Multiple sequence alignment - TraesCS5D01G481800

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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 TraesCS5D01G481800 chr5D 100.000 3504 0 0 1 3504 519544048 519547551 0.000000e+00 6471.0
1 TraesCS5D01G481800 chr5D 95.664 369 10 4 77 440 503736525 503736158 3.900000e-164 588.0
2 TraesCS5D01G481800 chr5B 92.680 2910 119 35 494 3356 654365148 654368010 0.000000e+00 4108.0
3 TraesCS5D01G481800 chr5B 89.394 66 7 0 430 495 425659940 425659875 2.240000e-12 84.2
4 TraesCS5D01G481800 chr5A 91.575 2445 146 37 1082 3501 646057998 646060407 0.000000e+00 3319.0
5 TraesCS5D01G481800 chr5A 87.420 628 24 23 494 1075 646057322 646057940 0.000000e+00 671.0
6 TraesCS5D01G481800 chr2D 84.553 738 114 0 1762 2499 573852730 573853467 0.000000e+00 732.0
7 TraesCS5D01G481800 chr2D 82.846 752 123 5 1762 2510 574346296 574345548 0.000000e+00 669.0
8 TraesCS5D01G481800 chr2D 95.913 367 11 3 77 440 48010798 48010433 3.010000e-165 592.0
9 TraesCS5D01G481800 chr2D 95.902 366 13 2 77 440 567014078 567013713 3.010000e-165 592.0
10 TraesCS5D01G481800 chr2D 95.628 366 13 3 77 440 78076458 78076094 5.040000e-163 584.0
11 TraesCS5D01G481800 chr2D 88.832 197 20 2 1501 1696 573852438 573852633 1.260000e-59 241.0
12 TraesCS5D01G481800 chr2D 80.930 215 40 1 3164 3377 375617630 375617844 6.020000e-38 169.0
13 TraesCS5D01G481800 chr2D 84.444 90 8 4 3413 3501 433725836 433725752 2.240000e-12 84.2
14 TraesCS5D01G481800 chr2B 82.846 752 123 5 1762 2510 690211345 690210597 0.000000e+00 669.0
15 TraesCS5D01G481800 chr2A 82.672 756 127 4 1762 2514 712707247 712706493 0.000000e+00 667.0
16 TraesCS5D01G481800 chr2A 86.224 196 27 0 1501 1696 712317781 712317976 2.740000e-51 213.0
17 TraesCS5D01G481800 chr2A 90.000 70 6 1 430 498 710477810 710477741 4.820000e-14 89.8
18 TraesCS5D01G481800 chr7D 96.467 368 9 2 77 440 501382034 501382401 3.870000e-169 604.0
19 TraesCS5D01G481800 chr7D 76.087 276 60 6 1890 2162 514075389 514075661 4.720000e-29 139.0
20 TraesCS5D01G481800 chr7D 87.500 72 9 0 429 500 254987773 254987702 2.240000e-12 84.2
21 TraesCS5D01G481800 chr6D 96.458 367 10 2 77 440 45624485 45624851 1.390000e-168 603.0
22 TraesCS5D01G481800 chr6D 96.185 367 11 2 77 440 349902494 349902860 6.470000e-167 597.0
23 TraesCS5D01G481800 chr6D 81.000 200 30 7 1883 2078 127379953 127379758 6.060000e-33 152.0
24 TraesCS5D01G481800 chr6D 98.795 83 1 0 1 83 414245440 414245522 7.840000e-32 148.0
25 TraesCS5D01G481800 chr6D 100.000 78 0 0 1 78 45499535 45499458 1.010000e-30 145.0
26 TraesCS5D01G481800 chr6D 88.889 108 12 0 3394 3501 41447969 41448076 2.190000e-27 134.0
27 TraesCS5D01G481800 chr1D 96.164 365 13 1 77 440 409814151 409814515 2.330000e-166 595.0
28 TraesCS5D01G481800 chr1D 100.000 78 0 0 1 78 49227587 49227510 1.010000e-30 145.0
29 TraesCS5D01G481800 chr1D 100.000 78 0 0 1 78 232433925 232433848 1.010000e-30 145.0
30 TraesCS5D01G481800 chr1D 92.647 68 5 0 429 496 424927855 424927788 8.000000e-17 99.0
31 TraesCS5D01G481800 chr4D 95.913 367 12 2 77 440 80138670 80138304 3.010000e-165 592.0
32 TraesCS5D01G481800 chr4D 100.000 78 0 0 1 78 165895182 165895105 1.010000e-30 145.0
33 TraesCS5D01G481800 chr4D 100.000 78 0 0 1 78 500474249 500474326 1.010000e-30 145.0
34 TraesCS5D01G481800 chr3A 98.795 83 1 0 1 83 16937155 16937073 7.840000e-32 148.0
35 TraesCS5D01G481800 chr3A 82.955 88 14 1 3396 3482 60198122 60198209 1.040000e-10 78.7
36 TraesCS5D01G481800 chr1A 98.795 83 1 0 1 83 407313506 407313424 7.840000e-32 148.0
37 TraesCS5D01G481800 chr1A 100.000 78 0 0 1 78 294511890 294511967 1.010000e-30 145.0
38 TraesCS5D01G481800 chr1A 100.000 30 0 0 3472 3501 479816789 479816760 4.890000e-04 56.5
39 TraesCS5D01G481800 chr1A 100.000 30 0 0 3472 3501 512011748 512011777 4.890000e-04 56.5
40 TraesCS5D01G481800 chr7B 76.173 277 58 6 1890 2162 544912286 544912558 4.720000e-29 139.0
41 TraesCS5D01G481800 chr7B 91.892 74 5 1 423 495 467444289 467444362 6.190000e-18 102.0
42 TraesCS5D01G481800 chr7B 89.231 65 6 1 430 494 721733624 721733687 2.900000e-11 80.5
43 TraesCS5D01G481800 chr1B 84.211 114 12 5 3394 3503 58267413 58267302 4.780000e-19 106.0
44 TraesCS5D01G481800 chr1B 91.045 67 6 0 429 495 453697487 453697421 1.340000e-14 91.6
45 TraesCS5D01G481800 chr4A 84.404 109 14 2 3394 3500 658038306 658038199 1.720000e-18 104.0
46 TraesCS5D01G481800 chr4A 89.855 69 7 0 430 498 567205727 567205795 4.820000e-14 89.8
47 TraesCS5D01G481800 chr6A 93.750 64 4 0 430 493 591155693 591155756 2.880000e-16 97.1
48 TraesCS5D01G481800 chr6A 100.000 30 0 0 3472 3501 65663269 65663240 4.890000e-04 56.5
49 TraesCS5D01G481800 chr6A 100.000 30 0 0 3472 3501 145132314 145132343 4.890000e-04 56.5


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 TraesCS5D01G481800 chr5D 519544048 519547551 3503 False 6471.0 6471 100.0000 1 3504 1 chr5D.!!$F1 3503
1 TraesCS5D01G481800 chr5B 654365148 654368010 2862 False 4108.0 4108 92.6800 494 3356 1 chr5B.!!$F1 2862
2 TraesCS5D01G481800 chr5A 646057322 646060407 3085 False 1995.0 3319 89.4975 494 3501 2 chr5A.!!$F1 3007
3 TraesCS5D01G481800 chr2D 574345548 574346296 748 True 669.0 669 82.8460 1762 2510 1 chr2D.!!$R5 748
4 TraesCS5D01G481800 chr2D 573852438 573853467 1029 False 486.5 732 86.6925 1501 2499 2 chr2D.!!$F2 998
5 TraesCS5D01G481800 chr2B 690210597 690211345 748 True 669.0 669 82.8460 1762 2510 1 chr2B.!!$R1 748
6 TraesCS5D01G481800 chr2A 712706493 712707247 754 True 667.0 667 82.6720 1762 2514 1 chr2A.!!$R2 752

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
455 456 0.040157 GTTTTACCCCAAACGGACGC 60.04 55.0 0.00 0.0 0.00 5.19 F
474 475 0.529992 CGCCCGGACAAGATAAGGTC 60.53 60.0 0.73 0.0 0.00 3.85 F
475 476 0.529992 GCCCGGACAAGATAAGGTCG 60.53 60.0 0.73 0.0 34.87 4.79 F
477 478 0.870307 CCGGACAAGATAAGGTCGCG 60.87 60.0 0.00 0.0 34.87 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1873 0.451628 CGAACAACACGCTCTGCATG 60.452 55.000 0.0 0.0 0.00 4.06 R
1760 1874 0.880278 ACGAACAACACGCTCTGCAT 60.880 50.000 0.0 0.0 0.00 3.96 R
2128 2272 4.715523 ACCCCGTTCATGGTGCCG 62.716 66.667 0.0 0.0 32.36 5.69 R
2528 2672 6.998802 AGAAGAAGGAAAAAGAAGATCGAGA 58.001 36.000 0.0 0.0 0.00 4.04 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
22 23 4.873129 GCGAAGAGGCCGCGATGA 62.873 66.667 8.23 0.00 43.28 2.92
23 24 2.028190 CGAAGAGGCCGCGATGAT 59.972 61.111 8.23 0.00 0.00 2.45
24 25 2.018866 CGAAGAGGCCGCGATGATC 61.019 63.158 8.23 0.00 0.00 2.92
25 26 1.068083 GAAGAGGCCGCGATGATCA 59.932 57.895 8.23 0.00 0.00 2.92
26 27 1.218230 GAAGAGGCCGCGATGATCAC 61.218 60.000 8.23 0.00 0.00 3.06
27 28 2.650813 AAGAGGCCGCGATGATCACC 62.651 60.000 8.23 0.00 0.00 4.02
28 29 3.157217 GAGGCCGCGATGATCACCT 62.157 63.158 8.23 0.00 0.00 4.00
29 30 2.663188 GGCCGCGATGATCACCTC 60.663 66.667 8.23 0.00 0.00 3.85
30 31 3.032609 GCCGCGATGATCACCTCG 61.033 66.667 8.23 13.20 37.26 4.63
31 32 2.721859 CCGCGATGATCACCTCGA 59.278 61.111 20.10 0.00 36.54 4.04
32 33 1.658717 CCGCGATGATCACCTCGAC 60.659 63.158 20.10 11.36 36.54 4.20
33 34 2.006062 CGCGATGATCACCTCGACG 61.006 63.158 20.10 17.54 36.54 5.12
34 35 2.296480 GCGATGATCACCTCGACGC 61.296 63.158 20.10 15.15 41.20 5.19
35 36 1.064134 CGATGATCACCTCGACGCA 59.936 57.895 12.36 0.00 36.54 5.24
36 37 0.932123 CGATGATCACCTCGACGCAG 60.932 60.000 12.36 0.00 36.54 5.18
37 38 1.211818 GATGATCACCTCGACGCAGC 61.212 60.000 0.00 0.00 0.00 5.25
38 39 1.948721 ATGATCACCTCGACGCAGCA 61.949 55.000 0.00 0.00 0.00 4.41
39 40 1.875813 GATCACCTCGACGCAGCAG 60.876 63.158 0.00 0.00 0.00 4.24
40 41 3.362399 ATCACCTCGACGCAGCAGG 62.362 63.158 0.00 0.00 0.00 4.85
47 48 4.643387 GACGCAGCAGGGGTGGTT 62.643 66.667 2.86 0.00 43.60 3.67
48 49 4.954970 ACGCAGCAGGGGTGGTTG 62.955 66.667 0.00 0.00 41.74 3.77
73 74 3.461773 GCTACTGGCCGCTCTGGA 61.462 66.667 0.00 0.00 42.00 3.86
74 75 2.811101 CTACTGGCCGCTCTGGAG 59.189 66.667 0.00 0.00 42.00 3.86
84 85 2.888863 CTCTGGAGCTCGTGTCCC 59.111 66.667 7.83 0.00 32.49 4.46
85 86 2.680352 TCTGGAGCTCGTGTCCCC 60.680 66.667 7.83 0.00 32.49 4.81
86 87 2.681778 CTGGAGCTCGTGTCCCCT 60.682 66.667 7.83 0.00 32.49 4.79
87 88 2.680352 TGGAGCTCGTGTCCCCTC 60.680 66.667 7.83 0.00 32.49 4.30
88 89 2.363147 GGAGCTCGTGTCCCCTCT 60.363 66.667 7.83 0.00 0.00 3.69
89 90 2.716017 GGAGCTCGTGTCCCCTCTG 61.716 68.421 7.83 0.00 0.00 3.35
90 91 3.363844 GAGCTCGTGTCCCCTCTGC 62.364 68.421 0.00 0.00 0.00 4.26
91 92 4.459089 GCTCGTGTCCCCTCTGCC 62.459 72.222 0.00 0.00 0.00 4.85
92 93 2.997315 CTCGTGTCCCCTCTGCCA 60.997 66.667 0.00 0.00 0.00 4.92
93 94 3.302347 CTCGTGTCCCCTCTGCCAC 62.302 68.421 0.00 0.00 0.00 5.01
94 95 4.394712 CGTGTCCCCTCTGCCACC 62.395 72.222 0.00 0.00 0.00 4.61
95 96 4.394712 GTGTCCCCTCTGCCACCG 62.395 72.222 0.00 0.00 0.00 4.94
112 113 4.090057 GGCAAAGACGGCGACAGC 62.090 66.667 16.62 13.22 44.18 4.40
122 123 2.032681 GCGACAGCCAAACCTCCT 59.967 61.111 0.00 0.00 37.42 3.69
123 124 2.035442 GCGACAGCCAAACCTCCTC 61.035 63.158 0.00 0.00 37.42 3.71
124 125 1.376037 CGACAGCCAAACCTCCTCC 60.376 63.158 0.00 0.00 0.00 4.30
125 126 1.376037 GACAGCCAAACCTCCTCCG 60.376 63.158 0.00 0.00 0.00 4.63
126 127 1.827399 GACAGCCAAACCTCCTCCGA 61.827 60.000 0.00 0.00 0.00 4.55
127 128 1.201429 ACAGCCAAACCTCCTCCGAT 61.201 55.000 0.00 0.00 0.00 4.18
128 129 0.462759 CAGCCAAACCTCCTCCGATC 60.463 60.000 0.00 0.00 0.00 3.69
129 130 1.521681 GCCAAACCTCCTCCGATCG 60.522 63.158 8.51 8.51 0.00 3.69
130 131 1.956629 GCCAAACCTCCTCCGATCGA 61.957 60.000 18.66 1.60 0.00 3.59
131 132 0.179108 CCAAACCTCCTCCGATCGAC 60.179 60.000 18.66 0.00 0.00 4.20
132 133 0.525668 CAAACCTCCTCCGATCGACG 60.526 60.000 18.66 6.66 42.18 5.12
141 142 3.870606 CGATCGACGGCCAAAACT 58.129 55.556 10.26 0.00 38.46 2.66
142 143 3.038946 CGATCGACGGCCAAAACTA 57.961 52.632 10.26 0.00 38.46 2.24
143 144 0.643820 CGATCGACGGCCAAAACTAC 59.356 55.000 10.26 0.00 38.46 2.73
144 145 0.643820 GATCGACGGCCAAAACTACG 59.356 55.000 2.24 0.00 0.00 3.51
145 146 0.738412 ATCGACGGCCAAAACTACGG 60.738 55.000 2.24 0.00 0.00 4.02
151 152 3.378013 GCCAAAACTACGGCGAAAG 57.622 52.632 16.62 13.35 38.82 2.62
179 180 4.451150 GTGGCGGCCATGTCGAGA 62.451 66.667 26.68 0.00 35.28 4.04
180 181 4.451150 TGGCGGCCATGTCGAGAC 62.451 66.667 19.77 0.00 29.41 3.36
182 183 4.796231 GCGGCCATGTCGAGACGT 62.796 66.667 2.24 0.00 29.41 4.34
183 184 2.880879 CGGCCATGTCGAGACGTG 60.881 66.667 16.25 16.25 45.43 4.49
189 190 0.708370 CATGTCGAGACGTGGTTTCG 59.292 55.000 15.59 2.68 42.91 3.46
190 191 0.313043 ATGTCGAGACGTGGTTTCGT 59.687 50.000 0.00 0.00 46.88 3.85
191 192 0.943673 TGTCGAGACGTGGTTTCGTA 59.056 50.000 0.00 0.00 44.21 3.43
192 193 1.536766 TGTCGAGACGTGGTTTCGTAT 59.463 47.619 0.00 0.00 44.21 3.06
193 194 1.909532 GTCGAGACGTGGTTTCGTATG 59.090 52.381 0.00 0.00 44.21 2.39
194 195 1.135603 TCGAGACGTGGTTTCGTATGG 60.136 52.381 0.00 0.00 44.21 2.74
195 196 1.135603 CGAGACGTGGTTTCGTATGGA 60.136 52.381 0.00 0.00 44.21 3.41
196 197 2.257034 GAGACGTGGTTTCGTATGGAC 58.743 52.381 0.00 0.00 44.21 4.02
234 235 3.231736 GGAGGCGGCCGGAGAATA 61.232 66.667 29.38 0.00 0.00 1.75
235 236 2.340443 GAGGCGGCCGGAGAATAG 59.660 66.667 29.38 0.00 0.00 1.73
236 237 3.867700 GAGGCGGCCGGAGAATAGC 62.868 68.421 29.38 6.89 0.00 2.97
277 278 4.779733 GCGGGGAGAGAGGGTGGA 62.780 72.222 0.00 0.00 0.00 4.02
278 279 2.038975 CGGGGAGAGAGGGTGGAA 59.961 66.667 0.00 0.00 0.00 3.53
279 280 2.060980 CGGGGAGAGAGGGTGGAAG 61.061 68.421 0.00 0.00 0.00 3.46
280 281 2.371259 GGGGAGAGAGGGTGGAAGC 61.371 68.421 0.00 0.00 0.00 3.86
281 282 2.726351 GGGAGAGAGGGTGGAAGCG 61.726 68.421 0.00 0.00 33.03 4.68
282 283 1.985116 GGAGAGAGGGTGGAAGCGT 60.985 63.158 0.00 0.00 33.03 5.07
283 284 1.545706 GGAGAGAGGGTGGAAGCGTT 61.546 60.000 0.00 0.00 33.03 4.84
284 285 0.390472 GAGAGAGGGTGGAAGCGTTG 60.390 60.000 0.00 0.00 33.03 4.10
285 286 1.376037 GAGAGGGTGGAAGCGTTGG 60.376 63.158 0.00 0.00 33.03 3.77
286 287 2.359975 GAGGGTGGAAGCGTTGGG 60.360 66.667 0.00 0.00 33.03 4.12
287 288 2.852075 AGGGTGGAAGCGTTGGGA 60.852 61.111 0.00 0.00 33.03 4.37
288 289 2.359975 GGGTGGAAGCGTTGGGAG 60.360 66.667 0.00 0.00 33.03 4.30
289 290 3.056328 GGTGGAAGCGTTGGGAGC 61.056 66.667 0.00 0.00 0.00 4.70
290 291 3.423154 GTGGAAGCGTTGGGAGCG 61.423 66.667 0.00 0.00 40.04 5.03
291 292 4.697756 TGGAAGCGTTGGGAGCGG 62.698 66.667 0.00 0.00 40.04 5.52
292 293 4.388499 GGAAGCGTTGGGAGCGGA 62.388 66.667 0.00 0.00 40.04 5.54
293 294 2.815647 GAAGCGTTGGGAGCGGAG 60.816 66.667 0.00 0.00 40.04 4.63
294 295 4.394712 AAGCGTTGGGAGCGGAGG 62.395 66.667 0.00 0.00 40.04 4.30
297 298 4.452733 CGTTGGGAGCGGAGGGAC 62.453 72.222 0.00 0.00 0.00 4.46
299 300 3.003173 TTGGGAGCGGAGGGACTG 61.003 66.667 0.00 0.00 41.55 3.51
311 312 2.893398 GGACTGCTAGTGTCCCCG 59.107 66.667 19.74 0.00 46.01 5.73
312 313 1.681327 GGACTGCTAGTGTCCCCGA 60.681 63.158 19.74 0.00 46.01 5.14
313 314 1.511768 GACTGCTAGTGTCCCCGAC 59.488 63.158 6.72 0.00 0.00 4.79
314 315 1.228769 ACTGCTAGTGTCCCCGACA 60.229 57.895 0.00 0.00 40.50 4.35
315 316 1.251527 ACTGCTAGTGTCCCCGACAG 61.252 60.000 0.00 0.00 43.57 3.51
316 317 1.949847 CTGCTAGTGTCCCCGACAGG 61.950 65.000 0.00 0.00 43.57 4.00
317 318 2.893398 CTAGTGTCCCCGACAGGC 59.107 66.667 0.00 0.00 43.57 4.85
318 319 3.064987 CTAGTGTCCCCGACAGGCG 62.065 68.421 0.00 0.00 43.57 5.52
374 375 4.973055 CGCGTCCGTTTCACCCCA 62.973 66.667 0.00 0.00 0.00 4.96
375 376 2.592287 GCGTCCGTTTCACCCCAA 60.592 61.111 0.00 0.00 0.00 4.12
376 377 2.188161 GCGTCCGTTTCACCCCAAA 61.188 57.895 0.00 0.00 0.00 3.28
377 378 1.650363 CGTCCGTTTCACCCCAAAC 59.350 57.895 0.00 0.00 33.57 2.93
378 379 1.788067 CGTCCGTTTCACCCCAAACC 61.788 60.000 0.00 0.00 33.37 3.27
379 380 1.526455 TCCGTTTCACCCCAAACCG 60.526 57.895 0.00 0.00 33.37 4.44
380 381 1.526455 CCGTTTCACCCCAAACCGA 60.526 57.895 0.00 0.00 33.37 4.69
381 382 1.512156 CCGTTTCACCCCAAACCGAG 61.512 60.000 0.00 0.00 33.37 4.63
382 383 1.658114 GTTTCACCCCAAACCGAGC 59.342 57.895 0.00 0.00 31.10 5.03
383 384 1.894756 TTTCACCCCAAACCGAGCG 60.895 57.895 0.00 0.00 0.00 5.03
386 387 4.572571 ACCCCAAACCGAGCGCAA 62.573 61.111 11.47 0.00 0.00 4.85
387 388 3.737172 CCCCAAACCGAGCGCAAG 61.737 66.667 11.47 1.89 43.44 4.01
388 389 2.978010 CCCAAACCGAGCGCAAGT 60.978 61.111 11.47 0.00 41.68 3.16
389 390 2.551912 CCCAAACCGAGCGCAAGTT 61.552 57.895 11.47 7.07 41.68 2.66
390 391 1.358759 CCAAACCGAGCGCAAGTTT 59.641 52.632 11.47 13.31 41.68 2.66
391 392 0.934436 CCAAACCGAGCGCAAGTTTG 60.934 55.000 28.51 28.51 46.28 2.93
399 400 3.683937 CGCAAGTTTGGGCCAGGG 61.684 66.667 6.23 0.00 34.31 4.45
400 401 2.203625 GCAAGTTTGGGCCAGGGA 60.204 61.111 6.23 0.00 0.00 4.20
401 402 1.610379 GCAAGTTTGGGCCAGGGAT 60.610 57.895 6.23 0.00 0.00 3.85
402 403 1.891722 GCAAGTTTGGGCCAGGGATG 61.892 60.000 6.23 6.71 0.00 3.51
403 404 1.079073 AAGTTTGGGCCAGGGATGG 59.921 57.895 6.23 0.00 0.00 3.51
404 405 2.364186 GTTTGGGCCAGGGATGGG 60.364 66.667 6.23 0.00 0.00 4.00
405 406 2.868566 TTTGGGCCAGGGATGGGT 60.869 61.111 6.23 0.00 0.00 4.51
406 407 2.929964 TTTGGGCCAGGGATGGGTC 61.930 63.158 6.23 0.00 0.00 4.46
409 410 3.407967 GGCCAGGGATGGGTCGAA 61.408 66.667 0.00 0.00 0.00 3.71
410 411 2.674754 GCCAGGGATGGGTCGAAA 59.325 61.111 0.00 0.00 0.00 3.46
411 412 1.001393 GCCAGGGATGGGTCGAAAA 60.001 57.895 0.00 0.00 0.00 2.29
412 413 1.313091 GCCAGGGATGGGTCGAAAAC 61.313 60.000 0.00 0.00 0.00 2.43
413 414 1.024579 CCAGGGATGGGTCGAAAACG 61.025 60.000 0.00 0.00 0.00 3.60
414 415 1.024579 CAGGGATGGGTCGAAAACGG 61.025 60.000 0.00 0.00 0.00 4.44
415 416 1.196104 AGGGATGGGTCGAAAACGGA 61.196 55.000 0.00 0.00 0.00 4.69
416 417 1.022982 GGGATGGGTCGAAAACGGAC 61.023 60.000 0.00 0.00 0.00 4.79
417 418 1.356527 GGATGGGTCGAAAACGGACG 61.357 60.000 0.00 0.00 35.24 4.79
418 419 1.356527 GATGGGTCGAAAACGGACGG 61.357 60.000 0.00 0.00 35.24 4.79
419 420 1.818959 ATGGGTCGAAAACGGACGGA 61.819 55.000 0.00 0.00 35.24 4.69
420 421 1.300853 GGGTCGAAAACGGACGGAA 60.301 57.895 0.00 0.00 35.24 4.30
421 422 0.671472 GGGTCGAAAACGGACGGAAT 60.671 55.000 0.00 0.00 35.24 3.01
422 423 0.717784 GGTCGAAAACGGACGGAATC 59.282 55.000 0.00 0.00 35.24 2.52
423 424 0.717784 GTCGAAAACGGACGGAATCC 59.282 55.000 0.00 0.00 45.20 3.01
435 436 2.024176 CGGAATCCGGACATTTGTCT 57.976 50.000 14.91 0.00 44.15 3.41
444 445 4.155310 CGGACATTTGTCTGTTTTACCC 57.845 45.455 10.73 0.00 44.33 3.69
445 446 3.057806 CGGACATTTGTCTGTTTTACCCC 60.058 47.826 10.73 0.00 44.33 4.95
446 447 3.892588 GGACATTTGTCTGTTTTACCCCA 59.107 43.478 10.32 0.00 44.20 4.96
447 448 4.342665 GGACATTTGTCTGTTTTACCCCAA 59.657 41.667 10.32 0.00 44.20 4.12
448 449 5.163395 GGACATTTGTCTGTTTTACCCCAAA 60.163 40.000 10.32 0.00 44.20 3.28
449 450 5.666462 ACATTTGTCTGTTTTACCCCAAAC 58.334 37.500 0.00 0.00 37.20 2.93
450 451 4.373348 TTTGTCTGTTTTACCCCAAACG 57.627 40.909 0.00 0.00 39.19 3.60
451 452 2.299521 TGTCTGTTTTACCCCAAACGG 58.700 47.619 0.00 0.00 42.30 4.44
452 453 2.092538 TGTCTGTTTTACCCCAAACGGA 60.093 45.455 4.11 4.11 45.70 4.69
453 454 2.574450 TCTGTTTTACCCCAAACGGAC 58.426 47.619 4.11 0.00 43.92 4.79
454 455 1.264826 CTGTTTTACCCCAAACGGACG 59.735 52.381 0.00 0.00 43.22 4.79
455 456 0.040157 GTTTTACCCCAAACGGACGC 60.040 55.000 0.00 0.00 0.00 5.19
456 457 1.505477 TTTTACCCCAAACGGACGCG 61.505 55.000 3.53 3.53 0.00 6.01
468 469 4.814294 GACGCGCCCGGACAAGAT 62.814 66.667 5.73 0.00 39.22 2.40
469 470 3.420214 GACGCGCCCGGACAAGATA 62.420 63.158 5.73 0.00 39.22 1.98
470 471 2.202824 CGCGCCCGGACAAGATAA 60.203 61.111 0.73 0.00 0.00 1.75
471 472 2.237751 CGCGCCCGGACAAGATAAG 61.238 63.158 0.73 0.00 0.00 1.73
472 473 1.887707 GCGCCCGGACAAGATAAGG 60.888 63.158 0.73 0.00 0.00 2.69
473 474 1.520666 CGCCCGGACAAGATAAGGT 59.479 57.895 0.73 0.00 0.00 3.50
474 475 0.529992 CGCCCGGACAAGATAAGGTC 60.530 60.000 0.73 0.00 0.00 3.85
475 476 0.529992 GCCCGGACAAGATAAGGTCG 60.530 60.000 0.73 0.00 34.87 4.79
476 477 0.529992 CCCGGACAAGATAAGGTCGC 60.530 60.000 0.73 0.00 34.87 5.19
477 478 0.870307 CCGGACAAGATAAGGTCGCG 60.870 60.000 0.00 0.00 34.87 5.87
478 479 1.480219 CGGACAAGATAAGGTCGCGC 61.480 60.000 0.00 0.00 34.87 6.86
479 480 1.480219 GGACAAGATAAGGTCGCGCG 61.480 60.000 26.76 26.76 34.87 6.86
480 481 1.480219 GACAAGATAAGGTCGCGCGG 61.480 60.000 31.69 12.05 0.00 6.46
481 482 1.518572 CAAGATAAGGTCGCGCGGT 60.519 57.895 31.69 15.28 0.00 5.68
482 483 1.518572 AAGATAAGGTCGCGCGGTG 60.519 57.895 31.69 1.17 0.00 4.94
483 484 2.901051 AAGATAAGGTCGCGCGGTGG 62.901 60.000 31.69 0.71 0.00 4.61
484 485 3.420214 GATAAGGTCGCGCGGTGGA 62.420 63.158 31.69 7.56 0.00 4.02
485 486 3.426117 ATAAGGTCGCGCGGTGGAG 62.426 63.158 31.69 0.00 0.00 3.86
518 519 1.213182 AGGAGCTCACTAGATCGTCCA 59.787 52.381 17.19 0.00 39.11 4.02
726 737 4.038633 ACCTCCCAAACCCTATAAGAGTC 58.961 47.826 0.00 0.00 0.00 3.36
731 765 4.344102 CCCAAACCCTATAAGAGTCGATCA 59.656 45.833 0.00 0.00 0.00 2.92
825 860 2.753043 CCACCCATGTGCTCTGGC 60.753 66.667 0.00 0.00 41.35 4.85
826 861 2.353958 CACCCATGTGCTCTGGCT 59.646 61.111 0.00 0.00 39.59 4.75
827 862 2.044555 CACCCATGTGCTCTGGCTG 61.045 63.158 0.00 0.00 39.59 4.85
828 863 2.439701 CCCATGTGCTCTGGCTGG 60.440 66.667 0.00 0.00 39.59 4.85
920 955 1.027255 GGAAGAGGAAGCGGAAAGGC 61.027 60.000 0.00 0.00 0.00 4.35
949 1003 8.391106 GGATATTAATTTATGCGCTTCTACTGG 58.609 37.037 9.73 0.00 0.00 4.00
1044 1098 3.172575 ATTGTCGTCGTCGCGCTG 61.173 61.111 5.56 0.00 36.96 5.18
1110 1215 5.467705 GTCACCTACAACGTCAAGAACTAT 58.532 41.667 0.00 0.00 0.00 2.12
1463 1576 2.701006 GCGCATTGCACGTACGAT 59.299 55.556 24.41 1.09 45.45 3.73
1490 1603 1.943693 ATTTTGTGTGCGTGCGTGC 60.944 52.632 0.00 0.00 0.00 5.34
1753 1867 2.424341 GCGCTGACCGTAAAATAAACG 58.576 47.619 0.00 0.00 39.71 3.60
1756 1870 3.722665 CGCTGACCGTAAAATAAACGTGG 60.723 47.826 0.00 0.00 38.67 4.94
1757 1871 3.739494 CTGACCGTAAAATAAACGTGGC 58.261 45.455 0.00 0.00 38.67 5.01
1758 1872 2.157279 TGACCGTAAAATAAACGTGGCG 59.843 45.455 0.00 0.00 38.67 5.69
1759 1873 1.136000 ACCGTAAAATAAACGTGGCGC 60.136 47.619 0.00 0.00 38.67 6.53
1760 1874 1.136029 CCGTAAAATAAACGTGGCGCA 60.136 47.619 10.83 0.00 38.67 6.09
2128 2272 2.338500 GTCAAGGACATGACCTTCGAC 58.662 52.381 24.04 25.47 46.94 4.20
2528 2672 2.706890 ACTACGACGGCCATTTTGATT 58.293 42.857 2.24 0.00 0.00 2.57
2572 2719 9.898152 TTCTTCTTCTTCTTCTTCTTCTTCTTT 57.102 29.630 0.00 0.00 0.00 2.52
2634 2787 5.062058 CGATTTTGTTGTTTCTTGTTGCTGT 59.938 36.000 0.00 0.00 0.00 4.40
2669 2822 8.576936 TTCGTTTTCTTTTTGTTTTAGTGTGT 57.423 26.923 0.00 0.00 0.00 3.72
2826 2980 5.663106 AGCTAGTTCATCCAGGAGATAAACA 59.337 40.000 0.00 0.00 35.77 2.83
2829 2983 6.319048 AGTTCATCCAGGAGATAAACACAT 57.681 37.500 0.00 0.00 35.77 3.21
2860 3021 3.577848 ACTGAACTCATGAGCACTTCTCT 59.422 43.478 22.83 5.85 42.38 3.10
2877 3038 6.016860 CACTTCTCTCAAAATGTGATGAACCA 60.017 38.462 0.00 0.00 35.07 3.67
2879 3040 4.456911 TCTCTCAAAATGTGATGAACCAGC 59.543 41.667 0.00 0.00 35.07 4.85
2933 3094 2.785258 GCCGCTTCGAACCATGAC 59.215 61.111 0.00 0.00 0.00 3.06
2993 3154 4.040217 ACAGTCATTGCATTTGGCCTTTAA 59.960 37.500 3.32 0.00 43.89 1.52
3033 3194 5.337250 CCCTTCAGTTTTATTTAGGGTTGCC 60.337 44.000 0.00 0.00 38.00 4.52
3080 3242 5.310857 CCCAATTCTACTAGCCCTAAATCCT 59.689 44.000 0.00 0.00 0.00 3.24
3087 3249 1.889174 AGCCCTAAATCCTAACGGGT 58.111 50.000 0.00 0.00 37.24 5.28
3104 3266 2.119495 GGGTCAAATCCCTAGCTCTCA 58.881 52.381 0.00 0.00 43.85 3.27
3111 3273 2.909504 TCCCTAGCTCTCACTCACTT 57.090 50.000 0.00 0.00 0.00 3.16
3123 3285 1.867233 CACTCACTTTCACCCAACTCG 59.133 52.381 0.00 0.00 0.00 4.18
3145 3307 3.691342 CTCGAACTGACCCCGCCA 61.691 66.667 0.00 0.00 0.00 5.69
3196 3358 1.530891 CGGCCGGAGAATAGGGAGA 60.531 63.158 20.10 0.00 0.00 3.71
3302 3465 0.460284 CAGACATGTACCGGCTGGAC 60.460 60.000 21.41 12.73 39.21 4.02
3339 3502 1.961277 GCGCTGCTTGGTACAGTGT 60.961 57.895 0.00 0.00 45.35 3.55
3353 3516 4.202070 GGTACAGTGTAAGAGGATCAGCTC 60.202 50.000 4.11 0.00 37.82 4.09
3405 3568 4.474113 GGCGACACTATTAGAGATAACGG 58.526 47.826 0.00 0.00 0.00 4.44
3411 3574 6.540995 ACACTATTAGAGATAACGGGCTAGA 58.459 40.000 0.00 0.00 0.00 2.43
3413 3576 7.337436 ACACTATTAGAGATAACGGGCTAGATC 59.663 40.741 0.00 0.00 0.00 2.75
3426 3589 4.452455 CGGGCTAGATCCATGTACAATTTC 59.548 45.833 0.00 0.00 0.00 2.17
3430 3593 6.203723 GGCTAGATCCATGTACAATTTCTGAC 59.796 42.308 0.00 0.00 0.00 3.51
3431 3594 6.763135 GCTAGATCCATGTACAATTTCTGACA 59.237 38.462 0.00 0.00 0.00 3.58
3443 3606 6.161381 ACAATTTCTGACATCTCAAATTGGC 58.839 36.000 20.83 0.00 38.17 4.52
3444 3607 4.789012 TTTCTGACATCTCAAATTGGCC 57.211 40.909 0.00 0.00 0.00 5.36
3477 3640 1.897560 GCAAGTGGTGGCTCTAAAGT 58.102 50.000 0.00 0.00 0.00 2.66
3490 3653 4.505808 GCTCTAAAGTTTAGTCCCACCTC 58.494 47.826 19.65 1.75 0.00 3.85
3491 3654 4.745649 CTCTAAAGTTTAGTCCCACCTCG 58.254 47.826 19.65 0.00 0.00 4.63
3501 3664 1.070289 GTCCCACCTCGAAAGTTGAGT 59.930 52.381 0.00 0.00 0.00 3.41
3502 3665 2.298163 GTCCCACCTCGAAAGTTGAGTA 59.702 50.000 0.00 0.00 0.00 2.59
3503 3666 3.056035 GTCCCACCTCGAAAGTTGAGTAT 60.056 47.826 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.018866 GATCATCGCGGCCTCTTCG 61.019 63.158 6.13 0.00 0.00 3.79
7 8 1.068083 TGATCATCGCGGCCTCTTC 59.932 57.895 6.13 0.00 0.00 2.87
8 9 1.227380 GTGATCATCGCGGCCTCTT 60.227 57.895 6.13 0.00 0.00 2.85
9 10 2.419198 GTGATCATCGCGGCCTCT 59.581 61.111 6.13 0.00 0.00 3.69
10 11 2.663188 GGTGATCATCGCGGCCTC 60.663 66.667 6.13 0.00 0.00 4.70
11 12 3.157217 GAGGTGATCATCGCGGCCT 62.157 63.158 6.13 0.00 0.00 5.19
12 13 2.663188 GAGGTGATCATCGCGGCC 60.663 66.667 6.13 0.00 0.00 6.13
13 14 3.032609 CGAGGTGATCATCGCGGC 61.033 66.667 22.57 3.04 40.70 6.53
14 15 1.658717 GTCGAGGTGATCATCGCGG 60.659 63.158 28.07 12.54 45.55 6.46
15 16 2.006062 CGTCGAGGTGATCATCGCG 61.006 63.158 24.02 24.02 45.55 5.87
16 17 2.296480 GCGTCGAGGTGATCATCGC 61.296 63.158 12.79 6.74 45.55 4.58
17 18 0.932123 CTGCGTCGAGGTGATCATCG 60.932 60.000 11.63 11.63 46.98 3.84
18 19 1.211818 GCTGCGTCGAGGTGATCATC 61.212 60.000 7.01 0.00 0.00 2.92
19 20 1.227089 GCTGCGTCGAGGTGATCAT 60.227 57.895 7.01 0.00 0.00 2.45
20 21 2.181777 GCTGCGTCGAGGTGATCA 59.818 61.111 7.01 0.00 0.00 2.92
21 22 1.875813 CTGCTGCGTCGAGGTGATC 60.876 63.158 7.01 0.00 0.00 2.92
22 23 2.182791 CTGCTGCGTCGAGGTGAT 59.817 61.111 7.01 0.00 0.00 3.06
23 24 4.056125 CCTGCTGCGTCGAGGTGA 62.056 66.667 7.01 0.00 0.00 4.02
30 31 4.643387 AACCACCCCTGCTGCGTC 62.643 66.667 0.00 0.00 0.00 5.19
31 32 4.954970 CAACCACCCCTGCTGCGT 62.955 66.667 0.00 0.00 0.00 5.24
56 57 3.438017 CTCCAGAGCGGCCAGTAGC 62.438 68.421 2.24 0.00 42.60 3.58
57 58 2.811101 CTCCAGAGCGGCCAGTAG 59.189 66.667 2.24 0.00 33.14 2.57
58 59 3.461773 GCTCCAGAGCGGCCAGTA 61.462 66.667 2.24 0.00 45.29 2.74
67 68 2.716017 GGGGACACGAGCTCCAGAG 61.716 68.421 8.47 0.00 0.00 3.35
68 69 2.680352 GGGGACACGAGCTCCAGA 60.680 66.667 8.47 0.00 0.00 3.86
69 70 2.681778 AGGGGACACGAGCTCCAG 60.682 66.667 8.47 3.10 0.00 3.86
70 71 2.680352 GAGGGGACACGAGCTCCA 60.680 66.667 8.47 0.00 0.00 3.86
71 72 2.363147 AGAGGGGACACGAGCTCC 60.363 66.667 8.47 0.00 0.00 4.70
72 73 2.888863 CAGAGGGGACACGAGCTC 59.111 66.667 2.73 2.73 0.00 4.09
73 74 3.386237 GCAGAGGGGACACGAGCT 61.386 66.667 0.00 0.00 0.00 4.09
74 75 4.459089 GGCAGAGGGGACACGAGC 62.459 72.222 0.00 0.00 0.00 5.03
75 76 2.997315 TGGCAGAGGGGACACGAG 60.997 66.667 0.00 0.00 0.00 4.18
76 77 3.311110 GTGGCAGAGGGGACACGA 61.311 66.667 0.00 0.00 37.00 4.35
78 79 4.394712 CGGTGGCAGAGGGGACAC 62.395 72.222 0.00 0.00 46.35 3.67
94 95 3.777925 CTGTCGCCGTCTTTGCCG 61.778 66.667 0.00 0.00 0.00 5.69
95 96 4.090057 GCTGTCGCCGTCTTTGCC 62.090 66.667 0.00 0.00 0.00 4.52
105 106 2.032681 AGGAGGTTTGGCTGTCGC 59.967 61.111 0.00 0.00 0.00 5.19
106 107 1.376037 GGAGGAGGTTTGGCTGTCG 60.376 63.158 0.00 0.00 0.00 4.35
107 108 1.376037 CGGAGGAGGTTTGGCTGTC 60.376 63.158 0.00 0.00 0.00 3.51
108 109 1.201429 ATCGGAGGAGGTTTGGCTGT 61.201 55.000 0.00 0.00 0.00 4.40
109 110 0.462759 GATCGGAGGAGGTTTGGCTG 60.463 60.000 0.00 0.00 0.00 4.85
110 111 1.908483 GATCGGAGGAGGTTTGGCT 59.092 57.895 0.00 0.00 0.00 4.75
111 112 1.521681 CGATCGGAGGAGGTTTGGC 60.522 63.158 7.38 0.00 0.00 4.52
112 113 0.179108 GTCGATCGGAGGAGGTTTGG 60.179 60.000 16.41 0.00 0.00 3.28
113 114 0.525668 CGTCGATCGGAGGAGGTTTG 60.526 60.000 16.41 0.00 35.71 2.93
114 115 1.807886 CGTCGATCGGAGGAGGTTT 59.192 57.895 16.41 0.00 35.71 3.27
115 116 3.510846 CGTCGATCGGAGGAGGTT 58.489 61.111 16.41 0.00 35.71 3.50
124 125 0.643820 GTAGTTTTGGCCGTCGATCG 59.356 55.000 9.36 9.36 39.52 3.69
125 126 0.643820 CGTAGTTTTGGCCGTCGATC 59.356 55.000 0.00 0.00 0.00 3.69
126 127 0.738412 CCGTAGTTTTGGCCGTCGAT 60.738 55.000 0.00 0.00 0.00 3.59
127 128 1.373246 CCGTAGTTTTGGCCGTCGA 60.373 57.895 0.00 0.00 0.00 4.20
128 129 3.018840 GCCGTAGTTTTGGCCGTCG 62.019 63.158 0.00 0.00 45.73 5.12
129 130 2.865308 GCCGTAGTTTTGGCCGTC 59.135 61.111 0.00 0.00 45.73 4.79
134 135 0.452122 CGCTTTCGCCGTAGTTTTGG 60.452 55.000 0.00 0.00 0.00 3.28
135 136 2.981969 CGCTTTCGCCGTAGTTTTG 58.018 52.632 0.00 0.00 0.00 2.44
162 163 4.451150 TCTCGACATGGCCGCCAC 62.451 66.667 16.16 0.61 35.80 5.01
163 164 4.451150 GTCTCGACATGGCCGCCA 62.451 66.667 16.17 16.17 38.19 5.69
165 166 4.796231 ACGTCTCGACATGGCCGC 62.796 66.667 0.00 0.00 0.00 6.53
166 167 2.880879 CACGTCTCGACATGGCCG 60.881 66.667 0.00 0.00 0.00 6.13
167 168 2.509336 CCACGTCTCGACATGGCC 60.509 66.667 0.00 0.00 37.88 5.36
170 171 0.708370 CGAAACCACGTCTCGACATG 59.292 55.000 0.00 0.00 34.52 3.21
171 172 0.313043 ACGAAACCACGTCTCGACAT 59.687 50.000 11.49 0.00 43.02 3.06
172 173 0.943673 TACGAAACCACGTCTCGACA 59.056 50.000 11.49 0.00 45.32 4.35
173 174 1.909532 CATACGAAACCACGTCTCGAC 59.090 52.381 11.49 0.00 45.32 4.20
174 175 1.135603 CCATACGAAACCACGTCTCGA 60.136 52.381 11.49 0.00 45.32 4.04
175 176 1.135603 TCCATACGAAACCACGTCTCG 60.136 52.381 0.00 0.00 45.32 4.04
176 177 2.257034 GTCCATACGAAACCACGTCTC 58.743 52.381 0.00 0.00 45.32 3.36
177 178 2.358939 GTCCATACGAAACCACGTCT 57.641 50.000 0.00 0.00 45.32 4.18
216 217 3.751049 TATTCTCCGGCCGCCTCCT 62.751 63.158 22.85 6.29 0.00 3.69
217 218 3.227792 CTATTCTCCGGCCGCCTCC 62.228 68.421 22.85 0.00 0.00 4.30
218 219 2.340443 CTATTCTCCGGCCGCCTC 59.660 66.667 22.85 0.00 0.00 4.70
219 220 3.930012 GCTATTCTCCGGCCGCCT 61.930 66.667 22.85 3.88 0.00 5.52
260 261 4.779733 TCCACCCTCTCTCCCCGC 62.780 72.222 0.00 0.00 0.00 6.13
261 262 2.038975 TTCCACCCTCTCTCCCCG 59.961 66.667 0.00 0.00 0.00 5.73
262 263 2.371259 GCTTCCACCCTCTCTCCCC 61.371 68.421 0.00 0.00 0.00 4.81
263 264 2.726351 CGCTTCCACCCTCTCTCCC 61.726 68.421 0.00 0.00 0.00 4.30
264 265 1.545706 AACGCTTCCACCCTCTCTCC 61.546 60.000 0.00 0.00 0.00 3.71
265 266 0.390472 CAACGCTTCCACCCTCTCTC 60.390 60.000 0.00 0.00 0.00 3.20
266 267 1.674057 CAACGCTTCCACCCTCTCT 59.326 57.895 0.00 0.00 0.00 3.10
267 268 1.376037 CCAACGCTTCCACCCTCTC 60.376 63.158 0.00 0.00 0.00 3.20
268 269 2.750350 CCAACGCTTCCACCCTCT 59.250 61.111 0.00 0.00 0.00 3.69
269 270 2.359975 CCCAACGCTTCCACCCTC 60.360 66.667 0.00 0.00 0.00 4.30
270 271 2.852075 TCCCAACGCTTCCACCCT 60.852 61.111 0.00 0.00 0.00 4.34
271 272 2.359975 CTCCCAACGCTTCCACCC 60.360 66.667 0.00 0.00 0.00 4.61
272 273 3.056328 GCTCCCAACGCTTCCACC 61.056 66.667 0.00 0.00 0.00 4.61
273 274 3.423154 CGCTCCCAACGCTTCCAC 61.423 66.667 0.00 0.00 0.00 4.02
274 275 4.697756 CCGCTCCCAACGCTTCCA 62.698 66.667 0.00 0.00 0.00 3.53
275 276 4.388499 TCCGCTCCCAACGCTTCC 62.388 66.667 0.00 0.00 0.00 3.46
276 277 2.815647 CTCCGCTCCCAACGCTTC 60.816 66.667 0.00 0.00 0.00 3.86
277 278 4.394712 CCTCCGCTCCCAACGCTT 62.395 66.667 0.00 0.00 0.00 4.68
280 281 4.452733 GTCCCTCCGCTCCCAACG 62.453 72.222 0.00 0.00 0.00 4.10
281 282 3.003763 AGTCCCTCCGCTCCCAAC 61.004 66.667 0.00 0.00 0.00 3.77
282 283 3.003173 CAGTCCCTCCGCTCCCAA 61.003 66.667 0.00 0.00 0.00 4.12
285 286 2.442272 TAGCAGTCCCTCCGCTCC 60.442 66.667 0.00 0.00 37.20 4.70
286 287 1.755008 ACTAGCAGTCCCTCCGCTC 60.755 63.158 0.00 0.00 37.20 5.03
287 288 2.055042 CACTAGCAGTCCCTCCGCT 61.055 63.158 0.00 0.00 39.80 5.52
288 289 2.286127 GACACTAGCAGTCCCTCCGC 62.286 65.000 4.92 0.00 0.00 5.54
289 290 1.810532 GACACTAGCAGTCCCTCCG 59.189 63.158 4.92 0.00 0.00 4.63
295 296 1.248785 TGTCGGGGACACTAGCAGTC 61.249 60.000 7.26 7.26 37.67 3.51
296 297 1.228769 TGTCGGGGACACTAGCAGT 60.229 57.895 0.00 0.00 37.67 4.40
297 298 1.513158 CTGTCGGGGACACTAGCAG 59.487 63.158 0.00 0.00 37.67 4.24
298 299 1.982395 CCTGTCGGGGACACTAGCA 60.982 63.158 0.00 0.00 37.67 3.49
299 300 2.893398 CCTGTCGGGGACACTAGC 59.107 66.667 0.00 0.00 37.67 3.42
300 301 2.893398 GCCTGTCGGGGACACTAG 59.107 66.667 0.00 0.00 37.67 2.57
301 302 3.066190 CGCCTGTCGGGGACACTA 61.066 66.667 0.00 0.00 45.63 2.74
357 358 4.973055 TGGGGTGAAACGGACGCG 62.973 66.667 3.53 3.53 38.12 6.01
358 359 2.188161 TTTGGGGTGAAACGGACGC 61.188 57.895 0.00 0.00 38.12 5.19
359 360 1.650363 GTTTGGGGTGAAACGGACG 59.350 57.895 0.00 0.00 38.12 4.79
360 361 1.788067 CGGTTTGGGGTGAAACGGAC 61.788 60.000 0.00 0.00 38.01 4.79
361 362 1.526455 CGGTTTGGGGTGAAACGGA 60.526 57.895 0.00 0.00 38.01 4.69
362 363 1.512156 CTCGGTTTGGGGTGAAACGG 61.512 60.000 0.00 0.00 38.12 4.44
363 364 1.946267 CTCGGTTTGGGGTGAAACG 59.054 57.895 0.00 0.00 38.12 3.60
364 365 1.658114 GCTCGGTTTGGGGTGAAAC 59.342 57.895 0.00 0.00 35.45 2.78
365 366 1.894756 CGCTCGGTTTGGGGTGAAA 60.895 57.895 0.00 0.00 0.00 2.69
366 367 2.281208 CGCTCGGTTTGGGGTGAA 60.281 61.111 0.00 0.00 0.00 3.18
369 370 4.572571 TTGCGCTCGGTTTGGGGT 62.573 61.111 9.73 0.00 0.00 4.95
370 371 3.737172 CTTGCGCTCGGTTTGGGG 61.737 66.667 9.73 0.00 0.00 4.96
371 372 2.070654 AAACTTGCGCTCGGTTTGGG 62.071 55.000 19.08 0.36 32.84 4.12
372 373 0.934436 CAAACTTGCGCTCGGTTTGG 60.934 55.000 28.14 17.85 43.19 3.28
373 374 0.934436 CCAAACTTGCGCTCGGTTTG 60.934 55.000 28.50 28.50 45.14 2.93
374 375 1.358759 CCAAACTTGCGCTCGGTTT 59.641 52.632 9.73 13.79 34.10 3.27
375 376 2.551912 CCCAAACTTGCGCTCGGTT 61.552 57.895 9.73 8.16 0.00 4.44
376 377 2.978010 CCCAAACTTGCGCTCGGT 60.978 61.111 9.73 1.34 0.00 4.69
377 378 4.404654 GCCCAAACTTGCGCTCGG 62.405 66.667 9.73 0.61 0.00 4.63
378 379 4.404654 GGCCCAAACTTGCGCTCG 62.405 66.667 9.73 1.27 32.76 5.03
379 380 3.273080 CTGGCCCAAACTTGCGCTC 62.273 63.158 9.73 0.00 32.76 5.03
380 381 3.297620 CTGGCCCAAACTTGCGCT 61.298 61.111 9.73 0.00 32.76 5.92
381 382 4.362476 CCTGGCCCAAACTTGCGC 62.362 66.667 0.00 0.00 0.00 6.09
382 383 3.683937 CCCTGGCCCAAACTTGCG 61.684 66.667 0.00 0.00 0.00 4.85
383 384 1.610379 ATCCCTGGCCCAAACTTGC 60.610 57.895 0.00 0.00 0.00 4.01
384 385 1.259840 CCATCCCTGGCCCAAACTTG 61.260 60.000 0.00 0.00 35.23 3.16
385 386 1.079073 CCATCCCTGGCCCAAACTT 59.921 57.895 0.00 0.00 35.23 2.66
386 387 2.772924 CCATCCCTGGCCCAAACT 59.227 61.111 0.00 0.00 35.23 2.66
387 388 2.364186 CCCATCCCTGGCCCAAAC 60.364 66.667 0.00 0.00 41.64 2.93
388 389 2.868566 ACCCATCCCTGGCCCAAA 60.869 61.111 0.00 0.00 41.64 3.28
389 390 3.346734 GACCCATCCCTGGCCCAA 61.347 66.667 0.00 0.00 41.64 4.12
392 393 2.493273 TTTTCGACCCATCCCTGGCC 62.493 60.000 0.00 0.00 41.64 5.36
393 394 1.001393 TTTTCGACCCATCCCTGGC 60.001 57.895 0.00 0.00 41.64 4.85
394 395 2.868253 GTTTTCGACCCATCCCTGG 58.132 57.895 0.00 0.00 42.73 4.45
413 414 1.014352 CAAATGTCCGGATTCCGTCC 58.986 55.000 22.83 13.25 46.80 4.79
414 415 1.664151 GACAAATGTCCGGATTCCGTC 59.336 52.381 22.83 15.53 46.80 4.79
415 416 1.278127 AGACAAATGTCCGGATTCCGT 59.722 47.619 22.83 1.21 46.80 4.69
416 417 1.665679 CAGACAAATGTCCGGATTCCG 59.334 52.381 18.33 18.33 45.85 4.30
417 418 2.711542 ACAGACAAATGTCCGGATTCC 58.288 47.619 7.81 0.00 45.85 3.01
418 419 4.766404 AAACAGACAAATGTCCGGATTC 57.234 40.909 7.81 0.00 45.85 2.52
419 420 5.048294 GGTAAAACAGACAAATGTCCGGATT 60.048 40.000 7.81 0.00 45.85 3.01
420 421 4.457949 GGTAAAACAGACAAATGTCCGGAT 59.542 41.667 7.81 0.00 45.85 4.18
421 422 3.816523 GGTAAAACAGACAAATGTCCGGA 59.183 43.478 0.00 0.00 45.85 5.14
422 423 3.057806 GGGTAAAACAGACAAATGTCCGG 60.058 47.826 9.84 0.00 45.85 5.14
423 424 3.057806 GGGGTAAAACAGACAAATGTCCG 60.058 47.826 9.84 2.65 45.85 4.79
424 425 3.892588 TGGGGTAAAACAGACAAATGTCC 59.107 43.478 9.84 0.00 45.85 4.02
425 426 5.523438 TTGGGGTAAAACAGACAAATGTC 57.477 39.130 5.40 5.40 45.08 3.06
426 427 5.666462 GTTTGGGGTAAAACAGACAAATGT 58.334 37.500 0.00 0.00 39.39 2.71
427 428 4.742659 CGTTTGGGGTAAAACAGACAAATG 59.257 41.667 0.00 0.00 39.53 2.32
428 429 4.202172 CCGTTTGGGGTAAAACAGACAAAT 60.202 41.667 0.00 0.00 39.53 2.32
429 430 3.130693 CCGTTTGGGGTAAAACAGACAAA 59.869 43.478 1.28 0.00 39.53 2.83
430 431 2.688958 CCGTTTGGGGTAAAACAGACAA 59.311 45.455 1.28 0.00 39.53 3.18
431 432 2.092538 TCCGTTTGGGGTAAAACAGACA 60.093 45.455 1.28 0.00 39.53 3.41
432 433 2.291465 GTCCGTTTGGGGTAAAACAGAC 59.709 50.000 1.66 1.66 39.16 3.51
433 434 2.574450 GTCCGTTTGGGGTAAAACAGA 58.426 47.619 1.28 0.00 39.53 3.41
434 435 1.264826 CGTCCGTTTGGGGTAAAACAG 59.735 52.381 1.28 0.00 39.53 3.16
435 436 1.307097 CGTCCGTTTGGGGTAAAACA 58.693 50.000 1.28 0.00 39.53 2.83
436 437 0.040157 GCGTCCGTTTGGGGTAAAAC 60.040 55.000 0.00 0.00 36.81 2.43
437 438 1.505477 CGCGTCCGTTTGGGGTAAAA 61.505 55.000 0.00 0.00 36.01 1.52
438 439 1.960250 CGCGTCCGTTTGGGGTAAA 60.960 57.895 0.00 0.00 36.01 2.01
439 440 2.357275 CGCGTCCGTTTGGGGTAA 60.357 61.111 0.00 0.00 36.01 2.85
451 452 2.894240 TTATCTTGTCCGGGCGCGTC 62.894 60.000 22.32 4.38 0.00 5.19
452 453 2.901051 CTTATCTTGTCCGGGCGCGT 62.901 60.000 22.32 3.86 0.00 6.01
453 454 2.202824 TTATCTTGTCCGGGCGCG 60.203 61.111 17.31 17.31 0.00 6.86
454 455 1.887707 CCTTATCTTGTCCGGGCGC 60.888 63.158 0.00 0.00 0.00 6.53
455 456 0.529992 GACCTTATCTTGTCCGGGCG 60.530 60.000 0.00 0.00 0.00 6.13
456 457 0.529992 CGACCTTATCTTGTCCGGGC 60.530 60.000 0.00 0.00 0.00 6.13
457 458 0.529992 GCGACCTTATCTTGTCCGGG 60.530 60.000 0.00 0.00 0.00 5.73
458 459 0.870307 CGCGACCTTATCTTGTCCGG 60.870 60.000 0.00 0.00 0.00 5.14
459 460 1.480219 GCGCGACCTTATCTTGTCCG 61.480 60.000 12.10 0.00 0.00 4.79
460 461 1.480219 CGCGCGACCTTATCTTGTCC 61.480 60.000 28.94 0.00 0.00 4.02
461 462 1.480219 CCGCGCGACCTTATCTTGTC 61.480 60.000 34.63 0.00 0.00 3.18
462 463 1.518572 CCGCGCGACCTTATCTTGT 60.519 57.895 34.63 0.00 0.00 3.16
463 464 1.518572 ACCGCGCGACCTTATCTTG 60.519 57.895 34.63 12.93 0.00 3.02
464 465 1.518572 CACCGCGCGACCTTATCTT 60.519 57.895 34.63 0.00 0.00 2.40
465 466 2.104331 CACCGCGCGACCTTATCT 59.896 61.111 34.63 0.00 0.00 1.98
466 467 2.960129 CCACCGCGCGACCTTATC 60.960 66.667 34.63 0.00 0.00 1.75
467 468 3.426117 CTCCACCGCGCGACCTTAT 62.426 63.158 34.63 6.07 0.00 1.73
468 469 4.124351 CTCCACCGCGCGACCTTA 62.124 66.667 34.63 11.52 0.00 2.69
476 477 3.599285 TAAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
477 478 2.038837 GTAAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 0.00 5.68
478 479 0.953960 GTGTAAGGCCAACTCCACCG 60.954 60.000 5.01 0.00 0.00 4.94
479 480 0.109723 TGTGTAAGGCCAACTCCACC 59.890 55.000 5.01 0.00 32.74 4.61
480 481 1.523758 CTGTGTAAGGCCAACTCCAC 58.476 55.000 5.01 4.77 33.74 4.02
481 482 0.400213 CCTGTGTAAGGCCAACTCCA 59.600 55.000 5.01 3.49 39.93 3.86
482 483 0.690762 TCCTGTGTAAGGCCAACTCC 59.309 55.000 5.01 0.00 46.92 3.85
483 484 1.946283 GCTCCTGTGTAAGGCCAACTC 60.946 57.143 5.01 4.34 46.92 3.01
484 485 0.036875 GCTCCTGTGTAAGGCCAACT 59.963 55.000 5.01 0.00 46.92 3.16
485 486 0.036875 AGCTCCTGTGTAAGGCCAAC 59.963 55.000 5.01 2.84 46.92 3.77
486 487 0.324943 GAGCTCCTGTGTAAGGCCAA 59.675 55.000 5.01 0.00 46.92 4.52
487 488 0.835971 TGAGCTCCTGTGTAAGGCCA 60.836 55.000 12.15 0.00 46.92 5.36
488 489 0.391793 GTGAGCTCCTGTGTAAGGCC 60.392 60.000 12.15 0.00 46.92 5.19
489 490 0.610687 AGTGAGCTCCTGTGTAAGGC 59.389 55.000 12.15 0.00 46.92 4.35
491 492 4.260990 CGATCTAGTGAGCTCCTGTGTAAG 60.261 50.000 12.15 2.40 0.00 2.34
492 493 3.628032 CGATCTAGTGAGCTCCTGTGTAA 59.372 47.826 12.15 0.00 0.00 2.41
509 510 1.821753 CAACTCCTGTCTGGACGATCT 59.178 52.381 0.00 0.00 40.56 2.75
511 512 0.898320 CCAACTCCTGTCTGGACGAT 59.102 55.000 0.00 0.00 40.56 3.73
518 519 4.320844 AGTGGCCAACTCCTGTCT 57.679 55.556 7.24 0.00 31.64 3.41
541 542 0.389948 ACTGCGGTCAAACTCGATCC 60.390 55.000 0.00 0.00 0.00 3.36
591 592 0.179111 GCGTCGATCCATGTCCTGAA 60.179 55.000 0.00 0.00 0.00 3.02
726 737 1.838568 CGGAGCATGCATGGTGATCG 61.839 60.000 34.35 27.09 38.85 3.69
731 765 1.105167 CCAATCGGAGCATGCATGGT 61.105 55.000 30.31 30.31 41.89 3.55
812 847 3.138798 GCCAGCCAGAGCACATGG 61.139 66.667 0.00 0.00 43.56 3.66
825 860 0.964700 TCACTCACTCAGTCAGCCAG 59.035 55.000 0.00 0.00 30.26 4.85
826 861 1.547820 GATCACTCACTCAGTCAGCCA 59.452 52.381 0.00 0.00 30.26 4.75
827 862 1.468908 CGATCACTCACTCAGTCAGCC 60.469 57.143 0.00 0.00 30.26 4.85
828 863 1.906757 CGATCACTCACTCAGTCAGC 58.093 55.000 0.00 0.00 30.26 4.26
920 955 7.383102 AGAAGCGCATAAATTAATATCCCTG 57.617 36.000 11.47 0.00 0.00 4.45
1194 1303 5.469373 TCACAAACAGATCATATCAACGC 57.531 39.130 0.00 0.00 0.00 4.84
1463 1576 1.327303 GCACACAAAATGAGTCCCCA 58.673 50.000 0.00 0.00 0.00 4.96
1494 1607 3.864686 GCGTACCCTGCATGCACG 61.865 66.667 18.46 19.25 35.78 5.34
1747 1861 1.024046 TCTGCATGCGCCACGTTTAT 61.024 50.000 14.09 0.00 37.32 1.40
1748 1862 1.634757 CTCTGCATGCGCCACGTTTA 61.635 55.000 14.09 0.00 37.32 2.01
1758 1872 0.727122 GAACAACACGCTCTGCATGC 60.727 55.000 11.82 11.82 0.00 4.06
1759 1873 0.451628 CGAACAACACGCTCTGCATG 60.452 55.000 0.00 0.00 0.00 4.06
1760 1874 0.880278 ACGAACAACACGCTCTGCAT 60.880 50.000 0.00 0.00 0.00 3.96
2128 2272 4.715523 ACCCCGTTCATGGTGCCG 62.716 66.667 0.00 0.00 32.36 5.69
2528 2672 6.998802 AGAAGAAGGAAAAAGAAGATCGAGA 58.001 36.000 0.00 0.00 0.00 4.04
2572 2719 8.744652 TCAACCAATCAAAACTAGAACAAGAAA 58.255 29.630 0.00 0.00 0.00 2.52
2578 2728 8.871686 AAACATCAACCAATCAAAACTAGAAC 57.128 30.769 0.00 0.00 0.00 3.01
2664 2817 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2665 2818 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2666 2819 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2667 2820 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2668 2821 0.167908 CCACACACACACACACACAC 59.832 55.000 0.00 0.00 0.00 3.82
2669 2822 1.581727 GCCACACACACACACACACA 61.582 55.000 0.00 0.00 0.00 3.72
2826 2980 4.257267 TGAGTTCAGTGACGAATGATGT 57.743 40.909 0.00 0.00 0.00 3.06
2829 2983 4.488879 CTCATGAGTTCAGTGACGAATGA 58.511 43.478 14.95 0.00 0.00 2.57
2860 3021 3.005684 GTGGCTGGTTCATCACATTTTGA 59.994 43.478 0.00 0.00 39.11 2.69
2877 3038 5.083533 TCATGAAACAAAACAAAGTGGCT 57.916 34.783 0.00 0.00 0.00 4.75
2879 3040 4.026640 CGCTCATGAAACAAAACAAAGTGG 60.027 41.667 0.00 0.00 0.00 4.00
2933 3094 2.355837 CACACCACGTCGACCCTG 60.356 66.667 10.58 5.43 0.00 4.45
2966 3127 1.673626 CCAAATGCAATGACTGTGGGC 60.674 52.381 4.54 0.00 0.00 5.36
2993 3154 1.122227 AGGGCCGCATTGCATAAAAT 58.878 45.000 9.69 0.00 0.00 1.82
3033 3194 6.044682 GGGATTTTACCTGAAATGCTGATTG 58.955 40.000 2.70 0.00 37.46 2.67
3087 3249 3.449018 GTGAGTGAGAGCTAGGGATTTGA 59.551 47.826 0.00 0.00 0.00 2.69
3104 3266 1.202651 CCGAGTTGGGTGAAAGTGAGT 60.203 52.381 0.00 0.00 0.00 3.41
3111 3273 2.029964 GCGACCGAGTTGGGTGAA 59.970 61.111 0.24 0.00 44.64 3.18
3145 3307 2.513753 CTCCATCTCGAGCTAGGTGAT 58.486 52.381 7.81 0.00 28.26 3.06
3196 3358 0.392193 CGCTGGGAAGAAGATGCACT 60.392 55.000 0.00 0.00 0.00 4.40
3266 3429 2.355837 GTCGTGCGCTGGAGAACA 60.356 61.111 9.73 0.00 0.00 3.18
3381 3544 2.708386 ATCTCTAATAGTGTCGCCGC 57.292 50.000 0.00 0.00 0.00 6.53
3405 3568 6.203723 GTCAGAAATTGTACATGGATCTAGCC 59.796 42.308 0.00 0.00 0.00 3.93
3411 3574 7.341030 TGAGATGTCAGAAATTGTACATGGAT 58.659 34.615 0.00 0.00 31.84 3.41
3413 3576 6.990341 TGAGATGTCAGAAATTGTACATGG 57.010 37.500 0.00 0.00 31.84 3.66
3426 3589 1.402968 CGGGCCAATTTGAGATGTCAG 59.597 52.381 4.39 0.00 32.98 3.51
3430 3593 1.462616 TCACGGGCCAATTTGAGATG 58.537 50.000 4.39 0.00 0.00 2.90
3431 3594 2.214376 TTCACGGGCCAATTTGAGAT 57.786 45.000 4.39 0.00 0.00 2.75
3443 3606 3.510719 CACTTGCCATTTTATTCACGGG 58.489 45.455 0.00 0.00 0.00 5.28
3444 3607 3.056891 ACCACTTGCCATTTTATTCACGG 60.057 43.478 0.00 0.00 0.00 4.94
3469 3632 4.461781 TCGAGGTGGGACTAAACTTTAGAG 59.538 45.833 14.37 0.00 0.00 2.43
3477 3640 3.388676 TCAACTTTCGAGGTGGGACTAAA 59.611 43.478 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.