Multiple sequence alignment - TraesCS4D01G122000

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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 TraesCS4D01G122000 chr4D 100.000 4682 0 0 1 4682 105134086 105138767 0.000000e+00 8647
1 TraesCS4D01G122000 chr4D 94.083 169 10 0 4 172 384969902 384969734 1.670000e-64 257
2 TraesCS4D01G122000 chr4D 93.750 96 6 0 391 486 436376810 436376715 1.360000e-30 145
3 TraesCS4D01G122000 chr4B 95.923 3998 111 17 638 4606 148920005 148923979 0.000000e+00 6433
4 TraesCS4D01G122000 chr4B 83.516 182 18 5 224 402 148919539 148919711 4.850000e-35 159
5 TraesCS4D01G122000 chr4A 96.079 3698 85 26 1009 4682 470689936 470686275 0.000000e+00 5971
6 TraesCS4D01G122000 chr4A 92.806 278 12 6 638 910 470690582 470690308 3.400000e-106 396
7 TraesCS4D01G122000 chr4A 90.541 148 9 3 230 372 470690998 470690851 1.720000e-44 191
8 TraesCS4D01G122000 chr5A 86.450 893 101 11 1717 2605 319753905 319753029 0.000000e+00 961
9 TraesCS4D01G122000 chr5A 84.360 422 66 0 3239 3660 319752481 319752060 9.370000e-112 414
10 TraesCS4D01G122000 chr5A 91.124 169 15 0 1448 1616 319754138 319753970 3.640000e-56 230
11 TraesCS4D01G122000 chr5B 86.399 897 89 17 1709 2601 270013469 270012602 0.000000e+00 950
12 TraesCS4D01G122000 chr5B 85.343 423 62 0 3238 3660 270011722 270011300 5.560000e-119 438
13 TraesCS4D01G122000 chr5B 91.124 169 15 0 1448 1616 270013689 270013521 3.640000e-56 230
14 TraesCS4D01G122000 chr5D 86.080 898 104 11 1709 2602 234821860 234822740 0.000000e+00 946
15 TraesCS4D01G122000 chr5D 84.360 422 66 0 3239 3660 234823309 234823730 9.370000e-112 414
16 TraesCS4D01G122000 chr5D 94.706 170 7 2 4 172 395704915 395704747 3.590000e-66 263
17 TraesCS4D01G122000 chr5D 91.124 169 15 0 1448 1616 234821634 234821802 3.640000e-56 230
18 TraesCS4D01G122000 chr5D 92.929 99 6 1 396 493 565655007 565654909 4.880000e-30 143
19 TraesCS4D01G122000 chr2D 95.930 172 7 0 1 172 364969017 364968846 3.570000e-71 279
20 TraesCS4D01G122000 chr2D 95.266 169 8 0 4 172 20775139 20774971 7.720000e-68 268
21 TraesCS4D01G122000 chr2D 86.179 123 12 5 366 486 532174661 532174780 1.370000e-25 128
22 TraesCS4D01G122000 chr3D 95.376 173 8 0 4 176 283322710 283322538 4.610000e-70 276
23 TraesCS4D01G122000 chr3D 94.083 169 10 0 4 172 496141357 496141189 1.670000e-64 257
24 TraesCS4D01G122000 chr6B 94.767 172 9 0 1 172 184630853 184631024 7.720000e-68 268
25 TraesCS4D01G122000 chr7B 94.083 169 10 0 4 172 718941657 718941489 1.670000e-64 257
26 TraesCS4D01G122000 chr7B 93.814 97 5 1 391 486 418204565 418204661 1.360000e-30 145
27 TraesCS4D01G122000 chr3B 93.491 169 11 0 1 169 168117864 168118032 7.780000e-63 252
28 TraesCS4D01G122000 chr3B 92.000 100 7 1 386 485 101314941 101315039 6.320000e-29 139
29 TraesCS4D01G122000 chr6D 94.681 94 5 0 391 484 30077358 30077451 3.780000e-31 147
30 TraesCS4D01G122000 chr1D 93.814 97 6 0 390 486 485967757 485967853 3.780000e-31 147
31 TraesCS4D01G122000 chr7D 92.157 102 8 0 393 494 1260943 1261044 1.360000e-30 145
32 TraesCS4D01G122000 chr6A 92.157 102 5 3 387 487 496842242 496842341 1.760000e-29 141


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 TraesCS4D01G122000 chr4D 105134086 105138767 4681 False 8647.000000 8647 100.000000 1 4682 1 chr4D.!!$F1 4681
1 TraesCS4D01G122000 chr4B 148919539 148923979 4440 False 3296.000000 6433 89.719500 224 4606 2 chr4B.!!$F1 4382
2 TraesCS4D01G122000 chr4A 470686275 470690998 4723 True 2186.000000 5971 93.142000 230 4682 3 chr4A.!!$R1 4452
3 TraesCS4D01G122000 chr5A 319752060 319754138 2078 True 535.000000 961 87.311333 1448 3660 3 chr5A.!!$R1 2212
4 TraesCS4D01G122000 chr5B 270011300 270013689 2389 True 539.333333 950 87.622000 1448 3660 3 chr5B.!!$R1 2212
5 TraesCS4D01G122000 chr5D 234821634 234823730 2096 False 530.000000 946 87.188000 1448 3660 3 chr5D.!!$F1 2212

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
74 75 0.036010 GACAGGATATGGCCGGGATG 60.036 60.0 2.18 0.0 0.00 3.51 F
168 169 0.168128 GACAGAATCCGGGCAAAACG 59.832 55.0 0.00 0.0 0.00 3.60 F
651 942 0.458669 TCGTTAGAGATGGGCGTTCC 59.541 55.0 0.00 0.0 0.00 3.62 F
657 948 1.087501 GAGATGGGCGTTCCTTTGTC 58.912 55.0 0.00 0.0 36.20 3.18 F
1181 1751 1.961180 CTAGACCACCAAGAGGGCGG 61.961 65.0 0.00 0.0 39.93 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1635 2205 3.418623 ATGGGGAGGAGGAGGAGGC 62.419 68.421 0.00 0.0 0.0 4.70 R
2777 3832 6.769822 AGAGCATAGAAAGTTGGTCATAATGG 59.230 38.462 5.11 0.0 41.6 3.16 R
3144 4233 1.861982 AATACAGAGTAGGGTGGCGT 58.138 50.000 0.00 0.0 0.0 5.68 R
3150 4239 5.187186 ACACAACCACTAATACAGAGTAGGG 59.813 44.000 0.00 0.0 0.0 3.53 R
3729 4831 1.067565 GCAGCTTAAGGGGCAAAAGAC 60.068 52.381 4.29 0.0 0.0 3.01 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
55 56 2.656085 TGCAAAGAAAAATGTACGCGG 58.344 42.857 12.47 0.00 0.00 6.46
56 57 2.290916 TGCAAAGAAAAATGTACGCGGA 59.709 40.909 12.47 0.00 0.00 5.54
57 58 2.655001 GCAAAGAAAAATGTACGCGGAC 59.345 45.455 16.44 16.44 0.00 4.79
58 59 3.850374 GCAAAGAAAAATGTACGCGGACA 60.850 43.478 29.06 29.06 0.00 4.02
59 60 3.806316 AAGAAAAATGTACGCGGACAG 57.194 42.857 30.25 0.00 31.51 3.51
60 61 2.073816 AGAAAAATGTACGCGGACAGG 58.926 47.619 30.25 0.00 31.51 4.00
61 62 2.070783 GAAAAATGTACGCGGACAGGA 58.929 47.619 30.25 6.34 31.51 3.86
62 63 2.396590 AAAATGTACGCGGACAGGAT 57.603 45.000 30.25 15.55 31.51 3.24
63 64 3.530265 AAAATGTACGCGGACAGGATA 57.470 42.857 30.25 5.45 31.51 2.59
64 65 3.746045 AAATGTACGCGGACAGGATAT 57.254 42.857 30.25 9.81 31.51 1.63
65 66 2.724977 ATGTACGCGGACAGGATATG 57.275 50.000 30.25 0.00 31.51 1.78
66 67 0.671796 TGTACGCGGACAGGATATGG 59.328 55.000 22.88 0.00 0.00 2.74
67 68 0.666577 GTACGCGGACAGGATATGGC 60.667 60.000 18.68 0.00 35.46 4.40
72 73 3.885814 GACAGGATATGGCCGGGA 58.114 61.111 2.18 0.00 0.00 5.14
73 74 2.377136 GACAGGATATGGCCGGGAT 58.623 57.895 2.18 0.00 0.00 3.85
74 75 0.036010 GACAGGATATGGCCGGGATG 60.036 60.000 2.18 0.00 0.00 3.51
75 76 1.377725 CAGGATATGGCCGGGATGC 60.378 63.158 2.18 0.00 0.00 3.91
76 77 2.436646 GGATATGGCCGGGATGCG 60.437 66.667 2.18 0.00 0.00 4.73
77 78 2.347490 GATATGGCCGGGATGCGT 59.653 61.111 2.18 0.00 0.00 5.24
78 79 1.741770 GATATGGCCGGGATGCGTC 60.742 63.158 2.18 0.00 0.00 5.19
79 80 2.172483 GATATGGCCGGGATGCGTCT 62.172 60.000 2.18 0.00 0.00 4.18
80 81 2.454832 ATATGGCCGGGATGCGTCTG 62.455 60.000 2.18 0.00 0.00 3.51
112 113 4.424711 GGCCACCGCATCCCAGAA 62.425 66.667 0.00 0.00 36.38 3.02
113 114 2.361104 GCCACCGCATCCCAGAAA 60.361 61.111 0.00 0.00 34.03 2.52
114 115 2.700773 GCCACCGCATCCCAGAAAC 61.701 63.158 0.00 0.00 34.03 2.78
115 116 1.002134 CCACCGCATCCCAGAAACT 60.002 57.895 0.00 0.00 0.00 2.66
116 117 1.308069 CCACCGCATCCCAGAAACTG 61.308 60.000 0.00 0.00 0.00 3.16
117 118 1.675641 ACCGCATCCCAGAAACTGC 60.676 57.895 0.00 0.00 0.00 4.40
118 119 2.409870 CCGCATCCCAGAAACTGCC 61.410 63.158 0.00 0.00 0.00 4.85
119 120 2.409870 CGCATCCCAGAAACTGCCC 61.410 63.158 0.00 0.00 0.00 5.36
120 121 2.409870 GCATCCCAGAAACTGCCCG 61.410 63.158 0.00 0.00 0.00 6.13
121 122 1.299648 CATCCCAGAAACTGCCCGA 59.700 57.895 0.00 0.00 0.00 5.14
122 123 0.322456 CATCCCAGAAACTGCCCGAA 60.322 55.000 0.00 0.00 0.00 4.30
123 124 0.322546 ATCCCAGAAACTGCCCGAAC 60.323 55.000 0.00 0.00 0.00 3.95
124 125 1.228124 CCCAGAAACTGCCCGAACA 60.228 57.895 0.00 0.00 0.00 3.18
125 126 1.515521 CCCAGAAACTGCCCGAACAC 61.516 60.000 0.00 0.00 0.00 3.32
126 127 1.569493 CAGAAACTGCCCGAACACG 59.431 57.895 0.00 0.00 0.00 4.49
127 128 0.878523 CAGAAACTGCCCGAACACGA 60.879 55.000 0.00 0.00 0.00 4.35
128 129 0.878961 AGAAACTGCCCGAACACGAC 60.879 55.000 0.00 0.00 0.00 4.34
129 130 1.838568 GAAACTGCCCGAACACGACC 61.839 60.000 0.00 0.00 0.00 4.79
130 131 3.819877 AACTGCCCGAACACGACCC 62.820 63.158 0.00 0.00 0.00 4.46
133 134 4.404098 GCCCGAACACGACCCCAT 62.404 66.667 0.00 0.00 0.00 4.00
134 135 2.349755 CCCGAACACGACCCCATT 59.650 61.111 0.00 0.00 0.00 3.16
135 136 1.597989 CCCGAACACGACCCCATTA 59.402 57.895 0.00 0.00 0.00 1.90
136 137 0.741927 CCCGAACACGACCCCATTAC 60.742 60.000 0.00 0.00 0.00 1.89
137 138 0.741927 CCGAACACGACCCCATTACC 60.742 60.000 0.00 0.00 0.00 2.85
138 139 0.741927 CGAACACGACCCCATTACCC 60.742 60.000 0.00 0.00 0.00 3.69
139 140 0.616891 GAACACGACCCCATTACCCT 59.383 55.000 0.00 0.00 0.00 4.34
140 141 1.832998 GAACACGACCCCATTACCCTA 59.167 52.381 0.00 0.00 0.00 3.53
141 142 1.197812 ACACGACCCCATTACCCTAC 58.802 55.000 0.00 0.00 0.00 3.18
142 143 0.466963 CACGACCCCATTACCCTACC 59.533 60.000 0.00 0.00 0.00 3.18
143 144 0.692083 ACGACCCCATTACCCTACCC 60.692 60.000 0.00 0.00 0.00 3.69
144 145 0.691748 CGACCCCATTACCCTACCCA 60.692 60.000 0.00 0.00 0.00 4.51
145 146 1.598869 GACCCCATTACCCTACCCAA 58.401 55.000 0.00 0.00 0.00 4.12
146 147 1.924552 GACCCCATTACCCTACCCAAA 59.075 52.381 0.00 0.00 0.00 3.28
147 148 1.642238 ACCCCATTACCCTACCCAAAC 59.358 52.381 0.00 0.00 0.00 2.93
148 149 1.409101 CCCCATTACCCTACCCAAACG 60.409 57.143 0.00 0.00 0.00 3.60
149 150 1.409101 CCCATTACCCTACCCAAACGG 60.409 57.143 0.00 0.00 37.81 4.44
150 151 1.560611 CCATTACCCTACCCAAACGGA 59.439 52.381 0.00 0.00 34.64 4.69
151 152 2.635714 CATTACCCTACCCAAACGGAC 58.364 52.381 0.00 0.00 34.64 4.79
152 153 1.727062 TTACCCTACCCAAACGGACA 58.273 50.000 0.00 0.00 34.64 4.02
153 154 1.269012 TACCCTACCCAAACGGACAG 58.731 55.000 0.00 0.00 34.64 3.51
154 155 0.472352 ACCCTACCCAAACGGACAGA 60.472 55.000 0.00 0.00 34.64 3.41
155 156 0.688487 CCCTACCCAAACGGACAGAA 59.312 55.000 0.00 0.00 34.64 3.02
156 157 1.280998 CCCTACCCAAACGGACAGAAT 59.719 52.381 0.00 0.00 34.64 2.40
157 158 2.629051 CCTACCCAAACGGACAGAATC 58.371 52.381 0.00 0.00 34.64 2.52
158 159 2.629051 CTACCCAAACGGACAGAATCC 58.371 52.381 0.00 0.00 45.20 3.01
165 166 4.734652 GGACAGAATCCGGGCAAA 57.265 55.556 0.00 0.00 37.88 3.68
166 167 2.955609 GGACAGAATCCGGGCAAAA 58.044 52.632 0.00 0.00 37.88 2.44
167 168 0.526211 GGACAGAATCCGGGCAAAAC 59.474 55.000 0.00 0.00 37.88 2.43
168 169 0.168128 GACAGAATCCGGGCAAAACG 59.832 55.000 0.00 0.00 0.00 3.60
175 176 3.666253 CGGGCAAAACGGACACCC 61.666 66.667 0.00 0.00 37.19 4.61
176 177 3.299977 GGGCAAAACGGACACCCC 61.300 66.667 0.00 0.00 34.23 4.95
177 178 3.299977 GGCAAAACGGACACCCCC 61.300 66.667 0.00 0.00 0.00 5.40
185 186 3.468140 GGACACCCCCGAGCTACC 61.468 72.222 0.00 0.00 0.00 3.18
186 187 3.468140 GACACCCCCGAGCTACCC 61.468 72.222 0.00 0.00 0.00 3.69
187 188 4.326227 ACACCCCCGAGCTACCCA 62.326 66.667 0.00 0.00 0.00 4.51
188 189 3.006728 CACCCCCGAGCTACCCAA 61.007 66.667 0.00 0.00 0.00 4.12
189 190 2.204029 ACCCCCGAGCTACCCAAA 60.204 61.111 0.00 0.00 0.00 3.28
190 191 2.271173 CCCCCGAGCTACCCAAAC 59.729 66.667 0.00 0.00 0.00 2.93
191 192 2.125269 CCCCGAGCTACCCAAACG 60.125 66.667 0.00 0.00 0.00 3.60
192 193 2.125269 CCCGAGCTACCCAAACGG 60.125 66.667 0.00 0.00 42.67 4.44
201 202 2.667199 CCCAAACGGGTCGTGGTC 60.667 66.667 0.00 0.00 39.99 4.02
202 203 3.039588 CCAAACGGGTCGTGGTCG 61.040 66.667 0.00 0.00 39.99 4.79
203 204 2.279650 CAAACGGGTCGTGGTCGT 60.280 61.111 0.00 0.00 39.99 4.34
204 205 2.279650 AAACGGGTCGTGGTCGTG 60.280 61.111 0.00 0.00 39.99 4.35
205 206 4.955774 AACGGGTCGTGGTCGTGC 62.956 66.667 0.00 0.00 39.99 5.34
213 214 4.295119 GTGGTCGTGCGGTGGAGT 62.295 66.667 0.00 0.00 0.00 3.85
214 215 3.542676 TGGTCGTGCGGTGGAGTT 61.543 61.111 0.00 0.00 0.00 3.01
215 216 3.041940 GGTCGTGCGGTGGAGTTG 61.042 66.667 0.00 0.00 0.00 3.16
216 217 3.041940 GTCGTGCGGTGGAGTTGG 61.042 66.667 0.00 0.00 0.00 3.77
217 218 4.980805 TCGTGCGGTGGAGTTGGC 62.981 66.667 0.00 0.00 0.00 4.52
219 220 4.643387 GTGCGGTGGAGTTGGCCT 62.643 66.667 3.32 0.00 0.00 5.19
220 221 3.884774 TGCGGTGGAGTTGGCCTT 61.885 61.111 3.32 0.00 0.00 4.35
221 222 2.349755 GCGGTGGAGTTGGCCTTA 59.650 61.111 3.32 0.00 0.00 2.69
222 223 1.077716 GCGGTGGAGTTGGCCTTAT 60.078 57.895 3.32 0.00 0.00 1.73
226 227 2.560981 CGGTGGAGTTGGCCTTATTTTT 59.439 45.455 3.32 0.00 0.00 1.94
228 229 3.576550 GGTGGAGTTGGCCTTATTTTTCA 59.423 43.478 3.32 0.00 0.00 2.69
239 240 9.784531 TTGGCCTTATTTTTCATGTTTTTCATA 57.215 25.926 3.32 0.00 34.67 2.15
270 271 7.732222 ATTTATAAACCAGATCAGCCCAAAA 57.268 32.000 0.00 0.00 0.00 2.44
303 307 7.334921 ACAAAGTGCCTACGTAATATTTTAGCA 59.665 33.333 0.00 0.00 0.00 3.49
404 408 8.411991 ACTCCTGCTACTTTATAATCTACTCC 57.588 38.462 0.00 0.00 0.00 3.85
405 409 8.228905 ACTCCTGCTACTTTATAATCTACTCCT 58.771 37.037 0.00 0.00 0.00 3.69
406 410 9.084533 CTCCTGCTACTTTATAATCTACTCCTT 57.915 37.037 0.00 0.00 0.00 3.36
407 411 9.080097 TCCTGCTACTTTATAATCTACTCCTTC 57.920 37.037 0.00 0.00 0.00 3.46
408 412 8.308207 CCTGCTACTTTATAATCTACTCCTTCC 58.692 40.741 0.00 0.00 0.00 3.46
409 413 7.883217 TGCTACTTTATAATCTACTCCTTCCG 58.117 38.462 0.00 0.00 0.00 4.30
410 414 7.504911 TGCTACTTTATAATCTACTCCTTCCGT 59.495 37.037 0.00 0.00 0.00 4.69
411 415 9.007901 GCTACTTTATAATCTACTCCTTCCGTA 57.992 37.037 0.00 0.00 0.00 4.02
426 430 9.418839 ACTCCTTCCGTAAACTAATATAAGAGT 57.581 33.333 0.00 0.00 0.00 3.24
427 431 9.680315 CTCCTTCCGTAAACTAATATAAGAGTG 57.320 37.037 0.00 0.00 0.00 3.51
428 432 9.193806 TCCTTCCGTAAACTAATATAAGAGTGT 57.806 33.333 0.00 0.00 0.00 3.55
429 433 9.813446 CCTTCCGTAAACTAATATAAGAGTGTT 57.187 33.333 0.00 0.00 0.00 3.32
481 485 9.832445 TGCTTTTATATTAGTTTACAGAGGGAG 57.168 33.333 0.00 0.00 0.00 4.30
482 486 9.833917 GCTTTTATATTAGTTTACAGAGGGAGT 57.166 33.333 0.00 0.00 0.00 3.85
490 494 6.742559 AGTTTACAGAGGGAGTACAAAAGA 57.257 37.500 0.00 0.00 0.00 2.52
491 495 7.133133 AGTTTACAGAGGGAGTACAAAAGAA 57.867 36.000 0.00 0.00 0.00 2.52
492 496 7.217906 AGTTTACAGAGGGAGTACAAAAGAAG 58.782 38.462 0.00 0.00 0.00 2.85
493 497 4.625607 ACAGAGGGAGTACAAAAGAAGG 57.374 45.455 0.00 0.00 0.00 3.46
496 500 5.132144 ACAGAGGGAGTACAAAAGAAGGAAA 59.868 40.000 0.00 0.00 0.00 3.13
498 502 4.399219 AGGGAGTACAAAAGAAGGAAAGC 58.601 43.478 0.00 0.00 0.00 3.51
518 522 8.416329 GGAAAGCCAAAGATACATATTGTGAAT 58.584 33.333 0.00 0.00 0.00 2.57
519 523 9.241317 GAAAGCCAAAGATACATATTGTGAATG 57.759 33.333 0.00 0.00 0.00 2.67
520 524 7.886629 AGCCAAAGATACATATTGTGAATGT 57.113 32.000 0.00 0.00 40.57 2.71
521 525 8.297470 AGCCAAAGATACATATTGTGAATGTT 57.703 30.769 0.00 0.00 38.49 2.71
522 526 8.408601 AGCCAAAGATACATATTGTGAATGTTC 58.591 33.333 0.00 0.00 38.49 3.18
523 527 7.649306 GCCAAAGATACATATTGTGAATGTTCC 59.351 37.037 0.00 0.00 38.49 3.62
524 528 8.685427 CCAAAGATACATATTGTGAATGTTCCA 58.315 33.333 0.00 0.00 38.49 3.53
525 529 9.507280 CAAAGATACATATTGTGAATGTTCCAC 57.493 33.333 0.00 0.00 38.49 4.02
526 530 8.806429 AAGATACATATTGTGAATGTTCCACA 57.194 30.769 0.00 0.00 42.16 4.17
527 531 8.213518 AGATACATATTGTGAATGTTCCACAC 57.786 34.615 0.00 0.00 43.37 3.82
528 532 8.049117 AGATACATATTGTGAATGTTCCACACT 58.951 33.333 0.00 0.00 43.37 3.55
529 533 6.899393 ACATATTGTGAATGTTCCACACTT 57.101 33.333 0.00 0.00 43.37 3.16
530 534 6.680810 ACATATTGTGAATGTTCCACACTTG 58.319 36.000 0.00 0.00 43.37 3.16
531 535 6.265196 ACATATTGTGAATGTTCCACACTTGT 59.735 34.615 0.00 0.00 43.37 3.16
532 536 7.446931 ACATATTGTGAATGTTCCACACTTGTA 59.553 33.333 0.00 0.00 43.37 2.41
533 537 5.493133 TTGTGAATGTTCCACACTTGTAC 57.507 39.130 0.00 0.00 43.37 2.90
534 538 3.880490 TGTGAATGTTCCACACTTGTACC 59.120 43.478 0.00 0.00 39.36 3.34
535 539 3.252458 GTGAATGTTCCACACTTGTACCC 59.748 47.826 0.00 0.00 34.81 3.69
536 540 3.137544 TGAATGTTCCACACTTGTACCCT 59.862 43.478 0.00 0.00 0.00 4.34
537 541 4.348461 TGAATGTTCCACACTTGTACCCTA 59.652 41.667 0.00 0.00 0.00 3.53
538 542 5.013704 TGAATGTTCCACACTTGTACCCTAT 59.986 40.000 0.00 0.00 0.00 2.57
539 543 4.546829 TGTTCCACACTTGTACCCTATC 57.453 45.455 0.00 0.00 0.00 2.08
540 544 4.164981 TGTTCCACACTTGTACCCTATCT 58.835 43.478 0.00 0.00 0.00 1.98
541 545 4.595781 TGTTCCACACTTGTACCCTATCTT 59.404 41.667 0.00 0.00 0.00 2.40
542 546 4.819105 TCCACACTTGTACCCTATCTTG 57.181 45.455 0.00 0.00 0.00 3.02
543 547 4.164981 TCCACACTTGTACCCTATCTTGT 58.835 43.478 0.00 0.00 0.00 3.16
544 548 5.335261 TCCACACTTGTACCCTATCTTGTA 58.665 41.667 0.00 0.00 0.00 2.41
545 549 5.781306 TCCACACTTGTACCCTATCTTGTAA 59.219 40.000 0.00 0.00 0.00 2.41
546 550 5.873164 CCACACTTGTACCCTATCTTGTAAC 59.127 44.000 0.00 0.00 0.00 2.50
547 551 6.295688 CCACACTTGTACCCTATCTTGTAACT 60.296 42.308 0.00 0.00 0.00 2.24
550 554 9.043548 ACACTTGTACCCTATCTTGTAACTTAT 57.956 33.333 0.00 0.00 0.00 1.73
596 759 9.948964 AGTTTATCTTGTAACCTATTTTACGGT 57.051 29.630 0.00 0.00 35.09 4.83
598 761 6.673154 ATCTTGTAACCTATTTTACGGTGC 57.327 37.500 0.00 0.00 35.09 5.01
651 942 0.458669 TCGTTAGAGATGGGCGTTCC 59.541 55.000 0.00 0.00 0.00 3.62
657 948 1.087501 GAGATGGGCGTTCCTTTGTC 58.912 55.000 0.00 0.00 36.20 3.18
758 1049 4.515028 ATGAGACACACATGGATGGATT 57.485 40.909 0.00 0.00 0.00 3.01
759 1050 4.305539 TGAGACACACATGGATGGATTT 57.694 40.909 0.00 0.00 0.00 2.17
841 1138 2.068837 TTACCGTCCTTGCTAACACG 57.931 50.000 0.00 0.00 0.00 4.49
1181 1751 1.961180 CTAGACCACCAAGAGGGCGG 61.961 65.000 0.00 0.00 39.93 6.13
1665 2250 3.170672 CCCCATCATCCGCCCTCA 61.171 66.667 0.00 0.00 0.00 3.86
2649 3330 8.739039 TGAATCTTCAAACTTTTCACTTCAGAA 58.261 29.630 0.00 0.00 33.55 3.02
2777 3832 5.306590 CGTTTAGAAGCTCTAAAAGTTCGC 58.693 41.667 15.46 6.09 46.72 4.70
2794 3863 4.156008 AGTTCGCCATTATGACCAACTTTC 59.844 41.667 0.00 0.00 0.00 2.62
3035 4124 5.127356 GTCATCTAACCTAGTGGCACTACTT 59.873 44.000 22.96 17.81 36.63 2.24
3108 4197 2.360165 GCATTGCATGGGGAACTAAGAG 59.640 50.000 3.15 0.00 0.00 2.85
3128 4217 6.983906 AGAGATCAACCAAAATGTCCTTTT 57.016 33.333 0.00 0.00 37.54 2.27
3144 4233 6.003326 TGTCCTTTTGACTTAGATGCATCAA 58.997 36.000 27.81 17.73 44.75 2.57
3150 4239 2.009774 ACTTAGATGCATCAACGCCAC 58.990 47.619 27.81 0.00 0.00 5.01
3199 4288 2.983229 AGTTCAGCAGCATCACCTTAG 58.017 47.619 0.00 0.00 0.00 2.18
3591 4691 0.456221 CGGATGGCTACACTCTCGTT 59.544 55.000 0.00 0.00 0.00 3.85
3714 4816 8.887717 AGCTAAAGCATCACTAGATTTTACTTG 58.112 33.333 4.54 0.00 45.16 3.16
3729 4831 1.299541 ACTTGGTGCAACTGTCTTCG 58.700 50.000 2.04 0.00 36.74 3.79
3739 4841 1.594331 ACTGTCTTCGTCTTTTGCCC 58.406 50.000 0.00 0.00 0.00 5.36
3766 4868 2.031437 GCTGCTCAGTTCGATCAATTCC 59.969 50.000 0.00 0.00 0.00 3.01
3771 4873 4.033817 GCTCAGTTCGATCAATTCCAAGAG 59.966 45.833 0.00 0.00 0.00 2.85
3915 5019 6.988522 TCTGGCCAATTAAGTTTACCTTTTC 58.011 36.000 7.01 0.00 34.46 2.29
3930 5034 3.641436 ACCTTTTCCATCTTGTGTTTCCC 59.359 43.478 0.00 0.00 0.00 3.97
4056 5160 8.143193 ACATGTGCATTTTCTAGTGAATCAAAA 58.857 29.630 0.00 0.00 31.56 2.44
4057 5161 9.146984 CATGTGCATTTTCTAGTGAATCAAAAT 57.853 29.630 0.00 0.00 31.56 1.82
4150 5256 7.823745 AGCTGTTGATTCCTTTTCTTTTCTA 57.176 32.000 0.00 0.00 0.00 2.10
4381 5489 7.289084 AGTTTGGGTATTTGTTAGTTCACCATT 59.711 33.333 0.00 0.00 0.00 3.16
4396 5504 2.036733 CACCATTCCCATCATGCAATCC 59.963 50.000 0.00 0.00 0.00 3.01
4459 5567 5.629435 GCTACTGATTGTTTTGTTAGCCAAC 59.371 40.000 0.00 0.00 31.20 3.77
4652 5763 6.071984 TCTTGTTTAACCCTTAGATTGCCAA 58.928 36.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.351948 TCTTTGCAAGCCCTTAACTTTTT 57.648 34.783 0.00 0.00 0.00 1.94
21 22 5.351948 TTCTTTGCAAGCCCTTAACTTTT 57.648 34.783 0.00 0.00 0.00 2.27
22 23 5.351948 TTTCTTTGCAAGCCCTTAACTTT 57.648 34.783 0.00 0.00 0.00 2.66
23 24 5.351948 TTTTCTTTGCAAGCCCTTAACTT 57.648 34.783 0.00 0.00 0.00 2.66
24 25 5.351948 TTTTTCTTTGCAAGCCCTTAACT 57.648 34.783 0.00 0.00 0.00 2.24
25 26 5.527214 ACATTTTTCTTTGCAAGCCCTTAAC 59.473 36.000 0.00 0.00 0.00 2.01
26 27 5.679601 ACATTTTTCTTTGCAAGCCCTTAA 58.320 33.333 0.00 0.00 0.00 1.85
27 28 5.289083 ACATTTTTCTTTGCAAGCCCTTA 57.711 34.783 0.00 0.00 0.00 2.69
28 29 4.155063 ACATTTTTCTTTGCAAGCCCTT 57.845 36.364 0.00 0.00 0.00 3.95
29 30 3.843893 ACATTTTTCTTTGCAAGCCCT 57.156 38.095 0.00 0.00 0.00 5.19
30 31 3.428534 CGTACATTTTTCTTTGCAAGCCC 59.571 43.478 0.00 0.00 0.00 5.19
31 32 3.121025 GCGTACATTTTTCTTTGCAAGCC 60.121 43.478 0.00 0.00 0.00 4.35
32 33 3.420417 CGCGTACATTTTTCTTTGCAAGC 60.420 43.478 0.00 0.00 0.00 4.01
33 34 3.119463 CCGCGTACATTTTTCTTTGCAAG 59.881 43.478 4.92 0.00 0.00 4.01
34 35 3.046390 CCGCGTACATTTTTCTTTGCAA 58.954 40.909 4.92 0.00 0.00 4.08
35 36 2.290916 TCCGCGTACATTTTTCTTTGCA 59.709 40.909 4.92 0.00 0.00 4.08
36 37 2.655001 GTCCGCGTACATTTTTCTTTGC 59.345 45.455 4.92 0.00 0.00 3.68
37 38 3.879427 TGTCCGCGTACATTTTTCTTTG 58.121 40.909 0.00 0.00 0.00 2.77
38 39 3.058501 CCTGTCCGCGTACATTTTTCTTT 60.059 43.478 4.55 0.00 0.00 2.52
39 40 2.482721 CCTGTCCGCGTACATTTTTCTT 59.517 45.455 4.55 0.00 0.00 2.52
40 41 2.073816 CCTGTCCGCGTACATTTTTCT 58.926 47.619 4.55 0.00 0.00 2.52
41 42 2.070783 TCCTGTCCGCGTACATTTTTC 58.929 47.619 4.55 0.00 0.00 2.29
42 43 2.172851 TCCTGTCCGCGTACATTTTT 57.827 45.000 4.55 0.00 0.00 1.94
43 44 2.396590 ATCCTGTCCGCGTACATTTT 57.603 45.000 4.55 0.00 0.00 1.82
44 45 3.390135 CATATCCTGTCCGCGTACATTT 58.610 45.455 4.55 0.00 0.00 2.32
45 46 2.288825 CCATATCCTGTCCGCGTACATT 60.289 50.000 4.55 0.00 0.00 2.71
46 47 1.272490 CCATATCCTGTCCGCGTACAT 59.728 52.381 4.55 0.00 0.00 2.29
47 48 0.671796 CCATATCCTGTCCGCGTACA 59.328 55.000 3.95 3.95 0.00 2.90
48 49 0.666577 GCCATATCCTGTCCGCGTAC 60.667 60.000 4.92 0.00 0.00 3.67
49 50 1.663739 GCCATATCCTGTCCGCGTA 59.336 57.895 4.92 0.00 0.00 4.42
50 51 2.421739 GCCATATCCTGTCCGCGT 59.578 61.111 4.92 0.00 0.00 6.01
51 52 2.357517 GGCCATATCCTGTCCGCG 60.358 66.667 0.00 0.00 0.00 6.46
52 53 2.357517 CGGCCATATCCTGTCCGC 60.358 66.667 2.24 0.00 33.36 5.54
53 54 2.343758 CCGGCCATATCCTGTCCG 59.656 66.667 2.24 0.00 39.79 4.79
54 55 1.201429 ATCCCGGCCATATCCTGTCC 61.201 60.000 2.24 0.00 0.00 4.02
55 56 0.036010 CATCCCGGCCATATCCTGTC 60.036 60.000 2.24 0.00 0.00 3.51
56 57 2.069776 CATCCCGGCCATATCCTGT 58.930 57.895 2.24 0.00 0.00 4.00
57 58 1.377725 GCATCCCGGCCATATCCTG 60.378 63.158 2.24 0.00 0.00 3.86
58 59 2.959484 CGCATCCCGGCCATATCCT 61.959 63.158 2.24 0.00 0.00 3.24
59 60 2.436646 CGCATCCCGGCCATATCC 60.437 66.667 2.24 0.00 0.00 2.59
60 61 1.741770 GACGCATCCCGGCCATATC 60.742 63.158 2.24 0.00 39.74 1.63
61 62 2.347490 GACGCATCCCGGCCATAT 59.653 61.111 2.24 0.00 39.74 1.78
95 96 3.936772 TTTCTGGGATGCGGTGGCC 62.937 63.158 0.00 0.00 38.85 5.36
96 97 2.361104 TTTCTGGGATGCGGTGGC 60.361 61.111 0.00 0.00 40.52 5.01
97 98 1.002134 AGTTTCTGGGATGCGGTGG 60.002 57.895 0.00 0.00 0.00 4.61
98 99 1.926511 GCAGTTTCTGGGATGCGGTG 61.927 60.000 0.00 0.00 31.21 4.94
99 100 1.675641 GCAGTTTCTGGGATGCGGT 60.676 57.895 0.00 0.00 31.21 5.68
100 101 2.409870 GGCAGTTTCTGGGATGCGG 61.410 63.158 0.00 0.00 39.58 5.69
101 102 2.409870 GGGCAGTTTCTGGGATGCG 61.410 63.158 0.00 0.00 39.58 4.73
102 103 2.409870 CGGGCAGTTTCTGGGATGC 61.410 63.158 0.00 0.00 37.95 3.91
103 104 0.322456 TTCGGGCAGTTTCTGGGATG 60.322 55.000 0.00 0.00 31.21 3.51
104 105 0.322546 GTTCGGGCAGTTTCTGGGAT 60.323 55.000 0.00 0.00 31.21 3.85
105 106 1.072505 GTTCGGGCAGTTTCTGGGA 59.927 57.895 0.00 0.00 31.21 4.37
106 107 1.228124 TGTTCGGGCAGTTTCTGGG 60.228 57.895 0.00 0.00 31.21 4.45
107 108 1.841663 CGTGTTCGGGCAGTTTCTGG 61.842 60.000 0.00 0.00 31.21 3.86
108 109 0.878523 TCGTGTTCGGGCAGTTTCTG 60.879 55.000 0.00 0.00 37.69 3.02
109 110 0.878961 GTCGTGTTCGGGCAGTTTCT 60.879 55.000 0.00 0.00 37.69 2.52
110 111 1.568025 GTCGTGTTCGGGCAGTTTC 59.432 57.895 0.00 0.00 37.69 2.78
111 112 1.890510 GGTCGTGTTCGGGCAGTTT 60.891 57.895 0.00 0.00 37.69 2.66
112 113 2.280592 GGTCGTGTTCGGGCAGTT 60.281 61.111 0.00 0.00 37.69 3.16
113 114 4.309950 GGGTCGTGTTCGGGCAGT 62.310 66.667 0.00 0.00 37.69 4.40
116 117 2.524951 TAATGGGGTCGTGTTCGGGC 62.525 60.000 0.00 0.00 37.69 6.13
117 118 0.741927 GTAATGGGGTCGTGTTCGGG 60.742 60.000 0.00 0.00 37.69 5.14
118 119 0.741927 GGTAATGGGGTCGTGTTCGG 60.742 60.000 0.00 0.00 37.69 4.30
119 120 0.741927 GGGTAATGGGGTCGTGTTCG 60.742 60.000 0.00 0.00 38.55 3.95
120 121 0.616891 AGGGTAATGGGGTCGTGTTC 59.383 55.000 0.00 0.00 0.00 3.18
121 122 1.556451 GTAGGGTAATGGGGTCGTGTT 59.444 52.381 0.00 0.00 0.00 3.32
122 123 1.197812 GTAGGGTAATGGGGTCGTGT 58.802 55.000 0.00 0.00 0.00 4.49
123 124 0.466963 GGTAGGGTAATGGGGTCGTG 59.533 60.000 0.00 0.00 0.00 4.35
124 125 0.692083 GGGTAGGGTAATGGGGTCGT 60.692 60.000 0.00 0.00 0.00 4.34
125 126 0.691748 TGGGTAGGGTAATGGGGTCG 60.692 60.000 0.00 0.00 0.00 4.79
126 127 1.598869 TTGGGTAGGGTAATGGGGTC 58.401 55.000 0.00 0.00 0.00 4.46
127 128 1.642238 GTTTGGGTAGGGTAATGGGGT 59.358 52.381 0.00 0.00 0.00 4.95
128 129 1.409101 CGTTTGGGTAGGGTAATGGGG 60.409 57.143 0.00 0.00 0.00 4.96
129 130 1.409101 CCGTTTGGGTAGGGTAATGGG 60.409 57.143 0.00 0.00 0.00 4.00
130 131 1.560611 TCCGTTTGGGTAGGGTAATGG 59.439 52.381 0.00 0.00 37.00 3.16
131 132 2.027007 TGTCCGTTTGGGTAGGGTAATG 60.027 50.000 0.00 0.00 37.00 1.90
132 133 2.237893 CTGTCCGTTTGGGTAGGGTAAT 59.762 50.000 0.00 0.00 37.00 1.89
133 134 1.624813 CTGTCCGTTTGGGTAGGGTAA 59.375 52.381 0.00 0.00 37.00 2.85
134 135 1.203162 TCTGTCCGTTTGGGTAGGGTA 60.203 52.381 0.00 0.00 37.00 3.69
135 136 0.472352 TCTGTCCGTTTGGGTAGGGT 60.472 55.000 0.00 0.00 37.00 4.34
136 137 0.688487 TTCTGTCCGTTTGGGTAGGG 59.312 55.000 0.00 0.00 37.00 3.53
137 138 2.629051 GATTCTGTCCGTTTGGGTAGG 58.371 52.381 0.00 0.00 37.00 3.18
138 139 2.629051 GGATTCTGTCCGTTTGGGTAG 58.371 52.381 0.00 0.00 37.23 3.18
139 140 2.773993 GGATTCTGTCCGTTTGGGTA 57.226 50.000 0.00 0.00 37.23 3.69
140 141 3.644861 GGATTCTGTCCGTTTGGGT 57.355 52.632 0.00 0.00 37.23 4.51
148 149 0.526211 GTTTTGCCCGGATTCTGTCC 59.474 55.000 0.73 0.00 44.10 4.02
149 150 0.168128 CGTTTTGCCCGGATTCTGTC 59.832 55.000 0.73 0.00 0.00 3.51
150 151 2.253513 CGTTTTGCCCGGATTCTGT 58.746 52.632 0.73 0.00 0.00 3.41
157 158 3.666253 GGTGTCCGTTTTGCCCGG 61.666 66.667 0.00 0.00 46.83 5.73
158 159 3.666253 GGGTGTCCGTTTTGCCCG 61.666 66.667 0.00 0.00 0.00 6.13
159 160 3.299977 GGGGTGTCCGTTTTGCCC 61.300 66.667 0.00 0.00 38.61 5.36
160 161 3.299977 GGGGGTGTCCGTTTTGCC 61.300 66.667 0.00 0.00 36.01 4.52
161 162 3.666253 CGGGGGTGTCCGTTTTGC 61.666 66.667 0.00 0.00 44.60 3.68
168 169 3.468140 GGTAGCTCGGGGGTGTCC 61.468 72.222 0.00 0.00 0.00 4.02
169 170 3.468140 GGGTAGCTCGGGGGTGTC 61.468 72.222 0.00 0.00 0.00 3.67
170 171 3.857521 TTGGGTAGCTCGGGGGTGT 62.858 63.158 0.00 0.00 0.00 4.16
171 172 2.598787 TTTGGGTAGCTCGGGGGTG 61.599 63.158 0.00 0.00 0.00 4.61
172 173 2.204029 TTTGGGTAGCTCGGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
173 174 2.271173 GTTTGGGTAGCTCGGGGG 59.729 66.667 0.00 0.00 0.00 5.40
174 175 2.125269 CGTTTGGGTAGCTCGGGG 60.125 66.667 0.00 0.00 0.00 5.73
175 176 2.125269 CCGTTTGGGTAGCTCGGG 60.125 66.667 0.00 0.00 37.92 5.14
185 186 3.039588 CGACCACGACCCGTTTGG 61.040 66.667 0.00 0.00 38.32 3.28
186 187 2.279650 ACGACCACGACCCGTTTG 60.280 61.111 0.00 0.00 38.32 2.93
187 188 2.279650 CACGACCACGACCCGTTT 60.280 61.111 0.00 0.00 38.32 3.60
188 189 4.955774 GCACGACCACGACCCGTT 62.956 66.667 0.00 0.00 38.32 4.44
196 197 3.802418 AACTCCACCGCACGACCAC 62.802 63.158 0.00 0.00 0.00 4.16
197 198 3.542676 AACTCCACCGCACGACCA 61.543 61.111 0.00 0.00 0.00 4.02
198 199 3.041940 CAACTCCACCGCACGACC 61.042 66.667 0.00 0.00 0.00 4.79
199 200 3.041940 CCAACTCCACCGCACGAC 61.042 66.667 0.00 0.00 0.00 4.34
200 201 4.980805 GCCAACTCCACCGCACGA 62.981 66.667 0.00 0.00 0.00 4.35
202 203 2.741486 TAAGGCCAACTCCACCGCAC 62.741 60.000 5.01 0.00 0.00 5.34
203 204 1.847798 ATAAGGCCAACTCCACCGCA 61.848 55.000 5.01 0.00 0.00 5.69
204 205 0.679960 AATAAGGCCAACTCCACCGC 60.680 55.000 5.01 0.00 0.00 5.68
205 206 1.834188 AAATAAGGCCAACTCCACCG 58.166 50.000 5.01 0.00 0.00 4.94
206 207 3.576550 TGAAAAATAAGGCCAACTCCACC 59.423 43.478 5.01 0.00 0.00 4.61
207 208 4.864704 TGAAAAATAAGGCCAACTCCAC 57.135 40.909 5.01 0.00 0.00 4.02
208 209 4.837860 ACATGAAAAATAAGGCCAACTCCA 59.162 37.500 5.01 0.00 0.00 3.86
209 210 5.405935 ACATGAAAAATAAGGCCAACTCC 57.594 39.130 5.01 0.00 0.00 3.85
210 211 7.728847 AAAACATGAAAAATAAGGCCAACTC 57.271 32.000 5.01 0.00 0.00 3.01
211 212 7.772757 TGAAAAACATGAAAAATAAGGCCAACT 59.227 29.630 5.01 0.00 0.00 3.16
212 213 7.924940 TGAAAAACATGAAAAATAAGGCCAAC 58.075 30.769 5.01 0.00 0.00 3.77
213 214 8.688747 ATGAAAAACATGAAAAATAAGGCCAA 57.311 26.923 5.01 0.00 37.87 4.52
214 215 9.956640 ATATGAAAAACATGAAAAATAAGGCCA 57.043 25.926 5.01 0.00 39.77 5.36
239 240 9.822185 GGCTGATCTGGTTTATAAATTTTTCAT 57.178 29.630 0.31 0.00 0.00 2.57
246 247 7.732222 TTTTGGGCTGATCTGGTTTATAAAT 57.268 32.000 0.31 0.00 0.00 1.40
270 271 7.916914 ATTACGTAGGCACTTTGTAGAATTT 57.083 32.000 0.00 0.00 41.75 1.82
358 362 9.689501 AGGAGTATATGCTAGTAGTAGAAATCC 57.310 37.037 8.87 5.93 0.00 3.01
360 364 8.962679 GCAGGAGTATATGCTAGTAGTAGAAAT 58.037 37.037 8.87 4.00 39.38 2.17
361 365 8.338072 GCAGGAGTATATGCTAGTAGTAGAAA 57.662 38.462 8.87 0.00 39.38 2.52
402 406 9.193806 ACACTCTTATATTAGTTTACGGAAGGA 57.806 33.333 0.00 0.00 0.00 3.36
403 407 9.813446 AACACTCTTATATTAGTTTACGGAAGG 57.187 33.333 0.00 0.00 0.00 3.46
455 459 9.832445 CTCCCTCTGTAAACTAATATAAAAGCA 57.168 33.333 0.00 0.00 0.00 3.91
456 460 9.833917 ACTCCCTCTGTAAACTAATATAAAAGC 57.166 33.333 0.00 0.00 0.00 3.51
464 468 8.877195 TCTTTTGTACTCCCTCTGTAAACTAAT 58.123 33.333 0.00 0.00 0.00 1.73
465 469 8.253867 TCTTTTGTACTCCCTCTGTAAACTAA 57.746 34.615 0.00 0.00 0.00 2.24
466 470 7.844493 TCTTTTGTACTCCCTCTGTAAACTA 57.156 36.000 0.00 0.00 0.00 2.24
467 471 6.742559 TCTTTTGTACTCCCTCTGTAAACT 57.257 37.500 0.00 0.00 0.00 2.66
468 472 6.427242 CCTTCTTTTGTACTCCCTCTGTAAAC 59.573 42.308 0.00 0.00 0.00 2.01
469 473 6.328148 TCCTTCTTTTGTACTCCCTCTGTAAA 59.672 38.462 0.00 0.00 0.00 2.01
470 474 5.842328 TCCTTCTTTTGTACTCCCTCTGTAA 59.158 40.000 0.00 0.00 0.00 2.41
471 475 5.399991 TCCTTCTTTTGTACTCCCTCTGTA 58.600 41.667 0.00 0.00 0.00 2.74
472 476 4.232091 TCCTTCTTTTGTACTCCCTCTGT 58.768 43.478 0.00 0.00 0.00 3.41
473 477 4.891992 TCCTTCTTTTGTACTCCCTCTG 57.108 45.455 0.00 0.00 0.00 3.35
474 478 5.746361 GCTTTCCTTCTTTTGTACTCCCTCT 60.746 44.000 0.00 0.00 0.00 3.69
475 479 4.456222 GCTTTCCTTCTTTTGTACTCCCTC 59.544 45.833 0.00 0.00 0.00 4.30
476 480 4.399219 GCTTTCCTTCTTTTGTACTCCCT 58.601 43.478 0.00 0.00 0.00 4.20
477 481 3.506455 GGCTTTCCTTCTTTTGTACTCCC 59.494 47.826 0.00 0.00 0.00 4.30
478 482 4.142038 TGGCTTTCCTTCTTTTGTACTCC 58.858 43.478 0.00 0.00 0.00 3.85
479 483 5.767816 TTGGCTTTCCTTCTTTTGTACTC 57.232 39.130 0.00 0.00 0.00 2.59
480 484 5.891551 TCTTTGGCTTTCCTTCTTTTGTACT 59.108 36.000 0.00 0.00 0.00 2.73
481 485 6.144078 TCTTTGGCTTTCCTTCTTTTGTAC 57.856 37.500 0.00 0.00 0.00 2.90
482 486 6.976934 ATCTTTGGCTTTCCTTCTTTTGTA 57.023 33.333 0.00 0.00 0.00 2.41
483 487 5.876651 ATCTTTGGCTTTCCTTCTTTTGT 57.123 34.783 0.00 0.00 0.00 2.83
484 488 6.748132 TGTATCTTTGGCTTTCCTTCTTTTG 58.252 36.000 0.00 0.00 0.00 2.44
485 489 6.976934 TGTATCTTTGGCTTTCCTTCTTTT 57.023 33.333 0.00 0.00 0.00 2.27
486 490 8.829373 ATATGTATCTTTGGCTTTCCTTCTTT 57.171 30.769 0.00 0.00 0.00 2.52
487 491 8.689972 CAATATGTATCTTTGGCTTTCCTTCTT 58.310 33.333 0.00 0.00 0.00 2.52
488 492 7.836183 ACAATATGTATCTTTGGCTTTCCTTCT 59.164 33.333 0.00 0.00 0.00 2.85
489 493 7.917505 CACAATATGTATCTTTGGCTTTCCTTC 59.082 37.037 0.00 0.00 0.00 3.46
490 494 7.615365 TCACAATATGTATCTTTGGCTTTCCTT 59.385 33.333 0.00 0.00 0.00 3.36
491 495 7.118723 TCACAATATGTATCTTTGGCTTTCCT 58.881 34.615 0.00 0.00 0.00 3.36
492 496 7.333528 TCACAATATGTATCTTTGGCTTTCC 57.666 36.000 0.00 0.00 0.00 3.13
493 497 9.241317 CATTCACAATATGTATCTTTGGCTTTC 57.759 33.333 0.00 0.00 0.00 2.62
496 500 7.886629 ACATTCACAATATGTATCTTTGGCT 57.113 32.000 0.00 0.00 34.59 4.75
498 502 8.685427 TGGAACATTCACAATATGTATCTTTGG 58.315 33.333 0.00 0.00 35.26 3.28
519 523 4.820894 AGATAGGGTACAAGTGTGGAAC 57.179 45.455 0.00 0.00 37.35 3.62
520 524 4.595781 ACAAGATAGGGTACAAGTGTGGAA 59.404 41.667 0.00 0.00 0.00 3.53
521 525 4.164981 ACAAGATAGGGTACAAGTGTGGA 58.835 43.478 0.00 0.00 0.00 4.02
522 526 4.553330 ACAAGATAGGGTACAAGTGTGG 57.447 45.455 0.00 0.00 0.00 4.17
523 527 6.698380 AGTTACAAGATAGGGTACAAGTGTG 58.302 40.000 0.00 0.00 0.00 3.82
524 528 6.930068 AGTTACAAGATAGGGTACAAGTGT 57.070 37.500 0.00 0.00 0.00 3.55
525 529 9.314321 CATAAGTTACAAGATAGGGTACAAGTG 57.686 37.037 0.00 0.00 0.00 3.16
526 530 9.043548 ACATAAGTTACAAGATAGGGTACAAGT 57.956 33.333 0.00 0.00 0.00 3.16
532 536 9.209048 TGACATACATAAGTTACAAGATAGGGT 57.791 33.333 0.00 0.00 0.00 4.34
572 576 8.667463 GCACCGTAAAATAGGTTACAAGATAAA 58.333 33.333 0.00 0.00 39.00 1.40
651 942 1.003696 GAGAGGGTTCCTGGGACAAAG 59.996 57.143 7.57 0.00 38.70 2.77
758 1049 9.173021 TCTGTGTCATTTGTTTCTCTCTAAAAA 57.827 29.630 0.00 0.00 0.00 1.94
759 1050 8.731275 TCTGTGTCATTTGTTTCTCTCTAAAA 57.269 30.769 0.00 0.00 0.00 1.52
766 1057 3.057946 GGGCTCTGTGTCATTTGTTTCTC 60.058 47.826 0.00 0.00 0.00 2.87
768 1059 2.622942 TGGGCTCTGTGTCATTTGTTTC 59.377 45.455 0.00 0.00 0.00 2.78
769 1060 2.665165 TGGGCTCTGTGTCATTTGTTT 58.335 42.857 0.00 0.00 0.00 2.83
772 1065 3.181493 GCTATTGGGCTCTGTGTCATTTG 60.181 47.826 0.00 0.00 0.00 2.32
774 1067 2.240667 AGCTATTGGGCTCTGTGTCATT 59.759 45.455 0.00 0.00 38.24 2.57
1635 2205 3.418623 ATGGGGAGGAGGAGGAGGC 62.419 68.421 0.00 0.00 0.00 4.70
2777 3832 6.769822 AGAGCATAGAAAGTTGGTCATAATGG 59.230 38.462 5.11 0.00 41.60 3.16
2794 3863 5.238868 CACCAAAGATCATGGAAGAGCATAG 59.761 44.000 20.76 0.00 40.56 2.23
3035 4124 5.744171 TGAGCTTAGCCTTGTCAATTGATA 58.256 37.500 12.12 6.04 0.00 2.15
3128 4217 2.279741 GGCGTTGATGCATCTAAGTCA 58.720 47.619 26.32 4.69 36.28 3.41
3144 4233 1.861982 AATACAGAGTAGGGTGGCGT 58.138 50.000 0.00 0.00 0.00 5.68
3150 4239 5.187186 ACACAACCACTAATACAGAGTAGGG 59.813 44.000 0.00 0.00 0.00 3.53
3199 4288 6.910972 CACATGTTAAGATCAGCACATCAATC 59.089 38.462 0.00 0.00 0.00 2.67
3591 4691 1.942776 TCAGAGTGCCATTCTCCTCA 58.057 50.000 0.00 0.00 32.93 3.86
3675 4775 7.435488 GTGATGCTTTAGCTCTAAATCTAACGA 59.565 37.037 3.10 0.00 42.66 3.85
3714 4816 1.583054 AAGACGAAGACAGTTGCACC 58.417 50.000 0.00 0.00 0.00 5.01
3729 4831 1.067565 GCAGCTTAAGGGGCAAAAGAC 60.068 52.381 4.29 0.00 0.00 3.01
3739 4841 2.370281 TCGAACTGAGCAGCTTAAGG 57.630 50.000 4.29 0.00 0.00 2.69
3766 4868 7.871463 AGAATGCTTTCATTTTTCCTTCTCTTG 59.129 33.333 14.15 0.00 42.60 3.02
3771 4873 7.816031 TGATCAGAATGCTTTCATTTTTCCTTC 59.184 33.333 14.15 0.45 42.60 3.46
3781 4884 6.376299 AGCAATTAGTGATCAGAATGCTTTCA 59.624 34.615 14.15 0.00 34.76 2.69
3854 4957 2.289072 TGAAGTGGACAGAAGCTACTGC 60.289 50.000 0.00 0.00 41.06 4.40
3855 4958 3.667497 TGAAGTGGACAGAAGCTACTG 57.333 47.619 0.00 0.00 42.78 2.74
3915 5019 2.017049 GGATCGGGAAACACAAGATGG 58.983 52.381 0.00 0.00 0.00 3.51
3930 5034 4.391216 GGCATCTGATATCAACAAGGATCG 59.609 45.833 6.90 2.97 0.00 3.69
4023 5127 6.529125 CACTAGAAAATGCACATGTGAATTCC 59.471 38.462 28.52 22.41 37.85 3.01
4056 5160 7.654520 GCCATTGACATTTGACAAAGCATATAT 59.345 33.333 6.77 0.00 35.19 0.86
4057 5161 6.979817 GCCATTGACATTTGACAAAGCATATA 59.020 34.615 6.77 0.00 35.19 0.86
4058 5162 5.813672 GCCATTGACATTTGACAAAGCATAT 59.186 36.000 6.77 0.00 35.19 1.78
4059 5163 5.170021 GCCATTGACATTTGACAAAGCATA 58.830 37.500 6.77 0.00 35.19 3.14
4060 5164 3.998341 GCCATTGACATTTGACAAAGCAT 59.002 39.130 6.77 0.00 35.19 3.79
4061 5165 3.181468 TGCCATTGACATTTGACAAAGCA 60.181 39.130 14.74 14.74 39.03 3.91
4062 5166 3.391965 TGCCATTGACATTTGACAAAGC 58.608 40.909 6.77 11.37 35.43 3.51
4063 5167 7.546316 TCAATATGCCATTGACATTTGACAAAG 59.454 33.333 6.77 1.89 33.55 2.77
4065 5169 6.932947 TCAATATGCCATTGACATTTGACAA 58.067 32.000 6.71 0.00 33.55 3.18
4066 5170 6.527057 TCAATATGCCATTGACATTTGACA 57.473 33.333 6.71 0.00 33.55 3.58
4067 5171 6.019318 GCTTCAATATGCCATTGACATTTGAC 60.019 38.462 9.65 0.39 37.71 3.18
4068 5172 6.044046 GCTTCAATATGCCATTGACATTTGA 58.956 36.000 9.65 0.00 37.71 2.69
4069 5173 6.281848 GCTTCAATATGCCATTGACATTTG 57.718 37.500 9.65 0.00 37.71 2.32
4123 5227 8.864087 AGAAAAGAAAAGGAATCAACAGCTATT 58.136 29.630 0.00 0.00 0.00 1.73
4150 5256 6.672266 TGAGAATCAACAGAACTTCTACCT 57.328 37.500 0.00 0.00 45.97 3.08
4269 5375 7.489160 AGTGAAAAGGATGTTGTTAAAAGGAC 58.511 34.615 0.00 0.00 0.00 3.85
4381 5489 0.928505 AGTGGGATTGCATGATGGGA 59.071 50.000 0.00 0.00 0.00 4.37
4396 5504 8.103948 AGAATTGTCAGAAAGTAATGAAGTGG 57.896 34.615 0.00 0.00 0.00 4.00
4459 5567 1.016130 CAGTGTCTAACAGCCAGGCG 61.016 60.000 5.55 3.56 0.00 5.52


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

AutoCloner maintained by Alex Coulton.