Multiple sequence alignment - TraesCS2D01G428000

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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 TraesCS2D01G428000 chr2D 100.000 3188 0 0 1 3188 539897240 539894053 0.000000e+00 5888.0
1 TraesCS2D01G428000 chr2B 86.195 2586 154 85 28 2527 644170113 644167645 0.000000e+00 2610.0
2 TraesCS2D01G428000 chr2B 88.889 162 16 2 2521 2681 644167541 644167381 6.980000e-47 198.0
3 TraesCS2D01G428000 chr2B 90.244 82 4 2 3107 3188 644167003 644166926 1.560000e-18 104.0
4 TraesCS2D01G428000 chr2B 97.436 39 1 0 113 151 368891836 368891798 2.050000e-07 67.6
5 TraesCS2D01G428000 chr2A 87.728 1646 103 51 544 2109 683537435 683535809 0.000000e+00 1829.0
6 TraesCS2D01G428000 chr2A 92.486 346 14 7 2840 3183 683534985 683534650 4.780000e-133 484.0
7 TraesCS2D01G428000 chr2A 84.029 407 54 11 152 551 683537860 683537458 6.450000e-102 381.0
8 TraesCS2D01G428000 chr2A 96.396 111 4 0 2413 2523 683535539 683535429 1.950000e-42 183.0
9 TraesCS2D01G428000 chr2A 92.647 68 5 0 89 156 683538987 683538920 7.280000e-17 99.0
10 TraesCS2D01G428000 chr7D 83.412 211 32 3 1298 1507 529956416 529956208 3.250000e-45 193.0
11 TraesCS2D01G428000 chr7B 82.464 211 34 3 1298 1507 568107384 568107176 7.020000e-42 182.0
12 TraesCS2D01G428000 chr7A 82.609 207 35 1 1301 1507 609431478 609431273 7.020000e-42 182.0
13 TraesCS2D01G428000 chr7A 88.889 63 4 3 2685 2746 212994303 212994363 1.230000e-09 75.0
14 TraesCS2D01G428000 chr3B 77.828 221 36 11 232 447 98023928 98024140 1.200000e-24 124.0
15 TraesCS2D01G428000 chr5D 78.344 157 32 2 233 388 533998155 533998000 2.020000e-17 100.0
16 TraesCS2D01G428000 chr4D 81.739 115 21 0 223 337 92077832 92077718 2.620000e-16 97.1
17 TraesCS2D01G428000 chr6B 75.127 197 38 7 232 426 437842367 437842554 7.330000e-12 82.4
18 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 12068892 12068835 4.410000e-09 73.1
19 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 144742348 144742291 4.410000e-09 73.1
20 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 144779459 144779402 4.410000e-09 73.1
21 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 144811927 144811870 4.410000e-09 73.1
22 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 144892462 144892405 4.410000e-09 73.1
23 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 144931000 144930943 4.410000e-09 73.1
24 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 179856173 179856116 4.410000e-09 73.1
25 TraesCS2D01G428000 chrUn 89.831 59 2 4 2692 2747 343171034 343170977 4.410000e-09 73.1


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 TraesCS2D01G428000 chr2D 539894053 539897240 3187 True 5888.000000 5888 100.000000 1 3188 1 chr2D.!!$R1 3187
1 TraesCS2D01G428000 chr2B 644166926 644170113 3187 True 970.666667 2610 88.442667 28 3188 3 chr2B.!!$R2 3160
2 TraesCS2D01G428000 chr2A 683534650 683538987 4337 True 595.200000 1829 90.657200 89 3183 5 chr2A.!!$R1 3094

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
339 1416 0.666913 GGCTCGTTCTCATAGCGGTA 59.333 55.0 0.0 0.0 37.11 4.02 F
1695 2885 0.178891 ACCTGACCACCATCCTGTCT 60.179 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3232 0.107508 CATCGCAACAGATCCCTGGT 60.108 55.0 0.00 0.0 44.6 4.00 R
3042 4572 0.035598 TCAATTTCAAGGTCGGCGGA 59.964 50.0 7.21 0.0 0.0 5.54 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
34 35 1.017387 GCGGATGGTGGTGATTCTTC 58.983 55.000 0.00 0.00 0.00 2.87
35 36 1.407437 GCGGATGGTGGTGATTCTTCT 60.407 52.381 0.00 0.00 0.00 2.85
41 42 2.003301 GGTGGTGATTCTTCTTCGAGC 58.997 52.381 0.00 0.00 0.00 5.03
43 44 2.670414 GTGGTGATTCTTCTTCGAGCTG 59.330 50.000 0.00 0.00 0.00 4.24
44 45 2.562738 TGGTGATTCTTCTTCGAGCTGA 59.437 45.455 0.00 0.00 0.00 4.26
45 46 3.196469 TGGTGATTCTTCTTCGAGCTGAT 59.804 43.478 0.00 0.00 0.00 2.90
52 53 2.568696 TCTTCGAGCTGATCTTTCGG 57.431 50.000 0.00 1.31 35.21 4.30
74 75 4.870991 GGGTTTCAATCCTTCTCTAGTTCG 59.129 45.833 0.00 0.00 0.00 3.95
80 81 5.422331 TCAATCCTTCTCTAGTTCGTCCATT 59.578 40.000 0.00 0.00 0.00 3.16
81 82 6.605995 TCAATCCTTCTCTAGTTCGTCCATTA 59.394 38.462 0.00 0.00 0.00 1.90
83 84 5.752650 TCCTTCTCTAGTTCGTCCATTAGA 58.247 41.667 0.00 0.00 0.00 2.10
109 110 1.679680 GTCGATGGATCTCCGGTGTAA 59.320 52.381 0.00 0.00 39.43 2.41
164 1230 1.990799 TTCTTGATGTACGTGCGAGG 58.009 50.000 0.00 0.00 0.00 4.63
195 1272 9.415544 GAGATTTGGTATGATCAATTTAATGGC 57.584 33.333 0.00 0.00 0.00 4.40
224 1301 2.753966 CGATGGCAGCTTTGGGACG 61.754 63.158 0.00 0.00 0.00 4.79
225 1302 3.056313 GATGGCAGCTTTGGGACGC 62.056 63.158 0.00 0.00 0.00 5.19
226 1303 3.574074 ATGGCAGCTTTGGGACGCT 62.574 57.895 0.00 0.00 36.83 5.07
238 1315 1.837439 TGGGACGCTGATTCTTATGGT 59.163 47.619 0.00 0.00 0.00 3.55
306 1383 1.281867 TCTGGTAAGGGAGTGGCAATG 59.718 52.381 0.00 0.00 0.00 2.82
308 1385 1.004277 TGGTAAGGGAGTGGCAATGAC 59.996 52.381 0.00 0.00 0.00 3.06
312 1389 1.003839 GGGAGTGGCAATGACGACA 60.004 57.895 0.00 0.00 0.00 4.35
330 1407 2.876645 CGTCAGCGGCTCGTTCTC 60.877 66.667 0.00 0.00 0.00 2.87
331 1408 2.258591 GTCAGCGGCTCGTTCTCA 59.741 61.111 0.00 0.00 0.00 3.27
339 1416 0.666913 GGCTCGTTCTCATAGCGGTA 59.333 55.000 0.00 0.00 37.11 4.02
347 1424 2.022195 TCTCATAGCGGTAGTGGTCAC 58.978 52.381 0.00 0.00 0.00 3.67
350 1427 1.749063 CATAGCGGTAGTGGTCACTCA 59.251 52.381 6.91 0.00 42.54 3.41
356 1433 1.000955 GGTAGTGGTCACTCAGTGGTG 59.999 57.143 4.57 5.63 42.54 4.17
381 1458 7.386025 TGCATGAATCTCGATGTAATTCTTAGG 59.614 37.037 0.00 0.00 31.99 2.69
409 1490 3.073209 TGGGGTGCTTTGTACATTCAGTA 59.927 43.478 0.00 0.00 0.00 2.74
411 1492 4.156008 GGGGTGCTTTGTACATTCAGTAAG 59.844 45.833 0.00 0.00 33.72 2.34
414 1495 4.215399 GTGCTTTGTACATTCAGTAAGCCA 59.785 41.667 19.76 9.29 34.59 4.75
451 1532 7.013846 TCCATACCCCTTTTCGCAAAAATATAG 59.986 37.037 0.00 0.00 34.00 1.31
455 1536 7.768240 ACCCCTTTTCGCAAAAATATAGTTAG 58.232 34.615 0.00 0.00 34.00 2.34
483 1564 5.934625 ACAAATGTTTTGTGCACTTTAACCA 59.065 32.000 19.41 8.77 0.00 3.67
587 1698 6.939163 TCCAAGAGGGTTACGACTATATACTC 59.061 42.308 0.00 0.00 38.11 2.59
632 1751 2.579410 AGGCTAACCGTCCACAAATT 57.421 45.000 0.00 0.00 42.76 1.82
706 1826 1.462731 ATTTTCGCCAGGCAGTTGCA 61.463 50.000 13.30 0.00 44.36 4.08
728 1852 1.047002 CCAGCACACATTTCCCCAAA 58.953 50.000 0.00 0.00 0.00 3.28
737 1861 1.055849 ATTTCCCCAAAGGTGGCAAC 58.944 50.000 0.00 0.00 44.46 4.17
828 1957 7.528996 ACTCCATTATTCAGAGAGATCAGAG 57.471 40.000 0.00 0.00 0.00 3.35
829 1958 7.296856 ACTCCATTATTCAGAGAGATCAGAGA 58.703 38.462 0.00 0.00 0.00 3.10
832 1961 9.156940 TCCATTATTCAGAGAGATCAGAGAAAT 57.843 33.333 0.00 0.00 0.00 2.17
988 2151 1.599606 AACAGCAACGCCACAACCAA 61.600 50.000 0.00 0.00 0.00 3.67
1023 2191 0.325272 AGGAGGAAAGGAAACGCTCC 59.675 55.000 0.00 0.00 45.81 4.70
1029 2197 2.113243 AAAGGAAACGCTCCCGCTCT 62.113 55.000 0.56 0.00 46.81 4.09
1031 2199 2.881352 GAAACGCTCCCGCTCTCG 60.881 66.667 0.00 0.00 38.22 4.04
1040 2208 4.735132 CCGCTCTCGCCCGTGAAA 62.735 66.667 0.00 0.00 0.00 2.69
1062 2231 2.109181 CCGCCCGAAGATCTTCCC 59.891 66.667 26.08 15.14 36.27 3.97
1063 2232 2.109181 CGCCCGAAGATCTTCCCC 59.891 66.667 26.08 14.84 36.27 4.81
1614 2798 3.533606 ACAACTCGCTCTGCAGATAAT 57.466 42.857 18.63 0.00 0.00 1.28
1615 2799 4.655762 ACAACTCGCTCTGCAGATAATA 57.344 40.909 18.63 2.47 0.00 0.98
1616 2800 5.011090 ACAACTCGCTCTGCAGATAATAA 57.989 39.130 18.63 0.65 0.00 1.40
1617 2801 5.046529 ACAACTCGCTCTGCAGATAATAAG 58.953 41.667 18.63 12.61 0.00 1.73
1618 2802 3.648009 ACTCGCTCTGCAGATAATAAGC 58.352 45.455 18.63 14.81 0.00 3.09
1619 2803 2.992543 CTCGCTCTGCAGATAATAAGCC 59.007 50.000 18.63 0.37 0.00 4.35
1620 2804 2.072298 CGCTCTGCAGATAATAAGCCC 58.928 52.381 18.63 0.00 0.00 5.19
1621 2805 2.072298 GCTCTGCAGATAATAAGCCCG 58.928 52.381 18.63 2.16 0.00 6.13
1669 2859 4.849310 TCGCCGGCCACCATTAGC 62.849 66.667 23.46 0.00 0.00 3.09
1671 2861 3.211963 GCCGGCCACCATTAGCAG 61.212 66.667 18.11 0.00 0.00 4.24
1692 2882 1.208052 CAGTACCTGACCACCATCCTG 59.792 57.143 0.00 0.00 32.44 3.86
1693 2883 1.203313 AGTACCTGACCACCATCCTGT 60.203 52.381 0.00 0.00 0.00 4.00
1694 2884 1.207329 GTACCTGACCACCATCCTGTC 59.793 57.143 0.00 0.00 0.00 3.51
1695 2885 0.178891 ACCTGACCACCATCCTGTCT 60.179 55.000 0.00 0.00 0.00 3.41
1696 2886 0.251354 CCTGACCACCATCCTGTCTG 59.749 60.000 0.00 0.00 0.00 3.51
1709 2899 2.105821 TCCTGTCTGTCCCACGAAAAAT 59.894 45.455 0.00 0.00 0.00 1.82
1710 2900 2.226437 CCTGTCTGTCCCACGAAAAATG 59.774 50.000 0.00 0.00 0.00 2.32
1711 2901 1.606668 TGTCTGTCCCACGAAAAATGC 59.393 47.619 0.00 0.00 0.00 3.56
1713 2904 2.095718 GTCTGTCCCACGAAAAATGCTC 60.096 50.000 0.00 0.00 0.00 4.26
1714 2905 1.200020 CTGTCCCACGAAAAATGCTCC 59.800 52.381 0.00 0.00 0.00 4.70
1716 2907 1.886542 GTCCCACGAAAAATGCTCCTT 59.113 47.619 0.00 0.00 0.00 3.36
1718 2909 2.962421 TCCCACGAAAAATGCTCCTTTT 59.038 40.909 0.00 0.00 0.00 2.27
1748 2942 4.457834 TCTTCTTCATCTTCTTCGGTCC 57.542 45.455 0.00 0.00 0.00 4.46
1848 3049 0.392461 TACCACTGCCCGCATTCTTC 60.392 55.000 0.00 0.00 0.00 2.87
1875 3076 2.329267 TGATGATCTGGATTAGCCGGT 58.671 47.619 1.90 0.00 44.00 5.28
1908 3120 1.280746 CATGCGGACGCCATTGATC 59.719 57.895 14.61 0.00 41.09 2.92
1976 3225 7.935338 TCTCTCTTGATTGATTTGTTTTTGC 57.065 32.000 0.00 0.00 0.00 3.68
1977 3226 6.925165 TCTCTCTTGATTGATTTGTTTTTGCC 59.075 34.615 0.00 0.00 0.00 4.52
1978 3227 5.990996 TCTCTTGATTGATTTGTTTTTGCCC 59.009 36.000 0.00 0.00 0.00 5.36
1979 3228 5.678583 TCTTGATTGATTTGTTTTTGCCCA 58.321 33.333 0.00 0.00 0.00 5.36
1980 3229 6.297582 TCTTGATTGATTTGTTTTTGCCCAT 58.702 32.000 0.00 0.00 0.00 4.00
1981 3230 6.771749 TCTTGATTGATTTGTTTTTGCCCATT 59.228 30.769 0.00 0.00 0.00 3.16
1982 3231 6.956202 TGATTGATTTGTTTTTGCCCATTT 57.044 29.167 0.00 0.00 0.00 2.32
1983 3232 8.455903 TTGATTGATTTGTTTTTGCCCATTTA 57.544 26.923 0.00 0.00 0.00 1.40
1984 3233 7.869800 TGATTGATTTGTTTTTGCCCATTTAC 58.130 30.769 0.00 0.00 0.00 2.01
1985 3234 6.625873 TTGATTTGTTTTTGCCCATTTACC 57.374 33.333 0.00 0.00 0.00 2.85
1986 3235 5.684704 TGATTTGTTTTTGCCCATTTACCA 58.315 33.333 0.00 0.00 0.00 3.25
1987 3236 5.762218 TGATTTGTTTTTGCCCATTTACCAG 59.238 36.000 0.00 0.00 0.00 4.00
1988 3237 3.760580 TGTTTTTGCCCATTTACCAGG 57.239 42.857 0.00 0.00 0.00 4.45
2013 3262 0.802494 GTTGCGATGTCACCGGAAAT 59.198 50.000 9.46 0.00 38.94 2.17
2027 3276 7.040062 TGTCACCGGAAATATTTTGAATGTTCT 60.040 33.333 9.46 0.00 0.00 3.01
2028 3277 7.484959 GTCACCGGAAATATTTTGAATGTTCTC 59.515 37.037 9.46 0.00 0.00 2.87
2032 3281 9.076596 CCGGAAATATTTTGAATGTTCTCTTTC 57.923 33.333 0.00 0.00 0.00 2.62
2215 3507 1.024579 ACGTGGTGCAATTCGATCCC 61.025 55.000 11.51 0.00 0.00 3.85
2249 3558 2.730928 CACATGCACCCAACGATTTTTC 59.269 45.455 0.00 0.00 0.00 2.29
2250 3559 2.627699 ACATGCACCCAACGATTTTTCT 59.372 40.909 0.00 0.00 0.00 2.52
2254 3563 5.461032 TGCACCCAACGATTTTTCTTAAT 57.539 34.783 0.00 0.00 0.00 1.40
2383 3692 2.751436 GGCATTGCCTGAAGCCGA 60.751 61.111 20.66 0.00 46.69 5.54
2384 3693 2.768492 GGCATTGCCTGAAGCCGAG 61.768 63.158 20.66 0.00 46.69 4.63
2385 3694 2.042831 GCATTGCCTGAAGCCGAGT 61.043 57.895 0.00 0.00 42.71 4.18
2386 3695 0.744414 GCATTGCCTGAAGCCGAGTA 60.744 55.000 0.00 0.00 42.71 2.59
2387 3696 1.009829 CATTGCCTGAAGCCGAGTAC 58.990 55.000 0.00 0.00 42.71 2.73
2388 3697 0.613260 ATTGCCTGAAGCCGAGTACA 59.387 50.000 0.00 0.00 42.71 2.90
2389 3698 0.037326 TTGCCTGAAGCCGAGTACAG 60.037 55.000 0.00 0.00 42.71 2.74
2390 3699 0.898326 TGCCTGAAGCCGAGTACAGA 60.898 55.000 0.00 0.00 42.71 3.41
2391 3700 0.246635 GCCTGAAGCCGAGTACAGAA 59.753 55.000 0.00 0.00 34.35 3.02
2392 3701 1.337823 GCCTGAAGCCGAGTACAGAAA 60.338 52.381 0.00 0.00 34.35 2.52
2403 3712 0.035820 GTACAGAAACGGCCATGGGA 60.036 55.000 15.13 0.00 0.00 4.37
2410 3719 2.223803 AACGGCCATGGGATAAAACA 57.776 45.000 15.13 0.00 0.00 2.83
2437 3746 1.117234 GTACGGTGCAAAGCAAAACG 58.883 50.000 0.00 9.40 41.47 3.60
2510 3819 1.077501 ACGGCACCCAGATTCATGG 60.078 57.895 0.00 0.00 40.29 3.66
2528 3955 0.250901 GGAGGCCACTGTTCATGTGT 60.251 55.000 5.01 0.00 33.92 3.72
2542 3969 8.257306 ACTGTTCATGTGTTTAATTTCCTTGTT 58.743 29.630 0.00 0.00 0.00 2.83
2543 3970 9.743057 CTGTTCATGTGTTTAATTTCCTTGTTA 57.257 29.630 0.00 0.00 0.00 2.41
2601 4029 3.014304 ACCTTCAGAGATGCATGCATT 57.986 42.857 32.60 21.88 36.70 3.56
2603 4031 2.688446 CCTTCAGAGATGCATGCATTGT 59.312 45.455 32.60 23.04 36.70 2.71
2619 4047 1.388547 TTGTGTCTGTTTGTGGCTCC 58.611 50.000 0.00 0.00 0.00 4.70
2664 4095 7.872483 AGTTCTTGTGTTTTCTGTTGTGATTTT 59.128 29.630 0.00 0.00 0.00 1.82
2677 4108 1.066303 GTGATTTTCACGGCACAACCA 59.934 47.619 0.00 0.00 37.67 3.67
2688 4119 3.344703 CACAACCAGGGCATTCAGA 57.655 52.632 0.00 0.00 0.00 3.27
2690 4121 0.773644 ACAACCAGGGCATTCAGAGT 59.226 50.000 0.00 0.00 0.00 3.24
2694 4125 2.269940 ACCAGGGCATTCAGAGTTACT 58.730 47.619 0.00 0.00 0.00 2.24
2695 4126 2.237392 ACCAGGGCATTCAGAGTTACTC 59.763 50.000 3.85 3.85 0.00 2.59
2697 4128 1.840635 AGGGCATTCAGAGTTACTCCC 59.159 52.381 8.96 1.76 0.00 4.30
2698 4129 1.840635 GGGCATTCAGAGTTACTCCCT 59.159 52.381 8.96 0.00 0.00 4.20
2699 4130 2.158885 GGGCATTCAGAGTTACTCCCTC 60.159 54.545 8.96 0.00 0.00 4.30
2700 4131 2.158885 GGCATTCAGAGTTACTCCCTCC 60.159 54.545 8.96 0.00 0.00 4.30
2701 4132 2.501723 GCATTCAGAGTTACTCCCTCCA 59.498 50.000 8.96 0.00 0.00 3.86
2702 4133 3.135530 GCATTCAGAGTTACTCCCTCCAT 59.864 47.826 8.96 0.00 0.00 3.41
2703 4134 4.742138 GCATTCAGAGTTACTCCCTCCATC 60.742 50.000 8.96 0.00 0.00 3.51
2704 4135 3.033659 TCAGAGTTACTCCCTCCATCC 57.966 52.381 8.96 0.00 0.00 3.51
2705 4136 2.043227 CAGAGTTACTCCCTCCATCCC 58.957 57.143 8.96 0.00 0.00 3.85
2706 4137 1.651770 AGAGTTACTCCCTCCATCCCA 59.348 52.381 8.96 0.00 0.00 4.37
2707 4138 2.251338 AGAGTTACTCCCTCCATCCCAT 59.749 50.000 8.96 0.00 0.00 4.00
2708 4139 3.471306 AGAGTTACTCCCTCCATCCCATA 59.529 47.826 8.96 0.00 0.00 2.74
2709 4140 4.077982 AGAGTTACTCCCTCCATCCCATAA 60.078 45.833 8.96 0.00 0.00 1.90
2710 4141 4.844348 AGTTACTCCCTCCATCCCATAAT 58.156 43.478 0.00 0.00 0.00 1.28
2711 4142 5.989717 AGTTACTCCCTCCATCCCATAATA 58.010 41.667 0.00 0.00 0.00 0.98
2712 4143 6.584950 AGTTACTCCCTCCATCCCATAATAT 58.415 40.000 0.00 0.00 0.00 1.28
2713 4144 7.729350 AGTTACTCCCTCCATCCCATAATATA 58.271 38.462 0.00 0.00 0.00 0.86
2714 4145 8.191110 AGTTACTCCCTCCATCCCATAATATAA 58.809 37.037 0.00 0.00 0.00 0.98
2715 4146 8.487028 GTTACTCCCTCCATCCCATAATATAAG 58.513 40.741 0.00 0.00 0.00 1.73
2716 4147 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
2717 4148 7.263901 ACTCCCTCCATCCCATAATATAAGAA 58.736 38.462 0.00 0.00 0.00 2.52
2718 4149 7.182930 ACTCCCTCCATCCCATAATATAAGAAC 59.817 40.741 0.00 0.00 0.00 3.01
2719 4150 6.156256 TCCCTCCATCCCATAATATAAGAACG 59.844 42.308 0.00 0.00 0.00 3.95
2720 4151 6.070194 CCCTCCATCCCATAATATAAGAACGT 60.070 42.308 0.00 0.00 0.00 3.99
2721 4152 7.394816 CCTCCATCCCATAATATAAGAACGTT 58.605 38.462 0.00 0.00 0.00 3.99
2722 4153 7.883311 CCTCCATCCCATAATATAAGAACGTTT 59.117 37.037 0.46 0.00 0.00 3.60
2723 4154 9.284968 CTCCATCCCATAATATAAGAACGTTTT 57.715 33.333 0.46 0.00 0.00 2.43
2724 4155 9.635404 TCCATCCCATAATATAAGAACGTTTTT 57.365 29.630 9.22 9.22 0.00 1.94
2775 4206 4.776743 GCATCTAGCACAACGGAATATTG 58.223 43.478 0.00 0.00 44.79 1.90
2780 4211 1.676006 GCACAACGGAATATTGGAGGG 59.324 52.381 0.00 0.00 0.00 4.30
2783 4214 2.210116 CAACGGAATATTGGAGGGTCG 58.790 52.381 0.00 0.00 0.00 4.79
2785 4216 1.411612 ACGGAATATTGGAGGGTCGTC 59.588 52.381 0.00 0.00 0.00 4.20
2786 4217 1.602165 CGGAATATTGGAGGGTCGTCG 60.602 57.143 0.00 0.00 0.00 5.12
2787 4218 1.684983 GGAATATTGGAGGGTCGTCGA 59.315 52.381 0.00 0.00 0.00 4.20
2814 4245 1.747355 TGAACGGACGAGGATCTAACC 59.253 52.381 0.00 0.00 0.00 2.85
2815 4246 0.737219 AACGGACGAGGATCTAACCG 59.263 55.000 0.00 0.00 43.88 4.44
2825 4313 5.221803 ACGAGGATCTAACCGACTAATCCTA 60.222 44.000 2.34 0.00 44.83 2.94
2838 4326 3.577415 ACTAATCCTACTTATCCACGGGC 59.423 47.826 0.00 0.00 0.00 6.13
2879 4377 1.667177 CGTTTGTTGTTGTGTGCCACA 60.667 47.619 0.00 0.00 43.02 4.17
2891 4389 3.311106 GTGTGCCACACTTTCATTCATG 58.689 45.455 20.46 0.00 45.27 3.07
2892 4390 3.004629 GTGTGCCACACTTTCATTCATGA 59.995 43.478 20.46 0.00 45.27 3.07
2924 4422 1.269723 GAGCCCGAACCAAAAGGAAAG 59.730 52.381 0.00 0.00 0.00 2.62
2926 4424 1.989706 CCCGAACCAAAAGGAAAGGA 58.010 50.000 0.00 0.00 0.00 3.36
2927 4425 2.312390 CCCGAACCAAAAGGAAAGGAA 58.688 47.619 0.00 0.00 0.00 3.36
2928 4426 2.696187 CCCGAACCAAAAGGAAAGGAAA 59.304 45.455 0.00 0.00 0.00 3.13
2929 4427 3.133183 CCCGAACCAAAAGGAAAGGAAAA 59.867 43.478 0.00 0.00 0.00 2.29
2930 4428 4.368315 CCGAACCAAAAGGAAAGGAAAAG 58.632 43.478 0.00 0.00 0.00 2.27
2931 4429 3.802139 CGAACCAAAAGGAAAGGAAAAGC 59.198 43.478 0.00 0.00 0.00 3.51
2936 4434 1.185618 AAGGAAAGGAAAAGCGGCCC 61.186 55.000 0.00 0.00 0.00 5.80
3058 4588 1.740296 CGTCCGCCGACCTTGAAAT 60.740 57.895 0.00 0.00 39.56 2.17
3059 4589 1.296056 CGTCCGCCGACCTTGAAATT 61.296 55.000 0.00 0.00 39.56 1.82
3060 4590 0.168128 GTCCGCCGACCTTGAAATTG 59.832 55.000 0.00 0.00 32.40 2.32
3061 4591 0.035598 TCCGCCGACCTTGAAATTGA 59.964 50.000 0.00 0.00 0.00 2.57
3062 4592 0.878416 CCGCCGACCTTGAAATTGAA 59.122 50.000 0.00 0.00 0.00 2.69
3063 4593 1.472480 CCGCCGACCTTGAAATTGAAT 59.528 47.619 0.00 0.00 0.00 2.57
3064 4594 2.518949 CGCCGACCTTGAAATTGAATG 58.481 47.619 0.00 0.00 0.00 2.67
3065 4595 2.731968 CGCCGACCTTGAAATTGAATGG 60.732 50.000 0.00 0.00 0.00 3.16
3066 4596 2.491693 GCCGACCTTGAAATTGAATGGA 59.508 45.455 0.00 0.00 0.00 3.41
3067 4597 3.131046 GCCGACCTTGAAATTGAATGGAT 59.869 43.478 0.00 0.00 0.00 3.41
3068 4598 4.675510 CCGACCTTGAAATTGAATGGATG 58.324 43.478 0.00 0.00 0.00 3.51
3069 4599 4.440525 CCGACCTTGAAATTGAATGGATGG 60.441 45.833 0.00 0.00 0.00 3.51
3070 4600 4.398988 CGACCTTGAAATTGAATGGATGGA 59.601 41.667 0.00 0.00 0.00 3.41
3071 4601 5.068198 CGACCTTGAAATTGAATGGATGGAT 59.932 40.000 0.00 0.00 0.00 3.41
3072 4602 6.475596 ACCTTGAAATTGAATGGATGGATC 57.524 37.500 0.00 0.00 0.00 3.36
3101 4631 2.127708 AGGTTTCTCTGGTCCAACAGT 58.872 47.619 0.00 0.00 39.48 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.752743 AATCACCACCATCCGCCATG 60.753 55.000 0.00 0.00 0.00 3.66
12 13 0.466189 GAATCACCACCATCCGCCAT 60.466 55.000 0.00 0.00 0.00 4.40
13 14 1.077787 GAATCACCACCATCCGCCA 60.078 57.895 0.00 0.00 0.00 5.69
14 15 0.394352 AAGAATCACCACCATCCGCC 60.394 55.000 0.00 0.00 0.00 6.13
15 16 1.017387 GAAGAATCACCACCATCCGC 58.983 55.000 0.00 0.00 0.00 5.54
16 17 2.698855 AGAAGAATCACCACCATCCG 57.301 50.000 0.00 0.00 0.00 4.18
17 18 2.939103 CGAAGAAGAATCACCACCATCC 59.061 50.000 0.00 0.00 0.00 3.51
18 19 3.861840 TCGAAGAAGAATCACCACCATC 58.138 45.455 0.00 0.00 0.00 3.51
19 20 3.866651 CTCGAAGAAGAATCACCACCAT 58.133 45.455 0.00 0.00 34.09 3.55
20 21 2.612972 GCTCGAAGAAGAATCACCACCA 60.613 50.000 0.00 0.00 34.09 4.17
21 22 2.003301 GCTCGAAGAAGAATCACCACC 58.997 52.381 0.00 0.00 34.09 4.61
22 23 2.670414 CAGCTCGAAGAAGAATCACCAC 59.330 50.000 0.00 0.00 34.09 4.16
23 24 2.562738 TCAGCTCGAAGAAGAATCACCA 59.437 45.455 0.00 0.00 34.09 4.17
24 25 3.238108 TCAGCTCGAAGAAGAATCACC 57.762 47.619 0.00 0.00 34.09 4.02
25 26 4.681744 AGATCAGCTCGAAGAAGAATCAC 58.318 43.478 0.00 0.00 34.09 3.06
26 27 4.998671 AGATCAGCTCGAAGAAGAATCA 57.001 40.909 0.00 0.00 34.09 2.57
34 35 1.134965 ACCCGAAAGATCAGCTCGAAG 60.135 52.381 11.36 6.27 34.52 3.79
35 36 0.895530 ACCCGAAAGATCAGCTCGAA 59.104 50.000 11.36 0.00 34.52 3.71
41 42 4.265073 AGGATTGAAACCCGAAAGATCAG 58.735 43.478 0.00 0.00 0.00 2.90
43 44 4.944317 AGAAGGATTGAAACCCGAAAGATC 59.056 41.667 0.00 0.00 0.00 2.75
44 45 4.923415 AGAAGGATTGAAACCCGAAAGAT 58.077 39.130 0.00 0.00 0.00 2.40
45 46 4.041691 AGAGAAGGATTGAAACCCGAAAGA 59.958 41.667 0.00 0.00 0.00 2.52
52 53 5.480205 ACGAACTAGAGAAGGATTGAAACC 58.520 41.667 0.00 0.00 0.00 3.27
74 75 8.908903 AGATCCATCGACTATATTCTAATGGAC 58.091 37.037 18.33 14.28 42.75 4.02
80 81 6.056236 CCGGAGATCCATCGACTATATTCTA 58.944 44.000 0.00 0.00 35.14 2.10
81 82 4.884744 CCGGAGATCCATCGACTATATTCT 59.115 45.833 0.00 0.00 35.14 2.40
83 84 4.399618 CACCGGAGATCCATCGACTATATT 59.600 45.833 9.46 0.00 35.14 1.28
109 110 2.176798 TCCCCAAGGAGACAACATGTTT 59.823 45.455 8.77 0.41 37.19 2.83
164 1230 3.381045 TGATCATACCAAATCTCGTCGC 58.619 45.455 0.00 0.00 0.00 5.19
192 1269 1.102154 CCATCGTTGCCATTAAGCCA 58.898 50.000 0.00 0.00 0.00 4.75
195 1272 1.534595 GCTGCCATCGTTGCCATTAAG 60.535 52.381 0.00 0.00 0.00 1.85
224 1301 3.628942 TGCACATGACCATAAGAATCAGC 59.371 43.478 0.00 0.00 0.00 4.26
225 1302 5.529800 TCATGCACATGACCATAAGAATCAG 59.470 40.000 9.23 0.00 42.42 2.90
226 1303 5.438833 TCATGCACATGACCATAAGAATCA 58.561 37.500 9.23 0.00 42.42 2.57
230 1307 4.877823 GTCTTCATGCACATGACCATAAGA 59.122 41.667 12.74 9.76 46.49 2.10
238 1315 2.715046 GGGAAGTCTTCATGCACATGA 58.285 47.619 14.49 9.23 45.30 3.07
312 1389 3.612371 GAGAACGAGCCGCTGACGT 62.612 63.158 0.00 0.00 41.97 4.34
320 1397 0.666913 TACCGCTATGAGAACGAGCC 59.333 55.000 0.00 0.00 32.35 4.70
330 1407 1.749063 TGAGTGACCACTACCGCTATG 59.251 52.381 2.23 0.00 42.66 2.23
331 1408 2.025155 CTGAGTGACCACTACCGCTAT 58.975 52.381 2.23 0.00 42.66 2.97
339 1416 1.337384 TGCACCACTGAGTGACCACT 61.337 55.000 15.33 1.78 45.84 4.00
347 1424 1.931841 CGAGATTCATGCACCACTGAG 59.068 52.381 0.00 0.00 0.00 3.35
350 1427 2.093288 ACATCGAGATTCATGCACCACT 60.093 45.455 0.00 0.00 0.00 4.00
356 1433 7.600375 TCCTAAGAATTACATCGAGATTCATGC 59.400 37.037 12.90 0.00 33.34 4.06
381 1458 2.625790 TGTACAAAGCACCCCAAACATC 59.374 45.455 0.00 0.00 0.00 3.06
409 1490 7.633391 AGGGGTATGGATCTATTATAATGGCTT 59.367 37.037 8.28 0.00 0.00 4.35
411 1492 7.394144 AGGGGTATGGATCTATTATAATGGC 57.606 40.000 8.28 0.00 0.00 4.40
429 1510 7.706100 AACTATATTTTTGCGAAAAGGGGTA 57.294 32.000 16.68 5.51 38.09 3.69
431 1512 7.992008 TCTAACTATATTTTTGCGAAAAGGGG 58.008 34.615 16.68 9.43 38.09 4.79
460 1541 6.414408 TGGTTAAAGTGCACAAAACATTTG 57.586 33.333 21.04 1.47 0.00 2.32
463 1544 5.918011 CGTATGGTTAAAGTGCACAAAACAT 59.082 36.000 24.35 24.35 33.92 2.71
464 1545 5.066117 TCGTATGGTTAAAGTGCACAAAACA 59.934 36.000 21.04 18.31 0.00 2.83
465 1546 5.397240 GTCGTATGGTTAAAGTGCACAAAAC 59.603 40.000 21.04 18.14 0.00 2.43
470 1551 2.417586 GGGTCGTATGGTTAAAGTGCAC 59.582 50.000 9.40 9.40 0.00 4.57
479 1560 4.628963 AGTTTGTTAGGGTCGTATGGTT 57.371 40.909 0.00 0.00 0.00 3.67
483 1564 4.248058 CCGAAAGTTTGTTAGGGTCGTAT 58.752 43.478 0.00 0.00 0.00 3.06
587 1698 2.047061 TCCAAGGGTAGATCGGAATGG 58.953 52.381 0.00 0.00 0.00 3.16
632 1751 1.090728 TGTGTTGCGCTTTGACTTGA 58.909 45.000 9.73 0.00 0.00 3.02
706 1826 1.607467 GGGAAATGTGTGCTGGCCT 60.607 57.895 3.32 0.00 0.00 5.19
728 1852 1.261480 TGTGTTTGTTGTTGCCACCT 58.739 45.000 0.00 0.00 0.00 4.00
737 1861 6.580041 GCATCTGAATAGACTTGTGTTTGTTG 59.420 38.462 0.00 0.00 35.34 3.33
745 1869 5.330455 TCGAAGCATCTGAATAGACTTGT 57.670 39.130 0.00 0.00 35.34 3.16
748 1872 5.347342 CAGTTCGAAGCATCTGAATAGACT 58.653 41.667 0.00 0.00 35.34 3.24
921 2065 0.683179 GCATTTAAAGGGCGAGGGGT 60.683 55.000 1.57 0.00 0.00 4.95
988 2151 0.996583 TCCTACGGGATTTTGGGCTT 59.003 50.000 0.00 0.00 36.57 4.35
1006 2169 1.019805 CGGGAGCGTTTCCTTTCCTC 61.020 60.000 0.00 0.00 45.98 3.71
1029 2197 2.592287 GGTGGTTTTCACGGGCGA 60.592 61.111 0.00 0.00 46.96 5.54
1031 2199 4.337060 GCGGTGGTTTTCACGGGC 62.337 66.667 5.99 1.68 46.96 6.13
1033 2201 3.666253 GGGCGGTGGTTTTCACGG 61.666 66.667 0.00 0.00 46.96 4.94
1034 2202 4.020378 CGGGCGGTGGTTTTCACG 62.020 66.667 0.00 0.00 46.96 4.35
1035 2203 2.125202 CTTCGGGCGGTGGTTTTCAC 62.125 60.000 0.00 0.00 45.34 3.18
1036 2204 1.894756 CTTCGGGCGGTGGTTTTCA 60.895 57.895 0.00 0.00 0.00 2.69
1037 2205 0.958876 ATCTTCGGGCGGTGGTTTTC 60.959 55.000 0.00 0.00 0.00 2.29
1039 2207 1.376812 GATCTTCGGGCGGTGGTTT 60.377 57.895 0.00 0.00 0.00 3.27
1040 2208 1.838073 AAGATCTTCGGGCGGTGGTT 61.838 55.000 0.88 0.00 0.00 3.67
1421 2593 1.615165 GGAACCCGAACTCCTCCTCC 61.615 65.000 0.00 0.00 0.00 4.30
1692 2882 1.880027 AGCATTTTTCGTGGGACAGAC 59.120 47.619 0.00 0.00 41.80 3.51
1693 2883 2.151202 GAGCATTTTTCGTGGGACAGA 58.849 47.619 0.00 0.00 41.80 3.41
1694 2884 1.200020 GGAGCATTTTTCGTGGGACAG 59.800 52.381 0.00 0.00 41.80 3.51
1695 2885 1.202879 AGGAGCATTTTTCGTGGGACA 60.203 47.619 0.00 0.00 0.00 4.02
1696 2886 1.534729 AGGAGCATTTTTCGTGGGAC 58.465 50.000 0.00 0.00 0.00 4.46
1718 2909 5.621193 AGAAGATGAAGAAGAACGGGAAAA 58.379 37.500 0.00 0.00 0.00 2.29
1721 2912 4.618460 CGAAGAAGATGAAGAAGAACGGGA 60.618 45.833 0.00 0.00 0.00 5.14
1722 2913 3.614616 CGAAGAAGATGAAGAAGAACGGG 59.385 47.826 0.00 0.00 0.00 5.28
1725 2916 4.627900 GGACCGAAGAAGATGAAGAAGAAC 59.372 45.833 0.00 0.00 0.00 3.01
1735 2929 4.040461 TGAGAAAACAGGACCGAAGAAGAT 59.960 41.667 0.00 0.00 0.00 2.40
1748 2942 1.487482 TCACGACGCTGAGAAAACAG 58.513 50.000 0.00 0.00 40.43 3.16
1848 3049 5.421277 GCTAATCCAGATCATCATCAGAGG 58.579 45.833 0.00 0.00 0.00 3.69
1908 3120 7.812690 TCACATCCAATCTTTCCATGATAAG 57.187 36.000 0.00 0.00 0.00 1.73
1967 3216 3.181450 CCCTGGTAAATGGGCAAAAACAA 60.181 43.478 0.00 0.00 36.61 2.83
1968 3217 2.370189 CCCTGGTAAATGGGCAAAAACA 59.630 45.455 0.00 0.00 36.61 2.83
1969 3218 2.635427 TCCCTGGTAAATGGGCAAAAAC 59.365 45.455 0.00 0.00 43.04 2.43
1970 3219 2.977808 TCCCTGGTAAATGGGCAAAAA 58.022 42.857 0.00 0.00 43.04 1.94
1971 3220 2.704190 TCCCTGGTAAATGGGCAAAA 57.296 45.000 0.00 0.00 43.04 2.44
1972 3221 2.314549 AGATCCCTGGTAAATGGGCAAA 59.685 45.455 0.00 0.00 43.04 3.68
1973 3222 1.929494 AGATCCCTGGTAAATGGGCAA 59.071 47.619 0.00 0.00 43.04 4.52
1974 3223 1.215173 CAGATCCCTGGTAAATGGGCA 59.785 52.381 0.00 0.00 43.04 5.36
1975 3224 1.215423 ACAGATCCCTGGTAAATGGGC 59.785 52.381 0.00 0.00 44.60 5.36
1976 3225 3.290710 CAACAGATCCCTGGTAAATGGG 58.709 50.000 0.00 0.00 44.60 4.00
1977 3226 2.689983 GCAACAGATCCCTGGTAAATGG 59.310 50.000 0.00 0.00 44.60 3.16
1978 3227 2.355756 CGCAACAGATCCCTGGTAAATG 59.644 50.000 0.00 0.00 44.60 2.32
1979 3228 2.238646 TCGCAACAGATCCCTGGTAAAT 59.761 45.455 0.00 0.00 44.60 1.40
1980 3229 1.626321 TCGCAACAGATCCCTGGTAAA 59.374 47.619 0.00 0.00 44.60 2.01
1981 3230 1.271856 TCGCAACAGATCCCTGGTAA 58.728 50.000 0.00 0.00 44.60 2.85
1982 3231 1.138859 CATCGCAACAGATCCCTGGTA 59.861 52.381 0.00 0.00 44.60 3.25
1983 3232 0.107508 CATCGCAACAGATCCCTGGT 60.108 55.000 0.00 0.00 44.60 4.00
1984 3233 0.107508 ACATCGCAACAGATCCCTGG 60.108 55.000 0.00 0.00 44.60 4.45
1985 3234 1.293924 GACATCGCAACAGATCCCTG 58.706 55.000 0.00 0.00 45.76 4.45
1986 3235 0.904649 TGACATCGCAACAGATCCCT 59.095 50.000 0.00 0.00 0.00 4.20
1987 3236 1.009829 GTGACATCGCAACAGATCCC 58.990 55.000 0.00 0.00 0.00 3.85
1988 3237 1.009829 GGTGACATCGCAACAGATCC 58.990 55.000 0.00 0.00 0.00 3.36
1989 3238 0.647410 CGGTGACATCGCAACAGATC 59.353 55.000 0.00 0.00 0.00 2.75
1990 3239 0.740868 CCGGTGACATCGCAACAGAT 60.741 55.000 1.54 0.00 0.00 2.90
1991 3240 1.374125 CCGGTGACATCGCAACAGA 60.374 57.895 1.54 0.00 0.00 3.41
2013 3262 8.946085 AGCGTATGAAAGAGAACATTCAAAATA 58.054 29.630 0.00 0.00 37.30 1.40
2027 3276 3.871006 CCATAACTGCAGCGTATGAAAGA 59.129 43.478 27.66 0.00 0.00 2.52
2028 3277 3.546815 GCCATAACTGCAGCGTATGAAAG 60.547 47.826 27.66 17.46 0.00 2.62
2032 3281 0.588252 GGCCATAACTGCAGCGTATG 59.412 55.000 22.54 22.54 0.00 2.39
2131 3395 0.461870 TGCGCGCCAATAGTCAAGAT 60.462 50.000 30.77 0.00 0.00 2.40
2162 3451 8.893727 CGATCTAAAGTTGGATTCATTTTACCT 58.106 33.333 0.00 0.00 0.00 3.08
2307 3616 5.632347 CGACCAGTGGTAAAAACAGTAGTAG 59.368 44.000 16.72 0.00 35.25 2.57
2308 3617 5.068987 ACGACCAGTGGTAAAAACAGTAGTA 59.931 40.000 16.72 0.00 35.25 1.82
2309 3618 4.141869 ACGACCAGTGGTAAAAACAGTAGT 60.142 41.667 16.72 0.23 35.25 2.73
2310 3619 4.374399 ACGACCAGTGGTAAAAACAGTAG 58.626 43.478 16.72 0.00 35.25 2.57
2351 3660 4.996434 GCCGCACAGTGCTCACCT 62.996 66.667 23.15 0.00 42.25 4.00
2369 3678 0.613260 TGTACTCGGCTTCAGGCAAT 59.387 50.000 0.82 0.00 44.01 3.56
2371 3680 0.898326 TCTGTACTCGGCTTCAGGCA 60.898 55.000 0.82 0.00 44.01 4.75
2374 3683 1.986378 CGTTTCTGTACTCGGCTTCAG 59.014 52.381 0.00 0.00 0.00 3.02
2376 3685 1.347320 CCGTTTCTGTACTCGGCTTC 58.653 55.000 0.00 0.00 36.68 3.86
2377 3686 3.509388 CCGTTTCTGTACTCGGCTT 57.491 52.632 0.00 0.00 36.68 4.35
2380 3689 0.108329 ATGGCCGTTTCTGTACTCGG 60.108 55.000 0.00 0.00 44.86 4.63
2381 3690 0.999406 CATGGCCGTTTCTGTACTCG 59.001 55.000 0.00 0.00 0.00 4.18
2382 3691 1.369625 CCATGGCCGTTTCTGTACTC 58.630 55.000 0.00 0.00 0.00 2.59
2383 3692 0.035439 CCCATGGCCGTTTCTGTACT 60.035 55.000 6.09 0.00 0.00 2.73
2384 3693 0.035820 TCCCATGGCCGTTTCTGTAC 60.036 55.000 6.09 0.00 0.00 2.90
2385 3694 0.916086 ATCCCATGGCCGTTTCTGTA 59.084 50.000 6.09 0.00 0.00 2.74
2386 3695 0.916086 TATCCCATGGCCGTTTCTGT 59.084 50.000 6.09 0.00 0.00 3.41
2387 3696 2.051334 TTATCCCATGGCCGTTTCTG 57.949 50.000 6.09 0.00 0.00 3.02
2388 3697 2.758423 GTTTTATCCCATGGCCGTTTCT 59.242 45.455 6.09 0.00 0.00 2.52
2389 3698 2.494073 TGTTTTATCCCATGGCCGTTTC 59.506 45.455 6.09 0.00 0.00 2.78
2390 3699 2.232696 GTGTTTTATCCCATGGCCGTTT 59.767 45.455 6.09 0.00 0.00 3.60
2391 3700 1.822371 GTGTTTTATCCCATGGCCGTT 59.178 47.619 6.09 0.00 0.00 4.44
2392 3701 1.272203 TGTGTTTTATCCCATGGCCGT 60.272 47.619 6.09 0.00 0.00 5.68
2403 3712 4.260866 GCACCGTACAAGTGTGTGTTTTAT 60.261 41.667 13.03 0.00 38.82 1.40
2410 3719 1.668751 CTTTGCACCGTACAAGTGTGT 59.331 47.619 13.03 0.00 42.09 3.72
2437 3746 4.054825 TCGTACGGTTGGTCGCCC 62.055 66.667 16.52 0.00 0.00 6.13
2490 3799 1.750399 ATGAATCTGGGTGCCGTGC 60.750 57.895 0.00 0.00 0.00 5.34
2510 3819 1.609208 AACACATGAACAGTGGCCTC 58.391 50.000 3.32 0.00 41.21 4.70
2601 4029 0.813610 CGGAGCCACAAACAGACACA 60.814 55.000 0.00 0.00 0.00 3.72
2603 4031 0.107410 AACGGAGCCACAAACAGACA 60.107 50.000 0.00 0.00 0.00 3.41
2619 4047 5.761726 AGAACTAAAAGGGGTAAACTGAACG 59.238 40.000 0.00 0.00 0.00 3.95
2664 4095 4.947147 GCCCTGGTTGTGCCGTGA 62.947 66.667 0.00 0.00 41.21 4.35
2668 4099 1.880819 CTGAATGCCCTGGTTGTGCC 61.881 60.000 0.00 0.00 37.90 5.01
2670 4101 1.171308 CTCTGAATGCCCTGGTTGTG 58.829 55.000 0.00 0.00 0.00 3.33
2671 4102 0.773644 ACTCTGAATGCCCTGGTTGT 59.226 50.000 0.00 0.00 0.00 3.32
2677 4108 1.840635 GGGAGTAACTCTGAATGCCCT 59.159 52.381 0.00 0.00 0.00 5.19
2686 4117 1.651770 TGGGATGGAGGGAGTAACTCT 59.348 52.381 0.00 0.00 35.34 3.24
2687 4118 2.176247 TGGGATGGAGGGAGTAACTC 57.824 55.000 0.00 0.00 0.00 3.01
2688 4119 2.897823 ATGGGATGGAGGGAGTAACT 57.102 50.000 0.00 0.00 0.00 2.24
2690 4121 8.414623 TCTTATATTATGGGATGGAGGGAGTAA 58.585 37.037 0.00 0.00 0.00 2.24
2694 4125 6.156256 CGTTCTTATATTATGGGATGGAGGGA 59.844 42.308 0.00 0.00 0.00 4.20
2695 4126 6.070194 ACGTTCTTATATTATGGGATGGAGGG 60.070 42.308 0.00 0.00 0.00 4.30
2697 4128 8.848474 AAACGTTCTTATATTATGGGATGGAG 57.152 34.615 0.00 0.00 0.00 3.86
2698 4129 9.635404 AAAAACGTTCTTATATTATGGGATGGA 57.365 29.630 0.00 0.00 0.00 3.41
2735 4166 9.698309 GCTAGATGCATCTCTTGTTTATAACTA 57.302 33.333 31.92 9.02 42.31 2.24
2736 4167 8.600449 GCTAGATGCATCTCTTGTTTATAACT 57.400 34.615 31.92 6.52 42.31 2.24
2770 4201 2.385803 AGTTCGACGACCCTCCAATAT 58.614 47.619 0.00 0.00 0.00 1.28
2775 4206 1.529865 CAAAAAGTTCGACGACCCTCC 59.470 52.381 0.00 0.00 0.00 4.30
2780 4211 2.282290 TCCGTTCAAAAAGTTCGACGAC 59.718 45.455 0.00 0.00 32.73 4.34
2783 4214 2.282290 TCGTCCGTTCAAAAAGTTCGAC 59.718 45.455 0.00 0.00 0.00 4.20
2785 4216 2.348218 CCTCGTCCGTTCAAAAAGTTCG 60.348 50.000 0.00 0.00 0.00 3.95
2786 4217 2.867975 TCCTCGTCCGTTCAAAAAGTTC 59.132 45.455 0.00 0.00 0.00 3.01
2787 4218 2.908916 TCCTCGTCCGTTCAAAAAGTT 58.091 42.857 0.00 0.00 0.00 2.66
2814 4245 4.082895 CCCGTGGATAAGTAGGATTAGTCG 60.083 50.000 0.00 0.00 0.00 4.18
2815 4246 4.321824 GCCCGTGGATAAGTAGGATTAGTC 60.322 50.000 0.00 0.00 0.00 2.59
2825 4313 0.400815 TATGGGGCCCGTGGATAAGT 60.401 55.000 27.99 2.26 0.00 2.24
2838 4326 2.489802 GGAAAAGCAGAGGGATATGGGG 60.490 54.545 0.00 0.00 0.00 4.96
2891 4389 1.078356 GGGCTCCCGAGAAAGGTTC 60.078 63.158 0.00 0.00 0.00 3.62
2892 4390 3.078817 GGGCTCCCGAGAAAGGTT 58.921 61.111 0.00 0.00 0.00 3.50
2924 4422 1.606601 AAAGAGGGGCCGCTTTTCC 60.607 57.895 24.96 11.03 41.89 3.13
2926 4424 4.619233 AAAAGAGGGGCCGCTTTT 57.381 50.000 24.96 21.59 46.03 2.27
2927 4425 2.574018 GCAAAAGAGGGGCCGCTTT 61.574 57.895 24.96 16.22 45.37 3.51
2928 4426 2.991540 GCAAAAGAGGGGCCGCTT 60.992 61.111 24.96 11.03 37.67 4.68
2929 4427 3.808218 TTGCAAAAGAGGGGCCGCT 62.808 57.895 24.42 24.42 0.00 5.52
2930 4428 3.286915 CTTGCAAAAGAGGGGCCGC 62.287 63.158 12.88 12.88 0.00 6.53
2931 4429 2.964978 CTTGCAAAAGAGGGGCCG 59.035 61.111 0.00 0.00 0.00 6.13
2936 4434 0.608035 TACCCGGCTTGCAAAAGAGG 60.608 55.000 0.00 2.03 0.00 3.69
2977 4478 1.373497 CGGAGACTCGTGCAAGCTT 60.373 57.895 0.00 0.00 0.00 3.74
2978 4479 2.206515 CTCGGAGACTCGTGCAAGCT 62.207 60.000 0.00 0.00 0.00 3.74
3042 4572 0.035598 TCAATTTCAAGGTCGGCGGA 59.964 50.000 7.21 0.00 0.00 5.54
3069 4599 4.512484 CAGAGAAACCTTTGGAGAGGATC 58.488 47.826 0.00 0.00 39.25 3.36
3070 4600 3.265479 CCAGAGAAACCTTTGGAGAGGAT 59.735 47.826 0.00 0.00 37.96 3.24
3071 4601 2.639839 CCAGAGAAACCTTTGGAGAGGA 59.360 50.000 0.00 0.00 37.96 3.71
3072 4602 2.373502 ACCAGAGAAACCTTTGGAGAGG 59.626 50.000 8.71 0.00 37.96 3.69
3073 4603 3.558109 GGACCAGAGAAACCTTTGGAGAG 60.558 52.174 8.71 0.00 37.96 3.20
3101 4631 3.950395 TCTTCTTCTCATCGAGATGCTCA 59.050 43.478 8.14 0.00 38.56 4.26


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

AutoCloner maintained by Alex Coulton.