Multiple sequence alignment - TraesCS3B01G143300

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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 TraesCS3B01G143300 chr3B 100.000 3975 0 0 1 3975 132088640 132092614 0.000000e+00 7341.0
1 TraesCS3B01G143300 chr3B 96.874 2623 66 12 1225 3841 132008737 132011349 0.000000e+00 4375.0
2 TraesCS3B01G143300 chr3B 94.130 2368 106 13 1225 3580 132903050 132900704 0.000000e+00 3572.0
3 TraesCS3B01G143300 chr3B 85.002 2627 263 51 421 2967 132906904 132904329 0.000000e+00 2547.0
4 TraesCS3B01G143300 chr3B 91.898 1370 80 10 1583 2943 133204198 133205545 0.000000e+00 1886.0
5 TraesCS3B01G143300 chr3B 84.330 1755 229 27 1225 2967 132005736 132007456 0.000000e+00 1676.0
6 TraesCS3B01G143300 chr3B 84.482 1727 226 23 1223 2940 133200425 133202118 0.000000e+00 1666.0
7 TraesCS3B01G143300 chr3B 84.598 870 54 24 426 1223 133199536 133200397 0.000000e+00 791.0
8 TraesCS3B01G143300 chr3B 89.796 392 31 6 3586 3975 133205526 133205910 9.920000e-136 494.0
9 TraesCS3B01G143300 chr3B 85.714 357 26 9 878 1223 132977050 132976708 1.760000e-93 353.0
10 TraesCS3B01G143300 chr3B 85.577 208 20 8 32 235 226725882 226726083 4.030000e-50 209.0
11 TraesCS3B01G143300 chr3B 89.313 131 14 0 1093 1223 132518611 132518741 8.840000e-37 165.0
12 TraesCS3B01G143300 chr3B 84.571 175 18 7 65 235 226785275 226785444 8.840000e-37 165.0
13 TraesCS3B01G143300 chr3B 100.000 79 0 0 3897 3975 132011582 132011660 3.200000e-31 147.0
14 TraesCS3B01G143300 chr3B 82.243 107 14 4 1 105 578589027 578589130 1.970000e-13 87.9
15 TraesCS3B01G143300 chr3B 92.857 56 4 0 871 926 133203360 133203415 9.160000e-12 82.4
16 TraesCS3B01G143300 chr3B 91.071 56 5 0 871 926 132903470 132903415 4.260000e-10 76.8
17 TraesCS3B01G143300 chr3D 95.874 2763 92 14 1225 3975 84498019 84495267 0.000000e+00 4451.0
18 TraesCS3B01G143300 chr3D 91.358 3020 122 56 426 3329 84565731 84562735 0.000000e+00 4002.0
19 TraesCS3B01G143300 chr3D 83.489 2144 255 44 871 2967 84501384 84499293 0.000000e+00 1906.0
20 TraesCS3B01G143300 chr3D 81.982 888 57 32 425 1223 84501906 84501033 0.000000e+00 658.0
21 TraesCS3B01G143300 chr3D 89.496 238 16 3 995 1223 84505761 84505524 3.890000e-75 292.0
22 TraesCS3B01G143300 chr3D 90.000 160 16 0 1064 1223 84498208 84498049 1.450000e-49 207.0
23 TraesCS3B01G143300 chr3D 84.409 186 21 6 47 230 110278107 110278286 4.080000e-40 176.0
24 TraesCS3B01G143300 chr3D 100.000 28 0 0 228 255 173703495 173703468 7.000000e-03 52.8
25 TraesCS3B01G143300 chr3A 95.221 2762 114 15 1225 3975 100842960 100840206 0.000000e+00 4353.0
26 TraesCS3B01G143300 chr3A 88.953 1738 141 22 1225 2943 100879645 100877940 0.000000e+00 2098.0
27 TraesCS3B01G143300 chr3A 81.685 2255 281 78 784 2967 100883139 100880946 0.000000e+00 1755.0
28 TraesCS3B01G143300 chr3A 81.477 880 56 29 425 1223 100845432 100844579 1.210000e-174 623.0
29 TraesCS3B01G143300 chr3A 81.751 674 91 25 1223 1886 100844551 100843900 5.850000e-148 534.0
30 TraesCS3B01G143300 chr3A 90.561 392 32 5 3586 3975 100877959 100877571 7.620000e-142 514.0
31 TraesCS3B01G143300 chr3A 85.319 470 56 8 3120 3580 100840394 100839929 1.290000e-129 473.0
32 TraesCS3B01G143300 chr3A 79.208 101 15 3 871 971 100843380 100843286 9.220000e-07 65.8
33 TraesCS3B01G143300 chr7B 90.000 230 15 6 1 227 530433540 530433764 1.400000e-74 291.0
34 TraesCS3B01G143300 chr1B 89.700 233 14 7 1 228 50211843 50211616 5.030000e-74 289.0
35 TraesCS3B01G143300 chr1B 84.577 201 24 6 33 230 31844827 31845023 4.050000e-45 193.0
36 TraesCS3B01G143300 chr6B 87.554 233 20 5 1 231 43803413 43803188 1.100000e-65 261.0
37 TraesCS3B01G143300 chr5B 83.691 233 31 6 1 230 709167357 709167585 3.110000e-51 213.0
38 TraesCS3B01G143300 chrUn 84.500 200 26 4 33 230 304675611 304675415 4.050000e-45 193.0
39 TraesCS3B01G143300 chrUn 93.333 45 2 1 385 429 17270380 17270423 9.220000e-07 65.8
40 TraesCS3B01G143300 chr7A 95.238 42 1 1 385 426 435835224 435835264 9.220000e-07 65.8
41 TraesCS3B01G143300 chr4B 95.238 42 1 1 385 426 464528085 464528125 9.220000e-07 65.8
42 TraesCS3B01G143300 chr2D 95.000 40 1 1 387 426 116643915 116643953 1.190000e-05 62.1
43 TraesCS3B01G143300 chr5D 100.000 28 0 0 228 255 328516666 328516639 7.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G143300 chr3B 132088640 132092614 3974 False 7341.000000 7341 100.000000 1 3975 1 chr3B.!!$F1 3974
1 TraesCS3B01G143300 chr3B 132005736 132011660 5924 False 2066.000000 4375 93.734667 1225 3975 3 chr3B.!!$F6 2750
2 TraesCS3B01G143300 chr3B 132900704 132906904 6200 True 2065.266667 3572 90.067667 421 3580 3 chr3B.!!$R2 3159
3 TraesCS3B01G143300 chr3B 133199536 133205910 6374 False 983.880000 1886 88.726200 426 3975 5 chr3B.!!$F7 3549
4 TraesCS3B01G143300 chr3D 84562735 84565731 2996 True 4002.000000 4002 91.358000 426 3329 1 chr3D.!!$R1 2903
5 TraesCS3B01G143300 chr3D 84495267 84505761 10494 True 1502.800000 4451 88.168200 425 3975 5 chr3D.!!$R3 3550
6 TraesCS3B01G143300 chr3A 100877571 100883139 5568 True 1455.666667 2098 87.066333 784 3975 3 chr3A.!!$R2 3191
7 TraesCS3B01G143300 chr3A 100839929 100845432 5503 True 1209.760000 4353 84.595200 425 3975 5 chr3A.!!$R1 3550

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
67 68 0.035915 TGCTATGTAGGCCGCAAACA 60.036 50.0 7.12 6.45 0.00 2.83 F
359 360 0.179006 GGGCTATTTCTGGGCTCCTG 60.179 60.0 0.00 0.00 0.00 3.86 F
460 3898 0.250727 GGGTGCACTGCCTTCACTAA 60.251 55.0 17.98 0.00 0.00 2.24 F
1487 11569 0.391661 GACATCGCAAGGGAGCTTGA 60.392 55.0 0.00 0.00 36.50 3.02 F
2204 12390 0.537371 CCCGCAAGAGGAAACAAGGT 60.537 55.0 0.00 0.00 43.02 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1059 4652 0.252761 TCATGGCTGATCGGCTGAAA 59.747 50.000 25.27 9.91 39.32 2.69 R
1508 11590 0.883833 CGAGAAGCCACAAAAGCCAT 59.116 50.000 0.00 0.00 0.00 4.40 R
2204 12390 2.815503 CACTGTGCTTCATCCATTGACA 59.184 45.455 0.00 0.00 32.84 3.58 R
2625 12811 0.178876 TCACTCCAACCTCCATCCCA 60.179 55.000 0.00 0.00 0.00 4.37 R
3869 14166 0.104144 TTCCTCCCCTTTCTGACCCA 60.104 55.000 0.00 0.00 0.00 4.51 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
19 20 1.073199 CAACGACTTCTTGGCCCCT 59.927 57.895 0.00 0.00 0.00 4.79
21 22 1.061546 AACGACTTCTTGGCCCCTTA 58.938 50.000 0.00 0.00 0.00 2.69
23 24 0.613777 CGACTTCTTGGCCCCTTAGT 59.386 55.000 0.00 0.00 0.00 2.24
24 25 1.003233 CGACTTCTTGGCCCCTTAGTT 59.997 52.381 0.00 0.00 0.00 2.24
25 26 2.235402 CGACTTCTTGGCCCCTTAGTTA 59.765 50.000 0.00 0.00 0.00 2.24
26 27 3.679083 CGACTTCTTGGCCCCTTAGTTAG 60.679 52.174 0.00 0.00 0.00 2.34
62 63 4.766404 ATAATTTTGCTATGTAGGCCGC 57.234 40.909 0.00 0.00 0.00 6.53
63 64 2.051334 ATTTTGCTATGTAGGCCGCA 57.949 45.000 0.00 0.22 0.00 5.69
65 66 1.827681 TTTGCTATGTAGGCCGCAAA 58.172 45.000 18.55 18.55 46.42 3.68
66 67 1.091537 TTGCTATGTAGGCCGCAAAC 58.908 50.000 10.56 2.73 39.19 2.93
67 68 0.035915 TGCTATGTAGGCCGCAAACA 60.036 50.000 7.12 6.45 0.00 2.83
69 70 1.002468 GCTATGTAGGCCGCAAACATG 60.002 52.381 19.79 13.25 35.54 3.21
70 71 2.288666 CTATGTAGGCCGCAAACATGT 58.711 47.619 19.79 0.00 35.54 3.21
73 74 1.276705 TGTAGGCCGCAAACATGTCTA 59.723 47.619 0.00 0.00 0.00 2.59
74 75 2.289756 TGTAGGCCGCAAACATGTCTAA 60.290 45.455 0.00 0.00 0.00 2.10
75 76 2.128771 AGGCCGCAAACATGTCTAAT 57.871 45.000 0.00 0.00 0.00 1.73
77 78 3.820557 AGGCCGCAAACATGTCTAATAT 58.179 40.909 0.00 0.00 0.00 1.28
79 80 5.560724 AGGCCGCAAACATGTCTAATATAT 58.439 37.500 0.00 0.00 0.00 0.86
80 81 5.412594 AGGCCGCAAACATGTCTAATATATG 59.587 40.000 0.00 0.00 33.16 1.78
82 83 5.631026 CCGCAAACATGTCTAATATATGCC 58.369 41.667 0.00 0.00 30.12 4.40
84 85 6.293900 CCGCAAACATGTCTAATATATGCCAA 60.294 38.462 0.00 0.00 30.12 4.52
85 86 6.798476 CGCAAACATGTCTAATATATGCCAAG 59.202 38.462 0.00 0.00 30.12 3.61
86 87 7.520453 CGCAAACATGTCTAATATATGCCAAGT 60.520 37.037 0.00 0.00 30.12 3.16
87 88 8.137437 GCAAACATGTCTAATATATGCCAAGTT 58.863 33.333 0.00 0.00 30.12 2.66
90 91 7.651808 ACATGTCTAATATATGCCAAGTTTGC 58.348 34.615 0.00 0.00 30.12 3.68
91 92 6.633500 TGTCTAATATATGCCAAGTTTGCC 57.367 37.500 0.00 0.00 0.00 4.52
94 95 6.017440 GTCTAATATATGCCAAGTTTGCCGAA 60.017 38.462 0.00 0.00 0.00 4.30
95 96 5.789643 AATATATGCCAAGTTTGCCGAAT 57.210 34.783 0.00 0.00 0.00 3.34
96 97 5.789643 ATATATGCCAAGTTTGCCGAATT 57.210 34.783 0.00 0.00 0.00 2.17
98 99 2.611225 TGCCAAGTTTGCCGAATTTT 57.389 40.000 0.00 0.00 0.00 1.82
99 100 3.735237 TGCCAAGTTTGCCGAATTTTA 57.265 38.095 0.00 0.00 0.00 1.52
100 101 3.648009 TGCCAAGTTTGCCGAATTTTAG 58.352 40.909 0.00 0.00 0.00 1.85
104 105 2.156098 AGTTTGCCGAATTTTAGCCGA 58.844 42.857 0.00 0.00 0.00 5.54
105 106 2.161609 AGTTTGCCGAATTTTAGCCGAG 59.838 45.455 0.00 0.00 0.00 4.63
106 107 1.816074 TTGCCGAATTTTAGCCGAGT 58.184 45.000 0.00 0.00 0.00 4.18
107 108 1.816074 TGCCGAATTTTAGCCGAGTT 58.184 45.000 0.00 0.00 0.00 3.01
108 109 2.156098 TGCCGAATTTTAGCCGAGTTT 58.844 42.857 0.00 0.00 0.00 2.66
109 110 3.336468 TGCCGAATTTTAGCCGAGTTTA 58.664 40.909 0.00 0.00 0.00 2.01
110 111 3.942748 TGCCGAATTTTAGCCGAGTTTAT 59.057 39.130 0.00 0.00 0.00 1.40
112 113 4.279659 CCGAATTTTAGCCGAGTTTATGC 58.720 43.478 0.00 0.00 0.00 3.14
113 114 3.960002 CGAATTTTAGCCGAGTTTATGCG 59.040 43.478 0.00 0.00 0.00 4.73
114 115 4.260051 CGAATTTTAGCCGAGTTTATGCGA 60.260 41.667 0.00 0.00 0.00 5.10
115 116 5.554822 AATTTTAGCCGAGTTTATGCGAA 57.445 34.783 0.00 0.00 0.00 4.70
117 118 2.953466 TAGCCGAGTTTATGCGAACT 57.047 45.000 0.22 0.22 42.31 3.01
118 119 2.094762 AGCCGAGTTTATGCGAACTT 57.905 45.000 2.11 0.00 39.84 2.66
119 120 2.000447 AGCCGAGTTTATGCGAACTTC 59.000 47.619 2.11 0.00 39.84 3.01
120 121 1.266891 GCCGAGTTTATGCGAACTTCG 60.267 52.381 6.82 6.82 39.84 3.79
130 131 2.738147 CGAACTTCGCCGAATGAGT 58.262 52.632 0.00 0.00 31.14 3.41
131 132 1.068474 CGAACTTCGCCGAATGAGTT 58.932 50.000 0.00 0.44 31.14 3.01
132 133 1.459592 CGAACTTCGCCGAATGAGTTT 59.540 47.619 0.00 0.00 31.14 2.66
133 134 2.096417 CGAACTTCGCCGAATGAGTTTT 60.096 45.455 0.00 0.00 31.14 2.43
134 135 3.606153 CGAACTTCGCCGAATGAGTTTTT 60.606 43.478 0.00 0.00 31.14 1.94
200 201 2.747686 GGAACCAACTCGCCTCCA 59.252 61.111 0.00 0.00 0.00 3.86
201 202 1.376037 GGAACCAACTCGCCTCCAG 60.376 63.158 0.00 0.00 0.00 3.86
202 203 1.376037 GAACCAACTCGCCTCCAGG 60.376 63.158 0.00 0.00 38.53 4.45
213 214 3.596362 CCTCCAGGCCCCTTTTTAG 57.404 57.895 0.00 0.00 0.00 1.85
214 215 0.684479 CCTCCAGGCCCCTTTTTAGC 60.684 60.000 0.00 0.00 0.00 3.09
215 216 1.001393 TCCAGGCCCCTTTTTAGCG 60.001 57.895 0.00 0.00 0.00 4.26
216 217 2.710902 CCAGGCCCCTTTTTAGCGC 61.711 63.158 0.00 0.00 0.00 5.92
217 218 2.362503 AGGCCCCTTTTTAGCGCC 60.363 61.111 2.29 0.00 40.03 6.53
218 219 3.822192 GGCCCCTTTTTAGCGCCG 61.822 66.667 2.29 0.00 0.00 6.46
237 238 4.722700 CTCACCCCCAACGGCTGG 62.723 72.222 0.00 0.00 45.97 4.85
245 246 3.805267 CAACGGCTGGAGATGCTC 58.195 61.111 0.00 0.00 0.00 4.26
246 247 1.220206 CAACGGCTGGAGATGCTCT 59.780 57.895 0.00 0.00 0.00 4.09
248 249 1.134699 CAACGGCTGGAGATGCTCTTA 60.135 52.381 0.00 0.00 0.00 2.10
249 250 0.749649 ACGGCTGGAGATGCTCTTAG 59.250 55.000 0.00 0.00 0.00 2.18
250 251 0.599728 CGGCTGGAGATGCTCTTAGC 60.600 60.000 12.47 12.47 42.82 3.09
251 252 0.758123 GGCTGGAGATGCTCTTAGCT 59.242 55.000 17.10 0.00 42.97 3.32
252 253 1.140652 GGCTGGAGATGCTCTTAGCTT 59.859 52.381 17.10 0.00 42.97 3.74
253 254 2.421248 GGCTGGAGATGCTCTTAGCTTT 60.421 50.000 17.10 0.00 42.97 3.51
254 255 2.613133 GCTGGAGATGCTCTTAGCTTTG 59.387 50.000 0.00 0.00 42.97 2.77
255 256 2.613133 CTGGAGATGCTCTTAGCTTTGC 59.387 50.000 0.00 0.00 42.97 3.68
256 257 1.596727 GGAGATGCTCTTAGCTTTGCG 59.403 52.381 0.00 0.00 42.97 4.85
257 258 1.596727 GAGATGCTCTTAGCTTTGCGG 59.403 52.381 0.00 0.00 42.97 5.69
258 259 0.659957 GATGCTCTTAGCTTTGCGGG 59.340 55.000 0.00 0.00 42.97 6.13
259 260 0.253044 ATGCTCTTAGCTTTGCGGGA 59.747 50.000 0.00 0.00 42.97 5.14
278 279 3.123620 CGCAAGCTGCTCACCTCC 61.124 66.667 1.00 0.00 42.25 4.30
280 281 2.345244 CAAGCTGCTCACCTCCGT 59.655 61.111 1.00 0.00 0.00 4.69
281 282 1.302033 CAAGCTGCTCACCTCCGTT 60.302 57.895 1.00 0.00 0.00 4.44
282 283 0.886490 CAAGCTGCTCACCTCCGTTT 60.886 55.000 1.00 0.00 0.00 3.60
283 284 0.886490 AAGCTGCTCACCTCCGTTTG 60.886 55.000 1.00 0.00 0.00 2.93
284 285 1.301716 GCTGCTCACCTCCGTTTGA 60.302 57.895 0.00 0.00 0.00 2.69
285 286 1.294659 GCTGCTCACCTCCGTTTGAG 61.295 60.000 0.00 0.00 41.96 3.02
287 288 4.285851 CTCACCTCCGTTTGAGCC 57.714 61.111 0.00 0.00 39.98 4.70
288 289 1.376037 CTCACCTCCGTTTGAGCCC 60.376 63.158 0.00 0.00 39.98 5.19
289 290 2.111999 CTCACCTCCGTTTGAGCCCA 62.112 60.000 0.00 0.00 39.98 5.36
291 292 2.747855 CCTCCGTTTGAGCCCAGC 60.748 66.667 0.00 0.00 39.98 4.85
292 293 2.348998 CTCCGTTTGAGCCCAGCT 59.651 61.111 0.00 0.00 43.88 4.24
305 306 4.007644 CAGCTCTGCCACCGGTGA 62.008 66.667 36.07 16.25 0.00 4.02
306 307 3.005539 AGCTCTGCCACCGGTGAT 61.006 61.111 36.07 3.78 0.00 3.06
307 308 2.045926 GCTCTGCCACCGGTGATT 60.046 61.111 36.07 0.00 0.00 2.57
308 309 1.220749 GCTCTGCCACCGGTGATTA 59.779 57.895 36.07 19.14 0.00 1.75
309 310 0.811616 GCTCTGCCACCGGTGATTAG 60.812 60.000 36.07 26.57 0.00 1.73
310 311 0.824109 CTCTGCCACCGGTGATTAGA 59.176 55.000 36.07 28.78 0.00 2.10
311 312 0.824109 TCTGCCACCGGTGATTAGAG 59.176 55.000 36.07 20.92 0.00 2.43
312 313 0.824109 CTGCCACCGGTGATTAGAGA 59.176 55.000 36.07 9.68 0.00 3.10
314 315 1.837439 TGCCACCGGTGATTAGAGATT 59.163 47.619 36.07 0.00 0.00 2.40
315 316 2.238646 TGCCACCGGTGATTAGAGATTT 59.761 45.455 36.07 0.00 0.00 2.17
316 317 3.279434 GCCACCGGTGATTAGAGATTTT 58.721 45.455 36.07 0.00 0.00 1.82
317 318 3.312697 GCCACCGGTGATTAGAGATTTTC 59.687 47.826 36.07 0.80 0.00 2.29
318 319 4.770795 CCACCGGTGATTAGAGATTTTCT 58.229 43.478 36.07 0.00 40.06 2.52
321 322 6.109359 CACCGGTGATTAGAGATTTTCTTCT 58.891 40.000 31.31 0.00 37.36 2.85
323 324 7.928706 CACCGGTGATTAGAGATTTTCTTCTAT 59.071 37.037 31.31 0.00 37.36 1.98
324 325 7.928706 ACCGGTGATTAGAGATTTTCTTCTATG 59.071 37.037 6.12 0.00 37.36 2.23
325 326 8.144478 CCGGTGATTAGAGATTTTCTTCTATGA 58.856 37.037 0.00 0.00 37.36 2.15
326 327 9.534565 CGGTGATTAGAGATTTTCTTCTATGAA 57.465 33.333 0.00 0.00 37.36 2.57
333 334 8.413899 AGAGATTTTCTTCTATGAAAGTACGC 57.586 34.615 0.00 0.00 37.27 4.42
334 335 7.492994 AGAGATTTTCTTCTATGAAAGTACGCC 59.507 37.037 0.00 0.00 37.27 5.68
335 336 5.773239 TTTTCTTCTATGAAAGTACGCCG 57.227 39.130 0.00 0.00 37.27 6.46
336 337 2.805845 TCTTCTATGAAAGTACGCCGC 58.194 47.619 0.00 0.00 0.00 6.53
337 338 1.859080 CTTCTATGAAAGTACGCCGCC 59.141 52.381 0.00 0.00 0.00 6.13
338 339 0.818938 TCTATGAAAGTACGCCGCCA 59.181 50.000 0.00 0.00 0.00 5.69
339 340 1.205179 TCTATGAAAGTACGCCGCCAA 59.795 47.619 0.00 0.00 0.00 4.52
340 341 1.593006 CTATGAAAGTACGCCGCCAAG 59.407 52.381 0.00 0.00 0.00 3.61
341 342 1.024579 ATGAAAGTACGCCGCCAAGG 61.025 55.000 0.00 0.00 44.97 3.61
353 354 2.812664 GCCAAGGGCTATTTCTGGG 58.187 57.895 0.00 0.00 46.69 4.45
354 355 1.395045 GCCAAGGGCTATTTCTGGGC 61.395 60.000 0.00 0.00 46.69 5.36
355 356 0.259938 CCAAGGGCTATTTCTGGGCT 59.740 55.000 0.00 0.00 0.00 5.19
356 357 1.685148 CAAGGGCTATTTCTGGGCTC 58.315 55.000 0.00 0.00 0.00 4.70
357 358 0.553333 AAGGGCTATTTCTGGGCTCC 59.447 55.000 0.00 0.00 0.00 4.70
358 359 0.327964 AGGGCTATTTCTGGGCTCCT 60.328 55.000 0.00 0.00 0.00 3.69
359 360 0.179006 GGGCTATTTCTGGGCTCCTG 60.179 60.000 0.00 0.00 0.00 3.86
361 362 0.821301 GCTATTTCTGGGCTCCTGGC 60.821 60.000 0.00 0.00 40.90 4.85
362 363 0.842635 CTATTTCTGGGCTCCTGGCT 59.157 55.000 0.00 0.00 41.46 4.75
363 364 0.548031 TATTTCTGGGCTCCTGGCTG 59.452 55.000 0.00 0.00 41.46 4.85
364 365 2.220786 ATTTCTGGGCTCCTGGCTGG 62.221 60.000 3.65 3.65 41.46 4.85
365 366 4.664267 TCTGGGCTCCTGGCTGGT 62.664 66.667 10.44 0.00 41.46 4.00
370 371 3.386237 GCTCCTGGCTGGTCTCGT 61.386 66.667 10.44 0.00 38.06 4.18
371 372 2.948720 GCTCCTGGCTGGTCTCGTT 61.949 63.158 10.44 0.00 38.06 3.85
372 373 1.674057 CTCCTGGCTGGTCTCGTTT 59.326 57.895 10.44 0.00 37.07 3.60
374 375 0.472471 TCCTGGCTGGTCTCGTTTTT 59.528 50.000 10.44 0.00 37.07 1.94
398 399 9.974980 TTTTGTATTCCCTGAACTAAAAATCAC 57.025 29.630 0.00 0.00 0.00 3.06
402 403 5.682943 TCCCTGAACTAAAAATCACAACG 57.317 39.130 0.00 0.00 0.00 4.10
403 404 5.369833 TCCCTGAACTAAAAATCACAACGA 58.630 37.500 0.00 0.00 0.00 3.85
404 405 5.468746 TCCCTGAACTAAAAATCACAACGAG 59.531 40.000 0.00 0.00 0.00 4.18
405 406 5.238650 CCCTGAACTAAAAATCACAACGAGT 59.761 40.000 0.00 0.00 0.00 4.18
406 407 6.425721 CCCTGAACTAAAAATCACAACGAGTA 59.574 38.462 0.00 0.00 0.00 2.59
407 408 7.041644 CCCTGAACTAAAAATCACAACGAGTAA 60.042 37.037 0.00 0.00 0.00 2.24
409 410 9.878599 CTGAACTAAAAATCACAACGAGTAAAT 57.121 29.630 0.00 0.00 0.00 1.40
410 411 9.872757 TGAACTAAAAATCACAACGAGTAAATC 57.127 29.630 0.00 0.00 0.00 2.17
430 3862 2.810274 TCGAAACGGAGGGAGTATATCG 59.190 50.000 0.00 0.00 0.00 2.92
454 3887 0.698238 TGAATAGGGTGCACTGCCTT 59.302 50.000 18.30 7.35 0.00 4.35
458 3896 1.127567 TAGGGTGCACTGCCTTCACT 61.128 55.000 18.30 0.00 0.00 3.41
460 3898 0.250727 GGGTGCACTGCCTTCACTAA 60.251 55.000 17.98 0.00 0.00 2.24
461 3899 1.604604 GGTGCACTGCCTTCACTAAA 58.395 50.000 17.98 0.00 0.00 1.85
531 3969 3.070734 TCTCTGCAGAAGCTTCTCACTTT 59.929 43.478 26.18 1.47 42.74 2.66
575 4027 8.204836 ACAGACCATACATAGTAATCTTTGACC 58.795 37.037 0.00 0.00 0.00 4.02
716 4201 1.128692 GAATTGAGTAGCACCACGCAC 59.871 52.381 0.00 0.00 46.13 5.34
757 4255 1.243342 CGGGCAGCCAAATTCAGTGA 61.243 55.000 15.19 0.00 0.00 3.41
796 4317 3.950794 TTGACCTGCGCCATCCGAC 62.951 63.158 4.18 0.00 40.02 4.79
800 4321 4.794439 CTGCGCCATCCGACGTCA 62.794 66.667 17.16 0.00 40.02 4.35
803 4324 4.794439 CGCCATCCGACGTCAGCA 62.794 66.667 17.16 0.00 40.02 4.41
804 4325 2.202932 GCCATCCGACGTCAGCAT 60.203 61.111 17.16 0.45 0.00 3.79
805 4326 2.240500 GCCATCCGACGTCAGCATC 61.241 63.158 17.16 0.00 0.00 3.91
1059 4652 2.093764 GCTTGACAGACTCCACTAGCAT 60.094 50.000 0.00 0.00 33.11 3.79
1307 4937 4.525949 GCGGAGTTCGGCCTACCC 62.526 72.222 0.00 2.12 39.69 3.69
1487 11569 0.391661 GACATCGCAAGGGAGCTTGA 60.392 55.000 0.00 0.00 36.50 3.02
1554 11636 8.944138 TCCCTCATCAGGTACAATCATAATAAA 58.056 33.333 0.00 0.00 38.30 1.40
1979 12165 1.002430 CCACTAGAGCTGACAAAGGCA 59.998 52.381 0.00 0.00 0.00 4.75
2204 12390 0.537371 CCCGCAAGAGGAAACAAGGT 60.537 55.000 0.00 0.00 43.02 3.50
2482 12668 0.910338 ACAGCTCATGATCCTGCAGT 59.090 50.000 13.81 9.39 0.00 4.40
2625 12811 2.028748 GCTGGTGGATGTGCTGAAAATT 60.029 45.455 0.00 0.00 0.00 1.82
2800 12993 3.593048 AGGCAAGGAGGGCTTTCA 58.407 55.556 0.00 0.00 41.46 2.69
3214 13497 8.040132 CAGAGTTGATAAGAGTTCAGAAAGGAT 58.960 37.037 0.00 0.00 0.00 3.24
3516 13806 5.000012 TGTTTTAAACGTGCTGGTTGATT 58.000 34.783 3.28 0.00 0.00 2.57
3602 13898 6.566197 ACTCAGTAAAATGAAAAGAGCCTG 57.434 37.500 0.00 0.00 0.00 4.85
3642 13938 8.322906 TGTTGTCATTAGAAAGAACCTACATG 57.677 34.615 0.00 0.00 0.00 3.21
3845 14142 5.633830 TGCTCTCCTTTTCATTTTGCTAG 57.366 39.130 0.00 0.00 0.00 3.42
3869 14166 7.256756 GCACTTGCTCATCAGAGTTAAATAT 57.743 36.000 0.00 0.00 44.00 1.28
3874 14171 6.291377 TGCTCATCAGAGTTAAATATGGGTC 58.709 40.000 0.00 0.00 44.00 4.46
3875 14172 6.126796 TGCTCATCAGAGTTAAATATGGGTCA 60.127 38.462 0.00 0.00 44.00 4.02
3877 14174 7.675161 TCATCAGAGTTAAATATGGGTCAGA 57.325 36.000 0.00 0.00 0.00 3.27
3880 14177 8.834465 CATCAGAGTTAAATATGGGTCAGAAAG 58.166 37.037 0.00 0.00 0.00 2.62
3883 14180 5.766590 AGTTAAATATGGGTCAGAAAGGGG 58.233 41.667 0.00 0.00 0.00 4.79
3884 14181 5.494706 AGTTAAATATGGGTCAGAAAGGGGA 59.505 40.000 0.00 0.00 0.00 4.81
3885 14182 4.526438 AAATATGGGTCAGAAAGGGGAG 57.474 45.455 0.00 0.00 0.00 4.30
3886 14183 1.893315 TATGGGTCAGAAAGGGGAGG 58.107 55.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.537371 AAGGGGCCAAGAAGTCGTTG 60.537 55.000 4.39 0.00 0.00 4.10
2 3 1.003233 CTAAGGGGCCAAGAAGTCGTT 59.997 52.381 4.39 0.00 0.00 3.85
4 5 0.613777 ACTAAGGGGCCAAGAAGTCG 59.386 55.000 4.39 0.00 0.00 4.18
5 6 2.881111 AACTAAGGGGCCAAGAAGTC 57.119 50.000 4.39 0.00 0.00 3.01
6 7 2.576648 CCTAACTAAGGGGCCAAGAAGT 59.423 50.000 4.39 0.00 42.32 3.01
7 8 2.844348 TCCTAACTAAGGGGCCAAGAAG 59.156 50.000 4.39 0.00 46.55 2.85
8 9 2.923908 TCCTAACTAAGGGGCCAAGAA 58.076 47.619 4.39 0.00 46.55 2.52
10 11 3.953542 AATCCTAACTAAGGGGCCAAG 57.046 47.619 4.39 1.52 46.55 3.61
11 12 4.685513 AAAATCCTAACTAAGGGGCCAA 57.314 40.909 4.39 0.00 46.55 4.52
12 13 4.685513 AAAAATCCTAACTAAGGGGCCA 57.314 40.909 4.39 0.00 46.55 5.36
37 38 7.608376 TGCGGCCTACATAGCAAAATTATATTA 59.392 33.333 0.00 0.00 36.60 0.98
38 39 6.432783 TGCGGCCTACATAGCAAAATTATATT 59.567 34.615 0.00 0.00 36.60 1.28
39 40 5.943416 TGCGGCCTACATAGCAAAATTATAT 59.057 36.000 0.00 0.00 36.60 0.86
40 41 5.309638 TGCGGCCTACATAGCAAAATTATA 58.690 37.500 0.00 0.00 36.60 0.98
41 42 4.141287 TGCGGCCTACATAGCAAAATTAT 58.859 39.130 0.00 0.00 36.60 1.28
42 43 3.546724 TGCGGCCTACATAGCAAAATTA 58.453 40.909 0.00 0.00 36.60 1.40
44 45 2.051334 TGCGGCCTACATAGCAAAAT 57.949 45.000 0.00 0.00 36.60 1.82
45 46 1.827681 TTGCGGCCTACATAGCAAAA 58.172 45.000 10.56 0.00 45.13 2.44
48 49 0.035915 TGTTTGCGGCCTACATAGCA 60.036 50.000 0.00 0.00 37.89 3.49
49 50 1.002468 CATGTTTGCGGCCTACATAGC 60.002 52.381 14.21 0.00 31.64 2.97
51 52 2.093181 AGACATGTTTGCGGCCTACATA 60.093 45.455 14.21 0.00 31.64 2.29
53 54 0.036164 AGACATGTTTGCGGCCTACA 59.964 50.000 0.00 6.71 0.00 2.74
54 55 2.018542 TAGACATGTTTGCGGCCTAC 57.981 50.000 0.00 0.00 0.00 3.18
56 57 2.128771 ATTAGACATGTTTGCGGCCT 57.871 45.000 0.00 0.00 0.00 5.19
57 58 5.631026 CATATATTAGACATGTTTGCGGCC 58.369 41.667 0.00 0.00 0.00 6.13
58 59 5.088739 GCATATATTAGACATGTTTGCGGC 58.911 41.667 0.00 0.00 0.00 6.53
60 61 6.239908 TGGCATATATTAGACATGTTTGCG 57.760 37.500 0.00 0.00 0.00 4.85
61 62 7.651808 ACTTGGCATATATTAGACATGTTTGC 58.348 34.615 0.00 0.20 0.00 3.68
65 66 7.651808 GCAAACTTGGCATATATTAGACATGT 58.348 34.615 0.00 0.00 0.00 3.21
82 83 2.661195 CGGCTAAAATTCGGCAAACTTG 59.339 45.455 0.00 0.00 0.00 3.16
84 85 2.156098 TCGGCTAAAATTCGGCAAACT 58.844 42.857 0.00 0.00 0.00 2.66
85 86 2.095415 ACTCGGCTAAAATTCGGCAAAC 60.095 45.455 0.00 0.00 0.00 2.93
86 87 2.156098 ACTCGGCTAAAATTCGGCAAA 58.844 42.857 0.00 0.00 0.00 3.68
87 88 1.816074 ACTCGGCTAAAATTCGGCAA 58.184 45.000 0.00 0.00 0.00 4.52
88 89 1.816074 AACTCGGCTAAAATTCGGCA 58.184 45.000 0.00 0.00 0.00 5.69
89 90 2.913777 AAACTCGGCTAAAATTCGGC 57.086 45.000 0.00 0.00 0.00 5.54
90 91 4.279659 GCATAAACTCGGCTAAAATTCGG 58.720 43.478 0.00 0.00 0.00 4.30
91 92 3.960002 CGCATAAACTCGGCTAAAATTCG 59.040 43.478 0.00 0.00 0.00 3.34
94 95 4.634443 AGTTCGCATAAACTCGGCTAAAAT 59.366 37.500 0.00 0.00 34.37 1.82
95 96 3.998341 AGTTCGCATAAACTCGGCTAAAA 59.002 39.130 0.00 0.00 34.37 1.52
96 97 3.592059 AGTTCGCATAAACTCGGCTAAA 58.408 40.909 0.00 0.00 34.37 1.85
98 99 2.953466 AGTTCGCATAAACTCGGCTA 57.047 45.000 0.00 0.00 34.37 3.93
99 100 2.000447 GAAGTTCGCATAAACTCGGCT 59.000 47.619 0.00 0.00 38.52 5.52
100 101 1.266891 CGAAGTTCGCATAAACTCGGC 60.267 52.381 13.08 0.00 38.52 5.54
112 113 1.068474 AACTCATTCGGCGAAGTTCG 58.932 50.000 27.35 20.87 43.89 3.95
113 114 3.537793 AAAACTCATTCGGCGAAGTTC 57.462 42.857 27.35 0.00 0.00 3.01
114 115 3.982576 AAAAACTCATTCGGCGAAGTT 57.017 38.095 27.35 21.87 0.00 2.66
142 143 1.677820 CCCCGGACAGCGTCTATTTTT 60.678 52.381 0.73 0.00 32.47 1.94
143 144 0.107848 CCCCGGACAGCGTCTATTTT 60.108 55.000 0.73 0.00 32.47 1.82
144 145 1.520666 CCCCGGACAGCGTCTATTT 59.479 57.895 0.73 0.00 32.47 1.40
145 146 3.090219 GCCCCGGACAGCGTCTATT 62.090 63.158 0.73 0.00 32.47 1.73
146 147 3.537874 GCCCCGGACAGCGTCTAT 61.538 66.667 0.73 0.00 32.47 1.98
170 171 4.754667 GTTCCCAGTCGCCGACCC 62.755 72.222 14.60 0.00 32.18 4.46
171 172 4.754667 GGTTCCCAGTCGCCGACC 62.755 72.222 14.60 0.00 32.18 4.79
172 173 3.524648 TTGGTTCCCAGTCGCCGAC 62.525 63.158 9.71 9.71 33.81 4.79
174 175 3.047877 GTTGGTTCCCAGTCGCCG 61.048 66.667 0.00 0.00 33.81 6.46
175 176 1.671379 GAGTTGGTTCCCAGTCGCC 60.671 63.158 0.00 0.00 33.81 5.54
176 177 2.027625 CGAGTTGGTTCCCAGTCGC 61.028 63.158 7.12 0.00 35.89 5.19
177 178 2.027625 GCGAGTTGGTTCCCAGTCG 61.028 63.158 13.48 13.48 41.59 4.18
178 179 1.671379 GGCGAGTTGGTTCCCAGTC 60.671 63.158 0.00 0.00 33.81 3.51
179 180 2.113243 GAGGCGAGTTGGTTCCCAGT 62.113 60.000 0.00 0.00 33.81 4.00
181 182 2.747686 GAGGCGAGTTGGTTCCCA 59.252 61.111 0.00 0.00 0.00 4.37
182 183 2.046217 GGAGGCGAGTTGGTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
183 184 1.376037 CTGGAGGCGAGTTGGTTCC 60.376 63.158 0.00 0.00 0.00 3.62
184 185 1.376037 CCTGGAGGCGAGTTGGTTC 60.376 63.158 0.00 0.00 0.00 3.62
185 186 2.750350 CCTGGAGGCGAGTTGGTT 59.250 61.111 0.00 0.00 0.00 3.67
195 196 0.684479 GCTAAAAAGGGGCCTGGAGG 60.684 60.000 0.84 0.00 38.53 4.30
197 198 1.001393 CGCTAAAAAGGGGCCTGGA 60.001 57.895 0.84 0.00 0.00 3.86
199 200 2.885113 GCGCTAAAAAGGGGCCTG 59.115 61.111 0.84 0.00 36.79 4.85
202 203 3.822192 CCGGCGCTAAAAAGGGGC 61.822 66.667 7.64 6.02 42.42 5.80
203 204 3.822192 GCCGGCGCTAAAAAGGGG 61.822 66.667 12.58 0.00 0.00 4.79
228 229 3.805267 GAGCATCTCCAGCCGTTG 58.195 61.111 0.00 0.00 0.00 4.10
239 240 0.659957 CCCGCAAAGCTAAGAGCATC 59.340 55.000 0.64 0.00 45.56 3.91
241 242 0.391661 CTCCCGCAAAGCTAAGAGCA 60.392 55.000 0.64 0.00 45.56 4.26
244 245 1.447838 CGCTCCCGCAAAGCTAAGA 60.448 57.895 0.00 0.00 37.62 2.10
245 246 3.093278 CGCTCCCGCAAAGCTAAG 58.907 61.111 0.00 0.00 37.62 2.18
262 263 3.123620 CGGAGGTGAGCAGCTTGC 61.124 66.667 0.00 0.47 45.46 4.01
263 264 0.886490 AAACGGAGGTGAGCAGCTTG 60.886 55.000 0.00 2.99 39.57 4.01
264 265 0.886490 CAAACGGAGGTGAGCAGCTT 60.886 55.000 0.00 0.00 39.57 3.74
267 268 2.832931 CTCAAACGGAGGTGAGCAG 58.167 57.895 0.00 0.00 40.13 4.24
270 271 1.376037 GGGCTCAAACGGAGGTGAG 60.376 63.158 0.00 0.00 44.22 3.51
273 274 2.750350 CTGGGCTCAAACGGAGGT 59.250 61.111 0.00 0.00 44.22 3.85
288 289 2.809861 AATCACCGGTGGCAGAGCTG 62.810 60.000 33.40 5.60 0.00 4.24
289 290 1.264749 TAATCACCGGTGGCAGAGCT 61.265 55.000 33.40 12.81 0.00 4.09
291 292 0.824109 TCTAATCACCGGTGGCAGAG 59.176 55.000 33.40 23.35 0.00 3.35
292 293 0.824109 CTCTAATCACCGGTGGCAGA 59.176 55.000 33.40 27.38 0.00 4.26
293 294 0.824109 TCTCTAATCACCGGTGGCAG 59.176 55.000 33.40 25.11 0.00 4.85
294 295 1.496060 ATCTCTAATCACCGGTGGCA 58.504 50.000 33.40 16.87 0.00 4.92
298 299 6.301169 AGAAGAAAATCTCTAATCACCGGT 57.699 37.500 0.00 0.00 32.46 5.28
299 300 8.144478 TCATAGAAGAAAATCTCTAATCACCGG 58.856 37.037 0.00 0.00 32.46 5.28
300 301 9.534565 TTCATAGAAGAAAATCTCTAATCACCG 57.465 33.333 0.00 0.00 32.46 4.94
307 308 9.517609 GCGTACTTTCATAGAAGAAAATCTCTA 57.482 33.333 0.00 0.00 37.09 2.43
308 309 7.492994 GGCGTACTTTCATAGAAGAAAATCTCT 59.507 37.037 0.00 0.00 37.09 3.10
309 310 7.515371 CGGCGTACTTTCATAGAAGAAAATCTC 60.515 40.741 0.00 0.00 37.09 2.75
310 311 6.255887 CGGCGTACTTTCATAGAAGAAAATCT 59.744 38.462 0.00 0.00 37.09 2.40
311 312 6.411652 CGGCGTACTTTCATAGAAGAAAATC 58.588 40.000 0.00 0.00 37.09 2.17
312 313 5.220605 GCGGCGTACTTTCATAGAAGAAAAT 60.221 40.000 9.37 0.00 37.09 1.82
314 315 3.615496 GCGGCGTACTTTCATAGAAGAAA 59.385 43.478 9.37 0.00 36.21 2.52
315 316 3.184541 GCGGCGTACTTTCATAGAAGAA 58.815 45.455 9.37 0.00 0.00 2.52
316 317 2.480759 GGCGGCGTACTTTCATAGAAGA 60.481 50.000 9.37 0.00 0.00 2.87
317 318 1.859080 GGCGGCGTACTTTCATAGAAG 59.141 52.381 9.37 0.00 0.00 2.85
318 319 1.205179 TGGCGGCGTACTTTCATAGAA 59.795 47.619 9.37 0.00 0.00 2.10
321 322 1.647346 CTTGGCGGCGTACTTTCATA 58.353 50.000 9.37 0.00 0.00 2.15
323 324 1.669760 CCTTGGCGGCGTACTTTCA 60.670 57.895 9.37 0.00 0.00 2.69
324 325 2.396157 CCCTTGGCGGCGTACTTTC 61.396 63.158 9.37 0.00 0.00 2.62
325 326 2.359478 CCCTTGGCGGCGTACTTT 60.359 61.111 9.37 0.00 0.00 2.66
336 337 0.259938 AGCCCAGAAATAGCCCTTGG 59.740 55.000 0.00 0.00 0.00 3.61
337 338 1.685148 GAGCCCAGAAATAGCCCTTG 58.315 55.000 0.00 0.00 0.00 3.61
338 339 0.553333 GGAGCCCAGAAATAGCCCTT 59.447 55.000 0.00 0.00 0.00 3.95
339 340 0.327964 AGGAGCCCAGAAATAGCCCT 60.328 55.000 0.00 0.00 0.00 5.19
340 341 0.179006 CAGGAGCCCAGAAATAGCCC 60.179 60.000 0.00 0.00 0.00 5.19
341 342 0.179006 CCAGGAGCCCAGAAATAGCC 60.179 60.000 0.00 0.00 0.00 3.93
343 344 0.842635 AGCCAGGAGCCCAGAAATAG 59.157 55.000 0.00 0.00 45.47 1.73
344 345 0.548031 CAGCCAGGAGCCCAGAAATA 59.452 55.000 0.00 0.00 45.47 1.40
345 346 1.305623 CAGCCAGGAGCCCAGAAAT 59.694 57.895 0.00 0.00 45.47 2.17
347 348 3.333219 CCAGCCAGGAGCCCAGAA 61.333 66.667 0.00 0.00 45.47 3.02
348 349 4.664267 ACCAGCCAGGAGCCCAGA 62.664 66.667 0.00 0.00 45.47 3.86
350 351 4.664267 AGACCAGCCAGGAGCCCA 62.664 66.667 0.00 0.00 45.47 5.36
352 353 4.154347 CGAGACCAGCCAGGAGCC 62.154 72.222 0.00 0.00 45.47 4.70
353 354 2.456287 AAACGAGACCAGCCAGGAGC 62.456 60.000 0.00 0.00 41.22 4.70
354 355 0.035458 AAAACGAGACCAGCCAGGAG 59.965 55.000 0.00 0.00 41.22 3.69
355 356 0.472471 AAAAACGAGACCAGCCAGGA 59.528 50.000 0.00 0.00 41.22 3.86
356 357 3.021451 AAAAACGAGACCAGCCAGG 57.979 52.632 0.00 0.00 45.67 4.45
372 373 9.974980 GTGATTTTTAGTTCAGGGAATACAAAA 57.025 29.630 0.00 0.00 0.00 2.44
374 375 8.698973 TGTGATTTTTAGTTCAGGGAATACAA 57.301 30.769 0.00 0.00 0.00 2.41
375 376 8.573035 GTTGTGATTTTTAGTTCAGGGAATACA 58.427 33.333 0.00 0.00 0.00 2.29
376 377 7.749126 CGTTGTGATTTTTAGTTCAGGGAATAC 59.251 37.037 0.00 0.00 0.00 1.89
377 378 7.662258 TCGTTGTGATTTTTAGTTCAGGGAATA 59.338 33.333 0.00 0.00 0.00 1.75
378 379 6.488683 TCGTTGTGATTTTTAGTTCAGGGAAT 59.511 34.615 0.00 0.00 0.00 3.01
379 380 5.823570 TCGTTGTGATTTTTAGTTCAGGGAA 59.176 36.000 0.00 0.00 0.00 3.97
380 381 5.369833 TCGTTGTGATTTTTAGTTCAGGGA 58.630 37.500 0.00 0.00 0.00 4.20
381 382 5.238650 ACTCGTTGTGATTTTTAGTTCAGGG 59.761 40.000 0.00 0.00 0.00 4.45
383 384 9.878599 ATTTACTCGTTGTGATTTTTAGTTCAG 57.121 29.630 0.00 0.00 0.00 3.02
384 385 9.872757 GATTTACTCGTTGTGATTTTTAGTTCA 57.127 29.630 0.00 0.00 0.00 3.18
385 386 9.037417 CGATTTACTCGTTGTGATTTTTAGTTC 57.963 33.333 0.00 0.00 42.56 3.01
386 387 8.928844 CGATTTACTCGTTGTGATTTTTAGTT 57.071 30.769 0.00 0.00 42.56 2.24
402 403 3.119209 ACTCCCTCCGTTTCGATTTACTC 60.119 47.826 0.00 0.00 0.00 2.59
403 404 2.830321 ACTCCCTCCGTTTCGATTTACT 59.170 45.455 0.00 0.00 0.00 2.24
404 405 3.242549 ACTCCCTCCGTTTCGATTTAC 57.757 47.619 0.00 0.00 0.00 2.01
405 406 6.348786 CGATATACTCCCTCCGTTTCGATTTA 60.349 42.308 0.00 0.00 0.00 1.40
406 407 5.564259 CGATATACTCCCTCCGTTTCGATTT 60.564 44.000 0.00 0.00 0.00 2.17
407 408 4.082895 CGATATACTCCCTCCGTTTCGATT 60.083 45.833 0.00 0.00 0.00 3.34
409 410 2.810274 CGATATACTCCCTCCGTTTCGA 59.190 50.000 0.00 0.00 0.00 3.71
410 411 2.095364 CCGATATACTCCCTCCGTTTCG 60.095 54.545 0.00 0.00 0.00 3.46
412 413 2.626743 CACCGATATACTCCCTCCGTTT 59.373 50.000 0.00 0.00 0.00 3.60
413 414 2.236766 CACCGATATACTCCCTCCGTT 58.763 52.381 0.00 0.00 0.00 4.44
414 415 1.144503 ACACCGATATACTCCCTCCGT 59.855 52.381 0.00 0.00 0.00 4.69
415 416 1.906990 ACACCGATATACTCCCTCCG 58.093 55.000 0.00 0.00 0.00 4.63
416 417 3.228453 TCAACACCGATATACTCCCTCC 58.772 50.000 0.00 0.00 0.00 4.30
418 419 5.480772 CCTATTCAACACCGATATACTCCCT 59.519 44.000 0.00 0.00 0.00 4.20
419 420 5.337330 CCCTATTCAACACCGATATACTCCC 60.337 48.000 0.00 0.00 0.00 4.30
430 3862 1.812571 CAGTGCACCCTATTCAACACC 59.187 52.381 14.63 0.00 0.00 4.16
454 3887 4.215399 CCATTTTTGGAGCGACTTTAGTGA 59.785 41.667 0.00 0.00 0.00 3.41
458 3896 4.394729 AGTCCATTTTTGGAGCGACTTTA 58.605 39.130 0.00 0.00 38.88 1.85
460 3898 2.863809 AGTCCATTTTTGGAGCGACTT 58.136 42.857 0.00 0.00 38.88 3.01
461 3899 2.554032 CAAGTCCATTTTTGGAGCGACT 59.446 45.455 0.00 0.00 38.88 4.18
531 3969 2.768527 CTGTATCCTCTCAGGCCTTTGA 59.231 50.000 0.00 2.92 34.61 2.69
689 4163 3.244526 TGGTGCTACTCAATTCTCAAGCA 60.245 43.478 0.00 0.00 37.62 3.91
716 4201 1.655484 TGATGCTGACTTGCCGTATG 58.345 50.000 0.00 0.00 0.00 2.39
757 4255 1.009829 GAAGAGCACGCCATTCGATT 58.990 50.000 0.00 0.00 41.67 3.34
796 4317 1.592669 GGTCCGGATGATGCTGACG 60.593 63.158 7.81 0.00 0.00 4.35
800 4321 4.241555 GGCGGTCCGGATGATGCT 62.242 66.667 14.38 0.00 0.00 3.79
802 4323 2.280389 CAGGCGGTCCGGATGATG 60.280 66.667 14.38 2.76 37.47 3.07
803 4324 3.550431 CCAGGCGGTCCGGATGAT 61.550 66.667 14.38 0.00 37.47 2.45
804 4325 4.770362 TCCAGGCGGTCCGGATGA 62.770 66.667 14.38 0.00 37.47 2.92
805 4326 4.530857 GTCCAGGCGGTCCGGATG 62.531 72.222 14.38 4.58 37.38 3.51
1059 4652 0.252761 TCATGGCTGATCGGCTGAAA 59.747 50.000 25.27 9.91 39.32 2.69
1155 4757 1.055849 CGGTCATGGGGATGGTATGA 58.944 55.000 0.00 0.00 0.00 2.15
1307 4937 4.796231 CGAGGTTCTCGCACCCGG 62.796 72.222 4.36 0.00 46.75 5.73
1508 11590 0.883833 CGAGAAGCCACAAAAGCCAT 59.116 50.000 0.00 0.00 0.00 4.40
1713 11883 8.575649 TCATCACACAAACTAGTACTCAGATA 57.424 34.615 0.00 0.00 0.00 1.98
1979 12165 7.176515 GGAATACAAAAATTTCCAGGGCATTTT 59.823 33.333 0.00 4.42 39.00 1.82
2204 12390 2.815503 CACTGTGCTTCATCCATTGACA 59.184 45.455 0.00 0.00 32.84 3.58
2482 12668 0.988832 AATCCTCCAACGGCTTGGTA 59.011 50.000 13.15 4.21 46.56 3.25
2625 12811 0.178876 TCACTCCAACCTCCATCCCA 60.179 55.000 0.00 0.00 0.00 4.37
2800 12993 4.030913 TCATACGAAGAACCTCCCTCATT 58.969 43.478 0.00 0.00 0.00 2.57
3516 13806 5.819991 AGATTGATTTTGGCAACTAGGAGA 58.180 37.500 0.00 0.00 37.61 3.71
3589 13879 8.947115 GTTATTTGTACTACAGGCTCTTTTCAT 58.053 33.333 0.00 0.00 0.00 2.57
3590 13880 7.389607 GGTTATTTGTACTACAGGCTCTTTTCA 59.610 37.037 0.00 0.00 0.00 2.69
3591 13881 7.606839 AGGTTATTTGTACTACAGGCTCTTTTC 59.393 37.037 0.00 0.00 0.00 2.29
3592 13882 7.390718 CAGGTTATTTGTACTACAGGCTCTTTT 59.609 37.037 0.00 0.00 0.00 2.27
3593 13883 6.879458 CAGGTTATTTGTACTACAGGCTCTTT 59.121 38.462 0.00 0.00 0.00 2.52
3683 13979 2.057922 CCCCACCAGTGAGCCTAATAT 58.942 52.381 0.00 0.00 0.00 1.28
3845 14142 5.557891 ATTTAACTCTGATGAGCAAGTGC 57.442 39.130 0.00 0.00 43.85 4.40
3869 14166 0.104144 TTCCTCCCCTTTCTGACCCA 60.104 55.000 0.00 0.00 0.00 4.51
3874 14171 7.179160 AGTTTATTTCATTTCCTCCCCTTTCTG 59.821 37.037 0.00 0.00 0.00 3.02
3875 14172 7.179160 CAGTTTATTTCATTTCCTCCCCTTTCT 59.821 37.037 0.00 0.00 0.00 2.52
3877 14174 6.787458 ACAGTTTATTTCATTTCCTCCCCTTT 59.213 34.615 0.00 0.00 0.00 3.11
3880 14177 7.684428 GCATACAGTTTATTTCATTTCCTCCCC 60.684 40.741 0.00 0.00 0.00 4.81
3883 14180 8.243426 TGTGCATACAGTTTATTTCATTTCCTC 58.757 33.333 0.00 0.00 31.91 3.71
3884 14181 8.121305 TGTGCATACAGTTTATTTCATTTCCT 57.879 30.769 0.00 0.00 31.91 3.36
3885 14182 8.931385 ATGTGCATACAGTTTATTTCATTTCC 57.069 30.769 0.00 0.00 40.79 3.13


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

AutoCloner maintained by Alex Coulton.