Multiple sequence alignment - TraesCS2D01G441200

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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 TraesCS2D01G441200 chr2D 100.000 2339 0 0 1 2339 551836417 551838755 0.000000e+00 4320.0
1 TraesCS2D01G441200 chr2D 80.049 411 58 16 1154 1556 466718308 466717914 1.370000e-72 283.0
2 TraesCS2D01G441200 chr2D 79.091 440 52 25 1153 1559 179937361 179936929 1.380000e-67 267.0
3 TraesCS2D01G441200 chr2D 77.253 466 48 31 1137 1567 569954232 569953790 1.090000e-53 220.0
4 TraesCS2D01G441200 chr2D 78.916 166 29 6 1021 1183 551837349 551837511 8.840000e-20 108.0
5 TraesCS2D01G441200 chr2D 78.916 166 29 6 933 1095 551837437 551837599 8.840000e-20 108.0
6 TraesCS2D01G441200 chr7A 89.139 755 56 6 802 1555 734916874 734917603 0.000000e+00 917.0
7 TraesCS2D01G441200 chr4B 86.364 792 73 21 1570 2339 657159311 657160089 0.000000e+00 832.0
8 TraesCS2D01G441200 chr4B 87.556 667 69 8 1683 2339 657142172 657142834 0.000000e+00 760.0
9 TraesCS2D01G441200 chr4B 100.000 28 0 0 432 459 4478241 4478214 4.000000e-03 52.8
10 TraesCS2D01G441200 chr3D 97.034 472 11 3 1 471 427302111 427301642 0.000000e+00 791.0
11 TraesCS2D01G441200 chr3D 93.536 263 16 1 1 262 135641640 135641902 7.840000e-105 390.0
12 TraesCS2D01G441200 chr3D 96.774 31 1 0 933 963 381889150 381889180 4.000000e-03 52.8
13 TraesCS2D01G441200 chr4D 93.348 466 31 0 1874 2339 509679131 509678666 0.000000e+00 689.0
14 TraesCS2D01G441200 chr4D 90.549 328 12 10 1556 1879 509679953 509679641 1.290000e-112 416.0
15 TraesCS2D01G441200 chr4D 78.082 438 74 18 1132 1557 421642014 421641587 8.290000e-65 257.0
16 TraesCS2D01G441200 chr5B 93.287 432 26 3 1090 1520 648610434 648610863 3.280000e-178 634.0
17 TraesCS2D01G441200 chr5B 95.195 333 13 2 463 793 648609932 648610263 7.410000e-145 523.0
18 TraesCS2D01G441200 chr5B 92.073 164 13 0 866 1029 648610262 648610425 5.030000e-57 231.0
19 TraesCS2D01G441200 chr3B 95.817 263 10 1 1 262 193628553 193628815 7.730000e-115 424.0
20 TraesCS2D01G441200 chr6A 77.395 522 82 25 1045 1563 318661721 318662209 6.370000e-71 278.0
21 TraesCS2D01G441200 chr1D 95.732 164 6 1 299 462 83696475 83696313 1.780000e-66 263.0
22 TraesCS2D01G441200 chr1D 98.039 51 1 0 261 311 83696532 83696482 3.200000e-14 89.8
23 TraesCS2D01G441200 chr6D 96.403 139 5 0 316 454 355880088 355880226 1.810000e-56 230.0
24 TraesCS2D01G441200 chr2B 77.241 435 61 22 1130 1555 11178545 11178140 1.090000e-53 220.0
25 TraesCS2D01G441200 chr2B 97.222 36 0 1 432 467 282563842 282563808 2.510000e-05 60.2
26 TraesCS2D01G441200 chr1B 87.333 150 17 2 1402 1549 461300338 461300189 1.110000e-38 171.0
27 TraesCS2D01G441200 chr4A 74.874 398 70 24 1130 1518 640055422 640055046 1.120000e-33 154.0
28 TraesCS2D01G441200 chr1A 84.444 90 11 3 1460 1547 516170893 516170981 4.140000e-13 86.1


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 TraesCS2D01G441200 chr2D 551836417 551838755 2338 False 1512.000000 4320 85.944000 1 2339 3 chr2D.!!$F1 2338
1 TraesCS2D01G441200 chr7A 734916874 734917603 729 False 917.000000 917 89.139000 802 1555 1 chr7A.!!$F1 753
2 TraesCS2D01G441200 chr4B 657159311 657160089 778 False 832.000000 832 86.364000 1570 2339 1 chr4B.!!$F2 769
3 TraesCS2D01G441200 chr4B 657142172 657142834 662 False 760.000000 760 87.556000 1683 2339 1 chr4B.!!$F1 656
4 TraesCS2D01G441200 chr4D 509678666 509679953 1287 True 552.500000 689 91.948500 1556 2339 2 chr4D.!!$R2 783
5 TraesCS2D01G441200 chr5B 648609932 648610863 931 False 462.666667 634 93.518333 463 1520 3 chr5B.!!$F1 1057

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
329 330 0.036294 GAGGAAAGAACGGGTGGAGG 60.036 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2648 0.459489 CTCTCCAGCTCTTCCTTCCG 59.541 60.0 0.0 0.0 0.0 4.3 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 4.760047 GGGCGTGCGGTCAGTGAT 62.760 66.667 0.00 0.00 0.00 3.06
38 39 3.490759 GGCGTGCGGTCAGTGATG 61.491 66.667 0.00 0.00 0.00 3.07
39 40 2.738521 GCGTGCGGTCAGTGATGT 60.739 61.111 0.00 0.00 0.00 3.06
40 41 2.317609 GCGTGCGGTCAGTGATGTT 61.318 57.895 0.00 0.00 0.00 2.71
41 42 1.492873 CGTGCGGTCAGTGATGTTG 59.507 57.895 0.00 0.00 0.00 3.33
42 43 0.943835 CGTGCGGTCAGTGATGTTGA 60.944 55.000 0.00 0.00 0.00 3.18
43 44 0.792640 GTGCGGTCAGTGATGTTGAG 59.207 55.000 0.00 0.00 0.00 3.02
44 45 0.950555 TGCGGTCAGTGATGTTGAGC 60.951 55.000 0.00 0.00 39.14 4.26
46 47 3.217242 GGTCAGTGATGTTGAGCGT 57.783 52.632 0.00 0.00 33.93 5.07
47 48 0.792640 GGTCAGTGATGTTGAGCGTG 59.207 55.000 0.00 0.00 33.93 5.34
48 49 1.605457 GGTCAGTGATGTTGAGCGTGA 60.605 52.381 0.00 0.00 33.93 4.35
49 50 1.457303 GTCAGTGATGTTGAGCGTGAC 59.543 52.381 0.00 0.00 0.00 3.67
50 51 0.436150 CAGTGATGTTGAGCGTGACG 59.564 55.000 0.00 0.00 0.00 4.35
51 52 0.313987 AGTGATGTTGAGCGTGACGA 59.686 50.000 10.10 0.00 0.00 4.20
52 53 1.136690 GTGATGTTGAGCGTGACGAA 58.863 50.000 10.10 0.00 0.00 3.85
53 54 1.525197 GTGATGTTGAGCGTGACGAAA 59.475 47.619 10.10 0.00 0.00 3.46
54 55 1.525197 TGATGTTGAGCGTGACGAAAC 59.475 47.619 10.10 10.27 0.00 2.78
55 56 0.865769 ATGTTGAGCGTGACGAAACC 59.134 50.000 10.10 0.00 0.00 3.27
56 57 1.200839 GTTGAGCGTGACGAAACCG 59.799 57.895 10.10 0.00 0.00 4.44
57 58 1.227031 TTGAGCGTGACGAAACCGT 60.227 52.632 10.10 0.00 43.79 4.83
58 59 0.806884 TTGAGCGTGACGAAACCGTT 60.807 50.000 10.10 0.00 40.80 4.44
59 60 1.200839 GAGCGTGACGAAACCGTTG 59.799 57.895 10.10 0.00 40.80 4.10
60 61 2.154427 GAGCGTGACGAAACCGTTGG 62.154 60.000 10.10 0.00 40.80 3.77
61 62 2.247267 CGTGACGAAACCGTTGGC 59.753 61.111 0.00 0.00 40.80 4.52
62 63 2.247267 GTGACGAAACCGTTGGCG 59.753 61.111 0.00 5.52 40.80 5.69
63 64 2.202905 TGACGAAACCGTTGGCGT 60.203 55.556 10.99 10.99 40.80 5.68
64 65 2.547798 GACGAAACCGTTGGCGTC 59.452 61.111 18.32 18.32 44.83 5.19
65 66 3.272420 GACGAAACCGTTGGCGTCG 62.272 63.158 18.32 11.27 42.71 5.12
120 121 4.779733 GGGGCGTGGAGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
121 122 3.151022 GGGCGTGGAGAGGAGGAG 61.151 72.222 0.00 0.00 0.00 3.69
122 123 3.151022 GGCGTGGAGAGGAGGAGG 61.151 72.222 0.00 0.00 0.00 4.30
123 124 2.043852 GCGTGGAGAGGAGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
124 125 2.124693 GCGTGGAGAGGAGGAGGAG 61.125 68.421 0.00 0.00 0.00 3.69
125 126 1.454847 CGTGGAGAGGAGGAGGAGG 60.455 68.421 0.00 0.00 0.00 4.30
126 127 1.760480 GTGGAGAGGAGGAGGAGGC 60.760 68.421 0.00 0.00 0.00 4.70
127 128 2.123033 GGAGAGGAGGAGGAGGCC 60.123 72.222 0.00 0.00 0.00 5.19
128 129 2.520741 GAGAGGAGGAGGAGGCCG 60.521 72.222 0.00 0.00 0.00 6.13
129 130 4.150454 AGAGGAGGAGGAGGCCGG 62.150 72.222 0.00 0.00 0.00 6.13
130 131 4.144727 GAGGAGGAGGAGGCCGGA 62.145 72.222 5.05 0.00 0.00 5.14
131 132 4.150454 AGGAGGAGGAGGCCGGAG 62.150 72.222 5.05 0.00 0.00 4.63
152 153 3.822192 TCGACGGCGAGGACCATG 61.822 66.667 10.67 0.00 42.51 3.66
153 154 4.873129 CGACGGCGAGGACCATGG 62.873 72.222 16.62 11.19 40.82 3.66
154 155 4.530857 GACGGCGAGGACCATGGG 62.531 72.222 16.62 0.00 0.00 4.00
165 166 4.375406 CCATGGGGTACTCGTCCT 57.625 61.111 2.85 0.00 0.00 3.85
166 167 2.604118 CCATGGGGTACTCGTCCTT 58.396 57.895 2.85 0.00 0.00 3.36
167 168 0.178068 CCATGGGGTACTCGTCCTTG 59.822 60.000 2.85 0.00 0.00 3.61
168 169 0.462047 CATGGGGTACTCGTCCTTGC 60.462 60.000 0.00 0.00 0.00 4.01
169 170 1.623542 ATGGGGTACTCGTCCTTGCC 61.624 60.000 0.00 0.00 0.00 4.52
170 171 2.183555 GGGTACTCGTCCTTGCCG 59.816 66.667 0.00 0.00 0.00 5.69
171 172 2.183555 GGTACTCGTCCTTGCCGG 59.816 66.667 0.00 0.00 0.00 6.13
172 173 2.183555 GTACTCGTCCTTGCCGGG 59.816 66.667 2.18 0.00 0.00 5.73
173 174 3.766691 TACTCGTCCTTGCCGGGC 61.767 66.667 13.32 13.32 0.00 6.13
204 205 4.314440 GCACGGTGAGCAGGGTGA 62.314 66.667 13.29 0.00 32.23 4.02
205 206 2.357517 CACGGTGAGCAGGGTGAC 60.358 66.667 0.74 0.00 32.23 3.67
206 207 3.991051 ACGGTGAGCAGGGTGACG 61.991 66.667 0.00 0.00 0.00 4.35
266 267 4.154347 GGAGGTCCTCGGCAGCTG 62.154 72.222 10.11 10.11 0.00 4.24
267 268 4.154347 GAGGTCCTCGGCAGCTGG 62.154 72.222 17.12 0.00 0.00 4.85
269 270 4.767255 GGTCCTCGGCAGCTGGTG 62.767 72.222 17.12 1.76 0.00 4.17
270 271 4.767255 GTCCTCGGCAGCTGGTGG 62.767 72.222 17.12 10.11 0.00 4.61
281 282 4.704833 CTGGTGGCTGGTGGTCGG 62.705 72.222 0.00 0.00 0.00 4.79
310 311 5.386958 CATGGGCAATGGAAGATAAGATG 57.613 43.478 0.00 0.00 32.10 2.90
311 312 4.794311 TGGGCAATGGAAGATAAGATGA 57.206 40.909 0.00 0.00 0.00 2.92
312 313 4.722220 TGGGCAATGGAAGATAAGATGAG 58.278 43.478 0.00 0.00 0.00 2.90
313 314 4.077822 GGGCAATGGAAGATAAGATGAGG 58.922 47.826 0.00 0.00 0.00 3.86
314 315 4.202503 GGGCAATGGAAGATAAGATGAGGA 60.203 45.833 0.00 0.00 0.00 3.71
315 316 5.380043 GGCAATGGAAGATAAGATGAGGAA 58.620 41.667 0.00 0.00 0.00 3.36
316 317 5.829924 GGCAATGGAAGATAAGATGAGGAAA 59.170 40.000 0.00 0.00 0.00 3.13
317 318 6.016443 GGCAATGGAAGATAAGATGAGGAAAG 60.016 42.308 0.00 0.00 0.00 2.62
318 319 6.769822 GCAATGGAAGATAAGATGAGGAAAGA 59.230 38.462 0.00 0.00 0.00 2.52
319 320 7.284034 GCAATGGAAGATAAGATGAGGAAAGAA 59.716 37.037 0.00 0.00 0.00 2.52
320 321 8.619546 CAATGGAAGATAAGATGAGGAAAGAAC 58.380 37.037 0.00 0.00 0.00 3.01
321 322 6.341316 TGGAAGATAAGATGAGGAAAGAACG 58.659 40.000 0.00 0.00 0.00 3.95
322 323 5.755861 GGAAGATAAGATGAGGAAAGAACGG 59.244 44.000 0.00 0.00 0.00 4.44
323 324 5.283457 AGATAAGATGAGGAAAGAACGGG 57.717 43.478 0.00 0.00 0.00 5.28
324 325 4.717280 AGATAAGATGAGGAAAGAACGGGT 59.283 41.667 0.00 0.00 0.00 5.28
325 326 2.770164 AGATGAGGAAAGAACGGGTG 57.230 50.000 0.00 0.00 0.00 4.61
326 327 1.279271 AGATGAGGAAAGAACGGGTGG 59.721 52.381 0.00 0.00 0.00 4.61
327 328 1.278127 GATGAGGAAAGAACGGGTGGA 59.722 52.381 0.00 0.00 0.00 4.02
328 329 0.685097 TGAGGAAAGAACGGGTGGAG 59.315 55.000 0.00 0.00 0.00 3.86
329 330 0.036294 GAGGAAAGAACGGGTGGAGG 60.036 60.000 0.00 0.00 0.00 4.30
330 331 0.473117 AGGAAAGAACGGGTGGAGGA 60.473 55.000 0.00 0.00 0.00 3.71
331 332 0.036294 GGAAAGAACGGGTGGAGGAG 60.036 60.000 0.00 0.00 0.00 3.69
332 333 0.673956 GAAAGAACGGGTGGAGGAGC 60.674 60.000 0.00 0.00 0.00 4.70
333 334 2.450479 AAAGAACGGGTGGAGGAGCG 62.450 60.000 0.00 0.00 0.00 5.03
334 335 4.452733 GAACGGGTGGAGGAGCGG 62.453 72.222 0.00 0.00 0.00 5.52
343 344 4.373116 GAGGAGCGGGCGTGTGAA 62.373 66.667 0.00 0.00 0.00 3.18
344 345 3.876589 GAGGAGCGGGCGTGTGAAA 62.877 63.158 0.00 0.00 0.00 2.69
345 346 3.423154 GGAGCGGGCGTGTGAAAG 61.423 66.667 0.00 0.00 0.00 2.62
346 347 2.357034 GAGCGGGCGTGTGAAAGA 60.357 61.111 0.00 0.00 0.00 2.52
347 348 2.357517 AGCGGGCGTGTGAAAGAG 60.358 61.111 0.00 0.00 0.00 2.85
348 349 2.357034 GCGGGCGTGTGAAAGAGA 60.357 61.111 0.00 0.00 0.00 3.10
349 350 1.741770 GCGGGCGTGTGAAAGAGAT 60.742 57.895 0.00 0.00 0.00 2.75
350 351 0.459585 GCGGGCGTGTGAAAGAGATA 60.460 55.000 0.00 0.00 0.00 1.98
351 352 2.004583 CGGGCGTGTGAAAGAGATAA 57.995 50.000 0.00 0.00 0.00 1.75
352 353 1.927174 CGGGCGTGTGAAAGAGATAAG 59.073 52.381 0.00 0.00 0.00 1.73
353 354 2.280628 GGGCGTGTGAAAGAGATAAGG 58.719 52.381 0.00 0.00 0.00 2.69
354 355 1.666189 GGCGTGTGAAAGAGATAAGGC 59.334 52.381 0.00 0.00 0.00 4.35
355 356 2.622436 GCGTGTGAAAGAGATAAGGCT 58.378 47.619 0.00 0.00 0.00 4.58
356 357 2.605366 GCGTGTGAAAGAGATAAGGCTC 59.395 50.000 0.00 0.00 35.11 4.70
357 358 2.854777 CGTGTGAAAGAGATAAGGCTCG 59.145 50.000 0.00 0.00 39.87 5.03
358 359 3.427638 CGTGTGAAAGAGATAAGGCTCGA 60.428 47.826 0.00 0.00 39.87 4.04
359 360 3.860536 GTGTGAAAGAGATAAGGCTCGAC 59.139 47.826 0.00 0.00 39.87 4.20
360 361 3.109619 GTGAAAGAGATAAGGCTCGACG 58.890 50.000 0.00 0.00 39.87 5.12
361 362 2.099263 TGAAAGAGATAAGGCTCGACGG 59.901 50.000 0.00 0.00 39.87 4.79
362 363 1.033574 AAGAGATAAGGCTCGACGGG 58.966 55.000 0.00 0.00 39.87 5.28
363 364 0.183014 AGAGATAAGGCTCGACGGGA 59.817 55.000 0.00 0.00 39.87 5.14
364 365 1.030457 GAGATAAGGCTCGACGGGAA 58.970 55.000 0.00 0.00 0.00 3.97
365 366 1.407979 GAGATAAGGCTCGACGGGAAA 59.592 52.381 0.00 0.00 0.00 3.13
366 367 1.409427 AGATAAGGCTCGACGGGAAAG 59.591 52.381 0.00 0.00 0.00 2.62
367 368 0.179081 ATAAGGCTCGACGGGAAAGC 60.179 55.000 0.00 0.00 35.27 3.51
368 369 2.552585 TAAGGCTCGACGGGAAAGCG 62.553 60.000 0.00 0.00 36.89 4.68
376 377 4.137872 CGGGAAAGCGGCGGACTA 62.138 66.667 9.78 0.00 0.00 2.59
377 378 2.202892 GGGAAAGCGGCGGACTAG 60.203 66.667 9.78 0.00 0.00 2.57
378 379 2.890961 GGAAAGCGGCGGACTAGC 60.891 66.667 9.78 0.00 0.00 3.42
379 380 2.184579 GAAAGCGGCGGACTAGCT 59.815 61.111 9.78 0.00 43.90 3.32
380 381 2.125512 AAAGCGGCGGACTAGCTG 60.126 61.111 9.78 0.00 45.82 4.24
381 382 2.558554 GAAAGCGGCGGACTAGCTGA 62.559 60.000 9.78 0.00 45.94 4.26
382 383 2.837371 AAAGCGGCGGACTAGCTGAC 62.837 60.000 9.78 0.00 45.94 3.51
387 388 4.003534 CGGACTAGCTGACGCATG 57.996 61.111 0.00 0.00 39.10 4.06
388 389 1.589993 CGGACTAGCTGACGCATGG 60.590 63.158 0.00 0.00 39.10 3.66
389 390 1.227380 GGACTAGCTGACGCATGGG 60.227 63.158 8.44 8.44 39.10 4.00
390 391 1.676678 GGACTAGCTGACGCATGGGA 61.677 60.000 17.76 0.00 39.10 4.37
391 392 0.528684 GACTAGCTGACGCATGGGAC 60.529 60.000 17.76 11.18 39.10 4.46
392 393 1.589993 CTAGCTGACGCATGGGACG 60.590 63.158 17.76 2.94 39.10 4.79
393 394 3.716539 TAGCTGACGCATGGGACGC 62.717 63.158 17.76 16.57 39.10 5.19
422 423 3.213264 GGGACCCGACTTATGCGA 58.787 61.111 0.00 0.00 0.00 5.10
423 424 1.227176 GGGACCCGACTTATGCGAC 60.227 63.158 0.00 0.00 0.00 5.19
424 425 1.588139 GGACCCGACTTATGCGACG 60.588 63.158 0.00 0.00 0.00 5.12
425 426 1.138247 GACCCGACTTATGCGACGT 59.862 57.895 0.00 0.00 0.00 4.34
426 427 0.457337 GACCCGACTTATGCGACGTT 60.457 55.000 0.00 0.00 0.00 3.99
427 428 0.734942 ACCCGACTTATGCGACGTTG 60.735 55.000 0.00 0.00 0.00 4.10
428 429 0.734942 CCCGACTTATGCGACGTTGT 60.735 55.000 4.37 0.00 0.00 3.32
429 430 1.065358 CCGACTTATGCGACGTTGTT 58.935 50.000 4.37 0.00 0.00 2.83
430 431 1.458064 CCGACTTATGCGACGTTGTTT 59.542 47.619 4.37 0.00 0.00 2.83
431 432 2.096614 CCGACTTATGCGACGTTGTTTT 60.097 45.455 4.37 0.00 0.00 2.43
432 433 3.143279 CGACTTATGCGACGTTGTTTTC 58.857 45.455 4.37 0.00 0.00 2.29
433 434 3.362207 CGACTTATGCGACGTTGTTTTCA 60.362 43.478 4.37 0.00 0.00 2.69
434 435 4.665645 CGACTTATGCGACGTTGTTTTCAT 60.666 41.667 4.37 1.97 0.00 2.57
435 436 4.708601 ACTTATGCGACGTTGTTTTCATC 58.291 39.130 4.37 0.00 0.00 2.92
436 437 2.611974 ATGCGACGTTGTTTTCATCC 57.388 45.000 4.37 0.00 0.00 3.51
437 438 0.233590 TGCGACGTTGTTTTCATCCG 59.766 50.000 4.37 0.00 0.00 4.18
438 439 0.452122 GCGACGTTGTTTTCATCCGG 60.452 55.000 4.37 0.00 0.00 5.14
439 440 0.863144 CGACGTTGTTTTCATCCGGT 59.137 50.000 0.00 0.00 0.00 5.28
440 441 1.262151 CGACGTTGTTTTCATCCGGTT 59.738 47.619 0.00 0.00 0.00 4.44
441 442 2.646250 GACGTTGTTTTCATCCGGTTG 58.354 47.619 6.15 6.15 0.00 3.77
442 443 2.288458 GACGTTGTTTTCATCCGGTTGA 59.712 45.455 11.25 11.25 0.00 3.18
443 444 2.882137 ACGTTGTTTTCATCCGGTTGAT 59.118 40.909 15.80 0.00 0.00 2.57
444 445 3.316868 ACGTTGTTTTCATCCGGTTGATT 59.683 39.130 15.80 0.00 0.00 2.57
445 446 4.202070 ACGTTGTTTTCATCCGGTTGATTT 60.202 37.500 15.80 0.00 0.00 2.17
446 447 5.008811 ACGTTGTTTTCATCCGGTTGATTTA 59.991 36.000 15.80 0.00 0.00 1.40
447 448 5.567534 CGTTGTTTTCATCCGGTTGATTTAG 59.432 40.000 15.80 1.74 0.00 1.85
448 449 6.566942 CGTTGTTTTCATCCGGTTGATTTAGA 60.567 38.462 15.80 0.00 0.00 2.10
449 450 7.312899 GTTGTTTTCATCCGGTTGATTTAGAT 58.687 34.615 15.80 0.00 0.00 1.98
450 451 8.455682 GTTGTTTTCATCCGGTTGATTTAGATA 58.544 33.333 15.80 0.00 0.00 1.98
451 452 7.981142 TGTTTTCATCCGGTTGATTTAGATAC 58.019 34.615 15.80 6.86 0.00 2.24
452 453 7.827236 TGTTTTCATCCGGTTGATTTAGATACT 59.173 33.333 15.80 0.00 0.00 2.12
453 454 8.674607 GTTTTCATCCGGTTGATTTAGATACTT 58.325 33.333 15.80 0.00 0.00 2.24
454 455 8.801882 TTTCATCCGGTTGATTTAGATACTTT 57.198 30.769 15.80 0.00 0.00 2.66
455 456 8.801882 TTCATCCGGTTGATTTAGATACTTTT 57.198 30.769 15.80 0.00 0.00 2.27
456 457 8.433421 TCATCCGGTTGATTTAGATACTTTTC 57.567 34.615 11.25 0.00 0.00 2.29
457 458 7.497909 TCATCCGGTTGATTTAGATACTTTTCC 59.502 37.037 11.25 0.00 0.00 3.13
458 459 6.954232 TCCGGTTGATTTAGATACTTTTCCT 58.046 36.000 0.00 0.00 0.00 3.36
459 460 8.081517 TCCGGTTGATTTAGATACTTTTCCTA 57.918 34.615 0.00 0.00 0.00 2.94
460 461 8.711170 TCCGGTTGATTTAGATACTTTTCCTAT 58.289 33.333 0.00 0.00 0.00 2.57
461 462 9.338622 CCGGTTGATTTAGATACTTTTCCTATT 57.661 33.333 0.00 0.00 0.00 1.73
480 481 7.767261 TCCTATTGTTTAAAATCAACCGGATG 58.233 34.615 9.46 7.03 36.02 3.51
490 491 2.139917 TCAACCGGATGAAAACTGTCG 58.860 47.619 12.63 0.00 0.00 4.35
550 551 4.436998 CTCGTCCACCGCTCCCAC 62.437 72.222 0.00 0.00 36.19 4.61
601 602 1.202842 TCCTCCACCCGTTTCCTTTTC 60.203 52.381 0.00 0.00 0.00 2.29
613 614 4.217767 CGTTTCCTTTTCCCCCTTTTCTAG 59.782 45.833 0.00 0.00 0.00 2.43
642 643 3.130160 GCAAAGGAGAGGCAGCGG 61.130 66.667 0.00 0.00 0.00 5.52
646 647 1.893919 AAAGGAGAGGCAGCGGAGAC 61.894 60.000 0.00 0.00 0.00 3.36
732 735 2.976840 GCAATTGAAGCGCCACCGA 61.977 57.895 10.34 0.00 36.29 4.69
745 748 0.676466 CCACCGAAGCTACATGGCAA 60.676 55.000 0.00 0.00 34.17 4.52
746 749 0.447801 CACCGAAGCTACATGGCAAC 59.552 55.000 0.00 0.00 34.17 4.17
784 787 4.889856 CATCCGCCGTCATCGCCA 62.890 66.667 0.00 0.00 35.54 5.69
791 794 3.842126 CGTCATCGCCACGCACTG 61.842 66.667 0.00 0.00 0.00 3.66
792 795 4.152625 GTCATCGCCACGCACTGC 62.153 66.667 0.00 0.00 0.00 4.40
804 807 2.878429 CACTGCGTCGTAGCTCCT 59.122 61.111 10.48 0.00 38.13 3.69
814 817 3.865383 TAGCTCCTGCCATGGCCG 61.865 66.667 33.44 26.87 41.09 6.13
835 838 2.557805 CATGTTGCGTCGCAGCTT 59.442 55.556 29.93 22.76 40.35 3.74
843 846 2.580470 CGTCGCAGCTTCCGCTATG 61.580 63.158 0.00 0.00 46.99 2.23
1014 1018 2.899339 GCAATGGAGCTCCGCCTC 60.899 66.667 27.43 13.05 39.43 4.70
1043 1047 3.059982 AGCTTCACCGCAGCTACA 58.940 55.556 0.00 0.00 46.18 2.74
1068 1072 0.602106 AGCGCATCCGAGATCATTGG 60.602 55.000 11.47 0.00 36.29 3.16
1125 1129 0.961019 GCAATGGAGCTTCACCACAA 59.039 50.000 0.00 0.00 40.36 3.33
1144 1148 4.089239 TACAATGGAGCGCGGCCA 62.089 61.111 23.84 23.84 40.24 5.36
1159 1163 1.825622 GCCAGGGCTGTAATGGAGC 60.826 63.158 2.30 0.00 36.09 4.70
1164 1168 3.941836 GCTGTAATGGAGCGCCGC 61.942 66.667 2.29 0.00 36.79 6.53
1185 1189 0.599558 GTGGCTGCAATGAAGCTTCA 59.400 50.000 30.23 30.23 40.64 3.02
1257 1261 2.056223 GCCATGGCTGCAATGGAGT 61.056 57.895 34.83 0.00 46.44 3.85
1265 1269 0.742281 CTGCAATGGAGTAGCACGCT 60.742 55.000 0.00 0.00 34.13 5.07
1306 1311 1.985447 AACGATGCAATGGAGCGCTG 61.985 55.000 18.48 0.53 37.31 5.18
1357 1362 0.886043 AAGATGTGTTGCAGCGCTCA 60.886 50.000 7.13 6.15 38.76 4.26
1400 1405 2.359850 GCAGGACGGATGTGCCAA 60.360 61.111 0.00 0.00 37.08 4.52
1407 1412 2.679716 GGATGTGCCAAGGGAGCT 59.320 61.111 0.00 0.00 36.34 4.09
1443 1448 0.463620 AGGCGATCAGAAGAGGAAGC 59.536 55.000 0.00 0.00 0.00 3.86
1449 1454 0.891373 TCAGAAGAGGAAGCCGTGAG 59.109 55.000 0.00 0.00 0.00 3.51
1506 1511 1.518572 AAATCGGACGGCTACGCAG 60.519 57.895 0.00 0.00 46.04 5.18
1561 1566 6.052360 TGATTTGTAGCAGTCGCCATATAAA 58.948 36.000 0.00 0.00 39.83 1.40
1593 1598 3.188460 TCAATTGAGTTTTCCACGCTAGC 59.812 43.478 3.38 4.06 0.00 3.42
1658 1668 2.809119 CAGATCAGGCAAGCATCTCATC 59.191 50.000 0.00 0.00 0.00 2.92
1659 1669 2.706723 AGATCAGGCAAGCATCTCATCT 59.293 45.455 0.00 0.00 0.00 2.90
1660 1670 2.616634 TCAGGCAAGCATCTCATCTC 57.383 50.000 0.00 0.00 0.00 2.75
1661 1671 1.835531 TCAGGCAAGCATCTCATCTCA 59.164 47.619 0.00 0.00 0.00 3.27
1662 1672 2.438392 TCAGGCAAGCATCTCATCTCAT 59.562 45.455 0.00 0.00 0.00 2.90
1663 1673 2.809119 CAGGCAAGCATCTCATCTCATC 59.191 50.000 0.00 0.00 0.00 2.92
1687 1697 3.296709 GACCAGCCATGTCGTCCGT 62.297 63.158 0.00 0.00 0.00 4.69
1692 1702 4.429212 CCATGTCGTCCGTCGCCA 62.429 66.667 0.00 0.00 39.67 5.69
1779 1789 2.408022 GCATCGACGGCTACTCGT 59.592 61.111 3.77 0.00 46.83 4.18
1816 1826 2.186384 CGGCCAGAAGCTCTCCTG 59.814 66.667 2.24 0.00 43.05 3.86
1846 1856 4.728102 CGTCGGCGGCCACAACTA 62.728 66.667 20.71 0.00 0.00 2.24
1893 2420 1.079405 GACGAATCCAACTCCGGCA 60.079 57.895 0.00 0.00 0.00 5.69
1907 2434 1.464376 CCGGCACCATCTCCGTCTAT 61.464 60.000 0.00 0.00 43.87 1.98
1960 2487 1.070105 AGGCGCGGTACAAGTTCAA 59.930 52.632 8.83 0.00 0.00 2.69
2022 2549 0.471780 TGAGACAGGCTCCTTCACCA 60.472 55.000 0.00 0.00 43.26 4.17
2118 2648 1.154205 CGGCCATGACGAGTTCATCC 61.154 60.000 2.24 0.00 43.68 3.51
2119 2649 1.154205 GGCCATGACGAGTTCATCCG 61.154 60.000 0.00 0.00 43.68 4.18
2139 2669 1.567357 GAAGGAAGAGCTGGAGAGGT 58.433 55.000 0.00 0.00 0.00 3.85
2189 2719 1.809619 CATGATCCGGTGCGACGTT 60.810 57.895 0.00 0.00 0.00 3.99
2213 2743 2.993899 CGTCACGCAGATTAACCTTTCT 59.006 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.466982 CCGGCTACTACGTCTGCGA 61.467 63.158 0.00 0.00 42.00 5.10
1 2 2.024305 CCGGCTACTACGTCTGCG 59.976 66.667 0.00 0.00 44.93 5.18
2 3 2.412112 CCCGGCTACTACGTCTGC 59.588 66.667 0.00 0.00 0.00 4.26
3 4 2.487532 CCCCCGGCTACTACGTCTG 61.488 68.421 0.00 0.00 0.00 3.51
4 5 2.123982 CCCCCGGCTACTACGTCT 60.124 66.667 0.00 0.00 0.00 4.18
20 21 4.760047 ATCACTGACCGCACGCCC 62.760 66.667 0.00 0.00 0.00 6.13
21 22 3.490759 CATCACTGACCGCACGCC 61.491 66.667 0.00 0.00 0.00 5.68
22 23 2.317609 AACATCACTGACCGCACGC 61.318 57.895 0.00 0.00 0.00 5.34
23 24 0.943835 TCAACATCACTGACCGCACG 60.944 55.000 0.00 0.00 0.00 5.34
24 25 0.792640 CTCAACATCACTGACCGCAC 59.207 55.000 0.00 0.00 0.00 5.34
25 26 0.950555 GCTCAACATCACTGACCGCA 60.951 55.000 0.00 0.00 0.00 5.69
26 27 1.790387 GCTCAACATCACTGACCGC 59.210 57.895 0.00 0.00 0.00 5.68
27 28 0.667487 ACGCTCAACATCACTGACCG 60.667 55.000 0.00 0.00 0.00 4.79
28 29 0.792640 CACGCTCAACATCACTGACC 59.207 55.000 0.00 0.00 0.00 4.02
29 30 1.457303 GTCACGCTCAACATCACTGAC 59.543 52.381 0.00 0.00 0.00 3.51
30 31 1.783284 GTCACGCTCAACATCACTGA 58.217 50.000 0.00 0.00 0.00 3.41
31 32 0.436150 CGTCACGCTCAACATCACTG 59.564 55.000 0.00 0.00 0.00 3.66
32 33 0.313987 TCGTCACGCTCAACATCACT 59.686 50.000 0.00 0.00 0.00 3.41
33 34 1.136690 TTCGTCACGCTCAACATCAC 58.863 50.000 0.00 0.00 0.00 3.06
34 35 1.525197 GTTTCGTCACGCTCAACATCA 59.475 47.619 0.00 0.00 0.00 3.07
35 36 1.136336 GGTTTCGTCACGCTCAACATC 60.136 52.381 0.00 0.00 0.00 3.06
36 37 0.865769 GGTTTCGTCACGCTCAACAT 59.134 50.000 0.00 0.00 0.00 2.71
37 38 1.484227 CGGTTTCGTCACGCTCAACA 61.484 55.000 0.00 0.00 0.00 3.33
38 39 1.200839 CGGTTTCGTCACGCTCAAC 59.799 57.895 0.00 0.00 0.00 3.18
39 40 3.620286 CGGTTTCGTCACGCTCAA 58.380 55.556 0.00 0.00 0.00 3.02
49 50 4.067016 CCGACGCCAACGGTTTCG 62.067 66.667 9.78 9.78 46.04 3.46
103 104 4.779733 TCCTCCTCTCCACGCCCC 62.780 72.222 0.00 0.00 0.00 5.80
104 105 3.151022 CTCCTCCTCTCCACGCCC 61.151 72.222 0.00 0.00 0.00 6.13
105 106 3.151022 CCTCCTCCTCTCCACGCC 61.151 72.222 0.00 0.00 0.00 5.68
106 107 2.043852 TCCTCCTCCTCTCCACGC 60.044 66.667 0.00 0.00 0.00 5.34
107 108 1.454847 CCTCCTCCTCCTCTCCACG 60.455 68.421 0.00 0.00 0.00 4.94
108 109 1.760480 GCCTCCTCCTCCTCTCCAC 60.760 68.421 0.00 0.00 0.00 4.02
109 110 2.693017 GCCTCCTCCTCCTCTCCA 59.307 66.667 0.00 0.00 0.00 3.86
110 111 2.123033 GGCCTCCTCCTCCTCTCC 60.123 72.222 0.00 0.00 0.00 3.71
111 112 2.520741 CGGCCTCCTCCTCCTCTC 60.521 72.222 0.00 0.00 0.00 3.20
112 113 4.150454 CCGGCCTCCTCCTCCTCT 62.150 72.222 0.00 0.00 0.00 3.69
113 114 4.144727 TCCGGCCTCCTCCTCCTC 62.145 72.222 0.00 0.00 0.00 3.71
114 115 4.150454 CTCCGGCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
134 135 3.823330 ATGGTCCTCGCCGTCGAC 61.823 66.667 5.18 5.18 40.21 4.20
135 136 3.822192 CATGGTCCTCGCCGTCGA 61.822 66.667 0.00 0.00 43.28 4.20
136 137 4.873129 CCATGGTCCTCGCCGTCG 62.873 72.222 2.57 0.00 0.00 5.12
137 138 4.530857 CCCATGGTCCTCGCCGTC 62.531 72.222 11.73 0.00 0.00 4.79
140 141 2.766651 TACCCCATGGTCCTCGCC 60.767 66.667 11.73 0.00 43.06 5.54
141 142 2.029307 GAGTACCCCATGGTCCTCGC 62.029 65.000 11.73 0.00 43.06 5.03
142 143 2.125178 GAGTACCCCATGGTCCTCG 58.875 63.158 11.73 0.00 43.06 4.63
143 144 0.686769 ACGAGTACCCCATGGTCCTC 60.687 60.000 11.73 8.79 43.06 3.71
144 145 0.686769 GACGAGTACCCCATGGTCCT 60.687 60.000 11.73 0.00 43.06 3.85
145 146 1.683418 GGACGAGTACCCCATGGTCC 61.683 65.000 11.73 4.41 43.06 4.46
146 147 0.686769 AGGACGAGTACCCCATGGTC 60.687 60.000 11.73 0.00 43.06 4.02
148 149 0.178068 CAAGGACGAGTACCCCATGG 59.822 60.000 4.14 4.14 37.80 3.66
149 150 0.462047 GCAAGGACGAGTACCCCATG 60.462 60.000 0.00 0.00 0.00 3.66
150 151 1.623542 GGCAAGGACGAGTACCCCAT 61.624 60.000 0.00 0.00 0.00 4.00
151 152 2.288025 GGCAAGGACGAGTACCCCA 61.288 63.158 0.00 0.00 0.00 4.96
152 153 2.582978 GGCAAGGACGAGTACCCC 59.417 66.667 0.00 0.00 0.00 4.95
153 154 2.183555 CGGCAAGGACGAGTACCC 59.816 66.667 0.00 0.00 35.20 3.69
154 155 2.183555 CCGGCAAGGACGAGTACC 59.816 66.667 0.00 0.00 45.00 3.34
155 156 2.183555 CCCGGCAAGGACGAGTAC 59.816 66.667 0.00 0.00 45.00 2.73
156 157 3.766691 GCCCGGCAAGGACGAGTA 61.767 66.667 3.91 0.00 45.00 2.59
187 188 4.314440 TCACCCTGCTCACCGTGC 62.314 66.667 0.00 0.00 0.00 5.34
188 189 2.357517 GTCACCCTGCTCACCGTG 60.358 66.667 0.00 0.00 0.00 4.94
189 190 3.991051 CGTCACCCTGCTCACCGT 61.991 66.667 0.00 0.00 0.00 4.83
249 250 4.154347 CAGCTGCCGAGGACCTCC 62.154 72.222 16.13 3.36 0.00 4.30
250 251 4.154347 CCAGCTGCCGAGGACCTC 62.154 72.222 11.87 11.87 0.00 3.85
252 253 4.767255 CACCAGCTGCCGAGGACC 62.767 72.222 8.66 0.00 0.00 4.46
253 254 4.767255 CCACCAGCTGCCGAGGAC 62.767 72.222 8.66 0.00 0.00 3.85
264 265 4.704833 CCGACCACCAGCCACCAG 62.705 72.222 0.00 0.00 0.00 4.00
288 289 5.074804 TCATCTTATCTTCCATTGCCCATG 58.925 41.667 0.00 0.00 0.00 3.66
289 290 5.322754 CTCATCTTATCTTCCATTGCCCAT 58.677 41.667 0.00 0.00 0.00 4.00
290 291 4.446745 CCTCATCTTATCTTCCATTGCCCA 60.447 45.833 0.00 0.00 0.00 5.36
291 292 4.077822 CCTCATCTTATCTTCCATTGCCC 58.922 47.826 0.00 0.00 0.00 5.36
292 293 4.978099 TCCTCATCTTATCTTCCATTGCC 58.022 43.478 0.00 0.00 0.00 4.52
293 294 6.769822 TCTTTCCTCATCTTATCTTCCATTGC 59.230 38.462 0.00 0.00 0.00 3.56
294 295 8.619546 GTTCTTTCCTCATCTTATCTTCCATTG 58.380 37.037 0.00 0.00 0.00 2.82
295 296 7.497249 CGTTCTTTCCTCATCTTATCTTCCATT 59.503 37.037 0.00 0.00 0.00 3.16
296 297 6.989169 CGTTCTTTCCTCATCTTATCTTCCAT 59.011 38.462 0.00 0.00 0.00 3.41
297 298 6.341316 CGTTCTTTCCTCATCTTATCTTCCA 58.659 40.000 0.00 0.00 0.00 3.53
298 299 5.755861 CCGTTCTTTCCTCATCTTATCTTCC 59.244 44.000 0.00 0.00 0.00 3.46
299 300 5.755861 CCCGTTCTTTCCTCATCTTATCTTC 59.244 44.000 0.00 0.00 0.00 2.87
300 301 5.189934 ACCCGTTCTTTCCTCATCTTATCTT 59.810 40.000 0.00 0.00 0.00 2.40
301 302 4.717280 ACCCGTTCTTTCCTCATCTTATCT 59.283 41.667 0.00 0.00 0.00 1.98
302 303 4.811557 CACCCGTTCTTTCCTCATCTTATC 59.188 45.833 0.00 0.00 0.00 1.75
303 304 4.384208 CCACCCGTTCTTTCCTCATCTTAT 60.384 45.833 0.00 0.00 0.00 1.73
304 305 3.055385 CCACCCGTTCTTTCCTCATCTTA 60.055 47.826 0.00 0.00 0.00 2.10
305 306 2.290323 CCACCCGTTCTTTCCTCATCTT 60.290 50.000 0.00 0.00 0.00 2.40
306 307 1.279271 CCACCCGTTCTTTCCTCATCT 59.721 52.381 0.00 0.00 0.00 2.90
307 308 1.278127 TCCACCCGTTCTTTCCTCATC 59.722 52.381 0.00 0.00 0.00 2.92
308 309 1.279271 CTCCACCCGTTCTTTCCTCAT 59.721 52.381 0.00 0.00 0.00 2.90
309 310 0.685097 CTCCACCCGTTCTTTCCTCA 59.315 55.000 0.00 0.00 0.00 3.86
310 311 0.036294 CCTCCACCCGTTCTTTCCTC 60.036 60.000 0.00 0.00 0.00 3.71
311 312 0.473117 TCCTCCACCCGTTCTTTCCT 60.473 55.000 0.00 0.00 0.00 3.36
312 313 0.036294 CTCCTCCACCCGTTCTTTCC 60.036 60.000 0.00 0.00 0.00 3.13
313 314 0.673956 GCTCCTCCACCCGTTCTTTC 60.674 60.000 0.00 0.00 0.00 2.62
314 315 1.375326 GCTCCTCCACCCGTTCTTT 59.625 57.895 0.00 0.00 0.00 2.52
315 316 2.943978 CGCTCCTCCACCCGTTCTT 61.944 63.158 0.00 0.00 0.00 2.52
316 317 3.382832 CGCTCCTCCACCCGTTCT 61.383 66.667 0.00 0.00 0.00 3.01
317 318 4.452733 CCGCTCCTCCACCCGTTC 62.453 72.222 0.00 0.00 0.00 3.95
326 327 3.876589 TTTCACACGCCCGCTCCTC 62.877 63.158 0.00 0.00 0.00 3.71
327 328 3.883744 CTTTCACACGCCCGCTCCT 62.884 63.158 0.00 0.00 0.00 3.69
328 329 3.423154 CTTTCACACGCCCGCTCC 61.423 66.667 0.00 0.00 0.00 4.70
329 330 2.357034 TCTTTCACACGCCCGCTC 60.357 61.111 0.00 0.00 0.00 5.03
330 331 2.172483 ATCTCTTTCACACGCCCGCT 62.172 55.000 0.00 0.00 0.00 5.52
331 332 0.459585 TATCTCTTTCACACGCCCGC 60.460 55.000 0.00 0.00 0.00 6.13
332 333 1.927174 CTTATCTCTTTCACACGCCCG 59.073 52.381 0.00 0.00 0.00 6.13
333 334 2.280628 CCTTATCTCTTTCACACGCCC 58.719 52.381 0.00 0.00 0.00 6.13
334 335 1.666189 GCCTTATCTCTTTCACACGCC 59.334 52.381 0.00 0.00 0.00 5.68
335 336 2.605366 GAGCCTTATCTCTTTCACACGC 59.395 50.000 0.00 0.00 0.00 5.34
336 337 2.854777 CGAGCCTTATCTCTTTCACACG 59.145 50.000 0.00 0.00 0.00 4.49
337 338 3.860536 GTCGAGCCTTATCTCTTTCACAC 59.139 47.826 0.00 0.00 0.00 3.82
338 339 3.427638 CGTCGAGCCTTATCTCTTTCACA 60.428 47.826 0.00 0.00 0.00 3.58
339 340 3.109619 CGTCGAGCCTTATCTCTTTCAC 58.890 50.000 0.00 0.00 0.00 3.18
340 341 2.099263 CCGTCGAGCCTTATCTCTTTCA 59.901 50.000 0.00 0.00 0.00 2.69
341 342 2.544069 CCCGTCGAGCCTTATCTCTTTC 60.544 54.545 0.00 0.00 0.00 2.62
342 343 1.409427 CCCGTCGAGCCTTATCTCTTT 59.591 52.381 0.00 0.00 0.00 2.52
343 344 1.033574 CCCGTCGAGCCTTATCTCTT 58.966 55.000 0.00 0.00 0.00 2.85
344 345 0.183014 TCCCGTCGAGCCTTATCTCT 59.817 55.000 0.00 0.00 0.00 3.10
345 346 1.030457 TTCCCGTCGAGCCTTATCTC 58.970 55.000 0.00 0.00 0.00 2.75
346 347 1.409427 CTTTCCCGTCGAGCCTTATCT 59.591 52.381 0.00 0.00 0.00 1.98
347 348 1.854227 CTTTCCCGTCGAGCCTTATC 58.146 55.000 0.00 0.00 0.00 1.75
348 349 0.179081 GCTTTCCCGTCGAGCCTTAT 60.179 55.000 0.00 0.00 0.00 1.73
349 350 1.217244 GCTTTCCCGTCGAGCCTTA 59.783 57.895 0.00 0.00 0.00 2.69
350 351 2.047179 GCTTTCCCGTCGAGCCTT 60.047 61.111 0.00 0.00 0.00 4.35
351 352 4.436998 CGCTTTCCCGTCGAGCCT 62.437 66.667 0.00 0.00 32.90 4.58
359 360 4.137872 TAGTCCGCCGCTTTCCCG 62.138 66.667 0.00 0.00 0.00 5.14
360 361 2.202892 CTAGTCCGCCGCTTTCCC 60.203 66.667 0.00 0.00 0.00 3.97
361 362 2.890961 GCTAGTCCGCCGCTTTCC 60.891 66.667 0.00 0.00 0.00 3.13
362 363 2.167861 CAGCTAGTCCGCCGCTTTC 61.168 63.158 0.00 0.00 0.00 2.62
363 364 2.125512 CAGCTAGTCCGCCGCTTT 60.126 61.111 0.00 0.00 0.00 3.51
364 365 3.068691 TCAGCTAGTCCGCCGCTT 61.069 61.111 0.00 0.00 0.00 4.68
365 366 3.827898 GTCAGCTAGTCCGCCGCT 61.828 66.667 0.00 0.00 0.00 5.52
368 369 3.432051 ATGCGTCAGCTAGTCCGCC 62.432 63.158 13.56 0.72 45.18 6.13
369 370 2.105128 ATGCGTCAGCTAGTCCGC 59.895 61.111 10.42 10.42 45.42 5.54
370 371 1.589993 CCATGCGTCAGCTAGTCCG 60.590 63.158 0.00 0.00 45.42 4.79
371 372 1.227380 CCCATGCGTCAGCTAGTCC 60.227 63.158 0.00 0.00 45.42 3.85
372 373 0.528684 GTCCCATGCGTCAGCTAGTC 60.529 60.000 0.00 0.00 45.42 2.59
373 374 1.517832 GTCCCATGCGTCAGCTAGT 59.482 57.895 0.00 0.00 45.42 2.57
374 375 1.589993 CGTCCCATGCGTCAGCTAG 60.590 63.158 0.00 0.00 45.42 3.42
375 376 2.494445 CGTCCCATGCGTCAGCTA 59.506 61.111 0.00 0.00 45.42 3.32
394 395 4.139234 GGGTCCCCTACGCGACAC 62.139 72.222 15.93 0.00 0.00 3.67
399 400 1.111715 ATAAGTCGGGTCCCCTACGC 61.112 60.000 1.00 0.00 36.95 4.42
400 401 0.672342 CATAAGTCGGGTCCCCTACG 59.328 60.000 1.00 0.00 36.95 3.51
401 402 0.391966 GCATAAGTCGGGTCCCCTAC 59.608 60.000 1.00 0.67 32.61 3.18
402 403 1.111116 CGCATAAGTCGGGTCCCCTA 61.111 60.000 1.00 0.00 0.00 3.53
403 404 2.432300 CGCATAAGTCGGGTCCCCT 61.432 63.158 1.00 0.00 0.00 4.79
404 405 2.108362 CGCATAAGTCGGGTCCCC 59.892 66.667 1.00 0.00 0.00 4.81
405 406 1.227176 GTCGCATAAGTCGGGTCCC 60.227 63.158 0.00 0.00 0.00 4.46
406 407 1.588139 CGTCGCATAAGTCGGGTCC 60.588 63.158 0.00 0.00 0.00 4.46
407 408 0.457337 AACGTCGCATAAGTCGGGTC 60.457 55.000 0.00 0.00 0.00 4.46
408 409 0.734942 CAACGTCGCATAAGTCGGGT 60.735 55.000 0.00 0.00 0.00 5.28
409 410 0.734942 ACAACGTCGCATAAGTCGGG 60.735 55.000 0.00 0.00 0.00 5.14
410 411 1.065358 AACAACGTCGCATAAGTCGG 58.935 50.000 0.00 0.00 0.00 4.79
411 412 2.848562 AAACAACGTCGCATAAGTCG 57.151 45.000 0.00 0.00 0.00 4.18
412 413 4.123276 TGAAAACAACGTCGCATAAGTC 57.877 40.909 0.00 0.00 0.00 3.01
413 414 4.378046 GGATGAAAACAACGTCGCATAAGT 60.378 41.667 0.00 0.00 0.00 2.24
414 415 4.088648 GGATGAAAACAACGTCGCATAAG 58.911 43.478 0.00 0.00 0.00 1.73
415 416 3.423776 CGGATGAAAACAACGTCGCATAA 60.424 43.478 0.00 0.00 0.00 1.90
416 417 2.092995 CGGATGAAAACAACGTCGCATA 59.907 45.455 0.00 0.00 0.00 3.14
417 418 1.136085 CGGATGAAAACAACGTCGCAT 60.136 47.619 0.00 0.00 0.00 4.73
418 419 0.233590 CGGATGAAAACAACGTCGCA 59.766 50.000 0.00 0.00 0.00 5.10
419 420 0.452122 CCGGATGAAAACAACGTCGC 60.452 55.000 0.00 0.00 0.00 5.19
420 421 0.863144 ACCGGATGAAAACAACGTCG 59.137 50.000 9.46 0.00 0.00 5.12
421 422 2.288458 TCAACCGGATGAAAACAACGTC 59.712 45.455 12.63 0.00 0.00 4.34
422 423 2.290464 TCAACCGGATGAAAACAACGT 58.710 42.857 12.63 0.00 0.00 3.99
423 424 3.552604 ATCAACCGGATGAAAACAACG 57.447 42.857 19.12 0.00 34.06 4.10
424 425 6.674066 TCTAAATCAACCGGATGAAAACAAC 58.326 36.000 19.12 0.00 36.02 3.32
425 426 6.885952 TCTAAATCAACCGGATGAAAACAA 57.114 33.333 19.12 2.14 36.02 2.83
426 427 7.827236 AGTATCTAAATCAACCGGATGAAAACA 59.173 33.333 19.12 2.59 36.02 2.83
427 428 8.209917 AGTATCTAAATCAACCGGATGAAAAC 57.790 34.615 19.12 8.87 36.02 2.43
428 429 8.801882 AAGTATCTAAATCAACCGGATGAAAA 57.198 30.769 19.12 6.21 36.02 2.29
429 430 8.801882 AAAGTATCTAAATCAACCGGATGAAA 57.198 30.769 19.12 6.56 36.02 2.69
430 431 8.801882 AAAAGTATCTAAATCAACCGGATGAA 57.198 30.769 19.12 1.69 36.02 2.57
431 432 7.497909 GGAAAAGTATCTAAATCAACCGGATGA 59.502 37.037 17.51 17.51 36.02 2.92
432 433 7.499232 AGGAAAAGTATCTAAATCAACCGGATG 59.501 37.037 9.46 7.03 36.02 3.51
433 434 7.574607 AGGAAAAGTATCTAAATCAACCGGAT 58.425 34.615 9.46 0.00 38.05 4.18
434 435 6.954232 AGGAAAAGTATCTAAATCAACCGGA 58.046 36.000 9.46 0.00 0.00 5.14
435 436 8.904099 ATAGGAAAAGTATCTAAATCAACCGG 57.096 34.615 0.00 0.00 0.00 5.28
450 451 9.471084 CGGTTGATTTTAAACAATAGGAAAAGT 57.529 29.630 0.00 0.00 0.00 2.66
451 452 8.921670 CCGGTTGATTTTAAACAATAGGAAAAG 58.078 33.333 0.00 0.00 31.93 2.27
452 453 8.639761 TCCGGTTGATTTTAAACAATAGGAAAA 58.360 29.630 0.00 0.00 34.37 2.29
453 454 8.179509 TCCGGTTGATTTTAAACAATAGGAAA 57.820 30.769 0.00 0.00 34.37 3.13
454 455 7.762588 TCCGGTTGATTTTAAACAATAGGAA 57.237 32.000 0.00 2.51 34.37 3.36
455 456 7.612244 TCATCCGGTTGATTTTAAACAATAGGA 59.388 33.333 11.25 14.43 38.08 2.94
456 457 7.767261 TCATCCGGTTGATTTTAAACAATAGG 58.233 34.615 11.25 0.00 0.00 2.57
457 458 9.632807 TTTCATCCGGTTGATTTTAAACAATAG 57.367 29.630 15.80 0.00 0.00 1.73
458 459 9.982651 TTTTCATCCGGTTGATTTTAAACAATA 57.017 25.926 15.80 0.00 0.00 1.90
459 460 8.769891 GTTTTCATCCGGTTGATTTTAAACAAT 58.230 29.630 23.42 0.00 31.79 2.71
460 461 7.982354 AGTTTTCATCCGGTTGATTTTAAACAA 59.018 29.630 26.85 12.66 32.80 2.83
461 462 7.436673 CAGTTTTCATCCGGTTGATTTTAAACA 59.563 33.333 26.85 8.50 32.80 2.83
550 551 2.909662 GGAGAAGATAAGATGGAGGGGG 59.090 54.545 0.00 0.00 0.00 5.40
559 560 1.319541 CGCTCGGGGAGAAGATAAGA 58.680 55.000 0.00 0.00 0.00 2.10
601 602 3.335579 CTTGACGAACTAGAAAAGGGGG 58.664 50.000 0.00 0.00 0.00 5.40
642 643 1.410517 TGAGGATGAATCAGGCGTCTC 59.589 52.381 0.00 0.00 0.00 3.36
646 647 1.493950 GCGTGAGGATGAATCAGGCG 61.494 60.000 5.06 0.00 45.26 5.52
732 735 2.102578 GGGAATGTTGCCATGTAGCTT 58.897 47.619 0.00 0.00 38.72 3.74
745 748 2.749865 CGATGCAACGCGGGAATGT 61.750 57.895 12.47 0.00 0.00 2.71
746 749 2.023181 CGATGCAACGCGGGAATG 59.977 61.111 12.47 5.00 0.00 2.67
788 791 3.343788 GCAGGAGCTACGACGCAGT 62.344 63.158 3.46 0.00 40.82 4.40
789 792 2.580867 GCAGGAGCTACGACGCAG 60.581 66.667 3.46 0.00 37.91 5.18
790 793 4.129737 GGCAGGAGCTACGACGCA 62.130 66.667 9.79 0.00 41.70 5.24
791 794 3.432051 ATGGCAGGAGCTACGACGC 62.432 63.158 0.00 0.00 41.70 5.19
792 795 1.589993 CATGGCAGGAGCTACGACG 60.590 63.158 0.00 0.00 41.70 5.12
793 796 1.227380 CCATGGCAGGAGCTACGAC 60.227 63.158 0.00 0.00 41.70 4.34
794 797 3.094062 GCCATGGCAGGAGCTACGA 62.094 63.158 32.08 0.00 41.70 3.43
795 798 2.590007 GCCATGGCAGGAGCTACG 60.590 66.667 32.08 0.00 41.70 3.51
796 799 2.203266 GGCCATGGCAGGAGCTAC 60.203 66.667 36.56 14.15 44.11 3.58
797 800 3.865383 CGGCCATGGCAGGAGCTA 61.865 66.667 36.56 0.00 44.11 3.32
885 888 2.380410 GGTGCACTCCGTTACAGCG 61.380 63.158 17.98 0.00 0.00 5.18
971 975 0.740737 GGCGGTGCTCTATTGCAAAT 59.259 50.000 1.71 0.00 45.12 2.32
1014 1018 0.109597 GTGAAGCTCCATTGCAACCG 60.110 55.000 0.00 0.00 34.99 4.44
1043 1047 0.107456 ATCTCGGATGCGCTCCATTT 59.893 50.000 20.87 4.90 45.24 2.32
1059 1063 0.106335 CGGCAGAGCTCCAATGATCT 59.894 55.000 10.93 0.00 32.39 2.75
1125 1129 2.511600 GCCGCGCTCCATTGTAGT 60.512 61.111 5.56 0.00 0.00 2.73
1144 1148 2.190578 GCGCTCCATTACAGCCCT 59.809 61.111 0.00 0.00 32.83 5.19
1164 1168 1.870055 AAGCTTCATTGCAGCCACGG 61.870 55.000 4.61 0.00 38.09 4.94
1185 1189 2.875485 CATGACGACGTCTCCGGT 59.125 61.111 26.86 3.51 38.78 5.28
1200 1204 0.881118 AAAAAGCATCGACACCGCAT 59.119 45.000 0.00 0.00 35.37 4.73
1287 1291 1.746615 AGCGCTCCATTGCATCGTT 60.747 52.632 2.64 0.00 0.00 3.85
1306 1311 3.643978 GATCGCTGCATCACCGGC 61.644 66.667 0.00 0.00 0.00 6.13
1400 1405 2.113986 AAAGCAACGCAGCTCCCT 59.886 55.556 2.44 0.00 45.89 4.20
1407 1412 1.732917 CTTCCACCAAAGCAACGCA 59.267 52.632 0.00 0.00 0.00 5.24
1443 1448 2.883828 AACACAGCCCTCCTCACGG 61.884 63.158 0.00 0.00 0.00 4.94
1449 1454 2.270986 CCAAGCAACACAGCCCTCC 61.271 63.158 0.00 0.00 34.23 4.30
1561 1566 9.696917 GTGGAAAACTCAATTGAAAACTGATAT 57.303 29.630 9.88 0.00 0.00 1.63
1576 1581 1.343142 TGAGCTAGCGTGGAAAACTCA 59.657 47.619 9.55 0.96 0.00 3.41
1593 1598 1.341156 GGTCAGGTGGGGGAGATGAG 61.341 65.000 0.00 0.00 0.00 2.90
1633 1639 2.438392 AGATGCTTGCCTGATCTGATCA 59.562 45.455 18.61 18.61 37.76 2.92
1638 1648 2.706723 AGATGAGATGCTTGCCTGATCT 59.293 45.455 0.00 0.00 30.35 2.75
1658 1668 2.279120 GCTGGTCGCCGAGATGAG 60.279 66.667 0.00 0.00 0.00 2.90
1779 1789 1.411216 GGGGAGGATCGTCTTGGTCTA 60.411 57.143 14.65 0.00 34.37 2.59
1816 1826 2.432628 CGACGTGGAACTCCTGGC 60.433 66.667 0.00 0.00 36.82 4.85
1846 1856 1.453762 GGGGTAGTAGTCGATGCGCT 61.454 60.000 9.73 0.00 0.00 5.92
1880 2404 1.224592 GATGGTGCCGGAGTTGGAT 59.775 57.895 5.05 0.00 0.00 3.41
1893 2420 2.870175 CTGGAGATAGACGGAGATGGT 58.130 52.381 0.00 0.00 0.00 3.55
1907 2434 3.695606 GCGTGGGTCAGCTGGAGA 61.696 66.667 15.13 0.00 0.00 3.71
2003 2530 0.471780 TGGTGAAGGAGCCTGTCTCA 60.472 55.000 0.00 0.00 43.70 3.27
2022 2549 1.301479 GGACGTTTGGGAAGACGCT 60.301 57.895 0.00 0.00 42.67 5.07
2105 2635 0.530744 CCTTCCGGATGAACTCGTCA 59.469 55.000 18.51 0.00 41.67 4.35
2118 2648 0.459489 CTCTCCAGCTCTTCCTTCCG 59.541 60.000 0.00 0.00 0.00 4.30
2119 2649 0.829990 CCTCTCCAGCTCTTCCTTCC 59.170 60.000 0.00 0.00 0.00 3.46
2139 2669 3.928779 GATCAGATCCCCGCGGCA 61.929 66.667 22.85 8.89 0.00 5.69
2159 2689 2.036346 CCGGATCATGATGCAGTAGTCA 59.964 50.000 24.65 0.00 0.00 3.41
2163 2693 1.541015 GCACCGGATCATGATGCAGTA 60.541 52.381 24.65 0.00 36.30 2.74
2213 2743 4.617520 TCGTCTTGCGCCAGCCAA 62.618 61.111 4.18 0.00 44.33 4.52
2265 2804 1.815421 GGCCATACAGGTCGTGCAG 60.815 63.158 0.00 0.00 40.61 4.41
2272 2811 1.762460 CGAGGAGGGCCATACAGGT 60.762 63.158 6.18 0.00 40.61 4.00


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

AutoCloner maintained by Alex Coulton.