Multiple sequence alignment - TraesCS2D01G057000

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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 TraesCS2D01G057000 chr2D 100.000 2933 0 0 1 2933 22766625 22769557 0.000000e+00 5417
1 TraesCS2D01G057000 chr2D 89.452 493 48 3 1 492 128971021 128971510 1.150000e-173 619
2 TraesCS2D01G057000 chr2A 94.858 1478 33 16 674 2124 24363615 24365076 0.000000e+00 2268
3 TraesCS2D01G057000 chr2A 91.801 622 34 8 2122 2742 24365836 24366441 0.000000e+00 850
4 TraesCS2D01G057000 chr2A 93.617 141 4 2 492 631 24363480 24363616 3.830000e-49 206
5 TraesCS2D01G057000 chr2A 97.674 43 1 0 2781 2823 24366440 24366482 1.130000e-09 75
6 TraesCS2D01G057000 chr1B 91.998 1612 48 29 491 2085 49016093 49017640 0.000000e+00 2187
7 TraesCS2D01G057000 chr1B 92.755 1532 58 22 510 2022 49429416 49430913 0.000000e+00 2165
8 TraesCS2D01G057000 chr1B 90.968 310 25 1 2622 2928 49446754 49447063 5.850000e-112 414
9 TraesCS2D01G057000 chr1B 93.525 278 15 1 2654 2928 49023887 49024164 7.570000e-111 411
10 TraesCS2D01G057000 chr1B 95.146 103 4 1 2022 2124 49446504 49446605 8.410000e-36 161
11 TraesCS2D01G057000 chr7B 93.418 471 28 3 2122 2591 727268144 727268612 0.000000e+00 695
12 TraesCS2D01G057000 chr1D 90.283 494 46 2 1 492 259597244 259596751 0.000000e+00 645
13 TraesCS2D01G057000 chr1D 93.750 304 17 2 2122 2425 402285437 402285136 3.450000e-124 455
14 TraesCS2D01G057000 chr1D 97.802 182 3 1 2412 2592 402156606 402156425 2.190000e-81 313
15 TraesCS2D01G057000 chr1A 86.207 522 41 12 1 492 325790451 325789931 1.200000e-148 536
16 TraesCS2D01G057000 chr5A 86.228 501 53 14 1 492 437910575 437911068 2.000000e-146 529
17 TraesCS2D01G057000 chr5A 75.130 579 121 19 1077 1646 531019311 531019875 1.750000e-62 250
18 TraesCS2D01G057000 chr7D 84.569 499 65 11 1 492 399645469 399645962 4.390000e-133 484
19 TraesCS2D01G057000 chr3D 84.787 493 47 15 1 492 79620790 79621255 1.230000e-128 470
20 TraesCS2D01G057000 chr6D 84.926 471 60 10 1 465 390170157 390169692 1.590000e-127 466
21 TraesCS2D01G057000 chr5D 82.834 501 74 11 1 492 442766210 442765713 3.470000e-119 438
22 TraesCS2D01G057000 chr7A 82.424 495 76 11 1 490 109070505 109070017 3.490000e-114 422
23 TraesCS2D01G057000 chr3B 81.644 365 57 9 134 492 410716915 410716555 7.950000e-76 294
24 TraesCS2D01G057000 chr5B 75.172 580 119 21 1077 1646 504775440 504776004 1.750000e-62 250


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 TraesCS2D01G057000 chr2D 22766625 22769557 2932 False 5417.00 5417 100.0000 1 2933 1 chr2D.!!$F1 2932
1 TraesCS2D01G057000 chr2A 24363480 24366482 3002 False 849.75 2268 94.4875 492 2823 4 chr2A.!!$F1 2331
2 TraesCS2D01G057000 chr1B 49016093 49017640 1547 False 2187.00 2187 91.9980 491 2085 1 chr1B.!!$F1 1594
3 TraesCS2D01G057000 chr1B 49429416 49430913 1497 False 2165.00 2165 92.7550 510 2022 1 chr1B.!!$F3 1512
4 TraesCS2D01G057000 chr1B 49446504 49447063 559 False 287.50 414 93.0570 2022 2928 2 chr1B.!!$F4 906
5 TraesCS2D01G057000 chr1A 325789931 325790451 520 True 536.00 536 86.2070 1 492 1 chr1A.!!$R1 491
6 TraesCS2D01G057000 chr5A 531019311 531019875 564 False 250.00 250 75.1300 1077 1646 1 chr5A.!!$F2 569
7 TraesCS2D01G057000 chr5B 504775440 504776004 564 False 250.00 250 75.1720 1077 1646 1 chr5B.!!$F1 569

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
207 208 0.102300 AAGCAACAGGTTTTGTCGGC 59.898 50.0 0.00 0.0 39.73 5.54 F
480 481 0.105246 TGTTGGCCATGGGGTCTTTT 60.105 50.0 15.13 0.0 40.42 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1848 1917 0.322098 TGACCCCGCCATAGTTGTTG 60.322 55.0 0.0 0.0 0.00 3.33 R
2405 3252 0.477204 AGATGATCCCCTACGGACGA 59.523 55.0 0.0 0.0 46.09 4.20 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
37 38 0.601057 CCGGGCGAAAGAACCAAAAT 59.399 50.000 0.00 0.00 0.00 1.82
40 41 2.668279 CGGGCGAAAGAACCAAAATCAG 60.668 50.000 0.00 0.00 0.00 2.90
41 42 2.328473 GGCGAAAGAACCAAAATCAGC 58.672 47.619 0.00 0.00 0.00 4.26
47 48 5.540911 GAAAGAACCAAAATCAGCCATCAA 58.459 37.500 0.00 0.00 0.00 2.57
54 55 2.425143 AATCAGCCATCAACGTCCAT 57.575 45.000 0.00 0.00 0.00 3.41
55 56 3.558931 AATCAGCCATCAACGTCCATA 57.441 42.857 0.00 0.00 0.00 2.74
56 57 3.777106 ATCAGCCATCAACGTCCATAT 57.223 42.857 0.00 0.00 0.00 1.78
57 58 3.558931 TCAGCCATCAACGTCCATATT 57.441 42.857 0.00 0.00 0.00 1.28
58 59 3.466836 TCAGCCATCAACGTCCATATTC 58.533 45.455 0.00 0.00 0.00 1.75
59 60 2.549754 CAGCCATCAACGTCCATATTCC 59.450 50.000 0.00 0.00 0.00 3.01
60 61 1.880027 GCCATCAACGTCCATATTCCC 59.120 52.381 0.00 0.00 0.00 3.97
61 62 2.143122 CCATCAACGTCCATATTCCCG 58.857 52.381 0.00 0.00 0.00 5.14
62 63 1.531149 CATCAACGTCCATATTCCCGC 59.469 52.381 0.00 0.00 0.00 6.13
63 64 0.528901 TCAACGTCCATATTCCCGCG 60.529 55.000 0.00 0.00 0.00 6.46
64 65 1.885850 AACGTCCATATTCCCGCGC 60.886 57.895 0.00 0.00 0.00 6.86
65 66 3.403057 CGTCCATATTCCCGCGCG 61.403 66.667 25.67 25.67 0.00 6.86
66 67 2.279918 GTCCATATTCCCGCGCGT 60.280 61.111 29.95 12.94 0.00 6.01
67 68 2.279851 TCCATATTCCCGCGCGTG 60.280 61.111 29.95 19.21 0.00 5.34
68 69 4.012895 CCATATTCCCGCGCGTGC 62.013 66.667 29.95 11.84 37.91 5.34
79 80 4.191485 CGCGTGCGAATCACCGTC 62.191 66.667 8.89 0.00 42.69 4.79
80 81 4.191485 GCGTGCGAATCACCGTCG 62.191 66.667 0.00 0.00 42.69 5.12
81 82 2.803670 CGTGCGAATCACCGTCGT 60.804 61.111 0.00 0.00 42.69 4.34
82 83 2.774951 CGTGCGAATCACCGTCGTC 61.775 63.158 0.00 0.00 42.69 4.20
83 84 1.731613 GTGCGAATCACCGTCGTCA 60.732 57.895 0.00 0.00 40.64 4.35
84 85 1.443702 TGCGAATCACCGTCGTCAG 60.444 57.895 0.00 0.00 40.64 3.51
85 86 2.789203 GCGAATCACCGTCGTCAGC 61.789 63.158 0.00 0.00 40.64 4.26
86 87 2.497092 CGAATCACCGTCGTCAGCG 61.497 63.158 0.00 0.00 39.92 5.18
87 88 1.443872 GAATCACCGTCGTCAGCGT 60.444 57.895 0.00 0.00 39.49 5.07
88 89 1.403972 GAATCACCGTCGTCAGCGTC 61.404 60.000 0.00 0.00 39.49 5.19
89 90 3.662623 ATCACCGTCGTCAGCGTCG 62.663 63.158 0.00 0.00 45.93 5.12
107 108 2.892425 CTGTCGCGCCTGGGAATC 60.892 66.667 0.00 0.00 38.96 2.52
108 109 3.664025 CTGTCGCGCCTGGGAATCA 62.664 63.158 0.00 0.00 38.96 2.57
109 110 2.892425 GTCGCGCCTGGGAATCAG 60.892 66.667 0.00 0.00 43.00 2.90
116 117 2.190578 CTGGGAATCAGGGCCGTC 59.809 66.667 0.00 0.00 39.76 4.79
117 118 2.609299 TGGGAATCAGGGCCGTCA 60.609 61.111 0.00 0.00 0.00 4.35
118 119 2.190578 GGGAATCAGGGCCGTCAG 59.809 66.667 0.00 0.00 0.00 3.51
119 120 2.514824 GGAATCAGGGCCGTCAGC 60.515 66.667 0.00 0.00 42.60 4.26
120 121 2.892425 GAATCAGGGCCGTCAGCG 60.892 66.667 0.00 0.00 45.17 5.18
121 122 3.665675 GAATCAGGGCCGTCAGCGT 62.666 63.158 0.00 0.00 45.17 5.07
122 123 3.958147 AATCAGGGCCGTCAGCGTG 62.958 63.158 0.00 0.00 45.17 5.34
155 156 3.847602 CAGAGAGGCCGCCTGGAG 61.848 72.222 19.21 0.00 37.49 3.86
156 157 4.390556 AGAGAGGCCGCCTGGAGT 62.391 66.667 19.21 0.00 37.49 3.85
157 158 2.442272 GAGAGGCCGCCTGGAGTA 60.442 66.667 19.21 0.00 37.49 2.59
158 159 2.443016 AGAGGCCGCCTGGAGTAG 60.443 66.667 19.21 0.00 37.49 2.57
159 160 2.760385 GAGGCCGCCTGGAGTAGT 60.760 66.667 19.21 0.00 37.49 2.73
160 161 3.077556 AGGCCGCCTGGAGTAGTG 61.078 66.667 12.38 0.00 37.49 2.74
161 162 4.162690 GGCCGCCTGGAGTAGTGG 62.163 72.222 0.71 0.00 37.49 4.00
162 163 4.840005 GCCGCCTGGAGTAGTGGC 62.840 72.222 0.00 0.00 42.94 5.01
165 166 4.840005 GCCTGGAGTAGTGGCGGC 62.840 72.222 0.00 0.00 37.11 6.53
166 167 4.514577 CCTGGAGTAGTGGCGGCG 62.515 72.222 0.51 0.51 0.00 6.46
167 168 3.760035 CTGGAGTAGTGGCGGCGT 61.760 66.667 9.37 0.00 0.00 5.68
168 169 3.989698 CTGGAGTAGTGGCGGCGTG 62.990 68.421 9.37 0.00 0.00 5.34
169 170 4.814294 GGAGTAGTGGCGGCGTGG 62.814 72.222 9.37 0.00 0.00 4.94
199 200 3.605664 GCCCGCAAGCAACAGGTT 61.606 61.111 0.00 0.00 0.00 3.50
200 201 3.128375 CCCGCAAGCAACAGGTTT 58.872 55.556 0.00 0.00 0.00 3.27
201 202 1.441311 CCCGCAAGCAACAGGTTTT 59.559 52.632 0.00 0.00 0.00 2.43
202 203 0.875474 CCCGCAAGCAACAGGTTTTG 60.875 55.000 0.00 0.00 0.00 2.44
203 204 0.179113 CCGCAAGCAACAGGTTTTGT 60.179 50.000 0.00 0.00 43.45 2.83
204 205 1.199624 CGCAAGCAACAGGTTTTGTC 58.800 50.000 0.00 0.00 39.73 3.18
205 206 1.199624 GCAAGCAACAGGTTTTGTCG 58.800 50.000 0.00 0.00 39.73 4.35
206 207 1.838913 CAAGCAACAGGTTTTGTCGG 58.161 50.000 0.00 0.00 39.73 4.79
207 208 0.102300 AAGCAACAGGTTTTGTCGGC 59.898 50.000 0.00 0.00 39.73 5.54
208 209 1.299850 GCAACAGGTTTTGTCGGCC 60.300 57.895 0.00 0.00 39.73 6.13
209 210 1.734388 GCAACAGGTTTTGTCGGCCT 61.734 55.000 0.00 0.00 39.73 5.19
211 212 2.644992 CAGGTTTTGTCGGCCTGC 59.355 61.111 0.00 0.00 42.54 4.85
212 213 2.192861 CAGGTTTTGTCGGCCTGCA 61.193 57.895 0.00 0.00 42.54 4.41
213 214 1.454847 AGGTTTTGTCGGCCTGCAA 60.455 52.632 0.00 2.57 0.00 4.08
214 215 1.007387 GGTTTTGTCGGCCTGCAAG 60.007 57.895 0.00 0.00 0.00 4.01
215 216 1.661509 GTTTTGTCGGCCTGCAAGC 60.662 57.895 0.00 0.00 0.00 4.01
216 217 3.192954 TTTTGTCGGCCTGCAAGCG 62.193 57.895 0.00 0.00 0.00 4.68
217 218 4.617520 TTGTCGGCCTGCAAGCGA 62.618 61.111 0.00 0.00 0.00 4.93
220 221 4.393155 TCGGCCTGCAAGCGACAT 62.393 61.111 0.00 0.00 0.00 3.06
221 222 4.170062 CGGCCTGCAAGCGACATG 62.170 66.667 0.00 0.00 0.00 3.21
222 223 3.058160 GGCCTGCAAGCGACATGT 61.058 61.111 0.00 0.00 0.00 3.21
223 224 2.177531 GCCTGCAAGCGACATGTG 59.822 61.111 1.15 0.00 0.00 3.21
224 225 2.177531 CCTGCAAGCGACATGTGC 59.822 61.111 1.15 7.67 38.78 4.57
225 226 2.619165 CCTGCAAGCGACATGTGCA 61.619 57.895 18.31 13.46 45.62 4.57
226 227 2.948323 TGCAAGCGACATGTGCAG 59.052 55.556 18.31 12.71 43.09 4.41
227 228 2.503375 GCAAGCGACATGTGCAGC 60.503 61.111 18.31 16.94 38.19 5.25
228 229 2.202260 CAAGCGACATGTGCAGCG 60.202 61.111 18.31 10.74 33.85 5.18
278 279 3.924507 CCAGGCCTGGCACATTAC 58.075 61.111 38.39 1.14 44.73 1.89
279 280 1.001020 CCAGGCCTGGCACATTACA 60.001 57.895 38.39 0.00 44.73 2.41
280 281 0.396139 CCAGGCCTGGCACATTACAT 60.396 55.000 38.39 0.00 44.73 2.29
281 282 1.027357 CAGGCCTGGCACATTACATC 58.973 55.000 26.14 0.00 38.20 3.06
282 283 0.106519 AGGCCTGGCACATTACATCC 60.107 55.000 22.05 0.00 38.20 3.51
283 284 1.109323 GGCCTGGCACATTACATCCC 61.109 60.000 22.05 0.00 38.20 3.85
284 285 1.447317 GCCTGGCACATTACATCCCG 61.447 60.000 15.17 0.00 38.20 5.14
285 286 0.819259 CCTGGCACATTACATCCCGG 60.819 60.000 0.00 0.00 38.20 5.73
286 287 1.447317 CTGGCACATTACATCCCGGC 61.447 60.000 0.00 0.00 38.20 6.13
287 288 1.152963 GGCACATTACATCCCGGCT 60.153 57.895 0.00 0.00 0.00 5.52
288 289 1.447317 GGCACATTACATCCCGGCTG 61.447 60.000 0.00 0.00 0.00 4.85
289 290 2.024918 CACATTACATCCCGGCTGC 58.975 57.895 0.00 0.00 0.00 5.25
290 291 0.464373 CACATTACATCCCGGCTGCT 60.464 55.000 0.00 0.00 0.00 4.24
291 292 0.464373 ACATTACATCCCGGCTGCTG 60.464 55.000 0.26 0.26 0.00 4.41
292 293 1.526917 ATTACATCCCGGCTGCTGC 60.527 57.895 7.10 7.10 38.76 5.25
293 294 4.529219 TACATCCCGGCTGCTGCG 62.529 66.667 9.65 5.10 40.82 5.18
308 309 3.409856 GCGCTGTGCATAATCCGT 58.590 55.556 8.57 0.00 45.45 4.69
309 310 1.721487 GCGCTGTGCATAATCCGTT 59.279 52.632 8.57 0.00 45.45 4.44
310 311 0.934496 GCGCTGTGCATAATCCGTTA 59.066 50.000 8.57 0.00 45.45 3.18
311 312 1.332904 GCGCTGTGCATAATCCGTTAC 60.333 52.381 8.57 0.00 45.45 2.50
312 313 1.930503 CGCTGTGCATAATCCGTTACA 59.069 47.619 0.00 0.00 0.00 2.41
313 314 2.285602 CGCTGTGCATAATCCGTTACAC 60.286 50.000 0.00 0.00 0.00 2.90
314 315 2.031683 GCTGTGCATAATCCGTTACACC 59.968 50.000 0.00 0.00 0.00 4.16
315 316 2.612212 CTGTGCATAATCCGTTACACCC 59.388 50.000 0.00 0.00 0.00 4.61
316 317 1.944709 GTGCATAATCCGTTACACCCC 59.055 52.381 0.00 0.00 0.00 4.95
317 318 1.223187 GCATAATCCGTTACACCCCG 58.777 55.000 0.00 0.00 0.00 5.73
318 319 1.223187 CATAATCCGTTACACCCCGC 58.777 55.000 0.00 0.00 0.00 6.13
319 320 0.249573 ATAATCCGTTACACCCCGCG 60.250 55.000 0.00 0.00 0.00 6.46
320 321 2.904470 TAATCCGTTACACCCCGCGC 62.904 60.000 0.00 0.00 0.00 6.86
420 421 3.966543 CACGGCCCAGGGGTCTTT 61.967 66.667 7.91 0.00 37.84 2.52
421 422 3.182996 ACGGCCCAGGGGTCTTTT 61.183 61.111 7.91 0.00 37.84 2.27
422 423 2.117423 CGGCCCAGGGGTCTTTTT 59.883 61.111 7.91 0.00 37.84 1.94
444 445 7.795482 TTTTGTCAAATATATCCACGGGTAG 57.205 36.000 0.00 0.00 0.00 3.18
445 446 6.488769 TTGTCAAATATATCCACGGGTAGT 57.511 37.500 0.00 0.00 0.00 2.73
446 447 6.092955 TGTCAAATATATCCACGGGTAGTC 57.907 41.667 0.00 0.00 0.00 2.59
447 448 5.011329 TGTCAAATATATCCACGGGTAGTCC 59.989 44.000 0.00 0.00 0.00 3.85
448 449 5.245526 GTCAAATATATCCACGGGTAGTCCT 59.754 44.000 0.00 0.00 0.00 3.85
449 450 5.842328 TCAAATATATCCACGGGTAGTCCTT 59.158 40.000 0.00 0.00 0.00 3.36
450 451 6.328148 TCAAATATATCCACGGGTAGTCCTTT 59.672 38.462 0.00 0.00 0.00 3.11
451 452 6.758806 AATATATCCACGGGTAGTCCTTTT 57.241 37.500 0.00 0.00 0.00 2.27
452 453 6.758806 ATATATCCACGGGTAGTCCTTTTT 57.241 37.500 0.00 0.00 0.00 1.94
453 454 2.554370 TCCACGGGTAGTCCTTTTTG 57.446 50.000 0.00 0.00 0.00 2.44
454 455 2.048601 TCCACGGGTAGTCCTTTTTGA 58.951 47.619 0.00 0.00 0.00 2.69
455 456 2.148768 CCACGGGTAGTCCTTTTTGAC 58.851 52.381 0.00 0.00 35.43 3.18
456 457 2.485835 CCACGGGTAGTCCTTTTTGACA 60.486 50.000 0.00 0.00 37.73 3.58
457 458 3.207778 CACGGGTAGTCCTTTTTGACAA 58.792 45.455 0.00 0.00 37.73 3.18
458 459 3.818773 CACGGGTAGTCCTTTTTGACAAT 59.181 43.478 0.00 0.00 37.73 2.71
459 460 4.277423 CACGGGTAGTCCTTTTTGACAATT 59.723 41.667 0.00 0.00 37.73 2.32
460 461 4.517832 ACGGGTAGTCCTTTTTGACAATTC 59.482 41.667 0.00 0.00 37.73 2.17
461 462 4.760204 CGGGTAGTCCTTTTTGACAATTCT 59.240 41.667 0.00 0.00 37.73 2.40
462 463 5.334879 CGGGTAGTCCTTTTTGACAATTCTG 60.335 44.000 0.00 0.00 37.73 3.02
463 464 5.535030 GGGTAGTCCTTTTTGACAATTCTGT 59.465 40.000 0.00 0.00 37.73 3.41
464 465 6.040504 GGGTAGTCCTTTTTGACAATTCTGTT 59.959 38.462 0.00 0.00 37.73 3.16
465 466 6.918022 GGTAGTCCTTTTTGACAATTCTGTTG 59.082 38.462 0.00 0.00 37.73 3.33
466 467 5.906073 AGTCCTTTTTGACAATTCTGTTGG 58.094 37.500 0.00 0.00 37.73 3.77
467 468 4.507756 GTCCTTTTTGACAATTCTGTTGGC 59.492 41.667 0.00 0.00 35.30 4.52
468 469 3.809279 CCTTTTTGACAATTCTGTTGGCC 59.191 43.478 0.00 0.00 35.30 5.36
469 470 4.440880 CTTTTTGACAATTCTGTTGGCCA 58.559 39.130 0.00 0.00 35.30 5.36
470 471 4.686191 TTTTGACAATTCTGTTGGCCAT 57.314 36.364 6.09 0.00 35.30 4.40
471 472 3.663995 TTGACAATTCTGTTGGCCATG 57.336 42.857 6.09 1.58 35.30 3.66
472 473 1.894466 TGACAATTCTGTTGGCCATGG 59.106 47.619 6.09 7.63 35.30 3.66
473 474 1.205417 GACAATTCTGTTGGCCATGGG 59.795 52.381 15.13 0.00 35.30 4.00
474 475 0.538118 CAATTCTGTTGGCCATGGGG 59.462 55.000 15.13 0.00 37.18 4.96
475 476 0.116940 AATTCTGTTGGCCATGGGGT 59.883 50.000 15.13 0.00 36.17 4.95
476 477 0.324645 ATTCTGTTGGCCATGGGGTC 60.325 55.000 15.13 0.00 40.08 4.46
477 478 1.434513 TTCTGTTGGCCATGGGGTCT 61.435 55.000 15.13 0.00 40.42 3.85
478 479 1.077265 CTGTTGGCCATGGGGTCTT 59.923 57.895 15.13 0.00 40.42 3.01
479 480 0.542702 CTGTTGGCCATGGGGTCTTT 60.543 55.000 15.13 0.00 40.42 2.52
480 481 0.105246 TGTTGGCCATGGGGTCTTTT 60.105 50.000 15.13 0.00 40.42 2.27
481 482 1.055849 GTTGGCCATGGGGTCTTTTT 58.944 50.000 15.13 0.00 40.42 1.94
482 483 1.055040 TTGGCCATGGGGTCTTTTTG 58.945 50.000 15.13 0.00 40.42 2.44
483 484 0.835543 TGGCCATGGGGTCTTTTTGG 60.836 55.000 15.13 0.00 40.42 3.28
484 485 0.544120 GGCCATGGGGTCTTTTTGGA 60.544 55.000 15.13 0.00 35.27 3.53
485 486 0.608130 GCCATGGGGTCTTTTTGGAC 59.392 55.000 15.13 0.00 36.17 4.02
486 487 2.008242 CCATGGGGTCTTTTTGGACA 57.992 50.000 2.85 0.00 37.91 4.02
487 488 2.324541 CCATGGGGTCTTTTTGGACAA 58.675 47.619 2.85 0.00 37.91 3.18
488 489 2.703007 CCATGGGGTCTTTTTGGACAAA 59.297 45.455 2.85 0.00 37.91 2.83
489 490 3.135530 CCATGGGGTCTTTTTGGACAAAA 59.864 43.478 2.85 6.14 38.40 2.44
490 491 4.384647 CCATGGGGTCTTTTTGGACAAAAA 60.385 41.667 18.58 18.58 44.98 1.94
532 533 7.136289 TGTAGCTAACTAACCGGAAAATTTG 57.864 36.000 9.46 0.00 0.00 2.32
533 534 6.711645 TGTAGCTAACTAACCGGAAAATTTGT 59.288 34.615 9.46 0.00 0.00 2.83
629 630 1.134340 ACCAAAGGAACACGCACTGTA 60.134 47.619 0.00 0.00 30.51 2.74
650 651 7.764901 ACTGTAACATTTTCTACTTAGCTAGCC 59.235 37.037 12.13 0.00 0.00 3.93
670 671 1.071987 TCCTGCACTGCACCTTCAG 59.928 57.895 0.00 0.00 39.86 3.02
791 802 1.502163 GCTCTGCACGTTCACTTGCT 61.502 55.000 9.55 0.00 41.12 3.91
792 803 0.940126 CTCTGCACGTTCACTTGCTT 59.060 50.000 9.55 0.00 41.12 3.91
855 873 4.759096 GCATTCCACGGCGCACAC 62.759 66.667 10.83 0.00 0.00 3.82
856 874 3.353029 CATTCCACGGCGCACACA 61.353 61.111 10.83 0.00 0.00 3.72
894 912 3.257127 CCTACTCCTACCTTAGCTGCATC 59.743 52.174 1.02 0.00 0.00 3.91
895 913 3.039252 ACTCCTACCTTAGCTGCATCT 57.961 47.619 1.02 0.00 0.00 2.90
896 914 4.186077 ACTCCTACCTTAGCTGCATCTA 57.814 45.455 1.02 0.00 0.00 1.98
897 915 4.746466 ACTCCTACCTTAGCTGCATCTAT 58.254 43.478 1.02 0.00 0.00 1.98
907 925 4.191033 AGCTGCATCTATCTATCTGTGC 57.809 45.455 1.02 0.00 0.00 4.57
998 1016 5.190528 ACAATATCCAGAACCATCTCACTGT 59.809 40.000 0.00 0.00 32.03 3.55
1031 1059 2.989639 CCCTCTCGCATTCCACCA 59.010 61.111 0.00 0.00 0.00 4.17
1032 1060 1.528824 CCCTCTCGCATTCCACCAT 59.471 57.895 0.00 0.00 0.00 3.55
1033 1061 0.816825 CCCTCTCGCATTCCACCATG 60.817 60.000 0.00 0.00 0.00 3.66
1034 1062 0.178767 CCTCTCGCATTCCACCATGA 59.821 55.000 0.00 0.00 0.00 3.07
1035 1063 1.579698 CTCTCGCATTCCACCATGAG 58.420 55.000 0.00 0.00 0.00 2.90
1036 1064 0.904649 TCTCGCATTCCACCATGAGT 59.095 50.000 0.00 0.00 0.00 3.41
1037 1065 1.012086 CTCGCATTCCACCATGAGTG 58.988 55.000 0.00 0.35 46.83 3.51
1038 1066 1.026182 TCGCATTCCACCATGAGTGC 61.026 55.000 8.37 0.00 45.83 4.40
1039 1067 1.307355 CGCATTCCACCATGAGTGCA 61.307 55.000 8.82 0.00 45.26 4.57
1040 1068 1.108776 GCATTCCACCATGAGTGCAT 58.891 50.000 8.37 1.81 44.62 3.96
1815 1884 2.344025 GCCGTTTACCTCAAGTACCTG 58.656 52.381 0.00 0.00 0.00 4.00
1848 1917 2.677875 CCCAAGGTGCAGAAGGCC 60.678 66.667 0.00 0.00 43.89 5.19
1971 2044 1.307097 ACAGCTACGGATCGGAGTAC 58.693 55.000 7.35 0.00 40.38 2.73
1980 2053 4.314121 ACGGATCGGAGTACATACTACTC 58.686 47.826 7.35 0.00 42.28 2.59
2100 2180 6.926630 AGGAATATGATCACTTCTCCTACC 57.073 41.667 13.27 1.94 30.01 3.18
2107 2187 6.928348 TGATCACTTCTCCTACCACTTTTA 57.072 37.500 0.00 0.00 0.00 1.52
2108 2188 6.698380 TGATCACTTCTCCTACCACTTTTAC 58.302 40.000 0.00 0.00 0.00 2.01
2112 2192 2.554563 TCTCCTACCACTTTTACCCCC 58.445 52.381 0.00 0.00 0.00 5.40
2128 2975 9.161629 CTTTTACCCCCAATAATTTTTGCTTAG 57.838 33.333 3.34 0.00 0.00 2.18
2130 2977 4.119136 CCCCCAATAATTTTTGCTTAGCG 58.881 43.478 0.00 0.00 0.00 4.26
2190 3037 0.818938 GGGGTCGTCTTCTTCCTCTC 59.181 60.000 0.00 0.00 0.00 3.20
2261 3108 4.436998 CTCGCGGTCCTGGGTGAC 62.437 72.222 6.13 0.00 34.42 3.67
2294 3141 3.154473 TTCCCCGGCTGGATCTCG 61.154 66.667 15.09 0.00 37.49 4.04
2328 3175 3.242673 CCAGATCAAGAAATCGAAGCTGC 60.243 47.826 0.00 0.00 0.00 5.25
2336 3183 4.507710 AGAAATCGAAGCTGCTGATGTTA 58.492 39.130 1.35 0.00 0.00 2.41
2340 3187 3.254060 TCGAAGCTGCTGATGTTAGAAC 58.746 45.455 1.35 0.00 0.00 3.01
2440 3287 5.653769 GGATCATCTTCATTCCAAGGTTTGA 59.346 40.000 0.00 0.00 0.00 2.69
2500 3348 2.664436 GCCGGCGTCACTGTGTTAC 61.664 63.158 12.58 0.00 0.00 2.50
2523 3371 5.163195 ACAGAAGGACCTGTGTGTTATTTCT 60.163 40.000 8.64 0.00 44.93 2.52
2544 3392 3.662759 TTCTTTGTGGGGTGTCTTTCT 57.337 42.857 0.00 0.00 0.00 2.52
2573 3421 8.627208 ATGTCTGGGCTTTAATATAATCAGTG 57.373 34.615 0.00 0.00 0.00 3.66
2614 3462 1.066303 CCTTTTTGTGCTGCCACGTTA 59.934 47.619 0.00 0.00 45.04 3.18
2615 3463 2.288152 CCTTTTTGTGCTGCCACGTTAT 60.288 45.455 0.00 0.00 45.04 1.89
2835 3690 1.375523 GCCAGTGGACCCAACGTAG 60.376 63.158 15.20 0.00 0.00 3.51
2849 3704 1.821216 ACGTAGGTGGGCTCAATTTG 58.179 50.000 0.00 0.00 0.00 2.32
2890 3745 0.887836 AGCACAGTACACGACCGAGA 60.888 55.000 0.00 0.00 0.00 4.04
2928 3783 1.539496 GGGCCAGTACGCGATCAATAA 60.539 52.381 15.93 0.00 0.00 1.40
2929 3784 2.413837 GGCCAGTACGCGATCAATAAT 58.586 47.619 15.93 0.00 0.00 1.28
2930 3785 3.581755 GGCCAGTACGCGATCAATAATA 58.418 45.455 15.93 0.00 0.00 0.98
2931 3786 3.612860 GGCCAGTACGCGATCAATAATAG 59.387 47.826 15.93 0.00 0.00 1.73
2932 3787 4.482386 GCCAGTACGCGATCAATAATAGA 58.518 43.478 15.93 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.832719 TTTCGCCCGGGAATCAGTCA 61.833 55.000 29.31 0.00 0.00 3.41
37 38 3.466836 GAATATGGACGTTGATGGCTGA 58.533 45.455 0.00 0.00 0.00 4.26
40 41 1.880027 GGGAATATGGACGTTGATGGC 59.120 52.381 0.00 0.00 0.00 4.40
41 42 2.143122 CGGGAATATGGACGTTGATGG 58.857 52.381 0.00 0.00 0.00 3.51
47 48 2.279918 GCGCGGGAATATGGACGT 60.280 61.111 8.83 0.00 0.00 4.34
65 66 1.674611 CTGACGACGGTGATTCGCAC 61.675 60.000 0.00 0.00 46.98 5.34
66 67 1.443702 CTGACGACGGTGATTCGCA 60.444 57.895 0.00 0.00 40.24 5.10
67 68 2.789203 GCTGACGACGGTGATTCGC 61.789 63.158 0.00 0.00 40.24 4.70
68 69 2.497092 CGCTGACGACGGTGATTCG 61.497 63.158 0.73 0.00 43.93 3.34
69 70 1.403972 GACGCTGACGACGGTGATTC 61.404 60.000 14.07 0.00 43.93 2.52
70 71 1.443872 GACGCTGACGACGGTGATT 60.444 57.895 14.07 0.00 43.93 2.57
71 72 2.178521 GACGCTGACGACGGTGAT 59.821 61.111 14.07 0.00 43.93 3.06
90 91 2.892425 GATTCCCAGGCGCGACAG 60.892 66.667 17.71 5.83 0.00 3.51
91 92 3.664025 CTGATTCCCAGGCGCGACA 62.664 63.158 17.71 0.00 39.23 4.35
92 93 2.892425 CTGATTCCCAGGCGCGAC 60.892 66.667 12.10 7.34 39.23 5.19
99 100 2.190578 GACGGCCCTGATTCCCAG 59.809 66.667 0.00 0.00 42.55 4.45
100 101 2.609299 TGACGGCCCTGATTCCCA 60.609 61.111 0.00 0.00 0.00 4.37
101 102 2.190578 CTGACGGCCCTGATTCCC 59.809 66.667 0.00 0.00 0.00 3.97
102 103 2.514824 GCTGACGGCCCTGATTCC 60.515 66.667 0.00 0.00 34.27 3.01
103 104 2.892425 CGCTGACGGCCCTGATTC 60.892 66.667 0.00 0.00 37.74 2.52
104 105 3.706373 ACGCTGACGGCCCTGATT 61.706 61.111 0.00 0.00 46.04 2.57
105 106 4.457496 CACGCTGACGGCCCTGAT 62.457 66.667 0.00 0.00 46.04 2.90
138 139 3.847602 CTCCAGGCGGCCTCTCTG 61.848 72.222 20.97 8.94 0.00 3.35
139 140 2.920076 CTACTCCAGGCGGCCTCTCT 62.920 65.000 20.97 4.38 0.00 3.10
140 141 2.442272 TACTCCAGGCGGCCTCTC 60.442 66.667 20.97 0.00 0.00 3.20
141 142 2.443016 CTACTCCAGGCGGCCTCT 60.443 66.667 20.97 4.39 0.00 3.69
142 143 2.760385 ACTACTCCAGGCGGCCTC 60.760 66.667 20.97 0.00 0.00 4.70
143 144 3.077556 CACTACTCCAGGCGGCCT 61.078 66.667 17.69 17.69 0.00 5.19
144 145 4.162690 CCACTACTCCAGGCGGCC 62.163 72.222 12.11 12.11 0.00 6.13
145 146 4.840005 GCCACTACTCCAGGCGGC 62.840 72.222 0.00 0.00 38.86 6.53
148 149 4.840005 GCCGCCACTACTCCAGGC 62.840 72.222 0.00 0.00 44.89 4.85
149 150 4.514577 CGCCGCCACTACTCCAGG 62.515 72.222 0.00 0.00 0.00 4.45
150 151 3.760035 ACGCCGCCACTACTCCAG 61.760 66.667 0.00 0.00 0.00 3.86
151 152 4.063967 CACGCCGCCACTACTCCA 62.064 66.667 0.00 0.00 0.00 3.86
152 153 4.814294 CCACGCCGCCACTACTCC 62.814 72.222 0.00 0.00 0.00 3.85
182 183 2.642996 AAAACCTGTTGCTTGCGGGC 62.643 55.000 0.00 0.00 35.84 6.13
183 184 0.875474 CAAAACCTGTTGCTTGCGGG 60.875 55.000 0.00 0.00 38.32 6.13
184 185 0.179113 ACAAAACCTGTTGCTTGCGG 60.179 50.000 0.00 0.00 32.99 5.69
185 186 1.199624 GACAAAACCTGTTGCTTGCG 58.800 50.000 0.00 0.00 38.84 4.85
186 187 1.199624 CGACAAAACCTGTTGCTTGC 58.800 50.000 0.00 0.00 38.84 4.01
187 188 1.838913 CCGACAAAACCTGTTGCTTG 58.161 50.000 0.00 0.00 38.84 4.01
188 189 0.102300 GCCGACAAAACCTGTTGCTT 59.898 50.000 0.00 0.00 38.84 3.91
189 190 1.733526 GCCGACAAAACCTGTTGCT 59.266 52.632 0.00 0.00 38.84 3.91
190 191 1.299850 GGCCGACAAAACCTGTTGC 60.300 57.895 0.00 0.00 38.84 4.17
191 192 0.030638 CAGGCCGACAAAACCTGTTG 59.969 55.000 0.00 0.00 44.91 3.33
192 193 2.414750 CAGGCCGACAAAACCTGTT 58.585 52.632 0.00 0.00 44.91 3.16
193 194 4.157607 CAGGCCGACAAAACCTGT 57.842 55.556 0.00 0.00 44.91 4.00
195 196 1.454847 TTGCAGGCCGACAAAACCT 60.455 52.632 10.63 0.00 0.00 3.50
196 197 1.007387 CTTGCAGGCCGACAAAACC 60.007 57.895 13.51 0.00 0.00 3.27
197 198 1.661509 GCTTGCAGGCCGACAAAAC 60.662 57.895 10.18 6.39 0.00 2.43
198 199 2.727544 GCTTGCAGGCCGACAAAA 59.272 55.556 10.18 0.00 0.00 2.44
199 200 3.659092 CGCTTGCAGGCCGACAAA 61.659 61.111 15.94 0.00 0.00 2.83
200 201 4.617520 TCGCTTGCAGGCCGACAA 62.618 61.111 15.94 12.21 0.00 3.18
203 204 4.393155 ATGTCGCTTGCAGGCCGA 62.393 61.111 15.94 12.74 0.00 5.54
204 205 4.170062 CATGTCGCTTGCAGGCCG 62.170 66.667 15.94 10.54 0.00 6.13
205 206 3.058160 ACATGTCGCTTGCAGGCC 61.058 61.111 15.94 2.43 0.00 5.19
206 207 2.177531 CACATGTCGCTTGCAGGC 59.822 61.111 11.41 11.41 0.00 4.85
207 208 2.177531 GCACATGTCGCTTGCAGG 59.822 61.111 11.51 0.00 36.22 4.85
208 209 2.948323 TGCACATGTCGCTTGCAG 59.052 55.556 17.30 0.00 41.29 4.41
209 210 2.948323 CTGCACATGTCGCTTGCA 59.052 55.556 17.30 12.94 43.89 4.08
210 211 2.503375 GCTGCACATGTCGCTTGC 60.503 61.111 17.30 16.50 36.76 4.01
211 212 2.202260 CGCTGCACATGTCGCTTG 60.202 61.111 17.30 12.43 0.00 4.01
212 213 4.093952 GCGCTGCACATGTCGCTT 62.094 61.111 19.04 0.00 43.70 4.68
262 263 1.027357 GATGTAATGTGCCAGGCCTG 58.973 55.000 26.87 26.87 0.00 4.85
263 264 0.106519 GGATGTAATGTGCCAGGCCT 60.107 55.000 9.64 0.00 0.00 5.19
264 265 1.109323 GGGATGTAATGTGCCAGGCC 61.109 60.000 9.64 0.00 0.00 5.19
265 266 1.447317 CGGGATGTAATGTGCCAGGC 61.447 60.000 3.66 3.66 0.00 4.85
266 267 0.819259 CCGGGATGTAATGTGCCAGG 60.819 60.000 0.00 0.00 0.00 4.45
267 268 1.447317 GCCGGGATGTAATGTGCCAG 61.447 60.000 2.18 0.00 0.00 4.85
268 269 1.453015 GCCGGGATGTAATGTGCCA 60.453 57.895 2.18 0.00 0.00 4.92
269 270 1.152963 AGCCGGGATGTAATGTGCC 60.153 57.895 2.18 0.00 0.00 5.01
270 271 2.024918 CAGCCGGGATGTAATGTGC 58.975 57.895 2.18 0.00 0.00 4.57
271 272 0.464373 AGCAGCCGGGATGTAATGTG 60.464 55.000 14.59 0.00 0.00 3.21
272 273 0.464373 CAGCAGCCGGGATGTAATGT 60.464 55.000 14.59 0.00 0.00 2.71
273 274 1.789078 GCAGCAGCCGGGATGTAATG 61.789 60.000 14.59 11.36 33.58 1.90
274 275 1.526917 GCAGCAGCCGGGATGTAAT 60.527 57.895 14.59 0.00 33.58 1.89
275 276 2.124736 GCAGCAGCCGGGATGTAA 60.125 61.111 14.59 0.00 33.58 2.41
276 277 4.529219 CGCAGCAGCCGGGATGTA 62.529 66.667 14.59 0.00 37.52 2.29
291 292 0.934496 TAACGGATTATGCACAGCGC 59.066 50.000 0.00 0.00 42.89 5.92
292 293 1.930503 TGTAACGGATTATGCACAGCG 59.069 47.619 0.00 0.00 0.00 5.18
293 294 2.031683 GGTGTAACGGATTATGCACAGC 59.968 50.000 0.00 0.00 38.12 4.40
294 295 2.612212 GGGTGTAACGGATTATGCACAG 59.388 50.000 0.00 0.00 38.12 3.66
295 296 2.634600 GGGTGTAACGGATTATGCACA 58.365 47.619 0.00 0.00 38.12 4.57
296 297 1.944709 GGGGTGTAACGGATTATGCAC 59.055 52.381 0.00 0.00 38.12 4.57
297 298 1.473610 CGGGGTGTAACGGATTATGCA 60.474 52.381 0.00 0.00 38.12 3.96
298 299 1.223187 CGGGGTGTAACGGATTATGC 58.777 55.000 0.00 0.00 38.12 3.14
299 300 1.223187 GCGGGGTGTAACGGATTATG 58.777 55.000 0.00 0.00 38.12 1.90
300 301 0.249573 CGCGGGGTGTAACGGATTAT 60.250 55.000 0.00 0.00 38.12 1.28
301 302 1.141449 CGCGGGGTGTAACGGATTA 59.859 57.895 0.00 0.00 38.12 1.75
302 303 2.125431 CGCGGGGTGTAACGGATT 60.125 61.111 0.00 0.00 38.12 3.01
303 304 4.825252 GCGCGGGGTGTAACGGAT 62.825 66.667 8.83 0.00 38.12 4.18
403 404 2.994643 AAAAAGACCCCTGGGCCGTG 62.995 60.000 7.39 0.00 39.32 4.94
404 405 2.774633 AAAAAGACCCCTGGGCCGT 61.775 57.895 7.39 0.00 39.32 5.68
405 406 2.117423 AAAAAGACCCCTGGGCCG 59.883 61.111 7.39 0.00 39.32 6.13
419 420 7.830201 ACTACCCGTGGATATATTTGACAAAAA 59.170 33.333 4.41 0.00 0.00 1.94
420 421 7.340256 ACTACCCGTGGATATATTTGACAAAA 58.660 34.615 4.41 0.00 0.00 2.44
421 422 6.891388 ACTACCCGTGGATATATTTGACAAA 58.109 36.000 2.48 2.48 0.00 2.83
422 423 6.463331 GGACTACCCGTGGATATATTTGACAA 60.463 42.308 0.00 0.00 0.00 3.18
423 424 5.011329 GGACTACCCGTGGATATATTTGACA 59.989 44.000 0.00 0.00 0.00 3.58
424 425 5.245526 AGGACTACCCGTGGATATATTTGAC 59.754 44.000 0.00 0.00 40.87 3.18
425 426 5.399991 AGGACTACCCGTGGATATATTTGA 58.600 41.667 0.00 0.00 40.87 2.69
426 427 5.740290 AGGACTACCCGTGGATATATTTG 57.260 43.478 0.00 0.00 40.87 2.32
427 428 6.758806 AAAGGACTACCCGTGGATATATTT 57.241 37.500 0.00 0.00 40.87 1.40
428 429 6.758806 AAAAGGACTACCCGTGGATATATT 57.241 37.500 0.00 0.00 40.87 1.28
429 430 6.328148 TCAAAAAGGACTACCCGTGGATATAT 59.672 38.462 0.00 0.00 40.87 0.86
430 431 5.662208 TCAAAAAGGACTACCCGTGGATATA 59.338 40.000 0.00 0.00 40.87 0.86
431 432 4.472108 TCAAAAAGGACTACCCGTGGATAT 59.528 41.667 0.00 0.00 40.87 1.63
432 433 3.839490 TCAAAAAGGACTACCCGTGGATA 59.161 43.478 0.00 0.00 40.87 2.59
433 434 2.640826 TCAAAAAGGACTACCCGTGGAT 59.359 45.455 0.00 0.00 40.87 3.41
434 435 2.048601 TCAAAAAGGACTACCCGTGGA 58.951 47.619 0.00 0.00 40.87 4.02
435 436 2.148768 GTCAAAAAGGACTACCCGTGG 58.851 52.381 0.00 0.00 40.87 4.94
436 437 2.841215 TGTCAAAAAGGACTACCCGTG 58.159 47.619 0.00 0.00 40.87 4.94
437 438 3.564053 TTGTCAAAAAGGACTACCCGT 57.436 42.857 0.00 0.00 40.87 5.28
438 439 4.760204 AGAATTGTCAAAAAGGACTACCCG 59.240 41.667 0.00 0.00 40.87 5.28
439 440 5.535030 ACAGAATTGTCAAAAAGGACTACCC 59.465 40.000 0.00 0.00 38.61 3.69
440 441 6.635030 ACAGAATTGTCAAAAAGGACTACC 57.365 37.500 0.00 0.00 38.61 3.18
441 442 6.918022 CCAACAGAATTGTCAAAAAGGACTAC 59.082 38.462 0.00 0.00 36.23 2.73
442 443 6.460953 GCCAACAGAATTGTCAAAAAGGACTA 60.461 38.462 0.00 0.00 36.23 2.59
443 444 5.682212 GCCAACAGAATTGTCAAAAAGGACT 60.682 40.000 0.00 0.00 36.23 3.85
444 445 4.507756 GCCAACAGAATTGTCAAAAAGGAC 59.492 41.667 0.00 0.00 36.23 3.85
445 446 4.442753 GGCCAACAGAATTGTCAAAAAGGA 60.443 41.667 0.00 0.00 36.23 3.36
446 447 3.809279 GGCCAACAGAATTGTCAAAAAGG 59.191 43.478 0.00 0.00 36.23 3.11
447 448 4.440880 TGGCCAACAGAATTGTCAAAAAG 58.559 39.130 0.61 0.00 36.23 2.27
448 449 4.478206 TGGCCAACAGAATTGTCAAAAA 57.522 36.364 0.61 0.00 36.23 1.94
449 450 4.378774 CATGGCCAACAGAATTGTCAAAA 58.621 39.130 10.96 0.00 36.23 2.44
450 451 3.244146 CCATGGCCAACAGAATTGTCAAA 60.244 43.478 10.96 0.00 36.23 2.69
451 452 2.299582 CCATGGCCAACAGAATTGTCAA 59.700 45.455 10.96 0.00 36.23 3.18
452 453 1.894466 CCATGGCCAACAGAATTGTCA 59.106 47.619 10.96 0.00 36.23 3.58
453 454 1.205417 CCCATGGCCAACAGAATTGTC 59.795 52.381 10.96 0.00 36.23 3.18
454 455 1.269012 CCCATGGCCAACAGAATTGT 58.731 50.000 10.96 0.00 39.87 2.71
455 456 0.538118 CCCCATGGCCAACAGAATTG 59.462 55.000 10.96 0.18 0.00 2.32
456 457 0.116940 ACCCCATGGCCAACAGAATT 59.883 50.000 10.96 0.00 33.59 2.17
457 458 0.324645 GACCCCATGGCCAACAGAAT 60.325 55.000 10.96 0.00 33.59 2.40
458 459 1.076549 GACCCCATGGCCAACAGAA 59.923 57.895 10.96 0.00 33.59 3.02
459 460 1.434513 AAGACCCCATGGCCAACAGA 61.435 55.000 10.96 0.00 33.59 3.41
460 461 0.542702 AAAGACCCCATGGCCAACAG 60.543 55.000 10.96 2.25 33.59 3.16
461 462 0.105246 AAAAGACCCCATGGCCAACA 60.105 50.000 10.96 0.00 33.59 3.33
462 463 1.055849 AAAAAGACCCCATGGCCAAC 58.944 50.000 10.96 0.00 33.59 3.77
463 464 1.055040 CAAAAAGACCCCATGGCCAA 58.945 50.000 10.96 0.00 33.59 4.52
464 465 0.835543 CCAAAAAGACCCCATGGCCA 60.836 55.000 8.56 8.56 33.59 5.36
465 466 0.544120 TCCAAAAAGACCCCATGGCC 60.544 55.000 6.09 0.00 33.59 5.36
466 467 0.608130 GTCCAAAAAGACCCCATGGC 59.392 55.000 6.09 0.00 33.59 4.40
467 468 2.008242 TGTCCAAAAAGACCCCATGG 57.992 50.000 4.14 4.14 35.83 3.66
468 469 4.414337 TTTTGTCCAAAAAGACCCCATG 57.586 40.909 2.82 0.00 37.35 3.66
487 488 4.141018 ACATAGGTCCTGGTTGAGGTTTTT 60.141 41.667 0.00 0.00 43.37 1.94
488 489 3.397955 ACATAGGTCCTGGTTGAGGTTTT 59.602 43.478 0.00 0.00 43.37 2.43
489 490 2.986728 ACATAGGTCCTGGTTGAGGTTT 59.013 45.455 0.00 0.00 43.37 3.27
490 491 2.632537 ACATAGGTCCTGGTTGAGGTT 58.367 47.619 0.00 0.00 43.37 3.50
491 492 2.344093 ACATAGGTCCTGGTTGAGGT 57.656 50.000 0.00 0.00 43.37 3.85
492 493 2.103263 GCTACATAGGTCCTGGTTGAGG 59.897 54.545 0.00 0.00 44.45 3.86
493 494 3.034635 AGCTACATAGGTCCTGGTTGAG 58.965 50.000 0.00 0.00 0.00 3.02
494 495 3.116096 AGCTACATAGGTCCTGGTTGA 57.884 47.619 0.00 0.00 0.00 3.18
495 496 4.406003 AGTTAGCTACATAGGTCCTGGTTG 59.594 45.833 0.00 2.33 35.39 3.77
504 505 5.779529 TTCCGGTTAGTTAGCTACATAGG 57.220 43.478 0.00 0.00 0.00 2.57
532 533 3.195825 TCTGCTAAAAGGTGGAGCTAGAC 59.804 47.826 0.00 0.00 37.12 2.59
533 534 3.441101 TCTGCTAAAAGGTGGAGCTAGA 58.559 45.455 0.00 0.00 37.12 2.43
584 585 1.356124 ACCAGATGCAAGACTCCAGT 58.644 50.000 0.00 0.00 0.00 4.00
585 586 2.486472 AACCAGATGCAAGACTCCAG 57.514 50.000 0.00 0.00 0.00 3.86
586 587 2.957402 AAACCAGATGCAAGACTCCA 57.043 45.000 0.00 0.00 0.00 3.86
587 588 4.333926 GTCATAAACCAGATGCAAGACTCC 59.666 45.833 0.00 0.00 0.00 3.85
629 630 5.731591 ACGGCTAGCTAAGTAGAAAATGTT 58.268 37.500 15.72 0.00 0.00 2.71
650 651 2.281070 AAGGTGCAGTGCAGGACG 60.281 61.111 20.42 0.00 40.08 4.79
670 671 5.652994 TTACAATGGGTGGCTTTATTGTC 57.347 39.130 0.00 0.00 41.38 3.18
742 743 3.895041 TGGGCATGACTGTTATCGATCTA 59.105 43.478 0.00 0.00 0.00 1.98
791 802 2.986019 TCAGGATGAAGAAACAGGGGAA 59.014 45.455 0.00 0.00 45.97 3.97
792 803 2.631384 TCAGGATGAAGAAACAGGGGA 58.369 47.619 0.00 0.00 45.97 4.81
855 873 4.451900 AGTAGGTCAAGTGTGTTTTCCTG 58.548 43.478 0.00 0.00 0.00 3.86
856 874 4.444449 GGAGTAGGTCAAGTGTGTTTTCCT 60.444 45.833 0.00 0.00 0.00 3.36
894 912 2.031595 ACACGAGCGCACAGATAGATAG 60.032 50.000 11.47 0.00 0.00 2.08
895 913 1.947456 ACACGAGCGCACAGATAGATA 59.053 47.619 11.47 0.00 0.00 1.98
896 914 0.741326 ACACGAGCGCACAGATAGAT 59.259 50.000 11.47 0.00 0.00 1.98
897 915 0.179163 CACACGAGCGCACAGATAGA 60.179 55.000 11.47 0.00 0.00 1.98
907 925 0.524392 TTTGTTTTGGCACACGAGCG 60.524 50.000 0.00 0.00 39.29 5.03
1031 1059 1.579698 GATCACGAGCATGCACTCAT 58.420 50.000 21.98 4.63 36.42 2.90
1032 1060 0.803380 CGATCACGAGCATGCACTCA 60.803 55.000 21.98 0.00 42.66 3.41
1033 1061 1.922903 CGATCACGAGCATGCACTC 59.077 57.895 21.98 8.78 42.66 3.51
1034 1062 2.169789 GCGATCACGAGCATGCACT 61.170 57.895 21.98 0.00 42.66 4.40
1035 1063 2.322422 GCGATCACGAGCATGCAC 59.678 61.111 21.98 13.43 42.66 4.57
1036 1064 2.857575 AAGGCGATCACGAGCATGCA 62.858 55.000 21.98 0.00 42.66 3.96
1037 1065 2.098842 GAAGGCGATCACGAGCATGC 62.099 60.000 10.51 10.51 42.66 4.06
1038 1066 1.815212 CGAAGGCGATCACGAGCATG 61.815 60.000 0.00 0.00 42.66 4.06
1039 1067 1.589993 CGAAGGCGATCACGAGCAT 60.590 57.895 0.00 0.00 42.66 3.79
1040 1068 2.202610 CGAAGGCGATCACGAGCA 60.203 61.111 0.00 0.00 42.66 4.26
1815 1884 1.141234 GGGCAGCAGGTCGTAGTAC 59.859 63.158 0.00 0.00 0.00 2.73
1848 1917 0.322098 TGACCCCGCCATAGTTGTTG 60.322 55.000 0.00 0.00 0.00 3.33
1971 2044 5.238868 ACGCATACACAGTAGGAGTAGTATG 59.761 44.000 0.00 0.00 40.85 2.39
1980 2053 2.363788 ACACACGCATACACAGTAGG 57.636 50.000 0.00 0.00 0.00 3.18
2100 2180 6.939730 AGCAAAAATTATTGGGGGTAAAAGTG 59.060 34.615 0.00 0.00 0.00 3.16
2107 2187 4.382577 CGCTAAGCAAAAATTATTGGGGGT 60.383 41.667 0.00 0.00 0.00 4.95
2108 2188 4.119136 CGCTAAGCAAAAATTATTGGGGG 58.881 43.478 0.00 0.00 0.00 5.40
2112 2192 3.242712 CCGCCGCTAAGCAAAAATTATTG 59.757 43.478 0.00 0.00 0.00 1.90
2156 3003 3.666253 CCCAAAACGCCGACCACC 61.666 66.667 0.00 0.00 0.00 4.61
2199 3046 2.391389 CCGAGGCTCCAAAGAACGC 61.391 63.158 9.32 0.00 0.00 4.84
2229 3076 3.775654 GAGCACAGGGGGAGGTCG 61.776 72.222 0.00 0.00 0.00 4.79
2294 3141 3.581687 GATCTGGATCCGCCGCTCC 62.582 68.421 7.39 0.00 40.66 4.70
2328 3175 0.999406 CGCCGGTGTTCTAACATCAG 59.001 55.000 6.91 0.00 40.02 2.90
2405 3252 0.477204 AGATGATCCCCTACGGACGA 59.523 55.000 0.00 0.00 46.09 4.20
2494 3342 3.131396 CACACAGGTCCTTCTGTAACAC 58.869 50.000 0.00 0.00 45.24 3.32
2500 3348 5.308825 AGAAATAACACACAGGTCCTTCTG 58.691 41.667 0.00 0.00 40.40 3.02
2523 3371 3.699038 CAGAAAGACACCCCACAAAGAAA 59.301 43.478 0.00 0.00 0.00 2.52
2592 3440 0.102120 CGTGGCAGCACAAAAAGGAA 59.898 50.000 0.00 0.00 0.00 3.36
2595 3443 2.483583 TAACGTGGCAGCACAAAAAG 57.516 45.000 0.00 0.00 0.00 2.27
2602 3450 0.959867 ATGCACATAACGTGGCAGCA 60.960 50.000 0.00 5.61 46.45 4.41
2604 3452 2.634982 AAATGCACATAACGTGGCAG 57.365 45.000 0.00 0.00 46.45 4.85
2614 3462 0.808125 TCGCCGCTTAAAATGCACAT 59.192 45.000 0.00 0.00 0.00 3.21
2615 3463 0.109964 GTCGCCGCTTAAAATGCACA 60.110 50.000 0.00 0.00 0.00 4.57
2618 3466 1.125847 CACGTCGCCGCTTAAAATGC 61.126 55.000 0.00 0.00 37.70 3.56
2835 3690 1.676615 CCAATGCAAATTGAGCCCACC 60.677 52.381 0.00 0.00 33.55 4.61
2879 3734 2.680352 AGCCCATCTCGGTCGTGT 60.680 61.111 0.00 0.00 0.00 4.49
2884 3739 1.755179 CAAATTCAGCCCATCTCGGT 58.245 50.000 0.00 0.00 0.00 4.69
2905 3760 1.883084 GATCGCGTACTGGCCCAAG 60.883 63.158 5.77 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.