Multiple sequence alignment - TraesCS7D01G216000

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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 TraesCS7D01G216000 chr7D 100.000 4216 0 0 1 4216 175919205 175923420 0.000000e+00 7786.0
1 TraesCS7D01G216000 chr7B 90.777 2201 132 36 1 2160 141798793 141800963 0.000000e+00 2874.0
2 TraesCS7D01G216000 chr7B 94.313 1143 35 18 2651 3767 141801478 141802616 0.000000e+00 1724.0
3 TraesCS7D01G216000 chr7B 94.958 357 18 0 2155 2511 141801035 141801391 1.020000e-155 560.0
4 TraesCS7D01G216000 chr7B 94.704 321 14 2 3794 4111 141802613 141802933 2.930000e-136 496.0
5 TraesCS7D01G216000 chr7A 84.009 1332 94 55 2601 3840 178006907 178008211 0.000000e+00 1170.0
6 TraesCS7D01G216000 chr7A 91.345 855 37 9 957 1775 178005022 178005875 0.000000e+00 1134.0
7 TraesCS7D01G216000 chr7A 94.618 353 19 0 2155 2507 178006507 178006859 7.970000e-152 547.0
8 TraesCS7D01G216000 chr7A 92.308 247 19 0 3941 4187 178008422 178008668 6.710000e-93 351.0
9 TraesCS7D01G216000 chr7A 88.732 284 29 3 1880 2160 178006153 178006436 1.120000e-90 344.0
10 TraesCS7D01G216000 chr7A 89.655 87 7 2 1798 1883 178005872 178005957 4.460000e-20 110.0
11 TraesCS7D01G216000 chr1B 91.031 223 16 3 2 221 429583994 429584215 8.860000e-77 298.0
12 TraesCS7D01G216000 chr1B 78.485 330 56 11 1661 1978 328140696 328141022 7.150000e-48 202.0
13 TraesCS7D01G216000 chr1B 88.350 103 9 3 750 850 45007804 45007703 2.060000e-23 121.0
14 TraesCS7D01G216000 chr2A 90.909 220 18 2 1 218 706751158 706751377 1.150000e-75 294.0
15 TraesCS7D01G216000 chr1A 90.583 223 18 2 2 221 398448440 398448662 4.120000e-75 292.0
16 TraesCS7D01G216000 chr1D 90.541 222 18 2 3 221 317427327 317427548 1.480000e-74 291.0
17 TraesCS7D01G216000 chr1D 78.133 375 59 16 1663 2026 228827109 228827471 2.550000e-52 217.0
18 TraesCS7D01G216000 chr1D 76.170 235 42 10 1719 1946 385603261 385603488 1.240000e-20 111.0
19 TraesCS7D01G216000 chr3D 89.778 225 20 2 1 222 375211019 375211243 6.900000e-73 285.0
20 TraesCS7D01G216000 chr3D 85.926 135 13 4 690 822 421735562 421735692 5.680000e-29 139.0
21 TraesCS7D01G216000 chr3D 76.256 219 42 7 1703 1914 121978643 121978428 1.600000e-19 108.0
22 TraesCS7D01G216000 chr3B 89.381 226 20 3 1 222 489361593 489361818 8.920000e-72 281.0
23 TraesCS7D01G216000 chr3B 88.235 136 9 5 690 822 549436687 549436818 5.640000e-34 156.0
24 TraesCS7D01G216000 chr3A 89.333 225 21 2 1 222 498246848 498247072 3.210000e-71 279.0
25 TraesCS7D01G216000 chr2B 89.202 213 22 1 7 218 679896586 679896798 8.990000e-67 265.0
26 TraesCS7D01G216000 chr2D 80.586 273 45 6 1750 2017 584461941 584461672 1.990000e-48 204.0
27 TraesCS7D01G216000 chr2D 77.982 327 57 12 1661 1975 593855053 593854730 1.550000e-44 191.0
28 TraesCS7D01G216000 chr6D 78.423 241 31 14 1684 1913 468348137 468348367 2.040000e-28 137.0
29 TraesCS7D01G216000 chr6B 89.320 103 8 3 750 850 405754349 405754248 4.430000e-25 126.0
30 TraesCS7D01G216000 chr6B 89.320 103 8 3 750 850 405799746 405799645 4.430000e-25 126.0
31 TraesCS7D01G216000 chrUn 88.350 103 9 3 750 850 219171335 219171436 2.060000e-23 121.0
32 TraesCS7D01G216000 chrUn 88.350 103 9 3 750 850 224097050 224096949 2.060000e-23 121.0
33 TraesCS7D01G216000 chr4B 88.350 103 9 3 750 850 121557340 121557441 2.060000e-23 121.0
34 TraesCS7D01G216000 chr5B 77.833 203 34 9 1806 2003 656452823 656452627 9.580000e-22 115.0
35 TraesCS7D01G216000 chr5D 88.095 84 6 2 1720 1800 220694727 220694809 3.470000e-16 97.1
36 TraesCS7D01G216000 chr5D 83.908 87 10 3 1921 2005 220694925 220695009 3.490000e-11 80.5
37 TraesCS7D01G216000 chr5A 84.884 86 8 4 1921 2005 295085814 295085895 9.720000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G216000 chr7D 175919205 175923420 4215 False 7786.000000 7786 100.000000 1 4216 1 chr7D.!!$F1 4215
1 TraesCS7D01G216000 chr7B 141798793 141802933 4140 False 1413.500000 2874 93.688000 1 4111 4 chr7B.!!$F1 4110
2 TraesCS7D01G216000 chr7A 178005022 178008668 3646 False 609.333333 1170 90.111167 957 4187 6 chr7A.!!$F1 3230

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
918 921 0.040067 CTGCCAACAAAGAACCGCTC 60.040 55.0 0.0 0.0 0.0 5.03 F
1036 1039 0.105760 ACCGATCTGCCTCCATCTCT 60.106 55.0 0.0 0.0 0.0 3.10 F
2562 2882 0.038599 ATGATGTGCTGCTGGTTGGA 59.961 50.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1817 0.323629 CGTGTGTCTACCCCCACATT 59.676 55.0 0.00 0.00 42.95 2.71 R
2585 2905 0.681733 AGCTGGCTACCATACGGATG 59.318 55.0 0.00 0.00 35.59 3.51 R
3780 4189 0.108804 CAGGCTCCATTTTGCAGCTG 60.109 55.0 10.11 10.11 33.38 4.24 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
117 118 5.614308 TGCCTGTAAGACCATATTGATCTG 58.386 41.667 0.00 0.00 34.07 2.90
120 121 6.543831 GCCTGTAAGACCATATTGATCTGTTT 59.456 38.462 0.00 0.00 34.07 2.83
158 159 8.764287 GGTAAATTAATTAGAATGTTGGCATGC 58.236 33.333 9.90 9.90 35.15 4.06
218 219 5.415701 TGTTTTGAAATCCTAGATCAGCCAC 59.584 40.000 0.00 0.00 0.00 5.01
234 235 0.254178 CCACTGGAAGCACTAGCCAT 59.746 55.000 0.00 0.00 43.56 4.40
275 276 3.782889 TCATCACATCCGACTAGTGTG 57.217 47.619 0.00 1.63 43.41 3.82
439 440 6.658816 AGATGCATAGTTGTTGGATGTGTAAA 59.341 34.615 0.00 0.00 0.00 2.01
493 494 6.682423 TGTTAGATGCATAGTTGTTGGATG 57.318 37.500 0.00 0.00 0.00 3.51
495 496 6.093909 TGTTAGATGCATAGTTGTTGGATGTG 59.906 38.462 0.00 0.00 0.00 3.21
505 506 5.680619 AGTTGTTGGATGTGTTACAGAAGA 58.319 37.500 0.00 0.00 0.00 2.87
515 516 8.616076 GGATGTGTTACAGAAGATTTATTCAGG 58.384 37.037 0.00 0.00 0.00 3.86
535 536 8.792830 TTCAGGTGGGTATGAAGTAGTATAAT 57.207 34.615 0.00 0.00 31.93 1.28
594 595 7.517614 TCAGTTGTTTACAAAGCATATTGGA 57.482 32.000 0.00 0.00 37.63 3.53
654 657 8.841444 AATTTTATAAAGCATAGTGACTTGCG 57.159 30.769 11.91 0.00 43.61 4.85
781 784 3.269592 TCTTCTCCCAGGTTGAAGGTA 57.730 47.619 14.98 0.00 38.10 3.08
789 792 4.352595 TCCCAGGTTGAAGGTAATTCTTGA 59.647 41.667 0.00 0.00 38.83 3.02
830 833 8.801715 AAAAATTACTGCTGTCTTGTTGTATG 57.198 30.769 0.00 0.00 0.00 2.39
831 834 6.500684 AATTACTGCTGTCTTGTTGTATGG 57.499 37.500 0.00 0.00 0.00 2.74
843 846 5.360429 TCTTGTTGTATGGCATGCATGTTAT 59.640 36.000 26.79 21.58 0.00 1.89
882 885 6.715347 AGATATTTTTCCCATGCTTGGTAC 57.285 37.500 16.81 0.00 41.91 3.34
900 903 1.394151 CCTCCCCCAGGTTCTCTCT 59.606 63.158 0.00 0.00 37.53 3.10
909 912 2.575532 CAGGTTCTCTCTGCCAACAAA 58.424 47.619 0.00 0.00 0.00 2.83
915 918 1.532868 CTCTCTGCCAACAAAGAACCG 59.467 52.381 0.00 0.00 0.00 4.44
918 921 0.040067 CTGCCAACAAAGAACCGCTC 60.040 55.000 0.00 0.00 0.00 5.03
922 925 1.227853 AACAAAGAACCGCTCCGCT 60.228 52.632 0.00 0.00 0.00 5.52
931 934 1.364171 CCGCTCCGCTGCTATACTT 59.636 57.895 0.00 0.00 0.00 2.24
932 935 0.941463 CCGCTCCGCTGCTATACTTG 60.941 60.000 0.00 0.00 0.00 3.16
952 955 1.620822 CTTGGACCCCTTGTTTCTGG 58.379 55.000 0.00 0.00 0.00 3.86
963 966 2.041115 GTTTCTGGGGCTTCCTCGC 61.041 63.158 0.00 0.00 36.20 5.03
1032 1035 2.502492 CGGACCGATCTGCCTCCAT 61.502 63.158 8.64 0.00 0.00 3.41
1036 1039 0.105760 ACCGATCTGCCTCCATCTCT 60.106 55.000 0.00 0.00 0.00 3.10
1044 1047 0.761802 GCCTCCATCTCTCCGGAATT 59.238 55.000 5.23 0.00 0.00 2.17
1110 1113 2.037367 ACCTGCTCTACCTCCGCA 59.963 61.111 0.00 0.00 0.00 5.69
1151 1154 3.891366 CACCACAATCTTGGAACCTTTCT 59.109 43.478 0.00 0.00 39.24 2.52
1162 1165 3.333381 TGGAACCTTTCTGGATTCCATCA 59.667 43.478 5.70 0.00 43.95 3.07
1200 1203 1.227674 CCTATCGAACCAGGCAGGC 60.228 63.158 0.00 0.00 43.14 4.85
1215 1218 3.589881 GGCGGTGATGGCAGCATC 61.590 66.667 9.36 7.51 42.53 3.91
1308 1311 1.067212 GTTGATCCTGCGGTCGACTAT 59.933 52.381 16.46 0.00 0.00 2.12
1364 1367 4.342092 CCTGAACCTTCCATCTTTTGTTGT 59.658 41.667 0.00 0.00 0.00 3.32
1383 1386 1.039068 TGTGTTTGTGGGCAATCAGG 58.961 50.000 0.00 0.00 35.66 3.86
1425 1428 3.492011 GTGTCTTTTGCTGAATTTGCTGG 59.508 43.478 6.07 0.00 0.00 4.85
1437 1440 6.969473 GCTGAATTTGCTGGTATTCTAGTTTC 59.031 38.462 0.00 0.00 33.08 2.78
1483 1486 3.691118 GTGAGAAAATGCTGCATCTGGTA 59.309 43.478 16.55 0.00 0.00 3.25
1517 1538 2.602878 CACACCTGAATTTGCTGCATC 58.397 47.619 1.84 0.00 0.00 3.91
1527 1548 6.270064 TGAATTTGCTGCATCATGATGTTAG 58.730 36.000 31.09 27.81 40.80 2.34
1528 1549 3.703286 TTGCTGCATCATGATGTTAGC 57.297 42.857 35.17 35.17 44.09 3.09
1529 1550 1.951602 TGCTGCATCATGATGTTAGCC 59.048 47.619 36.56 27.27 43.66 3.93
1532 1553 3.436015 GCTGCATCATGATGTTAGCCTAG 59.564 47.826 33.65 22.48 41.16 3.02
1534 1555 5.039920 TGCATCATGATGTTAGCCTAGTT 57.960 39.130 31.09 0.00 40.80 2.24
1535 1556 6.173427 TGCATCATGATGTTAGCCTAGTTA 57.827 37.500 31.09 2.94 40.80 2.24
1536 1557 6.226052 TGCATCATGATGTTAGCCTAGTTAG 58.774 40.000 31.09 6.55 40.80 2.34
1591 1626 5.129155 AGCAAGCAAAATAATAAGGCATGGA 59.871 36.000 0.00 0.00 0.00 3.41
1597 1632 5.535753 AAATAATAAGGCATGGAACTGGC 57.464 39.130 0.00 0.00 41.74 4.85
1620 1655 5.400485 GCTGATGAATGAACTTTTGTGTGTC 59.600 40.000 0.00 0.00 0.00 3.67
1623 1658 2.383298 ATGAACTTTTGTGTGTCGCG 57.617 45.000 0.00 0.00 0.00 5.87
1631 1666 0.522286 TTGTGTGTCGCGCAACTTTG 60.522 50.000 8.75 0.00 42.05 2.77
1658 1696 7.790027 ACCTATGATAACTGGATGCATATCTC 58.210 38.462 0.00 0.00 33.68 2.75
1670 1708 6.183361 TGGATGCATATCTCCTGTTGGAATTA 60.183 38.462 0.00 0.00 42.66 1.40
1771 1812 2.022918 ACACTTGTATCCTAGGCCTCCT 60.023 50.000 9.68 0.00 37.71 3.69
1772 1813 3.206866 ACACTTGTATCCTAGGCCTCCTA 59.793 47.826 9.68 0.00 34.61 2.94
1773 1814 4.140663 ACACTTGTATCCTAGGCCTCCTAT 60.141 45.833 9.68 3.36 35.36 2.57
1774 1815 5.076039 ACACTTGTATCCTAGGCCTCCTATA 59.924 44.000 9.68 2.22 35.36 1.31
1775 1816 6.198639 CACTTGTATCCTAGGCCTCCTATAT 58.801 44.000 9.68 0.00 35.36 0.86
1776 1817 7.036059 ACACTTGTATCCTAGGCCTCCTATATA 60.036 40.741 9.68 0.71 35.36 0.86
1777 1818 7.839705 CACTTGTATCCTAGGCCTCCTATATAA 59.160 40.741 9.68 9.10 35.36 0.98
1778 1819 8.579259 ACTTGTATCCTAGGCCTCCTATATAAT 58.421 37.037 9.68 0.00 35.36 1.28
1779 1820 8.783660 TTGTATCCTAGGCCTCCTATATAATG 57.216 38.462 9.68 0.00 35.36 1.90
1780 1821 7.894561 TGTATCCTAGGCCTCCTATATAATGT 58.105 38.462 9.68 0.00 35.36 2.71
1781 1822 7.785028 TGTATCCTAGGCCTCCTATATAATGTG 59.215 40.741 9.68 0.00 35.36 3.21
1782 1823 5.529289 TCCTAGGCCTCCTATATAATGTGG 58.471 45.833 9.68 0.00 35.36 4.17
1783 1824 4.656112 CCTAGGCCTCCTATATAATGTGGG 59.344 50.000 9.68 0.00 35.36 4.61
1784 1825 3.464828 AGGCCTCCTATATAATGTGGGG 58.535 50.000 0.00 0.00 28.47 4.96
1785 1826 2.509964 GGCCTCCTATATAATGTGGGGG 59.490 54.545 0.00 0.98 42.97 5.40
1786 1827 3.190439 GCCTCCTATATAATGTGGGGGT 58.810 50.000 6.54 0.00 42.12 4.95
1787 1828 4.368067 GCCTCCTATATAATGTGGGGGTA 58.632 47.826 6.54 0.00 42.12 3.69
1788 1829 4.409247 GCCTCCTATATAATGTGGGGGTAG 59.591 50.000 6.54 0.00 42.12 3.18
1789 1830 5.816739 GCCTCCTATATAATGTGGGGGTAGA 60.817 48.000 6.54 0.00 42.12 2.59
1790 1831 5.661759 CCTCCTATATAATGTGGGGGTAGAC 59.338 48.000 0.00 0.00 35.54 2.59
1791 1832 6.235765 TCCTATATAATGTGGGGGTAGACA 57.764 41.667 0.00 0.00 0.00 3.41
1792 1833 6.021030 TCCTATATAATGTGGGGGTAGACAC 58.979 44.000 0.00 0.00 38.08 3.67
1795 1836 3.462169 TGTGGGGGTAGACACACG 58.538 61.111 0.00 0.00 42.20 4.49
1796 1837 1.152504 TGTGGGGGTAGACACACGA 60.153 57.895 0.00 0.00 42.20 4.35
1827 1868 4.981806 TGCCAAAATAATAGCACAGGTC 57.018 40.909 0.00 0.00 0.00 3.85
1880 1922 2.112928 TCTGGTGTGCGGCATTGT 59.887 55.556 5.72 0.00 0.00 2.71
1883 2123 0.955428 CTGGTGTGCGGCATTGTAGT 60.955 55.000 5.72 0.00 0.00 2.73
1891 2131 1.518325 CGGCATTGTAGTGGTGTCAA 58.482 50.000 0.00 0.00 0.00 3.18
1904 2144 3.692406 GTCAACGGGGAGGAGCGT 61.692 66.667 0.00 0.00 0.00 5.07
1914 2154 1.428620 GAGGAGCGTCCGTAGTCAC 59.571 63.158 0.00 0.00 42.75 3.67
1949 2190 0.859232 CGAGTTCGGTGAACCTTGTG 59.141 55.000 6.09 0.00 42.85 3.33
1983 2224 1.227999 CCGTGCCTCGTGTGTGATTT 61.228 55.000 0.00 0.00 37.94 2.17
2005 2246 3.760151 TCTTGTCCTCGGAAAATCGACTA 59.240 43.478 0.00 0.00 35.18 2.59
2008 2249 2.795470 GTCCTCGGAAAATCGACTATGC 59.205 50.000 0.00 0.00 35.18 3.14
2021 2263 2.089121 CGACTATGCGATCGGATTTTCG 59.911 50.000 27.29 26.64 38.37 3.46
2080 2323 9.719355 CCTGTAATGCTACAATATTGTACCATA 57.281 33.333 25.97 15.59 38.39 2.74
2086 2329 8.690203 TGCTACAATATTGTACCATATGCTTT 57.310 30.769 21.73 0.00 42.35 3.51
2104 2347 5.316167 TGCTTTATCTCAACCATCACTTGT 58.684 37.500 0.00 0.00 0.00 3.16
2108 2351 7.362401 GCTTTATCTCAACCATCACTTGTTCAT 60.362 37.037 0.00 0.00 0.00 2.57
2123 2366 9.154847 TCACTTGTTCATGTCTTAGTAATCATG 57.845 33.333 15.90 15.90 38.96 3.07
2218 2538 6.047231 CGTAAAGGATACCAACTTAGAAGGG 58.953 44.000 0.00 0.00 37.17 3.95
2286 2606 7.286546 TCATTCTAAATCAGAGGTAGAGACTGG 59.713 40.741 0.00 0.00 33.83 4.00
2304 2624 4.662278 ACTGGCATCCTTAGCAAAAGTTA 58.338 39.130 0.00 0.00 0.00 2.24
2305 2625 4.459337 ACTGGCATCCTTAGCAAAAGTTAC 59.541 41.667 0.00 0.00 0.00 2.50
2363 2683 7.994911 TCTTTTGATATGGCTTATGTCTCATGT 59.005 33.333 0.00 0.00 0.00 3.21
2386 2706 2.777832 AAGAGAGAGATTTTGCGGCT 57.222 45.000 0.00 0.00 0.00 5.52
2464 2784 3.824443 GGGCATTGTACTTGGTAAGTTGT 59.176 43.478 0.00 0.00 42.81 3.32
2467 2787 5.240844 GGCATTGTACTTGGTAAGTTGTTCT 59.759 40.000 0.00 0.00 42.81 3.01
2474 2794 6.736110 ACTTGGTAAGTTGTTCTAGTGGTA 57.264 37.500 0.00 0.00 39.04 3.25
2477 2797 8.215736 ACTTGGTAAGTTGTTCTAGTGGTATTT 58.784 33.333 0.00 0.00 39.04 1.40
2497 2817 5.452078 TTTTTAAGTTCCACTGATGCAGG 57.548 39.130 0.00 0.00 35.51 4.85
2498 2818 2.113860 TAAGTTCCACTGATGCAGGC 57.886 50.000 0.00 0.00 35.51 4.85
2507 2827 0.806868 CTGATGCAGGCGTGTTCAAT 59.193 50.000 8.40 0.00 0.00 2.57
2511 2831 0.804364 TGCAGGCGTGTTCAATCATC 59.196 50.000 8.40 0.00 0.00 2.92
2512 2832 0.099436 GCAGGCGTGTTCAATCATCC 59.901 55.000 8.40 0.00 0.00 3.51
2513 2833 1.742761 CAGGCGTGTTCAATCATCCT 58.257 50.000 0.00 0.00 0.00 3.24
2514 2834 1.399440 CAGGCGTGTTCAATCATCCTG 59.601 52.381 0.00 0.00 35.95 3.86
2515 2835 1.278985 AGGCGTGTTCAATCATCCTGA 59.721 47.619 0.00 0.00 0.00 3.86
2516 2836 2.092753 AGGCGTGTTCAATCATCCTGAT 60.093 45.455 0.00 0.00 39.09 2.90
2517 2837 3.134623 AGGCGTGTTCAATCATCCTGATA 59.865 43.478 0.00 0.00 35.76 2.15
2518 2838 4.067896 GGCGTGTTCAATCATCCTGATAT 58.932 43.478 0.00 0.00 35.76 1.63
2519 2839 4.516698 GGCGTGTTCAATCATCCTGATATT 59.483 41.667 0.00 0.00 35.76 1.28
2520 2840 5.009010 GGCGTGTTCAATCATCCTGATATTT 59.991 40.000 0.00 0.00 35.76 1.40
2521 2841 6.138761 GCGTGTTCAATCATCCTGATATTTC 58.861 40.000 0.00 0.00 35.76 2.17
2522 2842 6.017605 GCGTGTTCAATCATCCTGATATTTCT 60.018 38.462 0.00 0.00 35.76 2.52
2523 2843 7.467811 GCGTGTTCAATCATCCTGATATTTCTT 60.468 37.037 0.00 0.00 35.76 2.52
2524 2844 8.400947 CGTGTTCAATCATCCTGATATTTCTTT 58.599 33.333 0.00 0.00 35.76 2.52
2536 2856 9.046296 TCCTGATATTTCTTTTTAATCGAGCTC 57.954 33.333 2.73 2.73 0.00 4.09
2552 2872 3.388308 GAGCTCGATGTAATGATGTGCT 58.612 45.455 0.00 0.00 32.67 4.40
2554 2874 2.349249 GCTCGATGTAATGATGTGCTGC 60.349 50.000 0.00 0.00 0.00 5.25
2562 2882 0.038599 ATGATGTGCTGCTGGTTGGA 59.961 50.000 0.00 0.00 0.00 3.53
2566 2886 2.203337 TGCTGCTGGTTGGACCAC 60.203 61.111 0.00 0.00 44.79 4.16
2572 2892 3.868200 CTGGTTGGACCACCCCAGC 62.868 68.421 21.05 6.34 44.79 4.85
2574 2894 3.580319 GTTGGACCACCCCAGCCT 61.580 66.667 0.00 0.00 37.53 4.58
2575 2895 2.208640 TTGGACCACCCCAGCCTA 59.791 61.111 0.00 0.00 37.53 3.93
2576 2896 1.923395 TTGGACCACCCCAGCCTAG 60.923 63.158 0.00 0.00 37.53 3.02
2577 2897 2.040606 GGACCACCCCAGCCTAGA 59.959 66.667 0.00 0.00 0.00 2.43
2578 2898 1.615424 GGACCACCCCAGCCTAGAA 60.615 63.158 0.00 0.00 0.00 2.10
2579 2899 0.988678 GGACCACCCCAGCCTAGAAT 60.989 60.000 0.00 0.00 0.00 2.40
2580 2900 1.694693 GGACCACCCCAGCCTAGAATA 60.695 57.143 0.00 0.00 0.00 1.75
2581 2901 2.124411 GACCACCCCAGCCTAGAATAA 58.876 52.381 0.00 0.00 0.00 1.40
2582 2902 2.508300 GACCACCCCAGCCTAGAATAAA 59.492 50.000 0.00 0.00 0.00 1.40
2583 2903 2.923629 ACCACCCCAGCCTAGAATAAAA 59.076 45.455 0.00 0.00 0.00 1.52
2584 2904 3.288092 CCACCCCAGCCTAGAATAAAAC 58.712 50.000 0.00 0.00 0.00 2.43
2585 2905 3.288092 CACCCCAGCCTAGAATAAAACC 58.712 50.000 0.00 0.00 0.00 3.27
2586 2906 2.923629 ACCCCAGCCTAGAATAAAACCA 59.076 45.455 0.00 0.00 0.00 3.67
2587 2907 3.531814 ACCCCAGCCTAGAATAAAACCAT 59.468 43.478 0.00 0.00 0.00 3.55
2588 2908 4.145052 CCCCAGCCTAGAATAAAACCATC 58.855 47.826 0.00 0.00 0.00 3.51
2589 2909 4.145052 CCCAGCCTAGAATAAAACCATCC 58.855 47.826 0.00 0.00 0.00 3.51
2590 2910 3.815401 CCAGCCTAGAATAAAACCATCCG 59.185 47.826 0.00 0.00 0.00 4.18
2591 2911 4.451900 CAGCCTAGAATAAAACCATCCGT 58.548 43.478 0.00 0.00 0.00 4.69
2592 2912 5.454187 CCAGCCTAGAATAAAACCATCCGTA 60.454 44.000 0.00 0.00 0.00 4.02
2593 2913 6.231211 CAGCCTAGAATAAAACCATCCGTAT 58.769 40.000 0.00 0.00 0.00 3.06
2594 2914 6.147821 CAGCCTAGAATAAAACCATCCGTATG 59.852 42.308 0.00 0.00 0.00 2.39
2605 2925 1.070758 CATCCGTATGGTAGCCAGCTT 59.929 52.381 0.00 0.00 36.75 3.74
2608 2928 2.026636 TCCGTATGGTAGCCAGCTTTTT 60.027 45.455 0.00 0.00 36.75 1.94
2631 2951 9.871175 TTTTTGGTTATAGGGAGTTCTTACTTT 57.129 29.630 0.00 0.00 33.84 2.66
2632 2952 9.871175 TTTTGGTTATAGGGAGTTCTTACTTTT 57.129 29.630 0.00 0.00 33.84 2.27
2633 2953 8.857694 TTGGTTATAGGGAGTTCTTACTTTTG 57.142 34.615 0.00 0.00 33.84 2.44
2634 2954 6.882678 TGGTTATAGGGAGTTCTTACTTTTGC 59.117 38.462 0.00 0.00 33.84 3.68
2635 2955 6.318144 GGTTATAGGGAGTTCTTACTTTTGCC 59.682 42.308 0.00 0.00 33.84 4.52
2636 2956 2.779506 AGGGAGTTCTTACTTTTGCCG 58.220 47.619 0.00 0.00 33.84 5.69
2637 2957 2.370849 AGGGAGTTCTTACTTTTGCCGA 59.629 45.455 0.00 0.00 33.84 5.54
2638 2958 2.483106 GGGAGTTCTTACTTTTGCCGAC 59.517 50.000 0.00 0.00 33.84 4.79
2639 2959 3.400255 GGAGTTCTTACTTTTGCCGACT 58.600 45.455 0.00 0.00 33.84 4.18
2640 2960 3.813724 GGAGTTCTTACTTTTGCCGACTT 59.186 43.478 0.00 0.00 33.84 3.01
2641 2961 4.992951 GGAGTTCTTACTTTTGCCGACTTA 59.007 41.667 0.00 0.00 33.84 2.24
2644 2964 7.332678 GGAGTTCTTACTTTTGCCGACTTATAA 59.667 37.037 0.00 0.00 33.84 0.98
2782 3102 6.708285 TCCAGAACTTCTTATGGAGGTAAAC 58.292 40.000 0.00 0.00 41.91 2.01
2783 3103 6.271391 TCCAGAACTTCTTATGGAGGTAAACA 59.729 38.462 0.00 0.00 41.91 2.83
2785 3105 7.611855 CCAGAACTTCTTATGGAGGTAAACAAT 59.388 37.037 0.00 0.00 40.74 2.71
2786 3106 8.669243 CAGAACTTCTTATGGAGGTAAACAATC 58.331 37.037 0.00 0.00 32.93 2.67
2787 3107 8.606830 AGAACTTCTTATGGAGGTAAACAATCT 58.393 33.333 0.00 0.00 32.93 2.40
2788 3108 8.794335 AACTTCTTATGGAGGTAAACAATCTC 57.206 34.615 0.00 0.00 32.93 2.75
2790 3110 7.182930 ACTTCTTATGGAGGTAAACAATCTCCT 59.817 37.037 5.93 0.00 45.36 3.69
2815 3138 1.585297 GCTTTTGCATGCAACCAACT 58.415 45.000 31.99 0.00 46.58 3.16
2824 3148 4.463539 TGCATGCAACCAACTAAATCATCT 59.536 37.500 20.30 0.00 0.00 2.90
2831 3155 8.677300 TGCAACCAACTAAATCATCTAATTCTC 58.323 33.333 0.00 0.00 0.00 2.87
2832 3156 8.897752 GCAACCAACTAAATCATCTAATTCTCT 58.102 33.333 0.00 0.00 0.00 3.10
2865 3206 9.807649 ATAACTGCAAGAATTAATCATTTCACC 57.192 29.630 0.00 0.00 37.43 4.02
2868 3215 6.632909 TGCAAGAATTAATCATTTCACCAGG 58.367 36.000 0.00 0.00 0.00 4.45
2886 3233 6.157820 TCACCAGGAAATATATCTCACCACAA 59.842 38.462 0.00 0.00 0.00 3.33
2894 3241 8.899427 AAATATATCTCACCACAAGATCACTG 57.101 34.615 0.00 0.00 35.20 3.66
3315 3663 1.977854 AGTCTGGTGGCTGACATGTTA 59.022 47.619 0.00 0.00 35.81 2.41
3682 4091 4.722700 GAGCCCGAAAGCCTGGCA 62.723 66.667 22.65 0.00 46.29 4.92
3744 4153 2.034685 GCTCCAAAACCTGACCTGAAAC 59.965 50.000 0.00 0.00 0.00 2.78
3763 4172 1.709147 CGCTGGAAGATTGAAGCCCG 61.709 60.000 0.00 0.00 34.07 6.13
3764 4173 0.392998 GCTGGAAGATTGAAGCCCGA 60.393 55.000 0.00 0.00 34.07 5.14
3765 4174 1.661341 CTGGAAGATTGAAGCCCGAG 58.339 55.000 0.00 0.00 34.07 4.63
3766 4175 0.392998 TGGAAGATTGAAGCCCGAGC 60.393 55.000 0.00 0.00 40.32 5.03
3767 4176 4.639051 CTGGAAGATTGAAGCCCGAGCT 62.639 54.545 0.00 0.00 46.59 4.09
3776 4185 2.282180 GCCCGAGCTTGTCCCAAA 60.282 61.111 0.00 0.00 35.50 3.28
3777 4186 1.678970 GCCCGAGCTTGTCCCAAAT 60.679 57.895 0.00 0.00 35.50 2.32
3778 4187 1.250840 GCCCGAGCTTGTCCCAAATT 61.251 55.000 0.00 0.00 35.50 1.82
3779 4188 1.256812 CCCGAGCTTGTCCCAAATTT 58.743 50.000 0.00 0.00 0.00 1.82
3780 4189 1.202348 CCCGAGCTTGTCCCAAATTTC 59.798 52.381 0.00 0.00 0.00 2.17
3781 4190 1.885887 CCGAGCTTGTCCCAAATTTCA 59.114 47.619 0.00 0.00 0.00 2.69
3782 4191 2.095059 CCGAGCTTGTCCCAAATTTCAG 60.095 50.000 0.00 0.00 0.00 3.02
3783 4192 2.669391 CGAGCTTGTCCCAAATTTCAGC 60.669 50.000 0.00 0.00 0.00 4.26
3784 4193 2.560105 GAGCTTGTCCCAAATTTCAGCT 59.440 45.455 0.00 0.00 0.00 4.24
3785 4194 2.298163 AGCTTGTCCCAAATTTCAGCTG 59.702 45.455 7.63 7.63 0.00 4.24
3786 4195 2.680577 CTTGTCCCAAATTTCAGCTGC 58.319 47.619 9.47 0.00 0.00 5.25
3787 4196 1.702182 TGTCCCAAATTTCAGCTGCA 58.298 45.000 9.47 0.00 0.00 4.41
3788 4197 2.037901 TGTCCCAAATTTCAGCTGCAA 58.962 42.857 9.47 4.65 0.00 4.08
3789 4198 2.433604 TGTCCCAAATTTCAGCTGCAAA 59.566 40.909 9.47 11.01 0.00 3.68
3790 4199 3.118482 TGTCCCAAATTTCAGCTGCAAAA 60.118 39.130 9.47 5.89 0.00 2.44
3791 4200 4.067192 GTCCCAAATTTCAGCTGCAAAAT 58.933 39.130 9.47 8.22 0.00 1.82
3792 4201 4.066490 TCCCAAATTTCAGCTGCAAAATG 58.934 39.130 9.47 8.08 0.00 2.32
3806 4250 1.619807 AAAATGGAGCCTGGGCATGC 61.620 55.000 9.90 9.90 44.88 4.06
3893 4360 4.749099 GGTGATCACTGCAAGATCTATCAC 59.251 45.833 24.50 18.26 41.85 3.06
3953 4514 4.202441 AGAACAATGCGCCATTAGAGATT 58.798 39.130 4.18 0.00 32.35 2.40
3965 4528 7.750903 GCGCCATTAGAGATTAATTGGATTTAC 59.249 37.037 0.00 0.00 0.00 2.01
4111 4675 5.461526 TGTGACTTCTGTGAAGACTTATCG 58.538 41.667 13.42 0.00 0.00 2.92
4119 4683 7.450124 TCTGTGAAGACTTATCGAGTACTTT 57.550 36.000 0.00 0.00 39.19 2.66
4127 4691 7.484975 AGACTTATCGAGTACTTTCATTCCAG 58.515 38.462 0.00 0.00 39.19 3.86
4183 4747 6.624352 TCCTTTTGAGAATTGTGTCTTCTG 57.376 37.500 0.00 0.00 33.18 3.02
4187 4751 3.405831 TGAGAATTGTGTCTTCTGGCTG 58.594 45.455 0.00 0.00 33.18 4.85
4188 4752 2.746362 GAGAATTGTGTCTTCTGGCTGG 59.254 50.000 0.00 0.00 33.18 4.85
4189 4753 2.373169 AGAATTGTGTCTTCTGGCTGGA 59.627 45.455 0.00 0.00 31.84 3.86
4190 4754 2.957402 ATTGTGTCTTCTGGCTGGAA 57.043 45.000 0.00 0.00 0.00 3.53
4191 4755 2.727123 TTGTGTCTTCTGGCTGGAAA 57.273 45.000 0.00 0.00 0.00 3.13
4192 4756 2.957402 TGTGTCTTCTGGCTGGAAAT 57.043 45.000 0.00 0.00 0.00 2.17
4193 4757 4.365514 TTGTGTCTTCTGGCTGGAAATA 57.634 40.909 0.00 0.00 0.00 1.40
4194 4758 3.674997 TGTGTCTTCTGGCTGGAAATAC 58.325 45.455 0.00 0.00 0.00 1.89
4195 4759 3.072330 TGTGTCTTCTGGCTGGAAATACA 59.928 43.478 0.00 0.00 0.00 2.29
4196 4760 3.437049 GTGTCTTCTGGCTGGAAATACAC 59.563 47.826 15.49 15.49 36.24 2.90
4197 4761 3.010420 GTCTTCTGGCTGGAAATACACC 58.990 50.000 0.00 0.00 0.00 4.16
4198 4762 2.026262 TCTTCTGGCTGGAAATACACCC 60.026 50.000 0.00 0.00 0.00 4.61
4199 4763 0.623723 TCTGGCTGGAAATACACCCC 59.376 55.000 0.00 0.00 0.00 4.95
4200 4764 0.748005 CTGGCTGGAAATACACCCCG 60.748 60.000 0.00 0.00 0.00 5.73
4201 4765 1.301954 GGCTGGAAATACACCCCGT 59.698 57.895 0.00 0.00 0.00 5.28
4202 4766 0.746923 GGCTGGAAATACACCCCGTC 60.747 60.000 0.00 0.00 0.00 4.79
4203 4767 0.746923 GCTGGAAATACACCCCGTCC 60.747 60.000 0.00 0.00 0.00 4.79
4204 4768 0.107361 CTGGAAATACACCCCGTCCC 60.107 60.000 0.00 0.00 0.00 4.46
4205 4769 1.225426 GGAAATACACCCCGTCCCC 59.775 63.158 0.00 0.00 0.00 4.81
4206 4770 1.225426 GAAATACACCCCGTCCCCC 59.775 63.158 0.00 0.00 0.00 5.40
4207 4771 2.598098 GAAATACACCCCGTCCCCCG 62.598 65.000 0.00 0.00 0.00 5.73
4208 4772 3.929723 AATACACCCCGTCCCCCGT 62.930 63.158 0.00 0.00 33.66 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.745227 ACCTTGAGAAGTTCAAAGAAGACA 58.255 37.500 16.06 0.00 44.84 3.41
133 134 8.764287 GGCATGCCAACATTCTAATTAATTTAC 58.236 33.333 32.08 0.00 32.87 2.01
218 219 0.531532 CCGATGGCTAGTGCTTCCAG 60.532 60.000 0.00 0.00 39.59 3.86
234 235 3.012934 TCACATGGATCAGTAGTCCGA 57.987 47.619 0.00 0.00 38.64 4.55
275 276 2.336809 CTCCTATCCGACGGCAGC 59.663 66.667 9.66 0.00 0.00 5.25
367 368 4.365514 ACAGGTTATGTCACATCCAACA 57.634 40.909 0.00 0.00 37.75 3.33
439 440 2.289694 ACGCACCTGAATACAGCTTCTT 60.290 45.455 0.00 0.00 42.25 2.52
486 487 9.774742 GAATAAATCTTCTGTAACACATCCAAC 57.225 33.333 0.00 0.00 0.00 3.77
493 494 7.148239 CCCACCTGAATAAATCTTCTGTAACAC 60.148 40.741 0.00 0.00 0.00 3.32
495 496 6.884836 ACCCACCTGAATAAATCTTCTGTAAC 59.115 38.462 0.00 0.00 0.00 2.50
505 506 8.102484 ACTACTTCATACCCACCTGAATAAAT 57.898 34.615 0.00 0.00 31.39 1.40
535 536 7.726216 ACTGTTATGCTGCTGACATTACTATA 58.274 34.615 0.00 0.00 30.43 1.31
584 585 8.523915 TGATAGTTTCACAAATCCAATATGCT 57.476 30.769 0.00 0.00 0.00 3.79
594 595 8.850156 AGCAACTAAACTGATAGTTTCACAAAT 58.150 29.630 9.95 0.00 44.47 2.32
628 629 9.929722 CGCAAGTCACTATGCTTTATAAAATTA 57.070 29.630 9.40 0.00 40.39 1.40
644 647 0.593128 GCATGAAACCGCAAGTCACT 59.407 50.000 0.00 0.00 0.00 3.41
715 718 2.733552 CACCACAATCTCAGACAGAACG 59.266 50.000 0.00 0.00 33.62 3.95
781 784 5.916318 TGCACAAAGTTTGGATCAAGAATT 58.084 33.333 19.45 0.00 34.12 2.17
810 813 3.751175 GCCATACAACAAGACAGCAGTAA 59.249 43.478 0.00 0.00 0.00 2.24
821 824 3.957591 AACATGCATGCCATACAACAA 57.042 38.095 26.53 0.00 31.47 2.83
830 833 4.114058 AGACACAAATAACATGCATGCC 57.886 40.909 26.53 0.00 0.00 4.40
831 834 6.092092 TGTAAGACACAAATAACATGCATGC 58.908 36.000 26.53 11.82 32.95 4.06
900 903 1.452145 GGAGCGGTTCTTTGTTGGCA 61.452 55.000 0.00 0.00 0.00 4.92
918 921 0.940126 CCAAGCAAGTATAGCAGCGG 59.060 55.000 0.00 0.00 0.00 5.52
922 925 1.211949 GGGGTCCAAGCAAGTATAGCA 59.788 52.381 0.00 0.00 0.00 3.49
931 934 0.555769 AGAAACAAGGGGTCCAAGCA 59.444 50.000 0.00 0.00 0.00 3.91
932 935 0.961753 CAGAAACAAGGGGTCCAAGC 59.038 55.000 0.00 0.00 0.00 4.01
1057 1060 4.065281 CTGTGGGGGTCGTCGGAC 62.065 72.222 0.00 0.00 42.66 4.79
1110 1113 3.274288 GTGGAAAGAGGATGAAGCGAAT 58.726 45.455 0.00 0.00 0.00 3.34
1200 1203 3.274586 CCGATGCTGCCATCACCG 61.275 66.667 0.00 0.00 46.59 4.94
1210 1213 4.521062 GCACTCTCCGCCGATGCT 62.521 66.667 0.00 0.00 33.44 3.79
1215 1218 4.504916 CTCCAGCACTCTCCGCCG 62.505 72.222 0.00 0.00 0.00 6.46
1221 1224 1.072159 GCCACAACTCCAGCACTCT 59.928 57.895 0.00 0.00 0.00 3.24
1278 1281 3.499737 GGATCAACGGGCTGCACG 61.500 66.667 24.43 24.43 37.36 5.34
1308 1311 3.691575 TCACAGGCCAAATATTCGGAAA 58.308 40.909 5.01 0.00 0.00 3.13
1364 1367 1.039068 CCTGATTGCCCACAAACACA 58.961 50.000 0.00 0.00 39.77 3.72
1591 1626 5.069516 ACAAAAGTTCATTCATCAGCCAGTT 59.930 36.000 0.00 0.00 0.00 3.16
1597 1632 5.622448 CGACACACAAAAGTTCATTCATCAG 59.378 40.000 0.00 0.00 0.00 2.90
1620 1655 1.996898 TCATAGGTACAAAGTTGCGCG 59.003 47.619 0.00 0.00 0.00 6.86
1623 1658 6.821665 TCCAGTTATCATAGGTACAAAGTTGC 59.178 38.462 0.00 0.00 0.00 4.17
1631 1666 8.700051 AGATATGCATCCAGTTATCATAGGTAC 58.300 37.037 0.19 0.00 0.00 3.34
1658 1696 8.620416 TGAAATATTCGACATAATTCCAACAGG 58.380 33.333 10.34 0.00 0.00 4.00
1670 1708 8.786826 TTAACCTGACTTGAAATATTCGACAT 57.213 30.769 0.00 0.00 0.00 3.06
1771 1812 5.244402 CGTGTGTCTACCCCCACATTATATA 59.756 44.000 0.00 0.00 42.95 0.86
1772 1813 4.039973 CGTGTGTCTACCCCCACATTATAT 59.960 45.833 0.00 0.00 42.95 0.86
1773 1814 3.385433 CGTGTGTCTACCCCCACATTATA 59.615 47.826 0.00 0.00 42.95 0.98
1774 1815 2.169769 CGTGTGTCTACCCCCACATTAT 59.830 50.000 0.00 0.00 42.95 1.28
1775 1816 1.551430 CGTGTGTCTACCCCCACATTA 59.449 52.381 0.00 0.00 42.95 1.90
1776 1817 0.323629 CGTGTGTCTACCCCCACATT 59.676 55.000 0.00 0.00 42.95 2.71
1777 1818 0.543410 TCGTGTGTCTACCCCCACAT 60.543 55.000 0.00 0.00 42.95 3.21
1778 1819 0.543410 ATCGTGTGTCTACCCCCACA 60.543 55.000 0.00 0.00 39.16 4.17
1779 1820 1.477553 TATCGTGTGTCTACCCCCAC 58.522 55.000 0.00 0.00 0.00 4.61
1780 1821 2.464796 ATATCGTGTGTCTACCCCCA 57.535 50.000 0.00 0.00 0.00 4.96
1781 1822 3.006217 GGTTATATCGTGTGTCTACCCCC 59.994 52.174 0.00 0.00 0.00 5.40
1782 1823 3.638160 TGGTTATATCGTGTGTCTACCCC 59.362 47.826 0.00 0.00 0.00 4.95
1783 1824 4.924305 TGGTTATATCGTGTGTCTACCC 57.076 45.455 0.00 0.00 0.00 3.69
1784 1825 5.176958 GCATTGGTTATATCGTGTGTCTACC 59.823 44.000 0.00 0.00 0.00 3.18
1785 1826 5.176958 GGCATTGGTTATATCGTGTGTCTAC 59.823 44.000 0.00 0.00 0.00 2.59
1786 1827 5.163395 TGGCATTGGTTATATCGTGTGTCTA 60.163 40.000 0.00 0.00 0.00 2.59
1787 1828 4.127171 GGCATTGGTTATATCGTGTGTCT 58.873 43.478 0.00 0.00 0.00 3.41
1788 1829 3.874543 TGGCATTGGTTATATCGTGTGTC 59.125 43.478 0.00 0.00 0.00 3.67
1789 1830 3.879998 TGGCATTGGTTATATCGTGTGT 58.120 40.909 0.00 0.00 0.00 3.72
1790 1831 4.891627 TTGGCATTGGTTATATCGTGTG 57.108 40.909 0.00 0.00 0.00 3.82
1791 1832 5.906113 TTTTGGCATTGGTTATATCGTGT 57.094 34.783 0.00 0.00 0.00 4.49
1794 1835 9.289303 GCTATTATTTTGGCATTGGTTATATCG 57.711 33.333 0.00 0.00 0.00 2.92
1796 1837 9.927668 GTGCTATTATTTTGGCATTGGTTATAT 57.072 29.630 0.00 0.00 37.05 0.86
1871 1913 0.953471 TGACACCACTACAATGCCGC 60.953 55.000 0.00 0.00 0.00 6.53
1875 1917 1.804151 CCCGTTGACACCACTACAATG 59.196 52.381 0.00 0.00 0.00 2.82
1880 1922 1.189524 CCTCCCCGTTGACACCACTA 61.190 60.000 0.00 0.00 0.00 2.74
1883 2123 2.122769 TCCTCCCCGTTGACACCA 60.123 61.111 0.00 0.00 0.00 4.17
1949 2190 1.400242 GCACGGCATCAAGACTTGTTC 60.400 52.381 14.75 5.53 0.00 3.18
1955 2196 2.456119 CGAGGCACGGCATCAAGAC 61.456 63.158 10.34 0.00 39.45 3.01
1983 2224 2.561419 AGTCGATTTTCCGAGGACAAGA 59.439 45.455 0.00 0.00 39.43 3.02
2005 2246 2.276201 TGTTCGAAAATCCGATCGCAT 58.724 42.857 10.32 0.00 38.45 4.73
2008 2249 4.267690 TGAAGATGTTCGAAAATCCGATCG 59.732 41.667 22.14 8.51 38.45 3.69
2021 2263 0.749454 ATGGGCGGCTGAAGATGTTC 60.749 55.000 9.56 0.00 0.00 3.18
2086 2329 6.475504 ACATGAACAAGTGATGGTTGAGATA 58.524 36.000 0.00 0.00 0.00 1.98
2091 2334 5.443185 AAGACATGAACAAGTGATGGTTG 57.557 39.130 0.00 0.00 0.00 3.77
2094 2337 7.905604 TTACTAAGACATGAACAAGTGATGG 57.094 36.000 0.00 0.00 0.00 3.51
2104 2347 9.889128 TCAATGACATGATTACTAAGACATGAA 57.111 29.630 17.93 10.52 41.45 2.57
2123 2366 9.206870 TCATTTTAAGGCAGAAAAATCAATGAC 57.793 29.630 1.41 0.00 34.01 3.06
2153 2396 9.810545 CCTACAGAAACCAGTTAAAATTTCAAA 57.189 29.630 0.00 0.00 34.22 2.69
2218 2538 4.632153 TCTTCTGCCAGTCTTTGTACTTC 58.368 43.478 0.00 0.00 0.00 3.01
2286 2606 7.862873 GGAATATGTAACTTTTGCTAAGGATGC 59.137 37.037 0.00 0.00 0.00 3.91
2304 2624 6.897413 AGGCTCAAACTAAAATGGGAATATGT 59.103 34.615 0.00 0.00 0.00 2.29
2305 2625 7.352079 AGGCTCAAACTAAAATGGGAATATG 57.648 36.000 0.00 0.00 0.00 1.78
2341 2661 8.193953 TCTACATGAGACATAAGCCATATCAA 57.806 34.615 0.00 0.00 0.00 2.57
2353 2673 8.537728 AATCTCTCTCTTTCTACATGAGACAT 57.462 34.615 0.00 0.00 33.24 3.06
2363 2683 4.081420 AGCCGCAAAATCTCTCTCTTTCTA 60.081 41.667 0.00 0.00 0.00 2.10
2386 2706 1.227943 GACAAGTGCTGACTGCCCA 60.228 57.895 1.50 0.00 42.00 5.36
2511 2831 8.006590 CGAGCTCGATTAAAAAGAAATATCAGG 58.993 37.037 32.06 0.00 43.02 3.86
2512 2832 8.755941 TCGAGCTCGATTAAAAAGAAATATCAG 58.244 33.333 33.84 0.00 44.22 2.90
2513 2833 8.642908 TCGAGCTCGATTAAAAAGAAATATCA 57.357 30.769 33.84 6.03 44.22 2.15
2530 2850 2.154580 GCACATCATTACATCGAGCTCG 59.845 50.000 30.03 30.03 41.45 5.03
2531 2851 3.183976 CAGCACATCATTACATCGAGCTC 59.816 47.826 2.73 2.73 0.00 4.09
2536 2856 2.032290 CCAGCAGCACATCATTACATCG 60.032 50.000 0.00 0.00 0.00 3.84
2539 2859 2.488937 CAACCAGCAGCACATCATTACA 59.511 45.455 0.00 0.00 0.00 2.41
2562 2882 2.280308 TTATTCTAGGCTGGGGTGGT 57.720 50.000 0.00 0.00 0.00 4.16
2566 2886 3.662759 TGGTTTTATTCTAGGCTGGGG 57.337 47.619 0.00 0.00 0.00 4.96
2585 2905 0.681733 AGCTGGCTACCATACGGATG 59.318 55.000 0.00 0.00 35.59 3.51
2586 2906 1.424638 AAGCTGGCTACCATACGGAT 58.575 50.000 0.00 0.00 35.59 4.18
2587 2907 1.200519 AAAGCTGGCTACCATACGGA 58.799 50.000 0.00 0.00 35.59 4.69
2588 2908 2.038387 AAAAGCTGGCTACCATACGG 57.962 50.000 0.00 0.00 38.77 4.02
2605 2925 9.871175 AAAGTAAGAACTCCCTATAACCAAAAA 57.129 29.630 0.00 0.00 33.75 1.94
2608 2928 7.392393 GCAAAAGTAAGAACTCCCTATAACCAA 59.608 37.037 0.00 0.00 33.75 3.67
2617 2937 2.483106 GTCGGCAAAAGTAAGAACTCCC 59.517 50.000 0.00 0.00 33.75 4.30
2618 2938 3.400255 AGTCGGCAAAAGTAAGAACTCC 58.600 45.455 0.00 0.00 33.75 3.85
2674 2994 4.651503 TGGTATGGTTGAAAAGCCTTTTGA 59.348 37.500 7.25 0.00 45.42 2.69
2680 3000 3.070302 TGGTTTGGTATGGTTGAAAAGCC 59.930 43.478 0.00 0.00 45.42 4.35
2782 3102 3.949754 TGCAAAAGCATAGGAGGAGATTG 59.050 43.478 0.00 0.00 0.00 2.67
2783 3103 4.240881 TGCAAAAGCATAGGAGGAGATT 57.759 40.909 0.00 0.00 0.00 2.40
2785 3105 3.548770 CATGCAAAAGCATAGGAGGAGA 58.451 45.455 2.28 0.00 0.00 3.71
2786 3106 2.034305 GCATGCAAAAGCATAGGAGGAG 59.966 50.000 14.21 0.00 0.00 3.69
2787 3107 2.026641 GCATGCAAAAGCATAGGAGGA 58.973 47.619 14.21 0.00 0.00 3.71
2788 3108 1.752498 TGCATGCAAAAGCATAGGAGG 59.248 47.619 20.30 0.00 35.51 4.30
2790 3110 2.094078 GGTTGCATGCAAAAGCATAGGA 60.094 45.455 33.42 5.95 40.94 2.94
2842 3166 7.230849 TGGTGAAATGATTAATTCTTGCAGT 57.769 32.000 0.00 0.00 0.00 4.40
2843 3167 6.755141 CCTGGTGAAATGATTAATTCTTGCAG 59.245 38.462 0.00 0.00 0.00 4.41
2845 3169 6.866480 TCCTGGTGAAATGATTAATTCTTGC 58.134 36.000 0.00 0.00 0.00 4.01
2862 3203 5.928976 TGTGGTGAGATATATTTCCTGGTG 58.071 41.667 1.06 0.00 0.00 4.17
2864 3205 6.830912 TCTTGTGGTGAGATATATTTCCTGG 58.169 40.000 1.06 0.00 0.00 4.45
2865 3206 8.152898 TGATCTTGTGGTGAGATATATTTCCTG 58.847 37.037 1.06 0.00 34.13 3.86
2868 3215 8.986847 CAGTGATCTTGTGGTGAGATATATTTC 58.013 37.037 0.00 0.00 34.13 2.17
2880 3227 4.422073 TTCTTCACAGTGATCTTGTGGT 57.578 40.909 22.33 1.92 34.60 4.16
2881 3228 5.297776 AGTTTTCTTCACAGTGATCTTGTGG 59.702 40.000 22.33 12.64 34.60 4.17
3289 3637 4.316823 AGCCACCAGACTCCCGGA 62.317 66.667 0.73 0.00 0.00 5.14
3315 3663 1.068741 GACTTCACTCAACCGACCTGT 59.931 52.381 0.00 0.00 0.00 4.00
3713 4122 0.521735 GTTTTGGAGCTGGGCTTACG 59.478 55.000 0.00 0.00 39.88 3.18
3744 4153 1.709147 CGGGCTTCAATCTTCCAGCG 61.709 60.000 0.00 0.00 32.68 5.18
3768 4177 1.702182 TGCAGCTGAAATTTGGGACA 58.298 45.000 20.43 0.00 0.00 4.02
3769 4178 2.818130 TTGCAGCTGAAATTTGGGAC 57.182 45.000 20.43 0.00 0.00 4.46
3770 4179 3.834489 TTTTGCAGCTGAAATTTGGGA 57.166 38.095 20.43 0.00 0.00 4.37
3771 4180 3.189702 CCATTTTGCAGCTGAAATTTGGG 59.810 43.478 20.43 9.13 0.00 4.12
3772 4181 4.066490 TCCATTTTGCAGCTGAAATTTGG 58.934 39.130 22.20 22.20 0.00 3.28
3773 4182 4.378046 GCTCCATTTTGCAGCTGAAATTTG 60.378 41.667 20.43 13.52 0.00 2.32
3774 4183 3.749609 GCTCCATTTTGCAGCTGAAATTT 59.250 39.130 20.43 0.16 0.00 1.82
3775 4184 3.332034 GCTCCATTTTGCAGCTGAAATT 58.668 40.909 20.43 8.73 0.00 1.82
3776 4185 2.354403 GGCTCCATTTTGCAGCTGAAAT 60.354 45.455 20.43 12.68 33.38 2.17
3777 4186 1.001181 GGCTCCATTTTGCAGCTGAAA 59.999 47.619 20.43 11.53 33.38 2.69
3778 4187 0.604578 GGCTCCATTTTGCAGCTGAA 59.395 50.000 20.43 2.96 33.38 3.02
3779 4188 0.251474 AGGCTCCATTTTGCAGCTGA 60.251 50.000 20.43 0.00 33.38 4.26
3780 4189 0.108804 CAGGCTCCATTTTGCAGCTG 60.109 55.000 10.11 10.11 33.38 4.24
3781 4190 1.255667 CCAGGCTCCATTTTGCAGCT 61.256 55.000 0.00 0.00 33.38 4.24
3782 4191 1.217244 CCAGGCTCCATTTTGCAGC 59.783 57.895 0.00 0.00 0.00 5.25
3783 4192 1.895238 CCCAGGCTCCATTTTGCAG 59.105 57.895 0.00 0.00 0.00 4.41
3784 4193 2.285024 GCCCAGGCTCCATTTTGCA 61.285 57.895 0.08 0.00 38.26 4.08
3785 4194 1.619807 ATGCCCAGGCTCCATTTTGC 61.620 55.000 10.58 0.00 42.51 3.68
3786 4195 0.177141 CATGCCCAGGCTCCATTTTG 59.823 55.000 10.58 0.00 42.51 2.44
3787 4196 1.619807 GCATGCCCAGGCTCCATTTT 61.620 55.000 6.36 0.00 42.51 1.82
3788 4197 2.062177 GCATGCCCAGGCTCCATTT 61.062 57.895 6.36 0.00 42.51 2.32
3789 4198 2.443390 GCATGCCCAGGCTCCATT 60.443 61.111 6.36 0.00 42.51 3.16
3790 4199 4.534824 GGCATGCCCAGGCTCCAT 62.535 66.667 27.24 0.00 42.51 3.41
3806 4250 3.204827 CGGGCTTGCCATTCGAGG 61.205 66.667 14.04 0.00 0.00 4.63
3893 4360 3.653344 TCAGAACTCGTCCAATCACTTG 58.347 45.455 0.00 0.00 0.00 3.16
4161 4725 5.766222 CCAGAAGACACAATTCTCAAAAGG 58.234 41.667 0.00 0.00 34.80 3.11
4162 4726 5.009410 AGCCAGAAGACACAATTCTCAAAAG 59.991 40.000 0.00 0.00 34.80 2.27
4187 4751 1.225426 GGGGACGGGGTGTATTTCC 59.775 63.158 0.00 0.00 0.00 3.13
4188 4752 1.225426 GGGGGACGGGGTGTATTTC 59.775 63.158 0.00 0.00 0.00 2.17
4189 4753 2.672181 CGGGGGACGGGGTGTATTT 61.672 63.158 0.00 0.00 39.42 1.40
4190 4754 3.085296 CGGGGGACGGGGTGTATT 61.085 66.667 0.00 0.00 39.42 1.89


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

AutoCloner maintained by Alex Coulton.