Multiple sequence alignment - TraesCS7A01G224300

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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 TraesCS7A01G224300 chr7A 100.000 3531 0 0 1 3531 193616600 193620130 0.000000e+00 6521
1 TraesCS7A01G224300 chr7A 73.181 1141 245 43 1436 2535 164793292 164792172 4.340000e-94 355
2 TraesCS7A01G224300 chr7A 91.954 87 2 4 367 449 316538466 316538381 2.230000e-22 117
3 TraesCS7A01G224300 chr7D 91.179 1984 95 31 572 2533 185811020 185812945 0.000000e+00 2621
4 TraesCS7A01G224300 chr7D 88.975 644 55 9 2610 3242 185812974 185813612 0.000000e+00 782
5 TraesCS7A01G224300 chr7D 91.102 236 17 2 3235 3470 185813964 185814195 2.050000e-82 316
6 TraesCS7A01G224300 chr7D 74.449 681 149 21 1870 2532 163593515 163592842 1.620000e-68 270
7 TraesCS7A01G224300 chr7D 90.805 87 3 4 367 449 283453547 283453632 1.040000e-20 111
8 TraesCS7A01G224300 chr7D 87.255 102 7 5 357 453 485090973 485090873 1.040000e-20 111
9 TraesCS7A01G224300 chr7B 87.189 2131 150 59 447 2534 328553592 328555642 0.000000e+00 2309
10 TraesCS7A01G224300 chr7B 87.651 413 38 7 2714 3118 328571094 328571501 5.340000e-128 468
11 TraesCS7A01G224300 chr7B 81.290 310 32 9 3240 3531 328584536 328584837 9.860000e-56 228
12 TraesCS7A01G224300 chr7B 90.845 142 8 3 2583 2722 328555655 328555793 6.020000e-43 185
13 TraesCS7A01G224300 chr7B 91.954 87 2 4 367 449 251666408 251666323 2.230000e-22 117
14 TraesCS7A01G224300 chrUn 99.772 879 2 0 2566 3444 462250173 462249295 0.000000e+00 1613
15 TraesCS7A01G224300 chrUn 99.870 771 1 0 1794 2564 382006201 382005431 0.000000e+00 1419
16 TraesCS7A01G224300 chrUn 90.805 87 3 4 366 448 68883267 68883352 1.040000e-20 111
17 TraesCS7A01G224300 chrUn 87.500 96 8 3 365 456 100223737 100223832 1.340000e-19 108
18 TraesCS7A01G224300 chr5A 87.500 168 5 3 1 163 709158866 709159022 2.800000e-41 180
19 TraesCS7A01G224300 chr6B 90.805 87 7 1 365 450 682857095 682857009 8.010000e-22 115
20 TraesCS7A01G224300 chr4B 89.011 91 7 2 361 448 108879953 108879863 3.730000e-20 110
21 TraesCS7A01G224300 chr3D 89.773 88 6 2 365 449 316561583 316561670 3.730000e-20 110


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 TraesCS7A01G224300 chr7A 193616600 193620130 3530 False 6521.000000 6521 100.000000 1 3531 1 chr7A.!!$F1 3530
1 TraesCS7A01G224300 chr7A 164792172 164793292 1120 True 355.000000 355 73.181000 1436 2535 1 chr7A.!!$R1 1099
2 TraesCS7A01G224300 chr7D 185811020 185814195 3175 False 1239.666667 2621 90.418667 572 3470 3 chr7D.!!$F2 2898
3 TraesCS7A01G224300 chr7D 163592842 163593515 673 True 270.000000 270 74.449000 1870 2532 1 chr7D.!!$R1 662
4 TraesCS7A01G224300 chr7B 328553592 328555793 2201 False 1247.000000 2309 89.017000 447 2722 2 chr7B.!!$F3 2275
5 TraesCS7A01G224300 chrUn 462249295 462250173 878 True 1613.000000 1613 99.772000 2566 3444 1 chrUn.!!$R2 878
6 TraesCS7A01G224300 chrUn 382005431 382006201 770 True 1419.000000 1419 99.870000 1794 2564 1 chrUn.!!$R1 770

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
353 354 0.031857 TTGAAAGCCGTCCGTCGTAA 59.968 50.0 0.0 0.0 37.94 3.18 F
356 357 0.032540 AAAGCCGTCCGTCGTAAGTT 59.967 50.0 0.0 0.0 37.94 2.66 F
705 709 0.039888 CGGGCGTTAAAACCTTGTGG 60.040 55.0 0.0 0.0 39.83 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1172 1212 1.300931 GCACGTCCTGTTGCAGAGA 60.301 57.895 0.0 0.0 32.44 3.10 R
1729 1774 1.600636 CTGCAGCCCGTTCTTCCAA 60.601 57.895 0.0 0.0 0.00 3.53 R
2564 2639 0.966875 ATGCACATTGATGGCCGTGT 60.967 50.000 0.0 0.0 0.00 4.49 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
25 26 5.163281 CATTTCATGGAGGGATAGGAGAG 57.837 47.826 0.00 0.00 0.00 3.20
26 27 4.559576 TTTCATGGAGGGATAGGAGAGA 57.440 45.455 0.00 0.00 0.00 3.10
27 28 3.824001 TCATGGAGGGATAGGAGAGAG 57.176 52.381 0.00 0.00 0.00 3.20
28 29 3.340403 TCATGGAGGGATAGGAGAGAGA 58.660 50.000 0.00 0.00 0.00 3.10
29 30 3.729524 TCATGGAGGGATAGGAGAGAGAA 59.270 47.826 0.00 0.00 0.00 2.87
30 31 3.893753 TGGAGGGATAGGAGAGAGAAG 57.106 52.381 0.00 0.00 0.00 2.85
31 32 2.448961 TGGAGGGATAGGAGAGAGAAGG 59.551 54.545 0.00 0.00 0.00 3.46
32 33 2.525368 GAGGGATAGGAGAGAGAAGGC 58.475 57.143 0.00 0.00 0.00 4.35
33 34 2.110011 GAGGGATAGGAGAGAGAAGGCT 59.890 54.545 0.00 0.00 0.00 4.58
34 35 2.522273 AGGGATAGGAGAGAGAAGGCTT 59.478 50.000 0.00 0.00 0.00 4.35
35 36 3.051419 AGGGATAGGAGAGAGAAGGCTTT 60.051 47.826 0.00 0.00 0.00 3.51
36 37 3.070878 GGGATAGGAGAGAGAAGGCTTTG 59.929 52.174 0.00 0.00 0.00 2.77
37 38 3.070878 GGATAGGAGAGAGAAGGCTTTGG 59.929 52.174 0.00 0.00 0.00 3.28
38 39 0.617935 AGGAGAGAGAAGGCTTTGGC 59.382 55.000 0.00 0.00 37.82 4.52
39 40 0.617935 GGAGAGAGAAGGCTTTGGCT 59.382 55.000 0.00 0.00 41.24 4.75
40 41 1.834263 GGAGAGAGAAGGCTTTGGCTA 59.166 52.381 0.00 0.00 37.50 3.93
41 42 2.237392 GGAGAGAGAAGGCTTTGGCTAA 59.763 50.000 0.00 0.00 37.50 3.09
42 43 3.307762 GGAGAGAGAAGGCTTTGGCTAAA 60.308 47.826 0.00 0.00 37.50 1.85
43 44 4.522114 GAGAGAGAAGGCTTTGGCTAAAT 58.478 43.478 0.00 0.00 37.50 1.40
44 45 4.268359 AGAGAGAAGGCTTTGGCTAAATG 58.732 43.478 0.00 0.00 37.50 2.32
45 46 3.359950 AGAGAAGGCTTTGGCTAAATGG 58.640 45.455 0.00 0.00 37.50 3.16
46 47 3.010584 AGAGAAGGCTTTGGCTAAATGGA 59.989 43.478 0.00 0.00 37.50 3.41
47 48 3.359950 AGAAGGCTTTGGCTAAATGGAG 58.640 45.455 0.00 0.00 37.50 3.86
48 49 2.149973 AGGCTTTGGCTAAATGGAGG 57.850 50.000 0.00 0.00 36.44 4.30
49 50 1.114627 GGCTTTGGCTAAATGGAGGG 58.885 55.000 0.00 0.00 38.73 4.30
50 51 1.619704 GGCTTTGGCTAAATGGAGGGT 60.620 52.381 0.00 0.00 38.73 4.34
51 52 2.179427 GCTTTGGCTAAATGGAGGGTT 58.821 47.619 0.00 0.00 35.22 4.11
52 53 2.567169 GCTTTGGCTAAATGGAGGGTTT 59.433 45.455 0.00 0.00 35.22 3.27
53 54 3.617288 GCTTTGGCTAAATGGAGGGTTTG 60.617 47.826 0.00 0.00 35.22 2.93
54 55 2.230130 TGGCTAAATGGAGGGTTTGG 57.770 50.000 0.00 0.00 0.00 3.28
55 56 1.272985 TGGCTAAATGGAGGGTTTGGG 60.273 52.381 0.00 0.00 0.00 4.12
56 57 0.824109 GCTAAATGGAGGGTTTGGGC 59.176 55.000 0.00 0.00 0.00 5.36
57 58 1.485124 CTAAATGGAGGGTTTGGGCC 58.515 55.000 0.00 0.00 0.00 5.80
58 59 1.007118 CTAAATGGAGGGTTTGGGCCT 59.993 52.381 4.53 0.00 0.00 5.19
59 60 0.545071 AAATGGAGGGTTTGGGCCTG 60.545 55.000 4.53 0.00 0.00 4.85
60 61 1.442886 AATGGAGGGTTTGGGCCTGA 61.443 55.000 4.53 0.00 0.00 3.86
61 62 1.224003 ATGGAGGGTTTGGGCCTGAT 61.224 55.000 4.53 0.00 0.00 2.90
62 63 1.388133 GGAGGGTTTGGGCCTGATT 59.612 57.895 4.53 0.00 0.00 2.57
63 64 0.684479 GGAGGGTTTGGGCCTGATTC 60.684 60.000 4.53 0.00 0.00 2.52
64 65 1.000896 AGGGTTTGGGCCTGATTCG 60.001 57.895 4.53 0.00 0.00 3.34
65 66 2.052104 GGGTTTGGGCCTGATTCGG 61.052 63.158 4.53 0.00 0.00 4.30
66 67 1.001393 GGTTTGGGCCTGATTCGGA 60.001 57.895 4.53 0.00 0.00 4.55
67 68 0.395724 GGTTTGGGCCTGATTCGGAT 60.396 55.000 4.53 0.00 0.00 4.18
68 69 1.474330 GTTTGGGCCTGATTCGGATT 58.526 50.000 4.53 0.00 0.00 3.01
69 70 1.824852 GTTTGGGCCTGATTCGGATTT 59.175 47.619 4.53 0.00 0.00 2.17
70 71 2.230130 TTGGGCCTGATTCGGATTTT 57.770 45.000 4.53 0.00 0.00 1.82
71 72 1.762708 TGGGCCTGATTCGGATTTTC 58.237 50.000 4.53 0.00 0.00 2.29
72 73 1.284785 TGGGCCTGATTCGGATTTTCT 59.715 47.619 4.53 0.00 0.00 2.52
73 74 1.678101 GGGCCTGATTCGGATTTTCTG 59.322 52.381 0.84 0.00 0.00 3.02
74 75 2.643551 GGCCTGATTCGGATTTTCTGA 58.356 47.619 0.00 0.00 0.00 3.27
75 76 3.016736 GGCCTGATTCGGATTTTCTGAA 58.983 45.455 0.00 1.51 44.92 3.02
76 77 3.443681 GGCCTGATTCGGATTTTCTGAAA 59.556 43.478 0.00 0.00 44.12 2.69
77 78 4.082245 GGCCTGATTCGGATTTTCTGAAAA 60.082 41.667 17.04 17.04 44.12 2.29
78 79 5.469479 GCCTGATTCGGATTTTCTGAAAAA 58.531 37.500 18.43 3.44 44.12 1.94
188 189 8.716646 TGTAACTGTCATGATATTACTTGGTG 57.283 34.615 19.26 0.26 0.00 4.17
189 190 8.318412 TGTAACTGTCATGATATTACTTGGTGT 58.682 33.333 19.26 0.75 0.00 4.16
190 191 7.849804 AACTGTCATGATATTACTTGGTGTC 57.150 36.000 0.00 0.00 0.00 3.67
191 192 7.187824 ACTGTCATGATATTACTTGGTGTCT 57.812 36.000 0.00 0.00 0.00 3.41
192 193 7.624549 ACTGTCATGATATTACTTGGTGTCTT 58.375 34.615 0.00 0.00 0.00 3.01
193 194 8.758829 ACTGTCATGATATTACTTGGTGTCTTA 58.241 33.333 0.00 0.00 0.00 2.10
194 195 9.254133 CTGTCATGATATTACTTGGTGTCTTAG 57.746 37.037 0.00 0.00 0.00 2.18
195 196 8.204160 TGTCATGATATTACTTGGTGTCTTAGG 58.796 37.037 0.00 0.00 0.00 2.69
196 197 8.421784 GTCATGATATTACTTGGTGTCTTAGGA 58.578 37.037 0.00 0.00 0.00 2.94
197 198 8.988060 TCATGATATTACTTGGTGTCTTAGGAA 58.012 33.333 0.00 0.00 0.00 3.36
198 199 9.613428 CATGATATTACTTGGTGTCTTAGGAAA 57.387 33.333 0.00 0.00 0.00 3.13
241 242 7.817418 AAGTACATTACTTGGTGTCATGTTT 57.183 32.000 0.00 0.00 46.58 2.83
242 243 7.202016 AGTACATTACTTGGTGTCATGTTTG 57.798 36.000 0.00 0.00 39.64 2.93
243 244 6.770785 AGTACATTACTTGGTGTCATGTTTGT 59.229 34.615 0.00 0.00 39.64 2.83
244 245 7.934665 AGTACATTACTTGGTGTCATGTTTGTA 59.065 33.333 0.00 0.00 39.64 2.41
245 246 7.202016 ACATTACTTGGTGTCATGTTTGTAG 57.798 36.000 0.00 0.00 39.64 2.74
246 247 6.995686 ACATTACTTGGTGTCATGTTTGTAGA 59.004 34.615 0.00 0.00 39.64 2.59
247 248 7.665559 ACATTACTTGGTGTCATGTTTGTAGAT 59.334 33.333 0.00 0.00 39.64 1.98
248 249 9.161629 CATTACTTGGTGTCATGTTTGTAGATA 57.838 33.333 0.00 0.00 33.93 1.98
249 250 9.733556 ATTACTTGGTGTCATGTTTGTAGATAA 57.266 29.630 0.00 0.00 33.93 1.75
250 251 9.733556 TTACTTGGTGTCATGTTTGTAGATAAT 57.266 29.630 0.00 0.00 33.93 1.28
251 252 8.635765 ACTTGGTGTCATGTTTGTAGATAATT 57.364 30.769 0.00 0.00 0.00 1.40
252 253 9.077885 ACTTGGTGTCATGTTTGTAGATAATTT 57.922 29.630 0.00 0.00 0.00 1.82
253 254 9.345517 CTTGGTGTCATGTTTGTAGATAATTTG 57.654 33.333 0.00 0.00 0.00 2.32
254 255 8.628630 TGGTGTCATGTTTGTAGATAATTTGA 57.371 30.769 0.00 0.00 0.00 2.69
255 256 9.072375 TGGTGTCATGTTTGTAGATAATTTGAA 57.928 29.630 0.00 0.00 0.00 2.69
256 257 9.559958 GGTGTCATGTTTGTAGATAATTTGAAG 57.440 33.333 0.00 0.00 0.00 3.02
264 265 9.569167 GTTTGTAGATAATTTGAAGTAAAGCCC 57.431 33.333 0.00 0.00 0.00 5.19
265 266 8.871629 TTGTAGATAATTTGAAGTAAAGCCCA 57.128 30.769 0.00 0.00 0.00 5.36
266 267 9.474313 TTGTAGATAATTTGAAGTAAAGCCCAT 57.526 29.630 0.00 0.00 0.00 4.00
321 322 4.942761 AAAATGGCATGGGATGTGTATC 57.057 40.909 0.00 0.00 0.00 2.24
322 323 3.598693 AATGGCATGGGATGTGTATCA 57.401 42.857 0.00 0.00 34.90 2.15
323 324 2.346766 TGGCATGGGATGTGTATCAC 57.653 50.000 0.00 0.00 37.24 3.06
336 337 5.733226 TGTGTATCACAGACTGTTTGTTG 57.267 39.130 5.04 0.00 39.62 3.33
337 338 5.423886 TGTGTATCACAGACTGTTTGTTGA 58.576 37.500 5.04 0.00 39.62 3.18
338 339 5.877564 TGTGTATCACAGACTGTTTGTTGAA 59.122 36.000 5.04 0.00 39.62 2.69
339 340 6.372937 TGTGTATCACAGACTGTTTGTTGAAA 59.627 34.615 5.04 0.00 39.62 2.69
340 341 6.907212 GTGTATCACAGACTGTTTGTTGAAAG 59.093 38.462 5.04 0.00 34.08 2.62
341 342 4.355543 TCACAGACTGTTTGTTGAAAGC 57.644 40.909 5.04 0.00 0.00 3.51
342 343 3.128589 TCACAGACTGTTTGTTGAAAGCC 59.871 43.478 5.04 0.00 0.00 4.35
343 344 2.097466 ACAGACTGTTTGTTGAAAGCCG 59.903 45.455 1.07 0.00 0.00 5.52
344 345 2.097466 CAGACTGTTTGTTGAAAGCCGT 59.903 45.455 0.00 0.00 0.00 5.68
345 346 2.354821 AGACTGTTTGTTGAAAGCCGTC 59.645 45.455 0.00 0.00 0.00 4.79
346 347 1.404035 ACTGTTTGTTGAAAGCCGTCC 59.596 47.619 0.00 0.00 0.00 4.79
347 348 0.378962 TGTTTGTTGAAAGCCGTCCG 59.621 50.000 0.00 0.00 0.00 4.79
348 349 0.379316 GTTTGTTGAAAGCCGTCCGT 59.621 50.000 0.00 0.00 0.00 4.69
349 350 0.658897 TTTGTTGAAAGCCGTCCGTC 59.341 50.000 0.00 0.00 0.00 4.79
350 351 1.492319 TTGTTGAAAGCCGTCCGTCG 61.492 55.000 0.00 0.00 39.52 5.12
351 352 1.952635 GTTGAAAGCCGTCCGTCGT 60.953 57.895 0.00 0.00 37.94 4.34
352 353 0.664166 GTTGAAAGCCGTCCGTCGTA 60.664 55.000 0.00 0.00 37.94 3.43
353 354 0.031857 TTGAAAGCCGTCCGTCGTAA 59.968 50.000 0.00 0.00 37.94 3.18
354 355 0.387622 TGAAAGCCGTCCGTCGTAAG 60.388 55.000 0.00 0.00 37.94 2.34
355 356 0.387750 GAAAGCCGTCCGTCGTAAGT 60.388 55.000 0.00 0.00 37.94 2.24
356 357 0.032540 AAAGCCGTCCGTCGTAAGTT 59.967 50.000 0.00 0.00 37.94 2.66
357 358 0.665369 AAGCCGTCCGTCGTAAGTTG 60.665 55.000 0.00 0.00 37.94 3.16
358 359 2.723719 GCCGTCCGTCGTAAGTTGC 61.724 63.158 0.00 0.00 37.94 4.17
359 360 1.080974 CCGTCCGTCGTAAGTTGCT 60.081 57.895 0.00 0.00 37.94 3.91
360 361 0.168788 CCGTCCGTCGTAAGTTGCTA 59.831 55.000 0.00 0.00 37.94 3.49
361 362 1.401409 CCGTCCGTCGTAAGTTGCTAA 60.401 52.381 0.00 0.00 37.94 3.09
362 363 2.318578 CGTCCGTCGTAAGTTGCTAAA 58.681 47.619 0.00 0.00 39.48 1.85
363 364 2.089581 CGTCCGTCGTAAGTTGCTAAAC 59.910 50.000 0.00 0.00 39.48 2.01
364 365 3.052036 GTCCGTCGTAAGTTGCTAAACA 58.948 45.455 0.00 0.00 38.88 2.83
365 366 3.052036 TCCGTCGTAAGTTGCTAAACAC 58.948 45.455 0.00 0.00 38.88 3.32
366 367 3.054878 CCGTCGTAAGTTGCTAAACACT 58.945 45.455 0.00 0.00 38.88 3.55
367 368 4.023279 TCCGTCGTAAGTTGCTAAACACTA 60.023 41.667 0.00 0.00 38.88 2.74
368 369 4.089065 CCGTCGTAAGTTGCTAAACACTAC 59.911 45.833 0.00 0.00 38.88 2.73
369 370 4.913924 CGTCGTAAGTTGCTAAACACTACT 59.086 41.667 0.00 0.00 38.88 2.57
370 371 5.058977 CGTCGTAAGTTGCTAAACACTACTC 59.941 44.000 0.00 0.00 38.88 2.59
371 372 5.344396 GTCGTAAGTTGCTAAACACTACTCC 59.656 44.000 0.00 0.00 38.88 3.85
372 373 4.624452 CGTAAGTTGCTAAACACTACTCCC 59.376 45.833 0.00 0.00 38.88 4.30
373 374 4.976540 AAGTTGCTAAACACTACTCCCT 57.023 40.909 0.00 0.00 38.88 4.20
374 375 4.538746 AGTTGCTAAACACTACTCCCTC 57.461 45.455 0.00 0.00 38.88 4.30
375 376 3.261137 AGTTGCTAAACACTACTCCCTCC 59.739 47.826 0.00 0.00 38.88 4.30
376 377 1.822990 TGCTAAACACTACTCCCTCCG 59.177 52.381 0.00 0.00 0.00 4.63
377 378 1.823610 GCTAAACACTACTCCCTCCGT 59.176 52.381 0.00 0.00 0.00 4.69
378 379 2.159268 GCTAAACACTACTCCCTCCGTC 60.159 54.545 0.00 0.00 0.00 4.79
379 380 2.305858 AAACACTACTCCCTCCGTCT 57.694 50.000 0.00 0.00 0.00 4.18
380 381 1.836802 AACACTACTCCCTCCGTCTC 58.163 55.000 0.00 0.00 0.00 3.36
381 382 0.697079 ACACTACTCCCTCCGTCTCA 59.303 55.000 0.00 0.00 0.00 3.27
382 383 1.285373 ACACTACTCCCTCCGTCTCAT 59.715 52.381 0.00 0.00 0.00 2.90
383 384 2.508716 ACACTACTCCCTCCGTCTCATA 59.491 50.000 0.00 0.00 0.00 2.15
384 385 3.053842 ACACTACTCCCTCCGTCTCATAA 60.054 47.826 0.00 0.00 0.00 1.90
385 386 4.145807 CACTACTCCCTCCGTCTCATAAT 58.854 47.826 0.00 0.00 0.00 1.28
386 387 5.163120 ACACTACTCCCTCCGTCTCATAATA 60.163 44.000 0.00 0.00 0.00 0.98
387 388 5.946972 CACTACTCCCTCCGTCTCATAATAT 59.053 44.000 0.00 0.00 0.00 1.28
388 389 7.110810 CACTACTCCCTCCGTCTCATAATATA 58.889 42.308 0.00 0.00 0.00 0.86
389 390 7.610692 CACTACTCCCTCCGTCTCATAATATAA 59.389 40.741 0.00 0.00 0.00 0.98
390 391 7.830201 ACTACTCCCTCCGTCTCATAATATAAG 59.170 40.741 0.00 0.00 0.00 1.73
391 392 6.791371 ACTCCCTCCGTCTCATAATATAAGA 58.209 40.000 0.00 0.00 0.00 2.10
392 393 6.887545 ACTCCCTCCGTCTCATAATATAAGAG 59.112 42.308 0.00 0.00 0.00 2.85
393 394 5.652891 TCCCTCCGTCTCATAATATAAGAGC 59.347 44.000 0.00 0.00 0.00 4.09
394 395 5.419155 CCCTCCGTCTCATAATATAAGAGCA 59.581 44.000 0.00 0.00 0.00 4.26
395 396 6.097554 CCCTCCGTCTCATAATATAAGAGCAT 59.902 42.308 0.00 0.00 0.00 3.79
396 397 7.364232 CCCTCCGTCTCATAATATAAGAGCATT 60.364 40.741 0.00 0.00 0.00 3.56
397 398 8.037758 CCTCCGTCTCATAATATAAGAGCATTT 58.962 37.037 0.00 0.00 0.00 2.32
398 399 9.429359 CTCCGTCTCATAATATAAGAGCATTTT 57.571 33.333 0.00 0.00 0.00 1.82
399 400 9.778741 TCCGTCTCATAATATAAGAGCATTTTT 57.221 29.630 0.00 0.00 0.00 1.94
424 425 9.720769 TTTGCACTACTAGTATAAAAAGCTTCT 57.279 29.630 2.33 0.00 0.00 2.85
425 426 9.720769 TTGCACTACTAGTATAAAAAGCTTCTT 57.279 29.630 2.33 0.00 0.00 2.52
439 440 7.745620 AAAAGCTTCTTATATTATGGGACGG 57.254 36.000 0.00 0.00 0.00 4.79
440 441 6.681729 AAGCTTCTTATATTATGGGACGGA 57.318 37.500 0.00 0.00 0.00 4.69
441 442 6.287589 AGCTTCTTATATTATGGGACGGAG 57.712 41.667 0.00 0.00 0.00 4.63
442 443 5.187967 AGCTTCTTATATTATGGGACGGAGG 59.812 44.000 0.00 0.00 0.00 4.30
443 444 5.627040 GCTTCTTATATTATGGGACGGAGGG 60.627 48.000 0.00 0.00 0.00 4.30
444 445 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
445 446 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
453 454 1.348696 GGGACGGAGGGAGTAACAAAA 59.651 52.381 0.00 0.00 0.00 2.44
475 476 4.884668 AACGGTCTGAGAGAACCATTTA 57.115 40.909 0.00 0.00 0.00 1.40
500 501 6.929606 ACGATTATCTTTGTATAAGACTGGGC 59.070 38.462 0.00 0.00 0.00 5.36
512 513 0.798776 GACTGGGCTGATGAAACGTG 59.201 55.000 0.00 0.00 0.00 4.49
513 514 0.108585 ACTGGGCTGATGAAACGTGT 59.891 50.000 0.00 0.00 0.00 4.49
543 544 0.815734 GCCTTAGGTGTGTCGAGCTA 59.184 55.000 0.00 0.00 0.00 3.32
555 556 5.512082 GTGTGTCGAGCTATTAGTGTACAAG 59.488 44.000 0.00 0.00 0.00 3.16
602 603 9.817365 CAACTTAGTACAATGAAGAAACTGATG 57.183 33.333 0.00 0.00 0.00 3.07
607 608 7.170965 AGTACAATGAAGAAACTGATGGACAT 58.829 34.615 0.00 0.00 0.00 3.06
634 635 4.192000 CAGTCTTACTGCGCCAGG 57.808 61.111 4.18 0.00 39.62 4.45
636 637 0.320771 CAGTCTTACTGCGCCAGGTT 60.321 55.000 4.18 0.00 39.62 3.50
639 640 2.000447 GTCTTACTGCGCCAGGTTAAG 59.000 52.381 4.18 7.72 35.51 1.85
642 643 2.843401 TACTGCGCCAGGTTAAGAAA 57.157 45.000 4.18 0.00 35.51 2.52
656 660 6.525578 GGTTAAGAAATTTAACCTCCCCAG 57.474 41.667 17.37 0.00 46.38 4.45
657 661 5.421056 GGTTAAGAAATTTAACCTCCCCAGG 59.579 44.000 17.37 0.00 46.38 4.45
705 709 0.039888 CGGGCGTTAAAACCTTGTGG 60.040 55.000 0.00 0.00 39.83 4.17
706 710 1.320507 GGGCGTTAAAACCTTGTGGA 58.679 50.000 0.00 0.00 37.04 4.02
729 733 0.817013 ACCTTTGGGCATAACGCATG 59.183 50.000 0.00 0.00 45.17 4.06
730 734 1.102154 CCTTTGGGCATAACGCATGA 58.898 50.000 0.00 0.00 45.17 3.07
731 735 1.202290 CCTTTGGGCATAACGCATGAC 60.202 52.381 0.00 0.00 45.17 3.06
756 760 8.344098 ACGAGAATATAAGAAAGGAAGACTACG 58.656 37.037 0.00 0.00 0.00 3.51
782 786 1.228245 GCACAAGGCTGGACTTCCA 60.228 57.895 0.00 0.00 45.30 3.53
789 793 3.109847 GCTGGACTTCCAACCAACA 57.890 52.632 0.00 0.00 46.97 3.33
803 807 4.202070 CCAACCAACAAAATAACTCCACGT 60.202 41.667 0.00 0.00 0.00 4.49
804 808 4.823790 ACCAACAAAATAACTCCACGTC 57.176 40.909 0.00 0.00 0.00 4.34
805 809 4.457466 ACCAACAAAATAACTCCACGTCT 58.543 39.130 0.00 0.00 0.00 4.18
806 810 4.514066 ACCAACAAAATAACTCCACGTCTC 59.486 41.667 0.00 0.00 0.00 3.36
822 826 6.055231 CACGTCTCTCTCTAGTGGATTAAG 57.945 45.833 0.00 0.00 0.00 1.85
835 839 4.872691 AGTGGATTAAGAACTGCTCAATCG 59.127 41.667 0.00 0.00 0.00 3.34
839 843 6.183360 TGGATTAAGAACTGCTCAATCGGATA 60.183 38.462 0.00 0.00 0.00 2.59
841 845 8.035394 GGATTAAGAACTGCTCAATCGGATATA 58.965 37.037 0.00 0.00 0.00 0.86
875 880 6.238103 CCACATCAACCAGTACGTATGATTTC 60.238 42.308 0.00 0.00 0.00 2.17
894 899 5.523438 TTTCCGTAAGACCAAGCATTTTT 57.477 34.783 0.00 0.00 43.02 1.94
942 964 1.915141 ACAAGAACAATGCTCCAGGG 58.085 50.000 0.00 0.00 0.00 4.45
947 969 1.792757 AACAATGCTCCAGGGCTCCA 61.793 55.000 0.00 0.00 0.00 3.86
948 970 1.453379 CAATGCTCCAGGGCTCCAG 60.453 63.158 0.00 0.00 0.00 3.86
949 971 2.687610 AATGCTCCAGGGCTCCAGG 61.688 63.158 0.00 0.00 0.00 4.45
993 1015 1.141019 GCGATCGAGTTACCCAGCA 59.859 57.895 21.57 0.00 0.00 4.41
994 1016 0.459585 GCGATCGAGTTACCCAGCAA 60.460 55.000 21.57 0.00 0.00 3.91
1072 1094 1.448540 CTTGGCAGCTCCTACCACG 60.449 63.158 0.00 0.00 31.83 4.94
1143 1183 1.147824 CTGCTCGCCCATCCATTCT 59.852 57.895 0.00 0.00 0.00 2.40
1158 1198 5.414789 TCCATTCTGGTGAAGTATTTCGA 57.585 39.130 0.00 0.00 39.03 3.71
1159 1199 5.989477 TCCATTCTGGTGAAGTATTTCGAT 58.011 37.500 0.00 0.00 39.03 3.59
1160 1200 6.049149 TCCATTCTGGTGAAGTATTTCGATC 58.951 40.000 0.00 0.00 39.03 3.69
1161 1201 5.237344 CCATTCTGGTGAAGTATTTCGATCC 59.763 44.000 0.00 0.00 36.04 3.36
1172 1212 9.184523 TGAAGTATTTCGATCCCACAAATTAAT 57.815 29.630 0.00 0.00 36.04 1.40
1184 1224 5.404946 CCACAAATTAATCTCTGCAACAGG 58.595 41.667 0.00 0.00 31.51 4.00
1191 1231 1.595109 CTCTGCAACAGGACGTGCA 60.595 57.895 10.52 2.53 35.83 4.57
1253 1298 2.278857 CGTCATTCTCCCCGCTCG 60.279 66.667 0.00 0.00 0.00 5.03
1320 1365 4.241999 GCCGCTGCCTGTAATGCG 62.242 66.667 0.00 0.00 46.74 4.73
1375 1420 1.979155 GGACCAAAGCAAGCCCTCC 60.979 63.158 0.00 0.00 0.00 4.30
1646 1691 2.424705 TTTCGACCCGTCCAAGTCCG 62.425 60.000 0.00 0.00 0.00 4.79
1729 1774 2.958204 CTGCACGCGCACACTCAAT 61.958 57.895 5.73 0.00 45.36 2.57
1747 1795 0.962356 ATTGGAAGAACGGGCTGCAG 60.962 55.000 10.11 10.11 0.00 4.41
3218 3304 5.508153 GGAAGAAGATAAGCATCGCTGTAGA 60.508 44.000 0.00 0.00 39.62 2.59
3220 3306 5.285651 AGAAGATAAGCATCGCTGTAGAAC 58.714 41.667 0.00 0.00 39.62 3.01
3529 3974 7.518731 TTTTCATAGTGTTTCACTGTTTTGC 57.481 32.000 11.92 0.00 45.01 3.68
3530 3975 5.826601 TCATAGTGTTTCACTGTTTTGCA 57.173 34.783 11.92 0.00 45.01 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.842948 TCTCTCCTATCCCTCCATGAAATG 59.157 45.833 0.00 0.00 46.21 2.32
4 5 5.092968 CTCTCTCCTATCCCTCCATGAAAT 58.907 45.833 0.00 0.00 0.00 2.17
5 6 4.170845 TCTCTCTCCTATCCCTCCATGAAA 59.829 45.833 0.00 0.00 0.00 2.69
6 7 3.729524 TCTCTCTCCTATCCCTCCATGAA 59.270 47.826 0.00 0.00 0.00 2.57
7 8 3.340403 TCTCTCTCCTATCCCTCCATGA 58.660 50.000 0.00 0.00 0.00 3.07
8 9 3.824001 TCTCTCTCCTATCCCTCCATG 57.176 52.381 0.00 0.00 0.00 3.66
9 10 3.077391 CCTTCTCTCTCCTATCCCTCCAT 59.923 52.174 0.00 0.00 0.00 3.41
10 11 2.448961 CCTTCTCTCTCCTATCCCTCCA 59.551 54.545 0.00 0.00 0.00 3.86
11 12 2.821625 GCCTTCTCTCTCCTATCCCTCC 60.822 59.091 0.00 0.00 0.00 4.30
12 13 2.110011 AGCCTTCTCTCTCCTATCCCTC 59.890 54.545 0.00 0.00 0.00 4.30
13 14 2.152123 AGCCTTCTCTCTCCTATCCCT 58.848 52.381 0.00 0.00 0.00 4.20
14 15 2.694616 AGCCTTCTCTCTCCTATCCC 57.305 55.000 0.00 0.00 0.00 3.85
15 16 3.070878 CCAAAGCCTTCTCTCTCCTATCC 59.929 52.174 0.00 0.00 0.00 2.59
16 17 3.494223 GCCAAAGCCTTCTCTCTCCTATC 60.494 52.174 0.00 0.00 0.00 2.08
17 18 2.437651 GCCAAAGCCTTCTCTCTCCTAT 59.562 50.000 0.00 0.00 0.00 2.57
18 19 1.834263 GCCAAAGCCTTCTCTCTCCTA 59.166 52.381 0.00 0.00 0.00 2.94
19 20 0.617935 GCCAAAGCCTTCTCTCTCCT 59.382 55.000 0.00 0.00 0.00 3.69
20 21 0.617935 AGCCAAAGCCTTCTCTCTCC 59.382 55.000 0.00 0.00 41.25 3.71
21 22 3.618690 TTAGCCAAAGCCTTCTCTCTC 57.381 47.619 0.00 0.00 41.25 3.20
22 23 4.268359 CATTTAGCCAAAGCCTTCTCTCT 58.732 43.478 0.00 0.00 41.25 3.10
23 24 3.379688 CCATTTAGCCAAAGCCTTCTCTC 59.620 47.826 0.00 0.00 41.25 3.20
24 25 3.010584 TCCATTTAGCCAAAGCCTTCTCT 59.989 43.478 0.00 0.00 41.25 3.10
25 26 3.356290 TCCATTTAGCCAAAGCCTTCTC 58.644 45.455 0.00 0.00 41.25 2.87
26 27 3.359950 CTCCATTTAGCCAAAGCCTTCT 58.640 45.455 0.00 0.00 41.25 2.85
27 28 2.428530 CCTCCATTTAGCCAAAGCCTTC 59.571 50.000 0.00 0.00 41.25 3.46
28 29 2.460669 CCTCCATTTAGCCAAAGCCTT 58.539 47.619 0.00 0.00 41.25 4.35
29 30 1.342374 CCCTCCATTTAGCCAAAGCCT 60.342 52.381 0.00 0.00 41.25 4.58
30 31 1.114627 CCCTCCATTTAGCCAAAGCC 58.885 55.000 0.00 0.00 41.25 4.35
31 32 1.852633 ACCCTCCATTTAGCCAAAGC 58.147 50.000 0.00 0.00 40.32 3.51
32 33 3.055891 CCAAACCCTCCATTTAGCCAAAG 60.056 47.826 0.00 0.00 0.00 2.77
33 34 2.903135 CCAAACCCTCCATTTAGCCAAA 59.097 45.455 0.00 0.00 0.00 3.28
34 35 2.534990 CCAAACCCTCCATTTAGCCAA 58.465 47.619 0.00 0.00 0.00 4.52
35 36 1.272985 CCCAAACCCTCCATTTAGCCA 60.273 52.381 0.00 0.00 0.00 4.75
36 37 1.485124 CCCAAACCCTCCATTTAGCC 58.515 55.000 0.00 0.00 0.00 3.93
37 38 0.824109 GCCCAAACCCTCCATTTAGC 59.176 55.000 0.00 0.00 0.00 3.09
38 39 1.007118 AGGCCCAAACCCTCCATTTAG 59.993 52.381 0.00 0.00 0.00 1.85
39 40 1.089123 AGGCCCAAACCCTCCATTTA 58.911 50.000 0.00 0.00 0.00 1.40
40 41 0.545071 CAGGCCCAAACCCTCCATTT 60.545 55.000 0.00 0.00 0.00 2.32
41 42 1.079073 CAGGCCCAAACCCTCCATT 59.921 57.895 0.00 0.00 0.00 3.16
42 43 1.224003 ATCAGGCCCAAACCCTCCAT 61.224 55.000 0.00 0.00 0.00 3.41
43 44 1.442886 AATCAGGCCCAAACCCTCCA 61.443 55.000 0.00 0.00 0.00 3.86
44 45 0.684479 GAATCAGGCCCAAACCCTCC 60.684 60.000 0.00 0.00 0.00 4.30
45 46 1.032114 CGAATCAGGCCCAAACCCTC 61.032 60.000 0.00 0.00 0.00 4.30
46 47 1.000896 CGAATCAGGCCCAAACCCT 60.001 57.895 0.00 0.00 0.00 4.34
47 48 2.052104 CCGAATCAGGCCCAAACCC 61.052 63.158 0.00 0.00 0.00 4.11
48 49 0.395724 ATCCGAATCAGGCCCAAACC 60.396 55.000 0.00 0.00 0.00 3.27
49 50 1.474330 AATCCGAATCAGGCCCAAAC 58.526 50.000 0.00 0.00 0.00 2.93
50 51 2.230130 AAATCCGAATCAGGCCCAAA 57.770 45.000 0.00 0.00 0.00 3.28
51 52 2.099405 GAAAATCCGAATCAGGCCCAA 58.901 47.619 0.00 0.00 0.00 4.12
52 53 1.284785 AGAAAATCCGAATCAGGCCCA 59.715 47.619 0.00 0.00 0.00 5.36
53 54 1.678101 CAGAAAATCCGAATCAGGCCC 59.322 52.381 0.00 0.00 0.00 5.80
54 55 2.643551 TCAGAAAATCCGAATCAGGCC 58.356 47.619 0.00 0.00 0.00 5.19
55 56 4.701956 TTTCAGAAAATCCGAATCAGGC 57.298 40.909 0.00 0.00 0.00 4.85
162 163 9.330063 CACCAAGTAATATCATGACAGTTACAT 57.670 33.333 20.12 11.37 0.00 2.29
163 164 8.318412 ACACCAAGTAATATCATGACAGTTACA 58.682 33.333 20.12 0.00 0.00 2.41
164 165 8.718102 ACACCAAGTAATATCATGACAGTTAC 57.282 34.615 14.33 14.33 0.00 2.50
165 166 8.758829 AGACACCAAGTAATATCATGACAGTTA 58.241 33.333 0.00 0.00 0.00 2.24
166 167 7.624549 AGACACCAAGTAATATCATGACAGTT 58.375 34.615 0.00 0.00 0.00 3.16
167 168 7.187824 AGACACCAAGTAATATCATGACAGT 57.812 36.000 0.00 0.00 0.00 3.55
168 169 9.254133 CTAAGACACCAAGTAATATCATGACAG 57.746 37.037 0.00 0.00 0.00 3.51
169 170 8.204160 CCTAAGACACCAAGTAATATCATGACA 58.796 37.037 0.00 0.00 0.00 3.58
170 171 8.421784 TCCTAAGACACCAAGTAATATCATGAC 58.578 37.037 0.00 0.00 0.00 3.06
171 172 8.547481 TCCTAAGACACCAAGTAATATCATGA 57.453 34.615 0.00 0.00 0.00 3.07
172 173 9.613428 TTTCCTAAGACACCAAGTAATATCATG 57.387 33.333 0.00 0.00 0.00 3.07
212 213 9.383519 CATGACACCAAGTAATGTACTTATCTT 57.616 33.333 0.51 0.00 46.66 2.40
213 214 8.948631 CATGACACCAAGTAATGTACTTATCT 57.051 34.615 0.51 0.00 46.66 1.98
222 223 7.433708 TCTACAAACATGACACCAAGTAATG 57.566 36.000 0.00 0.00 43.70 1.90
223 224 9.733556 TTATCTACAAACATGACACCAAGTAAT 57.266 29.630 0.00 0.00 0.00 1.89
224 225 9.733556 ATTATCTACAAACATGACACCAAGTAA 57.266 29.630 0.00 0.00 0.00 2.24
225 226 9.733556 AATTATCTACAAACATGACACCAAGTA 57.266 29.630 0.00 0.00 0.00 2.24
226 227 8.635765 AATTATCTACAAACATGACACCAAGT 57.364 30.769 0.00 0.00 0.00 3.16
227 228 9.345517 CAAATTATCTACAAACATGACACCAAG 57.654 33.333 0.00 0.00 0.00 3.61
228 229 9.072375 TCAAATTATCTACAAACATGACACCAA 57.928 29.630 0.00 0.00 0.00 3.67
229 230 8.628630 TCAAATTATCTACAAACATGACACCA 57.371 30.769 0.00 0.00 0.00 4.17
230 231 9.559958 CTTCAAATTATCTACAAACATGACACC 57.440 33.333 0.00 0.00 0.00 4.16
238 239 9.569167 GGGCTTTACTTCAAATTATCTACAAAC 57.431 33.333 0.00 0.00 0.00 2.93
239 240 9.303116 TGGGCTTTACTTCAAATTATCTACAAA 57.697 29.630 0.00 0.00 0.00 2.83
240 241 8.871629 TGGGCTTTACTTCAAATTATCTACAA 57.128 30.769 0.00 0.00 0.00 2.41
299 300 4.715792 TGATACACATCCCATGCCATTTTT 59.284 37.500 0.00 0.00 0.00 1.94
300 301 4.099881 GTGATACACATCCCATGCCATTTT 59.900 41.667 0.00 0.00 34.08 1.82
301 302 3.638160 GTGATACACATCCCATGCCATTT 59.362 43.478 0.00 0.00 34.08 2.32
302 303 3.225104 GTGATACACATCCCATGCCATT 58.775 45.455 0.00 0.00 34.08 3.16
303 304 2.175284 TGTGATACACATCCCATGCCAT 59.825 45.455 0.25 0.00 39.62 4.40
304 305 1.563410 TGTGATACACATCCCATGCCA 59.437 47.619 0.25 0.00 39.62 4.92
305 306 2.158769 TCTGTGATACACATCCCATGCC 60.159 50.000 5.07 0.00 43.71 4.40
306 307 2.874701 GTCTGTGATACACATCCCATGC 59.125 50.000 5.07 0.00 43.71 4.06
307 308 4.124970 CAGTCTGTGATACACATCCCATG 58.875 47.826 5.07 0.00 43.71 3.66
308 309 3.776969 ACAGTCTGTGATACACATCCCAT 59.223 43.478 4.21 0.00 43.71 4.00
309 310 3.173151 ACAGTCTGTGATACACATCCCA 58.827 45.455 4.21 0.00 43.71 4.37
310 311 3.895232 ACAGTCTGTGATACACATCCC 57.105 47.619 4.21 0.00 43.71 3.85
311 312 4.997395 ACAAACAGTCTGTGATACACATCC 59.003 41.667 6.18 0.07 43.71 3.51
312 313 6.202762 TCAACAAACAGTCTGTGATACACATC 59.797 38.462 6.18 2.92 43.71 3.06
313 314 6.054941 TCAACAAACAGTCTGTGATACACAT 58.945 36.000 6.18 0.00 43.71 3.21
314 315 5.423886 TCAACAAACAGTCTGTGATACACA 58.576 37.500 6.18 4.56 42.45 3.72
315 316 5.984233 TCAACAAACAGTCTGTGATACAC 57.016 39.130 6.18 0.00 34.56 2.90
316 317 6.458206 GCTTTCAACAAACAGTCTGTGATACA 60.458 38.462 6.18 0.00 0.00 2.29
317 318 5.909610 GCTTTCAACAAACAGTCTGTGATAC 59.090 40.000 6.18 0.00 0.00 2.24
318 319 5.008613 GGCTTTCAACAAACAGTCTGTGATA 59.991 40.000 6.18 0.00 0.00 2.15
319 320 4.202050 GGCTTTCAACAAACAGTCTGTGAT 60.202 41.667 6.18 0.00 0.00 3.06
320 321 3.128589 GGCTTTCAACAAACAGTCTGTGA 59.871 43.478 6.18 0.00 0.00 3.58
321 322 3.438360 GGCTTTCAACAAACAGTCTGTG 58.562 45.455 6.18 0.00 0.00 3.66
322 323 2.097466 CGGCTTTCAACAAACAGTCTGT 59.903 45.455 0.00 0.00 0.00 3.41
323 324 2.097466 ACGGCTTTCAACAAACAGTCTG 59.903 45.455 0.00 0.00 0.00 3.51
324 325 2.354821 GACGGCTTTCAACAAACAGTCT 59.645 45.455 0.00 0.00 0.00 3.24
325 326 2.540973 GGACGGCTTTCAACAAACAGTC 60.541 50.000 0.00 0.00 0.00 3.51
326 327 1.404035 GGACGGCTTTCAACAAACAGT 59.596 47.619 0.00 0.00 0.00 3.55
327 328 1.596954 CGGACGGCTTTCAACAAACAG 60.597 52.381 0.00 0.00 0.00 3.16
328 329 0.378962 CGGACGGCTTTCAACAAACA 59.621 50.000 0.00 0.00 0.00 2.83
329 330 0.379316 ACGGACGGCTTTCAACAAAC 59.621 50.000 0.00 0.00 0.00 2.93
330 331 0.658897 GACGGACGGCTTTCAACAAA 59.341 50.000 0.00 0.00 0.00 2.83
331 332 1.492319 CGACGGACGGCTTTCAACAA 61.492 55.000 0.00 0.00 38.46 2.83
332 333 1.952133 CGACGGACGGCTTTCAACA 60.952 57.895 0.00 0.00 38.46 3.33
333 334 2.851104 CGACGGACGGCTTTCAAC 59.149 61.111 0.00 0.00 38.46 3.18
342 343 4.392324 TGTTTAGCAACTTACGACGGACG 61.392 47.826 0.00 0.00 39.72 4.79
343 344 3.052036 TGTTTAGCAACTTACGACGGAC 58.948 45.455 0.00 0.00 33.58 4.79
344 345 3.052036 GTGTTTAGCAACTTACGACGGA 58.948 45.455 0.00 0.00 33.58 4.69
345 346 3.054878 AGTGTTTAGCAACTTACGACGG 58.945 45.455 0.00 0.00 33.58 4.79
346 347 4.913924 AGTAGTGTTTAGCAACTTACGACG 59.086 41.667 0.00 0.00 32.95 5.12
347 348 5.344396 GGAGTAGTGTTTAGCAACTTACGAC 59.656 44.000 0.00 0.00 32.95 4.34
348 349 5.464168 GGAGTAGTGTTTAGCAACTTACGA 58.536 41.667 0.00 0.00 32.95 3.43
349 350 4.624452 GGGAGTAGTGTTTAGCAACTTACG 59.376 45.833 0.00 0.00 32.95 3.18
350 351 5.791666 AGGGAGTAGTGTTTAGCAACTTAC 58.208 41.667 0.00 0.00 33.58 2.34
351 352 5.046807 GGAGGGAGTAGTGTTTAGCAACTTA 60.047 44.000 0.00 0.00 33.58 2.24
352 353 4.262938 GGAGGGAGTAGTGTTTAGCAACTT 60.263 45.833 0.00 0.00 33.58 2.66
353 354 3.261137 GGAGGGAGTAGTGTTTAGCAACT 59.739 47.826 0.00 0.00 33.58 3.16
354 355 3.597255 GGAGGGAGTAGTGTTTAGCAAC 58.403 50.000 0.00 0.00 0.00 4.17
355 356 2.232941 CGGAGGGAGTAGTGTTTAGCAA 59.767 50.000 0.00 0.00 0.00 3.91
356 357 1.822990 CGGAGGGAGTAGTGTTTAGCA 59.177 52.381 0.00 0.00 0.00 3.49
357 358 1.823610 ACGGAGGGAGTAGTGTTTAGC 59.176 52.381 0.00 0.00 0.00 3.09
358 359 3.354467 AGACGGAGGGAGTAGTGTTTAG 58.646 50.000 0.00 0.00 0.00 1.85
359 360 3.245016 TGAGACGGAGGGAGTAGTGTTTA 60.245 47.826 0.00 0.00 0.00 2.01
360 361 2.169330 GAGACGGAGGGAGTAGTGTTT 58.831 52.381 0.00 0.00 0.00 2.83
361 362 1.075050 TGAGACGGAGGGAGTAGTGTT 59.925 52.381 0.00 0.00 0.00 3.32
362 363 0.697079 TGAGACGGAGGGAGTAGTGT 59.303 55.000 0.00 0.00 0.00 3.55
363 364 2.060050 ATGAGACGGAGGGAGTAGTG 57.940 55.000 0.00 0.00 0.00 2.74
364 365 3.947612 TTATGAGACGGAGGGAGTAGT 57.052 47.619 0.00 0.00 0.00 2.73
365 366 8.047911 TCTTATATTATGAGACGGAGGGAGTAG 58.952 40.741 0.00 0.00 0.00 2.57
366 367 7.925622 TCTTATATTATGAGACGGAGGGAGTA 58.074 38.462 0.00 0.00 0.00 2.59
367 368 6.791371 TCTTATATTATGAGACGGAGGGAGT 58.209 40.000 0.00 0.00 0.00 3.85
368 369 6.183360 GCTCTTATATTATGAGACGGAGGGAG 60.183 46.154 0.00 0.00 33.20 4.30
369 370 5.652891 GCTCTTATATTATGAGACGGAGGGA 59.347 44.000 0.00 0.00 33.20 4.20
370 371 5.419155 TGCTCTTATATTATGAGACGGAGGG 59.581 44.000 0.00 0.00 33.20 4.30
371 372 6.516739 TGCTCTTATATTATGAGACGGAGG 57.483 41.667 0.00 0.00 33.20 4.30
372 373 8.994429 AAATGCTCTTATATTATGAGACGGAG 57.006 34.615 0.00 0.00 33.20 4.63
373 374 9.778741 AAAAATGCTCTTATATTATGAGACGGA 57.221 29.630 0.00 0.00 33.20 4.69
398 399 9.720769 AGAAGCTTTTTATACTAGTAGTGCAAA 57.279 29.630 13.29 9.53 0.00 3.68
399 400 9.720769 AAGAAGCTTTTTATACTAGTAGTGCAA 57.279 29.630 13.29 3.92 0.00 4.08
413 414 9.280174 CCGTCCCATAATATAAGAAGCTTTTTA 57.720 33.333 11.47 11.47 0.00 1.52
414 415 7.996644 TCCGTCCCATAATATAAGAAGCTTTTT 59.003 33.333 7.46 7.46 0.00 1.94
415 416 7.514721 TCCGTCCCATAATATAAGAAGCTTTT 58.485 34.615 0.00 0.00 0.00 2.27
416 417 7.074653 TCCGTCCCATAATATAAGAAGCTTT 57.925 36.000 0.00 0.00 0.00 3.51
417 418 6.295916 CCTCCGTCCCATAATATAAGAAGCTT 60.296 42.308 0.00 0.00 0.00 3.74
418 419 5.187967 CCTCCGTCCCATAATATAAGAAGCT 59.812 44.000 0.00 0.00 0.00 3.74
419 420 5.420409 CCTCCGTCCCATAATATAAGAAGC 58.580 45.833 0.00 0.00 0.00 3.86
420 421 5.720041 TCCCTCCGTCCCATAATATAAGAAG 59.280 44.000 0.00 0.00 0.00 2.85
421 422 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
422 423 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
423 424 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
424 425 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
425 426 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
426 427 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
427 428 4.154942 GTTACTCCCTCCGTCCCATAATA 58.845 47.826 0.00 0.00 0.00 0.98
428 429 2.970640 GTTACTCCCTCCGTCCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
429 430 2.292389 TGTTACTCCCTCCGTCCCATAA 60.292 50.000 0.00 0.00 0.00 1.90
430 431 1.288633 TGTTACTCCCTCCGTCCCATA 59.711 52.381 0.00 0.00 0.00 2.74
431 432 0.042131 TGTTACTCCCTCCGTCCCAT 59.958 55.000 0.00 0.00 0.00 4.00
432 433 0.178926 TTGTTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
433 434 0.978907 TTTGTTACTCCCTCCGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
434 435 2.845363 TTTTGTTACTCCCTCCGTCC 57.155 50.000 0.00 0.00 0.00 4.79
453 454 3.771577 AATGGTTCTCTCAGACCGTTT 57.228 42.857 0.00 0.00 27.62 3.60
457 458 4.451629 TCGTAAATGGTTCTCTCAGACC 57.548 45.455 0.00 0.00 0.00 3.85
461 462 9.098355 CAAAGATAATCGTAAATGGTTCTCTCA 57.902 33.333 0.00 0.00 0.00 3.27
475 476 6.929606 GCCCAGTCTTATACAAAGATAATCGT 59.070 38.462 0.00 0.00 0.00 3.73
489 490 3.055094 ACGTTTCATCAGCCCAGTCTTAT 60.055 43.478 0.00 0.00 0.00 1.73
495 496 0.518636 CACACGTTTCATCAGCCCAG 59.481 55.000 0.00 0.00 0.00 4.45
496 497 0.107643 TCACACGTTTCATCAGCCCA 59.892 50.000 0.00 0.00 0.00 5.36
497 498 0.798776 CTCACACGTTTCATCAGCCC 59.201 55.000 0.00 0.00 0.00 5.19
500 501 3.123621 GGTTAGCTCACACGTTTCATCAG 59.876 47.826 0.00 0.00 0.00 2.90
512 513 2.317530 CCTAAGGCAGGTTAGCTCAC 57.682 55.000 0.00 0.00 39.91 3.51
569 570 7.990917 TCTTCATTGTACTAAGTTGCAAAACA 58.009 30.769 0.00 0.00 0.00 2.83
581 582 7.676004 TGTCCATCAGTTTCTTCATTGTACTA 58.324 34.615 0.00 0.00 0.00 1.82
582 583 6.533730 TGTCCATCAGTTTCTTCATTGTACT 58.466 36.000 0.00 0.00 0.00 2.73
583 584 6.801539 TGTCCATCAGTTTCTTCATTGTAC 57.198 37.500 0.00 0.00 0.00 2.90
602 603 1.204941 AGACTGCCAACGTCTATGTCC 59.795 52.381 0.00 0.00 39.80 4.02
607 608 3.570926 CAGTAAGACTGCCAACGTCTA 57.429 47.619 0.00 0.00 39.62 2.59
634 635 5.105473 GCCTGGGGAGGTTAAATTTCTTAAC 60.105 44.000 0.00 0.00 34.92 2.01
636 637 4.571148 GGCCTGGGGAGGTTAAATTTCTTA 60.571 45.833 0.00 0.00 0.00 2.10
639 640 2.108168 GGCCTGGGGAGGTTAAATTTC 58.892 52.381 0.00 0.00 0.00 2.17
642 643 0.631212 CTGGCCTGGGGAGGTTAAAT 59.369 55.000 3.32 0.00 0.00 1.40
667 671 2.894387 GAGCGACTGCCATGGAGC 60.894 66.667 18.40 11.91 44.31 4.70
705 709 2.415491 GCGTTATGCCCAAAGGTTTCTC 60.415 50.000 0.00 0.00 37.76 2.87
706 710 1.544246 GCGTTATGCCCAAAGGTTTCT 59.456 47.619 0.00 0.00 37.76 2.52
729 733 9.667989 GTAGTCTTCCTTTCTTATATTCTCGTC 57.332 37.037 0.00 0.00 0.00 4.20
730 734 8.344098 CGTAGTCTTCCTTTCTTATATTCTCGT 58.656 37.037 0.00 0.00 0.00 4.18
731 735 8.344098 ACGTAGTCTTCCTTTCTTATATTCTCG 58.656 37.037 0.00 0.00 29.74 4.04
756 760 1.089920 CCAGCCTTGTGCATAGTCAC 58.910 55.000 0.00 0.00 44.83 3.67
782 786 4.885325 AGACGTGGAGTTATTTTGTTGGTT 59.115 37.500 0.00 0.00 0.00 3.67
787 791 5.244178 AGAGAGAGACGTGGAGTTATTTTGT 59.756 40.000 0.00 0.00 0.00 2.83
789 793 5.986501 AGAGAGAGACGTGGAGTTATTTT 57.013 39.130 0.00 0.00 0.00 1.82
803 807 6.320164 GCAGTTCTTAATCCACTAGAGAGAGA 59.680 42.308 0.00 0.00 0.00 3.10
804 808 6.321181 AGCAGTTCTTAATCCACTAGAGAGAG 59.679 42.308 0.00 0.00 0.00 3.20
805 809 6.191315 AGCAGTTCTTAATCCACTAGAGAGA 58.809 40.000 0.00 0.00 0.00 3.10
806 810 6.096141 TGAGCAGTTCTTAATCCACTAGAGAG 59.904 42.308 0.00 0.00 0.00 3.20
835 839 8.046708 TGGTTGATGTGGCAAGTATATATATCC 58.953 37.037 0.00 0.00 0.00 2.59
839 843 6.841601 ACTGGTTGATGTGGCAAGTATATAT 58.158 36.000 0.00 0.00 0.00 0.86
841 845 5.116084 ACTGGTTGATGTGGCAAGTATAT 57.884 39.130 0.00 0.00 0.00 0.86
900 905 1.004610 TGCTCTCGCGTACGTACATAC 60.005 52.381 24.50 12.49 41.18 2.39
902 907 0.247974 GTGCTCTCGCGTACGTACAT 60.248 55.000 24.50 0.00 41.18 2.29
904 909 0.453282 TTGTGCTCTCGCGTACGTAC 60.453 55.000 17.90 15.90 41.18 3.67
906 911 1.728426 GTTGTGCTCTCGCGTACGT 60.728 57.895 17.90 0.00 41.18 3.57
907 912 1.272784 TTGTTGTGCTCTCGCGTACG 61.273 55.000 11.84 11.84 39.65 3.67
908 913 0.435008 CTTGTTGTGCTCTCGCGTAC 59.565 55.000 5.77 0.00 39.65 3.67
909 914 0.312729 TCTTGTTGTGCTCTCGCGTA 59.687 50.000 5.77 0.00 39.65 4.42
942 964 4.503296 CGTTATATATATGGGGCCTGGAGC 60.503 50.000 0.84 0.00 42.60 4.70
947 969 4.686122 GCTTGCGTTATATATATGGGGCCT 60.686 45.833 0.84 0.00 0.00 5.19
948 970 3.564225 GCTTGCGTTATATATATGGGGCC 59.436 47.826 5.44 0.00 0.00 5.80
949 971 4.451900 AGCTTGCGTTATATATATGGGGC 58.548 43.478 5.44 6.21 0.00 5.80
950 972 6.258727 CAGAAGCTTGCGTTATATATATGGGG 59.741 42.308 2.10 0.00 0.00 4.96
951 973 6.238211 GCAGAAGCTTGCGTTATATATATGGG 60.238 42.308 2.10 0.00 37.91 4.00
952 974 6.709643 GCAGAAGCTTGCGTTATATATATGG 58.290 40.000 2.10 0.00 37.91 2.74
993 1015 1.327303 TGGCCGAAGACATTTTGCTT 58.673 45.000 0.00 0.00 0.00 3.91
994 1016 1.549203 ATGGCCGAAGACATTTTGCT 58.451 45.000 0.00 0.00 0.00 3.91
1065 1087 3.385749 ATGCCTTCCGCCGTGGTAG 62.386 63.158 0.00 0.00 39.52 3.18
1072 1094 3.195698 GACGACATGCCTTCCGCC 61.196 66.667 0.00 0.00 36.24 6.13
1143 1183 3.262151 TGTGGGATCGAAATACTTCACCA 59.738 43.478 0.00 0.00 0.00 4.17
1158 1198 5.716228 TGTTGCAGAGATTAATTTGTGGGAT 59.284 36.000 5.44 0.00 0.00 3.85
1159 1199 5.076182 TGTTGCAGAGATTAATTTGTGGGA 58.924 37.500 5.44 0.00 0.00 4.37
1160 1200 5.389859 TGTTGCAGAGATTAATTTGTGGG 57.610 39.130 5.44 0.00 0.00 4.61
1161 1201 5.183713 TCCTGTTGCAGAGATTAATTTGTGG 59.816 40.000 5.44 0.00 32.44 4.17
1172 1212 1.300931 GCACGTCCTGTTGCAGAGA 60.301 57.895 0.00 0.00 32.44 3.10
1210 1255 4.098960 ACGACCGTGACCAACTCATTATAT 59.901 41.667 0.00 0.00 0.00 0.86
1211 1256 3.444742 ACGACCGTGACCAACTCATTATA 59.555 43.478 0.00 0.00 0.00 0.98
1356 1401 2.282462 AGGGCTTGCTTTGGTCCG 60.282 61.111 0.00 0.00 0.00 4.79
1411 1456 1.807573 CTTCCCGAAGAGCGTGCTC 60.808 63.158 13.90 13.90 40.79 4.26
1478 1523 4.112341 GTGGTACTCGGACGCGCT 62.112 66.667 5.73 0.00 0.00 5.92
1646 1691 2.187163 GACGTAGGCAAGGGAGGC 59.813 66.667 0.00 0.00 0.00 4.70
1690 1735 4.803426 CGTCCCCTGCACTCGCTC 62.803 72.222 0.00 0.00 39.64 5.03
1729 1774 1.600636 CTGCAGCCCGTTCTTCCAA 60.601 57.895 0.00 0.00 0.00 3.53
1747 1795 3.241177 GTCACGAAGGTGGCGTTC 58.759 61.111 0.00 0.00 44.50 3.95
2564 2639 0.966875 ATGCACATTGATGGCCGTGT 60.967 50.000 0.00 0.00 0.00 4.49
3504 3949 7.600375 TGCAAAACAGTGAAACACTATGAAAAA 59.400 29.630 0.00 0.00 43.43 1.94
3505 3950 7.093354 TGCAAAACAGTGAAACACTATGAAAA 58.907 30.769 0.00 0.00 43.43 2.29
3506 3951 6.625362 TGCAAAACAGTGAAACACTATGAAA 58.375 32.000 0.00 0.00 43.43 2.69
3507 3952 6.201226 TGCAAAACAGTGAAACACTATGAA 57.799 33.333 0.00 0.00 43.43 2.57
3508 3953 5.826601 TGCAAAACAGTGAAACACTATGA 57.173 34.783 0.00 0.00 43.43 2.15


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

AutoCloner maintained by Alex Coulton.