Multiple sequence alignment - TraesCS3B01G172500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G172500 chr3B 100.000 2264 0 0 1 2264 173075512 173077775 0.000000e+00 4181.0
1 TraesCS3B01G172500 chr2D 93.377 1223 74 4 645 1866 641205460 641204244 0.000000e+00 1803.0
2 TraesCS3B01G172500 chr6D 92.457 1233 79 5 645 1866 293060304 293059075 0.000000e+00 1749.0
3 TraesCS3B01G172500 chr6D 89.825 855 67 14 1 836 293061038 293060185 0.000000e+00 1079.0
4 TraesCS3B01G172500 chr3D 89.061 1417 115 11 645 2024 62369953 62368540 0.000000e+00 1722.0
5 TraesCS3B01G172500 chr3D 89.789 852 59 16 1 829 549427507 549428353 0.000000e+00 1066.0
6 TraesCS3B01G172500 chr3D 89.240 855 72 12 1 836 62370687 62369834 0.000000e+00 1051.0
7 TraesCS3B01G172500 chr5B 89.424 1267 104 15 656 1908 428831940 428833190 0.000000e+00 1570.0
8 TraesCS3B01G172500 chr5B 89.943 1223 106 9 645 1866 578836893 578835687 0.000000e+00 1561.0
9 TraesCS3B01G172500 chr5B 89.170 1265 111 12 656 1908 428826489 428827739 0.000000e+00 1554.0
10 TraesCS3B01G172500 chr5B 89.591 855 69 12 1 836 491841038 491840185 0.000000e+00 1068.0
11 TraesCS3B01G172500 chr5B 91.316 737 48 10 1 721 565841710 565842446 0.000000e+00 992.0
12 TraesCS3B01G172500 chr5B 100.000 31 0 0 2119 2149 297112670 297112640 8.730000e-05 58.4
13 TraesCS3B01G172500 chr2B 89.424 1267 103 19 656 1908 29753886 29752637 0.000000e+00 1568.0
14 TraesCS3B01G172500 chr2B 85.417 192 22 1 2073 2264 596100845 596101030 6.380000e-46 195.0
15 TraesCS3B01G172500 chr2B 81.481 108 13 3 1920 2026 102804385 102804486 5.180000e-12 82.4
16 TraesCS3B01G172500 chr7B 89.336 1266 107 14 656 1908 27327257 27328507 0.000000e+00 1565.0
17 TraesCS3B01G172500 chr7B 88.902 856 74 10 1 836 315291461 315290607 0.000000e+00 1035.0
18 TraesCS3B01G172500 chr7B 83.478 115 17 2 1910 2023 34280114 34280001 3.080000e-19 106.0
19 TraesCS3B01G172500 chr4B 88.862 1239 113 15 677 1908 74252598 74253818 0.000000e+00 1500.0
20 TraesCS3B01G172500 chr5D 89.161 858 71 12 1 836 313383557 313382700 0.000000e+00 1050.0
21 TraesCS3B01G172500 chr5D 88.717 842 70 13 1 823 485079130 485078295 0.000000e+00 1005.0
22 TraesCS3B01G172500 chr1D 89.006 855 66 13 1 836 297552218 297551373 0.000000e+00 1033.0
23 TraesCS3B01G172500 chr1D 90.155 193 17 2 2072 2264 487706895 487706705 1.340000e-62 250.0
24 TraesCS3B01G172500 chr4A 83.420 193 27 1 2072 2264 737662666 737662853 8.310000e-40 174.0
25 TraesCS3B01G172500 chr3A 90.909 110 10 0 656 765 145558262 145558153 5.040000e-32 148.0
26 TraesCS3B01G172500 chr3A 89.565 115 12 0 651 765 22603613 22603499 1.810000e-31 147.0
27 TraesCS3B01G172500 chr7D 91.346 104 9 0 1920 2023 16797420 16797317 2.340000e-30 143.0
28 TraesCS3B01G172500 chr7D 91.346 104 9 0 1920 2023 16797491 16797388 2.340000e-30 143.0
29 TraesCS3B01G172500 chr7D 87.500 104 13 0 1920 2023 16797562 16797459 1.100000e-23 121.0
30 TraesCS3B01G172500 chr7A 85.000 100 15 0 1924 2023 7462546 7462447 3.980000e-18 102.0


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 TraesCS3B01G172500 chr3B 173075512 173077775 2263 False 4181.0 4181 100.0000 1 2264 1 chr3B.!!$F1 2263
1 TraesCS3B01G172500 chr2D 641204244 641205460 1216 True 1803.0 1803 93.3770 645 1866 1 chr2D.!!$R1 1221
2 TraesCS3B01G172500 chr6D 293059075 293061038 1963 True 1414.0 1749 91.1410 1 1866 2 chr6D.!!$R1 1865
3 TraesCS3B01G172500 chr3D 62368540 62370687 2147 True 1386.5 1722 89.1505 1 2024 2 chr3D.!!$R1 2023
4 TraesCS3B01G172500 chr3D 549427507 549428353 846 False 1066.0 1066 89.7890 1 829 1 chr3D.!!$F1 828
5 TraesCS3B01G172500 chr5B 428831940 428833190 1250 False 1570.0 1570 89.4240 656 1908 1 chr5B.!!$F2 1252
6 TraesCS3B01G172500 chr5B 578835687 578836893 1206 True 1561.0 1561 89.9430 645 1866 1 chr5B.!!$R3 1221
7 TraesCS3B01G172500 chr5B 428826489 428827739 1250 False 1554.0 1554 89.1700 656 1908 1 chr5B.!!$F1 1252
8 TraesCS3B01G172500 chr5B 491840185 491841038 853 True 1068.0 1068 89.5910 1 836 1 chr5B.!!$R2 835
9 TraesCS3B01G172500 chr5B 565841710 565842446 736 False 992.0 992 91.3160 1 721 1 chr5B.!!$F3 720
10 TraesCS3B01G172500 chr2B 29752637 29753886 1249 True 1568.0 1568 89.4240 656 1908 1 chr2B.!!$R1 1252
11 TraesCS3B01G172500 chr7B 27327257 27328507 1250 False 1565.0 1565 89.3360 656 1908 1 chr7B.!!$F1 1252
12 TraesCS3B01G172500 chr7B 315290607 315291461 854 True 1035.0 1035 88.9020 1 836 1 chr7B.!!$R2 835
13 TraesCS3B01G172500 chr4B 74252598 74253818 1220 False 1500.0 1500 88.8620 677 1908 1 chr4B.!!$F1 1231
14 TraesCS3B01G172500 chr5D 313382700 313383557 857 True 1050.0 1050 89.1610 1 836 1 chr5D.!!$R1 835
15 TraesCS3B01G172500 chr5D 485078295 485079130 835 True 1005.0 1005 88.7170 1 823 1 chr5D.!!$R2 822
16 TraesCS3B01G172500 chr1D 297551373 297552218 845 True 1033.0 1033 89.0060 1 836 1 chr1D.!!$R1 835

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
789 1003 1.157513 TGCTAGAGGTGGTGGTGGA 59.842 57.895 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2360 0.039527 GTTGCCCAAGTAGCCAAACG 60.04 55.0 0.0 0.0 0.0 3.6 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
127 129 8.473358 AATGATCTATCAAATTGATGAGCCAA 57.527 30.769 17.93 3.37 40.69 4.52
144 146 1.229428 CAAGTGGCACAACACGAGAT 58.771 50.000 21.41 0.00 44.16 2.75
210 213 1.672356 GTGGTGCCAGTGCGAGATT 60.672 57.895 0.00 0.00 41.78 2.40
376 379 2.054021 TCTTGGACCAATCACAGTGGA 58.946 47.619 7.54 0.00 39.62 4.02
426 429 2.192263 GACCCTCTCTTGAAGGTGGAT 58.808 52.381 0.00 0.00 37.16 3.41
443 446 3.134262 GTGGATACCAAGGGTAGAAGGAC 59.866 52.174 1.24 0.00 41.83 3.85
490 493 2.543037 TGACCTGGCTGGATACACTA 57.457 50.000 18.12 0.00 46.17 2.74
550 553 2.567169 CCTGACACTATCAACTGTGGGA 59.433 50.000 0.00 0.00 36.69 4.37
555 561 2.303022 CACTATCAACTGTGGGAGGTGT 59.697 50.000 0.00 0.00 40.70 4.16
602 609 4.516321 GGCATGCAAGAAAAGGAAAACATT 59.484 37.500 21.36 0.00 0.00 2.71
649 785 3.235195 CGTAGAGGAAAGACAAGTCGTG 58.765 50.000 0.00 0.00 34.09 4.35
665 801 1.821061 CGTGGAGGGAGCAGAAGTGT 61.821 60.000 0.00 0.00 0.00 3.55
670 806 2.167487 GGAGGGAGCAGAAGTGTTAGAG 59.833 54.545 0.00 0.00 0.00 2.43
671 807 2.167487 GAGGGAGCAGAAGTGTTAGAGG 59.833 54.545 0.00 0.00 0.00 3.69
672 808 1.903183 GGGAGCAGAAGTGTTAGAGGT 59.097 52.381 0.00 0.00 0.00 3.85
673 809 2.354203 GGGAGCAGAAGTGTTAGAGGTG 60.354 54.545 0.00 0.00 0.00 4.00
674 810 2.300437 GGAGCAGAAGTGTTAGAGGTGT 59.700 50.000 0.00 0.00 0.00 4.16
675 811 3.244249 GGAGCAGAAGTGTTAGAGGTGTT 60.244 47.826 0.00 0.00 0.00 3.32
764 978 1.192428 GGTGGTGGTCGTAGAGGAAT 58.808 55.000 0.00 0.00 36.95 3.01
789 1003 1.157513 TGCTAGAGGTGGTGGTGGA 59.842 57.895 0.00 0.00 0.00 4.02
848 1071 6.139048 TCGTAGACGAATGGTTGATAATGA 57.861 37.500 1.51 0.00 46.30 2.57
869 1092 1.621992 TCGGCCTTTGGTTATTTGCA 58.378 45.000 0.00 0.00 0.00 4.08
988 1213 5.960113 TGTGTCTTGTGCTAACAATTGTTT 58.040 33.333 27.66 12.78 45.12 2.83
1013 1238 1.284491 TGTAGGCATGGCTTCATCCAA 59.716 47.619 28.30 4.07 39.96 3.53
1072 1297 1.945354 GCCGAAGACGTGGATGGAGA 61.945 60.000 0.00 0.00 37.88 3.71
1076 1301 2.422479 CGAAGACGTGGATGGAGACTAA 59.578 50.000 0.00 0.00 34.56 2.24
1095 1320 4.846940 ACTAAGTTGGACAAGGAGAAGGAT 59.153 41.667 0.00 0.00 0.00 3.24
1150 1375 0.459489 TGTTTGCAAGGTGAAGGTGC 59.541 50.000 0.00 0.00 38.78 5.01
1206 1431 4.901250 AGAAGGTTTTTCATGTGTCCCAAT 59.099 37.500 0.00 0.00 0.00 3.16
1222 1447 4.036734 GTCCCAATTATGCACATGATCGTT 59.963 41.667 0.00 0.00 0.00 3.85
1253 1478 3.958798 ACTAACGCATATGACCTACCACT 59.041 43.478 6.97 0.00 0.00 4.00
1378 1604 3.381590 TCACTTGGATAGATCACGAGGTG 59.618 47.826 0.00 1.06 34.45 4.00
1451 1677 1.347707 TGTTCGAGGAGTCCTTTGCAT 59.652 47.619 14.41 0.00 31.76 3.96
1480 1706 2.490217 CGGGAGCGTCGTGAGAAT 59.510 61.111 0.00 0.00 45.01 2.40
1521 1747 0.250295 CGTGAGGAAAAGAGGGCACA 60.250 55.000 0.00 0.00 0.00 4.57
1541 1767 2.231478 CACAAAGAGAAGGAGGCTCGTA 59.769 50.000 10.52 0.00 37.46 3.43
1547 1773 4.027437 AGAGAAGGAGGCTCGTAAAGAAT 58.973 43.478 10.52 0.00 37.46 2.40
1641 1867 2.648059 GCCCCGTACTACTCAGTAGAA 58.352 52.381 19.25 0.00 38.29 2.10
1658 1884 4.898861 AGTAGAAAAATGGAAAAGGCACCA 59.101 37.500 0.00 0.00 40.57 4.17
1688 1914 5.462530 TGATGGACTTTCGAGACTTTGTA 57.537 39.130 0.00 0.00 0.00 2.41
1744 1970 9.643693 GTGGTCATGAAAAATTTATGTCATTCT 57.356 29.630 0.00 0.00 0.00 2.40
1760 1986 6.101997 TGTCATTCTAGACATCATGTGTGAC 58.898 40.000 0.00 0.00 43.18 3.67
1770 1996 4.686091 ACATCATGTGTGACGAACTTGTAG 59.314 41.667 0.00 0.00 40.28 2.74
1796 2032 7.468922 TTGAGACTATTTGAGATTATGTGCG 57.531 36.000 0.00 0.00 0.00 5.34
1837 2077 7.768240 TCGAGACTAGTATGCTTTGTTCATAA 58.232 34.615 0.00 0.00 0.00 1.90
1841 2081 9.890629 AGACTAGTATGCTTTGTTCATAATTGA 57.109 29.630 0.00 0.00 0.00 2.57
1849 2089 8.883954 TGCTTTGTTCATAATTGAATGTTTCA 57.116 26.923 0.00 0.00 43.49 2.69
1872 2138 9.724839 TTCAACTAGTATGCTTTGTTTAACAAC 57.275 29.630 10.28 0.89 37.90 3.32
1920 2186 6.944557 AAAATTAACAAGTTGCTATTCGGC 57.055 33.333 1.81 0.00 0.00 5.54
1921 2187 5.637006 AATTAACAAGTTGCTATTCGGCA 57.363 34.783 1.81 0.00 40.74 5.69
1922 2188 2.989422 AACAAGTTGCTATTCGGCAC 57.011 45.000 1.81 0.00 42.27 5.01
1923 2189 1.890876 ACAAGTTGCTATTCGGCACA 58.109 45.000 1.81 0.00 42.27 4.57
1924 2190 1.535462 ACAAGTTGCTATTCGGCACAC 59.465 47.619 1.81 0.00 42.27 3.82
1936 2202 2.267642 GCACACCCAGACGCCATA 59.732 61.111 0.00 0.00 0.00 2.74
1950 2216 3.127099 CCATAGACCCTGGCGTCTA 57.873 57.895 20.21 20.21 46.59 2.59
1970 2236 1.292242 AGGTCCCTATCCAGAGAGCAA 59.708 52.381 0.00 0.00 0.00 3.91
1975 2241 4.819088 GTCCCTATCCAGAGAGCAATTTTC 59.181 45.833 0.00 0.00 0.00 2.29
1976 2242 4.140536 CCCTATCCAGAGAGCAATTTTCC 58.859 47.826 0.00 0.00 0.00 3.13
1977 2243 4.385643 CCCTATCCAGAGAGCAATTTTCCA 60.386 45.833 0.00 0.00 0.00 3.53
1978 2244 5.195940 CCTATCCAGAGAGCAATTTTCCAA 58.804 41.667 0.00 0.00 0.00 3.53
1983 2249 3.985925 CAGAGAGCAATTTTCCAAGTTGC 59.014 43.478 8.27 8.27 46.37 4.17
2007 2274 3.434319 GCACACCCAGACGCCATG 61.434 66.667 0.00 0.00 0.00 3.66
2008 2275 2.032528 CACACCCAGACGCCATGT 59.967 61.111 0.00 0.00 0.00 3.21
2009 2276 1.600636 CACACCCAGACGCCATGTT 60.601 57.895 0.00 0.00 0.00 2.71
2024 2291 4.021925 GTTCCCTGGCGTCTGGCT 62.022 66.667 7.54 0.00 42.94 4.75
2025 2292 2.284331 TTCCCTGGCGTCTGGCTA 60.284 61.111 7.54 0.00 42.94 3.93
2030 2297 2.460330 CTGGCGTCTGGCTAGTTTG 58.540 57.895 0.00 0.00 44.55 2.93
2031 2298 1.003839 TGGCGTCTGGCTAGTTTGG 60.004 57.895 0.00 0.00 42.94 3.28
2032 2299 1.003718 GGCGTCTGGCTAGTTTGGT 60.004 57.895 0.00 0.00 42.94 3.67
2033 2300 1.019805 GGCGTCTGGCTAGTTTGGTC 61.020 60.000 0.00 0.00 42.94 4.02
2034 2301 0.320421 GCGTCTGGCTAGTTTGGTCA 60.320 55.000 0.00 0.00 39.11 4.02
2035 2302 1.429463 CGTCTGGCTAGTTTGGTCAC 58.571 55.000 0.00 0.00 0.00 3.67
2036 2303 1.429463 GTCTGGCTAGTTTGGTCACG 58.571 55.000 0.00 0.00 0.00 4.35
2037 2304 0.320421 TCTGGCTAGTTTGGTCACGC 60.320 55.000 0.00 0.00 0.00 5.34
2038 2305 0.602638 CTGGCTAGTTTGGTCACGCA 60.603 55.000 0.00 0.00 0.00 5.24
2039 2306 0.602638 TGGCTAGTTTGGTCACGCAG 60.603 55.000 0.00 0.00 0.00 5.18
2040 2307 1.298859 GGCTAGTTTGGTCACGCAGG 61.299 60.000 0.00 0.00 0.00 4.85
2041 2308 0.320421 GCTAGTTTGGTCACGCAGGA 60.320 55.000 0.00 0.00 0.00 3.86
2042 2309 1.876416 GCTAGTTTGGTCACGCAGGAA 60.876 52.381 0.00 0.00 0.00 3.36
2043 2310 2.069273 CTAGTTTGGTCACGCAGGAAG 58.931 52.381 0.00 0.00 0.00 3.46
2044 2311 1.166531 AGTTTGGTCACGCAGGAAGC 61.167 55.000 0.00 0.00 40.87 3.86
2045 2312 1.896660 TTTGGTCACGCAGGAAGCC 60.897 57.895 0.00 0.00 41.38 4.35
2046 2313 2.616797 TTTGGTCACGCAGGAAGCCA 62.617 55.000 0.00 0.00 41.38 4.75
2047 2314 2.743928 GGTCACGCAGGAAGCCAG 60.744 66.667 0.00 0.00 41.38 4.85
2048 2315 2.343758 GTCACGCAGGAAGCCAGA 59.656 61.111 0.00 0.00 41.38 3.86
2049 2316 2.029844 GTCACGCAGGAAGCCAGAC 61.030 63.158 0.00 0.00 41.38 3.51
2050 2317 2.031012 CACGCAGGAAGCCAGACA 59.969 61.111 0.00 0.00 41.38 3.41
2051 2318 2.031163 ACGCAGGAAGCCAGACAC 59.969 61.111 0.00 0.00 41.38 3.67
2052 2319 2.031012 CGCAGGAAGCCAGACACA 59.969 61.111 0.00 0.00 41.38 3.72
2053 2320 1.376424 CGCAGGAAGCCAGACACAT 60.376 57.895 0.00 0.00 41.38 3.21
2054 2321 1.642037 CGCAGGAAGCCAGACACATG 61.642 60.000 0.00 0.00 41.38 3.21
2055 2322 0.607489 GCAGGAAGCCAGACACATGT 60.607 55.000 0.00 0.00 37.23 3.21
2056 2323 1.446907 CAGGAAGCCAGACACATGTC 58.553 55.000 3.72 3.72 45.08 3.06
2065 2332 2.785868 GACACATGTCTGATGGCCC 58.214 57.895 0.00 0.00 41.65 5.80
2066 2333 1.078214 ACACATGTCTGATGGCCCG 60.078 57.895 0.00 0.00 0.00 6.13
2067 2334 2.124570 ACATGTCTGATGGCCCGC 60.125 61.111 0.00 0.00 0.00 6.13
2068 2335 3.274586 CATGTCTGATGGCCCGCG 61.275 66.667 0.00 0.00 0.00 6.46
2086 2353 3.691342 CCGACCAGACGCCAAGGA 61.691 66.667 0.00 0.00 0.00 3.36
2087 2354 2.432628 CGACCAGACGCCAAGGAC 60.433 66.667 0.00 0.00 0.00 3.85
2088 2355 2.047179 GACCAGACGCCAAGGACC 60.047 66.667 0.00 0.00 0.00 4.46
2089 2356 2.847234 ACCAGACGCCAAGGACCA 60.847 61.111 0.00 0.00 0.00 4.02
2090 2357 2.185310 GACCAGACGCCAAGGACCAT 62.185 60.000 0.00 0.00 0.00 3.55
2091 2358 1.746615 CCAGACGCCAAGGACCATG 60.747 63.158 0.00 0.00 0.00 3.66
2092 2359 1.746615 CAGACGCCAAGGACCATGG 60.747 63.158 11.19 11.19 41.08 3.66
2097 2364 4.095590 CCAAGGACCATGGCGTTT 57.904 55.556 13.04 0.00 0.00 3.60
2098 2365 1.586028 CCAAGGACCATGGCGTTTG 59.414 57.895 13.04 13.10 0.00 2.93
2099 2366 1.586028 CAAGGACCATGGCGTTTGG 59.414 57.895 13.04 0.00 40.26 3.28
2100 2367 2.275380 AAGGACCATGGCGTTTGGC 61.275 57.895 13.04 0.00 37.81 4.52
2101 2368 2.676471 GGACCATGGCGTTTGGCT 60.676 61.111 13.04 0.00 42.94 4.75
2102 2369 1.377987 GGACCATGGCGTTTGGCTA 60.378 57.895 13.04 0.00 42.94 3.93
2103 2370 1.654023 GGACCATGGCGTTTGGCTAC 61.654 60.000 13.04 0.00 42.94 3.58
2104 2371 0.676782 GACCATGGCGTTTGGCTACT 60.677 55.000 13.04 0.00 42.94 2.57
2105 2372 0.251165 ACCATGGCGTTTGGCTACTT 60.251 50.000 13.04 0.00 42.94 2.24
2106 2373 0.171007 CCATGGCGTTTGGCTACTTG 59.829 55.000 0.00 0.00 42.94 3.16
2107 2374 0.171007 CATGGCGTTTGGCTACTTGG 59.829 55.000 0.00 0.00 42.94 3.61
2108 2375 0.965363 ATGGCGTTTGGCTACTTGGG 60.965 55.000 0.00 0.00 42.94 4.12
2109 2376 2.566529 GCGTTTGGCTACTTGGGC 59.433 61.111 0.00 0.00 39.11 5.36
2110 2377 2.265182 GCGTTTGGCTACTTGGGCA 61.265 57.895 0.00 0.00 39.99 5.36
2113 2380 4.073052 TTGGCTACTTGGGCAACG 57.927 55.556 0.00 0.00 44.72 4.10
2114 2381 1.149627 TTGGCTACTTGGGCAACGT 59.850 52.632 0.00 0.00 44.72 3.99
2115 2382 0.887387 TTGGCTACTTGGGCAACGTC 60.887 55.000 0.00 0.00 44.72 4.34
2116 2383 1.302192 GGCTACTTGGGCAACGTCA 60.302 57.895 0.00 0.00 37.60 4.35
2117 2384 0.887387 GGCTACTTGGGCAACGTCAA 60.887 55.000 0.00 0.00 37.60 3.18
2118 2385 0.237498 GCTACTTGGGCAACGTCAAC 59.763 55.000 0.00 0.00 37.60 3.18
2119 2386 0.872388 CTACTTGGGCAACGTCAACC 59.128 55.000 0.00 0.00 37.60 3.77
2120 2387 0.180642 TACTTGGGCAACGTCAACCA 59.819 50.000 0.00 0.00 37.60 3.67
2121 2388 1.101049 ACTTGGGCAACGTCAACCAG 61.101 55.000 5.40 3.81 33.96 4.00
2122 2389 0.817634 CTTGGGCAACGTCAACCAGA 60.818 55.000 5.40 0.00 33.96 3.86
2123 2390 1.098712 TTGGGCAACGTCAACCAGAC 61.099 55.000 5.40 0.00 44.02 3.51
2130 2397 2.358737 GTCAACCAGACGCCAGGG 60.359 66.667 0.00 0.00 37.53 4.45
2131 2398 2.525629 TCAACCAGACGCCAGGGA 60.526 61.111 0.00 0.00 0.00 4.20
2132 2399 2.358737 CAACCAGACGCCAGGGAC 60.359 66.667 0.00 0.00 0.00 4.46
2133 2400 3.637273 AACCAGACGCCAGGGACC 61.637 66.667 0.00 0.00 0.00 4.46
2136 2403 4.742201 CAGACGCCAGGGACCGTG 62.742 72.222 7.23 7.23 37.87 4.94
2143 2410 4.742201 CAGGGACCGTGGCGTCTG 62.742 72.222 6.27 0.00 33.07 3.51
2149 2416 4.619227 CCGTGGCGTCTGGGTGTT 62.619 66.667 0.00 0.00 0.00 3.32
2150 2417 3.345808 CGTGGCGTCTGGGTGTTG 61.346 66.667 0.00 0.00 0.00 3.33
2151 2418 3.660111 GTGGCGTCTGGGTGTTGC 61.660 66.667 0.00 0.00 0.00 4.17
2152 2419 4.182433 TGGCGTCTGGGTGTTGCA 62.182 61.111 0.00 0.00 0.00 4.08
2153 2420 3.660111 GGCGTCTGGGTGTTGCAC 61.660 66.667 0.00 0.00 0.00 4.57
2154 2421 2.899838 GCGTCTGGGTGTTGCACA 60.900 61.111 1.61 0.00 35.86 4.57
2160 2427 1.674359 CTGGGTGTTGCACAGTTACA 58.326 50.000 1.61 0.00 43.50 2.41
2161 2428 2.229792 CTGGGTGTTGCACAGTTACAT 58.770 47.619 1.61 0.00 43.50 2.29
2162 2429 2.622942 CTGGGTGTTGCACAGTTACATT 59.377 45.455 1.61 0.00 43.50 2.71
2163 2430 3.027412 TGGGTGTTGCACAGTTACATTT 58.973 40.909 1.61 0.00 35.86 2.32
2164 2431 3.067461 TGGGTGTTGCACAGTTACATTTC 59.933 43.478 1.61 0.00 35.86 2.17
2165 2432 3.296628 GGTGTTGCACAGTTACATTTCG 58.703 45.455 1.61 0.00 35.86 3.46
2166 2433 2.719046 GTGTTGCACAGTTACATTTCGC 59.281 45.455 0.00 0.00 34.08 4.70
2167 2434 2.616376 TGTTGCACAGTTACATTTCGCT 59.384 40.909 0.00 0.00 0.00 4.93
2168 2435 3.066064 TGTTGCACAGTTACATTTCGCTT 59.934 39.130 0.00 0.00 0.00 4.68
2169 2436 3.536158 TGCACAGTTACATTTCGCTTC 57.464 42.857 0.00 0.00 0.00 3.86
2170 2437 3.138304 TGCACAGTTACATTTCGCTTCT 58.862 40.909 0.00 0.00 0.00 2.85
2171 2438 3.058983 TGCACAGTTACATTTCGCTTCTG 60.059 43.478 0.00 0.00 0.00 3.02
2172 2439 3.058914 GCACAGTTACATTTCGCTTCTGT 60.059 43.478 0.00 0.00 35.49 3.41
2173 2440 4.554723 GCACAGTTACATTTCGCTTCTGTT 60.555 41.667 0.00 0.00 33.35 3.16
2174 2441 4.905866 CACAGTTACATTTCGCTTCTGTTG 59.094 41.667 0.00 0.00 33.35 3.33
2175 2442 4.814234 ACAGTTACATTTCGCTTCTGTTGA 59.186 37.500 0.00 0.00 31.95 3.18
2176 2443 5.470098 ACAGTTACATTTCGCTTCTGTTGAT 59.530 36.000 0.00 0.00 31.95 2.57
2177 2444 6.017109 ACAGTTACATTTCGCTTCTGTTGATT 60.017 34.615 0.00 0.00 31.95 2.57
2178 2445 6.857964 CAGTTACATTTCGCTTCTGTTGATTT 59.142 34.615 0.00 0.00 0.00 2.17
2179 2446 7.379529 CAGTTACATTTCGCTTCTGTTGATTTT 59.620 33.333 0.00 0.00 0.00 1.82
2180 2447 7.379529 AGTTACATTTCGCTTCTGTTGATTTTG 59.620 33.333 0.00 0.00 0.00 2.44
2181 2448 4.984161 ACATTTCGCTTCTGTTGATTTTGG 59.016 37.500 0.00 0.00 0.00 3.28
2182 2449 3.641437 TTCGCTTCTGTTGATTTTGGG 57.359 42.857 0.00 0.00 0.00 4.12
2183 2450 1.885887 TCGCTTCTGTTGATTTTGGGG 59.114 47.619 0.00 0.00 0.00 4.96
2184 2451 1.067635 CGCTTCTGTTGATTTTGGGGG 60.068 52.381 0.00 0.00 0.00 5.40
2207 2474 4.672251 GGTACCAGACGCTAGGGA 57.328 61.111 14.59 0.00 0.00 4.20
2208 2475 2.113767 GGTACCAGACGCTAGGGAC 58.886 63.158 14.59 7.54 38.06 4.46
2209 2476 2.113767 GTACCAGACGCTAGGGACC 58.886 63.158 14.59 4.92 32.28 4.46
2210 2477 1.076485 TACCAGACGCTAGGGACCC 60.076 63.158 14.59 0.59 0.00 4.46
2211 2478 1.578215 TACCAGACGCTAGGGACCCT 61.578 60.000 19.48 19.48 37.71 4.34
2212 2479 2.427245 CCAGACGCTAGGGACCCTG 61.427 68.421 24.42 13.88 34.61 4.45
2213 2480 2.042843 AGACGCTAGGGACCCTGG 60.043 66.667 24.42 21.88 34.61 4.45
2218 2485 3.400188 CTAGGGACCCTGGCGTTT 58.600 61.111 24.42 0.00 34.61 3.60
2219 2486 1.078426 CTAGGGACCCTGGCGTTTG 60.078 63.158 24.42 0.73 34.61 2.93
2220 2487 2.536997 CTAGGGACCCTGGCGTTTGG 62.537 65.000 24.42 0.00 34.61 3.28
2221 2488 3.961414 GGGACCCTGGCGTTTGGA 61.961 66.667 2.09 0.00 0.00 3.53
2222 2489 2.355115 GGACCCTGGCGTTTGGAT 59.645 61.111 0.00 0.00 0.00 3.41
2223 2490 1.605453 GGACCCTGGCGTTTGGATA 59.395 57.895 0.00 0.00 0.00 2.59
2224 2491 0.182775 GGACCCTGGCGTTTGGATAT 59.817 55.000 0.00 0.00 0.00 1.63
2225 2492 1.409661 GGACCCTGGCGTTTGGATATT 60.410 52.381 0.00 0.00 0.00 1.28
2226 2493 2.375146 GACCCTGGCGTTTGGATATTT 58.625 47.619 0.00 0.00 0.00 1.40
2227 2494 2.099098 GACCCTGGCGTTTGGATATTTG 59.901 50.000 0.00 0.00 0.00 2.32
2228 2495 1.408702 CCCTGGCGTTTGGATATTTGG 59.591 52.381 0.00 0.00 0.00 3.28
2229 2496 1.408702 CCTGGCGTTTGGATATTTGGG 59.591 52.381 0.00 0.00 0.00 4.12
2230 2497 0.820871 TGGCGTTTGGATATTTGGGC 59.179 50.000 0.00 0.00 0.00 5.36
2231 2498 0.104120 GGCGTTTGGATATTTGGGCC 59.896 55.000 0.00 0.00 0.00 5.80
2232 2499 0.820871 GCGTTTGGATATTTGGGCCA 59.179 50.000 0.00 0.00 0.00 5.36
2233 2500 1.412343 GCGTTTGGATATTTGGGCCAT 59.588 47.619 7.26 0.00 0.00 4.40
2234 2501 2.802774 GCGTTTGGATATTTGGGCCATG 60.803 50.000 7.26 0.00 0.00 3.66
2235 2502 2.430332 CGTTTGGATATTTGGGCCATGT 59.570 45.455 7.26 0.94 0.00 3.21
2236 2503 3.490761 CGTTTGGATATTTGGGCCATGTC 60.491 47.826 7.26 0.29 0.00 3.06
2237 2504 3.395054 TTGGATATTTGGGCCATGTCA 57.605 42.857 7.26 0.00 0.00 3.58
2238 2505 3.395054 TGGATATTTGGGCCATGTCAA 57.605 42.857 7.26 0.00 0.00 3.18
2239 2506 3.030291 TGGATATTTGGGCCATGTCAAC 58.970 45.455 7.26 0.00 0.00 3.18
2240 2507 2.365293 GGATATTTGGGCCATGTCAACC 59.635 50.000 7.26 3.65 0.00 3.77
2241 2508 2.612285 TATTTGGGCCATGTCAACCA 57.388 45.000 7.26 0.00 0.00 3.67
2242 2509 1.269012 ATTTGGGCCATGTCAACCAG 58.731 50.000 7.26 0.00 33.96 4.00
2243 2510 0.187117 TTTGGGCCATGTCAACCAGA 59.813 50.000 7.26 0.00 33.96 3.86
2244 2511 0.409092 TTGGGCCATGTCAACCAGAT 59.591 50.000 7.26 0.00 33.96 2.90
2245 2512 0.323633 TGGGCCATGTCAACCAGATG 60.324 55.000 0.00 0.00 0.00 2.90
2246 2513 1.669999 GGGCCATGTCAACCAGATGC 61.670 60.000 4.39 0.00 0.00 3.91
2247 2514 1.669999 GGCCATGTCAACCAGATGCC 61.670 60.000 0.00 0.00 0.00 4.40
2248 2515 1.996786 GCCATGTCAACCAGATGCCG 61.997 60.000 0.00 0.00 0.00 5.69
2249 2516 0.392863 CCATGTCAACCAGATGCCGA 60.393 55.000 0.00 0.00 0.00 5.54
2250 2517 1.012086 CATGTCAACCAGATGCCGAG 58.988 55.000 0.00 0.00 0.00 4.63
2251 2518 0.107508 ATGTCAACCAGATGCCGAGG 60.108 55.000 0.00 0.00 0.00 4.63
2252 2519 1.191489 TGTCAACCAGATGCCGAGGA 61.191 55.000 0.00 0.00 0.00 3.71
2253 2520 0.741221 GTCAACCAGATGCCGAGGAC 60.741 60.000 0.00 0.00 0.00 3.85
2254 2521 1.450312 CAACCAGATGCCGAGGACC 60.450 63.158 0.00 0.00 0.00 4.46
2255 2522 2.670148 AACCAGATGCCGAGGACCC 61.670 63.158 0.00 0.00 0.00 4.46
2256 2523 2.765807 CCAGATGCCGAGGACCCT 60.766 66.667 0.00 0.00 0.00 4.34
2257 2524 2.503061 CAGATGCCGAGGACCCTG 59.497 66.667 0.00 0.00 0.00 4.45
2258 2525 2.765807 AGATGCCGAGGACCCTGG 60.766 66.667 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.147629 CAGCCATTCATCAATCTCTCCC 58.852 50.000 0.00 0.00 0.00 4.30
28 29 2.950309 ACTGCAGCCATTCATCAATCTC 59.050 45.455 15.27 0.00 0.00 2.75
31 33 4.018490 TGTAACTGCAGCCATTCATCAAT 58.982 39.130 15.27 0.00 0.00 2.57
127 129 0.603707 CCATCTCGTGTTGTGCCACT 60.604 55.000 0.00 0.00 33.07 4.00
144 146 3.257873 CAGCACCACCATATTGAAAACCA 59.742 43.478 0.00 0.00 0.00 3.67
210 213 5.513094 GCATGGCCAATGATACTTACTAGGA 60.513 44.000 10.96 0.00 38.72 2.94
296 299 2.306805 TCCACATGGAACTCTTGCATCT 59.693 45.455 0.00 0.00 39.89 2.90
376 379 2.180946 TGAGGGCCATGATACTCAGT 57.819 50.000 6.18 0.00 35.24 3.41
426 429 3.865571 AGTTGTCCTTCTACCCTTGGTA 58.134 45.455 0.00 0.00 37.09 3.25
443 446 4.286297 TCACCCATGAACCTCTTAGTTG 57.714 45.455 0.00 0.00 0.00 3.16
490 493 3.367292 CCGCTACCAAATTGTTTCATGCT 60.367 43.478 0.00 0.00 0.00 3.79
550 553 1.152756 GTTGCCCTTCACCACACCT 60.153 57.895 0.00 0.00 0.00 4.00
555 561 1.039068 CATTGTGTTGCCCTTCACCA 58.961 50.000 0.00 0.00 34.14 4.17
580 586 5.236911 TCAATGTTTTCCTTTTCTTGCATGC 59.763 36.000 11.82 11.82 0.00 4.06
602 609 0.258774 GCTAGGAATGCCCCCTTTCA 59.741 55.000 0.00 0.00 35.30 2.69
649 785 2.167487 CTCTAACACTTCTGCTCCCTCC 59.833 54.545 0.00 0.00 0.00 4.30
665 801 1.416243 ACGACCACCAACACCTCTAA 58.584 50.000 0.00 0.00 0.00 2.10
670 806 0.037605 CCTCTACGACCACCAACACC 60.038 60.000 0.00 0.00 0.00 4.16
671 807 0.963962 TCCTCTACGACCACCAACAC 59.036 55.000 0.00 0.00 0.00 3.32
672 808 1.616865 CTTCCTCTACGACCACCAACA 59.383 52.381 0.00 0.00 0.00 3.33
673 809 1.672145 GCTTCCTCTACGACCACCAAC 60.672 57.143 0.00 0.00 0.00 3.77
674 810 0.606604 GCTTCCTCTACGACCACCAA 59.393 55.000 0.00 0.00 0.00 3.67
675 811 0.541063 TGCTTCCTCTACGACCACCA 60.541 55.000 0.00 0.00 0.00 4.17
704 846 0.324614 TCTACCACCACCAGCACATG 59.675 55.000 0.00 0.00 0.00 3.21
706 848 2.057830 CTCTACCACCACCAGCACA 58.942 57.895 0.00 0.00 0.00 4.57
764 978 1.344438 CACCACCTCTAGCACTTGTGA 59.656 52.381 4.79 0.00 0.00 3.58
789 1003 2.370189 AGCACTTGTGCTTCCTCTAAGT 59.630 45.455 20.95 0.00 43.52 2.24
812 1035 1.549170 GTCTACGACCACCACATCCTT 59.451 52.381 0.00 0.00 0.00 3.36
816 1039 2.951269 TCGTCTACGACCACCACAT 58.049 52.632 0.14 0.00 44.22 3.21
817 1040 4.479303 TCGTCTACGACCACCACA 57.521 55.556 0.14 0.00 44.22 4.17
832 1055 4.466828 GCCGATTCATTATCAACCATTCG 58.533 43.478 0.00 0.00 32.45 3.34
848 1071 2.564947 TGCAAATAACCAAAGGCCGATT 59.435 40.909 0.00 0.00 0.00 3.34
952 1177 8.220755 AGCACAAGACACAAAAAGAGTAAATA 57.779 30.769 0.00 0.00 0.00 1.40
1013 1238 1.299976 GACGGCCTTGTCCTGGAAT 59.700 57.895 0.00 0.00 32.61 3.01
1072 1297 4.232091 TCCTTCTCCTTGTCCAACTTAGT 58.768 43.478 0.00 0.00 0.00 2.24
1076 1301 4.226168 CCTTATCCTTCTCCTTGTCCAACT 59.774 45.833 0.00 0.00 0.00 3.16
1095 1320 0.037590 GTGGTGTGGGCACATCCTTA 59.962 55.000 13.04 0.00 46.95 2.69
1150 1375 0.951040 GACTTCTTGCGGTCAGTGGG 60.951 60.000 0.00 0.00 33.19 4.61
1206 1431 3.123050 CCGAGAACGATCATGTGCATAA 58.877 45.455 0.00 0.00 42.66 1.90
1222 1447 0.818938 TATGCGTTAGTTGGCCGAGA 59.181 50.000 0.00 0.00 0.00 4.04
1378 1604 2.795329 TCCTCTTGGACATCTTTTGGC 58.205 47.619 0.00 0.00 37.46 4.52
1451 1677 3.089874 CTCCCGCTCCAATCCCCA 61.090 66.667 0.00 0.00 0.00 4.96
1480 1706 0.313987 TCTTGCGCTCGTTCTTCTCA 59.686 50.000 9.73 0.00 0.00 3.27
1511 1737 2.487986 CCTTCTCTTTGTGTGCCCTCTT 60.488 50.000 0.00 0.00 0.00 2.85
1521 1747 1.343069 ACGAGCCTCCTTCTCTTTGT 58.657 50.000 0.00 0.00 0.00 2.83
1641 1867 3.922171 TGTTGGTGCCTTTTCCATTTT 57.078 38.095 0.00 0.00 33.50 1.82
1658 1884 4.115516 CTCGAAAGTCCATCATCGATGTT 58.884 43.478 24.09 14.06 42.66 2.71
1688 1914 5.349817 GTCTCGAATGACAAGTTCATCACAT 59.650 40.000 0.22 0.00 44.86 3.21
1744 1970 4.783764 AGTTCGTCACACATGATGTCTA 57.216 40.909 0.00 0.00 40.64 2.59
1752 1978 5.113383 TCAAACTACAAGTTCGTCACACAT 58.887 37.500 0.00 0.00 37.47 3.21
1760 1986 8.294341 TCAAATAGTCTCAAACTACAAGTTCG 57.706 34.615 0.00 0.00 43.21 3.95
1770 1996 7.848051 CGCACATAATCTCAAATAGTCTCAAAC 59.152 37.037 0.00 0.00 0.00 2.93
1796 2032 6.952935 AGTCTCGAATGACAAACATAGTTC 57.047 37.500 7.47 0.00 38.38 3.01
1840 2080 9.463443 AAACAAAGCATACTAGTTGAAACATTC 57.537 29.630 0.00 0.00 0.00 2.67
1843 2083 9.724839 GTTAAACAAAGCATACTAGTTGAAACA 57.275 29.630 0.00 0.00 30.73 2.83
1844 2084 9.724839 TGTTAAACAAAGCATACTAGTTGAAAC 57.275 29.630 0.00 1.62 30.85 2.78
1846 2086 9.724839 GTTGTTAAACAAAGCATACTAGTTGAA 57.275 29.630 0.00 0.00 40.15 2.69
1847 2087 8.065407 CGTTGTTAAACAAAGCATACTAGTTGA 58.935 33.333 0.00 0.00 40.15 3.18
1848 2088 7.853929 ACGTTGTTAAACAAAGCATACTAGTTG 59.146 33.333 0.00 0.52 40.44 3.16
1849 2089 7.853929 CACGTTGTTAAACAAAGCATACTAGTT 59.146 33.333 0.00 0.00 40.44 2.24
1871 2137 4.783903 GCAACTTGTTGCACACGT 57.216 50.000 27.19 0.00 46.60 4.49
1899 2165 5.048364 TGTGCCGAATAGCAACTTGTTAATT 60.048 36.000 0.00 0.00 46.19 1.40
1908 2174 0.958382 TGGGTGTGCCGAATAGCAAC 60.958 55.000 0.00 0.00 46.19 4.17
1909 2175 0.676466 CTGGGTGTGCCGAATAGCAA 60.676 55.000 0.00 0.00 46.19 3.91
1910 2176 1.078497 CTGGGTGTGCCGAATAGCA 60.078 57.895 0.00 0.00 41.46 3.49
1911 2177 1.090052 GTCTGGGTGTGCCGAATAGC 61.090 60.000 0.00 0.00 34.97 2.97
1912 2178 0.806102 CGTCTGGGTGTGCCGAATAG 60.806 60.000 0.00 0.00 34.97 1.73
1913 2179 1.216977 CGTCTGGGTGTGCCGAATA 59.783 57.895 0.00 0.00 34.97 1.75
1914 2180 2.047274 CGTCTGGGTGTGCCGAAT 60.047 61.111 0.00 0.00 34.97 3.34
1915 2181 4.980805 GCGTCTGGGTGTGCCGAA 62.981 66.667 0.00 0.00 34.97 4.30
1919 2185 1.815421 CTATGGCGTCTGGGTGTGC 60.815 63.158 0.00 0.00 0.00 4.57
1920 2186 0.460284 GTCTATGGCGTCTGGGTGTG 60.460 60.000 0.00 0.00 0.00 3.82
1921 2187 1.614241 GGTCTATGGCGTCTGGGTGT 61.614 60.000 0.00 0.00 0.00 4.16
1922 2188 1.144057 GGTCTATGGCGTCTGGGTG 59.856 63.158 0.00 0.00 0.00 4.61
1923 2189 2.064581 GGGTCTATGGCGTCTGGGT 61.065 63.158 0.00 0.00 0.00 4.51
1924 2190 1.762460 AGGGTCTATGGCGTCTGGG 60.762 63.158 0.00 0.00 0.00 4.45
1950 2216 0.937441 TGCTCTCTGGATAGGGACCT 59.063 55.000 0.00 0.00 0.00 3.85
1970 2236 2.223845 GCGCAATTGCAACTTGGAAAAT 59.776 40.909 28.77 0.00 42.21 1.82
1975 2241 4.340076 TGCGCAATTGCAACTTGG 57.660 50.000 28.77 13.15 43.02 3.61
1983 2249 1.081242 GTCTGGGTGTGCGCAATTG 60.081 57.895 14.00 0.00 37.11 2.32
1984 2250 2.616330 CGTCTGGGTGTGCGCAATT 61.616 57.895 14.00 0.00 37.11 2.32
2006 2273 4.329545 GCCAGACGCCAGGGAACA 62.330 66.667 0.00 0.00 0.00 3.18
2007 2274 2.579684 CTAGCCAGACGCCAGGGAAC 62.580 65.000 0.00 0.00 38.78 3.62
2008 2275 2.284331 TAGCCAGACGCCAGGGAA 60.284 61.111 0.00 0.00 38.78 3.97
2009 2276 2.759973 CTAGCCAGACGCCAGGGA 60.760 66.667 0.00 0.00 38.78 4.20
2024 2291 1.876416 GCTTCCTGCGTGACCAAACTA 60.876 52.381 0.00 0.00 0.00 2.24
2025 2292 1.166531 GCTTCCTGCGTGACCAAACT 61.167 55.000 0.00 0.00 0.00 2.66
2026 2293 1.282875 GCTTCCTGCGTGACCAAAC 59.717 57.895 0.00 0.00 0.00 2.93
2027 2294 1.896660 GGCTTCCTGCGTGACCAAA 60.897 57.895 0.00 0.00 44.05 3.28
2028 2295 2.281484 GGCTTCCTGCGTGACCAA 60.281 61.111 0.00 0.00 44.05 3.67
2029 2296 3.535629 CTGGCTTCCTGCGTGACCA 62.536 63.158 0.00 0.00 44.05 4.02
2030 2297 2.743928 CTGGCTTCCTGCGTGACC 60.744 66.667 0.00 0.00 44.05 4.02
2031 2298 2.029844 GTCTGGCTTCCTGCGTGAC 61.030 63.158 0.00 0.00 44.05 3.67
2032 2299 2.343758 GTCTGGCTTCCTGCGTGA 59.656 61.111 0.00 0.00 44.05 4.35
2033 2300 2.031012 TGTCTGGCTTCCTGCGTG 59.969 61.111 0.00 0.00 44.05 5.34
2034 2301 2.031163 GTGTCTGGCTTCCTGCGT 59.969 61.111 0.00 0.00 44.05 5.24
2035 2302 1.376424 ATGTGTCTGGCTTCCTGCG 60.376 57.895 0.00 0.00 44.05 5.18
2036 2303 0.607489 ACATGTGTCTGGCTTCCTGC 60.607 55.000 0.00 0.00 41.94 4.85
2037 2304 1.446907 GACATGTGTCTGGCTTCCTG 58.553 55.000 1.15 0.00 41.65 3.86
2038 2305 3.944476 GACATGTGTCTGGCTTCCT 57.056 52.632 1.15 0.00 41.65 3.36
2047 2314 1.091771 CGGGCCATCAGACATGTGTC 61.092 60.000 1.15 5.01 45.08 3.67
2048 2315 1.078214 CGGGCCATCAGACATGTGT 60.078 57.895 1.15 0.00 0.00 3.72
2049 2316 2.475466 GCGGGCCATCAGACATGTG 61.475 63.158 1.15 0.00 0.00 3.21
2050 2317 2.124570 GCGGGCCATCAGACATGT 60.125 61.111 4.39 0.00 0.00 3.21
2051 2318 3.274586 CGCGGGCCATCAGACATG 61.275 66.667 4.39 0.00 0.00 3.21
2069 2336 3.691342 TCCTTGGCGTCTGGTCGG 61.691 66.667 0.00 0.00 0.00 4.79
2070 2337 2.432628 GTCCTTGGCGTCTGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
2071 2338 2.047179 GGTCCTTGGCGTCTGGTC 60.047 66.667 0.00 0.00 0.00 4.02
2072 2339 2.224159 ATGGTCCTTGGCGTCTGGT 61.224 57.895 0.00 0.00 0.00 4.00
2073 2340 1.746615 CATGGTCCTTGGCGTCTGG 60.747 63.158 0.00 0.00 0.00 3.86
2074 2341 1.746615 CCATGGTCCTTGGCGTCTG 60.747 63.158 10.74 0.00 0.00 3.51
2075 2342 2.671070 CCATGGTCCTTGGCGTCT 59.329 61.111 10.74 0.00 0.00 4.18
2080 2347 1.586028 CAAACGCCATGGTCCTTGG 59.414 57.895 17.78 17.78 37.31 3.61
2081 2348 1.586028 CCAAACGCCATGGTCCTTG 59.414 57.895 14.67 13.23 33.08 3.61
2082 2349 2.275380 GCCAAACGCCATGGTCCTT 61.275 57.895 14.67 0.89 40.23 3.36
2083 2350 1.847798 TAGCCAAACGCCATGGTCCT 61.848 55.000 14.67 2.32 40.23 3.85
2084 2351 1.377987 TAGCCAAACGCCATGGTCC 60.378 57.895 14.67 0.00 40.23 4.46
2085 2352 0.676782 AGTAGCCAAACGCCATGGTC 60.677 55.000 14.67 4.79 40.23 4.02
2086 2353 0.251165 AAGTAGCCAAACGCCATGGT 60.251 50.000 14.67 0.00 40.23 3.55
2087 2354 0.171007 CAAGTAGCCAAACGCCATGG 59.829 55.000 7.63 7.63 41.08 3.66
2088 2355 0.171007 CCAAGTAGCCAAACGCCATG 59.829 55.000 0.00 0.00 38.78 3.66
2089 2356 0.965363 CCCAAGTAGCCAAACGCCAT 60.965 55.000 0.00 0.00 38.78 4.40
2090 2357 1.602323 CCCAAGTAGCCAAACGCCA 60.602 57.895 0.00 0.00 38.78 5.69
2091 2358 2.989881 GCCCAAGTAGCCAAACGCC 61.990 63.158 0.00 0.00 38.78 5.68
2092 2359 1.801309 TTGCCCAAGTAGCCAAACGC 61.801 55.000 0.00 0.00 37.98 4.84
2093 2360 0.039527 GTTGCCCAAGTAGCCAAACG 60.040 55.000 0.00 0.00 0.00 3.60
2094 2361 0.039527 CGTTGCCCAAGTAGCCAAAC 60.040 55.000 0.00 0.00 0.00 2.93
2095 2362 0.466555 ACGTTGCCCAAGTAGCCAAA 60.467 50.000 0.00 0.00 0.00 3.28
2096 2363 0.887387 GACGTTGCCCAAGTAGCCAA 60.887 55.000 0.00 0.00 0.00 4.52
2097 2364 1.302192 GACGTTGCCCAAGTAGCCA 60.302 57.895 0.00 0.00 0.00 4.75
2098 2365 0.887387 TTGACGTTGCCCAAGTAGCC 60.887 55.000 0.00 0.00 0.00 3.93
2099 2366 0.237498 GTTGACGTTGCCCAAGTAGC 59.763 55.000 0.00 0.00 0.00 3.58
2100 2367 0.872388 GGTTGACGTTGCCCAAGTAG 59.128 55.000 0.00 0.00 0.00 2.57
2101 2368 0.180642 TGGTTGACGTTGCCCAAGTA 59.819 50.000 0.00 0.00 0.00 2.24
2102 2369 1.077357 TGGTTGACGTTGCCCAAGT 60.077 52.632 0.00 0.00 0.00 3.16
2103 2370 0.817634 TCTGGTTGACGTTGCCCAAG 60.818 55.000 0.00 0.00 0.00 3.61
2104 2371 1.098712 GTCTGGTTGACGTTGCCCAA 61.099 55.000 0.00 0.00 35.81 4.12
2105 2372 1.525077 GTCTGGTTGACGTTGCCCA 60.525 57.895 0.00 0.00 35.81 5.36
2106 2373 3.340789 GTCTGGTTGACGTTGCCC 58.659 61.111 0.00 0.00 35.81 5.36
2113 2380 2.358737 CCCTGGCGTCTGGTTGAC 60.359 66.667 12.29 0.00 42.06 3.18
2114 2381 2.525629 TCCCTGGCGTCTGGTTGA 60.526 61.111 12.29 0.00 0.00 3.18
2115 2382 2.358737 GTCCCTGGCGTCTGGTTG 60.359 66.667 12.29 0.00 0.00 3.77
2116 2383 3.637273 GGTCCCTGGCGTCTGGTT 61.637 66.667 12.29 0.00 0.00 3.67
2119 2386 4.742201 CACGGTCCCTGGCGTCTG 62.742 72.222 0.00 0.00 0.00 3.51
2126 2393 4.742201 CAGACGCCACGGTCCCTG 62.742 72.222 0.00 0.00 37.66 4.45
2132 2399 4.619227 AACACCCAGACGCCACGG 62.619 66.667 0.00 0.00 0.00 4.94
2133 2400 3.345808 CAACACCCAGACGCCACG 61.346 66.667 0.00 0.00 0.00 4.94
2134 2401 3.660111 GCAACACCCAGACGCCAC 61.660 66.667 0.00 0.00 0.00 5.01
2135 2402 4.182433 TGCAACACCCAGACGCCA 62.182 61.111 0.00 0.00 0.00 5.69
2136 2403 3.660111 GTGCAACACCCAGACGCC 61.660 66.667 0.00 0.00 36.32 5.68
2137 2404 2.896801 CTGTGCAACACCCAGACGC 61.897 63.158 0.00 0.00 45.67 5.19
2138 2405 1.095228 AACTGTGCAACACCCAGACG 61.095 55.000 8.15 0.00 45.67 4.18
2139 2406 1.602377 GTAACTGTGCAACACCCAGAC 59.398 52.381 8.15 0.00 45.67 3.51
2140 2407 1.210722 TGTAACTGTGCAACACCCAGA 59.789 47.619 8.15 0.00 45.67 3.86
2141 2408 1.674359 TGTAACTGTGCAACACCCAG 58.326 50.000 0.00 0.00 45.67 4.45
2142 2409 2.356665 ATGTAACTGTGCAACACCCA 57.643 45.000 0.00 0.00 45.67 4.51
2143 2410 3.638484 GAAATGTAACTGTGCAACACCC 58.362 45.455 0.00 0.00 45.67 4.61
2144 2411 3.296628 CGAAATGTAACTGTGCAACACC 58.703 45.455 0.00 0.00 45.67 4.16
2145 2412 2.719046 GCGAAATGTAACTGTGCAACAC 59.281 45.455 0.00 0.00 45.67 3.32
2147 2414 3.268013 AGCGAAATGTAACTGTGCAAC 57.732 42.857 0.00 0.00 37.35 4.17
2148 2415 3.563808 AGAAGCGAAATGTAACTGTGCAA 59.436 39.130 0.00 0.00 0.00 4.08
2149 2416 3.058983 CAGAAGCGAAATGTAACTGTGCA 60.059 43.478 0.00 0.00 0.00 4.57
2150 2417 3.058914 ACAGAAGCGAAATGTAACTGTGC 60.059 43.478 0.00 0.00 0.00 4.57
2151 2418 4.732285 ACAGAAGCGAAATGTAACTGTG 57.268 40.909 0.00 0.00 0.00 3.66
2152 2419 4.814234 TCAACAGAAGCGAAATGTAACTGT 59.186 37.500 0.00 0.00 0.00 3.55
2153 2420 5.342806 TCAACAGAAGCGAAATGTAACTG 57.657 39.130 0.00 0.00 0.00 3.16
2154 2421 6.560253 AATCAACAGAAGCGAAATGTAACT 57.440 33.333 0.00 0.00 0.00 2.24
2155 2422 7.358352 CCAAAATCAACAGAAGCGAAATGTAAC 60.358 37.037 0.00 0.00 0.00 2.50
2156 2423 6.640499 CCAAAATCAACAGAAGCGAAATGTAA 59.360 34.615 0.00 0.00 0.00 2.41
2157 2424 6.148948 CCAAAATCAACAGAAGCGAAATGTA 58.851 36.000 0.00 0.00 0.00 2.29
2158 2425 4.984161 CCAAAATCAACAGAAGCGAAATGT 59.016 37.500 0.00 0.00 0.00 2.71
2159 2426 4.386652 CCCAAAATCAACAGAAGCGAAATG 59.613 41.667 0.00 0.00 0.00 2.32
2160 2427 4.559153 CCCAAAATCAACAGAAGCGAAAT 58.441 39.130 0.00 0.00 0.00 2.17
2161 2428 3.243704 CCCCAAAATCAACAGAAGCGAAA 60.244 43.478 0.00 0.00 0.00 3.46
2162 2429 2.295909 CCCCAAAATCAACAGAAGCGAA 59.704 45.455 0.00 0.00 0.00 4.70
2163 2430 1.885887 CCCCAAAATCAACAGAAGCGA 59.114 47.619 0.00 0.00 0.00 4.93
2164 2431 1.067635 CCCCCAAAATCAACAGAAGCG 60.068 52.381 0.00 0.00 0.00 4.68
2165 2432 2.749280 CCCCCAAAATCAACAGAAGC 57.251 50.000 0.00 0.00 0.00 3.86
2187 2454 2.132352 CCTAGCGTCTGGTACCCCC 61.132 68.421 10.07 0.00 0.00 5.40
2188 2455 2.132352 CCCTAGCGTCTGGTACCCC 61.132 68.421 10.07 0.00 0.00 4.95
2189 2456 1.076485 TCCCTAGCGTCTGGTACCC 60.076 63.158 10.07 0.00 0.00 3.69
2190 2457 1.390383 GGTCCCTAGCGTCTGGTACC 61.390 65.000 4.43 4.43 0.00 3.34
2191 2458 1.390383 GGGTCCCTAGCGTCTGGTAC 61.390 65.000 0.00 0.00 0.00 3.34
2192 2459 1.076485 GGGTCCCTAGCGTCTGGTA 60.076 63.158 0.00 0.00 0.00 3.25
2193 2460 2.363925 GGGTCCCTAGCGTCTGGT 60.364 66.667 0.00 0.00 0.00 4.00
2194 2461 2.042843 AGGGTCCCTAGCGTCTGG 60.043 66.667 9.39 0.00 28.47 3.86
2195 2462 2.427245 CCAGGGTCCCTAGCGTCTG 61.427 68.421 11.12 0.00 29.64 3.51
2196 2463 2.042843 CCAGGGTCCCTAGCGTCT 60.043 66.667 11.12 0.00 29.64 4.18
2197 2464 3.851128 GCCAGGGTCCCTAGCGTC 61.851 72.222 12.97 0.00 27.51 5.19
2200 2467 2.967946 AAACGCCAGGGTCCCTAGC 61.968 63.158 17.82 17.82 35.00 3.42
2201 2468 1.078426 CAAACGCCAGGGTCCCTAG 60.078 63.158 11.12 4.06 29.64 3.02
2202 2469 2.598787 CCAAACGCCAGGGTCCCTA 61.599 63.158 11.12 0.00 29.64 3.53
2203 2470 3.966543 CCAAACGCCAGGGTCCCT 61.967 66.667 3.85 3.85 0.00 4.20
2204 2471 1.917336 TATCCAAACGCCAGGGTCCC 61.917 60.000 0.00 0.00 0.00 4.46
2205 2472 0.182775 ATATCCAAACGCCAGGGTCC 59.817 55.000 0.00 0.00 0.00 4.46
2206 2473 2.052782 AATATCCAAACGCCAGGGTC 57.947 50.000 0.00 0.00 0.00 4.46
2207 2474 2.099405 CAAATATCCAAACGCCAGGGT 58.901 47.619 0.00 0.00 0.00 4.34
2208 2475 1.408702 CCAAATATCCAAACGCCAGGG 59.591 52.381 0.00 0.00 0.00 4.45
2209 2476 1.408702 CCCAAATATCCAAACGCCAGG 59.591 52.381 0.00 0.00 0.00 4.45
2210 2477 1.202405 GCCCAAATATCCAAACGCCAG 60.202 52.381 0.00 0.00 0.00 4.85
2211 2478 0.820871 GCCCAAATATCCAAACGCCA 59.179 50.000 0.00 0.00 0.00 5.69
2212 2479 0.104120 GGCCCAAATATCCAAACGCC 59.896 55.000 0.00 0.00 0.00 5.68
2213 2480 0.820871 TGGCCCAAATATCCAAACGC 59.179 50.000 0.00 0.00 0.00 4.84
2214 2481 2.430332 ACATGGCCCAAATATCCAAACG 59.570 45.455 0.00 0.00 33.04 3.60
2215 2482 3.450457 TGACATGGCCCAAATATCCAAAC 59.550 43.478 0.00 0.00 33.04 2.93
2216 2483 3.717576 TGACATGGCCCAAATATCCAAA 58.282 40.909 0.00 0.00 33.04 3.28
2217 2484 3.395054 TGACATGGCCCAAATATCCAA 57.605 42.857 0.00 0.00 33.04 3.53
2218 2485 3.030291 GTTGACATGGCCCAAATATCCA 58.970 45.455 0.00 0.00 0.00 3.41
2219 2486 2.365293 GGTTGACATGGCCCAAATATCC 59.635 50.000 0.00 0.00 0.00 2.59
2220 2487 3.030291 TGGTTGACATGGCCCAAATATC 58.970 45.455 0.00 0.00 0.00 1.63
2221 2488 3.033184 CTGGTTGACATGGCCCAAATAT 58.967 45.455 0.00 0.00 0.00 1.28
2222 2489 2.042297 TCTGGTTGACATGGCCCAAATA 59.958 45.455 0.00 0.00 0.00 1.40
2223 2490 1.203162 TCTGGTTGACATGGCCCAAAT 60.203 47.619 0.00 0.00 0.00 2.32
2224 2491 0.187117 TCTGGTTGACATGGCCCAAA 59.813 50.000 0.00 0.00 0.00 3.28
2225 2492 0.409092 ATCTGGTTGACATGGCCCAA 59.591 50.000 0.00 0.00 0.00 4.12
2226 2493 0.323633 CATCTGGTTGACATGGCCCA 60.324 55.000 0.00 0.00 0.00 5.36
2227 2494 1.669999 GCATCTGGTTGACATGGCCC 61.670 60.000 0.00 0.00 0.00 5.80
2228 2495 1.669999 GGCATCTGGTTGACATGGCC 61.670 60.000 0.00 0.00 33.98 5.36
2229 2496 1.811860 GGCATCTGGTTGACATGGC 59.188 57.895 0.00 0.00 0.00 4.40
2230 2497 0.392863 TCGGCATCTGGTTGACATGG 60.393 55.000 0.00 0.00 0.00 3.66
2231 2498 1.012086 CTCGGCATCTGGTTGACATG 58.988 55.000 0.00 0.00 0.00 3.21
2232 2499 0.107508 CCTCGGCATCTGGTTGACAT 60.108 55.000 0.00 0.00 0.00 3.06
2233 2500 1.191489 TCCTCGGCATCTGGTTGACA 61.191 55.000 0.00 0.00 0.00 3.58
2234 2501 0.741221 GTCCTCGGCATCTGGTTGAC 60.741 60.000 0.00 0.00 0.00 3.18
2235 2502 1.596934 GTCCTCGGCATCTGGTTGA 59.403 57.895 0.00 0.00 0.00 3.18
2236 2503 1.450312 GGTCCTCGGCATCTGGTTG 60.450 63.158 0.00 0.00 0.00 3.77
2237 2504 2.670148 GGGTCCTCGGCATCTGGTT 61.670 63.158 0.00 0.00 0.00 3.67
2238 2505 3.083997 GGGTCCTCGGCATCTGGT 61.084 66.667 0.00 0.00 0.00 4.00
2239 2506 2.765807 AGGGTCCTCGGCATCTGG 60.766 66.667 0.00 0.00 0.00 3.86
2240 2507 2.503061 CAGGGTCCTCGGCATCTG 59.497 66.667 0.00 0.00 0.00 2.90
2241 2508 2.765807 CCAGGGTCCTCGGCATCT 60.766 66.667 0.00 0.00 0.00 2.90
2242 2509 4.554036 GCCAGGGTCCTCGGCATC 62.554 72.222 18.82 0.00 45.52 3.91


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

AutoCloner maintained by Alex Coulton.