Multiple sequence alignment - TraesCS5B01G327300

Loading Multiple Alignment...

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 TraesCS5B01G327300 chr5B 100.000 2741 0 0 1 2741 511291410 511294150 0.000000e+00 5062.0
1 TraesCS5B01G327300 chr5B 98.925 186 1 1 1 185 445179429 445179614 5.660000e-87 331.0
2 TraesCS5B01G327300 chr5B 98.387 186 2 1 1 185 695754815 695754630 2.630000e-85 326.0
3 TraesCS5B01G327300 chr5D 91.528 1747 73 26 762 2466 423474088 423475801 0.000000e+00 2337.0
4 TraesCS5B01G327300 chr5D 87.567 563 52 13 2188 2741 423486441 423486994 1.070000e-178 636.0
5 TraesCS5B01G327300 chr5D 89.560 364 21 4 181 539 423473208 423473559 1.940000e-121 446.0
6 TraesCS5B01G327300 chr5D 90.000 170 9 2 2026 2191 423476657 423476822 2.140000e-51 213.0
7 TraesCS5B01G327300 chr5D 95.161 124 4 1 571 692 423473562 423473685 7.740000e-46 195.0
8 TraesCS5B01G327300 chr5A 87.030 1303 74 32 480 1737 536970152 536971404 0.000000e+00 1382.0
9 TraesCS5B01G327300 chr5A 87.792 557 52 6 2189 2741 536973461 536974005 2.980000e-179 638.0
10 TraesCS5B01G327300 chr5A 91.558 308 21 2 181 483 536948570 536948877 1.170000e-113 420.0
11 TraesCS5B01G327300 chr5A 86.310 336 12 14 1871 2201 536971703 536972009 4.370000e-88 335.0
12 TraesCS5B01G327300 chr3B 80.952 1596 180 62 612 2153 542897189 542898714 0.000000e+00 1149.0
13 TraesCS5B01G327300 chr3B 80.012 1606 144 82 612 2153 542929230 542930722 0.000000e+00 1024.0
14 TraesCS5B01G327300 chr3B 83.178 428 59 8 1286 1712 543067779 543068194 1.990000e-101 379.0
15 TraesCS5B01G327300 chr3B 98.925 186 1 1 1 185 62389450 62389265 5.660000e-87 331.0
16 TraesCS5B01G327300 chr3B 98.396 187 2 1 1 186 471474125 471474311 7.320000e-86 327.0
17 TraesCS5B01G327300 chr3B 78.113 530 54 28 1359 1850 542748676 542749181 2.080000e-71 279.0
18 TraesCS5B01G327300 chr3B 77.290 524 60 32 1446 1966 543181483 543181950 1.260000e-63 254.0
19 TraesCS5B01G327300 chr3B 78.992 238 30 15 902 1135 543093382 543093603 7.910000e-31 145.0
20 TraesCS5B01G327300 chr3D 79.687 1595 160 72 613 2153 416575226 416576710 0.000000e+00 1000.0
21 TraesCS5B01G327300 chr3D 79.704 675 78 21 1046 1712 416951673 416952296 1.510000e-117 433.0
22 TraesCS5B01G327300 chr3D 81.431 517 60 18 1287 1776 416937081 416936574 9.200000e-105 390.0
23 TraesCS5B01G327300 chr3D 79.439 428 48 28 390 802 416561704 416562106 1.620000e-67 267.0
24 TraesCS5B01G327300 chr3D 79.439 214 35 5 989 1194 416934960 416935172 2.850000e-30 143.0
25 TraesCS5B01G327300 chr3D 77.885 208 37 7 2338 2545 416576954 416577152 1.330000e-23 121.0
26 TraesCS5B01G327300 chr3D 85.567 97 12 1 435 529 416405038 416405134 1.740000e-17 100.0
27 TraesCS5B01G327300 chr3D 74.086 301 41 17 2162 2442 416952676 416952959 3.760000e-14 89.8
28 TraesCS5B01G327300 chr3D 92.727 55 2 1 385 437 416985208 416985262 8.140000e-11 78.7
29 TraesCS5B01G327300 chr3A 81.942 1174 128 46 625 1776 533995479 533994368 0.000000e+00 917.0
30 TraesCS5B01G327300 chr3A 85.238 210 25 5 379 584 534162843 534162636 7.690000e-51 211.0
31 TraesCS5B01G327300 chr3A 77.824 239 25 13 1734 1968 534166299 534166085 3.710000e-24 122.0
32 TraesCS5B01G327300 chr3A 85.366 123 11 5 1655 1776 533979904 533979788 1.330000e-23 121.0
33 TraesCS5B01G327300 chr3A 79.730 148 13 9 732 877 534167168 534167036 1.050000e-14 91.6
34 TraesCS5B01G327300 chr7B 98.404 188 2 1 1 187 735986875 735987062 2.030000e-86 329.0
35 TraesCS5B01G327300 chr7B 98.396 187 2 1 1 186 312406966 312407152 7.320000e-86 327.0
36 TraesCS5B01G327300 chr6D 98.387 186 2 1 1 185 143958627 143958442 2.630000e-85 326.0
37 TraesCS5B01G327300 chr2B 98.387 186 2 1 1 185 748070685 748070500 2.630000e-85 326.0
38 TraesCS5B01G327300 chr2B 94.634 205 8 3 1 203 436266274 436266071 5.700000e-82 315.0
39 TraesCS5B01G327300 chr7D 84.158 101 6 7 795 892 6445238 6445331 3.760000e-14 89.8


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 TraesCS5B01G327300 chr5B 511291410 511294150 2740 False 5062.00 5062 100.00000 1 2741 1 chr5B.!!$F2 2740
1 TraesCS5B01G327300 chr5D 423473208 423476822 3614 False 797.75 2337 91.56225 181 2466 4 chr5D.!!$F2 2285
2 TraesCS5B01G327300 chr5D 423486441 423486994 553 False 636.00 636 87.56700 2188 2741 1 chr5D.!!$F1 553
3 TraesCS5B01G327300 chr5A 536970152 536974005 3853 False 785.00 1382 87.04400 480 2741 3 chr5A.!!$F2 2261
4 TraesCS5B01G327300 chr3B 542897189 542898714 1525 False 1149.00 1149 80.95200 612 2153 1 chr3B.!!$F3 1541
5 TraesCS5B01G327300 chr3B 542929230 542930722 1492 False 1024.00 1024 80.01200 612 2153 1 chr3B.!!$F4 1541
6 TraesCS5B01G327300 chr3B 542748676 542749181 505 False 279.00 279 78.11300 1359 1850 1 chr3B.!!$F2 491
7 TraesCS5B01G327300 chr3D 416575226 416577152 1926 False 560.50 1000 78.78600 613 2545 2 chr3D.!!$F5 1932
8 TraesCS5B01G327300 chr3D 416936574 416937081 507 True 390.00 390 81.43100 1287 1776 1 chr3D.!!$R1 489
9 TraesCS5B01G327300 chr3D 416951673 416952959 1286 False 261.40 433 76.89500 1046 2442 2 chr3D.!!$F6 1396
10 TraesCS5B01G327300 chr3A 533994368 533995479 1111 True 917.00 917 81.94200 625 1776 1 chr3A.!!$R2 1151

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
556 562 0.037975 TCGCGGTAGTTTCCCTTGTC 60.038 55.0 6.13 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 4661 0.322187 TCGACTCGGTGATCTGACCA 60.322 55.0 0.0 0.0 35.5 4.02 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
20 21 2.404083 CAACAAGTTGTGCCCGACT 58.596 52.632 9.79 0.00 36.86 4.18
21 22 0.307760 CAACAAGTTGTGCCCGACTC 59.692 55.000 9.79 0.00 34.00 3.36
22 23 0.818040 AACAAGTTGTGCCCGACTCC 60.818 55.000 9.79 0.00 34.00 3.85
23 24 2.030562 AAGTTGTGCCCGACTCCG 59.969 61.111 0.00 0.00 34.00 4.63
40 41 4.996434 GGCGATGGAGGGGCGATG 62.996 72.222 0.00 0.00 0.00 3.84
41 42 3.928779 GCGATGGAGGGGCGATGA 61.929 66.667 0.00 0.00 0.00 2.92
42 43 2.029666 CGATGGAGGGGCGATGAC 59.970 66.667 0.00 0.00 0.00 3.06
43 44 2.029666 GATGGAGGGGCGATGACG 59.970 66.667 0.00 0.00 42.93 4.35
44 45 3.521529 GATGGAGGGGCGATGACGG 62.522 68.421 0.00 0.00 40.15 4.79
68 69 3.191539 GCCTTCGGCTCGCTTCAG 61.192 66.667 0.00 0.00 46.69 3.02
69 70 2.262915 CCTTCGGCTCGCTTCAGT 59.737 61.111 0.00 0.00 0.00 3.41
70 71 2.097038 CCTTCGGCTCGCTTCAGTG 61.097 63.158 0.00 0.00 0.00 3.66
71 72 2.734673 CTTCGGCTCGCTTCAGTGC 61.735 63.158 0.00 0.00 0.00 4.40
72 73 3.226429 TTCGGCTCGCTTCAGTGCT 62.226 57.895 0.00 0.00 0.00 4.40
73 74 3.485431 CGGCTCGCTTCAGTGCTG 61.485 66.667 0.00 0.00 0.00 4.41
74 75 3.123620 GGCTCGCTTCAGTGCTGG 61.124 66.667 0.00 0.00 0.00 4.85
75 76 2.358003 GCTCGCTTCAGTGCTGGT 60.358 61.111 0.00 0.00 0.00 4.00
76 77 1.079819 GCTCGCTTCAGTGCTGGTA 60.080 57.895 0.00 0.00 0.00 3.25
77 78 1.080995 GCTCGCTTCAGTGCTGGTAG 61.081 60.000 0.00 0.00 0.00 3.18
78 79 0.244994 CTCGCTTCAGTGCTGGTAGT 59.755 55.000 0.00 0.00 0.00 2.73
79 80 0.243907 TCGCTTCAGTGCTGGTAGTC 59.756 55.000 0.00 0.00 0.00 2.59
80 81 1.073216 CGCTTCAGTGCTGGTAGTCG 61.073 60.000 0.00 3.25 0.00 4.18
81 82 0.038159 GCTTCAGTGCTGGTAGTCGT 60.038 55.000 0.00 0.00 0.00 4.34
82 83 1.983972 CTTCAGTGCTGGTAGTCGTC 58.016 55.000 0.00 0.00 0.00 4.20
83 84 0.240145 TTCAGTGCTGGTAGTCGTCG 59.760 55.000 0.00 0.00 0.00 5.12
84 85 1.154016 CAGTGCTGGTAGTCGTCGG 60.154 63.158 0.00 0.00 0.00 4.79
85 86 1.602888 AGTGCTGGTAGTCGTCGGT 60.603 57.895 0.00 0.00 0.00 4.69
86 87 0.321919 AGTGCTGGTAGTCGTCGGTA 60.322 55.000 0.00 0.00 0.00 4.02
87 88 0.098376 GTGCTGGTAGTCGTCGGTAG 59.902 60.000 0.00 0.00 0.00 3.18
88 89 1.028330 TGCTGGTAGTCGTCGGTAGG 61.028 60.000 0.00 0.00 0.00 3.18
89 90 1.028868 GCTGGTAGTCGTCGGTAGGT 61.029 60.000 0.00 0.00 0.00 3.08
90 91 0.731417 CTGGTAGTCGTCGGTAGGTG 59.269 60.000 0.00 0.00 0.00 4.00
91 92 0.677731 TGGTAGTCGTCGGTAGGTGG 60.678 60.000 0.00 0.00 0.00 4.61
92 93 0.678048 GGTAGTCGTCGGTAGGTGGT 60.678 60.000 0.00 0.00 0.00 4.16
93 94 0.729690 GTAGTCGTCGGTAGGTGGTC 59.270 60.000 0.00 0.00 0.00 4.02
94 95 0.615331 TAGTCGTCGGTAGGTGGTCT 59.385 55.000 0.00 0.00 0.00 3.85
95 96 0.615331 AGTCGTCGGTAGGTGGTCTA 59.385 55.000 0.00 0.00 0.00 2.59
96 97 1.211457 AGTCGTCGGTAGGTGGTCTAT 59.789 52.381 0.00 0.00 0.00 1.98
97 98 1.332997 GTCGTCGGTAGGTGGTCTATG 59.667 57.143 0.00 0.00 0.00 2.23
98 99 0.666913 CGTCGGTAGGTGGTCTATGG 59.333 60.000 0.00 0.00 0.00 2.74
99 100 1.748244 CGTCGGTAGGTGGTCTATGGA 60.748 57.143 0.00 0.00 0.00 3.41
100 101 2.595238 GTCGGTAGGTGGTCTATGGAT 58.405 52.381 0.00 0.00 0.00 3.41
101 102 2.557490 GTCGGTAGGTGGTCTATGGATC 59.443 54.545 0.00 0.00 0.00 3.36
102 103 2.445905 TCGGTAGGTGGTCTATGGATCT 59.554 50.000 0.00 0.00 0.00 2.75
103 104 2.558795 CGGTAGGTGGTCTATGGATCTG 59.441 54.545 0.00 0.00 0.00 2.90
104 105 2.900546 GGTAGGTGGTCTATGGATCTGG 59.099 54.545 0.00 0.00 0.00 3.86
105 106 3.438078 GGTAGGTGGTCTATGGATCTGGA 60.438 52.174 0.00 0.00 0.00 3.86
106 107 3.645053 AGGTGGTCTATGGATCTGGAT 57.355 47.619 0.00 0.00 0.00 3.41
107 108 3.246301 AGGTGGTCTATGGATCTGGATG 58.754 50.000 0.00 0.00 0.00 3.51
108 109 2.975489 GGTGGTCTATGGATCTGGATGT 59.025 50.000 0.00 0.00 0.00 3.06
109 110 4.140686 AGGTGGTCTATGGATCTGGATGTA 60.141 45.833 0.00 0.00 0.00 2.29
110 111 4.593206 GGTGGTCTATGGATCTGGATGTAA 59.407 45.833 0.00 0.00 0.00 2.41
111 112 5.249393 GGTGGTCTATGGATCTGGATGTAAT 59.751 44.000 0.00 0.00 0.00 1.89
112 113 6.240002 GGTGGTCTATGGATCTGGATGTAATT 60.240 42.308 0.00 0.00 0.00 1.40
113 114 7.227156 GTGGTCTATGGATCTGGATGTAATTT 58.773 38.462 0.00 0.00 0.00 1.82
114 115 7.721399 GTGGTCTATGGATCTGGATGTAATTTT 59.279 37.037 0.00 0.00 0.00 1.82
115 116 8.281531 TGGTCTATGGATCTGGATGTAATTTTT 58.718 33.333 0.00 0.00 0.00 1.94
116 117 9.793259 GGTCTATGGATCTGGATGTAATTTTTA 57.207 33.333 0.00 0.00 0.00 1.52
141 142 5.796350 ATTTCTGGTATTCGTTGTACTGC 57.204 39.130 0.00 0.00 0.00 4.40
142 143 3.241067 TCTGGTATTCGTTGTACTGCC 57.759 47.619 0.00 0.00 0.00 4.85
143 144 2.563620 TCTGGTATTCGTTGTACTGCCA 59.436 45.455 0.00 0.00 0.00 4.92
144 145 3.196901 TCTGGTATTCGTTGTACTGCCAT 59.803 43.478 0.00 0.00 0.00 4.40
145 146 3.266636 TGGTATTCGTTGTACTGCCATG 58.733 45.455 0.00 0.00 0.00 3.66
146 147 3.055747 TGGTATTCGTTGTACTGCCATGA 60.056 43.478 0.00 0.00 0.00 3.07
147 148 4.127171 GGTATTCGTTGTACTGCCATGAT 58.873 43.478 0.00 0.00 0.00 2.45
148 149 4.574828 GGTATTCGTTGTACTGCCATGATT 59.425 41.667 0.00 0.00 0.00 2.57
149 150 4.621068 ATTCGTTGTACTGCCATGATTG 57.379 40.909 0.00 0.00 0.00 2.67
150 151 3.326836 TCGTTGTACTGCCATGATTGA 57.673 42.857 0.00 0.00 0.00 2.57
151 152 3.669536 TCGTTGTACTGCCATGATTGAA 58.330 40.909 0.00 0.00 0.00 2.69
152 153 3.684305 TCGTTGTACTGCCATGATTGAAG 59.316 43.478 0.00 0.00 0.00 3.02
153 154 3.684305 CGTTGTACTGCCATGATTGAAGA 59.316 43.478 0.00 0.00 0.00 2.87
154 155 4.333649 CGTTGTACTGCCATGATTGAAGAT 59.666 41.667 0.00 0.00 0.00 2.40
155 156 5.575957 GTTGTACTGCCATGATTGAAGATG 58.424 41.667 0.00 0.00 0.00 2.90
156 157 5.101648 TGTACTGCCATGATTGAAGATGA 57.898 39.130 0.00 0.00 0.00 2.92
157 158 5.499313 TGTACTGCCATGATTGAAGATGAA 58.501 37.500 0.00 0.00 0.00 2.57
158 159 6.124340 TGTACTGCCATGATTGAAGATGAAT 58.876 36.000 0.00 0.00 0.00 2.57
159 160 7.281841 TGTACTGCCATGATTGAAGATGAATA 58.718 34.615 0.00 0.00 0.00 1.75
160 161 6.879276 ACTGCCATGATTGAAGATGAATAG 57.121 37.500 0.00 0.00 0.00 1.73
161 162 6.363065 ACTGCCATGATTGAAGATGAATAGT 58.637 36.000 0.00 0.00 0.00 2.12
162 163 6.485984 ACTGCCATGATTGAAGATGAATAGTC 59.514 38.462 0.00 0.00 0.00 2.59
163 164 5.467735 TGCCATGATTGAAGATGAATAGTCG 59.532 40.000 0.00 0.00 0.00 4.18
164 165 5.106791 GCCATGATTGAAGATGAATAGTCGG 60.107 44.000 0.00 0.00 0.00 4.79
165 166 6.226052 CCATGATTGAAGATGAATAGTCGGA 58.774 40.000 0.00 0.00 0.00 4.55
166 167 6.707608 CCATGATTGAAGATGAATAGTCGGAA 59.292 38.462 0.00 0.00 0.00 4.30
167 168 7.227314 CCATGATTGAAGATGAATAGTCGGAAA 59.773 37.037 0.00 0.00 0.00 3.13
168 169 8.781196 CATGATTGAAGATGAATAGTCGGAAAT 58.219 33.333 0.00 0.00 0.00 2.17
169 170 8.737168 TGATTGAAGATGAATAGTCGGAAATT 57.263 30.769 0.00 0.00 0.00 1.82
170 171 9.177608 TGATTGAAGATGAATAGTCGGAAATTT 57.822 29.630 0.00 0.00 0.00 1.82
173 174 8.792830 TGAAGATGAATAGTCGGAAATTTTCT 57.207 30.769 8.93 0.00 0.00 2.52
174 175 8.883731 TGAAGATGAATAGTCGGAAATTTTCTC 58.116 33.333 8.93 0.00 0.00 2.87
175 176 7.470289 AGATGAATAGTCGGAAATTTTCTCG 57.530 36.000 8.93 10.38 0.00 4.04
176 177 5.464965 TGAATAGTCGGAAATTTTCTCGC 57.535 39.130 8.93 7.39 0.00 5.03
177 178 4.932799 TGAATAGTCGGAAATTTTCTCGCA 59.067 37.500 8.93 1.97 0.00 5.10
178 179 5.410132 TGAATAGTCGGAAATTTTCTCGCAA 59.590 36.000 8.93 1.91 0.00 4.85
179 180 5.873179 ATAGTCGGAAATTTTCTCGCAAA 57.127 34.783 8.93 1.64 0.00 3.68
221 223 2.009051 TGCTTTGGTAGATGCATGTCG 58.991 47.619 2.46 0.00 0.00 4.35
274 278 4.346734 TCGAGTTGAACCGTGTAGATAC 57.653 45.455 6.20 0.00 0.00 2.24
277 281 5.048504 TCGAGTTGAACCGTGTAGATACTTT 60.049 40.000 6.20 0.00 0.00 2.66
280 284 5.694910 AGTTGAACCGTGTAGATACTTTGTG 59.305 40.000 0.00 0.00 0.00 3.33
298 302 5.627499 TTGTGGAGCATAAGTTGATGAAC 57.373 39.130 0.00 0.00 0.00 3.18
307 311 1.568504 AGTTGATGAACGGGCTCCTA 58.431 50.000 0.00 0.00 37.15 2.94
311 315 3.426787 TGATGAACGGGCTCCTAAAAA 57.573 42.857 0.00 0.00 0.00 1.94
340 344 3.179443 GATGGCTATCGGAGTGTCAAA 57.821 47.619 0.00 0.00 0.00 2.69
341 345 3.531538 GATGGCTATCGGAGTGTCAAAA 58.468 45.455 0.00 0.00 0.00 2.44
342 346 3.410631 TGGCTATCGGAGTGTCAAAAA 57.589 42.857 0.00 0.00 0.00 1.94
500 506 3.947196 CACACCTGCAAAGATATTAGGCA 59.053 43.478 0.00 0.29 31.69 4.75
539 545 1.070289 GAGGGTATAGGGGCAACTTCG 59.930 57.143 0.00 0.00 0.00 3.79
541 547 0.878961 GGTATAGGGGCAACTTCGCG 60.879 60.000 0.00 0.00 0.00 5.87
542 548 0.878961 GTATAGGGGCAACTTCGCGG 60.879 60.000 6.13 0.00 0.00 6.46
543 549 1.332144 TATAGGGGCAACTTCGCGGT 61.332 55.000 6.13 0.00 0.00 5.68
544 550 1.332144 ATAGGGGCAACTTCGCGGTA 61.332 55.000 6.13 0.00 0.00 4.02
545 551 1.952102 TAGGGGCAACTTCGCGGTAG 61.952 60.000 6.13 6.96 0.00 3.18
546 552 2.047560 GGGCAACTTCGCGGTAGT 60.048 61.111 6.13 7.70 0.00 2.73
547 553 1.670083 GGGCAACTTCGCGGTAGTT 60.670 57.895 17.84 17.84 36.31 2.24
548 554 1.232621 GGGCAACTTCGCGGTAGTTT 61.233 55.000 20.03 7.59 33.73 2.66
549 555 0.165295 GGCAACTTCGCGGTAGTTTC 59.835 55.000 20.03 16.49 33.73 2.78
550 556 0.165295 GCAACTTCGCGGTAGTTTCC 59.835 55.000 20.03 12.78 33.73 3.13
551 557 0.794473 CAACTTCGCGGTAGTTTCCC 59.206 55.000 20.03 0.00 33.73 3.97
552 558 0.683412 AACTTCGCGGTAGTTTCCCT 59.317 50.000 17.84 1.00 32.06 4.20
553 559 0.683412 ACTTCGCGGTAGTTTCCCTT 59.317 50.000 6.13 0.00 0.00 3.95
554 560 1.076332 CTTCGCGGTAGTTTCCCTTG 58.924 55.000 6.13 0.00 0.00 3.61
555 561 0.393820 TTCGCGGTAGTTTCCCTTGT 59.606 50.000 6.13 0.00 0.00 3.16
556 562 0.037975 TCGCGGTAGTTTCCCTTGTC 60.038 55.000 6.13 0.00 0.00 3.18
557 563 0.320073 CGCGGTAGTTTCCCTTGTCA 60.320 55.000 0.00 0.00 0.00 3.58
558 564 1.154197 GCGGTAGTTTCCCTTGTCAC 58.846 55.000 0.00 0.00 0.00 3.67
559 565 1.270678 GCGGTAGTTTCCCTTGTCACT 60.271 52.381 0.00 0.00 0.00 3.41
560 566 2.413837 CGGTAGTTTCCCTTGTCACTG 58.586 52.381 0.00 0.00 0.00 3.66
561 567 2.152016 GGTAGTTTCCCTTGTCACTGC 58.848 52.381 0.00 0.00 0.00 4.40
562 568 2.152016 GTAGTTTCCCTTGTCACTGCC 58.848 52.381 0.00 0.00 0.00 4.85
563 569 0.178990 AGTTTCCCTTGTCACTGCCC 60.179 55.000 0.00 0.00 0.00 5.36
564 570 0.178990 GTTTCCCTTGTCACTGCCCT 60.179 55.000 0.00 0.00 0.00 5.19
565 571 0.178992 TTTCCCTTGTCACTGCCCTG 60.179 55.000 0.00 0.00 0.00 4.45
566 572 1.059584 TTCCCTTGTCACTGCCCTGA 61.060 55.000 0.00 0.00 0.00 3.86
567 573 1.002868 CCCTTGTCACTGCCCTGAG 60.003 63.158 0.00 0.00 0.00 3.35
568 574 1.483595 CCCTTGTCACTGCCCTGAGA 61.484 60.000 0.00 0.00 0.00 3.27
569 575 0.617413 CCTTGTCACTGCCCTGAGAT 59.383 55.000 0.00 0.00 0.00 2.75
758 849 1.962822 TTGCAGCTCGAGCACCTTG 60.963 57.895 36.87 26.64 42.54 3.61
794 1178 4.187694 CCAAGCTAACAAGCTAGGAAGAG 58.812 47.826 0.00 0.00 45.54 2.85
797 1181 5.746990 AGCTAACAAGCTAGGAAGAGAAA 57.253 39.130 0.00 0.00 44.28 2.52
863 1249 0.394565 ATCTCCGGCCATCTTGCTAC 59.605 55.000 2.24 0.00 0.00 3.58
995 1389 2.115595 GTTGCTGATCTCGTGATCTCG 58.884 52.381 23.64 10.84 46.84 4.04
1037 1440 0.107214 GGATCTCCATGGACGGCAAA 60.107 55.000 11.44 0.00 35.64 3.68
1137 1549 2.094659 AACGCCTTCAGCATCGTCG 61.095 57.895 0.00 0.00 44.04 5.12
1138 1550 2.507102 CGCCTTCAGCATCGTCGT 60.507 61.111 0.00 0.00 44.04 4.34
1194 1609 1.257750 TGTCTCGTGCAGCCAGGTAT 61.258 55.000 0.00 0.00 0.00 2.73
1195 1610 0.744874 GTCTCGTGCAGCCAGGTATA 59.255 55.000 0.00 0.00 0.00 1.47
1243 1690 5.905532 GCTTTTGCTTGGCATTATTGCGAA 61.906 41.667 6.82 6.82 45.61 4.70
1336 1783 1.372499 CTGACGGACGCGGAGAAAA 60.372 57.895 12.47 0.00 0.00 2.29
1730 2252 5.590259 AGCGTACTTCTAGGGAATAACGTAA 59.410 40.000 0.00 0.00 39.48 3.18
1797 2482 8.700644 CCGTAGTATTGTATTTGTGAATCTAGC 58.299 37.037 0.00 0.00 0.00 3.42
1798 2483 9.464714 CGTAGTATTGTATTTGTGAATCTAGCT 57.535 33.333 0.00 0.00 0.00 3.32
1801 2486 9.482627 AGTATTGTATTTGTGAATCTAGCTAGC 57.517 33.333 16.35 6.62 0.00 3.42
1812 2497 5.422331 TGAATCTAGCTAGCAGTAACTGGTT 59.578 40.000 18.83 0.95 42.44 3.67
1843 2538 6.995511 AATATCCAGATCGACTCTAGTAGC 57.004 41.667 0.00 0.00 31.13 3.58
1991 2752 7.769272 AAATTGATATTGCGGTGTAATTTGG 57.231 32.000 0.00 0.00 0.00 3.28
1992 2753 4.300189 TGATATTGCGGTGTAATTTGGC 57.700 40.909 0.00 0.00 0.00 4.52
2092 2863 2.801579 GCTAGCGCGCGTATCCTC 60.802 66.667 32.35 13.54 0.00 3.71
2093 2864 2.947542 CTAGCGCGCGTATCCTCT 59.052 61.111 32.35 20.35 0.00 3.69
2094 2865 1.909141 GCTAGCGCGCGTATCCTCTA 61.909 60.000 32.35 20.38 0.00 2.43
2095 2866 0.095589 CTAGCGCGCGTATCCTCTAG 59.904 60.000 32.35 25.14 0.00 2.43
2194 4469 1.630878 CCCTCCTGCAAAGTAAGGTCT 59.369 52.381 0.00 0.00 34.94 3.85
2278 4555 1.264826 GTATTTGCGGTTTCACCACGT 59.735 47.619 0.00 0.00 38.47 4.49
2352 4691 5.748630 CAGATCACCGAGTCGAATATTTGAA 59.251 40.000 15.64 0.00 0.00 2.69
2411 4750 3.712733 TGTTCCACAACTTACACCTACCT 59.287 43.478 0.00 0.00 33.17 3.08
2431 4770 3.071023 CCTGAACACCTGAAACTACTGGA 59.929 47.826 0.00 0.00 33.93 3.86
2557 5542 5.524646 TCCAACTTCAAAACCAGTTAGTACG 59.475 40.000 0.00 0.00 31.78 3.67
2574 5560 1.957668 ACGCAACCCTAAACTTTCGT 58.042 45.000 0.00 0.00 0.00 3.85
2589 5575 5.924475 ACTTTCGTCACCATTCAGTTTAG 57.076 39.130 0.00 0.00 0.00 1.85
2660 5658 4.118410 AGTCAACAATGATCTCGCATCTC 58.882 43.478 0.00 0.00 38.01 2.75
2665 5663 3.869832 ACAATGATCTCGCATCTCAGTTG 59.130 43.478 0.00 0.00 0.00 3.16
2666 5664 1.931906 TGATCTCGCATCTCAGTTGC 58.068 50.000 0.00 0.00 36.74 4.17
2669 5667 2.168326 TCTCGCATCTCAGTTGCAAA 57.832 45.000 0.00 0.00 40.14 3.68
2670 5668 2.493035 TCTCGCATCTCAGTTGCAAAA 58.507 42.857 0.00 0.00 40.14 2.44
2671 5669 2.877786 TCTCGCATCTCAGTTGCAAAAA 59.122 40.909 0.00 0.00 40.14 1.94
2672 5670 2.975851 CTCGCATCTCAGTTGCAAAAAC 59.024 45.455 0.00 0.00 40.14 2.43
2673 5671 2.357323 TCGCATCTCAGTTGCAAAAACA 59.643 40.909 0.00 0.00 40.14 2.83
2675 5673 4.215185 TCGCATCTCAGTTGCAAAAACATA 59.785 37.500 0.00 0.00 40.14 2.29
2677 5675 5.164158 CGCATCTCAGTTGCAAAAACATAAC 60.164 40.000 0.00 0.00 40.14 1.89
2678 5676 5.922544 GCATCTCAGTTGCAAAAACATAACT 59.077 36.000 0.00 0.00 39.90 2.24
2679 5677 6.129009 GCATCTCAGTTGCAAAAACATAACTG 60.129 38.462 0.00 2.20 46.94 3.16
2730 5730 6.493189 AAATCATCTTCTTCCTCCTCTACC 57.507 41.667 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.134340 AGTCGGGCACAACTTGTTGTA 60.134 47.619 17.26 1.01 33.17 2.41
1 2 0.393808 AGTCGGGCACAACTTGTTGT 60.394 50.000 12.73 12.73 35.14 3.32
3 4 0.818040 GGAGTCGGGCACAACTTGTT 60.818 55.000 0.00 0.00 0.00 2.83
4 5 1.227853 GGAGTCGGGCACAACTTGT 60.228 57.895 0.00 0.00 0.00 3.16
5 6 2.317609 CGGAGTCGGGCACAACTTG 61.318 63.158 0.00 0.00 0.00 3.16
6 7 2.030562 CGGAGTCGGGCACAACTT 59.969 61.111 0.00 0.00 0.00 2.66
23 24 4.996434 CATCGCCCCTCCATCGCC 62.996 72.222 0.00 0.00 0.00 5.54
24 25 3.928779 TCATCGCCCCTCCATCGC 61.929 66.667 0.00 0.00 0.00 4.58
25 26 2.029666 GTCATCGCCCCTCCATCG 59.970 66.667 0.00 0.00 0.00 3.84
26 27 2.029666 CGTCATCGCCCCTCCATC 59.970 66.667 0.00 0.00 0.00 3.51
27 28 3.550431 CCGTCATCGCCCCTCCAT 61.550 66.667 0.00 0.00 35.54 3.41
53 54 2.734673 GCACTGAAGCGAGCCGAAG 61.735 63.158 0.00 0.00 0.00 3.79
54 55 2.738521 GCACTGAAGCGAGCCGAA 60.739 61.111 0.00 0.00 0.00 4.30
55 56 3.684990 AGCACTGAAGCGAGCCGA 61.685 61.111 0.00 0.00 40.15 5.54
56 57 3.485431 CAGCACTGAAGCGAGCCG 61.485 66.667 0.00 0.00 40.15 5.52
57 58 2.507110 TACCAGCACTGAAGCGAGCC 62.507 60.000 0.00 0.00 40.15 4.70
58 59 1.079819 TACCAGCACTGAAGCGAGC 60.080 57.895 0.00 0.00 40.15 5.03
59 60 0.244994 ACTACCAGCACTGAAGCGAG 59.755 55.000 0.00 0.00 40.15 5.03
60 61 0.243907 GACTACCAGCACTGAAGCGA 59.756 55.000 0.00 0.00 40.15 4.93
61 62 1.073216 CGACTACCAGCACTGAAGCG 61.073 60.000 0.00 1.97 40.15 4.68
62 63 0.038159 ACGACTACCAGCACTGAAGC 60.038 55.000 0.00 0.00 0.00 3.86
63 64 1.729472 CGACGACTACCAGCACTGAAG 60.729 57.143 0.00 0.00 0.00 3.02
64 65 0.240145 CGACGACTACCAGCACTGAA 59.760 55.000 0.00 0.00 0.00 3.02
65 66 1.583495 CCGACGACTACCAGCACTGA 61.583 60.000 0.00 0.00 0.00 3.41
66 67 1.154016 CCGACGACTACCAGCACTG 60.154 63.158 0.00 0.00 0.00 3.66
67 68 0.321919 TACCGACGACTACCAGCACT 60.322 55.000 0.00 0.00 0.00 4.40
68 69 0.098376 CTACCGACGACTACCAGCAC 59.902 60.000 0.00 0.00 0.00 4.40
69 70 1.028330 CCTACCGACGACTACCAGCA 61.028 60.000 0.00 0.00 0.00 4.41
70 71 1.028868 ACCTACCGACGACTACCAGC 61.029 60.000 0.00 0.00 0.00 4.85
71 72 0.731417 CACCTACCGACGACTACCAG 59.269 60.000 0.00 0.00 0.00 4.00
72 73 0.677731 CCACCTACCGACGACTACCA 60.678 60.000 0.00 0.00 0.00 3.25
73 74 0.678048 ACCACCTACCGACGACTACC 60.678 60.000 0.00 0.00 0.00 3.18
74 75 0.729690 GACCACCTACCGACGACTAC 59.270 60.000 0.00 0.00 0.00 2.73
75 76 0.615331 AGACCACCTACCGACGACTA 59.385 55.000 0.00 0.00 0.00 2.59
76 77 0.615331 TAGACCACCTACCGACGACT 59.385 55.000 0.00 0.00 0.00 4.18
77 78 1.332997 CATAGACCACCTACCGACGAC 59.667 57.143 0.00 0.00 0.00 4.34
78 79 1.671979 CATAGACCACCTACCGACGA 58.328 55.000 0.00 0.00 0.00 4.20
79 80 0.666913 CCATAGACCACCTACCGACG 59.333 60.000 0.00 0.00 0.00 5.12
80 81 2.062971 TCCATAGACCACCTACCGAC 57.937 55.000 0.00 0.00 0.00 4.79
81 82 2.445905 AGATCCATAGACCACCTACCGA 59.554 50.000 0.00 0.00 0.00 4.69
82 83 2.558795 CAGATCCATAGACCACCTACCG 59.441 54.545 0.00 0.00 0.00 4.02
83 84 2.900546 CCAGATCCATAGACCACCTACC 59.099 54.545 0.00 0.00 0.00 3.18
84 85 3.845860 TCCAGATCCATAGACCACCTAC 58.154 50.000 0.00 0.00 0.00 3.18
85 86 4.140686 ACATCCAGATCCATAGACCACCTA 60.141 45.833 0.00 0.00 0.00 3.08
86 87 3.246301 CATCCAGATCCATAGACCACCT 58.754 50.000 0.00 0.00 0.00 4.00
87 88 2.975489 ACATCCAGATCCATAGACCACC 59.025 50.000 0.00 0.00 0.00 4.61
88 89 5.808366 TTACATCCAGATCCATAGACCAC 57.192 43.478 0.00 0.00 0.00 4.16
89 90 7.392766 AAATTACATCCAGATCCATAGACCA 57.607 36.000 0.00 0.00 0.00 4.02
90 91 8.697507 AAAAATTACATCCAGATCCATAGACC 57.302 34.615 0.00 0.00 0.00 3.85
115 116 9.037737 GCAGTACAACGAATACCAGAAATAATA 57.962 33.333 0.00 0.00 0.00 0.98
116 117 7.012044 GGCAGTACAACGAATACCAGAAATAAT 59.988 37.037 0.00 0.00 0.00 1.28
117 118 6.314400 GGCAGTACAACGAATACCAGAAATAA 59.686 38.462 0.00 0.00 0.00 1.40
118 119 5.813672 GGCAGTACAACGAATACCAGAAATA 59.186 40.000 0.00 0.00 0.00 1.40
119 120 4.634443 GGCAGTACAACGAATACCAGAAAT 59.366 41.667 0.00 0.00 0.00 2.17
120 121 3.998341 GGCAGTACAACGAATACCAGAAA 59.002 43.478 0.00 0.00 0.00 2.52
121 122 3.007074 TGGCAGTACAACGAATACCAGAA 59.993 43.478 0.00 0.00 0.00 3.02
122 123 2.563620 TGGCAGTACAACGAATACCAGA 59.436 45.455 0.00 0.00 0.00 3.86
123 124 2.967362 TGGCAGTACAACGAATACCAG 58.033 47.619 0.00 0.00 0.00 4.00
124 125 3.055747 TCATGGCAGTACAACGAATACCA 60.056 43.478 0.00 0.00 0.00 3.25
125 126 3.527533 TCATGGCAGTACAACGAATACC 58.472 45.455 0.00 0.00 0.00 2.73
126 127 5.293324 TCAATCATGGCAGTACAACGAATAC 59.707 40.000 0.00 0.00 0.00 1.89
127 128 5.423886 TCAATCATGGCAGTACAACGAATA 58.576 37.500 0.00 0.00 0.00 1.75
128 129 4.260985 TCAATCATGGCAGTACAACGAAT 58.739 39.130 0.00 0.00 0.00 3.34
129 130 3.669536 TCAATCATGGCAGTACAACGAA 58.330 40.909 0.00 0.00 0.00 3.85
130 131 3.326836 TCAATCATGGCAGTACAACGA 57.673 42.857 0.00 0.00 0.00 3.85
131 132 3.684305 TCTTCAATCATGGCAGTACAACG 59.316 43.478 0.00 0.00 0.00 4.10
132 133 5.355071 TCATCTTCAATCATGGCAGTACAAC 59.645 40.000 0.00 0.00 0.00 3.32
133 134 5.499313 TCATCTTCAATCATGGCAGTACAA 58.501 37.500 0.00 0.00 0.00 2.41
134 135 5.101648 TCATCTTCAATCATGGCAGTACA 57.898 39.130 0.00 0.00 0.00 2.90
135 136 6.630444 ATTCATCTTCAATCATGGCAGTAC 57.370 37.500 0.00 0.00 0.00 2.73
136 137 7.512130 ACTATTCATCTTCAATCATGGCAGTA 58.488 34.615 0.00 0.00 0.00 2.74
137 138 6.363065 ACTATTCATCTTCAATCATGGCAGT 58.637 36.000 0.00 0.00 0.00 4.40
138 139 6.347483 CGACTATTCATCTTCAATCATGGCAG 60.347 42.308 0.00 0.00 0.00 4.85
139 140 5.467735 CGACTATTCATCTTCAATCATGGCA 59.532 40.000 0.00 0.00 0.00 4.92
140 141 5.106791 CCGACTATTCATCTTCAATCATGGC 60.107 44.000 0.00 0.00 0.00 4.40
141 142 6.226052 TCCGACTATTCATCTTCAATCATGG 58.774 40.000 0.00 0.00 0.00 3.66
142 143 7.719778 TTCCGACTATTCATCTTCAATCATG 57.280 36.000 0.00 0.00 0.00 3.07
143 144 8.915057 ATTTCCGACTATTCATCTTCAATCAT 57.085 30.769 0.00 0.00 0.00 2.45
144 145 8.737168 AATTTCCGACTATTCATCTTCAATCA 57.263 30.769 0.00 0.00 0.00 2.57
147 148 9.231297 AGAAAATTTCCGACTATTCATCTTCAA 57.769 29.630 1.57 0.00 0.00 2.69
148 149 8.792830 AGAAAATTTCCGACTATTCATCTTCA 57.207 30.769 1.57 0.00 0.00 3.02
149 150 8.058915 CGAGAAAATTTCCGACTATTCATCTTC 58.941 37.037 1.57 0.00 0.00 2.87
150 151 7.466050 GCGAGAAAATTTCCGACTATTCATCTT 60.466 37.037 16.61 0.00 0.00 2.40
151 152 6.018669 GCGAGAAAATTTCCGACTATTCATCT 60.019 38.462 16.61 0.00 0.00 2.90
152 153 6.130058 GCGAGAAAATTTCCGACTATTCATC 58.870 40.000 16.61 0.00 0.00 2.92
153 154 5.584649 TGCGAGAAAATTTCCGACTATTCAT 59.415 36.000 16.61 0.00 0.00 2.57
154 155 4.932799 TGCGAGAAAATTTCCGACTATTCA 59.067 37.500 16.61 5.18 0.00 2.57
155 156 5.464965 TGCGAGAAAATTTCCGACTATTC 57.535 39.130 16.61 1.18 0.00 1.75
156 157 5.873179 TTGCGAGAAAATTTCCGACTATT 57.127 34.783 16.61 0.00 0.00 1.73
157 158 5.873179 TTTGCGAGAAAATTTCCGACTAT 57.127 34.783 16.61 0.00 0.00 2.12
158 159 5.676532 TTTTGCGAGAAAATTTCCGACTA 57.323 34.783 16.61 6.17 0.00 2.59
159 160 4.561735 TTTTGCGAGAAAATTTCCGACT 57.438 36.364 16.61 0.82 0.00 4.18
221 223 6.816140 TCAAAAGAAGGAAAAACACCATTGAC 59.184 34.615 0.00 0.00 0.00 3.18
252 254 4.639310 AGTATCTACACGGTTCAACTCGAT 59.361 41.667 5.55 0.00 0.00 3.59
255 257 5.924825 ACAAAGTATCTACACGGTTCAACTC 59.075 40.000 0.00 0.00 0.00 3.01
274 278 5.885230 TCATCAACTTATGCTCCACAAAG 57.115 39.130 0.00 0.00 0.00 2.77
277 281 3.684305 CGTTCATCAACTTATGCTCCACA 59.316 43.478 0.00 0.00 0.00 4.17
280 284 2.614057 CCCGTTCATCAACTTATGCTCC 59.386 50.000 0.00 0.00 0.00 4.70
321 325 3.627395 TTTTGACACTCCGATAGCCAT 57.373 42.857 0.00 0.00 0.00 4.40
363 367 5.605534 AGCTAGCACGATTATTTGACTGAT 58.394 37.500 18.83 0.00 0.00 2.90
364 368 5.011090 AGCTAGCACGATTATTTGACTGA 57.989 39.130 18.83 0.00 0.00 3.41
397 401 3.173540 TGGCTCATCCACATTTCGG 57.826 52.632 0.00 0.00 40.72 4.30
417 421 0.880278 CACCACTCCAACGACTGGTG 60.880 60.000 7.94 1.44 46.51 4.17
418 422 1.445942 CACCACTCCAACGACTGGT 59.554 57.895 7.94 0.00 46.51 4.00
461 467 3.000177 GGTGTGCAAAAACGTGAATGAAC 60.000 43.478 0.00 0.00 0.00 3.18
539 545 1.154197 GTGACAAGGGAAACTACCGC 58.846 55.000 0.00 0.00 0.00 5.68
541 547 2.152016 GCAGTGACAAGGGAAACTACC 58.848 52.381 0.00 0.00 0.00 3.18
542 548 2.152016 GGCAGTGACAAGGGAAACTAC 58.848 52.381 0.00 0.00 0.00 2.73
543 549 1.073284 GGGCAGTGACAAGGGAAACTA 59.927 52.381 0.00 0.00 0.00 2.24
544 550 0.178990 GGGCAGTGACAAGGGAAACT 60.179 55.000 0.00 0.00 0.00 2.66
545 551 0.178990 AGGGCAGTGACAAGGGAAAC 60.179 55.000 0.00 0.00 0.00 2.78
546 552 0.178992 CAGGGCAGTGACAAGGGAAA 60.179 55.000 0.00 0.00 0.00 3.13
547 553 1.059584 TCAGGGCAGTGACAAGGGAA 61.060 55.000 0.00 0.00 0.00 3.97
548 554 1.461268 TCAGGGCAGTGACAAGGGA 60.461 57.895 0.00 0.00 0.00 4.20
549 555 1.002868 CTCAGGGCAGTGACAAGGG 60.003 63.158 0.00 0.00 0.00 3.95
550 556 0.617413 ATCTCAGGGCAGTGACAAGG 59.383 55.000 0.00 0.00 0.00 3.61
551 557 1.277273 TCATCTCAGGGCAGTGACAAG 59.723 52.381 0.00 0.00 0.00 3.16
552 558 1.277273 CTCATCTCAGGGCAGTGACAA 59.723 52.381 0.00 0.00 0.00 3.18
553 559 0.900421 CTCATCTCAGGGCAGTGACA 59.100 55.000 0.00 0.00 0.00 3.58
554 560 1.134848 GTCTCATCTCAGGGCAGTGAC 60.135 57.143 0.00 0.00 0.00 3.67
555 561 1.189752 GTCTCATCTCAGGGCAGTGA 58.810 55.000 0.00 0.00 0.00 3.41
556 562 0.177604 GGTCTCATCTCAGGGCAGTG 59.822 60.000 0.00 0.00 0.00 3.66
557 563 1.326213 CGGTCTCATCTCAGGGCAGT 61.326 60.000 0.00 0.00 0.00 4.40
558 564 1.326213 ACGGTCTCATCTCAGGGCAG 61.326 60.000 0.00 0.00 0.00 4.85
559 565 1.305297 ACGGTCTCATCTCAGGGCA 60.305 57.895 0.00 0.00 0.00 5.36
560 566 1.323271 TGACGGTCTCATCTCAGGGC 61.323 60.000 9.88 0.00 0.00 5.19
561 567 0.457851 GTGACGGTCTCATCTCAGGG 59.542 60.000 9.88 0.00 0.00 4.45
562 568 1.177401 TGTGACGGTCTCATCTCAGG 58.823 55.000 9.88 0.00 0.00 3.86
563 569 2.807044 CATGTGACGGTCTCATCTCAG 58.193 52.381 19.62 7.92 29.13 3.35
564 570 1.134995 GCATGTGACGGTCTCATCTCA 60.135 52.381 19.62 6.11 29.13 3.27
565 571 1.135915 AGCATGTGACGGTCTCATCTC 59.864 52.381 19.62 14.85 29.13 2.75
566 572 1.189752 AGCATGTGACGGTCTCATCT 58.810 50.000 19.62 16.37 29.13 2.90
567 573 1.929836 GAAGCATGTGACGGTCTCATC 59.070 52.381 19.62 14.86 29.13 2.92
568 574 1.406069 GGAAGCATGTGACGGTCTCAT 60.406 52.381 17.41 17.41 31.48 2.90
569 575 0.037326 GGAAGCATGTGACGGTCTCA 60.037 55.000 14.46 14.46 0.00 3.27
724 802 3.429547 GCTGCAACTACAGAGCTAGCTAA 60.430 47.826 19.38 2.74 40.25 3.09
758 849 0.957888 GCTTGGTGTGCTTCCCTCTC 60.958 60.000 0.00 0.00 0.00 3.20
794 1178 1.087501 GTCGGATGCAAGGGAGTTTC 58.912 55.000 0.00 0.00 0.00 2.78
797 1181 1.903877 CTGGTCGGATGCAAGGGAGT 61.904 60.000 0.00 0.00 0.00 3.85
863 1249 8.143835 AGAAGAAGAAGAAGAAGAAGAAGACAG 58.856 37.037 0.00 0.00 0.00 3.51
995 1389 4.980339 AGCTACTAGGTAGGAGTAGGAC 57.020 50.000 10.87 0.00 44.42 3.85
1070 1482 0.032678 CGTCATCCCGGATCTCCTTG 59.967 60.000 0.73 0.00 0.00 3.61
1170 1585 1.812922 GGCTGCACGAGACATGGAG 60.813 63.158 0.50 0.00 38.46 3.86
1194 1609 0.850784 GGGGTACGGGTAGGTAGGTA 59.149 60.000 0.00 0.00 0.00 3.08
1195 1610 0.926220 AGGGGTACGGGTAGGTAGGT 60.926 60.000 0.00 0.00 0.00 3.08
1243 1690 1.153188 TTGGCGCATGATGGATCGT 60.153 52.632 10.83 0.00 0.00 3.73
1712 2216 9.268268 TGCATAATTTACGTTATTCCCTAGAAG 57.732 33.333 0.00 0.00 34.86 2.85
1730 2252 6.457392 CGTCACAGCAGACTTAATGCATAATT 60.457 38.462 0.00 0.00 46.31 1.40
1797 2482 8.773404 ATTAACACTAAACCAGTTACTGCTAG 57.227 34.615 6.88 9.29 34.26 3.42
1799 2484 9.379791 GATATTAACACTAAACCAGTTACTGCT 57.620 33.333 6.88 0.00 34.26 4.24
1800 2485 8.610035 GGATATTAACACTAAACCAGTTACTGC 58.390 37.037 6.88 0.00 34.26 4.40
1801 2486 9.661563 TGGATATTAACACTAAACCAGTTACTG 57.338 33.333 5.22 5.22 34.26 2.74
1812 2497 8.693120 AGAGTCGATCTGGATATTAACACTAA 57.307 34.615 0.00 0.00 36.69 2.24
1843 2538 6.765036 CAGCATATATAGCCCAAATGGAGTAG 59.235 42.308 0.00 0.00 37.39 2.57
1975 2733 0.885196 ACGCCAAATTACACCGCAAT 59.115 45.000 0.00 0.00 0.00 3.56
1991 2752 0.660005 TGCAACGATTTCAGCAACGC 60.660 50.000 0.00 0.00 33.48 4.84
1992 2753 1.321016 CTGCAACGATTTCAGCAACG 58.679 50.000 0.00 0.00 36.44 4.10
2032 2797 8.702163 AGAAACAATTTTTAACACCAGAACAG 57.298 30.769 0.00 0.00 0.00 3.16
2090 2861 2.820973 GCAGCCCAGCCTCTAGAG 59.179 66.667 13.18 13.18 0.00 2.43
2091 2862 3.150335 CGCAGCCCAGCCTCTAGA 61.150 66.667 0.00 0.00 0.00 2.43
2092 2863 3.465403 ACGCAGCCCAGCCTCTAG 61.465 66.667 0.00 0.00 0.00 2.43
2093 2864 3.774528 CACGCAGCCCAGCCTCTA 61.775 66.667 0.00 0.00 0.00 2.43
2278 4555 2.457598 AGGAGGATTGTTGCGTCTAGA 58.542 47.619 0.00 0.00 0.00 2.43
2324 4661 0.322187 TCGACTCGGTGATCTGACCA 60.322 55.000 0.00 0.00 35.50 4.02
2329 4666 5.515797 TCAAATATTCGACTCGGTGATCT 57.484 39.130 0.00 0.00 0.00 2.75
2352 4691 4.207891 AGATGGTTGCTTAACTCGTGAT 57.792 40.909 0.00 0.00 0.00 3.06
2411 4750 3.709653 ACTCCAGTAGTTTCAGGTGTTCA 59.290 43.478 0.00 0.00 33.35 3.18
2533 5518 5.524646 CGTACTAACTGGTTTTGAAGTTGGA 59.475 40.000 6.00 0.00 0.00 3.53
2574 5560 1.707989 TGGGGCTAAACTGAATGGTGA 59.292 47.619 0.00 0.00 0.00 4.02
2620 5618 6.839124 TTGACTAGTCAAAAATGATGCCAT 57.161 33.333 31.26 0.00 45.56 4.40
2646 5644 2.159000 TGCAACTGAGATGCGAGATCAT 60.159 45.455 10.13 0.00 46.76 2.45
2660 5658 9.424659 GAAAAATCAGTTATGTTTTTGCAACTG 57.575 29.630 0.00 0.98 45.89 3.16
2665 5663 7.172654 ACCGAAAAATCAGTTATGTTTTTGC 57.827 32.000 0.00 0.00 38.01 3.68
2666 5664 7.095816 GGGACCGAAAAATCAGTTATGTTTTTG 60.096 37.037 0.00 0.00 38.01 2.44
2669 5667 5.536916 TGGGACCGAAAAATCAGTTATGTTT 59.463 36.000 0.00 0.00 0.00 2.83
2670 5668 5.074115 TGGGACCGAAAAATCAGTTATGTT 58.926 37.500 0.00 0.00 0.00 2.71
2671 5669 4.658063 TGGGACCGAAAAATCAGTTATGT 58.342 39.130 0.00 0.00 0.00 2.29
2672 5670 5.835113 ATGGGACCGAAAAATCAGTTATG 57.165 39.130 0.00 0.00 0.00 1.90
2673 5671 7.060421 ACATATGGGACCGAAAAATCAGTTAT 58.940 34.615 7.80 0.00 0.00 1.89
2675 5673 5.261216 ACATATGGGACCGAAAAATCAGTT 58.739 37.500 7.80 0.00 0.00 3.16
2677 5675 4.881273 TGACATATGGGACCGAAAAATCAG 59.119 41.667 7.80 0.00 0.00 2.90
2678 5676 4.849518 TGACATATGGGACCGAAAAATCA 58.150 39.130 7.80 0.00 0.00 2.57
2679 5677 7.687941 ATATGACATATGGGACCGAAAAATC 57.312 36.000 7.17 0.00 0.00 2.17
2680 5678 9.753674 ATTATATGACATATGGGACCGAAAAAT 57.246 29.630 16.73 3.34 0.00 1.82
2686 5686 9.830975 TGATTTATTATATGACATATGGGACCG 57.169 33.333 16.73 0.00 0.00 4.79
2709 5709 4.488770 GGGTAGAGGAGGAAGAAGATGAT 58.511 47.826 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.