Multiple sequence alignment - TraesCS1D01G051000

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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 TraesCS1D01G051000 chr1D 100.000 3609 0 0 1 3609 31059344 31062952 0.000000e+00 6665.0
1 TraesCS1D01G051000 chr1D 89.583 1872 181 9 788 2651 30651860 30653725 0.000000e+00 2364.0
2 TraesCS1D01G051000 chr1D 83.150 1911 273 27 762 2658 30572533 30574408 0.000000e+00 1700.0
3 TraesCS1D01G051000 chr1D 82.890 1917 273 34 764 2635 30429996 30431902 0.000000e+00 1672.0
4 TraesCS1D01G051000 chr1D 83.610 1385 193 21 1095 2469 31038496 31039856 0.000000e+00 1269.0
5 TraesCS1D01G051000 chr1D 79.733 750 119 14 116 864 30665972 30666689 2.490000e-141 512.0
6 TraesCS1D01G051000 chr1D 84.350 492 65 6 310 796 31352443 31352927 4.220000e-129 472.0
7 TraesCS1D01G051000 chr1D 78.534 573 102 9 1 556 31029624 31030192 1.230000e-94 357.0
8 TraesCS1D01G051000 chr1D 82.973 370 54 6 47 413 30310265 30310628 3.470000e-85 326.0
9 TraesCS1D01G051000 chr1D 78.378 518 98 9 47 556 30537729 30538240 1.250000e-84 324.0
10 TraesCS1D01G051000 chr1D 82.500 360 39 10 3167 3504 30431996 30432353 9.800000e-76 294.0
11 TraesCS1D01G051000 chr1D 80.851 376 68 2 116 491 30310761 30311132 3.520000e-75 292.0
12 TraesCS1D01G051000 chr1D 79.814 431 51 17 2463 2882 31050752 31051157 7.630000e-72 281.0
13 TraesCS1D01G051000 chr1D 86.528 193 25 1 577 768 30538583 30538775 1.020000e-50 211.0
14 TraesCS1D01G051000 chr1D 89.189 111 5 4 3158 3262 30277936 30278045 8.130000e-27 132.0
15 TraesCS1D01G051000 chr1D 85.833 120 15 2 579 697 31285613 31285731 3.780000e-25 126.0
16 TraesCS1D01G051000 chr1D 93.220 59 4 0 3105 3163 30277849 30277907 1.790000e-13 87.9
17 TraesCS1D01G051000 chr1D 88.406 69 6 2 3096 3163 30671594 30671661 8.310000e-12 82.4
18 TraesCS1D01G051000 chr1D 100.000 33 0 0 3226 3258 30381974 30382006 1.080000e-05 62.1
19 TraesCS1D01G051000 chr1D 95.000 40 1 1 3 42 30537662 30537700 1.080000e-05 62.1
20 TraesCS1D01G051000 chr1B 89.415 1899 194 5 758 2651 48997050 48998946 0.000000e+00 2386.0
21 TraesCS1D01G051000 chr1B 89.406 1869 192 6 788 2651 48932918 48934785 0.000000e+00 2350.0
22 TraesCS1D01G051000 chr1B 83.646 1810 255 19 1076 2872 49663580 49665361 0.000000e+00 1664.0
23 TraesCS1D01G051000 chr1B 89.010 1010 108 3 788 1796 48981920 48982927 0.000000e+00 1247.0
24 TraesCS1D01G051000 chr1B 84.628 1184 165 13 1459 2635 49643368 49644541 0.000000e+00 1162.0
25 TraesCS1D01G051000 chr1B 85.439 1037 144 3 263 1298 49642144 49643174 0.000000e+00 1072.0
26 TraesCS1D01G051000 chr1B 82.353 748 117 9 121 865 49675181 49675916 1.410000e-178 636.0
27 TraesCS1D01G051000 chr1B 81.923 780 113 22 2077 2845 49612164 49612926 5.080000e-178 634.0
28 TraesCS1D01G051000 chr1B 86.374 455 57 4 395 846 49166168 49166620 3.240000e-135 492.0
29 TraesCS1D01G051000 chr1B 79.492 512 90 10 47 555 48995899 48996398 2.060000e-92 350.0
30 TraesCS1D01G051000 chr1B 82.338 385 65 1 47 431 49634153 49634534 7.470000e-87 331.0
31 TraesCS1D01G051000 chr1B 81.176 170 13 13 3012 3163 49644724 49644892 6.330000e-23 119.0
32 TraesCS1D01G051000 chr1B 88.750 80 7 1 3147 3224 49665595 49665674 2.970000e-16 97.1
33 TraesCS1D01G051000 chr1B 79.070 129 16 10 3036 3163 49614613 49614731 1.070000e-10 78.7
34 TraesCS1D01G051000 chr1A 85.537 1929 247 23 1004 2908 30334281 30336201 0.000000e+00 1988.0
35 TraesCS1D01G051000 chr1A 91.769 1227 95 4 1390 2610 30389377 30390603 0.000000e+00 1701.0
36 TraesCS1D01G051000 chr1A 93.596 406 24 2 990 1395 30388592 30388995 3.990000e-169 604.0
37 TraesCS1D01G051000 chr1A 80.640 656 114 11 116 766 30455502 30456149 2.500000e-136 496.0
38 TraesCS1D01G051000 chr1A 83.871 496 67 9 309 797 30771198 30771687 9.130000e-126 460.0


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 TraesCS1D01G051000 chr1D 31059344 31062952 3608 False 6665.000000 6665 100.000000 1 3609 1 chr1D.!!$F9 3608
1 TraesCS1D01G051000 chr1D 30651860 30653725 1865 False 2364.000000 2364 89.583000 788 2651 1 chr1D.!!$F3 1863
2 TraesCS1D01G051000 chr1D 30572533 30574408 1875 False 1700.000000 1700 83.150000 762 2658 1 chr1D.!!$F2 1896
3 TraesCS1D01G051000 chr1D 31038496 31039856 1360 False 1269.000000 1269 83.610000 1095 2469 1 chr1D.!!$F7 1374
4 TraesCS1D01G051000 chr1D 30429996 30432353 2357 False 983.000000 1672 82.695000 764 3504 2 chr1D.!!$F14 2740
5 TraesCS1D01G051000 chr1D 30665972 30666689 717 False 512.000000 512 79.733000 116 864 1 chr1D.!!$F4 748
6 TraesCS1D01G051000 chr1D 31029624 31030192 568 False 357.000000 357 78.534000 1 556 1 chr1D.!!$F6 555
7 TraesCS1D01G051000 chr1D 30310265 30311132 867 False 309.000000 326 81.912000 47 491 2 chr1D.!!$F13 444
8 TraesCS1D01G051000 chr1B 48932918 48934785 1867 False 2350.000000 2350 89.406000 788 2651 1 chr1B.!!$F1 1863
9 TraesCS1D01G051000 chr1B 48995899 48998946 3047 False 1368.000000 2386 84.453500 47 2651 2 chr1B.!!$F6 2604
10 TraesCS1D01G051000 chr1B 48981920 48982927 1007 False 1247.000000 1247 89.010000 788 1796 1 chr1B.!!$F2 1008
11 TraesCS1D01G051000 chr1B 49663580 49665674 2094 False 880.550000 1664 86.198000 1076 3224 2 chr1B.!!$F9 2148
12 TraesCS1D01G051000 chr1B 49642144 49644892 2748 False 784.333333 1162 83.747667 263 3163 3 chr1B.!!$F8 2900
13 TraesCS1D01G051000 chr1B 49675181 49675916 735 False 636.000000 636 82.353000 121 865 1 chr1B.!!$F5 744
14 TraesCS1D01G051000 chr1B 49612164 49614731 2567 False 356.350000 634 80.496500 2077 3163 2 chr1B.!!$F7 1086
15 TraesCS1D01G051000 chr1A 30334281 30336201 1920 False 1988.000000 1988 85.537000 1004 2908 1 chr1A.!!$F1 1904
16 TraesCS1D01G051000 chr1A 30388592 30390603 2011 False 1152.500000 1701 92.682500 990 2610 2 chr1A.!!$F4 1620
17 TraesCS1D01G051000 chr1A 30455502 30456149 647 False 496.000000 496 80.640000 116 766 1 chr1A.!!$F2 650

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
867 1972 0.034477 GGATCACGGGTTCCATTGGT 60.034 55.0 10.00 0.00 33.77 3.67 F
870 1975 0.035820 TCACGGGTTCCATTGGTAGC 60.036 55.0 1.86 2.56 0.00 3.58 F
2278 3832 0.249322 AGTGCGACGTGTACAGCTTT 60.249 50.0 0.00 0.00 35.35 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2326 3880 0.881796 GGCAAAAGAACGGAAGGAGG 59.118 55.0 0.00 0.0 0.0 4.30 R
2404 3958 1.658686 CCTTCTCCTCCTCGACGGTG 61.659 65.0 0.00 0.0 0.0 4.94 R
3440 6619 0.104120 TCCTTCACTGTGTGACCACG 59.896 55.0 7.79 0.0 42.6 4.94 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
82 98 3.347958 TTGTGTCCAACATTTCGCTTC 57.652 42.857 0.00 0.00 38.99 3.86
83 99 1.606668 TGTGTCCAACATTTCGCTTCC 59.393 47.619 0.00 0.00 32.36 3.46
85 101 0.454452 GTCCAACATTTCGCTTCCGC 60.454 55.000 0.00 0.00 0.00 5.54
86 102 0.605319 TCCAACATTTCGCTTCCGCT 60.605 50.000 0.00 0.00 0.00 5.52
87 103 1.083489 CCAACATTTCGCTTCCGCTA 58.917 50.000 0.00 0.00 0.00 4.26
92 108 1.665679 CATTTCGCTTCCGCTATGTGT 59.334 47.619 0.00 0.00 0.00 3.72
153 169 9.217278 GACTTGCATCATCTTGTATATCTGAAT 57.783 33.333 0.00 0.00 0.00 2.57
166 182 9.817809 TTGTATATCTGAATCTCAGTTACAACC 57.182 33.333 16.46 2.91 44.58 3.77
177 193 2.496070 CAGTTACAACCATCTCTCGGGA 59.504 50.000 0.00 0.00 0.00 5.14
233 249 2.028658 TCACTCACTTGGATCTGTCTGC 60.029 50.000 0.00 0.00 0.00 4.26
246 262 0.178995 TGTCTGCCAATGACCTGCAA 60.179 50.000 0.00 0.00 34.06 4.08
284 301 9.709495 AACGTCCTTATGTAATTGTACTAAACA 57.291 29.630 0.00 0.00 35.88 2.83
315 332 9.350951 TCCATCGATCTCTCTTACTACAATTTA 57.649 33.333 0.00 0.00 0.00 1.40
331 934 9.338622 ACTACAATTTATTTCTACCATGCCTAC 57.661 33.333 0.00 0.00 0.00 3.18
339 942 7.670605 ATTTCTACCATGCCTACTACAGTAA 57.329 36.000 0.00 0.00 0.00 2.24
347 950 5.640189 TGCCTACTACAGTAAGAACACTC 57.360 43.478 0.00 0.00 0.00 3.51
374 977 6.153510 GGAATTTAATGAGCCTCTCCACTTTT 59.846 38.462 0.00 0.00 0.00 2.27
375 978 7.310052 GGAATTTAATGAGCCTCTCCACTTTTT 60.310 37.037 0.00 0.00 0.00 1.94
398 1001 3.010027 TGCAGATTTACCCCATCTTGTCA 59.990 43.478 0.00 0.00 0.00 3.58
399 1002 3.629398 GCAGATTTACCCCATCTTGTCAG 59.371 47.826 0.00 0.00 0.00 3.51
414 1017 2.796557 TGTCAGTCTGGACCTCAGTAG 58.203 52.381 0.00 0.00 43.76 2.57
426 1206 3.088532 ACCTCAGTAGCAACTCTCTCTG 58.911 50.000 0.00 0.00 31.97 3.35
436 1216 1.867363 ACTCTCTCTGGGGCGTAATT 58.133 50.000 0.00 0.00 0.00 1.40
445 1225 1.283613 TGGGGCGTAATTCCATCAAGT 59.716 47.619 0.00 0.00 0.00 3.16
469 1249 4.157958 GCTCTTGCCAAGCTCGCG 62.158 66.667 0.00 0.00 36.80 5.87
470 1250 4.157958 CTCTTGCCAAGCTCGCGC 62.158 66.667 0.00 0.00 0.00 6.86
525 1330 1.208052 CATCCCGCCATCCATAGGTAG 59.792 57.143 0.00 0.00 0.00 3.18
701 1518 2.949177 ACAACACTGGCACTTGGATA 57.051 45.000 0.00 0.00 0.00 2.59
726 1543 2.367567 TCAGCTTAAGGGCCTATTACCG 59.632 50.000 6.41 0.00 0.00 4.02
730 1547 3.725490 CTTAAGGGCCTATTACCGTCAC 58.275 50.000 6.41 0.00 0.00 3.67
806 1911 2.230660 GGGTTCCATTGGTAGCATAGC 58.769 52.381 12.71 0.00 40.09 2.97
840 1945 8.797438 ACAAGTTTAGAATTTCTGGATCTTTCC 58.203 33.333 9.22 0.00 42.94 3.13
852 1957 4.820284 GGATCTTTCCAACAATCGGATC 57.180 45.455 0.00 0.00 42.12 3.36
853 1958 4.199310 GGATCTTTCCAACAATCGGATCA 58.801 43.478 0.00 0.00 42.12 2.92
854 1959 4.035675 GGATCTTTCCAACAATCGGATCAC 59.964 45.833 0.00 0.00 42.12 3.06
855 1960 3.000041 TCTTTCCAACAATCGGATCACG 59.000 45.455 0.00 0.00 46.11 4.35
856 1961 1.732941 TTCCAACAATCGGATCACGG 58.267 50.000 0.00 0.00 44.45 4.94
857 1962 0.107897 TCCAACAATCGGATCACGGG 60.108 55.000 0.00 0.00 44.45 5.28
858 1963 0.392461 CCAACAATCGGATCACGGGT 60.392 55.000 0.00 0.00 44.45 5.28
859 1964 1.448985 CAACAATCGGATCACGGGTT 58.551 50.000 0.00 0.29 44.45 4.11
860 1965 1.396996 CAACAATCGGATCACGGGTTC 59.603 52.381 0.00 0.00 44.45 3.62
861 1966 0.107848 ACAATCGGATCACGGGTTCC 60.108 55.000 4.56 4.56 44.45 3.62
862 1967 0.107897 CAATCGGATCACGGGTTCCA 60.108 55.000 14.99 2.87 44.45 3.53
863 1968 0.837272 AATCGGATCACGGGTTCCAT 59.163 50.000 14.99 5.00 44.45 3.41
864 1969 0.837272 ATCGGATCACGGGTTCCATT 59.163 50.000 14.99 0.00 44.45 3.16
865 1970 0.107897 TCGGATCACGGGTTCCATTG 60.108 55.000 14.99 0.00 44.45 2.82
866 1971 1.095228 CGGATCACGGGTTCCATTGG 61.095 60.000 14.99 0.00 39.42 3.16
867 1972 0.034477 GGATCACGGGTTCCATTGGT 60.034 55.000 10.00 0.00 33.77 3.67
868 1973 1.210967 GGATCACGGGTTCCATTGGTA 59.789 52.381 10.00 0.00 33.77 3.25
869 1974 2.561569 GATCACGGGTTCCATTGGTAG 58.438 52.381 1.86 0.00 0.00 3.18
870 1975 0.035820 TCACGGGTTCCATTGGTAGC 60.036 55.000 1.86 2.56 0.00 3.58
871 1976 0.322098 CACGGGTTCCATTGGTAGCA 60.322 55.000 12.71 0.00 0.00 3.49
872 1977 0.322187 ACGGGTTCCATTGGTAGCAC 60.322 55.000 12.71 2.87 0.00 4.40
873 1978 0.322098 CGGGTTCCATTGGTAGCACA 60.322 55.000 12.71 0.00 0.00 4.57
874 1979 1.463674 GGGTTCCATTGGTAGCACAG 58.536 55.000 12.71 0.00 0.00 3.66
875 1980 1.463674 GGTTCCATTGGTAGCACAGG 58.536 55.000 6.64 0.00 0.00 4.00
876 1981 1.004277 GGTTCCATTGGTAGCACAGGA 59.996 52.381 9.77 9.77 0.00 3.86
877 1982 2.554344 GGTTCCATTGGTAGCACAGGAA 60.554 50.000 18.43 18.43 33.10 3.36
878 1983 3.153919 GTTCCATTGGTAGCACAGGAAA 58.846 45.455 22.06 9.40 36.95 3.13
879 1984 3.737559 TCCATTGGTAGCACAGGAAAT 57.262 42.857 11.09 0.00 0.00 2.17
880 1985 3.620488 TCCATTGGTAGCACAGGAAATC 58.380 45.455 11.09 0.00 0.00 2.17
881 1986 3.266772 TCCATTGGTAGCACAGGAAATCT 59.733 43.478 11.09 0.00 0.00 2.40
882 1987 4.473196 TCCATTGGTAGCACAGGAAATCTA 59.527 41.667 11.09 0.00 0.00 1.98
883 1988 5.045213 TCCATTGGTAGCACAGGAAATCTAA 60.045 40.000 11.09 0.00 0.00 2.10
884 1989 5.066505 CCATTGGTAGCACAGGAAATCTAAC 59.933 44.000 6.04 0.00 0.00 2.34
885 1990 4.901197 TGGTAGCACAGGAAATCTAACA 57.099 40.909 0.00 0.00 0.00 2.41
886 1991 5.235850 TGGTAGCACAGGAAATCTAACAA 57.764 39.130 0.00 0.00 0.00 2.83
887 1992 5.245531 TGGTAGCACAGGAAATCTAACAAG 58.754 41.667 0.00 0.00 0.00 3.16
888 1993 5.221843 TGGTAGCACAGGAAATCTAACAAGT 60.222 40.000 0.00 0.00 0.00 3.16
889 1994 5.705905 GGTAGCACAGGAAATCTAACAAGTT 59.294 40.000 0.00 0.00 0.00 2.66
890 1995 6.206829 GGTAGCACAGGAAATCTAACAAGTTT 59.793 38.462 0.00 0.00 0.00 2.66
891 1996 7.389607 GGTAGCACAGGAAATCTAACAAGTTTA 59.610 37.037 0.00 0.00 0.00 2.01
892 1997 7.440523 AGCACAGGAAATCTAACAAGTTTAG 57.559 36.000 0.00 0.00 0.00 1.85
893 1998 7.224297 AGCACAGGAAATCTAACAAGTTTAGA 58.776 34.615 0.00 0.00 35.71 2.10
894 1999 7.389053 AGCACAGGAAATCTAACAAGTTTAGAG 59.611 37.037 0.69 0.00 34.84 2.43
954 2059 6.318648 CCATCCCTTCGACATTCTCAAAATTA 59.681 38.462 0.00 0.00 0.00 1.40
1159 2264 4.346709 TGACAGGACAGATACCACAAGAAA 59.653 41.667 0.00 0.00 0.00 2.52
1177 2282 6.870769 CAAGAAATTGGATATCTTGCCAACT 58.129 36.000 2.05 0.00 46.06 3.16
1188 2293 7.279758 GGATATCTTGCCAACTTATATGAGCTC 59.720 40.741 6.82 6.82 0.00 4.09
1348 2465 4.239304 CCATAATACGTACTTATGCGGCA 58.761 43.478 20.62 4.58 38.39 5.69
1395 2920 2.341101 ACCGAAGCTCGACGTGGAT 61.341 57.895 0.00 0.00 43.74 3.41
1854 3385 2.695666 TCTTATCGAGAGGGGAAGCTTG 59.304 50.000 2.10 0.00 0.00 4.01
2070 3601 0.449388 CGAGGAAACTGAAGCATGGC 59.551 55.000 0.00 0.00 44.43 4.40
2118 3649 1.959042 GCACATGTGGCTACATAGCT 58.041 50.000 26.55 6.89 45.53 3.32
2128 3659 3.651803 GCTACATAGCTCCTGGTACTG 57.348 52.381 3.56 0.00 45.62 2.74
2134 3667 1.944177 AGCTCCTGGTACTGACATGT 58.056 50.000 0.00 0.00 0.00 3.21
2153 3686 9.585099 TGACATGTGCTTAATCCATTTTTATTC 57.415 29.630 1.15 0.00 0.00 1.75
2248 3802 3.110705 AGAGCTGTCATCTACCATGGTT 58.889 45.455 25.38 1.14 0.00 3.67
2278 3832 0.249322 AGTGCGACGTGTACAGCTTT 60.249 50.000 0.00 0.00 35.35 3.51
2302 3856 1.335496 GTGGTTGCGCTGGAAGTTTTA 59.665 47.619 9.73 0.00 35.30 1.52
2326 3880 1.078143 AAAGCACCCAGGCGATCTC 60.078 57.895 0.00 0.00 39.27 2.75
2358 3912 1.100463 TTTTGCCGAACAGAGCAGCA 61.100 50.000 0.00 0.00 40.73 4.41
2376 3930 3.691609 CAGCAAGGGAAGTTCAAGGATAC 59.308 47.826 5.01 0.00 0.00 2.24
2479 4036 0.396974 TGCAAGTCAACCCCAAAGCT 60.397 50.000 0.00 0.00 0.00 3.74
2506 4063 4.261322 CCAACAATGCAGCAGGTATATCAC 60.261 45.833 0.00 0.00 0.00 3.06
2553 4110 0.179936 CTCATGCTCAGACCCCTTCC 59.820 60.000 0.00 0.00 0.00 3.46
2571 4128 4.699257 CCTTCCTGAAATCAGTCTTCAAGG 59.301 45.833 9.43 8.22 42.27 3.61
2572 4129 4.292186 TCCTGAAATCAGTCTTCAAGGG 57.708 45.455 9.43 0.00 42.27 3.95
2581 4138 2.486982 CAGTCTTCAAGGGTTGCATGAG 59.513 50.000 0.00 0.00 0.00 2.90
2634 4194 6.616947 GCTATATAGCTAGTCTCCTGTGTTG 58.383 44.000 24.63 0.00 45.62 3.33
2636 4196 2.310779 AGCTAGTCTCCTGTGTTGGA 57.689 50.000 0.00 0.00 34.52 3.53
2651 4211 9.928618 TCCTGTGTTGGAAATTATATATTTGGA 57.071 29.630 0.00 0.00 32.39 3.53
2698 4315 5.119931 CTTCGAGACAGAAGGATGGATAG 57.880 47.826 0.00 0.00 42.78 2.08
2828 4447 2.725221 ATCTGGCCCTCTTCATTCAC 57.275 50.000 0.00 0.00 0.00 3.18
2915 4535 4.400120 AGGAGGAATAGATACCGTCTGTC 58.600 47.826 0.00 0.00 37.83 3.51
2919 4539 6.072563 GGAGGAATAGATACCGTCTGTCTTAC 60.073 46.154 0.00 0.00 37.83 2.34
2942 4564 2.819608 GGAAACTTATGCAACAGGCTGA 59.180 45.455 23.66 0.00 45.15 4.26
2945 4567 5.473039 GAAACTTATGCAACAGGCTGAATT 58.527 37.500 23.66 2.46 45.15 2.17
2985 4624 3.003378 ACAACCGAAGCTTTTTAGCTGTC 59.997 43.478 0.00 0.95 45.54 3.51
3001 4640 2.607187 CTGTCACGATCCCACTTACAC 58.393 52.381 0.00 0.00 0.00 2.90
3004 4643 3.007506 TGTCACGATCCCACTTACACATT 59.992 43.478 0.00 0.00 0.00 2.71
3009 4992 3.618752 CGATCCCACTTACACATTGGTCA 60.619 47.826 0.00 0.00 0.00 4.02
3010 4993 4.526970 GATCCCACTTACACATTGGTCAT 58.473 43.478 0.00 0.00 0.00 3.06
3074 6208 3.045601 ACCAGATCTCAAGTTCAACCG 57.954 47.619 0.00 0.00 0.00 4.44
3081 6215 5.701290 AGATCTCAAGTTCAACCGGTTTTAG 59.299 40.000 19.55 6.99 0.00 1.85
3086 6220 4.684484 AGTTCAACCGGTTTTAGTCTCT 57.316 40.909 19.55 6.60 0.00 3.10
3087 6221 5.032327 AGTTCAACCGGTTTTAGTCTCTT 57.968 39.130 19.55 0.00 0.00 2.85
3088 6222 4.814771 AGTTCAACCGGTTTTAGTCTCTTG 59.185 41.667 19.55 2.73 0.00 3.02
3089 6223 4.411256 TCAACCGGTTTTAGTCTCTTGT 57.589 40.909 19.55 0.00 0.00 3.16
3090 6224 4.374399 TCAACCGGTTTTAGTCTCTTGTC 58.626 43.478 19.55 0.00 0.00 3.18
3091 6225 4.100498 TCAACCGGTTTTAGTCTCTTGTCT 59.900 41.667 19.55 0.00 0.00 3.41
3092 6226 4.684484 ACCGGTTTTAGTCTCTTGTCTT 57.316 40.909 0.00 0.00 0.00 3.01
3093 6227 5.032327 ACCGGTTTTAGTCTCTTGTCTTT 57.968 39.130 0.00 0.00 0.00 2.52
3164 6321 1.204467 GAAGCTCTCACACTCCAGAGG 59.796 57.143 0.00 0.00 37.26 3.69
3170 6327 4.320844 ACACTCCAGAGGGTGCTT 57.679 55.556 0.72 0.00 44.74 3.91
3225 6384 7.043565 CCCAACATGGAAGGAAGAATATTTTG 58.956 38.462 0.00 0.00 40.96 2.44
3226 6385 7.043565 CCAACATGGAAGGAAGAATATTTTGG 58.956 38.462 0.00 0.00 40.96 3.28
3231 6409 9.135189 CATGGAAGGAAGAATATTTTGGTCATA 57.865 33.333 0.00 0.00 0.00 2.15
3263 6441 5.841957 AATTTCCATCCTTGTCTATGTGC 57.158 39.130 0.00 0.00 0.00 4.57
3292 6470 2.159114 GCTCTGAGCTTAGAGTTCCTGG 60.159 54.545 29.88 10.14 44.77 4.45
3296 6474 4.780021 TCTGAGCTTAGAGTTCCTGGAAAT 59.220 41.667 11.40 10.41 0.00 2.17
3310 6488 9.936329 AGTTCCTGGAAATATTTTATGTATGGT 57.064 29.630 11.40 0.00 0.00 3.55
3317 6495 9.463443 GGAAATATTTTATGTATGGTTGCAGTC 57.537 33.333 1.43 0.00 0.00 3.51
3323 6501 4.558226 ATGTATGGTTGCAGTCTCTGAA 57.442 40.909 0.66 0.00 32.44 3.02
3328 6506 3.930336 TGGTTGCAGTCTCTGAATACTG 58.070 45.455 12.97 12.97 44.79 2.74
3330 6508 3.055819 GGTTGCAGTCTCTGAATACTGGA 60.056 47.826 16.93 13.25 42.72 3.86
3332 6510 4.662468 TGCAGTCTCTGAATACTGGATC 57.338 45.455 16.93 5.84 42.72 3.36
3333 6511 4.285020 TGCAGTCTCTGAATACTGGATCT 58.715 43.478 16.93 0.00 42.72 2.75
3334 6512 4.713814 TGCAGTCTCTGAATACTGGATCTT 59.286 41.667 16.93 0.00 42.72 2.40
3335 6513 5.163468 TGCAGTCTCTGAATACTGGATCTTC 60.163 44.000 16.93 4.81 42.72 2.87
3337 6515 6.462768 GCAGTCTCTGAATACTGGATCTTCAT 60.463 42.308 16.93 0.00 42.72 2.57
3341 6519 8.203485 GTCTCTGAATACTGGATCTTCATCTTT 58.797 37.037 0.00 0.00 0.00 2.52
3342 6520 8.766476 TCTCTGAATACTGGATCTTCATCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
3343 6521 8.954950 TCTGAATACTGGATCTTCATCTTTTC 57.045 34.615 0.00 0.00 0.00 2.29
3344 6522 8.766476 TCTGAATACTGGATCTTCATCTTTTCT 58.234 33.333 0.00 0.00 0.00 2.52
3345 6523 8.728337 TGAATACTGGATCTTCATCTTTTCTG 57.272 34.615 0.00 0.00 0.00 3.02
3354 6533 7.748241 GGATCTTCATCTTTTCTGTTCTTTTCG 59.252 37.037 0.00 0.00 0.00 3.46
3360 6539 6.753107 TCTTTTCTGTTCTTTTCGTTTCCT 57.247 33.333 0.00 0.00 0.00 3.36
3373 6552 8.298140 TCTTTTCGTTTCCTTTTTAAGAACACA 58.702 29.630 0.00 0.00 0.00 3.72
3391 6570 4.079253 ACACATTTTGTATGGAGGTGGAC 58.921 43.478 0.00 0.00 36.32 4.02
3411 6590 4.789123 GTAATGCGGGGCGGTGGT 62.789 66.667 0.00 0.00 0.00 4.16
3440 6619 1.202114 CAGAGGATAGCGAGGAGATGC 59.798 57.143 0.00 0.00 0.00 3.91
3449 6628 1.591703 GAGGAGATGCGTGGTCACA 59.408 57.895 1.90 0.00 0.00 3.58
3465 6644 2.558795 GTCACACAGTGAAGGAGCTCTA 59.441 50.000 14.64 0.00 44.49 2.43
3470 6649 1.134848 CAGTGAAGGAGCTCTACTGGC 60.135 57.143 22.00 5.50 36.12 4.85
3471 6650 0.898320 GTGAAGGAGCTCTACTGGCA 59.102 55.000 14.64 3.04 0.00 4.92
3475 6654 1.944177 AGGAGCTCTACTGGCAGAAA 58.056 50.000 23.66 7.84 0.00 2.52
3478 6657 3.640967 AGGAGCTCTACTGGCAGAAATAG 59.359 47.826 23.66 12.71 0.00 1.73
3487 6666 4.573900 ACTGGCAGAAATAGACAGAACAG 58.426 43.478 23.66 0.00 45.12 3.16
3499 6678 2.676839 GACAGAACAGGATCATGTGCAG 59.323 50.000 20.24 14.71 30.33 4.41
3504 6683 1.542915 ACAGGATCATGTGCAGTTTGC 59.457 47.619 13.05 0.00 45.29 3.68
3513 6692 4.831698 GCAGTTTGCAGTTTGGCA 57.168 50.000 0.00 0.00 44.26 4.92
3514 6693 2.596875 GCAGTTTGCAGTTTGGCAG 58.403 52.632 0.00 0.00 45.88 4.85
3515 6694 0.179103 GCAGTTTGCAGTTTGGCAGT 60.179 50.000 0.00 0.00 45.88 4.40
3516 6695 1.066908 GCAGTTTGCAGTTTGGCAGTA 59.933 47.619 0.00 0.00 45.88 2.74
3517 6696 2.731217 CAGTTTGCAGTTTGGCAGTAC 58.269 47.619 0.00 0.00 45.88 2.73
3518 6697 1.681264 AGTTTGCAGTTTGGCAGTACC 59.319 47.619 0.00 0.00 45.88 3.34
3534 6713 3.520862 CCATTCATTGGCGGCGCT 61.521 61.111 32.30 9.47 39.09 5.92
3535 6714 2.186160 CCATTCATTGGCGGCGCTA 61.186 57.895 32.30 24.91 39.09 4.26
3536 6715 1.518056 CCATTCATTGGCGGCGCTAT 61.518 55.000 32.30 21.54 39.09 2.97
3537 6716 1.155889 CATTCATTGGCGGCGCTATA 58.844 50.000 32.30 17.14 0.00 1.31
3538 6717 1.739466 CATTCATTGGCGGCGCTATAT 59.261 47.619 32.30 18.64 0.00 0.86
3539 6718 2.753055 TTCATTGGCGGCGCTATATA 57.247 45.000 32.30 11.68 0.00 0.86
3540 6719 2.979814 TCATTGGCGGCGCTATATAT 57.020 45.000 32.30 13.72 0.00 0.86
3541 6720 2.549926 TCATTGGCGGCGCTATATATG 58.450 47.619 32.30 24.49 0.00 1.78
3542 6721 2.093711 TCATTGGCGGCGCTATATATGT 60.094 45.455 32.30 6.53 0.00 2.29
3543 6722 2.465860 TTGGCGGCGCTATATATGTT 57.534 45.000 32.30 0.00 0.00 2.71
3544 6723 2.465860 TGGCGGCGCTATATATGTTT 57.534 45.000 32.30 0.00 0.00 2.83
3545 6724 2.343101 TGGCGGCGCTATATATGTTTC 58.657 47.619 32.30 10.65 0.00 2.78
3546 6725 2.289133 TGGCGGCGCTATATATGTTTCA 60.289 45.455 32.30 13.36 0.00 2.69
3547 6726 2.936498 GGCGGCGCTATATATGTTTCAT 59.064 45.455 32.30 0.00 0.00 2.57
3548 6727 3.001330 GGCGGCGCTATATATGTTTCATC 59.999 47.826 32.30 4.75 0.00 2.92
3549 6728 3.616821 GCGGCGCTATATATGTTTCATCA 59.383 43.478 26.86 0.00 0.00 3.07
3550 6729 4.259970 GCGGCGCTATATATGTTTCATCAG 60.260 45.833 26.86 0.00 0.00 2.90
3551 6730 4.864806 CGGCGCTATATATGTTTCATCAGT 59.135 41.667 7.64 0.00 0.00 3.41
3552 6731 6.033966 CGGCGCTATATATGTTTCATCAGTA 58.966 40.000 7.64 0.00 0.00 2.74
3553 6732 6.697455 CGGCGCTATATATGTTTCATCAGTAT 59.303 38.462 7.64 0.00 0.00 2.12
3554 6733 7.096436 CGGCGCTATATATGTTTCATCAGTATC 60.096 40.741 7.64 0.00 0.00 2.24
3555 6734 7.923344 GGCGCTATATATGTTTCATCAGTATCT 59.077 37.037 7.64 0.00 0.00 1.98
3556 6735 8.750416 GCGCTATATATGTTTCATCAGTATCTG 58.250 37.037 0.00 0.00 0.00 2.90
3557 6736 8.750416 CGCTATATATGTTTCATCAGTATCTGC 58.250 37.037 0.00 0.00 0.00 4.26
3558 6737 9.814899 GCTATATATGTTTCATCAGTATCTGCT 57.185 33.333 0.00 0.00 0.00 4.24
3560 6739 8.923609 ATATATGTTTCATCAGTATCTGCTCG 57.076 34.615 0.00 0.00 0.00 5.03
3561 6740 4.718940 TGTTTCATCAGTATCTGCTCGA 57.281 40.909 0.00 0.00 0.00 4.04
3562 6741 5.072040 TGTTTCATCAGTATCTGCTCGAA 57.928 39.130 0.00 0.00 0.00 3.71
3563 6742 5.105063 TGTTTCATCAGTATCTGCTCGAAG 58.895 41.667 0.00 0.00 0.00 3.79
3564 6743 3.361794 TCATCAGTATCTGCTCGAAGC 57.638 47.619 0.00 0.00 42.82 3.86
3565 6744 2.954989 TCATCAGTATCTGCTCGAAGCT 59.045 45.455 8.07 0.00 42.97 3.74
3566 6745 2.859526 TCAGTATCTGCTCGAAGCTG 57.140 50.000 8.07 7.61 42.97 4.24
3571 6750 2.280835 TCTGCTCGAAGCTGATGGT 58.719 52.632 10.70 0.00 42.93 3.55
3572 6751 0.174389 TCTGCTCGAAGCTGATGGTC 59.826 55.000 10.70 0.00 42.93 4.02
3573 6752 1.144565 CTGCTCGAAGCTGATGGTCG 61.145 60.000 8.07 0.00 41.94 4.79
3574 6753 2.520904 GCTCGAAGCTGATGGTCGC 61.521 63.158 0.00 0.00 38.45 5.19
3575 6754 2.202610 TCGAAGCTGATGGTCGCG 60.203 61.111 0.00 0.00 0.00 5.87
3576 6755 2.202610 CGAAGCTGATGGTCGCGA 60.203 61.111 3.71 3.71 0.00 5.87
3577 6756 1.589993 CGAAGCTGATGGTCGCGAT 60.590 57.895 14.06 0.00 0.00 4.58
3578 6757 1.815212 CGAAGCTGATGGTCGCGATG 61.815 60.000 14.06 0.00 0.00 3.84
3579 6758 0.528466 GAAGCTGATGGTCGCGATGA 60.528 55.000 14.06 1.40 0.00 2.92
3580 6759 0.529337 AAGCTGATGGTCGCGATGAG 60.529 55.000 14.06 0.12 0.00 2.90
3581 6760 1.953138 GCTGATGGTCGCGATGAGG 60.953 63.158 14.06 2.15 0.00 3.86
3582 6761 1.300465 CTGATGGTCGCGATGAGGG 60.300 63.158 14.06 0.00 0.00 4.30
3583 6762 2.663188 GATGGTCGCGATGAGGGC 60.663 66.667 14.06 0.00 0.00 5.19
3591 6770 3.327148 CGATGAGGGCGCTGAATG 58.673 61.111 8.56 0.00 0.00 2.67
3592 6771 2.249535 CGATGAGGGCGCTGAATGG 61.250 63.158 8.56 0.00 0.00 3.16
3593 6772 1.153086 GATGAGGGCGCTGAATGGT 60.153 57.895 8.56 0.00 0.00 3.55
3594 6773 1.442526 GATGAGGGCGCTGAATGGTG 61.443 60.000 8.56 0.00 0.00 4.17
3595 6774 1.913951 ATGAGGGCGCTGAATGGTGA 61.914 55.000 8.56 0.00 0.00 4.02
3596 6775 1.817099 GAGGGCGCTGAATGGTGAG 60.817 63.158 8.56 0.00 0.00 3.51
3597 6776 2.045926 GGGCGCTGAATGGTGAGT 60.046 61.111 7.64 0.00 0.00 3.41
3598 6777 1.675641 GGGCGCTGAATGGTGAGTT 60.676 57.895 7.64 0.00 0.00 3.01
3599 6778 1.503542 GGCGCTGAATGGTGAGTTG 59.496 57.895 7.64 0.00 0.00 3.16
3600 6779 1.154150 GCGCTGAATGGTGAGTTGC 60.154 57.895 0.00 0.00 0.00 4.17
3601 6780 1.503542 CGCTGAATGGTGAGTTGCC 59.496 57.895 0.00 0.00 0.00 4.52
3602 6781 0.957395 CGCTGAATGGTGAGTTGCCT 60.957 55.000 0.00 0.00 0.00 4.75
3603 6782 0.524862 GCTGAATGGTGAGTTGCCTG 59.475 55.000 0.00 0.00 0.00 4.85
3604 6783 1.901591 CTGAATGGTGAGTTGCCTGT 58.098 50.000 0.00 0.00 0.00 4.00
3605 6784 1.808945 CTGAATGGTGAGTTGCCTGTC 59.191 52.381 0.00 0.00 0.00 3.51
3606 6785 1.142667 TGAATGGTGAGTTGCCTGTCA 59.857 47.619 0.00 0.00 0.00 3.58
3607 6786 2.229792 GAATGGTGAGTTGCCTGTCAA 58.770 47.619 0.00 0.00 0.00 3.18
3608 6787 2.363306 ATGGTGAGTTGCCTGTCAAA 57.637 45.000 0.00 0.00 36.26 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.267961 CGGTCCAGTTACAGGGGC 59.732 66.667 0.00 0.00 0.00 5.80
42 43 2.874648 CTAAGGCAGCATCACCGGCA 62.875 60.000 0.00 0.00 0.00 5.69
82 98 1.586422 CCATCAAGGACACATAGCGG 58.414 55.000 0.00 0.00 41.22 5.52
83 99 0.940126 GCCATCAAGGACACATAGCG 59.060 55.000 0.00 0.00 41.22 4.26
85 101 2.569059 CCTGCCATCAAGGACACATAG 58.431 52.381 0.00 0.00 41.22 2.23
86 102 1.408683 GCCTGCCATCAAGGACACATA 60.409 52.381 0.00 0.00 41.22 2.29
87 103 0.682209 GCCTGCCATCAAGGACACAT 60.682 55.000 0.00 0.00 41.22 3.21
92 108 1.924939 TCCAGCCTGCCATCAAGGA 60.925 57.895 0.00 0.00 41.22 3.36
153 169 3.444034 CCGAGAGATGGTTGTAACTGAGA 59.556 47.826 0.00 0.00 0.00 3.27
166 182 3.997672 GGATTGGTCCCGAGAGATG 57.002 57.895 0.00 0.00 38.69 2.90
233 249 2.431954 AGATCCTTGCAGGTCATTGG 57.568 50.000 0.00 0.00 36.53 3.16
246 262 2.777459 AGGACGTTGGGATAGATCCT 57.223 50.000 8.45 0.00 46.35 3.24
268 284 8.927675 ATGGAGGTTTGTTTAGTACAATTACA 57.072 30.769 0.00 0.00 45.72 2.41
284 301 5.205056 AGTAAGAGAGATCGATGGAGGTTT 58.795 41.667 0.54 0.00 0.00 3.27
315 332 7.563924 TCTTACTGTAGTAGGCATGGTAGAAAT 59.436 37.037 0.00 0.00 0.00 2.17
331 934 4.778534 TTCCCGAGTGTTCTTACTGTAG 57.221 45.455 0.00 0.00 0.00 2.74
339 942 4.636206 GCTCATTAAATTCCCGAGTGTTCT 59.364 41.667 0.00 0.00 0.00 3.01
347 950 3.142174 GGAGAGGCTCATTAAATTCCCG 58.858 50.000 18.26 0.00 31.08 5.14
374 977 4.415596 ACAAGATGGGGTAAATCTGCAAA 58.584 39.130 0.00 0.00 34.59 3.68
375 978 4.016444 GACAAGATGGGGTAAATCTGCAA 58.984 43.478 0.00 0.00 34.59 4.08
376 979 3.010027 TGACAAGATGGGGTAAATCTGCA 59.990 43.478 0.00 0.00 34.59 4.41
385 988 0.987294 CCAGACTGACAAGATGGGGT 59.013 55.000 3.32 0.00 33.06 4.95
398 1001 1.896465 GTTGCTACTGAGGTCCAGACT 59.104 52.381 0.00 0.00 45.78 3.24
399 1002 1.896465 AGTTGCTACTGAGGTCCAGAC 59.104 52.381 0.00 0.00 45.78 3.51
414 1017 1.605058 TACGCCCCAGAGAGAGTTGC 61.605 60.000 0.00 0.00 0.00 4.17
426 1206 2.052782 ACTTGATGGAATTACGCCCC 57.947 50.000 0.00 0.00 0.00 5.80
436 1216 1.486310 AGAGCGCCAATACTTGATGGA 59.514 47.619 2.29 0.00 39.12 3.41
469 1249 8.806146 AGAAGATTGAAGGATAGATCTAAGAGC 58.194 37.037 6.52 0.00 0.00 4.09
525 1330 9.356433 GATCAAGAGAGGTTAGTTTAGTACAAC 57.644 37.037 0.00 0.00 0.00 3.32
584 1397 6.369059 ACTCATCAAATTTCCTATGCTTCG 57.631 37.500 0.00 0.00 0.00 3.79
701 1518 4.526438 AATAGGCCCTTAAGCTGATTGT 57.474 40.909 0.00 0.00 0.00 2.71
831 1936 4.035675 GTGATCCGATTGTTGGAAAGATCC 59.964 45.833 0.00 0.00 46.76 3.36
832 1937 4.260375 CGTGATCCGATTGTTGGAAAGATC 60.260 45.833 0.00 0.00 39.39 2.75
833 1938 3.623060 CGTGATCCGATTGTTGGAAAGAT 59.377 43.478 0.00 0.00 39.39 2.40
834 1939 3.000041 CGTGATCCGATTGTTGGAAAGA 59.000 45.455 0.00 0.00 39.39 2.52
835 1940 2.095853 CCGTGATCCGATTGTTGGAAAG 59.904 50.000 5.32 0.00 39.39 2.62
836 1941 2.080693 CCGTGATCCGATTGTTGGAAA 58.919 47.619 5.32 0.00 39.39 3.13
837 1942 1.677518 CCCGTGATCCGATTGTTGGAA 60.678 52.381 5.32 0.00 39.39 3.53
838 1943 0.107897 CCCGTGATCCGATTGTTGGA 60.108 55.000 5.32 0.00 39.56 3.53
839 1944 0.392461 ACCCGTGATCCGATTGTTGG 60.392 55.000 5.32 0.54 39.56 3.77
840 1945 1.396996 GAACCCGTGATCCGATTGTTG 59.603 52.381 5.32 0.00 39.56 3.33
841 1946 1.677820 GGAACCCGTGATCCGATTGTT 60.678 52.381 5.32 5.80 39.56 2.83
842 1947 0.107848 GGAACCCGTGATCCGATTGT 60.108 55.000 5.32 0.00 39.56 2.71
843 1948 0.107897 TGGAACCCGTGATCCGATTG 60.108 55.000 5.32 0.00 38.63 2.67
844 1949 0.837272 ATGGAACCCGTGATCCGATT 59.163 50.000 5.32 0.49 38.63 3.34
845 1950 0.837272 AATGGAACCCGTGATCCGAT 59.163 50.000 5.32 0.00 38.63 4.18
846 1951 0.107897 CAATGGAACCCGTGATCCGA 60.108 55.000 5.32 0.00 38.63 4.55
847 1952 1.095228 CCAATGGAACCCGTGATCCG 61.095 60.000 0.00 0.00 38.63 4.18
848 1953 0.034477 ACCAATGGAACCCGTGATCC 60.034 55.000 6.16 0.00 36.21 3.36
849 1954 2.561569 CTACCAATGGAACCCGTGATC 58.438 52.381 6.16 0.00 0.00 2.92
850 1955 1.408266 GCTACCAATGGAACCCGTGAT 60.408 52.381 6.16 0.00 0.00 3.06
851 1956 0.035820 GCTACCAATGGAACCCGTGA 60.036 55.000 6.16 0.00 0.00 4.35
852 1957 0.322098 TGCTACCAATGGAACCCGTG 60.322 55.000 6.16 0.00 0.00 4.94
853 1958 0.322187 GTGCTACCAATGGAACCCGT 60.322 55.000 6.16 0.00 0.00 5.28
854 1959 0.322098 TGTGCTACCAATGGAACCCG 60.322 55.000 6.16 0.00 0.00 5.28
855 1960 1.463674 CTGTGCTACCAATGGAACCC 58.536 55.000 6.16 0.00 0.00 4.11
856 1961 1.004277 TCCTGTGCTACCAATGGAACC 59.996 52.381 6.16 0.00 0.00 3.62
857 1962 2.489938 TCCTGTGCTACCAATGGAAC 57.510 50.000 6.16 0.00 0.00 3.62
858 1963 3.517296 TTTCCTGTGCTACCAATGGAA 57.483 42.857 6.16 0.00 34.73 3.53
859 1964 3.266772 AGATTTCCTGTGCTACCAATGGA 59.733 43.478 6.16 0.00 0.00 3.41
860 1965 3.624777 AGATTTCCTGTGCTACCAATGG 58.375 45.455 0.00 0.00 0.00 3.16
861 1966 5.647658 TGTTAGATTTCCTGTGCTACCAATG 59.352 40.000 0.00 0.00 0.00 2.82
862 1967 5.815581 TGTTAGATTTCCTGTGCTACCAAT 58.184 37.500 0.00 0.00 0.00 3.16
863 1968 5.235850 TGTTAGATTTCCTGTGCTACCAA 57.764 39.130 0.00 0.00 0.00 3.67
864 1969 4.901197 TGTTAGATTTCCTGTGCTACCA 57.099 40.909 0.00 0.00 0.00 3.25
865 1970 5.246307 ACTTGTTAGATTTCCTGTGCTACC 58.754 41.667 0.00 0.00 0.00 3.18
866 1971 6.803154 AACTTGTTAGATTTCCTGTGCTAC 57.197 37.500 0.00 0.00 0.00 3.58
867 1972 8.372459 TCTAAACTTGTTAGATTTCCTGTGCTA 58.628 33.333 0.00 0.00 0.00 3.49
868 1973 7.224297 TCTAAACTTGTTAGATTTCCTGTGCT 58.776 34.615 0.00 0.00 0.00 4.40
869 1974 7.173390 ACTCTAAACTTGTTAGATTTCCTGTGC 59.827 37.037 0.00 0.00 31.36 4.57
870 1975 8.608844 ACTCTAAACTTGTTAGATTTCCTGTG 57.391 34.615 0.00 0.00 31.36 3.66
871 1976 9.274206 GAACTCTAAACTTGTTAGATTTCCTGT 57.726 33.333 11.99 0.00 35.98 4.00
872 1977 9.495572 AGAACTCTAAACTTGTTAGATTTCCTG 57.504 33.333 16.39 1.58 39.49 3.86
876 1981 9.847224 TCCAAGAACTCTAAACTTGTTAGATTT 57.153 29.630 0.00 0.00 39.19 2.17
878 1983 9.660180 GATCCAAGAACTCTAAACTTGTTAGAT 57.340 33.333 0.00 0.00 39.19 1.98
879 1984 8.871125 AGATCCAAGAACTCTAAACTTGTTAGA 58.129 33.333 0.00 0.00 39.19 2.10
880 1985 9.495572 AAGATCCAAGAACTCTAAACTTGTTAG 57.504 33.333 0.00 0.00 39.19 2.34
881 1986 9.847224 AAAGATCCAAGAACTCTAAACTTGTTA 57.153 29.630 0.00 0.00 39.19 2.41
882 1987 8.753497 AAAGATCCAAGAACTCTAAACTTGTT 57.247 30.769 0.00 0.00 39.19 2.83
883 1988 7.445707 GGAAAGATCCAAGAACTCTAAACTTGT 59.554 37.037 0.00 0.00 45.79 3.16
884 1989 7.811653 GGAAAGATCCAAGAACTCTAAACTTG 58.188 38.462 0.00 0.00 45.79 3.16
885 1990 7.987750 GGAAAGATCCAAGAACTCTAAACTT 57.012 36.000 0.00 0.00 45.79 2.66
954 2059 8.354711 TGAGTGATAGTGTTGTAAGAGAGATT 57.645 34.615 0.00 0.00 0.00 2.40
978 2083 5.902613 TTCCATTAAGCTGATTGGACTTG 57.097 39.130 13.42 0.00 37.97 3.16
1159 2264 9.458727 CTCATATAAGTTGGCAAGATATCCAAT 57.541 33.333 0.00 0.00 43.43 3.16
1188 2293 9.993881 CTGCTTAAATTGTTTTTACTCAAATCG 57.006 29.630 0.00 0.00 0.00 3.34
1348 2465 6.663093 TCACATGGAGTTAAGCCATACAAATT 59.337 34.615 8.95 0.00 44.08 1.82
1395 2920 6.074648 ACTTGGATGTTTCCTATTTTGGTGA 58.925 36.000 0.00 0.00 43.07 4.02
1782 3313 5.852763 TGGGAACAGAAGCCATACAGCTTA 61.853 45.833 0.00 0.00 44.74 3.09
1854 3385 2.212652 TGCTCGTGCATAATGGATGAC 58.787 47.619 8.30 0.00 45.31 3.06
2070 3601 4.399004 AATAGTGCTCCAGCTTGAGTAG 57.601 45.455 15.66 0.00 42.66 2.57
2118 3649 1.644509 AGCACATGTCAGTACCAGGA 58.355 50.000 0.00 0.00 0.00 3.86
2128 3659 9.807649 AGAATAAAAATGGATTAAGCACATGTC 57.192 29.630 0.00 0.00 0.00 3.06
2220 3774 7.310299 CCATGGTAGATGACAGCTCTGTAATAT 60.310 40.741 2.57 1.31 45.05 1.28
2248 3802 1.202371 ACGTCGCACTTCTCAGTCAAA 60.202 47.619 0.00 0.00 0.00 2.69
2278 3832 3.705934 TTCCAGCGCAACCACACCA 62.706 57.895 11.47 0.00 0.00 4.17
2326 3880 0.881796 GGCAAAAGAACGGAAGGAGG 59.118 55.000 0.00 0.00 0.00 4.30
2358 3912 3.267031 CAGGGTATCCTTGAACTTCCCTT 59.733 47.826 0.00 0.00 42.67 3.95
2404 3958 1.658686 CCTTCTCCTCCTCGACGGTG 61.659 65.000 0.00 0.00 0.00 4.94
2408 3962 1.679153 GACATCCTTCTCCTCCTCGAC 59.321 57.143 0.00 0.00 0.00 4.20
2413 3967 3.950395 CCAAAATGACATCCTTCTCCTCC 59.050 47.826 0.00 0.00 0.00 4.30
2470 4027 3.373565 GTTGGCCGAGCTTTGGGG 61.374 66.667 0.00 0.00 0.00 4.96
2479 4036 2.596923 TGCTGCATTGTTGGCCGA 60.597 55.556 0.00 0.00 0.00 5.54
2506 4063 4.461431 GGGTGGTTTCTATTTGTTAGTGGG 59.539 45.833 0.00 0.00 0.00 4.61
2507 4064 5.074115 TGGGTGGTTTCTATTTGTTAGTGG 58.926 41.667 0.00 0.00 0.00 4.00
2571 4128 1.818060 TGCCACAATACTCATGCAACC 59.182 47.619 0.00 0.00 0.00 3.77
2572 4129 2.415893 GGTGCCACAATACTCATGCAAC 60.416 50.000 0.00 0.00 0.00 4.17
2667 4229 3.355626 TCTGTCTCGAAGTCAACACAG 57.644 47.619 0.00 0.00 33.90 3.66
2673 4235 2.493675 CCATCCTTCTGTCTCGAAGTCA 59.506 50.000 0.00 0.00 38.95 3.41
2680 4242 3.006752 CCTGCTATCCATCCTTCTGTCTC 59.993 52.174 0.00 0.00 0.00 3.36
2698 4315 5.123344 ACGTACAAAGGATGTATTTTCCTGC 59.877 40.000 0.00 0.00 42.90 4.85
2889 4509 6.156429 ACAGACGGTATCTATTCCTCCTTTTT 59.844 38.462 0.00 0.00 35.15 1.94
2890 4510 5.661759 ACAGACGGTATCTATTCCTCCTTTT 59.338 40.000 0.00 0.00 35.15 2.27
2894 4514 4.400120 AGACAGACGGTATCTATTCCTCC 58.600 47.826 0.00 0.00 35.15 4.30
2902 4522 4.232188 TCCAGTAAGACAGACGGTATCT 57.768 45.455 0.00 0.00 38.66 1.98
2909 4529 5.932303 TGCATAAGTTTCCAGTAAGACAGAC 59.068 40.000 0.00 0.00 0.00 3.51
2911 4531 6.204688 TGTTGCATAAGTTTCCAGTAAGACAG 59.795 38.462 0.00 0.00 0.00 3.51
2915 4535 5.619981 GCCTGTTGCATAAGTTTCCAGTAAG 60.620 44.000 0.00 0.00 40.77 2.34
2919 4539 2.821969 AGCCTGTTGCATAAGTTTCCAG 59.178 45.455 0.00 0.00 44.83 3.86
2942 4564 9.900710 GGTTGTTTCAGGTTTTTGTTAAAAATT 57.099 25.926 3.17 0.00 41.85 1.82
2945 4567 6.927381 TCGGTTGTTTCAGGTTTTTGTTAAAA 59.073 30.769 0.00 0.00 0.00 1.52
2985 4624 2.677836 CCAATGTGTAAGTGGGATCGTG 59.322 50.000 0.00 0.00 0.00 4.35
3004 4643 9.944376 GCCTAAATATATCAGTAAAGATGACCA 57.056 33.333 0.00 0.00 0.00 4.02
3074 6208 9.504710 GAAAAGAAAAGACAAGAGACTAAAACC 57.495 33.333 0.00 0.00 0.00 3.27
3108 6242 5.673337 TCACTGGCTAATGCGAATAAATC 57.327 39.130 0.00 0.00 40.82 2.17
3109 6243 5.009010 CCTTCACTGGCTAATGCGAATAAAT 59.991 40.000 0.00 0.00 40.82 1.40
3111 6245 3.876914 CCTTCACTGGCTAATGCGAATAA 59.123 43.478 0.00 0.00 40.82 1.40
3113 6247 2.292267 CCTTCACTGGCTAATGCGAAT 58.708 47.619 0.00 0.00 40.82 3.34
3117 6251 2.409948 AGACCTTCACTGGCTAATGC 57.590 50.000 0.00 0.00 38.76 3.56
3164 6321 0.801251 CAGTCAGCAGCTTAAGCACC 59.199 55.000 28.39 17.97 45.16 5.01
3170 6327 2.893489 TCAGAGTTCAGTCAGCAGCTTA 59.107 45.455 0.00 0.00 0.00 3.09
3225 6384 8.406297 GGATGGAAATTAACTTCAGTTATGACC 58.594 37.037 0.00 3.92 39.89 4.02
3226 6385 9.178758 AGGATGGAAATTAACTTCAGTTATGAC 57.821 33.333 0.00 0.00 39.89 3.06
3231 6409 7.725844 AGACAAGGATGGAAATTAACTTCAGTT 59.274 33.333 0.00 0.00 41.73 3.16
3246 6424 1.586422 CCGCACATAGACAAGGATGG 58.414 55.000 0.00 0.00 0.00 3.51
3263 6441 0.462581 TAAGCTCAGAGCATTGCCCG 60.463 55.000 24.64 0.00 45.56 6.13
3296 6474 8.264347 TCAGAGACTGCAACCATACATAAAATA 58.736 33.333 0.00 0.00 0.00 1.40
3310 6488 4.713814 AGATCCAGTATTCAGAGACTGCAA 59.286 41.667 8.46 1.60 42.40 4.08
3317 6495 8.961294 AAAAGATGAAGATCCAGTATTCAGAG 57.039 34.615 1.51 0.00 41.00 3.35
3323 6501 8.547173 AGAACAGAAAAGATGAAGATCCAGTAT 58.453 33.333 0.00 0.00 0.00 2.12
3328 6506 7.748241 CGAAAAGAACAGAAAAGATGAAGATCC 59.252 37.037 0.00 0.00 0.00 3.36
3330 6508 8.159344 ACGAAAAGAACAGAAAAGATGAAGAT 57.841 30.769 0.00 0.00 0.00 2.40
3332 6510 8.620533 AAACGAAAAGAACAGAAAAGATGAAG 57.379 30.769 0.00 0.00 0.00 3.02
3333 6511 7.700656 GGAAACGAAAAGAACAGAAAAGATGAA 59.299 33.333 0.00 0.00 0.00 2.57
3334 6512 7.067008 AGGAAACGAAAAGAACAGAAAAGATGA 59.933 33.333 0.00 0.00 0.00 2.92
3335 6513 7.196331 AGGAAACGAAAAGAACAGAAAAGATG 58.804 34.615 0.00 0.00 0.00 2.90
3337 6515 6.753107 AGGAAACGAAAAGAACAGAAAAGA 57.247 33.333 0.00 0.00 0.00 2.52
3341 6519 9.349145 CTTAAAAAGGAAACGAAAAGAACAGAA 57.651 29.630 0.00 0.00 0.00 3.02
3342 6520 8.732531 TCTTAAAAAGGAAACGAAAAGAACAGA 58.267 29.630 0.00 0.00 0.00 3.41
3343 6521 8.905103 TCTTAAAAAGGAAACGAAAAGAACAG 57.095 30.769 0.00 0.00 0.00 3.16
3344 6522 9.131416 GTTCTTAAAAAGGAAACGAAAAGAACA 57.869 29.630 15.85 0.00 45.40 3.18
3345 6523 9.131416 TGTTCTTAAAAAGGAAACGAAAAGAAC 57.869 29.630 14.52 14.52 45.88 3.01
3360 6539 9.757227 CCTCCATACAAAATGTGTTCTTAAAAA 57.243 29.630 0.00 0.00 41.98 1.94
3373 6552 3.333680 ACAGGTCCACCTCCATACAAAAT 59.666 43.478 0.00 0.00 46.65 1.82
3391 6570 4.483243 ACCGCCCCGCATTACAGG 62.483 66.667 0.00 0.00 0.00 4.00
3419 6598 1.202114 CATCTCCTCGCTATCCTCTGC 59.798 57.143 0.00 0.00 0.00 4.26
3426 6605 1.109920 ACCACGCATCTCCTCGCTAT 61.110 55.000 0.00 0.00 0.00 2.97
3427 6606 1.725557 GACCACGCATCTCCTCGCTA 61.726 60.000 0.00 0.00 0.00 4.26
3432 6611 1.293498 GTGTGACCACGCATCTCCT 59.707 57.895 8.65 0.00 41.22 3.69
3440 6619 0.104120 TCCTTCACTGTGTGACCACG 59.896 55.000 7.79 0.00 42.60 4.94
3449 6628 2.175202 CCAGTAGAGCTCCTTCACTGT 58.825 52.381 23.13 4.42 35.85 3.55
3452 6631 0.898320 TGCCAGTAGAGCTCCTTCAC 59.102 55.000 10.93 3.67 0.00 3.18
3465 6644 4.564406 CCTGTTCTGTCTATTTCTGCCAGT 60.564 45.833 0.00 0.00 0.00 4.00
3470 6649 7.011202 CACATGATCCTGTTCTGTCTATTTCTG 59.989 40.741 0.00 0.00 0.00 3.02
3471 6650 7.046652 CACATGATCCTGTTCTGTCTATTTCT 58.953 38.462 0.00 0.00 0.00 2.52
3475 6654 4.162888 TGCACATGATCCTGTTCTGTCTAT 59.837 41.667 0.00 0.00 0.00 1.98
3478 6657 2.676839 CTGCACATGATCCTGTTCTGTC 59.323 50.000 0.00 0.00 0.00 3.51
3499 6678 1.407258 TGGTACTGCCAAACTGCAAAC 59.593 47.619 0.00 0.00 45.94 2.93
3518 6697 1.155889 TATAGCGCCGCCAATGAATG 58.844 50.000 4.98 0.00 0.00 2.67
3519 6698 2.113860 ATATAGCGCCGCCAATGAAT 57.886 45.000 4.98 0.00 0.00 2.57
3520 6699 2.753055 TATATAGCGCCGCCAATGAA 57.247 45.000 4.98 0.00 0.00 2.57
3521 6700 2.093711 ACATATATAGCGCCGCCAATGA 60.094 45.455 4.98 0.00 0.00 2.57
3522 6701 2.279741 ACATATATAGCGCCGCCAATG 58.720 47.619 4.98 5.91 0.00 2.82
3523 6702 2.691409 ACATATATAGCGCCGCCAAT 57.309 45.000 4.98 2.05 0.00 3.16
3524 6703 2.465860 AACATATATAGCGCCGCCAA 57.534 45.000 4.98 0.00 0.00 4.52
3525 6704 2.289133 TGAAACATATATAGCGCCGCCA 60.289 45.455 4.98 0.00 0.00 5.69
3526 6705 2.343101 TGAAACATATATAGCGCCGCC 58.657 47.619 4.98 0.00 0.00 6.13
3527 6706 3.616821 TGATGAAACATATATAGCGCCGC 59.383 43.478 2.29 0.00 0.00 6.53
3528 6707 4.864806 ACTGATGAAACATATATAGCGCCG 59.135 41.667 2.29 0.00 0.00 6.46
3529 6708 7.923344 AGATACTGATGAAACATATATAGCGCC 59.077 37.037 2.29 0.00 0.00 6.53
3530 6709 8.750416 CAGATACTGATGAAACATATATAGCGC 58.250 37.037 0.00 0.00 32.44 5.92
3531 6710 8.750416 GCAGATACTGATGAAACATATATAGCG 58.250 37.037 2.81 0.00 32.44 4.26
3532 6711 9.814899 AGCAGATACTGATGAAACATATATAGC 57.185 33.333 2.81 0.00 32.44 2.97
3535 6714 8.743714 TCGAGCAGATACTGATGAAACATATAT 58.256 33.333 2.81 0.00 32.44 0.86
3536 6715 8.110860 TCGAGCAGATACTGATGAAACATATA 57.889 34.615 2.81 0.00 32.44 0.86
3537 6716 6.986250 TCGAGCAGATACTGATGAAACATAT 58.014 36.000 2.81 0.00 32.44 1.78
3538 6717 6.391227 TCGAGCAGATACTGATGAAACATA 57.609 37.500 2.81 0.00 32.44 2.29
3539 6718 5.268118 TCGAGCAGATACTGATGAAACAT 57.732 39.130 2.81 0.00 32.44 2.71
3540 6719 4.718940 TCGAGCAGATACTGATGAAACA 57.281 40.909 2.81 0.00 32.44 2.83
3541 6720 4.026145 GCTTCGAGCAGATACTGATGAAAC 60.026 45.833 2.81 0.00 41.89 2.78
3542 6721 4.115516 GCTTCGAGCAGATACTGATGAAA 58.884 43.478 2.81 0.00 41.89 2.69
3543 6722 3.382865 AGCTTCGAGCAGATACTGATGAA 59.617 43.478 9.09 3.26 45.56 2.57
3544 6723 2.954989 AGCTTCGAGCAGATACTGATGA 59.045 45.455 9.09 0.00 45.56 2.92
3545 6724 3.051327 CAGCTTCGAGCAGATACTGATG 58.949 50.000 9.09 0.00 45.56 3.07
3546 6725 2.954989 TCAGCTTCGAGCAGATACTGAT 59.045 45.455 9.09 0.00 45.56 2.90
3547 6726 2.369394 TCAGCTTCGAGCAGATACTGA 58.631 47.619 9.09 9.20 45.56 3.41
3548 6727 2.859526 TCAGCTTCGAGCAGATACTG 57.140 50.000 9.09 0.00 45.56 2.74
3549 6728 2.035704 CCATCAGCTTCGAGCAGATACT 59.964 50.000 12.06 0.00 44.18 2.12
3550 6729 2.223923 ACCATCAGCTTCGAGCAGATAC 60.224 50.000 12.06 0.00 44.18 2.24
3551 6730 2.034878 ACCATCAGCTTCGAGCAGATA 58.965 47.619 12.06 0.00 44.18 1.98
3552 6731 0.829333 ACCATCAGCTTCGAGCAGAT 59.171 50.000 9.09 8.66 46.45 2.90
3553 6732 0.174389 GACCATCAGCTTCGAGCAGA 59.826 55.000 9.09 6.94 45.56 4.26
3554 6733 1.144565 CGACCATCAGCTTCGAGCAG 61.145 60.000 0.00 2.13 45.56 4.24
3555 6734 1.153765 CGACCATCAGCTTCGAGCA 60.154 57.895 0.00 0.00 45.56 4.26
3556 6735 2.520904 GCGACCATCAGCTTCGAGC 61.521 63.158 8.87 0.00 42.84 5.03
3557 6736 2.226896 CGCGACCATCAGCTTCGAG 61.227 63.158 0.00 1.59 34.62 4.04
3558 6737 2.004808 ATCGCGACCATCAGCTTCGA 62.005 55.000 12.93 0.00 34.62 3.71
3559 6738 1.589993 ATCGCGACCATCAGCTTCG 60.590 57.895 12.93 0.35 35.82 3.79
3560 6739 0.528466 TCATCGCGACCATCAGCTTC 60.528 55.000 12.93 0.00 0.00 3.86
3561 6740 0.529337 CTCATCGCGACCATCAGCTT 60.529 55.000 12.93 0.00 0.00 3.74
3562 6741 1.067084 CTCATCGCGACCATCAGCT 59.933 57.895 12.93 0.00 0.00 4.24
3563 6742 1.953138 CCTCATCGCGACCATCAGC 60.953 63.158 12.93 0.00 0.00 4.26
3564 6743 1.300465 CCCTCATCGCGACCATCAG 60.300 63.158 12.93 2.57 0.00 2.90
3565 6744 2.814604 CCCTCATCGCGACCATCA 59.185 61.111 12.93 0.00 0.00 3.07
3566 6745 2.663188 GCCCTCATCGCGACCATC 60.663 66.667 12.93 0.00 0.00 3.51
3574 6753 2.249535 CCATTCAGCGCCCTCATCG 61.250 63.158 2.29 0.00 0.00 3.84
3575 6754 1.153086 ACCATTCAGCGCCCTCATC 60.153 57.895 2.29 0.00 0.00 2.92
3576 6755 1.452651 CACCATTCAGCGCCCTCAT 60.453 57.895 2.29 0.00 0.00 2.90
3577 6756 2.046023 CACCATTCAGCGCCCTCA 60.046 61.111 2.29 0.00 0.00 3.86
3578 6757 1.817099 CTCACCATTCAGCGCCCTC 60.817 63.158 2.29 0.00 0.00 4.30
3579 6758 2.129555 AACTCACCATTCAGCGCCCT 62.130 55.000 2.29 0.00 0.00 5.19
3580 6759 1.675641 AACTCACCATTCAGCGCCC 60.676 57.895 2.29 0.00 0.00 6.13
3581 6760 1.503542 CAACTCACCATTCAGCGCC 59.496 57.895 2.29 0.00 0.00 6.53
3582 6761 1.154150 GCAACTCACCATTCAGCGC 60.154 57.895 0.00 0.00 0.00 5.92
3583 6762 1.503542 GGCAACTCACCATTCAGCG 59.496 57.895 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.