Multiple sequence alignment - TraesCS2A01G448200

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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 TraesCS2A01G448200 chr2A 100.000 2767 0 0 1 2767 697095651 697092885 0.000000e+00 5110.0
1 TraesCS2A01G448200 chr2B 89.474 1140 53 21 789 1885 664414123 664413008 0.000000e+00 1378.0
2 TraesCS2A01G448200 chr2B 91.036 357 20 4 1899 2250 664412953 664412604 3.230000e-129 472.0
3 TraesCS2A01G448200 chr2B 85.618 445 22 9 2282 2699 664412518 664412089 1.970000e-116 429.0
4 TraesCS2A01G448200 chr2B 86.496 274 35 2 117 389 664429615 664429343 1.610000e-77 300.0
5 TraesCS2A01G448200 chr2D 89.245 1060 55 22 862 1885 557173667 557172631 0.000000e+00 1271.0
6 TraesCS2A01G448200 chr2D 87.528 890 43 21 1885 2723 557172563 557171691 0.000000e+00 966.0
7 TraesCS2A01G448200 chr2D 83.673 588 86 10 118 701 557174330 557173749 1.870000e-151 545.0
8 TraesCS2A01G448200 chr2D 89.474 57 2 2 789 841 557173722 557173666 4.940000e-08 69.4
9 TraesCS2A01G448200 chr4B 90.066 151 9 1 1339 1489 216840015 216840159 1.010000e-44 191.0


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 TraesCS2A01G448200 chr2A 697092885 697095651 2766 True 5110.000000 5110 100.000000 1 2767 1 chr2A.!!$R1 2766
1 TraesCS2A01G448200 chr2B 664412089 664414123 2034 True 759.666667 1378 88.709333 789 2699 3 chr2B.!!$R2 1910
2 TraesCS2A01G448200 chr2D 557171691 557174330 2639 True 712.850000 1271 87.480000 118 2723 4 chr2D.!!$R1 2605

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
727 729 0.037882 CTCACTCTGTCGTGCCACAT 60.038 55.0 0.0 0.0 34.92 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1851 0.112412 TTCCAAGGCTGGGGAAGAAC 59.888 55.0 8.41 0.0 43.71 3.01 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
28 29 9.979897 ACCATATATCTAATTGCCATTGTATGT 57.020 29.630 0.00 0.00 0.00 2.29
33 34 9.890629 ATATCTAATTGCCATTGTATGTACGAT 57.109 29.630 0.00 0.00 0.00 3.73
34 35 7.420184 TCTAATTGCCATTGTATGTACGATG 57.580 36.000 11.76 11.76 44.20 3.84
35 36 7.213678 TCTAATTGCCATTGTATGTACGATGA 58.786 34.615 17.93 3.35 46.38 2.92
36 37 5.673337 ATTGCCATTGTATGTACGATGAC 57.327 39.130 17.93 9.87 46.38 3.06
37 38 4.130286 TGCCATTGTATGTACGATGACA 57.870 40.909 17.93 11.95 46.38 3.58
38 39 4.508662 TGCCATTGTATGTACGATGACAA 58.491 39.130 17.93 4.74 46.38 3.18
39 40 5.122519 TGCCATTGTATGTACGATGACAAT 58.877 37.500 17.93 8.04 46.38 2.71
40 41 5.236263 TGCCATTGTATGTACGATGACAATC 59.764 40.000 17.93 6.08 46.38 2.67
41 42 5.466728 GCCATTGTATGTACGATGACAATCT 59.533 40.000 17.93 0.00 46.38 2.40
42 43 6.564686 GCCATTGTATGTACGATGACAATCTG 60.565 42.308 17.93 4.80 46.38 2.90
43 44 6.701400 CCATTGTATGTACGATGACAATCTGA 59.299 38.462 17.93 0.00 46.38 3.27
44 45 7.306807 CCATTGTATGTACGATGACAATCTGAC 60.307 40.741 17.93 0.00 46.38 3.51
45 46 5.588240 TGTATGTACGATGACAATCTGACC 58.412 41.667 0.00 0.00 31.83 4.02
46 47 5.359860 TGTATGTACGATGACAATCTGACCT 59.640 40.000 0.00 0.00 31.83 3.85
47 48 4.371855 TGTACGATGACAATCTGACCTC 57.628 45.455 0.00 0.00 0.00 3.85
48 49 3.761752 TGTACGATGACAATCTGACCTCA 59.238 43.478 0.00 0.00 0.00 3.86
49 50 3.961480 ACGATGACAATCTGACCTCAA 57.039 42.857 0.00 0.00 0.00 3.02
50 51 3.854666 ACGATGACAATCTGACCTCAAG 58.145 45.455 0.00 0.00 0.00 3.02
51 52 3.511540 ACGATGACAATCTGACCTCAAGA 59.488 43.478 0.00 0.00 0.00 3.02
52 53 4.161189 ACGATGACAATCTGACCTCAAGAT 59.839 41.667 0.00 0.00 0.00 2.40
53 54 4.507021 CGATGACAATCTGACCTCAAGATG 59.493 45.833 0.00 0.00 0.00 2.90
54 55 4.897509 TGACAATCTGACCTCAAGATGT 57.102 40.909 0.00 0.00 0.00 3.06
55 56 6.550938 ATGACAATCTGACCTCAAGATGTA 57.449 37.500 0.00 0.00 0.00 2.29
56 57 6.550938 TGACAATCTGACCTCAAGATGTAT 57.449 37.500 0.00 0.00 0.00 2.29
57 58 6.343703 TGACAATCTGACCTCAAGATGTATG 58.656 40.000 0.00 0.00 0.00 2.39
58 59 6.155049 TGACAATCTGACCTCAAGATGTATGA 59.845 38.462 0.00 0.00 0.00 2.15
59 60 6.344500 ACAATCTGACCTCAAGATGTATGAC 58.656 40.000 0.00 0.00 0.00 3.06
60 61 5.543507 ATCTGACCTCAAGATGTATGACC 57.456 43.478 0.00 0.00 0.00 4.02
61 62 4.614475 TCTGACCTCAAGATGTATGACCT 58.386 43.478 0.00 0.00 0.00 3.85
62 63 4.646945 TCTGACCTCAAGATGTATGACCTC 59.353 45.833 0.00 0.00 0.00 3.85
63 64 4.352893 TGACCTCAAGATGTATGACCTCA 58.647 43.478 0.00 0.00 0.00 3.86
64 65 4.160439 TGACCTCAAGATGTATGACCTCAC 59.840 45.833 0.00 0.00 0.00 3.51
65 66 4.357325 ACCTCAAGATGTATGACCTCACT 58.643 43.478 0.00 0.00 0.00 3.41
66 67 4.404073 ACCTCAAGATGTATGACCTCACTC 59.596 45.833 0.00 0.00 0.00 3.51
67 68 4.648762 CCTCAAGATGTATGACCTCACTCT 59.351 45.833 0.00 0.00 0.00 3.24
68 69 5.451659 CCTCAAGATGTATGACCTCACTCTG 60.452 48.000 0.00 0.00 0.00 3.35
69 70 5.019470 TCAAGATGTATGACCTCACTCTGT 58.981 41.667 0.00 0.00 0.00 3.41
70 71 5.481824 TCAAGATGTATGACCTCACTCTGTT 59.518 40.000 0.00 0.00 0.00 3.16
71 72 5.336150 AGATGTATGACCTCACTCTGTTG 57.664 43.478 0.00 0.00 0.00 3.33
72 73 4.774726 AGATGTATGACCTCACTCTGTTGT 59.225 41.667 0.00 0.00 0.00 3.32
73 74 4.257267 TGTATGACCTCACTCTGTTGTG 57.743 45.455 0.00 0.00 39.15 3.33
74 75 3.641436 TGTATGACCTCACTCTGTTGTGT 59.359 43.478 0.00 0.00 38.90 3.72
75 76 2.890808 TGACCTCACTCTGTTGTGTC 57.109 50.000 0.00 0.00 38.90 3.67
76 77 2.107366 TGACCTCACTCTGTTGTGTCA 58.893 47.619 0.00 0.00 38.90 3.58
77 78 2.159099 TGACCTCACTCTGTTGTGTCAC 60.159 50.000 0.00 0.00 38.90 3.67
78 79 1.202417 ACCTCACTCTGTTGTGTCACG 60.202 52.381 0.00 0.00 38.90 4.35
79 80 1.202417 CCTCACTCTGTTGTGTCACGT 60.202 52.381 0.00 0.00 38.90 4.49
80 81 1.854743 CTCACTCTGTTGTGTCACGTG 59.145 52.381 9.94 9.94 38.90 4.49
81 82 0.930310 CACTCTGTTGTGTCACGTGG 59.070 55.000 17.00 0.00 33.61 4.94
82 83 0.821517 ACTCTGTTGTGTCACGTGGA 59.178 50.000 17.00 0.00 0.00 4.02
83 84 1.202417 ACTCTGTTGTGTCACGTGGAG 60.202 52.381 17.00 13.49 0.00 3.86
84 85 0.529773 TCTGTTGTGTCACGTGGAGC 60.530 55.000 17.00 7.20 0.00 4.70
85 86 0.809636 CTGTTGTGTCACGTGGAGCA 60.810 55.000 17.00 9.84 0.00 4.26
86 87 0.179059 TGTTGTGTCACGTGGAGCAT 60.179 50.000 17.00 0.00 0.00 3.79
87 88 0.512952 GTTGTGTCACGTGGAGCATC 59.487 55.000 17.00 7.45 0.00 3.91
102 103 4.485024 GAGCATCCAACACATCATCATC 57.515 45.455 0.00 0.00 0.00 2.92
103 104 4.135306 GAGCATCCAACACATCATCATCT 58.865 43.478 0.00 0.00 0.00 2.90
104 105 4.533815 AGCATCCAACACATCATCATCTT 58.466 39.130 0.00 0.00 0.00 2.40
105 106 4.579340 AGCATCCAACACATCATCATCTTC 59.421 41.667 0.00 0.00 0.00 2.87
106 107 4.261489 GCATCCAACACATCATCATCTTCC 60.261 45.833 0.00 0.00 0.00 3.46
107 108 3.889815 TCCAACACATCATCATCTTCCC 58.110 45.455 0.00 0.00 0.00 3.97
108 109 3.524789 TCCAACACATCATCATCTTCCCT 59.475 43.478 0.00 0.00 0.00 4.20
109 110 4.018141 TCCAACACATCATCATCTTCCCTT 60.018 41.667 0.00 0.00 0.00 3.95
110 111 5.191522 TCCAACACATCATCATCTTCCCTTA 59.808 40.000 0.00 0.00 0.00 2.69
111 112 6.066690 CCAACACATCATCATCTTCCCTTAT 58.933 40.000 0.00 0.00 0.00 1.73
112 113 6.016527 CCAACACATCATCATCTTCCCTTATG 60.017 42.308 0.00 0.00 0.00 1.90
113 114 5.628130 ACACATCATCATCTTCCCTTATGG 58.372 41.667 0.00 0.00 0.00 2.74
114 115 5.133322 ACACATCATCATCTTCCCTTATGGT 59.867 40.000 0.00 0.00 34.77 3.55
115 116 6.066690 CACATCATCATCTTCCCTTATGGTT 58.933 40.000 0.00 0.00 34.77 3.67
116 117 6.016527 CACATCATCATCTTCCCTTATGGTTG 60.017 42.308 0.00 0.00 34.77 3.77
131 132 0.173708 GGTTGACAACCGCACCAAAA 59.826 50.000 21.24 0.00 42.62 2.44
132 133 1.404315 GGTTGACAACCGCACCAAAAA 60.404 47.619 21.24 0.00 42.62 1.94
140 141 2.227568 CGCACCAAAAACACGGCAC 61.228 57.895 0.00 0.00 0.00 5.01
178 179 0.465460 GGTGAGTGTTGGTTGGCTCA 60.465 55.000 0.00 0.00 35.85 4.26
179 180 1.388547 GTGAGTGTTGGTTGGCTCAA 58.611 50.000 0.00 0.00 39.33 3.02
180 181 1.334869 GTGAGTGTTGGTTGGCTCAAG 59.665 52.381 0.00 0.00 39.33 3.02
181 182 0.954452 GAGTGTTGGTTGGCTCAAGG 59.046 55.000 0.00 0.00 0.00 3.61
182 183 0.550914 AGTGTTGGTTGGCTCAAGGA 59.449 50.000 0.00 0.00 0.00 3.36
184 185 2.375174 AGTGTTGGTTGGCTCAAGGATA 59.625 45.455 0.00 0.00 0.00 2.59
185 186 3.153919 GTGTTGGTTGGCTCAAGGATAA 58.846 45.455 0.00 0.00 0.00 1.75
189 190 5.306678 TGTTGGTTGGCTCAAGGATAATTTT 59.693 36.000 0.00 0.00 0.00 1.82
191 192 4.222588 TGGTTGGCTCAAGGATAATTTTGG 59.777 41.667 0.00 0.00 0.00 3.28
192 193 4.222810 GGTTGGCTCAAGGATAATTTTGGT 59.777 41.667 0.00 0.00 0.00 3.67
193 194 5.170748 GTTGGCTCAAGGATAATTTTGGTG 58.829 41.667 0.00 0.00 0.00 4.17
195 196 4.706476 TGGCTCAAGGATAATTTTGGTGAG 59.294 41.667 0.00 0.00 35.28 3.51
204 205 6.948309 AGGATAATTTTGGTGAGCTACTTGTT 59.052 34.615 0.00 0.00 0.00 2.83
207 208 6.655078 AATTTTGGTGAGCTACTTGTTGAT 57.345 33.333 0.00 0.00 0.00 2.57
217 218 4.708421 AGCTACTTGTTGATGGCATGATTT 59.292 37.500 3.81 0.00 0.00 2.17
219 220 5.393352 GCTACTTGTTGATGGCATGATTTGA 60.393 40.000 3.81 0.00 0.00 2.69
226 227 4.684877 TGATGGCATGATTTGATTTTCCG 58.315 39.130 3.81 0.00 0.00 4.30
229 230 3.257873 TGGCATGATTTGATTTTCCGTGT 59.742 39.130 0.00 0.00 0.00 4.49
233 234 3.648009 TGATTTGATTTTCCGTGTTGGC 58.352 40.909 0.00 0.00 37.80 4.52
242 243 1.281656 CCGTGTTGGCGGTTTTCTC 59.718 57.895 0.00 0.00 46.11 2.87
244 245 1.768112 CGTGTTGGCGGTTTTCTCGT 61.768 55.000 0.00 0.00 0.00 4.18
270 271 1.207089 CCGTTGGAGCTCCATCTTGTA 59.793 52.381 35.42 17.44 46.97 2.41
277 278 4.718774 TGGAGCTCCATCTTGTAATCTTCT 59.281 41.667 32.00 0.00 42.01 2.85
294 296 1.348064 TCTGAGTTTCCCCATGTCGT 58.652 50.000 0.00 0.00 0.00 4.34
298 300 0.613777 AGTTTCCCCATGTCGTCTCC 59.386 55.000 0.00 0.00 0.00 3.71
299 301 0.739813 GTTTCCCCATGTCGTCTCCG 60.740 60.000 0.00 0.00 0.00 4.63
306 308 1.153369 ATGTCGTCTCCGGGCATTG 60.153 57.895 0.00 0.00 33.95 2.82
307 309 3.195698 GTCGTCTCCGGGCATTGC 61.196 66.667 0.00 0.00 33.95 3.56
319 321 2.670210 GCATTGCGTTTGCCTTGGC 61.670 57.895 4.43 4.43 41.78 4.52
321 323 2.895680 TTGCGTTTGCCTTGGCAA 59.104 50.000 21.59 21.59 42.54 4.52
335 337 2.696989 TGGCAACATCGATCATCTGT 57.303 45.000 0.00 0.00 46.17 3.41
336 338 3.817709 TGGCAACATCGATCATCTGTA 57.182 42.857 0.00 0.00 46.17 2.74
339 341 3.496130 GGCAACATCGATCATCTGTAAGG 59.504 47.826 0.00 0.00 0.00 2.69
352 354 7.496346 TCATCTGTAAGGGTTGTCTTCTATT 57.504 36.000 0.00 0.00 0.00 1.73
353 355 7.918076 TCATCTGTAAGGGTTGTCTTCTATTT 58.082 34.615 0.00 0.00 0.00 1.40
361 363 6.721318 AGGGTTGTCTTCTATTTGCTTATCA 58.279 36.000 0.00 0.00 0.00 2.15
364 366 7.067494 GGGTTGTCTTCTATTTGCTTATCACAT 59.933 37.037 0.00 0.00 0.00 3.21
368 370 9.890629 TGTCTTCTATTTGCTTATCACATAACT 57.109 29.630 0.00 0.00 0.00 2.24
382 384 4.766373 TCACATAACTGGTGTTGCATCATT 59.234 37.500 0.00 0.00 37.59 2.57
389 391 2.035704 TGGTGTTGCATCATTCAACCAC 59.964 45.455 0.00 0.00 42.17 4.16
390 392 2.297033 GGTGTTGCATCATTCAACCACT 59.703 45.455 0.00 0.00 42.17 4.00
401 403 8.877779 GCATCATTCAACCACTGATATATCTAC 58.122 37.037 13.79 0.00 32.78 2.59
437 439 5.000591 TCTATGTGTTGTGTGGTAACCATG 58.999 41.667 0.00 0.00 35.28 3.66
439 441 2.685388 TGTGTTGTGTGGTAACCATGTG 59.315 45.455 0.00 0.00 35.28 3.21
444 446 3.821748 TGTGTGGTAACCATGTGCTTTA 58.178 40.909 0.00 0.00 35.28 1.85
461 463 8.749841 TGTGCTTTATATTTTGCGTTTTATGT 57.250 26.923 0.00 0.00 0.00 2.29
462 464 8.642885 TGTGCTTTATATTTTGCGTTTTATGTG 58.357 29.630 0.00 0.00 0.00 3.21
486 488 6.595326 TGTTTCTTGCTTCGATGAGATGTATT 59.405 34.615 1.89 0.00 0.00 1.89
487 489 7.119699 TGTTTCTTGCTTCGATGAGATGTATTT 59.880 33.333 1.89 0.00 0.00 1.40
490 492 4.380531 TGCTTCGATGAGATGTATTTCCC 58.619 43.478 1.89 0.00 0.00 3.97
497 499 4.778213 TGAGATGTATTTCCCCTCAAGG 57.222 45.455 0.00 0.00 31.72 3.61
499 501 4.164221 TGAGATGTATTTCCCCTCAAGGTC 59.836 45.833 0.00 0.00 31.72 3.85
500 502 4.111577 AGATGTATTTCCCCTCAAGGTCA 58.888 43.478 0.00 0.00 0.00 4.02
502 504 4.946160 TGTATTTCCCCTCAAGGTCATT 57.054 40.909 0.00 0.00 0.00 2.57
504 506 6.395780 TGTATTTCCCCTCAAGGTCATTAA 57.604 37.500 0.00 0.00 0.00 1.40
505 507 6.795590 TGTATTTCCCCTCAAGGTCATTAAA 58.204 36.000 0.00 0.00 0.00 1.52
506 508 7.242359 TGTATTTCCCCTCAAGGTCATTAAAA 58.758 34.615 0.00 0.00 0.00 1.52
508 510 7.813087 ATTTCCCCTCAAGGTCATTAAAATT 57.187 32.000 0.00 0.00 0.00 1.82
526 528 8.819643 TTAAAATTTTAATCCAACCTTCCACG 57.180 30.769 17.45 0.00 0.00 4.94
533 535 2.841215 TCCAACCTTCCACGTAAACTG 58.159 47.619 0.00 0.00 0.00 3.16
537 539 3.329929 ACCTTCCACGTAAACTGGATC 57.670 47.619 0.00 0.00 37.65 3.36
545 547 5.584649 TCCACGTAAACTGGATCATGATTTC 59.415 40.000 10.14 6.37 32.52 2.17
551 553 8.070171 CGTAAACTGGATCATGATTTCCAATAC 58.930 37.037 16.90 16.72 41.36 1.89
555 557 5.445069 TGGATCATGATTTCCAATACGGTT 58.555 37.500 14.45 0.00 39.05 4.44
559 561 4.642885 TCATGATTTCCAATACGGTTTCCC 59.357 41.667 0.00 0.00 35.57 3.97
572 574 1.173913 GTTTCCCGCATAAGCCAACT 58.826 50.000 0.00 0.00 37.52 3.16
580 582 3.129287 CCGCATAAGCCAACTCAATTTCT 59.871 43.478 0.00 0.00 37.52 2.52
582 584 5.163513 CGCATAAGCCAACTCAATTTCTTT 58.836 37.500 0.00 0.00 37.52 2.52
588 590 7.719778 AAGCCAACTCAATTTCTTTTGAATC 57.280 32.000 0.00 0.00 38.37 2.52
608 610 3.186909 TCGAGATCAATTTACAGGTGCG 58.813 45.455 0.00 0.00 0.00 5.34
609 611 2.285834 CGAGATCAATTTACAGGTGCGC 60.286 50.000 0.00 0.00 0.00 6.09
610 612 2.017049 AGATCAATTTACAGGTGCGCC 58.983 47.619 8.71 8.71 0.00 6.53
613 615 0.965363 CAATTTACAGGTGCGCCCCT 60.965 55.000 14.07 5.25 34.57 4.79
615 617 1.562672 ATTTACAGGTGCGCCCCTCT 61.563 55.000 9.08 0.00 34.57 3.69
626 628 2.360980 CCCCTCTCTCGGGTGACT 59.639 66.667 0.00 0.00 43.06 3.41
630 632 1.316706 CCTCTCTCGGGTGACTGACC 61.317 65.000 0.00 0.00 42.04 4.02
642 644 3.053455 GTGACTGACCGAAAGAGTGAAG 58.947 50.000 0.00 0.00 0.00 3.02
644 646 3.243434 TGACTGACCGAAAGAGTGAAGAC 60.243 47.826 0.00 0.00 0.00 3.01
660 662 4.688879 GTGAAGACGTGAAACCATACATCA 59.311 41.667 0.00 0.00 0.00 3.07
661 663 4.688879 TGAAGACGTGAAACCATACATCAC 59.311 41.667 0.00 0.00 39.98 3.06
680 682 6.038161 ACATCACATCACCATTTTACATACCG 59.962 38.462 0.00 0.00 0.00 4.02
688 690 4.034742 ACCATTTTACATACCGCGACAATC 59.965 41.667 8.23 0.00 0.00 2.67
689 691 4.272504 CCATTTTACATACCGCGACAATCT 59.727 41.667 8.23 0.00 0.00 2.40
690 692 5.464057 CCATTTTACATACCGCGACAATCTA 59.536 40.000 8.23 0.00 0.00 1.98
696 698 0.530744 ACCGCGACAATCTAAGCTCA 59.469 50.000 8.23 0.00 0.00 4.26
701 703 3.060674 CGCGACAATCTAAGCTCAAGATG 60.061 47.826 0.00 8.67 33.95 2.90
702 704 3.868077 GCGACAATCTAAGCTCAAGATGT 59.132 43.478 11.24 11.02 33.95 3.06
703 705 4.026145 GCGACAATCTAAGCTCAAGATGTC 60.026 45.833 11.24 16.00 33.95 3.06
704 706 4.505922 CGACAATCTAAGCTCAAGATGTCC 59.494 45.833 20.64 11.32 33.95 4.02
705 707 4.437239 ACAATCTAAGCTCAAGATGTCCG 58.563 43.478 11.24 5.04 33.95 4.79
706 708 4.160439 ACAATCTAAGCTCAAGATGTCCGA 59.840 41.667 11.24 0.00 33.95 4.55
707 709 3.784701 TCTAAGCTCAAGATGTCCGAC 57.215 47.619 0.00 0.00 0.00 4.79
708 710 2.427453 TCTAAGCTCAAGATGTCCGACC 59.573 50.000 0.00 0.00 0.00 4.79
709 711 1.270907 AAGCTCAAGATGTCCGACCT 58.729 50.000 0.00 0.00 0.00 3.85
710 712 0.820871 AGCTCAAGATGTCCGACCTC 59.179 55.000 0.00 0.00 0.00 3.85
711 713 0.532573 GCTCAAGATGTCCGACCTCA 59.467 55.000 6.59 0.00 0.00 3.86
712 714 1.737363 GCTCAAGATGTCCGACCTCAC 60.737 57.143 6.59 0.00 0.00 3.51
713 715 1.821753 CTCAAGATGTCCGACCTCACT 59.178 52.381 6.59 0.00 0.00 3.41
714 716 1.819288 TCAAGATGTCCGACCTCACTC 59.181 52.381 6.59 0.00 0.00 3.51
715 717 1.821753 CAAGATGTCCGACCTCACTCT 59.178 52.381 6.59 0.00 0.00 3.24
716 718 1.468985 AGATGTCCGACCTCACTCTG 58.531 55.000 6.59 0.00 0.00 3.35
717 719 1.178276 GATGTCCGACCTCACTCTGT 58.822 55.000 0.00 0.00 0.00 3.41
718 720 1.133407 GATGTCCGACCTCACTCTGTC 59.867 57.143 0.00 0.00 0.00 3.51
721 723 4.849336 CGACCTCACTCTGTCGTG 57.151 61.111 4.04 0.00 46.83 4.35
722 724 1.442857 CGACCTCACTCTGTCGTGC 60.443 63.158 4.04 0.00 46.83 5.34
723 725 1.080434 GACCTCACTCTGTCGTGCC 60.080 63.158 0.00 0.00 34.92 5.01
724 726 1.806461 GACCTCACTCTGTCGTGCCA 61.806 60.000 0.00 0.00 34.92 4.92
725 727 1.373497 CCTCACTCTGTCGTGCCAC 60.373 63.158 0.00 0.00 34.92 5.01
726 728 1.363807 CTCACTCTGTCGTGCCACA 59.636 57.895 0.00 0.00 34.92 4.17
727 729 0.037882 CTCACTCTGTCGTGCCACAT 60.038 55.000 0.00 0.00 34.92 3.21
728 730 0.319813 TCACTCTGTCGTGCCACATG 60.320 55.000 0.00 0.00 34.92 3.21
733 735 0.670239 CTGTCGTGCCACATGTAGCA 60.670 55.000 15.25 15.25 36.44 3.49
748 750 3.740513 GCATCCAGCGCATCATCA 58.259 55.556 11.47 0.00 0.00 3.07
751 753 1.129998 GCATCCAGCGCATCATCATAC 59.870 52.381 11.47 0.00 0.00 2.39
754 756 0.957395 CCAGCGCATCATCATACCCC 60.957 60.000 11.47 0.00 0.00 4.95
755 757 0.957395 CAGCGCATCATCATACCCCC 60.957 60.000 11.47 0.00 0.00 5.40
821 823 2.223688 TGTTGGCAAGATGGAAAACACG 60.224 45.455 0.00 0.00 0.00 4.49
824 826 0.313672 GCAAGATGGAAAACACGCCA 59.686 50.000 0.00 0.00 38.78 5.69
864 870 0.911769 TGGATCTCCAAGAACCGCAT 59.088 50.000 0.00 0.00 44.35 4.73
899 905 2.434359 GAGAAAGTCCGTGGGCCG 60.434 66.667 0.00 0.00 0.00 6.13
918 936 2.907179 GCCCTGGCCCCGCTTATAT 61.907 63.158 0.00 0.00 34.56 0.86
965 983 1.077429 CCCTAGAGCCAAGCCAACC 60.077 63.158 0.00 0.00 0.00 3.77
983 1001 3.698463 AACGAACGCCGCAACTCG 61.698 61.111 0.00 4.66 43.32 4.18
1036 1071 2.505982 CGGGATCCATCGCAGGTT 59.494 61.111 15.23 0.00 39.45 3.50
1037 1072 1.595382 CGGGATCCATCGCAGGTTC 60.595 63.158 15.23 0.00 39.45 3.62
1038 1073 1.595382 GGGATCCATCGCAGGTTCG 60.595 63.158 15.23 0.00 39.31 3.95
1039 1074 2.247437 GGATCCATCGCAGGTTCGC 61.247 63.158 6.95 0.00 0.00 4.70
1040 1075 1.521457 GATCCATCGCAGGTTCGCA 60.521 57.895 0.00 0.00 0.00 5.10
1041 1076 1.078497 ATCCATCGCAGGTTCGCAA 60.078 52.632 0.00 0.00 0.00 4.85
1652 1713 1.325355 AGGTCGTCTTCTTTCCGTGA 58.675 50.000 0.00 0.00 0.00 4.35
1700 1761 1.340697 GGTTGGTGATCCTGTAACCCC 60.341 57.143 0.00 0.00 33.66 4.95
1723 1784 4.111053 GTCCCGGCCCCTTCCTTC 62.111 72.222 0.00 0.00 0.00 3.46
1777 1838 3.940852 TGTGCATAGAATGTGTTAGCTGG 59.059 43.478 0.00 0.00 0.00 4.85
1790 1851 0.758734 TAGCTGGTGATCCAATCCCG 59.241 55.000 0.00 0.00 43.81 5.14
1834 1901 1.541588 GGTTCCACAGTTCATTCTGGC 59.458 52.381 0.00 0.00 39.48 4.85
1837 1904 1.699083 TCCACAGTTCATTCTGGCTCA 59.301 47.619 0.00 0.00 39.48 4.26
1838 1905 2.082231 CCACAGTTCATTCTGGCTCAG 58.918 52.381 0.00 0.00 39.48 3.35
1839 1906 2.082231 CACAGTTCATTCTGGCTCAGG 58.918 52.381 2.86 0.00 39.48 3.86
1840 1907 1.701847 ACAGTTCATTCTGGCTCAGGT 59.298 47.619 2.86 0.00 39.48 4.00
1841 1908 2.107204 ACAGTTCATTCTGGCTCAGGTT 59.893 45.455 2.86 0.00 39.48 3.50
1842 1909 2.746362 CAGTTCATTCTGGCTCAGGTTC 59.254 50.000 2.86 0.00 31.51 3.62
1843 1910 2.373169 AGTTCATTCTGGCTCAGGTTCA 59.627 45.455 2.86 0.00 31.51 3.18
1863 1930 2.763249 GCAATGGCGATCGATTTCTT 57.237 45.000 21.57 1.10 0.00 2.52
1879 1946 5.276114 CGATTTCTTAACTGATCTGTGCGAG 60.276 44.000 5.96 5.23 0.00 5.03
1913 2048 4.849329 GTCCTGTAGCCGGCGTCG 62.849 72.222 23.20 0.29 0.00 5.12
2160 2299 2.943653 GAAGCCGTTGTCCCGTTG 59.056 61.111 0.00 0.00 0.00 4.10
2234 2373 4.631740 TCTGCTGGGACGGGTGGA 62.632 66.667 0.00 0.00 33.56 4.02
2394 2589 4.415332 CTCCGTGGTGACGTCCGG 62.415 72.222 20.69 20.69 44.54 5.14
2590 2813 0.399454 CATGTCCTCCTATGCCAGGG 59.601 60.000 1.85 0.00 45.58 4.45
2591 2814 1.422161 ATGTCCTCCTATGCCAGGGC 61.422 60.000 2.62 2.62 45.58 5.19
2592 2815 2.448542 TCCTCCTATGCCAGGGCC 60.449 66.667 8.02 0.00 45.58 5.80
2593 2816 3.574237 CCTCCTATGCCAGGGCCC 61.574 72.222 16.46 16.46 45.58 5.80
2594 2817 2.773918 CTCCTATGCCAGGGCCCA 60.774 66.667 27.56 2.25 45.58 5.36
2595 2818 2.773918 TCCTATGCCAGGGCCCAG 60.774 66.667 27.56 17.69 45.58 4.45
2596 2819 3.894638 CCTATGCCAGGGCCCAGG 61.895 72.222 28.81 28.81 41.26 4.45
2648 2871 1.207089 TGAATGCGTCCCCTGTCTAAG 59.793 52.381 0.00 0.00 0.00 2.18
2649 2872 0.107654 AATGCGTCCCCTGTCTAAGC 60.108 55.000 0.00 0.00 0.00 3.09
2723 2950 2.927004 ACACGCCGTGACATTCATT 58.073 47.368 25.94 0.00 36.96 2.57
2724 2951 0.516877 ACACGCCGTGACATTCATTG 59.483 50.000 25.94 0.00 36.96 2.82
2725 2952 0.794229 CACGCCGTGACATTCATTGC 60.794 55.000 12.85 0.00 35.23 3.56
2726 2953 0.955428 ACGCCGTGACATTCATTGCT 60.955 50.000 0.00 0.00 0.00 3.91
2727 2954 0.247814 CGCCGTGACATTCATTGCTC 60.248 55.000 0.00 0.00 0.00 4.26
2728 2955 1.089920 GCCGTGACATTCATTGCTCT 58.910 50.000 0.00 0.00 0.00 4.09
2729 2956 1.470098 GCCGTGACATTCATTGCTCTT 59.530 47.619 0.00 0.00 0.00 2.85
2730 2957 2.095059 GCCGTGACATTCATTGCTCTTT 60.095 45.455 0.00 0.00 0.00 2.52
2731 2958 3.612479 GCCGTGACATTCATTGCTCTTTT 60.612 43.478 0.00 0.00 0.00 2.27
2732 2959 4.549458 CCGTGACATTCATTGCTCTTTTT 58.451 39.130 0.00 0.00 0.00 1.94
2760 2987 9.638239 TTGGACAAATATTCATTGCTCTTAAAC 57.362 29.630 0.00 0.00 0.00 2.01
2761 2988 8.801299 TGGACAAATATTCATTGCTCTTAAACA 58.199 29.630 0.00 0.00 0.00 2.83
2762 2989 9.294030 GGACAAATATTCATTGCTCTTAAACAG 57.706 33.333 0.00 0.00 0.00 3.16
2763 2990 8.693542 ACAAATATTCATTGCTCTTAAACAGC 57.306 30.769 0.00 0.00 37.40 4.40
2764 2991 7.761249 ACAAATATTCATTGCTCTTAAACAGCC 59.239 33.333 4.08 0.00 35.89 4.85
2765 2992 7.408756 AATATTCATTGCTCTTAAACAGCCA 57.591 32.000 4.08 0.00 35.89 4.75
2766 2993 5.927281 ATTCATTGCTCTTAAACAGCCAT 57.073 34.783 4.08 0.00 35.89 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.979897 ACATACAATGGCAATTAGATATATGGT 57.020 29.630 0.00 0.00 33.60 3.55
7 8 9.890629 ATCGTACATACAATGGCAATTAGATAT 57.109 29.630 0.00 0.00 33.60 1.63
8 9 9.150348 CATCGTACATACAATGGCAATTAGATA 57.850 33.333 0.00 0.00 33.60 1.98
9 10 7.877612 TCATCGTACATACAATGGCAATTAGAT 59.122 33.333 0.00 0.00 33.60 1.98
10 11 7.170828 GTCATCGTACATACAATGGCAATTAGA 59.829 37.037 0.00 0.00 26.37 2.10
11 12 7.042119 TGTCATCGTACATACAATGGCAATTAG 60.042 37.037 0.00 0.00 32.83 1.73
12 13 6.763610 TGTCATCGTACATACAATGGCAATTA 59.236 34.615 0.00 0.00 32.83 1.40
13 14 5.588246 TGTCATCGTACATACAATGGCAATT 59.412 36.000 0.00 0.00 32.83 2.32
14 15 5.122519 TGTCATCGTACATACAATGGCAAT 58.877 37.500 0.00 0.00 32.83 3.56
15 16 4.508662 TGTCATCGTACATACAATGGCAA 58.491 39.130 0.00 0.00 32.83 4.52
16 17 4.130286 TGTCATCGTACATACAATGGCA 57.870 40.909 0.00 0.00 33.29 4.92
17 18 5.466728 AGATTGTCATCGTACATACAATGGC 59.533 40.000 13.60 3.09 41.37 4.40
18 19 6.701400 TCAGATTGTCATCGTACATACAATGG 59.299 38.462 13.60 8.20 41.37 3.16
19 20 7.306807 GGTCAGATTGTCATCGTACATACAATG 60.307 40.741 13.60 5.78 41.37 2.82
20 21 6.701841 GGTCAGATTGTCATCGTACATACAAT 59.298 38.462 10.24 10.24 43.36 2.71
21 22 6.040247 GGTCAGATTGTCATCGTACATACAA 58.960 40.000 0.00 0.00 36.37 2.41
22 23 5.359860 AGGTCAGATTGTCATCGTACATACA 59.640 40.000 0.00 0.00 34.17 2.29
23 24 5.833082 AGGTCAGATTGTCATCGTACATAC 58.167 41.667 0.00 0.00 34.17 2.39
24 25 5.592688 TGAGGTCAGATTGTCATCGTACATA 59.407 40.000 0.00 0.00 34.17 2.29
25 26 4.402474 TGAGGTCAGATTGTCATCGTACAT 59.598 41.667 0.00 0.00 34.17 2.29
26 27 3.761752 TGAGGTCAGATTGTCATCGTACA 59.238 43.478 0.00 0.00 34.17 2.90
27 28 4.371855 TGAGGTCAGATTGTCATCGTAC 57.628 45.455 0.00 0.00 34.17 3.67
28 29 4.705023 TCTTGAGGTCAGATTGTCATCGTA 59.295 41.667 0.00 0.00 34.17 3.43
29 30 3.511540 TCTTGAGGTCAGATTGTCATCGT 59.488 43.478 0.00 0.00 34.17 3.73
30 31 4.115401 TCTTGAGGTCAGATTGTCATCG 57.885 45.455 0.00 0.00 34.17 3.84
31 32 5.426504 ACATCTTGAGGTCAGATTGTCATC 58.573 41.667 0.00 0.00 0.00 2.92
32 33 5.432680 ACATCTTGAGGTCAGATTGTCAT 57.567 39.130 0.00 0.00 0.00 3.06
33 34 4.897509 ACATCTTGAGGTCAGATTGTCA 57.102 40.909 0.00 0.00 0.00 3.58
34 35 6.478344 GTCATACATCTTGAGGTCAGATTGTC 59.522 42.308 0.00 0.00 0.00 3.18
35 36 6.344500 GTCATACATCTTGAGGTCAGATTGT 58.656 40.000 0.00 0.00 0.00 2.71
36 37 5.757320 GGTCATACATCTTGAGGTCAGATTG 59.243 44.000 0.00 0.00 0.00 2.67
37 38 5.664908 AGGTCATACATCTTGAGGTCAGATT 59.335 40.000 0.00 0.00 0.00 2.40
38 39 5.215069 AGGTCATACATCTTGAGGTCAGAT 58.785 41.667 0.00 0.00 0.00 2.90
39 40 4.614475 AGGTCATACATCTTGAGGTCAGA 58.386 43.478 0.00 0.00 0.00 3.27
40 41 4.403752 TGAGGTCATACATCTTGAGGTCAG 59.596 45.833 0.00 0.00 29.01 3.51
41 42 4.160439 GTGAGGTCATACATCTTGAGGTCA 59.840 45.833 0.00 0.00 29.01 4.02
42 43 4.404073 AGTGAGGTCATACATCTTGAGGTC 59.596 45.833 0.00 0.00 29.01 3.85
43 44 4.357325 AGTGAGGTCATACATCTTGAGGT 58.643 43.478 0.00 0.00 29.01 3.85
44 45 4.648762 AGAGTGAGGTCATACATCTTGAGG 59.351 45.833 0.00 0.00 29.01 3.86
45 46 5.126869 ACAGAGTGAGGTCATACATCTTGAG 59.873 44.000 0.00 0.00 29.01 3.02
46 47 5.019470 ACAGAGTGAGGTCATACATCTTGA 58.981 41.667 0.00 0.00 29.01 3.02
47 48 5.336150 ACAGAGTGAGGTCATACATCTTG 57.664 43.478 0.00 0.00 29.01 3.02
48 49 5.247110 ACAACAGAGTGAGGTCATACATCTT 59.753 40.000 0.00 0.00 29.01 2.40
49 50 4.774726 ACAACAGAGTGAGGTCATACATCT 59.225 41.667 0.00 0.00 29.01 2.90
50 51 4.867047 CACAACAGAGTGAGGTCATACATC 59.133 45.833 0.00 0.00 42.05 3.06
51 52 4.284490 ACACAACAGAGTGAGGTCATACAT 59.716 41.667 0.57 0.00 42.05 2.29
52 53 3.641436 ACACAACAGAGTGAGGTCATACA 59.359 43.478 0.57 0.00 42.05 2.29
53 54 4.238514 GACACAACAGAGTGAGGTCATAC 58.761 47.826 0.57 0.00 42.05 2.39
54 55 3.895041 TGACACAACAGAGTGAGGTCATA 59.105 43.478 0.57 0.00 42.05 2.15
55 56 2.700371 TGACACAACAGAGTGAGGTCAT 59.300 45.455 0.57 0.00 42.05 3.06
56 57 2.107366 TGACACAACAGAGTGAGGTCA 58.893 47.619 0.57 0.00 42.05 4.02
57 58 2.474816 GTGACACAACAGAGTGAGGTC 58.525 52.381 0.00 0.00 42.05 3.85
58 59 1.202417 CGTGACACAACAGAGTGAGGT 60.202 52.381 6.37 0.00 42.05 3.85
59 60 1.202417 ACGTGACACAACAGAGTGAGG 60.202 52.381 6.37 0.00 42.05 3.86
60 61 1.854743 CACGTGACACAACAGAGTGAG 59.145 52.381 10.90 0.00 42.05 3.51
61 62 1.470805 CCACGTGACACAACAGAGTGA 60.471 52.381 19.30 0.00 42.05 3.41
62 63 0.930310 CCACGTGACACAACAGAGTG 59.070 55.000 19.30 4.40 44.93 3.51
63 64 0.821517 TCCACGTGACACAACAGAGT 59.178 50.000 19.30 0.00 0.00 3.24
64 65 1.491670 CTCCACGTGACACAACAGAG 58.508 55.000 19.30 8.45 0.00 3.35
65 66 0.529773 GCTCCACGTGACACAACAGA 60.530 55.000 19.30 1.60 0.00 3.41
66 67 0.809636 TGCTCCACGTGACACAACAG 60.810 55.000 19.30 0.00 0.00 3.16
67 68 0.179059 ATGCTCCACGTGACACAACA 60.179 50.000 19.30 6.62 0.00 3.33
68 69 0.512952 GATGCTCCACGTGACACAAC 59.487 55.000 19.30 6.64 0.00 3.32
69 70 0.602638 GGATGCTCCACGTGACACAA 60.603 55.000 19.30 0.00 36.28 3.33
70 71 1.005037 GGATGCTCCACGTGACACA 60.005 57.895 19.30 11.90 36.28 3.72
71 72 1.005037 TGGATGCTCCACGTGACAC 60.005 57.895 19.30 5.90 42.67 3.67
72 73 3.465701 TGGATGCTCCACGTGACA 58.534 55.556 19.30 12.68 42.67 3.58
79 80 2.026075 TGATGATGTGTTGGATGCTCCA 60.026 45.455 1.25 1.25 46.61 3.86
80 81 2.646930 TGATGATGTGTTGGATGCTCC 58.353 47.619 0.00 0.00 36.96 4.70
81 82 4.135306 AGATGATGATGTGTTGGATGCTC 58.865 43.478 0.00 0.00 0.00 4.26
82 83 4.166246 AGATGATGATGTGTTGGATGCT 57.834 40.909 0.00 0.00 0.00 3.79
83 84 4.261489 GGAAGATGATGATGTGTTGGATGC 60.261 45.833 0.00 0.00 0.00 3.91
84 85 4.277672 GGGAAGATGATGATGTGTTGGATG 59.722 45.833 0.00 0.00 0.00 3.51
85 86 4.167502 AGGGAAGATGATGATGTGTTGGAT 59.832 41.667 0.00 0.00 0.00 3.41
86 87 3.524789 AGGGAAGATGATGATGTGTTGGA 59.475 43.478 0.00 0.00 0.00 3.53
87 88 3.894759 AGGGAAGATGATGATGTGTTGG 58.105 45.455 0.00 0.00 0.00 3.77
88 89 6.016527 CCATAAGGGAAGATGATGATGTGTTG 60.017 42.308 0.00 0.00 40.01 3.33
89 90 6.066690 CCATAAGGGAAGATGATGATGTGTT 58.933 40.000 0.00 0.00 40.01 3.32
90 91 5.133322 ACCATAAGGGAAGATGATGATGTGT 59.867 40.000 0.00 0.00 41.15 3.72
91 92 5.628130 ACCATAAGGGAAGATGATGATGTG 58.372 41.667 0.00 0.00 41.15 3.21
92 93 5.919348 ACCATAAGGGAAGATGATGATGT 57.081 39.130 0.00 0.00 41.15 3.06
93 94 6.206243 GTCAACCATAAGGGAAGATGATGATG 59.794 42.308 0.00 0.00 41.15 3.07
94 95 6.126390 TGTCAACCATAAGGGAAGATGATGAT 60.126 38.462 0.00 0.00 41.15 2.45
95 96 5.191522 TGTCAACCATAAGGGAAGATGATGA 59.808 40.000 0.00 0.00 41.15 2.92
96 97 5.439721 TGTCAACCATAAGGGAAGATGATG 58.560 41.667 0.00 0.00 41.15 3.07
97 98 5.715439 TGTCAACCATAAGGGAAGATGAT 57.285 39.130 0.00 0.00 41.15 2.45
98 99 5.253330 GTTGTCAACCATAAGGGAAGATGA 58.747 41.667 4.21 0.00 41.15 2.92
99 100 5.567138 GTTGTCAACCATAAGGGAAGATG 57.433 43.478 4.21 0.00 41.15 2.90
113 114 1.656594 GTTTTTGGTGCGGTTGTCAAC 59.343 47.619 7.20 7.20 0.00 3.18
114 115 1.272490 TGTTTTTGGTGCGGTTGTCAA 59.728 42.857 0.00 0.00 0.00 3.18
115 116 0.888619 TGTTTTTGGTGCGGTTGTCA 59.111 45.000 0.00 0.00 0.00 3.58
116 117 1.273688 GTGTTTTTGGTGCGGTTGTC 58.726 50.000 0.00 0.00 0.00 3.18
158 159 0.465460 GAGCCAACCAACACTCACCA 60.465 55.000 0.00 0.00 0.00 4.17
161 162 1.679139 CTTGAGCCAACCAACACTCA 58.321 50.000 0.00 0.00 37.38 3.41
178 179 6.948309 ACAAGTAGCTCACCAAAATTATCCTT 59.052 34.615 0.00 0.00 0.00 3.36
179 180 6.485171 ACAAGTAGCTCACCAAAATTATCCT 58.515 36.000 0.00 0.00 0.00 3.24
180 181 6.759497 ACAAGTAGCTCACCAAAATTATCC 57.241 37.500 0.00 0.00 0.00 2.59
181 182 7.816640 TCAACAAGTAGCTCACCAAAATTATC 58.183 34.615 0.00 0.00 0.00 1.75
182 183 7.759489 TCAACAAGTAGCTCACCAAAATTAT 57.241 32.000 0.00 0.00 0.00 1.28
184 185 6.449698 CATCAACAAGTAGCTCACCAAAATT 58.550 36.000 0.00 0.00 0.00 1.82
185 186 5.047802 CCATCAACAAGTAGCTCACCAAAAT 60.048 40.000 0.00 0.00 0.00 1.82
189 190 2.875672 GCCATCAACAAGTAGCTCACCA 60.876 50.000 0.00 0.00 0.00 4.17
191 192 2.426522 TGCCATCAACAAGTAGCTCAC 58.573 47.619 0.00 0.00 0.00 3.51
192 193 2.857186 TGCCATCAACAAGTAGCTCA 57.143 45.000 0.00 0.00 0.00 4.26
193 194 3.273434 TCATGCCATCAACAAGTAGCTC 58.727 45.455 0.00 0.00 0.00 4.09
195 196 4.644103 AATCATGCCATCAACAAGTAGC 57.356 40.909 0.00 0.00 0.00 3.58
204 205 4.160065 ACGGAAAATCAAATCATGCCATCA 59.840 37.500 0.00 0.00 0.00 3.07
207 208 3.257873 ACACGGAAAATCAAATCATGCCA 59.742 39.130 0.00 0.00 0.00 4.92
226 227 1.193874 CTACGAGAAAACCGCCAACAC 59.806 52.381 0.00 0.00 0.00 3.32
229 230 0.034337 AGCTACGAGAAAACCGCCAA 59.966 50.000 0.00 0.00 0.00 4.52
233 234 1.683790 CGGCAGCTACGAGAAAACCG 61.684 60.000 4.11 0.00 0.00 4.44
240 241 1.517257 CTCCAACGGCAGCTACGAG 60.517 63.158 15.81 8.16 34.93 4.18
242 243 3.188786 GCTCCAACGGCAGCTACG 61.189 66.667 8.28 8.28 32.48 3.51
244 245 2.579201 GAGCTCCAACGGCAGCTA 59.421 61.111 0.87 0.00 46.31 3.32
294 296 2.033448 AAACGCAATGCCCGGAGA 59.967 55.556 0.73 0.00 0.00 3.71
316 318 2.696989 ACAGATGATCGATGTTGCCA 57.303 45.000 0.54 0.00 0.00 4.92
319 321 4.697514 ACCCTTACAGATGATCGATGTTG 58.302 43.478 0.54 0.00 0.00 3.33
321 323 4.162320 ACAACCCTTACAGATGATCGATGT 59.838 41.667 0.54 0.00 0.00 3.06
326 328 5.983540 AGAAGACAACCCTTACAGATGATC 58.016 41.667 0.00 0.00 0.00 2.92
330 332 6.599638 GCAAATAGAAGACAACCCTTACAGAT 59.400 38.462 0.00 0.00 0.00 2.90
332 334 5.940470 AGCAAATAGAAGACAACCCTTACAG 59.060 40.000 0.00 0.00 0.00 2.74
335 337 8.325787 TGATAAGCAAATAGAAGACAACCCTTA 58.674 33.333 0.00 0.00 0.00 2.69
336 338 7.121315 GTGATAAGCAAATAGAAGACAACCCTT 59.879 37.037 0.00 0.00 0.00 3.95
339 341 7.377766 TGTGATAAGCAAATAGAAGACAACC 57.622 36.000 0.00 0.00 0.00 3.77
352 354 5.335583 GCAACACCAGTTATGTGATAAGCAA 60.336 40.000 0.00 0.00 35.85 3.91
353 355 4.155826 GCAACACCAGTTATGTGATAAGCA 59.844 41.667 0.00 0.00 35.85 3.91
361 363 4.766373 TGAATGATGCAACACCAGTTATGT 59.234 37.500 0.00 0.00 35.85 2.29
364 366 4.022416 GGTTGAATGATGCAACACCAGTTA 60.022 41.667 17.54 0.00 45.58 2.24
367 369 2.296752 TGGTTGAATGATGCAACACCAG 59.703 45.455 17.54 0.00 45.58 4.00
368 370 2.035704 GTGGTTGAATGATGCAACACCA 59.964 45.455 17.54 5.77 45.58 4.17
382 384 6.844388 ACCAAGGTAGATATATCAGTGGTTGA 59.156 38.462 15.08 0.00 40.85 3.18
401 403 3.955471 ACACATAGATCAACCACCAAGG 58.045 45.455 0.00 0.00 45.67 3.61
437 439 8.643752 ACACATAAAACGCAAAATATAAAGCAC 58.356 29.630 0.00 0.00 0.00 4.40
444 446 8.220434 GCAAGAAACACATAAAACGCAAAATAT 58.780 29.630 0.00 0.00 0.00 1.28
461 463 4.318332 ACATCTCATCGAAGCAAGAAACA 58.682 39.130 0.00 0.00 0.00 2.83
462 464 4.935885 ACATCTCATCGAAGCAAGAAAC 57.064 40.909 0.00 0.00 0.00 2.78
486 488 7.625498 AAAATTTTAATGACCTTGAGGGGAA 57.375 32.000 0.37 0.00 40.27 3.97
487 489 8.728596 TTAAAATTTTAATGACCTTGAGGGGA 57.271 30.769 17.45 0.00 40.27 4.81
500 502 9.430623 CGTGGAAGGTTGGATTAAAATTTTAAT 57.569 29.630 28.11 28.11 43.83 1.40
502 504 7.953752 ACGTGGAAGGTTGGATTAAAATTTTA 58.046 30.769 6.54 6.54 0.00 1.52
504 506 6.413783 ACGTGGAAGGTTGGATTAAAATTT 57.586 33.333 0.00 0.00 0.00 1.82
505 507 7.527568 TTACGTGGAAGGTTGGATTAAAATT 57.472 32.000 0.00 0.00 35.89 1.82
506 508 7.231925 AGTTTACGTGGAAGGTTGGATTAAAAT 59.768 33.333 0.00 0.00 35.89 1.82
508 510 6.016943 CAGTTTACGTGGAAGGTTGGATTAAA 60.017 38.462 0.00 0.00 35.89 1.52
523 525 5.353956 TGGAAATCATGATCCAGTTTACGTG 59.646 40.000 13.08 0.00 40.74 4.49
526 528 8.070171 CGTATTGGAAATCATGATCCAGTTTAC 58.930 37.037 16.01 16.14 45.94 2.01
533 535 6.391227 AAACCGTATTGGAAATCATGATCC 57.609 37.500 9.06 8.59 42.00 3.36
537 539 4.932146 GGGAAACCGTATTGGAAATCATG 58.068 43.478 0.00 0.00 43.64 3.07
555 557 0.326595 TGAGTTGGCTTATGCGGGAA 59.673 50.000 0.00 0.00 40.82 3.97
559 561 4.361451 AGAAATTGAGTTGGCTTATGCG 57.639 40.909 0.00 0.00 40.82 4.73
563 565 7.594758 CGATTCAAAAGAAATTGAGTTGGCTTA 59.405 33.333 0.00 0.00 40.21 3.09
580 582 8.236586 CACCTGTAAATTGATCTCGATTCAAAA 58.763 33.333 13.09 2.64 0.00 2.44
582 584 6.183360 GCACCTGTAAATTGATCTCGATTCAA 60.183 38.462 11.87 11.87 0.00 2.69
588 590 2.285834 GCGCACCTGTAAATTGATCTCG 60.286 50.000 0.30 0.00 0.00 4.04
598 600 2.606519 AGAGGGGCGCACCTGTAA 60.607 61.111 41.14 0.00 42.10 2.41
613 615 4.417641 GGTCAGTCACCCGAGAGA 57.582 61.111 0.00 0.00 39.69 3.10
626 628 1.679680 ACGTCTTCACTCTTTCGGTCA 59.320 47.619 0.00 0.00 0.00 4.02
630 632 3.060473 GGTTTCACGTCTTCACTCTTTCG 60.060 47.826 0.00 0.00 0.00 3.46
635 637 4.304110 TGTATGGTTTCACGTCTTCACTC 58.696 43.478 0.00 0.00 0.00 3.51
642 644 5.143916 GATGTGATGTATGGTTTCACGTC 57.856 43.478 8.29 8.29 44.51 4.34
644 646 4.201812 GGTGATGTGATGTATGGTTTCACG 60.202 45.833 0.00 0.00 42.07 4.35
660 662 3.311322 CGCGGTATGTAAAATGGTGATGT 59.689 43.478 0.00 0.00 0.00 3.06
661 663 3.558006 TCGCGGTATGTAAAATGGTGATG 59.442 43.478 6.13 0.00 0.00 3.07
680 682 3.868077 ACATCTTGAGCTTAGATTGTCGC 59.132 43.478 9.00 0.00 30.05 5.19
688 690 2.428890 AGGTCGGACATCTTGAGCTTAG 59.571 50.000 10.76 0.00 37.16 2.18
689 691 2.427453 GAGGTCGGACATCTTGAGCTTA 59.573 50.000 15.01 0.00 40.28 3.09
690 692 1.205893 GAGGTCGGACATCTTGAGCTT 59.794 52.381 15.01 0.00 40.28 3.74
696 698 1.821753 CAGAGTGAGGTCGGACATCTT 59.178 52.381 21.63 11.30 29.01 2.40
705 707 1.080434 GGCACGACAGAGTGAGGTC 60.080 63.158 0.88 0.00 44.43 3.85
706 708 1.832608 TGGCACGACAGAGTGAGGT 60.833 57.895 0.88 0.00 44.43 3.85
707 709 1.373497 GTGGCACGACAGAGTGAGG 60.373 63.158 0.00 0.00 44.43 3.86
708 710 0.037882 ATGTGGCACGACAGAGTGAG 60.038 55.000 13.77 0.00 44.43 3.51
709 711 0.319813 CATGTGGCACGACAGAGTGA 60.320 55.000 13.77 0.00 44.43 3.41
710 712 0.601046 ACATGTGGCACGACAGAGTG 60.601 55.000 13.77 5.53 44.47 3.51
711 713 0.966179 TACATGTGGCACGACAGAGT 59.034 50.000 13.77 7.31 0.00 3.24
712 714 1.633561 CTACATGTGGCACGACAGAG 58.366 55.000 13.77 2.69 0.00 3.35
713 715 0.389817 GCTACATGTGGCACGACAGA 60.390 55.000 27.25 0.00 37.02 3.41
714 716 0.670239 TGCTACATGTGGCACGACAG 60.670 55.000 30.41 8.16 42.20 3.51
715 717 1.369321 TGCTACATGTGGCACGACA 59.631 52.632 30.41 9.86 42.20 4.35
716 718 4.277239 TGCTACATGTGGCACGAC 57.723 55.556 30.41 4.86 42.20 4.34
721 723 1.779025 CGCTGGATGCTACATGTGGC 61.779 60.000 25.76 25.76 40.11 5.01
722 724 1.779025 GCGCTGGATGCTACATGTGG 61.779 60.000 9.11 6.75 40.11 4.17
723 725 1.091197 TGCGCTGGATGCTACATGTG 61.091 55.000 9.73 0.00 40.11 3.21
724 726 0.179037 ATGCGCTGGATGCTACATGT 60.179 50.000 9.73 2.69 40.11 3.21
725 727 0.516001 GATGCGCTGGATGCTACATG 59.484 55.000 9.73 0.00 36.62 3.21
726 728 0.107268 TGATGCGCTGGATGCTACAT 59.893 50.000 9.73 0.00 38.33 2.29
727 729 0.107268 ATGATGCGCTGGATGCTACA 59.893 50.000 9.73 0.00 40.11 2.74
728 730 0.795085 GATGATGCGCTGGATGCTAC 59.205 55.000 9.73 0.00 40.11 3.58
733 735 1.339438 GGGTATGATGATGCGCTGGAT 60.339 52.381 9.73 0.00 0.00 3.41
777 779 1.072015 CATTGCAGGGCCCTTCAAAAA 59.928 47.619 35.80 18.14 33.42 1.94
778 780 0.686224 CATTGCAGGGCCCTTCAAAA 59.314 50.000 35.80 18.89 33.42 2.44
779 781 1.193462 CCATTGCAGGGCCCTTCAAA 61.193 55.000 35.80 23.77 33.42 2.69
780 782 1.610086 CCATTGCAGGGCCCTTCAA 60.610 57.895 34.64 34.64 34.12 2.69
781 783 2.037687 CCATTGCAGGGCCCTTCA 59.962 61.111 26.10 23.53 0.00 3.02
782 784 1.610379 AACCATTGCAGGGCCCTTC 60.610 57.895 26.10 20.41 0.00 3.46
783 785 1.914764 CAACCATTGCAGGGCCCTT 60.915 57.895 26.10 4.10 0.00 3.95
784 786 2.284112 CAACCATTGCAGGGCCCT 60.284 61.111 22.28 22.28 0.00 5.19
785 787 2.216331 AACAACCATTGCAGGGCCC 61.216 57.895 16.46 16.46 0.00 5.80
786 788 1.004679 CAACAACCATTGCAGGGCC 60.005 57.895 0.00 0.00 0.00 5.80
787 789 1.004679 CCAACAACCATTGCAGGGC 60.005 57.895 6.41 0.00 0.00 5.19
864 870 3.015677 CGGTGAACGGCGTTTTGA 58.984 55.556 27.48 11.19 39.42 2.69
900 906 2.907179 ATATAAGCGGGGCCAGGGC 61.907 63.158 4.39 3.77 41.06 5.19
901 907 1.002134 CATATAAGCGGGGCCAGGG 60.002 63.158 4.39 0.00 0.00 4.45
902 908 0.036010 CTCATATAAGCGGGGCCAGG 60.036 60.000 4.39 0.00 0.00 4.45
903 909 0.976641 TCTCATATAAGCGGGGCCAG 59.023 55.000 4.39 1.12 0.00 4.85
904 910 0.976641 CTCTCATATAAGCGGGGCCA 59.023 55.000 4.39 0.00 0.00 5.36
918 936 1.679305 GCAGAGGGTCCGTCTCTCA 60.679 63.158 11.25 0.00 45.59 3.27
957 975 2.719354 GCGTTCGTTGGTTGGCTT 59.281 55.556 0.00 0.00 0.00 4.35
965 983 2.127758 GAGTTGCGGCGTTCGTTG 60.128 61.111 9.37 0.00 41.72 4.10
990 1008 2.585153 GGTTTCGGAGGGAGAGGC 59.415 66.667 0.00 0.00 0.00 4.70
1034 1069 2.547798 GTCCGTTCGGTTGCGAAC 59.452 61.111 11.04 0.00 43.19 3.95
1035 1070 3.031457 CGTCCGTTCGGTTGCGAA 61.031 61.111 11.04 0.00 0.00 4.70
1254 1315 1.588403 CTCGATGAGGCTGCAGACG 60.588 63.158 20.43 11.99 0.00 4.18
1396 1457 2.489275 GCTCCTCCTCGCTCTCCAG 61.489 68.421 0.00 0.00 0.00 3.86
1441 1502 2.154798 CTCGACCGCTCCAACTCCAA 62.155 60.000 0.00 0.00 0.00 3.53
1442 1503 2.599281 TCGACCGCTCCAACTCCA 60.599 61.111 0.00 0.00 0.00 3.86
1443 1504 2.182030 CTCGACCGCTCCAACTCC 59.818 66.667 0.00 0.00 0.00 3.85
1444 1505 2.507324 GCTCGACCGCTCCAACTC 60.507 66.667 0.00 0.00 0.00 3.01
1445 1506 2.992114 AGCTCGACCGCTCCAACT 60.992 61.111 0.00 0.00 34.57 3.16
1597 1658 0.179124 GCGATCTCACCTCACCTCAC 60.179 60.000 0.00 0.00 0.00 3.51
1598 1659 1.323271 GGCGATCTCACCTCACCTCA 61.323 60.000 0.00 0.00 0.00 3.86
1599 1660 1.439644 GGCGATCTCACCTCACCTC 59.560 63.158 0.00 0.00 0.00 3.85
1600 1661 2.418910 CGGCGATCTCACCTCACCT 61.419 63.158 0.00 0.00 0.00 4.00
1601 1662 2.105128 CGGCGATCTCACCTCACC 59.895 66.667 0.00 0.00 0.00 4.02
1637 1698 2.135664 ACAGTCACGGAAAGAAGACG 57.864 50.000 0.00 0.00 35.03 4.18
1652 1713 4.515028 ATCCATGGATCATCACAACAGT 57.485 40.909 22.15 0.00 0.00 3.55
1727 1788 2.743636 ATGTATAATCACGGGCGAGG 57.256 50.000 0.00 0.00 0.00 4.63
1777 1838 2.289565 GGAAGAACGGGATTGGATCAC 58.710 52.381 0.00 0.00 0.00 3.06
1790 1851 0.112412 TTCCAAGGCTGGGGAAGAAC 59.888 55.000 8.41 0.00 43.71 3.01
1827 1894 0.694771 TGCTGAACCTGAGCCAGAAT 59.305 50.000 4.00 0.00 35.43 2.40
1834 1901 0.674581 TCGCCATTGCTGAACCTGAG 60.675 55.000 0.00 0.00 34.43 3.35
1837 1904 1.091771 CGATCGCCATTGCTGAACCT 61.092 55.000 0.26 0.00 34.43 3.50
1838 1905 1.089481 TCGATCGCCATTGCTGAACC 61.089 55.000 11.09 0.00 34.43 3.62
1839 1906 0.940126 ATCGATCGCCATTGCTGAAC 59.060 50.000 11.09 0.00 34.43 3.18
1840 1907 1.667236 AATCGATCGCCATTGCTGAA 58.333 45.000 11.09 0.00 34.43 3.02
1841 1908 1.599071 GAAATCGATCGCCATTGCTGA 59.401 47.619 11.09 0.00 34.43 4.26
1842 1909 1.600957 AGAAATCGATCGCCATTGCTG 59.399 47.619 11.09 0.00 34.43 4.41
1843 1910 1.959042 AGAAATCGATCGCCATTGCT 58.041 45.000 11.09 7.23 34.43 3.91
1863 1930 3.585862 GAAACCTCGCACAGATCAGTTA 58.414 45.455 0.00 0.00 0.00 2.24
1879 1946 1.000145 GACGCATTCTCCTCGAAACC 59.000 55.000 0.00 0.00 34.79 3.27
2143 2282 2.613506 CCAACGGGACAACGGCTTC 61.614 63.158 0.00 0.00 38.39 3.86
2211 2350 3.991051 CGTCCCAGCAGACCACGT 61.991 66.667 0.00 0.00 32.91 4.49
2217 2356 4.631740 TCCACCCGTCCCAGCAGA 62.632 66.667 0.00 0.00 0.00 4.26
2324 2519 3.948086 CTCGTGCAGTCCGTCCGTC 62.948 68.421 0.00 0.00 0.00 4.79
2325 2520 4.039357 CTCGTGCAGTCCGTCCGT 62.039 66.667 0.00 0.00 0.00 4.69
2544 2762 2.583593 GCACAGATCGCTCGACCC 60.584 66.667 0.00 0.00 0.00 4.46
2567 2790 2.609825 GCATAGGAGGACATGCACG 58.390 57.895 0.00 0.00 45.51 5.34
2591 2814 4.227134 CATCCGAGCGTCCCTGGG 62.227 72.222 6.33 6.33 40.54 4.45
2592 2815 4.227134 CCATCCGAGCGTCCCTGG 62.227 72.222 0.00 0.00 0.00 4.45
2593 2816 4.227134 CCCATCCGAGCGTCCCTG 62.227 72.222 0.00 0.00 0.00 4.45
2596 2819 4.593864 GAGCCCATCCGAGCGTCC 62.594 72.222 0.00 0.00 0.00 4.79
2601 2824 1.301558 GATGCAGAGCCCATCCGAG 60.302 63.158 0.00 0.00 34.43 4.63
2649 2872 2.949678 CTACTGTACGCGCGCCAG 60.950 66.667 34.60 34.60 0.00 4.85
2734 2961 9.638239 GTTTAAGAGCAATGAATATTTGTCCAA 57.362 29.630 0.00 0.00 0.00 3.53
2735 2962 8.801299 TGTTTAAGAGCAATGAATATTTGTCCA 58.199 29.630 0.00 0.00 0.00 4.02
2736 2963 9.294030 CTGTTTAAGAGCAATGAATATTTGTCC 57.706 33.333 0.00 0.00 0.00 4.02
2737 2964 8.801913 GCTGTTTAAGAGCAATGAATATTTGTC 58.198 33.333 9.28 0.00 36.40 3.18
2738 2965 7.761249 GGCTGTTTAAGAGCAATGAATATTTGT 59.239 33.333 15.78 0.00 38.27 2.83
2739 2966 7.760794 TGGCTGTTTAAGAGCAATGAATATTTG 59.239 33.333 15.78 0.00 38.27 2.32
2740 2967 7.839907 TGGCTGTTTAAGAGCAATGAATATTT 58.160 30.769 15.78 0.00 38.27 1.40
2741 2968 7.408756 TGGCTGTTTAAGAGCAATGAATATT 57.591 32.000 15.78 0.00 38.27 1.28
2742 2969 7.592885 ATGGCTGTTTAAGAGCAATGAATAT 57.407 32.000 15.78 0.00 38.27 1.28
2744 2971 5.927281 ATGGCTGTTTAAGAGCAATGAAT 57.073 34.783 15.78 0.00 38.27 2.57


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

AutoCloner maintained by Alex Coulton.