Multiple sequence alignment - TraesCS2B01G225200

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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 TraesCS2B01G225200 chr2B 100.000 9258 0 0 1 9258 215197840 215207097 0.000000e+00 17097.0
1 TraesCS2B01G225200 chr2B 98.263 518 8 1 8742 9258 215242282 215241765 0.000000e+00 905.0
2 TraesCS2B01G225200 chr2B 94.402 518 29 0 8741 9258 583343219 583342702 0.000000e+00 797.0
3 TraesCS2B01G225200 chr2A 94.597 8607 216 91 268 8699 167946796 167955328 0.000000e+00 13088.0
4 TraesCS2B01G225200 chr2D 95.404 5461 120 39 3358 8741 157887923 157893329 0.000000e+00 8573.0
5 TraesCS2B01G225200 chr2D 94.072 3087 92 30 269 3314 157884890 157887926 0.000000e+00 4602.0
6 TraesCS2B01G225200 chr1A 86.613 493 50 12 8774 9254 551811176 551810688 1.770000e-146 531.0
7 TraesCS2B01G225200 chr1A 89.098 266 27 2 1 266 153336857 153337120 6.930000e-86 329.0
8 TraesCS2B01G225200 chr6B 93.214 280 19 0 8902 9181 601083113 601082834 6.690000e-111 412.0
9 TraesCS2B01G225200 chr6B 77.246 167 34 4 8741 8905 262721176 262721012 2.750000e-15 95.3
10 TraesCS2B01G225200 chr6B 96.970 33 1 0 237 269 80213737 80213705 1.000000e-03 56.5
11 TraesCS2B01G225200 chrUn 88.213 263 21 1 4 266 324122386 324122134 1.170000e-78 305.0
12 TraesCS2B01G225200 chrUn 88.213 263 21 1 4 266 353963457 353963205 1.170000e-78 305.0
13 TraesCS2B01G225200 chr7B 86.121 281 23 2 1 266 439011602 439011323 1.180000e-73 289.0
14 TraesCS2B01G225200 chr7B 83.146 178 24 4 8741 8916 34618463 34618290 3.460000e-34 158.0
15 TraesCS2B01G225200 chr5B 85.714 175 23 2 8740 8913 44023625 44023798 5.710000e-42 183.0
16 TraesCS2B01G225200 chr4D 79.245 212 36 6 8884 9089 35588420 35588211 3.490000e-29 141.0
17 TraesCS2B01G225200 chr1B 84.058 69 5 6 201 266 551835488 551835553 2.790000e-05 62.1
18 TraesCS2B01G225200 chr7A 100.000 30 0 0 237 266 719019559 719019530 1.000000e-03 56.5
19 TraesCS2B01G225200 chr7A 100.000 30 0 0 237 266 719295145 719295116 1.000000e-03 56.5


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 TraesCS2B01G225200 chr2B 215197840 215207097 9257 False 17097.0 17097 100.000 1 9258 1 chr2B.!!$F1 9257
1 TraesCS2B01G225200 chr2B 215241765 215242282 517 True 905.0 905 98.263 8742 9258 1 chr2B.!!$R1 516
2 TraesCS2B01G225200 chr2B 583342702 583343219 517 True 797.0 797 94.402 8741 9258 1 chr2B.!!$R2 517
3 TraesCS2B01G225200 chr2A 167946796 167955328 8532 False 13088.0 13088 94.597 268 8699 1 chr2A.!!$F1 8431
4 TraesCS2B01G225200 chr2D 157884890 157893329 8439 False 6587.5 8573 94.738 269 8741 2 chr2D.!!$F1 8472

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
129 130 0.108615 AGAACAGATGGGCTTCGTCG 60.109 55.000 0.00 0.00 36.53 5.12 F
131 132 0.108615 AACAGATGGGCTTCGTCGAG 60.109 55.000 0.00 0.00 36.53 4.04 F
708 743 0.318360 TGCGTGGAGTGTAACGAGTG 60.318 55.000 0.00 0.00 45.86 3.51 F
1854 1943 0.179089 TGCACCGCAAAACAAGCAAT 60.179 45.000 0.00 0.00 34.76 3.56 F
2389 2482 2.281484 GAACCACAAGCCGGAGCA 60.281 61.111 5.05 0.00 43.56 4.26 F
2844 2940 0.260230 AAGAGATCCAGAGCTCCGGA 59.740 55.000 20.94 20.94 44.40 5.14 F
3569 3678 0.537188 GAAAGATGGCGAGAGGACCA 59.463 55.000 0.00 0.00 41.06 4.02 F
5339 5466 0.176680 CCGACAGGATCCAGACAAGG 59.823 60.000 15.82 5.59 41.02 3.61 F
6474 6613 0.321122 GTGTCAGCTCCACCTTCAGG 60.321 60.000 2.23 0.00 42.17 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1283 1368 0.108963 CCGATCTCCCTCCTAGTCGT 59.891 60.000 0.00 0.0 0.00 4.34 R
1854 1943 0.387565 GCGGCAAGAAGGGTGAAAAA 59.612 50.000 0.00 0.0 0.00 1.94 R
2487 2580 4.265073 AGATTAAAATTGACGAGCTGCCT 58.735 39.130 0.00 0.0 0.00 4.75 R
2844 2940 0.248661 CGTCGATCTGATTCGCTGGT 60.249 55.000 0.00 0.0 38.97 4.00 R
4091 4201 0.251077 CAGCAGAAGTCCCTGGCTTT 60.251 55.000 0.00 0.0 34.82 3.51 R
4245 4355 3.124466 GTGCGATGTAACAATGTGTAGCA 59.876 43.478 0.00 0.0 0.00 3.49 R
5513 5640 1.000896 CAATTCGAACCCCCTGGCT 60.001 57.895 0.00 0.0 33.59 4.75 R
6601 6740 0.181350 GGGAGTGGCCAATCTTCGAT 59.819 55.000 30.44 0.0 38.95 3.59 R
8298 8519 0.108186 TGCCGAGTCATCACACATCC 60.108 55.000 0.00 0.0 0.00 3.51 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
17 18 3.394836 GGAAGGAGGCGAGCACCT 61.395 66.667 7.11 7.11 45.04 4.00
18 19 2.058595 GGAAGGAGGCGAGCACCTA 61.059 63.158 11.90 0.00 41.32 3.08
19 20 1.439644 GAAGGAGGCGAGCACCTAG 59.560 63.158 11.90 0.00 41.32 3.02
20 21 1.305381 AAGGAGGCGAGCACCTAGT 60.305 57.895 11.90 0.00 41.32 2.57
21 22 1.324005 AAGGAGGCGAGCACCTAGTC 61.324 60.000 11.90 0.00 41.32 2.59
22 23 2.787567 GGAGGCGAGCACCTAGTCC 61.788 68.421 0.00 0.00 41.32 3.85
23 24 2.037367 AGGCGAGCACCTAGTCCA 59.963 61.111 0.00 0.00 38.67 4.02
24 25 2.184579 GGCGAGCACCTAGTCCAC 59.815 66.667 0.00 0.00 0.00 4.02
25 26 2.202623 GCGAGCACCTAGTCCACG 60.203 66.667 0.00 0.00 0.00 4.94
26 27 2.697761 GCGAGCACCTAGTCCACGA 61.698 63.158 0.00 0.00 0.00 4.35
27 28 1.136984 CGAGCACCTAGTCCACGAC 59.863 63.158 0.00 0.00 0.00 4.34
28 29 1.136984 GAGCACCTAGTCCACGACG 59.863 63.158 0.00 0.00 37.67 5.12
29 30 2.181021 GCACCTAGTCCACGACGG 59.819 66.667 0.00 0.00 37.67 4.79
30 31 2.181021 CACCTAGTCCACGACGGC 59.819 66.667 0.00 0.00 37.67 5.68
31 32 2.282674 ACCTAGTCCACGACGGCA 60.283 61.111 0.00 0.00 37.67 5.69
32 33 2.181021 CCTAGTCCACGACGGCAC 59.819 66.667 0.00 0.00 37.67 5.01
33 34 2.181021 CTAGTCCACGACGGCACC 59.819 66.667 0.00 0.00 37.67 5.01
34 35 3.678717 CTAGTCCACGACGGCACCG 62.679 68.421 7.71 7.71 46.03 4.94
56 57 4.052229 CCTTGGGCGAGACGACGT 62.052 66.667 0.00 0.00 34.63 4.34
57 58 2.805353 CTTGGGCGAGACGACGTG 60.805 66.667 4.58 0.00 34.63 4.49
58 59 4.351938 TTGGGCGAGACGACGTGG 62.352 66.667 4.58 0.00 34.63 4.94
60 61 4.047059 GGGCGAGACGACGTGGAA 62.047 66.667 4.58 0.00 34.63 3.53
61 62 2.504244 GGCGAGACGACGTGGAAG 60.504 66.667 4.58 0.00 35.59 3.46
62 63 2.559840 GCGAGACGACGTGGAAGA 59.440 61.111 4.58 0.00 35.59 2.87
63 64 1.081641 GCGAGACGACGTGGAAGAA 60.082 57.895 4.58 0.00 35.59 2.52
64 65 1.066114 GCGAGACGACGTGGAAGAAG 61.066 60.000 4.58 0.00 35.59 2.85
65 66 1.066114 CGAGACGACGTGGAAGAAGC 61.066 60.000 4.58 0.00 0.00 3.86
66 67 0.241481 GAGACGACGTGGAAGAAGCT 59.759 55.000 4.58 0.00 0.00 3.74
67 68 0.241481 AGACGACGTGGAAGAAGCTC 59.759 55.000 4.58 0.00 0.00 4.09
68 69 0.241481 GACGACGTGGAAGAAGCTCT 59.759 55.000 4.58 0.00 0.00 4.09
69 70 0.241481 ACGACGTGGAAGAAGCTCTC 59.759 55.000 3.97 0.00 0.00 3.20
70 71 0.456995 CGACGTGGAAGAAGCTCTCC 60.457 60.000 0.00 0.00 0.00 3.71
71 72 0.456995 GACGTGGAAGAAGCTCTCCG 60.457 60.000 0.00 0.00 0.00 4.63
72 73 1.153745 CGTGGAAGAAGCTCTCCGG 60.154 63.158 0.00 0.00 0.00 5.14
73 74 1.595993 CGTGGAAGAAGCTCTCCGGA 61.596 60.000 2.93 2.93 0.00 5.14
74 75 0.174617 GTGGAAGAAGCTCTCCGGAG 59.825 60.000 26.32 26.32 42.18 4.63
94 95 4.592192 GCGAGCGCTATGGCTGGA 62.592 66.667 11.50 0.00 44.93 3.86
95 96 2.659897 CGAGCGCTATGGCTGGAC 60.660 66.667 11.50 0.00 44.93 4.02
96 97 2.659897 GAGCGCTATGGCTGGACG 60.660 66.667 11.50 0.00 44.93 4.79
97 98 4.227134 AGCGCTATGGCTGGACGG 62.227 66.667 8.99 0.00 42.86 4.79
99 100 3.536917 CGCTATGGCTGGACGGGA 61.537 66.667 0.00 0.00 36.09 5.14
100 101 2.109181 GCTATGGCTGGACGGGAC 59.891 66.667 0.00 0.00 35.22 4.46
117 118 4.402056 GGGACGAATGGATAAGAACAGA 57.598 45.455 0.00 0.00 0.00 3.41
118 119 4.962155 GGGACGAATGGATAAGAACAGAT 58.038 43.478 0.00 0.00 0.00 2.90
119 120 4.752101 GGGACGAATGGATAAGAACAGATG 59.248 45.833 0.00 0.00 0.00 2.90
120 121 4.752101 GGACGAATGGATAAGAACAGATGG 59.248 45.833 0.00 0.00 0.00 3.51
121 122 4.708177 ACGAATGGATAAGAACAGATGGG 58.292 43.478 0.00 0.00 0.00 4.00
122 123 3.499918 CGAATGGATAAGAACAGATGGGC 59.500 47.826 0.00 0.00 0.00 5.36
123 124 4.723309 GAATGGATAAGAACAGATGGGCT 58.277 43.478 0.00 0.00 0.00 5.19
124 125 4.803329 ATGGATAAGAACAGATGGGCTT 57.197 40.909 0.00 0.00 0.00 4.35
125 126 4.156455 TGGATAAGAACAGATGGGCTTC 57.844 45.455 0.00 0.00 0.00 3.86
126 127 3.134458 GGATAAGAACAGATGGGCTTCG 58.866 50.000 0.00 0.00 0.00 3.79
127 128 3.432326 GGATAAGAACAGATGGGCTTCGT 60.432 47.826 0.00 0.00 0.00 3.85
128 129 2.100605 AAGAACAGATGGGCTTCGTC 57.899 50.000 0.00 0.00 0.00 4.20
129 130 0.108615 AGAACAGATGGGCTTCGTCG 60.109 55.000 0.00 0.00 36.53 5.12
130 131 0.108804 GAACAGATGGGCTTCGTCGA 60.109 55.000 0.00 0.00 36.53 4.20
131 132 0.108615 AACAGATGGGCTTCGTCGAG 60.109 55.000 0.00 0.00 36.53 4.04
132 133 1.880340 CAGATGGGCTTCGTCGAGC 60.880 63.158 7.80 7.80 41.96 5.03
133 134 2.956964 GATGGGCTTCGTCGAGCG 60.957 66.667 0.00 0.00 43.62 5.03
134 135 4.514577 ATGGGCTTCGTCGAGCGG 62.515 66.667 0.00 0.00 43.62 5.52
149 150 4.501714 CGGCGTCGGATCGGGAAA 62.502 66.667 0.00 0.00 0.00 3.13
150 151 2.889018 GGCGTCGGATCGGGAAAC 60.889 66.667 0.00 0.00 0.00 2.78
169 170 4.091939 GCCCCGACCAGGTACCAC 62.092 72.222 15.94 1.58 38.74 4.16
170 171 3.396570 CCCCGACCAGGTACCACC 61.397 72.222 15.94 0.00 38.99 4.61
179 180 4.687464 GGTACCACCTGACCAACG 57.313 61.111 7.15 0.00 34.73 4.10
180 181 1.670083 GGTACCACCTGACCAACGC 60.670 63.158 7.15 0.00 34.73 4.84
181 182 2.025418 GTACCACCTGACCAACGCG 61.025 63.158 3.53 3.53 0.00 6.01
182 183 3.869473 TACCACCTGACCAACGCGC 62.869 63.158 5.73 0.00 0.00 6.86
200 201 4.477413 GGGACGATAGGAGCGAGA 57.523 61.111 0.00 0.00 43.77 4.04
201 202 2.949826 GGGACGATAGGAGCGAGAT 58.050 57.895 0.00 0.00 43.77 2.75
202 203 0.806241 GGGACGATAGGAGCGAGATC 59.194 60.000 0.00 0.00 43.77 2.75
203 204 0.444651 GGACGATAGGAGCGAGATCG 59.555 60.000 10.46 10.46 46.12 3.69
205 206 3.666784 CGATAGGAGCGAGATCGTG 57.333 57.895 3.94 0.00 42.22 4.35
206 207 0.453615 CGATAGGAGCGAGATCGTGC 60.454 60.000 3.94 4.27 42.22 5.34
207 208 0.453615 GATAGGAGCGAGATCGTGCG 60.454 60.000 3.94 4.31 42.22 5.34
208 209 1.857318 ATAGGAGCGAGATCGTGCGG 61.857 60.000 3.94 0.00 42.22 5.69
214 215 3.838271 GAGATCGTGCGGCCAGGA 61.838 66.667 2.24 0.00 39.85 3.86
215 216 3.781770 GAGATCGTGCGGCCAGGAG 62.782 68.421 2.24 0.00 39.02 3.69
235 236 4.838486 GGCCGCTCGACTCGTCTG 62.838 72.222 0.00 0.00 0.00 3.51
236 237 3.800863 GCCGCTCGACTCGTCTGA 61.801 66.667 0.00 0.00 0.00 3.27
237 238 2.868196 CCGCTCGACTCGTCTGAA 59.132 61.111 0.00 0.00 0.00 3.02
238 239 1.429825 CCGCTCGACTCGTCTGAAT 59.570 57.895 0.00 0.00 0.00 2.57
239 240 0.656259 CCGCTCGACTCGTCTGAATA 59.344 55.000 0.00 0.00 0.00 1.75
240 241 1.333347 CCGCTCGACTCGTCTGAATAG 60.333 57.143 0.00 0.00 0.00 1.73
241 242 1.328069 CGCTCGACTCGTCTGAATAGT 59.672 52.381 0.00 0.00 0.00 2.12
242 243 2.710760 GCTCGACTCGTCTGAATAGTG 58.289 52.381 0.00 0.00 0.00 2.74
243 244 2.710760 CTCGACTCGTCTGAATAGTGC 58.289 52.381 0.00 0.00 0.00 4.40
244 245 1.062148 TCGACTCGTCTGAATAGTGCG 59.938 52.381 0.00 0.00 0.00 5.34
245 246 1.192793 GACTCGTCTGAATAGTGCGC 58.807 55.000 0.00 0.00 0.00 6.09
246 247 0.523546 ACTCGTCTGAATAGTGCGCG 60.524 55.000 0.00 0.00 0.00 6.86
247 248 0.523546 CTCGTCTGAATAGTGCGCGT 60.524 55.000 8.43 0.00 0.00 6.01
248 249 0.796870 TCGTCTGAATAGTGCGCGTG 60.797 55.000 8.43 0.00 0.00 5.34
249 250 1.345176 GTCTGAATAGTGCGCGTGC 59.655 57.895 15.48 15.48 43.20 5.34
260 261 3.448076 GCGCGTGCACTTTTTAGAA 57.552 47.368 17.66 0.00 42.15 2.10
261 262 1.963747 GCGCGTGCACTTTTTAGAAT 58.036 45.000 17.66 0.00 42.15 2.40
262 263 2.315901 GCGCGTGCACTTTTTAGAATT 58.684 42.857 17.66 0.00 42.15 2.17
263 264 2.724174 GCGCGTGCACTTTTTAGAATTT 59.276 40.909 17.66 0.00 42.15 1.82
264 265 3.909574 GCGCGTGCACTTTTTAGAATTTA 59.090 39.130 17.66 0.00 42.15 1.40
265 266 4.029087 GCGCGTGCACTTTTTAGAATTTAG 59.971 41.667 17.66 0.00 42.15 1.85
266 267 4.029087 CGCGTGCACTTTTTAGAATTTAGC 59.971 41.667 16.19 4.43 0.00 3.09
322 324 6.739331 AATCCATTGAGAGTAGAAGTAGGG 57.261 41.667 0.00 0.00 0.00 3.53
369 375 4.747529 GGGCCCCACGTACGTCAC 62.748 72.222 19.94 4.39 0.00 3.67
408 414 0.739813 GCCCACGAGCAGAACGTTAT 60.740 55.000 0.00 0.00 42.07 1.89
431 437 9.965824 TTATGCGAAAGAGAAAAAGAAAAGAAT 57.034 25.926 0.00 0.00 0.00 2.40
434 440 8.076178 TGCGAAAGAGAAAAAGAAAAGAATAGG 58.924 33.333 0.00 0.00 0.00 2.57
457 482 1.072489 AGCGGATGAGACGGAGAGATA 59.928 52.381 0.00 0.00 0.00 1.98
505 532 2.268280 CACTGCCTGCCTGGAGAG 59.732 66.667 0.00 0.00 38.35 3.20
506 533 2.121385 ACTGCCTGCCTGGAGAGA 59.879 61.111 0.00 0.00 38.35 3.10
507 534 2.289532 ACTGCCTGCCTGGAGAGAC 61.290 63.158 0.00 0.00 38.35 3.36
509 536 1.537397 TGCCTGCCTGGAGAGACTT 60.537 57.895 0.00 0.00 38.35 3.01
510 537 1.130054 TGCCTGCCTGGAGAGACTTT 61.130 55.000 0.00 0.00 38.35 2.66
675 710 5.448632 CGTAGCGCCATTTCTTTATTCCTTT 60.449 40.000 2.29 0.00 0.00 3.11
676 711 6.238266 CGTAGCGCCATTTCTTTATTCCTTTA 60.238 38.462 2.29 0.00 0.00 1.85
701 736 8.101654 ACTTTATTTATTTTGCGTGGAGTGTA 57.898 30.769 0.00 0.00 0.00 2.90
703 738 8.730970 TTTATTTATTTTGCGTGGAGTGTAAC 57.269 30.769 0.00 0.00 0.00 2.50
705 740 1.937278 TTTTGCGTGGAGTGTAACGA 58.063 45.000 0.00 0.00 45.86 3.85
706 741 1.493772 TTTGCGTGGAGTGTAACGAG 58.506 50.000 0.00 0.00 45.86 4.18
707 742 0.386476 TTGCGTGGAGTGTAACGAGT 59.614 50.000 0.00 0.00 45.86 4.18
708 743 0.318360 TGCGTGGAGTGTAACGAGTG 60.318 55.000 0.00 0.00 45.86 3.51
709 744 0.318445 GCGTGGAGTGTAACGAGTGT 60.318 55.000 0.00 0.00 45.86 3.55
710 745 1.866880 GCGTGGAGTGTAACGAGTGTT 60.867 52.381 0.00 0.00 45.86 3.32
711 746 2.605338 GCGTGGAGTGTAACGAGTGTTA 60.605 50.000 0.00 0.00 45.86 2.41
712 747 3.631144 CGTGGAGTGTAACGAGTGTTAA 58.369 45.455 0.00 0.00 45.86 2.01
713 748 3.667261 CGTGGAGTGTAACGAGTGTTAAG 59.333 47.826 0.00 0.00 45.86 1.85
805 855 4.303993 CGTGGACGGTTCGGGGTT 62.304 66.667 0.00 0.00 35.37 4.11
1854 1943 0.179089 TGCACCGCAAAACAAGCAAT 60.179 45.000 0.00 0.00 34.76 3.56
2113 2202 3.357482 TCCATCTCCCCTCATGATTCT 57.643 47.619 0.00 0.00 0.00 2.40
2389 2482 2.281484 GAACCACAAGCCGGAGCA 60.281 61.111 5.05 0.00 43.56 4.26
2390 2483 2.281761 AACCACAAGCCGGAGCAG 60.282 61.111 5.05 0.00 43.56 4.24
2487 2580 3.722627 AGCCTCTCTCACCACTATAGGTA 59.277 47.826 4.43 0.00 40.77 3.08
2505 2598 3.055385 AGGTAGGCAGCTCGTCAATTTTA 60.055 43.478 0.00 0.00 0.00 1.52
2547 2640 4.078639 TGCTAATTTTGGTTTTGTGGGG 57.921 40.909 0.00 0.00 0.00 4.96
2844 2940 0.260230 AAGAGATCCAGAGCTCCGGA 59.740 55.000 20.94 20.94 44.40 5.14
3163 3272 6.272090 TCTCATGGTGGGTATATGCTTTCATA 59.728 38.462 0.00 0.00 39.31 2.15
3167 3276 6.609876 TGGTGGGTATATGCTTTCATATGTT 58.390 36.000 1.90 0.00 43.66 2.71
3456 3565 3.445096 CCAATTCTGTTGATTGACCTCCC 59.555 47.826 0.00 0.00 0.00 4.30
3461 3570 1.559682 TGTTGATTGACCTCCCTAGCC 59.440 52.381 0.00 0.00 0.00 3.93
3514 3623 5.858581 CGGTCCATTTCTTGTTCATCTTTTC 59.141 40.000 0.00 0.00 0.00 2.29
3530 3639 2.879103 TTTCCTCCGATTTCAGGCTT 57.121 45.000 0.00 0.00 0.00 4.35
3569 3678 0.537188 GAAAGATGGCGAGAGGACCA 59.463 55.000 0.00 0.00 41.06 4.02
3601 3710 2.035321 GGAGATCAATCTGGAGGACGAC 59.965 54.545 0.00 0.00 37.25 4.34
3649 3758 1.196354 CTTGCTCCAAAGAAGCTCACG 59.804 52.381 0.00 0.00 0.00 4.35
3723 3832 2.749044 CAGACAGCCGCCATTGCT 60.749 61.111 0.00 0.00 40.41 3.91
4013 4122 6.889722 CCCTGAAGGATTTGTGGTCTAAAATA 59.110 38.462 0.00 0.00 38.24 1.40
4091 4201 4.225942 GGGCTTCATCATCCTATGGACATA 59.774 45.833 0.00 0.00 32.98 2.29
4137 4247 2.221981 CAGGTTCGCTTTCTCACTTCAC 59.778 50.000 0.00 0.00 0.00 3.18
4404 4520 1.364721 CATTCAACATGGGCGTCGTA 58.635 50.000 0.00 0.00 0.00 3.43
4687 4803 9.935241 ATGCTATTCATTACTAGTATCTTGTGG 57.065 33.333 2.79 0.00 29.16 4.17
4688 4804 8.924303 TGCTATTCATTACTAGTATCTTGTGGT 58.076 33.333 2.79 0.00 0.00 4.16
4732 4850 2.052782 ATAATTTCCCGTGCACCCTC 57.947 50.000 12.15 0.00 0.00 4.30
5339 5466 0.176680 CCGACAGGATCCAGACAAGG 59.823 60.000 15.82 5.59 41.02 3.61
5513 5640 1.227823 CAGCCACCAACCAGTCGAA 60.228 57.895 0.00 0.00 0.00 3.71
6148 6284 2.561885 CAGCAGCAGCAGCAACTC 59.438 61.111 12.92 0.00 45.49 3.01
6162 6298 1.152902 AACTCCAGCAGCAGCAACA 60.153 52.632 3.17 0.00 45.49 3.33
6163 6299 1.170919 AACTCCAGCAGCAGCAACAG 61.171 55.000 3.17 0.00 45.49 3.16
6217 6356 2.255554 CAACAGCAGCAGCAGCAG 59.744 61.111 12.92 6.60 45.49 4.24
6474 6613 0.321122 GTGTCAGCTCCACCTTCAGG 60.321 60.000 2.23 0.00 42.17 3.86
6507 6646 0.599728 GCTGCATCCTCGCCTTCTAG 60.600 60.000 0.00 0.00 0.00 2.43
6586 6725 1.553690 CCACCCCGAATCACCAGTCT 61.554 60.000 0.00 0.00 0.00 3.24
6744 6883 1.076485 GCCCACCTGCATCTGGAAT 60.076 57.895 10.73 0.00 0.00 3.01
6814 6953 1.462670 GCAGCAAAGAACTCTCCTTCG 59.537 52.381 0.00 0.00 0.00 3.79
7222 7376 0.627451 AGGCCAATCTTCATCCAGCA 59.373 50.000 5.01 0.00 0.00 4.41
7245 7399 1.967066 TGGTGGTTTTATGCACCTTGG 59.033 47.619 0.00 0.00 38.46 3.61
7286 7440 0.827925 TGGTTCGCCTCACTCTCACT 60.828 55.000 0.00 0.00 38.36 3.41
7287 7441 0.109039 GGTTCGCCTCACTCTCACTC 60.109 60.000 0.00 0.00 0.00 3.51
7288 7442 0.885196 GTTCGCCTCACTCTCACTCT 59.115 55.000 0.00 0.00 0.00 3.24
7289 7443 1.135517 GTTCGCCTCACTCTCACTCTC 60.136 57.143 0.00 0.00 0.00 3.20
7290 7444 0.036875 TCGCCTCACTCTCACTCTCA 59.963 55.000 0.00 0.00 0.00 3.27
7291 7445 0.170116 CGCCTCACTCTCACTCTCAC 59.830 60.000 0.00 0.00 0.00 3.51
7522 7676 2.228343 GCATGGGAATGCTGCTAATCTC 59.772 50.000 0.00 0.00 43.79 2.75
7618 7772 2.608825 CGAGAGCCGGATCGTCGAT 61.609 63.158 26.65 7.63 34.30 3.59
7689 7844 3.566742 GTGGAGTAAAAATGTGGAACGGT 59.433 43.478 0.00 0.00 42.39 4.83
7707 7862 1.386533 GTTGGCTGATGGGAGTGATG 58.613 55.000 0.00 0.00 0.00 3.07
7761 7916 3.439857 AAGCTGGAGGTGCATAGAAAA 57.560 42.857 0.00 0.00 0.00 2.29
7816 7973 3.399440 AAGCTGGTCTCTCTGAACTTG 57.601 47.619 0.00 0.00 32.49 3.16
7818 7975 2.703007 AGCTGGTCTCTCTGAACTTGTT 59.297 45.455 0.00 0.00 32.49 2.83
7834 7991 1.383386 GTTCCCTCCCCTCTCCTCC 60.383 68.421 0.00 0.00 0.00 4.30
7835 7992 1.866997 TTCCCTCCCCTCTCCTCCA 60.867 63.158 0.00 0.00 0.00 3.86
7836 7993 1.460839 TTCCCTCCCCTCTCCTCCAA 61.461 60.000 0.00 0.00 0.00 3.53
7837 7994 1.690985 CCCTCCCCTCTCCTCCAAC 60.691 68.421 0.00 0.00 0.00 3.77
7838 7995 1.394151 CCTCCCCTCTCCTCCAACT 59.606 63.158 0.00 0.00 0.00 3.16
7843 8015 1.078567 CCTCTCCTCCAACTGCTGC 60.079 63.158 0.00 0.00 0.00 5.25
8009 8189 7.778470 TTTTTCCATGTGTTTTGTCAATACC 57.222 32.000 4.03 0.00 0.00 2.73
8096 8282 8.848182 AGTAGTAGTAGTAGTATGTTGGATTGC 58.152 37.037 0.00 0.00 0.00 3.56
8109 8298 6.214191 TGTTGGATTGCTTTAGAAACAACA 57.786 33.333 0.00 0.00 42.96 3.33
8110 8299 6.634805 TGTTGGATTGCTTTAGAAACAACAA 58.365 32.000 0.00 0.00 42.45 2.83
8111 8300 6.533367 TGTTGGATTGCTTTAGAAACAACAAC 59.467 34.615 0.00 0.00 42.45 3.32
8129 8318 2.203983 TGGGGCTGAGGCAGAGAA 60.204 61.111 8.68 0.00 40.87 2.87
8145 8334 5.278758 GGCAGAGAAGGCAGATAAGTAGTAG 60.279 48.000 0.00 0.00 0.00 2.57
8147 8336 6.514376 GCAGAGAAGGCAGATAAGTAGTAGTC 60.514 46.154 0.00 0.00 0.00 2.59
8155 8344 5.908499 GCAGATAAGTAGTAGTCGTAGTTGC 59.092 44.000 0.00 0.00 0.00 4.17
8197 8398 1.064906 AGAATGACCATGACCTGCCTG 60.065 52.381 0.00 0.00 0.00 4.85
8247 8464 6.950041 AGAAATGAATCAATCAAGAAGGTGGA 59.050 34.615 0.00 0.00 42.54 4.02
8248 8465 7.618512 AGAAATGAATCAATCAAGAAGGTGGAT 59.381 33.333 0.00 0.00 42.54 3.41
8249 8466 6.710597 ATGAATCAATCAAGAAGGTGGATG 57.289 37.500 0.00 0.00 42.54 3.51
8294 8515 6.151648 TGTTAAGATAGCAAAGCAGAGCAATT 59.848 34.615 0.00 0.00 0.00 2.32
8295 8516 4.897025 AGATAGCAAAGCAGAGCAATTC 57.103 40.909 0.00 0.00 0.00 2.17
8296 8517 4.525024 AGATAGCAAAGCAGAGCAATTCT 58.475 39.130 0.00 0.00 36.25 2.40
8461 8682 8.707796 ATCTTCTTCCTAATCGTACCAATCTA 57.292 34.615 0.00 0.00 0.00 1.98
8462 8683 8.707796 TCTTCTTCCTAATCGTACCAATCTAT 57.292 34.615 0.00 0.00 0.00 1.98
8463 8684 8.794553 TCTTCTTCCTAATCGTACCAATCTATC 58.205 37.037 0.00 0.00 0.00 2.08
8507 8735 0.033796 ATGACACTTGGGCTGGATGG 60.034 55.000 0.00 0.00 0.00 3.51
8524 8752 4.070716 GGATGGTGATGATCTCATTCACC 58.929 47.826 21.95 21.95 44.91 4.02
8526 8754 4.412796 TGGTGATGATCTCATTCACCTC 57.587 45.455 25.28 12.58 44.93 3.85
8527 8755 3.135348 TGGTGATGATCTCATTCACCTCC 59.865 47.826 25.28 12.83 44.93 4.30
8529 8757 4.125703 GTGATGATCTCATTCACCTCCAC 58.874 47.826 0.00 0.00 36.57 4.02
8531 8759 2.550175 TGATCTCATTCACCTCCACCA 58.450 47.619 0.00 0.00 0.00 4.17
8532 8760 2.912295 TGATCTCATTCACCTCCACCAA 59.088 45.455 0.00 0.00 0.00 3.67
8533 8761 3.330405 TGATCTCATTCACCTCCACCAAA 59.670 43.478 0.00 0.00 0.00 3.28
8541 8771 1.743252 CCTCCACCAAAGCTCTCGC 60.743 63.158 0.00 0.00 0.00 5.03
8544 8774 2.348998 CACCAAAGCTCTCGCCCT 59.651 61.111 0.00 0.00 36.60 5.19
8606 8836 7.890655 AGGCTGAAAAGTAAAGTATCTGGAAAT 59.109 33.333 0.00 0.00 0.00 2.17
8617 8847 5.482006 AGTATCTGGAAATTTTTGCCTTGC 58.518 37.500 0.00 0.00 0.00 4.01
8652 8882 1.178534 TTCCTTTCCCTTGGCGCAAG 61.179 55.000 10.83 11.08 40.75 4.01
8715 8945 1.666888 CGCATGGAGCTTTTTGTCCAC 60.667 52.381 0.00 0.00 45.72 4.02
8835 9065 1.595311 TCTTGCACCCATGACCCTAT 58.405 50.000 0.00 0.00 0.00 2.57
9167 9398 0.251165 TGGGCCACTTGCTAAAGGTC 60.251 55.000 0.00 0.00 40.92 3.85
9175 9406 4.280677 CCACTTGCTAAAGGTCAAAATGGA 59.719 41.667 0.00 0.00 37.76 3.41
9208 9439 8.387354 CAAGCGTGTGAATAACATACAGAATAA 58.613 33.333 0.00 0.00 41.97 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.022240 CTAGGTGCTCGCCTCCTTCC 62.022 65.000 5.10 0.00 39.94 3.46
1 2 1.324005 ACTAGGTGCTCGCCTCCTTC 61.324 60.000 5.10 0.00 39.94 3.46
2 3 1.305381 ACTAGGTGCTCGCCTCCTT 60.305 57.895 5.10 0.00 39.94 3.36
3 4 1.755008 GACTAGGTGCTCGCCTCCT 60.755 63.158 5.10 4.59 39.94 3.69
4 5 2.787567 GGACTAGGTGCTCGCCTCC 61.788 68.421 5.10 0.00 39.94 4.30
5 6 2.052690 TGGACTAGGTGCTCGCCTC 61.053 63.158 5.10 0.00 39.94 4.70
6 7 2.037367 TGGACTAGGTGCTCGCCT 59.963 61.111 7.21 7.21 42.43 5.52
7 8 2.184579 GTGGACTAGGTGCTCGCC 59.815 66.667 0.00 0.00 0.00 5.54
8 9 2.202623 CGTGGACTAGGTGCTCGC 60.203 66.667 0.00 0.00 34.72 5.03
9 10 1.136984 GTCGTGGACTAGGTGCTCG 59.863 63.158 7.17 7.17 40.89 5.03
10 11 1.136984 CGTCGTGGACTAGGTGCTC 59.863 63.158 0.00 0.00 0.00 4.26
11 12 2.341101 CCGTCGTGGACTAGGTGCT 61.341 63.158 0.00 0.00 42.00 4.40
12 13 2.181021 CCGTCGTGGACTAGGTGC 59.819 66.667 0.00 0.00 42.00 5.01
13 14 2.181021 GCCGTCGTGGACTAGGTG 59.819 66.667 0.00 0.00 42.00 4.00
14 15 2.282674 TGCCGTCGTGGACTAGGT 60.283 61.111 0.00 0.00 42.00 3.08
15 16 2.181021 GTGCCGTCGTGGACTAGG 59.819 66.667 0.00 0.00 42.00 3.02
16 17 2.181021 GGTGCCGTCGTGGACTAG 59.819 66.667 0.51 0.00 42.00 2.57
17 18 3.740397 CGGTGCCGTCGTGGACTA 61.740 66.667 1.93 0.00 42.00 2.59
39 40 4.052229 ACGTCGTCTCGCCCAAGG 62.052 66.667 0.00 0.00 0.00 3.61
40 41 2.805353 CACGTCGTCTCGCCCAAG 60.805 66.667 0.00 0.00 0.00 3.61
41 42 4.351938 CCACGTCGTCTCGCCCAA 62.352 66.667 0.00 0.00 0.00 4.12
43 44 3.966026 CTTCCACGTCGTCTCGCCC 62.966 68.421 0.00 0.00 0.00 6.13
44 45 2.467946 TTCTTCCACGTCGTCTCGCC 62.468 60.000 0.00 0.00 0.00 5.54
45 46 1.066114 CTTCTTCCACGTCGTCTCGC 61.066 60.000 0.00 0.00 0.00 5.03
46 47 1.066114 GCTTCTTCCACGTCGTCTCG 61.066 60.000 0.00 0.00 0.00 4.04
47 48 0.241481 AGCTTCTTCCACGTCGTCTC 59.759 55.000 0.00 0.00 0.00 3.36
48 49 0.241481 GAGCTTCTTCCACGTCGTCT 59.759 55.000 0.00 0.00 0.00 4.18
49 50 0.241481 AGAGCTTCTTCCACGTCGTC 59.759 55.000 0.00 0.00 0.00 4.20
50 51 0.241481 GAGAGCTTCTTCCACGTCGT 59.759 55.000 0.00 0.00 0.00 4.34
51 52 0.456995 GGAGAGCTTCTTCCACGTCG 60.457 60.000 7.71 0.00 0.00 5.12
52 53 0.456995 CGGAGAGCTTCTTCCACGTC 60.457 60.000 11.83 0.00 0.00 4.34
53 54 1.587054 CGGAGAGCTTCTTCCACGT 59.413 57.895 11.83 0.00 0.00 4.49
54 55 1.153745 CCGGAGAGCTTCTTCCACG 60.154 63.158 0.00 0.00 0.00 4.94
55 56 0.174617 CTCCGGAGAGCTTCTTCCAC 59.825 60.000 28.21 0.00 32.13 4.02
56 57 2.584673 CTCCGGAGAGCTTCTTCCA 58.415 57.895 28.21 0.00 32.13 3.53
77 78 4.592192 TCCAGCCATAGCGCTCGC 62.592 66.667 16.34 15.07 46.67 5.03
78 79 2.659897 GTCCAGCCATAGCGCTCG 60.660 66.667 16.34 6.46 46.67 5.03
79 80 2.659897 CGTCCAGCCATAGCGCTC 60.660 66.667 16.34 0.00 46.67 5.03
80 81 4.227134 CCGTCCAGCCATAGCGCT 62.227 66.667 17.26 17.26 46.67 5.92
82 83 3.536917 TCCCGTCCAGCCATAGCG 61.537 66.667 0.00 0.00 46.67 4.26
83 84 2.109181 GTCCCGTCCAGCCATAGC 59.891 66.667 0.00 0.00 40.32 2.97
84 85 1.672854 TTCGTCCCGTCCAGCCATAG 61.673 60.000 0.00 0.00 0.00 2.23
85 86 1.046472 ATTCGTCCCGTCCAGCCATA 61.046 55.000 0.00 0.00 0.00 2.74
86 87 2.367202 ATTCGTCCCGTCCAGCCAT 61.367 57.895 0.00 0.00 0.00 4.40
87 88 3.000819 ATTCGTCCCGTCCAGCCA 61.001 61.111 0.00 0.00 0.00 4.75
88 89 2.511600 CATTCGTCCCGTCCAGCC 60.512 66.667 0.00 0.00 0.00 4.85
89 90 2.311688 ATCCATTCGTCCCGTCCAGC 62.312 60.000 0.00 0.00 0.00 4.85
90 91 1.037493 TATCCATTCGTCCCGTCCAG 58.963 55.000 0.00 0.00 0.00 3.86
91 92 1.411246 CTTATCCATTCGTCCCGTCCA 59.589 52.381 0.00 0.00 0.00 4.02
92 93 1.684983 TCTTATCCATTCGTCCCGTCC 59.315 52.381 0.00 0.00 0.00 4.79
93 94 3.121544 GTTCTTATCCATTCGTCCCGTC 58.878 50.000 0.00 0.00 0.00 4.79
94 95 2.498481 TGTTCTTATCCATTCGTCCCGT 59.502 45.455 0.00 0.00 0.00 5.28
95 96 3.123804 CTGTTCTTATCCATTCGTCCCG 58.876 50.000 0.00 0.00 0.00 5.14
96 97 4.402056 TCTGTTCTTATCCATTCGTCCC 57.598 45.455 0.00 0.00 0.00 4.46
97 98 4.752101 CCATCTGTTCTTATCCATTCGTCC 59.248 45.833 0.00 0.00 0.00 4.79
98 99 4.752101 CCCATCTGTTCTTATCCATTCGTC 59.248 45.833 0.00 0.00 0.00 4.20
99 100 4.708177 CCCATCTGTTCTTATCCATTCGT 58.292 43.478 0.00 0.00 0.00 3.85
100 101 3.499918 GCCCATCTGTTCTTATCCATTCG 59.500 47.826 0.00 0.00 0.00 3.34
101 102 4.723309 AGCCCATCTGTTCTTATCCATTC 58.277 43.478 0.00 0.00 0.00 2.67
102 103 4.803329 AGCCCATCTGTTCTTATCCATT 57.197 40.909 0.00 0.00 0.00 3.16
103 104 4.723309 GAAGCCCATCTGTTCTTATCCAT 58.277 43.478 0.00 0.00 0.00 3.41
104 105 3.432186 CGAAGCCCATCTGTTCTTATCCA 60.432 47.826 0.00 0.00 0.00 3.41
105 106 3.134458 CGAAGCCCATCTGTTCTTATCC 58.866 50.000 0.00 0.00 0.00 2.59
106 107 3.798202 ACGAAGCCCATCTGTTCTTATC 58.202 45.455 0.00 0.00 0.00 1.75
107 108 3.738281 CGACGAAGCCCATCTGTTCTTAT 60.738 47.826 0.00 0.00 0.00 1.73
108 109 2.416836 CGACGAAGCCCATCTGTTCTTA 60.417 50.000 0.00 0.00 0.00 2.10
109 110 1.673033 CGACGAAGCCCATCTGTTCTT 60.673 52.381 0.00 0.00 0.00 2.52
110 111 0.108615 CGACGAAGCCCATCTGTTCT 60.109 55.000 0.00 0.00 0.00 3.01
111 112 0.108804 TCGACGAAGCCCATCTGTTC 60.109 55.000 0.00 0.00 0.00 3.18
112 113 0.108615 CTCGACGAAGCCCATCTGTT 60.109 55.000 0.00 0.00 0.00 3.16
113 114 1.513158 CTCGACGAAGCCCATCTGT 59.487 57.895 0.00 0.00 0.00 3.41
114 115 1.880340 GCTCGACGAAGCCCATCTG 60.880 63.158 0.00 0.00 36.22 2.90
115 116 2.496817 GCTCGACGAAGCCCATCT 59.503 61.111 0.00 0.00 36.22 2.90
132 133 4.501714 TTTCCCGATCCGACGCCG 62.502 66.667 0.00 0.00 0.00 6.46
133 134 2.889018 GTTTCCCGATCCGACGCC 60.889 66.667 0.00 0.00 0.00 5.68
134 135 2.889018 GGTTTCCCGATCCGACGC 60.889 66.667 0.00 0.00 0.00 5.19
152 153 4.091939 GTGGTACCTGGTCGGGGC 62.092 72.222 14.36 0.00 36.97 5.80
153 154 3.396570 GGTGGTACCTGGTCGGGG 61.397 72.222 14.36 0.00 34.73 5.73
162 163 1.670083 GCGTTGGTCAGGTGGTACC 60.670 63.158 4.43 4.43 38.99 3.34
163 164 2.025418 CGCGTTGGTCAGGTGGTAC 61.025 63.158 0.00 0.00 0.00 3.34
164 165 2.340809 CGCGTTGGTCAGGTGGTA 59.659 61.111 0.00 0.00 0.00 3.25
174 175 4.858433 TATCGTCCCGCGCGTTGG 62.858 66.667 29.95 23.42 41.07 3.77
175 176 3.320078 CTATCGTCCCGCGCGTTG 61.320 66.667 29.95 19.43 41.07 4.10
176 177 4.564116 CCTATCGTCCCGCGCGTT 62.564 66.667 29.95 8.35 41.07 4.84
178 179 4.685026 CTCCTATCGTCCCGCGCG 62.685 72.222 25.67 25.67 41.07 6.86
180 181 4.685026 CGCTCCTATCGTCCCGCG 62.685 72.222 0.00 0.00 43.01 6.46
181 182 3.256716 CTCGCTCCTATCGTCCCGC 62.257 68.421 0.00 0.00 0.00 6.13
182 183 0.956410 ATCTCGCTCCTATCGTCCCG 60.956 60.000 0.00 0.00 0.00 5.14
183 184 0.806241 GATCTCGCTCCTATCGTCCC 59.194 60.000 0.00 0.00 0.00 4.46
184 185 0.444651 CGATCTCGCTCCTATCGTCC 59.555 60.000 0.00 0.00 38.12 4.79
185 186 3.959520 CGATCTCGCTCCTATCGTC 57.040 57.895 0.00 0.00 38.12 4.20
187 188 0.453615 GCACGATCTCGCTCCTATCG 60.454 60.000 0.00 0.00 46.02 2.92
188 189 0.453615 CGCACGATCTCGCTCCTATC 60.454 60.000 0.00 0.00 44.43 2.08
189 190 1.576920 CGCACGATCTCGCTCCTAT 59.423 57.895 0.00 0.00 44.43 2.57
190 191 2.543802 CCGCACGATCTCGCTCCTA 61.544 63.158 0.00 0.00 44.43 2.94
191 192 3.893763 CCGCACGATCTCGCTCCT 61.894 66.667 0.00 0.00 44.43 3.69
197 198 3.781770 CTCCTGGCCGCACGATCTC 62.782 68.421 0.00 0.00 0.00 2.75
198 199 3.842923 CTCCTGGCCGCACGATCT 61.843 66.667 0.00 0.00 0.00 2.75
218 219 4.838486 CAGACGAGTCGAGCGGCC 62.838 72.222 21.50 0.00 37.53 6.13
219 220 2.600122 ATTCAGACGAGTCGAGCGGC 62.600 60.000 21.50 8.76 36.94 6.53
220 221 0.656259 TATTCAGACGAGTCGAGCGG 59.344 55.000 21.50 11.34 34.09 5.52
221 222 1.328069 ACTATTCAGACGAGTCGAGCG 59.672 52.381 21.50 6.52 34.09 5.03
222 223 2.710760 CACTATTCAGACGAGTCGAGC 58.289 52.381 21.50 10.74 34.09 5.03
223 224 2.710760 GCACTATTCAGACGAGTCGAG 58.289 52.381 21.50 6.57 34.09 4.04
224 225 1.062148 CGCACTATTCAGACGAGTCGA 59.938 52.381 21.50 0.00 34.09 4.20
225 226 1.457738 CGCACTATTCAGACGAGTCG 58.542 55.000 11.85 11.85 34.09 4.18
226 227 1.192793 GCGCACTATTCAGACGAGTC 58.807 55.000 0.30 0.00 0.00 3.36
227 228 0.523546 CGCGCACTATTCAGACGAGT 60.524 55.000 8.75 0.00 0.00 4.18
228 229 0.523546 ACGCGCACTATTCAGACGAG 60.524 55.000 5.73 0.00 33.54 4.18
229 230 0.796870 CACGCGCACTATTCAGACGA 60.797 55.000 5.73 0.00 0.00 4.20
230 231 1.625870 CACGCGCACTATTCAGACG 59.374 57.895 5.73 0.00 0.00 4.18
231 232 1.345176 GCACGCGCACTATTCAGAC 59.655 57.895 5.73 0.00 38.36 3.51
232 233 1.080161 TGCACGCGCACTATTCAGA 60.080 52.632 5.73 0.00 45.36 3.27
233 234 3.473669 TGCACGCGCACTATTCAG 58.526 55.556 5.73 0.00 45.36 3.02
242 243 1.963747 ATTCTAAAAAGTGCACGCGC 58.036 45.000 12.01 0.00 39.24 6.86
243 244 4.029087 GCTAAATTCTAAAAAGTGCACGCG 59.971 41.667 12.01 3.53 0.00 6.01
244 245 5.154222 AGCTAAATTCTAAAAAGTGCACGC 58.846 37.500 12.01 3.27 0.00 5.34
245 246 8.722342 TTAAGCTAAATTCTAAAAAGTGCACG 57.278 30.769 12.01 0.00 0.00 5.34
255 256 9.444600 CACCCACTAGTTTAAGCTAAATTCTAA 57.555 33.333 0.00 0.00 0.00 2.10
256 257 8.599792 ACACCCACTAGTTTAAGCTAAATTCTA 58.400 33.333 0.00 0.00 0.00 2.10
257 258 7.459234 ACACCCACTAGTTTAAGCTAAATTCT 58.541 34.615 0.00 0.00 0.00 2.40
258 259 7.683437 ACACCCACTAGTTTAAGCTAAATTC 57.317 36.000 0.00 0.00 0.00 2.17
259 260 8.473358 AAACACCCACTAGTTTAAGCTAAATT 57.527 30.769 0.00 0.00 36.28 1.82
260 261 8.473358 AAAACACCCACTAGTTTAAGCTAAAT 57.527 30.769 0.00 0.00 36.98 1.40
261 262 7.885009 AAAACACCCACTAGTTTAAGCTAAA 57.115 32.000 0.00 0.00 36.98 1.85
262 263 7.885009 AAAAACACCCACTAGTTTAAGCTAA 57.115 32.000 0.00 0.00 36.98 3.09
263 264 8.977267 TTAAAAACACCCACTAGTTTAAGCTA 57.023 30.769 0.00 0.00 36.98 3.32
264 265 7.013942 CCTTAAAAACACCCACTAGTTTAAGCT 59.986 37.037 11.45 0.00 37.28 3.74
265 266 7.013559 TCCTTAAAAACACCCACTAGTTTAAGC 59.986 37.037 11.45 0.00 37.28 3.09
266 267 8.454570 TCCTTAAAAACACCCACTAGTTTAAG 57.545 34.615 10.49 10.49 36.98 1.85
302 303 3.706594 TGCCCTACTTCTACTCTCAATGG 59.293 47.826 0.00 0.00 0.00 3.16
322 324 0.602905 AACCTTCACCGCACTACTGC 60.603 55.000 0.00 0.00 40.38 4.40
386 392 2.343758 GTTCTGCTCGTGGGCTCA 59.656 61.111 0.00 0.00 0.00 4.26
408 414 8.076178 CCTATTCTTTTCTTTTTCTCTTTCGCA 58.924 33.333 0.00 0.00 0.00 5.10
431 437 0.744874 CCGTCTCATCCGCTTTCCTA 59.255 55.000 0.00 0.00 0.00 2.94
434 440 0.456221 TCTCCGTCTCATCCGCTTTC 59.544 55.000 0.00 0.00 0.00 2.62
505 532 1.605753 AAAAGGGCACGAGGAAAGTC 58.394 50.000 0.00 0.00 0.00 3.01
506 533 2.882761 GTTAAAAGGGCACGAGGAAAGT 59.117 45.455 0.00 0.00 0.00 2.66
507 534 2.228103 GGTTAAAAGGGCACGAGGAAAG 59.772 50.000 0.00 0.00 0.00 2.62
509 536 1.546099 GGGTTAAAAGGGCACGAGGAA 60.546 52.381 0.00 0.00 0.00 3.36
510 537 0.037160 GGGTTAAAAGGGCACGAGGA 59.963 55.000 0.00 0.00 0.00 3.71
675 710 8.101654 ACACTCCACGCAAAATAAATAAAGTA 57.898 30.769 0.00 0.00 0.00 2.24
676 711 6.977213 ACACTCCACGCAAAATAAATAAAGT 58.023 32.000 0.00 0.00 0.00 2.66
701 736 8.416329 TCCTCTAGTAAAAACTTAACACTCGTT 58.584 33.333 0.00 0.00 39.24 3.85
703 738 8.983307 ATCCTCTAGTAAAAACTTAACACTCG 57.017 34.615 0.00 0.00 0.00 4.18
738 773 3.501385 CCCATTTGTTCCCTTCCCTAACA 60.501 47.826 0.00 0.00 0.00 2.41
742 777 0.252239 GCCCATTTGTTCCCTTCCCT 60.252 55.000 0.00 0.00 0.00 4.20
1283 1368 0.108963 CCGATCTCCCTCCTAGTCGT 59.891 60.000 0.00 0.00 0.00 4.34
1854 1943 0.387565 GCGGCAAGAAGGGTGAAAAA 59.612 50.000 0.00 0.00 0.00 1.94
2113 2202 5.497474 GAAATCAGTAAGGGCAGGAGTTAA 58.503 41.667 0.00 0.00 0.00 2.01
2487 2580 4.265073 AGATTAAAATTGACGAGCTGCCT 58.735 39.130 0.00 0.00 0.00 4.75
2547 2640 7.674471 AAAGCAGTGAGGAAGTTTATTAGAC 57.326 36.000 0.00 0.00 0.00 2.59
2714 2807 4.295119 ACAGCCGACACCGACACC 62.295 66.667 0.00 0.00 38.22 4.16
2715 2808 3.036084 CACAGCCGACACCGACAC 61.036 66.667 0.00 0.00 38.22 3.67
2716 2809 4.293648 CCACAGCCGACACCGACA 62.294 66.667 0.00 0.00 38.22 4.35
2844 2940 0.248661 CGTCGATCTGATTCGCTGGT 60.249 55.000 0.00 0.00 38.97 4.00
2892 3000 2.743928 GTCGGGCTTGACTGCTGG 60.744 66.667 0.00 0.00 35.95 4.85
3163 3272 4.734398 ATTCAACCACACACACAAACAT 57.266 36.364 0.00 0.00 0.00 2.71
3167 3276 2.828520 ACCAATTCAACCACACACACAA 59.171 40.909 0.00 0.00 0.00 3.33
3456 3565 1.890979 CCAATGCTCCAGCGGCTAG 60.891 63.158 0.26 0.00 45.83 3.42
3461 3570 0.813184 AAACATCCAATGCTCCAGCG 59.187 50.000 0.00 0.00 45.83 5.18
3514 3623 2.012673 CTCAAAGCCTGAAATCGGAGG 58.987 52.381 0.00 0.00 32.17 4.30
3530 3639 8.752005 TCTTTCTTTTCAGAATTTCCTCTCAA 57.248 30.769 0.00 0.00 38.89 3.02
3569 3678 5.320636 AGATTGATCTCCAGGCCTCTCCT 62.321 52.174 0.00 0.00 38.08 3.69
3601 3710 1.137404 CGGAATCCTTTGCGCCTTG 59.863 57.895 4.18 0.00 39.82 3.61
3649 3758 0.679002 TCTCCAAATCCAGCTGCAGC 60.679 55.000 31.53 31.53 42.49 5.25
3658 3767 1.039785 GGCTGGGCTTCTCCAAATCC 61.040 60.000 0.00 0.00 36.21 3.01
3748 3857 3.633361 CTCGGACTTTGAGGGCTTT 57.367 52.632 0.00 0.00 0.00 3.51
3936 4045 4.578928 GCAGTGAAAACTCACCTAAAAGGA 59.421 41.667 0.00 0.00 41.26 3.36
4013 4122 3.832527 ACTGCCAAGGTAAGAACAACAT 58.167 40.909 0.00 0.00 0.00 2.71
4091 4201 0.251077 CAGCAGAAGTCCCTGGCTTT 60.251 55.000 0.00 0.00 34.82 3.51
4137 4247 3.703001 AGACAGAAACCACACCATAGG 57.297 47.619 0.00 0.00 0.00 2.57
4245 4355 3.124466 GTGCGATGTAACAATGTGTAGCA 59.876 43.478 0.00 0.00 0.00 3.49
4904 5022 1.589716 AAGCTCAAGTTCATGGCCGC 61.590 55.000 0.00 0.00 0.00 6.53
5339 5466 1.375098 GACTGGCCATCTTGCAGAGC 61.375 60.000 5.51 0.00 0.00 4.09
5513 5640 1.000896 CAATTCGAACCCCCTGGCT 60.001 57.895 0.00 0.00 33.59 4.75
6145 6281 1.600076 CTGTTGCTGCTGCTGGAGT 60.600 57.895 17.00 0.00 40.48 3.85
6147 6283 2.981909 GCTGTTGCTGCTGCTGGA 60.982 61.111 17.00 2.36 40.48 3.86
6148 6284 3.268965 CTGCTGTTGCTGCTGCTGG 62.269 63.158 17.00 5.42 40.48 4.85
6178 6314 2.979197 CTGCTGGAGTTGCTGCTGC 61.979 63.158 8.89 8.89 44.20 5.25
6217 6356 1.947642 GTGCTGCTGCTGTTGTTGC 60.948 57.895 17.00 0.00 40.48 4.17
6474 6613 2.331132 GCAGCAGGGACAGAAGCAC 61.331 63.158 0.00 0.00 0.00 4.40
6507 6646 7.820648 ACCACTGTTCTTCATCATAATCAAAC 58.179 34.615 0.00 0.00 0.00 2.93
6586 6725 4.568956 TCTTCGATGAACTCATGCTTTGA 58.431 39.130 0.00 0.00 36.57 2.69
6601 6740 0.181350 GGGAGTGGCCAATCTTCGAT 59.819 55.000 30.44 0.00 38.95 3.59
6814 6953 1.740718 GCCGACTTGGATCCAGAAGTC 60.741 57.143 26.90 26.90 43.11 3.01
7245 7399 2.825836 CAGATTGCCCCGCTGTCC 60.826 66.667 0.00 0.00 0.00 4.02
7286 7440 1.301716 GTGCCGCTGAAAGGTGAGA 60.302 57.895 0.00 0.00 0.00 3.27
7287 7441 1.165907 TTGTGCCGCTGAAAGGTGAG 61.166 55.000 0.00 0.00 0.00 3.51
7288 7442 0.537143 ATTGTGCCGCTGAAAGGTGA 60.537 50.000 0.00 0.00 0.00 4.02
7289 7443 0.314935 AATTGTGCCGCTGAAAGGTG 59.685 50.000 0.00 0.00 0.00 4.00
7290 7444 0.314935 CAATTGTGCCGCTGAAAGGT 59.685 50.000 0.00 0.00 0.00 3.50
7291 7445 0.597568 TCAATTGTGCCGCTGAAAGG 59.402 50.000 5.13 0.00 0.00 3.11
7522 7676 2.161486 GCAGTTAGCTCGCCGACTG 61.161 63.158 14.31 14.31 41.76 3.51
7618 7772 0.621280 TGGGTGCATCATCCTCCTCA 60.621 55.000 0.00 0.00 35.30 3.86
7689 7844 0.394762 GCATCACTCCCATCAGCCAA 60.395 55.000 0.00 0.00 0.00 4.52
7707 7862 5.340439 AGGATAACCTACTACACACAAGC 57.660 43.478 0.00 0.00 45.83 4.01
7816 7973 1.383386 GGAGGAGAGGGGAGGGAAC 60.383 68.421 0.00 0.00 0.00 3.62
7818 7975 1.866997 TTGGAGGAGAGGGGAGGGA 60.867 63.158 0.00 0.00 0.00 4.20
7834 7991 0.321021 AGAGACCAGAGCAGCAGTTG 59.679 55.000 0.00 0.00 0.00 3.16
7835 7992 1.055040 AAGAGACCAGAGCAGCAGTT 58.945 50.000 0.00 0.00 0.00 3.16
7836 7993 1.055040 AAAGAGACCAGAGCAGCAGT 58.945 50.000 0.00 0.00 0.00 4.40
7837 7994 2.495270 TCTAAAGAGACCAGAGCAGCAG 59.505 50.000 0.00 0.00 0.00 4.24
7838 7995 2.529632 TCTAAAGAGACCAGAGCAGCA 58.470 47.619 0.00 0.00 0.00 4.41
7843 8015 8.614469 AAAGAACAAATCTAAAGAGACCAGAG 57.386 34.615 0.00 0.00 37.42 3.35
8009 8189 7.147312 TGTTTCTAAAACAATCCAAGCAGATG 58.853 34.615 2.90 0.00 0.00 2.90
8096 8282 3.636764 AGCCCCAGTTGTTGTTTCTAAAG 59.363 43.478 0.00 0.00 0.00 1.85
8109 8298 2.530151 TCTGCCTCAGCCCCAGTT 60.530 61.111 0.00 0.00 38.69 3.16
8110 8299 3.007920 CTCTGCCTCAGCCCCAGT 61.008 66.667 0.00 0.00 38.69 4.00
8111 8300 2.254737 CTTCTCTGCCTCAGCCCCAG 62.255 65.000 0.00 0.00 38.69 4.45
8129 8318 5.927819 ACTACGACTACTACTTATCTGCCT 58.072 41.667 0.00 0.00 0.00 4.75
8155 8344 4.189231 TCATGCTATGCTATGCTATGCAG 58.811 43.478 0.00 0.00 43.65 4.41
8197 8398 0.733729 TTACAACGCACACACCCAAC 59.266 50.000 0.00 0.00 0.00 3.77
8240 8457 2.109480 CCATCCATCCATCATCCACCTT 59.891 50.000 0.00 0.00 0.00 3.50
8241 8458 1.709115 CCATCCATCCATCATCCACCT 59.291 52.381 0.00 0.00 0.00 4.00
8247 8464 7.040913 ACAAGATTATCCATCCATCCATCAT 57.959 36.000 0.00 0.00 31.20 2.45
8248 8465 6.458630 ACAAGATTATCCATCCATCCATCA 57.541 37.500 0.00 0.00 31.20 3.07
8249 8466 8.868522 TTAACAAGATTATCCATCCATCCATC 57.131 34.615 0.00 0.00 31.20 3.51
8294 8515 1.478105 CGAGTCATCACACATCCCAGA 59.522 52.381 0.00 0.00 0.00 3.86
8295 8516 1.472201 CCGAGTCATCACACATCCCAG 60.472 57.143 0.00 0.00 0.00 4.45
8296 8517 0.536724 CCGAGTCATCACACATCCCA 59.463 55.000 0.00 0.00 0.00 4.37
8298 8519 0.108186 TGCCGAGTCATCACACATCC 60.108 55.000 0.00 0.00 0.00 3.51
8299 8520 1.002366 GTGCCGAGTCATCACACATC 58.998 55.000 6.83 0.00 34.07 3.06
8300 8521 0.610174 AGTGCCGAGTCATCACACAT 59.390 50.000 12.52 0.00 35.56 3.21
8496 8724 0.475475 GATCATCACCATCCAGCCCA 59.525 55.000 0.00 0.00 0.00 5.36
8507 8735 4.125703 GTGGAGGTGAATGAGATCATCAC 58.874 47.826 12.86 12.86 41.91 3.06
8541 8771 2.357034 CCGGACACGTGTGAAGGG 60.357 66.667 28.82 16.83 38.78 3.95
8544 8774 1.746322 TTAGGCCGGACACGTGTGAA 61.746 55.000 28.82 5.46 38.78 3.18
8570 8800 2.652382 TTTTCAGCCTGCACGTCGGA 62.652 55.000 0.00 0.00 0.00 4.55
8606 8836 3.237741 CCCCGGGCAAGGCAAAAA 61.238 61.111 17.73 0.00 0.00 1.94
8617 8847 4.109675 AAAGCGATGTCCCCCGGG 62.110 66.667 15.80 15.80 0.00 5.73
8732 8962 0.179020 TGCCAGGTTGAGTCACCAAG 60.179 55.000 12.45 5.90 39.62 3.61
9167 9398 2.491693 ACGCTTGGTATGGTCCATTTTG 59.508 45.455 10.33 0.00 37.33 2.44
9175 9406 2.489938 ATTCACACGCTTGGTATGGT 57.510 45.000 0.00 0.00 0.00 3.55
9208 9439 0.185901 ACCACAACCATCACCAAGCT 59.814 50.000 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.