Multiple sequence alignment - TraesCS4D01G016600

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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 TraesCS4D01G016600 chr4D 100.000 4180 0 0 1 4180 7463331 7459152 0.000000e+00 7720
1 TraesCS4D01G016600 chr4D 98.727 550 7 0 3631 4180 394130456 394129907 0.000000e+00 977
2 TraesCS4D01G016600 chr4D 98.000 550 11 0 3631 4180 235440156 235440705 0.000000e+00 955
3 TraesCS4D01G016600 chr4D 98.000 550 11 0 3631 4180 509516962 509516413 0.000000e+00 955
4 TraesCS4D01G016600 chr4A 90.037 2168 99 30 404 2542 596158676 596160755 0.000000e+00 2699
5 TraesCS4D01G016600 chr4A 92.605 879 35 17 2761 3627 596161479 596162339 0.000000e+00 1236
6 TraesCS4D01G016600 chr4A 87.733 375 26 9 2312 2681 596161120 596161479 1.800000e-113 420
7 TraesCS4D01G016600 chr4A 87.681 276 23 5 2 273 596158372 596158640 1.130000e-80 311
8 TraesCS4D01G016600 chr4A 88.344 163 13 5 131 292 596153764 596153921 1.530000e-44 191
9 TraesCS4D01G016600 chr4B 88.129 2047 134 50 1 2010 13302862 13300888 0.000000e+00 2333
10 TraesCS4D01G016600 chr4B 87.865 890 49 31 2766 3620 13300244 13299379 0.000000e+00 990
11 TraesCS4D01G016600 chr4B 87.879 660 36 21 2057 2683 13300892 13300244 0.000000e+00 736
12 TraesCS4D01G016600 chr4B 88.991 109 9 3 2678 2786 283233866 283233761 9.430000e-27 132
13 TraesCS4D01G016600 chr7D 99.091 550 5 0 3631 4180 26398878 26398329 0.000000e+00 989
14 TraesCS4D01G016600 chr6D 99.091 550 5 0 3631 4180 468548415 468547866 0.000000e+00 989
15 TraesCS4D01G016600 chr6D 98.364 550 9 0 3631 4180 181724831 181724282 0.000000e+00 966
16 TraesCS4D01G016600 chr1D 99.091 550 5 0 3631 4180 224482760 224483309 0.000000e+00 989
17 TraesCS4D01G016600 chr1D 98.909 550 6 0 3631 4180 315024322 315024871 0.000000e+00 983
18 TraesCS4D01G016600 chr2D 98.545 550 8 0 3631 4180 455988089 455987540 0.000000e+00 972
19 TraesCS4D01G016600 chr6B 82.496 617 44 26 2077 2681 643477183 643476619 2.260000e-132 483
20 TraesCS4D01G016600 chr6B 87.246 345 24 10 2077 2412 473184737 473184404 3.950000e-100 375
21 TraesCS4D01G016600 chr6B 86.667 345 26 8 2077 2412 616756659 616756326 8.540000e-97 364
22 TraesCS4D01G016600 chr6B 82.353 357 32 15 2313 2662 643476386 643476054 8.850000e-72 281
23 TraesCS4D01G016600 chr6B 81.793 357 34 15 2313 2662 62202217 62201885 1.920000e-68 270
24 TraesCS4D01G016600 chr6B 82.319 345 30 15 2313 2650 616756072 616755752 1.920000e-68 270
25 TraesCS4D01G016600 chr6B 90.000 210 12 7 2459 2662 473184024 473183818 3.200000e-66 263
26 TraesCS4D01G016600 chr6B 87.500 104 10 3 2763 2866 643476620 643476520 2.640000e-22 117
27 TraesCS4D01G016600 chr6B 87.500 104 6 5 2763 2866 62202447 62202351 3.420000e-21 113
28 TraesCS4D01G016600 chr6B 87.500 104 6 3 2763 2866 473184380 473184284 3.420000e-21 113
29 TraesCS4D01G016600 chr2B 86.957 345 25 10 2077 2412 764924993 764924660 1.840000e-98 370
30 TraesCS4D01G016600 chr2B 88.561 271 15 7 2077 2342 161977760 161977501 8.720000e-82 315
31 TraesCS4D01G016600 chr2B 88.991 109 8 4 2680 2786 682450991 682450885 9.430000e-27 132
32 TraesCS4D01G016600 chr5B 86.667 345 26 10 2077 2412 657063454 657063121 8.540000e-97 364
33 TraesCS4D01G016600 chr5B 88.889 108 9 3 2657 2764 318105245 318105349 3.390000e-26 130
34 TraesCS4D01G016600 chr7B 88.449 303 22 7 2119 2412 135316650 135316948 1.850000e-93 353
35 TraesCS4D01G016600 chr7B 85.673 342 35 11 2077 2412 721374981 721375314 8.600000e-92 348
36 TraesCS4D01G016600 chr7B 85.423 343 27 9 2079 2412 574880535 574880863 6.700000e-88 335
37 TraesCS4D01G016600 chr7B 83.188 345 27 15 2313 2650 708809048 708808728 1.900000e-73 287
38 TraesCS4D01G016600 chr7B 82.073 357 32 16 2313 2662 135317202 135317533 4.120000e-70 276
39 TraesCS4D01G016600 chr7B 87.500 104 6 5 2763 2866 135316972 135317068 3.420000e-21 113
40 TraesCS4D01G016600 chr7B 86.538 104 7 5 2763 2866 708809278 708809182 1.590000e-19 108
41 TraesCS4D01G016600 chr7B 85.577 104 8 4 2763 2866 721375398 721375494 7.390000e-18 102
42 TraesCS4D01G016600 chr3B 87.823 271 17 7 2077 2342 557358190 557357931 1.890000e-78 303
43 TraesCS4D01G016600 chr3B 81.322 348 34 15 2313 2653 446994072 446994395 1.930000e-63 254
44 TraesCS4D01G016600 chr3B 90.909 99 8 1 2678 2776 468222286 468222383 9.430000e-27 132
45 TraesCS4D01G016600 chr3B 86.538 104 7 5 2763 2866 710944601 710944697 1.590000e-19 108
46 TraesCS4D01G016600 chr2A 93.617 94 6 0 2673 2766 714303008 714302915 1.570000e-29 141
47 TraesCS4D01G016600 chr3D 89.815 108 8 3 2658 2764 123309600 123309495 7.290000e-28 135
48 TraesCS4D01G016600 chr3D 85.981 107 13 2 1917 2023 588061541 588061645 3.420000e-21 113
49 TraesCS4D01G016600 chr7A 90.291 103 7 3 2671 2772 14632135 14632035 9.430000e-27 132
50 TraesCS4D01G016600 chr1B 88.991 109 9 3 2678 2786 404679814 404679709 9.430000e-27 132
51 TraesCS4D01G016600 chr1B 88.785 107 8 4 2680 2786 487349206 487349104 1.220000e-25 128


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 TraesCS4D01G016600 chr4D 7459152 7463331 4179 True 7720.000000 7720 100.000000 1 4180 1 chr4D.!!$R1 4179
1 TraesCS4D01G016600 chr4D 394129907 394130456 549 True 977.000000 977 98.727000 3631 4180 1 chr4D.!!$R2 549
2 TraesCS4D01G016600 chr4D 235440156 235440705 549 False 955.000000 955 98.000000 3631 4180 1 chr4D.!!$F1 549
3 TraesCS4D01G016600 chr4D 509516413 509516962 549 True 955.000000 955 98.000000 3631 4180 1 chr4D.!!$R3 549
4 TraesCS4D01G016600 chr4A 596158372 596162339 3967 False 1166.500000 2699 89.514000 2 3627 4 chr4A.!!$F2 3625
5 TraesCS4D01G016600 chr4B 13299379 13302862 3483 True 1353.000000 2333 87.957667 1 3620 3 chr4B.!!$R2 3619
6 TraesCS4D01G016600 chr7D 26398329 26398878 549 True 989.000000 989 99.091000 3631 4180 1 chr7D.!!$R1 549
7 TraesCS4D01G016600 chr6D 468547866 468548415 549 True 989.000000 989 99.091000 3631 4180 1 chr6D.!!$R2 549
8 TraesCS4D01G016600 chr6D 181724282 181724831 549 True 966.000000 966 98.364000 3631 4180 1 chr6D.!!$R1 549
9 TraesCS4D01G016600 chr1D 224482760 224483309 549 False 989.000000 989 99.091000 3631 4180 1 chr1D.!!$F1 549
10 TraesCS4D01G016600 chr1D 315024322 315024871 549 False 983.000000 983 98.909000 3631 4180 1 chr1D.!!$F2 549
11 TraesCS4D01G016600 chr2D 455987540 455988089 549 True 972.000000 972 98.545000 3631 4180 1 chr2D.!!$R1 549
12 TraesCS4D01G016600 chr6B 616755752 616756659 907 True 317.000000 364 84.493000 2077 2650 2 chr6B.!!$R3 573
13 TraesCS4D01G016600 chr6B 643476054 643477183 1129 True 293.666667 483 84.116333 2077 2866 3 chr6B.!!$R4 789
14 TraesCS4D01G016600 chr6B 473183818 473184737 919 True 250.333333 375 88.248667 2077 2866 3 chr6B.!!$R2 789
15 TraesCS4D01G016600 chr7B 135316650 135317533 883 False 247.333333 353 86.007333 2119 2866 3 chr7B.!!$F2 747
16 TraesCS4D01G016600 chr7B 721374981 721375494 513 False 225.000000 348 85.625000 2077 2866 2 chr7B.!!$F3 789

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
855 865 0.383949 TTTGTGGTGAGCTTTTCGGC 59.616 50.000 0.00 0.0 0.00 5.54 F
856 866 1.452145 TTGTGGTGAGCTTTTCGGCC 61.452 55.000 0.00 0.0 0.00 6.13 F
1401 1417 2.136878 CAGGATCCAGGTCCCCTCG 61.137 68.421 15.82 0.0 39.17 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1699 1736 0.450983 GCATGGCAAGAGCTCAAGAC 59.549 55.000 17.77 10.54 41.7 3.01 R
1956 2013 1.335964 CGTGTCTCCAAGCTTCGAGAA 60.336 52.381 23.07 12.12 36.9 2.87 R
3243 4562 0.105964 TCGGTTATTCAGGGCCATCG 59.894 55.000 6.18 0.00 0.0 3.84 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
51 56 3.963129 TGCAATTAGGTCTAAAGTGGGG 58.037 45.455 0.00 0.00 0.00 4.96
58 63 1.844497 GGTCTAAAGTGGGGCCATAGT 59.156 52.381 4.39 0.00 0.00 2.12
71 76 2.484264 GGCCATAGTGAAACGCATATCC 59.516 50.000 0.00 0.00 45.86 2.59
77 82 6.447162 CATAGTGAAACGCATATCCACTCTA 58.553 40.000 0.00 0.00 45.86 2.43
78 83 4.683832 AGTGAAACGCATATCCACTCTAC 58.316 43.478 0.00 0.00 45.86 2.59
79 84 4.402793 AGTGAAACGCATATCCACTCTACT 59.597 41.667 0.00 0.00 45.86 2.57
80 85 4.740695 GTGAAACGCATATCCACTCTACTC 59.259 45.833 0.00 0.00 0.00 2.59
89 94 6.237888 GCATATCCACTCTACTCTATCGTACG 60.238 46.154 9.53 9.53 0.00 3.67
94 99 5.164070 CCACTCTACTCTATCGTACGAATCG 60.164 48.000 23.56 13.18 0.00 3.34
99 104 5.080642 ACTCTATCGTACGAATCGAACAG 57.919 43.478 23.56 12.91 40.61 3.16
100 105 4.569966 ACTCTATCGTACGAATCGAACAGT 59.430 41.667 23.56 13.50 40.61 3.55
142 147 4.624024 TCAAACGAAGATAACACGGTCATC 59.376 41.667 0.00 0.00 0.00 2.92
167 172 6.741992 TCACTAGCATGACCACAATTAAAG 57.258 37.500 0.00 0.00 0.00 1.85
168 173 6.472016 TCACTAGCATGACCACAATTAAAGA 58.528 36.000 0.00 0.00 0.00 2.52
261 266 4.452447 CGTCATCAAAGATCGCATCAATC 58.548 43.478 0.00 0.00 0.00 2.67
275 280 6.495706 TCGCATCAATCACAGTTAGTAGTAG 58.504 40.000 0.00 0.00 0.00 2.57
298 303 5.591643 CACTCGTTGCAAATAAGTACAGT 57.408 39.130 0.00 0.00 0.00 3.55
299 304 6.699895 CACTCGTTGCAAATAAGTACAGTA 57.300 37.500 0.00 0.00 0.00 2.74
300 305 7.112528 CACTCGTTGCAAATAAGTACAGTAA 57.887 36.000 0.00 0.00 0.00 2.24
301 306 7.569297 CACTCGTTGCAAATAAGTACAGTAAA 58.431 34.615 0.00 0.00 0.00 2.01
302 307 8.065407 CACTCGTTGCAAATAAGTACAGTAAAA 58.935 33.333 0.00 0.00 0.00 1.52
303 308 8.780249 ACTCGTTGCAAATAAGTACAGTAAAAT 58.220 29.630 0.00 0.00 0.00 1.82
304 309 9.607285 CTCGTTGCAAATAAGTACAGTAAAATT 57.393 29.630 0.00 0.00 0.00 1.82
344 349 6.019479 GTCAATTATTGTTCTCCGAGCTAGTG 60.019 42.308 4.77 0.00 0.00 2.74
374 380 2.848679 TCTCTGCCAGTGTGCCCA 60.849 61.111 0.00 0.00 0.00 5.36
375 381 2.359602 CTCTGCCAGTGTGCCCAG 60.360 66.667 0.00 0.00 0.00 4.45
390 396 9.651913 CAGTGTGCCCAGTTTATTTATTTTATT 57.348 29.630 0.00 0.00 0.00 1.40
415 421 2.463047 TAAGGGCCTCCTCTTCTCTC 57.537 55.000 6.46 0.00 44.07 3.20
430 436 1.307866 TCTCCCATGTCCCCTTCCC 60.308 63.158 0.00 0.00 0.00 3.97
481 487 1.037493 GGGGTAAAAATGGATCGGGC 58.963 55.000 0.00 0.00 0.00 6.13
577 583 2.265904 GGCTTTCCGGCGGTTTTCT 61.266 57.895 27.32 0.00 0.00 2.52
597 603 2.437359 GCGGCTGGTTGCTCATCT 60.437 61.111 0.00 0.00 42.39 2.90
626 632 1.175983 TTCCGGCGGAATTTGTGCTT 61.176 50.000 35.71 0.00 36.71 3.91
649 655 2.038007 TCCTGCTTCTCCTCGGCT 59.962 61.111 0.00 0.00 0.00 5.52
734 741 1.743958 TCGATTCCAGAACGAGACTCC 59.256 52.381 0.00 0.00 0.00 3.85
738 745 0.538977 TCCAGAACGAGACTCCGGTT 60.539 55.000 0.00 0.00 0.00 4.44
746 753 1.187087 GAGACTCCGGTTCCTGACAT 58.813 55.000 0.00 0.00 0.00 3.06
749 756 2.100989 GACTCCGGTTCCTGACATAGT 58.899 52.381 0.00 0.00 0.00 2.12
805 815 1.737793 CCATTGTAGTTGGAGCGGTTC 59.262 52.381 0.00 0.00 36.26 3.62
817 827 4.587189 CGGTTCCGGCTCGATCCC 62.587 72.222 0.00 0.00 0.00 3.85
826 836 3.288290 CTCGATCCCTCCGTCCGG 61.288 72.222 0.00 0.00 0.00 5.14
852 862 2.860136 GTTGCTTTGTGGTGAGCTTTTC 59.140 45.455 0.00 0.00 39.60 2.29
854 864 1.600413 GCTTTGTGGTGAGCTTTTCGG 60.600 52.381 0.00 0.00 36.01 4.30
855 865 0.383949 TTTGTGGTGAGCTTTTCGGC 59.616 50.000 0.00 0.00 0.00 5.54
856 866 1.452145 TTGTGGTGAGCTTTTCGGCC 61.452 55.000 0.00 0.00 0.00 6.13
857 867 2.282180 TGGTGAGCTTTTCGGCCC 60.282 61.111 0.00 0.00 0.00 5.80
858 868 3.062466 GGTGAGCTTTTCGGCCCC 61.062 66.667 0.00 0.00 0.00 5.80
859 869 3.062466 GTGAGCTTTTCGGCCCCC 61.062 66.667 0.00 0.00 0.00 5.40
1246 1262 4.214327 CGCCCTTCCTCTCGGAGC 62.214 72.222 0.00 0.00 41.25 4.70
1398 1414 2.447714 GCTCAGGATCCAGGTCCCC 61.448 68.421 15.82 0.00 39.17 4.81
1401 1417 2.136878 CAGGATCCAGGTCCCCTCG 61.137 68.421 15.82 0.00 39.17 4.63
1627 1655 3.560826 GACTGCATAGTCGAGAGCC 57.439 57.895 0.00 0.00 43.49 4.70
1751 1791 2.966915 ACTTGGGCATGCCAATGATAT 58.033 42.857 36.56 13.13 35.67 1.63
1777 1821 4.695455 TCATCCATCGGTGAGTTTTCTTTC 59.305 41.667 0.00 0.00 0.00 2.62
1817 1861 9.226345 CTTTAAAGATTTATCACTCGCCATTTC 57.774 33.333 9.77 0.00 0.00 2.17
1949 2006 8.939929 CGAATGGTCTGTTCATGCTAAATATAT 58.060 33.333 0.00 0.00 0.00 0.86
1975 2032 2.062519 GTTCTCGAAGCTTGGAGACAC 58.937 52.381 32.96 27.55 40.91 3.67
2016 2073 7.405469 CATGATCTGCTAGATGTGAACTTAC 57.595 40.000 0.00 0.00 34.53 2.34
2027 2084 4.617253 TGTGAACTTACACTGCAGGTAT 57.383 40.909 19.93 5.22 40.87 2.73
2110 2167 8.902540 AATTTCTGAATGTACTGTCACAACTA 57.097 30.769 0.00 0.00 30.84 2.24
2111 2168 7.709269 TTTCTGAATGTACTGTCACAACTAC 57.291 36.000 0.00 0.00 30.84 2.73
2112 2169 6.650427 TCTGAATGTACTGTCACAACTACT 57.350 37.500 0.00 0.00 30.84 2.57
2113 2170 7.754851 TCTGAATGTACTGTCACAACTACTA 57.245 36.000 0.00 0.00 30.84 1.82
2114 2171 7.817641 TCTGAATGTACTGTCACAACTACTAG 58.182 38.462 0.00 0.00 30.84 2.57
2115 2172 7.447545 TCTGAATGTACTGTCACAACTACTAGT 59.552 37.037 0.00 0.00 30.84 2.57
2116 2173 8.625786 TGAATGTACTGTCACAACTACTAGTA 57.374 34.615 1.89 1.89 30.84 1.82
2209 2266 9.780186 AATTCTCAGTTTTTAGTTACTGCTAGT 57.220 29.630 0.00 0.00 41.16 2.57
2211 2268 9.688592 TTCTCAGTTTTTAGTTACTGCTAGTAC 57.311 33.333 0.00 0.00 41.16 2.73
2212 2269 9.075678 TCTCAGTTTTTAGTTACTGCTAGTACT 57.924 33.333 0.00 0.00 41.16 2.73
2261 2323 9.709495 ATTGCAAGTTTTATGTGTGTAATCATT 57.291 25.926 4.94 0.00 0.00 2.57
2333 2399 7.160049 CAGTATACTTCATCAAGATCATGGCT 58.840 38.462 1.56 0.00 33.34 4.75
2382 3055 3.118629 TGGATGGGTCTGATTCTTCTTCG 60.119 47.826 0.00 0.00 0.00 3.79
2389 3062 6.106673 GGGTCTGATTCTTCTTCGTTATTGA 58.893 40.000 0.00 0.00 0.00 2.57
2396 3069 9.214957 TGATTCTTCTTCGTTATTGAAGCTTAA 57.785 29.630 0.00 0.00 44.01 1.85
2422 3099 1.073923 AGAGTAGGCCTTGTTTGGTGG 59.926 52.381 12.58 0.00 0.00 4.61
2433 3110 5.744594 GCCTTGTTTGGTGGGAACAAAATAT 60.745 40.000 4.29 0.00 43.89 1.28
2434 3111 5.700373 CCTTGTTTGGTGGGAACAAAATATG 59.300 40.000 4.29 0.00 43.89 1.78
2435 3112 5.878406 TGTTTGGTGGGAACAAAATATGT 57.122 34.783 0.00 0.00 46.06 2.29
2436 3113 5.848406 TGTTTGGTGGGAACAAAATATGTC 58.152 37.500 0.00 0.00 46.06 3.06
2437 3114 5.221541 TGTTTGGTGGGAACAAAATATGTCC 60.222 40.000 0.00 0.00 46.06 4.02
2440 3117 4.526262 TGGTGGGAACAAAATATGTCCTTG 59.474 41.667 0.00 0.00 46.06 3.61
2441 3118 4.526650 GGTGGGAACAAAATATGTCCTTGT 59.473 41.667 0.00 0.00 46.06 3.16
2690 3988 6.380079 AAAAGAATCACATACTCCCTCTGT 57.620 37.500 0.00 0.00 0.00 3.41
2691 3989 5.606348 AAGAATCACATACTCCCTCTGTC 57.394 43.478 0.00 0.00 0.00 3.51
2692 3990 3.964031 AGAATCACATACTCCCTCTGTCC 59.036 47.826 0.00 0.00 0.00 4.02
2693 3991 2.160721 TCACATACTCCCTCTGTCCC 57.839 55.000 0.00 0.00 0.00 4.46
2694 3992 1.361197 TCACATACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 0.00 4.37
2695 3993 2.023015 TCACATACTCCCTCTGTCCCAT 60.023 50.000 0.00 0.00 0.00 4.00
2696 3994 3.206639 TCACATACTCCCTCTGTCCCATA 59.793 47.826 0.00 0.00 0.00 2.74
2697 3995 3.967326 CACATACTCCCTCTGTCCCATAA 59.033 47.826 0.00 0.00 0.00 1.90
2698 3996 4.594920 CACATACTCCCTCTGTCCCATAAT 59.405 45.833 0.00 0.00 0.00 1.28
2699 3997 5.780282 CACATACTCCCTCTGTCCCATAATA 59.220 44.000 0.00 0.00 0.00 0.98
2700 3998 6.441924 CACATACTCCCTCTGTCCCATAATAT 59.558 42.308 0.00 0.00 0.00 1.28
2701 3999 7.619698 CACATACTCCCTCTGTCCCATAATATA 59.380 40.741 0.00 0.00 0.00 0.86
2702 4000 8.184249 ACATACTCCCTCTGTCCCATAATATAA 58.816 37.037 0.00 0.00 0.00 0.98
2703 4001 8.700051 CATACTCCCTCTGTCCCATAATATAAG 58.300 40.741 0.00 0.00 0.00 1.73
2704 4002 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
2705 4003 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
2706 4004 7.456269 ACTCCCTCTGTCCCATAATATAAGAAG 59.544 40.741 0.00 0.00 0.00 2.85
2707 4005 6.730977 TCCCTCTGTCCCATAATATAAGAAGG 59.269 42.308 0.00 0.00 0.00 3.46
2708 4006 6.502158 CCCTCTGTCCCATAATATAAGAAGGT 59.498 42.308 0.00 0.00 0.00 3.50
2709 4007 7.017651 CCCTCTGTCCCATAATATAAGAAGGTT 59.982 40.741 0.00 0.00 0.00 3.50
2710 4008 8.440771 CCTCTGTCCCATAATATAAGAAGGTTT 58.559 37.037 0.00 0.00 0.00 3.27
2711 4009 9.853177 CTCTGTCCCATAATATAAGAAGGTTTT 57.147 33.333 0.00 0.00 0.00 2.43
2712 4010 9.847224 TCTGTCCCATAATATAAGAAGGTTTTC 57.153 33.333 0.00 0.00 0.00 2.29
2713 4011 8.671384 TGTCCCATAATATAAGAAGGTTTTCG 57.329 34.615 0.00 0.00 38.38 3.46
2714 4012 8.487848 TGTCCCATAATATAAGAAGGTTTTCGA 58.512 33.333 0.00 0.00 38.38 3.71
2715 4013 8.771766 GTCCCATAATATAAGAAGGTTTTCGAC 58.228 37.037 0.00 0.00 38.38 4.20
2716 4014 8.487848 TCCCATAATATAAGAAGGTTTTCGACA 58.512 33.333 0.00 0.00 38.38 4.35
2717 4015 8.557029 CCCATAATATAAGAAGGTTTTCGACAC 58.443 37.037 0.00 0.00 38.38 3.67
2718 4016 9.326413 CCATAATATAAGAAGGTTTTCGACACT 57.674 33.333 0.00 0.00 38.38 3.55
2722 4020 8.699283 ATATAAGAAGGTTTTCGACACTACAC 57.301 34.615 0.00 0.00 38.38 2.90
2723 4021 4.667519 AGAAGGTTTTCGACACTACACT 57.332 40.909 0.00 0.00 38.38 3.55
2724 4022 5.779529 AGAAGGTTTTCGACACTACACTA 57.220 39.130 0.00 0.00 38.38 2.74
2725 4023 5.770417 AGAAGGTTTTCGACACTACACTAG 58.230 41.667 0.00 0.00 38.38 2.57
2726 4024 5.301298 AGAAGGTTTTCGACACTACACTAGT 59.699 40.000 0.00 0.00 37.70 2.57
2737 4035 3.800531 ACTACACTAGTGCCAAAAACGT 58.199 40.909 22.90 2.45 37.69 3.99
2738 4036 4.193865 ACTACACTAGTGCCAAAAACGTT 58.806 39.130 22.90 0.00 37.69 3.99
2739 4037 3.685836 ACACTAGTGCCAAAAACGTTC 57.314 42.857 22.90 0.00 0.00 3.95
2740 4038 3.275999 ACACTAGTGCCAAAAACGTTCT 58.724 40.909 22.90 0.00 0.00 3.01
2741 4039 3.692593 ACACTAGTGCCAAAAACGTTCTT 59.307 39.130 22.90 0.00 0.00 2.52
2742 4040 4.877251 ACACTAGTGCCAAAAACGTTCTTA 59.123 37.500 22.90 0.00 0.00 2.10
2743 4041 5.529800 ACACTAGTGCCAAAAACGTTCTTAT 59.470 36.000 22.90 0.00 0.00 1.73
2744 4042 6.707161 ACACTAGTGCCAAAAACGTTCTTATA 59.293 34.615 22.90 0.00 0.00 0.98
2745 4043 7.389607 ACACTAGTGCCAAAAACGTTCTTATAT 59.610 33.333 22.90 0.00 0.00 0.86
2746 4044 8.234546 CACTAGTGCCAAAAACGTTCTTATATT 58.765 33.333 10.54 0.00 0.00 1.28
2747 4045 9.439500 ACTAGTGCCAAAAACGTTCTTATATTA 57.561 29.630 0.00 0.00 0.00 0.98
2750 4048 8.188139 AGTGCCAAAAACGTTCTTATATTATGG 58.812 33.333 0.00 3.63 0.00 2.74
2751 4049 7.434013 GTGCCAAAAACGTTCTTATATTATGGG 59.566 37.037 0.00 0.00 0.00 4.00
2752 4050 7.339721 TGCCAAAAACGTTCTTATATTATGGGA 59.660 33.333 0.00 1.11 0.00 4.37
2753 4051 7.646526 GCCAAAAACGTTCTTATATTATGGGAC 59.353 37.037 0.00 0.00 0.00 4.46
2754 4052 7.853929 CCAAAAACGTTCTTATATTATGGGACG 59.146 37.037 0.00 9.33 0.00 4.79
2755 4053 8.392612 CAAAAACGTTCTTATATTATGGGACGT 58.607 33.333 0.00 10.25 0.00 4.34
2756 4054 9.598517 AAAAACGTTCTTATATTATGGGACGTA 57.401 29.630 0.00 0.00 0.00 3.57
2757 4055 8.807667 AAACGTTCTTATATTATGGGACGTAG 57.192 34.615 0.00 0.00 0.00 3.51
2758 4056 6.917533 ACGTTCTTATATTATGGGACGTAGG 58.082 40.000 12.88 0.00 0.00 3.18
2759 4057 6.071728 ACGTTCTTATATTATGGGACGTAGGG 60.072 42.308 12.88 0.00 0.00 3.53
2770 4068 6.898171 ATGGGACGTAGGGAGTAGTATATA 57.102 41.667 0.00 0.00 0.00 0.86
2771 4069 6.702449 TGGGACGTAGGGAGTAGTATATAA 57.298 41.667 0.00 0.00 0.00 0.98
2955 4253 4.887748 TCTTCTCGATCAGAGCAGTTTTT 58.112 39.130 11.54 0.00 46.44 1.94
2965 4263 4.340666 TCAGAGCAGTTTTTATTTGTGCCA 59.659 37.500 0.00 0.00 34.56 4.92
2975 4278 0.598158 ATTTGTGCCACTGCTTTGCG 60.598 50.000 0.00 0.00 38.71 4.85
3193 4507 0.318784 CGCTAGCTAGCTAAACGGGG 60.319 60.000 36.02 18.73 46.85 5.73
3226 4545 5.118203 GTGCATTTCACAAGAGAATTTCAGC 59.882 40.000 0.00 0.00 44.98 4.26
3242 4561 1.687146 AGCGGAGGAGAAGGCATGA 60.687 57.895 0.00 0.00 0.00 3.07
3243 4562 1.522580 GCGGAGGAGAAGGCATGAC 60.523 63.158 0.00 0.00 0.00 3.06
3275 4598 7.547370 CCCTGAATAACCGAGATGAGATTTATC 59.453 40.741 0.00 0.00 0.00 1.75
3349 4676 7.174413 TGGTCATGGAGAACAGAATGATTTTA 58.826 34.615 0.00 0.00 39.57 1.52
3351 4678 7.192232 GTCATGGAGAACAGAATGATTTTAGC 58.808 38.462 0.00 0.00 39.69 3.09
3374 4702 1.524848 TTGCCGCGGATTAAAAGACA 58.475 45.000 33.48 11.24 0.00 3.41
3378 4706 3.057174 TGCCGCGGATTAAAAGACATTTT 60.057 39.130 33.48 0.00 41.48 1.82
3379 4707 3.303229 GCCGCGGATTAAAAGACATTTTG 59.697 43.478 33.48 0.00 39.01 2.44
3383 4711 4.815269 CGGATTAAAAGACATTTTGCCCA 58.185 39.130 0.00 0.00 39.01 5.36
3384 4712 4.625311 CGGATTAAAAGACATTTTGCCCAC 59.375 41.667 0.00 0.00 39.01 4.61
3385 4713 5.566627 CGGATTAAAAGACATTTTGCCCACT 60.567 40.000 0.00 0.00 39.01 4.00
3386 4714 6.230472 GGATTAAAAGACATTTTGCCCACTT 58.770 36.000 0.00 0.00 39.01 3.16
3387 4715 6.710295 GGATTAAAAGACATTTTGCCCACTTT 59.290 34.615 0.00 0.00 39.01 2.66
3389 4717 5.816449 AAAAGACATTTTGCCCACTTTTG 57.184 34.783 0.00 0.00 37.24 2.44
3390 4718 2.837498 AGACATTTTGCCCACTTTTGC 58.163 42.857 0.00 0.00 0.00 3.68
3391 4719 2.170187 AGACATTTTGCCCACTTTTGCA 59.830 40.909 0.00 0.00 35.27 4.08
3392 4720 2.941720 GACATTTTGCCCACTTTTGCAA 59.058 40.909 0.00 0.00 45.12 4.08
3395 4723 2.600470 TTTGCCCACTTTTGCAAGAG 57.400 45.000 15.05 15.05 46.99 2.85
3396 4724 0.752054 TTGCCCACTTTTGCAAGAGG 59.248 50.000 20.04 8.27 42.19 3.69
3397 4725 0.396974 TGCCCACTTTTGCAAGAGGT 60.397 50.000 20.04 8.31 38.72 3.85
3398 4726 0.752658 GCCCACTTTTGCAAGAGGTT 59.247 50.000 20.04 0.00 38.72 3.50
3399 4727 1.538849 GCCCACTTTTGCAAGAGGTTG 60.539 52.381 20.04 10.54 38.72 3.77
3407 4735 2.856032 CAAGAGGTTGCGCTGTCG 59.144 61.111 9.73 0.00 39.07 4.35
3408 4736 2.357517 AAGAGGTTGCGCTGTCGG 60.358 61.111 9.73 0.00 35.95 4.79
3409 4737 3.883744 AAGAGGTTGCGCTGTCGGG 62.884 63.158 9.73 0.00 35.95 5.14
3413 4741 4.681978 GTTGCGCTGTCGGGGACT 62.682 66.667 9.73 0.00 35.95 3.85
3474 4805 1.347707 CAGTGTTCTTCTACCCTGCCA 59.652 52.381 0.00 0.00 0.00 4.92
3567 4905 9.447040 GAAAGAAACTGTGTTCATTAAACTACC 57.553 33.333 5.82 0.00 38.76 3.18
3586 4927 1.824230 CCGGGAAAGCAAAATCATCCA 59.176 47.619 0.00 0.00 31.63 3.41
3594 4935 2.835764 AGCAAAATCATCCACATGGCTT 59.164 40.909 0.00 0.00 34.44 4.35
3595 4936 3.262405 AGCAAAATCATCCACATGGCTTT 59.738 39.130 0.00 0.00 34.44 3.51
3627 4968 7.587037 AGATCCACTCTGATCAAAACAAAAA 57.413 32.000 0.00 0.00 42.95 1.94
3628 4969 7.428826 AGATCCACTCTGATCAAAACAAAAAC 58.571 34.615 0.00 0.00 42.95 2.43
3629 4970 5.577835 TCCACTCTGATCAAAACAAAAACG 58.422 37.500 0.00 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 7.093771 CCACTTTAGACCTAATTGCAAGGATTT 60.094 37.037 9.96 0.00 37.57 2.17
24 26 6.378280 CCACTTTAGACCTAATTGCAAGGATT 59.622 38.462 9.96 0.00 37.57 3.01
25 27 5.888161 CCACTTTAGACCTAATTGCAAGGAT 59.112 40.000 9.96 0.00 37.57 3.24
28 30 4.399303 CCCCACTTTAGACCTAATTGCAAG 59.601 45.833 4.94 0.00 0.00 4.01
32 34 3.288092 GGCCCCACTTTAGACCTAATTG 58.712 50.000 0.00 0.00 0.00 2.32
51 56 3.058914 GTGGATATGCGTTTCACTATGGC 60.059 47.826 0.00 0.00 0.00 4.40
58 63 4.645136 AGAGTAGAGTGGATATGCGTTTCA 59.355 41.667 0.00 0.00 0.00 2.69
71 76 5.628606 TCGATTCGTACGATAGAGTAGAGTG 59.371 44.000 20.27 0.00 41.38 3.51
77 82 4.569966 ACTGTTCGATTCGTACGATAGAGT 59.430 41.667 20.27 12.48 39.45 3.24
78 83 5.080642 ACTGTTCGATTCGTACGATAGAG 57.919 43.478 20.27 11.04 39.45 2.43
79 84 5.475273 AACTGTTCGATTCGTACGATAGA 57.525 39.130 20.27 15.26 39.45 1.98
80 85 4.669728 GGAACTGTTCGATTCGTACGATAG 59.330 45.833 20.27 13.18 39.45 2.08
89 94 4.545823 TTTGTGTGGAACTGTTCGATTC 57.454 40.909 13.89 8.26 38.04 2.52
94 99 7.425606 ACATTATCTTTTGTGTGGAACTGTTC 58.574 34.615 12.05 12.05 38.04 3.18
99 104 7.096640 CGTTTGACATTATCTTTTGTGTGGAAC 60.097 37.037 0.00 0.00 37.35 3.62
100 105 6.915300 CGTTTGACATTATCTTTTGTGTGGAA 59.085 34.615 0.00 0.00 0.00 3.53
142 147 6.682423 TTAATTGTGGTCATGCTAGTGATG 57.318 37.500 0.00 0.00 0.00 3.07
261 266 4.681835 ACGAGTGCTACTACTAACTGTG 57.318 45.455 0.00 0.00 0.00 3.66
307 312 8.356657 AGAACAATAATTGACCATCGTTTTTGA 58.643 29.630 0.00 0.00 0.00 2.69
314 319 4.808895 TCGGAGAACAATAATTGACCATCG 59.191 41.667 0.00 0.00 0.00 3.84
319 324 6.019479 CACTAGCTCGGAGAACAATAATTGAC 60.019 42.308 9.69 0.00 34.09 3.18
344 349 1.893919 GCAGAGAGGGACCTGTGGAC 61.894 65.000 0.00 0.00 33.19 4.02
390 396 3.852578 AGAAGAGGAGGCCCTTATTTGAA 59.147 43.478 0.00 0.00 44.53 2.69
415 421 3.429580 GGGGGAAGGGGACATGGG 61.430 72.222 0.00 0.00 0.00 4.00
626 632 1.859302 GAGGAGAAGCAGGAGAGGAA 58.141 55.000 0.00 0.00 0.00 3.36
649 655 1.138266 GAATGCTTGCCGAGGTAGGTA 59.862 52.381 0.00 0.00 0.00 3.08
720 727 0.109226 GAACCGGAGTCTCGTTCTGG 60.109 60.000 9.46 0.00 44.99 3.86
734 741 4.083749 CGATCTAGACTATGTCAGGAACCG 60.084 50.000 0.00 3.42 34.60 4.44
738 745 4.804597 GCCTCGATCTAGACTATGTCAGGA 60.805 50.000 0.00 0.00 34.60 3.86
746 753 3.304726 CGCATTTGCCTCGATCTAGACTA 60.305 47.826 0.00 0.00 37.91 2.59
749 756 1.409064 ACGCATTTGCCTCGATCTAGA 59.591 47.619 0.00 0.00 37.91 2.43
826 836 1.098712 TCACCACAAAGCAACGTCCC 61.099 55.000 0.00 0.00 0.00 4.46
839 849 2.626780 GGGCCGAAAAGCTCACCAC 61.627 63.158 0.00 0.00 31.68 4.16
861 871 1.151777 AATAATCAGCGACGGTGGCG 61.152 55.000 25.25 1.74 35.00 5.69
862 872 0.582005 GAATAATCAGCGACGGTGGC 59.418 55.000 25.25 7.06 0.00 5.01
863 873 2.225068 AGAATAATCAGCGACGGTGG 57.775 50.000 25.25 8.47 0.00 4.61
864 874 5.712217 TTAAAGAATAATCAGCGACGGTG 57.288 39.130 20.57 20.57 0.00 4.94
865 875 5.220605 GCTTTAAAGAATAATCAGCGACGGT 60.221 40.000 19.48 0.00 0.00 4.83
927 937 0.323633 CAGGCCATGACCAACCATGA 60.324 55.000 5.01 0.00 44.98 3.07
987 997 2.755876 AGCATCGCCTCAGACGGA 60.756 61.111 0.00 0.00 0.00 4.69
990 1000 3.260483 CGCAGCATCGCCTCAGAC 61.260 66.667 0.00 0.00 0.00 3.51
991 1001 4.519437 CCGCAGCATCGCCTCAGA 62.519 66.667 0.00 0.00 0.00 3.27
992 1002 4.519437 TCCGCAGCATCGCCTCAG 62.519 66.667 0.00 0.00 0.00 3.35
993 1003 4.081185 TTCCGCAGCATCGCCTCA 62.081 61.111 0.00 0.00 0.00 3.86
1083 1096 2.047844 GAAGACTGAGCAGCGGCA 60.048 61.111 12.44 0.00 44.61 5.69
1263 1279 4.451150 GCGGCCGTCTCCATGTGA 62.451 66.667 28.70 0.00 0.00 3.58
1412 1428 2.607750 GGGAGGACACCAGCTCCA 60.608 66.667 0.00 0.00 37.71 3.86
1690 1727 2.811317 GCTCAAGACACCGCTCGG 60.811 66.667 6.79 6.79 42.03 4.63
1699 1736 0.450983 GCATGGCAAGAGCTCAAGAC 59.549 55.000 17.77 10.54 41.70 3.01
1751 1791 3.981071 AAACTCACCGATGGATGAAGA 57.019 42.857 0.00 0.00 0.00 2.87
1798 1842 5.741388 AGTGAAATGGCGAGTGATAAATC 57.259 39.130 0.00 0.00 0.00 2.17
1805 1849 5.942872 AGAAAATTAGTGAAATGGCGAGTG 58.057 37.500 0.00 0.00 0.00 3.51
1845 1891 9.955102 ATCATCAACATATATGCAGTGTCTATT 57.045 29.630 12.79 0.00 0.00 1.73
1949 2006 4.462834 TCTCCAAGCTTCGAGAACATCTTA 59.537 41.667 19.85 0.00 32.22 2.10
1950 2007 3.259374 TCTCCAAGCTTCGAGAACATCTT 59.741 43.478 19.85 0.00 32.22 2.40
1956 2013 1.335964 CGTGTCTCCAAGCTTCGAGAA 60.336 52.381 23.07 12.12 36.90 2.87
1961 2018 4.024048 TCAAAATTCGTGTCTCCAAGCTTC 60.024 41.667 0.00 0.00 0.00 3.86
1975 2032 5.803461 AGATCATGCATGTTGTCAAAATTCG 59.197 36.000 25.43 0.00 0.00 3.34
2005 2062 3.492102 ACCTGCAGTGTAAGTTCACAT 57.508 42.857 13.81 0.00 40.37 3.21
2006 2063 4.617253 ATACCTGCAGTGTAAGTTCACA 57.383 40.909 13.81 0.00 40.37 3.58
2007 2064 4.994852 TCAATACCTGCAGTGTAAGTTCAC 59.005 41.667 13.81 0.00 38.46 3.18
2016 2073 4.202000 TGTGTTGTTTCAATACCTGCAGTG 60.202 41.667 13.81 6.81 0.00 3.66
2054 2111 4.679639 GCTCCATGATGTCAATGCACATTT 60.680 41.667 0.00 0.00 37.11 2.32
2065 2122 6.630444 AATTACATTCTGCTCCATGATGTC 57.370 37.500 0.00 0.00 0.00 3.06
2209 2266 7.823799 TGATGAAGCACTCATGTCAAATAAGTA 59.176 33.333 6.08 0.00 45.23 2.24
2210 2267 6.656270 TGATGAAGCACTCATGTCAAATAAGT 59.344 34.615 6.08 0.00 45.23 2.24
2211 2268 7.080353 TGATGAAGCACTCATGTCAAATAAG 57.920 36.000 6.08 0.00 45.23 1.73
2212 2269 7.634671 ATGATGAAGCACTCATGTCAAATAA 57.365 32.000 6.08 0.00 45.23 1.40
2261 2323 9.777297 TGCTATATATCAACAATCAGCAAGTTA 57.223 29.630 1.03 0.00 35.03 2.24
2294 2360 8.763049 TGAAGTATACTGCAGATGTATTATGC 57.237 34.615 23.35 10.02 40.40 3.14
2347 2413 3.395941 GACCCATCCACAAAGATCCCTAT 59.604 47.826 0.00 0.00 0.00 2.57
2389 3062 7.125963 ACAAGGCCTACTCTACTAATTAAGCTT 59.874 37.037 5.16 3.48 0.00 3.74
2396 3069 5.487845 ACCAAACAAGGCCTACTCTACTAAT 59.512 40.000 5.16 0.00 0.00 1.73
2436 3113 3.486383 TCAAAACAGCTCCCTTACAAGG 58.514 45.455 0.66 0.66 46.06 3.61
2437 3114 5.617751 CGAATCAAAACAGCTCCCTTACAAG 60.618 44.000 0.00 0.00 0.00 3.16
2440 3117 4.000988 TCGAATCAAAACAGCTCCCTTAC 58.999 43.478 0.00 0.00 0.00 2.34
2441 3118 4.000988 GTCGAATCAAAACAGCTCCCTTA 58.999 43.478 0.00 0.00 0.00 2.69
2689 3987 8.771766 GTCGAAAACCTTCTTATATTATGGGAC 58.228 37.037 0.00 0.00 0.00 4.46
2690 3988 8.487848 TGTCGAAAACCTTCTTATATTATGGGA 58.512 33.333 0.00 0.00 0.00 4.37
2691 3989 8.557029 GTGTCGAAAACCTTCTTATATTATGGG 58.443 37.037 0.00 0.00 0.00 4.00
2692 3990 9.326413 AGTGTCGAAAACCTTCTTATATTATGG 57.674 33.333 0.00 0.00 0.00 2.74
2696 3994 9.148104 GTGTAGTGTCGAAAACCTTCTTATATT 57.852 33.333 0.00 0.00 0.00 1.28
2697 3995 8.529476 AGTGTAGTGTCGAAAACCTTCTTATAT 58.471 33.333 0.00 0.00 0.00 0.86
2698 3996 7.889469 AGTGTAGTGTCGAAAACCTTCTTATA 58.111 34.615 0.00 0.00 0.00 0.98
2699 3997 6.756221 AGTGTAGTGTCGAAAACCTTCTTAT 58.244 36.000 0.00 0.00 0.00 1.73
2700 3998 6.152932 AGTGTAGTGTCGAAAACCTTCTTA 57.847 37.500 0.00 0.00 0.00 2.10
2701 3999 5.019785 AGTGTAGTGTCGAAAACCTTCTT 57.980 39.130 0.00 0.00 0.00 2.52
2702 4000 4.667519 AGTGTAGTGTCGAAAACCTTCT 57.332 40.909 0.00 0.00 0.00 2.85
2703 4001 5.527033 ACTAGTGTAGTGTCGAAAACCTTC 58.473 41.667 0.00 0.00 37.69 3.46
2704 4002 5.526506 ACTAGTGTAGTGTCGAAAACCTT 57.473 39.130 0.00 0.00 37.69 3.50
2716 4014 3.800531 ACGTTTTTGGCACTAGTGTAGT 58.199 40.909 23.44 9.54 40.28 2.73
2717 4015 4.510340 AGAACGTTTTTGGCACTAGTGTAG 59.490 41.667 23.44 8.99 0.00 2.74
2718 4016 4.444536 AGAACGTTTTTGGCACTAGTGTA 58.555 39.130 23.44 10.89 0.00 2.90
2719 4017 3.275999 AGAACGTTTTTGGCACTAGTGT 58.724 40.909 23.44 0.00 0.00 3.55
2720 4018 3.963383 AGAACGTTTTTGGCACTAGTG 57.037 42.857 18.93 18.93 0.00 2.74
2721 4019 7.916914 ATATAAGAACGTTTTTGGCACTAGT 57.083 32.000 13.87 0.00 0.00 2.57
2724 4022 8.188139 CCATAATATAAGAACGTTTTTGGCACT 58.812 33.333 13.87 0.00 0.00 4.40
2725 4023 7.434013 CCCATAATATAAGAACGTTTTTGGCAC 59.566 37.037 13.87 0.00 0.00 5.01
2726 4024 7.339721 TCCCATAATATAAGAACGTTTTTGGCA 59.660 33.333 13.87 0.01 0.00 4.92
2727 4025 7.646526 GTCCCATAATATAAGAACGTTTTTGGC 59.353 37.037 13.87 0.00 0.00 4.52
2728 4026 7.853929 CGTCCCATAATATAAGAACGTTTTTGG 59.146 37.037 13.87 5.54 0.00 3.28
2729 4027 8.392612 ACGTCCCATAATATAAGAACGTTTTTG 58.607 33.333 13.87 0.00 0.00 2.44
2730 4028 8.496707 ACGTCCCATAATATAAGAACGTTTTT 57.503 30.769 9.22 9.22 0.00 1.94
2731 4029 9.252962 CTACGTCCCATAATATAAGAACGTTTT 57.747 33.333 0.46 0.00 0.00 2.43
2732 4030 7.869429 CCTACGTCCCATAATATAAGAACGTTT 59.131 37.037 0.46 0.00 0.00 3.60
2733 4031 7.373493 CCTACGTCCCATAATATAAGAACGTT 58.627 38.462 0.00 0.00 0.00 3.99
2734 4032 6.071728 CCCTACGTCCCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
2735 4033 6.151648 TCCCTACGTCCCATAATATAAGAACG 59.848 42.308 0.00 0.00 0.00 3.95
2736 4034 7.178097 ACTCCCTACGTCCCATAATATAAGAAC 59.822 40.741 0.00 0.00 0.00 3.01
2737 4035 7.243824 ACTCCCTACGTCCCATAATATAAGAA 58.756 38.462 0.00 0.00 0.00 2.52
2738 4036 6.797707 ACTCCCTACGTCCCATAATATAAGA 58.202 40.000 0.00 0.00 0.00 2.10
2739 4037 7.833183 ACTACTCCCTACGTCCCATAATATAAG 59.167 40.741 0.00 0.00 0.00 1.73
2740 4038 7.702785 ACTACTCCCTACGTCCCATAATATAA 58.297 38.462 0.00 0.00 0.00 0.98
2741 4039 7.276088 ACTACTCCCTACGTCCCATAATATA 57.724 40.000 0.00 0.00 0.00 0.86
2742 4040 6.150034 ACTACTCCCTACGTCCCATAATAT 57.850 41.667 0.00 0.00 0.00 1.28
2743 4041 5.589367 ACTACTCCCTACGTCCCATAATA 57.411 43.478 0.00 0.00 0.00 0.98
2744 4042 4.466255 ACTACTCCCTACGTCCCATAAT 57.534 45.455 0.00 0.00 0.00 1.28
2745 4043 3.959495 ACTACTCCCTACGTCCCATAA 57.041 47.619 0.00 0.00 0.00 1.90
2746 4044 6.898171 ATATACTACTCCCTACGTCCCATA 57.102 41.667 0.00 0.00 0.00 2.74
2747 4045 5.793034 ATATACTACTCCCTACGTCCCAT 57.207 43.478 0.00 0.00 0.00 4.00
2748 4046 6.702449 TTATATACTACTCCCTACGTCCCA 57.298 41.667 0.00 0.00 0.00 4.37
2749 4047 7.416101 GCAATTATATACTACTCCCTACGTCCC 60.416 44.444 0.00 0.00 0.00 4.46
2750 4048 7.338957 AGCAATTATATACTACTCCCTACGTCC 59.661 40.741 0.00 0.00 0.00 4.79
2751 4049 8.278729 AGCAATTATATACTACTCCCTACGTC 57.721 38.462 0.00 0.00 0.00 4.34
2752 4050 9.393512 CTAGCAATTATATACTACTCCCTACGT 57.606 37.037 0.00 0.00 0.00 3.57
2753 4051 9.393512 ACTAGCAATTATATACTACTCCCTACG 57.606 37.037 0.00 0.00 0.00 3.51
2770 4068 5.393461 GCATAAGGCTGTCAAACTAGCAATT 60.393 40.000 0.00 0.00 41.63 2.32
2771 4069 4.096984 GCATAAGGCTGTCAAACTAGCAAT 59.903 41.667 0.00 0.00 41.63 3.56
2955 4253 1.335780 CGCAAAGCAGTGGCACAAATA 60.336 47.619 21.41 0.00 44.16 1.40
2975 4278 3.536158 TGTTCATGTTACGCTCTTTGC 57.464 42.857 0.00 0.00 38.57 3.68
2984 4287 4.432712 GGGGCAATTGATGTTCATGTTAC 58.567 43.478 10.34 0.00 0.00 2.50
3053 4361 8.408601 GGACAAATTATATCACAGAAATGTGCT 58.591 33.333 3.51 0.00 39.49 4.40
3193 4507 1.002624 TGAAATGCACCGTCCCTCC 60.003 57.895 0.00 0.00 0.00 4.30
3206 4520 4.761739 TCCGCTGAAATTCTCTTGTGAAAT 59.238 37.500 0.00 0.00 0.00 2.17
3226 4545 1.227089 CGTCATGCCTTCTCCTCCG 60.227 63.158 0.00 0.00 0.00 4.63
3242 4561 0.179056 CGGTTATTCAGGGCCATCGT 60.179 55.000 6.18 0.00 0.00 3.73
3243 4562 0.105964 TCGGTTATTCAGGGCCATCG 59.894 55.000 6.18 0.00 0.00 3.84
3286 4609 4.034048 GTCTTGCAAAGTCGAGAAGAAACA 59.966 41.667 0.00 0.00 46.34 2.83
3349 4676 0.963355 TTAATCCGCGGCAAAAGGCT 60.963 50.000 23.51 0.15 44.01 4.58
3351 4678 2.094957 TCTTTTAATCCGCGGCAAAAGG 60.095 45.455 34.06 26.50 38.14 3.11
3378 4706 0.396974 ACCTCTTGCAAAAGTGGGCA 60.397 50.000 10.46 0.00 37.66 5.36
3379 4707 0.752658 AACCTCTTGCAAAAGTGGGC 59.247 50.000 10.46 0.00 37.66 5.36
3390 4718 2.671177 CCGACAGCGCAACCTCTTG 61.671 63.158 11.47 0.00 35.83 3.02
3391 4719 2.357517 CCGACAGCGCAACCTCTT 60.358 61.111 11.47 0.00 35.83 2.85
3392 4720 4.379243 CCCGACAGCGCAACCTCT 62.379 66.667 11.47 0.00 35.83 3.69
3396 4724 4.681978 AGTCCCCGACAGCGCAAC 62.682 66.667 11.47 0.00 34.60 4.17
3397 4725 4.680237 CAGTCCCCGACAGCGCAA 62.680 66.667 11.47 0.00 34.60 4.85
3399 4727 4.148825 ATCAGTCCCCGACAGCGC 62.149 66.667 0.00 0.00 34.60 5.92
3400 4728 2.202797 CATCAGTCCCCGACAGCG 60.203 66.667 0.00 0.00 34.60 5.18
3401 4729 0.741221 GAACATCAGTCCCCGACAGC 60.741 60.000 0.00 0.00 34.60 4.40
3402 4730 0.458543 CGAACATCAGTCCCCGACAG 60.459 60.000 0.00 0.00 34.60 3.51
3403 4731 0.896479 TCGAACATCAGTCCCCGACA 60.896 55.000 0.00 0.00 34.60 4.35
3404 4732 0.458025 GTCGAACATCAGTCCCCGAC 60.458 60.000 0.00 0.00 37.60 4.79
3405 4733 1.888018 GTCGAACATCAGTCCCCGA 59.112 57.895 0.00 0.00 0.00 5.14
3406 4734 1.516386 CGTCGAACATCAGTCCCCG 60.516 63.158 0.00 0.00 0.00 5.73
3407 4735 0.037605 AACGTCGAACATCAGTCCCC 60.038 55.000 0.00 0.00 0.00 4.81
3408 4736 1.067776 AGAACGTCGAACATCAGTCCC 60.068 52.381 0.00 0.00 0.00 4.46
3409 4737 2.349297 AGAACGTCGAACATCAGTCC 57.651 50.000 0.00 0.00 0.00 3.85
3410 4738 4.080969 ACTAGAACGTCGAACATCAGTC 57.919 45.455 0.00 0.00 0.00 3.51
3411 4739 4.500603 AACTAGAACGTCGAACATCAGT 57.499 40.909 0.00 0.00 0.00 3.41
3412 4740 6.922980 TTTAACTAGAACGTCGAACATCAG 57.077 37.500 0.00 0.00 0.00 2.90
3413 4741 7.085746 TCATTTAACTAGAACGTCGAACATCA 58.914 34.615 0.00 0.00 0.00 3.07
3474 4805 4.213906 GCCAAAATTTAACTTGCAGCACAT 59.786 37.500 0.00 0.00 0.00 3.21
3567 4905 2.230992 TGTGGATGATTTTGCTTTCCCG 59.769 45.455 0.00 0.00 0.00 5.14
3627 4968 0.032714 GGAACCCTAGTCCTACCCGT 60.033 60.000 0.00 0.00 0.00 5.28
3628 4969 0.261109 AGGAACCCTAGTCCTACCCG 59.739 60.000 0.00 0.00 31.06 5.28
3629 4970 2.956132 GTAGGAACCCTAGTCCTACCC 58.044 57.143 20.22 4.17 46.18 3.69
3998 5339 3.074412 CGCCAACACTATCCAGACTTTT 58.926 45.455 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.