Multiple sequence alignment - TraesCS1D01G347100

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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 TraesCS1D01G347100 chr1D 100.000 3502 0 0 1 3502 434280823 434284324 0.000000e+00 6468.0
1 TraesCS1D01G347100 chr1D 100.000 2714 0 0 3756 6469 434284578 434287291 0.000000e+00 5012.0
2 TraesCS1D01G347100 chr1D 78.440 1628 314 24 3768 5375 434370181 434371791 0.000000e+00 1027.0
3 TraesCS1D01G347100 chr1D 83.593 1091 159 16 3790 4872 434338019 434339097 0.000000e+00 1005.0
4 TraesCS1D01G347100 chr1D 87.309 851 75 15 975 1816 434321515 434322341 0.000000e+00 942.0
5 TraesCS1D01G347100 chr1D 87.431 541 57 8 2964 3500 434337419 434337952 4.290000e-171 612.0
6 TraesCS1D01G347100 chr1D 78.132 910 144 29 4877 5765 434339136 434340011 1.600000e-145 527.0
7 TraesCS1D01G347100 chr1D 83.424 549 74 14 1987 2531 434322404 434322939 1.620000e-135 494.0
8 TraesCS1D01G347100 chr1D 77.830 848 152 29 979 1811 434367046 434367872 5.830000e-135 492.0
9 TraesCS1D01G347100 chr1D 90.358 363 29 3 2964 3325 434528833 434529190 7.590000e-129 472.0
10 TraesCS1D01G347100 chr1D 78.598 528 91 16 2976 3494 434369617 434370131 4.840000e-86 329.0
11 TraesCS1D01G347100 chr1D 74.749 499 100 19 1245 1727 434274202 434274690 3.960000e-47 200.0
12 TraesCS1D01G347100 chr1D 71.629 571 131 22 2011 2558 434368667 434369229 1.890000e-25 128.0
13 TraesCS1D01G347100 chr1B 92.330 2725 186 13 3756 6469 587991672 587994384 0.000000e+00 3853.0
14 TraesCS1D01G347100 chr1B 90.977 2527 164 25 51 2550 587988234 587990723 0.000000e+00 3345.0
15 TraesCS1D01G347100 chr1B 80.309 2006 319 49 3790 5765 588005693 588007652 0.000000e+00 1447.0
16 TraesCS1D01G347100 chr1B 94.524 913 49 1 2588 3500 587990723 587991634 0.000000e+00 1408.0
17 TraesCS1D01G347100 chr1B 77.587 1633 325 29 3765 5375 588153656 588155269 0.000000e+00 950.0
18 TraesCS1D01G347100 chr1B 86.192 898 89 15 975 1864 588002778 588003648 0.000000e+00 939.0
19 TraesCS1D01G347100 chr1B 86.271 539 66 8 2964 3500 588005098 588005630 4.350000e-161 579.0
20 TraesCS1D01G347100 chr1B 79.688 512 87 13 2987 3495 588153115 588153612 2.870000e-93 353.0
21 TraesCS1D01G347100 chr1B 78.271 451 84 13 4155 4598 622704780 622704337 1.780000e-70 278.0
22 TraesCS1D01G347100 chr1B 74.219 512 105 21 1232 1727 587981987 587982487 8.560000e-44 189.0
23 TraesCS1D01G347100 chr1B 94.495 109 6 0 984 1092 588150773 588150881 1.120000e-37 169.0
24 TraesCS1D01G347100 chr1B 79.612 206 37 5 4383 4586 588312581 588312783 6.760000e-30 143.0
25 TraesCS1D01G347100 chr1B 75.600 250 53 4 2011 2253 588151700 588151948 4.100000e-22 117.0
26 TraesCS1D01G347100 chr1B 93.103 58 4 0 2915 2972 510799147 510799090 1.160000e-12 86.1
27 TraesCS1D01G347100 chr1B 83.133 83 12 2 6098 6179 299058993 299059074 2.500000e-09 75.0
28 TraesCS1D01G347100 chr1B 82.222 90 12 3 1879 1967 492787896 492787982 2.500000e-09 75.0
29 TraesCS1D01G347100 chr1A 88.995 2735 234 31 3787 6467 532477630 532480351 0.000000e+00 3321.0
30 TraesCS1D01G347100 chr1A 93.524 942 39 9 2577 3499 532476628 532477566 0.000000e+00 1382.0
31 TraesCS1D01G347100 chr1A 91.958 858 47 7 1052 1889 532457830 532458685 0.000000e+00 1182.0
32 TraesCS1D01G347100 chr1A 77.409 1567 301 30 3765 5303 532488452 532489993 0.000000e+00 883.0
33 TraesCS1D01G347100 chr1A 95.890 292 11 1 2012 2302 532458736 532459027 7.590000e-129 472.0
34 TraesCS1D01G347100 chr1A 89.394 264 18 4 550 812 532452275 532452529 2.250000e-84 324.0
35 TraesCS1D01G347100 chr1A 91.064 235 21 0 2299 2533 532471267 532471501 1.050000e-82 318.0
36 TraesCS1D01G347100 chr1A 74.950 499 99 21 1245 1727 532435908 532436396 8.500000e-49 206.0
37 TraesCS1D01G347100 chr1A 93.893 131 8 0 923 1053 532456866 532456996 1.420000e-46 198.0
38 TraesCS1D01G347100 chr1A 96.552 58 2 0 2526 2583 532475827 532475884 5.340000e-16 97.1
39 TraesCS1D01G347100 chr7A 76.541 1168 248 20 4150 5299 77562568 77561409 3.310000e-172 616.0
40 TraesCS1D01G347100 chr5D 77.710 489 90 16 5936 6417 377480409 377479933 1.370000e-71 281.0
41 TraesCS1D01G347100 chr5D 77.273 440 84 14 102 532 398563544 398563112 1.800000e-60 244.0
42 TraesCS1D01G347100 chr5D 89.394 66 7 0 2915 2980 520110237 520110172 4.160000e-12 84.2
43 TraesCS1D01G347100 chr7D 78.125 352 63 13 5939 6283 164493548 164493204 1.830000e-50 211.0
44 TraesCS1D01G347100 chr6A 74.545 495 105 21 55 541 501180069 501180550 5.120000e-46 196.0
45 TraesCS1D01G347100 chr6A 78.378 111 19 5 1859 1965 606995500 606995609 4.190000e-07 67.6
46 TraesCS1D01G347100 chr3D 78.924 223 36 10 103 319 359599652 359599435 2.430000e-29 141.0
47 TraesCS1D01G347100 chr3D 87.037 54 6 1 1877 1929 536429819 536429872 7.000000e-05 60.2
48 TraesCS1D01G347100 chr4B 74.570 291 66 8 1406 1692 5406465 5406751 3.170000e-23 121.0
49 TraesCS1D01G347100 chr2A 88.158 76 9 0 1887 1962 61385914 61385989 2.480000e-14 91.6
50 TraesCS1D01G347100 chr2A 91.304 46 4 0 1888 1933 20489125 20489170 5.410000e-06 63.9
51 TraesCS1D01G347100 chr4D 91.935 62 5 0 2915 2976 324227814 324227753 3.210000e-13 87.9
52 TraesCS1D01G347100 chr4D 90.476 42 3 1 5950 5991 443157898 443157938 3.000000e-03 54.7
53 TraesCS1D01G347100 chr6B 77.124 153 31 4 136 285 219565907 219566058 1.160000e-12 86.1
54 TraesCS1D01G347100 chr6D 92.982 57 4 0 2915 2971 296699545 296699489 4.160000e-12 84.2
55 TraesCS1D01G347100 chr6D 92.982 57 4 0 2915 2971 446899128 446899072 4.160000e-12 84.2
56 TraesCS1D01G347100 chr5B 92.982 57 4 0 2915 2971 264876355 264876299 4.160000e-12 84.2
57 TraesCS1D01G347100 chrUn 92.727 55 4 0 2915 2969 29029233 29029287 5.380000e-11 80.5
58 TraesCS1D01G347100 chr4A 95.455 44 2 0 1921 1964 615882148 615882105 3.240000e-08 71.3
59 TraesCS1D01G347100 chr4A 92.000 50 4 0 1921 1970 615884848 615884799 3.240000e-08 71.3
60 TraesCS1D01G347100 chr4A 85.714 70 5 2 1902 1967 647387628 647387560 1.160000e-07 69.4
61 TraesCS1D01G347100 chr3A 90.196 51 4 1 1920 1969 710276373 710276323 1.510000e-06 65.8
62 TraesCS1D01G347100 chr2B 82.051 78 10 2 1890 1963 72603597 72603674 5.410000e-06 63.9
63 TraesCS1D01G347100 chr3B 87.037 54 6 1 1877 1929 708944266 708944319 7.000000e-05 60.2


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 TraesCS1D01G347100 chr1D 434280823 434287291 6468 False 5740.000000 6468 100.000000 1 6469 2 chr1D.!!$F3 6468
1 TraesCS1D01G347100 chr1D 434321515 434322939 1424 False 718.000000 942 85.366500 975 2531 2 chr1D.!!$F4 1556
2 TraesCS1D01G347100 chr1D 434337419 434340011 2592 False 714.666667 1005 83.052000 2964 5765 3 chr1D.!!$F5 2801
3 TraesCS1D01G347100 chr1D 434367046 434371791 4745 False 494.000000 1027 76.624250 979 5375 4 chr1D.!!$F6 4396
4 TraesCS1D01G347100 chr1B 587988234 587994384 6150 False 2868.666667 3853 92.610333 51 6469 3 chr1B.!!$F5 6418
5 TraesCS1D01G347100 chr1B 588002778 588007652 4874 False 988.333333 1447 84.257333 975 5765 3 chr1B.!!$F6 4790
6 TraesCS1D01G347100 chr1B 588150773 588155269 4496 False 397.250000 950 81.842500 984 5375 4 chr1B.!!$F7 4391
7 TraesCS1D01G347100 chr1A 532475827 532480351 4524 False 1600.033333 3321 93.023667 2526 6467 3 chr1A.!!$F6 3941
8 TraesCS1D01G347100 chr1A 532488452 532489993 1541 False 883.000000 883 77.409000 3765 5303 1 chr1A.!!$F4 1538
9 TraesCS1D01G347100 chr1A 532456866 532459027 2161 False 617.333333 1182 93.913667 923 2302 3 chr1A.!!$F5 1379
10 TraesCS1D01G347100 chr7A 77561409 77562568 1159 True 616.000000 616 76.541000 4150 5299 1 chr7A.!!$R1 1149

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
34 35 0.029567 CTCGCGGACTATCTGGACAC 59.970 60.000 6.13 0.00 0.00 3.67 F
398 399 0.037326 CGCTAGCTTGAACCCTGTGA 60.037 55.000 13.93 0.00 0.00 3.58 F
451 452 0.179084 TTTCTTAGGCGGGCATCTCG 60.179 55.000 3.78 0.00 0.00 4.04 F
644 645 0.528249 GTGTTTGTGCTGTTGCCCTG 60.528 55.000 0.00 0.00 38.71 4.45 F
864 867 1.004440 GCCCACTCTTGAGCGACTT 60.004 57.895 0.00 0.00 0.00 3.01 F
877 880 1.071567 GCGACTTGCCGTAGACACTC 61.072 60.000 0.00 0.00 37.76 3.51 F
880 883 1.153823 CTTGCCGTAGACACTCCGG 60.154 63.158 0.00 0.00 44.46 5.14 F
2134 3832 1.171308 CCTCTTTGAGGTACCGACGA 58.829 55.000 6.18 2.04 44.25 4.20 F
2425 4393 1.473965 CCATCATTCCCACCGTCAGAG 60.474 57.143 0.00 0.00 0.00 3.35 F
3993 7384 1.741706 CATAGGCAAGAGCACAACCAG 59.258 52.381 0.00 0.00 44.61 4.00 F
4770 8194 1.133823 TCCAAACACATGAGCACTGGT 60.134 47.619 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1527 2435 0.329596 GAGGTCAAAGATGGGTGGCT 59.670 55.000 0.00 0.0 0.00 4.75 R
2091 3783 0.742505 CCGGTATGACCTTGCTCGTA 59.257 55.000 0.00 0.0 35.66 3.43 R
2181 3879 1.351017 TCAGGGTCCCAAGACAATGAC 59.649 52.381 11.55 0.0 45.48 3.06 R
2425 4393 1.714899 ATGATAGGCGGTTGCGTTGC 61.715 55.000 0.00 0.0 44.10 4.17 R
2831 6194 0.902531 ACACCATAACAGTCTCCGGG 59.097 55.000 0.00 0.0 0.00 5.73 R
2891 6254 8.997323 TCTAGTACTTACAAGCGTATAATCCTC 58.003 37.037 0.00 0.0 0.00 3.71 R
2921 6284 6.268825 AGAGCGTTTAGATCACTACTTTCA 57.731 37.500 0.00 0.0 37.82 2.69 R
3884 7275 1.695242 ACAACCACAGGGACGACAATA 59.305 47.619 0.00 0.0 38.05 1.90 R
4361 7765 0.331616 GGCACAATCCCTACCTTGGT 59.668 55.000 0.00 0.0 0.00 3.67 R
4915 8373 0.719465 CACGTAGTCATTTCCGCCAC 59.281 55.000 0.00 0.0 41.61 5.01 R
6048 9568 0.407918 GGGGGTCACCTTCCATTTCA 59.592 55.000 0.00 0.0 40.03 2.69 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
25 26 2.202878 GCCAATGCTCGCGGACTA 60.203 61.111 6.13 0.00 33.53 2.59
26 27 1.595382 GCCAATGCTCGCGGACTAT 60.595 57.895 6.13 0.00 33.53 2.12
27 28 1.560860 GCCAATGCTCGCGGACTATC 61.561 60.000 6.13 0.00 33.53 2.08
28 29 0.032678 CCAATGCTCGCGGACTATCT 59.967 55.000 6.13 0.00 0.00 1.98
29 30 1.135046 CAATGCTCGCGGACTATCTG 58.865 55.000 6.13 0.00 0.00 2.90
30 31 0.032678 AATGCTCGCGGACTATCTGG 59.967 55.000 6.13 0.00 0.00 3.86
31 32 0.823769 ATGCTCGCGGACTATCTGGA 60.824 55.000 6.13 0.00 0.00 3.86
32 33 1.008309 GCTCGCGGACTATCTGGAC 60.008 63.158 6.13 0.00 0.00 4.02
33 34 1.725557 GCTCGCGGACTATCTGGACA 61.726 60.000 6.13 0.00 0.00 4.02
34 35 0.029567 CTCGCGGACTATCTGGACAC 59.970 60.000 6.13 0.00 0.00 3.67
35 36 1.065928 CGCGGACTATCTGGACACC 59.934 63.158 0.00 0.00 0.00 4.16
36 37 1.663379 CGCGGACTATCTGGACACCA 61.663 60.000 0.00 0.00 0.00 4.17
37 38 0.753262 GCGGACTATCTGGACACCAT 59.247 55.000 0.00 0.00 30.82 3.55
38 39 1.139058 GCGGACTATCTGGACACCATT 59.861 52.381 0.00 0.00 30.82 3.16
39 40 2.420129 GCGGACTATCTGGACACCATTT 60.420 50.000 0.00 0.00 30.82 2.32
40 41 3.458189 CGGACTATCTGGACACCATTTC 58.542 50.000 0.00 0.00 30.82 2.17
41 42 3.133003 CGGACTATCTGGACACCATTTCT 59.867 47.826 0.00 0.00 30.82 2.52
42 43 4.383118 CGGACTATCTGGACACCATTTCTT 60.383 45.833 0.00 0.00 30.82 2.52
43 44 4.878397 GGACTATCTGGACACCATTTCTTG 59.122 45.833 0.00 0.00 30.82 3.02
73 74 7.066043 GCTGTCATCTCTTTCATGAATCTTTCT 59.934 37.037 9.40 0.00 31.98 2.52
78 79 9.985318 CATCTCTTTCATGAATCTTTCTGTTAC 57.015 33.333 9.40 0.00 0.00 2.50
79 80 8.244494 TCTCTTTCATGAATCTTTCTGTTACG 57.756 34.615 9.40 0.00 0.00 3.18
100 101 2.814336 GGAAAACACCCTTGTAGCTGAG 59.186 50.000 0.00 0.00 33.55 3.35
132 133 4.340666 TCTTTTGTTTGGCAACTGCTATGA 59.659 37.500 0.00 0.00 41.70 2.15
170 171 1.927174 GATGGAGGTGATCAAACGACG 59.073 52.381 0.00 0.00 0.00 5.12
176 177 0.788391 GTGATCAAACGACGTGACCC 59.212 55.000 0.00 0.00 0.00 4.46
209 210 5.476945 GGTTGTGTCCCATTTATGAAGTTCT 59.523 40.000 4.17 0.00 0.00 3.01
211 212 5.875224 TGTGTCCCATTTATGAAGTTCTGA 58.125 37.500 4.17 0.00 0.00 3.27
215 216 6.655003 TGTCCCATTTATGAAGTTCTGAAGAC 59.345 38.462 4.17 5.22 0.00 3.01
224 225 0.391597 GTTCTGAAGACGGGGACACA 59.608 55.000 0.00 0.00 0.00 3.72
234 235 4.514401 AGACGGGGACACATATTTTTCTC 58.486 43.478 0.00 0.00 0.00 2.87
242 243 4.312443 ACACATATTTTTCTCGTCCACGT 58.688 39.130 0.00 0.00 40.80 4.49
243 244 4.387862 ACACATATTTTTCTCGTCCACGTC 59.612 41.667 0.00 0.00 40.80 4.34
244 245 3.611113 ACATATTTTTCTCGTCCACGTCG 59.389 43.478 0.00 0.00 40.80 5.12
245 246 1.425412 ATTTTTCTCGTCCACGTCGG 58.575 50.000 0.00 0.00 40.80 4.79
246 247 1.216941 TTTTTCTCGTCCACGTCGGC 61.217 55.000 0.00 0.00 40.80 5.54
247 248 3.884581 TTTCTCGTCCACGTCGGCG 62.885 63.158 8.42 8.42 44.93 6.46
251 252 4.175489 CGTCCACGTCGGCGAGAT 62.175 66.667 20.03 0.00 42.00 2.75
252 253 2.181021 GTCCACGTCGGCGAGATT 59.819 61.111 20.03 0.00 42.00 2.40
253 254 1.445582 GTCCACGTCGGCGAGATTT 60.446 57.895 20.03 0.00 42.00 2.17
254 255 1.153901 TCCACGTCGGCGAGATTTC 60.154 57.895 20.03 0.00 42.00 2.17
255 256 1.153823 CCACGTCGGCGAGATTTCT 60.154 57.895 20.03 0.00 42.00 2.52
256 257 0.736325 CCACGTCGGCGAGATTTCTT 60.736 55.000 20.03 0.00 42.00 2.52
257 258 1.068474 CACGTCGGCGAGATTTCTTT 58.932 50.000 20.03 0.00 42.00 2.52
258 259 1.068474 ACGTCGGCGAGATTTCTTTG 58.932 50.000 20.03 0.00 42.00 2.77
259 260 0.370273 CGTCGGCGAGATTTCTTTGG 59.630 55.000 11.20 0.00 41.33 3.28
260 261 1.722011 GTCGGCGAGATTTCTTTGGA 58.278 50.000 11.20 0.00 0.00 3.53
261 262 1.661112 GTCGGCGAGATTTCTTTGGAG 59.339 52.381 11.20 0.00 0.00 3.86
262 263 0.375106 CGGCGAGATTTCTTTGGAGC 59.625 55.000 0.00 0.00 0.00 4.70
306 307 0.614979 GACTGGGAGGCACTAGACCA 60.615 60.000 0.00 0.00 41.55 4.02
326 327 3.264450 CCAGTCTGGGTTCCTACAAATCT 59.736 47.826 11.46 0.00 32.67 2.40
331 332 1.737793 GGGTTCCTACAAATCTGTGCG 59.262 52.381 0.00 0.00 36.96 5.34
340 341 1.197721 CAAATCTGTGCGAACCAGACC 59.802 52.381 0.00 0.00 41.47 3.85
341 342 0.670546 AATCTGTGCGAACCAGACCG 60.671 55.000 0.00 0.00 41.47 4.79
344 345 3.998672 GTGCGAACCAGACCGGGA 61.999 66.667 6.32 0.00 40.22 5.14
345 346 3.691342 TGCGAACCAGACCGGGAG 61.691 66.667 6.32 0.00 40.22 4.30
361 362 0.458260 GGAGGAGGAGACGCTTCTTC 59.542 60.000 0.00 0.00 36.48 2.87
369 370 1.462670 GAGACGCTTCTTCTGGCTTTG 59.537 52.381 0.00 0.00 29.47 2.77
375 376 2.603173 GCTTCTTCTGGCTTTGTGTTCG 60.603 50.000 0.00 0.00 0.00 3.95
376 377 2.613026 TCTTCTGGCTTTGTGTTCGA 57.387 45.000 0.00 0.00 0.00 3.71
379 380 0.884704 TCTGGCTTTGTGTTCGAGGC 60.885 55.000 0.00 0.00 36.59 4.70
388 389 1.446099 TGTTCGAGGCGCTAGCTTG 60.446 57.895 13.93 0.00 44.37 4.01
389 390 1.153823 GTTCGAGGCGCTAGCTTGA 60.154 57.895 13.93 2.22 44.37 3.02
398 399 0.037326 CGCTAGCTTGAACCCTGTGA 60.037 55.000 13.93 0.00 0.00 3.58
413 414 3.519579 CCTGTGAACAACATGCAACAAA 58.480 40.909 0.00 0.00 38.39 2.83
450 451 1.139058 TCTTTCTTAGGCGGGCATCTC 59.861 52.381 3.78 0.00 0.00 2.75
451 452 0.179084 TTTCTTAGGCGGGCATCTCG 60.179 55.000 3.78 0.00 0.00 4.04
469 470 5.860941 TCTCGCTCTATCTTCAAATTCCT 57.139 39.130 0.00 0.00 0.00 3.36
471 472 7.348080 TCTCGCTCTATCTTCAAATTCCTTA 57.652 36.000 0.00 0.00 0.00 2.69
483 484 8.203485 TCTTCAAATTCCTTACATTTTTGCAGT 58.797 29.630 0.00 0.00 0.00 4.40
489 490 8.630054 ATTCCTTACATTTTTGCAGTACTGTA 57.370 30.769 23.44 17.20 0.00 2.74
502 503 4.421948 CAGTACTGTAACCCGCTTTCTAG 58.578 47.826 15.06 0.00 0.00 2.43
517 518 4.734917 CTTTCTAGATAGCGGGATTACGG 58.265 47.826 0.00 0.00 0.00 4.02
519 520 1.134560 CTAGATAGCGGGATTACGGCC 59.865 57.143 0.00 0.00 45.68 6.13
537 538 2.036958 CCGGTTTGGCTACATGATGA 57.963 50.000 0.00 0.00 0.00 2.92
541 542 2.747446 GGTTTGGCTACATGATGAACGT 59.253 45.455 0.00 0.00 0.00 3.99
545 546 3.197265 TGGCTACATGATGAACGTGATG 58.803 45.455 0.00 0.00 38.72 3.07
562 563 3.869272 GATTGCTGCCTCACGCCG 61.869 66.667 0.00 0.00 36.24 6.46
574 575 4.664677 ACGCCGTCTTGCTTCGCT 62.665 61.111 0.00 0.00 0.00 4.93
581 582 1.227943 TCTTGCTTCGCTGCCAACT 60.228 52.632 0.00 0.00 0.00 3.16
591 592 1.318576 GCTGCCAACTACTTGTGGTT 58.681 50.000 0.00 0.00 0.00 3.67
644 645 0.528249 GTGTTTGTGCTGTTGCCCTG 60.528 55.000 0.00 0.00 38.71 4.45
753 754 1.461268 TGTCAACTCTCCAGCCCCA 60.461 57.895 0.00 0.00 0.00 4.96
801 804 2.413765 GATCGAGTCGTGGCCTCC 59.586 66.667 13.12 0.00 0.00 4.30
823 826 1.228003 TGGGTACAAAGTGGTGGCG 60.228 57.895 0.00 0.00 0.00 5.69
840 843 1.683917 GGCGAGAGAATTCAGGCTAGA 59.316 52.381 8.44 0.00 0.00 2.43
854 857 1.382420 CTAGAGCAGGGCCCACTCT 60.382 63.158 36.16 36.16 43.12 3.24
859 862 2.045536 CAGGGCCCACTCTTGAGC 60.046 66.667 27.56 0.00 0.00 4.26
864 867 1.004440 GCCCACTCTTGAGCGACTT 60.004 57.895 0.00 0.00 0.00 3.01
865 868 1.294659 GCCCACTCTTGAGCGACTTG 61.295 60.000 0.00 0.00 0.00 3.16
877 880 1.071567 GCGACTTGCCGTAGACACTC 61.072 60.000 0.00 0.00 37.76 3.51
880 883 1.153823 CTTGCCGTAGACACTCCGG 60.154 63.158 0.00 0.00 44.46 5.14
889 892 3.787394 ACACTCCGGGGTGTAGTG 58.213 61.111 38.57 26.33 46.89 2.74
920 923 4.346139 GCGTTAACTAAGGTTATACGCG 57.654 45.455 20.23 3.53 45.51 6.01
921 924 3.180387 GCGTTAACTAAGGTTATACGCGG 59.820 47.826 12.47 0.00 45.51 6.46
926 945 4.820284 ACTAAGGTTATACGCGGAGTAC 57.180 45.455 12.47 3.73 38.29 2.73
927 946 3.565902 ACTAAGGTTATACGCGGAGTACC 59.434 47.826 12.47 14.04 38.29 3.34
1103 1960 8.570488 TGACAGTAACGGTATGTACTTATATGG 58.430 37.037 0.00 0.00 0.00 2.74
1222 2123 1.750351 TATATCTGCGCGTGTTCGAC 58.250 50.000 8.43 0.00 39.71 4.20
1892 3523 9.544579 AGTACTACCTTTGTTCCTAAATACTCT 57.455 33.333 0.00 0.00 0.00 3.24
1893 3524 9.800433 GTACTACCTTTGTTCCTAAATACTCTC 57.200 37.037 0.00 0.00 0.00 3.20
1894 3525 7.545489 ACTACCTTTGTTCCTAAATACTCTCG 58.455 38.462 0.00 0.00 0.00 4.04
1897 3528 3.431922 TGTTCCTAAATACTCTCGCCG 57.568 47.619 0.00 0.00 0.00 6.46
1900 3531 4.179298 GTTCCTAAATACTCTCGCCGTTT 58.821 43.478 0.00 0.00 0.00 3.60
1926 3557 8.952278 TCAAAATAAGTGTGTCAACTTTGTACT 58.048 29.630 0.00 0.00 40.77 2.73
1934 3565 8.188139 AGTGTGTCAACTTTGTACTAATTTTGG 58.812 33.333 9.87 0.00 0.00 3.28
1951 3588 9.203421 CTAATTTTGGGACACTTATTTTGGAAC 57.797 33.333 0.00 0.00 39.29 3.62
1966 3603 3.675348 TGGAACGGAGGGAGTATAAGA 57.325 47.619 0.00 0.00 0.00 2.10
1975 3612 5.163343 CGGAGGGAGTATAAGACATTTTGGA 60.163 44.000 0.00 0.00 0.00 3.53
1976 3613 6.631766 CGGAGGGAGTATAAGACATTTTGGAA 60.632 42.308 0.00 0.00 0.00 3.53
1977 3614 6.768381 GGAGGGAGTATAAGACATTTTGGAAG 59.232 42.308 0.00 0.00 0.00 3.46
1978 3615 6.663734 AGGGAGTATAAGACATTTTGGAAGG 58.336 40.000 0.00 0.00 0.00 3.46
1979 3616 5.828328 GGGAGTATAAGACATTTTGGAAGGG 59.172 44.000 0.00 0.00 0.00 3.95
1981 3618 6.318900 GGAGTATAAGACATTTTGGAAGGGTG 59.681 42.308 0.00 0.00 0.00 4.61
1982 3619 6.790319 AGTATAAGACATTTTGGAAGGGTGT 58.210 36.000 0.00 0.00 0.00 4.16
1983 3620 7.924541 AGTATAAGACATTTTGGAAGGGTGTA 58.075 34.615 0.00 0.00 0.00 2.90
1984 3621 8.557450 AGTATAAGACATTTTGGAAGGGTGTAT 58.443 33.333 0.00 0.00 0.00 2.29
1985 3622 9.185680 GTATAAGACATTTTGGAAGGGTGTATT 57.814 33.333 0.00 0.00 0.00 1.89
1998 3635 3.437741 AGGGTGTATTTTTAACCGCGAAG 59.562 43.478 8.23 0.00 34.62 3.79
1999 3636 3.189080 GGGTGTATTTTTAACCGCGAAGT 59.811 43.478 8.23 0.00 34.62 3.01
2027 3719 1.893137 TCAATCGATCAGGTATCCCGG 59.107 52.381 0.00 0.00 35.12 5.73
2091 3783 7.517361 CTGGAACATATACCGAGGTATCGACT 61.517 46.154 17.21 2.96 46.03 4.18
2134 3832 1.171308 CCTCTTTGAGGTACCGACGA 58.829 55.000 6.18 2.04 44.25 4.20
2181 3879 1.530441 CGAAATGTCTCAAGCGGCATG 60.530 52.381 1.45 0.00 0.00 4.06
2295 3994 2.051879 ATGTCACACGTGAGTTCTCG 57.948 50.000 25.01 2.42 46.40 4.04
2310 4009 4.899502 AGTTCTCGATCAACCTCAACAAT 58.100 39.130 4.23 0.00 0.00 2.71
2425 4393 1.473965 CCATCATTCCCACCGTCAGAG 60.474 57.143 0.00 0.00 0.00 3.35
2459 4427 6.082338 CGCCTATCATCAATGCTATTGAAAC 58.918 40.000 13.21 1.97 31.55 2.78
2523 5113 6.055588 CCTGGATGGTACGTTTTATTCAGAT 58.944 40.000 12.75 0.00 29.40 2.90
2601 5941 9.912634 CATAAGTGGCTTGAGATTCTTTTAAAA 57.087 29.630 0.00 0.00 0.00 1.52
2880 6243 2.371306 TGACATGTAGCTACGCCACTA 58.629 47.619 18.74 0.44 0.00 2.74
2960 6323 6.839820 AACGCTCTTATATTTCTTTACGGG 57.160 37.500 0.00 0.00 0.00 5.28
3008 6371 9.550811 GTTAGGATTTTATGTTAGTGAAAACCG 57.449 33.333 0.00 0.00 0.00 4.44
3069 6439 8.988064 TTCTACTATCATCAACTGAAACTGAC 57.012 34.615 0.00 0.00 37.44 3.51
3086 6456 2.422479 CTGACCCACTGATCATTTGCTG 59.578 50.000 0.00 0.00 0.00 4.41
3135 6505 6.276847 GTCTGAACGGTGATATCTCATCTTT 58.723 40.000 3.98 0.00 32.98 2.52
3175 6545 5.066246 AGCTATCCAGTACTTGTACGTCTTC 59.934 44.000 0.00 0.00 0.00 2.87
3277 6649 8.980481 ATCTATCAAACAATAACTTGGTAGGG 57.020 34.615 3.06 0.00 37.03 3.53
3363 6735 5.248020 TGTCAAAATTTAGCCATTCCCATGT 59.752 36.000 0.00 0.00 0.00 3.21
3372 6744 4.729868 AGCCATTCCCATGTATTACTTCC 58.270 43.478 0.00 0.00 0.00 3.46
3384 6756 7.709182 CCATGTATTACTTCCGAGTCATGTAAA 59.291 37.037 0.00 0.00 34.79 2.01
3500 6875 2.102588 CACTGAATCTAAGGTACCCCCG 59.897 54.545 8.74 0.00 38.74 5.73
3861 7243 8.663305 ACAATTCATGTCGGTTGGAACCTAAAT 61.663 37.037 6.97 0.00 41.44 1.40
3875 7266 5.654209 GGAACCTAAATGGAAGAGCAATCTT 59.346 40.000 0.00 0.00 39.71 2.40
3914 7305 2.517959 CCTGTGGTTGTGTCCATGATT 58.482 47.619 0.00 0.00 39.81 2.57
3941 7332 7.012232 GTGGTGATAGTAGTGGTAGTACTCTTC 59.988 44.444 0.00 0.00 35.97 2.87
3947 7338 4.035612 AGTGGTAGTACTCTTCTGCTCA 57.964 45.455 0.00 0.00 0.00 4.26
3956 7347 3.150767 ACTCTTCTGCTCACTAAGACGT 58.849 45.455 0.00 0.00 0.00 4.34
3993 7384 1.741706 CATAGGCAAGAGCACAACCAG 59.258 52.381 0.00 0.00 44.61 4.00
3996 7387 2.253758 GCAAGAGCACAACCAGCGA 61.254 57.895 0.00 0.00 41.58 4.93
3997 7388 1.785041 GCAAGAGCACAACCAGCGAA 61.785 55.000 0.00 0.00 41.58 4.70
4009 7400 3.747099 ACCAGCGAATGATCTTTTTCG 57.253 42.857 16.50 16.50 45.61 3.46
4108 7504 2.517450 GCCACGACGAGCTATGTGC 61.517 63.158 0.00 0.00 43.29 4.57
4188 7584 3.190744 TCACGTACGAAGAGCTCAAGATT 59.809 43.478 24.41 0.20 0.00 2.40
4301 7697 4.189639 AGTTACGGTCTCATTCTTCCAC 57.810 45.455 0.00 0.00 0.00 4.02
4351 7755 4.082026 AGGTACATGCCTTTCTTTGATTGC 60.082 41.667 0.00 0.00 34.71 3.56
4361 7765 6.680810 CCTTTCTTTGATTGCACTTGATGTA 58.319 36.000 0.00 0.00 0.00 2.29
4441 7857 7.547227 GTTTGTCCAGGCTCATATTTTAACAT 58.453 34.615 0.00 0.00 0.00 2.71
4466 7882 7.724287 TGGATTCATCACAAAAATCTTGTCAA 58.276 30.769 0.00 0.00 31.53 3.18
4655 8073 2.029918 GGAAGCAAACACAATGGAGGAC 60.030 50.000 0.00 0.00 0.00 3.85
4770 8194 1.133823 TCCAAACACATGAGCACTGGT 60.134 47.619 0.00 0.00 0.00 4.00
4915 8373 3.861840 TCGGCTTATCCAAGACTTTCAG 58.138 45.455 0.00 0.00 37.69 3.02
4922 8380 0.250295 CCAAGACTTTCAGTGGCGGA 60.250 55.000 0.00 0.00 0.00 5.54
5054 8515 0.317160 TGCTACTGGAACTGGTCACG 59.683 55.000 0.00 0.00 0.00 4.35
5122 8583 1.290955 GGTCACGACAACGGATGGA 59.709 57.895 0.00 0.00 44.46 3.41
5180 8641 3.755905 TGTGTGGCATTTACGATGTCAAT 59.244 39.130 0.00 0.00 35.22 2.57
5224 8685 3.767287 CACTCAAGTGCACTGCATG 57.233 52.632 22.49 15.51 41.91 4.06
5252 8713 1.302511 GCAACGACCCACCATGACT 60.303 57.895 0.00 0.00 0.00 3.41
5351 8816 1.672356 GAGTGGTGGCAGCGACAAT 60.672 57.895 12.58 0.00 0.00 2.71
5413 8878 7.997482 TCCAGTGATAGTACTACATTTCAGAC 58.003 38.462 4.31 0.00 0.00 3.51
5422 8887 4.307432 ACTACATTTCAGACTGAACACGG 58.693 43.478 17.52 9.61 35.89 4.94
5516 8989 9.669353 AATTTCGTATGAATGCAACAATAGATC 57.331 29.630 0.00 0.00 33.20 2.75
5566 9046 5.221541 GGGATCCAGACGAGATACTGAAATT 60.222 44.000 15.23 0.00 36.38 1.82
5603 9086 6.652062 GTGAGTGCACATGGATTCATATATCA 59.348 38.462 21.04 5.58 44.51 2.15
5628 9111 3.528532 CTCATCAAGAGTGTAGCATGCA 58.471 45.455 21.98 2.77 39.62 3.96
5629 9112 4.127907 CTCATCAAGAGTGTAGCATGCAT 58.872 43.478 21.98 7.68 39.62 3.96
5664 9147 6.075315 TGGAAATAGGACCTTGAGATCGATA 58.925 40.000 0.00 0.00 0.00 2.92
5701 9192 5.391312 AGTATGCCATTCTTGGTTGTTTC 57.609 39.130 0.00 0.00 45.57 2.78
5718 9209 8.713271 TGGTTGTTTCTTGTTAATTGACAAAAC 58.287 29.630 15.67 16.66 38.90 2.43
5901 9418 6.312426 ACATCGAAGTAGAAAGAGAAATGCTG 59.688 38.462 0.00 0.00 0.00 4.41
5916 9433 8.138712 AGAGAAATGCTGCTACATAACTACTAC 58.861 37.037 0.00 0.00 0.00 2.73
5998 9515 4.386867 TGTCAACATATCTCGAGGAACC 57.613 45.455 13.56 0.00 0.00 3.62
6093 9614 9.086336 CACAAATTTACATGAAGACAAGTGTTT 57.914 29.630 0.00 0.00 0.00 2.83
6104 9625 1.750778 ACAAGTGTTTGTCAAGCCCAG 59.249 47.619 0.00 0.00 44.00 4.45
6154 9681 3.932545 AGATCACATCGAGTCCATAGC 57.067 47.619 0.00 0.00 0.00 2.97
6157 9684 1.409064 TCACATCGAGTCCATAGCCAC 59.591 52.381 0.00 0.00 0.00 5.01
6188 9715 2.279173 ACAATAGGGGACAAGGAAGCT 58.721 47.619 0.00 0.00 0.00 3.74
6276 9806 7.508296 TCAAACCTCCACTATATCTACCTAACC 59.492 40.741 0.00 0.00 0.00 2.85
6297 9827 3.522553 CTTCATACACTTCGGAGTTCCC 58.477 50.000 0.00 0.00 32.54 3.97
6331 9861 1.463674 GGAATTGGCGAGTGGTTCAT 58.536 50.000 0.00 0.00 0.00 2.57
6344 9874 2.996621 GTGGTTCATCAGATATAGCCGC 59.003 50.000 0.00 0.00 0.00 6.53
6391 9922 3.442273 TGCCAACTATTTCATTCGGAACC 59.558 43.478 0.00 0.00 34.56 3.62
6392 9923 3.442273 GCCAACTATTTCATTCGGAACCA 59.558 43.478 0.00 0.00 34.56 3.67
6395 9926 5.878116 CCAACTATTTCATTCGGAACCACTA 59.122 40.000 0.00 0.00 34.56 2.74
6405 9936 2.158871 TCGGAACCACTAAAGCACTTGT 60.159 45.455 0.00 0.00 0.00 3.16
6406 9937 2.032030 CGGAACCACTAAAGCACTTGTG 60.032 50.000 0.00 0.00 0.00 3.33
6416 9947 2.985957 AGCACTTGTGGCAAACATTT 57.014 40.000 2.81 0.00 38.99 2.32
6431 9962 3.252974 ACATTTAGTCGCCTTCTCAGG 57.747 47.619 0.00 0.00 44.28 3.86
6460 9991 1.746470 ACCATTCGGTCGGAATTTCC 58.254 50.000 5.28 5.28 44.71 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.560860 GATAGTCCGCGAGCATTGGC 61.561 60.000 8.23 0.00 41.61 4.52
9 10 0.032678 AGATAGTCCGCGAGCATTGG 59.967 55.000 8.23 0.00 0.00 3.16
10 11 1.135046 CAGATAGTCCGCGAGCATTG 58.865 55.000 8.23 0.00 0.00 2.82
11 12 0.032678 CCAGATAGTCCGCGAGCATT 59.967 55.000 8.23 0.00 0.00 3.56
12 13 0.823769 TCCAGATAGTCCGCGAGCAT 60.824 55.000 8.23 0.00 0.00 3.79
13 14 1.453197 TCCAGATAGTCCGCGAGCA 60.453 57.895 8.23 0.00 0.00 4.26
14 15 1.008309 GTCCAGATAGTCCGCGAGC 60.008 63.158 8.23 0.00 0.00 5.03
15 16 0.029567 GTGTCCAGATAGTCCGCGAG 59.970 60.000 8.23 0.00 0.00 5.03
16 17 1.381928 GGTGTCCAGATAGTCCGCGA 61.382 60.000 8.23 0.00 0.00 5.87
17 18 1.065928 GGTGTCCAGATAGTCCGCG 59.934 63.158 0.00 0.00 0.00 6.46
18 19 0.753262 ATGGTGTCCAGATAGTCCGC 59.247 55.000 0.00 0.00 36.75 5.54
19 20 3.133003 AGAAATGGTGTCCAGATAGTCCG 59.867 47.826 0.00 0.00 36.75 4.79
20 21 4.762289 AGAAATGGTGTCCAGATAGTCC 57.238 45.455 0.00 0.00 36.75 3.85
21 22 4.878397 CCAAGAAATGGTGTCCAGATAGTC 59.122 45.833 0.00 0.00 44.85 2.59
22 23 4.848357 CCAAGAAATGGTGTCCAGATAGT 58.152 43.478 0.00 0.00 44.85 2.12
35 36 2.753452 AGATGACAGCTGCCAAGAAATG 59.247 45.455 15.27 0.00 0.00 2.32
36 37 3.015327 GAGATGACAGCTGCCAAGAAAT 58.985 45.455 15.27 0.00 0.00 2.17
37 38 2.039480 AGAGATGACAGCTGCCAAGAAA 59.961 45.455 15.27 0.00 0.00 2.52
38 39 1.627329 AGAGATGACAGCTGCCAAGAA 59.373 47.619 15.27 0.00 0.00 2.52
39 40 1.273759 AGAGATGACAGCTGCCAAGA 58.726 50.000 15.27 0.00 0.00 3.02
40 41 2.110901 AAGAGATGACAGCTGCCAAG 57.889 50.000 15.27 0.00 0.00 3.61
41 42 2.224597 TGAAAGAGATGACAGCTGCCAA 60.225 45.455 15.27 0.00 0.00 4.52
42 43 1.348696 TGAAAGAGATGACAGCTGCCA 59.651 47.619 15.27 10.11 0.00 4.92
43 44 2.105006 TGAAAGAGATGACAGCTGCC 57.895 50.000 15.27 2.30 0.00 4.85
44 45 3.268330 TCATGAAAGAGATGACAGCTGC 58.732 45.455 15.27 7.45 0.00 5.25
45 46 5.818336 AGATTCATGAAAGAGATGACAGCTG 59.182 40.000 13.09 13.48 29.39 4.24
46 47 5.991861 AGATTCATGAAAGAGATGACAGCT 58.008 37.500 13.09 0.00 29.39 4.24
47 48 6.680874 AAGATTCATGAAAGAGATGACAGC 57.319 37.500 13.09 0.00 29.39 4.40
48 49 8.391859 CAGAAAGATTCATGAAAGAGATGACAG 58.608 37.037 13.09 0.00 29.39 3.51
49 50 7.881751 ACAGAAAGATTCATGAAAGAGATGACA 59.118 33.333 13.09 0.00 29.39 3.58
73 74 3.002038 ACAAGGGTGTTTTCCGTAACA 57.998 42.857 0.00 0.00 32.58 2.41
78 79 1.535462 CAGCTACAAGGGTGTTTTCCG 59.465 52.381 0.00 0.00 39.30 4.30
79 80 2.814336 CTCAGCTACAAGGGTGTTTTCC 59.186 50.000 0.00 0.00 39.30 3.13
176 177 0.611896 GGGACACAACCCATTCCCAG 60.612 60.000 0.37 0.00 46.35 4.45
209 210 3.992943 AAATATGTGTCCCCGTCTTCA 57.007 42.857 0.00 0.00 0.00 3.02
211 212 4.918588 AGAAAAATATGTGTCCCCGTCTT 58.081 39.130 0.00 0.00 0.00 3.01
215 216 3.267483 ACGAGAAAAATATGTGTCCCCG 58.733 45.455 0.00 0.00 0.00 5.73
224 225 3.184541 CCGACGTGGACGAGAAAAATAT 58.815 45.455 6.12 0.00 42.00 1.28
234 235 3.678717 AATCTCGCCGACGTGGACG 62.679 63.158 0.00 0.00 42.00 4.79
242 243 2.007049 GCTCCAAAGAAATCTCGCCGA 61.007 52.381 0.00 0.00 0.00 5.54
243 244 0.375106 GCTCCAAAGAAATCTCGCCG 59.625 55.000 0.00 0.00 0.00 6.46
244 245 1.743996 AGCTCCAAAGAAATCTCGCC 58.256 50.000 0.00 0.00 0.00 5.54
245 246 3.057946 ACAAAGCTCCAAAGAAATCTCGC 60.058 43.478 0.00 0.00 0.00 5.03
246 247 4.378874 GGACAAAGCTCCAAAGAAATCTCG 60.379 45.833 0.00 0.00 0.00 4.04
247 248 4.378874 CGGACAAAGCTCCAAAGAAATCTC 60.379 45.833 0.00 0.00 0.00 2.75
248 249 3.503748 CGGACAAAGCTCCAAAGAAATCT 59.496 43.478 0.00 0.00 0.00 2.40
249 250 3.253432 ACGGACAAAGCTCCAAAGAAATC 59.747 43.478 0.00 0.00 0.00 2.17
250 251 3.004734 CACGGACAAAGCTCCAAAGAAAT 59.995 43.478 0.00 0.00 0.00 2.17
251 252 2.357637 CACGGACAAAGCTCCAAAGAAA 59.642 45.455 0.00 0.00 0.00 2.52
252 253 1.946768 CACGGACAAAGCTCCAAAGAA 59.053 47.619 0.00 0.00 0.00 2.52
253 254 1.140052 TCACGGACAAAGCTCCAAAGA 59.860 47.619 0.00 0.00 0.00 2.52
254 255 1.532868 CTCACGGACAAAGCTCCAAAG 59.467 52.381 0.00 0.00 0.00 2.77
255 256 1.593196 CTCACGGACAAAGCTCCAAA 58.407 50.000 0.00 0.00 0.00 3.28
256 257 0.250295 CCTCACGGACAAAGCTCCAA 60.250 55.000 0.00 0.00 0.00 3.53
257 258 1.371183 CCTCACGGACAAAGCTCCA 59.629 57.895 0.00 0.00 0.00 3.86
258 259 2.035442 GCCTCACGGACAAAGCTCC 61.035 63.158 0.00 0.00 0.00 4.70
259 260 1.004440 AGCCTCACGGACAAAGCTC 60.004 57.895 0.00 0.00 0.00 4.09
260 261 1.004440 GAGCCTCACGGACAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
261 262 1.004440 AGAGCCTCACGGACAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
262 263 0.671781 CCAGAGCCTCACGGACAAAG 60.672 60.000 0.00 0.00 0.00 2.77
283 284 1.965754 CTAGTGCCTCCCAGTCTGGC 61.966 65.000 13.99 2.44 46.26 4.85
285 286 0.820871 GTCTAGTGCCTCCCAGTCTG 59.179 60.000 0.00 0.00 0.00 3.51
286 287 0.324830 GGTCTAGTGCCTCCCAGTCT 60.325 60.000 0.00 0.00 0.00 3.24
291 292 0.324830 AGACTGGTCTAGTGCCTCCC 60.325 60.000 0.95 0.00 40.53 4.30
306 307 3.910627 ACAGATTTGTAGGAACCCAGACT 59.089 43.478 0.00 0.00 35.25 3.24
326 327 4.308458 CCCGGTCTGGTTCGCACA 62.308 66.667 0.00 0.00 35.15 4.57
331 332 2.359967 CCTCCTCCCGGTCTGGTTC 61.360 68.421 0.00 0.00 35.15 3.62
340 341 2.756283 AAGCGTCTCCTCCTCCCG 60.756 66.667 0.00 0.00 0.00 5.14
341 342 0.973496 AAGAAGCGTCTCCTCCTCCC 60.973 60.000 1.62 0.00 30.70 4.30
344 345 1.181786 CAGAAGAAGCGTCTCCTCCT 58.818 55.000 1.62 0.00 30.70 3.69
345 346 0.174617 CCAGAAGAAGCGTCTCCTCC 59.825 60.000 1.62 0.00 30.70 4.30
346 347 0.459411 GCCAGAAGAAGCGTCTCCTC 60.459 60.000 1.62 0.00 30.70 3.71
347 348 0.902516 AGCCAGAAGAAGCGTCTCCT 60.903 55.000 1.62 0.00 30.70 3.69
348 349 0.036858 AAGCCAGAAGAAGCGTCTCC 60.037 55.000 1.62 0.00 30.70 3.71
349 350 1.462670 CAAAGCCAGAAGAAGCGTCTC 59.537 52.381 1.62 0.00 30.70 3.36
350 351 1.202698 ACAAAGCCAGAAGAAGCGTCT 60.203 47.619 0.00 0.00 34.72 4.18
356 357 2.872245 CTCGAACACAAAGCCAGAAGAA 59.128 45.455 0.00 0.00 0.00 2.52
361 362 1.576421 GCCTCGAACACAAAGCCAG 59.424 57.895 0.00 0.00 0.00 4.85
369 370 1.446272 AAGCTAGCGCCTCGAACAC 60.446 57.895 9.55 0.00 36.60 3.32
375 376 1.815840 GGGTTCAAGCTAGCGCCTC 60.816 63.158 9.55 0.42 36.60 4.70
376 377 2.269241 GGGTTCAAGCTAGCGCCT 59.731 61.111 9.55 0.00 36.60 5.52
379 380 0.037326 TCACAGGGTTCAAGCTAGCG 60.037 55.000 9.55 0.00 0.00 4.26
388 389 1.680735 TGCATGTTGTTCACAGGGTTC 59.319 47.619 0.00 0.00 39.40 3.62
389 390 1.774110 TGCATGTTGTTCACAGGGTT 58.226 45.000 0.00 0.00 39.40 4.11
413 414 6.906157 AGAAAGATCCACACAATCAACATT 57.094 33.333 0.00 0.00 0.00 2.71
424 425 1.209504 CCCGCCTAAGAAAGATCCACA 59.790 52.381 0.00 0.00 0.00 4.17
431 432 1.587547 GAGATGCCCGCCTAAGAAAG 58.412 55.000 0.00 0.00 0.00 2.62
450 451 7.721286 ATGTAAGGAATTTGAAGATAGAGCG 57.279 36.000 0.00 0.00 0.00 5.03
469 470 6.293516 CGGGTTACAGTACTGCAAAAATGTAA 60.294 38.462 22.90 13.79 32.38 2.41
471 472 4.023536 CGGGTTACAGTACTGCAAAAATGT 60.024 41.667 22.90 4.09 0.00 2.71
483 484 5.009410 GCTATCTAGAAAGCGGGTTACAGTA 59.991 44.000 0.00 0.00 0.00 2.74
502 503 1.445582 CGGCCGTAATCCCGCTATC 60.446 63.158 19.50 0.00 37.85 2.08
519 520 2.223021 CGTTCATCATGTAGCCAAACCG 60.223 50.000 0.00 0.00 0.00 4.44
527 528 5.235831 AGCAATCATCACGTTCATCATGTAG 59.764 40.000 0.00 0.00 0.00 2.74
537 538 1.089920 GAGGCAGCAATCATCACGTT 58.910 50.000 0.00 0.00 0.00 3.99
541 542 1.371337 GCGTGAGGCAGCAATCATCA 61.371 55.000 3.08 0.00 42.87 3.07
568 569 1.195448 CACAAGTAGTTGGCAGCGAAG 59.805 52.381 14.69 0.00 38.07 3.79
669 670 8.775220 TCACGTTCATACAACAAAATTAAGTG 57.225 30.769 0.00 0.00 0.00 3.16
676 677 6.362016 GCAATCATCACGTTCATACAACAAAA 59.638 34.615 0.00 0.00 0.00 2.44
801 804 1.508632 CACCACTTTGTACCCACGAG 58.491 55.000 0.00 0.00 0.00 4.18
823 826 3.243839 CCTGCTCTAGCCTGAATTCTCTC 60.244 52.174 7.05 0.00 41.18 3.20
840 843 2.530151 TCAAGAGTGGGCCCTGCT 60.530 61.111 25.70 21.04 0.00 4.24
854 857 0.388134 GTCTACGGCAAGTCGCTCAA 60.388 55.000 0.00 0.00 41.91 3.02
859 862 0.456312 GGAGTGTCTACGGCAAGTCG 60.456 60.000 0.00 0.00 0.00 4.18
874 877 1.608627 GGACACTACACCCCGGAGT 60.609 63.158 0.73 0.00 0.00 3.85
896 899 5.878261 CGTATAACCTTAGTTAACGCCTG 57.122 43.478 0.00 0.00 41.68 4.85
920 923 0.531200 CCAACAGGACTCGGTACTCC 59.469 60.000 0.00 0.00 0.00 3.85
921 924 1.542492 TCCAACAGGACTCGGTACTC 58.458 55.000 0.00 0.00 0.00 2.59
926 945 3.198068 CAACATATCCAACAGGACTCGG 58.802 50.000 0.00 0.00 33.38 4.63
927 946 3.198068 CCAACATATCCAACAGGACTCG 58.802 50.000 0.00 0.00 33.38 4.18
1020 1041 0.901124 GGCTGAGGCAGAGAAGAAGA 59.099 55.000 0.00 0.00 40.87 2.87
1122 1981 5.764686 TGTGTCAACTTGCAGTAATCATCTT 59.235 36.000 0.00 0.00 0.00 2.40
1126 1985 5.826601 TTTGTGTCAACTTGCAGTAATCA 57.173 34.783 0.00 0.00 0.00 2.57
1222 2123 2.096406 CAAACAGCACGCGATCGG 59.904 61.111 15.93 9.59 40.69 4.18
1243 2148 4.694509 CAGTCTATGCTTATGAATCCTGCC 59.305 45.833 0.00 0.00 0.00 4.85
1400 2308 0.944311 CTGCGGACGGTATACATGCC 60.944 60.000 5.01 1.41 0.00 4.40
1527 2435 0.329596 GAGGTCAAAGATGGGTGGCT 59.670 55.000 0.00 0.00 0.00 4.75
1744 2652 2.757508 TCAGAGAGCAGGAGCCCG 60.758 66.667 0.00 0.00 43.56 6.13
1888 3519 4.062991 ACTTATTTTGAAACGGCGAGAGT 58.937 39.130 16.62 0.00 0.00 3.24
1892 3523 3.312973 ACACACTTATTTTGAAACGGCGA 59.687 39.130 16.62 0.00 0.00 5.54
1893 3524 3.623863 ACACACTTATTTTGAAACGGCG 58.376 40.909 4.80 4.80 0.00 6.46
1894 3525 4.602995 TGACACACTTATTTTGAAACGGC 58.397 39.130 0.00 0.00 0.00 5.68
1897 3528 8.921670 ACAAAGTTGACACACTTATTTTGAAAC 58.078 29.630 0.00 0.00 35.87 2.78
1900 3531 8.952278 AGTACAAAGTTGACACACTTATTTTGA 58.048 29.630 0.00 0.00 35.87 2.69
1926 3557 7.868415 CGTTCCAAAATAAGTGTCCCAAAATTA 59.132 33.333 0.00 0.00 0.00 1.40
1934 3565 3.439129 CCTCCGTTCCAAAATAAGTGTCC 59.561 47.826 0.00 0.00 0.00 4.02
1951 3588 5.057149 CCAAAATGTCTTATACTCCCTCCG 58.943 45.833 0.00 0.00 0.00 4.63
1966 3603 7.934665 GGTTAAAAATACACCCTTCCAAAATGT 59.065 33.333 0.00 0.00 0.00 2.71
1975 3612 3.410508 TCGCGGTTAAAAATACACCCTT 58.589 40.909 6.13 0.00 0.00 3.95
1976 3613 3.056588 TCGCGGTTAAAAATACACCCT 57.943 42.857 6.13 0.00 0.00 4.34
1977 3614 3.189080 ACTTCGCGGTTAAAAATACACCC 59.811 43.478 6.13 0.00 0.00 4.61
1978 3615 4.083908 TGACTTCGCGGTTAAAAATACACC 60.084 41.667 6.13 0.00 0.00 4.16
1979 3616 5.021120 TGACTTCGCGGTTAAAAATACAC 57.979 39.130 6.13 0.00 0.00 2.90
1981 3618 5.446899 CGAATGACTTCGCGGTTAAAAATAC 59.553 40.000 6.13 0.00 46.76 1.89
1982 3619 5.552807 CGAATGACTTCGCGGTTAAAAATA 58.447 37.500 6.13 0.00 46.76 1.40
1983 3620 4.399978 CGAATGACTTCGCGGTTAAAAAT 58.600 39.130 6.13 0.00 46.76 1.82
1984 3621 3.801293 CGAATGACTTCGCGGTTAAAAA 58.199 40.909 6.13 0.00 46.76 1.94
1985 3622 3.443054 CGAATGACTTCGCGGTTAAAA 57.557 42.857 6.13 0.00 46.76 1.52
2027 3719 6.197282 CGTCCATATTCTGTCATATGTATCGC 59.803 42.308 1.90 0.00 35.94 4.58
2091 3783 0.742505 CCGGTATGACCTTGCTCGTA 59.257 55.000 0.00 0.00 35.66 3.43
2181 3879 1.351017 TCAGGGTCCCAAGACAATGAC 59.649 52.381 11.55 0.00 45.48 3.06
2310 4009 2.934932 TCTGGGTGCCATGGCTCA 60.935 61.111 35.53 26.99 42.51 4.26
2425 4393 1.714899 ATGATAGGCGGTTGCGTTGC 61.715 55.000 0.00 0.00 44.10 4.17
2533 5123 4.024556 GTGTGTGCTTGTCCATCTATATGC 60.025 45.833 0.00 0.00 0.00 3.14
2601 5941 9.220767 CAATTTTAGTTAGCAGGTTAGAAGAGT 57.779 33.333 0.00 0.00 0.00 3.24
2702 6047 5.448360 GCTAATTCACAGTTGCTTCAGATCC 60.448 44.000 0.00 0.00 0.00 3.36
2831 6194 0.902531 ACACCATAACAGTCTCCGGG 59.097 55.000 0.00 0.00 0.00 5.73
2891 6254 8.997323 TCTAGTACTTACAAGCGTATAATCCTC 58.003 37.037 0.00 0.00 0.00 3.71
2921 6284 6.268825 AGAGCGTTTAGATCACTACTTTCA 57.731 37.500 0.00 0.00 37.82 2.69
2922 6285 8.859517 ATAAGAGCGTTTAGATCACTACTTTC 57.140 34.615 0.00 0.00 37.82 2.62
2960 6323 9.482627 CTAACAGATTGATATGAACTACTTCCC 57.517 37.037 0.00 0.00 0.00 3.97
2990 6353 7.498570 ACCAGTTACGGTTTTCACTAACATAAA 59.501 33.333 0.00 0.00 34.91 1.40
3069 6439 3.243301 GCATACAGCAAATGATCAGTGGG 60.243 47.826 0.09 0.00 44.79 4.61
3094 6464 2.028567 CAGACCTCTCAAGGACAAGTCC 60.029 54.545 11.29 11.29 46.67 3.85
3135 6505 6.009589 TGGATAGCTTTGAGATTGGTGAAAA 58.990 36.000 0.00 0.00 0.00 2.29
3175 6545 7.225538 GTGGACATTAAGACAGATCCATAACAG 59.774 40.741 0.00 0.00 38.45 3.16
3277 6649 2.098117 CGAAAGGGCATCTGGAATTGAC 59.902 50.000 0.00 0.00 0.00 3.18
3363 6735 9.661563 ACAATTTTACATGACTCGGAAGTAATA 57.338 29.630 0.00 0.00 35.28 0.98
3372 6744 7.827819 TCCTAAGACAATTTTACATGACTCG 57.172 36.000 0.00 0.00 0.00 4.18
3384 6756 8.181904 TGCAGAAAAGAAATCCTAAGACAATT 57.818 30.769 0.00 0.00 0.00 2.32
3815 7197 2.040544 ATTGGCGCAAAGGTCTCGG 61.041 57.895 10.83 0.00 0.00 4.63
3875 7266 3.006859 CAGGGACGACAATATAGATGGCA 59.993 47.826 0.00 0.00 0.00 4.92
3884 7275 1.695242 ACAACCACAGGGACGACAATA 59.305 47.619 0.00 0.00 38.05 1.90
3914 7305 6.069789 AGAGTACTACCACTACTATCACCACA 60.070 42.308 0.00 0.00 0.00 4.17
3941 7332 4.154375 TGTCTCTTACGTCTTAGTGAGCAG 59.846 45.833 0.00 0.00 0.00 4.24
3947 7338 5.068636 TCACCTTGTCTCTTACGTCTTAGT 58.931 41.667 0.00 0.00 0.00 2.24
3956 7347 3.706594 CCTATGCCTCACCTTGTCTCTTA 59.293 47.826 0.00 0.00 0.00 2.10
3996 7387 6.017400 AGTGTGATTGCGAAAAAGATCATT 57.983 33.333 0.00 0.00 31.85 2.57
3997 7388 5.633830 AGTGTGATTGCGAAAAAGATCAT 57.366 34.783 0.00 0.00 31.85 2.45
4009 7400 7.091443 ACAACTAGACTTAGTAGTGTGATTGC 58.909 38.462 0.00 0.00 39.20 3.56
4108 7504 1.949525 CCTATGAGCATTGTTTCCCGG 59.050 52.381 0.00 0.00 0.00 5.73
4188 7584 5.531634 ACTCGTTGGAAGTTGTTCGTTATA 58.468 37.500 0.00 0.00 32.92 0.98
4301 7697 4.092116 AGGAACTCCTTGAAACCTTGAG 57.908 45.455 0.00 0.00 46.09 3.02
4351 7755 3.517901 TCCCTACCTTGGTACATCAAGTG 59.482 47.826 9.97 5.47 41.72 3.16
4361 7765 0.331616 GGCACAATCCCTACCTTGGT 59.668 55.000 0.00 0.00 0.00 3.67
4407 7822 1.336755 GCCTGGACAAACGTTCACAAT 59.663 47.619 0.00 0.00 0.00 2.71
4441 7857 7.287512 TGACAAGATTTTTGTGATGAATCCA 57.712 32.000 0.00 0.00 31.70 3.41
4466 7882 4.098914 TCCTTGCAGTAACCAATCAAGT 57.901 40.909 0.00 0.00 34.07 3.16
4770 8194 1.002659 CCCTGGAAATCACCGTACACA 59.997 52.381 0.00 0.00 0.00 3.72
4915 8373 0.719465 CACGTAGTCATTTCCGCCAC 59.281 55.000 0.00 0.00 41.61 5.01
5122 8583 1.613437 CACTTTCAATGTTTCCCCGCT 59.387 47.619 0.00 0.00 0.00 5.52
5180 8641 2.120312 TCCACCACTTTCCACACACTA 58.880 47.619 0.00 0.00 0.00 2.74
5252 8713 1.293179 CAGCTGATCCACCACGTCA 59.707 57.895 8.42 0.00 0.00 4.35
5413 8878 1.502231 CCTCTTGACACCGTGTTCAG 58.498 55.000 5.45 5.27 0.00 3.02
5422 8887 1.896220 TGAATGCACCCTCTTGACAC 58.104 50.000 0.00 0.00 0.00 3.67
5531 9006 3.133721 CGTCTGGATCCCTTCAAGAGAAT 59.866 47.826 9.90 0.00 34.94 2.40
5548 9023 6.958193 GCAAAAGAATTTCAGTATCTCGTCTG 59.042 38.462 0.00 0.00 37.28 3.51
5566 9046 0.944386 GCACTCACTTCGGCAAAAGA 59.056 50.000 4.50 0.00 0.00 2.52
5771 9264 5.833082 TCTACTCTAATCATTCGCCTGTTC 58.167 41.667 0.00 0.00 0.00 3.18
5828 9345 2.940561 CGGTTACCGTGGTTGTGC 59.059 61.111 16.53 0.00 42.73 4.57
5839 9356 6.608610 AGTTTTCTTACATGATTGCGGTTAC 58.391 36.000 0.00 0.00 0.00 2.50
5885 9402 8.260818 AGTTATGTAGCAGCATTTCTCTTTCTA 58.739 33.333 0.00 0.00 0.00 2.10
5901 9418 8.674263 TGAGTTCCTAGTAGTAGTTATGTAGC 57.326 38.462 3.91 0.00 0.00 3.58
5916 9433 4.537751 TCACCTGGAGTATGAGTTCCTAG 58.462 47.826 0.00 0.00 34.48 3.02
5998 9515 8.184192 CCTAAAATGAACTTGTAGTAGGCATTG 58.816 37.037 0.00 0.00 30.44 2.82
6048 9568 0.407918 GGGGGTCACCTTCCATTTCA 59.592 55.000 0.00 0.00 40.03 2.69
6093 9614 1.004745 GAAGAATCCCTGGGCTTGACA 59.995 52.381 8.22 0.00 0.00 3.58
6097 9618 3.479866 AAATGAAGAATCCCTGGGCTT 57.520 42.857 8.22 4.21 0.00 4.35
6131 9658 4.500545 GCTATGGACTCGATGTGATCTTGT 60.501 45.833 0.00 0.00 0.00 3.16
6143 9670 1.589993 CAGCGTGGCTATGGACTCG 60.590 63.158 1.55 1.55 36.40 4.18
6154 9681 4.307432 CCCTATTGTTAGTATCAGCGTGG 58.693 47.826 0.00 0.00 0.00 4.94
6157 9684 4.038763 TGTCCCCTATTGTTAGTATCAGCG 59.961 45.833 0.00 0.00 0.00 5.18
6209 9736 6.121776 TGGAGTTTGATCCTTAAGCACTTA 57.878 37.500 0.00 0.00 40.29 2.24
6237 9764 3.384789 GGAGGTTTGAAGGCTTTTGAGTT 59.615 43.478 0.00 0.00 0.00 3.01
6238 9765 2.959030 GGAGGTTTGAAGGCTTTTGAGT 59.041 45.455 0.00 0.00 0.00 3.41
6255 9782 7.239438 TGAAGGTTAGGTAGATATAGTGGAGG 58.761 42.308 0.00 0.00 0.00 4.30
6256 9783 8.887264 ATGAAGGTTAGGTAGATATAGTGGAG 57.113 38.462 0.00 0.00 0.00 3.86
6276 9806 3.522553 GGGAACTCCGAAGTGTATGAAG 58.477 50.000 0.00 0.00 35.36 3.02
6297 9827 0.600255 ATTCCGGCCGAAATAGCTCG 60.600 55.000 30.73 6.27 38.58 5.03
6310 9840 1.644786 GAACCACTCGCCAATTCCGG 61.645 60.000 0.00 0.00 0.00 5.14
6331 9861 2.908688 TTTGCAGCGGCTATATCTGA 57.091 45.000 10.92 0.00 41.91 3.27
6344 9874 4.245660 TCCGAATGACTAGACTTTTGCAG 58.754 43.478 0.00 0.00 0.00 4.41
6391 9922 3.115554 GTTTGCCACAAGTGCTTTAGTG 58.884 45.455 0.00 0.00 0.00 2.74
6392 9923 2.757868 TGTTTGCCACAAGTGCTTTAGT 59.242 40.909 0.00 0.00 29.87 2.24
6395 9926 2.985957 ATGTTTGCCACAAGTGCTTT 57.014 40.000 0.00 0.00 39.50 3.51
6405 9936 1.904287 AGGCGACTAAATGTTTGCCA 58.096 45.000 0.00 0.00 46.43 4.92
6406 9937 2.488153 AGAAGGCGACTAAATGTTTGCC 59.512 45.455 0.00 0.00 45.23 4.52
6416 9947 2.431057 GGAAATCCTGAGAAGGCGACTA 59.569 50.000 0.00 0.00 42.68 2.59


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

AutoCloner maintained by Alex Coulton.