Multiple sequence alignment - TraesCS2D01G514200

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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 TraesCS2D01G514200 chr2D 100.000 2267 0 0 1 2267 606131775 606134041 0.000000e+00 4187.0
1 TraesCS2D01G514200 chr2D 86.667 60 3 5 836 892 606625393 606625450 6.760000e-06 62.1
2 TraesCS2D01G514200 chr2B 91.168 1789 110 16 482 2266 737049735 737051479 0.000000e+00 2385.0
3 TraesCS2D01G514200 chr2B 83.508 382 46 13 957 1331 737449854 737450225 7.760000e-90 340.0
4 TraesCS2D01G514200 chr2B 88.034 117 11 2 201 317 737049624 737049737 3.930000e-28 135.0
5 TraesCS2D01G514200 chr2B 90.698 43 1 2 796 838 737449634 737449673 1.000000e-03 54.7
6 TraesCS2D01G514200 chr2A 88.383 835 54 18 794 1609 737644771 737645581 0.000000e+00 965.0
7 TraesCS2D01G514200 chr2A 83.980 980 59 33 678 1609 737829345 737830274 0.000000e+00 850.0
8 TraesCS2D01G514200 chr2A 86.969 683 58 12 1600 2267 737833447 737834113 0.000000e+00 739.0
9 TraesCS2D01G514200 chr2A 88.732 213 18 4 2056 2266 737731255 737731463 2.890000e-64 255.0
10 TraesCS2D01G514200 chr2A 85.246 183 23 3 132 314 737826797 737826975 3.850000e-43 185.0
11 TraesCS2D01G514200 chr2A 91.736 121 10 0 1600 1720 737730697 737730817 3.870000e-38 169.0
12 TraesCS2D01G514200 chr2A 88.000 100 6 6 315 413 537510621 537510715 1.840000e-21 113.0
13 TraesCS2D01G514200 chr3D 89.222 167 12 5 317 482 497819060 497819221 1.060000e-48 204.0
14 TraesCS2D01G514200 chr4D 94.624 93 5 0 392 484 311157087 311156995 6.530000e-31 145.0
15 TraesCS2D01G514200 chr5B 91.837 98 7 1 1 98 564472145 564472241 3.930000e-28 135.0
16 TraesCS2D01G514200 chr5B 89.286 84 9 0 21 104 564317668 564317751 3.080000e-19 106.0
17 TraesCS2D01G514200 chr5B 89.286 84 9 0 21 104 564378385 564378468 3.080000e-19 106.0
18 TraesCS2D01G514200 chr5B 89.286 84 9 0 21 104 564446714 564446797 3.080000e-19 106.0
19 TraesCS2D01G514200 chr5B 89.024 82 9 0 23 104 564440536 564440617 3.980000e-18 102.0
20 TraesCS2D01G514200 chr5B 87.640 89 10 1 8 96 564530870 564530957 3.980000e-18 102.0
21 TraesCS2D01G514200 chr5B 85.000 100 13 2 6 104 564180111 564180209 1.430000e-17 100.0
22 TraesCS2D01G514200 chr5B 88.095 84 10 0 21 104 564212867 564212950 1.430000e-17 100.0
23 TraesCS2D01G514200 chr5A 86.667 90 12 0 21 110 579847860 579847771 1.430000e-17 100.0


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 TraesCS2D01G514200 chr2D 606131775 606134041 2266 False 4187.000000 4187 100.000000 1 2267 1 chr2D.!!$F1 2266
1 TraesCS2D01G514200 chr2B 737049624 737051479 1855 False 1260.000000 2385 89.601000 201 2266 2 chr2B.!!$F1 2065
2 TraesCS2D01G514200 chr2A 737644771 737645581 810 False 965.000000 965 88.383000 794 1609 1 chr2A.!!$F2 815
3 TraesCS2D01G514200 chr2A 737826797 737834113 7316 False 591.333333 850 85.398333 132 2267 3 chr2A.!!$F4 2135
4 TraesCS2D01G514200 chr2A 737730697 737731463 766 False 212.000000 255 90.234000 1600 2266 2 chr2A.!!$F3 666

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
390 391 0.038526 GGAAACGAGGAGCGACAGAA 60.039 55.0 0.0 0.0 44.57 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1319 3568 0.179043 TTTCCTACGCCACAGCAACA 60.179 50.0 0.0 0.0 39.83 3.33 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
59 60 9.947669 TTCACAAATTTTGAATTTAGCATTTGG 57.052 25.926 15.81 8.36 36.40 3.28
60 61 9.334947 TCACAAATTTTGAATTTAGCATTTGGA 57.665 25.926 15.81 9.70 36.40 3.53
61 62 9.601971 CACAAATTTTGAATTTAGCATTTGGAG 57.398 29.630 15.81 7.88 36.40 3.86
62 63 8.785946 ACAAATTTTGAATTTAGCATTTGGAGG 58.214 29.630 15.81 0.00 36.40 4.30
63 64 6.990341 ATTTTGAATTTAGCATTTGGAGGC 57.010 33.333 0.00 0.00 0.00 4.70
64 65 4.470334 TTGAATTTAGCATTTGGAGGCC 57.530 40.909 0.00 0.00 31.67 5.19
65 66 3.711863 TGAATTTAGCATTTGGAGGCCT 58.288 40.909 3.86 3.86 31.67 5.19
66 67 3.701040 TGAATTTAGCATTTGGAGGCCTC 59.299 43.478 25.59 25.59 31.67 4.70
77 78 1.144936 GAGGCCTCCATGGAGTTCG 59.855 63.158 34.49 22.84 40.44 3.95
78 79 2.190578 GGCCTCCATGGAGTTCGG 59.809 66.667 34.49 23.81 40.44 4.30
79 80 2.514824 GCCTCCATGGAGTTCGGC 60.515 66.667 34.49 28.63 40.44 5.54
80 81 2.190578 CCTCCATGGAGTTCGGCC 59.809 66.667 34.49 0.00 40.44 6.13
81 82 2.370445 CCTCCATGGAGTTCGGCCT 61.370 63.158 34.49 0.00 40.44 5.19
82 83 1.144936 CTCCATGGAGTTCGGCCTC 59.855 63.158 30.55 0.00 37.47 4.70
89 90 1.876664 GAGTTCGGCCTCCAAAAGC 59.123 57.895 0.00 0.00 0.00 3.51
90 91 0.889186 GAGTTCGGCCTCCAAAAGCA 60.889 55.000 0.00 0.00 0.00 3.91
91 92 0.890996 AGTTCGGCCTCCAAAAGCAG 60.891 55.000 0.00 0.00 0.00 4.24
92 93 1.150536 TTCGGCCTCCAAAAGCAGT 59.849 52.632 0.00 0.00 0.00 4.40
93 94 0.467290 TTCGGCCTCCAAAAGCAGTT 60.467 50.000 0.00 0.00 0.00 3.16
94 95 0.467290 TCGGCCTCCAAAAGCAGTTT 60.467 50.000 0.00 0.00 0.00 2.66
95 96 0.039165 CGGCCTCCAAAAGCAGTTTC 60.039 55.000 0.00 0.00 0.00 2.78
96 97 1.332195 GGCCTCCAAAAGCAGTTTCT 58.668 50.000 0.00 0.00 0.00 2.52
97 98 1.000171 GGCCTCCAAAAGCAGTTTCTG 60.000 52.381 0.00 0.00 34.12 3.02
98 99 1.000171 GCCTCCAAAAGCAGTTTCTGG 60.000 52.381 0.00 0.00 31.21 3.86
99 100 2.310538 CCTCCAAAAGCAGTTTCTGGT 58.689 47.619 0.00 0.00 44.48 4.00
106 107 2.355010 AGCAGTTTCTGGTTTGAGCT 57.645 45.000 0.00 0.00 39.27 4.09
107 108 2.225467 AGCAGTTTCTGGTTTGAGCTC 58.775 47.619 6.82 6.82 39.27 4.09
108 109 1.268079 GCAGTTTCTGGTTTGAGCTCC 59.732 52.381 12.15 0.00 31.21 4.70
109 110 2.575532 CAGTTTCTGGTTTGAGCTCCA 58.424 47.619 12.15 0.80 0.00 3.86
110 111 2.951642 CAGTTTCTGGTTTGAGCTCCAA 59.048 45.455 12.15 3.14 33.06 3.53
111 112 2.952310 AGTTTCTGGTTTGAGCTCCAAC 59.048 45.455 19.76 19.76 33.85 3.77
112 113 1.981256 TTCTGGTTTGAGCTCCAACC 58.019 50.000 32.83 32.83 33.85 3.77
113 114 1.140312 TCTGGTTTGAGCTCCAACCT 58.860 50.000 36.26 0.00 33.85 3.50
114 115 1.202806 TCTGGTTTGAGCTCCAACCTG 60.203 52.381 36.26 34.79 33.85 4.00
115 116 0.843309 TGGTTTGAGCTCCAACCTGA 59.157 50.000 36.26 22.58 33.85 3.86
116 117 1.239347 GGTTTGAGCTCCAACCTGAC 58.761 55.000 32.42 13.67 33.85 3.51
117 118 1.239347 GTTTGAGCTCCAACCTGACC 58.761 55.000 17.74 0.00 33.85 4.02
118 119 1.140312 TTTGAGCTCCAACCTGACCT 58.860 50.000 12.15 0.00 33.85 3.85
119 120 0.687354 TTGAGCTCCAACCTGACCTC 59.313 55.000 12.15 0.00 0.00 3.85
120 121 1.194781 TGAGCTCCAACCTGACCTCC 61.195 60.000 12.15 0.00 0.00 4.30
121 122 1.152030 AGCTCCAACCTGACCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
122 123 1.197430 AGCTCCAACCTGACCTCCAG 61.197 60.000 0.00 0.00 42.55 3.86
140 141 2.434428 CAGGCTATGGATGCAATCTCC 58.566 52.381 0.00 0.00 44.71 3.71
159 160 0.893447 CGGAGGTAGGGAAAACTCGT 59.107 55.000 0.00 0.00 0.00 4.18
160 161 1.274447 CGGAGGTAGGGAAAACTCGTT 59.726 52.381 0.00 0.00 0.00 3.85
167 168 2.096248 AGGGAAAACTCGTTGTGCAAA 58.904 42.857 0.00 0.00 0.00 3.68
172 173 1.745232 AACTCGTTGTGCAAACTCCA 58.255 45.000 0.00 0.00 0.00 3.86
177 178 2.490115 TCGTTGTGCAAACTCCACTTTT 59.510 40.909 0.00 0.00 34.38 2.27
178 179 2.598192 CGTTGTGCAAACTCCACTTTTG 59.402 45.455 0.00 0.00 37.07 2.44
179 180 3.584834 GTTGTGCAAACTCCACTTTTGT 58.415 40.909 0.00 0.00 36.50 2.83
181 182 2.159448 TGTGCAAACTCCACTTTTGTCG 60.159 45.455 0.00 0.00 36.50 4.35
224 225 1.472904 CGAGGAGAAGTGCTGCATCAT 60.473 52.381 5.27 0.00 37.43 2.45
226 227 1.558294 AGGAGAAGTGCTGCATCATCA 59.442 47.619 5.27 0.00 37.43 3.07
227 228 2.172930 AGGAGAAGTGCTGCATCATCAT 59.827 45.455 5.27 0.00 37.43 2.45
228 229 2.290916 GGAGAAGTGCTGCATCATCATG 59.709 50.000 5.27 0.00 34.66 3.07
229 230 2.943690 GAGAAGTGCTGCATCATCATGT 59.056 45.455 5.27 0.00 31.86 3.21
230 231 4.124970 GAGAAGTGCTGCATCATCATGTA 58.875 43.478 5.27 0.00 31.86 2.29
231 232 4.520179 AGAAGTGCTGCATCATCATGTAA 58.480 39.130 5.27 0.00 31.86 2.41
232 233 4.945543 AGAAGTGCTGCATCATCATGTAAA 59.054 37.500 5.27 0.00 31.86 2.01
233 234 5.593095 AGAAGTGCTGCATCATCATGTAAAT 59.407 36.000 5.27 0.00 31.86 1.40
241 242 7.514784 TGCATCATCATGTAAATAAAGGAGG 57.485 36.000 0.00 0.00 31.86 4.30
247 248 9.793259 TCATCATGTAAATAAAGGAGGAATACC 57.207 33.333 0.00 0.00 0.00 2.73
278 279 4.307032 AAGAAGCTGGAAGGAAATGCTA 57.693 40.909 0.00 0.00 33.28 3.49
295 296 1.611519 CTAGGGAGCGGGAAGTAGAG 58.388 60.000 0.00 0.00 0.00 2.43
306 307 3.409570 GGGAAGTAGAGTTGGTGGAAAC 58.590 50.000 0.00 0.00 0.00 2.78
317 318 6.594159 AGAGTTGGTGGAAACGTATCATTTAG 59.406 38.462 0.00 0.00 35.13 1.85
318 319 5.646360 AGTTGGTGGAAACGTATCATTTAGG 59.354 40.000 0.00 0.00 35.13 2.69
319 320 3.942748 TGGTGGAAACGTATCATTTAGGC 59.057 43.478 0.00 0.00 0.00 3.93
320 321 3.314357 GGTGGAAACGTATCATTTAGGCC 59.686 47.826 0.00 0.00 0.00 5.19
321 322 3.314357 GTGGAAACGTATCATTTAGGCCC 59.686 47.826 0.00 0.00 0.00 5.80
322 323 2.882761 GGAAACGTATCATTTAGGCCCC 59.117 50.000 0.00 0.00 0.00 5.80
324 325 1.125633 ACGTATCATTTAGGCCCCGT 58.874 50.000 0.00 0.00 0.00 5.28
325 326 1.487558 ACGTATCATTTAGGCCCCGTT 59.512 47.619 0.00 0.00 0.00 4.44
326 327 2.140717 CGTATCATTTAGGCCCCGTTC 58.859 52.381 0.00 0.00 0.00 3.95
327 328 2.140717 GTATCATTTAGGCCCCGTTCG 58.859 52.381 0.00 0.00 0.00 3.95
328 329 0.179029 ATCATTTAGGCCCCGTTCGG 60.179 55.000 0.00 4.08 0.00 4.30
338 339 2.125269 CCGTTCGGGATGGACCAC 60.125 66.667 0.00 0.00 41.20 4.16
339 340 2.656069 CCGTTCGGGATGGACCACT 61.656 63.158 0.00 0.00 41.20 4.00
340 341 1.153628 CGTTCGGGATGGACCACTC 60.154 63.158 0.00 0.00 41.20 3.51
341 342 1.221021 GTTCGGGATGGACCACTCC 59.779 63.158 0.00 5.36 41.20 3.85
342 343 1.993391 TTCGGGATGGACCACTCCC 60.993 63.158 22.77 22.77 46.59 4.30
344 345 3.648694 GGGATGGACCACTCCCTC 58.351 66.667 24.27 8.62 46.55 4.30
345 346 1.003573 GGGATGGACCACTCCCTCT 59.996 63.158 24.27 0.00 46.55 3.69
346 347 1.341156 GGGATGGACCACTCCCTCTG 61.341 65.000 24.27 0.00 46.55 3.35
347 348 1.524482 GATGGACCACTCCCTCTGC 59.476 63.158 0.00 0.00 35.34 4.26
348 349 0.980231 GATGGACCACTCCCTCTGCT 60.980 60.000 0.00 0.00 35.34 4.24
349 350 0.980231 ATGGACCACTCCCTCTGCTC 60.980 60.000 0.00 0.00 35.34 4.26
350 351 1.305718 GGACCACTCCCTCTGCTCT 60.306 63.158 0.00 0.00 0.00 4.09
351 352 1.612395 GGACCACTCCCTCTGCTCTG 61.612 65.000 0.00 0.00 0.00 3.35
352 353 2.237534 GACCACTCCCTCTGCTCTGC 62.238 65.000 0.00 0.00 0.00 4.26
353 354 1.988956 CCACTCCCTCTGCTCTGCT 60.989 63.158 0.00 0.00 0.00 4.24
354 355 1.516892 CACTCCCTCTGCTCTGCTC 59.483 63.158 0.00 0.00 0.00 4.26
355 356 1.685421 ACTCCCTCTGCTCTGCTCC 60.685 63.158 0.00 0.00 0.00 4.70
356 357 2.757508 TCCCTCTGCTCTGCTCCG 60.758 66.667 0.00 0.00 0.00 4.63
357 358 4.527583 CCCTCTGCTCTGCTCCGC 62.528 72.222 0.00 0.00 0.00 5.54
358 359 3.459965 CCTCTGCTCTGCTCCGCT 61.460 66.667 0.00 0.00 0.00 5.52
359 360 2.104729 CTCTGCTCTGCTCCGCTC 59.895 66.667 0.00 0.00 0.00 5.03
360 361 3.429080 CTCTGCTCTGCTCCGCTCC 62.429 68.421 0.00 0.00 0.00 4.70
361 362 4.869440 CTGCTCTGCTCCGCTCCG 62.869 72.222 0.00 0.00 0.00 4.63
364 365 4.567385 CTCTGCTCCGCTCCGCTC 62.567 72.222 0.00 0.00 0.00 5.03
374 375 4.069232 CTCCGCTCGGTGCTGGAA 62.069 66.667 8.28 0.00 41.28 3.53
375 376 3.589654 CTCCGCTCGGTGCTGGAAA 62.590 63.158 8.28 0.00 41.28 3.13
376 377 3.423154 CCGCTCGGTGCTGGAAAC 61.423 66.667 0.00 0.00 40.11 2.78
377 378 3.777925 CGCTCGGTGCTGGAAACG 61.778 66.667 0.23 0.00 40.11 3.60
378 379 2.357034 GCTCGGTGCTGGAAACGA 60.357 61.111 0.00 0.00 38.95 3.85
379 380 3.862124 CTCGGTGCTGGAAACGAG 58.138 61.111 1.38 1.38 45.34 4.18
380 381 1.738099 CTCGGTGCTGGAAACGAGG 60.738 63.158 8.07 0.00 46.44 4.63
381 382 2.154798 CTCGGTGCTGGAAACGAGGA 62.155 60.000 8.07 0.00 46.44 3.71
382 383 1.738099 CGGTGCTGGAAACGAGGAG 60.738 63.158 0.00 0.00 0.00 3.69
383 384 2.035442 GGTGCTGGAAACGAGGAGC 61.035 63.158 0.00 0.00 0.00 4.70
385 386 2.261671 GCTGGAAACGAGGAGCGA 59.738 61.111 0.00 0.00 44.57 4.93
386 387 2.095252 GCTGGAAACGAGGAGCGAC 61.095 63.158 0.00 0.00 44.57 5.19
387 388 1.289066 CTGGAAACGAGGAGCGACA 59.711 57.895 0.00 0.00 44.57 4.35
388 389 0.734253 CTGGAAACGAGGAGCGACAG 60.734 60.000 0.00 0.00 44.57 3.51
389 390 1.176619 TGGAAACGAGGAGCGACAGA 61.177 55.000 0.00 0.00 44.57 3.41
390 391 0.038526 GGAAACGAGGAGCGACAGAA 60.039 55.000 0.00 0.00 44.57 3.02
391 392 1.404315 GGAAACGAGGAGCGACAGAAT 60.404 52.381 0.00 0.00 44.57 2.40
392 393 2.159282 GGAAACGAGGAGCGACAGAATA 60.159 50.000 0.00 0.00 44.57 1.75
393 394 2.853731 AACGAGGAGCGACAGAATAG 57.146 50.000 0.00 0.00 44.57 1.73
394 395 0.382515 ACGAGGAGCGACAGAATAGC 59.617 55.000 0.00 0.00 44.57 2.97
395 396 0.665835 CGAGGAGCGACAGAATAGCT 59.334 55.000 0.00 0.00 44.57 3.32
396 397 1.874231 CGAGGAGCGACAGAATAGCTA 59.126 52.381 0.00 0.00 44.57 3.32
397 398 2.350007 CGAGGAGCGACAGAATAGCTAC 60.350 54.545 0.00 0.00 44.57 3.58
398 399 2.938838 AGGAGCGACAGAATAGCTACT 58.061 47.619 0.00 0.00 46.50 2.57
399 400 3.276882 GGAGCGACAGAATAGCTACTC 57.723 52.381 0.00 0.00 41.84 2.59
400 401 2.030628 GGAGCGACAGAATAGCTACTCC 60.031 54.545 0.00 2.97 41.84 3.85
401 402 1.957877 AGCGACAGAATAGCTACTCCC 59.042 52.381 0.00 0.00 39.74 4.30
402 403 1.000052 GCGACAGAATAGCTACTCCCC 60.000 57.143 0.00 0.00 0.00 4.81
403 404 2.307768 CGACAGAATAGCTACTCCCCA 58.692 52.381 0.00 0.00 0.00 4.96
404 405 2.693591 CGACAGAATAGCTACTCCCCAA 59.306 50.000 0.00 0.00 0.00 4.12
405 406 3.132289 CGACAGAATAGCTACTCCCCAAA 59.868 47.826 0.00 0.00 0.00 3.28
406 407 4.382685 CGACAGAATAGCTACTCCCCAAAA 60.383 45.833 0.00 0.00 0.00 2.44
407 408 5.497474 GACAGAATAGCTACTCCCCAAAAA 58.503 41.667 0.00 0.00 0.00 1.94
408 409 6.079712 ACAGAATAGCTACTCCCCAAAAAT 57.920 37.500 0.00 0.00 0.00 1.82
409 410 5.888161 ACAGAATAGCTACTCCCCAAAAATG 59.112 40.000 0.00 0.00 0.00 2.32
410 411 6.122277 CAGAATAGCTACTCCCCAAAAATGA 58.878 40.000 0.00 0.00 0.00 2.57
411 412 6.603201 CAGAATAGCTACTCCCCAAAAATGAA 59.397 38.462 0.00 0.00 0.00 2.57
412 413 6.603599 AGAATAGCTACTCCCCAAAAATGAAC 59.396 38.462 0.00 0.00 0.00 3.18
413 414 4.388577 AGCTACTCCCCAAAAATGAACT 57.611 40.909 0.00 0.00 0.00 3.01
414 415 5.514500 AGCTACTCCCCAAAAATGAACTA 57.486 39.130 0.00 0.00 0.00 2.24
415 416 5.254115 AGCTACTCCCCAAAAATGAACTAC 58.746 41.667 0.00 0.00 0.00 2.73
416 417 4.094442 GCTACTCCCCAAAAATGAACTACG 59.906 45.833 0.00 0.00 0.00 3.51
417 418 2.817844 ACTCCCCAAAAATGAACTACGC 59.182 45.455 0.00 0.00 0.00 4.42
418 419 2.163613 CTCCCCAAAAATGAACTACGCC 59.836 50.000 0.00 0.00 0.00 5.68
419 420 1.203758 CCCCAAAAATGAACTACGCCC 59.796 52.381 0.00 0.00 0.00 6.13
420 421 1.203758 CCCAAAAATGAACTACGCCCC 59.796 52.381 0.00 0.00 0.00 5.80
421 422 2.167662 CCAAAAATGAACTACGCCCCT 58.832 47.619 0.00 0.00 0.00 4.79
422 423 2.163613 CCAAAAATGAACTACGCCCCTC 59.836 50.000 0.00 0.00 0.00 4.30
423 424 3.081804 CAAAAATGAACTACGCCCCTCT 58.918 45.455 0.00 0.00 0.00 3.69
424 425 2.693267 AAATGAACTACGCCCCTCTC 57.307 50.000 0.00 0.00 0.00 3.20
425 426 0.831307 AATGAACTACGCCCCTCTCC 59.169 55.000 0.00 0.00 0.00 3.71
426 427 1.392710 ATGAACTACGCCCCTCTCCG 61.393 60.000 0.00 0.00 0.00 4.63
427 428 3.427598 GAACTACGCCCCTCTCCGC 62.428 68.421 0.00 0.00 0.00 5.54
428 429 3.959329 AACTACGCCCCTCTCCGCT 62.959 63.158 0.00 0.00 0.00 5.52
429 430 3.597728 CTACGCCCCTCTCCGCTC 61.598 72.222 0.00 0.00 0.00 5.03
435 436 2.765807 CCCTCTCCGCTCCACCAT 60.766 66.667 0.00 0.00 0.00 3.55
436 437 2.370445 CCCTCTCCGCTCCACCATT 61.370 63.158 0.00 0.00 0.00 3.16
437 438 1.604378 CCTCTCCGCTCCACCATTT 59.396 57.895 0.00 0.00 0.00 2.32
438 439 0.462759 CCTCTCCGCTCCACCATTTC 60.463 60.000 0.00 0.00 0.00 2.17
439 440 0.250234 CTCTCCGCTCCACCATTTCA 59.750 55.000 0.00 0.00 0.00 2.69
440 441 0.250234 TCTCCGCTCCACCATTTCAG 59.750 55.000 0.00 0.00 0.00 3.02
441 442 1.372087 CTCCGCTCCACCATTTCAGC 61.372 60.000 0.00 0.00 0.00 4.26
442 443 1.377725 CCGCTCCACCATTTCAGCT 60.378 57.895 0.00 0.00 0.00 4.24
443 444 1.372087 CCGCTCCACCATTTCAGCTC 61.372 60.000 0.00 0.00 0.00 4.09
444 445 1.372087 CGCTCCACCATTTCAGCTCC 61.372 60.000 0.00 0.00 0.00 4.70
445 446 0.322816 GCTCCACCATTTCAGCTCCA 60.323 55.000 0.00 0.00 0.00 3.86
446 447 1.457346 CTCCACCATTTCAGCTCCAC 58.543 55.000 0.00 0.00 0.00 4.02
447 448 0.321564 TCCACCATTTCAGCTCCACG 60.322 55.000 0.00 0.00 0.00 4.94
448 449 0.321564 CCACCATTTCAGCTCCACGA 60.322 55.000 0.00 0.00 0.00 4.35
449 450 1.522668 CACCATTTCAGCTCCACGAA 58.477 50.000 0.00 0.00 0.00 3.85
450 451 1.466167 CACCATTTCAGCTCCACGAAG 59.534 52.381 0.00 0.00 0.00 3.79
452 453 2.154462 CCATTTCAGCTCCACGAAGTT 58.846 47.619 0.00 0.00 41.61 2.66
453 454 2.095567 CCATTTCAGCTCCACGAAGTTG 60.096 50.000 0.00 0.00 41.61 3.16
454 455 1.593196 TTTCAGCTCCACGAAGTTGG 58.407 50.000 0.00 0.00 41.61 3.77
455 456 0.250295 TTCAGCTCCACGAAGTTGGG 60.250 55.000 0.00 0.00 41.61 4.12
456 457 1.118965 TCAGCTCCACGAAGTTGGGA 61.119 55.000 0.00 0.00 41.61 4.37
458 459 4.285851 CTCCACGAAGTTGGGAGC 57.714 61.111 0.00 0.00 42.46 4.70
459 460 1.376037 CTCCACGAAGTTGGGAGCC 60.376 63.158 0.00 0.00 42.46 4.70
460 461 2.111999 CTCCACGAAGTTGGGAGCCA 62.112 60.000 0.00 0.00 42.46 4.75
461 462 1.672356 CCACGAAGTTGGGAGCCAG 60.672 63.158 0.00 0.00 41.61 4.85
462 463 1.371183 CACGAAGTTGGGAGCCAGA 59.629 57.895 0.00 0.00 41.61 3.86
463 464 0.671781 CACGAAGTTGGGAGCCAGAG 60.672 60.000 0.00 0.00 41.61 3.35
464 465 1.122019 ACGAAGTTGGGAGCCAGAGT 61.122 55.000 0.00 0.00 37.78 3.24
465 466 0.671781 CGAAGTTGGGAGCCAGAGTG 60.672 60.000 0.00 0.00 33.81 3.51
466 467 0.398318 GAAGTTGGGAGCCAGAGTGT 59.602 55.000 0.00 0.00 33.81 3.55
467 468 0.846693 AAGTTGGGAGCCAGAGTGTT 59.153 50.000 0.00 0.00 33.81 3.32
468 469 0.109342 AGTTGGGAGCCAGAGTGTTG 59.891 55.000 0.00 0.00 33.81 3.33
469 470 1.228245 TTGGGAGCCAGAGTGTTGC 60.228 57.895 0.00 0.00 33.81 4.17
470 471 2.360475 GGGAGCCAGAGTGTTGCC 60.360 66.667 0.00 0.00 0.00 4.52
471 472 2.743928 GGAGCCAGAGTGTTGCCG 60.744 66.667 0.00 0.00 0.00 5.69
472 473 2.343758 GAGCCAGAGTGTTGCCGA 59.656 61.111 0.00 0.00 0.00 5.54
473 474 1.301716 GAGCCAGAGTGTTGCCGAA 60.302 57.895 0.00 0.00 0.00 4.30
474 475 1.569479 GAGCCAGAGTGTTGCCGAAC 61.569 60.000 0.00 0.00 0.00 3.95
475 476 2.954753 GCCAGAGTGTTGCCGAACG 61.955 63.158 0.00 0.00 34.49 3.95
476 477 2.317609 CCAGAGTGTTGCCGAACGG 61.318 63.158 9.00 9.00 34.49 4.44
477 478 2.030562 AGAGTGTTGCCGAACGGG 59.969 61.111 15.01 0.00 34.49 5.28
486 487 2.435410 CCGAACGGGCCCTTACAC 60.435 66.667 22.43 5.10 0.00 2.90
487 488 2.660802 CGAACGGGCCCTTACACT 59.339 61.111 22.43 0.00 0.00 3.55
488 489 1.004200 CGAACGGGCCCTTACACTT 60.004 57.895 22.43 0.00 0.00 3.16
489 490 0.604511 CGAACGGGCCCTTACACTTT 60.605 55.000 22.43 0.66 0.00 2.66
490 491 0.879090 GAACGGGCCCTTACACTTTG 59.121 55.000 22.43 2.61 0.00 2.77
491 492 0.475044 AACGGGCCCTTACACTTTGA 59.525 50.000 22.43 0.00 0.00 2.69
566 571 2.238646 AGACGAATACCATGGGCTTTGA 59.761 45.455 18.09 0.00 0.00 2.69
579 584 4.512484 TGGGCTTTGACTTTTCCTTTTTG 58.488 39.130 0.00 0.00 0.00 2.44
643 650 3.006537 GGGTGCTTTGAGACACTAGTACA 59.993 47.826 0.00 0.00 36.99 2.90
660 667 1.174712 ACATGTTCCAGCACAGCACC 61.175 55.000 0.00 0.00 0.00 5.01
664 671 4.994471 TCCAGCACAGCACCGCAG 62.994 66.667 0.00 0.00 0.00 5.18
690 697 1.098712 GGCCCGCCGTGAAATAATCA 61.099 55.000 0.00 0.00 35.05 2.57
767 2958 3.141398 CCCCTCGTCACATTCATATTGG 58.859 50.000 0.00 0.00 0.00 3.16
791 2982 2.895372 CCGGCCAAGATGCGTACC 60.895 66.667 2.24 0.00 0.00 3.34
802 3002 3.090037 AGATGCGTACCTACTCACAACT 58.910 45.455 0.00 0.00 0.00 3.16
981 3203 2.164865 CTGTGGACTGAGCCGAGCTT 62.165 60.000 0.00 0.00 39.88 3.74
984 3206 2.264166 GACTGAGCCGAGCTTGCT 59.736 61.111 11.09 11.09 39.88 3.91
985 3207 1.513158 GACTGAGCCGAGCTTGCTA 59.487 57.895 11.23 1.39 39.88 3.49
986 3208 0.527385 GACTGAGCCGAGCTTGCTAG 60.527 60.000 11.23 11.05 39.88 3.42
1272 3521 1.397692 GACGTCTTCTACTGACCGAGG 59.602 57.143 8.70 0.00 0.00 4.63
1276 3525 0.179161 CTTCTACTGACCGAGGTGCG 60.179 60.000 0.00 0.00 40.47 5.34
1317 3566 3.494336 CGCTCGCTGCTTCCCTTG 61.494 66.667 0.00 0.00 40.11 3.61
1318 3567 3.808656 GCTCGCTGCTTCCCTTGC 61.809 66.667 0.00 0.00 38.95 4.01
1319 3568 2.046507 CTCGCTGCTTCCCTTGCT 60.047 61.111 0.00 0.00 0.00 3.91
1320 3569 2.359107 TCGCTGCTTCCCTTGCTG 60.359 61.111 0.00 0.00 0.00 4.41
1522 3773 6.087952 CGATCAGCGATTTCTTCTTATGAGAG 59.912 42.308 0.00 0.00 44.57 3.20
1617 7052 6.204882 ACACTGGCTTAAAGATTTACAGTCAC 59.795 38.462 0.00 0.00 35.72 3.67
1621 7056 5.705905 GGCTTAAAGATTTACAGTCACAGGT 59.294 40.000 0.00 0.00 0.00 4.00
1629 7064 8.553459 AGATTTACAGTCACAGGTAAAATGAG 57.447 34.615 8.38 0.00 41.30 2.90
1713 7148 7.572523 TTTTGGATCATCCTACAATCATCAC 57.427 36.000 4.96 0.00 37.46 3.06
1732 7167 8.234136 TCATCACTAACTAACTGATAACCGAT 57.766 34.615 0.00 0.00 0.00 4.18
1749 7184 2.680841 CCGATGAACGAAGGGCATAAAA 59.319 45.455 0.00 0.00 45.77 1.52
1797 7233 7.094162 TGCTATCCAGAGTAGTATGAACTATGC 60.094 40.741 0.00 0.00 40.30 3.14
1862 7298 2.906691 TGCACCCCTCAACAAAAATG 57.093 45.000 0.00 0.00 0.00 2.32
1863 7299 2.114616 TGCACCCCTCAACAAAAATGT 58.885 42.857 0.00 0.00 0.00 2.71
1902 7340 5.060506 TCAAATGCAAAAACTCCTCGACTA 58.939 37.500 0.00 0.00 0.00 2.59
1903 7341 5.705441 TCAAATGCAAAAACTCCTCGACTAT 59.295 36.000 0.00 0.00 0.00 2.12
1921 7359 8.468720 TCGACTATTGATCAAATTCGTAAACA 57.531 30.769 24.37 11.15 0.00 2.83
1930 7368 6.671614 TCAAATTCGTAAACACAACAGTCT 57.328 33.333 0.00 0.00 0.00 3.24
1962 7400 0.108424 TTGTGCTTTTTGTGGCGCTT 60.108 45.000 7.64 0.00 39.38 4.68
2030 7468 1.634960 TGTGGAGTTGTATCCGGTCA 58.365 50.000 0.00 0.00 42.77 4.02
2073 7650 4.568592 CCCCCTCTTCTTTTGTTGAGCTAT 60.569 45.833 0.00 0.00 0.00 2.97
2118 7695 6.486993 GGTGGGACTGAATAGATGTTTATTCC 59.513 42.308 3.98 0.00 38.63 3.01
2141 7718 1.094785 TTGGCTTTTCTAGGATGCGC 58.905 50.000 0.00 0.00 0.00 6.09
2163 7747 5.163540 CGCTGGGTTCTTTGTACTACTAGAT 60.164 44.000 0.00 0.00 0.00 1.98
2164 7748 6.627508 CGCTGGGTTCTTTGTACTACTAGATT 60.628 42.308 0.00 0.00 0.00 2.40
2165 7749 7.104290 GCTGGGTTCTTTGTACTACTAGATTT 58.896 38.462 0.00 0.00 0.00 2.17
2166 7750 7.606839 GCTGGGTTCTTTGTACTACTAGATTTT 59.393 37.037 0.00 0.00 0.00 1.82
2167 7751 9.503399 CTGGGTTCTTTGTACTACTAGATTTTT 57.497 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.947669 CCAAATGCTAAATTCAAAATTTGTGAA 57.052 25.926 4.51 4.51 39.24 3.18
34 35 9.334947 TCCAAATGCTAAATTCAAAATTTGTGA 57.665 25.926 5.56 0.00 34.65 3.58
35 36 9.601971 CTCCAAATGCTAAATTCAAAATTTGTG 57.398 29.630 5.56 0.00 34.65 3.33
36 37 8.785946 CCTCCAAATGCTAAATTCAAAATTTGT 58.214 29.630 5.56 0.00 34.65 2.83
37 38 7.751793 GCCTCCAAATGCTAAATTCAAAATTTG 59.248 33.333 0.00 0.00 35.68 2.32
38 39 7.094248 GGCCTCCAAATGCTAAATTCAAAATTT 60.094 33.333 0.00 3.43 0.00 1.82
39 40 6.375174 GGCCTCCAAATGCTAAATTCAAAATT 59.625 34.615 0.00 0.00 0.00 1.82
40 41 5.882000 GGCCTCCAAATGCTAAATTCAAAAT 59.118 36.000 0.00 0.00 0.00 1.82
41 42 5.012975 AGGCCTCCAAATGCTAAATTCAAAA 59.987 36.000 0.00 0.00 0.00 2.44
42 43 4.531732 AGGCCTCCAAATGCTAAATTCAAA 59.468 37.500 0.00 0.00 0.00 2.69
43 44 4.095946 AGGCCTCCAAATGCTAAATTCAA 58.904 39.130 0.00 0.00 0.00 2.69
44 45 3.701040 GAGGCCTCCAAATGCTAAATTCA 59.299 43.478 23.19 0.00 0.00 2.57
45 46 4.313277 GAGGCCTCCAAATGCTAAATTC 57.687 45.455 23.19 0.00 0.00 2.17
59 60 1.144936 CGAACTCCATGGAGGCCTC 59.855 63.158 38.54 29.39 45.88 4.70
60 61 2.370445 CCGAACTCCATGGAGGCCT 61.370 63.158 38.54 25.36 45.88 5.19
61 62 2.190578 CCGAACTCCATGGAGGCC 59.809 66.667 38.54 28.56 45.88 5.19
62 63 2.514824 GCCGAACTCCATGGAGGC 60.515 66.667 38.54 30.70 45.88 4.70
63 64 2.190578 GGCCGAACTCCATGGAGG 59.809 66.667 38.54 26.01 45.88 4.30
64 65 1.144936 GAGGCCGAACTCCATGGAG 59.855 63.158 35.55 35.55 46.91 3.86
65 66 3.309582 GAGGCCGAACTCCATGGA 58.690 61.111 15.27 15.27 0.00 3.41
71 72 0.889186 TGCTTTTGGAGGCCGAACTC 60.889 55.000 0.00 0.00 36.76 3.01
72 73 0.890996 CTGCTTTTGGAGGCCGAACT 60.891 55.000 0.00 0.00 33.97 3.01
73 74 1.172812 ACTGCTTTTGGAGGCCGAAC 61.173 55.000 0.00 0.00 42.59 3.95
74 75 0.467290 AACTGCTTTTGGAGGCCGAA 60.467 50.000 0.00 0.00 42.59 4.30
75 76 0.467290 AAACTGCTTTTGGAGGCCGA 60.467 50.000 0.00 0.00 42.59 5.54
76 77 0.039165 GAAACTGCTTTTGGAGGCCG 60.039 55.000 0.00 0.00 42.59 6.13
77 78 1.000171 CAGAAACTGCTTTTGGAGGCC 60.000 52.381 0.00 0.00 42.59 5.19
78 79 1.000171 CCAGAAACTGCTTTTGGAGGC 60.000 52.381 0.00 0.00 42.59 4.70
79 80 2.310538 ACCAGAAACTGCTTTTGGAGG 58.689 47.619 7.30 0.00 42.59 4.30
80 81 4.114794 CAAACCAGAAACTGCTTTTGGAG 58.885 43.478 7.30 0.00 43.99 3.86
81 82 3.766591 TCAAACCAGAAACTGCTTTTGGA 59.233 39.130 7.30 3.40 35.52 3.53
82 83 4.114794 CTCAAACCAGAAACTGCTTTTGG 58.885 43.478 16.45 0.00 35.52 3.28
83 84 3.553105 GCTCAAACCAGAAACTGCTTTTG 59.447 43.478 13.17 13.17 35.82 2.44
84 85 3.448660 AGCTCAAACCAGAAACTGCTTTT 59.551 39.130 0.00 0.00 0.00 2.27
85 86 3.026694 AGCTCAAACCAGAAACTGCTTT 58.973 40.909 0.00 0.00 0.00 3.51
86 87 2.620585 GAGCTCAAACCAGAAACTGCTT 59.379 45.455 9.40 0.00 0.00 3.91
87 88 2.225467 GAGCTCAAACCAGAAACTGCT 58.775 47.619 9.40 0.00 0.00 4.24
88 89 1.268079 GGAGCTCAAACCAGAAACTGC 59.732 52.381 17.19 0.00 0.00 4.40
89 90 2.575532 TGGAGCTCAAACCAGAAACTG 58.424 47.619 17.19 0.00 0.00 3.16
90 91 2.952310 GTTGGAGCTCAAACCAGAAACT 59.048 45.455 21.59 0.00 37.08 2.66
91 92 2.034685 GGTTGGAGCTCAAACCAGAAAC 59.965 50.000 37.92 16.78 37.09 2.78
92 93 2.091885 AGGTTGGAGCTCAAACCAGAAA 60.092 45.455 41.46 11.66 43.90 2.52
93 94 1.494721 AGGTTGGAGCTCAAACCAGAA 59.505 47.619 41.46 7.53 43.90 3.02
94 95 1.140312 AGGTTGGAGCTCAAACCAGA 58.860 50.000 41.46 5.54 43.90 3.86
95 96 1.202806 TCAGGTTGGAGCTCAAACCAG 60.203 52.381 41.46 36.11 43.90 4.00
96 97 0.843309 TCAGGTTGGAGCTCAAACCA 59.157 50.000 41.46 26.69 43.90 3.67
97 98 1.239347 GTCAGGTTGGAGCTCAAACC 58.761 55.000 36.73 36.73 43.90 3.27
98 99 1.202818 AGGTCAGGTTGGAGCTCAAAC 60.203 52.381 23.65 23.65 41.51 2.93
99 100 1.140312 AGGTCAGGTTGGAGCTCAAA 58.860 50.000 17.19 7.99 41.51 2.69
100 101 2.854253 AGGTCAGGTTGGAGCTCAA 58.146 52.632 17.19 0.00 41.51 3.02
101 102 4.648007 AGGTCAGGTTGGAGCTCA 57.352 55.556 17.19 0.00 41.51 4.26
104 105 1.298014 CTGGAGGTCAGGTTGGAGC 59.702 63.158 0.00 0.00 39.76 4.70
120 121 2.434428 GGAGATTGCATCCATAGCCTG 58.566 52.381 0.00 0.00 36.79 4.85
121 122 1.002888 CGGAGATTGCATCCATAGCCT 59.997 52.381 5.70 0.00 36.57 4.58
122 123 1.446907 CGGAGATTGCATCCATAGCC 58.553 55.000 5.70 0.00 36.57 3.93
123 124 1.002430 TCCGGAGATTGCATCCATAGC 59.998 52.381 0.00 0.00 36.57 2.97
124 125 2.354503 CCTCCGGAGATTGCATCCATAG 60.355 54.545 33.39 7.09 36.57 2.23
125 126 1.625315 CCTCCGGAGATTGCATCCATA 59.375 52.381 33.39 0.00 36.57 2.74
126 127 0.399454 CCTCCGGAGATTGCATCCAT 59.601 55.000 33.39 0.00 36.57 3.41
127 128 0.982852 ACCTCCGGAGATTGCATCCA 60.983 55.000 33.39 0.00 36.57 3.41
128 129 1.001406 CTACCTCCGGAGATTGCATCC 59.999 57.143 33.39 0.00 0.00 3.51
129 130 1.001406 CCTACCTCCGGAGATTGCATC 59.999 57.143 33.39 0.00 0.00 3.91
130 131 1.051812 CCTACCTCCGGAGATTGCAT 58.948 55.000 33.39 12.51 0.00 3.96
131 132 1.048724 CCCTACCTCCGGAGATTGCA 61.049 60.000 33.39 11.17 0.00 4.08
132 133 0.759436 TCCCTACCTCCGGAGATTGC 60.759 60.000 33.39 0.00 0.00 3.56
133 134 1.789523 TTCCCTACCTCCGGAGATTG 58.210 55.000 33.39 17.46 0.00 2.67
134 135 2.504585 GTTTTCCCTACCTCCGGAGATT 59.495 50.000 33.39 20.66 0.00 2.40
135 136 2.117051 GTTTTCCCTACCTCCGGAGAT 58.883 52.381 33.39 20.31 0.00 2.75
136 137 1.078324 AGTTTTCCCTACCTCCGGAGA 59.922 52.381 33.39 13.15 0.00 3.71
137 138 1.481363 GAGTTTTCCCTACCTCCGGAG 59.519 57.143 25.36 25.36 0.00 4.63
138 139 1.565067 GAGTTTTCCCTACCTCCGGA 58.435 55.000 2.93 2.93 0.00 5.14
139 140 0.175073 CGAGTTTTCCCTACCTCCGG 59.825 60.000 0.00 0.00 0.00 5.14
140 141 0.893447 ACGAGTTTTCCCTACCTCCG 59.107 55.000 0.00 0.00 0.00 4.63
159 160 3.671971 CGACAAAAGTGGAGTTTGCACAA 60.672 43.478 3.61 0.00 41.46 3.33
160 161 2.159448 CGACAAAAGTGGAGTTTGCACA 60.159 45.455 3.61 0.00 41.46 4.57
167 168 1.485066 AGTGGTCGACAAAAGTGGAGT 59.515 47.619 18.91 0.00 0.00 3.85
172 173 3.757745 CACAAAGTGGTCGACAAAAGT 57.242 42.857 18.91 4.89 0.00 2.66
194 195 0.036952 CTTCTCCTCGCAGCCAAGAA 60.037 55.000 0.00 0.00 0.00 2.52
202 203 2.047844 GCAGCACTTCTCCTCGCA 60.048 61.111 0.00 0.00 0.00 5.10
224 225 8.998814 TCTGGTATTCCTCCTTTATTTACATGA 58.001 33.333 0.00 0.00 34.23 3.07
226 227 8.440771 CCTCTGGTATTCCTCCTTTATTTACAT 58.559 37.037 0.00 0.00 34.23 2.29
227 228 7.626084 TCCTCTGGTATTCCTCCTTTATTTACA 59.374 37.037 0.00 0.00 34.23 2.41
228 229 8.030913 TCCTCTGGTATTCCTCCTTTATTTAC 57.969 38.462 0.00 0.00 34.23 2.01
229 230 8.632731 TTCCTCTGGTATTCCTCCTTTATTTA 57.367 34.615 0.00 0.00 34.23 1.40
230 231 7.525158 TTCCTCTGGTATTCCTCCTTTATTT 57.475 36.000 0.00 0.00 34.23 1.40
231 232 7.713704 ATTCCTCTGGTATTCCTCCTTTATT 57.286 36.000 0.00 0.00 34.23 1.40
232 233 8.814448 TTATTCCTCTGGTATTCCTCCTTTAT 57.186 34.615 0.00 0.00 34.23 1.40
233 234 8.632731 TTTATTCCTCTGGTATTCCTCCTTTA 57.367 34.615 0.00 0.00 34.23 1.85
241 242 6.484977 CCAGCTTCTTTATTCCTCTGGTATTC 59.515 42.308 0.00 0.00 35.97 1.75
247 248 4.880696 CCTTCCAGCTTCTTTATTCCTCTG 59.119 45.833 0.00 0.00 0.00 3.35
278 279 0.041386 AACTCTACTTCCCGCTCCCT 59.959 55.000 0.00 0.00 0.00 4.20
289 290 4.525487 TGATACGTTTCCACCAACTCTACT 59.475 41.667 0.00 0.00 0.00 2.57
295 296 5.675323 GCCTAAATGATACGTTTCCACCAAC 60.675 44.000 0.00 0.00 0.00 3.77
306 307 2.140717 GAACGGGGCCTAAATGATACG 58.859 52.381 0.84 0.00 0.00 3.06
321 322 2.125269 GTGGTCCATCCCGAACGG 60.125 66.667 6.25 6.25 34.77 4.44
322 323 1.153628 GAGTGGTCCATCCCGAACG 60.154 63.158 0.00 0.00 34.77 3.95
324 325 1.993391 GGGAGTGGTCCATCCCGAA 60.993 63.158 18.31 0.00 45.63 4.30
325 326 2.365105 GGGAGTGGTCCATCCCGA 60.365 66.667 18.31 0.00 45.63 5.14
330 331 0.980231 GAGCAGAGGGAGTGGTCCAT 60.980 60.000 0.00 0.00 46.07 3.41
331 332 1.610673 GAGCAGAGGGAGTGGTCCA 60.611 63.158 0.00 0.00 46.07 4.02
332 333 1.305718 AGAGCAGAGGGAGTGGTCC 60.306 63.158 0.00 0.00 42.29 4.46
333 334 1.896694 CAGAGCAGAGGGAGTGGTC 59.103 63.158 0.00 0.00 41.76 4.02
334 335 2.289532 GCAGAGCAGAGGGAGTGGT 61.290 63.158 0.00 0.00 0.00 4.16
335 336 1.958902 GAGCAGAGCAGAGGGAGTGG 61.959 65.000 0.00 0.00 0.00 4.00
336 337 1.516892 GAGCAGAGCAGAGGGAGTG 59.483 63.158 0.00 0.00 0.00 3.51
337 338 1.685421 GGAGCAGAGCAGAGGGAGT 60.685 63.158 0.00 0.00 0.00 3.85
338 339 2.784356 CGGAGCAGAGCAGAGGGAG 61.784 68.421 0.00 0.00 0.00 4.30
339 340 2.757508 CGGAGCAGAGCAGAGGGA 60.758 66.667 0.00 0.00 0.00 4.20
361 362 2.357034 TCGTTTCCAGCACCGAGC 60.357 61.111 0.00 0.00 46.19 5.03
362 363 1.738099 CCTCGTTTCCAGCACCGAG 60.738 63.158 0.00 0.00 44.72 4.63
363 364 2.154798 CTCCTCGTTTCCAGCACCGA 62.155 60.000 0.00 0.00 0.00 4.69
364 365 1.738099 CTCCTCGTTTCCAGCACCG 60.738 63.158 0.00 0.00 0.00 4.94
365 366 2.035442 GCTCCTCGTTTCCAGCACC 61.035 63.158 0.00 0.00 0.00 5.01
366 367 2.383527 CGCTCCTCGTTTCCAGCAC 61.384 63.158 0.00 0.00 0.00 4.40
367 368 2.048222 CGCTCCTCGTTTCCAGCA 60.048 61.111 0.00 0.00 0.00 4.41
368 369 2.095252 GTCGCTCCTCGTTTCCAGC 61.095 63.158 0.00 0.00 39.67 4.85
369 370 0.734253 CTGTCGCTCCTCGTTTCCAG 60.734 60.000 0.00 0.00 39.67 3.86
370 371 1.176619 TCTGTCGCTCCTCGTTTCCA 61.177 55.000 0.00 0.00 39.67 3.53
371 372 0.038526 TTCTGTCGCTCCTCGTTTCC 60.039 55.000 0.00 0.00 39.67 3.13
372 373 1.997669 ATTCTGTCGCTCCTCGTTTC 58.002 50.000 0.00 0.00 39.67 2.78
373 374 2.735762 GCTATTCTGTCGCTCCTCGTTT 60.736 50.000 0.00 0.00 39.67 3.60
374 375 1.202313 GCTATTCTGTCGCTCCTCGTT 60.202 52.381 0.00 0.00 39.67 3.85
375 376 0.382515 GCTATTCTGTCGCTCCTCGT 59.617 55.000 0.00 0.00 39.67 4.18
376 377 0.665835 AGCTATTCTGTCGCTCCTCG 59.334 55.000 0.00 0.00 40.15 4.63
377 378 2.882137 AGTAGCTATTCTGTCGCTCCTC 59.118 50.000 0.00 0.00 35.33 3.71
378 379 2.882137 GAGTAGCTATTCTGTCGCTCCT 59.118 50.000 8.90 0.00 35.33 3.69
379 380 2.030628 GGAGTAGCTATTCTGTCGCTCC 60.031 54.545 15.07 10.79 35.33 4.70
380 381 2.030628 GGGAGTAGCTATTCTGTCGCTC 60.031 54.545 15.07 5.82 35.33 5.03
381 382 1.957877 GGGAGTAGCTATTCTGTCGCT 59.042 52.381 15.07 0.00 37.77 4.93
382 383 1.000052 GGGGAGTAGCTATTCTGTCGC 60.000 57.143 15.07 4.65 0.00 5.19
383 384 2.307768 TGGGGAGTAGCTATTCTGTCG 58.692 52.381 15.07 0.00 0.00 4.35
384 385 4.755266 TTTGGGGAGTAGCTATTCTGTC 57.245 45.455 15.07 6.64 0.00 3.51
385 386 5.514500 TTTTTGGGGAGTAGCTATTCTGT 57.486 39.130 15.07 0.00 0.00 3.41
386 387 6.122277 TCATTTTTGGGGAGTAGCTATTCTG 58.878 40.000 15.07 4.32 0.00 3.02
387 388 6.327386 TCATTTTTGGGGAGTAGCTATTCT 57.673 37.500 15.07 0.00 0.00 2.40
388 389 6.603599 AGTTCATTTTTGGGGAGTAGCTATTC 59.396 38.462 7.70 7.70 0.00 1.75
389 390 6.494059 AGTTCATTTTTGGGGAGTAGCTATT 58.506 36.000 0.00 0.00 0.00 1.73
390 391 6.079712 AGTTCATTTTTGGGGAGTAGCTAT 57.920 37.500 0.00 0.00 0.00 2.97
391 392 5.514500 AGTTCATTTTTGGGGAGTAGCTA 57.486 39.130 0.00 0.00 0.00 3.32
392 393 4.388577 AGTTCATTTTTGGGGAGTAGCT 57.611 40.909 0.00 0.00 0.00 3.32
393 394 4.094442 CGTAGTTCATTTTTGGGGAGTAGC 59.906 45.833 0.00 0.00 0.00 3.58
394 395 4.094442 GCGTAGTTCATTTTTGGGGAGTAG 59.906 45.833 0.00 0.00 0.00 2.57
395 396 4.004982 GCGTAGTTCATTTTTGGGGAGTA 58.995 43.478 0.00 0.00 0.00 2.59
396 397 2.817844 GCGTAGTTCATTTTTGGGGAGT 59.182 45.455 0.00 0.00 0.00 3.85
397 398 2.163613 GGCGTAGTTCATTTTTGGGGAG 59.836 50.000 0.00 0.00 0.00 4.30
398 399 2.164338 GGCGTAGTTCATTTTTGGGGA 58.836 47.619 0.00 0.00 0.00 4.81
399 400 1.203758 GGGCGTAGTTCATTTTTGGGG 59.796 52.381 0.00 0.00 0.00 4.96
400 401 1.203758 GGGGCGTAGTTCATTTTTGGG 59.796 52.381 0.00 0.00 0.00 4.12
401 402 2.163613 GAGGGGCGTAGTTCATTTTTGG 59.836 50.000 0.00 0.00 0.00 3.28
402 403 3.081804 AGAGGGGCGTAGTTCATTTTTG 58.918 45.455 0.00 0.00 0.00 2.44
403 404 3.344515 GAGAGGGGCGTAGTTCATTTTT 58.655 45.455 0.00 0.00 0.00 1.94
404 405 2.355818 GGAGAGGGGCGTAGTTCATTTT 60.356 50.000 0.00 0.00 0.00 1.82
405 406 1.209747 GGAGAGGGGCGTAGTTCATTT 59.790 52.381 0.00 0.00 0.00 2.32
406 407 0.831307 GGAGAGGGGCGTAGTTCATT 59.169 55.000 0.00 0.00 0.00 2.57
407 408 1.392710 CGGAGAGGGGCGTAGTTCAT 61.393 60.000 0.00 0.00 0.00 2.57
408 409 2.050350 CGGAGAGGGGCGTAGTTCA 61.050 63.158 0.00 0.00 0.00 3.18
409 410 2.806237 CGGAGAGGGGCGTAGTTC 59.194 66.667 0.00 0.00 0.00 3.01
410 411 3.459063 GCGGAGAGGGGCGTAGTT 61.459 66.667 0.00 0.00 0.00 2.24
411 412 4.444081 AGCGGAGAGGGGCGTAGT 62.444 66.667 0.00 0.00 0.00 2.73
412 413 3.597728 GAGCGGAGAGGGGCGTAG 61.598 72.222 0.00 0.00 0.00 3.51
418 419 1.915078 AAATGGTGGAGCGGAGAGGG 61.915 60.000 0.00 0.00 0.00 4.30
419 420 0.462759 GAAATGGTGGAGCGGAGAGG 60.463 60.000 0.00 0.00 0.00 3.69
420 421 0.250234 TGAAATGGTGGAGCGGAGAG 59.750 55.000 0.00 0.00 0.00 3.20
421 422 0.250234 CTGAAATGGTGGAGCGGAGA 59.750 55.000 0.00 0.00 0.00 3.71
422 423 1.372087 GCTGAAATGGTGGAGCGGAG 61.372 60.000 0.00 0.00 0.00 4.63
423 424 1.377202 GCTGAAATGGTGGAGCGGA 60.377 57.895 0.00 0.00 0.00 5.54
424 425 1.372087 GAGCTGAAATGGTGGAGCGG 61.372 60.000 0.00 0.00 36.52 5.52
425 426 1.372087 GGAGCTGAAATGGTGGAGCG 61.372 60.000 0.00 0.00 36.52 5.03
426 427 0.322816 TGGAGCTGAAATGGTGGAGC 60.323 55.000 0.00 0.00 0.00 4.70
427 428 1.457346 GTGGAGCTGAAATGGTGGAG 58.543 55.000 0.00 0.00 0.00 3.86
428 429 0.321564 CGTGGAGCTGAAATGGTGGA 60.322 55.000 0.00 0.00 0.00 4.02
429 430 0.321564 TCGTGGAGCTGAAATGGTGG 60.322 55.000 0.00 0.00 0.00 4.61
430 431 1.466167 CTTCGTGGAGCTGAAATGGTG 59.534 52.381 0.00 0.00 0.00 4.17
431 432 1.072331 ACTTCGTGGAGCTGAAATGGT 59.928 47.619 0.00 0.00 0.00 3.55
432 433 1.813513 ACTTCGTGGAGCTGAAATGG 58.186 50.000 0.00 0.00 0.00 3.16
433 434 2.095567 CCAACTTCGTGGAGCTGAAATG 60.096 50.000 0.00 0.00 41.65 2.32
434 435 2.154462 CCAACTTCGTGGAGCTGAAAT 58.846 47.619 0.00 0.00 41.65 2.17
435 436 1.593196 CCAACTTCGTGGAGCTGAAA 58.407 50.000 0.00 0.00 41.65 2.69
436 437 0.250295 CCCAACTTCGTGGAGCTGAA 60.250 55.000 0.00 0.00 41.65 3.02
437 438 1.118965 TCCCAACTTCGTGGAGCTGA 61.119 55.000 0.00 0.00 41.65 4.26
438 439 0.671781 CTCCCAACTTCGTGGAGCTG 60.672 60.000 0.00 0.00 41.65 4.24
439 440 1.674057 CTCCCAACTTCGTGGAGCT 59.326 57.895 0.00 0.00 41.65 4.09
440 441 4.285851 CTCCCAACTTCGTGGAGC 57.714 61.111 0.00 0.00 41.65 4.70
441 442 1.376037 GGCTCCCAACTTCGTGGAG 60.376 63.158 0.00 0.00 46.87 3.86
442 443 2.111999 CTGGCTCCCAACTTCGTGGA 62.112 60.000 0.00 0.00 41.65 4.02
443 444 1.672356 CTGGCTCCCAACTTCGTGG 60.672 63.158 0.00 0.00 38.51 4.94
444 445 0.671781 CTCTGGCTCCCAACTTCGTG 60.672 60.000 0.00 0.00 30.80 4.35
445 446 1.122019 ACTCTGGCTCCCAACTTCGT 61.122 55.000 0.00 0.00 30.80 3.85
446 447 0.671781 CACTCTGGCTCCCAACTTCG 60.672 60.000 0.00 0.00 30.80 3.79
447 448 0.398318 ACACTCTGGCTCCCAACTTC 59.602 55.000 0.00 0.00 30.80 3.01
448 449 0.846693 AACACTCTGGCTCCCAACTT 59.153 50.000 0.00 0.00 30.80 2.66
449 450 0.109342 CAACACTCTGGCTCCCAACT 59.891 55.000 0.00 0.00 30.80 3.16
450 451 1.518903 GCAACACTCTGGCTCCCAAC 61.519 60.000 0.00 0.00 30.80 3.77
451 452 1.228245 GCAACACTCTGGCTCCCAA 60.228 57.895 0.00 0.00 30.80 4.12
452 453 2.431683 GCAACACTCTGGCTCCCA 59.568 61.111 0.00 0.00 0.00 4.37
453 454 2.360475 GGCAACACTCTGGCTCCC 60.360 66.667 0.00 0.00 38.77 4.30
454 455 2.731691 TTCGGCAACACTCTGGCTCC 62.732 60.000 0.00 0.00 39.65 4.70
455 456 1.301716 TTCGGCAACACTCTGGCTC 60.302 57.895 0.00 0.00 39.65 4.70
456 457 1.598130 GTTCGGCAACACTCTGGCT 60.598 57.895 0.00 0.00 39.65 4.75
457 458 2.946762 GTTCGGCAACACTCTGGC 59.053 61.111 0.00 0.00 38.47 4.85
458 459 2.317609 CCGTTCGGCAACACTCTGG 61.318 63.158 0.00 0.00 32.14 3.86
459 460 2.317609 CCCGTTCGGCAACACTCTG 61.318 63.158 5.66 0.00 32.14 3.35
460 461 2.030562 CCCGTTCGGCAACACTCT 59.969 61.111 5.66 0.00 32.14 3.24
469 470 2.435410 GTGTAAGGGCCCGTTCGG 60.435 66.667 17.88 4.08 0.00 4.30
470 471 0.604511 AAAGTGTAAGGGCCCGTTCG 60.605 55.000 17.88 0.00 0.00 3.95
471 472 0.879090 CAAAGTGTAAGGGCCCGTTC 59.121 55.000 17.88 12.10 0.00 3.95
472 473 0.475044 TCAAAGTGTAAGGGCCCGTT 59.525 50.000 17.88 13.55 0.00 4.44
473 474 0.696501 ATCAAAGTGTAAGGGCCCGT 59.303 50.000 18.44 17.51 0.00 5.28
474 475 1.834188 AATCAAAGTGTAAGGGCCCG 58.166 50.000 18.44 0.00 0.00 6.13
475 476 4.617253 AAAAATCAAAGTGTAAGGGCCC 57.383 40.909 16.46 16.46 0.00 5.80
511 516 7.440556 AGACCAATGATGAGATCTAATCAAACG 59.559 37.037 23.96 16.14 36.44 3.60
544 549 2.614057 CAAAGCCCATGGTATTCGTCTC 59.386 50.000 11.73 0.00 0.00 3.36
566 571 6.170506 GGTTTTCTCCACAAAAAGGAAAAGT 58.829 36.000 0.00 0.00 36.83 2.66
579 584 5.710099 TGACAAATCCTATGGTTTTCTCCAC 59.290 40.000 0.00 0.00 40.51 4.02
643 650 1.968017 CGGTGCTGTGCTGGAACAT 60.968 57.895 0.00 0.00 38.20 2.71
690 697 6.461640 ACGCAATTACTACTTACTTTCAGGT 58.538 36.000 0.00 0.00 0.00 4.00
791 2982 2.409715 TCGTCGTCGTAGTTGTGAGTAG 59.590 50.000 1.33 0.00 38.33 2.57
802 3002 4.270808 TGAGCTGTTATTATCGTCGTCGTA 59.729 41.667 0.00 0.00 38.33 3.43
984 3206 1.399744 CCATCGGTGGCTACTGGCTA 61.400 60.000 0.00 0.00 39.01 3.93
985 3207 2.735772 CCATCGGTGGCTACTGGCT 61.736 63.158 0.00 0.00 39.01 4.75
986 3208 2.203070 CCATCGGTGGCTACTGGC 60.203 66.667 0.00 0.00 39.01 4.85
987 3209 2.505982 CCCATCGGTGGCTACTGG 59.494 66.667 9.99 4.60 44.62 4.00
988 3210 2.505982 CCCCATCGGTGGCTACTG 59.494 66.667 9.99 1.91 44.62 2.74
989 3211 3.480133 GCCCCATCGGTGGCTACT 61.480 66.667 9.99 0.00 44.62 2.57
1315 3564 1.506309 CTACGCCACAGCAACAGCAA 61.506 55.000 0.00 0.00 39.83 3.91
1316 3565 1.960763 CTACGCCACAGCAACAGCA 60.961 57.895 0.00 0.00 39.83 4.41
1317 3566 2.680913 CCTACGCCACAGCAACAGC 61.681 63.158 0.00 0.00 39.83 4.40
1318 3567 0.602638 TTCCTACGCCACAGCAACAG 60.603 55.000 0.00 0.00 39.83 3.16
1319 3568 0.179043 TTTCCTACGCCACAGCAACA 60.179 50.000 0.00 0.00 39.83 3.33
1320 3569 1.165270 ATTTCCTACGCCACAGCAAC 58.835 50.000 0.00 0.00 39.83 4.17
1469 3720 1.084370 CGAAACAGAGGATCCGCCAC 61.084 60.000 12.40 2.70 40.02 5.01
1544 3797 6.762108 AGTCGACAACTATTTTGCGAATTAG 58.238 36.000 19.50 12.21 36.07 1.73
1553 3806 5.638234 GCTACTCCAAGTCGACAACTATTTT 59.362 40.000 19.50 0.00 37.17 1.82
1617 7052 7.393234 TGAATGGAGTTAACCTCATTTTACCTG 59.607 37.037 18.82 0.00 42.40 4.00
1621 7056 9.177608 CTCATGAATGGAGTTAACCTCATTTTA 57.822 33.333 18.82 13.83 42.40 1.52
1627 7062 6.535508 GTGTACTCATGAATGGAGTTAACCTC 59.464 42.308 0.88 0.00 42.77 3.85
1629 7064 6.313905 CAGTGTACTCATGAATGGAGTTAACC 59.686 42.308 0.88 0.00 42.77 2.85
1713 7148 7.191551 TCGTTCATCGGTTATCAGTTAGTTAG 58.808 38.462 0.00 0.00 40.32 2.34
1732 7167 3.149005 AGGTTTTATGCCCTTCGTTCA 57.851 42.857 0.00 0.00 0.00 3.18
1749 7184 7.444299 AGCATGACAAATTGACAAATAAAGGT 58.556 30.769 0.00 0.00 0.00 3.50
1777 7213 5.239744 ACGAGCATAGTTCATACTACTCTGG 59.760 44.000 0.00 0.00 39.59 3.86
1902 7340 8.134895 ACTGTTGTGTTTACGAATTTGATCAAT 58.865 29.630 9.40 0.00 0.00 2.57
1903 7341 7.476667 ACTGTTGTGTTTACGAATTTGATCAA 58.523 30.769 3.38 3.38 0.00 2.57
1921 7359 5.615925 AAAGTCAGACCTAAGACTGTTGT 57.384 39.130 0.00 0.00 43.88 3.32
1930 7368 6.071616 ACAAAAAGCACAAAAGTCAGACCTAA 60.072 34.615 0.00 0.00 0.00 2.69
1962 7400 5.427481 AGAAAATACGGTTAGGATCTTCCCA 59.573 40.000 0.00 0.00 37.19 4.37
2030 7468 0.615331 ACCAGTTGACATCGAGCCAT 59.385 50.000 0.00 0.00 0.00 4.40
2073 7650 2.223688 CCAACTGATTTGCAACGGAACA 60.224 45.455 0.00 0.00 33.34 3.18
2118 7695 2.159379 GCATCCTAGAAAAGCCAAACCG 60.159 50.000 0.00 0.00 0.00 4.44
2141 7718 9.503399 AAAAATCTAGTAGTACAAAGAACCCAG 57.497 33.333 2.52 0.00 0.00 4.45
2191 7775 5.508200 CAAACAGTTAGCAGGTTTGGTAA 57.492 39.130 14.74 0.00 44.59 2.85
2199 7783 6.983890 ACCAATTTAAACAAACAGTTAGCAGG 59.016 34.615 0.00 0.00 40.26 4.85


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

AutoCloner maintained by Alex Coulton.