Multiple sequence alignment - TraesCS4A01G466200

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 TraesCS4A01G466200 chr4A 100.000 3203 0 0 1 3203 729156302 729159504 0.000000e+00 5915.0
1 TraesCS4A01G466200 chr4A 84.865 2590 290 58 159 2706 729818414 729820943 0.000000e+00 2518.0
2 TraesCS4A01G466200 chr4A 89.133 1638 143 19 1087 2708 728443472 728441854 0.000000e+00 2006.0
3 TraesCS4A01G466200 chr4A 95.849 1036 41 1 1708 2741 729678543 729679578 0.000000e+00 1674.0
4 TraesCS4A01G466200 chr4A 82.580 1791 225 56 997 2744 729880854 729882600 0.000000e+00 1498.0
5 TraesCS4A01G466200 chr4A 77.837 1877 314 61 932 2765 727080858 727079041 0.000000e+00 1068.0
6 TraesCS4A01G466200 chr4A 77.634 1775 308 52 999 2744 729236752 729238466 0.000000e+00 996.0
7 TraesCS4A01G466200 chr4A 82.075 1166 131 31 564 1710 729677355 729678461 0.000000e+00 924.0
8 TraesCS4A01G466200 chr4A 79.043 1317 221 30 998 2278 730322761 730324058 0.000000e+00 852.0
9 TraesCS4A01G466200 chr4A 78.112 1165 173 44 753 1863 729925309 729926445 0.000000e+00 664.0
10 TraesCS4A01G466200 chr4A 79.624 692 95 19 2 662 729924552 729925228 3.770000e-124 455.0
11 TraesCS4A01G466200 chr4A 79.963 534 69 24 42 553 730005673 730005156 3.040000e-95 359.0
12 TraesCS4A01G466200 chr4A 79.545 484 54 14 801 1247 728662496 728662021 1.440000e-78 303.0
13 TraesCS4A01G466200 chr4A 91.045 201 16 2 2682 2880 730002310 730002110 1.460000e-68 270.0
14 TraesCS4A01G466200 chr4A 82.353 340 29 7 810 1122 730061513 730061178 1.890000e-67 267.0
15 TraesCS4A01G466200 chr4A 83.333 258 37 3 2949 3203 728569512 728569258 1.920000e-57 233.0
16 TraesCS4A01G466200 chr4A 88.000 175 12 4 602 770 728698558 728698387 7.010000e-47 198.0
17 TraesCS4A01G466200 chr4A 89.231 130 13 1 2808 2936 728441843 728441714 9.200000e-36 161.0
18 TraesCS4A01G466200 chr4A 90.435 115 11 0 3089 3203 729821055 729821169 5.530000e-33 152.0
19 TraesCS4A01G466200 chr4A 89.412 85 8 1 551 634 730005005 730004921 4.370000e-19 106.0
20 TraesCS4A01G466200 chr4A 94.000 50 3 0 813 862 730004754 730004705 3.430000e-10 76.8
21 TraesCS4A01G466200 chr7D 88.710 2418 172 40 563 2930 8818414 8820780 0.000000e+00 2859.0
22 TraesCS4A01G466200 chr7D 77.602 1768 300 63 998 2721 109144722 109143007 0.000000e+00 983.0
23 TraesCS4A01G466200 chr7D 76.780 2037 296 83 479 2444 10466140 10464210 0.000000e+00 977.0
24 TraesCS4A01G466200 chr7D 78.198 1376 220 48 1089 2408 10910347 10908996 0.000000e+00 806.0
25 TraesCS4A01G466200 chr7D 78.818 1303 197 48 1097 2357 9223956 9225221 0.000000e+00 804.0
26 TraesCS4A01G466200 chr7D 83.516 273 37 7 2936 3203 8871610 8871879 6.860000e-62 248.0
27 TraesCS4A01G466200 chr7D 80.586 273 36 12 2936 3203 9389067 9388807 9.070000e-46 195.0
28 TraesCS4A01G466200 chr7D 88.235 68 6 1 596 663 9223144 9223209 2.650000e-11 80.5
29 TraesCS4A01G466200 chr7A 87.795 1524 132 21 801 2300 9381809 9383302 0.000000e+00 1735.0
30 TraesCS4A01G466200 chr7A 77.237 1933 299 83 848 2734 10269523 10271360 0.000000e+00 1002.0
31 TraesCS4A01G466200 chr7A 76.905 1693 286 63 998 2623 10092034 10090380 0.000000e+00 863.0
32 TraesCS4A01G466200 chr7A 79.977 879 129 36 1890 2746 10168140 10167287 3.530000e-169 604.0
33 TraesCS4A01G466200 chr7A 79.245 583 100 9 1718 2299 10106083 10105521 1.390000e-103 387.0
34 TraesCS4A01G466200 chr7A 85.765 281 37 3 998 1278 1526780 1526503 8.690000e-76 294.0
35 TraesCS4A01G466200 chr7A 83.026 271 39 5 2936 3203 9488219 9488485 4.130000e-59 239.0
36 TraesCS4A01G466200 chr7A 88.889 72 3 2 714 780 9381737 9381808 2.050000e-12 84.2
37 TraesCS4A01G466200 chr4D 81.863 1814 233 53 998 2769 507352244 507350485 0.000000e+00 1439.0
38 TraesCS4A01G466200 chr4D 83.704 270 38 4 2938 3203 507350710 507350443 1.910000e-62 250.0
39 TraesCS4A01G466200 chr4D 90.361 166 13 3 2773 2936 507350454 507350290 6.960000e-52 215.0
40 TraesCS4A01G466200 chr4B 81.874 1804 239 46 1001 2769 654201948 654203698 0.000000e+00 1439.0
41 TraesCS4A01G466200 chr4B 88.024 167 17 3 2773 2936 654203729 654203895 9.070000e-46 195.0
42 TraesCS4A01G466200 chr5A 79.975 1623 226 55 807 2363 691820781 691822370 0.000000e+00 1105.0
43 TraesCS4A01G466200 chr5A 90.566 371 29 5 2403 2769 691822371 691822739 1.340000e-133 486.0
44 TraesCS4A01G466200 chr5A 92.188 128 8 2 2811 2936 691822820 691822947 2.540000e-41 180.0
45 TraesCS4A01G466200 chr6D 77.133 1207 199 44 998 2173 84280119 84281279 2.100000e-176 628.0
46 TraesCS4A01G466200 chr1B 100.000 64 0 0 734 797 65683969 65684032 5.610000e-23 119.0


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 TraesCS4A01G466200 chr4A 729156302 729159504 3202 False 5915.000000 5915 100.000000 1 3203 1 chr4A.!!$F1 3202
1 TraesCS4A01G466200 chr4A 729880854 729882600 1746 False 1498.000000 1498 82.580000 997 2744 1 chr4A.!!$F3 1747
2 TraesCS4A01G466200 chr4A 729818414 729821169 2755 False 1335.000000 2518 87.650000 159 3203 2 chr4A.!!$F6 3044
3 TraesCS4A01G466200 chr4A 729677355 729679578 2223 False 1299.000000 1674 88.962000 564 2741 2 chr4A.!!$F5 2177
4 TraesCS4A01G466200 chr4A 728441714 728443472 1758 True 1083.500000 2006 89.182000 1087 2936 2 chr4A.!!$R6 1849
5 TraesCS4A01G466200 chr4A 727079041 727080858 1817 True 1068.000000 1068 77.837000 932 2765 1 chr4A.!!$R1 1833
6 TraesCS4A01G466200 chr4A 729236752 729238466 1714 False 996.000000 996 77.634000 999 2744 1 chr4A.!!$F2 1745
7 TraesCS4A01G466200 chr4A 730322761 730324058 1297 False 852.000000 852 79.043000 998 2278 1 chr4A.!!$F4 1280
8 TraesCS4A01G466200 chr4A 729924552 729926445 1893 False 559.500000 664 78.868000 2 1863 2 chr4A.!!$F7 1861
9 TraesCS4A01G466200 chr4A 730002110 730005673 3563 True 202.950000 359 88.605000 42 2880 4 chr4A.!!$R7 2838
10 TraesCS4A01G466200 chr7D 8818414 8820780 2366 False 2859.000000 2859 88.710000 563 2930 1 chr7D.!!$F1 2367
11 TraesCS4A01G466200 chr7D 109143007 109144722 1715 True 983.000000 983 77.602000 998 2721 1 chr7D.!!$R4 1723
12 TraesCS4A01G466200 chr7D 10464210 10466140 1930 True 977.000000 977 76.780000 479 2444 1 chr7D.!!$R2 1965
13 TraesCS4A01G466200 chr7D 10908996 10910347 1351 True 806.000000 806 78.198000 1089 2408 1 chr7D.!!$R3 1319
14 TraesCS4A01G466200 chr7D 9223144 9225221 2077 False 442.250000 804 83.526500 596 2357 2 chr7D.!!$F3 1761
15 TraesCS4A01G466200 chr7A 10269523 10271360 1837 False 1002.000000 1002 77.237000 848 2734 1 chr7A.!!$F2 1886
16 TraesCS4A01G466200 chr7A 9381737 9383302 1565 False 909.600000 1735 88.342000 714 2300 2 chr7A.!!$F3 1586
17 TraesCS4A01G466200 chr7A 10090380 10092034 1654 True 863.000000 863 76.905000 998 2623 1 chr7A.!!$R2 1625
18 TraesCS4A01G466200 chr7A 10167287 10168140 853 True 604.000000 604 79.977000 1890 2746 1 chr7A.!!$R4 856
19 TraesCS4A01G466200 chr7A 10105521 10106083 562 True 387.000000 387 79.245000 1718 2299 1 chr7A.!!$R3 581
20 TraesCS4A01G466200 chr4D 507350290 507352244 1954 True 634.666667 1439 85.309333 998 3203 3 chr4D.!!$R1 2205
21 TraesCS4A01G466200 chr4B 654201948 654203895 1947 False 817.000000 1439 84.949000 1001 2936 2 chr4B.!!$F1 1935
22 TraesCS4A01G466200 chr5A 691820781 691822947 2166 False 590.333333 1105 87.576333 807 2936 3 chr5A.!!$F1 2129
23 TraesCS4A01G466200 chr6D 84280119 84281279 1160 False 628.000000 628 77.133000 998 2173 1 chr6D.!!$F1 1175

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
148 150 0.251787 GGGCCCAAGTTGGAGATGTT 60.252 55.0 24.06 0.0 40.96 2.71 F
149 151 1.177401 GGCCCAAGTTGGAGATGTTC 58.823 55.0 24.06 3.2 40.96 3.18 F
1519 2448 0.829990 TTGCCATATCGCAGGTCTGA 59.170 50.0 1.65 0.0 40.53 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 2448 0.173708 GAGACCGCTGGATCGAAAGT 59.826 55.000 0.00 0.0 0.00 2.66 R
1978 3018 2.723563 TCTCCCCAATCATGCCCATAAT 59.276 45.455 0.00 0.0 0.00 1.28 R
3155 4943 0.179181 CACCTGCACGCTGCTATTTG 60.179 55.000 10.54 0.0 45.31 2.32 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
28 29 2.320745 AGAAACACGAAGAACCGGTT 57.679 45.000 22.50 22.50 0.00 4.44
29 30 2.635714 AGAAACACGAAGAACCGGTTT 58.364 42.857 23.22 6.19 36.44 3.27
37 38 2.708051 GAAGAACCGGTTTAGGGAAGG 58.292 52.381 23.22 0.00 35.02 3.46
38 39 0.327259 AGAACCGGTTTAGGGAAGGC 59.673 55.000 23.22 4.93 35.02 4.35
40 41 0.775542 AACCGGTTTAGGGAAGGCTT 59.224 50.000 15.86 0.00 35.02 4.35
47 48 4.154176 GGTTTAGGGAAGGCTTAAAACCA 58.846 43.478 25.57 8.39 43.34 3.67
57 58 1.893137 GCTTAAAACCAGTGGGGGAAG 59.107 52.381 15.21 11.84 42.91 3.46
91 93 2.038975 CTCGGACAAGGAGGGGGA 59.961 66.667 0.00 0.00 0.00 4.81
115 117 1.421646 CTTGGAGAAGGTGGTCTTGGT 59.578 52.381 0.00 0.00 35.50 3.67
123 125 1.746517 GTGGTCTTGGTGGTCGACT 59.253 57.895 16.46 0.00 0.00 4.18
131 133 1.004918 GGTGGTCGACTCAGTTGGG 60.005 63.158 16.46 0.00 0.00 4.12
136 138 2.144078 TCGACTCAGTTGGGCCCAA 61.144 57.895 34.07 34.07 0.00 4.12
148 150 0.251787 GGGCCCAAGTTGGAGATGTT 60.252 55.000 24.06 0.00 40.96 2.71
149 151 1.177401 GGCCCAAGTTGGAGATGTTC 58.823 55.000 24.06 3.20 40.96 3.18
150 152 1.547675 GGCCCAAGTTGGAGATGTTCA 60.548 52.381 24.06 0.00 40.96 3.18
152 154 2.627699 GCCCAAGTTGGAGATGTTCAAA 59.372 45.455 24.06 0.00 40.96 2.69
153 155 3.069443 GCCCAAGTTGGAGATGTTCAAAA 59.931 43.478 24.06 0.00 40.96 2.44
253 271 2.125512 GTGCAACTCGAGGCGGAT 60.126 61.111 18.41 0.00 0.00 4.18
287 305 2.836793 GCCCTCGTCGAGCTCTACC 61.837 68.421 17.02 0.00 0.00 3.18
295 313 3.075005 GAGCTCTACCACGGCCCA 61.075 66.667 6.43 0.00 0.00 5.36
300 318 3.873812 CTACCACGGCCCATCCCC 61.874 72.222 0.00 0.00 0.00 4.81
318 336 2.760159 CCATTGCCGAAATCCGCGT 61.760 57.895 4.92 0.00 36.84 6.01
332 350 1.280142 CGCGTCATCCTAGAGTCCG 59.720 63.158 0.00 0.00 0.00 4.79
347 365 4.933064 CCGTCGAGGATGAGCGGC 62.933 72.222 6.70 0.00 45.00 6.53
350 368 2.440247 TCGAGGATGAGCGGCTGA 60.440 61.111 7.50 0.00 0.00 4.26
353 371 1.960250 GAGGATGAGCGGCTGATGC 60.960 63.158 12.70 12.70 38.76 3.91
387 405 3.639094 CGTAGGATCTTCATTCCTGACCT 59.361 47.826 2.50 0.00 43.52 3.85
393 411 2.690497 TCTTCATTCCTGACCTAGAGCG 59.310 50.000 0.00 0.00 0.00 5.03
421 445 2.270352 ACTTTGCAAATGAGGACGGA 57.730 45.000 13.23 0.00 0.00 4.69
424 448 1.974265 TTGCAAATGAGGACGGACAA 58.026 45.000 0.00 0.00 0.00 3.18
476 501 2.031465 GTTTCGGCGAAGGGGTGA 59.969 61.111 22.52 3.68 0.00 4.02
517 542 6.951971 ACAAGGAGCAGATAGATTAGTTTGT 58.048 36.000 0.00 0.00 0.00 2.83
594 775 9.703892 GAATCTATGAATGAGTTGTAGCTGTAT 57.296 33.333 0.00 0.00 0.00 2.29
597 778 8.355913 TCTATGAATGAGTTGTAGCTGTATCTG 58.644 37.037 0.00 0.00 0.00 2.90
682 896 9.815306 AATAGTGAGTCAGACATACATATAGGT 57.185 33.333 2.66 0.00 0.00 3.08
697 913 5.888161 ACATATAGGTGGCAAGAAGGAAAAG 59.112 40.000 0.00 0.00 0.00 2.27
698 914 2.001076 AGGTGGCAAGAAGGAAAAGG 57.999 50.000 0.00 0.00 0.00 3.11
701 923 2.899900 GGTGGCAAGAAGGAAAAGGAAT 59.100 45.455 0.00 0.00 0.00 3.01
710 932 5.019470 AGAAGGAAAAGGAATAGCCCAAAG 58.981 41.667 0.00 0.00 37.37 2.77
1105 1933 3.669036 CTGCTCACCGACGACCTCG 62.669 68.421 0.00 0.00 46.33 4.63
1287 2133 2.259818 CACTTCGCCAGCGTCTCT 59.740 61.111 12.32 0.00 40.74 3.10
1519 2448 0.829990 TTGCCATATCGCAGGTCTGA 59.170 50.000 1.65 0.00 40.53 3.27
1978 3018 2.743664 CGTTCTGCCAACATCAATGAGA 59.256 45.455 0.00 0.00 0.00 3.27
2224 3517 3.499021 GCTTTACCTTCAAACCACCCCTA 60.499 47.826 0.00 0.00 0.00 3.53
2381 3688 2.813754 TGGCAAACTACAGATGAAGCAC 59.186 45.455 0.00 0.00 0.00 4.40
2395 3708 3.644823 TGAAGCACAATGTCATTTGCAG 58.355 40.909 23.02 7.10 37.44 4.41
2486 3827 8.686334 CCATGTGGCTAAATTCTACTGTAATTT 58.314 33.333 6.53 6.53 39.31 1.82
2510 3851 7.020827 TCTCTTCCTTTCCATAACAATCAGT 57.979 36.000 0.00 0.00 0.00 3.41
2782 4556 6.715344 TGTACAAATACGGCAGAGTTTTAG 57.285 37.500 0.00 0.00 33.60 1.85
2786 4560 5.938125 ACAAATACGGCAGAGTTTTAGTGAT 59.062 36.000 0.00 0.00 0.00 3.06
2838 4624 7.042725 TCAGCTTCATACACGATATTAGTTTGC 60.043 37.037 0.00 0.00 0.00 3.68
2854 4641 0.249699 TTGCGACACGACTGAATGGT 60.250 50.000 0.00 0.00 0.00 3.55
2881 4669 7.004086 ACCAAAAATAAGATCTCTTGGTGTGA 58.996 34.615 18.10 0.00 43.68 3.58
2893 4681 6.003326 TCTCTTGGTGTGATTGATTGCTTTA 58.997 36.000 0.00 0.00 0.00 1.85
2901 4689 5.091431 GTGATTGATTGCTTTAGCTGTGTC 58.909 41.667 0.00 0.00 42.66 3.67
2941 4729 3.234368 CAACCAGCGTTGTGTGAAC 57.766 52.632 0.00 0.00 43.73 3.18
2942 4730 0.248458 CAACCAGCGTTGTGTGAACC 60.248 55.000 0.00 0.00 43.73 3.62
2943 4731 0.393808 AACCAGCGTTGTGTGAACCT 60.394 50.000 0.00 0.00 0.00 3.50
2944 4732 1.095228 ACCAGCGTTGTGTGAACCTG 61.095 55.000 0.00 0.00 0.00 4.00
2945 4733 1.009675 CAGCGTTGTGTGAACCTGC 60.010 57.895 0.00 0.00 0.00 4.85
2946 4734 1.153168 AGCGTTGTGTGAACCTGCT 60.153 52.632 0.00 0.00 0.00 4.24
2947 4735 0.105964 AGCGTTGTGTGAACCTGCTA 59.894 50.000 0.00 0.00 0.00 3.49
2948 4736 0.512952 GCGTTGTGTGAACCTGCTAG 59.487 55.000 0.00 0.00 0.00 3.42
2949 4737 1.865865 CGTTGTGTGAACCTGCTAGT 58.134 50.000 0.00 0.00 0.00 2.57
2950 4738 1.526887 CGTTGTGTGAACCTGCTAGTG 59.473 52.381 0.00 0.00 0.00 2.74
2951 4739 2.561569 GTTGTGTGAACCTGCTAGTGT 58.438 47.619 0.00 0.00 0.00 3.55
2952 4740 3.724374 GTTGTGTGAACCTGCTAGTGTA 58.276 45.455 0.00 0.00 0.00 2.90
2953 4741 3.380479 TGTGTGAACCTGCTAGTGTAC 57.620 47.619 0.00 0.00 0.00 2.90
2954 4742 2.963101 TGTGTGAACCTGCTAGTGTACT 59.037 45.455 0.00 0.00 0.00 2.73
2955 4743 4.146564 TGTGTGAACCTGCTAGTGTACTA 58.853 43.478 0.00 0.00 0.00 1.82
2956 4744 4.585581 TGTGTGAACCTGCTAGTGTACTAA 59.414 41.667 0.00 0.00 0.00 2.24
2957 4745 5.069383 TGTGTGAACCTGCTAGTGTACTAAA 59.931 40.000 0.00 0.00 0.00 1.85
2958 4746 5.987347 GTGTGAACCTGCTAGTGTACTAAAA 59.013 40.000 0.00 0.00 0.00 1.52
2959 4747 6.145696 GTGTGAACCTGCTAGTGTACTAAAAG 59.854 42.308 0.00 0.00 0.00 2.27
2960 4748 5.638234 GTGAACCTGCTAGTGTACTAAAAGG 59.362 44.000 13.94 13.94 37.24 3.11
2961 4749 5.306160 TGAACCTGCTAGTGTACTAAAAGGT 59.694 40.000 14.85 14.85 41.98 3.50
2962 4750 5.820404 ACCTGCTAGTGTACTAAAAGGTT 57.180 39.130 14.85 5.14 39.45 3.50
2963 4751 6.183810 ACCTGCTAGTGTACTAAAAGGTTT 57.816 37.500 14.85 0.96 39.45 3.27
2964 4752 7.307131 ACCTGCTAGTGTACTAAAAGGTTTA 57.693 36.000 14.85 0.00 39.45 2.01
2965 4753 7.738847 ACCTGCTAGTGTACTAAAAGGTTTAA 58.261 34.615 14.85 0.00 39.45 1.52
2966 4754 8.380867 ACCTGCTAGTGTACTAAAAGGTTTAAT 58.619 33.333 14.85 0.00 39.45 1.40
2967 4755 8.880750 CCTGCTAGTGTACTAAAAGGTTTAATC 58.119 37.037 9.80 0.00 31.42 1.75
2968 4756 9.431887 CTGCTAGTGTACTAAAAGGTTTAATCA 57.568 33.333 0.00 0.00 0.00 2.57
2969 4757 9.431887 TGCTAGTGTACTAAAAGGTTTAATCAG 57.568 33.333 0.00 0.00 0.00 2.90
2970 4758 9.649167 GCTAGTGTACTAAAAGGTTTAATCAGA 57.351 33.333 0.00 0.00 0.00 3.27
2973 4761 9.490379 AGTGTACTAAAAGGTTTAATCAGACTG 57.510 33.333 0.00 0.00 0.00 3.51
2974 4762 8.718734 GTGTACTAAAAGGTTTAATCAGACTGG 58.281 37.037 1.81 0.00 0.00 4.00
2975 4763 8.434392 TGTACTAAAAGGTTTAATCAGACTGGT 58.566 33.333 1.81 0.00 0.00 4.00
2976 4764 9.281371 GTACTAAAAGGTTTAATCAGACTGGTT 57.719 33.333 6.17 6.17 0.00 3.67
2978 4766 9.281371 ACTAAAAGGTTTAATCAGACTGGTTAC 57.719 33.333 7.71 0.40 0.00 2.50
2979 4767 9.503399 CTAAAAGGTTTAATCAGACTGGTTACT 57.497 33.333 7.71 0.00 0.00 2.24
2980 4768 7.745620 AAAGGTTTAATCAGACTGGTTACTG 57.254 36.000 7.71 0.00 35.72 2.74
2981 4769 5.805728 AGGTTTAATCAGACTGGTTACTGG 58.194 41.667 7.71 0.00 35.20 4.00
2982 4770 5.309806 AGGTTTAATCAGACTGGTTACTGGT 59.690 40.000 7.71 0.00 35.20 4.00
2983 4771 5.411669 GGTTTAATCAGACTGGTTACTGGTG 59.588 44.000 7.71 0.00 35.20 4.17
2984 4772 5.818678 TTAATCAGACTGGTTACTGGTGT 57.181 39.130 7.71 0.00 35.20 4.16
2985 4773 3.685139 ATCAGACTGGTTACTGGTGTG 57.315 47.619 1.81 0.00 35.20 3.82
2986 4774 1.070134 TCAGACTGGTTACTGGTGTGC 59.930 52.381 1.81 0.00 35.20 4.57
2987 4775 1.070758 CAGACTGGTTACTGGTGTGCT 59.929 52.381 0.00 0.00 0.00 4.40
2988 4776 1.070758 AGACTGGTTACTGGTGTGCTG 59.929 52.381 0.00 0.00 0.00 4.41
2989 4777 0.837272 ACTGGTTACTGGTGTGCTGT 59.163 50.000 0.00 0.00 0.00 4.40
2990 4778 1.202651 ACTGGTTACTGGTGTGCTGTC 60.203 52.381 0.00 0.00 0.00 3.51
2991 4779 1.070758 CTGGTTACTGGTGTGCTGTCT 59.929 52.381 0.00 0.00 0.00 3.41
2992 4780 2.299013 CTGGTTACTGGTGTGCTGTCTA 59.701 50.000 0.00 0.00 0.00 2.59
2993 4781 2.299013 TGGTTACTGGTGTGCTGTCTAG 59.701 50.000 0.00 0.00 0.00 2.43
2994 4782 2.299297 GGTTACTGGTGTGCTGTCTAGT 59.701 50.000 0.00 0.00 0.00 2.57
2995 4783 3.244112 GGTTACTGGTGTGCTGTCTAGTT 60.244 47.826 0.00 0.00 0.00 2.24
2996 4784 2.533266 ACTGGTGTGCTGTCTAGTTG 57.467 50.000 0.00 0.00 0.00 3.16
2997 4785 2.039418 ACTGGTGTGCTGTCTAGTTGA 58.961 47.619 0.00 0.00 0.00 3.18
2998 4786 2.224066 ACTGGTGTGCTGTCTAGTTGAC 60.224 50.000 0.00 0.00 45.54 3.18
2999 4787 1.070134 TGGTGTGCTGTCTAGTTGACC 59.930 52.381 2.18 0.00 44.75 4.02
3000 4788 1.344763 GGTGTGCTGTCTAGTTGACCT 59.655 52.381 2.18 0.00 44.75 3.85
3001 4789 2.224305 GGTGTGCTGTCTAGTTGACCTT 60.224 50.000 2.18 0.00 44.75 3.50
3002 4790 3.006537 GGTGTGCTGTCTAGTTGACCTTA 59.993 47.826 2.18 0.00 44.75 2.69
3003 4791 4.322801 GGTGTGCTGTCTAGTTGACCTTAT 60.323 45.833 2.18 0.00 44.75 1.73
3004 4792 5.238583 GTGTGCTGTCTAGTTGACCTTATT 58.761 41.667 2.18 0.00 44.75 1.40
3005 4793 5.348997 GTGTGCTGTCTAGTTGACCTTATTC 59.651 44.000 2.18 0.00 44.75 1.75
3006 4794 5.011635 TGTGCTGTCTAGTTGACCTTATTCA 59.988 40.000 2.18 0.00 44.75 2.57
3007 4795 6.109359 GTGCTGTCTAGTTGACCTTATTCAT 58.891 40.000 2.18 0.00 44.75 2.57
3008 4796 6.595716 GTGCTGTCTAGTTGACCTTATTCATT 59.404 38.462 2.18 0.00 44.75 2.57
3009 4797 7.119846 GTGCTGTCTAGTTGACCTTATTCATTT 59.880 37.037 2.18 0.00 44.75 2.32
3010 4798 8.318412 TGCTGTCTAGTTGACCTTATTCATTTA 58.682 33.333 2.18 0.00 44.75 1.40
3011 4799 8.821894 GCTGTCTAGTTGACCTTATTCATTTAG 58.178 37.037 2.18 0.00 44.75 1.85
3012 4800 9.877178 CTGTCTAGTTGACCTTATTCATTTAGT 57.123 33.333 2.18 0.00 44.75 2.24
3037 4825 2.699251 GGTAAAACACCGCCTTTGAG 57.301 50.000 0.00 0.00 37.63 3.02
3038 4826 1.335597 GGTAAAACACCGCCTTTGAGC 60.336 52.381 0.00 0.00 37.63 4.26
3039 4827 1.335496 GTAAAACACCGCCTTTGAGCA 59.665 47.619 0.00 0.00 0.00 4.26
3040 4828 0.820871 AAAACACCGCCTTTGAGCAA 59.179 45.000 0.00 0.00 0.00 3.91
3041 4829 0.385390 AAACACCGCCTTTGAGCAAG 59.615 50.000 0.00 0.00 0.00 4.01
3042 4830 0.751643 AACACCGCCTTTGAGCAAGT 60.752 50.000 0.00 0.00 0.00 3.16
3043 4831 0.751643 ACACCGCCTTTGAGCAAGTT 60.752 50.000 0.00 0.00 0.00 2.66
3044 4832 0.385390 CACCGCCTTTGAGCAAGTTT 59.615 50.000 0.00 0.00 0.00 2.66
3045 4833 1.111277 ACCGCCTTTGAGCAAGTTTT 58.889 45.000 0.00 0.00 0.00 2.43
3046 4834 1.480545 ACCGCCTTTGAGCAAGTTTTT 59.519 42.857 0.00 0.00 0.00 1.94
3067 4855 5.881637 TTTTTATGCGTGTTTGCTCTTTC 57.118 34.783 0.00 0.00 35.36 2.62
3068 4856 4.829064 TTTATGCGTGTTTGCTCTTTCT 57.171 36.364 0.00 0.00 35.36 2.52
3069 4857 5.933187 TTTATGCGTGTTTGCTCTTTCTA 57.067 34.783 0.00 0.00 35.36 2.10
3070 4858 5.530519 TTATGCGTGTTTGCTCTTTCTAG 57.469 39.130 0.00 0.00 35.36 2.43
3071 4859 2.833794 TGCGTGTTTGCTCTTTCTAGT 58.166 42.857 0.00 0.00 35.36 2.57
3072 4860 2.543848 TGCGTGTTTGCTCTTTCTAGTG 59.456 45.455 0.00 0.00 35.36 2.74
3073 4861 2.800544 GCGTGTTTGCTCTTTCTAGTGA 59.199 45.455 0.00 0.00 0.00 3.41
3074 4862 3.247648 GCGTGTTTGCTCTTTCTAGTGAA 59.752 43.478 0.00 0.00 0.00 3.18
3075 4863 4.260620 GCGTGTTTGCTCTTTCTAGTGAAA 60.261 41.667 0.00 0.00 39.59 2.69
3076 4864 5.198274 CGTGTTTGCTCTTTCTAGTGAAAC 58.802 41.667 0.00 0.00 37.27 2.78
3093 4881 6.793492 GTGAAACTAGAGCTTTTGATCTGT 57.207 37.500 0.00 0.00 45.75 3.41
3094 4882 7.195839 GTGAAACTAGAGCTTTTGATCTGTT 57.804 36.000 0.00 0.00 45.75 3.16
3095 4883 8.311650 GTGAAACTAGAGCTTTTGATCTGTTA 57.688 34.615 0.00 0.00 45.75 2.41
3096 4884 8.439286 GTGAAACTAGAGCTTTTGATCTGTTAG 58.561 37.037 0.00 0.00 45.75 2.34
3097 4885 8.150945 TGAAACTAGAGCTTTTGATCTGTTAGT 58.849 33.333 0.00 0.00 45.75 2.24
3098 4886 8.541133 AAACTAGAGCTTTTGATCTGTTAGTC 57.459 34.615 0.00 0.00 45.75 2.59
3099 4887 7.233389 ACTAGAGCTTTTGATCTGTTAGTCA 57.767 36.000 0.00 0.00 45.75 3.41
3100 4888 7.093992 ACTAGAGCTTTTGATCTGTTAGTCAC 58.906 38.462 0.00 0.00 45.75 3.67
3101 4889 5.858381 AGAGCTTTTGATCTGTTAGTCACA 58.142 37.500 0.00 0.00 44.39 3.58
3114 4902 6.486253 TGTTAGTCACAGAGAAATTGCATC 57.514 37.500 0.00 0.00 0.00 3.91
3115 4903 5.997129 TGTTAGTCACAGAGAAATTGCATCA 59.003 36.000 0.00 0.00 0.00 3.07
3116 4904 6.486320 TGTTAGTCACAGAGAAATTGCATCAA 59.514 34.615 0.00 0.00 0.00 2.57
3117 4905 7.175467 TGTTAGTCACAGAGAAATTGCATCAAT 59.825 33.333 0.00 0.00 35.39 2.57
3118 4906 6.192234 AGTCACAGAGAAATTGCATCAATC 57.808 37.500 0.00 0.00 32.43 2.67
3119 4907 5.026462 GTCACAGAGAAATTGCATCAATCG 58.974 41.667 0.00 0.00 32.43 3.34
3120 4908 3.789756 CACAGAGAAATTGCATCAATCGC 59.210 43.478 0.00 0.00 32.43 4.58
3121 4909 3.441222 ACAGAGAAATTGCATCAATCGCA 59.559 39.130 0.00 0.00 32.43 5.10
3135 4923 9.964303 TGCATCAATCGCAATATAAAATAAACT 57.036 25.926 0.00 0.00 36.17 2.66
3144 4932 9.365311 CGCAATATAAAATAAACTTGGAGTACG 57.635 33.333 0.00 0.00 0.00 3.67
3162 4950 7.662182 GAGTACGTACTCTTGTACAAATAGC 57.338 40.000 37.02 14.91 46.88 2.97
3163 4951 7.149569 AGTACGTACTCTTGTACAAATAGCA 57.850 36.000 22.45 0.00 46.88 3.49
3164 4952 7.249147 AGTACGTACTCTTGTACAAATAGCAG 58.751 38.462 22.45 7.59 46.88 4.24
3165 4953 4.863131 ACGTACTCTTGTACAAATAGCAGC 59.137 41.667 10.03 3.94 46.88 5.25
3166 4954 4.027621 CGTACTCTTGTACAAATAGCAGCG 60.028 45.833 10.03 10.76 46.88 5.18
3167 4955 3.926616 ACTCTTGTACAAATAGCAGCGT 58.073 40.909 10.03 0.00 0.00 5.07
3168 4956 3.679980 ACTCTTGTACAAATAGCAGCGTG 59.320 43.478 10.03 0.00 0.00 5.34
3169 4957 2.415168 TCTTGTACAAATAGCAGCGTGC 59.585 45.455 10.03 2.28 45.46 5.34
3180 4968 4.876701 AGCGTGCAGGTGAAAGAA 57.123 50.000 8.40 0.00 0.00 2.52
3181 4969 3.094386 AGCGTGCAGGTGAAAGAAA 57.906 47.368 8.40 0.00 0.00 2.52
3182 4970 1.609208 AGCGTGCAGGTGAAAGAAAT 58.391 45.000 8.40 0.00 0.00 2.17
3183 4971 1.537202 AGCGTGCAGGTGAAAGAAATC 59.463 47.619 8.40 0.00 0.00 2.17
3184 4972 1.266718 GCGTGCAGGTGAAAGAAATCA 59.733 47.619 8.40 0.00 0.00 2.57
3185 4973 2.666619 GCGTGCAGGTGAAAGAAATCAG 60.667 50.000 8.40 0.00 0.00 2.90
3186 4974 2.549754 CGTGCAGGTGAAAGAAATCAGT 59.450 45.455 0.00 0.00 0.00 3.41
3187 4975 3.745975 CGTGCAGGTGAAAGAAATCAGTA 59.254 43.478 0.00 0.00 0.00 2.74
3188 4976 4.377431 CGTGCAGGTGAAAGAAATCAGTAC 60.377 45.833 0.00 0.00 0.00 2.73
3189 4977 3.745975 TGCAGGTGAAAGAAATCAGTACG 59.254 43.478 0.00 0.00 0.00 3.67
3190 4978 3.125316 GCAGGTGAAAGAAATCAGTACGG 59.875 47.826 0.00 0.00 0.00 4.02
3191 4979 3.125316 CAGGTGAAAGAAATCAGTACGGC 59.875 47.826 0.00 0.00 0.00 5.68
3192 4980 3.008049 AGGTGAAAGAAATCAGTACGGCT 59.992 43.478 0.00 0.00 0.00 5.52
3193 4981 3.125316 GGTGAAAGAAATCAGTACGGCTG 59.875 47.826 3.27 3.27 46.34 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.805971 ACCGGTTCTTCGTGTTTCTTTAG 59.194 43.478 0.00 0.00 0.00 1.85
6 7 3.795877 ACCGGTTCTTCGTGTTTCTTTA 58.204 40.909 0.00 0.00 0.00 1.85
10 11 3.059393 CCTAAACCGGTTCTTCGTGTTTC 60.059 47.826 22.53 0.00 36.14 2.78
16 17 2.344025 CTTCCCTAAACCGGTTCTTCG 58.656 52.381 22.53 9.13 0.00 3.79
20 21 0.327259 AGCCTTCCCTAAACCGGTTC 59.673 55.000 22.53 4.38 0.00 3.62
23 24 2.793288 TTAAGCCTTCCCTAAACCGG 57.207 50.000 0.00 0.00 0.00 5.28
24 25 3.192001 GGTTTTAAGCCTTCCCTAAACCG 59.808 47.826 0.00 0.00 36.34 4.44
28 29 4.403734 CACTGGTTTTAAGCCTTCCCTAA 58.596 43.478 0.00 0.00 0.00 2.69
29 30 3.245122 CCACTGGTTTTAAGCCTTCCCTA 60.245 47.826 0.00 0.00 0.00 3.53
37 38 1.893137 CTTCCCCCACTGGTTTTAAGC 59.107 52.381 0.00 0.00 0.00 3.09
38 39 3.518992 TCTTCCCCCACTGGTTTTAAG 57.481 47.619 0.00 0.00 0.00 1.85
40 41 3.245479 GGATTCTTCCCCCACTGGTTTTA 60.245 47.826 0.00 0.00 35.84 1.52
47 48 2.592512 TCTAGAGGATTCTTCCCCCACT 59.407 50.000 0.00 0.00 43.76 4.00
57 58 2.556622 CCGAGCCTTCTCTAGAGGATTC 59.443 54.545 19.67 8.29 37.19 2.52
91 93 0.402121 GACCACCTTCTCCAAGCCTT 59.598 55.000 0.00 0.00 0.00 4.35
115 117 2.741092 GCCCAACTGAGTCGACCA 59.259 61.111 13.01 9.18 0.00 4.02
123 125 1.152567 CCAACTTGGGCCCAACTGA 60.153 57.895 34.07 14.07 32.67 3.41
131 133 1.909700 TGAACATCTCCAACTTGGGC 58.090 50.000 8.01 0.00 38.32 5.36
136 138 3.319122 GCTGGTTTTGAACATCTCCAACT 59.681 43.478 0.00 0.00 0.00 3.16
148 150 0.541764 GGGGGTGATGCTGGTTTTGA 60.542 55.000 0.00 0.00 0.00 2.69
149 151 0.831288 TGGGGGTGATGCTGGTTTTG 60.831 55.000 0.00 0.00 0.00 2.44
150 152 0.831711 GTGGGGGTGATGCTGGTTTT 60.832 55.000 0.00 0.00 0.00 2.43
152 154 2.440599 GTGGGGGTGATGCTGGTT 59.559 61.111 0.00 0.00 0.00 3.67
153 155 3.661648 GGTGGGGGTGATGCTGGT 61.662 66.667 0.00 0.00 0.00 4.00
227 245 2.971598 CGAGTTGCACCTCCCCCAT 61.972 63.158 5.59 0.00 0.00 4.00
287 305 4.141876 AATGGGGGATGGGCCGTG 62.142 66.667 1.02 0.00 37.63 4.94
295 313 0.469892 GGATTTCGGCAATGGGGGAT 60.470 55.000 0.00 0.00 0.00 3.85
300 318 2.024588 CGCGGATTTCGGCAATGG 59.975 61.111 0.00 0.00 41.54 3.16
318 336 1.202663 CCTCGACGGACTCTAGGATGA 60.203 57.143 0.00 0.00 33.16 2.92
332 350 2.081425 ATCAGCCGCTCATCCTCGAC 62.081 60.000 0.00 0.00 0.00 4.20
347 365 1.815212 CGGCGATTCGTCAGCATCAG 61.815 60.000 11.66 0.00 0.00 2.90
350 368 0.595053 CTACGGCGATTCGTCAGCAT 60.595 55.000 16.62 0.00 42.82 3.79
353 371 0.311165 ATCCTACGGCGATTCGTCAG 59.689 55.000 16.62 6.25 42.82 3.51
381 399 1.028905 CTTCTCCCGCTCTAGGTCAG 58.971 60.000 0.00 0.00 0.00 3.51
387 405 2.353803 GCAAAGTTCTTCTCCCGCTCTA 60.354 50.000 0.00 0.00 0.00 2.43
393 411 4.321527 CCTCATTTGCAAAGTTCTTCTCCC 60.322 45.833 18.19 0.00 0.00 4.30
458 482 3.053896 CACCCCTTCGCCGAAACC 61.054 66.667 0.00 0.00 0.00 3.27
476 501 0.031111 TGTCTGAGGGGATCGGGATT 60.031 55.000 0.00 0.00 34.76 3.01
526 551 8.510132 AAAACTACGTCCGGAAATAAAAATTG 57.490 30.769 5.23 0.00 0.00 2.32
589 767 8.873830 CAACATAGAACTACAAACCAGATACAG 58.126 37.037 0.00 0.00 0.00 2.74
594 775 5.616270 TGCAACATAGAACTACAAACCAGA 58.384 37.500 0.00 0.00 0.00 3.86
597 778 6.677913 ACAATGCAACATAGAACTACAAACC 58.322 36.000 0.00 0.00 0.00 3.27
674 888 5.300286 CCTTTTCCTTCTTGCCACCTATATG 59.700 44.000 0.00 0.00 0.00 1.78
676 890 4.538490 TCCTTTTCCTTCTTGCCACCTATA 59.462 41.667 0.00 0.00 0.00 1.31
677 891 3.333680 TCCTTTTCCTTCTTGCCACCTAT 59.666 43.478 0.00 0.00 0.00 2.57
678 892 2.714250 TCCTTTTCCTTCTTGCCACCTA 59.286 45.455 0.00 0.00 0.00 3.08
679 893 1.499007 TCCTTTTCCTTCTTGCCACCT 59.501 47.619 0.00 0.00 0.00 4.00
682 896 3.763897 GCTATTCCTTTTCCTTCTTGCCA 59.236 43.478 0.00 0.00 0.00 4.92
697 913 1.685180 GGTGTCCCTTTGGGCTATTCC 60.685 57.143 0.00 0.00 43.94 3.01
698 914 1.285078 AGGTGTCCCTTTGGGCTATTC 59.715 52.381 0.00 0.00 43.94 1.75
701 923 1.205460 GGAGGTGTCCCTTTGGGCTA 61.205 60.000 0.00 0.00 42.86 3.93
710 932 2.926242 TCCGGTTGGAGGTGTCCC 60.926 66.667 0.00 0.00 43.15 4.46
770 1041 1.374125 CGAATGTGTGGACGCTCCA 60.374 57.895 3.02 3.02 45.98 3.86
771 1042 1.352156 GACGAATGTGTGGACGCTCC 61.352 60.000 0.00 0.00 36.96 4.70
1083 1558 4.988716 TCGTCGGTGAGCAGGGGT 62.989 66.667 0.00 0.00 0.00 4.95
1519 2448 0.173708 GAGACCGCTGGATCGAAAGT 59.826 55.000 0.00 0.00 0.00 2.66
1978 3018 2.723563 TCTCCCCAATCATGCCCATAAT 59.276 45.455 0.00 0.00 0.00 1.28
2381 3688 5.924254 ACAATGTTCTCTGCAAATGACATTG 59.076 36.000 26.95 26.95 44.82 2.82
2395 3708 8.398665 ACACAGAAAAAGAGTAACAATGTTCTC 58.601 33.333 0.22 9.34 0.00 2.87
2486 3827 7.020827 ACTGATTGTTATGGAAAGGAAGAGA 57.979 36.000 0.00 0.00 0.00 3.10
2751 4498 6.167685 TCTGCCGTATTTGTACAACAATACT 58.832 36.000 20.41 3.37 38.00 2.12
2755 4502 4.382291 ACTCTGCCGTATTTGTACAACAA 58.618 39.130 8.07 0.00 36.11 2.83
2757 4504 5.352643 AAACTCTGCCGTATTTGTACAAC 57.647 39.130 8.07 0.00 0.00 3.32
2838 4624 1.060713 GTGACCATTCAGTCGTGTCG 58.939 55.000 0.00 0.00 39.77 4.35
2881 4669 3.426695 GCGACACAGCTAAAGCAATCAAT 60.427 43.478 4.54 0.00 45.16 2.57
2901 4689 0.736325 CCGACTCAAACAGGGTAGCG 60.736 60.000 0.00 0.00 0.00 4.26
2936 4724 5.638234 CCTTTTAGTACACTAGCAGGTTCAC 59.362 44.000 0.00 0.00 30.54 3.18
2937 4725 5.306160 ACCTTTTAGTACACTAGCAGGTTCA 59.694 40.000 12.61 0.00 38.52 3.18
2938 4726 5.791666 ACCTTTTAGTACACTAGCAGGTTC 58.208 41.667 12.61 0.00 38.52 3.62
2939 4727 5.820404 ACCTTTTAGTACACTAGCAGGTT 57.180 39.130 12.61 2.74 38.52 3.50
2940 4728 5.820404 AACCTTTTAGTACACTAGCAGGT 57.180 39.130 12.61 12.61 41.10 4.00
2941 4729 8.788325 ATTAAACCTTTTAGTACACTAGCAGG 57.212 34.615 11.68 11.68 36.38 4.85
2942 4730 9.431887 TGATTAAACCTTTTAGTACACTAGCAG 57.568 33.333 0.00 0.00 0.00 4.24
2943 4731 9.431887 CTGATTAAACCTTTTAGTACACTAGCA 57.568 33.333 0.00 0.00 0.00 3.49
2944 4732 9.649167 TCTGATTAAACCTTTTAGTACACTAGC 57.351 33.333 0.00 0.00 0.00 3.42
2947 4735 9.490379 CAGTCTGATTAAACCTTTTAGTACACT 57.510 33.333 0.00 0.00 0.00 3.55
2948 4736 8.718734 CCAGTCTGATTAAACCTTTTAGTACAC 58.281 37.037 0.00 0.00 0.00 2.90
2949 4737 8.434392 ACCAGTCTGATTAAACCTTTTAGTACA 58.566 33.333 0.00 0.00 0.00 2.90
2950 4738 8.843885 ACCAGTCTGATTAAACCTTTTAGTAC 57.156 34.615 0.00 0.00 0.00 2.73
2952 4740 9.281371 GTAACCAGTCTGATTAAACCTTTTAGT 57.719 33.333 0.00 0.00 0.00 2.24
2953 4741 9.503399 AGTAACCAGTCTGATTAAACCTTTTAG 57.497 33.333 0.00 0.00 0.00 1.85
2954 4742 9.280174 CAGTAACCAGTCTGATTAAACCTTTTA 57.720 33.333 0.00 0.00 34.02 1.52
2955 4743 7.230712 CCAGTAACCAGTCTGATTAAACCTTTT 59.769 37.037 0.00 0.00 34.02 2.27
2956 4744 6.715264 CCAGTAACCAGTCTGATTAAACCTTT 59.285 38.462 0.00 0.00 34.02 3.11
2957 4745 6.183361 ACCAGTAACCAGTCTGATTAAACCTT 60.183 38.462 0.00 0.00 34.02 3.50
2958 4746 5.309806 ACCAGTAACCAGTCTGATTAAACCT 59.690 40.000 0.00 0.00 34.02 3.50
2959 4747 5.411669 CACCAGTAACCAGTCTGATTAAACC 59.588 44.000 0.00 0.00 34.02 3.27
2960 4748 5.995897 ACACCAGTAACCAGTCTGATTAAAC 59.004 40.000 0.00 0.00 34.02 2.01
2961 4749 5.995282 CACACCAGTAACCAGTCTGATTAAA 59.005 40.000 0.00 0.00 34.02 1.52
2962 4750 5.547465 CACACCAGTAACCAGTCTGATTAA 58.453 41.667 0.00 0.00 34.02 1.40
2963 4751 4.562757 GCACACCAGTAACCAGTCTGATTA 60.563 45.833 0.00 0.00 34.02 1.75
2964 4752 3.807209 GCACACCAGTAACCAGTCTGATT 60.807 47.826 0.00 0.00 34.02 2.57
2965 4753 2.289694 GCACACCAGTAACCAGTCTGAT 60.290 50.000 0.00 0.00 34.02 2.90
2966 4754 1.070134 GCACACCAGTAACCAGTCTGA 59.930 52.381 0.00 0.00 34.02 3.27
2967 4755 1.070758 AGCACACCAGTAACCAGTCTG 59.929 52.381 0.00 0.00 0.00 3.51
2968 4756 1.070758 CAGCACACCAGTAACCAGTCT 59.929 52.381 0.00 0.00 0.00 3.24
2969 4757 1.202651 ACAGCACACCAGTAACCAGTC 60.203 52.381 0.00 0.00 0.00 3.51
2970 4758 0.837272 ACAGCACACCAGTAACCAGT 59.163 50.000 0.00 0.00 0.00 4.00
2971 4759 1.070758 AGACAGCACACCAGTAACCAG 59.929 52.381 0.00 0.00 0.00 4.00
2972 4760 1.128200 AGACAGCACACCAGTAACCA 58.872 50.000 0.00 0.00 0.00 3.67
2973 4761 2.299297 ACTAGACAGCACACCAGTAACC 59.701 50.000 0.00 0.00 0.00 2.85
2974 4762 3.662247 ACTAGACAGCACACCAGTAAC 57.338 47.619 0.00 0.00 0.00 2.50
2975 4763 3.639561 TCAACTAGACAGCACACCAGTAA 59.360 43.478 0.00 0.00 0.00 2.24
2976 4764 3.005472 GTCAACTAGACAGCACACCAGTA 59.995 47.826 0.00 0.00 46.77 2.74
2977 4765 2.039418 TCAACTAGACAGCACACCAGT 58.961 47.619 0.00 0.00 0.00 4.00
2978 4766 2.408050 GTCAACTAGACAGCACACCAG 58.592 52.381 0.00 0.00 46.77 4.00
2979 4767 2.526304 GTCAACTAGACAGCACACCA 57.474 50.000 0.00 0.00 46.77 4.17
3018 4806 1.335597 GCTCAAAGGCGGTGTTTTACC 60.336 52.381 0.00 0.00 46.56 2.85
3019 4807 1.335496 TGCTCAAAGGCGGTGTTTTAC 59.665 47.619 0.00 0.00 34.52 2.01
3020 4808 1.681538 TGCTCAAAGGCGGTGTTTTA 58.318 45.000 0.00 0.00 34.52 1.52
3021 4809 0.820871 TTGCTCAAAGGCGGTGTTTT 59.179 45.000 0.00 0.00 34.52 2.43
3022 4810 0.385390 CTTGCTCAAAGGCGGTGTTT 59.615 50.000 0.00 0.00 34.52 2.83
3023 4811 0.751643 ACTTGCTCAAAGGCGGTGTT 60.752 50.000 0.00 0.00 40.51 3.32
3024 4812 0.751643 AACTTGCTCAAAGGCGGTGT 60.752 50.000 0.00 0.00 40.51 4.16
3025 4813 0.385390 AAACTTGCTCAAAGGCGGTG 59.615 50.000 0.00 0.00 40.51 4.94
3026 4814 1.111277 AAAACTTGCTCAAAGGCGGT 58.889 45.000 0.00 0.00 40.51 5.68
3027 4815 2.223537 AAAAACTTGCTCAAAGGCGG 57.776 45.000 0.00 0.00 40.51 6.13
3045 4833 5.587289 AGAAAGAGCAAACACGCATAAAAA 58.413 33.333 0.00 0.00 0.00 1.94
3046 4834 5.181690 AGAAAGAGCAAACACGCATAAAA 57.818 34.783 0.00 0.00 0.00 1.52
3047 4835 4.829064 AGAAAGAGCAAACACGCATAAA 57.171 36.364 0.00 0.00 0.00 1.40
3048 4836 4.994852 ACTAGAAAGAGCAAACACGCATAA 59.005 37.500 0.00 0.00 0.00 1.90
3049 4837 4.388773 CACTAGAAAGAGCAAACACGCATA 59.611 41.667 0.00 0.00 0.00 3.14
3050 4838 3.187227 CACTAGAAAGAGCAAACACGCAT 59.813 43.478 0.00 0.00 0.00 4.73
3051 4839 2.543848 CACTAGAAAGAGCAAACACGCA 59.456 45.455 0.00 0.00 0.00 5.24
3052 4840 2.800544 TCACTAGAAAGAGCAAACACGC 59.199 45.455 0.00 0.00 0.00 5.34
3053 4841 5.006746 AGTTTCACTAGAAAGAGCAAACACG 59.993 40.000 0.00 0.00 43.95 4.49
3054 4842 6.364945 AGTTTCACTAGAAAGAGCAAACAC 57.635 37.500 0.00 0.00 43.95 3.32
3068 4856 7.671302 ACAGATCAAAAGCTCTAGTTTCACTA 58.329 34.615 0.00 0.00 0.00 2.74
3069 4857 6.529220 ACAGATCAAAAGCTCTAGTTTCACT 58.471 36.000 0.00 0.00 0.00 3.41
3070 4858 6.793492 ACAGATCAAAAGCTCTAGTTTCAC 57.207 37.500 0.00 0.00 0.00 3.18
3071 4859 8.150945 ACTAACAGATCAAAAGCTCTAGTTTCA 58.849 33.333 0.00 0.00 0.00 2.69
3072 4860 8.541133 ACTAACAGATCAAAAGCTCTAGTTTC 57.459 34.615 0.00 0.00 0.00 2.78
3073 4861 8.150945 TGACTAACAGATCAAAAGCTCTAGTTT 58.849 33.333 0.00 0.00 0.00 2.66
3074 4862 7.600752 GTGACTAACAGATCAAAAGCTCTAGTT 59.399 37.037 0.00 0.00 0.00 2.24
3075 4863 7.093992 GTGACTAACAGATCAAAAGCTCTAGT 58.906 38.462 0.00 0.00 0.00 2.57
3076 4864 7.093354 TGTGACTAACAGATCAAAAGCTCTAG 58.907 38.462 0.00 0.00 33.78 2.43
3077 4865 6.993079 TGTGACTAACAGATCAAAAGCTCTA 58.007 36.000 0.00 0.00 33.78 2.43
3078 4866 5.858381 TGTGACTAACAGATCAAAAGCTCT 58.142 37.500 0.00 0.00 33.78 4.09
3091 4879 5.997129 TGATGCAATTTCTCTGTGACTAACA 59.003 36.000 0.00 0.00 37.22 2.41
3092 4880 6.486253 TGATGCAATTTCTCTGTGACTAAC 57.514 37.500 0.00 0.00 0.00 2.34
3093 4881 7.413328 CGATTGATGCAATTTCTCTGTGACTAA 60.413 37.037 0.00 0.00 33.90 2.24
3094 4882 6.036408 CGATTGATGCAATTTCTCTGTGACTA 59.964 38.462 0.00 0.00 33.90 2.59
3095 4883 5.163784 CGATTGATGCAATTTCTCTGTGACT 60.164 40.000 0.00 0.00 33.90 3.41
3096 4884 5.026462 CGATTGATGCAATTTCTCTGTGAC 58.974 41.667 0.00 0.00 33.90 3.67
3097 4885 4.437794 GCGATTGATGCAATTTCTCTGTGA 60.438 41.667 0.00 0.00 33.90 3.58
3098 4886 3.789756 GCGATTGATGCAATTTCTCTGTG 59.210 43.478 0.00 0.00 33.90 3.66
3099 4887 3.441222 TGCGATTGATGCAATTTCTCTGT 59.559 39.130 0.00 0.00 39.87 3.41
3100 4888 4.023739 TGCGATTGATGCAATTTCTCTG 57.976 40.909 0.00 0.00 39.87 3.35
3101 4889 4.707030 TTGCGATTGATGCAATTTCTCT 57.293 36.364 0.00 0.00 46.62 3.10
3109 4897 9.964303 AGTTTATTTTATATTGCGATTGATGCA 57.036 25.926 0.00 0.00 41.38 3.96
3118 4906 9.365311 CGTACTCCAAGTTTATTTTATATTGCG 57.635 33.333 0.00 0.00 0.00 4.85
3144 4932 8.553921 GCACGCTGCTATTTGTACAAGAGTAC 62.554 46.154 8.56 0.00 44.29 2.73
3145 4933 4.862574 CACGCTGCTATTTGTACAAGAGTA 59.137 41.667 8.56 8.91 0.00 2.59
3146 4934 3.679980 CACGCTGCTATTTGTACAAGAGT 59.320 43.478 8.56 1.00 0.00 3.24
3147 4935 3.484229 GCACGCTGCTATTTGTACAAGAG 60.484 47.826 8.56 11.16 40.96 2.85
3148 4936 2.415168 GCACGCTGCTATTTGTACAAGA 59.585 45.455 8.56 0.37 40.96 3.02
3149 4937 2.159430 TGCACGCTGCTATTTGTACAAG 59.841 45.455 8.56 0.00 45.31 3.16
3150 4938 2.147150 TGCACGCTGCTATTTGTACAA 58.853 42.857 3.59 3.59 45.31 2.41
3151 4939 1.731709 CTGCACGCTGCTATTTGTACA 59.268 47.619 10.54 0.00 45.31 2.90
3152 4940 1.062587 CCTGCACGCTGCTATTTGTAC 59.937 52.381 10.54 0.00 45.31 2.90
3153 4941 1.338674 ACCTGCACGCTGCTATTTGTA 60.339 47.619 10.54 0.00 45.31 2.41
3154 4942 0.606401 ACCTGCACGCTGCTATTTGT 60.606 50.000 10.54 0.00 45.31 2.83
3155 4943 0.179181 CACCTGCACGCTGCTATTTG 60.179 55.000 10.54 0.00 45.31 2.32
3156 4944 0.321564 TCACCTGCACGCTGCTATTT 60.322 50.000 10.54 0.00 45.31 1.40
3157 4945 0.321564 TTCACCTGCACGCTGCTATT 60.322 50.000 10.54 0.00 45.31 1.73
3158 4946 0.321564 TTTCACCTGCACGCTGCTAT 60.322 50.000 10.54 0.00 45.31 2.97
3159 4947 0.950555 CTTTCACCTGCACGCTGCTA 60.951 55.000 10.54 0.00 45.31 3.49
3160 4948 2.203195 TTTCACCTGCACGCTGCT 60.203 55.556 10.54 0.00 45.31 4.24
3161 4949 1.785041 TTCTTTCACCTGCACGCTGC 61.785 55.000 3.44 3.44 45.29 5.25
3162 4950 0.662619 TTTCTTTCACCTGCACGCTG 59.337 50.000 0.00 0.00 0.00 5.18
3163 4951 1.537202 GATTTCTTTCACCTGCACGCT 59.463 47.619 0.00 0.00 0.00 5.07
3164 4952 1.266718 TGATTTCTTTCACCTGCACGC 59.733 47.619 0.00 0.00 0.00 5.34
3165 4953 2.549754 ACTGATTTCTTTCACCTGCACG 59.450 45.455 0.00 0.00 0.00 5.34
3166 4954 4.377431 CGTACTGATTTCTTTCACCTGCAC 60.377 45.833 0.00 0.00 0.00 4.57
3167 4955 3.745975 CGTACTGATTTCTTTCACCTGCA 59.254 43.478 0.00 0.00 0.00 4.41
3168 4956 3.125316 CCGTACTGATTTCTTTCACCTGC 59.875 47.826 0.00 0.00 0.00 4.85
3169 4957 3.125316 GCCGTACTGATTTCTTTCACCTG 59.875 47.826 0.00 0.00 0.00 4.00
3170 4958 3.008049 AGCCGTACTGATTTCTTTCACCT 59.992 43.478 0.00 0.00 0.00 4.00
3171 4959 3.335579 AGCCGTACTGATTTCTTTCACC 58.664 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.