Multiple sequence alignment - TraesCS7D01G044700

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 TraesCS7D01G044700 chr7D 100.000 2959 0 0 1 2959 22649367 22652325 0.000000e+00 5465.0
1 TraesCS7D01G044700 chr4A 90.259 1273 82 17 705 1958 705628558 705627309 0.000000e+00 1626.0
2 TraesCS7D01G044700 chr4A 86.694 496 28 6 2499 2959 705626964 705626472 1.570000e-142 516.0
3 TraesCS7D01G044700 chr4A 92.742 124 7 1 2331 2452 705627088 705626965 8.430000e-41 178.0
4 TraesCS7D01G044700 chr7A 91.286 1205 75 17 803 1991 23107911 23109101 0.000000e+00 1616.0
5 TraesCS7D01G044700 chr7A 90.964 332 30 0 2496 2827 23110644 23110975 5.820000e-122 448.0
6 TraesCS7D01G044700 chr7A 91.667 300 24 1 2659 2957 23109422 23109721 5.900000e-112 414.0
7 TraesCS7D01G044700 chr7A 88.017 242 11 9 1647 1888 23109944 23110167 1.350000e-68 270.0
8 TraesCS7D01G044700 chr7A 93.277 119 3 2 2362 2475 23110534 23110652 1.410000e-38 171.0
9 TraesCS7D01G044700 chr7A 95.960 99 4 0 2060 2158 23110423 23110521 8.490000e-36 161.0
10 TraesCS7D01G044700 chr7A 86.567 134 9 1 2826 2959 23111415 23111539 3.980000e-29 139.0
11 TraesCS7D01G044700 chr7A 97.917 48 1 0 763 810 23107554 23107601 1.890000e-12 84.2
12 TraesCS7D01G044700 chr7A 89.831 59 6 0 705 763 23107398 23107456 3.160000e-10 76.8
13 TraesCS7D01G044700 chr2D 96.028 705 21 5 1 705 217501253 217501950 0.000000e+00 1140.0
14 TraesCS7D01G044700 chr2D 96.000 100 2 1 2360 2457 39524539 39524638 8.490000e-36 161.0
15 TraesCS7D01G044700 chr5B 95.461 705 25 3 1 705 324250411 324251108 0.000000e+00 1118.0
16 TraesCS7D01G044700 chr3B 95.455 704 25 3 4 707 662018656 662017960 0.000000e+00 1116.0
17 TraesCS7D01G044700 chr6D 95.319 705 25 5 1 705 45667350 45666654 0.000000e+00 1112.0
18 TraesCS7D01G044700 chr6D 94.901 706 28 4 1 705 472371319 472372017 0.000000e+00 1098.0
19 TraesCS7D01G044700 chr6D 80.247 891 132 31 795 1676 353100540 353099685 5.380000e-177 630.0
20 TraesCS7D01G044700 chr6D 96.000 100 2 1 2360 2457 124511006 124511105 8.490000e-36 161.0
21 TraesCS7D01G044700 chr6D 96.000 100 2 1 2360 2457 425949517 425949616 8.490000e-36 161.0
22 TraesCS7D01G044700 chr2B 95.191 707 27 3 1 707 745724904 745725603 0.000000e+00 1110.0
23 TraesCS7D01G044700 chr2B 88.950 543 59 1 1071 1613 717630072 717629531 0.000000e+00 669.0
24 TraesCS7D01G044700 chr6B 95.170 704 27 3 1 704 704887288 704887984 0.000000e+00 1105.0
25 TraesCS7D01G044700 chr6B 79.422 899 141 31 792 1676 525313442 525314310 1.960000e-166 595.0
26 TraesCS7D01G044700 chr5D 95.164 703 27 7 1 703 443763200 443763895 0.000000e+00 1103.0
27 TraesCS7D01G044700 chr3D 94.872 702 29 4 1 702 520151500 520150806 0.000000e+00 1090.0
28 TraesCS7D01G044700 chr4B 89.981 539 53 1 1076 1613 605788321 605788859 0.000000e+00 695.0
29 TraesCS7D01G044700 chr4B 89.338 544 57 1 1071 1613 605846644 605846101 0.000000e+00 682.0
30 TraesCS7D01G044700 chr4B 88.787 544 59 2 1071 1613 90266454 90266996 0.000000e+00 665.0
31 TraesCS7D01G044700 chr4B 96.000 100 2 1 2360 2457 209293308 209293407 8.490000e-36 161.0
32 TraesCS7D01G044700 chr7B 88.582 543 62 0 1071 1613 169124332 169124874 0.000000e+00 660.0
33 TraesCS7D01G044700 chr7B 96.000 100 2 1 2360 2457 716846613 716846514 8.490000e-36 161.0
34 TraesCS7D01G044700 chr6A 80.045 897 129 37 792 1676 489441371 489442229 1.170000e-173 619.0
35 TraesCS7D01G044700 chr6A 91.304 46 0 2 1739 1784 489442301 489442342 3.190000e-05 60.2
36 TraesCS7D01G044700 chr4D 96.000 100 2 1 2360 2457 123297196 123297295 8.490000e-36 161.0
37 TraesCS7D01G044700 chr4D 96.000 100 2 1 2360 2457 123328951 123329050 8.490000e-36 161.0


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 TraesCS7D01G044700 chr7D 22649367 22652325 2958 False 5465.000000 5465 100.000000 1 2959 1 chr7D.!!$F1 2958
1 TraesCS7D01G044700 chr4A 705626472 705628558 2086 True 773.333333 1626 89.898333 705 2959 3 chr4A.!!$R1 2254
2 TraesCS7D01G044700 chr7A 23107398 23111539 4141 False 375.555556 1616 91.720667 705 2959 9 chr7A.!!$F1 2254
3 TraesCS7D01G044700 chr2D 217501253 217501950 697 False 1140.000000 1140 96.028000 1 705 1 chr2D.!!$F2 704
4 TraesCS7D01G044700 chr5B 324250411 324251108 697 False 1118.000000 1118 95.461000 1 705 1 chr5B.!!$F1 704
5 TraesCS7D01G044700 chr3B 662017960 662018656 696 True 1116.000000 1116 95.455000 4 707 1 chr3B.!!$R1 703
6 TraesCS7D01G044700 chr6D 45666654 45667350 696 True 1112.000000 1112 95.319000 1 705 1 chr6D.!!$R1 704
7 TraesCS7D01G044700 chr6D 472371319 472372017 698 False 1098.000000 1098 94.901000 1 705 1 chr6D.!!$F3 704
8 TraesCS7D01G044700 chr6D 353099685 353100540 855 True 630.000000 630 80.247000 795 1676 1 chr6D.!!$R2 881
9 TraesCS7D01G044700 chr2B 745724904 745725603 699 False 1110.000000 1110 95.191000 1 707 1 chr2B.!!$F1 706
10 TraesCS7D01G044700 chr2B 717629531 717630072 541 True 669.000000 669 88.950000 1071 1613 1 chr2B.!!$R1 542
11 TraesCS7D01G044700 chr6B 704887288 704887984 696 False 1105.000000 1105 95.170000 1 704 1 chr6B.!!$F2 703
12 TraesCS7D01G044700 chr6B 525313442 525314310 868 False 595.000000 595 79.422000 792 1676 1 chr6B.!!$F1 884
13 TraesCS7D01G044700 chr5D 443763200 443763895 695 False 1103.000000 1103 95.164000 1 703 1 chr5D.!!$F1 702
14 TraesCS7D01G044700 chr3D 520150806 520151500 694 True 1090.000000 1090 94.872000 1 702 1 chr3D.!!$R1 701
15 TraesCS7D01G044700 chr4B 605788321 605788859 538 False 695.000000 695 89.981000 1076 1613 1 chr4B.!!$F3 537
16 TraesCS7D01G044700 chr4B 605846101 605846644 543 True 682.000000 682 89.338000 1071 1613 1 chr4B.!!$R1 542
17 TraesCS7D01G044700 chr4B 90266454 90266996 542 False 665.000000 665 88.787000 1071 1613 1 chr4B.!!$F1 542
18 TraesCS7D01G044700 chr7B 169124332 169124874 542 False 660.000000 660 88.582000 1071 1613 1 chr7B.!!$F1 542
19 TraesCS7D01G044700 chr6A 489441371 489442342 971 False 339.600000 619 85.674500 792 1784 2 chr6A.!!$F1 992

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
382 384 1.408127 CCATCCATGAACCCTAACGCA 60.408 52.381 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 3970 0.03213 TTCTGAGCCACGATATCGCC 59.968 55.0 24.59 13.13 44.43 5.54 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
172 174 1.771255 AGGAAACCAGAACTGTCAGCT 59.229 47.619 0.00 0.00 0.00 4.24
308 310 2.111043 CGCCATAGCAACGGGGAT 59.889 61.111 0.00 0.00 39.83 3.85
341 343 1.895798 GAGACACACCTGATGGAGTCA 59.104 52.381 0.00 0.00 34.94 3.41
382 384 1.408127 CCATCCATGAACCCTAACGCA 60.408 52.381 0.00 0.00 0.00 5.24
472 474 2.111384 GTATGGGAGTGAAGCTGAGGA 58.889 52.381 0.00 0.00 0.00 3.71
551 553 7.287810 ACAAATCCAAAACCTAACTACAGAGT 58.712 34.615 0.00 0.00 37.59 3.24
559 561 4.949121 ACCTAACTACAGAGTGGAGGAAT 58.051 43.478 11.42 0.00 40.11 3.01
674 676 2.770048 CCTCCCTAGTGGCCTGGG 60.770 72.222 3.32 10.77 42.20 4.45
743 745 8.777865 ATTCGACTGAGAGTGAAATCAAAATA 57.222 30.769 0.00 0.00 0.00 1.40
793 893 8.943909 AAATGAATCCTAAACTTACGGAGTAG 57.056 34.615 0.00 0.00 46.93 2.57
1365 1810 4.443266 GAGCTGCTCTTCGCCGGT 62.443 66.667 21.93 0.00 38.05 5.28
1512 1958 1.079750 GTTCGTCAGGGAGAGCACC 60.080 63.158 0.00 0.00 0.00 5.01
1515 1961 3.695606 GTCAGGGAGAGCACCGCA 61.696 66.667 0.00 0.00 0.00 5.69
1548 1994 1.118965 TGGAGCTCAAGGTTGTCGGA 61.119 55.000 17.19 0.00 0.00 4.55
1554 2000 1.001406 CTCAAGGTTGTCGGAGAGCTT 59.999 52.381 0.00 1.24 36.95 3.74
1559 2005 1.275573 GGTTGTCGGAGAGCTTAGGTT 59.724 52.381 0.00 0.00 36.95 3.50
1594 2040 3.978723 CTGCAGAGACTGGACGCGG 62.979 68.421 8.42 0.00 31.21 6.46
1596 2042 2.651361 CAGAGACTGGACGCGGTT 59.349 61.111 12.47 0.00 0.00 4.44
1681 2127 2.864946 GCCGTTTTTACTAGCTAGCTCC 59.135 50.000 23.26 2.46 0.00 4.70
1798 3427 4.083537 CGCCTCTAGCTAGAGTCATTACAG 60.084 50.000 36.92 24.62 46.52 2.74
1820 3449 8.288689 ACAGTACATTACATTACATTTTCCCC 57.711 34.615 0.00 0.00 0.00 4.81
1821 3450 7.340999 ACAGTACATTACATTACATTTTCCCCC 59.659 37.037 0.00 0.00 0.00 5.40
1888 3517 9.225436 AGCTAGTCTCTTTTCCTCTTTTTAATG 57.775 33.333 0.00 0.00 0.00 1.90
1889 3518 9.220767 GCTAGTCTCTTTTCCTCTTTTTAATGA 57.779 33.333 0.00 0.00 0.00 2.57
1891 3520 8.628630 AGTCTCTTTTCCTCTTTTTAATGAGG 57.371 34.615 14.96 14.96 46.37 3.86
1908 3538 4.513198 TGAGGTTTTTAATTTGGAGGCG 57.487 40.909 0.00 0.00 0.00 5.52
1931 3672 6.201425 GCGAATTAACTACGTTATTGGGATGA 59.799 38.462 0.00 0.00 0.00 2.92
1950 3691 4.732285 TGACATTGTTTTCTTCTCGAGC 57.268 40.909 7.81 0.00 0.00 5.03
1959 3700 9.994432 ATTGTTTTCTTCTCGAGCATAATAAAG 57.006 29.630 7.81 4.48 0.00 1.85
1960 3701 8.771920 TGTTTTCTTCTCGAGCATAATAAAGA 57.228 30.769 7.81 6.97 0.00 2.52
1961 3702 9.214957 TGTTTTCTTCTCGAGCATAATAAAGAA 57.785 29.630 15.37 15.37 31.45 2.52
1997 3738 9.969001 ATATACACCATTTGTTTAGTGTAGGTT 57.031 29.630 7.76 0.00 45.83 3.50
2040 3790 7.035004 TGTCACCTAATTTTGAATATTGCTGC 58.965 34.615 0.00 0.00 0.00 5.25
2041 3791 6.197096 GTCACCTAATTTTGAATATTGCTGCG 59.803 38.462 0.00 0.00 0.00 5.18
2042 3792 6.035843 CACCTAATTTTGAATATTGCTGCGT 58.964 36.000 0.00 0.00 0.00 5.24
2043 3793 6.531240 CACCTAATTTTGAATATTGCTGCGTT 59.469 34.615 0.00 0.00 0.00 4.84
2045 3795 8.413229 ACCTAATTTTGAATATTGCTGCGTTAT 58.587 29.630 0.00 0.00 0.00 1.89
2046 3796 9.248291 CCTAATTTTGAATATTGCTGCGTTATT 57.752 29.630 0.00 6.60 0.00 1.40
2151 3926 9.995003 TGTTGATCCAAAAGCTTAAAAATATGT 57.005 25.926 0.00 0.00 0.00 2.29
2153 3928 9.651913 TTGATCCAAAAGCTTAAAAATATGTCC 57.348 29.630 0.00 0.00 0.00 4.02
2154 3929 8.811017 TGATCCAAAAGCTTAAAAATATGTCCA 58.189 29.630 0.00 0.00 0.00 4.02
2155 3930 9.651913 GATCCAAAAGCTTAAAAATATGTCCAA 57.348 29.630 0.00 0.00 0.00 3.53
2157 3932 9.267084 TCCAAAAGCTTAAAAATATGTCCAAAC 57.733 29.630 0.00 0.00 0.00 2.93
2158 3933 9.271828 CCAAAAGCTTAAAAATATGTCCAAACT 57.728 29.630 0.00 0.00 0.00 2.66
2174 3949 7.754625 TGTCCAAACTATAGTTTAAAATCGCC 58.245 34.615 26.38 11.63 45.54 5.54
2175 3950 6.903479 GTCCAAACTATAGTTTAAAATCGCCG 59.097 38.462 26.38 13.11 45.54 6.46
2176 3951 6.037391 TCCAAACTATAGTTTAAAATCGCCGG 59.963 38.462 26.38 19.88 45.54 6.13
2177 3952 5.413969 AACTATAGTTTAAAATCGCCGGC 57.586 39.130 19.07 19.07 33.93 6.13
2178 3953 3.492011 ACTATAGTTTAAAATCGCCGGCG 59.508 43.478 42.13 42.13 41.35 6.46
2187 3962 3.788817 TCGCCGGCGAAATTACAG 58.211 55.556 46.56 17.71 46.01 2.74
2188 3963 2.022762 CGCCGGCGAAATTACAGC 59.977 61.111 44.86 1.62 42.83 4.40
2189 3964 2.461110 CGCCGGCGAAATTACAGCT 61.461 57.895 44.86 0.00 42.83 4.24
2190 3965 1.149361 CGCCGGCGAAATTACAGCTA 61.149 55.000 44.86 0.00 42.83 3.32
2191 3966 1.226746 GCCGGCGAAATTACAGCTAT 58.773 50.000 12.58 0.00 0.00 2.97
2192 3967 2.409975 GCCGGCGAAATTACAGCTATA 58.590 47.619 12.58 0.00 0.00 1.31
2193 3968 2.412089 GCCGGCGAAATTACAGCTATAG 59.588 50.000 12.58 0.00 0.00 1.31
2194 3969 2.412089 CCGGCGAAATTACAGCTATAGC 59.588 50.000 17.33 17.33 42.49 2.97
2205 3980 3.920144 GCTATAGCGGCGATATCGT 57.080 52.632 21.97 8.93 42.22 3.73
2206 3981 1.467875 GCTATAGCGGCGATATCGTG 58.532 55.000 21.97 18.55 42.22 4.35
2207 3982 1.860399 GCTATAGCGGCGATATCGTGG 60.860 57.143 21.97 17.71 42.22 4.94
2208 3983 0.099968 TATAGCGGCGATATCGTGGC 59.900 55.000 21.97 25.11 42.22 5.01
2209 3984 1.595993 ATAGCGGCGATATCGTGGCT 61.596 55.000 32.20 32.20 46.01 4.75
2210 3985 2.196382 TAGCGGCGATATCGTGGCTC 62.196 60.000 33.00 16.52 44.28 4.70
2211 3986 2.335011 CGGCGATATCGTGGCTCA 59.665 61.111 24.99 0.00 42.22 4.26
2212 3987 1.730902 CGGCGATATCGTGGCTCAG 60.731 63.158 24.99 6.25 42.22 3.35
2213 3988 1.660355 GGCGATATCGTGGCTCAGA 59.340 57.895 24.99 0.00 42.22 3.27
2214 3989 0.032130 GGCGATATCGTGGCTCAGAA 59.968 55.000 24.99 0.00 42.22 3.02
2215 3990 1.337260 GGCGATATCGTGGCTCAGAAT 60.337 52.381 24.99 0.00 42.22 2.40
2216 3991 1.989165 GCGATATCGTGGCTCAGAATC 59.011 52.381 24.99 1.39 42.22 2.52
2217 3992 2.352225 GCGATATCGTGGCTCAGAATCT 60.352 50.000 24.99 0.00 42.22 2.40
2218 3993 3.858877 GCGATATCGTGGCTCAGAATCTT 60.859 47.826 24.99 0.00 42.22 2.40
2219 3994 3.917380 CGATATCGTGGCTCAGAATCTTC 59.083 47.826 17.06 0.00 34.11 2.87
2220 3995 2.611225 ATCGTGGCTCAGAATCTTCC 57.389 50.000 0.00 0.00 0.00 3.46
2221 3996 1.561643 TCGTGGCTCAGAATCTTCCT 58.438 50.000 0.00 0.00 0.00 3.36
2222 3997 1.902508 TCGTGGCTCAGAATCTTCCTT 59.097 47.619 0.00 0.00 0.00 3.36
2223 3998 2.005451 CGTGGCTCAGAATCTTCCTTG 58.995 52.381 0.00 0.00 0.00 3.61
2224 3999 1.742268 GTGGCTCAGAATCTTCCTTGC 59.258 52.381 0.00 0.00 0.00 4.01
2225 4000 1.012841 GGCTCAGAATCTTCCTTGCG 58.987 55.000 0.00 0.00 0.00 4.85
2226 4001 1.406069 GGCTCAGAATCTTCCTTGCGA 60.406 52.381 0.00 0.00 0.00 5.10
2227 4002 2.559440 GCTCAGAATCTTCCTTGCGAT 58.441 47.619 0.00 0.00 0.00 4.58
2228 4003 2.941720 GCTCAGAATCTTCCTTGCGATT 59.058 45.455 0.00 0.00 32.86 3.34
2229 4004 3.002144 GCTCAGAATCTTCCTTGCGATTC 59.998 47.826 0.00 0.00 43.56 2.52
2230 4005 3.190079 TCAGAATCTTCCTTGCGATTCG 58.810 45.455 0.62 0.62 46.24 3.34
2241 4016 4.932789 CGATTCGCTTCCTTCCCA 57.067 55.556 0.00 0.00 0.00 4.37
2242 4017 3.153024 CGATTCGCTTCCTTCCCAA 57.847 52.632 0.00 0.00 0.00 4.12
2243 4018 1.448985 CGATTCGCTTCCTTCCCAAA 58.551 50.000 0.00 0.00 0.00 3.28
2244 4019 1.810151 CGATTCGCTTCCTTCCCAAAA 59.190 47.619 0.00 0.00 0.00 2.44
2245 4020 2.423538 CGATTCGCTTCCTTCCCAAAAT 59.576 45.455 0.00 0.00 0.00 1.82
2246 4021 3.487544 CGATTCGCTTCCTTCCCAAAATC 60.488 47.826 0.00 0.00 0.00 2.17
2247 4022 1.448985 TCGCTTCCTTCCCAAAATCG 58.551 50.000 0.00 0.00 0.00 3.34
2248 4023 0.179163 CGCTTCCTTCCCAAAATCGC 60.179 55.000 0.00 0.00 0.00 4.58
2249 4024 0.179163 GCTTCCTTCCCAAAATCGCG 60.179 55.000 0.00 0.00 0.00 5.87
2250 4025 0.451783 CTTCCTTCCCAAAATCGCGG 59.548 55.000 6.13 0.00 0.00 6.46
2251 4026 0.963355 TTCCTTCCCAAAATCGCGGG 60.963 55.000 6.13 0.00 44.60 6.13
2254 4029 3.394494 TCCCAAAATCGCGGGAGA 58.606 55.556 6.13 0.00 46.93 3.71
2255 4030 1.912220 TCCCAAAATCGCGGGAGAT 59.088 52.632 6.13 0.00 46.93 2.75
2256 4031 0.179056 TCCCAAAATCGCGGGAGATC 60.179 55.000 6.13 0.00 46.93 2.75
2257 4032 1.498865 CCCAAAATCGCGGGAGATCG 61.499 60.000 6.13 0.00 46.34 3.69
2266 4041 3.527641 GGGAGATCGCGACTTCCT 58.472 61.111 29.16 17.67 30.78 3.36
2267 4042 1.817209 GGGAGATCGCGACTTCCTT 59.183 57.895 29.16 8.83 30.78 3.36
2268 4043 0.249114 GGGAGATCGCGACTTCCTTC 60.249 60.000 29.16 16.46 30.78 3.46
2269 4044 0.249114 GGAGATCGCGACTTCCTTCC 60.249 60.000 25.55 14.98 0.00 3.46
2270 4045 0.741915 GAGATCGCGACTTCCTTCCT 59.258 55.000 12.93 0.00 0.00 3.36
2271 4046 1.948145 GAGATCGCGACTTCCTTCCTA 59.052 52.381 12.93 0.00 0.00 2.94
2272 4047 2.554893 GAGATCGCGACTTCCTTCCTAT 59.445 50.000 12.93 0.00 0.00 2.57
2273 4048 3.752222 GAGATCGCGACTTCCTTCCTATA 59.248 47.826 12.93 0.00 0.00 1.31
2274 4049 4.142790 AGATCGCGACTTCCTTCCTATAA 58.857 43.478 12.93 0.00 0.00 0.98
2275 4050 4.767928 AGATCGCGACTTCCTTCCTATAAT 59.232 41.667 12.93 0.00 0.00 1.28
2276 4051 4.931661 TCGCGACTTCCTTCCTATAATT 57.068 40.909 3.71 0.00 0.00 1.40
2277 4052 5.272283 TCGCGACTTCCTTCCTATAATTT 57.728 39.130 3.71 0.00 0.00 1.82
2278 4053 5.287226 TCGCGACTTCCTTCCTATAATTTC 58.713 41.667 3.71 0.00 0.00 2.17
2279 4054 4.148348 CGCGACTTCCTTCCTATAATTTCG 59.852 45.833 0.00 0.00 0.00 3.46
2280 4055 4.084485 GCGACTTCCTTCCTATAATTTCGC 60.084 45.833 0.00 0.00 0.00 4.70
2281 4056 5.290386 CGACTTCCTTCCTATAATTTCGCT 58.710 41.667 0.00 0.00 0.00 4.93
2282 4057 5.175856 CGACTTCCTTCCTATAATTTCGCTG 59.824 44.000 0.00 0.00 0.00 5.18
2283 4058 4.816925 ACTTCCTTCCTATAATTTCGCTGC 59.183 41.667 0.00 0.00 0.00 5.25
2284 4059 3.740115 TCCTTCCTATAATTTCGCTGCC 58.260 45.455 0.00 0.00 0.00 4.85
2285 4060 3.135712 TCCTTCCTATAATTTCGCTGCCA 59.864 43.478 0.00 0.00 0.00 4.92
2286 4061 3.882888 CCTTCCTATAATTTCGCTGCCAA 59.117 43.478 0.00 0.00 0.00 4.52
2287 4062 4.338118 CCTTCCTATAATTTCGCTGCCAAA 59.662 41.667 0.00 0.00 0.00 3.28
2288 4063 5.010012 CCTTCCTATAATTTCGCTGCCAAAT 59.990 40.000 0.00 0.00 0.00 2.32
2289 4064 6.461509 CCTTCCTATAATTTCGCTGCCAAATT 60.462 38.462 19.13 19.13 37.27 1.82
2290 4065 6.463995 TCCTATAATTTCGCTGCCAAATTT 57.536 33.333 20.09 12.00 35.52 1.82
2291 4066 6.503524 TCCTATAATTTCGCTGCCAAATTTC 58.496 36.000 20.09 0.00 35.52 2.17
2292 4067 5.691754 CCTATAATTTCGCTGCCAAATTTCC 59.308 40.000 20.09 0.00 35.52 3.13
2293 4068 3.683365 AATTTCGCTGCCAAATTTCCT 57.317 38.095 11.40 0.00 30.74 3.36
2294 4069 4.799564 AATTTCGCTGCCAAATTTCCTA 57.200 36.364 11.40 0.00 30.74 2.94
2295 4070 3.569250 TTTCGCTGCCAAATTTCCTAC 57.431 42.857 0.00 0.00 0.00 3.18
2296 4071 1.459450 TCGCTGCCAAATTTCCTACC 58.541 50.000 0.00 0.00 0.00 3.18
2297 4072 1.004277 TCGCTGCCAAATTTCCTACCT 59.996 47.619 0.00 0.00 0.00 3.08
2298 4073 1.401905 CGCTGCCAAATTTCCTACCTC 59.598 52.381 0.00 0.00 0.00 3.85
2299 4074 2.728007 GCTGCCAAATTTCCTACCTCT 58.272 47.619 0.00 0.00 0.00 3.69
2300 4075 3.681594 CGCTGCCAAATTTCCTACCTCTA 60.682 47.826 0.00 0.00 0.00 2.43
2301 4076 4.270008 GCTGCCAAATTTCCTACCTCTAA 58.730 43.478 0.00 0.00 0.00 2.10
2302 4077 4.705023 GCTGCCAAATTTCCTACCTCTAAA 59.295 41.667 0.00 0.00 0.00 1.85
2303 4078 5.393135 GCTGCCAAATTTCCTACCTCTAAAC 60.393 44.000 0.00 0.00 0.00 2.01
2304 4079 5.887754 TGCCAAATTTCCTACCTCTAAACT 58.112 37.500 0.00 0.00 0.00 2.66
2305 4080 5.944007 TGCCAAATTTCCTACCTCTAAACTC 59.056 40.000 0.00 0.00 0.00 3.01
2306 4081 5.357314 GCCAAATTTCCTACCTCTAAACTCC 59.643 44.000 0.00 0.00 0.00 3.85
2307 4082 6.722328 CCAAATTTCCTACCTCTAAACTCCT 58.278 40.000 0.00 0.00 0.00 3.69
2308 4083 7.175797 CCAAATTTCCTACCTCTAAACTCCTT 58.824 38.462 0.00 0.00 0.00 3.36
2309 4084 7.670140 CCAAATTTCCTACCTCTAAACTCCTTT 59.330 37.037 0.00 0.00 0.00 3.11
2310 4085 8.515414 CAAATTTCCTACCTCTAAACTCCTTTG 58.485 37.037 0.00 0.00 0.00 2.77
2311 4086 4.820894 TCCTACCTCTAAACTCCTTTGC 57.179 45.455 0.00 0.00 0.00 3.68
2312 4087 3.518303 TCCTACCTCTAAACTCCTTTGCC 59.482 47.826 0.00 0.00 0.00 4.52
2313 4088 2.881111 ACCTCTAAACTCCTTTGCCC 57.119 50.000 0.00 0.00 0.00 5.36
2314 4089 1.003233 ACCTCTAAACTCCTTTGCCCG 59.997 52.381 0.00 0.00 0.00 6.13
2315 4090 1.087501 CTCTAAACTCCTTTGCCCGC 58.912 55.000 0.00 0.00 0.00 6.13
2316 4091 0.672401 TCTAAACTCCTTTGCCCGCG 60.672 55.000 0.00 0.00 0.00 6.46
2317 4092 0.672401 CTAAACTCCTTTGCCCGCGA 60.672 55.000 8.23 0.00 0.00 5.87
2318 4093 0.035820 TAAACTCCTTTGCCCGCGAT 60.036 50.000 8.23 0.00 0.00 4.58
2319 4094 0.893727 AAACTCCTTTGCCCGCGATT 60.894 50.000 8.23 0.00 0.00 3.34
2320 4095 0.893727 AACTCCTTTGCCCGCGATTT 60.894 50.000 8.23 0.00 0.00 2.17
2321 4096 0.893727 ACTCCTTTGCCCGCGATTTT 60.894 50.000 8.23 0.00 0.00 1.82
2322 4097 1.091537 CTCCTTTGCCCGCGATTTTA 58.908 50.000 8.23 0.00 0.00 1.52
2323 4098 1.470890 CTCCTTTGCCCGCGATTTTAA 59.529 47.619 8.23 0.00 0.00 1.52
2324 4099 2.096248 TCCTTTGCCCGCGATTTTAAT 58.904 42.857 8.23 0.00 0.00 1.40
2325 4100 2.098443 TCCTTTGCCCGCGATTTTAATC 59.902 45.455 8.23 0.00 0.00 1.75
2326 4101 2.099098 CCTTTGCCCGCGATTTTAATCT 59.901 45.455 8.23 0.00 33.24 2.40
2327 4102 3.314080 CCTTTGCCCGCGATTTTAATCTA 59.686 43.478 8.23 0.00 33.24 1.98
2328 4103 4.023193 CCTTTGCCCGCGATTTTAATCTAT 60.023 41.667 8.23 0.00 33.24 1.98
2329 4104 4.481930 TTGCCCGCGATTTTAATCTATG 57.518 40.909 8.23 0.00 33.24 2.23
2374 4149 4.287067 ACCATAATTGATGAGCTACCCGAT 59.713 41.667 0.00 0.00 37.82 4.18
2447 4227 4.545610 TGTCATTTTGCGATTTGAGTTCC 58.454 39.130 0.00 0.00 0.00 3.62
2564 4344 6.685657 TCTATAGCTGACAATAGATGCACAG 58.314 40.000 0.00 0.00 38.75 3.66
2573 4353 8.414629 TGACAATAGATGCACAGATAGTAGAT 57.585 34.615 0.00 0.00 0.00 1.98
2609 4389 8.408043 AAAATATCACTGTCATTCCAACTCAA 57.592 30.769 0.00 0.00 0.00 3.02
2707 4487 5.503927 AGCAAATTGGAGAGTACATCACAT 58.496 37.500 0.00 0.00 0.00 3.21
2708 4488 5.356190 AGCAAATTGGAGAGTACATCACATG 59.644 40.000 0.00 0.00 0.00 3.21
2722 4502 4.040829 ACATCACATGACAGAGAGGAAACA 59.959 41.667 0.00 0.00 0.00 2.83
2739 4519 7.874528 AGAGGAAACATTGAAAAATGCTTTAGG 59.125 33.333 0.00 0.00 33.57 2.69
2754 4534 2.238942 TTAGGTATGCATGTGCTCCG 57.761 50.000 10.16 0.00 42.66 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.759516 TTCTTTCAACGGCTATGGTTTC 57.240 40.909 0.00 0.00 0.00 2.78
172 174 0.257328 TGCTGGGTCTGTGGTTGAAA 59.743 50.000 0.00 0.00 0.00 2.69
308 310 3.085533 GTGTGTCTCTCCTTCTGCTCTA 58.914 50.000 0.00 0.00 0.00 2.43
472 474 2.351726 GGCGCACAGACGAATAAATCTT 59.648 45.455 10.83 0.00 34.06 2.40
707 709 4.641396 TCTCAGTCGAATTGTTGTCCATT 58.359 39.130 0.00 0.00 0.00 3.16
743 745 9.841295 TTTTACTAGTAATTTTCAGTGGACAGT 57.159 29.630 15.92 0.00 0.00 3.55
793 893 1.670791 TGTCAAACAAGGAACGTCCC 58.329 50.000 0.00 0.00 37.19 4.46
1515 1961 4.974438 TCCAGCCGGAACACCCCT 62.974 66.667 5.05 0.00 38.83 4.79
1571 2017 2.046507 CCAGTCTCTGCAGGTGGC 60.047 66.667 15.13 9.00 45.13 5.01
1581 2027 2.668280 GCAAACCGCGTCCAGTCTC 61.668 63.158 4.92 0.00 0.00 3.36
1594 2040 2.644992 CAACTCCAGCGGGCAAAC 59.355 61.111 0.00 0.00 0.00 2.93
1681 2127 3.058450 GGCATGAAGAGATGTCATCGAG 58.942 50.000 7.18 0.00 33.37 4.04
1818 3447 5.046807 TCGTTCTAGTAGAAAAGAAAGGGGG 60.047 44.000 14.20 0.00 35.75 5.40
1819 3448 6.034161 TCGTTCTAGTAGAAAAGAAAGGGG 57.966 41.667 14.20 0.00 35.75 4.79
1820 3449 7.321153 TGATCGTTCTAGTAGAAAAGAAAGGG 58.679 38.462 14.20 0.00 35.75 3.95
1821 3450 8.244802 TCTGATCGTTCTAGTAGAAAAGAAAGG 58.755 37.037 14.20 10.28 35.75 3.11
1834 3463 3.366883 GCTAGCCCATCTGATCGTTCTAG 60.367 52.174 2.29 0.00 0.00 2.43
1888 3517 4.776795 TCGCCTCCAAATTAAAAACCTC 57.223 40.909 0.00 0.00 0.00 3.85
1889 3518 5.738619 ATTCGCCTCCAAATTAAAAACCT 57.261 34.783 0.00 0.00 0.00 3.50
1890 3519 7.601130 AGTTAATTCGCCTCCAAATTAAAAACC 59.399 33.333 0.00 0.00 38.42 3.27
1891 3520 8.528917 AGTTAATTCGCCTCCAAATTAAAAAC 57.471 30.769 0.00 0.00 38.42 2.43
1895 3525 6.594937 ACGTAGTTAATTCGCCTCCAAATTAA 59.405 34.615 0.00 0.00 37.78 1.40
1931 3672 6.801539 TTATGCTCGAGAAGAAAACAATGT 57.198 33.333 18.75 0.00 0.00 2.71
1975 3716 9.223099 GTATAACCTACACTAAACAAATGGTGT 57.777 33.333 0.00 0.00 44.64 4.16
2014 3756 7.707893 GCAGCAATATTCAAAATTAGGTGACAT 59.292 33.333 0.00 0.00 0.00 3.06
2047 3797 7.282224 AGACGTAGCAATATAGATTGGCAAAAA 59.718 33.333 11.83 0.00 42.44 1.94
2049 3799 6.288294 AGACGTAGCAATATAGATTGGCAAA 58.712 36.000 11.83 0.00 42.44 3.68
2050 3800 5.853936 AGACGTAGCAATATAGATTGGCAA 58.146 37.500 11.83 0.68 42.44 4.52
2051 3801 5.468540 AGACGTAGCAATATAGATTGGCA 57.531 39.130 11.83 0.00 42.44 4.92
2053 3803 8.709646 GGTTTTAGACGTAGCAATATAGATTGG 58.290 37.037 11.83 0.00 42.44 3.16
2054 3804 8.425491 CGGTTTTAGACGTAGCAATATAGATTG 58.575 37.037 5.69 5.69 44.62 2.67
2055 3805 7.115947 GCGGTTTTAGACGTAGCAATATAGATT 59.884 37.037 0.00 0.00 0.00 2.40
2056 3806 6.585322 GCGGTTTTAGACGTAGCAATATAGAT 59.415 38.462 0.00 0.00 0.00 1.98
2057 3807 5.916883 GCGGTTTTAGACGTAGCAATATAGA 59.083 40.000 0.00 0.00 0.00 1.98
2058 3808 5.688621 TGCGGTTTTAGACGTAGCAATATAG 59.311 40.000 0.00 0.00 33.22 1.31
2059 3809 5.459762 GTGCGGTTTTAGACGTAGCAATATA 59.540 40.000 0.00 0.00 36.25 0.86
2060 3810 4.269363 GTGCGGTTTTAGACGTAGCAATAT 59.731 41.667 0.00 0.00 36.25 1.28
2061 3811 3.613737 GTGCGGTTTTAGACGTAGCAATA 59.386 43.478 0.00 0.00 36.25 1.90
2062 3812 2.414138 GTGCGGTTTTAGACGTAGCAAT 59.586 45.455 0.00 0.00 36.25 3.56
2070 3820 6.956299 TGTTAGATAAGTGCGGTTTTAGAC 57.044 37.500 0.00 0.00 0.00 2.59
2148 3923 8.403236 GGCGATTTTAAACTATAGTTTGGACAT 58.597 33.333 31.97 20.95 46.56 3.06
2150 3925 6.903479 CGGCGATTTTAAACTATAGTTTGGAC 59.097 38.462 31.97 19.68 46.56 4.02
2151 3926 6.037391 CCGGCGATTTTAAACTATAGTTTGGA 59.963 38.462 31.97 20.94 46.56 3.53
2152 3927 6.196571 CCGGCGATTTTAAACTATAGTTTGG 58.803 40.000 31.97 20.50 46.56 3.28
2153 3928 5.679792 GCCGGCGATTTTAAACTATAGTTTG 59.320 40.000 31.97 19.25 46.56 2.93
2154 3929 5.502869 CGCCGGCGATTTTAAACTATAGTTT 60.503 40.000 44.86 28.78 44.99 2.66
2155 3930 4.025480 CGCCGGCGATTTTAAACTATAGTT 60.025 41.667 44.86 12.50 42.83 2.24
2156 3931 3.492011 CGCCGGCGATTTTAAACTATAGT 59.508 43.478 44.86 0.00 42.83 2.12
2157 3932 3.737266 TCGCCGGCGATTTTAAACTATAG 59.263 43.478 45.37 14.10 44.01 1.31
2158 3933 3.715495 TCGCCGGCGATTTTAAACTATA 58.285 40.909 45.37 20.80 44.01 1.31
2159 3934 2.553086 TCGCCGGCGATTTTAAACTAT 58.447 42.857 45.37 0.00 44.01 2.12
2160 3935 2.007360 TCGCCGGCGATTTTAAACTA 57.993 45.000 45.37 21.61 44.01 2.24
2161 3936 2.843669 TCGCCGGCGATTTTAAACT 58.156 47.368 45.37 0.00 44.01 2.66
2171 3946 1.149361 TAGCTGTAATTTCGCCGGCG 61.149 55.000 42.13 42.13 41.35 6.46
2172 3947 1.226746 ATAGCTGTAATTTCGCCGGC 58.773 50.000 19.07 19.07 0.00 6.13
2173 3948 2.412089 GCTATAGCTGTAATTTCGCCGG 59.588 50.000 17.75 0.00 38.21 6.13
2174 3949 2.090658 CGCTATAGCTGTAATTTCGCCG 59.909 50.000 21.98 0.00 39.32 6.46
2175 3950 2.412089 CCGCTATAGCTGTAATTTCGCC 59.588 50.000 21.98 0.00 39.32 5.54
2176 3951 2.159827 GCCGCTATAGCTGTAATTTCGC 60.160 50.000 21.98 8.89 39.32 4.70
2177 3952 2.090658 CGCCGCTATAGCTGTAATTTCG 59.909 50.000 21.98 9.64 39.32 3.46
2178 3953 3.314553 TCGCCGCTATAGCTGTAATTTC 58.685 45.455 21.98 1.69 39.32 2.17
2179 3954 3.380479 TCGCCGCTATAGCTGTAATTT 57.620 42.857 21.98 0.00 39.32 1.82
2180 3955 3.594603 ATCGCCGCTATAGCTGTAATT 57.405 42.857 21.98 0.63 39.32 1.40
2181 3956 4.554919 CGATATCGCCGCTATAGCTGTAAT 60.555 45.833 21.98 14.49 39.32 1.89
2182 3957 3.242641 CGATATCGCCGCTATAGCTGTAA 60.243 47.826 21.98 8.76 39.32 2.41
2183 3958 2.287103 CGATATCGCCGCTATAGCTGTA 59.713 50.000 21.98 9.09 39.32 2.74
2184 3959 1.064208 CGATATCGCCGCTATAGCTGT 59.936 52.381 21.98 1.54 39.32 4.40
2185 3960 1.064208 ACGATATCGCCGCTATAGCTG 59.936 52.381 24.59 16.77 44.43 4.24
2186 3961 1.064208 CACGATATCGCCGCTATAGCT 59.936 52.381 24.59 5.94 44.43 3.32
2187 3962 1.467875 CACGATATCGCCGCTATAGC 58.532 55.000 24.59 15.09 44.43 2.97
2188 3963 1.860399 GCCACGATATCGCCGCTATAG 60.860 57.143 24.59 6.07 44.43 1.31
2189 3964 0.099968 GCCACGATATCGCCGCTATA 59.900 55.000 24.59 0.00 44.43 1.31
2190 3965 1.153823 GCCACGATATCGCCGCTAT 60.154 57.895 24.59 1.13 44.43 2.97
2191 3966 2.196382 GAGCCACGATATCGCCGCTA 62.196 60.000 29.09 0.00 43.83 4.26
2192 3967 3.559657 GAGCCACGATATCGCCGCT 62.560 63.158 29.31 29.31 45.58 5.52
2193 3968 3.106407 GAGCCACGATATCGCCGC 61.106 66.667 24.59 23.52 44.43 6.53
2194 3969 1.730902 CTGAGCCACGATATCGCCG 60.731 63.158 24.59 15.60 44.43 6.46
2195 3970 0.032130 TTCTGAGCCACGATATCGCC 59.968 55.000 24.59 13.13 44.43 5.54
2196 3971 1.989165 GATTCTGAGCCACGATATCGC 59.011 52.381 24.59 8.94 44.43 4.58
2197 3972 3.567576 AGATTCTGAGCCACGATATCG 57.432 47.619 23.18 23.18 46.33 2.92
2198 3973 4.021544 AGGAAGATTCTGAGCCACGATATC 60.022 45.833 0.00 0.00 0.00 1.63
2199 3974 3.900601 AGGAAGATTCTGAGCCACGATAT 59.099 43.478 0.00 0.00 0.00 1.63
2200 3975 3.300388 AGGAAGATTCTGAGCCACGATA 58.700 45.455 0.00 0.00 0.00 2.92
2201 3976 2.114616 AGGAAGATTCTGAGCCACGAT 58.885 47.619 0.00 0.00 0.00 3.73
2202 3977 1.561643 AGGAAGATTCTGAGCCACGA 58.438 50.000 0.00 0.00 0.00 4.35
2203 3978 2.005451 CAAGGAAGATTCTGAGCCACG 58.995 52.381 0.00 0.00 0.00 4.94
2204 3979 1.742268 GCAAGGAAGATTCTGAGCCAC 59.258 52.381 0.00 0.00 0.00 5.01
2205 3980 1.676916 CGCAAGGAAGATTCTGAGCCA 60.677 52.381 0.00 0.00 0.00 4.75
2206 3981 1.012841 CGCAAGGAAGATTCTGAGCC 58.987 55.000 0.00 0.00 0.00 4.70
2207 3982 2.015736 TCGCAAGGAAGATTCTGAGC 57.984 50.000 0.00 0.00 38.47 4.26
2208 3983 3.244814 CGAATCGCAAGGAAGATTCTGAG 59.755 47.826 13.88 0.00 46.24 3.35
2209 3984 3.190079 CGAATCGCAAGGAAGATTCTGA 58.810 45.455 13.88 0.00 46.24 3.27
2210 3985 3.582444 CGAATCGCAAGGAAGATTCTG 57.418 47.619 13.88 6.27 46.24 3.02
2224 3999 1.448985 TTTGGGAAGGAAGCGAATCG 58.551 50.000 0.00 0.00 0.00 3.34
2225 4000 3.487544 CGATTTTGGGAAGGAAGCGAATC 60.488 47.826 0.00 0.00 34.46 2.52
2226 4001 2.423538 CGATTTTGGGAAGGAAGCGAAT 59.576 45.455 0.00 0.00 34.46 3.34
2227 4002 1.810151 CGATTTTGGGAAGGAAGCGAA 59.190 47.619 0.00 0.00 34.46 4.70
2228 4003 1.448985 CGATTTTGGGAAGGAAGCGA 58.551 50.000 0.00 0.00 34.46 4.93
2229 4004 0.179163 GCGATTTTGGGAAGGAAGCG 60.179 55.000 0.00 0.00 35.52 4.68
2230 4005 0.179163 CGCGATTTTGGGAAGGAAGC 60.179 55.000 0.00 0.00 0.00 3.86
2231 4006 0.451783 CCGCGATTTTGGGAAGGAAG 59.548 55.000 8.23 0.00 0.00 3.46
2232 4007 2.562125 CCGCGATTTTGGGAAGGAA 58.438 52.632 8.23 0.00 0.00 3.36
2233 4008 4.312052 CCGCGATTTTGGGAAGGA 57.688 55.556 8.23 0.00 0.00 3.36
2239 4014 1.934463 CGATCTCCCGCGATTTTGG 59.066 57.895 8.23 0.00 0.00 3.28
2240 4015 1.276844 GCGATCTCCCGCGATTTTG 59.723 57.895 8.23 0.00 45.86 2.44
2241 4016 3.719214 GCGATCTCCCGCGATTTT 58.281 55.556 8.23 0.00 45.86 1.82
2248 4023 2.005960 AAGGAAGTCGCGATCTCCCG 62.006 60.000 26.81 0.00 0.00 5.14
2249 4024 0.249114 GAAGGAAGTCGCGATCTCCC 60.249 60.000 26.81 17.47 0.00 4.30
2250 4025 0.249114 GGAAGGAAGTCGCGATCTCC 60.249 60.000 24.48 24.48 0.00 3.71
2251 4026 0.741915 AGGAAGGAAGTCGCGATCTC 59.258 55.000 14.06 12.10 0.00 2.75
2252 4027 2.054232 TAGGAAGGAAGTCGCGATCT 57.946 50.000 14.06 8.87 0.00 2.75
2253 4028 4.500603 TTATAGGAAGGAAGTCGCGATC 57.499 45.455 14.06 6.63 0.00 3.69
2254 4029 5.470047 AATTATAGGAAGGAAGTCGCGAT 57.530 39.130 14.06 0.00 0.00 4.58
2255 4030 4.931661 AATTATAGGAAGGAAGTCGCGA 57.068 40.909 3.71 3.71 0.00 5.87
2256 4031 4.148348 CGAAATTATAGGAAGGAAGTCGCG 59.852 45.833 0.00 0.00 0.00 5.87
2257 4032 4.084485 GCGAAATTATAGGAAGGAAGTCGC 60.084 45.833 0.00 0.00 0.00 5.19
2258 4033 5.175856 CAGCGAAATTATAGGAAGGAAGTCG 59.824 44.000 0.00 0.00 0.00 4.18
2259 4034 5.050023 GCAGCGAAATTATAGGAAGGAAGTC 60.050 44.000 0.00 0.00 0.00 3.01
2260 4035 4.816925 GCAGCGAAATTATAGGAAGGAAGT 59.183 41.667 0.00 0.00 0.00 3.01
2261 4036 4.214332 GGCAGCGAAATTATAGGAAGGAAG 59.786 45.833 0.00 0.00 0.00 3.46
2262 4037 4.134563 GGCAGCGAAATTATAGGAAGGAA 58.865 43.478 0.00 0.00 0.00 3.36
2263 4038 3.135712 TGGCAGCGAAATTATAGGAAGGA 59.864 43.478 0.00 0.00 0.00 3.36
2264 4039 3.476552 TGGCAGCGAAATTATAGGAAGG 58.523 45.455 0.00 0.00 0.00 3.46
2265 4040 5.499139 TTTGGCAGCGAAATTATAGGAAG 57.501 39.130 0.00 0.00 0.00 3.46
2266 4041 6.463995 AATTTGGCAGCGAAATTATAGGAA 57.536 33.333 22.50 0.00 31.86 3.36
2267 4042 6.460953 GGAAATTTGGCAGCGAAATTATAGGA 60.461 38.462 23.64 0.00 32.30 2.94
2268 4043 5.691754 GGAAATTTGGCAGCGAAATTATAGG 59.308 40.000 23.64 0.00 32.30 2.57
2269 4044 6.507023 AGGAAATTTGGCAGCGAAATTATAG 58.493 36.000 23.64 0.00 32.30 1.31
2270 4045 6.463995 AGGAAATTTGGCAGCGAAATTATA 57.536 33.333 23.64 0.00 32.30 0.98
2271 4046 5.343307 AGGAAATTTGGCAGCGAAATTAT 57.657 34.783 23.64 15.53 32.30 1.28
2272 4047 4.799564 AGGAAATTTGGCAGCGAAATTA 57.200 36.364 23.64 0.00 32.30 1.40
2273 4048 3.683365 AGGAAATTTGGCAGCGAAATT 57.317 38.095 19.32 19.32 34.27 1.82
2274 4049 3.119137 GGTAGGAAATTTGGCAGCGAAAT 60.119 43.478 9.44 9.44 0.00 2.17
2275 4050 2.230266 GGTAGGAAATTTGGCAGCGAAA 59.770 45.455 4.92 4.92 0.00 3.46
2276 4051 1.816224 GGTAGGAAATTTGGCAGCGAA 59.184 47.619 0.00 0.00 0.00 4.70
2277 4052 1.004277 AGGTAGGAAATTTGGCAGCGA 59.996 47.619 0.00 0.00 0.00 4.93
2278 4053 1.401905 GAGGTAGGAAATTTGGCAGCG 59.598 52.381 0.00 0.00 0.00 5.18
2279 4054 2.728007 AGAGGTAGGAAATTTGGCAGC 58.272 47.619 0.00 0.00 0.00 5.25
2280 4055 5.946377 AGTTTAGAGGTAGGAAATTTGGCAG 59.054 40.000 0.00 0.00 0.00 4.85
2281 4056 5.887754 AGTTTAGAGGTAGGAAATTTGGCA 58.112 37.500 0.00 0.00 0.00 4.92
2282 4057 5.357314 GGAGTTTAGAGGTAGGAAATTTGGC 59.643 44.000 0.00 0.00 0.00 4.52
2283 4058 6.722328 AGGAGTTTAGAGGTAGGAAATTTGG 58.278 40.000 0.00 0.00 0.00 3.28
2284 4059 8.515414 CAAAGGAGTTTAGAGGTAGGAAATTTG 58.485 37.037 0.00 0.00 0.00 2.32
2285 4060 7.176865 GCAAAGGAGTTTAGAGGTAGGAAATTT 59.823 37.037 0.00 0.00 0.00 1.82
2286 4061 6.659668 GCAAAGGAGTTTAGAGGTAGGAAATT 59.340 38.462 0.00 0.00 0.00 1.82
2287 4062 6.181190 GCAAAGGAGTTTAGAGGTAGGAAAT 58.819 40.000 0.00 0.00 0.00 2.17
2288 4063 5.514310 GGCAAAGGAGTTTAGAGGTAGGAAA 60.514 44.000 0.00 0.00 0.00 3.13
2289 4064 4.019591 GGCAAAGGAGTTTAGAGGTAGGAA 60.020 45.833 0.00 0.00 0.00 3.36
2290 4065 3.518303 GGCAAAGGAGTTTAGAGGTAGGA 59.482 47.826 0.00 0.00 0.00 2.94
2291 4066 3.370633 GGGCAAAGGAGTTTAGAGGTAGG 60.371 52.174 0.00 0.00 0.00 3.18
2292 4067 3.679083 CGGGCAAAGGAGTTTAGAGGTAG 60.679 52.174 0.00 0.00 0.00 3.18
2293 4068 2.235402 CGGGCAAAGGAGTTTAGAGGTA 59.765 50.000 0.00 0.00 0.00 3.08
2294 4069 1.003233 CGGGCAAAGGAGTTTAGAGGT 59.997 52.381 0.00 0.00 0.00 3.85
2295 4070 1.739067 CGGGCAAAGGAGTTTAGAGG 58.261 55.000 0.00 0.00 0.00 3.69
2296 4071 1.087501 GCGGGCAAAGGAGTTTAGAG 58.912 55.000 0.00 0.00 0.00 2.43
2297 4072 0.672401 CGCGGGCAAAGGAGTTTAGA 60.672 55.000 0.00 0.00 0.00 2.10
2298 4073 0.672401 TCGCGGGCAAAGGAGTTTAG 60.672 55.000 6.13 0.00 0.00 1.85
2299 4074 0.035820 ATCGCGGGCAAAGGAGTTTA 60.036 50.000 6.13 0.00 0.00 2.01
2300 4075 0.893727 AATCGCGGGCAAAGGAGTTT 60.894 50.000 6.13 0.00 0.00 2.66
2301 4076 0.893727 AAATCGCGGGCAAAGGAGTT 60.894 50.000 6.13 0.00 0.00 3.01
2302 4077 0.893727 AAAATCGCGGGCAAAGGAGT 60.894 50.000 6.13 0.00 0.00 3.85
2303 4078 1.091537 TAAAATCGCGGGCAAAGGAG 58.908 50.000 6.13 0.00 0.00 3.69
2304 4079 1.535833 TTAAAATCGCGGGCAAAGGA 58.464 45.000 6.13 0.00 0.00 3.36
2305 4080 2.099098 AGATTAAAATCGCGGGCAAAGG 59.901 45.455 6.13 0.00 40.35 3.11
2306 4081 3.420839 AGATTAAAATCGCGGGCAAAG 57.579 42.857 6.13 0.00 40.35 2.77
2307 4082 4.261405 CCATAGATTAAAATCGCGGGCAAA 60.261 41.667 6.13 0.00 40.35 3.68
2308 4083 3.252215 CCATAGATTAAAATCGCGGGCAA 59.748 43.478 6.13 0.00 40.35 4.52
2309 4084 2.811431 CCATAGATTAAAATCGCGGGCA 59.189 45.455 6.13 0.00 40.35 5.36
2310 4085 2.812011 ACCATAGATTAAAATCGCGGGC 59.188 45.455 6.13 0.00 40.35 6.13
2311 4086 3.435671 GGACCATAGATTAAAATCGCGGG 59.564 47.826 6.13 0.00 40.35 6.13
2312 4087 4.062293 TGGACCATAGATTAAAATCGCGG 58.938 43.478 6.13 2.75 40.35 6.46
2313 4088 5.666969 TTGGACCATAGATTAAAATCGCG 57.333 39.130 0.00 0.00 40.35 5.87
2314 4089 6.206498 GGTTTGGACCATAGATTAAAATCGC 58.794 40.000 0.00 0.00 45.77 4.58
2329 4104 2.673258 TCCCTCTTTTTGGTTTGGACC 58.327 47.619 0.00 0.00 46.71 4.46
2374 4149 1.087202 GTACGAATGCACATCGGCCA 61.087 55.000 22.95 8.98 44.32 5.36
2447 4227 8.888579 ATTACTTAAAAGGATGTGTATCTCCG 57.111 34.615 0.00 0.00 36.62 4.63
2501 4281 9.151471 GCAACACACATCTTTATCTTCTAGTAA 57.849 33.333 0.00 0.00 0.00 2.24
2502 4282 7.764443 GGCAACACACATCTTTATCTTCTAGTA 59.236 37.037 0.00 0.00 0.00 1.82
2503 4283 6.595716 GGCAACACACATCTTTATCTTCTAGT 59.404 38.462 0.00 0.00 0.00 2.57
2504 4284 6.595326 TGGCAACACACATCTTTATCTTCTAG 59.405 38.462 0.00 0.00 46.17 2.43
2505 4285 6.472016 TGGCAACACACATCTTTATCTTCTA 58.528 36.000 0.00 0.00 46.17 2.10
2506 4286 5.316167 TGGCAACACACATCTTTATCTTCT 58.684 37.500 0.00 0.00 46.17 2.85
2585 4365 8.585471 ATTGAGTTGGAATGACAGTGATATTT 57.415 30.769 0.00 0.00 0.00 1.40
2594 4374 5.412594 GCTGAACTATTGAGTTGGAATGACA 59.587 40.000 0.00 0.00 46.23 3.58
2609 4389 6.166982 GTTCTTGTAAGAGTGGCTGAACTAT 58.833 40.000 0.00 0.00 36.22 2.12
2657 4437 7.039504 ACAAATGACATATTTGTGCTCTCCTTT 60.040 33.333 14.98 0.00 46.67 3.11
2707 4487 7.428020 CATTTTTCAATGTTTCCTCTCTGTCA 58.572 34.615 0.00 0.00 35.86 3.58
2708 4488 6.364435 GCATTTTTCAATGTTTCCTCTCTGTC 59.636 38.462 0.00 0.00 41.84 3.51
2722 4502 8.042515 ACATGCATACCTAAAGCATTTTTCAAT 58.957 29.630 0.00 0.00 45.98 2.57
2739 4519 1.217882 GGTACGGAGCACATGCATAC 58.782 55.000 6.64 3.34 45.16 2.39
2754 4534 7.122055 TCAATGGAAAATGTGGATTACTGGTAC 59.878 37.037 0.00 0.00 0.00 3.34
2807 4611 1.052124 TCAACTTCCCACTCCACGGT 61.052 55.000 0.00 0.00 0.00 4.83
2808 4612 0.320771 CTCAACTTCCCACTCCACGG 60.321 60.000 0.00 0.00 0.00 4.94
2862 5107 6.069684 ACTCAAAGTGCTCTCATTTTCTTG 57.930 37.500 0.00 0.00 30.96 3.02
2873 5118 6.647067 ACTTCAACATACTACTCAAAGTGCTC 59.353 38.462 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.