Multiple sequence alignment - TraesCS2D01G104200

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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 TraesCS2D01G104200 chr2D 100.000 3946 0 0 1 3946 56203785 56199840 0.000000e+00 7287.0
1 TraesCS2D01G104200 chr2D 90.882 340 15 4 2605 2942 56191468 56191143 3.620000e-120 442.0
2 TraesCS2D01G104200 chr2D 81.944 360 39 16 3486 3842 56190470 56190134 8.350000e-72 281.0
3 TraesCS2D01G104200 chr2D 93.798 129 7 1 3254 3382 56190872 56190745 4.020000e-45 193.0
4 TraesCS2D01G104200 chr2D 85.915 142 18 2 2260 2400 56192369 56192229 2.460000e-32 150.0
5 TraesCS2D01G104200 chr2D 92.857 98 4 3 3380 3477 56190648 56190554 5.320000e-29 139.0
6 TraesCS2D01G104200 chr2D 90.476 105 10 0 2399 2503 56191576 56191472 5.320000e-29 139.0
7 TraesCS2D01G104200 chr2B 96.295 3158 85 16 3 3142 88933628 88930485 0.000000e+00 5155.0
8 TraesCS2D01G104200 chr2B 95.679 162 6 1 2609 2769 88919424 88919263 3.910000e-65 259.0
9 TraesCS2D01G104200 chr2B 80.833 360 37 18 3488 3842 88918549 88918217 1.820000e-63 254.0
10 TraesCS2D01G104200 chr2B 86.577 149 19 1 2265 2413 88925647 88925500 3.160000e-36 163.0
11 TraesCS2D01G104200 chr2B 96.471 85 3 0 2858 2942 88919242 88919158 1.480000e-29 141.0
12 TraesCS2D01G104200 chr2B 92.857 98 4 3 3380 3477 88918718 88918624 5.320000e-29 139.0
13 TraesCS2D01G104200 chr2B 91.250 80 7 0 2424 2503 88919512 88919433 4.170000e-20 110.0
14 TraesCS2D01G104200 chr2B 100.000 29 0 0 3185 3213 683060068 683060040 2.000000e-03 54.7
15 TraesCS2D01G104200 chr2A 94.708 3137 116 19 1 3108 57833081 57829966 0.000000e+00 4828.0
16 TraesCS2D01G104200 chr2A 95.745 94 4 0 3853 3946 57829875 57829782 6.830000e-33 152.0
17 TraesCS2D01G104200 chr2A 94.667 75 4 0 3139 3213 424544451 424544377 2.490000e-22 117.0
18 TraesCS2D01G104200 chr4D 77.460 630 132 9 1041 1665 300783379 300784003 6.230000e-98 368.0
19 TraesCS2D01G104200 chr4D 98.000 50 1 0 3135 3184 12415629 12415678 1.950000e-13 87.9
20 TraesCS2D01G104200 chr4D 89.583 48 4 1 3135 3182 500684124 500684170 4.260000e-05 60.2
21 TraesCS2D01G104200 chr4B 78.087 575 116 9 1096 1665 373981843 373982412 4.850000e-94 355.0
22 TraesCS2D01G104200 chr4B 98.039 51 1 0 3135 3185 191365337 191365387 5.430000e-14 89.8
23 TraesCS2D01G104200 chr7D 90.667 75 7 0 3139 3213 638017638 638017564 2.510000e-17 100.0
24 TraesCS2D01G104200 chr7A 90.123 81 3 5 3136 3213 696822204 696822126 2.510000e-17 100.0
25 TraesCS2D01G104200 chr3B 92.537 67 4 1 3135 3200 42157173 42157239 1.170000e-15 95.3
26 TraesCS2D01G104200 chr6D 98.039 51 1 0 3135 3185 87598714 87598664 5.430000e-14 89.8
27 TraesCS2D01G104200 chr3A 96.296 54 1 1 3133 3185 647142366 647142313 1.950000e-13 87.9
28 TraesCS2D01G104200 chr7B 83.951 81 7 4 3137 3212 20647031 20647110 5.470000e-09 73.1
29 TraesCS2D01G104200 chr6A 100.000 29 0 0 3185 3213 198074940 198074912 2.000000e-03 54.7


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 TraesCS2D01G104200 chr2D 56199840 56203785 3945 True 7287 7287 100.0000 1 3946 1 chr2D.!!$R1 3945
1 TraesCS2D01G104200 chr2D 56190134 56192369 2235 True 224 442 89.3120 2260 3842 6 chr2D.!!$R2 1582
2 TraesCS2D01G104200 chr2B 88930485 88933628 3143 True 5155 5155 96.2950 3 3142 1 chr2B.!!$R2 3139
3 TraesCS2D01G104200 chr2A 57829782 57833081 3299 True 2490 4828 95.2265 1 3946 2 chr2A.!!$R2 3945
4 TraesCS2D01G104200 chr4D 300783379 300784003 624 False 368 368 77.4600 1041 1665 1 chr4D.!!$F2 624
5 TraesCS2D01G104200 chr4B 373981843 373982412 569 False 355 355 78.0870 1096 1665 1 chr4B.!!$F2 569

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
106 117 0.036022 AGGCACACTCTCCTGCTTTC 59.964 55.000 0.00 0.00 33.63 2.62 F
396 417 0.676184 GTGAGAGGTGCTGACAGTCA 59.324 55.000 2.48 2.48 30.37 3.41 F
500 521 0.819259 TGGTTGCTTCTGGTGTCAGC 60.819 55.000 0.00 0.00 40.69 4.26 F
864 885 1.620819 TCAAGGCCTCTCTCTTCACAC 59.379 52.381 5.23 0.00 0.00 3.82 F
2589 3275 0.822164 AGCATGAGAGCAAATTGGCC 59.178 50.000 0.00 0.00 36.85 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1207 1228 0.419459 ACCTCCTCAGGGGACTCAAT 59.581 55.000 0.00 0.00 45.53 2.57 R
2101 2123 4.408921 TCAGTTAGCATGGCCTATAACAGT 59.591 41.667 3.32 0.00 31.90 3.55 R
2349 2371 7.283354 GCAAAGAGTAGGAAGTTATAAGCCATT 59.717 37.037 0.00 0.00 0.00 3.16 R
2636 3324 3.573558 CGCTTGCCGGCTTCTTTA 58.426 55.556 29.70 1.94 0.00 1.85 R
3621 4589 0.109153 TGGAGAGCTGCTTTGCTGAA 59.891 50.000 12.62 0.00 44.17 3.02 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
33 36 0.320374 TAGGCTGGTTCGAGGTGTTG 59.680 55.000 0.00 0.00 0.00 3.33
34 37 1.070786 GGCTGGTTCGAGGTGTTGA 59.929 57.895 0.00 0.00 0.00 3.18
35 38 0.534203 GGCTGGTTCGAGGTGTTGAA 60.534 55.000 0.00 0.00 0.00 2.69
96 107 5.221244 ACAATTTTGGTCTAAAGGCACACTC 60.221 40.000 0.00 0.00 0.00 3.51
106 117 0.036022 AGGCACACTCTCCTGCTTTC 59.964 55.000 0.00 0.00 33.63 2.62
165 179 6.164176 TCTGGAAGTAACTTTCGAGAAATCC 58.836 40.000 0.00 3.29 38.46 3.01
167 181 5.932303 TGGAAGTAACTTTCGAGAAATCCTG 59.068 40.000 12.19 0.21 0.00 3.86
396 417 0.676184 GTGAGAGGTGCTGACAGTCA 59.324 55.000 2.48 2.48 30.37 3.41
451 472 7.338196 TCAACTGATTGTCCTTTAGTTTTGTCA 59.662 33.333 0.00 0.00 37.11 3.58
483 504 2.101249 ACAGTTTTCCTGCAACACATGG 59.899 45.455 0.00 0.00 45.68 3.66
500 521 0.819259 TGGTTGCTTCTGGTGTCAGC 60.819 55.000 0.00 0.00 40.69 4.26
683 704 8.774546 TTCTTCCAATACTAGATGAGACTGAT 57.225 34.615 0.00 0.00 0.00 2.90
746 767 2.771943 AGTCCAGGAAGAACAACACTGA 59.228 45.455 0.00 0.00 0.00 3.41
857 878 2.810852 CAACTTGTTCAAGGCCTCTCTC 59.189 50.000 5.23 0.00 0.00 3.20
864 885 1.620819 TCAAGGCCTCTCTCTTCACAC 59.379 52.381 5.23 0.00 0.00 3.82
1670 1691 4.828072 ACTCCTTTCAGGTAGGTCATTC 57.172 45.455 0.00 0.00 36.53 2.67
1774 1795 4.715713 GACTTTACCTTGTCCTGGACTTT 58.284 43.478 26.03 10.95 33.15 2.66
1777 1798 4.513406 TTACCTTGTCCTGGACTTTGTT 57.487 40.909 26.03 10.31 33.15 2.83
1926 1948 2.930682 GGAGGAACTTGCACGAATCTAC 59.069 50.000 0.00 0.00 41.55 2.59
1929 1951 3.064207 GGAACTTGCACGAATCTACACA 58.936 45.455 0.00 0.00 0.00 3.72
2088 2110 4.339530 TCCTCTTCGGTTATCTGACATCTG 59.660 45.833 0.00 0.00 0.00 2.90
2093 2115 5.147330 TCGGTTATCTGACATCTGTTTGT 57.853 39.130 0.00 0.00 0.00 2.83
2101 2123 2.757314 TGACATCTGTTTGTTTGTGCCA 59.243 40.909 0.00 0.00 0.00 4.92
2347 2369 1.940613 GAGGTTTTCTGTGCAGACGTT 59.059 47.619 0.79 0.00 37.14 3.99
2349 2371 3.537580 AGGTTTTCTGTGCAGACGTTTA 58.462 40.909 0.79 0.00 37.14 2.01
2496 3173 4.377897 CTGAAAGGAGTACGTTTTCCAGT 58.622 43.478 17.23 6.90 35.88 4.00
2589 3275 0.822164 AGCATGAGAGCAAATTGGCC 59.178 50.000 0.00 0.00 36.85 5.36
2602 3288 5.126384 AGCAAATTGGCCGCTTAACTATTTA 59.874 36.000 0.00 0.00 29.87 1.40
2636 3324 9.439500 AAAATAACAATATTTCAGTTGCTGCAT 57.561 25.926 1.84 0.00 40.10 3.96
2891 3579 0.696501 ACTTTGCGGGGTTCACCTAT 59.303 50.000 0.00 0.00 40.03 2.57
2933 3622 3.706373 GACCTGAAGCCGCCCTCA 61.706 66.667 0.00 0.00 0.00 3.86
2938 3627 2.821810 GAAGCCGCCCTCAAGCTC 60.822 66.667 0.00 0.00 35.30 4.09
2939 3628 3.322318 GAAGCCGCCCTCAAGCTCT 62.322 63.158 0.00 0.00 35.30 4.09
2940 3629 1.961180 GAAGCCGCCCTCAAGCTCTA 61.961 60.000 0.00 0.00 35.30 2.43
2941 3630 1.965754 AAGCCGCCCTCAAGCTCTAG 61.966 60.000 0.00 0.00 35.30 2.43
2980 3669 0.460284 CGCTCTAGTGCACCCGAAAT 60.460 55.000 14.63 0.00 0.00 2.17
3039 3779 2.280628 GCTGTGTTCTATGGCCTGTAC 58.719 52.381 3.32 0.00 0.00 2.90
3117 3860 5.355596 ACAGAGAGCAACTACAATATCTGC 58.644 41.667 0.00 0.00 37.11 4.26
3131 3874 7.775397 ACAATATCTGCAATTACAAATTGGC 57.225 32.000 12.82 7.02 0.00 4.52
3142 3885 7.857885 GCAATTACAAATTGGCTGATAGTACTC 59.142 37.037 0.00 0.00 0.00 2.59
3145 3888 4.475016 ACAAATTGGCTGATAGTACTCCCT 59.525 41.667 0.00 0.00 0.00 4.20
3146 3889 4.965200 AATTGGCTGATAGTACTCCCTC 57.035 45.455 0.00 0.00 0.00 4.30
3147 3890 2.383442 TGGCTGATAGTACTCCCTCC 57.617 55.000 0.00 0.00 0.00 4.30
3148 3891 1.249407 GGCTGATAGTACTCCCTCCG 58.751 60.000 0.00 0.00 0.00 4.63
3149 3892 1.479021 GGCTGATAGTACTCCCTCCGT 60.479 57.143 0.00 0.00 0.00 4.69
3150 3893 1.881324 GCTGATAGTACTCCCTCCGTC 59.119 57.143 0.00 0.00 0.00 4.79
3151 3894 2.506444 CTGATAGTACTCCCTCCGTCC 58.494 57.143 0.00 0.00 0.00 4.79
3152 3895 1.202734 TGATAGTACTCCCTCCGTCCG 60.203 57.143 0.00 0.00 0.00 4.79
3153 3896 0.110104 ATAGTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
3154 3897 0.982852 TAGTACTCCCTCCGTCCGGA 60.983 60.000 0.00 0.00 42.90 5.14
3155 3898 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3156 3899 0.754587 GTACTCCCTCCGTCCGGAAT 60.755 60.000 5.23 0.00 44.66 3.01
3157 3900 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
3158 3901 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
3159 3902 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
3160 3903 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
3161 3904 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
3162 3905 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3163 3906 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3164 3907 2.354403 CCTCCGTCCGGAATTACTTGTT 60.354 50.000 5.23 0.00 44.66 2.83
3165 3908 2.671396 CTCCGTCCGGAATTACTTGTTG 59.329 50.000 5.23 0.00 44.66 3.33
3166 3909 1.129811 CCGTCCGGAATTACTTGTTGC 59.870 52.381 5.23 0.00 37.50 4.17
3167 3910 1.801771 CGTCCGGAATTACTTGTTGCA 59.198 47.619 5.23 0.00 0.00 4.08
3168 3911 2.159707 CGTCCGGAATTACTTGTTGCAG 60.160 50.000 5.23 0.00 0.00 4.41
3169 3912 3.071479 GTCCGGAATTACTTGTTGCAGA 58.929 45.455 5.23 0.00 0.00 4.26
3170 3913 3.500680 GTCCGGAATTACTTGTTGCAGAA 59.499 43.478 5.23 0.00 0.00 3.02
3171 3914 4.023536 GTCCGGAATTACTTGTTGCAGAAA 60.024 41.667 5.23 0.00 0.00 2.52
3172 3915 4.764823 TCCGGAATTACTTGTTGCAGAAAT 59.235 37.500 0.00 0.00 0.00 2.17
3173 3916 4.858692 CCGGAATTACTTGTTGCAGAAATG 59.141 41.667 0.00 0.00 0.00 2.32
3174 3917 4.858692 CGGAATTACTTGTTGCAGAAATGG 59.141 41.667 0.00 0.00 0.00 3.16
3175 3918 5.335583 CGGAATTACTTGTTGCAGAAATGGA 60.336 40.000 0.00 0.00 0.00 3.41
3176 3919 6.625740 CGGAATTACTTGTTGCAGAAATGGAT 60.626 38.462 0.00 0.00 0.00 3.41
3177 3920 6.532657 GGAATTACTTGTTGCAGAAATGGATG 59.467 38.462 0.00 0.00 0.00 3.51
3178 3921 6.594788 ATTACTTGTTGCAGAAATGGATGT 57.405 33.333 0.00 0.00 0.00 3.06
3179 3922 7.701539 ATTACTTGTTGCAGAAATGGATGTA 57.298 32.000 0.00 0.00 0.00 2.29
3180 3923 7.701539 TTACTTGTTGCAGAAATGGATGTAT 57.298 32.000 0.00 0.00 0.00 2.29
3181 3924 6.199937 ACTTGTTGCAGAAATGGATGTATC 57.800 37.500 0.00 0.00 0.00 2.24
3182 3925 5.948162 ACTTGTTGCAGAAATGGATGTATCT 59.052 36.000 0.00 0.00 0.00 1.98
3183 3926 7.112122 ACTTGTTGCAGAAATGGATGTATCTA 58.888 34.615 0.00 0.00 0.00 1.98
3184 3927 7.281774 ACTTGTTGCAGAAATGGATGTATCTAG 59.718 37.037 0.00 0.00 0.00 2.43
3185 3928 6.653020 TGTTGCAGAAATGGATGTATCTAGT 58.347 36.000 0.00 0.00 0.00 2.57
3186 3929 7.791029 TGTTGCAGAAATGGATGTATCTAGTA 58.209 34.615 0.00 0.00 0.00 1.82
3187 3930 7.928167 TGTTGCAGAAATGGATGTATCTAGTAG 59.072 37.037 0.00 0.00 0.00 2.57
3188 3931 7.839680 TGCAGAAATGGATGTATCTAGTAGA 57.160 36.000 1.45 1.45 0.00 2.59
3189 3932 8.427902 TGCAGAAATGGATGTATCTAGTAGAT 57.572 34.615 16.75 16.75 38.70 1.98
3190 3933 9.533831 TGCAGAAATGGATGTATCTAGTAGATA 57.466 33.333 14.72 14.72 36.20 1.98
3209 3952 9.770097 AGTAGATACATCCATTTATGTGACAAG 57.230 33.333 0.00 0.00 40.29 3.16
3210 3953 9.547753 GTAGATACATCCATTTATGTGACAAGT 57.452 33.333 0.00 0.00 40.29 3.16
3214 3957 9.905713 ATACATCCATTTATGTGACAAGTAAGT 57.094 29.630 0.00 0.00 40.29 2.24
3216 3959 9.733556 ACATCCATTTATGTGACAAGTAAGTAA 57.266 29.630 0.00 0.00 38.65 2.24
3221 3964 9.702726 CATTTATGTGACAAGTAAGTAATTCCG 57.297 33.333 0.00 0.00 0.00 4.30
3222 3965 7.837202 TTATGTGACAAGTAAGTAATTCCGG 57.163 36.000 0.00 0.00 0.00 5.14
3223 3966 5.471556 TGTGACAAGTAAGTAATTCCGGA 57.528 39.130 0.00 0.00 0.00 5.14
3224 3967 6.045072 TGTGACAAGTAAGTAATTCCGGAT 57.955 37.500 4.15 0.00 0.00 4.18
3225 3968 5.872617 TGTGACAAGTAAGTAATTCCGGATG 59.127 40.000 4.15 0.00 0.00 3.51
3226 3969 5.293569 GTGACAAGTAAGTAATTCCGGATGG 59.706 44.000 4.15 0.00 0.00 3.51
3227 3970 4.777463 ACAAGTAAGTAATTCCGGATGGG 58.223 43.478 4.15 0.00 35.24 4.00
3228 3971 4.134563 CAAGTAAGTAATTCCGGATGGGG 58.865 47.826 4.15 0.00 36.01 4.96
3251 3994 1.770658 TGTCCCCAGGATATGCTCAAG 59.229 52.381 0.00 0.00 32.73 3.02
3252 3995 2.050144 GTCCCCAGGATATGCTCAAGA 58.950 52.381 0.00 0.00 32.73 3.02
3262 4054 2.649331 ATGCTCAAGAGTTGCATTGC 57.351 45.000 0.46 0.46 43.85 3.56
3311 4103 5.163652 ACTCAGAAACAAGAAAGGAAAACCG 60.164 40.000 0.00 0.00 0.00 4.44
3356 4148 2.303175 GAGTCGGCTCTCAAGGTAGAT 58.697 52.381 10.47 0.00 38.66 1.98
3360 4152 3.251487 GTCGGCTCTCAAGGTAGATCTAC 59.749 52.174 22.47 22.47 35.40 2.59
3477 4367 5.336744 GCTTACTGCTTGTCTAGTCTACTG 58.663 45.833 0.00 0.00 38.95 2.74
3479 4369 3.426615 ACTGCTTGTCTAGTCTACTGCT 58.573 45.455 0.00 0.00 0.00 4.24
3480 4370 3.442273 ACTGCTTGTCTAGTCTACTGCTC 59.558 47.826 0.00 0.00 0.00 4.26
3482 4372 3.020984 GCTTGTCTAGTCTACTGCTCCT 58.979 50.000 0.00 0.00 0.00 3.69
3483 4373 4.200874 GCTTGTCTAGTCTACTGCTCCTA 58.799 47.826 0.00 0.00 0.00 2.94
3484 4374 4.035909 GCTTGTCTAGTCTACTGCTCCTAC 59.964 50.000 0.00 0.00 0.00 3.18
3494 4459 6.668283 AGTCTACTGCTCCTACTTATTTCCAA 59.332 38.462 0.00 0.00 0.00 3.53
3526 4494 3.377485 TGTATCTCTCCCTTCGAAGTTCG 59.623 47.826 23.03 19.23 42.10 3.95
3551 4519 3.615709 GGGGCAGCACCAAACACC 61.616 66.667 9.59 0.00 42.05 4.16
3582 4550 1.065701 GCAGATTCAGCAATCAGCAGG 59.934 52.381 8.65 0.00 46.06 4.85
3592 4560 2.196749 CAATCAGCAGGTACTACGCAG 58.803 52.381 0.00 0.00 36.02 5.18
3593 4561 1.763968 ATCAGCAGGTACTACGCAGA 58.236 50.000 0.00 0.00 36.02 4.26
3594 4562 1.763968 TCAGCAGGTACTACGCAGAT 58.236 50.000 0.00 0.00 36.02 2.90
3595 4563 2.927028 TCAGCAGGTACTACGCAGATA 58.073 47.619 0.00 0.00 36.02 1.98
3596 4564 2.617308 TCAGCAGGTACTACGCAGATAC 59.383 50.000 0.00 0.00 36.02 2.24
3597 4565 1.602851 AGCAGGTACTACGCAGATACG 59.397 52.381 0.00 0.00 36.02 3.06
3598 4566 1.925068 GCAGGTACTACGCAGATACGC 60.925 57.143 0.00 0.00 36.02 4.42
3599 4567 1.332686 CAGGTACTACGCAGATACGCA 59.667 52.381 0.00 0.00 36.02 5.24
3600 4568 1.602851 AGGTACTACGCAGATACGCAG 59.397 52.381 0.00 0.00 36.02 5.18
3601 4569 1.334779 GGTACTACGCAGATACGCAGG 60.335 57.143 0.00 0.00 36.19 4.85
3602 4570 1.332997 GTACTACGCAGATACGCAGGT 59.667 52.381 0.00 0.00 36.19 4.00
3603 4571 1.671979 ACTACGCAGATACGCAGGTA 58.328 50.000 0.00 0.00 36.19 3.08
3604 4572 1.332997 ACTACGCAGATACGCAGGTAC 59.667 52.381 0.00 0.00 36.19 3.34
3605 4573 1.602851 CTACGCAGATACGCAGGTACT 59.397 52.381 0.00 0.00 35.85 2.73
3606 4574 1.671979 ACGCAGATACGCAGGTACTA 58.328 50.000 0.00 0.00 33.64 1.82
3607 4575 1.332997 ACGCAGATACGCAGGTACTAC 59.667 52.381 0.00 0.00 33.64 2.73
3615 4583 2.033793 CGCAGGTACTACGCAGATAC 57.966 55.000 0.00 0.00 38.82 2.24
3616 4584 1.659491 CGCAGGTACTACGCAGATACG 60.659 57.143 0.00 0.00 38.82 3.06
3617 4585 1.925068 GCAGGTACTACGCAGATACGC 60.925 57.143 0.00 0.00 36.02 4.42
3618 4586 1.332686 CAGGTACTACGCAGATACGCA 59.667 52.381 0.00 0.00 36.02 5.24
3619 4587 1.602851 AGGTACTACGCAGATACGCAG 59.397 52.381 0.00 0.00 36.02 5.18
3620 4588 1.600957 GGTACTACGCAGATACGCAGA 59.399 52.381 0.00 0.00 36.19 4.26
3621 4589 2.225963 GGTACTACGCAGATACGCAGAT 59.774 50.000 0.00 0.00 36.19 2.90
3622 4590 3.304525 GGTACTACGCAGATACGCAGATT 60.305 47.826 0.00 0.00 36.19 2.40
3623 4591 3.001395 ACTACGCAGATACGCAGATTC 57.999 47.619 0.00 0.00 36.19 2.52
3624 4592 2.357952 ACTACGCAGATACGCAGATTCA 59.642 45.455 0.00 0.00 36.19 2.57
3625 4593 1.845266 ACGCAGATACGCAGATTCAG 58.155 50.000 0.00 0.00 36.19 3.02
3626 4594 0.506080 CGCAGATACGCAGATTCAGC 59.494 55.000 0.00 0.00 0.00 4.26
3627 4595 1.575244 GCAGATACGCAGATTCAGCA 58.425 50.000 1.84 0.00 0.00 4.41
3628 4596 1.935873 GCAGATACGCAGATTCAGCAA 59.064 47.619 1.84 0.00 0.00 3.91
3629 4597 2.352651 GCAGATACGCAGATTCAGCAAA 59.647 45.455 1.84 0.00 0.00 3.68
3630 4598 3.545624 GCAGATACGCAGATTCAGCAAAG 60.546 47.826 1.84 0.00 0.00 2.77
3631 4599 2.611292 AGATACGCAGATTCAGCAAAGC 59.389 45.455 1.84 0.00 0.00 3.51
3632 4600 1.807139 TACGCAGATTCAGCAAAGCA 58.193 45.000 1.84 0.00 0.00 3.91
3650 4618 1.305718 AGCTCTCCACTCCCTGGAC 60.306 63.158 0.00 0.00 44.99 4.02
3656 4624 0.613260 TCCACTCCCTGGACAAATCG 59.387 55.000 0.00 0.00 44.99 3.34
3662 4630 3.009033 ACTCCCTGGACAAATCGATTCAA 59.991 43.478 11.83 0.00 0.00 2.69
3673 4641 4.627611 AATCGATTCAACAATCAGCAGG 57.372 40.909 4.39 0.00 38.77 4.85
3676 4644 4.183865 TCGATTCAACAATCAGCAGGTAG 58.816 43.478 0.00 0.00 38.77 3.18
3720 4711 4.454161 GCTTCTCTCTTTCTTTCTCAACCC 59.546 45.833 0.00 0.00 0.00 4.11
3724 4715 3.328050 TCTCTTTCTTTCTCAACCCCCTC 59.672 47.826 0.00 0.00 0.00 4.30
3732 4723 1.150135 TCTCAACCCCCTCTCTGAACT 59.850 52.381 0.00 0.00 0.00 3.01
3739 4730 2.843113 CCCCCTCTCTGAACTCTGATTT 59.157 50.000 0.00 0.00 0.00 2.17
3747 4738 5.095145 TCTGAACTCTGATTTATGCAGCT 57.905 39.130 0.00 0.00 33.45 4.24
3768 4759 1.204704 GCCAAACAGCCAGAATAACCC 59.795 52.381 0.00 0.00 0.00 4.11
3769 4760 2.524306 CCAAACAGCCAGAATAACCCA 58.476 47.619 0.00 0.00 0.00 4.51
3790 4781 3.000727 ACGGTTTCATGCAAGCTACTAC 58.999 45.455 5.77 0.00 0.00 2.73
3791 4782 3.262420 CGGTTTCATGCAAGCTACTACT 58.738 45.455 5.77 0.00 0.00 2.57
3794 4785 5.350365 CGGTTTCATGCAAGCTACTACTAAA 59.650 40.000 5.77 0.00 0.00 1.85
3795 4786 6.128391 CGGTTTCATGCAAGCTACTACTAAAA 60.128 38.462 5.77 0.00 0.00 1.52
3796 4787 7.572353 CGGTTTCATGCAAGCTACTACTAAAAA 60.572 37.037 5.77 0.00 0.00 1.94
3836 4827 2.622942 TGTCACAAAGGATCACAAAGGC 59.377 45.455 0.00 0.00 0.00 4.35
3842 4833 2.226962 AGGATCACAAAGGCAGCATT 57.773 45.000 0.00 0.00 0.00 3.56
3843 4834 1.822990 AGGATCACAAAGGCAGCATTG 59.177 47.619 8.27 8.27 0.00 2.82
3844 4835 1.134907 GGATCACAAAGGCAGCATTGG 60.135 52.381 13.11 3.98 0.00 3.16
3845 4836 1.547372 GATCACAAAGGCAGCATTGGT 59.453 47.619 13.11 4.63 0.00 3.67
3846 4837 1.412079 TCACAAAGGCAGCATTGGTT 58.588 45.000 13.11 0.00 0.00 3.67
3847 4838 1.761784 TCACAAAGGCAGCATTGGTTT 59.238 42.857 13.11 0.00 0.00 3.27
3848 4839 2.170187 TCACAAAGGCAGCATTGGTTTT 59.830 40.909 13.11 0.00 0.00 2.43
3849 4840 2.288458 CACAAAGGCAGCATTGGTTTTG 59.712 45.455 13.11 9.01 0.00 2.44
3850 4841 1.264826 CAAAGGCAGCATTGGTTTTGC 59.735 47.619 0.00 0.00 40.45 3.68
3851 4842 0.469070 AAGGCAGCATTGGTTTTGCA 59.531 45.000 0.00 0.00 42.62 4.08
3863 4854 1.606668 GGTTTTGCAGTCCGACAATGA 59.393 47.619 0.40 0.00 0.00 2.57
3869 4860 1.014044 CAGTCCGACAATGACACCGG 61.014 60.000 0.00 0.00 43.02 5.28
3876 4867 2.537401 GACAATGACACCGGCTACTAC 58.463 52.381 0.00 0.00 0.00 2.73
3898 4889 1.070786 GACCACGGTGAAGCCAAGA 59.929 57.895 10.28 0.00 36.97 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.035385 TCGAACCAGCCTAGCATCGA 61.035 55.000 0.00 0.00 37.02 3.59
33 36 2.100916 TCCTAGCCACGCTATGTTCTTC 59.899 50.000 0.00 0.00 40.54 2.87
34 37 2.108168 TCCTAGCCACGCTATGTTCTT 58.892 47.619 0.00 0.00 40.54 2.52
35 38 1.776662 TCCTAGCCACGCTATGTTCT 58.223 50.000 0.00 0.00 40.54 3.01
106 117 2.893637 AGGCATACTACGTGCTTTCTG 58.106 47.619 0.00 0.00 42.16 3.02
396 417 2.106566 AGGATCTCAGTTCGCATCACT 58.893 47.619 0.00 0.00 0.00 3.41
483 504 0.880278 TCGCTGACACCAGAAGCAAC 60.880 55.000 0.00 0.00 43.02 4.17
500 521 6.927294 ATCTTGCTAGGATTTAAACCTTCG 57.073 37.500 12.60 7.56 38.76 3.79
683 704 5.147330 ACGGACACAGAACAGATAAATCA 57.853 39.130 0.00 0.00 0.00 2.57
746 767 4.945543 TGCTGAATATGACTTGCTTGATGT 59.054 37.500 0.00 0.00 0.00 3.06
857 878 7.433708 TGTAAAATGATGTACTGGTGTGAAG 57.566 36.000 0.00 0.00 0.00 3.02
864 885 6.828273 TCCAAGGATGTAAAATGATGTACTGG 59.172 38.462 0.00 0.00 0.00 4.00
1207 1228 0.419459 ACCTCCTCAGGGGACTCAAT 59.581 55.000 0.00 0.00 45.53 2.57
1670 1691 9.052080 CAACGTAGAGATGACAATATGTATACG 57.948 37.037 8.03 8.03 43.08 3.06
1929 1951 5.105392 GGCTACAGCAGATATAATCTCAGCT 60.105 44.000 3.24 0.00 44.36 4.24
2088 2110 5.219633 CCTATAACAGTGGCACAAACAAAC 58.780 41.667 21.41 0.00 44.16 2.93
2101 2123 4.408921 TCAGTTAGCATGGCCTATAACAGT 59.591 41.667 3.32 0.00 31.90 3.55
2349 2371 7.283354 GCAAAGAGTAGGAAGTTATAAGCCATT 59.717 37.037 0.00 0.00 0.00 3.16
2518 3195 6.195700 ACATGGTACTATGAGTTACTCCTGT 58.804 40.000 24.30 8.28 0.00 4.00
2519 3196 6.716934 ACATGGTACTATGAGTTACTCCTG 57.283 41.667 24.30 2.73 0.00 3.86
2636 3324 3.573558 CGCTTGCCGGCTTCTTTA 58.426 55.556 29.70 1.94 0.00 1.85
2876 3564 1.195442 TGACATAGGTGAACCCCGCA 61.195 55.000 0.00 0.00 36.42 5.69
2938 3627 1.000731 CCTTGCAGCCTAGCTAGCTAG 59.999 57.143 35.39 35.39 44.07 3.42
2939 3628 1.043816 CCTTGCAGCCTAGCTAGCTA 58.956 55.000 22.85 22.85 38.95 3.32
2940 3629 0.980231 ACCTTGCAGCCTAGCTAGCT 60.980 55.000 23.12 23.12 42.70 3.32
2941 3630 0.107459 AACCTTGCAGCCTAGCTAGC 60.107 55.000 15.74 6.62 36.40 3.42
2980 3669 2.152297 ATCAAAATTGCGCGCACCCA 62.152 50.000 36.72 21.36 0.00 4.51
3053 3793 3.427233 GCAAGTAAAGCAGATGCAGAAGG 60.427 47.826 7.68 0.00 45.16 3.46
3117 3860 8.345565 GGAGTACTATCAGCCAATTTGTAATTG 58.654 37.037 0.00 5.39 0.00 2.32
3131 3874 2.506444 GGACGGAGGGAGTACTATCAG 58.494 57.143 0.00 0.00 0.00 2.90
3142 3885 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3145 3888 2.690786 CAACAAGTAATTCCGGACGGA 58.309 47.619 1.83 9.76 43.52 4.69
3146 3889 1.129811 GCAACAAGTAATTCCGGACGG 59.870 52.381 1.83 3.96 0.00 4.79
3147 3890 1.801771 TGCAACAAGTAATTCCGGACG 59.198 47.619 1.83 0.00 0.00 4.79
3148 3891 3.071479 TCTGCAACAAGTAATTCCGGAC 58.929 45.455 1.83 0.00 0.00 4.79
3149 3892 3.410631 TCTGCAACAAGTAATTCCGGA 57.589 42.857 0.00 0.00 0.00 5.14
3150 3893 4.497473 TTTCTGCAACAAGTAATTCCGG 57.503 40.909 0.00 0.00 0.00 5.14
3151 3894 4.858692 CCATTTCTGCAACAAGTAATTCCG 59.141 41.667 0.00 0.00 0.00 4.30
3152 3895 6.024552 TCCATTTCTGCAACAAGTAATTCC 57.975 37.500 0.00 0.00 0.00 3.01
3153 3896 7.092716 ACATCCATTTCTGCAACAAGTAATTC 58.907 34.615 0.00 0.00 0.00 2.17
3154 3897 6.996509 ACATCCATTTCTGCAACAAGTAATT 58.003 32.000 0.00 0.00 0.00 1.40
3155 3898 6.594788 ACATCCATTTCTGCAACAAGTAAT 57.405 33.333 0.00 0.00 0.00 1.89
3156 3899 7.611467 AGATACATCCATTTCTGCAACAAGTAA 59.389 33.333 0.00 0.00 0.00 2.24
3157 3900 7.112122 AGATACATCCATTTCTGCAACAAGTA 58.888 34.615 0.00 0.00 0.00 2.24
3158 3901 5.948162 AGATACATCCATTTCTGCAACAAGT 59.052 36.000 0.00 0.00 0.00 3.16
3159 3902 6.446781 AGATACATCCATTTCTGCAACAAG 57.553 37.500 0.00 0.00 0.00 3.16
3160 3903 7.112122 ACTAGATACATCCATTTCTGCAACAA 58.888 34.615 0.00 0.00 0.00 2.83
3161 3904 6.653020 ACTAGATACATCCATTTCTGCAACA 58.347 36.000 0.00 0.00 0.00 3.33
3162 3905 8.144478 TCTACTAGATACATCCATTTCTGCAAC 58.856 37.037 0.00 0.00 0.00 4.17
3163 3906 8.250143 TCTACTAGATACATCCATTTCTGCAA 57.750 34.615 0.00 0.00 0.00 4.08
3164 3907 7.839680 TCTACTAGATACATCCATTTCTGCA 57.160 36.000 0.00 0.00 0.00 4.41
3183 3926 9.770097 CTTGTCACATAAATGGATGTATCTACT 57.230 33.333 0.00 0.00 37.99 2.57
3184 3927 9.547753 ACTTGTCACATAAATGGATGTATCTAC 57.452 33.333 0.00 0.00 37.99 2.59
3188 3931 9.905713 ACTTACTTGTCACATAAATGGATGTAT 57.094 29.630 0.00 0.00 37.99 2.29
3190 3933 9.733556 TTACTTACTTGTCACATAAATGGATGT 57.266 29.630 0.00 0.00 40.78 3.06
3195 3938 9.702726 CGGAATTACTTACTTGTCACATAAATG 57.297 33.333 0.00 0.00 0.00 2.32
3196 3939 8.889717 CCGGAATTACTTACTTGTCACATAAAT 58.110 33.333 0.00 0.00 0.00 1.40
3197 3940 8.095792 TCCGGAATTACTTACTTGTCACATAAA 58.904 33.333 0.00 0.00 0.00 1.40
3198 3941 7.613585 TCCGGAATTACTTACTTGTCACATAA 58.386 34.615 0.00 0.00 0.00 1.90
3199 3942 7.172868 TCCGGAATTACTTACTTGTCACATA 57.827 36.000 0.00 0.00 0.00 2.29
3200 3943 6.045072 TCCGGAATTACTTACTTGTCACAT 57.955 37.500 0.00 0.00 0.00 3.21
3201 3944 5.471556 TCCGGAATTACTTACTTGTCACA 57.528 39.130 0.00 0.00 0.00 3.58
3202 3945 5.293569 CCATCCGGAATTACTTACTTGTCAC 59.706 44.000 9.01 0.00 0.00 3.67
3203 3946 5.424757 CCATCCGGAATTACTTACTTGTCA 58.575 41.667 9.01 0.00 0.00 3.58
3204 3947 4.814771 CCCATCCGGAATTACTTACTTGTC 59.185 45.833 9.01 0.00 0.00 3.18
3205 3948 4.384868 CCCCATCCGGAATTACTTACTTGT 60.385 45.833 9.01 0.00 0.00 3.16
3206 3949 4.134563 CCCCATCCGGAATTACTTACTTG 58.865 47.826 9.01 0.00 0.00 3.16
3207 3950 3.434596 GCCCCATCCGGAATTACTTACTT 60.435 47.826 9.01 0.00 0.00 2.24
3208 3951 2.105993 GCCCCATCCGGAATTACTTACT 59.894 50.000 9.01 0.00 0.00 2.24
3209 3952 2.158726 TGCCCCATCCGGAATTACTTAC 60.159 50.000 9.01 0.00 0.00 2.34
3210 3953 2.128535 TGCCCCATCCGGAATTACTTA 58.871 47.619 9.01 0.00 0.00 2.24
3211 3954 0.923358 TGCCCCATCCGGAATTACTT 59.077 50.000 9.01 0.00 0.00 2.24
3212 3955 1.149101 ATGCCCCATCCGGAATTACT 58.851 50.000 9.01 0.00 0.00 2.24
3213 3956 1.247567 CATGCCCCATCCGGAATTAC 58.752 55.000 9.01 0.00 0.00 1.89
3214 3957 0.850100 ACATGCCCCATCCGGAATTA 59.150 50.000 9.01 0.00 0.00 1.40
3215 3958 0.468029 GACATGCCCCATCCGGAATT 60.468 55.000 9.01 0.00 0.00 2.17
3216 3959 1.151450 GACATGCCCCATCCGGAAT 59.849 57.895 9.01 0.00 0.00 3.01
3217 3960 2.595095 GACATGCCCCATCCGGAA 59.405 61.111 9.01 0.00 0.00 4.30
3218 3961 3.488569 GGACATGCCCCATCCGGA 61.489 66.667 6.61 6.61 0.00 5.14
3227 3970 3.658398 CATATCCTGGGGACATGCC 57.342 57.895 0.00 0.00 41.51 4.40
3251 3994 1.214589 CAGGGCTGCAATGCAACTC 59.785 57.895 9.92 4.55 38.41 3.01
3252 3995 1.532316 ACAGGGCTGCAATGCAACT 60.532 52.632 9.92 5.14 38.41 3.16
3262 4054 2.093075 AGATTCATCAGTCACAGGGCTG 60.093 50.000 0.00 0.00 0.00 4.85
3311 4103 0.385974 CGCAGCCAGTTTTGCACTAC 60.386 55.000 0.00 0.00 40.28 2.73
3333 4125 0.534412 ACCTTGAGAGCCGACTCATG 59.466 55.000 0.35 7.19 46.09 3.07
3339 4131 2.738587 AGATCTACCTTGAGAGCCGA 57.261 50.000 0.00 0.00 32.04 5.54
3360 4152 8.465201 ACCGTAACTATTAGTCAAAACTCTAGG 58.535 37.037 0.00 0.00 36.92 3.02
3378 4170 7.172757 CGCATACGTTAAATTTAACCGTAACT 58.827 34.615 28.55 19.65 39.81 2.24
3402 4292 7.769044 ACTGCTATTAGCCCCATATAATTAACG 59.231 37.037 13.01 0.00 41.51 3.18
3410 4300 6.448369 TGTAAACTGCTATTAGCCCCATAT 57.552 37.500 13.01 0.00 41.51 1.78
3412 4302 4.788925 TGTAAACTGCTATTAGCCCCAT 57.211 40.909 13.01 0.61 41.51 4.00
3413 4303 4.165180 TGATGTAAACTGCTATTAGCCCCA 59.835 41.667 13.01 1.80 41.51 4.96
3414 4304 4.714632 TGATGTAAACTGCTATTAGCCCC 58.285 43.478 13.01 0.00 41.51 5.80
3470 4360 6.466885 TGGAAATAAGTAGGAGCAGTAGAC 57.533 41.667 0.00 0.00 0.00 2.59
3477 4367 5.735766 AGAGTGTTGGAAATAAGTAGGAGC 58.264 41.667 0.00 0.00 0.00 4.70
3479 4369 7.554959 AAGAGAGTGTTGGAAATAAGTAGGA 57.445 36.000 0.00 0.00 0.00 2.94
3480 4370 7.661847 ACAAAGAGAGTGTTGGAAATAAGTAGG 59.338 37.037 0.00 0.00 0.00 3.18
3483 4373 9.220767 GATACAAAGAGAGTGTTGGAAATAAGT 57.779 33.333 0.00 0.00 0.00 2.24
3484 4374 9.442047 AGATACAAAGAGAGTGTTGGAAATAAG 57.558 33.333 0.00 0.00 0.00 1.73
3494 4459 4.941713 AGGGAGAGATACAAAGAGAGTGT 58.058 43.478 0.00 0.00 0.00 3.55
3526 4494 4.792804 GTGCTGCCCCTGCTCCTC 62.793 72.222 0.00 0.00 38.71 3.71
3532 4500 2.521465 TGTTTGGTGCTGCCCCTG 60.521 61.111 2.15 0.00 36.04 4.45
3551 4519 2.596452 CTGAATCTGCTGCTTTGCTTG 58.404 47.619 0.00 0.00 0.00 4.01
3582 4550 1.332997 ACCTGCGTATCTGCGTAGTAC 59.667 52.381 0.00 2.23 41.74 2.73
3592 4560 1.600957 TCTGCGTAGTACCTGCGTATC 59.399 52.381 0.00 0.00 41.34 2.24
3593 4561 1.671979 TCTGCGTAGTACCTGCGTAT 58.328 50.000 0.00 0.00 41.34 3.06
3594 4562 1.671979 ATCTGCGTAGTACCTGCGTA 58.328 50.000 0.00 0.00 41.34 4.42
3595 4563 1.332997 GTATCTGCGTAGTACCTGCGT 59.667 52.381 0.00 0.00 41.34 5.24
3596 4564 1.659491 CGTATCTGCGTAGTACCTGCG 60.659 57.143 0.00 0.00 42.13 5.18
3597 4565 1.925068 GCGTATCTGCGTAGTACCTGC 60.925 57.143 0.00 0.00 0.00 4.85
3598 4566 1.332686 TGCGTATCTGCGTAGTACCTG 59.667 52.381 0.00 0.00 37.81 4.00
3599 4567 1.602851 CTGCGTATCTGCGTAGTACCT 59.397 52.381 0.00 0.00 39.21 3.08
3600 4568 1.600957 TCTGCGTATCTGCGTAGTACC 59.399 52.381 0.00 0.00 43.32 3.34
3601 4569 3.539431 ATCTGCGTATCTGCGTAGTAC 57.461 47.619 0.00 2.23 43.32 2.73
3602 4570 3.562557 TGAATCTGCGTATCTGCGTAGTA 59.437 43.478 0.00 0.00 43.32 1.82
3603 4571 2.357952 TGAATCTGCGTATCTGCGTAGT 59.642 45.455 0.00 0.00 43.32 2.73
3604 4572 2.976509 CTGAATCTGCGTATCTGCGTAG 59.023 50.000 0.00 0.00 44.00 3.51
3605 4573 2.858646 GCTGAATCTGCGTATCTGCGTA 60.859 50.000 0.00 0.00 37.81 4.42
3606 4574 1.845266 CTGAATCTGCGTATCTGCGT 58.155 50.000 0.00 0.00 37.81 5.24
3607 4575 0.506080 GCTGAATCTGCGTATCTGCG 59.494 55.000 0.00 0.00 37.81 5.18
3608 4576 1.575244 TGCTGAATCTGCGTATCTGC 58.425 50.000 7.58 0.00 38.18 4.26
3609 4577 3.545624 GCTTTGCTGAATCTGCGTATCTG 60.546 47.826 7.58 0.00 0.00 2.90
3610 4578 2.611292 GCTTTGCTGAATCTGCGTATCT 59.389 45.455 7.58 0.00 0.00 1.98
3611 4579 2.352651 TGCTTTGCTGAATCTGCGTATC 59.647 45.455 7.58 0.00 0.00 2.24
3612 4580 2.353889 CTGCTTTGCTGAATCTGCGTAT 59.646 45.455 7.58 0.00 0.00 3.06
3613 4581 1.733912 CTGCTTTGCTGAATCTGCGTA 59.266 47.619 7.58 0.00 0.00 4.42
3614 4582 0.520404 CTGCTTTGCTGAATCTGCGT 59.480 50.000 7.58 0.00 0.00 5.24
3615 4583 0.797249 GCTGCTTTGCTGAATCTGCG 60.797 55.000 7.58 0.00 0.00 5.18
3616 4584 0.526662 AGCTGCTTTGCTGAATCTGC 59.473 50.000 5.11 5.11 42.33 4.26
3617 4585 2.085320 AGAGCTGCTTTGCTGAATCTG 58.915 47.619 2.53 0.00 44.17 2.90
3618 4586 2.358015 GAGAGCTGCTTTGCTGAATCT 58.642 47.619 2.53 0.00 44.17 2.40
3619 4587 1.401199 GGAGAGCTGCTTTGCTGAATC 59.599 52.381 2.53 0.00 44.17 2.52
3620 4588 1.271762 TGGAGAGCTGCTTTGCTGAAT 60.272 47.619 12.62 0.00 44.17 2.57
3621 4589 0.109153 TGGAGAGCTGCTTTGCTGAA 59.891 50.000 12.62 0.00 44.17 3.02
3622 4590 0.604780 GTGGAGAGCTGCTTTGCTGA 60.605 55.000 12.62 0.00 44.17 4.26
3623 4591 0.605860 AGTGGAGAGCTGCTTTGCTG 60.606 55.000 12.62 0.00 44.17 4.41
3625 4593 1.304509 GGAGTGGAGAGCTGCTTTGC 61.305 60.000 2.53 3.77 0.00 3.68
3626 4594 0.676151 GGGAGTGGAGAGCTGCTTTG 60.676 60.000 2.53 0.00 0.00 2.77
3627 4595 0.839853 AGGGAGTGGAGAGCTGCTTT 60.840 55.000 2.53 0.00 0.00 3.51
3628 4596 1.229464 AGGGAGTGGAGAGCTGCTT 60.229 57.895 2.53 0.00 0.00 3.91
3629 4597 1.988956 CAGGGAGTGGAGAGCTGCT 60.989 63.158 0.00 0.00 0.00 4.24
3630 4598 2.583520 CAGGGAGTGGAGAGCTGC 59.416 66.667 0.00 0.00 0.00 5.25
3650 4618 4.796830 CCTGCTGATTGTTGAATCGATTTG 59.203 41.667 12.81 0.00 40.96 2.32
3656 4624 4.033358 CGACTACCTGCTGATTGTTGAATC 59.967 45.833 0.00 0.00 38.85 2.52
3662 4630 5.339008 TTTATCGACTACCTGCTGATTGT 57.661 39.130 0.00 0.00 0.00 2.71
3673 4641 3.961182 TCGGTGCAGATTTATCGACTAC 58.039 45.455 0.00 0.00 0.00 2.73
3676 4644 1.523095 GCTCGGTGCAGATTTATCGAC 59.477 52.381 0.00 0.00 42.31 4.20
3720 4711 5.055812 GCATAAATCAGAGTTCAGAGAGGG 58.944 45.833 0.00 0.00 0.00 4.30
3724 4715 5.006844 CAGCTGCATAAATCAGAGTTCAGAG 59.993 44.000 0.00 0.00 33.54 3.35
3732 4723 2.423446 TGGCAGCTGCATAAATCAGA 57.577 45.000 37.63 8.54 44.36 3.27
3768 4759 1.806542 AGTAGCTTGCATGAAACCGTG 59.193 47.619 3.33 0.00 0.00 4.94
3769 4760 2.185004 AGTAGCTTGCATGAAACCGT 57.815 45.000 3.33 0.00 0.00 4.83
3794 4785 9.614792 GTGACAGGGTATGTTATTATCTCTTTT 57.385 33.333 0.00 0.00 44.17 2.27
3795 4786 8.768397 TGTGACAGGGTATGTTATTATCTCTTT 58.232 33.333 0.00 0.00 44.17 2.52
3796 4787 8.319057 TGTGACAGGGTATGTTATTATCTCTT 57.681 34.615 0.00 0.00 44.17 2.85
3797 4788 7.914427 TGTGACAGGGTATGTTATTATCTCT 57.086 36.000 0.00 0.00 44.17 3.10
3836 4827 1.787012 GGACTGCAAAACCAATGCTG 58.213 50.000 4.21 4.21 44.14 4.41
3842 4833 1.336440 CATTGTCGGACTGCAAAACCA 59.664 47.619 9.88 0.00 0.00 3.67
3843 4834 1.606668 TCATTGTCGGACTGCAAAACC 59.393 47.619 9.88 0.00 0.00 3.27
3844 4835 2.032799 TGTCATTGTCGGACTGCAAAAC 59.967 45.455 9.88 1.63 36.26 2.43
3845 4836 2.032799 GTGTCATTGTCGGACTGCAAAA 59.967 45.455 9.88 0.00 36.26 2.44
3846 4837 1.601903 GTGTCATTGTCGGACTGCAAA 59.398 47.619 9.88 0.00 36.26 3.68
3847 4838 1.225855 GTGTCATTGTCGGACTGCAA 58.774 50.000 9.88 0.00 36.26 4.08
3848 4839 0.602638 GGTGTCATTGTCGGACTGCA 60.603 55.000 9.88 0.00 36.26 4.41
3849 4840 1.626654 CGGTGTCATTGTCGGACTGC 61.627 60.000 9.88 0.00 36.26 4.40
3850 4841 1.014044 CCGGTGTCATTGTCGGACTG 61.014 60.000 9.88 0.24 44.69 3.51
3851 4842 1.292223 CCGGTGTCATTGTCGGACT 59.708 57.895 9.88 0.00 44.69 3.85
3863 4854 0.737219 GTCATCGTAGTAGCCGGTGT 59.263 55.000 1.90 0.00 37.67 4.16
3869 4860 0.737219 ACCGTGGTCATCGTAGTAGC 59.263 55.000 0.00 0.00 0.00 3.58
3876 4867 2.100631 GGCTTCACCGTGGTCATCG 61.101 63.158 0.00 0.00 0.00 3.84
3898 4889 1.271597 GGAGTTGAGCTTGTCCATGGT 60.272 52.381 12.58 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.