Multiple sequence alignment - TraesCS5D01G179200

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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 TraesCS5D01G179200 chr5D 100.000 2498 0 0 1 2498 278357370 278359867 0.000000e+00 4614.0
1 TraesCS5D01G179200 chr5D 90.560 2055 115 33 512 2498 278440866 278442909 0.000000e+00 2647.0
2 TraesCS5D01G179200 chr5D 90.357 280 11 7 110 373 278440589 278440868 1.100000e-93 353.0
3 TraesCS5D01G179200 chr5D 87.681 138 16 1 374 511 549553511 549553647 2.570000e-35 159.0
4 TraesCS5D01G179200 chr5D 79.000 100 7 11 1743 1839 6385594 6385682 3.470000e-04 56.5
5 TraesCS5D01G179200 chr5A 90.988 1720 99 24 512 2207 370107554 370105867 0.000000e+00 2266.0
6 TraesCS5D01G179200 chr5A 83.178 214 23 9 115 320 370107790 370107582 1.530000e-42 183.0
7 TraesCS5D01G179200 chr5A 84.746 59 1 7 1743 1798 3286476 3286423 4.000000e-03 52.8
8 TraesCS5D01G179200 chr5B 86.155 1979 174 60 512 2435 316531256 316533189 0.000000e+00 2045.0
9 TraesCS5D01G179200 chr5B 91.057 1409 90 24 645 2029 316561256 316562652 0.000000e+00 1871.0
10 TraesCS5D01G179200 chr5B 84.286 280 21 11 110 373 316530986 316531258 4.120000e-63 252.0
11 TraesCS5D01G179200 chr5B 90.517 116 6 3 258 373 316561043 316561153 5.570000e-32 148.0
12 TraesCS5D01G179200 chr5B 76.522 115 17 8 1743 1855 545190513 545190407 1.000000e-03 54.7
13 TraesCS5D01G179200 chr7D 99.107 112 1 0 1 112 595690074 595690185 4.210000e-48 202.0
14 TraesCS5D01G179200 chr7D 96.639 119 3 1 1 118 478326294 478326412 1.960000e-46 196.0
15 TraesCS5D01G179200 chr6A 99.107 112 1 0 2 113 68950798 68950909 4.210000e-48 202.0
16 TraesCS5D01G179200 chr3B 92.806 139 10 0 373 511 392812643 392812505 4.210000e-48 202.0
17 TraesCS5D01G179200 chr3B 91.724 145 9 3 371 514 475495300 475495158 5.450000e-47 198.0
18 TraesCS5D01G179200 chr2D 97.436 117 2 1 1 117 515619587 515619702 5.450000e-47 198.0
19 TraesCS5D01G179200 chr2D 90.278 144 14 0 371 514 544345264 544345407 3.280000e-44 189.0
20 TraesCS5D01G179200 chrUn 98.214 112 2 0 1 112 10694162 10694051 1.960000e-46 196.0
21 TraesCS5D01G179200 chr4D 97.391 115 3 0 1 115 340840025 340840139 1.960000e-46 196.0
22 TraesCS5D01G179200 chr1D 98.214 112 2 0 1 112 222341 222452 1.960000e-46 196.0
23 TraesCS5D01G179200 chr1D 98.214 112 2 0 1 112 352405787 352405676 1.960000e-46 196.0
24 TraesCS5D01G179200 chr7B 91.489 141 12 0 372 512 641682067 641682207 7.050000e-46 195.0
25 TraesCS5D01G179200 chr2B 91.429 140 12 0 373 512 97183488 97183349 2.540000e-45 193.0
26 TraesCS5D01G179200 chr3D 95.041 121 5 1 5 124 58053150 58053030 3.280000e-44 189.0
27 TraesCS5D01G179200 chr3D 85.315 143 18 3 371 512 473448570 473448430 7.200000e-31 145.0
28 TraesCS5D01G179200 chr6B 90.714 140 13 0 373 512 63665644 63665783 1.180000e-43 187.0
29 TraesCS5D01G179200 chr2A 89.726 146 13 2 370 514 631635576 631635720 4.240000e-43 185.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G179200 chr5D 278357370 278359867 2497 False 4614.0 4614 100.0000 1 2498 1 chr5D.!!$F2 2497
1 TraesCS5D01G179200 chr5D 278440589 278442909 2320 False 1500.0 2647 90.4585 110 2498 2 chr5D.!!$F4 2388
2 TraesCS5D01G179200 chr5A 370105867 370107790 1923 True 1224.5 2266 87.0830 115 2207 2 chr5A.!!$R2 2092
3 TraesCS5D01G179200 chr5B 316530986 316533189 2203 False 1148.5 2045 85.2205 110 2435 2 chr5B.!!$F1 2325
4 TraesCS5D01G179200 chr5B 316561043 316562652 1609 False 1009.5 1871 90.7870 258 2029 2 chr5B.!!$F2 1771

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
19 20 0.035725 CCGGGGTGGGACTAAACTTC 60.036 60.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 2055 0.25064 GGCAGCCATGAAGATCGGAT 60.251 55.0 6.55 0.0 0.0 4.18 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 3.816054 CCGGGGTGGGACTAAACT 58.184 61.111 0.00 0.00 0.00 2.66
18 19 2.072366 CCGGGGTGGGACTAAACTT 58.928 57.895 0.00 0.00 0.00 2.66
19 20 0.035725 CCGGGGTGGGACTAAACTTC 60.036 60.000 0.00 0.00 0.00 3.01
20 21 0.035725 CGGGGTGGGACTAAACTTCC 60.036 60.000 0.00 0.00 0.00 3.46
29 30 3.935315 GGACTAAACTTCCCACTACACC 58.065 50.000 0.00 0.00 0.00 4.16
30 31 3.581770 GGACTAAACTTCCCACTACACCT 59.418 47.826 0.00 0.00 0.00 4.00
31 32 4.774200 GGACTAAACTTCCCACTACACCTA 59.226 45.833 0.00 0.00 0.00 3.08
32 33 5.105432 GGACTAAACTTCCCACTACACCTAG 60.105 48.000 0.00 0.00 0.00 3.02
33 34 5.400870 ACTAAACTTCCCACTACACCTAGT 58.599 41.667 0.00 0.00 33.01 2.57
34 35 4.618920 AAACTTCCCACTACACCTAGTG 57.381 45.455 1.51 1.51 46.77 2.74
35 36 3.255634 ACTTCCCACTACACCTAGTGT 57.744 47.619 5.60 5.60 46.07 3.55
36 37 3.163467 ACTTCCCACTACACCTAGTGTC 58.837 50.000 3.18 0.00 43.92 3.67
37 38 2.984435 TCCCACTACACCTAGTGTCA 57.016 50.000 3.18 0.00 43.92 3.58
38 39 3.468071 TCCCACTACACCTAGTGTCAT 57.532 47.619 3.18 0.00 43.92 3.06
39 40 4.596354 TCCCACTACACCTAGTGTCATA 57.404 45.455 3.18 0.00 43.92 2.15
40 41 5.138758 TCCCACTACACCTAGTGTCATAT 57.861 43.478 3.18 0.00 43.92 1.78
41 42 6.270219 TCCCACTACACCTAGTGTCATATA 57.730 41.667 3.18 0.00 43.92 0.86
42 43 6.675565 TCCCACTACACCTAGTGTCATATAA 58.324 40.000 3.18 0.00 43.92 0.98
43 44 6.548622 TCCCACTACACCTAGTGTCATATAAC 59.451 42.308 3.18 0.00 43.92 1.89
44 45 6.239232 CCCACTACACCTAGTGTCATATAACC 60.239 46.154 3.18 0.00 43.92 2.85
45 46 6.239232 CCACTACACCTAGTGTCATATAACCC 60.239 46.154 3.18 0.00 43.92 4.11
46 47 6.322969 CACTACACCTAGTGTCATATAACCCA 59.677 42.308 3.18 0.00 43.92 4.51
47 48 5.609533 ACACCTAGTGTCATATAACCCAC 57.390 43.478 0.00 0.00 43.92 4.61
48 49 5.027460 ACACCTAGTGTCATATAACCCACA 58.973 41.667 0.00 0.00 43.92 4.17
49 50 5.665812 ACACCTAGTGTCATATAACCCACAT 59.334 40.000 0.00 0.00 43.92 3.21
50 51 5.991606 CACCTAGTGTCATATAACCCACATG 59.008 44.000 0.00 0.00 0.00 3.21
51 52 5.071788 ACCTAGTGTCATATAACCCACATGG 59.928 44.000 0.00 0.00 41.37 3.66
62 63 2.620234 CCACATGGGCCCTTAGAGA 58.380 57.895 25.70 0.07 0.00 3.10
63 64 1.143813 CCACATGGGCCCTTAGAGAT 58.856 55.000 25.70 3.22 0.00 2.75
64 65 1.496429 CCACATGGGCCCTTAGAGATT 59.504 52.381 25.70 0.00 0.00 2.40
65 66 2.091665 CCACATGGGCCCTTAGAGATTT 60.092 50.000 25.70 0.00 0.00 2.17
66 67 3.628257 CCACATGGGCCCTTAGAGATTTT 60.628 47.826 25.70 0.00 0.00 1.82
67 68 4.026052 CACATGGGCCCTTAGAGATTTTT 58.974 43.478 25.70 0.00 0.00 1.94
68 69 4.098501 CACATGGGCCCTTAGAGATTTTTC 59.901 45.833 25.70 0.00 0.00 2.29
69 70 4.264352 ACATGGGCCCTTAGAGATTTTTCA 60.264 41.667 25.70 0.00 0.00 2.69
70 71 3.968265 TGGGCCCTTAGAGATTTTTCAG 58.032 45.455 25.70 0.00 0.00 3.02
71 72 3.591527 TGGGCCCTTAGAGATTTTTCAGA 59.408 43.478 25.70 0.00 0.00 3.27
72 73 4.044065 TGGGCCCTTAGAGATTTTTCAGAA 59.956 41.667 25.70 0.00 0.00 3.02
73 74 5.016831 GGGCCCTTAGAGATTTTTCAGAAA 58.983 41.667 17.04 0.00 0.00 2.52
74 75 5.658634 GGGCCCTTAGAGATTTTTCAGAAAT 59.341 40.000 17.04 0.00 0.00 2.17
75 76 6.155221 GGGCCCTTAGAGATTTTTCAGAAATT 59.845 38.462 17.04 0.00 0.00 1.82
76 77 7.038048 GGCCCTTAGAGATTTTTCAGAAATTG 58.962 38.462 0.00 0.00 0.00 2.32
77 78 6.533012 GCCCTTAGAGATTTTTCAGAAATTGC 59.467 38.462 0.00 0.00 0.00 3.56
78 79 7.578380 GCCCTTAGAGATTTTTCAGAAATTGCT 60.578 37.037 0.00 0.00 0.00 3.91
79 80 8.960591 CCCTTAGAGATTTTTCAGAAATTGCTA 58.039 33.333 0.00 0.00 0.00 3.49
85 86 9.741647 GAGATTTTTCAGAAATTGCTATAAGGG 57.258 33.333 0.00 0.00 0.00 3.95
86 87 8.200120 AGATTTTTCAGAAATTGCTATAAGGGC 58.800 33.333 0.00 0.00 0.00 5.19
87 88 5.852282 TTTCAGAAATTGCTATAAGGGCC 57.148 39.130 0.00 0.00 0.00 5.80
88 89 4.796110 TCAGAAATTGCTATAAGGGCCT 57.204 40.909 0.00 0.00 0.00 5.19
89 90 5.904984 TCAGAAATTGCTATAAGGGCCTA 57.095 39.130 6.41 0.00 0.00 3.93
90 91 5.869579 TCAGAAATTGCTATAAGGGCCTAG 58.130 41.667 6.41 0.85 0.00 3.02
91 92 5.606749 TCAGAAATTGCTATAAGGGCCTAGA 59.393 40.000 6.41 0.00 0.00 2.43
92 93 5.936956 CAGAAATTGCTATAAGGGCCTAGAG 59.063 44.000 6.41 5.62 0.00 2.43
93 94 3.990959 ATTGCTATAAGGGCCTAGAGC 57.009 47.619 21.38 21.38 36.79 4.09
104 105 2.947127 GCCTAGAGCCCATCTCAAAT 57.053 50.000 0.00 0.00 44.35 2.32
105 106 3.220674 GCCTAGAGCCCATCTCAAATT 57.779 47.619 0.00 0.00 44.35 1.82
106 107 3.560105 GCCTAGAGCCCATCTCAAATTT 58.440 45.455 0.00 0.00 44.35 1.82
107 108 3.567585 GCCTAGAGCCCATCTCAAATTTC 59.432 47.826 0.00 0.00 44.35 2.17
108 109 4.785301 CCTAGAGCCCATCTCAAATTTCA 58.215 43.478 0.00 0.00 44.35 2.69
109 110 4.820716 CCTAGAGCCCATCTCAAATTTCAG 59.179 45.833 0.00 0.00 44.35 3.02
110 111 3.022406 AGAGCCCATCTCAAATTTCAGC 58.978 45.455 0.00 0.00 44.35 4.26
111 112 2.756760 GAGCCCATCTCAAATTTCAGCA 59.243 45.455 0.00 0.00 41.51 4.41
112 113 2.494870 AGCCCATCTCAAATTTCAGCAC 59.505 45.455 0.00 0.00 0.00 4.40
113 114 2.494870 GCCCATCTCAAATTTCAGCACT 59.505 45.455 0.00 0.00 0.00 4.40
179 181 0.262876 AATCAGAGATTTGGGGCCCC 59.737 55.000 36.14 36.14 0.00 5.80
181 183 0.045623 TCAGAGATTTGGGGCCCCTA 59.954 55.000 40.66 32.25 36.94 3.53
204 206 0.941463 CGACACCTCACTGTCACTGC 60.941 60.000 0.63 0.00 40.67 4.40
239 241 0.388520 TGCGTCTGTTCACTGGATCG 60.389 55.000 0.00 0.00 0.00 3.69
244 246 0.458543 CTGTTCACTGGATCGTCCCG 60.459 60.000 2.23 0.00 35.03 5.14
250 252 0.396695 ACTGGATCGTCCCGTGGTAT 60.397 55.000 2.23 0.00 32.52 2.73
298 315 7.424803 CAATCACCAGACAAATTACTGAACAA 58.575 34.615 0.00 0.00 36.38 2.83
339 356 2.796032 GCCATCAGTTACGTACGTACCC 60.796 54.545 26.83 19.41 0.00 3.69
373 390 4.688879 TGCCACGAACATCTTACAAGTTAG 59.311 41.667 0.00 0.00 0.00 2.34
374 391 4.092968 GCCACGAACATCTTACAAGTTAGG 59.907 45.833 0.00 0.00 0.00 2.69
375 392 4.630069 CCACGAACATCTTACAAGTTAGGG 59.370 45.833 0.00 0.00 0.00 3.53
376 393 4.630069 CACGAACATCTTACAAGTTAGGGG 59.370 45.833 0.00 0.00 0.00 4.79
377 394 3.621715 CGAACATCTTACAAGTTAGGGGC 59.378 47.826 0.00 0.00 0.00 5.80
378 395 3.646736 ACATCTTACAAGTTAGGGGCC 57.353 47.619 0.00 0.00 0.00 5.80
379 396 2.093128 ACATCTTACAAGTTAGGGGCCG 60.093 50.000 0.00 0.00 0.00 6.13
380 397 1.648116 TCTTACAAGTTAGGGGCCGT 58.352 50.000 3.37 3.37 0.00 5.68
381 398 1.980036 TCTTACAAGTTAGGGGCCGTT 59.020 47.619 3.09 0.00 0.00 4.44
382 399 2.027837 TCTTACAAGTTAGGGGCCGTTC 60.028 50.000 3.09 0.00 0.00 3.95
383 400 0.247185 TACAAGTTAGGGGCCGTTCG 59.753 55.000 3.09 0.00 0.00 3.95
384 401 1.743995 CAAGTTAGGGGCCGTTCGG 60.744 63.158 3.09 6.90 0.00 4.30
385 402 1.914764 AAGTTAGGGGCCGTTCGGA 60.915 57.895 15.69 0.00 0.00 4.55
386 403 1.896122 AAGTTAGGGGCCGTTCGGAG 61.896 60.000 15.69 0.00 0.00 4.63
387 404 3.078836 TTAGGGGCCGTTCGGAGG 61.079 66.667 15.69 0.00 0.00 4.30
411 428 4.882396 GCTCCGCGCCTTCTCTCC 62.882 72.222 0.00 0.00 0.00 3.71
412 429 4.214327 CTCCGCGCCTTCTCTCCC 62.214 72.222 0.00 0.00 0.00 4.30
416 433 4.214327 GCGCCTTCTCTCCCGGAG 62.214 72.222 8.30 8.30 43.12 4.63
417 434 4.214327 CGCCTTCTCTCCCGGAGC 62.214 72.222 9.87 0.00 41.60 4.70
418 435 4.214327 GCCTTCTCTCCCGGAGCG 62.214 72.222 9.87 3.52 41.60 5.03
434 451 4.124351 CGGACGGAGCTGCGGTTA 62.124 66.667 31.29 0.00 0.00 2.85
435 452 2.202756 GGACGGAGCTGCGGTTAG 60.203 66.667 31.29 3.87 0.00 2.34
436 453 2.707849 GGACGGAGCTGCGGTTAGA 61.708 63.158 31.29 0.00 0.00 2.10
437 454 1.214589 GACGGAGCTGCGGTTAGAA 59.785 57.895 31.29 0.00 0.00 2.10
438 455 0.389426 GACGGAGCTGCGGTTAGAAA 60.389 55.000 31.29 0.00 0.00 2.52
439 456 0.249398 ACGGAGCTGCGGTTAGAAAT 59.751 50.000 31.29 4.81 0.00 2.17
440 457 1.338769 ACGGAGCTGCGGTTAGAAATT 60.339 47.619 31.29 4.00 0.00 1.82
441 458 1.737793 CGGAGCTGCGGTTAGAAATTT 59.262 47.619 21.08 0.00 0.00 1.82
442 459 2.223044 CGGAGCTGCGGTTAGAAATTTC 60.223 50.000 21.08 10.33 0.00 2.17
443 460 2.747446 GGAGCTGCGGTTAGAAATTTCA 59.253 45.455 19.99 3.83 0.00 2.69
444 461 3.181506 GGAGCTGCGGTTAGAAATTTCAG 60.182 47.826 19.99 8.44 0.00 3.02
445 462 3.674997 AGCTGCGGTTAGAAATTTCAGA 58.325 40.909 19.99 4.91 0.00 3.27
446 463 3.686726 AGCTGCGGTTAGAAATTTCAGAG 59.313 43.478 19.99 7.66 0.00 3.35
447 464 3.729163 GCTGCGGTTAGAAATTTCAGAGC 60.729 47.826 19.99 16.11 0.00 4.09
448 465 3.674997 TGCGGTTAGAAATTTCAGAGCT 58.325 40.909 19.99 1.71 0.00 4.09
449 466 3.436704 TGCGGTTAGAAATTTCAGAGCTG 59.563 43.478 19.99 14.14 0.00 4.24
450 467 3.181506 GCGGTTAGAAATTTCAGAGCTGG 60.182 47.826 19.99 7.10 0.00 4.85
451 468 3.181506 CGGTTAGAAATTTCAGAGCTGGC 60.182 47.826 19.99 1.94 0.00 4.85
452 469 3.181506 GGTTAGAAATTTCAGAGCTGGCG 60.182 47.826 19.99 0.00 0.00 5.69
453 470 2.479566 AGAAATTTCAGAGCTGGCGA 57.520 45.000 19.99 0.00 0.00 5.54
454 471 2.783135 AGAAATTTCAGAGCTGGCGAA 58.217 42.857 19.99 0.00 0.00 4.70
455 472 3.149196 AGAAATTTCAGAGCTGGCGAAA 58.851 40.909 19.99 0.00 33.48 3.46
456 473 2.997485 AATTTCAGAGCTGGCGAAAC 57.003 45.000 0.00 0.00 31.87 2.78
457 474 0.798776 ATTTCAGAGCTGGCGAAACG 59.201 50.000 0.00 0.00 31.87 3.60
458 475 1.227999 TTTCAGAGCTGGCGAAACGG 61.228 55.000 0.00 0.00 0.00 4.44
459 476 2.357517 CAGAGCTGGCGAAACGGT 60.358 61.111 0.00 0.00 0.00 4.83
460 477 2.357517 AGAGCTGGCGAAACGGTG 60.358 61.111 0.00 0.00 0.00 4.94
461 478 4.090057 GAGCTGGCGAAACGGTGC 62.090 66.667 0.00 0.00 0.00 5.01
462 479 4.626081 AGCTGGCGAAACGGTGCT 62.626 61.111 0.00 0.00 0.00 4.40
463 480 2.740826 GCTGGCGAAACGGTGCTA 60.741 61.111 0.00 0.00 0.00 3.49
464 481 3.023591 GCTGGCGAAACGGTGCTAC 62.024 63.158 0.00 0.00 0.00 3.58
465 482 2.357760 TGGCGAAACGGTGCTACC 60.358 61.111 0.00 0.00 34.05 3.18
466 483 3.122971 GGCGAAACGGTGCTACCC 61.123 66.667 0.00 0.00 33.75 3.69
467 484 2.357760 GCGAAACGGTGCTACCCA 60.358 61.111 0.00 0.00 33.75 4.51
468 485 2.388232 GCGAAACGGTGCTACCCAG 61.388 63.158 0.00 0.00 33.75 4.45
477 494 3.524606 GCTACCCAGCTCCGCGTA 61.525 66.667 4.92 0.00 44.93 4.42
478 495 2.857744 GCTACCCAGCTCCGCGTAT 61.858 63.158 4.92 0.00 44.93 3.06
479 496 1.740285 CTACCCAGCTCCGCGTATT 59.260 57.895 4.92 0.00 0.00 1.89
480 497 0.104304 CTACCCAGCTCCGCGTATTT 59.896 55.000 4.92 0.00 0.00 1.40
481 498 0.538118 TACCCAGCTCCGCGTATTTT 59.462 50.000 4.92 0.00 0.00 1.82
482 499 1.024579 ACCCAGCTCCGCGTATTTTG 61.025 55.000 4.92 0.00 0.00 2.44
483 500 0.742990 CCCAGCTCCGCGTATTTTGA 60.743 55.000 4.92 0.00 0.00 2.69
484 501 0.652592 CCAGCTCCGCGTATTTTGAG 59.347 55.000 4.92 4.23 0.00 3.02
485 502 0.652592 CAGCTCCGCGTATTTTGAGG 59.347 55.000 4.92 0.00 0.00 3.86
486 503 0.535335 AGCTCCGCGTATTTTGAGGA 59.465 50.000 4.92 0.00 34.02 3.71
488 505 0.931005 CTCCGCGTATTTTGAGGAGC 59.069 55.000 4.92 0.00 44.58 4.70
489 506 0.535335 TCCGCGTATTTTGAGGAGCT 59.465 50.000 4.92 0.00 31.32 4.09
490 507 0.652592 CCGCGTATTTTGAGGAGCTG 59.347 55.000 4.92 0.00 0.00 4.24
491 508 1.640428 CGCGTATTTTGAGGAGCTGA 58.360 50.000 0.00 0.00 0.00 4.26
492 509 2.205074 CGCGTATTTTGAGGAGCTGAT 58.795 47.619 0.00 0.00 0.00 2.90
493 510 2.033407 CGCGTATTTTGAGGAGCTGATG 60.033 50.000 0.00 0.00 0.00 3.07
494 511 2.289002 GCGTATTTTGAGGAGCTGATGG 59.711 50.000 0.00 0.00 0.00 3.51
495 512 3.797039 CGTATTTTGAGGAGCTGATGGA 58.203 45.455 0.00 0.00 0.00 3.41
496 513 4.384056 CGTATTTTGAGGAGCTGATGGAT 58.616 43.478 0.00 0.00 0.00 3.41
497 514 4.450419 CGTATTTTGAGGAGCTGATGGATC 59.550 45.833 0.00 0.00 0.00 3.36
501 518 2.746359 GGAGCTGATGGATCCCCG 59.254 66.667 9.90 0.00 44.19 5.73
502 519 1.838846 GGAGCTGATGGATCCCCGA 60.839 63.158 9.90 0.00 44.19 5.14
503 520 1.410850 GGAGCTGATGGATCCCCGAA 61.411 60.000 9.90 0.00 44.19 4.30
504 521 0.250081 GAGCTGATGGATCCCCGAAC 60.250 60.000 9.90 0.00 34.29 3.95
505 522 1.595382 GCTGATGGATCCCCGAACG 60.595 63.158 9.90 0.00 34.29 3.95
506 523 1.069765 CTGATGGATCCCCGAACGG 59.930 63.158 9.90 6.25 34.29 4.44
712 737 5.281693 TCGTTCATGCAATGTAGACAAAG 57.718 39.130 0.00 0.00 46.80 2.77
808 834 2.605837 TAAAACCTGACGTGCACAGA 57.394 45.000 18.64 0.00 37.54 3.41
1688 1752 7.169158 TCTTGTCATTCTTTTTGTTGGTCTT 57.831 32.000 0.00 0.00 0.00 3.01
1710 1774 2.106477 TGCAACGGATTATGAGCACA 57.894 45.000 0.00 0.00 0.00 4.57
1881 1951 5.546621 TCTATAAAGCATGGTGAGTACCC 57.453 43.478 0.00 0.00 46.96 3.69
1898 1968 4.803908 CCGCCTCCTTGGGGCTTC 62.804 72.222 3.10 0.00 46.73 3.86
1934 2004 1.086696 ATCCGCATTGTCCGTTTCAG 58.913 50.000 0.00 0.00 0.00 3.02
1964 2045 1.407437 CGCCAATTTCTCCTAGGCACT 60.407 52.381 2.96 0.00 45.47 4.40
1972 2053 1.658686 CTCCTAGGCACTCTTCGCGT 61.659 60.000 5.77 0.00 41.75 6.01
1974 2055 1.506718 CTAGGCACTCTTCGCGTCA 59.493 57.895 5.77 0.00 41.75 4.35
1975 2056 0.101399 CTAGGCACTCTTCGCGTCAT 59.899 55.000 5.77 0.00 41.75 3.06
1976 2057 0.100682 TAGGCACTCTTCGCGTCATC 59.899 55.000 5.77 0.00 41.75 2.92
1977 2058 2.167861 GGCACTCTTCGCGTCATCC 61.168 63.158 5.77 0.00 0.00 3.51
1978 2059 2.508891 GCACTCTTCGCGTCATCCG 61.509 63.158 5.77 0.00 40.40 4.18
1983 2064 0.738975 TCTTCGCGTCATCCGATCTT 59.261 50.000 5.77 0.00 39.56 2.40
1985 2071 0.454196 TTCGCGTCATCCGATCTTCA 59.546 50.000 5.77 0.00 39.56 3.02
2030 2116 0.546747 TCCTCGGGGATCCACAACTT 60.547 55.000 16.00 0.00 36.57 2.66
2071 2177 6.740944 TCATATTTCTATTCCTTCGGGTGA 57.259 37.500 0.00 0.00 36.28 4.02
2084 2190 2.726274 GGTGAGTCGTGGACGTGT 59.274 61.111 0.00 0.00 40.80 4.49
2099 2229 1.152546 GTGTCTGGGGCCACCTTTT 60.153 57.895 0.20 0.00 41.11 2.27
2119 2249 3.469564 GGTTATCATCGCACCCACA 57.530 52.632 0.00 0.00 0.00 4.17
2162 2296 2.044650 ACGCGGTAGGTGAGCCTA 60.045 61.111 12.47 0.00 44.90 3.93
2176 2310 5.132648 AGGTGAGCCTAATCCATGTTATCAA 59.867 40.000 0.00 0.00 44.90 2.57
2177 2311 5.827797 GGTGAGCCTAATCCATGTTATCAAA 59.172 40.000 0.00 0.00 0.00 2.69
2179 2313 5.532406 TGAGCCTAATCCATGTTATCAAAGC 59.468 40.000 0.00 0.00 0.00 3.51
2192 2326 1.451387 CAAAGCCGTTCGCCCCTAT 60.451 57.895 0.00 0.00 38.78 2.57
2207 2341 3.740128 CTATGGGGCTGCGTCGCTT 62.740 63.158 19.50 0.00 0.00 4.68
2218 2352 1.446792 CGTCGCTTGAGTGAGCCAT 60.447 57.895 0.00 0.00 39.51 4.40
2321 2458 2.030363 GTGCATCATCGTTTGTTTCCCA 60.030 45.455 0.00 0.00 0.00 4.37
2324 2461 3.825308 CATCATCGTTTGTTTCCCACTG 58.175 45.455 0.00 0.00 0.00 3.66
2327 2464 1.104577 TCGTTTGTTTCCCACTGGGC 61.105 55.000 9.60 0.00 43.94 5.36
2328 2465 1.388065 CGTTTGTTTCCCACTGGGCA 61.388 55.000 9.60 0.00 43.94 5.36
2333 2470 1.119684 GTTTCCCACTGGGCAGTTTT 58.880 50.000 9.60 0.00 43.94 2.43
2340 2477 1.034838 ACTGGGCAGTTTTGTTCGCA 61.035 50.000 0.00 0.00 38.83 5.10
2346 2483 0.657368 CAGTTTTGTTCGCACGAGCC 60.657 55.000 4.44 0.00 37.52 4.70
2372 2509 0.110486 GGGTCTGAGCAAAGGAACCA 59.890 55.000 9.30 0.00 36.87 3.67
2452 2591 1.812571 GTGCTTCATGGGTGTTTCGAT 59.187 47.619 0.00 0.00 0.00 3.59
2458 2597 5.106317 GCTTCATGGGTGTTTCGATCTTTTA 60.106 40.000 0.00 0.00 0.00 1.52
2460 2599 7.461182 TTCATGGGTGTTTCGATCTTTTATT 57.539 32.000 0.00 0.00 0.00 1.40
2465 2604 6.127842 TGGGTGTTTCGATCTTTTATTAAGGC 60.128 38.462 0.00 0.00 0.00 4.35
2466 2605 6.263344 GGTGTTTCGATCTTTTATTAAGGCC 58.737 40.000 0.00 0.00 0.00 5.19
2472 2611 3.750639 TCTTTTATTAAGGCCGTTGCG 57.249 42.857 0.00 0.00 38.85 4.85
2487 2628 4.552276 GCCGTTGCGTTTTTCTATAAGTTC 59.448 41.667 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.035725 GAAGTTTAGTCCCACCCCGG 60.036 60.000 0.00 0.00 0.00 5.73
2 3 3.972368 GGAAGTTTAGTCCCACCCC 57.028 57.895 0.00 0.00 0.00 4.95
8 9 3.581770 AGGTGTAGTGGGAAGTTTAGTCC 59.418 47.826 0.00 0.00 0.00 3.85
9 10 4.886496 AGGTGTAGTGGGAAGTTTAGTC 57.114 45.455 0.00 0.00 0.00 2.59
10 11 5.400870 ACTAGGTGTAGTGGGAAGTTTAGT 58.599 41.667 0.00 0.00 38.14 2.24
11 12 5.997384 ACTAGGTGTAGTGGGAAGTTTAG 57.003 43.478 0.00 0.00 38.14 1.85
26 27 5.607939 TGTGGGTTATATGACACTAGGTG 57.392 43.478 1.17 0.00 39.75 4.00
27 28 5.071788 CCATGTGGGTTATATGACACTAGGT 59.928 44.000 1.17 0.00 35.02 3.08
28 29 5.551233 CCATGTGGGTTATATGACACTAGG 58.449 45.833 1.17 0.00 35.02 3.02
44 45 1.143813 ATCTCTAAGGGCCCATGTGG 58.856 55.000 27.56 11.04 37.09 4.17
45 46 3.303351 AAATCTCTAAGGGCCCATGTG 57.697 47.619 27.56 13.94 0.00 3.21
46 47 4.264352 TGAAAAATCTCTAAGGGCCCATGT 60.264 41.667 27.56 11.59 0.00 3.21
47 48 4.280819 TGAAAAATCTCTAAGGGCCCATG 58.719 43.478 27.56 13.67 0.00 3.66
48 49 4.230502 TCTGAAAAATCTCTAAGGGCCCAT 59.769 41.667 27.56 16.50 0.00 4.00
49 50 3.591527 TCTGAAAAATCTCTAAGGGCCCA 59.408 43.478 27.56 2.12 0.00 5.36
50 51 4.236527 TCTGAAAAATCTCTAAGGGCCC 57.763 45.455 16.46 16.46 0.00 5.80
51 52 6.782082 ATTTCTGAAAAATCTCTAAGGGCC 57.218 37.500 6.95 0.00 0.00 5.80
52 53 6.533012 GCAATTTCTGAAAAATCTCTAAGGGC 59.467 38.462 6.95 0.00 0.00 5.19
53 54 7.834803 AGCAATTTCTGAAAAATCTCTAAGGG 58.165 34.615 6.95 0.00 0.00 3.95
59 60 9.741647 CCCTTATAGCAATTTCTGAAAAATCTC 57.258 33.333 6.95 0.00 0.00 2.75
60 61 8.200120 GCCCTTATAGCAATTTCTGAAAAATCT 58.800 33.333 6.95 6.75 0.00 2.40
61 62 7.439356 GGCCCTTATAGCAATTTCTGAAAAATC 59.561 37.037 6.95 0.00 0.00 2.17
62 63 7.126268 AGGCCCTTATAGCAATTTCTGAAAAAT 59.874 33.333 6.95 0.00 0.00 1.82
63 64 6.440328 AGGCCCTTATAGCAATTTCTGAAAAA 59.560 34.615 6.95 0.00 0.00 1.94
64 65 5.957774 AGGCCCTTATAGCAATTTCTGAAAA 59.042 36.000 6.95 0.00 0.00 2.29
65 66 5.518865 AGGCCCTTATAGCAATTTCTGAAA 58.481 37.500 5.15 5.15 0.00 2.69
66 67 5.129368 AGGCCCTTATAGCAATTTCTGAA 57.871 39.130 0.00 0.00 0.00 3.02
67 68 4.796110 AGGCCCTTATAGCAATTTCTGA 57.204 40.909 0.00 0.00 0.00 3.27
68 69 5.869579 TCTAGGCCCTTATAGCAATTTCTG 58.130 41.667 0.00 0.00 0.00 3.02
69 70 5.513962 GCTCTAGGCCCTTATAGCAATTTCT 60.514 44.000 0.00 0.00 34.27 2.52
70 71 4.697828 GCTCTAGGCCCTTATAGCAATTTC 59.302 45.833 0.00 0.00 34.27 2.17
71 72 4.657013 GCTCTAGGCCCTTATAGCAATTT 58.343 43.478 0.00 0.00 34.27 1.82
72 73 4.293662 GCTCTAGGCCCTTATAGCAATT 57.706 45.455 0.00 0.00 34.27 2.32
73 74 3.990959 GCTCTAGGCCCTTATAGCAAT 57.009 47.619 0.00 0.00 34.27 3.56
85 86 2.947127 ATTTGAGATGGGCTCTAGGC 57.053 50.000 0.00 0.00 44.27 3.93
86 87 4.785301 TGAAATTTGAGATGGGCTCTAGG 58.215 43.478 0.00 0.00 44.27 3.02
87 88 4.275443 GCTGAAATTTGAGATGGGCTCTAG 59.725 45.833 9.00 0.00 44.27 2.43
88 89 4.202441 GCTGAAATTTGAGATGGGCTCTA 58.798 43.478 9.00 0.00 44.27 2.43
89 90 3.022406 GCTGAAATTTGAGATGGGCTCT 58.978 45.455 9.00 0.00 44.27 4.09
90 91 2.756760 TGCTGAAATTTGAGATGGGCTC 59.243 45.455 9.00 0.00 44.21 4.70
91 92 2.494870 GTGCTGAAATTTGAGATGGGCT 59.505 45.455 9.00 0.00 0.00 5.19
92 93 2.494870 AGTGCTGAAATTTGAGATGGGC 59.505 45.455 9.00 0.00 0.00 5.36
93 94 4.796038 AAGTGCTGAAATTTGAGATGGG 57.204 40.909 9.00 0.00 0.00 4.00
94 95 6.145048 GTGAAAAGTGCTGAAATTTGAGATGG 59.855 38.462 9.00 0.00 0.00 3.51
95 96 6.921857 AGTGAAAAGTGCTGAAATTTGAGATG 59.078 34.615 9.00 0.00 0.00 2.90
96 97 6.921857 CAGTGAAAAGTGCTGAAATTTGAGAT 59.078 34.615 9.00 0.00 32.39 2.75
97 98 6.267817 CAGTGAAAAGTGCTGAAATTTGAGA 58.732 36.000 9.00 0.00 32.39 3.27
98 99 5.461078 CCAGTGAAAAGTGCTGAAATTTGAG 59.539 40.000 0.00 0.00 32.39 3.02
99 100 5.105392 ACCAGTGAAAAGTGCTGAAATTTGA 60.105 36.000 0.00 0.00 32.39 2.69
100 101 5.111293 ACCAGTGAAAAGTGCTGAAATTTG 58.889 37.500 0.00 0.00 32.39 2.32
101 102 5.127682 AGACCAGTGAAAAGTGCTGAAATTT 59.872 36.000 0.00 0.00 32.39 1.82
102 103 4.646492 AGACCAGTGAAAAGTGCTGAAATT 59.354 37.500 0.00 0.00 32.39 1.82
103 104 4.210331 AGACCAGTGAAAAGTGCTGAAAT 58.790 39.130 0.00 0.00 32.39 2.17
104 105 3.620488 AGACCAGTGAAAAGTGCTGAAA 58.380 40.909 0.00 0.00 32.39 2.69
105 106 3.281727 AGACCAGTGAAAAGTGCTGAA 57.718 42.857 0.00 0.00 32.39 3.02
106 107 2.945008 CAAGACCAGTGAAAAGTGCTGA 59.055 45.455 0.00 0.00 32.39 4.26
107 108 2.542411 GCAAGACCAGTGAAAAGTGCTG 60.542 50.000 0.00 0.00 0.00 4.41
108 109 1.678101 GCAAGACCAGTGAAAAGTGCT 59.322 47.619 0.00 0.00 0.00 4.40
109 110 1.678101 AGCAAGACCAGTGAAAAGTGC 59.322 47.619 0.00 0.00 0.00 4.40
110 111 3.209410 AGAGCAAGACCAGTGAAAAGTG 58.791 45.455 0.00 0.00 0.00 3.16
111 112 3.135530 AGAGAGCAAGACCAGTGAAAAGT 59.864 43.478 0.00 0.00 0.00 2.66
112 113 3.497640 CAGAGAGCAAGACCAGTGAAAAG 59.502 47.826 0.00 0.00 0.00 2.27
113 114 3.118261 ACAGAGAGCAAGACCAGTGAAAA 60.118 43.478 0.00 0.00 0.00 2.29
179 181 0.598562 ACAGTGAGGTGTCGTGCTAG 59.401 55.000 0.00 0.00 0.00 3.42
181 183 1.364171 GACAGTGAGGTGTCGTGCT 59.636 57.895 0.00 0.00 37.69 4.40
239 241 4.243270 GTCATGCTATTATACCACGGGAC 58.757 47.826 0.00 0.00 0.00 4.46
244 246 7.710907 TGTCTTCTTGTCATGCTATTATACCAC 59.289 37.037 0.00 0.00 0.00 4.16
298 315 3.522553 GCGAGTACAGTTGCTCCTAATT 58.477 45.455 0.00 0.00 30.95 1.40
395 412 4.214327 GGGAGAGAAGGCGCGGAG 62.214 72.222 8.83 0.00 0.00 4.63
399 416 4.214327 CTCCGGGAGAGAAGGCGC 62.214 72.222 19.57 0.00 46.50 6.53
400 417 4.214327 GCTCCGGGAGAGAAGGCG 62.214 72.222 27.95 0.00 46.50 5.52
401 418 4.214327 CGCTCCGGGAGAGAAGGC 62.214 72.222 27.95 10.83 46.50 4.35
402 419 3.532155 CCGCTCCGGGAGAGAAGG 61.532 72.222 27.95 18.59 46.50 3.46
417 434 4.124351 TAACCGCAGCTCCGTCCG 62.124 66.667 0.00 0.00 0.00 4.79
418 435 2.202756 CTAACCGCAGCTCCGTCC 60.203 66.667 0.00 0.00 0.00 4.79
419 436 0.389426 TTTCTAACCGCAGCTCCGTC 60.389 55.000 0.00 0.00 0.00 4.79
420 437 0.249398 ATTTCTAACCGCAGCTCCGT 59.751 50.000 0.00 0.00 0.00 4.69
421 438 1.369625 AATTTCTAACCGCAGCTCCG 58.630 50.000 0.00 0.00 0.00 4.63
422 439 2.747446 TGAAATTTCTAACCGCAGCTCC 59.253 45.455 18.64 0.00 0.00 4.70
423 440 3.684788 TCTGAAATTTCTAACCGCAGCTC 59.315 43.478 18.64 0.00 0.00 4.09
424 441 3.674997 TCTGAAATTTCTAACCGCAGCT 58.325 40.909 18.64 0.00 0.00 4.24
425 442 3.729163 GCTCTGAAATTTCTAACCGCAGC 60.729 47.826 18.64 10.85 0.00 5.25
426 443 3.686726 AGCTCTGAAATTTCTAACCGCAG 59.313 43.478 18.64 7.04 0.00 5.18
427 444 3.436704 CAGCTCTGAAATTTCTAACCGCA 59.563 43.478 18.64 0.00 0.00 5.69
428 445 3.181506 CCAGCTCTGAAATTTCTAACCGC 60.182 47.826 18.64 13.06 0.00 5.68
429 446 3.181506 GCCAGCTCTGAAATTTCTAACCG 60.182 47.826 18.64 4.85 0.00 4.44
430 447 3.181506 CGCCAGCTCTGAAATTTCTAACC 60.182 47.826 18.64 5.73 0.00 2.85
431 448 3.684788 TCGCCAGCTCTGAAATTTCTAAC 59.315 43.478 18.64 6.39 0.00 2.34
432 449 3.937814 TCGCCAGCTCTGAAATTTCTAA 58.062 40.909 18.64 6.36 0.00 2.10
433 450 3.610040 TCGCCAGCTCTGAAATTTCTA 57.390 42.857 18.64 6.68 0.00 2.10
434 451 2.479566 TCGCCAGCTCTGAAATTTCT 57.520 45.000 18.64 0.00 0.00 2.52
435 452 3.237628 GTTTCGCCAGCTCTGAAATTTC 58.762 45.455 11.41 11.41 34.47 2.17
436 453 2.350772 CGTTTCGCCAGCTCTGAAATTT 60.351 45.455 7.55 0.00 34.47 1.82
437 454 1.197721 CGTTTCGCCAGCTCTGAAATT 59.802 47.619 7.55 0.00 34.47 1.82
438 455 0.798776 CGTTTCGCCAGCTCTGAAAT 59.201 50.000 7.55 0.00 34.47 2.17
439 456 1.227999 CCGTTTCGCCAGCTCTGAAA 61.228 55.000 0.00 1.47 0.00 2.69
440 457 1.667830 CCGTTTCGCCAGCTCTGAA 60.668 57.895 0.00 0.00 0.00 3.02
441 458 2.048222 CCGTTTCGCCAGCTCTGA 60.048 61.111 0.00 0.00 0.00 3.27
442 459 2.357517 ACCGTTTCGCCAGCTCTG 60.358 61.111 0.00 0.00 0.00 3.35
443 460 2.357517 CACCGTTTCGCCAGCTCT 60.358 61.111 0.00 0.00 0.00 4.09
444 461 4.090057 GCACCGTTTCGCCAGCTC 62.090 66.667 0.00 0.00 0.00 4.09
445 462 3.234630 TAGCACCGTTTCGCCAGCT 62.235 57.895 0.00 0.00 36.20 4.24
446 463 2.740826 TAGCACCGTTTCGCCAGC 60.741 61.111 0.00 0.00 0.00 4.85
447 464 2.388232 GGTAGCACCGTTTCGCCAG 61.388 63.158 0.00 0.00 0.00 4.85
448 465 2.357760 GGTAGCACCGTTTCGCCA 60.358 61.111 0.00 0.00 0.00 5.69
449 466 3.122971 GGGTAGCACCGTTTCGCC 61.123 66.667 0.00 0.00 39.83 5.54
450 467 2.357760 TGGGTAGCACCGTTTCGC 60.358 61.111 0.00 0.00 39.83 4.70
451 468 3.870606 CTGGGTAGCACCGTTTCG 58.129 61.111 0.00 0.00 39.83 3.46
469 486 0.931005 GCTCCTCAAAATACGCGGAG 59.069 55.000 12.47 5.90 43.18 4.63
470 487 0.535335 AGCTCCTCAAAATACGCGGA 59.465 50.000 12.47 0.00 0.00 5.54
471 488 0.652592 CAGCTCCTCAAAATACGCGG 59.347 55.000 12.47 0.00 0.00 6.46
472 489 1.640428 TCAGCTCCTCAAAATACGCG 58.360 50.000 3.53 3.53 0.00 6.01
473 490 2.289002 CCATCAGCTCCTCAAAATACGC 59.711 50.000 0.00 0.00 0.00 4.42
474 491 3.797039 TCCATCAGCTCCTCAAAATACG 58.203 45.455 0.00 0.00 0.00 3.06
475 492 4.759183 GGATCCATCAGCTCCTCAAAATAC 59.241 45.833 6.95 0.00 0.00 1.89
476 493 4.202503 GGGATCCATCAGCTCCTCAAAATA 60.203 45.833 15.23 0.00 0.00 1.40
477 494 3.436180 GGGATCCATCAGCTCCTCAAAAT 60.436 47.826 15.23 0.00 0.00 1.82
478 495 2.092212 GGGATCCATCAGCTCCTCAAAA 60.092 50.000 15.23 0.00 0.00 2.44
479 496 1.492176 GGGATCCATCAGCTCCTCAAA 59.508 52.381 15.23 0.00 0.00 2.69
480 497 1.135094 GGGATCCATCAGCTCCTCAA 58.865 55.000 15.23 0.00 0.00 3.02
481 498 0.765903 GGGGATCCATCAGCTCCTCA 60.766 60.000 15.23 0.00 29.39 3.86
482 499 1.825281 CGGGGATCCATCAGCTCCTC 61.825 65.000 15.23 0.00 0.00 3.71
483 500 1.840650 CGGGGATCCATCAGCTCCT 60.841 63.158 15.23 0.00 0.00 3.69
484 501 1.410850 TTCGGGGATCCATCAGCTCC 61.411 60.000 15.23 2.23 0.00 4.70
485 502 0.250081 GTTCGGGGATCCATCAGCTC 60.250 60.000 15.23 0.00 0.00 4.09
486 503 1.832912 GTTCGGGGATCCATCAGCT 59.167 57.895 15.23 0.00 0.00 4.24
487 504 1.595382 CGTTCGGGGATCCATCAGC 60.595 63.158 15.23 0.00 0.00 4.26
488 505 1.069765 CCGTTCGGGGATCCATCAG 59.930 63.158 15.23 1.23 0.00 2.90
489 506 3.226242 CCGTTCGGGGATCCATCA 58.774 61.111 15.23 0.00 0.00 3.07
499 516 1.078001 ATTGTAAGGGCCCGTTCGG 60.078 57.895 17.88 4.08 0.00 4.30
500 517 0.391927 TGATTGTAAGGGCCCGTTCG 60.392 55.000 17.88 0.00 0.00 3.95
501 518 1.092348 GTGATTGTAAGGGCCCGTTC 58.908 55.000 17.88 12.10 0.00 3.95
502 519 0.402504 TGTGATTGTAAGGGCCCGTT 59.597 50.000 17.88 13.55 0.00 4.44
503 520 0.623723 ATGTGATTGTAAGGGCCCGT 59.376 50.000 18.44 17.51 0.00 5.28
504 521 1.308998 GATGTGATTGTAAGGGCCCG 58.691 55.000 18.44 0.00 0.00 6.13
505 522 2.435372 TGATGTGATTGTAAGGGCCC 57.565 50.000 16.46 16.46 0.00 5.80
506 523 5.072741 ACATATGATGTGATTGTAAGGGCC 58.927 41.667 10.38 0.00 43.01 5.80
507 524 7.928307 ATACATATGATGTGATTGTAAGGGC 57.072 36.000 10.38 0.00 44.60 5.19
508 525 9.383519 GGTATACATATGATGTGATTGTAAGGG 57.616 37.037 10.38 0.00 44.60 3.95
509 526 9.383519 GGGTATACATATGATGTGATTGTAAGG 57.616 37.037 10.38 0.00 44.60 2.69
510 527 9.942850 TGGGTATACATATGATGTGATTGTAAG 57.057 33.333 10.38 0.00 44.60 2.34
513 530 9.812347 AAATGGGTATACATATGATGTGATTGT 57.188 29.630 10.38 0.00 44.60 2.71
574 591 4.389687 GGACTAGATCGAGATCTACGAACC 59.610 50.000 16.39 13.14 45.69 3.62
712 737 3.463944 TCTCAAGAAACAACGGAGAACC 58.536 45.455 0.00 0.00 32.10 3.62
808 834 1.164411 TTGTCGATCCAATTGCGCTT 58.836 45.000 9.73 0.00 0.00 4.68
1575 1609 6.915300 CACTCATTTTATTTTGAACGACCACA 59.085 34.615 0.00 0.00 0.00 4.17
1688 1752 3.194861 GTGCTCATAATCCGTTGCACTA 58.805 45.455 8.40 0.00 44.80 2.74
1710 1774 3.503800 AGCAGCATCCACATATGACAT 57.496 42.857 10.38 0.00 0.00 3.06
1940 2011 2.746472 GCCTAGGAGAAATTGGCGTGAT 60.746 50.000 14.75 0.00 33.96 3.06
1951 2032 0.818296 GCGAAGAGTGCCTAGGAGAA 59.182 55.000 14.75 0.00 0.00 2.87
1964 2045 0.738975 AAGATCGGATGACGCGAAGA 59.261 50.000 15.93 2.57 43.86 2.87
1972 2053 1.541889 GCAGCCATGAAGATCGGATGA 60.542 52.381 6.08 0.00 38.50 2.92
1974 2055 0.250640 GGCAGCCATGAAGATCGGAT 60.251 55.000 6.55 0.00 0.00 4.18
1975 2056 1.146930 GGCAGCCATGAAGATCGGA 59.853 57.895 6.55 0.00 0.00 4.55
1976 2057 1.895707 GGGCAGCCATGAAGATCGG 60.896 63.158 15.19 0.00 0.00 4.18
1977 2058 1.895707 GGGGCAGCCATGAAGATCG 60.896 63.158 15.19 0.00 0.00 3.69
1978 2059 1.895707 CGGGGCAGCCATGAAGATC 60.896 63.158 15.19 0.00 0.00 2.75
2002 2088 4.338710 CCCCGAGGAAAACCGGCA 62.339 66.667 0.00 0.00 44.07 5.69
2071 2177 2.561956 CCCAGACACGTCCACGACT 61.562 63.158 6.03 0.00 43.02 4.18
2084 2190 2.525592 CCAAAAGGTGGCCCCAGA 59.474 61.111 12.24 0.00 41.72 3.86
2113 2243 1.453745 CAATATGGCGCCTGTGGGT 60.454 57.895 29.70 8.99 34.45 4.51
2141 2271 4.111016 CTCACCTACCGCGTGCGA 62.111 66.667 16.91 0.00 42.83 5.10
2162 2296 4.201910 CGAACGGCTTTGATAACATGGATT 60.202 41.667 0.00 0.00 0.00 3.01
2163 2297 3.312421 CGAACGGCTTTGATAACATGGAT 59.688 43.478 0.00 0.00 0.00 3.41
2164 2298 2.675844 CGAACGGCTTTGATAACATGGA 59.324 45.455 0.00 0.00 0.00 3.41
2168 2302 0.800012 GGCGAACGGCTTTGATAACA 59.200 50.000 13.15 0.00 42.94 2.41
2172 2306 1.906105 TAGGGGCGAACGGCTTTGAT 61.906 55.000 18.90 5.23 42.94 2.57
2176 2310 2.189521 CATAGGGGCGAACGGCTT 59.810 61.111 18.90 11.00 42.94 4.35
2177 2311 3.861797 CCATAGGGGCGAACGGCT 61.862 66.667 18.90 4.47 42.94 5.52
2207 2341 2.743538 GCGTGCATGGCTCACTCA 60.744 61.111 8.27 0.00 32.54 3.41
2235 2369 3.744719 CGACGCTCACCCCGAGAA 61.745 66.667 0.00 0.00 45.45 2.87
2256 2390 3.435186 GAAACAGCTCGGCAGGGC 61.435 66.667 0.00 0.00 46.47 5.19
2294 2431 2.819984 AAACGATGATGCACCCCGCT 62.820 55.000 0.00 0.00 43.06 5.52
2305 2442 2.226330 CCAGTGGGAAACAAACGATGA 58.774 47.619 0.00 0.00 35.59 2.92
2321 2458 1.034838 TGCGAACAAAACTGCCCAGT 61.035 50.000 0.00 0.00 44.94 4.00
2324 2461 1.657181 CGTGCGAACAAAACTGCCC 60.657 57.895 0.00 0.00 0.00 5.36
2327 2464 0.657368 GGCTCGTGCGAACAAAACTG 60.657 55.000 3.02 0.00 40.82 3.16
2328 2465 1.647084 GGCTCGTGCGAACAAAACT 59.353 52.632 3.02 0.00 40.82 2.66
2352 2489 0.609406 GGTTCCTTTGCTCAGACCCC 60.609 60.000 0.00 0.00 0.00 4.95
2357 2494 1.151668 CGACTGGTTCCTTTGCTCAG 58.848 55.000 0.00 0.00 0.00 3.35
2365 2502 2.637383 GCCTCGACGACTGGTTCCT 61.637 63.158 5.18 0.00 0.00 3.36
2409 2548 0.514691 GACTCACAAAAGCCGAGCAG 59.485 55.000 0.00 0.00 0.00 4.24
2420 2559 1.070786 GAAGCACCCCGACTCACAA 59.929 57.895 0.00 0.00 0.00 3.33
2452 2591 3.075884 ACGCAACGGCCTTAATAAAAGA 58.924 40.909 0.00 0.00 36.38 2.52
2458 2597 2.295070 AGAAAAACGCAACGGCCTTAAT 59.705 40.909 0.00 0.00 36.38 1.40
2460 2599 1.310904 AGAAAAACGCAACGGCCTTA 58.689 45.000 0.00 0.00 36.38 2.69
2465 2604 4.779523 CGAACTTATAGAAAAACGCAACGG 59.220 41.667 0.00 0.00 0.00 4.44
2466 2605 5.368374 ACGAACTTATAGAAAAACGCAACG 58.632 37.500 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.