Multiple sequence alignment - TraesCS3B01G152700

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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 TraesCS3B01G152700 chr3B 100.000 4828 0 0 1 4828 144817743 144812916 0.000000e+00 8916.0
1 TraesCS3B01G152700 chr3A 93.834 3114 125 30 76 3150 547481174 547478089 0.000000e+00 4625.0
2 TraesCS3B01G152700 chr3A 93.686 1362 61 10 3469 4828 547478086 547476748 0.000000e+00 2015.0
3 TraesCS3B01G152700 chr3D 95.534 1657 52 8 1507 3150 94496738 94495091 0.000000e+00 2630.0
4 TraesCS3B01G152700 chr3D 93.988 1364 62 8 3469 4828 94495088 94493741 0.000000e+00 2047.0
5 TraesCS3B01G152700 chr3D 93.052 1396 59 15 141 1517 94498642 94497266 0.000000e+00 2006.0
6 TraesCS3B01G152700 chr2D 94.118 272 13 2 3149 3417 491802870 491802599 1.250000e-110 411.0
7 TraesCS3B01G152700 chr2D 81.564 179 24 6 2844 3021 12567071 12567241 6.520000e-29 139.0
8 TraesCS3B01G152700 chr2A 93.750 272 14 2 3149 3417 636904688 636904417 5.820000e-109 405.0
9 TraesCS3B01G152700 chr7A 93.358 271 16 1 3144 3412 595822709 595822979 2.710000e-107 399.0
10 TraesCS3B01G152700 chr7A 89.073 302 30 2 3150 3448 712627477 712627176 5.900000e-99 372.0
11 TraesCS3B01G152700 chr1A 93.893 262 13 3 3150 3410 533464756 533465015 4.530000e-105 392.0
12 TraesCS3B01G152700 chr1A 78.554 401 60 14 900 1287 420387617 420388004 1.740000e-59 241.0
13 TraesCS3B01G152700 chr5D 92.857 266 17 1 3149 3412 135656704 135656969 7.580000e-103 385.0
14 TraesCS3B01G152700 chr5A 92.884 267 16 3 3150 3415 688730854 688730590 7.580000e-103 385.0
15 TraesCS3B01G152700 chr2B 92.537 268 16 4 3149 3413 576085417 576085151 9.810000e-102 381.0
16 TraesCS3B01G152700 chr7B 90.345 290 25 2 3148 3435 726018477 726018189 1.270000e-100 377.0
17 TraesCS3B01G152700 chr1B 77.045 379 63 21 881 1247 98804744 98805110 3.810000e-46 196.0
18 TraesCS3B01G152700 chr1B 82.584 178 18 8 2848 3024 563296739 563296574 1.400000e-30 145.0
19 TraesCS3B01G152700 chr1D 83.889 180 15 8 2844 3021 175819835 175820002 5.000000e-35 159.0
20 TraesCS3B01G152700 chr1D 90.196 51 4 1 2 52 487025598 487025647 1.120000e-06 65.8
21 TraesCS3B01G152700 chrUn 82.609 184 18 9 2844 3025 279937719 279937548 3.010000e-32 150.0
22 TraesCS3B01G152700 chrUn 82.609 184 18 9 2844 3025 292395668 292395497 3.010000e-32 150.0
23 TraesCS3B01G152700 chr4D 81.152 191 21 10 2838 3025 293386045 293386223 6.520000e-29 139.0
24 TraesCS3B01G152700 chr7D 81.081 185 22 7 2844 3027 530124002 530123830 8.430000e-28 135.0
25 TraesCS3B01G152700 chr4A 90.741 54 4 1 2 54 119637536 119637589 2.410000e-08 71.3
26 TraesCS3B01G152700 chr6D 90.741 54 2 3 2 53 10362277 10362225 8.670000e-08 69.4


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 TraesCS3B01G152700 chr3B 144812916 144817743 4827 True 8916.000000 8916 100.000000 1 4828 1 chr3B.!!$R1 4827
1 TraesCS3B01G152700 chr3A 547476748 547481174 4426 True 3320.000000 4625 93.760000 76 4828 2 chr3A.!!$R1 4752
2 TraesCS3B01G152700 chr3D 94493741 94498642 4901 True 2227.666667 2630 94.191333 141 4828 3 chr3D.!!$R1 4687

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
735 741 0.329596 GGGAGGAGCATGGTTGTTCT 59.670 55.0 0.0 0.0 33.89 3.01 F
1656 2229 0.674581 GCAGCACAGCACATGTAGGA 60.675 55.0 0.0 0.0 41.41 2.94 F
2381 2959 0.035056 CCTTCACCCTTCTGCGGATT 60.035 55.0 0.0 0.0 0.00 3.01 F
3313 3900 0.110056 GTGTTGAGCGCTCACCATTG 60.110 55.0 35.4 0.0 39.66 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 2920 0.036022 GGAACACAGGAGCTCAGCTT 59.964 55.0 17.19 2.63 39.88 3.74 R
2879 3461 0.027590 AATCCTTCCCCAGGCCCTAT 60.028 55.0 0.00 0.00 43.55 2.57 R
3355 3942 0.181350 AGGGGCAGATCCAACGAATC 59.819 55.0 0.00 0.00 36.21 2.52 R
4398 5001 0.035915 GACTTGGGTTCAGGAGCTCC 60.036 60.0 26.22 26.22 0.00 4.70 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
74 75 9.956720 AAAATAAAAATAAGAGCGATGATGGAG 57.043 29.630 0.00 0.00 0.00 3.86
75 76 8.682936 AATAAAAATAAGAGCGATGATGGAGT 57.317 30.769 0.00 0.00 0.00 3.85
76 77 9.778741 AATAAAAATAAGAGCGATGATGGAGTA 57.221 29.630 0.00 0.00 0.00 2.59
77 78 7.721286 AAAAATAAGAGCGATGATGGAGTAG 57.279 36.000 0.00 0.00 0.00 2.57
78 79 6.412362 AAATAAGAGCGATGATGGAGTAGT 57.588 37.500 0.00 0.00 0.00 2.73
79 80 6.412362 AATAAGAGCGATGATGGAGTAGTT 57.588 37.500 0.00 0.00 0.00 2.24
95 96 9.811995 ATGGAGTAGTTTTTAAAAAGTGGAAAC 57.188 29.630 24.83 16.92 33.79 2.78
111 112 5.242393 AGTGGAAACAAATCATCCAAGACAG 59.758 40.000 0.00 0.00 44.41 3.51
114 115 6.494491 TGGAAACAAATCATCCAAGACAGAAT 59.506 34.615 0.00 0.00 40.19 2.40
130 131 7.043961 AGACAGAATTTCTTTTTGAGGGAAC 57.956 36.000 0.00 0.00 0.00 3.62
149 152 4.827284 GGAACCCAAGAGAATTTCAACTCA 59.173 41.667 0.00 0.00 35.83 3.41
176 179 1.458445 GTACGCTTTCGGAACTGGAAC 59.542 52.381 0.00 0.00 40.69 3.62
180 183 1.860676 CTTTCGGAACTGGAACACGA 58.139 50.000 0.00 0.00 0.00 4.35
181 184 2.413837 CTTTCGGAACTGGAACACGAT 58.586 47.619 0.00 0.00 33.26 3.73
183 186 3.880047 TTCGGAACTGGAACACGATAT 57.120 42.857 0.00 0.00 33.26 1.63
190 193 3.782046 ACTGGAACACGATATCCGAAAG 58.218 45.455 0.00 0.00 41.76 2.62
396 399 0.671251 GTTCTCATCTCCGGCGATCT 59.329 55.000 9.30 0.00 0.00 2.75
399 402 0.521291 CTCATCTCCGGCGATCTCTC 59.479 60.000 9.30 0.00 0.00 3.20
401 404 1.969064 ATCTCCGGCGATCTCTCGG 60.969 63.158 9.30 10.65 45.15 4.63
528 531 3.006430 TGGTGAGCTCTATTCAAACACGA 59.994 43.478 16.19 0.00 0.00 4.35
536 539 5.982516 GCTCTATTCAAACACGAGAGATCAT 59.017 40.000 0.00 0.00 36.55 2.45
544 547 3.779759 ACACGAGAGATCATGCTTCTTC 58.220 45.455 0.00 0.00 0.00 2.87
578 583 0.442310 TTATCGCTGCACGCTTGTTC 59.558 50.000 0.00 0.00 43.23 3.18
581 586 2.327940 GCTGCACGCTTGTTCGTT 59.672 55.556 0.00 0.00 41.21 3.85
706 712 5.134339 AGGGGGATCAGATGTTGCTTAAATA 59.866 40.000 0.00 0.00 0.00 1.40
735 741 0.329596 GGGAGGAGCATGGTTGTTCT 59.670 55.000 0.00 0.00 33.89 3.01
742 754 4.520492 AGGAGCATGGTTGTTCTGTTAAAG 59.480 41.667 0.00 0.00 33.89 1.85
743 755 4.229876 GAGCATGGTTGTTCTGTTAAAGC 58.770 43.478 0.00 0.00 30.99 3.51
748 760 2.296190 GGTTGTTCTGTTAAAGCTGGGG 59.704 50.000 0.00 0.00 0.00 4.96
761 773 0.815615 GCTGGGGGCGATTTAGACAG 60.816 60.000 0.00 0.00 0.00 3.51
817 829 7.016268 CCCAACTTTATATCCTTCTGGTAGCTA 59.984 40.741 0.00 0.00 34.23 3.32
818 830 7.873505 CCAACTTTATATCCTTCTGGTAGCTAC 59.126 40.741 15.88 15.88 34.23 3.58
856 869 3.454371 TTTAGTAGCTGGCCGAGAATC 57.546 47.619 0.00 0.00 0.00 2.52
1146 1160 1.500108 CCTTCGAGCATCTCATCAGC 58.500 55.000 0.00 0.00 0.00 4.26
1150 1164 1.962100 TCGAGCATCTCATCAGCAGAT 59.038 47.619 0.00 0.00 33.87 2.90
1272 1294 5.352643 ACACGGTAAAGCTACAATTGTTC 57.647 39.130 17.78 9.27 0.00 3.18
1589 2162 8.701895 AGTTCAATCTCATGCCATTGAAATTAT 58.298 29.630 23.07 12.95 45.89 1.28
1656 2229 0.674581 GCAGCACAGCACATGTAGGA 60.675 55.000 0.00 0.00 41.41 2.94
1792 2365 5.699143 ACAGCCATCATTAGCTTCCTTTAT 58.301 37.500 0.00 0.00 37.18 1.40
1827 2400 7.233389 ACTGTTATGCTTTCTGAGAAGTCTA 57.767 36.000 0.00 0.00 0.00 2.59
2247 2825 4.080863 AGTGTCATAATGGAGTGGAGAACC 60.081 45.833 0.00 0.00 0.00 3.62
2377 2955 2.045926 CCCCTTCACCCTTCTGCG 60.046 66.667 0.00 0.00 0.00 5.18
2381 2959 0.035056 CCTTCACCCTTCTGCGGATT 60.035 55.000 0.00 0.00 0.00 3.01
2407 2985 6.316390 GGTGTTAATAAGGAGACAGATGTTGG 59.684 42.308 0.00 0.00 0.00 3.77
2422 3000 3.019799 TGTTGGGTTGTAAAGGCTCAA 57.980 42.857 0.00 0.00 0.00 3.02
2510 3088 2.760092 TGAAGTGATATTTGGGCTTGGC 59.240 45.455 0.00 0.00 0.00 4.52
2527 3108 1.618837 TGGCGTGAGAATATAGGGCTC 59.381 52.381 0.00 0.00 0.00 4.70
2566 3147 6.092670 ACAGTCTGTTGGATCAATTTATCACG 59.907 38.462 0.00 0.00 0.00 4.35
2578 3159 0.606944 TTATCACGCCACAACCCCAC 60.607 55.000 0.00 0.00 0.00 4.61
2723 3304 3.065925 GCCATCTCAAACTAGGTGCAATC 59.934 47.826 0.00 0.00 0.00 2.67
2772 3353 3.341823 GAGGTCAGTTGAATGCATCAGT 58.658 45.455 0.00 0.00 39.77 3.41
2794 3376 8.980596 TCAGTAAATAATTCCCTGCAAATTGAT 58.019 29.630 0.00 0.00 0.00 2.57
2796 3378 9.205513 AGTAAATAATTCCCTGCAAATTGATCT 57.794 29.630 0.00 0.00 0.00 2.75
2879 3461 1.561643 CTAGAAGCTCCCACACCAGA 58.438 55.000 0.00 0.00 0.00 3.86
2885 3467 1.832912 CTCCCACACCAGATAGGGC 59.167 63.158 0.00 0.00 43.89 5.19
2961 3548 1.974343 AGAGAGGCTGCGTCGAACT 60.974 57.895 15.71 13.27 0.00 3.01
2990 3577 1.758592 TGGCACAAGTGGGGAGTAC 59.241 57.895 2.00 0.00 31.92 2.73
2991 3578 0.766674 TGGCACAAGTGGGGAGTACT 60.767 55.000 0.00 0.00 31.92 2.73
2992 3579 0.400594 GGCACAAGTGGGGAGTACTT 59.599 55.000 0.00 0.00 38.84 2.24
3150 3737 3.036091 TCATAGTGCCCCCTGTACTTAC 58.964 50.000 0.00 0.00 40.66 2.34
3151 3738 2.934263 TAGTGCCCCCTGTACTTACT 57.066 50.000 0.00 0.00 40.66 2.24
3152 3739 2.934263 AGTGCCCCCTGTACTTACTA 57.066 50.000 0.00 0.00 36.38 1.82
3153 3740 2.748388 AGTGCCCCCTGTACTTACTAG 58.252 52.381 0.00 0.00 36.38 2.57
3154 3741 2.044077 AGTGCCCCCTGTACTTACTAGT 59.956 50.000 0.00 0.00 36.38 2.57
3155 3742 3.270433 AGTGCCCCCTGTACTTACTAGTA 59.730 47.826 0.00 0.00 36.38 1.82
3156 3743 4.026052 GTGCCCCCTGTACTTACTAGTAA 58.974 47.826 14.52 14.52 38.55 2.24
3157 3744 4.467438 GTGCCCCCTGTACTTACTAGTAAA 59.533 45.833 15.95 0.00 38.55 2.01
3158 3745 5.129980 GTGCCCCCTGTACTTACTAGTAAAT 59.870 44.000 15.95 9.21 38.55 1.40
3159 3746 5.129815 TGCCCCCTGTACTTACTAGTAAATG 59.870 44.000 15.95 8.32 38.55 2.32
3160 3747 5.129980 GCCCCCTGTACTTACTAGTAAATGT 59.870 44.000 15.95 13.27 38.55 2.71
3161 3748 6.579865 CCCCCTGTACTTACTAGTAAATGTG 58.420 44.000 15.95 7.32 38.55 3.21
3162 3749 6.155737 CCCCCTGTACTTACTAGTAAATGTGT 59.844 42.308 15.95 12.32 38.55 3.72
3163 3750 7.342799 CCCCCTGTACTTACTAGTAAATGTGTA 59.657 40.741 15.95 11.43 38.55 2.90
3164 3751 8.193438 CCCCTGTACTTACTAGTAAATGTGTAC 58.807 40.741 23.31 23.31 38.55 2.90
3165 3752 7.912250 CCCTGTACTTACTAGTAAATGTGTACG 59.088 40.741 23.84 20.06 38.55 3.67
3166 3753 8.454106 CCTGTACTTACTAGTAAATGTGTACGT 58.546 37.037 23.84 15.99 38.55 3.57
3167 3754 9.270576 CTGTACTTACTAGTAAATGTGTACGTG 57.729 37.037 23.84 18.83 38.55 4.49
3168 3755 7.750458 TGTACTTACTAGTAAATGTGTACGTGC 59.250 37.037 23.84 16.63 38.55 5.34
3169 3756 6.680810 ACTTACTAGTAAATGTGTACGTGCA 58.319 36.000 15.95 0.82 31.21 4.57
3170 3757 7.147312 ACTTACTAGTAAATGTGTACGTGCAA 58.853 34.615 15.95 0.00 31.21 4.08
3171 3758 7.816031 ACTTACTAGTAAATGTGTACGTGCAAT 59.184 33.333 15.95 1.77 31.21 3.56
3172 3759 6.403333 ACTAGTAAATGTGTACGTGCAATG 57.597 37.500 8.25 0.00 0.00 2.82
3173 3760 4.078363 AGTAAATGTGTACGTGCAATGC 57.922 40.909 8.25 0.00 0.00 3.56
3174 3761 3.500299 AGTAAATGTGTACGTGCAATGCA 59.500 39.130 8.25 2.72 35.60 3.96
3187 3774 3.509740 TGCAATGCACGTTGATATTTGG 58.490 40.909 2.72 0.00 31.71 3.28
3188 3775 3.056962 TGCAATGCACGTTGATATTTGGT 60.057 39.130 2.72 0.00 31.71 3.67
3189 3776 4.156739 TGCAATGCACGTTGATATTTGGTA 59.843 37.500 2.72 0.00 31.71 3.25
3190 3777 5.098893 GCAATGCACGTTGATATTTGGTAA 58.901 37.500 0.00 0.00 0.00 2.85
3191 3778 5.748152 GCAATGCACGTTGATATTTGGTAAT 59.252 36.000 0.00 0.00 0.00 1.89
3192 3779 6.915300 GCAATGCACGTTGATATTTGGTAATA 59.085 34.615 0.00 0.00 0.00 0.98
3193 3780 7.594758 GCAATGCACGTTGATATTTGGTAATAT 59.405 33.333 0.00 0.00 39.17 1.28
3256 3843 9.778993 GCATATTAAGTATGTGATTAGCATTGG 57.221 33.333 0.00 0.00 41.86 3.16
3257 3844 9.778993 CATATTAAGTATGTGATTAGCATTGGC 57.221 33.333 0.00 0.00 36.28 4.52
3258 3845 7.822161 ATTAAGTATGTGATTAGCATTGGCA 57.178 32.000 0.00 0.00 44.61 4.92
3259 3846 7.822161 TTAAGTATGTGATTAGCATTGGCAT 57.178 32.000 0.00 0.00 44.61 4.40
3260 3847 6.720112 AAGTATGTGATTAGCATTGGCATT 57.280 33.333 0.00 0.00 44.61 3.56
3261 3848 7.822161 AAGTATGTGATTAGCATTGGCATTA 57.178 32.000 0.00 0.00 44.61 1.90
3262 3849 7.822161 AGTATGTGATTAGCATTGGCATTAA 57.178 32.000 0.00 0.00 44.61 1.40
3263 3850 8.413309 AGTATGTGATTAGCATTGGCATTAAT 57.587 30.769 0.00 0.00 44.61 1.40
3264 3851 9.519191 AGTATGTGATTAGCATTGGCATTAATA 57.481 29.630 0.00 0.00 44.61 0.98
3268 3855 9.478768 TGTGATTAGCATTGGCATTAATATTTG 57.521 29.630 0.00 0.00 44.61 2.32
3269 3856 8.928733 GTGATTAGCATTGGCATTAATATTTGG 58.071 33.333 0.00 0.00 44.61 3.28
3270 3857 8.649591 TGATTAGCATTGGCATTAATATTTGGT 58.350 29.630 0.00 0.00 44.61 3.67
3273 3860 9.926158 TTAGCATTGGCATTAATATTTGGTATG 57.074 29.630 0.00 0.00 44.61 2.39
3274 3861 8.192743 AGCATTGGCATTAATATTTGGTATGA 57.807 30.769 0.00 0.00 44.61 2.15
3275 3862 8.818860 AGCATTGGCATTAATATTTGGTATGAT 58.181 29.630 0.00 0.00 44.61 2.45
3289 3876 8.752005 ATTTGGTATGATATTAACTGCACACT 57.248 30.769 0.00 0.00 0.00 3.55
3290 3877 9.845740 ATTTGGTATGATATTAACTGCACACTA 57.154 29.630 0.00 0.00 0.00 2.74
3291 3878 9.674068 TTTGGTATGATATTAACTGCACACTAA 57.326 29.630 0.00 0.00 0.00 2.24
3292 3879 9.674068 TTGGTATGATATTAACTGCACACTAAA 57.326 29.630 0.00 0.00 0.00 1.85
3293 3880 9.104965 TGGTATGATATTAACTGCACACTAAAC 57.895 33.333 0.00 0.00 0.00 2.01
3294 3881 8.273557 GGTATGATATTAACTGCACACTAAACG 58.726 37.037 0.00 0.00 0.00 3.60
3295 3882 7.843490 ATGATATTAACTGCACACTAAACGT 57.157 32.000 0.00 0.00 0.00 3.99
3304 3891 3.345087 CACTAAACGTGTTGAGCGC 57.655 52.632 0.00 0.00 38.84 5.92
3305 3892 0.859232 CACTAAACGTGTTGAGCGCT 59.141 50.000 11.27 11.27 38.84 5.92
3306 3893 1.136611 CACTAAACGTGTTGAGCGCTC 60.137 52.381 30.42 30.42 38.84 5.03
3307 3894 1.136690 CTAAACGTGTTGAGCGCTCA 58.863 50.000 35.30 35.30 37.91 4.26
3308 3895 0.856641 TAAACGTGTTGAGCGCTCAC 59.143 50.000 38.36 29.97 39.66 3.51
3309 3896 1.772063 AAACGTGTTGAGCGCTCACC 61.772 55.000 38.36 32.16 39.66 4.02
3310 3897 2.661537 CGTGTTGAGCGCTCACCA 60.662 61.111 38.36 34.47 39.66 4.17
3311 3898 2.029288 CGTGTTGAGCGCTCACCAT 61.029 57.895 35.40 1.89 39.66 3.55
3312 3899 1.568612 CGTGTTGAGCGCTCACCATT 61.569 55.000 35.40 1.02 39.66 3.16
3313 3900 0.110056 GTGTTGAGCGCTCACCATTG 60.110 55.000 35.40 0.00 39.66 2.82
3314 3901 1.236616 TGTTGAGCGCTCACCATTGG 61.237 55.000 38.36 0.00 39.66 3.16
3315 3902 0.955428 GTTGAGCGCTCACCATTGGA 60.955 55.000 38.36 20.24 39.66 3.53
3316 3903 0.674581 TTGAGCGCTCACCATTGGAG 60.675 55.000 38.36 0.83 39.66 3.86
3321 3908 3.915575 CTCACCATTGGAGCAGCC 58.084 61.111 10.37 0.00 37.10 4.85
3322 3909 1.302285 CTCACCATTGGAGCAGCCT 59.698 57.895 10.37 0.00 37.63 4.58
3323 3910 1.001764 TCACCATTGGAGCAGCCTG 60.002 57.895 10.37 0.00 37.63 4.85
3324 3911 1.001764 CACCATTGGAGCAGCCTGA 60.002 57.895 10.37 0.00 37.63 3.86
3325 3912 1.030488 CACCATTGGAGCAGCCTGAG 61.030 60.000 10.37 0.00 37.63 3.35
3326 3913 1.302285 CCATTGGAGCAGCCTGAGT 59.698 57.895 0.00 0.00 37.63 3.41
3327 3914 0.747283 CCATTGGAGCAGCCTGAGTC 60.747 60.000 0.00 0.00 37.63 3.36
3328 3915 1.088340 CATTGGAGCAGCCTGAGTCG 61.088 60.000 0.00 0.00 37.63 4.18
3329 3916 1.548357 ATTGGAGCAGCCTGAGTCGT 61.548 55.000 0.00 0.00 37.63 4.34
3330 3917 1.758440 TTGGAGCAGCCTGAGTCGTT 61.758 55.000 0.00 0.00 37.63 3.85
3331 3918 1.739562 GGAGCAGCCTGAGTCGTTG 60.740 63.158 0.00 0.00 0.00 4.10
3332 3919 1.739562 GAGCAGCCTGAGTCGTTGG 60.740 63.158 0.00 0.00 0.00 3.77
3333 3920 2.159819 GAGCAGCCTGAGTCGTTGGA 62.160 60.000 0.00 0.00 0.00 3.53
3334 3921 1.078848 GCAGCCTGAGTCGTTGGAT 60.079 57.895 0.00 0.00 0.00 3.41
3335 3922 0.674895 GCAGCCTGAGTCGTTGGATT 60.675 55.000 0.00 0.00 0.00 3.01
3336 3923 1.081892 CAGCCTGAGTCGTTGGATTG 58.918 55.000 0.00 0.00 0.00 2.67
3337 3924 0.976641 AGCCTGAGTCGTTGGATTGA 59.023 50.000 1.44 0.00 0.00 2.57
3338 3925 1.079503 GCCTGAGTCGTTGGATTGAC 58.920 55.000 1.44 0.00 35.33 3.18
3339 3926 1.726853 CCTGAGTCGTTGGATTGACC 58.273 55.000 0.00 0.00 35.71 4.02
3340 3927 1.276421 CCTGAGTCGTTGGATTGACCT 59.724 52.381 0.00 0.00 39.86 3.85
3341 3928 2.341257 CTGAGTCGTTGGATTGACCTG 58.659 52.381 0.00 0.00 39.86 4.00
3342 3929 1.967779 TGAGTCGTTGGATTGACCTGA 59.032 47.619 0.00 0.00 39.86 3.86
3343 3930 2.567169 TGAGTCGTTGGATTGACCTGAT 59.433 45.455 0.00 0.00 39.86 2.90
3344 3931 3.007940 TGAGTCGTTGGATTGACCTGATT 59.992 43.478 0.00 0.00 39.86 2.57
3345 3932 4.003648 GAGTCGTTGGATTGACCTGATTT 58.996 43.478 0.00 0.00 39.86 2.17
3346 3933 3.753272 AGTCGTTGGATTGACCTGATTTG 59.247 43.478 0.00 0.00 39.86 2.32
3347 3934 3.751175 GTCGTTGGATTGACCTGATTTGA 59.249 43.478 0.00 0.00 39.86 2.69
3348 3935 3.751175 TCGTTGGATTGACCTGATTTGAC 59.249 43.478 0.00 0.00 39.86 3.18
3349 3936 3.424829 CGTTGGATTGACCTGATTTGACG 60.425 47.826 0.00 0.00 39.86 4.35
3350 3937 2.710377 TGGATTGACCTGATTTGACGG 58.290 47.619 0.00 0.00 39.86 4.79
3351 3938 1.401905 GGATTGACCTGATTTGACGGC 59.598 52.381 0.00 0.00 35.41 5.68
3352 3939 1.401905 GATTGACCTGATTTGACGGCC 59.598 52.381 0.00 0.00 0.00 6.13
3353 3940 0.953471 TTGACCTGATTTGACGGCCG 60.953 55.000 26.86 26.86 0.00 6.13
3354 3941 2.046314 ACCTGATTTGACGGCCGG 60.046 61.111 31.76 11.88 0.00 6.13
3355 3942 2.824041 CCTGATTTGACGGCCGGG 60.824 66.667 31.76 14.60 0.00 5.73
3356 3943 2.267642 CTGATTTGACGGCCGGGA 59.732 61.111 31.76 12.83 0.00 5.14
3357 3944 1.153168 CTGATTTGACGGCCGGGAT 60.153 57.895 31.76 16.88 0.00 3.85
3358 3945 0.748005 CTGATTTGACGGCCGGGATT 60.748 55.000 31.76 8.20 0.00 3.01
3359 3946 0.746563 TGATTTGACGGCCGGGATTC 60.747 55.000 31.76 18.48 0.00 2.52
3360 3947 1.772063 GATTTGACGGCCGGGATTCG 61.772 60.000 31.76 1.69 38.88 3.34
3361 3948 2.530958 ATTTGACGGCCGGGATTCGT 62.531 55.000 31.76 5.85 39.99 3.85
3362 3949 2.734948 TTTGACGGCCGGGATTCGTT 62.735 55.000 31.76 4.91 37.25 3.85
3363 3950 3.192922 GACGGCCGGGATTCGTTG 61.193 66.667 31.76 0.00 37.25 4.10
3364 3951 4.770874 ACGGCCGGGATTCGTTGG 62.771 66.667 31.76 0.00 37.11 3.77
3365 3952 4.460683 CGGCCGGGATTCGTTGGA 62.461 66.667 20.10 0.00 37.11 3.53
3366 3953 2.192175 GGCCGGGATTCGTTGGAT 59.808 61.111 2.18 0.00 37.11 3.41
3367 3954 1.892391 GGCCGGGATTCGTTGGATC 60.892 63.158 2.18 0.00 37.11 3.36
3368 3955 1.146263 GCCGGGATTCGTTGGATCT 59.854 57.895 2.18 0.00 37.11 2.75
3369 3956 1.160329 GCCGGGATTCGTTGGATCTG 61.160 60.000 2.18 0.00 37.11 2.90
3370 3957 1.160329 CCGGGATTCGTTGGATCTGC 61.160 60.000 0.00 0.00 37.11 4.26
3371 3958 1.160329 CGGGATTCGTTGGATCTGCC 61.160 60.000 0.00 0.00 37.10 4.85
3372 3959 0.819666 GGGATTCGTTGGATCTGCCC 60.820 60.000 0.00 0.00 34.97 5.36
3373 3960 0.819666 GGATTCGTTGGATCTGCCCC 60.820 60.000 0.00 0.00 34.97 5.80
3374 3961 0.181350 GATTCGTTGGATCTGCCCCT 59.819 55.000 0.00 0.00 34.97 4.79
3375 3962 0.625849 ATTCGTTGGATCTGCCCCTT 59.374 50.000 0.00 0.00 34.97 3.95
3376 3963 0.404040 TTCGTTGGATCTGCCCCTTT 59.596 50.000 0.00 0.00 34.97 3.11
3377 3964 0.322456 TCGTTGGATCTGCCCCTTTG 60.322 55.000 0.00 0.00 34.97 2.77
3378 3965 1.315257 CGTTGGATCTGCCCCTTTGG 61.315 60.000 0.00 0.00 34.97 3.28
3394 3981 6.867519 CCCTTTGGGTCTTTTTATTGGTAT 57.132 37.500 0.00 0.00 38.25 2.73
3395 3982 7.964666 CCCTTTGGGTCTTTTTATTGGTATA 57.035 36.000 0.00 0.00 38.25 1.47
3396 3983 8.547481 CCCTTTGGGTCTTTTTATTGGTATAT 57.453 34.615 0.00 0.00 38.25 0.86
3397 3984 9.649316 CCCTTTGGGTCTTTTTATTGGTATATA 57.351 33.333 0.00 0.00 38.25 0.86
3589 4176 9.743057 CCAGTTACTTGTGATTCAACAATTTTA 57.257 29.630 0.00 0.00 39.25 1.52
4191 4779 1.017387 CCAATAGACTTTGCTCCCGC 58.983 55.000 0.00 0.00 0.00 6.13
4208 4796 0.038159 CGCGGAGTCTCCTGTTCTTT 60.038 55.000 17.00 0.00 33.30 2.52
4223 4811 6.325545 TCCTGTTCTTTAACTTCTGGAGTGTA 59.674 38.462 0.00 0.00 39.00 2.90
4262 4850 3.206150 GCCACATCATTATCCGTGACTT 58.794 45.455 0.00 0.00 0.00 3.01
4347 4935 0.671251 GGATGTAGTCCTGAGAGCCG 59.329 60.000 0.00 0.00 44.16 5.52
4348 4936 0.031449 GATGTAGTCCTGAGAGCCGC 59.969 60.000 0.00 0.00 0.00 6.53
4349 4937 1.395826 ATGTAGTCCTGAGAGCCGCC 61.396 60.000 0.00 0.00 0.00 6.13
4350 4938 1.755008 GTAGTCCTGAGAGCCGCCT 60.755 63.158 0.00 0.00 0.00 5.52
4351 4939 1.454111 TAGTCCTGAGAGCCGCCTC 60.454 63.158 0.00 0.00 38.42 4.70
4352 4940 2.912987 TAGTCCTGAGAGCCGCCTCC 62.913 65.000 0.00 0.00 38.96 4.30
4353 4941 4.067512 TCCTGAGAGCCGCCTCCT 62.068 66.667 0.00 0.00 38.96 3.69
4354 4942 3.847602 CCTGAGAGCCGCCTCCTG 61.848 72.222 0.00 0.00 38.96 3.86
4355 4943 2.757508 CTGAGAGCCGCCTCCTGA 60.758 66.667 0.00 0.00 38.96 3.86
4356 4944 2.283894 TGAGAGCCGCCTCCTGAA 60.284 61.111 0.00 0.00 38.96 3.02
4357 4945 2.295472 CTGAGAGCCGCCTCCTGAAG 62.295 65.000 0.00 0.00 38.96 3.02
4398 5001 4.785301 ACCATTCTGATTCCCACAGTATG 58.215 43.478 0.00 0.00 40.36 2.39
4461 5064 0.957395 AACTGGAGCTGTTGCGGATG 60.957 55.000 0.00 0.00 45.42 3.51
4483 5086 1.167851 GCCTGTATCTTGTGCAGCAA 58.832 50.000 0.00 0.00 39.01 3.91
4503 5106 1.339055 ACCGCATCTGCTGTATGTGTT 60.339 47.619 0.09 0.97 36.73 3.32
4585 5188 4.062991 GGTTGGTCCTTGTAGTGTTACTG 58.937 47.826 0.00 0.00 0.00 2.74
4611 5214 0.165295 CTGCTGATGACACAGTTGCG 59.835 55.000 0.00 0.00 39.73 4.85
4673 5276 6.494893 TGAGTGTTGTTATTATGTTGCTCC 57.505 37.500 0.00 0.00 0.00 4.70
4684 5287 1.961793 TGTTGCTCCTGTGTTGGTAC 58.038 50.000 0.00 0.00 0.00 3.34
4685 5288 1.488812 TGTTGCTCCTGTGTTGGTACT 59.511 47.619 0.00 0.00 0.00 2.73
4686 5289 2.092646 TGTTGCTCCTGTGTTGGTACTT 60.093 45.455 0.00 0.00 0.00 2.24
4687 5290 2.949644 GTTGCTCCTGTGTTGGTACTTT 59.050 45.455 0.00 0.00 0.00 2.66
4688 5291 3.290948 TGCTCCTGTGTTGGTACTTTT 57.709 42.857 0.00 0.00 0.00 2.27
4740 5346 2.483491 CTGCAAGAGAAGGAAGAAGCAC 59.517 50.000 0.00 0.00 34.07 4.40
4801 5407 1.371183 GTATATGGCAGAGGCGGCA 59.629 57.895 13.08 0.00 46.50 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 9.956720 CTCCATCATCGCTCTTATTTTTATTTT 57.043 29.630 0.00 0.00 0.00 1.82
49 50 9.125026 ACTCCATCATCGCTCTTATTTTTATTT 57.875 29.630 0.00 0.00 0.00 1.40
50 51 8.682936 ACTCCATCATCGCTCTTATTTTTATT 57.317 30.769 0.00 0.00 0.00 1.40
51 52 9.429359 CTACTCCATCATCGCTCTTATTTTTAT 57.571 33.333 0.00 0.00 0.00 1.40
52 53 8.421784 ACTACTCCATCATCGCTCTTATTTTTA 58.578 33.333 0.00 0.00 0.00 1.52
53 54 7.275920 ACTACTCCATCATCGCTCTTATTTTT 58.724 34.615 0.00 0.00 0.00 1.94
54 55 6.821388 ACTACTCCATCATCGCTCTTATTTT 58.179 36.000 0.00 0.00 0.00 1.82
55 56 6.412362 ACTACTCCATCATCGCTCTTATTT 57.588 37.500 0.00 0.00 0.00 1.40
56 57 6.412362 AACTACTCCATCATCGCTCTTATT 57.588 37.500 0.00 0.00 0.00 1.40
57 58 6.412362 AAACTACTCCATCATCGCTCTTAT 57.588 37.500 0.00 0.00 0.00 1.73
58 59 5.854010 AAACTACTCCATCATCGCTCTTA 57.146 39.130 0.00 0.00 0.00 2.10
59 60 4.744795 AAACTACTCCATCATCGCTCTT 57.255 40.909 0.00 0.00 0.00 2.85
60 61 4.744795 AAAACTACTCCATCATCGCTCT 57.255 40.909 0.00 0.00 0.00 4.09
61 62 6.903883 TTAAAAACTACTCCATCATCGCTC 57.096 37.500 0.00 0.00 0.00 5.03
62 63 7.681939 TTTTAAAAACTACTCCATCATCGCT 57.318 32.000 0.00 0.00 0.00 4.93
63 64 8.021396 ACTTTTTAAAAACTACTCCATCATCGC 58.979 33.333 9.31 0.00 0.00 4.58
64 65 9.329913 CACTTTTTAAAAACTACTCCATCATCG 57.670 33.333 9.31 0.00 0.00 3.84
65 66 9.626045 CCACTTTTTAAAAACTACTCCATCATC 57.374 33.333 9.31 0.00 0.00 2.92
66 67 9.362151 TCCACTTTTTAAAAACTACTCCATCAT 57.638 29.630 9.31 0.00 0.00 2.45
67 68 8.754991 TCCACTTTTTAAAAACTACTCCATCA 57.245 30.769 9.31 0.00 0.00 3.07
69 70 9.811995 GTTTCCACTTTTTAAAAACTACTCCAT 57.188 29.630 9.31 0.00 0.00 3.41
70 71 8.804204 TGTTTCCACTTTTTAAAAACTACTCCA 58.196 29.630 9.31 0.00 32.44 3.86
71 72 9.642327 TTGTTTCCACTTTTTAAAAACTACTCC 57.358 29.630 9.31 0.00 32.44 3.85
79 80 9.672673 TGGATGATTTGTTTCCACTTTTTAAAA 57.327 25.926 0.00 0.00 34.65 1.52
95 96 9.485206 AAAAGAAATTCTGTCTTGGATGATTTG 57.515 29.630 0.00 0.00 35.50 2.32
98 99 8.863086 TCAAAAAGAAATTCTGTCTTGGATGAT 58.137 29.630 0.00 0.00 35.50 2.45
99 100 8.236585 TCAAAAAGAAATTCTGTCTTGGATGA 57.763 30.769 0.00 0.00 35.50 2.92
100 101 7.597743 CCTCAAAAAGAAATTCTGTCTTGGATG 59.402 37.037 0.00 0.00 35.50 3.51
101 102 7.256083 CCCTCAAAAAGAAATTCTGTCTTGGAT 60.256 37.037 0.00 0.00 35.50 3.41
102 103 6.040842 CCCTCAAAAAGAAATTCTGTCTTGGA 59.959 38.462 0.00 0.00 35.50 3.53
103 104 6.040842 TCCCTCAAAAAGAAATTCTGTCTTGG 59.959 38.462 0.00 0.00 35.50 3.61
111 112 5.545063 TGGGTTCCCTCAAAAAGAAATTC 57.455 39.130 9.43 0.00 0.00 2.17
114 115 4.615513 TCTTGGGTTCCCTCAAAAAGAAA 58.384 39.130 9.43 0.00 0.00 2.52
130 131 4.829492 AGGTTGAGTTGAAATTCTCTTGGG 59.171 41.667 0.00 0.00 0.00 4.12
149 152 0.963962 TCCGAAAGCGTACTCAGGTT 59.036 50.000 0.00 0.00 35.23 3.50
176 179 1.934589 TGCACCTTTCGGATATCGTG 58.065 50.000 0.00 0.00 40.32 4.35
180 183 3.587061 TGGGATATGCACCTTTCGGATAT 59.413 43.478 0.00 0.00 30.93 1.63
181 184 2.976185 TGGGATATGCACCTTTCGGATA 59.024 45.455 0.00 0.00 0.00 2.59
183 186 1.208706 TGGGATATGCACCTTTCGGA 58.791 50.000 0.00 0.00 0.00 4.55
190 193 3.068590 CCACTGAAAATGGGATATGCACC 59.931 47.826 0.00 0.00 33.18 5.01
192 195 2.694628 GCCACTGAAAATGGGATATGCA 59.305 45.455 0.00 0.00 37.73 3.96
193 196 2.694628 TGCCACTGAAAATGGGATATGC 59.305 45.455 0.00 0.00 37.73 3.14
195 198 4.613437 AGTTGCCACTGAAAATGGGATAT 58.387 39.130 0.00 0.00 37.41 1.63
196 199 4.046286 AGTTGCCACTGAAAATGGGATA 57.954 40.909 0.00 0.00 37.41 2.59
197 200 2.893424 AGTTGCCACTGAAAATGGGAT 58.107 42.857 0.00 0.00 37.41 3.85
198 201 2.380064 AGTTGCCACTGAAAATGGGA 57.620 45.000 0.00 0.00 37.73 4.37
383 386 1.969064 CCGAGAGATCGCCGGAGAT 60.969 63.158 21.54 21.54 45.58 2.75
528 531 9.545105 CTATTAACAAGAAGAAGCATGATCTCT 57.455 33.333 0.00 0.00 0.00 3.10
706 712 0.624500 TGCTCCTCCCTAAGGCCAAT 60.625 55.000 5.01 0.00 45.78 3.16
735 741 0.039035 AATCGCCCCCAGCTTTAACA 59.961 50.000 0.00 0.00 40.39 2.41
742 754 0.815615 CTGTCTAAATCGCCCCCAGC 60.816 60.000 0.00 0.00 38.52 4.85
743 755 0.830648 TCTGTCTAAATCGCCCCCAG 59.169 55.000 0.00 0.00 0.00 4.45
748 760 5.649602 CAGAAGAATCTGTCTAAATCGCC 57.350 43.478 0.00 0.00 46.60 5.54
761 773 2.478894 TGTCGCGAAAACCAGAAGAATC 59.521 45.455 12.06 0.00 0.00 2.52
1243 1265 3.680937 TGTAGCTTTACCGTGTTGCATAC 59.319 43.478 0.00 0.00 0.00 2.39
1272 1294 8.447833 TGCAGAAATTGGATAAAAGTAAGTACG 58.552 33.333 0.00 0.00 0.00 3.67
1557 2130 5.016051 TGGCATGAGATTGAACTAGAGTC 57.984 43.478 0.00 0.00 0.00 3.36
1650 2223 4.661709 AGGGGTCAAAGTAAGTTTCCTACA 59.338 41.667 0.00 0.00 0.00 2.74
1656 2229 3.437491 GGGGAAGGGGTCAAAGTAAGTTT 60.437 47.826 0.00 0.00 0.00 2.66
1792 2365 3.346315 AGCATAACAGTTGCAGCATACA 58.654 40.909 2.55 0.00 42.62 2.29
1972 2549 6.299141 AGTGTGTTAATGTCAGAATGGAGTT 58.701 36.000 0.00 0.00 36.16 3.01
2342 2920 0.036022 GGAACACAGGAGCTCAGCTT 59.964 55.000 17.19 2.63 39.88 3.74
2377 2955 6.650120 TCTGTCTCCTTATTAACACCAATCC 58.350 40.000 0.00 0.00 0.00 3.01
2381 2959 6.620877 ACATCTGTCTCCTTATTAACACCA 57.379 37.500 0.00 0.00 0.00 4.17
2510 3088 4.592485 ACTTGAGCCCTATATTCTCACG 57.408 45.455 0.00 0.00 36.67 4.35
2527 3108 3.100817 CAGACTGTTCGCAACAAACTTG 58.899 45.455 0.00 0.00 41.61 3.16
2566 3147 1.818674 CAAATCTAGTGGGGTTGTGGC 59.181 52.381 0.00 0.00 0.00 5.01
2772 3353 8.641541 GGAGATCAATTTGCAGGGAATTATTTA 58.358 33.333 0.00 0.00 0.00 1.40
2794 3376 4.132336 GACATATCATTGCAAGCAGGAGA 58.868 43.478 4.94 0.00 0.00 3.71
2796 3378 4.132336 GAGACATATCATTGCAAGCAGGA 58.868 43.478 4.94 0.12 0.00 3.86
2879 3461 0.027590 AATCCTTCCCCAGGCCCTAT 60.028 55.000 0.00 0.00 43.55 2.57
2885 3467 0.475906 CAGCCTAATCCTTCCCCAGG 59.524 60.000 0.00 0.00 45.64 4.45
2961 3548 0.397941 CTTGTGCCAAGAGGTCCTGA 59.602 55.000 0.00 0.00 37.19 3.86
2990 3577 1.610102 CCTGAGGCAGTGGTGAAGAAG 60.610 57.143 0.00 0.00 0.00 2.85
2991 3578 0.397941 CCTGAGGCAGTGGTGAAGAA 59.602 55.000 0.00 0.00 0.00 2.52
2992 3579 2.061220 CCTGAGGCAGTGGTGAAGA 58.939 57.895 0.00 0.00 0.00 2.87
3150 3737 5.163903 TGCATTGCACGTACACATTTACTAG 60.164 40.000 7.38 0.00 31.71 2.57
3151 3738 4.691216 TGCATTGCACGTACACATTTACTA 59.309 37.500 7.38 0.00 31.71 1.82
3152 3739 3.500299 TGCATTGCACGTACACATTTACT 59.500 39.130 7.38 0.00 31.71 2.24
3153 3740 3.816091 TGCATTGCACGTACACATTTAC 58.184 40.909 7.38 0.00 31.71 2.01
3166 3753 3.056962 ACCAAATATCAACGTGCATTGCA 60.057 39.130 7.38 7.38 35.60 4.08
3167 3754 3.510719 ACCAAATATCAACGTGCATTGC 58.489 40.909 0.46 0.46 0.00 3.56
3230 3817 9.778993 CCAATGCTAATCACATACTTAATATGC 57.221 33.333 0.00 0.00 44.12 3.14
3231 3818 9.778993 GCCAATGCTAATCACATACTTAATATG 57.221 33.333 0.00 0.00 39.66 1.78
3232 3819 9.519191 TGCCAATGCTAATCACATACTTAATAT 57.481 29.630 0.00 0.00 38.71 1.28
3233 3820 8.916628 TGCCAATGCTAATCACATACTTAATA 57.083 30.769 0.00 0.00 38.71 0.98
3234 3821 7.822161 TGCCAATGCTAATCACATACTTAAT 57.178 32.000 0.00 0.00 38.71 1.40
3235 3822 7.822161 ATGCCAATGCTAATCACATACTTAA 57.178 32.000 0.00 0.00 38.71 1.85
3236 3823 7.822161 AATGCCAATGCTAATCACATACTTA 57.178 32.000 0.00 0.00 38.71 2.24
3237 3824 6.720112 AATGCCAATGCTAATCACATACTT 57.280 33.333 0.00 0.00 38.71 2.24
3238 3825 7.822161 TTAATGCCAATGCTAATCACATACT 57.178 32.000 0.00 0.00 38.71 2.12
3242 3829 9.478768 CAAATATTAATGCCAATGCTAATCACA 57.521 29.630 0.00 0.00 38.71 3.58
3243 3830 8.928733 CCAAATATTAATGCCAATGCTAATCAC 58.071 33.333 0.00 0.00 38.71 3.06
3244 3831 8.649591 ACCAAATATTAATGCCAATGCTAATCA 58.350 29.630 0.00 0.00 38.71 2.57
3247 3834 9.926158 CATACCAAATATTAATGCCAATGCTAA 57.074 29.630 0.00 0.00 38.71 3.09
3248 3835 9.306777 TCATACCAAATATTAATGCCAATGCTA 57.693 29.630 0.00 0.00 38.71 3.49
3249 3836 8.192743 TCATACCAAATATTAATGCCAATGCT 57.807 30.769 0.00 0.00 38.71 3.79
3263 3850 9.845740 AGTGTGCAGTTAATATCATACCAAATA 57.154 29.630 0.00 0.00 0.00 1.40
3264 3851 8.752005 AGTGTGCAGTTAATATCATACCAAAT 57.248 30.769 0.00 0.00 0.00 2.32
3265 3852 9.674068 TTAGTGTGCAGTTAATATCATACCAAA 57.326 29.630 0.00 0.00 0.00 3.28
3266 3853 9.674068 TTTAGTGTGCAGTTAATATCATACCAA 57.326 29.630 0.00 0.00 0.00 3.67
3267 3854 9.104965 GTTTAGTGTGCAGTTAATATCATACCA 57.895 33.333 0.00 0.00 0.00 3.25
3268 3855 8.273557 CGTTTAGTGTGCAGTTAATATCATACC 58.726 37.037 0.00 0.00 0.00 2.73
3269 3856 8.814235 ACGTTTAGTGTGCAGTTAATATCATAC 58.186 33.333 0.00 0.00 0.00 2.39
3270 3857 8.813282 CACGTTTAGTGTGCAGTTAATATCATA 58.187 33.333 0.00 0.00 45.51 2.15
3271 3858 7.684670 CACGTTTAGTGTGCAGTTAATATCAT 58.315 34.615 0.00 0.00 45.51 2.45
3272 3859 7.056002 CACGTTTAGTGTGCAGTTAATATCA 57.944 36.000 0.00 0.00 45.51 2.15
3286 3873 3.675666 TGAGCGCTCAACACGTTTAGTG 61.676 50.000 36.62 1.23 44.66 2.74
3287 3874 1.137513 GAGCGCTCAACACGTTTAGT 58.862 50.000 31.91 0.00 0.00 2.24
3288 3875 1.136611 GTGAGCGCTCAACACGTTTAG 60.137 52.381 39.63 0.00 41.85 1.85
3289 3876 0.856641 GTGAGCGCTCAACACGTTTA 59.143 50.000 39.63 13.11 41.85 2.01
3290 3877 1.641677 GTGAGCGCTCAACACGTTT 59.358 52.632 39.63 0.00 41.85 3.60
3291 3878 2.244651 GGTGAGCGCTCAACACGTT 61.245 57.895 42.62 4.93 46.18 3.99
3292 3879 2.661866 GGTGAGCGCTCAACACGT 60.662 61.111 42.62 5.80 46.18 4.49
3297 3884 0.674581 CTCCAATGGTGAGCGCTCAA 60.675 55.000 39.63 26.77 41.85 3.02
3298 3885 1.078918 CTCCAATGGTGAGCGCTCA 60.079 57.895 35.30 35.30 37.24 4.26
3299 3886 2.467826 GCTCCAATGGTGAGCGCTC 61.468 63.158 30.42 30.42 45.05 5.03
3300 3887 2.437359 GCTCCAATGGTGAGCGCT 60.437 61.111 11.27 11.27 45.05 5.92
3304 3891 1.030488 CAGGCTGCTCCAATGGTGAG 61.030 60.000 0.00 0.00 37.29 3.51
3305 3892 1.001764 CAGGCTGCTCCAATGGTGA 60.002 57.895 0.00 0.00 37.29 4.02
3306 3893 1.001764 TCAGGCTGCTCCAATGGTG 60.002 57.895 10.34 0.00 37.29 4.17
3307 3894 1.302285 CTCAGGCTGCTCCAATGGT 59.698 57.895 10.34 0.00 37.29 3.55
3308 3895 0.747283 GACTCAGGCTGCTCCAATGG 60.747 60.000 10.34 0.00 37.29 3.16
3309 3896 1.088340 CGACTCAGGCTGCTCCAATG 61.088 60.000 10.34 0.00 37.29 2.82
3310 3897 1.220206 CGACTCAGGCTGCTCCAAT 59.780 57.895 10.34 0.00 37.29 3.16
3311 3898 1.758440 AACGACTCAGGCTGCTCCAA 61.758 55.000 10.34 0.00 37.29 3.53
3312 3899 2.210013 AACGACTCAGGCTGCTCCA 61.210 57.895 10.34 0.00 37.29 3.86
3313 3900 1.739562 CAACGACTCAGGCTGCTCC 60.740 63.158 10.34 0.00 0.00 4.70
3314 3901 1.739562 CCAACGACTCAGGCTGCTC 60.740 63.158 10.34 5.79 0.00 4.26
3315 3902 1.548357 ATCCAACGACTCAGGCTGCT 61.548 55.000 10.34 0.00 0.00 4.24
3316 3903 0.674895 AATCCAACGACTCAGGCTGC 60.675 55.000 10.34 0.00 0.00 5.25
3317 3904 1.081892 CAATCCAACGACTCAGGCTG 58.918 55.000 8.58 8.58 0.00 4.85
3318 3905 0.976641 TCAATCCAACGACTCAGGCT 59.023 50.000 0.00 0.00 0.00 4.58
3319 3906 1.079503 GTCAATCCAACGACTCAGGC 58.920 55.000 0.00 0.00 0.00 4.85
3320 3907 1.276421 AGGTCAATCCAACGACTCAGG 59.724 52.381 0.00 0.00 39.02 3.86
3321 3908 2.029020 TCAGGTCAATCCAACGACTCAG 60.029 50.000 0.00 0.00 39.02 3.35
3322 3909 1.967779 TCAGGTCAATCCAACGACTCA 59.032 47.619 0.00 0.00 39.02 3.41
3323 3910 2.743636 TCAGGTCAATCCAACGACTC 57.256 50.000 0.00 0.00 39.02 3.36
3324 3911 3.703001 AATCAGGTCAATCCAACGACT 57.297 42.857 0.00 0.00 39.02 4.18
3325 3912 3.751175 TCAAATCAGGTCAATCCAACGAC 59.249 43.478 0.00 0.00 39.02 4.34
3326 3913 3.751175 GTCAAATCAGGTCAATCCAACGA 59.249 43.478 0.00 0.00 39.02 3.85
3327 3914 3.424829 CGTCAAATCAGGTCAATCCAACG 60.425 47.826 0.00 0.00 39.02 4.10
3328 3915 3.119849 CCGTCAAATCAGGTCAATCCAAC 60.120 47.826 0.00 0.00 39.02 3.77
3329 3916 3.081061 CCGTCAAATCAGGTCAATCCAA 58.919 45.455 0.00 0.00 39.02 3.53
3330 3917 2.710377 CCGTCAAATCAGGTCAATCCA 58.290 47.619 0.00 0.00 39.02 3.41
3331 3918 1.401905 GCCGTCAAATCAGGTCAATCC 59.598 52.381 0.00 0.00 0.00 3.01
3332 3919 1.401905 GGCCGTCAAATCAGGTCAATC 59.598 52.381 0.00 0.00 0.00 2.67
3333 3920 1.463674 GGCCGTCAAATCAGGTCAAT 58.536 50.000 0.00 0.00 0.00 2.57
3334 3921 0.953471 CGGCCGTCAAATCAGGTCAA 60.953 55.000 19.50 0.00 0.00 3.18
3335 3922 1.375396 CGGCCGTCAAATCAGGTCA 60.375 57.895 19.50 0.00 0.00 4.02
3336 3923 2.106683 CCGGCCGTCAAATCAGGTC 61.107 63.158 26.12 0.00 0.00 3.85
3337 3924 2.046314 CCGGCCGTCAAATCAGGT 60.046 61.111 26.12 0.00 0.00 4.00
3338 3925 2.608970 ATCCCGGCCGTCAAATCAGG 62.609 60.000 26.12 15.50 0.00 3.86
3339 3926 0.748005 AATCCCGGCCGTCAAATCAG 60.748 55.000 26.12 5.50 0.00 2.90
3340 3927 0.746563 GAATCCCGGCCGTCAAATCA 60.747 55.000 26.12 0.00 0.00 2.57
3341 3928 1.772063 CGAATCCCGGCCGTCAAATC 61.772 60.000 26.12 14.09 33.91 2.17
3342 3929 1.817941 CGAATCCCGGCCGTCAAAT 60.818 57.895 26.12 8.69 33.91 2.32
3343 3930 2.435234 CGAATCCCGGCCGTCAAA 60.435 61.111 26.12 6.42 33.91 2.69
3344 3931 3.242897 AACGAATCCCGGCCGTCAA 62.243 57.895 26.12 9.29 43.93 3.18
3345 3932 3.697747 AACGAATCCCGGCCGTCA 61.698 61.111 26.12 10.46 43.93 4.35
3346 3933 3.192922 CAACGAATCCCGGCCGTC 61.193 66.667 26.12 14.15 43.93 4.79
3347 3934 4.770874 CCAACGAATCCCGGCCGT 62.771 66.667 26.12 4.65 43.93 5.68
3348 3935 3.750373 ATCCAACGAATCCCGGCCG 62.750 63.158 21.04 21.04 43.93 6.13
3349 3936 1.892391 GATCCAACGAATCCCGGCC 60.892 63.158 0.00 0.00 43.93 6.13
3350 3937 1.146263 AGATCCAACGAATCCCGGC 59.854 57.895 0.00 0.00 43.93 6.13
3351 3938 1.160329 GCAGATCCAACGAATCCCGG 61.160 60.000 0.00 0.00 43.93 5.73
3352 3939 1.160329 GGCAGATCCAACGAATCCCG 61.160 60.000 0.00 0.00 38.46 5.14
3353 3940 0.819666 GGGCAGATCCAACGAATCCC 60.820 60.000 0.00 0.00 36.21 3.85
3354 3941 0.819666 GGGGCAGATCCAACGAATCC 60.820 60.000 0.00 0.00 36.21 3.01
3355 3942 0.181350 AGGGGCAGATCCAACGAATC 59.819 55.000 0.00 0.00 36.21 2.52
3356 3943 0.625849 AAGGGGCAGATCCAACGAAT 59.374 50.000 0.00 0.00 36.21 3.34
3357 3944 0.404040 AAAGGGGCAGATCCAACGAA 59.596 50.000 0.00 0.00 36.21 3.85
3358 3945 0.322456 CAAAGGGGCAGATCCAACGA 60.322 55.000 0.00 0.00 36.21 3.85
3359 3946 1.315257 CCAAAGGGGCAGATCCAACG 61.315 60.000 0.00 0.00 36.21 4.10
3360 3947 2.583472 CCAAAGGGGCAGATCCAAC 58.417 57.895 0.00 0.00 36.21 3.77
3456 4043 9.807921 TCTACATGTTGGTCACATCTATATCTA 57.192 33.333 2.30 0.00 43.17 1.98
3457 4044 8.712228 TCTACATGTTGGTCACATCTATATCT 57.288 34.615 2.30 0.00 43.17 1.98
3458 4045 9.935241 ATTCTACATGTTGGTCACATCTATATC 57.065 33.333 2.30 0.00 43.17 1.63
3461 4048 9.770097 CTAATTCTACATGTTGGTCACATCTAT 57.230 33.333 2.30 0.00 43.17 1.98
3462 4049 8.204160 CCTAATTCTACATGTTGGTCACATCTA 58.796 37.037 2.30 0.00 43.17 1.98
3463 4050 7.050377 CCTAATTCTACATGTTGGTCACATCT 58.950 38.462 2.30 0.00 43.17 2.90
3464 4051 6.823689 ACCTAATTCTACATGTTGGTCACATC 59.176 38.462 2.30 0.00 43.17 3.06
3466 4053 6.013725 AGACCTAATTCTACATGTTGGTCACA 60.014 38.462 2.30 0.00 43.49 3.58
3467 4054 6.407202 AGACCTAATTCTACATGTTGGTCAC 58.593 40.000 2.30 0.00 43.49 3.67
3589 4176 8.514594 ACACGTCTCAAATCATAAATCACAAAT 58.485 29.630 0.00 0.00 0.00 2.32
4191 4779 4.522722 AGTTAAAGAACAGGAGACTCCG 57.477 45.455 15.97 12.90 40.21 4.63
4208 4796 4.101898 TGCCAAAGTACACTCCAGAAGTTA 59.898 41.667 0.00 0.00 35.45 2.24
4223 4811 0.675633 GCACCTTGACATGCCAAAGT 59.324 50.000 0.00 0.00 35.73 2.66
4262 4850 0.907486 CATCCCTTCTGACTGCTCCA 59.093 55.000 0.00 0.00 0.00 3.86
4315 4903 2.159421 ACTACATCCAGCTTGTACGACG 60.159 50.000 0.00 0.00 0.00 5.12
4343 4931 3.780173 GCTCTTCAGGAGGCGGCT 61.780 66.667 13.09 13.09 42.08 5.52
4344 4932 3.780173 AGCTCTTCAGGAGGCGGC 61.780 66.667 0.00 0.00 42.08 6.53
4345 4933 2.177594 AACAGCTCTTCAGGAGGCGG 62.178 60.000 0.00 0.00 42.08 6.13
4346 4934 1.018226 CAACAGCTCTTCAGGAGGCG 61.018 60.000 0.00 0.00 42.08 5.52
4347 4935 1.304509 GCAACAGCTCTTCAGGAGGC 61.305 60.000 0.00 0.00 42.08 4.70
4348 4936 0.324285 AGCAACAGCTCTTCAGGAGG 59.676 55.000 0.00 0.00 42.08 4.30
4349 4937 1.270732 ACAGCAACAGCTCTTCAGGAG 60.271 52.381 0.00 0.00 44.49 3.69
4350 4938 0.761187 ACAGCAACAGCTCTTCAGGA 59.239 50.000 0.00 0.00 36.19 3.86
4351 4939 1.155042 GACAGCAACAGCTCTTCAGG 58.845 55.000 0.00 0.00 36.19 3.86
4352 4940 0.788995 CGACAGCAACAGCTCTTCAG 59.211 55.000 0.00 0.00 36.19 3.02
4353 4941 0.601046 CCGACAGCAACAGCTCTTCA 60.601 55.000 0.00 0.00 36.19 3.02
4354 4942 1.905922 GCCGACAGCAACAGCTCTTC 61.906 60.000 0.00 0.00 42.97 2.87
4355 4943 1.963338 GCCGACAGCAACAGCTCTT 60.963 57.895 0.00 0.00 42.97 2.85
4356 4944 2.358003 GCCGACAGCAACAGCTCT 60.358 61.111 0.00 0.00 42.97 4.09
4357 4945 3.782244 CGCCGACAGCAACAGCTC 61.782 66.667 0.00 0.00 44.04 4.09
4398 5001 0.035915 GACTTGGGTTCAGGAGCTCC 60.036 60.000 26.22 26.22 0.00 4.70
4461 5064 1.709147 CTGCACAAGATACAGGCGCC 61.709 60.000 21.89 21.89 0.00 6.53
4520 5123 1.835494 CTGGTACTCCAAGGACTCGA 58.165 55.000 0.00 0.00 43.81 4.04
4585 5188 1.001293 TGTGTCATCAGCAGACCAGAC 59.999 52.381 0.00 0.00 35.15 3.51
4611 5214 2.047939 GTTGCAGCATGGCCAACC 60.048 61.111 10.96 3.14 35.86 3.77
4650 5253 6.149308 CAGGAGCAACATAATAACAACACTCA 59.851 38.462 0.00 0.00 0.00 3.41
4651 5254 6.149474 ACAGGAGCAACATAATAACAACACTC 59.851 38.462 0.00 0.00 0.00 3.51
4656 5259 6.294453 CCAACACAGGAGCAACATAATAACAA 60.294 38.462 0.00 0.00 0.00 2.83
4686 5289 4.583871 TCTTTCTTTGCCTTTGCCAAAAA 58.416 34.783 0.00 0.00 36.33 1.94
4687 5290 4.213564 TCTTTCTTTGCCTTTGCCAAAA 57.786 36.364 0.00 0.00 36.33 2.44
4688 5291 3.902881 TCTTTCTTTGCCTTTGCCAAA 57.097 38.095 0.00 0.00 36.33 3.28
4699 5305 4.318546 GCAGCTTTGCAACATCTTTCTTTG 60.319 41.667 0.00 0.00 34.41 2.77
4801 5407 3.692406 GGGGTCGTCCACTTCGCT 61.692 66.667 0.04 0.00 37.22 4.93


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

AutoCloner maintained by Alex Coulton.