Multiple sequence alignment - TraesCS7D01G209000

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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 TraesCS7D01G209000 chr7D 100.000 3666 0 0 1 3666 167227162 167230827 0.000000e+00 6770.0
1 TraesCS7D01G209000 chr7D 90.741 54 1 3 499 551 610697287 610697337 6.570000e-08 69.4
2 TraesCS7D01G209000 chr7A 97.084 2126 47 11 555 2674 168811852 168813968 0.000000e+00 3568.0
3 TraesCS7D01G209000 chr7A 87.719 57 5 1 491 547 694257618 694257672 8.500000e-07 65.8
4 TraesCS7D01G209000 chr7B 95.904 2075 55 9 594 2643 131376198 131378267 0.000000e+00 3334.0
5 TraesCS7D01G209000 chr7B 91.765 85 6 1 281 365 131375848 131375931 2.310000e-22 117.0
6 TraesCS7D01G209000 chr5A 96.134 983 32 3 2690 3666 28764758 28763776 0.000000e+00 1600.0
7 TraesCS7D01G209000 chr6B 93.516 987 57 4 2685 3665 134684699 134683714 0.000000e+00 1461.0
8 TraesCS7D01G209000 chr6B 77.371 464 78 21 1142 1584 572393743 572393286 2.190000e-62 250.0
9 TraesCS7D01G209000 chr6B 87.425 167 19 2 2215 2380 572392592 572392427 1.340000e-44 191.0
10 TraesCS7D01G209000 chr3B 92.199 987 71 3 2685 3665 224934493 224933507 0.000000e+00 1391.0
11 TraesCS7D01G209000 chr3B 85.606 132 15 2 1735 1862 11577032 11577163 6.390000e-28 135.0
12 TraesCS7D01G209000 chr2B 91.768 984 74 4 2689 3665 602108118 602107135 0.000000e+00 1362.0
13 TraesCS7D01G209000 chr3A 90.549 984 87 3 2688 3665 458916786 458915803 0.000000e+00 1297.0
14 TraesCS7D01G209000 chr5B 90.293 989 87 6 2686 3666 65515203 65516190 0.000000e+00 1286.0
15 TraesCS7D01G209000 chr5B 89.501 981 97 3 2692 3666 196249075 196248095 0.000000e+00 1236.0
16 TraesCS7D01G209000 chr2A 91.569 854 66 3 2818 3665 706285407 706286260 0.000000e+00 1173.0
17 TraesCS7D01G209000 chr4A 90.725 593 50 3 3079 3666 688709773 688709181 0.000000e+00 785.0
18 TraesCS7D01G209000 chr4A 91.525 354 29 1 2689 3041 688710122 688709769 1.530000e-133 486.0
19 TraesCS7D01G209000 chr4A 95.588 136 4 2 2234 2368 580734809 580734675 2.220000e-52 217.0
20 TraesCS7D01G209000 chr6D 88.701 177 14 5 2215 2390 382588787 382588616 1.030000e-50 211.0
21 TraesCS7D01G209000 chr4D 94.853 136 5 2 2234 2368 21775588 21775454 1.030000e-50 211.0
22 TraesCS7D01G209000 chr4B 94.853 136 5 2 2234 2368 32897830 32897964 1.030000e-50 211.0
23 TraesCS7D01G209000 chr4B 75.457 383 68 12 1138 1508 582158160 582158528 2.930000e-36 163.0
24 TraesCS7D01G209000 chr3D 79.902 204 34 5 1689 1886 193248279 193248077 3.820000e-30 143.0
25 TraesCS7D01G209000 chr3D 86.364 66 3 3 497 558 591618638 591618701 2.360000e-07 67.6
26 TraesCS7D01G209000 chr1B 90.741 54 3 1 504 557 579608069 579608120 1.830000e-08 71.3
27 TraesCS7D01G209000 chr1B 87.931 58 4 2 501 557 411211871 411211926 8.500000e-07 65.8
28 TraesCS7D01G209000 chr5D 86.885 61 6 2 497 557 416973295 416973237 2.360000e-07 67.6
29 TraesCS7D01G209000 chr5D 89.091 55 4 1 497 551 482013897 482013949 2.360000e-07 67.6
30 TraesCS7D01G209000 chr5D 88.889 54 4 1 493 546 549851441 549851390 8.500000e-07 65.8
31 TraesCS7D01G209000 chr2D 84.058 69 6 4 479 547 100900205 100900268 1.100000e-05 62.1


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 TraesCS7D01G209000 chr7D 167227162 167230827 3665 False 6770.0 6770 100.0000 1 3666 1 chr7D.!!$F1 3665
1 TraesCS7D01G209000 chr7A 168811852 168813968 2116 False 3568.0 3568 97.0840 555 2674 1 chr7A.!!$F1 2119
2 TraesCS7D01G209000 chr7B 131375848 131378267 2419 False 1725.5 3334 93.8345 281 2643 2 chr7B.!!$F1 2362
3 TraesCS7D01G209000 chr5A 28763776 28764758 982 True 1600.0 1600 96.1340 2690 3666 1 chr5A.!!$R1 976
4 TraesCS7D01G209000 chr6B 134683714 134684699 985 True 1461.0 1461 93.5160 2685 3665 1 chr6B.!!$R1 980
5 TraesCS7D01G209000 chr6B 572392427 572393743 1316 True 220.5 250 82.3980 1142 2380 2 chr6B.!!$R2 1238
6 TraesCS7D01G209000 chr3B 224933507 224934493 986 True 1391.0 1391 92.1990 2685 3665 1 chr3B.!!$R1 980
7 TraesCS7D01G209000 chr2B 602107135 602108118 983 True 1362.0 1362 91.7680 2689 3665 1 chr2B.!!$R1 976
8 TraesCS7D01G209000 chr3A 458915803 458916786 983 True 1297.0 1297 90.5490 2688 3665 1 chr3A.!!$R1 977
9 TraesCS7D01G209000 chr5B 65515203 65516190 987 False 1286.0 1286 90.2930 2686 3666 1 chr5B.!!$F1 980
10 TraesCS7D01G209000 chr5B 196248095 196249075 980 True 1236.0 1236 89.5010 2692 3666 1 chr5B.!!$R1 974
11 TraesCS7D01G209000 chr2A 706285407 706286260 853 False 1173.0 1173 91.5690 2818 3665 1 chr2A.!!$F1 847
12 TraesCS7D01G209000 chr4A 688709181 688710122 941 True 635.5 785 91.1250 2689 3666 2 chr4A.!!$R2 977

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
692 799 0.108756 ACTTCTTTAGTCTCGGCCGC 60.109 55.0 23.51 6.72 28.23 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2683 2928 1.470979 GCTCGAAGTGGAATCGCCTAA 60.471 52.381 0.0 0.0 40.04 2.69 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
31 32 7.745620 CCAGACCATGGGTTAATAAATACTC 57.254 40.000 18.09 0.00 46.36 2.59
32 33 6.715264 CCAGACCATGGGTTAATAAATACTCC 59.285 42.308 18.09 0.00 46.36 3.85
33 34 6.715264 CAGACCATGGGTTAATAAATACTCCC 59.285 42.308 18.09 0.00 35.25 4.30
34 35 6.624021 AGACCATGGGTTAATAAATACTCCCT 59.376 38.462 18.09 0.00 35.25 4.20
35 36 6.849151 ACCATGGGTTAATAAATACTCCCTC 58.151 40.000 18.09 0.00 36.23 4.30
36 37 6.391649 ACCATGGGTTAATAAATACTCCCTCA 59.608 38.462 18.09 0.00 36.23 3.86
37 38 6.942576 CCATGGGTTAATAAATACTCCCTCAG 59.057 42.308 2.85 0.00 36.23 3.35
38 39 7.421382 CCATGGGTTAATAAATACTCCCTCAGT 60.421 40.741 2.85 0.00 39.41 3.41
39 40 7.519347 TGGGTTAATAAATACTCCCTCAGTT 57.481 36.000 0.00 0.00 36.43 3.16
40 41 7.935405 TGGGTTAATAAATACTCCCTCAGTTT 58.065 34.615 0.00 0.00 36.43 2.66
41 42 8.050930 TGGGTTAATAAATACTCCCTCAGTTTC 58.949 37.037 0.00 0.00 36.43 2.78
42 43 8.050930 GGGTTAATAAATACTCCCTCAGTTTCA 58.949 37.037 0.00 0.00 36.43 2.69
43 44 9.457436 GGTTAATAAATACTCCCTCAGTTTCAA 57.543 33.333 0.00 0.00 36.43 2.69
47 48 9.753674 AATAAATACTCCCTCAGTTTCAATTCA 57.246 29.630 0.00 0.00 36.43 2.57
48 49 7.454260 AAATACTCCCTCAGTTTCAATTCAC 57.546 36.000 0.00 0.00 36.43 3.18
49 50 4.437682 ACTCCCTCAGTTTCAATTCACA 57.562 40.909 0.00 0.00 26.56 3.58
50 51 4.792068 ACTCCCTCAGTTTCAATTCACAA 58.208 39.130 0.00 0.00 26.56 3.33
51 52 5.388654 ACTCCCTCAGTTTCAATTCACAAT 58.611 37.500 0.00 0.00 26.56 2.71
52 53 5.242393 ACTCCCTCAGTTTCAATTCACAATG 59.758 40.000 0.00 0.00 26.56 2.82
53 54 5.384336 TCCCTCAGTTTCAATTCACAATGA 58.616 37.500 0.00 0.00 0.00 2.57
54 55 5.474532 TCCCTCAGTTTCAATTCACAATGAG 59.525 40.000 0.00 0.00 34.18 2.90
55 56 5.242393 CCCTCAGTTTCAATTCACAATGAGT 59.758 40.000 0.00 0.00 32.86 3.41
56 57 6.376978 CCTCAGTTTCAATTCACAATGAGTC 58.623 40.000 0.00 0.00 32.86 3.36
57 58 6.206243 CCTCAGTTTCAATTCACAATGAGTCT 59.794 38.462 0.00 0.00 32.86 3.24
58 59 7.255381 CCTCAGTTTCAATTCACAATGAGTCTT 60.255 37.037 0.00 0.00 32.86 3.01
59 60 8.675705 TCAGTTTCAATTCACAATGAGTCTTA 57.324 30.769 0.00 0.00 0.00 2.10
60 61 8.559536 TCAGTTTCAATTCACAATGAGTCTTAC 58.440 33.333 0.00 0.00 0.00 2.34
61 62 8.344831 CAGTTTCAATTCACAATGAGTCTTACA 58.655 33.333 0.00 0.00 0.00 2.41
62 63 9.071276 AGTTTCAATTCACAATGAGTCTTACAT 57.929 29.630 0.00 0.00 0.00 2.29
63 64 9.683069 GTTTCAATTCACAATGAGTCTTACATT 57.317 29.630 0.00 0.00 38.30 2.71
73 74 8.955061 CAATGAGTCTTACATTGGTTGTTAAG 57.045 34.615 0.00 0.00 45.92 1.85
74 75 8.783093 CAATGAGTCTTACATTGGTTGTTAAGA 58.217 33.333 0.00 0.00 45.92 2.10
75 76 7.724305 TGAGTCTTACATTGGTTGTTAAGAC 57.276 36.000 12.70 12.70 42.15 3.01
76 77 6.708949 TGAGTCTTACATTGGTTGTTAAGACC 59.291 38.462 15.26 10.34 42.41 3.85
77 78 6.597562 AGTCTTACATTGGTTGTTAAGACCA 58.402 36.000 15.26 6.55 45.09 4.02
85 86 5.766150 TGGTTGTTAAGACCAACATTGAG 57.234 39.130 7.93 0.00 43.87 3.02
86 87 4.037446 TGGTTGTTAAGACCAACATTGAGC 59.963 41.667 7.93 0.00 43.87 4.26
87 88 4.219033 GTTGTTAAGACCAACATTGAGCG 58.781 43.478 3.30 0.00 41.40 5.03
88 89 3.734463 TGTTAAGACCAACATTGAGCGA 58.266 40.909 0.00 0.00 33.55 4.93
89 90 3.745975 TGTTAAGACCAACATTGAGCGAG 59.254 43.478 0.00 0.00 33.55 5.03
90 91 1.160137 AAGACCAACATTGAGCGAGC 58.840 50.000 0.00 0.00 0.00 5.03
91 92 0.674895 AGACCAACATTGAGCGAGCC 60.675 55.000 0.00 0.00 0.00 4.70
92 93 0.955428 GACCAACATTGAGCGAGCCA 60.955 55.000 0.00 0.00 0.00 4.75
93 94 0.537143 ACCAACATTGAGCGAGCCAA 60.537 50.000 0.00 0.00 0.00 4.52
94 95 0.813184 CCAACATTGAGCGAGCCAAT 59.187 50.000 6.14 6.14 34.83 3.16
95 96 2.016318 CCAACATTGAGCGAGCCAATA 58.984 47.619 10.03 0.00 33.35 1.90
96 97 2.223340 CCAACATTGAGCGAGCCAATAC 60.223 50.000 10.03 0.00 33.35 1.89
97 98 1.668419 ACATTGAGCGAGCCAATACC 58.332 50.000 10.03 0.00 33.35 2.73
98 99 1.210478 ACATTGAGCGAGCCAATACCT 59.790 47.619 10.03 0.00 33.35 3.08
99 100 1.600957 CATTGAGCGAGCCAATACCTG 59.399 52.381 10.03 0.09 33.35 4.00
100 101 0.744414 TTGAGCGAGCCAATACCTGC 60.744 55.000 0.00 0.00 0.00 4.85
101 102 1.153369 GAGCGAGCCAATACCTGCA 60.153 57.895 0.00 0.00 0.00 4.41
102 103 0.533755 GAGCGAGCCAATACCTGCAT 60.534 55.000 0.00 0.00 0.00 3.96
103 104 0.816825 AGCGAGCCAATACCTGCATG 60.817 55.000 0.00 0.00 0.00 4.06
104 105 1.097547 GCGAGCCAATACCTGCATGT 61.098 55.000 0.00 0.00 0.00 3.21
105 106 0.659427 CGAGCCAATACCTGCATGTG 59.341 55.000 4.73 0.00 0.00 3.21
106 107 0.383231 GAGCCAATACCTGCATGTGC 59.617 55.000 4.73 0.00 42.50 4.57
121 122 4.804108 GCATGTGCATTTGGTAACTAACA 58.196 39.130 0.00 0.00 41.59 2.41
122 123 4.858692 GCATGTGCATTTGGTAACTAACAG 59.141 41.667 0.00 0.00 41.59 3.16
123 124 5.564651 GCATGTGCATTTGGTAACTAACAGT 60.565 40.000 0.00 0.00 41.59 3.55
124 125 6.446318 CATGTGCATTTGGTAACTAACAGTT 58.554 36.000 0.00 0.00 41.97 3.16
125 126 5.826586 TGTGCATTTGGTAACTAACAGTTG 58.173 37.500 0.00 0.00 39.11 3.16
126 127 5.358442 TGTGCATTTGGTAACTAACAGTTGT 59.642 36.000 0.00 0.00 39.11 3.32
127 128 6.542735 TGTGCATTTGGTAACTAACAGTTGTA 59.457 34.615 0.00 0.00 39.11 2.41
128 129 7.229707 TGTGCATTTGGTAACTAACAGTTGTAT 59.770 33.333 0.00 0.00 39.11 2.29
129 130 8.723311 GTGCATTTGGTAACTAACAGTTGTATA 58.277 33.333 0.00 0.00 39.11 1.47
130 131 9.286170 TGCATTTGGTAACTAACAGTTGTATAA 57.714 29.630 0.00 0.00 39.11 0.98
131 132 9.769093 GCATTTGGTAACTAACAGTTGTATAAG 57.231 33.333 0.00 0.00 39.11 1.73
134 135 8.767478 TTGGTAACTAACAGTTGTATAAGAGC 57.233 34.615 0.00 0.00 39.11 4.09
135 136 7.898918 TGGTAACTAACAGTTGTATAAGAGCA 58.101 34.615 0.00 0.00 39.11 4.26
136 137 8.537016 TGGTAACTAACAGTTGTATAAGAGCAT 58.463 33.333 0.00 0.00 39.11 3.79
137 138 9.032420 GGTAACTAACAGTTGTATAAGAGCATC 57.968 37.037 0.00 0.00 39.11 3.91
138 139 9.804758 GTAACTAACAGTTGTATAAGAGCATCT 57.195 33.333 0.00 0.00 43.45 2.90
139 140 8.934507 AACTAACAGTTGTATAAGAGCATCTC 57.065 34.615 0.00 0.00 40.46 2.75
140 141 7.982354 AACTAACAGTTGTATAAGAGCATCTCC 59.018 37.037 0.00 0.00 40.46 3.71
149 150 2.475666 GAGCATCTCCAACAGCCAC 58.524 57.895 0.00 0.00 0.00 5.01
150 151 0.321919 GAGCATCTCCAACAGCCACA 60.322 55.000 0.00 0.00 0.00 4.17
151 152 0.607489 AGCATCTCCAACAGCCACAC 60.607 55.000 0.00 0.00 0.00 3.82
152 153 0.607489 GCATCTCCAACAGCCACACT 60.607 55.000 0.00 0.00 0.00 3.55
153 154 1.339055 GCATCTCCAACAGCCACACTA 60.339 52.381 0.00 0.00 0.00 2.74
154 155 2.875672 GCATCTCCAACAGCCACACTAA 60.876 50.000 0.00 0.00 0.00 2.24
155 156 3.411446 CATCTCCAACAGCCACACTAAA 58.589 45.455 0.00 0.00 0.00 1.85
156 157 3.788227 TCTCCAACAGCCACACTAAAT 57.212 42.857 0.00 0.00 0.00 1.40
157 158 4.901197 TCTCCAACAGCCACACTAAATA 57.099 40.909 0.00 0.00 0.00 1.40
158 159 5.435686 TCTCCAACAGCCACACTAAATAT 57.564 39.130 0.00 0.00 0.00 1.28
159 160 5.428253 TCTCCAACAGCCACACTAAATATC 58.572 41.667 0.00 0.00 0.00 1.63
160 161 4.188462 TCCAACAGCCACACTAAATATCG 58.812 43.478 0.00 0.00 0.00 2.92
161 162 3.242739 CCAACAGCCACACTAAATATCGC 60.243 47.826 0.00 0.00 0.00 4.58
162 163 3.260475 ACAGCCACACTAAATATCGCA 57.740 42.857 0.00 0.00 0.00 5.10
163 164 2.936498 ACAGCCACACTAAATATCGCAC 59.064 45.455 0.00 0.00 0.00 5.34
164 165 2.033747 CAGCCACACTAAATATCGCACG 60.034 50.000 0.00 0.00 0.00 5.34
165 166 1.332904 GCCACACTAAATATCGCACGC 60.333 52.381 0.00 0.00 0.00 5.34
166 167 1.071502 CCACACTAAATATCGCACGCG 60.072 52.381 3.53 3.53 41.35 6.01
167 168 1.071502 CACACTAAATATCGCACGCGG 60.072 52.381 12.47 0.00 40.25 6.46
168 169 0.506932 CACTAAATATCGCACGCGGG 59.493 55.000 12.47 7.92 40.25 6.13
169 170 0.599204 ACTAAATATCGCACGCGGGG 60.599 55.000 11.92 7.97 40.25 5.73
170 171 1.289109 CTAAATATCGCACGCGGGGG 61.289 60.000 20.80 20.80 40.25 5.40
171 172 1.746322 TAAATATCGCACGCGGGGGA 61.746 55.000 30.90 30.90 40.25 4.81
172 173 2.596553 AAATATCGCACGCGGGGGAA 62.597 55.000 32.31 20.50 40.25 3.97
173 174 2.596553 AATATCGCACGCGGGGGAAA 62.597 55.000 32.31 11.16 40.25 3.13
174 175 2.596553 ATATCGCACGCGGGGGAAAA 62.597 55.000 32.31 22.62 40.25 2.29
191 192 4.747810 GGAAAAGCCCATATGAGTGTTTG 58.252 43.478 3.65 0.00 0.00 2.93
192 193 3.874392 AAAGCCCATATGAGTGTTTGC 57.126 42.857 3.65 0.00 0.00 3.68
193 194 2.512692 AGCCCATATGAGTGTTTGCA 57.487 45.000 3.65 0.00 0.00 4.08
194 195 3.022557 AGCCCATATGAGTGTTTGCAT 57.977 42.857 3.65 0.00 0.00 3.96
195 196 2.954318 AGCCCATATGAGTGTTTGCATC 59.046 45.455 3.65 0.00 0.00 3.91
196 197 2.954318 GCCCATATGAGTGTTTGCATCT 59.046 45.455 3.65 0.00 0.00 2.90
197 198 4.136796 GCCCATATGAGTGTTTGCATCTA 58.863 43.478 3.65 0.00 0.00 1.98
198 199 4.763793 GCCCATATGAGTGTTTGCATCTAT 59.236 41.667 3.65 0.00 0.00 1.98
199 200 5.242393 GCCCATATGAGTGTTTGCATCTATT 59.758 40.000 3.65 0.00 0.00 1.73
200 201 6.239120 GCCCATATGAGTGTTTGCATCTATTT 60.239 38.462 3.65 0.00 0.00 1.40
201 202 7.685155 GCCCATATGAGTGTTTGCATCTATTTT 60.685 37.037 3.65 0.00 0.00 1.82
202 203 8.849168 CCCATATGAGTGTTTGCATCTATTTTA 58.151 33.333 3.65 0.00 0.00 1.52
207 208 9.979578 ATGAGTGTTTGCATCTATTTTAAACAA 57.020 25.926 0.00 0.00 41.26 2.83
208 209 9.243637 TGAGTGTTTGCATCTATTTTAAACAAC 57.756 29.630 0.00 0.00 41.26 3.32
209 210 8.587952 AGTGTTTGCATCTATTTTAAACAACC 57.412 30.769 0.00 0.00 41.26 3.77
210 211 7.655732 AGTGTTTGCATCTATTTTAAACAACCC 59.344 33.333 0.00 0.00 41.26 4.11
211 212 7.655732 GTGTTTGCATCTATTTTAAACAACCCT 59.344 33.333 0.00 0.00 41.26 4.34
212 213 8.207545 TGTTTGCATCTATTTTAAACAACCCTT 58.792 29.630 0.00 0.00 38.03 3.95
213 214 8.708742 GTTTGCATCTATTTTAAACAACCCTTC 58.291 33.333 0.00 0.00 32.92 3.46
214 215 7.531857 TGCATCTATTTTAAACAACCCTTCA 57.468 32.000 0.00 0.00 0.00 3.02
215 216 8.133024 TGCATCTATTTTAAACAACCCTTCAT 57.867 30.769 0.00 0.00 0.00 2.57
216 217 8.592809 TGCATCTATTTTAAACAACCCTTCATT 58.407 29.630 0.00 0.00 0.00 2.57
217 218 9.435688 GCATCTATTTTAAACAACCCTTCATTT 57.564 29.630 0.00 0.00 0.00 2.32
228 229 7.169158 ACAACCCTTCATTTGTATACATTGG 57.831 36.000 6.36 3.41 34.12 3.16
229 230 6.723977 ACAACCCTTCATTTGTATACATTGGT 59.276 34.615 6.36 3.48 34.12 3.67
230 231 7.234577 ACAACCCTTCATTTGTATACATTGGTT 59.765 33.333 6.36 8.82 34.12 3.67
231 232 7.790782 ACCCTTCATTTGTATACATTGGTTT 57.209 32.000 6.36 0.00 0.00 3.27
232 233 8.201242 ACCCTTCATTTGTATACATTGGTTTT 57.799 30.769 6.36 0.00 0.00 2.43
233 234 8.655901 ACCCTTCATTTGTATACATTGGTTTTT 58.344 29.630 6.36 0.00 0.00 1.94
278 279 7.807977 AAAAAGAGAGAGCATAAGAAACACA 57.192 32.000 0.00 0.00 0.00 3.72
279 280 7.807977 AAAAGAGAGAGCATAAGAAACACAA 57.192 32.000 0.00 0.00 0.00 3.33
284 285 9.323985 AGAGAGAGCATAAGAAACACAAATATC 57.676 33.333 0.00 0.00 0.00 1.63
419 452 7.739498 AATTAAGTTGGTGTATGTTTCGAGT 57.261 32.000 0.00 0.00 0.00 4.18
420 453 6.533819 TTAAGTTGGTGTATGTTTCGAGTG 57.466 37.500 0.00 0.00 0.00 3.51
422 455 5.204409 AGTTGGTGTATGTTTCGAGTGTA 57.796 39.130 0.00 0.00 0.00 2.90
423 456 5.603596 AGTTGGTGTATGTTTCGAGTGTAA 58.396 37.500 0.00 0.00 0.00 2.41
427 460 6.893759 TGGTGTATGTTTCGAGTGTAATTTG 58.106 36.000 0.00 0.00 0.00 2.32
428 461 6.072948 TGGTGTATGTTTCGAGTGTAATTTGG 60.073 38.462 0.00 0.00 0.00 3.28
430 463 7.013529 GTGTATGTTTCGAGTGTAATTTGGTC 58.986 38.462 0.00 0.00 0.00 4.02
441 511 8.664798 CGAGTGTAATTTGGTCAAATATCAAGA 58.335 33.333 9.06 0.00 39.88 3.02
450 520 9.883142 TTTGGTCAAATATCAAGAAGTTTGTTT 57.117 25.926 9.07 0.00 34.20 2.83
460 530 7.903995 TCAAGAAGTTTGTTTTGAGCAAAAT 57.096 28.000 11.11 0.00 41.64 1.82
506 576 7.045126 AGATTGAGTAGCACTAAGATGTACC 57.955 40.000 0.00 0.00 0.00 3.34
507 577 5.593679 TTGAGTAGCACTAAGATGTACCC 57.406 43.478 0.00 0.00 0.00 3.69
508 578 4.606210 TGAGTAGCACTAAGATGTACCCA 58.394 43.478 0.00 0.00 0.00 4.51
509 579 4.401519 TGAGTAGCACTAAGATGTACCCAC 59.598 45.833 0.00 0.00 0.00 4.61
510 580 4.611367 AGTAGCACTAAGATGTACCCACT 58.389 43.478 0.00 0.00 0.00 4.00
511 581 4.645588 AGTAGCACTAAGATGTACCCACTC 59.354 45.833 0.00 0.00 0.00 3.51
512 582 2.766828 AGCACTAAGATGTACCCACTCC 59.233 50.000 0.00 0.00 0.00 3.85
513 583 2.481449 GCACTAAGATGTACCCACTCCG 60.481 54.545 0.00 0.00 0.00 4.63
514 584 2.758979 CACTAAGATGTACCCACTCCGT 59.241 50.000 0.00 0.00 0.00 4.69
515 585 3.949754 CACTAAGATGTACCCACTCCGTA 59.050 47.826 0.00 0.00 0.00 4.02
516 586 4.400251 CACTAAGATGTACCCACTCCGTAA 59.600 45.833 0.00 0.00 0.00 3.18
517 587 5.018809 ACTAAGATGTACCCACTCCGTAAA 58.981 41.667 0.00 0.00 0.00 2.01
518 588 4.895668 AAGATGTACCCACTCCGTAAAA 57.104 40.909 0.00 0.00 0.00 1.52
519 589 4.895668 AGATGTACCCACTCCGTAAAAA 57.104 40.909 0.00 0.00 0.00 1.94
520 590 4.828829 AGATGTACCCACTCCGTAAAAAG 58.171 43.478 0.00 0.00 0.00 2.27
521 591 4.529377 AGATGTACCCACTCCGTAAAAAGA 59.471 41.667 0.00 0.00 0.00 2.52
522 592 4.686191 TGTACCCACTCCGTAAAAAGAA 57.314 40.909 0.00 0.00 0.00 2.52
523 593 5.033589 TGTACCCACTCCGTAAAAAGAAA 57.966 39.130 0.00 0.00 0.00 2.52
524 594 5.623169 TGTACCCACTCCGTAAAAAGAAAT 58.377 37.500 0.00 0.00 0.00 2.17
525 595 6.767456 TGTACCCACTCCGTAAAAAGAAATA 58.233 36.000 0.00 0.00 0.00 1.40
526 596 7.396418 TGTACCCACTCCGTAAAAAGAAATAT 58.604 34.615 0.00 0.00 0.00 1.28
527 597 8.538701 TGTACCCACTCCGTAAAAAGAAATATA 58.461 33.333 0.00 0.00 0.00 0.86
528 598 9.382275 GTACCCACTCCGTAAAAAGAAATATAA 57.618 33.333 0.00 0.00 0.00 0.98
529 599 8.502105 ACCCACTCCGTAAAAAGAAATATAAG 57.498 34.615 0.00 0.00 0.00 1.73
530 600 8.323567 ACCCACTCCGTAAAAAGAAATATAAGA 58.676 33.333 0.00 0.00 0.00 2.10
531 601 8.827677 CCCACTCCGTAAAAAGAAATATAAGAG 58.172 37.037 0.00 0.00 0.00 2.85
532 602 8.336080 CCACTCCGTAAAAAGAAATATAAGAGC 58.664 37.037 0.00 0.00 0.00 4.09
533 603 8.056571 CACTCCGTAAAAAGAAATATAAGAGCG 58.943 37.037 0.00 0.00 0.00 5.03
534 604 7.763071 ACTCCGTAAAAAGAAATATAAGAGCGT 59.237 33.333 0.00 0.00 0.00 5.07
535 605 8.483307 TCCGTAAAAAGAAATATAAGAGCGTT 57.517 30.769 0.00 0.00 0.00 4.84
536 606 8.938906 TCCGTAAAAAGAAATATAAGAGCGTTT 58.061 29.630 0.00 0.00 0.00 3.60
551 621 6.320494 AGAGCGTTTAGATCACTACATAGG 57.680 41.667 0.00 0.00 37.82 2.57
552 622 5.241949 AGAGCGTTTAGATCACTACATAGGG 59.758 44.000 0.00 0.00 37.82 3.53
553 623 5.138276 AGCGTTTAGATCACTACATAGGGA 58.862 41.667 0.00 0.00 40.55 4.20
558 628 8.452534 CGTTTAGATCACTACATAGGGAGTATC 58.547 40.741 0.00 0.00 39.45 2.24
623 725 5.694006 CGTTGGCAGTGAATTTTAATGGAAA 59.306 36.000 0.00 0.00 0.00 3.13
626 728 6.825610 TGGCAGTGAATTTTAATGGAAAAGT 58.174 32.000 0.00 0.00 40.34 2.66
654 757 2.026822 TCAGGGCAGAATGGAAGAGAAC 60.027 50.000 0.00 0.00 35.86 3.01
666 772 2.761767 GGAAGAGAACCTAGTCAGTCCC 59.238 54.545 0.00 0.00 0.00 4.46
682 788 6.042638 TCAGTCCCAGAATGACTTCTTTAG 57.957 41.667 0.00 0.00 41.02 1.85
692 799 0.108756 ACTTCTTTAGTCTCGGCCGC 60.109 55.000 23.51 6.72 28.23 6.53
695 802 1.215647 CTTTAGTCTCGGCCGCAGT 59.784 57.895 23.51 14.86 0.00 4.40
823 930 2.194326 GCCAATCAGAGGCCTCCC 59.806 66.667 29.54 6.19 46.50 4.30
1700 1832 1.668151 GCGCCGGTTCAGTTCTTCT 60.668 57.895 1.90 0.00 0.00 2.85
3362 3652 3.793144 CTGAGTTCTTGCGCGCCC 61.793 66.667 30.77 11.12 0.00 6.13
3416 3706 3.522553 GCTTTCGACAAGCTATACCACT 58.477 45.455 18.85 0.00 40.01 4.00
3430 3720 0.041090 ACCACTTTAATGGCCTGGGG 59.959 55.000 3.32 0.03 44.33 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.645884 TTTATTAACCCATGGTCTGGTAGT 57.354 37.500 11.73 0.00 44.30 2.73
4 5 8.437575 AGTATTTATTAACCCATGGTCTGGTAG 58.562 37.037 11.73 0.00 44.30 3.18
5 6 8.339720 AGTATTTATTAACCCATGGTCTGGTA 57.660 34.615 11.73 0.00 44.30 3.25
6 7 7.220890 AGTATTTATTAACCCATGGTCTGGT 57.779 36.000 11.73 0.00 44.30 4.00
7 8 6.715264 GGAGTATTTATTAACCCATGGTCTGG 59.285 42.308 11.73 0.00 45.51 3.86
8 9 6.715264 GGGAGTATTTATTAACCCATGGTCTG 59.285 42.308 11.73 0.00 33.12 3.51
9 10 6.624021 AGGGAGTATTTATTAACCCATGGTCT 59.376 38.462 11.73 0.00 39.73 3.85
10 11 6.849151 AGGGAGTATTTATTAACCCATGGTC 58.151 40.000 11.73 0.00 39.73 4.02
11 12 6.391649 TGAGGGAGTATTTATTAACCCATGGT 59.608 38.462 11.73 0.00 39.73 3.55
12 13 6.848069 TGAGGGAGTATTTATTAACCCATGG 58.152 40.000 4.14 4.14 39.73 3.66
13 14 7.518188 ACTGAGGGAGTATTTATTAACCCATG 58.482 38.462 0.00 0.00 39.73 3.66
14 15 7.707467 ACTGAGGGAGTATTTATTAACCCAT 57.293 36.000 0.00 0.00 39.73 4.00
15 16 7.519347 AACTGAGGGAGTATTTATTAACCCA 57.481 36.000 0.00 0.00 39.73 4.51
16 17 8.050930 TGAAACTGAGGGAGTATTTATTAACCC 58.949 37.037 0.00 0.00 33.09 4.11
17 18 9.457436 TTGAAACTGAGGGAGTATTTATTAACC 57.543 33.333 0.00 0.00 33.09 2.85
21 22 9.753674 TGAATTGAAACTGAGGGAGTATTTATT 57.246 29.630 0.00 0.00 33.09 1.40
22 23 9.178758 GTGAATTGAAACTGAGGGAGTATTTAT 57.821 33.333 0.00 0.00 33.09 1.40
23 24 8.160765 TGTGAATTGAAACTGAGGGAGTATTTA 58.839 33.333 0.00 0.00 33.09 1.40
24 25 7.004086 TGTGAATTGAAACTGAGGGAGTATTT 58.996 34.615 0.00 0.00 33.09 1.40
25 26 6.542821 TGTGAATTGAAACTGAGGGAGTATT 58.457 36.000 0.00 0.00 33.09 1.89
26 27 6.126863 TGTGAATTGAAACTGAGGGAGTAT 57.873 37.500 0.00 0.00 33.09 2.12
27 28 5.560722 TGTGAATTGAAACTGAGGGAGTA 57.439 39.130 0.00 0.00 33.09 2.59
28 29 4.437682 TGTGAATTGAAACTGAGGGAGT 57.562 40.909 0.00 0.00 35.94 3.85
29 30 5.474532 TCATTGTGAATTGAAACTGAGGGAG 59.525 40.000 0.00 0.00 0.00 4.30
30 31 5.384336 TCATTGTGAATTGAAACTGAGGGA 58.616 37.500 0.00 0.00 0.00 4.20
31 32 5.242393 ACTCATTGTGAATTGAAACTGAGGG 59.758 40.000 7.24 0.00 34.58 4.30
32 33 6.206243 AGACTCATTGTGAATTGAAACTGAGG 59.794 38.462 7.24 0.00 34.58 3.86
33 34 7.199541 AGACTCATTGTGAATTGAAACTGAG 57.800 36.000 1.62 1.62 35.99 3.35
34 35 7.572523 AAGACTCATTGTGAATTGAAACTGA 57.427 32.000 0.00 0.00 0.00 3.41
35 36 8.344831 TGTAAGACTCATTGTGAATTGAAACTG 58.655 33.333 0.00 0.00 0.00 3.16
36 37 8.450578 TGTAAGACTCATTGTGAATTGAAACT 57.549 30.769 0.00 0.00 0.00 2.66
37 38 9.683069 AATGTAAGACTCATTGTGAATTGAAAC 57.317 29.630 0.00 0.00 34.74 2.78
38 39 9.681692 CAATGTAAGACTCATTGTGAATTGAAA 57.318 29.630 8.16 0.00 43.81 2.69
39 40 8.298854 CCAATGTAAGACTCATTGTGAATTGAA 58.701 33.333 13.13 0.00 45.91 2.69
40 41 7.448161 ACCAATGTAAGACTCATTGTGAATTGA 59.552 33.333 13.13 0.00 45.91 2.57
41 42 7.596494 ACCAATGTAAGACTCATTGTGAATTG 58.404 34.615 13.13 0.00 45.91 2.32
42 43 7.765695 ACCAATGTAAGACTCATTGTGAATT 57.234 32.000 13.13 0.00 45.91 2.17
43 44 7.231317 ACAACCAATGTAAGACTCATTGTGAAT 59.769 33.333 13.13 0.00 45.91 2.57
44 45 6.545666 ACAACCAATGTAAGACTCATTGTGAA 59.454 34.615 13.13 0.00 45.91 3.18
45 46 6.061441 ACAACCAATGTAAGACTCATTGTGA 58.939 36.000 13.13 0.00 45.91 3.58
46 47 6.317789 ACAACCAATGTAAGACTCATTGTG 57.682 37.500 13.13 9.49 45.91 3.33
47 48 6.959639 AACAACCAATGTAAGACTCATTGT 57.040 33.333 13.13 0.00 45.91 2.71
48 49 8.783093 TCTTAACAACCAATGTAAGACTCATTG 58.217 33.333 9.05 9.05 46.50 2.82
49 50 8.784043 GTCTTAACAACCAATGTAAGACTCATT 58.216 33.333 12.82 0.00 42.99 2.57
50 51 7.390718 GGTCTTAACAACCAATGTAAGACTCAT 59.609 37.037 17.34 0.00 42.99 2.90
51 52 6.708949 GGTCTTAACAACCAATGTAAGACTCA 59.291 38.462 17.34 0.00 42.99 3.41
52 53 6.708949 TGGTCTTAACAACCAATGTAAGACTC 59.291 38.462 17.34 10.81 43.72 3.36
53 54 6.597562 TGGTCTTAACAACCAATGTAAGACT 58.402 36.000 17.34 0.00 43.72 3.24
54 55 6.870971 TGGTCTTAACAACCAATGTAAGAC 57.129 37.500 12.02 12.02 43.72 3.01
63 64 4.037446 GCTCAATGTTGGTCTTAACAACCA 59.963 41.667 5.44 3.54 45.72 3.67
64 65 4.546570 GCTCAATGTTGGTCTTAACAACC 58.453 43.478 5.44 1.18 45.72 3.77
65 66 4.024387 TCGCTCAATGTTGGTCTTAACAAC 60.024 41.667 0.85 0.85 46.30 3.32
66 67 4.130857 TCGCTCAATGTTGGTCTTAACAA 58.869 39.130 0.00 0.00 43.13 2.83
67 68 3.734463 TCGCTCAATGTTGGTCTTAACA 58.266 40.909 0.00 0.00 43.93 2.41
68 69 3.424962 GCTCGCTCAATGTTGGTCTTAAC 60.425 47.826 0.00 0.00 0.00 2.01
69 70 2.742053 GCTCGCTCAATGTTGGTCTTAA 59.258 45.455 0.00 0.00 0.00 1.85
70 71 2.346803 GCTCGCTCAATGTTGGTCTTA 58.653 47.619 0.00 0.00 0.00 2.10
71 72 1.160137 GCTCGCTCAATGTTGGTCTT 58.840 50.000 0.00 0.00 0.00 3.01
72 73 0.674895 GGCTCGCTCAATGTTGGTCT 60.675 55.000 0.00 0.00 0.00 3.85
73 74 0.955428 TGGCTCGCTCAATGTTGGTC 60.955 55.000 0.00 0.00 0.00 4.02
74 75 0.537143 TTGGCTCGCTCAATGTTGGT 60.537 50.000 0.00 0.00 0.00 3.67
75 76 0.813184 ATTGGCTCGCTCAATGTTGG 59.187 50.000 5.28 0.00 34.01 3.77
76 77 2.223340 GGTATTGGCTCGCTCAATGTTG 60.223 50.000 12.67 0.00 36.40 3.33
77 78 2.017049 GGTATTGGCTCGCTCAATGTT 58.983 47.619 12.67 0.00 36.40 2.71
78 79 1.210478 AGGTATTGGCTCGCTCAATGT 59.790 47.619 12.67 0.53 36.40 2.71
79 80 1.600957 CAGGTATTGGCTCGCTCAATG 59.399 52.381 12.67 0.00 36.40 2.82
80 81 1.959042 CAGGTATTGGCTCGCTCAAT 58.041 50.000 9.44 9.44 38.29 2.57
81 82 0.744414 GCAGGTATTGGCTCGCTCAA 60.744 55.000 0.00 0.00 0.00 3.02
82 83 1.153369 GCAGGTATTGGCTCGCTCA 60.153 57.895 0.00 0.00 0.00 4.26
83 84 0.533755 ATGCAGGTATTGGCTCGCTC 60.534 55.000 0.00 0.00 0.00 5.03
84 85 0.816825 CATGCAGGTATTGGCTCGCT 60.817 55.000 0.00 0.00 0.00 4.93
85 86 1.097547 ACATGCAGGTATTGGCTCGC 61.098 55.000 0.06 0.00 0.00 5.03
86 87 0.659427 CACATGCAGGTATTGGCTCG 59.341 55.000 2.51 0.00 0.00 5.03
87 88 0.383231 GCACATGCAGGTATTGGCTC 59.617 55.000 2.51 0.00 41.59 4.70
88 89 2.496942 GCACATGCAGGTATTGGCT 58.503 52.632 2.51 0.00 41.59 4.75
98 99 9.294288 AACTGTTAGTTACCAAATGCACATGCA 62.294 37.037 9.36 9.36 45.70 3.96
99 100 4.804108 TGTTAGTTACCAAATGCACATGC 58.196 39.130 0.00 0.00 42.50 4.06
100 101 6.012658 ACTGTTAGTTACCAAATGCACATG 57.987 37.500 0.00 0.00 0.00 3.21
101 102 6.040391 ACAACTGTTAGTTACCAAATGCACAT 59.960 34.615 0.00 0.00 36.03 3.21
102 103 5.358442 ACAACTGTTAGTTACCAAATGCACA 59.642 36.000 0.00 0.00 36.03 4.57
103 104 5.827666 ACAACTGTTAGTTACCAAATGCAC 58.172 37.500 0.00 0.00 36.03 4.57
104 105 7.753309 ATACAACTGTTAGTTACCAAATGCA 57.247 32.000 0.00 0.00 36.03 3.96
105 106 9.769093 CTTATACAACTGTTAGTTACCAAATGC 57.231 33.333 0.00 0.00 36.03 3.56
108 109 9.211485 GCTCTTATACAACTGTTAGTTACCAAA 57.789 33.333 0.00 0.00 36.03 3.28
109 110 8.369424 TGCTCTTATACAACTGTTAGTTACCAA 58.631 33.333 0.00 0.00 36.03 3.67
110 111 7.898918 TGCTCTTATACAACTGTTAGTTACCA 58.101 34.615 0.00 0.00 36.03 3.25
111 112 8.943909 ATGCTCTTATACAACTGTTAGTTACC 57.056 34.615 0.00 0.00 36.03 2.85
112 113 9.804758 AGATGCTCTTATACAACTGTTAGTTAC 57.195 33.333 0.00 0.00 36.03 2.50
114 115 7.982354 GGAGATGCTCTTATACAACTGTTAGTT 59.018 37.037 0.00 0.00 39.39 2.24
115 116 7.124298 TGGAGATGCTCTTATACAACTGTTAGT 59.876 37.037 0.00 0.00 0.00 2.24
116 117 7.492524 TGGAGATGCTCTTATACAACTGTTAG 58.507 38.462 0.00 0.00 0.00 2.34
117 118 7.418337 TGGAGATGCTCTTATACAACTGTTA 57.582 36.000 0.00 0.00 0.00 2.41
118 119 6.299805 TGGAGATGCTCTTATACAACTGTT 57.700 37.500 0.00 0.00 0.00 3.16
119 120 5.939764 TGGAGATGCTCTTATACAACTGT 57.060 39.130 0.00 0.00 0.00 3.55
120 121 6.108687 TGTTGGAGATGCTCTTATACAACTG 58.891 40.000 0.00 0.00 38.15 3.16
121 122 6.299805 TGTTGGAGATGCTCTTATACAACT 57.700 37.500 0.00 0.00 38.15 3.16
122 123 5.007136 GCTGTTGGAGATGCTCTTATACAAC 59.993 44.000 0.00 0.00 37.90 3.32
123 124 5.118990 GCTGTTGGAGATGCTCTTATACAA 58.881 41.667 0.00 0.00 0.00 2.41
124 125 4.443457 GGCTGTTGGAGATGCTCTTATACA 60.443 45.833 0.00 0.00 0.00 2.29
125 126 4.061596 GGCTGTTGGAGATGCTCTTATAC 58.938 47.826 0.00 0.00 0.00 1.47
126 127 3.711190 TGGCTGTTGGAGATGCTCTTATA 59.289 43.478 0.00 0.00 0.00 0.98
127 128 2.507058 TGGCTGTTGGAGATGCTCTTAT 59.493 45.455 0.00 0.00 0.00 1.73
128 129 1.908619 TGGCTGTTGGAGATGCTCTTA 59.091 47.619 0.00 0.00 0.00 2.10
129 130 0.694771 TGGCTGTTGGAGATGCTCTT 59.305 50.000 0.00 0.00 0.00 2.85
130 131 0.035630 GTGGCTGTTGGAGATGCTCT 60.036 55.000 0.00 0.00 0.00 4.09
131 132 0.321919 TGTGGCTGTTGGAGATGCTC 60.322 55.000 0.00 0.00 0.00 4.26
132 133 0.607489 GTGTGGCTGTTGGAGATGCT 60.607 55.000 0.00 0.00 0.00 3.79
133 134 0.607489 AGTGTGGCTGTTGGAGATGC 60.607 55.000 0.00 0.00 0.00 3.91
134 135 2.768253 TAGTGTGGCTGTTGGAGATG 57.232 50.000 0.00 0.00 0.00 2.90
135 136 3.788227 TTTAGTGTGGCTGTTGGAGAT 57.212 42.857 0.00 0.00 0.00 2.75
136 137 3.788227 ATTTAGTGTGGCTGTTGGAGA 57.212 42.857 0.00 0.00 0.00 3.71
137 138 4.271049 CGATATTTAGTGTGGCTGTTGGAG 59.729 45.833 0.00 0.00 0.00 3.86
138 139 4.188462 CGATATTTAGTGTGGCTGTTGGA 58.812 43.478 0.00 0.00 0.00 3.53
139 140 3.242739 GCGATATTTAGTGTGGCTGTTGG 60.243 47.826 0.00 0.00 0.00 3.77
140 141 3.373748 TGCGATATTTAGTGTGGCTGTTG 59.626 43.478 0.00 0.00 0.00 3.33
141 142 3.374058 GTGCGATATTTAGTGTGGCTGTT 59.626 43.478 0.00 0.00 0.00 3.16
142 143 2.936498 GTGCGATATTTAGTGTGGCTGT 59.064 45.455 0.00 0.00 0.00 4.40
143 144 2.033747 CGTGCGATATTTAGTGTGGCTG 60.034 50.000 0.00 0.00 0.00 4.85
144 145 2.201732 CGTGCGATATTTAGTGTGGCT 58.798 47.619 0.00 0.00 0.00 4.75
145 146 1.332904 GCGTGCGATATTTAGTGTGGC 60.333 52.381 0.00 0.00 0.00 5.01
146 147 1.071502 CGCGTGCGATATTTAGTGTGG 60.072 52.381 8.89 0.00 42.83 4.17
147 148 1.071502 CCGCGTGCGATATTTAGTGTG 60.072 52.381 16.91 0.00 42.83 3.82
148 149 1.205657 CCGCGTGCGATATTTAGTGT 58.794 50.000 16.91 0.00 42.83 3.55
149 150 0.506932 CCCGCGTGCGATATTTAGTG 59.493 55.000 16.91 0.00 42.83 2.74
150 151 0.599204 CCCCGCGTGCGATATTTAGT 60.599 55.000 16.91 0.00 42.83 2.24
151 152 1.289109 CCCCCGCGTGCGATATTTAG 61.289 60.000 16.91 0.00 42.83 1.85
152 153 1.301087 CCCCCGCGTGCGATATTTA 60.301 57.895 16.91 0.00 42.83 1.40
153 154 2.590575 CCCCCGCGTGCGATATTT 60.591 61.111 16.91 0.00 42.83 1.40
154 155 2.596553 TTTCCCCCGCGTGCGATATT 62.597 55.000 16.91 0.00 42.83 1.28
155 156 2.596553 TTTTCCCCCGCGTGCGATAT 62.597 55.000 16.91 0.00 42.83 1.63
156 157 3.312285 TTTTCCCCCGCGTGCGATA 62.312 57.895 16.91 0.00 42.83 2.92
157 158 4.708386 TTTTCCCCCGCGTGCGAT 62.708 61.111 16.91 0.00 42.83 4.58
169 170 4.747810 CAAACACTCATATGGGCTTTTCC 58.252 43.478 1.33 0.00 0.00 3.13
170 171 4.176271 GCAAACACTCATATGGGCTTTTC 58.824 43.478 1.33 0.00 0.00 2.29
171 172 3.577848 TGCAAACACTCATATGGGCTTTT 59.422 39.130 1.33 0.00 0.00 2.27
172 173 3.164268 TGCAAACACTCATATGGGCTTT 58.836 40.909 1.33 0.00 0.00 3.51
173 174 2.806434 TGCAAACACTCATATGGGCTT 58.194 42.857 1.33 0.00 0.00 4.35
174 175 2.512692 TGCAAACACTCATATGGGCT 57.487 45.000 1.33 0.00 0.00 5.19
175 176 2.954318 AGATGCAAACACTCATATGGGC 59.046 45.455 1.33 0.00 0.00 5.36
176 177 6.889301 AATAGATGCAAACACTCATATGGG 57.111 37.500 0.00 0.00 0.00 4.00
181 182 9.979578 TTGTTTAAAATAGATGCAAACACTCAT 57.020 25.926 0.00 0.00 38.45 2.90
182 183 9.243637 GTTGTTTAAAATAGATGCAAACACTCA 57.756 29.630 0.00 0.00 38.45 3.41
183 184 8.699749 GGTTGTTTAAAATAGATGCAAACACTC 58.300 33.333 0.00 0.00 38.45 3.51
184 185 7.655732 GGGTTGTTTAAAATAGATGCAAACACT 59.344 33.333 0.00 0.00 38.45 3.55
185 186 7.655732 AGGGTTGTTTAAAATAGATGCAAACAC 59.344 33.333 0.00 0.00 38.45 3.32
186 187 7.731054 AGGGTTGTTTAAAATAGATGCAAACA 58.269 30.769 0.00 0.00 37.33 2.83
187 188 8.601845 AAGGGTTGTTTAAAATAGATGCAAAC 57.398 30.769 0.00 0.00 0.00 2.93
188 189 8.424918 TGAAGGGTTGTTTAAAATAGATGCAAA 58.575 29.630 0.00 0.00 0.00 3.68
189 190 7.957002 TGAAGGGTTGTTTAAAATAGATGCAA 58.043 30.769 0.00 0.00 0.00 4.08
190 191 7.531857 TGAAGGGTTGTTTAAAATAGATGCA 57.468 32.000 0.00 0.00 0.00 3.96
191 192 9.435688 AAATGAAGGGTTGTTTAAAATAGATGC 57.564 29.630 0.00 0.00 0.00 3.91
202 203 8.093927 CCAATGTATACAAATGAAGGGTTGTTT 58.906 33.333 18.59 0.00 38.80 2.83
203 204 7.234577 ACCAATGTATACAAATGAAGGGTTGTT 59.765 33.333 18.59 0.44 38.80 2.83
204 205 6.723977 ACCAATGTATACAAATGAAGGGTTGT 59.276 34.615 18.59 7.42 40.88 3.32
205 206 7.169158 ACCAATGTATACAAATGAAGGGTTG 57.831 36.000 18.59 11.48 0.00 3.77
206 207 7.790782 AACCAATGTATACAAATGAAGGGTT 57.209 32.000 18.59 15.56 0.00 4.11
207 208 7.790782 AAACCAATGTATACAAATGAAGGGT 57.209 32.000 18.59 11.77 0.00 4.34
254 255 7.807977 TGTGTTTCTTATGCTCTCTCTTTTT 57.192 32.000 0.00 0.00 0.00 1.94
255 256 7.807977 TTGTGTTTCTTATGCTCTCTCTTTT 57.192 32.000 0.00 0.00 0.00 2.27
256 257 7.807977 TTTGTGTTTCTTATGCTCTCTCTTT 57.192 32.000 0.00 0.00 0.00 2.52
257 258 7.992754 ATTTGTGTTTCTTATGCTCTCTCTT 57.007 32.000 0.00 0.00 0.00 2.85
258 259 9.323985 GATATTTGTGTTTCTTATGCTCTCTCT 57.676 33.333 0.00 0.00 0.00 3.10
259 260 8.555361 GGATATTTGTGTTTCTTATGCTCTCTC 58.445 37.037 0.00 0.00 0.00 3.20
260 261 8.270744 AGGATATTTGTGTTTCTTATGCTCTCT 58.729 33.333 0.00 0.00 0.00 3.10
261 262 8.443953 AGGATATTTGTGTTTCTTATGCTCTC 57.556 34.615 0.00 0.00 0.00 3.20
401 434 5.910637 TTACACTCGAAACATACACCAAC 57.089 39.130 0.00 0.00 0.00 3.77
409 442 6.627395 TTGACCAAATTACACTCGAAACAT 57.373 33.333 0.00 0.00 0.00 2.71
410 443 6.438259 TTTGACCAAATTACACTCGAAACA 57.562 33.333 0.00 0.00 0.00 2.83
411 444 9.274065 GATATTTGACCAAATTACACTCGAAAC 57.726 33.333 12.51 0.00 40.99 2.78
412 445 9.004717 TGATATTTGACCAAATTACACTCGAAA 57.995 29.630 12.51 0.00 40.99 3.46
414 447 8.554835 TTGATATTTGACCAAATTACACTCGA 57.445 30.769 12.51 0.00 40.99 4.04
415 448 8.664798 TCTTGATATTTGACCAAATTACACTCG 58.335 33.333 12.51 6.11 40.99 4.18
427 460 9.528018 TCAAAACAAACTTCTTGATATTTGACC 57.472 29.630 11.54 0.00 35.93 4.02
430 463 9.033481 TGCTCAAAACAAACTTCTTGATATTTG 57.967 29.630 0.00 0.00 37.91 2.32
481 551 7.230913 GGGTACATCTTAGTGCTACTCAATCTA 59.769 40.741 0.00 0.00 0.00 1.98
484 554 5.661312 TGGGTACATCTTAGTGCTACTCAAT 59.339 40.000 0.00 0.00 0.00 2.57
497 567 4.895668 TTTTACGGAGTGGGTACATCTT 57.104 40.909 0.00 0.00 45.73 2.40
501 571 4.686191 TTCTTTTTACGGAGTGGGTACA 57.314 40.909 0.00 0.00 45.73 2.90
502 572 7.854557 ATATTTCTTTTTACGGAGTGGGTAC 57.145 36.000 0.00 0.00 45.73 3.34
503 573 9.603921 CTTATATTTCTTTTTACGGAGTGGGTA 57.396 33.333 0.00 0.00 45.73 3.69
504 574 8.323567 TCTTATATTTCTTTTTACGGAGTGGGT 58.676 33.333 0.00 0.00 45.73 4.51
505 575 8.726870 TCTTATATTTCTTTTTACGGAGTGGG 57.273 34.615 0.00 0.00 45.73 4.61
506 576 8.336080 GCTCTTATATTTCTTTTTACGGAGTGG 58.664 37.037 0.00 0.00 45.73 4.00
507 577 8.056571 CGCTCTTATATTTCTTTTTACGGAGTG 58.943 37.037 0.00 0.00 45.73 3.51
509 579 8.128016 ACGCTCTTATATTTCTTTTTACGGAG 57.872 34.615 0.00 0.00 0.00 4.63
510 580 8.483307 AACGCTCTTATATTTCTTTTTACGGA 57.517 30.769 0.00 0.00 0.00 4.69
525 595 8.516234 CCTATGTAGTGATCTAAACGCTCTTAT 58.484 37.037 0.00 0.00 0.00 1.73
526 596 7.040617 CCCTATGTAGTGATCTAAACGCTCTTA 60.041 40.741 0.00 0.00 0.00 2.10
527 597 6.239064 CCCTATGTAGTGATCTAAACGCTCTT 60.239 42.308 0.00 0.00 0.00 2.85
528 598 5.241949 CCCTATGTAGTGATCTAAACGCTCT 59.758 44.000 0.00 0.00 0.00 4.09
529 599 5.241064 TCCCTATGTAGTGATCTAAACGCTC 59.759 44.000 0.00 0.00 0.00 5.03
530 600 5.138276 TCCCTATGTAGTGATCTAAACGCT 58.862 41.667 0.00 0.00 0.00 5.07
531 601 5.009811 ACTCCCTATGTAGTGATCTAAACGC 59.990 44.000 0.00 0.00 0.00 4.84
532 602 6.636562 ACTCCCTATGTAGTGATCTAAACG 57.363 41.667 0.00 0.00 0.00 3.60
533 603 8.741841 GGATACTCCCTATGTAGTGATCTAAAC 58.258 40.741 0.00 0.00 0.00 2.01
534 604 8.880991 GGATACTCCCTATGTAGTGATCTAAA 57.119 38.462 0.00 0.00 0.00 1.85
553 623 6.214412 AGAGTGTTCTGAAATTCCAGGATACT 59.786 38.462 1.81 1.81 43.85 2.12
558 628 7.693969 ATAAAGAGTGTTCTGAAATTCCAGG 57.306 36.000 0.00 0.00 34.99 4.45
626 728 2.647299 TCCATTCTGCCCTGAAAAGGTA 59.353 45.455 8.49 0.00 31.46 3.08
634 736 2.363683 GTTCTCTTCCATTCTGCCCTG 58.636 52.381 0.00 0.00 0.00 4.45
639 742 5.186797 ACTGACTAGGTTCTCTTCCATTCTG 59.813 44.000 0.00 0.00 0.00 3.02
654 757 3.370104 AGTCATTCTGGGACTGACTAGG 58.630 50.000 15.49 0.00 45.93 3.02
677 783 0.802607 GACTGCGGCCGAGACTAAAG 60.803 60.000 33.48 15.32 0.00 1.85
692 799 3.596066 CTGGCAGTGGGACCGACTG 62.596 68.421 27.35 27.35 43.22 3.51
823 930 1.628340 TGGGTAATATCCATCCAGCGG 59.372 52.381 0.00 0.00 0.00 5.52
1231 1342 4.228567 TGGCACAGGAACGCGTCA 62.229 61.111 14.44 0.00 0.00 4.35
2674 2919 5.784177 AGTGGAATCGCCTAACATATACAG 58.216 41.667 0.00 0.00 37.63 2.74
2675 2920 5.801531 AGTGGAATCGCCTAACATATACA 57.198 39.130 0.00 0.00 37.63 2.29
2676 2921 5.345202 CGAAGTGGAATCGCCTAACATATAC 59.655 44.000 0.00 0.00 37.63 1.47
2677 2922 5.242171 TCGAAGTGGAATCGCCTAACATATA 59.758 40.000 0.00 0.00 40.04 0.86
2678 2923 4.038763 TCGAAGTGGAATCGCCTAACATAT 59.961 41.667 0.00 0.00 40.04 1.78
2679 2924 3.382227 TCGAAGTGGAATCGCCTAACATA 59.618 43.478 0.00 0.00 40.04 2.29
2680 2925 2.167693 TCGAAGTGGAATCGCCTAACAT 59.832 45.455 0.00 0.00 40.04 2.71
2681 2926 1.546923 TCGAAGTGGAATCGCCTAACA 59.453 47.619 0.00 0.00 40.04 2.41
2682 2927 2.194271 CTCGAAGTGGAATCGCCTAAC 58.806 52.381 0.00 0.00 40.04 2.34
2683 2928 1.470979 GCTCGAAGTGGAATCGCCTAA 60.471 52.381 0.00 0.00 40.04 2.69
3030 3277 1.965219 CTAGTATCGCCTTCCCGGG 59.035 63.158 16.85 16.85 0.00 5.73
3362 3652 0.602638 TGCTTAACAGTGTCCCAGCG 60.603 55.000 13.65 0.00 0.00 5.18
3482 3777 1.416772 GGCCTATAGTCCACAAGGGTC 59.583 57.143 0.00 0.00 38.11 4.46


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

AutoCloner maintained by Alex Coulton.