Multiple sequence alignment - TraesCS1D01G237500

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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 TraesCS1D01G237500 chr1D 100.000 5790 0 0 1 5790 326913285 326907496 0.000000e+00 10693.0
1 TraesCS1D01G237500 chr1D 97.714 175 4 0 3165 3339 372878804 372878630 9.430000e-78 302.0
2 TraesCS1D01G237500 chr1D 95.556 180 7 1 3161 3340 427704713 427704535 2.640000e-73 287.0
3 TraesCS1D01G237500 chr1D 94.595 185 8 2 3160 3342 297155797 297155981 9.500000e-73 285.0
4 TraesCS1D01G237500 chr1A 91.366 3243 132 45 1 3165 410152049 410155221 0.000000e+00 4301.0
5 TraesCS1D01G237500 chr1A 95.306 1896 66 15 3388 5266 410155258 410157147 0.000000e+00 2987.0
6 TraesCS1D01G237500 chr1A 90.359 529 36 3 5263 5790 410157175 410157689 0.000000e+00 680.0
7 TraesCS1D01G237500 chr1B 95.874 1939 54 8 3340 5266 441386647 441384723 0.000000e+00 3114.0
8 TraesCS1D01G237500 chr1B 94.298 1175 36 15 2005 3170 441387785 441386633 0.000000e+00 1770.0
9 TraesCS1D01G237500 chr1B 91.831 1114 62 18 1 1102 441389816 441388720 0.000000e+00 1526.0
10 TraesCS1D01G237500 chr1B 93.226 930 44 11 1082 1996 441388692 441387767 0.000000e+00 1351.0
11 TraesCS1D01G237500 chr1B 89.720 535 28 7 5262 5790 441384696 441384183 0.000000e+00 658.0
12 TraesCS1D01G237500 chr7A 92.068 996 69 5 3813 4798 730504584 730505579 0.000000e+00 1393.0
13 TraesCS1D01G237500 chr7A 79.452 657 86 18 282 922 730501139 730501762 2.490000e-113 420.0
14 TraesCS1D01G237500 chr7A 82.849 344 35 11 4855 5176 730505660 730506001 2.640000e-73 287.0
15 TraesCS1D01G237500 chr7A 78.125 480 48 36 1393 1864 730502348 730502778 9.630000e-63 252.0
16 TraesCS1D01G237500 chr7A 88.235 170 17 3 1806 1974 730528279 730528446 3.540000e-47 200.0
17 TraesCS1D01G237500 chr7A 100.000 36 0 0 2054 2089 730502992 730503027 3.740000e-07 67.6
18 TraesCS1D01G237500 chr7D 91.784 998 72 5 3813 4800 635517893 635516896 0.000000e+00 1380.0
19 TraesCS1D01G237500 chr7D 79.032 496 48 28 1559 2042 635519946 635519495 7.340000e-74 289.0
20 TraesCS1D01G237500 chr7D 87.805 246 17 10 4978 5214 635516311 635516070 5.720000e-70 276.0
21 TraesCS1D01G237500 chr7D 82.938 211 17 8 1082 1274 635520296 635520087 7.710000e-39 172.0
22 TraesCS1D01G237500 chr7D 90.476 63 5 1 1325 1387 635520056 635519995 1.340000e-11 82.4
23 TraesCS1D01G237500 chr7D 97.059 34 1 0 2056 2089 635519461 635519428 2.250000e-04 58.4
24 TraesCS1D01G237500 chr7B 89.389 999 95 6 3813 4801 740261015 740262012 0.000000e+00 1247.0
25 TraesCS1D01G237500 chr7B 92.794 569 37 4 4234 4800 740301807 740302373 0.000000e+00 821.0
26 TraesCS1D01G237500 chr7B 90.084 474 42 3 3813 4281 740238717 740239190 1.380000e-170 610.0
27 TraesCS1D01G237500 chr7B 90.150 467 33 6 3813 4270 740763913 740764375 3.860000e-166 595.0
28 TraesCS1D01G237500 chr7B 89.722 467 35 6 3813 4270 740723052 740723514 8.360000e-163 584.0
29 TraesCS1D01G237500 chr7B 78.408 829 98 49 1079 1874 740720502 740721282 1.140000e-126 464.0
30 TraesCS1D01G237500 chr7B 83.575 414 44 10 4855 5246 740240306 740240717 3.300000e-97 366.0
31 TraesCS1D01G237500 chr7B 79.061 554 61 22 282 819 740254586 740255100 4.330000e-86 329.0
32 TraesCS1D01G237500 chr7B 79.683 315 38 18 1324 1636 740287103 740287393 2.740000e-48 204.0
33 TraesCS1D01G237500 chr7B 85.955 178 19 4 1806 1978 740716486 740716662 9.910000e-43 185.0
34 TraesCS1D01G237500 chr7B 83.178 214 18 10 1079 1274 740286868 740287081 4.610000e-41 180.0
35 TraesCS1D01G237500 chr7B 84.831 178 21 4 1806 1978 740673606 740673782 2.140000e-39 174.0
36 TraesCS1D01G237500 chr7B 94.286 105 5 1 999 1102 740720389 740720493 6.010000e-35 159.0
37 TraesCS1D01G237500 chr7B 94.286 105 5 1 999 1102 740758176 740758280 6.010000e-35 159.0
38 TraesCS1D01G237500 chr7B 96.552 87 3 0 996 1082 740286751 740286837 1.680000e-30 145.0
39 TraesCS1D01G237500 chr7B 78.369 282 16 25 2233 2478 740256575 740256847 2.180000e-29 141.0
40 TraesCS1D01G237500 chr7B 96.104 77 3 0 999 1075 740676958 740677034 6.090000e-25 126.0
41 TraesCS1D01G237500 chr7B 96.104 77 3 0 999 1075 740705567 740705643 6.090000e-25 126.0
42 TraesCS1D01G237500 chr7B 79.268 164 14 12 2268 2411 740300195 740300358 4.780000e-16 97.1
43 TraesCS1D01G237500 chr7B 78.659 164 15 11 2268 2411 740721449 740721612 2.220000e-14 91.6
44 TraesCS1D01G237500 chr7B 85.393 89 9 1 1153 1237 740256487 740256575 7.990000e-14 89.8
45 TraesCS1D01G237500 chr7B 78.912 147 12 10 2268 2395 740240908 740241054 1.340000e-11 82.4
46 TraesCS1D01G237500 chr7B 100.000 34 0 0 2056 2089 740240861 740240894 4.840000e-06 63.9
47 TraesCS1D01G237500 chr7B 100.000 34 0 0 2056 2089 740721402 740721435 4.840000e-06 63.9
48 TraesCS1D01G237500 chr3B 75.000 932 206 24 3873 4787 773542576 773543497 6.990000e-109 405.0
49 TraesCS1D01G237500 chr3D 74.484 921 219 15 3878 4787 579292708 579293623 9.100000e-103 385.0
50 TraesCS1D01G237500 chr3D 93.651 189 10 2 3158 3345 587946843 587946656 1.230000e-71 281.0
51 TraesCS1D01G237500 chr3A 74.582 897 213 13 3873 4758 714535182 714536074 4.230000e-101 379.0
52 TraesCS1D01G237500 chr3A 72.571 875 194 31 3865 4719 711297361 711296513 1.610000e-60 244.0
53 TraesCS1D01G237500 chr5D 97.765 179 3 1 3161 3338 380079619 380079441 2.030000e-79 307.0
54 TraesCS1D01G237500 chr5D 95.480 177 8 0 3165 3341 539072647 539072823 3.420000e-72 283.0
55 TraesCS1D01G237500 chr4D 96.067 178 7 0 3163 3340 381560208 381560031 2.040000e-74 291.0
56 TraesCS1D01G237500 chr4D 94.086 186 11 0 3161 3346 3846932 3846747 3.420000e-72 283.0
57 TraesCS1D01G237500 chr4D 89.286 224 17 6 3162 3384 506103788 506104005 2.060000e-69 274.0


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 TraesCS1D01G237500 chr1D 326907496 326913285 5789 True 10693.000000 10693 100.000000 1 5790 1 chr1D.!!$R1 5789
1 TraesCS1D01G237500 chr1A 410152049 410157689 5640 False 2656.000000 4301 92.343667 1 5790 3 chr1A.!!$F1 5789
2 TraesCS1D01G237500 chr1B 441384183 441389816 5633 True 1683.800000 3114 92.989800 1 5790 5 chr1B.!!$R1 5789
3 TraesCS1D01G237500 chr7A 730501139 730506001 4862 False 483.920000 1393 86.498800 282 5176 5 chr7A.!!$F2 4894
4 TraesCS1D01G237500 chr7D 635516070 635520296 4226 True 376.300000 1380 88.182333 1082 5214 6 chr7D.!!$R1 4132
5 TraesCS1D01G237500 chr7B 740261015 740262012 997 False 1247.000000 1247 89.389000 3813 4801 1 chr7B.!!$F1 988
6 TraesCS1D01G237500 chr7B 740300195 740302373 2178 False 459.050000 821 86.031000 2268 4800 2 chr7B.!!$F8 2532
7 TraesCS1D01G237500 chr7B 740238717 740241054 2337 False 280.575000 610 88.142750 2056 5246 4 chr7B.!!$F5 3190
8 TraesCS1D01G237500 chr7B 740716486 740723514 7028 False 257.916667 584 87.838333 999 4270 6 chr7B.!!$F10 3271
9 TraesCS1D01G237500 chr3B 773542576 773543497 921 False 405.000000 405 75.000000 3873 4787 1 chr3B.!!$F1 914
10 TraesCS1D01G237500 chr3D 579292708 579293623 915 False 385.000000 385 74.484000 3878 4787 1 chr3D.!!$F1 909
11 TraesCS1D01G237500 chr3A 714535182 714536074 892 False 379.000000 379 74.582000 3873 4758 1 chr3A.!!$F1 885
12 TraesCS1D01G237500 chr3A 711296513 711297361 848 True 244.000000 244 72.571000 3865 4719 1 chr3A.!!$R1 854

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
992 1032 1.202245 CCTCAACGCAGCTAGAGAGAC 60.202 57.143 0.00 0.0 0.00 3.36 F
2451 6094 0.315251 GTTGGTTCTGCTGGCCTTTC 59.685 55.000 3.32 0.0 0.00 2.62 F
3573 7567 0.028505 GAAGCTACACGCATGCATGG 59.971 55.000 27.34 19.0 42.61 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2632 6276 0.891449 CGGCTGCTCCTAGCTAGCTA 60.891 60.0 22.85 22.85 42.97 3.32 R
3651 7649 0.238025 GCGATGCATGAACACACACA 59.762 50.0 2.46 0.00 0.00 3.72 R
5378 10819 2.073252 AGGCAGGATCGTCTACATCA 57.927 50.0 0.00 0.00 0.00 3.07 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
35 36 5.105513 ACAACAAGTCCAAAAGTTTAGTGGG 60.106 40.000 6.51 0.00 32.95 4.61
236 243 8.511748 AAAAGTGATATAGACCCCACTATGAT 57.488 34.615 0.00 0.00 38.75 2.45
274 290 4.081420 AGTGACGAAAGGCTTCTGATGTAT 60.081 41.667 0.00 0.00 42.42 2.29
324 341 9.016623 TCGCGGATATTCATTACTAAAATATCG 57.983 33.333 6.13 0.00 40.71 2.92
950 988 5.164954 GCTTTAGAGCGAGAGAAAGAAAGA 58.835 41.667 0.00 0.00 39.48 2.52
951 989 5.061684 GCTTTAGAGCGAGAGAAAGAAAGAC 59.938 44.000 0.00 0.00 39.48 3.01
952 990 5.707242 TTAGAGCGAGAGAAAGAAAGACA 57.293 39.130 0.00 0.00 0.00 3.41
954 992 3.319405 AGAGCGAGAGAAAGAAAGACACA 59.681 43.478 0.00 0.00 0.00 3.72
955 993 4.021544 AGAGCGAGAGAAAGAAAGACACAT 60.022 41.667 0.00 0.00 0.00 3.21
964 1002 5.527582 AGAAAGAAAGACACATACACACACC 59.472 40.000 0.00 0.00 0.00 4.16
983 1021 2.591715 ACACACCCTCAACGCAGC 60.592 61.111 0.00 0.00 0.00 5.25
992 1032 1.202245 CCTCAACGCAGCTAGAGAGAC 60.202 57.143 0.00 0.00 0.00 3.36
1159 4130 3.006247 GCAGGGAGTTTGCTTAGAAGAG 58.994 50.000 0.00 0.00 38.51 2.85
1450 4607 3.211045 TGGGAGCACAGTAACTTTTCAC 58.789 45.455 0.00 0.00 0.00 3.18
1591 4754 6.348132 CCAAGATAAAAGTGCACGTGTAATCA 60.348 38.462 18.38 3.18 0.00 2.57
1593 4756 7.377766 AGATAAAAGTGCACGTGTAATCAAT 57.622 32.000 18.38 6.46 0.00 2.57
1598 4761 4.569943 AGTGCACGTGTAATCAATCTTCT 58.430 39.130 18.38 0.00 0.00 2.85
1836 5006 8.600625 GTTGATCGTACACTATAAAGCATCAAA 58.399 33.333 0.00 0.00 31.39 2.69
1864 5034 3.665871 GCTTGCAAATGAAGTCTCGAAAC 59.334 43.478 0.00 0.00 0.00 2.78
1870 5040 5.498159 CAAATGAAGTCTCGAAACGTTTGA 58.502 37.500 20.10 14.47 38.75 2.69
1873 5043 4.364860 TGAAGTCTCGAAACGTTTGATGA 58.635 39.130 20.10 12.08 0.00 2.92
1874 5044 4.988540 TGAAGTCTCGAAACGTTTGATGAT 59.011 37.500 20.10 0.00 0.00 2.45
2166 5421 2.095372 CCGTCGCTAACCATCTTTTTCC 59.905 50.000 0.00 0.00 0.00 3.13
2183 5440 1.580059 TCCTATTCCTTTGGTCCGCT 58.420 50.000 0.00 0.00 0.00 5.52
2185 5442 1.017387 CTATTCCTTTGGTCCGCTGC 58.983 55.000 0.00 0.00 0.00 5.25
2448 6091 1.529244 GTGTTGGTTCTGCTGGCCT 60.529 57.895 3.32 0.00 0.00 5.19
2449 6092 1.109323 GTGTTGGTTCTGCTGGCCTT 61.109 55.000 3.32 0.00 0.00 4.35
2450 6093 0.396974 TGTTGGTTCTGCTGGCCTTT 60.397 50.000 3.32 0.00 0.00 3.11
2451 6094 0.315251 GTTGGTTCTGCTGGCCTTTC 59.685 55.000 3.32 0.00 0.00 2.62
2452 6095 0.827507 TTGGTTCTGCTGGCCTTTCC 60.828 55.000 3.32 0.00 0.00 3.13
2453 6096 1.228552 GGTTCTGCTGGCCTTTCCA 60.229 57.895 3.32 0.00 44.18 3.53
2632 6276 2.417787 GCTAGACCGTTAATTGGACCGT 60.418 50.000 0.00 0.00 0.00 4.83
2633 6277 3.181487 GCTAGACCGTTAATTGGACCGTA 60.181 47.826 0.00 0.00 0.00 4.02
2634 6278 3.515330 AGACCGTTAATTGGACCGTAG 57.485 47.619 3.91 0.00 0.00 3.51
2635 6279 1.929169 GACCGTTAATTGGACCGTAGC 59.071 52.381 3.91 0.00 0.00 3.58
2790 6435 1.960689 GCATGAGGTCTCTACTCTCCC 59.039 57.143 0.00 0.00 35.98 4.30
2792 6437 3.486383 CATGAGGTCTCTACTCTCCCTC 58.514 54.545 0.00 0.00 41.69 4.30
2794 6439 2.775384 TGAGGTCTCTACTCTCCCTCTC 59.225 54.545 0.00 0.00 41.83 3.20
2795 6440 2.105993 GAGGTCTCTACTCTCCCTCTCC 59.894 59.091 0.00 0.00 38.90 3.71
2796 6441 1.847737 GGTCTCTACTCTCCCTCTCCA 59.152 57.143 0.00 0.00 0.00 3.86
2797 6442 2.445525 GGTCTCTACTCTCCCTCTCCAT 59.554 54.545 0.00 0.00 0.00 3.41
2798 6443 3.486383 GTCTCTACTCTCCCTCTCCATG 58.514 54.545 0.00 0.00 0.00 3.66
2799 6444 3.117663 GTCTCTACTCTCCCTCTCCATGT 60.118 52.174 0.00 0.00 0.00 3.21
2896 6545 6.526674 GTCCGCTTGTTTAATAAATCCAACTG 59.473 38.462 0.00 0.00 0.00 3.16
2929 6578 6.091577 CCGTGCAAGTACTACACAATTTATGA 59.908 38.462 22.07 0.00 33.89 2.15
2965 6625 8.094548 TGCATTCTTAAGAGTACATGTACTGTT 58.905 33.333 36.27 36.27 46.84 3.16
3052 6716 9.774071 ACTAAATTAGGGTAGAGTTAGTTGGTA 57.226 33.333 4.92 0.00 29.71 3.25
3085 6749 7.475840 CAAATCAGCTAGGGTAAAAGATTCAC 58.524 38.462 0.00 0.00 0.00 3.18
3086 6750 6.567602 ATCAGCTAGGGTAAAAGATTCACT 57.432 37.500 0.00 0.00 0.00 3.41
3087 6751 5.734720 TCAGCTAGGGTAAAAGATTCACTG 58.265 41.667 0.00 0.00 0.00 3.66
3088 6752 4.333926 CAGCTAGGGTAAAAGATTCACTGC 59.666 45.833 0.00 0.00 0.00 4.40
3089 6753 4.019321 AGCTAGGGTAAAAGATTCACTGCA 60.019 41.667 0.00 0.00 0.00 4.41
3156 6825 2.928416 GCACGAGTAGCCAAAGGTT 58.072 52.632 0.00 0.00 0.00 3.50
3157 6826 1.235724 GCACGAGTAGCCAAAGGTTT 58.764 50.000 0.00 0.00 0.00 3.27
3158 6827 2.419667 GCACGAGTAGCCAAAGGTTTA 58.580 47.619 0.00 0.00 0.00 2.01
3159 6828 3.007635 GCACGAGTAGCCAAAGGTTTAT 58.992 45.455 0.00 0.00 0.00 1.40
3160 6829 4.186159 GCACGAGTAGCCAAAGGTTTATA 58.814 43.478 0.00 0.00 0.00 0.98
3161 6830 4.814771 GCACGAGTAGCCAAAGGTTTATAT 59.185 41.667 0.00 0.00 0.00 0.86
3162 6831 5.296035 GCACGAGTAGCCAAAGGTTTATATT 59.704 40.000 0.00 0.00 0.00 1.28
3163 6832 6.183360 GCACGAGTAGCCAAAGGTTTATATTT 60.183 38.462 0.00 0.00 0.00 1.40
3164 6833 7.011669 GCACGAGTAGCCAAAGGTTTATATTTA 59.988 37.037 0.00 0.00 0.00 1.40
3165 6834 8.333186 CACGAGTAGCCAAAGGTTTATATTTAC 58.667 37.037 0.00 0.00 0.00 2.01
3166 6835 8.042515 ACGAGTAGCCAAAGGTTTATATTTACA 58.957 33.333 0.00 0.00 0.00 2.41
3167 6836 8.548721 CGAGTAGCCAAAGGTTTATATTTACAG 58.451 37.037 0.00 0.00 0.00 2.74
3168 6837 9.392259 GAGTAGCCAAAGGTTTATATTTACAGT 57.608 33.333 0.00 0.00 0.00 3.55
3169 6838 9.749340 AGTAGCCAAAGGTTTATATTTACAGTT 57.251 29.630 0.00 0.00 0.00 3.16
3172 6841 9.705290 AGCCAAAGGTTTATATTTACAGTTTTG 57.295 29.630 0.00 0.00 0.00 2.44
3173 6842 8.440059 GCCAAAGGTTTATATTTACAGTTTTGC 58.560 33.333 0.00 0.00 0.00 3.68
3174 6843 9.705290 CCAAAGGTTTATATTTACAGTTTTGCT 57.295 29.630 0.00 0.00 0.00 3.91
3182 6851 9.742144 TTATATTTACAGTTTTGCTAGAACCCA 57.258 29.630 0.00 0.00 0.00 4.51
3183 6852 8.823220 ATATTTACAGTTTTGCTAGAACCCAT 57.177 30.769 0.00 0.00 0.00 4.00
3184 6853 6.569179 TTTACAGTTTTGCTAGAACCCATC 57.431 37.500 0.00 0.00 0.00 3.51
3185 6854 4.373156 ACAGTTTTGCTAGAACCCATCT 57.627 40.909 0.00 0.00 42.48 2.90
3186 6855 5.499004 ACAGTTTTGCTAGAACCCATCTA 57.501 39.130 0.00 0.00 39.71 1.98
3201 6870 9.836179 AGAACCCATCTAGATGAGATATAGTTT 57.164 33.333 30.40 8.71 43.52 2.66
3202 6871 9.868277 GAACCCATCTAGATGAGATATAGTTTG 57.132 37.037 30.40 11.28 43.52 2.93
3203 6872 8.372877 ACCCATCTAGATGAGATATAGTTTGG 57.627 38.462 30.40 20.19 43.52 3.28
3204 6873 7.958583 ACCCATCTAGATGAGATATAGTTTGGT 59.041 37.037 30.40 20.75 43.52 3.67
3205 6874 8.474025 CCCATCTAGATGAGATATAGTTTGGTC 58.526 40.741 30.40 0.00 43.52 4.02
3206 6875 9.253832 CCATCTAGATGAGATATAGTTTGGTCT 57.746 37.037 30.40 0.00 43.52 3.85
3214 6883 7.500992 TGAGATATAGTTTGGTCTCATTCACC 58.499 38.462 0.16 0.00 41.40 4.02
3215 6884 7.345653 TGAGATATAGTTTGGTCTCATTCACCT 59.654 37.037 0.16 0.00 41.40 4.00
3216 6885 8.095452 AGATATAGTTTGGTCTCATTCACCTT 57.905 34.615 0.00 0.00 34.66 3.50
3217 6886 8.552296 AGATATAGTTTGGTCTCATTCACCTTT 58.448 33.333 0.00 0.00 34.66 3.11
3218 6887 9.178758 GATATAGTTTGGTCTCATTCACCTTTT 57.821 33.333 0.00 0.00 34.66 2.27
3222 6891 8.567285 AGTTTGGTCTCATTCACCTTTTATAG 57.433 34.615 0.00 0.00 34.66 1.31
3223 6892 7.121315 AGTTTGGTCTCATTCACCTTTTATAGC 59.879 37.037 0.00 0.00 34.66 2.97
3224 6893 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
3225 6894 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
3226 6895 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
3227 6896 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
3228 6897 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
3229 6898 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
3230 6899 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
3231 6900 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
3232 6901 6.713762 TTCACCTTTTATAGCCATTGGATG 57.286 37.500 6.95 0.00 0.00 3.51
3233 6902 5.765510 TCACCTTTTATAGCCATTGGATGT 58.234 37.500 6.95 0.10 0.00 3.06
3234 6903 5.593909 TCACCTTTTATAGCCATTGGATGTG 59.406 40.000 6.95 2.95 0.00 3.21
3235 6904 5.593909 CACCTTTTATAGCCATTGGATGTGA 59.406 40.000 6.95 0.00 0.00 3.58
3236 6905 6.266103 CACCTTTTATAGCCATTGGATGTGAT 59.734 38.462 6.95 0.00 0.00 3.06
3237 6906 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
3238 6907 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
3239 6908 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
3240 6909 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
3241 6910 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
3242 6911 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
3243 6912 4.989277 AGCCATTGGATGTGATGCTATAA 58.011 39.130 6.95 0.00 0.00 0.98
3244 6913 5.008331 AGCCATTGGATGTGATGCTATAAG 58.992 41.667 6.95 0.00 0.00 1.73
3245 6914 5.005740 GCCATTGGATGTGATGCTATAAGA 58.994 41.667 6.95 0.00 0.00 2.10
3246 6915 5.651139 GCCATTGGATGTGATGCTATAAGAT 59.349 40.000 6.95 0.00 0.00 2.40
3247 6916 6.404403 GCCATTGGATGTGATGCTATAAGATG 60.404 42.308 6.95 0.00 0.00 2.90
3248 6917 6.404403 CCATTGGATGTGATGCTATAAGATGC 60.404 42.308 0.00 0.00 0.00 3.91
3249 6918 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
3250 6919 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
3251 6920 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
3252 6921 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
3253 6922 3.803778 TGTGATGCTATAAGATGCGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
3254 6923 3.804325 GTGATGCTATAAGATGCGTGTGT 59.196 43.478 0.00 0.00 0.00 3.72
3255 6924 3.803778 TGATGCTATAAGATGCGTGTGTG 59.196 43.478 0.00 0.00 0.00 3.82
3256 6925 1.933181 TGCTATAAGATGCGTGTGTGC 59.067 47.619 0.00 0.00 0.00 4.57
3257 6926 2.205074 GCTATAAGATGCGTGTGTGCT 58.795 47.619 0.00 0.00 35.36 4.40
3258 6927 2.033407 GCTATAAGATGCGTGTGTGCTG 60.033 50.000 0.00 0.00 35.36 4.41
3259 6928 2.385013 ATAAGATGCGTGTGTGCTGA 57.615 45.000 0.00 0.00 35.36 4.26
3260 6929 1.428448 TAAGATGCGTGTGTGCTGAC 58.572 50.000 0.00 0.00 35.36 3.51
3261 6930 0.250038 AAGATGCGTGTGTGCTGACT 60.250 50.000 0.00 0.00 35.36 3.41
3262 6931 0.250038 AGATGCGTGTGTGCTGACTT 60.250 50.000 0.00 0.00 35.36 3.01
3263 6932 0.110509 GATGCGTGTGTGCTGACTTG 60.111 55.000 0.00 0.00 35.36 3.16
3264 6933 1.509644 ATGCGTGTGTGCTGACTTGG 61.510 55.000 0.00 0.00 35.36 3.61
3265 6934 2.896801 GCGTGTGTGCTGACTTGGG 61.897 63.158 0.00 0.00 0.00 4.12
3266 6935 1.523711 CGTGTGTGCTGACTTGGGT 60.524 57.895 0.00 0.00 0.00 4.51
3267 6936 1.095228 CGTGTGTGCTGACTTGGGTT 61.095 55.000 0.00 0.00 0.00 4.11
3268 6937 0.381801 GTGTGTGCTGACTTGGGTTG 59.618 55.000 0.00 0.00 0.00 3.77
3269 6938 1.360192 GTGTGCTGACTTGGGTTGC 59.640 57.895 0.00 0.00 0.00 4.17
3270 6939 1.103398 GTGTGCTGACTTGGGTTGCT 61.103 55.000 0.00 0.00 0.00 3.91
3271 6940 0.395586 TGTGCTGACTTGGGTTGCTT 60.396 50.000 0.00 0.00 0.00 3.91
3272 6941 0.746659 GTGCTGACTTGGGTTGCTTT 59.253 50.000 0.00 0.00 0.00 3.51
3273 6942 1.136891 GTGCTGACTTGGGTTGCTTTT 59.863 47.619 0.00 0.00 0.00 2.27
3274 6943 1.136695 TGCTGACTTGGGTTGCTTTTG 59.863 47.619 0.00 0.00 0.00 2.44
3275 6944 1.136891 GCTGACTTGGGTTGCTTTTGT 59.863 47.619 0.00 0.00 0.00 2.83
3276 6945 2.418609 GCTGACTTGGGTTGCTTTTGTT 60.419 45.455 0.00 0.00 0.00 2.83
3277 6946 3.860641 CTGACTTGGGTTGCTTTTGTTT 58.139 40.909 0.00 0.00 0.00 2.83
3278 6947 4.252878 CTGACTTGGGTTGCTTTTGTTTT 58.747 39.130 0.00 0.00 0.00 2.43
3279 6948 4.249661 TGACTTGGGTTGCTTTTGTTTTC 58.750 39.130 0.00 0.00 0.00 2.29
3280 6949 3.258228 ACTTGGGTTGCTTTTGTTTTCG 58.742 40.909 0.00 0.00 0.00 3.46
3281 6950 3.258228 CTTGGGTTGCTTTTGTTTTCGT 58.742 40.909 0.00 0.00 0.00 3.85
3282 6951 3.320673 TGGGTTGCTTTTGTTTTCGTT 57.679 38.095 0.00 0.00 0.00 3.85
3283 6952 3.665190 TGGGTTGCTTTTGTTTTCGTTT 58.335 36.364 0.00 0.00 0.00 3.60
3284 6953 4.065789 TGGGTTGCTTTTGTTTTCGTTTT 58.934 34.783 0.00 0.00 0.00 2.43
3285 6954 4.152580 TGGGTTGCTTTTGTTTTCGTTTTC 59.847 37.500 0.00 0.00 0.00 2.29
3286 6955 4.152580 GGGTTGCTTTTGTTTTCGTTTTCA 59.847 37.500 0.00 0.00 0.00 2.69
3287 6956 5.334182 GGGTTGCTTTTGTTTTCGTTTTCAA 60.334 36.000 0.00 0.00 0.00 2.69
3288 6957 5.788041 GGTTGCTTTTGTTTTCGTTTTCAAG 59.212 36.000 0.00 0.00 0.00 3.02
3289 6958 5.523013 TGCTTTTGTTTTCGTTTTCAAGG 57.477 34.783 0.00 0.00 0.00 3.61
3290 6959 4.991687 TGCTTTTGTTTTCGTTTTCAAGGT 59.008 33.333 0.00 0.00 0.00 3.50
3291 6960 5.107298 TGCTTTTGTTTTCGTTTTCAAGGTG 60.107 36.000 0.00 0.00 0.00 4.00
3292 6961 5.119434 GCTTTTGTTTTCGTTTTCAAGGTGA 59.881 36.000 0.00 0.00 0.00 4.02
3293 6962 6.346999 GCTTTTGTTTTCGTTTTCAAGGTGAA 60.347 34.615 0.00 0.00 34.03 3.18
3294 6963 7.623297 GCTTTTGTTTTCGTTTTCAAGGTGAAT 60.623 33.333 0.00 0.00 36.11 2.57
3295 6964 6.639671 TTGTTTTCGTTTTCAAGGTGAATG 57.360 33.333 0.00 0.00 36.11 2.67
3296 6965 5.955488 TGTTTTCGTTTTCAAGGTGAATGA 58.045 33.333 0.00 0.00 36.11 2.57
3297 6966 6.033341 TGTTTTCGTTTTCAAGGTGAATGAG 58.967 36.000 0.00 0.00 36.11 2.90
3298 6967 6.127869 TGTTTTCGTTTTCAAGGTGAATGAGA 60.128 34.615 0.00 0.00 36.11 3.27
3299 6968 5.418310 TTCGTTTTCAAGGTGAATGAGAC 57.582 39.130 0.00 0.00 36.11 3.36
3300 6969 3.813166 TCGTTTTCAAGGTGAATGAGACC 59.187 43.478 0.00 0.00 36.11 3.85
3301 6970 3.563808 CGTTTTCAAGGTGAATGAGACCA 59.436 43.478 0.00 0.00 36.11 4.02
3302 6971 4.036262 CGTTTTCAAGGTGAATGAGACCAA 59.964 41.667 0.00 0.00 36.11 3.67
3303 6972 5.449862 CGTTTTCAAGGTGAATGAGACCAAA 60.450 40.000 0.00 0.00 36.11 3.28
3304 6973 6.515832 GTTTTCAAGGTGAATGAGACCAAAT 58.484 36.000 0.00 0.00 36.11 2.32
3305 6974 6.729690 TTTCAAGGTGAATGAGACCAAATT 57.270 33.333 0.00 0.00 36.11 1.82
3306 6975 7.831691 TTTCAAGGTGAATGAGACCAAATTA 57.168 32.000 0.00 0.00 36.11 1.40
3307 6976 8.421249 TTTCAAGGTGAATGAGACCAAATTAT 57.579 30.769 0.00 0.00 36.11 1.28
3308 6977 9.527157 TTTCAAGGTGAATGAGACCAAATTATA 57.473 29.630 0.00 0.00 36.11 0.98
3309 6978 9.699410 TTCAAGGTGAATGAGACCAAATTATAT 57.301 29.630 0.00 0.00 35.76 0.86
3310 6979 9.342308 TCAAGGTGAATGAGACCAAATTATATC 57.658 33.333 0.00 0.00 35.76 1.63
3311 6980 9.347240 CAAGGTGAATGAGACCAAATTATATCT 57.653 33.333 0.00 0.00 35.76 1.98
3312 6981 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
3334 7003 6.798427 TCATCTAAATGAGTTCTAGGCACT 57.202 37.500 0.00 0.00 38.74 4.40
3335 7004 6.810911 TCATCTAAATGAGTTCTAGGCACTC 58.189 40.000 13.40 13.40 37.09 3.51
3336 7005 5.599999 TCTAAATGAGTTCTAGGCACTCC 57.400 43.478 16.20 4.17 40.12 3.85
3337 7006 3.636153 AAATGAGTTCTAGGCACTCCC 57.364 47.619 16.20 0.00 40.12 4.30
3338 7007 9.047928 CATCTAAATGAGTTCTAGGCACTCCCT 62.048 44.444 16.20 5.46 40.12 4.20
3381 7055 0.815734 TCCTTGCTCGTGGTAGCTAC 59.184 55.000 15.88 15.88 43.19 3.58
3383 7057 1.202313 CCTTGCTCGTGGTAGCTACTC 60.202 57.143 22.74 13.53 43.19 2.59
3384 7058 0.815734 TTGCTCGTGGTAGCTACTCC 59.184 55.000 22.74 12.53 43.19 3.85
3385 7059 0.034380 TGCTCGTGGTAGCTACTCCT 60.034 55.000 22.74 0.00 43.19 3.69
3386 7060 1.211212 TGCTCGTGGTAGCTACTCCTA 59.789 52.381 22.74 6.60 43.19 2.94
3387 7061 1.603326 GCTCGTGGTAGCTACTCCTAC 59.397 57.143 22.74 14.94 39.50 3.18
3388 7062 2.745812 GCTCGTGGTAGCTACTCCTACT 60.746 54.545 22.74 0.00 39.50 2.57
3389 7063 3.494048 GCTCGTGGTAGCTACTCCTACTA 60.494 52.174 22.74 8.83 39.50 1.82
3390 7064 4.309099 CTCGTGGTAGCTACTCCTACTAG 58.691 52.174 22.74 13.52 38.18 2.57
3391 7065 2.807392 CGTGGTAGCTACTCCTACTAGC 59.193 54.545 22.74 4.13 38.18 3.42
3392 7066 3.494749 CGTGGTAGCTACTCCTACTAGCT 60.495 52.174 22.74 5.35 46.95 3.32
3393 7067 4.262377 CGTGGTAGCTACTCCTACTAGCTA 60.262 50.000 22.74 3.53 44.24 3.32
3573 7567 0.028505 GAAGCTACACGCATGCATGG 59.971 55.000 27.34 19.00 42.61 3.66
3651 7649 1.402787 CCAACAGGTCAAAAGGCTGT 58.597 50.000 0.00 0.00 0.00 4.40
3652 7650 1.067516 CCAACAGGTCAAAAGGCTGTG 59.932 52.381 0.00 0.00 0.00 3.66
4261 8713 4.015406 TCGGTGTCGCAGGCCATT 62.015 61.111 5.01 0.00 36.13 3.16
4869 9883 1.382419 GCGTATAAGAGCGTGTATGCG 59.618 52.381 8.78 8.78 40.67 4.73
4902 9920 5.588648 GTGCACATTATGTATTGTACAGGGT 59.411 40.000 13.17 0.00 42.77 4.34
4946 9968 1.226802 CAGCTCAGATGCGTACGCT 60.227 57.895 36.99 24.06 42.51 5.07
5164 10534 4.398673 GGCGAGACCGAAGTATTCCTATAT 59.601 45.833 0.00 0.00 43.81 0.86
5167 10538 6.527372 GCGAGACCGAAGTATTCCTATATTTC 59.473 42.308 0.00 0.00 43.81 2.17
5230 10603 6.405731 CGGAAACACAATTAATCACATCCCAT 60.406 38.462 0.00 0.00 0.00 4.00
5305 10735 2.517919 GGGTGGCCCAGATGGATC 59.482 66.667 0.00 0.00 44.65 3.36
5370 10811 4.500116 GAGAGAGGGACGCACGCC 62.500 72.222 0.00 0.00 0.00 5.68
5378 10819 3.537874 GACGCACGCCCTAGGGAT 61.538 66.667 33.21 15.94 37.50 3.85
5379 10820 3.792053 GACGCACGCCCTAGGGATG 62.792 68.421 33.21 27.00 37.50 3.51
5397 10838 2.073252 TGATGTAGACGATCCTGCCT 57.927 50.000 0.00 0.00 0.00 4.75
5513 10959 5.175859 CAGTAGGTATCATCCGTGTGTTTT 58.824 41.667 0.00 0.00 0.00 2.43
5538 10984 3.752747 TGGATACGTATATCTCGCCGAAA 59.247 43.478 8.34 0.00 37.85 3.46
5542 10988 2.287427 ACGTATATCTCGCCGAAACCTG 60.287 50.000 0.00 0.00 0.00 4.00
5575 11021 3.842869 GAGCAACCCTCTGATCGTT 57.157 52.632 0.00 0.00 37.60 3.85
5584 11030 1.354040 CTCTGATCGTTCCTGTGCAC 58.646 55.000 10.75 10.75 0.00 4.57
5687 11134 6.054295 GCTCCAGATGATAATGTTCAGACTT 58.946 40.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 9.968743 CGTATACTTTTTCAAACAAGACCTATC 57.031 33.333 0.56 0.00 0.00 2.08
236 243 6.882610 TTCGTCACTCTACCTTTTACTACA 57.117 37.500 0.00 0.00 0.00 2.74
936 974 5.920840 TGTGTATGTGTCTTTCTTTCTCTCG 59.079 40.000 0.00 0.00 0.00 4.04
950 988 1.210722 TGTGTGGGTGTGTGTATGTGT 59.789 47.619 0.00 0.00 0.00 3.72
951 989 1.601903 GTGTGTGGGTGTGTGTATGTG 59.398 52.381 0.00 0.00 0.00 3.21
952 990 1.476110 GGTGTGTGGGTGTGTGTATGT 60.476 52.381 0.00 0.00 0.00 2.29
954 992 0.109723 GGGTGTGTGGGTGTGTGTAT 59.890 55.000 0.00 0.00 0.00 2.29
955 993 0.983905 AGGGTGTGTGGGTGTGTGTA 60.984 55.000 0.00 0.00 0.00 2.90
964 1002 2.203139 TGCGTTGAGGGTGTGTGG 60.203 61.111 0.00 0.00 0.00 4.17
983 1021 4.097135 TCGCCATTCTCTTTGTCTCTCTAG 59.903 45.833 0.00 0.00 0.00 2.43
992 1032 1.131883 CTTGGCTCGCCATTCTCTTTG 59.868 52.381 12.00 0.00 46.64 2.77
1159 4130 9.657121 AAGCTAAGATTAACGTACGTATTACTC 57.343 33.333 23.12 14.28 0.00 2.59
1188 4325 9.203163 ACCTAGCTAGCTAATTCTTCTCTTAAA 57.797 33.333 24.20 0.00 0.00 1.52
1512 4671 2.957680 TGCAGCAAATTCCAAGACTCAA 59.042 40.909 0.00 0.00 0.00 3.02
1513 4672 2.555325 CTGCAGCAAATTCCAAGACTCA 59.445 45.455 0.00 0.00 0.00 3.41
1825 4995 5.114780 TGCAAGCTTTTGTTTGATGCTTTA 58.885 33.333 0.00 0.00 42.20 1.85
1836 5006 5.014808 AGACTTCATTTGCAAGCTTTTGT 57.985 34.783 0.00 0.00 0.00 2.83
1864 5034 4.201881 ACTGACATGCATGATCATCAAACG 60.202 41.667 32.75 18.44 0.00 3.60
1870 5040 3.819337 GGCTAACTGACATGCATGATCAT 59.181 43.478 32.75 18.26 0.00 2.45
1873 5043 3.286329 TGGCTAACTGACATGCATGAT 57.714 42.857 32.75 16.80 0.00 2.45
1874 5044 2.785540 TGGCTAACTGACATGCATGA 57.214 45.000 32.75 10.86 0.00 3.07
1998 5232 9.647797 GGGAAGAAGAAAAACTTTTAGTTCAAA 57.352 29.630 10.11 0.00 37.47 2.69
1999 5233 9.031537 AGGGAAGAAGAAAAACTTTTAGTTCAA 57.968 29.630 10.11 0.00 37.47 2.69
2000 5234 8.466798 CAGGGAAGAAGAAAAACTTTTAGTTCA 58.533 33.333 10.11 0.00 37.47 3.18
2001 5235 7.435488 GCAGGGAAGAAGAAAAACTTTTAGTTC 59.565 37.037 0.00 0.00 37.47 3.01
2002 5236 7.093509 TGCAGGGAAGAAGAAAAACTTTTAGTT 60.094 33.333 0.00 0.00 40.80 2.24
2003 5237 6.379988 TGCAGGGAAGAAGAAAAACTTTTAGT 59.620 34.615 0.00 0.00 39.13 2.24
2004 5238 6.805713 TGCAGGGAAGAAGAAAAACTTTTAG 58.194 36.000 0.00 0.00 39.13 1.85
2005 5239 6.783708 TGCAGGGAAGAAGAAAAACTTTTA 57.216 33.333 0.00 0.00 39.13 1.52
2006 5240 5.675684 TGCAGGGAAGAAGAAAAACTTTT 57.324 34.783 0.00 0.00 39.13 2.27
2166 5421 1.017387 GCAGCGGACCAAAGGAATAG 58.983 55.000 0.00 0.00 0.00 1.73
2185 5442 1.289109 AAACGTCAAGATGCGACCGG 61.289 55.000 0.00 0.00 0.00 5.28
2632 6276 0.891449 CGGCTGCTCCTAGCTAGCTA 60.891 60.000 22.85 22.85 42.97 3.32
2633 6277 2.199652 CGGCTGCTCCTAGCTAGCT 61.200 63.158 23.12 23.12 42.97 3.32
2634 6278 2.338257 CGGCTGCTCCTAGCTAGC 59.662 66.667 15.74 6.62 42.97 3.42
2635 6279 1.523154 CTCCGGCTGCTCCTAGCTAG 61.523 65.000 14.20 14.20 42.97 3.42
2790 6435 4.020662 GGAAGCCTAGGAATACATGGAGAG 60.021 50.000 14.75 0.00 0.00 3.20
2792 6437 3.906846 AGGAAGCCTAGGAATACATGGAG 59.093 47.826 14.75 0.00 28.47 3.86
2794 6439 3.808618 GCAGGAAGCCTAGGAATACATGG 60.809 52.174 14.75 0.00 37.23 3.66
2795 6440 3.406764 GCAGGAAGCCTAGGAATACATG 58.593 50.000 14.75 9.22 37.23 3.21
2796 6441 3.778954 GCAGGAAGCCTAGGAATACAT 57.221 47.619 14.75 0.00 37.23 2.29
2929 6578 7.944729 ACTCTTAAGAATGCAAATGGTATGT 57.055 32.000 6.63 0.00 0.00 2.29
3085 6749 2.462456 TTGACTAGCTTCCAGTGCAG 57.538 50.000 0.00 0.00 0.00 4.41
3086 6750 2.104792 ACTTTGACTAGCTTCCAGTGCA 59.895 45.455 0.00 0.00 0.00 4.57
3087 6751 2.772287 ACTTTGACTAGCTTCCAGTGC 58.228 47.619 0.00 0.00 0.00 4.40
3088 6752 4.380531 TGAACTTTGACTAGCTTCCAGTG 58.619 43.478 0.00 0.00 0.00 3.66
3089 6753 4.689612 TGAACTTTGACTAGCTTCCAGT 57.310 40.909 0.00 0.00 0.00 4.00
3156 6825 9.742144 TGGGTTCTAGCAAAACTGTAAATATAA 57.258 29.630 0.00 0.00 0.00 0.98
3157 6826 9.914834 ATGGGTTCTAGCAAAACTGTAAATATA 57.085 29.630 0.00 0.00 0.00 0.86
3158 6827 8.823220 ATGGGTTCTAGCAAAACTGTAAATAT 57.177 30.769 0.00 0.00 0.00 1.28
3159 6828 8.107095 AGATGGGTTCTAGCAAAACTGTAAATA 58.893 33.333 0.00 0.00 30.96 1.40
3160 6829 6.948309 AGATGGGTTCTAGCAAAACTGTAAAT 59.052 34.615 0.00 0.00 30.96 1.40
3161 6830 6.303839 AGATGGGTTCTAGCAAAACTGTAAA 58.696 36.000 0.00 0.00 30.96 2.01
3162 6831 5.876357 AGATGGGTTCTAGCAAAACTGTAA 58.124 37.500 0.00 0.00 30.96 2.41
3163 6832 5.499004 AGATGGGTTCTAGCAAAACTGTA 57.501 39.130 0.00 0.00 30.96 2.74
3164 6833 4.373156 AGATGGGTTCTAGCAAAACTGT 57.627 40.909 0.00 0.00 30.96 3.55
3175 6844 9.836179 AAACTATATCTCATCTAGATGGGTTCT 57.164 33.333 27.95 16.81 44.95 3.01
3176 6845 9.868277 CAAACTATATCTCATCTAGATGGGTTC 57.132 37.037 27.95 0.00 44.95 3.62
3177 6846 8.820831 CCAAACTATATCTCATCTAGATGGGTT 58.179 37.037 27.95 22.87 44.95 4.11
3178 6847 7.958583 ACCAAACTATATCTCATCTAGATGGGT 59.041 37.037 27.95 19.82 44.95 4.51
3179 6848 8.372877 ACCAAACTATATCTCATCTAGATGGG 57.627 38.462 28.30 26.46 44.95 4.00
3180 6849 9.253832 AGACCAAACTATATCTCATCTAGATGG 57.746 37.037 28.30 19.83 44.95 3.51
3190 6859 7.731054 AGGTGAATGAGACCAAACTATATCTC 58.269 38.462 0.00 0.00 38.46 2.75
3191 6860 7.682787 AGGTGAATGAGACCAAACTATATCT 57.317 36.000 0.00 0.00 35.76 1.98
3192 6861 8.738645 AAAGGTGAATGAGACCAAACTATATC 57.261 34.615 0.00 0.00 35.76 1.63
3196 6865 9.667107 CTATAAAAGGTGAATGAGACCAAACTA 57.333 33.333 0.00 0.00 35.76 2.24
3197 6866 7.121315 GCTATAAAAGGTGAATGAGACCAAACT 59.879 37.037 0.00 0.00 35.76 2.66
3198 6867 7.251281 GCTATAAAAGGTGAATGAGACCAAAC 58.749 38.462 0.00 0.00 35.76 2.93
3199 6868 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
3200 6869 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
3201 6870 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
3202 6871 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
3203 6872 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
3204 6873 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
3205 6874 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
3206 6875 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
3207 6876 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
3208 6877 6.840705 ACATCCAATGGCTATAAAAGGTGAAT 59.159 34.615 0.00 0.00 33.60 2.57
3209 6878 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
3210 6879 5.593909 CACATCCAATGGCTATAAAAGGTGA 59.406 40.000 0.00 0.00 33.60 4.02
3211 6880 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
3212 6881 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
3213 6882 6.684686 CATCACATCCAATGGCTATAAAAGG 58.315 40.000 0.00 0.00 33.60 3.11
3214 6883 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
3215 6884 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
3216 6885 5.387788 AGCATCACATCCAATGGCTATAAA 58.612 37.500 0.00 0.00 33.60 1.40
3217 6886 4.989277 AGCATCACATCCAATGGCTATAA 58.011 39.130 0.00 0.00 33.60 0.98
3218 6887 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
3219 6888 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
3220 6889 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
3221 6890 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
3222 6891 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40
3223 6892 6.404403 GCATCTTATAGCATCACATCCAATGG 60.404 42.308 0.00 0.00 33.60 3.16
3224 6893 6.552629 GCATCTTATAGCATCACATCCAATG 58.447 40.000 0.00 0.00 0.00 2.82
3225 6894 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
3226 6895 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
3227 6896 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
3228 6897 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
3229 6898 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
3230 6899 4.450080 CACACGCATCTTATAGCATCACAT 59.550 41.667 0.00 0.00 0.00 3.21
3231 6900 3.803778 CACACGCATCTTATAGCATCACA 59.196 43.478 0.00 0.00 0.00 3.58
3232 6901 3.804325 ACACACGCATCTTATAGCATCAC 59.196 43.478 0.00 0.00 0.00 3.06
3233 6902 3.803778 CACACACGCATCTTATAGCATCA 59.196 43.478 0.00 0.00 0.00 3.07
3234 6903 3.363378 GCACACACGCATCTTATAGCATC 60.363 47.826 0.00 0.00 0.00 3.91
3235 6904 2.545526 GCACACACGCATCTTATAGCAT 59.454 45.455 0.00 0.00 0.00 3.79
3236 6905 1.933181 GCACACACGCATCTTATAGCA 59.067 47.619 0.00 0.00 0.00 3.49
3237 6906 2.033407 CAGCACACACGCATCTTATAGC 60.033 50.000 0.00 0.00 0.00 2.97
3238 6907 3.243877 GTCAGCACACACGCATCTTATAG 59.756 47.826 0.00 0.00 0.00 1.31
3239 6908 3.119137 AGTCAGCACACACGCATCTTATA 60.119 43.478 0.00 0.00 0.00 0.98
3240 6909 2.002586 GTCAGCACACACGCATCTTAT 58.997 47.619 0.00 0.00 0.00 1.73
3241 6910 1.000843 AGTCAGCACACACGCATCTTA 59.999 47.619 0.00 0.00 0.00 2.10
3242 6911 0.250038 AGTCAGCACACACGCATCTT 60.250 50.000 0.00 0.00 0.00 2.40
3243 6912 0.250038 AAGTCAGCACACACGCATCT 60.250 50.000 0.00 0.00 0.00 2.90
3244 6913 0.110509 CAAGTCAGCACACACGCATC 60.111 55.000 0.00 0.00 0.00 3.91
3245 6914 1.509644 CCAAGTCAGCACACACGCAT 61.510 55.000 0.00 0.00 0.00 4.73
3246 6915 2.179547 CCAAGTCAGCACACACGCA 61.180 57.895 0.00 0.00 0.00 5.24
3247 6916 2.633657 CCAAGTCAGCACACACGC 59.366 61.111 0.00 0.00 0.00 5.34
3248 6917 1.095228 AACCCAAGTCAGCACACACG 61.095 55.000 0.00 0.00 0.00 4.49
3249 6918 0.381801 CAACCCAAGTCAGCACACAC 59.618 55.000 0.00 0.00 0.00 3.82
3250 6919 1.383456 GCAACCCAAGTCAGCACACA 61.383 55.000 0.00 0.00 0.00 3.72
3251 6920 1.103398 AGCAACCCAAGTCAGCACAC 61.103 55.000 0.00 0.00 31.33 3.82
3252 6921 0.395586 AAGCAACCCAAGTCAGCACA 60.396 50.000 0.00 0.00 31.33 4.57
3253 6922 0.746659 AAAGCAACCCAAGTCAGCAC 59.253 50.000 0.00 0.00 31.33 4.40
3254 6923 1.136695 CAAAAGCAACCCAAGTCAGCA 59.863 47.619 0.00 0.00 31.33 4.41
3255 6924 1.136891 ACAAAAGCAACCCAAGTCAGC 59.863 47.619 0.00 0.00 0.00 4.26
3256 6925 3.525268 AACAAAAGCAACCCAAGTCAG 57.475 42.857 0.00 0.00 0.00 3.51
3257 6926 3.971245 AAACAAAAGCAACCCAAGTCA 57.029 38.095 0.00 0.00 0.00 3.41
3258 6927 3.305897 CGAAAACAAAAGCAACCCAAGTC 59.694 43.478 0.00 0.00 0.00 3.01
3259 6928 3.258228 CGAAAACAAAAGCAACCCAAGT 58.742 40.909 0.00 0.00 0.00 3.16
3260 6929 3.258228 ACGAAAACAAAAGCAACCCAAG 58.742 40.909 0.00 0.00 0.00 3.61
3261 6930 3.320673 ACGAAAACAAAAGCAACCCAA 57.679 38.095 0.00 0.00 0.00 4.12
3262 6931 3.320673 AACGAAAACAAAAGCAACCCA 57.679 38.095 0.00 0.00 0.00 4.51
3263 6932 4.152580 TGAAAACGAAAACAAAAGCAACCC 59.847 37.500 0.00 0.00 0.00 4.11
3264 6933 5.270812 TGAAAACGAAAACAAAAGCAACC 57.729 34.783 0.00 0.00 0.00 3.77
3265 6934 5.788041 CCTTGAAAACGAAAACAAAAGCAAC 59.212 36.000 0.00 0.00 0.00 4.17
3266 6935 5.467063 ACCTTGAAAACGAAAACAAAAGCAA 59.533 32.000 0.00 0.00 0.00 3.91
3267 6936 4.991687 ACCTTGAAAACGAAAACAAAAGCA 59.008 33.333 0.00 0.00 0.00 3.91
3268 6937 5.119434 TCACCTTGAAAACGAAAACAAAAGC 59.881 36.000 0.00 0.00 0.00 3.51
3269 6938 6.698359 TCACCTTGAAAACGAAAACAAAAG 57.302 33.333 0.00 0.00 0.00 2.27
3270 6939 7.385205 TCATTCACCTTGAAAACGAAAACAAAA 59.615 29.630 0.00 0.00 40.12 2.44
3271 6940 6.868864 TCATTCACCTTGAAAACGAAAACAAA 59.131 30.769 0.00 0.00 40.12 2.83
3272 6941 6.390721 TCATTCACCTTGAAAACGAAAACAA 58.609 32.000 0.00 0.00 40.12 2.83
3273 6942 5.955488 TCATTCACCTTGAAAACGAAAACA 58.045 33.333 0.00 0.00 40.12 2.83
3274 6943 6.196538 GTCTCATTCACCTTGAAAACGAAAAC 59.803 38.462 0.00 0.00 40.12 2.43
3275 6944 6.262601 GTCTCATTCACCTTGAAAACGAAAA 58.737 36.000 0.00 0.00 40.12 2.29
3276 6945 5.220970 GGTCTCATTCACCTTGAAAACGAAA 60.221 40.000 0.00 0.00 40.12 3.46
3277 6946 4.274950 GGTCTCATTCACCTTGAAAACGAA 59.725 41.667 0.00 0.00 40.12 3.85
3278 6947 3.813166 GGTCTCATTCACCTTGAAAACGA 59.187 43.478 0.00 0.00 40.12 3.85
3279 6948 3.563808 TGGTCTCATTCACCTTGAAAACG 59.436 43.478 0.00 0.00 40.12 3.60
3280 6949 5.514274 TTGGTCTCATTCACCTTGAAAAC 57.486 39.130 0.00 0.00 40.12 2.43
3281 6950 6.729690 ATTTGGTCTCATTCACCTTGAAAA 57.270 33.333 0.00 0.00 40.12 2.29
3282 6951 6.729690 AATTTGGTCTCATTCACCTTGAAA 57.270 33.333 0.00 0.00 40.12 2.69
3283 6952 9.699410 ATATAATTTGGTCTCATTCACCTTGAA 57.301 29.630 0.00 0.00 41.09 2.69
3284 6953 9.342308 GATATAATTTGGTCTCATTCACCTTGA 57.658 33.333 0.00 0.00 34.66 3.02
3285 6954 9.347240 AGATATAATTTGGTCTCATTCACCTTG 57.653 33.333 0.00 0.00 34.66 3.61
3286 6955 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
3287 6956 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
3288 6957 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
3311 6980 6.183360 GGAGTGCCTAGAACTCATTTAGATGA 60.183 42.308 20.54 0.00 44.86 2.92
3312 6981 5.988561 GGAGTGCCTAGAACTCATTTAGATG 59.011 44.000 20.54 0.00 44.86 2.90
3313 6982 5.071115 GGGAGTGCCTAGAACTCATTTAGAT 59.929 44.000 20.54 0.00 44.86 1.98
3314 6983 4.406003 GGGAGTGCCTAGAACTCATTTAGA 59.594 45.833 20.54 0.00 44.86 2.10
3315 6984 4.407296 AGGGAGTGCCTAGAACTCATTTAG 59.593 45.833 20.54 0.00 44.86 1.85
3316 6985 4.362677 AGGGAGTGCCTAGAACTCATTTA 58.637 43.478 20.54 0.00 44.86 1.40
3317 6986 3.185455 AGGGAGTGCCTAGAACTCATTT 58.815 45.455 20.54 8.10 44.86 2.32
3318 6987 2.839228 AGGGAGTGCCTAGAACTCATT 58.161 47.619 20.54 9.88 44.86 2.57
3319 6988 2.559381 AGGGAGTGCCTAGAACTCAT 57.441 50.000 20.54 10.40 44.86 2.90
3320 6989 2.327325 AAGGGAGTGCCTAGAACTCA 57.673 50.000 20.54 0.39 44.86 3.41
3321 6990 6.673839 AATATAAGGGAGTGCCTAGAACTC 57.326 41.667 2.47 14.10 42.79 3.01
3322 6991 8.743636 ATAAATATAAGGGAGTGCCTAGAACT 57.256 34.615 2.47 0.00 0.00 3.01
3323 6992 8.041919 GGATAAATATAAGGGAGTGCCTAGAAC 58.958 40.741 2.47 0.00 0.00 3.01
3324 6993 7.737607 TGGATAAATATAAGGGAGTGCCTAGAA 59.262 37.037 2.47 0.00 0.00 2.10
3325 6994 7.253421 TGGATAAATATAAGGGAGTGCCTAGA 58.747 38.462 2.47 0.00 0.00 2.43
3326 6995 7.181125 ACTGGATAAATATAAGGGAGTGCCTAG 59.819 40.741 2.47 0.00 0.00 3.02
3327 6996 7.023120 ACTGGATAAATATAAGGGAGTGCCTA 58.977 38.462 2.47 0.00 0.00 3.93
3328 6997 5.852250 ACTGGATAAATATAAGGGAGTGCCT 59.148 40.000 0.00 0.00 0.00 4.75
3329 6998 6.128138 ACTGGATAAATATAAGGGAGTGCC 57.872 41.667 0.00 0.00 0.00 5.01
3330 6999 6.655425 GGAACTGGATAAATATAAGGGAGTGC 59.345 42.308 0.00 0.00 0.00 4.40
3331 7000 7.978925 AGGAACTGGATAAATATAAGGGAGTG 58.021 38.462 0.00 0.00 37.18 3.51
3332 7001 8.582891 AAGGAACTGGATAAATATAAGGGAGT 57.417 34.615 0.00 0.00 40.86 3.85
3333 7002 9.868160 AAAAGGAACTGGATAAATATAAGGGAG 57.132 33.333 0.00 0.00 40.86 4.30
3388 7062 2.943690 CCGACTTGTCACTAGCTAGCTA 59.056 50.000 22.85 22.85 0.00 3.32
3389 7063 1.746220 CCGACTTGTCACTAGCTAGCT 59.254 52.381 23.12 23.12 0.00 3.32
3390 7064 1.473278 ACCGACTTGTCACTAGCTAGC 59.527 52.381 20.91 6.62 0.00 3.42
3391 7065 2.747989 TGACCGACTTGTCACTAGCTAG 59.252 50.000 19.44 19.44 40.22 3.42
3392 7066 2.786777 TGACCGACTTGTCACTAGCTA 58.213 47.619 0.00 0.00 40.22 3.32
3393 7067 1.617322 TGACCGACTTGTCACTAGCT 58.383 50.000 0.00 0.00 40.22 3.32
3425 7099 3.788797 GCCGAGGAACATTGCTATTTTCG 60.789 47.826 0.00 0.00 0.00 3.46
3573 7567 5.888105 ACTGAAATCTTGTAAGCATGCATC 58.112 37.500 21.98 10.00 0.00 3.91
3582 7579 8.441312 AAGGACGTTTAACTGAAATCTTGTAA 57.559 30.769 0.00 0.00 0.00 2.41
3651 7649 0.238025 GCGATGCATGAACACACACA 59.762 50.000 2.46 0.00 0.00 3.72
3652 7650 0.454957 GGCGATGCATGAACACACAC 60.455 55.000 2.46 0.00 0.00 3.82
3712 7815 6.952083 CGTGATGACATGCGATTGAATATAAG 59.048 38.462 0.00 0.00 0.00 1.73
3725 7828 1.524621 CCTCCCCGTGATGACATGC 60.525 63.158 0.00 0.00 0.00 4.06
3768 7958 7.524717 ACAAAATTATTCACACCAAGCTAGT 57.475 32.000 0.00 0.00 0.00 2.57
4869 9883 7.042321 ACAATACATAATGTGCACATACGTACC 60.042 37.037 31.55 0.00 35.10 3.34
4902 9920 2.519780 GTCGCACCCCAACCCAAA 60.520 61.111 0.00 0.00 0.00 3.28
4946 9968 7.613022 ACACTACTACAGCAAACCACTACTATA 59.387 37.037 0.00 0.00 0.00 1.31
5164 10534 6.262273 GGAGTTAGTGTGGACATTTCAAGAAA 59.738 38.462 0.00 0.00 34.46 2.52
5167 10538 5.063204 TGGAGTTAGTGTGGACATTTCAAG 58.937 41.667 0.00 0.00 0.00 3.02
5370 10811 3.697045 GGATCGTCTACATCATCCCTAGG 59.303 52.174 0.06 0.06 30.17 3.02
5371 10812 4.397730 CAGGATCGTCTACATCATCCCTAG 59.602 50.000 0.00 0.00 36.22 3.02
5374 10815 2.353208 GCAGGATCGTCTACATCATCCC 60.353 54.545 0.00 0.00 36.22 3.85
5375 10816 2.353208 GGCAGGATCGTCTACATCATCC 60.353 54.545 0.00 0.00 35.87 3.51
5377 10818 2.603021 AGGCAGGATCGTCTACATCAT 58.397 47.619 0.00 0.00 0.00 2.45
5378 10819 2.073252 AGGCAGGATCGTCTACATCA 57.927 50.000 0.00 0.00 0.00 3.07
5379 10820 4.096682 GGTATAGGCAGGATCGTCTACATC 59.903 50.000 0.00 0.00 0.00 3.06
5397 10838 7.773690 GGAGCAGTAAAGGAAGAAAATGGTATA 59.226 37.037 0.00 0.00 0.00 1.47
5513 10959 3.120095 CGGCGAGATATACGTATCCACAA 60.120 47.826 12.24 0.00 37.94 3.33
5570 11016 2.351276 GGGGTGCACAGGAACGAT 59.649 61.111 20.43 0.00 0.00 3.73
5575 11021 2.435663 CATGTGGGGTGCACAGGA 59.564 61.111 20.43 0.00 36.57 3.86
5584 11030 5.148502 AGTACTACTTATCTCCATGTGGGG 58.851 45.833 0.00 0.00 37.22 4.96
5627 11074 7.950512 TGTATCAATTCACACTCACCATTTTT 58.049 30.769 0.00 0.00 0.00 1.94
5714 11161 9.421399 CCCCATTTGAGGAATTAATTAACTAGT 57.579 33.333 0.00 0.00 0.00 2.57
5715 11162 8.360390 GCCCCATTTGAGGAATTAATTAACTAG 58.640 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.