Multiple sequence alignment - TraesCS5D01G486400

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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 TraesCS5D01G486400 chr5D 100.000 5785 0 0 1 5785 521526604 521520820 0.000000e+00 10683.0
1 TraesCS5D01G486400 chr5D 97.436 117 2 1 2798 2914 408792009 408791894 1.270000e-46 198.0
2 TraesCS5D01G486400 chr5D 98.214 112 1 1 2804 2915 555341063 555341173 1.640000e-45 195.0
3 TraesCS5D01G486400 chr5B 91.972 2815 119 44 2994 5755 657885813 657883053 0.000000e+00 3847.0
4 TraesCS5D01G486400 chr5B 93.151 1898 67 26 937 2809 657887812 657885953 0.000000e+00 2726.0
5 TraesCS5D01G486400 chr5B 93.621 486 31 0 433 918 657888577 657888092 0.000000e+00 726.0
6 TraesCS5D01G486400 chr5B 86.638 464 34 10 1 437 657889126 657888664 6.740000e-134 488.0
7 TraesCS5D01G486400 chr5B 97.647 85 2 0 2912 2996 657885955 657885871 4.670000e-31 147.0
8 TraesCS5D01G486400 chr5A 91.471 2345 127 38 2912 5205 649854647 649852325 0.000000e+00 3155.0
9 TraesCS5D01G486400 chr5A 93.282 1429 51 18 1390 2809 649856037 649854645 0.000000e+00 2065.0
10 TraesCS5D01G486400 chr5A 92.534 509 33 5 437 943 649856938 649856433 0.000000e+00 725.0
11 TraesCS5D01G486400 chr5A 91.579 95 8 0 4691 4785 649861439 649861533 1.310000e-26 132.0
12 TraesCS5D01G486400 chr7D 96.532 519 5 4 884 1401 82900237 82900743 0.000000e+00 846.0
13 TraesCS5D01G486400 chr7B 90.031 642 25 21 972 1602 591221904 591221291 0.000000e+00 795.0
14 TraesCS5D01G486400 chr7B 86.364 198 24 3 2206 2401 397211153 397211349 4.540000e-51 213.0
15 TraesCS5D01G486400 chr7B 86.364 198 24 3 2206 2401 397278799 397278995 4.540000e-51 213.0
16 TraesCS5D01G486400 chr7B 96.610 118 3 1 2798 2915 730205229 730205113 1.640000e-45 195.0
17 TraesCS5D01G486400 chr2B 83.623 403 41 14 2330 2729 105842044 105842424 7.130000e-94 355.0
18 TraesCS5D01G486400 chr2B 87.255 102 13 0 4650 4751 176168150 176168049 3.660000e-22 117.0
19 TraesCS5D01G486400 chr1B 83.457 405 42 14 2330 2731 682391579 682391961 2.560000e-93 353.0
20 TraesCS5D01G486400 chr4D 84.492 374 37 11 2357 2729 452847254 452846901 3.320000e-92 350.0
21 TraesCS5D01G486400 chr4D 99.099 111 1 0 2805 2915 401095121 401095011 3.540000e-47 200.0
22 TraesCS5D01G486400 chr6B 82.878 403 44 14 2330 2729 19972614 19972994 7.180000e-89 339.0
23 TraesCS5D01G486400 chr6B 86.283 226 24 6 2330 2553 19949734 19949954 7.490000e-59 239.0
24 TraesCS5D01G486400 chr6B 85.841 226 25 6 2330 2553 19930315 19930535 3.490000e-57 233.0
25 TraesCS5D01G486400 chr2D 83.556 225 35 2 1403 1626 261957192 261957415 5.870000e-50 209.0
26 TraesCS5D01G486400 chr2D 87.255 102 13 0 4650 4751 123213503 123213402 3.660000e-22 117.0
27 TraesCS5D01G486400 chr4B 99.099 111 1 0 2805 2915 242910304 242910414 3.540000e-47 200.0
28 TraesCS5D01G486400 chr6D 97.414 116 3 0 2807 2922 397359923 397359808 1.270000e-46 198.0
29 TraesCS5D01G486400 chr3D 95.082 122 5 1 2797 2918 591339540 591339420 2.130000e-44 191.0
30 TraesCS5D01G486400 chr3B 94.355 124 5 2 2792 2915 216502114 216502235 7.650000e-44 189.0
31 TraesCS5D01G486400 chr1A 93.651 126 6 2 2789 2914 584968558 584968681 2.750000e-43 187.0
32 TraesCS5D01G486400 chr7A 94.000 50 3 0 5116 5165 46396816 46396865 6.220000e-10 76.8


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 TraesCS5D01G486400 chr5D 521520820 521526604 5784 True 10683.000000 10683 100.0000 1 5785 1 chr5D.!!$R2 5784
1 TraesCS5D01G486400 chr5B 657883053 657889126 6073 True 1586.800000 3847 92.6058 1 5755 5 chr5B.!!$R1 5754
2 TraesCS5D01G486400 chr5A 649852325 649856938 4613 True 1981.666667 3155 92.4290 437 5205 3 chr5A.!!$R1 4768
3 TraesCS5D01G486400 chr7D 82900237 82900743 506 False 846.000000 846 96.5320 884 1401 1 chr7D.!!$F1 517
4 TraesCS5D01G486400 chr7B 591221291 591221904 613 True 795.000000 795 90.0310 972 1602 1 chr7B.!!$R1 630

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
78 79 0.107848 CACGACAGTCCCCAATACCC 60.108 60.000 0.00 0.0 0.00 3.69 F
1681 2112 0.247460 TGGTGCCTCTGACGATTGAG 59.753 55.000 0.00 0.0 0.00 3.02 F
1682 2113 0.532573 GGTGCCTCTGACGATTGAGA 59.467 55.000 0.00 0.0 32.44 3.27 F
2821 3263 2.029623 GCTATGTACTCCCTCCGTTCA 58.970 52.381 0.00 0.0 0.00 3.18 F
3390 3896 0.825010 CCTTGTGCAGCTTCAGGGTT 60.825 55.000 9.85 0.0 0.00 4.11 F
3718 4241 1.956477 TGCTCACTTGAGGGCTTTTTC 59.044 47.619 8.32 0.0 42.29 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2283 1.114722 ACATGCACCAACCACCAAGG 61.115 55.0 0.00 0.00 45.67 3.61 R
2901 3343 0.038744 TCGGTTCTACTCCCTCCGTT 59.961 55.0 0.00 0.00 41.58 4.44 R
2902 3344 0.038744 TTCGGTTCTACTCCCTCCGT 59.961 55.0 0.00 0.00 41.58 4.69 R
3910 4452 0.108520 GCATCATTTGCCCTGTGTGG 60.109 55.0 0.00 0.00 46.15 4.17 R
4284 4838 0.603707 CTGAACAAGCGCTTCCTGGA 60.604 55.0 22.21 2.36 0.00 3.86 R
5150 5716 0.745468 CCTGTACTTCCGCTAGGGTC 59.255 60.0 6.02 0.00 38.33 4.46 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
18 19 1.966451 GGACAAAGCCACTCCACCG 60.966 63.158 0.00 0.00 0.00 4.94
38 39 3.073735 CAGAGCTCGGCTGGACCT 61.074 66.667 8.37 0.00 39.88 3.85
39 40 3.073735 AGAGCTCGGCTGGACCTG 61.074 66.667 8.37 0.00 39.88 4.00
40 41 4.828925 GAGCTCGGCTGGACCTGC 62.829 72.222 14.68 14.68 39.88 4.85
42 43 4.400961 GCTCGGCTGGACCTGCTT 62.401 66.667 21.23 0.00 35.61 3.91
43 44 2.125350 CTCGGCTGGACCTGCTTC 60.125 66.667 21.23 6.45 35.61 3.86
44 45 3.997064 CTCGGCTGGACCTGCTTCG 62.997 68.421 21.23 17.00 35.61 3.79
69 70 2.661866 ACAAGCGCACGACAGTCC 60.662 61.111 11.47 0.00 0.00 3.85
73 74 4.980805 GCGCACGACAGTCCCCAA 62.981 66.667 0.30 0.00 0.00 4.12
78 79 0.107848 CACGACAGTCCCCAATACCC 60.108 60.000 0.00 0.00 0.00 3.69
79 80 0.545787 ACGACAGTCCCCAATACCCA 60.546 55.000 0.00 0.00 0.00 4.51
86 87 1.006639 GTCCCCAATACCCACCAACAT 59.993 52.381 0.00 0.00 0.00 2.71
91 92 1.750778 CAATACCCACCAACATGAGCC 59.249 52.381 0.00 0.00 0.00 4.70
114 115 3.171828 ATCGTCACCACAACGCCCA 62.172 57.895 0.00 0.00 39.90 5.36
116 117 3.660111 GTCACCACAACGCCCAGC 61.660 66.667 0.00 0.00 0.00 4.85
131 132 1.339055 CCCAGCTGAAGAAACGATCCA 60.339 52.381 17.39 0.00 0.00 3.41
137 138 1.737236 TGAAGAAACGATCCAATGCCG 59.263 47.619 0.00 0.00 0.00 5.69
170 171 3.545703 CAAAATCTATGAGCCCCTCGTT 58.454 45.455 0.00 0.00 32.35 3.85
178 179 4.778143 GCCCCTCGTTGACGCCAT 62.778 66.667 0.00 0.00 39.60 4.40
180 181 2.819595 CCCTCGTTGACGCCATGG 60.820 66.667 7.63 7.63 39.60 3.66
181 182 2.047274 CCTCGTTGACGCCATGGT 60.047 61.111 14.67 0.00 39.60 3.55
182 183 2.100631 CCTCGTTGACGCCATGGTC 61.101 63.158 14.67 4.33 39.60 4.02
183 184 2.431771 TCGTTGACGCCATGGTCG 60.432 61.111 21.83 21.83 39.83 4.79
191 192 4.899239 GCCATGGTCGCCGGAGAG 62.899 72.222 14.67 0.00 0.00 3.20
192 193 3.147595 CCATGGTCGCCGGAGAGA 61.148 66.667 8.65 0.00 0.00 3.10
193 194 2.105128 CATGGTCGCCGGAGAGAC 59.895 66.667 8.65 12.24 35.07 3.36
194 195 2.362503 ATGGTCGCCGGAGAGACA 60.363 61.111 21.14 17.66 36.88 3.41
195 196 1.982395 ATGGTCGCCGGAGAGACAA 60.982 57.895 21.14 13.87 36.88 3.18
196 197 1.949847 ATGGTCGCCGGAGAGACAAG 61.950 60.000 21.14 0.00 36.88 3.16
205 233 2.700897 CCGGAGAGACAAGTATTCCCAT 59.299 50.000 0.00 0.00 0.00 4.00
211 239 0.539986 ACAAGTATTCCCATCGCCGT 59.460 50.000 0.00 0.00 0.00 5.68
216 244 2.396747 TATTCCCATCGCCGTCGTCG 62.397 60.000 0.00 0.00 36.96 5.12
220 248 3.594827 CATCGCCGTCGTCGTTCG 61.595 66.667 0.71 4.65 41.41 3.95
228 256 2.099638 TCGTCGTTCGCTCCATCG 59.900 61.111 0.00 0.00 39.67 3.84
267 295 7.308109 CGAGGACACTAAGCCTAGATAAACTAG 60.308 44.444 0.00 0.00 45.77 2.57
402 430 4.667573 TCCCTATCTACTGTAGCATGGAG 58.332 47.826 9.98 2.99 0.00 3.86
506 625 1.179174 CCTCATCTGGGCCGTCGATA 61.179 60.000 0.00 0.00 0.00 2.92
526 645 3.838271 GAGATCCGACGGCAGGCA 61.838 66.667 9.66 0.00 0.00 4.75
570 689 1.513373 CGTCGCGATTCCGAACTCA 60.513 57.895 14.06 0.00 39.17 3.41
628 747 0.468214 TGAGATAGTCGGGCTCAGGG 60.468 60.000 0.00 0.00 34.02 4.45
708 827 2.343758 CCCGTGTCTCCACCACAG 59.656 66.667 0.00 0.00 38.41 3.66
715 834 3.625897 CTCCACCACAGTCCCGCA 61.626 66.667 0.00 0.00 0.00 5.69
801 921 3.364964 ACCTCCCTCGGATCCCCA 61.365 66.667 6.06 0.00 0.00 4.96
837 958 1.602323 ACGCAAATCCTTTCGGCCA 60.602 52.632 2.24 0.00 0.00 5.36
1642 2047 4.083696 CCAACGAACGGTAATTTTACTGCT 60.084 41.667 8.81 0.00 42.44 4.24
1681 2112 0.247460 TGGTGCCTCTGACGATTGAG 59.753 55.000 0.00 0.00 0.00 3.02
1682 2113 0.532573 GGTGCCTCTGACGATTGAGA 59.467 55.000 0.00 0.00 32.44 3.27
1693 2124 8.454106 CCTCTGACGATTGAGAAAAATATTTGT 58.546 33.333 0.39 0.00 32.44 2.83
1847 2283 5.495640 TGATGGCCCATTTATTTTGTTTCC 58.504 37.500 0.00 0.00 0.00 3.13
1907 2343 3.733337 TCTTGTGCTCCTCTCTTTGTTC 58.267 45.455 0.00 0.00 0.00 3.18
2017 2453 3.419858 CCCTCTGGGCTTGATGGT 58.580 61.111 0.00 0.00 35.35 3.55
2083 2522 3.431415 ACTGCCCCCTTTCACTTTATTC 58.569 45.455 0.00 0.00 0.00 1.75
2223 2662 5.314923 GACAAACTATGCCACATTGTCAT 57.685 39.130 10.98 0.00 45.63 3.06
2238 2677 5.355350 ACATTGTCATAACTTGCTCTAAGCC 59.645 40.000 0.00 0.00 41.51 4.35
2646 3086 8.568794 AGTAAGAAGCAACTATTCCTTTTTCAC 58.431 33.333 0.00 0.00 0.00 3.18
2696 3136 6.583806 CACAAATAAAGGACAATGTGCTTCTC 59.416 38.462 19.99 0.00 43.05 2.87
2701 3141 4.833478 AGGACAATGTGCTTCTCTGTAT 57.167 40.909 0.28 0.00 27.37 2.29
2721 3161 2.747855 CCCAGTTTCGGCTGCTCC 60.748 66.667 0.00 0.00 35.28 4.70
2750 3190 9.657419 AGAATTTTAATGTCCAGCCTATTTTTG 57.343 29.630 0.00 0.00 0.00 2.44
2771 3211 3.761218 TGTGTTTGTGGTGATGAACTGTT 59.239 39.130 0.00 0.00 0.00 3.16
2779 3221 3.569277 TGGTGATGAACTGTTCCACATTG 59.431 43.478 22.57 0.00 0.00 2.82
2809 3251 6.508777 ACTTGCTCTAAGCTTAGCTATGTAC 58.491 40.000 25.83 11.38 42.97 2.90
2810 3252 6.322712 ACTTGCTCTAAGCTTAGCTATGTACT 59.677 38.462 25.83 4.10 42.97 2.73
2811 3253 6.320494 TGCTCTAAGCTTAGCTATGTACTC 57.680 41.667 25.83 8.87 42.97 2.59
2812 3254 5.241949 TGCTCTAAGCTTAGCTATGTACTCC 59.758 44.000 25.83 7.01 42.97 3.85
2813 3255 5.336134 GCTCTAAGCTTAGCTATGTACTCCC 60.336 48.000 25.83 2.41 38.25 4.30
2814 3256 5.954757 TCTAAGCTTAGCTATGTACTCCCT 58.045 41.667 25.83 0.00 38.25 4.20
2815 3257 6.005198 TCTAAGCTTAGCTATGTACTCCCTC 58.995 44.000 25.83 0.00 38.25 4.30
2816 3258 3.502356 AGCTTAGCTATGTACTCCCTCC 58.498 50.000 4.30 0.00 36.99 4.30
2817 3259 2.229302 GCTTAGCTATGTACTCCCTCCG 59.771 54.545 8.30 0.00 0.00 4.63
2818 3260 3.488363 CTTAGCTATGTACTCCCTCCGT 58.512 50.000 0.00 0.00 0.00 4.69
2819 3261 2.456073 AGCTATGTACTCCCTCCGTT 57.544 50.000 0.00 0.00 0.00 4.44
2820 3262 2.308690 AGCTATGTACTCCCTCCGTTC 58.691 52.381 0.00 0.00 0.00 3.95
2821 3263 2.029623 GCTATGTACTCCCTCCGTTCA 58.970 52.381 0.00 0.00 0.00 3.18
2822 3264 2.034812 GCTATGTACTCCCTCCGTTCAG 59.965 54.545 0.00 0.00 0.00 3.02
2823 3265 2.526888 ATGTACTCCCTCCGTTCAGA 57.473 50.000 0.00 0.00 0.00 3.27
2824 3266 2.297698 TGTACTCCCTCCGTTCAGAA 57.702 50.000 0.00 0.00 0.00 3.02
2825 3267 2.816411 TGTACTCCCTCCGTTCAGAAT 58.184 47.619 0.00 0.00 0.00 2.40
2826 3268 3.170717 TGTACTCCCTCCGTTCAGAATT 58.829 45.455 0.00 0.00 0.00 2.17
2827 3269 4.346730 TGTACTCCCTCCGTTCAGAATTA 58.653 43.478 0.00 0.00 0.00 1.40
2828 3270 3.889520 ACTCCCTCCGTTCAGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2829 3271 3.442076 ACTCCCTCCGTTCAGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2830 3272 3.447944 ACTCCCTCCGTTCAGAATTACTC 59.552 47.826 0.00 0.00 0.00 2.59
2831 3273 2.426024 TCCCTCCGTTCAGAATTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
2832 3274 2.165845 CCCTCCGTTCAGAATTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
2833 3275 3.436496 CCTCCGTTCAGAATTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
2834 3276 3.436496 CTCCGTTCAGAATTACTCGTCC 58.564 50.000 0.00 0.00 0.00 4.79
2835 3277 2.821378 TCCGTTCAGAATTACTCGTCCA 59.179 45.455 0.00 0.00 0.00 4.02
2836 3278 3.256383 TCCGTTCAGAATTACTCGTCCAA 59.744 43.478 0.00 0.00 0.00 3.53
2837 3279 3.612860 CCGTTCAGAATTACTCGTCCAAG 59.387 47.826 0.00 0.00 0.00 3.61
2838 3280 4.482386 CGTTCAGAATTACTCGTCCAAGA 58.518 43.478 0.00 0.00 0.00 3.02
2839 3281 4.921515 CGTTCAGAATTACTCGTCCAAGAA 59.078 41.667 0.00 0.00 0.00 2.52
2840 3282 5.404366 CGTTCAGAATTACTCGTCCAAGAAA 59.596 40.000 0.00 0.00 0.00 2.52
2841 3283 6.090898 CGTTCAGAATTACTCGTCCAAGAAAT 59.909 38.462 0.00 0.00 0.00 2.17
2842 3284 6.968131 TCAGAATTACTCGTCCAAGAAATG 57.032 37.500 0.00 0.00 0.00 2.32
2843 3285 6.697395 TCAGAATTACTCGTCCAAGAAATGA 58.303 36.000 0.00 0.00 0.00 2.57
2844 3286 7.158697 TCAGAATTACTCGTCCAAGAAATGAA 58.841 34.615 0.00 0.00 0.00 2.57
2845 3287 7.824289 TCAGAATTACTCGTCCAAGAAATGAAT 59.176 33.333 0.00 0.00 0.00 2.57
2846 3288 7.907045 CAGAATTACTCGTCCAAGAAATGAATG 59.093 37.037 0.00 0.00 0.00 2.67
2847 3289 7.607991 AGAATTACTCGTCCAAGAAATGAATGT 59.392 33.333 0.00 0.00 0.00 2.71
2848 3290 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2849 3291 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2850 3292 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2851 3293 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2852 3294 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2853 3295 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2854 3296 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
2855 3297 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
2856 3298 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
2857 3299 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
2888 3330 8.862325 AGTTGTAGATACATCCATTTTTGTGA 57.138 30.769 0.00 0.00 35.89 3.58
2889 3331 8.730680 AGTTGTAGATACATCCATTTTTGTGAC 58.269 33.333 0.00 0.00 35.89 3.67
2890 3332 8.511321 GTTGTAGATACATCCATTTTTGTGACA 58.489 33.333 0.00 0.00 35.89 3.58
2891 3333 8.628630 TGTAGATACATCCATTTTTGTGACAA 57.371 30.769 0.00 0.00 0.00 3.18
2892 3334 8.729756 TGTAGATACATCCATTTTTGTGACAAG 58.270 33.333 0.00 0.00 0.00 3.16
2893 3335 7.765695 AGATACATCCATTTTTGTGACAAGT 57.234 32.000 0.00 0.00 0.00 3.16
2894 3336 8.862325 AGATACATCCATTTTTGTGACAAGTA 57.138 30.769 0.00 0.00 0.00 2.24
2895 3337 9.295825 AGATACATCCATTTTTGTGACAAGTAA 57.704 29.630 0.00 0.00 0.00 2.24
2898 3340 8.816640 ACATCCATTTTTGTGACAAGTAATTC 57.183 30.769 0.00 0.00 0.00 2.17
2899 3341 7.872483 ACATCCATTTTTGTGACAAGTAATTCC 59.128 33.333 0.00 0.00 0.00 3.01
2900 3342 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
2901 3343 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
2902 3344 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
2903 3345 7.096230 CCATTTTTGTGACAAGTAATTCCGAAC 60.096 37.037 0.00 0.00 0.00 3.95
2904 3346 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
2905 3347 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
2906 3348 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
2907 3349 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
2908 3350 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2909 3351 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2910 3352 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2911 3353 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2912 3354 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2913 3355 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3171 3675 3.140325 TCTGCGGGAAAGATGAAAACT 57.860 42.857 0.00 0.00 0.00 2.66
3390 3896 0.825010 CCTTGTGCAGCTTCAGGGTT 60.825 55.000 9.85 0.00 0.00 4.11
3398 3904 2.810400 GCAGCTTCAGGGTTCTGTGTTA 60.810 50.000 0.00 0.00 41.59 2.41
3487 3996 6.719829 TCTTCACTTCAGTATCACACTCCTTA 59.280 38.462 0.00 0.00 34.26 2.69
3526 4036 4.341366 TGTCAGTGTGTCACTCATCATT 57.659 40.909 4.27 0.00 43.43 2.57
3537 4047 4.749099 GTCACTCATCATTGCCATCTCTAC 59.251 45.833 0.00 0.00 0.00 2.59
3597 4108 7.289317 TGGACCACGATATTCTTTAGTTATCCT 59.711 37.037 0.00 0.00 0.00 3.24
3659 4170 9.092876 GGTTTTGTTTTCACTTGAATGTTCATA 57.907 29.630 0.00 0.00 37.00 2.15
3718 4241 1.956477 TGCTCACTTGAGGGCTTTTTC 59.044 47.619 8.32 0.00 42.29 2.29
3731 4254 6.101650 AGGGCTTTTTCTGGAACAAATTAG 57.898 37.500 0.00 0.00 38.70 1.73
3734 4257 6.765989 GGGCTTTTTCTGGAACAAATTAGTTT 59.234 34.615 0.00 0.00 38.70 2.66
3820 4345 7.649973 CCACGCTAGTAATCTATTTACAGTCT 58.350 38.462 0.00 0.00 42.30 3.24
3849 4374 3.673809 CCGTTCTCTTGTGTTAGCACTAC 59.326 47.826 11.22 0.00 45.44 2.73
3891 4433 4.037222 TCTGTGAAGCCTATATTGTGGGA 58.963 43.478 0.00 0.00 0.00 4.37
4008 4555 6.801539 TCTGTTATTTAGTTCTTGCCACAG 57.198 37.500 0.00 0.00 0.00 3.66
4078 4625 6.593770 ACAAGAAAACTGGTTCCATGTTTTTC 59.406 34.615 21.00 18.96 41.89 2.29
4079 4626 6.544928 AGAAAACTGGTTCCATGTTTTTCT 57.455 33.333 21.00 20.10 41.89 2.52
4080 4627 6.946340 AGAAAACTGGTTCCATGTTTTTCTT 58.054 32.000 21.00 13.41 41.89 2.52
4102 4649 7.760437 TCTTTTTCTTTTCAAAAGGCCATTTG 58.240 30.769 24.24 24.24 40.33 2.32
4103 4650 7.609532 TCTTTTTCTTTTCAAAAGGCCATTTGA 59.390 29.630 27.71 27.71 45.07 2.69
4104 4651 6.923928 TTTCTTTTCAAAAGGCCATTTGAG 57.076 33.333 29.05 20.59 46.63 3.02
4105 4652 5.612725 TCTTTTCAAAAGGCCATTTGAGT 57.387 34.783 29.05 0.00 46.63 3.41
4106 4653 6.723298 TCTTTTCAAAAGGCCATTTGAGTA 57.277 33.333 29.05 20.75 46.63 2.59
4107 4654 6.512297 TCTTTTCAAAAGGCCATTTGAGTAC 58.488 36.000 29.05 0.00 46.63 2.73
4111 4658 5.841810 TCAAAAGGCCATTTGAGTACTTTG 58.158 37.500 27.71 4.65 42.68 2.77
4113 4660 2.875296 AGGCCATTTGAGTACTTTGCA 58.125 42.857 5.01 0.00 0.00 4.08
4114 4661 3.230134 AGGCCATTTGAGTACTTTGCAA 58.770 40.909 5.01 0.00 0.00 4.08
4116 4663 4.284234 AGGCCATTTGAGTACTTTGCAAAT 59.716 37.500 13.23 12.80 41.44 2.32
4117 4664 4.996758 GGCCATTTGAGTACTTTGCAAATT 59.003 37.500 13.23 9.97 39.46 1.82
4118 4665 5.120674 GGCCATTTGAGTACTTTGCAAATTC 59.879 40.000 13.23 8.90 39.46 2.17
4122 4674 7.116805 CCATTTGAGTACTTTGCAAATTCCTTC 59.883 37.037 13.23 7.91 39.46 3.46
4284 4838 1.670811 CGTTTCTGTGCCTTGTGTCTT 59.329 47.619 0.00 0.00 0.00 3.01
4426 4980 1.429463 CCAAAGGTACGCTGACTGAC 58.571 55.000 0.00 0.00 0.00 3.51
4526 5081 1.790623 GCAATTTGTTCTGTGCAGCAG 59.209 47.619 0.00 9.27 46.34 4.24
4592 5147 1.130938 GAAGAAGACGAGGACGAGGAC 59.869 57.143 0.00 0.00 42.66 3.85
5032 5598 1.593196 CAGGTGTGGACAATGTCGTT 58.407 50.000 7.35 0.00 32.65 3.85
5121 5687 5.911752 TGCAAAATGAACTGCCTTTCTTTA 58.088 33.333 0.00 0.00 37.79 1.85
5242 5808 4.883585 ACTGTTCATCTGTTTGAGCTTCAA 59.116 37.500 0.00 0.00 34.03 2.69
5276 5842 7.004086 ACCAAAGTGAAGGATTTCTACAATCA 58.996 34.615 0.00 0.00 34.31 2.57
5277 5843 7.671398 ACCAAAGTGAAGGATTTCTACAATCAT 59.329 33.333 0.00 0.00 34.31 2.45
5278 5844 7.972277 CCAAAGTGAAGGATTTCTACAATCATG 59.028 37.037 0.00 0.00 34.31 3.07
5280 5846 6.962182 AGTGAAGGATTTCTACAATCATGGA 58.038 36.000 0.00 0.00 34.31 3.41
5281 5847 7.052873 AGTGAAGGATTTCTACAATCATGGAG 58.947 38.462 0.00 0.00 39.04 3.86
5282 5848 5.824624 TGAAGGATTTCTACAATCATGGAGC 59.175 40.000 0.00 0.00 37.43 4.70
5283 5849 5.643421 AGGATTTCTACAATCATGGAGCT 57.357 39.130 0.00 0.00 37.43 4.09
5284 5850 5.619220 AGGATTTCTACAATCATGGAGCTC 58.381 41.667 4.71 4.71 37.43 4.09
5285 5851 5.369110 AGGATTTCTACAATCATGGAGCTCT 59.631 40.000 14.64 0.00 37.43 4.09
5286 5852 6.556495 AGGATTTCTACAATCATGGAGCTCTA 59.444 38.462 14.64 8.26 37.43 2.43
5287 5853 7.237263 AGGATTTCTACAATCATGGAGCTCTAT 59.763 37.037 14.64 10.73 37.43 1.98
5288 5854 7.333921 GGATTTCTACAATCATGGAGCTCTATG 59.666 40.741 28.88 28.88 37.43 2.23
5289 5855 6.737720 TTCTACAATCATGGAGCTCTATGT 57.262 37.500 31.71 20.69 37.43 2.29
5290 5856 7.839680 TTCTACAATCATGGAGCTCTATGTA 57.160 36.000 31.71 20.70 37.43 2.29
5291 5857 7.459795 TCTACAATCATGGAGCTCTATGTAG 57.540 40.000 31.71 26.89 37.43 2.74
5292 5858 7.234355 TCTACAATCATGGAGCTCTATGTAGA 58.766 38.462 31.71 28.26 43.20 2.59
5293 5859 6.737720 ACAATCATGGAGCTCTATGTAGAA 57.262 37.500 31.71 17.99 36.40 2.10
5294 5860 7.313740 ACAATCATGGAGCTCTATGTAGAAT 57.686 36.000 31.71 19.22 36.40 2.40
5295 5861 7.743749 ACAATCATGGAGCTCTATGTAGAATT 58.256 34.615 31.71 22.90 36.40 2.17
5302 5868 7.050377 TGGAGCTCTATGTAGAATTTCTTTGG 58.950 38.462 14.64 0.00 0.00 3.28
5305 5871 6.758886 AGCTCTATGTAGAATTTCTTTGGACG 59.241 38.462 3.86 0.00 0.00 4.79
5308 5874 8.475331 TCTATGTAGAATTTCTTTGGACGAAC 57.525 34.615 3.86 0.00 0.00 3.95
5334 5900 4.343814 CCAAGGTCTATTTGGTGGTTTGTT 59.656 41.667 0.00 0.00 40.15 2.83
5397 5963 5.687166 ATTCCTACGAATTGGACACCTAA 57.313 39.130 0.00 0.00 35.00 2.69
5398 5964 4.460948 TCCTACGAATTGGACACCTAAC 57.539 45.455 0.00 0.00 0.00 2.34
5401 5967 4.159879 CCTACGAATTGGACACCTAACTCT 59.840 45.833 0.00 0.00 0.00 3.24
5409 5975 5.105567 TGGACACCTAACTCTTGACAAAA 57.894 39.130 0.00 0.00 0.00 2.44
5431 5998 0.890996 CCCTTGCACAACTCTCCCAC 60.891 60.000 0.00 0.00 0.00 4.61
5449 6016 1.597027 CGGAAGAAGCCACGGTTGT 60.597 57.895 0.00 0.00 0.00 3.32
5471 6039 2.183679 CCCTACTCCAAGTTCTGCTCT 58.816 52.381 0.00 0.00 0.00 4.09
5500 6068 1.832883 CAATCCCCACCGAAATGTCA 58.167 50.000 0.00 0.00 0.00 3.58
5508 6076 1.603802 CACCGAAATGTCACTGCACTT 59.396 47.619 0.00 0.00 0.00 3.16
5531 6099 3.445096 GCTAATGTTTGAGGAACCTGCAT 59.555 43.478 0.00 0.00 37.45 3.96
5561 6129 5.579119 CACACATCAATAGTTAACCGCACTA 59.421 40.000 0.88 0.00 0.00 2.74
5571 6139 4.279169 AGTTAACCGCACTACTTGACAGTA 59.721 41.667 0.88 0.00 34.06 2.74
5580 6148 7.744715 CCGCACTACTTGACAGTAAAATAAAAG 59.255 37.037 0.00 0.00 34.94 2.27
5622 6207 1.314730 GCCTCACCCGTGAAAAGAAA 58.685 50.000 0.00 0.00 39.39 2.52
5667 6252 1.621072 CCTCCAACAGCTCCCTACTCT 60.621 57.143 0.00 0.00 0.00 3.24
5670 6255 0.827368 CAACAGCTCCCTACTCTCCC 59.173 60.000 0.00 0.00 0.00 4.30
5769 6354 0.591659 AAAAACGCTCTTCTTCCGCC 59.408 50.000 0.00 0.00 0.00 6.13
5770 6355 0.534203 AAAACGCTCTTCTTCCGCCA 60.534 50.000 0.00 0.00 0.00 5.69
5771 6356 0.321653 AAACGCTCTTCTTCCGCCAT 60.322 50.000 0.00 0.00 0.00 4.40
5772 6357 0.535335 AACGCTCTTCTTCCGCCATA 59.465 50.000 0.00 0.00 0.00 2.74
5773 6358 0.179108 ACGCTCTTCTTCCGCCATAC 60.179 55.000 0.00 0.00 0.00 2.39
5774 6359 1.209275 CGCTCTTCTTCCGCCATACG 61.209 60.000 0.00 0.00 43.15 3.06
5775 6360 1.491505 GCTCTTCTTCCGCCATACGC 61.492 60.000 0.00 0.00 41.76 4.42
5776 6361 0.179111 CTCTTCTTCCGCCATACGCA 60.179 55.000 0.00 0.00 41.76 5.24
5777 6362 0.248012 TCTTCTTCCGCCATACGCAA 59.752 50.000 0.00 0.00 41.76 4.85
5778 6363 1.134521 TCTTCTTCCGCCATACGCAAT 60.135 47.619 0.00 0.00 41.76 3.56
5779 6364 1.670811 CTTCTTCCGCCATACGCAATT 59.329 47.619 0.00 0.00 41.76 2.32
5780 6365 1.013596 TCTTCCGCCATACGCAATTG 58.986 50.000 0.00 0.00 41.76 2.32
5781 6366 1.013596 CTTCCGCCATACGCAATTGA 58.986 50.000 10.34 0.00 41.76 2.57
5782 6367 1.400142 CTTCCGCCATACGCAATTGAA 59.600 47.619 10.34 0.00 41.76 2.69
5783 6368 1.013596 TCCGCCATACGCAATTGAAG 58.986 50.000 10.34 4.66 41.76 3.02
5784 6369 0.592247 CCGCCATACGCAATTGAAGC 60.592 55.000 10.34 0.94 41.76 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.397413 CTGGTCGGTGGAGTGGCTTT 62.397 60.000 0.00 0.00 0.00 3.51
38 39 1.234615 GCTTGTGTAAGGGCGAAGCA 61.235 55.000 0.00 0.00 45.15 3.91
39 40 1.502190 GCTTGTGTAAGGGCGAAGC 59.498 57.895 0.00 0.00 43.57 3.86
45 46 1.666553 TCGTGCGCTTGTGTAAGGG 60.667 57.895 9.73 0.00 46.39 3.95
46 47 1.218875 TGTCGTGCGCTTGTGTAAGG 61.219 55.000 9.73 0.00 34.40 2.69
69 70 2.378038 CTCATGTTGGTGGGTATTGGG 58.622 52.381 0.00 0.00 0.00 4.12
73 74 0.998928 TGGCTCATGTTGGTGGGTAT 59.001 50.000 0.00 0.00 0.00 2.73
78 79 3.327600 TGAGTGGCTCATGTTGGTG 57.672 52.632 0.00 0.00 35.39 4.17
86 87 1.184970 TGGTGACGATGAGTGGCTCA 61.185 55.000 1.06 1.06 44.99 4.26
91 92 0.784178 CGTTGTGGTGACGATGAGTG 59.216 55.000 0.00 0.00 42.82 3.51
114 115 2.421424 GCATTGGATCGTTTCTTCAGCT 59.579 45.455 0.00 0.00 0.00 4.24
116 117 2.223112 CGGCATTGGATCGTTTCTTCAG 60.223 50.000 0.00 0.00 0.00 3.02
176 177 2.105128 GTCTCTCCGGCGACCATG 59.895 66.667 9.30 0.00 0.00 3.66
177 178 1.949847 CTTGTCTCTCCGGCGACCAT 61.950 60.000 9.30 0.00 0.00 3.55
178 179 2.599281 TTGTCTCTCCGGCGACCA 60.599 61.111 9.30 1.35 0.00 4.02
180 181 0.739561 ATACTTGTCTCTCCGGCGAC 59.260 55.000 9.30 3.84 0.00 5.19
181 182 1.404391 GAATACTTGTCTCTCCGGCGA 59.596 52.381 9.30 0.00 0.00 5.54
182 183 1.536284 GGAATACTTGTCTCTCCGGCG 60.536 57.143 0.00 0.00 0.00 6.46
183 184 1.202545 GGGAATACTTGTCTCTCCGGC 60.203 57.143 0.00 0.00 0.00 6.13
186 187 3.800604 GCGATGGGAATACTTGTCTCTCC 60.801 52.174 0.00 0.00 0.00 3.71
187 188 3.385577 GCGATGGGAATACTTGTCTCTC 58.614 50.000 0.00 0.00 0.00 3.20
188 189 2.103263 GGCGATGGGAATACTTGTCTCT 59.897 50.000 0.00 0.00 0.00 3.10
191 192 1.217882 CGGCGATGGGAATACTTGTC 58.782 55.000 0.00 0.00 0.00 3.18
192 193 0.539986 ACGGCGATGGGAATACTTGT 59.460 50.000 16.62 0.00 0.00 3.16
193 194 1.217882 GACGGCGATGGGAATACTTG 58.782 55.000 16.62 0.00 0.00 3.16
194 195 0.249322 CGACGGCGATGGGAATACTT 60.249 55.000 16.62 0.00 40.82 2.24
195 196 1.362717 CGACGGCGATGGGAATACT 59.637 57.895 16.62 0.00 40.82 2.12
196 197 0.938168 GACGACGGCGATGGGAATAC 60.938 60.000 22.49 0.00 41.64 1.89
211 239 1.914531 TTCGATGGAGCGAACGACGA 61.915 55.000 0.00 0.00 44.43 4.20
220 248 2.799540 GACGGCGTTTCGATGGAGC 61.800 63.158 16.19 0.00 0.00 4.70
267 295 2.677037 GCCCGGTATGCATACATCTACC 60.677 54.545 32.19 19.15 37.74 3.18
278 306 3.199891 GTTGTCCGCCCGGTATGC 61.200 66.667 6.61 0.00 36.47 3.14
359 387 3.195698 GGAAGACGGTGCCATCGC 61.196 66.667 0.00 0.00 0.00 4.58
362 390 1.141053 GGATAAGGAAGACGGTGCCAT 59.859 52.381 0.00 0.00 0.00 4.40
402 430 2.607635 TGTTTTCGAACAGAGTGTGCTC 59.392 45.455 0.00 0.00 41.94 4.26
506 625 3.893763 CTGCCGTCGGATCTCGCT 61.894 66.667 17.49 0.00 39.05 4.93
540 659 4.070818 GCGACGTGACATTGCGCA 62.071 61.111 5.66 5.66 46.19 6.09
702 821 4.250305 GGTGTGCGGGACTGTGGT 62.250 66.667 0.31 0.00 0.00 4.16
788 908 2.205462 ATCCTGGGGATCCGAGGG 59.795 66.667 22.50 15.87 38.09 4.30
815 935 1.578926 CGAAAGGATTTGCGTGGCA 59.421 52.632 0.00 0.00 39.27 4.92
837 958 4.010667 TCGGTTTTATTACACTGTGCCT 57.989 40.909 7.90 0.00 0.00 4.75
928 1050 2.443016 CTCGAGGGAGAGGGGTGG 60.443 72.222 3.91 0.00 43.27 4.61
930 1052 3.351885 AGCTCGAGGGAGAGGGGT 61.352 66.667 15.58 0.00 43.27 4.95
1642 2047 4.220821 ACCAAGCTGAGAGAAATCGAACTA 59.779 41.667 0.00 0.00 0.00 2.24
1847 2283 1.114722 ACATGCACCAACCACCAAGG 61.115 55.000 0.00 0.00 45.67 3.61
1907 2343 5.853282 CGATACACTCAAAGCAAAGAAAAGG 59.147 40.000 0.00 0.00 0.00 3.11
2017 2453 8.439971 ACAGCTGAAAACCTATGGATTATATCA 58.560 33.333 23.35 0.00 0.00 2.15
2036 2472 4.502105 TTTCATATGGCCTAACAGCTGA 57.498 40.909 23.35 0.00 0.00 4.26
2095 2534 7.468441 CACGCAATCCTTTATTTGTGTATGTA 58.532 34.615 1.99 0.00 31.31 2.29
2183 2622 4.371855 TGTCACCGCAAACACAAAAATA 57.628 36.364 0.00 0.00 0.00 1.40
2223 2662 6.732896 AATAGCTAGGCTTAGAGCAAGTTA 57.267 37.500 7.11 2.25 44.75 2.24
2590 3030 9.774413 CCGAACTCCACCTTTATATTTACTTAT 57.226 33.333 0.00 0.00 0.00 1.73
2591 3031 7.712205 GCCGAACTCCACCTTTATATTTACTTA 59.288 37.037 0.00 0.00 0.00 2.24
2614 3054 5.177696 GGAATAGTTGCTTCTTACTATGCCG 59.822 44.000 0.00 0.00 41.16 5.69
2686 3126 4.018960 ACTGGGAAATACAGAGAAGCACAT 60.019 41.667 0.00 0.00 39.24 3.21
2696 3136 2.420022 CAGCCGAAACTGGGAAATACAG 59.580 50.000 0.00 0.00 41.64 2.74
2701 3141 0.889186 GAGCAGCCGAAACTGGGAAA 60.889 55.000 0.00 0.00 38.16 3.13
2721 3161 9.657419 AAATAGGCTGGACATTAAAATTCTTTG 57.343 29.630 0.00 0.00 0.00 2.77
2750 3190 4.351192 GAACAGTTCATCACCACAAACAC 58.649 43.478 8.54 0.00 0.00 3.32
2771 3211 0.388659 GCAAGTTGTGGCAATGTGGA 59.611 50.000 4.48 0.00 0.00 4.02
2779 3221 1.528129 AGCTTAGAGCAAGTTGTGGC 58.472 50.000 4.48 1.06 45.56 5.01
2809 3251 3.489398 CGAGTAATTCTGAACGGAGGGAG 60.489 52.174 0.00 0.00 0.00 4.30
2810 3252 2.426024 CGAGTAATTCTGAACGGAGGGA 59.574 50.000 0.00 0.00 0.00 4.20
2811 3253 2.165845 ACGAGTAATTCTGAACGGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
2812 3254 3.436496 GACGAGTAATTCTGAACGGAGG 58.564 50.000 0.00 0.00 0.00 4.30
2813 3255 3.119602 TGGACGAGTAATTCTGAACGGAG 60.120 47.826 0.00 0.00 0.00 4.63
2814 3256 2.821378 TGGACGAGTAATTCTGAACGGA 59.179 45.455 0.00 0.00 0.00 4.69
2815 3257 3.226346 TGGACGAGTAATTCTGAACGG 57.774 47.619 0.00 0.00 0.00 4.44
2816 3258 4.482386 TCTTGGACGAGTAATTCTGAACG 58.518 43.478 0.00 0.00 0.00 3.95
2817 3259 6.780706 TTTCTTGGACGAGTAATTCTGAAC 57.219 37.500 0.00 0.00 0.00 3.18
2818 3260 7.158697 TCATTTCTTGGACGAGTAATTCTGAA 58.841 34.615 0.00 0.00 0.00 3.02
2819 3261 6.697395 TCATTTCTTGGACGAGTAATTCTGA 58.303 36.000 0.00 0.00 0.00 3.27
2820 3262 6.968131 TCATTTCTTGGACGAGTAATTCTG 57.032 37.500 0.00 0.00 0.00 3.02
2821 3263 7.607991 ACATTCATTTCTTGGACGAGTAATTCT 59.392 33.333 0.00 0.00 0.00 2.40
2822 3264 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2823 3265 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2824 3266 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2825 3267 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2826 3268 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
2827 3269 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
2828 3270 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
2829 3271 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
2830 3272 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
2831 3273 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
2862 3304 9.952030 TCACAAAAATGGATGTATCTACAACTA 57.048 29.630 0.00 0.00 39.99 2.24
2863 3305 8.730680 GTCACAAAAATGGATGTATCTACAACT 58.269 33.333 0.00 0.00 39.99 3.16
2864 3306 8.511321 TGTCACAAAAATGGATGTATCTACAAC 58.489 33.333 0.00 0.00 39.99 3.32
2865 3307 8.628630 TGTCACAAAAATGGATGTATCTACAA 57.371 30.769 0.00 0.00 39.99 2.41
2866 3308 8.628630 TTGTCACAAAAATGGATGTATCTACA 57.371 30.769 0.00 0.00 40.98 2.74
2867 3309 8.730680 ACTTGTCACAAAAATGGATGTATCTAC 58.269 33.333 0.00 0.00 0.00 2.59
2868 3310 8.862325 ACTTGTCACAAAAATGGATGTATCTA 57.138 30.769 0.00 0.00 0.00 1.98
2869 3311 7.765695 ACTTGTCACAAAAATGGATGTATCT 57.234 32.000 0.00 0.00 0.00 1.98
2872 3314 9.906660 GAATTACTTGTCACAAAAATGGATGTA 57.093 29.630 0.00 0.00 0.00 2.29
2873 3315 7.872483 GGAATTACTTGTCACAAAAATGGATGT 59.128 33.333 0.00 0.00 0.00 3.06
2874 3316 7.062138 CGGAATTACTTGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
2875 3317 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
2876 3318 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
2877 3319 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
2878 3320 7.357206 CGTTCGGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
2879 3321 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
2880 3322 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
2881 3323 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
2882 3324 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
2883 3325 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
2884 3326 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
2885 3327 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
2886 3328 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
2887 3329 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2888 3330 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2889 3331 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2890 3332 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2891 3333 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2892 3334 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2893 3335 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2894 3336 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2895 3337 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
2896 3338 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
2897 3339 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
2898 3340 0.455005 GTTCTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30
2899 3341 0.455005 GGTTCTACTCCCTCCGTTCG 59.545 60.000 0.00 0.00 0.00 3.95
2900 3342 0.455005 CGGTTCTACTCCCTCCGTTC 59.545 60.000 0.00 0.00 36.99 3.95
2901 3343 0.038744 TCGGTTCTACTCCCTCCGTT 59.961 55.000 0.00 0.00 41.58 4.44
2902 3344 0.038744 TTCGGTTCTACTCCCTCCGT 59.961 55.000 0.00 0.00 41.58 4.69
2903 3345 0.739561 CTTCGGTTCTACTCCCTCCG 59.260 60.000 0.00 0.00 42.12 4.63
2904 3346 2.140839 TCTTCGGTTCTACTCCCTCC 57.859 55.000 0.00 0.00 0.00 4.30
2905 3347 3.288964 TGATCTTCGGTTCTACTCCCTC 58.711 50.000 0.00 0.00 0.00 4.30
2906 3348 3.383698 TGATCTTCGGTTCTACTCCCT 57.616 47.619 0.00 0.00 0.00 4.20
2907 3349 4.081586 ACTTTGATCTTCGGTTCTACTCCC 60.082 45.833 0.00 0.00 0.00 4.30
2908 3350 4.865365 CACTTTGATCTTCGGTTCTACTCC 59.135 45.833 0.00 0.00 0.00 3.85
2909 3351 4.327627 GCACTTTGATCTTCGGTTCTACTC 59.672 45.833 0.00 0.00 0.00 2.59
2910 3352 4.246458 GCACTTTGATCTTCGGTTCTACT 58.754 43.478 0.00 0.00 0.00 2.57
2911 3353 3.371285 GGCACTTTGATCTTCGGTTCTAC 59.629 47.826 0.00 0.00 0.00 2.59
2912 3354 3.007506 TGGCACTTTGATCTTCGGTTCTA 59.992 43.478 0.00 0.00 0.00 2.10
2913 3355 2.224523 TGGCACTTTGATCTTCGGTTCT 60.225 45.455 0.00 0.00 0.00 3.01
3086 3588 8.844244 AGAAACAGAATGAACTCATAATATGCC 58.156 33.333 0.00 0.00 39.69 4.40
3190 3696 9.120538 GGTTGCTATTAACTCCATTTTGAGATA 57.879 33.333 0.00 0.00 36.22 1.98
3265 3771 6.954232 AGTGTAAGAAAGATTCCGGGATTAA 58.046 36.000 0.00 0.00 0.00 1.40
3270 3776 5.731591 AGTTAGTGTAAGAAAGATTCCGGG 58.268 41.667 0.00 0.00 0.00 5.73
3390 3896 9.838975 CAAAATTATGCACATTACTAACACAGA 57.161 29.630 0.00 0.00 0.00 3.41
3398 3904 8.121305 TGAAGGTCAAAATTATGCACATTACT 57.879 30.769 0.00 0.00 0.00 2.24
3487 3996 3.646162 TGACAAGATGTAACAGGTCCACT 59.354 43.478 0.00 0.00 0.00 4.00
3526 4036 7.395772 TCCAATTGTTAATTTGTAGAGATGGCA 59.604 33.333 4.43 0.00 0.00 4.92
3537 4047 6.007936 TCTCGTGGTCCAATTGTTAATTTG 57.992 37.500 4.43 0.00 0.00 2.32
3638 4149 8.519526 GGGTATATGAACATTCAAGTGAAAACA 58.480 33.333 0.00 0.00 41.13 2.83
3718 4241 7.454260 AGCCTTCTAAACTAATTTGTTCCAG 57.546 36.000 5.74 6.82 0.00 3.86
3798 4323 8.343366 TCACAGACTGTAAATAGATTACTAGCG 58.657 37.037 8.02 0.00 43.60 4.26
3820 4345 1.754803 ACACAAGAGAACGGAGTCACA 59.245 47.619 0.00 0.00 45.00 3.58
3849 4374 1.211457 AGCAGAGTGGGCCTTTATCTG 59.789 52.381 17.83 17.83 40.26 2.90
3909 4451 1.548081 CATCATTTGCCCTGTGTGGA 58.452 50.000 0.00 0.00 38.35 4.02
3910 4452 0.108520 GCATCATTTGCCCTGTGTGG 60.109 55.000 0.00 0.00 46.15 4.17
3911 4453 3.429043 GCATCATTTGCCCTGTGTG 57.571 52.632 0.00 0.00 46.15 3.82
3935 4482 2.512692 ATAGCAAGTGCATGGAACCA 57.487 45.000 6.00 0.00 45.16 3.67
4008 4555 3.343617 TGGCATAAACTTGACAGCTACC 58.656 45.455 0.00 0.00 29.17 3.18
4078 4625 7.760437 TCAAATGGCCTTTTGAAAAGAAAAAG 58.240 30.769 33.20 12.04 41.39 2.27
4079 4626 7.392953 ACTCAAATGGCCTTTTGAAAAGAAAAA 59.607 29.630 33.85 17.32 43.12 1.94
4080 4627 6.883756 ACTCAAATGGCCTTTTGAAAAGAAAA 59.116 30.769 33.85 17.86 43.12 2.29
4102 4649 6.739112 ACAAGAAGGAATTTGCAAAGTACTC 58.261 36.000 23.63 16.42 0.00 2.59
4103 4650 6.715347 ACAAGAAGGAATTTGCAAAGTACT 57.285 33.333 18.41 18.41 0.00 2.73
4104 4651 7.168135 CAGAACAAGAAGGAATTTGCAAAGTAC 59.832 37.037 18.19 16.09 0.00 2.73
4105 4652 7.147915 ACAGAACAAGAAGGAATTTGCAAAGTA 60.148 33.333 18.19 0.00 0.00 2.24
4106 4653 6.044682 CAGAACAAGAAGGAATTTGCAAAGT 58.955 36.000 18.19 15.58 0.00 2.66
4107 4654 6.044682 ACAGAACAAGAAGGAATTTGCAAAG 58.955 36.000 18.19 2.98 0.00 2.77
4111 4658 9.346725 CTAATAACAGAACAAGAAGGAATTTGC 57.653 33.333 0.00 0.00 0.00 3.68
4114 4661 9.574516 ACACTAATAACAGAACAAGAAGGAATT 57.425 29.630 0.00 0.00 0.00 2.17
4116 4663 8.974060 AACACTAATAACAGAACAAGAAGGAA 57.026 30.769 0.00 0.00 0.00 3.36
4142 4694 5.541953 AAAAGCAGCCAAGAGAAAAAGAT 57.458 34.783 0.00 0.00 0.00 2.40
4284 4838 0.603707 CTGAACAAGCGCTTCCTGGA 60.604 55.000 22.21 2.36 0.00 3.86
4592 5147 2.348591 GGTTTCGCTGTGTTCTTCTTCG 60.349 50.000 0.00 0.00 0.00 3.79
5039 5605 5.232202 GCACAATTCAATCATCATCAGCAAG 59.768 40.000 0.00 0.00 0.00 4.01
5074 5640 4.961438 AACACAAGCCAATCAGGAAATT 57.039 36.364 0.00 0.00 41.22 1.82
5079 5645 2.545106 GCAAAAACACAAGCCAATCAGG 59.455 45.455 0.00 0.00 41.84 3.86
5121 5687 2.363795 TCGGCCCTCAGACGGATT 60.364 61.111 0.00 0.00 0.00 3.01
5145 5711 1.453379 CTTCCGCTAGGGTCGAGGA 60.453 63.158 6.02 0.00 38.33 3.71
5150 5716 0.745468 CCTGTACTTCCGCTAGGGTC 59.255 60.000 6.02 0.00 38.33 4.46
5242 5808 6.983906 ATCCTTCACTTTGGTTCATTTCTT 57.016 33.333 0.00 0.00 0.00 2.52
5276 5842 7.718753 CCAAAGAAATTCTACATAGAGCTCCAT 59.281 37.037 10.93 0.00 33.21 3.41
5277 5843 7.050377 CCAAAGAAATTCTACATAGAGCTCCA 58.950 38.462 10.93 0.00 33.21 3.86
5278 5844 7.225734 GTCCAAAGAAATTCTACATAGAGCTCC 59.774 40.741 10.93 0.00 33.21 4.70
5280 5846 6.758886 CGTCCAAAGAAATTCTACATAGAGCT 59.241 38.462 0.00 0.00 33.21 4.09
5281 5847 6.757010 TCGTCCAAAGAAATTCTACATAGAGC 59.243 38.462 0.00 0.00 33.21 4.09
5282 5848 8.596380 GTTCGTCCAAAGAAATTCTACATAGAG 58.404 37.037 0.00 0.00 33.21 2.43
5283 5849 8.311836 AGTTCGTCCAAAGAAATTCTACATAGA 58.688 33.333 0.00 0.00 0.00 1.98
5284 5850 8.480643 AGTTCGTCCAAAGAAATTCTACATAG 57.519 34.615 0.00 0.00 0.00 2.23
5285 5851 9.362539 GTAGTTCGTCCAAAGAAATTCTACATA 57.637 33.333 0.00 0.00 31.07 2.29
5286 5852 7.333672 GGTAGTTCGTCCAAAGAAATTCTACAT 59.666 37.037 0.00 0.00 31.71 2.29
5287 5853 6.647895 GGTAGTTCGTCCAAAGAAATTCTACA 59.352 38.462 0.00 0.00 31.71 2.74
5288 5854 6.647895 TGGTAGTTCGTCCAAAGAAATTCTAC 59.352 38.462 0.00 0.00 30.47 2.59
5289 5855 6.761312 TGGTAGTTCGTCCAAAGAAATTCTA 58.239 36.000 0.00 0.00 0.00 2.10
5290 5856 5.617252 TGGTAGTTCGTCCAAAGAAATTCT 58.383 37.500 0.00 0.00 0.00 2.40
5291 5857 5.934935 TGGTAGTTCGTCCAAAGAAATTC 57.065 39.130 0.00 0.00 0.00 2.17
5292 5858 5.240844 CCTTGGTAGTTCGTCCAAAGAAATT 59.759 40.000 0.00 0.00 42.14 1.82
5293 5859 4.760204 CCTTGGTAGTTCGTCCAAAGAAAT 59.240 41.667 0.00 0.00 42.14 2.17
5294 5860 4.131596 CCTTGGTAGTTCGTCCAAAGAAA 58.868 43.478 0.00 0.00 42.14 2.52
5295 5861 3.135167 ACCTTGGTAGTTCGTCCAAAGAA 59.865 43.478 0.00 0.00 42.14 2.52
5302 5868 4.868734 CCAAATAGACCTTGGTAGTTCGTC 59.131 45.833 0.00 0.00 38.85 4.20
5359 5925 7.214381 TCGTAGGAATTGAAGAAACAAGAGAA 58.786 34.615 0.00 0.00 33.22 2.87
5389 5955 6.294010 GGGATTTTTGTCAAGAGTTAGGTGTC 60.294 42.308 0.00 0.00 0.00 3.67
5397 5963 3.960102 TGCAAGGGATTTTTGTCAAGAGT 59.040 39.130 0.00 0.00 0.00 3.24
5398 5964 4.202141 TGTGCAAGGGATTTTTGTCAAGAG 60.202 41.667 0.00 0.00 0.00 2.85
5401 5967 4.081198 AGTTGTGCAAGGGATTTTTGTCAA 60.081 37.500 0.00 0.00 0.00 3.18
5409 5975 1.272147 GGGAGAGTTGTGCAAGGGATT 60.272 52.381 0.00 0.00 0.00 3.01
5431 5998 1.164041 AACAACCGTGGCTTCTTCCG 61.164 55.000 0.00 0.00 0.00 4.30
5449 6016 2.567615 GAGCAGAACTTGGAGTAGGGAA 59.432 50.000 0.00 0.00 0.00 3.97
5471 6039 1.484038 GTGGGGATTGCTTTATGGCA 58.516 50.000 0.00 0.00 40.74 4.92
5500 6068 3.254166 CCTCAAACATTAGCAAGTGCAGT 59.746 43.478 6.00 0.00 45.16 4.40
5508 6076 2.819608 GCAGGTTCCTCAAACATTAGCA 59.180 45.455 0.00 0.00 39.81 3.49
5531 6099 6.348132 CGGTTAACTATTGATGTGTGCTTGAA 60.348 38.462 5.42 0.00 0.00 2.69
5580 6148 6.092122 GGCCAAAGTTTAGGATGTTAAAATGC 59.908 38.462 0.00 0.00 0.00 3.56
5622 6207 9.190317 GGAGAAATTAGATCTTAACCCACATTT 57.810 33.333 0.00 0.00 0.00 2.32
5677 6262 5.815581 TGTGGCAACTTCTCTTATACCAAT 58.184 37.500 0.00 0.00 37.61 3.16
5707 6292 1.192146 TAGGGAAGTTGCTGGAGCGT 61.192 55.000 0.00 0.00 45.83 5.07
5713 6298 7.410120 AAAAATAGGAATAGGGAAGTTGCTG 57.590 36.000 0.00 0.00 0.00 4.41
5750 6335 0.591659 GGCGGAAGAAGAGCGTTTTT 59.408 50.000 0.00 0.00 0.00 1.94
5755 6340 1.209275 CGTATGGCGGAAGAAGAGCG 61.209 60.000 0.00 0.00 36.85 5.03
5756 6341 1.491505 GCGTATGGCGGAAGAAGAGC 61.492 60.000 0.00 0.00 41.69 4.09
5757 6342 1.739035 TTGCGTATGGCGGAAGAAGAG 60.739 52.381 0.00 0.00 45.65 2.85
5758 6343 0.248012 TTGCGTATGGCGGAAGAAGA 59.752 50.000 0.00 0.00 45.65 2.87
5759 6344 2.762360 TTGCGTATGGCGGAAGAAG 58.238 52.632 0.00 0.00 45.65 2.85


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

AutoCloner maintained by Alex Coulton.