Multiple sequence alignment - TraesCS7D01G347900

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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 TraesCS7D01G347900 chr7D 100.000 5299 0 0 1 5299 447064972 447070270 0.000000e+00 9786
1 TraesCS7D01G347900 chr7B 96.748 3536 85 10 559 4075 464558344 464561868 0.000000e+00 5866
2 TraesCS7D01G347900 chr7B 89.772 1095 43 28 4241 5299 464561872 464562933 0.000000e+00 1338
3 TraesCS7D01G347900 chr7B 84.874 119 12 3 1772 1884 464559430 464559548 1.210000e-21 115
4 TraesCS7D01G347900 chr7B 87.000 100 10 3 475 571 464557405 464557504 5.610000e-20 110
5 TraesCS7D01G347900 chr7A 92.490 1558 80 10 1772 3312 498935671 498937208 0.000000e+00 2194
6 TraesCS7D01G347900 chr7A 88.558 1678 138 28 123 1772 498934147 498935798 0.000000e+00 1986
7 TraesCS7D01G347900 chr7A 82.301 1017 92 43 3714 4708 498937798 498938748 0.000000e+00 800
8 TraesCS7D01G347900 chr7A 90.076 524 38 3 4789 5299 498938876 498939398 0.000000e+00 667
9 TraesCS7D01G347900 chr7A 94.866 409 18 2 3307 3714 498937363 498937769 2.080000e-178 636


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 TraesCS7D01G347900 chr7D 447064972 447070270 5298 False 9786.00 9786 100.0000 1 5299 1 chr7D.!!$F1 5298
1 TraesCS7D01G347900 chr7B 464557405 464562933 5528 False 1857.25 5866 89.5985 475 5299 4 chr7B.!!$F1 4824
2 TraesCS7D01G347900 chr7A 498934147 498939398 5251 False 1256.60 2194 89.6582 123 5299 5 chr7A.!!$F1 5176

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
536 553 0.030773 TCGATTTGGAGAGATCCGCG 59.969 55.000 0.0 0.0 0.0 6.46 F
1693 2573 1.351017 TCCACATTTCACTGGTCTCCC 59.649 52.381 0.0 0.0 0.0 4.30 F
3273 4176 0.037303 CGCCTCTGATGCCCCAATAT 59.963 55.000 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 2692 2.175499 TGAAATGAATAGGGGAGGCCAG 59.825 50.0 5.01 0.0 0.0 4.85 R
3374 4438 0.948623 ACTGCAGCGCGAATAACACA 60.949 50.0 15.27 0.0 0.0 3.72 R
4720 5845 0.036577 CAGAACTCCTCACCAGCCAG 60.037 60.0 0.00 0.0 0.0 4.85 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
21 22 2.808543 ACTTGCTCTTCGTCAAATGTCC 59.191 45.455 0.00 0.00 0.00 4.02
22 23 1.428448 TGCTCTTCGTCAAATGTCCG 58.572 50.000 0.00 0.00 0.00 4.79
23 24 0.095417 GCTCTTCGTCAAATGTCCGC 59.905 55.000 0.00 0.00 0.00 5.54
24 25 1.428448 CTCTTCGTCAAATGTCCGCA 58.572 50.000 0.00 0.00 0.00 5.69
25 26 1.126846 CTCTTCGTCAAATGTCCGCAC 59.873 52.381 0.00 0.00 0.00 5.34
26 27 1.148310 CTTCGTCAAATGTCCGCACT 58.852 50.000 0.00 0.00 0.00 4.40
27 28 1.531149 CTTCGTCAAATGTCCGCACTT 59.469 47.619 0.00 0.00 0.00 3.16
28 29 1.588674 TCGTCAAATGTCCGCACTTT 58.411 45.000 0.00 0.00 0.00 2.66
29 30 1.529438 TCGTCAAATGTCCGCACTTTC 59.471 47.619 0.00 0.00 0.00 2.62
30 31 1.531149 CGTCAAATGTCCGCACTTTCT 59.469 47.619 0.00 0.00 0.00 2.52
31 32 2.411547 CGTCAAATGTCCGCACTTTCTC 60.412 50.000 0.00 0.00 0.00 2.87
32 33 2.095718 GTCAAATGTCCGCACTTTCTCC 60.096 50.000 0.00 0.00 0.00 3.71
33 34 2.154462 CAAATGTCCGCACTTTCTCCT 58.846 47.619 0.00 0.00 0.00 3.69
34 35 2.100605 AATGTCCGCACTTTCTCCTC 57.899 50.000 0.00 0.00 0.00 3.71
35 36 0.250513 ATGTCCGCACTTTCTCCTCC 59.749 55.000 0.00 0.00 0.00 4.30
36 37 1.446272 GTCCGCACTTTCTCCTCCG 60.446 63.158 0.00 0.00 0.00 4.63
37 38 1.605451 TCCGCACTTTCTCCTCCGA 60.605 57.895 0.00 0.00 0.00 4.55
38 39 1.153745 CCGCACTTTCTCCTCCGAG 60.154 63.158 0.00 0.00 37.48 4.63
39 40 1.595993 CCGCACTTTCTCCTCCGAGA 61.596 60.000 0.00 0.00 43.62 4.04
40 41 0.179150 CGCACTTTCTCCTCCGAGAG 60.179 60.000 0.00 0.00 45.86 3.20
41 42 0.459411 GCACTTTCTCCTCCGAGAGC 60.459 60.000 0.00 0.00 45.86 4.09
42 43 0.179150 CACTTTCTCCTCCGAGAGCG 60.179 60.000 0.00 0.00 45.86 5.03
81 82 2.287829 GGAACCGACATCCCAGAGT 58.712 57.895 0.00 0.00 0.00 3.24
82 83 0.108138 GGAACCGACATCCCAGAGTG 60.108 60.000 0.00 0.00 0.00 3.51
83 84 0.108138 GAACCGACATCCCAGAGTGG 60.108 60.000 0.00 0.00 37.25 4.00
84 85 2.185310 AACCGACATCCCAGAGTGGC 62.185 60.000 0.00 0.00 35.79 5.01
85 86 2.659063 CCGACATCCCAGAGTGGCA 61.659 63.158 0.00 0.00 35.79 4.92
86 87 1.524002 CGACATCCCAGAGTGGCAT 59.476 57.895 0.00 0.00 35.79 4.40
87 88 0.531532 CGACATCCCAGAGTGGCATC 60.532 60.000 0.00 0.00 35.79 3.91
88 89 0.179034 GACATCCCAGAGTGGCATCC 60.179 60.000 0.00 0.00 35.79 3.51
89 90 1.227764 CATCCCAGAGTGGCATCCG 60.228 63.158 0.00 0.00 35.79 4.18
90 91 1.383109 ATCCCAGAGTGGCATCCGA 60.383 57.895 0.00 0.00 35.79 4.55
91 92 0.765903 ATCCCAGAGTGGCATCCGAT 60.766 55.000 0.00 0.00 35.79 4.18
92 93 0.982852 TCCCAGAGTGGCATCCGATT 60.983 55.000 0.00 0.00 35.79 3.34
93 94 0.758734 CCCAGAGTGGCATCCGATTA 59.241 55.000 0.00 0.00 35.79 1.75
94 95 1.140852 CCCAGAGTGGCATCCGATTAA 59.859 52.381 0.00 0.00 35.79 1.40
95 96 2.213499 CCAGAGTGGCATCCGATTAAC 58.787 52.381 0.00 0.00 0.00 2.01
96 97 1.860950 CAGAGTGGCATCCGATTAACG 59.139 52.381 0.00 0.00 42.18 3.18
107 108 1.841450 CGATTAACGGAGCTGTCCTC 58.159 55.000 0.00 0.00 41.34 3.71
108 109 1.841450 GATTAACGGAGCTGTCCTCG 58.159 55.000 0.00 0.00 41.34 4.63
109 110 0.460311 ATTAACGGAGCTGTCCTCGG 59.540 55.000 0.00 0.00 44.11 4.63
110 111 0.609957 TTAACGGAGCTGTCCTCGGA 60.610 55.000 0.00 0.00 41.90 4.55
111 112 0.395311 TAACGGAGCTGTCCTCGGAT 60.395 55.000 0.00 0.00 41.90 4.18
112 113 1.668101 AACGGAGCTGTCCTCGGATC 61.668 60.000 0.00 0.00 41.90 3.36
113 114 1.826054 CGGAGCTGTCCTCGGATCT 60.826 63.158 0.00 0.00 41.90 2.75
114 115 1.739049 GGAGCTGTCCTCGGATCTG 59.261 63.158 0.00 0.00 41.71 2.90
115 116 1.739049 GAGCTGTCCTCGGATCTGG 59.261 63.158 0.62 0.00 33.15 3.86
116 117 0.753479 GAGCTGTCCTCGGATCTGGA 60.753 60.000 0.62 0.16 33.15 3.86
117 118 0.754957 AGCTGTCCTCGGATCTGGAG 60.755 60.000 0.62 4.63 32.36 3.86
118 119 1.040339 GCTGTCCTCGGATCTGGAGT 61.040 60.000 0.62 0.00 32.36 3.85
119 120 1.028905 CTGTCCTCGGATCTGGAGTC 58.971 60.000 0.62 1.85 32.36 3.36
120 121 0.748367 TGTCCTCGGATCTGGAGTCG 60.748 60.000 0.62 0.00 32.36 4.18
121 122 1.152943 TCCTCGGATCTGGAGTCGG 60.153 63.158 0.62 0.00 0.00 4.79
139 140 1.227853 GGCACCGACAACCACTTCT 60.228 57.895 0.00 0.00 0.00 2.85
140 141 1.228657 GGCACCGACAACCACTTCTC 61.229 60.000 0.00 0.00 0.00 2.87
187 192 1.073025 GGAGGTGTGATGGTGTGCA 59.927 57.895 0.00 0.00 0.00 4.57
209 214 0.034059 GGCCGGTGGATATGTGAGAG 59.966 60.000 1.90 0.00 0.00 3.20
220 225 5.222505 TGGATATGTGAGAGAGGATGAGGAT 60.223 44.000 0.00 0.00 0.00 3.24
237 243 0.808755 GATTGTGCGGGTAGGGTTTG 59.191 55.000 0.00 0.00 0.00 2.93
239 245 2.281900 GTGCGGGTAGGGTTTGCA 60.282 61.111 0.00 0.00 0.00 4.08
243 249 1.078426 CGGGTAGGGTTTGCAGAGG 60.078 63.158 0.00 0.00 0.00 3.69
249 255 0.037447 AGGGTTTGCAGAGGAGAAGC 59.963 55.000 0.00 0.00 0.00 3.86
251 257 1.301677 GGTTTGCAGAGGAGAAGCCG 61.302 60.000 0.00 0.00 43.43 5.52
253 259 1.768684 TTTGCAGAGGAGAAGCCGGT 61.769 55.000 1.90 0.00 43.43 5.28
254 260 2.172483 TTGCAGAGGAGAAGCCGGTC 62.172 60.000 1.90 0.00 43.43 4.79
256 262 1.984570 CAGAGGAGAAGCCGGTCCA 60.985 63.158 11.16 0.00 43.43 4.02
257 263 1.229209 AGAGGAGAAGCCGGTCCAA 60.229 57.895 11.16 0.00 43.43 3.53
258 264 0.618968 AGAGGAGAAGCCGGTCCAAT 60.619 55.000 11.16 0.00 43.43 3.16
266 272 3.056821 AGAAGCCGGTCCAATTTTAAAGC 60.057 43.478 1.90 0.00 0.00 3.51
267 273 2.525368 AGCCGGTCCAATTTTAAAGCT 58.475 42.857 1.90 0.00 0.00 3.74
270 276 2.823154 CCGGTCCAATTTTAAAGCTGGA 59.177 45.455 13.61 13.61 35.58 3.86
271 277 3.119495 CCGGTCCAATTTTAAAGCTGGAG 60.119 47.826 16.63 9.07 38.63 3.86
283 289 1.040339 AGCTGGAGTAGGCTTCTCGG 61.040 60.000 13.99 10.59 34.96 4.63
287 293 1.726533 GGAGTAGGCTTCTCGGTCGG 61.727 65.000 13.99 0.00 33.26 4.79
290 296 1.303888 TAGGCTTCTCGGTCGGTGT 60.304 57.895 0.00 0.00 0.00 4.16
295 301 3.509137 TTCTCGGTCGGTGTGCCAC 62.509 63.158 0.00 0.00 34.09 5.01
304 310 4.895854 GTGTGCCACCATGAATGC 57.104 55.556 0.00 0.00 0.00 3.56
306 312 2.341875 TGTGCCACCATGAATGCGG 61.342 57.895 0.00 0.00 0.00 5.69
307 313 2.755064 TGCCACCATGAATGCGGG 60.755 61.111 0.00 0.00 0.00 6.13
312 318 1.152963 ACCATGAATGCGGGTAGGC 60.153 57.895 0.00 0.00 31.89 3.93
313 319 1.149174 CCATGAATGCGGGTAGGCT 59.851 57.895 0.00 0.00 0.00 4.58
314 320 1.168407 CCATGAATGCGGGTAGGCTG 61.168 60.000 0.00 0.00 0.00 4.85
315 321 0.179048 CATGAATGCGGGTAGGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
316 322 0.546122 ATGAATGCGGGTAGGCTGAA 59.454 50.000 0.00 0.00 0.00 3.02
317 323 0.107703 TGAATGCGGGTAGGCTGAAG 60.108 55.000 0.00 0.00 0.00 3.02
318 324 0.178068 GAATGCGGGTAGGCTGAAGA 59.822 55.000 0.00 0.00 0.00 2.87
322 328 2.901042 GGGTAGGCTGAAGACCGG 59.099 66.667 0.00 0.00 33.77 5.28
339 345 2.641197 GGTTTGCCGGAGTGAATGT 58.359 52.632 5.05 0.00 0.00 2.71
342 348 1.606668 GTTTGCCGGAGTGAATGTGAA 59.393 47.619 5.05 0.00 0.00 3.18
348 354 1.740380 CGGAGTGAATGTGAAGCCGAT 60.740 52.381 0.00 0.00 39.62 4.18
350 356 2.350522 GAGTGAATGTGAAGCCGATGT 58.649 47.619 0.00 0.00 0.00 3.06
351 357 2.079158 AGTGAATGTGAAGCCGATGTG 58.921 47.619 0.00 0.00 0.00 3.21
353 359 1.271325 TGAATGTGAAGCCGATGTGGT 60.271 47.619 0.00 0.00 41.21 4.16
362 368 4.814900 CGATGTGGTCGGAGAAGG 57.185 61.111 0.00 0.00 46.47 3.46
363 369 1.890894 CGATGTGGTCGGAGAAGGT 59.109 57.895 0.00 0.00 46.47 3.50
364 370 0.246635 CGATGTGGTCGGAGAAGGTT 59.753 55.000 0.00 0.00 46.47 3.50
365 371 1.726853 GATGTGGTCGGAGAAGGTTG 58.273 55.000 0.00 0.00 39.69 3.77
371 387 2.359975 CGGAGAAGGTTGTGGGCC 60.360 66.667 0.00 0.00 0.00 5.80
374 390 1.303643 GAGAAGGTTGTGGGCCTGG 60.304 63.158 4.53 0.00 36.30 4.45
375 391 2.283173 GAAGGTTGTGGGCCTGGG 60.283 66.667 4.53 0.00 36.30 4.45
396 412 1.594269 CGTTGGAGTTCGACGTGACG 61.594 60.000 2.24 2.24 45.60 4.35
397 413 1.008194 TTGGAGTTCGACGTGACGG 60.008 57.895 10.66 0.00 0.00 4.79
398 414 2.126580 GGAGTTCGACGTGACGGG 60.127 66.667 10.66 0.23 0.00 5.28
399 415 2.804090 GAGTTCGACGTGACGGGC 60.804 66.667 10.66 0.00 0.00 6.13
400 416 4.695231 AGTTCGACGTGACGGGCG 62.695 66.667 10.66 12.98 0.00 6.13
401 417 4.988486 GTTCGACGTGACGGGCGT 62.988 66.667 18.64 1.10 45.86 5.68
402 418 3.353029 TTCGACGTGACGGGCGTA 61.353 61.111 18.64 9.43 43.04 4.42
404 420 1.365368 TTCGACGTGACGGGCGTATA 61.365 55.000 18.64 6.55 43.04 1.47
405 421 1.159713 TCGACGTGACGGGCGTATAT 61.160 55.000 18.64 0.00 43.04 0.86
406 422 0.317269 CGACGTGACGGGCGTATATT 60.317 55.000 10.66 0.00 43.04 1.28
407 423 1.126079 GACGTGACGGGCGTATATTG 58.874 55.000 10.66 0.00 43.04 1.90
409 425 0.872451 CGTGACGGGCGTATATTGCA 60.872 55.000 0.00 0.00 0.00 4.08
413 429 1.964373 CGGGCGTATATTGCACCCC 60.964 63.158 0.95 0.00 37.25 4.95
414 430 1.602605 GGGCGTATATTGCACCCCC 60.603 63.158 0.00 0.00 34.23 5.40
431 447 4.060667 CCTCCCCGCCCCAATTGT 62.061 66.667 4.43 0.00 0.00 2.71
434 450 2.603171 CCCCGCCCCAATTGTTGT 60.603 61.111 4.43 0.00 0.00 3.32
446 462 3.305110 CAATTGTTGTCAGTTTACGGGC 58.695 45.455 0.00 0.00 0.00 6.13
448 464 0.881159 TGTTGTCAGTTTACGGGCGG 60.881 55.000 0.00 0.00 0.00 6.13
450 466 0.600782 TTGTCAGTTTACGGGCGGTC 60.601 55.000 0.00 0.00 0.00 4.79
452 468 0.527565 GTCAGTTTACGGGCGGTCTA 59.472 55.000 0.00 0.00 0.00 2.59
463 479 2.669950 CGGGCGGTCTAAACAAATTTGG 60.670 50.000 21.74 4.61 0.00 3.28
465 481 3.313690 GGCGGTCTAAACAAATTTGGTG 58.686 45.455 21.74 5.22 0.00 4.17
469 485 4.542735 GGTCTAAACAAATTTGGTGACCG 58.457 43.478 22.84 8.39 35.89 4.79
472 488 2.507339 AACAAATTTGGTGACCGCAG 57.493 45.000 21.74 0.00 0.00 5.18
474 490 1.754226 ACAAATTTGGTGACCGCAGTT 59.246 42.857 21.74 0.00 0.00 3.16
475 491 2.126467 CAAATTTGGTGACCGCAGTTG 58.874 47.619 10.49 0.00 0.00 3.16
476 492 0.673437 AATTTGGTGACCGCAGTTGG 59.327 50.000 0.00 0.00 0.00 3.77
477 493 0.179004 ATTTGGTGACCGCAGTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
478 494 1.098712 TTTGGTGACCGCAGTTGGAC 61.099 55.000 0.00 0.00 0.00 4.02
479 495 3.041940 GGTGACCGCAGTTGGACG 61.042 66.667 0.00 0.00 0.00 4.79
490 506 2.788786 GCAGTTGGACGTCAAAATTGTG 59.211 45.455 18.91 9.21 37.08 3.33
508 525 1.959226 GCTGACCGTCCGCTTTGAA 60.959 57.895 7.62 0.00 0.00 2.69
511 528 1.128692 CTGACCGTCCGCTTTGAAATC 59.871 52.381 0.00 0.00 0.00 2.17
515 532 2.028385 ACCGTCCGCTTTGAAATCTACT 60.028 45.455 0.00 0.00 0.00 2.57
534 551 2.099921 ACTGTCGATTTGGAGAGATCCG 59.900 50.000 0.00 0.00 32.10 4.18
535 552 1.202417 TGTCGATTTGGAGAGATCCGC 60.202 52.381 0.00 0.00 0.00 5.54
536 553 0.030773 TCGATTTGGAGAGATCCGCG 59.969 55.000 0.00 0.00 0.00 6.46
927 1806 5.003804 TCCAAATTCCTCTTCTCCTTTTCG 58.996 41.667 0.00 0.00 0.00 3.46
1147 2027 7.010460 TCACATCATTGATGAACTCGTATCAAC 59.990 37.037 28.81 0.00 43.66 3.18
1189 2069 5.362105 AATGCCATATTGCAGTGGAAATT 57.638 34.783 16.33 12.08 45.93 1.82
1192 2072 4.114794 GCCATATTGCAGTGGAAATTGAC 58.885 43.478 16.33 0.00 37.72 3.18
1312 2192 2.120909 CAAATGCCCACCCTAGCCG 61.121 63.158 0.00 0.00 0.00 5.52
1360 2240 6.935240 TTCTGTGATATTACCCCCTATCTG 57.065 41.667 0.00 0.00 0.00 2.90
1688 2568 3.075283 TGGGTAATCCACATTTCACTGGT 59.925 43.478 0.00 0.00 41.46 4.00
1693 2573 1.351017 TCCACATTTCACTGGTCTCCC 59.649 52.381 0.00 0.00 0.00 4.30
1714 2594 3.248602 CCCTATTCATTACAGAAGCGTGC 59.751 47.826 0.00 0.00 0.00 5.34
2031 2916 1.725164 GAGAAATGTGTCCGGTTCGTC 59.275 52.381 0.00 0.00 0.00 4.20
2178 3063 8.322091 AGGTGAAGTTCACTATAATTTAGCACT 58.678 33.333 29.89 14.24 46.19 4.40
2580 3470 6.821160 TGAACAGATGGATTAATAGCGTTCAA 59.179 34.615 0.00 0.00 37.77 2.69
3080 3975 9.512435 CTGAAATTTTCCTTACTGATAATGCTG 57.488 33.333 6.68 0.00 0.00 4.41
3125 4020 5.820947 GGAACGAAGAAAGGGATTGCTATTA 59.179 40.000 0.00 0.00 0.00 0.98
3273 4176 0.037303 CGCCTCTGATGCCCCAATAT 59.963 55.000 0.00 0.00 0.00 1.28
3374 4438 2.317371 TGGGTTGGGCAAATACACAT 57.683 45.000 0.00 0.00 0.00 3.21
3400 4464 1.368641 TTCGCGCTGCAGTTCATAAT 58.631 45.000 16.64 0.00 0.00 1.28
3820 4916 4.729868 ACCAGCCTAACTTTGTTCTCAAT 58.270 39.130 0.00 0.00 33.32 2.57
3833 4929 7.667219 ACTTTGTTCTCAATCACAATATGGTCT 59.333 33.333 0.00 0.00 32.96 3.85
3992 5088 6.318648 TGGCAAATAGTAGGTTCTTGCTATTG 59.681 38.462 5.21 0.00 41.62 1.90
4049 5146 0.240945 ACTTGTGTTATGCAAGCGCC 59.759 50.000 2.29 0.00 45.09 6.53
4061 5158 1.469079 GCAAGCGCCGTCCATTTTTAT 60.469 47.619 2.29 0.00 0.00 1.40
4091 5188 1.276138 GGCTGTTTGCTAATGCCCTTT 59.724 47.619 13.74 0.00 42.39 3.11
4116 5213 6.976088 TGTATGTCAAATTTTGTGGTAGGTG 58.024 36.000 8.89 0.00 0.00 4.00
4117 5214 6.547880 TGTATGTCAAATTTTGTGGTAGGTGT 59.452 34.615 8.89 0.00 0.00 4.16
4118 5215 5.255710 TGTCAAATTTTGTGGTAGGTGTG 57.744 39.130 8.89 0.00 0.00 3.82
4119 5216 4.950475 TGTCAAATTTTGTGGTAGGTGTGA 59.050 37.500 8.89 0.00 0.00 3.58
4120 5217 5.163602 TGTCAAATTTTGTGGTAGGTGTGAC 60.164 40.000 8.89 0.00 33.84 3.67
4121 5218 4.950475 TCAAATTTTGTGGTAGGTGTGACA 59.050 37.500 8.89 0.00 0.00 3.58
4122 5219 5.596361 TCAAATTTTGTGGTAGGTGTGACAT 59.404 36.000 8.89 0.00 0.00 3.06
4123 5220 5.705609 AATTTTGTGGTAGGTGTGACATC 57.294 39.130 0.00 0.00 0.00 3.06
4124 5221 3.847671 TTTGTGGTAGGTGTGACATCA 57.152 42.857 0.00 0.00 0.00 3.07
4125 5222 4.365514 TTTGTGGTAGGTGTGACATCAT 57.634 40.909 0.00 0.00 0.00 2.45
4126 5223 3.610040 TGTGGTAGGTGTGACATCATC 57.390 47.619 0.00 0.00 0.00 2.92
4127 5224 2.903135 TGTGGTAGGTGTGACATCATCA 59.097 45.455 0.00 0.00 33.79 3.07
4128 5225 3.326297 TGTGGTAGGTGTGACATCATCAA 59.674 43.478 0.00 0.00 39.72 2.57
4129 5226 3.935203 GTGGTAGGTGTGACATCATCAAG 59.065 47.826 0.00 0.00 39.72 3.02
4130 5227 2.939103 GGTAGGTGTGACATCATCAAGC 59.061 50.000 0.00 0.00 39.72 4.01
4131 5228 2.865119 AGGTGTGACATCATCAAGCA 57.135 45.000 0.00 0.00 39.72 3.91
4132 5229 3.144657 AGGTGTGACATCATCAAGCAA 57.855 42.857 0.00 0.00 39.72 3.91
4133 5230 3.489355 AGGTGTGACATCATCAAGCAAA 58.511 40.909 0.00 0.00 39.72 3.68
4134 5231 3.890756 AGGTGTGACATCATCAAGCAAAA 59.109 39.130 0.00 0.00 39.72 2.44
4135 5232 4.525487 AGGTGTGACATCATCAAGCAAAAT 59.475 37.500 0.00 0.00 39.72 1.82
4173 5270 1.667236 TGGTGATGCGCTTTCCATAG 58.333 50.000 9.73 0.00 0.00 2.23
4176 5273 2.279741 GTGATGCGCTTTCCATAGACA 58.720 47.619 9.73 0.00 0.00 3.41
4180 5277 2.346803 TGCGCTTTCCATAGACAGAAC 58.653 47.619 9.73 0.00 0.00 3.01
4187 5284 5.351740 GCTTTCCATAGACAGAACTGTAACC 59.648 44.000 7.46 0.00 45.05 2.85
4188 5285 6.428083 TTTCCATAGACAGAACTGTAACCA 57.572 37.500 7.46 0.00 45.05 3.67
4203 5300 5.660629 TGTAACCAACAGTTTATCGTGTG 57.339 39.130 0.00 0.00 40.05 3.82
4238 5335 7.127012 TCAATGTTGCCCATTATTCATTCAT 57.873 32.000 0.00 0.00 41.93 2.57
4290 5387 1.246056 GCAGAAAGACATGCCAGCCA 61.246 55.000 0.00 0.00 36.41 4.75
4473 5572 5.163754 CCCTTGATCCTCGTTGATTGTAAAC 60.164 44.000 0.00 0.00 0.00 2.01
4481 5580 8.610248 TCCTCGTTGATTGTAAACTAAATTGA 57.390 30.769 0.00 0.00 0.00 2.57
4551 5653 0.538516 AGCTGACTGTCGGTCTGTCT 60.539 55.000 17.36 12.63 44.74 3.41
4561 5663 2.557490 GTCGGTCTGTCTGGAAACTACT 59.443 50.000 0.00 0.00 0.00 2.57
4562 5664 3.755378 GTCGGTCTGTCTGGAAACTACTA 59.245 47.826 0.00 0.00 0.00 1.82
4564 5666 3.504906 CGGTCTGTCTGGAAACTACTACA 59.495 47.826 0.00 0.00 0.00 2.74
4565 5667 4.379603 CGGTCTGTCTGGAAACTACTACAG 60.380 50.000 0.00 0.00 36.52 2.74
4566 5668 4.082136 GGTCTGTCTGGAAACTACTACAGG 60.082 50.000 0.00 0.00 36.01 4.00
4568 5670 3.507411 TGTCTGGAAACTACTACAGGCT 58.493 45.455 0.00 0.00 36.57 4.58
4569 5671 4.669700 TGTCTGGAAACTACTACAGGCTA 58.330 43.478 0.00 0.00 36.57 3.93
4570 5672 5.269991 TGTCTGGAAACTACTACAGGCTAT 58.730 41.667 0.00 0.00 36.57 2.97
4571 5673 5.360144 TGTCTGGAAACTACTACAGGCTATC 59.640 44.000 0.00 0.00 36.57 2.08
4575 5684 3.309600 AACTACTACAGGCTATCCGGT 57.690 47.619 0.00 0.00 43.31 5.28
4586 5695 4.095932 CAGGCTATCCGGTAAAAGGAAAAC 59.904 45.833 0.00 0.00 41.69 2.43
4608 5717 6.660887 ACCTGCAACACTTTATTTTGTTTG 57.339 33.333 0.00 0.00 33.59 2.93
4610 5719 5.064452 CCTGCAACACTTTATTTTGTTTGCA 59.936 36.000 6.00 6.00 37.39 4.08
4611 5720 6.402983 CCTGCAACACTTTATTTTGTTTGCAA 60.403 34.615 0.00 0.00 38.29 4.08
4612 5721 6.541086 TGCAACACTTTATTTTGTTTGCAAG 58.459 32.000 0.00 0.00 37.09 4.01
4613 5722 6.148480 TGCAACACTTTATTTTGTTTGCAAGT 59.852 30.769 0.00 0.00 37.09 3.16
4614 5723 6.682441 GCAACACTTTATTTTGTTTGCAAGTC 59.318 34.615 0.00 0.00 33.59 3.01
4615 5724 7.623089 GCAACACTTTATTTTGTTTGCAAGTCA 60.623 33.333 0.00 0.47 33.59 3.41
4616 5725 7.897575 ACACTTTATTTTGTTTGCAAGTCAA 57.102 28.000 12.80 12.80 35.82 3.18
4617 5726 8.316640 ACACTTTATTTTGTTTGCAAGTCAAA 57.683 26.923 20.21 20.21 42.01 2.69
4618 5727 8.778358 ACACTTTATTTTGTTTGCAAGTCAAAA 58.222 25.926 28.90 28.90 45.35 2.44
4619 5728 9.604626 CACTTTATTTTGTTTGCAAGTCAAAAA 57.395 25.926 29.68 21.11 45.35 1.94
4638 5747 0.615850 AACTACAGCTTCCCTCCAGC 59.384 55.000 0.00 0.00 37.56 4.85
4722 5847 9.855021 AACGGTTTCTGGATAATTTTAATTCTG 57.145 29.630 0.00 0.00 0.00 3.02
4723 5848 8.466798 ACGGTTTCTGGATAATTTTAATTCTGG 58.533 33.333 0.00 0.00 0.00 3.86
4724 5849 7.435192 CGGTTTCTGGATAATTTTAATTCTGGC 59.565 37.037 0.00 0.00 0.00 4.85
4725 5850 8.478066 GGTTTCTGGATAATTTTAATTCTGGCT 58.522 33.333 0.00 0.00 0.00 4.75
4726 5851 9.305925 GTTTCTGGATAATTTTAATTCTGGCTG 57.694 33.333 0.00 0.00 0.00 4.85
4727 5852 7.587037 TCTGGATAATTTTAATTCTGGCTGG 57.413 36.000 0.00 0.00 0.00 4.85
4728 5853 7.125391 TCTGGATAATTTTAATTCTGGCTGGT 58.875 34.615 0.00 0.00 0.00 4.00
4729 5854 7.068593 TCTGGATAATTTTAATTCTGGCTGGTG 59.931 37.037 0.00 0.00 0.00 4.17
4730 5855 6.894654 TGGATAATTTTAATTCTGGCTGGTGA 59.105 34.615 0.00 0.00 0.00 4.02
4731 5856 7.068593 TGGATAATTTTAATTCTGGCTGGTGAG 59.931 37.037 0.00 0.00 0.00 3.51
4750 5875 4.636206 GTGAGGAGTTCTGTGAACTTTGTT 59.364 41.667 13.25 1.90 0.00 2.83
4760 5885 7.310072 TCTGTGAACTTTGTTCAAACGATAA 57.690 32.000 13.69 0.00 0.00 1.75
4773 5898 6.176975 TCAAACGATAAATTCTGCGACATT 57.823 33.333 0.00 0.00 0.00 2.71
4774 5899 6.020984 TCAAACGATAAATTCTGCGACATTG 58.979 36.000 0.00 0.00 0.00 2.82
4775 5900 4.536364 ACGATAAATTCTGCGACATTGG 57.464 40.909 0.00 0.00 0.00 3.16
4776 5901 4.188462 ACGATAAATTCTGCGACATTGGA 58.812 39.130 0.00 0.00 0.00 3.53
4777 5902 4.634004 ACGATAAATTCTGCGACATTGGAA 59.366 37.500 0.00 0.00 0.00 3.53
4778 5903 5.296780 ACGATAAATTCTGCGACATTGGAAT 59.703 36.000 0.00 0.00 0.00 3.01
4779 5904 6.183360 ACGATAAATTCTGCGACATTGGAATT 60.183 34.615 0.00 0.00 39.22 2.17
4781 5906 7.305590 CGATAAATTCTGCGACATTGGAATTTG 60.306 37.037 17.28 3.51 43.57 2.32
4783 5908 5.587388 ATTCTGCGACATTGGAATTTGAT 57.413 34.783 0.00 0.00 0.00 2.57
4784 5909 6.698008 ATTCTGCGACATTGGAATTTGATA 57.302 33.333 0.00 0.00 0.00 2.15
4785 5910 6.698008 TTCTGCGACATTGGAATTTGATAT 57.302 33.333 0.00 0.00 0.00 1.63
4790 5977 6.082338 GCGACATTGGAATTTGATATAGCAG 58.918 40.000 0.00 0.00 0.00 4.24
4846 6033 3.766591 TGGAATTTGATAACATTGCCCGT 59.233 39.130 0.00 0.00 0.00 5.28
4933 6121 2.671396 CACAGGCTATTACAACCACGAC 59.329 50.000 0.00 0.00 0.00 4.34
5042 6232 7.336931 CCATATTTACAAGCAAACTACCTCTGT 59.663 37.037 0.00 0.00 0.00 3.41
5074 6275 5.539574 CACTGTATCATCTCCATCCTCTTCT 59.460 44.000 0.00 0.00 0.00 2.85
5086 6287 1.612395 CCTCTTCTCTTCCTGGCGCT 61.612 60.000 7.64 0.00 0.00 5.92
5138 6346 8.635765 ACTATAGAAAAATGAGTTGCAAGGAA 57.364 30.769 6.78 0.00 0.00 3.36
5267 6475 0.036732 CAAGGTAGCAGAGCCCACAA 59.963 55.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.808543 GGACATTTGACGAAGAGCAAGT 59.191 45.455 0.00 0.00 0.00 3.16
1 2 2.159787 CGGACATTTGACGAAGAGCAAG 60.160 50.000 0.00 0.00 0.00 4.01
2 3 1.798223 CGGACATTTGACGAAGAGCAA 59.202 47.619 0.00 0.00 0.00 3.91
3 4 1.428448 CGGACATTTGACGAAGAGCA 58.572 50.000 0.00 0.00 0.00 4.26
4 5 0.095417 GCGGACATTTGACGAAGAGC 59.905 55.000 0.00 0.00 0.00 4.09
5 6 1.126846 GTGCGGACATTTGACGAAGAG 59.873 52.381 0.63 0.00 0.00 2.85
6 7 1.144969 GTGCGGACATTTGACGAAGA 58.855 50.000 0.63 0.00 0.00 2.87
7 8 1.148310 AGTGCGGACATTTGACGAAG 58.852 50.000 10.52 0.00 0.00 3.79
8 9 1.588674 AAGTGCGGACATTTGACGAA 58.411 45.000 10.52 0.00 0.00 3.85
9 10 1.529438 GAAAGTGCGGACATTTGACGA 59.471 47.619 10.52 0.00 0.00 4.20
10 11 1.531149 AGAAAGTGCGGACATTTGACG 59.469 47.619 10.52 0.00 0.00 4.35
11 12 2.095718 GGAGAAAGTGCGGACATTTGAC 60.096 50.000 10.52 0.00 0.00 3.18
12 13 2.151202 GGAGAAAGTGCGGACATTTGA 58.849 47.619 10.52 0.00 0.00 2.69
13 14 2.154462 AGGAGAAAGTGCGGACATTTG 58.846 47.619 10.52 0.00 0.00 2.32
14 15 2.427506 GAGGAGAAAGTGCGGACATTT 58.572 47.619 10.52 7.01 0.00 2.32
15 16 1.339151 GGAGGAGAAAGTGCGGACATT 60.339 52.381 10.52 2.77 0.00 2.71
16 17 0.250513 GGAGGAGAAAGTGCGGACAT 59.749 55.000 10.52 0.00 0.00 3.06
17 18 1.671742 GGAGGAGAAAGTGCGGACA 59.328 57.895 10.52 0.00 0.00 4.02
18 19 1.446272 CGGAGGAGAAAGTGCGGAC 60.446 63.158 0.00 0.00 0.00 4.79
19 20 1.595993 CTCGGAGGAGAAAGTGCGGA 61.596 60.000 0.00 0.00 43.27 5.54
20 21 1.153745 CTCGGAGGAGAAAGTGCGG 60.154 63.158 0.00 0.00 43.27 5.69
21 22 1.883732 TCTCGGAGGAGAAAGTGCG 59.116 57.895 4.96 0.00 46.11 5.34
55 56 2.907897 GATGTCGGTTCCCCTGCGAG 62.908 65.000 0.00 0.00 0.00 5.03
56 57 3.000819 ATGTCGGTTCCCCTGCGA 61.001 61.111 0.00 0.00 0.00 5.10
57 58 2.511600 GATGTCGGTTCCCCTGCG 60.512 66.667 0.00 0.00 0.00 5.18
58 59 2.124695 GGATGTCGGTTCCCCTGC 60.125 66.667 0.00 0.00 0.00 4.85
59 60 2.590092 GGGATGTCGGTTCCCCTG 59.410 66.667 6.91 0.00 46.20 4.45
63 64 0.108138 CACTCTGGGATGTCGGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
64 65 0.108138 CCACTCTGGGATGTCGGTTC 60.108 60.000 0.00 0.00 32.67 3.62
65 66 1.983224 CCACTCTGGGATGTCGGTT 59.017 57.895 0.00 0.00 32.67 4.44
66 67 2.660064 GCCACTCTGGGATGTCGGT 61.660 63.158 0.00 0.00 38.19 4.69
67 68 2.187946 GCCACTCTGGGATGTCGG 59.812 66.667 0.00 0.00 38.19 4.79
68 69 2.981302 TGCCACTCTGGGATGTCG 59.019 61.111 0.00 0.00 38.19 4.35
73 74 0.982852 AATCGGATGCCACTCTGGGA 60.983 55.000 0.00 0.00 43.78 4.37
74 75 0.758734 TAATCGGATGCCACTCTGGG 59.241 55.000 0.00 0.00 38.19 4.45
75 76 2.213499 GTTAATCGGATGCCACTCTGG 58.787 52.381 0.00 0.00 41.55 3.86
76 77 1.860950 CGTTAATCGGATGCCACTCTG 59.139 52.381 0.00 0.00 35.71 3.35
77 78 2.225068 CGTTAATCGGATGCCACTCT 57.775 50.000 0.00 0.00 35.71 3.24
88 89 1.841450 GAGGACAGCTCCGTTAATCG 58.159 55.000 0.00 0.00 42.22 3.34
89 90 1.536284 CCGAGGACAGCTCCGTTAATC 60.536 57.143 0.00 0.00 42.22 1.75
90 91 0.460311 CCGAGGACAGCTCCGTTAAT 59.540 55.000 0.00 0.00 42.22 1.40
91 92 0.609957 TCCGAGGACAGCTCCGTTAA 60.610 55.000 0.00 0.00 42.22 2.01
92 93 0.395311 ATCCGAGGACAGCTCCGTTA 60.395 55.000 0.00 0.00 42.22 3.18
93 94 1.668101 GATCCGAGGACAGCTCCGTT 61.668 60.000 0.00 0.00 42.22 4.44
94 95 2.043852 ATCCGAGGACAGCTCCGT 60.044 61.111 0.00 0.00 42.22 4.69
95 96 1.826054 AGATCCGAGGACAGCTCCG 60.826 63.158 0.00 0.00 42.22 4.63
96 97 1.739049 CAGATCCGAGGACAGCTCC 59.261 63.158 0.00 0.00 36.71 4.70
97 98 0.753479 TCCAGATCCGAGGACAGCTC 60.753 60.000 0.00 0.00 0.00 4.09
98 99 0.754957 CTCCAGATCCGAGGACAGCT 60.755 60.000 0.00 0.00 0.00 4.24
99 100 1.040339 ACTCCAGATCCGAGGACAGC 61.040 60.000 11.13 0.00 0.00 4.40
100 101 1.028905 GACTCCAGATCCGAGGACAG 58.971 60.000 11.13 0.02 0.00 3.51
101 102 0.748367 CGACTCCAGATCCGAGGACA 60.748 60.000 11.13 0.00 0.00 4.02
102 103 1.448922 CCGACTCCAGATCCGAGGAC 61.449 65.000 11.13 5.16 0.00 3.85
103 104 1.152943 CCGACTCCAGATCCGAGGA 60.153 63.158 11.13 5.83 0.00 3.71
104 105 2.196925 CCCGACTCCAGATCCGAGG 61.197 68.421 11.13 1.86 0.00 4.63
105 106 2.851071 GCCCGACTCCAGATCCGAG 61.851 68.421 5.98 5.98 0.00 4.63
106 107 2.833582 GCCCGACTCCAGATCCGA 60.834 66.667 0.00 0.00 0.00 4.55
107 108 3.147595 TGCCCGACTCCAGATCCG 61.148 66.667 0.00 0.00 0.00 4.18
108 109 2.501610 GTGCCCGACTCCAGATCC 59.498 66.667 0.00 0.00 0.00 3.36
109 110 2.501610 GGTGCCCGACTCCAGATC 59.498 66.667 0.00 0.00 31.85 2.75
120 121 2.203294 AAGTGGTTGTCGGTGCCC 60.203 61.111 0.00 0.00 0.00 5.36
121 122 1.227853 AGAAGTGGTTGTCGGTGCC 60.228 57.895 0.00 0.00 0.00 5.01
130 131 0.107410 TGCAACACCGAGAAGTGGTT 60.107 50.000 0.00 0.00 42.28 3.67
155 156 4.415332 CTCCGACCACCACGACGG 62.415 72.222 0.00 0.00 45.61 4.79
156 157 4.415332 CCTCCGACCACCACGACG 62.415 72.222 0.00 0.00 0.00 5.12
187 192 3.161450 ACATATCCACCGGCCGCT 61.161 61.111 22.85 2.01 0.00 5.52
201 206 4.101274 CACAATCCTCATCCTCTCTCACAT 59.899 45.833 0.00 0.00 0.00 3.21
209 214 0.533755 CCCGCACAATCCTCATCCTC 60.534 60.000 0.00 0.00 0.00 3.71
220 225 1.899534 GCAAACCCTACCCGCACAA 60.900 57.895 0.00 0.00 0.00 3.33
237 243 2.185608 GACCGGCTTCTCCTCTGC 59.814 66.667 0.00 0.00 0.00 4.26
239 245 0.618968 ATTGGACCGGCTTCTCCTCT 60.619 55.000 0.00 0.00 0.00 3.69
243 249 4.733850 CTTTAAAATTGGACCGGCTTCTC 58.266 43.478 0.00 0.00 0.00 2.87
249 255 2.823154 TCCAGCTTTAAAATTGGACCGG 59.177 45.455 13.61 0.00 34.90 5.28
251 257 5.125578 CCTACTCCAGCTTTAAAATTGGACC 59.874 44.000 13.61 0.00 34.90 4.46
253 259 4.705023 GCCTACTCCAGCTTTAAAATTGGA 59.295 41.667 15.73 15.73 37.38 3.53
254 260 4.706962 AGCCTACTCCAGCTTTAAAATTGG 59.293 41.667 10.13 10.13 35.22 3.16
266 272 0.741915 GACCGAGAAGCCTACTCCAG 59.258 60.000 0.00 0.00 0.00 3.86
267 273 1.030488 CGACCGAGAAGCCTACTCCA 61.030 60.000 0.00 0.00 0.00 3.86
270 276 1.001145 ACCGACCGAGAAGCCTACT 60.001 57.895 0.00 0.00 0.00 2.57
271 277 1.139095 CACCGACCGAGAAGCCTAC 59.861 63.158 0.00 0.00 0.00 3.18
290 296 2.203549 TACCCGCATTCATGGTGGCA 62.204 55.000 0.00 0.00 34.56 4.92
295 301 1.149174 AGCCTACCCGCATTCATGG 59.851 57.895 0.00 0.00 0.00 3.66
304 310 2.494918 CGGTCTTCAGCCTACCCG 59.505 66.667 0.00 0.00 0.00 5.28
306 312 0.323957 AAACCGGTCTTCAGCCTACC 59.676 55.000 8.04 0.00 0.00 3.18
307 313 1.439679 CAAACCGGTCTTCAGCCTAC 58.560 55.000 8.04 0.00 0.00 3.18
322 328 1.234821 TCACATTCACTCCGGCAAAC 58.765 50.000 0.00 0.00 0.00 2.93
348 354 0.105964 CACAACCTTCTCCGACCACA 59.894 55.000 0.00 0.00 0.00 4.17
350 356 1.752198 CCACAACCTTCTCCGACCA 59.248 57.895 0.00 0.00 0.00 4.02
351 357 1.003718 CCCACAACCTTCTCCGACC 60.004 63.158 0.00 0.00 0.00 4.79
353 359 2.747686 GCCCACAACCTTCTCCGA 59.252 61.111 0.00 0.00 0.00 4.55
356 362 1.303643 CCAGGCCCACAACCTTCTC 60.304 63.158 0.00 0.00 34.42 2.87
357 363 2.845345 CCCAGGCCCACAACCTTCT 61.845 63.158 0.00 0.00 34.42 2.85
359 365 3.914713 CCCCAGGCCCACAACCTT 61.915 66.667 0.00 0.00 34.42 3.50
371 387 2.742372 CGAACTCCAACGCCCCAG 60.742 66.667 0.00 0.00 0.00 4.45
374 390 3.110178 CGTCGAACTCCAACGCCC 61.110 66.667 0.00 0.00 0.00 6.13
375 391 2.355481 ACGTCGAACTCCAACGCC 60.355 61.111 0.00 0.00 39.93 5.68
378 394 1.273455 CCGTCACGTCGAACTCCAAC 61.273 60.000 0.00 0.00 0.00 3.77
380 396 2.640989 CCGTCACGTCGAACTCCA 59.359 61.111 0.00 0.00 0.00 3.86
382 398 2.804090 GCCCGTCACGTCGAACTC 60.804 66.667 0.00 0.00 0.00 3.01
391 407 0.580104 GTGCAATATACGCCCGTCAC 59.420 55.000 0.00 0.00 0.00 3.67
397 413 4.074647 GGGGGTGCAATATACGCC 57.925 61.111 0.00 0.00 46.90 5.68
413 429 4.839706 CAATTGGGGCGGGGAGGG 62.840 72.222 0.00 0.00 0.00 4.30
414 430 3.600410 AACAATTGGGGCGGGGAGG 62.600 63.158 10.83 0.00 0.00 4.30
415 431 2.037208 AACAATTGGGGCGGGGAG 59.963 61.111 10.83 0.00 0.00 4.30
416 432 2.283532 CAACAATTGGGGCGGGGA 60.284 61.111 10.83 0.00 0.00 4.81
418 434 1.876497 CTGACAACAATTGGGGCGGG 61.876 60.000 10.83 0.00 34.12 6.13
421 437 2.908688 AAACTGACAACAATTGGGGC 57.091 45.000 10.83 4.26 34.12 5.80
422 438 3.305064 CCGTAAACTGACAACAATTGGGG 60.305 47.826 10.83 3.71 34.12 4.96
423 439 3.305064 CCCGTAAACTGACAACAATTGGG 60.305 47.826 10.83 4.09 34.12 4.12
424 440 3.855524 GCCCGTAAACTGACAACAATTGG 60.856 47.826 10.83 0.00 34.12 3.16
425 441 3.305110 GCCCGTAAACTGACAACAATTG 58.695 45.455 3.24 3.24 0.00 2.32
426 442 2.031508 CGCCCGTAAACTGACAACAATT 60.032 45.455 0.00 0.00 0.00 2.32
427 443 1.533731 CGCCCGTAAACTGACAACAAT 59.466 47.619 0.00 0.00 0.00 2.71
431 447 0.600782 GACCGCCCGTAAACTGACAA 60.601 55.000 0.00 0.00 0.00 3.18
434 450 1.255882 TTAGACCGCCCGTAAACTGA 58.744 50.000 0.00 0.00 0.00 3.41
446 462 4.542735 GGTCACCAAATTTGTTTAGACCG 58.457 43.478 21.90 8.33 35.49 4.79
448 464 3.978855 GCGGTCACCAAATTTGTTTAGAC 59.021 43.478 16.73 15.94 0.00 2.59
450 466 3.971150 TGCGGTCACCAAATTTGTTTAG 58.029 40.909 16.73 4.22 0.00 1.85
452 468 2.167487 ACTGCGGTCACCAAATTTGTTT 59.833 40.909 16.73 0.71 0.00 2.83
463 479 2.279918 ACGTCCAACTGCGGTCAC 60.280 61.111 0.00 0.00 0.00 3.67
465 481 1.155424 TTTGACGTCCAACTGCGGTC 61.155 55.000 14.12 0.00 33.85 4.79
469 485 2.788786 CACAATTTTGACGTCCAACTGC 59.211 45.455 14.12 0.00 33.85 4.40
472 488 2.788786 CAGCACAATTTTGACGTCCAAC 59.211 45.455 14.12 0.00 33.85 3.77
474 490 2.032799 GTCAGCACAATTTTGACGTCCA 59.967 45.455 14.12 0.00 32.81 4.02
475 491 2.604614 GGTCAGCACAATTTTGACGTCC 60.605 50.000 14.12 0.00 41.57 4.79
476 492 2.650608 GGTCAGCACAATTTTGACGTC 58.349 47.619 9.11 9.11 41.57 4.34
477 493 1.002900 CGGTCAGCACAATTTTGACGT 60.003 47.619 0.00 0.00 41.57 4.34
478 494 1.002900 ACGGTCAGCACAATTTTGACG 60.003 47.619 0.00 0.00 41.57 4.35
479 495 2.604614 GGACGGTCAGCACAATTTTGAC 60.605 50.000 10.76 0.00 40.29 3.18
490 506 1.503818 TTTCAAAGCGGACGGTCAGC 61.504 55.000 22.98 22.98 37.86 4.26
508 525 6.239176 GGATCTCTCCAAATCGACAGTAGATT 60.239 42.308 3.18 3.18 41.64 2.40
511 528 4.555708 CGGATCTCTCCAAATCGACAGTAG 60.556 50.000 0.00 0.00 42.19 2.57
515 532 1.202417 GCGGATCTCTCCAAATCGACA 60.202 52.381 0.00 0.00 42.19 4.35
534 551 2.681344 CCAATTAGGGTAACTCCAACGC 59.319 50.000 0.00 0.00 38.11 4.84
535 552 2.681344 GCCAATTAGGGTAACTCCAACG 59.319 50.000 0.00 0.00 38.09 4.10
596 1472 2.704725 TCTCGGTCAAAATTGCAAGC 57.295 45.000 4.94 0.00 0.00 4.01
927 1806 2.482864 CAACCAAATCCTGCACAAACC 58.517 47.619 0.00 0.00 0.00 3.27
996 1875 2.814269 TGTACTCGATTCTGCATGAGC 58.186 47.619 0.00 0.00 42.57 4.26
1360 2240 3.248266 AGTAATGCTAACGGTTGTCGAC 58.752 45.455 9.11 9.11 42.43 4.20
1688 2568 4.039245 CGCTTCTGTAATGAATAGGGGAGA 59.961 45.833 0.00 0.00 0.00 3.71
1693 2573 3.248602 GGCACGCTTCTGTAATGAATAGG 59.751 47.826 0.00 0.00 0.00 2.57
1812 2692 2.175499 TGAAATGAATAGGGGAGGCCAG 59.825 50.000 5.01 0.00 0.00 4.85
1888 2773 6.827251 AGGCTGCCATATATGATACTTTCATG 59.173 38.462 22.65 0.00 44.90 3.07
1985 2870 8.576442 CCTGAATGTGTACTGGAAAGTAAATTT 58.424 33.333 0.00 0.00 0.00 1.82
2031 2916 5.533482 AGTTGCTAGTTGCGGATCTAATAG 58.467 41.667 0.00 0.00 46.63 1.73
2178 3063 6.315642 TGCTGACAAAATTCAAAAGATTTGCA 59.684 30.769 0.00 0.00 36.48 4.08
2319 3204 8.593945 AAAATATGACACCCATAAATCACAGT 57.406 30.769 0.00 0.00 40.79 3.55
2320 3205 9.950680 GTAAAATATGACACCCATAAATCACAG 57.049 33.333 0.00 0.00 40.79 3.66
2381 3266 7.383572 CAGAAGTTAAATATGAGATACTGCGCT 59.616 37.037 9.73 0.00 0.00 5.92
2455 3342 7.281999 TGCGTGGAAATGATAACATCAGATTTA 59.718 33.333 0.00 0.00 43.53 1.40
2580 3470 1.047801 GTTTCAACCCCAGGCATTGT 58.952 50.000 1.82 0.00 0.00 2.71
2887 3781 3.767673 TGGGACTGGTACTGTGATTCTAC 59.232 47.826 0.00 0.00 41.64 2.59
3080 3975 7.484324 CGTTCCAGTAACTCTAAAACTACTAGC 59.516 40.741 0.00 0.00 35.81 3.42
3273 4176 7.338703 GGTATCAGATACGGATATGACACCTTA 59.661 40.741 22.74 2.23 44.26 2.69
3374 4438 0.948623 ACTGCAGCGCGAATAACACA 60.949 50.000 15.27 0.00 0.00 3.72
3419 4483 7.255942 CCATCCTCAAGGTTAACAAAAAGATGT 60.256 37.037 8.10 0.00 36.34 3.06
3776 4869 7.405292 TGGTAATCATGACTCCTTTCTTGATT 58.595 34.615 14.83 14.83 45.40 2.57
3778 4871 6.373005 TGGTAATCATGACTCCTTTCTTGA 57.627 37.500 0.00 0.00 34.99 3.02
3779 4872 5.065731 GCTGGTAATCATGACTCCTTTCTTG 59.934 44.000 0.00 0.00 0.00 3.02
3820 4916 9.996554 CTGTATTAACCATAGACCATATTGTGA 57.003 33.333 0.00 0.00 0.00 3.58
3833 4929 5.588246 CACATGTGCCACTGTATTAACCATA 59.412 40.000 13.94 0.00 0.00 2.74
3928 5024 8.449251 TCCGTTTTACAAAAACATACTAGGTT 57.551 30.769 13.83 0.00 0.00 3.50
4020 5116 7.517614 TTGCATAACACAAGTCCTTCAATAA 57.482 32.000 0.00 0.00 0.00 1.40
4049 5146 5.967088 GCCGGTAGTAAAATAAAAATGGACG 59.033 40.000 1.90 0.00 0.00 4.79
4091 5188 7.068839 ACACCTACCACAAAATTTGACATACAA 59.931 33.333 13.19 0.00 36.65 2.41
4116 5213 4.239304 TGCATTTTGCTTGATGATGTCAC 58.761 39.130 0.75 0.00 45.31 3.67
4117 5214 4.522722 TGCATTTTGCTTGATGATGTCA 57.477 36.364 0.75 0.00 45.31 3.58
4118 5215 6.270815 AGTATGCATTTTGCTTGATGATGTC 58.729 36.000 3.54 0.00 45.31 3.06
4119 5216 6.216801 AGTATGCATTTTGCTTGATGATGT 57.783 33.333 3.54 0.00 45.31 3.06
4120 5217 8.812147 ATTAGTATGCATTTTGCTTGATGATG 57.188 30.769 3.54 0.00 45.31 3.07
4156 5253 2.279741 TGTCTATGGAAAGCGCATCAC 58.720 47.619 11.47 2.02 0.00 3.06
4158 5255 2.826428 TCTGTCTATGGAAAGCGCATC 58.174 47.619 11.47 7.52 0.00 3.91
4162 5259 3.589988 ACAGTTCTGTCTATGGAAAGCG 58.410 45.455 0.00 0.00 0.00 4.68
4220 5317 6.017192 CGAGTACATGAATGAATAATGGGCAA 60.017 38.462 0.00 0.00 0.00 4.52
4238 5335 5.854010 AGAAATAAGATCAGGCGAGTACA 57.146 39.130 0.00 0.00 0.00 2.90
4290 5387 6.071952 CCAGTACCTTGCATGATTTAGTTTGT 60.072 38.462 0.00 0.00 0.00 2.83
4551 5653 3.635373 CGGATAGCCTGTAGTAGTTTCCA 59.365 47.826 0.00 0.00 0.00 3.53
4561 5663 3.645434 TCCTTTTACCGGATAGCCTGTA 58.355 45.455 9.46 0.00 33.34 2.74
4562 5664 2.474112 TCCTTTTACCGGATAGCCTGT 58.526 47.619 9.46 0.00 35.62 4.00
4564 5666 4.267536 GTTTTCCTTTTACCGGATAGCCT 58.732 43.478 9.46 0.00 0.00 4.58
4565 5667 3.379372 GGTTTTCCTTTTACCGGATAGCC 59.621 47.826 9.46 0.00 36.94 3.93
4566 5668 4.627611 GGTTTTCCTTTTACCGGATAGC 57.372 45.455 9.46 0.00 36.94 2.97
4586 5695 5.064452 TGCAAACAAAATAAAGTGTTGCAGG 59.936 36.000 4.19 0.00 37.99 4.85
4616 5725 3.756117 CTGGAGGGAAGCTGTAGTTTTT 58.244 45.455 0.00 0.00 0.00 1.94
4617 5726 2.553247 GCTGGAGGGAAGCTGTAGTTTT 60.553 50.000 0.00 0.00 37.69 2.43
4618 5727 1.003696 GCTGGAGGGAAGCTGTAGTTT 59.996 52.381 0.00 0.00 37.69 2.66
4619 5728 0.615850 GCTGGAGGGAAGCTGTAGTT 59.384 55.000 0.00 0.00 37.69 2.24
4620 5729 1.608717 CGCTGGAGGGAAGCTGTAGT 61.609 60.000 0.00 0.00 38.57 2.73
4621 5730 1.142748 CGCTGGAGGGAAGCTGTAG 59.857 63.158 0.00 0.00 38.57 2.74
4622 5731 1.304962 TCGCTGGAGGGAAGCTGTA 60.305 57.895 0.00 0.00 38.57 2.74
4623 5732 2.604686 TCGCTGGAGGGAAGCTGT 60.605 61.111 0.00 0.00 38.57 4.40
4624 5733 2.125350 GTCGCTGGAGGGAAGCTG 60.125 66.667 0.00 0.00 38.57 4.24
4625 5734 3.764466 CGTCGCTGGAGGGAAGCT 61.764 66.667 0.00 0.00 38.57 3.74
4626 5735 3.708220 CTCGTCGCTGGAGGGAAGC 62.708 68.421 2.40 0.00 38.76 3.86
4631 5740 3.119709 GAGCTCTCGTCGCTGGAGG 62.120 68.421 6.43 0.00 37.96 4.30
4638 5747 0.457851 ATGGGAAAGAGCTCTCGTCG 59.542 55.000 18.55 0.00 34.09 5.12
4712 5837 4.202567 ACTCCTCACCAGCCAGAATTAAAA 60.203 41.667 0.00 0.00 0.00 1.52
4718 5843 0.687354 GAACTCCTCACCAGCCAGAA 59.313 55.000 0.00 0.00 0.00 3.02
4719 5844 0.178921 AGAACTCCTCACCAGCCAGA 60.179 55.000 0.00 0.00 0.00 3.86
4720 5845 0.036577 CAGAACTCCTCACCAGCCAG 60.037 60.000 0.00 0.00 0.00 4.85
4721 5846 0.764369 ACAGAACTCCTCACCAGCCA 60.764 55.000 0.00 0.00 0.00 4.75
4722 5847 0.321122 CACAGAACTCCTCACCAGCC 60.321 60.000 0.00 0.00 0.00 4.85
4723 5848 0.681733 TCACAGAACTCCTCACCAGC 59.318 55.000 0.00 0.00 0.00 4.85
4724 5849 2.366916 AGTTCACAGAACTCCTCACCAG 59.633 50.000 6.58 0.00 0.00 4.00
4725 5850 2.398588 AGTTCACAGAACTCCTCACCA 58.601 47.619 6.58 0.00 0.00 4.17
4726 5851 3.477210 AAGTTCACAGAACTCCTCACC 57.523 47.619 12.31 0.00 0.00 4.02
4727 5852 4.192317 ACAAAGTTCACAGAACTCCTCAC 58.808 43.478 12.31 0.00 0.00 3.51
4728 5853 4.487714 ACAAAGTTCACAGAACTCCTCA 57.512 40.909 12.31 0.00 0.00 3.86
4729 5854 4.876107 TGAACAAAGTTCACAGAACTCCTC 59.124 41.667 12.31 7.77 0.00 3.71
4730 5855 4.843728 TGAACAAAGTTCACAGAACTCCT 58.156 39.130 12.31 1.58 0.00 3.69
4731 5856 5.560966 TTGAACAAAGTTCACAGAACTCC 57.439 39.130 11.73 2.42 0.00 3.85
4750 5875 5.794687 ATGTCGCAGAATTTATCGTTTGA 57.205 34.783 0.00 0.00 39.69 2.69
4760 5885 5.389859 TCAAATTCCAATGTCGCAGAATT 57.610 34.783 0.00 0.00 39.69 2.17
4846 6033 0.253044 GCCTTGGTCTGGTGCTGATA 59.747 55.000 0.00 0.00 0.00 2.15
4896 6084 3.786635 CCTGTGGTTCTTAGGAATCTCG 58.213 50.000 0.00 0.00 33.95 4.04
4933 6121 6.471976 TGAATCTTGAGAGTTTGATCGTTG 57.528 37.500 0.00 0.00 0.00 4.10
4992 6182 2.215942 AGGTTTAGTTGCCATCACCC 57.784 50.000 0.00 0.00 0.00 4.61
5042 6232 5.203528 TGGAGATGATACAGTGAGATGTCA 58.796 41.667 0.00 0.00 34.56 3.58
5074 6275 1.758440 AACAGTCAGCGCCAGGAAGA 61.758 55.000 2.29 0.00 0.00 2.87
5086 6287 7.608761 AGTTAGGTTTAAACAGAACAACAGTCA 59.391 33.333 24.79 0.00 31.33 3.41
5124 6325 1.620323 GCCCTTTTCCTTGCAACTCAT 59.380 47.619 0.00 0.00 0.00 2.90
5138 6346 0.106015 ACAACAGCTGAAGGCCCTTT 60.106 50.000 23.35 0.00 43.05 3.11


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

AutoCloner maintained by Alex Coulton.