Multiple sequence alignment - TraesCS4D01G130700

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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 TraesCS4D01G130700 chr4D 100.000 4040 0 0 1 4040 116824138 116820099 0.000000e+00 7461
1 TraesCS4D01G130700 chr4D 100.000 1709 0 0 4380 6088 116819759 116818051 0.000000e+00 3157
2 TraesCS4D01G130700 chr4A 92.015 1578 67 24 584 2121 459627152 459628710 0.000000e+00 2161
3 TraesCS4D01G130700 chr4A 95.920 1054 31 1 5047 6088 459631461 459632514 0.000000e+00 1698
4 TraesCS4D01G130700 chr4A 90.625 1312 54 21 2744 4040 459629403 459630660 0.000000e+00 1677
5 TraesCS4D01G130700 chr4A 97.615 671 16 0 4380 5050 459630763 459631433 0.000000e+00 1151
6 TraesCS4D01G130700 chr4A 94.667 450 17 3 2297 2740 459628708 459629156 0.000000e+00 691
7 TraesCS4D01G130700 chr4A 78.683 319 66 1 275 591 181703705 181703387 1.720000e-50 211
8 TraesCS4D01G130700 chr4A 77.489 231 46 6 1133 1360 132703126 132702899 3.830000e-27 134
9 TraesCS4D01G130700 chr4B 92.355 1452 55 23 701 2125 178854297 178852875 0.000000e+00 2015
10 TraesCS4D01G130700 chr4B 92.175 1329 52 19 2564 3877 178852554 178851263 0.000000e+00 1831
11 TraesCS4D01G130700 chr4B 91.398 930 31 22 4446 5328 178851220 178850293 0.000000e+00 1229
12 TraesCS4D01G130700 chr4B 97.156 633 18 0 5456 6088 178849974 178849342 0.000000e+00 1070
13 TraesCS4D01G130700 chr4B 93.462 260 13 4 2297 2554 178852874 178852617 3.440000e-102 383
14 TraesCS4D01G130700 chr4B 76.955 243 47 9 1133 1370 418752298 418752536 4.950000e-26 130
15 TraesCS4D01G130700 chr4B 91.139 79 6 1 2230 2308 630098810 630098733 8.350000e-19 106
16 TraesCS4D01G130700 chr7D 89.189 592 54 6 1 590 94762168 94761585 0.000000e+00 730
17 TraesCS4D01G130700 chr7D 92.208 77 5 1 2227 2302 580814961 580815037 2.320000e-19 108
18 TraesCS4D01G130700 chr1A 86.125 591 73 5 4 589 560254639 560254053 4.010000e-176 628
19 TraesCS4D01G130700 chr1A 92.208 77 5 1 2227 2302 558981479 558981555 2.320000e-19 108
20 TraesCS4D01G130700 chr1B 84.874 595 82 4 1 591 478537319 478537909 1.460000e-165 593
21 TraesCS4D01G130700 chr5B 83.430 519 69 15 4398 4911 282267962 282268468 3.320000e-127 466
22 TraesCS4D01G130700 chr5B 91.597 238 20 0 1116 1353 282264887 282265124 4.550000e-86 329
23 TraesCS4D01G130700 chr5B 76.585 615 100 26 3236 3820 282267155 282267755 1.280000e-76 298
24 TraesCS4D01G130700 chr5B 97.403 77 2 0 2394 2470 282265977 282266053 1.380000e-26 132
25 TraesCS4D01G130700 chr5B 90.722 97 9 0 1470 1566 282265253 282265349 4.950000e-26 130
26 TraesCS4D01G130700 chr2D 80.640 594 101 10 1 588 44461447 44460862 1.200000e-121 448
27 TraesCS4D01G130700 chr2D 89.062 128 4 8 2124 2244 189371229 189371353 3.800000e-32 150
28 TraesCS4D01G130700 chr2D 77.350 234 48 5 1133 1363 35686231 35686000 3.830000e-27 134
29 TraesCS4D01G130700 chr2D 93.506 77 5 0 2227 2303 526080464 526080540 1.390000e-21 115
30 TraesCS4D01G130700 chr5D 82.812 512 67 16 4398 4902 249526676 249527173 7.240000e-119 438
31 TraesCS4D01G130700 chr5D 90.756 238 22 0 1116 1353 249523616 249523853 9.850000e-83 318
32 TraesCS4D01G130700 chr5D 77.148 547 105 16 53 589 200495996 200495460 3.570000e-77 300
33 TraesCS4D01G130700 chr5D 76.623 616 100 29 3236 3820 249525874 249526476 3.570000e-77 300
34 TraesCS4D01G130700 chr5D 97.403 77 2 0 2394 2470 249524677 249524753 1.380000e-26 132
35 TraesCS4D01G130700 chr5D 90.722 97 9 0 1470 1566 249523992 249524088 4.950000e-26 130
36 TraesCS4D01G130700 chr5A 82.129 526 71 20 4398 4911 332218622 332219136 4.360000e-116 429
37 TraesCS4D01G130700 chr5A 90.756 238 22 0 1116 1353 332215293 332215530 9.850000e-83 318
38 TraesCS4D01G130700 chr5A 76.461 616 101 29 3236 3820 332217819 332218421 1.660000e-75 294
39 TraesCS4D01G130700 chr5A 88.372 172 18 2 420 590 269280713 269280883 8.000000e-49 206
40 TraesCS4D01G130700 chr5A 93.269 104 5 2 2133 2236 466005805 466005704 1.060000e-32 152
41 TraesCS4D01G130700 chr5A 93.814 97 6 0 1470 1566 332215658 332215754 4.920000e-31 147
42 TraesCS4D01G130700 chr5A 97.403 77 2 0 2394 2470 332216397 332216473 1.380000e-26 132
43 TraesCS4D01G130700 chr2A 79.730 592 111 6 1 589 778844096 778843511 2.620000e-113 420
44 TraesCS4D01G130700 chr2A 76.923 234 49 5 1133 1363 38915265 38915034 1.780000e-25 128
45 TraesCS4D01G130700 chr2A 94.444 72 4 0 2230 2301 166785052 166784981 1.790000e-20 111
46 TraesCS4D01G130700 chr2A 94.444 72 4 0 2227 2298 771521828 771521899 1.790000e-20 111
47 TraesCS4D01G130700 chr3D 79.097 598 109 12 1 590 451156400 451156989 1.230000e-106 398
48 TraesCS4D01G130700 chr3D 85.517 145 13 7 2139 2279 76376779 76376639 1.770000e-30 145
49 TraesCS4D01G130700 chr3D 95.890 73 3 0 2230 2302 505561921 505561849 1.070000e-22 119
50 TraesCS4D01G130700 chr7A 75.253 594 131 12 4 589 680604195 680603610 1.010000e-67 268
51 TraesCS4D01G130700 chr2B 77.961 304 65 1 286 587 531519907 531520210 8.060000e-44 189
52 TraesCS4D01G130700 chr2B 97.849 93 1 1 2140 2231 496962095 496962187 6.320000e-35 159
53 TraesCS4D01G130700 chr2B 94.444 72 4 0 2230 2301 470530803 470530732 1.790000e-20 111
54 TraesCS4D01G130700 chr6B 93.269 104 6 1 2127 2230 672159157 672159259 1.060000e-32 152
55 TraesCS4D01G130700 chr6B 94.000 100 5 1 2137 2236 252247779 252247877 3.800000e-32 150
56 TraesCS4D01G130700 chr3B 94.118 102 3 3 2136 2237 771328929 771329027 1.060000e-32 152
57 TraesCS4D01G130700 chr3B 91.743 109 6 2 2124 2229 806472630 806472738 1.370000e-31 148
58 TraesCS4D01G130700 chr6A 91.667 108 7 1 2136 2241 592530732 592530839 1.370000e-31 148
59 TraesCS4D01G130700 chr6A 95.833 72 3 0 2227 2298 107695211 107695282 3.860000e-22 117


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 TraesCS4D01G130700 chr4D 116818051 116824138 6087 True 5309.0 7461 100.0000 1 6088 2 chr4D.!!$R1 6087
1 TraesCS4D01G130700 chr4A 459627152 459632514 5362 False 1475.6 2161 94.1684 584 6088 5 chr4A.!!$F1 5504
2 TraesCS4D01G130700 chr4B 178849342 178854297 4955 True 1305.6 2015 93.3092 701 6088 5 chr4B.!!$R2 5387
3 TraesCS4D01G130700 chr7D 94761585 94762168 583 True 730.0 730 89.1890 1 590 1 chr7D.!!$R1 589
4 TraesCS4D01G130700 chr1A 560254053 560254639 586 True 628.0 628 86.1250 4 589 1 chr1A.!!$R1 585
5 TraesCS4D01G130700 chr1B 478537319 478537909 590 False 593.0 593 84.8740 1 591 1 chr1B.!!$F1 590
6 TraesCS4D01G130700 chr5B 282264887 282268468 3581 False 271.0 466 87.9474 1116 4911 5 chr5B.!!$F1 3795
7 TraesCS4D01G130700 chr2D 44460862 44461447 585 True 448.0 448 80.6400 1 588 1 chr2D.!!$R2 587
8 TraesCS4D01G130700 chr5D 200495460 200495996 536 True 300.0 300 77.1480 53 589 1 chr5D.!!$R1 536
9 TraesCS4D01G130700 chr5D 249523616 249527173 3557 False 263.6 438 87.6632 1116 4902 5 chr5D.!!$F1 3786
10 TraesCS4D01G130700 chr5A 332215293 332219136 3843 False 264.0 429 88.1126 1116 4911 5 chr5A.!!$F2 3795
11 TraesCS4D01G130700 chr2A 778843511 778844096 585 True 420.0 420 79.7300 1 589 1 chr2A.!!$R3 588
12 TraesCS4D01G130700 chr3D 451156400 451156989 589 False 398.0 398 79.0970 1 590 1 chr3D.!!$F1 589
13 TraesCS4D01G130700 chr7A 680603610 680604195 585 True 268.0 268 75.2530 4 589 1 chr7A.!!$R1 585

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
202 204 0.036388 GGCTTGTGTGTAGCTGCCTA 60.036 55.0 0.00 0.00 38.67 3.93 F
278 280 0.232303 GTCGGGCGATTAATCTTGCG 59.768 55.0 13.45 2.12 0.00 4.85 F
323 325 1.028905 TCTTCAAAACGGGTTGCCTG 58.971 50.0 0.00 0.00 35.68 4.85 F
1966 2150 0.382873 GACAAAAACGTGGGTCACCC 59.617 55.0 5.63 5.63 45.71 4.61 F
3121 4140 0.875059 GCCCTTTTCAGTCAGGTTCG 59.125 55.0 0.00 0.00 0.00 3.95 F
4405 5525 1.317613 TTCACCAGCGCTCAATGTTT 58.682 45.0 7.13 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 2149 1.008995 CTTGTGCCCGTCGTTTTGG 60.009 57.895 0.0 0.0 0.00 3.28 R
1966 2150 1.657181 GCTTGTGCCCGTCGTTTTG 60.657 57.895 0.0 0.0 0.00 2.44 R
2135 2330 2.019807 TGGAACGGAGGGAGTAGTTT 57.980 50.000 0.0 0.0 0.00 2.66 R
3414 4492 0.321346 TGAGCCATTGCAGAAGACGA 59.679 50.000 0.0 0.0 41.13 4.20 R
4443 5563 1.210478 GGTAGCTCCATTCCTGCAAGA 59.790 52.381 0.0 0.0 33.33 3.02 R
5534 6991 0.807667 GGTGATGCAGCGGTAGAGTG 60.808 60.000 0.0 0.0 0.00 3.51 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
65 66 2.282251 AGGCGTGAGACCTCGTCA 60.282 61.111 0.00 0.00 43.69 4.35
67 68 2.627737 GGCGTGAGACCTCGTCACT 61.628 63.158 2.06 0.00 41.91 3.41
69 70 0.520404 GCGTGAGACCTCGTCACTAA 59.480 55.000 2.06 0.00 41.91 2.24
72 73 2.418976 CGTGAGACCTCGTCACTAATCA 59.581 50.000 2.06 0.00 41.91 2.57
114 116 1.202891 GGGTACAGTGGTGGCTTTCTT 60.203 52.381 0.00 0.00 0.00 2.52
121 123 1.340889 GTGGTGGCTTTCTTTGATGCA 59.659 47.619 0.00 0.00 0.00 3.96
122 124 2.037901 TGGTGGCTTTCTTTGATGCAA 58.962 42.857 0.00 0.00 0.00 4.08
123 125 2.224018 TGGTGGCTTTCTTTGATGCAAC 60.224 45.455 0.00 0.00 0.00 4.17
124 126 2.036346 GGTGGCTTTCTTTGATGCAACT 59.964 45.455 0.00 0.00 30.69 3.16
125 127 3.311966 GTGGCTTTCTTTGATGCAACTC 58.688 45.455 0.00 0.00 0.00 3.01
126 128 3.005155 GTGGCTTTCTTTGATGCAACTCT 59.995 43.478 0.00 0.00 0.00 3.24
129 131 4.022503 GGCTTTCTTTGATGCAACTCTCTT 60.023 41.667 0.00 0.00 0.00 2.85
148 150 0.689055 TTGTCTGAGGAGCTGCACAT 59.311 50.000 8.35 0.00 0.00 3.21
176 178 0.844661 TAGGGGTGGTGGTGCTCAAT 60.845 55.000 0.00 0.00 0.00 2.57
202 204 0.036388 GGCTTGTGTGTAGCTGCCTA 60.036 55.000 0.00 0.00 38.67 3.93
242 244 0.319728 CACTGTCTCCAGAGGTGGTG 59.680 60.000 0.00 0.00 45.28 4.17
278 280 0.232303 GTCGGGCGATTAATCTTGCG 59.768 55.000 13.45 2.12 0.00 4.85
323 325 1.028905 TCTTCAAAACGGGTTGCCTG 58.971 50.000 0.00 0.00 35.68 4.85
333 335 1.756561 GGTTGCCTGTTGGTGGTGT 60.757 57.895 0.00 0.00 35.27 4.16
361 363 5.503634 TTGAAATCTTCATCCAGAGACCA 57.496 39.130 0.00 0.00 39.84 4.02
446 450 1.301716 AGCATGTTCGTCGGCAGTT 60.302 52.632 0.00 0.00 0.00 3.16
528 532 1.679680 CATTCTGCTCCGGATTGCATT 59.320 47.619 17.78 4.80 38.59 3.56
541 545 1.442769 TTGCATTCGGAAGACTCTGC 58.557 50.000 6.36 6.36 41.84 4.26
573 577 3.554934 TGCTTGATCAATAAAGGCCGAT 58.445 40.909 8.96 0.00 0.00 4.18
609 613 2.993264 TTCCGACACCTCCCGTCC 60.993 66.667 0.00 0.00 0.00 4.79
622 626 1.338136 CCCGTCCCCAGAGCAATAGT 61.338 60.000 0.00 0.00 0.00 2.12
628 632 1.148157 CCCAGAGCAATAGTCGTGCG 61.148 60.000 0.00 0.00 46.86 5.34
677 681 2.840651 GGGAAAGGTGGAGATCTGAAGA 59.159 50.000 0.00 0.00 0.00 2.87
679 683 3.118445 GGAAAGGTGGAGATCTGAAGAGG 60.118 52.174 0.00 0.00 0.00 3.69
681 685 1.648568 AGGTGGAGATCTGAAGAGGGA 59.351 52.381 0.00 0.00 0.00 4.20
686 690 1.219213 GAGATCTGAAGAGGGAGGGGA 59.781 57.143 0.00 0.00 0.00 4.81
692 696 1.133009 TGAAGAGGGAGGGGATCTAGC 60.133 57.143 0.00 0.00 0.00 3.42
709 713 1.486211 AGCAGGCGTCAACTAGGTAT 58.514 50.000 0.00 0.00 0.00 2.73
719 724 6.018994 GGCGTCAACTAGGTATGTATTTTCTG 60.019 42.308 0.00 0.00 0.00 3.02
772 778 9.897744 ATTTAGTTTAGAAACACACATGTCATG 57.102 29.630 11.41 11.41 38.45 3.07
921 927 1.819632 GCACCGGTCCATCCATCAC 60.820 63.158 2.59 0.00 35.57 3.06
980 987 4.662278 TGGCTTATAAATAGCACCCATCC 58.338 43.478 0.00 0.00 40.42 3.51
983 990 2.949177 ATAAATAGCACCCATCCGCA 57.051 45.000 0.00 0.00 0.00 5.69
1492 1521 1.533033 TGGTCACGGGAGCTTCTCA 60.533 57.895 19.03 0.00 42.05 3.27
1587 1616 6.429692 TGGTTAGCATCTTTCGATTTTTCTCA 59.570 34.615 0.00 0.00 0.00 3.27
1588 1617 7.121168 TGGTTAGCATCTTTCGATTTTTCTCAT 59.879 33.333 0.00 0.00 0.00 2.90
1626 1660 4.760204 AGACAGTTTAGTATGCACCCAAAC 59.240 41.667 0.00 0.00 33.42 2.93
1634 1668 2.363306 ATGCACCCAAACTCTGAACA 57.637 45.000 0.00 0.00 0.00 3.18
1646 1680 6.127814 CCAAACTCTGAACATGCACAGATTAT 60.128 38.462 18.33 8.37 41.35 1.28
1738 1788 3.504906 CGGGCTGCAATTTCTATCATGAT 59.495 43.478 13.81 13.81 0.00 2.45
1741 1791 5.924825 GGGCTGCAATTTCTATCATGATTTC 59.075 40.000 14.65 0.00 0.00 2.17
1789 1839 6.603201 TCATGAAAAGGAGCTAAAATTCGGAT 59.397 34.615 0.00 0.00 0.00 4.18
1828 1878 4.848757 ACAAGATGCGAAACAGAGTTTTC 58.151 39.130 0.00 0.00 32.92 2.29
1835 1885 1.947456 GAAACAGAGTTTTCGCACCCT 59.053 47.619 0.00 0.00 0.00 4.34
1842 1908 5.766174 ACAGAGTTTTCGCACCCTATTAAAA 59.234 36.000 0.00 0.00 0.00 1.52
1961 2145 3.886324 TGGAGACAAAAACGTGGGT 57.114 47.368 0.00 0.00 37.44 4.51
1963 2147 1.065345 TGGAGACAAAAACGTGGGTCA 60.065 47.619 10.47 0.00 37.44 4.02
1964 2148 1.332686 GGAGACAAAAACGTGGGTCAC 59.667 52.381 10.47 5.43 32.79 3.67
1965 2149 1.332686 GAGACAAAAACGTGGGTCACC 59.667 52.381 10.47 0.00 32.79 4.02
1966 2150 0.382873 GACAAAAACGTGGGTCACCC 59.617 55.000 5.63 5.63 45.71 4.61
2059 2246 2.053627 GGTTCTGCATTTTCTTGTGCG 58.946 47.619 0.00 0.00 44.11 5.34
2144 2339 8.530804 TTATTACTCCCTCTGTAAACTACTCC 57.469 38.462 0.00 0.00 34.20 3.85
2145 2340 3.710724 ACTCCCTCTGTAAACTACTCCC 58.289 50.000 0.00 0.00 0.00 4.30
2146 2341 3.337301 ACTCCCTCTGTAAACTACTCCCT 59.663 47.826 0.00 0.00 0.00 4.20
2147 2342 3.955551 CTCCCTCTGTAAACTACTCCCTC 59.044 52.174 0.00 0.00 0.00 4.30
2148 2343 3.032459 CCCTCTGTAAACTACTCCCTCC 58.968 54.545 0.00 0.00 0.00 4.30
2149 2344 2.688958 CCTCTGTAAACTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
2150 2345 3.354467 CTCTGTAAACTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
2151 2346 3.762823 CTCTGTAAACTACTCCCTCCGTT 59.237 47.826 0.00 0.00 0.00 4.44
2152 2347 3.760684 TCTGTAAACTACTCCCTCCGTTC 59.239 47.826 0.00 0.00 0.00 3.95
2153 2348 2.827921 TGTAAACTACTCCCTCCGTTCC 59.172 50.000 0.00 0.00 0.00 3.62
2154 2349 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2155 2350 2.019807 AACTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2156 2351 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2157 2352 2.332117 ACTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2158 2353 2.910977 ACTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2159 2354 4.098894 ACTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2160 2355 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2161 2356 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2162 2357 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2163 2358 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2164 2359 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2165 2360 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2166 2361 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2167 2362 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2168 2363 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2169 2364 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2170 2365 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2171 2366 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2172 2367 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2173 2368 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2174 2369 7.094549 CGTTCCAAAATAGATGACCCAACTTTA 60.095 37.037 0.00 0.00 0.00 1.85
2175 2370 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
2176 2371 9.983024 TTCCAAAATAGATGACCCAACTTTATA 57.017 29.630 0.00 0.00 0.00 0.98
2177 2372 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
2178 2373 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
2200 2395 9.716531 ATACTAAAGTTAGTACAAAGTTGGGTC 57.283 33.333 12.07 0.00 45.86 4.46
2201 2396 7.567458 ACTAAAGTTAGTACAAAGTTGGGTCA 58.433 34.615 1.81 0.00 41.92 4.02
2202 2397 8.215736 ACTAAAGTTAGTACAAAGTTGGGTCAT 58.784 33.333 1.81 0.00 41.92 3.06
2203 2398 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
2204 2399 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
2205 2400 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
2206 2401 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
2207 2402 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
2208 2403 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2209 2404 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2210 2405 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2211 2406 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
2212 2407 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
2213 2408 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
2214 2409 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
2215 2410 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
2216 2411 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
2217 2412 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
2218 2413 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
2219 2414 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
2220 2415 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
2221 2416 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
2222 2417 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
2223 2418 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
2224 2419 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
2225 2420 6.363167 TCTATTTTGAAACGGAGGGAGTAA 57.637 37.500 0.00 0.00 0.00 2.24
2226 2421 6.954232 TCTATTTTGAAACGGAGGGAGTAAT 58.046 36.000 0.00 0.00 0.00 1.89
2227 2422 8.081517 TCTATTTTGAAACGGAGGGAGTAATA 57.918 34.615 0.00 0.00 0.00 0.98
2228 2423 6.997239 ATTTTGAAACGGAGGGAGTAATAC 57.003 37.500 0.00 0.00 0.00 1.89
2229 2424 5.750352 TTTGAAACGGAGGGAGTAATACT 57.250 39.130 0.00 0.00 0.00 2.12
2230 2425 6.855763 TTTGAAACGGAGGGAGTAATACTA 57.144 37.500 0.00 0.00 0.00 1.82
2231 2426 7.427989 TTTGAAACGGAGGGAGTAATACTAT 57.572 36.000 0.00 0.00 0.00 2.12
2232 2427 8.537728 TTTGAAACGGAGGGAGTAATACTATA 57.462 34.615 0.00 0.00 0.00 1.31
2233 2428 8.537728 TTGAAACGGAGGGAGTAATACTATAA 57.462 34.615 0.00 0.00 0.00 0.98
2234 2429 8.174733 TGAAACGGAGGGAGTAATACTATAAG 57.825 38.462 0.00 0.00 0.00 1.73
2235 2430 8.000709 TGAAACGGAGGGAGTAATACTATAAGA 58.999 37.037 0.00 0.00 0.00 2.10
2236 2431 7.999450 AACGGAGGGAGTAATACTATAAGAG 57.001 40.000 0.00 0.00 0.00 2.85
2237 2432 7.089106 ACGGAGGGAGTAATACTATAAGAGT 57.911 40.000 0.00 0.00 42.69 3.24
2238 2433 6.941436 ACGGAGGGAGTAATACTATAAGAGTG 59.059 42.308 0.00 0.00 39.39 3.51
2239 2434 6.941436 CGGAGGGAGTAATACTATAAGAGTGT 59.059 42.308 0.00 0.00 39.39 3.55
2240 2435 7.447853 CGGAGGGAGTAATACTATAAGAGTGTT 59.552 40.741 0.00 0.00 41.83 3.32
2241 2436 9.145442 GGAGGGAGTAATACTATAAGAGTGTTT 57.855 37.037 0.00 0.00 39.87 2.83
2286 2481 9.309516 TCTAAACACTCTTATATTAGTTTGCGG 57.690 33.333 0.00 0.00 32.23 5.69
2287 2482 9.309516 CTAAACACTCTTATATTAGTTTGCGGA 57.690 33.333 0.00 0.00 32.23 5.54
2288 2483 7.772332 AACACTCTTATATTAGTTTGCGGAG 57.228 36.000 0.00 0.00 0.00 4.63
2289 2484 6.281405 ACACTCTTATATTAGTTTGCGGAGG 58.719 40.000 0.00 0.00 0.00 4.30
2290 2485 5.696724 CACTCTTATATTAGTTTGCGGAGGG 59.303 44.000 0.00 0.00 0.00 4.30
2291 2486 5.601313 ACTCTTATATTAGTTTGCGGAGGGA 59.399 40.000 0.00 0.00 0.00 4.20
2292 2487 6.097915 TCTTATATTAGTTTGCGGAGGGAG 57.902 41.667 0.00 0.00 0.00 4.30
2293 2488 5.601313 TCTTATATTAGTTTGCGGAGGGAGT 59.399 40.000 0.00 0.00 0.00 3.85
2294 2489 6.779049 TCTTATATTAGTTTGCGGAGGGAGTA 59.221 38.462 0.00 0.00 0.00 2.59
2295 2490 7.453752 TCTTATATTAGTTTGCGGAGGGAGTAT 59.546 37.037 0.00 0.00 0.00 2.12
2320 2515 2.276472 TGCGGTGCAGCAATTAATTC 57.724 45.000 17.33 0.00 45.06 2.17
2539 2847 2.429971 CAGATTCAGAGCTGCTAGACCA 59.570 50.000 0.15 0.00 31.79 4.02
2540 2848 3.069872 CAGATTCAGAGCTGCTAGACCAT 59.930 47.826 0.15 0.00 31.79 3.55
2542 2850 3.533606 TTCAGAGCTGCTAGACCATTC 57.466 47.619 0.15 0.00 0.00 2.67
2729 3053 2.616765 GGAGCAGAAAAGGGGAGAGAAC 60.617 54.545 0.00 0.00 0.00 3.01
2767 3334 6.939163 AGATATGATTAGGCTGCCAAACTAAG 59.061 38.462 22.65 0.00 31.02 2.18
2787 3354 1.546548 GCTGCCCCTAAAGATCCATCC 60.547 57.143 0.00 0.00 0.00 3.51
2788 3355 1.776667 CTGCCCCTAAAGATCCATCCA 59.223 52.381 0.00 0.00 0.00 3.41
2789 3356 2.377869 CTGCCCCTAAAGATCCATCCAT 59.622 50.000 0.00 0.00 0.00 3.41
2790 3357 2.376518 TGCCCCTAAAGATCCATCCATC 59.623 50.000 0.00 0.00 0.00 3.51
2842 3578 2.627221 GGTCCGTCCTTTCCTAGATACC 59.373 54.545 0.00 0.00 0.00 2.73
2849 3585 6.294473 CGTCCTTTCCTAGATACCACTACTA 58.706 44.000 0.00 0.00 0.00 1.82
2998 3776 2.545946 GCATCGAATCTTACCTTGGCTC 59.454 50.000 0.00 0.00 0.00 4.70
3117 4136 1.251251 CCTTGCCCTTTTCAGTCAGG 58.749 55.000 0.00 0.00 0.00 3.86
3118 4137 1.479389 CCTTGCCCTTTTCAGTCAGGT 60.479 52.381 0.00 0.00 0.00 4.00
3121 4140 0.875059 GCCCTTTTCAGTCAGGTTCG 59.125 55.000 0.00 0.00 0.00 3.95
3130 4149 2.669569 TCAGGTTCGGCTGCTTGC 60.670 61.111 0.00 0.00 41.94 4.01
3162 4181 2.296752 TGGTTGTGGCATCAGTCAATTG 59.703 45.455 0.00 0.00 0.00 2.32
3163 4182 2.331194 GTTGTGGCATCAGTCAATTGC 58.669 47.619 0.00 0.00 35.64 3.56
3165 4184 1.962100 TGTGGCATCAGTCAATTGCAA 59.038 42.857 0.00 0.00 38.12 4.08
3166 4185 2.563620 TGTGGCATCAGTCAATTGCAAT 59.436 40.909 5.99 5.99 38.12 3.56
3167 4186 3.007074 TGTGGCATCAGTCAATTGCAATT 59.993 39.130 18.99 18.99 38.12 2.32
3168 4187 3.998341 GTGGCATCAGTCAATTGCAATTT 59.002 39.130 21.95 5.46 38.12 1.82
3169 4188 4.453136 GTGGCATCAGTCAATTGCAATTTT 59.547 37.500 21.95 8.20 38.12 1.82
3171 4190 6.147492 GTGGCATCAGTCAATTGCAATTTTAA 59.853 34.615 21.95 8.11 38.12 1.52
3172 4191 6.147492 TGGCATCAGTCAATTGCAATTTTAAC 59.853 34.615 21.95 18.41 38.12 2.01
3173 4192 6.402442 GGCATCAGTCAATTGCAATTTTAACC 60.402 38.462 21.95 11.38 38.12 2.85
3174 4193 6.147492 GCATCAGTCAATTGCAATTTTAACCA 59.853 34.615 21.95 10.27 36.40 3.67
3175 4194 7.307870 GCATCAGTCAATTGCAATTTTAACCAA 60.308 33.333 21.95 11.21 36.40 3.67
3178 4197 7.984050 TCAGTCAATTGCAATTTTAACCAAGAA 59.016 29.630 21.95 0.00 0.00 2.52
3179 4198 8.610896 CAGTCAATTGCAATTTTAACCAAGAAA 58.389 29.630 21.95 0.00 0.00 2.52
3180 4199 9.171877 AGTCAATTGCAATTTTAACCAAGAAAA 57.828 25.926 21.95 0.00 0.00 2.29
3181 4200 9.780413 GTCAATTGCAATTTTAACCAAGAAAAA 57.220 25.926 21.95 0.00 30.03 1.94
3261 4327 6.115446 TGAATTGAGCAGATTACCGAGAATT 58.885 36.000 0.00 0.00 0.00 2.17
3414 4492 4.098349 TCAGCTGAAAAACTGCACTGAATT 59.902 37.500 15.67 0.00 44.13 2.17
3458 4536 1.374947 GCAGTGGTACAGAAGCCCA 59.625 57.895 0.00 0.00 41.80 5.36
3470 4548 3.133365 AAGCCCAGGCAAGAACGGT 62.133 57.895 12.03 0.00 44.88 4.83
3569 4647 1.554891 CGATGATCGCGCTGCTCATT 61.555 55.000 15.80 4.77 31.14 2.57
3907 5017 7.825681 AGATCCATCTACGAATAGTTCATGAG 58.174 38.462 0.00 0.00 34.85 2.90
3908 5018 6.961360 TCCATCTACGAATAGTTCATGAGT 57.039 37.500 0.00 0.00 0.00 3.41
3909 5019 7.348080 TCCATCTACGAATAGTTCATGAGTT 57.652 36.000 0.00 0.00 0.00 3.01
3910 5020 8.459911 TCCATCTACGAATAGTTCATGAGTTA 57.540 34.615 0.00 0.00 0.00 2.24
3911 5021 8.568794 TCCATCTACGAATAGTTCATGAGTTAG 58.431 37.037 0.00 0.00 0.00 2.34
3912 5022 7.327275 CCATCTACGAATAGTTCATGAGTTAGC 59.673 40.741 0.00 0.00 0.00 3.09
3913 5023 7.329588 TCTACGAATAGTTCATGAGTTAGCA 57.670 36.000 0.00 0.00 0.00 3.49
3914 5024 7.418408 TCTACGAATAGTTCATGAGTTAGCAG 58.582 38.462 0.00 0.00 0.00 4.24
3915 5025 6.208988 ACGAATAGTTCATGAGTTAGCAGA 57.791 37.500 0.00 0.00 0.00 4.26
3916 5026 6.037098 ACGAATAGTTCATGAGTTAGCAGAC 58.963 40.000 0.00 0.00 0.00 3.51
3917 5027 6.127591 ACGAATAGTTCATGAGTTAGCAGACT 60.128 38.462 0.00 0.00 0.00 3.24
3918 5028 7.067129 ACGAATAGTTCATGAGTTAGCAGACTA 59.933 37.037 0.00 0.00 0.00 2.59
3919 5029 8.079203 CGAATAGTTCATGAGTTAGCAGACTAT 58.921 37.037 6.61 6.61 0.00 2.12
3920 5030 9.757227 GAATAGTTCATGAGTTAGCAGACTATT 57.243 33.333 18.42 18.42 31.79 1.73
3921 5031 9.539825 AATAGTTCATGAGTTAGCAGACTATTG 57.460 33.333 17.97 0.00 0.00 1.90
3922 5032 6.940739 AGTTCATGAGTTAGCAGACTATTGT 58.059 36.000 0.00 0.00 0.00 2.71
3923 5033 7.390027 AGTTCATGAGTTAGCAGACTATTGTT 58.610 34.615 0.00 0.00 0.00 2.83
3924 5034 7.880195 AGTTCATGAGTTAGCAGACTATTGTTT 59.120 33.333 0.00 0.00 0.00 2.83
3925 5035 7.834068 TCATGAGTTAGCAGACTATTGTTTC 57.166 36.000 0.00 0.00 0.00 2.78
3926 5036 6.818644 TCATGAGTTAGCAGACTATTGTTTCC 59.181 38.462 0.00 0.00 0.00 3.13
3927 5037 6.109156 TGAGTTAGCAGACTATTGTTTCCA 57.891 37.500 0.00 0.00 0.00 3.53
3928 5038 6.530120 TGAGTTAGCAGACTATTGTTTCCAA 58.470 36.000 0.00 0.00 34.45 3.53
3929 5039 6.995686 TGAGTTAGCAGACTATTGTTTCCAAA 59.004 34.615 0.00 0.00 33.44 3.28
3930 5040 7.500892 TGAGTTAGCAGACTATTGTTTCCAAAA 59.499 33.333 0.00 0.00 33.44 2.44
3931 5041 8.232913 AGTTAGCAGACTATTGTTTCCAAAAA 57.767 30.769 0.00 0.00 33.44 1.94
4405 5525 1.317613 TTCACCAGCGCTCAATGTTT 58.682 45.000 7.13 0.00 0.00 2.83
4413 5533 3.539563 CAGCGCTCAATGTTTATTTGTCG 59.460 43.478 7.13 0.00 0.00 4.35
4649 5773 7.096884 TGTACTTACCTACTAATGCTGAGTG 57.903 40.000 0.00 0.00 0.00 3.51
4908 6038 4.409570 GCAAGCACAAGTGATGTAAGATG 58.590 43.478 4.04 0.00 41.46 2.90
4939 6069 4.708177 TCATAGCCTGCTGGAGAAATTAC 58.292 43.478 14.77 0.00 34.57 1.89
4973 6103 5.314923 TCCTGCTAAAATCAAAGCATGTC 57.685 39.130 0.00 0.00 46.96 3.06
5063 6224 6.071952 GCATTCTCCAATCTTACCAGTTTTGA 60.072 38.462 0.00 0.00 0.00 2.69
5329 6502 3.447229 ACCATAAGCATAACAAGTTGGCC 59.553 43.478 7.96 0.00 0.00 5.36
5352 6525 6.568869 CCAAATTCCCAACGCTGAAAATATA 58.431 36.000 0.00 0.00 0.00 0.86
5362 6535 7.201513 CCAACGCTGAAAATATAAAATGTTGGG 60.202 37.037 0.00 0.00 45.39 4.12
5375 6548 2.572209 TGTTGGGCCACTAACCTTAC 57.428 50.000 5.23 0.00 37.28 2.34
5378 6551 3.224269 GTTGGGCCACTAACCTTACAAA 58.776 45.455 5.23 0.00 32.49 2.83
5432 6605 7.862675 AGTTGGCCAAACTCTTAGATACTAAT 58.137 34.615 22.47 0.00 46.60 1.73
5493 6950 6.539173 TGAACCTACAAATTAGCAGGAGAAA 58.461 36.000 6.23 0.00 32.25 2.52
5518 6975 2.176045 CCAAACCTGGAATTACCCACC 58.824 52.381 0.00 0.00 46.92 4.61
5534 6991 2.213499 CCACCGATTATGGACTTCAGC 58.787 52.381 0.00 0.00 39.87 4.26
5543 7000 0.888619 TGGACTTCAGCACTCTACCG 59.111 55.000 0.00 0.00 0.00 4.02
5618 7075 9.894783 ACAATCGATATATACTTGCCGATATAC 57.105 33.333 0.00 0.00 35.98 1.47
5787 7244 3.727726 CAAACCTCCAAAACCATTGTCC 58.272 45.455 0.00 0.00 0.00 4.02
5874 7331 1.421646 CACTTGACCTTCAGTTCCCCT 59.578 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 3.511934 GGCGGAGACCATAGATGATTAGT 59.488 47.826 0.00 0.00 0.00 2.24
67 68 2.492088 CGGCGGAGACCATAGATGATTA 59.508 50.000 0.00 0.00 0.00 1.75
69 70 0.891373 CGGCGGAGACCATAGATGAT 59.109 55.000 0.00 0.00 0.00 2.45
72 73 2.574955 GGCGGCGGAGACCATAGAT 61.575 63.158 9.78 0.00 0.00 1.98
114 116 4.707105 TCAGACAAAGAGAGTTGCATCAA 58.293 39.130 0.00 0.00 31.29 2.57
121 123 3.006752 CAGCTCCTCAGACAAAGAGAGTT 59.993 47.826 0.00 0.00 35.09 3.01
122 124 2.562298 CAGCTCCTCAGACAAAGAGAGT 59.438 50.000 0.00 0.00 35.09 3.24
123 125 2.674747 GCAGCTCCTCAGACAAAGAGAG 60.675 54.545 0.00 0.00 35.09 3.20
124 126 1.274728 GCAGCTCCTCAGACAAAGAGA 59.725 52.381 0.00 0.00 35.09 3.10
125 127 1.001746 TGCAGCTCCTCAGACAAAGAG 59.998 52.381 0.00 0.00 0.00 2.85
126 128 1.051008 TGCAGCTCCTCAGACAAAGA 58.949 50.000 0.00 0.00 0.00 2.52
129 131 0.689055 ATGTGCAGCTCCTCAGACAA 59.311 50.000 0.00 0.00 0.00 3.18
148 150 1.203212 CCACCACCCCTATACCGGATA 60.203 57.143 9.46 0.44 0.00 2.59
176 178 2.026915 AGCTACACACAAGCCATCATGA 60.027 45.455 0.00 0.00 41.02 3.07
202 204 1.064825 ACCCCTCAACGGTTCAGAAT 58.935 50.000 0.00 0.00 0.00 2.40
242 244 3.534721 ACGGAGTGCTAAAGCTTCC 57.465 52.632 0.00 13.03 42.51 3.46
278 280 3.049080 ATCAAAGCCCTCCTCCCGC 62.049 63.158 0.00 0.00 0.00 6.13
316 318 0.951558 CTACACCACCAACAGGCAAC 59.048 55.000 0.00 0.00 0.00 4.17
323 325 1.301423 TCAAACGCTACACCACCAAC 58.699 50.000 0.00 0.00 0.00 3.77
333 335 5.487433 TCTGGATGAAGATTTCAAACGCTA 58.513 37.500 0.00 0.00 43.95 4.26
361 363 4.954118 TGGAGCCCACCACCGAGT 62.954 66.667 0.00 0.00 34.77 4.18
446 450 7.076842 GCTAAGACATGAGCTAAAACATTGA 57.923 36.000 0.00 0.00 35.73 2.57
528 532 3.587797 AATTTACGCAGAGTCTTCCGA 57.412 42.857 14.88 0.00 0.00 4.55
541 545 9.941991 CTTTATTGATCAAGCAACAAATTTACG 57.058 29.630 14.54 0.00 0.00 3.18
592 596 2.993264 GGACGGGAGGTGTCGGAA 60.993 66.667 0.00 0.00 37.22 4.30
596 600 3.391382 CTGGGGACGGGAGGTGTC 61.391 72.222 0.00 0.00 35.60 3.67
597 601 3.907027 CTCTGGGGACGGGAGGTGT 62.907 68.421 0.00 0.00 37.31 4.16
609 613 1.148157 CGCACGACTATTGCTCTGGG 61.148 60.000 0.00 0.00 37.87 4.45
611 615 0.179137 TCCGCACGACTATTGCTCTG 60.179 55.000 0.00 0.00 37.87 3.35
622 626 1.372499 CGGTTCTCTTTCCGCACGA 60.372 57.895 0.00 0.00 40.28 4.35
628 632 3.125573 GCCGGCGGTTCTCTTTCC 61.126 66.667 28.82 2.84 0.00 3.13
652 656 0.106967 GATCTCCACCTTTCCCAGCC 60.107 60.000 0.00 0.00 0.00 4.85
655 659 2.342406 TCAGATCTCCACCTTTCCCA 57.658 50.000 0.00 0.00 0.00 4.37
661 665 1.648568 TCCCTCTTCAGATCTCCACCT 59.351 52.381 0.00 0.00 0.00 4.00
677 681 1.551358 CCTGCTAGATCCCCTCCCT 59.449 63.158 0.00 0.00 0.00 4.20
679 683 2.578714 CGCCTGCTAGATCCCCTCC 61.579 68.421 0.00 0.00 0.00 4.30
681 685 1.834822 GACGCCTGCTAGATCCCCT 60.835 63.158 0.00 0.00 0.00 4.79
686 690 1.683917 CCTAGTTGACGCCTGCTAGAT 59.316 52.381 0.00 0.00 34.46 1.98
692 696 2.961526 ACATACCTAGTTGACGCCTG 57.038 50.000 0.00 0.00 0.00 4.85
745 751 9.897744 ATGACATGTGTGTTTCTAAACTAAATG 57.102 29.630 1.15 8.74 39.09 2.32
980 987 4.284860 TGGCCGGAGATCGATGCG 62.285 66.667 5.05 0.00 42.43 4.73
983 990 2.443952 TGGTGGCCGGAGATCGAT 60.444 61.111 5.05 0.00 42.43 3.59
1023 1030 2.736826 GGGAAAGCGGGGAGAGAGG 61.737 68.421 0.00 0.00 0.00 3.69
1392 1411 4.735578 GCGACGATCTGGTTAACTAATGGA 60.736 45.833 5.42 0.00 0.00 3.41
1588 1617 9.826574 ACTAAACTGTCTGTGTTTATGTTAAGA 57.173 29.630 0.00 0.00 38.62 2.10
1626 1660 6.093082 TGTTCATAATCTGTGCATGTTCAGAG 59.907 38.462 20.25 8.89 42.67 3.35
1634 1668 5.393124 CGTTTGTGTTCATAATCTGTGCAT 58.607 37.500 0.00 0.00 0.00 3.96
1646 1680 2.575694 ATTTGCAGCGTTTGTGTTCA 57.424 40.000 0.00 0.00 0.00 3.18
1761 1811 8.405531 CCGAATTTTAGCTCCTTTTCATGATTA 58.594 33.333 0.00 0.00 0.00 1.75
1845 2024 7.497579 GGGAGATATTTCTCTGAACCTTTTCTC 59.502 40.741 12.20 0.00 46.46 2.87
1856 2035 5.011090 TGTTGTCGGGAGATATTTCTCTG 57.989 43.478 12.20 6.43 46.46 3.35
1960 2144 3.336566 CCCGTCGTTTTGGGTGAC 58.663 61.111 0.00 0.00 40.76 3.67
1965 2149 1.008995 CTTGTGCCCGTCGTTTTGG 60.009 57.895 0.00 0.00 0.00 3.28
1966 2150 1.657181 GCTTGTGCCCGTCGTTTTG 60.657 57.895 0.00 0.00 0.00 2.44
2059 2246 5.731967 GCCCCGCAAAAATAAATAAATTGCC 60.732 40.000 0.00 0.00 42.47 4.52
2122 2317 5.016031 AGGGAGTAGTTTACAGAGGGAGTAA 59.984 44.000 0.00 0.00 0.00 2.24
2123 2318 4.543337 AGGGAGTAGTTTACAGAGGGAGTA 59.457 45.833 0.00 0.00 0.00 2.59
2125 2320 3.955551 GAGGGAGTAGTTTACAGAGGGAG 59.044 52.174 0.00 0.00 0.00 4.30
2127 2322 3.032459 GGAGGGAGTAGTTTACAGAGGG 58.968 54.545 0.00 0.00 0.00 4.30
2128 2323 2.688958 CGGAGGGAGTAGTTTACAGAGG 59.311 54.545 0.00 0.00 0.00 3.69
2129 2324 3.354467 ACGGAGGGAGTAGTTTACAGAG 58.646 50.000 0.00 0.00 0.00 3.35
2130 2325 3.446442 ACGGAGGGAGTAGTTTACAGA 57.554 47.619 0.00 0.00 0.00 3.41
2131 2326 3.119209 GGAACGGAGGGAGTAGTTTACAG 60.119 52.174 0.00 0.00 0.00 2.74
2132 2327 2.827921 GGAACGGAGGGAGTAGTTTACA 59.172 50.000 0.00 0.00 0.00 2.41
2133 2328 2.827921 TGGAACGGAGGGAGTAGTTTAC 59.172 50.000 0.00 0.00 0.00 2.01
2134 2329 3.173953 TGGAACGGAGGGAGTAGTTTA 57.826 47.619 0.00 0.00 0.00 2.01
2135 2330 2.019807 TGGAACGGAGGGAGTAGTTT 57.980 50.000 0.00 0.00 0.00 2.66
2136 2331 2.019807 TTGGAACGGAGGGAGTAGTT 57.980 50.000 0.00 0.00 0.00 2.24
2137 2332 2.019807 TTTGGAACGGAGGGAGTAGT 57.980 50.000 0.00 0.00 0.00 2.73
2138 2333 3.629142 ATTTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
2139 2334 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2140 2335 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2141 2336 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2142 2337 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2143 2338 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2144 2339 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2145 2340 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2146 2341 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2147 2342 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2148 2343 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2149 2344 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2150 2345 8.893563 ATAAAGTTGGGTCATCTATTTTGGAA 57.106 30.769 0.00 0.00 0.00 3.53
2151 2346 9.403583 GTATAAAGTTGGGTCATCTATTTTGGA 57.596 33.333 0.00 0.00 0.00 3.53
2152 2347 9.408648 AGTATAAAGTTGGGTCATCTATTTTGG 57.591 33.333 0.00 0.00 0.00 3.28
2174 2369 9.716531 GACCCAACTTTGTACTAACTTTAGTAT 57.283 33.333 11.18 0.00 45.11 2.12
2175 2370 8.703743 TGACCCAACTTTGTACTAACTTTAGTA 58.296 33.333 4.98 4.98 43.36 1.82
2176 2371 7.567458 TGACCCAACTTTGTACTAACTTTAGT 58.433 34.615 6.85 6.85 45.39 2.24
2177 2372 8.617290 ATGACCCAACTTTGTACTAACTTTAG 57.383 34.615 0.00 0.00 36.82 1.85
2178 2373 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
2179 2374 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
2180 2375 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
2181 2376 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
2182 2377 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2183 2378 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2184 2379 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2185 2380 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
2186 2381 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
2187 2382 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
2188 2383 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
2189 2384 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
2190 2385 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
2191 2386 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
2192 2387 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
2193 2388 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
2194 2389 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
2195 2390 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
2196 2391 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
2197 2392 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
2198 2393 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2199 2394 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
2200 2395 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2201 2396 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2202 2397 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2203 2398 7.985752 AGTATTACTCCCTCCGTTTCAAAATAG 59.014 37.037 0.00 0.00 0.00 1.73
2204 2399 7.854337 AGTATTACTCCCTCCGTTTCAAAATA 58.146 34.615 0.00 0.00 0.00 1.40
2205 2400 6.718294 AGTATTACTCCCTCCGTTTCAAAAT 58.282 36.000 0.00 0.00 0.00 1.82
2206 2401 6.117975 AGTATTACTCCCTCCGTTTCAAAA 57.882 37.500 0.00 0.00 0.00 2.44
2207 2402 5.750352 AGTATTACTCCCTCCGTTTCAAA 57.250 39.130 0.00 0.00 0.00 2.69
2208 2403 8.537728 TTATAGTATTACTCCCTCCGTTTCAA 57.462 34.615 0.00 0.00 0.00 2.69
2209 2404 8.000709 TCTTATAGTATTACTCCCTCCGTTTCA 58.999 37.037 0.00 0.00 0.00 2.69
2210 2405 8.401490 TCTTATAGTATTACTCCCTCCGTTTC 57.599 38.462 0.00 0.00 0.00 2.78
2211 2406 8.003629 ACTCTTATAGTATTACTCCCTCCGTTT 58.996 37.037 0.00 0.00 36.36 3.60
2212 2407 7.447853 CACTCTTATAGTATTACTCCCTCCGTT 59.552 40.741 0.00 0.00 35.76 4.44
2213 2408 6.941436 CACTCTTATAGTATTACTCCCTCCGT 59.059 42.308 0.00 0.00 35.76 4.69
2214 2409 6.941436 ACACTCTTATAGTATTACTCCCTCCG 59.059 42.308 0.00 0.00 35.76 4.63
2215 2410 8.709272 AACACTCTTATAGTATTACTCCCTCC 57.291 38.462 0.00 0.00 35.76 4.30
2260 2455 9.309516 CCGCAAACTAATATAAGAGTGTTTAGA 57.690 33.333 0.00 0.00 0.00 2.10
2261 2456 9.309516 TCCGCAAACTAATATAAGAGTGTTTAG 57.690 33.333 0.00 0.00 0.00 1.85
2262 2457 9.309516 CTCCGCAAACTAATATAAGAGTGTTTA 57.690 33.333 0.00 0.00 0.00 2.01
2263 2458 7.280205 CCTCCGCAAACTAATATAAGAGTGTTT 59.720 37.037 0.00 0.00 0.00 2.83
2264 2459 6.761714 CCTCCGCAAACTAATATAAGAGTGTT 59.238 38.462 0.00 0.00 0.00 3.32
2265 2460 6.281405 CCTCCGCAAACTAATATAAGAGTGT 58.719 40.000 0.00 0.00 0.00 3.55
2266 2461 5.696724 CCCTCCGCAAACTAATATAAGAGTG 59.303 44.000 0.00 0.00 0.00 3.51
2267 2462 5.601313 TCCCTCCGCAAACTAATATAAGAGT 59.399 40.000 0.00 0.00 0.00 3.24
2268 2463 6.097915 TCCCTCCGCAAACTAATATAAGAG 57.902 41.667 0.00 0.00 0.00 2.85
2269 2464 5.601313 ACTCCCTCCGCAAACTAATATAAGA 59.399 40.000 0.00 0.00 0.00 2.10
2270 2465 5.855045 ACTCCCTCCGCAAACTAATATAAG 58.145 41.667 0.00 0.00 0.00 1.73
2271 2466 5.881923 ACTCCCTCCGCAAACTAATATAA 57.118 39.130 0.00 0.00 0.00 0.98
2272 2467 7.549147 AATACTCCCTCCGCAAACTAATATA 57.451 36.000 0.00 0.00 0.00 0.86
2273 2468 6.435292 AATACTCCCTCCGCAAACTAATAT 57.565 37.500 0.00 0.00 0.00 1.28
2274 2469 5.881923 AATACTCCCTCCGCAAACTAATA 57.118 39.130 0.00 0.00 0.00 0.98
2275 2470 4.772886 AATACTCCCTCCGCAAACTAAT 57.227 40.909 0.00 0.00 0.00 1.73
2276 2471 4.563140 AAATACTCCCTCCGCAAACTAA 57.437 40.909 0.00 0.00 0.00 2.24
2277 2472 4.563140 AAAATACTCCCTCCGCAAACTA 57.437 40.909 0.00 0.00 0.00 2.24
2278 2473 3.434940 AAAATACTCCCTCCGCAAACT 57.565 42.857 0.00 0.00 0.00 2.66
2319 2514 5.526479 GCATCACTAGATCAAAGCATCAAGA 59.474 40.000 0.00 0.00 30.20 3.02
2320 2515 5.527951 AGCATCACTAGATCAAAGCATCAAG 59.472 40.000 0.00 0.00 30.20 3.02
2539 2847 7.952671 TCTTAGCCTACAAATATCTGTCGAAT 58.047 34.615 0.00 0.00 0.00 3.34
2540 2848 7.342769 TCTTAGCCTACAAATATCTGTCGAA 57.657 36.000 0.00 0.00 0.00 3.71
2542 2850 9.862371 AATATCTTAGCCTACAAATATCTGTCG 57.138 33.333 0.00 0.00 0.00 4.35
2678 3002 0.462225 CACTCTGCATCTCAGGCTGG 60.462 60.000 15.73 5.63 43.06 4.85
2715 3039 1.777272 AGCAGTGTTCTCTCCCCTTTT 59.223 47.619 0.00 0.00 0.00 2.27
2729 3053 7.257003 CCTAATCATATCTACTAGCAGCAGTG 58.743 42.308 0.00 0.00 0.00 3.66
2767 3334 1.546548 GGATGGATCTTTAGGGGCAGC 60.547 57.143 0.00 0.00 0.00 5.25
2842 3578 6.127758 TGTTTGGCTGGCATTATTTAGTAGTG 60.128 38.462 4.22 0.00 0.00 2.74
2849 3585 4.317488 CTTGTGTTTGGCTGGCATTATTT 58.683 39.130 4.22 0.00 0.00 1.40
2998 3776 1.202879 TGGTGGGTGACTAAGCAAAGG 60.203 52.381 0.00 0.00 0.00 3.11
3130 4149 1.024271 CCACAACCACAACTCCACAG 58.976 55.000 0.00 0.00 0.00 3.66
3178 4197 7.944000 AGGATCCTGGTTAAAATTGCAATTTTT 59.056 29.630 40.12 28.15 43.91 1.94
3179 4198 7.460910 AGGATCCTGGTTAAAATTGCAATTTT 58.539 30.769 38.15 38.15 46.85 1.82
3180 4199 7.019656 AGGATCCTGGTTAAAATTGCAATTT 57.980 32.000 27.73 27.73 40.15 1.82
3181 4200 6.625532 AGGATCCTGGTTAAAATTGCAATT 57.374 33.333 18.99 18.99 0.00 2.32
3183 4202 7.015682 TGTTAAGGATCCTGGTTAAAATTGCAA 59.984 33.333 17.02 0.00 0.00 4.08
3184 4203 6.495181 TGTTAAGGATCCTGGTTAAAATTGCA 59.505 34.615 17.02 1.81 0.00 4.08
3261 4327 2.265367 TGGCTCCATCTCCTTGTACAA 58.735 47.619 8.28 8.28 0.00 2.41
3414 4492 0.321346 TGAGCCATTGCAGAAGACGA 59.679 50.000 0.00 0.00 41.13 4.20
3458 4536 0.889186 AATGCGAACCGTTCTTGCCT 60.889 50.000 9.55 0.00 0.00 4.75
3470 4548 1.000385 CTGCTTGGGTTGAAATGCGAA 60.000 47.619 0.00 0.00 0.00 4.70
3569 4647 2.124060 AAACACACACGCCATGGCA 61.124 52.632 34.93 0.00 42.06 4.92
3674 4769 3.120792 GTTAGTTGTTCAGTGCGAGTGA 58.879 45.455 0.00 0.00 0.00 3.41
3880 4987 8.300286 TCATGAACTATTCGTAGATGGATCTTC 58.700 37.037 0.00 0.00 38.32 2.87
3883 4990 7.598278 ACTCATGAACTATTCGTAGATGGATC 58.402 38.462 0.00 0.00 35.04 3.36
3895 5005 9.539825 CAATAGTCTGCTAACTCATGAACTATT 57.460 33.333 14.92 14.92 0.00 1.73
3928 5038 6.991938 TGACAAATAGGCTGCTAACATTTTT 58.008 32.000 0.00 0.00 0.00 1.94
3929 5039 6.588719 TGACAAATAGGCTGCTAACATTTT 57.411 33.333 0.00 0.00 0.00 1.82
3930 5040 6.406177 CCATGACAAATAGGCTGCTAACATTT 60.406 38.462 0.00 0.00 0.00 2.32
3931 5041 5.068198 CCATGACAAATAGGCTGCTAACATT 59.932 40.000 0.00 0.00 0.00 2.71
3932 5042 4.581824 CCATGACAAATAGGCTGCTAACAT 59.418 41.667 0.00 0.00 0.00 2.71
3933 5043 3.947196 CCATGACAAATAGGCTGCTAACA 59.053 43.478 0.00 0.00 0.00 2.41
3949 5059 2.557924 TGTTTGTTCCATCTGCCATGAC 59.442 45.455 0.00 0.00 0.00 3.06
3985 5097 7.673641 AGATGTTCAGAAGATGAGGTAATCT 57.326 36.000 0.00 0.00 39.68 2.40
4443 5563 1.210478 GGTAGCTCCATTCCTGCAAGA 59.790 52.381 0.00 0.00 33.33 3.02
4444 5564 1.211457 AGGTAGCTCCATTCCTGCAAG 59.789 52.381 0.00 0.00 39.02 4.01
4649 5773 1.725164 GCCGTAGTTTCAGTACACAGC 59.275 52.381 0.00 0.00 0.00 4.40
4815 5945 2.349886 GACAACATCTCCAACATCGCTC 59.650 50.000 0.00 0.00 0.00 5.03
4908 6038 3.132646 CCAGCAGGCTATGATATCTCTCC 59.867 52.174 3.98 0.58 0.00 3.71
4939 6069 2.747855 GCAGGAAGCCCGTTCTGG 60.748 66.667 0.00 0.00 37.23 3.86
5288 6461 3.074412 GGTGGTGTAGGTTCATGTTGAG 58.926 50.000 0.00 0.00 0.00 3.02
5329 6502 8.472683 TTTATATTTTCAGCGTTGGGAATTTG 57.527 30.769 0.00 0.00 0.00 2.32
5341 6514 6.037062 GTGGCCCAACATTTTATATTTTCAGC 59.963 38.462 0.00 0.00 0.00 4.26
5352 6525 2.970987 AGGTTAGTGGCCCAACATTTT 58.029 42.857 0.00 0.00 0.00 1.82
5362 6535 8.495148 CAAATTGAAATTTGTAAGGTTAGTGGC 58.505 33.333 16.80 0.00 46.27 5.01
5378 6551 4.226761 GCGACGAAGGTTCAAATTGAAAT 58.773 39.130 10.27 0.00 38.22 2.17
5398 6571 1.061857 GTTTGGCCAACTTGTTTTGCG 59.938 47.619 20.35 0.00 31.92 4.85
5427 6600 7.792032 TGCTAGTGGCTTACATTCTAATTAGT 58.208 34.615 12.19 0.00 42.39 2.24
5432 6605 8.044309 TGTAAATGCTAGTGGCTTACATTCTAA 58.956 33.333 8.62 0.00 36.96 2.10
5441 6614 7.880160 TGAAATATGTAAATGCTAGTGGCTT 57.120 32.000 0.00 0.00 42.39 4.35
5493 6950 2.837591 GGTAATTCCAGGTTTGGCCAAT 59.162 45.455 21.26 0.42 44.63 3.16
5518 6975 4.052159 AGAGTGCTGAAGTCCATAATCG 57.948 45.455 0.00 0.00 0.00 3.34
5534 6991 0.807667 GGTGATGCAGCGGTAGAGTG 60.808 60.000 0.00 0.00 0.00 3.51
5543 7000 5.934043 TCACTGTTATATATGGTGATGCAGC 59.066 40.000 0.00 0.00 32.91 5.25
5618 7075 3.726291 TGATGATGCATTGCCTTCATG 57.274 42.857 21.86 0.00 32.98 3.07
5787 7244 1.451567 CATGGCAGCAGTCAGGGAG 60.452 63.158 0.00 0.00 29.55 4.30
5948 7405 1.202568 TCGGTGCAATGGAGCAGATAG 60.203 52.381 4.63 0.00 46.69 2.08


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

AutoCloner maintained by Alex Coulton.