Multiple sequence alignment - TraesCS6B01G058600

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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 TraesCS6B01G058600 chr6B 100.000 3602 0 0 1 3602 38886363 38882762 0.000000e+00 6652.0
1 TraesCS6B01G058600 chr6A 88.752 3574 277 58 73 3602 22531887 22528395 0.000000e+00 4257.0
2 TraesCS6B01G058600 chr6D 91.802 2842 155 28 502 3315 24010185 24007394 0.000000e+00 3886.0
3 TraesCS6B01G058600 chr6D 89.262 298 24 2 3313 3602 24007137 24006840 2.040000e-97 366.0
4 TraesCS6B01G058600 chr3D 95.238 84 3 1 991 1073 24265568 24265485 8.110000e-27 132.0
5 TraesCS6B01G058600 chr3D 92.857 84 5 1 991 1073 405719036 405719119 1.760000e-23 121.0
6 TraesCS6B01G058600 chr3D 97.436 39 1 0 1 39 582172674 582172636 2.320000e-07 67.6
7 TraesCS6B01G058600 chr3B 94.048 84 4 1 991 1073 791789571 791789654 3.780000e-25 126.0
8 TraesCS6B01G058600 chr3B 97.500 40 1 0 1 40 786762285 786762324 6.450000e-08 69.4
9 TraesCS6B01G058600 chr1B 94.048 84 4 1 991 1073 107876258 107876341 3.780000e-25 126.0
10 TraesCS6B01G058600 chr4D 96.053 76 3 0 998 1073 487245067 487245142 1.360000e-24 124.0
11 TraesCS6B01G058600 chr1D 92.857 84 5 1 991 1073 425478399 425478482 1.760000e-23 121.0
12 TraesCS6B01G058600 chr1A 92.857 84 5 1 991 1073 418722593 418722676 1.760000e-23 121.0
13 TraesCS6B01G058600 chr1A 97.436 39 1 0 1 39 593633433 593633395 2.320000e-07 67.6
14 TraesCS6B01G058600 chrUn 97.500 40 1 0 1 40 116883368 116883329 6.450000e-08 69.4
15 TraesCS6B01G058600 chrUn 97.436 39 1 0 1 39 16253656 16253694 2.320000e-07 67.6
16 TraesCS6B01G058600 chrUn 97.436 39 1 0 2 40 60983069 60983107 2.320000e-07 67.6
17 TraesCS6B01G058600 chr5B 97.500 40 1 0 1 40 7205517 7205556 6.450000e-08 69.4
18 TraesCS6B01G058600 chr2B 97.500 40 1 0 1 40 756108986 756109025 6.450000e-08 69.4
19 TraesCS6B01G058600 chr5D 97.436 39 1 0 1 39 531228006 531227968 2.320000e-07 67.6


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 TraesCS6B01G058600 chr6B 38882762 38886363 3601 True 6652 6652 100.000 1 3602 1 chr6B.!!$R1 3601
1 TraesCS6B01G058600 chr6A 22528395 22531887 3492 True 4257 4257 88.752 73 3602 1 chr6A.!!$R1 3529
2 TraesCS6B01G058600 chr6D 24006840 24010185 3345 True 2126 3886 90.532 502 3602 2 chr6D.!!$R1 3100

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
29 30 0.033504 CGGGACTAATGCATAGCCGT 59.966 55.0 0.00 0.0 34.44 5.68 F
512 516 0.174617 GGAGCTCTCCTTTCCAGACG 59.825 60.0 14.64 0.0 46.16 4.18 F
1122 1181 0.396435 ACCAGTCCATCTCGTGCAAA 59.604 50.0 0.00 0.0 0.00 3.68 F
1990 2049 0.181350 GGACATGCTAAGGTCTGGGG 59.819 60.0 0.00 0.0 37.28 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1431 1490 0.438445 CGCACCGGCAATACATATCG 59.562 55.000 0.00 0.0 41.24 2.92 R
1968 2027 1.202463 CCAGACCTTAGCATGTCCTCG 60.202 57.143 0.00 0.0 31.76 4.63 R
2475 2534 1.382522 TTTCCCTTCGAGCATCATGC 58.617 50.000 0.00 0.0 45.46 4.06 R
3191 3261 0.390340 GAGCAACCATGTGAGCTCGA 60.390 55.000 9.64 0.0 43.27 4.04 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
17 18 2.259204 CAACGCGAACCGGGACTA 59.741 61.111 15.93 0.00 42.31 2.59
18 19 1.373246 CAACGCGAACCGGGACTAA 60.373 57.895 15.93 0.00 42.31 2.24
19 20 0.738412 CAACGCGAACCGGGACTAAT 60.738 55.000 15.93 0.00 42.31 1.73
20 21 0.738412 AACGCGAACCGGGACTAATG 60.738 55.000 15.93 0.00 42.31 1.90
21 22 2.522638 CGCGAACCGGGACTAATGC 61.523 63.158 6.32 0.00 42.31 3.56
22 23 1.448893 GCGAACCGGGACTAATGCA 60.449 57.895 6.32 0.00 0.00 3.96
23 24 0.814010 GCGAACCGGGACTAATGCAT 60.814 55.000 6.32 0.00 0.00 3.96
24 25 1.539496 GCGAACCGGGACTAATGCATA 60.539 52.381 6.32 0.00 0.00 3.14
25 26 2.404215 CGAACCGGGACTAATGCATAG 58.596 52.381 6.32 0.44 37.66 2.23
26 27 2.143925 GAACCGGGACTAATGCATAGC 58.856 52.381 6.32 0.00 34.78 2.97
27 28 0.396811 ACCGGGACTAATGCATAGCC 59.603 55.000 6.32 0.00 34.78 3.93
28 29 0.670546 CCGGGACTAATGCATAGCCG 60.671 60.000 0.00 7.30 37.15 5.52
29 30 0.033504 CGGGACTAATGCATAGCCGT 59.966 55.000 0.00 0.00 34.44 5.68
30 31 1.540363 CGGGACTAATGCATAGCCGTT 60.540 52.381 0.00 0.00 34.44 4.44
31 32 2.143925 GGGACTAATGCATAGCCGTTC 58.856 52.381 0.00 0.00 34.78 3.95
32 33 1.792949 GGACTAATGCATAGCCGTTCG 59.207 52.381 0.00 0.00 34.78 3.95
33 34 2.545113 GGACTAATGCATAGCCGTTCGA 60.545 50.000 0.00 0.00 34.78 3.71
34 35 3.120792 GACTAATGCATAGCCGTTCGAA 58.879 45.455 0.00 0.00 34.78 3.71
35 36 2.864343 ACTAATGCATAGCCGTTCGAAC 59.136 45.455 18.47 18.47 34.78 3.95
36 37 1.014352 AATGCATAGCCGTTCGAACC 58.986 50.000 22.07 9.45 0.00 3.62
37 38 1.151777 ATGCATAGCCGTTCGAACCG 61.152 55.000 22.07 16.66 0.00 4.44
43 44 2.356553 CCGTTCGAACCGGCTGAA 60.357 61.111 22.07 0.00 38.85 3.02
44 45 2.664436 CCGTTCGAACCGGCTGAAC 61.664 63.158 22.07 18.90 38.85 3.18
45 46 1.952133 CGTTCGAACCGGCTGAACA 60.952 57.895 24.80 0.00 41.52 3.18
46 47 1.289109 CGTTCGAACCGGCTGAACAT 61.289 55.000 24.80 0.00 41.52 2.71
47 48 0.872388 GTTCGAACCGGCTGAACATT 59.128 50.000 22.15 0.42 41.20 2.71
48 49 2.070783 GTTCGAACCGGCTGAACATTA 58.929 47.619 22.15 0.00 41.20 1.90
49 50 2.004583 TCGAACCGGCTGAACATTAG 57.995 50.000 0.00 0.00 0.00 1.73
50 51 1.006832 CGAACCGGCTGAACATTAGG 58.993 55.000 0.00 0.00 0.00 2.69
51 52 1.674817 CGAACCGGCTGAACATTAGGT 60.675 52.381 0.00 0.00 0.00 3.08
52 53 2.433436 GAACCGGCTGAACATTAGGTT 58.567 47.619 0.00 0.00 43.72 3.50
76 77 4.467198 TTTTCTACTAGCTAGTGTGGCC 57.533 45.455 32.21 0.00 37.10 5.36
99 100 3.175438 AGCTCTGGCCCTAAAATTTGT 57.825 42.857 0.00 0.00 39.73 2.83
100 101 3.092301 AGCTCTGGCCCTAAAATTTGTC 58.908 45.455 0.00 0.00 39.73 3.18
102 103 3.511540 GCTCTGGCCCTAAAATTTGTCTT 59.488 43.478 0.00 0.00 0.00 3.01
109 110 5.014202 GCCCTAAAATTTGTCTTGTCCCTA 58.986 41.667 0.00 0.00 0.00 3.53
110 111 5.125578 GCCCTAAAATTTGTCTTGTCCCTAG 59.874 44.000 0.00 0.00 0.00 3.02
115 116 0.394938 TTGTCTTGTCCCTAGCGCAA 59.605 50.000 11.47 0.00 0.00 4.85
116 117 0.394938 TGTCTTGTCCCTAGCGCAAA 59.605 50.000 11.47 0.00 0.00 3.68
117 118 1.079503 GTCTTGTCCCTAGCGCAAAG 58.920 55.000 11.47 6.47 0.00 2.77
123 124 1.134371 GTCCCTAGCGCAAAGAAGGAT 60.134 52.381 11.47 0.00 0.00 3.24
156 158 9.901724 CAATCGCATTATTATAACTCGGATAAC 57.098 33.333 7.48 0.00 0.00 1.89
160 162 8.328146 CGCATTATTATAACTCGGATAACATGG 58.672 37.037 0.00 0.00 0.00 3.66
168 170 3.322254 ACTCGGATAACATGGAGGTGATC 59.678 47.826 0.00 0.00 0.00 2.92
170 172 2.296190 CGGATAACATGGAGGTGATCGA 59.704 50.000 0.00 0.00 30.50 3.59
176 178 3.242867 ACATGGAGGTGATCGATACCAT 58.757 45.455 19.59 15.73 40.74 3.55
193 195 0.179134 CATGACGGAAGGAGGACGAC 60.179 60.000 0.00 0.00 0.00 4.34
194 196 1.321074 ATGACGGAAGGAGGACGACC 61.321 60.000 0.00 0.00 0.00 4.79
207 210 4.069232 CGACCTTCAGGGCAGCGA 62.069 66.667 0.00 0.00 46.09 4.93
218 221 2.427410 GCAGCGACGGCAGTTTTG 60.427 61.111 0.00 0.00 43.41 2.44
220 223 1.868997 CAGCGACGGCAGTTTTGAT 59.131 52.632 0.00 0.00 43.41 2.57
226 230 2.540769 CGACGGCAGTTTTGATTGTTGT 60.541 45.455 0.00 0.00 0.00 3.32
230 234 4.328712 ACGGCAGTTTTGATTGTTGTTTTC 59.671 37.500 0.00 0.00 0.00 2.29
238 242 9.382275 AGTTTTGATTGTTGTTTTCATTTAGCT 57.618 25.926 0.00 0.00 0.00 3.32
250 254 9.809096 TGTTTTCATTTAGCTTGTGATTTTACA 57.191 25.926 0.00 0.00 0.00 2.41
261 265 9.515226 AGCTTGTGATTTTACAATTTCTAGGTA 57.485 29.630 0.00 0.00 39.60 3.08
262 266 9.556030 GCTTGTGATTTTACAATTTCTAGGTAC 57.444 33.333 0.00 0.00 39.60 3.34
273 277 6.757010 ACAATTTCTAGGTACGAGCATTGTAG 59.243 38.462 15.11 0.00 40.19 2.74
285 289 4.790140 CGAGCATTGTAGCAAAGAATCAAC 59.210 41.667 0.00 0.00 36.85 3.18
286 290 5.617529 CGAGCATTGTAGCAAAGAATCAACA 60.618 40.000 0.00 0.00 36.85 3.33
287 291 5.464168 AGCATTGTAGCAAAGAATCAACAC 58.536 37.500 0.00 0.00 36.85 3.32
290 294 6.200665 GCATTGTAGCAAAGAATCAACACAAA 59.799 34.615 0.00 0.00 0.00 2.83
291 295 7.568134 GCATTGTAGCAAAGAATCAACACAAAG 60.568 37.037 0.00 0.00 0.00 2.77
292 296 5.830912 TGTAGCAAAGAATCAACACAAAGG 58.169 37.500 0.00 0.00 0.00 3.11
293 297 5.359576 TGTAGCAAAGAATCAACACAAAGGT 59.640 36.000 0.00 0.00 0.00 3.50
307 311 1.939934 CAAAGGTGCTCACGAACTTGA 59.060 47.619 0.00 0.00 0.00 3.02
309 313 0.597637 AGGTGCTCACGAACTTGACG 60.598 55.000 0.00 0.00 0.00 4.35
311 315 0.596600 GTGCTCACGAACTTGACGGA 60.597 55.000 0.00 0.00 34.93 4.69
313 317 0.992802 GCTCACGAACTTGACGGATC 59.007 55.000 0.00 0.00 34.93 3.36
317 321 1.153823 CGAACTTGACGGATCGGCT 60.154 57.895 0.00 0.00 35.04 5.52
335 339 4.032445 TCGGCTAGATTTTCGTTCATTTCG 59.968 41.667 0.00 0.00 0.00 3.46
336 340 4.032445 CGGCTAGATTTTCGTTCATTTCGA 59.968 41.667 0.00 0.00 35.50 3.71
337 341 5.493735 GGCTAGATTTTCGTTCATTTCGAG 58.506 41.667 0.00 0.00 38.52 4.04
339 343 5.954349 GCTAGATTTTCGTTCATTTCGAGTG 59.046 40.000 0.00 0.00 38.52 3.51
341 345 4.755123 AGATTTTCGTTCATTTCGAGTGGT 59.245 37.500 0.80 0.00 38.52 4.16
344 348 3.870723 TCGTTCATTTCGAGTGGTTTG 57.129 42.857 0.80 0.00 33.38 2.93
345 349 3.459145 TCGTTCATTTCGAGTGGTTTGA 58.541 40.909 0.80 0.00 33.38 2.69
346 350 3.493129 TCGTTCATTTCGAGTGGTTTGAG 59.507 43.478 0.80 0.00 33.38 3.02
347 351 3.363970 CGTTCATTTCGAGTGGTTTGAGG 60.364 47.826 0.80 0.00 0.00 3.86
348 352 3.762407 TCATTTCGAGTGGTTTGAGGA 57.238 42.857 0.80 0.00 0.00 3.71
349 353 3.664107 TCATTTCGAGTGGTTTGAGGAG 58.336 45.455 0.80 0.00 0.00 3.69
350 354 1.878953 TTTCGAGTGGTTTGAGGAGC 58.121 50.000 0.00 0.00 0.00 4.70
351 355 0.319555 TTCGAGTGGTTTGAGGAGCG 60.320 55.000 0.00 0.00 0.00 5.03
352 356 1.176619 TCGAGTGGTTTGAGGAGCGA 61.177 55.000 0.00 0.00 0.00 4.93
353 357 0.319555 CGAGTGGTTTGAGGAGCGAA 60.320 55.000 0.00 0.00 0.00 4.70
355 359 2.427506 GAGTGGTTTGAGGAGCGAAAT 58.572 47.619 0.00 0.00 0.00 2.17
356 360 2.154462 AGTGGTTTGAGGAGCGAAATG 58.846 47.619 0.00 0.00 0.00 2.32
357 361 1.880027 GTGGTTTGAGGAGCGAAATGT 59.120 47.619 0.00 0.00 0.00 2.71
358 362 2.293399 GTGGTTTGAGGAGCGAAATGTT 59.707 45.455 0.00 0.00 0.00 2.71
359 363 2.293122 TGGTTTGAGGAGCGAAATGTTG 59.707 45.455 0.00 0.00 0.00 3.33
360 364 2.552315 GGTTTGAGGAGCGAAATGTTGA 59.448 45.455 0.00 0.00 0.00 3.18
361 365 3.004315 GGTTTGAGGAGCGAAATGTTGAA 59.996 43.478 0.00 0.00 0.00 2.69
363 367 5.222631 GTTTGAGGAGCGAAATGTTGAAAT 58.777 37.500 0.00 0.00 0.00 2.17
364 368 5.452078 TTGAGGAGCGAAATGTTGAAATT 57.548 34.783 0.00 0.00 0.00 1.82
365 369 4.797471 TGAGGAGCGAAATGTTGAAATTG 58.203 39.130 0.00 0.00 0.00 2.32
366 370 4.278170 TGAGGAGCGAAATGTTGAAATTGT 59.722 37.500 0.00 0.00 0.00 2.71
367 371 5.471797 TGAGGAGCGAAATGTTGAAATTGTA 59.528 36.000 0.00 0.00 0.00 2.41
368 372 5.699839 AGGAGCGAAATGTTGAAATTGTAC 58.300 37.500 0.00 0.00 0.00 2.90
369 373 4.857037 GGAGCGAAATGTTGAAATTGTACC 59.143 41.667 0.00 0.00 0.00 3.34
370 374 5.446143 AGCGAAATGTTGAAATTGTACCA 57.554 34.783 0.00 0.00 0.00 3.25
372 376 6.092748 AGCGAAATGTTGAAATTGTACCATC 58.907 36.000 0.00 0.00 0.00 3.51
373 377 5.288472 GCGAAATGTTGAAATTGTACCATCC 59.712 40.000 0.00 0.00 0.00 3.51
374 378 5.804979 CGAAATGTTGAAATTGTACCATCCC 59.195 40.000 0.00 0.00 0.00 3.85
376 380 6.530019 AATGTTGAAATTGTACCATCCCTC 57.470 37.500 0.00 0.00 0.00 4.30
378 382 5.579047 TGTTGAAATTGTACCATCCCTCAT 58.421 37.500 0.00 0.00 0.00 2.90
379 383 6.726379 TGTTGAAATTGTACCATCCCTCATA 58.274 36.000 0.00 0.00 0.00 2.15
380 384 6.601613 TGTTGAAATTGTACCATCCCTCATAC 59.398 38.462 0.00 0.00 0.00 2.39
381 385 5.690865 TGAAATTGTACCATCCCTCATACC 58.309 41.667 0.00 0.00 0.00 2.73
382 386 4.724279 AATTGTACCATCCCTCATACCC 57.276 45.455 0.00 0.00 0.00 3.69
383 387 2.112279 TGTACCATCCCTCATACCCC 57.888 55.000 0.00 0.00 0.00 4.95
384 388 1.583611 TGTACCATCCCTCATACCCCT 59.416 52.381 0.00 0.00 0.00 4.79
385 389 2.798972 TGTACCATCCCTCATACCCCTA 59.201 50.000 0.00 0.00 0.00 3.53
386 390 3.210305 TGTACCATCCCTCATACCCCTAA 59.790 47.826 0.00 0.00 0.00 2.69
387 391 3.448277 ACCATCCCTCATACCCCTAAA 57.552 47.619 0.00 0.00 0.00 1.85
388 392 3.053826 ACCATCCCTCATACCCCTAAAC 58.946 50.000 0.00 0.00 0.00 2.01
389 393 2.375509 CCATCCCTCATACCCCTAAACC 59.624 54.545 0.00 0.00 0.00 3.27
390 394 3.327439 CATCCCTCATACCCCTAAACCT 58.673 50.000 0.00 0.00 0.00 3.50
391 395 3.519370 TCCCTCATACCCCTAAACCTT 57.481 47.619 0.00 0.00 0.00 3.50
392 396 4.647710 TCCCTCATACCCCTAAACCTTA 57.352 45.455 0.00 0.00 0.00 2.69
393 397 4.301205 TCCCTCATACCCCTAAACCTTAC 58.699 47.826 0.00 0.00 0.00 2.34
394 398 4.014973 TCCCTCATACCCCTAAACCTTACT 60.015 45.833 0.00 0.00 0.00 2.24
400 404 4.838904 ACCCCTAAACCTTACTTAGCTG 57.161 45.455 0.00 0.00 0.00 4.24
401 405 3.522343 ACCCCTAAACCTTACTTAGCTGG 59.478 47.826 0.00 0.00 0.00 4.85
403 407 4.514401 CCCTAAACCTTACTTAGCTGGTG 58.486 47.826 0.00 0.00 32.53 4.17
444 448 7.475137 TTTTCTTTCTTTCTGAAAACCAGGA 57.525 32.000 4.18 0.00 43.25 3.86
445 449 7.660030 TTTCTTTCTTTCTGAAAACCAGGAT 57.340 32.000 4.18 0.00 43.25 3.24
464 468 3.596214 GATGACAACGGCGGGAATATAT 58.404 45.455 13.24 0.00 0.00 0.86
466 470 2.103432 TGACAACGGCGGGAATATATGT 59.897 45.455 13.24 2.79 0.00 2.29
474 478 2.160417 GCGGGAATATATGTGCAGCTTC 59.840 50.000 0.00 0.00 0.00 3.86
499 503 3.151022 CGTGGGAGGAGGGAGCTC 61.151 72.222 4.71 4.71 0.00 4.09
500 504 2.366570 GTGGGAGGAGGGAGCTCT 59.633 66.667 14.64 0.00 0.00 4.09
512 516 0.174617 GGAGCTCTCCTTTCCAGACG 59.825 60.000 14.64 0.00 46.16 4.18
513 517 0.892063 GAGCTCTCCTTTCCAGACGT 59.108 55.000 6.43 0.00 0.00 4.34
584 594 2.617021 CGCTAGGGTTTTAAAGAGGCCA 60.617 50.000 5.01 0.00 0.00 5.36
628 639 1.563577 GGAAACCACTCCCTCCCTCC 61.564 65.000 0.00 0.00 0.00 4.30
629 640 1.541620 AAACCACTCCCTCCCTCCC 60.542 63.158 0.00 0.00 0.00 4.30
630 641 2.062448 AAACCACTCCCTCCCTCCCT 62.062 60.000 0.00 0.00 0.00 4.20
631 642 2.041405 CCACTCCCTCCCTCCCTC 60.041 72.222 0.00 0.00 0.00 4.30
632 643 2.041405 CACTCCCTCCCTCCCTCC 60.041 72.222 0.00 0.00 0.00 4.30
633 644 3.369388 ACTCCCTCCCTCCCTCCC 61.369 72.222 0.00 0.00 0.00 4.30
634 645 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
635 646 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
638 649 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
757 790 2.419198 CCTCTCGAATCCCCAGCG 59.581 66.667 0.00 0.00 0.00 5.18
773 806 1.380650 GCGAACCTCTCCCTCTCCT 60.381 63.158 0.00 0.00 0.00 3.69
787 830 2.411904 CTCTCCTCGCCATGATTTAGC 58.588 52.381 0.00 0.00 0.00 3.09
837 880 3.820467 TCATTCCACGAGCTGAAAAATGT 59.180 39.130 0.00 0.00 0.00 2.71
847 890 1.226018 GAAAAATGTCCGGAGCGCG 60.226 57.895 3.06 0.00 0.00 6.86
848 891 1.632046 GAAAAATGTCCGGAGCGCGA 61.632 55.000 12.10 0.00 0.00 5.87
849 892 1.635663 AAAAATGTCCGGAGCGCGAG 61.636 55.000 12.10 0.00 0.00 5.03
885 928 0.598680 CGCCTAGATTTCTCCTGGCG 60.599 60.000 19.45 19.45 45.79 5.69
902 945 2.452813 CGTTTGTCCAGATCCGCGG 61.453 63.158 22.12 22.12 0.00 6.46
946 989 1.511768 GGTCGCCAGTAGAGTGGAC 59.488 63.158 7.62 0.00 40.44 4.02
952 995 1.471119 CCAGTAGAGTGGACCGCTTA 58.529 55.000 9.42 1.24 40.44 3.09
954 997 1.134560 CAGTAGAGTGGACCGCTTACC 59.865 57.143 9.42 0.00 0.00 2.85
960 1003 1.972795 AGTGGACCGCTTACCAGTTTA 59.027 47.619 0.29 0.00 36.56 2.01
961 1004 2.028385 AGTGGACCGCTTACCAGTTTAG 60.028 50.000 0.29 0.00 36.56 1.85
993 1036 0.815615 GCTCTAATTCCAGGTGGCCG 60.816 60.000 0.00 0.00 34.44 6.13
1014 1073 0.741221 GGTGGATGAACAGGAGCGTC 60.741 60.000 0.00 0.00 0.00 5.19
1020 1079 1.078848 GAACAGGAGCGTCTGCCAT 60.079 57.895 8.85 0.00 44.31 4.40
1122 1181 0.396435 ACCAGTCCATCTCGTGCAAA 59.604 50.000 0.00 0.00 0.00 3.68
1123 1182 1.202758 ACCAGTCCATCTCGTGCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
1314 1373 3.508840 CCCGATGGCTTTGCGGTC 61.509 66.667 0.00 0.00 43.35 4.79
1364 1423 3.918220 CGATCTGCGCGCTGGTTC 61.918 66.667 33.04 26.97 0.00 3.62
1365 1424 2.815211 GATCTGCGCGCTGGTTCA 60.815 61.111 33.04 17.54 0.00 3.18
1377 1436 2.362889 GGTTCAGGGGTGCATGGG 60.363 66.667 0.00 0.00 0.00 4.00
1545 1604 4.854173 TGCATGGGTATATGAAGTGTGTT 58.146 39.130 0.00 0.00 0.00 3.32
1557 1616 1.165907 AGTGTGTTGGTGTGGATGCG 61.166 55.000 0.00 0.00 0.00 4.73
1620 1679 1.069765 CTGGACAGCGTTGGTGACT 59.930 57.895 3.74 0.00 34.87 3.41
1698 1757 4.759893 GAGGGTCACCGTCCTACT 57.240 61.111 5.09 0.00 43.47 2.57
1704 1763 1.134560 GGTCACCGTCCTACTCATGTC 59.865 57.143 0.00 0.00 0.00 3.06
1719 1778 6.109156 ACTCATGTCACAATTGTAGGTGTA 57.891 37.500 11.53 0.00 36.43 2.90
1728 1787 3.611766 ATTGTAGGTGTACTGTCTGCC 57.388 47.619 0.00 0.00 0.00 4.85
1785 1844 6.260936 GTGTCATTCATGGGTATGGAAGTAAG 59.739 42.308 0.00 0.00 34.97 2.34
1863 1922 5.073437 AGAGTGGAAGTATAGAGATGGCT 57.927 43.478 0.00 0.00 0.00 4.75
1968 2027 4.574421 GGGATAAAAGCTCTTGAGCTCTTC 59.426 45.833 23.17 16.45 45.54 2.87
1990 2049 0.181350 GGACATGCTAAGGTCTGGGG 59.819 60.000 0.00 0.00 37.28 4.96
2016 2075 5.654650 TGTTCCAAATAGTGTGACCTTTGTT 59.345 36.000 0.00 0.00 0.00 2.83
2019 2078 5.888724 TCCAAATAGTGTGACCTTTGTTTCA 59.111 36.000 0.00 0.00 0.00 2.69
2270 2329 3.501445 GGCAATGATAGATTGGCTGAGAC 59.499 47.826 12.33 0.00 46.82 3.36
2334 2393 4.222810 GGGGTTTATGTGCTTCTTTGGAAT 59.777 41.667 0.00 0.00 0.00 3.01
2337 2396 7.203218 GGGTTTATGTGCTTCTTTGGAATATC 58.797 38.462 0.00 0.00 0.00 1.63
2379 2438 5.994668 GTGGAAAGAAGCTCTGGATATAAGG 59.005 44.000 0.00 0.00 0.00 2.69
2400 2459 6.484364 AGGAAACAAATGTTGACAAGGAAT 57.516 33.333 0.00 0.00 38.44 3.01
2475 2534 0.320374 TCTTGGTACAGGACAAGGCG 59.680 55.000 8.99 0.00 40.33 5.52
2629 2688 8.627208 ATGTATACTGGCCATTTCTTCATTAG 57.373 34.615 5.51 0.00 0.00 1.73
2635 2694 6.948309 ACTGGCCATTTCTTCATTAGTAACTT 59.052 34.615 5.51 0.00 0.00 2.66
2636 2695 8.107095 ACTGGCCATTTCTTCATTAGTAACTTA 58.893 33.333 5.51 0.00 0.00 2.24
2706 2767 6.880529 CCAGAATTTTTGGATTTTGTAGCCAT 59.119 34.615 0.00 0.00 37.96 4.40
2838 2903 2.666272 TTGGGGTTTCACATGCTGTA 57.334 45.000 0.00 0.00 0.00 2.74
2856 2924 9.264719 CATGCTGTAGAGTCATTAACATTCATA 57.735 33.333 0.00 0.00 0.00 2.15
2858 2926 9.836864 TGCTGTAGAGTCATTAACATTCATATT 57.163 29.630 0.00 0.00 0.00 1.28
2903 2971 3.365868 GCGATACTTGCATTGGTTGTTGA 60.366 43.478 0.00 0.00 0.00 3.18
2904 2972 4.675146 GCGATACTTGCATTGGTTGTTGAT 60.675 41.667 0.00 0.00 0.00 2.57
2967 3035 8.604640 ATGTACATGTTTGCAATCATTTTCAA 57.395 26.923 18.26 6.28 0.00 2.69
2970 3038 9.881529 GTACATGTTTGCAATCATTTTCAATTT 57.118 25.926 18.26 0.00 0.00 1.82
3000 3068 6.922247 TTTGTTCTGTTTGTATTCGGTACA 57.078 33.333 0.00 0.00 41.46 2.90
3087 3157 6.719829 TCACTACTGTTAGATGTCTTCTGGAA 59.280 38.462 0.00 0.00 35.79 3.53
3155 3225 6.753180 AGATATTAGACGCATCAAGTGTGAT 58.247 36.000 0.00 0.00 45.80 3.06
3191 3261 7.437713 TGTTAGGTCCAAGATGTATCTCATT 57.562 36.000 0.00 0.00 36.83 2.57
3284 3354 3.225104 TCTTCTTTGTGCTGAAAGGCAT 58.775 40.909 7.81 0.00 44.34 4.40
3343 3672 6.366061 GTGTATCTTTTCTCATTTTTGCCCAC 59.634 38.462 0.00 0.00 0.00 4.61
3347 3676 6.413892 TCTTTTCTCATTTTTGCCCACTTTT 58.586 32.000 0.00 0.00 0.00 2.27
3386 3722 8.918202 TCATCAAGTTGTAAATAACTTCACCT 57.082 30.769 2.11 0.00 45.15 4.00
3391 3727 6.735130 AGTTGTAAATAACTTCACCTTGCAC 58.265 36.000 0.00 0.00 37.62 4.57
3422 3758 3.508762 GCGAGAACGAAATCTTAGGTGA 58.491 45.455 0.00 0.00 42.66 4.02
3464 3801 1.205657 ACGCCTATCGCAACATTACG 58.794 50.000 0.00 0.00 43.23 3.18
3484 3821 2.289072 CGACCACTCAACCAGAATCACT 60.289 50.000 0.00 0.00 0.00 3.41
3533 3871 6.645003 CAGACTTGCATTGTAGTGTAACACTA 59.355 38.462 0.00 0.00 43.46 2.74
3534 3872 7.170828 CAGACTTGCATTGTAGTGTAACACTAA 59.829 37.037 0.00 0.00 46.55 2.24
3535 3873 7.385205 AGACTTGCATTGTAGTGTAACACTAAG 59.615 37.037 0.00 0.00 46.55 2.18
3536 3874 6.426937 ACTTGCATTGTAGTGTAACACTAAGG 59.573 38.462 0.00 0.00 46.55 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.738412 ATTAGTCCCGGTTCGCGTTG 60.738 55.000 5.77 0.00 0.00 4.10
1 2 0.738412 CATTAGTCCCGGTTCGCGTT 60.738 55.000 5.77 0.00 0.00 4.84
2 3 1.153706 CATTAGTCCCGGTTCGCGT 60.154 57.895 5.77 0.00 0.00 6.01
3 4 2.522638 GCATTAGTCCCGGTTCGCG 61.523 63.158 0.00 0.00 0.00 5.87
4 5 0.814010 ATGCATTAGTCCCGGTTCGC 60.814 55.000 0.00 0.00 0.00 4.70
5 6 2.404215 CTATGCATTAGTCCCGGTTCG 58.596 52.381 3.54 0.00 0.00 3.95
6 7 2.143925 GCTATGCATTAGTCCCGGTTC 58.856 52.381 3.54 0.00 0.00 3.62
7 8 1.202770 GGCTATGCATTAGTCCCGGTT 60.203 52.381 3.54 0.00 0.00 4.44
8 9 0.396811 GGCTATGCATTAGTCCCGGT 59.603 55.000 3.54 0.00 0.00 5.28
9 10 0.670546 CGGCTATGCATTAGTCCCGG 60.671 60.000 3.54 0.00 32.79 5.73
10 11 0.033504 ACGGCTATGCATTAGTCCCG 59.966 55.000 3.54 12.43 38.68 5.14
11 12 2.143925 GAACGGCTATGCATTAGTCCC 58.856 52.381 3.54 0.00 0.00 4.46
12 13 1.792949 CGAACGGCTATGCATTAGTCC 59.207 52.381 3.54 0.17 0.00 3.85
13 14 2.739292 TCGAACGGCTATGCATTAGTC 58.261 47.619 3.54 0.95 0.00 2.59
14 15 2.864343 GTTCGAACGGCTATGCATTAGT 59.136 45.455 13.36 0.00 0.00 2.24
15 16 2.221055 GGTTCGAACGGCTATGCATTAG 59.779 50.000 21.34 1.51 0.00 1.73
16 17 2.206750 GGTTCGAACGGCTATGCATTA 58.793 47.619 21.34 0.00 0.00 1.90
17 18 1.014352 GGTTCGAACGGCTATGCATT 58.986 50.000 21.34 0.00 0.00 3.56
18 19 1.151777 CGGTTCGAACGGCTATGCAT 61.152 55.000 21.34 3.79 0.00 3.96
19 20 1.807981 CGGTTCGAACGGCTATGCA 60.808 57.895 21.34 0.00 0.00 3.96
20 21 2.522638 CCGGTTCGAACGGCTATGC 61.523 63.158 25.58 8.97 45.34 3.14
21 22 3.700961 CCGGTTCGAACGGCTATG 58.299 61.111 25.58 11.66 45.34 2.23
27 28 1.289109 ATGTTCAGCCGGTTCGAACG 61.289 55.000 21.34 15.88 41.52 3.95
28 29 0.872388 AATGTTCAGCCGGTTCGAAC 59.128 50.000 20.14 20.14 39.56 3.95
29 30 2.343101 CTAATGTTCAGCCGGTTCGAA 58.657 47.619 1.90 0.00 0.00 3.71
30 31 1.404986 CCTAATGTTCAGCCGGTTCGA 60.405 52.381 1.90 0.00 0.00 3.71
31 32 1.006832 CCTAATGTTCAGCCGGTTCG 58.993 55.000 1.90 0.00 0.00 3.95
32 33 2.109425 ACCTAATGTTCAGCCGGTTC 57.891 50.000 1.90 0.00 0.00 3.62
33 34 2.579410 AACCTAATGTTCAGCCGGTT 57.421 45.000 1.90 0.00 28.45 4.44
46 47 9.086758 ACACTAGCTAGTAGAAAAAGAACCTAA 57.913 33.333 25.63 0.00 34.13 2.69
47 48 8.521176 CACACTAGCTAGTAGAAAAAGAACCTA 58.479 37.037 25.63 0.00 34.13 3.08
48 49 7.379750 CACACTAGCTAGTAGAAAAAGAACCT 58.620 38.462 25.63 0.00 34.13 3.50
49 50 6.590677 CCACACTAGCTAGTAGAAAAAGAACC 59.409 42.308 25.63 0.00 34.13 3.62
50 51 6.091034 GCCACACTAGCTAGTAGAAAAAGAAC 59.909 42.308 25.63 4.46 34.13 3.01
51 52 6.164176 GCCACACTAGCTAGTAGAAAAAGAA 58.836 40.000 25.63 0.00 34.13 2.52
52 53 5.337330 GGCCACACTAGCTAGTAGAAAAAGA 60.337 44.000 25.63 0.00 34.13 2.52
53 54 4.870991 GGCCACACTAGCTAGTAGAAAAAG 59.129 45.833 25.63 13.92 34.13 2.27
54 55 4.619863 CGGCCACACTAGCTAGTAGAAAAA 60.620 45.833 25.63 0.00 34.13 1.94
55 56 3.119245 CGGCCACACTAGCTAGTAGAAAA 60.119 47.826 25.63 0.00 34.13 2.29
56 57 2.426024 CGGCCACACTAGCTAGTAGAAA 59.574 50.000 25.63 0.00 34.13 2.52
57 58 2.022195 CGGCCACACTAGCTAGTAGAA 58.978 52.381 25.63 0.00 34.13 2.10
58 59 1.211212 TCGGCCACACTAGCTAGTAGA 59.789 52.381 25.63 14.51 34.13 2.59
59 60 1.676746 TCGGCCACACTAGCTAGTAG 58.323 55.000 25.63 20.42 34.13 2.57
60 61 2.022195 CTTCGGCCACACTAGCTAGTA 58.978 52.381 25.63 6.12 34.13 1.82
61 62 0.818296 CTTCGGCCACACTAGCTAGT 59.182 55.000 20.95 20.95 36.90 2.57
62 63 0.528684 GCTTCGGCCACACTAGCTAG 60.529 60.000 19.44 19.44 34.32 3.42
63 64 0.970937 AGCTTCGGCCACACTAGCTA 60.971 55.000 2.24 0.00 40.19 3.32
64 65 2.232298 GAGCTTCGGCCACACTAGCT 62.232 60.000 2.24 8.69 44.32 3.32
65 66 1.811679 GAGCTTCGGCCACACTAGC 60.812 63.158 2.24 3.37 43.01 3.42
66 67 0.459237 CAGAGCTTCGGCCACACTAG 60.459 60.000 2.24 0.00 43.01 2.57
67 68 1.591703 CAGAGCTTCGGCCACACTA 59.408 57.895 2.24 0.00 43.01 2.74
68 69 2.345244 CAGAGCTTCGGCCACACT 59.655 61.111 2.24 0.00 43.01 3.55
69 70 2.743928 CCAGAGCTTCGGCCACAC 60.744 66.667 2.24 0.00 43.01 3.82
70 71 4.704833 GCCAGAGCTTCGGCCACA 62.705 66.667 14.82 0.00 42.82 4.17
76 77 2.044123 ATTTTAGGGCCAGAGCTTCG 57.956 50.000 6.18 0.00 39.73 3.79
99 100 0.973632 TCTTTGCGCTAGGGACAAGA 59.026 50.000 11.61 12.98 0.00 3.02
100 101 1.734465 CTTCTTTGCGCTAGGGACAAG 59.266 52.381 11.61 10.93 0.00 3.16
102 103 0.036388 CCTTCTTTGCGCTAGGGACA 60.036 55.000 11.61 5.44 0.00 4.02
109 110 2.843701 CATCCTATCCTTCTTTGCGCT 58.156 47.619 9.73 0.00 0.00 5.92
110 111 1.265365 GCATCCTATCCTTCTTTGCGC 59.735 52.381 0.00 0.00 0.00 6.09
115 116 3.406764 GCGATTGCATCCTATCCTTCTT 58.593 45.455 0.00 0.00 42.15 2.52
116 117 3.051081 GCGATTGCATCCTATCCTTCT 57.949 47.619 0.00 0.00 42.15 2.85
156 158 3.593096 CATGGTATCGATCACCTCCATG 58.407 50.000 20.70 20.70 43.61 3.66
160 162 2.351835 CCGTCATGGTATCGATCACCTC 60.352 54.545 18.66 9.90 36.96 3.85
168 170 1.000163 CCTCCTTCCGTCATGGTATCG 60.000 57.143 0.00 0.00 39.52 2.92
170 172 2.040178 GTCCTCCTTCCGTCATGGTAT 58.960 52.381 0.00 0.00 39.52 2.73
176 178 1.975407 GGTCGTCCTCCTTCCGTCA 60.975 63.158 0.00 0.00 0.00 4.35
207 210 3.518634 AACAACAATCAAAACTGCCGT 57.481 38.095 0.00 0.00 0.00 5.68
210 213 9.424659 CTAAATGAAAACAACAATCAAAACTGC 57.575 29.630 0.00 0.00 0.00 4.40
211 214 9.424659 GCTAAATGAAAACAACAATCAAAACTG 57.575 29.630 0.00 0.00 0.00 3.16
218 221 8.351495 TCACAAGCTAAATGAAAACAACAATC 57.649 30.769 0.00 0.00 0.00 2.67
220 223 8.715191 AATCACAAGCTAAATGAAAACAACAA 57.285 26.923 0.00 0.00 0.00 2.83
238 242 9.491675 TCGTACCTAGAAATTGTAAAATCACAA 57.508 29.630 0.00 0.00 42.32 3.33
250 254 5.753921 GCTACAATGCTCGTACCTAGAAATT 59.246 40.000 0.00 0.00 0.00 1.82
259 263 4.921470 TTCTTTGCTACAATGCTCGTAC 57.079 40.909 0.00 0.00 0.00 3.67
261 265 4.002982 TGATTCTTTGCTACAATGCTCGT 58.997 39.130 0.00 0.00 0.00 4.18
262 266 4.604843 TGATTCTTTGCTACAATGCTCG 57.395 40.909 0.00 0.00 0.00 5.03
273 277 3.245990 GCACCTTTGTGTTGATTCTTTGC 59.754 43.478 0.00 0.00 44.65 3.68
276 280 3.953612 TGAGCACCTTTGTGTTGATTCTT 59.046 39.130 0.00 0.00 44.65 2.52
277 281 3.316308 GTGAGCACCTTTGTGTTGATTCT 59.684 43.478 0.00 0.00 44.65 2.40
285 289 1.299541 AGTTCGTGAGCACCTTTGTG 58.700 50.000 0.00 0.00 45.65 3.33
286 290 1.670811 CAAGTTCGTGAGCACCTTTGT 59.329 47.619 0.00 0.00 0.00 2.83
287 291 1.939934 TCAAGTTCGTGAGCACCTTTG 59.060 47.619 0.00 0.00 0.00 2.77
290 294 0.597637 CGTCAAGTTCGTGAGCACCT 60.598 55.000 0.00 0.00 0.00 4.00
291 295 1.557443 CCGTCAAGTTCGTGAGCACC 61.557 60.000 0.00 0.00 0.00 5.01
292 296 0.596600 TCCGTCAAGTTCGTGAGCAC 60.597 55.000 0.00 0.00 0.00 4.40
293 297 0.317160 ATCCGTCAAGTTCGTGAGCA 59.683 50.000 0.00 0.00 0.00 4.26
294 298 0.992802 GATCCGTCAAGTTCGTGAGC 59.007 55.000 0.00 0.00 0.00 4.26
296 300 0.109458 CCGATCCGTCAAGTTCGTGA 60.109 55.000 0.00 0.00 0.00 4.35
299 303 0.099968 TAGCCGATCCGTCAAGTTCG 59.900 55.000 0.00 0.00 0.00 3.95
307 311 1.407979 ACGAAAATCTAGCCGATCCGT 59.592 47.619 0.00 0.00 0.00 4.69
309 313 3.454375 TGAACGAAAATCTAGCCGATCC 58.546 45.455 0.00 0.00 0.00 3.36
311 315 5.276868 CGAAATGAACGAAAATCTAGCCGAT 60.277 40.000 0.00 0.00 0.00 4.18
313 317 4.032445 TCGAAATGAACGAAAATCTAGCCG 59.968 41.667 0.00 0.00 36.84 5.52
317 321 5.929992 ACCACTCGAAATGAACGAAAATCTA 59.070 36.000 0.00 0.00 39.23 1.98
335 339 1.878953 TTTCGCTCCTCAAACCACTC 58.121 50.000 0.00 0.00 0.00 3.51
336 340 2.154462 CATTTCGCTCCTCAAACCACT 58.846 47.619 0.00 0.00 0.00 4.00
337 341 1.880027 ACATTTCGCTCCTCAAACCAC 59.120 47.619 0.00 0.00 0.00 4.16
339 343 2.552315 TCAACATTTCGCTCCTCAAACC 59.448 45.455 0.00 0.00 0.00 3.27
341 345 4.909696 TTTCAACATTTCGCTCCTCAAA 57.090 36.364 0.00 0.00 0.00 2.69
344 348 4.798574 ACAATTTCAACATTTCGCTCCTC 58.201 39.130 0.00 0.00 0.00 3.71
345 349 4.853924 ACAATTTCAACATTTCGCTCCT 57.146 36.364 0.00 0.00 0.00 3.69
346 350 4.857037 GGTACAATTTCAACATTTCGCTCC 59.143 41.667 0.00 0.00 0.00 4.70
347 351 5.457140 TGGTACAATTTCAACATTTCGCTC 58.543 37.500 0.00 0.00 31.92 5.03
348 352 5.446143 TGGTACAATTTCAACATTTCGCT 57.554 34.783 0.00 0.00 31.92 4.93
365 369 2.417719 AGGGGTATGAGGGATGGTAC 57.582 55.000 0.00 0.00 0.00 3.34
366 370 4.237018 GTTTAGGGGTATGAGGGATGGTA 58.763 47.826 0.00 0.00 0.00 3.25
367 371 3.053826 GTTTAGGGGTATGAGGGATGGT 58.946 50.000 0.00 0.00 0.00 3.55
368 372 2.375509 GGTTTAGGGGTATGAGGGATGG 59.624 54.545 0.00 0.00 0.00 3.51
369 373 3.327439 AGGTTTAGGGGTATGAGGGATG 58.673 50.000 0.00 0.00 0.00 3.51
370 374 3.745678 AGGTTTAGGGGTATGAGGGAT 57.254 47.619 0.00 0.00 0.00 3.85
372 376 4.304659 AGTAAGGTTTAGGGGTATGAGGG 58.695 47.826 0.00 0.00 0.00 4.30
373 377 5.970501 AAGTAAGGTTTAGGGGTATGAGG 57.029 43.478 0.00 0.00 0.00 3.86
374 378 6.326843 AGCTAAGTAAGGTTTAGGGGTATGAG 59.673 42.308 0.00 0.00 29.36 2.90
376 380 6.289064 CAGCTAAGTAAGGTTTAGGGGTATG 58.711 44.000 0.00 0.00 32.16 2.39
378 382 4.718276 CCAGCTAAGTAAGGTTTAGGGGTA 59.282 45.833 0.00 0.00 32.16 3.69
379 383 3.522343 CCAGCTAAGTAAGGTTTAGGGGT 59.478 47.826 0.00 0.00 32.16 4.95
380 384 3.522343 ACCAGCTAAGTAAGGTTTAGGGG 59.478 47.826 0.00 0.00 32.16 4.79
381 385 4.224370 TCACCAGCTAAGTAAGGTTTAGGG 59.776 45.833 0.00 0.00 32.16 3.53
382 386 5.416271 TCACCAGCTAAGTAAGGTTTAGG 57.584 43.478 0.00 0.00 32.16 2.69
383 387 7.201530 CGAAATCACCAGCTAAGTAAGGTTTAG 60.202 40.741 0.00 0.00 32.16 1.85
384 388 6.592607 CGAAATCACCAGCTAAGTAAGGTTTA 59.407 38.462 0.00 0.00 32.16 2.01
385 389 5.411669 CGAAATCACCAGCTAAGTAAGGTTT 59.588 40.000 0.00 0.00 32.16 3.27
386 390 4.935808 CGAAATCACCAGCTAAGTAAGGTT 59.064 41.667 0.00 0.00 32.16 3.50
387 391 4.020485 ACGAAATCACCAGCTAAGTAAGGT 60.020 41.667 0.00 0.00 35.94 3.50
388 392 4.504858 ACGAAATCACCAGCTAAGTAAGG 58.495 43.478 0.00 0.00 0.00 2.69
389 393 5.637810 TGAACGAAATCACCAGCTAAGTAAG 59.362 40.000 0.00 0.00 0.00 2.34
390 394 5.543714 TGAACGAAATCACCAGCTAAGTAA 58.456 37.500 0.00 0.00 0.00 2.24
391 395 5.142061 TGAACGAAATCACCAGCTAAGTA 57.858 39.130 0.00 0.00 0.00 2.24
392 396 3.997021 CTGAACGAAATCACCAGCTAAGT 59.003 43.478 0.00 0.00 0.00 2.24
393 397 3.997021 ACTGAACGAAATCACCAGCTAAG 59.003 43.478 0.00 0.00 0.00 2.18
394 398 4.002906 ACTGAACGAAATCACCAGCTAA 57.997 40.909 0.00 0.00 0.00 3.09
422 426 6.833416 TCATCCTGGTTTTCAGAAAGAAAGAA 59.167 34.615 0.00 0.00 46.24 2.52
423 427 6.263168 GTCATCCTGGTTTTCAGAAAGAAAGA 59.737 38.462 0.00 0.00 46.24 2.52
424 428 6.039717 TGTCATCCTGGTTTTCAGAAAGAAAG 59.960 38.462 0.00 0.00 46.24 2.62
426 430 5.445069 TGTCATCCTGGTTTTCAGAAAGAA 58.555 37.500 0.00 0.00 46.18 2.52
427 431 5.047566 TGTCATCCTGGTTTTCAGAAAGA 57.952 39.130 0.00 0.00 46.18 2.52
428 432 5.523369 GTTGTCATCCTGGTTTTCAGAAAG 58.477 41.667 0.00 0.00 46.18 2.62
429 433 4.036262 CGTTGTCATCCTGGTTTTCAGAAA 59.964 41.667 0.00 0.00 46.18 2.52
430 434 3.563808 CGTTGTCATCCTGGTTTTCAGAA 59.436 43.478 0.00 0.00 46.18 3.02
431 435 3.138304 CGTTGTCATCCTGGTTTTCAGA 58.862 45.455 0.00 0.00 46.18 3.27
432 436 2.226437 CCGTTGTCATCCTGGTTTTCAG 59.774 50.000 0.00 0.00 43.00 3.02
444 448 3.244422 ACATATATTCCCGCCGTTGTCAT 60.244 43.478 0.00 0.00 0.00 3.06
445 449 2.103432 ACATATATTCCCGCCGTTGTCA 59.897 45.455 0.00 0.00 0.00 3.58
494 498 0.892063 ACGTCTGGAAAGGAGAGCTC 59.108 55.000 5.27 5.27 0.00 4.09
495 499 0.892063 GACGTCTGGAAAGGAGAGCT 59.108 55.000 8.70 0.00 0.00 4.09
496 500 0.456995 CGACGTCTGGAAAGGAGAGC 60.457 60.000 14.70 0.00 0.00 4.09
497 501 0.882474 ACGACGTCTGGAAAGGAGAG 59.118 55.000 14.70 0.00 0.00 3.20
498 502 0.879765 GACGACGTCTGGAAAGGAGA 59.120 55.000 20.52 0.00 0.00 3.71
499 503 0.596577 TGACGACGTCTGGAAAGGAG 59.403 55.000 26.86 0.00 33.15 3.69
500 504 0.596577 CTGACGACGTCTGGAAAGGA 59.403 55.000 26.86 4.98 33.15 3.36
512 516 4.148825 AGCGGATGGGCTGACGAC 62.149 66.667 0.00 0.00 42.86 4.34
584 594 1.207488 TGTTATGGAGGCTGGCTGGT 61.207 55.000 9.06 0.00 0.00 4.00
598 608 3.421844 GAGTGGTTTCCTTGGCTGTTAT 58.578 45.455 0.00 0.00 0.00 1.89
757 790 1.388837 GCGAGGAGAGGGAGAGGTTC 61.389 65.000 0.00 0.00 0.00 3.62
773 806 0.179234 TTCGGGCTAAATCATGGCGA 59.821 50.000 0.00 0.00 0.00 5.54
885 928 2.750888 GCCGCGGATCTGGACAAAC 61.751 63.158 33.48 1.41 0.00 2.93
902 945 4.876081 CAAATCGCCGCAGCTCGC 62.876 66.667 0.00 0.00 36.60 5.03
927 970 2.044555 TCCACTCTACTGGCGACCG 61.045 63.158 0.00 0.00 0.00 4.79
929 972 1.511768 GGTCCACTCTACTGGCGAC 59.488 63.158 0.00 0.00 0.00 5.19
946 989 1.338769 ACTGGCTAAACTGGTAAGCGG 60.339 52.381 0.00 0.00 37.11 5.52
952 995 3.596214 CGACATTACTGGCTAAACTGGT 58.404 45.455 0.00 0.00 0.00 4.00
954 997 2.351726 GCCGACATTACTGGCTAAACTG 59.648 50.000 0.00 0.00 45.40 3.16
993 1036 2.109126 GCTCCTGTTCATCCACCGC 61.109 63.158 0.00 0.00 0.00 5.68
1014 1073 3.200593 GCGAGCAGGTGATGGCAG 61.201 66.667 0.00 0.00 35.26 4.85
1020 1079 4.007644 CACTGGGCGAGCAGGTGA 62.008 66.667 0.00 0.00 0.00 4.02
1078 1137 1.396653 GGATGGAGGCCATTGACAAG 58.603 55.000 5.01 0.00 45.26 3.16
1080 1139 1.213619 TGGGATGGAGGCCATTGACA 61.214 55.000 5.01 0.00 45.26 3.58
1081 1140 0.466922 CTGGGATGGAGGCCATTGAC 60.467 60.000 5.01 0.00 45.26 3.18
1082 1141 0.920763 ACTGGGATGGAGGCCATTGA 60.921 55.000 5.01 0.00 45.26 2.57
1084 1143 1.215423 GTTACTGGGATGGAGGCCATT 59.785 52.381 5.01 0.00 45.26 3.16
1095 1154 2.467880 GAGATGGACTGGTTACTGGGA 58.532 52.381 0.00 0.00 0.00 4.37
1347 1406 3.918220 GAACCAGCGCGCAGATCG 61.918 66.667 35.10 15.27 42.12 3.69
1364 1423 2.866523 AATGAGCCCATGCACCCCTG 62.867 60.000 0.00 0.00 41.13 4.45
1365 1424 2.172229 AAATGAGCCCATGCACCCCT 62.172 55.000 0.00 0.00 41.13 4.79
1422 1481 2.663602 GCAATACATATCGACCAGAGCG 59.336 50.000 0.00 0.00 0.00 5.03
1431 1490 0.438445 CGCACCGGCAATACATATCG 59.562 55.000 0.00 0.00 41.24 2.92
1464 1523 2.992689 TCGAACACCCCTAGCGCA 60.993 61.111 11.47 0.00 0.00 6.09
1557 1616 1.578206 GGTCAAAGAAGGACAGCGCC 61.578 60.000 2.29 0.00 37.00 6.53
1561 1620 2.350522 CATCCGGTCAAAGAAGGACAG 58.649 52.381 0.00 0.00 37.00 3.51
1644 1703 4.202050 CCAAAAATTTCTAGAGCCCGGATG 60.202 45.833 0.73 0.00 0.00 3.51
1650 1709 6.039829 CCATCCTACCAAAAATTTCTAGAGCC 59.960 42.308 0.00 0.00 0.00 4.70
1698 1757 5.931724 CAGTACACCTACAATTGTGACATGA 59.068 40.000 21.42 0.00 36.35 3.07
1704 1763 4.152402 GCAGACAGTACACCTACAATTGTG 59.848 45.833 21.42 7.85 38.44 3.33
1719 1778 3.619767 TCAGCGCAGGCAGACAGT 61.620 61.111 11.47 0.00 43.41 3.55
1728 1787 1.703438 GAGAGCCAATGTCAGCGCAG 61.703 60.000 11.47 0.00 0.00 5.18
1806 1865 5.528690 GTCCATCAGAGCATTGCTAACAATA 59.471 40.000 11.96 0.00 44.83 1.90
1863 1922 2.011222 ACTTCTTCGAACACGGCAAAA 58.989 42.857 0.00 0.00 0.00 2.44
1968 2027 1.202463 CCAGACCTTAGCATGTCCTCG 60.202 57.143 0.00 0.00 31.76 4.63
2016 2075 1.677576 CTGCAGGCTGACAAAACTGAA 59.322 47.619 20.86 0.00 32.86 3.02
2019 2078 1.458639 GGCTGCAGGCTGACAAAACT 61.459 55.000 31.40 0.00 41.46 2.66
2283 2342 7.350921 TCATCCCCTGGTTCTCTCTTTATAATT 59.649 37.037 0.00 0.00 0.00 1.40
2334 2393 5.896106 CCACCTATCTGATGAGGCATAGATA 59.104 44.000 0.00 0.00 36.17 1.98
2337 2396 4.092279 TCCACCTATCTGATGAGGCATAG 58.908 47.826 0.00 0.00 36.17 2.23
2379 2438 9.696917 AAGATATTCCTTGTCAACATTTGTTTC 57.303 29.630 0.00 0.00 35.83 2.78
2475 2534 1.382522 TTTCCCTTCGAGCATCATGC 58.617 50.000 0.00 0.00 45.46 4.06
2550 2609 6.716628 AGATTAATGAGTTTTCTTCCAGTGCA 59.283 34.615 0.00 0.00 0.00 4.57
2551 2610 7.025963 CAGATTAATGAGTTTTCTTCCAGTGC 58.974 38.462 0.00 0.00 0.00 4.40
2706 2767 8.962884 ATGAACAGTGCATTAATCACAGTATA 57.037 30.769 15.69 9.45 33.90 1.47
2804 2865 6.014669 TGAAACCCCAATCAGAAAAATACAGG 60.015 38.462 0.00 0.00 0.00 4.00
2878 2946 3.005261 ACAACCAATGCAAGTATCGCAAA 59.995 39.130 0.00 0.00 43.84 3.68
2879 2947 2.556189 ACAACCAATGCAAGTATCGCAA 59.444 40.909 0.00 0.00 43.84 4.85
2935 3003 7.304735 TGATTGCAAACATGTACATAACTCAC 58.695 34.615 8.32 0.00 0.00 3.51
2970 3038 7.486551 CCGAATACAAACAGAACAAAACAAGAA 59.513 33.333 0.00 0.00 0.00 2.52
3059 3127 7.371159 CAGAAGACATCTAACAGTAGTGAACA 58.629 38.462 4.09 0.00 36.32 3.18
3060 3128 6.809196 CCAGAAGACATCTAACAGTAGTGAAC 59.191 42.308 4.09 0.00 36.32 3.18
3087 3157 4.712051 TTTCATCTCCATCGATCCCATT 57.288 40.909 0.00 0.00 0.00 3.16
3155 3225 3.764434 TGGACCTAACAACAGTGCAAAAA 59.236 39.130 0.00 0.00 0.00 1.94
3191 3261 0.390340 GAGCAACCATGTGAGCTCGA 60.390 55.000 9.64 0.00 43.27 4.04
3386 3722 2.048597 CGCCTGGTCTACGTGCAA 60.049 61.111 0.00 0.00 0.00 4.08
3391 3727 1.226323 CGTTCTCGCCTGGTCTACG 60.226 63.158 0.00 0.00 0.00 3.51
3464 3801 3.070018 CAGTGATTCTGGTTGAGTGGTC 58.930 50.000 0.00 0.00 40.23 4.02
3484 3821 0.538746 TCGGGGTCATAGCTATCGCA 60.539 55.000 2.34 0.00 39.10 5.10
3561 3899 6.787458 TCCTATTTGAAGTAGGATGAGGCATA 59.213 38.462 11.88 0.00 42.07 3.14


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

AutoCloner maintained by Alex Coulton.