Multiple sequence alignment - TraesCS5A01G228300

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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 TraesCS5A01G228300 chr5A 100.000 3060 0 0 1 3060 444547325 444550384 0.000000e+00 5651.0
1 TraesCS5A01G228300 chr5A 97.233 253 7 0 1 253 9329812 9330064 2.180000e-116 429.0
2 TraesCS5A01G228300 chr5A 84.196 367 46 10 2702 3060 444544616 444544254 2.260000e-91 346.0
3 TraesCS5A01G228300 chr5D 86.863 1667 133 48 1446 3060 347393274 347391642 0.000000e+00 1786.0
4 TraesCS5A01G228300 chr5D 87.632 1043 58 30 443 1450 347395740 347394734 0.000000e+00 1146.0
5 TraesCS5A01G228300 chr5D 80.716 363 46 17 2702 3055 347432591 347432938 8.420000e-66 261.0
6 TraesCS5A01G228300 chr5D 91.195 159 12 1 260 418 347431332 347431176 6.650000e-52 215.0
7 TraesCS5A01G228300 chr5B 83.276 873 78 37 2211 3060 403777310 403778137 0.000000e+00 741.0
8 TraesCS5A01G228300 chr5B 86.613 493 28 16 564 1035 403749971 403750446 7.570000e-141 510.0
9 TraesCS5A01G228300 chr5B 95.294 255 12 0 1 255 461691811 461691557 3.670000e-109 405.0
10 TraesCS5A01G228300 chr5B 78.669 511 68 26 2403 2882 403723695 403723195 4.960000e-78 302.0
11 TraesCS5A01G228300 chr5B 96.111 180 7 0 264 443 403749421 403749600 8.300000e-76 294.0
12 TraesCS5A01G228300 chr5B 97.059 102 3 0 468 569 403749720 403749821 4.060000e-39 172.0
13 TraesCS5A01G228300 chr5B 97.619 42 1 0 443 484 403749664 403749705 4.230000e-09 73.1
14 TraesCS5A01G228300 chr4D 97.222 252 7 0 1 252 479377039 479376788 7.840000e-116 427.0
15 TraesCS5A01G228300 chr6A 96.109 257 10 0 1 257 2935415 2935159 1.310000e-113 420.0
16 TraesCS5A01G228300 chr6A 96.063 254 9 1 1 254 89298137 89297885 2.200000e-111 412.0
17 TraesCS5A01G228300 chr2B 96.109 257 10 0 1 257 785266557 785266813 1.310000e-113 420.0
18 TraesCS5A01G228300 chr1A 96.800 250 8 0 1 250 552336649 552336400 4.720000e-113 418.0
19 TraesCS5A01G228300 chr6B 95.720 257 11 0 1 257 689941636 689941892 6.100000e-112 414.0
20 TraesCS5A01G228300 chr3B 95.984 249 10 0 1 249 100958668 100958916 3.670000e-109 405.0
21 TraesCS5A01G228300 chr3A 81.818 132 15 6 568 695 16993609 16993735 5.400000e-18 102.0
22 TraesCS5A01G228300 chr3A 92.188 64 5 0 1075 1138 37499124 37499187 1.170000e-14 91.6


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 TraesCS5A01G228300 chr5A 444547325 444550384 3059 False 5651.000 5651 100.0000 1 3060 1 chr5A.!!$F2 3059
1 TraesCS5A01G228300 chr5D 347391642 347395740 4098 True 1466.000 1786 87.2475 443 3060 2 chr5D.!!$R2 2617
2 TraesCS5A01G228300 chr5B 403777310 403778137 827 False 741.000 741 83.2760 2211 3060 1 chr5B.!!$F1 849
3 TraesCS5A01G228300 chr5B 403723195 403723695 500 True 302.000 302 78.6690 2403 2882 1 chr5B.!!$R1 479
4 TraesCS5A01G228300 chr5B 403749421 403750446 1025 False 262.275 510 94.3505 264 1035 4 chr5B.!!$F2 771

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
977 1250 0.024619 GTTCGTTGCTAATCGCCGAC 59.975 55.0 0.00 0.0 38.05 4.79 F
1568 3318 0.094046 GGTCACGGCGTTCAAATACG 59.906 55.0 11.19 0.0 44.09 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 3637 0.957888 GACACTGAGGAAGGCAAGCC 60.958 60.000 2.02 2.02 0.0 4.35 R
2817 4634 3.826466 GCTTAAACTTCAGCGCAGAAAT 58.174 40.909 16.37 3.34 0.0 2.17 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
19 20 1.967319 ATGCTTGTTTCGTGGACTGT 58.033 45.000 0.00 0.00 0.00 3.55
20 21 1.295792 TGCTTGTTTCGTGGACTGTC 58.704 50.000 0.00 0.00 0.00 3.51
21 22 1.134521 TGCTTGTTTCGTGGACTGTCT 60.135 47.619 7.85 0.00 0.00 3.41
22 23 1.261619 GCTTGTTTCGTGGACTGTCTG 59.738 52.381 7.85 0.00 0.00 3.51
23 24 1.867233 CTTGTTTCGTGGACTGTCTGG 59.133 52.381 7.85 0.00 0.00 3.86
24 25 1.116308 TGTTTCGTGGACTGTCTGGA 58.884 50.000 7.85 0.22 0.00 3.86
25 26 1.483004 TGTTTCGTGGACTGTCTGGAA 59.517 47.619 7.85 6.25 0.00 3.53
26 27 1.865340 GTTTCGTGGACTGTCTGGAAC 59.135 52.381 7.85 5.83 0.00 3.62
27 28 0.031585 TTCGTGGACTGTCTGGAACG 59.968 55.000 7.85 12.25 0.00 3.95
28 29 0.820482 TCGTGGACTGTCTGGAACGA 60.820 55.000 17.65 17.65 37.68 3.85
29 30 0.387367 CGTGGACTGTCTGGAACGAG 60.387 60.000 7.85 0.00 33.03 4.18
30 31 0.667792 GTGGACTGTCTGGAACGAGC 60.668 60.000 7.85 0.00 0.00 5.03
31 32 1.444553 GGACTGTCTGGAACGAGCG 60.445 63.158 7.85 0.00 0.00 5.03
32 33 1.579932 GACTGTCTGGAACGAGCGA 59.420 57.895 0.00 0.00 0.00 4.93
33 34 0.039437 GACTGTCTGGAACGAGCGAA 60.039 55.000 0.00 0.00 0.00 4.70
34 35 0.387929 ACTGTCTGGAACGAGCGAAA 59.612 50.000 0.00 0.00 0.00 3.46
35 36 0.784778 CTGTCTGGAACGAGCGAAAC 59.215 55.000 0.00 0.00 0.00 2.78
36 37 0.937699 TGTCTGGAACGAGCGAAACG 60.938 55.000 0.00 0.00 0.00 3.60
48 49 2.612200 CGAAACGCAAGGGTCTTCA 58.388 52.632 0.00 0.00 46.39 3.02
49 50 0.941542 CGAAACGCAAGGGTCTTCAA 59.058 50.000 0.00 0.00 46.39 2.69
50 51 1.069906 CGAAACGCAAGGGTCTTCAAG 60.070 52.381 0.00 0.00 46.39 3.02
51 52 0.668535 AAACGCAAGGGTCTTCAAGC 59.331 50.000 0.00 0.00 46.39 4.01
52 53 0.465460 AACGCAAGGGTCTTCAAGCA 60.465 50.000 0.00 0.00 46.39 3.91
53 54 1.166531 ACGCAAGGGTCTTCAAGCAC 61.167 55.000 0.00 0.00 46.39 4.40
54 55 1.165907 CGCAAGGGTCTTCAAGCACA 61.166 55.000 0.00 0.00 0.00 4.57
55 56 1.032014 GCAAGGGTCTTCAAGCACAA 58.968 50.000 0.00 0.00 0.00 3.33
56 57 1.000938 GCAAGGGTCTTCAAGCACAAG 60.001 52.381 0.00 0.00 0.00 3.16
57 58 2.575532 CAAGGGTCTTCAAGCACAAGA 58.424 47.619 0.00 0.00 0.00 3.02
58 59 2.551459 CAAGGGTCTTCAAGCACAAGAG 59.449 50.000 0.00 0.00 30.32 2.85
59 60 0.877743 GGGTCTTCAAGCACAAGAGC 59.122 55.000 11.17 11.17 44.32 4.09
60 61 0.514691 GGTCTTCAAGCACAAGAGCG 59.485 55.000 5.95 0.00 38.30 5.03
61 62 0.110464 GTCTTCAAGCACAAGAGCGC 60.110 55.000 0.00 0.00 40.15 5.92
62 63 0.250038 TCTTCAAGCACAAGAGCGCT 60.250 50.000 11.27 11.27 41.20 5.92
63 64 0.165511 CTTCAAGCACAAGAGCGCTC 59.834 55.000 30.01 30.01 37.54 5.03
64 65 1.230635 TTCAAGCACAAGAGCGCTCC 61.231 55.000 32.94 17.61 37.54 4.70
65 66 1.670406 CAAGCACAAGAGCGCTCCT 60.670 57.895 32.94 19.32 37.54 3.69
66 67 1.375268 AAGCACAAGAGCGCTCCTC 60.375 57.895 32.94 17.13 37.54 3.71
67 68 2.794820 AAGCACAAGAGCGCTCCTCC 62.795 60.000 32.94 16.90 41.74 4.30
68 69 2.659016 CACAAGAGCGCTCCTCCA 59.341 61.111 32.94 0.00 41.74 3.86
69 70 1.004560 CACAAGAGCGCTCCTCCAA 60.005 57.895 32.94 0.00 41.74 3.53
70 71 1.004440 ACAAGAGCGCTCCTCCAAC 60.004 57.895 32.94 7.95 41.74 3.77
71 72 1.294780 CAAGAGCGCTCCTCCAACT 59.705 57.895 32.94 10.71 41.74 3.16
72 73 0.532573 CAAGAGCGCTCCTCCAACTA 59.467 55.000 32.94 0.00 41.74 2.24
73 74 1.137872 CAAGAGCGCTCCTCCAACTAT 59.862 52.381 32.94 9.10 41.74 2.12
74 75 1.490574 AGAGCGCTCCTCCAACTATT 58.509 50.000 32.94 8.29 41.74 1.73
75 76 1.834263 AGAGCGCTCCTCCAACTATTT 59.166 47.619 32.94 7.72 41.74 1.40
76 77 2.237392 AGAGCGCTCCTCCAACTATTTT 59.763 45.455 32.94 7.50 41.74 1.82
77 78 2.352960 GAGCGCTCCTCCAACTATTTTG 59.647 50.000 27.22 0.00 34.35 2.44
78 79 1.202188 GCGCTCCTCCAACTATTTTGC 60.202 52.381 0.00 0.00 0.00 3.68
79 80 2.359900 CGCTCCTCCAACTATTTTGCT 58.640 47.619 0.00 0.00 0.00 3.91
80 81 2.749621 CGCTCCTCCAACTATTTTGCTT 59.250 45.455 0.00 0.00 0.00 3.91
81 82 3.426695 CGCTCCTCCAACTATTTTGCTTG 60.427 47.826 0.00 0.00 0.00 4.01
82 83 3.674410 GCTCCTCCAACTATTTTGCTTGC 60.674 47.826 0.00 0.00 0.00 4.01
83 84 2.825532 TCCTCCAACTATTTTGCTTGCC 59.174 45.455 0.00 0.00 0.00 4.52
84 85 2.827921 CCTCCAACTATTTTGCTTGCCT 59.172 45.455 0.00 0.00 0.00 4.75
85 86 3.119352 CCTCCAACTATTTTGCTTGCCTC 60.119 47.826 0.00 0.00 0.00 4.70
86 87 2.825532 TCCAACTATTTTGCTTGCCTCC 59.174 45.455 0.00 0.00 0.00 4.30
87 88 2.562298 CCAACTATTTTGCTTGCCTCCA 59.438 45.455 0.00 0.00 0.00 3.86
88 89 3.196254 CCAACTATTTTGCTTGCCTCCAT 59.804 43.478 0.00 0.00 0.00 3.41
89 90 4.402155 CCAACTATTTTGCTTGCCTCCATA 59.598 41.667 0.00 0.00 0.00 2.74
90 91 5.450965 CCAACTATTTTGCTTGCCTCCATAG 60.451 44.000 0.00 0.00 0.00 2.23
91 92 5.116084 ACTATTTTGCTTGCCTCCATAGA 57.884 39.130 0.00 0.00 0.00 1.98
92 93 5.128919 ACTATTTTGCTTGCCTCCATAGAG 58.871 41.667 0.00 0.00 40.09 2.43
93 94 3.719268 TTTTGCTTGCCTCCATAGAGA 57.281 42.857 0.00 0.00 43.39 3.10
94 95 2.698855 TTGCTTGCCTCCATAGAGAC 57.301 50.000 0.00 0.00 43.39 3.36
95 96 0.833287 TGCTTGCCTCCATAGAGACC 59.167 55.000 0.00 0.00 43.39 3.85
96 97 0.249657 GCTTGCCTCCATAGAGACCG 60.250 60.000 0.00 0.00 43.39 4.79
97 98 1.403814 CTTGCCTCCATAGAGACCGA 58.596 55.000 0.00 0.00 43.39 4.69
98 99 1.339610 CTTGCCTCCATAGAGACCGAG 59.660 57.143 0.00 0.00 43.39 4.63
99 100 0.468214 TGCCTCCATAGAGACCGAGG 60.468 60.000 0.00 0.00 43.39 4.63
100 101 2.346597 CCTCCATAGAGACCGAGGC 58.653 63.158 0.00 0.00 43.39 4.70
101 102 1.182385 CCTCCATAGAGACCGAGGCC 61.182 65.000 0.00 0.00 43.39 5.19
102 103 0.468214 CTCCATAGAGACCGAGGCCA 60.468 60.000 5.01 0.00 43.39 5.36
103 104 0.032515 TCCATAGAGACCGAGGCCAA 60.033 55.000 5.01 0.00 0.00 4.52
104 105 0.105039 CCATAGAGACCGAGGCCAAC 59.895 60.000 5.01 0.00 0.00 3.77
105 106 0.105039 CATAGAGACCGAGGCCAACC 59.895 60.000 5.01 0.00 0.00 3.77
120 121 0.378257 CAACCTTTGGATCATCGCCG 59.622 55.000 0.00 0.00 0.00 6.46
121 122 0.748005 AACCTTTGGATCATCGCCGG 60.748 55.000 0.00 0.00 0.00 6.13
122 123 1.153168 CCTTTGGATCATCGCCGGT 60.153 57.895 1.90 0.00 0.00 5.28
123 124 1.439353 CCTTTGGATCATCGCCGGTG 61.439 60.000 9.28 9.28 0.00 4.94
124 125 2.051804 CTTTGGATCATCGCCGGTGC 62.052 60.000 11.05 0.00 0.00 5.01
125 126 4.545706 TGGATCATCGCCGGTGCC 62.546 66.667 11.05 5.84 0.00 5.01
126 127 4.545706 GGATCATCGCCGGTGCCA 62.546 66.667 11.05 0.00 0.00 4.92
127 128 2.513666 GATCATCGCCGGTGCCAA 60.514 61.111 11.05 0.00 0.00 4.52
128 129 2.045438 ATCATCGCCGGTGCCAAA 60.045 55.556 11.05 0.00 0.00 3.28
129 130 1.653094 GATCATCGCCGGTGCCAAAA 61.653 55.000 11.05 0.00 0.00 2.44
130 131 1.247419 ATCATCGCCGGTGCCAAAAA 61.247 50.000 11.05 0.00 0.00 1.94
151 152 7.899178 AAAAATTAGGGTCCTTTATTTTGCG 57.101 32.000 10.43 0.00 33.50 4.85
152 153 6.844097 AAATTAGGGTCCTTTATTTTGCGA 57.156 33.333 0.00 0.00 0.00 5.10
153 154 6.451064 AATTAGGGTCCTTTATTTTGCGAG 57.549 37.500 0.00 0.00 0.00 5.03
154 155 3.713826 AGGGTCCTTTATTTTGCGAGA 57.286 42.857 0.00 0.00 0.00 4.04
155 156 3.610911 AGGGTCCTTTATTTTGCGAGAG 58.389 45.455 0.00 0.00 0.00 3.20
156 157 3.009143 AGGGTCCTTTATTTTGCGAGAGT 59.991 43.478 0.00 0.00 0.00 3.24
157 158 3.127030 GGGTCCTTTATTTTGCGAGAGTG 59.873 47.826 0.00 0.00 0.00 3.51
158 159 4.000988 GGTCCTTTATTTTGCGAGAGTGA 58.999 43.478 0.00 0.00 0.00 3.41
159 160 4.636206 GGTCCTTTATTTTGCGAGAGTGAT 59.364 41.667 0.00 0.00 0.00 3.06
160 161 5.220681 GGTCCTTTATTTTGCGAGAGTGATC 60.221 44.000 0.00 0.00 0.00 2.92
161 162 5.582665 GTCCTTTATTTTGCGAGAGTGATCT 59.417 40.000 0.00 0.00 0.00 2.75
162 163 5.812642 TCCTTTATTTTGCGAGAGTGATCTC 59.187 40.000 0.00 0.00 40.70 2.75
163 164 5.582269 CCTTTATTTTGCGAGAGTGATCTCA 59.418 40.000 6.12 0.00 42.66 3.27
164 165 6.259608 CCTTTATTTTGCGAGAGTGATCTCAT 59.740 38.462 6.12 0.00 42.66 2.90
165 166 6.594284 TTATTTTGCGAGAGTGATCTCATG 57.406 37.500 6.12 0.00 42.66 3.07
166 167 1.931906 TTGCGAGAGTGATCTCATGC 58.068 50.000 6.12 2.86 42.66 4.06
167 168 0.103755 TGCGAGAGTGATCTCATGCC 59.896 55.000 6.12 0.00 42.66 4.40
168 169 0.938637 GCGAGAGTGATCTCATGCCG 60.939 60.000 6.12 0.00 42.66 5.69
169 170 0.383590 CGAGAGTGATCTCATGCCGT 59.616 55.000 6.12 0.00 42.66 5.68
170 171 1.850377 GAGAGTGATCTCATGCCGTG 58.150 55.000 0.43 0.00 42.66 4.94
171 172 1.135915 GAGAGTGATCTCATGCCGTGT 59.864 52.381 0.43 0.00 42.66 4.49
172 173 2.359214 GAGAGTGATCTCATGCCGTGTA 59.641 50.000 0.43 0.00 42.66 2.90
173 174 2.961741 AGAGTGATCTCATGCCGTGTAT 59.038 45.455 0.00 0.00 42.66 2.29
174 175 3.386078 AGAGTGATCTCATGCCGTGTATT 59.614 43.478 0.00 0.00 42.66 1.89
175 176 3.461061 AGTGATCTCATGCCGTGTATTG 58.539 45.455 0.00 0.00 0.00 1.90
176 177 3.132824 AGTGATCTCATGCCGTGTATTGA 59.867 43.478 0.00 0.00 0.00 2.57
177 178 3.492383 GTGATCTCATGCCGTGTATTGAG 59.508 47.826 0.00 0.00 0.00 3.02
178 179 3.132824 TGATCTCATGCCGTGTATTGAGT 59.867 43.478 0.00 0.00 0.00 3.41
179 180 2.892374 TCTCATGCCGTGTATTGAGTG 58.108 47.619 0.00 0.00 0.00 3.51
180 181 2.495669 TCTCATGCCGTGTATTGAGTGA 59.504 45.455 0.00 0.00 0.00 3.41
181 182 2.604914 CTCATGCCGTGTATTGAGTGAC 59.395 50.000 0.00 0.00 0.00 3.67
182 183 2.233676 TCATGCCGTGTATTGAGTGACT 59.766 45.455 0.00 0.00 0.00 3.41
183 184 2.831685 TGCCGTGTATTGAGTGACTT 57.168 45.000 0.00 0.00 0.00 3.01
184 185 2.412870 TGCCGTGTATTGAGTGACTTG 58.587 47.619 0.00 0.00 0.00 3.16
185 186 2.224185 TGCCGTGTATTGAGTGACTTGT 60.224 45.455 0.00 0.00 0.00 3.16
186 187 3.006003 TGCCGTGTATTGAGTGACTTGTA 59.994 43.478 0.00 0.00 0.00 2.41
187 188 3.991773 GCCGTGTATTGAGTGACTTGTAA 59.008 43.478 0.00 0.00 0.00 2.41
188 189 4.143179 GCCGTGTATTGAGTGACTTGTAAC 60.143 45.833 0.00 0.00 0.00 2.50
189 190 4.986034 CCGTGTATTGAGTGACTTGTAACA 59.014 41.667 0.00 0.00 0.00 2.41
190 191 5.464057 CCGTGTATTGAGTGACTTGTAACAA 59.536 40.000 0.00 0.00 0.00 2.83
191 192 6.018588 CCGTGTATTGAGTGACTTGTAACAAA 60.019 38.462 0.00 0.00 0.00 2.83
192 193 6.844279 CGTGTATTGAGTGACTTGTAACAAAC 59.156 38.462 0.00 0.00 0.00 2.93
193 194 7.254319 CGTGTATTGAGTGACTTGTAACAAACT 60.254 37.037 0.00 0.00 0.00 2.66
194 195 8.062448 GTGTATTGAGTGACTTGTAACAAACTC 58.938 37.037 0.00 0.00 35.66 3.01
195 196 7.985184 TGTATTGAGTGACTTGTAACAAACTCT 59.015 33.333 0.00 0.00 36.01 3.24
196 197 9.472361 GTATTGAGTGACTTGTAACAAACTCTA 57.528 33.333 0.00 0.00 36.01 2.43
198 199 8.958119 TTGAGTGACTTGTAACAAACTCTATT 57.042 30.769 0.00 0.00 36.01 1.73
225 226 8.455903 TCTCTTATTTAATGGATGAGGCAAAG 57.544 34.615 0.00 0.00 0.00 2.77
226 227 7.013655 TCTCTTATTTAATGGATGAGGCAAAGC 59.986 37.037 0.00 0.00 0.00 3.51
227 228 6.835488 TCTTATTTAATGGATGAGGCAAAGCT 59.165 34.615 0.00 0.00 0.00 3.74
228 229 5.945144 ATTTAATGGATGAGGCAAAGCTT 57.055 34.783 0.00 0.00 0.00 3.74
229 230 5.743636 TTTAATGGATGAGGCAAAGCTTT 57.256 34.783 5.69 5.69 0.00 3.51
230 231 5.743636 TTAATGGATGAGGCAAAGCTTTT 57.256 34.783 9.53 0.00 0.00 2.27
231 232 3.604875 ATGGATGAGGCAAAGCTTTTG 57.395 42.857 9.53 6.62 0.00 2.44
243 244 3.957383 GCTTTTGCCTCCGTTTCAA 57.043 47.368 0.00 0.00 40.15 2.69
244 245 2.217429 GCTTTTGCCTCCGTTTCAAA 57.783 45.000 0.00 0.00 40.15 2.69
245 246 2.545731 GCTTTTGCCTCCGTTTCAAAA 58.454 42.857 0.00 0.00 40.15 2.44
246 247 2.933260 GCTTTTGCCTCCGTTTCAAAAA 59.067 40.909 0.00 0.00 38.65 1.94
272 273 0.242017 AAAAGCAAGCATGGCGTCTC 59.758 50.000 0.00 0.00 42.81 3.36
330 331 2.030946 GCGTCAATGGAGATAGTGTTGC 59.969 50.000 0.00 0.00 0.00 4.17
383 384 3.606846 CGACAACGACTTGACATGCAATT 60.607 43.478 0.00 0.00 42.66 2.32
408 409 3.812262 CCATGATCTCCAACACATGCTA 58.188 45.455 0.00 0.00 38.79 3.49
411 412 4.128925 TGATCTCCAACACATGCTACTC 57.871 45.455 0.00 0.00 0.00 2.59
415 416 2.234661 CTCCAACACATGCTACTCTCCA 59.765 50.000 0.00 0.00 0.00 3.86
429 430 2.271800 CTCTCCATTGCCGTAACAGTC 58.728 52.381 0.00 0.00 0.00 3.51
487 583 7.354312 ACTTCAACTTATTATGGGCCTTACAT 58.646 34.615 4.53 0.00 0.00 2.29
644 895 8.783833 AGTTAGCGCTGATTCATATGATTATT 57.216 30.769 22.90 0.00 0.00 1.40
645 896 8.663025 AGTTAGCGCTGATTCATATGATTATTG 58.337 33.333 22.90 0.00 0.00 1.90
646 897 8.659491 GTTAGCGCTGATTCATATGATTATTGA 58.341 33.333 22.90 0.00 0.00 2.57
648 899 8.277490 AGCGCTGATTCATATGATTATTGATT 57.723 30.769 10.39 0.00 0.00 2.57
649 900 9.387257 AGCGCTGATTCATATGATTATTGATTA 57.613 29.630 10.39 0.00 0.00 1.75
650 901 9.430838 GCGCTGATTCATATGATTATTGATTAC 57.569 33.333 6.17 0.00 0.00 1.89
696 947 2.008543 GCATCTTCGGACTGACATGCA 61.009 52.381 17.32 0.00 40.56 3.96
697 948 2.558378 CATCTTCGGACTGACATGCAT 58.442 47.619 0.00 0.00 0.00 3.96
701 952 2.183478 TCGGACTGACATGCATGTTT 57.817 45.000 31.82 19.55 41.95 2.83
715 984 4.334552 TGCATGTTTAGCTGGAATCTTGA 58.665 39.130 0.00 0.00 0.00 3.02
751 1020 3.362706 AGCCGGATTCAGACACTACTAA 58.637 45.455 5.05 0.00 0.00 2.24
797 1070 3.782244 CGAACAGAGGCTGCACGC 61.782 66.667 0.50 0.11 34.37 5.34
839 1112 4.862641 ACTTTGGCCCTTCATATACAGT 57.137 40.909 0.00 0.00 0.00 3.55
852 1125 9.077674 CCTTCATATACAGTTACATAGATTCGC 57.922 37.037 0.00 0.00 0.00 4.70
891 1164 2.525368 CCGGGAGTCCCTCAAATTTTT 58.475 47.619 26.04 0.00 42.67 1.94
913 1186 0.161024 GTTGAACTCTCGTTTCGCCG 59.839 55.000 0.00 0.00 32.39 6.46
977 1250 0.024619 GTTCGTTGCTAATCGCCGAC 59.975 55.000 0.00 0.00 38.05 4.79
985 1258 1.529865 GCTAATCGCCGACATAAACCC 59.470 52.381 0.00 0.00 0.00 4.11
1063 1336 4.824515 AGGAGGGAGAGGGCGTCG 62.825 72.222 0.96 0.00 0.00 5.12
1092 1365 2.029844 GAAGGACGTGCTGGACTGC 61.030 63.158 11.44 0.00 0.00 4.40
1106 1379 4.767255 CTGCCCCGTCTGCTCCAC 62.767 72.222 0.00 0.00 0.00 4.02
1143 1416 7.020827 TCCCATCTTCCAGGTAATCATATTC 57.979 40.000 0.00 0.00 0.00 1.75
1192 1471 4.613925 ACTCTCATCACTCATGTGTTGT 57.386 40.909 0.00 0.00 44.14 3.32
1193 1472 4.965814 ACTCTCATCACTCATGTGTTGTT 58.034 39.130 0.00 0.00 44.14 2.83
1194 1473 4.753610 ACTCTCATCACTCATGTGTTGTTG 59.246 41.667 0.00 0.00 44.14 3.33
1195 1474 4.959723 TCTCATCACTCATGTGTTGTTGA 58.040 39.130 0.00 1.66 44.14 3.18
1196 1475 5.554070 TCTCATCACTCATGTGTTGTTGAT 58.446 37.500 0.00 0.00 44.14 2.57
1209 1488 7.022055 TGTGTTGTTGATGACGTTAATTCTT 57.978 32.000 0.00 0.00 0.00 2.52
1215 1494 7.577979 TGTTGATGACGTTAATTCTTAACCAC 58.422 34.615 0.00 1.09 41.87 4.16
1348 1634 2.202919 TCCAGACGATGCCATGCG 60.203 61.111 0.00 0.00 0.00 4.73
1530 3280 1.289066 CGCTCCTGAACCACTTCGA 59.711 57.895 0.00 0.00 0.00 3.71
1568 3318 0.094046 GGTCACGGCGTTCAAATACG 59.906 55.000 11.19 0.00 44.09 3.06
1640 3390 3.238570 CAGCGAAGAATACGAAGAAGACG 59.761 47.826 0.00 0.00 0.00 4.18
1645 3395 5.966503 CGAAGAATACGAAGAAGACGAAGAT 59.033 40.000 0.00 0.00 34.70 2.40
1648 3398 7.033530 AGAATACGAAGAAGACGAAGATGAT 57.966 36.000 0.00 0.00 34.70 2.45
1697 3447 3.061848 CCCCGGACACCACAATGC 61.062 66.667 0.73 0.00 0.00 3.56
1698 3448 3.430862 CCCGGACACCACAATGCG 61.431 66.667 0.73 0.00 0.00 4.73
1699 3449 4.101790 CCGGACACCACAATGCGC 62.102 66.667 0.00 0.00 0.00 6.09
1754 3504 1.245732 GGAGTACGATATCGGGTGCT 58.754 55.000 27.58 16.62 44.95 4.40
1755 3505 1.199558 GGAGTACGATATCGGGTGCTC 59.800 57.143 27.58 22.71 42.76 4.26
1877 3627 4.000620 TACCCGAGGCTCCACCCA 62.001 66.667 9.32 0.00 40.58 4.51
1878 3628 3.326385 TACCCGAGGCTCCACCCAT 62.326 63.158 9.32 0.00 40.58 4.00
1904 3654 1.676967 GGGCTTGCCTTCCTCAGTG 60.677 63.158 11.71 0.00 0.00 3.66
1914 3664 1.546029 CTTCCTCAGTGTCACCATCGA 59.454 52.381 0.00 0.00 0.00 3.59
1948 3707 0.965866 ATGACGACGAGCAGGAGGAA 60.966 55.000 0.00 0.00 0.00 3.36
2023 3782 0.036765 TACCTGCCAACGGTGATGAC 60.037 55.000 0.00 0.00 35.98 3.06
2033 3792 2.583143 ACGGTGATGACGAGGATGATA 58.417 47.619 0.00 0.00 34.93 2.15
2043 3802 1.546029 CGAGGATGATAAGGCGGATGA 59.454 52.381 0.00 0.00 0.00 2.92
2052 3811 2.715749 AAGGCGGATGATCACAATGA 57.284 45.000 0.00 0.00 0.00 2.57
2068 3827 5.578336 TCACAATGATGATTGACGAACTCTC 59.422 40.000 12.12 0.00 41.49 3.20
2070 3829 4.549680 CAATGATGATTGACGAACTCTCGC 60.550 45.833 0.00 0.00 41.49 5.03
2081 3840 1.663135 GAACTCTCGCATTTGGAGCTC 59.337 52.381 4.71 4.71 0.00 4.09
2092 3851 4.033014 GCATTTGGAGCTCGTTAACTAGTC 59.967 45.833 7.83 5.44 0.00 2.59
2096 3863 3.120060 TGGAGCTCGTTAACTAGTCGTTC 60.120 47.826 7.83 2.96 37.05 3.95
2104 3871 5.048504 TCGTTAACTAGTCGTTCAAGGATGT 60.049 40.000 3.71 0.00 37.05 3.06
2107 3874 7.487189 CGTTAACTAGTCGTTCAAGGATGTATT 59.513 37.037 3.71 0.00 37.05 1.89
2108 3875 8.592998 GTTAACTAGTCGTTCAAGGATGTATTG 58.407 37.037 0.00 0.00 37.05 1.90
2110 3877 6.565234 ACTAGTCGTTCAAGGATGTATTGAG 58.435 40.000 0.00 0.00 37.91 3.02
2111 3878 5.661056 AGTCGTTCAAGGATGTATTGAGA 57.339 39.130 0.00 0.00 37.91 3.27
2112 3879 5.411781 AGTCGTTCAAGGATGTATTGAGAC 58.588 41.667 0.00 0.00 37.91 3.36
2113 3880 5.186021 AGTCGTTCAAGGATGTATTGAGACT 59.814 40.000 5.32 5.32 37.36 3.24
2114 3881 5.869888 GTCGTTCAAGGATGTATTGAGACTT 59.130 40.000 0.00 0.00 37.91 3.01
2119 3889 8.821894 GTTCAAGGATGTATTGAGACTTCATAC 58.178 37.037 0.00 0.00 37.91 2.39
2132 3902 5.615289 AGACTTCATACATACAATCTGGGC 58.385 41.667 0.00 0.00 0.00 5.36
2138 3908 8.450578 TTCATACATACAATCTGGGCTTTTAG 57.549 34.615 0.00 0.00 0.00 1.85
2139 3909 6.486657 TCATACATACAATCTGGGCTTTTAGC 59.513 38.462 0.00 0.00 41.46 3.09
2140 3910 4.599041 ACATACAATCTGGGCTTTTAGCA 58.401 39.130 0.67 0.00 44.75 3.49
2186 3958 4.899352 AGTGGTTCTGTTCTAATCTGCT 57.101 40.909 0.00 0.00 0.00 4.24
2196 3968 6.095580 TCTGTTCTAATCTGCTATTCAGTCGT 59.904 38.462 0.00 0.00 43.32 4.34
2212 3986 4.449743 TCAGTCGTTTAAAAAGTGATCGGG 59.550 41.667 5.63 0.00 0.00 5.14
2221 3995 4.965119 AAAAGTGATCGGGTTAATGCTC 57.035 40.909 0.00 0.00 0.00 4.26
2241 4016 4.384056 CTCCATTGGCGATTCAGTATCTT 58.616 43.478 0.00 0.00 0.00 2.40
2250 4025 6.127451 TGGCGATTCAGTATCTTTCTTCAGTA 60.127 38.462 0.00 0.00 0.00 2.74
2376 4155 3.996150 AACTCAAAATGTGCCTGTCAG 57.004 42.857 0.00 0.00 0.00 3.51
2405 4193 9.395707 ACGAGTCATGATTATACTACGATTTTC 57.604 33.333 0.00 0.00 0.00 2.29
2495 4285 7.715264 AGTTAACTATTTTACGCGCAAAATC 57.285 32.000 28.24 15.66 38.65 2.17
2500 4290 7.892445 ACTATTTTACGCGCAAAATCAATAG 57.108 32.000 28.24 22.24 38.65 1.73
2682 4497 9.846248 AAAATTAGAAACCTCATTTTCGAGATG 57.154 29.630 4.89 4.89 39.96 2.90
2684 4499 7.596749 TTAGAAACCTCATTTTCGAGATGTC 57.403 36.000 9.73 2.21 39.96 3.06
2688 4503 6.633500 AACCTCATTTTCGAGATGTCAAAA 57.367 33.333 9.73 0.00 34.79 2.44
2700 4515 6.537301 TCGAGATGTCAAAATATGGTGGTTAC 59.463 38.462 0.00 0.00 0.00 2.50
2718 4533 8.027189 GGTGGTTACAATAGAAACCTCATTTTC 58.973 37.037 5.88 0.00 44.55 2.29
2905 4727 5.009631 TGGTGGTGAAATAGAAACCTCATG 58.990 41.667 0.00 0.00 34.90 3.07
3047 4871 6.822676 AGATTTCAGCATTTTGGTCAAAACAA 59.177 30.769 10.56 0.00 42.32 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.873591 GACAGTCCACGAAACAAGCAT 59.126 47.619 0.00 0.00 0.00 3.79
1 2 1.134521 AGACAGTCCACGAAACAAGCA 60.135 47.619 0.00 0.00 0.00 3.91
2 3 1.261619 CAGACAGTCCACGAAACAAGC 59.738 52.381 0.00 0.00 0.00 4.01
3 4 1.867233 CCAGACAGTCCACGAAACAAG 59.133 52.381 0.00 0.00 0.00 3.16
4 5 1.483004 TCCAGACAGTCCACGAAACAA 59.517 47.619 0.00 0.00 0.00 2.83
5 6 1.116308 TCCAGACAGTCCACGAAACA 58.884 50.000 0.00 0.00 0.00 2.83
6 7 1.865340 GTTCCAGACAGTCCACGAAAC 59.135 52.381 0.00 0.00 0.00 2.78
7 8 1.537348 CGTTCCAGACAGTCCACGAAA 60.537 52.381 0.00 0.00 0.00 3.46
8 9 0.031585 CGTTCCAGACAGTCCACGAA 59.968 55.000 0.00 0.00 0.00 3.85
9 10 0.820482 TCGTTCCAGACAGTCCACGA 60.820 55.000 9.65 9.65 34.45 4.35
10 11 0.387367 CTCGTTCCAGACAGTCCACG 60.387 60.000 0.00 1.60 0.00 4.94
11 12 0.667792 GCTCGTTCCAGACAGTCCAC 60.668 60.000 0.00 0.00 0.00 4.02
12 13 1.666011 GCTCGTTCCAGACAGTCCA 59.334 57.895 0.00 0.00 0.00 4.02
13 14 1.444553 CGCTCGTTCCAGACAGTCC 60.445 63.158 0.00 0.00 0.00 3.85
14 15 0.039437 TTCGCTCGTTCCAGACAGTC 60.039 55.000 0.00 0.00 0.00 3.51
15 16 0.387929 TTTCGCTCGTTCCAGACAGT 59.612 50.000 0.00 0.00 0.00 3.55
16 17 0.784778 GTTTCGCTCGTTCCAGACAG 59.215 55.000 0.00 0.00 0.00 3.51
17 18 0.937699 CGTTTCGCTCGTTCCAGACA 60.938 55.000 0.00 0.00 0.00 3.41
18 19 1.773496 CGTTTCGCTCGTTCCAGAC 59.227 57.895 0.00 0.00 0.00 3.51
19 20 4.238385 CGTTTCGCTCGTTCCAGA 57.762 55.556 0.00 0.00 0.00 3.86
30 31 0.941542 TTGAAGACCCTTGCGTTTCG 59.058 50.000 0.00 0.00 0.00 3.46
31 32 1.335051 GCTTGAAGACCCTTGCGTTTC 60.335 52.381 0.00 0.00 0.00 2.78
32 33 0.668535 GCTTGAAGACCCTTGCGTTT 59.331 50.000 0.00 0.00 0.00 3.60
33 34 0.465460 TGCTTGAAGACCCTTGCGTT 60.465 50.000 0.00 0.00 0.00 4.84
34 35 1.148273 TGCTTGAAGACCCTTGCGT 59.852 52.632 0.00 0.00 0.00 5.24
35 36 1.165907 TGTGCTTGAAGACCCTTGCG 61.166 55.000 0.00 0.00 0.00 4.85
36 37 1.000938 CTTGTGCTTGAAGACCCTTGC 60.001 52.381 0.00 0.00 0.00 4.01
37 38 2.551459 CTCTTGTGCTTGAAGACCCTTG 59.449 50.000 0.00 0.00 0.00 3.61
38 39 2.856222 CTCTTGTGCTTGAAGACCCTT 58.144 47.619 0.00 0.00 0.00 3.95
39 40 1.544314 GCTCTTGTGCTTGAAGACCCT 60.544 52.381 0.00 0.00 0.00 4.34
40 41 0.877743 GCTCTTGTGCTTGAAGACCC 59.122 55.000 0.00 0.00 0.00 4.46
41 42 0.514691 CGCTCTTGTGCTTGAAGACC 59.485 55.000 0.00 0.00 0.00 3.85
42 43 0.110464 GCGCTCTTGTGCTTGAAGAC 60.110 55.000 0.00 0.00 45.43 3.01
43 44 2.238353 GCGCTCTTGTGCTTGAAGA 58.762 52.632 0.00 0.00 45.43 2.87
44 45 4.834828 GCGCTCTTGTGCTTGAAG 57.165 55.556 0.00 0.00 45.43 3.02
51 52 1.004560 TTGGAGGAGCGCTCTTGTG 60.005 57.895 34.46 0.00 0.00 3.33
52 53 1.004440 GTTGGAGGAGCGCTCTTGT 60.004 57.895 34.46 20.59 0.00 3.16
53 54 0.532573 TAGTTGGAGGAGCGCTCTTG 59.467 55.000 34.46 0.00 0.00 3.02
54 55 1.490574 ATAGTTGGAGGAGCGCTCTT 58.509 50.000 34.46 29.44 0.00 2.85
55 56 1.490574 AATAGTTGGAGGAGCGCTCT 58.509 50.000 34.46 21.46 0.00 4.09
56 57 2.317530 AAATAGTTGGAGGAGCGCTC 57.682 50.000 29.38 29.38 0.00 5.03
57 58 2.359900 CAAAATAGTTGGAGGAGCGCT 58.640 47.619 11.27 11.27 0.00 5.92
58 59 1.202188 GCAAAATAGTTGGAGGAGCGC 60.202 52.381 0.00 0.00 0.00 5.92
59 60 2.359900 AGCAAAATAGTTGGAGGAGCG 58.640 47.619 0.00 0.00 0.00 5.03
60 61 3.674410 GCAAGCAAAATAGTTGGAGGAGC 60.674 47.826 0.00 0.00 0.00 4.70
61 62 3.119352 GGCAAGCAAAATAGTTGGAGGAG 60.119 47.826 0.00 0.00 0.00 3.69
62 63 2.825532 GGCAAGCAAAATAGTTGGAGGA 59.174 45.455 0.00 0.00 0.00 3.71
63 64 2.827921 AGGCAAGCAAAATAGTTGGAGG 59.172 45.455 0.00 0.00 0.00 4.30
64 65 3.119352 GGAGGCAAGCAAAATAGTTGGAG 60.119 47.826 0.00 0.00 0.00 3.86
65 66 2.825532 GGAGGCAAGCAAAATAGTTGGA 59.174 45.455 0.00 0.00 0.00 3.53
66 67 2.562298 TGGAGGCAAGCAAAATAGTTGG 59.438 45.455 0.00 0.00 0.00 3.77
67 68 3.940209 TGGAGGCAAGCAAAATAGTTG 57.060 42.857 0.00 0.00 0.00 3.16
68 69 5.509498 TCTATGGAGGCAAGCAAAATAGTT 58.491 37.500 0.00 0.00 0.00 2.24
69 70 5.104360 TCTCTATGGAGGCAAGCAAAATAGT 60.104 40.000 6.21 0.00 39.86 2.12
70 71 5.238214 GTCTCTATGGAGGCAAGCAAAATAG 59.762 44.000 5.72 0.00 43.17 1.73
71 72 5.126067 GTCTCTATGGAGGCAAGCAAAATA 58.874 41.667 5.72 0.00 43.17 1.40
72 73 3.950395 GTCTCTATGGAGGCAAGCAAAAT 59.050 43.478 5.72 0.00 43.17 1.82
73 74 3.347216 GTCTCTATGGAGGCAAGCAAAA 58.653 45.455 5.72 0.00 43.17 2.44
74 75 2.356125 GGTCTCTATGGAGGCAAGCAAA 60.356 50.000 13.11 0.00 45.27 3.68
75 76 1.210478 GGTCTCTATGGAGGCAAGCAA 59.790 52.381 13.11 0.00 45.27 3.91
76 77 0.833287 GGTCTCTATGGAGGCAAGCA 59.167 55.000 13.11 0.00 45.27 3.91
77 78 0.249657 CGGTCTCTATGGAGGCAAGC 60.250 60.000 13.11 0.00 45.27 4.01
78 79 1.339610 CTCGGTCTCTATGGAGGCAAG 59.660 57.143 13.11 5.56 45.27 4.01
79 80 1.403814 CTCGGTCTCTATGGAGGCAA 58.596 55.000 13.11 0.00 45.27 4.52
80 81 0.468214 CCTCGGTCTCTATGGAGGCA 60.468 60.000 13.11 0.00 45.27 4.75
81 82 2.346597 CCTCGGTCTCTATGGAGGC 58.653 63.158 6.21 3.87 42.96 4.70
83 84 0.468214 TGGCCTCGGTCTCTATGGAG 60.468 60.000 3.32 0.00 40.73 3.86
84 85 0.032515 TTGGCCTCGGTCTCTATGGA 60.033 55.000 3.32 0.00 0.00 3.41
85 86 0.105039 GTTGGCCTCGGTCTCTATGG 59.895 60.000 3.32 0.00 0.00 2.74
86 87 0.105039 GGTTGGCCTCGGTCTCTATG 59.895 60.000 3.32 0.00 0.00 2.23
87 88 0.032017 AGGTTGGCCTCGGTCTCTAT 60.032 55.000 3.32 0.00 42.67 1.98
88 89 0.252103 AAGGTTGGCCTCGGTCTCTA 60.252 55.000 3.32 0.00 46.33 2.43
89 90 1.128188 AAAGGTTGGCCTCGGTCTCT 61.128 55.000 3.32 0.00 46.33 3.10
90 91 0.955919 CAAAGGTTGGCCTCGGTCTC 60.956 60.000 3.32 0.00 46.33 3.36
91 92 1.073199 CAAAGGTTGGCCTCGGTCT 59.927 57.895 3.32 0.00 46.33 3.85
92 93 1.971695 CCAAAGGTTGGCCTCGGTC 60.972 63.158 3.32 0.00 46.33 4.79
93 94 2.115266 CCAAAGGTTGGCCTCGGT 59.885 61.111 3.32 0.00 46.33 4.69
101 102 0.378257 CGGCGATGATCCAAAGGTTG 59.622 55.000 0.00 0.00 0.00 3.77
102 103 0.748005 CCGGCGATGATCCAAAGGTT 60.748 55.000 9.30 0.00 0.00 3.50
103 104 1.153168 CCGGCGATGATCCAAAGGT 60.153 57.895 9.30 0.00 0.00 3.50
104 105 1.153168 ACCGGCGATGATCCAAAGG 60.153 57.895 9.30 0.00 0.00 3.11
105 106 2.016961 CACCGGCGATGATCCAAAG 58.983 57.895 9.30 0.00 0.00 2.77
106 107 2.112198 GCACCGGCGATGATCCAAA 61.112 57.895 4.84 0.00 0.00 3.28
107 108 2.513666 GCACCGGCGATGATCCAA 60.514 61.111 4.84 0.00 0.00 3.53
108 109 4.545706 GGCACCGGCGATGATCCA 62.546 66.667 4.84 0.00 42.47 3.41
109 110 4.545706 TGGCACCGGCGATGATCC 62.546 66.667 4.84 0.00 42.47 3.36
110 111 1.653094 TTTTGGCACCGGCGATGATC 61.653 55.000 4.84 0.00 42.47 2.92
111 112 1.247419 TTTTTGGCACCGGCGATGAT 61.247 50.000 4.84 0.00 42.47 2.45
112 113 1.899054 TTTTTGGCACCGGCGATGA 60.899 52.632 4.84 0.00 42.47 2.92
113 114 2.647875 TTTTTGGCACCGGCGATG 59.352 55.556 9.30 0.65 42.47 3.84
127 128 7.672240 TCGCAAAATAAAGGACCCTAATTTTT 58.328 30.769 14.43 7.59 33.41 1.94
128 129 7.177744 TCTCGCAAAATAAAGGACCCTAATTTT 59.822 33.333 12.56 12.56 34.72 1.82
129 130 6.661805 TCTCGCAAAATAAAGGACCCTAATTT 59.338 34.615 0.00 0.00 0.00 1.82
130 131 6.184789 TCTCGCAAAATAAAGGACCCTAATT 58.815 36.000 0.00 0.00 0.00 1.40
131 132 5.751586 TCTCGCAAAATAAAGGACCCTAAT 58.248 37.500 0.00 0.00 0.00 1.73
132 133 5.168647 TCTCGCAAAATAAAGGACCCTAA 57.831 39.130 0.00 0.00 0.00 2.69
133 134 4.224370 ACTCTCGCAAAATAAAGGACCCTA 59.776 41.667 0.00 0.00 0.00 3.53
134 135 3.009143 ACTCTCGCAAAATAAAGGACCCT 59.991 43.478 0.00 0.00 0.00 4.34
135 136 3.127030 CACTCTCGCAAAATAAAGGACCC 59.873 47.826 0.00 0.00 0.00 4.46
136 137 4.000988 TCACTCTCGCAAAATAAAGGACC 58.999 43.478 0.00 0.00 0.00 4.46
137 138 5.582665 AGATCACTCTCGCAAAATAAAGGAC 59.417 40.000 0.00 0.00 0.00 3.85
138 139 5.734720 AGATCACTCTCGCAAAATAAAGGA 58.265 37.500 0.00 0.00 0.00 3.36
139 140 6.042144 GAGATCACTCTCGCAAAATAAAGG 57.958 41.667 0.00 0.00 38.70 3.11
151 152 1.135915 ACACGGCATGAGATCACTCTC 59.864 52.381 0.00 0.00 46.89 3.20
152 153 1.189752 ACACGGCATGAGATCACTCT 58.810 50.000 0.00 0.00 42.99 3.24
153 154 2.871182 TACACGGCATGAGATCACTC 57.129 50.000 0.00 0.00 42.88 3.51
154 155 3.132824 TCAATACACGGCATGAGATCACT 59.867 43.478 0.00 0.00 0.00 3.41
155 156 3.457234 TCAATACACGGCATGAGATCAC 58.543 45.455 0.00 0.00 0.00 3.06
156 157 3.132824 ACTCAATACACGGCATGAGATCA 59.867 43.478 8.48 0.00 41.38 2.92
157 158 3.492383 CACTCAATACACGGCATGAGATC 59.508 47.826 8.48 0.00 41.38 2.75
158 159 3.132824 TCACTCAATACACGGCATGAGAT 59.867 43.478 8.48 0.00 41.38 2.75
159 160 2.495669 TCACTCAATACACGGCATGAGA 59.504 45.455 8.48 0.00 41.38 3.27
160 161 2.604914 GTCACTCAATACACGGCATGAG 59.395 50.000 0.00 0.00 43.79 2.90
161 162 2.233676 AGTCACTCAATACACGGCATGA 59.766 45.455 0.00 0.00 0.00 3.07
162 163 2.621338 AGTCACTCAATACACGGCATG 58.379 47.619 0.00 0.00 0.00 4.06
163 164 3.002791 CAAGTCACTCAATACACGGCAT 58.997 45.455 0.00 0.00 0.00 4.40
164 165 2.224185 ACAAGTCACTCAATACACGGCA 60.224 45.455 0.00 0.00 0.00 5.69
165 166 2.413837 ACAAGTCACTCAATACACGGC 58.586 47.619 0.00 0.00 0.00 5.68
166 167 4.986034 TGTTACAAGTCACTCAATACACGG 59.014 41.667 0.00 0.00 0.00 4.94
167 168 6.519353 TTGTTACAAGTCACTCAATACACG 57.481 37.500 0.00 0.00 0.00 4.49
168 169 7.916552 AGTTTGTTACAAGTCACTCAATACAC 58.083 34.615 0.00 0.00 0.00 2.90
169 170 7.985184 AGAGTTTGTTACAAGTCACTCAATACA 59.015 33.333 22.46 0.00 34.33 2.29
170 171 8.366671 AGAGTTTGTTACAAGTCACTCAATAC 57.633 34.615 22.46 6.26 34.33 1.89
172 173 9.561069 AATAGAGTTTGTTACAAGTCACTCAAT 57.439 29.630 22.46 11.04 34.33 2.57
173 174 8.958119 AATAGAGTTTGTTACAAGTCACTCAA 57.042 30.769 22.46 4.15 34.33 3.02
199 200 9.075678 CTTTGCCTCATCCATTAAATAAGAGAT 57.924 33.333 0.00 0.00 0.00 2.75
200 201 7.013655 GCTTTGCCTCATCCATTAAATAAGAGA 59.986 37.037 0.00 0.00 0.00 3.10
201 202 7.014038 AGCTTTGCCTCATCCATTAAATAAGAG 59.986 37.037 0.00 0.00 0.00 2.85
202 203 6.835488 AGCTTTGCCTCATCCATTAAATAAGA 59.165 34.615 0.00 0.00 0.00 2.10
203 204 7.047460 AGCTTTGCCTCATCCATTAAATAAG 57.953 36.000 0.00 0.00 0.00 1.73
204 205 7.422465 AAGCTTTGCCTCATCCATTAAATAA 57.578 32.000 0.00 0.00 0.00 1.40
205 206 7.422465 AAAGCTTTGCCTCATCCATTAAATA 57.578 32.000 11.80 0.00 0.00 1.40
206 207 5.945144 AAGCTTTGCCTCATCCATTAAAT 57.055 34.783 0.00 0.00 0.00 1.40
207 208 5.743636 AAAGCTTTGCCTCATCCATTAAA 57.256 34.783 11.80 0.00 0.00 1.52
208 209 5.481105 CAAAAGCTTTGCCTCATCCATTAA 58.519 37.500 13.54 0.00 0.00 1.40
209 210 4.621274 GCAAAAGCTTTGCCTCATCCATTA 60.621 41.667 13.54 0.00 39.38 1.90
210 211 3.867216 GCAAAAGCTTTGCCTCATCCATT 60.867 43.478 13.54 0.00 39.38 3.16
211 212 2.354403 GCAAAAGCTTTGCCTCATCCAT 60.354 45.455 13.54 0.00 39.38 3.41
212 213 1.001181 GCAAAAGCTTTGCCTCATCCA 59.999 47.619 13.54 0.00 39.38 3.41
213 214 1.718396 GCAAAAGCTTTGCCTCATCC 58.282 50.000 13.54 0.00 39.38 3.51
220 221 0.249447 AACGGAGGCAAAAGCTTTGC 60.249 50.000 13.54 17.13 44.22 3.68
221 222 2.127251 GAAACGGAGGCAAAAGCTTTG 58.873 47.619 13.54 8.26 0.00 2.77
222 223 1.754226 TGAAACGGAGGCAAAAGCTTT 59.246 42.857 5.69 5.69 0.00 3.51
223 224 1.398692 TGAAACGGAGGCAAAAGCTT 58.601 45.000 0.00 0.00 0.00 3.74
224 225 1.398692 TTGAAACGGAGGCAAAAGCT 58.601 45.000 0.00 0.00 0.00 3.74
225 226 2.217429 TTTGAAACGGAGGCAAAAGC 57.783 45.000 0.00 0.00 0.00 3.51
252 253 0.675633 AGACGCCATGCTTGCTTTTT 59.324 45.000 0.00 0.00 0.00 1.94
253 254 0.242017 GAGACGCCATGCTTGCTTTT 59.758 50.000 0.00 0.00 0.00 2.27
254 255 1.878775 GAGACGCCATGCTTGCTTT 59.121 52.632 0.00 0.00 0.00 3.51
255 256 2.393768 CGAGACGCCATGCTTGCTT 61.394 57.895 0.00 0.00 0.00 3.91
256 257 2.816958 CGAGACGCCATGCTTGCT 60.817 61.111 0.00 0.00 0.00 3.91
257 258 3.869272 CCGAGACGCCATGCTTGC 61.869 66.667 0.00 0.00 0.00 4.01
258 259 3.869272 GCCGAGACGCCATGCTTG 61.869 66.667 0.00 0.00 0.00 4.01
259 260 3.687321 ATGCCGAGACGCCATGCTT 62.687 57.895 0.00 0.00 0.00 3.91
260 261 4.166888 ATGCCGAGACGCCATGCT 62.167 61.111 0.00 0.00 0.00 3.79
261 262 3.945434 CATGCCGAGACGCCATGC 61.945 66.667 2.56 0.00 0.00 4.06
262 263 3.274586 CCATGCCGAGACGCCATG 61.275 66.667 7.87 7.87 0.00 3.66
272 273 1.227764 CTGGTCCATCTCCATGCCG 60.228 63.158 0.00 0.00 34.26 5.69
330 331 2.707849 GCATCTGCAAGGCCTGGTG 61.708 63.158 5.69 2.04 41.59 4.17
383 384 0.034186 GTGTTGGAGATCATGGCCCA 60.034 55.000 0.00 0.00 0.00 5.36
408 409 1.623811 ACTGTTACGGCAATGGAGAGT 59.376 47.619 0.00 0.00 0.00 3.24
411 412 2.271800 GAGACTGTTACGGCAATGGAG 58.728 52.381 0.00 0.00 0.00 3.86
415 416 1.271379 TGACGAGACTGTTACGGCAAT 59.729 47.619 12.19 0.00 42.07 3.56
429 430 2.627515 AATGATCCATGGGTGACGAG 57.372 50.000 13.02 0.00 0.00 4.18
606 857 7.843490 TCAGCGCTAACTAACTCATATTTTT 57.157 32.000 10.99 0.00 0.00 1.94
614 865 6.863645 TCATATGAATCAGCGCTAACTAACTC 59.136 38.462 10.99 0.55 0.00 3.01
620 871 8.659491 TCAATAATCATATGAATCAGCGCTAAC 58.341 33.333 10.99 2.20 0.00 2.34
649 900 9.793259 TTTGGAAACTCTTTTCAGATATACTGT 57.207 29.630 0.00 0.00 45.86 3.55
651 902 8.951243 GCTTTGGAAACTCTTTTCAGATATACT 58.049 33.333 0.00 0.00 42.72 2.12
652 903 8.730680 TGCTTTGGAAACTCTTTTCAGATATAC 58.269 33.333 0.00 0.00 42.72 1.47
653 904 8.862325 TGCTTTGGAAACTCTTTTCAGATATA 57.138 30.769 0.00 0.00 42.72 0.86
654 905 7.765695 TGCTTTGGAAACTCTTTTCAGATAT 57.234 32.000 0.00 0.00 42.72 1.63
655 906 7.667219 AGATGCTTTGGAAACTCTTTTCAGATA 59.333 33.333 0.00 0.00 42.72 1.98
656 907 6.492772 AGATGCTTTGGAAACTCTTTTCAGAT 59.507 34.615 0.00 0.00 42.72 2.90
696 947 3.941483 CCGTCAAGATTCCAGCTAAACAT 59.059 43.478 0.00 0.00 0.00 2.71
697 948 3.007506 TCCGTCAAGATTCCAGCTAAACA 59.992 43.478 0.00 0.00 0.00 2.83
701 952 2.457598 AGTCCGTCAAGATTCCAGCTA 58.542 47.619 0.00 0.00 0.00 3.32
715 984 0.942962 CGGCTCGTATAGAAGTCCGT 59.057 55.000 0.00 0.00 0.00 4.69
751 1020 6.594159 CAGATAGGAGGTGTGTTTTCGTTTAT 59.406 38.462 0.00 0.00 0.00 1.40
797 1070 3.520290 TGTCCGTTTCCTAGTAGCATG 57.480 47.619 0.00 0.00 0.00 4.06
830 1103 6.757010 GGGGCGAATCTATGTAACTGTATATG 59.243 42.308 0.00 0.00 0.00 1.78
839 1112 5.617528 TTACAAGGGGCGAATCTATGTAA 57.382 39.130 0.00 0.00 31.49 2.41
852 1125 1.376609 GCTGTGGCGATTACAAGGGG 61.377 60.000 0.00 0.00 0.00 4.79
913 1186 2.385013 AAATCGGCAATTTCTTGGGC 57.615 45.000 0.00 0.00 31.78 5.36
953 1226 2.873170 CGATTAGCAACGAACAAGCA 57.127 45.000 0.00 0.00 0.00 3.91
977 1250 0.176219 TCCACTACCGCGGGTTTATG 59.824 55.000 31.76 18.82 37.09 1.90
985 1258 2.586079 CATGCCTCCACTACCGCG 60.586 66.667 0.00 0.00 0.00 6.46
1084 1357 4.767255 GCAGACGGGGCAGTCCAG 62.767 72.222 8.43 0.00 41.83 3.86
1181 1460 4.472691 AACGTCATCAACAACACATGAG 57.527 40.909 0.00 0.00 0.00 2.90
1215 1494 0.389817 TGCAGAGAATCAACCGGACG 60.390 55.000 9.46 0.00 37.82 4.79
1348 1634 4.531912 TCGACGACGCGCTCCATC 62.532 66.667 5.73 0.00 39.58 3.51
1520 3270 2.049433 CTCGGCGTCGAAGTGGTT 60.049 61.111 15.23 0.00 45.47 3.67
1622 3372 6.967767 TCATCTTCGTCTTCTTCGTATTCTTC 59.032 38.462 0.00 0.00 0.00 2.87
1640 3390 2.100584 AGAGGTCGCTGTCATCATCTTC 59.899 50.000 0.00 0.00 0.00 2.87
1645 3395 0.532573 GGAAGAGGTCGCTGTCATCA 59.467 55.000 0.00 0.00 0.00 3.07
1648 3398 1.967535 CAGGAAGAGGTCGCTGTCA 59.032 57.895 0.00 0.00 0.00 3.58
1705 3455 3.916392 CTGGACGCGGACCAGTGAC 62.916 68.421 31.90 7.91 46.71 3.67
1754 3504 3.452786 CCAGGAGAAGCTCGCGGA 61.453 66.667 6.13 0.00 0.00 5.54
1755 3505 3.302347 AACCAGGAGAAGCTCGCGG 62.302 63.158 6.13 0.00 0.00 6.46
1847 3597 2.230940 CGGGTACGATGCAGAAGCG 61.231 63.158 0.00 0.00 43.52 4.68
1887 3637 0.957888 GACACTGAGGAAGGCAAGCC 60.958 60.000 2.02 2.02 0.00 4.35
1904 3654 2.205074 GACATCCACATCGATGGTGAC 58.795 52.381 28.09 16.47 43.34 3.67
1914 3664 1.067669 CGTCATCCTCGACATCCACAT 59.932 52.381 0.00 0.00 35.54 3.21
1939 3698 1.522580 GTCATCCGCTTCCTCCTGC 60.523 63.158 0.00 0.00 0.00 4.85
1948 3707 1.152652 ATCCTCCTCGTCATCCGCT 60.153 57.895 0.00 0.00 36.19 5.52
1966 3725 1.884464 GCGCATCCATTCGCTCTCA 60.884 57.895 0.30 0.00 46.92 3.27
1967 3726 2.934428 GCGCATCCATTCGCTCTC 59.066 61.111 0.30 0.00 46.92 3.20
2023 3782 1.546029 TCATCCGCCTTATCATCCTCG 59.454 52.381 0.00 0.00 0.00 4.63
2033 3792 2.715749 TCATTGTGATCATCCGCCTT 57.284 45.000 0.00 0.00 0.00 4.35
2043 3802 6.111382 AGAGTTCGTCAATCATCATTGTGAT 58.889 36.000 0.00 0.00 40.47 3.06
2068 3827 1.732259 AGTTAACGAGCTCCAAATGCG 59.268 47.619 8.47 0.00 35.28 4.73
2070 3829 4.265556 CGACTAGTTAACGAGCTCCAAATG 59.734 45.833 14.82 0.00 0.00 2.32
2081 3840 5.159209 ACATCCTTGAACGACTAGTTAACG 58.841 41.667 0.00 0.00 44.35 3.18
2092 3851 5.869344 TGAAGTCTCAATACATCCTTGAACG 59.131 40.000 0.00 0.00 32.53 3.95
2096 3863 8.899427 ATGTATGAAGTCTCAATACATCCTTG 57.101 34.615 11.81 0.00 34.58 3.61
2104 3871 9.987272 CCAGATTGTATGTATGAAGTCTCAATA 57.013 33.333 0.00 0.00 34.49 1.90
2107 3874 6.686378 GCCCAGATTGTATGTATGAAGTCTCA 60.686 42.308 0.00 0.00 35.56 3.27
2108 3875 5.698545 GCCCAGATTGTATGTATGAAGTCTC 59.301 44.000 0.00 0.00 0.00 3.36
2110 3877 5.615289 AGCCCAGATTGTATGTATGAAGTC 58.385 41.667 0.00 0.00 0.00 3.01
2111 3878 5.636903 AGCCCAGATTGTATGTATGAAGT 57.363 39.130 0.00 0.00 0.00 3.01
2112 3879 6.949352 AAAGCCCAGATTGTATGTATGAAG 57.051 37.500 0.00 0.00 0.00 3.02
2113 3880 7.013274 GCTAAAAGCCCAGATTGTATGTATGAA 59.987 37.037 0.00 0.00 34.48 2.57
2114 3881 6.486657 GCTAAAAGCCCAGATTGTATGTATGA 59.513 38.462 0.00 0.00 34.48 2.15
2119 3889 4.398988 TGTGCTAAAAGCCCAGATTGTATG 59.601 41.667 0.00 0.00 41.51 2.39
2186 3958 7.148540 CCCGATCACTTTTTAAACGACTGAATA 60.149 37.037 0.00 0.00 0.00 1.75
2196 3968 7.222000 AGCATTAACCCGATCACTTTTTAAA 57.778 32.000 0.00 0.00 0.00 1.52
2212 3986 3.066621 TGAATCGCCAATGGAGCATTAAC 59.933 43.478 2.05 0.00 32.35 2.01
2221 3995 4.818546 AGAAAGATACTGAATCGCCAATGG 59.181 41.667 0.00 0.00 39.79 3.16
2347 4126 6.311200 CAGGCACATTTTGAGTTAATAAAGGC 59.689 38.462 0.00 0.00 0.00 4.35
2349 4128 8.081633 TGACAGGCACATTTTGAGTTAATAAAG 58.918 33.333 0.00 0.00 0.00 1.85
2376 4155 8.951954 ATCGTAGTATAATCATGACTCGTTTC 57.048 34.615 0.00 0.00 0.00 2.78
2500 4290 7.136119 TCCGTTTTGACAGTATTTGATCAAAC 58.864 34.615 22.71 12.26 36.96 2.93
2522 4314 7.320443 TCATATCTTGAAAATGAGGTTTCCG 57.680 36.000 0.00 0.00 36.80 4.30
2621 4418 6.012658 ACGCTTAAATTTCAGCATTTCAGA 57.987 33.333 21.06 0.00 35.60 3.27
2622 4419 6.695292 AACGCTTAAATTTCAGCATTTCAG 57.305 33.333 21.06 8.59 35.60 3.02
2623 4420 7.343691 CAAAACGCTTAAATTTCAGCATTTCA 58.656 30.769 21.06 0.00 30.49 2.69
2624 4421 6.791775 CCAAAACGCTTAAATTTCAGCATTTC 59.208 34.615 21.06 0.00 30.49 2.17
2625 4422 6.259829 ACCAAAACGCTTAAATTTCAGCATTT 59.740 30.769 21.06 16.40 33.01 2.32
2659 4474 7.824289 TGACATCTCGAAAATGAGGTTTCTAAT 59.176 33.333 12.95 0.00 35.70 1.73
2660 4475 7.158697 TGACATCTCGAAAATGAGGTTTCTAA 58.841 34.615 12.95 0.00 35.70 2.10
2662 4477 5.551233 TGACATCTCGAAAATGAGGTTTCT 58.449 37.500 12.95 0.00 35.70 2.52
2663 4478 5.862924 TGACATCTCGAAAATGAGGTTTC 57.137 39.130 12.95 2.57 36.61 2.78
2667 4482 7.859377 CCATATTTTGACATCTCGAAAATGAGG 59.141 37.037 12.95 0.00 34.10 3.86
2671 4486 7.122650 ACCACCATATTTTGACATCTCGAAAAT 59.877 33.333 0.00 0.00 34.10 1.82
2677 4492 7.624360 TGTAACCACCATATTTTGACATCTC 57.376 36.000 0.00 0.00 0.00 2.75
2684 4499 9.581099 GGTTTCTATTGTAACCACCATATTTTG 57.419 33.333 10.08 0.00 41.45 2.44
2688 4503 7.867921 TGAGGTTTCTATTGTAACCACCATAT 58.132 34.615 15.75 0.00 43.39 1.78
2811 4628 9.722056 CTTAAACTTCAGCGCAGAAATTATTAT 57.278 29.630 16.37 0.67 0.00 1.28
2812 4629 7.696453 GCTTAAACTTCAGCGCAGAAATTATTA 59.304 33.333 16.37 9.86 0.00 0.98
2817 4634 3.826466 GCTTAAACTTCAGCGCAGAAAT 58.174 40.909 16.37 3.34 0.00 2.17
3013 4837 6.814644 CCAAAATGCTGAAATCTCTATGCAAA 59.185 34.615 0.00 0.00 34.07 3.68
3023 4847 6.601741 TGTTTTGACCAAAATGCTGAAATC 57.398 33.333 10.61 0.00 41.64 2.17


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

AutoCloner maintained by Alex Coulton.