Multiple sequence alignment - TraesCS4A01G128900

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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 TraesCS4A01G128900 chr4A 100.000 4016 0 0 1 4016 165758569 165754554 0.000000e+00 7417.0
1 TraesCS4A01G128900 chr4D 91.763 3885 147 63 226 4016 309498955 309502760 0.000000e+00 5241.0
2 TraesCS4A01G128900 chr4D 92.308 52 4 0 1475 1526 493017018 493017069 1.550000e-09 75.0
3 TraesCS4A01G128900 chr4B 89.866 3286 129 79 261 3451 386201975 386205151 0.000000e+00 4036.0
4 TraesCS4A01G128900 chr4B 92.374 577 33 7 3445 4016 386207812 386208382 0.000000e+00 811.0
5 TraesCS4A01G128900 chr4B 92.308 52 4 0 1475 1526 631608671 631608620 1.550000e-09 75.0
6 TraesCS4A01G128900 chr2D 94.231 52 3 0 1475 1526 592411306 592411357 3.330000e-11 80.5
7 TraesCS4A01G128900 chr2D 92.308 52 4 0 1475 1526 619046361 619046310 1.550000e-09 75.0
8 TraesCS4A01G128900 chr2B 94.231 52 3 0 1475 1526 718396650 718396701 3.330000e-11 80.5
9 TraesCS4A01G128900 chr2B 92.308 52 4 0 1475 1526 756553073 756553022 1.550000e-09 75.0
10 TraesCS4A01G128900 chr2A 94.231 52 3 0 1475 1526 726986425 726986476 3.330000e-11 80.5


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 TraesCS4A01G128900 chr4A 165754554 165758569 4015 True 7417.0 7417 100.000 1 4016 1 chr4A.!!$R1 4015
1 TraesCS4A01G128900 chr4D 309498955 309502760 3805 False 5241.0 5241 91.763 226 4016 1 chr4D.!!$F1 3790
2 TraesCS4A01G128900 chr4B 386201975 386208382 6407 False 2423.5 4036 91.120 261 4016 2 chr4B.!!$F1 3755

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
48 49 0.041663 ATTTGTGACGAAACACGCCG 60.042 50.0 0.0 0.0 46.94 6.46 F
184 185 0.110486 ATTGGCCCTCAGACAACGTT 59.890 50.0 0.0 0.0 0.00 3.99 F
1600 1669 0.036010 AGCTCACCCACTCCGATTTG 60.036 55.0 0.0 0.0 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1664 1.800681 GTGTACGCCTGCCCAAATC 59.199 57.895 0.0 0.0 0.0 2.17 R
2091 2203 0.107945 AGATGAAGCGGTGAGAAGGC 60.108 55.000 0.0 0.0 0.0 4.35 R
3378 3513 0.109597 CCCGCTGATCTTTTGTGTGC 60.110 55.000 0.0 0.0 0.0 4.57 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
42 43 8.389586 AGTTTTAGTTGAATTTGTGACGAAAC 57.610 30.769 0.00 0.00 0.00 2.78
43 44 8.024285 AGTTTTAGTTGAATTTGTGACGAAACA 58.976 29.630 0.00 0.00 31.53 2.83
44 45 7.728580 TTTAGTTGAATTTGTGACGAAACAC 57.271 32.000 0.00 0.00 40.68 3.32
46 47 2.710760 TGAATTTGTGACGAAACACGC 58.289 42.857 0.00 0.00 46.94 5.34
47 48 2.041244 GAATTTGTGACGAAACACGCC 58.959 47.619 0.00 0.00 46.94 5.68
48 49 0.041663 ATTTGTGACGAAACACGCCG 60.042 50.000 0.00 0.00 46.94 6.46
49 50 1.082679 TTTGTGACGAAACACGCCGA 61.083 50.000 0.00 0.00 46.94 5.54
50 51 1.082679 TTGTGACGAAACACGCCGAA 61.083 50.000 0.00 0.00 46.94 4.30
51 52 0.876777 TGTGACGAAACACGCCGAAT 60.877 50.000 0.00 0.00 46.94 3.34
52 53 0.450482 GTGACGAAACACGCCGAATG 60.450 55.000 0.00 0.00 46.94 2.67
53 54 0.876777 TGACGAAACACGCCGAATGT 60.877 50.000 0.00 0.00 46.94 2.71
54 55 0.450482 GACGAAACACGCCGAATGTG 60.450 55.000 0.00 0.00 46.94 3.21
55 56 1.154488 CGAAACACGCCGAATGTGG 60.154 57.895 0.00 0.00 41.64 4.17
56 57 1.209127 GAAACACGCCGAATGTGGG 59.791 57.895 0.00 0.00 41.64 4.61
63 64 3.607163 CCGAATGTGGGCAGCATT 58.393 55.556 5.63 5.63 39.04 3.56
64 65 1.892338 CCGAATGTGGGCAGCATTT 59.108 52.632 7.10 0.00 36.77 2.32
65 66 0.458889 CCGAATGTGGGCAGCATTTG 60.459 55.000 11.34 11.34 36.77 2.32
66 67 0.458889 CGAATGTGGGCAGCATTTGG 60.459 55.000 10.74 3.27 36.77 3.28
67 68 0.896923 GAATGTGGGCAGCATTTGGA 59.103 50.000 7.10 0.00 36.77 3.53
68 69 1.483415 GAATGTGGGCAGCATTTGGAT 59.517 47.619 7.10 0.00 36.77 3.41
69 70 1.117150 ATGTGGGCAGCATTTGGATC 58.883 50.000 0.00 0.00 0.00 3.36
70 71 0.251698 TGTGGGCAGCATTTGGATCA 60.252 50.000 0.00 0.00 0.00 2.92
71 72 0.896923 GTGGGCAGCATTTGGATCAA 59.103 50.000 0.00 0.00 0.00 2.57
72 73 1.483415 GTGGGCAGCATTTGGATCAAT 59.517 47.619 0.00 0.00 0.00 2.57
73 74 2.093341 GTGGGCAGCATTTGGATCAATT 60.093 45.455 0.00 0.00 0.00 2.32
74 75 2.572556 TGGGCAGCATTTGGATCAATTT 59.427 40.909 0.00 0.00 0.00 1.82
75 76 2.940410 GGGCAGCATTTGGATCAATTTG 59.060 45.455 0.00 0.00 0.00 2.32
76 77 2.353579 GGCAGCATTTGGATCAATTTGC 59.646 45.455 0.00 0.00 34.94 3.68
77 78 2.029970 GCAGCATTTGGATCAATTTGCG 59.970 45.455 0.00 0.00 37.67 4.85
78 79 3.255725 CAGCATTTGGATCAATTTGCGT 58.744 40.909 0.00 0.00 37.67 5.24
79 80 3.305094 CAGCATTTGGATCAATTTGCGTC 59.695 43.478 0.00 0.00 37.67 5.19
80 81 3.194116 AGCATTTGGATCAATTTGCGTCT 59.806 39.130 0.00 0.00 37.67 4.18
81 82 4.398988 AGCATTTGGATCAATTTGCGTCTA 59.601 37.500 0.00 0.00 37.67 2.59
82 83 5.101628 GCATTTGGATCAATTTGCGTCTAA 58.898 37.500 0.00 0.00 0.00 2.10
83 84 5.576384 GCATTTGGATCAATTTGCGTCTAAA 59.424 36.000 12.12 12.12 0.00 1.85
84 85 6.256321 GCATTTGGATCAATTTGCGTCTAAAT 59.744 34.615 14.34 14.34 33.75 1.40
85 86 7.201548 GCATTTGGATCAATTTGCGTCTAAATT 60.202 33.333 16.05 0.00 40.00 1.82
90 91 3.848726 CAATTTGCGTCTAAATTGGGCT 58.151 40.909 18.51 0.00 46.59 5.19
91 92 3.508744 ATTTGCGTCTAAATTGGGCTG 57.491 42.857 0.00 0.00 0.00 4.85
92 93 2.192664 TTGCGTCTAAATTGGGCTGA 57.807 45.000 0.00 0.00 0.00 4.26
93 94 2.192664 TGCGTCTAAATTGGGCTGAA 57.807 45.000 0.00 0.00 0.00 3.02
94 95 2.509569 TGCGTCTAAATTGGGCTGAAA 58.490 42.857 0.00 0.00 0.00 2.69
95 96 3.088532 TGCGTCTAAATTGGGCTGAAAT 58.911 40.909 0.00 0.00 0.00 2.17
96 97 3.128589 TGCGTCTAAATTGGGCTGAAATC 59.871 43.478 0.00 0.00 0.00 2.17
97 98 3.788797 GCGTCTAAATTGGGCTGAAATCG 60.789 47.826 0.00 0.00 0.00 3.34
98 99 3.621268 CGTCTAAATTGGGCTGAAATCGA 59.379 43.478 0.00 0.00 0.00 3.59
99 100 4.273480 CGTCTAAATTGGGCTGAAATCGAT 59.727 41.667 0.00 0.00 0.00 3.59
100 101 5.514279 GTCTAAATTGGGCTGAAATCGATG 58.486 41.667 0.00 0.00 0.00 3.84
101 102 5.296780 GTCTAAATTGGGCTGAAATCGATGA 59.703 40.000 0.00 0.00 0.00 2.92
102 103 4.376340 AAATTGGGCTGAAATCGATGAC 57.624 40.909 0.00 0.00 0.00 3.06
103 104 2.787473 TTGGGCTGAAATCGATGACT 57.213 45.000 0.00 0.00 0.00 3.41
104 105 3.904800 TTGGGCTGAAATCGATGACTA 57.095 42.857 0.00 0.00 0.00 2.59
105 106 3.459232 TGGGCTGAAATCGATGACTAG 57.541 47.619 0.00 0.00 0.00 2.57
106 107 2.103094 TGGGCTGAAATCGATGACTAGG 59.897 50.000 0.00 0.00 0.00 3.02
107 108 2.548920 GGGCTGAAATCGATGACTAGGG 60.549 54.545 0.00 0.00 0.00 3.53
108 109 2.548920 GGCTGAAATCGATGACTAGGGG 60.549 54.545 0.00 0.00 0.00 4.79
109 110 2.365617 GCTGAAATCGATGACTAGGGGA 59.634 50.000 0.00 0.00 0.00 4.81
110 111 3.007398 GCTGAAATCGATGACTAGGGGAT 59.993 47.826 0.00 0.00 0.00 3.85
111 112 4.564041 CTGAAATCGATGACTAGGGGATG 58.436 47.826 0.00 0.00 0.00 3.51
112 113 4.223144 TGAAATCGATGACTAGGGGATGA 58.777 43.478 0.00 0.00 0.00 2.92
113 114 4.653801 TGAAATCGATGACTAGGGGATGAA 59.346 41.667 0.00 0.00 0.00 2.57
114 115 4.608948 AATCGATGACTAGGGGATGAAC 57.391 45.455 0.00 0.00 0.00 3.18
115 116 3.314307 TCGATGACTAGGGGATGAACT 57.686 47.619 0.00 0.00 0.00 3.01
116 117 3.643237 TCGATGACTAGGGGATGAACTT 58.357 45.455 0.00 0.00 0.00 2.66
117 118 4.800023 TCGATGACTAGGGGATGAACTTA 58.200 43.478 0.00 0.00 0.00 2.24
118 119 4.827835 TCGATGACTAGGGGATGAACTTAG 59.172 45.833 0.00 0.00 0.00 2.18
119 120 4.021894 CGATGACTAGGGGATGAACTTAGG 60.022 50.000 0.00 0.00 0.00 2.69
120 121 3.654273 TGACTAGGGGATGAACTTAGGG 58.346 50.000 0.00 0.00 0.00 3.53
121 122 2.973406 GACTAGGGGATGAACTTAGGGG 59.027 54.545 0.00 0.00 0.00 4.79
122 123 1.700186 CTAGGGGATGAACTTAGGGGC 59.300 57.143 0.00 0.00 0.00 5.80
123 124 0.994050 AGGGGATGAACTTAGGGGCC 60.994 60.000 0.00 0.00 0.00 5.80
124 125 1.148498 GGGATGAACTTAGGGGCCG 59.852 63.158 0.00 0.00 0.00 6.13
125 126 1.148498 GGATGAACTTAGGGGCCGG 59.852 63.158 0.00 0.00 0.00 6.13
126 127 1.526225 GATGAACTTAGGGGCCGGC 60.526 63.158 21.18 21.18 0.00 6.13
127 128 3.400599 ATGAACTTAGGGGCCGGCG 62.401 63.158 22.54 7.92 0.00 6.46
128 129 4.851179 GAACTTAGGGGCCGGCGG 62.851 72.222 24.35 24.35 0.00 6.13
151 152 4.754667 GAACCCGAGCCCCACGTC 62.755 72.222 0.00 0.00 0.00 4.34
155 156 4.143333 CCGAGCCCCACGTCGATT 62.143 66.667 0.00 0.00 38.50 3.34
156 157 2.125673 CGAGCCCCACGTCGATTT 60.126 61.111 0.00 0.00 38.50 2.17
157 158 1.740296 CGAGCCCCACGTCGATTTT 60.740 57.895 0.00 0.00 38.50 1.82
158 159 0.458889 CGAGCCCCACGTCGATTTTA 60.459 55.000 0.00 0.00 38.50 1.52
159 160 1.805120 CGAGCCCCACGTCGATTTTAT 60.805 52.381 0.00 0.00 38.50 1.40
160 161 1.865340 GAGCCCCACGTCGATTTTATC 59.135 52.381 0.00 0.00 0.00 1.75
179 180 2.989639 CCGATTGGCCCTCAGACA 59.010 61.111 0.00 0.00 0.00 3.41
180 181 1.299648 CCGATTGGCCCTCAGACAA 59.700 57.895 0.00 0.00 0.00 3.18
181 182 1.026718 CCGATTGGCCCTCAGACAAC 61.027 60.000 0.00 0.00 0.00 3.32
182 183 1.361668 CGATTGGCCCTCAGACAACG 61.362 60.000 0.00 0.00 0.00 4.10
183 184 0.321653 GATTGGCCCTCAGACAACGT 60.322 55.000 0.00 0.00 0.00 3.99
184 185 0.110486 ATTGGCCCTCAGACAACGTT 59.890 50.000 0.00 0.00 0.00 3.99
185 186 0.759959 TTGGCCCTCAGACAACGTTA 59.240 50.000 0.00 0.00 0.00 3.18
186 187 0.981183 TGGCCCTCAGACAACGTTAT 59.019 50.000 0.00 0.00 0.00 1.89
187 188 1.349688 TGGCCCTCAGACAACGTTATT 59.650 47.619 0.00 0.00 0.00 1.40
188 189 2.224670 TGGCCCTCAGACAACGTTATTT 60.225 45.455 0.00 0.00 0.00 1.40
189 190 2.817844 GGCCCTCAGACAACGTTATTTT 59.182 45.455 0.00 0.00 0.00 1.82
190 191 4.004982 GGCCCTCAGACAACGTTATTTTA 58.995 43.478 0.00 0.00 0.00 1.52
191 192 4.456566 GGCCCTCAGACAACGTTATTTTAA 59.543 41.667 0.00 0.00 0.00 1.52
192 193 5.391629 GGCCCTCAGACAACGTTATTTTAAG 60.392 44.000 0.00 0.00 0.00 1.85
193 194 5.628134 CCCTCAGACAACGTTATTTTAAGC 58.372 41.667 0.00 0.00 0.00 3.09
194 195 5.391629 CCCTCAGACAACGTTATTTTAAGCC 60.392 44.000 0.00 0.00 0.00 4.35
195 196 5.411669 CCTCAGACAACGTTATTTTAAGCCT 59.588 40.000 0.00 0.00 0.00 4.58
196 197 6.402226 CCTCAGACAACGTTATTTTAAGCCTC 60.402 42.308 0.00 0.00 0.00 4.70
197 198 6.228258 TCAGACAACGTTATTTTAAGCCTCT 58.772 36.000 0.00 0.00 0.00 3.69
198 199 7.380536 TCAGACAACGTTATTTTAAGCCTCTA 58.619 34.615 0.00 0.00 0.00 2.43
199 200 8.038944 TCAGACAACGTTATTTTAAGCCTCTAT 58.961 33.333 0.00 0.00 0.00 1.98
200 201 8.116753 CAGACAACGTTATTTTAAGCCTCTATG 58.883 37.037 0.00 0.00 0.00 2.23
201 202 7.280205 AGACAACGTTATTTTAAGCCTCTATGG 59.720 37.037 0.00 0.00 39.35 2.74
202 203 6.317893 ACAACGTTATTTTAAGCCTCTATGGG 59.682 38.462 0.00 0.00 36.00 4.00
203 204 5.374071 ACGTTATTTTAAGCCTCTATGGGG 58.626 41.667 0.00 0.00 36.00 4.96
209 210 2.111251 GCCTCTATGGGGCCGAAC 59.889 66.667 0.00 0.00 43.49 3.95
210 211 2.421739 CCTCTATGGGGCCGAACG 59.578 66.667 0.00 0.00 0.00 3.95
211 212 2.421739 CTCTATGGGGCCGAACGG 59.578 66.667 9.00 9.00 38.57 4.44
212 213 2.042741 TCTATGGGGCCGAACGGA 60.043 61.111 17.63 0.00 37.50 4.69
213 214 1.458777 TCTATGGGGCCGAACGGAT 60.459 57.895 17.63 4.09 37.50 4.18
214 215 1.301716 CTATGGGGCCGAACGGATG 60.302 63.158 17.63 0.00 37.50 3.51
215 216 2.731691 CTATGGGGCCGAACGGATGG 62.732 65.000 17.63 0.00 37.50 3.51
217 218 4.547367 GGGGCCGAACGGATGGAG 62.547 72.222 17.63 0.00 37.50 3.86
218 219 3.467226 GGGCCGAACGGATGGAGA 61.467 66.667 17.63 0.00 37.50 3.71
219 220 2.808206 GGGCCGAACGGATGGAGAT 61.808 63.158 17.63 0.00 37.50 2.75
220 221 1.595382 GGCCGAACGGATGGAGATG 60.595 63.158 17.63 0.00 37.50 2.90
221 222 1.144057 GCCGAACGGATGGAGATGT 59.856 57.895 17.63 0.00 37.50 3.06
222 223 0.462047 GCCGAACGGATGGAGATGTT 60.462 55.000 17.63 0.00 37.50 2.71
223 224 1.571919 CCGAACGGATGGAGATGTTC 58.428 55.000 7.53 0.00 37.84 3.18
224 225 1.571919 CGAACGGATGGAGATGTTCC 58.428 55.000 0.00 0.00 46.98 3.62
238 239 0.620410 TGTTCCCATCGGGTCATCCT 60.620 55.000 0.00 0.00 44.74 3.24
242 243 1.528824 CCATCGGGTCATCCTTGCT 59.471 57.895 0.00 0.00 0.00 3.91
314 317 3.185455 AGAGCCTAGAGGTCAAACCAAT 58.815 45.455 11.39 0.00 45.87 3.16
315 318 3.054802 AGAGCCTAGAGGTCAAACCAATG 60.055 47.826 11.39 0.00 45.87 2.82
316 319 2.644798 AGCCTAGAGGTCAAACCAATGT 59.355 45.455 0.00 0.00 41.95 2.71
317 320 2.749621 GCCTAGAGGTCAAACCAATGTG 59.250 50.000 0.00 0.00 41.95 3.21
318 321 2.749621 CCTAGAGGTCAAACCAATGTGC 59.250 50.000 0.00 0.00 41.95 4.57
319 322 1.620822 AGAGGTCAAACCAATGTGCC 58.379 50.000 0.00 0.00 41.95 5.01
320 323 0.603065 GAGGTCAAACCAATGTGCCC 59.397 55.000 0.00 0.00 41.95 5.36
321 324 1.178534 AGGTCAAACCAATGTGCCCG 61.179 55.000 0.00 0.00 41.95 6.13
322 325 1.460273 GGTCAAACCAATGTGCCCGT 61.460 55.000 0.00 0.00 38.42 5.28
401 404 3.849951 GGCTCCCGCTCGGAATGA 61.850 66.667 10.28 0.00 41.40 2.57
407 410 1.356624 CCGCTCGGAATGATTTGCC 59.643 57.895 1.35 0.00 37.50 4.52
466 490 4.440839 AGGTCGAAATTCCAGCAAATTC 57.559 40.909 0.00 0.00 0.00 2.17
488 512 1.511850 CACAGCACGTCTGAATGGAA 58.488 50.000 17.99 0.00 45.72 3.53
545 569 1.136984 GACCCGCTGTCACTACTCG 59.863 63.158 0.00 0.00 43.85 4.18
546 570 1.303074 ACCCGCTGTCACTACTCGA 60.303 57.895 0.00 0.00 0.00 4.04
547 571 0.680280 ACCCGCTGTCACTACTCGAT 60.680 55.000 0.00 0.00 0.00 3.59
548 572 1.306148 CCCGCTGTCACTACTCGATA 58.694 55.000 0.00 0.00 0.00 2.92
549 573 1.002684 CCCGCTGTCACTACTCGATAC 60.003 57.143 0.00 0.00 0.00 2.24
550 574 1.002684 CCGCTGTCACTACTCGATACC 60.003 57.143 0.00 0.00 0.00 2.73
551 575 1.941294 CGCTGTCACTACTCGATACCT 59.059 52.381 0.00 0.00 0.00 3.08
552 576 2.286477 CGCTGTCACTACTCGATACCTG 60.286 54.545 0.00 0.00 0.00 4.00
553 577 2.541999 GCTGTCACTACTCGATACCTGC 60.542 54.545 0.00 0.00 0.00 4.85
554 578 2.946329 CTGTCACTACTCGATACCTGCT 59.054 50.000 0.00 0.00 0.00 4.24
555 579 2.943690 TGTCACTACTCGATACCTGCTC 59.056 50.000 0.00 0.00 0.00 4.26
559 583 2.224233 ACTACTCGATACCTGCTCGCTA 60.224 50.000 0.00 0.00 36.11 4.26
655 690 2.071540 GGAATTGAAAGCAAAGCCAGC 58.928 47.619 0.00 0.00 37.59 4.85
701 736 0.254462 CAGGAGCTCTTTTCCCCTCC 59.746 60.000 14.64 0.00 43.29 4.30
703 738 1.610327 GAGCTCTTTTCCCCTCCCC 59.390 63.158 6.43 0.00 0.00 4.81
731 775 3.020274 GCTCCTCCCTTTTTGGATTCTC 58.980 50.000 0.00 0.00 38.35 2.87
812 856 3.433740 GGAATCGTAAATCCTTGCCTCCT 60.434 47.826 0.00 0.00 32.75 3.69
815 867 2.168521 TCGTAAATCCTTGCCTCCTCTG 59.831 50.000 0.00 0.00 0.00 3.35
818 870 0.545646 AATCCTTGCCTCCTCTGCTC 59.454 55.000 0.00 0.00 0.00 4.26
877 929 1.004862 CCAAGGGAAGGGAAAGGAGAC 59.995 57.143 0.00 0.00 0.00 3.36
878 930 1.705186 CAAGGGAAGGGAAAGGAGACA 59.295 52.381 0.00 0.00 0.00 3.41
946 998 1.264288 CGTTTCTTGCAGGTGTTCCTC 59.736 52.381 0.00 0.00 43.07 3.71
986 1046 2.752354 CTCTACTGGTGAGTGAGGAGTG 59.248 54.545 0.00 0.00 33.21 3.51
987 1047 2.375509 TCTACTGGTGAGTGAGGAGTGA 59.624 50.000 0.00 0.00 33.21 3.41
988 1048 1.626686 ACTGGTGAGTGAGGAGTGAG 58.373 55.000 0.00 0.00 0.00 3.51
989 1049 1.133325 ACTGGTGAGTGAGGAGTGAGT 60.133 52.381 0.00 0.00 0.00 3.41
990 1050 1.271934 CTGGTGAGTGAGGAGTGAGTG 59.728 57.143 0.00 0.00 0.00 3.51
991 1051 0.605589 GGTGAGTGAGGAGTGAGTGG 59.394 60.000 0.00 0.00 0.00 4.00
992 1052 0.605589 GTGAGTGAGGAGTGAGTGGG 59.394 60.000 0.00 0.00 0.00 4.61
993 1053 0.188587 TGAGTGAGGAGTGAGTGGGT 59.811 55.000 0.00 0.00 0.00 4.51
1583 1652 0.525242 TTTGTTGCACGCTCACAAGC 60.525 50.000 1.53 0.00 45.56 4.01
1590 1659 2.031012 CGCTCACAAGCTCACCCA 59.969 61.111 0.00 0.00 46.91 4.51
1595 1664 1.669115 CACAAGCTCACCCACTCCG 60.669 63.158 0.00 0.00 0.00 4.63
1597 1666 1.194781 ACAAGCTCACCCACTCCGAT 61.195 55.000 0.00 0.00 0.00 4.18
1599 1668 0.693049 AAGCTCACCCACTCCGATTT 59.307 50.000 0.00 0.00 0.00 2.17
1600 1669 0.036010 AGCTCACCCACTCCGATTTG 60.036 55.000 0.00 0.00 0.00 2.32
1681 1763 3.306780 GCAGCTCAGGAGTTACAAGGTAA 60.307 47.826 0.00 0.00 0.00 2.85
1682 1764 4.624125 GCAGCTCAGGAGTTACAAGGTAAT 60.624 45.833 0.00 0.00 0.00 1.89
1683 1765 5.395324 GCAGCTCAGGAGTTACAAGGTAATA 60.395 44.000 0.00 0.00 0.00 0.98
1684 1766 6.043411 CAGCTCAGGAGTTACAAGGTAATAC 58.957 44.000 0.00 0.00 0.00 1.89
1685 1767 5.958987 AGCTCAGGAGTTACAAGGTAATACT 59.041 40.000 0.00 0.00 0.00 2.12
1692 1774 6.556974 AGTTACAAGGTAATACTCCTTCCC 57.443 41.667 0.00 0.00 42.57 3.97
1693 1775 6.027482 AGTTACAAGGTAATACTCCTTCCCA 58.973 40.000 0.00 0.00 42.57 4.37
1694 1776 6.502863 AGTTACAAGGTAATACTCCTTCCCAA 59.497 38.462 0.00 0.00 42.57 4.12
1695 1777 5.175388 ACAAGGTAATACTCCTTCCCAAC 57.825 43.478 0.00 0.00 42.57 3.77
1696 1778 4.850386 ACAAGGTAATACTCCTTCCCAACT 59.150 41.667 0.00 0.00 42.57 3.16
1699 1808 6.809976 AGGTAATACTCCTTCCCAACTAAG 57.190 41.667 0.00 0.00 30.18 2.18
1709 1818 6.947464 TCCTTCCCAACTAAGTAAATCTCAG 58.053 40.000 0.00 0.00 0.00 3.35
1717 1826 7.064728 CCAACTAAGTAAATCTCAGGTTGCTAC 59.935 40.741 0.00 0.00 33.26 3.58
1727 1836 3.188786 GTTGCTACGCAGGCTCGG 61.189 66.667 10.29 0.00 40.61 4.63
1736 1845 1.519719 GCAGGCTCGGTCAAGAGAT 59.480 57.895 0.00 0.00 40.57 2.75
1740 1849 1.205893 AGGCTCGGTCAAGAGATGAAC 59.794 52.381 0.00 0.00 42.69 3.18
1744 1853 3.615110 GCTCGGTCAAGAGATGAACTTCA 60.615 47.826 0.00 0.00 44.03 3.02
1783 1892 5.095490 CCACTTCTTGTCGATTTTTATGCC 58.905 41.667 0.00 0.00 0.00 4.40
1970 2079 2.485124 GGTCTGCTATTGCTGATGAGCT 60.485 50.000 5.57 0.00 46.12 4.09
2089 2201 3.173953 AGTTCTGCCCAATCAAATGGA 57.826 42.857 0.00 0.00 43.54 3.41
2091 2203 1.462616 TCTGCCCAATCAAATGGACG 58.537 50.000 0.00 0.00 43.54 4.79
2096 2208 1.134946 CCCAATCAAATGGACGCCTTC 59.865 52.381 0.00 0.00 43.54 3.46
2101 2213 0.804989 CAAATGGACGCCTTCTCACC 59.195 55.000 0.00 0.00 0.00 4.02
2120 2232 2.287788 ACCGCTTCATCTTGCACAAAAG 60.288 45.455 0.00 0.00 0.00 2.27
2127 2239 6.579666 TTCATCTTGCACAAAAGCTTATCT 57.420 33.333 0.00 0.00 34.99 1.98
2298 2419 3.706389 TTCCATCTATCTCACCTCCCA 57.294 47.619 0.00 0.00 0.00 4.37
2332 2453 1.952296 CAATGCCTATTCCCTGCTGAC 59.048 52.381 0.00 0.00 0.00 3.51
2453 2574 0.946221 CTCGTTGTCTGCCACCTCAC 60.946 60.000 0.00 0.00 0.00 3.51
2542 2666 0.030705 AATAGCTCCTCCCCAGCTCA 60.031 55.000 0.00 0.00 44.25 4.26
2634 2758 8.043429 ACTGGTATCCATGTAGTAGTAGTAGT 57.957 38.462 0.00 0.00 30.82 2.73
2688 2812 1.778591 CGCGCATTTTTCGTTTTCTGT 59.221 42.857 8.75 0.00 0.00 3.41
2695 2819 6.566065 CGCATTTTTCGTTTTCTGTGATTTTC 59.434 34.615 0.00 0.00 0.00 2.29
2697 2821 7.789302 GCATTTTTCGTTTTCTGTGATTTTCTC 59.211 33.333 0.00 0.00 0.00 2.87
2776 2900 0.250727 TAAGCCTGCCAGTGACAACC 60.251 55.000 0.00 0.00 0.00 3.77
2913 3042 0.468226 AGTTTTGCAGACCTGACGGA 59.532 50.000 0.47 0.00 0.00 4.69
2916 3045 0.036388 TTTGCAGACCTGACGGATCC 60.036 55.000 0.00 0.00 0.00 3.36
2940 3069 0.179145 GCTGTGTGATGCAGGCATTC 60.179 55.000 8.34 5.93 36.70 2.67
3067 3196 2.750237 CCCGGCACTAAGGTTGCC 60.750 66.667 0.00 3.13 44.69 4.52
3068 3197 2.750237 CCGGCACTAAGGTTGCCC 60.750 66.667 7.76 0.00 45.30 5.36
3083 3212 3.320826 GGTTGCCCAATTTGTAACTGACT 59.679 43.478 5.91 0.00 0.00 3.41
3152 3281 1.078848 ATCTCCGACTTGCTGTGGC 60.079 57.895 0.00 0.00 39.26 5.01
3154 3283 3.865929 CTCCGACTTGCTGTGGCGT 62.866 63.158 0.00 0.00 42.25 5.68
3200 3329 1.966493 GCACACCGCATTGTACTCCG 61.966 60.000 0.00 0.00 41.79 4.63
3264 3393 3.311871 CAGCCTGTGATTGCAAGAGTATC 59.688 47.826 4.94 0.00 0.00 2.24
3278 3407 4.744795 AGAGTATCCCAGTTAAGCTGTG 57.255 45.455 0.00 0.00 43.55 3.66
3279 3408 4.097418 AGAGTATCCCAGTTAAGCTGTGT 58.903 43.478 0.00 0.00 43.55 3.72
3280 3409 5.269991 AGAGTATCCCAGTTAAGCTGTGTA 58.730 41.667 0.00 0.00 43.55 2.90
3281 3410 5.361285 AGAGTATCCCAGTTAAGCTGTGTAG 59.639 44.000 0.00 0.00 43.55 2.74
3325 3457 3.783191 GCTAGCCTAGCGGTAATATTCC 58.217 50.000 8.18 0.00 42.62 3.01
3326 3458 3.194968 GCTAGCCTAGCGGTAATATTCCA 59.805 47.826 8.18 0.00 42.62 3.53
3327 3459 3.963428 AGCCTAGCGGTAATATTCCAG 57.037 47.619 0.00 0.00 0.00 3.86
3328 3460 3.240302 AGCCTAGCGGTAATATTCCAGT 58.760 45.455 0.00 0.00 0.00 4.00
3329 3461 3.258622 AGCCTAGCGGTAATATTCCAGTC 59.741 47.826 0.00 0.00 0.00 3.51
3330 3462 3.258622 GCCTAGCGGTAATATTCCAGTCT 59.741 47.826 0.00 0.00 0.00 3.24
3406 3541 6.473455 CACAAAAGATCAGCGGGATTTATTTC 59.527 38.462 0.00 0.00 36.00 2.17
3440 3575 7.290061 ACATAAACTATACATCAATGTGCCCT 58.710 34.615 5.89 0.00 41.89 5.19
3443 3578 6.455360 AACTATACATCAATGTGCCCTTTG 57.545 37.500 5.89 0.00 41.89 2.77
3444 3579 3.806625 ATACATCAATGTGCCCTTTGC 57.193 42.857 5.89 0.00 41.89 3.68
3445 3580 1.636148 ACATCAATGTGCCCTTTGCT 58.364 45.000 0.00 0.00 40.03 3.91
3451 3615 5.991933 TCAATGTGCCCTTTGCTTTATAA 57.008 34.783 0.00 0.00 42.00 0.98
3453 3617 6.397272 TCAATGTGCCCTTTGCTTTATAAAG 58.603 36.000 19.08 19.08 42.00 1.85
3495 6299 5.767168 ACTCTCATCCTCAAAACTTTTCAGG 59.233 40.000 0.00 0.00 0.00 3.86
3512 6316 1.405821 CAGGTGTAGTCAGGATCGTCC 59.594 57.143 0.00 0.00 36.58 4.79
3624 6428 8.826241 TGGAACAAGCTGCAAACAGAGAAATG 62.826 42.308 1.02 0.00 40.83 2.32
3699 6505 9.293404 ACCACCAATTGAATGAGATCTATAATG 57.707 33.333 7.12 0.00 0.00 1.90
3791 6597 6.667414 ACCCAAAAATCACTGCAGGAATTATA 59.333 34.615 19.93 0.00 0.00 0.98
3841 6647 3.118531 AGCCACCCAATGTCTTCTCTAT 58.881 45.455 0.00 0.00 0.00 1.98
3892 6698 4.697352 GCCGATTCTAGCATTTCCATGTAT 59.303 41.667 0.00 0.00 32.28 2.29
3893 6699 5.874810 GCCGATTCTAGCATTTCCATGTATA 59.125 40.000 0.00 0.00 32.28 1.47
3896 6702 7.063898 CCGATTCTAGCATTTCCATGTATACAG 59.936 40.741 11.91 3.82 32.28 2.74
3900 6706 7.791029 TCTAGCATTTCCATGTATACAGAACA 58.209 34.615 11.91 2.93 32.28 3.18
3941 6747 7.401321 ATCAGAACGTGAGGGATAGGAGACT 62.401 48.000 0.00 0.00 41.36 3.24
3942 6748 2.060050 ACGTGAGGGATAGGAGACTG 57.940 55.000 0.00 0.00 43.88 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.493206 GTTTCGTCACAAATTCAACTAAAACTA 57.507 29.630 0.00 0.00 0.00 2.24
17 18 8.024285 TGTTTCGTCACAAATTCAACTAAAACT 58.976 29.630 0.00 0.00 0.00 2.66
18 19 8.099704 GTGTTTCGTCACAAATTCAACTAAAAC 58.900 33.333 0.00 0.00 38.12 2.43
19 20 7.007546 CGTGTTTCGTCACAAATTCAACTAAAA 59.992 33.333 8.28 0.00 38.12 1.52
20 21 6.466413 CGTGTTTCGTCACAAATTCAACTAAA 59.534 34.615 8.28 0.00 38.12 1.85
21 22 5.960683 CGTGTTTCGTCACAAATTCAACTAA 59.039 36.000 8.28 0.00 38.12 2.24
22 23 5.494618 CGTGTTTCGTCACAAATTCAACTA 58.505 37.500 8.28 0.00 38.12 2.24
23 24 4.339429 CGTGTTTCGTCACAAATTCAACT 58.661 39.130 8.28 0.00 38.12 3.16
24 25 3.062124 GCGTGTTTCGTCACAAATTCAAC 60.062 43.478 8.28 0.00 42.13 3.18
25 26 3.102276 GCGTGTTTCGTCACAAATTCAA 58.898 40.909 8.28 0.00 42.13 2.69
26 27 2.539953 GGCGTGTTTCGTCACAAATTCA 60.540 45.455 8.28 0.00 44.22 2.57
27 28 2.041244 GGCGTGTTTCGTCACAAATTC 58.959 47.619 8.28 0.00 44.22 2.17
28 29 1.595976 CGGCGTGTTTCGTCACAAATT 60.596 47.619 0.00 0.00 45.17 1.82
29 30 0.041663 CGGCGTGTTTCGTCACAAAT 60.042 50.000 0.00 0.00 45.17 2.32
30 31 1.082679 TCGGCGTGTTTCGTCACAAA 61.083 50.000 6.85 0.00 45.17 2.83
31 32 1.082679 TTCGGCGTGTTTCGTCACAA 61.083 50.000 6.85 0.00 45.17 3.33
32 33 0.876777 ATTCGGCGTGTTTCGTCACA 60.877 50.000 6.85 0.00 45.17 3.58
33 34 0.450482 CATTCGGCGTGTTTCGTCAC 60.450 55.000 6.85 0.00 45.17 3.67
34 35 0.876777 ACATTCGGCGTGTTTCGTCA 60.877 50.000 6.85 0.00 45.17 4.35
35 36 0.450482 CACATTCGGCGTGTTTCGTC 60.450 55.000 6.85 0.00 42.13 4.20
36 37 1.567537 CACATTCGGCGTGTTTCGT 59.432 52.632 6.85 0.00 42.13 3.85
37 38 1.154488 CCACATTCGGCGTGTTTCG 60.154 57.895 6.85 0.00 43.12 3.46
38 39 1.209127 CCCACATTCGGCGTGTTTC 59.791 57.895 6.85 0.00 32.26 2.78
39 40 2.914908 GCCCACATTCGGCGTGTTT 61.915 57.895 6.85 0.00 36.47 2.83
40 41 3.361977 GCCCACATTCGGCGTGTT 61.362 61.111 6.85 0.00 36.47 3.32
46 47 0.458889 CAAATGCTGCCCACATTCGG 60.459 55.000 0.00 0.00 36.74 4.30
47 48 0.458889 CCAAATGCTGCCCACATTCG 60.459 55.000 0.00 0.00 36.74 3.34
48 49 0.896923 TCCAAATGCTGCCCACATTC 59.103 50.000 0.00 0.00 36.74 2.67
49 50 1.483415 GATCCAAATGCTGCCCACATT 59.517 47.619 0.00 0.00 39.38 2.71
50 51 1.117150 GATCCAAATGCTGCCCACAT 58.883 50.000 0.00 0.00 0.00 3.21
51 52 0.251698 TGATCCAAATGCTGCCCACA 60.252 50.000 0.00 0.00 0.00 4.17
52 53 0.896923 TTGATCCAAATGCTGCCCAC 59.103 50.000 0.00 0.00 0.00 4.61
53 54 1.868713 ATTGATCCAAATGCTGCCCA 58.131 45.000 0.00 0.00 0.00 5.36
54 55 2.940410 CAAATTGATCCAAATGCTGCCC 59.060 45.455 0.00 0.00 0.00 5.36
55 56 2.353579 GCAAATTGATCCAAATGCTGCC 59.646 45.455 0.00 0.00 37.32 4.85
56 57 2.029970 CGCAAATTGATCCAAATGCTGC 59.970 45.455 0.00 0.00 37.78 5.25
57 58 3.255725 ACGCAAATTGATCCAAATGCTG 58.744 40.909 0.00 11.51 37.78 4.41
58 59 3.194116 AGACGCAAATTGATCCAAATGCT 59.806 39.130 0.00 6.16 37.78 3.79
59 60 3.514645 AGACGCAAATTGATCCAAATGC 58.485 40.909 0.00 0.00 37.10 3.56
60 61 7.760131 ATTTAGACGCAAATTGATCCAAATG 57.240 32.000 0.00 0.00 0.00 2.32
70 71 3.509575 TCAGCCCAATTTAGACGCAAATT 59.490 39.130 0.00 0.00 38.37 1.82
71 72 3.088532 TCAGCCCAATTTAGACGCAAAT 58.911 40.909 0.00 0.00 0.00 2.32
72 73 2.509569 TCAGCCCAATTTAGACGCAAA 58.490 42.857 0.00 0.00 0.00 3.68
73 74 2.192664 TCAGCCCAATTTAGACGCAA 57.807 45.000 0.00 0.00 0.00 4.85
74 75 2.192664 TTCAGCCCAATTTAGACGCA 57.807 45.000 0.00 0.00 0.00 5.24
75 76 3.695816 GATTTCAGCCCAATTTAGACGC 58.304 45.455 0.00 0.00 0.00 5.19
76 77 3.621268 TCGATTTCAGCCCAATTTAGACG 59.379 43.478 0.00 0.00 0.00 4.18
77 78 5.296780 TCATCGATTTCAGCCCAATTTAGAC 59.703 40.000 0.00 0.00 0.00 2.59
78 79 5.296780 GTCATCGATTTCAGCCCAATTTAGA 59.703 40.000 0.00 0.00 0.00 2.10
79 80 5.297776 AGTCATCGATTTCAGCCCAATTTAG 59.702 40.000 0.00 0.00 0.00 1.85
80 81 5.192927 AGTCATCGATTTCAGCCCAATTTA 58.807 37.500 0.00 0.00 0.00 1.40
81 82 4.019174 AGTCATCGATTTCAGCCCAATTT 58.981 39.130 0.00 0.00 0.00 1.82
82 83 3.624777 AGTCATCGATTTCAGCCCAATT 58.375 40.909 0.00 0.00 0.00 2.32
83 84 3.287867 AGTCATCGATTTCAGCCCAAT 57.712 42.857 0.00 0.00 0.00 3.16
84 85 2.787473 AGTCATCGATTTCAGCCCAA 57.213 45.000 0.00 0.00 0.00 4.12
85 86 2.103094 CCTAGTCATCGATTTCAGCCCA 59.897 50.000 0.00 0.00 0.00 5.36
86 87 2.548920 CCCTAGTCATCGATTTCAGCCC 60.549 54.545 0.00 0.00 0.00 5.19
87 88 2.548920 CCCCTAGTCATCGATTTCAGCC 60.549 54.545 0.00 0.00 0.00 4.85
88 89 2.365617 TCCCCTAGTCATCGATTTCAGC 59.634 50.000 0.00 0.00 0.00 4.26
89 90 4.281941 TCATCCCCTAGTCATCGATTTCAG 59.718 45.833 0.00 0.00 0.00 3.02
90 91 4.223144 TCATCCCCTAGTCATCGATTTCA 58.777 43.478 0.00 0.00 0.00 2.69
91 92 4.873746 TCATCCCCTAGTCATCGATTTC 57.126 45.455 0.00 0.00 0.00 2.17
92 93 4.656112 AGTTCATCCCCTAGTCATCGATTT 59.344 41.667 0.00 0.00 0.00 2.17
93 94 4.227197 AGTTCATCCCCTAGTCATCGATT 58.773 43.478 0.00 0.00 0.00 3.34
94 95 3.850752 AGTTCATCCCCTAGTCATCGAT 58.149 45.455 0.00 0.00 0.00 3.59
95 96 3.314307 AGTTCATCCCCTAGTCATCGA 57.686 47.619 0.00 0.00 0.00 3.59
96 97 4.021894 CCTAAGTTCATCCCCTAGTCATCG 60.022 50.000 0.00 0.00 0.00 3.84
97 98 4.284746 CCCTAAGTTCATCCCCTAGTCATC 59.715 50.000 0.00 0.00 0.00 2.92
98 99 4.235372 CCCTAAGTTCATCCCCTAGTCAT 58.765 47.826 0.00 0.00 0.00 3.06
99 100 3.632645 CCCCTAAGTTCATCCCCTAGTCA 60.633 52.174 0.00 0.00 0.00 3.41
100 101 2.973406 CCCCTAAGTTCATCCCCTAGTC 59.027 54.545 0.00 0.00 0.00 2.59
101 102 2.964803 GCCCCTAAGTTCATCCCCTAGT 60.965 54.545 0.00 0.00 0.00 2.57
102 103 1.700186 GCCCCTAAGTTCATCCCCTAG 59.300 57.143 0.00 0.00 0.00 3.02
103 104 1.697945 GGCCCCTAAGTTCATCCCCTA 60.698 57.143 0.00 0.00 0.00 3.53
104 105 0.994050 GGCCCCTAAGTTCATCCCCT 60.994 60.000 0.00 0.00 0.00 4.79
105 106 1.537172 GGCCCCTAAGTTCATCCCC 59.463 63.158 0.00 0.00 0.00 4.81
106 107 1.148498 CGGCCCCTAAGTTCATCCC 59.852 63.158 0.00 0.00 0.00 3.85
107 108 1.148498 CCGGCCCCTAAGTTCATCC 59.852 63.158 0.00 0.00 0.00 3.51
108 109 1.526225 GCCGGCCCCTAAGTTCATC 60.526 63.158 18.11 0.00 0.00 2.92
109 110 2.595655 GCCGGCCCCTAAGTTCAT 59.404 61.111 18.11 0.00 0.00 2.57
110 111 4.090588 CGCCGGCCCCTAAGTTCA 62.091 66.667 23.46 0.00 0.00 3.18
111 112 4.851179 CCGCCGGCCCCTAAGTTC 62.851 72.222 23.46 0.00 0.00 3.01
134 135 4.754667 GACGTGGGGCTCGGGTTC 62.755 72.222 0.00 0.00 0.00 3.62
138 139 3.659089 AAATCGACGTGGGGCTCGG 62.659 63.158 0.00 0.00 0.00 4.63
139 140 0.458889 TAAAATCGACGTGGGGCTCG 60.459 55.000 0.00 0.00 0.00 5.03
140 141 1.865340 GATAAAATCGACGTGGGGCTC 59.135 52.381 0.00 0.00 0.00 4.70
141 142 1.949465 GATAAAATCGACGTGGGGCT 58.051 50.000 0.00 0.00 0.00 5.19
162 163 1.026718 GTTGTCTGAGGGCCAATCGG 61.027 60.000 6.18 7.45 0.00 4.18
163 164 1.361668 CGTTGTCTGAGGGCCAATCG 61.362 60.000 6.18 0.00 0.00 3.34
164 165 0.321653 ACGTTGTCTGAGGGCCAATC 60.322 55.000 6.18 1.94 0.00 2.67
165 166 0.110486 AACGTTGTCTGAGGGCCAAT 59.890 50.000 6.18 0.00 0.00 3.16
166 167 0.759959 TAACGTTGTCTGAGGGCCAA 59.240 50.000 11.99 0.00 0.00 4.52
167 168 0.981183 ATAACGTTGTCTGAGGGCCA 59.019 50.000 11.99 0.00 0.00 5.36
168 169 2.109425 AATAACGTTGTCTGAGGGCC 57.891 50.000 11.99 0.00 0.00 5.80
169 170 5.616488 TTAAAATAACGTTGTCTGAGGGC 57.384 39.130 11.99 0.00 0.00 5.19
170 171 5.391629 GGCTTAAAATAACGTTGTCTGAGGG 60.392 44.000 11.99 0.00 0.00 4.30
171 172 5.411669 AGGCTTAAAATAACGTTGTCTGAGG 59.588 40.000 11.99 0.00 0.00 3.86
172 173 6.369065 AGAGGCTTAAAATAACGTTGTCTGAG 59.631 38.462 11.99 3.07 0.00 3.35
173 174 6.228258 AGAGGCTTAAAATAACGTTGTCTGA 58.772 36.000 11.99 0.00 0.00 3.27
174 175 6.481954 AGAGGCTTAAAATAACGTTGTCTG 57.518 37.500 11.99 0.00 0.00 3.51
175 176 7.280205 CCATAGAGGCTTAAAATAACGTTGTCT 59.720 37.037 11.99 0.00 0.00 3.41
176 177 7.407337 CCATAGAGGCTTAAAATAACGTTGTC 58.593 38.462 11.99 0.00 0.00 3.18
177 178 6.317893 CCCATAGAGGCTTAAAATAACGTTGT 59.682 38.462 11.99 0.00 35.39 3.32
178 179 6.238648 CCCCATAGAGGCTTAAAATAACGTTG 60.239 42.308 11.99 0.00 35.39 4.10
179 180 5.826208 CCCCATAGAGGCTTAAAATAACGTT 59.174 40.000 5.88 5.88 35.39 3.99
180 181 5.374071 CCCCATAGAGGCTTAAAATAACGT 58.626 41.667 0.00 0.00 35.39 3.99
181 182 5.941948 CCCCATAGAGGCTTAAAATAACG 57.058 43.478 0.00 0.00 35.39 3.18
193 194 2.421739 CGTTCGGCCCCATAGAGG 59.578 66.667 0.00 0.00 37.03 3.69
194 195 1.472662 ATCCGTTCGGCCCCATAGAG 61.473 60.000 6.35 0.00 0.00 2.43
195 196 1.458777 ATCCGTTCGGCCCCATAGA 60.459 57.895 6.35 0.00 0.00 1.98
196 197 1.301716 CATCCGTTCGGCCCCATAG 60.302 63.158 6.35 0.00 0.00 2.23
197 198 2.813726 CCATCCGTTCGGCCCCATA 61.814 63.158 6.35 0.00 0.00 2.74
198 199 4.189580 CCATCCGTTCGGCCCCAT 62.190 66.667 6.35 0.00 0.00 4.00
200 201 4.547367 CTCCATCCGTTCGGCCCC 62.547 72.222 6.35 0.00 0.00 5.80
201 202 2.808206 ATCTCCATCCGTTCGGCCC 61.808 63.158 6.35 0.00 0.00 5.80
202 203 1.595382 CATCTCCATCCGTTCGGCC 60.595 63.158 6.35 0.00 0.00 6.13
203 204 0.462047 AACATCTCCATCCGTTCGGC 60.462 55.000 6.35 0.00 0.00 5.54
204 205 1.571919 GAACATCTCCATCCGTTCGG 58.428 55.000 4.74 4.74 0.00 4.30
205 206 1.571919 GGAACATCTCCATCCGTTCG 58.428 55.000 0.00 0.00 44.67 3.95
224 225 0.107017 AAGCAAGGATGACCCGATGG 60.107 55.000 0.00 0.00 40.87 3.51
229 230 0.811281 CCGAAAAGCAAGGATGACCC 59.189 55.000 0.00 0.00 36.73 4.46
238 239 2.727544 GCTGGTGCCGAAAAGCAA 59.272 55.556 0.00 0.00 46.19 3.91
314 317 2.115911 GTGAACCACAACGGGCACA 61.116 57.895 0.00 0.00 41.40 4.57
315 318 2.115911 TGTGAACCACAACGGGCAC 61.116 57.895 0.00 0.00 41.69 5.01
316 319 2.115911 GTGTGAACCACAACGGGCA 61.116 57.895 0.95 0.00 46.28 5.36
317 320 2.719354 GTGTGAACCACAACGGGC 59.281 61.111 0.95 0.00 46.28 6.13
392 395 1.747355 AGCAAGGCAAATCATTCCGAG 59.253 47.619 0.00 0.00 0.00 4.63
401 404 2.880443 TCTCCTCAAAGCAAGGCAAAT 58.120 42.857 0.00 0.00 33.65 2.32
407 410 1.936547 GCCGTATCTCCTCAAAGCAAG 59.063 52.381 0.00 0.00 0.00 4.01
466 490 0.165295 CATTCAGACGTGCTGTGCAG 59.835 55.000 0.00 0.00 45.14 4.41
488 512 4.681978 GCCCGCTCAACAGTCCGT 62.682 66.667 0.00 0.00 0.00 4.69
510 534 2.433838 CAGCGAGTGCCACAGAGG 60.434 66.667 0.00 0.00 44.31 3.69
541 565 1.231221 CTAGCGAGCAGGTATCGAGT 58.769 55.000 0.00 0.00 42.76 4.18
553 577 4.906792 GGCTGCCTGGCTAGCGAG 62.907 72.222 25.81 19.00 40.78 5.03
594 619 7.960195 CGGTGGAATTTTTATTTTATTTGTGGC 59.040 33.333 0.00 0.00 0.00 5.01
655 690 3.058160 CGAGGCCAGCCAAGGTTG 61.058 66.667 12.03 0.00 38.92 3.77
703 738 1.268283 AAAAGGGAGGAGCGAGAGGG 61.268 60.000 0.00 0.00 0.00 4.30
710 754 3.020274 GAGAATCCAAAAAGGGAGGAGC 58.980 50.000 0.00 0.00 41.08 4.70
731 775 1.895707 GCGATGCCTCAAGATGGGG 60.896 63.158 0.00 0.00 42.32 4.96
812 856 4.590647 TGAAGAAGAAGAAGAAGGAGCAGA 59.409 41.667 0.00 0.00 0.00 4.26
815 867 3.684305 GCTGAAGAAGAAGAAGAAGGAGC 59.316 47.826 0.00 0.00 0.00 4.70
818 870 4.640364 ACAGCTGAAGAAGAAGAAGAAGG 58.360 43.478 23.35 0.00 0.00 3.46
877 929 4.988598 ACGCCGCTCCACCACTTG 62.989 66.667 0.00 0.00 0.00 3.16
878 930 4.681978 GACGCCGCTCCACCACTT 62.682 66.667 0.00 0.00 0.00 3.16
986 1046 0.984230 TCCCATTCACTCACCCACTC 59.016 55.000 0.00 0.00 0.00 3.51
987 1047 1.073923 GTTCCCATTCACTCACCCACT 59.926 52.381 0.00 0.00 0.00 4.00
988 1048 1.073923 AGTTCCCATTCACTCACCCAC 59.926 52.381 0.00 0.00 0.00 4.61
989 1049 1.351017 GAGTTCCCATTCACTCACCCA 59.649 52.381 0.00 0.00 39.49 4.51
990 1050 1.351017 TGAGTTCCCATTCACTCACCC 59.649 52.381 0.00 0.00 43.63 4.61
991 1051 2.616510 CCTGAGTTCCCATTCACTCACC 60.617 54.545 0.00 0.00 43.63 4.02
992 1052 2.704572 CCTGAGTTCCCATTCACTCAC 58.295 52.381 0.00 0.00 43.63 3.51
993 1053 1.003580 GCCTGAGTTCCCATTCACTCA 59.996 52.381 2.23 2.23 45.77 3.41
1467 1533 3.691609 GGTTCTTGATCATCCGCTTCTTT 59.308 43.478 0.00 0.00 0.00 2.52
1538 1604 2.498078 AGAGAGATTTGGGGTCTCGAAC 59.502 50.000 0.00 0.00 45.26 3.95
1583 1652 3.159298 CCAAATCGGAGTGGGTGAG 57.841 57.895 3.16 0.00 36.56 3.51
1590 1659 2.044946 GCCTGCCCAAATCGGAGT 60.045 61.111 0.00 0.00 36.56 3.85
1595 1664 1.800681 GTGTACGCCTGCCCAAATC 59.199 57.895 0.00 0.00 0.00 2.17
1597 1666 2.661840 TTCGTGTACGCCTGCCCAAA 62.662 55.000 0.00 0.00 39.60 3.28
1599 1668 3.617735 TTCGTGTACGCCTGCCCA 61.618 61.111 0.00 0.00 39.60 5.36
1600 1669 3.116531 GTTCGTGTACGCCTGCCC 61.117 66.667 0.00 0.00 39.60 5.36
1681 1763 8.625467 AGATTTACTTAGTTGGGAAGGAGTAT 57.375 34.615 0.00 0.00 0.00 2.12
1682 1764 7.676893 TGAGATTTACTTAGTTGGGAAGGAGTA 59.323 37.037 0.00 0.00 0.00 2.59
1683 1765 6.500751 TGAGATTTACTTAGTTGGGAAGGAGT 59.499 38.462 0.00 0.00 0.00 3.85
1684 1766 6.947464 TGAGATTTACTTAGTTGGGAAGGAG 58.053 40.000 0.00 0.00 0.00 3.69
1685 1767 6.070194 CCTGAGATTTACTTAGTTGGGAAGGA 60.070 42.308 0.00 0.00 31.41 3.36
1687 1769 6.712276 ACCTGAGATTTACTTAGTTGGGAAG 58.288 40.000 0.00 0.00 31.41 3.46
1688 1770 6.697641 ACCTGAGATTTACTTAGTTGGGAA 57.302 37.500 0.00 0.00 31.41 3.97
1689 1771 6.472887 CAACCTGAGATTTACTTAGTTGGGA 58.527 40.000 0.00 0.00 33.57 4.37
1691 1773 5.940470 AGCAACCTGAGATTTACTTAGTTGG 59.060 40.000 0.00 0.00 35.59 3.77
1692 1774 7.201444 CGTAGCAACCTGAGATTTACTTAGTTG 60.201 40.741 0.00 0.00 36.82 3.16
1693 1775 6.812160 CGTAGCAACCTGAGATTTACTTAGTT 59.188 38.462 0.00 0.00 31.41 2.24
1694 1776 6.331061 CGTAGCAACCTGAGATTTACTTAGT 58.669 40.000 0.00 0.00 31.41 2.24
1695 1777 6.814076 CGTAGCAACCTGAGATTTACTTAG 57.186 41.667 0.00 0.00 32.87 2.18
1717 1826 2.290122 ATCTCTTGACCGAGCCTGCG 62.290 60.000 0.00 0.00 0.00 5.18
1970 2079 2.341846 AAGAAAGAAACACAGGCCGA 57.658 45.000 0.00 0.00 0.00 5.54
2089 2201 2.048127 GAAGCGGTGAGAAGGCGT 60.048 61.111 0.00 0.00 0.00 5.68
2091 2203 0.107945 AGATGAAGCGGTGAGAAGGC 60.108 55.000 0.00 0.00 0.00 4.35
2096 2208 0.445436 GTGCAAGATGAAGCGGTGAG 59.555 55.000 0.00 0.00 0.00 3.51
2101 2213 1.717645 GCTTTTGTGCAAGATGAAGCG 59.282 47.619 0.00 0.00 31.51 4.68
2120 2232 7.948278 ATTGACATAAGGTAACGAGATAAGC 57.052 36.000 0.00 0.00 46.39 3.09
2192 2305 6.155565 TCCACGATTGTATCTTCCTTAGGAAA 59.844 38.462 15.17 6.74 41.54 3.13
2193 2306 5.659525 TCCACGATTGTATCTTCCTTAGGAA 59.340 40.000 13.60 13.60 39.66 3.36
2194 2307 5.205821 TCCACGATTGTATCTTCCTTAGGA 58.794 41.667 0.00 0.00 0.00 2.94
2195 2308 5.531122 TCCACGATTGTATCTTCCTTAGG 57.469 43.478 0.00 0.00 0.00 2.69
2298 2419 6.949117 ATAGGCATTGACTATTCCTCTGAT 57.051 37.500 6.19 0.00 27.85 2.90
2382 2503 8.851541 ATTTTAGTTCCATCCAGTACGTTAAA 57.148 30.769 0.00 0.00 0.00 1.52
2383 2504 8.851541 AATTTTAGTTCCATCCAGTACGTTAA 57.148 30.769 0.00 0.00 0.00 2.01
2384 2505 9.590451 CTAATTTTAGTTCCATCCAGTACGTTA 57.410 33.333 0.00 0.00 0.00 3.18
2385 2506 7.551617 CCTAATTTTAGTTCCATCCAGTACGTT 59.448 37.037 0.00 0.00 0.00 3.99
2386 2507 7.046033 CCTAATTTTAGTTCCATCCAGTACGT 58.954 38.462 0.00 0.00 0.00 3.57
2387 2508 6.482308 CCCTAATTTTAGTTCCATCCAGTACG 59.518 42.308 0.00 0.00 0.00 3.67
2388 2509 6.262496 GCCCTAATTTTAGTTCCATCCAGTAC 59.738 42.308 0.00 0.00 0.00 2.73
2453 2574 6.176183 AGTAGTGAATTGGTGATGAAGGAAG 58.824 40.000 0.00 0.00 0.00 3.46
2513 2634 6.494952 TGGGGAGGAGCTATTATCTTACTAG 58.505 44.000 0.00 0.00 0.00 2.57
2542 2666 9.512588 CTGGAGGAGTATTTATTTATCAGCATT 57.487 33.333 0.00 0.00 0.00 3.56
2572 2696 0.449388 GCTGAAAGAGATGGGCAACG 59.551 55.000 0.00 0.00 34.07 4.10
2671 2795 7.621102 AGAAAATCACAGAAAACGAAAAATGC 58.379 30.769 0.00 0.00 0.00 3.56
2688 2812 7.201626 GCACGAGACTAGTACTAGAGAAAATCA 60.202 40.741 31.93 0.00 36.97 2.57
2695 2819 4.053295 GGAGCACGAGACTAGTACTAGAG 58.947 52.174 31.93 21.35 36.97 2.43
2697 2821 4.062677 AGGAGCACGAGACTAGTACTAG 57.937 50.000 25.30 25.30 39.04 2.57
2776 2900 3.681897 CACAAATCTCACCTTTCGGAGAG 59.318 47.826 0.00 0.15 45.95 3.20
2830 2954 3.943137 TAGGCAGTGGGGGTCAGGG 62.943 68.421 0.00 0.00 0.00 4.45
2913 3042 2.165641 CTGCATCACACAGCAATTGGAT 59.834 45.455 7.72 0.00 40.73 3.41
2916 3045 1.990799 CCTGCATCACACAGCAATTG 58.009 50.000 0.00 0.00 40.73 2.32
2940 3069 3.345808 CAGTGCACCACCGGTTCG 61.346 66.667 14.63 0.00 34.49 3.95
3045 3174 1.196104 AACCTTAGTGCCGGGCAGTA 61.196 55.000 28.36 28.36 42.60 2.74
3067 3196 5.929992 TCGGAGTAAGTCAGTTACAAATTGG 59.070 40.000 5.17 0.00 43.26 3.16
3068 3197 7.416154 TTCGGAGTAAGTCAGTTACAAATTG 57.584 36.000 5.17 0.00 43.26 2.32
3083 3212 9.362539 CTACTAGCTAAATGTTTTTCGGAGTAA 57.637 33.333 0.00 0.00 0.00 2.24
3152 3281 0.847670 CAATTGCGCATTGCCATACG 59.152 50.000 12.75 0.00 45.60 3.06
3278 3407 7.907214 ATTCTGTTTCCAGATACAACACTAC 57.093 36.000 0.00 0.00 46.80 2.73
3279 3408 7.094805 GCAATTCTGTTTCCAGATACAACACTA 60.095 37.037 0.00 0.00 46.80 2.74
3280 3409 6.294176 GCAATTCTGTTTCCAGATACAACACT 60.294 38.462 0.00 0.00 46.80 3.55
3281 3410 5.858581 GCAATTCTGTTTCCAGATACAACAC 59.141 40.000 0.00 0.00 46.80 3.32
3318 3450 5.707066 AGAGCTGGAAAGACTGGAATATT 57.293 39.130 0.00 0.00 0.00 1.28
3322 3454 3.864789 AAAGAGCTGGAAAGACTGGAA 57.135 42.857 0.00 0.00 0.00 3.53
3323 3455 3.008049 GGTAAAGAGCTGGAAAGACTGGA 59.992 47.826 0.00 0.00 0.00 3.86
3324 3456 3.244561 TGGTAAAGAGCTGGAAAGACTGG 60.245 47.826 0.00 0.00 0.00 4.00
3325 3457 4.008074 TGGTAAAGAGCTGGAAAGACTG 57.992 45.455 0.00 0.00 0.00 3.51
3326 3458 4.323868 GGATGGTAAAGAGCTGGAAAGACT 60.324 45.833 0.00 0.00 0.00 3.24
3327 3459 3.942115 GGATGGTAAAGAGCTGGAAAGAC 59.058 47.826 0.00 0.00 0.00 3.01
3328 3460 3.054361 GGGATGGTAAAGAGCTGGAAAGA 60.054 47.826 0.00 0.00 0.00 2.52
3329 3461 3.054065 AGGGATGGTAAAGAGCTGGAAAG 60.054 47.826 0.00 0.00 0.00 2.62
3330 3462 2.919602 AGGGATGGTAAAGAGCTGGAAA 59.080 45.455 0.00 0.00 0.00 3.13
3376 3511 1.200716 CCGCTGATCTTTTGTGTGCAT 59.799 47.619 0.00 0.00 0.00 3.96
3378 3513 0.109597 CCCGCTGATCTTTTGTGTGC 60.110 55.000 0.00 0.00 0.00 4.57
3440 3575 9.357161 TCACCTAGTTTTCCTTTATAAAGCAAA 57.643 29.630 18.18 13.95 34.69 3.68
3477 6281 6.365520 ACTACACCTGAAAAGTTTTGAGGAT 58.634 36.000 32.51 23.24 0.00 3.24
3479 6283 5.588648 TGACTACACCTGAAAAGTTTTGAGG 59.411 40.000 26.54 26.54 0.00 3.86
3512 6316 5.712446 TGATCTTAGATTGATACTCCCCGAG 59.288 44.000 0.00 0.00 35.52 4.63
3647 6451 7.615365 TGCCAATCTTAGATTTATGTTGACCTT 59.385 33.333 4.51 0.00 0.00 3.50
3670 6476 2.170166 TCTCATTCAATTGGTGGTGCC 58.830 47.619 5.42 0.00 37.90 5.01
3699 6505 7.492352 TTGAGGTAAAGTACAGCTCTTTTTC 57.508 36.000 10.97 2.70 40.41 2.29
3701 6507 7.497925 CTTTGAGGTAAAGTACAGCTCTTTT 57.502 36.000 10.97 0.00 40.71 2.27
3758 6564 4.680440 GCAGTGATTTTTGGGTTGTCAACT 60.680 41.667 15.17 0.00 0.00 3.16
3766 6572 2.380064 TCCTGCAGTGATTTTTGGGT 57.620 45.000 13.81 0.00 0.00 4.51
3791 6597 2.158325 TGTTCTTTCATCCCCAAGGCTT 60.158 45.455 0.00 0.00 0.00 4.35
3841 6647 4.487714 AGCGAGGATTTGAAGGATACAA 57.512 40.909 0.00 0.00 41.41 2.41
3914 6720 3.133003 CCTATCCCTCACGTTCTGATTGT 59.867 47.826 0.00 0.00 0.00 2.71
3915 6721 3.384789 TCCTATCCCTCACGTTCTGATTG 59.615 47.826 0.00 0.00 0.00 2.67
3916 6722 3.639094 CTCCTATCCCTCACGTTCTGATT 59.361 47.826 0.00 0.00 0.00 2.57
3917 6723 3.117474 TCTCCTATCCCTCACGTTCTGAT 60.117 47.826 0.00 0.00 0.00 2.90
3941 6747 6.096141 GGAAATGTCTCTGTGATCTCTACTCA 59.904 42.308 0.00 0.00 0.00 3.41
3942 6748 6.096141 TGGAAATGTCTCTGTGATCTCTACTC 59.904 42.308 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.