Multiple sequence alignment - TraesCS7A01G506800

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 TraesCS7A01G506800 chr7A 100.000 2521 0 0 1 2521 694054914 694052394 0.000000e+00 4656.0
1 TraesCS7A01G506800 chr7A 88.729 417 36 6 2104 2519 671452493 671452899 1.350000e-137 499.0
2 TraesCS7A01G506800 chr7A 87.893 413 46 2 2104 2516 202364379 202364787 1.360000e-132 483.0
3 TraesCS7A01G506800 chr7A 96.386 249 8 1 1972 2219 694051744 694051992 2.330000e-110 409.0
4 TraesCS7A01G506800 chr7A 92.391 276 21 0 1976 2251 671452500 671452775 6.540000e-106 394.0
5 TraesCS7A01G506800 chr7A 100.000 30 0 0 709 738 694054074 694054045 3.500000e-04 56.5
6 TraesCS7A01G506800 chr7A 100.000 30 0 0 841 870 694054206 694054177 3.500000e-04 56.5
7 TraesCS7A01G506800 chr7D 93.598 1640 65 14 161 1794 602303101 602301496 0.000000e+00 2410.0
8 TraesCS7A01G506800 chr7D 89.336 422 40 5 2104 2521 581388474 581388054 2.220000e-145 525.0
9 TraesCS7A01G506800 chr7D 88.305 419 32 8 2104 2521 555198640 555199042 1.050000e-133 486.0
10 TraesCS7A01G506800 chr7D 87.351 419 45 6 2104 2521 366899714 366900125 8.160000e-130 473.0
11 TraesCS7A01G506800 chr7D 90.391 281 20 6 1972 2251 555198642 555198916 1.840000e-96 363.0
12 TraesCS7A01G506800 chr7D 100.000 30 0 0 841 870 602302558 602302529 3.500000e-04 56.5
13 TraesCS7A01G506800 chr7D 100.000 28 0 0 1772 1799 107381438 107381411 5.000000e-03 52.8
14 TraesCS7A01G506800 chrUn 88.889 1062 63 24 748 1793 87125463 87124441 0.000000e+00 1256.0
15 TraesCS7A01G506800 chrUn 90.629 747 64 6 1 746 87126868 87126127 0.000000e+00 987.0
16 TraesCS7A01G506800 chrUn 90.580 276 22 2 1972 2246 27960699 27960427 1.840000e-96 363.0
17 TraesCS7A01G506800 chrUn 94.118 102 5 1 703 804 87125441 87125341 1.210000e-33 154.0
18 TraesCS7A01G506800 chrUn 95.312 64 3 0 709 772 87125403 87125340 4.440000e-18 102.0
19 TraesCS7A01G506800 chr6D 89.336 422 39 6 2104 2521 20198698 20198279 2.220000e-145 525.0
20 TraesCS7A01G506800 chr3D 90.052 382 38 0 2140 2521 182824363 182823982 1.740000e-136 496.0
21 TraesCS7A01G506800 chr3A 87.879 396 45 3 2129 2521 360903430 360903825 1.770000e-126 462.0
22 TraesCS7A01G506800 chr3A 89.571 163 15 2 1818 1980 648732074 648731914 3.290000e-49 206.0
23 TraesCS7A01G506800 chr5D 89.037 374 38 2 2140 2513 175585784 175585414 6.350000e-126 460.0
24 TraesCS7A01G506800 chr5D 100.000 28 0 0 1773 1800 204310794 204310821 5.000000e-03 52.8
25 TraesCS7A01G506800 chr6A 92.527 281 20 1 1972 2251 143145370 143145090 3.910000e-108 401.0
26 TraesCS7A01G506800 chr6A 89.560 182 17 2 1796 1977 539371370 539371191 1.950000e-56 230.0
27 TraesCS7A01G506800 chr6A 87.425 167 19 2 1811 1977 581835131 581835295 9.200000e-45 191.0
28 TraesCS7A01G506800 chr5A 78.251 446 67 13 42 484 363420161 363419743 2.490000e-65 259.0
29 TraesCS7A01G506800 chr5A 89.474 133 11 2 1847 1977 382563190 382563059 5.580000e-37 165.0
30 TraesCS7A01G506800 chr1B 91.892 185 11 4 1795 1977 597399775 597399957 3.220000e-64 255.0
31 TraesCS7A01G506800 chr1B 89.944 179 16 2 1799 1976 314560298 314560475 1.950000e-56 230.0
32 TraesCS7A01G506800 chr2A 92.262 168 13 0 1802 1969 49171414 49171247 3.240000e-59 239.0
33 TraesCS7A01G506800 chr2A 91.061 179 13 3 1799 1977 194134966 194134791 3.240000e-59 239.0
34 TraesCS7A01G506800 chr6B 87.027 185 16 5 1797 1977 439357244 439357424 4.250000e-48 202.0
35 TraesCS7A01G506800 chr6B 85.965 57 6 2 1794 1849 703397603 703397658 2.710000e-05 60.2
36 TraesCS7A01G506800 chr2B 87.273 55 6 1 1795 1849 541908580 541908633 7.530000e-06 62.1
37 TraesCS7A01G506800 chr4A 100.000 30 0 0 1771 1800 554640911 554640882 3.500000e-04 56.5


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 TraesCS7A01G506800 chr7A 694052394 694054914 2520 True 1589.666667 4656 100.000 1 2521 3 chr7A.!!$R1 2520
1 TraesCS7A01G506800 chr7D 602301496 602303101 1605 True 1233.250000 2410 96.799 161 1794 2 chr7D.!!$R3 1633
2 TraesCS7A01G506800 chrUn 87124441 87126868 2427 True 624.750000 1256 92.237 1 1793 4 chrUn.!!$R2 1792

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
145 146 0.036388 GATCGTGCCACCTCCTTTCA 60.036 55.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 2338 0.172578 TTCGCTGTATGGACACGAGG 59.827 55.0 0.0 0.0 38.98 4.63 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
18 19 1.807165 CGTCCTCTGTGATGCCGTG 60.807 63.158 0.00 0.00 0.00 4.94
28 29 0.908910 TGATGCCGTGTACCCAGATT 59.091 50.000 0.00 0.00 0.00 2.40
32 33 1.654023 GCCGTGTACCCAGATTTGGC 61.654 60.000 0.00 0.00 43.58 4.52
57 58 4.314440 GGTGTCACGGCAGCCAGA 62.314 66.667 13.30 5.79 0.00 3.86
80 81 1.006758 TCGAGTTGGAGGTAGGGATGT 59.993 52.381 0.00 0.00 0.00 3.06
84 85 2.590611 AGTTGGAGGTAGGGATGTAGGA 59.409 50.000 0.00 0.00 0.00 2.94
92 93 3.136077 GGTAGGGATGTAGGAAGGGAAAC 59.864 52.174 0.00 0.00 0.00 2.78
138 139 1.739067 GCTAAAAGATCGTGCCACCT 58.261 50.000 0.00 0.00 0.00 4.00
145 146 0.036388 GATCGTGCCACCTCCTTTCA 60.036 55.000 0.00 0.00 0.00 2.69
153 154 2.888212 CCACCTCCTTTCATTTTCCCA 58.112 47.619 0.00 0.00 0.00 4.37
237 238 0.178900 AGAAGGGACGGGAGAAACCT 60.179 55.000 0.00 0.00 38.98 3.50
277 278 1.184970 ATGGGCGTTGGGTTTGGAAG 61.185 55.000 0.00 0.00 0.00 3.46
278 279 2.570284 GGGCGTTGGGTTTGGAAGG 61.570 63.158 0.00 0.00 0.00 3.46
313 314 6.677781 TGGGAATAGATCGAAATGTGTTTC 57.322 37.500 0.00 0.00 40.25 2.78
335 337 7.553504 TTCTTTATATGATGGATCGGGAAGA 57.446 36.000 0.00 0.00 0.00 2.87
338 340 9.267071 TCTTTATATGATGGATCGGGAAGAATA 57.733 33.333 0.00 0.00 0.00 1.75
374 376 2.225727 GGAACGGAGCGAAAACAATCTT 59.774 45.455 0.00 0.00 0.00 2.40
473 475 2.494073 GTGTGAGGTGGAACAAAAACCA 59.506 45.455 0.00 0.00 44.16 3.67
485 487 2.242708 ACAAAAACCAGTGGGAGGTGTA 59.757 45.455 15.21 0.00 39.86 2.90
506 508 0.520404 TGAACGAGCGACTGACCTAC 59.480 55.000 0.00 0.00 0.00 3.18
524 526 1.669760 CGTGCTGCCCGTTTAGGAA 60.670 57.895 0.00 0.00 45.00 3.36
641 643 5.655893 ACAATTGATTTGGCGTGAAAAAG 57.344 34.783 13.59 0.00 39.80 2.27
806 1470 7.837202 TTAATGATTGAGTACCGACGAAATT 57.163 32.000 0.00 0.00 0.00 1.82
823 1487 7.116061 ACGAAATTTGTTTGCATTAATGACC 57.884 32.000 19.73 2.94 0.00 4.02
830 1494 4.759693 TGTTTGCATTAATGACCGAGAACT 59.240 37.500 19.73 0.00 0.00 3.01
888 1552 0.321122 ACGACGTACGAACTCCCTCT 60.321 55.000 24.41 0.00 45.77 3.69
889 1553 1.066858 ACGACGTACGAACTCCCTCTA 60.067 52.381 24.41 0.00 45.77 2.43
890 1554 2.208431 CGACGTACGAACTCCCTCTAT 58.792 52.381 24.41 0.00 45.77 1.98
891 1555 2.220593 CGACGTACGAACTCCCTCTATC 59.779 54.545 24.41 3.05 45.77 2.08
976 1640 7.841758 GTCGAACAAATATTTCTCATCGAGAAC 59.158 37.037 17.46 8.75 46.54 3.01
1169 1840 3.496130 TCTGCTTCTCTCTTTCGCAAAAG 59.504 43.478 0.00 0.00 42.77 2.27
1170 1841 2.549754 TGCTTCTCTCTTTCGCAAAAGG 59.450 45.455 0.00 0.00 41.88 3.11
1173 1844 4.083057 GCTTCTCTCTTTCGCAAAAGGAAT 60.083 41.667 0.00 0.00 41.88 3.01
1174 1845 5.122396 GCTTCTCTCTTTCGCAAAAGGAATA 59.878 40.000 0.00 0.00 41.88 1.75
1178 1849 7.383687 TCTCTCTTTCGCAAAAGGAATAGTTA 58.616 34.615 0.00 0.00 41.88 2.24
1499 2176 1.279271 ACGACATCCCTTCCTCCTTTG 59.721 52.381 0.00 0.00 0.00 2.77
1534 2211 9.685276 TTTTCCATCATAGACATAATGTTCTGT 57.315 29.630 0.00 0.00 0.00 3.41
1561 2238 9.831737 ATTGCGCAATAAGAGTTGATTAATATC 57.168 29.630 33.14 0.00 0.00 1.63
1593 2270 9.725019 AAGCTGGTGATAATATATTTCGATGAA 57.275 29.630 2.68 0.00 0.00 2.57
1655 2332 7.114388 GCATGTATAATATCGTTCTCGTGTTCA 59.886 37.037 0.00 0.00 38.33 3.18
1656 2333 9.129209 CATGTATAATATCGTTCTCGTGTTCAT 57.871 33.333 0.00 0.00 38.33 2.57
1658 2335 9.603298 TGTATAATATCGTTCTCGTGTTCATAC 57.397 33.333 0.00 0.00 38.33 2.39
1659 2336 9.603298 GTATAATATCGTTCTCGTGTTCATACA 57.397 33.333 0.00 0.00 38.33 2.29
1660 2337 8.729529 ATAATATCGTTCTCGTGTTCATACAG 57.270 34.615 0.00 0.00 34.24 2.74
1661 2338 2.592194 TCGTTCTCGTGTTCATACAGC 58.408 47.619 0.00 0.00 34.24 4.40
1662 2339 1.654105 CGTTCTCGTGTTCATACAGCC 59.346 52.381 0.00 0.00 34.24 4.85
1663 2340 2.671351 CGTTCTCGTGTTCATACAGCCT 60.671 50.000 0.00 0.00 34.24 4.58
1664 2341 2.924290 GTTCTCGTGTTCATACAGCCTC 59.076 50.000 0.00 0.00 34.24 4.70
1665 2342 1.132453 TCTCGTGTTCATACAGCCTCG 59.868 52.381 0.00 0.00 34.24 4.63
1666 2343 0.885879 TCGTGTTCATACAGCCTCGT 59.114 50.000 0.00 0.00 34.24 4.18
1667 2344 0.992072 CGTGTTCATACAGCCTCGTG 59.008 55.000 0.00 0.00 34.24 4.35
1668 2345 1.668919 CGTGTTCATACAGCCTCGTGT 60.669 52.381 0.00 0.00 34.24 4.49
1669 2346 1.993370 GTGTTCATACAGCCTCGTGTC 59.007 52.381 0.00 0.00 34.24 3.67
1670 2347 1.067142 TGTTCATACAGCCTCGTGTCC 60.067 52.381 0.00 0.00 31.46 4.02
1683 2360 1.749063 TCGTGTCCATACAGCGAAGAT 59.251 47.619 0.00 0.00 36.72 2.40
1687 2364 4.051922 GTGTCCATACAGCGAAGATAAGG 58.948 47.826 0.00 0.00 35.91 2.69
1700 2377 5.109903 CGAAGATAAGGGACGATCTGTTTT 58.890 41.667 0.00 0.00 36.34 2.43
1785 2465 9.757227 CAGGCCTAAGCAATTCTATATCTATAC 57.243 37.037 3.98 0.00 42.56 1.47
1810 2490 9.490379 ACCTAATATTAAAAGGCGAGTAATCTG 57.510 33.333 3.09 0.00 33.42 2.90
1811 2491 8.443937 CCTAATATTAAAAGGCGAGTAATCTGC 58.556 37.037 0.00 0.00 0.00 4.26
1812 2492 4.795970 ATTAAAAGGCGAGTAATCTGCG 57.204 40.909 0.00 0.00 0.00 5.18
1816 2496 2.278596 GCGAGTAATCTGCGCCGA 60.279 61.111 4.18 3.73 44.55 5.54
1817 2497 2.577785 GCGAGTAATCTGCGCCGAC 61.578 63.158 4.18 0.00 44.55 4.79
1818 2498 2.286559 CGAGTAATCTGCGCCGACG 61.287 63.158 4.18 0.00 44.07 5.12
1833 2513 4.887190 ACGCACCGGCCCAAAGTT 62.887 61.111 0.00 0.00 36.38 2.66
1834 2514 3.601685 CGCACCGGCCCAAAGTTT 61.602 61.111 0.00 0.00 36.38 2.66
1835 2515 2.028925 GCACCGGCCCAAAGTTTG 59.971 61.111 8.73 8.73 0.00 2.93
1844 2524 2.642700 CAAAGTTTGGGCCGGTCG 59.357 61.111 7.78 0.00 0.00 4.79
1845 2525 3.292159 AAAGTTTGGGCCGGTCGC 61.292 61.111 1.90 4.53 0.00 5.19
1846 2526 4.572571 AAGTTTGGGCCGGTCGCA 62.573 61.111 1.90 7.47 40.31 5.10
1858 2538 4.530857 GTCGCACCCTAGCCGCAT 62.531 66.667 0.00 0.00 0.00 4.73
1859 2539 4.529219 TCGCACCCTAGCCGCATG 62.529 66.667 0.00 0.00 0.00 4.06
1860 2540 4.529219 CGCACCCTAGCCGCATGA 62.529 66.667 0.00 0.00 0.00 3.07
1861 2541 2.111878 GCACCCTAGCCGCATGAT 59.888 61.111 0.00 0.00 0.00 2.45
1862 2542 2.256591 GCACCCTAGCCGCATGATG 61.257 63.158 0.00 0.00 0.00 3.07
1863 2543 2.111878 ACCCTAGCCGCATGATGC 59.888 61.111 7.49 7.49 40.69 3.91
1864 2544 2.670934 CCCTAGCCGCATGATGCC 60.671 66.667 12.40 0.00 41.12 4.40
1865 2545 2.111669 CCTAGCCGCATGATGCCA 59.888 61.111 12.40 0.00 41.12 4.92
1866 2546 1.303074 CCTAGCCGCATGATGCCAT 60.303 57.895 12.40 0.27 41.12 4.40
1867 2547 0.892358 CCTAGCCGCATGATGCCATT 60.892 55.000 12.40 0.00 41.12 3.16
1868 2548 0.956633 CTAGCCGCATGATGCCATTT 59.043 50.000 12.40 0.00 41.12 2.32
1869 2549 2.153645 CTAGCCGCATGATGCCATTTA 58.846 47.619 12.40 0.00 41.12 1.40
1870 2550 1.624336 AGCCGCATGATGCCATTTAT 58.376 45.000 12.40 0.00 41.12 1.40
1871 2551 1.965643 AGCCGCATGATGCCATTTATT 59.034 42.857 12.40 0.00 41.12 1.40
1872 2552 2.029649 AGCCGCATGATGCCATTTATTC 60.030 45.455 12.40 0.00 41.12 1.75
1873 2553 2.029649 GCCGCATGATGCCATTTATTCT 60.030 45.455 12.40 0.00 41.12 2.40
1874 2554 3.191162 GCCGCATGATGCCATTTATTCTA 59.809 43.478 12.40 0.00 41.12 2.10
1875 2555 4.673580 GCCGCATGATGCCATTTATTCTAG 60.674 45.833 12.40 0.00 41.12 2.43
1876 2556 4.409570 CGCATGATGCCATTTATTCTAGC 58.590 43.478 12.40 0.00 41.12 3.42
1877 2557 4.673580 CGCATGATGCCATTTATTCTAGCC 60.674 45.833 12.40 0.00 41.12 3.93
1878 2558 4.673580 GCATGATGCCATTTATTCTAGCCG 60.674 45.833 6.04 0.00 37.42 5.52
1879 2559 4.085357 TGATGCCATTTATTCTAGCCGT 57.915 40.909 0.00 0.00 0.00 5.68
1880 2560 4.460263 TGATGCCATTTATTCTAGCCGTT 58.540 39.130 0.00 0.00 0.00 4.44
1881 2561 4.515191 TGATGCCATTTATTCTAGCCGTTC 59.485 41.667 0.00 0.00 0.00 3.95
1882 2562 3.879998 TGCCATTTATTCTAGCCGTTCA 58.120 40.909 0.00 0.00 0.00 3.18
1883 2563 4.265893 TGCCATTTATTCTAGCCGTTCAA 58.734 39.130 0.00 0.00 0.00 2.69
1884 2564 4.887071 TGCCATTTATTCTAGCCGTTCAAT 59.113 37.500 0.00 0.00 0.00 2.57
1885 2565 5.008613 TGCCATTTATTCTAGCCGTTCAATC 59.991 40.000 0.00 0.00 0.00 2.67
1886 2566 5.239525 GCCATTTATTCTAGCCGTTCAATCT 59.760 40.000 0.00 0.00 0.00 2.40
1887 2567 6.426937 GCCATTTATTCTAGCCGTTCAATCTA 59.573 38.462 0.00 0.00 0.00 1.98
1888 2568 7.360438 GCCATTTATTCTAGCCGTTCAATCTAG 60.360 40.741 0.00 0.00 33.04 2.43
1889 2569 7.360438 CCATTTATTCTAGCCGTTCAATCTAGC 60.360 40.741 0.00 0.00 32.10 3.42
1890 2570 2.776312 TCTAGCCGTTCAATCTAGCG 57.224 50.000 0.00 0.00 32.10 4.26
1891 2571 1.337071 TCTAGCCGTTCAATCTAGCGG 59.663 52.381 0.00 0.00 46.17 5.52
1892 2572 0.387929 TAGCCGTTCAATCTAGCGGG 59.612 55.000 6.39 0.00 43.90 6.13
1893 2573 1.143183 GCCGTTCAATCTAGCGGGA 59.857 57.895 6.39 0.00 43.90 5.14
1894 2574 0.461339 GCCGTTCAATCTAGCGGGAA 60.461 55.000 6.39 0.00 43.90 3.97
1895 2575 2.010043 GCCGTTCAATCTAGCGGGAAA 61.010 52.381 6.39 0.00 43.90 3.13
1896 2576 2.352388 CCGTTCAATCTAGCGGGAAAA 58.648 47.619 0.00 0.00 40.45 2.29
1897 2577 2.745281 CCGTTCAATCTAGCGGGAAAAA 59.255 45.455 0.00 0.00 40.45 1.94
1918 2598 6.442513 AAAAATGATTCGTCCCAGATCTTC 57.557 37.500 0.00 0.00 0.00 2.87
1919 2599 5.365021 AAATGATTCGTCCCAGATCTTCT 57.635 39.130 0.00 0.00 0.00 2.85
1920 2600 5.365021 AATGATTCGTCCCAGATCTTCTT 57.635 39.130 0.00 0.00 0.00 2.52
1921 2601 4.392921 TGATTCGTCCCAGATCTTCTTC 57.607 45.455 0.00 0.00 0.00 2.87
1922 2602 3.133003 TGATTCGTCCCAGATCTTCTTCC 59.867 47.826 0.00 0.00 0.00 3.46
1923 2603 2.534042 TCGTCCCAGATCTTCTTCCT 57.466 50.000 0.00 0.00 0.00 3.36
1924 2604 2.379972 TCGTCCCAGATCTTCTTCCTC 58.620 52.381 0.00 0.00 0.00 3.71
1925 2605 1.410882 CGTCCCAGATCTTCTTCCTCC 59.589 57.143 0.00 0.00 0.00 4.30
1926 2606 2.758130 GTCCCAGATCTTCTTCCTCCT 58.242 52.381 0.00 0.00 0.00 3.69
1927 2607 2.698274 GTCCCAGATCTTCTTCCTCCTC 59.302 54.545 0.00 0.00 0.00 3.71
1928 2608 1.686052 CCCAGATCTTCTTCCTCCTCG 59.314 57.143 0.00 0.00 0.00 4.63
1929 2609 1.068434 CCAGATCTTCTTCCTCCTCGC 59.932 57.143 0.00 0.00 0.00 5.03
1930 2610 1.028905 AGATCTTCTTCCTCCTCGCG 58.971 55.000 0.00 0.00 0.00 5.87
1931 2611 0.596341 GATCTTCTTCCTCCTCGCGC 60.596 60.000 0.00 0.00 0.00 6.86
1932 2612 1.323271 ATCTTCTTCCTCCTCGCGCA 61.323 55.000 8.75 0.00 0.00 6.09
1933 2613 1.142748 CTTCTTCCTCCTCGCGCAT 59.857 57.895 8.75 0.00 0.00 4.73
1934 2614 0.873743 CTTCTTCCTCCTCGCGCATC 60.874 60.000 8.75 0.00 0.00 3.91
1935 2615 1.323271 TTCTTCCTCCTCGCGCATCT 61.323 55.000 8.75 0.00 0.00 2.90
1936 2616 1.299773 CTTCCTCCTCGCGCATCTC 60.300 63.158 8.75 0.00 0.00 2.75
1937 2617 2.009424 CTTCCTCCTCGCGCATCTCA 62.009 60.000 8.75 0.00 0.00 3.27
1938 2618 2.279120 CCTCCTCGCGCATCTCAC 60.279 66.667 8.75 0.00 0.00 3.51
1939 2619 2.653448 CTCCTCGCGCATCTCACG 60.653 66.667 8.75 0.00 0.00 4.35
1946 2626 3.906649 CGCATCTCACGCTCGTGC 61.907 66.667 16.66 0.00 45.04 5.34
1947 2627 2.810887 GCATCTCACGCTCGTGCA 60.811 61.111 16.66 6.90 45.04 4.57
1948 2628 2.796425 GCATCTCACGCTCGTGCAG 61.796 63.158 16.66 14.13 45.04 4.41
1949 2629 1.153958 CATCTCACGCTCGTGCAGA 60.154 57.895 16.66 18.02 45.04 4.26
1950 2630 0.527169 CATCTCACGCTCGTGCAGAT 60.527 55.000 20.67 20.67 45.04 2.90
1951 2631 0.248825 ATCTCACGCTCGTGCAGATC 60.249 55.000 20.67 0.00 45.04 2.75
1952 2632 1.875813 CTCACGCTCGTGCAGATCC 60.876 63.158 16.66 0.00 45.04 3.36
1953 2633 2.887568 CACGCTCGTGCAGATCCC 60.888 66.667 9.55 0.00 39.39 3.85
1954 2634 4.148825 ACGCTCGTGCAGATCCCC 62.149 66.667 10.43 0.00 39.64 4.81
1957 2637 4.147449 CTCGTGCAGATCCCCGCA 62.147 66.667 0.00 0.00 35.30 5.69
1958 2638 3.451556 CTCGTGCAGATCCCCGCAT 62.452 63.158 5.47 0.00 40.89 4.73
1959 2639 2.969238 CGTGCAGATCCCCGCATC 60.969 66.667 5.47 0.48 40.89 3.91
1960 2640 2.507944 GTGCAGATCCCCGCATCT 59.492 61.111 5.47 0.00 40.89 2.90
1961 2641 1.596477 GTGCAGATCCCCGCATCTC 60.596 63.158 5.47 0.00 40.89 2.75
1962 2642 1.763655 TGCAGATCCCCGCATCTCT 60.764 57.895 0.00 0.00 30.07 3.10
1963 2643 1.301558 GCAGATCCCCGCATCTCTG 60.302 63.158 0.00 0.00 38.49 3.35
1964 2644 1.301558 CAGATCCCCGCATCTCTGC 60.302 63.158 0.00 0.00 45.31 4.26
1965 2645 2.031768 GATCCCCGCATCTCTGCC 59.968 66.667 0.00 0.00 46.07 4.85
1966 2646 3.873026 GATCCCCGCATCTCTGCCG 62.873 68.421 0.00 0.00 46.07 5.69
1968 2648 4.899239 CCCCGCATCTCTGCCGTC 62.899 72.222 0.00 0.00 46.07 4.79
1969 2649 4.899239 CCCGCATCTCTGCCGTCC 62.899 72.222 0.00 0.00 46.07 4.79
1970 2650 3.842923 CCGCATCTCTGCCGTCCT 61.843 66.667 0.00 0.00 46.07 3.85
1971 2651 2.279120 CGCATCTCTGCCGTCCTC 60.279 66.667 0.00 0.00 46.07 3.71
1972 2652 2.279120 GCATCTCTGCCGTCCTCG 60.279 66.667 0.00 0.00 42.88 4.63
1973 2653 2.279120 CATCTCTGCCGTCCTCGC 60.279 66.667 0.00 0.00 35.54 5.03
1974 2654 3.893763 ATCTCTGCCGTCCTCGCG 61.894 66.667 0.00 0.00 35.54 5.87
2024 2704 3.823330 GCTGCAGCTGCCATCCAC 61.823 66.667 34.64 14.22 41.18 4.02
2025 2705 3.138798 CTGCAGCTGCCATCCACC 61.139 66.667 34.64 6.50 41.18 4.61
2043 2723 3.930012 GCCCCGCCCTAGCTACAG 61.930 72.222 0.00 0.00 36.60 2.74
2044 2724 2.444140 CCCCGCCCTAGCTACAGT 60.444 66.667 0.00 0.00 36.60 3.55
2045 2725 2.797278 CCCCGCCCTAGCTACAGTG 61.797 68.421 0.00 0.00 36.60 3.66
2046 2726 2.797278 CCCGCCCTAGCTACAGTGG 61.797 68.421 9.88 9.88 36.60 4.00
2047 2727 2.107141 CGCCCTAGCTACAGTGGC 59.893 66.667 0.00 0.00 38.74 5.01
2048 2728 2.721167 CGCCCTAGCTACAGTGGCA 61.721 63.158 12.02 0.00 42.27 4.92
2049 2729 1.144936 GCCCTAGCTACAGTGGCAG 59.855 63.158 12.02 6.53 41.76 4.85
2050 2730 1.144936 CCCTAGCTACAGTGGCAGC 59.855 63.158 12.02 10.21 38.09 5.25
2051 2731 1.144936 CCTAGCTACAGTGGCAGCC 59.855 63.158 12.02 3.66 38.61 4.85
2052 2732 1.227089 CTAGCTACAGTGGCAGCCG 60.227 63.158 12.02 0.00 38.61 5.52
2053 2733 3.371097 TAGCTACAGTGGCAGCCGC 62.371 63.158 18.07 18.07 38.61 6.53
2159 2839 3.823330 GCTGCAGCTGCCATCCAC 61.823 66.667 34.64 14.22 41.18 4.02
2160 2840 3.138798 CTGCAGCTGCCATCCACC 61.139 66.667 34.64 6.50 41.18 4.61
2169 2849 4.033776 CCATCCACCGCCACCACT 62.034 66.667 0.00 0.00 0.00 4.00
2170 2850 2.747460 CATCCACCGCCACCACTG 60.747 66.667 0.00 0.00 0.00 3.66
2171 2851 4.722700 ATCCACCGCCACCACTGC 62.723 66.667 0.00 0.00 0.00 4.40
2187 2867 4.537433 GCCTCGCCCTGGCTACAG 62.537 72.222 6.60 0.00 46.38 2.74
2188 2868 3.077556 CCTCGCCCTGGCTACAGT 61.078 66.667 6.60 0.00 43.36 3.55
2189 2869 2.185350 CTCGCCCTGGCTACAGTG 59.815 66.667 6.60 0.00 43.36 3.66
2190 2870 3.376935 CTCGCCCTGGCTACAGTGG 62.377 68.421 6.60 0.00 43.36 4.00
2214 2894 4.785453 CCACTCCTGGCGGCCTTC 62.785 72.222 21.46 0.00 0.00 3.46
2300 2980 4.060038 GCCGCTGCAACTGCCATT 62.060 61.111 0.00 0.00 41.18 3.16
2301 2981 2.180017 CCGCTGCAACTGCCATTC 59.820 61.111 0.00 0.00 41.18 2.67
2302 2982 2.628696 CCGCTGCAACTGCCATTCA 61.629 57.895 0.00 0.00 41.18 2.57
2303 2983 1.443194 CGCTGCAACTGCCATTCAC 60.443 57.895 0.00 0.00 41.18 3.18
2304 2984 1.080298 GCTGCAACTGCCATTCACC 60.080 57.895 0.00 0.00 41.18 4.02
2305 2985 1.210931 CTGCAACTGCCATTCACCG 59.789 57.895 0.00 0.00 41.18 4.94
2306 2986 2.126346 GCAACTGCCATTCACCGC 60.126 61.111 0.00 0.00 34.31 5.68
2307 2987 2.568090 CAACTGCCATTCACCGCC 59.432 61.111 0.00 0.00 0.00 6.13
2308 2988 2.115052 AACTGCCATTCACCGCCA 59.885 55.556 0.00 0.00 0.00 5.69
2309 2989 2.268076 AACTGCCATTCACCGCCAC 61.268 57.895 0.00 0.00 0.00 5.01
2310 2990 3.443045 CTGCCATTCACCGCCACC 61.443 66.667 0.00 0.00 0.00 4.61
2311 2991 4.277009 TGCCATTCACCGCCACCA 62.277 61.111 0.00 0.00 0.00 4.17
2312 2992 3.747976 GCCATTCACCGCCACCAC 61.748 66.667 0.00 0.00 0.00 4.16
2313 2993 2.034066 CCATTCACCGCCACCACT 59.966 61.111 0.00 0.00 0.00 4.00
2314 2994 2.334946 CCATTCACCGCCACCACTG 61.335 63.158 0.00 0.00 0.00 3.66
2315 2995 2.672996 ATTCACCGCCACCACTGC 60.673 61.111 0.00 0.00 0.00 4.40
2316 2996 4.947147 TTCACCGCCACCACTGCC 62.947 66.667 0.00 0.00 0.00 4.85
2324 3004 4.666253 CACCACTGCCCCACCCTG 62.666 72.222 0.00 0.00 0.00 4.45
2335 3015 4.778143 CACCCTGGCTACGGTGGC 62.778 72.222 8.09 8.09 44.89 5.01
2417 3097 4.899239 CTCCAGCCCCGCATCGAC 62.899 72.222 0.00 0.00 0.00 4.20
2444 3124 2.365105 GGGAGTCCCGATCCACCA 60.365 66.667 13.89 0.00 38.70 4.17
2445 3125 1.766461 GGGAGTCCCGATCCACCAT 60.766 63.158 13.89 0.00 38.70 3.55
2446 3126 0.471211 GGGAGTCCCGATCCACCATA 60.471 60.000 13.89 0.00 38.70 2.74
2447 3127 1.645710 GGAGTCCCGATCCACCATAT 58.354 55.000 0.00 0.00 36.79 1.78
2448 3128 1.550976 GGAGTCCCGATCCACCATATC 59.449 57.143 0.00 0.00 36.79 1.63
2449 3129 2.248248 GAGTCCCGATCCACCATATCA 58.752 52.381 0.00 0.00 0.00 2.15
2450 3130 2.632996 GAGTCCCGATCCACCATATCAA 59.367 50.000 0.00 0.00 0.00 2.57
2451 3131 2.634940 AGTCCCGATCCACCATATCAAG 59.365 50.000 0.00 0.00 0.00 3.02
2452 3132 2.368875 GTCCCGATCCACCATATCAAGT 59.631 50.000 0.00 0.00 0.00 3.16
2453 3133 3.045634 TCCCGATCCACCATATCAAGTT 58.954 45.455 0.00 0.00 0.00 2.66
2454 3134 3.071023 TCCCGATCCACCATATCAAGTTC 59.929 47.826 0.00 0.00 0.00 3.01
2455 3135 3.403038 CCGATCCACCATATCAAGTTCC 58.597 50.000 0.00 0.00 0.00 3.62
2456 3136 3.403038 CGATCCACCATATCAAGTTCCC 58.597 50.000 0.00 0.00 0.00 3.97
2457 3137 3.403038 GATCCACCATATCAAGTTCCCG 58.597 50.000 0.00 0.00 0.00 5.14
2458 3138 2.193127 TCCACCATATCAAGTTCCCGT 58.807 47.619 0.00 0.00 0.00 5.28
2459 3139 2.169769 TCCACCATATCAAGTTCCCGTC 59.830 50.000 0.00 0.00 0.00 4.79
2460 3140 2.201732 CACCATATCAAGTTCCCGTCG 58.798 52.381 0.00 0.00 0.00 5.12
2461 3141 1.829222 ACCATATCAAGTTCCCGTCGT 59.171 47.619 0.00 0.00 0.00 4.34
2462 3142 2.159142 ACCATATCAAGTTCCCGTCGTC 60.159 50.000 0.00 0.00 0.00 4.20
2463 3143 2.117137 CATATCAAGTTCCCGTCGTCG 58.883 52.381 0.00 0.00 0.00 5.12
2464 3144 0.179156 TATCAAGTTCCCGTCGTCGC 60.179 55.000 0.00 0.00 35.54 5.19
2465 3145 2.830704 ATCAAGTTCCCGTCGTCGCC 62.831 60.000 0.00 0.00 35.54 5.54
2466 3146 3.608662 AAGTTCCCGTCGTCGCCA 61.609 61.111 0.00 0.00 35.54 5.69
2467 3147 2.939261 AAGTTCCCGTCGTCGCCAT 61.939 57.895 0.00 0.00 35.54 4.40
2468 3148 2.433664 GTTCCCGTCGTCGCCATT 60.434 61.111 0.00 0.00 35.54 3.16
2469 3149 1.153784 GTTCCCGTCGTCGCCATTA 60.154 57.895 0.00 0.00 35.54 1.90
2470 3150 1.153784 TTCCCGTCGTCGCCATTAC 60.154 57.895 0.00 0.00 35.54 1.89
2471 3151 2.561549 TTCCCGTCGTCGCCATTACC 62.562 60.000 0.00 0.00 35.54 2.85
2472 3152 2.952783 CCGTCGTCGCCATTACCG 60.953 66.667 0.00 0.00 35.54 4.02
2473 3153 3.613702 CGTCGTCGCCATTACCGC 61.614 66.667 0.00 0.00 0.00 5.68
2474 3154 2.202703 GTCGTCGCCATTACCGCT 60.203 61.111 0.00 0.00 0.00 5.52
2475 3155 1.808390 GTCGTCGCCATTACCGCTT 60.808 57.895 0.00 0.00 0.00 4.68
2476 3156 1.517694 TCGTCGCCATTACCGCTTC 60.518 57.895 0.00 0.00 0.00 3.86
2477 3157 2.522638 CGTCGCCATTACCGCTTCC 61.523 63.158 0.00 0.00 0.00 3.46
2478 3158 2.178235 GTCGCCATTACCGCTTCCC 61.178 63.158 0.00 0.00 0.00 3.97
2479 3159 2.900337 CGCCATTACCGCTTCCCC 60.900 66.667 0.00 0.00 0.00 4.81
2480 3160 2.274104 GCCATTACCGCTTCCCCA 59.726 61.111 0.00 0.00 0.00 4.96
2481 3161 1.823899 GCCATTACCGCTTCCCCAG 60.824 63.158 0.00 0.00 0.00 4.45
2482 3162 1.152963 CCATTACCGCTTCCCCAGG 60.153 63.158 0.00 0.00 0.00 4.45
2483 3163 1.152963 CATTACCGCTTCCCCAGGG 60.153 63.158 0.00 0.00 35.12 4.45
2484 3164 3.056754 ATTACCGCTTCCCCAGGGC 62.057 63.158 0.00 0.00 33.95 5.19
2499 3179 4.864334 GGCGTCCCCATCCAGCAG 62.864 72.222 0.00 0.00 0.00 4.24
2500 3180 3.785859 GCGTCCCCATCCAGCAGA 61.786 66.667 0.00 0.00 0.00 4.26
2501 3181 3.112205 GCGTCCCCATCCAGCAGAT 62.112 63.158 0.00 0.00 34.66 2.90
2502 3182 1.070445 CGTCCCCATCCAGCAGATC 59.930 63.158 0.00 0.00 30.59 2.75
2503 3183 1.689243 CGTCCCCATCCAGCAGATCA 61.689 60.000 0.00 0.00 30.59 2.92
2504 3184 0.548031 GTCCCCATCCAGCAGATCAA 59.452 55.000 0.00 0.00 30.59 2.57
2505 3185 0.841961 TCCCCATCCAGCAGATCAAG 59.158 55.000 0.00 0.00 30.59 3.02
2506 3186 0.549950 CCCCATCCAGCAGATCAAGT 59.450 55.000 0.00 0.00 30.59 3.16
2507 3187 1.064166 CCCCATCCAGCAGATCAAGTT 60.064 52.381 0.00 0.00 30.59 2.66
2508 3188 2.295885 CCCATCCAGCAGATCAAGTTC 58.704 52.381 0.00 0.00 30.59 3.01
2509 3189 2.295885 CCATCCAGCAGATCAAGTTCC 58.704 52.381 0.00 0.00 30.59 3.62
2510 3190 2.295885 CATCCAGCAGATCAAGTTCCC 58.704 52.381 0.00 0.00 30.59 3.97
2511 3191 0.250234 TCCAGCAGATCAAGTTCCCG 59.750 55.000 0.00 0.00 0.00 5.14
2512 3192 1.372087 CCAGCAGATCAAGTTCCCGC 61.372 60.000 0.00 0.00 0.00 6.13
2513 3193 1.078143 AGCAGATCAAGTTCCCGCC 60.078 57.895 0.00 0.00 0.00 6.13
2514 3194 2.464459 GCAGATCAAGTTCCCGCCG 61.464 63.158 0.00 0.00 0.00 6.46
2515 3195 1.079127 CAGATCAAGTTCCCGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
2516 3196 1.084370 CAGATCAAGTTCCCGCCGTC 61.084 60.000 0.00 0.00 0.00 4.79
2517 3197 2.125673 ATCAAGTTCCCGCCGTCG 60.126 61.111 0.00 0.00 0.00 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.029947 GGCCAAATCTGGGTACACGG 61.030 60.000 0.00 0.00 43.74 4.94
16 17 2.024414 GATGGCCAAATCTGGGTACAC 58.976 52.381 10.96 0.00 43.74 2.90
18 19 2.301346 CAGATGGCCAAATCTGGGTAC 58.699 52.381 23.49 1.82 46.57 3.34
48 49 1.506493 CAACTCGATATCTGGCTGCC 58.494 55.000 12.87 12.87 0.00 4.85
57 58 3.897657 TCCCTACCTCCAACTCGATAT 57.102 47.619 0.00 0.00 0.00 1.63
80 81 2.983192 TGTGTCATGGTTTCCCTTCCTA 59.017 45.455 0.00 0.00 0.00 2.94
84 85 1.963515 GCTTGTGTCATGGTTTCCCTT 59.036 47.619 0.00 0.00 0.00 3.95
92 93 1.211969 GCTGCTGCTTGTGTCATGG 59.788 57.895 8.53 0.00 36.03 3.66
120 121 2.093447 AGGAGGTGGCACGATCTTTTAG 60.093 50.000 12.17 0.00 0.00 1.85
122 123 0.693049 AGGAGGTGGCACGATCTTTT 59.307 50.000 12.17 0.64 0.00 2.27
124 125 0.693049 AAAGGAGGTGGCACGATCTT 59.307 50.000 12.17 11.26 0.00 2.40
125 126 0.250513 GAAAGGAGGTGGCACGATCT 59.749 55.000 12.17 2.73 0.00 2.75
138 139 3.216187 TCACGTGGGAAAATGAAAGGA 57.784 42.857 17.00 0.00 0.00 3.36
237 238 4.373156 TCCGATCTGGATCTACATGAGA 57.627 45.455 0.00 0.00 43.74 3.27
313 314 9.539825 CTATTCTTCCCGATCCATCATATAAAG 57.460 37.037 0.00 0.00 0.00 1.85
335 337 9.331282 CTCCGTTCCTATTTCTTTTCATCTATT 57.669 33.333 0.00 0.00 0.00 1.73
338 340 5.586643 GCTCCGTTCCTATTTCTTTTCATCT 59.413 40.000 0.00 0.00 0.00 2.90
352 354 1.804748 GATTGTTTTCGCTCCGTTCCT 59.195 47.619 0.00 0.00 0.00 3.36
374 376 5.640158 TTGACTGGGGTTTTTCTCTTCTA 57.360 39.130 0.00 0.00 0.00 2.10
473 475 2.233922 CTCGTTCATTACACCTCCCACT 59.766 50.000 0.00 0.00 0.00 4.00
485 487 0.603569 AGGTCAGTCGCTCGTTCATT 59.396 50.000 0.00 0.00 0.00 2.57
506 508 1.024579 ATTCCTAAACGGGCAGCACG 61.025 55.000 17.63 17.63 37.36 5.34
596 598 9.585099 TTGTAAAATTGAGCCATTAATGTGATC 57.415 29.630 14.25 13.23 0.00 2.92
599 601 9.976255 CAATTGTAAAATTGAGCCATTAATGTG 57.024 29.630 12.35 7.06 41.44 3.21
600 602 9.941325 TCAATTGTAAAATTGAGCCATTAATGT 57.059 25.926 15.76 0.00 42.39 2.71
806 1470 5.240623 AGTTCTCGGTCATTAATGCAAACAA 59.759 36.000 10.76 0.00 0.00 2.83
823 1487 6.233430 ACAAACAGATTTCATCAGTTCTCG 57.767 37.500 0.00 0.00 37.93 4.04
976 1640 1.106944 ACGCAGGAACCCAGTTTTGG 61.107 55.000 0.00 0.00 44.60 3.28
1178 1849 9.654663 AGTACATACTTCTTAGAAAAGCGAAAT 57.345 29.630 0.00 0.00 31.13 2.17
1499 2176 4.819088 GTCTATGATGGAAAAGGAGAAGGC 59.181 45.833 0.00 0.00 0.00 4.35
1609 2286 7.721402 ACATGCCAATTTTACTTTTAGTCACA 58.279 30.769 0.00 0.00 0.00 3.58
1655 2332 2.362397 CTGTATGGACACGAGGCTGTAT 59.638 50.000 0.00 0.00 0.00 2.29
1656 2333 1.749063 CTGTATGGACACGAGGCTGTA 59.251 52.381 0.00 0.00 0.00 2.74
1657 2334 0.532573 CTGTATGGACACGAGGCTGT 59.467 55.000 0.00 0.00 0.00 4.40
1658 2335 0.807667 GCTGTATGGACACGAGGCTG 60.808 60.000 0.00 0.00 0.00 4.85
1659 2336 1.517832 GCTGTATGGACACGAGGCT 59.482 57.895 0.00 0.00 0.00 4.58
1660 2337 1.878522 CGCTGTATGGACACGAGGC 60.879 63.158 0.00 0.00 34.23 4.70
1661 2338 0.172578 TTCGCTGTATGGACACGAGG 59.827 55.000 0.00 0.00 38.98 4.63
1662 2339 1.132453 TCTTCGCTGTATGGACACGAG 59.868 52.381 0.00 0.00 38.98 4.18
1663 2340 1.170442 TCTTCGCTGTATGGACACGA 58.830 50.000 0.00 0.00 37.34 4.35
1664 2341 2.209838 ATCTTCGCTGTATGGACACG 57.790 50.000 0.00 0.00 33.88 4.49
1665 2342 4.051922 CCTTATCTTCGCTGTATGGACAC 58.948 47.826 0.00 0.00 0.00 3.67
1666 2343 3.069586 CCCTTATCTTCGCTGTATGGACA 59.930 47.826 0.00 0.00 0.00 4.02
1667 2344 3.321111 TCCCTTATCTTCGCTGTATGGAC 59.679 47.826 0.00 0.00 0.00 4.02
1668 2345 3.321111 GTCCCTTATCTTCGCTGTATGGA 59.679 47.826 0.00 0.00 0.00 3.41
1669 2346 3.654414 GTCCCTTATCTTCGCTGTATGG 58.346 50.000 0.00 0.00 0.00 2.74
1670 2347 3.004419 TCGTCCCTTATCTTCGCTGTATG 59.996 47.826 0.00 0.00 0.00 2.39
1683 2360 7.218614 TCTTTTGTAAAACAGATCGTCCCTTA 58.781 34.615 0.00 0.00 0.00 2.69
1687 2364 8.623310 TTTTTCTTTTGTAAAACAGATCGTCC 57.377 30.769 0.00 0.00 0.00 4.79
1732 2409 3.966154 TGAGATCGTAGATTTTCCTCGC 58.034 45.455 0.00 0.00 45.12 5.03
1733 2410 5.340803 TGTTGAGATCGTAGATTTTCCTCG 58.659 41.667 0.00 0.00 45.12 4.63
1734 2411 6.237969 GCTTGTTGAGATCGTAGATTTTCCTC 60.238 42.308 0.00 0.00 45.12 3.71
1735 2412 5.582665 GCTTGTTGAGATCGTAGATTTTCCT 59.417 40.000 0.00 0.00 45.12 3.36
1743 2423 1.929836 GCCTGCTTGTTGAGATCGTAG 59.070 52.381 0.00 0.00 0.00 3.51
1785 2465 8.443937 GCAGATTACTCGCCTTTTAATATTAGG 58.556 37.037 0.00 0.00 0.00 2.69
1789 2469 5.107065 GCGCAGATTACTCGCCTTTTAATAT 60.107 40.000 0.30 0.00 42.71 1.28
1790 2470 4.210537 GCGCAGATTACTCGCCTTTTAATA 59.789 41.667 0.30 0.00 42.71 0.98
1791 2471 3.002348 GCGCAGATTACTCGCCTTTTAAT 59.998 43.478 0.30 0.00 42.71 1.40
1793 2473 1.931172 GCGCAGATTACTCGCCTTTTA 59.069 47.619 0.30 0.00 42.71 1.52
1794 2474 0.727398 GCGCAGATTACTCGCCTTTT 59.273 50.000 0.30 0.00 42.71 2.27
1795 2475 2.384203 GCGCAGATTACTCGCCTTT 58.616 52.632 0.30 0.00 42.71 3.11
1796 2476 4.110493 GCGCAGATTACTCGCCTT 57.890 55.556 0.30 0.00 42.71 4.35
1800 2480 2.286559 CGTCGGCGCAGATTACTCG 61.287 63.158 14.65 8.34 0.00 4.18
1801 2481 3.601981 CGTCGGCGCAGATTACTC 58.398 61.111 14.65 0.00 0.00 2.59
1816 2496 4.887190 AACTTTGGGCCGGTGCGT 62.887 61.111 1.90 0.00 38.85 5.24
1817 2497 3.601685 AAACTTTGGGCCGGTGCG 61.602 61.111 1.90 0.00 38.85 5.34
1818 2498 2.028925 CAAACTTTGGGCCGGTGC 59.971 61.111 1.90 0.00 0.00 5.01
1827 2507 2.642700 CGACCGGCCCAAACTTTG 59.357 61.111 0.00 0.00 0.00 2.77
1828 2508 3.292159 GCGACCGGCCCAAACTTT 61.292 61.111 0.00 0.00 34.80 2.66
1829 2509 4.572571 TGCGACCGGCCCAAACTT 62.573 61.111 0.00 0.00 42.61 2.66
1841 2521 4.530857 ATGCGGCTAGGGTGCGAC 62.531 66.667 0.00 0.00 0.00 5.19
1842 2522 4.529219 CATGCGGCTAGGGTGCGA 62.529 66.667 0.00 0.00 0.00 5.10
1843 2523 3.814615 ATCATGCGGCTAGGGTGCG 62.815 63.158 0.00 0.00 0.00 5.34
1844 2524 2.111878 ATCATGCGGCTAGGGTGC 59.888 61.111 0.00 0.00 0.00 5.01
1845 2525 2.256591 GCATCATGCGGCTAGGGTG 61.257 63.158 0.00 0.00 31.71 4.61
1846 2526 2.111878 GCATCATGCGGCTAGGGT 59.888 61.111 0.00 0.00 31.71 4.34
1847 2527 2.670934 GGCATCATGCGGCTAGGG 60.671 66.667 2.82 0.00 46.21 3.53
1848 2528 0.892358 AATGGCATCATGCGGCTAGG 60.892 55.000 2.82 0.00 46.21 3.02
1849 2529 0.956633 AAATGGCATCATGCGGCTAG 59.043 50.000 2.82 0.00 46.21 3.42
1850 2530 2.268762 TAAATGGCATCATGCGGCTA 57.731 45.000 2.82 3.93 46.21 3.93
1851 2531 1.624336 ATAAATGGCATCATGCGGCT 58.376 45.000 2.82 0.00 46.21 5.52
1852 2532 2.029649 AGAATAAATGGCATCATGCGGC 60.030 45.455 2.82 0.00 46.21 6.53
1853 2533 3.928727 AGAATAAATGGCATCATGCGG 57.071 42.857 2.82 0.00 46.21 5.69
1854 2534 4.409570 GCTAGAATAAATGGCATCATGCG 58.590 43.478 2.82 0.00 46.21 4.73
1855 2535 4.673580 CGGCTAGAATAAATGGCATCATGC 60.674 45.833 0.00 0.00 44.08 4.06
1856 2536 4.456911 ACGGCTAGAATAAATGGCATCATG 59.543 41.667 0.00 0.00 33.18 3.07
1857 2537 4.655963 ACGGCTAGAATAAATGGCATCAT 58.344 39.130 0.00 0.00 34.56 2.45
1858 2538 4.085357 ACGGCTAGAATAAATGGCATCA 57.915 40.909 0.00 0.00 0.00 3.07
1859 2539 4.515191 TGAACGGCTAGAATAAATGGCATC 59.485 41.667 0.00 0.00 0.00 3.91
1860 2540 4.460263 TGAACGGCTAGAATAAATGGCAT 58.540 39.130 0.00 0.00 0.00 4.40
1861 2541 3.879998 TGAACGGCTAGAATAAATGGCA 58.120 40.909 0.00 0.00 0.00 4.92
1862 2542 4.893424 TTGAACGGCTAGAATAAATGGC 57.107 40.909 0.00 0.00 0.00 4.40
1863 2543 6.867662 AGATTGAACGGCTAGAATAAATGG 57.132 37.500 0.00 0.00 0.00 3.16
1864 2544 7.513968 GCTAGATTGAACGGCTAGAATAAATG 58.486 38.462 0.00 0.00 34.88 2.32
1865 2545 6.366332 CGCTAGATTGAACGGCTAGAATAAAT 59.634 38.462 0.00 0.00 34.88 1.40
1866 2546 5.690409 CGCTAGATTGAACGGCTAGAATAAA 59.310 40.000 0.00 0.00 34.88 1.40
1867 2547 5.220381 CGCTAGATTGAACGGCTAGAATAA 58.780 41.667 0.00 0.00 34.88 1.40
1868 2548 4.321008 CCGCTAGATTGAACGGCTAGAATA 60.321 45.833 0.00 0.00 39.08 1.75
1869 2549 3.553096 CCGCTAGATTGAACGGCTAGAAT 60.553 47.826 0.00 0.00 39.08 2.40
1870 2550 2.223735 CCGCTAGATTGAACGGCTAGAA 60.224 50.000 0.00 0.00 39.08 2.10
1871 2551 1.337071 CCGCTAGATTGAACGGCTAGA 59.663 52.381 0.00 0.00 39.08 2.43
1872 2552 1.603172 CCCGCTAGATTGAACGGCTAG 60.603 57.143 0.00 0.00 44.29 3.42
1873 2553 0.387929 CCCGCTAGATTGAACGGCTA 59.612 55.000 0.00 0.00 44.29 3.93
1874 2554 1.144057 CCCGCTAGATTGAACGGCT 59.856 57.895 0.00 0.00 44.29 5.52
1875 2555 0.461339 TTCCCGCTAGATTGAACGGC 60.461 55.000 0.00 0.00 44.29 5.68
1876 2556 2.018542 TTTCCCGCTAGATTGAACGG 57.981 50.000 0.00 0.00 45.21 4.44
1895 2575 6.183347 AGAAGATCTGGGACGAATCATTTTT 58.817 36.000 0.00 0.00 0.00 1.94
1896 2576 5.749462 AGAAGATCTGGGACGAATCATTTT 58.251 37.500 0.00 0.00 0.00 1.82
1897 2577 5.365021 AGAAGATCTGGGACGAATCATTT 57.635 39.130 0.00 0.00 0.00 2.32
1898 2578 5.363939 GAAGAAGATCTGGGACGAATCATT 58.636 41.667 0.00 0.00 0.00 2.57
1899 2579 4.202305 GGAAGAAGATCTGGGACGAATCAT 60.202 45.833 0.00 0.00 0.00 2.45
1900 2580 3.133003 GGAAGAAGATCTGGGACGAATCA 59.867 47.826 0.00 0.00 0.00 2.57
1901 2581 3.386402 AGGAAGAAGATCTGGGACGAATC 59.614 47.826 0.00 0.00 0.00 2.52
1902 2582 3.379452 AGGAAGAAGATCTGGGACGAAT 58.621 45.455 0.00 0.00 0.00 3.34
1903 2583 2.761208 GAGGAAGAAGATCTGGGACGAA 59.239 50.000 0.00 0.00 0.00 3.85
1904 2584 2.379972 GAGGAAGAAGATCTGGGACGA 58.620 52.381 0.00 0.00 0.00 4.20
1905 2585 1.410882 GGAGGAAGAAGATCTGGGACG 59.589 57.143 0.00 0.00 0.00 4.79
1906 2586 2.698274 GAGGAGGAAGAAGATCTGGGAC 59.302 54.545 0.00 0.00 0.00 4.46
1907 2587 2.688214 CGAGGAGGAAGAAGATCTGGGA 60.688 54.545 0.00 0.00 0.00 4.37
1908 2588 1.686052 CGAGGAGGAAGAAGATCTGGG 59.314 57.143 0.00 0.00 0.00 4.45
1909 2589 1.068434 GCGAGGAGGAAGAAGATCTGG 59.932 57.143 0.00 0.00 0.00 3.86
1910 2590 1.268999 CGCGAGGAGGAAGAAGATCTG 60.269 57.143 0.00 0.00 0.00 2.90
1911 2591 1.028905 CGCGAGGAGGAAGAAGATCT 58.971 55.000 0.00 0.00 0.00 2.75
1912 2592 0.596341 GCGCGAGGAGGAAGAAGATC 60.596 60.000 12.10 0.00 0.00 2.75
1913 2593 1.323271 TGCGCGAGGAGGAAGAAGAT 61.323 55.000 12.10 0.00 0.00 2.40
1914 2594 1.323271 ATGCGCGAGGAGGAAGAAGA 61.323 55.000 12.10 0.00 32.19 2.87
1915 2595 0.873743 GATGCGCGAGGAGGAAGAAG 60.874 60.000 12.10 0.00 32.19 2.85
1916 2596 1.141881 GATGCGCGAGGAGGAAGAA 59.858 57.895 12.10 0.00 32.19 2.52
1917 2597 1.729470 GAGATGCGCGAGGAGGAAGA 61.729 60.000 12.10 0.00 32.19 2.87
1918 2598 1.299773 GAGATGCGCGAGGAGGAAG 60.300 63.158 12.10 0.00 32.19 3.46
1919 2599 2.052104 TGAGATGCGCGAGGAGGAA 61.052 57.895 12.10 0.00 32.19 3.36
1920 2600 2.440247 TGAGATGCGCGAGGAGGA 60.440 61.111 12.10 0.00 32.19 3.71
1921 2601 2.279120 GTGAGATGCGCGAGGAGG 60.279 66.667 12.10 0.00 32.19 4.30
1937 2617 4.148825 GGGGATCTGCACGAGCGT 62.149 66.667 0.00 0.00 46.23 5.07
1945 2625 1.301558 CAGAGATGCGGGGATCTGC 60.302 63.158 7.46 0.00 45.23 4.26
1946 2626 1.301558 GCAGAGATGCGGGGATCTG 60.302 63.158 7.46 0.00 41.68 2.90
1947 2627 2.515071 GGCAGAGATGCGGGGATCT 61.515 63.158 2.08 2.08 35.27 2.75
1948 2628 2.031768 GGCAGAGATGCGGGGATC 59.968 66.667 0.00 0.00 35.24 3.36
1949 2629 3.933722 CGGCAGAGATGCGGGGAT 61.934 66.667 0.31 0.00 35.24 3.85
1951 2631 4.899239 GACGGCAGAGATGCGGGG 62.899 72.222 11.67 0.00 39.09 5.73
1952 2632 4.899239 GGACGGCAGAGATGCGGG 62.899 72.222 11.67 1.40 39.09 6.13
1953 2633 3.781770 GAGGACGGCAGAGATGCGG 62.782 68.421 6.28 6.28 40.35 5.69
1954 2634 2.279120 GAGGACGGCAGAGATGCG 60.279 66.667 0.00 0.00 35.24 4.73
1955 2635 2.279120 CGAGGACGGCAGAGATGC 60.279 66.667 0.00 0.00 35.72 3.91
1956 2636 2.279120 GCGAGGACGGCAGAGATG 60.279 66.667 0.00 0.00 40.15 2.90
1957 2637 3.893763 CGCGAGGACGGCAGAGAT 61.894 66.667 0.00 0.00 40.15 2.75
2007 2687 3.823330 GTGGATGGCAGCTGCAGC 61.823 66.667 37.63 31.53 44.36 5.25
2008 2688 3.138798 GGTGGATGGCAGCTGCAG 61.139 66.667 37.63 10.11 44.36 4.41
2026 2706 3.930012 CTGTAGCTAGGGCGGGGC 61.930 72.222 0.00 0.00 44.37 5.80
2027 2707 2.444140 ACTGTAGCTAGGGCGGGG 60.444 66.667 0.00 0.00 44.37 5.73
2028 2708 2.797278 CCACTGTAGCTAGGGCGGG 61.797 68.421 0.00 0.00 44.37 6.13
2029 2709 2.815308 CCACTGTAGCTAGGGCGG 59.185 66.667 0.00 0.00 44.37 6.13
2030 2710 2.107141 GCCACTGTAGCTAGGGCG 59.893 66.667 9.19 0.00 44.37 6.13
2031 2711 1.144936 CTGCCACTGTAGCTAGGGC 59.855 63.158 15.28 15.28 44.82 5.19
2032 2712 1.144936 GCTGCCACTGTAGCTAGGG 59.855 63.158 0.00 0.00 45.63 3.53
2033 2713 4.844420 GCTGCCACTGTAGCTAGG 57.156 61.111 0.00 0.00 45.63 3.02
2142 2822 3.823330 GTGGATGGCAGCTGCAGC 61.823 66.667 37.63 31.53 44.36 5.25
2143 2823 3.138798 GGTGGATGGCAGCTGCAG 61.139 66.667 37.63 10.11 44.36 4.41
2152 2832 4.033776 AGTGGTGGCGGTGGATGG 62.034 66.667 0.00 0.00 0.00 3.51
2153 2833 2.747460 CAGTGGTGGCGGTGGATG 60.747 66.667 0.00 0.00 0.00 3.51
2154 2834 4.722700 GCAGTGGTGGCGGTGGAT 62.723 66.667 0.00 0.00 0.00 3.41
2175 2855 3.984193 CTGCCACTGTAGCCAGGGC 62.984 68.421 0.97 0.97 46.68 5.19
2176 2856 2.270205 CTGCCACTGTAGCCAGGG 59.730 66.667 0.00 0.00 43.36 4.45
2177 2857 2.437359 GCTGCCACTGTAGCCAGG 60.437 66.667 0.00 0.00 43.62 4.45
2283 2963 3.976902 GAATGGCAGTTGCAGCGGC 62.977 63.158 16.87 16.87 44.36 6.53
2284 2964 2.180017 GAATGGCAGTTGCAGCGG 59.820 61.111 6.43 0.00 44.36 5.52
2285 2965 1.443194 GTGAATGGCAGTTGCAGCG 60.443 57.895 6.43 0.00 44.36 5.18
2286 2966 1.080298 GGTGAATGGCAGTTGCAGC 60.080 57.895 6.43 0.00 44.36 5.25
2287 2967 1.210931 CGGTGAATGGCAGTTGCAG 59.789 57.895 6.43 0.00 44.36 4.41
2288 2968 2.918345 GCGGTGAATGGCAGTTGCA 61.918 57.895 6.43 0.00 44.36 4.08
2289 2969 2.126346 GCGGTGAATGGCAGTTGC 60.126 61.111 0.00 0.00 41.14 4.17
2290 2970 2.267351 TGGCGGTGAATGGCAGTTG 61.267 57.895 0.00 0.00 36.93 3.16
2291 2971 2.115052 TGGCGGTGAATGGCAGTT 59.885 55.556 0.00 0.00 36.93 3.16
2292 2972 2.672996 GTGGCGGTGAATGGCAGT 60.673 61.111 0.00 0.00 43.05 4.40
2293 2973 3.443045 GGTGGCGGTGAATGGCAG 61.443 66.667 0.00 0.00 43.05 4.85
2294 2974 4.277009 TGGTGGCGGTGAATGGCA 62.277 61.111 0.00 0.00 39.86 4.92
2295 2975 3.747976 GTGGTGGCGGTGAATGGC 61.748 66.667 0.00 0.00 0.00 4.40
2296 2976 2.034066 AGTGGTGGCGGTGAATGG 59.966 61.111 0.00 0.00 0.00 3.16
2297 2977 2.981560 GCAGTGGTGGCGGTGAATG 61.982 63.158 0.00 0.00 0.00 2.67
2298 2978 2.672996 GCAGTGGTGGCGGTGAAT 60.673 61.111 0.00 0.00 0.00 2.57
2299 2979 4.947147 GGCAGTGGTGGCGGTGAA 62.947 66.667 0.00 0.00 39.84 3.18
2307 2987 4.666253 CAGGGTGGGGCAGTGGTG 62.666 72.222 0.00 0.00 0.00 4.17
2320 3000 4.473520 CTGCCACCGTAGCCAGGG 62.474 72.222 0.00 0.00 35.72 4.45
2400 3080 4.899239 GTCGATGCGGGGCTGGAG 62.899 72.222 0.00 0.00 0.00 3.86
2427 3107 0.471211 TATGGTGGATCGGGACTCCC 60.471 60.000 3.63 3.63 41.09 4.30
2428 3108 1.550976 GATATGGTGGATCGGGACTCC 59.449 57.143 0.00 0.00 0.00 3.85
2429 3109 2.248248 TGATATGGTGGATCGGGACTC 58.752 52.381 0.00 0.00 0.00 3.36
2430 3110 2.398754 TGATATGGTGGATCGGGACT 57.601 50.000 0.00 0.00 0.00 3.85
2431 3111 2.368875 ACTTGATATGGTGGATCGGGAC 59.631 50.000 0.00 0.00 0.00 4.46
2432 3112 2.689658 ACTTGATATGGTGGATCGGGA 58.310 47.619 0.00 0.00 0.00 5.14
2433 3113 3.403038 GAACTTGATATGGTGGATCGGG 58.597 50.000 0.00 0.00 0.00 5.14
2434 3114 3.403038 GGAACTTGATATGGTGGATCGG 58.597 50.000 0.00 0.00 0.00 4.18
2435 3115 3.403038 GGGAACTTGATATGGTGGATCG 58.597 50.000 0.00 0.00 0.00 3.69
2436 3116 3.181454 ACGGGAACTTGATATGGTGGATC 60.181 47.826 0.00 0.00 0.00 3.36
2437 3117 2.777692 ACGGGAACTTGATATGGTGGAT 59.222 45.455 0.00 0.00 0.00 3.41
2438 3118 2.169769 GACGGGAACTTGATATGGTGGA 59.830 50.000 0.00 0.00 0.00 4.02
2439 3119 2.561569 GACGGGAACTTGATATGGTGG 58.438 52.381 0.00 0.00 0.00 4.61
2440 3120 2.201732 CGACGGGAACTTGATATGGTG 58.798 52.381 0.00 0.00 0.00 4.17
2441 3121 1.829222 ACGACGGGAACTTGATATGGT 59.171 47.619 0.00 0.00 0.00 3.55
2442 3122 2.470821 GACGACGGGAACTTGATATGG 58.529 52.381 0.00 0.00 0.00 2.74
2443 3123 2.117137 CGACGACGGGAACTTGATATG 58.883 52.381 0.00 0.00 35.72 1.78
2444 3124 1.535437 GCGACGACGGGAACTTGATAT 60.535 52.381 9.67 0.00 40.15 1.63
2445 3125 0.179156 GCGACGACGGGAACTTGATA 60.179 55.000 9.67 0.00 40.15 2.15
2446 3126 1.445582 GCGACGACGGGAACTTGAT 60.446 57.895 9.67 0.00 40.15 2.57
2447 3127 2.049802 GCGACGACGGGAACTTGA 60.050 61.111 9.67 0.00 40.15 3.02
2448 3128 3.110178 GGCGACGACGGGAACTTG 61.110 66.667 9.67 0.00 40.15 3.16
2449 3129 2.444700 AATGGCGACGACGGGAACTT 62.445 55.000 9.67 0.00 40.15 2.66
2450 3130 1.597797 TAATGGCGACGACGGGAACT 61.598 55.000 9.67 0.00 40.15 3.01
2451 3131 1.153784 TAATGGCGACGACGGGAAC 60.154 57.895 9.67 0.00 40.15 3.62
2452 3132 1.153784 GTAATGGCGACGACGGGAA 60.154 57.895 9.67 0.00 40.15 3.97
2453 3133 2.491152 GTAATGGCGACGACGGGA 59.509 61.111 9.67 0.00 40.15 5.14
2454 3134 2.584143 GGTAATGGCGACGACGGG 60.584 66.667 9.67 0.00 40.15 5.28
2455 3135 2.952783 CGGTAATGGCGACGACGG 60.953 66.667 9.67 0.00 40.15 4.79
2456 3136 3.613702 GCGGTAATGGCGACGACG 61.614 66.667 2.12 2.12 42.93 5.12
2457 3137 1.749609 GAAGCGGTAATGGCGACGAC 61.750 60.000 0.00 0.00 35.00 4.34
2458 3138 1.517694 GAAGCGGTAATGGCGACGA 60.518 57.895 0.00 0.00 35.00 4.20
2459 3139 2.522638 GGAAGCGGTAATGGCGACG 61.523 63.158 0.00 0.00 35.00 5.12
2460 3140 2.178235 GGGAAGCGGTAATGGCGAC 61.178 63.158 0.00 0.00 35.00 5.19
2461 3141 2.188469 GGGAAGCGGTAATGGCGA 59.812 61.111 0.00 0.00 35.00 5.54
2462 3142 2.900337 GGGGAAGCGGTAATGGCG 60.900 66.667 0.00 0.00 35.00 5.69
2463 3143 1.823899 CTGGGGAAGCGGTAATGGC 60.824 63.158 0.00 0.00 0.00 4.40
2464 3144 1.152963 CCTGGGGAAGCGGTAATGG 60.153 63.158 0.00 0.00 0.00 3.16
2465 3145 1.152963 CCCTGGGGAAGCGGTAATG 60.153 63.158 4.27 0.00 37.50 1.90
2466 3146 3.056754 GCCCTGGGGAAGCGGTAAT 62.057 63.158 16.03 0.00 37.50 1.89
2467 3147 3.723922 GCCCTGGGGAAGCGGTAA 61.724 66.667 16.03 0.00 37.50 2.85
2479 3159 4.181010 CTGGATGGGGACGCCCTG 62.181 72.222 13.58 0.00 44.66 4.45
2482 3162 4.864334 CTGCTGGATGGGGACGCC 62.864 72.222 0.53 0.53 0.00 5.68
2483 3163 3.112205 ATCTGCTGGATGGGGACGC 62.112 63.158 0.00 0.00 32.69 5.19
2484 3164 1.070445 GATCTGCTGGATGGGGACG 59.930 63.158 0.00 0.00 34.33 4.79
2485 3165 0.548031 TTGATCTGCTGGATGGGGAC 59.452 55.000 0.00 0.00 34.33 4.46
2486 3166 0.841961 CTTGATCTGCTGGATGGGGA 59.158 55.000 0.00 0.00 34.33 4.81
2487 3167 0.549950 ACTTGATCTGCTGGATGGGG 59.450 55.000 0.00 0.00 34.33 4.96
2488 3168 2.295885 GAACTTGATCTGCTGGATGGG 58.704 52.381 0.00 0.00 34.33 4.00
2489 3169 2.295885 GGAACTTGATCTGCTGGATGG 58.704 52.381 0.00 0.00 34.33 3.51
2490 3170 2.295885 GGGAACTTGATCTGCTGGATG 58.704 52.381 0.00 0.00 34.33 3.51
2491 3171 1.134280 CGGGAACTTGATCTGCTGGAT 60.134 52.381 0.00 0.00 37.37 3.41
2492 3172 0.250234 CGGGAACTTGATCTGCTGGA 59.750 55.000 0.00 0.00 0.00 3.86
2493 3173 1.372087 GCGGGAACTTGATCTGCTGG 61.372 60.000 0.00 0.00 0.00 4.85
2494 3174 1.372087 GGCGGGAACTTGATCTGCTG 61.372 60.000 0.00 0.00 0.00 4.41
2495 3175 1.078143 GGCGGGAACTTGATCTGCT 60.078 57.895 0.00 0.00 0.00 4.24
2496 3176 2.464459 CGGCGGGAACTTGATCTGC 61.464 63.158 0.00 0.00 0.00 4.26
2497 3177 1.079127 ACGGCGGGAACTTGATCTG 60.079 57.895 13.24 0.00 0.00 2.90
2498 3178 1.218316 GACGGCGGGAACTTGATCT 59.782 57.895 13.24 0.00 0.00 2.75
2499 3179 2.165301 CGACGGCGGGAACTTGATC 61.165 63.158 13.24 0.00 0.00 2.92
2500 3180 2.125673 CGACGGCGGGAACTTGAT 60.126 61.111 13.24 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.