Multiple sequence alignment - TraesCS4A01G080500

Loading Multiple Alignment...

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 TraesCS4A01G080500 chr4A 100.000 2389 0 0 4001 6389 83319210 83321598 0.000000e+00 4412.0
1 TraesCS4A01G080500 chr4A 100.000 1828 0 0 1875 3702 83317084 83318911 0.000000e+00 3376.0
2 TraesCS4A01G080500 chr4A 100.000 1635 0 0 1 1635 83315210 83316844 0.000000e+00 3020.0
3 TraesCS4A01G080500 chr4A 96.835 158 2 2 1875 2029 11366047 11366204 1.770000e-65 261.0
4 TraesCS4A01G080500 chr4A 86.700 203 22 4 1433 1633 625794152 625794351 3.000000e-53 220.0
5 TraesCS4A01G080500 chr4A 98.000 50 1 0 2522 2571 714406239 714406288 3.170000e-13 87.9
6 TraesCS4A01G080500 chr4D 93.579 1869 95 14 4524 6389 380460843 380458997 0.000000e+00 2763.0
7 TraesCS4A01G080500 chr4D 95.470 1722 61 7 1983 3700 380464020 380462312 0.000000e+00 2732.0
8 TraesCS4A01G080500 chr4D 92.419 1174 45 16 471 1626 380465112 380463965 0.000000e+00 1635.0
9 TraesCS4A01G080500 chr4D 86.237 465 38 14 1 455 380466201 380465753 1.250000e-131 481.0
10 TraesCS4A01G080500 chr4D 91.775 231 10 4 4001 4231 380462254 380462033 4.810000e-81 313.0
11 TraesCS4A01G080500 chr4D 97.959 98 2 0 4262 4359 380460948 380460851 3.060000e-38 171.0
12 TraesCS4A01G080500 chr4D 90.323 93 6 1 5259 5351 380460198 380460109 1.130000e-22 119.0
13 TraesCS4A01G080500 chr4B 94.197 1775 75 10 4001 5771 467916529 467914779 0.000000e+00 2682.0
14 TraesCS4A01G080500 chr4B 94.480 1721 80 6 1983 3700 467918295 467916587 0.000000e+00 2638.0
15 TraesCS4A01G080500 chr4B 88.556 1669 108 44 5 1628 467919868 467918238 0.000000e+00 1947.0
16 TraesCS4A01G080500 chr4B 87.520 617 42 13 5807 6389 467912833 467912218 0.000000e+00 680.0
17 TraesCS4A01G080500 chr4B 92.208 77 3 1 5259 5335 467915372 467915299 8.760000e-19 106.0
18 TraesCS4A01G080500 chr2A 91.528 1865 112 24 4001 5838 14941144 14939299 0.000000e+00 2527.0
19 TraesCS4A01G080500 chr2A 96.835 158 3 2 1875 2030 88796062 88796219 4.910000e-66 263.0
20 TraesCS4A01G080500 chr2A 93.529 170 9 2 1875 2042 505337218 505337049 1.060000e-62 252.0
21 TraesCS4A01G080500 chr2A 86.124 209 23 4 1420 1628 584149440 584149642 3.000000e-53 220.0
22 TraesCS4A01G080500 chr2A 85.238 210 27 4 1423 1631 278996248 278996454 5.020000e-51 213.0
23 TraesCS4A01G080500 chr2A 92.683 41 2 1 346 385 543744674 543744714 2.490000e-04 58.4
24 TraesCS4A01G080500 chr6A 96.835 158 2 2 1875 2029 180309182 180309339 1.770000e-65 261.0
25 TraesCS4A01G080500 chr6A 96.203 158 6 0 1875 2032 147454486 147454329 6.350000e-65 259.0
26 TraesCS4A01G080500 chr6A 95.706 163 3 2 1875 2033 273584407 273584245 6.350000e-65 259.0
27 TraesCS4A01G080500 chr7A 96.226 159 5 1 1875 2032 701621270 701621112 6.350000e-65 259.0
28 TraesCS4A01G080500 chr7A 94.048 168 8 1 1875 2040 162776273 162776106 2.960000e-63 254.0
29 TraesCS4A01G080500 chr7A 94.083 169 5 3 1875 2039 130378218 130378385 1.060000e-62 252.0
30 TraesCS4A01G080500 chr5D 88.000 200 16 7 1433 1628 482454462 482454267 4.980000e-56 230.0
31 TraesCS4A01G080500 chr5D 94.444 36 2 0 350 385 564952487 564952452 8.950000e-04 56.5
32 TraesCS4A01G080500 chr5B 86.275 204 25 2 1422 1625 383538648 383538848 1.080000e-52 219.0
33 TraesCS4A01G080500 chr1A 85.990 207 23 5 1427 1630 271887426 271887629 3.880000e-52 217.0
34 TraesCS4A01G080500 chr1A 85.646 209 23 6 1420 1627 17244416 17244618 5.020000e-51 213.0
35 TraesCS4A01G080500 chr1A 98.000 50 0 1 2522 2571 27398438 27398486 1.140000e-12 86.1
36 TraesCS4A01G080500 chr7D 98.000 50 0 1 2522 2571 568198682 568198634 1.140000e-12 86.1
37 TraesCS4A01G080500 chr2D 96.000 50 2 0 2522 2571 107866649 107866698 1.480000e-11 82.4


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 TraesCS4A01G080500 chr4A 83315210 83321598 6388 False 3602.666667 4412 100.000000 1 6389 3 chr4A.!!$F4 6388
1 TraesCS4A01G080500 chr4D 380458997 380466201 7204 True 1173.428571 2763 92.537429 1 6389 7 chr4D.!!$R1 6388
2 TraesCS4A01G080500 chr4B 467912218 467919868 7650 True 1610.600000 2682 91.392200 5 6389 5 chr4B.!!$R1 6384
3 TraesCS4A01G080500 chr2A 14939299 14941144 1845 True 2527.000000 2527 91.528000 4001 5838 1 chr2A.!!$R1 1837

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
704 1364 0.324943 TGTTTCTCAGTAGCCCAGCC 59.675 55.0 0.00 0.0 0.00 4.85 F
1451 2138 0.466124 GGTCTGTCTAGGGCACATCC 59.534 60.0 0.00 0.0 0.00 3.51 F
2032 2719 0.328258 GTGCCCTAGACACACCCAAT 59.672 55.0 10.07 0.0 37.96 3.16 F
2529 3216 0.529378 CTGCAGGCAAACCCAAGATC 59.471 55.0 5.57 0.0 36.11 2.75 F
4105 4800 0.183014 TAACTCCCAACGGTGGCAAA 59.817 50.0 16.13 0.0 44.46 3.68 F
4658 6426 0.179045 AGCTTGGTGGTGTGAGTGTC 60.179 55.0 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2697 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.0 18.92 18.25 46.66 3.06 R
3220 3913 0.107459 GATGGCTCAGTTCCCAGTCC 60.107 60.0 0.00 0.00 34.01 3.85 R
3610 4305 0.612453 CCTATCTACGCCTCCTCCCC 60.612 65.0 0.00 0.00 0.00 4.81 R
4151 4846 2.393271 ATCTCGTTTCCCAGCTTCTG 57.607 50.0 0.00 0.00 0.00 3.02 R
5091 6863 0.536460 AAGGCGTTTTGACCGGTGAT 60.536 50.0 14.63 0.00 0.00 3.06 R
6349 10088 0.102120 TTTTGTTTCAGCCGGCACAG 59.898 50.0 31.54 18.31 0.00 3.66 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
27 28 4.344968 AGTGGCTCCCATAAATAAAATGCC 59.655 41.667 0.00 0.00 35.28 4.40
45 46 6.645790 AATGCCAAACCATAAATGCAAAAA 57.354 29.167 0.00 0.00 31.81 1.94
74 79 7.630606 CCGAAAGAAAACGAAGAAAAACATTTG 59.369 33.333 0.00 0.00 0.00 2.32
77 82 7.289587 AGAAAACGAAGAAAAACATTTGTGG 57.710 32.000 0.00 0.00 0.00 4.17
84 89 7.386573 ACGAAGAAAAACATTTGTGGAAAAACT 59.613 29.630 0.00 0.00 0.00 2.66
91 96 6.969993 ACATTTGTGGAAAAACTAGCCTAA 57.030 33.333 0.00 0.00 0.00 2.69
93 98 5.427036 TTTGTGGAAAAACTAGCCTAACG 57.573 39.130 0.00 0.00 0.00 3.18
94 99 4.339872 TGTGGAAAAACTAGCCTAACGA 57.660 40.909 0.00 0.00 0.00 3.85
95 100 4.312443 TGTGGAAAAACTAGCCTAACGAG 58.688 43.478 0.00 0.00 0.00 4.18
97 102 3.007614 TGGAAAAACTAGCCTAACGAGCT 59.992 43.478 0.00 0.00 44.49 4.09
100 105 5.816258 GGAAAAACTAGCCTAACGAGCTATT 59.184 40.000 0.00 0.00 41.79 1.73
101 106 6.018913 GGAAAAACTAGCCTAACGAGCTATTC 60.019 42.308 0.00 0.00 41.79 1.75
104 109 1.789523 AGCCTAACGAGCTATTCCCA 58.210 50.000 0.00 0.00 39.29 4.37
105 110 2.330216 AGCCTAACGAGCTATTCCCAT 58.670 47.619 0.00 0.00 39.29 4.00
106 111 2.300437 AGCCTAACGAGCTATTCCCATC 59.700 50.000 0.00 0.00 39.29 3.51
122 127 3.706086 TCCCATCGAGATGTGAAGAATCA 59.294 43.478 11.59 0.00 37.11 2.57
150 162 2.550180 GCTATTCCCATCGCTTTCTTCC 59.450 50.000 0.00 0.00 0.00 3.46
152 164 0.695924 TTCCCATCGCTTTCTTCCCA 59.304 50.000 0.00 0.00 0.00 4.37
153 165 0.695924 TCCCATCGCTTTCTTCCCAA 59.304 50.000 0.00 0.00 0.00 4.12
168 180 3.438131 TCCCAAGACCTCCTATTCCAT 57.562 47.619 0.00 0.00 0.00 3.41
189 201 5.451798 CCATGCCTTAATTAAGCGTGGAATT 60.452 40.000 31.76 7.78 42.50 2.17
197 209 9.706691 CTTAATTAAGCGTGGAATTATAGAGGA 57.293 33.333 12.15 0.00 29.87 3.71
213 225 4.085357 AGAGGAAACACATGTGCTTACA 57.915 40.909 25.68 0.00 0.00 2.41
227 239 8.978564 CATGTGCTTACATGGTTTGTTATTTA 57.021 30.769 11.53 0.00 42.63 1.40
228 240 9.416794 CATGTGCTTACATGGTTTGTTATTTAA 57.583 29.630 11.53 0.00 42.63 1.52
229 241 9.988815 ATGTGCTTACATGGTTTGTTATTTAAA 57.011 25.926 0.00 0.00 39.87 1.52
230 242 9.817809 TGTGCTTACATGGTTTGTTATTTAAAA 57.182 25.926 0.00 0.00 39.87 1.52
331 356 6.018425 GGGAAATATGCATGCTCGTATATCTG 60.018 42.308 20.33 0.00 0.00 2.90
335 360 8.552083 AATATGCATGCTCGTATATCTGAAAA 57.448 30.769 20.33 0.00 0.00 2.29
503 1160 4.911390 ACCATCAGAAAACTCGGAAGAAT 58.089 39.130 0.00 0.00 41.32 2.40
559 1217 8.687242 AGAAGAAGAAAAAGACGGAAGAAAAAT 58.313 29.630 0.00 0.00 0.00 1.82
567 1225 1.194218 CGGAAGAAAAATGGCCCCAT 58.806 50.000 0.00 0.00 38.46 4.00
610 1268 1.890174 CCACGGGGATTTGCCTTTC 59.110 57.895 0.00 0.00 35.59 2.62
616 1276 1.195115 GGGATTTGCCTTTCCCTTCC 58.805 55.000 7.51 0.00 46.91 3.46
638 1298 1.671379 GTCCAGTCCAACGAAGCCC 60.671 63.158 0.00 0.00 0.00 5.19
659 1319 1.586154 CGTGGCCCCACTTGAATCAC 61.586 60.000 14.93 0.00 44.16 3.06
704 1364 0.324943 TGTTTCTCAGTAGCCCAGCC 59.675 55.000 0.00 0.00 0.00 4.85
1067 1739 1.208165 AATCCGCCCAAGAAGGAGGT 61.208 55.000 0.11 0.00 46.35 3.85
1273 1957 1.213430 AGGAAGAGGAGGAGTACGAGG 59.787 57.143 0.00 0.00 0.00 4.63
1274 1958 1.212441 GGAAGAGGAGGAGTACGAGGA 59.788 57.143 0.00 0.00 0.00 3.71
1275 1959 2.567985 GAAGAGGAGGAGTACGAGGAG 58.432 57.143 0.00 0.00 0.00 3.69
1451 2138 0.466124 GGTCTGTCTAGGGCACATCC 59.534 60.000 0.00 0.00 0.00 3.51
1477 2164 1.340017 TGCCCTAGTTCTTGCACATCC 60.340 52.381 0.00 0.00 0.00 3.51
1485 2172 1.896220 TCTTGCACATCCAAGTGACC 58.104 50.000 0.00 0.00 42.16 4.02
1545 2232 7.839680 AAAGAAATTACCCACACAAATCTCT 57.160 32.000 0.00 0.00 0.00 3.10
1569 2256 4.383052 GCGTAAGATCAATGACATAGGACG 59.617 45.833 0.00 0.00 43.02 4.79
1899 2586 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
1900 2587 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
1901 2588 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
1902 2589 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
1903 2590 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
1904 2591 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
1908 2595 8.824159 AGTATTGCACATCTAAGTCATATGTC 57.176 34.615 1.90 0.00 31.60 3.06
1909 2596 8.424133 AGTATTGCACATCTAAGTCATATGTCA 58.576 33.333 1.90 0.00 31.60 3.58
1910 2597 9.212641 GTATTGCACATCTAAGTCATATGTCAT 57.787 33.333 1.90 0.00 31.60 3.06
1911 2598 8.687292 ATTGCACATCTAAGTCATATGTCATT 57.313 30.769 1.90 0.00 31.60 2.57
1912 2599 7.486802 TGCACATCTAAGTCATATGTCATTG 57.513 36.000 1.90 0.00 31.60 2.82
1913 2600 7.274447 TGCACATCTAAGTCATATGTCATTGA 58.726 34.615 1.90 0.00 31.60 2.57
1914 2601 7.935210 TGCACATCTAAGTCATATGTCATTGAT 59.065 33.333 1.90 0.00 31.60 2.57
1915 2602 8.441608 GCACATCTAAGTCATATGTCATTGATC 58.558 37.037 1.90 0.00 31.60 2.92
1916 2603 9.708092 CACATCTAAGTCATATGTCATTGATCT 57.292 33.333 1.90 0.00 31.60 2.75
1944 2631 9.436957 ACATTAAGATTCGTGTGAATACTTTCT 57.563 29.630 0.00 0.00 44.79 2.52
1948 2635 8.608844 AAGATTCGTGTGAATACTTTCTTTCT 57.391 30.769 0.00 0.00 44.79 2.52
1949 2636 8.245701 AGATTCGTGTGAATACTTTCTTTCTC 57.754 34.615 0.00 0.00 44.79 2.87
1950 2637 8.091449 AGATTCGTGTGAATACTTTCTTTCTCT 58.909 33.333 0.00 0.00 44.79 3.10
1951 2638 8.608844 ATTCGTGTGAATACTTTCTTTCTCTT 57.391 30.769 0.00 0.00 42.99 2.85
1952 2639 8.433421 TTCGTGTGAATACTTTCTTTCTCTTT 57.567 30.769 0.00 0.00 32.78 2.52
1953 2640 8.433421 TCGTGTGAATACTTTCTTTCTCTTTT 57.567 30.769 0.00 0.00 32.78 2.27
1954 2641 8.889717 TCGTGTGAATACTTTCTTTCTCTTTTT 58.110 29.630 0.00 0.00 32.78 1.94
1979 2666 9.814899 TTTTTCTTTTTATGCTTGATTCACTCA 57.185 25.926 0.00 0.00 0.00 3.41
1980 2667 8.801715 TTTCTTTTTATGCTTGATTCACTCAC 57.198 30.769 0.00 0.00 32.17 3.51
1981 2668 7.750229 TCTTTTTATGCTTGATTCACTCACT 57.250 32.000 0.00 0.00 32.17 3.41
1982 2669 8.169977 TCTTTTTATGCTTGATTCACTCACTT 57.830 30.769 0.00 0.00 32.17 3.16
1983 2670 9.283768 TCTTTTTATGCTTGATTCACTCACTTA 57.716 29.630 0.00 0.00 32.17 2.24
1984 2671 9.552114 CTTTTTATGCTTGATTCACTCACTTAG 57.448 33.333 0.00 0.00 32.17 2.18
1985 2672 8.846943 TTTTATGCTTGATTCACTCACTTAGA 57.153 30.769 0.00 0.00 32.17 2.10
1986 2673 9.453572 TTTTATGCTTGATTCACTCACTTAGAT 57.546 29.630 0.00 0.00 32.17 1.98
1987 2674 6.922247 ATGCTTGATTCACTCACTTAGATG 57.078 37.500 0.00 0.00 32.17 2.90
1988 2675 5.798132 TGCTTGATTCACTCACTTAGATGT 58.202 37.500 0.00 0.00 32.17 3.06
1989 2676 5.640783 TGCTTGATTCACTCACTTAGATGTG 59.359 40.000 0.00 0.00 39.15 3.21
1990 2677 5.447010 GCTTGATTCACTCACTTAGATGTGC 60.447 44.000 0.00 0.00 37.81 4.57
1991 2678 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
1992 2679 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
1993 2680 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
1994 2681 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
1995 2682 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
1996 2683 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
1997 2684 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
1998 2685 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
1999 2686 7.976175 TCACTCACTTAGATGTGCAATAACTAG 59.024 37.037 0.00 0.00 37.81 2.57
2000 2687 7.976175 CACTCACTTAGATGTGCAATAACTAGA 59.024 37.037 0.00 0.00 37.81 2.43
2001 2688 8.194104 ACTCACTTAGATGTGCAATAACTAGAG 58.806 37.037 0.00 0.00 37.81 2.43
2002 2689 6.980978 TCACTTAGATGTGCAATAACTAGAGC 59.019 38.462 0.00 0.00 37.81 4.09
2003 2690 6.758416 CACTTAGATGTGCAATAACTAGAGCA 59.242 38.462 0.00 0.00 34.10 4.26
2025 2712 4.250116 CATCTAGATGTGCCCTAGACAC 57.750 50.000 22.42 8.47 43.57 3.67
2029 2716 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
2030 2717 1.460497 TGTGCCCTAGACACACCCA 60.460 57.895 12.81 0.00 42.88 4.51
2031 2718 1.057275 TGTGCCCTAGACACACCCAA 61.057 55.000 12.81 0.00 42.88 4.12
2032 2719 0.328258 GTGCCCTAGACACACCCAAT 59.672 55.000 10.07 0.00 37.96 3.16
2033 2720 1.072266 TGCCCTAGACACACCCAATT 58.928 50.000 0.00 0.00 0.00 2.32
2034 2721 1.427368 TGCCCTAGACACACCCAATTT 59.573 47.619 0.00 0.00 0.00 1.82
2035 2722 2.158385 TGCCCTAGACACACCCAATTTT 60.158 45.455 0.00 0.00 0.00 1.82
2036 2723 2.897326 GCCCTAGACACACCCAATTTTT 59.103 45.455 0.00 0.00 0.00 1.94
2174 2861 2.683211 ATTGGAGGGTTGTCAAGCTT 57.317 45.000 14.11 6.92 0.00 3.74
2281 2968 2.784347 CTGGTTTCTCCCAGTCTTTCC 58.216 52.381 0.00 0.00 45.81 3.13
2493 3180 3.243367 TGTGGACTTTTCAGCCAAAATCG 60.243 43.478 0.00 0.00 33.34 3.34
2514 3201 1.001746 CAGAAGAGAAGTCCAGCTGCA 59.998 52.381 8.66 0.00 0.00 4.41
2529 3216 0.529378 CTGCAGGCAAACCCAAGATC 59.471 55.000 5.57 0.00 36.11 2.75
2674 3364 8.581253 AATAAAGAAGGAAGTTGGTATCAAGG 57.419 34.615 0.00 0.00 32.92 3.61
2852 3542 6.046593 TCATACGGAGCAATAATCGTTTTCT 58.953 36.000 0.00 0.00 37.10 2.52
2960 3650 7.706281 GTGAGATACCACATCTATGAAACAG 57.294 40.000 0.00 0.00 37.04 3.16
3060 3753 4.168101 TCCAAGAATCACAGTAGAACCCT 58.832 43.478 0.00 0.00 0.00 4.34
3220 3913 5.806654 CCAATAATTTCTGGGTATTGGGG 57.193 43.478 12.03 0.00 45.58 4.96
3250 3943 3.460825 ACTGAGCCATCCCCTAAACTTA 58.539 45.455 0.00 0.00 0.00 2.24
3261 3954 6.222227 TCCCCTAAACTTAACTCCCATTTT 57.778 37.500 0.00 0.00 0.00 1.82
3262 3955 6.626238 TCCCCTAAACTTAACTCCCATTTTT 58.374 36.000 0.00 0.00 0.00 1.94
3409 4102 4.776322 CCGCTGCGGTGGATGGAA 62.776 66.667 31.72 0.00 45.39 3.53
3455 4150 1.617018 CCTGATTCCCTGCCTCGACA 61.617 60.000 0.00 0.00 0.00 4.35
3488 4183 1.954362 CTTCTCGGCTCAGGAGGTGG 61.954 65.000 0.00 0.00 32.34 4.61
3489 4184 2.681778 CTCGGCTCAGGAGGTGGT 60.682 66.667 0.00 0.00 0.00 4.16
3490 4185 2.997315 TCGGCTCAGGAGGTGGTG 60.997 66.667 0.00 0.00 0.00 4.17
3582 4277 1.154221 GGAGGAGGCGGAGATAGGT 59.846 63.158 0.00 0.00 0.00 3.08
3631 4326 0.539901 GGAGGAGGCGTAGATAGGCA 60.540 60.000 6.84 0.00 38.72 4.75
3676 4371 1.898574 CTTGGCCGGAGTTGTTGCT 60.899 57.895 5.05 0.00 0.00 3.91
3700 4395 4.887190 AACTTTGGCGGTGGCGGT 62.887 61.111 0.00 0.00 41.24 5.68
3701 4396 4.887190 ACTTTGGCGGTGGCGGTT 62.887 61.111 0.00 0.00 41.24 4.44
4105 4800 0.183014 TAACTCCCAACGGTGGCAAA 59.817 50.000 16.13 0.00 44.46 3.68
4110 4805 1.486726 TCCCAACGGTGGCAAATTTTT 59.513 42.857 16.13 0.00 44.46 1.94
4151 4846 3.265995 TGGGATGGGTTAGAGTTCCTTTC 59.734 47.826 0.00 0.00 0.00 2.62
4178 4873 6.174720 AGCTGGGAAACGAGATATAAATCA 57.825 37.500 0.00 0.00 38.67 2.57
4420 6186 7.885297 TGGTAGATTAATGCAATATCAAAGGC 58.115 34.615 0.00 0.00 0.00 4.35
4454 6220 5.417580 TCAGTTAAAACTTGAAAGCACCAGT 59.582 36.000 0.00 0.00 37.08 4.00
4474 6240 8.616076 CACCAGTATTTTTAATCTCCACTGATC 58.384 37.037 0.00 0.00 35.12 2.92
4658 6426 0.179045 AGCTTGGTGGTGTGAGTGTC 60.179 55.000 0.00 0.00 0.00 3.67
4687 6455 4.224147 TGTAGGTTGTATGCTTCTGCCTTA 59.776 41.667 0.00 0.00 38.71 2.69
4737 6505 4.704833 GCTTGCAGCCGAGGTCCA 62.705 66.667 0.00 0.00 34.48 4.02
4738 6506 2.743928 CTTGCAGCCGAGGTCCAC 60.744 66.667 0.00 0.00 0.00 4.02
4760 6528 5.301805 CACTTTTCTTGGGTAAACATGAGGT 59.698 40.000 0.00 0.00 0.00 3.85
4817 6588 8.612619 CATCAATTACTAATAAACCTCGCTTGT 58.387 33.333 0.00 0.00 0.00 3.16
4917 6689 5.235305 ACTTGTAGCTTGTGTGTTGAAAG 57.765 39.130 0.00 0.00 0.00 2.62
4925 6697 6.630071 AGCTTGTGTGTTGAAAGTGTTATTT 58.370 32.000 0.00 0.00 0.00 1.40
4989 6761 6.014156 AGTTCCTCTGATGTAAGCAAGTAACT 60.014 38.462 0.00 0.00 0.00 2.24
5057 6829 1.634702 GCTACAGAGGTCTTTGCGAG 58.365 55.000 0.00 0.00 0.00 5.03
5091 6863 5.359194 AGAAACAGGTTCTGAAACTGAGA 57.641 39.130 35.08 0.00 45.29 3.27
5337 7118 0.803117 ACACAGATGACGACGACGAT 59.197 50.000 15.32 0.00 42.66 3.73
5394 7179 7.666623 AGCAAAAGATCTCTAGCTAAGTATCC 58.333 38.462 12.43 0.00 30.46 2.59
5436 7221 4.578928 GTGTCCTTTGTGTTACCATTGACT 59.421 41.667 0.00 0.00 0.00 3.41
5441 7226 6.829298 TCCTTTGTGTTACCATTGACTTTGTA 59.171 34.615 0.00 0.00 0.00 2.41
5468 7253 7.052142 AGATCAGTATAACCTTAGGAAACGG 57.948 40.000 4.77 0.00 0.00 4.44
5479 7270 4.451435 CCTTAGGAAACGGTGAGACTTTTC 59.549 45.833 0.00 0.00 0.00 2.29
5483 7274 4.383173 GGAAACGGTGAGACTTTTCCTTA 58.617 43.478 7.94 0.00 42.53 2.69
5547 7339 2.386661 ACTATTGAGGTGTGAAGCGG 57.613 50.000 0.00 0.00 0.00 5.52
5551 7343 3.414700 GAGGTGTGAAGCGGTGCG 61.415 66.667 0.00 0.00 0.00 5.34
5608 7400 6.046593 TCATGTTATCCATCGTGAACCTTAC 58.953 40.000 0.00 0.00 0.00 2.34
5649 7441 2.279136 GCAGTACTTGCGTAGTGATTCG 59.721 50.000 9.90 0.00 45.71 3.34
5693 7485 5.607939 TTCTACTGAGGTTGACAAACTGA 57.392 39.130 11.31 0.25 36.48 3.41
5709 7501 7.013178 TGACAAACTGAAGCATCATTTTCTACA 59.987 33.333 4.50 3.67 36.59 2.74
5773 7565 4.704057 AGCTGAATGTTTCTTCTCCCATTC 59.296 41.667 0.00 0.00 42.11 2.67
5776 7568 6.375455 GCTGAATGTTTCTTCTCCCATTCTTA 59.625 38.462 11.23 0.00 42.21 2.10
5782 7574 6.881065 TGTTTCTTCTCCCATTCTTACATCAG 59.119 38.462 0.00 0.00 0.00 2.90
5790 9487 5.248248 TCCCATTCTTACATCAGAACACAGA 59.752 40.000 0.00 0.00 35.57 3.41
5791 9488 6.070021 TCCCATTCTTACATCAGAACACAGAT 60.070 38.462 0.00 0.00 35.57 2.90
5792 9489 7.125659 TCCCATTCTTACATCAGAACACAGATA 59.874 37.037 0.00 0.00 35.57 1.98
5815 9520 1.914634 CTTTCGCACGTAGCATCTCT 58.085 50.000 9.95 0.00 46.13 3.10
5860 9565 6.165577 GCAGTAACATTTCCCATTGACAATT 58.834 36.000 0.00 0.00 0.00 2.32
5963 9689 4.110036 GGTTCCAATCAACCATAGCAAC 57.890 45.455 0.00 0.00 44.79 4.17
6237 9966 0.038526 GAACTCCGCTTCTTCGACCA 60.039 55.000 0.00 0.00 0.00 4.02
6346 10085 3.192844 TCTCCAGTAAACATCACGGTCTC 59.807 47.826 0.00 0.00 0.00 3.36
6348 10087 2.094906 CCAGTAAACATCACGGTCTCGA 60.095 50.000 0.00 0.00 40.11 4.04
6349 10088 2.915463 CAGTAAACATCACGGTCTCGAC 59.085 50.000 0.00 0.00 40.11 4.20
6374 10113 2.809696 GCCGGCTGAAACAAAACTAGTA 59.190 45.455 22.15 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.291971 GCATTTTATTTATGGGAGCCACTG 58.708 41.667 0.00 0.00 35.80 3.66
45 46 4.968812 TTTCTTCGTTTTCTTTCGGGTT 57.031 36.364 0.00 0.00 0.00 4.11
47 48 5.096849 TGTTTTTCTTCGTTTTCTTTCGGG 58.903 37.500 0.00 0.00 0.00 5.14
48 49 6.806120 ATGTTTTTCTTCGTTTTCTTTCGG 57.194 33.333 0.00 0.00 0.00 4.30
50 51 9.249844 CACAAATGTTTTTCTTCGTTTTCTTTC 57.750 29.630 0.00 0.00 0.00 2.62
51 52 8.227119 CCACAAATGTTTTTCTTCGTTTTCTTT 58.773 29.630 0.00 0.00 0.00 2.52
52 53 7.600752 TCCACAAATGTTTTTCTTCGTTTTCTT 59.399 29.630 0.00 0.00 0.00 2.52
53 54 7.093992 TCCACAAATGTTTTTCTTCGTTTTCT 58.906 30.769 0.00 0.00 0.00 2.52
54 55 7.284518 TCCACAAATGTTTTTCTTCGTTTTC 57.715 32.000 0.00 0.00 0.00 2.29
57 58 7.659652 TTTTCCACAAATGTTTTTCTTCGTT 57.340 28.000 0.00 0.00 0.00 3.85
59 60 7.738345 AGTTTTTCCACAAATGTTTTTCTTCG 58.262 30.769 0.00 0.00 0.00 3.79
61 62 8.664798 GCTAGTTTTTCCACAAATGTTTTTCTT 58.335 29.630 0.00 0.00 0.00 2.52
62 63 7.279981 GGCTAGTTTTTCCACAAATGTTTTTCT 59.720 33.333 0.00 0.00 0.00 2.52
63 64 7.279981 AGGCTAGTTTTTCCACAAATGTTTTTC 59.720 33.333 0.00 0.00 0.00 2.29
74 79 3.124806 GCTCGTTAGGCTAGTTTTTCCAC 59.875 47.826 0.00 0.00 0.00 4.02
77 82 6.018913 GGAATAGCTCGTTAGGCTAGTTTTTC 60.019 42.308 0.00 0.00 44.05 2.29
84 89 2.953453 TGGGAATAGCTCGTTAGGCTA 58.047 47.619 0.00 0.00 44.76 3.93
91 96 1.982660 TCTCGATGGGAATAGCTCGT 58.017 50.000 0.00 0.00 33.10 4.18
93 98 3.583806 CACATCTCGATGGGAATAGCTC 58.416 50.000 11.25 0.00 44.83 4.09
94 99 3.674528 CACATCTCGATGGGAATAGCT 57.325 47.619 11.25 0.00 44.83 3.32
101 106 4.063998 TGATTCTTCACATCTCGATGGG 57.936 45.455 11.25 7.30 43.43 4.00
104 109 6.739112 TCGTTATGATTCTTCACATCTCGAT 58.261 36.000 0.00 0.00 33.85 3.59
105 110 6.131544 TCGTTATGATTCTTCACATCTCGA 57.868 37.500 0.00 0.00 33.85 4.04
106 111 5.108065 GCTCGTTATGATTCTTCACATCTCG 60.108 44.000 0.00 0.00 33.85 4.04
122 127 2.563179 AGCGATGGGAATAGCTCGTTAT 59.437 45.455 0.00 0.00 34.48 1.89
150 162 2.487986 GGCATGGAATAGGAGGTCTTGG 60.488 54.545 0.00 0.00 0.00 3.61
152 164 2.781667 AGGCATGGAATAGGAGGTCTT 58.218 47.619 0.00 0.00 0.00 3.01
153 165 2.503869 AGGCATGGAATAGGAGGTCT 57.496 50.000 0.00 0.00 0.00 3.85
168 180 6.952773 ATAATTCCACGCTTAATTAAGGCA 57.047 33.333 23.37 2.22 32.80 4.75
189 201 6.941857 TGTAAGCACATGTGTTTCCTCTATA 58.058 36.000 28.21 9.17 35.63 1.31
460 492 9.278978 GATGGTTTCTTTCTTTCTCTCTTACTT 57.721 33.333 0.00 0.00 0.00 2.24
461 493 8.432805 TGATGGTTTCTTTCTTTCTCTCTTACT 58.567 33.333 0.00 0.00 0.00 2.24
462 494 8.608844 TGATGGTTTCTTTCTTTCTCTCTTAC 57.391 34.615 0.00 0.00 0.00 2.34
463 495 8.651389 TCTGATGGTTTCTTTCTTTCTCTCTTA 58.349 33.333 0.00 0.00 0.00 2.10
468 1125 8.409371 AGTTTTCTGATGGTTTCTTTCTTTCTC 58.591 33.333 0.00 0.00 0.00 2.87
594 1252 4.434483 GGAAAGGCAAATCCCCGT 57.566 55.556 0.00 0.00 34.51 5.28
610 1268 2.301738 GGACTGGACTGGGGAAGGG 61.302 68.421 0.00 0.00 0.00 3.95
616 1276 0.320771 CTTCGTTGGACTGGACTGGG 60.321 60.000 0.00 0.00 0.00 4.45
648 1308 0.518636 CCGCCACTGTGATTCAAGTG 59.481 55.000 9.86 15.94 0.00 3.16
695 1355 2.754648 CCGGTATTAGGCTGGGCTA 58.245 57.895 0.00 0.00 0.00 3.93
704 1364 2.702592 TGACCAAAGGCCGGTATTAG 57.297 50.000 1.90 0.00 36.69 1.73
788 1458 1.695597 ATGGGGAAGAGGCAGAGGG 60.696 63.158 0.00 0.00 0.00 4.30
962 1633 1.873863 GAGGGTTTCGGCTTTTCGG 59.126 57.895 0.00 0.00 0.00 4.30
1043 1715 2.257286 CTTCTTGGGCGGATTGTGCG 62.257 60.000 0.00 0.00 0.00 5.34
1047 1719 0.749454 CCTCCTTCTTGGGCGGATTG 60.749 60.000 0.00 0.00 36.20 2.67
1066 1738 2.515641 TCATCGTCTTCGTCGTACAC 57.484 50.000 0.00 0.00 38.33 2.90
1067 1739 3.541071 TTTCATCGTCTTCGTCGTACA 57.459 42.857 0.00 0.00 38.33 2.90
1144 1816 1.981495 CTCCTCCTTCTTGACCTTGGT 59.019 52.381 0.00 0.00 0.00 3.67
1273 1957 0.256464 TCGTCTTCCTCCTCCTCCTC 59.744 60.000 0.00 0.00 0.00 3.71
1274 1958 0.033894 GTCGTCTTCCTCCTCCTCCT 60.034 60.000 0.00 0.00 0.00 3.69
1275 1959 1.378124 CGTCGTCTTCCTCCTCCTCC 61.378 65.000 0.00 0.00 0.00 4.30
1451 2138 2.557924 TGCAAGAACTAGGGCACATTTG 59.442 45.455 0.00 0.00 0.00 2.32
1477 2164 9.868277 TTTTTATGCTTATAATTGGGTCACTTG 57.132 29.630 0.00 0.00 0.00 3.16
1545 2232 5.289595 GTCCTATGTCATTGATCTTACGCA 58.710 41.667 0.00 0.00 0.00 5.24
1876 2563 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
1877 2564 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
1878 2565 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
1882 2569 9.265901 GACATATGACTTAGATGTGCAATACTT 57.734 33.333 10.38 0.00 41.09 2.24
1883 2570 8.424133 TGACATATGACTTAGATGTGCAATACT 58.576 33.333 10.38 0.00 41.09 2.12
1884 2571 8.593492 TGACATATGACTTAGATGTGCAATAC 57.407 34.615 10.38 0.00 41.09 1.89
1885 2572 9.783081 AATGACATATGACTTAGATGTGCAATA 57.217 29.630 10.38 0.00 41.09 1.90
1886 2573 8.565416 CAATGACATATGACTTAGATGTGCAAT 58.435 33.333 10.38 0.00 41.09 3.56
1887 2574 7.769970 TCAATGACATATGACTTAGATGTGCAA 59.230 33.333 10.38 0.00 41.09 4.08
1888 2575 7.274447 TCAATGACATATGACTTAGATGTGCA 58.726 34.615 10.38 0.00 41.09 4.57
1889 2576 7.719778 TCAATGACATATGACTTAGATGTGC 57.280 36.000 10.38 0.00 41.09 4.57
1890 2577 9.708092 AGATCAATGACATATGACTTAGATGTG 57.292 33.333 10.38 0.00 41.09 3.21
1918 2605 9.436957 AGAAAGTATTCACACGAATCTTAATGT 57.563 29.630 0.00 0.00 41.09 2.71
1922 2609 9.706691 AGAAAGAAAGTATTCACACGAATCTTA 57.293 29.630 0.00 0.00 41.09 2.10
1923 2610 8.608844 AGAAAGAAAGTATTCACACGAATCTT 57.391 30.769 0.00 0.00 41.09 2.40
1924 2611 8.091449 AGAGAAAGAAAGTATTCACACGAATCT 58.909 33.333 0.00 0.00 41.09 2.40
1925 2612 8.245701 AGAGAAAGAAAGTATTCACACGAATC 57.754 34.615 0.00 0.00 41.09 2.52
1926 2613 8.608844 AAGAGAAAGAAAGTATTCACACGAAT 57.391 30.769 0.00 0.00 44.24 3.34
1927 2614 8.433421 AAAGAGAAAGAAAGTATTCACACGAA 57.567 30.769 0.00 0.00 38.06 3.85
1928 2615 8.433421 AAAAGAGAAAGAAAGTATTCACACGA 57.567 30.769 0.00 0.00 38.06 4.35
1953 2640 9.814899 TGAGTGAATCAAGCATAAAAAGAAAAA 57.185 25.926 0.00 0.00 34.02 1.94
1954 2641 9.248291 GTGAGTGAATCAAGCATAAAAAGAAAA 57.752 29.630 0.00 0.00 40.43 2.29
1955 2642 8.632679 AGTGAGTGAATCAAGCATAAAAAGAAA 58.367 29.630 0.00 0.00 40.43 2.52
1956 2643 8.169977 AGTGAGTGAATCAAGCATAAAAAGAA 57.830 30.769 0.00 0.00 40.43 2.52
1957 2644 7.750229 AGTGAGTGAATCAAGCATAAAAAGA 57.250 32.000 0.00 0.00 40.43 2.52
1958 2645 9.552114 CTAAGTGAGTGAATCAAGCATAAAAAG 57.448 33.333 0.00 0.00 40.43 2.27
1959 2646 9.283768 TCTAAGTGAGTGAATCAAGCATAAAAA 57.716 29.630 0.00 0.00 40.43 1.94
1960 2647 8.846943 TCTAAGTGAGTGAATCAAGCATAAAA 57.153 30.769 0.00 0.00 40.43 1.52
1961 2648 8.886719 CATCTAAGTGAGTGAATCAAGCATAAA 58.113 33.333 0.00 0.00 40.43 1.40
1962 2649 8.043113 ACATCTAAGTGAGTGAATCAAGCATAA 58.957 33.333 0.00 0.00 40.43 1.90
1963 2650 7.493645 CACATCTAAGTGAGTGAATCAAGCATA 59.506 37.037 0.00 0.00 42.05 3.14
1964 2651 6.315642 CACATCTAAGTGAGTGAATCAAGCAT 59.684 38.462 0.00 0.00 42.05 3.79
1965 2652 5.640783 CACATCTAAGTGAGTGAATCAAGCA 59.359 40.000 0.00 0.00 42.05 3.91
1966 2653 5.447010 GCACATCTAAGTGAGTGAATCAAGC 60.447 44.000 0.00 0.00 42.05 4.01
1967 2654 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
1968 2655 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
1969 2656 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
1970 2657 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
1971 2658 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
1972 2659 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
1973 2660 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
1974 2661 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
1975 2662 8.067751 TCTAGTTATTGCACATCTAAGTGAGT 57.932 34.615 0.00 0.00 42.05 3.41
1976 2663 7.168972 GCTCTAGTTATTGCACATCTAAGTGAG 59.831 40.741 0.00 0.00 42.05 3.51
1977 2664 6.980978 GCTCTAGTTATTGCACATCTAAGTGA 59.019 38.462 0.00 0.00 42.05 3.41
1978 2665 6.758416 TGCTCTAGTTATTGCACATCTAAGTG 59.242 38.462 0.00 0.00 42.37 3.16
1979 2666 6.878317 TGCTCTAGTTATTGCACATCTAAGT 58.122 36.000 0.00 0.00 0.00 2.24
2004 2691 3.638627 TGTGTCTAGGGCACATCTAGATG 59.361 47.826 27.63 27.63 43.25 2.90
2005 2692 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
2006 2693 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
2007 2694 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
2008 2695 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
2009 2696 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
2010 2697 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
2011 2698 0.840288 TGGGTGTGTCTAGGGCACAT 60.840 55.000 18.92 0.00 46.66 3.21
2012 2699 1.057275 TTGGGTGTGTCTAGGGCACA 61.057 55.000 14.22 14.22 43.60 4.57
2013 2700 0.328258 ATTGGGTGTGTCTAGGGCAC 59.672 55.000 10.20 10.20 37.37 5.01
2014 2701 1.072266 AATTGGGTGTGTCTAGGGCA 58.928 50.000 0.00 0.00 0.00 5.36
2015 2702 2.215942 AAATTGGGTGTGTCTAGGGC 57.784 50.000 0.00 0.00 0.00 5.19
2016 2703 6.435904 TCAATAAAAATTGGGTGTGTCTAGGG 59.564 38.462 0.00 0.00 32.65 3.53
2017 2704 7.040062 TGTCAATAAAAATTGGGTGTGTCTAGG 60.040 37.037 0.00 0.00 32.65 3.02
2018 2705 7.881142 TGTCAATAAAAATTGGGTGTGTCTAG 58.119 34.615 0.00 0.00 32.65 2.43
2019 2706 7.825331 TGTCAATAAAAATTGGGTGTGTCTA 57.175 32.000 0.00 0.00 32.65 2.59
2020 2707 6.723298 TGTCAATAAAAATTGGGTGTGTCT 57.277 33.333 0.00 0.00 32.65 3.41
2021 2708 7.272515 CGTATGTCAATAAAAATTGGGTGTGTC 59.727 37.037 0.00 0.00 32.65 3.67
2022 2709 7.087639 CGTATGTCAATAAAAATTGGGTGTGT 58.912 34.615 0.00 0.00 32.65 3.72
2023 2710 6.529829 CCGTATGTCAATAAAAATTGGGTGTG 59.470 38.462 0.00 0.00 32.65 3.82
2024 2711 6.350612 CCCGTATGTCAATAAAAATTGGGTGT 60.351 38.462 0.00 0.00 32.65 4.16
2025 2712 6.039616 CCCGTATGTCAATAAAAATTGGGTG 58.960 40.000 0.00 0.00 32.65 4.61
2026 2713 5.128008 CCCCGTATGTCAATAAAAATTGGGT 59.872 40.000 0.00 0.00 32.65 4.51
2027 2714 5.361285 TCCCCGTATGTCAATAAAAATTGGG 59.639 40.000 0.00 0.00 32.65 4.12
2028 2715 6.458232 TCCCCGTATGTCAATAAAAATTGG 57.542 37.500 0.00 0.00 32.65 3.16
2029 2716 8.940768 AAATCCCCGTATGTCAATAAAAATTG 57.059 30.769 0.00 0.00 0.00 2.32
2030 2717 8.977412 AGAAATCCCCGTATGTCAATAAAAATT 58.023 29.630 0.00 0.00 0.00 1.82
2031 2718 8.533569 AGAAATCCCCGTATGTCAATAAAAAT 57.466 30.769 0.00 0.00 0.00 1.82
2032 2719 7.948034 AGAAATCCCCGTATGTCAATAAAAA 57.052 32.000 0.00 0.00 0.00 1.94
2033 2720 7.948034 AAGAAATCCCCGTATGTCAATAAAA 57.052 32.000 0.00 0.00 0.00 1.52
2034 2721 7.225145 CGTAAGAAATCCCCGTATGTCAATAAA 59.775 37.037 0.00 0.00 43.02 1.40
2035 2722 6.702723 CGTAAGAAATCCCCGTATGTCAATAA 59.297 38.462 0.00 0.00 43.02 1.40
2036 2723 6.218019 CGTAAGAAATCCCCGTATGTCAATA 58.782 40.000 0.00 0.00 43.02 1.90
2115 2802 2.058001 ATCCGGCGACATGTCCAGA 61.058 57.895 20.03 11.50 0.00 3.86
2174 2861 1.141019 GCTACGAATCGCTGTGGGA 59.859 57.895 1.15 0.00 0.00 4.37
2281 2968 9.941664 CAGCAATGTTATCTTTATACAAGGAAG 57.058 33.333 0.00 0.00 0.00 3.46
2386 3073 3.952323 CCTTGCATTCATCATCAGAACCT 59.048 43.478 0.00 0.00 0.00 3.50
2493 3180 1.724429 CAGCTGGACTTCTCTTCTGC 58.276 55.000 5.57 0.00 0.00 4.26
2514 3201 1.075601 TGGAGATCTTGGGTTTGCCT 58.924 50.000 0.00 0.00 34.45 4.75
2529 3216 8.796475 TCATCTTTTGGTTTCTTAATCTTGGAG 58.204 33.333 0.00 0.00 0.00 3.86
2576 3266 9.761504 ACAACACAACATAAATCATGAAAATGA 57.238 25.926 17.39 0.00 38.10 2.57
2674 3364 3.119566 CCAGCAGCCTTCTTTTCATCTTC 60.120 47.826 0.00 0.00 0.00 2.87
2852 3542 5.779241 ATGGATCCCTCTGTAACAAGAAA 57.221 39.130 9.90 0.00 0.00 2.52
3005 3698 7.910441 TGTTTAAATACCCTGTACAAGCTAC 57.090 36.000 0.00 0.00 0.00 3.58
3220 3913 0.107459 GATGGCTCAGTTCCCAGTCC 60.107 60.000 0.00 0.00 34.01 3.85
3261 3954 4.479158 AGGAGGTGTGAATTAGCCAAAAA 58.521 39.130 0.00 0.00 0.00 1.94
3262 3955 4.112634 AGGAGGTGTGAATTAGCCAAAA 57.887 40.909 0.00 0.00 0.00 2.44
3396 4089 3.727258 CCCCTTCCATCCACCGCA 61.727 66.667 0.00 0.00 0.00 5.69
3455 4150 3.050275 GAAGCGGCCTTCAGCGTT 61.050 61.111 0.00 0.00 45.44 4.84
3480 4175 4.202030 ACCACCCCACCACCTCCT 62.202 66.667 0.00 0.00 0.00 3.69
3610 4305 0.612453 CCTATCTACGCCTCCTCCCC 60.612 65.000 0.00 0.00 0.00 4.81
4151 4846 2.393271 ATCTCGTTTCCCAGCTTCTG 57.607 50.000 0.00 0.00 0.00 3.02
4234 6000 4.047142 GGTACAAGTAACGCTGGCTATAC 58.953 47.826 0.00 0.00 0.00 1.47
4337 6103 2.778659 GCAAGACGCAATGATCACTTC 58.221 47.619 0.00 0.00 41.79 3.01
4474 6240 8.345565 GCTGACCTTCAATATTTAACACCATAG 58.654 37.037 0.00 0.00 0.00 2.23
4531 6297 9.778741 CACTACTAAGCCAGGATTTTATTATCA 57.221 33.333 0.00 0.00 0.00 2.15
4658 6426 4.451096 AGAAGCATACAACCTACACAAACG 59.549 41.667 0.00 0.00 0.00 3.60
4687 6455 9.295825 TGTTTCATAACAACAATTGAGAGGTAT 57.704 29.630 13.59 6.84 41.15 2.73
4737 6505 5.454966 ACCTCATGTTTACCCAAGAAAAGT 58.545 37.500 0.00 0.00 0.00 2.66
4738 6506 5.048013 GGACCTCATGTTTACCCAAGAAAAG 60.048 44.000 0.00 0.00 0.00 2.27
4760 6528 2.762887 GGTCACATCTCTGACTCATGGA 59.237 50.000 0.00 0.00 40.50 3.41
4804 6575 8.611654 ATCTAACTAAAAACAAGCGAGGTTTA 57.388 30.769 4.31 0.00 37.47 2.01
4811 6582 7.360361 AGTGGAAATCTAACTAAAAACAAGCG 58.640 34.615 0.00 0.00 0.00 4.68
4840 6612 2.176045 TGATTCGGTCAGGAGCAACTA 58.824 47.619 0.00 0.00 31.80 2.24
4844 6616 2.107366 TGTATGATTCGGTCAGGAGCA 58.893 47.619 0.00 0.00 40.92 4.26
4965 6737 6.091441 CAGTTACTTGCTTACATCAGAGGAAC 59.909 42.308 0.00 0.00 0.00 3.62
4989 6761 4.078537 CCATCAACCTGTACATCCAAACA 58.921 43.478 0.00 0.00 0.00 2.83
5057 6829 2.230660 CCTGTTTCTGACCCTGTTTCC 58.769 52.381 0.00 0.00 0.00 3.13
5091 6863 0.536460 AAGGCGTTTTGACCGGTGAT 60.536 50.000 14.63 0.00 0.00 3.06
5224 6996 1.068472 GTCCTCGTCGTCATCAGTGTT 60.068 52.381 0.00 0.00 0.00 3.32
5229 7001 1.792301 GTCGTCCTCGTCGTCATCA 59.208 57.895 0.00 0.00 38.33 3.07
5257 7038 2.223805 CCTTTGTGGCTGAGTTGGTTTC 60.224 50.000 0.00 0.00 0.00 2.78
5441 7226 8.848182 CGTTTCCTAAGGTTATACTGATCTAGT 58.152 37.037 0.00 0.00 43.56 2.57
5465 7250 4.576879 GGAATAAGGAAAAGTCTCACCGT 58.423 43.478 0.00 0.00 0.00 4.83
5468 7253 4.142881 GCACGGAATAAGGAAAAGTCTCAC 60.143 45.833 0.00 0.00 0.00 3.51
5479 7270 0.999406 CGTCAGTGCACGGAATAAGG 59.001 55.000 21.46 5.24 36.07 2.69
5483 7274 2.029288 CAGCGTCAGTGCACGGAAT 61.029 57.895 21.46 7.93 40.29 3.01
5608 7400 5.106948 ACTGCAAGACATGTCAATAGTTTCG 60.107 40.000 27.02 8.78 37.43 3.46
5649 7441 7.675478 AGAATTCAAAGCGAAAAGAAAAACAC 58.325 30.769 8.44 0.00 37.12 3.32
5693 7485 9.846248 GTAATCTTTGTGTAGAAAATGATGCTT 57.154 29.630 0.00 0.00 0.00 3.91
5773 7565 7.783090 AGCATTATCTGTGTTCTGATGTAAG 57.217 36.000 0.00 0.00 34.79 2.34
5776 7568 6.183360 CGAAAGCATTATCTGTGTTCTGATGT 60.183 38.462 0.00 0.00 34.79 3.06
5815 9520 1.889454 GCGAATGCATTGGTTGGGA 59.111 52.632 18.59 0.00 42.15 4.37
6197 9926 1.739562 GAAGCTGCTGACGGAGGTG 60.740 63.158 1.35 0.00 39.36 4.00
6346 10085 2.664851 TTTCAGCCGGCACAGTCG 60.665 61.111 31.54 9.44 0.00 4.18
6348 10087 1.034838 TTTGTTTCAGCCGGCACAGT 61.035 50.000 31.54 4.11 0.00 3.55
6349 10088 0.102120 TTTTGTTTCAGCCGGCACAG 59.898 50.000 31.54 18.31 0.00 3.66


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

AutoCloner maintained by Alex Coulton.