Multiple sequence alignment - TraesCS2A01G199500

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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 TraesCS2A01G199500 chr2A 100.000 3220 0 0 1 3220 171955931 171959150 0.000000e+00 5947.0
1 TraesCS2A01G199500 chr2D 91.238 1712 82 28 1 1671 160605974 160607658 0.000000e+00 2268.0
2 TraesCS2A01G199500 chr2D 89.595 740 60 11 2385 3121 160608793 160609518 0.000000e+00 924.0
3 TraesCS2A01G199500 chr2D 81.395 946 71 42 1403 2303 160607893 160608778 0.000000e+00 675.0
4 TraesCS2A01G199500 chr2D 96.203 158 6 0 1686 1843 160607709 160607866 3.190000e-65 259.0
5 TraesCS2A01G199500 chr2B 90.421 1545 79 28 1 1504 217408874 217410390 0.000000e+00 1969.0
6 TraesCS2A01G199500 chr2B 91.734 738 42 10 2390 3121 217415231 217415955 0.000000e+00 1007.0
7 TraesCS2A01G199500 chr2B 87.700 626 35 14 1697 2303 217414598 217415200 0.000000e+00 691.0
8 TraesCS2A01G199500 chr7D 88.779 303 31 2 126 427 140758018 140757718 5.070000e-98 368.0
9 TraesCS2A01G199500 chr7D 98.000 50 1 0 2341 2390 410056876 410056925 1.590000e-13 87.9
10 TraesCS2A01G199500 chr7D 91.667 48 4 0 1023 1070 556434465 556434512 2.070000e-07 67.6
11 TraesCS2A01G199500 chrUn 87.789 303 33 4 126 427 64366649 64366350 5.110000e-93 351.0
12 TraesCS2A01G199500 chrUn 97.778 45 1 0 2343 2387 312871118 312871074 9.580000e-11 78.7
13 TraesCS2A01G199500 chrUn 97.778 45 1 0 2343 2387 312872711 312872755 9.580000e-11 78.7
14 TraesCS2A01G199500 chr1A 89.571 163 16 1 263 424 11790755 11790917 4.210000e-49 206.0
15 TraesCS2A01G199500 chr3B 91.034 145 13 0 128 272 805667268 805667412 2.530000e-46 196.0
16 TraesCS2A01G199500 chr3B 93.220 118 7 1 308 424 805667418 805667535 4.270000e-39 172.0
17 TraesCS2A01G199500 chr5D 91.837 98 8 0 129 226 483284916 483284819 1.560000e-28 137.0
18 TraesCS2A01G199500 chr5D 87.850 107 11 2 3 107 489311133 489311239 1.210000e-24 124.0
19 TraesCS2A01G199500 chr5D 93.878 49 3 0 2343 2391 22864596 22864644 1.240000e-09 75.0
20 TraesCS2A01G199500 chr5B 88.785 107 10 2 3 107 603456223 603456329 2.610000e-26 130.0
21 TraesCS2A01G199500 chr5B 95.745 47 2 0 2342 2388 472674584 472674538 3.440000e-10 76.8
22 TraesCS2A01G199500 chr5A 86.916 107 12 2 3 107 610463095 610463201 5.640000e-23 119.0
23 TraesCS2A01G199500 chr5A 97.826 46 1 0 2342 2387 574342970 574343015 2.660000e-11 80.5
24 TraesCS2A01G199500 chr6B 96.000 50 2 0 2341 2390 91854106 91854057 7.400000e-12 82.4
25 TraesCS2A01G199500 chr4A 95.833 48 2 0 2342 2389 488112953 488113000 9.580000e-11 78.7
26 TraesCS2A01G199500 chr4B 93.750 48 3 0 2342 2389 473859610 473859657 4.460000e-09 73.1
27 TraesCS2A01G199500 chr1B 93.750 48 3 0 57 104 410814022 410814069 4.460000e-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 TraesCS2A01G199500 chr2A 171955931 171959150 3219 False 5947.0 5947 100.00000 1 3220 1 chr2A.!!$F1 3219
1 TraesCS2A01G199500 chr2D 160605974 160609518 3544 False 1031.5 2268 89.60775 1 3121 4 chr2D.!!$F1 3120
2 TraesCS2A01G199500 chr2B 217408874 217410390 1516 False 1969.0 1969 90.42100 1 1504 1 chr2B.!!$F1 1503
3 TraesCS2A01G199500 chr2B 217414598 217415955 1357 False 849.0 1007 89.71700 1697 3121 2 chr2B.!!$F2 1424

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
298 313 0.248907 CCACCCATACGCTGACTACG 60.249 60.0 0.00 0.0 0.00 3.51 F
896 934 0.541863 CGACTCAACCTATGGGCCTT 59.458 55.0 4.53 0.0 35.63 4.35 F
1856 1975 0.037975 GAAGTAGTCCCGCCGTTTCA 60.038 55.0 0.00 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1689 0.096454 GTTCCTGCGCATTCCGTAAC 59.904 55.0 12.24 5.76 39.71 2.50 R
1868 1987 0.322816 ATGGCATGGACTGTGACCAC 60.323 55.0 0.00 0.00 40.36 4.16 R
2997 3632 0.034059 CCGACAAGCTATAGCAGGGG 59.966 60.0 26.07 17.69 45.16 4.79 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
63 65 4.790765 AATTTCTGGCAACTTAAGAGGC 57.209 40.909 10.09 13.54 37.61 4.70
85 87 1.573108 TCTCAGAGGGTGAATGGACC 58.427 55.000 0.00 0.00 33.60 4.46
112 114 8.548877 ACCACCAACTCAGATATTATAACAGTT 58.451 33.333 0.00 0.00 0.00 3.16
113 115 9.396022 CCACCAACTCAGATATTATAACAGTTT 57.604 33.333 0.00 0.00 0.00 2.66
181 196 5.064452 GTGAACAAGAACTGGAGCATCTATG 59.936 44.000 0.00 0.00 33.73 2.23
189 204 8.148437 AGAACTGGAGCATCTATGATGATATT 57.852 34.615 11.25 0.00 33.73 1.28
225 240 1.754745 GACTCTGCACTGGAACCCA 59.245 57.895 0.00 0.00 0.00 4.51
259 274 1.069596 GTTTGGGGCTTGGCTTGTG 59.930 57.895 0.00 0.00 0.00 3.33
298 313 0.248907 CCACCCATACGCTGACTACG 60.249 60.000 0.00 0.00 0.00 3.51
400 415 2.357517 CGCGCAAACTCCTCCAGT 60.358 61.111 8.75 0.00 36.64 4.00
407 422 1.134965 CAAACTCCTCCAGTAGGCTCG 60.135 57.143 0.00 0.00 46.10 5.03
440 456 6.203723 CAGAAAATCCAAGAGAGAAAACGAGT 59.796 38.462 0.00 0.00 0.00 4.18
441 457 7.385205 CAGAAAATCCAAGAGAGAAAACGAGTA 59.615 37.037 0.00 0.00 0.00 2.59
536 552 1.209640 GAAGTCTCGGCGTCGTCTT 59.790 57.895 10.18 12.77 37.69 3.01
643 671 1.906824 GCCTACCGATCCCGATCCA 60.907 63.158 0.00 0.00 38.22 3.41
657 685 2.666596 GATCCAGGTGTCCCCATCGC 62.667 65.000 0.00 0.00 34.66 4.58
815 843 2.029221 GATCTTACGGGCCCTCGC 59.971 66.667 22.43 0.00 0.00 5.03
841 876 2.034376 ATTTGGGTTGGCCGCGTA 59.966 55.556 4.92 0.00 34.97 4.42
896 934 0.541863 CGACTCAACCTATGGGCCTT 59.458 55.000 4.53 0.00 35.63 4.35
1008 1046 1.807886 GGCAAAGAGGATGCAGCTG 59.192 57.895 10.11 10.11 45.60 4.24
1013 1051 3.270839 GAGGATGCAGCTGCGCTC 61.271 66.667 32.11 28.22 45.83 5.03
1138 1182 3.068691 CGTCGGAGAAGGAGGGCA 61.069 66.667 0.00 0.00 39.69 5.36
1265 1310 2.107366 CCCGGGTAATCATTGCCTTTT 58.893 47.619 14.18 0.00 35.54 2.27
1271 1316 3.769300 GGTAATCATTGCCTTTTCCCACT 59.231 43.478 0.00 0.00 32.08 4.00
1373 1418 6.421501 GTCGTCTAGAGTTCGAGATCTTCATA 59.578 42.308 4.34 0.00 34.33 2.15
1396 1441 5.772521 AGCGGCCAATAATAATTGATTCAC 58.227 37.500 2.24 0.00 44.50 3.18
1423 1469 2.717809 GCCGTTCGCGTGTTCTCTC 61.718 63.158 5.77 0.00 39.32 3.20
1437 1483 6.961554 GCGTGTTCTCTCGAATGAAAATTTAT 59.038 34.615 0.00 0.00 33.21 1.40
1438 1484 7.481798 GCGTGTTCTCTCGAATGAAAATTTATT 59.518 33.333 0.00 0.00 33.21 1.40
1439 1485 9.967245 CGTGTTCTCTCGAATGAAAATTTATTA 57.033 29.630 0.00 0.00 33.21 0.98
1469 1515 2.358582 GCCTAACCTACGGAGAAGAGAC 59.641 54.545 0.00 0.00 0.00 3.36
1484 1530 6.232581 AGAAGAGACGGATCAATCTTCAAT 57.767 37.500 20.89 7.36 46.51 2.57
1485 1531 7.353414 AGAAGAGACGGATCAATCTTCAATA 57.647 36.000 20.89 0.00 46.51 1.90
1486 1532 7.786030 AGAAGAGACGGATCAATCTTCAATAA 58.214 34.615 20.89 0.00 46.51 1.40
1487 1533 7.708752 AGAAGAGACGGATCAATCTTCAATAAC 59.291 37.037 20.89 2.47 46.51 1.89
1488 1534 6.284459 AGAGACGGATCAATCTTCAATAACC 58.716 40.000 0.00 0.00 0.00 2.85
1514 1560 2.414481 CTGAAACAACTGCTCGATGGAG 59.586 50.000 0.00 0.00 43.46 3.86
1536 1587 2.416547 CAGGTCATTTGTTAGCCTCGTG 59.583 50.000 0.00 0.00 0.00 4.35
1537 1588 1.737793 GGTCATTTGTTAGCCTCGTGG 59.262 52.381 0.00 0.00 0.00 4.94
1538 1589 2.423577 GTCATTTGTTAGCCTCGTGGT 58.576 47.619 5.26 0.00 35.27 4.16
1539 1590 2.159627 GTCATTTGTTAGCCTCGTGGTG 59.840 50.000 5.26 0.00 35.27 4.17
1540 1591 1.135689 CATTTGTTAGCCTCGTGGTGC 60.136 52.381 5.26 0.00 35.27 5.01
1560 1625 6.831868 TGGTGCATACTTCAGTATACAGTAGA 59.168 38.462 5.50 0.00 39.06 2.59
1582 1647 6.862209 AGAGCTAGTCATTTCTCAAGTACTG 58.138 40.000 0.00 0.00 0.00 2.74
1583 1648 6.435904 AGAGCTAGTCATTTCTCAAGTACTGT 59.564 38.462 0.00 0.00 0.00 3.55
1595 1668 7.783090 TCTCAAGTACTGTACCTACGAATAG 57.217 40.000 14.05 2.37 0.00 1.73
1596 1669 7.334090 TCTCAAGTACTGTACCTACGAATAGT 58.666 38.462 14.05 0.00 0.00 2.12
1614 1687 9.846248 ACGAATAGTAGACGTATTACTGTTTTT 57.154 29.630 17.85 8.84 38.47 1.94
1621 1694 7.109006 AGACGTATTACTGTTTTTGGTTACG 57.891 36.000 0.00 0.00 37.70 3.18
1628 1701 2.977169 CTGTTTTTGGTTACGGAATGCG 59.023 45.455 0.00 0.00 0.00 4.73
1632 1705 1.302383 TTGGTTACGGAATGCGCAGG 61.302 55.000 18.32 7.65 0.00 4.85
1635 1708 0.096454 GTTACGGAATGCGCAGGAAC 59.904 55.000 18.32 11.67 0.00 3.62
1656 1729 6.986231 GGAACTGTTCATTTCCTCATTTGTTT 59.014 34.615 21.01 0.00 38.65 2.83
1671 1744 7.117241 TCATTTGTTTCTTTCGTAGCAGTAG 57.883 36.000 0.00 0.00 0.00 2.57
1674 1747 6.998258 TTGTTTCTTTCGTAGCAGTAGTAC 57.002 37.500 0.00 0.00 0.00 2.73
1675 1748 6.075762 TGTTTCTTTCGTAGCAGTAGTACA 57.924 37.500 2.52 0.00 0.00 2.90
1676 1749 6.147581 TGTTTCTTTCGTAGCAGTAGTACAG 58.852 40.000 2.52 0.00 0.00 2.74
1677 1750 5.954296 TTCTTTCGTAGCAGTAGTACAGT 57.046 39.130 2.52 0.00 0.00 3.55
1678 1751 5.292671 TCTTTCGTAGCAGTAGTACAGTG 57.707 43.478 2.52 0.00 0.00 3.66
1679 1752 4.155462 TCTTTCGTAGCAGTAGTACAGTGG 59.845 45.833 2.52 0.00 0.00 4.00
1680 1753 1.741706 TCGTAGCAGTAGTACAGTGGC 59.258 52.381 2.52 0.94 0.00 5.01
1681 1754 1.471287 CGTAGCAGTAGTACAGTGGCA 59.529 52.381 2.52 0.00 0.00 4.92
1682 1755 2.731341 CGTAGCAGTAGTACAGTGGCAC 60.731 54.545 10.29 10.29 0.00 5.01
1683 1756 1.633774 AGCAGTAGTACAGTGGCACT 58.366 50.000 15.88 15.88 0.00 4.40
1684 1757 1.971357 AGCAGTAGTACAGTGGCACTT 59.029 47.619 19.43 12.08 0.00 3.16
1745 1858 2.858344 CCGAGTGATCCGTACAATTCAC 59.142 50.000 9.78 9.78 38.97 3.18
1810 1923 5.275630 TCCTACTTTTTCTAGGGGAGTACC 58.724 45.833 0.00 0.00 32.79 3.34
1821 1934 2.380410 GGAGTACCGTGTGCTTGCG 61.380 63.158 0.00 0.00 0.00 4.85
1843 1962 3.801698 AGCATAGCATGTGTGGAAGTAG 58.198 45.455 0.00 0.00 0.00 2.57
1844 1963 3.198635 AGCATAGCATGTGTGGAAGTAGT 59.801 43.478 0.00 0.00 0.00 2.73
1845 1964 3.557595 GCATAGCATGTGTGGAAGTAGTC 59.442 47.826 0.00 0.00 0.00 2.59
1853 1972 2.976356 GGAAGTAGTCCCGCCGTT 59.024 61.111 0.00 0.00 41.10 4.44
1854 1973 1.294459 GGAAGTAGTCCCGCCGTTT 59.706 57.895 0.00 0.00 41.10 3.60
1855 1974 0.738762 GGAAGTAGTCCCGCCGTTTC 60.739 60.000 0.00 0.00 41.10 2.78
1856 1975 0.037975 GAAGTAGTCCCGCCGTTTCA 60.038 55.000 0.00 0.00 0.00 2.69
1857 1976 0.393820 AAGTAGTCCCGCCGTTTCAA 59.606 50.000 0.00 0.00 0.00 2.69
1858 1977 0.393820 AGTAGTCCCGCCGTTTCAAA 59.606 50.000 0.00 0.00 0.00 2.69
1859 1978 1.002773 AGTAGTCCCGCCGTTTCAAAT 59.997 47.619 0.00 0.00 0.00 2.32
1861 1980 2.188062 AGTCCCGCCGTTTCAAATTA 57.812 45.000 0.00 0.00 0.00 1.40
1868 1987 2.754478 GCCGTTTCAAATTACTCGTCG 58.246 47.619 0.00 0.00 0.00 5.12
1870 1989 3.717830 CCGTTTCAAATTACTCGTCGTG 58.282 45.455 0.00 0.00 0.00 4.35
1874 1993 3.646611 TCAAATTACTCGTCGTGGTCA 57.353 42.857 0.00 0.00 0.00 4.02
1875 1994 3.311106 TCAAATTACTCGTCGTGGTCAC 58.689 45.455 0.00 0.00 0.00 3.67
1912 2519 1.817357 TGCCTGCTTGATCACTTCTG 58.183 50.000 0.00 0.00 0.00 3.02
1913 2520 1.348696 TGCCTGCTTGATCACTTCTGA 59.651 47.619 0.00 0.00 0.00 3.27
1914 2521 1.736681 GCCTGCTTGATCACTTCTGAC 59.263 52.381 0.00 0.00 0.00 3.51
1915 2522 2.614987 GCCTGCTTGATCACTTCTGACT 60.615 50.000 0.00 0.00 0.00 3.41
1916 2523 3.672808 CCTGCTTGATCACTTCTGACTT 58.327 45.455 0.00 0.00 0.00 3.01
1917 2524 3.683822 CCTGCTTGATCACTTCTGACTTC 59.316 47.826 0.00 0.00 0.00 3.01
1918 2525 4.563168 CCTGCTTGATCACTTCTGACTTCT 60.563 45.833 0.00 0.00 0.00 2.85
1956 2563 8.818860 TCTGTATGGGTACTTGTGTATTTACTT 58.181 33.333 0.00 0.00 0.00 2.24
1957 2564 9.095065 CTGTATGGGTACTTGTGTATTTACTTC 57.905 37.037 0.00 0.00 0.00 3.01
1958 2565 8.818860 TGTATGGGTACTTGTGTATTTACTTCT 58.181 33.333 0.00 0.00 0.00 2.85
1959 2566 9.095065 GTATGGGTACTTGTGTATTTACTTCTG 57.905 37.037 0.00 0.00 0.00 3.02
1961 2568 7.511268 TGGGTACTTGTGTATTTACTTCTGTT 58.489 34.615 0.00 0.00 0.00 3.16
1962 2569 7.994334 TGGGTACTTGTGTATTTACTTCTGTTT 59.006 33.333 0.00 0.00 0.00 2.83
1963 2570 8.843262 GGGTACTTGTGTATTTACTTCTGTTTT 58.157 33.333 0.00 0.00 0.00 2.43
1964 2571 9.659830 GGTACTTGTGTATTTACTTCTGTTTTG 57.340 33.333 0.00 0.00 0.00 2.44
2209 2822 0.107703 CAGCCCGGCAATTCTAGTGA 60.108 55.000 13.15 0.00 0.00 3.41
2222 2835 5.849357 ATTCTAGTGATAGCTCGTAGACG 57.151 43.478 0.00 0.00 41.45 4.18
2231 2844 5.585047 TGATAGCTCGTAGACGTATATGCAT 59.415 40.000 3.79 3.79 40.80 3.96
2254 2867 8.004344 GCATGACACGATAATACAGTTTGATAC 58.996 37.037 0.00 0.00 0.00 2.24
2256 2869 8.628882 TGACACGATAATACAGTTTGATACAG 57.371 34.615 0.00 0.00 0.00 2.74
2257 2870 8.248253 TGACACGATAATACAGTTTGATACAGT 58.752 33.333 0.00 0.00 0.00 3.55
2258 2871 8.407457 ACACGATAATACAGTTTGATACAGTG 57.593 34.615 0.00 0.00 0.00 3.66
2259 2872 7.491372 ACACGATAATACAGTTTGATACAGTGG 59.509 37.037 0.00 0.00 0.00 4.00
2260 2873 6.479001 ACGATAATACAGTTTGATACAGTGGC 59.521 38.462 0.00 0.00 0.00 5.01
2286 2904 2.791004 GCTGTGCTTTGCAAGTTAACTG 59.209 45.455 9.34 4.88 41.47 3.16
2290 2908 3.487207 GTGCTTTGCAAGTTAACTGAAGC 59.513 43.478 24.57 24.57 41.47 3.86
2301 2919 0.111061 AACTGAAGCCATGTGCCTCA 59.889 50.000 7.11 7.11 42.71 3.86
2302 2920 0.330604 ACTGAAGCCATGTGCCTCAT 59.669 50.000 7.61 0.00 39.63 2.90
2303 2921 1.022735 CTGAAGCCATGTGCCTCATC 58.977 55.000 7.61 1.91 39.63 2.92
2304 2922 0.394762 TGAAGCCATGTGCCTCATCC 60.395 55.000 4.06 0.00 42.71 3.51
2305 2923 1.076485 AAGCCATGTGCCTCATCCC 60.076 57.895 2.95 0.00 42.71 3.85
2306 2924 1.578215 AAGCCATGTGCCTCATCCCT 61.578 55.000 2.95 0.00 42.71 4.20
2307 2925 1.527844 GCCATGTGCCTCATCCCTC 60.528 63.158 0.00 0.00 34.09 4.30
2316 2934 1.808945 GCCTCATCCCTCATATTTGCG 59.191 52.381 0.00 0.00 0.00 4.85
2317 2935 2.430465 CCTCATCCCTCATATTTGCGG 58.570 52.381 0.00 0.00 0.00 5.69
2321 2939 2.363306 TCCCTCATATTTGCGGCATT 57.637 45.000 2.28 0.00 0.00 3.56
2324 2942 3.758023 TCCCTCATATTTGCGGCATTATG 59.242 43.478 19.53 19.53 0.00 1.90
2325 2943 3.507233 CCCTCATATTTGCGGCATTATGT 59.493 43.478 22.35 9.81 0.00 2.29
2326 2944 4.699735 CCCTCATATTTGCGGCATTATGTA 59.300 41.667 22.35 13.81 0.00 2.29
2327 2945 5.391950 CCCTCATATTTGCGGCATTATGTAC 60.392 44.000 22.35 0.00 0.00 2.90
2328 2946 5.412594 CCTCATATTTGCGGCATTATGTACT 59.587 40.000 22.35 0.89 0.00 2.73
2329 2947 6.402550 CCTCATATTTGCGGCATTATGTACTC 60.403 42.308 22.35 0.00 0.00 2.59
2330 2948 5.411361 TCATATTTGCGGCATTATGTACTCC 59.589 40.000 22.35 0.00 0.00 3.85
2331 2949 1.961793 TTGCGGCATTATGTACTCCC 58.038 50.000 2.28 0.00 0.00 4.30
2332 2950 1.128200 TGCGGCATTATGTACTCCCT 58.872 50.000 0.00 0.00 0.00 4.20
2333 2951 1.070134 TGCGGCATTATGTACTCCCTC 59.930 52.381 0.00 0.00 0.00 4.30
2334 2952 1.608283 GCGGCATTATGTACTCCCTCC 60.608 57.143 0.00 0.00 0.00 4.30
2335 2953 1.336887 CGGCATTATGTACTCCCTCCG 60.337 57.143 0.00 0.00 0.00 4.63
2336 2954 1.692519 GGCATTATGTACTCCCTCCGT 59.307 52.381 0.00 0.00 0.00 4.69
2337 2955 2.288886 GGCATTATGTACTCCCTCCGTC 60.289 54.545 0.00 0.00 0.00 4.79
2338 2956 2.288886 GCATTATGTACTCCCTCCGTCC 60.289 54.545 0.00 0.00 0.00 4.79
2339 2957 2.077687 TTATGTACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
2340 2958 1.229131 TATGTACTCCCTCCGTCCCT 58.771 55.000 0.00 0.00 0.00 4.20
2341 2959 0.106116 ATGTACTCCCTCCGTCCCTC 60.106 60.000 0.00 0.00 0.00 4.30
2342 2960 1.823041 GTACTCCCTCCGTCCCTCG 60.823 68.421 0.00 0.00 39.52 4.63
2343 2961 2.304056 TACTCCCTCCGTCCCTCGT 61.304 63.158 0.00 0.00 37.94 4.18
2344 2962 0.982852 TACTCCCTCCGTCCCTCGTA 60.983 60.000 0.00 0.00 37.94 3.43
2345 2963 1.150992 CTCCCTCCGTCCCTCGTAT 59.849 63.158 0.00 0.00 37.94 3.06
2346 2964 0.467659 CTCCCTCCGTCCCTCGTATT 60.468 60.000 0.00 0.00 37.94 1.89
2347 2965 0.032813 TCCCTCCGTCCCTCGTATTT 60.033 55.000 0.00 0.00 37.94 1.40
2348 2966 1.215173 TCCCTCCGTCCCTCGTATTTA 59.785 52.381 0.00 0.00 37.94 1.40
2349 2967 1.612463 CCCTCCGTCCCTCGTATTTAG 59.388 57.143 0.00 0.00 37.94 1.85
2350 2968 2.579873 CCTCCGTCCCTCGTATTTAGA 58.420 52.381 0.00 0.00 37.94 2.10
2351 2969 2.292845 CCTCCGTCCCTCGTATTTAGAC 59.707 54.545 0.00 0.00 37.94 2.59
2352 2970 2.947652 CTCCGTCCCTCGTATTTAGACA 59.052 50.000 0.00 0.00 37.94 3.41
2353 2971 3.355378 TCCGTCCCTCGTATTTAGACAA 58.645 45.455 0.00 0.00 37.94 3.18
2354 2972 3.763360 TCCGTCCCTCGTATTTAGACAAA 59.237 43.478 0.00 0.00 37.94 2.83
2355 2973 4.403432 TCCGTCCCTCGTATTTAGACAAAT 59.597 41.667 0.00 0.00 36.21 2.32
2356 2974 5.105228 TCCGTCCCTCGTATTTAGACAAATT 60.105 40.000 0.00 0.00 35.00 1.82
2357 2975 5.583457 CCGTCCCTCGTATTTAGACAAATTT 59.417 40.000 0.00 0.00 35.00 1.82
2358 2976 6.757947 CCGTCCCTCGTATTTAGACAAATTTA 59.242 38.462 0.00 0.00 35.00 1.40
2359 2977 7.278424 CCGTCCCTCGTATTTAGACAAATTTAA 59.722 37.037 0.00 0.00 35.00 1.52
2360 2978 8.325997 CGTCCCTCGTATTTAGACAAATTTAAG 58.674 37.037 0.00 0.00 35.88 1.85
2361 2979 9.374838 GTCCCTCGTATTTAGACAAATTTAAGA 57.625 33.333 0.00 0.00 35.88 2.10
2362 2980 9.374838 TCCCTCGTATTTAGACAAATTTAAGAC 57.625 33.333 0.00 0.00 35.88 3.01
2363 2981 9.158233 CCCTCGTATTTAGACAAATTTAAGACA 57.842 33.333 0.00 0.00 35.88 3.41
2382 3000 9.738832 TTAAGACAAAAATTTTAAGACGAAGGG 57.261 29.630 3.34 0.00 0.00 3.95
2383 3001 7.576861 AGACAAAAATTTTAAGACGAAGGGA 57.423 32.000 3.34 0.00 0.00 4.20
2410 3039 3.788227 AAGACCCACATGCTCTAAACA 57.212 42.857 0.00 0.00 0.00 2.83
2415 3044 2.163010 CCCACATGCTCTAAACAAGCTG 59.837 50.000 0.00 0.00 40.50 4.24
2418 3047 2.227388 ACATGCTCTAAACAAGCTGTGC 59.773 45.455 0.00 0.00 40.50 4.57
2420 3049 1.875514 TGCTCTAAACAAGCTGTGCTG 59.124 47.619 0.00 0.00 39.62 4.41
2432 3061 3.730761 GTGCTGTTGCTGGCCTCG 61.731 66.667 3.32 0.00 40.48 4.63
2446 3075 4.821935 CTCGGCCTTGAGGGTTTT 57.178 55.556 0.00 0.00 37.43 2.43
2448 3077 0.250727 CTCGGCCTTGAGGGTTTTCA 60.251 55.000 0.00 0.00 37.43 2.69
2498 3128 0.107017 CCATGGGGCTTCACCTGTAG 60.107 60.000 2.85 0.00 39.10 2.74
2504 3134 2.420129 GGGGCTTCACCTGTAGTATGTG 60.420 54.545 0.00 0.00 39.10 3.21
2632 3263 6.202570 CCCAACTTGTGAACCAATTAATTGTG 59.797 38.462 23.24 17.42 36.06 3.33
2647 3278 1.725641 TTGTGTCAGCGGTGATCATC 58.274 50.000 21.66 8.30 34.36 2.92
2654 3285 2.580470 GCGGTGATCATCGACGCTG 61.580 63.158 31.70 7.87 46.02 5.18
2777 3408 0.812811 CGACATGGATGAGCTGTGGG 60.813 60.000 0.00 0.00 0.00 4.61
2873 3504 3.348119 TCTGCGATCTTCTACTGTGTCT 58.652 45.455 0.00 0.00 0.00 3.41
2995 3630 4.724074 TGTTTCGTCCGGATTATACACT 57.276 40.909 7.81 0.00 0.00 3.55
2997 3632 2.787601 TCGTCCGGATTATACACTGC 57.212 50.000 7.81 0.00 0.00 4.40
2999 3634 1.604693 CGTCCGGATTATACACTGCCC 60.605 57.143 7.81 0.00 0.00 5.36
3005 3640 2.637872 GGATTATACACTGCCCCTGCTA 59.362 50.000 0.00 0.00 38.71 3.49
3008 3643 5.395768 GGATTATACACTGCCCCTGCTATAG 60.396 48.000 0.00 0.00 38.71 1.31
3010 3645 0.692419 ACACTGCCCCTGCTATAGCT 60.692 55.000 24.61 0.00 42.66 3.32
3088 3723 4.697514 CTTTCCCTATGCAAGATTCTCGA 58.302 43.478 0.00 0.00 0.00 4.04
3121 3756 6.260271 CCTATCGTAGACACAGTACATCTTGA 59.740 42.308 0.00 0.00 42.51 3.02
3122 3757 6.701145 ATCGTAGACACAGTACATCTTGAT 57.299 37.500 0.00 0.00 42.51 2.57
3123 3758 6.120378 TCGTAGACACAGTACATCTTGATC 57.880 41.667 0.00 0.00 0.00 2.92
3124 3759 5.880887 TCGTAGACACAGTACATCTTGATCT 59.119 40.000 0.00 0.00 0.00 2.75
3125 3760 5.968261 CGTAGACACAGTACATCTTGATCTG 59.032 44.000 0.00 0.00 0.00 2.90
3126 3761 5.991933 AGACACAGTACATCTTGATCTGT 57.008 39.130 0.00 0.00 36.20 3.41
3127 3762 5.960113 AGACACAGTACATCTTGATCTGTC 58.040 41.667 0.00 0.00 34.74 3.51
3128 3763 5.714333 AGACACAGTACATCTTGATCTGTCT 59.286 40.000 0.00 0.00 34.74 3.41
3129 3764 5.960113 ACACAGTACATCTTGATCTGTCTC 58.040 41.667 0.00 0.00 34.74 3.36
3130 3765 5.105554 ACACAGTACATCTTGATCTGTCTCC 60.106 44.000 0.00 0.00 34.74 3.71
3131 3766 5.126869 CACAGTACATCTTGATCTGTCTCCT 59.873 44.000 0.00 0.00 34.74 3.69
3132 3767 6.319911 CACAGTACATCTTGATCTGTCTCCTA 59.680 42.308 0.00 0.00 34.74 2.94
3133 3768 7.014134 CACAGTACATCTTGATCTGTCTCCTAT 59.986 40.741 0.00 0.00 34.74 2.57
3134 3769 7.563188 ACAGTACATCTTGATCTGTCTCCTATT 59.437 37.037 0.00 0.00 32.98 1.73
3135 3770 8.420222 CAGTACATCTTGATCTGTCTCCTATTT 58.580 37.037 0.00 0.00 0.00 1.40
3136 3771 8.637986 AGTACATCTTGATCTGTCTCCTATTTC 58.362 37.037 0.00 0.00 0.00 2.17
3137 3772 6.825610 ACATCTTGATCTGTCTCCTATTTCC 58.174 40.000 0.00 0.00 0.00 3.13
3138 3773 6.614906 ACATCTTGATCTGTCTCCTATTTCCT 59.385 38.462 0.00 0.00 0.00 3.36
3139 3774 6.723298 TCTTGATCTGTCTCCTATTTCCTC 57.277 41.667 0.00 0.00 0.00 3.71
3140 3775 6.197903 TCTTGATCTGTCTCCTATTTCCTCA 58.802 40.000 0.00 0.00 0.00 3.86
3141 3776 5.860941 TGATCTGTCTCCTATTTCCTCAC 57.139 43.478 0.00 0.00 0.00 3.51
3142 3777 5.272402 TGATCTGTCTCCTATTTCCTCACA 58.728 41.667 0.00 0.00 0.00 3.58
3143 3778 5.362143 TGATCTGTCTCCTATTTCCTCACAG 59.638 44.000 0.00 0.00 0.00 3.66
3144 3779 3.449018 TCTGTCTCCTATTTCCTCACAGC 59.551 47.826 0.00 0.00 31.69 4.40
3145 3780 3.445008 TGTCTCCTATTTCCTCACAGCT 58.555 45.455 0.00 0.00 0.00 4.24
3146 3781 3.449018 TGTCTCCTATTTCCTCACAGCTC 59.551 47.826 0.00 0.00 0.00 4.09
3147 3782 2.690497 TCTCCTATTTCCTCACAGCTCG 59.310 50.000 0.00 0.00 0.00 5.03
3148 3783 2.690497 CTCCTATTTCCTCACAGCTCGA 59.310 50.000 0.00 0.00 0.00 4.04
3149 3784 2.690497 TCCTATTTCCTCACAGCTCGAG 59.310 50.000 8.45 8.45 0.00 4.04
3150 3785 2.468831 CTATTTCCTCACAGCTCGAGC 58.531 52.381 30.01 30.01 42.49 5.03
3151 3786 0.107945 ATTTCCTCACAGCTCGAGCC 60.108 55.000 32.94 15.76 43.38 4.70
3152 3787 1.471829 TTTCCTCACAGCTCGAGCCA 61.472 55.000 32.94 14.15 43.38 4.75
3153 3788 1.260538 TTCCTCACAGCTCGAGCCAT 61.261 55.000 32.94 19.20 43.38 4.40
3154 3789 1.220206 CCTCACAGCTCGAGCCATT 59.780 57.895 32.94 15.29 43.38 3.16
3155 3790 0.809241 CCTCACAGCTCGAGCCATTC 60.809 60.000 32.94 6.32 43.38 2.67
3156 3791 0.809241 CTCACAGCTCGAGCCATTCC 60.809 60.000 32.94 5.52 43.38 3.01
3157 3792 1.220206 CACAGCTCGAGCCATTCCT 59.780 57.895 32.94 11.52 43.38 3.36
3158 3793 0.461548 CACAGCTCGAGCCATTCCTA 59.538 55.000 32.94 0.00 43.38 2.94
3159 3794 1.134699 CACAGCTCGAGCCATTCCTAA 60.135 52.381 32.94 0.00 43.38 2.69
3160 3795 1.765314 ACAGCTCGAGCCATTCCTAAT 59.235 47.619 32.94 9.10 43.38 1.73
3161 3796 2.171448 ACAGCTCGAGCCATTCCTAATT 59.829 45.455 32.94 8.29 43.38 1.40
3162 3797 3.209410 CAGCTCGAGCCATTCCTAATTT 58.791 45.455 32.94 7.72 43.38 1.82
3163 3798 3.629398 CAGCTCGAGCCATTCCTAATTTT 59.371 43.478 32.94 7.50 43.38 1.82
3164 3799 4.096984 CAGCTCGAGCCATTCCTAATTTTT 59.903 41.667 32.94 7.02 43.38 1.94
3165 3800 4.336713 AGCTCGAGCCATTCCTAATTTTTC 59.663 41.667 32.94 0.00 43.38 2.29
3166 3801 4.336713 GCTCGAGCCATTCCTAATTTTTCT 59.663 41.667 27.22 0.00 34.31 2.52
3167 3802 5.504830 GCTCGAGCCATTCCTAATTTTTCTC 60.505 44.000 27.22 0.00 34.31 2.87
3168 3803 5.496556 TCGAGCCATTCCTAATTTTTCTCA 58.503 37.500 0.00 0.00 0.00 3.27
3169 3804 6.122277 TCGAGCCATTCCTAATTTTTCTCAT 58.878 36.000 0.00 0.00 0.00 2.90
3170 3805 6.603201 TCGAGCCATTCCTAATTTTTCTCATT 59.397 34.615 0.00 0.00 0.00 2.57
3171 3806 7.122650 TCGAGCCATTCCTAATTTTTCTCATTT 59.877 33.333 0.00 0.00 0.00 2.32
3172 3807 7.761249 CGAGCCATTCCTAATTTTTCTCATTTT 59.239 33.333 0.00 0.00 0.00 1.82
3208 3843 8.934023 TCTTTGGTTTCATTAGAAATACCAGT 57.066 30.769 0.00 0.00 42.54 4.00
3211 3846 9.802039 TTTGGTTTCATTAGAAATACCAGTAGT 57.198 29.630 0.00 0.00 42.54 2.73
3212 3847 9.802039 TTGGTTTCATTAGAAATACCAGTAGTT 57.198 29.630 0.00 0.00 42.54 2.24
3213 3848 9.802039 TGGTTTCATTAGAAATACCAGTAGTTT 57.198 29.630 0.00 0.00 44.87 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 3.539604 GTCCATTCACCCTCTGAGATTG 58.460 50.000 6.17 2.79 0.00 2.67
85 87 7.987458 ACTGTTATAATATCTGAGTTGGTGGTG 59.013 37.037 0.00 0.00 0.00 4.17
112 114 9.542462 GATACCACAAACTGCAGTATATCTTAA 57.458 33.333 22.01 3.22 0.00 1.85
113 115 8.148351 GGATACCACAAACTGCAGTATATCTTA 58.852 37.037 22.01 8.56 0.00 2.10
115 117 6.099701 TGGATACCACAAACTGCAGTATATCT 59.900 38.462 22.01 0.00 0.00 1.98
116 118 6.288294 TGGATACCACAAACTGCAGTATATC 58.712 40.000 22.01 17.73 0.00 1.63
117 119 6.247229 TGGATACCACAAACTGCAGTATAT 57.753 37.500 22.01 10.94 0.00 0.86
118 120 5.685520 TGGATACCACAAACTGCAGTATA 57.314 39.130 22.01 6.56 0.00 1.47
172 187 8.371571 TGGACTACAATATCATCATAGATGCT 57.628 34.615 2.19 0.00 0.00 3.79
225 240 1.039856 AAACTGGCCATCGCTGTTTT 58.960 45.000 5.51 0.00 37.91 2.43
259 274 3.135895 TGGATAAACCCTAGTTGGCTAGC 59.864 47.826 6.04 6.04 42.51 3.42
289 304 1.956620 GCTTTGTCGCCGTAGTCAGC 61.957 60.000 0.00 0.00 0.00 4.26
298 313 1.154035 CGGGAATTGCTTTGTCGCC 60.154 57.895 0.00 0.00 0.00 5.54
305 320 2.690778 GCGCTGTCGGGAATTGCTT 61.691 57.895 0.00 0.00 35.95 3.91
407 422 5.316987 TCTCTTGGATTTTCTGGAAAGGTC 58.683 41.667 0.00 0.55 0.00 3.85
440 456 2.096980 CCTGCGATGTTACGAGTGAGTA 59.903 50.000 0.00 0.00 35.09 2.59
441 457 1.135373 CCTGCGATGTTACGAGTGAGT 60.135 52.381 0.00 0.00 35.09 3.41
454 470 0.692419 AGGATCCAACTCCCTGCGAT 60.692 55.000 15.82 0.00 35.79 4.58
619 635 3.992317 GGATCGGTAGGCGAGCCC 61.992 72.222 10.95 0.00 36.08 5.19
629 645 2.134287 CACCTGGATCGGGATCGGT 61.134 63.158 0.00 3.08 38.69 4.69
684 712 3.148031 GATACCCACCGTCTCCGCC 62.148 68.421 0.00 0.00 0.00 6.13
815 843 2.755103 GGCCAACCCAAATCTTCTACTG 59.245 50.000 0.00 0.00 0.00 2.74
987 1025 3.104602 CTGCATCCTCTTTGCCGCG 62.105 63.158 0.00 0.00 39.39 6.46
1074 1112 0.108567 GCTTCCTTCTCTCCGTCACC 60.109 60.000 0.00 0.00 0.00 4.02
1091 1129 0.374758 CGCGTTGCAACATATCTGCT 59.625 50.000 28.01 0.00 40.59 4.24
1265 1310 1.677966 CGAGGAGAACGGAGTGGGA 60.678 63.158 0.00 0.00 45.00 4.37
1271 1316 2.154798 CTTGGCACGAGGAGAACGGA 62.155 60.000 0.00 0.00 34.93 4.69
1339 1384 4.789119 CGAACTCTAGACGACTGATTGAAC 59.211 45.833 0.00 0.00 0.00 3.18
1373 1418 5.562696 CGTGAATCAATTATTATTGGCCGCT 60.563 40.000 0.00 0.00 41.23 5.52
1396 1441 2.389143 GCGAACGGCGAACTTACG 59.611 61.111 16.62 10.48 44.57 3.18
1423 1469 7.254084 GCAGCCCAACTAATAAATTTTCATTCG 60.254 37.037 0.00 0.00 0.00 3.34
1437 1483 1.368374 AGGTTAGGCAGCCCAACTAA 58.632 50.000 20.55 4.83 0.00 2.24
1438 1484 1.835531 GTAGGTTAGGCAGCCCAACTA 59.164 52.381 20.55 11.72 0.00 2.24
1439 1485 0.618981 GTAGGTTAGGCAGCCCAACT 59.381 55.000 20.55 12.72 0.00 3.16
1469 1515 7.383572 CAGAGTAGGTTATTGAAGATTGATCCG 59.616 40.741 0.00 0.00 0.00 4.18
1484 1530 5.539048 GAGCAGTTGTTTCAGAGTAGGTTA 58.461 41.667 0.00 0.00 0.00 2.85
1485 1531 4.381411 GAGCAGTTGTTTCAGAGTAGGTT 58.619 43.478 0.00 0.00 0.00 3.50
1486 1532 3.553096 CGAGCAGTTGTTTCAGAGTAGGT 60.553 47.826 0.00 0.00 0.00 3.08
1487 1533 2.989840 CGAGCAGTTGTTTCAGAGTAGG 59.010 50.000 0.00 0.00 0.00 3.18
1488 1534 3.902150 TCGAGCAGTTGTTTCAGAGTAG 58.098 45.455 0.00 0.00 0.00 2.57
1514 1560 1.398390 CGAGGCTAACAAATGACCTGC 59.602 52.381 0.00 0.00 0.00 4.85
1536 1587 7.273320 TCTACTGTATACTGAAGTATGCACC 57.727 40.000 15.84 2.29 44.65 5.01
1537 1588 6.858993 GCTCTACTGTATACTGAAGTATGCAC 59.141 42.308 15.84 6.75 44.65 4.57
1538 1589 6.773200 AGCTCTACTGTATACTGAAGTATGCA 59.227 38.462 16.97 16.97 46.35 3.96
1539 1590 7.209471 AGCTCTACTGTATACTGAAGTATGC 57.791 40.000 15.84 11.40 41.03 3.14
1540 1591 9.496873 ACTAGCTCTACTGTATACTGAAGTATG 57.503 37.037 15.84 7.04 41.03 2.39
1560 1625 6.597832 ACAGTACTTGAGAAATGACTAGCT 57.402 37.500 0.00 0.00 0.00 3.32
1582 1647 9.413048 AGTAATACGTCTACTATTCGTAGGTAC 57.587 37.037 8.16 0.00 44.66 3.34
1583 1648 9.411801 CAGTAATACGTCTACTATTCGTAGGTA 57.588 37.037 9.29 0.00 44.66 3.08
1595 1668 8.155923 CGTAACCAAAAACAGTAATACGTCTAC 58.844 37.037 0.00 0.00 32.56 2.59
1596 1669 7.328249 CCGTAACCAAAAACAGTAATACGTCTA 59.672 37.037 0.00 0.00 34.65 2.59
1599 1672 5.988561 TCCGTAACCAAAAACAGTAATACGT 59.011 36.000 0.00 0.00 34.65 3.57
1600 1673 6.464895 TCCGTAACCAAAAACAGTAATACG 57.535 37.500 0.00 0.00 35.82 3.06
1601 1674 7.271868 GCATTCCGTAACCAAAAACAGTAATAC 59.728 37.037 0.00 0.00 0.00 1.89
1603 1676 6.153756 GCATTCCGTAACCAAAAACAGTAAT 58.846 36.000 0.00 0.00 0.00 1.89
1604 1677 5.521544 GCATTCCGTAACCAAAAACAGTAA 58.478 37.500 0.00 0.00 0.00 2.24
1605 1678 4.319622 CGCATTCCGTAACCAAAAACAGTA 60.320 41.667 0.00 0.00 0.00 2.74
1606 1679 3.549221 CGCATTCCGTAACCAAAAACAGT 60.549 43.478 0.00 0.00 0.00 3.55
1607 1680 2.977169 CGCATTCCGTAACCAAAAACAG 59.023 45.455 0.00 0.00 0.00 3.16
1608 1681 2.859032 GCGCATTCCGTAACCAAAAACA 60.859 45.455 0.30 0.00 39.71 2.83
1609 1682 1.717113 GCGCATTCCGTAACCAAAAAC 59.283 47.619 0.30 0.00 39.71 2.43
1610 1683 1.337071 TGCGCATTCCGTAACCAAAAA 59.663 42.857 5.66 0.00 39.71 1.94
1611 1684 0.952280 TGCGCATTCCGTAACCAAAA 59.048 45.000 5.66 0.00 39.71 2.44
1612 1685 0.519519 CTGCGCATTCCGTAACCAAA 59.480 50.000 12.24 0.00 39.71 3.28
1613 1686 1.302383 CCTGCGCATTCCGTAACCAA 61.302 55.000 12.24 0.00 39.71 3.67
1614 1687 1.743623 CCTGCGCATTCCGTAACCA 60.744 57.895 12.24 0.00 39.71 3.67
1615 1688 1.022451 TTCCTGCGCATTCCGTAACC 61.022 55.000 12.24 0.00 39.71 2.85
1616 1689 0.096454 GTTCCTGCGCATTCCGTAAC 59.904 55.000 12.24 5.76 39.71 2.50
1621 1694 0.169009 GAACAGTTCCTGCGCATTCC 59.831 55.000 12.24 0.00 34.37 3.01
1632 1705 7.922811 AGAAACAAATGAGGAAATGAACAGTTC 59.077 33.333 6.32 6.32 34.94 3.01
1635 1708 8.652810 AAAGAAACAAATGAGGAAATGAACAG 57.347 30.769 0.00 0.00 0.00 3.16
1656 1729 4.155462 CCACTGTACTACTGCTACGAAAGA 59.845 45.833 0.00 0.00 0.00 2.52
1671 1744 4.151867 GCTGTAAAGTAAGTGCCACTGTAC 59.848 45.833 0.00 3.78 37.28 2.90
1674 1747 2.157668 CGCTGTAAAGTAAGTGCCACTG 59.842 50.000 0.00 0.00 0.00 3.66
1675 1748 2.224209 ACGCTGTAAAGTAAGTGCCACT 60.224 45.455 0.00 0.00 0.00 4.00
1676 1749 2.140717 ACGCTGTAAAGTAAGTGCCAC 58.859 47.619 0.00 0.00 0.00 5.01
1677 1750 2.536761 ACGCTGTAAAGTAAGTGCCA 57.463 45.000 0.00 0.00 0.00 4.92
1678 1751 3.841643 TCTACGCTGTAAAGTAAGTGCC 58.158 45.455 0.00 0.00 0.00 5.01
1679 1752 3.303760 GCTCTACGCTGTAAAGTAAGTGC 59.696 47.826 0.00 0.00 35.14 4.40
1680 1753 3.542704 CGCTCTACGCTGTAAAGTAAGTG 59.457 47.826 0.00 0.00 36.13 3.16
1681 1754 3.438087 TCGCTCTACGCTGTAAAGTAAGT 59.562 43.478 0.00 0.00 43.23 2.24
1682 1755 4.012319 TCGCTCTACGCTGTAAAGTAAG 57.988 45.455 0.00 0.00 43.23 2.34
1683 1756 4.348656 CATCGCTCTACGCTGTAAAGTAA 58.651 43.478 0.00 0.00 43.23 2.24
1684 1757 3.791122 GCATCGCTCTACGCTGTAAAGTA 60.791 47.826 0.00 0.00 40.01 2.24
1702 1811 5.423886 GGGCTTGGTATATCTAGAAGCATC 58.576 45.833 11.39 1.49 40.68 3.91
1745 1858 1.741770 GTCGTGGCCTAGCAACTGG 60.742 63.158 3.32 0.00 28.79 4.00
1821 1934 2.636830 ACTTCCACACATGCTATGCTC 58.363 47.619 0.00 0.00 0.00 4.26
1843 1962 1.808343 AGTAATTTGAAACGGCGGGAC 59.192 47.619 13.24 1.88 0.00 4.46
1844 1963 2.078392 GAGTAATTTGAAACGGCGGGA 58.922 47.619 13.24 0.00 0.00 5.14
1845 1964 1.201987 CGAGTAATTTGAAACGGCGGG 60.202 52.381 13.24 0.00 0.00 6.13
1846 1965 1.461897 ACGAGTAATTTGAAACGGCGG 59.538 47.619 13.24 0.00 0.00 6.13
1847 1966 2.754478 GACGAGTAATTTGAAACGGCG 58.246 47.619 4.80 4.80 0.00 6.46
1848 1967 2.156310 ACGACGAGTAATTTGAAACGGC 59.844 45.455 0.00 0.00 0.00 5.68
1849 1968 3.422603 CCACGACGAGTAATTTGAAACGG 60.423 47.826 0.00 0.00 0.00 4.44
1850 1969 3.182972 ACCACGACGAGTAATTTGAAACG 59.817 43.478 0.00 0.00 0.00 3.60
1851 1970 4.209703 TGACCACGACGAGTAATTTGAAAC 59.790 41.667 0.00 0.00 0.00 2.78
1852 1971 4.209703 GTGACCACGACGAGTAATTTGAAA 59.790 41.667 0.00 0.00 0.00 2.69
1853 1972 3.737266 GTGACCACGACGAGTAATTTGAA 59.263 43.478 0.00 0.00 0.00 2.69
1854 1973 3.243468 TGTGACCACGACGAGTAATTTGA 60.243 43.478 0.00 0.00 0.00 2.69
1855 1974 3.054166 TGTGACCACGACGAGTAATTTG 58.946 45.455 0.00 0.00 0.00 2.32
1856 1975 3.243636 ACTGTGACCACGACGAGTAATTT 60.244 43.478 0.00 0.00 0.00 1.82
1857 1976 2.295349 ACTGTGACCACGACGAGTAATT 59.705 45.455 0.00 0.00 0.00 1.40
1858 1977 1.884579 ACTGTGACCACGACGAGTAAT 59.115 47.619 0.00 0.00 0.00 1.89
1859 1978 1.265095 GACTGTGACCACGACGAGTAA 59.735 52.381 0.00 0.00 0.00 2.24
1861 1980 1.653115 GACTGTGACCACGACGAGT 59.347 57.895 0.00 0.00 0.00 4.18
1868 1987 0.322816 ATGGCATGGACTGTGACCAC 60.323 55.000 0.00 0.00 40.36 4.16
1870 1989 0.813184 CAATGGCATGGACTGTGACC 59.187 55.000 0.00 0.00 0.00 4.02
1874 1993 1.274167 CAAAGCAATGGCATGGACTGT 59.726 47.619 5.91 0.00 44.61 3.55
1875 1994 2.004583 CAAAGCAATGGCATGGACTG 57.995 50.000 5.91 0.00 44.61 3.51
1912 2519 5.385509 ACAGAGAAGTTAGCAGAGAAGTC 57.614 43.478 0.00 0.00 0.00 3.01
1913 2520 6.127479 CCATACAGAGAAGTTAGCAGAGAAGT 60.127 42.308 0.00 0.00 0.00 3.01
1914 2521 6.272318 CCATACAGAGAAGTTAGCAGAGAAG 58.728 44.000 0.00 0.00 0.00 2.85
1915 2522 5.127845 CCCATACAGAGAAGTTAGCAGAGAA 59.872 44.000 0.00 0.00 0.00 2.87
1916 2523 4.646945 CCCATACAGAGAAGTTAGCAGAGA 59.353 45.833 0.00 0.00 0.00 3.10
1917 2524 4.404073 ACCCATACAGAGAAGTTAGCAGAG 59.596 45.833 0.00 0.00 0.00 3.35
1918 2525 4.353777 ACCCATACAGAGAAGTTAGCAGA 58.646 43.478 0.00 0.00 0.00 4.26
1957 2564 6.135290 TGAAAGGATCTGTGAACAAAACAG 57.865 37.500 0.00 0.00 45.26 3.16
1958 2565 6.461370 CCATGAAAGGATCTGTGAACAAAACA 60.461 38.462 0.00 0.00 0.00 2.83
1959 2566 5.922544 CCATGAAAGGATCTGTGAACAAAAC 59.077 40.000 0.00 0.00 0.00 2.43
1961 2568 5.241506 GTCCATGAAAGGATCTGTGAACAAA 59.758 40.000 0.00 0.00 40.42 2.83
1962 2569 4.761739 GTCCATGAAAGGATCTGTGAACAA 59.238 41.667 0.00 0.00 40.42 2.83
1963 2570 4.326826 GTCCATGAAAGGATCTGTGAACA 58.673 43.478 0.00 0.00 40.42 3.18
1964 2571 3.691609 GGTCCATGAAAGGATCTGTGAAC 59.308 47.826 0.00 0.00 40.42 3.18
2209 2822 5.585047 TCATGCATATACGTCTACGAGCTAT 59.415 40.000 9.86 0.00 43.02 2.97
2222 2835 8.689251 ACTGTATTATCGTGTCATGCATATAC 57.311 34.615 0.00 1.18 0.00 1.47
2231 2844 8.248253 ACTGTATCAAACTGTATTATCGTGTCA 58.752 33.333 0.00 0.00 38.38 3.58
2254 2867 3.677648 GCACAGCCCTTGCCACTG 61.678 66.667 0.00 0.00 38.69 3.66
2256 2869 2.501602 AAAGCACAGCCCTTGCCAC 61.502 57.895 0.00 0.00 41.18 5.01
2257 2870 2.123338 AAAGCACAGCCCTTGCCA 60.123 55.556 0.00 0.00 41.18 4.92
2258 2871 2.341176 CAAAGCACAGCCCTTGCC 59.659 61.111 0.00 0.00 41.18 4.52
2259 2872 2.356673 GCAAAGCACAGCCCTTGC 60.357 61.111 9.64 9.64 39.45 4.01
2260 2873 0.599204 CTTGCAAAGCACAGCCCTTG 60.599 55.000 0.00 0.00 38.71 3.61
2290 2908 0.477204 ATGAGGGATGAGGCACATGG 59.523 55.000 1.04 0.00 39.56 3.66
2303 2921 3.507233 ACATAATGCCGCAAATATGAGGG 59.493 43.478 25.02 8.70 45.75 4.30
2305 2923 6.402550 GGAGTACATAATGCCGCAAATATGAG 60.403 42.308 25.02 9.45 31.71 2.90
2306 2924 5.411361 GGAGTACATAATGCCGCAAATATGA 59.589 40.000 25.02 12.91 31.71 2.15
2307 2925 5.391950 GGGAGTACATAATGCCGCAAATATG 60.392 44.000 20.04 20.04 33.12 1.78
2316 2934 1.692519 ACGGAGGGAGTACATAATGCC 59.307 52.381 0.00 0.00 31.56 4.40
2317 2935 2.288886 GGACGGAGGGAGTACATAATGC 60.289 54.545 0.00 0.00 0.00 3.56
2321 2939 1.144503 GAGGGACGGAGGGAGTACATA 59.855 57.143 0.00 0.00 0.00 2.29
2324 2942 1.823041 CGAGGGACGGAGGGAGTAC 60.823 68.421 0.00 0.00 38.46 2.73
2325 2943 2.593978 CGAGGGACGGAGGGAGTA 59.406 66.667 0.00 0.00 38.46 2.59
2330 2948 9.719437 AATTTGTCTAAATACGAGGGACGGAGG 62.719 44.444 0.00 0.00 39.74 4.30
2331 2949 6.903542 AATTTGTCTAAATACGAGGGACGGAG 60.904 42.308 0.00 0.00 39.74 4.63
2332 2950 5.105228 AATTTGTCTAAATACGAGGGACGGA 60.105 40.000 0.00 0.00 39.74 4.69
2333 2951 5.114081 AATTTGTCTAAATACGAGGGACGG 58.886 41.667 0.00 0.00 39.74 4.79
2334 2952 6.657836 AAATTTGTCTAAATACGAGGGACG 57.342 37.500 0.00 0.00 40.54 4.79
2335 2953 9.374838 TCTTAAATTTGTCTAAATACGAGGGAC 57.625 33.333 0.00 0.00 35.50 4.46
2336 2954 9.374838 GTCTTAAATTTGTCTAAATACGAGGGA 57.625 33.333 0.00 0.00 35.50 4.20
2337 2955 9.158233 TGTCTTAAATTTGTCTAAATACGAGGG 57.842 33.333 0.00 0.00 35.50 4.30
2356 2974 9.738832 CCCTTCGTCTTAAAATTTTTGTCTTAA 57.261 29.630 9.06 0.00 0.00 1.85
2357 2975 9.122779 TCCCTTCGTCTTAAAATTTTTGTCTTA 57.877 29.630 9.06 0.00 0.00 2.10
2358 2976 8.002984 TCCCTTCGTCTTAAAATTTTTGTCTT 57.997 30.769 9.06 0.00 0.00 3.01
2359 2977 7.284716 ACTCCCTTCGTCTTAAAATTTTTGTCT 59.715 33.333 9.06 0.00 0.00 3.41
2360 2978 7.423199 ACTCCCTTCGTCTTAAAATTTTTGTC 58.577 34.615 9.06 0.62 0.00 3.18
2361 2979 7.342769 ACTCCCTTCGTCTTAAAATTTTTGT 57.657 32.000 9.06 0.00 0.00 2.83
2362 2980 9.908152 AATACTCCCTTCGTCTTAAAATTTTTG 57.092 29.630 9.06 3.23 0.00 2.44
2368 2986 9.428097 GTCTTAAATACTCCCTTCGTCTTAAAA 57.572 33.333 0.00 0.00 0.00 1.52
2369 2987 8.037166 GGTCTTAAATACTCCCTTCGTCTTAAA 58.963 37.037 0.00 0.00 0.00 1.52
2370 2988 7.364144 GGGTCTTAAATACTCCCTTCGTCTTAA 60.364 40.741 0.00 0.00 35.63 1.85
2371 2989 6.097412 GGGTCTTAAATACTCCCTTCGTCTTA 59.903 42.308 0.00 0.00 35.63 2.10
2372 2990 5.105023 GGGTCTTAAATACTCCCTTCGTCTT 60.105 44.000 0.00 0.00 35.63 3.01
2373 2991 4.405036 GGGTCTTAAATACTCCCTTCGTCT 59.595 45.833 0.00 0.00 35.63 4.18
2374 2992 4.161001 TGGGTCTTAAATACTCCCTTCGTC 59.839 45.833 0.00 0.00 38.95 4.20
2375 2993 4.081254 GTGGGTCTTAAATACTCCCTTCGT 60.081 45.833 0.00 0.00 38.95 3.85
2376 2994 4.081309 TGTGGGTCTTAAATACTCCCTTCG 60.081 45.833 0.00 0.00 38.95 3.79
2377 2995 5.431179 TGTGGGTCTTAAATACTCCCTTC 57.569 43.478 0.00 0.00 38.95 3.46
2378 2996 5.755849 CATGTGGGTCTTAAATACTCCCTT 58.244 41.667 0.00 0.00 38.95 3.95
2379 2997 4.385310 GCATGTGGGTCTTAAATACTCCCT 60.385 45.833 0.00 0.00 38.95 4.20
2380 2998 3.883489 GCATGTGGGTCTTAAATACTCCC 59.117 47.826 0.00 0.00 38.68 4.30
2381 2999 4.781934 AGCATGTGGGTCTTAAATACTCC 58.218 43.478 0.00 0.00 0.00 3.85
2382 3000 5.993106 GAGCATGTGGGTCTTAAATACTC 57.007 43.478 0.00 0.00 40.87 2.59
2392 3021 2.162408 GCTTGTTTAGAGCATGTGGGTC 59.838 50.000 0.00 0.00 44.43 4.46
2410 3039 2.853290 GCCAGCAACAGCACAGCTT 61.853 57.895 0.00 0.00 36.40 3.74
2415 3044 3.730761 CGAGGCCAGCAACAGCAC 61.731 66.667 5.01 0.00 0.00 4.40
2432 3061 1.923356 TGATGAAAACCCTCAAGGCC 58.077 50.000 0.00 0.00 40.58 5.19
2433 3062 5.452356 CCATAATGATGAAAACCCTCAAGGC 60.452 44.000 0.00 0.00 35.22 4.35
2435 3064 7.093814 TGTTCCATAATGATGAAAACCCTCAAG 60.094 37.037 0.00 0.00 34.73 3.02
2443 3072 6.211184 AGCACCTTGTTCCATAATGATGAAAA 59.789 34.615 0.00 0.00 34.73 2.29
2444 3073 5.716228 AGCACCTTGTTCCATAATGATGAAA 59.284 36.000 0.00 0.00 34.73 2.69
2445 3074 5.125900 CAGCACCTTGTTCCATAATGATGAA 59.874 40.000 0.00 0.00 34.73 2.57
2446 3075 4.641541 CAGCACCTTGTTCCATAATGATGA 59.358 41.667 0.00 0.00 34.73 2.92
2448 3077 3.382546 GCAGCACCTTGTTCCATAATGAT 59.617 43.478 0.00 0.00 0.00 2.45
2532 3163 2.315925 TCATTGAGTCGATGGAAGCC 57.684 50.000 18.52 0.00 0.00 4.35
2632 3263 1.202973 CGTCGATGATCACCGCTGAC 61.203 60.000 4.00 4.75 0.00 3.51
2647 3278 1.347817 GCTCTCCAAGTTCAGCGTCG 61.348 60.000 0.00 0.00 0.00 5.12
2654 3285 2.560105 AGGCAATTTGCTCTCCAAGTTC 59.440 45.455 20.06 0.62 44.28 3.01
2777 3408 4.759096 GTGCCGCACGACCATTGC 62.759 66.667 7.96 0.00 36.57 3.56
2955 3590 6.129561 CGAAACAAGCTAAATACAACAAACGG 60.130 38.462 0.00 0.00 0.00 4.44
2970 3605 2.754946 TAATCCGGACGAAACAAGCT 57.245 45.000 6.12 0.00 0.00 3.74
2995 3630 0.469917 GACAAGCTATAGCAGGGGCA 59.530 55.000 26.07 0.00 45.16 5.36
2997 3632 0.034059 CCGACAAGCTATAGCAGGGG 59.966 60.000 26.07 17.69 45.16 4.79
2999 3634 0.104855 TGCCGACAAGCTATAGCAGG 59.895 55.000 26.07 18.73 45.16 4.85
3005 3640 2.350522 CAAGAACTGCCGACAAGCTAT 58.649 47.619 0.00 0.00 0.00 2.97
3008 3643 1.576421 CCAAGAACTGCCGACAAGC 59.424 57.895 0.00 0.00 0.00 4.01
3010 3645 0.106918 AACCCAAGAACTGCCGACAA 60.107 50.000 0.00 0.00 0.00 3.18
3088 3723 5.105310 ACTGTGTCTACGATAGGAAAGCAAT 60.105 40.000 0.00 0.00 43.77 3.56
3121 3756 4.100808 GCTGTGAGGAAATAGGAGACAGAT 59.899 45.833 0.00 0.00 32.78 2.90
3122 3757 3.449018 GCTGTGAGGAAATAGGAGACAGA 59.551 47.826 0.00 0.00 32.78 3.41
3123 3758 3.450457 AGCTGTGAGGAAATAGGAGACAG 59.550 47.826 0.00 0.00 33.91 3.51
3124 3759 3.445008 AGCTGTGAGGAAATAGGAGACA 58.555 45.455 0.00 0.00 0.00 3.41
3125 3760 3.490078 CGAGCTGTGAGGAAATAGGAGAC 60.490 52.174 0.00 0.00 0.00 3.36
3126 3761 2.690497 CGAGCTGTGAGGAAATAGGAGA 59.310 50.000 0.00 0.00 0.00 3.71
3127 3762 2.690497 TCGAGCTGTGAGGAAATAGGAG 59.310 50.000 0.00 0.00 0.00 3.69
3128 3763 2.690497 CTCGAGCTGTGAGGAAATAGGA 59.310 50.000 0.00 0.00 0.00 2.94
3129 3764 2.801342 GCTCGAGCTGTGAGGAAATAGG 60.801 54.545 29.88 0.00 38.21 2.57
3130 3765 2.468831 GCTCGAGCTGTGAGGAAATAG 58.531 52.381 29.88 0.00 38.21 1.73
3131 3766 1.137086 GGCTCGAGCTGTGAGGAAATA 59.863 52.381 34.46 0.00 41.70 1.40
3132 3767 0.107945 GGCTCGAGCTGTGAGGAAAT 60.108 55.000 34.46 0.00 41.70 2.17
3133 3768 1.293498 GGCTCGAGCTGTGAGGAAA 59.707 57.895 34.46 0.00 41.70 3.13
3134 3769 1.260538 ATGGCTCGAGCTGTGAGGAA 61.261 55.000 34.46 12.11 41.70 3.36
3135 3770 1.260538 AATGGCTCGAGCTGTGAGGA 61.261 55.000 34.46 11.94 41.70 3.71
3136 3771 0.809241 GAATGGCTCGAGCTGTGAGG 60.809 60.000 34.46 0.00 41.70 3.86
3137 3772 0.809241 GGAATGGCTCGAGCTGTGAG 60.809 60.000 34.46 7.98 41.70 3.51
3138 3773 1.219124 GGAATGGCTCGAGCTGTGA 59.781 57.895 34.46 17.65 41.70 3.58
3139 3774 0.461548 TAGGAATGGCTCGAGCTGTG 59.538 55.000 34.46 0.00 41.70 3.66
3140 3775 1.195115 TTAGGAATGGCTCGAGCTGT 58.805 50.000 34.46 21.31 41.70 4.40
3141 3776 2.540265 ATTAGGAATGGCTCGAGCTG 57.460 50.000 34.46 0.84 41.70 4.24
3142 3777 3.567478 AAATTAGGAATGGCTCGAGCT 57.433 42.857 34.46 17.49 41.70 4.09
3143 3778 4.336713 AGAAAAATTAGGAATGGCTCGAGC 59.663 41.667 29.38 29.38 41.14 5.03
3144 3779 5.586243 TGAGAAAAATTAGGAATGGCTCGAG 59.414 40.000 8.45 8.45 0.00 4.04
3145 3780 5.496556 TGAGAAAAATTAGGAATGGCTCGA 58.503 37.500 0.00 0.00 0.00 4.04
3146 3781 5.818136 TGAGAAAAATTAGGAATGGCTCG 57.182 39.130 0.00 0.00 0.00 5.03
3182 3817 9.362151 ACTGGTATTTCTAATGAAACCAAAGAA 57.638 29.630 0.00 0.00 43.90 2.52
3183 3818 8.934023 ACTGGTATTTCTAATGAAACCAAAGA 57.066 30.769 0.00 0.00 43.90 2.52
3185 3820 9.802039 ACTACTGGTATTTCTAATGAAACCAAA 57.198 29.630 0.00 0.00 43.90 3.28
3186 3821 9.802039 AACTACTGGTATTTCTAATGAAACCAA 57.198 29.630 0.00 0.00 43.90 3.67
3187 3822 9.802039 AAACTACTGGTATTTCTAATGAAACCA 57.198 29.630 0.00 0.00 43.90 3.67


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

AutoCloner maintained by Alex Coulton.