Multiple sequence alignment - TraesCS6B01G163100

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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 TraesCS6B01G163100 chr6B 100.000 3476 0 0 1 3476 169319561 169316086 0.000000e+00 6420.0
1 TraesCS6B01G163100 chr6D 92.297 2168 101 26 480 2612 89004763 89002627 0.000000e+00 3018.0
2 TraesCS6B01G163100 chr6D 81.266 806 136 13 1019 1818 88884959 88884163 3.780000e-179 638.0
3 TraesCS6B01G163100 chr6D 92.290 428 24 5 2614 3033 89002560 89002134 1.790000e-167 599.0
4 TraesCS6B01G163100 chr6D 87.251 251 17 5 1 247 89005230 89004991 4.420000e-69 272.0
5 TraesCS6B01G163100 chr6D 85.366 82 6 3 2403 2478 89002874 89002793 2.880000e-11 80.5
6 TraesCS6B01G163100 chr6A 93.445 1907 78 13 570 2435 107113845 107111945 0.000000e+00 2785.0
7 TraesCS6B01G163100 chr6A 85.152 559 35 21 2617 3165 107111728 107111208 2.380000e-146 529.0
8 TraesCS6B01G163100 chr6A 83.008 512 48 18 1 487 107115075 107114578 8.920000e-116 427.0
9 TraesCS6B01G163100 chr6A 93.220 236 13 2 2377 2612 107112030 107111798 9.240000e-91 344.0
10 TraesCS6B01G163100 chr6A 85.393 178 24 1 3299 3474 107111113 107110936 2.130000e-42 183.0
11 TraesCS6B01G163100 chr6A 100.000 35 0 0 538 572 107114169 107114135 8.050000e-07 65.8
12 TraesCS6B01G163100 chr3D 78.094 1406 288 18 986 2381 453097341 453098736 0.000000e+00 872.0
13 TraesCS6B01G163100 chr3A 78.587 1345 270 15 986 2321 595434911 595436246 0.000000e+00 872.0
14 TraesCS6B01G163100 chr3B 78.395 1333 272 14 986 2310 595288572 595289896 0.000000e+00 852.0
15 TraesCS6B01G163100 chr4B 93.750 80 5 0 3183 3262 464528046 464528125 1.690000e-23 121.0
16 TraesCS6B01G163100 chr4B 92.105 76 4 1 3187 3262 668868291 668868218 4.740000e-19 106.0
17 TraesCS6B01G163100 chr4B 87.640 89 5 2 3183 3266 653543910 653543823 7.940000e-17 99.0
18 TraesCS6B01G163100 chr5B 92.593 81 3 2 3187 3267 660271255 660271178 2.840000e-21 113.0
19 TraesCS6B01G163100 chr2B 92.405 79 5 1 3184 3262 772053325 772053248 1.020000e-20 111.0
20 TraesCS6B01G163100 chr5D 92.105 76 6 0 3187 3262 169535243 169535168 1.320000e-19 108.0
21 TraesCS6B01G163100 chr2D 92.105 76 6 0 3187 3262 379701801 379701726 1.320000e-19 108.0
22 TraesCS6B01G163100 chr5A 90.361 83 4 2 3187 3266 55409950 55409869 4.740000e-19 106.0
23 TraesCS6B01G163100 chr1D 90.909 77 5 1 3187 3263 28967323 28967249 6.140000e-18 102.0


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 TraesCS6B01G163100 chr6B 169316086 169319561 3475 True 6420.000 6420 100.000000 1 3476 1 chr6B.!!$R1 3475
1 TraesCS6B01G163100 chr6D 89002134 89005230 3096 True 992.375 3018 89.301000 1 3033 4 chr6D.!!$R2 3032
2 TraesCS6B01G163100 chr6D 88884163 88884959 796 True 638.000 638 81.266000 1019 1818 1 chr6D.!!$R1 799
3 TraesCS6B01G163100 chr6A 107110936 107115075 4139 True 722.300 2785 90.036333 1 3474 6 chr6A.!!$R1 3473
4 TraesCS6B01G163100 chr3D 453097341 453098736 1395 False 872.000 872 78.094000 986 2381 1 chr3D.!!$F1 1395
5 TraesCS6B01G163100 chr3A 595434911 595436246 1335 False 872.000 872 78.587000 986 2321 1 chr3A.!!$F1 1335
6 TraesCS6B01G163100 chr3B 595288572 595289896 1324 False 852.000 852 78.395000 986 2310 1 chr3B.!!$F1 1324

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
188 215 0.039165 CTTTTTGTCTTCTGCCGGCC 60.039 55.0 26.77 7.71 0.00 6.13 F
374 464 0.321298 TTACTGGAGCAGCCGGAAAC 60.321 55.0 5.05 0.00 46.81 2.78 F
455 545 0.396556 TCATACCACTAGCTGGCCGA 60.397 55.0 0.00 3.69 45.32 5.54 F
2374 3165 0.242017 GCAGTCACCTTTGCCATCAC 59.758 55.0 0.00 0.00 34.28 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 1892 1.086696 TCTTTATCGCAACAGCCTGC 58.913 50.0 0.00 0.0 39.04 4.85 R
1995 2786 1.107538 TCCGGCCATACTTCTCCTCG 61.108 60.0 2.24 0.0 0.00 4.63 R
2387 3178 0.167470 CTGCTGCGATGACAAAGGTG 59.833 55.0 0.00 0.0 0.00 4.00 R
3266 4136 0.109597 CAGCGATGCAAGGTTCCAAC 60.110 55.0 0.00 0.0 0.00 3.77 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.414158 CGACTATCTGGGACCCACAT 58.586 55.000 9.95 7.99 0.00 3.21
32 33 1.521681 GACCCACATACAGCGCCTC 60.522 63.158 2.29 0.00 0.00 4.70
33 34 1.961180 GACCCACATACAGCGCCTCT 61.961 60.000 2.29 0.00 0.00 3.69
34 35 1.227380 CCCACATACAGCGCCTCTC 60.227 63.158 2.29 0.00 0.00 3.20
35 36 1.227380 CCACATACAGCGCCTCTCC 60.227 63.158 2.29 0.00 0.00 3.71
36 37 1.589993 CACATACAGCGCCTCTCCG 60.590 63.158 2.29 0.00 0.00 4.63
82 91 0.323629 CCACCAGGTAAAGCTTCGGA 59.676 55.000 0.00 0.00 0.00 4.55
161 179 0.745468 CTTCCCGACCTAGTAGTGCC 59.255 60.000 0.00 0.00 0.00 5.01
175 198 0.954452 AGTGCCTTCTCGCCTTTTTG 59.046 50.000 0.00 0.00 0.00 2.44
182 205 3.058639 CCTTCTCGCCTTTTTGTCTTCTG 60.059 47.826 0.00 0.00 0.00 3.02
183 206 1.873591 TCTCGCCTTTTTGTCTTCTGC 59.126 47.619 0.00 0.00 0.00 4.26
188 215 0.039165 CTTTTTGTCTTCTGCCGGCC 60.039 55.000 26.77 7.71 0.00 6.13
189 216 1.791103 TTTTTGTCTTCTGCCGGCCG 61.791 55.000 26.77 21.04 0.00 6.13
191 218 3.876589 TTGTCTTCTGCCGGCCGTC 62.877 63.158 26.77 13.25 0.00 4.79
247 274 2.622977 GGGGGATTTTGCTGATGTGGTA 60.623 50.000 0.00 0.00 0.00 3.25
248 275 2.427095 GGGGATTTTGCTGATGTGGTAC 59.573 50.000 0.00 0.00 0.00 3.34
249 276 3.088532 GGGATTTTGCTGATGTGGTACA 58.911 45.455 0.00 0.00 0.00 2.90
250 277 3.129287 GGGATTTTGCTGATGTGGTACAG 59.871 47.826 0.00 0.00 41.80 2.74
251 278 4.009675 GGATTTTGCTGATGTGGTACAGA 58.990 43.478 0.00 0.00 41.80 3.41
277 316 0.815615 GATTTCGGTGCTAGCCCCTG 60.816 60.000 14.68 9.12 0.00 4.45
281 320 3.813724 GGTGCTAGCCCCTGCCAT 61.814 66.667 13.29 0.00 38.69 4.40
292 346 0.890683 CCCTGCCATGTTCTTGTTCC 59.109 55.000 0.00 0.00 0.00 3.62
317 371 1.065854 ACCGGAAGAAGAAGCTGATGG 60.066 52.381 9.46 0.00 0.00 3.51
318 372 1.012841 CGGAAGAAGAAGCTGATGGC 58.987 55.000 0.00 0.00 42.19 4.40
374 464 0.321298 TTACTGGAGCAGCCGGAAAC 60.321 55.000 5.05 0.00 46.81 2.78
376 466 4.344865 TGGAGCAGCCGGAAACCC 62.345 66.667 5.05 0.00 40.66 4.11
377 467 4.035102 GGAGCAGCCGGAAACCCT 62.035 66.667 5.05 0.00 0.00 4.34
378 468 2.747855 GAGCAGCCGGAAACCCTG 60.748 66.667 5.05 3.10 0.00 4.45
379 469 3.553095 GAGCAGCCGGAAACCCTGT 62.553 63.158 5.05 0.00 0.00 4.00
380 470 2.180159 GAGCAGCCGGAAACCCTGTA 62.180 60.000 5.05 0.00 0.00 2.74
381 471 2.038837 GCAGCCGGAAACCCTGTAC 61.039 63.158 5.05 0.00 0.00 2.90
382 472 1.376812 CAGCCGGAAACCCTGTACC 60.377 63.158 5.05 0.00 0.00 3.34
383 473 1.538135 AGCCGGAAACCCTGTACCT 60.538 57.895 5.05 0.00 0.00 3.08
403 493 3.570125 CCTCTGTAGCATCAGACCGATTA 59.430 47.826 6.74 0.00 39.20 1.75
448 538 6.583562 AGGTGTCTAATTTCATACCACTAGC 58.416 40.000 0.00 0.00 0.00 3.42
455 545 0.396556 TCATACCACTAGCTGGCCGA 60.397 55.000 0.00 3.69 45.32 5.54
465 555 1.889573 GCTGGCCGACCTGATTAGC 60.890 63.158 0.00 0.00 37.06 3.09
496 588 1.702182 TGCCATTTCAGTGCTTTGGA 58.298 45.000 8.67 0.00 0.00 3.53
501 593 3.007182 CCATTTCAGTGCTTTGGATGGTT 59.993 43.478 11.97 0.00 32.40 3.67
506 598 3.010027 TCAGTGCTTTGGATGGTTGGATA 59.990 43.478 0.00 0.00 0.00 2.59
510 603 4.947388 GTGCTTTGGATGGTTGGATAAGTA 59.053 41.667 0.00 0.00 0.00 2.24
513 606 6.667414 TGCTTTGGATGGTTGGATAAGTATTT 59.333 34.615 0.00 0.00 0.00 1.40
536 629 6.478512 TTTTTCCCCAATAATGGCAGATAC 57.521 37.500 0.00 0.00 46.09 2.24
583 1324 3.120546 GGTGCTATGTATGTATGCTTGCG 60.121 47.826 0.00 0.00 0.00 4.85
598 1339 2.535732 GCTTGCGAAATCACGATGAGAC 60.536 50.000 0.00 0.00 35.09 3.36
619 1363 3.636153 AGGCAATAGTCCCTGAAAGAC 57.364 47.619 0.00 0.00 34.07 3.01
653 1397 9.710900 GGATTTTCTTAATTTTGTCATGGACTT 57.289 29.630 0.00 0.00 33.15 3.01
670 1425 3.242543 GGACTTCTGAATATGCTTGTGCG 60.243 47.826 0.00 0.00 43.34 5.34
677 1432 5.180304 TCTGAATATGCTTGTGCGTTTGTAA 59.820 36.000 0.00 0.00 43.34 2.41
710 1482 5.367302 CCCCATTTGTGTTTGTTCTGATTT 58.633 37.500 0.00 0.00 0.00 2.17
713 1485 5.277442 CCATTTGTGTTTGTTCTGATTTGGC 60.277 40.000 0.00 0.00 0.00 4.52
722 1494 7.437862 TGTTTGTTCTGATTTGGCTTGTTTATC 59.562 33.333 0.00 0.00 0.00 1.75
727 1499 6.611381 TCTGATTTGGCTTGTTTATCTTTCG 58.389 36.000 0.00 0.00 0.00 3.46
740 1512 2.613026 TCTTTCGTTGCAGTTCTGGA 57.387 45.000 1.97 0.00 0.00 3.86
834 1606 5.545063 TGTTGAGTTATCACAAGAGTGGA 57.455 39.130 0.00 0.00 45.91 4.02
861 1635 3.064820 CCATACTGGTTCGGTATTTGTGC 59.935 47.826 0.00 0.00 34.13 4.57
862 1636 1.153353 ACTGGTTCGGTATTTGTGCG 58.847 50.000 0.00 0.00 0.00 5.34
930 1718 6.088819 AGGCCACATACCTATTAATAGACCA 58.911 40.000 21.75 8.21 35.10 4.02
932 1720 5.867716 GCCACATACCTATTAATAGACCACG 59.132 44.000 21.75 8.68 32.05 4.94
955 1743 2.273370 AACGTAGTGCATAGTGGACG 57.727 50.000 0.00 0.00 45.00 4.79
1017 1805 4.932200 GCTATAATGGATGAAAGGAGGACG 59.068 45.833 0.00 0.00 0.00 4.79
1104 1892 0.804989 GTCGGAATCTTGCAACTGGG 59.195 55.000 0.00 0.00 0.00 4.45
1176 1964 5.126067 GGCCTAATTGTGCAGATAAAGAGA 58.874 41.667 0.00 0.00 0.00 3.10
1269 2057 7.781056 AGAGCAAGATTTACTTTGTTTTGGAA 58.219 30.769 0.00 0.00 36.61 3.53
1461 2252 4.833390 ACCTTAAAGTCTCTGATTTCGGG 58.167 43.478 0.00 0.00 0.00 5.14
1638 2429 1.613925 GCTGGTTTCCTTCCTTTCCAC 59.386 52.381 0.00 0.00 0.00 4.02
1716 2507 2.151202 CGCCCTTTTTCTGTTGAGCTA 58.849 47.619 0.00 0.00 0.00 3.32
1895 2686 3.009916 ACCTCTGAATCAACAGAAGGCAT 59.990 43.478 0.00 0.00 44.62 4.40
1900 2691 5.124936 TCTGAATCAACAGAAGGCATCAATG 59.875 40.000 0.00 0.00 42.79 2.82
1971 2762 7.120432 GCCTTTGACATAATTTCTCTCTCAACT 59.880 37.037 0.00 0.00 0.00 3.16
1992 2783 4.772100 ACTGGGTTTGACCTATCCAATTTG 59.228 41.667 0.00 0.00 38.64 2.32
1995 2786 5.245075 TGGGTTTGACCTATCCAATTTGTTC 59.755 40.000 0.00 0.00 38.64 3.18
2374 3165 0.242017 GCAGTCACCTTTGCCATCAC 59.758 55.000 0.00 0.00 34.28 3.06
2375 3166 1.901591 CAGTCACCTTTGCCATCACT 58.098 50.000 0.00 0.00 0.00 3.41
2394 3185 3.117589 GCAGCAGCAATCACCTTTG 57.882 52.632 0.00 0.00 41.58 2.77
2395 3186 0.316204 GCAGCAGCAATCACCTTTGT 59.684 50.000 0.00 0.00 41.58 2.83
2396 3187 1.668047 GCAGCAGCAATCACCTTTGTC 60.668 52.381 0.00 0.00 41.58 3.18
2397 3188 1.610038 CAGCAGCAATCACCTTTGTCA 59.390 47.619 0.00 0.00 0.00 3.58
2398 3189 2.230508 CAGCAGCAATCACCTTTGTCAT 59.769 45.455 0.00 0.00 0.00 3.06
2399 3190 2.490903 AGCAGCAATCACCTTTGTCATC 59.509 45.455 0.00 0.00 0.00 2.92
2612 3406 2.713967 GCATTGCAACGGCCAGGAT 61.714 57.895 12.66 0.00 40.13 3.24
2664 3526 6.183360 CCTGTGTTAGTAGATCAGTTGCCTAT 60.183 42.308 0.00 0.00 0.00 2.57
2792 3657 3.119209 TGCACTGCAGAAATTTGTGTTCA 60.119 39.130 23.35 6.37 33.32 3.18
2793 3658 3.243643 GCACTGCAGAAATTTGTGTTCAC 59.756 43.478 23.35 1.15 0.00 3.18
2798 3663 3.798337 GCAGAAATTTGTGTTCACTGTGG 59.202 43.478 15.91 0.00 0.00 4.17
2817 3682 4.751600 TGTGGCTGAAGATATTGAATAGCG 59.248 41.667 0.00 0.00 0.00 4.26
2822 3687 8.043113 TGGCTGAAGATATTGAATAGCGATAAT 58.957 33.333 0.00 0.00 0.00 1.28
2837 3705 4.520111 AGCGATAATAGAAATGGCATGCAA 59.480 37.500 21.36 9.21 31.22 4.08
2845 3713 1.811195 ATGGCATGCAACCATCACG 59.189 52.632 21.36 0.00 44.85 4.35
2848 3716 0.248743 GGCATGCAACCATCACGATG 60.249 55.000 21.36 0.00 38.51 3.84
2853 3721 2.892374 TGCAACCATCACGATGTCTAG 58.108 47.619 6.30 0.00 37.11 2.43
2860 3728 3.448686 CATCACGATGTCTAGGAACACC 58.551 50.000 0.00 0.00 34.23 4.16
2903 3772 2.852449 ACCATGTGATATGTGGAACCCT 59.148 45.455 0.00 0.00 36.82 4.34
2998 3868 8.443953 TCATTTTTCTGGTTAAAATTGGTTGG 57.556 30.769 0.00 0.00 34.01 3.77
3033 3903 9.866936 CCAGTTTTTGTATTTTGAATGTTCATG 57.133 29.630 0.00 0.00 37.00 3.07
3078 3948 7.386299 AGTGCTTTATGAAGGAGCTAAATATCG 59.614 37.037 0.00 0.00 33.59 2.92
3146 4016 4.634349 TGTGTGTTAATAGCGAAACGAC 57.366 40.909 0.00 0.00 0.00 4.34
3147 4017 4.049869 TGTGTGTTAATAGCGAAACGACA 58.950 39.130 0.00 0.00 0.00 4.35
3158 4028 2.029728 GCGAAACGACATCATCTTCTGG 59.970 50.000 0.00 0.00 0.00 3.86
3160 4030 3.061295 CGAAACGACATCATCTTCTGGTG 59.939 47.826 0.00 0.00 42.09 4.17
3161 4031 2.015736 ACGACATCATCTTCTGGTGC 57.984 50.000 0.00 0.00 39.81 5.01
3162 4032 1.276138 ACGACATCATCTTCTGGTGCA 59.724 47.619 0.00 0.00 39.81 4.57
3163 4033 2.093288 ACGACATCATCTTCTGGTGCAT 60.093 45.455 0.00 0.00 39.81 3.96
3164 4034 2.543012 CGACATCATCTTCTGGTGCATC 59.457 50.000 0.00 0.00 39.81 3.91
3166 4036 3.542648 ACATCATCTTCTGGTGCATCAG 58.457 45.455 21.48 21.48 39.81 2.90
3167 4037 2.034104 TCATCTTCTGGTGCATCAGC 57.966 50.000 22.65 0.00 42.57 4.26
3189 4059 3.268023 GGAAGTGCCTTGCTATGTACT 57.732 47.619 0.00 0.00 0.00 2.73
3190 4060 3.198872 GGAAGTGCCTTGCTATGTACTC 58.801 50.000 0.00 0.00 0.00 2.59
3191 4061 2.990066 AGTGCCTTGCTATGTACTCC 57.010 50.000 0.00 0.00 0.00 3.85
3192 4062 2.472029 AGTGCCTTGCTATGTACTCCT 58.528 47.619 0.00 0.00 0.00 3.69
3193 4063 2.840651 AGTGCCTTGCTATGTACTCCTT 59.159 45.455 0.00 0.00 0.00 3.36
3194 4064 3.118592 AGTGCCTTGCTATGTACTCCTTC 60.119 47.826 0.00 0.00 0.00 3.46
3195 4065 2.170607 TGCCTTGCTATGTACTCCTTCC 59.829 50.000 0.00 0.00 0.00 3.46
3196 4066 2.170607 GCCTTGCTATGTACTCCTTCCA 59.829 50.000 0.00 0.00 0.00 3.53
3197 4067 3.181450 GCCTTGCTATGTACTCCTTCCAT 60.181 47.826 0.00 0.00 0.00 3.41
3198 4068 4.687219 GCCTTGCTATGTACTCCTTCCATT 60.687 45.833 0.00 0.00 0.00 3.16
3199 4069 5.059833 CCTTGCTATGTACTCCTTCCATTC 58.940 45.833 0.00 0.00 0.00 2.67
3200 4070 4.689612 TGCTATGTACTCCTTCCATTCC 57.310 45.455 0.00 0.00 0.00 3.01
3201 4071 4.037222 TGCTATGTACTCCTTCCATTCCA 58.963 43.478 0.00 0.00 0.00 3.53
3202 4072 4.473196 TGCTATGTACTCCTTCCATTCCAA 59.527 41.667 0.00 0.00 0.00 3.53
3203 4073 5.132648 TGCTATGTACTCCTTCCATTCCAAT 59.867 40.000 0.00 0.00 0.00 3.16
3204 4074 6.064717 GCTATGTACTCCTTCCATTCCAATT 58.935 40.000 0.00 0.00 0.00 2.32
3205 4075 6.547510 GCTATGTACTCCTTCCATTCCAATTT 59.452 38.462 0.00 0.00 0.00 1.82
3206 4076 7.719633 GCTATGTACTCCTTCCATTCCAATTTA 59.280 37.037 0.00 0.00 0.00 1.40
3207 4077 7.881775 ATGTACTCCTTCCATTCCAATTTAC 57.118 36.000 0.00 0.00 0.00 2.01
3208 4078 7.027874 TGTACTCCTTCCATTCCAATTTACT 57.972 36.000 0.00 0.00 0.00 2.24
3209 4079 7.110155 TGTACTCCTTCCATTCCAATTTACTC 58.890 38.462 0.00 0.00 0.00 2.59
3210 4080 5.186198 ACTCCTTCCATTCCAATTTACTCG 58.814 41.667 0.00 0.00 0.00 4.18
3211 4081 5.174037 TCCTTCCATTCCAATTTACTCGT 57.826 39.130 0.00 0.00 0.00 4.18
3212 4082 5.183228 TCCTTCCATTCCAATTTACTCGTC 58.817 41.667 0.00 0.00 0.00 4.20
3213 4083 4.034048 CCTTCCATTCCAATTTACTCGTCG 59.966 45.833 0.00 0.00 0.00 5.12
3214 4084 4.196626 TCCATTCCAATTTACTCGTCGT 57.803 40.909 0.00 0.00 0.00 4.34
3215 4085 3.930229 TCCATTCCAATTTACTCGTCGTG 59.070 43.478 0.00 0.00 0.00 4.35
3216 4086 3.063452 CCATTCCAATTTACTCGTCGTGG 59.937 47.826 0.00 0.00 0.00 4.94
3217 4087 3.389925 TTCCAATTTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
3218 4088 3.389925 TCCAATTTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
3219 4089 3.731089 TCCAATTTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
3220 4090 4.128643 TCCAATTTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
3221 4091 4.575645 TCCAATTTACTCGTCGTGGTTTTT 59.424 37.500 0.00 0.00 0.00 1.94
3222 4092 4.673311 CCAATTTACTCGTCGTGGTTTTTG 59.327 41.667 0.00 0.00 0.00 2.44
3223 4093 5.503498 CAATTTACTCGTCGTGGTTTTTGA 58.497 37.500 0.00 0.00 0.00 2.69
3224 4094 5.738118 ATTTACTCGTCGTGGTTTTTGAA 57.262 34.783 0.00 0.00 0.00 2.69
3225 4095 4.519191 TTACTCGTCGTGGTTTTTGAAC 57.481 40.909 0.00 0.00 0.00 3.18
3226 4096 2.624636 ACTCGTCGTGGTTTTTGAACT 58.375 42.857 0.00 0.00 0.00 3.01
3227 4097 3.784338 ACTCGTCGTGGTTTTTGAACTA 58.216 40.909 0.00 0.00 0.00 2.24
3228 4098 4.183101 ACTCGTCGTGGTTTTTGAACTAA 58.817 39.130 0.00 0.00 0.00 2.24
3229 4099 4.630940 ACTCGTCGTGGTTTTTGAACTAAA 59.369 37.500 0.00 0.00 0.00 1.85
3230 4100 5.122082 ACTCGTCGTGGTTTTTGAACTAAAA 59.878 36.000 0.00 0.00 36.51 1.52
3231 4101 5.323105 TCGTCGTGGTTTTTGAACTAAAAC 58.677 37.500 13.17 13.17 43.78 2.43
3238 4108 5.594215 GTTTTTGAACTAAAACCACGACG 57.406 39.130 11.38 0.00 40.46 5.12
3239 4109 5.323105 GTTTTTGAACTAAAACCACGACGA 58.677 37.500 0.00 0.00 40.46 4.20
3240 4110 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
3241 4111 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
3242 4112 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
3243 4113 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
3244 4114 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
3245 4115 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
3246 4116 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
3247 4117 5.531634 ACTAAAACCACGACGAGTAAATCA 58.468 37.500 0.00 0.00 0.00 2.57
3248 4118 4.985044 AAAACCACGACGAGTAAATCAG 57.015 40.909 0.00 0.00 0.00 2.90
3249 4119 3.928727 AACCACGACGAGTAAATCAGA 57.071 42.857 0.00 0.00 0.00 3.27
3250 4120 3.928727 ACCACGACGAGTAAATCAGAA 57.071 42.857 0.00 0.00 0.00 3.02
3251 4121 3.572584 ACCACGACGAGTAAATCAGAAC 58.427 45.455 0.00 0.00 0.00 3.01
3252 4122 2.592897 CCACGACGAGTAAATCAGAACG 59.407 50.000 0.00 0.00 0.00 3.95
3253 4123 2.592897 CACGACGAGTAAATCAGAACGG 59.407 50.000 0.00 0.00 0.00 4.44
3254 4124 2.485426 ACGACGAGTAAATCAGAACGGA 59.515 45.455 0.00 0.00 0.00 4.69
3255 4125 3.099362 CGACGAGTAAATCAGAACGGAG 58.901 50.000 0.00 0.00 0.00 4.63
3256 4126 3.436496 GACGAGTAAATCAGAACGGAGG 58.564 50.000 0.00 0.00 0.00 4.30
3257 4127 2.165845 ACGAGTAAATCAGAACGGAGGG 59.834 50.000 0.00 0.00 0.00 4.30
3258 4128 2.426024 CGAGTAAATCAGAACGGAGGGA 59.574 50.000 0.00 0.00 0.00 4.20
3259 4129 3.489398 CGAGTAAATCAGAACGGAGGGAG 60.489 52.174 0.00 0.00 0.00 4.30
3260 4130 3.442076 AGTAAATCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
3261 4131 4.607239 AGTAAATCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
3262 4132 5.021458 AGTAAATCAGAACGGAGGGAGTAA 58.979 41.667 0.00 0.00 0.00 2.24
3263 4133 4.473477 AAATCAGAACGGAGGGAGTAAG 57.527 45.455 0.00 0.00 0.00 2.34
3264 4134 2.893215 TCAGAACGGAGGGAGTAAGA 57.107 50.000 0.00 0.00 0.00 2.10
3265 4135 3.383698 TCAGAACGGAGGGAGTAAGAT 57.616 47.619 0.00 0.00 0.00 2.40
3266 4136 3.024547 TCAGAACGGAGGGAGTAAGATG 58.975 50.000 0.00 0.00 0.00 2.90
3267 4137 2.761208 CAGAACGGAGGGAGTAAGATGT 59.239 50.000 0.00 0.00 0.00 3.06
3268 4138 3.195825 CAGAACGGAGGGAGTAAGATGTT 59.804 47.826 0.00 0.00 0.00 2.71
3269 4139 3.195825 AGAACGGAGGGAGTAAGATGTTG 59.804 47.826 0.00 0.00 0.00 3.33
3270 4140 1.831736 ACGGAGGGAGTAAGATGTTGG 59.168 52.381 0.00 0.00 0.00 3.77
3271 4141 2.108168 CGGAGGGAGTAAGATGTTGGA 58.892 52.381 0.00 0.00 0.00 3.53
3272 4142 2.500098 CGGAGGGAGTAAGATGTTGGAA 59.500 50.000 0.00 0.00 0.00 3.53
3273 4143 3.679083 CGGAGGGAGTAAGATGTTGGAAC 60.679 52.174 0.00 0.00 0.00 3.62
3274 4144 3.370633 GGAGGGAGTAAGATGTTGGAACC 60.371 52.174 0.00 0.00 0.00 3.62
3275 4145 3.519913 GAGGGAGTAAGATGTTGGAACCT 59.480 47.826 0.00 0.00 0.00 3.50
3276 4146 3.916989 AGGGAGTAAGATGTTGGAACCTT 59.083 43.478 0.00 0.00 0.00 3.50
3277 4147 4.010349 GGGAGTAAGATGTTGGAACCTTG 58.990 47.826 0.00 0.00 0.00 3.61
3278 4148 3.440522 GGAGTAAGATGTTGGAACCTTGC 59.559 47.826 0.00 0.00 0.00 4.01
3279 4149 4.072131 GAGTAAGATGTTGGAACCTTGCA 58.928 43.478 0.00 0.00 0.00 4.08
3280 4150 4.666512 AGTAAGATGTTGGAACCTTGCAT 58.333 39.130 0.00 0.00 0.00 3.96
3281 4151 4.702131 AGTAAGATGTTGGAACCTTGCATC 59.298 41.667 0.00 11.54 36.97 3.91
3282 4152 2.086869 AGATGTTGGAACCTTGCATCG 58.913 47.619 0.00 0.00 40.37 3.84
3283 4153 0.527565 ATGTTGGAACCTTGCATCGC 59.472 50.000 0.00 0.00 0.00 4.58
3284 4154 0.537143 TGTTGGAACCTTGCATCGCT 60.537 50.000 0.00 0.00 0.00 4.93
3285 4155 0.109597 GTTGGAACCTTGCATCGCTG 60.110 55.000 0.00 0.00 0.00 5.18
3294 4164 2.125391 GCATCGCTGCTCACCAGA 60.125 61.111 3.51 0.00 44.64 3.86
3295 4165 1.523258 GCATCGCTGCTCACCAGAT 60.523 57.895 3.51 0.00 44.64 2.90
3296 4166 0.249615 GCATCGCTGCTCACCAGATA 60.250 55.000 3.51 0.00 44.64 1.98
3311 4181 6.291377 TCACCAGATATCTATGTTTGCCTTC 58.709 40.000 4.54 0.00 0.00 3.46
3312 4182 5.471456 CACCAGATATCTATGTTTGCCTTCC 59.529 44.000 4.54 0.00 0.00 3.46
3323 4193 2.985847 GCCTTCCGCCTTGCAGTT 60.986 61.111 0.00 0.00 0.00 3.16
3382 4329 1.783711 GCACGCGAGATATGTTGAGAG 59.216 52.381 15.93 0.00 0.00 3.20
3384 4331 3.855154 GCACGCGAGATATGTTGAGAGAT 60.855 47.826 15.93 0.00 0.00 2.75
3388 4335 3.240884 CGAGATATGTTGAGAGATGCCG 58.759 50.000 0.00 0.00 0.00 5.69
3390 4337 4.083271 CGAGATATGTTGAGAGATGCCGTA 60.083 45.833 0.00 0.00 0.00 4.02
3393 4340 2.654749 TGTTGAGAGATGCCGTACAG 57.345 50.000 0.00 0.00 0.00 2.74
3408 4355 0.393808 TACAGCGCCCCTGGAATTTC 60.394 55.000 2.29 0.00 46.14 2.17
3409 4356 2.438434 AGCGCCCCTGGAATTTCG 60.438 61.111 2.29 0.00 0.00 3.46
3417 4364 2.706190 CCCCTGGAATTTCGTCTATCCT 59.294 50.000 0.00 0.00 33.02 3.24
3422 4369 6.217294 CCTGGAATTTCGTCTATCCTTCTAC 58.783 44.000 0.00 0.00 33.02 2.59
3451 4400 9.757227 TTCAAGATAATTTAAGTTTGTTGGTGG 57.243 29.630 0.00 0.00 0.00 4.61
3458 4407 3.971245 AAGTTTGTTGGTGGAAAAGCA 57.029 38.095 0.00 0.00 0.00 3.91
3474 4423 5.926542 GGAAAAGCAAAGAAATGGGTTAGTC 59.073 40.000 0.00 0.00 0.00 2.59
3475 4424 6.462347 GGAAAAGCAAAGAAATGGGTTAGTCA 60.462 38.462 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.826754 CTGCGGAGAGGCGCTGTA 61.827 66.667 7.64 0.00 35.06 2.74
146 164 1.677052 GAGAAGGCACTACTAGGTCGG 59.323 57.143 0.00 0.00 38.49 4.79
161 179 3.608008 GCAGAAGACAAAAAGGCGAGAAG 60.608 47.826 0.00 0.00 0.00 2.85
189 216 3.400054 AACTAGCCGGCCAGGGAC 61.400 66.667 25.90 0.00 41.48 4.46
191 218 2.666596 GATCAACTAGCCGGCCAGGG 62.667 65.000 25.90 16.97 41.48 4.45
222 249 3.962718 CACATCAGCAAAATCCCCCTATT 59.037 43.478 0.00 0.00 0.00 1.73
247 274 0.252742 ACCGAAATCCCTCCCTCTGT 60.253 55.000 0.00 0.00 0.00 3.41
248 275 0.179000 CACCGAAATCCCTCCCTCTG 59.821 60.000 0.00 0.00 0.00 3.35
249 276 1.627297 GCACCGAAATCCCTCCCTCT 61.627 60.000 0.00 0.00 0.00 3.69
250 277 1.153147 GCACCGAAATCCCTCCCTC 60.153 63.158 0.00 0.00 0.00 4.30
251 278 0.326238 TAGCACCGAAATCCCTCCCT 60.326 55.000 0.00 0.00 0.00 4.20
277 316 1.816074 TACCGGAACAAGAACATGGC 58.184 50.000 9.46 0.00 0.00 4.40
279 318 2.158841 CGGTTACCGGAACAAGAACATG 59.841 50.000 17.00 0.00 44.15 3.21
280 319 2.419667 CGGTTACCGGAACAAGAACAT 58.580 47.619 17.00 0.00 44.15 2.71
281 320 1.868469 CGGTTACCGGAACAAGAACA 58.132 50.000 17.00 0.00 44.15 3.18
350 434 1.221414 CGGCTGCTCCAGTAAATAGC 58.779 55.000 0.00 0.00 36.77 2.97
353 437 0.618458 TTCCGGCTGCTCCAGTAAAT 59.382 50.000 0.00 0.00 33.43 1.40
374 464 2.363680 CTGATGCTACAGAGGTACAGGG 59.636 54.545 0.00 0.00 39.94 4.45
376 466 3.067461 GGTCTGATGCTACAGAGGTACAG 59.933 52.174 12.22 0.00 45.67 2.74
377 467 3.024547 GGTCTGATGCTACAGAGGTACA 58.975 50.000 12.22 0.00 45.67 2.90
378 468 2.033550 CGGTCTGATGCTACAGAGGTAC 59.966 54.545 12.22 3.69 45.67 3.34
379 469 2.092592 TCGGTCTGATGCTACAGAGGTA 60.093 50.000 12.22 1.10 45.67 3.08
380 470 1.107114 CGGTCTGATGCTACAGAGGT 58.893 55.000 12.22 0.00 45.67 3.85
381 471 1.393603 TCGGTCTGATGCTACAGAGG 58.606 55.000 12.22 8.65 45.67 3.69
382 472 3.724508 AATCGGTCTGATGCTACAGAG 57.275 47.619 12.22 4.39 45.67 3.35
383 473 3.003378 CGTAATCGGTCTGATGCTACAGA 59.997 47.826 8.80 8.80 43.39 3.41
424 514 6.384305 AGCTAGTGGTATGAAATTAGACACCT 59.616 38.462 0.00 0.00 0.00 4.00
448 538 0.179000 AAGCTAATCAGGTCGGCCAG 59.821 55.000 9.71 0.00 37.19 4.85
455 545 4.322057 ACAATTGGGAAGCTAATCAGGT 57.678 40.909 10.83 0.00 0.00 4.00
513 606 5.068460 CGTATCTGCCATTATTGGGGAAAAA 59.932 40.000 5.82 0.00 43.84 1.94
516 609 3.750371 CGTATCTGCCATTATTGGGGAA 58.250 45.455 5.82 0.00 43.84 3.97
518 611 1.812571 GCGTATCTGCCATTATTGGGG 59.187 52.381 5.82 0.00 43.84 4.96
523 616 5.934625 CCTAAAGAAGCGTATCTGCCATTAT 59.065 40.000 0.00 0.00 34.65 1.28
528 621 1.867865 GCCTAAAGAAGCGTATCTGCC 59.132 52.381 0.00 0.00 34.65 4.85
536 629 4.095610 CGGTTAATTTGCCTAAAGAAGCG 58.904 43.478 0.00 0.00 38.74 4.68
583 1324 2.621338 TGCCTGTCTCATCGTGATTTC 58.379 47.619 0.00 0.00 0.00 2.17
653 1397 3.501828 ACAAACGCACAAGCATATTCAGA 59.498 39.130 0.00 0.00 42.27 3.27
670 1425 3.025262 TGGGGGTCAAGTTGTTACAAAC 58.975 45.455 0.00 0.00 0.00 2.93
677 1432 2.038659 CACAAATGGGGGTCAAGTTGT 58.961 47.619 2.11 0.00 37.84 3.32
710 1482 3.316588 TGCAACGAAAGATAAACAAGCCA 59.683 39.130 0.00 0.00 0.00 4.75
713 1485 6.358030 CAGAACTGCAACGAAAGATAAACAAG 59.642 38.462 0.00 0.00 0.00 3.16
722 1494 2.213499 AGTCCAGAACTGCAACGAAAG 58.787 47.619 0.00 0.00 36.65 2.62
740 1512 1.364901 CCGTTACGGTGTCACCAGT 59.635 57.895 21.91 20.18 42.73 4.00
802 1574 8.463930 TTGTGATAACTCAACAAGGAAATTCT 57.536 30.769 0.00 0.00 31.85 2.40
861 1635 0.732880 CTCCAGACGCAGGTGTAACG 60.733 60.000 0.00 0.00 38.12 3.18
862 1636 1.014564 GCTCCAGACGCAGGTGTAAC 61.015 60.000 0.00 0.00 0.00 2.50
932 1720 3.861689 GTCCACTATGCACTACGTTTACC 59.138 47.826 0.00 0.00 0.00 2.85
955 1743 1.373570 AGCCGAATAGTGCTTTCAGC 58.626 50.000 0.00 0.00 42.82 4.26
1008 1796 3.610911 GTCCATCAAAATCGTCCTCCTT 58.389 45.455 0.00 0.00 0.00 3.36
1017 1805 6.632834 CGATTTCATAACGGTCCATCAAAATC 59.367 38.462 0.00 0.00 0.00 2.17
1104 1892 1.086696 TCTTTATCGCAACAGCCTGC 58.913 50.000 0.00 0.00 39.04 4.85
1176 1964 6.776887 ACCAATCCCATTATTGAGATCTCT 57.223 37.500 22.95 6.99 38.84 3.10
1461 2252 4.096003 TCGGCCAGGGCACTTAGC 62.096 66.667 14.59 0.00 44.11 3.09
1895 2686 4.365514 TCTTGGTTAACCTCTGCATTGA 57.634 40.909 24.78 8.73 36.82 2.57
1900 2691 1.464997 CGCTTCTTGGTTAACCTCTGC 59.535 52.381 24.78 18.46 36.82 4.26
1971 2762 4.746466 ACAAATTGGATAGGTCAAACCCA 58.254 39.130 0.00 0.00 39.75 4.51
1992 2783 1.536284 CGGCCATACTTCTCCTCGAAC 60.536 57.143 2.24 0.00 0.00 3.95
1995 2786 1.107538 TCCGGCCATACTTCTCCTCG 61.108 60.000 2.24 0.00 0.00 4.63
2021 2812 2.170607 GGCTGCCTAGTGGTAAATCTGA 59.829 50.000 12.43 0.00 35.27 3.27
2223 3014 9.656323 TTATACTCTATAGTGTCTCCATTGGTT 57.344 33.333 10.62 0.00 36.36 3.67
2385 3176 1.089920 GCTGCGATGACAAAGGTGAT 58.910 50.000 0.00 0.00 0.00 3.06
2386 3177 0.250252 TGCTGCGATGACAAAGGTGA 60.250 50.000 0.00 0.00 0.00 4.02
2387 3178 0.167470 CTGCTGCGATGACAAAGGTG 59.833 55.000 0.00 0.00 0.00 4.00
2388 3179 1.580845 GCTGCTGCGATGACAAAGGT 61.581 55.000 0.00 0.00 0.00 3.50
2389 3180 1.136147 GCTGCTGCGATGACAAAGG 59.864 57.895 0.00 0.00 0.00 3.11
2390 3181 0.179197 CTGCTGCTGCGATGACAAAG 60.179 55.000 11.21 0.00 43.34 2.77
2391 3182 1.871077 CTGCTGCTGCGATGACAAA 59.129 52.632 11.21 0.00 43.34 2.83
2392 3183 2.683859 GCTGCTGCTGCGATGACAA 61.684 57.895 15.65 0.00 43.34 3.18
2393 3184 3.122971 GCTGCTGCTGCGATGACA 61.123 61.111 15.65 0.00 43.34 3.58
2394 3185 1.989966 ATTGCTGCTGCTGCGATGAC 61.990 55.000 27.06 3.54 43.34 3.06
2395 3186 1.712018 GATTGCTGCTGCTGCGATGA 61.712 55.000 31.02 16.04 43.34 2.92
2396 3187 1.298413 GATTGCTGCTGCTGCGATG 60.298 57.895 31.02 5.04 43.34 3.84
2397 3188 1.747745 TGATTGCTGCTGCTGCGAT 60.748 52.632 27.72 27.72 43.34 4.58
2398 3189 2.358984 TGATTGCTGCTGCTGCGA 60.359 55.556 21.42 21.42 43.34 5.10
2399 3190 2.202440 GTGATTGCTGCTGCTGCG 60.202 61.111 23.38 7.03 43.34 5.18
2532 3326 1.524393 TACTGCTGATGCCATGGCG 60.524 57.895 30.87 17.94 45.51 5.69
2596 3390 0.034574 TGTATCCTGGCCGTTGCAAT 60.035 50.000 0.59 0.00 40.13 3.56
2612 3406 3.582647 ACCTGATGAACCAGTGACATGTA 59.417 43.478 0.00 0.00 32.43 2.29
2664 3526 2.187100 GAAGGGGGAAATGCCAAATGA 58.813 47.619 0.00 0.00 38.95 2.57
2792 3657 5.762218 GCTATTCAATATCTTCAGCCACAGT 59.238 40.000 0.00 0.00 0.00 3.55
2793 3658 5.107182 CGCTATTCAATATCTTCAGCCACAG 60.107 44.000 0.00 0.00 0.00 3.66
2817 3682 6.088016 TGGTTGCATGCCATTTCTATTATC 57.912 37.500 16.68 0.00 0.00 1.75
2822 3687 3.130869 GTGATGGTTGCATGCCATTTCTA 59.869 43.478 16.68 8.47 45.87 2.10
2837 3705 3.096852 TGTTCCTAGACATCGTGATGGT 58.903 45.455 13.95 3.93 42.91 3.55
2845 3713 3.515901 AGTTCAGGGTGTTCCTAGACATC 59.484 47.826 0.00 0.00 46.12 3.06
2848 3716 3.447944 CCTAGTTCAGGGTGTTCCTAGAC 59.552 52.174 0.00 0.00 46.12 2.59
2860 3728 6.126883 TGGTTACATCCATTACCTAGTTCAGG 60.127 42.308 0.00 0.00 40.47 3.86
2903 3772 7.284261 TCCAAATAGATGTTTGTTCACTCACAA 59.716 33.333 2.09 0.00 37.37 3.33
2998 3868 9.528018 TCAAAATACAAAAACTGGAAAGATGAC 57.472 29.630 0.00 0.00 0.00 3.06
3043 3913 8.314751 GCTCCTTCATAAAGCACTAGGATATAA 58.685 37.037 0.00 0.00 36.06 0.98
3044 3914 7.676043 AGCTCCTTCATAAAGCACTAGGATATA 59.324 37.037 0.00 0.00 38.51 0.86
3045 3915 6.500049 AGCTCCTTCATAAAGCACTAGGATAT 59.500 38.462 0.00 0.00 38.51 1.63
3046 3916 5.841237 AGCTCCTTCATAAAGCACTAGGATA 59.159 40.000 0.00 0.00 38.51 2.59
3047 3917 4.657969 AGCTCCTTCATAAAGCACTAGGAT 59.342 41.667 0.00 0.00 38.51 3.24
3048 3918 4.033709 AGCTCCTTCATAAAGCACTAGGA 58.966 43.478 0.00 0.00 38.51 2.94
3049 3919 4.414337 AGCTCCTTCATAAAGCACTAGG 57.586 45.455 0.00 0.00 38.51 3.02
3057 3927 9.778741 AATCACGATATTTAGCTCCTTCATAAA 57.221 29.630 0.00 0.00 0.00 1.40
3094 3964 9.690913 TGACATAATCATTTTCTCAAAGAGGAT 57.309 29.630 0.00 0.00 29.99 3.24
3095 3965 9.690913 ATGACATAATCATTTTCTCAAAGAGGA 57.309 29.630 0.00 0.00 46.54 3.71
3117 3987 9.793245 GTTTCGCTATTAACACACATATATGAC 57.207 33.333 19.63 0.00 0.00 3.06
3130 4000 6.512177 AGATGATGTCGTTTCGCTATTAAC 57.488 37.500 0.00 0.00 0.00 2.01
3132 4002 6.417930 CAGAAGATGATGTCGTTTCGCTATTA 59.582 38.462 0.00 0.00 0.00 0.98
3134 4004 4.742167 CAGAAGATGATGTCGTTTCGCTAT 59.258 41.667 0.00 0.00 0.00 2.97
3135 4005 4.105486 CAGAAGATGATGTCGTTTCGCTA 58.895 43.478 0.00 0.00 0.00 4.26
3136 4006 2.926200 CAGAAGATGATGTCGTTTCGCT 59.074 45.455 0.00 0.00 0.00 4.93
3137 4007 2.029728 CCAGAAGATGATGTCGTTTCGC 59.970 50.000 0.00 0.00 0.00 4.70
3138 4008 3.061295 CACCAGAAGATGATGTCGTTTCG 59.939 47.826 0.00 0.00 0.00 3.46
3139 4009 3.181516 GCACCAGAAGATGATGTCGTTTC 60.182 47.826 0.00 0.00 0.00 2.78
3140 4010 2.744202 GCACCAGAAGATGATGTCGTTT 59.256 45.455 0.00 0.00 0.00 3.60
3146 4016 2.290916 GCTGATGCACCAGAAGATGATG 59.709 50.000 13.88 0.00 39.41 3.07
3147 4017 2.092592 TGCTGATGCACCAGAAGATGAT 60.093 45.455 13.88 0.00 45.31 2.45
3158 4028 1.505353 GCACTTCCTGCTGATGCAC 59.495 57.895 0.00 0.00 45.31 4.57
3160 4030 1.378250 AGGCACTTCCTGCTGATGC 60.378 57.895 0.00 0.00 45.54 3.91
3173 4043 2.990066 AGGAGTACATAGCAAGGCAC 57.010 50.000 0.00 0.00 0.00 5.01
3174 4044 2.170607 GGAAGGAGTACATAGCAAGGCA 59.829 50.000 0.00 0.00 0.00 4.75
3175 4045 2.170607 TGGAAGGAGTACATAGCAAGGC 59.829 50.000 0.00 0.00 0.00 4.35
3176 4046 4.696479 ATGGAAGGAGTACATAGCAAGG 57.304 45.455 0.00 0.00 0.00 3.61
3179 4049 4.037222 TGGAATGGAAGGAGTACATAGCA 58.963 43.478 0.00 0.00 0.00 3.49
3180 4050 4.689612 TGGAATGGAAGGAGTACATAGC 57.310 45.455 0.00 0.00 0.00 2.97
3181 4051 9.057089 GTAAATTGGAATGGAAGGAGTACATAG 57.943 37.037 0.00 0.00 0.00 2.23
3182 4052 8.778059 AGTAAATTGGAATGGAAGGAGTACATA 58.222 33.333 0.00 0.00 0.00 2.29
3183 4053 7.643123 AGTAAATTGGAATGGAAGGAGTACAT 58.357 34.615 0.00 0.00 0.00 2.29
3184 4054 7.027874 AGTAAATTGGAATGGAAGGAGTACA 57.972 36.000 0.00 0.00 0.00 2.90
3185 4055 6.258068 CGAGTAAATTGGAATGGAAGGAGTAC 59.742 42.308 0.00 0.00 0.00 2.73
3186 4056 6.070424 ACGAGTAAATTGGAATGGAAGGAGTA 60.070 38.462 0.00 0.00 0.00 2.59
3187 4057 5.186198 CGAGTAAATTGGAATGGAAGGAGT 58.814 41.667 0.00 0.00 0.00 3.85
3188 4058 5.186198 ACGAGTAAATTGGAATGGAAGGAG 58.814 41.667 0.00 0.00 0.00 3.69
3189 4059 5.174037 ACGAGTAAATTGGAATGGAAGGA 57.826 39.130 0.00 0.00 0.00 3.36
3190 4060 4.034048 CGACGAGTAAATTGGAATGGAAGG 59.966 45.833 0.00 0.00 0.00 3.46
3191 4061 4.630069 ACGACGAGTAAATTGGAATGGAAG 59.370 41.667 0.00 0.00 0.00 3.46
3192 4062 4.390603 CACGACGAGTAAATTGGAATGGAA 59.609 41.667 0.00 0.00 0.00 3.53
3193 4063 3.930229 CACGACGAGTAAATTGGAATGGA 59.070 43.478 0.00 0.00 0.00 3.41
3194 4064 3.063452 CCACGACGAGTAAATTGGAATGG 59.937 47.826 0.00 0.00 0.00 3.16
3195 4065 3.682858 ACCACGACGAGTAAATTGGAATG 59.317 43.478 0.00 0.00 0.00 2.67
3196 4066 3.934068 ACCACGACGAGTAAATTGGAAT 58.066 40.909 0.00 0.00 0.00 3.01
3197 4067 3.389925 ACCACGACGAGTAAATTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
3198 4068 3.389925 AACCACGACGAGTAAATTGGA 57.610 42.857 0.00 0.00 0.00 3.53
3199 4069 4.477302 AAAACCACGACGAGTAAATTGG 57.523 40.909 0.00 0.00 0.00 3.16
3200 4070 5.503498 TCAAAAACCACGACGAGTAAATTG 58.497 37.500 0.00 5.55 0.00 2.32
3201 4071 5.738118 TCAAAAACCACGACGAGTAAATT 57.262 34.783 0.00 0.00 0.00 1.82
3202 4072 5.295045 AGTTCAAAAACCACGACGAGTAAAT 59.705 36.000 0.00 0.00 35.92 1.40
3203 4073 4.630940 AGTTCAAAAACCACGACGAGTAAA 59.369 37.500 0.00 0.00 35.92 2.01
3204 4074 4.183101 AGTTCAAAAACCACGACGAGTAA 58.817 39.130 0.00 0.00 35.92 2.24
3205 4075 3.784338 AGTTCAAAAACCACGACGAGTA 58.216 40.909 0.00 0.00 35.92 2.59
3206 4076 2.624636 AGTTCAAAAACCACGACGAGT 58.375 42.857 0.00 0.00 35.92 4.18
3207 4077 4.782252 TTAGTTCAAAAACCACGACGAG 57.218 40.909 0.00 0.00 35.92 4.18
3208 4078 5.323105 GTTTTAGTTCAAAAACCACGACGA 58.677 37.500 0.00 0.00 41.43 4.20
3209 4079 5.594215 GTTTTAGTTCAAAAACCACGACG 57.406 39.130 0.00 0.00 41.43 5.12
3216 4086 5.323105 TCGTCGTGGTTTTAGTTCAAAAAC 58.677 37.500 4.09 4.09 44.80 2.43
3217 4087 5.122082 ACTCGTCGTGGTTTTAGTTCAAAAA 59.878 36.000 0.00 0.00 37.85 1.94
3218 4088 4.630940 ACTCGTCGTGGTTTTAGTTCAAAA 59.369 37.500 0.00 0.00 33.66 2.44
3219 4089 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
3220 4090 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
3221 4091 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
3222 4092 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
3223 4093 5.984926 TGATTTACTCGTCGTGGTTTTAGTT 59.015 36.000 0.00 0.00 0.00 2.24
3224 4094 5.531634 TGATTTACTCGTCGTGGTTTTAGT 58.468 37.500 0.00 0.00 0.00 2.24
3225 4095 5.860182 TCTGATTTACTCGTCGTGGTTTTAG 59.140 40.000 0.00 0.00 0.00 1.85
3226 4096 5.771469 TCTGATTTACTCGTCGTGGTTTTA 58.229 37.500 0.00 0.00 0.00 1.52
3227 4097 4.624015 TCTGATTTACTCGTCGTGGTTTT 58.376 39.130 0.00 0.00 0.00 2.43
3228 4098 4.247267 TCTGATTTACTCGTCGTGGTTT 57.753 40.909 0.00 0.00 0.00 3.27
3229 4099 3.928727 TCTGATTTACTCGTCGTGGTT 57.071 42.857 0.00 0.00 0.00 3.67
3230 4100 3.572584 GTTCTGATTTACTCGTCGTGGT 58.427 45.455 0.00 0.00 0.00 4.16
3231 4101 2.592897 CGTTCTGATTTACTCGTCGTGG 59.407 50.000 0.00 0.00 0.00 4.94
3232 4102 2.592897 CCGTTCTGATTTACTCGTCGTG 59.407 50.000 0.00 0.00 0.00 4.35
3233 4103 2.485426 TCCGTTCTGATTTACTCGTCGT 59.515 45.455 0.00 0.00 0.00 4.34
3234 4104 3.099362 CTCCGTTCTGATTTACTCGTCG 58.901 50.000 0.00 0.00 0.00 5.12
3235 4105 3.436496 CCTCCGTTCTGATTTACTCGTC 58.564 50.000 0.00 0.00 0.00 4.20
3236 4106 2.165845 CCCTCCGTTCTGATTTACTCGT 59.834 50.000 0.00 0.00 0.00 4.18
3237 4107 2.426024 TCCCTCCGTTCTGATTTACTCG 59.574 50.000 0.00 0.00 0.00 4.18
3238 4108 3.447944 ACTCCCTCCGTTCTGATTTACTC 59.552 47.826 0.00 0.00 0.00 2.59
3239 4109 3.442076 ACTCCCTCCGTTCTGATTTACT 58.558 45.455 0.00 0.00 0.00 2.24
3240 4110 3.889520 ACTCCCTCCGTTCTGATTTAC 57.110 47.619 0.00 0.00 0.00 2.01
3241 4111 5.266788 TCTTACTCCCTCCGTTCTGATTTA 58.733 41.667 0.00 0.00 0.00 1.40
3242 4112 4.094476 TCTTACTCCCTCCGTTCTGATTT 58.906 43.478 0.00 0.00 0.00 2.17
3243 4113 3.709587 TCTTACTCCCTCCGTTCTGATT 58.290 45.455 0.00 0.00 0.00 2.57
3244 4114 3.383698 TCTTACTCCCTCCGTTCTGAT 57.616 47.619 0.00 0.00 0.00 2.90
3245 4115 2.893215 TCTTACTCCCTCCGTTCTGA 57.107 50.000 0.00 0.00 0.00 3.27
3246 4116 2.761208 ACATCTTACTCCCTCCGTTCTG 59.239 50.000 0.00 0.00 0.00 3.02
3247 4117 3.103080 ACATCTTACTCCCTCCGTTCT 57.897 47.619 0.00 0.00 0.00 3.01
3248 4118 3.522553 CAACATCTTACTCCCTCCGTTC 58.477 50.000 0.00 0.00 0.00 3.95
3249 4119 2.236395 CCAACATCTTACTCCCTCCGTT 59.764 50.000 0.00 0.00 0.00 4.44
3250 4120 1.831736 CCAACATCTTACTCCCTCCGT 59.168 52.381 0.00 0.00 0.00 4.69
3251 4121 2.108168 TCCAACATCTTACTCCCTCCG 58.892 52.381 0.00 0.00 0.00 4.63
3252 4122 3.370633 GGTTCCAACATCTTACTCCCTCC 60.371 52.174 0.00 0.00 0.00 4.30
3253 4123 3.519913 AGGTTCCAACATCTTACTCCCTC 59.480 47.826 0.00 0.00 0.00 4.30
3254 4124 3.532102 AGGTTCCAACATCTTACTCCCT 58.468 45.455 0.00 0.00 0.00 4.20
3255 4125 4.010349 CAAGGTTCCAACATCTTACTCCC 58.990 47.826 0.00 0.00 0.00 4.30
3256 4126 3.440522 GCAAGGTTCCAACATCTTACTCC 59.559 47.826 0.00 0.00 0.00 3.85
3257 4127 4.072131 TGCAAGGTTCCAACATCTTACTC 58.928 43.478 0.00 0.00 0.00 2.59
3258 4128 4.098914 TGCAAGGTTCCAACATCTTACT 57.901 40.909 0.00 0.00 0.00 2.24
3259 4129 4.437390 CGATGCAAGGTTCCAACATCTTAC 60.437 45.833 0.00 0.00 35.96 2.34
3260 4130 3.689161 CGATGCAAGGTTCCAACATCTTA 59.311 43.478 0.00 0.00 35.96 2.10
3261 4131 2.489329 CGATGCAAGGTTCCAACATCTT 59.511 45.455 0.00 0.00 35.96 2.40
3262 4132 2.086869 CGATGCAAGGTTCCAACATCT 58.913 47.619 0.00 0.00 35.96 2.90
3263 4133 1.468054 GCGATGCAAGGTTCCAACATC 60.468 52.381 0.00 0.00 35.01 3.06
3264 4134 0.527565 GCGATGCAAGGTTCCAACAT 59.472 50.000 0.00 0.00 0.00 2.71
3265 4135 0.537143 AGCGATGCAAGGTTCCAACA 60.537 50.000 0.00 0.00 0.00 3.33
3266 4136 0.109597 CAGCGATGCAAGGTTCCAAC 60.110 55.000 0.00 0.00 0.00 3.77
3267 4137 1.865788 GCAGCGATGCAAGGTTCCAA 61.866 55.000 22.72 0.00 34.41 3.53
3268 4138 2.334946 GCAGCGATGCAAGGTTCCA 61.335 57.895 22.72 0.00 34.41 3.53
3269 4139 1.986575 GAGCAGCGATGCAAGGTTCC 61.987 60.000 29.24 3.66 37.25 3.62
3270 4140 1.300971 TGAGCAGCGATGCAAGGTTC 61.301 55.000 29.24 16.41 37.25 3.62
3271 4141 1.302752 TGAGCAGCGATGCAAGGTT 60.303 52.632 29.24 6.17 37.25 3.50
3272 4142 2.037136 GTGAGCAGCGATGCAAGGT 61.037 57.895 29.24 6.63 37.25 3.50
3273 4143 2.758089 GGTGAGCAGCGATGCAAGG 61.758 63.158 29.24 0.00 37.25 3.61
3274 4144 1.978712 CTGGTGAGCAGCGATGCAAG 61.979 60.000 29.24 12.62 37.25 4.01
3275 4145 2.032376 TGGTGAGCAGCGATGCAA 59.968 55.556 29.24 13.06 37.25 4.08
3276 4146 2.248086 ATCTGGTGAGCAGCGATGCA 62.248 55.000 29.24 4.69 37.25 3.96
3277 4147 0.249615 TATCTGGTGAGCAGCGATGC 60.250 55.000 19.88 19.88 0.00 3.91
3278 4148 2.029200 AGATATCTGGTGAGCAGCGATG 60.029 50.000 6.80 0.00 0.00 3.84
3279 4149 2.246469 AGATATCTGGTGAGCAGCGAT 58.754 47.619 6.80 2.32 0.00 4.58
3280 4150 1.697284 AGATATCTGGTGAGCAGCGA 58.303 50.000 6.80 0.00 0.00 4.93
3281 4151 3.056962 ACATAGATATCTGGTGAGCAGCG 60.057 47.826 15.79 0.00 0.00 5.18
3282 4152 4.533919 ACATAGATATCTGGTGAGCAGC 57.466 45.455 15.79 0.00 0.00 5.25
3283 4153 5.178996 GCAAACATAGATATCTGGTGAGCAG 59.821 44.000 15.79 5.07 0.00 4.24
3284 4154 5.059161 GCAAACATAGATATCTGGTGAGCA 58.941 41.667 15.79 0.00 0.00 4.26
3285 4155 4.453819 GGCAAACATAGATATCTGGTGAGC 59.546 45.833 15.79 17.29 0.00 4.26
3286 4156 5.862845 AGGCAAACATAGATATCTGGTGAG 58.137 41.667 15.79 10.12 0.00 3.51
3287 4157 5.894298 AGGCAAACATAGATATCTGGTGA 57.106 39.130 15.79 0.00 0.00 4.02
3288 4158 5.471456 GGAAGGCAAACATAGATATCTGGTG 59.529 44.000 15.79 15.20 0.00 4.17
3289 4159 5.625150 GGAAGGCAAACATAGATATCTGGT 58.375 41.667 15.79 10.39 0.00 4.00
3290 4160 4.692625 CGGAAGGCAAACATAGATATCTGG 59.307 45.833 15.79 9.76 0.00 3.86
3291 4161 4.153117 GCGGAAGGCAAACATAGATATCTG 59.847 45.833 15.79 2.92 42.87 2.90
3292 4162 4.319177 GCGGAAGGCAAACATAGATATCT 58.681 43.478 10.73 10.73 42.87 1.98
3293 4163 4.670227 GCGGAAGGCAAACATAGATATC 57.330 45.455 0.00 0.00 42.87 1.63
3311 4181 2.986479 GACAAATAAAACTGCAAGGCGG 59.014 45.455 0.00 0.00 39.30 6.13
3312 4182 3.425193 GTGACAAATAAAACTGCAAGGCG 59.575 43.478 0.00 0.00 39.30 5.52
3323 4193 6.952773 AAGTTACAGCAGGTGACAAATAAA 57.047 33.333 6.61 0.00 38.40 1.40
3372 4319 3.490933 GCTGTACGGCATCTCTCAACATA 60.491 47.826 21.95 0.00 0.00 2.29
3388 4335 0.679960 AAATTCCAGGGGCGCTGTAC 60.680 55.000 27.08 0.00 0.00 2.90
3390 4337 1.678970 GAAATTCCAGGGGCGCTGT 60.679 57.895 27.08 10.78 0.00 4.40
3393 4340 2.750237 ACGAAATTCCAGGGGCGC 60.750 61.111 0.00 0.00 0.00 6.53
3399 4346 7.045126 AGTAGAAGGATAGACGAAATTCCAG 57.955 40.000 0.00 0.00 0.00 3.86
3437 4386 5.407407 TTGCTTTTCCACCAACAAACTTA 57.593 34.783 0.00 0.00 0.00 2.24
3439 4388 3.971245 TTGCTTTTCCACCAACAAACT 57.029 38.095 0.00 0.00 0.00 2.66
3440 4389 4.249661 TCTTTGCTTTTCCACCAACAAAC 58.750 39.130 0.00 0.00 0.00 2.93
3442 4391 4.543590 TTCTTTGCTTTTCCACCAACAA 57.456 36.364 0.00 0.00 0.00 2.83
3449 4398 4.769345 AACCCATTTCTTTGCTTTTCCA 57.231 36.364 0.00 0.00 0.00 3.53
3451 4400 6.512297 TGACTAACCCATTTCTTTGCTTTTC 58.488 36.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.