Multiple sequence alignment - TraesCS1A01G145400

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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 TraesCS1A01G145400 chr1A 100.000 2826 0 0 1 2826 251533820 251530995 0.000000e+00 5219
1 TraesCS1A01G145400 chr1A 93.193 1572 72 3 430 1966 278501230 278502801 0.000000e+00 2278
2 TraesCS1A01G145400 chr7B 93.393 1574 67 4 430 1966 698140555 698142128 0.000000e+00 2296
3 TraesCS1A01G145400 chrUn 93.333 1575 67 4 430 1966 223706539 223704965 0.000000e+00 2292
4 TraesCS1A01G145400 chrUn 95.849 265 11 0 430 694 266187687 266187423 2.010000e-116 429
5 TraesCS1A01G145400 chr2A 93.270 1575 68 4 430 1966 605912482 605910908 0.000000e+00 2287
6 TraesCS1A01G145400 chr2A 92.939 1572 76 6 430 1966 563257037 563258608 0.000000e+00 2255
7 TraesCS1A01G145400 chr2A 95.360 431 14 6 1 429 364671784 364672210 0.000000e+00 680
8 TraesCS1A01G145400 chr2A 95.128 431 16 5 1 429 642145495 642145068 0.000000e+00 675
9 TraesCS1A01G145400 chr2A 96.525 259 9 0 430 688 735137185 735137443 2.010000e-116 429
10 TraesCS1A01G145400 chr6B 93.147 1576 69 4 430 1966 128903929 128905504 0.000000e+00 2276
11 TraesCS1A01G145400 chr1B 92.943 1573 75 18 430 1966 683733747 683732175 0.000000e+00 2257
12 TraesCS1A01G145400 chr1B 96.525 259 9 0 430 688 338893212 338893470 2.010000e-116 429
13 TraesCS1A01G145400 chr3B 92.884 1574 75 18 430 1966 92143319 92144892 0.000000e+00 2252
14 TraesCS1A01G145400 chr4B 92.743 1571 80 13 430 1966 495542373 495540803 0.000000e+00 2239
15 TraesCS1A01G145400 chr7D 93.418 866 52 5 1963 2824 334872474 334873338 0.000000e+00 1279
16 TraesCS1A01G145400 chr7D 92.907 860 56 5 1969 2824 473903117 473903975 0.000000e+00 1245
17 TraesCS1A01G145400 chr3D 93.380 861 49 7 1969 2824 217570916 217570059 0.000000e+00 1267
18 TraesCS1A01G145400 chr3D 93.031 861 55 5 1969 2824 386035430 386034570 0.000000e+00 1253
19 TraesCS1A01G145400 chr1D 93.279 863 53 5 1966 2824 387933849 387934710 0.000000e+00 1267
20 TraesCS1A01G145400 chr1D 93.256 860 52 6 1969 2824 357311953 357311096 0.000000e+00 1262
21 TraesCS1A01G145400 chr1D 96.139 259 10 0 430 688 351042087 351042345 9.360000e-115 424
22 TraesCS1A01G145400 chr5D 93.039 862 56 4 1966 2824 191921725 191922585 0.000000e+00 1256
23 TraesCS1A01G145400 chr5D 92.759 870 59 4 1959 2824 96264790 96265659 0.000000e+00 1254
24 TraesCS1A01G145400 chr2B 93.015 859 56 4 1969 2824 463865979 463865122 0.000000e+00 1251
25 TraesCS1A01G145400 chr6A 95.116 430 17 3 1 429 399812371 399812797 0.000000e+00 675
26 TraesCS1A01G145400 chr5A 95.128 431 15 6 1 429 195782944 195783370 0.000000e+00 675
27 TraesCS1A01G145400 chr5A 95.139 432 14 7 1 429 230853377 230853804 0.000000e+00 675
28 TraesCS1A01G145400 chr5A 95.128 431 15 6 1 429 261777714 261777288 0.000000e+00 675
29 TraesCS1A01G145400 chr4A 95.128 431 15 6 1 429 493162894 493163320 0.000000e+00 675
30 TraesCS1A01G145400 chr4A 94.907 432 17 4 1 430 147393667 147394095 0.000000e+00 671
31 TraesCS1A01G145400 chr3A 94.907 432 16 6 1 429 269335713 269336141 0.000000e+00 671
32 TraesCS1A01G145400 chr6D 96.525 259 9 0 430 688 430482156 430482414 2.010000e-116 429
33 TraesCS1A01G145400 chr5B 95.849 265 11 0 430 694 713081823 713081559 2.010000e-116 429
34 TraesCS1A01G145400 chr2D 96.525 259 9 0 430 688 634995571 634995829 2.010000e-116 429


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 TraesCS1A01G145400 chr1A 251530995 251533820 2825 True 5219 5219 100.000 1 2826 1 chr1A.!!$R1 2825
1 TraesCS1A01G145400 chr1A 278501230 278502801 1571 False 2278 2278 93.193 430 1966 1 chr1A.!!$F1 1536
2 TraesCS1A01G145400 chr7B 698140555 698142128 1573 False 2296 2296 93.393 430 1966 1 chr7B.!!$F1 1536
3 TraesCS1A01G145400 chrUn 223704965 223706539 1574 True 2292 2292 93.333 430 1966 1 chrUn.!!$R1 1536
4 TraesCS1A01G145400 chr2A 605910908 605912482 1574 True 2287 2287 93.270 430 1966 1 chr2A.!!$R1 1536
5 TraesCS1A01G145400 chr2A 563257037 563258608 1571 False 2255 2255 92.939 430 1966 1 chr2A.!!$F2 1536
6 TraesCS1A01G145400 chr6B 128903929 128905504 1575 False 2276 2276 93.147 430 1966 1 chr6B.!!$F1 1536
7 TraesCS1A01G145400 chr1B 683732175 683733747 1572 True 2257 2257 92.943 430 1966 1 chr1B.!!$R1 1536
8 TraesCS1A01G145400 chr3B 92143319 92144892 1573 False 2252 2252 92.884 430 1966 1 chr3B.!!$F1 1536
9 TraesCS1A01G145400 chr4B 495540803 495542373 1570 True 2239 2239 92.743 430 1966 1 chr4B.!!$R1 1536
10 TraesCS1A01G145400 chr7D 334872474 334873338 864 False 1279 1279 93.418 1963 2824 1 chr7D.!!$F1 861
11 TraesCS1A01G145400 chr7D 473903117 473903975 858 False 1245 1245 92.907 1969 2824 1 chr7D.!!$F2 855
12 TraesCS1A01G145400 chr3D 217570059 217570916 857 True 1267 1267 93.380 1969 2824 1 chr3D.!!$R1 855
13 TraesCS1A01G145400 chr3D 386034570 386035430 860 True 1253 1253 93.031 1969 2824 1 chr3D.!!$R2 855
14 TraesCS1A01G145400 chr1D 387933849 387934710 861 False 1267 1267 93.279 1966 2824 1 chr1D.!!$F2 858
15 TraesCS1A01G145400 chr1D 357311096 357311953 857 True 1262 1262 93.256 1969 2824 1 chr1D.!!$R1 855
16 TraesCS1A01G145400 chr5D 191921725 191922585 860 False 1256 1256 93.039 1966 2824 1 chr5D.!!$F2 858
17 TraesCS1A01G145400 chr5D 96264790 96265659 869 False 1254 1254 92.759 1959 2824 1 chr5D.!!$F1 865
18 TraesCS1A01G145400 chr2B 463865122 463865979 857 True 1251 1251 93.015 1969 2824 1 chr2B.!!$R1 855

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
329 330 0.033991 CTCTCTCCGAGGGTCCTTGA 60.034 60.0 5.84 0.0 36.06 3.02 F
332 333 0.114560 TCTCCGAGGGTCCTTGAGTT 59.885 55.0 5.84 0.0 31.48 3.01 F
1460 1496 0.174162 GGGCGCTCCGAAGTAAAGTA 59.826 55.0 7.64 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1801 0.529773 GGTCGCACATAAGCCATCGA 60.530 55.000 0.0 0.0 0.00 3.59 R
1820 1861 1.067776 GGGTCGAATCAGAGTTCACGT 60.068 52.381 0.0 0.0 0.00 4.49 R
2665 2711 5.070047 ACCTTTATCGGTCGAACCTTATGAT 59.930 40.000 0.0 0.0 35.66 2.45 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
23 24 5.701224 TCCCGAAATATAATTTTCCTGGCT 58.299 37.500 0.00 0.00 33.02 4.75
24 25 6.133356 TCCCGAAATATAATTTTCCTGGCTT 58.867 36.000 0.00 0.00 33.02 4.35
25 26 6.264518 TCCCGAAATATAATTTTCCTGGCTTC 59.735 38.462 0.00 0.00 33.02 3.86
26 27 6.265422 CCCGAAATATAATTTTCCTGGCTTCT 59.735 38.462 0.00 0.00 33.02 2.85
27 28 7.447238 CCCGAAATATAATTTTCCTGGCTTCTA 59.553 37.037 0.00 0.00 33.02 2.10
28 29 8.846211 CCGAAATATAATTTTCCTGGCTTCTAA 58.154 33.333 0.00 0.00 33.02 2.10
36 37 5.391312 TTTCCTGGCTTCTAAAATCAAGC 57.609 39.130 0.00 0.00 43.72 4.01
40 41 2.919666 GCTTCTAAAATCAAGCCGCA 57.080 45.000 0.00 0.00 39.36 5.69
41 42 2.519963 GCTTCTAAAATCAAGCCGCAC 58.480 47.619 0.00 0.00 39.36 5.34
42 43 2.095263 GCTTCTAAAATCAAGCCGCACA 60.095 45.455 0.00 0.00 39.36 4.57
43 44 3.751621 CTTCTAAAATCAAGCCGCACAG 58.248 45.455 0.00 0.00 0.00 3.66
44 45 2.083774 TCTAAAATCAAGCCGCACAGG 58.916 47.619 0.00 0.00 44.97 4.00
45 46 2.083774 CTAAAATCAAGCCGCACAGGA 58.916 47.619 0.00 0.00 45.00 3.86
46 47 1.549203 AAAATCAAGCCGCACAGGAT 58.451 45.000 0.00 0.00 45.00 3.24
47 48 0.813184 AAATCAAGCCGCACAGGATG 59.187 50.000 0.00 0.00 45.00 3.51
48 49 0.035152 AATCAAGCCGCACAGGATGA 60.035 50.000 0.00 0.00 45.00 2.92
49 50 0.035152 ATCAAGCCGCACAGGATGAA 60.035 50.000 0.00 0.00 45.00 2.57
50 51 0.955428 TCAAGCCGCACAGGATGAAC 60.955 55.000 0.00 0.00 45.00 3.18
51 52 1.073025 AAGCCGCACAGGATGAACA 59.927 52.632 0.00 0.00 45.00 3.18
52 53 0.322816 AAGCCGCACAGGATGAACAT 60.323 50.000 0.00 0.00 45.00 2.71
53 54 0.322816 AGCCGCACAGGATGAACATT 60.323 50.000 0.00 0.00 45.00 2.71
54 55 0.527565 GCCGCACAGGATGAACATTT 59.472 50.000 0.00 0.00 45.00 2.32
55 56 1.742831 GCCGCACAGGATGAACATTTA 59.257 47.619 0.00 0.00 45.00 1.40
56 57 2.358898 GCCGCACAGGATGAACATTTAT 59.641 45.455 0.00 0.00 45.00 1.40
57 58 3.181487 GCCGCACAGGATGAACATTTATT 60.181 43.478 0.00 0.00 45.00 1.40
58 59 4.677779 GCCGCACAGGATGAACATTTATTT 60.678 41.667 0.00 0.00 45.00 1.40
59 60 4.799949 CCGCACAGGATGAACATTTATTTG 59.200 41.667 0.00 0.00 45.00 2.32
60 61 5.392919 CCGCACAGGATGAACATTTATTTGA 60.393 40.000 0.00 0.00 45.00 2.69
61 62 5.740569 CGCACAGGATGAACATTTATTTGAG 59.259 40.000 0.00 0.00 39.69 3.02
62 63 6.623549 CGCACAGGATGAACATTTATTTGAGT 60.624 38.462 0.00 0.00 39.69 3.41
63 64 6.749118 GCACAGGATGAACATTTATTTGAGTC 59.251 38.462 0.00 0.00 39.69 3.36
64 65 7.253422 CACAGGATGAACATTTATTTGAGTCC 58.747 38.462 0.00 0.00 39.69 3.85
65 66 7.121759 CACAGGATGAACATTTATTTGAGTCCT 59.878 37.037 0.00 0.00 39.69 3.85
66 67 8.328758 ACAGGATGAACATTTATTTGAGTCCTA 58.671 33.333 0.00 0.00 39.69 2.94
67 68 9.177608 CAGGATGAACATTTATTTGAGTCCTAA 57.822 33.333 0.00 0.00 39.69 2.69
68 69 9.753674 AGGATGAACATTTATTTGAGTCCTAAA 57.246 29.630 0.00 0.00 31.03 1.85
71 72 9.807649 ATGAACATTTATTTGAGTCCTAAATGC 57.192 29.630 19.58 11.35 42.50 3.56
72 73 8.801299 TGAACATTTATTTGAGTCCTAAATGCA 58.199 29.630 19.58 12.83 42.50 3.96
73 74 9.638239 GAACATTTATTTGAGTCCTAAATGCAA 57.362 29.630 19.58 7.06 42.50 4.08
81 82 8.954950 TTTGAGTCCTAAATGCAATTTTGAAA 57.045 26.923 0.00 0.00 46.10 2.69
82 83 8.954950 TTGAGTCCTAAATGCAATTTTGAAAA 57.045 26.923 0.00 0.00 46.10 2.29
83 84 8.954950 TGAGTCCTAAATGCAATTTTGAAAAA 57.045 26.923 0.00 0.00 46.10 1.94
84 85 8.825745 TGAGTCCTAAATGCAATTTTGAAAAAC 58.174 29.630 0.00 0.00 46.10 2.43
85 86 7.850501 AGTCCTAAATGCAATTTTGAAAAACG 58.149 30.769 0.00 0.00 46.10 3.60
86 87 6.573357 GTCCTAAATGCAATTTTGAAAAACGC 59.427 34.615 7.47 7.47 46.10 4.84
87 88 5.559632 CCTAAATGCAATTTTGAAAAACGCG 59.440 36.000 3.53 3.53 46.10 6.01
88 89 2.359523 TGCAATTTTGAAAAACGCGC 57.640 40.000 5.73 0.00 34.25 6.86
89 90 1.660607 TGCAATTTTGAAAAACGCGCA 59.339 38.095 5.73 6.43 34.25 6.09
90 91 2.286294 TGCAATTTTGAAAAACGCGCAT 59.714 36.364 5.73 0.00 34.25 4.73
91 92 3.242543 TGCAATTTTGAAAAACGCGCATT 60.243 34.783 5.73 0.00 34.25 3.56
92 93 3.723272 GCAATTTTGAAAAACGCGCATTT 59.277 34.783 5.73 7.87 0.00 2.32
93 94 4.203966 GCAATTTTGAAAAACGCGCATTTT 59.796 33.333 19.32 19.32 33.13 1.82
94 95 5.275649 GCAATTTTGAAAAACGCGCATTTTT 60.276 32.000 25.00 25.00 42.94 1.94
99 100 4.957832 GAAAAACGCGCATTTTTCCTAA 57.042 36.364 32.90 0.00 46.17 2.69
100 101 5.509605 GAAAAACGCGCATTTTTCCTAAT 57.490 34.783 32.90 11.43 46.17 1.73
101 102 5.911421 GAAAAACGCGCATTTTTCCTAATT 58.089 33.333 32.90 10.75 46.17 1.40
102 103 5.915812 AAAACGCGCATTTTTCCTAATTT 57.084 30.435 8.60 0.00 0.00 1.82
103 104 5.509605 AAACGCGCATTTTTCCTAATTTC 57.490 34.783 5.73 0.00 0.00 2.17
104 105 4.167554 ACGCGCATTTTTCCTAATTTCA 57.832 36.364 5.73 0.00 0.00 2.69
105 106 4.551388 ACGCGCATTTTTCCTAATTTCAA 58.449 34.783 5.73 0.00 0.00 2.69
106 107 4.985409 ACGCGCATTTTTCCTAATTTCAAA 59.015 33.333 5.73 0.00 0.00 2.69
107 108 5.637387 ACGCGCATTTTTCCTAATTTCAAAT 59.363 32.000 5.73 0.00 0.00 2.32
108 109 6.809196 ACGCGCATTTTTCCTAATTTCAAATA 59.191 30.769 5.73 0.00 0.00 1.40
109 110 7.329717 ACGCGCATTTTTCCTAATTTCAAATAA 59.670 29.630 5.73 0.00 0.00 1.40
110 111 8.165428 CGCGCATTTTTCCTAATTTCAAATAAA 58.835 29.630 8.75 0.00 0.00 1.40
111 112 9.818796 GCGCATTTTTCCTAATTTCAAATAAAA 57.181 25.926 0.30 0.00 0.00 1.52
182 183 9.728100 AATCCTCAATATTTCCTTATTTTGGGA 57.272 29.630 0.00 0.00 0.00 4.37
183 184 9.728100 ATCCTCAATATTTCCTTATTTTGGGAA 57.272 29.630 0.00 0.00 39.52 3.97
204 205 7.561021 GGAAAGTCATTTTATTCCCTCTCTC 57.439 40.000 0.00 0.00 36.21 3.20
205 206 7.112779 GGAAAGTCATTTTATTCCCTCTCTCA 58.887 38.462 0.00 0.00 36.21 3.27
206 207 7.777440 GGAAAGTCATTTTATTCCCTCTCTCAT 59.223 37.037 0.00 0.00 36.21 2.90
207 208 9.183368 GAAAGTCATTTTATTCCCTCTCTCATT 57.817 33.333 0.00 0.00 0.00 2.57
208 209 9.539194 AAAGTCATTTTATTCCCTCTCTCATTT 57.461 29.630 0.00 0.00 0.00 2.32
209 210 9.539194 AAGTCATTTTATTCCCTCTCTCATTTT 57.461 29.630 0.00 0.00 0.00 1.82
210 211 9.539194 AGTCATTTTATTCCCTCTCTCATTTTT 57.461 29.630 0.00 0.00 0.00 1.94
278 279 9.947433 AATGATCCTATTTTCAAAATTTGAGCA 57.053 25.926 8.51 12.09 41.38 4.26
279 280 9.947433 ATGATCCTATTTTCAAAATTTGAGCAA 57.053 25.926 13.15 6.69 41.38 3.91
280 281 9.775854 TGATCCTATTTTCAAAATTTGAGCAAA 57.224 25.926 8.51 8.05 41.38 3.68
282 283 9.783081 ATCCTATTTTCAAAATTTGAGCAAACT 57.217 25.926 8.51 0.00 41.38 2.66
283 284 9.260002 TCCTATTTTCAAAATTTGAGCAAACTC 57.740 29.630 8.51 0.00 41.38 3.01
300 301 8.687824 AGCAAACTCAAATATGAAAATAACGG 57.312 30.769 0.00 0.00 34.49 4.44
301 302 8.519526 AGCAAACTCAAATATGAAAATAACGGA 58.480 29.630 0.00 0.00 34.49 4.69
302 303 9.134734 GCAAACTCAAATATGAAAATAACGGAA 57.865 29.630 0.00 0.00 34.49 4.30
306 307 8.630037 ACTCAAATATGAAAATAACGGAATCCC 58.370 33.333 0.00 0.00 34.49 3.85
307 308 7.947282 TCAAATATGAAAATAACGGAATCCCC 58.053 34.615 0.00 0.00 30.99 4.81
308 309 7.561722 TCAAATATGAAAATAACGGAATCCCCA 59.438 33.333 0.00 0.00 30.99 4.96
309 310 7.906199 AATATGAAAATAACGGAATCCCCAA 57.094 32.000 0.00 0.00 34.14 4.12
310 311 5.592104 ATGAAAATAACGGAATCCCCAAC 57.408 39.130 0.00 0.00 34.14 3.77
311 312 4.668636 TGAAAATAACGGAATCCCCAACT 58.331 39.130 0.00 0.00 34.14 3.16
312 313 4.703093 TGAAAATAACGGAATCCCCAACTC 59.297 41.667 0.00 0.00 34.14 3.01
313 314 4.586306 AAATAACGGAATCCCCAACTCT 57.414 40.909 0.00 0.00 34.14 3.24
314 315 3.840124 ATAACGGAATCCCCAACTCTC 57.160 47.619 0.00 0.00 34.14 3.20
315 316 1.657804 AACGGAATCCCCAACTCTCT 58.342 50.000 0.00 0.00 34.14 3.10
316 317 1.196012 ACGGAATCCCCAACTCTCTC 58.804 55.000 0.00 0.00 34.14 3.20
317 318 0.466124 CGGAATCCCCAACTCTCTCC 59.534 60.000 0.00 0.00 34.14 3.71
318 319 0.466124 GGAATCCCCAACTCTCTCCG 59.534 60.000 0.00 0.00 34.14 4.63
319 320 1.486211 GAATCCCCAACTCTCTCCGA 58.514 55.000 0.00 0.00 0.00 4.55
320 321 1.410882 GAATCCCCAACTCTCTCCGAG 59.589 57.143 0.00 0.00 45.56 4.63
321 322 0.397816 ATCCCCAACTCTCTCCGAGG 60.398 60.000 0.00 0.00 44.33 4.63
322 323 2.060980 CCCCAACTCTCTCCGAGGG 61.061 68.421 0.00 0.00 44.33 4.30
323 324 1.305381 CCCAACTCTCTCCGAGGGT 60.305 63.158 0.00 0.00 46.42 4.34
324 325 1.324005 CCCAACTCTCTCCGAGGGTC 61.324 65.000 0.00 0.00 43.29 4.46
325 326 1.324005 CCAACTCTCTCCGAGGGTCC 61.324 65.000 0.00 0.00 43.29 4.46
326 327 0.323908 CAACTCTCTCCGAGGGTCCT 60.324 60.000 0.00 0.00 43.29 3.85
327 328 0.410270 AACTCTCTCCGAGGGTCCTT 59.590 55.000 0.00 0.00 43.29 3.36
328 329 0.323908 ACTCTCTCCGAGGGTCCTTG 60.324 60.000 0.00 0.00 39.45 3.61
329 330 0.033991 CTCTCTCCGAGGGTCCTTGA 60.034 60.000 5.84 0.00 36.06 3.02
330 331 0.033991 TCTCTCCGAGGGTCCTTGAG 60.034 60.000 5.84 8.15 0.00 3.02
331 332 0.323908 CTCTCCGAGGGTCCTTGAGT 60.324 60.000 5.84 0.00 31.48 3.41
332 333 0.114560 TCTCCGAGGGTCCTTGAGTT 59.885 55.000 5.84 0.00 31.48 3.01
333 334 0.247736 CTCCGAGGGTCCTTGAGTTG 59.752 60.000 5.84 0.00 0.00 3.16
334 335 1.376037 CCGAGGGTCCTTGAGTTGC 60.376 63.158 5.84 0.00 0.00 4.17
335 336 1.738099 CGAGGGTCCTTGAGTTGCG 60.738 63.158 0.00 0.00 0.00 4.85
336 337 1.371558 GAGGGTCCTTGAGTTGCGT 59.628 57.895 0.00 0.00 0.00 5.24
337 338 0.606604 GAGGGTCCTTGAGTTGCGTA 59.393 55.000 0.00 0.00 0.00 4.42
338 339 0.608640 AGGGTCCTTGAGTTGCGTAG 59.391 55.000 0.00 0.00 0.00 3.51
339 340 0.606604 GGGTCCTTGAGTTGCGTAGA 59.393 55.000 0.00 0.00 0.00 2.59
340 341 1.001633 GGGTCCTTGAGTTGCGTAGAA 59.998 52.381 0.00 0.00 0.00 2.10
341 342 2.354805 GGGTCCTTGAGTTGCGTAGAAT 60.355 50.000 0.00 0.00 0.00 2.40
342 343 3.335579 GGTCCTTGAGTTGCGTAGAATT 58.664 45.455 0.00 0.00 0.00 2.17
343 344 3.751698 GGTCCTTGAGTTGCGTAGAATTT 59.248 43.478 0.00 0.00 0.00 1.82
344 345 4.142881 GGTCCTTGAGTTGCGTAGAATTTC 60.143 45.833 0.00 0.00 0.00 2.17
345 346 4.691216 GTCCTTGAGTTGCGTAGAATTTCT 59.309 41.667 4.03 4.03 0.00 2.52
346 347 5.867716 GTCCTTGAGTTGCGTAGAATTTCTA 59.132 40.000 1.90 1.90 0.00 2.10
347 348 6.035112 GTCCTTGAGTTGCGTAGAATTTCTAG 59.965 42.308 6.37 3.18 28.01 2.43
348 349 5.292101 CCTTGAGTTGCGTAGAATTTCTAGG 59.708 44.000 17.73 17.73 37.76 3.02
349 350 5.654603 TGAGTTGCGTAGAATTTCTAGGA 57.345 39.130 23.59 10.26 37.10 2.94
350 351 6.222038 TGAGTTGCGTAGAATTTCTAGGAT 57.778 37.500 23.59 10.22 37.10 3.24
351 352 6.273825 TGAGTTGCGTAGAATTTCTAGGATC 58.726 40.000 23.59 16.26 37.10 3.36
352 353 6.127451 TGAGTTGCGTAGAATTTCTAGGATCA 60.127 38.462 23.59 17.90 37.10 2.92
353 354 6.640518 AGTTGCGTAGAATTTCTAGGATCAA 58.359 36.000 23.59 17.13 37.10 2.57
354 355 6.535508 AGTTGCGTAGAATTTCTAGGATCAAC 59.464 38.462 23.59 23.86 37.68 3.18
355 356 5.357257 TGCGTAGAATTTCTAGGATCAACC 58.643 41.667 23.59 9.87 37.10 3.77
356 357 5.105106 TGCGTAGAATTTCTAGGATCAACCA 60.105 40.000 23.59 11.77 37.10 3.67
357 358 5.815740 GCGTAGAATTTCTAGGATCAACCAA 59.184 40.000 23.59 0.00 37.10 3.67
358 359 6.315393 GCGTAGAATTTCTAGGATCAACCAAA 59.685 38.462 23.59 0.00 37.10 3.28
359 360 7.012421 GCGTAGAATTTCTAGGATCAACCAAAT 59.988 37.037 23.59 0.00 37.10 2.32
360 361 8.338259 CGTAGAATTTCTAGGATCAACCAAATG 58.662 37.037 17.32 0.00 37.10 2.32
361 362 7.105241 AGAATTTCTAGGATCAACCAAATGC 57.895 36.000 0.00 0.00 42.04 3.56
362 363 6.664816 AGAATTTCTAGGATCAACCAAATGCA 59.335 34.615 0.00 0.00 42.04 3.96
363 364 6.855763 ATTTCTAGGATCAACCAAATGCAA 57.144 33.333 0.00 0.00 42.04 4.08
364 365 6.855763 TTTCTAGGATCAACCAAATGCAAT 57.144 33.333 0.00 0.00 42.04 3.56
365 366 7.953005 TTTCTAGGATCAACCAAATGCAATA 57.047 32.000 0.00 0.00 42.04 1.90
366 367 7.953005 TTCTAGGATCAACCAAATGCAATAA 57.047 32.000 0.00 0.00 42.04 1.40
367 368 7.953005 TCTAGGATCAACCAAATGCAATAAA 57.047 32.000 0.00 0.00 42.04 1.40
368 369 8.359875 TCTAGGATCAACCAAATGCAATAAAA 57.640 30.769 0.00 0.00 42.04 1.52
369 370 8.980596 TCTAGGATCAACCAAATGCAATAAAAT 58.019 29.630 0.00 0.00 42.04 1.82
372 373 9.550406 AGGATCAACCAAATGCAATAAAATATG 57.450 29.630 0.00 0.00 42.04 1.78
373 374 9.545105 GGATCAACCAAATGCAATAAAATATGA 57.455 29.630 0.00 0.00 38.79 2.15
442 443 6.443849 TGGGATGTTACACCTCTAGAAAGATT 59.556 38.462 0.00 0.00 0.00 2.40
484 485 8.712285 AGCTGTAATTGTACGTACATGTAAAT 57.288 30.769 27.82 15.57 35.89 1.40
561 562 6.655078 TCAAGAAGGAAATCCAAAAGGAAG 57.345 37.500 1.67 0.00 38.89 3.46
571 572 4.893424 TCCAAAAGGAAGTCGAGTTTTG 57.107 40.909 6.99 7.47 38.87 2.44
596 597 1.536072 CGATCGCTCGGGAATTGAGAA 60.536 52.381 0.26 0.00 41.27 2.87
611 612 9.525409 GGGAATTGAGAATTATGAATTTCACTG 57.475 33.333 5.77 0.00 0.00 3.66
836 871 9.680315 TTTATTGAAAACGTTCGAAAACCATAT 57.320 25.926 0.00 0.00 36.46 1.78
904 939 7.544566 GTCTTCAAACTAGTCATTAATGGTCGA 59.455 37.037 15.36 5.21 0.00 4.20
945 980 1.463528 GGTATGCGTTGCGAACACTTC 60.464 52.381 0.00 0.00 0.00 3.01
1014 1049 3.110705 AGAGCAGATGGTCCAACTACAT 58.889 45.455 8.34 0.00 43.11 2.29
1043 1078 6.924111 TCTTCTTTTTCATTACTTCCATGGC 58.076 36.000 6.96 0.00 0.00 4.40
1068 1103 2.827190 CGTGGCATGGCAGCATCT 60.827 61.111 24.03 0.00 35.83 2.90
1073 1108 1.450531 GGCATGGCAGCATCTGTACC 61.451 60.000 15.47 0.00 35.83 3.34
1097 1132 6.489675 CATTGAAATGGTTCGTCAATAGAGG 58.510 40.000 0.00 0.00 39.40 3.69
1223 1258 2.303022 TGGACAGAGCTAAAAGTGGAGG 59.697 50.000 0.00 0.00 0.00 4.30
1282 1317 4.263639 ACAAAATGGAGAGAAGCTCATCCA 60.264 41.667 10.49 10.49 45.81 3.41
1312 1347 8.688747 AAATGCTTTATTTCATTTTGTTCCCA 57.311 26.923 0.00 0.00 39.15 4.37
1317 1352 8.659491 GCTTTATTTCATTTTGTTCCCATTCTC 58.341 33.333 0.00 0.00 0.00 2.87
1333 1368 8.056088 TCCCATTCTCCATTTCCTTATTATCA 57.944 34.615 0.00 0.00 0.00 2.15
1343 1378 7.820872 CCATTTCCTTATTATCAAATCCATGGC 59.179 37.037 6.96 0.00 0.00 4.40
1369 1405 9.967346 CGGACTTGTCATATTAGAATCTTTCTA 57.033 33.333 3.08 0.00 41.14 2.10
1430 1466 4.469586 TCTTTACCATGTGATAGGTCAGCA 59.530 41.667 0.00 0.00 39.31 4.41
1459 1495 1.079336 GGGCGCTCCGAAGTAAAGT 60.079 57.895 7.64 0.00 0.00 2.66
1460 1496 0.174162 GGGCGCTCCGAAGTAAAGTA 59.826 55.000 7.64 0.00 0.00 2.24
1464 1500 2.091744 GCGCTCCGAAGTAAAGTACAAC 59.908 50.000 0.00 0.00 0.00 3.32
1467 1503 3.678548 GCTCCGAAGTAAAGTACAACCAG 59.321 47.826 0.00 0.00 0.00 4.00
1485 1521 2.777692 CCAGTTCAGCCTAAGGGGAATA 59.222 50.000 0.00 0.00 37.23 1.75
1514 1550 1.293062 ATGACAAGATGAGGTGCCCT 58.707 50.000 0.00 0.00 36.03 5.19
1546 1582 5.304614 CCCATATAGAAAGAAGGGTCGAAGA 59.695 44.000 0.00 0.00 0.00 2.87
1571 1607 1.450211 GCCTATAGCTTTCCCCGCA 59.550 57.895 0.00 0.00 38.99 5.69
1634 1675 2.046892 GCGGGCTTGAAGCTCTCA 60.047 61.111 15.93 0.00 40.30 3.27
1654 1695 0.813184 CCTTACCAACGAGCCGACTA 59.187 55.000 1.50 0.00 0.00 2.59
1675 1716 2.224523 ACTGATGGTTGTTGGTCACGAT 60.225 45.455 0.00 0.00 0.00 3.73
1756 1797 0.828022 TGGGTGTTCTTCTGTCGTGT 59.172 50.000 0.00 0.00 0.00 4.49
1760 1801 2.481449 GGTGTTCTTCTGTCGTGTGACT 60.481 50.000 0.00 0.00 45.70 3.41
1820 1861 2.186602 TATTTGTTCAGGGCGGGCGA 62.187 55.000 0.00 0.00 0.00 5.54
1838 1879 1.905687 CGACGTGAACTCTGATTCGAC 59.094 52.381 0.00 0.00 0.00 4.20
1861 1902 1.594331 GGTATTCAATCCCGCCACTC 58.406 55.000 0.00 0.00 0.00 3.51
1871 1912 1.078918 CCGCCACTCAGATGCTCAA 60.079 57.895 0.00 0.00 0.00 3.02
1893 1934 7.918076 TCAATTGACTCCTTAACCTTGATAGT 58.082 34.615 3.38 0.00 0.00 2.12
1928 1969 3.192422 TCCAAAATTCGTGCATAAGGGTG 59.808 43.478 0.00 0.00 0.00 4.61
1951 1992 7.093771 GGTGAGGAACTTTGGATGAATTAATGT 60.094 37.037 0.00 0.00 41.55 2.71
1961 2002 6.193504 TGGATGAATTAATGTGAATGGGTGA 58.806 36.000 0.00 0.00 0.00 4.02
1988 2029 5.013183 GCTAAAGGAAATATGCCCTAGAGGA 59.987 44.000 0.00 0.00 38.24 3.71
2145 2188 7.715657 ACTAGACTAGCTCATTGATCAAAGAG 58.284 38.462 28.22 28.22 38.68 2.85
2148 2191 2.652590 AGCTCATTGATCAAAGAGGGC 58.347 47.619 31.25 24.75 36.83 5.19
2203 2246 8.849168 GTCATTTGATAATGGGATCACAACATA 58.151 33.333 0.00 0.00 41.23 2.29
2242 2285 1.207329 ACAAGACCCATCCGTTAGCTC 59.793 52.381 0.00 0.00 0.00 4.09
2243 2286 0.460311 AAGACCCATCCGTTAGCTCG 59.540 55.000 0.00 0.00 0.00 5.03
2244 2287 0.395311 AGACCCATCCGTTAGCTCGA 60.395 55.000 0.00 0.00 0.00 4.04
2486 2530 0.644937 AGGTATCTCTGGGCCCTCTT 59.355 55.000 25.70 5.92 0.00 2.85
2507 2551 9.784531 CCTCTTGGTAATACACATCATAAGAAT 57.215 33.333 0.00 0.00 0.00 2.40
2517 2561 6.182627 ACACATCATAAGAATCCTTGCAAGA 58.817 36.000 28.05 13.93 33.94 3.02
2524 2568 5.859205 AAGAATCCTTGCAAGAAAAGTGT 57.141 34.783 28.05 7.76 0.00 3.55
2544 2590 9.694137 AAAGTGTCTAATGAGTTAGTTGTAGAC 57.306 33.333 0.00 0.00 38.72 2.59
2625 2671 1.647629 CCGACGATCGAATCTCGGT 59.352 57.895 27.43 3.73 43.74 4.69
2665 2711 9.707957 AATGGACAAAGGGAATTACATATGTTA 57.292 29.630 14.77 5.16 0.00 2.41
2688 2735 4.940463 TCATAAGGTTCGACCGATAAAGG 58.060 43.478 0.00 0.00 44.90 3.11
2782 2830 8.247562 GTCTCAGTCATGTCTACATAGTTCTTT 58.752 37.037 0.00 0.00 34.26 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.701224 AGCCAGGAAAATTATATTTCGGGA 58.299 37.500 11.10 0.00 39.64 5.14
1 2 6.265422 AGAAGCCAGGAAAATTATATTTCGGG 59.735 38.462 0.00 0.00 39.64 5.14
2 3 7.277174 AGAAGCCAGGAAAATTATATTTCGG 57.723 36.000 0.00 0.00 39.64 4.30
10 11 8.034804 GCTTGATTTTAGAAGCCAGGAAAATTA 58.965 33.333 0.00 0.00 38.96 1.40
11 12 6.875726 GCTTGATTTTAGAAGCCAGGAAAATT 59.124 34.615 0.00 0.00 38.96 1.82
12 13 6.401394 GCTTGATTTTAGAAGCCAGGAAAAT 58.599 36.000 0.00 0.00 38.96 1.82
13 14 5.783111 GCTTGATTTTAGAAGCCAGGAAAA 58.217 37.500 0.00 0.00 38.96 2.29
14 15 5.391312 GCTTGATTTTAGAAGCCAGGAAA 57.609 39.130 0.00 0.00 38.96 3.13
21 22 2.095263 TGTGCGGCTTGATTTTAGAAGC 60.095 45.455 0.00 0.00 43.27 3.86
22 23 3.426695 CCTGTGCGGCTTGATTTTAGAAG 60.427 47.826 0.00 0.00 0.00 2.85
23 24 2.487762 CCTGTGCGGCTTGATTTTAGAA 59.512 45.455 0.00 0.00 0.00 2.10
24 25 2.083774 CCTGTGCGGCTTGATTTTAGA 58.916 47.619 0.00 0.00 0.00 2.10
25 26 2.083774 TCCTGTGCGGCTTGATTTTAG 58.916 47.619 0.00 0.00 0.00 1.85
26 27 2.192664 TCCTGTGCGGCTTGATTTTA 57.807 45.000 0.00 0.00 0.00 1.52
27 28 1.203052 CATCCTGTGCGGCTTGATTTT 59.797 47.619 0.00 0.00 0.00 1.82
28 29 0.813184 CATCCTGTGCGGCTTGATTT 59.187 50.000 0.00 0.00 0.00 2.17
29 30 0.035152 TCATCCTGTGCGGCTTGATT 60.035 50.000 0.00 0.00 0.00 2.57
30 31 0.035152 TTCATCCTGTGCGGCTTGAT 60.035 50.000 0.00 0.00 0.00 2.57
31 32 0.955428 GTTCATCCTGTGCGGCTTGA 60.955 55.000 0.00 0.00 0.00 3.02
32 33 1.236616 TGTTCATCCTGTGCGGCTTG 61.237 55.000 0.00 0.00 0.00 4.01
33 34 0.322816 ATGTTCATCCTGTGCGGCTT 60.323 50.000 0.00 0.00 0.00 4.35
34 35 0.322816 AATGTTCATCCTGTGCGGCT 60.323 50.000 0.00 0.00 0.00 5.52
35 36 0.527565 AAATGTTCATCCTGTGCGGC 59.472 50.000 0.00 0.00 0.00 6.53
36 37 4.637483 AATAAATGTTCATCCTGTGCGG 57.363 40.909 0.00 0.00 0.00 5.69
37 38 5.639757 TCAAATAAATGTTCATCCTGTGCG 58.360 37.500 0.00 0.00 0.00 5.34
38 39 6.624423 ACTCAAATAAATGTTCATCCTGTGC 58.376 36.000 0.00 0.00 0.00 4.57
39 40 7.121759 AGGACTCAAATAAATGTTCATCCTGTG 59.878 37.037 0.00 0.00 31.65 3.66
40 41 7.177878 AGGACTCAAATAAATGTTCATCCTGT 58.822 34.615 0.00 0.00 31.65 4.00
41 42 7.636150 AGGACTCAAATAAATGTTCATCCTG 57.364 36.000 0.00 0.00 31.65 3.86
42 43 9.753674 TTTAGGACTCAAATAAATGTTCATCCT 57.246 29.630 0.00 0.00 36.77 3.24
45 46 9.807649 GCATTTAGGACTCAAATAAATGTTCAT 57.192 29.630 14.77 0.00 43.75 2.57
46 47 8.801299 TGCATTTAGGACTCAAATAAATGTTCA 58.199 29.630 14.77 6.16 43.75 3.18
47 48 9.638239 TTGCATTTAGGACTCAAATAAATGTTC 57.362 29.630 14.77 4.28 43.75 3.18
55 56 9.558396 TTTCAAAATTGCATTTAGGACTCAAAT 57.442 25.926 0.00 0.00 0.00 2.32
56 57 8.954950 TTTCAAAATTGCATTTAGGACTCAAA 57.045 26.923 0.00 0.00 0.00 2.69
57 58 8.954950 TTTTCAAAATTGCATTTAGGACTCAA 57.045 26.923 0.00 0.00 0.00 3.02
58 59 8.825745 GTTTTTCAAAATTGCATTTAGGACTCA 58.174 29.630 0.00 0.00 0.00 3.41
59 60 8.003784 CGTTTTTCAAAATTGCATTTAGGACTC 58.996 33.333 0.00 0.00 0.00 3.36
60 61 7.518211 GCGTTTTTCAAAATTGCATTTAGGACT 60.518 33.333 0.00 0.00 34.39 3.85
61 62 6.573357 GCGTTTTTCAAAATTGCATTTAGGAC 59.427 34.615 0.00 0.00 34.39 3.85
62 63 6.563010 CGCGTTTTTCAAAATTGCATTTAGGA 60.563 34.615 0.00 0.00 34.09 2.94
63 64 5.559632 CGCGTTTTTCAAAATTGCATTTAGG 59.440 36.000 0.00 0.00 34.09 2.69
64 65 5.056687 GCGCGTTTTTCAAAATTGCATTTAG 59.943 36.000 8.43 0.00 34.09 1.85
65 66 4.900747 GCGCGTTTTTCAAAATTGCATTTA 59.099 33.333 8.43 0.00 34.09 1.40
66 67 3.723272 GCGCGTTTTTCAAAATTGCATTT 59.277 34.783 8.43 0.00 34.09 2.32
67 68 3.242543 TGCGCGTTTTTCAAAATTGCATT 60.243 34.783 8.43 0.00 34.09 3.56
68 69 2.286294 TGCGCGTTTTTCAAAATTGCAT 59.714 36.364 8.43 0.00 34.09 3.96
69 70 1.660607 TGCGCGTTTTTCAAAATTGCA 59.339 38.095 8.43 8.11 34.09 4.08
70 71 2.359523 TGCGCGTTTTTCAAAATTGC 57.640 40.000 8.43 0.00 0.00 3.56
71 72 5.846555 AAAATGCGCGTTTTTCAAAATTG 57.153 30.435 29.75 0.00 0.00 2.32
79 80 5.915812 AATTAGGAAAAATGCGCGTTTTT 57.084 30.435 39.28 39.28 42.29 1.94
80 81 5.463724 TGAAATTAGGAAAAATGCGCGTTTT 59.536 32.000 29.75 29.75 32.94 2.43
81 82 4.985409 TGAAATTAGGAAAAATGCGCGTTT 59.015 33.333 21.59 21.59 0.00 3.60
82 83 4.551388 TGAAATTAGGAAAAATGCGCGTT 58.449 34.783 9.57 9.57 0.00 4.84
83 84 4.167554 TGAAATTAGGAAAAATGCGCGT 57.832 36.364 8.43 0.00 0.00 6.01
84 85 5.508124 TTTGAAATTAGGAAAAATGCGCG 57.492 34.783 0.00 0.00 0.00 6.86
85 86 9.818796 TTTTATTTGAAATTAGGAAAAATGCGC 57.181 25.926 0.00 0.00 0.00 6.09
156 157 9.728100 TCCCAAAATAAGGAAATATTGAGGATT 57.272 29.630 0.00 0.00 0.00 3.01
157 158 9.728100 TTCCCAAAATAAGGAAATATTGAGGAT 57.272 29.630 0.00 0.00 39.21 3.24
158 159 9.554053 TTTCCCAAAATAAGGAAATATTGAGGA 57.446 29.630 0.15 0.00 45.09 3.71
180 181 7.112779 TGAGAGAGGGAATAAAATGACTTTCC 58.887 38.462 0.00 0.00 37.49 3.13
181 182 8.744568 ATGAGAGAGGGAATAAAATGACTTTC 57.255 34.615 0.00 0.00 0.00 2.62
182 183 9.539194 AAATGAGAGAGGGAATAAAATGACTTT 57.461 29.630 0.00 0.00 0.00 2.66
183 184 9.539194 AAAATGAGAGAGGGAATAAAATGACTT 57.461 29.630 0.00 0.00 0.00 3.01
184 185 9.539194 AAAAATGAGAGAGGGAATAAAATGACT 57.461 29.630 0.00 0.00 0.00 3.41
252 253 9.947433 TGCTCAAATTTTGAAAATAGGATCATT 57.053 25.926 12.62 0.00 39.58 2.57
253 254 9.947433 TTGCTCAAATTTTGAAAATAGGATCAT 57.053 25.926 12.62 0.00 39.58 2.45
254 255 9.775854 TTTGCTCAAATTTTGAAAATAGGATCA 57.224 25.926 12.62 4.22 39.58 2.92
256 257 9.783081 AGTTTGCTCAAATTTTGAAAATAGGAT 57.217 25.926 12.62 0.00 39.58 3.24
257 258 9.260002 GAGTTTGCTCAAATTTTGAAAATAGGA 57.740 29.630 12.62 4.15 41.29 2.94
274 275 8.798153 CCGTTATTTTCATATTTGAGTTTGCTC 58.202 33.333 0.00 0.00 41.97 4.26
275 276 8.519526 TCCGTTATTTTCATATTTGAGTTTGCT 58.480 29.630 0.00 0.00 32.27 3.91
276 277 8.682128 TCCGTTATTTTCATATTTGAGTTTGC 57.318 30.769 0.00 0.00 32.27 3.68
280 281 8.630037 GGGATTCCGTTATTTTCATATTTGAGT 58.370 33.333 0.00 0.00 32.27 3.41
281 282 8.082242 GGGGATTCCGTTATTTTCATATTTGAG 58.918 37.037 0.00 0.00 32.27 3.02
282 283 7.561722 TGGGGATTCCGTTATTTTCATATTTGA 59.438 33.333 0.00 0.00 38.76 2.69
283 284 7.721402 TGGGGATTCCGTTATTTTCATATTTG 58.279 34.615 0.00 0.00 38.76 2.32
284 285 7.906199 TGGGGATTCCGTTATTTTCATATTT 57.094 32.000 0.00 0.00 38.76 1.40
285 286 7.563556 AGTTGGGGATTCCGTTATTTTCATATT 59.436 33.333 0.00 0.00 38.76 1.28
286 287 7.066781 AGTTGGGGATTCCGTTATTTTCATAT 58.933 34.615 0.00 0.00 38.76 1.78
287 288 6.428295 AGTTGGGGATTCCGTTATTTTCATA 58.572 36.000 0.00 0.00 38.76 2.15
288 289 5.269189 AGTTGGGGATTCCGTTATTTTCAT 58.731 37.500 0.00 0.00 38.76 2.57
289 290 4.668636 AGTTGGGGATTCCGTTATTTTCA 58.331 39.130 0.00 0.00 38.76 2.69
290 291 4.948004 AGAGTTGGGGATTCCGTTATTTTC 59.052 41.667 0.00 0.00 38.76 2.29
291 292 4.930696 AGAGTTGGGGATTCCGTTATTTT 58.069 39.130 0.00 0.00 38.76 1.82
292 293 4.227527 AGAGAGTTGGGGATTCCGTTATTT 59.772 41.667 0.00 0.00 38.76 1.40
293 294 3.780850 AGAGAGTTGGGGATTCCGTTATT 59.219 43.478 0.00 0.00 38.76 1.40
294 295 3.385115 AGAGAGTTGGGGATTCCGTTAT 58.615 45.455 0.00 0.00 38.76 1.89
295 296 2.764572 GAGAGAGTTGGGGATTCCGTTA 59.235 50.000 0.00 0.00 38.76 3.18
296 297 1.555533 GAGAGAGTTGGGGATTCCGTT 59.444 52.381 0.00 0.00 38.76 4.44
297 298 1.196012 GAGAGAGTTGGGGATTCCGT 58.804 55.000 0.00 0.00 38.76 4.69
298 299 0.466124 GGAGAGAGTTGGGGATTCCG 59.534 60.000 0.00 0.00 38.76 4.30
299 300 0.466124 CGGAGAGAGTTGGGGATTCC 59.534 60.000 0.00 0.00 0.00 3.01
300 301 1.486211 TCGGAGAGAGTTGGGGATTC 58.514 55.000 0.00 0.00 0.00 2.52
301 302 3.711849 TCGGAGAGAGTTGGGGATT 57.288 52.632 0.00 0.00 0.00 3.01
313 314 0.114560 AACTCAAGGACCCTCGGAGA 59.885 55.000 18.66 3.61 33.98 3.71
314 315 0.247736 CAACTCAAGGACCCTCGGAG 59.752 60.000 13.11 13.11 35.13 4.63
315 316 1.827399 GCAACTCAAGGACCCTCGGA 61.827 60.000 0.00 0.00 0.00 4.55
316 317 1.376037 GCAACTCAAGGACCCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
317 318 1.738099 CGCAACTCAAGGACCCTCG 60.738 63.158 0.00 0.00 0.00 4.63
318 319 0.606604 TACGCAACTCAAGGACCCTC 59.393 55.000 0.00 0.00 0.00 4.30
319 320 0.608640 CTACGCAACTCAAGGACCCT 59.391 55.000 0.00 0.00 0.00 4.34
320 321 0.606604 TCTACGCAACTCAAGGACCC 59.393 55.000 0.00 0.00 0.00 4.46
321 322 2.450609 TTCTACGCAACTCAAGGACC 57.549 50.000 0.00 0.00 0.00 4.46
322 323 4.691216 AGAAATTCTACGCAACTCAAGGAC 59.309 41.667 0.00 0.00 0.00 3.85
323 324 4.894784 AGAAATTCTACGCAACTCAAGGA 58.105 39.130 0.00 0.00 0.00 3.36
324 325 5.292101 CCTAGAAATTCTACGCAACTCAAGG 59.708 44.000 0.00 0.00 0.00 3.61
325 326 6.100004 TCCTAGAAATTCTACGCAACTCAAG 58.900 40.000 0.00 0.00 0.00 3.02
326 327 6.032956 TCCTAGAAATTCTACGCAACTCAA 57.967 37.500 0.00 0.00 0.00 3.02
327 328 5.654603 TCCTAGAAATTCTACGCAACTCA 57.345 39.130 0.00 0.00 0.00 3.41
328 329 6.273825 TGATCCTAGAAATTCTACGCAACTC 58.726 40.000 0.00 0.00 0.00 3.01
329 330 6.222038 TGATCCTAGAAATTCTACGCAACT 57.778 37.500 0.00 0.00 0.00 3.16
330 331 6.238130 GGTTGATCCTAGAAATTCTACGCAAC 60.238 42.308 16.04 16.04 0.00 4.17
331 332 5.815740 GGTTGATCCTAGAAATTCTACGCAA 59.184 40.000 0.00 0.00 0.00 4.85
332 333 5.105106 TGGTTGATCCTAGAAATTCTACGCA 60.105 40.000 0.00 0.00 37.07 5.24
333 334 5.357257 TGGTTGATCCTAGAAATTCTACGC 58.643 41.667 0.00 0.00 37.07 4.42
334 335 7.843490 TTTGGTTGATCCTAGAAATTCTACG 57.157 36.000 0.00 0.00 37.07 3.51
335 336 8.131731 GCATTTGGTTGATCCTAGAAATTCTAC 58.868 37.037 0.00 0.00 37.07 2.59
336 337 7.833682 TGCATTTGGTTGATCCTAGAAATTCTA 59.166 33.333 2.44 2.44 37.07 2.10
337 338 6.664816 TGCATTTGGTTGATCCTAGAAATTCT 59.335 34.615 0.00 0.00 37.07 2.40
338 339 6.866480 TGCATTTGGTTGATCCTAGAAATTC 58.134 36.000 0.00 0.00 37.07 2.17
339 340 6.855763 TGCATTTGGTTGATCCTAGAAATT 57.144 33.333 0.00 0.00 37.07 1.82
340 341 6.855763 TTGCATTTGGTTGATCCTAGAAAT 57.144 33.333 0.00 0.00 37.07 2.17
341 342 6.855763 ATTGCATTTGGTTGATCCTAGAAA 57.144 33.333 0.00 0.00 37.07 2.52
342 343 7.953005 TTATTGCATTTGGTTGATCCTAGAA 57.047 32.000 0.00 0.00 37.07 2.10
343 344 7.953005 TTTATTGCATTTGGTTGATCCTAGA 57.047 32.000 0.00 0.00 37.07 2.43
346 347 9.550406 CATATTTTATTGCATTTGGTTGATCCT 57.450 29.630 0.00 0.00 37.07 3.24
347 348 9.545105 TCATATTTTATTGCATTTGGTTGATCC 57.455 29.630 0.00 0.00 0.00 3.36
403 404 8.288913 GTGTAACATCCCAAATTTTCAATTTGG 58.711 33.333 25.00 25.00 45.86 3.28
404 405 8.288913 GGTGTAACATCCCAAATTTTCAATTTG 58.711 33.333 12.97 12.97 39.98 2.32
405 406 8.217111 AGGTGTAACATCCCAAATTTTCAATTT 58.783 29.630 0.00 0.00 39.98 1.82
406 407 7.744733 AGGTGTAACATCCCAAATTTTCAATT 58.255 30.769 0.00 0.00 39.98 2.32
407 408 7.315066 AGGTGTAACATCCCAAATTTTCAAT 57.685 32.000 0.00 0.00 39.98 2.57
408 409 6.739331 AGGTGTAACATCCCAAATTTTCAA 57.261 33.333 0.00 0.00 39.98 2.69
409 410 6.339587 GAGGTGTAACATCCCAAATTTTCA 57.660 37.500 0.00 0.00 42.84 2.69
421 422 9.256228 TGTCTAATCTTTCTAGAGGTGTAACAT 57.744 33.333 0.00 0.00 32.31 2.71
422 423 8.645814 TGTCTAATCTTTCTAGAGGTGTAACA 57.354 34.615 0.00 0.00 32.31 2.41
423 424 8.958506 TCTGTCTAATCTTTCTAGAGGTGTAAC 58.041 37.037 0.00 0.00 32.92 2.50
424 425 9.529823 TTCTGTCTAATCTTTCTAGAGGTGTAA 57.470 33.333 0.00 0.00 32.92 2.41
425 426 9.179909 CTTCTGTCTAATCTTTCTAGAGGTGTA 57.820 37.037 0.00 0.00 32.92 2.90
426 427 7.672239 ACTTCTGTCTAATCTTTCTAGAGGTGT 59.328 37.037 0.00 0.00 32.92 4.16
427 428 8.062065 ACTTCTGTCTAATCTTTCTAGAGGTG 57.938 38.462 0.00 0.00 32.92 4.00
428 429 9.756571 TTACTTCTGTCTAATCTTTCTAGAGGT 57.243 33.333 0.00 0.00 32.92 3.85
442 443 4.325119 ACAGCTCGTCTTACTTCTGTCTA 58.675 43.478 0.00 0.00 29.81 2.59
484 485 8.806429 ATCATACCATTGTCACATTTGAGTTA 57.194 30.769 0.00 0.00 30.10 2.24
561 562 0.442699 GATCGCACCCAAAACTCGAC 59.557 55.000 0.00 0.00 31.74 4.20
596 597 9.730705 TGAGACTCTTTCAGTGAAATTCATAAT 57.269 29.630 18.35 2.75 34.41 1.28
611 612 3.446873 TCAGGAGCTCATGAGACTCTTTC 59.553 47.826 26.22 20.33 34.37 2.62
730 765 9.962809 TTCGAACCCTTCCTTTTATTAAGATTA 57.037 29.630 0.00 0.00 0.00 1.75
945 980 5.814705 AGAGAAGATGAGACGCTAAAAATGG 59.185 40.000 0.00 0.00 0.00 3.16
984 1019 2.362397 GACCATCTGCTCTATCCGTTCA 59.638 50.000 0.00 0.00 0.00 3.18
1073 1108 6.094048 ACCTCTATTGACGAACCATTTCAATG 59.906 38.462 6.35 0.00 39.68 2.82
1191 1226 1.613925 GCTCTGTCCATGGAGCGTATA 59.386 52.381 16.81 0.00 44.01 1.47
1212 1247 3.955524 TTGACCAACCCTCCACTTTTA 57.044 42.857 0.00 0.00 0.00 1.52
1223 1258 1.007387 CGGCTTGCTTTGACCAACC 60.007 57.895 0.00 0.00 0.00 3.77
1317 1352 7.820872 GCCATGGATTTGATAATAAGGAAATGG 59.179 37.037 18.40 0.00 0.00 3.16
1343 1378 8.879342 AGAAAGATTCTAATATGACAAGTCCG 57.121 34.615 0.00 0.00 38.49 4.79
1369 1405 5.978814 AGAATTGTAAATAGAGCAGACCGT 58.021 37.500 0.00 0.00 0.00 4.83
1459 1495 2.304761 CCCTTAGGCTGAACTGGTTGTA 59.695 50.000 0.00 0.00 0.00 2.41
1460 1496 1.073923 CCCTTAGGCTGAACTGGTTGT 59.926 52.381 0.00 0.00 0.00 3.32
1464 1500 0.991920 TTCCCCTTAGGCTGAACTGG 59.008 55.000 0.00 0.00 34.51 4.00
1467 1503 3.215151 GCTTATTCCCCTTAGGCTGAAC 58.785 50.000 0.00 0.00 34.51 3.18
1485 1521 5.069516 ACCTCATCTTGTCATTTTGTTGCTT 59.930 36.000 0.00 0.00 0.00 3.91
1546 1582 3.576861 GGGAAAGCTATAGGCCCAAAAT 58.423 45.455 0.00 0.00 43.05 1.82
1634 1675 1.183676 AGTCGGCTCGTTGGTAAGGT 61.184 55.000 0.00 0.00 0.00 3.50
1654 1695 1.140052 TCGTGACCAACAACCATCAGT 59.860 47.619 0.00 0.00 0.00 3.41
1695 1736 6.763135 TCCTCCATGTGAAATAGAAAGATTCG 59.237 38.462 0.00 0.00 34.02 3.34
1756 1797 1.802508 CGCACATAAGCCATCGAGTCA 60.803 52.381 0.00 0.00 0.00 3.41
1760 1801 0.529773 GGTCGCACATAAGCCATCGA 60.530 55.000 0.00 0.00 0.00 3.59
1820 1861 1.067776 GGGTCGAATCAGAGTTCACGT 60.068 52.381 0.00 0.00 0.00 4.49
1858 1899 3.518705 AGGAGTCAATTGAGCATCTGAGT 59.481 43.478 8.80 0.00 34.92 3.41
1861 1902 5.065731 GGTTAAGGAGTCAATTGAGCATCTG 59.934 44.000 8.80 0.00 34.92 2.90
1871 1912 9.268282 TCTTACTATCAAGGTTAAGGAGTCAAT 57.732 33.333 0.00 0.00 0.00 2.57
1893 1934 7.479980 CACGAATTTTGGAATAAGCCATCTTA 58.520 34.615 0.00 0.00 37.86 2.10
1928 1969 8.055279 TCACATTAATTCATCCAAAGTTCCTC 57.945 34.615 0.00 0.00 0.00 3.71
1951 1992 4.380843 TCCTTTAGCTTTCACCCATTCA 57.619 40.909 0.00 0.00 0.00 2.57
1961 2002 6.911308 TCTAGGGCATATTTCCTTTAGCTTT 58.089 36.000 0.00 0.00 34.75 3.51
2203 2246 4.849813 TGTCCATCACATCATTCTCCTT 57.150 40.909 0.00 0.00 0.00 3.36
2242 2285 7.318909 GCAATAAACTGAACGATCAATATGTCG 59.681 37.037 0.00 4.46 43.13 4.35
2243 2286 8.338259 AGCAATAAACTGAACGATCAATATGTC 58.662 33.333 0.00 0.00 34.49 3.06
2244 2287 8.213518 AGCAATAAACTGAACGATCAATATGT 57.786 30.769 0.00 0.00 34.49 2.29
2486 2530 9.559732 CAAGGATTCTTATGATGTGTATTACCA 57.440 33.333 0.00 0.00 0.00 3.25
2507 2551 6.061441 TCATTAGACACTTTTCTTGCAAGGA 58.939 36.000 25.73 15.86 0.00 3.36
2524 2568 8.277490 ACATCGTCTACAACTAACTCATTAGA 57.723 34.615 1.17 0.00 40.38 2.10
2544 2590 8.074370 TCTCTTTACTCGTTCCATAATACATCG 58.926 37.037 0.00 0.00 0.00 3.84
2625 2671 6.432783 CCTTTGTCCATTGGTATGTTACTTGA 59.567 38.462 1.86 0.00 0.00 3.02
2665 2711 5.070047 ACCTTTATCGGTCGAACCTTATGAT 59.930 40.000 0.00 0.00 35.66 2.45


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

AutoCloner maintained by Alex Coulton.