Multiple sequence alignment - TraesCS6D01G241900

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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 TraesCS6D01G241900 chr6D 100.000 4548 0 0 1 4548 344180553 344176006 0.000000e+00 8399.0
1 TraesCS6D01G241900 chr6B 94.483 2157 76 20 2160 4287 519405563 519403421 0.000000e+00 3284.0
2 TraesCS6D01G241900 chr6B 86.216 1081 59 35 8 1041 519407679 519406642 0.000000e+00 1088.0
3 TraesCS6D01G241900 chr6B 93.738 527 15 5 1120 1645 519406544 519406035 0.000000e+00 774.0
4 TraesCS6D01G241900 chr6B 96.413 446 12 2 1716 2161 519406037 519405596 0.000000e+00 732.0
5 TraesCS6D01G241900 chr6B 92.823 209 8 2 4295 4503 519403318 519403117 3.440000e-76 296.0
6 TraesCS6D01G241900 chr6A 94.257 1515 47 9 2803 4283 484568767 484567259 0.000000e+00 2279.0
7 TraesCS6D01G241900 chr6A 87.684 1697 85 53 1 1643 484571658 484570032 0.000000e+00 1862.0
8 TraesCS6D01G241900 chr6A 96.552 435 12 1 1715 2149 484570034 484569603 0.000000e+00 717.0
9 TraesCS6D01G241900 chr6A 91.403 221 10 6 4283 4503 484567175 484566964 1.240000e-75 294.0
10 TraesCS6D01G241900 chr5B 93.151 73 4 1 2504 2576 437935493 437935422 6.220000e-19 106.0
11 TraesCS6D01G241900 chr2A 81.600 125 19 4 2360 2480 572599411 572599287 2.900000e-17 100.0
12 TraesCS6D01G241900 chr7D 89.041 73 8 0 2504 2576 509502194 509502122 1.740000e-14 91.6
13 TraesCS6D01G241900 chr4A 90.164 61 4 2 2504 2562 673474597 673474537 1.360000e-10 78.7
14 TraesCS6D01G241900 chrUn 81.707 82 13 2 2374 2453 74039635 74039554 2.940000e-07 67.6


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 TraesCS6D01G241900 chr6D 344176006 344180553 4547 True 8399.0 8399 100.0000 1 4548 1 chr6D.!!$R1 4547
1 TraesCS6D01G241900 chr6B 519403117 519407679 4562 True 1234.8 3284 92.7346 8 4503 5 chr6B.!!$R1 4495
2 TraesCS6D01G241900 chr6A 484566964 484571658 4694 True 1288.0 2279 92.4740 1 4503 4 chr6A.!!$R1 4502

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
457 501 0.109532 TGTGATTTCCTCCGGTGCAA 59.890 50.0 0.00 0.00 0.00 4.08 F
1265 1392 0.244178 AAAACCCGCGTGTTTGTGTT 59.756 45.0 20.16 1.81 38.41 3.32 F
1691 1826 0.035881 CACGGATCATCCATGGGAGG 59.964 60.0 13.02 1.63 35.91 4.30 F
2615 3191 0.038166 AAGAGCCCAAATTCGAGCCA 59.962 50.0 0.00 0.00 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1656 1791 0.163788 CGTGACTTACTTTGGCAGCG 59.836 55.0 0.00 0.00 0.00 5.18 R
3224 3816 0.040058 TGGTGCTGATTTGGAGCCAT 59.960 50.0 0.00 0.00 35.43 4.40 R
3393 3991 0.385473 CTTTGTTAACCGCGGCACAG 60.385 55.0 28.58 13.63 0.00 3.66 R
4292 4929 0.113190 CTGGTTTTGAAGCTCCCCCT 59.887 55.0 0.00 0.00 0.00 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
205 216 1.587034 GCGATTTTTCTACTCCGTCCG 59.413 52.381 0.00 0.00 0.00 4.79
335 355 2.331194 CGTCGATGGTCTAAAAACGGT 58.669 47.619 0.00 0.00 0.00 4.83
336 356 2.733026 CGTCGATGGTCTAAAAACGGTT 59.267 45.455 0.00 0.00 0.00 4.44
337 357 3.181537 CGTCGATGGTCTAAAAACGGTTC 60.182 47.826 0.00 0.00 0.00 3.62
338 358 3.742369 GTCGATGGTCTAAAAACGGTTCA 59.258 43.478 0.00 0.00 0.00 3.18
339 359 3.742369 TCGATGGTCTAAAAACGGTTCAC 59.258 43.478 0.00 0.00 0.00 3.18
342 362 3.888583 TGGTCTAAAAACGGTTCACCTT 58.111 40.909 0.00 0.00 0.00 3.50
343 363 3.878699 TGGTCTAAAAACGGTTCACCTTC 59.121 43.478 0.00 0.00 0.00 3.46
345 365 5.163322 TGGTCTAAAAACGGTTCACCTTCTA 60.163 40.000 0.00 0.00 0.00 2.10
346 366 5.178252 GGTCTAAAAACGGTTCACCTTCTAC 59.822 44.000 0.00 0.00 0.00 2.59
347 367 5.178252 GTCTAAAAACGGTTCACCTTCTACC 59.822 44.000 0.00 0.00 0.00 3.18
457 501 0.109532 TGTGATTTCCTCCGGTGCAA 59.890 50.000 0.00 0.00 0.00 4.08
549 593 2.441901 CAGGCGGAGAGGAGAGCT 60.442 66.667 0.00 0.00 0.00 4.09
550 594 2.123897 AGGCGGAGAGGAGAGCTC 60.124 66.667 5.27 5.27 0.00 4.09
551 595 2.441164 GGCGGAGAGGAGAGCTCA 60.441 66.667 17.77 0.00 34.07 4.26
552 596 1.832167 GGCGGAGAGGAGAGCTCAT 60.832 63.158 17.77 0.42 34.07 2.90
553 597 1.363443 GCGGAGAGGAGAGCTCATG 59.637 63.158 17.77 0.00 34.07 3.07
554 598 1.391157 GCGGAGAGGAGAGCTCATGT 61.391 60.000 17.77 0.00 34.07 3.21
555 599 1.110442 CGGAGAGGAGAGCTCATGTT 58.890 55.000 17.77 0.00 34.07 2.71
556 600 1.066908 CGGAGAGGAGAGCTCATGTTC 59.933 57.143 17.77 4.16 34.07 3.18
557 601 2.387757 GGAGAGGAGAGCTCATGTTCT 58.612 52.381 17.77 12.58 36.45 3.01
558 602 2.362077 GGAGAGGAGAGCTCATGTTCTC 59.638 54.545 17.77 19.45 45.83 2.87
567 615 1.139989 CTCATGTTCTCACACGCGTT 58.860 50.000 10.22 0.00 35.03 4.84
568 616 0.858583 TCATGTTCTCACACGCGTTG 59.141 50.000 10.22 12.12 35.03 4.10
819 908 2.483889 CCCTCTCTTTTATGCGACTCCC 60.484 54.545 0.00 0.00 0.00 4.30
828 917 3.213402 GCGACTCCCCTCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
839 928 2.123640 CTCCTCGTCCCCTCTCCC 60.124 72.222 0.00 0.00 0.00 4.30
880 969 3.016736 CTCTTCGCCTCTCTTCTCTTCT 58.983 50.000 0.00 0.00 0.00 2.85
881 970 3.013921 TCTTCGCCTCTCTTCTCTTCTC 58.986 50.000 0.00 0.00 0.00 2.87
883 972 1.283613 TCGCCTCTCTTCTCTTCTCCT 59.716 52.381 0.00 0.00 0.00 3.69
884 973 1.405105 CGCCTCTCTTCTCTTCTCCTG 59.595 57.143 0.00 0.00 0.00 3.86
885 974 1.136891 GCCTCTCTTCTCTTCTCCTGC 59.863 57.143 0.00 0.00 0.00 4.85
889 978 0.901124 TCTTCTCTTCTCCTGCCTGC 59.099 55.000 0.00 0.00 0.00 4.85
1049 1139 2.552585 TTCTTCCGGGTGCGATCGAC 62.553 60.000 21.57 13.74 0.00 4.20
1063 1190 3.544244 GCGATCGACTTAAAATGGTGCTC 60.544 47.826 21.57 0.00 0.00 4.26
1064 1191 3.865745 CGATCGACTTAAAATGGTGCTCT 59.134 43.478 10.26 0.00 0.00 4.09
1065 1192 4.026475 CGATCGACTTAAAATGGTGCTCTC 60.026 45.833 10.26 0.00 0.00 3.20
1066 1193 3.250744 TCGACTTAAAATGGTGCTCTCG 58.749 45.455 0.00 0.00 0.00 4.04
1067 1194 3.057104 TCGACTTAAAATGGTGCTCTCGA 60.057 43.478 0.00 0.00 0.00 4.04
1069 1196 4.026475 CGACTTAAAATGGTGCTCTCGATC 60.026 45.833 0.00 0.00 0.00 3.69
1074 1201 0.387202 ATGGTGCTCTCGATCGGAAG 59.613 55.000 16.41 13.65 0.00 3.46
1079 1206 0.317770 GCTCTCGATCGGAAGCAGAG 60.318 60.000 26.97 23.92 34.79 3.35
1102 1229 3.361281 TGGATGCTCATGCTTCTTCTT 57.639 42.857 3.18 0.00 41.41 2.52
1112 1239 2.244695 TGCTTCTTCTTCTCCGTGGTA 58.755 47.619 0.00 0.00 0.00 3.25
1265 1392 0.244178 AAAACCCGCGTGTTTGTGTT 59.756 45.000 20.16 1.81 38.41 3.32
1271 1398 1.332178 CGCGTGTTTGTGTTTGTGTT 58.668 45.000 0.00 0.00 0.00 3.32
1272 1399 1.716581 CGCGTGTTTGTGTTTGTGTTT 59.283 42.857 0.00 0.00 0.00 2.83
1273 1400 2.469820 CGCGTGTTTGTGTTTGTGTTTG 60.470 45.455 0.00 0.00 0.00 2.93
1274 1401 2.473235 GCGTGTTTGTGTTTGTGTTTGT 59.527 40.909 0.00 0.00 0.00 2.83
1275 1402 3.660389 GCGTGTTTGTGTTTGTGTTTGTG 60.660 43.478 0.00 0.00 0.00 3.33
1276 1403 3.487574 CGTGTTTGTGTTTGTGTTTGTGT 59.512 39.130 0.00 0.00 0.00 3.72
1513 1648 4.767841 CTCTGTGCGCGCTCTCGT 62.768 66.667 33.29 0.00 38.14 4.18
1538 1673 1.078497 CATAGGCACCAAGACGGCA 60.078 57.895 0.00 0.00 39.03 5.69
1611 1746 2.571653 TCCCTCACCATCTAACCAACTG 59.428 50.000 0.00 0.00 0.00 3.16
1612 1747 2.305927 CCCTCACCATCTAACCAACTGT 59.694 50.000 0.00 0.00 0.00 3.55
1613 1748 3.600388 CCTCACCATCTAACCAACTGTC 58.400 50.000 0.00 0.00 0.00 3.51
1614 1749 3.261897 CCTCACCATCTAACCAACTGTCT 59.738 47.826 0.00 0.00 0.00 3.41
1615 1750 4.499183 CTCACCATCTAACCAACTGTCTC 58.501 47.826 0.00 0.00 0.00 3.36
1616 1751 3.901222 TCACCATCTAACCAACTGTCTCA 59.099 43.478 0.00 0.00 0.00 3.27
1617 1752 4.532126 TCACCATCTAACCAACTGTCTCAT 59.468 41.667 0.00 0.00 0.00 2.90
1622 1757 5.392767 TCTAACCAACTGTCTCATCTCAC 57.607 43.478 0.00 0.00 0.00 3.51
1661 1796 3.449322 TTTAATTCGTGAACTCGCTGC 57.551 42.857 0.00 0.00 0.00 5.25
1662 1797 1.355971 TAATTCGTGAACTCGCTGCC 58.644 50.000 0.00 0.00 0.00 4.85
1663 1798 0.602638 AATTCGTGAACTCGCTGCCA 60.603 50.000 0.00 0.00 0.00 4.92
1664 1799 0.602638 ATTCGTGAACTCGCTGCCAA 60.603 50.000 0.00 0.00 0.00 4.52
1665 1800 0.812014 TTCGTGAACTCGCTGCCAAA 60.812 50.000 0.00 0.00 0.00 3.28
1666 1801 1.205064 CGTGAACTCGCTGCCAAAG 59.795 57.895 0.00 0.00 0.00 2.77
1667 1802 1.498865 CGTGAACTCGCTGCCAAAGT 61.499 55.000 0.00 0.00 0.00 2.66
1668 1803 1.508632 GTGAACTCGCTGCCAAAGTA 58.491 50.000 0.00 0.00 0.00 2.24
1669 1804 1.871039 GTGAACTCGCTGCCAAAGTAA 59.129 47.619 0.00 0.00 0.00 2.24
1670 1805 2.096218 GTGAACTCGCTGCCAAAGTAAG 60.096 50.000 0.00 0.00 0.00 2.34
1671 1806 2.143925 GAACTCGCTGCCAAAGTAAGT 58.856 47.619 0.00 0.00 0.00 2.24
1672 1807 1.797025 ACTCGCTGCCAAAGTAAGTC 58.203 50.000 0.00 0.00 0.00 3.01
1673 1808 1.070134 ACTCGCTGCCAAAGTAAGTCA 59.930 47.619 0.00 0.00 0.00 3.41
1674 1809 1.461127 CTCGCTGCCAAAGTAAGTCAC 59.539 52.381 0.00 0.00 0.00 3.67
1675 1810 0.163788 CGCTGCCAAAGTAAGTCACG 59.836 55.000 0.00 0.00 0.00 4.35
1676 1811 0.517316 GCTGCCAAAGTAAGTCACGG 59.483 55.000 0.00 0.00 0.00 4.94
1677 1812 1.876416 GCTGCCAAAGTAAGTCACGGA 60.876 52.381 0.00 0.00 0.00 4.69
1678 1813 2.699954 CTGCCAAAGTAAGTCACGGAT 58.300 47.619 0.00 0.00 0.00 4.18
1679 1814 2.673368 CTGCCAAAGTAAGTCACGGATC 59.327 50.000 0.00 0.00 0.00 3.36
1680 1815 2.037902 TGCCAAAGTAAGTCACGGATCA 59.962 45.455 0.00 0.00 0.00 2.92
1681 1816 3.270877 GCCAAAGTAAGTCACGGATCAT 58.729 45.455 0.00 0.00 0.00 2.45
1682 1817 3.309954 GCCAAAGTAAGTCACGGATCATC 59.690 47.826 0.00 0.00 0.00 2.92
1683 1818 3.871594 CCAAAGTAAGTCACGGATCATCC 59.128 47.826 0.00 0.00 0.00 3.51
1684 1819 4.503910 CAAAGTAAGTCACGGATCATCCA 58.496 43.478 4.06 0.00 35.91 3.41
1685 1820 5.118990 CAAAGTAAGTCACGGATCATCCAT 58.881 41.667 4.06 0.00 35.91 3.41
1686 1821 4.327982 AGTAAGTCACGGATCATCCATG 57.672 45.455 4.06 0.00 35.91 3.66
1687 1822 2.627515 AAGTCACGGATCATCCATGG 57.372 50.000 4.97 4.97 35.91 3.66
1688 1823 0.761187 AGTCACGGATCATCCATGGG 59.239 55.000 13.02 0.00 35.91 4.00
1689 1824 0.758734 GTCACGGATCATCCATGGGA 59.241 55.000 13.02 1.95 35.91 4.37
1690 1825 1.051008 TCACGGATCATCCATGGGAG 58.949 55.000 13.02 4.86 35.91 4.30
1691 1826 0.035881 CACGGATCATCCATGGGAGG 59.964 60.000 13.02 1.63 35.91 4.30
1692 1827 0.400525 ACGGATCATCCATGGGAGGT 60.401 55.000 13.02 0.00 35.91 3.85
1693 1828 0.322975 CGGATCATCCATGGGAGGTC 59.677 60.000 13.02 10.35 35.91 3.85
1694 1829 0.695347 GGATCATCCATGGGAGGTCC 59.305 60.000 17.40 17.40 36.28 4.46
1695 1830 0.322975 GATCATCCATGGGAGGTCCG 59.677 60.000 13.02 0.00 34.82 4.79
1696 1831 0.400525 ATCATCCATGGGAGGTCCGT 60.401 55.000 13.02 0.00 34.82 4.69
1701 1836 2.284625 ATGGGAGGTCCGTGAGCA 60.285 61.111 6.00 0.00 38.76 4.26
1702 1837 2.362369 ATGGGAGGTCCGTGAGCAG 61.362 63.158 6.00 0.00 38.76 4.24
1703 1838 2.680352 GGGAGGTCCGTGAGCAGA 60.680 66.667 6.00 0.00 36.71 4.26
1704 1839 2.060980 GGGAGGTCCGTGAGCAGAT 61.061 63.158 6.00 0.00 36.71 2.90
1705 1840 1.142748 GGAGGTCCGTGAGCAGATG 59.857 63.158 6.00 0.00 31.89 2.90
1706 1841 1.323271 GGAGGTCCGTGAGCAGATGA 61.323 60.000 6.00 0.00 31.89 2.92
1707 1842 0.179124 GAGGTCCGTGAGCAGATGAC 60.179 60.000 6.00 0.00 31.89 3.06
1708 1843 1.517257 GGTCCGTGAGCAGATGACG 60.517 63.158 0.00 0.00 0.00 4.35
1709 1844 1.213013 GTCCGTGAGCAGATGACGT 59.787 57.895 0.00 0.00 0.00 4.34
1710 1845 0.798771 GTCCGTGAGCAGATGACGTC 60.799 60.000 9.11 9.11 0.00 4.34
1711 1846 1.869574 CCGTGAGCAGATGACGTCG 60.870 63.158 11.62 0.00 0.00 5.12
1712 1847 1.869574 CGTGAGCAGATGACGTCGG 60.870 63.158 11.62 1.50 0.00 4.79
1713 1848 1.213013 GTGAGCAGATGACGTCGGT 59.787 57.895 11.62 1.47 0.00 4.69
1718 1853 2.334838 AGCAGATGACGTCGGTTTTAC 58.665 47.619 11.62 0.00 0.00 2.01
1724 1859 1.620413 GACGTCGGTTTTACCAGCCG 61.620 60.000 0.00 0.00 46.12 5.52
1728 1863 2.358984 GGTTTTACCAGCCGCGGA 60.359 61.111 33.48 3.64 38.42 5.54
1788 1923 2.438795 GAGAGTCGTCCGGGAGCT 60.439 66.667 0.00 0.00 0.00 4.09
1862 1997 4.715523 CCGCGGCCCAAGAGGAAA 62.716 66.667 14.67 0.00 38.24 3.13
2135 2270 0.664767 GCTGCCTCTCGCCTAATACG 60.665 60.000 0.00 0.00 36.24 3.06
2136 2271 0.952280 CTGCCTCTCGCCTAATACGA 59.048 55.000 0.00 0.00 38.02 3.43
2137 2272 0.666913 TGCCTCTCGCCTAATACGAC 59.333 55.000 0.00 0.00 35.35 4.34
2150 2285 5.334182 GCCTAATACGACTAAGGTACCGTAC 60.334 48.000 6.18 0.00 39.77 3.67
2165 2418 8.757982 AGGTACCGTACTCTTTTCTAATATCA 57.242 34.615 6.18 0.00 0.00 2.15
2244 2501 9.706691 AAATTTCAGTCAATCGTCTTAGACTTA 57.293 29.630 10.83 0.00 39.17 2.24
2265 2522 9.181805 GACTTAAGTTTGCCTTGAGATTAAAAC 57.818 33.333 10.02 0.00 38.69 2.43
2266 2523 8.141909 ACTTAAGTTTGCCTTGAGATTAAAACC 58.858 33.333 1.12 0.00 38.69 3.27
2267 2524 5.121221 AGTTTGCCTTGAGATTAAAACCG 57.879 39.130 0.00 0.00 0.00 4.44
2268 2525 4.825085 AGTTTGCCTTGAGATTAAAACCGA 59.175 37.500 0.00 0.00 0.00 4.69
2270 2527 5.975693 TTGCCTTGAGATTAAAACCGATT 57.024 34.783 0.00 0.00 0.00 3.34
2272 2529 4.157656 TGCCTTGAGATTAAAACCGATTGG 59.842 41.667 0.00 0.00 42.84 3.16
2274 2531 4.440112 CCTTGAGATTAAAACCGATTGGCC 60.440 45.833 0.00 0.00 39.70 5.36
2275 2532 3.691575 TGAGATTAAAACCGATTGGCCA 58.308 40.909 0.00 0.00 39.70 5.36
2276 2533 4.277476 TGAGATTAAAACCGATTGGCCAT 58.723 39.130 6.09 0.00 39.70 4.40
2415 2984 4.876125 AGATGTGTCCTAGATATTGCACG 58.124 43.478 0.00 0.00 0.00 5.34
2428 2997 2.433868 TTGCACGTCTAAGTGACTCC 57.566 50.000 0.88 0.00 44.43 3.85
2429 2998 0.240145 TGCACGTCTAAGTGACTCCG 59.760 55.000 0.88 0.00 44.43 4.63
2431 3000 1.728502 GCACGTCTAAGTGACTCCGTC 60.729 57.143 0.88 0.00 44.43 4.79
2438 3007 5.860182 CGTCTAAGTGACTCCGTCAAATTAA 59.140 40.000 0.00 0.00 44.49 1.40
2486 3056 2.177394 TGGTTGCACGAATCTTAGCA 57.823 45.000 0.00 0.00 34.79 3.49
2489 3059 4.450976 TGGTTGCACGAATCTTAGCATAT 58.549 39.130 0.00 0.00 36.80 1.78
2490 3060 4.881273 TGGTTGCACGAATCTTAGCATATT 59.119 37.500 0.00 0.00 36.80 1.28
2521 3095 7.519057 TCTAGAGTAGCTTTATAGAAGGCAGA 58.481 38.462 6.98 0.00 40.04 4.26
2539 3113 8.814038 AAGGCAGAATATCAGTTACAAGAAAT 57.186 30.769 0.00 0.00 0.00 2.17
2547 3121 5.756950 TCAGTTACAAGAAATTACGCTCG 57.243 39.130 0.00 0.00 0.00 5.03
2577 3151 4.512944 ACAATGAGAGTAGCACAAACACTG 59.487 41.667 0.00 0.00 0.00 3.66
2615 3191 0.038166 AAGAGCCCAAATTCGAGCCA 59.962 50.000 0.00 0.00 0.00 4.75
2677 3261 9.623000 GTGGTTTAATAAGAGGATAAAGGCTAA 57.377 33.333 0.00 0.00 0.00 3.09
2735 3327 6.345920 TCACTTCGAGAAGAAAACAAACTC 57.654 37.500 18.54 0.00 40.79 3.01
2840 3432 5.484715 CTCCGGTACCTTTCAATTCTAACA 58.515 41.667 10.90 0.00 0.00 2.41
3013 3605 2.676471 AACCCGCAGAATGGTGGC 60.676 61.111 0.00 0.00 37.11 5.01
3187 3779 0.899717 AATCTGCGGTGCCATGGTTT 60.900 50.000 14.67 0.00 0.00 3.27
3224 3816 2.161855 CAATGTTCTACCAGCAAGCCA 58.838 47.619 0.00 0.00 0.00 4.75
3319 3917 0.038744 CAGGATCAAACACTGGCCCT 59.961 55.000 0.00 0.00 0.00 5.19
3376 3974 0.980423 GAGGGAGAGGAAACAGCAGT 59.020 55.000 0.00 0.00 0.00 4.40
3436 4034 1.271102 GAGAGCTCTGTTTCGGTCAGT 59.729 52.381 23.91 0.00 34.86 3.41
3795 4400 6.757010 TGTTTTTGTTCTCTACAGAGTGTCTC 59.243 38.462 6.16 0.00 42.60 3.36
3796 4401 6.716934 TTTTGTTCTCTACAGAGTGTCTCT 57.283 37.500 6.16 0.00 42.11 3.10
3949 4555 9.836864 AGTCTGCATTCTGTAAAACATATGATA 57.163 29.630 10.38 0.00 0.00 2.15
4024 4633 2.344093 ATACCTGGACTTGGGTCTGT 57.656 50.000 0.00 0.00 41.82 3.41
4183 4817 1.591059 GCACAATGTTGTTGCGGCA 60.591 52.632 0.00 0.00 39.91 5.69
4200 4834 1.377725 CAGCACCAACAGGGCTAGG 60.378 63.158 0.00 0.00 42.05 3.02
4246 4880 3.062466 CACGCGACAGAGGGGAGA 61.062 66.667 15.93 0.00 0.00 3.71
4247 4881 2.043852 ACGCGACAGAGGGGAGAT 60.044 61.111 15.93 0.00 0.00 2.75
4268 4902 3.826754 TAGCCGTGGAGCTCTGCG 61.827 66.667 14.64 17.10 43.67 5.18
4284 4921 3.775654 CGAAAGCGGGGAGGAGCT 61.776 66.667 0.00 0.00 46.97 4.09
4285 4922 2.423898 CGAAAGCGGGGAGGAGCTA 61.424 63.158 0.00 0.00 43.78 3.32
4286 4923 1.443828 GAAAGCGGGGAGGAGCTAG 59.556 63.158 0.00 0.00 43.78 3.42
4287 4924 2.652382 GAAAGCGGGGAGGAGCTAGC 62.652 65.000 6.62 6.62 43.78 3.42
4288 4925 3.984186 AAGCGGGGAGGAGCTAGCA 62.984 63.158 18.83 0.00 43.78 3.49
4289 4926 3.922640 GCGGGGAGGAGCTAGCAG 61.923 72.222 18.83 0.00 0.00 4.24
4291 4928 3.555324 GGGGAGGAGCTAGCAGGC 61.555 72.222 18.83 5.58 0.00 4.85
4292 4929 2.765807 GGGAGGAGCTAGCAGGCA 60.766 66.667 18.83 0.00 34.17 4.75
4391 5119 6.151691 CCAATGAATCCACACTACAAACTTG 58.848 40.000 0.00 0.00 0.00 3.16
4406 5134 2.086054 ACTTGCATCCGAGTTCTGAC 57.914 50.000 0.00 0.00 31.43 3.51
4407 5135 1.620819 ACTTGCATCCGAGTTCTGACT 59.379 47.619 0.00 0.00 39.32 3.41
4408 5136 2.037772 ACTTGCATCCGAGTTCTGACTT 59.962 45.455 0.00 0.00 35.88 3.01
4409 5137 2.370281 TGCATCCGAGTTCTGACTTC 57.630 50.000 0.00 0.00 35.88 3.01
4410 5138 1.895798 TGCATCCGAGTTCTGACTTCT 59.104 47.619 0.00 0.00 35.88 2.85
4411 5139 2.266554 GCATCCGAGTTCTGACTTCTG 58.733 52.381 0.00 0.00 35.88 3.02
4412 5140 2.094494 GCATCCGAGTTCTGACTTCTGA 60.094 50.000 0.00 0.00 35.88 3.27
4413 5141 3.768406 CATCCGAGTTCTGACTTCTGAG 58.232 50.000 0.00 0.00 35.88 3.35
4447 5175 2.439507 TCAAGAGGAGGCATCATAACCC 59.560 50.000 0.00 0.00 0.00 4.11
4503 5231 5.855040 ACATCATATAGGGGTTAACCATGGA 59.145 40.000 25.71 12.75 42.91 3.41
4504 5232 6.012508 ACATCATATAGGGGTTAACCATGGAG 60.013 42.308 25.71 16.19 42.91 3.86
4505 5233 5.482580 TCATATAGGGGTTAACCATGGAGT 58.517 41.667 25.71 8.44 42.91 3.85
4506 5234 6.636003 TCATATAGGGGTTAACCATGGAGTA 58.364 40.000 25.71 7.31 42.91 2.59
4507 5235 6.499350 TCATATAGGGGTTAACCATGGAGTAC 59.501 42.308 25.71 12.17 42.91 2.73
4508 5236 2.923908 AGGGGTTAACCATGGAGTACA 58.076 47.619 25.71 0.00 42.91 2.90
4509 5237 3.261962 AGGGGTTAACCATGGAGTACAA 58.738 45.455 25.71 1.41 42.91 2.41
4510 5238 3.856206 AGGGGTTAACCATGGAGTACAAT 59.144 43.478 25.71 0.00 42.91 2.71
4511 5239 3.951680 GGGGTTAACCATGGAGTACAATG 59.048 47.826 25.71 0.00 42.91 2.82
4512 5240 3.380320 GGGTTAACCATGGAGTACAATGC 59.620 47.826 25.71 0.00 39.85 3.56
4513 5241 4.013728 GGTTAACCATGGAGTACAATGCA 58.986 43.478 21.47 0.00 35.64 3.96
4514 5242 4.461081 GGTTAACCATGGAGTACAATGCAA 59.539 41.667 21.47 0.00 35.64 4.08
4515 5243 5.393027 GGTTAACCATGGAGTACAATGCAAG 60.393 44.000 21.47 0.00 35.64 4.01
4516 5244 3.439857 ACCATGGAGTACAATGCAAGT 57.560 42.857 21.47 0.00 0.00 3.16
4517 5245 3.084039 ACCATGGAGTACAATGCAAGTG 58.916 45.455 21.47 2.53 38.30 3.16
4518 5246 2.424601 CCATGGAGTACAATGCAAGTGG 59.575 50.000 5.56 0.00 35.33 4.00
4519 5247 2.949177 TGGAGTACAATGCAAGTGGT 57.051 45.000 5.51 0.00 35.33 4.16
4520 5248 4.260985 CATGGAGTACAATGCAAGTGGTA 58.739 43.478 5.51 0.00 35.33 3.25
4521 5249 4.359434 TGGAGTACAATGCAAGTGGTAA 57.641 40.909 5.51 0.00 35.33 2.85
4522 5250 4.917385 TGGAGTACAATGCAAGTGGTAAT 58.083 39.130 5.51 0.00 35.33 1.89
4523 5251 4.699735 TGGAGTACAATGCAAGTGGTAATG 59.300 41.667 5.51 0.00 35.33 1.90
4524 5252 4.700213 GGAGTACAATGCAAGTGGTAATGT 59.300 41.667 5.51 0.00 35.33 2.71
4525 5253 5.183140 GGAGTACAATGCAAGTGGTAATGTT 59.817 40.000 5.51 0.00 35.33 2.71
4526 5254 6.012658 AGTACAATGCAAGTGGTAATGTTG 57.987 37.500 5.51 0.00 35.33 3.33
4527 5255 3.652274 ACAATGCAAGTGGTAATGTTGC 58.348 40.909 0.00 0.00 45.56 4.17
4534 5262 6.393720 GCAAGTGGTAATGTTGCAATTTAG 57.606 37.500 0.59 0.00 44.87 1.85
4535 5263 5.925969 GCAAGTGGTAATGTTGCAATTTAGT 59.074 36.000 0.59 0.00 44.87 2.24
4536 5264 6.423604 GCAAGTGGTAATGTTGCAATTTAGTT 59.576 34.615 0.59 0.00 44.87 2.24
4537 5265 7.359181 GCAAGTGGTAATGTTGCAATTTAGTTC 60.359 37.037 0.59 0.00 44.87 3.01
4538 5266 7.524717 AGTGGTAATGTTGCAATTTAGTTCT 57.475 32.000 0.59 0.96 0.00 3.01
4539 5267 7.370383 AGTGGTAATGTTGCAATTTAGTTCTG 58.630 34.615 0.59 0.00 0.00 3.02
4540 5268 6.089417 GTGGTAATGTTGCAATTTAGTTCTGC 59.911 38.462 0.59 0.00 36.60 4.26
4541 5269 6.155827 GGTAATGTTGCAATTTAGTTCTGCA 58.844 36.000 0.59 0.00 44.04 4.41
4547 5275 4.050553 TGCAATTTAGTTCTGCAAACTGC 58.949 39.130 18.57 15.04 42.84 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.071206 TCCTGGCCACGAGCTCTC 61.071 66.667 12.85 0.00 43.05 3.20
47 48 2.534903 GGATAGGCGTGCCTTTCGC 61.535 63.158 20.08 10.66 45.70 4.70
48 49 2.237751 CGGATAGGCGTGCCTTTCG 61.238 63.158 20.08 15.70 45.70 3.46
49 50 1.143183 TCGGATAGGCGTGCCTTTC 59.857 57.895 20.08 19.64 45.70 2.62
50 51 1.153429 GTCGGATAGGCGTGCCTTT 60.153 57.895 20.08 11.53 45.70 3.11
54 55 3.845259 TGGGTCGGATAGGCGTGC 61.845 66.667 0.00 0.00 0.00 5.34
55 56 1.956629 AAGTGGGTCGGATAGGCGTG 61.957 60.000 0.00 0.00 0.00 5.34
231 251 2.490993 GATTTGTTGGGGCGCCACAG 62.491 60.000 33.21 0.00 0.00 3.66
232 252 2.522923 ATTTGTTGGGGCGCCACA 60.523 55.556 31.83 31.83 0.00 4.17
233 253 2.212900 GAGATTTGTTGGGGCGCCAC 62.213 60.000 30.85 28.40 0.00 5.01
234 254 1.976474 GAGATTTGTTGGGGCGCCA 60.976 57.895 30.85 20.22 0.00 5.69
235 255 2.885113 GAGATTTGTTGGGGCGCC 59.115 61.111 21.18 21.18 0.00 6.53
236 256 2.332654 ACGAGATTTGTTGGGGCGC 61.333 57.895 0.00 0.00 0.00 6.53
237 257 1.501741 CACGAGATTTGTTGGGGCG 59.498 57.895 0.00 0.00 0.00 6.13
238 258 1.883021 CCACGAGATTTGTTGGGGC 59.117 57.895 0.00 0.00 0.00 5.80
239 259 0.609131 AGCCACGAGATTTGTTGGGG 60.609 55.000 0.00 0.00 0.00 4.96
286 306 3.679389 TGTGCTCCAGAGGAAGAAAATC 58.321 45.455 0.00 0.00 0.00 2.17
287 307 3.560882 CCTGTGCTCCAGAGGAAGAAAAT 60.561 47.826 2.46 0.00 46.28 1.82
289 309 1.349026 CCTGTGCTCCAGAGGAAGAAA 59.651 52.381 2.46 0.00 46.28 2.52
290 310 0.979665 CCTGTGCTCCAGAGGAAGAA 59.020 55.000 2.46 0.00 46.28 2.52
291 311 0.178921 ACCTGTGCTCCAGAGGAAGA 60.179 55.000 14.47 0.00 46.28 2.87
292 312 1.480137 CTACCTGTGCTCCAGAGGAAG 59.520 57.143 14.47 0.00 46.28 3.46
310 330 1.766494 TTTAGACCATCGACGGCCTA 58.234 50.000 0.00 0.00 0.00 3.93
335 355 4.165565 TCTCTCCTATCGGTAGAAGGTGAA 59.834 45.833 3.68 0.00 33.72 3.18
336 356 3.715315 TCTCTCCTATCGGTAGAAGGTGA 59.285 47.826 3.68 0.00 33.23 4.02
337 357 4.088056 TCTCTCCTATCGGTAGAAGGTG 57.912 50.000 3.68 0.00 0.00 4.00
338 358 4.166531 ACTTCTCTCCTATCGGTAGAAGGT 59.833 45.833 22.80 12.99 45.47 3.50
339 359 4.517453 CACTTCTCTCCTATCGGTAGAAGG 59.483 50.000 22.80 14.23 45.47 3.46
342 362 4.744259 GCTCACTTCTCTCCTATCGGTAGA 60.744 50.000 3.68 0.00 0.00 2.59
343 363 3.500680 GCTCACTTCTCTCCTATCGGTAG 59.499 52.174 0.00 0.00 0.00 3.18
345 365 2.303175 GCTCACTTCTCTCCTATCGGT 58.697 52.381 0.00 0.00 0.00 4.69
346 366 1.265635 CGCTCACTTCTCTCCTATCGG 59.734 57.143 0.00 0.00 0.00 4.18
347 367 1.944024 ACGCTCACTTCTCTCCTATCG 59.056 52.381 0.00 0.00 0.00 2.92
348 368 2.685897 ACACGCTCACTTCTCTCCTATC 59.314 50.000 0.00 0.00 0.00 2.08
349 369 2.685897 GACACGCTCACTTCTCTCCTAT 59.314 50.000 0.00 0.00 0.00 2.57
549 593 0.858583 CAACGCGTGTGAGAACATGA 59.141 50.000 14.98 0.00 0.00 3.07
550 594 0.110688 CCAACGCGTGTGAGAACATG 60.111 55.000 14.98 3.19 0.00 3.21
551 595 0.249699 TCCAACGCGTGTGAGAACAT 60.250 50.000 14.98 0.00 0.00 2.71
552 596 0.874175 CTCCAACGCGTGTGAGAACA 60.874 55.000 25.79 0.56 30.28 3.18
553 597 1.557443 CCTCCAACGCGTGTGAGAAC 61.557 60.000 29.49 0.00 30.28 3.01
554 598 1.300620 CCTCCAACGCGTGTGAGAA 60.301 57.895 29.49 12.44 30.28 2.87
555 599 2.338620 CCTCCAACGCGTGTGAGA 59.661 61.111 29.49 16.86 30.28 3.27
556 600 3.414700 GCCTCCAACGCGTGTGAG 61.415 66.667 24.00 24.00 0.00 3.51
557 601 4.980805 GGCCTCCAACGCGTGTGA 62.981 66.667 14.98 11.96 0.00 3.58
559 603 4.555709 TTGGCCTCCAACGCGTGT 62.556 61.111 14.98 0.00 38.75 4.49
560 604 3.726517 CTTGGCCTCCAACGCGTG 61.727 66.667 14.98 7.16 38.75 5.34
567 615 0.475044 ACCGTAAAACTTGGCCTCCA 59.525 50.000 3.32 0.00 0.00 3.86
568 616 0.879090 CACCGTAAAACTTGGCCTCC 59.121 55.000 3.32 0.00 0.00 4.30
703 782 1.669265 GTCGGACGGGATTTTTCCATC 59.331 52.381 0.00 0.00 0.00 3.51
784 863 0.967380 AGAGGGGTACGTTACGTGGG 60.967 60.000 21.22 0.00 41.39 4.61
785 864 0.453390 GAGAGGGGTACGTTACGTGG 59.547 60.000 21.22 0.00 41.39 4.94
787 866 2.206576 AAGAGAGGGGTACGTTACGT 57.793 50.000 16.31 16.31 44.35 3.57
788 867 3.582714 AAAAGAGAGGGGTACGTTACG 57.417 47.619 2.19 2.19 0.00 3.18
789 868 4.807834 GCATAAAAGAGAGGGGTACGTTAC 59.192 45.833 0.00 0.00 0.00 2.50
790 869 4.440525 CGCATAAAAGAGAGGGGTACGTTA 60.441 45.833 0.00 0.00 0.00 3.18
819 908 1.152839 GAGAGGGGACGAGGAGAGG 60.153 68.421 0.00 0.00 0.00 3.69
828 917 2.442458 GGAGTCGGGAGAGGGGAC 60.442 72.222 0.00 0.00 41.26 4.46
839 928 1.758319 GCGAGAGACGAGAGGAGTCG 61.758 65.000 0.00 0.00 45.77 4.18
933 1023 2.430332 CACCAAAAGCCAAGACCAAGAA 59.570 45.455 0.00 0.00 0.00 2.52
1049 1139 3.246226 CCGATCGAGAGCACCATTTTAAG 59.754 47.826 18.66 0.00 0.00 1.85
1063 1190 2.351253 CCATACTCTGCTTCCGATCGAG 60.351 54.545 18.66 8.18 0.00 4.04
1064 1191 1.609072 CCATACTCTGCTTCCGATCGA 59.391 52.381 18.66 0.00 0.00 3.59
1065 1192 1.609072 TCCATACTCTGCTTCCGATCG 59.391 52.381 8.51 8.51 0.00 3.69
1066 1193 3.583806 CATCCATACTCTGCTTCCGATC 58.416 50.000 0.00 0.00 0.00 3.69
1067 1194 2.289320 GCATCCATACTCTGCTTCCGAT 60.289 50.000 0.00 0.00 33.15 4.18
1069 1196 1.069823 AGCATCCATACTCTGCTTCCG 59.930 52.381 0.00 0.00 43.44 4.30
1074 1201 1.805345 GCATGAGCATCCATACTCTGC 59.195 52.381 0.00 0.00 41.58 4.26
1079 1206 4.387598 AGAAGAAGCATGAGCATCCATAC 58.612 43.478 0.00 0.00 45.49 2.39
1090 1217 2.005451 CCACGGAGAAGAAGAAGCATG 58.995 52.381 0.00 0.00 0.00 4.06
1112 1239 2.203195 TCCTGCAAGCAAGCACGT 60.203 55.556 0.00 0.00 40.11 4.49
1245 1372 1.093159 ACACAAACACGCGGGTTTTA 58.907 45.000 35.24 0.00 38.86 1.52
1293 1420 3.906008 CGAGCAACAAATTCGTTCGATTT 59.094 39.130 0.00 0.00 0.00 2.17
1457 1587 0.729140 CGTGCGAAATTGGTTGGCTC 60.729 55.000 0.00 0.00 41.26 4.70
1460 1590 0.729140 GAGCGTGCGAAATTGGTTGG 60.729 55.000 0.00 0.00 0.00 3.77
1513 1648 2.168521 GTCTTGGTGCCTATGTGCTCTA 59.831 50.000 0.00 0.00 0.00 2.43
1538 1673 1.675641 GTGGCTCCGGATTTGCACT 60.676 57.895 15.29 0.00 0.00 4.40
1642 1777 1.730064 GGCAGCGAGTTCACGAATTAA 59.270 47.619 0.00 0.00 35.09 1.40
1643 1778 1.337354 TGGCAGCGAGTTCACGAATTA 60.337 47.619 0.00 0.00 35.09 1.40
1644 1779 0.602638 TGGCAGCGAGTTCACGAATT 60.603 50.000 0.00 0.00 35.09 2.17
1645 1780 0.602638 TTGGCAGCGAGTTCACGAAT 60.603 50.000 0.00 0.00 35.09 3.34
1646 1781 0.812014 TTTGGCAGCGAGTTCACGAA 60.812 50.000 0.00 0.00 35.09 3.85
1647 1782 1.221466 CTTTGGCAGCGAGTTCACGA 61.221 55.000 0.00 0.00 35.09 4.35
1648 1783 1.205064 CTTTGGCAGCGAGTTCACG 59.795 57.895 0.00 0.00 0.00 4.35
1649 1784 1.508632 TACTTTGGCAGCGAGTTCAC 58.491 50.000 5.73 0.00 0.00 3.18
1650 1785 2.143122 CTTACTTTGGCAGCGAGTTCA 58.857 47.619 5.73 0.00 0.00 3.18
1651 1786 2.143925 ACTTACTTTGGCAGCGAGTTC 58.856 47.619 5.73 0.00 0.00 3.01
1652 1787 2.143925 GACTTACTTTGGCAGCGAGTT 58.856 47.619 5.73 0.00 0.00 3.01
1653 1788 1.070134 TGACTTACTTTGGCAGCGAGT 59.930 47.619 5.73 5.73 0.00 4.18
1654 1789 1.461127 GTGACTTACTTTGGCAGCGAG 59.539 52.381 0.00 0.00 0.00 5.03
1655 1790 1.508632 GTGACTTACTTTGGCAGCGA 58.491 50.000 0.00 0.00 0.00 4.93
1656 1791 0.163788 CGTGACTTACTTTGGCAGCG 59.836 55.000 0.00 0.00 0.00 5.18
1657 1792 0.517316 CCGTGACTTACTTTGGCAGC 59.483 55.000 0.00 0.00 0.00 5.25
1658 1793 2.163818 TCCGTGACTTACTTTGGCAG 57.836 50.000 0.00 0.00 0.00 4.85
1659 1794 2.037902 TGATCCGTGACTTACTTTGGCA 59.962 45.455 0.00 0.00 0.00 4.92
1660 1795 2.695359 TGATCCGTGACTTACTTTGGC 58.305 47.619 0.00 0.00 0.00 4.52
1661 1796 3.871594 GGATGATCCGTGACTTACTTTGG 59.128 47.826 0.00 0.00 0.00 3.28
1662 1797 4.503910 TGGATGATCCGTGACTTACTTTG 58.496 43.478 7.03 0.00 40.17 2.77
1663 1798 4.819105 TGGATGATCCGTGACTTACTTT 57.181 40.909 7.03 0.00 40.17 2.66
1673 1808 0.400525 ACCTCCCATGGATGATCCGT 60.401 55.000 15.22 3.19 40.17 4.69
1674 1809 0.322975 GACCTCCCATGGATGATCCG 59.677 60.000 15.22 0.00 40.17 4.18
1675 1810 0.695347 GGACCTCCCATGGATGATCC 59.305 60.000 15.22 11.15 33.88 3.36
1676 1811 0.322975 CGGACCTCCCATGGATGATC 59.677 60.000 15.22 5.39 34.14 2.92
1677 1812 0.400525 ACGGACCTCCCATGGATGAT 60.401 55.000 15.22 0.00 34.14 2.45
1678 1813 1.002921 ACGGACCTCCCATGGATGA 59.997 57.895 15.22 1.25 34.14 2.92
1679 1814 1.146930 CACGGACCTCCCATGGATG 59.853 63.158 15.22 5.06 34.14 3.51
1680 1815 1.002921 TCACGGACCTCCCATGGAT 59.997 57.895 15.22 0.00 34.14 3.41
1681 1816 1.685765 CTCACGGACCTCCCATGGA 60.686 63.158 15.22 0.00 34.14 3.41
1682 1817 2.903357 CTCACGGACCTCCCATGG 59.097 66.667 4.14 4.14 34.14 3.66
1683 1818 2.187946 GCTCACGGACCTCCCATG 59.812 66.667 0.00 0.00 34.14 3.66
1684 1819 2.284625 TGCTCACGGACCTCCCAT 60.285 61.111 0.00 0.00 34.14 4.00
1685 1820 2.805313 ATCTGCTCACGGACCTCCCA 62.805 60.000 0.00 0.00 32.77 4.37
1686 1821 2.060980 ATCTGCTCACGGACCTCCC 61.061 63.158 0.00 0.00 32.77 4.30
1687 1822 1.142748 CATCTGCTCACGGACCTCC 59.857 63.158 0.00 0.00 32.77 4.30
1688 1823 0.179124 GTCATCTGCTCACGGACCTC 60.179 60.000 0.00 0.00 32.77 3.85
1689 1824 1.893786 GTCATCTGCTCACGGACCT 59.106 57.895 0.00 0.00 32.77 3.85
1690 1825 1.517257 CGTCATCTGCTCACGGACC 60.517 63.158 0.00 0.00 32.77 4.46
1691 1826 0.798771 GACGTCATCTGCTCACGGAC 60.799 60.000 11.55 0.00 37.86 4.79
1692 1827 1.506718 GACGTCATCTGCTCACGGA 59.493 57.895 11.55 0.00 37.86 4.69
1693 1828 1.869574 CGACGTCATCTGCTCACGG 60.870 63.158 17.16 0.00 37.86 4.94
1694 1829 1.869574 CCGACGTCATCTGCTCACG 60.870 63.158 17.16 0.00 39.48 4.35
1695 1830 0.388649 AACCGACGTCATCTGCTCAC 60.389 55.000 17.16 0.00 0.00 3.51
1696 1831 0.317160 AAACCGACGTCATCTGCTCA 59.683 50.000 17.16 0.00 0.00 4.26
1697 1832 1.429463 AAAACCGACGTCATCTGCTC 58.571 50.000 17.16 0.00 0.00 4.26
1698 1833 2.334838 GTAAAACCGACGTCATCTGCT 58.665 47.619 17.16 0.00 0.00 4.24
1699 1834 1.392510 GGTAAAACCGACGTCATCTGC 59.607 52.381 17.16 0.00 0.00 4.26
1700 1835 2.666508 CTGGTAAAACCGACGTCATCTG 59.333 50.000 17.16 3.12 42.58 2.90
1701 1836 2.929592 GCTGGTAAAACCGACGTCATCT 60.930 50.000 17.16 0.00 42.58 2.90
1702 1837 1.392510 GCTGGTAAAACCGACGTCATC 59.607 52.381 17.16 0.00 42.58 2.92
1703 1838 1.435577 GCTGGTAAAACCGACGTCAT 58.564 50.000 17.16 0.00 42.58 3.06
1704 1839 0.600782 GGCTGGTAAAACCGACGTCA 60.601 55.000 17.16 0.00 42.58 4.35
1705 1840 2.156542 GGCTGGTAAAACCGACGTC 58.843 57.895 5.18 5.18 42.58 4.34
1706 1841 4.366603 GGCTGGTAAAACCGACGT 57.633 55.556 0.00 0.00 42.58 4.34
1711 1846 1.310216 AATCCGCGGCTGGTAAAACC 61.310 55.000 23.51 0.00 39.22 3.27
1712 1847 0.524414 AAATCCGCGGCTGGTAAAAC 59.476 50.000 23.51 0.00 0.00 2.43
1713 1848 1.200484 GAAAATCCGCGGCTGGTAAAA 59.800 47.619 23.51 0.00 0.00 1.52
1718 1853 2.438434 AGGAAAATCCGCGGCTGG 60.438 61.111 23.51 0.00 42.75 4.85
1724 1859 2.791927 GGCGTCAGGAAAATCCGC 59.208 61.111 0.00 0.00 42.75 5.54
1728 1863 1.379527 GAATCCGGCGTCAGGAAAAT 58.620 50.000 6.01 0.00 41.69 1.82
2037 2172 2.047274 GCTGCCGCTGGAGTTGTA 60.047 61.111 0.00 0.00 0.00 2.41
2135 2270 6.507958 AGAAAAGAGTACGGTACCTTAGTC 57.492 41.667 20.58 20.58 0.00 2.59
2136 2271 8.586879 ATTAGAAAAGAGTACGGTACCTTAGT 57.413 34.615 14.41 7.99 0.00 2.24
2233 2490 6.929606 TCTCAAGGCAAACTTAAGTCTAAGAC 59.070 38.462 8.95 1.57 37.29 3.01
2244 2501 5.300792 TCGGTTTTAATCTCAAGGCAAACTT 59.699 36.000 0.00 0.00 41.00 2.66
2265 2522 5.977635 TCTATTGAGTATATGGCCAATCGG 58.022 41.667 10.96 0.00 32.28 4.18
2266 2523 7.495901 AGATCTATTGAGTATATGGCCAATCG 58.504 38.462 10.96 0.00 32.28 3.34
2270 2527 8.762645 CCTTTAGATCTATTGAGTATATGGCCA 58.237 37.037 8.56 8.56 0.00 5.36
2272 2529 9.593134 CACCTTTAGATCTATTGAGTATATGGC 57.407 37.037 2.58 0.00 0.00 4.40
2372 2936 1.985159 AGATGTGCCCTAAACAGACCA 59.015 47.619 0.00 0.00 0.00 4.02
2469 3039 7.740519 AAAAATATGCTAAGATTCGTGCAAC 57.259 32.000 0.00 0.00 38.96 4.17
2498 3068 8.713708 ATTCTGCCTTCTATAAAGCTACTCTA 57.286 34.615 0.00 0.00 0.00 2.43
2511 3081 8.306313 TCTTGTAACTGATATTCTGCCTTCTA 57.694 34.615 0.00 0.00 0.00 2.10
2512 3082 7.187824 TCTTGTAACTGATATTCTGCCTTCT 57.812 36.000 0.00 0.00 0.00 2.85
2521 3095 8.540492 CGAGCGTAATTTCTTGTAACTGATATT 58.460 33.333 0.00 0.00 0.00 1.28
2547 3121 1.325943 GCTACTCTCATTGTTCGCAGC 59.674 52.381 0.00 0.00 0.00 5.25
2552 3126 5.237344 AGTGTTTGTGCTACTCTCATTGTTC 59.763 40.000 0.00 0.00 0.00 3.18
2558 3132 3.819564 ACAGTGTTTGTGCTACTCTCA 57.180 42.857 0.00 0.00 38.99 3.27
2615 3191 0.106015 AGCTGGGTGAAGCCAAACTT 60.106 50.000 2.40 0.00 44.68 2.66
2677 3261 3.838565 TGTTTATGTCCCATGTGGTGTT 58.161 40.909 0.00 0.00 34.77 3.32
2718 3310 4.570772 TGTCTGGAGTTTGTTTTCTTCTCG 59.429 41.667 0.00 0.00 0.00 4.04
2735 3327 1.279496 TTCACAGGGAGGATGTCTGG 58.721 55.000 0.00 0.00 33.19 3.86
3013 3605 0.663568 AAGCTTCAGTTCCGACGTCG 60.664 55.000 30.33 30.33 39.44 5.12
3224 3816 0.040058 TGGTGCTGATTTGGAGCCAT 59.960 50.000 0.00 0.00 35.43 4.40
3393 3991 0.385473 CTTTGTTAACCGCGGCACAG 60.385 55.000 28.58 13.63 0.00 3.66
3436 4034 1.888512 GGCATGAAACCTCTTTGCAGA 59.111 47.619 0.00 0.00 34.79 4.26
3795 4400 3.574614 CGATTTGGGGTAAAAACTGCAG 58.425 45.455 13.48 13.48 0.00 4.41
3796 4401 2.297597 CCGATTTGGGGTAAAAACTGCA 59.702 45.455 0.00 0.00 0.00 4.41
3797 4402 2.954316 CCGATTTGGGGTAAAAACTGC 58.046 47.619 0.00 0.00 0.00 4.40
3949 4555 2.031683 CGTTTTTGTTCGTCTTCTGCCT 59.968 45.455 0.00 0.00 0.00 4.75
4024 4633 4.305539 TCCTGGAAAGAAGATGAATGCA 57.694 40.909 0.00 0.00 0.00 3.96
4183 4817 2.606587 CCCTAGCCCTGTTGGTGCT 61.607 63.158 0.00 0.00 40.93 4.40
4229 4863 2.418910 ATCTCCCCTCTGTCGCGTG 61.419 63.158 5.77 0.00 0.00 5.34
4234 4868 0.671251 CTACGCATCTCCCCTCTGTC 59.329 60.000 0.00 0.00 0.00 3.51
4237 4871 1.834822 GGCTACGCATCTCCCCTCT 60.835 63.158 0.00 0.00 0.00 3.69
4246 4880 3.432051 GAGCTCCACGGCTACGCAT 62.432 63.158 0.87 0.00 46.04 4.73
4247 4881 4.129737 GAGCTCCACGGCTACGCA 62.130 66.667 0.87 0.00 46.04 5.24
4257 4891 2.433145 CGCTTTCGCAGAGCTCCA 60.433 61.111 10.93 0.00 38.43 3.86
4263 4897 4.082523 CCTCCCCGCTTTCGCAGA 62.083 66.667 0.00 0.00 35.30 4.26
4268 4902 1.443828 CTAGCTCCTCCCCGCTTTC 59.556 63.158 0.00 0.00 37.68 2.62
4269 4903 2.736826 GCTAGCTCCTCCCCGCTTT 61.737 63.158 7.70 0.00 37.68 3.51
4283 4920 3.871395 GCTCCCCCTGCCTGCTAG 61.871 72.222 0.00 0.00 0.00 3.42
4284 4921 3.950861 AAGCTCCCCCTGCCTGCTA 62.951 63.158 0.00 0.00 33.28 3.49
4286 4923 4.811364 GAAGCTCCCCCTGCCTGC 62.811 72.222 0.00 0.00 0.00 4.85
4287 4924 2.430704 TTTGAAGCTCCCCCTGCCTG 62.431 60.000 0.00 0.00 0.00 4.85
4288 4925 1.729267 TTTTGAAGCTCCCCCTGCCT 61.729 55.000 0.00 0.00 0.00 4.75
4289 4926 1.228862 TTTTGAAGCTCCCCCTGCC 60.229 57.895 0.00 0.00 0.00 4.85
4291 4928 0.178964 TGGTTTTGAAGCTCCCCCTG 60.179 55.000 0.00 0.00 0.00 4.45
4292 4929 0.113190 CTGGTTTTGAAGCTCCCCCT 59.887 55.000 0.00 0.00 0.00 4.79
4391 5119 2.094494 TCAGAAGTCAGAACTCGGATGC 60.094 50.000 0.00 0.00 33.48 3.91
4447 5175 5.413309 AGGTCTGAGTTGAGTTGGATTAG 57.587 43.478 0.00 0.00 0.00 1.73
4503 5231 5.564651 GCAACATTACCACTTGCATTGTACT 60.565 40.000 0.00 0.00 40.09 2.73
4504 5232 4.621034 GCAACATTACCACTTGCATTGTAC 59.379 41.667 0.00 0.00 40.09 2.90
4505 5233 4.279420 TGCAACATTACCACTTGCATTGTA 59.721 37.500 0.24 0.00 44.09 2.41
4506 5234 3.069300 TGCAACATTACCACTTGCATTGT 59.931 39.130 0.24 0.00 44.09 2.71
4507 5235 3.651206 TGCAACATTACCACTTGCATTG 58.349 40.909 0.24 0.00 44.09 2.82
4510 5238 4.333913 AATTGCAACATTACCACTTGCA 57.666 36.364 0.00 0.24 46.55 4.08
4511 5239 5.925969 ACTAAATTGCAACATTACCACTTGC 59.074 36.000 0.00 0.00 40.63 4.01
4512 5240 7.867403 AGAACTAAATTGCAACATTACCACTTG 59.133 33.333 0.00 0.00 0.00 3.16
4513 5241 7.867403 CAGAACTAAATTGCAACATTACCACTT 59.133 33.333 0.00 0.00 0.00 3.16
4514 5242 7.370383 CAGAACTAAATTGCAACATTACCACT 58.630 34.615 0.00 0.00 0.00 4.00
4515 5243 6.089417 GCAGAACTAAATTGCAACATTACCAC 59.911 38.462 0.00 0.00 37.75 4.16
4516 5244 6.155827 GCAGAACTAAATTGCAACATTACCA 58.844 36.000 0.00 0.00 37.75 3.25
4517 5245 6.155827 TGCAGAACTAAATTGCAACATTACC 58.844 36.000 0.00 0.00 44.13 2.85
4525 5253 4.050553 GCAGTTTGCAGAACTAAATTGCA 58.949 39.130 12.06 0.00 44.14 4.08
4526 5254 4.635961 GCAGTTTGCAGAACTAAATTGC 57.364 40.909 12.06 6.22 44.26 3.56


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

AutoCloner maintained by Alex Coulton.