Multiple sequence alignment - TraesCS7A01G050300

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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 TraesCS7A01G050300 chr7A 100.000 4330 0 0 1 4330 23385185 23389514 0.000000e+00 7997.0
1 TraesCS7A01G050300 chr7A 96.154 2834 69 17 742 3544 23523720 23520896 0.000000e+00 4593.0
2 TraesCS7A01G050300 chr7A 100.000 30 0 0 3542 3571 23357128 23357157 6.050000e-04 56.5
3 TraesCS7A01G050300 chr4A 94.011 3590 160 22 769 4330 706839017 706835455 0.000000e+00 5387.0
4 TraesCS7A01G050300 chr4A 95.452 2133 80 7 984 3106 706706705 706708830 0.000000e+00 3386.0
5 TraesCS7A01G050300 chr7D 94.067 3118 111 34 721 3790 22943616 22946707 0.000000e+00 4665.0
6 TraesCS7A01G050300 chr7D 95.384 2816 102 12 989 3788 22974907 22972104 0.000000e+00 4455.0
7 TraesCS7A01G050300 chr7D 83.692 2465 309 53 1111 3538 22904421 22906829 0.000000e+00 2239.0
8 TraesCS7A01G050300 chr7D 95.652 276 8 1 4055 4330 22946715 22946986 1.430000e-119 440.0
9 TraesCS7A01G050300 chr7D 93.478 276 14 1 4055 4330 22972094 22971823 1.450000e-109 407.0
10 TraesCS7A01G050300 chr7D 86.385 213 10 6 755 955 22975098 22974893 9.430000e-52 215.0
11 TraesCS7A01G050300 chrUn 93.995 2631 99 24 989 3584 89917659 89915053 0.000000e+00 3928.0
12 TraesCS7A01G050300 chrUn 93.995 2631 99 24 989 3584 89979649 89982255 0.000000e+00 3928.0
13 TraesCS7A01G050300 chrUn 86.385 213 10 6 755 955 89917850 89917645 9.430000e-52 215.0
14 TraesCS7A01G050300 chrUn 86.111 216 11 6 752 955 89979455 89979663 9.430000e-52 215.0
15 TraesCS7A01G050300 chr5D 91.676 1742 103 21 904 2620 361184199 361182475 0.000000e+00 2375.0
16 TraesCS7A01G050300 chr5D 83.725 510 50 19 389 867 361185285 361184778 6.600000e-123 451.0
17 TraesCS7A01G050300 chr5A 84.567 2242 275 43 1091 3311 41966817 41969008 0.000000e+00 2158.0
18 TraesCS7A01G050300 chr5A 89.119 386 38 4 3 385 458271997 458272381 1.090000e-130 477.0
19 TraesCS7A01G050300 chr5A 88.191 398 40 5 1 396 641735932 641735540 6.560000e-128 468.0
20 TraesCS7A01G050300 chr3D 90.814 381 28 4 3 382 586036787 586036413 1.800000e-138 503.0
21 TraesCS7A01G050300 chr6B 90.130 385 31 6 1 382 64169181 64169561 1.080000e-135 494.0
22 TraesCS7A01G050300 chr6B 89.583 384 37 3 1 381 8444369 8444752 6.510000e-133 484.0
23 TraesCS7A01G050300 chr2D 89.817 383 37 2 1 382 124475108 124474727 1.400000e-134 490.0
24 TraesCS7A01G050300 chr2B 89.791 382 38 1 2 382 771922398 771922779 5.030000e-134 488.0
25 TraesCS7A01G050300 chr1B 89.583 384 37 3 1 382 684914704 684914322 6.510000e-133 484.0
26 TraesCS7A01G050300 chr4D 89.062 384 40 2 1 383 447286114 447285732 3.920000e-130 475.0


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 TraesCS7A01G050300 chr7A 23385185 23389514 4329 False 7997.000000 7997 100.0000 1 4330 1 chr7A.!!$F2 4329
1 TraesCS7A01G050300 chr7A 23520896 23523720 2824 True 4593.000000 4593 96.1540 742 3544 1 chr7A.!!$R1 2802
2 TraesCS7A01G050300 chr4A 706835455 706839017 3562 True 5387.000000 5387 94.0110 769 4330 1 chr4A.!!$R1 3561
3 TraesCS7A01G050300 chr4A 706706705 706708830 2125 False 3386.000000 3386 95.4520 984 3106 1 chr4A.!!$F1 2122
4 TraesCS7A01G050300 chr7D 22943616 22946986 3370 False 2552.500000 4665 94.8595 721 4330 2 chr7D.!!$F2 3609
5 TraesCS7A01G050300 chr7D 22904421 22906829 2408 False 2239.000000 2239 83.6920 1111 3538 1 chr7D.!!$F1 2427
6 TraesCS7A01G050300 chr7D 22971823 22975098 3275 True 1692.333333 4455 91.7490 755 4330 3 chr7D.!!$R1 3575
7 TraesCS7A01G050300 chrUn 89915053 89917850 2797 True 2071.500000 3928 90.1900 755 3584 2 chrUn.!!$R1 2829
8 TraesCS7A01G050300 chrUn 89979455 89982255 2800 False 2071.500000 3928 90.0530 752 3584 2 chrUn.!!$F1 2832
9 TraesCS7A01G050300 chr5D 361182475 361185285 2810 True 1413.000000 2375 87.7005 389 2620 2 chr5D.!!$R1 2231
10 TraesCS7A01G050300 chr5A 41966817 41969008 2191 False 2158.000000 2158 84.5670 1091 3311 1 chr5A.!!$F1 2220

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
370 371 0.251165 GGGGTGCAGGTGCTCTAAAA 60.251 55.000 3.18 0.00 42.66 1.52 F
733 770 0.319641 GGGGAACGAGTATGATCGGC 60.320 60.000 6.38 0.00 46.91 5.54 F
883 934 1.916506 ATCAGCTGCGCTAGATAGGA 58.083 50.000 9.47 0.00 36.40 2.94 F
966 1590 2.028130 TCAGAAGATCGCTCCTCTTCC 58.972 52.381 13.14 1.25 46.39 3.46 F
968 1592 2.034558 CAGAAGATCGCTCCTCTTCCTC 59.965 54.545 13.14 0.00 46.39 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 3042 0.439985 CAGACATGTCAAAGCGGACG 59.560 55.0 27.02 1.02 40.72 4.79 R
2729 3413 0.107703 CGGCCATTCCAGCTAACAGA 60.108 55.0 2.24 0.00 34.01 3.41 R
2734 3418 1.909459 TTCTGCGGCCATTCCAGCTA 61.909 55.0 2.24 0.00 36.05 3.32 R
2832 3516 5.986135 GGTAAATATGTCGATCAGCAGAGTT 59.014 40.0 0.00 0.00 0.00 3.01 R
3523 4255 7.419711 AGAGGTTCGATCAAGGAAGTATAAA 57.580 36.0 0.00 0.00 0.00 1.40 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
33 34 9.739276 TTTGTTTCTTCCACATAGAACATATCT 57.261 29.630 0.00 0.00 42.48 1.98
34 35 9.739276 TTGTTTCTTCCACATAGAACATATCTT 57.261 29.630 0.00 0.00 39.71 2.40
35 36 9.166173 TGTTTCTTCCACATAGAACATATCTTG 57.834 33.333 0.00 0.00 39.71 3.02
36 37 9.383519 GTTTCTTCCACATAGAACATATCTTGA 57.616 33.333 0.00 0.00 39.71 3.02
37 38 9.958180 TTTCTTCCACATAGAACATATCTTGAA 57.042 29.630 0.00 0.00 39.71 2.69
38 39 9.605275 TTCTTCCACATAGAACATATCTTGAAG 57.395 33.333 0.00 0.00 39.71 3.02
39 40 8.762645 TCTTCCACATAGAACATATCTTGAAGT 58.237 33.333 0.00 0.00 39.71 3.01
40 41 9.388506 CTTCCACATAGAACATATCTTGAAGTT 57.611 33.333 0.00 0.00 39.71 2.66
41 42 9.739276 TTCCACATAGAACATATCTTGAAGTTT 57.261 29.630 0.00 0.00 39.71 2.66
55 56 7.072177 TCTTGAAGTTTAAATCTATGCACCG 57.928 36.000 0.00 0.00 0.00 4.94
56 57 6.653320 TCTTGAAGTTTAAATCTATGCACCGT 59.347 34.615 0.00 0.00 0.00 4.83
57 58 6.176975 TGAAGTTTAAATCTATGCACCGTG 57.823 37.500 0.00 0.00 0.00 4.94
58 59 5.123186 TGAAGTTTAAATCTATGCACCGTGG 59.877 40.000 0.00 0.00 0.00 4.94
59 60 4.585879 AGTTTAAATCTATGCACCGTGGT 58.414 39.130 0.00 0.00 0.00 4.16
60 61 5.736813 AGTTTAAATCTATGCACCGTGGTA 58.263 37.500 0.00 0.00 0.00 3.25
61 62 6.174760 AGTTTAAATCTATGCACCGTGGTAA 58.825 36.000 0.00 0.00 0.00 2.85
62 63 6.655848 AGTTTAAATCTATGCACCGTGGTAAA 59.344 34.615 0.00 0.00 0.00 2.01
63 64 4.957759 AAATCTATGCACCGTGGTAAAC 57.042 40.909 0.00 0.00 0.00 2.01
64 65 2.389962 TCTATGCACCGTGGTAAACC 57.610 50.000 0.00 0.00 0.00 3.27
65 66 1.903860 TCTATGCACCGTGGTAAACCT 59.096 47.619 0.00 0.00 36.82 3.50
66 67 2.303600 TCTATGCACCGTGGTAAACCTT 59.696 45.455 0.00 0.00 36.82 3.50
67 68 1.989706 ATGCACCGTGGTAAACCTTT 58.010 45.000 0.00 0.00 36.82 3.11
68 69 1.310904 TGCACCGTGGTAAACCTTTC 58.689 50.000 0.00 0.00 36.82 2.62
69 70 1.134037 TGCACCGTGGTAAACCTTTCT 60.134 47.619 0.00 0.00 36.82 2.52
70 71 2.104451 TGCACCGTGGTAAACCTTTCTA 59.896 45.455 0.00 0.00 36.82 2.10
71 72 3.140623 GCACCGTGGTAAACCTTTCTAA 58.859 45.455 0.00 0.00 36.82 2.10
72 73 3.058708 GCACCGTGGTAAACCTTTCTAAC 60.059 47.826 0.00 0.00 36.82 2.34
73 74 4.383173 CACCGTGGTAAACCTTTCTAACT 58.617 43.478 0.02 0.00 36.82 2.24
74 75 5.540911 CACCGTGGTAAACCTTTCTAACTA 58.459 41.667 0.02 0.00 36.82 2.24
75 76 5.636543 CACCGTGGTAAACCTTTCTAACTAG 59.363 44.000 0.02 0.00 36.82 2.57
76 77 5.539955 ACCGTGGTAAACCTTTCTAACTAGA 59.460 40.000 0.00 0.00 36.82 2.43
77 78 6.041979 ACCGTGGTAAACCTTTCTAACTAGAA 59.958 38.462 0.00 0.00 40.33 2.10
78 79 7.101700 CCGTGGTAAACCTTTCTAACTAGAAT 58.898 38.462 0.00 0.00 41.52 2.40
79 80 7.277319 CCGTGGTAAACCTTTCTAACTAGAATC 59.723 40.741 0.00 0.00 41.52 2.52
80 81 8.033626 CGTGGTAAACCTTTCTAACTAGAATCT 58.966 37.037 0.00 0.00 41.52 2.40
206 207 9.534565 TTCTGAAAGATTTATCCTAGATTGTCG 57.465 33.333 0.00 0.00 46.36 4.35
207 208 8.696374 TCTGAAAGATTTATCCTAGATTGTCGT 58.304 33.333 0.00 0.00 38.67 4.34
208 209 9.319143 CTGAAAGATTTATCCTAGATTGTCGTT 57.681 33.333 0.00 0.00 34.07 3.85
215 216 8.644318 TTTATCCTAGATTGTCGTTAGAAAGC 57.356 34.615 0.00 0.00 0.00 3.51
216 217 5.916661 TCCTAGATTGTCGTTAGAAAGCT 57.083 39.130 0.00 0.00 0.00 3.74
217 218 6.282199 TCCTAGATTGTCGTTAGAAAGCTT 57.718 37.500 0.00 0.00 0.00 3.74
218 219 6.698380 TCCTAGATTGTCGTTAGAAAGCTTT 58.302 36.000 12.53 12.53 0.00 3.51
219 220 6.590292 TCCTAGATTGTCGTTAGAAAGCTTTG 59.410 38.462 18.30 1.32 0.00 2.77
220 221 5.035784 AGATTGTCGTTAGAAAGCTTTGC 57.964 39.130 18.30 8.41 0.00 3.68
221 222 4.757149 AGATTGTCGTTAGAAAGCTTTGCT 59.243 37.500 18.30 15.16 42.56 3.91
222 223 5.932303 AGATTGTCGTTAGAAAGCTTTGCTA 59.068 36.000 18.30 14.18 38.25 3.49
223 224 4.985044 TGTCGTTAGAAAGCTTTGCTAC 57.015 40.909 18.30 9.91 38.25 3.58
224 225 3.427528 TGTCGTTAGAAAGCTTTGCTACG 59.572 43.478 18.30 20.30 38.25 3.51
225 226 2.410730 TCGTTAGAAAGCTTTGCTACGC 59.589 45.455 18.30 11.23 38.25 4.42
226 227 2.412089 CGTTAGAAAGCTTTGCTACGCT 59.588 45.455 18.30 8.71 38.25 5.07
227 228 3.722082 CGTTAGAAAGCTTTGCTACGCTG 60.722 47.826 18.30 4.47 38.25 5.18
228 229 0.519077 AGAAAGCTTTGCTACGCTGC 59.481 50.000 18.30 0.00 38.25 5.25
229 230 0.455126 GAAAGCTTTGCTACGCTGCC 60.455 55.000 18.30 0.00 38.25 4.85
230 231 1.172180 AAAGCTTTGCTACGCTGCCA 61.172 50.000 11.80 0.00 38.25 4.92
231 232 1.172180 AAGCTTTGCTACGCTGCCAA 61.172 50.000 0.00 0.00 38.25 4.52
232 233 1.154150 GCTTTGCTACGCTGCCAAG 60.154 57.895 8.90 8.90 38.32 3.61
233 234 1.503542 CTTTGCTACGCTGCCAAGG 59.496 57.895 0.00 0.00 33.67 3.61
234 235 1.228124 TTTGCTACGCTGCCAAGGT 60.228 52.632 0.00 0.00 0.00 3.50
235 236 0.821711 TTTGCTACGCTGCCAAGGTT 60.822 50.000 0.00 0.00 0.00 3.50
236 237 0.821711 TTGCTACGCTGCCAAGGTTT 60.822 50.000 0.00 0.00 0.00 3.27
237 238 1.210155 GCTACGCTGCCAAGGTTTG 59.790 57.895 0.00 0.00 0.00 2.93
238 239 1.234615 GCTACGCTGCCAAGGTTTGA 61.235 55.000 0.00 0.00 0.00 2.69
239 240 1.234821 CTACGCTGCCAAGGTTTGAA 58.765 50.000 0.00 0.00 0.00 2.69
240 241 0.948678 TACGCTGCCAAGGTTTGAAC 59.051 50.000 0.00 0.00 0.00 3.18
241 242 0.751643 ACGCTGCCAAGGTTTGAACT 60.752 50.000 0.00 0.00 0.00 3.01
242 243 0.385390 CGCTGCCAAGGTTTGAACTT 59.615 50.000 0.00 0.00 0.00 2.66
243 244 1.600413 CGCTGCCAAGGTTTGAACTTC 60.600 52.381 0.00 0.00 0.00 3.01
244 245 1.408702 GCTGCCAAGGTTTGAACTTCA 59.591 47.619 0.00 0.00 0.00 3.02
245 246 2.159114 GCTGCCAAGGTTTGAACTTCAA 60.159 45.455 0.00 0.00 34.03 2.69
246 247 3.709987 CTGCCAAGGTTTGAACTTCAAG 58.290 45.455 4.43 0.00 37.70 3.02
247 248 3.360867 TGCCAAGGTTTGAACTTCAAGA 58.639 40.909 4.43 0.00 37.70 3.02
248 249 3.960102 TGCCAAGGTTTGAACTTCAAGAT 59.040 39.130 4.43 0.00 37.70 2.40
249 250 5.136828 TGCCAAGGTTTGAACTTCAAGATA 58.863 37.500 4.43 0.00 37.70 1.98
250 251 5.774690 TGCCAAGGTTTGAACTTCAAGATAT 59.225 36.000 4.43 0.00 37.70 1.63
251 252 6.945435 TGCCAAGGTTTGAACTTCAAGATATA 59.055 34.615 4.43 0.00 37.70 0.86
252 253 7.615365 TGCCAAGGTTTGAACTTCAAGATATAT 59.385 33.333 4.43 0.00 37.70 0.86
253 254 8.470002 GCCAAGGTTTGAACTTCAAGATATATT 58.530 33.333 4.43 0.00 37.70 1.28
311 312 4.688511 AAAAAGTTAGTTGTGTCGCACA 57.311 36.364 8.32 8.32 43.02 4.57
312 313 3.944422 AAAGTTAGTTGTGTCGCACAG 57.056 42.857 11.48 0.00 45.39 3.66
313 314 2.882927 AGTTAGTTGTGTCGCACAGA 57.117 45.000 11.48 0.00 45.39 3.41
314 315 3.386768 AGTTAGTTGTGTCGCACAGAT 57.613 42.857 11.48 7.96 45.39 2.90
315 316 3.318017 AGTTAGTTGTGTCGCACAGATC 58.682 45.455 11.48 7.75 45.39 2.75
316 317 3.005897 AGTTAGTTGTGTCGCACAGATCT 59.994 43.478 11.48 12.72 45.39 2.75
317 318 2.533266 AGTTGTGTCGCACAGATCTT 57.467 45.000 11.48 0.00 45.39 2.40
318 319 3.660501 AGTTGTGTCGCACAGATCTTA 57.339 42.857 11.48 0.00 45.39 2.10
319 320 3.990092 AGTTGTGTCGCACAGATCTTAA 58.010 40.909 11.48 0.00 45.39 1.85
320 321 4.377021 AGTTGTGTCGCACAGATCTTAAA 58.623 39.130 11.48 0.00 45.39 1.52
321 322 4.814234 AGTTGTGTCGCACAGATCTTAAAA 59.186 37.500 11.48 0.00 45.39 1.52
322 323 4.725556 TGTGTCGCACAGATCTTAAAAC 57.274 40.909 8.32 0.00 39.62 2.43
323 324 3.183574 TGTGTCGCACAGATCTTAAAACG 59.816 43.478 8.32 0.00 39.62 3.60
324 325 3.427528 GTGTCGCACAGATCTTAAAACGA 59.572 43.478 0.00 0.00 34.08 3.85
325 326 4.091509 GTGTCGCACAGATCTTAAAACGAT 59.908 41.667 0.00 0.00 34.08 3.73
326 327 5.287752 GTGTCGCACAGATCTTAAAACGATA 59.712 40.000 0.00 0.00 34.08 2.92
327 328 6.019801 GTGTCGCACAGATCTTAAAACGATAT 60.020 38.462 0.00 0.00 34.08 1.63
328 329 6.533723 TGTCGCACAGATCTTAAAACGATATT 59.466 34.615 0.00 0.00 0.00 1.28
329 330 6.841286 GTCGCACAGATCTTAAAACGATATTG 59.159 38.462 0.00 0.00 0.00 1.90
330 331 6.019075 TCGCACAGATCTTAAAACGATATTGG 60.019 38.462 0.00 0.00 0.00 3.16
331 332 6.019075 CGCACAGATCTTAAAACGATATTGGA 60.019 38.462 0.00 0.00 0.00 3.53
332 333 7.348201 GCACAGATCTTAAAACGATATTGGAG 58.652 38.462 0.00 0.00 0.00 3.86
333 334 7.224753 GCACAGATCTTAAAACGATATTGGAGA 59.775 37.037 0.00 0.00 0.00 3.71
334 335 8.759641 CACAGATCTTAAAACGATATTGGAGAG 58.240 37.037 0.00 0.00 0.00 3.20
335 336 8.696374 ACAGATCTTAAAACGATATTGGAGAGA 58.304 33.333 0.00 0.00 0.00 3.10
336 337 9.703892 CAGATCTTAAAACGATATTGGAGAGAT 57.296 33.333 0.00 0.00 0.00 2.75
340 341 9.363401 TCTTAAAACGATATTGGAGAGATAGGA 57.637 33.333 0.00 0.00 0.00 2.94
344 345 6.952773 ACGATATTGGAGAGATAGGATAGC 57.047 41.667 0.00 0.00 0.00 2.97
345 346 6.427441 ACGATATTGGAGAGATAGGATAGCA 58.573 40.000 0.00 0.00 0.00 3.49
346 347 6.545666 ACGATATTGGAGAGATAGGATAGCAG 59.454 42.308 0.00 0.00 0.00 4.24
347 348 6.770303 CGATATTGGAGAGATAGGATAGCAGA 59.230 42.308 0.00 0.00 0.00 4.26
348 349 7.041167 CGATATTGGAGAGATAGGATAGCAGAG 60.041 44.444 0.00 0.00 0.00 3.35
349 350 3.696045 TGGAGAGATAGGATAGCAGAGC 58.304 50.000 0.00 0.00 0.00 4.09
350 351 3.023832 GGAGAGATAGGATAGCAGAGCC 58.976 54.545 0.00 0.00 0.00 4.70
351 352 2.682856 GAGAGATAGGATAGCAGAGCCG 59.317 54.545 0.00 0.00 39.29 5.52
352 353 1.748493 GAGATAGGATAGCAGAGCCGG 59.252 57.143 0.00 0.00 39.29 6.13
353 354 0.820871 GATAGGATAGCAGAGCCGGG 59.179 60.000 2.18 0.00 39.29 5.73
354 355 0.616111 ATAGGATAGCAGAGCCGGGG 60.616 60.000 2.18 0.00 39.29 5.73
355 356 2.020100 TAGGATAGCAGAGCCGGGGT 62.020 60.000 2.18 0.00 39.29 4.95
356 357 2.423446 GATAGCAGAGCCGGGGTG 59.577 66.667 2.05 0.00 0.00 4.61
357 358 3.816367 GATAGCAGAGCCGGGGTGC 62.816 68.421 2.05 1.19 37.48 5.01
367 368 3.390521 CGGGGTGCAGGTGCTCTA 61.391 66.667 3.18 0.00 42.66 2.43
368 369 2.954684 CGGGGTGCAGGTGCTCTAA 61.955 63.158 3.18 0.00 42.66 2.10
369 370 1.378762 GGGGTGCAGGTGCTCTAAA 59.621 57.895 3.18 0.00 42.66 1.85
370 371 0.251165 GGGGTGCAGGTGCTCTAAAA 60.251 55.000 3.18 0.00 42.66 1.52
371 372 1.616159 GGGTGCAGGTGCTCTAAAAA 58.384 50.000 3.18 0.00 42.66 1.94
372 373 2.171003 GGGTGCAGGTGCTCTAAAAAT 58.829 47.619 3.18 0.00 42.66 1.82
373 374 2.164422 GGGTGCAGGTGCTCTAAAAATC 59.836 50.000 3.18 0.00 42.66 2.17
374 375 2.164422 GGTGCAGGTGCTCTAAAAATCC 59.836 50.000 3.18 0.00 42.66 3.01
375 376 2.819608 GTGCAGGTGCTCTAAAAATCCA 59.180 45.455 3.18 0.00 42.66 3.41
376 377 2.819608 TGCAGGTGCTCTAAAAATCCAC 59.180 45.455 3.18 0.00 42.66 4.02
377 378 2.159517 GCAGGTGCTCTAAAAATCCACG 60.160 50.000 0.00 0.00 38.21 4.94
378 379 3.074412 CAGGTGCTCTAAAAATCCACGT 58.926 45.455 0.00 0.00 0.00 4.49
379 380 3.125316 CAGGTGCTCTAAAAATCCACGTC 59.875 47.826 0.00 0.00 0.00 4.34
380 381 2.418976 GGTGCTCTAAAAATCCACGTCC 59.581 50.000 0.00 0.00 0.00 4.79
381 382 2.093783 GTGCTCTAAAAATCCACGTCCG 59.906 50.000 0.00 0.00 0.00 4.79
382 383 1.664151 GCTCTAAAAATCCACGTCCGG 59.336 52.381 0.00 0.00 0.00 5.14
383 384 2.675889 GCTCTAAAAATCCACGTCCGGA 60.676 50.000 0.00 0.00 40.07 5.14
384 385 3.592059 CTCTAAAAATCCACGTCCGGAA 58.408 45.455 5.23 0.00 38.95 4.30
385 386 4.189231 CTCTAAAAATCCACGTCCGGAAT 58.811 43.478 5.23 0.00 38.95 3.01
386 387 4.581868 TCTAAAAATCCACGTCCGGAATT 58.418 39.130 5.23 0.00 38.95 2.17
387 388 3.569250 AAAAATCCACGTCCGGAATTG 57.431 42.857 5.23 6.09 38.95 2.32
393 394 2.824041 CGTCCGGAATTGGGCCTG 60.824 66.667 5.23 0.00 0.00 4.85
451 452 2.654749 TGAACACTACGATGCTCCAG 57.345 50.000 0.00 0.00 0.00 3.86
466 467 4.063335 CAGATCCCTCTGGTGGCT 57.937 61.111 0.00 0.00 44.40 4.75
467 468 1.828768 CAGATCCCTCTGGTGGCTC 59.171 63.158 0.00 0.00 44.40 4.70
469 470 0.398381 AGATCCCTCTGGTGGCTCTC 60.398 60.000 0.00 0.00 0.00 3.20
472 473 3.385384 CCTCTGGTGGCTCTCGCA 61.385 66.667 0.00 0.00 38.10 5.10
514 538 2.164663 CGGCAAAGCGTCGATGCTA 61.165 57.895 31.20 0.00 46.60 3.49
515 539 1.348594 GGCAAAGCGTCGATGCTAC 59.651 57.895 31.20 22.18 46.60 3.58
516 540 1.013323 GCAAAGCGTCGATGCTACG 60.013 57.895 31.20 24.30 46.60 3.51
517 541 1.410737 GCAAAGCGTCGATGCTACGA 61.411 55.000 31.20 4.06 46.60 3.43
518 542 0.567968 CAAAGCGTCGATGCTACGAG 59.432 55.000 31.20 17.22 46.60 4.18
519 543 1.140407 AAAGCGTCGATGCTACGAGC 61.140 55.000 31.20 6.75 46.60 5.03
520 544 3.379625 GCGTCGATGCTACGAGCG 61.380 66.667 22.31 1.92 46.26 5.03
521 545 2.722548 CGTCGATGCTACGAGCGG 60.723 66.667 6.11 0.00 46.26 5.52
540 564 2.642129 CGTCACCGGCAATGCAAA 59.358 55.556 7.79 0.00 0.00 3.68
546 570 1.203052 CACCGGCAATGCAAAGAAGAT 59.797 47.619 7.79 0.00 0.00 2.40
551 575 1.917273 CAATGCAAAGAAGATGCGGG 58.083 50.000 0.00 0.00 46.76 6.13
572 596 4.155733 CGGCTACATGGACCGGCA 62.156 66.667 13.66 0.00 43.23 5.69
601 625 2.672996 ATGGTGGGTGTTGCGAGC 60.673 61.111 0.00 0.00 0.00 5.03
704 741 2.169978 AGGTAATAGTTTGCGGGGAGAC 59.830 50.000 0.00 0.00 0.00 3.36
733 770 0.319641 GGGGAACGAGTATGATCGGC 60.320 60.000 6.38 0.00 46.91 5.54
883 934 1.916506 ATCAGCTGCGCTAGATAGGA 58.083 50.000 9.47 0.00 36.40 2.94
892 943 7.001674 AGCTGCGCTAGATAGGAGTATATATT 58.998 38.462 9.73 0.00 36.99 1.28
964 1588 4.405358 AGAAATCAGAAGATCGCTCCTCTT 59.595 41.667 0.00 0.00 35.69 2.85
965 1589 4.320608 AATCAGAAGATCGCTCCTCTTC 57.679 45.455 10.23 10.23 45.85 2.87
966 1590 2.028130 TCAGAAGATCGCTCCTCTTCC 58.972 52.381 13.14 1.25 46.39 3.46
967 1591 2.031120 CAGAAGATCGCTCCTCTTCCT 58.969 52.381 13.14 2.91 46.39 3.36
968 1592 2.034558 CAGAAGATCGCTCCTCTTCCTC 59.965 54.545 13.14 0.00 46.39 3.71
969 1593 2.028130 GAAGATCGCTCCTCTTCCTCA 58.972 52.381 8.00 0.00 41.74 3.86
970 1594 2.380064 AGATCGCTCCTCTTCCTCAT 57.620 50.000 0.00 0.00 0.00 2.90
971 1595 2.676748 AGATCGCTCCTCTTCCTCATT 58.323 47.619 0.00 0.00 0.00 2.57
987 1611 4.695455 TCCTCATTGTTTGGATCGAAAGAC 59.305 41.667 2.80 0.00 46.97 3.01
988 1612 4.436050 CCTCATTGTTTGGATCGAAAGACG 60.436 45.833 2.80 0.00 46.97 4.18
1044 1678 2.122564 GTATTGGCCGTTACTAGCGTC 58.877 52.381 0.00 0.00 0.00 5.19
1213 1856 2.669569 GCCGCTCCAAGAACTGCA 60.670 61.111 0.00 0.00 0.00 4.41
1934 2591 7.047271 AGTTGCATCAACCAAAACAAATTAGT 58.953 30.769 6.12 0.00 44.49 2.24
2041 2698 8.867935 CCTTGCTAATAATCGAATCTGTATGAG 58.132 37.037 0.00 0.00 0.00 2.90
2042 2699 9.416794 CTTGCTAATAATCGAATCTGTATGAGT 57.583 33.333 0.00 0.00 0.00 3.41
2369 3042 5.855395 GCTGTTTGACAATGAGAAGATGTTC 59.145 40.000 0.00 0.00 0.00 3.18
2444 3126 9.840236 CTCATTGGAGGACCTCGAAGGTTTAAA 62.840 44.444 24.38 9.16 40.76 1.52
2452 3134 3.541711 CTCGAAGGTTTAAACTTGCACG 58.458 45.455 17.50 15.45 0.00 5.34
2506 3190 7.547370 ACTTCCTTCTCATATCTCACTTTTTCG 59.453 37.037 0.00 0.00 0.00 3.46
2832 3516 4.410883 TCTCTTTGTAAAGTCCACTTGGGA 59.589 41.667 4.45 0.00 37.84 4.37
3523 4255 4.595762 AATGTTTGTTGCTTGCTGAGAT 57.404 36.364 0.00 0.00 0.00 2.75
3683 4437 7.576666 GCAAGTATCCGATGATTCAGATAGACT 60.577 40.741 0.00 0.00 32.18 3.24
3686 4440 4.729868 TCCGATGATTCAGATAGACTCCA 58.270 43.478 0.00 0.00 0.00 3.86
3701 4455 1.142060 ACTCCACGGTGTCCATTTTGA 59.858 47.619 7.45 0.00 0.00 2.69
3764 4518 2.303600 ACGCCATTGTAAAGTACTCCCA 59.696 45.455 0.00 0.00 0.00 4.37
3791 4545 6.817641 TGTCCCGAAATATAAGAGCGTTTTTA 59.182 34.615 0.00 0.00 0.00 1.52
3825 4579 5.514914 ACAAAACTTGTCACGCTACAAAATG 59.485 36.000 4.90 4.61 40.56 2.32
3899 4653 0.103208 ATTCCACTCTCGTCATCGCC 59.897 55.000 0.00 0.00 36.96 5.54
3967 4721 2.360483 CCCTCCATCTATCCATCGATCG 59.640 54.545 9.36 9.36 0.00 3.69
3978 4732 1.804748 CCATCGATCGATCTACACCGA 59.195 52.381 27.20 14.53 39.25 4.69
3982 4736 2.737252 TCGATCGATCTACACCGATGAG 59.263 50.000 22.43 3.30 44.40 2.90
3995 4749 1.156736 CGATGAGAAGGCAAAACGGT 58.843 50.000 0.00 0.00 0.00 4.83
3996 4750 1.135972 CGATGAGAAGGCAAAACGGTG 60.136 52.381 0.00 0.00 0.00 4.94
4003 4757 2.193536 GGCAAAACGGTGGCTCTGT 61.194 57.895 0.00 0.00 40.77 3.41
4020 4774 3.581755 TCTGTCCGGAGTAAACATTTCG 58.418 45.455 3.06 0.00 0.00 3.46
4062 4816 3.644966 TGGATAAAGGGCACTACTTGG 57.355 47.619 0.00 0.00 0.00 3.61
4071 4825 1.732259 GGCACTACTTGGTTGTGATCG 59.268 52.381 14.22 0.00 40.56 3.69
4298 5052 8.129496 TGTTATGTACTCCAGAATGTTCAGTA 57.871 34.615 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.739276 AGATATGTTCTATGTGGAAGAAACAAA 57.261 29.630 0.00 0.00 34.86 2.83
8 9 9.739276 AAGATATGTTCTATGTGGAAGAAACAA 57.261 29.630 0.00 0.00 34.86 2.83
9 10 9.166173 CAAGATATGTTCTATGTGGAAGAAACA 57.834 33.333 0.00 0.00 34.86 2.83
10 11 9.383519 TCAAGATATGTTCTATGTGGAAGAAAC 57.616 33.333 0.00 0.00 34.86 2.78
11 12 9.958180 TTCAAGATATGTTCTATGTGGAAGAAA 57.042 29.630 0.00 0.00 34.86 2.52
12 13 9.605275 CTTCAAGATATGTTCTATGTGGAAGAA 57.395 33.333 0.00 0.00 33.05 2.52
13 14 8.762645 ACTTCAAGATATGTTCTATGTGGAAGA 58.237 33.333 11.43 0.00 33.05 2.87
14 15 8.954950 ACTTCAAGATATGTTCTATGTGGAAG 57.045 34.615 0.00 0.00 33.05 3.46
15 16 9.739276 AAACTTCAAGATATGTTCTATGTGGAA 57.261 29.630 0.00 0.00 33.05 3.53
29 30 8.826710 CGGTGCATAGATTTAAACTTCAAGATA 58.173 33.333 0.00 0.00 0.00 1.98
30 31 7.336931 ACGGTGCATAGATTTAAACTTCAAGAT 59.663 33.333 0.00 0.00 0.00 2.40
31 32 6.653320 ACGGTGCATAGATTTAAACTTCAAGA 59.347 34.615 0.00 0.00 0.00 3.02
32 33 6.742718 CACGGTGCATAGATTTAAACTTCAAG 59.257 38.462 0.00 0.00 0.00 3.02
33 34 6.348950 CCACGGTGCATAGATTTAAACTTCAA 60.349 38.462 1.68 0.00 0.00 2.69
34 35 5.123186 CCACGGTGCATAGATTTAAACTTCA 59.877 40.000 1.68 0.00 0.00 3.02
35 36 5.123344 ACCACGGTGCATAGATTTAAACTTC 59.877 40.000 1.68 0.00 0.00 3.01
36 37 5.007682 ACCACGGTGCATAGATTTAAACTT 58.992 37.500 1.68 0.00 0.00 2.66
37 38 4.585879 ACCACGGTGCATAGATTTAAACT 58.414 39.130 1.68 0.00 0.00 2.66
38 39 4.957759 ACCACGGTGCATAGATTTAAAC 57.042 40.909 1.68 0.00 0.00 2.01
39 40 6.127952 GGTTTACCACGGTGCATAGATTTAAA 60.128 38.462 1.68 0.00 35.64 1.52
40 41 5.354792 GGTTTACCACGGTGCATAGATTTAA 59.645 40.000 1.68 0.00 35.64 1.52
41 42 4.877251 GGTTTACCACGGTGCATAGATTTA 59.123 41.667 1.68 0.00 35.64 1.40
42 43 3.692593 GGTTTACCACGGTGCATAGATTT 59.307 43.478 1.68 0.00 35.64 2.17
43 44 3.054655 AGGTTTACCACGGTGCATAGATT 60.055 43.478 1.68 0.00 38.89 2.40
44 45 2.504175 AGGTTTACCACGGTGCATAGAT 59.496 45.455 1.68 0.00 38.89 1.98
45 46 1.903860 AGGTTTACCACGGTGCATAGA 59.096 47.619 1.68 0.00 38.89 1.98
46 47 2.396590 AGGTTTACCACGGTGCATAG 57.603 50.000 1.68 0.00 38.89 2.23
47 48 2.863132 AAGGTTTACCACGGTGCATA 57.137 45.000 1.68 0.00 38.89 3.14
48 49 1.883926 GAAAGGTTTACCACGGTGCAT 59.116 47.619 1.68 0.00 38.89 3.96
49 50 1.134037 AGAAAGGTTTACCACGGTGCA 60.134 47.619 1.68 0.00 38.89 4.57
50 51 1.601166 AGAAAGGTTTACCACGGTGC 58.399 50.000 1.68 0.00 38.89 5.01
51 52 4.383173 AGTTAGAAAGGTTTACCACGGTG 58.617 43.478 0.00 0.00 38.89 4.94
52 53 4.694760 AGTTAGAAAGGTTTACCACGGT 57.305 40.909 1.13 0.00 38.89 4.83
53 54 6.029346 TCTAGTTAGAAAGGTTTACCACGG 57.971 41.667 1.13 0.00 38.89 4.94
54 55 8.033626 AGATTCTAGTTAGAAAGGTTTACCACG 58.966 37.037 5.75 0.00 44.63 4.94
180 181 9.534565 CGACAATCTAGGATAAATCTTTCAGAA 57.465 33.333 0.00 0.00 0.00 3.02
181 182 8.696374 ACGACAATCTAGGATAAATCTTTCAGA 58.304 33.333 0.00 0.00 0.00 3.27
182 183 8.879342 ACGACAATCTAGGATAAATCTTTCAG 57.121 34.615 0.00 0.00 0.00 3.02
189 190 9.262358 GCTTTCTAACGACAATCTAGGATAAAT 57.738 33.333 0.00 0.00 0.00 1.40
190 191 8.475639 AGCTTTCTAACGACAATCTAGGATAAA 58.524 33.333 0.00 0.00 0.00 1.40
191 192 8.008513 AGCTTTCTAACGACAATCTAGGATAA 57.991 34.615 0.00 0.00 0.00 1.75
192 193 7.584122 AGCTTTCTAACGACAATCTAGGATA 57.416 36.000 0.00 0.00 0.00 2.59
193 194 6.472686 AGCTTTCTAACGACAATCTAGGAT 57.527 37.500 0.00 0.00 0.00 3.24
194 195 5.916661 AGCTTTCTAACGACAATCTAGGA 57.083 39.130 0.00 0.00 0.00 2.94
195 196 6.673316 GCAAAGCTTTCTAACGACAATCTAGG 60.673 42.308 9.23 0.00 0.00 3.02
196 197 6.091441 AGCAAAGCTTTCTAACGACAATCTAG 59.909 38.462 9.23 0.00 33.89 2.43
197 198 5.932303 AGCAAAGCTTTCTAACGACAATCTA 59.068 36.000 9.23 0.00 33.89 1.98
198 199 4.757149 AGCAAAGCTTTCTAACGACAATCT 59.243 37.500 9.23 0.00 33.89 2.40
199 200 5.035784 AGCAAAGCTTTCTAACGACAATC 57.964 39.130 9.23 0.00 33.89 2.67
200 201 5.389516 CGTAGCAAAGCTTTCTAACGACAAT 60.390 40.000 22.69 0.00 37.68 2.71
201 202 4.084745 CGTAGCAAAGCTTTCTAACGACAA 60.085 41.667 22.69 2.51 37.68 3.18
202 203 3.427528 CGTAGCAAAGCTTTCTAACGACA 59.572 43.478 22.69 3.05 37.68 4.35
203 204 3.975093 CGTAGCAAAGCTTTCTAACGAC 58.025 45.455 22.69 12.94 37.68 4.34
220 221 1.069227 GTTCAAACCTTGGCAGCGTAG 60.069 52.381 0.00 0.00 0.00 3.51
221 222 0.948678 GTTCAAACCTTGGCAGCGTA 59.051 50.000 0.00 0.00 0.00 4.42
222 223 0.751643 AGTTCAAACCTTGGCAGCGT 60.752 50.000 0.00 0.00 0.00 5.07
223 224 0.385390 AAGTTCAAACCTTGGCAGCG 59.615 50.000 0.00 0.00 0.00 5.18
224 225 1.408702 TGAAGTTCAAACCTTGGCAGC 59.591 47.619 2.20 0.00 0.00 5.25
225 226 3.381272 TCTTGAAGTTCAAACCTTGGCAG 59.619 43.478 18.55 4.64 35.73 4.85
226 227 3.360867 TCTTGAAGTTCAAACCTTGGCA 58.639 40.909 18.55 0.00 35.73 4.92
227 228 4.590850 ATCTTGAAGTTCAAACCTTGGC 57.409 40.909 18.55 0.00 35.73 4.52
285 286 9.205719 TGTGCGACACAACTAACTTTTTATATA 57.794 29.630 9.71 0.00 41.69 0.86
286 287 8.090250 TGTGCGACACAACTAACTTTTTATAT 57.910 30.769 9.71 0.00 41.69 0.86
287 288 7.438757 TCTGTGCGACACAACTAACTTTTTATA 59.561 33.333 12.53 0.00 44.08 0.98
288 289 6.259167 TCTGTGCGACACAACTAACTTTTTAT 59.741 34.615 12.53 0.00 44.08 1.40
289 290 5.581479 TCTGTGCGACACAACTAACTTTTTA 59.419 36.000 12.53 0.00 44.08 1.52
290 291 4.393680 TCTGTGCGACACAACTAACTTTTT 59.606 37.500 12.53 0.00 44.08 1.94
291 292 3.936453 TCTGTGCGACACAACTAACTTTT 59.064 39.130 12.53 0.00 44.08 2.27
292 293 3.527533 TCTGTGCGACACAACTAACTTT 58.472 40.909 12.53 0.00 44.08 2.66
293 294 3.173668 TCTGTGCGACACAACTAACTT 57.826 42.857 12.53 0.00 44.08 2.66
294 295 2.882927 TCTGTGCGACACAACTAACT 57.117 45.000 12.53 0.00 44.08 2.24
295 296 3.318017 AGATCTGTGCGACACAACTAAC 58.682 45.455 12.53 4.95 44.08 2.34
296 297 3.660501 AGATCTGTGCGACACAACTAA 57.339 42.857 12.53 1.97 44.08 2.24
297 298 3.660501 AAGATCTGTGCGACACAACTA 57.339 42.857 12.53 3.90 44.08 2.24
298 299 2.533266 AAGATCTGTGCGACACAACT 57.467 45.000 12.53 9.69 44.08 3.16
299 300 4.725556 TTTAAGATCTGTGCGACACAAC 57.274 40.909 12.53 8.08 44.08 3.32
300 301 4.318475 CGTTTTAAGATCTGTGCGACACAA 60.318 41.667 12.53 5.97 44.08 3.33
301 302 3.183574 CGTTTTAAGATCTGTGCGACACA 59.816 43.478 11.28 11.28 42.45 3.72
302 303 3.427528 TCGTTTTAAGATCTGTGCGACAC 59.572 43.478 0.00 3.44 34.56 3.67
303 304 3.644823 TCGTTTTAAGATCTGTGCGACA 58.355 40.909 0.00 0.00 0.00 4.35
304 305 4.842139 ATCGTTTTAAGATCTGTGCGAC 57.158 40.909 0.00 0.00 0.00 5.19
305 306 6.019075 CCAATATCGTTTTAAGATCTGTGCGA 60.019 38.462 0.00 3.38 0.00 5.10
306 307 6.019075 TCCAATATCGTTTTAAGATCTGTGCG 60.019 38.462 0.00 0.00 0.00 5.34
307 308 7.224753 TCTCCAATATCGTTTTAAGATCTGTGC 59.775 37.037 0.00 0.00 0.00 4.57
308 309 8.648557 TCTCCAATATCGTTTTAAGATCTGTG 57.351 34.615 0.00 0.00 0.00 3.66
309 310 8.696374 TCTCTCCAATATCGTTTTAAGATCTGT 58.304 33.333 0.00 0.00 0.00 3.41
310 311 9.703892 ATCTCTCCAATATCGTTTTAAGATCTG 57.296 33.333 0.00 0.00 0.00 2.90
314 315 9.363401 TCCTATCTCTCCAATATCGTTTTAAGA 57.637 33.333 0.00 0.00 0.00 2.10
318 319 8.254508 GCTATCCTATCTCTCCAATATCGTTTT 58.745 37.037 0.00 0.00 0.00 2.43
319 320 7.397476 TGCTATCCTATCTCTCCAATATCGTTT 59.603 37.037 0.00 0.00 0.00 3.60
320 321 6.892456 TGCTATCCTATCTCTCCAATATCGTT 59.108 38.462 0.00 0.00 0.00 3.85
321 322 6.427441 TGCTATCCTATCTCTCCAATATCGT 58.573 40.000 0.00 0.00 0.00 3.73
322 323 6.770303 TCTGCTATCCTATCTCTCCAATATCG 59.230 42.308 0.00 0.00 0.00 2.92
323 324 7.255590 GCTCTGCTATCCTATCTCTCCAATATC 60.256 44.444 0.00 0.00 0.00 1.63
324 325 6.550854 GCTCTGCTATCCTATCTCTCCAATAT 59.449 42.308 0.00 0.00 0.00 1.28
325 326 5.890985 GCTCTGCTATCCTATCTCTCCAATA 59.109 44.000 0.00 0.00 0.00 1.90
326 327 4.711355 GCTCTGCTATCCTATCTCTCCAAT 59.289 45.833 0.00 0.00 0.00 3.16
327 328 4.085733 GCTCTGCTATCCTATCTCTCCAA 58.914 47.826 0.00 0.00 0.00 3.53
328 329 3.563261 GGCTCTGCTATCCTATCTCTCCA 60.563 52.174 0.00 0.00 0.00 3.86
329 330 3.023832 GGCTCTGCTATCCTATCTCTCC 58.976 54.545 0.00 0.00 0.00 3.71
330 331 2.682856 CGGCTCTGCTATCCTATCTCTC 59.317 54.545 0.00 0.00 0.00 3.20
331 332 2.620367 CCGGCTCTGCTATCCTATCTCT 60.620 54.545 0.00 0.00 0.00 3.10
332 333 1.748493 CCGGCTCTGCTATCCTATCTC 59.252 57.143 0.00 0.00 0.00 2.75
333 334 1.618345 CCCGGCTCTGCTATCCTATCT 60.618 57.143 0.00 0.00 0.00 1.98
334 335 0.820871 CCCGGCTCTGCTATCCTATC 59.179 60.000 0.00 0.00 0.00 2.08
335 336 0.616111 CCCCGGCTCTGCTATCCTAT 60.616 60.000 0.00 0.00 0.00 2.57
336 337 1.228894 CCCCGGCTCTGCTATCCTA 60.229 63.158 0.00 0.00 0.00 2.94
337 338 2.525381 CCCCGGCTCTGCTATCCT 60.525 66.667 0.00 0.00 0.00 3.24
338 339 2.844839 ACCCCGGCTCTGCTATCC 60.845 66.667 0.00 0.00 0.00 2.59
339 340 2.423446 CACCCCGGCTCTGCTATC 59.577 66.667 0.00 0.00 0.00 2.08
340 341 3.866582 GCACCCCGGCTCTGCTAT 61.867 66.667 0.00 0.00 0.00 2.97
350 351 2.463589 TTTAGAGCACCTGCACCCCG 62.464 60.000 0.00 0.00 45.16 5.73
351 352 0.251165 TTTTAGAGCACCTGCACCCC 60.251 55.000 0.00 0.00 45.16 4.95
352 353 1.616159 TTTTTAGAGCACCTGCACCC 58.384 50.000 0.00 0.00 45.16 4.61
353 354 2.164422 GGATTTTTAGAGCACCTGCACC 59.836 50.000 0.00 0.00 45.16 5.01
354 355 2.819608 TGGATTTTTAGAGCACCTGCAC 59.180 45.455 0.00 0.00 45.16 4.57
355 356 2.819608 GTGGATTTTTAGAGCACCTGCA 59.180 45.455 0.00 0.00 45.16 4.41
356 357 2.159517 CGTGGATTTTTAGAGCACCTGC 60.160 50.000 0.00 0.00 42.49 4.85
357 358 3.074412 ACGTGGATTTTTAGAGCACCTG 58.926 45.455 0.00 0.00 0.00 4.00
358 359 3.335579 GACGTGGATTTTTAGAGCACCT 58.664 45.455 0.00 0.00 0.00 4.00
359 360 2.418976 GGACGTGGATTTTTAGAGCACC 59.581 50.000 0.00 0.00 0.00 5.01
360 361 2.093783 CGGACGTGGATTTTTAGAGCAC 59.906 50.000 0.00 0.00 0.00 4.40
361 362 2.343101 CGGACGTGGATTTTTAGAGCA 58.657 47.619 0.00 0.00 0.00 4.26
362 363 1.664151 CCGGACGTGGATTTTTAGAGC 59.336 52.381 0.00 0.00 0.00 4.09
363 364 3.241067 TCCGGACGTGGATTTTTAGAG 57.759 47.619 0.00 0.00 31.53 2.43
364 365 3.681593 TTCCGGACGTGGATTTTTAGA 57.318 42.857 1.83 0.00 38.00 2.10
365 366 4.438200 CCAATTCCGGACGTGGATTTTTAG 60.438 45.833 23.06 1.32 38.00 1.85
366 367 3.440872 CCAATTCCGGACGTGGATTTTTA 59.559 43.478 23.06 0.00 38.00 1.52
367 368 2.230266 CCAATTCCGGACGTGGATTTTT 59.770 45.455 23.06 0.00 38.00 1.94
368 369 1.816224 CCAATTCCGGACGTGGATTTT 59.184 47.619 23.06 0.00 38.00 1.82
369 370 1.459450 CCAATTCCGGACGTGGATTT 58.541 50.000 23.06 0.00 38.00 2.17
370 371 0.393808 CCCAATTCCGGACGTGGATT 60.394 55.000 27.31 12.49 38.00 3.01
371 372 1.223487 CCCAATTCCGGACGTGGAT 59.777 57.895 27.31 6.95 38.00 3.41
372 373 2.666207 CCCAATTCCGGACGTGGA 59.334 61.111 27.31 4.68 35.83 4.02
373 374 3.131478 GCCCAATTCCGGACGTGG 61.131 66.667 21.25 21.25 0.00 4.94
374 375 3.131478 GGCCCAATTCCGGACGTG 61.131 66.667 1.83 4.90 0.00 4.49
375 376 3.327404 AGGCCCAATTCCGGACGT 61.327 61.111 1.83 0.00 31.53 4.34
376 377 2.824041 CAGGCCCAATTCCGGACG 60.824 66.667 1.83 0.00 31.53 4.79
377 378 3.140814 GCAGGCCCAATTCCGGAC 61.141 66.667 1.83 0.00 0.00 4.79
378 379 3.338250 AGCAGGCCCAATTCCGGA 61.338 61.111 0.00 0.00 0.00 5.14
379 380 3.142838 CAGCAGGCCCAATTCCGG 61.143 66.667 0.00 0.00 0.00 5.14
380 381 3.830192 GCAGCAGGCCCAATTCCG 61.830 66.667 0.00 0.00 36.11 4.30
381 382 2.285024 TTGCAGCAGGCCCAATTCC 61.285 57.895 0.00 0.00 43.89 3.01
382 383 1.079612 GTTGCAGCAGGCCCAATTC 60.080 57.895 0.00 0.00 43.89 2.17
383 384 2.586293 GGTTGCAGCAGGCCCAATT 61.586 57.895 0.00 0.00 43.89 2.32
384 385 2.999063 GGTTGCAGCAGGCCCAAT 60.999 61.111 0.00 0.00 43.89 3.16
410 411 1.498865 CGTGCCGGTCATAGAATGGC 61.499 60.000 1.90 4.37 45.91 4.40
411 412 0.104120 TCGTGCCGGTCATAGAATGG 59.896 55.000 1.90 0.00 0.00 3.16
429 430 3.521560 TGGAGCATCGTAGTGTTCAATC 58.478 45.455 0.00 0.00 34.37 2.67
437 438 1.133325 AGGGATCTGGAGCATCGTAGT 60.133 52.381 0.00 0.00 34.37 2.73
441 442 0.317799 CAGAGGGATCTGGAGCATCG 59.682 60.000 0.00 0.00 34.37 3.84
451 452 1.743321 CGAGAGCCACCAGAGGGATC 61.743 65.000 0.00 0.00 41.11 3.36
497 521 1.348594 GTAGCATCGACGCTTTGCC 59.651 57.895 12.80 0.00 43.56 4.52
505 529 2.353607 CCCGCTCGTAGCATCGAC 60.354 66.667 7.47 0.00 42.58 4.20
506 530 4.266070 GCCCGCTCGTAGCATCGA 62.266 66.667 7.47 0.00 42.58 3.59
538 562 1.450312 CGCTCCCCGCATCTTCTTT 60.450 57.895 0.00 0.00 39.08 2.52
540 564 3.854669 CCGCTCCCCGCATCTTCT 61.855 66.667 0.00 0.00 39.08 2.85
551 575 2.109181 GGTCCATGTAGCCGCTCC 59.891 66.667 0.00 0.00 0.00 4.70
572 596 2.360350 CACCATGGGCAAGCTCGT 60.360 61.111 18.09 0.00 0.00 4.18
652 679 2.747855 GCACTAGCAGCACCCCAC 60.748 66.667 0.00 0.00 41.58 4.61
675 702 3.114065 GCAAACTATTACCTCCGTCTCG 58.886 50.000 0.00 0.00 0.00 4.04
692 729 1.198094 TCCATCTGTCTCCCCGCAAA 61.198 55.000 0.00 0.00 0.00 3.68
704 741 0.176680 CTCGTTCCCCTGTCCATCTG 59.823 60.000 0.00 0.00 0.00 2.90
733 770 2.279517 GGACTCACGCATAGCCGG 60.280 66.667 0.00 0.00 0.00 6.13
772 813 1.439644 GTCCGATCTGGGCTCACTC 59.560 63.158 1.59 0.00 40.15 3.51
883 934 9.338622 GCTTTCAAGGGTACACAAATATATACT 57.661 33.333 0.00 0.00 0.00 2.12
892 943 2.173782 TCTGGCTTTCAAGGGTACACAA 59.826 45.455 0.00 0.00 0.00 3.33
898 959 2.158325 TGGATTTCTGGCTTTCAAGGGT 60.158 45.455 0.00 0.00 0.00 4.34
936 1525 4.583871 AGCGATCTTCTGATTTCTTTGGT 58.416 39.130 0.00 0.00 32.19 3.67
937 1526 4.034975 GGAGCGATCTTCTGATTTCTTTGG 59.965 45.833 0.00 0.00 32.19 3.28
940 1553 4.405358 AGAGGAGCGATCTTCTGATTTCTT 59.595 41.667 15.04 0.00 32.19 2.52
964 1588 4.695455 GTCTTTCGATCCAAACAATGAGGA 59.305 41.667 0.00 0.00 35.59 3.71
965 1589 4.436050 CGTCTTTCGATCCAAACAATGAGG 60.436 45.833 0.00 0.00 42.86 3.86
966 1590 4.388773 TCGTCTTTCGATCCAAACAATGAG 59.611 41.667 0.00 0.00 44.01 2.90
967 1591 4.311606 TCGTCTTTCGATCCAAACAATGA 58.688 39.130 0.00 0.00 44.01 2.57
968 1592 4.661993 TCGTCTTTCGATCCAAACAATG 57.338 40.909 0.00 0.00 44.01 2.82
987 1611 0.311790 GCTCCATCTCTGCTCTCTCG 59.688 60.000 0.00 0.00 0.00 4.04
988 1612 1.338973 CTGCTCCATCTCTGCTCTCTC 59.661 57.143 0.00 0.00 0.00 3.20
995 1629 2.459060 CATAGCCTGCTCCATCTCTG 57.541 55.000 0.00 0.00 0.00 3.35
1044 1678 1.289109 CTACTGCCCACGACAAACCG 61.289 60.000 0.00 0.00 0.00 4.44
2369 3042 0.439985 CAGACATGTCAAAGCGGACG 59.560 55.000 27.02 1.02 40.72 4.79
2452 3134 3.813529 AGAAATACGTGTGCAAAGAGC 57.186 42.857 0.00 0.00 45.96 4.09
2506 3190 7.426929 TCTTCATAGCTTCAGAAAGTCAAAC 57.573 36.000 0.00 0.00 34.79 2.93
2729 3413 0.107703 CGGCCATTCCAGCTAACAGA 60.108 55.000 2.24 0.00 34.01 3.41
2734 3418 1.909459 TTCTGCGGCCATTCCAGCTA 61.909 55.000 2.24 0.00 36.05 3.32
2832 3516 5.986135 GGTAAATATGTCGATCAGCAGAGTT 59.014 40.000 0.00 0.00 0.00 3.01
3523 4255 7.419711 AGAGGTTCGATCAAGGAAGTATAAA 57.580 36.000 0.00 0.00 0.00 1.40
3594 4343 2.682836 GTCTCAAGACTGAAGACTGGC 58.317 52.381 2.86 0.00 41.65 4.85
3618 4367 2.679996 GGCAGCGGGGTTTTGGAT 60.680 61.111 0.00 0.00 0.00 3.41
3683 4437 1.600023 GTCAAAATGGACACCGTGGA 58.400 50.000 3.03 0.00 37.73 4.02
3686 4440 1.604604 CTGGTCAAAATGGACACCGT 58.395 50.000 0.00 0.00 39.59 4.83
3701 4455 3.550431 ACGGCACACTGAGCTGGT 61.550 61.111 11.44 1.97 42.62 4.00
3764 4518 3.383825 ACGCTCTTATATTTCGGGACAGT 59.616 43.478 0.00 0.00 0.00 3.55
3791 4545 5.277779 CGTGACAAGTTTTGTACATGGATGT 60.278 40.000 0.00 0.00 45.52 3.06
3825 4579 3.001838 GGGCATTTTTGGAAACGAACAAC 59.998 43.478 0.00 0.00 31.96 3.32
3899 4653 3.517100 TGGAGAGATGGAGTGAAGGAAAG 59.483 47.826 0.00 0.00 0.00 2.62
3967 4721 2.362397 TGCCTTCTCATCGGTGTAGATC 59.638 50.000 0.00 0.00 0.00 2.75
3978 4732 1.247567 CCACCGTTTTGCCTTCTCAT 58.752 50.000 0.00 0.00 0.00 2.90
3982 4736 1.172812 AGAGCCACCGTTTTGCCTTC 61.173 55.000 0.00 0.00 0.00 3.46
3995 4749 0.606604 GTTTACTCCGGACAGAGCCA 59.393 55.000 0.00 0.00 37.39 4.75
3996 4750 0.606604 TGTTTACTCCGGACAGAGCC 59.393 55.000 0.00 0.00 37.39 4.70
4003 4757 2.564062 ACTCCGAAATGTTTACTCCGGA 59.436 45.455 2.93 2.93 42.92 5.14
4020 4774 2.841442 ACCAAACTGCAGTCTACTCC 57.159 50.000 21.95 0.00 0.00 3.85
4062 4816 0.249398 AGTGGGCCTACGATCACAAC 59.751 55.000 14.26 0.00 33.01 3.32
4071 4825 3.840124 ATTTAGCACTAGTGGGCCTAC 57.160 47.619 23.95 12.09 0.00 3.18


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

AutoCloner maintained by Alex Coulton.