Multiple sequence alignment - TraesCS7D01G387600

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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 TraesCS7D01G387600 chr7D 100.000 2763 0 0 1 2763 501507763 501510525 0.000000e+00 5103.0
1 TraesCS7D01G387600 chr7D 83.554 681 53 24 1178 1827 501609973 501609321 1.430000e-162 582.0
2 TraesCS7D01G387600 chr7D 85.799 169 18 5 438 603 501611586 501611421 1.020000e-39 174.0
3 TraesCS7D01G387600 chr7A 87.032 1681 118 51 175 1829 567791320 567792926 0.000000e+00 1805.0
4 TraesCS7D01G387600 chr7A 94.603 315 17 0 2277 2591 567798478 567798792 3.200000e-134 488.0
5 TraesCS7D01G387600 chr7A 80.620 645 55 45 961 1569 568129651 568130261 4.230000e-118 435.0
6 TraesCS7D01G387600 chr7A 94.265 279 13 3 1177 1455 569112478 569112203 9.150000e-115 424.0
7 TraesCS7D01G387600 chr7A 88.724 337 29 6 1183 1513 568695653 568695320 1.190000e-108 403.0
8 TraesCS7D01G387600 chr7A 92.553 282 18 2 1174 1455 568579867 568580145 4.290000e-108 401.0
9 TraesCS7D01G387600 chr7A 84.018 438 41 21 1836 2262 567798076 567798495 7.170000e-106 394.0
10 TraesCS7D01G387600 chr7A 96.335 191 4 2 2576 2763 567798960 567799150 7.430000e-81 311.0
11 TraesCS7D01G387600 chr7A 82.635 167 8 10 1618 1765 568695231 568695067 8.030000e-26 128.0
12 TraesCS7D01G387600 chr7A 87.963 108 11 2 101 207 567731234 567731340 2.890000e-25 126.0
13 TraesCS7D01G387600 chr7A 90.426 94 6 2 453 546 568696329 568696239 1.340000e-23 121.0
14 TraesCS7D01G387600 chr7A 92.000 50 4 0 750 799 569112970 569112921 1.370000e-08 71.3
15 TraesCS7D01G387600 chr7A 93.478 46 3 0 438 483 568129338 568129383 4.940000e-08 69.4
16 TraesCS7D01G387600 chr7A 90.196 51 5 0 362 412 567731672 567731722 1.780000e-07 67.6
17 TraesCS7D01G387600 chr7B 86.862 1606 114 36 293 1830 530869028 530870604 0.000000e+00 1707.0
18 TraesCS7D01G387600 chr7B 78.049 1230 127 75 749 1893 531222785 531221614 0.000000e+00 643.0
19 TraesCS7D01G387600 chr7B 79.936 623 79 30 854 1455 531179858 531180455 1.530000e-112 416.0
20 TraesCS7D01G387600 chr7B 94.231 52 3 0 119 170 531231215 531231164 2.280000e-11 80.5
21 TraesCS7D01G387600 chr5D 81.410 468 83 4 2278 2743 450110238 450110703 2.010000e-101 379.0
22 TraesCS7D01G387600 chr5A 88.462 52 6 0 14 65 680505134 680505185 2.300000e-06 63.9


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 TraesCS7D01G387600 chr7D 501507763 501510525 2762 False 5103.000000 5103 100.000000 1 2763 1 chr7D.!!$F1 2762
1 TraesCS7D01G387600 chr7D 501609321 501611586 2265 True 378.000000 582 84.676500 438 1827 2 chr7D.!!$R1 1389
2 TraesCS7D01G387600 chr7A 567791320 567792926 1606 False 1805.000000 1805 87.032000 175 1829 1 chr7A.!!$F1 1654
3 TraesCS7D01G387600 chr7A 567798076 567799150 1074 False 397.666667 488 91.652000 1836 2763 3 chr7A.!!$F4 927
4 TraesCS7D01G387600 chr7A 568129338 568130261 923 False 252.200000 435 87.049000 438 1569 2 chr7A.!!$F5 1131
5 TraesCS7D01G387600 chr7A 569112203 569112970 767 True 247.650000 424 93.132500 750 1455 2 chr7A.!!$R2 705
6 TraesCS7D01G387600 chr7A 568695067 568696329 1262 True 217.333333 403 87.261667 453 1765 3 chr7A.!!$R1 1312
7 TraesCS7D01G387600 chr7B 530869028 530870604 1576 False 1707.000000 1707 86.862000 293 1830 1 chr7B.!!$F1 1537
8 TraesCS7D01G387600 chr7B 531221614 531222785 1171 True 643.000000 643 78.049000 749 1893 1 chr7B.!!$R1 1144
9 TraesCS7D01G387600 chr7B 531179858 531180455 597 False 416.000000 416 79.936000 854 1455 1 chr7B.!!$F2 601

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
90 91 0.171903 TAGCCCGCACGTAAGAGAAC 59.828 55.0 0.00 0.0 43.62 3.01 F
425 448 0.175531 GCCGGGCAAGCATACATTTT 59.824 50.0 15.62 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1589 2775 0.240145 CTACAGACAGAACACGCGGA 59.760 55.0 12.47 0.0 0.00 5.54 R
2176 3423 0.315251 GTTTCTTGGGCCAACTGCTC 59.685 55.0 16.66 1.5 42.61 4.26 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 2.500509 GTGTGGTCGGCAATTCAAAA 57.499 45.000 0.00 0.00 0.00 2.44
20 21 2.815478 GTGTGGTCGGCAATTCAAAAA 58.185 42.857 0.00 0.00 0.00 1.94
21 22 3.389221 GTGTGGTCGGCAATTCAAAAAT 58.611 40.909 0.00 0.00 0.00 1.82
22 23 4.551388 GTGTGGTCGGCAATTCAAAAATA 58.449 39.130 0.00 0.00 0.00 1.40
23 24 4.985409 GTGTGGTCGGCAATTCAAAAATAA 59.015 37.500 0.00 0.00 0.00 1.40
24 25 5.463724 GTGTGGTCGGCAATTCAAAAATAAA 59.536 36.000 0.00 0.00 0.00 1.40
25 26 6.018669 GTGTGGTCGGCAATTCAAAAATAAAA 60.019 34.615 0.00 0.00 0.00 1.52
26 27 6.018669 TGTGGTCGGCAATTCAAAAATAAAAC 60.019 34.615 0.00 0.00 0.00 2.43
27 28 5.467063 TGGTCGGCAATTCAAAAATAAAACC 59.533 36.000 0.00 0.00 0.00 3.27
28 29 5.467063 GGTCGGCAATTCAAAAATAAAACCA 59.533 36.000 0.00 0.00 0.00 3.67
29 30 6.017852 GGTCGGCAATTCAAAAATAAAACCAA 60.018 34.615 0.00 0.00 0.00 3.67
30 31 7.410485 GTCGGCAATTCAAAAATAAAACCAAA 58.590 30.769 0.00 0.00 0.00 3.28
31 32 7.374754 GTCGGCAATTCAAAAATAAAACCAAAC 59.625 33.333 0.00 0.00 0.00 2.93
32 33 7.065803 TCGGCAATTCAAAAATAAAACCAAACA 59.934 29.630 0.00 0.00 0.00 2.83
33 34 7.375544 CGGCAATTCAAAAATAAAACCAAACAG 59.624 33.333 0.00 0.00 0.00 3.16
34 35 7.167302 GGCAATTCAAAAATAAAACCAAACAGC 59.833 33.333 0.00 0.00 0.00 4.40
35 36 7.167302 GCAATTCAAAAATAAAACCAAACAGCC 59.833 33.333 0.00 0.00 0.00 4.85
36 37 7.872113 ATTCAAAAATAAAACCAAACAGCCA 57.128 28.000 0.00 0.00 0.00 4.75
37 38 7.687941 TTCAAAAATAAAACCAAACAGCCAA 57.312 28.000 0.00 0.00 0.00 4.52
38 39 7.313951 TCAAAAATAAAACCAAACAGCCAAG 57.686 32.000 0.00 0.00 0.00 3.61
39 40 6.881602 TCAAAAATAAAACCAAACAGCCAAGT 59.118 30.769 0.00 0.00 0.00 3.16
40 41 6.676237 AAAATAAAACCAAACAGCCAAGTG 57.324 33.333 0.00 0.00 0.00 3.16
41 42 2.689553 AAAACCAAACAGCCAAGTGG 57.310 45.000 0.00 0.00 37.17 4.00
42 43 1.567357 AAACCAAACAGCCAAGTGGT 58.433 45.000 0.00 0.00 46.38 4.16
43 44 1.567357 AACCAAACAGCCAAGTGGTT 58.433 45.000 6.64 6.64 46.96 3.67
44 45 2.445682 ACCAAACAGCCAAGTGGTTA 57.554 45.000 0.00 0.00 41.68 2.85
45 46 2.741145 ACCAAACAGCCAAGTGGTTAA 58.259 42.857 0.00 0.00 41.68 2.01
46 47 2.429250 ACCAAACAGCCAAGTGGTTAAC 59.571 45.455 0.00 0.00 41.68 2.01
47 48 2.428890 CCAAACAGCCAAGTGGTTAACA 59.571 45.455 8.10 0.00 37.57 2.41
48 49 3.069443 CCAAACAGCCAAGTGGTTAACAT 59.931 43.478 8.10 0.00 37.57 2.71
49 50 4.442753 CCAAACAGCCAAGTGGTTAACATT 60.443 41.667 8.10 0.00 37.57 2.71
50 51 5.115480 CAAACAGCCAAGTGGTTAACATTT 58.885 37.500 8.10 0.00 37.57 2.32
51 52 4.320608 ACAGCCAAGTGGTTAACATTTG 57.679 40.909 8.10 8.20 43.95 2.32
52 53 3.957497 ACAGCCAAGTGGTTAACATTTGA 59.043 39.130 7.07 0.00 46.34 2.69
53 54 4.588528 ACAGCCAAGTGGTTAACATTTGAT 59.411 37.500 7.07 0.00 46.34 2.57
54 55 5.163513 CAGCCAAGTGGTTAACATTTGATC 58.836 41.667 7.07 0.00 46.34 2.92
55 56 4.832266 AGCCAAGTGGTTAACATTTGATCA 59.168 37.500 7.07 0.00 46.34 2.92
56 57 5.047802 AGCCAAGTGGTTAACATTTGATCAG 60.048 40.000 7.07 0.00 46.34 2.90
57 58 5.713025 CCAAGTGGTTAACATTTGATCAGG 58.287 41.667 7.07 0.00 46.34 3.86
58 59 5.243730 CCAAGTGGTTAACATTTGATCAGGT 59.756 40.000 7.07 0.00 46.34 4.00
59 60 6.239289 CCAAGTGGTTAACATTTGATCAGGTT 60.239 38.462 7.07 12.27 46.34 3.50
60 61 6.976934 AGTGGTTAACATTTGATCAGGTTT 57.023 33.333 8.10 1.78 0.00 3.27
61 62 8.356657 CAAGTGGTTAACATTTGATCAGGTTTA 58.643 33.333 8.10 4.02 46.34 2.01
62 63 8.650143 AGTGGTTAACATTTGATCAGGTTTAT 57.350 30.769 8.10 0.00 0.00 1.40
63 64 8.522830 AGTGGTTAACATTTGATCAGGTTTATG 58.477 33.333 8.10 7.98 0.00 1.90
64 65 8.519526 GTGGTTAACATTTGATCAGGTTTATGA 58.480 33.333 8.10 0.00 0.00 2.15
65 66 9.253832 TGGTTAACATTTGATCAGGTTTATGAT 57.746 29.630 8.10 0.00 42.62 2.45
69 70 7.516198 ACATTTGATCAGGTTTATGATAGGC 57.484 36.000 0.00 0.00 40.02 3.93
70 71 6.491403 ACATTTGATCAGGTTTATGATAGGCC 59.509 38.462 0.00 0.00 40.02 5.19
71 72 5.912149 TTGATCAGGTTTATGATAGGCCT 57.088 39.130 11.78 11.78 40.02 5.19
72 73 7.387265 TTTGATCAGGTTTATGATAGGCCTA 57.613 36.000 16.60 16.60 40.02 3.93
73 74 6.611613 TGATCAGGTTTATGATAGGCCTAG 57.388 41.667 19.33 0.08 40.02 3.02
74 75 4.891992 TCAGGTTTATGATAGGCCTAGC 57.108 45.455 21.41 21.41 0.00 3.42
75 76 4.226168 ATCAGGTTTATGATAGGCCTAGCC 59.774 45.833 24.83 15.65 39.65 3.93
76 77 6.815497 ATCAGGTTTATGATAGGCCTAGCCC 61.815 48.000 24.83 17.47 39.95 5.19
84 85 4.151582 GGCCTAGCCCGCACGTAA 62.152 66.667 0.00 0.00 44.06 3.18
86 87 3.072486 GCCTAGCCCGCACGTAAGA 62.072 63.158 0.00 0.00 43.62 2.10
87 88 1.065928 CCTAGCCCGCACGTAAGAG 59.934 63.158 0.00 0.00 43.62 2.85
88 89 1.381928 CCTAGCCCGCACGTAAGAGA 61.382 60.000 0.00 0.00 43.62 3.10
89 90 0.454600 CTAGCCCGCACGTAAGAGAA 59.545 55.000 0.00 0.00 43.62 2.87
90 91 0.171903 TAGCCCGCACGTAAGAGAAC 59.828 55.000 0.00 0.00 43.62 3.01
97 98 4.979204 CGTAAGAGAACGGGTGCA 57.021 55.556 0.00 0.00 39.19 4.57
98 99 3.436001 CGTAAGAGAACGGGTGCAT 57.564 52.632 0.00 0.00 39.19 3.96
99 100 2.572191 CGTAAGAGAACGGGTGCATA 57.428 50.000 0.00 0.00 39.19 3.14
100 101 3.093717 CGTAAGAGAACGGGTGCATAT 57.906 47.619 0.00 0.00 39.19 1.78
101 102 4.233123 CGTAAGAGAACGGGTGCATATA 57.767 45.455 0.00 0.00 39.19 0.86
102 103 4.806330 CGTAAGAGAACGGGTGCATATAT 58.194 43.478 0.00 0.00 39.19 0.86
103 104 4.621460 CGTAAGAGAACGGGTGCATATATG 59.379 45.833 8.45 8.45 39.19 1.78
104 105 3.685139 AGAGAACGGGTGCATATATGG 57.315 47.619 14.51 0.00 0.00 2.74
105 106 3.239449 AGAGAACGGGTGCATATATGGA 58.761 45.455 14.51 8.93 0.00 3.41
106 107 3.840666 AGAGAACGGGTGCATATATGGAT 59.159 43.478 14.51 0.00 0.00 3.41
107 108 4.081420 AGAGAACGGGTGCATATATGGATC 60.081 45.833 14.51 11.74 0.00 3.36
108 109 3.582647 AGAACGGGTGCATATATGGATCA 59.417 43.478 18.02 3.91 29.98 2.92
109 110 4.225942 AGAACGGGTGCATATATGGATCAT 59.774 41.667 18.02 4.05 29.98 2.45
110 111 3.877559 ACGGGTGCATATATGGATCATG 58.122 45.455 18.02 12.25 29.98 3.07
111 112 2.615447 CGGGTGCATATATGGATCATGC 59.385 50.000 18.02 7.77 44.23 4.06
112 113 2.954318 GGGTGCATATATGGATCATGCC 59.046 50.000 18.02 10.31 43.51 4.40
113 114 2.615447 GGTGCATATATGGATCATGCCG 59.385 50.000 12.24 0.00 43.51 5.69
114 115 3.534554 GTGCATATATGGATCATGCCGA 58.465 45.455 14.51 0.00 43.51 5.54
115 116 3.558829 GTGCATATATGGATCATGCCGAG 59.441 47.826 14.51 0.00 43.51 4.63
116 117 3.136763 GCATATATGGATCATGCCGAGG 58.863 50.000 14.51 0.00 39.30 4.63
117 118 2.988010 TATATGGATCATGCCGAGGC 57.012 50.000 7.26 7.26 42.35 4.70
118 119 0.254178 ATATGGATCATGCCGAGGCC 59.746 55.000 12.05 0.00 41.09 5.19
119 120 1.841302 TATGGATCATGCCGAGGCCC 61.841 60.000 12.05 5.56 41.09 5.80
120 121 3.564218 GGATCATGCCGAGGCCCT 61.564 66.667 12.05 0.00 41.09 5.19
121 122 2.281345 GATCATGCCGAGGCCCTG 60.281 66.667 12.05 9.30 41.09 4.45
122 123 3.839353 GATCATGCCGAGGCCCTGG 62.839 68.421 12.05 1.82 41.09 4.45
124 125 4.864334 CATGCCGAGGCCCTGGAC 62.864 72.222 14.92 6.68 41.09 4.02
135 136 2.261671 CCTGGACCAGGTTCGTCG 59.738 66.667 29.93 4.84 45.82 5.12
136 137 2.273179 CCTGGACCAGGTTCGTCGA 61.273 63.158 29.93 0.00 45.82 4.20
137 138 1.605058 CCTGGACCAGGTTCGTCGAT 61.605 60.000 29.93 0.00 45.82 3.59
138 139 0.458543 CTGGACCAGGTTCGTCGATG 60.459 60.000 14.26 0.00 0.00 3.84
139 140 1.153628 GGACCAGGTTCGTCGATGG 60.154 63.158 11.05 11.05 38.83 3.51
140 141 3.787394 ACCAGGTTCGTCGATGGT 58.213 55.556 12.26 12.26 41.22 3.55
141 142 1.590147 ACCAGGTTCGTCGATGGTC 59.410 57.895 12.26 0.00 42.35 4.02
142 143 1.516386 CCAGGTTCGTCGATGGTCG 60.516 63.158 4.48 0.00 42.10 4.79
151 152 3.571748 TCGATGGTCGACTCCTTCT 57.428 52.632 16.46 0.00 44.82 2.85
152 153 1.095600 TCGATGGTCGACTCCTTCTG 58.904 55.000 16.46 4.88 44.82 3.02
153 154 0.811915 CGATGGTCGACTCCTTCTGT 59.188 55.000 16.46 0.00 43.74 3.41
154 155 1.202582 CGATGGTCGACTCCTTCTGTT 59.797 52.381 16.46 0.00 43.74 3.16
155 156 2.422479 CGATGGTCGACTCCTTCTGTTA 59.578 50.000 16.46 0.00 43.74 2.41
156 157 3.066900 CGATGGTCGACTCCTTCTGTTAT 59.933 47.826 16.46 0.00 43.74 1.89
157 158 4.612943 GATGGTCGACTCCTTCTGTTATC 58.387 47.826 16.46 0.00 0.00 1.75
158 159 3.427573 TGGTCGACTCCTTCTGTTATCA 58.572 45.455 16.46 0.00 0.00 2.15
159 160 3.192844 TGGTCGACTCCTTCTGTTATCAC 59.807 47.826 16.46 0.00 0.00 3.06
160 161 3.427243 GTCGACTCCTTCTGTTATCACG 58.573 50.000 8.70 0.00 0.00 4.35
161 162 2.422479 TCGACTCCTTCTGTTATCACGG 59.578 50.000 0.00 0.00 0.00 4.94
162 163 2.541556 GACTCCTTCTGTTATCACGGC 58.458 52.381 0.00 0.00 0.00 5.68
163 164 1.899814 ACTCCTTCTGTTATCACGGCA 59.100 47.619 0.00 0.00 0.00 5.69
164 165 2.301870 ACTCCTTCTGTTATCACGGCAA 59.698 45.455 0.00 0.00 0.00 4.52
165 166 2.932614 CTCCTTCTGTTATCACGGCAAG 59.067 50.000 0.00 0.00 0.00 4.01
166 167 2.009774 CCTTCTGTTATCACGGCAAGG 58.990 52.381 0.00 3.97 33.71 3.61
167 168 2.615493 CCTTCTGTTATCACGGCAAGGT 60.615 50.000 8.06 0.00 34.74 3.50
168 169 2.851263 TCTGTTATCACGGCAAGGTT 57.149 45.000 0.00 0.00 0.00 3.50
169 170 2.695359 TCTGTTATCACGGCAAGGTTC 58.305 47.619 0.00 0.00 0.00 3.62
170 171 1.393539 CTGTTATCACGGCAAGGTTCG 59.606 52.381 0.00 0.00 0.00 3.95
171 172 1.270412 TGTTATCACGGCAAGGTTCGT 60.270 47.619 0.00 0.00 40.49 3.85
172 173 1.802365 GTTATCACGGCAAGGTTCGTT 59.198 47.619 0.00 0.00 37.53 3.85
173 174 1.434555 TATCACGGCAAGGTTCGTTG 58.565 50.000 1.56 1.56 37.53 4.10
183 184 2.365408 AGGTTCGTTGAATCTCCGTC 57.635 50.000 0.00 0.00 24.45 4.79
189 190 1.084370 GTTGAATCTCCGTCGCCCTG 61.084 60.000 0.00 0.00 0.00 4.45
218 219 5.402398 GGGTAGTGCTTGAAATGAATGAAC 58.598 41.667 0.00 0.00 0.00 3.18
220 221 6.350445 GGGTAGTGCTTGAAATGAATGAACAT 60.350 38.462 0.00 0.00 0.00 2.71
221 222 7.148086 GGGTAGTGCTTGAAATGAATGAACATA 60.148 37.037 0.00 0.00 0.00 2.29
222 223 8.408601 GGTAGTGCTTGAAATGAATGAACATAT 58.591 33.333 0.00 0.00 0.00 1.78
226 227 9.740239 GTGCTTGAAATGAATGAACATATACAT 57.260 29.630 0.00 0.00 0.00 2.29
300 306 1.278238 CATCTTACTCCGTTGGCGAC 58.722 55.000 0.00 0.00 41.33 5.19
309 315 2.902419 CGTTGGCGACCATGCAACA 61.902 57.895 11.90 0.00 41.33 3.33
321 327 4.324424 GCAACACAATGCGCTGTT 57.676 50.000 9.73 8.07 36.45 3.16
328 334 0.880278 ACAATGCGCTGTTCGTCACT 60.880 50.000 9.73 0.00 41.07 3.41
329 335 0.235665 CAATGCGCTGTTCGTCACTT 59.764 50.000 9.73 0.00 41.07 3.16
341 347 1.278637 GTCACTTCGCCGTTGGTTG 59.721 57.895 0.00 0.00 0.00 3.77
342 348 1.153329 TCACTTCGCCGTTGGTTGT 60.153 52.632 0.00 0.00 0.00 3.32
344 350 0.316689 CACTTCGCCGTTGGTTGTTC 60.317 55.000 0.00 0.00 0.00 3.18
346 352 1.440938 CTTCGCCGTTGGTTGTTCCA 61.441 55.000 0.00 0.00 45.60 3.53
356 369 0.942252 GGTTGTTCCAGAACGTGTCC 59.058 55.000 6.08 2.68 43.94 4.02
358 371 1.329599 GTTGTTCCAGAACGTGTCCAC 59.670 52.381 6.08 0.00 43.94 4.02
359 372 0.828022 TGTTCCAGAACGTGTCCACT 59.172 50.000 6.08 0.00 43.94 4.00
360 373 1.217882 GTTCCAGAACGTGTCCACTG 58.782 55.000 0.00 0.00 0.00 3.66
364 377 1.491670 CAGAACGTGTCCACTGTCAG 58.508 55.000 0.00 0.00 0.00 3.51
366 379 1.548973 GAACGTGTCCACTGTCAGCG 61.549 60.000 0.00 0.00 0.00 5.18
379 392 3.120385 CAGCGAGGCGTGCATCAA 61.120 61.111 7.32 0.00 33.85 2.57
425 448 0.175531 GCCGGGCAAGCATACATTTT 59.824 50.000 15.62 0.00 0.00 1.82
449 480 7.804614 TTTGTTTTATACCATGCGTTTGATC 57.195 32.000 0.00 0.00 0.00 2.92
521 563 2.032528 TGCCAGTGCCAGTACAGC 59.967 61.111 0.00 0.00 36.33 4.40
522 564 2.747855 GCCAGTGCCAGTACAGCC 60.748 66.667 5.55 0.00 0.00 4.85
523 565 2.749682 CCAGTGCCAGTACAGCCA 59.250 61.111 5.55 0.00 0.00 4.75
524 566 1.376424 CCAGTGCCAGTACAGCCAG 60.376 63.158 5.55 0.00 0.00 4.85
525 567 1.372683 CAGTGCCAGTACAGCCAGT 59.627 57.895 5.55 0.00 0.00 4.00
573 617 2.230508 AGTATCCGCTTCTCGTTTCACA 59.769 45.455 0.00 0.00 36.19 3.58
600 645 6.128172 CGTATCTTTGCAGAAACTTCCAGAAT 60.128 38.462 0.00 0.00 30.76 2.40
616 694 4.464244 TCCAGAATCTACTCACTGAGGTTG 59.536 45.833 10.86 0.75 33.35 3.77
618 696 5.047021 CCAGAATCTACTCACTGAGGTTGAA 60.047 44.000 10.86 0.00 33.35 2.69
619 697 6.459066 CAGAATCTACTCACTGAGGTTGAAA 58.541 40.000 10.86 0.00 33.35 2.69
620 698 7.102346 CAGAATCTACTCACTGAGGTTGAAAT 58.898 38.462 10.86 0.52 33.35 2.17
624 702 9.793259 AATCTACTCACTGAGGTTGAAATTAAA 57.207 29.630 10.86 0.00 33.35 1.52
626 704 9.793259 TCTACTCACTGAGGTTGAAATTAAATT 57.207 29.630 10.86 0.00 33.35 1.82
724 805 1.076777 CCACCTATGTTGGGCAGGG 60.077 63.158 0.00 0.00 33.48 4.45
738 819 3.947041 AGGGCCCCACCTGTCTCT 61.947 66.667 21.43 0.00 40.04 3.10
739 820 3.403558 GGGCCCCACCTGTCTCTC 61.404 72.222 12.23 0.00 39.10 3.20
743 824 1.000771 CCCCACCTGTCTCTCGAGA 60.001 63.158 15.70 15.70 34.56 4.04
758 839 1.574702 CGAGACCCGAAAAACCAGGC 61.575 60.000 0.00 0.00 41.76 4.85
976 2057 0.622136 GGGGCCCCTATAAATACCGG 59.378 60.000 35.49 0.00 0.00 5.28
1053 2140 0.234884 GAACAAGCGAGAAACCACCG 59.765 55.000 0.00 0.00 0.00 4.94
1083 2202 0.596577 TGTACGCACACAGAGAGGAC 59.403 55.000 0.00 0.00 0.00 3.85
1092 2211 2.034812 ACACAGAGAGGACGAAACAGAC 59.965 50.000 0.00 0.00 0.00 3.51
1407 2584 2.186903 GTCGTCATCATGGCCGGT 59.813 61.111 1.90 0.00 0.00 5.28
1589 2775 7.044798 CGTCAGATTTTCTCCTAGGATTTTCT 58.955 38.462 13.12 7.85 0.00 2.52
1831 3055 4.011023 CGTTTGGGTGGGTGATATTACAA 58.989 43.478 0.00 0.00 0.00 2.41
1832 3056 4.142556 CGTTTGGGTGGGTGATATTACAAC 60.143 45.833 0.00 0.00 0.00 3.32
1833 3057 3.655615 TGGGTGGGTGATATTACAACC 57.344 47.619 11.30 11.30 46.73 3.77
1856 3080 5.751990 CCATATTATAAATACTCGCCCGTCC 59.248 44.000 0.00 0.00 0.00 4.79
1910 3134 2.029288 CGCAGTCGCAGGTCACAAT 61.029 57.895 0.00 0.00 38.40 2.71
1978 3220 6.114187 TCTTCTGGCCGTTCATCATTATAT 57.886 37.500 0.00 0.00 0.00 0.86
1979 3221 7.239763 TCTTCTGGCCGTTCATCATTATATA 57.760 36.000 0.00 0.00 0.00 0.86
1980 3222 7.851228 TCTTCTGGCCGTTCATCATTATATAT 58.149 34.615 0.00 0.00 0.00 0.86
1981 3223 7.765819 TCTTCTGGCCGTTCATCATTATATATG 59.234 37.037 0.00 0.00 0.00 1.78
1982 3224 6.946340 TCTGGCCGTTCATCATTATATATGT 58.054 36.000 0.00 0.00 0.00 2.29
2023 3265 5.220416 GCCGTCATGTATGTTTCTGTCTTAC 60.220 44.000 0.00 0.00 0.00 2.34
2024 3266 5.004440 CCGTCATGTATGTTTCTGTCTTACG 59.996 44.000 0.00 0.00 0.00 3.18
2025 3267 5.571741 CGTCATGTATGTTTCTGTCTTACGT 59.428 40.000 0.00 0.00 0.00 3.57
2026 3268 6.089016 CGTCATGTATGTTTCTGTCTTACGTT 59.911 38.462 0.00 0.00 0.00 3.99
2027 3269 7.271868 CGTCATGTATGTTTCTGTCTTACGTTA 59.728 37.037 0.00 0.00 0.00 3.18
2028 3270 8.918658 GTCATGTATGTTTCTGTCTTACGTTAA 58.081 33.333 0.00 0.00 0.00 2.01
2029 3271 9.478768 TCATGTATGTTTCTGTCTTACGTTAAA 57.521 29.630 0.00 0.00 0.00 1.52
2035 3277 8.441312 TGTTTCTGTCTTACGTTAAAATTCCT 57.559 30.769 0.00 0.00 0.00 3.36
2036 3278 8.895737 TGTTTCTGTCTTACGTTAAAATTCCTT 58.104 29.630 0.00 0.00 0.00 3.36
2037 3279 9.726232 GTTTCTGTCTTACGTTAAAATTCCTTT 57.274 29.630 0.00 0.00 0.00 3.11
2078 3320 7.916977 ACGTTAAAATTCCTTAAAACGCTCTTT 59.083 29.630 5.43 0.00 38.86 2.52
2103 3346 0.036875 ACAGGCTCTTACACTTGGGC 59.963 55.000 0.00 0.00 0.00 5.36
2172 3419 0.725784 GCAAAATCTGTGGACGCACG 60.726 55.000 0.00 0.00 0.00 5.34
2175 3422 1.291877 AAATCTGTGGACGCACGAGC 61.292 55.000 0.00 0.00 37.42 5.03
2202 3449 1.358759 GGCCCAAGAAACACACACG 59.641 57.895 0.00 0.00 0.00 4.49
2205 3452 0.307760 CCCAAGAAACACACACGAGC 59.692 55.000 0.00 0.00 0.00 5.03
2233 3480 5.298026 AGGTCAAGAAGCAAAAGAAACTCTC 59.702 40.000 0.00 0.00 0.00 3.20
2239 3486 4.889832 AGCAAAAGAAACTCTCACTGTG 57.110 40.909 0.17 0.17 0.00 3.66
2255 3502 4.115516 CACTGTGCACTAAAGCTCGATAT 58.884 43.478 19.41 0.00 34.99 1.63
2256 3503 4.026228 CACTGTGCACTAAAGCTCGATATG 60.026 45.833 19.41 0.00 34.99 1.78
2257 3504 3.457234 TGTGCACTAAAGCTCGATATGG 58.543 45.455 19.41 0.00 34.99 2.74
2258 3505 3.118775 TGTGCACTAAAGCTCGATATGGT 60.119 43.478 19.41 0.00 34.99 3.55
2259 3506 3.246226 GTGCACTAAAGCTCGATATGGTG 59.754 47.826 10.32 0.00 34.99 4.17
2260 3507 3.132111 TGCACTAAAGCTCGATATGGTGA 59.868 43.478 7.30 0.00 34.99 4.02
2261 3508 4.119862 GCACTAAAGCTCGATATGGTGAA 58.880 43.478 7.30 0.00 0.00 3.18
2262 3509 4.752101 GCACTAAAGCTCGATATGGTGAAT 59.248 41.667 7.30 0.00 0.00 2.57
2263 3510 5.237344 GCACTAAAGCTCGATATGGTGAATT 59.763 40.000 7.30 0.00 0.00 2.17
2264 3511 6.564873 GCACTAAAGCTCGATATGGTGAATTC 60.565 42.308 0.00 0.00 0.00 2.17
2265 3512 5.992217 ACTAAAGCTCGATATGGTGAATTCC 59.008 40.000 2.27 0.00 0.00 3.01
2266 3513 3.409026 AGCTCGATATGGTGAATTCCC 57.591 47.619 2.27 4.57 0.00 3.97
2267 3514 2.039084 AGCTCGATATGGTGAATTCCCC 59.961 50.000 2.27 0.63 0.00 4.81
2268 3515 2.039084 GCTCGATATGGTGAATTCCCCT 59.961 50.000 8.51 2.85 0.00 4.79
2269 3516 3.260884 GCTCGATATGGTGAATTCCCCTA 59.739 47.826 8.51 4.83 0.00 3.53
2270 3517 4.262894 GCTCGATATGGTGAATTCCCCTAA 60.263 45.833 8.51 0.00 0.00 2.69
2271 3518 5.744887 GCTCGATATGGTGAATTCCCCTAAA 60.745 44.000 8.51 0.00 0.00 1.85
2272 3519 6.255294 TCGATATGGTGAATTCCCCTAAAA 57.745 37.500 8.51 0.00 0.00 1.52
2273 3520 6.664714 TCGATATGGTGAATTCCCCTAAAAA 58.335 36.000 8.51 0.00 0.00 1.94
2296 3543 3.340814 AAAGCTCGATGTGATGAAGGT 57.659 42.857 0.00 0.00 0.00 3.50
2317 3564 7.437713 AGGTGTATGATAGAGTTGAATGGAA 57.562 36.000 0.00 0.00 0.00 3.53
2329 3576 7.441017 AGAGTTGAATGGAACTATCTAGATGC 58.559 38.462 15.79 2.28 36.27 3.91
2367 3614 1.479757 GGTTGGAGCAAGGTTGGGTTA 60.480 52.381 0.00 0.00 0.00 2.85
2370 3617 1.777878 TGGAGCAAGGTTGGGTTAAGA 59.222 47.619 0.00 0.00 0.00 2.10
2385 3632 6.414732 TGGGTTAAGAGAATTATGAGGTGTG 58.585 40.000 0.00 0.00 0.00 3.82
2393 3640 4.287067 AGAATTATGAGGTGTGTGTCCACT 59.713 41.667 0.00 0.00 42.34 4.00
2404 3651 3.438781 TGTGTGTCCACTGTGACTTTTTC 59.561 43.478 9.86 0.00 42.34 2.29
2408 3655 3.938963 TGTCCACTGTGACTTTTTCTGTC 59.061 43.478 9.86 0.00 36.21 3.51
2418 3665 4.573201 TGACTTTTTCTGTCCTGGTTAACG 59.427 41.667 0.00 0.00 33.83 3.18
2433 3680 4.773674 TGGTTAACGGAGTAAAGATGGAGA 59.226 41.667 0.00 0.00 45.00 3.71
2461 3708 2.029623 GCCAACTAGAGGGATACGACA 58.970 52.381 0.00 0.00 37.60 4.35
2492 3739 5.544176 TCCCATATCTCCATACTTGTTCCTC 59.456 44.000 0.00 0.00 0.00 3.71
2574 3821 1.219935 GTGGTTGTAGCCCCTACGG 59.780 63.158 0.00 0.00 39.58 4.02
2602 4034 4.157840 ACCGGTAAATCATCTCCTTTTTGC 59.842 41.667 4.49 0.00 0.00 3.68
2604 4036 4.094294 CGGTAAATCATCTCCTTTTTGCGA 59.906 41.667 0.00 0.00 0.00 5.10
2606 4038 6.564328 GGTAAATCATCTCCTTTTTGCGAAT 58.436 36.000 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.500509 TTTTGAATTGCCGACCACAC 57.499 45.000 0.00 0.00 0.00 3.82
1 2 3.742433 ATTTTTGAATTGCCGACCACA 57.258 38.095 0.00 0.00 0.00 4.17
2 3 6.359545 GTTTTATTTTTGAATTGCCGACCAC 58.640 36.000 0.00 0.00 0.00 4.16
3 4 5.467063 GGTTTTATTTTTGAATTGCCGACCA 59.533 36.000 0.00 0.00 0.00 4.02
4 5 5.467063 TGGTTTTATTTTTGAATTGCCGACC 59.533 36.000 0.00 0.00 0.00 4.79
5 6 6.532365 TGGTTTTATTTTTGAATTGCCGAC 57.468 33.333 0.00 0.00 0.00 4.79
6 7 7.065803 TGTTTGGTTTTATTTTTGAATTGCCGA 59.934 29.630 0.00 0.00 0.00 5.54
7 8 7.189512 TGTTTGGTTTTATTTTTGAATTGCCG 58.810 30.769 0.00 0.00 0.00 5.69
8 9 7.167302 GCTGTTTGGTTTTATTTTTGAATTGCC 59.833 33.333 0.00 0.00 0.00 4.52
9 10 7.167302 GGCTGTTTGGTTTTATTTTTGAATTGC 59.833 33.333 0.00 0.00 0.00 3.56
10 11 8.186821 TGGCTGTTTGGTTTTATTTTTGAATTG 58.813 29.630 0.00 0.00 0.00 2.32
11 12 8.286191 TGGCTGTTTGGTTTTATTTTTGAATT 57.714 26.923 0.00 0.00 0.00 2.17
12 13 7.872113 TGGCTGTTTGGTTTTATTTTTGAAT 57.128 28.000 0.00 0.00 0.00 2.57
13 14 7.391833 ACTTGGCTGTTTGGTTTTATTTTTGAA 59.608 29.630 0.00 0.00 0.00 2.69
14 15 6.881602 ACTTGGCTGTTTGGTTTTATTTTTGA 59.118 30.769 0.00 0.00 0.00 2.69
15 16 6.966066 CACTTGGCTGTTTGGTTTTATTTTTG 59.034 34.615 0.00 0.00 0.00 2.44
16 17 6.094742 CCACTTGGCTGTTTGGTTTTATTTTT 59.905 34.615 0.00 0.00 0.00 1.94
17 18 5.588246 CCACTTGGCTGTTTGGTTTTATTTT 59.412 36.000 0.00 0.00 0.00 1.82
18 19 5.122519 CCACTTGGCTGTTTGGTTTTATTT 58.877 37.500 0.00 0.00 0.00 1.40
19 20 4.163268 ACCACTTGGCTGTTTGGTTTTATT 59.837 37.500 0.00 0.00 39.41 1.40
20 21 3.709141 ACCACTTGGCTGTTTGGTTTTAT 59.291 39.130 0.00 0.00 39.41 1.40
21 22 3.100671 ACCACTTGGCTGTTTGGTTTTA 58.899 40.909 0.00 0.00 39.41 1.52
22 23 1.905894 ACCACTTGGCTGTTTGGTTTT 59.094 42.857 0.00 0.00 39.41 2.43
23 24 1.567357 ACCACTTGGCTGTTTGGTTT 58.433 45.000 0.00 0.00 39.41 3.27
24 25 1.567357 AACCACTTGGCTGTTTGGTT 58.433 45.000 7.31 7.31 45.59 3.67
25 26 2.429250 GTTAACCACTTGGCTGTTTGGT 59.571 45.455 0.00 0.00 44.52 3.67
26 27 2.428890 TGTTAACCACTTGGCTGTTTGG 59.571 45.455 2.48 0.00 39.32 3.28
27 28 3.791973 TGTTAACCACTTGGCTGTTTG 57.208 42.857 2.48 0.00 39.32 2.93
28 29 5.105146 TCAAATGTTAACCACTTGGCTGTTT 60.105 36.000 2.48 0.00 39.32 2.83
29 30 4.404073 TCAAATGTTAACCACTTGGCTGTT 59.596 37.500 2.48 0.00 39.32 3.16
30 31 3.957497 TCAAATGTTAACCACTTGGCTGT 59.043 39.130 2.48 0.00 39.32 4.40
31 32 4.582701 TCAAATGTTAACCACTTGGCTG 57.417 40.909 2.48 0.00 39.32 4.85
32 33 4.832266 TGATCAAATGTTAACCACTTGGCT 59.168 37.500 2.48 0.00 39.32 4.75
33 34 5.132897 TGATCAAATGTTAACCACTTGGC 57.867 39.130 2.48 1.99 39.32 4.52
34 35 5.243730 ACCTGATCAAATGTTAACCACTTGG 59.756 40.000 2.48 0.00 42.17 3.61
35 36 6.331369 ACCTGATCAAATGTTAACCACTTG 57.669 37.500 2.48 4.35 0.00 3.16
36 37 6.976934 AACCTGATCAAATGTTAACCACTT 57.023 33.333 2.48 0.00 0.00 3.16
37 38 6.976934 AAACCTGATCAAATGTTAACCACT 57.023 33.333 2.48 0.00 0.00 4.00
38 39 8.519526 TCATAAACCTGATCAAATGTTAACCAC 58.480 33.333 2.48 0.00 0.00 4.16
39 40 8.642935 TCATAAACCTGATCAAATGTTAACCA 57.357 30.769 2.48 0.00 0.00 3.67
43 44 9.066892 GCCTATCATAAACCTGATCAAATGTTA 57.933 33.333 0.00 0.00 37.13 2.41
44 45 7.014615 GGCCTATCATAAACCTGATCAAATGTT 59.985 37.037 0.00 0.00 37.13 2.71
45 46 6.491403 GGCCTATCATAAACCTGATCAAATGT 59.509 38.462 0.00 0.00 37.13 2.71
46 47 6.718454 AGGCCTATCATAAACCTGATCAAATG 59.282 38.462 1.29 0.00 37.13 2.32
47 48 6.856757 AGGCCTATCATAAACCTGATCAAAT 58.143 36.000 1.29 0.00 37.13 2.32
48 49 6.266131 AGGCCTATCATAAACCTGATCAAA 57.734 37.500 1.29 0.00 37.13 2.69
49 50 5.912149 AGGCCTATCATAAACCTGATCAA 57.088 39.130 1.29 0.00 37.13 2.57
50 51 5.046304 GCTAGGCCTATCATAAACCTGATCA 60.046 44.000 14.30 0.00 37.13 2.92
51 52 5.423886 GCTAGGCCTATCATAAACCTGATC 58.576 45.833 14.30 0.00 37.13 2.92
52 53 4.226168 GGCTAGGCCTATCATAAACCTGAT 59.774 45.833 14.30 0.00 46.69 2.90
53 54 3.583086 GGCTAGGCCTATCATAAACCTGA 59.417 47.826 14.30 0.00 46.69 3.86
54 55 3.944087 GGCTAGGCCTATCATAAACCTG 58.056 50.000 14.30 0.00 46.69 4.00
68 69 2.585247 CTTACGTGCGGGCTAGGC 60.585 66.667 8.00 8.00 0.00 3.93
69 70 1.065928 CTCTTACGTGCGGGCTAGG 59.934 63.158 0.00 0.00 0.00 3.02
70 71 0.454600 TTCTCTTACGTGCGGGCTAG 59.545 55.000 0.00 0.00 0.00 3.42
71 72 0.171903 GTTCTCTTACGTGCGGGCTA 59.828 55.000 0.00 0.00 0.00 3.93
72 73 1.080025 GTTCTCTTACGTGCGGGCT 60.080 57.895 0.00 0.00 0.00 5.19
73 74 2.442188 CGTTCTCTTACGTGCGGGC 61.442 63.158 0.00 0.00 36.80 6.13
74 75 1.804326 CCGTTCTCTTACGTGCGGG 60.804 63.158 0.00 0.00 39.81 6.13
75 76 1.804326 CCCGTTCTCTTACGTGCGG 60.804 63.158 0.00 0.67 39.81 5.69
76 77 1.080974 ACCCGTTCTCTTACGTGCG 60.081 57.895 0.00 0.00 39.81 5.34
77 78 1.623973 GCACCCGTTCTCTTACGTGC 61.624 60.000 0.00 0.00 39.81 5.34
78 79 0.319211 TGCACCCGTTCTCTTACGTG 60.319 55.000 0.00 0.00 39.81 4.49
79 80 0.606604 ATGCACCCGTTCTCTTACGT 59.393 50.000 0.00 0.00 39.81 3.57
80 81 2.572191 TATGCACCCGTTCTCTTACG 57.428 50.000 0.00 0.00 41.06 3.18
81 82 4.929808 CCATATATGCACCCGTTCTCTTAC 59.070 45.833 7.24 0.00 0.00 2.34
82 83 4.836175 TCCATATATGCACCCGTTCTCTTA 59.164 41.667 7.24 0.00 0.00 2.10
83 84 3.646162 TCCATATATGCACCCGTTCTCTT 59.354 43.478 7.24 0.00 0.00 2.85
84 85 3.239449 TCCATATATGCACCCGTTCTCT 58.761 45.455 7.24 0.00 0.00 3.10
85 86 3.678056 TCCATATATGCACCCGTTCTC 57.322 47.619 7.24 0.00 0.00 2.87
86 87 3.582647 TGATCCATATATGCACCCGTTCT 59.417 43.478 7.24 0.00 0.00 3.01
87 88 3.937814 TGATCCATATATGCACCCGTTC 58.062 45.455 7.24 0.00 0.00 3.95
88 89 4.264253 CATGATCCATATATGCACCCGTT 58.736 43.478 7.24 0.00 0.00 4.44
89 90 3.877559 CATGATCCATATATGCACCCGT 58.122 45.455 7.24 0.00 0.00 5.28
90 91 2.615447 GCATGATCCATATATGCACCCG 59.385 50.000 7.24 0.00 44.88 5.28
91 92 2.954318 GGCATGATCCATATATGCACCC 59.046 50.000 14.71 1.95 46.74 4.61
92 93 2.615447 CGGCATGATCCATATATGCACC 59.385 50.000 14.71 0.00 46.74 5.01
93 94 3.534554 TCGGCATGATCCATATATGCAC 58.465 45.455 14.71 5.69 46.74 4.57
94 95 3.432608 CCTCGGCATGATCCATATATGCA 60.433 47.826 14.71 0.76 46.74 3.96
95 96 3.136763 CCTCGGCATGATCCATATATGC 58.863 50.000 7.24 6.44 44.81 3.14
96 97 3.136763 GCCTCGGCATGATCCATATATG 58.863 50.000 5.68 5.68 41.49 1.78
97 98 2.105477 GGCCTCGGCATGATCCATATAT 59.895 50.000 10.51 0.00 44.11 0.86
98 99 1.486310 GGCCTCGGCATGATCCATATA 59.514 52.381 10.51 0.00 44.11 0.86
99 100 0.254178 GGCCTCGGCATGATCCATAT 59.746 55.000 10.51 0.00 44.11 1.78
100 101 1.679311 GGCCTCGGCATGATCCATA 59.321 57.895 10.51 0.00 44.11 2.74
101 102 2.433446 GGCCTCGGCATGATCCAT 59.567 61.111 10.51 0.00 44.11 3.41
102 103 3.877450 GGGCCTCGGCATGATCCA 61.877 66.667 10.51 0.00 44.11 3.41
103 104 3.564218 AGGGCCTCGGCATGATCC 61.564 66.667 10.51 1.16 44.11 3.36
104 105 2.281345 CAGGGCCTCGGCATGATC 60.281 66.667 0.95 0.00 44.11 2.92
105 106 3.882326 CCAGGGCCTCGGCATGAT 61.882 66.667 0.95 0.00 44.11 2.45
107 108 4.864334 GTCCAGGGCCTCGGCATG 62.864 72.222 0.95 7.74 44.11 4.06
119 120 0.458543 CATCGACGAACCTGGTCCAG 60.459 60.000 12.40 12.40 0.00 3.86
120 121 1.589630 CATCGACGAACCTGGTCCA 59.410 57.895 0.00 0.00 0.00 4.02
121 122 1.153628 CCATCGACGAACCTGGTCC 60.154 63.158 0.00 0.00 0.00 4.46
122 123 1.590147 ACCATCGACGAACCTGGTC 59.410 57.895 14.42 0.00 37.43 4.02
123 124 1.590147 GACCATCGACGAACCTGGT 59.410 57.895 18.98 18.98 44.52 4.00
124 125 1.516386 CGACCATCGACGAACCTGG 60.516 63.158 13.21 13.21 43.74 4.45
125 126 1.504900 TCGACCATCGACGAACCTG 59.495 57.895 0.00 0.00 44.82 4.00
126 127 3.991999 TCGACCATCGACGAACCT 58.008 55.556 0.00 0.00 44.82 3.50
134 135 0.811915 ACAGAAGGAGTCGACCATCG 59.188 55.000 13.01 5.19 42.10 3.84
135 136 4.098044 TGATAACAGAAGGAGTCGACCATC 59.902 45.833 13.01 3.87 0.00 3.51
136 137 4.023980 TGATAACAGAAGGAGTCGACCAT 58.976 43.478 13.01 0.00 0.00 3.55
137 138 3.192844 GTGATAACAGAAGGAGTCGACCA 59.807 47.826 13.01 0.00 0.00 4.02
138 139 3.731264 CGTGATAACAGAAGGAGTCGACC 60.731 52.174 13.01 3.55 0.00 4.79
139 140 3.427243 CGTGATAACAGAAGGAGTCGAC 58.573 50.000 7.70 7.70 0.00 4.20
140 141 2.422479 CCGTGATAACAGAAGGAGTCGA 59.578 50.000 0.00 0.00 0.00 4.20
141 142 2.798680 CCGTGATAACAGAAGGAGTCG 58.201 52.381 0.00 0.00 0.00 4.18
142 143 2.094182 TGCCGTGATAACAGAAGGAGTC 60.094 50.000 0.00 0.00 0.00 3.36
143 144 1.899814 TGCCGTGATAACAGAAGGAGT 59.100 47.619 0.00 0.00 0.00 3.85
144 145 2.672961 TGCCGTGATAACAGAAGGAG 57.327 50.000 0.00 0.00 0.00 3.69
145 146 2.354704 CCTTGCCGTGATAACAGAAGGA 60.355 50.000 0.00 0.00 31.85 3.36
146 147 2.009774 CCTTGCCGTGATAACAGAAGG 58.990 52.381 0.00 0.00 0.00 3.46
147 148 2.699954 ACCTTGCCGTGATAACAGAAG 58.300 47.619 0.00 0.00 0.00 2.85
148 149 2.851263 ACCTTGCCGTGATAACAGAA 57.149 45.000 0.00 0.00 0.00 3.02
149 150 2.695359 GAACCTTGCCGTGATAACAGA 58.305 47.619 0.00 0.00 0.00 3.41
150 151 1.393539 CGAACCTTGCCGTGATAACAG 59.606 52.381 0.00 0.00 0.00 3.16
151 152 1.270412 ACGAACCTTGCCGTGATAACA 60.270 47.619 0.00 0.00 37.64 2.41
152 153 1.435577 ACGAACCTTGCCGTGATAAC 58.564 50.000 0.00 0.00 37.64 1.89
153 154 1.801771 CAACGAACCTTGCCGTGATAA 59.198 47.619 0.00 0.00 39.14 1.75
154 155 1.001068 TCAACGAACCTTGCCGTGATA 59.999 47.619 0.00 0.00 39.14 2.15
155 156 0.250124 TCAACGAACCTTGCCGTGAT 60.250 50.000 0.00 0.00 39.14 3.06
156 157 0.462225 TTCAACGAACCTTGCCGTGA 60.462 50.000 0.00 0.00 39.14 4.35
157 158 0.591170 ATTCAACGAACCTTGCCGTG 59.409 50.000 0.00 0.00 39.14 4.94
158 159 0.872388 GATTCAACGAACCTTGCCGT 59.128 50.000 0.00 0.00 41.14 5.68
159 160 1.128692 GAGATTCAACGAACCTTGCCG 59.871 52.381 0.00 0.00 0.00 5.69
160 161 1.468914 GGAGATTCAACGAACCTTGCC 59.531 52.381 0.00 0.00 0.00 4.52
161 162 1.128692 CGGAGATTCAACGAACCTTGC 59.871 52.381 0.00 0.00 0.00 4.01
162 163 2.412089 GACGGAGATTCAACGAACCTTG 59.588 50.000 6.96 0.00 0.00 3.61
163 164 2.685100 GACGGAGATTCAACGAACCTT 58.315 47.619 6.96 0.00 0.00 3.50
164 165 1.402456 CGACGGAGATTCAACGAACCT 60.402 52.381 6.96 0.00 0.00 3.50
165 166 0.989890 CGACGGAGATTCAACGAACC 59.010 55.000 6.96 0.00 0.00 3.62
166 167 0.365859 GCGACGGAGATTCAACGAAC 59.634 55.000 0.00 1.40 0.00 3.95
167 168 0.734942 GGCGACGGAGATTCAACGAA 60.735 55.000 0.00 0.00 0.00 3.85
168 169 1.153901 GGCGACGGAGATTCAACGA 60.154 57.895 0.00 0.00 0.00 3.85
169 170 2.165301 GGGCGACGGAGATTCAACG 61.165 63.158 0.00 0.00 0.00 4.10
170 171 1.084370 CAGGGCGACGGAGATTCAAC 61.084 60.000 0.00 0.00 0.00 3.18
171 172 1.218047 CAGGGCGACGGAGATTCAA 59.782 57.895 0.00 0.00 0.00 2.69
172 173 1.945354 GACAGGGCGACGGAGATTCA 61.945 60.000 0.00 0.00 0.00 2.57
173 174 1.227002 GACAGGGCGACGGAGATTC 60.227 63.158 0.00 0.00 0.00 2.52
189 190 3.975168 TTTCAAGCACTACCCCTAGAC 57.025 47.619 0.00 0.00 0.00 2.59
269 271 6.100004 ACGGAGTAAGATGTAACATGTTCTG 58.900 40.000 15.85 4.26 41.94 3.02
277 279 2.601763 CGCCAACGGAGTAAGATGTAAC 59.398 50.000 0.00 0.00 45.00 2.50
281 283 1.278238 GTCGCCAACGGAGTAAGATG 58.722 55.000 0.00 0.00 45.00 2.90
284 290 0.108329 ATGGTCGCCAACGGAGTAAG 60.108 55.000 2.68 0.00 45.00 2.34
285 291 0.390603 CATGGTCGCCAACGGAGTAA 60.391 55.000 2.68 0.00 45.00 2.24
289 295 3.834013 TTGCATGGTCGCCAACGGA 62.834 57.895 2.68 0.00 36.95 4.69
290 296 3.361158 TTGCATGGTCGCCAACGG 61.361 61.111 2.68 0.00 36.95 4.44
291 297 2.126888 GTTGCATGGTCGCCAACG 60.127 61.111 2.68 0.00 36.95 4.10
300 306 1.080366 AGCGCATTGTGTTGCATGG 60.080 52.632 11.47 0.00 42.91 3.66
309 315 0.880278 AGTGACGAACAGCGCATTGT 60.880 50.000 11.47 2.50 46.04 2.71
321 327 2.355363 CCAACGGCGAAGTGACGA 60.355 61.111 16.62 0.00 35.09 4.20
328 334 1.451567 TGGAACAACCAACGGCGAA 60.452 52.632 16.62 0.00 46.75 4.70
329 335 2.189784 TGGAACAACCAACGGCGA 59.810 55.556 16.62 0.00 46.75 5.54
341 347 1.217882 CAGTGGACACGTTCTGGAAC 58.782 55.000 3.62 3.62 37.92 3.62
342 348 0.828022 ACAGTGGACACGTTCTGGAA 59.172 50.000 0.00 0.00 36.20 3.53
344 350 0.104120 TGACAGTGGACACGTTCTGG 59.896 55.000 0.00 0.00 36.20 3.86
346 352 0.249489 GCTGACAGTGGACACGTTCT 60.249 55.000 3.99 0.00 36.20 3.01
347 353 1.548973 CGCTGACAGTGGACACGTTC 61.549 60.000 8.20 0.00 36.20 3.95
350 363 1.730902 CTCGCTGACAGTGGACACG 60.731 63.158 15.79 4.02 36.20 4.49
356 369 3.108289 CACGCCTCGCTGACAGTG 61.108 66.667 9.85 9.85 0.00 3.66
359 372 4.377708 ATGCACGCCTCGCTGACA 62.378 61.111 0.00 0.00 0.00 3.58
360 373 3.558411 GATGCACGCCTCGCTGAC 61.558 66.667 0.00 0.00 0.00 3.51
364 377 4.166011 GGTTGATGCACGCCTCGC 62.166 66.667 0.00 0.00 0.00 5.03
366 379 3.499737 CGGGTTGATGCACGCCTC 61.500 66.667 0.00 0.00 0.00 4.70
374 387 1.123077 TCCAGGAGATCGGGTTGATG 58.877 55.000 0.00 0.00 37.47 3.07
379 392 0.978146 CTTGGTCCAGGAGATCGGGT 60.978 60.000 0.00 0.00 32.28 5.28
425 448 7.598278 AGATCAAACGCATGGTATAAAACAAA 58.402 30.769 0.00 0.00 0.00 2.83
428 451 6.183360 TGGAGATCAAACGCATGGTATAAAAC 60.183 38.462 0.00 0.00 0.00 2.43
429 452 5.883115 TGGAGATCAAACGCATGGTATAAAA 59.117 36.000 0.00 0.00 0.00 1.52
433 457 3.206150 GTGGAGATCAAACGCATGGTAT 58.794 45.455 0.00 0.00 0.00 2.73
435 459 1.271325 TGTGGAGATCAAACGCATGGT 60.271 47.619 0.00 0.00 0.00 3.55
449 480 1.556911 AGTGAACCTAGCCATGTGGAG 59.443 52.381 2.55 0.00 37.39 3.86
521 563 2.738521 CGCCGAGGTGTGAACTGG 60.739 66.667 0.00 0.00 0.00 4.00
522 564 1.557443 GAACGCCGAGGTGTGAACTG 61.557 60.000 9.28 0.00 38.98 3.16
523 565 1.300697 GAACGCCGAGGTGTGAACT 60.301 57.895 9.28 0.00 38.98 3.01
524 566 2.315386 GGAACGCCGAGGTGTGAAC 61.315 63.158 9.28 4.56 38.98 3.18
525 567 2.029964 GGAACGCCGAGGTGTGAA 59.970 61.111 9.28 0.00 38.98 3.18
573 617 3.751698 GGAAGTTTCTGCAAAGATACGGT 59.248 43.478 0.00 0.00 0.00 4.83
600 645 9.793259 AATTTAATTTCAACCTCAGTGAGTAGA 57.207 29.630 18.74 10.30 0.00 2.59
624 702 9.134055 GAGTGTACCAGTAAGTAGAAGGATAAT 57.866 37.037 0.00 0.00 0.00 1.28
626 704 7.636579 TGAGTGTACCAGTAAGTAGAAGGATA 58.363 38.462 0.00 0.00 0.00 2.59
627 705 6.491383 TGAGTGTACCAGTAAGTAGAAGGAT 58.509 40.000 0.00 0.00 0.00 3.24
630 708 7.760340 GGAATTGAGTGTACCAGTAAGTAGAAG 59.240 40.741 0.00 0.00 0.00 2.85
632 710 6.722590 TGGAATTGAGTGTACCAGTAAGTAGA 59.277 38.462 0.00 0.00 0.00 2.59
633 711 6.931838 TGGAATTGAGTGTACCAGTAAGTAG 58.068 40.000 0.00 0.00 0.00 2.57
634 712 6.921486 TGGAATTGAGTGTACCAGTAAGTA 57.079 37.500 0.00 0.00 0.00 2.24
635 713 5.818678 TGGAATTGAGTGTACCAGTAAGT 57.181 39.130 0.00 0.00 0.00 2.24
636 714 7.687941 AAATGGAATTGAGTGTACCAGTAAG 57.312 36.000 0.00 0.00 36.10 2.34
637 715 8.472007 AAAAATGGAATTGAGTGTACCAGTAA 57.528 30.769 0.00 0.00 36.10 2.24
724 805 2.680352 TCGAGAGACAGGTGGGGC 60.680 66.667 0.00 0.00 33.31 5.80
739 820 1.574702 GCCTGGTTTTTCGGGTCTCG 61.575 60.000 0.00 0.00 40.90 4.04
743 824 2.203582 GGGCCTGGTTTTTCGGGT 60.204 61.111 0.84 0.00 35.63 5.28
747 828 0.835971 ATGGTGGGGCCTGGTTTTTC 60.836 55.000 0.84 0.00 38.35 2.29
871 1913 1.213799 CAGCTCTGCTCTGCGTGTA 59.786 57.895 0.00 0.00 36.40 2.90
918 1984 2.594962 CGGAAAAGTGACTGCGCGT 61.595 57.895 8.43 3.28 0.00 6.01
960 2041 1.065636 GGAGCCGGTATTTATAGGGGC 60.066 57.143 1.90 0.00 40.80 5.80
962 2043 2.500504 GAGGGAGCCGGTATTTATAGGG 59.499 54.545 1.90 0.00 0.00 3.53
976 2057 2.123033 GAGAGGAGGGGAGGGAGC 60.123 72.222 0.00 0.00 0.00 4.70
1083 2202 5.119898 CCTGATCTTTCTCTTGTCTGTTTCG 59.880 44.000 0.00 0.00 0.00 3.46
1092 2211 5.395546 CCCTCTTCTCCTGATCTTTCTCTTG 60.396 48.000 0.00 0.00 0.00 3.02
1589 2775 0.240145 CTACAGACAGAACACGCGGA 59.760 55.000 12.47 0.00 0.00 5.54
1693 2906 3.288809 TCACTCACAGATCTCAACGTG 57.711 47.619 4.87 4.87 0.00 4.49
1831 3055 6.290294 ACGGGCGAGTATTTATAATATGGT 57.710 37.500 0.00 0.00 0.00 3.55
1832 3056 5.751990 GGACGGGCGAGTATTTATAATATGG 59.248 44.000 0.00 0.00 0.00 2.74
1833 3057 6.570692 AGGACGGGCGAGTATTTATAATATG 58.429 40.000 0.00 0.00 0.00 1.78
1834 3058 6.459298 CGAGGACGGGCGAGTATTTATAATAT 60.459 42.308 0.00 0.00 35.72 1.28
1856 3080 4.196193 AGACAGTCTCCTAGAATGACGAG 58.804 47.826 10.98 0.00 42.41 4.18
1943 3183 7.936847 TGAACGGCCAGAAGATACATATAAAAT 59.063 33.333 2.24 0.00 0.00 1.82
1944 3184 7.276658 TGAACGGCCAGAAGATACATATAAAA 58.723 34.615 2.24 0.00 0.00 1.52
1952 3194 3.179443 TGATGAACGGCCAGAAGATAC 57.821 47.619 2.24 0.00 0.00 2.24
2047 3289 8.834212 GCGTTTTAAGGAATTTTAACGTAAGAG 58.166 33.333 0.00 0.00 37.64 2.85
2048 3290 8.558700 AGCGTTTTAAGGAATTTTAACGTAAGA 58.441 29.630 0.00 0.00 37.64 2.10
2049 3291 8.718047 AGCGTTTTAAGGAATTTTAACGTAAG 57.282 30.769 0.00 0.00 37.64 2.34
2050 3292 8.558700 AGAGCGTTTTAAGGAATTTTAACGTAA 58.441 29.630 0.00 0.00 37.64 3.18
2051 3293 8.086851 AGAGCGTTTTAAGGAATTTTAACGTA 57.913 30.769 0.00 0.00 37.64 3.57
2052 3294 6.962686 AGAGCGTTTTAAGGAATTTTAACGT 58.037 32.000 0.00 0.00 37.64 3.99
2078 3320 1.961394 AGTGTAAGAGCCTGTGAACGA 59.039 47.619 0.00 0.00 0.00 3.85
2172 3419 4.704833 TGGGCCAACTGCTCGCTC 62.705 66.667 2.13 0.00 46.64 5.03
2175 3422 1.172180 TTTCTTGGGCCAACTGCTCG 61.172 55.000 16.66 4.57 46.64 5.03
2176 3423 0.315251 GTTTCTTGGGCCAACTGCTC 59.685 55.000 16.66 1.50 42.61 4.26
2202 3449 0.319900 TGCTTCTTGACCTCGTGCTC 60.320 55.000 0.00 0.00 0.00 4.26
2205 3452 2.872245 TCTTTTGCTTCTTGACCTCGTG 59.128 45.455 0.00 0.00 0.00 4.35
2233 3480 1.783284 TCGAGCTTTAGTGCACAGTG 58.217 50.000 21.04 7.18 34.99 3.66
2239 3486 3.717707 TCACCATATCGAGCTTTAGTGC 58.282 45.455 0.00 0.00 0.00 4.40
2274 3521 4.074970 ACCTTCATCACATCGAGCTTTTT 58.925 39.130 0.00 0.00 0.00 1.94
2275 3522 3.438087 CACCTTCATCACATCGAGCTTTT 59.562 43.478 0.00 0.00 0.00 2.27
2276 3523 3.005554 CACCTTCATCACATCGAGCTTT 58.994 45.455 0.00 0.00 0.00 3.51
2277 3524 2.027745 ACACCTTCATCACATCGAGCTT 60.028 45.455 0.00 0.00 0.00 3.74
2278 3525 1.552337 ACACCTTCATCACATCGAGCT 59.448 47.619 0.00 0.00 0.00 4.09
2279 3526 2.015736 ACACCTTCATCACATCGAGC 57.984 50.000 0.00 0.00 0.00 5.03
2280 3527 4.936891 TCATACACCTTCATCACATCGAG 58.063 43.478 0.00 0.00 0.00 4.04
2281 3528 5.535753 ATCATACACCTTCATCACATCGA 57.464 39.130 0.00 0.00 0.00 3.59
2282 3529 6.681777 TCTATCATACACCTTCATCACATCG 58.318 40.000 0.00 0.00 0.00 3.84
2283 3530 7.665690 ACTCTATCATACACCTTCATCACATC 58.334 38.462 0.00 0.00 0.00 3.06
2284 3531 7.609097 ACTCTATCATACACCTTCATCACAT 57.391 36.000 0.00 0.00 0.00 3.21
2285 3532 7.124147 TCAACTCTATCATACACCTTCATCACA 59.876 37.037 0.00 0.00 0.00 3.58
2286 3533 7.492524 TCAACTCTATCATACACCTTCATCAC 58.507 38.462 0.00 0.00 0.00 3.06
2317 3564 9.319143 GTTTTAACATCACAGCATCTAGATAGT 57.681 33.333 4.54 1.97 0.00 2.12
2327 3574 3.957497 ACCCAAGTTTTAACATCACAGCA 59.043 39.130 0.00 0.00 0.00 4.41
2329 3576 5.068460 TCCAACCCAAGTTTTAACATCACAG 59.932 40.000 0.00 0.00 32.45 3.66
2367 3614 5.013079 TGGACACACACCTCATAATTCTCTT 59.987 40.000 0.00 0.00 0.00 2.85
2370 3617 4.579869 GTGGACACACACCTCATAATTCT 58.420 43.478 0.00 0.00 46.90 2.40
2385 3632 3.689649 ACAGAAAAAGTCACAGTGGACAC 59.310 43.478 12.45 0.00 40.29 3.67
2393 3640 3.644966 ACCAGGACAGAAAAAGTCACA 57.355 42.857 0.00 0.00 37.74 3.58
2404 3651 3.947910 TTACTCCGTTAACCAGGACAG 57.052 47.619 0.00 0.00 32.33 3.51
2408 3655 4.081309 TCCATCTTTACTCCGTTAACCAGG 60.081 45.833 0.00 0.00 0.00 4.45
2418 3665 5.352846 GCTTGAACTTCTCCATCTTTACTCC 59.647 44.000 0.00 0.00 0.00 3.85
2433 3680 2.979678 TCCCTCTAGTTGGCTTGAACTT 59.020 45.455 0.00 0.00 37.38 2.66
2492 3739 1.040339 AGAGACCCTCGGCAGCTAAG 61.040 60.000 0.00 0.00 35.36 2.18
2574 3821 0.814010 AGATGATTTACCGGTGGCGC 60.814 55.000 19.93 0.00 0.00 6.53
2577 3824 3.560636 AAGGAGATGATTTACCGGTGG 57.439 47.619 19.93 0.00 0.00 4.61
2602 4034 7.061441 CCTTGAAGATCAACAAACAATCATTCG 59.939 37.037 0.00 0.00 32.21 3.34
2604 4036 6.647895 GCCTTGAAGATCAACAAACAATCATT 59.352 34.615 0.00 0.00 32.21 2.57
2606 4038 5.068855 TGCCTTGAAGATCAACAAACAATCA 59.931 36.000 0.00 0.00 32.21 2.57
2681 4114 1.946984 TTAACCCTCTGACCCGATGT 58.053 50.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.