Multiple sequence alignment - TraesCS5A01G399600

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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 TraesCS5A01G399600 chr5A 100.000 3136 0 0 320 3455 593077648 593080783 0.000000e+00 5792.0
1 TraesCS5A01G399600 chr5A 100.000 102 0 0 1 102 593077329 593077430 4.550000e-44 189.0
2 TraesCS5A01G399600 chr5D 93.532 2984 82 28 500 3455 473096180 473099080 0.000000e+00 4338.0
3 TraesCS5A01G399600 chr5D 95.833 48 2 0 1 48 28160937 28160984 1.030000e-10 78.7
4 TraesCS5A01G399600 chr5B 95.170 2298 49 15 508 2796 580490308 580492552 0.000000e+00 3572.0
5 TraesCS5A01G399600 chr5B 97.143 35 1 0 3199 3233 611992999 611992965 3.720000e-05 60.2
6 TraesCS5A01G399600 chr5B 96.970 33 1 0 3207 3239 508775521 508775489 4.820000e-04 56.5
7 TraesCS5A01G399600 chr7A 94.621 409 7 3 2784 3185 130440619 130440219 1.360000e-173 619.0
8 TraesCS5A01G399600 chr7A 95.455 220 9 1 3237 3455 130440221 130440002 1.970000e-92 350.0
9 TraesCS5A01G399600 chr7A 80.800 125 14 6 378 498 723309743 723309625 4.750000e-14 89.8
10 TraesCS5A01G399600 chr7A 97.917 48 1 0 1 48 527599448 527599401 2.210000e-12 84.2
11 TraesCS5A01G399600 chr6A 94.335 406 8 3 2784 3182 26755720 26756117 2.950000e-170 608.0
12 TraesCS5A01G399600 chr6A 96.364 220 7 1 3237 3455 26756118 26756337 9.120000e-96 361.0
13 TraesCS5A01G399600 chr6A 100.000 31 0 0 3206 3236 222554979 222555009 1.340000e-04 58.4
14 TraesCS5A01G399600 chr6A 100.000 31 0 0 3206 3236 446725130 446725100 1.340000e-04 58.4
15 TraesCS5A01G399600 chrUn 79.003 381 77 3 2488 2865 413095334 413094954 1.230000e-64 257.0
16 TraesCS5A01G399600 chrUn 84.559 136 11 7 374 504 73964951 73965081 3.620000e-25 126.0
17 TraesCS5A01G399600 chrUn 95.833 48 2 0 1 48 110998801 110998754 1.030000e-10 78.7
18 TraesCS5A01G399600 chr6B 79.003 381 77 3 2488 2865 560700949 560700569 1.230000e-64 257.0
19 TraesCS5A01G399600 chr6B 79.003 381 77 3 2488 2865 560740396 560740016 1.230000e-64 257.0
20 TraesCS5A01G399600 chr6B 78.478 381 79 3 2488 2865 560793302 560792922 2.660000e-61 246.0
21 TraesCS5A01G399600 chr6B 95.556 45 2 0 374 418 592946985 592947029 4.780000e-09 73.1
22 TraesCS5A01G399600 chr3D 82.963 135 13 7 375 504 458607513 458607642 2.820000e-21 113.0
23 TraesCS5A01G399600 chr3D 83.486 109 10 7 374 477 299556857 299556962 1.020000e-15 95.3
24 TraesCS5A01G399600 chr3D 96.296 54 1 1 48 100 427818657 427818710 1.710000e-13 87.9
25 TraesCS5A01G399600 chr3D 95.833 48 2 0 1 48 47240928 47240975 1.030000e-10 78.7
26 TraesCS5A01G399600 chr3B 81.481 135 19 5 374 504 66191073 66191205 4.720000e-19 106.0
27 TraesCS5A01G399600 chr3B 88.000 50 6 0 3191 3240 6249685 6249734 3.720000e-05 60.2
28 TraesCS5A01G399600 chr7D 98.113 53 0 1 49 100 565623976 565623924 1.320000e-14 91.6
29 TraesCS5A01G399600 chr7D 98.113 53 0 1 49 100 565636908 565636856 1.320000e-14 91.6
30 TraesCS5A01G399600 chr7D 98.113 53 0 1 49 100 565639477 565639425 1.320000e-14 91.6
31 TraesCS5A01G399600 chr7D 98.039 51 0 1 49 98 565622365 565622315 1.710000e-13 87.9
32 TraesCS5A01G399600 chr7D 94.340 53 2 1 49 100 565638048 565637996 2.860000e-11 80.5
33 TraesCS5A01G399600 chr7D 94.340 53 2 1 49 100 565638234 565638182 2.860000e-11 80.5
34 TraesCS5A01G399600 chr7D 81.481 108 11 5 378 480 624828798 624828695 2.860000e-11 80.5
35 TraesCS5A01G399600 chr7D 97.674 43 1 0 327 369 565624214 565624172 1.330000e-09 75.0
36 TraesCS5A01G399600 chr7D 92.453 53 3 1 49 100 565639661 565639609 1.330000e-09 75.0
37 TraesCS5A01G399600 chr2D 83.019 106 9 5 378 478 82911587 82911688 1.710000e-13 87.9
38 TraesCS5A01G399600 chr1D 96.226 53 1 1 49 100 416093359 416093307 6.140000e-13 86.1
39 TraesCS5A01G399600 chr1D 95.833 48 2 0 1 48 431510815 431510862 1.030000e-10 78.7
40 TraesCS5A01G399600 chr4B 81.250 112 14 4 374 480 648173609 648173718 2.210000e-12 84.2
41 TraesCS5A01G399600 chr4B 90.476 63 5 1 3171 3232 563209586 563209524 7.950000e-12 82.4
42 TraesCS5A01G399600 chr4B 95.833 48 2 0 1 48 617916830 617916783 1.030000e-10 78.7
43 TraesCS5A01G399600 chr4A 90.476 63 5 1 3171 3232 16470342 16470404 7.950000e-12 82.4
44 TraesCS5A01G399600 chr2B 92.727 55 4 0 1 55 80671990 80671936 2.860000e-11 80.5
45 TraesCS5A01G399600 chr7B 95.833 48 2 0 1 48 605818760 605818807 1.030000e-10 78.7
46 TraesCS5A01G399600 chr1A 95.833 48 2 0 1 48 579963940 579963987 1.030000e-10 78.7
47 TraesCS5A01G399600 chr4D 88.889 63 6 1 3171 3232 450202766 450202704 3.700000e-10 76.8


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 TraesCS5A01G399600 chr5A 593077329 593080783 3454 False 2990.5 5792 100.0000 1 3455 2 chr5A.!!$F1 3454
1 TraesCS5A01G399600 chr5D 473096180 473099080 2900 False 4338.0 4338 93.5320 500 3455 1 chr5D.!!$F2 2955
2 TraesCS5A01G399600 chr5B 580490308 580492552 2244 False 3572.0 3572 95.1700 508 2796 1 chr5B.!!$F1 2288
3 TraesCS5A01G399600 chr7A 130440002 130440619 617 True 484.5 619 95.0380 2784 3455 2 chr7A.!!$R3 671
4 TraesCS5A01G399600 chr6A 26755720 26756337 617 False 484.5 608 95.3495 2784 3455 2 chr6A.!!$F2 671

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
610 611 0.036388 CCTGCTCAAGCCCTAAACGA 60.036 55.0 0.00 0.0 41.18 3.85 F
613 614 0.442699 GCTCAAGCCCTAAACGAACG 59.557 55.0 0.00 0.0 34.31 3.95 F
1459 1471 0.811616 GGCGCAGAAGGTCGATGAAT 60.812 55.0 10.83 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1923 1.167851 CCACAACATCTGGCACGATT 58.832 50.000 0.00 0.00 0.00 3.34 R
2124 2136 4.960938 TGGTGTATGTATCAGAATCTGGC 58.039 43.478 10.71 2.31 31.51 4.85 R
3032 3044 0.104934 AACCTGAGGACTGGGTGACT 60.105 55.000 4.99 0.00 39.06 3.41 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
45 46 4.383850 GAGAGCTGCTCAGATGTCTAAA 57.616 45.455 29.49 0.00 43.38 1.85
46 47 4.947645 GAGAGCTGCTCAGATGTCTAAAT 58.052 43.478 29.49 5.90 43.38 1.40
47 48 4.695396 AGAGCTGCTCAGATGTCTAAATG 58.305 43.478 29.49 0.00 32.06 2.32
48 49 3.204526 AGCTGCTCAGATGTCTAAATGC 58.795 45.455 0.00 0.00 0.00 3.56
49 50 2.941064 GCTGCTCAGATGTCTAAATGCA 59.059 45.455 0.29 0.00 0.00 3.96
50 51 3.376234 GCTGCTCAGATGTCTAAATGCAA 59.624 43.478 0.29 0.00 0.00 4.08
51 52 4.036498 GCTGCTCAGATGTCTAAATGCAAT 59.964 41.667 0.29 0.00 0.00 3.56
52 53 5.237996 GCTGCTCAGATGTCTAAATGCAATA 59.762 40.000 0.29 0.00 0.00 1.90
53 54 6.238566 GCTGCTCAGATGTCTAAATGCAATAA 60.239 38.462 0.29 0.00 0.00 1.40
54 55 7.521748 GCTGCTCAGATGTCTAAATGCAATAAT 60.522 37.037 0.29 0.00 0.00 1.28
55 56 7.645402 TGCTCAGATGTCTAAATGCAATAATG 58.355 34.615 0.00 0.00 0.00 1.90
71 72 6.274001 CAATAATGCTACACCTACAACGAG 57.726 41.667 0.00 0.00 0.00 4.18
72 73 2.295253 ATGCTACACCTACAACGAGC 57.705 50.000 0.00 0.00 0.00 5.03
73 74 1.254026 TGCTACACCTACAACGAGCT 58.746 50.000 0.00 0.00 0.00 4.09
74 75 1.616865 TGCTACACCTACAACGAGCTT 59.383 47.619 0.00 0.00 0.00 3.74
75 76 2.821378 TGCTACACCTACAACGAGCTTA 59.179 45.455 0.00 0.00 0.00 3.09
76 77 3.177487 GCTACACCTACAACGAGCTTAC 58.823 50.000 0.00 0.00 0.00 2.34
77 78 2.342910 ACACCTACAACGAGCTTACG 57.657 50.000 0.00 0.00 39.31 3.18
78 79 1.881973 ACACCTACAACGAGCTTACGA 59.118 47.619 1.33 0.00 37.03 3.43
79 80 2.294233 ACACCTACAACGAGCTTACGAA 59.706 45.455 1.33 0.00 37.03 3.85
80 81 2.915463 CACCTACAACGAGCTTACGAAG 59.085 50.000 1.33 0.00 37.03 3.79
81 82 2.816087 ACCTACAACGAGCTTACGAAGA 59.184 45.455 1.33 0.00 37.03 2.87
82 83 3.169733 CCTACAACGAGCTTACGAAGAC 58.830 50.000 1.33 0.00 37.03 3.01
83 84 3.119919 CCTACAACGAGCTTACGAAGACT 60.120 47.826 1.33 0.00 37.03 3.24
84 85 3.366440 ACAACGAGCTTACGAAGACTT 57.634 42.857 1.33 0.00 37.03 3.01
85 86 4.494350 ACAACGAGCTTACGAAGACTTA 57.506 40.909 1.33 0.00 37.03 2.24
86 87 4.225208 ACAACGAGCTTACGAAGACTTAC 58.775 43.478 1.33 0.00 37.03 2.34
87 88 3.114693 ACGAGCTTACGAAGACTTACG 57.885 47.619 1.33 0.00 37.03 3.18
88 89 2.481952 ACGAGCTTACGAAGACTTACGT 59.518 45.455 14.22 14.22 44.72 3.57
89 90 3.679980 ACGAGCTTACGAAGACTTACGTA 59.320 43.478 12.73 12.73 42.61 3.57
91 92 4.490191 CGAGCTTACGAAGACTTACGTAAC 59.510 45.833 19.54 16.96 45.48 2.50
92 93 5.619625 AGCTTACGAAGACTTACGTAACT 57.380 39.130 19.54 18.09 45.48 2.24
93 94 6.006759 AGCTTACGAAGACTTACGTAACTT 57.993 37.500 19.54 7.38 45.48 2.66
94 95 6.442112 AGCTTACGAAGACTTACGTAACTTT 58.558 36.000 19.54 0.00 45.48 2.66
95 96 6.580416 AGCTTACGAAGACTTACGTAACTTTC 59.420 38.462 19.54 7.59 45.48 2.62
96 97 6.183359 GCTTACGAAGACTTACGTAACTTTCC 60.183 42.308 19.54 0.00 45.48 3.13
97 98 4.550422 ACGAAGACTTACGTAACTTTCCC 58.450 43.478 3.29 0.00 40.92 3.97
98 99 4.279420 ACGAAGACTTACGTAACTTTCCCT 59.721 41.667 3.29 0.00 40.92 4.20
99 100 4.855937 CGAAGACTTACGTAACTTTCCCTC 59.144 45.833 3.29 1.46 0.00 4.30
100 101 4.797800 AGACTTACGTAACTTTCCCTCC 57.202 45.455 3.29 0.00 0.00 4.30
101 102 4.154942 AGACTTACGTAACTTTCCCTCCA 58.845 43.478 3.29 0.00 0.00 3.86
342 343 6.476243 GTCAGCCTTTACGTAAAAATCTCA 57.524 37.500 20.47 3.30 0.00 3.27
343 344 6.304882 GTCAGCCTTTACGTAAAAATCTCAC 58.695 40.000 20.47 10.94 0.00 3.51
344 345 5.992829 TCAGCCTTTACGTAAAAATCTCACA 59.007 36.000 20.47 0.00 0.00 3.58
345 346 6.653320 TCAGCCTTTACGTAAAAATCTCACAT 59.347 34.615 20.47 0.00 0.00 3.21
346 347 7.820386 TCAGCCTTTACGTAAAAATCTCACATA 59.180 33.333 20.47 0.00 0.00 2.29
347 348 8.447833 CAGCCTTTACGTAAAAATCTCACATAA 58.552 33.333 20.47 0.00 0.00 1.90
348 349 8.448615 AGCCTTTACGTAAAAATCTCACATAAC 58.551 33.333 20.47 0.52 0.00 1.89
349 350 8.448615 GCCTTTACGTAAAAATCTCACATAACT 58.551 33.333 20.47 0.00 0.00 2.24
356 357 9.246423 CGTAAAAATCTCACATAACTTTACGTG 57.754 33.333 13.26 0.00 42.17 4.49
357 358 9.537848 GTAAAAATCTCACATAACTTTACGTGG 57.462 33.333 0.00 0.00 28.68 4.94
358 359 6.737254 AAATCTCACATAACTTTACGTGGG 57.263 37.500 0.00 0.00 29.08 4.61
359 360 4.877378 TCTCACATAACTTTACGTGGGT 57.123 40.909 0.00 0.00 29.98 4.51
360 361 4.813027 TCTCACATAACTTTACGTGGGTC 58.187 43.478 0.00 0.00 29.98 4.46
361 362 4.525487 TCTCACATAACTTTACGTGGGTCT 59.475 41.667 0.00 0.00 29.98 3.85
362 363 5.711506 TCTCACATAACTTTACGTGGGTCTA 59.288 40.000 0.00 0.00 29.98 2.59
363 364 5.957798 TCACATAACTTTACGTGGGTCTAG 58.042 41.667 0.00 0.00 28.68 2.43
364 365 5.477984 TCACATAACTTTACGTGGGTCTAGT 59.522 40.000 0.00 0.00 28.68 2.57
365 366 6.658816 TCACATAACTTTACGTGGGTCTAGTA 59.341 38.462 0.00 0.00 28.68 1.82
366 367 7.340232 TCACATAACTTTACGTGGGTCTAGTAT 59.660 37.037 0.00 0.00 28.68 2.12
367 368 7.646922 CACATAACTTTACGTGGGTCTAGTATC 59.353 40.741 0.00 0.00 0.00 2.24
368 369 4.889832 ACTTTACGTGGGTCTAGTATCG 57.110 45.455 0.00 0.00 0.00 2.92
369 370 3.629398 ACTTTACGTGGGTCTAGTATCGG 59.371 47.826 0.00 0.00 0.00 4.18
370 371 3.281727 TTACGTGGGTCTAGTATCGGT 57.718 47.619 0.00 0.00 0.00 4.69
371 372 2.134789 ACGTGGGTCTAGTATCGGTT 57.865 50.000 0.00 0.00 0.00 4.44
372 373 2.019984 ACGTGGGTCTAGTATCGGTTC 58.980 52.381 0.00 0.00 0.00 3.62
373 374 1.003116 CGTGGGTCTAGTATCGGTTCG 60.003 57.143 0.00 0.00 0.00 3.95
374 375 2.019984 GTGGGTCTAGTATCGGTTCGT 58.980 52.381 0.00 0.00 0.00 3.85
375 376 2.032675 GTGGGTCTAGTATCGGTTCGTC 59.967 54.545 0.00 0.00 0.00 4.20
376 377 2.092753 TGGGTCTAGTATCGGTTCGTCT 60.093 50.000 0.00 0.00 0.00 4.18
377 378 3.134623 TGGGTCTAGTATCGGTTCGTCTA 59.865 47.826 0.00 0.00 0.00 2.59
378 379 4.130118 GGGTCTAGTATCGGTTCGTCTAA 58.870 47.826 0.00 0.00 0.00 2.10
379 380 4.576463 GGGTCTAGTATCGGTTCGTCTAAA 59.424 45.833 0.00 0.00 0.00 1.85
380 381 5.240403 GGGTCTAGTATCGGTTCGTCTAAAT 59.760 44.000 0.00 0.00 0.00 1.40
381 382 6.141462 GGTCTAGTATCGGTTCGTCTAAATG 58.859 44.000 0.00 0.00 0.00 2.32
382 383 6.017605 GGTCTAGTATCGGTTCGTCTAAATGA 60.018 42.308 0.00 0.00 0.00 2.57
383 384 6.850317 GTCTAGTATCGGTTCGTCTAAATGAC 59.150 42.308 0.00 0.00 42.06 3.06
384 385 5.831702 AGTATCGGTTCGTCTAAATGACT 57.168 39.130 0.00 0.00 43.25 3.41
385 386 6.205101 AGTATCGGTTCGTCTAAATGACTT 57.795 37.500 0.00 0.00 43.25 3.01
386 387 6.034591 AGTATCGGTTCGTCTAAATGACTTG 58.965 40.000 0.00 0.00 43.25 3.16
387 388 4.508461 TCGGTTCGTCTAAATGACTTGA 57.492 40.909 0.00 0.00 43.25 3.02
388 389 4.873817 TCGGTTCGTCTAAATGACTTGAA 58.126 39.130 0.00 0.00 43.25 2.69
389 390 5.291178 TCGGTTCGTCTAAATGACTTGAAA 58.709 37.500 0.00 0.00 43.25 2.69
390 391 5.929992 TCGGTTCGTCTAAATGACTTGAAAT 59.070 36.000 0.00 0.00 43.25 2.17
391 392 6.425721 TCGGTTCGTCTAAATGACTTGAAATT 59.574 34.615 0.00 0.00 43.25 1.82
392 393 7.041644 TCGGTTCGTCTAAATGACTTGAAATTT 60.042 33.333 0.00 0.00 43.25 1.82
393 394 7.059488 CGGTTCGTCTAAATGACTTGAAATTTG 59.941 37.037 0.00 0.00 43.25 2.32
394 395 7.326063 GGTTCGTCTAAATGACTTGAAATTTGG 59.674 37.037 0.00 0.00 43.25 3.28
395 396 7.737972 TCGTCTAAATGACTTGAAATTTGGA 57.262 32.000 0.00 0.00 43.25 3.53
396 397 7.806690 TCGTCTAAATGACTTGAAATTTGGAG 58.193 34.615 0.00 0.00 43.25 3.86
397 398 6.524586 CGTCTAAATGACTTGAAATTTGGAGC 59.475 38.462 0.00 0.00 43.25 4.70
398 399 6.524586 GTCTAAATGACTTGAAATTTGGAGCG 59.475 38.462 0.00 0.00 42.21 5.03
399 400 3.855689 ATGACTTGAAATTTGGAGCGG 57.144 42.857 0.00 0.00 0.00 5.52
400 401 2.857483 TGACTTGAAATTTGGAGCGGA 58.143 42.857 0.00 0.00 0.00 5.54
401 402 2.552315 TGACTTGAAATTTGGAGCGGAC 59.448 45.455 0.00 0.00 0.00 4.79
402 403 1.886542 ACTTGAAATTTGGAGCGGACC 59.113 47.619 0.00 0.00 0.00 4.46
403 404 2.162681 CTTGAAATTTGGAGCGGACCT 58.837 47.619 0.00 0.00 0.00 3.85
404 405 1.821216 TGAAATTTGGAGCGGACCTC 58.179 50.000 0.00 0.00 39.98 3.85
405 406 1.073125 TGAAATTTGGAGCGGACCTCA 59.927 47.619 0.00 0.00 42.62 3.86
406 407 1.468914 GAAATTTGGAGCGGACCTCAC 59.531 52.381 0.00 0.00 42.62 3.51
407 408 0.400213 AATTTGGAGCGGACCTCACA 59.600 50.000 0.00 0.00 42.62 3.58
408 409 0.321653 ATTTGGAGCGGACCTCACAC 60.322 55.000 0.00 0.00 42.62 3.82
409 410 1.691195 TTTGGAGCGGACCTCACACA 61.691 55.000 0.00 0.00 42.62 3.72
410 411 1.480212 TTGGAGCGGACCTCACACAT 61.480 55.000 0.00 0.00 42.62 3.21
411 412 1.153549 GGAGCGGACCTCACACATC 60.154 63.158 0.00 0.00 42.62 3.06
412 413 1.591703 GAGCGGACCTCACACATCA 59.408 57.895 0.00 0.00 40.45 3.07
413 414 0.037326 GAGCGGACCTCACACATCAA 60.037 55.000 0.00 0.00 40.45 2.57
414 415 0.396435 AGCGGACCTCACACATCAAA 59.604 50.000 0.00 0.00 0.00 2.69
415 416 1.003580 AGCGGACCTCACACATCAAAT 59.996 47.619 0.00 0.00 0.00 2.32
416 417 1.812571 GCGGACCTCACACATCAAATT 59.187 47.619 0.00 0.00 0.00 1.82
417 418 2.228822 GCGGACCTCACACATCAAATTT 59.771 45.455 0.00 0.00 0.00 1.82
418 419 3.305335 GCGGACCTCACACATCAAATTTT 60.305 43.478 0.00 0.00 0.00 1.82
419 420 4.795962 GCGGACCTCACACATCAAATTTTT 60.796 41.667 0.00 0.00 0.00 1.94
494 495 4.771590 TTTTTCTAACCAGCTGCAGATG 57.228 40.909 24.93 24.93 0.00 2.90
495 496 3.701205 TTTCTAACCAGCTGCAGATGA 57.299 42.857 32.59 12.55 32.25 2.92
496 497 2.975732 TCTAACCAGCTGCAGATGAG 57.024 50.000 32.59 23.22 32.25 2.90
497 498 1.134580 TCTAACCAGCTGCAGATGAGC 60.135 52.381 32.59 10.44 36.65 4.26
511 512 4.442472 GCAGATGAGCTGGGCATTATTTTT 60.442 41.667 0.00 0.00 45.03 1.94
576 577 0.948678 AACGCATACACACCCAACAC 59.051 50.000 0.00 0.00 0.00 3.32
606 607 2.677228 GGCCTGCTCAAGCCCTAA 59.323 61.111 0.00 0.00 43.76 2.69
607 608 1.000896 GGCCTGCTCAAGCCCTAAA 60.001 57.895 0.00 0.00 43.76 1.85
608 609 1.315981 GGCCTGCTCAAGCCCTAAAC 61.316 60.000 0.00 0.00 43.76 2.01
609 610 1.648467 GCCTGCTCAAGCCCTAAACG 61.648 60.000 0.00 0.00 41.18 3.60
610 611 0.036388 CCTGCTCAAGCCCTAAACGA 60.036 55.000 0.00 0.00 41.18 3.85
611 612 1.610624 CCTGCTCAAGCCCTAAACGAA 60.611 52.381 0.00 0.00 41.18 3.85
612 613 1.464997 CTGCTCAAGCCCTAAACGAAC 59.535 52.381 0.00 0.00 41.18 3.95
613 614 0.442699 GCTCAAGCCCTAAACGAACG 59.557 55.000 0.00 0.00 34.31 3.95
614 615 1.076332 CTCAAGCCCTAAACGAACGG 58.924 55.000 0.00 0.00 0.00 4.44
615 616 0.952010 TCAAGCCCTAAACGAACGGC 60.952 55.000 0.00 0.00 41.96 5.68
616 617 3.066198 AGCCCTAAACGAACGGCT 58.934 55.556 0.00 0.00 46.96 5.52
617 618 3.976758 GCCCTAAACGAACGGCTT 58.023 55.556 0.00 0.00 38.41 4.35
618 619 1.500396 GCCCTAAACGAACGGCTTG 59.500 57.895 0.00 0.00 38.41 4.01
619 620 1.500396 CCCTAAACGAACGGCTTGC 59.500 57.895 0.00 0.00 0.00 4.01
620 621 1.500396 CCTAAACGAACGGCTTGCC 59.500 57.895 0.75 0.75 0.00 4.52
621 622 1.131826 CTAAACGAACGGCTTGCCG 59.868 57.895 29.32 29.32 39.31 5.69
622 623 1.286354 CTAAACGAACGGCTTGCCGA 61.286 55.000 35.96 14.10 36.94 5.54
623 624 0.879400 TAAACGAACGGCTTGCCGAA 60.879 50.000 35.96 12.08 36.94 4.30
624 625 1.716826 AAACGAACGGCTTGCCGAAA 61.717 50.000 35.96 0.00 36.94 3.46
625 626 2.127383 CGAACGGCTTGCCGAAAC 60.127 61.111 35.96 23.78 36.94 2.78
626 627 2.887889 CGAACGGCTTGCCGAAACA 61.888 57.895 35.96 0.00 36.94 2.83
627 628 1.082104 GAACGGCTTGCCGAAACAG 60.082 57.895 35.96 10.40 36.94 3.16
628 629 1.503818 GAACGGCTTGCCGAAACAGA 61.504 55.000 35.96 0.00 36.94 3.41
629 630 0.889186 AACGGCTTGCCGAAACAGAT 60.889 50.000 35.96 12.67 36.94 2.90
671 672 3.372458 GGCCATTTTCTCTCCCTCAATCT 60.372 47.826 0.00 0.00 0.00 2.40
675 676 4.737855 TTTTCTCTCCCTCAATCTACGG 57.262 45.455 0.00 0.00 0.00 4.02
680 682 0.899720 TCCCTCAATCTACGGCGTTT 59.100 50.000 21.24 3.07 0.00 3.60
722 724 1.671901 CGAGGAGAGGTTGAGAGGGC 61.672 65.000 0.00 0.00 0.00 5.19
765 769 0.980231 CTTGAGGTGGAGGGAGGGAG 60.980 65.000 0.00 0.00 0.00 4.30
766 770 2.041405 GAGGTGGAGGGAGGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
767 771 3.700350 AGGTGGAGGGAGGGAGGG 61.700 72.222 0.00 0.00 0.00 4.30
768 772 3.695825 GGTGGAGGGAGGGAGGGA 61.696 72.222 0.00 0.00 0.00 4.20
769 773 2.041405 GTGGAGGGAGGGAGGGAG 60.041 72.222 0.00 0.00 0.00 4.30
770 774 3.368501 TGGAGGGAGGGAGGGAGG 61.369 72.222 0.00 0.00 0.00 4.30
771 775 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
772 776 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
773 777 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
774 778 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
775 779 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
776 780 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
777 781 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
778 782 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
779 783 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
780 784 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
781 785 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
782 786 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
783 787 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
784 788 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
785 789 3.039526 AGGGAGGGAGGGAGGGAG 61.040 72.222 0.00 0.00 0.00 4.30
786 790 4.179599 GGGAGGGAGGGAGGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
787 791 4.179599 GGAGGGAGGGAGGGAGGG 62.180 77.778 0.00 0.00 0.00 4.30
788 792 3.036959 GAGGGAGGGAGGGAGGGA 61.037 72.222 0.00 0.00 0.00 4.20
812 816 3.224324 GAGCGGTGGAGGCGGATA 61.224 66.667 0.00 0.00 35.00 2.59
840 844 2.298610 CTACAGCTGGAGGTCGATACA 58.701 52.381 19.10 0.00 0.00 2.29
990 1002 4.988598 CAGCGTGTGGAAGGCGGT 62.989 66.667 0.00 0.00 44.54 5.68
997 1009 1.883084 GTGGAAGGCGGTGATAGCG 60.883 63.158 0.00 0.00 42.73 4.26
1020 1032 1.671379 GGCCAGTTTCCGTCTCACC 60.671 63.158 0.00 0.00 0.00 4.02
1072 1084 1.956629 GCTTAGCAGCGGGACAGGTA 61.957 60.000 0.00 0.00 35.91 3.08
1375 1387 4.953868 TGTGGGACGTCGTTGCCG 62.954 66.667 9.92 0.00 0.00 5.69
1381 1393 1.010419 GGACGTCGTTGCCGTAATGT 61.010 55.000 9.92 0.00 38.92 2.71
1459 1471 0.811616 GGCGCAGAAGGTCGATGAAT 60.812 55.000 10.83 0.00 0.00 2.57
1592 1604 6.822170 CAGGAGATCTTTGAACAGATGAATGA 59.178 38.462 0.00 0.00 33.36 2.57
1911 1923 1.788229 TGGATATGCAGAAGGACGGA 58.212 50.000 0.00 0.00 0.00 4.69
2124 2136 1.193203 CGTATGATAAAGCGCTGCCAG 59.807 52.381 12.58 0.00 0.00 4.85
2756 2768 9.871238 CTACAGTTACTTCATAAGTACCACATT 57.129 33.333 0.00 0.00 43.30 2.71
2819 2831 6.995091 GTCCTATCAGCATCTTCCTTACATTT 59.005 38.462 0.00 0.00 0.00 2.32
3031 3043 9.923786 GGTAAAATTGTACATTTTTGTTTGGTC 57.076 29.630 27.00 13.99 33.73 4.02
3034 3046 8.785329 AAATTGTACATTTTTGTTTGGTCAGT 57.215 26.923 9.40 0.00 0.00 3.41
3035 3047 8.419076 AATTGTACATTTTTGTTTGGTCAGTC 57.581 30.769 0.00 0.00 0.00 3.51
3036 3048 6.516739 TGTACATTTTTGTTTGGTCAGTCA 57.483 33.333 0.00 0.00 0.00 3.41
3037 3049 6.326375 TGTACATTTTTGTTTGGTCAGTCAC 58.674 36.000 0.00 0.00 0.00 3.67
3223 3259 6.918892 TCAATGACAACTAATATGGAACGG 57.081 37.500 0.00 0.00 0.00 4.44
3224 3260 6.645306 TCAATGACAACTAATATGGAACGGA 58.355 36.000 0.00 0.00 0.00 4.69
3254 3290 3.105959 ACCTAGCAGATTTTGGGCATT 57.894 42.857 0.00 0.00 0.00 3.56
3325 3361 2.437200 TTGCTAAAATGCACAGTGCC 57.563 45.000 23.06 5.93 44.23 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.971481 TGAGCAGCTCTCAGCAAAAA 58.029 45.000 23.15 0.00 46.34 1.94
17 18 3.711937 TGAGCAGCTCTCAGCAAAA 57.288 47.368 23.15 0.00 46.34 2.44
24 25 4.383850 TTTAGACATCTGAGCAGCTCTC 57.616 45.455 23.15 11.79 42.23 3.20
25 26 4.695396 CATTTAGACATCTGAGCAGCTCT 58.305 43.478 23.15 2.04 0.00 4.09
26 27 3.248125 GCATTTAGACATCTGAGCAGCTC 59.752 47.826 16.21 16.21 0.00 4.09
27 28 3.204526 GCATTTAGACATCTGAGCAGCT 58.795 45.455 0.00 0.00 0.00 4.24
28 29 2.941064 TGCATTTAGACATCTGAGCAGC 59.059 45.455 0.00 0.00 0.00 5.25
29 30 5.752892 ATTGCATTTAGACATCTGAGCAG 57.247 39.130 0.00 0.00 31.87 4.24
30 31 7.645402 CATTATTGCATTTAGACATCTGAGCA 58.355 34.615 0.00 0.00 0.00 4.26
48 49 5.276868 GCTCGTTGTAGGTGTAGCATTATTG 60.277 44.000 0.00 0.00 0.00 1.90
49 50 4.809426 GCTCGTTGTAGGTGTAGCATTATT 59.191 41.667 0.00 0.00 0.00 1.40
50 51 4.099573 AGCTCGTTGTAGGTGTAGCATTAT 59.900 41.667 0.00 0.00 32.42 1.28
51 52 3.446161 AGCTCGTTGTAGGTGTAGCATTA 59.554 43.478 0.00 0.00 32.42 1.90
52 53 2.233922 AGCTCGTTGTAGGTGTAGCATT 59.766 45.455 0.00 0.00 32.42 3.56
53 54 1.825474 AGCTCGTTGTAGGTGTAGCAT 59.175 47.619 0.00 0.00 32.42 3.79
54 55 1.254026 AGCTCGTTGTAGGTGTAGCA 58.746 50.000 0.00 0.00 32.42 3.49
55 56 2.365408 AAGCTCGTTGTAGGTGTAGC 57.635 50.000 0.00 0.00 0.00 3.58
56 57 3.125829 TCGTAAGCTCGTTGTAGGTGTAG 59.874 47.826 0.00 0.00 37.18 2.74
57 58 3.073678 TCGTAAGCTCGTTGTAGGTGTA 58.926 45.455 0.00 0.00 37.18 2.90
58 59 1.881973 TCGTAAGCTCGTTGTAGGTGT 59.118 47.619 0.00 0.00 37.18 4.16
59 60 2.624316 TCGTAAGCTCGTTGTAGGTG 57.376 50.000 0.00 0.00 37.18 4.00
60 61 2.816087 TCTTCGTAAGCTCGTTGTAGGT 59.184 45.455 0.00 0.00 37.18 3.08
61 62 3.119919 AGTCTTCGTAAGCTCGTTGTAGG 60.120 47.826 0.00 0.00 37.18 3.18
62 63 4.080969 AGTCTTCGTAAGCTCGTTGTAG 57.919 45.455 0.00 0.00 37.18 2.74
63 64 4.494350 AAGTCTTCGTAAGCTCGTTGTA 57.506 40.909 0.00 0.00 37.18 2.41
64 65 3.366440 AAGTCTTCGTAAGCTCGTTGT 57.634 42.857 0.00 0.00 37.18 3.32
65 66 3.297461 CGTAAGTCTTCGTAAGCTCGTTG 59.703 47.826 0.00 0.00 37.18 4.10
66 67 3.486584 CGTAAGTCTTCGTAAGCTCGTT 58.513 45.455 0.00 0.00 37.18 3.85
67 68 3.114693 CGTAAGTCTTCGTAAGCTCGT 57.885 47.619 0.00 0.00 37.18 4.18
319 320 6.073440 TGTGAGATTTTTACGTAAAGGCTGAC 60.073 38.462 19.31 19.35 0.00 3.51
320 321 5.992829 TGTGAGATTTTTACGTAAAGGCTGA 59.007 36.000 19.31 10.37 0.00 4.26
321 322 6.236017 TGTGAGATTTTTACGTAAAGGCTG 57.764 37.500 19.31 0.00 0.00 4.85
322 323 8.448615 GTTATGTGAGATTTTTACGTAAAGGCT 58.551 33.333 19.31 16.83 30.28 4.58
323 324 8.448615 AGTTATGTGAGATTTTTACGTAAAGGC 58.551 33.333 19.31 13.01 30.28 4.35
341 342 5.717119 ACTAGACCCACGTAAAGTTATGTG 58.283 41.667 14.04 14.04 45.67 3.21
342 343 5.990120 ACTAGACCCACGTAAAGTTATGT 57.010 39.130 0.00 0.00 33.34 2.29
343 344 6.854892 CGATACTAGACCCACGTAAAGTTATG 59.145 42.308 0.00 0.00 0.00 1.90
344 345 6.016777 CCGATACTAGACCCACGTAAAGTTAT 60.017 42.308 0.00 0.00 0.00 1.89
345 346 5.296780 CCGATACTAGACCCACGTAAAGTTA 59.703 44.000 0.00 0.00 0.00 2.24
346 347 4.096984 CCGATACTAGACCCACGTAAAGTT 59.903 45.833 0.00 0.00 0.00 2.66
347 348 3.629398 CCGATACTAGACCCACGTAAAGT 59.371 47.826 0.00 0.00 0.00 2.66
348 349 3.629398 ACCGATACTAGACCCACGTAAAG 59.371 47.826 0.00 0.00 0.00 1.85
349 350 3.620488 ACCGATACTAGACCCACGTAAA 58.380 45.455 0.00 0.00 0.00 2.01
350 351 3.281727 ACCGATACTAGACCCACGTAA 57.718 47.619 0.00 0.00 0.00 3.18
351 352 3.206150 GAACCGATACTAGACCCACGTA 58.794 50.000 0.00 0.00 0.00 3.57
352 353 2.019984 GAACCGATACTAGACCCACGT 58.980 52.381 0.00 0.00 0.00 4.49
353 354 1.003116 CGAACCGATACTAGACCCACG 60.003 57.143 0.00 0.00 0.00 4.94
354 355 2.019984 ACGAACCGATACTAGACCCAC 58.980 52.381 0.00 0.00 0.00 4.61
355 356 2.092753 AGACGAACCGATACTAGACCCA 60.093 50.000 0.00 0.00 0.00 4.51
356 357 2.570135 AGACGAACCGATACTAGACCC 58.430 52.381 0.00 0.00 0.00 4.46
357 358 5.741388 TTTAGACGAACCGATACTAGACC 57.259 43.478 0.00 0.00 0.00 3.85
358 359 6.850317 GTCATTTAGACGAACCGATACTAGAC 59.150 42.308 0.00 0.00 37.53 2.59
359 360 6.952743 GTCATTTAGACGAACCGATACTAGA 58.047 40.000 0.00 0.00 37.53 2.43
374 375 6.349280 CCGCTCCAAATTTCAAGTCATTTAGA 60.349 38.462 0.00 0.00 0.00 2.10
375 376 5.801947 CCGCTCCAAATTTCAAGTCATTTAG 59.198 40.000 0.00 0.00 0.00 1.85
376 377 5.475220 TCCGCTCCAAATTTCAAGTCATTTA 59.525 36.000 0.00 0.00 0.00 1.40
377 378 4.280677 TCCGCTCCAAATTTCAAGTCATTT 59.719 37.500 0.00 0.00 0.00 2.32
378 379 3.826157 TCCGCTCCAAATTTCAAGTCATT 59.174 39.130 0.00 0.00 0.00 2.57
379 380 3.191371 GTCCGCTCCAAATTTCAAGTCAT 59.809 43.478 0.00 0.00 0.00 3.06
380 381 2.552315 GTCCGCTCCAAATTTCAAGTCA 59.448 45.455 0.00 0.00 0.00 3.41
381 382 2.095212 GGTCCGCTCCAAATTTCAAGTC 60.095 50.000 0.00 0.00 0.00 3.01
382 383 1.886542 GGTCCGCTCCAAATTTCAAGT 59.113 47.619 0.00 0.00 0.00 3.16
383 384 2.162408 GAGGTCCGCTCCAAATTTCAAG 59.838 50.000 0.00 0.00 0.00 3.02
384 385 2.159382 GAGGTCCGCTCCAAATTTCAA 58.841 47.619 0.00 0.00 0.00 2.69
385 386 1.073125 TGAGGTCCGCTCCAAATTTCA 59.927 47.619 0.00 0.00 0.00 2.69
386 387 1.468914 GTGAGGTCCGCTCCAAATTTC 59.531 52.381 0.00 0.00 0.00 2.17
387 388 1.202879 TGTGAGGTCCGCTCCAAATTT 60.203 47.619 0.00 0.00 0.00 1.82
388 389 0.400213 TGTGAGGTCCGCTCCAAATT 59.600 50.000 0.00 0.00 0.00 1.82
389 390 0.321653 GTGTGAGGTCCGCTCCAAAT 60.322 55.000 0.00 0.00 0.00 2.32
390 391 1.070786 GTGTGAGGTCCGCTCCAAA 59.929 57.895 0.00 0.00 0.00 3.28
391 392 1.480212 ATGTGTGAGGTCCGCTCCAA 61.480 55.000 0.00 0.00 0.00 3.53
392 393 1.888436 GATGTGTGAGGTCCGCTCCA 61.888 60.000 0.00 0.00 0.00 3.86
393 394 1.153549 GATGTGTGAGGTCCGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
394 395 0.037326 TTGATGTGTGAGGTCCGCTC 60.037 55.000 0.00 0.00 0.00 5.03
395 396 0.396435 TTTGATGTGTGAGGTCCGCT 59.604 50.000 0.00 0.00 0.00 5.52
396 397 1.453155 ATTTGATGTGTGAGGTCCGC 58.547 50.000 0.00 0.00 0.00 5.54
397 398 4.503741 AAAATTTGATGTGTGAGGTCCG 57.496 40.909 0.00 0.00 0.00 4.79
473 474 4.397420 TCATCTGCAGCTGGTTAGAAAAA 58.603 39.130 17.12 0.00 0.00 1.94
474 475 4.005650 CTCATCTGCAGCTGGTTAGAAAA 58.994 43.478 17.12 0.00 0.00 2.29
475 476 3.603532 CTCATCTGCAGCTGGTTAGAAA 58.396 45.455 17.12 0.00 0.00 2.52
476 477 2.679059 GCTCATCTGCAGCTGGTTAGAA 60.679 50.000 17.12 0.00 33.75 2.10
477 478 1.134580 GCTCATCTGCAGCTGGTTAGA 60.135 52.381 17.12 5.49 33.75 2.10
478 479 1.134461 AGCTCATCTGCAGCTGGTTAG 60.134 52.381 17.12 8.76 45.85 2.34
479 480 0.907486 AGCTCATCTGCAGCTGGTTA 59.093 50.000 17.12 0.00 45.85 2.85
480 481 1.684035 AGCTCATCTGCAGCTGGTT 59.316 52.632 17.12 3.99 45.85 3.67
481 482 3.401332 AGCTCATCTGCAGCTGGT 58.599 55.556 17.12 5.94 45.85 4.00
485 486 3.210528 GCCCAGCTCATCTGCAGC 61.211 66.667 9.47 0.00 41.50 5.25
486 487 0.752009 AATGCCCAGCTCATCTGCAG 60.752 55.000 7.63 7.63 41.50 4.41
487 488 0.547553 TAATGCCCAGCTCATCTGCA 59.452 50.000 0.00 0.00 41.50 4.41
488 489 1.906990 ATAATGCCCAGCTCATCTGC 58.093 50.000 0.00 0.00 41.50 4.26
489 490 4.931661 AAAATAATGCCCAGCTCATCTG 57.068 40.909 0.00 0.00 42.49 2.90
490 491 4.037208 CGAAAAATAATGCCCAGCTCATCT 59.963 41.667 0.00 0.00 0.00 2.90
491 492 4.293415 CGAAAAATAATGCCCAGCTCATC 58.707 43.478 0.00 0.00 0.00 2.92
492 493 3.068590 CCGAAAAATAATGCCCAGCTCAT 59.931 43.478 0.00 0.00 0.00 2.90
493 494 2.426738 CCGAAAAATAATGCCCAGCTCA 59.573 45.455 0.00 0.00 0.00 4.26
494 495 2.687935 TCCGAAAAATAATGCCCAGCTC 59.312 45.455 0.00 0.00 0.00 4.09
495 496 2.733956 TCCGAAAAATAATGCCCAGCT 58.266 42.857 0.00 0.00 0.00 4.24
496 497 3.518634 TTCCGAAAAATAATGCCCAGC 57.481 42.857 0.00 0.00 0.00 4.85
497 498 5.072040 AGTTTCCGAAAAATAATGCCCAG 57.928 39.130 0.00 0.00 0.00 4.45
498 499 5.011125 TGAAGTTTCCGAAAAATAATGCCCA 59.989 36.000 0.00 0.00 0.00 5.36
511 512 5.223449 AGGATACAAACTGAAGTTTCCGA 57.777 39.130 5.46 0.00 45.54 4.55
576 577 1.669115 CAGGCCGAGTGAACCTGTG 60.669 63.158 0.00 0.00 44.91 3.66
613 614 0.678048 AGGATCTGTTTCGGCAAGCC 60.678 55.000 0.00 0.00 0.00 4.35
614 615 0.449388 CAGGATCTGTTTCGGCAAGC 59.551 55.000 0.00 0.00 0.00 4.01
615 616 0.449388 GCAGGATCTGTTTCGGCAAG 59.551 55.000 0.00 0.00 33.43 4.01
616 617 0.036732 AGCAGGATCTGTTTCGGCAA 59.963 50.000 0.00 0.00 33.43 4.52
617 618 0.036732 AAGCAGGATCTGTTTCGGCA 59.963 50.000 0.00 0.00 29.26 5.69
618 619 0.729690 GAAGCAGGATCTGTTTCGGC 59.270 55.000 8.33 0.00 40.59 5.54
621 622 4.470334 AGAGAGAAGCAGGATCTGTTTC 57.530 45.455 13.96 13.96 46.84 2.78
622 623 4.323409 GGAAGAGAGAAGCAGGATCTGTTT 60.323 45.833 0.00 0.00 37.60 2.83
623 624 3.197549 GGAAGAGAGAAGCAGGATCTGTT 59.802 47.826 0.00 0.00 33.43 3.16
624 625 2.765699 GGAAGAGAGAAGCAGGATCTGT 59.234 50.000 0.00 0.00 33.43 3.41
625 626 2.765135 TGGAAGAGAGAAGCAGGATCTG 59.235 50.000 0.00 0.00 34.12 2.90
626 627 2.765699 GTGGAAGAGAGAAGCAGGATCT 59.234 50.000 0.00 0.00 0.00 2.75
627 628 2.499289 TGTGGAAGAGAGAAGCAGGATC 59.501 50.000 0.00 0.00 0.00 3.36
628 629 2.500910 CTGTGGAAGAGAGAAGCAGGAT 59.499 50.000 0.00 0.00 0.00 3.24
629 630 1.898472 CTGTGGAAGAGAGAAGCAGGA 59.102 52.381 0.00 0.00 0.00 3.86
671 672 1.072116 CGTCGGAATCAAACGCCGTA 61.072 55.000 0.00 0.00 45.02 4.02
675 676 2.097728 GCCGTCGGAATCAAACGC 59.902 61.111 17.49 0.00 35.17 4.84
680 682 3.833645 CGGAGGCCGTCGGAATCA 61.834 66.667 17.49 0.00 42.73 2.57
707 709 1.671901 CGGAGCCCTCTCAACCTCTC 61.672 65.000 0.00 0.00 41.13 3.20
708 710 1.684049 CGGAGCCCTCTCAACCTCT 60.684 63.158 0.00 0.00 41.13 3.69
709 711 1.545706 AACGGAGCCCTCTCAACCTC 61.546 60.000 0.00 0.00 41.13 3.85
743 747 1.920325 CTCCCTCCACCTCAAGCCA 60.920 63.158 0.00 0.00 0.00 4.75
765 769 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
766 770 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
767 771 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
768 772 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
769 773 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
770 774 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
771 775 2.613576 CTTCCCTCCCTCCCTCCCTC 62.614 70.000 0.00 0.00 0.00 4.30
772 776 2.543637 TTCCCTCCCTCCCTCCCT 60.544 66.667 0.00 0.00 0.00 4.20
773 777 2.040359 CTTCCCTCCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
774 778 0.983905 GTTCTTCCCTCCCTCCCTCC 60.984 65.000 0.00 0.00 0.00 4.30
775 779 0.252742 TGTTCTTCCCTCCCTCCCTC 60.253 60.000 0.00 0.00 0.00 4.30
776 780 0.252927 CTGTTCTTCCCTCCCTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
777 781 0.252742 TCTGTTCTTCCCTCCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
778 782 1.199615 CTCTGTTCTTCCCTCCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
779 783 0.539518 GCTCTGTTCTTCCCTCCCTC 59.460 60.000 0.00 0.00 0.00 4.30
780 784 1.261238 CGCTCTGTTCTTCCCTCCCT 61.261 60.000 0.00 0.00 0.00 4.20
781 785 1.219393 CGCTCTGTTCTTCCCTCCC 59.781 63.158 0.00 0.00 0.00 4.30
782 786 1.219393 CCGCTCTGTTCTTCCCTCC 59.781 63.158 0.00 0.00 0.00 4.30
783 787 0.390472 CACCGCTCTGTTCTTCCCTC 60.390 60.000 0.00 0.00 0.00 4.30
784 788 1.674057 CACCGCTCTGTTCTTCCCT 59.326 57.895 0.00 0.00 0.00 4.20
785 789 1.376037 CCACCGCTCTGTTCTTCCC 60.376 63.158 0.00 0.00 0.00 3.97
786 790 0.390472 CTCCACCGCTCTGTTCTTCC 60.390 60.000 0.00 0.00 0.00 3.46
787 791 0.390472 CCTCCACCGCTCTGTTCTTC 60.390 60.000 0.00 0.00 0.00 2.87
788 792 1.674057 CCTCCACCGCTCTGTTCTT 59.326 57.895 0.00 0.00 0.00 2.52
812 816 4.742201 CCAGCTGTAGCCGCACGT 62.742 66.667 13.81 0.00 43.38 4.49
840 844 1.809619 CGCGATCACCACACCGAAT 60.810 57.895 0.00 0.00 0.00 3.34
910 921 1.662438 CCTCACTGAGGTCTCGCTCC 61.662 65.000 16.18 0.00 44.25 4.70
931 942 0.391263 CAGAAGCCCCGTACTTCACC 60.391 60.000 10.70 0.00 44.87 4.02
945 956 2.125350 GGTGAGCTCGGGCAGAAG 60.125 66.667 11.40 0.00 41.70 2.85
952 963 2.433838 CTGCTGTGGTGAGCTCGG 60.434 66.667 9.64 0.00 39.90 4.63
990 1002 0.546122 AACTGGCCATTCCGCTATCA 59.454 50.000 5.51 0.00 37.80 2.15
997 1009 0.322546 AGACGGAAACTGGCCATTCC 60.323 55.000 23.28 23.28 41.39 3.01
1020 1032 4.680237 TTGCGTGCCTCCAGACCG 62.680 66.667 0.00 0.00 0.00 4.79
1459 1471 5.049749 CCATGACATTGAACGTGTAAACAGA 60.050 40.000 0.00 0.00 0.00 3.41
1536 1548 2.620115 CACATTCTTGGACTTGCACAGT 59.380 45.455 0.00 0.00 39.07 3.55
1566 1578 5.752036 TCATCTGTTCAAAGATCTCCTGT 57.248 39.130 0.00 0.00 34.60 4.00
1592 1604 2.671070 CATCAGGGCTGAACCGGT 59.329 61.111 0.00 0.00 43.58 5.28
1911 1923 1.167851 CCACAACATCTGGCACGATT 58.832 50.000 0.00 0.00 0.00 3.34
2124 2136 4.960938 TGGTGTATGTATCAGAATCTGGC 58.039 43.478 10.71 2.31 31.51 4.85
2796 2808 6.769822 ACAAATGTAAGGAAGATGCTGATAGG 59.230 38.462 0.00 0.00 0.00 2.57
2819 2831 6.488344 TGCAACATATTAACAGAAGTGGAACA 59.512 34.615 0.00 0.00 41.43 3.18
3031 3043 0.833834 ACCTGAGGACTGGGTGACTG 60.834 60.000 4.99 0.00 39.06 3.51
3032 3044 0.104934 AACCTGAGGACTGGGTGACT 60.105 55.000 4.99 0.00 39.06 3.41
3033 3045 0.321996 GAACCTGAGGACTGGGTGAC 59.678 60.000 4.99 0.00 39.06 3.67
3034 3046 0.105194 TGAACCTGAGGACTGGGTGA 60.105 55.000 4.99 0.00 39.06 4.02
3035 3047 0.322975 CTGAACCTGAGGACTGGGTG 59.677 60.000 4.99 0.00 39.06 4.61
3036 3048 0.104934 ACTGAACCTGAGGACTGGGT 60.105 55.000 4.99 0.00 39.06 4.51
3037 3049 0.610687 GACTGAACCTGAGGACTGGG 59.389 60.000 4.99 0.00 39.06 4.45
3038 3050 1.548269 GAGACTGAACCTGAGGACTGG 59.452 57.143 4.99 0.00 40.30 4.00
3204 3240 4.141801 CCCTCCGTTCCATATTAGTTGTCA 60.142 45.833 0.00 0.00 0.00 3.58
3206 3242 4.035112 TCCCTCCGTTCCATATTAGTTGT 58.965 43.478 0.00 0.00 0.00 3.32
3207 3243 4.101119 ACTCCCTCCGTTCCATATTAGTTG 59.899 45.833 0.00 0.00 0.00 3.16
3223 3259 3.300239 TCTGCTAGGTTCTACTCCCTC 57.700 52.381 0.00 0.00 32.08 4.30
3224 3260 3.983533 ATCTGCTAGGTTCTACTCCCT 57.016 47.619 0.00 0.00 34.74 4.20
3254 3290 6.993902 AGTACGGTCAAAAAGGAAATCTGTAA 59.006 34.615 0.00 0.00 0.00 2.41
3432 3469 4.590850 ACTTTGCAATCAAGGAACCTTC 57.409 40.909 0.00 0.00 33.93 3.46


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

AutoCloner maintained by Alex Coulton.