Multiple sequence alignment - TraesCS5D01G215100

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 TraesCS5D01G215100 chr5D 100.000 3170 0 0 1 3170 324475308 324478477 0.000000e+00 5854
1 TraesCS5D01G215100 chr5D 96.601 353 12 0 2606 2958 173388805 173388453 1.270000e-163 586
2 TraesCS5D01G215100 chr5D 94.648 355 19 0 2604 2958 11426397 11426751 4.620000e-153 551
3 TraesCS5D01G215100 chr5D 94.681 188 9 1 2983 3170 173388099 173387913 1.110000e-74 291
4 TraesCS5D01G215100 chr5B 92.314 1223 51 20 1416 2602 375948695 375949910 0.000000e+00 1698
5 TraesCS5D01G215100 chr5B 91.326 1199 61 16 208 1397 375947482 375948646 0.000000e+00 1598
6 TraesCS5D01G215100 chr5B 95.775 355 14 1 2604 2958 688081102 688081455 3.550000e-159 571
7 TraesCS5D01G215100 chr5A 95.017 903 31 7 1412 2308 422053061 422053955 0.000000e+00 1406
8 TraesCS5D01G215100 chr5A 93.473 858 36 6 557 1397 422052163 422053017 0.000000e+00 1256
9 TraesCS5D01G215100 chr5A 99.038 208 1 1 1 207 238855427 238855634 3.860000e-99 372
10 TraesCS5D01G215100 chr7D 97.838 555 12 0 2604 3158 402334300 402333746 0.000000e+00 959
11 TraesCS5D01G215100 chr7D 96.154 520 18 2 2651 3170 223845089 223845606 0.000000e+00 848
12 TraesCS5D01G215100 chr7D 96.056 355 13 1 2604 2958 156774028 156773675 7.620000e-161 577
13 TraesCS5D01G215100 chr7D 99.519 208 0 1 1 207 626644210 626644417 8.300000e-101 377
14 TraesCS5D01G215100 chr7B 96.610 354 12 0 2605 2958 680778837 680779190 3.520000e-164 588
15 TraesCS5D01G215100 chr1D 95.775 355 14 1 2604 2958 304333805 304333452 3.550000e-159 571
16 TraesCS5D01G215100 chr1D 99.519 208 0 1 1 207 493798427 493798634 8.300000e-101 377
17 TraesCS5D01G215100 chr3D 94.901 353 18 0 2606 2958 157759583 157759935 1.280000e-153 553
18 TraesCS5D01G215100 chr1B 99.519 208 0 1 1 207 339068767 339068560 8.300000e-101 377
19 TraesCS5D01G215100 chr4A 99.038 208 1 1 1 207 552131957 552132164 3.860000e-99 372
20 TraesCS5D01G215100 chr4A 81.221 213 30 5 726 930 494037294 494037504 2.530000e-36 163
21 TraesCS5D01G215100 chr2D 99.038 208 1 1 1 207 39711495 39711702 3.860000e-99 372
22 TraesCS5D01G215100 chr6D 98.558 208 2 1 1 207 159816852 159817059 1.800000e-97 366
23 TraesCS5D01G215100 chr6A 98.558 208 2 1 1 207 155840618 155840825 1.800000e-97 366
24 TraesCS5D01G215100 chr1A 98.558 208 2 1 1 207 334086854 334087061 1.800000e-97 366
25 TraesCS5D01G215100 chr7A 91.935 186 13 2 2979 3164 602472711 602472894 3.140000e-65 259
26 TraesCS5D01G215100 chr7A 85.204 196 14 4 2976 3170 239777858 239778039 1.500000e-43 187
27 TraesCS5D01G215100 chr7A 83.163 196 11 12 2975 3170 602471625 602471798 3.270000e-35 159
28 TraesCS5D01G215100 chr7A 92.727 110 8 0 3061 3170 602474757 602474866 3.270000e-35 159


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 TraesCS5D01G215100 chr5D 324475308 324478477 3169 False 5854.0 5854 100.000 1 3170 1 chr5D.!!$F2 3169
1 TraesCS5D01G215100 chr5D 173387913 173388805 892 True 438.5 586 95.641 2606 3170 2 chr5D.!!$R1 564
2 TraesCS5D01G215100 chr5B 375947482 375949910 2428 False 1648.0 1698 91.820 208 2602 2 chr5B.!!$F2 2394
3 TraesCS5D01G215100 chr5A 422052163 422053955 1792 False 1331.0 1406 94.245 557 2308 2 chr5A.!!$F2 1751
4 TraesCS5D01G215100 chr7D 402333746 402334300 554 True 959.0 959 97.838 2604 3158 1 chr7D.!!$R2 554
5 TraesCS5D01G215100 chr7D 223845089 223845606 517 False 848.0 848 96.154 2651 3170 1 chr7D.!!$F1 519

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
230 231 0.830444 TCAGTAGTGACGCTGGGGTT 60.830 55.0 9.54 0.0 33.81 4.11 F
1145 1174 0.037232 AGCAAGGTAAGGAGTGACGC 60.037 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1643 2.131183 CTCTCGCTTTATACCAGCAGC 58.869 52.381 4.39 0.0 37.07 5.25 R
2482 2583 0.682209 CTGATGTGGGGGAAAGCAGG 60.682 60.000 0.00 0.0 0.00 4.85 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
26 27 9.938280 AACTTGTATCTATGCAGTACTGTTTAA 57.062 29.630 23.44 8.24 0.00 1.52
29 30 9.884636 TTGTATCTATGCAGTACTGTTTAATGT 57.115 29.630 23.44 8.04 0.00 2.71
30 31 9.313118 TGTATCTATGCAGTACTGTTTAATGTG 57.687 33.333 23.44 10.11 0.00 3.21
31 32 7.792374 ATCTATGCAGTACTGTTTAATGTGG 57.208 36.000 23.44 5.32 0.00 4.17
32 33 6.941857 TCTATGCAGTACTGTTTAATGTGGA 58.058 36.000 23.44 7.29 0.00 4.02
33 34 7.390823 TCTATGCAGTACTGTTTAATGTGGAA 58.609 34.615 23.44 0.00 0.00 3.53
34 35 5.940192 TGCAGTACTGTTTAATGTGGAAG 57.060 39.130 23.44 0.00 0.00 3.46
35 36 5.616270 TGCAGTACTGTTTAATGTGGAAGA 58.384 37.500 23.44 0.00 0.00 2.87
36 37 6.058833 TGCAGTACTGTTTAATGTGGAAGAA 58.941 36.000 23.44 0.00 0.00 2.52
37 38 6.204688 TGCAGTACTGTTTAATGTGGAAGAAG 59.795 38.462 23.44 0.00 0.00 2.85
38 39 6.204882 GCAGTACTGTTTAATGTGGAAGAAGT 59.795 38.462 23.44 0.00 0.00 3.01
39 40 7.576236 CAGTACTGTTTAATGTGGAAGAAGTG 58.424 38.462 15.06 0.00 0.00 3.16
40 41 7.226720 CAGTACTGTTTAATGTGGAAGAAGTGT 59.773 37.037 15.06 0.00 0.00 3.55
41 42 7.773690 AGTACTGTTTAATGTGGAAGAAGTGTT 59.226 33.333 0.00 0.00 0.00 3.32
42 43 7.404671 ACTGTTTAATGTGGAAGAAGTGTTT 57.595 32.000 0.00 0.00 0.00 2.83
43 44 7.836842 ACTGTTTAATGTGGAAGAAGTGTTTT 58.163 30.769 0.00 0.00 0.00 2.43
44 45 8.311109 ACTGTTTAATGTGGAAGAAGTGTTTTT 58.689 29.630 0.00 0.00 0.00 1.94
45 46 8.472683 TGTTTAATGTGGAAGAAGTGTTTTTG 57.527 30.769 0.00 0.00 0.00 2.44
46 47 8.091449 TGTTTAATGTGGAAGAAGTGTTTTTGT 58.909 29.630 0.00 0.00 0.00 2.83
47 48 9.575783 GTTTAATGTGGAAGAAGTGTTTTTGTA 57.424 29.630 0.00 0.00 0.00 2.41
48 49 9.575783 TTTAATGTGGAAGAAGTGTTTTTGTAC 57.424 29.630 0.00 0.00 0.00 2.90
49 50 7.404671 AATGTGGAAGAAGTGTTTTTGTACT 57.595 32.000 0.00 0.00 0.00 2.73
50 51 8.514330 AATGTGGAAGAAGTGTTTTTGTACTA 57.486 30.769 0.00 0.00 0.00 1.82
51 52 7.925043 TGTGGAAGAAGTGTTTTTGTACTAA 57.075 32.000 0.00 0.00 0.00 2.24
52 53 7.754625 TGTGGAAGAAGTGTTTTTGTACTAAC 58.245 34.615 0.00 0.00 0.00 2.34
53 54 7.390996 TGTGGAAGAAGTGTTTTTGTACTAACA 59.609 33.333 0.00 0.00 32.21 2.41
54 55 8.238631 GTGGAAGAAGTGTTTTTGTACTAACAA 58.761 33.333 9.34 0.00 43.85 2.83
55 56 8.238631 TGGAAGAAGTGTTTTTGTACTAACAAC 58.761 33.333 9.34 8.38 45.18 3.32
56 57 8.238631 GGAAGAAGTGTTTTTGTACTAACAACA 58.761 33.333 9.34 10.20 45.18 3.33
57 58 9.783256 GAAGAAGTGTTTTTGTACTAACAACAT 57.217 29.630 15.00 6.24 45.18 2.71
68 69 9.562408 TTTGTACTAACAACATAGAAACCATGA 57.438 29.630 0.00 0.00 45.18 3.07
69 70 9.733556 TTGTACTAACAACATAGAAACCATGAT 57.266 29.630 0.00 0.00 40.69 2.45
72 73 8.732746 ACTAACAACATAGAAACCATGATACC 57.267 34.615 0.00 0.00 0.00 2.73
73 74 8.325787 ACTAACAACATAGAAACCATGATACCA 58.674 33.333 0.00 0.00 0.00 3.25
74 75 7.630242 AACAACATAGAAACCATGATACCAG 57.370 36.000 0.00 0.00 0.00 4.00
75 76 6.721318 ACAACATAGAAACCATGATACCAGT 58.279 36.000 0.00 0.00 0.00 4.00
76 77 6.599244 ACAACATAGAAACCATGATACCAGTG 59.401 38.462 0.00 0.00 0.00 3.66
77 78 5.126067 ACATAGAAACCATGATACCAGTGC 58.874 41.667 0.00 0.00 0.00 4.40
78 79 3.719268 AGAAACCATGATACCAGTGCA 57.281 42.857 0.00 0.00 0.00 4.57
79 80 4.240881 AGAAACCATGATACCAGTGCAT 57.759 40.909 0.00 0.00 0.00 3.96
80 81 5.372343 AGAAACCATGATACCAGTGCATA 57.628 39.130 0.00 0.00 0.00 3.14
81 82 5.754782 AGAAACCATGATACCAGTGCATAA 58.245 37.500 0.00 0.00 0.00 1.90
82 83 5.824624 AGAAACCATGATACCAGTGCATAAG 59.175 40.000 0.00 0.00 0.00 1.73
83 84 3.480470 ACCATGATACCAGTGCATAAGC 58.520 45.455 0.00 0.00 42.57 3.09
100 101 6.814343 GCATAAGCATGAAAAACTCACTTTG 58.186 36.000 0.00 0.00 41.58 2.77
101 102 6.421801 GCATAAGCATGAAAAACTCACTTTGT 59.578 34.615 0.00 0.00 41.58 2.83
102 103 7.568134 GCATAAGCATGAAAAACTCACTTTGTG 60.568 37.037 0.00 0.00 41.58 3.33
103 104 5.581126 AGCATGAAAAACTCACTTTGTGA 57.419 34.783 0.00 0.37 40.50 3.58
104 105 6.152932 AGCATGAAAAACTCACTTTGTGAT 57.847 33.333 0.00 0.00 41.94 3.06
105 106 6.211515 AGCATGAAAAACTCACTTTGTGATC 58.788 36.000 0.00 0.00 41.94 2.92
106 107 5.978919 GCATGAAAAACTCACTTTGTGATCA 59.021 36.000 0.00 0.00 41.94 2.92
107 108 6.143438 GCATGAAAAACTCACTTTGTGATCAG 59.857 38.462 0.00 0.00 41.94 2.90
108 109 7.420002 CATGAAAAACTCACTTTGTGATCAGA 58.580 34.615 0.00 0.00 41.94 3.27
109 110 7.572523 TGAAAAACTCACTTTGTGATCAGAT 57.427 32.000 0.00 0.00 41.94 2.90
110 111 7.999679 TGAAAAACTCACTTTGTGATCAGATT 58.000 30.769 0.00 0.00 41.94 2.40
111 112 7.916977 TGAAAAACTCACTTTGTGATCAGATTG 59.083 33.333 0.00 0.00 41.94 2.67
112 113 7.572523 AAAACTCACTTTGTGATCAGATTGA 57.427 32.000 0.00 0.00 41.94 2.57
113 114 7.756395 AAACTCACTTTGTGATCAGATTGAT 57.244 32.000 0.00 0.00 41.94 2.57
127 128 6.358974 TCAGATTGATCAAGGTTGTAGTCA 57.641 37.500 14.54 0.00 0.00 3.41
128 129 6.950842 TCAGATTGATCAAGGTTGTAGTCAT 58.049 36.000 14.54 0.00 0.00 3.06
129 130 7.397221 TCAGATTGATCAAGGTTGTAGTCATT 58.603 34.615 14.54 0.00 0.00 2.57
130 131 7.550551 TCAGATTGATCAAGGTTGTAGTCATTC 59.449 37.037 14.54 1.78 0.00 2.67
131 132 6.536582 AGATTGATCAAGGTTGTAGTCATTCG 59.463 38.462 14.54 0.00 0.00 3.34
132 133 5.400066 TGATCAAGGTTGTAGTCATTCGA 57.600 39.130 0.00 0.00 0.00 3.71
133 134 5.789521 TGATCAAGGTTGTAGTCATTCGAA 58.210 37.500 0.00 0.00 0.00 3.71
134 135 6.406370 TGATCAAGGTTGTAGTCATTCGAAT 58.594 36.000 4.39 4.39 0.00 3.34
135 136 6.878923 TGATCAAGGTTGTAGTCATTCGAATT 59.121 34.615 8.21 0.00 0.00 2.17
136 137 7.390440 TGATCAAGGTTGTAGTCATTCGAATTT 59.610 33.333 8.21 0.00 0.00 1.82
137 138 8.786826 ATCAAGGTTGTAGTCATTCGAATTTA 57.213 30.769 8.21 0.00 0.00 1.40
138 139 8.025243 TCAAGGTTGTAGTCATTCGAATTTAC 57.975 34.615 8.21 9.90 0.00 2.01
139 140 7.876068 TCAAGGTTGTAGTCATTCGAATTTACT 59.124 33.333 20.81 20.81 0.00 2.24
140 141 9.146984 CAAGGTTGTAGTCATTCGAATTTACTA 57.853 33.333 19.28 19.28 0.00 1.82
141 142 8.699283 AGGTTGTAGTCATTCGAATTTACTAC 57.301 34.615 31.30 31.30 41.74 2.73
142 143 8.529476 AGGTTGTAGTCATTCGAATTTACTACT 58.471 33.333 33.94 23.25 41.85 2.57
143 144 9.148104 GGTTGTAGTCATTCGAATTTACTACTT 57.852 33.333 33.94 16.62 41.85 2.24
145 146 8.610855 TGTAGTCATTCGAATTTACTACTTCG 57.389 34.615 33.94 15.58 41.85 3.79
146 147 8.239314 TGTAGTCATTCGAATTTACTACTTCGT 58.761 33.333 33.94 15.46 43.49 3.85
147 148 9.070149 GTAGTCATTCGAATTTACTACTTCGTT 57.930 33.333 31.01 12.62 43.49 3.85
149 150 9.630098 AGTCATTCGAATTTACTACTTCGTTAA 57.370 29.630 17.33 0.00 43.49 2.01
156 157 9.632969 CGAATTTACTACTTCGTTAAATGATGG 57.367 33.333 0.00 0.00 39.42 3.51
157 158 9.434559 GAATTTACTACTTCGTTAAATGATGGC 57.565 33.333 0.00 0.00 0.00 4.40
158 159 8.732746 ATTTACTACTTCGTTAAATGATGGCT 57.267 30.769 0.00 0.00 0.00 4.75
159 160 7.534085 TTACTACTTCGTTAAATGATGGCTG 57.466 36.000 0.00 0.00 0.00 4.85
160 161 5.488341 ACTACTTCGTTAAATGATGGCTGT 58.512 37.500 0.00 0.00 0.00 4.40
161 162 5.938125 ACTACTTCGTTAAATGATGGCTGTT 59.062 36.000 0.00 0.00 0.00 3.16
162 163 5.705609 ACTTCGTTAAATGATGGCTGTTT 57.294 34.783 0.00 0.00 0.00 2.83
163 164 6.811253 ACTTCGTTAAATGATGGCTGTTTA 57.189 33.333 0.00 0.00 0.00 2.01
164 165 7.209471 ACTTCGTTAAATGATGGCTGTTTAA 57.791 32.000 0.00 0.00 0.00 1.52
165 166 7.653647 ACTTCGTTAAATGATGGCTGTTTAAA 58.346 30.769 0.00 0.00 31.42 1.52
166 167 7.807907 ACTTCGTTAAATGATGGCTGTTTAAAG 59.192 33.333 0.00 0.00 31.42 1.85
167 168 6.616947 TCGTTAAATGATGGCTGTTTAAAGG 58.383 36.000 0.00 0.00 31.91 3.11
168 169 6.207810 TCGTTAAATGATGGCTGTTTAAAGGT 59.792 34.615 0.00 0.00 31.91 3.50
169 170 6.307800 CGTTAAATGATGGCTGTTTAAAGGTG 59.692 38.462 0.00 0.00 31.42 4.00
170 171 5.806654 AAATGATGGCTGTTTAAAGGTGT 57.193 34.783 0.00 0.00 0.00 4.16
171 172 5.391312 AATGATGGCTGTTTAAAGGTGTC 57.609 39.130 0.00 0.00 0.00 3.67
172 173 4.098914 TGATGGCTGTTTAAAGGTGTCT 57.901 40.909 0.00 0.00 0.00 3.41
173 174 5.235850 TGATGGCTGTTTAAAGGTGTCTA 57.764 39.130 0.00 0.00 0.00 2.59
174 175 5.001232 TGATGGCTGTTTAAAGGTGTCTAC 58.999 41.667 0.00 0.00 0.00 2.59
188 189 5.622770 GGTGTCTACCATAGTTTGTTTGG 57.377 43.478 0.00 0.00 46.71 3.28
189 190 5.310451 GGTGTCTACCATAGTTTGTTTGGA 58.690 41.667 0.00 0.00 46.71 3.53
190 191 5.180680 GGTGTCTACCATAGTTTGTTTGGAC 59.819 44.000 0.00 0.00 46.71 4.02
191 192 5.761234 GTGTCTACCATAGTTTGTTTGGACA 59.239 40.000 0.00 0.00 34.52 4.02
192 193 6.261381 GTGTCTACCATAGTTTGTTTGGACAA 59.739 38.462 0.00 0.00 43.73 3.18
193 194 7.001674 TGTCTACCATAGTTTGTTTGGACAAT 58.998 34.615 0.00 0.00 44.71 2.71
194 195 7.040755 TGTCTACCATAGTTTGTTTGGACAATG 60.041 37.037 0.00 0.00 44.71 2.82
195 196 7.001674 TCTACCATAGTTTGTTTGGACAATGT 58.998 34.615 0.00 0.00 44.71 2.71
196 197 6.084326 ACCATAGTTTGTTTGGACAATGTC 57.916 37.500 4.51 4.51 44.71 3.06
214 215 3.654273 TGTCCTTAGTAATCCCCCTCAG 58.346 50.000 0.00 0.00 0.00 3.35
221 222 3.644335 AGTAATCCCCCTCAGTAGTGAC 58.356 50.000 0.00 0.00 0.00 3.67
224 225 1.682684 CCCCCTCAGTAGTGACGCT 60.683 63.158 0.00 0.00 0.00 5.07
229 230 1.228769 TCAGTAGTGACGCTGGGGT 60.229 57.895 9.54 0.00 33.81 4.95
230 231 0.830444 TCAGTAGTGACGCTGGGGTT 60.830 55.000 9.54 0.00 33.81 4.11
242 243 1.760479 CTGGGGTTGTCCACGGTGTA 61.760 60.000 7.45 0.00 40.71 2.90
243 244 1.343431 TGGGGTTGTCCACGGTGTAA 61.343 55.000 7.45 0.00 40.71 2.41
260 261 2.426024 TGTAACCATGTAGAGCTCGGTC 59.574 50.000 8.37 3.55 0.00 4.79
278 279 1.089112 TCGTTGTCTAATCCGAGCGA 58.911 50.000 0.00 0.00 0.00 4.93
288 289 1.429463 ATCCGAGCGACACTCAAAAC 58.571 50.000 0.00 0.00 46.63 2.43
327 328 1.633945 CACCTACAAACCCTAGGCCTT 59.366 52.381 12.58 0.00 35.04 4.35
329 330 2.842496 ACCTACAAACCCTAGGCCTTAC 59.158 50.000 12.58 0.00 35.04 2.34
356 357 4.293648 TGACACCACGACCAGCCG 62.294 66.667 0.00 0.00 0.00 5.52
379 380 4.131088 GTCCCAGTCTCCGGCGAC 62.131 72.222 16.93 16.93 0.00 5.19
401 402 1.000396 GAGGTCCTGGCTTGGCATT 60.000 57.895 0.00 0.00 0.00 3.56
402 403 1.000396 AGGTCCTGGCTTGGCATTC 60.000 57.895 0.00 0.00 0.00 2.67
412 413 2.345880 CTTGGCATTCGCAGGGATGC 62.346 60.000 11.19 11.19 43.20 3.91
420 421 2.693762 CGCAGGGATGCCACAACTG 61.694 63.158 5.86 0.00 0.00 3.16
424 425 2.040544 GGGATGCCACAACTGGTCG 61.041 63.158 0.00 0.00 40.17 4.79
429 430 3.403057 CCACAACTGGTCGCGTCG 61.403 66.667 5.77 0.00 32.03 5.12
430 431 4.059459 CACAACTGGTCGCGTCGC 62.059 66.667 7.29 7.29 0.00 5.19
431 432 4.280494 ACAACTGGTCGCGTCGCT 62.280 61.111 16.36 0.00 0.00 4.93
441 442 4.742201 GCGTCGCTGCCCTTCTCA 62.742 66.667 10.68 0.00 0.00 3.27
442 443 2.507992 CGTCGCTGCCCTTCTCAG 60.508 66.667 0.00 0.00 34.79 3.35
447 448 3.396767 CTGCCCTTCTCAGCCTCA 58.603 61.111 0.00 0.00 0.00 3.86
455 456 2.421619 CTTCTCAGCCTCACCTTGTTC 58.578 52.381 0.00 0.00 0.00 3.18
488 489 4.643463 TGACTAAGGCAACGGAAAATGTA 58.357 39.130 0.00 0.00 46.39 2.29
489 490 4.693566 TGACTAAGGCAACGGAAAATGTAG 59.306 41.667 0.00 0.00 46.39 2.74
491 492 2.579410 AGGCAACGGAAAATGTAGGT 57.421 45.000 0.00 0.00 46.39 3.08
492 493 2.159382 AGGCAACGGAAAATGTAGGTG 58.841 47.619 0.00 0.00 46.39 4.00
493 494 1.883926 GGCAACGGAAAATGTAGGTGT 59.116 47.619 0.00 0.00 0.00 4.16
494 495 3.075884 GGCAACGGAAAATGTAGGTGTA 58.924 45.455 0.00 0.00 0.00 2.90
495 496 3.692593 GGCAACGGAAAATGTAGGTGTAT 59.307 43.478 0.00 0.00 0.00 2.29
496 497 4.438200 GGCAACGGAAAATGTAGGTGTATG 60.438 45.833 0.00 0.00 0.00 2.39
497 498 4.393680 GCAACGGAAAATGTAGGTGTATGA 59.606 41.667 0.00 0.00 0.00 2.15
511 513 8.661257 TGTAGGTGTATGATCAAATAACAAACG 58.339 33.333 0.00 0.00 0.00 3.60
676 678 0.982704 AAGTCCATGCAGCTGTCTCT 59.017 50.000 16.64 3.16 0.00 3.10
722 727 8.940952 GTTTCTACCAATCATATTAGAGCATCC 58.059 37.037 0.00 0.00 33.66 3.51
748 753 3.481028 CGTACCACGTGAATCATAAGACG 59.519 47.826 19.30 6.62 36.74 4.18
763 768 6.330278 TCATAAGACGCCCAAGATATTATCG 58.670 40.000 0.00 0.00 0.00 2.92
767 772 3.914312 ACGCCCAAGATATTATCGTCTG 58.086 45.455 0.00 0.00 0.00 3.51
930 952 5.788450 CACTAATCTTAGCCCTCCATGTAG 58.212 45.833 0.00 0.00 34.09 2.74
1090 1116 3.164977 GCTACTGCTCCCCCTCCC 61.165 72.222 0.00 0.00 36.03 4.30
1092 1118 4.103928 TACTGCTCCCCCTCCCCC 62.104 72.222 0.00 0.00 0.00 5.40
1145 1174 0.037232 AGCAAGGTAAGGAGTGACGC 60.037 55.000 0.00 0.00 0.00 5.19
1149 1178 1.218316 GGTAAGGAGTGACGCTGGG 59.782 63.158 0.00 0.00 0.00 4.45
1173 1202 0.940991 GAAACGGACGCTGTTACGGT 60.941 55.000 4.80 0.00 37.37 4.83
1344 1373 2.257371 CTCCTCGCCGTCGTCAAA 59.743 61.111 0.00 0.00 36.96 2.69
1379 1408 2.669229 TGAGTGACCGTACCGCGA 60.669 61.111 8.23 0.00 44.77 5.87
1390 1419 1.467883 CGTACCGCGATAACCAGTGAA 60.468 52.381 8.23 0.00 44.77 3.18
1402 1467 7.360946 GCGATAACCAGTGAAGTACATTTTCTT 60.361 37.037 0.00 0.00 0.00 2.52
1409 1474 6.697019 CAGTGAAGTACATTTTCTTTTGTGGG 59.303 38.462 0.00 0.00 0.00 4.61
1410 1475 6.605594 AGTGAAGTACATTTTCTTTTGTGGGA 59.394 34.615 0.00 0.00 0.00 4.37
1411 1476 6.918022 GTGAAGTACATTTTCTTTTGTGGGAG 59.082 38.462 0.00 0.00 0.00 4.30
1412 1477 6.605594 TGAAGTACATTTTCTTTTGTGGGAGT 59.394 34.615 0.00 0.00 0.00 3.85
1413 1478 6.391227 AGTACATTTTCTTTTGTGGGAGTG 57.609 37.500 0.00 0.00 0.00 3.51
1414 1479 4.670896 ACATTTTCTTTTGTGGGAGTGG 57.329 40.909 0.00 0.00 0.00 4.00
1417 1482 3.611025 TTTCTTTTGTGGGAGTGGGAT 57.389 42.857 0.00 0.00 0.00 3.85
1430 1495 5.841237 TGGGAGTGGGATTTTGTTGAAATTA 59.159 36.000 0.00 0.00 38.06 1.40
1535 1600 1.035932 ATGCCATGAGGAGCTTGTGC 61.036 55.000 0.00 0.00 36.89 4.57
1632 1710 2.605366 GCTAGTTCTAAAAGGCAGCGAG 59.395 50.000 0.00 0.00 0.00 5.03
1672 1750 4.454717 AATTTCGGCCGAACGCGC 62.455 61.111 38.87 0.00 38.94 6.86
1777 1858 0.798776 ACGAGAAAGCAATTCCGCAG 59.201 50.000 0.00 0.65 38.94 5.18
1837 1919 3.640029 GCCCATGATTGATTGATTGGTCT 59.360 43.478 0.00 0.00 0.00 3.85
1838 1920 4.828939 GCCCATGATTGATTGATTGGTCTA 59.171 41.667 0.00 0.00 0.00 2.59
2172 2257 0.532573 TCTGGCTCCTCGCTTAGTTG 59.467 55.000 0.00 0.00 39.13 3.16
2177 2262 2.413837 GCTCCTCGCTTAGTTGTTCAA 58.586 47.619 0.00 0.00 35.14 2.69
2304 2401 3.618774 GCATTGCTGCTAGCTGAAC 57.381 52.632 24.19 8.78 45.32 3.18
2328 2425 3.617284 TCGTATCTCTGTACTGCCTTGA 58.383 45.455 0.00 0.00 0.00 3.02
2482 2583 6.140303 ACATTTATGGATCAGTTCACATGC 57.860 37.500 0.00 0.00 0.00 4.06
2484 2585 4.508551 TTATGGATCAGTTCACATGCCT 57.491 40.909 0.00 0.00 0.00 4.75
2486 2587 0.737219 GGATCAGTTCACATGCCTGC 59.263 55.000 0.00 0.00 0.00 4.85
2489 2590 1.985473 TCAGTTCACATGCCTGCTTT 58.015 45.000 0.00 0.00 0.00 3.51
2500 2601 1.383799 CCTGCTTTCCCCCACATCA 59.616 57.895 0.00 0.00 0.00 3.07
2525 2626 2.741612 CAAATTTGCGGAGACTTTGCA 58.258 42.857 5.01 0.00 36.72 4.08
2526 2627 2.712057 AATTTGCGGAGACTTTGCAG 57.288 45.000 3.26 0.00 40.15 4.41
2545 2646 3.570540 CAGGAGTCTAGACATCATGGGA 58.429 50.000 24.44 0.00 0.00 4.37
2547 2648 4.039004 CAGGAGTCTAGACATCATGGGAAG 59.961 50.000 24.44 2.30 0.00 3.46
2595 2696 2.892852 CCACATGTTCTCACAACCCATT 59.107 45.455 0.00 0.00 36.16 3.16
2602 2703 4.081198 TGTTCTCACAACCCATTTGCTTTT 60.081 37.500 0.00 0.00 39.01 2.27
2722 2823 2.117779 TTTGGCAACGCAGCTGTGA 61.118 52.632 32.90 7.95 42.51 3.58
2738 2839 3.381045 CTGTGAAAACGACTGTGAGCTA 58.619 45.455 0.00 0.00 0.00 3.32
2776 2877 2.169352 GCCCTTAGAGCACTGAGATCAA 59.831 50.000 4.47 0.00 34.30 2.57
3105 3535 4.286910 CAAATTTCAAACGGACGTGTGAT 58.713 39.130 17.39 2.22 41.45 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.938280 TTAAACAGTACTGCATAGATACAAGTT 57.062 29.630 22.90 1.85 0.00 2.66
3 4 9.884636 ACATTAAACAGTACTGCATAGATACAA 57.115 29.630 22.90 4.81 0.00 2.41
6 7 8.700973 TCCACATTAAACAGTACTGCATAGATA 58.299 33.333 22.90 4.55 0.00 1.98
7 8 7.564793 TCCACATTAAACAGTACTGCATAGAT 58.435 34.615 22.90 7.98 0.00 1.98
8 9 6.941857 TCCACATTAAACAGTACTGCATAGA 58.058 36.000 22.90 5.94 0.00 1.98
9 10 7.549134 TCTTCCACATTAAACAGTACTGCATAG 59.451 37.037 22.90 10.39 0.00 2.23
10 11 7.390823 TCTTCCACATTAAACAGTACTGCATA 58.609 34.615 22.90 12.84 0.00 3.14
11 12 6.237901 TCTTCCACATTAAACAGTACTGCAT 58.762 36.000 22.90 13.85 0.00 3.96
12 13 5.616270 TCTTCCACATTAAACAGTACTGCA 58.384 37.500 22.90 5.56 0.00 4.41
13 14 6.204882 ACTTCTTCCACATTAAACAGTACTGC 59.795 38.462 22.90 0.00 0.00 4.40
14 15 7.226720 ACACTTCTTCCACATTAAACAGTACTG 59.773 37.037 21.44 21.44 0.00 2.74
15 16 7.280356 ACACTTCTTCCACATTAAACAGTACT 58.720 34.615 0.00 0.00 0.00 2.73
16 17 7.492352 ACACTTCTTCCACATTAAACAGTAC 57.508 36.000 0.00 0.00 0.00 2.73
17 18 8.514330 AAACACTTCTTCCACATTAAACAGTA 57.486 30.769 0.00 0.00 0.00 2.74
18 19 7.404671 AAACACTTCTTCCACATTAAACAGT 57.595 32.000 0.00 0.00 0.00 3.55
19 20 8.594687 CAAAAACACTTCTTCCACATTAAACAG 58.405 33.333 0.00 0.00 0.00 3.16
20 21 8.091449 ACAAAAACACTTCTTCCACATTAAACA 58.909 29.630 0.00 0.00 0.00 2.83
21 22 8.474006 ACAAAAACACTTCTTCCACATTAAAC 57.526 30.769 0.00 0.00 0.00 2.01
22 23 9.575783 GTACAAAAACACTTCTTCCACATTAAA 57.424 29.630 0.00 0.00 0.00 1.52
23 24 8.962679 AGTACAAAAACACTTCTTCCACATTAA 58.037 29.630 0.00 0.00 0.00 1.40
24 25 8.514330 AGTACAAAAACACTTCTTCCACATTA 57.486 30.769 0.00 0.00 0.00 1.90
25 26 7.404671 AGTACAAAAACACTTCTTCCACATT 57.595 32.000 0.00 0.00 0.00 2.71
26 27 8.403236 GTTAGTACAAAAACACTTCTTCCACAT 58.597 33.333 0.00 0.00 0.00 3.21
27 28 7.390996 TGTTAGTACAAAAACACTTCTTCCACA 59.609 33.333 0.00 0.00 30.88 4.17
28 29 7.754625 TGTTAGTACAAAAACACTTCTTCCAC 58.245 34.615 0.00 0.00 30.88 4.02
29 30 7.925043 TGTTAGTACAAAAACACTTCTTCCA 57.075 32.000 0.00 0.00 30.88 3.53
30 31 8.238631 TGTTGTTAGTACAAAAACACTTCTTCC 58.761 33.333 7.67 0.00 45.33 3.46
31 32 9.783256 ATGTTGTTAGTACAAAAACACTTCTTC 57.217 29.630 12.87 2.36 45.33 2.87
42 43 9.562408 TCATGGTTTCTATGTTGTTAGTACAAA 57.438 29.630 0.00 0.00 45.33 2.83
43 44 9.733556 ATCATGGTTTCTATGTTGTTAGTACAA 57.266 29.630 0.00 0.00 41.82 2.41
46 47 9.826574 GGTATCATGGTTTCTATGTTGTTAGTA 57.173 33.333 0.00 0.00 0.00 1.82
47 48 8.325787 TGGTATCATGGTTTCTATGTTGTTAGT 58.674 33.333 0.00 0.00 0.00 2.24
48 49 8.731275 TGGTATCATGGTTTCTATGTTGTTAG 57.269 34.615 0.00 0.00 0.00 2.34
49 50 8.325787 ACTGGTATCATGGTTTCTATGTTGTTA 58.674 33.333 0.00 0.00 0.00 2.41
50 51 7.121168 CACTGGTATCATGGTTTCTATGTTGTT 59.879 37.037 0.00 0.00 0.00 2.83
51 52 6.599244 CACTGGTATCATGGTTTCTATGTTGT 59.401 38.462 0.00 0.00 0.00 3.32
52 53 6.458751 GCACTGGTATCATGGTTTCTATGTTG 60.459 42.308 0.00 0.00 0.00 3.33
53 54 5.590259 GCACTGGTATCATGGTTTCTATGTT 59.410 40.000 0.00 0.00 0.00 2.71
54 55 5.126067 GCACTGGTATCATGGTTTCTATGT 58.874 41.667 0.00 0.00 0.00 2.29
55 56 5.125356 TGCACTGGTATCATGGTTTCTATG 58.875 41.667 0.00 0.00 0.00 2.23
56 57 5.372343 TGCACTGGTATCATGGTTTCTAT 57.628 39.130 0.00 0.00 0.00 1.98
57 58 4.835284 TGCACTGGTATCATGGTTTCTA 57.165 40.909 0.00 0.00 0.00 2.10
58 59 3.719268 TGCACTGGTATCATGGTTTCT 57.281 42.857 0.00 0.00 0.00 2.52
59 60 5.506317 GCTTATGCACTGGTATCATGGTTTC 60.506 44.000 0.00 0.00 39.41 2.78
60 61 4.339247 GCTTATGCACTGGTATCATGGTTT 59.661 41.667 0.00 0.00 39.41 3.27
61 62 3.885297 GCTTATGCACTGGTATCATGGTT 59.115 43.478 0.00 0.00 39.41 3.67
62 63 3.117926 TGCTTATGCACTGGTATCATGGT 60.118 43.478 0.00 0.00 45.31 3.55
63 64 3.479489 TGCTTATGCACTGGTATCATGG 58.521 45.455 0.00 0.00 45.31 3.66
76 77 6.421801 ACAAAGTGAGTTTTTCATGCTTATGC 59.578 34.615 0.00 0.00 38.29 3.14
77 78 7.648908 TCACAAAGTGAGTTTTTCATGCTTATG 59.351 33.333 0.00 0.00 37.67 1.90
78 79 7.715657 TCACAAAGTGAGTTTTTCATGCTTAT 58.284 30.769 0.00 0.00 37.67 1.73
79 80 7.094508 TCACAAAGTGAGTTTTTCATGCTTA 57.905 32.000 0.00 0.00 37.67 3.09
80 81 5.964758 TCACAAAGTGAGTTTTTCATGCTT 58.035 33.333 0.00 0.00 37.67 3.91
81 82 5.581126 TCACAAAGTGAGTTTTTCATGCT 57.419 34.783 0.00 0.00 37.67 3.79
82 83 5.978919 TGATCACAAAGTGAGTTTTTCATGC 59.021 36.000 6.01 0.00 46.04 4.06
83 84 7.420002 TCTGATCACAAAGTGAGTTTTTCATG 58.580 34.615 6.01 0.00 46.04 3.07
84 85 7.572523 TCTGATCACAAAGTGAGTTTTTCAT 57.427 32.000 6.01 0.00 46.04 2.57
85 86 7.572523 ATCTGATCACAAAGTGAGTTTTTCA 57.427 32.000 6.01 3.66 46.04 2.69
86 87 8.131100 TCAATCTGATCACAAAGTGAGTTTTTC 58.869 33.333 6.01 0.00 46.04 2.29
87 88 7.999679 TCAATCTGATCACAAAGTGAGTTTTT 58.000 30.769 6.01 0.00 46.04 1.94
88 89 7.572523 TCAATCTGATCACAAAGTGAGTTTT 57.427 32.000 6.01 0.00 46.04 2.43
89 90 7.756395 ATCAATCTGATCACAAAGTGAGTTT 57.244 32.000 6.01 0.00 46.04 2.66
103 104 6.950842 TGACTACAACCTTGATCAATCTGAT 58.049 36.000 8.96 0.00 40.34 2.90
104 105 6.358974 TGACTACAACCTTGATCAATCTGA 57.641 37.500 8.96 0.00 0.00 3.27
105 106 7.465111 CGAATGACTACAACCTTGATCAATCTG 60.465 40.741 8.96 9.01 0.00 2.90
106 107 6.536582 CGAATGACTACAACCTTGATCAATCT 59.463 38.462 8.96 0.00 0.00 2.40
107 108 6.535150 TCGAATGACTACAACCTTGATCAATC 59.465 38.462 8.96 1.55 0.00 2.67
108 109 6.406370 TCGAATGACTACAACCTTGATCAAT 58.594 36.000 8.96 0.00 0.00 2.57
109 110 5.789521 TCGAATGACTACAACCTTGATCAA 58.210 37.500 8.12 8.12 0.00 2.57
110 111 5.400066 TCGAATGACTACAACCTTGATCA 57.600 39.130 0.00 0.00 0.00 2.92
111 112 6.910536 ATTCGAATGACTACAACCTTGATC 57.089 37.500 10.50 0.00 0.00 2.92
112 113 7.687941 AAATTCGAATGACTACAACCTTGAT 57.312 32.000 12.25 0.00 0.00 2.57
113 114 7.876068 AGTAAATTCGAATGACTACAACCTTGA 59.124 33.333 19.35 0.00 0.00 3.02
114 115 8.029642 AGTAAATTCGAATGACTACAACCTTG 57.970 34.615 19.35 0.00 0.00 3.61
115 116 9.148104 GTAGTAAATTCGAATGACTACAACCTT 57.852 33.333 33.32 17.86 37.93 3.50
116 117 8.529476 AGTAGTAAATTCGAATGACTACAACCT 58.471 33.333 35.96 25.03 39.14 3.50
117 118 8.699283 AGTAGTAAATTCGAATGACTACAACC 57.301 34.615 35.96 23.54 39.14 3.77
131 132 9.434559 GCCATCATTTAACGAAGTAGTAAATTC 57.565 33.333 0.00 0.00 45.00 2.17
132 133 9.174166 AGCCATCATTTAACGAAGTAGTAAATT 57.826 29.630 0.00 0.00 45.00 1.82
133 134 8.612619 CAGCCATCATTTAACGAAGTAGTAAAT 58.387 33.333 0.00 0.00 45.00 1.40
134 135 7.604927 ACAGCCATCATTTAACGAAGTAGTAAA 59.395 33.333 0.00 0.00 45.00 2.01
135 136 7.101054 ACAGCCATCATTTAACGAAGTAGTAA 58.899 34.615 0.00 0.00 45.00 2.24
136 137 6.636705 ACAGCCATCATTTAACGAAGTAGTA 58.363 36.000 0.00 0.00 45.00 1.82
137 138 5.488341 ACAGCCATCATTTAACGAAGTAGT 58.512 37.500 0.00 0.00 45.00 2.73
138 139 6.422776 AACAGCCATCATTTAACGAAGTAG 57.577 37.500 0.00 0.00 45.00 2.57
139 140 6.811253 AAACAGCCATCATTTAACGAAGTA 57.189 33.333 0.00 0.00 45.00 2.24
141 142 7.273381 CCTTTAAACAGCCATCATTTAACGAAG 59.727 37.037 0.00 0.00 29.76 3.79
142 143 7.087639 CCTTTAAACAGCCATCATTTAACGAA 58.912 34.615 0.00 0.00 29.76 3.85
143 144 6.207810 ACCTTTAAACAGCCATCATTTAACGA 59.792 34.615 0.00 0.00 29.76 3.85
144 145 6.307800 CACCTTTAAACAGCCATCATTTAACG 59.692 38.462 0.00 0.00 29.76 3.18
145 146 7.151976 ACACCTTTAAACAGCCATCATTTAAC 58.848 34.615 0.00 0.00 29.76 2.01
146 147 7.232534 AGACACCTTTAAACAGCCATCATTTAA 59.767 33.333 0.00 0.00 0.00 1.52
147 148 6.719370 AGACACCTTTAAACAGCCATCATTTA 59.281 34.615 0.00 0.00 0.00 1.40
148 149 5.539955 AGACACCTTTAAACAGCCATCATTT 59.460 36.000 0.00 0.00 0.00 2.32
149 150 5.079643 AGACACCTTTAAACAGCCATCATT 58.920 37.500 0.00 0.00 0.00 2.57
150 151 4.666512 AGACACCTTTAAACAGCCATCAT 58.333 39.130 0.00 0.00 0.00 2.45
151 152 4.098914 AGACACCTTTAAACAGCCATCA 57.901 40.909 0.00 0.00 0.00 3.07
152 153 4.395231 GGTAGACACCTTTAAACAGCCATC 59.605 45.833 0.00 0.00 42.11 3.51
153 154 4.202524 TGGTAGACACCTTTAAACAGCCAT 60.203 41.667 0.00 0.00 45.98 4.40
154 155 3.136809 TGGTAGACACCTTTAAACAGCCA 59.863 43.478 0.00 0.00 45.98 4.75
155 156 3.746940 TGGTAGACACCTTTAAACAGCC 58.253 45.455 0.00 0.00 45.98 4.85
156 157 6.171213 ACTATGGTAGACACCTTTAAACAGC 58.829 40.000 0.00 0.00 45.98 4.40
157 158 8.504005 CAAACTATGGTAGACACCTTTAAACAG 58.496 37.037 0.00 0.00 45.98 3.16
158 159 7.994334 ACAAACTATGGTAGACACCTTTAAACA 59.006 33.333 0.00 0.00 45.98 2.83
159 160 8.387190 ACAAACTATGGTAGACACCTTTAAAC 57.613 34.615 0.00 0.00 45.98 2.01
160 161 8.983702 AACAAACTATGGTAGACACCTTTAAA 57.016 30.769 0.00 0.00 45.98 1.52
161 162 8.842280 CAAACAAACTATGGTAGACACCTTTAA 58.158 33.333 0.00 0.00 45.98 1.52
162 163 7.446013 CCAAACAAACTATGGTAGACACCTTTA 59.554 37.037 0.00 0.00 45.98 1.85
163 164 6.264518 CCAAACAAACTATGGTAGACACCTTT 59.735 38.462 0.00 0.00 45.98 3.11
164 165 5.768164 CCAAACAAACTATGGTAGACACCTT 59.232 40.000 0.00 0.00 45.98 3.50
165 166 5.072600 TCCAAACAAACTATGGTAGACACCT 59.927 40.000 0.00 0.00 45.98 4.00
166 167 5.180680 GTCCAAACAAACTATGGTAGACACC 59.819 44.000 0.00 0.00 46.00 4.16
167 168 5.761234 TGTCCAAACAAACTATGGTAGACAC 59.239 40.000 0.00 0.00 37.28 3.67
168 169 5.931294 TGTCCAAACAAACTATGGTAGACA 58.069 37.500 0.00 0.00 38.90 3.41
169 170 6.870971 TTGTCCAAACAAACTATGGTAGAC 57.129 37.500 0.00 0.00 42.34 2.59
188 189 4.412528 AGGGGGATTACTAAGGACATTGTC 59.587 45.833 8.34 8.34 0.00 3.18
189 190 4.380791 AGGGGGATTACTAAGGACATTGT 58.619 43.478 0.00 0.00 0.00 2.71
190 191 4.412199 TGAGGGGGATTACTAAGGACATTG 59.588 45.833 0.00 0.00 0.00 2.82
191 192 4.641868 TGAGGGGGATTACTAAGGACATT 58.358 43.478 0.00 0.00 0.00 2.71
192 193 4.235372 CTGAGGGGGATTACTAAGGACAT 58.765 47.826 0.00 0.00 0.00 3.06
193 194 3.013648 ACTGAGGGGGATTACTAAGGACA 59.986 47.826 0.00 0.00 0.00 4.02
194 195 3.655384 ACTGAGGGGGATTACTAAGGAC 58.345 50.000 0.00 0.00 0.00 3.85
195 196 4.485021 ACTACTGAGGGGGATTACTAAGGA 59.515 45.833 0.00 0.00 0.00 3.36
196 197 4.589374 CACTACTGAGGGGGATTACTAAGG 59.411 50.000 0.00 0.00 0.00 2.69
197 198 5.302313 GTCACTACTGAGGGGGATTACTAAG 59.698 48.000 0.00 0.00 0.00 2.18
198 199 5.206587 GTCACTACTGAGGGGGATTACTAA 58.793 45.833 0.00 0.00 0.00 2.24
199 200 4.688045 CGTCACTACTGAGGGGGATTACTA 60.688 50.000 0.00 0.00 0.00 1.82
200 201 3.644335 GTCACTACTGAGGGGGATTACT 58.356 50.000 0.00 0.00 0.00 2.24
201 202 2.361438 CGTCACTACTGAGGGGGATTAC 59.639 54.545 0.00 0.00 0.00 1.89
202 203 2.662866 CGTCACTACTGAGGGGGATTA 58.337 52.381 0.00 0.00 0.00 1.75
203 204 1.486211 CGTCACTACTGAGGGGGATT 58.514 55.000 0.00 0.00 0.00 3.01
204 205 1.043673 GCGTCACTACTGAGGGGGAT 61.044 60.000 0.00 0.00 33.59 3.85
205 206 1.681327 GCGTCACTACTGAGGGGGA 60.681 63.158 0.00 0.00 33.59 4.81
206 207 1.682684 AGCGTCACTACTGAGGGGG 60.683 63.158 0.00 0.00 33.59 5.40
214 215 0.669625 GACAACCCCAGCGTCACTAC 60.670 60.000 0.00 0.00 0.00 2.73
224 225 1.343431 TTACACCGTGGACAACCCCA 61.343 55.000 3.03 0.00 34.81 4.96
242 243 0.456221 CGACCGAGCTCTACATGGTT 59.544 55.000 12.85 0.00 31.86 3.67
243 244 0.680280 ACGACCGAGCTCTACATGGT 60.680 55.000 12.85 11.12 35.14 3.55
260 261 1.189403 GTCGCTCGGATTAGACAACG 58.811 55.000 3.74 0.00 34.09 4.10
278 279 3.008049 AGAGGCCTATTCGTTTTGAGTGT 59.992 43.478 4.42 0.00 0.00 3.55
288 289 1.218230 GCAAGCGAGAGGCCTATTCG 61.218 60.000 26.66 26.66 45.17 3.34
327 328 2.280552 GGTGTCAGCGACCCAGGTA 61.281 63.158 6.30 0.00 0.00 3.08
329 330 3.625897 TGGTGTCAGCGACCCAGG 61.626 66.667 11.68 0.00 32.25 4.45
337 338 3.044305 GCTGGTCGTGGTGTCAGC 61.044 66.667 0.00 0.00 44.34 4.26
338 339 2.357517 GGCTGGTCGTGGTGTCAG 60.358 66.667 0.00 0.00 0.00 3.51
356 357 0.531200 CCGGAGACTGGGACTAACAC 59.469 60.000 0.00 0.00 0.00 3.32
360 361 2.439701 CGCCGGAGACTGGGACTA 60.440 66.667 5.05 0.00 0.00 2.59
362 363 4.131088 GTCGCCGGAGACTGGGAC 62.131 72.222 28.62 9.57 46.74 4.46
379 380 2.046892 CAAGCCAGGACCTCACCG 60.047 66.667 0.00 0.00 34.73 4.94
380 381 2.352805 CCAAGCCAGGACCTCACC 59.647 66.667 0.00 0.00 0.00 4.02
381 382 2.360475 GCCAAGCCAGGACCTCAC 60.360 66.667 0.00 0.00 0.00 3.51
382 383 1.792757 AATGCCAAGCCAGGACCTCA 61.793 55.000 0.00 0.00 0.00 3.86
383 384 1.000396 AATGCCAAGCCAGGACCTC 60.000 57.895 0.00 0.00 0.00 3.85
384 385 1.000396 GAATGCCAAGCCAGGACCT 60.000 57.895 0.00 0.00 0.00 3.85
424 425 4.742201 TGAGAAGGGCAGCGACGC 62.742 66.667 13.03 13.03 0.00 5.19
430 431 1.078567 GTGAGGCTGAGAAGGGCAG 60.079 63.158 0.00 0.00 36.47 4.85
431 432 2.596851 GGTGAGGCTGAGAAGGGCA 61.597 63.158 0.00 0.00 0.00 5.36
433 434 0.035630 CAAGGTGAGGCTGAGAAGGG 60.036 60.000 0.00 0.00 0.00 3.95
434 435 0.689623 ACAAGGTGAGGCTGAGAAGG 59.310 55.000 0.00 0.00 0.00 3.46
435 436 2.038295 AGAACAAGGTGAGGCTGAGAAG 59.962 50.000 0.00 0.00 0.00 2.85
436 437 2.037772 GAGAACAAGGTGAGGCTGAGAA 59.962 50.000 0.00 0.00 0.00 2.87
437 438 1.620819 GAGAACAAGGTGAGGCTGAGA 59.379 52.381 0.00 0.00 0.00 3.27
438 439 1.338579 GGAGAACAAGGTGAGGCTGAG 60.339 57.143 0.00 0.00 0.00 3.35
439 440 0.687354 GGAGAACAAGGTGAGGCTGA 59.313 55.000 0.00 0.00 0.00 4.26
440 441 0.397941 TGGAGAACAAGGTGAGGCTG 59.602 55.000 0.00 0.00 0.00 4.85
441 442 0.398318 GTGGAGAACAAGGTGAGGCT 59.602 55.000 0.00 0.00 0.00 4.58
442 443 0.108585 TGTGGAGAACAAGGTGAGGC 59.891 55.000 0.00 0.00 35.24 4.70
443 444 2.867109 ATGTGGAGAACAAGGTGAGG 57.133 50.000 0.00 0.00 43.61 3.86
444 445 5.939883 TCAATTATGTGGAGAACAAGGTGAG 59.060 40.000 0.00 0.00 43.61 3.51
445 446 5.705441 GTCAATTATGTGGAGAACAAGGTGA 59.295 40.000 0.00 0.00 43.61 4.02
446 447 5.707298 AGTCAATTATGTGGAGAACAAGGTG 59.293 40.000 0.00 0.00 43.61 4.00
447 448 5.880901 AGTCAATTATGTGGAGAACAAGGT 58.119 37.500 0.00 0.00 43.61 3.50
455 456 5.220662 CGTTGCCTTAGTCAATTATGTGGAG 60.221 44.000 0.00 0.00 0.00 3.86
488 489 7.389330 TCACGTTTGTTATTTGATCATACACCT 59.611 33.333 0.00 0.00 0.00 4.00
489 490 7.523219 TCACGTTTGTTATTTGATCATACACC 58.477 34.615 0.00 0.00 0.00 4.16
619 621 9.762933 AGACACATTTGTATTTAAGCATTTTGT 57.237 25.926 0.00 0.00 35.47 2.83
627 629 9.831737 CTTCCAGAAGACACATTTGTATTTAAG 57.168 33.333 0.90 0.00 37.29 1.85
748 753 5.169295 GGTACAGACGATAATATCTTGGGC 58.831 45.833 0.00 0.00 0.00 5.36
876 898 4.589374 GGGGATGCTTATATATACGCCTCT 59.411 45.833 19.06 6.95 0.00 3.69
877 899 4.558898 CGGGGATGCTTATATATACGCCTC 60.559 50.000 16.22 15.21 0.00 4.70
878 900 3.321111 CGGGGATGCTTATATATACGCCT 59.679 47.826 16.22 8.38 0.00 5.52
879 901 3.069158 ACGGGGATGCTTATATATACGCC 59.931 47.826 16.22 9.94 0.00 5.68
930 952 4.762251 ACAAGGAAAAGCTGTGGAGTATTC 59.238 41.667 0.00 0.00 0.00 1.75
1145 1174 2.359975 GTCCGTTTCCTGCCCCAG 60.360 66.667 0.00 0.00 0.00 4.45
1149 1178 3.423154 CAGCGTCCGTTTCCTGCC 61.423 66.667 0.00 0.00 0.00 4.85
1379 1408 9.965824 CAAAAGAAAATGTACTTCACTGGTTAT 57.034 29.630 0.00 0.00 0.00 1.89
1390 1419 5.301805 CCACTCCCACAAAAGAAAATGTACT 59.698 40.000 0.00 0.00 0.00 2.73
1402 1467 3.039252 ACAAAATCCCACTCCCACAAA 57.961 42.857 0.00 0.00 0.00 2.83
1409 1474 6.921307 ACGTTAATTTCAACAAAATCCCACTC 59.079 34.615 0.00 0.00 36.54 3.51
1410 1475 6.811954 ACGTTAATTTCAACAAAATCCCACT 58.188 32.000 0.00 0.00 36.54 4.00
1411 1476 8.576936 TTACGTTAATTTCAACAAAATCCCAC 57.423 30.769 0.00 0.00 36.54 4.61
1412 1477 9.595823 TTTTACGTTAATTTCAACAAAATCCCA 57.404 25.926 0.00 0.00 36.54 4.37
1535 1600 3.057547 CTCTGGCCTGGTCGACTCG 62.058 68.421 16.46 6.59 0.00 4.18
1575 1643 2.131183 CTCTCGCTTTATACCAGCAGC 58.869 52.381 4.39 0.00 37.07 5.25
1581 1649 8.704234 CAGTTTGATATTCTCTCGCTTTATACC 58.296 37.037 0.00 0.00 0.00 2.73
1711 1789 8.606602 GCCAAAAGCAAATAAATTCATTCCTAG 58.393 33.333 0.00 0.00 42.97 3.02
1777 1858 8.372459 TGTTGATCCACTACCACCATATATTAC 58.628 37.037 0.00 0.00 0.00 1.89
1837 1919 8.716646 AACGTTGATTCTTGTGTCATCATATA 57.283 30.769 0.00 0.00 0.00 0.86
1838 1920 7.615582 AACGTTGATTCTTGTGTCATCATAT 57.384 32.000 0.00 0.00 0.00 1.78
2172 2257 3.487563 GGTTGAACCGATGGATTGAAC 57.512 47.619 0.00 0.00 0.00 3.18
2304 2401 5.470437 TCAAGGCAGTACAGAGATACGATAG 59.530 44.000 0.00 0.00 46.19 2.08
2382 2480 2.649816 AGGTAAAGTTTGGAGATGCCCT 59.350 45.455 0.00 0.00 34.97 5.19
2383 2481 3.017442 GAGGTAAAGTTTGGAGATGCCC 58.983 50.000 0.00 0.00 34.97 5.36
2482 2583 0.682209 CTGATGTGGGGGAAAGCAGG 60.682 60.000 0.00 0.00 0.00 4.85
2484 2585 0.776810 TTCTGATGTGGGGGAAAGCA 59.223 50.000 0.00 0.00 0.00 3.91
2486 2587 1.272092 TGCTTCTGATGTGGGGGAAAG 60.272 52.381 0.00 0.00 0.00 2.62
2489 2590 0.776810 TTTGCTTCTGATGTGGGGGA 59.223 50.000 0.00 0.00 0.00 4.81
2513 2614 3.129792 GACTCCTGCAAAGTCTCCG 57.870 57.895 17.55 0.00 40.03 4.63
2523 2624 2.036992 CCCATGATGTCTAGACTCCTGC 59.963 54.545 23.01 8.78 0.00 4.85
2525 2626 3.981516 TCCCATGATGTCTAGACTCCT 57.018 47.619 23.01 8.47 0.00 3.69
2526 2627 4.038642 GTCTTCCCATGATGTCTAGACTCC 59.961 50.000 23.01 14.64 0.00 3.85
2545 2646 2.231380 AGTGGGCCAATCGGGTCTT 61.231 57.895 8.40 0.00 42.62 3.01
2547 2648 2.438434 CAGTGGGCCAATCGGGTC 60.438 66.667 8.40 0.00 42.12 4.46
2595 2696 3.188048 CCAAACAAACACAGCAAAAGCAA 59.812 39.130 0.00 0.00 0.00 3.91
2602 2703 0.901124 AAGCCCAAACAAACACAGCA 59.099 45.000 0.00 0.00 0.00 4.41
2722 2823 3.728076 TCACTAGCTCACAGTCGTTTT 57.272 42.857 0.00 0.00 0.00 2.43
2738 2839 1.620323 GGGCATTTCAGGCTTTTCACT 59.380 47.619 0.00 0.00 0.00 3.41
3105 3535 1.378382 ACGCCTATGCATGCACCAA 60.378 52.632 25.37 10.83 37.32 3.67
3140 3570 1.420514 TCGTCAACCAAACCACCCATA 59.579 47.619 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.