Multiple sequence alignment - TraesCS2B01G405900

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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 TraesCS2B01G405900 chr2B 100.000 5409 0 0 1 5409 574708081 574713489 0.000000e+00 9989.0
1 TraesCS2B01G405900 chr2B 85.944 1181 133 17 4066 5225 575133619 575134787 0.000000e+00 1230.0
2 TraesCS2B01G405900 chr2B 88.679 901 67 11 437 1333 575115001 575115870 0.000000e+00 1066.0
3 TraesCS2B01G405900 chr2B 88.469 503 57 1 920 1421 574661015 574661517 1.670000e-169 606.0
4 TraesCS2B01G405900 chr2B 95.527 313 12 2 2343 2655 574662779 574663089 2.910000e-137 499.0
5 TraesCS2B01G405900 chr2B 84.571 525 48 7 1564 2082 574661417 574661914 1.750000e-134 490.0
6 TraesCS2B01G405900 chr2B 93.396 318 20 1 5091 5407 574670723 574671040 2.280000e-128 470.0
7 TraesCS2B01G405900 chr2B 95.798 238 10 0 2645 2882 574663110 574663347 8.500000e-103 385.0
8 TraesCS2B01G405900 chr2B 93.333 180 8 2 2165 2343 118465813 118465637 4.150000e-66 263.0
9 TraesCS2B01G405900 chr2B 82.105 285 44 5 3073 3353 575115951 575116232 2.520000e-58 237.0
10 TraesCS2B01G405900 chr2B 89.474 171 16 2 631 800 574660667 574660836 1.180000e-51 215.0
11 TraesCS2B01G405900 chr2B 80.000 330 25 18 3335 3652 575116687 575116987 7.100000e-49 206.0
12 TraesCS2B01G405900 chr2B 90.210 143 12 2 3304 3444 574663964 574664106 9.250000e-43 185.0
13 TraesCS2B01G405900 chr2B 98.571 70 1 0 2081 2150 574662694 574662763 2.050000e-24 124.0
14 TraesCS2B01G405900 chr2D 92.689 1190 33 8 2892 4071 490568592 490569737 0.000000e+00 1666.0
15 TraesCS2B01G405900 chr2D 90.472 1270 89 16 825 2070 490564809 490566070 0.000000e+00 1646.0
16 TraesCS2B01G405900 chr2D 95.207 918 36 5 4072 4985 490569813 490570726 0.000000e+00 1445.0
17 TraesCS2B01G405900 chr2D 95.385 780 29 3 4072 4847 490643353 490644129 0.000000e+00 1234.0
18 TraesCS2B01G405900 chr2D 85.739 1171 136 16 4073 5222 490645510 490646670 0.000000e+00 1208.0
19 TraesCS2B01G405900 chr2D 89.958 946 61 12 406 1333 490618219 490619148 0.000000e+00 1190.0
20 TraesCS2B01G405900 chr2D 95.185 540 24 2 2343 2882 490566796 490567333 0.000000e+00 852.0
21 TraesCS2B01G405900 chr2D 91.902 531 25 4 3542 4071 490642764 490643277 0.000000e+00 726.0
22 TraesCS2B01G405900 chr2D 93.147 394 25 2 5015 5407 490570728 490571120 1.310000e-160 577.0
23 TraesCS2B01G405900 chr2D 86.364 550 50 14 2906 3448 490620653 490621184 1.310000e-160 577.0
24 TraesCS2B01G405900 chr2D 86.744 430 50 7 375 800 490564315 490564741 6.340000e-129 472.0
25 TraesCS2B01G405900 chr2D 85.539 408 47 10 3674 4071 490645028 490645433 3.010000e-112 416.0
26 TraesCS2B01G405900 chr2D 84.887 397 44 10 4190 4577 490129425 490129036 2.360000e-103 387.0
27 TraesCS2B01G405900 chr2D 91.579 190 13 2 2155 2343 101884253 101884066 5.370000e-65 259.0
28 TraesCS2B01G405900 chr2D 92.308 182 11 2 2162 2343 175757121 175757299 6.950000e-64 255.0
29 TraesCS2B01G405900 chr2D 91.935 186 10 5 2162 2345 534482805 534482987 6.950000e-64 255.0
30 TraesCS2B01G405900 chr2D 93.007 143 8 2 3304 3444 490567950 490568092 1.970000e-49 207.0
31 TraesCS2B01G405900 chr2D 80.077 261 41 5 3073 3330 490619217 490619469 3.330000e-42 183.0
32 TraesCS2B01G405900 chr2D 96.970 99 3 0 3449 3547 490621157 490621255 3.350000e-37 167.0
33 TraesCS2B01G405900 chr2D 83.146 178 16 10 3672 3849 490568339 490568502 3.370000e-32 150.0
34 TraesCS2B01G405900 chr2D 72.093 387 85 17 1072 1454 490131995 490131628 1.600000e-15 95.3
35 TraesCS2B01G405900 chr2D 85.507 69 7 2 1851 1919 490131012 490130947 9.720000e-08 69.4
36 TraesCS2B01G405900 chr2D 79.775 89 15 3 3735 3822 490130013 490129927 1.630000e-05 62.1
37 TraesCS2B01G405900 chr2A 89.825 1258 105 11 825 2061 634091433 634092688 0.000000e+00 1592.0
38 TraesCS2B01G405900 chr2A 94.310 949 41 7 4237 5184 634104741 634105677 0.000000e+00 1441.0
39 TraesCS2B01G405900 chr2A 91.019 913 50 10 432 1333 634598673 634599564 0.000000e+00 1203.0
40 TraesCS2B01G405900 chr2A 85.702 1161 141 17 4072 5222 634603145 634604290 0.000000e+00 1201.0
41 TraesCS2B01G405900 chr2A 95.722 561 15 3 2892 3445 634099255 634099813 0.000000e+00 894.0
42 TraesCS2B01G405900 chr2A 93.095 391 25 2 2493 2882 634097604 634097993 6.080000e-159 571.0
43 TraesCS2B01G405900 chr2A 95.796 333 13 1 1 332 634598127 634598459 2.220000e-148 536.0
44 TraesCS2B01G405900 chr2A 87.879 429 43 7 375 800 634090943 634091365 3.760000e-136 496.0
45 TraesCS2B01G405900 chr2A 94.554 202 8 3 2343 2543 634097418 634097617 5.260000e-80 309.0
46 TraesCS2B01G405900 chr2A 91.748 206 17 0 3865 4070 634602863 634603068 2.470000e-73 287.0
47 TraesCS2B01G405900 chr2A 80.978 368 25 14 3304 3656 634098609 634098946 3.230000e-62 250.0
48 TraesCS2B01G405900 chr2A 87.356 174 21 1 3674 3847 634602637 634602809 1.190000e-46 198.0
49 TraesCS2B01G405900 chr2A 83.799 179 14 11 3672 3849 634099000 634099164 7.250000e-34 156.0
50 TraesCS2B01G405900 chr2A 98.718 78 1 0 2081 2158 634097339 634097416 7.310000e-29 139.0
51 TraesCS2B01G405900 chr2A 92.135 89 7 0 361 449 634598459 634598547 5.690000e-25 126.0
52 TraesCS2B01G405900 chr2A 80.124 161 26 5 1564 1718 634091944 634092104 1.230000e-21 115.0
53 TraesCS2B01G405900 chr2A 91.549 71 6 0 3584 3654 634602513 634602583 1.240000e-16 99.0
54 TraesCS2B01G405900 chr7D 82.852 554 65 11 2343 2882 135433796 135434333 2.280000e-128 470.0
55 TraesCS2B01G405900 chr5A 83.176 529 74 13 2358 2882 452419469 452419986 2.280000e-128 470.0
56 TraesCS2B01G405900 chr5A 82.987 529 75 13 2358 2882 452415614 452416131 1.060000e-126 464.0
57 TraesCS2B01G405900 chr5A 82.987 529 75 13 2358 2882 452423333 452423850 1.060000e-126 464.0
58 TraesCS2B01G405900 chr5A 93.913 115 6 1 45 158 82871487 82871373 7.200000e-39 172.0
59 TraesCS2B01G405900 chr6B 92.818 181 12 1 2162 2342 176254525 176254346 1.490000e-65 261.0
60 TraesCS2B01G405900 chr5D 92.391 184 11 2 2162 2343 429353716 429353534 5.370000e-65 259.0
61 TraesCS2B01G405900 chr5D 89.510 143 12 3 45 186 6108057 6107917 1.550000e-40 178.0
62 TraesCS2B01G405900 chr5D 93.043 115 7 1 45 158 88878609 88878495 3.350000e-37 167.0
63 TraesCS2B01G405900 chr3D 92.350 183 13 1 2162 2343 517482287 517482469 5.370000e-65 259.0
64 TraesCS2B01G405900 chr3D 91.176 136 11 1 42 176 382002237 382002372 3.330000e-42 183.0
65 TraesCS2B01G405900 chr4D 89.899 198 12 5 2153 2345 29656462 29656656 1.160000e-61 248.0
66 TraesCS2B01G405900 chr1A 89.163 203 17 3 2148 2345 557897498 557897700 1.160000e-61 248.0
67 TraesCS2B01G405900 chrUn 83.406 229 29 4 4074 4294 259672391 259672164 2.550000e-48 204.0
68 TraesCS2B01G405900 chr5B 93.220 118 7 1 42 158 95512943 95513060 7.200000e-39 172.0


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 TraesCS2B01G405900 chr2B 574708081 574713489 5408 False 9989.000000 9989 100.000000 1 5409 1 chr2B.!!$F2 5408
1 TraesCS2B01G405900 chr2B 575133619 575134787 1168 False 1230.000000 1230 85.944000 4066 5225 1 chr2B.!!$F3 1159
2 TraesCS2B01G405900 chr2B 575115001 575116987 1986 False 503.000000 1066 83.594667 437 3652 3 chr2B.!!$F5 3215
3 TraesCS2B01G405900 chr2B 574660667 574664106 3439 False 357.714286 606 91.802857 631 3444 7 chr2B.!!$F4 2813
4 TraesCS2B01G405900 chr2D 490642764 490646670 3906 False 896.000000 1234 89.641250 3542 5222 4 chr2D.!!$F5 1680
5 TraesCS2B01G405900 chr2D 490564315 490571120 6805 False 876.875000 1666 91.199625 375 5407 8 chr2D.!!$F3 5032
6 TraesCS2B01G405900 chr2D 490618219 490621255 3036 False 529.250000 1190 88.342250 406 3547 4 chr2D.!!$F4 3141
7 TraesCS2B01G405900 chr2A 634104741 634105677 936 False 1441.000000 1441 94.310000 4237 5184 1 chr2A.!!$F1 947
8 TraesCS2B01G405900 chr2A 634090943 634092688 1745 False 734.333333 1592 85.942667 375 2061 3 chr2A.!!$F2 1686
9 TraesCS2B01G405900 chr2A 634598127 634604290 6163 False 521.428571 1203 90.757857 1 5222 7 chr2A.!!$F4 5221
10 TraesCS2B01G405900 chr2A 634097339 634099813 2474 False 386.500000 894 91.144333 2081 3849 6 chr2A.!!$F3 1768
11 TraesCS2B01G405900 chr7D 135433796 135434333 537 False 470.000000 470 82.852000 2343 2882 1 chr7D.!!$F1 539
12 TraesCS2B01G405900 chr5A 452415614 452423850 8236 False 466.000000 470 83.050000 2358 2882 3 chr5A.!!$F1 524

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
151 153 0.036010 ATTGGGTCTGCTTCCGTCTG 60.036 55.0 0.00 0.0 0.00 3.51 F
354 356 0.747852 GCTAGACCAGTAGGACTGCC 59.252 60.0 0.00 0.0 44.63 4.85 F
358 360 0.905357 GACCAGTAGGACTGCCATGT 59.095 55.0 0.89 0.0 44.63 3.21 F
974 1216 1.011968 TCGTCCGTTTCCATTCGCTG 61.012 55.0 0.00 0.0 0.00 5.18 F
2689 4471 0.235926 GAACTCTGTGCGGAAACAGC 59.764 55.0 6.43 0.0 45.93 4.40 F
2893 8541 0.250234 GCAGCAGATGGTCACTGGTA 59.750 55.0 0.00 0.0 42.85 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1821 0.542333 TTGTCACCAACTGGAACCGA 59.458 50.000 1.86 0.0 38.94 4.69 R
1931 2201 1.299541 AGCAGTGTTCAGTGTTTCCG 58.700 50.000 9.02 0.0 0.00 4.30 R
2073 2351 2.173669 CCGGGCACTCGCATACTTG 61.174 63.158 0.00 0.0 41.24 3.16 R
2898 8884 2.311542 ACCCCCAGATTAATTGCTGACA 59.688 45.455 5.87 0.0 34.06 3.58 R
3993 11866 1.063616 CTCAAAGCATGACATGGCTCG 59.936 52.381 17.03 9.3 40.01 5.03 R
4767 12735 1.024579 CCGGGTTTTCGATGGACAGG 61.025 60.000 0.00 0.0 0.00 4.00 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
99 101 3.103742 GAGAGATGTCCCTCCTGAAACT 58.896 50.000 0.00 0.00 33.76 2.66
108 110 1.271543 CCTCCTGAAACTGTGGATGCA 60.272 52.381 0.00 0.00 0.00 3.96
125 127 5.246656 TGGATGCAATGAAGAGGAATGTTTT 59.753 36.000 0.00 0.00 0.00 2.43
146 148 1.133668 AGGCATATTGGGTCTGCTTCC 60.134 52.381 0.00 0.00 36.18 3.46
151 153 0.036010 ATTGGGTCTGCTTCCGTCTG 60.036 55.000 0.00 0.00 0.00 3.51
165 167 1.683319 CCGTCTGATCAGTGAGAGGGA 60.683 57.143 21.92 0.00 43.58 4.20
193 195 0.905337 GCCTGGTGTACTGAGAGGGT 60.905 60.000 0.00 0.00 0.00 4.34
295 297 5.649782 TTTGAAGCATCAGGAGGATTTTC 57.350 39.130 0.00 0.00 36.78 2.29
345 347 7.661536 TTTGAGTATCTATTGCTAGACCAGT 57.338 36.000 0.00 0.00 36.81 4.00
347 349 7.987750 TGAGTATCTATTGCTAGACCAGTAG 57.012 40.000 0.00 0.00 36.81 2.57
348 350 6.943146 TGAGTATCTATTGCTAGACCAGTAGG 59.057 42.308 0.00 0.00 36.81 3.18
349 351 7.092748 AGTATCTATTGCTAGACCAGTAGGA 57.907 40.000 0.00 0.00 36.81 2.94
350 352 6.943718 AGTATCTATTGCTAGACCAGTAGGAC 59.056 42.308 0.00 0.00 36.81 3.85
354 356 0.747852 GCTAGACCAGTAGGACTGCC 59.252 60.000 0.00 0.00 44.63 4.85
355 357 1.960471 GCTAGACCAGTAGGACTGCCA 60.960 57.143 0.00 0.00 44.63 4.92
356 358 2.672098 CTAGACCAGTAGGACTGCCAT 58.328 52.381 0.89 0.00 44.63 4.40
357 359 1.198713 AGACCAGTAGGACTGCCATG 58.801 55.000 0.89 0.00 44.63 3.66
358 360 0.905357 GACCAGTAGGACTGCCATGT 59.095 55.000 0.89 0.00 44.63 3.21
359 361 2.108168 GACCAGTAGGACTGCCATGTA 58.892 52.381 0.89 0.00 44.63 2.29
360 362 2.700897 GACCAGTAGGACTGCCATGTAT 59.299 50.000 0.89 0.00 44.63 2.29
759 925 5.964958 TGTTAGCCTTCCAGAAAAATCAG 57.035 39.130 0.00 0.00 0.00 2.90
871 1097 2.257409 CTGGAGTGTTCCCATCCCGG 62.257 65.000 0.00 0.00 43.33 5.73
898 1124 1.152030 TCAACACTCCCCTCTGGCT 60.152 57.895 0.00 0.00 0.00 4.75
974 1216 1.011968 TCGTCCGTTTCCATTCGCTG 61.012 55.000 0.00 0.00 0.00 5.18
1443 1685 2.037136 CAGCGTTGGGAGCAAGGAG 61.037 63.158 0.00 0.00 37.01 3.69
1461 1703 2.204090 AAGCGGAAGGGGAAGGGA 60.204 61.111 0.00 0.00 0.00 4.20
1507 1749 4.185413 AATCTCGTGTGCGCGATT 57.815 50.000 12.10 1.05 44.52 3.34
1508 1750 3.339061 AATCTCGTGTGCGCGATTA 57.661 47.368 12.10 0.00 46.52 1.75
1530 1772 2.257980 CCTGCGCATCGGCAAAAA 59.742 55.556 12.24 0.00 43.39 1.94
1543 1785 2.482864 GGCAAAAAGTGTTGGTGATGG 58.517 47.619 0.00 0.00 0.00 3.51
1567 1809 1.283736 CAAGGTTACACGATACGGGC 58.716 55.000 0.00 0.00 31.12 6.13
1579 1821 3.873679 TACGGGCAGGACGAGGTGT 62.874 63.158 0.00 0.00 34.93 4.16
1696 1938 2.913617 GGGAAGAAGGAGAAGGGAAAGA 59.086 50.000 0.00 0.00 0.00 2.52
1748 1990 2.375766 CGCTGAAGTCTCGTGTGGC 61.376 63.158 0.00 0.00 0.00 5.01
1757 1999 1.811266 CTCGTGTGGCCGATTCCAG 60.811 63.158 0.00 0.00 36.67 3.86
1796 2042 2.674796 AAATCGTTTCTCCCCTCTCG 57.325 50.000 0.00 0.00 0.00 4.04
1822 2069 7.672738 AGTTAAATATGTGTCGCGTTTCTAAG 58.327 34.615 5.77 0.00 0.00 2.18
1828 2075 1.269883 TGTCGCGTTTCTAAGGCAGAA 60.270 47.619 5.77 0.00 42.10 3.02
1834 2081 4.143597 CGCGTTTCTAAGGCAGAATATACG 60.144 45.833 0.00 6.13 43.27 3.06
1836 2083 4.982916 CGTTTCTAAGGCAGAATATACGCT 59.017 41.667 0.00 0.00 42.88 5.07
1881 2128 5.188751 ACAGGGTCAGAAGGAGAAGAATAAG 59.811 44.000 0.00 0.00 0.00 1.73
1895 2144 7.120726 GGAGAAGAATAAGGAACGGAAAAATGA 59.879 37.037 0.00 0.00 0.00 2.57
2033 2307 4.821805 ACTAGAGATGTGGTTTGTGGTTTG 59.178 41.667 0.00 0.00 0.00 2.93
2073 2351 7.363094 GGGTAGATATGCCACATAAGAGTCTAC 60.363 44.444 13.08 13.08 36.45 2.59
2105 3797 1.984288 GCCCGGCTGGATTAAGAGGT 61.984 60.000 15.09 0.00 37.49 3.85
2159 3857 6.285224 TCGATTTGACAAGTAGAAAACTGGA 58.715 36.000 0.00 0.00 38.88 3.86
2160 3858 6.423905 TCGATTTGACAAGTAGAAAACTGGAG 59.576 38.462 0.00 0.00 38.88 3.86
2161 3859 5.751243 TTTGACAAGTAGAAAACTGGAGC 57.249 39.130 0.00 0.00 38.88 4.70
2162 3860 4.415881 TGACAAGTAGAAAACTGGAGCA 57.584 40.909 0.00 0.00 38.88 4.26
2163 3861 4.380531 TGACAAGTAGAAAACTGGAGCAG 58.619 43.478 0.00 0.00 38.88 4.24
2176 3874 4.973168 ACTGGAGCAGTTTGTCTAATTCA 58.027 39.130 0.00 0.00 42.59 2.57
2177 3875 4.757149 ACTGGAGCAGTTTGTCTAATTCAC 59.243 41.667 0.00 0.00 42.59 3.18
2178 3876 4.713553 TGGAGCAGTTTGTCTAATTCACA 58.286 39.130 0.00 0.00 0.00 3.58
2179 3877 5.316167 TGGAGCAGTTTGTCTAATTCACAT 58.684 37.500 0.00 0.00 0.00 3.21
2180 3878 5.181811 TGGAGCAGTTTGTCTAATTCACATG 59.818 40.000 0.00 0.00 0.00 3.21
2181 3879 5.182001 GGAGCAGTTTGTCTAATTCACATGT 59.818 40.000 0.00 0.00 0.00 3.21
2182 3880 6.371548 GGAGCAGTTTGTCTAATTCACATGTA 59.628 38.462 0.00 0.00 0.00 2.29
2183 3881 7.369803 AGCAGTTTGTCTAATTCACATGTAG 57.630 36.000 0.00 0.00 0.00 2.74
2184 3882 7.161404 AGCAGTTTGTCTAATTCACATGTAGA 58.839 34.615 0.00 0.00 0.00 2.59
2185 3883 7.826252 AGCAGTTTGTCTAATTCACATGTAGAT 59.174 33.333 0.00 0.00 0.00 1.98
2186 3884 7.907045 GCAGTTTGTCTAATTCACATGTAGATG 59.093 37.037 0.00 0.00 35.49 2.90
2187 3885 8.939929 CAGTTTGTCTAATTCACATGTAGATGT 58.060 33.333 0.00 0.00 44.08 3.06
2188 3886 9.507329 AGTTTGTCTAATTCACATGTAGATGTT 57.493 29.630 2.09 0.00 41.12 2.71
2213 3911 7.849804 TTTTAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
2214 3912 4.414337 AAGGATGTCACATCTAAGCTCC 57.586 45.455 17.46 0.18 0.00 4.70
2215 3913 2.703007 AGGATGTCACATCTAAGCTCCC 59.297 50.000 17.46 0.00 0.00 4.30
2216 3914 2.435805 GGATGTCACATCTAAGCTCCCA 59.564 50.000 17.46 0.00 0.00 4.37
2217 3915 3.072184 GGATGTCACATCTAAGCTCCCAT 59.928 47.826 17.46 0.00 0.00 4.00
2218 3916 4.284490 GGATGTCACATCTAAGCTCCCATA 59.716 45.833 17.46 0.00 0.00 2.74
2219 3917 5.221722 GGATGTCACATCTAAGCTCCCATAA 60.222 44.000 17.46 0.00 0.00 1.90
2220 3918 5.692115 TGTCACATCTAAGCTCCCATAAA 57.308 39.130 0.00 0.00 0.00 1.40
2221 3919 6.252599 TGTCACATCTAAGCTCCCATAAAT 57.747 37.500 0.00 0.00 0.00 1.40
2222 3920 7.373617 TGTCACATCTAAGCTCCCATAAATA 57.626 36.000 0.00 0.00 0.00 1.40
2223 3921 7.977818 TGTCACATCTAAGCTCCCATAAATAT 58.022 34.615 0.00 0.00 0.00 1.28
2224 3922 9.100197 TGTCACATCTAAGCTCCCATAAATATA 57.900 33.333 0.00 0.00 0.00 0.86
2230 3928 9.765795 ATCTAAGCTCCCATAAATATATAACGC 57.234 33.333 0.00 0.00 0.00 4.84
2231 3929 8.755028 TCTAAGCTCCCATAAATATATAACGCA 58.245 33.333 0.00 0.00 0.00 5.24
2232 3930 7.849804 AAGCTCCCATAAATATATAACGCAG 57.150 36.000 0.00 0.00 0.00 5.18
2233 3931 5.817816 AGCTCCCATAAATATATAACGCAGC 59.182 40.000 0.00 0.00 0.00 5.25
2234 3932 5.584649 GCTCCCATAAATATATAACGCAGCA 59.415 40.000 0.00 0.00 0.00 4.41
2235 3933 6.093495 GCTCCCATAAATATATAACGCAGCAA 59.907 38.462 0.00 0.00 0.00 3.91
2236 3934 7.372451 TCCCATAAATATATAACGCAGCAAC 57.628 36.000 0.00 0.00 0.00 4.17
2237 3935 6.937465 TCCCATAAATATATAACGCAGCAACA 59.063 34.615 0.00 0.00 0.00 3.33
2238 3936 7.445707 TCCCATAAATATATAACGCAGCAACAA 59.554 33.333 0.00 0.00 0.00 2.83
2239 3937 7.750458 CCCATAAATATATAACGCAGCAACAAG 59.250 37.037 0.00 0.00 0.00 3.16
2240 3938 8.503196 CCATAAATATATAACGCAGCAACAAGA 58.497 33.333 0.00 0.00 0.00 3.02
2241 3939 9.877137 CATAAATATATAACGCAGCAACAAGAA 57.123 29.630 0.00 0.00 0.00 2.52
2243 3941 8.614994 AAATATATAACGCAGCAACAAGAAAC 57.385 30.769 0.00 0.00 0.00 2.78
2244 3942 3.980646 ATAACGCAGCAACAAGAAACA 57.019 38.095 0.00 0.00 0.00 2.83
2245 3943 2.645730 AACGCAGCAACAAGAAACAA 57.354 40.000 0.00 0.00 0.00 2.83
2246 3944 2.645730 ACGCAGCAACAAGAAACAAA 57.354 40.000 0.00 0.00 0.00 2.83
2247 3945 2.953020 ACGCAGCAACAAGAAACAAAA 58.047 38.095 0.00 0.00 0.00 2.44
2248 3946 3.321497 ACGCAGCAACAAGAAACAAAAA 58.679 36.364 0.00 0.00 0.00 1.94
2287 3985 5.968528 AAAGACCACAAACAAAGTGTACA 57.031 34.783 0.00 0.00 35.24 2.90
2288 3986 6.524101 AAAGACCACAAACAAAGTGTACAT 57.476 33.333 0.00 0.00 35.24 2.29
2289 3987 5.751243 AGACCACAAACAAAGTGTACATC 57.249 39.130 0.00 0.00 35.24 3.06
2290 3988 5.189928 AGACCACAAACAAAGTGTACATCA 58.810 37.500 0.00 0.00 35.24 3.07
2291 3989 5.296780 AGACCACAAACAAAGTGTACATCAG 59.703 40.000 0.00 0.00 35.24 2.90
2292 3990 4.202010 ACCACAAACAAAGTGTACATCAGC 60.202 41.667 0.00 0.00 35.24 4.26
2293 3991 4.036734 CCACAAACAAAGTGTACATCAGCT 59.963 41.667 0.00 0.00 35.24 4.24
2294 3992 5.450412 CCACAAACAAAGTGTACATCAGCTT 60.450 40.000 0.00 0.00 35.24 3.74
2295 3993 6.238621 CCACAAACAAAGTGTACATCAGCTTA 60.239 38.462 0.00 0.00 35.24 3.09
2296 3994 6.852853 CACAAACAAAGTGTACATCAGCTTAG 59.147 38.462 0.00 0.00 32.44 2.18
2297 3995 6.765989 ACAAACAAAGTGTACATCAGCTTAGA 59.234 34.615 0.00 0.00 0.00 2.10
2298 3996 7.445402 ACAAACAAAGTGTACATCAGCTTAGAT 59.555 33.333 0.00 0.00 0.00 1.98
2311 4009 8.877808 CATCAGCTTAGATGTGACATAACTAA 57.122 34.615 0.00 2.45 40.35 2.24
2312 4010 8.976471 CATCAGCTTAGATGTGACATAACTAAG 58.024 37.037 20.91 20.91 40.35 2.18
2313 4011 8.067751 TCAGCTTAGATGTGACATAACTAAGT 57.932 34.615 23.60 14.11 40.82 2.24
2314 4012 8.191446 TCAGCTTAGATGTGACATAACTAAGTC 58.809 37.037 23.60 18.48 40.82 3.01
2315 4013 7.976175 CAGCTTAGATGTGACATAACTAAGTCA 59.024 37.037 23.60 0.00 42.06 3.41
2340 4038 5.916661 TCTAGATGTGTCCTAAACAGACC 57.083 43.478 0.00 0.00 38.97 3.85
2341 4039 3.983044 AGATGTGTCCTAAACAGACCC 57.017 47.619 0.00 0.00 38.97 4.46
2462 4173 1.546923 TGCATTGCAAGTGAAGGGATG 59.453 47.619 9.33 0.00 34.76 3.51
2546 4296 7.445402 CCAGAAAAGAATTCTGAACTGAAGGTA 59.555 37.037 24.58 0.00 46.57 3.08
2633 4383 0.663153 GTGCCGTCAAAAGTCTGCTT 59.337 50.000 0.00 0.00 36.30 3.91
2689 4471 0.235926 GAACTCTGTGCGGAAACAGC 59.764 55.000 6.43 0.00 45.93 4.40
2705 4488 5.470845 AAACAGCGATAAATAGTGAGCAC 57.529 39.130 0.00 0.00 0.00 4.40
2741 4524 7.186804 AGAAAACAATTTCAGTCTACACAACG 58.813 34.615 4.34 0.00 46.03 4.10
2756 4539 9.726232 GTCTACACAACGTAAATATCATAGTCA 57.274 33.333 0.00 0.00 0.00 3.41
2839 8486 9.013490 CACAACATTTCTTCTGACTGTAAAAAG 57.987 33.333 0.00 0.00 0.00 2.27
2856 8504 4.759205 GCCGGCACCAATTCCCCT 62.759 66.667 24.80 0.00 0.00 4.79
2861 8509 1.571955 GGCACCAATTCCCCTTTGAT 58.428 50.000 0.00 0.00 0.00 2.57
2882 8530 3.095332 TCTCACAGTTCTAGCAGCAGAT 58.905 45.455 0.00 0.00 0.00 2.90
2885 8533 1.905215 ACAGTTCTAGCAGCAGATGGT 59.095 47.619 0.00 0.00 43.56 3.55
2886 8534 2.093764 ACAGTTCTAGCAGCAGATGGTC 60.094 50.000 0.00 0.00 40.89 4.02
2888 8536 2.093764 AGTTCTAGCAGCAGATGGTCAC 60.094 50.000 0.00 0.00 40.89 3.67
2889 8537 1.857965 TCTAGCAGCAGATGGTCACT 58.142 50.000 0.00 0.00 40.89 3.41
2890 8538 1.479730 TCTAGCAGCAGATGGTCACTG 59.520 52.381 0.00 0.00 40.89 3.66
2892 8540 1.002868 GCAGCAGATGGTCACTGGT 60.003 57.895 0.00 0.00 45.03 4.00
2893 8541 0.250234 GCAGCAGATGGTCACTGGTA 59.750 55.000 0.00 0.00 42.85 3.25
2898 8884 5.371526 CAGCAGATGGTCACTGGTATATTT 58.628 41.667 0.00 0.00 42.85 1.40
2899 8885 5.237996 CAGCAGATGGTCACTGGTATATTTG 59.762 44.000 0.00 0.00 42.85 2.32
2916 8902 8.299570 GGTATATTTGTCAGCAATTAATCTGGG 58.700 37.037 4.76 0.00 34.18 4.45
2920 8906 2.952310 GTCAGCAATTAATCTGGGGGTC 59.048 50.000 4.76 0.00 0.00 4.46
2935 8921 2.835764 GGGGGTCGCTGGTATCAATATA 59.164 50.000 0.00 0.00 0.00 0.86
2975 8970 4.946478 ATGGAGTATACCTTGTCTCAGC 57.054 45.455 0.00 0.00 0.00 4.26
3000 8995 7.068226 GCAAGTAGCCCATTTAGGATTTAAGAA 59.932 37.037 0.00 0.00 41.22 2.52
3137 10904 1.900585 GCGCTGAAATCTCGTGTGCA 61.901 55.000 0.00 0.00 35.53 4.57
3255 11052 5.529060 TGTTACATACACATGTGCAAACAGA 59.471 36.000 25.68 4.11 45.17 3.41
3382 11182 7.416964 TTGTGAAGAGGAAAAGGAAATCAAA 57.583 32.000 0.00 0.00 0.00 2.69
3439 11239 6.152661 TCGGTGAGAATTTCCTATGCATTTTT 59.847 34.615 3.54 0.00 0.00 1.94
3461 11261 4.989279 TTTCAGCCAGAATTTCCTATGC 57.011 40.909 0.00 0.00 35.83 3.14
3462 11262 3.650281 TCAGCCAGAATTTCCTATGCA 57.350 42.857 0.00 0.00 0.00 3.96
3463 11263 4.174704 TCAGCCAGAATTTCCTATGCAT 57.825 40.909 3.79 3.79 0.00 3.96
3464 11264 4.539726 TCAGCCAGAATTTCCTATGCATT 58.460 39.130 3.54 0.00 0.00 3.56
3559 11359 9.154632 TGGTAGATGTATCTTGTACCACATAAT 57.845 33.333 9.77 0.00 37.86 1.28
3626 11426 3.609853 TGATGCTTCCTACAACATGTCC 58.390 45.455 0.00 0.00 0.00 4.02
3677 11511 5.975344 CACATAAACATGGAGCATCATTCAC 59.025 40.000 0.00 0.00 36.25 3.18
3703 11537 4.210955 TCAAAGTTGAATTTTGGATTGCGC 59.789 37.500 12.27 0.00 36.44 6.09
3725 11559 3.096092 GTGGGCCTTATTCATTGGAACA 58.904 45.455 4.53 0.00 35.46 3.18
3993 11866 0.691078 TATGGAGGGAGGACTGGCAC 60.691 60.000 0.00 0.00 0.00 5.01
4078 12026 6.753913 TGGATGGAGCAAAATACTCTCTAT 57.246 37.500 0.00 0.00 34.46 1.98
4115 12063 6.153340 ACATATTAAACTCATGGTGCTTTGCT 59.847 34.615 0.00 0.00 0.00 3.91
4141 12089 0.875059 GGCACACTTTGACTAGGCAC 59.125 55.000 0.00 0.00 0.00 5.01
4235 12188 5.730550 ACATGTTCGCTTCTAACCAATCTA 58.269 37.500 0.00 0.00 0.00 1.98
4335 12288 0.249868 TTGTCGCACTTCCAGACTGG 60.250 55.000 15.99 15.99 39.43 4.00
4336 12289 2.029844 GTCGCACTTCCAGACTGGC 61.030 63.158 17.33 3.58 37.47 4.85
4337 12290 2.031012 CGCACTTCCAGACTGGCA 59.969 61.111 17.33 4.94 37.47 4.92
4598 12552 5.469479 AGGTTTTTCGAGTAATTGGCAATG 58.531 37.500 14.47 0.48 0.00 2.82
4599 12553 4.091365 GGTTTTTCGAGTAATTGGCAATGC 59.909 41.667 14.47 9.99 0.00 3.56
4629 12583 7.375053 GCCTTTCAATTACAAGAACATGGTTA 58.625 34.615 0.00 0.00 0.00 2.85
4680 12648 4.487714 TTGGGAAGTATAGTTGAGGCAG 57.512 45.455 0.00 0.00 0.00 4.85
4684 12652 2.990066 AGTATAGTTGAGGCAGGTGC 57.010 50.000 0.00 0.00 41.14 5.01
4689 12657 0.987294 AGTTGAGGCAGGTGCACTAT 59.013 50.000 17.98 2.70 44.36 2.12
4702 12670 1.291132 GCACTATTCGTGAAGGAGGC 58.709 55.000 0.00 0.00 46.81 4.70
4767 12735 4.498009 CGCCACAACCTGATAAATCATTCC 60.498 45.833 0.00 0.00 36.02 3.01
4776 12744 5.709164 CCTGATAAATCATTCCCTGTCCATC 59.291 44.000 0.00 0.00 36.02 3.51
4832 12800 7.451731 TTCCATAGGGTGTAGATCAAATTCT 57.548 36.000 0.00 0.00 34.93 2.40
4945 15079 0.036732 GGGACACATGGCAGTCTTGA 59.963 55.000 12.81 0.00 35.18 3.02
4965 15099 0.937304 CATTCACCGCCTTCCATACG 59.063 55.000 0.00 0.00 0.00 3.06
4990 15124 4.401925 CTTTGAGAAGGGACAATCCTTGT 58.598 43.478 0.39 0.00 46.31 3.16
5013 15147 1.577328 GGTGGCACGGTGTCTCATTG 61.577 60.000 14.54 0.00 0.00 2.82
5105 15241 1.518056 CCATGCAACACGAGCCAAGT 61.518 55.000 0.00 0.00 0.00 3.16
5152 15288 3.035363 GTTTCCTTCCAAACCTTCCCAA 58.965 45.455 0.00 0.00 31.10 4.12
5198 15334 9.127277 GCCAAGGGTATCTTATACACAAATTTA 57.873 33.333 2.40 0.00 33.68 1.40
5225 15361 3.398292 AGAATTCATCTGAGGCCATCCAT 59.602 43.478 5.01 0.00 36.88 3.41
5259 15395 0.609662 GGGTGTTAAGGCCTACGACA 59.390 55.000 5.16 8.82 0.00 4.35
5260 15396 1.002315 GGGTGTTAAGGCCTACGACAA 59.998 52.381 5.16 0.00 0.00 3.18
5261 15397 2.071540 GGTGTTAAGGCCTACGACAAC 58.928 52.381 5.16 10.67 0.00 3.32
5280 15416 4.788617 ACAACTGTTATCCACTTATCCCCT 59.211 41.667 0.00 0.00 0.00 4.79
5281 15417 5.126067 CAACTGTTATCCACTTATCCCCTG 58.874 45.833 0.00 0.00 0.00 4.45
5283 15419 3.973973 CTGTTATCCACTTATCCCCTGGA 59.026 47.826 0.00 0.00 38.47 3.86
5284 15420 3.973973 TGTTATCCACTTATCCCCTGGAG 59.026 47.826 0.00 0.00 37.51 3.86
5285 15421 4.232091 GTTATCCACTTATCCCCTGGAGA 58.768 47.826 0.00 0.00 37.51 3.71
5286 15422 2.176247 TCCACTTATCCCCTGGAGAC 57.824 55.000 0.00 0.00 34.05 3.36
5295 15431 1.538876 CCCTGGAGACCCTGGTTCA 60.539 63.158 0.00 0.00 46.77 3.18
5303 15439 0.108138 GACCCTGGTTCATCGTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
5342 15478 2.282462 AAAAGCTCTGGGGCACGG 60.282 61.111 0.00 0.00 34.17 4.94
5364 15500 1.476488 GCAAAGTGCGGAATACCCAAT 59.524 47.619 0.00 0.00 31.71 3.16
5403 15539 0.735978 CTTGTCTACACGCCATCGCA 60.736 55.000 0.00 0.00 39.84 5.10
5407 15543 0.319986 TCTACACGCCATCGCAAACA 60.320 50.000 0.00 0.00 39.84 2.83
5408 15544 0.095245 CTACACGCCATCGCAAACAG 59.905 55.000 0.00 0.00 39.84 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 54 6.043938 TGGACTACACTTAGATCCAAAGGTTT 59.956 38.462 9.54 0.00 34.87 3.27
99 101 3.438216 TTCCTCTTCATTGCATCCACA 57.562 42.857 0.00 0.00 0.00 4.17
108 110 8.773033 ATATGCCTAAAACATTCCTCTTCATT 57.227 30.769 0.00 0.00 0.00 2.57
146 148 1.675483 CTCCCTCTCACTGATCAGACG 59.325 57.143 29.27 18.40 0.00 4.18
151 153 1.408969 GGGTCTCCCTCTCACTGATC 58.591 60.000 0.00 0.00 41.34 2.92
165 167 3.188355 TACACCAGGCCAGGGGTCT 62.188 63.158 27.73 9.77 43.31 3.85
193 195 2.187958 CCTGTATGGACTCACCCTTCA 58.812 52.381 0.00 0.00 38.35 3.02
335 337 0.747852 GGCAGTCCTACTGGTCTAGC 59.252 60.000 8.99 0.00 46.01 3.42
336 338 2.145397 TGGCAGTCCTACTGGTCTAG 57.855 55.000 8.99 0.00 46.01 2.43
338 340 1.198713 CATGGCAGTCCTACTGGTCT 58.801 55.000 8.99 0.00 46.01 3.85
339 341 0.905357 ACATGGCAGTCCTACTGGTC 59.095 55.000 8.99 0.00 46.01 4.02
340 342 2.247699 TACATGGCAGTCCTACTGGT 57.752 50.000 8.99 1.47 46.01 4.00
343 345 4.684485 GCAAAGATACATGGCAGTCCTACT 60.684 45.833 0.00 0.00 0.00 2.57
344 346 3.561725 GCAAAGATACATGGCAGTCCTAC 59.438 47.826 0.00 0.00 0.00 3.18
345 347 3.433598 GGCAAAGATACATGGCAGTCCTA 60.434 47.826 0.00 0.00 41.38 2.94
347 349 1.678101 GGCAAAGATACATGGCAGTCC 59.322 52.381 0.00 0.00 41.38 3.85
348 350 1.331756 CGGCAAAGATACATGGCAGTC 59.668 52.381 0.00 0.00 41.79 3.51
349 351 1.382522 CGGCAAAGATACATGGCAGT 58.617 50.000 0.00 0.00 41.79 4.40
350 352 0.029834 GCGGCAAAGATACATGGCAG 59.970 55.000 0.00 0.00 41.79 4.85
354 356 2.419673 TCAACAGCGGCAAAGATACATG 59.580 45.455 1.45 0.00 0.00 3.21
355 357 2.710377 TCAACAGCGGCAAAGATACAT 58.290 42.857 1.45 0.00 0.00 2.29
356 358 2.177394 TCAACAGCGGCAAAGATACA 57.823 45.000 1.45 0.00 0.00 2.29
357 359 2.223340 CCATCAACAGCGGCAAAGATAC 60.223 50.000 1.45 0.00 0.00 2.24
358 360 2.016318 CCATCAACAGCGGCAAAGATA 58.984 47.619 1.45 0.00 0.00 1.98
359 361 0.813184 CCATCAACAGCGGCAAAGAT 59.187 50.000 1.45 0.00 0.00 2.40
360 362 1.243342 CCCATCAACAGCGGCAAAGA 61.243 55.000 1.45 0.00 0.00 2.52
759 925 8.669394 AGCAAGTTTTAATTCGTAATTACAGC 57.331 30.769 15.67 0.00 33.32 4.40
871 1097 0.108756 GGGAGTGTTGACTAGACGGC 60.109 60.000 0.00 0.00 30.16 5.68
877 1103 1.938585 CCAGAGGGGAGTGTTGACTA 58.061 55.000 0.00 0.00 40.01 2.59
898 1124 2.159099 ACAGCCGAATATCTTGCGAGAA 60.159 45.455 7.99 0.00 35.07 2.87
974 1216 1.227234 GCTTTGTGTGTGGGTTGGC 60.227 57.895 0.00 0.00 0.00 4.52
1168 1410 4.430765 GCGGTCGCTTCCTTCCGA 62.431 66.667 8.20 0.00 44.86 4.55
1186 1428 1.546961 GAGTTCTTCTCCTCCACCGA 58.453 55.000 0.00 0.00 37.22 4.69
1348 1590 2.749621 CTGCCCCATTAGACTTGTCAAC 59.250 50.000 3.49 0.00 0.00 3.18
1443 1685 1.848886 TTCCCTTCCCCTTCCGCTTC 61.849 60.000 0.00 0.00 0.00 3.86
1461 1703 2.746277 GTGATCGCCGCCACCTTT 60.746 61.111 0.00 0.00 0.00 3.11
1483 1725 0.670546 CGCACACGAGATTTCCCACT 60.671 55.000 0.00 0.00 43.93 4.00
1507 1749 4.201679 CCGATGCGCAGGGTCGTA 62.202 66.667 25.10 0.00 33.77 3.43
1543 1785 1.922545 GTATCGTGTAACCTTGCGGTC 59.077 52.381 0.00 0.00 44.73 4.79
1567 1809 1.080705 GAACCGACACCTCGTCCTG 60.081 63.158 0.00 0.00 42.07 3.86
1579 1821 0.542333 TTGTCACCAACTGGAACCGA 59.458 50.000 1.86 0.00 38.94 4.69
1696 1938 4.162690 GATCGCCGCCACCTTCCT 62.163 66.667 0.00 0.00 0.00 3.36
1748 1990 2.537560 GGATGCGCACTGGAATCGG 61.538 63.158 14.90 0.00 0.00 4.18
1796 2042 6.091123 AGAAACGCGACACATATTTAACTC 57.909 37.500 15.93 0.00 0.00 3.01
1834 2081 7.792925 TGTTCGCACATGTATATATAACAAGC 58.207 34.615 0.00 0.00 0.00 4.01
1836 2083 7.386573 CCCTGTTCGCACATGTATATATAACAA 59.613 37.037 0.00 0.00 30.39 2.83
1881 2128 5.560966 TCTTAGCATCATTTTTCCGTTCC 57.439 39.130 0.00 0.00 0.00 3.62
1895 2144 3.549794 GCCACCTTCATCTTCTTAGCAT 58.450 45.455 0.00 0.00 0.00 3.79
1931 2201 1.299541 AGCAGTGTTCAGTGTTTCCG 58.700 50.000 9.02 0.00 0.00 4.30
1941 2211 4.142881 GGAATTCTTACCGAAGCAGTGTTC 60.143 45.833 5.23 0.00 34.56 3.18
1991 2262 2.626743 AGTACTAAGACACGGTGCAGTT 59.373 45.455 8.30 1.88 0.00 3.16
2033 2307 6.204882 GCATATCTACCCATAACCACAAAGAC 59.795 42.308 0.00 0.00 0.00 3.01
2073 2351 2.173669 CCGGGCACTCGCATACTTG 61.174 63.158 0.00 0.00 41.24 3.16
2105 3797 6.892658 ATGTCAGCTAAAACACAACCAATA 57.107 33.333 0.00 0.00 0.00 1.90
2159 3857 7.161404 TCTACATGTGAATTAGACAAACTGCT 58.839 34.615 9.11 0.00 0.00 4.24
2160 3858 7.364522 TCTACATGTGAATTAGACAAACTGC 57.635 36.000 9.11 0.00 0.00 4.40
2161 3859 8.939929 ACATCTACATGTGAATTAGACAAACTG 58.060 33.333 9.11 0.51 42.05 3.16
2162 3860 9.507329 AACATCTACATGTGAATTAGACAAACT 57.493 29.630 9.11 0.00 42.89 2.66
2188 3886 7.336931 GGAGCTTAGATGTGACATCCTTAAAAA 59.663 37.037 21.05 6.46 0.00 1.94
2189 3887 6.823689 GGAGCTTAGATGTGACATCCTTAAAA 59.176 38.462 21.05 8.00 0.00 1.52
2190 3888 6.349300 GGAGCTTAGATGTGACATCCTTAAA 58.651 40.000 21.05 10.18 0.00 1.52
2191 3889 5.163301 GGGAGCTTAGATGTGACATCCTTAA 60.163 44.000 21.05 13.11 0.00 1.85
2192 3890 4.345257 GGGAGCTTAGATGTGACATCCTTA 59.655 45.833 21.05 6.22 0.00 2.69
2193 3891 3.135530 GGGAGCTTAGATGTGACATCCTT 59.864 47.826 21.05 7.22 0.00 3.36
2194 3892 2.703007 GGGAGCTTAGATGTGACATCCT 59.297 50.000 21.05 11.37 0.00 3.24
2195 3893 2.435805 TGGGAGCTTAGATGTGACATCC 59.564 50.000 21.05 6.28 0.00 3.51
2196 3894 3.827008 TGGGAGCTTAGATGTGACATC 57.173 47.619 17.46 17.46 0.00 3.06
2197 3895 5.894298 TTATGGGAGCTTAGATGTGACAT 57.106 39.130 0.00 0.00 0.00 3.06
2198 3896 5.692115 TTTATGGGAGCTTAGATGTGACA 57.308 39.130 0.00 0.00 0.00 3.58
2204 3902 9.765795 GCGTTATATATTTATGGGAGCTTAGAT 57.234 33.333 0.00 0.00 0.00 1.98
2205 3903 8.755028 TGCGTTATATATTTATGGGAGCTTAGA 58.245 33.333 0.00 0.00 0.00 2.10
2206 3904 8.942338 TGCGTTATATATTTATGGGAGCTTAG 57.058 34.615 0.00 0.00 0.00 2.18
2207 3905 7.494625 GCTGCGTTATATATTTATGGGAGCTTA 59.505 37.037 0.00 0.00 0.00 3.09
2208 3906 6.316390 GCTGCGTTATATATTTATGGGAGCTT 59.684 38.462 0.00 0.00 0.00 3.74
2209 3907 5.817816 GCTGCGTTATATATTTATGGGAGCT 59.182 40.000 0.00 0.00 0.00 4.09
2210 3908 5.584649 TGCTGCGTTATATATTTATGGGAGC 59.415 40.000 0.00 9.06 0.00 4.70
2211 3909 7.119116 TGTTGCTGCGTTATATATTTATGGGAG 59.881 37.037 0.00 0.00 0.00 4.30
2212 3910 6.937465 TGTTGCTGCGTTATATATTTATGGGA 59.063 34.615 0.00 0.00 0.00 4.37
2213 3911 7.139896 TGTTGCTGCGTTATATATTTATGGG 57.860 36.000 0.00 0.00 0.00 4.00
2214 3912 8.503196 TCTTGTTGCTGCGTTATATATTTATGG 58.497 33.333 0.00 0.00 0.00 2.74
2215 3913 9.877137 TTCTTGTTGCTGCGTTATATATTTATG 57.123 29.630 0.00 0.00 0.00 1.90
2217 3915 9.710979 GTTTCTTGTTGCTGCGTTATATATTTA 57.289 29.630 0.00 0.00 0.00 1.40
2218 3916 8.240682 TGTTTCTTGTTGCTGCGTTATATATTT 58.759 29.630 0.00 0.00 0.00 1.40
2219 3917 7.757526 TGTTTCTTGTTGCTGCGTTATATATT 58.242 30.769 0.00 0.00 0.00 1.28
2220 3918 7.315247 TGTTTCTTGTTGCTGCGTTATATAT 57.685 32.000 0.00 0.00 0.00 0.86
2221 3919 6.729391 TGTTTCTTGTTGCTGCGTTATATA 57.271 33.333 0.00 0.00 0.00 0.86
2222 3920 5.621197 TGTTTCTTGTTGCTGCGTTATAT 57.379 34.783 0.00 0.00 0.00 0.86
2223 3921 5.425577 TTGTTTCTTGTTGCTGCGTTATA 57.574 34.783 0.00 0.00 0.00 0.98
2224 3922 3.980646 TGTTTCTTGTTGCTGCGTTAT 57.019 38.095 0.00 0.00 0.00 1.89
2225 3923 3.766676 TTGTTTCTTGTTGCTGCGTTA 57.233 38.095 0.00 0.00 0.00 3.18
2226 3924 2.645730 TTGTTTCTTGTTGCTGCGTT 57.354 40.000 0.00 0.00 0.00 4.84
2227 3925 2.645730 TTTGTTTCTTGTTGCTGCGT 57.354 40.000 0.00 0.00 0.00 5.24
2228 3926 3.987807 TTTTTGTTTCTTGTTGCTGCG 57.012 38.095 0.00 0.00 0.00 5.18
2263 3961 6.750148 TGTACACTTTGTTTGTGGTCTTTTT 58.250 32.000 0.00 0.00 39.52 1.94
2264 3962 6.334102 TGTACACTTTGTTTGTGGTCTTTT 57.666 33.333 0.00 0.00 39.52 2.27
2265 3963 5.968528 TGTACACTTTGTTTGTGGTCTTT 57.031 34.783 0.00 0.00 39.52 2.52
2266 3964 5.650266 TGATGTACACTTTGTTTGTGGTCTT 59.350 36.000 0.00 0.00 39.52 3.01
2267 3965 5.189928 TGATGTACACTTTGTTTGTGGTCT 58.810 37.500 0.00 0.00 39.52 3.85
2268 3966 5.493133 TGATGTACACTTTGTTTGTGGTC 57.507 39.130 0.00 0.00 39.52 4.02
2269 3967 4.202010 GCTGATGTACACTTTGTTTGTGGT 60.202 41.667 0.00 0.00 39.52 4.16
2270 3968 4.036734 AGCTGATGTACACTTTGTTTGTGG 59.963 41.667 0.00 0.00 39.52 4.17
2271 3969 5.173774 AGCTGATGTACACTTTGTTTGTG 57.826 39.130 0.00 0.00 40.87 3.33
2272 3970 5.835113 AAGCTGATGTACACTTTGTTTGT 57.165 34.783 0.00 0.00 0.00 2.83
2273 3971 7.189693 TCTAAGCTGATGTACACTTTGTTTG 57.810 36.000 0.00 0.00 0.00 2.93
2274 3972 7.810658 CATCTAAGCTGATGTACACTTTGTTT 58.189 34.615 0.00 0.00 39.05 2.83
2275 3973 7.369803 CATCTAAGCTGATGTACACTTTGTT 57.630 36.000 0.00 0.00 39.05 2.83
2276 3974 6.974932 CATCTAAGCTGATGTACACTTTGT 57.025 37.500 0.00 0.00 39.05 2.83
2286 3984 8.877808 TTAGTTATGTCACATCTAAGCTGATG 57.122 34.615 11.48 11.48 46.61 3.07
2287 3985 8.700051 ACTTAGTTATGTCACATCTAAGCTGAT 58.300 33.333 19.38 4.62 40.32 2.90
2288 3986 8.067751 ACTTAGTTATGTCACATCTAAGCTGA 57.932 34.615 19.38 0.00 40.32 4.26
2289 3987 7.976175 TGACTTAGTTATGTCACATCTAAGCTG 59.024 37.037 19.38 5.03 40.32 4.24
2290 3988 8.067751 TGACTTAGTTATGTCACATCTAAGCT 57.932 34.615 19.38 11.02 40.32 3.74
2316 4014 6.276847 GGTCTGTTTAGGACACATCTAGATG 58.723 44.000 27.63 27.63 44.15 2.90
2317 4015 5.364157 GGGTCTGTTTAGGACACATCTAGAT 59.636 44.000 0.00 0.00 37.11 1.98
2318 4016 4.710375 GGGTCTGTTTAGGACACATCTAGA 59.290 45.833 0.00 0.00 37.11 2.43
2319 4017 4.466370 TGGGTCTGTTTAGGACACATCTAG 59.534 45.833 0.00 0.00 41.46 2.43
2320 4018 4.422057 TGGGTCTGTTTAGGACACATCTA 58.578 43.478 0.00 0.00 41.46 1.98
2321 4019 3.248024 TGGGTCTGTTTAGGACACATCT 58.752 45.455 0.00 0.00 41.46 2.90
2322 4020 3.695830 TGGGTCTGTTTAGGACACATC 57.304 47.619 0.00 0.00 41.46 3.06
2323 4021 4.398319 CTTTGGGTCTGTTTAGGACACAT 58.602 43.478 0.00 0.00 44.98 3.21
2324 4022 3.434453 CCTTTGGGTCTGTTTAGGACACA 60.434 47.826 0.00 0.00 44.14 3.72
2325 4023 3.146847 CCTTTGGGTCTGTTTAGGACAC 58.853 50.000 0.00 0.00 37.60 3.67
2326 4024 2.781174 ACCTTTGGGTCTGTTTAGGACA 59.219 45.455 0.00 0.00 43.38 4.02
2327 4025 3.146847 CACCTTTGGGTCTGTTTAGGAC 58.853 50.000 0.00 0.00 45.41 3.85
2328 4026 2.781174 ACACCTTTGGGTCTGTTTAGGA 59.219 45.455 0.00 0.00 45.41 2.94
2329 4027 3.223674 ACACCTTTGGGTCTGTTTAGG 57.776 47.619 0.00 0.00 45.41 2.69
2330 4028 6.677913 CAATAACACCTTTGGGTCTGTTTAG 58.322 40.000 0.00 0.00 45.41 1.85
2331 4029 5.010213 GCAATAACACCTTTGGGTCTGTTTA 59.990 40.000 0.00 0.00 45.41 2.01
2332 4030 4.202212 GCAATAACACCTTTGGGTCTGTTT 60.202 41.667 0.00 0.00 45.41 2.83
2333 4031 3.320826 GCAATAACACCTTTGGGTCTGTT 59.679 43.478 0.00 0.00 45.41 3.16
2334 4032 2.890945 GCAATAACACCTTTGGGTCTGT 59.109 45.455 0.00 0.00 45.41 3.41
2335 4033 3.157087 AGCAATAACACCTTTGGGTCTG 58.843 45.455 0.00 0.00 45.41 3.51
2336 4034 3.525800 AGCAATAACACCTTTGGGTCT 57.474 42.857 0.00 0.00 45.41 3.85
2337 4035 4.585879 TCTAGCAATAACACCTTTGGGTC 58.414 43.478 0.00 0.00 45.41 4.46
2339 4037 6.332630 CAAATCTAGCAATAACACCTTTGGG 58.667 40.000 0.00 0.00 38.88 4.12
2340 4038 5.807011 GCAAATCTAGCAATAACACCTTTGG 59.193 40.000 0.00 0.00 0.00 3.28
2341 4039 5.807011 GGCAAATCTAGCAATAACACCTTTG 59.193 40.000 0.00 0.00 0.00 2.77
2432 4143 4.162131 TCACTTGCAATGCACTCTAGGATA 59.838 41.667 7.72 0.00 38.71 2.59
2546 4296 8.869109 TCAGAATTTTCAGGGTAACATCATTTT 58.131 29.630 0.00 0.00 39.74 1.82
2633 4383 3.107601 CCCCTTGACCTCACATTCTAGA 58.892 50.000 0.00 0.00 0.00 2.43
2689 4471 6.377327 AAAATGGGTGCTCACTATTTATCG 57.623 37.500 12.44 0.00 32.33 2.92
2756 4539 4.770010 GCCAGCTCTTGATACTACCTAGAT 59.230 45.833 0.00 0.00 0.00 1.98
2757 4540 4.141135 AGCCAGCTCTTGATACTACCTAGA 60.141 45.833 0.00 0.00 0.00 2.43
2839 8486 4.759205 AGGGGAATTGGTGCCGGC 62.759 66.667 22.73 22.73 39.07 6.13
2856 8504 4.248859 GCTGCTAGAACTGTGAGATCAAA 58.751 43.478 0.00 0.00 0.00 2.69
2861 8509 2.519013 TCTGCTGCTAGAACTGTGAGA 58.481 47.619 0.00 0.00 0.00 3.27
2882 8530 4.019771 TGCTGACAAATATACCAGTGACCA 60.020 41.667 0.00 0.00 0.00 4.02
2885 8533 8.800370 TTAATTGCTGACAAATATACCAGTGA 57.200 30.769 0.00 0.00 39.77 3.41
2886 8534 9.669353 GATTAATTGCTGACAAATATACCAGTG 57.331 33.333 0.00 0.00 39.77 3.66
2888 8536 9.888878 CAGATTAATTGCTGACAAATATACCAG 57.111 33.333 0.00 0.00 39.77 4.00
2889 8537 8.849168 CCAGATTAATTGCTGACAAATATACCA 58.151 33.333 5.87 0.00 39.77 3.25
2890 8538 8.299570 CCCAGATTAATTGCTGACAAATATACC 58.700 37.037 5.87 0.00 39.77 2.73
2892 8540 7.451255 CCCCCAGATTAATTGCTGACAAATATA 59.549 37.037 5.87 0.00 39.77 0.86
2893 8541 6.268387 CCCCCAGATTAATTGCTGACAAATAT 59.732 38.462 5.87 0.00 39.77 1.28
2898 8884 2.311542 ACCCCCAGATTAATTGCTGACA 59.688 45.455 5.87 0.00 34.06 3.58
2899 8885 2.952310 GACCCCCAGATTAATTGCTGAC 59.048 50.000 5.87 0.00 34.06 3.51
2916 8902 8.556213 TTTTAATATATTGATACCAGCGACCC 57.444 34.615 8.28 0.00 0.00 4.46
2952 8938 5.897250 TGCTGAGACAAGGTATACTCCATAA 59.103 40.000 2.25 0.00 0.00 1.90
2975 8970 8.519799 TTCTTAAATCCTAAATGGGCTACTTG 57.480 34.615 0.00 0.00 36.20 3.16
3000 8995 6.100279 TGAAATGCATCTCCTCCTTAGTACAT 59.900 38.462 0.00 0.00 0.00 2.29
3009 10776 6.515272 TTTAGTTTGAAATGCATCTCCTCC 57.485 37.500 0.00 0.00 0.00 4.30
3137 10904 0.248907 CGGATGCGTAGTGGAATCGT 60.249 55.000 0.00 0.00 0.00 3.73
3255 11052 4.764172 CGTCCATTCTTCTCCTTCTGAAT 58.236 43.478 0.00 0.00 0.00 2.57
3382 11182 5.234329 CGAGACTCGGCATTTTGTACATTAT 59.766 40.000 17.27 0.00 36.00 1.28
3439 11239 4.771577 TGCATAGGAAATTCTGGCTGAAAA 59.228 37.500 10.95 0.00 38.29 2.29
3441 11241 3.966979 TGCATAGGAAATTCTGGCTGAA 58.033 40.909 9.33 9.33 39.24 3.02
3443 11243 4.931661 AATGCATAGGAAATTCTGGCTG 57.068 40.909 0.00 0.00 0.00 4.85
3444 11244 5.945144 AAAATGCATAGGAAATTCTGGCT 57.055 34.783 0.00 0.00 0.00 4.75
3533 11333 8.541899 TTATGTGGTACAAGATACATCTACCA 57.458 34.615 7.85 7.85 44.16 3.25
3656 11456 4.276678 CCGTGAATGATGCTCCATGTTTAT 59.723 41.667 0.00 0.00 0.00 1.40
3661 11495 1.600957 GACCGTGAATGATGCTCCATG 59.399 52.381 0.00 0.00 0.00 3.66
3677 11511 5.333263 GCAATCCAAAATTCAACTTTGACCG 60.333 40.000 0.00 0.00 36.83 4.79
3703 11537 2.051334 TCCAATGAATAAGGCCCACG 57.949 50.000 0.00 0.00 0.00 4.94
3725 11559 7.619965 CATCTCTCTTCTTTAGTTCTCCCTTT 58.380 38.462 0.00 0.00 0.00 3.11
3733 11567 8.627208 TTGAAATGCATCTCTCTTCTTTAGTT 57.373 30.769 0.00 0.00 0.00 2.24
3838 11675 9.817809 AGAGTTATCATGTGTTGATATTACGTT 57.182 29.630 0.00 0.00 44.77 3.99
3883 11756 8.985315 TCATTAAACAGATCCTTGATGCTAAT 57.015 30.769 0.00 0.00 0.00 1.73
3993 11866 1.063616 CTCAAAGCATGACATGGCTCG 59.936 52.381 17.03 9.30 40.01 5.03
4115 12063 2.639065 AGTCAAAGTGTGCCGAAAGAA 58.361 42.857 0.00 0.00 0.00 2.52
4219 12172 9.438291 CATAAAAATGTAGATTGGTTAGAAGCG 57.562 33.333 0.00 0.00 0.00 4.68
4235 12188 6.653320 ACCACACGACTATGTCATAAAAATGT 59.347 34.615 0.00 0.00 32.09 2.71
4335 12288 1.926510 GTTGTGGCTTTCTGTTGTTGC 59.073 47.619 0.00 0.00 0.00 4.17
4336 12289 3.508744 AGTTGTGGCTTTCTGTTGTTG 57.491 42.857 0.00 0.00 0.00 3.33
4337 12290 3.427503 CGAAGTTGTGGCTTTCTGTTGTT 60.428 43.478 0.00 0.00 0.00 2.83
4577 12530 4.923281 AGCATTGCCAATTACTCGAAAAAC 59.077 37.500 4.70 0.00 0.00 2.43
4598 12552 3.188460 TCTTGTAATTGAAAGGCGACAGC 59.812 43.478 0.00 0.00 44.18 4.40
4599 12553 5.147162 GTTCTTGTAATTGAAAGGCGACAG 58.853 41.667 0.00 0.00 0.00 3.51
4629 12583 6.416750 GTCGCTTGTAAAAGCAGTTGTAAAAT 59.583 34.615 17.74 0.00 45.75 1.82
4689 12657 1.689813 TGTAGTTGCCTCCTTCACGAA 59.310 47.619 0.00 0.00 0.00 3.85
4702 12670 3.249799 TCCGTGCACAATTCTTGTAGTTG 59.750 43.478 18.64 0.00 43.23 3.16
4716 12684 1.337260 CCCTAGCAGATATCCGTGCAC 60.337 57.143 16.66 6.82 42.47 4.57
4750 12718 5.044179 TGGACAGGGAATGATTTATCAGGTT 60.044 40.000 0.00 0.00 40.64 3.50
4767 12735 1.024579 CCGGGTTTTCGATGGACAGG 61.025 60.000 0.00 0.00 0.00 4.00
4776 12744 1.702491 GAGGAATCGCCGGGTTTTCG 61.702 60.000 2.18 0.00 43.43 3.46
4832 12800 4.083590 GCAAAGTTTGAAGGTGCAAAACAA 60.084 37.500 19.82 3.86 39.26 2.83
4915 15049 2.092807 CCATGTGTCCCTGATGATGACA 60.093 50.000 0.00 0.00 36.71 3.58
4916 15050 2.569059 CCATGTGTCCCTGATGATGAC 58.431 52.381 0.00 0.00 0.00 3.06
4925 15059 0.037303 CAAGACTGCCATGTGTCCCT 59.963 55.000 7.00 0.00 34.02 4.20
4945 15079 1.742411 CGTATGGAAGGCGGTGAATGT 60.742 52.381 0.00 0.00 0.00 2.71
4990 15124 0.034337 GAGACACCGTGCCACCTTTA 59.966 55.000 0.00 0.00 0.00 1.85
5002 15136 2.271800 CTTAGCGACCAATGAGACACC 58.728 52.381 0.00 0.00 0.00 4.16
5013 15147 3.063588 GGTTTCACTTATGCTTAGCGACC 59.936 47.826 0.00 0.00 0.00 4.79
5066 15202 0.673985 TAGAATCCTGATGACGGCGG 59.326 55.000 13.24 0.00 0.00 6.13
5105 15241 3.507233 CACTCCCAAATGCAAGCTTTCTA 59.493 43.478 0.00 0.00 0.00 2.10
5152 15288 1.745087 CCATGTGCAGCCTTTTCGTAT 59.255 47.619 0.00 0.00 0.00 3.06
5198 15334 3.265221 TGGCCTCAGATGAATTCTTGACT 59.735 43.478 3.32 0.00 29.93 3.41
5236 15372 0.107993 GTAGGCCTTAACACCCCGAC 60.108 60.000 12.58 0.00 0.00 4.79
5239 15375 0.107993 GTCGTAGGCCTTAACACCCC 60.108 60.000 12.58 0.00 0.00 4.95
5259 15395 4.166144 CCAGGGGATAAGTGGATAACAGTT 59.834 45.833 0.00 0.00 44.67 3.16
5260 15396 3.716872 CCAGGGGATAAGTGGATAACAGT 59.283 47.826 0.00 0.00 32.60 3.55
5261 15397 3.973973 TCCAGGGGATAAGTGGATAACAG 59.026 47.826 0.00 0.00 35.36 3.16
5280 15416 0.544357 ACGATGAACCAGGGTCTCCA 60.544 55.000 5.94 0.00 34.83 3.86
5281 15417 0.175989 GACGATGAACCAGGGTCTCC 59.824 60.000 5.94 0.00 0.00 3.71
5283 15419 0.252284 AGGACGATGAACCAGGGTCT 60.252 55.000 5.94 0.00 0.00 3.85
5284 15420 0.108138 CAGGACGATGAACCAGGGTC 60.108 60.000 0.00 0.00 0.00 4.46
5285 15421 0.544357 TCAGGACGATGAACCAGGGT 60.544 55.000 0.00 0.00 0.00 4.34
5286 15422 0.833287 ATCAGGACGATGAACCAGGG 59.167 55.000 0.00 0.00 31.20 4.45
5295 15431 3.068873 GCAACTAGGAAGATCAGGACGAT 59.931 47.826 0.00 0.00 36.91 3.73
5303 15439 6.992063 TTCAAGATTGCAACTAGGAAGATC 57.008 37.500 0.00 0.00 0.00 2.75
5342 15478 0.170339 GGGTATTCCGCACTTTGCAC 59.830 55.000 0.00 0.00 45.36 4.57
5380 15516 2.478894 CGATGGCGTGTAGACAAGTTTT 59.521 45.455 0.00 0.00 44.01 2.43


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

AutoCloner maintained by Alex Coulton.