Multiple sequence alignment - TraesCS2D01G106000

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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 TraesCS2D01G106000 chr2D 100.000 2825 0 0 1 2825 57263904 57266728 0.000000e+00 5217.0
1 TraesCS2D01G106000 chr2D 93.865 163 9 1 1 163 480849227 480849066 7.820000e-61 244.0
2 TraesCS2D01G106000 chr2D 83.916 143 20 2 164 305 569258684 569258544 1.770000e-27 134.0
3 TraesCS2D01G106000 chr2A 91.589 2259 118 28 312 2512 58459778 58462022 0.000000e+00 3053.0
4 TraesCS2D01G106000 chr2A 95.318 299 13 1 2528 2825 58462007 58462305 9.160000e-130 473.0
5 TraesCS2D01G106000 chr2B 91.568 1601 91 20 389 1982 90571030 90572593 0.000000e+00 2169.0
6 TraesCS2D01G106000 chr2B 93.364 648 19 3 2198 2822 90574197 90574843 0.000000e+00 937.0
7 TraesCS2D01G106000 chr2B 91.328 369 9 3 2198 2544 90613563 90613930 1.520000e-132 483.0
8 TraesCS2D01G106000 chr2B 90.836 371 10 3 2198 2544 90593434 90593804 2.550000e-130 475.0
9 TraesCS2D01G106000 chr2B 90.541 370 12 2 2198 2544 90590991 90591360 4.260000e-128 468.0
10 TraesCS2D01G106000 chr2B 90.541 370 12 2 2198 2544 90598362 90598731 4.260000e-128 468.0
11 TraesCS2D01G106000 chr2B 90.541 370 10 7 2198 2544 90599985 90600352 1.530000e-127 466.0
12 TraesCS2D01G106000 chr2B 90.270 370 12 3 2198 2544 90595056 90595424 1.980000e-126 462.0
13 TraesCS2D01G106000 chr2B 90.270 370 11 4 2198 2544 90590170 90590537 7.130000e-126 460.0
14 TraesCS2D01G106000 chr2B 90.270 370 9 7 2198 2544 90591814 90592179 2.560000e-125 459.0
15 TraesCS2D01G106000 chr2B 90.000 370 13 3 2198 2544 90597540 90597908 9.220000e-125 457.0
16 TraesCS2D01G106000 chr2B 89.295 383 15 10 2198 2557 90601625 90602004 9.220000e-125 457.0
17 TraesCS2D01G106000 chr2B 90.000 370 13 3 2198 2544 90612742 90613110 9.220000e-125 457.0
18 TraesCS2D01G106000 chr2B 90.000 370 12 7 2198 2544 90599164 90599531 3.320000e-124 455.0
19 TraesCS2D01G106000 chr2B 89.730 370 14 7 2198 2544 90592633 90593001 4.290000e-123 451.0
20 TraesCS2D01G106000 chr2B 89.730 370 13 8 2198 2544 90596721 90597088 1.540000e-122 449.0
21 TraesCS2D01G106000 chr2B 89.459 370 14 6 2198 2544 90595879 90596246 7.180000e-121 444.0
22 TraesCS2D01G106000 chr2B 94.444 162 9 0 1 162 689425947 689426108 1.680000e-62 250.0
23 TraesCS2D01G106000 chr2B 97.753 89 2 0 2002 2090 90572580 90572668 1.360000e-33 154.0
24 TraesCS2D01G106000 chr2B 97.619 42 0 1 2150 2191 90573805 90573845 1.400000e-08 71.3
25 TraesCS2D01G106000 chr3B 80.223 718 103 17 997 1713 124388814 124389493 1.170000e-138 503.0
26 TraesCS2D01G106000 chr7B 78.999 719 113 18 997 1713 704264586 704265268 9.220000e-125 457.0
27 TraesCS2D01G106000 chr7B 91.525 177 13 2 1 176 125896625 125896450 2.810000e-60 243.0
28 TraesCS2D01G106000 chr6B 78.631 716 115 18 1000 1713 222857215 222856536 9.290000e-120 440.0
29 TraesCS2D01G106000 chr6B 97.500 40 1 0 2106 2145 503536321 503536360 5.050000e-08 69.4
30 TraesCS2D01G106000 chr6B 90.196 51 5 0 2100 2150 653615510 653615460 1.820000e-07 67.6
31 TraesCS2D01G106000 chr3D 82.150 493 79 7 1000 1491 114082963 114082479 5.630000e-112 414.0
32 TraesCS2D01G106000 chr3D 94.512 164 9 0 1 164 608675129 608675292 1.300000e-63 254.0
33 TraesCS2D01G106000 chr3D 85.517 145 19 1 161 305 10378005 10377863 1.750000e-32 150.0
34 TraesCS2D01G106000 chr3D 85.211 142 20 1 164 305 532103235 532103095 8.160000e-31 145.0
35 TraesCS2D01G106000 chr4A 79.525 547 93 10 1000 1546 714048891 714048364 3.440000e-99 372.0
36 TraesCS2D01G106000 chr4D 95.152 165 8 0 1 165 245570901 245570737 7.760000e-66 261.0
37 TraesCS2D01G106000 chr4D 94.444 162 9 0 1 162 268974457 268974618 1.680000e-62 250.0
38 TraesCS2D01G106000 chr5D 95.652 161 7 0 1 161 479783522 479783362 2.790000e-65 259.0
39 TraesCS2D01G106000 chr5D 94.479 163 9 0 1 163 287228329 287228491 4.670000e-63 252.0
40 TraesCS2D01G106000 chr5D 95.652 46 2 0 2105 2150 401280395 401280440 1.090000e-09 75.0
41 TraesCS2D01G106000 chr5B 94.444 162 9 0 1 162 432326031 432326192 1.680000e-62 250.0
42 TraesCS2D01G106000 chr5B 90.000 60 4 2 2087 2146 398069846 398069789 3.020000e-10 76.8
43 TraesCS2D01G106000 chr4B 95.070 142 6 1 163 304 568608556 568608416 3.660000e-54 222.0
44 TraesCS2D01G106000 chr4B 97.500 40 1 0 2106 2145 632332095 632332134 5.050000e-08 69.4
45 TraesCS2D01G106000 chr1A 94.444 144 8 0 163 306 298118479 298118622 3.660000e-54 222.0
46 TraesCS2D01G106000 chr1A 84.028 144 21 1 161 304 403625897 403625756 1.360000e-28 137.0
47 TraesCS2D01G106000 chr3A 92.958 142 10 0 163 304 20303457 20303316 1.030000e-49 207.0
48 TraesCS2D01G106000 chr6A 84.828 145 20 1 161 305 602340263 602340405 8.160000e-31 145.0
49 TraesCS2D01G106000 chr6A 91.304 46 4 0 2105 2150 29544863 29544908 2.350000e-06 63.9
50 TraesCS2D01G106000 chr1D 84.722 144 20 1 161 304 50917899 50917758 2.930000e-30 143.0
51 TraesCS2D01G106000 chr1D 93.478 46 3 0 2105 2150 22943484 22943529 5.050000e-08 69.4
52 TraesCS2D01G106000 chr1B 91.549 71 4 2 2756 2824 74648606 74648536 2.320000e-16 97.1
53 TraesCS2D01G106000 chr7D 93.478 46 3 0 2105 2150 75551071 75551026 5.050000e-08 69.4


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 TraesCS2D01G106000 chr2D 57263904 57266728 2824 False 5217.000000 5217 100.000000 1 2825 1 chr2D.!!$F1 2824
1 TraesCS2D01G106000 chr2A 58459778 58462305 2527 False 1763.000000 3053 93.453500 312 2825 2 chr2A.!!$F1 2513
2 TraesCS2D01G106000 chr2B 90571030 90574843 3813 False 832.825000 2169 95.076000 389 2822 4 chr2B.!!$F2 2433
3 TraesCS2D01G106000 chr2B 90612742 90613930 1188 False 470.000000 483 90.664000 2198 2544 2 chr2B.!!$F4 346
4 TraesCS2D01G106000 chr2B 90590170 90602004 11834 False 459.307692 475 90.114077 2198 2557 13 chr2B.!!$F3 359
5 TraesCS2D01G106000 chr3B 124388814 124389493 679 False 503.000000 503 80.223000 997 1713 1 chr3B.!!$F1 716
6 TraesCS2D01G106000 chr7B 704264586 704265268 682 False 457.000000 457 78.999000 997 1713 1 chr7B.!!$F1 716
7 TraesCS2D01G106000 chr6B 222856536 222857215 679 True 440.000000 440 78.631000 1000 1713 1 chr6B.!!$R1 713
8 TraesCS2D01G106000 chr4A 714048364 714048891 527 True 372.000000 372 79.525000 1000 1546 1 chr4A.!!$R1 546

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
113 114 0.034337 AGCCGAAACGAGCCAAACTA 59.966 50.0 0.0 0.0 0.0 2.24 F
243 244 0.038166 GGTCAGCCCAATGGTCTTCA 59.962 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1665 0.835276 CCACCAGCATCTCCATCAGA 59.165 55.0 0.0 0.0 34.78 3.27 R
2144 3316 0.815734 TCGAAGCTACTACCACTGGC 59.184 55.0 0.0 0.0 0.00 4.85 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
24 25 2.731451 TCTCGTGAAACTCATTTGCTCG 59.269 45.455 0.00 0.00 31.75 5.03
25 26 1.194547 TCGTGAAACTCATTTGCTCGC 59.805 47.619 0.00 0.00 31.75 5.03
27 28 2.349817 CGTGAAACTCATTTGCTCGCTT 60.350 45.455 0.00 0.00 31.75 4.68
29 30 2.618241 TGAAACTCATTTGCTCGCTTGT 59.382 40.909 0.00 0.00 0.00 3.16
31 32 4.274705 TGAAACTCATTTGCTCGCTTGTTA 59.725 37.500 0.00 0.00 0.00 2.41
33 34 4.410492 ACTCATTTGCTCGCTTGTTAAG 57.590 40.909 0.00 0.00 0.00 1.85
74 75 3.535280 AAAAACATTGTTCGGCTTGGT 57.465 38.095 1.83 0.00 0.00 3.67
75 76 3.535280 AAAACATTGTTCGGCTTGGTT 57.465 38.095 1.83 0.00 0.00 3.67
76 77 2.793278 AACATTGTTCGGCTTGGTTC 57.207 45.000 0.00 0.00 0.00 3.62
77 78 1.686355 ACATTGTTCGGCTTGGTTCA 58.314 45.000 0.00 0.00 0.00 3.18
78 79 2.238521 ACATTGTTCGGCTTGGTTCAT 58.761 42.857 0.00 0.00 0.00 2.57
80 81 3.823873 ACATTGTTCGGCTTGGTTCATTA 59.176 39.130 0.00 0.00 0.00 1.90
81 82 4.279671 ACATTGTTCGGCTTGGTTCATTAA 59.720 37.500 0.00 0.00 0.00 1.40
82 83 3.907894 TGTTCGGCTTGGTTCATTAAC 57.092 42.857 0.00 0.00 34.66 2.01
84 85 4.643463 TGTTCGGCTTGGTTCATTAACTA 58.357 39.130 0.00 0.00 35.81 2.24
85 86 5.064558 TGTTCGGCTTGGTTCATTAACTAA 58.935 37.500 0.00 0.00 35.14 2.24
86 87 5.049267 TGTTCGGCTTGGTTCATTAACTAAC 60.049 40.000 0.00 0.00 33.14 2.34
87 88 3.680937 TCGGCTTGGTTCATTAACTAACG 59.319 43.478 0.00 0.00 33.14 3.18
88 89 3.680937 CGGCTTGGTTCATTAACTAACGA 59.319 43.478 0.00 0.00 33.14 3.85
89 90 4.201685 CGGCTTGGTTCATTAACTAACGAG 60.202 45.833 0.00 0.00 33.14 4.18
90 91 4.436986 GGCTTGGTTCATTAACTAACGAGC 60.437 45.833 14.18 14.18 35.99 5.03
92 93 5.600908 TTGGTTCATTAACTAACGAGCAC 57.399 39.130 0.00 0.00 31.83 4.40
93 94 3.676172 TGGTTCATTAACTAACGAGCACG 59.324 43.478 0.76 0.76 39.36 5.34
94 95 3.922240 GGTTCATTAACTAACGAGCACGA 59.078 43.478 11.40 0.00 38.07 4.35
95 96 4.031426 GGTTCATTAACTAACGAGCACGAG 59.969 45.833 11.40 0.04 38.07 4.18
96 97 3.176708 TCATTAACTAACGAGCACGAGC 58.823 45.455 11.40 0.00 42.66 5.03
97 98 1.986698 TTAACTAACGAGCACGAGCC 58.013 50.000 11.40 0.00 43.56 4.70
99 100 1.859427 AACTAACGAGCACGAGCCGA 61.859 55.000 18.72 1.31 43.56 5.54
100 101 1.154093 CTAACGAGCACGAGCCGAA 60.154 57.895 18.72 8.29 43.56 4.30
102 103 1.005294 TAACGAGCACGAGCCGAAAC 61.005 55.000 18.72 0.00 43.56 2.78
103 104 3.827784 CGAGCACGAGCCGAAACG 61.828 66.667 0.00 0.00 43.56 3.60
105 106 2.430921 AGCACGAGCCGAAACGAG 60.431 61.111 0.00 0.00 43.56 4.18
108 109 3.986006 ACGAGCCGAAACGAGCCA 61.986 61.111 1.50 0.00 0.00 4.75
110 111 2.314647 CGAGCCGAAACGAGCCAAA 61.315 57.895 0.00 0.00 0.00 3.28
113 114 0.034337 AGCCGAAACGAGCCAAACTA 59.966 50.000 0.00 0.00 0.00 2.24
114 115 1.084289 GCCGAAACGAGCCAAACTAT 58.916 50.000 0.00 0.00 0.00 2.12
115 116 1.062148 GCCGAAACGAGCCAAACTATC 59.938 52.381 0.00 0.00 0.00 2.08
116 117 1.323534 CCGAAACGAGCCAAACTATCG 59.676 52.381 0.00 0.00 42.04 2.92
117 118 2.256174 CGAAACGAGCCAAACTATCGA 58.744 47.619 0.30 0.00 39.66 3.59
118 119 2.279136 CGAAACGAGCCAAACTATCGAG 59.721 50.000 0.30 0.00 39.66 4.04
120 121 0.525668 ACGAGCCAAACTATCGAGCG 60.526 55.000 0.30 0.00 39.66 5.03
121 122 0.525668 CGAGCCAAACTATCGAGCGT 60.526 55.000 0.00 0.00 38.72 5.07
122 123 1.641577 GAGCCAAACTATCGAGCGTT 58.358 50.000 0.00 0.00 0.00 4.84
123 124 2.000447 GAGCCAAACTATCGAGCGTTT 59.000 47.619 8.54 8.54 33.92 3.60
124 125 3.184541 GAGCCAAACTATCGAGCGTTTA 58.815 45.455 12.67 0.00 32.52 2.01
125 126 3.793559 AGCCAAACTATCGAGCGTTTAT 58.206 40.909 12.67 2.80 32.52 1.40
127 128 5.353938 AGCCAAACTATCGAGCGTTTATTA 58.646 37.500 12.67 0.00 32.52 0.98
128 129 5.989777 AGCCAAACTATCGAGCGTTTATTAT 59.010 36.000 12.67 0.91 32.52 1.28
130 131 6.071463 CCAAACTATCGAGCGTTTATTATGC 58.929 40.000 12.67 0.00 39.16 3.14
137 138 1.787155 AGCGTTTATTATGCTCGCGAG 59.213 47.619 31.37 31.37 46.18 5.03
138 139 3.981937 AGCGTTTATTATGCTCGCGAGC 61.982 50.000 45.38 45.38 46.18 5.03
159 160 2.391389 CGAGCTTTTCGTCCAGCCC 61.391 63.158 0.00 0.00 44.27 5.19
161 162 0.249398 GAGCTTTTCGTCCAGCCCTA 59.751 55.000 0.00 0.00 36.62 3.53
162 163 0.912486 AGCTTTTCGTCCAGCCCTAT 59.088 50.000 0.00 0.00 36.62 2.57
163 164 1.134371 AGCTTTTCGTCCAGCCCTATC 60.134 52.381 0.00 0.00 36.62 2.08
164 165 1.571919 CTTTTCGTCCAGCCCTATCG 58.428 55.000 0.00 0.00 0.00 2.92
165 166 1.136305 CTTTTCGTCCAGCCCTATCGA 59.864 52.381 0.00 0.00 0.00 3.59
166 167 0.744874 TTTCGTCCAGCCCTATCGAG 59.255 55.000 0.00 0.00 32.39 4.04
167 168 1.107538 TTCGTCCAGCCCTATCGAGG 61.108 60.000 0.00 0.00 43.33 4.63
177 178 1.482593 CCCTATCGAGGCTCACAAACT 59.517 52.381 15.95 0.00 42.21 2.66
178 179 2.482142 CCCTATCGAGGCTCACAAACTC 60.482 54.545 15.95 0.00 42.21 3.01
180 181 3.159984 CGAGGCTCACAAACTCGC 58.840 61.111 15.95 0.00 45.97 5.03
181 182 2.720758 CGAGGCTCACAAACTCGCG 61.721 63.158 15.95 0.00 45.97 5.87
182 183 1.372997 GAGGCTCACAAACTCGCGA 60.373 57.895 9.26 9.26 0.00 5.87
183 184 0.944311 GAGGCTCACAAACTCGCGAA 60.944 55.000 11.33 0.00 0.00 4.70
184 185 0.946221 AGGCTCACAAACTCGCGAAG 60.946 55.000 11.33 7.16 0.00 3.79
201 202 2.983136 CGAAGCACGCATTATCTCTAGG 59.017 50.000 0.00 0.00 34.51 3.02
203 204 1.620819 AGCACGCATTATCTCTAGGGG 59.379 52.381 0.00 0.00 0.00 4.79
204 205 1.941668 GCACGCATTATCTCTAGGGGC 60.942 57.143 0.00 0.00 0.00 5.80
208 209 1.339535 GCATTATCTCTAGGGGCTGGC 60.340 57.143 0.00 0.00 0.00 4.85
210 211 1.722034 TTATCTCTAGGGGCTGGCTG 58.278 55.000 0.00 0.00 0.00 4.85
220 221 2.263540 GCTGGCTGCCATGTTTGG 59.736 61.111 23.64 10.50 46.66 3.28
221 222 2.576832 GCTGGCTGCCATGTTTGGT 61.577 57.895 23.64 0.00 45.57 3.67
222 223 2.051941 CTGGCTGCCATGTTTGGTT 58.948 52.632 23.64 0.00 45.57 3.67
223 224 1.255882 CTGGCTGCCATGTTTGGTTA 58.744 50.000 23.64 0.00 45.57 2.85
224 225 1.203052 CTGGCTGCCATGTTTGGTTAG 59.797 52.381 23.64 2.01 45.57 2.34
227 228 1.202348 GCTGCCATGTTTGGTTAGGTC 59.798 52.381 0.00 0.00 45.57 3.85
228 229 2.513753 CTGCCATGTTTGGTTAGGTCA 58.486 47.619 0.00 0.00 45.57 4.02
230 231 1.202348 GCCATGTTTGGTTAGGTCAGC 59.798 52.381 0.00 0.00 45.57 4.26
231 232 1.818674 CCATGTTTGGTTAGGTCAGCC 59.181 52.381 0.00 0.00 38.30 4.85
233 234 0.847373 TGTTTGGTTAGGTCAGCCCA 59.153 50.000 0.00 0.00 34.66 5.36
234 235 1.215673 TGTTTGGTTAGGTCAGCCCAA 59.784 47.619 0.00 0.00 35.25 4.12
237 238 0.331278 TGGTTAGGTCAGCCCAATGG 59.669 55.000 0.00 0.00 34.66 3.16
238 239 0.331616 GGTTAGGTCAGCCCAATGGT 59.668 55.000 0.00 0.00 34.66 3.55
239 240 1.682087 GGTTAGGTCAGCCCAATGGTC 60.682 57.143 0.00 0.00 34.66 4.02
241 242 1.668826 TAGGTCAGCCCAATGGTCTT 58.331 50.000 0.00 0.00 34.66 3.01
242 243 0.329596 AGGTCAGCCCAATGGTCTTC 59.670 55.000 0.00 0.00 34.66 2.87
243 244 0.038166 GGTCAGCCCAATGGTCTTCA 59.962 55.000 0.00 0.00 0.00 3.02
246 247 2.827921 GTCAGCCCAATGGTCTTCATTT 59.172 45.455 0.00 0.00 43.04 2.32
247 248 3.091545 TCAGCCCAATGGTCTTCATTTC 58.908 45.455 0.00 0.00 43.04 2.17
249 250 1.818674 GCCCAATGGTCTTCATTTCGT 59.181 47.619 0.00 0.00 43.04 3.85
250 251 2.159379 GCCCAATGGTCTTCATTTCGTC 60.159 50.000 0.00 0.00 43.04 4.20
251 252 2.423538 CCCAATGGTCTTCATTTCGTCC 59.576 50.000 0.00 0.00 43.04 4.79
252 253 2.423538 CCAATGGTCTTCATTTCGTCCC 59.576 50.000 0.00 0.00 43.04 4.46
253 254 3.347216 CAATGGTCTTCATTTCGTCCCT 58.653 45.455 0.00 0.00 43.04 4.20
255 256 1.697432 TGGTCTTCATTTCGTCCCTGT 59.303 47.619 0.00 0.00 0.00 4.00
256 257 2.901192 TGGTCTTCATTTCGTCCCTGTA 59.099 45.455 0.00 0.00 0.00 2.74
257 258 3.325425 TGGTCTTCATTTCGTCCCTGTAA 59.675 43.478 0.00 0.00 0.00 2.41
258 259 4.202377 TGGTCTTCATTTCGTCCCTGTAAA 60.202 41.667 0.00 0.00 0.00 2.01
259 260 4.153655 GGTCTTCATTTCGTCCCTGTAAAC 59.846 45.833 0.00 0.00 0.00 2.01
260 261 4.753107 GTCTTCATTTCGTCCCTGTAAACA 59.247 41.667 0.00 0.00 0.00 2.83
261 262 5.411669 GTCTTCATTTCGTCCCTGTAAACAT 59.588 40.000 0.00 0.00 0.00 2.71
263 264 5.621197 TCATTTCGTCCCTGTAAACATTG 57.379 39.130 0.00 0.00 0.00 2.82
264 265 5.067273 TCATTTCGTCCCTGTAAACATTGT 58.933 37.500 0.00 0.00 0.00 2.71
266 267 3.755112 TCGTCCCTGTAAACATTGTGA 57.245 42.857 0.00 0.00 0.00 3.58
267 268 3.395639 TCGTCCCTGTAAACATTGTGAC 58.604 45.455 0.00 0.00 0.00 3.67
268 269 2.156891 CGTCCCTGTAAACATTGTGACG 59.843 50.000 8.54 8.54 38.42 4.35
269 270 3.395639 GTCCCTGTAAACATTGTGACGA 58.604 45.455 0.00 0.00 0.00 4.20
272 273 4.454161 TCCCTGTAAACATTGTGACGATTG 59.546 41.667 0.00 0.00 0.00 2.67
273 274 4.454161 CCCTGTAAACATTGTGACGATTGA 59.546 41.667 0.00 0.00 0.00 2.57
274 275 5.049060 CCCTGTAAACATTGTGACGATTGAA 60.049 40.000 0.00 0.00 0.00 2.69
275 276 6.349280 CCCTGTAAACATTGTGACGATTGAAT 60.349 38.462 0.00 0.00 0.00 2.57
276 277 7.148323 CCCTGTAAACATTGTGACGATTGAATA 60.148 37.037 0.00 0.00 0.00 1.75
277 278 8.233868 CCTGTAAACATTGTGACGATTGAATAA 58.766 33.333 0.00 0.00 0.00 1.40
278 279 9.605955 CTGTAAACATTGTGACGATTGAATAAA 57.394 29.630 0.00 0.00 0.00 1.40
279 280 9.952188 TGTAAACATTGTGACGATTGAATAAAA 57.048 25.926 0.00 0.00 0.00 1.52
328 329 0.537143 TCAAAGACCTTGCGCCATGT 60.537 50.000 4.18 0.00 34.76 3.21
336 337 0.396435 CTTGCGCCATGTCCCCTATA 59.604 55.000 4.18 0.00 0.00 1.31
338 339 1.945580 TGCGCCATGTCCCCTATATA 58.054 50.000 4.18 0.00 0.00 0.86
340 341 2.170397 TGCGCCATGTCCCCTATATATG 59.830 50.000 4.18 0.00 0.00 1.78
343 344 3.742327 CGCCATGTCCCCTATATATGCTG 60.742 52.174 0.00 0.00 0.00 4.41
355 356 9.167311 CCCCTATATATGCTGTCAAACTAATTC 57.833 37.037 0.00 0.00 0.00 2.17
412 413 7.538303 AGCAACAAAGTAAACCATTTTCTTG 57.462 32.000 0.00 0.00 0.00 3.02
413 414 6.538381 AGCAACAAAGTAAACCATTTTCTTGG 59.462 34.615 0.00 0.00 42.82 3.61
450 451 7.707893 ACAAAGAAGAACACATCAAAGGAATTG 59.292 33.333 0.00 0.00 40.58 2.32
459 460 4.763793 ACATCAAAGGAATTGTCAGGTCAG 59.236 41.667 0.00 0.00 40.11 3.51
460 461 4.705110 TCAAAGGAATTGTCAGGTCAGA 57.295 40.909 0.00 0.00 40.11 3.27
461 462 4.389374 TCAAAGGAATTGTCAGGTCAGAC 58.611 43.478 0.00 0.00 40.11 3.51
480 481 1.515954 GATCGTCGCTCTGGGGAAA 59.484 57.895 0.00 0.00 36.19 3.13
547 548 1.144936 CAATGGACGCCTCCTCCTC 59.855 63.158 3.30 0.00 37.48 3.71
548 549 2.066999 AATGGACGCCTCCTCCTCC 61.067 63.158 3.30 0.00 37.48 4.30
586 602 1.378250 CAAGGGCTGCAGCTAGCTT 60.378 57.895 35.82 15.14 45.94 3.74
589 605 2.749044 GGCTGCAGCTAGCTTGCA 60.749 61.111 35.82 28.27 45.94 4.08
616 632 8.450964 ACCAACTGTTACATCATTTCTTAATCG 58.549 33.333 0.00 0.00 0.00 3.34
617 633 7.429340 CCAACTGTTACATCATTTCTTAATCGC 59.571 37.037 0.00 0.00 0.00 4.58
662 679 8.050930 TCAAGTAAGTCTTCATATTAAACCCCC 58.949 37.037 0.00 0.00 33.63 5.40
670 689 5.897851 TCATATTAAACCCCCGAAGATCA 57.102 39.130 0.00 0.00 0.00 2.92
716 735 3.612423 TCTGCACGTAAATCATGTTCTCG 59.388 43.478 0.00 0.00 0.00 4.04
902 931 0.512952 CAAAGACCTTCGCGACCAAG 59.487 55.000 9.15 3.21 0.00 3.61
942 971 0.385723 GTAGCCGGCGACTCTAATCG 60.386 60.000 29.75 0.00 45.09 3.34
946 975 4.610844 GGCGACTCTAATCGACGG 57.389 61.111 0.00 0.00 45.13 4.79
948 977 1.063649 GCGACTCTAATCGACGGCA 59.936 57.895 0.00 0.00 45.13 5.69
951 980 0.100682 GACTCTAATCGACGGCAGCA 59.899 55.000 0.00 0.00 0.00 4.41
953 982 1.203928 CTCTAATCGACGGCAGCAAG 58.796 55.000 0.00 0.00 0.00 4.01
1812 1851 0.040870 CATCCGAGTCGTCCGATGAG 60.041 60.000 19.48 0.48 39.48 2.90
1830 1869 1.947642 GTCGACTGTTTGACCGCGT 60.948 57.895 8.70 0.00 30.50 6.01
1888 1928 2.124860 GGTGGACCCGTATGTGGC 60.125 66.667 0.00 0.00 0.00 5.01
1966 2008 1.518325 TGTCCAAGGCGTTGTATGTG 58.482 50.000 17.23 2.58 30.95 3.21
1969 2011 0.810648 CCAAGGCGTTGTATGTGCAT 59.189 50.000 17.23 0.00 30.95 3.96
1983 2025 1.888512 TGTGCATCTCTTTTTCCTGCC 59.111 47.619 0.00 0.00 31.89 4.85
2042 2086 1.471684 CATTGCTGAGAGGCTTGTTCC 59.528 52.381 0.00 0.00 0.00 3.62
2043 2087 0.473755 TTGCTGAGAGGCTTGTTCCA 59.526 50.000 0.00 0.00 0.00 3.53
2116 3288 7.282450 CCAATAAATGAAGTAAGTACCACCTCC 59.718 40.741 0.00 0.00 0.00 4.30
2121 3293 2.720915 AGTAAGTACCACCTCCGTCTC 58.279 52.381 0.00 0.00 0.00 3.36
2191 3367 2.990735 CGCGCTTGAAGCTCTACG 59.009 61.111 15.92 9.64 39.60 3.51
2194 3370 1.009389 GCGCTTGAAGCTCTACGTGT 61.009 55.000 15.92 0.00 39.60 4.49
2197 3373 1.727335 GCTTGAAGCTCTACGTGTTCC 59.273 52.381 10.44 0.00 38.45 3.62
2198 3374 2.610727 GCTTGAAGCTCTACGTGTTCCT 60.611 50.000 10.44 0.00 38.45 3.36
2221 6575 3.251004 CCCTTTGTTTCACTCTTTCCTCG 59.749 47.826 0.00 0.00 0.00 4.63
2227 6581 1.420430 TCACTCTTTCCTCGGTGGTT 58.580 50.000 0.00 0.00 37.07 3.67
2265 6619 3.053991 TCTCCCTCTCAATCTCGTTCTCT 60.054 47.826 0.00 0.00 0.00 3.10
2626 14249 5.590530 TGATTTGGTTGTTAGTTTGTGCT 57.409 34.783 0.00 0.00 0.00 4.40
2677 14300 8.268850 TCTAGCCTTTGTTGTAATCTGATTTC 57.731 34.615 8.38 4.12 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.062183 CGAGCAAATGAGTTTCACGAGATAA 59.938 40.000 0.00 0.00 0.00 1.75
2 3 3.369147 CGAGCAAATGAGTTTCACGAGAT 59.631 43.478 0.00 0.00 0.00 2.75
3 4 2.731451 CGAGCAAATGAGTTTCACGAGA 59.269 45.455 0.00 0.00 0.00 4.04
6 7 1.195448 AGCGAGCAAATGAGTTTCACG 59.805 47.619 0.00 0.00 0.00 4.35
7 8 2.975851 CAAGCGAGCAAATGAGTTTCAC 59.024 45.455 0.00 0.00 0.00 3.18
8 9 2.618241 ACAAGCGAGCAAATGAGTTTCA 59.382 40.909 0.00 0.00 0.00 2.69
9 10 3.273919 ACAAGCGAGCAAATGAGTTTC 57.726 42.857 0.00 0.00 0.00 2.78
10 11 3.715628 AACAAGCGAGCAAATGAGTTT 57.284 38.095 0.00 0.00 0.00 2.66
11 12 4.787598 CTTAACAAGCGAGCAAATGAGTT 58.212 39.130 0.00 0.00 0.00 3.01
12 13 3.365364 GCTTAACAAGCGAGCAAATGAGT 60.365 43.478 0.00 0.00 45.74 3.41
13 14 3.166657 GCTTAACAAGCGAGCAAATGAG 58.833 45.455 0.00 0.00 45.74 2.90
14 15 3.201726 GCTTAACAAGCGAGCAAATGA 57.798 42.857 0.00 0.00 45.74 2.57
54 55 3.535280 ACCAAGCCGAACAATGTTTTT 57.465 38.095 0.00 0.00 0.00 1.94
57 58 2.028130 TGAACCAAGCCGAACAATGTT 58.972 42.857 0.00 0.00 0.00 2.71
58 59 1.686355 TGAACCAAGCCGAACAATGT 58.314 45.000 0.00 0.00 0.00 2.71
59 60 3.302365 AATGAACCAAGCCGAACAATG 57.698 42.857 0.00 0.00 0.00 2.82
60 61 4.522789 AGTTAATGAACCAAGCCGAACAAT 59.477 37.500 0.00 0.00 36.08 2.71
61 62 3.886505 AGTTAATGAACCAAGCCGAACAA 59.113 39.130 0.00 0.00 36.08 2.83
63 64 5.388111 GTTAGTTAATGAACCAAGCCGAAC 58.612 41.667 0.00 0.00 36.08 3.95
64 65 4.152759 CGTTAGTTAATGAACCAAGCCGAA 59.847 41.667 0.00 0.00 36.08 4.30
67 68 4.436986 GCTCGTTAGTTAATGAACCAAGCC 60.437 45.833 10.41 0.00 36.08 4.35
68 69 4.153475 TGCTCGTTAGTTAATGAACCAAGC 59.847 41.667 12.70 12.70 36.08 4.01
69 70 5.618561 GTGCTCGTTAGTTAATGAACCAAG 58.381 41.667 0.00 0.00 36.08 3.61
72 73 3.922240 TCGTGCTCGTTAGTTAATGAACC 59.078 43.478 8.17 0.00 35.93 3.62
73 74 4.490479 GCTCGTGCTCGTTAGTTAATGAAC 60.490 45.833 8.17 0.00 38.33 3.18
74 75 3.611113 GCTCGTGCTCGTTAGTTAATGAA 59.389 43.478 8.17 0.00 38.33 2.57
75 76 3.176708 GCTCGTGCTCGTTAGTTAATGA 58.823 45.455 8.17 0.00 38.33 2.57
76 77 2.281762 GGCTCGTGCTCGTTAGTTAATG 59.718 50.000 9.61 0.00 39.59 1.90
77 78 2.537401 GGCTCGTGCTCGTTAGTTAAT 58.463 47.619 9.61 0.00 39.59 1.40
78 79 1.730121 CGGCTCGTGCTCGTTAGTTAA 60.730 52.381 9.61 0.00 39.59 2.01
80 81 1.443872 CGGCTCGTGCTCGTTAGTT 60.444 57.895 9.61 0.00 39.59 2.24
81 82 1.859427 TTCGGCTCGTGCTCGTTAGT 61.859 55.000 9.61 0.00 39.59 2.24
82 83 0.731514 TTTCGGCTCGTGCTCGTTAG 60.732 55.000 9.61 0.27 39.59 2.34
84 85 2.028484 TTTCGGCTCGTGCTCGTT 59.972 55.556 9.61 0.00 39.59 3.85
85 86 2.733593 GTTTCGGCTCGTGCTCGT 60.734 61.111 9.61 0.00 39.59 4.18
86 87 3.827784 CGTTTCGGCTCGTGCTCG 61.828 66.667 9.61 11.11 39.59 5.03
87 88 2.430244 TCGTTTCGGCTCGTGCTC 60.430 61.111 9.61 0.00 39.59 4.26
88 89 2.430921 CTCGTTTCGGCTCGTGCT 60.431 61.111 9.61 0.00 39.59 4.40
89 90 4.135493 GCTCGTTTCGGCTCGTGC 62.135 66.667 0.00 0.00 38.82 5.34
90 91 3.479269 GGCTCGTTTCGGCTCGTG 61.479 66.667 0.00 0.00 0.00 4.35
92 93 2.314647 TTTGGCTCGTTTCGGCTCG 61.315 57.895 0.00 0.00 0.00 5.03
93 94 1.206831 GTTTGGCTCGTTTCGGCTC 59.793 57.895 0.00 0.00 0.00 4.70
94 95 0.034337 TAGTTTGGCTCGTTTCGGCT 59.966 50.000 0.00 0.00 0.00 5.52
95 96 1.062148 GATAGTTTGGCTCGTTTCGGC 59.938 52.381 0.00 0.00 0.00 5.54
96 97 1.323534 CGATAGTTTGGCTCGTTTCGG 59.676 52.381 0.00 0.00 0.00 4.30
97 98 2.256174 TCGATAGTTTGGCTCGTTTCG 58.744 47.619 0.00 0.00 34.19 3.46
99 100 2.000447 GCTCGATAGTTTGGCTCGTTT 59.000 47.619 0.00 0.00 34.19 3.60
100 101 1.641577 GCTCGATAGTTTGGCTCGTT 58.358 50.000 0.00 0.00 34.19 3.85
102 103 0.525668 ACGCTCGATAGTTTGGCTCG 60.526 55.000 0.00 0.00 37.40 5.03
103 104 1.641577 AACGCTCGATAGTTTGGCTC 58.358 50.000 0.00 0.00 37.40 4.70
105 106 4.531659 AATAAACGCTCGATAGTTTGGC 57.468 40.909 21.28 4.87 40.34 4.52
108 109 7.106663 GAGCATAATAAACGCTCGATAGTTT 57.893 36.000 18.17 18.17 42.42 2.66
116 117 1.784856 TCGCGAGCATAATAAACGCTC 59.215 47.619 3.71 0.00 46.91 5.03
117 118 1.787155 CTCGCGAGCATAATAAACGCT 59.213 47.619 25.07 0.00 45.64 5.07
118 119 2.198273 CTCGCGAGCATAATAAACGC 57.802 50.000 25.07 0.00 44.64 4.84
142 143 0.249398 TAGGGCTGGACGAAAAGCTC 59.751 55.000 0.00 0.00 40.40 4.09
143 144 0.912486 ATAGGGCTGGACGAAAAGCT 59.088 50.000 0.00 0.00 39.46 3.74
144 145 1.300481 GATAGGGCTGGACGAAAAGC 58.700 55.000 0.00 0.00 38.76 3.51
145 146 1.136305 TCGATAGGGCTGGACGAAAAG 59.864 52.381 0.00 0.00 0.00 2.27
146 147 1.136305 CTCGATAGGGCTGGACGAAAA 59.864 52.381 0.00 0.00 32.85 2.29
147 148 0.744874 CTCGATAGGGCTGGACGAAA 59.255 55.000 0.00 0.00 32.85 3.46
148 149 1.107538 CCTCGATAGGGCTGGACGAA 61.108 60.000 0.00 0.00 39.48 3.85
150 151 3.043419 CCTCGATAGGGCTGGACG 58.957 66.667 0.00 0.00 39.48 4.79
151 152 2.737830 GCCTCGATAGGGCTGGAC 59.262 66.667 6.91 0.00 45.38 4.02
157 158 1.482593 AGTTTGTGAGCCTCGATAGGG 59.517 52.381 0.00 0.00 43.87 3.53
164 165 0.944311 TTCGCGAGTTTGTGAGCCTC 60.944 55.000 9.59 0.00 0.00 4.70
165 166 0.946221 CTTCGCGAGTTTGTGAGCCT 60.946 55.000 9.59 0.00 0.00 4.58
166 167 1.493311 CTTCGCGAGTTTGTGAGCC 59.507 57.895 9.59 0.00 0.00 4.70
167 168 1.154580 GCTTCGCGAGTTTGTGAGC 60.155 57.895 9.59 10.16 0.00 4.26
168 169 0.111089 GTGCTTCGCGAGTTTGTGAG 60.111 55.000 9.59 2.69 0.00 3.51
169 170 1.817217 CGTGCTTCGCGAGTTTGTGA 61.817 55.000 9.59 0.00 39.94 3.58
171 172 2.928361 CGTGCTTCGCGAGTTTGT 59.072 55.556 9.59 0.00 39.94 2.83
180 181 2.983136 CCTAGAGATAATGCGTGCTTCG 59.017 50.000 0.00 0.00 43.12 3.79
181 182 3.321497 CCCTAGAGATAATGCGTGCTTC 58.679 50.000 0.00 0.00 0.00 3.86
182 183 2.037772 CCCCTAGAGATAATGCGTGCTT 59.962 50.000 0.00 0.00 0.00 3.91
183 184 1.620819 CCCCTAGAGATAATGCGTGCT 59.379 52.381 0.00 0.00 0.00 4.40
184 185 1.941668 GCCCCTAGAGATAATGCGTGC 60.942 57.143 0.00 0.00 0.00 5.34
185 186 1.620819 AGCCCCTAGAGATAATGCGTG 59.379 52.381 0.00 0.00 0.00 5.34
186 187 1.620819 CAGCCCCTAGAGATAATGCGT 59.379 52.381 0.00 0.00 0.00 5.24
187 188 1.066573 CCAGCCCCTAGAGATAATGCG 60.067 57.143 0.00 0.00 0.00 4.73
188 189 1.339535 GCCAGCCCCTAGAGATAATGC 60.340 57.143 0.00 0.00 0.00 3.56
189 190 2.027377 CAGCCAGCCCCTAGAGATAATG 60.027 54.545 0.00 0.00 0.00 1.90
190 191 2.264455 CAGCCAGCCCCTAGAGATAAT 58.736 52.381 0.00 0.00 0.00 1.28
191 192 1.722034 CAGCCAGCCCCTAGAGATAA 58.278 55.000 0.00 0.00 0.00 1.75
193 194 2.146061 GCAGCCAGCCCCTAGAGAT 61.146 63.158 0.00 0.00 37.23 2.75
194 195 2.765807 GCAGCCAGCCCCTAGAGA 60.766 66.667 0.00 0.00 37.23 3.10
203 204 2.103339 AACCAAACATGGCAGCCAGC 62.103 55.000 21.51 0.00 44.65 4.85
204 205 1.203052 CTAACCAAACATGGCAGCCAG 59.797 52.381 21.51 14.22 36.75 4.85
208 209 2.489329 CTGACCTAACCAAACATGGCAG 59.511 50.000 0.00 0.00 0.00 4.85
210 211 1.202348 GCTGACCTAACCAAACATGGC 59.798 52.381 0.00 0.00 0.00 4.40
212 213 1.818674 GGGCTGACCTAACCAAACATG 59.181 52.381 0.00 0.00 35.85 3.21
213 214 1.427368 TGGGCTGACCTAACCAAACAT 59.573 47.619 0.00 0.00 41.11 2.71
215 216 1.989706 TTGGGCTGACCTAACCAAAC 58.010 50.000 0.00 0.00 39.83 2.93
216 217 2.524306 CATTGGGCTGACCTAACCAAA 58.476 47.619 0.00 0.00 45.18 3.28
217 218 1.272425 CCATTGGGCTGACCTAACCAA 60.272 52.381 0.00 0.00 45.99 3.67
220 221 1.282157 AGACCATTGGGCTGACCTAAC 59.718 52.381 11.25 0.00 41.17 2.34
221 222 1.668826 AGACCATTGGGCTGACCTAA 58.331 50.000 11.25 0.00 41.17 2.69
222 223 1.559682 GAAGACCATTGGGCTGACCTA 59.440 52.381 13.09 0.00 42.44 3.08
223 224 0.329596 GAAGACCATTGGGCTGACCT 59.670 55.000 13.09 0.00 42.44 3.85
224 225 0.038166 TGAAGACCATTGGGCTGACC 59.962 55.000 13.09 5.38 42.44 4.02
227 228 2.159338 CGAAATGAAGACCATTGGGCTG 60.159 50.000 13.09 0.00 42.44 4.85
230 231 2.423538 GGACGAAATGAAGACCATTGGG 59.576 50.000 7.78 0.00 44.28 4.12
231 232 2.423538 GGGACGAAATGAAGACCATTGG 59.576 50.000 0.00 0.00 44.28 3.16
233 234 3.244911 ACAGGGACGAAATGAAGACCATT 60.245 43.478 0.00 0.00 46.86 3.16
234 235 2.305927 ACAGGGACGAAATGAAGACCAT 59.694 45.455 0.00 0.00 36.99 3.55
237 238 4.753107 TGTTTACAGGGACGAAATGAAGAC 59.247 41.667 0.00 0.00 0.00 3.01
238 239 4.963373 TGTTTACAGGGACGAAATGAAGA 58.037 39.130 0.00 0.00 0.00 2.87
239 240 5.880054 ATGTTTACAGGGACGAAATGAAG 57.120 39.130 0.00 0.00 0.00 3.02
241 242 5.049060 CACAATGTTTACAGGGACGAAATGA 60.049 40.000 0.00 0.00 0.00 2.57
242 243 5.049060 TCACAATGTTTACAGGGACGAAATG 60.049 40.000 0.00 0.00 0.00 2.32
243 244 5.048991 GTCACAATGTTTACAGGGACGAAAT 60.049 40.000 0.00 0.00 0.00 2.17
246 247 3.395639 GTCACAATGTTTACAGGGACGA 58.604 45.455 0.00 0.00 0.00 4.20
247 248 2.156891 CGTCACAATGTTTACAGGGACG 59.843 50.000 11.00 11.00 40.45 4.79
249 250 3.755112 TCGTCACAATGTTTACAGGGA 57.245 42.857 0.00 0.00 0.00 4.20
250 251 4.454161 TCAATCGTCACAATGTTTACAGGG 59.546 41.667 0.00 0.00 0.00 4.45
251 252 5.605564 TCAATCGTCACAATGTTTACAGG 57.394 39.130 0.00 0.00 0.00 4.00
252 253 9.605955 TTTATTCAATCGTCACAATGTTTACAG 57.394 29.630 0.00 0.00 0.00 2.74
253 254 9.952188 TTTTATTCAATCGTCACAATGTTTACA 57.048 25.926 0.00 0.00 0.00 2.41
301 302 3.616821 GCGCAAGGTCTTTGAAAAGTTTT 59.383 39.130 0.30 0.00 39.21 2.43
302 303 3.186909 GCGCAAGGTCTTTGAAAAGTTT 58.813 40.909 0.30 0.00 39.21 2.66
303 304 2.481276 GGCGCAAGGTCTTTGAAAAGTT 60.481 45.455 10.83 0.00 39.21 2.66
305 306 1.066908 TGGCGCAAGGTCTTTGAAAAG 59.933 47.619 10.83 0.00 39.21 2.27
306 307 1.107114 TGGCGCAAGGTCTTTGAAAA 58.893 45.000 10.83 0.00 39.21 2.29
307 308 1.000385 CATGGCGCAAGGTCTTTGAAA 60.000 47.619 10.83 0.00 39.21 2.69
308 309 0.597568 CATGGCGCAAGGTCTTTGAA 59.402 50.000 10.83 0.00 39.21 2.69
310 311 0.109597 GACATGGCGCAAGGTCTTTG 60.110 55.000 21.86 0.25 39.88 2.77
328 329 7.865530 TTAGTTTGACAGCATATATAGGGGA 57.134 36.000 0.00 0.00 0.00 4.81
336 337 4.275936 GGGCGAATTAGTTTGACAGCATAT 59.724 41.667 0.00 0.00 0.00 1.78
338 339 2.423538 GGGCGAATTAGTTTGACAGCAT 59.576 45.455 0.00 0.00 0.00 3.79
340 341 1.132453 GGGGCGAATTAGTTTGACAGC 59.868 52.381 0.00 0.00 0.00 4.40
343 344 4.995487 CCTATAGGGGCGAATTAGTTTGAC 59.005 45.833 11.33 0.00 0.00 3.18
355 356 3.553828 TTCTTTGTTCCTATAGGGGCG 57.446 47.619 18.97 2.59 35.41 6.13
450 451 0.247735 CGACGATCGTCTGACCTGAC 60.248 60.000 37.12 15.57 42.54 3.51
459 460 2.024871 CCCAGAGCGACGATCGTC 59.975 66.667 33.22 33.22 42.81 4.20
460 461 3.518998 CCCCAGAGCGACGATCGT 61.519 66.667 22.97 22.97 42.81 3.73
461 462 2.279502 TTTCCCCAGAGCGACGATCG 62.280 60.000 14.88 14.88 43.89 3.69
494 495 6.438763 AGCAGCAAAGTTCTTTGTATAACAC 58.561 36.000 21.20 7.56 34.56 3.32
514 515 1.401409 CCATTGGTACGTGCAAAGCAG 60.401 52.381 5.86 0.00 40.08 4.24
547 548 4.871513 TGCAGAGTAATCGTAATGCTAGG 58.128 43.478 4.17 0.00 34.80 3.02
548 549 5.403766 CCTTGCAGAGTAATCGTAATGCTAG 59.596 44.000 6.61 6.61 36.64 3.42
579 595 0.954452 ACAGTTGGTTGCAAGCTAGC 59.046 50.000 27.31 17.13 0.00 3.42
616 632 5.112220 TGATGATAATCGCAAAATGAGGC 57.888 39.130 0.00 0.00 0.00 4.70
617 633 6.732154 ACTTGATGATAATCGCAAAATGAGG 58.268 36.000 0.00 0.00 0.00 3.86
662 679 7.747799 CGGAAATATTTGGATTCATGATCTTCG 59.252 37.037 5.17 0.00 35.02 3.79
670 689 8.206189 AGAAAATGCGGAAATATTTGGATTCAT 58.794 29.630 5.17 0.00 0.00 2.57
705 724 1.418334 AGCTAGGGCGAGAACATGAT 58.582 50.000 0.00 0.00 44.37 2.45
706 725 1.195115 AAGCTAGGGCGAGAACATGA 58.805 50.000 0.00 0.00 44.37 3.07
909 938 1.070376 CGGCTACGATGATTGCATGTG 60.070 52.381 0.00 0.00 44.60 3.21
942 971 1.081840 GTTCTTGCTTGCTGCCGTC 60.082 57.895 0.00 0.00 42.00 4.79
945 974 0.595825 GTGTGTTCTTGCTTGCTGCC 60.596 55.000 0.00 0.00 42.00 4.85
946 975 0.931662 CGTGTGTTCTTGCTTGCTGC 60.932 55.000 0.00 0.00 43.25 5.25
948 977 2.024918 CCGTGTGTTCTTGCTTGCT 58.975 52.632 0.00 0.00 0.00 3.91
951 980 2.542907 CCGCCGTGTGTTCTTGCTT 61.543 57.895 0.00 0.00 0.00 3.91
953 982 2.054140 TTTCCGCCGTGTGTTCTTGC 62.054 55.000 0.00 0.00 0.00 4.01
960 989 2.280524 TGACCTTTCCGCCGTGTG 60.281 61.111 0.00 0.00 0.00 3.82
962 991 2.725203 TTCCTGACCTTTCCGCCGTG 62.725 60.000 0.00 0.00 0.00 4.94
998 1031 2.592032 TTGCACTCCCTCGGCATGA 61.592 57.895 0.00 0.00 37.39 3.07
1626 1665 0.835276 CCACCAGCATCTCCATCAGA 59.165 55.000 0.00 0.00 34.78 3.27
1812 1851 1.947642 ACGCGGTCAAACAGTCGAC 60.948 57.895 12.47 7.70 0.00 4.20
1845 1884 2.067365 AGGGACAAACTGAAACCACC 57.933 50.000 0.00 0.00 0.00 4.61
1847 1886 4.394729 GTCATAGGGACAAACTGAAACCA 58.605 43.478 0.00 0.00 46.19 3.67
1966 2008 3.949842 AAAGGCAGGAAAAAGAGATGC 57.050 42.857 0.00 0.00 36.16 3.91
2042 2086 9.573133 GTATCATTTCCATTTTCTTTAGGTGTG 57.427 33.333 0.00 0.00 0.00 3.82
2043 2087 9.308000 TGTATCATTTCCATTTTCTTTAGGTGT 57.692 29.630 0.00 0.00 0.00 4.16
2121 3293 9.868277 TGGCCTACAAAAATGTCTTATATTTTG 57.132 29.630 3.32 7.95 44.34 2.44
2144 3316 0.815734 TCGAAGCTACTACCACTGGC 59.184 55.000 0.00 0.00 0.00 4.85
2148 3320 1.340568 GGGGATCGAAGCTACTACCAC 59.659 57.143 0.00 0.00 0.00 4.16
2191 3367 3.288092 AGTGAAACAAAGGGAGGAACAC 58.712 45.455 0.00 0.00 41.43 3.32
2194 3370 4.519906 AAGAGTGAAACAAAGGGAGGAA 57.480 40.909 0.00 0.00 41.43 3.36
2197 3373 4.464947 AGGAAAGAGTGAAACAAAGGGAG 58.535 43.478 0.00 0.00 41.43 4.30
2198 3374 4.461198 GAGGAAAGAGTGAAACAAAGGGA 58.539 43.478 0.00 0.00 41.43 4.20
2221 6575 5.476945 AGAAGAAATACATCAACCAACCACC 59.523 40.000 0.00 0.00 0.00 4.61
2227 6581 5.488919 AGAGGGAGAAGAAATACATCAACCA 59.511 40.000 0.00 0.00 0.00 3.67
2265 6619 6.499106 TGCATCCAACCAGATCTAGAAATA 57.501 37.500 0.00 0.00 0.00 1.40
2455 7630 1.290955 CTTCGTTGGGGCGACACTA 59.709 57.895 0.00 0.00 40.85 2.74
2457 7632 1.005867 TACTTCGTTGGGGCGACAC 60.006 57.895 0.00 0.00 40.85 3.67


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

AutoCloner maintained by Alex Coulton.