Multiple sequence alignment - TraesCS3A01G103000

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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 TraesCS3A01G103000 chr3A 100.000 4245 0 0 1 4245 66510670 66506426 0.000000e+00 7840.0
1 TraesCS3A01G103000 chr3B 92.840 2053 98 14 1867 3884 90471891 90469853 0.000000e+00 2931.0
2 TraesCS3A01G103000 chr3B 93.121 1352 49 11 509 1841 90473211 90471885 0.000000e+00 1941.0
3 TraesCS3A01G103000 chr3B 87.048 525 39 13 1 509 90473753 90473242 2.220000e-157 566.0
4 TraesCS3A01G103000 chr3B 93.782 193 12 0 4053 4245 90469850 90469658 1.490000e-74 291.0
5 TraesCS3A01G103000 chr3B 93.143 175 12 0 3874 4048 602591114 602591288 1.510000e-64 257.0
6 TraesCS3A01G103000 chr3B 95.556 45 2 0 3699 3743 669921189 669921233 5.890000e-09 73.1
7 TraesCS3A01G103000 chr3D 92.233 2060 96 22 1867 3880 57506631 57504590 0.000000e+00 2859.0
8 TraesCS3A01G103000 chr3D 93.472 1348 68 8 511 1841 57507969 57506625 0.000000e+00 1984.0
9 TraesCS3A01G103000 chr3D 87.091 519 48 9 1 509 57508510 57508001 1.710000e-158 569.0
10 TraesCS3A01G103000 chr3D 90.449 178 9 5 4053 4230 57504477 57504308 1.190000e-55 228.0
11 TraesCS3A01G103000 chr4B 97.006 167 5 0 3875 4041 407061169 407061335 8.990000e-72 281.0
12 TraesCS3A01G103000 chr4B 94.737 171 8 1 3877 4046 25530391 25530221 9.050000e-67 265.0
13 TraesCS3A01G103000 chr4B 95.732 164 7 0 3879 4042 658025698 658025535 9.050000e-67 265.0
14 TraesCS3A01G103000 chr4B 91.398 186 15 1 3862 4047 643895652 643895836 1.960000e-63 254.0
15 TraesCS3A01G103000 chr5B 97.531 162 4 0 3880 4041 349382616 349382777 1.160000e-70 278.0
16 TraesCS3A01G103000 chr2B 96.970 165 5 0 3877 4041 237581574 237581410 1.160000e-70 278.0
17 TraesCS3A01G103000 chr6B 96.914 162 5 0 3880 4041 699977610 699977449 5.410000e-69 272.0
18 TraesCS3A01G103000 chr1B 96.296 162 6 0 3880 4041 662157524 662157363 2.520000e-67 267.0
19 TraesCS3A01G103000 chr6D 97.561 41 1 0 3698 3738 9669750 9669790 2.120000e-08 71.3
20 TraesCS3A01G103000 chr6D 88.525 61 3 4 3701 3758 24554633 24554574 2.120000e-08 71.3
21 TraesCS3A01G103000 chr6D 97.561 41 1 0 3698 3738 298384566 298384606 2.120000e-08 71.3
22 TraesCS3A01G103000 chr6D 95.455 44 2 0 3698 3741 447633854 447633811 2.120000e-08 71.3
23 TraesCS3A01G103000 chr1A 89.474 57 4 2 3683 3738 75916366 75916421 2.120000e-08 71.3
24 TraesCS3A01G103000 chr2D 89.286 56 4 2 3687 3741 43945954 43946008 7.620000e-08 69.4


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 TraesCS3A01G103000 chr3A 66506426 66510670 4244 True 7840.00 7840 100.00000 1 4245 1 chr3A.!!$R1 4244
1 TraesCS3A01G103000 chr3B 90469658 90473753 4095 True 1432.25 2931 91.69775 1 4245 4 chr3B.!!$R1 4244
2 TraesCS3A01G103000 chr3D 57504308 57508510 4202 True 1410.00 2859 90.81125 1 4230 4 chr3D.!!$R1 4229

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
223 238 0.768221 ATCACCTGCCATATCCGGGT 60.768 55.0 0.0 0.0 42.62 5.28 F
967 1037 0.825010 ACAGGGCTGTTTCTTGGCTG 60.825 55.0 0.0 0.0 41.83 4.85 F
1848 1918 0.034089 GCTAATGCACTCCCCCAAGT 60.034 55.0 0.0 0.0 39.41 3.16 F
2005 2077 0.254462 TGCGAATTATCAGTGCCCCA 59.746 50.0 0.0 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1636 1706 0.038310 AAGCTGGCCTAGGTTCCAAC 59.962 55.0 11.31 5.69 43.30 3.77 R
2200 2279 0.743688 TTGGCAAACATCGCACTGTT 59.256 45.0 0.00 0.00 41.01 3.16 R
3145 3236 0.543749 GCCTGCACTTCAGTATCCCT 59.456 55.0 0.00 0.00 41.25 4.20 R
3592 3687 0.719465 GCATACCCAACGACGTCAAG 59.281 55.0 17.16 2.29 0.00 3.02 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
32 37 6.379133 TCCTGATTTCTTTGATTGATTCCCAG 59.621 38.462 0.00 0.00 0.00 4.45
48 53 1.068474 CCAGTAGTTGCCGTTTCTCG 58.932 55.000 0.00 0.00 39.52 4.04
70 75 7.330454 TCTCGCCAATTATAGTACGAGTAGTAG 59.670 40.741 9.68 0.00 45.30 2.57
71 76 6.931281 TCGCCAATTATAGTACGAGTAGTAGT 59.069 38.462 0.00 0.00 41.56 2.73
72 77 8.088365 TCGCCAATTATAGTACGAGTAGTAGTA 58.912 37.037 1.05 1.05 43.24 1.82
86 91 6.579292 CGAGTAGTAGTATCTTGCTTGTATGC 59.421 42.308 0.00 0.00 0.00 3.14
87 92 6.439599 AGTAGTAGTATCTTGCTTGTATGCG 58.560 40.000 0.00 0.00 35.36 4.73
213 228 6.492254 CCGTAGTTTTTATTTATCACCTGCC 58.508 40.000 0.00 0.00 0.00 4.85
214 229 6.094325 CCGTAGTTTTTATTTATCACCTGCCA 59.906 38.462 0.00 0.00 0.00 4.92
219 234 8.860088 AGTTTTTATTTATCACCTGCCATATCC 58.140 33.333 0.00 0.00 0.00 2.59
223 238 0.768221 ATCACCTGCCATATCCGGGT 60.768 55.000 0.00 0.00 42.62 5.28
233 248 1.070758 CATATCCGGGTCCAGGTTCAG 59.929 57.143 8.03 0.00 0.00 3.02
240 255 2.537143 GGGTCCAGGTTCAGAACTCTA 58.463 52.381 13.13 0.00 0.00 2.43
259 274 5.634020 ACTCTAGAATCGCTGTTTGTTGTAC 59.366 40.000 0.00 0.00 0.00 2.90
295 316 2.579207 TCTTGGTCGTCGATTGATCC 57.421 50.000 0.00 0.00 0.00 3.36
346 367 5.106317 CGGGATGCTTGTTTGTACTGTTTAT 60.106 40.000 0.00 0.00 0.00 1.40
348 369 7.361371 CGGGATGCTTGTTTGTACTGTTTATTA 60.361 37.037 0.00 0.00 0.00 0.98
349 370 8.466798 GGGATGCTTGTTTGTACTGTTTATTAT 58.533 33.333 0.00 0.00 0.00 1.28
360 381 8.271312 TGTACTGTTTATTATTACTTGTGGCC 57.729 34.615 0.00 0.00 0.00 5.36
361 382 8.104566 TGTACTGTTTATTATTACTTGTGGCCT 58.895 33.333 3.32 0.00 0.00 5.19
363 384 8.732746 ACTGTTTATTATTACTTGTGGCCTAG 57.267 34.615 3.32 0.94 0.00 3.02
364 385 7.773690 ACTGTTTATTATTACTTGTGGCCTAGG 59.226 37.037 3.67 3.67 0.00 3.02
365 386 7.635648 TGTTTATTATTACTTGTGGCCTAGGT 58.364 34.615 11.31 2.14 0.00 3.08
368 389 3.629142 ATTACTTGTGGCCTAGGTGAC 57.371 47.619 11.31 7.96 0.00 3.67
370 391 0.977395 ACTTGTGGCCTAGGTGACTC 59.023 55.000 11.31 3.29 43.67 3.36
399 420 5.491635 TGATGATAGAACAGAGTCAGTCG 57.508 43.478 0.00 0.00 0.00 4.18
402 423 4.072839 TGATAGAACAGAGTCAGTCGTGT 58.927 43.478 0.00 0.00 0.00 4.49
423 444 0.835941 CATGCTAGGTTGCTCCTCCT 59.164 55.000 4.41 0.38 44.42 3.69
523 575 7.850501 CCAGTTTGGTCAAATAACATGTTTTC 58.149 34.615 17.78 0.00 31.35 2.29
526 578 6.739331 TTGGTCAAATAACATGTTTTCCCT 57.261 33.333 17.78 0.00 0.00 4.20
535 587 2.559668 ACATGTTTTCCCTGTGCATCTG 59.440 45.455 0.00 0.00 0.00 2.90
579 647 7.877097 CCTGTTTCTATCAGCTGCTATATTCTT 59.123 37.037 9.47 0.00 0.00 2.52
606 674 6.507023 ACAAGAATTTGTTGTTAGAAGCCAG 58.493 36.000 6.13 0.00 45.01 4.85
634 702 4.671831 TCCATTTAGAAGGGCAATGTTCA 58.328 39.130 0.00 0.00 30.92 3.18
653 722 4.360951 TCACCCCTTTTGTCGTAATTCT 57.639 40.909 0.00 0.00 0.00 2.40
664 733 5.681337 TGTCGTAATTCTTCACATTTGCA 57.319 34.783 0.00 0.00 0.00 4.08
667 736 6.636447 TGTCGTAATTCTTCACATTTGCAAAG 59.364 34.615 18.19 11.80 0.00 2.77
802 872 9.507329 AGTATATGAAGTCAGTTTCATGTTTGT 57.493 29.630 10.58 0.00 45.00 2.83
873 943 4.916983 TGCTAGCACATTGTTTTCAGTT 57.083 36.364 14.93 0.00 0.00 3.16
885 955 8.850156 ACATTGTTTTCAGTTAGACTAGCATTT 58.150 29.630 0.00 0.00 0.00 2.32
886 956 9.683069 CATTGTTTTCAGTTAGACTAGCATTTT 57.317 29.630 0.00 0.00 0.00 1.82
926 996 9.630098 GACTATTGATGTTCATTCAATTTGTGT 57.370 29.630 4.43 0.91 40.08 3.72
967 1037 0.825010 ACAGGGCTGTTTCTTGGCTG 60.825 55.000 0.00 0.00 41.83 4.85
1064 1134 6.267014 CCTGTGCCTTTAGGTAGCTATACTTA 59.733 42.308 1.80 0.00 37.57 2.24
1097 1167 7.412455 GCTCTGTTCTGCTGTTTATCTTAGTTC 60.412 40.741 0.00 0.00 0.00 3.01
1297 1367 4.927267 AGGGACCTCACATGTTTCATTA 57.073 40.909 0.00 0.00 0.00 1.90
1462 1532 4.760530 TGACTATTATGTTGGCAGCTCT 57.239 40.909 2.28 0.00 0.00 4.09
1484 1554 4.527509 TCCAACAGTCACTTCTCTGATC 57.472 45.455 0.00 0.00 35.84 2.92
1513 1583 3.264450 AGCCAAATCCTAGTGCACTTACT 59.736 43.478 27.06 2.51 34.71 2.24
1542 1612 1.468054 GCATCCGCAAGTGCCTTTAAG 60.468 52.381 0.00 0.00 38.36 1.85
1544 1614 1.154225 CCGCAAGTGCCTTTAAGCG 60.154 57.895 0.00 0.00 44.24 4.68
1615 1685 1.067283 CAGAGGAATGTCAGAGCACGT 60.067 52.381 0.00 0.00 0.00 4.49
1636 1706 5.232202 ACGTCATGATAGTGCTAATGTTTCG 59.768 40.000 0.00 0.00 0.00 3.46
1700 1770 1.758936 TCAGCTGCCATTCCATTCAG 58.241 50.000 9.47 0.00 0.00 3.02
1714 1784 2.608752 CCATTCAGCCACAAGTGCTTTC 60.609 50.000 0.00 0.00 36.81 2.62
1716 1786 0.463654 TCAGCCACAAGTGCTTTCGT 60.464 50.000 0.00 0.00 36.81 3.85
1845 1915 3.833653 TGCTAATGCACTCCCCCA 58.166 55.556 0.00 0.00 45.31 4.96
1846 1916 2.082834 TGCTAATGCACTCCCCCAA 58.917 52.632 0.00 0.00 45.31 4.12
1847 1917 0.034186 TGCTAATGCACTCCCCCAAG 60.034 55.000 0.00 0.00 45.31 3.61
1848 1918 0.034089 GCTAATGCACTCCCCCAAGT 60.034 55.000 0.00 0.00 39.41 3.16
1849 1919 1.616994 GCTAATGCACTCCCCCAAGTT 60.617 52.381 0.00 0.00 39.41 2.66
1850 1920 2.807676 CTAATGCACTCCCCCAAGTTT 58.192 47.619 0.00 0.00 0.00 2.66
1851 1921 2.101640 AATGCACTCCCCCAAGTTTT 57.898 45.000 0.00 0.00 0.00 2.43
1852 1922 2.101640 ATGCACTCCCCCAAGTTTTT 57.898 45.000 0.00 0.00 0.00 1.94
1853 1923 1.408969 TGCACTCCCCCAAGTTTTTC 58.591 50.000 0.00 0.00 0.00 2.29
1854 1924 0.679505 GCACTCCCCCAAGTTTTTCC 59.320 55.000 0.00 0.00 0.00 3.13
1855 1925 1.338107 CACTCCCCCAAGTTTTTCCC 58.662 55.000 0.00 0.00 0.00 3.97
1856 1926 1.133167 CACTCCCCCAAGTTTTTCCCT 60.133 52.381 0.00 0.00 0.00 4.20
1857 1927 1.578703 ACTCCCCCAAGTTTTTCCCTT 59.421 47.619 0.00 0.00 0.00 3.95
1858 1928 1.970640 CTCCCCCAAGTTTTTCCCTTG 59.029 52.381 0.00 0.00 39.19 3.61
1859 1929 1.576272 TCCCCCAAGTTTTTCCCTTGA 59.424 47.619 1.89 0.00 41.44 3.02
1860 1930 1.691976 CCCCCAAGTTTTTCCCTTGAC 59.308 52.381 1.89 0.00 41.44 3.18
1861 1931 2.393646 CCCCAAGTTTTTCCCTTGACA 58.606 47.619 1.89 0.00 41.44 3.58
1862 1932 2.769095 CCCCAAGTTTTTCCCTTGACAA 59.231 45.455 1.89 0.00 41.44 3.18
1863 1933 3.390967 CCCCAAGTTTTTCCCTTGACAAT 59.609 43.478 1.89 0.00 41.44 2.71
1864 1934 4.141505 CCCCAAGTTTTTCCCTTGACAATT 60.142 41.667 1.89 0.00 41.44 2.32
1865 1935 5.071115 CCCCAAGTTTTTCCCTTGACAATTA 59.929 40.000 1.89 0.00 41.44 1.40
1866 1936 6.223120 CCCAAGTTTTTCCCTTGACAATTAG 58.777 40.000 1.89 0.00 41.44 1.73
1867 1937 5.696270 CCAAGTTTTTCCCTTGACAATTAGC 59.304 40.000 1.89 0.00 41.44 3.09
1927 1997 3.781079 TGAGGTTGCTTTTGTGACTTG 57.219 42.857 0.00 0.00 0.00 3.16
1946 2016 6.588756 TGACTTGATTTTAGTAGTTACCTGCG 59.411 38.462 0.00 0.00 0.00 5.18
1951 2021 2.133281 TAGTAGTTACCTGCGGCTGA 57.867 50.000 8.57 0.00 0.00 4.26
1952 2022 1.486211 AGTAGTTACCTGCGGCTGAT 58.514 50.000 8.57 0.00 0.00 2.90
1988 2058 9.202273 TGTGATACAATTTTACCAGAAAAATGC 57.798 29.630 0.00 0.00 38.68 3.56
1990 2060 8.300286 TGATACAATTTTACCAGAAAAATGCGA 58.700 29.630 0.00 0.00 38.68 5.10
2001 2073 5.230726 CCAGAAAAATGCGAATTATCAGTGC 59.769 40.000 0.00 0.00 0.00 4.40
2005 2077 0.254462 TGCGAATTATCAGTGCCCCA 59.746 50.000 0.00 0.00 0.00 4.96
2050 2122 6.378582 AGCATACGAGGTTGTTGTTTTTATG 58.621 36.000 0.00 0.00 0.00 1.90
2058 2130 9.567848 CGAGGTTGTTGTTTTTATGCTATTTAT 57.432 29.630 0.00 0.00 0.00 1.40
2137 2216 5.080337 TCACTGGTAGGATCTACCATCATC 58.920 45.833 22.41 0.00 45.53 2.92
2138 2217 4.221703 CACTGGTAGGATCTACCATCATCC 59.778 50.000 22.41 2.79 45.53 3.51
2140 2219 5.316183 ACTGGTAGGATCTACCATCATCCTA 59.684 44.000 22.41 9.39 46.10 2.94
2200 2279 3.221771 CCAACTGTCCATGGTTCTTCAA 58.778 45.455 12.58 0.00 31.84 2.69
2429 2508 2.291365 CCATGATGCAGTCATTCCGAA 58.709 47.619 8.38 0.00 45.25 4.30
2436 2515 2.766263 TGCAGTCATTCCGAACTATCCT 59.234 45.455 0.00 0.00 0.00 3.24
2440 2519 3.452627 AGTCATTCCGAACTATCCTGCTT 59.547 43.478 0.00 0.00 0.00 3.91
2457 2536 4.346418 CCTGCTTCTACCTCTACATCCATT 59.654 45.833 0.00 0.00 0.00 3.16
2490 2572 2.352225 GCCATCTCCTATCAGTACTGCG 60.352 54.545 18.45 8.60 0.00 5.18
2523 2605 0.557238 ATGCAAGGGTATCCATGGCA 59.443 50.000 6.96 4.99 38.98 4.92
2606 2688 3.243771 ACACAGGTAGAGGTCTTGTTTCG 60.244 47.826 0.00 0.00 0.00 3.46
2622 2704 8.124199 GTCTTGTTTCGTGTTTTCAGGTAATTA 58.876 33.333 0.00 0.00 37.06 1.40
2768 2850 5.702670 GGACTTGAGACTGAACATTGATGAA 59.297 40.000 0.00 0.00 0.00 2.57
2812 2894 3.321111 TGGTCGTTTGCTTCTTCTACTCT 59.679 43.478 0.00 0.00 0.00 3.24
2958 3041 2.171448 AGAAGTGGTCTGTTGCAGTTCT 59.829 45.455 0.00 0.00 34.29 3.01
2966 3049 2.634453 TCTGTTGCAGTTCTGATGAGGA 59.366 45.455 3.84 0.00 32.61 3.71
2967 3050 3.001414 CTGTTGCAGTTCTGATGAGGAG 58.999 50.000 3.84 0.00 0.00 3.69
2976 3059 1.747924 TCTGATGAGGAGCAAGACGAG 59.252 52.381 0.00 0.00 0.00 4.18
3049 3132 6.780031 TCCTAATTTCCAGTTCCATGTTGAAA 59.220 34.615 0.00 0.00 0.00 2.69
3062 3145 8.711457 GTTCCATGTTGAAAAATTCATTACAGG 58.289 33.333 0.00 4.13 39.84 4.00
3084 3167 0.960364 TGCCCTGAATCGTTTGCTCC 60.960 55.000 0.00 0.00 0.00 4.70
3145 3236 6.897966 AGGAGTACAAAGACAATGATCTCCTA 59.102 38.462 16.09 0.00 42.84 2.94
3148 3239 5.365021 ACAAAGACAATGATCTCCTAGGG 57.635 43.478 9.46 0.00 0.00 3.53
3151 3242 6.846505 ACAAAGACAATGATCTCCTAGGGATA 59.153 38.462 9.46 0.00 0.00 2.59
3178 3269 1.961277 CAGGCACGACTTCCACACC 60.961 63.158 0.00 0.00 0.00 4.16
3202 3293 2.030371 TGCATCAAGAAGTGGTTGCAA 58.970 42.857 0.00 0.00 41.09 4.08
3223 3314 1.448893 GAAGAACGCATGCCCGGTA 60.449 57.895 13.15 0.00 0.00 4.02
3315 3407 3.179443 TGAGATTGAGTTATGCGGTCC 57.821 47.619 0.00 0.00 0.00 4.46
3469 3564 7.572523 TTCTCCAGCCATTTATTTATCTGTG 57.427 36.000 0.00 0.00 0.00 3.66
3582 3677 0.478072 AGGTTGTTGGCATGAGACCA 59.522 50.000 0.00 0.00 34.65 4.02
3592 3687 2.035066 GGCATGAGACCAATAATGTGGC 59.965 50.000 0.00 0.00 43.00 5.01
3600 3695 2.747446 ACCAATAATGTGGCTTGACGTC 59.253 45.455 9.11 9.11 43.00 4.34
3602 3697 2.380084 ATAATGTGGCTTGACGTCGT 57.620 45.000 11.62 0.00 0.00 4.34
3623 3718 1.876714 GGTATGCGCATGTCGTCGT 60.877 57.895 32.48 7.17 41.07 4.34
3892 4017 7.938715 TCTTGAACTATATACTTCCTCCGTTC 58.061 38.462 0.00 0.00 0.00 3.95
3894 4019 6.371278 TGAACTATATACTTCCTCCGTTCCT 58.629 40.000 0.00 0.00 31.17 3.36
3895 4020 7.520798 TGAACTATATACTTCCTCCGTTCCTA 58.479 38.462 0.00 0.00 31.17 2.94
3897 4022 8.773033 AACTATATACTTCCTCCGTTCCTAAA 57.227 34.615 0.00 0.00 0.00 1.85
3906 4031 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3907 4032 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
3909 4034 8.202137 TCCTCCGTTCCTAAATATAAGTCTTTG 58.798 37.037 0.00 0.00 0.00 2.77
3910 4035 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3927 4052 8.621532 AGTCTTTGTAGAAATTTCACTATGCA 57.378 30.769 19.99 6.42 30.65 3.96
3928 4053 8.507249 AGTCTTTGTAGAAATTTCACTATGCAC 58.493 33.333 19.99 8.80 30.65 4.57
3929 4054 8.507249 GTCTTTGTAGAAATTTCACTATGCACT 58.493 33.333 19.99 0.00 30.65 4.40
3930 4055 9.719355 TCTTTGTAGAAATTTCACTATGCACTA 57.281 29.630 19.99 0.00 0.00 2.74
3931 4056 9.760660 CTTTGTAGAAATTTCACTATGCACTAC 57.239 33.333 19.99 10.34 0.00 2.73
3932 4057 8.840833 TTGTAGAAATTTCACTATGCACTACA 57.159 30.769 19.99 12.52 36.83 2.74
3933 4058 9.448438 TTGTAGAAATTTCACTATGCACTACAT 57.552 29.630 19.99 0.00 43.18 2.29
3936 4061 8.131455 AGAAATTTCACTATGCACTACATACG 57.869 34.615 19.99 0.00 40.38 3.06
3937 4062 6.844696 AATTTCACTATGCACTACATACGG 57.155 37.500 0.00 0.00 40.38 4.02
3938 4063 5.585820 TTTCACTATGCACTACATACGGA 57.414 39.130 0.00 0.00 40.38 4.69
3939 4064 4.830826 TCACTATGCACTACATACGGAG 57.169 45.455 0.00 0.00 40.38 4.63
3940 4065 3.004419 TCACTATGCACTACATACGGAGC 59.996 47.826 0.00 0.00 40.38 4.70
3941 4066 2.956333 ACTATGCACTACATACGGAGCA 59.044 45.455 0.00 0.00 40.38 4.26
3942 4067 2.979814 ATGCACTACATACGGAGCAA 57.020 45.000 0.00 0.00 37.17 3.91
3943 4068 2.753055 TGCACTACATACGGAGCAAA 57.247 45.000 0.00 0.00 0.00 3.68
3944 4069 3.046968 TGCACTACATACGGAGCAAAA 57.953 42.857 0.00 0.00 0.00 2.44
3945 4070 3.605634 TGCACTACATACGGAGCAAAAT 58.394 40.909 0.00 0.00 0.00 1.82
3946 4071 3.373748 TGCACTACATACGGAGCAAAATG 59.626 43.478 0.00 0.00 0.00 2.32
3947 4072 3.621268 GCACTACATACGGAGCAAAATGA 59.379 43.478 0.00 0.00 0.00 2.57
3948 4073 4.260375 GCACTACATACGGAGCAAAATGAG 60.260 45.833 0.00 0.00 0.00 2.90
3949 4074 4.870426 CACTACATACGGAGCAAAATGAGT 59.130 41.667 0.00 0.00 0.00 3.41
3950 4075 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3951 4076 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3952 4077 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3953 4078 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3954 4079 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3955 4080 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3956 4081 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3957 4082 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3998 4123 6.951256 CATACATCCGTATGTGGTTCATAG 57.049 41.667 3.56 0.00 46.70 2.23
3999 4124 6.455647 CATACATCCGTATGTGGTTCATAGT 58.544 40.000 3.56 0.00 46.70 2.12
4000 4125 4.693283 ACATCCGTATGTGGTTCATAGTG 58.307 43.478 0.00 0.00 44.79 2.74
4001 4126 3.812156 TCCGTATGTGGTTCATAGTGG 57.188 47.619 0.00 0.00 39.36 4.00
4002 4127 3.367321 TCCGTATGTGGTTCATAGTGGA 58.633 45.455 0.00 0.00 39.94 4.02
4003 4128 3.770388 TCCGTATGTGGTTCATAGTGGAA 59.230 43.478 0.00 0.00 39.60 3.53
4004 4129 4.407621 TCCGTATGTGGTTCATAGTGGAAT 59.592 41.667 0.00 0.00 39.60 3.01
4005 4130 4.750098 CCGTATGTGGTTCATAGTGGAATC 59.250 45.833 0.00 0.00 39.36 2.52
4006 4131 5.453339 CCGTATGTGGTTCATAGTGGAATCT 60.453 44.000 0.00 0.00 39.36 2.40
4007 4132 5.692204 CGTATGTGGTTCATAGTGGAATCTC 59.308 44.000 0.00 0.00 39.36 2.75
4008 4133 5.965033 ATGTGGTTCATAGTGGAATCTCT 57.035 39.130 0.00 0.00 34.67 3.10
4009 4134 5.344743 TGTGGTTCATAGTGGAATCTCTC 57.655 43.478 0.00 0.00 0.00 3.20
4012 4137 8.954344 ATGTGGTTCATAGTGGAATCTCTCCAA 61.954 40.741 0.00 0.00 44.66 3.53
4039 4164 8.068733 AGACTTATATTTAGGAACAGAGGGAGT 58.931 37.037 0.00 0.00 0.00 3.85
4040 4165 9.364653 GACTTATATTTAGGAACAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
4041 4166 9.900112 ACTTATATTTAGGAACAGAGGGAGTAT 57.100 33.333 0.00 0.00 0.00 2.12
4045 4170 6.697641 TTTAGGAACAGAGGGAGTATTTGT 57.302 37.500 0.00 0.00 0.00 2.83
4046 4171 6.697641 TTAGGAACAGAGGGAGTATTTGTT 57.302 37.500 0.00 0.00 34.91 2.83
4047 4172 7.801893 TTAGGAACAGAGGGAGTATTTGTTA 57.198 36.000 0.00 0.00 32.58 2.41
4048 4173 6.301169 AGGAACAGAGGGAGTATTTGTTAG 57.699 41.667 0.00 0.00 32.58 2.34
4049 4174 5.785940 AGGAACAGAGGGAGTATTTGTTAGT 59.214 40.000 0.00 0.00 32.58 2.24
4050 4175 6.958192 AGGAACAGAGGGAGTATTTGTTAGTA 59.042 38.462 0.00 0.00 32.58 1.82
4051 4176 7.040494 GGAACAGAGGGAGTATTTGTTAGTAC 58.960 42.308 0.00 0.00 32.58 2.73
4113 4238 2.996249 TGGGCTTCACAAAATTGCAA 57.004 40.000 0.00 0.00 0.00 4.08
4121 4246 3.443037 TCACAAAATTGCAACCAGTTCG 58.557 40.909 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 75 2.221981 GCCTCGCATACAAGCAAGATAC 59.778 50.000 0.00 0.00 0.00 2.24
71 76 2.483876 GCCTCGCATACAAGCAAGATA 58.516 47.619 0.00 0.00 0.00 1.98
72 77 1.303309 GCCTCGCATACAAGCAAGAT 58.697 50.000 0.00 0.00 0.00 2.40
123 138 2.437716 ATGCGGTACCCAAAGCGG 60.438 61.111 6.25 0.00 40.57 5.52
142 157 5.274823 CGCGAGTAAAATTTCAAATTCGCTC 60.275 40.000 22.96 14.00 46.92 5.03
144 159 4.771741 GCGCGAGTAAAATTTCAAATTCGC 60.772 41.667 12.10 19.18 46.00 4.70
213 228 1.070758 CTGAACCTGGACCCGGATATG 59.929 57.143 9.25 0.00 0.00 1.78
214 229 1.062428 TCTGAACCTGGACCCGGATAT 60.062 52.381 9.25 0.00 0.00 1.63
219 234 0.037232 GAGTTCTGAACCTGGACCCG 60.037 60.000 16.48 0.00 0.00 5.28
223 238 4.399618 CGATTCTAGAGTTCTGAACCTGGA 59.600 45.833 16.48 15.99 0.00 3.86
233 248 5.177696 ACAACAAACAGCGATTCTAGAGTTC 59.822 40.000 0.00 0.00 0.00 3.01
240 255 5.334879 GGATTGTACAACAAACAGCGATTCT 60.335 40.000 11.22 0.00 41.96 2.40
259 274 1.856629 AGAATTGGTGCCAGGGATTG 58.143 50.000 0.00 0.00 0.00 2.67
286 307 2.848887 GAGCATATCGACGGATCAATCG 59.151 50.000 10.70 10.70 39.72 3.34
295 316 1.399572 CCAACGAGAGCATATCGACG 58.600 55.000 11.48 0.00 42.76 5.12
346 367 4.781087 AGTCACCTAGGCCACAAGTAATAA 59.219 41.667 9.30 0.00 0.00 1.40
348 369 3.182152 AGTCACCTAGGCCACAAGTAAT 58.818 45.455 9.30 0.00 0.00 1.89
349 370 2.565834 GAGTCACCTAGGCCACAAGTAA 59.434 50.000 9.30 0.00 0.00 2.24
351 372 0.977395 GAGTCACCTAGGCCACAAGT 59.023 55.000 9.30 0.00 0.00 3.16
352 373 1.270907 AGAGTCACCTAGGCCACAAG 58.729 55.000 9.30 0.00 0.00 3.16
353 374 1.729586 AAGAGTCACCTAGGCCACAA 58.270 50.000 9.30 0.00 0.00 3.33
356 377 4.534500 TCAAATTAAGAGTCACCTAGGCCA 59.466 41.667 9.30 0.00 0.00 5.36
357 378 5.099042 TCAAATTAAGAGTCACCTAGGCC 57.901 43.478 9.30 0.00 0.00 5.19
358 379 6.349300 TCATCAAATTAAGAGTCACCTAGGC 58.651 40.000 9.30 0.00 0.00 3.93
359 380 9.703892 CTATCATCAAATTAAGAGTCACCTAGG 57.296 37.037 7.41 7.41 0.00 3.02
363 384 9.383519 TGTTCTATCATCAAATTAAGAGTCACC 57.616 33.333 0.00 0.00 0.00 4.02
387 408 0.676184 ATGCACACGACTGACTCTGT 59.324 50.000 0.00 0.00 0.00 3.41
399 420 0.449388 GAGCAACCTAGCATGCACAC 59.551 55.000 21.98 1.58 44.95 3.82
402 423 4.643795 GGAGCAACCTAGCATGCA 57.356 55.556 21.98 5.01 44.95 3.96
423 444 4.459685 TCCGTTTTGTTTCCTTTGTCAGAA 59.540 37.500 0.00 0.00 0.00 3.02
440 461 2.086869 CCATCAGAGTGCAATCCGTTT 58.913 47.619 11.14 0.00 0.00 3.60
442 463 0.107508 CCCATCAGAGTGCAATCCGT 60.108 55.000 11.14 0.00 0.00 4.69
443 464 0.107508 ACCCATCAGAGTGCAATCCG 60.108 55.000 11.14 0.00 0.00 4.18
523 575 1.162698 CAGTCAACAGATGCACAGGG 58.837 55.000 0.00 0.00 0.00 4.45
526 578 4.002982 GGTTATCAGTCAACAGATGCACA 58.997 43.478 0.00 0.00 0.00 4.57
535 587 2.749621 CAGGGCAAGGTTATCAGTCAAC 59.250 50.000 0.00 0.00 0.00 3.18
606 674 6.998673 ACATTGCCCTTCTAAATGGAGTATAC 59.001 38.462 0.00 0.00 35.95 1.47
634 702 4.517832 GTGAAGAATTACGACAAAAGGGGT 59.482 41.667 0.00 0.00 0.00 4.95
653 722 5.769662 AGGTGAGATACTTTGCAAATGTGAA 59.230 36.000 13.23 0.15 35.64 3.18
664 733 5.234466 AGCACTTGAAGGTGAGATACTTT 57.766 39.130 0.00 0.00 39.34 2.66
667 736 7.224949 GGTAATTAGCACTTGAAGGTGAGATAC 59.775 40.741 9.77 0.00 39.34 2.24
802 872 1.324740 ACCGCCGCAACTCAGGTATA 61.325 55.000 0.00 0.00 32.76 1.47
885 955 8.258007 ACATCAATAGTCTAGAATCGGACAAAA 58.742 33.333 0.00 0.00 35.18 2.44
886 956 7.782049 ACATCAATAGTCTAGAATCGGACAAA 58.218 34.615 0.00 1.49 35.18 2.83
887 957 7.348080 ACATCAATAGTCTAGAATCGGACAA 57.652 36.000 0.00 0.00 35.18 3.18
892 962 9.468532 TGAATGAACATCAATAGTCTAGAATCG 57.531 33.333 0.00 0.00 0.00 3.34
926 996 2.003937 GGTTGCCCTTAACCTGGAAA 57.996 50.000 0.00 0.00 45.29 3.13
967 1037 3.135348 TGGAGATGGTTCAGATGATGTCC 59.865 47.826 0.00 0.00 0.00 4.02
1064 1134 0.471617 AGCAGAACAGAGCACAGGTT 59.528 50.000 0.00 0.00 0.00 3.50
1114 1184 6.267699 TCTGACCTGAGATTGAAACAAGAGTA 59.732 38.462 0.00 0.00 0.00 2.59
1462 1532 4.590647 AGATCAGAGAAGTGACTGTTGGAA 59.409 41.667 0.00 0.00 35.84 3.53
1484 1554 2.163010 CACTAGGATTTGGCTGCACAAG 59.837 50.000 0.50 0.00 0.00 3.16
1532 1602 0.240145 GGACCAACGCTTAAAGGCAC 59.760 55.000 0.00 0.00 0.00 5.01
1542 1612 1.008538 CAGTTGCTTGGACCAACGC 60.009 57.895 17.01 17.01 45.38 4.84
1544 1614 3.109847 TCCAGTTGCTTGGACCAAC 57.890 52.632 1.69 1.39 42.24 3.77
1615 1685 6.037062 CCAACGAAACATTAGCACTATCATGA 59.963 38.462 0.00 0.00 0.00 3.07
1631 1701 1.162698 GGCCTAGGTTCCAACGAAAC 58.837 55.000 11.31 0.00 35.79 2.78
1636 1706 0.038310 AAGCTGGCCTAGGTTCCAAC 59.962 55.000 11.31 5.69 43.30 3.77
1700 1770 1.602377 ACTTACGAAAGCACTTGTGGC 59.398 47.619 2.81 0.00 36.05 5.01
1716 1786 1.897133 TCCTTTCTGCTGCCGTACTTA 59.103 47.619 0.00 0.00 0.00 2.24
1724 1794 0.038801 GCTTGGTTCCTTTCTGCTGC 60.039 55.000 0.00 0.00 0.00 5.25
1806 1876 5.617751 GCAAGACAATAAAGACGCATCAAGT 60.618 40.000 0.00 0.00 0.00 3.16
1837 1907 1.241485 AGGGAAAAACTTGGGGGAGT 58.759 50.000 0.00 0.00 0.00 3.85
1838 1908 1.970640 CAAGGGAAAAACTTGGGGGAG 59.029 52.381 0.00 0.00 41.16 4.30
1839 1909 1.576272 TCAAGGGAAAAACTTGGGGGA 59.424 47.619 5.46 0.00 44.13 4.81
1840 1910 1.691976 GTCAAGGGAAAAACTTGGGGG 59.308 52.381 5.46 0.00 44.13 5.40
1841 1911 2.393646 TGTCAAGGGAAAAACTTGGGG 58.606 47.619 5.46 0.00 44.13 4.96
1842 1912 4.687901 ATTGTCAAGGGAAAAACTTGGG 57.312 40.909 5.46 0.00 44.13 4.12
1843 1913 5.696270 GCTAATTGTCAAGGGAAAAACTTGG 59.304 40.000 5.46 0.00 44.13 3.61
1844 1914 6.279882 TGCTAATTGTCAAGGGAAAAACTTG 58.720 36.000 0.00 0.00 45.08 3.16
1845 1915 6.478512 TGCTAATTGTCAAGGGAAAAACTT 57.521 33.333 0.00 0.00 0.00 2.66
1846 1916 6.494835 AGATGCTAATTGTCAAGGGAAAAACT 59.505 34.615 0.00 0.00 0.00 2.66
1847 1917 6.691508 AGATGCTAATTGTCAAGGGAAAAAC 58.308 36.000 0.00 0.00 0.00 2.43
1848 1918 6.493115 TGAGATGCTAATTGTCAAGGGAAAAA 59.507 34.615 0.00 0.00 0.00 1.94
1849 1919 6.009589 TGAGATGCTAATTGTCAAGGGAAAA 58.990 36.000 0.00 0.00 0.00 2.29
1850 1920 5.569355 TGAGATGCTAATTGTCAAGGGAAA 58.431 37.500 0.00 0.00 0.00 3.13
1851 1921 5.178096 TGAGATGCTAATTGTCAAGGGAA 57.822 39.130 0.00 0.00 0.00 3.97
1852 1922 4.842531 TGAGATGCTAATTGTCAAGGGA 57.157 40.909 0.00 0.00 0.00 4.20
1853 1923 5.434352 CATGAGATGCTAATTGTCAAGGG 57.566 43.478 0.00 0.00 0.00 3.95
1867 1937 2.306341 ACAGAAGACCGCATGAGATG 57.694 50.000 0.00 0.00 0.00 2.90
1876 1946 6.727824 ATTAAAGATGTGAACAGAAGACCG 57.272 37.500 0.00 0.00 0.00 4.79
1952 2022 8.573035 GGTAAAATTGTATCACAGGACTGAAAA 58.427 33.333 6.29 0.00 0.00 2.29
1987 2057 1.388547 TTGGGGCACTGATAATTCGC 58.611 50.000 0.00 0.00 0.00 4.70
1988 2058 3.631686 TGATTTGGGGCACTGATAATTCG 59.368 43.478 0.00 0.00 0.00 3.34
1990 2060 5.461327 AGATGATTTGGGGCACTGATAATT 58.539 37.500 0.00 0.00 0.00 1.40
1996 2068 2.173519 ACAAGATGATTTGGGGCACTG 58.826 47.619 0.00 0.00 32.32 3.66
2029 2101 6.569179 AGCATAAAAACAACAACCTCGTAT 57.431 33.333 0.00 0.00 0.00 3.06
2032 2104 7.867445 AAATAGCATAAAAACAACAACCTCG 57.133 32.000 0.00 0.00 0.00 4.63
2075 2152 9.577110 CTAAACAGTCAAAATACATAGACCGTA 57.423 33.333 0.00 0.00 0.00 4.02
2078 2155 8.665685 CACCTAAACAGTCAAAATACATAGACC 58.334 37.037 0.00 0.00 0.00 3.85
2091 2168 1.202758 CCAGTGCCACCTAAACAGTCA 60.203 52.381 0.00 0.00 0.00 3.41
2141 2220 0.887836 GCTGCTGCTATGCATAGGCA 60.888 55.000 30.14 27.93 45.10 4.75
2142 2221 1.874562 GCTGCTGCTATGCATAGGC 59.125 57.895 30.14 25.46 42.48 3.93
2200 2279 0.743688 TTGGCAAACATCGCACTGTT 59.256 45.000 0.00 0.00 41.01 3.16
2429 2508 5.390087 TGTAGAGGTAGAAGCAGGATAGT 57.610 43.478 0.00 0.00 0.00 2.12
2436 2515 5.540337 CCTAATGGATGTAGAGGTAGAAGCA 59.460 44.000 0.00 0.00 34.57 3.91
2467 2549 3.553922 GCAGTACTGATAGGAGATGGCAC 60.554 52.174 27.08 0.00 0.00 5.01
2490 2572 1.607628 CTTGCATGCCTAGAAGATGCC 59.392 52.381 16.68 2.62 41.54 4.40
2531 2613 6.216569 TCTACGAATCTATTCATTCCAGTGC 58.783 40.000 3.76 0.00 36.61 4.40
2534 2616 8.961634 TCCTATCTACGAATCTATTCATTCCAG 58.038 37.037 3.76 0.00 36.61 3.86
2540 2622 7.168905 TGAGCTCCTATCTACGAATCTATTCA 58.831 38.462 12.15 0.00 36.61 2.57
2606 2688 6.327279 ACCAGCTTAATTACCTGAAAACAC 57.673 37.500 11.91 0.00 0.00 3.32
2622 2704 7.775053 TTCAAACTTAAATGGATACCAGCTT 57.225 32.000 0.00 0.00 36.75 3.74
2768 2850 9.950496 GACCATGATTATACCTCATAACTCATT 57.050 33.333 0.00 0.00 31.77 2.57
2777 2859 4.814234 GCAAACGACCATGATTATACCTCA 59.186 41.667 0.00 0.00 0.00 3.86
2786 2868 3.679389 AGAAGAAGCAAACGACCATGAT 58.321 40.909 0.00 0.00 0.00 2.45
2787 2869 3.126001 AGAAGAAGCAAACGACCATGA 57.874 42.857 0.00 0.00 0.00 3.07
2788 2870 3.997021 AGTAGAAGAAGCAAACGACCATG 59.003 43.478 0.00 0.00 0.00 3.66
2812 2894 7.230712 GGTTAAGAAAAGATCCTGAAGTTTCCA 59.769 37.037 0.00 0.00 0.00 3.53
2958 3041 0.820226 CCTCGTCTTGCTCCTCATCA 59.180 55.000 0.00 0.00 0.00 3.07
2966 3049 2.158986 CCATCATCTTCCTCGTCTTGCT 60.159 50.000 0.00 0.00 0.00 3.91
2967 3050 2.208431 CCATCATCTTCCTCGTCTTGC 58.792 52.381 0.00 0.00 0.00 4.01
2976 3059 1.153086 ACAGCGCCCATCATCTTCC 60.153 57.895 2.29 0.00 0.00 3.46
3049 3132 3.133362 CAGGGCATGCCTGTAATGAATTT 59.867 43.478 34.70 4.89 36.10 1.82
3062 3145 0.803380 GCAAACGATTCAGGGCATGC 60.803 55.000 9.90 9.90 0.00 4.06
3145 3236 0.543749 GCCTGCACTTCAGTATCCCT 59.456 55.000 0.00 0.00 41.25 4.20
3148 3239 1.002366 CGTGCCTGCACTTCAGTATC 58.998 55.000 19.07 0.00 44.16 2.24
3151 3242 1.595382 GTCGTGCCTGCACTTCAGT 60.595 57.895 19.07 0.00 44.16 3.41
3178 3269 1.800805 ACCACTTCTTGATGCAGTCG 58.199 50.000 0.00 0.00 0.00 4.18
3202 3293 2.034879 CGGGCATGCGTTCTTCACT 61.035 57.895 12.44 0.00 0.00 3.41
3248 3339 2.168521 CGGTTATTCTGCTTCCTCTCCA 59.831 50.000 0.00 0.00 0.00 3.86
3467 3562 2.346803 ACGGCTCAACATGTGATACAC 58.653 47.619 0.00 0.00 35.07 2.90
3469 3564 2.742053 ACAACGGCTCAACATGTGATAC 59.258 45.455 0.00 0.00 35.07 2.24
3582 3677 2.695359 ACGACGTCAAGCCACATTATT 58.305 42.857 17.16 0.00 0.00 1.40
3592 3687 0.719465 GCATACCCAACGACGTCAAG 59.281 55.000 17.16 2.29 0.00 3.02
3600 3695 1.351707 GACATGCGCATACCCAACG 59.648 57.895 24.84 11.44 0.00 4.10
3602 3697 1.078778 ACGACATGCGCATACCCAA 60.079 52.632 24.84 0.00 46.04 4.12
3623 3718 1.891919 GTCACAGCCAACGAGCCAA 60.892 57.895 0.00 0.00 0.00 4.52
3868 3987 7.014422 AGGAACGGAGGAAGTATATAGTTCAAG 59.986 40.741 24.93 16.72 38.62 3.02
3901 4026 9.066892 TGCATAGTGAAATTTCTACAAAGACTT 57.933 29.630 18.64 2.00 0.00 3.01
3902 4027 8.507249 GTGCATAGTGAAATTTCTACAAAGACT 58.493 33.333 18.64 13.41 0.00 3.24
3906 4031 9.278978 TGTAGTGCATAGTGAAATTTCTACAAA 57.721 29.630 18.64 8.40 34.46 2.83
3907 4032 8.840833 TGTAGTGCATAGTGAAATTTCTACAA 57.159 30.769 18.64 3.14 34.46 2.41
3910 4035 9.244799 CGTATGTAGTGCATAGTGAAATTTCTA 57.755 33.333 18.64 4.82 40.42 2.10
3912 4037 7.223971 TCCGTATGTAGTGCATAGTGAAATTTC 59.776 37.037 11.41 11.41 40.42 2.17
3913 4038 7.045416 TCCGTATGTAGTGCATAGTGAAATTT 58.955 34.615 0.61 0.00 40.42 1.82
3914 4039 6.578944 TCCGTATGTAGTGCATAGTGAAATT 58.421 36.000 0.61 0.00 40.42 1.82
3915 4040 6.156748 TCCGTATGTAGTGCATAGTGAAAT 57.843 37.500 0.61 0.00 40.42 2.17
3916 4041 5.585820 TCCGTATGTAGTGCATAGTGAAA 57.414 39.130 0.61 0.00 40.42 2.69
3918 4043 3.004419 GCTCCGTATGTAGTGCATAGTGA 59.996 47.826 0.61 1.11 40.42 3.41
3919 4044 3.243401 TGCTCCGTATGTAGTGCATAGTG 60.243 47.826 0.61 0.00 40.42 2.74
3921 4046 3.643159 TGCTCCGTATGTAGTGCATAG 57.357 47.619 0.61 0.00 40.42 2.23
3922 4047 4.394439 TTTGCTCCGTATGTAGTGCATA 57.606 40.909 0.00 0.00 38.94 3.14
3923 4048 2.979814 TTGCTCCGTATGTAGTGCAT 57.020 45.000 0.00 0.00 41.42 3.96
3924 4049 2.753055 TTTGCTCCGTATGTAGTGCA 57.247 45.000 0.00 0.00 0.00 4.57
3925 4050 3.621268 TCATTTTGCTCCGTATGTAGTGC 59.379 43.478 0.00 0.00 0.00 4.40
3926 4051 4.870426 ACTCATTTTGCTCCGTATGTAGTG 59.130 41.667 0.00 0.00 0.00 2.74
3927 4052 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3928 4053 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3929 4054 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3930 4055 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3931 4056 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3932 4057 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3933 4058 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3934 4059 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3935 4060 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3936 4061 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3937 4062 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3984 4109 6.821388 AGAGATTCCACTATGAACCACATAC 58.179 40.000 0.00 0.00 40.07 2.39
3986 4111 5.163258 GGAGAGATTCCACTATGAACCACAT 60.163 44.000 0.00 0.00 46.01 3.21
3988 4113 4.698575 GGAGAGATTCCACTATGAACCAC 58.301 47.826 0.00 0.00 46.01 4.16
4009 4134 9.331282 CCTCTGTTCCTAAATATAAGTCTTTGG 57.669 37.037 0.00 0.00 0.00 3.28
4012 4137 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
4013 4138 8.068733 ACTCCCTCTGTTCCTAAATATAAGTCT 58.931 37.037 0.00 0.00 0.00 3.24
4019 4144 9.004231 ACAAATACTCCCTCTGTTCCTAAATAT 57.996 33.333 0.00 0.00 0.00 1.28
4022 4147 6.697641 ACAAATACTCCCTCTGTTCCTAAA 57.302 37.500 0.00 0.00 0.00 1.85
4024 4149 6.958192 ACTAACAAATACTCCCTCTGTTCCTA 59.042 38.462 0.00 0.00 32.69 2.94
4025 4150 5.785940 ACTAACAAATACTCCCTCTGTTCCT 59.214 40.000 0.00 0.00 32.69 3.36
4031 4156 9.544579 AAACTAGTACTAACAAATACTCCCTCT 57.455 33.333 3.76 0.00 33.65 3.69
4040 4165 9.317827 TCCCTCTGTAAACTAGTACTAACAAAT 57.682 33.333 3.76 0.00 0.00 2.32
4041 4166 8.710749 TCCCTCTGTAAACTAGTACTAACAAA 57.289 34.615 3.76 0.00 0.00 2.83
4042 4167 7.946776 ACTCCCTCTGTAAACTAGTACTAACAA 59.053 37.037 3.76 0.00 0.00 2.83
4043 4168 7.465116 ACTCCCTCTGTAAACTAGTACTAACA 58.535 38.462 3.76 4.66 0.00 2.41
4044 4169 7.936496 ACTCCCTCTGTAAACTAGTACTAAC 57.064 40.000 3.76 0.00 0.00 2.34
4045 4170 8.830741 AGTACTCCCTCTGTAAACTAGTACTAA 58.169 37.037 9.79 0.00 43.72 2.24
4046 4171 8.386012 AGTACTCCCTCTGTAAACTAGTACTA 57.614 38.462 9.79 1.89 43.72 1.82
4047 4172 7.269522 AGTACTCCCTCTGTAAACTAGTACT 57.730 40.000 0.00 0.00 41.86 2.73
4048 4173 7.628153 GCAAGTACTCCCTCTGTAAACTAGTAC 60.628 44.444 0.00 0.00 38.59 2.73
4049 4174 6.376581 GCAAGTACTCCCTCTGTAAACTAGTA 59.623 42.308 0.00 0.00 0.00 1.82
4050 4175 5.185442 GCAAGTACTCCCTCTGTAAACTAGT 59.815 44.000 0.00 0.00 0.00 2.57
4051 4176 5.394333 GGCAAGTACTCCCTCTGTAAACTAG 60.394 48.000 0.00 0.00 0.00 2.57
4113 4238 6.056884 TGGTAATCAAAGTTTACGAACTGGT 58.943 36.000 0.00 0.00 45.18 4.00


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

AutoCloner maintained by Alex Coulton.