Multiple sequence alignment - TraesCS1B01G295600

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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 TraesCS1B01G295600 chr1B 100.000 4815 0 0 1 4815 513543381 513538567 0.000000e+00 8892.0
1 TraesCS1B01G295600 chr1B 85.714 77 9 2 4568 4643 33857205 33857280 3.990000e-11 80.5
2 TraesCS1B01G295600 chr1B 85.714 77 9 2 4568 4643 33946579 33946654 3.990000e-11 80.5
3 TraesCS1B01G295600 chr1D 92.310 3602 159 41 1100 4648 383317002 383313466 0.000000e+00 5009.0
4 TraesCS1B01G295600 chr1D 89.041 584 32 18 547 1120 383318019 383317458 0.000000e+00 695.0
5 TraesCS1B01G295600 chr1D 78.650 548 81 21 22 557 383318842 383318319 9.990000e-87 331.0
6 TraesCS1B01G295600 chr1D 87.013 77 8 2 4568 4643 20062075 20062000 8.590000e-13 86.1
7 TraesCS1B01G295600 chr1A 94.441 1835 58 14 2077 3894 483028413 483026606 0.000000e+00 2784.0
8 TraesCS1B01G295600 chr1A 88.043 1564 112 39 547 2079 483030204 483028685 0.000000e+00 1783.0
9 TraesCS1B01G295600 chr1A 88.020 601 28 15 4237 4812 483025650 483025069 0.000000e+00 671.0
10 TraesCS1B01G295600 chr1A 87.013 77 8 2 4568 4643 22282785 22282860 8.590000e-13 86.1
11 TraesCS1B01G295600 chr3B 81.496 254 34 12 3119 3362 612101897 612102147 3.800000e-46 196.0
12 TraesCS1B01G295600 chr3B 78.986 276 32 16 2749 3004 612101076 612101345 1.070000e-36 165.0
13 TraesCS1B01G295600 chr3B 90.426 94 7 1 1293 1386 612098431 612098522 6.540000e-24 122.0
14 TraesCS1B01G295600 chr3D 80.859 256 33 14 3119 3362 461311185 461311436 2.290000e-43 187.0
15 TraesCS1B01G295600 chr3D 78.671 286 35 15 2739 3004 461310302 461310581 2.980000e-37 167.0
16 TraesCS1B01G295600 chr3D 90.217 92 6 2 1296 1386 461307923 461308012 3.040000e-22 117.0
17 TraesCS1B01G295600 chr3A 80.297 269 36 14 2749 3004 603810664 603810928 2.290000e-43 187.0
18 TraesCS1B01G295600 chr3A 80.632 253 38 10 3119 3362 603811283 603811533 8.230000e-43 185.0
19 TraesCS1B01G295600 chr3A 91.011 89 6 1 1298 1386 603807978 603808064 8.470000e-23 119.0
20 TraesCS1B01G295600 chr3A 91.860 86 5 1 1312 1397 698010707 698010790 8.470000e-23 119.0
21 TraesCS1B01G295600 chr5D 90.323 93 5 3 1305 1397 524586647 524586735 8.470000e-23 119.0
22 TraesCS1B01G295600 chr5B 90.323 93 5 2 1305 1397 659169297 659169385 8.470000e-23 119.0
23 TraesCS1B01G295600 chr5A 90.323 93 5 2 1305 1397 650834309 650834397 8.470000e-23 119.0


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 TraesCS1B01G295600 chr1B 513538567 513543381 4814 True 8892.000000 8892 100.000 1 4815 1 chr1B.!!$R1 4814
1 TraesCS1B01G295600 chr1D 383313466 383318842 5376 True 2011.666667 5009 86.667 22 4648 3 chr1D.!!$R2 4626
2 TraesCS1B01G295600 chr1A 483025069 483030204 5135 True 1746.000000 2784 90.168 547 4812 3 chr1A.!!$R1 4265

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
343 350 0.034767 TGGAATGCAGAGCTTCCAGG 60.035 55.000 14.20 0.00 44.56 4.45 F
713 1037 0.035152 ACACATGATCGCCACACCAT 60.035 50.000 0.00 0.00 0.00 3.55 F
805 1129 0.108898 CCACAGGTCAGCTTCTCGAG 60.109 60.000 5.93 5.93 0.00 4.04 F
1279 2087 0.350904 TAGGAGGAGGAGGAGGAGGA 59.649 60.000 0.00 0.00 0.00 3.71 F
1959 2774 0.250295 CAAGGCCGGACAGAGAACAA 60.250 55.000 11.69 0.00 0.00 2.83 F
1961 2776 0.832135 AGGCCGGACAGAGAACAAGA 60.832 55.000 11.69 0.00 0.00 3.02 F
3027 4123 1.138464 GTACACGAATCCTCTTCCCCC 59.862 57.143 0.00 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1961 0.540597 GGGAGGGATAATGGCTTGCC 60.541 60.000 4.43 4.43 0.00 4.52 R
1707 2517 0.611200 TGGCTCGAAATTCTCCCGAA 59.389 50.000 0.00 0.00 31.59 4.30 R
1725 2535 0.761802 GCAACCTATCCCCTCTCCTG 59.238 60.000 0.00 0.00 0.00 3.86 R
3009 4105 0.252742 AGGGGGAAGAGGATTCGTGT 60.253 55.000 0.00 0.00 0.00 4.49 R
3402 4507 2.774799 GGGCACCGAACATGATGGC 61.775 63.158 0.00 1.82 40.86 4.40 R
3802 4910 5.210715 GCATATTGATTGCTCGGAAAGAAG 58.789 41.667 0.00 0.00 37.14 2.85 R
4214 5894 0.255890 AGGGGTGAATCCGTGAATGG 59.744 55.000 0.00 0.00 37.00 3.16 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
61 62 2.294512 GCTTTTGCTTGTAACTGGCTCT 59.705 45.455 0.00 0.00 43.35 4.09
88 90 3.303049 CCCTCCTACGGTATAGTGGTTT 58.697 50.000 0.00 0.00 0.00 3.27
101 103 0.385598 GTGGTTTTCGAAAGCTCGCC 60.386 55.000 21.70 14.67 45.04 5.54
104 106 2.248135 TTTTCGAAAGCTCGCCGCA 61.248 52.632 10.98 0.00 45.04 5.69
105 107 1.573829 TTTTCGAAAGCTCGCCGCAT 61.574 50.000 10.98 0.00 45.04 4.73
106 108 1.966493 TTTCGAAAGCTCGCCGCATC 61.966 55.000 6.47 0.00 45.04 3.91
108 110 2.864931 CGAAAGCTCGCCGCATCTC 61.865 63.158 0.00 0.00 42.61 2.75
109 111 1.520342 GAAAGCTCGCCGCATCTCT 60.520 57.895 0.00 0.00 42.61 3.10
110 112 1.486644 GAAAGCTCGCCGCATCTCTC 61.487 60.000 0.00 0.00 42.61 3.20
131 133 0.951558 GGTCATGGTTTTCGCACACT 59.048 50.000 0.00 0.00 0.00 3.55
143 145 3.063670 TCGCACACTCAACATTGTTTG 57.936 42.857 0.00 0.00 0.00 2.93
145 147 2.472816 GCACACTCAACATTGTTTGGG 58.527 47.619 0.00 0.00 32.72 4.12
152 154 5.241506 CACTCAACATTGTTTGGGTACATCT 59.758 40.000 0.00 0.00 38.17 2.90
153 155 5.833131 ACTCAACATTGTTTGGGTACATCTT 59.167 36.000 0.00 0.00 38.48 2.40
179 181 7.489574 TTTCCTTTTTGCCATCACAATAAAC 57.510 32.000 0.00 0.00 0.00 2.01
182 184 5.107530 CCTTTTTGCCATCACAATAAACGTG 60.108 40.000 0.00 0.00 35.63 4.49
183 185 2.627863 TGCCATCACAATAAACGTGC 57.372 45.000 0.00 0.00 34.27 5.34
185 187 2.556189 TGCCATCACAATAAACGTGCTT 59.444 40.909 0.00 0.00 34.27 3.91
187 189 3.364621 GCCATCACAATAAACGTGCTTTG 59.635 43.478 0.00 0.00 34.27 2.77
188 190 3.364621 CCATCACAATAAACGTGCTTTGC 59.635 43.478 0.00 0.00 34.27 3.68
189 191 3.699779 TCACAATAAACGTGCTTTGCA 57.300 38.095 0.00 0.00 35.60 4.08
191 193 4.424626 TCACAATAAACGTGCTTTGCAAA 58.575 34.783 12.14 12.14 41.47 3.68
193 195 4.267452 CACAATAAACGTGCTTTGCAAAGT 59.733 37.500 33.47 18.99 41.47 2.66
194 196 4.267452 ACAATAAACGTGCTTTGCAAAGTG 59.733 37.500 33.47 25.99 41.47 3.16
196 198 0.179113 AACGTGCTTTGCAAAGTGGG 60.179 50.000 33.47 24.96 41.47 4.61
212 218 2.168936 AGTGGGTCGACACAAGTTACAA 59.831 45.455 24.60 0.00 43.72 2.41
225 231 9.807386 GACACAAGTTACAAATCATACTTACAC 57.193 33.333 0.00 0.00 30.19 2.90
231 237 7.874016 AGTTACAAATCATACTTACACACCGAA 59.126 33.333 0.00 0.00 0.00 4.30
232 238 8.662141 GTTACAAATCATACTTACACACCGAAT 58.338 33.333 0.00 0.00 0.00 3.34
233 239 7.072177 ACAAATCATACTTACACACCGAATG 57.928 36.000 0.00 0.00 0.00 2.67
234 240 6.876789 ACAAATCATACTTACACACCGAATGA 59.123 34.615 0.00 0.00 0.00 2.57
235 241 7.064609 ACAAATCATACTTACACACCGAATGAG 59.935 37.037 0.00 0.00 0.00 2.90
236 242 5.654603 TCATACTTACACACCGAATGAGT 57.345 39.130 0.00 0.00 36.04 3.41
237 243 6.762702 TCATACTTACACACCGAATGAGTA 57.237 37.500 0.00 0.00 33.72 2.59
238 244 6.558009 TCATACTTACACACCGAATGAGTAC 58.442 40.000 0.00 0.00 34.53 2.73
239 245 4.859304 ACTTACACACCGAATGAGTACA 57.141 40.909 0.00 0.00 34.53 2.90
241 247 2.450609 ACACACCGAATGAGTACACC 57.549 50.000 0.00 0.00 29.28 4.16
242 248 1.001633 ACACACCGAATGAGTACACCC 59.998 52.381 0.00 0.00 29.28 4.61
243 249 1.275291 CACACCGAATGAGTACACCCT 59.725 52.381 0.00 0.00 0.00 4.34
244 250 2.494471 CACACCGAATGAGTACACCCTA 59.506 50.000 0.00 0.00 0.00 3.53
245 251 3.056393 CACACCGAATGAGTACACCCTAA 60.056 47.826 0.00 0.00 0.00 2.69
246 252 3.194968 ACACCGAATGAGTACACCCTAAG 59.805 47.826 0.00 0.00 0.00 2.18
248 254 2.483188 CCGAATGAGTACACCCTAAGGC 60.483 54.545 0.00 0.00 36.11 4.35
249 255 2.483188 CGAATGAGTACACCCTAAGGCC 60.483 54.545 0.00 0.00 36.11 5.19
250 256 2.570386 ATGAGTACACCCTAAGGCCT 57.430 50.000 0.00 0.00 36.11 5.19
251 257 2.337359 TGAGTACACCCTAAGGCCTT 57.663 50.000 24.18 24.18 36.11 4.35
252 258 1.906574 TGAGTACACCCTAAGGCCTTG 59.093 52.381 28.77 14.28 36.11 3.61
253 259 1.907255 GAGTACACCCTAAGGCCTTGT 59.093 52.381 28.77 19.60 36.11 3.16
264 270 1.072266 AGGCCTTGTACAATGGTGGA 58.928 50.000 9.13 0.00 0.00 4.02
268 274 2.726821 CCTTGTACAATGGTGGATGCT 58.273 47.619 9.13 0.00 0.00 3.79
301 307 5.756347 TGTACTTAAAGAAAAAGAGCAGCGA 59.244 36.000 0.00 0.00 0.00 4.93
305 311 1.527034 AGAAAAAGAGCAGCGATGCA 58.473 45.000 29.24 0.00 37.25 3.96
326 333 4.274069 CATCGCAAATAATGTCGTCTTGG 58.726 43.478 0.00 0.00 32.69 3.61
328 335 3.997681 TCGCAAATAATGTCGTCTTGGAA 59.002 39.130 0.00 0.00 32.69 3.53
330 337 4.730042 CGCAAATAATGTCGTCTTGGAATG 59.270 41.667 0.00 0.00 0.00 2.67
331 338 4.500477 GCAAATAATGTCGTCTTGGAATGC 59.500 41.667 0.00 0.00 0.00 3.56
332 339 5.639757 CAAATAATGTCGTCTTGGAATGCA 58.360 37.500 0.00 0.00 0.00 3.96
336 343 0.723981 GTCGTCTTGGAATGCAGAGC 59.276 55.000 0.00 0.00 0.00 4.09
337 344 0.610174 TCGTCTTGGAATGCAGAGCT 59.390 50.000 0.00 0.00 0.00 4.09
338 345 1.002430 TCGTCTTGGAATGCAGAGCTT 59.998 47.619 0.00 0.00 0.00 3.74
339 346 1.396301 CGTCTTGGAATGCAGAGCTTC 59.604 52.381 0.00 0.00 0.00 3.86
340 347 1.742268 GTCTTGGAATGCAGAGCTTCC 59.258 52.381 9.47 9.47 41.13 3.46
342 349 3.564262 TGGAATGCAGAGCTTCCAG 57.436 52.632 14.20 0.00 44.56 3.86
343 350 0.034767 TGGAATGCAGAGCTTCCAGG 60.035 55.000 14.20 0.00 44.56 4.45
344 351 1.382692 GGAATGCAGAGCTTCCAGGC 61.383 60.000 11.20 0.00 40.57 4.85
345 352 0.679002 GAATGCAGAGCTTCCAGGCA 60.679 55.000 0.00 0.00 39.03 4.75
346 353 0.251474 AATGCAGAGCTTCCAGGCAA 60.251 50.000 0.00 0.00 38.08 4.52
347 354 0.251474 ATGCAGAGCTTCCAGGCAAA 60.251 50.000 0.00 0.00 38.08 3.68
348 355 0.467844 TGCAGAGCTTCCAGGCAAAA 60.468 50.000 0.00 0.00 34.17 2.44
365 372 3.118542 CAAAAGTGCTTCAGTTGCTTCC 58.881 45.455 0.00 0.00 0.00 3.46
366 373 0.947244 AAGTGCTTCAGTTGCTTCCG 59.053 50.000 0.00 0.00 0.00 4.30
371 378 1.301677 CTTCAGTTGCTTCCGCCTCC 61.302 60.000 0.00 0.00 34.43 4.30
375 382 2.041115 GTTGCTTCCGCCTCCCTTC 61.041 63.158 0.00 0.00 34.43 3.46
376 383 2.224159 TTGCTTCCGCCTCCCTTCT 61.224 57.895 0.00 0.00 34.43 2.85
384 391 1.817099 GCCTCCCTTCTGCATGACG 60.817 63.158 0.00 0.00 0.00 4.35
386 393 0.036010 CCTCCCTTCTGCATGACGTT 60.036 55.000 0.00 0.00 0.00 3.99
387 394 1.081892 CTCCCTTCTGCATGACGTTG 58.918 55.000 0.00 0.00 0.00 4.10
390 397 1.338105 CCCTTCTGCATGACGTTGAGA 60.338 52.381 0.00 0.00 0.00 3.27
398 405 2.257894 CATGACGTTGAGAGAGCACTC 58.742 52.381 2.51 2.51 42.90 3.51
399 406 0.598562 TGACGTTGAGAGAGCACTCC 59.401 55.000 7.60 0.47 43.53 3.85
400 407 0.885196 GACGTTGAGAGAGCACTCCT 59.115 55.000 7.60 0.00 43.53 3.69
401 408 1.271102 GACGTTGAGAGAGCACTCCTT 59.729 52.381 7.60 0.00 43.53 3.36
416 423 0.749818 TCCTTTTGTGCAAGCACCGA 60.750 50.000 21.19 8.30 45.63 4.69
419 426 1.601903 CTTTTGTGCAAGCACCGACTA 59.398 47.619 21.19 0.43 45.63 2.59
421 428 1.227999 TTGTGCAAGCACCGACTAGC 61.228 55.000 21.19 0.00 45.63 3.42
425 432 1.005037 CAAGCACCGACTAGCACCA 60.005 57.895 0.00 0.00 0.00 4.17
433 440 1.406069 CCGACTAGCACCAGAAGCAAT 60.406 52.381 0.00 0.00 0.00 3.56
436 443 1.630369 ACTAGCACCAGAAGCAATCCA 59.370 47.619 0.00 0.00 0.00 3.41
437 444 2.040278 ACTAGCACCAGAAGCAATCCAA 59.960 45.455 0.00 0.00 0.00 3.53
439 446 3.370840 AGCACCAGAAGCAATCCAATA 57.629 42.857 0.00 0.00 0.00 1.90
440 447 3.700538 AGCACCAGAAGCAATCCAATAA 58.299 40.909 0.00 0.00 0.00 1.40
448 460 4.103153 AGAAGCAATCCAATAATCTCGGGA 59.897 41.667 0.00 0.00 0.00 5.14
449 461 4.013267 AGCAATCCAATAATCTCGGGAG 57.987 45.455 0.00 0.00 31.96 4.30
468 480 2.964209 AGAAGACCTCTCAAGTGTCCA 58.036 47.619 0.00 0.00 0.00 4.02
471 483 2.614259 AGACCTCTCAAGTGTCCATGT 58.386 47.619 0.00 0.00 0.00 3.21
476 488 2.926200 CTCTCAAGTGTCCATGTAAGCG 59.074 50.000 0.00 0.00 0.00 4.68
477 489 2.299013 TCTCAAGTGTCCATGTAAGCGT 59.701 45.455 0.00 0.00 0.00 5.07
479 491 2.299013 TCAAGTGTCCATGTAAGCGTCT 59.701 45.455 0.00 0.00 0.00 4.18
486 498 0.095245 CATGTAAGCGTCTGCCGTTG 59.905 55.000 0.00 0.00 44.31 4.10
492 504 2.380410 GCGTCTGCCGTTGTACAGG 61.380 63.158 0.00 0.00 39.32 4.00
494 506 1.375523 GTCTGCCGTTGTACAGGGG 60.376 63.158 14.69 12.10 34.57 4.79
514 526 2.633488 GCTAAGCGATCCAAGTTCCTT 58.367 47.619 0.00 0.00 0.00 3.36
518 530 1.347707 AGCGATCCAAGTTCCTTGTGA 59.652 47.619 3.53 1.59 39.58 3.58
527 539 6.630071 TCCAAGTTCCTTGTGAAAAGAAAAG 58.370 36.000 3.53 0.00 39.58 2.27
530 542 5.654497 AGTTCCTTGTGAAAAGAAAAGCAG 58.346 37.500 0.00 0.00 33.94 4.24
533 545 5.650543 TCCTTGTGAAAAGAAAAGCAGAAC 58.349 37.500 0.00 0.00 0.00 3.01
570 892 4.761739 CCTTGTGCTTGATTTGAAGGTAGA 59.238 41.667 0.00 0.00 0.00 2.59
579 901 8.084684 GCTTGATTTGAAGGTAGATTTCTTGTT 58.915 33.333 0.00 0.00 0.00 2.83
593 915 5.694674 TTTCTTGTTGAAATTTCACGCAC 57.305 34.783 20.35 15.91 39.50 5.34
594 916 4.630894 TCTTGTTGAAATTTCACGCACT 57.369 36.364 20.35 0.00 36.83 4.40
602 924 2.995466 ATTTCACGCACTTCATGGTG 57.005 45.000 0.00 0.00 39.91 4.17
608 930 1.093972 CGCACTTCATGGTGGCATTA 58.906 50.000 4.55 0.00 37.65 1.90
609 931 1.064505 CGCACTTCATGGTGGCATTAG 59.935 52.381 4.55 0.00 37.65 1.73
610 932 1.202336 GCACTTCATGGTGGCATTAGC 60.202 52.381 4.55 0.00 37.65 3.09
612 934 2.492881 CACTTCATGGTGGCATTAGCAA 59.507 45.455 0.00 0.00 44.61 3.91
613 935 2.756760 ACTTCATGGTGGCATTAGCAAG 59.243 45.455 0.00 0.00 44.61 4.01
614 936 2.512692 TCATGGTGGCATTAGCAAGT 57.487 45.000 0.00 0.00 44.61 3.16
615 937 2.368439 TCATGGTGGCATTAGCAAGTC 58.632 47.619 0.00 0.00 44.61 3.01
616 938 2.093890 CATGGTGGCATTAGCAAGTCA 58.906 47.619 0.00 0.00 44.61 3.41
619 941 2.961741 TGGTGGCATTAGCAAGTCAAAA 59.038 40.909 0.00 0.00 44.61 2.44
623 945 5.229423 GTGGCATTAGCAAGTCAAAATTGA 58.771 37.500 0.00 0.00 44.61 2.57
635 957 7.201600 GCAAGTCAAAATTGAAAAGTTAGGCAA 60.202 33.333 0.00 0.00 39.21 4.52
638 960 9.394767 AGTCAAAATTGAAAAGTTAGGCAAAAT 57.605 25.926 0.00 0.00 39.21 1.82
656 979 6.404293 GGCAAAATTATTTGTCGCTCCTCTTA 60.404 38.462 3.55 0.00 46.19 2.10
662 985 1.183549 TGTCGCTCCTCTTAGAACCC 58.816 55.000 0.00 0.00 0.00 4.11
679 1003 3.043713 CGAGGCAGCAACGCAAGA 61.044 61.111 0.00 0.00 43.62 3.02
696 1020 2.677337 CAAGATCACACACACACACACA 59.323 45.455 0.00 0.00 0.00 3.72
697 1021 2.279741 AGATCACACACACACACACAC 58.720 47.619 0.00 0.00 0.00 3.82
698 1022 2.006169 GATCACACACACACACACACA 58.994 47.619 0.00 0.00 0.00 3.72
711 1035 0.955428 ACACACATGATCGCCACACC 60.955 55.000 0.00 0.00 0.00 4.16
712 1036 0.954938 CACACATGATCGCCACACCA 60.955 55.000 0.00 0.00 0.00 4.17
713 1037 0.035152 ACACATGATCGCCACACCAT 60.035 50.000 0.00 0.00 0.00 3.55
714 1038 1.209261 ACACATGATCGCCACACCATA 59.791 47.619 0.00 0.00 0.00 2.74
723 1047 6.805713 TGATCGCCACACCATATATATACAG 58.194 40.000 0.00 0.00 0.00 2.74
746 1070 0.181350 AAGTTCCATCCGATCTGGCC 59.819 55.000 0.00 0.00 37.80 5.36
798 1122 3.644606 CTGCCCCACAGGTCAGCT 61.645 66.667 0.00 0.00 43.19 4.24
803 1127 1.079543 CCCACAGGTCAGCTTCTCG 60.080 63.158 0.00 0.00 0.00 4.04
805 1129 0.108898 CCACAGGTCAGCTTCTCGAG 60.109 60.000 5.93 5.93 0.00 4.04
807 1131 1.254284 ACAGGTCAGCTTCTCGAGGG 61.254 60.000 13.56 7.26 0.00 4.30
808 1132 2.185608 GGTCAGCTTCTCGAGGGC 59.814 66.667 13.56 16.76 0.00 5.19
809 1133 2.185608 GTCAGCTTCTCGAGGGCC 59.814 66.667 21.38 0.00 0.00 5.80
895 1219 3.059982 CGGGAGCAGTGTCTTCCA 58.940 61.111 11.15 0.00 30.76 3.53
896 1220 1.371183 CGGGAGCAGTGTCTTCCAA 59.629 57.895 11.15 0.00 30.76 3.53
998 1332 1.002366 CAGAGGCCGACGAATCAAAG 58.998 55.000 0.00 0.00 0.00 2.77
1189 1996 1.845809 CTCGCCGGCAAGCCATTATC 61.846 60.000 28.98 0.00 35.37 1.75
1194 2001 0.890996 CGGCAAGCCATTATCCCTCC 60.891 60.000 12.19 0.00 35.37 4.30
1218 2025 1.082104 GACGCTCGTTTTGGCCTTG 60.082 57.895 3.32 0.00 0.00 3.61
1219 2026 2.429069 CGCTCGTTTTGGCCTTGC 60.429 61.111 3.32 0.00 0.00 4.01
1244 2052 3.083997 GTCGGGGGATCAGCACCT 61.084 66.667 0.00 0.00 41.14 4.00
1278 2086 0.481128 GTAGGAGGAGGAGGAGGAGG 59.519 65.000 0.00 0.00 0.00 4.30
1279 2087 0.350904 TAGGAGGAGGAGGAGGAGGA 59.649 60.000 0.00 0.00 0.00 3.71
1280 2088 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1286 2094 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1410 2218 4.609098 CCCCCGCTAGATCTCTGT 57.391 61.111 0.00 0.00 0.00 3.41
1517 2326 2.009774 CTCGCAGGGATTCGTCATTTT 58.990 47.619 0.00 0.00 0.00 1.82
1518 2327 2.420022 CTCGCAGGGATTCGTCATTTTT 59.580 45.455 0.00 0.00 0.00 1.94
1725 2535 3.453559 TTCGGGAGAATTTCGAGCC 57.546 52.632 0.00 0.00 45.39 4.70
1752 2562 0.676782 GGGATAGGTTGCGTGTTGCT 60.677 55.000 0.00 0.00 46.63 3.91
1754 2564 1.156736 GATAGGTTGCGTGTTGCTGT 58.843 50.000 0.00 0.00 46.63 4.40
1761 2571 3.181575 GGTTGCGTGTTGCTGTTATTTTC 59.818 43.478 0.00 0.00 46.63 2.29
1880 2690 6.683974 GCTTGGTAGATTAAGCATCAAGAA 57.316 37.500 18.23 0.00 46.43 2.52
1924 2734 2.289002 GGCAGGCTTGACTTTATCATCG 59.711 50.000 0.00 0.00 37.11 3.84
1925 2735 2.939103 GCAGGCTTGACTTTATCATCGT 59.061 45.455 0.00 0.00 37.11 3.73
1926 2736 4.119862 GCAGGCTTGACTTTATCATCGTA 58.880 43.478 0.00 0.00 37.11 3.43
1930 2745 7.348201 CAGGCTTGACTTTATCATCGTATTTC 58.652 38.462 0.00 0.00 37.11 2.17
1959 2774 0.250295 CAAGGCCGGACAGAGAACAA 60.250 55.000 11.69 0.00 0.00 2.83
1961 2776 0.832135 AGGCCGGACAGAGAACAAGA 60.832 55.000 11.69 0.00 0.00 3.02
1994 2809 3.430779 GCATTCTTTTGCTGCTCCC 57.569 52.632 0.00 0.00 39.57 4.30
2033 2848 7.173390 AGAGGTTAAGAATGTGTAGCTTGAAAC 59.827 37.037 0.00 0.00 0.00 2.78
2036 2851 8.082242 GGTTAAGAATGTGTAGCTTGAAACATT 58.918 33.333 4.94 4.94 43.91 2.71
2037 2852 8.905702 GTTAAGAATGTGTAGCTTGAAACATTG 58.094 33.333 9.35 0.00 41.91 2.82
2046 2861 6.544197 TGTAGCTTGAAACATTGGTTACTTCA 59.456 34.615 0.00 0.00 35.82 3.02
2082 3171 7.149202 AGATGCCTCCTTTTGGTGTTATATA 57.851 36.000 0.00 0.00 41.38 0.86
2181 3270 1.575447 GGGAGTCCCTTGCTTCCCAT 61.575 60.000 22.04 0.00 41.34 4.00
2495 3588 7.175990 CCTTTGTTGCCCTACACTAATTCTTAA 59.824 37.037 0.00 0.00 0.00 1.85
2648 3741 6.017605 GGATTGTTCCAATCTGCTATACTGTG 60.018 42.308 14.60 0.00 42.12 3.66
3009 4105 6.670464 TGGATGAGAGTAAAAGGGTATGTGTA 59.330 38.462 0.00 0.00 0.00 2.90
3019 4115 3.371965 AGGGTATGTGTACACGAATCCT 58.628 45.455 20.94 20.94 39.28 3.24
3022 4118 4.142004 GGGTATGTGTACACGAATCCTCTT 60.142 45.833 20.61 0.60 32.25 2.85
3027 4123 1.138464 GTACACGAATCCTCTTCCCCC 59.862 57.143 0.00 0.00 0.00 5.40
3032 4128 2.026169 ACGAATCCTCTTCCCCCTTTTC 60.026 50.000 0.00 0.00 0.00 2.29
3386 4488 8.462143 ACAGACAATAACTGTACTCAATTACG 57.538 34.615 0.00 0.00 45.10 3.18
3394 4499 5.899299 ACTGTACTCAATTACGTATGTCCC 58.101 41.667 0.00 0.00 0.00 4.46
3408 4513 4.770362 TCCCGGTCTCCGCCATCA 62.770 66.667 0.00 0.00 46.86 3.07
3802 4910 2.049433 CTGTTGGCTTGCTGCTGC 60.049 61.111 8.89 8.89 42.39 5.25
3918 5026 3.994392 CTCGCTCACTTTTTGTAGCCTTA 59.006 43.478 0.00 0.00 0.00 2.69
3958 5270 4.556233 TCAACGGTGTTCTGTCTTATCTG 58.444 43.478 0.00 0.00 32.07 2.90
4006 5441 6.409524 AATGGTAATTGCATATTGGTCTGG 57.590 37.500 0.00 0.00 0.00 3.86
4007 5442 3.636300 TGGTAATTGCATATTGGTCTGGC 59.364 43.478 0.00 0.00 0.00 4.85
4011 5446 0.106569 TGCATATTGGTCTGGCCTGG 60.107 55.000 10.07 0.00 38.35 4.45
4014 5449 2.579873 CATATTGGTCTGGCCTGGAAG 58.420 52.381 10.07 0.00 38.35 3.46
4063 5604 1.129811 GGCAACCGAGAAATACCAACG 59.870 52.381 0.00 0.00 0.00 4.10
4099 5640 2.226437 CACGGCTTAACAAAGACAGCAT 59.774 45.455 0.00 0.00 33.64 3.79
4229 5924 3.996825 GTGCCATTCACGGATTCAC 57.003 52.632 0.00 0.00 35.76 3.18
4250 5974 0.179108 CCTAGTAGCGTTCCTGCACC 60.179 60.000 0.00 0.00 37.31 5.01
4252 5976 0.530744 TAGTAGCGTTCCTGCACCTG 59.469 55.000 0.00 0.00 37.31 4.00
4283 6007 3.741476 CCTGCGCCAGGTTCAAGC 61.741 66.667 4.18 0.00 45.82 4.01
4766 6517 1.466025 AACGAAGGGTACGTGCTCCA 61.466 55.000 0.00 0.00 43.16 3.86
4767 6518 1.445582 CGAAGGGTACGTGCTCCAC 60.446 63.158 0.00 0.00 0.00 4.02
4814 6565 3.693245 CGCAGCGTACATGGAGTC 58.307 61.111 6.65 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.806739 GCAACAAACATCCAATCTACTTTACC 59.193 38.462 0.00 0.00 0.00 2.85
1 2 7.367285 TGCAACAAACATCCAATCTACTTTAC 58.633 34.615 0.00 0.00 0.00 2.01
2 3 7.517614 TGCAACAAACATCCAATCTACTTTA 57.482 32.000 0.00 0.00 0.00 1.85
3 4 6.403866 TGCAACAAACATCCAATCTACTTT 57.596 33.333 0.00 0.00 0.00 2.66
4 5 6.403866 TTGCAACAAACATCCAATCTACTT 57.596 33.333 0.00 0.00 0.00 2.24
5 6 5.565439 GCTTGCAACAAACATCCAATCTACT 60.565 40.000 0.00 0.00 0.00 2.57
6 7 4.622740 GCTTGCAACAAACATCCAATCTAC 59.377 41.667 0.00 0.00 0.00 2.59
7 8 4.280425 TGCTTGCAACAAACATCCAATCTA 59.720 37.500 0.00 0.00 0.00 1.98
8 9 3.069872 TGCTTGCAACAAACATCCAATCT 59.930 39.130 0.00 0.00 0.00 2.40
9 10 3.391965 TGCTTGCAACAAACATCCAATC 58.608 40.909 0.00 0.00 0.00 2.67
10 11 3.472283 TGCTTGCAACAAACATCCAAT 57.528 38.095 0.00 0.00 0.00 3.16
11 12 2.975732 TGCTTGCAACAAACATCCAA 57.024 40.000 0.00 0.00 0.00 3.53
12 13 2.629137 AGATGCTTGCAACAAACATCCA 59.371 40.909 16.18 0.00 38.28 3.41
13 14 2.991190 CAGATGCTTGCAACAAACATCC 59.009 45.455 16.18 3.78 38.28 3.51
14 15 3.904571 TCAGATGCTTGCAACAAACATC 58.095 40.909 13.29 13.29 37.89 3.06
15 16 4.219944 AGATCAGATGCTTGCAACAAACAT 59.780 37.500 0.00 0.00 0.00 2.71
16 17 3.570975 AGATCAGATGCTTGCAACAAACA 59.429 39.130 0.00 0.00 0.00 2.83
17 18 4.170292 AGATCAGATGCTTGCAACAAAC 57.830 40.909 0.00 0.00 0.00 2.93
18 19 4.142534 GCTAGATCAGATGCTTGCAACAAA 60.143 41.667 0.00 0.00 33.94 2.83
19 20 3.376234 GCTAGATCAGATGCTTGCAACAA 59.624 43.478 0.00 0.00 33.94 2.83
20 21 2.941064 GCTAGATCAGATGCTTGCAACA 59.059 45.455 0.00 0.00 33.94 3.33
58 59 2.714259 CGTAGGAGGGCTCTCAGAG 58.286 63.158 17.22 0.00 41.69 3.35
74 75 3.681417 GCTTTCGAAAACCACTATACCGT 59.319 43.478 12.41 0.00 0.00 4.83
101 103 0.463204 ACCATGACCTGAGAGATGCG 59.537 55.000 0.00 0.00 0.00 4.73
104 106 3.866651 CGAAAACCATGACCTGAGAGAT 58.133 45.455 0.00 0.00 0.00 2.75
105 107 2.612972 GCGAAAACCATGACCTGAGAGA 60.613 50.000 0.00 0.00 0.00 3.10
106 108 1.734465 GCGAAAACCATGACCTGAGAG 59.266 52.381 0.00 0.00 0.00 3.20
108 110 1.197721 GTGCGAAAACCATGACCTGAG 59.802 52.381 0.00 0.00 0.00 3.35
109 111 1.234821 GTGCGAAAACCATGACCTGA 58.765 50.000 0.00 0.00 0.00 3.86
110 112 0.950836 TGTGCGAAAACCATGACCTG 59.049 50.000 0.00 0.00 0.00 4.00
131 133 6.723298 AAAGATGTACCCAAACAATGTTGA 57.277 33.333 0.00 0.00 32.02 3.18
153 155 8.401709 GTTTATTGTGATGGCAAAAAGGAAAAA 58.598 29.630 0.00 0.00 31.63 1.94
159 161 5.612276 GCACGTTTATTGTGATGGCAAAAAG 60.612 40.000 0.00 0.00 39.73 2.27
160 162 4.210120 GCACGTTTATTGTGATGGCAAAAA 59.790 37.500 0.00 0.00 39.73 1.94
163 165 2.556189 AGCACGTTTATTGTGATGGCAA 59.444 40.909 0.00 0.00 39.73 4.52
164 166 2.158559 AGCACGTTTATTGTGATGGCA 58.841 42.857 0.00 0.00 39.73 4.92
167 169 3.980134 TGCAAAGCACGTTTATTGTGATG 59.020 39.130 0.00 0.00 39.73 3.07
172 174 4.317980 CCACTTTGCAAAGCACGTTTATTG 60.318 41.667 33.72 21.74 38.71 1.90
179 181 0.594796 GACCCACTTTGCAAAGCACG 60.595 55.000 33.72 23.49 38.71 5.34
182 184 0.317854 GTCGACCCACTTTGCAAAGC 60.318 55.000 33.72 18.69 39.63 3.51
183 185 1.021202 TGTCGACCCACTTTGCAAAG 58.979 50.000 32.53 32.53 41.73 2.77
185 187 0.393132 TGTGTCGACCCACTTTGCAA 60.393 50.000 14.12 0.00 36.30 4.08
187 189 0.307760 CTTGTGTCGACCCACTTTGC 59.692 55.000 14.12 0.00 36.30 3.68
188 190 1.663695 ACTTGTGTCGACCCACTTTG 58.336 50.000 14.12 0.87 36.30 2.77
189 191 2.413310 AACTTGTGTCGACCCACTTT 57.587 45.000 14.12 0.11 36.30 2.66
191 193 1.758280 TGTAACTTGTGTCGACCCACT 59.242 47.619 14.12 0.00 36.30 4.00
193 195 2.983907 TTGTAACTTGTGTCGACCCA 57.016 45.000 14.12 4.45 0.00 4.51
194 196 3.810941 TGATTTGTAACTTGTGTCGACCC 59.189 43.478 14.12 0.94 0.00 4.46
196 198 7.347508 AGTATGATTTGTAACTTGTGTCGAC 57.652 36.000 9.11 9.11 0.00 4.20
212 218 6.640518 ACTCATTCGGTGTGTAAGTATGATT 58.359 36.000 0.00 0.00 33.06 2.57
225 231 3.430374 CCTTAGGGTGTACTCATTCGGTG 60.430 52.174 0.00 0.00 0.00 4.94
231 237 2.505819 CAAGGCCTTAGGGTGTACTCAT 59.494 50.000 20.00 0.00 34.45 2.90
232 238 1.906574 CAAGGCCTTAGGGTGTACTCA 59.093 52.381 20.00 0.00 34.45 3.41
233 239 1.907255 ACAAGGCCTTAGGGTGTACTC 59.093 52.381 20.00 0.00 34.45 2.59
234 240 2.040342 ACAAGGCCTTAGGGTGTACT 57.960 50.000 20.00 0.00 34.45 2.73
235 241 2.568509 TGTACAAGGCCTTAGGGTGTAC 59.431 50.000 27.19 27.19 40.26 2.90
236 242 2.905246 TGTACAAGGCCTTAGGGTGTA 58.095 47.619 20.00 14.03 34.45 2.90
237 243 1.737199 TGTACAAGGCCTTAGGGTGT 58.263 50.000 20.00 15.18 34.45 4.16
238 244 2.871096 TTGTACAAGGCCTTAGGGTG 57.129 50.000 20.00 9.01 34.45 4.61
239 245 2.025321 CCATTGTACAAGGCCTTAGGGT 60.025 50.000 20.00 14.93 34.45 4.34
241 247 3.016736 CACCATTGTACAAGGCCTTAGG 58.983 50.000 20.00 9.74 0.00 2.69
242 248 3.016736 CCACCATTGTACAAGGCCTTAG 58.983 50.000 20.00 15.05 0.00 2.18
243 249 2.645297 TCCACCATTGTACAAGGCCTTA 59.355 45.455 20.00 1.64 0.00 2.69
244 250 1.427368 TCCACCATTGTACAAGGCCTT 59.573 47.619 13.78 13.78 0.00 4.35
245 251 1.072266 TCCACCATTGTACAAGGCCT 58.928 50.000 14.66 0.00 0.00 5.19
246 252 1.750778 CATCCACCATTGTACAAGGCC 59.249 52.381 14.66 0.00 0.00 5.19
248 254 2.726821 AGCATCCACCATTGTACAAGG 58.273 47.619 14.65 13.92 0.00 3.61
249 255 4.201812 CGTAAGCATCCACCATTGTACAAG 60.202 45.833 14.65 3.88 0.00 3.16
250 256 3.687212 CGTAAGCATCCACCATTGTACAA 59.313 43.478 11.41 11.41 0.00 2.41
251 257 3.266636 CGTAAGCATCCACCATTGTACA 58.733 45.455 0.00 0.00 0.00 2.90
252 258 3.944422 CGTAAGCATCCACCATTGTAC 57.056 47.619 0.00 0.00 0.00 2.90
268 274 8.828644 TCTTTTTCTTTAAGTACATGTGCGTAA 58.171 29.630 15.96 15.96 0.00 3.18
280 286 5.693814 CATCGCTGCTCTTTTTCTTTAAGT 58.306 37.500 0.00 0.00 0.00 2.24
301 307 3.561310 AGACGACATTATTTGCGATGCAT 59.439 39.130 0.00 0.00 38.76 3.96
305 311 4.188462 TCCAAGACGACATTATTTGCGAT 58.812 39.130 0.00 0.00 0.00 4.58
310 316 5.647658 TCTGCATTCCAAGACGACATTATTT 59.352 36.000 0.00 0.00 0.00 1.40
326 333 0.679002 TGCCTGGAAGCTCTGCATTC 60.679 55.000 0.00 0.00 0.00 2.67
328 335 0.251474 TTTGCCTGGAAGCTCTGCAT 60.251 50.000 0.00 0.00 0.00 3.96
330 337 0.243095 CTTTTGCCTGGAAGCTCTGC 59.757 55.000 0.00 0.00 0.00 4.26
331 338 1.268899 CACTTTTGCCTGGAAGCTCTG 59.731 52.381 0.00 0.00 0.00 3.35
332 339 1.613836 CACTTTTGCCTGGAAGCTCT 58.386 50.000 0.00 0.00 0.00 4.09
344 351 3.118542 GGAAGCAACTGAAGCACTTTTG 58.881 45.455 0.00 0.00 0.00 2.44
345 352 2.223572 CGGAAGCAACTGAAGCACTTTT 60.224 45.455 0.00 0.00 0.00 2.27
346 353 1.334869 CGGAAGCAACTGAAGCACTTT 59.665 47.619 0.00 0.00 0.00 2.66
347 354 0.947244 CGGAAGCAACTGAAGCACTT 59.053 50.000 0.00 0.00 0.00 3.16
348 355 2.621763 CGGAAGCAACTGAAGCACT 58.378 52.632 0.00 0.00 0.00 4.40
361 368 2.124942 GCAGAAGGGAGGCGGAAG 60.125 66.667 0.00 0.00 0.00 3.46
365 372 1.817099 GTCATGCAGAAGGGAGGCG 60.817 63.158 0.00 0.00 0.00 5.52
366 373 1.817099 CGTCATGCAGAAGGGAGGC 60.817 63.158 0.00 0.00 0.00 4.70
371 378 1.998315 CTCTCAACGTCATGCAGAAGG 59.002 52.381 0.00 0.00 0.00 3.46
375 382 0.997932 GCTCTCTCAACGTCATGCAG 59.002 55.000 0.00 0.00 0.00 4.41
376 383 0.318120 TGCTCTCTCAACGTCATGCA 59.682 50.000 0.00 0.00 0.00 3.96
384 391 3.249559 CACAAAAGGAGTGCTCTCTCAAC 59.750 47.826 14.98 0.00 40.29 3.18
386 393 3.117491 CACAAAAGGAGTGCTCTCTCA 57.883 47.619 14.98 0.00 40.29 3.27
398 405 0.594796 GTCGGTGCTTGCACAAAAGG 60.595 55.000 24.34 9.88 0.00 3.11
399 406 0.381801 AGTCGGTGCTTGCACAAAAG 59.618 50.000 24.34 13.55 0.00 2.27
400 407 1.601903 CTAGTCGGTGCTTGCACAAAA 59.398 47.619 24.34 8.58 0.00 2.44
401 408 1.225855 CTAGTCGGTGCTTGCACAAA 58.774 50.000 24.34 10.84 0.00 2.83
410 417 0.737715 CTTCTGGTGCTAGTCGGTGC 60.738 60.000 0.00 0.00 0.00 5.01
416 423 1.630369 TGGATTGCTTCTGGTGCTAGT 59.370 47.619 0.00 0.00 0.00 2.57
419 426 2.226962 ATTGGATTGCTTCTGGTGCT 57.773 45.000 0.00 0.00 0.00 4.40
421 428 5.277683 CGAGATTATTGGATTGCTTCTGGTG 60.278 44.000 0.00 0.00 0.00 4.17
425 432 4.103153 TCCCGAGATTATTGGATTGCTTCT 59.897 41.667 0.00 0.00 33.64 2.85
433 440 3.641906 GGTCTTCTCCCGAGATTATTGGA 59.358 47.826 0.00 0.00 37.29 3.53
436 443 4.810345 AGAGGTCTTCTCCCGAGATTATT 58.190 43.478 0.00 0.00 43.44 1.40
437 444 4.403734 GAGAGGTCTTCTCCCGAGATTAT 58.596 47.826 0.40 0.00 45.53 1.28
439 446 2.661718 GAGAGGTCTTCTCCCGAGATT 58.338 52.381 0.40 0.00 45.53 2.40
440 447 2.358322 GAGAGGTCTTCTCCCGAGAT 57.642 55.000 0.40 0.00 45.53 2.75
448 460 2.964209 TGGACACTTGAGAGGTCTTCT 58.036 47.619 0.00 0.00 39.43 2.85
449 461 3.007398 ACATGGACACTTGAGAGGTCTTC 59.993 47.826 0.00 0.00 0.00 2.87
461 473 1.673033 GCAGACGCTTACATGGACACT 60.673 52.381 0.00 0.00 34.30 3.55
463 475 0.391130 GGCAGACGCTTACATGGACA 60.391 55.000 0.00 0.00 38.60 4.02
464 476 1.421410 CGGCAGACGCTTACATGGAC 61.421 60.000 0.00 0.00 38.60 4.02
465 477 1.153647 CGGCAGACGCTTACATGGA 60.154 57.895 0.00 0.00 38.60 3.41
476 488 1.375523 CCCCTGTACAACGGCAGAC 60.376 63.158 0.00 0.00 34.87 3.51
477 489 3.065306 CCCCTGTACAACGGCAGA 58.935 61.111 0.00 0.00 34.87 4.26
479 491 1.481901 TTAGCCCCTGTACAACGGCA 61.482 55.000 26.54 14.55 44.18 5.69
486 498 0.033642 GGATCGCTTAGCCCCTGTAC 59.966 60.000 0.00 0.00 0.00 2.90
492 504 1.300481 GAACTTGGATCGCTTAGCCC 58.700 55.000 0.00 0.00 30.06 5.19
494 506 2.317530 AGGAACTTGGATCGCTTAGC 57.682 50.000 0.00 0.00 27.25 3.09
514 526 5.384063 TGTGTTCTGCTTTTCTTTTCACA 57.616 34.783 0.00 0.00 0.00 3.58
518 530 5.177326 TGCATTGTGTTCTGCTTTTCTTTT 58.823 33.333 0.00 0.00 39.16 2.27
527 539 2.925563 GGCTTTATGCATTGTGTTCTGC 59.074 45.455 3.54 0.00 45.15 4.26
579 901 3.317711 ACCATGAAGTGCGTGAAATTTCA 59.682 39.130 16.91 16.91 35.44 2.69
590 912 1.202336 GCTAATGCCACCATGAAGTGC 60.202 52.381 0.00 0.00 36.38 4.40
593 915 2.756760 ACTTGCTAATGCCACCATGAAG 59.243 45.455 0.00 0.00 38.71 3.02
594 916 2.754552 GACTTGCTAATGCCACCATGAA 59.245 45.455 0.00 0.00 38.71 2.57
602 924 6.783892 TTTCAATTTTGACTTGCTAATGCC 57.216 33.333 0.00 0.00 36.83 4.40
608 930 6.479990 GCCTAACTTTTCAATTTTGACTTGCT 59.520 34.615 0.00 0.00 36.83 3.91
609 931 6.257630 TGCCTAACTTTTCAATTTTGACTTGC 59.742 34.615 0.00 0.00 36.83 4.01
610 932 7.769272 TGCCTAACTTTTCAATTTTGACTTG 57.231 32.000 0.00 0.00 36.83 3.16
612 934 8.785329 TTTTGCCTAACTTTTCAATTTTGACT 57.215 26.923 0.00 0.00 36.83 3.41
623 945 7.655732 AGCGACAAATAATTTTGCCTAACTTTT 59.344 29.630 0.00 0.00 45.01 2.27
630 952 3.763897 AGGAGCGACAAATAATTTTGCCT 59.236 39.130 0.00 0.00 45.01 4.75
635 957 7.065923 GGTTCTAAGAGGAGCGACAAATAATTT 59.934 37.037 0.00 0.00 0.00 1.82
638 960 5.416947 GGTTCTAAGAGGAGCGACAAATAA 58.583 41.667 0.00 0.00 0.00 1.40
656 979 2.032681 GTTGCTGCCTCGGGTTCT 59.967 61.111 0.00 0.00 0.00 3.01
662 985 2.301902 GATCTTGCGTTGCTGCCTCG 62.302 60.000 0.00 3.09 0.00 4.63
679 1003 2.106477 TGTGTGTGTGTGTGTGTGAT 57.894 45.000 0.00 0.00 0.00 3.06
696 1020 2.936919 ATATGGTGTGGCGATCATGT 57.063 45.000 0.00 0.00 0.00 3.21
697 1021 7.209475 TGTATATATATGGTGTGGCGATCATG 58.791 38.462 5.44 0.00 0.00 3.07
698 1022 7.360113 TGTATATATATGGTGTGGCGATCAT 57.640 36.000 5.44 0.00 0.00 2.45
711 1035 9.113838 GGATGGAACTTTGGCTGTATATATATG 57.886 37.037 5.44 0.00 0.00 1.78
712 1036 7.987458 CGGATGGAACTTTGGCTGTATATATAT 59.013 37.037 0.00 0.00 0.00 0.86
713 1037 7.179516 TCGGATGGAACTTTGGCTGTATATATA 59.820 37.037 0.00 0.00 0.00 0.86
714 1038 6.013725 TCGGATGGAACTTTGGCTGTATATAT 60.014 38.462 0.00 0.00 0.00 0.86
723 1047 1.672881 CAGATCGGATGGAACTTTGGC 59.327 52.381 0.00 0.00 0.00 4.52
798 1122 2.869503 GAAATGGCGGCCCTCGAGAA 62.870 60.000 17.97 0.00 42.43 2.87
803 1127 3.508840 CGTGAAATGGCGGCCCTC 61.509 66.667 17.97 11.00 0.00 4.30
813 1137 3.419759 GGTCGTGCCGCGTGAAAT 61.420 61.111 4.92 0.00 42.13 2.17
880 1204 1.003580 TGGATTGGAAGACACTGCTCC 59.996 52.381 0.00 0.00 0.00 4.70
882 1206 2.957402 TTGGATTGGAAGACACTGCT 57.043 45.000 0.00 0.00 0.00 4.24
884 1208 3.689347 TGGATTGGATTGGAAGACACTG 58.311 45.455 0.00 0.00 0.00 3.66
885 1209 4.338879 CTTGGATTGGATTGGAAGACACT 58.661 43.478 0.00 0.00 0.00 3.55
886 1210 3.119352 GCTTGGATTGGATTGGAAGACAC 60.119 47.826 0.00 0.00 0.00 3.67
887 1211 3.091545 GCTTGGATTGGATTGGAAGACA 58.908 45.455 0.00 0.00 0.00 3.41
888 1212 2.098117 CGCTTGGATTGGATTGGAAGAC 59.902 50.000 0.00 0.00 0.00 3.01
889 1213 2.026356 TCGCTTGGATTGGATTGGAAGA 60.026 45.455 0.00 0.00 0.00 2.87
892 1216 1.681780 GGTCGCTTGGATTGGATTGGA 60.682 52.381 0.00 0.00 0.00 3.53
893 1217 0.740737 GGTCGCTTGGATTGGATTGG 59.259 55.000 0.00 0.00 0.00 3.16
895 1219 0.748005 CGGGTCGCTTGGATTGGATT 60.748 55.000 0.00 0.00 0.00 3.01
896 1220 1.153168 CGGGTCGCTTGGATTGGAT 60.153 57.895 0.00 0.00 0.00 3.41
998 1332 0.543174 TGGGGGTTAAATGGTGGTGC 60.543 55.000 0.00 0.00 0.00 5.01
1175 1960 0.890996 GGAGGGATAATGGCTTGCCG 60.891 60.000 7.18 0.00 0.00 5.69
1176 1961 0.540597 GGGAGGGATAATGGCTTGCC 60.541 60.000 4.43 4.43 0.00 4.52
1179 1986 1.456287 GCGGGAGGGATAATGGCTT 59.544 57.895 0.00 0.00 0.00 4.35
1278 2086 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1279 2087 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1280 2088 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1410 2218 4.798682 GAAGCGGGGAGAGGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
1467 2276 2.180204 CCACGCGCCCAAATCCTAG 61.180 63.158 5.73 0.00 0.00 3.02
1517 2326 1.514678 AATTCGCTCGCAGGCAACAA 61.515 50.000 0.00 0.00 41.41 2.83
1518 2327 1.911293 GAATTCGCTCGCAGGCAACA 61.911 55.000 0.00 0.00 41.41 3.33
1576 2386 2.912956 AGAGGCTATTCAGGAAACACCA 59.087 45.455 0.00 0.00 42.04 4.17
1577 2387 3.274288 CAGAGGCTATTCAGGAAACACC 58.726 50.000 0.00 0.00 39.35 4.16
1578 2388 2.680339 GCAGAGGCTATTCAGGAAACAC 59.320 50.000 0.00 0.00 36.96 3.32
1646 2456 2.295885 CCTCATCCTAAAGCCAGCAAG 58.704 52.381 0.00 0.00 0.00 4.01
1707 2517 0.611200 TGGCTCGAAATTCTCCCGAA 59.389 50.000 0.00 0.00 31.59 4.30
1725 2535 0.761802 GCAACCTATCCCCTCTCCTG 59.238 60.000 0.00 0.00 0.00 3.86
1891 2701 1.542492 AGCCTGCCTCACAATCTTTG 58.458 50.000 0.00 0.00 0.00 2.77
1924 2734 7.170489 GTCCGGCCTTGTAAACTATAGAAATAC 59.830 40.741 6.78 7.01 0.00 1.89
1925 2735 7.147689 TGTCCGGCCTTGTAAACTATAGAAATA 60.148 37.037 6.78 0.00 0.00 1.40
1926 2736 6.053650 GTCCGGCCTTGTAAACTATAGAAAT 58.946 40.000 6.78 0.00 0.00 2.17
1930 2745 4.098960 TCTGTCCGGCCTTGTAAACTATAG 59.901 45.833 0.00 0.00 0.00 1.31
1959 2774 7.458409 AAGAATGCTAAATGATTGTGTGTCT 57.542 32.000 0.00 0.00 0.00 3.41
1961 2776 7.095523 GCAAAAGAATGCTAAATGATTGTGTGT 60.096 33.333 0.00 0.00 43.06 3.72
1994 2809 5.657474 TCTTAACCTCTTTACCATACAGCG 58.343 41.667 0.00 0.00 0.00 5.18
2033 2848 4.696877 TGACATGCTCTGAAGTAACCAATG 59.303 41.667 0.00 0.00 0.00 2.82
2036 2851 4.350368 TTGACATGCTCTGAAGTAACCA 57.650 40.909 0.00 0.00 0.00 3.67
2037 2852 4.997395 TCTTTGACATGCTCTGAAGTAACC 59.003 41.667 0.00 0.00 0.00 2.85
2046 2861 2.641305 GAGGCATCTTTGACATGCTCT 58.359 47.619 4.75 0.97 45.18 4.09
2082 3171 5.860941 ACTAGCTAGTCACATAACAGCAT 57.139 39.130 20.95 0.00 34.65 3.79
2181 3270 4.194678 AGTTAACTCCGATCATCCCCTA 57.805 45.455 1.12 0.00 0.00 3.53
2495 3588 8.547967 AAGTCAATACTACACGAACAAATGAT 57.452 30.769 0.00 0.00 33.75 2.45
2648 3741 6.968131 TCTATCACAATAACTTCACAGCAC 57.032 37.500 0.00 0.00 0.00 4.40
3009 4105 0.252742 AGGGGGAAGAGGATTCGTGT 60.253 55.000 0.00 0.00 0.00 4.49
3019 4115 4.240323 ACTAGAACAGAAAAGGGGGAAGA 58.760 43.478 0.00 0.00 0.00 2.87
3022 4118 4.759953 ACTACTAGAACAGAAAAGGGGGA 58.240 43.478 0.00 0.00 0.00 4.81
3073 4169 8.827677 AGTGATTTCGAACCTATAATACAAAGC 58.172 33.333 0.00 0.00 0.00 3.51
3374 4476 4.202050 ACCGGGACATACGTAATTGAGTAC 60.202 45.833 6.32 0.00 0.00 2.73
3402 4507 2.774799 GGGCACCGAACATGATGGC 61.775 63.158 0.00 1.82 40.86 4.40
3802 4910 5.210715 GCATATTGATTGCTCGGAAAGAAG 58.789 41.667 0.00 0.00 37.14 2.85
3918 5026 6.151691 CCGTTGATTGTTGTTCAGAATTCAT 58.848 36.000 8.44 0.00 0.00 2.57
3977 5289 8.076910 ACCAATATGCAATTACCATTTGAGAA 57.923 30.769 0.00 0.00 0.00 2.87
4006 5441 2.226674 GTGCTCACTTTAACTTCCAGGC 59.773 50.000 0.00 0.00 0.00 4.85
4007 5442 3.744660 AGTGCTCACTTTAACTTCCAGG 58.255 45.455 0.00 0.00 38.83 4.45
4011 5446 7.647715 TGCAATTTTAGTGCTCACTTTAACTTC 59.352 33.333 7.92 0.00 42.69 3.01
4014 5449 7.873739 ATGCAATTTTAGTGCTCACTTTAAC 57.126 32.000 7.92 0.00 42.69 2.01
4063 5604 2.162408 AGCCGTGCTTTTTATTCTCAGC 59.838 45.455 0.00 0.00 33.89 4.26
4099 5640 7.546250 TTCCAATTCCAAATGCCTACTTTTA 57.454 32.000 0.00 0.00 0.00 1.52
4214 5894 0.255890 AGGGGTGAATCCGTGAATGG 59.744 55.000 0.00 0.00 37.00 3.16
4228 5923 1.328430 GCAGGAACGCTACTAGGGGT 61.328 60.000 5.22 0.00 31.71 4.95
4229 5924 1.327690 TGCAGGAACGCTACTAGGGG 61.328 60.000 5.22 0.00 31.71 4.79
4283 6007 4.247380 GGCCGAGATCTGCCTGGG 62.247 72.222 15.24 3.50 42.13 4.45
4346 6070 4.072088 GAACGCGAACGGCACCAG 62.072 66.667 15.93 0.00 46.04 4.00
4490 6223 4.292178 CCTCGAGATCCGGCTGCC 62.292 72.222 15.71 9.11 39.14 4.85
4709 6460 1.673923 CGACATGAGCAAGAGAAGGCA 60.674 52.381 0.00 0.00 0.00 4.75
4712 6463 3.519579 ACATCGACATGAGCAAGAGAAG 58.480 45.455 0.00 0.00 33.72 2.85
4713 6464 3.515630 GACATCGACATGAGCAAGAGAA 58.484 45.455 0.00 0.00 33.72 2.87
4714 6465 2.478539 CGACATCGACATGAGCAAGAGA 60.479 50.000 0.00 0.00 43.02 3.10
4753 6504 2.264794 CCTGTGGAGCACGTACCC 59.735 66.667 0.00 0.00 37.14 3.69
4786 6537 2.159296 TGTACGCTGCGCTATATATGGG 60.159 50.000 23.51 1.27 0.00 4.00


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

AutoCloner maintained by Alex Coulton.