Multiple sequence alignment - TraesCS2D01G469000

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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 TraesCS2D01G469000 chr2D 100.000 2402 0 0 1 2402 574120392 574117991 0.000000e+00 4436.0
1 TraesCS2D01G469000 chr2A 91.807 1721 82 28 586 2284 712588358 712586675 0.000000e+00 2342.0
2 TraesCS2D01G469000 chr2A 91.667 48 4 0 523 570 712588391 712588344 1.540000e-07 67.6
3 TraesCS2D01G469000 chr2B 90.479 1565 105 24 586 2119 690039964 690038413 0.000000e+00 2025.0
4 TraesCS2D01G469000 chr2B 85.864 382 30 20 196 570 690040314 690039950 3.750000e-103 385.0
5 TraesCS2D01G469000 chr2B 84.267 375 41 6 1916 2284 690038664 690038302 1.370000e-92 350.0
6 TraesCS2D01G469000 chr2B 92.857 84 4 2 2279 2361 762916545 762916463 1.170000e-23 121.0
7 TraesCS2D01G469000 chrUn 84.416 154 18 5 254 406 96471182 96471034 1.920000e-31 147.0
8 TraesCS2D01G469000 chr6D 82.468 154 16 9 254 406 426078335 426078478 9.020000e-25 124.0
9 TraesCS2D01G469000 chr6B 92.593 81 5 1 2278 2358 149447254 149447175 5.430000e-22 115.0
10 TraesCS2D01G469000 chr6B 94.595 74 4 0 2282 2355 693939313 693939386 5.430000e-22 115.0
11 TraesCS2D01G469000 chr3D 92.593 81 4 2 2276 2355 169888136 169888215 5.430000e-22 115.0
12 TraesCS2D01G469000 chr4D 92.593 81 3 2 2279 2357 402527928 402528007 1.950000e-21 113.0
13 TraesCS2D01G469000 chr4B 88.542 96 7 3 2271 2366 269174157 269174066 1.950000e-21 113.0
14 TraesCS2D01G469000 chr4B 92.593 81 3 2 2279 2357 498374457 498374536 1.950000e-21 113.0
15 TraesCS2D01G469000 chr5B 89.773 88 6 3 2279 2365 664376103 664376018 2.520000e-20 110.0
16 TraesCS2D01G469000 chr5B 85.484 62 4 5 346 406 70392286 70392343 2.580000e-05 60.2
17 TraesCS2D01G469000 chr6A 90.476 84 5 1 2282 2362 91911617 91911534 9.080000e-20 108.0
18 TraesCS2D01G469000 chr7A 79.200 125 16 9 286 406 164660508 164660626 7.120000e-11 78.7
19 TraesCS2D01G469000 chr7A 89.362 47 4 1 250 296 563839928 563839973 9.270000e-05 58.4
20 TraesCS2D01G469000 chr7D 76.774 155 23 11 251 402 578051354 578051498 9.210000e-10 75.0
21 TraesCS2D01G469000 chr1B 97.297 37 0 1 371 406 17525368 17525332 7.170000e-06 62.1
22 TraesCS2D01G469000 chr1B 100.000 28 0 0 251 278 519518091 519518118 4.000000e-03 52.8
23 TraesCS2D01G469000 chr5D 85.484 62 4 5 346 406 60252814 60252757 2.580000e-05 60.2
24 TraesCS2D01G469000 chr3A 96.875 32 1 0 375 406 149563385 149563416 1.000000e-03 54.7


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 TraesCS2D01G469000 chr2D 574117991 574120392 2401 True 4436.0 4436 100.000 1 2402 1 chr2D.!!$R1 2401
1 TraesCS2D01G469000 chr2A 712586675 712588391 1716 True 1204.8 2342 91.737 523 2284 2 chr2A.!!$R1 1761
2 TraesCS2D01G469000 chr2B 690038302 690040314 2012 True 920.0 2025 86.870 196 2284 3 chr2B.!!$R2 2088

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
75 76 0.040646 ACTCCACCCGATGACCACTA 59.959 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1728 3.536956 TTGAATTCCCCTAGTACTGCG 57.463 47.619 5.39 0.0 0.0 5.18 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
25 26 7.902920 ACATGGCACCTAGAAATAATTTCAT 57.097 32.000 0.00 0.00 42.10 2.57
26 27 8.995027 ACATGGCACCTAGAAATAATTTCATA 57.005 30.769 0.00 0.00 42.10 2.15
27 28 9.420118 ACATGGCACCTAGAAATAATTTCATAA 57.580 29.630 0.00 0.00 42.10 1.90
45 46 8.969121 TTTCATAAATAACATTGCACAGACTG 57.031 30.769 0.00 0.00 0.00 3.51
46 47 7.686438 TCATAAATAACATTGCACAGACTGT 57.314 32.000 1.07 1.07 0.00 3.55
47 48 8.109705 TCATAAATAACATTGCACAGACTGTT 57.890 30.769 5.04 0.00 36.00 3.16
48 49 9.225436 TCATAAATAACATTGCACAGACTGTTA 57.775 29.630 5.04 0.00 38.16 2.41
49 50 9.494479 CATAAATAACATTGCACAGACTGTTAG 57.506 33.333 5.04 0.00 37.46 2.34
50 51 6.500684 AATAACATTGCACAGACTGTTAGG 57.499 37.500 5.04 0.00 37.46 2.69
51 52 2.783135 ACATTGCACAGACTGTTAGGG 58.217 47.619 5.04 0.00 0.00 3.53
52 53 2.371841 ACATTGCACAGACTGTTAGGGA 59.628 45.455 5.04 0.00 0.00 4.20
53 54 3.009473 ACATTGCACAGACTGTTAGGGAT 59.991 43.478 5.04 0.00 0.00 3.85
54 55 3.788227 TTGCACAGACTGTTAGGGATT 57.212 42.857 5.04 0.00 0.00 3.01
55 56 3.334583 TGCACAGACTGTTAGGGATTC 57.665 47.619 5.04 0.00 0.00 2.52
56 57 2.637382 TGCACAGACTGTTAGGGATTCA 59.363 45.455 5.04 0.00 0.00 2.57
57 58 3.003480 GCACAGACTGTTAGGGATTCAC 58.997 50.000 5.04 0.00 0.00 3.18
58 59 3.307059 GCACAGACTGTTAGGGATTCACT 60.307 47.826 5.04 0.00 0.00 3.41
59 60 4.499183 CACAGACTGTTAGGGATTCACTC 58.501 47.826 5.04 0.00 0.00 3.51
60 61 3.515901 ACAGACTGTTAGGGATTCACTCC 59.484 47.826 1.07 0.00 44.11 3.85
61 62 3.515502 CAGACTGTTAGGGATTCACTCCA 59.484 47.826 0.00 0.00 46.98 3.86
62 63 3.515901 AGACTGTTAGGGATTCACTCCAC 59.484 47.826 0.00 0.00 46.98 4.02
63 64 2.572104 ACTGTTAGGGATTCACTCCACC 59.428 50.000 0.00 0.00 46.98 4.61
64 65 1.913419 TGTTAGGGATTCACTCCACCC 59.087 52.381 0.00 0.00 46.98 4.61
65 66 1.134491 GTTAGGGATTCACTCCACCCG 60.134 57.143 0.00 0.00 46.98 5.28
66 67 0.337082 TAGGGATTCACTCCACCCGA 59.663 55.000 0.00 0.00 46.98 5.14
67 68 0.326618 AGGGATTCACTCCACCCGAT 60.327 55.000 0.00 0.00 46.98 4.18
68 69 0.179045 GGGATTCACTCCACCCGATG 60.179 60.000 0.00 0.00 46.98 3.84
69 70 0.830648 GGATTCACTCCACCCGATGA 59.169 55.000 0.00 0.00 44.26 2.92
70 71 1.473434 GGATTCACTCCACCCGATGAC 60.473 57.143 0.00 0.00 44.26 3.06
71 72 0.541863 ATTCACTCCACCCGATGACC 59.458 55.000 0.00 0.00 0.00 4.02
72 73 0.834261 TTCACTCCACCCGATGACCA 60.834 55.000 0.00 0.00 0.00 4.02
73 74 1.079127 CACTCCACCCGATGACCAC 60.079 63.158 0.00 0.00 0.00 4.16
74 75 1.229209 ACTCCACCCGATGACCACT 60.229 57.895 0.00 0.00 0.00 4.00
75 76 0.040646 ACTCCACCCGATGACCACTA 59.959 55.000 0.00 0.00 0.00 2.74
76 77 1.191535 CTCCACCCGATGACCACTAA 58.808 55.000 0.00 0.00 0.00 2.24
77 78 1.553248 CTCCACCCGATGACCACTAAA 59.447 52.381 0.00 0.00 0.00 1.85
78 79 1.979308 TCCACCCGATGACCACTAAAA 59.021 47.619 0.00 0.00 0.00 1.52
79 80 2.027561 TCCACCCGATGACCACTAAAAG 60.028 50.000 0.00 0.00 0.00 2.27
80 81 2.356135 CACCCGATGACCACTAAAAGG 58.644 52.381 0.00 0.00 0.00 3.11
81 82 1.339727 ACCCGATGACCACTAAAAGGC 60.340 52.381 0.00 0.00 0.00 4.35
82 83 1.065418 CCCGATGACCACTAAAAGGCT 60.065 52.381 0.00 0.00 0.00 4.58
83 84 2.280628 CCGATGACCACTAAAAGGCTC 58.719 52.381 0.00 0.00 0.00 4.70
84 85 2.280628 CGATGACCACTAAAAGGCTCC 58.719 52.381 0.00 0.00 0.00 4.70
85 86 2.093447 CGATGACCACTAAAAGGCTCCT 60.093 50.000 0.00 0.00 0.00 3.69
86 87 3.132289 CGATGACCACTAAAAGGCTCCTA 59.868 47.826 0.00 0.00 0.00 2.94
87 88 4.202264 CGATGACCACTAAAAGGCTCCTAT 60.202 45.833 0.00 0.00 0.00 2.57
88 89 5.010719 CGATGACCACTAAAAGGCTCCTATA 59.989 44.000 0.00 0.00 0.00 1.31
89 90 6.462487 CGATGACCACTAAAAGGCTCCTATAA 60.462 42.308 0.00 0.00 0.00 0.98
90 91 6.630203 TGACCACTAAAAGGCTCCTATAAA 57.370 37.500 0.00 0.00 0.00 1.40
91 92 7.023171 TGACCACTAAAAGGCTCCTATAAAA 57.977 36.000 0.00 0.00 0.00 1.52
92 93 7.463431 TGACCACTAAAAGGCTCCTATAAAAA 58.537 34.615 0.00 0.00 0.00 1.94
93 94 7.392393 TGACCACTAAAAGGCTCCTATAAAAAC 59.608 37.037 0.00 0.00 0.00 2.43
94 95 7.235804 ACCACTAAAAGGCTCCTATAAAAACA 58.764 34.615 0.00 0.00 0.00 2.83
95 96 7.726738 ACCACTAAAAGGCTCCTATAAAAACAA 59.273 33.333 0.00 0.00 0.00 2.83
96 97 8.581578 CCACTAAAAGGCTCCTATAAAAACAAA 58.418 33.333 0.00 0.00 0.00 2.83
97 98 9.626045 CACTAAAAGGCTCCTATAAAAACAAAG 57.374 33.333 0.00 0.00 0.00 2.77
98 99 8.304596 ACTAAAAGGCTCCTATAAAAACAAAGC 58.695 33.333 0.00 0.00 0.00 3.51
99 100 6.664428 AAAGGCTCCTATAAAAACAAAGCA 57.336 33.333 0.00 0.00 0.00 3.91
100 101 6.664428 AAGGCTCCTATAAAAACAAAGCAA 57.336 33.333 0.00 0.00 0.00 3.91
101 102 6.272822 AGGCTCCTATAAAAACAAAGCAAG 57.727 37.500 0.00 0.00 0.00 4.01
102 103 6.010219 AGGCTCCTATAAAAACAAAGCAAGA 58.990 36.000 0.00 0.00 0.00 3.02
103 104 6.665248 AGGCTCCTATAAAAACAAAGCAAGAT 59.335 34.615 0.00 0.00 0.00 2.40
104 105 7.834181 AGGCTCCTATAAAAACAAAGCAAGATA 59.166 33.333 0.00 0.00 0.00 1.98
105 106 8.633561 GGCTCCTATAAAAACAAAGCAAGATAT 58.366 33.333 0.00 0.00 0.00 1.63
106 107 9.670719 GCTCCTATAAAAACAAAGCAAGATATC 57.329 33.333 0.00 0.00 0.00 1.63
112 113 7.951530 AAAAACAAAGCAAGATATCAGTTGG 57.048 32.000 5.32 0.00 0.00 3.77
113 114 6.899393 AAACAAAGCAAGATATCAGTTGGA 57.101 33.333 5.32 0.00 0.00 3.53
114 115 6.506500 AACAAAGCAAGATATCAGTTGGAG 57.493 37.500 5.32 0.00 0.00 3.86
115 116 4.946157 ACAAAGCAAGATATCAGTTGGAGG 59.054 41.667 5.32 0.00 0.00 4.30
116 117 3.205784 AGCAAGATATCAGTTGGAGGC 57.794 47.619 5.32 0.00 0.00 4.70
117 118 2.507058 AGCAAGATATCAGTTGGAGGCA 59.493 45.455 5.32 0.00 0.00 4.75
118 119 3.054139 AGCAAGATATCAGTTGGAGGCAA 60.054 43.478 5.32 0.00 0.00 4.52
119 120 3.696051 GCAAGATATCAGTTGGAGGCAAA 59.304 43.478 5.32 0.00 0.00 3.68
120 121 4.439289 GCAAGATATCAGTTGGAGGCAAAC 60.439 45.833 5.32 0.00 0.00 2.93
121 122 4.574674 AGATATCAGTTGGAGGCAAACA 57.425 40.909 5.32 0.00 0.00 2.83
122 123 4.922206 AGATATCAGTTGGAGGCAAACAA 58.078 39.130 5.32 0.00 0.00 2.83
123 124 5.513233 AGATATCAGTTGGAGGCAAACAAT 58.487 37.500 5.32 0.00 0.00 2.71
124 125 5.954150 AGATATCAGTTGGAGGCAAACAATT 59.046 36.000 5.32 0.00 0.00 2.32
125 126 4.525912 ATCAGTTGGAGGCAAACAATTC 57.474 40.909 0.00 0.00 0.00 2.17
126 127 2.293122 TCAGTTGGAGGCAAACAATTCG 59.707 45.455 0.00 0.00 0.00 3.34
127 128 2.293122 CAGTTGGAGGCAAACAATTCGA 59.707 45.455 0.00 0.00 0.00 3.71
128 129 2.554032 AGTTGGAGGCAAACAATTCGAG 59.446 45.455 0.00 0.00 0.00 4.04
129 130 1.533625 TGGAGGCAAACAATTCGAGG 58.466 50.000 0.00 0.00 0.00 4.63
130 131 1.073125 TGGAGGCAAACAATTCGAGGA 59.927 47.619 0.00 0.00 0.00 3.71
131 132 2.159382 GGAGGCAAACAATTCGAGGAA 58.841 47.619 0.00 0.00 0.00 3.36
132 133 2.556622 GGAGGCAAACAATTCGAGGAAA 59.443 45.455 0.00 0.00 0.00 3.13
133 134 3.005367 GGAGGCAAACAATTCGAGGAAAA 59.995 43.478 0.00 0.00 0.00 2.29
134 135 4.500716 GGAGGCAAACAATTCGAGGAAAAA 60.501 41.667 0.00 0.00 0.00 1.94
158 159 8.504812 AAAAACCTAACCGTTCTTGTACTTAA 57.495 30.769 0.00 0.00 0.00 1.85
159 160 8.681486 AAAACCTAACCGTTCTTGTACTTAAT 57.319 30.769 0.00 0.00 0.00 1.40
160 161 7.662604 AACCTAACCGTTCTTGTACTTAATG 57.337 36.000 0.00 0.00 0.00 1.90
161 162 6.762333 ACCTAACCGTTCTTGTACTTAATGT 58.238 36.000 0.00 0.00 0.00 2.71
162 163 6.870439 ACCTAACCGTTCTTGTACTTAATGTC 59.130 38.462 0.00 0.00 0.00 3.06
163 164 7.095270 CCTAACCGTTCTTGTACTTAATGTCT 58.905 38.462 0.00 0.00 0.00 3.41
164 165 7.601508 CCTAACCGTTCTTGTACTTAATGTCTT 59.398 37.037 0.00 0.00 0.00 3.01
165 166 9.630098 CTAACCGTTCTTGTACTTAATGTCTTA 57.370 33.333 0.00 0.00 0.00 2.10
166 167 8.530269 AACCGTTCTTGTACTTAATGTCTTAG 57.470 34.615 0.00 0.00 0.00 2.18
167 168 7.664758 ACCGTTCTTGTACTTAATGTCTTAGT 58.335 34.615 0.00 0.00 0.00 2.24
168 169 8.146412 ACCGTTCTTGTACTTAATGTCTTAGTT 58.854 33.333 0.00 0.00 0.00 2.24
169 170 8.985805 CCGTTCTTGTACTTAATGTCTTAGTTT 58.014 33.333 0.00 0.00 0.00 2.66
249 250 9.934190 AATGCACAAAAACAAAAATGATTAGTC 57.066 25.926 0.00 0.00 0.00 2.59
265 266 6.942976 TGATTAGTCAAATACTTCCTCCGTT 58.057 36.000 0.00 0.00 39.80 4.44
271 272 5.237779 GTCAAATACTTCCTCCGTTCACAAA 59.762 40.000 0.00 0.00 0.00 2.83
280 281 3.869246 CCTCCGTTCACAAATATAAGCGT 59.131 43.478 0.00 0.00 0.00 5.07
315 316 7.715266 TTTGTGAATTGGATGGATATTGACA 57.285 32.000 0.00 0.00 0.00 3.58
338 339 5.464057 CACGATTTAGTGTGTTTGTCCACTA 59.536 40.000 0.00 0.00 41.85 2.74
344 345 7.867305 TTAGTGTGTTTGTCCACTAATTTCA 57.133 32.000 7.87 0.00 44.81 2.69
345 346 6.377327 AGTGTGTTTGTCCACTAATTTCAG 57.623 37.500 0.00 0.00 40.03 3.02
346 347 5.885912 AGTGTGTTTGTCCACTAATTTCAGT 59.114 36.000 0.00 0.00 40.03 3.41
347 348 6.377146 AGTGTGTTTGTCCACTAATTTCAGTT 59.623 34.615 0.00 0.00 40.03 3.16
348 349 6.691388 GTGTGTTTGTCCACTAATTTCAGTTC 59.309 38.462 0.00 0.00 36.30 3.01
349 350 6.601613 TGTGTTTGTCCACTAATTTCAGTTCT 59.398 34.615 0.00 0.00 36.30 3.01
350 351 7.771361 TGTGTTTGTCCACTAATTTCAGTTCTA 59.229 33.333 0.00 0.00 36.30 2.10
351 352 8.617809 GTGTTTGTCCACTAATTTCAGTTCTAA 58.382 33.333 0.00 0.00 32.50 2.10
352 353 9.349713 TGTTTGTCCACTAATTTCAGTTCTAAT 57.650 29.630 0.00 0.00 0.00 1.73
353 354 9.612620 GTTTGTCCACTAATTTCAGTTCTAATG 57.387 33.333 0.00 0.00 0.00 1.90
354 355 8.918202 TTGTCCACTAATTTCAGTTCTAATGT 57.082 30.769 0.00 0.00 0.00 2.71
356 357 9.653287 TGTCCACTAATTTCAGTTCTAATGTAG 57.347 33.333 0.00 0.00 0.00 2.74
357 358 9.654663 GTCCACTAATTTCAGTTCTAATGTAGT 57.345 33.333 0.00 0.00 0.00 2.73
405 406 8.848474 AATATCTTATATTTGTGAACGGAGGG 57.152 34.615 0.00 0.00 0.00 4.30
406 407 5.687166 TCTTATATTTGTGAACGGAGGGT 57.313 39.130 0.00 0.00 0.00 4.34
415 416 3.949754 TGTGAACGGAGGGTACTGTATAG 59.050 47.826 0.00 0.00 0.00 1.31
459 463 9.054922 CAAGAAACAAAAACACCAATATTCCAT 57.945 29.630 0.00 0.00 0.00 3.41
473 477 5.833406 ATATTCCATCGCAATGTCAAACA 57.167 34.783 0.00 0.00 0.00 2.83
481 485 7.700234 TCCATCGCAATGTCAAACAAATATTAC 59.300 33.333 0.00 0.00 0.00 1.89
483 487 9.075519 CATCGCAATGTCAAACAAATATTACTT 57.924 29.630 0.00 0.00 0.00 2.24
486 490 8.577939 CGCAATGTCAAACAAATATTACTTCTG 58.422 33.333 0.00 0.00 0.00 3.02
487 491 9.624697 GCAATGTCAAACAAATATTACTTCTGA 57.375 29.630 0.00 0.00 0.00 3.27
496 500 8.425577 ACAAATATTACTTCTGACTGATTCGG 57.574 34.615 0.00 0.00 0.00 4.30
497 501 7.495934 ACAAATATTACTTCTGACTGATTCGGG 59.504 37.037 0.00 0.00 0.00 5.14
570 578 3.319689 CCCAATTTTAGAAACCCACACGT 59.680 43.478 0.00 0.00 0.00 4.49
571 579 4.202172 CCCAATTTTAGAAACCCACACGTT 60.202 41.667 0.00 0.00 0.00 3.99
572 580 5.353111 CCAATTTTAGAAACCCACACGTTT 58.647 37.500 0.00 0.00 38.65 3.60
573 581 5.813157 CCAATTTTAGAAACCCACACGTTTT 59.187 36.000 0.00 0.00 36.10 2.43
574 582 6.314152 CCAATTTTAGAAACCCACACGTTTTT 59.686 34.615 0.00 0.00 36.10 1.94
600 608 5.838531 TTTGAAATTAGAAACCCACACGT 57.161 34.783 0.00 0.00 0.00 4.49
809 831 2.987125 GGCCCCACACGTCATACT 59.013 61.111 0.00 0.00 0.00 2.12
859 881 3.009695 AGTGAACATACGAATTTCCCCCA 59.990 43.478 0.00 0.00 0.00 4.96
863 885 5.047660 TGAACATACGAATTTCCCCCAAAAG 60.048 40.000 0.00 0.00 0.00 2.27
877 899 2.046292 CCAAAAGCTTTTCCCTCCCAA 58.954 47.619 21.45 0.00 0.00 4.12
880 902 0.542938 AAGCTTTTCCCTCCCAAGGC 60.543 55.000 0.00 0.00 41.85 4.35
957 980 2.141011 CTTCCACAGCATCCCACCCA 62.141 60.000 0.00 0.00 0.00 4.51
975 998 0.398806 CATCCCATTGGCCCAATCCA 60.399 55.000 5.84 0.00 31.05 3.41
1248 1278 3.695022 CTACTTCGTGCCCGGGTCG 62.695 68.421 24.63 25.62 33.95 4.79
1429 1462 1.580704 CCGTCGTGTTGTATTAGTCGC 59.419 52.381 0.00 0.00 0.00 5.19
1445 1478 6.624352 TTAGTCGCGGTATACTTGTAGATT 57.376 37.500 6.13 1.26 0.00 2.40
1457 1490 5.799827 ACTTGTAGATTCAGGGATCTAGC 57.200 43.478 0.00 0.00 38.84 3.42
1469 1502 1.512735 GATCTAGCCCCTCCCTTGTT 58.487 55.000 0.00 0.00 0.00 2.83
1470 1503 1.847088 GATCTAGCCCCTCCCTTGTTT 59.153 52.381 0.00 0.00 0.00 2.83
1471 1504 0.991920 TCTAGCCCCTCCCTTGTTTG 59.008 55.000 0.00 0.00 0.00 2.93
1472 1505 0.991920 CTAGCCCCTCCCTTGTTTGA 59.008 55.000 0.00 0.00 0.00 2.69
1473 1506 1.566231 CTAGCCCCTCCCTTGTTTGAT 59.434 52.381 0.00 0.00 0.00 2.57
1475 1508 1.149923 AGCCCCTCCCTTGTTTGATTT 59.850 47.619 0.00 0.00 0.00 2.17
1476 1509 2.381961 AGCCCCTCCCTTGTTTGATTTA 59.618 45.455 0.00 0.00 0.00 1.40
1477 1510 2.760650 GCCCCTCCCTTGTTTGATTTAG 59.239 50.000 0.00 0.00 0.00 1.85
1481 1514 4.156008 CCCTCCCTTGTTTGATTTAGTTCG 59.844 45.833 0.00 0.00 0.00 3.95
1499 1532 8.922058 TTAGTTCGATGTCTTACAGTTTATCC 57.078 34.615 0.00 0.00 0.00 2.59
1601 1637 2.978156 AAATGGGGAAGAGAAGTGCA 57.022 45.000 0.00 0.00 0.00 4.57
1692 1728 3.251004 GGCTTGCTTATAGGCACATACAC 59.749 47.826 9.35 0.00 42.27 2.90
1774 1810 7.520798 TCATCAGCATCTGGTTATCCTTTTAT 58.479 34.615 0.00 0.00 31.51 1.40
1913 1950 6.179756 TGGTTGATGTAGATACATGCTGTTT 58.820 36.000 10.13 0.00 46.20 2.83
1931 1978 4.739195 TGTTTGTAGTTCAACTTGGTTGC 58.261 39.130 0.00 0.00 42.55 4.17
2016 2066 4.035208 CCGTTAGCAGTTCAACTCTTGTTT 59.965 41.667 0.00 0.00 33.52 2.83
2040 2090 5.862924 ACTTGGTTGATTCTGATTACACG 57.137 39.130 0.00 0.00 0.00 4.49
2049 2099 2.695359 TCTGATTACACGAACCTTGCC 58.305 47.619 0.00 0.00 0.00 4.52
2087 2137 5.305585 TCTAGTTCAAGTTGGGTGATGTTC 58.694 41.667 2.34 0.00 0.00 3.18
2235 2285 8.995027 TTTTGACCTATTGATGCTTATGGTAT 57.005 30.769 0.00 0.00 0.00 2.73
2287 2337 9.498176 TTTGTTAAGAAACACTATACTTCCCTC 57.502 33.333 0.00 0.00 45.18 4.30
2288 2338 7.618137 TGTTAAGAAACACTATACTTCCCTCC 58.382 38.462 0.00 0.00 40.69 4.30
2289 2339 5.695424 AAGAAACACTATACTTCCCTCCC 57.305 43.478 0.00 0.00 0.00 4.30
2290 2340 4.961585 AGAAACACTATACTTCCCTCCCT 58.038 43.478 0.00 0.00 0.00 4.20
2291 2341 6.101274 AGAAACACTATACTTCCCTCCCTA 57.899 41.667 0.00 0.00 0.00 3.53
2292 2342 6.509386 AGAAACACTATACTTCCCTCCCTAA 58.491 40.000 0.00 0.00 0.00 2.69
2293 2343 6.964086 AGAAACACTATACTTCCCTCCCTAAA 59.036 38.462 0.00 0.00 0.00 1.85
2294 2344 6.809976 AACACTATACTTCCCTCCCTAAAG 57.190 41.667 0.00 0.00 0.00 1.85
2295 2345 6.101274 ACACTATACTTCCCTCCCTAAAGA 57.899 41.667 0.00 0.00 0.00 2.52
2296 2346 6.509386 ACACTATACTTCCCTCCCTAAAGAA 58.491 40.000 0.00 0.00 0.00 2.52
2297 2347 6.964086 ACACTATACTTCCCTCCCTAAAGAAA 59.036 38.462 0.00 0.00 0.00 2.52
2298 2348 7.628101 ACACTATACTTCCCTCCCTAAAGAAAT 59.372 37.037 0.00 0.00 0.00 2.17
2299 2349 9.155785 CACTATACTTCCCTCCCTAAAGAAATA 57.844 37.037 0.00 0.00 0.00 1.40
2300 2350 9.915564 ACTATACTTCCCTCCCTAAAGAAATAT 57.084 33.333 0.00 0.00 0.00 1.28
2304 2354 8.871570 ACTTCCCTCCCTAAAGAAATATAAGA 57.128 34.615 0.00 0.00 0.00 2.10
2305 2355 8.939932 ACTTCCCTCCCTAAAGAAATATAAGAG 58.060 37.037 0.00 0.00 0.00 2.85
2306 2356 7.317722 TCCCTCCCTAAAGAAATATAAGAGC 57.682 40.000 0.00 0.00 0.00 4.09
2307 2357 6.014499 TCCCTCCCTAAAGAAATATAAGAGCG 60.014 42.308 0.00 0.00 0.00 5.03
2308 2358 6.239629 CCCTCCCTAAAGAAATATAAGAGCGT 60.240 42.308 0.00 0.00 0.00 5.07
2309 2359 7.217906 CCTCCCTAAAGAAATATAAGAGCGTT 58.782 38.462 0.00 0.00 0.00 4.84
2310 2360 7.715686 CCTCCCTAAAGAAATATAAGAGCGTTT 59.284 37.037 0.00 0.00 0.00 3.60
2311 2361 9.760077 CTCCCTAAAGAAATATAAGAGCGTTTA 57.240 33.333 0.00 0.00 0.00 2.01
2312 2362 9.760077 TCCCTAAAGAAATATAAGAGCGTTTAG 57.240 33.333 0.00 0.00 0.00 1.85
2313 2363 9.760077 CCCTAAAGAAATATAAGAGCGTTTAGA 57.240 33.333 0.00 0.00 30.96 2.10
2345 2395 8.348983 TCTAAACGCTCTTATATTTCTTTCCG 57.651 34.615 0.00 0.00 0.00 4.30
2346 2396 5.986004 AACGCTCTTATATTTCTTTCCGG 57.014 39.130 0.00 0.00 0.00 5.14
2347 2397 5.272283 ACGCTCTTATATTTCTTTCCGGA 57.728 39.130 0.00 0.00 0.00 5.14
2348 2398 5.290386 ACGCTCTTATATTTCTTTCCGGAG 58.710 41.667 3.34 0.00 0.00 4.63
2364 2414 2.946785 CGGAGGGAGTACATCTTAGGT 58.053 52.381 0.00 0.00 0.00 3.08
2365 2415 3.297736 CGGAGGGAGTACATCTTAGGTT 58.702 50.000 0.00 0.00 0.00 3.50
2366 2416 3.705072 CGGAGGGAGTACATCTTAGGTTT 59.295 47.826 0.00 0.00 0.00 3.27
2367 2417 4.202131 CGGAGGGAGTACATCTTAGGTTTC 60.202 50.000 0.00 0.00 0.00 2.78
2368 2418 4.963628 GGAGGGAGTACATCTTAGGTTTCT 59.036 45.833 0.00 0.00 0.00 2.52
2369 2419 5.425862 GGAGGGAGTACATCTTAGGTTTCTT 59.574 44.000 0.00 0.00 0.00 2.52
2370 2420 6.610425 GGAGGGAGTACATCTTAGGTTTCTTA 59.390 42.308 0.00 0.00 0.00 2.10
2371 2421 7.290481 GGAGGGAGTACATCTTAGGTTTCTTAT 59.710 40.741 0.00 0.00 0.00 1.73
2372 2422 8.024145 AGGGAGTACATCTTAGGTTTCTTATG 57.976 38.462 0.00 0.00 0.00 1.90
2373 2423 7.624077 AGGGAGTACATCTTAGGTTTCTTATGT 59.376 37.037 0.00 0.00 0.00 2.29
2374 2424 8.265764 GGGAGTACATCTTAGGTTTCTTATGTT 58.734 37.037 0.00 0.00 0.00 2.71
2375 2425 9.099454 GGAGTACATCTTAGGTTTCTTATGTTG 57.901 37.037 0.00 0.00 0.00 3.33
2376 2426 9.654663 GAGTACATCTTAGGTTTCTTATGTTGT 57.345 33.333 0.00 0.00 0.00 3.32
2379 2429 8.110860 ACATCTTAGGTTTCTTATGTTGTTGG 57.889 34.615 0.00 0.00 0.00 3.77
2380 2430 7.942341 ACATCTTAGGTTTCTTATGTTGTTGGA 59.058 33.333 0.00 0.00 0.00 3.53
2381 2431 7.739498 TCTTAGGTTTCTTATGTTGTTGGAC 57.261 36.000 0.00 0.00 0.00 4.02
2382 2432 7.284074 TCTTAGGTTTCTTATGTTGTTGGACA 58.716 34.615 0.00 0.00 0.00 4.02
2383 2433 7.942341 TCTTAGGTTTCTTATGTTGTTGGACAT 59.058 33.333 0.00 0.00 42.57 3.06
2384 2434 6.976934 AGGTTTCTTATGTTGTTGGACATT 57.023 33.333 0.00 0.00 40.54 2.71
2385 2435 6.748132 AGGTTTCTTATGTTGTTGGACATTG 58.252 36.000 0.00 0.00 40.54 2.82
2386 2436 5.405269 GGTTTCTTATGTTGTTGGACATTGC 59.595 40.000 0.00 0.00 40.54 3.56
2387 2437 4.782019 TCTTATGTTGTTGGACATTGCC 57.218 40.909 0.00 0.00 40.54 4.52
2388 2438 4.148079 TCTTATGTTGTTGGACATTGCCA 58.852 39.130 0.00 0.00 40.54 4.92
2389 2439 4.771577 TCTTATGTTGTTGGACATTGCCAT 59.228 37.500 0.00 0.00 40.54 4.40
2390 2440 3.598019 ATGTTGTTGGACATTGCCATC 57.402 42.857 1.47 2.27 36.92 3.51
2391 2441 2.596346 TGTTGTTGGACATTGCCATCT 58.404 42.857 1.47 0.00 37.86 2.90
2392 2442 2.964464 TGTTGTTGGACATTGCCATCTT 59.036 40.909 1.47 0.00 37.86 2.40
2393 2443 3.005684 TGTTGTTGGACATTGCCATCTTC 59.994 43.478 1.47 1.23 37.86 2.87
2394 2444 3.159213 TGTTGGACATTGCCATCTTCT 57.841 42.857 1.47 0.00 37.86 2.85
2395 2445 2.821378 TGTTGGACATTGCCATCTTCTG 59.179 45.455 1.47 0.00 37.86 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.995027 ATGAAATTATTTCTAGGTGCCATGTA 57.005 30.769 17.16 0.00 40.32 2.29
19 20 9.577110 CAGTCTGTGCAATGTTATTTATGAAAT 57.423 29.630 0.00 0.00 34.90 2.17
20 21 8.575589 ACAGTCTGTGCAATGTTATTTATGAAA 58.424 29.630 4.21 0.00 0.00 2.69
21 22 8.109705 ACAGTCTGTGCAATGTTATTTATGAA 57.890 30.769 4.21 0.00 0.00 2.57
22 23 7.686438 ACAGTCTGTGCAATGTTATTTATGA 57.314 32.000 4.21 0.00 0.00 2.15
23 24 9.494479 CTAACAGTCTGTGCAATGTTATTTATG 57.506 33.333 6.18 0.00 37.46 1.90
24 25 8.677300 CCTAACAGTCTGTGCAATGTTATTTAT 58.323 33.333 6.18 0.00 37.46 1.40
25 26 7.120579 CCCTAACAGTCTGTGCAATGTTATTTA 59.879 37.037 6.18 0.00 37.46 1.40
26 27 6.071952 CCCTAACAGTCTGTGCAATGTTATTT 60.072 38.462 6.18 0.00 37.46 1.40
27 28 5.415701 CCCTAACAGTCTGTGCAATGTTATT 59.584 40.000 6.18 0.00 37.46 1.40
28 29 4.943705 CCCTAACAGTCTGTGCAATGTTAT 59.056 41.667 6.18 0.00 37.46 1.89
29 30 4.041075 TCCCTAACAGTCTGTGCAATGTTA 59.959 41.667 6.18 0.00 37.15 2.41
30 31 3.149196 CCCTAACAGTCTGTGCAATGTT 58.851 45.455 6.18 0.00 39.16 2.71
31 32 2.371841 TCCCTAACAGTCTGTGCAATGT 59.628 45.455 6.18 0.00 0.00 2.71
32 33 3.057969 TCCCTAACAGTCTGTGCAATG 57.942 47.619 6.18 0.00 0.00 2.82
33 34 4.263462 TGAATCCCTAACAGTCTGTGCAAT 60.263 41.667 6.18 0.00 0.00 3.56
34 35 3.072330 TGAATCCCTAACAGTCTGTGCAA 59.928 43.478 6.18 0.00 0.00 4.08
35 36 2.637382 TGAATCCCTAACAGTCTGTGCA 59.363 45.455 6.18 0.00 0.00 4.57
36 37 3.003480 GTGAATCCCTAACAGTCTGTGC 58.997 50.000 6.18 0.00 0.00 4.57
37 38 4.499183 GAGTGAATCCCTAACAGTCTGTG 58.501 47.826 6.18 0.00 33.05 3.66
38 39 3.515901 GGAGTGAATCCCTAACAGTCTGT 59.484 47.826 0.00 0.00 43.01 3.41
39 40 4.130286 GGAGTGAATCCCTAACAGTCTG 57.870 50.000 0.00 0.00 43.01 3.51
51 52 1.473434 GGTCATCGGGTGGAGTGAATC 60.473 57.143 0.00 0.00 0.00 2.52
52 53 0.541863 GGTCATCGGGTGGAGTGAAT 59.458 55.000 0.00 0.00 0.00 2.57
53 54 0.834261 TGGTCATCGGGTGGAGTGAA 60.834 55.000 0.00 0.00 0.00 3.18
54 55 1.229051 TGGTCATCGGGTGGAGTGA 60.229 57.895 0.00 0.00 0.00 3.41
55 56 1.079127 GTGGTCATCGGGTGGAGTG 60.079 63.158 0.00 0.00 0.00 3.51
56 57 0.040646 TAGTGGTCATCGGGTGGAGT 59.959 55.000 0.00 0.00 0.00 3.85
57 58 1.191535 TTAGTGGTCATCGGGTGGAG 58.808 55.000 0.00 0.00 0.00 3.86
58 59 1.646912 TTTAGTGGTCATCGGGTGGA 58.353 50.000 0.00 0.00 0.00 4.02
59 60 2.356135 CTTTTAGTGGTCATCGGGTGG 58.644 52.381 0.00 0.00 0.00 4.61
60 61 2.356135 CCTTTTAGTGGTCATCGGGTG 58.644 52.381 0.00 0.00 0.00 4.61
61 62 1.339727 GCCTTTTAGTGGTCATCGGGT 60.340 52.381 0.00 0.00 0.00 5.28
62 63 1.065418 AGCCTTTTAGTGGTCATCGGG 60.065 52.381 0.00 0.00 0.00 5.14
63 64 2.280628 GAGCCTTTTAGTGGTCATCGG 58.719 52.381 0.00 0.00 0.00 4.18
64 65 2.093447 AGGAGCCTTTTAGTGGTCATCG 60.093 50.000 0.00 0.00 0.00 3.84
65 66 3.636153 AGGAGCCTTTTAGTGGTCATC 57.364 47.619 0.00 0.00 0.00 2.92
66 67 6.824958 TTATAGGAGCCTTTTAGTGGTCAT 57.175 37.500 0.00 0.00 0.00 3.06
67 68 6.630203 TTTATAGGAGCCTTTTAGTGGTCA 57.370 37.500 0.00 0.00 0.00 4.02
68 69 7.392393 TGTTTTTATAGGAGCCTTTTAGTGGTC 59.608 37.037 0.00 0.00 0.00 4.02
69 70 7.235804 TGTTTTTATAGGAGCCTTTTAGTGGT 58.764 34.615 0.00 0.00 0.00 4.16
70 71 7.696992 TGTTTTTATAGGAGCCTTTTAGTGG 57.303 36.000 0.00 0.00 0.00 4.00
71 72 9.626045 CTTTGTTTTTATAGGAGCCTTTTAGTG 57.374 33.333 0.00 0.00 0.00 2.74
72 73 8.304596 GCTTTGTTTTTATAGGAGCCTTTTAGT 58.695 33.333 0.00 0.00 0.00 2.24
73 74 8.303876 TGCTTTGTTTTTATAGGAGCCTTTTAG 58.696 33.333 0.00 0.00 0.00 1.85
74 75 8.184304 TGCTTTGTTTTTATAGGAGCCTTTTA 57.816 30.769 0.00 0.00 0.00 1.52
75 76 7.061566 TGCTTTGTTTTTATAGGAGCCTTTT 57.938 32.000 0.00 0.00 0.00 2.27
76 77 6.664428 TGCTTTGTTTTTATAGGAGCCTTT 57.336 33.333 0.00 0.00 0.00 3.11
77 78 6.493458 TCTTGCTTTGTTTTTATAGGAGCCTT 59.507 34.615 0.00 0.00 0.00 4.35
78 79 6.010219 TCTTGCTTTGTTTTTATAGGAGCCT 58.990 36.000 0.00 0.00 0.00 4.58
79 80 6.267496 TCTTGCTTTGTTTTTATAGGAGCC 57.733 37.500 0.00 0.00 0.00 4.70
80 81 9.670719 GATATCTTGCTTTGTTTTTATAGGAGC 57.329 33.333 0.00 0.00 0.00 4.70
86 87 9.643693 CCAACTGATATCTTGCTTTGTTTTTAT 57.356 29.630 3.98 0.00 0.00 1.40
87 88 8.855110 TCCAACTGATATCTTGCTTTGTTTTTA 58.145 29.630 3.98 0.00 0.00 1.52
88 89 7.725251 TCCAACTGATATCTTGCTTTGTTTTT 58.275 30.769 3.98 0.00 0.00 1.94
89 90 7.288810 TCCAACTGATATCTTGCTTTGTTTT 57.711 32.000 3.98 0.00 0.00 2.43
90 91 6.071728 CCTCCAACTGATATCTTGCTTTGTTT 60.072 38.462 3.98 0.00 0.00 2.83
91 92 5.416952 CCTCCAACTGATATCTTGCTTTGTT 59.583 40.000 3.98 0.00 0.00 2.83
92 93 4.946157 CCTCCAACTGATATCTTGCTTTGT 59.054 41.667 3.98 0.00 0.00 2.83
93 94 4.201990 GCCTCCAACTGATATCTTGCTTTG 60.202 45.833 3.98 0.81 0.00 2.77
94 95 3.950395 GCCTCCAACTGATATCTTGCTTT 59.050 43.478 3.98 0.00 0.00 3.51
95 96 3.054139 TGCCTCCAACTGATATCTTGCTT 60.054 43.478 3.98 0.00 0.00 3.91
96 97 2.507058 TGCCTCCAACTGATATCTTGCT 59.493 45.455 3.98 0.00 0.00 3.91
97 98 2.923121 TGCCTCCAACTGATATCTTGC 58.077 47.619 3.98 0.00 0.00 4.01
98 99 4.701651 TGTTTGCCTCCAACTGATATCTTG 59.298 41.667 3.98 1.15 0.00 3.02
99 100 4.922206 TGTTTGCCTCCAACTGATATCTT 58.078 39.130 3.98 0.00 0.00 2.40
100 101 4.574674 TGTTTGCCTCCAACTGATATCT 57.425 40.909 3.98 0.00 0.00 1.98
101 102 5.841957 ATTGTTTGCCTCCAACTGATATC 57.158 39.130 0.00 0.00 0.00 1.63
102 103 5.163622 CGAATTGTTTGCCTCCAACTGATAT 60.164 40.000 0.00 0.00 0.00 1.63
103 104 4.155826 CGAATTGTTTGCCTCCAACTGATA 59.844 41.667 0.00 0.00 0.00 2.15
104 105 3.057315 CGAATTGTTTGCCTCCAACTGAT 60.057 43.478 0.00 0.00 0.00 2.90
105 106 2.293122 CGAATTGTTTGCCTCCAACTGA 59.707 45.455 0.00 0.00 0.00 3.41
106 107 2.293122 TCGAATTGTTTGCCTCCAACTG 59.707 45.455 0.00 0.00 0.00 3.16
107 108 2.554032 CTCGAATTGTTTGCCTCCAACT 59.446 45.455 0.00 0.00 0.00 3.16
108 109 2.351738 CCTCGAATTGTTTGCCTCCAAC 60.352 50.000 0.00 0.00 0.00 3.77
109 110 1.885887 CCTCGAATTGTTTGCCTCCAA 59.114 47.619 0.00 0.00 0.00 3.53
110 111 1.073125 TCCTCGAATTGTTTGCCTCCA 59.927 47.619 0.00 0.00 0.00 3.86
111 112 1.821216 TCCTCGAATTGTTTGCCTCC 58.179 50.000 0.00 0.00 0.00 4.30
112 113 3.915437 TTTCCTCGAATTGTTTGCCTC 57.085 42.857 0.00 0.00 0.00 4.70
113 114 4.664150 TTTTTCCTCGAATTGTTTGCCT 57.336 36.364 0.00 0.00 0.00 4.75
133 134 8.504812 TTAAGTACAAGAACGGTTAGGTTTTT 57.495 30.769 0.00 0.00 0.00 1.94
134 135 8.562052 CATTAAGTACAAGAACGGTTAGGTTTT 58.438 33.333 0.00 0.00 0.00 2.43
135 136 7.716560 ACATTAAGTACAAGAACGGTTAGGTTT 59.283 33.333 0.00 0.00 0.00 3.27
136 137 7.219322 ACATTAAGTACAAGAACGGTTAGGTT 58.781 34.615 0.00 0.00 0.00 3.50
137 138 6.762333 ACATTAAGTACAAGAACGGTTAGGT 58.238 36.000 0.00 0.00 0.00 3.08
138 139 7.095270 AGACATTAAGTACAAGAACGGTTAGG 58.905 38.462 0.00 0.00 0.00 2.69
139 140 8.530269 AAGACATTAAGTACAAGAACGGTTAG 57.470 34.615 0.00 0.00 0.00 2.34
140 141 9.630098 CTAAGACATTAAGTACAAGAACGGTTA 57.370 33.333 0.00 0.00 0.00 2.85
141 142 8.146412 ACTAAGACATTAAGTACAAGAACGGTT 58.854 33.333 0.00 0.00 0.00 4.44
142 143 7.664758 ACTAAGACATTAAGTACAAGAACGGT 58.335 34.615 0.00 0.00 0.00 4.83
143 144 8.530269 AACTAAGACATTAAGTACAAGAACGG 57.470 34.615 0.00 0.00 0.00 4.44
170 171 9.897744 CTTTTGTGAGATGTACAAATATGTTGT 57.102 29.630 0.00 7.92 44.63 3.32
191 192 9.987272 GGGATCCCTATGAATATTTTTCTTTTG 57.013 33.333 24.69 0.00 0.00 2.44
192 193 9.958125 AGGGATCCCTATGAATATTTTTCTTTT 57.042 29.630 33.08 0.02 46.14 2.27
249 250 5.682943 TTTGTGAACGGAGGAAGTATTTG 57.317 39.130 0.00 0.00 0.00 2.32
259 260 4.328983 ACACGCTTATATTTGTGAACGGAG 59.671 41.667 0.00 0.00 36.25 4.63
265 266 8.542497 AAAGTTAGACACGCTTATATTTGTGA 57.458 30.769 0.00 0.00 36.25 3.58
293 294 5.296531 CGTGTCAATATCCATCCAATTCACA 59.703 40.000 0.00 0.00 0.00 3.58
294 295 5.527214 TCGTGTCAATATCCATCCAATTCAC 59.473 40.000 0.00 0.00 0.00 3.18
296 297 6.808008 ATCGTGTCAATATCCATCCAATTC 57.192 37.500 0.00 0.00 0.00 2.17
310 311 5.220700 GGACAAACACACTAAATCGTGTCAA 60.221 40.000 0.00 0.00 45.74 3.18
312 313 4.271533 TGGACAAACACACTAAATCGTGTC 59.728 41.667 0.00 0.00 45.74 3.67
315 316 4.448210 AGTGGACAAACACACTAAATCGT 58.552 39.130 0.00 0.00 45.45 3.73
415 416 7.040686 TGTTTCTTGCCCTATTTTTGTCTACTC 60.041 37.037 0.00 0.00 0.00 2.59
432 436 7.011857 TGGAATATTGGTGTTTTTGTTTCTTGC 59.988 33.333 0.00 0.00 0.00 4.01
459 463 8.511321 AGAAGTAATATTTGTTTGACATTGCGA 58.489 29.630 0.00 0.00 0.00 5.10
473 477 7.792032 TCCCGAATCAGTCAGAAGTAATATTT 58.208 34.615 0.00 0.00 0.00 1.40
576 584 6.631962 ACGTGTGGGTTTCTAATTTCAAAAA 58.368 32.000 0.00 0.00 0.00 1.94
577 585 6.210287 ACGTGTGGGTTTCTAATTTCAAAA 57.790 33.333 0.00 0.00 0.00 2.44
578 586 5.838531 ACGTGTGGGTTTCTAATTTCAAA 57.161 34.783 0.00 0.00 0.00 2.69
579 587 5.357314 TCAACGTGTGGGTTTCTAATTTCAA 59.643 36.000 0.00 0.00 0.00 2.69
580 588 4.882427 TCAACGTGTGGGTTTCTAATTTCA 59.118 37.500 0.00 0.00 0.00 2.69
581 589 5.427036 TCAACGTGTGGGTTTCTAATTTC 57.573 39.130 0.00 0.00 0.00 2.17
582 590 6.399639 AATCAACGTGTGGGTTTCTAATTT 57.600 33.333 0.00 0.00 0.00 1.82
583 591 6.347888 CGTAATCAACGTGTGGGTTTCTAATT 60.348 38.462 0.00 0.00 46.72 1.40
584 592 5.121142 CGTAATCAACGTGTGGGTTTCTAAT 59.879 40.000 0.00 0.00 46.72 1.73
585 593 4.448395 CGTAATCAACGTGTGGGTTTCTAA 59.552 41.667 0.00 0.00 46.72 2.10
586 594 3.989167 CGTAATCAACGTGTGGGTTTCTA 59.011 43.478 0.00 0.00 46.72 2.10
587 595 2.803956 CGTAATCAACGTGTGGGTTTCT 59.196 45.455 0.00 0.00 46.72 2.52
588 596 3.177605 CGTAATCAACGTGTGGGTTTC 57.822 47.619 0.00 0.00 46.72 2.78
599 607 3.713936 GCCTTTGCCCGTAATCAAC 57.286 52.632 0.00 0.00 0.00 3.18
610 618 2.046988 GCAATGGGTGGCCTTTGC 60.047 61.111 3.32 8.15 36.26 3.68
635 646 2.887568 GCTGTCATCTCGCCCACG 60.888 66.667 0.00 0.00 42.01 4.94
636 647 2.887568 CGCTGTCATCTCGCCCAC 60.888 66.667 0.00 0.00 0.00 4.61
637 648 4.819761 GCGCTGTCATCTCGCCCA 62.820 66.667 0.00 0.00 42.71 5.36
643 654 2.958543 CGATGCGCGCTGTCATCT 60.959 61.111 33.29 7.68 37.52 2.90
735 757 2.884207 CGTTCTTACCGAGCGGGC 60.884 66.667 14.07 0.00 41.85 6.13
740 762 0.179258 GTTTGCGCGTTCTTACCGAG 60.179 55.000 8.43 0.00 0.00 4.63
742 764 1.154543 GGTTTGCGCGTTCTTACCG 60.155 57.895 8.43 0.00 0.00 4.02
788 810 1.669049 TATGACGTGTGGGGCCGTAG 61.669 60.000 0.00 0.00 37.44 3.51
789 811 1.681666 TATGACGTGTGGGGCCGTA 60.682 57.895 0.00 0.00 37.44 4.02
818 840 1.653094 TTCCAAATCGGTGATGGCGC 61.653 55.000 0.00 0.00 34.13 6.53
859 881 2.329267 CCTTGGGAGGGAAAAGCTTTT 58.671 47.619 24.08 24.08 39.55 2.27
863 885 0.967887 GAGCCTTGGGAGGGAAAAGC 60.968 60.000 0.00 0.00 43.75 3.51
957 980 0.398948 GTGGATTGGGCCAATGGGAT 60.399 55.000 35.23 13.22 40.20 3.85
1011 1035 4.547367 GGGGATCGGGTCTTGCGG 62.547 72.222 0.00 0.00 0.00 5.69
1429 1462 6.434652 AGATCCCTGAATCTACAAGTATACCG 59.565 42.308 0.00 0.00 34.21 4.02
1457 1490 4.047627 ACTAAATCAAACAAGGGAGGGG 57.952 45.455 0.00 0.00 0.00 4.79
1461 1494 6.001460 ACATCGAACTAAATCAAACAAGGGA 58.999 36.000 0.00 0.00 0.00 4.20
1462 1495 6.149474 AGACATCGAACTAAATCAAACAAGGG 59.851 38.462 0.00 0.00 0.00 3.95
1469 1502 8.827177 AACTGTAAGACATCGAACTAAATCAA 57.173 30.769 0.00 0.00 37.43 2.57
1470 1503 8.827177 AAACTGTAAGACATCGAACTAAATCA 57.173 30.769 0.00 0.00 37.43 2.57
1473 1506 9.362539 GGATAAACTGTAAGACATCGAACTAAA 57.637 33.333 0.00 0.00 37.43 1.85
1475 1508 8.289939 AGGATAAACTGTAAGACATCGAACTA 57.710 34.615 0.00 0.00 37.43 2.24
1476 1509 7.171630 AGGATAAACTGTAAGACATCGAACT 57.828 36.000 0.00 0.00 37.43 3.01
1477 1510 7.829378 AAGGATAAACTGTAAGACATCGAAC 57.171 36.000 0.00 0.00 37.43 3.95
1481 1514 9.668497 AAGGTAAAGGATAAACTGTAAGACATC 57.332 33.333 0.00 0.00 37.43 3.06
1499 1532 6.687081 TTGGTACAGACAAACAAGGTAAAG 57.313 37.500 0.00 0.00 42.39 1.85
1601 1637 8.106247 TCGTAGAAGGAAAGCATAACAAATTT 57.894 30.769 0.00 0.00 0.00 1.82
1692 1728 3.536956 TTGAATTCCCCTAGTACTGCG 57.463 47.619 5.39 0.00 0.00 5.18
1850 1886 5.045215 TCTTAACCAATAATACTGTCGGCG 58.955 41.667 0.00 0.00 0.00 6.46
1887 1923 6.682423 CAGCATGTATCTACATCAACCAAA 57.318 37.500 0.00 0.00 44.57 3.28
1913 1950 6.116806 TCTAAAGCAACCAAGTTGAACTACA 58.883 36.000 11.50 0.00 45.28 2.74
2016 2066 7.156000 TCGTGTAATCAGAATCAACCAAGTTA 58.844 34.615 0.00 0.00 0.00 2.24
2049 2099 5.220381 TGAACTAGAGTTGAACTGCTAACG 58.780 41.667 0.90 0.00 38.56 3.18
2087 2137 7.224753 ACTGCTAACGGTAAGATTCATGTAATG 59.775 37.037 0.00 0.00 38.75 1.90
2281 2331 7.472945 CGCTCTTATATTTCTTTAGGGAGGGAA 60.473 40.741 0.00 0.00 34.63 3.97
2284 2334 6.760291 ACGCTCTTATATTTCTTTAGGGAGG 58.240 40.000 0.00 0.00 0.00 4.30
2285 2335 8.664211 AAACGCTCTTATATTTCTTTAGGGAG 57.336 34.615 0.00 0.00 0.00 4.30
2286 2336 9.760077 CTAAACGCTCTTATATTTCTTTAGGGA 57.240 33.333 0.00 0.00 0.00 4.20
2287 2337 9.760077 TCTAAACGCTCTTATATTTCTTTAGGG 57.240 33.333 0.00 0.00 0.00 3.53
2319 2369 8.979574 CGGAAAGAAATATAAGAGCGTTTAGAT 58.020 33.333 0.00 0.00 0.00 1.98
2320 2370 7.437267 CCGGAAAGAAATATAAGAGCGTTTAGA 59.563 37.037 0.00 0.00 0.00 2.10
2321 2371 7.437267 TCCGGAAAGAAATATAAGAGCGTTTAG 59.563 37.037 0.00 0.00 0.00 1.85
2322 2372 7.267128 TCCGGAAAGAAATATAAGAGCGTTTA 58.733 34.615 0.00 0.00 0.00 2.01
2323 2373 6.110707 TCCGGAAAGAAATATAAGAGCGTTT 58.889 36.000 0.00 0.00 0.00 3.60
2324 2374 5.667466 TCCGGAAAGAAATATAAGAGCGTT 58.333 37.500 0.00 0.00 0.00 4.84
2325 2375 5.272283 TCCGGAAAGAAATATAAGAGCGT 57.728 39.130 0.00 0.00 0.00 5.07
2326 2376 4.686554 CCTCCGGAAAGAAATATAAGAGCG 59.313 45.833 5.23 0.00 0.00 5.03
2327 2377 4.998033 CCCTCCGGAAAGAAATATAAGAGC 59.002 45.833 5.23 0.00 0.00 4.09
2328 2378 6.042208 ACTCCCTCCGGAAAGAAATATAAGAG 59.958 42.308 5.23 2.37 37.86 2.85
2329 2379 5.903589 ACTCCCTCCGGAAAGAAATATAAGA 59.096 40.000 5.23 0.00 37.86 2.10
2330 2380 6.176014 ACTCCCTCCGGAAAGAAATATAAG 57.824 41.667 5.23 0.00 37.86 1.73
2331 2381 6.612456 TGTACTCCCTCCGGAAAGAAATATAA 59.388 38.462 5.23 0.00 37.86 0.98
2332 2382 6.138263 TGTACTCCCTCCGGAAAGAAATATA 58.862 40.000 5.23 0.00 37.86 0.86
2333 2383 4.966805 TGTACTCCCTCCGGAAAGAAATAT 59.033 41.667 5.23 0.00 37.86 1.28
2334 2384 4.355549 TGTACTCCCTCCGGAAAGAAATA 58.644 43.478 5.23 0.00 37.86 1.40
2335 2385 3.178865 TGTACTCCCTCCGGAAAGAAAT 58.821 45.455 5.23 0.00 37.86 2.17
2336 2386 2.612000 TGTACTCCCTCCGGAAAGAAA 58.388 47.619 5.23 0.00 37.86 2.52
2337 2387 2.314071 TGTACTCCCTCCGGAAAGAA 57.686 50.000 5.23 0.00 37.86 2.52
2338 2388 2.024273 AGATGTACTCCCTCCGGAAAGA 60.024 50.000 5.23 4.03 37.86 2.52
2339 2389 2.389715 AGATGTACTCCCTCCGGAAAG 58.610 52.381 5.23 6.10 37.86 2.62
2340 2390 2.544844 AGATGTACTCCCTCCGGAAA 57.455 50.000 5.23 0.00 37.86 3.13
2341 2391 2.544844 AAGATGTACTCCCTCCGGAA 57.455 50.000 5.23 0.00 37.86 4.30
2342 2392 2.158505 CCTAAGATGTACTCCCTCCGGA 60.159 54.545 2.93 2.93 36.45 5.14
2343 2393 2.240279 CCTAAGATGTACTCCCTCCGG 58.760 57.143 0.00 0.00 0.00 5.14
2344 2394 2.946785 ACCTAAGATGTACTCCCTCCG 58.053 52.381 0.00 0.00 0.00 4.63
2345 2395 4.963628 AGAAACCTAAGATGTACTCCCTCC 59.036 45.833 0.00 0.00 0.00 4.30
2346 2396 6.547930 AAGAAACCTAAGATGTACTCCCTC 57.452 41.667 0.00 0.00 0.00 4.30
2347 2397 7.624077 ACATAAGAAACCTAAGATGTACTCCCT 59.376 37.037 0.00 0.00 0.00 4.20
2348 2398 7.793036 ACATAAGAAACCTAAGATGTACTCCC 58.207 38.462 0.00 0.00 0.00 4.30
2349 2399 9.099454 CAACATAAGAAACCTAAGATGTACTCC 57.901 37.037 0.00 0.00 0.00 3.85
2350 2400 9.654663 ACAACATAAGAAACCTAAGATGTACTC 57.345 33.333 0.00 0.00 0.00 2.59
2353 2403 9.226606 CCAACAACATAAGAAACCTAAGATGTA 57.773 33.333 0.00 0.00 0.00 2.29
2354 2404 7.942341 TCCAACAACATAAGAAACCTAAGATGT 59.058 33.333 0.00 0.00 0.00 3.06
2355 2405 8.237267 GTCCAACAACATAAGAAACCTAAGATG 58.763 37.037 0.00 0.00 0.00 2.90
2356 2406 7.942341 TGTCCAACAACATAAGAAACCTAAGAT 59.058 33.333 0.00 0.00 0.00 2.40
2357 2407 7.284074 TGTCCAACAACATAAGAAACCTAAGA 58.716 34.615 0.00 0.00 0.00 2.10
2358 2408 7.504924 TGTCCAACAACATAAGAAACCTAAG 57.495 36.000 0.00 0.00 0.00 2.18
2359 2409 8.356657 CAATGTCCAACAACATAAGAAACCTAA 58.643 33.333 0.00 0.00 38.92 2.69
2360 2410 7.523052 GCAATGTCCAACAACATAAGAAACCTA 60.523 37.037 0.00 0.00 38.92 3.08
2361 2411 6.738453 GCAATGTCCAACAACATAAGAAACCT 60.738 38.462 0.00 0.00 38.92 3.50
2362 2412 5.405269 GCAATGTCCAACAACATAAGAAACC 59.595 40.000 0.00 0.00 38.92 3.27
2363 2413 5.405269 GGCAATGTCCAACAACATAAGAAAC 59.595 40.000 0.00 0.00 38.92 2.78
2364 2414 5.069648 TGGCAATGTCCAACAACATAAGAAA 59.930 36.000 0.00 0.00 38.92 2.52
2365 2415 4.586421 TGGCAATGTCCAACAACATAAGAA 59.414 37.500 0.00 0.00 38.92 2.52
2366 2416 4.148079 TGGCAATGTCCAACAACATAAGA 58.852 39.130 0.00 0.00 38.92 2.10
2367 2417 4.517952 TGGCAATGTCCAACAACATAAG 57.482 40.909 0.00 0.00 38.92 1.73
2368 2418 4.771577 AGATGGCAATGTCCAACAACATAA 59.228 37.500 0.00 0.00 38.92 1.90
2369 2419 4.343231 AGATGGCAATGTCCAACAACATA 58.657 39.130 0.00 0.00 38.92 2.29
2370 2420 3.167485 AGATGGCAATGTCCAACAACAT 58.833 40.909 0.00 0.00 41.60 2.71
2371 2421 2.596346 AGATGGCAATGTCCAACAACA 58.404 42.857 0.00 0.00 39.96 3.33
2372 2422 3.256631 AGAAGATGGCAATGTCCAACAAC 59.743 43.478 0.00 0.00 39.96 3.32
2373 2423 3.256383 CAGAAGATGGCAATGTCCAACAA 59.744 43.478 0.00 0.00 39.96 2.83
2374 2424 2.821378 CAGAAGATGGCAATGTCCAACA 59.179 45.455 0.00 0.00 39.96 3.33
2375 2425 2.165030 CCAGAAGATGGCAATGTCCAAC 59.835 50.000 0.00 0.00 43.83 3.77
2376 2426 2.449464 CCAGAAGATGGCAATGTCCAA 58.551 47.619 0.00 0.00 43.83 3.53
2377 2427 2.133281 CCAGAAGATGGCAATGTCCA 57.867 50.000 0.00 0.00 43.83 4.02


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

AutoCloner maintained by Alex Coulton.