Multiple sequence alignment - TraesCS1B01G212700

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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 TraesCS1B01G212700 chr1B 100.000 3368 0 0 1 3368 386199871 386196504 0.000000e+00 6220
1 TraesCS1B01G212700 chr1A 92.620 2534 76 47 667 3103 355722687 355720168 0.000000e+00 3541
2 TraesCS1B01G212700 chr1D 94.450 2054 55 16 667 2701 284247165 284245152 0.000000e+00 3107
3 TraesCS1B01G212700 chr1D 86.797 409 23 6 2716 3103 284245078 284244680 8.640000e-116 427
4 TraesCS1B01G212700 chr6B 93.814 679 24 11 1 667 131698378 131699050 0.000000e+00 1005
5 TraesCS1B01G212700 chr5B 92.960 696 20 9 1 667 398151344 398150649 0.000000e+00 987
6 TraesCS1B01G212700 chr5D 87.717 692 49 21 4 667 86736695 86737378 0.000000e+00 774
7 TraesCS1B01G212700 chr6A 86.628 688 56 27 1 668 199467940 199467269 0.000000e+00 728
8 TraesCS1B01G212700 chr6A 87.526 481 39 17 1 472 137546759 137546291 1.380000e-148 536
9 TraesCS1B01G212700 chr7D 86.297 686 55 27 1 667 106598313 106598978 0.000000e+00 710
10 TraesCS1B01G212700 chr7D 85.191 655 58 24 36 667 14844628 14845266 1.320000e-178 636
11 TraesCS1B01G212700 chr3A 85.465 688 54 27 1 667 545878499 545879161 0.000000e+00 675
12 TraesCS1B01G212700 chr3A 93.671 237 15 0 3132 3368 678509470 678509234 4.130000e-94 355
13 TraesCS1B01G212700 chr2B 89.781 548 20 7 1 537 219598574 219599096 0.000000e+00 669
14 TraesCS1B01G212700 chr3B 84.526 685 50 19 1 667 795042130 795041484 7.930000e-176 627
15 TraesCS1B01G212700 chr2D 90.702 484 21 12 1 465 43230479 43230001 1.030000e-174 623
16 TraesCS1B01G212700 chr2D 95.902 122 4 1 548 668 43229707 43229586 2.650000e-46 196
17 TraesCS1B01G212700 chr2A 95.359 237 11 0 3132 3368 32775633 32775397 8.820000e-101 377
18 TraesCS1B01G212700 chr2A 94.937 237 12 0 3132 3368 81462124 81461888 4.100000e-99 372
19 TraesCS1B01G212700 chr3D 94.309 246 13 1 3123 3368 383591178 383591422 3.170000e-100 375
20 TraesCS1B01G212700 chr3D 93.089 246 16 1 3123 3368 336825630 336825874 3.200000e-95 359
21 TraesCS1B01G212700 chr7A 93.496 246 16 0 3123 3368 701287956 701288201 1.910000e-97 366
22 TraesCS1B01G212700 chr7A 93.089 246 16 1 3123 3368 445605245 445605489 3.200000e-95 359
23 TraesCS1B01G212700 chr7A 92.827 237 17 0 3132 3368 287009473 287009237 8.950000e-91 344
24 TraesCS1B01G212700 chr5A 93.671 237 15 0 3132 3368 558928234 558927998 4.130000e-94 355


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 TraesCS1B01G212700 chr1B 386196504 386199871 3367 True 6220.0 6220 100.0000 1 3368 1 chr1B.!!$R1 3367
1 TraesCS1B01G212700 chr1A 355720168 355722687 2519 True 3541.0 3541 92.6200 667 3103 1 chr1A.!!$R1 2436
2 TraesCS1B01G212700 chr1D 284244680 284247165 2485 True 1767.0 3107 90.6235 667 3103 2 chr1D.!!$R1 2436
3 TraesCS1B01G212700 chr6B 131698378 131699050 672 False 1005.0 1005 93.8140 1 667 1 chr6B.!!$F1 666
4 TraesCS1B01G212700 chr5B 398150649 398151344 695 True 987.0 987 92.9600 1 667 1 chr5B.!!$R1 666
5 TraesCS1B01G212700 chr5D 86736695 86737378 683 False 774.0 774 87.7170 4 667 1 chr5D.!!$F1 663
6 TraesCS1B01G212700 chr6A 199467269 199467940 671 True 728.0 728 86.6280 1 668 1 chr6A.!!$R2 667
7 TraesCS1B01G212700 chr7D 106598313 106598978 665 False 710.0 710 86.2970 1 667 1 chr7D.!!$F2 666
8 TraesCS1B01G212700 chr7D 14844628 14845266 638 False 636.0 636 85.1910 36 667 1 chr7D.!!$F1 631
9 TraesCS1B01G212700 chr3A 545878499 545879161 662 False 675.0 675 85.4650 1 667 1 chr3A.!!$F1 666
10 TraesCS1B01G212700 chr2B 219598574 219599096 522 False 669.0 669 89.7810 1 537 1 chr2B.!!$F1 536
11 TraesCS1B01G212700 chr3B 795041484 795042130 646 True 627.0 627 84.5260 1 667 1 chr3B.!!$R1 666
12 TraesCS1B01G212700 chr2D 43229586 43230479 893 True 409.5 623 93.3020 1 668 2 chr2D.!!$R1 667

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
819 1266 0.178947 ATTAGGAGGAGGAGGCGGAG 60.179 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 3298 0.53646 TTTTGTTGGAGCCGGAGTCC 60.536 55.0 5.05 11.5 34.31 3.85 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
128 258 7.836358 TTCTCAAATCGAATGAACTTTTTCG 57.164 32.000 5.86 0.00 44.53 3.46
174 305 7.930513 AATCGACTGAACTTTTTCCAAAATC 57.069 32.000 0.00 0.00 0.00 2.17
175 306 6.443934 TCGACTGAACTTTTTCCAAAATCA 57.556 33.333 0.00 0.00 0.00 2.57
178 309 7.434897 TCGACTGAACTTTTTCCAAAATCAATG 59.565 33.333 0.00 0.00 0.00 2.82
180 311 9.097257 GACTGAACTTTTTCCAAAATCAATGAA 57.903 29.630 0.00 0.00 0.00 2.57
181 312 8.882736 ACTGAACTTTTTCCAAAATCAATGAAC 58.117 29.630 0.00 0.00 0.00 3.18
384 596 2.635915 TGGTTAACTGGTCAGACCGATT 59.364 45.455 15.24 13.30 42.58 3.34
559 998 3.566322 CGATGACCTGTTTTTGGTGGTAA 59.434 43.478 0.00 0.00 38.03 2.85
598 1037 2.428491 CAGTACGTGTTTATGGGCCAA 58.572 47.619 11.89 0.00 0.00 4.52
700 1139 4.327680 CTTTCTGGAGAAGGAAACGGAAT 58.672 43.478 0.00 0.00 33.54 3.01
813 1260 7.302184 CCCTAGGATTATATTAGGAGGAGGAG 58.698 46.154 11.48 0.00 36.83 3.69
818 1265 1.155323 TATTAGGAGGAGGAGGCGGA 58.845 55.000 0.00 0.00 0.00 5.54
819 1266 0.178947 ATTAGGAGGAGGAGGCGGAG 60.179 60.000 0.00 0.00 0.00 4.63
820 1267 2.299727 TTAGGAGGAGGAGGCGGAGG 62.300 65.000 0.00 0.00 0.00 4.30
841 1288 0.310854 GGTGGCGAAGGTTCTTGTTG 59.689 55.000 0.00 0.00 0.00 3.33
874 1321 3.824133 TCTCCGTGGGTTCGATCTATTA 58.176 45.455 0.00 0.00 0.00 0.98
887 1338 4.155462 TCGATCTATTAATACGCGCTTCCT 59.845 41.667 5.73 0.00 0.00 3.36
975 1427 8.812329 CGATTCGTTTCTCAGATCTTAATCTTT 58.188 33.333 0.00 0.00 40.38 2.52
1103 1561 1.600164 CGCCAACAACATGAACACCAG 60.600 52.381 0.00 0.00 0.00 4.00
1118 1576 1.824230 CACCAGGTGGAGAGAGAGAAG 59.176 57.143 12.40 0.00 38.94 2.85
1188 1682 0.965866 AGCATCAGCAGCAACAGCAT 60.966 50.000 0.00 0.00 45.49 3.79
1194 1688 1.443872 GCAGCAACAGCATCAGCAC 60.444 57.895 0.00 0.00 45.49 4.40
1215 1709 1.319614 ACCACCAACAACAGCACCAC 61.320 55.000 0.00 0.00 0.00 4.16
1218 1712 1.319614 ACCAACAACAGCACCACCAC 61.320 55.000 0.00 0.00 0.00 4.16
1221 1715 1.319614 AACAACAGCACCACCACCAC 61.320 55.000 0.00 0.00 0.00 4.16
1230 1724 2.519063 CACCACCACCAGCAGCAA 60.519 61.111 0.00 0.00 0.00 3.91
1252 1746 1.800315 CGCTACCGTCCTGTCAACG 60.800 63.158 0.00 0.00 39.78 4.10
1259 1753 0.790207 CGTCCTGTCAACGACAATGG 59.210 55.000 0.00 0.00 42.26 3.16
1788 2282 1.000618 GAAGACGACGACCCCTTTCTT 59.999 52.381 0.00 0.00 0.00 2.52
2116 2610 2.498726 GCGGGAGAGCAAGAGGAG 59.501 66.667 0.00 0.00 37.05 3.69
2329 2826 1.192146 TTCCGGTGGTGGAAGAGGAG 61.192 60.000 0.00 0.00 43.01 3.69
2580 3077 7.553760 TGCATGCTATATTACTTCATGGTATGG 59.446 37.037 20.33 0.00 36.11 2.74
2625 3130 0.035439 ATTGGTACAGAAGGTGGCCG 60.035 55.000 0.00 0.00 42.39 6.13
2632 3137 2.214216 AGAAGGTGGCCGTGCTGTA 61.214 57.895 0.00 0.00 0.00 2.74
2712 3271 1.376037 CAGGACAAGAACTCGGCCC 60.376 63.158 0.00 0.00 0.00 5.80
2731 3298 3.458189 CCCAGTTAGGATAGAGCAAACG 58.542 50.000 0.00 0.00 41.22 3.60
2737 3304 1.757699 AGGATAGAGCAAACGGACTCC 59.242 52.381 0.00 0.00 33.18 3.85
2778 3345 6.428159 CACTCAAAGCCAACTACTGTCTAAAT 59.572 38.462 0.00 0.00 0.00 1.40
2785 3352 7.048512 AGCCAACTACTGTCTAAATTATCACC 58.951 38.462 0.00 0.00 0.00 4.02
2810 3377 3.512724 CCATCTCTTTGGCAAACTTCCAT 59.487 43.478 8.93 0.00 32.92 3.41
2811 3378 4.491676 CATCTCTTTGGCAAACTTCCATG 58.508 43.478 8.93 3.80 32.92 3.66
2816 3383 0.469705 TGGCAAACTTCCATGGCTGT 60.470 50.000 6.96 5.17 42.17 4.40
3048 3640 5.079643 ACCAAACCTGTTAAGATCTTGCAT 58.920 37.500 18.47 0.90 0.00 3.96
3089 3681 3.632643 TGTCATCTTGAAGGCTATGCA 57.367 42.857 0.00 0.00 0.00 3.96
3103 3695 2.364970 GCTATGCAGGACTCTGTGATCT 59.635 50.000 0.00 0.00 42.78 2.75
3104 3696 2.983907 ATGCAGGACTCTGTGATCTG 57.016 50.000 0.00 0.00 42.78 2.90
3105 3697 1.928868 TGCAGGACTCTGTGATCTGA 58.071 50.000 0.00 0.00 42.78 3.27
3106 3698 1.547820 TGCAGGACTCTGTGATCTGAC 59.452 52.381 0.00 0.00 42.78 3.51
3107 3699 1.468908 GCAGGACTCTGTGATCTGACG 60.469 57.143 0.00 0.00 42.78 4.35
3108 3700 1.815613 CAGGACTCTGTGATCTGACGT 59.184 52.381 0.00 0.00 36.30 4.34
3109 3701 2.088423 AGGACTCTGTGATCTGACGTC 58.912 52.381 9.11 9.11 0.00 4.34
3110 3702 1.133407 GGACTCTGTGATCTGACGTCC 59.867 57.143 14.12 0.00 35.36 4.79
3111 3703 1.813178 GACTCTGTGATCTGACGTCCA 59.187 52.381 14.12 0.00 0.00 4.02
3112 3704 1.815613 ACTCTGTGATCTGACGTCCAG 59.184 52.381 14.12 11.69 44.27 3.86
3119 3711 3.672066 TCTGACGTCCAGATCCTGT 57.328 52.632 14.12 0.00 46.38 4.00
3120 3712 2.801077 TCTGACGTCCAGATCCTGTA 57.199 50.000 14.12 0.00 46.38 2.74
3121 3713 2.366533 TCTGACGTCCAGATCCTGTAC 58.633 52.381 14.12 0.00 46.38 2.90
3122 3714 2.026169 TCTGACGTCCAGATCCTGTACT 60.026 50.000 14.12 0.00 46.38 2.73
3123 3715 2.092323 TGACGTCCAGATCCTGTACTG 58.908 52.381 14.12 0.00 0.00 2.74
3124 3716 0.818296 ACGTCCAGATCCTGTACTGC 59.182 55.000 0.00 0.00 33.40 4.40
3125 3717 0.248661 CGTCCAGATCCTGTACTGCG 60.249 60.000 0.00 0.00 33.40 5.18
3126 3718 1.103803 GTCCAGATCCTGTACTGCGA 58.896 55.000 0.00 0.00 33.40 5.10
3127 3719 1.103803 TCCAGATCCTGTACTGCGAC 58.896 55.000 0.00 0.00 33.40 5.19
3128 3720 1.107114 CCAGATCCTGTACTGCGACT 58.893 55.000 0.00 0.00 33.40 4.18
3129 3721 1.478510 CCAGATCCTGTACTGCGACTT 59.521 52.381 0.00 0.00 33.40 3.01
3130 3722 2.688446 CCAGATCCTGTACTGCGACTTA 59.312 50.000 0.00 0.00 33.40 2.24
3131 3723 3.319405 CCAGATCCTGTACTGCGACTTAT 59.681 47.826 0.00 0.00 33.40 1.73
3132 3724 4.202161 CCAGATCCTGTACTGCGACTTATT 60.202 45.833 0.00 0.00 33.40 1.40
3133 3725 5.352284 CAGATCCTGTACTGCGACTTATTT 58.648 41.667 0.00 0.00 0.00 1.40
3134 3726 5.233050 CAGATCCTGTACTGCGACTTATTTG 59.767 44.000 0.00 0.00 0.00 2.32
3135 3727 3.259064 TCCTGTACTGCGACTTATTTGC 58.741 45.455 0.00 0.00 34.74 3.68
3136 3728 3.056107 TCCTGTACTGCGACTTATTTGCT 60.056 43.478 0.00 0.00 35.31 3.91
3137 3729 3.684788 CCTGTACTGCGACTTATTTGCTT 59.315 43.478 0.00 0.00 35.31 3.91
3138 3730 4.436050 CCTGTACTGCGACTTATTTGCTTG 60.436 45.833 0.00 0.00 35.31 4.01
3139 3731 3.435327 TGTACTGCGACTTATTTGCTTGG 59.565 43.478 0.00 0.00 35.31 3.61
3140 3732 1.200020 ACTGCGACTTATTTGCTTGGC 59.800 47.619 0.00 0.00 35.31 4.52
3141 3733 1.470098 CTGCGACTTATTTGCTTGGCT 59.530 47.619 0.00 0.00 35.31 4.75
3142 3734 2.677836 CTGCGACTTATTTGCTTGGCTA 59.322 45.455 0.00 0.00 35.31 3.93
3143 3735 2.677836 TGCGACTTATTTGCTTGGCTAG 59.322 45.455 0.00 0.00 35.31 3.42
3144 3736 2.678336 GCGACTTATTTGCTTGGCTAGT 59.322 45.455 0.00 0.00 0.00 2.57
3145 3737 3.127030 GCGACTTATTTGCTTGGCTAGTT 59.873 43.478 0.00 0.00 0.00 2.24
3146 3738 4.331717 GCGACTTATTTGCTTGGCTAGTTA 59.668 41.667 0.00 0.00 0.00 2.24
3147 3739 5.007724 GCGACTTATTTGCTTGGCTAGTTAT 59.992 40.000 0.00 0.00 0.00 1.89
3148 3740 6.650372 CGACTTATTTGCTTGGCTAGTTATC 58.350 40.000 0.00 0.00 0.00 1.75
3149 3741 6.257849 CGACTTATTTGCTTGGCTAGTTATCA 59.742 38.462 0.00 0.00 0.00 2.15
3150 3742 7.201609 CGACTTATTTGCTTGGCTAGTTATCAA 60.202 37.037 0.00 0.00 0.00 2.57
3151 3743 8.525290 ACTTATTTGCTTGGCTAGTTATCAAT 57.475 30.769 0.00 0.00 0.00 2.57
3152 3744 9.627123 ACTTATTTGCTTGGCTAGTTATCAATA 57.373 29.630 0.00 0.00 0.00 1.90
3155 3747 7.695480 TTTGCTTGGCTAGTTATCAATAACA 57.305 32.000 13.76 1.85 43.83 2.41
3156 3748 6.925610 TGCTTGGCTAGTTATCAATAACAG 57.074 37.500 13.76 10.18 43.83 3.16
3157 3749 5.822519 TGCTTGGCTAGTTATCAATAACAGG 59.177 40.000 13.76 7.76 43.83 4.00
3158 3750 6.055588 GCTTGGCTAGTTATCAATAACAGGA 58.944 40.000 13.76 0.65 43.83 3.86
3159 3751 6.712547 GCTTGGCTAGTTATCAATAACAGGAT 59.287 38.462 13.76 0.00 43.83 3.24
3160 3752 7.095017 GCTTGGCTAGTTATCAATAACAGGATC 60.095 40.741 13.76 0.00 43.83 3.36
3161 3753 7.618019 TGGCTAGTTATCAATAACAGGATCT 57.382 36.000 13.76 0.00 43.83 2.75
3162 3754 7.445121 TGGCTAGTTATCAATAACAGGATCTG 58.555 38.462 13.76 0.00 43.83 2.90
3163 3755 6.876257 GGCTAGTTATCAATAACAGGATCTGG 59.124 42.308 13.76 0.00 43.83 3.86
3164 3756 7.256332 GGCTAGTTATCAATAACAGGATCTGGA 60.256 40.741 13.76 0.00 43.83 3.86
3165 3757 7.600752 GCTAGTTATCAATAACAGGATCTGGAC 59.399 40.741 13.76 0.00 43.83 4.02
3166 3758 6.516718 AGTTATCAATAACAGGATCTGGACG 58.483 40.000 13.76 0.00 43.83 4.79
3167 3759 3.819564 TCAATAACAGGATCTGGACGG 57.180 47.619 0.00 0.00 35.51 4.79
3168 3760 2.158957 TCAATAACAGGATCTGGACGGC 60.159 50.000 0.00 0.00 35.51 5.68
3169 3761 0.759346 ATAACAGGATCTGGACGGCC 59.241 55.000 0.00 0.00 35.51 6.13
3170 3762 1.672854 TAACAGGATCTGGACGGCCG 61.673 60.000 26.86 26.86 35.51 6.13
3171 3763 3.147595 CAGGATCTGGACGGCCGA 61.148 66.667 35.90 9.64 36.79 5.54
3172 3764 3.148279 AGGATCTGGACGGCCGAC 61.148 66.667 35.90 27.37 36.79 4.79
3173 3765 3.458163 GGATCTGGACGGCCGACA 61.458 66.667 35.90 27.50 36.79 4.35
3174 3766 2.105128 GATCTGGACGGCCGACAG 59.895 66.667 33.38 33.38 36.79 3.51
3175 3767 3.432051 GATCTGGACGGCCGACAGG 62.432 68.421 35.77 24.99 41.62 4.00
3192 3784 4.038080 GCTTCAACGCCGGGGTTG 62.038 66.667 42.87 42.87 46.70 3.77
3193 3785 3.361977 CTTCAACGCCGGGGTTGG 61.362 66.667 44.89 33.14 45.66 3.77
3201 3793 2.045340 CCGGGGTTGGCCTAACTG 60.045 66.667 3.32 0.00 39.31 3.16
3202 3794 2.750237 CGGGGTTGGCCTAACTGC 60.750 66.667 3.32 0.00 39.31 4.40
3203 3795 2.750237 GGGGTTGGCCTAACTGCG 60.750 66.667 3.32 0.00 39.31 5.18
3204 3796 2.349755 GGGTTGGCCTAACTGCGA 59.650 61.111 3.32 0.00 39.31 5.10
3205 3797 2.038837 GGGTTGGCCTAACTGCGAC 61.039 63.158 3.32 0.00 39.31 5.19
3206 3798 2.038837 GGTTGGCCTAACTGCGACC 61.039 63.158 3.32 0.00 39.31 4.79
3207 3799 1.302192 GTTGGCCTAACTGCGACCA 60.302 57.895 3.32 0.00 36.34 4.02
3208 3800 0.676782 GTTGGCCTAACTGCGACCAT 60.677 55.000 3.32 0.00 36.34 3.55
3209 3801 0.037590 TTGGCCTAACTGCGACCATT 59.962 50.000 3.32 0.00 0.00 3.16
3210 3802 0.676466 TGGCCTAACTGCGACCATTG 60.676 55.000 3.32 0.00 0.00 2.82
3211 3803 1.429423 GCCTAACTGCGACCATTGC 59.571 57.895 0.00 0.00 0.00 3.56
3212 3804 1.993369 GCCTAACTGCGACCATTGCC 61.993 60.000 0.00 0.00 0.00 4.52
3213 3805 1.376609 CCTAACTGCGACCATTGCCC 61.377 60.000 0.00 0.00 0.00 5.36
3214 3806 0.676466 CTAACTGCGACCATTGCCCA 60.676 55.000 0.00 0.00 0.00 5.36
3215 3807 0.958382 TAACTGCGACCATTGCCCAC 60.958 55.000 0.00 0.00 0.00 4.61
3216 3808 2.360350 CTGCGACCATTGCCCACT 60.360 61.111 0.00 0.00 0.00 4.00
3217 3809 1.078497 CTGCGACCATTGCCCACTA 60.078 57.895 0.00 0.00 0.00 2.74
3218 3810 0.464373 CTGCGACCATTGCCCACTAT 60.464 55.000 0.00 0.00 0.00 2.12
3219 3811 0.747644 TGCGACCATTGCCCACTATG 60.748 55.000 0.00 0.00 0.00 2.23
3220 3812 2.024918 CGACCATTGCCCACTATGC 58.975 57.895 0.00 0.00 0.00 3.14
3221 3813 0.747644 CGACCATTGCCCACTATGCA 60.748 55.000 0.00 0.00 36.84 3.96
3228 3820 1.993956 TGCCCACTATGCAAACAAGT 58.006 45.000 0.00 0.00 35.40 3.16
3229 3821 2.315176 TGCCCACTATGCAAACAAGTT 58.685 42.857 0.00 0.00 35.40 2.66
3230 3822 2.295909 TGCCCACTATGCAAACAAGTTC 59.704 45.455 0.00 0.00 35.40 3.01
3231 3823 2.295909 GCCCACTATGCAAACAAGTTCA 59.704 45.455 0.00 0.00 0.00 3.18
3232 3824 3.243704 GCCCACTATGCAAACAAGTTCAA 60.244 43.478 0.00 0.00 0.00 2.69
3233 3825 4.549458 CCCACTATGCAAACAAGTTCAAG 58.451 43.478 0.00 0.00 0.00 3.02
3234 3826 4.278170 CCCACTATGCAAACAAGTTCAAGA 59.722 41.667 0.00 0.00 0.00 3.02
3235 3827 5.221224 CCCACTATGCAAACAAGTTCAAGAA 60.221 40.000 0.00 0.00 0.00 2.52
3236 3828 6.449698 CCACTATGCAAACAAGTTCAAGAAT 58.550 36.000 0.00 0.00 0.00 2.40
3237 3829 6.583806 CCACTATGCAAACAAGTTCAAGAATC 59.416 38.462 0.00 0.00 0.00 2.52
3238 3830 6.583806 CACTATGCAAACAAGTTCAAGAATCC 59.416 38.462 0.00 0.00 0.00 3.01
3239 3831 3.963665 TGCAAACAAGTTCAAGAATCCG 58.036 40.909 0.00 0.00 0.00 4.18
3240 3832 2.726241 GCAAACAAGTTCAAGAATCCGC 59.274 45.455 0.00 0.00 0.00 5.54
3241 3833 2.969443 AACAAGTTCAAGAATCCGCG 57.031 45.000 0.00 0.00 0.00 6.46
3242 3834 1.156736 ACAAGTTCAAGAATCCGCGG 58.843 50.000 22.12 22.12 0.00 6.46
3243 3835 0.179189 CAAGTTCAAGAATCCGCGGC 60.179 55.000 23.51 6.72 0.00 6.53
3244 3836 1.305930 AAGTTCAAGAATCCGCGGCC 61.306 55.000 23.51 12.26 0.00 6.13
3245 3837 2.437716 TTCAAGAATCCGCGGCCC 60.438 61.111 23.51 11.86 0.00 5.80
3246 3838 3.261039 TTCAAGAATCCGCGGCCCA 62.261 57.895 23.51 3.06 0.00 5.36
3247 3839 3.508840 CAAGAATCCGCGGCCCAC 61.509 66.667 23.51 11.73 0.00 4.61
3248 3840 4.796495 AAGAATCCGCGGCCCACC 62.796 66.667 23.51 7.52 0.00 4.61
3250 3842 3.857038 GAATCCGCGGCCCACCTA 61.857 66.667 23.51 0.16 0.00 3.08
3251 3843 4.171103 AATCCGCGGCCCACCTAC 62.171 66.667 23.51 0.00 0.00 3.18
3255 3847 4.388499 CGCGGCCCACCTACTGTT 62.388 66.667 0.00 0.00 0.00 3.16
3256 3848 2.033602 GCGGCCCACCTACTGTTT 59.966 61.111 0.00 0.00 0.00 2.83
3257 3849 2.038837 GCGGCCCACCTACTGTTTC 61.039 63.158 0.00 0.00 0.00 2.78
3258 3850 1.373435 CGGCCCACCTACTGTTTCA 59.627 57.895 0.00 0.00 0.00 2.69
3259 3851 0.250553 CGGCCCACCTACTGTTTCAA 60.251 55.000 0.00 0.00 0.00 2.69
3260 3852 1.613255 CGGCCCACCTACTGTTTCAAT 60.613 52.381 0.00 0.00 0.00 2.57
3261 3853 1.818674 GGCCCACCTACTGTTTCAATG 59.181 52.381 0.00 0.00 0.00 2.82
3262 3854 1.202348 GCCCACCTACTGTTTCAATGC 59.798 52.381 0.00 0.00 0.00 3.56
3263 3855 1.818674 CCCACCTACTGTTTCAATGCC 59.181 52.381 0.00 0.00 0.00 4.40
3264 3856 2.513753 CCACCTACTGTTTCAATGCCA 58.486 47.619 0.00 0.00 0.00 4.92
3265 3857 2.228822 CCACCTACTGTTTCAATGCCAC 59.771 50.000 0.00 0.00 0.00 5.01
3266 3858 3.149196 CACCTACTGTTTCAATGCCACT 58.851 45.455 0.00 0.00 0.00 4.00
3267 3859 4.323417 CACCTACTGTTTCAATGCCACTA 58.677 43.478 0.00 0.00 0.00 2.74
3268 3860 4.154195 CACCTACTGTTTCAATGCCACTAC 59.846 45.833 0.00 0.00 0.00 2.73
3269 3861 4.202419 ACCTACTGTTTCAATGCCACTACA 60.202 41.667 0.00 0.00 0.00 2.74
3270 3862 4.154195 CCTACTGTTTCAATGCCACTACAC 59.846 45.833 0.00 0.00 0.00 2.90
3271 3863 2.548057 ACTGTTTCAATGCCACTACACG 59.452 45.455 0.00 0.00 0.00 4.49
3272 3864 1.876799 TGTTTCAATGCCACTACACGG 59.123 47.619 0.00 0.00 0.00 4.94
3273 3865 1.877443 GTTTCAATGCCACTACACGGT 59.123 47.619 0.00 0.00 0.00 4.83
3274 3866 2.264005 TTCAATGCCACTACACGGTT 57.736 45.000 0.00 0.00 0.00 4.44
3275 3867 1.803334 TCAATGCCACTACACGGTTC 58.197 50.000 0.00 0.00 0.00 3.62
3276 3868 0.442310 CAATGCCACTACACGGTTCG 59.558 55.000 0.00 0.00 0.00 3.95
3277 3869 0.319083 AATGCCACTACACGGTTCGA 59.681 50.000 0.00 0.00 0.00 3.71
3278 3870 0.108804 ATGCCACTACACGGTTCGAG 60.109 55.000 0.00 0.00 0.00 4.04
3279 3871 1.288127 GCCACTACACGGTTCGAGT 59.712 57.895 0.00 0.00 34.76 4.18
3280 3872 0.319297 GCCACTACACGGTTCGAGTT 60.319 55.000 0.00 0.00 32.48 3.01
3281 3873 1.870993 GCCACTACACGGTTCGAGTTT 60.871 52.381 0.00 0.00 32.48 2.66
3282 3874 1.790623 CCACTACACGGTTCGAGTTTG 59.209 52.381 0.00 0.00 32.48 2.93
3283 3875 1.790623 CACTACACGGTTCGAGTTTGG 59.209 52.381 0.00 0.00 32.48 3.28
3284 3876 1.269936 ACTACACGGTTCGAGTTTGGG 60.270 52.381 0.00 0.00 32.48 4.12
3285 3877 0.033781 TACACGGTTCGAGTTTGGGG 59.966 55.000 0.00 0.00 32.48 4.96
3286 3878 1.070105 CACGGTTCGAGTTTGGGGA 59.930 57.895 0.00 0.00 0.00 4.81
3287 3879 0.533308 CACGGTTCGAGTTTGGGGAA 60.533 55.000 0.00 0.00 0.00 3.97
3288 3880 0.399075 ACGGTTCGAGTTTGGGGAAT 59.601 50.000 0.00 0.00 0.00 3.01
3289 3881 0.802494 CGGTTCGAGTTTGGGGAATG 59.198 55.000 0.00 0.00 0.00 2.67
3290 3882 1.609580 CGGTTCGAGTTTGGGGAATGA 60.610 52.381 0.00 0.00 0.00 2.57
3291 3883 2.723273 GGTTCGAGTTTGGGGAATGAT 58.277 47.619 0.00 0.00 0.00 2.45
3292 3884 2.683362 GGTTCGAGTTTGGGGAATGATC 59.317 50.000 0.00 0.00 0.00 2.92
3293 3885 3.343617 GTTCGAGTTTGGGGAATGATCA 58.656 45.455 0.00 0.00 0.00 2.92
3294 3886 3.712016 TCGAGTTTGGGGAATGATCAA 57.288 42.857 0.00 0.00 0.00 2.57
3295 3887 3.609853 TCGAGTTTGGGGAATGATCAAG 58.390 45.455 0.00 0.00 0.00 3.02
3296 3888 3.009033 TCGAGTTTGGGGAATGATCAAGT 59.991 43.478 0.00 0.00 0.00 3.16
3297 3889 3.375299 CGAGTTTGGGGAATGATCAAGTC 59.625 47.826 0.00 0.00 0.00 3.01
3298 3890 4.593956 GAGTTTGGGGAATGATCAAGTCT 58.406 43.478 0.00 0.00 0.00 3.24
3299 3891 5.003096 AGTTTGGGGAATGATCAAGTCTT 57.997 39.130 0.00 0.00 0.00 3.01
3300 3892 4.768968 AGTTTGGGGAATGATCAAGTCTTG 59.231 41.667 6.21 6.21 0.00 3.02
3301 3893 3.370840 TGGGGAATGATCAAGTCTTGG 57.629 47.619 12.66 0.00 0.00 3.61
3302 3894 2.027385 GGGGAATGATCAAGTCTTGGC 58.973 52.381 12.66 6.15 0.00 4.52
3303 3895 2.357569 GGGGAATGATCAAGTCTTGGCT 60.358 50.000 12.66 0.76 0.00 4.75
3304 3896 3.359950 GGGAATGATCAAGTCTTGGCTT 58.640 45.455 12.66 1.90 0.00 4.35
3305 3897 3.129988 GGGAATGATCAAGTCTTGGCTTG 59.870 47.826 12.66 8.51 45.18 4.01
3306 3898 3.129988 GGAATGATCAAGTCTTGGCTTGG 59.870 47.826 12.66 0.00 44.26 3.61
3307 3899 1.538047 TGATCAAGTCTTGGCTTGGC 58.462 50.000 12.66 8.05 44.26 4.52
3308 3900 1.074405 TGATCAAGTCTTGGCTTGGCT 59.926 47.619 12.66 3.48 44.26 4.75
3309 3901 2.165998 GATCAAGTCTTGGCTTGGCTT 58.834 47.619 12.66 1.43 44.26 4.35
3310 3902 1.321474 TCAAGTCTTGGCTTGGCTTG 58.679 50.000 12.66 15.01 44.26 4.01
3311 3903 0.316204 CAAGTCTTGGCTTGGCTTGG 59.684 55.000 13.88 0.64 41.41 3.61
3312 3904 0.106015 AAGTCTTGGCTTGGCTTGGT 60.106 50.000 0.00 0.00 0.00 3.67
3313 3905 0.825010 AGTCTTGGCTTGGCTTGGTG 60.825 55.000 0.00 0.00 0.00 4.17
3314 3906 1.531365 TCTTGGCTTGGCTTGGTGG 60.531 57.895 0.00 0.00 0.00 4.61
3315 3907 1.531365 CTTGGCTTGGCTTGGTGGA 60.531 57.895 0.00 0.00 0.00 4.02
3316 3908 0.901580 CTTGGCTTGGCTTGGTGGAT 60.902 55.000 0.00 0.00 0.00 3.41
3317 3909 1.186917 TTGGCTTGGCTTGGTGGATG 61.187 55.000 0.00 0.00 0.00 3.51
3318 3910 1.607467 GGCTTGGCTTGGTGGATGT 60.607 57.895 0.00 0.00 0.00 3.06
3319 3911 1.588082 GCTTGGCTTGGTGGATGTG 59.412 57.895 0.00 0.00 0.00 3.21
3320 3912 1.588082 CTTGGCTTGGTGGATGTGC 59.412 57.895 0.00 0.00 0.00 4.57
3321 3913 1.152589 TTGGCTTGGTGGATGTGCA 60.153 52.632 0.00 0.00 0.00 4.57
3322 3914 1.462731 TTGGCTTGGTGGATGTGCAC 61.463 55.000 10.75 10.75 0.00 4.57
3323 3915 2.639327 GGCTTGGTGGATGTGCACC 61.639 63.158 15.69 15.80 41.64 5.01
3324 3916 2.639327 GCTTGGTGGATGTGCACCC 61.639 63.158 19.16 9.94 40.61 4.61
3325 3917 1.075482 CTTGGTGGATGTGCACCCT 59.925 57.895 19.16 0.70 40.61 4.34
3326 3918 0.540365 CTTGGTGGATGTGCACCCTT 60.540 55.000 19.16 0.00 40.61 3.95
3327 3919 0.539438 TTGGTGGATGTGCACCCTTC 60.539 55.000 19.16 8.63 40.61 3.46
3328 3920 1.380302 GGTGGATGTGCACCCTTCT 59.620 57.895 15.69 0.00 35.53 2.85
3329 3921 0.962356 GGTGGATGTGCACCCTTCTG 60.962 60.000 15.69 0.00 35.53 3.02
3330 3922 1.303561 TGGATGTGCACCCTTCTGC 60.304 57.895 15.69 0.00 37.70 4.26
3331 3923 1.001641 GGATGTGCACCCTTCTGCT 60.002 57.895 15.69 0.00 38.07 4.24
3332 3924 0.610232 GGATGTGCACCCTTCTGCTT 60.610 55.000 15.69 0.00 38.07 3.91
3333 3925 0.524862 GATGTGCACCCTTCTGCTTG 59.475 55.000 15.69 0.00 38.07 4.01
3334 3926 0.896940 ATGTGCACCCTTCTGCTTGG 60.897 55.000 15.69 0.00 38.07 3.61
3335 3927 1.228245 GTGCACCCTTCTGCTTGGA 60.228 57.895 5.22 0.00 38.07 3.53
3336 3928 0.610232 GTGCACCCTTCTGCTTGGAT 60.610 55.000 5.22 0.00 38.07 3.41
3337 3929 0.609957 TGCACCCTTCTGCTTGGATG 60.610 55.000 0.00 0.00 38.07 3.51
3338 3930 1.318158 GCACCCTTCTGCTTGGATGG 61.318 60.000 0.00 0.00 34.06 3.51
3339 3931 1.000396 ACCCTTCTGCTTGGATGGC 60.000 57.895 0.00 0.00 31.58 4.40
3340 3932 1.305623 CCCTTCTGCTTGGATGGCT 59.694 57.895 0.00 0.00 31.58 4.75
3341 3933 0.548031 CCCTTCTGCTTGGATGGCTA 59.452 55.000 0.00 0.00 31.58 3.93
3342 3934 1.144503 CCCTTCTGCTTGGATGGCTAT 59.855 52.381 0.00 0.00 31.58 2.97
3343 3935 2.502295 CCTTCTGCTTGGATGGCTATC 58.498 52.381 0.51 0.51 0.00 2.08
3357 3949 3.295973 TGGCTATCCATTTGGTAAAGGC 58.704 45.455 12.03 12.03 37.47 4.35
3358 3950 2.628178 GGCTATCCATTTGGTAAAGGCC 59.372 50.000 0.00 0.00 36.34 5.19
3359 3951 3.566351 GCTATCCATTTGGTAAAGGCCT 58.434 45.455 0.00 0.00 36.34 5.19
3360 3952 3.319122 GCTATCCATTTGGTAAAGGCCTG 59.681 47.826 5.69 0.00 36.34 4.85
3361 3953 2.230130 TCCATTTGGTAAAGGCCTGG 57.770 50.000 5.69 0.00 36.34 4.45
3362 3954 1.431243 TCCATTTGGTAAAGGCCTGGT 59.569 47.619 5.69 0.00 36.34 4.00
3363 3955 1.550072 CCATTTGGTAAAGGCCTGGTG 59.450 52.381 5.69 0.00 0.00 4.17
3364 3956 1.550072 CATTTGGTAAAGGCCTGGTGG 59.450 52.381 5.69 0.00 0.00 4.61
3365 3957 0.854218 TTTGGTAAAGGCCTGGTGGA 59.146 50.000 5.69 0.00 34.57 4.02
3366 3958 0.854218 TTGGTAAAGGCCTGGTGGAA 59.146 50.000 5.69 0.00 34.57 3.53
3367 3959 0.111639 TGGTAAAGGCCTGGTGGAAC 59.888 55.000 5.69 0.00 34.57 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 615 9.793259 AATTAGGACAAGTTCACTAATTTGAGA 57.207 29.630 0.00 0.00 41.03 3.27
423 635 4.991056 TCTAGCTGCGCTATTTGAATTAGG 59.009 41.667 9.73 0.00 40.54 2.69
559 998 3.440173 ACTGCAATACTGTAGCGCAAAAT 59.560 39.130 11.47 0.00 38.75 1.82
598 1037 3.772025 CTCACAGGAGAATCTTAGTGGGT 59.228 47.826 9.58 0.00 44.26 4.51
700 1139 6.034790 CGCATTGGATTGAAATTCGATTTTGA 59.965 34.615 9.85 0.00 31.47 2.69
791 1238 6.637493 CGCCTCCTCCTCCTAATATAATCCTA 60.637 46.154 0.00 0.00 0.00 2.94
818 1265 4.699522 GAACCTTCGCCACCGCCT 62.700 66.667 0.00 0.00 0.00 5.52
819 1266 4.699522 AGAACCTTCGCCACCGCC 62.700 66.667 0.00 0.00 0.00 6.13
820 1267 2.668550 AAGAACCTTCGCCACCGC 60.669 61.111 0.00 0.00 0.00 5.68
821 1268 1.164041 AACAAGAACCTTCGCCACCG 61.164 55.000 0.00 0.00 0.00 4.94
822 1269 0.310854 CAACAAGAACCTTCGCCACC 59.689 55.000 0.00 0.00 0.00 4.61
823 1270 0.317854 GCAACAAGAACCTTCGCCAC 60.318 55.000 0.00 0.00 0.00 5.01
862 1309 5.219987 GGAAGCGCGTATTAATAGATCGAAC 60.220 44.000 8.43 0.00 0.00 3.95
905 1356 1.759459 GAAAGGGGATCGGGAGCGAT 61.759 60.000 0.00 0.00 0.00 4.58
975 1427 3.394606 GGATTGGTCTGGAATAGCCCTAA 59.605 47.826 0.00 0.00 34.97 2.69
1094 1552 1.133167 TCTCTCTCCACCTGGTGTTCA 60.133 52.381 24.32 7.98 36.34 3.18
1095 1553 1.548269 CTCTCTCTCCACCTGGTGTTC 59.452 57.143 24.32 0.00 36.34 3.18
1096 1554 1.148027 TCTCTCTCTCCACCTGGTGTT 59.852 52.381 24.32 0.00 36.34 3.32
1103 1561 0.616111 TGGCCTTCTCTCTCTCCACC 60.616 60.000 3.32 0.00 0.00 4.61
1173 1634 1.583495 GCTGATGCTGTTGCTGCTGA 61.583 55.000 0.00 0.00 40.48 4.26
1176 1637 1.443872 GTGCTGATGCTGTTGCTGC 60.444 57.895 0.00 0.00 40.48 5.25
1188 1682 1.034838 GTTGTTGGTGGTGGTGCTGA 61.035 55.000 0.00 0.00 0.00 4.26
1194 1688 1.437160 GTGCTGTTGTTGGTGGTGG 59.563 57.895 0.00 0.00 0.00 4.61
1215 1709 1.870055 GATGTTGCTGCTGGTGGTGG 61.870 60.000 0.00 0.00 0.00 4.61
1218 1712 2.872557 CGATGTTGCTGCTGGTGG 59.127 61.111 0.00 0.00 0.00 4.61
1221 1715 1.709147 GGTAGCGATGTTGCTGCTGG 61.709 60.000 9.68 0.00 46.70 4.85
1230 1724 0.963856 TGACAGGACGGTAGCGATGT 60.964 55.000 22.88 20.45 0.00 3.06
1252 1746 2.109126 GCGAGGAGTGGCCATTGTC 61.109 63.158 9.72 6.43 40.02 3.18
1295 1789 2.997897 GGTGTCGGTCCAGCTCCT 60.998 66.667 0.00 0.00 0.00 3.69
1641 2135 3.169155 AACAGACGCTGCAGAGCCA 62.169 57.895 20.43 0.00 42.91 4.75
1725 2219 3.883830 TTCAAGTTGGAAGCAGCAAAA 57.116 38.095 2.34 0.00 0.00 2.44
1788 2282 4.382040 CCAAAGCGAAGACTAATCTCCTCA 60.382 45.833 0.00 0.00 32.34 3.86
2116 2610 9.941619 ATCGTTGAAATGATCTGCAGATGTTGC 62.942 40.741 33.33 23.70 40.63 4.17
2329 2826 2.250237 GCCTCCTGCTATTCTGCGC 61.250 63.158 0.00 0.00 36.87 6.09
2557 3054 9.672673 GAACCATACCATGAAGTAATATAGCAT 57.327 33.333 0.00 0.00 0.00 3.79
2566 3063 7.661437 GCATCAATAGAACCATACCATGAAGTA 59.339 37.037 0.00 0.00 0.00 2.24
2611 3108 2.214216 AGCACGGCCACCTTCTGTA 61.214 57.895 2.24 0.00 0.00 2.74
2625 3130 9.197694 CTAACATTTACATAGGATCTACAGCAC 57.802 37.037 0.00 0.00 0.00 4.40
2712 3271 4.113354 GTCCGTTTGCTCTATCCTAACTG 58.887 47.826 0.00 0.00 0.00 3.16
2731 3298 0.536460 TTTTGTTGGAGCCGGAGTCC 60.536 55.000 5.05 11.50 34.31 3.85
2737 3304 0.738389 AGTGTGTTTTGTTGGAGCCG 59.262 50.000 0.00 0.00 0.00 5.52
2738 3305 1.748493 TGAGTGTGTTTTGTTGGAGCC 59.252 47.619 0.00 0.00 0.00 4.70
2778 3345 4.079844 TGCCAAAGAGATGGATGGTGATAA 60.080 41.667 0.00 0.00 43.54 1.75
2785 3352 4.381292 GGAAGTTTGCCAAAGAGATGGATG 60.381 45.833 0.00 0.00 43.54 3.51
2810 3377 7.707624 ATCTCATTTTTCTGAATTACAGCCA 57.292 32.000 0.00 0.00 45.38 4.75
2811 3378 7.490402 CCAATCTCATTTTTCTGAATTACAGCC 59.510 37.037 0.00 0.00 45.38 4.85
2816 3383 7.479352 TGGCCAATCTCATTTTTCTGAATTA 57.521 32.000 0.61 0.00 0.00 1.40
3037 3629 7.070447 TCCTGTTATCTCTGTATGCAAGATCTT 59.930 37.037 0.88 0.88 32.25 2.40
3048 3640 4.716784 ACATGGCTTCCTGTTATCTCTGTA 59.283 41.667 0.00 0.00 0.00 2.74
3089 3681 2.088423 GACGTCAGATCACAGAGTCCT 58.912 52.381 11.55 0.00 0.00 3.85
3107 3699 1.103803 TCGCAGTACAGGATCTGGAC 58.896 55.000 2.21 2.21 45.06 4.02
3108 3700 1.103803 GTCGCAGTACAGGATCTGGA 58.896 55.000 0.00 0.00 35.51 3.86
3109 3701 1.107114 AGTCGCAGTACAGGATCTGG 58.893 55.000 0.00 0.00 35.51 3.86
3110 3702 2.949451 AAGTCGCAGTACAGGATCTG 57.051 50.000 0.00 0.00 37.52 2.90
3111 3703 5.352284 CAAATAAGTCGCAGTACAGGATCT 58.648 41.667 0.00 0.00 0.00 2.75
3112 3704 4.025647 GCAAATAAGTCGCAGTACAGGATC 60.026 45.833 0.00 0.00 0.00 3.36
3113 3705 3.871594 GCAAATAAGTCGCAGTACAGGAT 59.128 43.478 0.00 0.00 0.00 3.24
3114 3706 3.056107 AGCAAATAAGTCGCAGTACAGGA 60.056 43.478 0.00 0.00 0.00 3.86
3115 3707 3.262420 AGCAAATAAGTCGCAGTACAGG 58.738 45.455 0.00 0.00 0.00 4.00
3116 3708 4.436050 CCAAGCAAATAAGTCGCAGTACAG 60.436 45.833 0.00 0.00 0.00 2.74
3117 3709 3.435327 CCAAGCAAATAAGTCGCAGTACA 59.565 43.478 0.00 0.00 0.00 2.90
3118 3710 3.727970 GCCAAGCAAATAAGTCGCAGTAC 60.728 47.826 0.00 0.00 0.00 2.73
3119 3711 2.418628 GCCAAGCAAATAAGTCGCAGTA 59.581 45.455 0.00 0.00 0.00 2.74
3120 3712 1.200020 GCCAAGCAAATAAGTCGCAGT 59.800 47.619 0.00 0.00 0.00 4.40
3121 3713 1.470098 AGCCAAGCAAATAAGTCGCAG 59.530 47.619 0.00 0.00 0.00 5.18
3122 3714 1.533625 AGCCAAGCAAATAAGTCGCA 58.466 45.000 0.00 0.00 0.00 5.10
3123 3715 2.678336 ACTAGCCAAGCAAATAAGTCGC 59.322 45.455 0.00 0.00 0.00 5.19
3124 3716 4.946784 AACTAGCCAAGCAAATAAGTCG 57.053 40.909 0.00 0.00 0.00 4.18
3125 3717 7.553881 TGATAACTAGCCAAGCAAATAAGTC 57.446 36.000 0.00 0.00 0.00 3.01
3126 3718 7.938140 TTGATAACTAGCCAAGCAAATAAGT 57.062 32.000 0.00 0.00 0.00 2.24
3129 3721 9.402320 TGTTATTGATAACTAGCCAAGCAAATA 57.598 29.630 13.35 0.00 42.32 1.40
3130 3722 8.292444 TGTTATTGATAACTAGCCAAGCAAAT 57.708 30.769 13.35 0.00 42.32 2.32
3131 3723 7.148086 CCTGTTATTGATAACTAGCCAAGCAAA 60.148 37.037 13.35 0.00 42.32 3.68
3132 3724 6.318648 CCTGTTATTGATAACTAGCCAAGCAA 59.681 38.462 13.35 0.00 42.32 3.91
3133 3725 5.822519 CCTGTTATTGATAACTAGCCAAGCA 59.177 40.000 13.35 0.00 42.32 3.91
3134 3726 6.055588 TCCTGTTATTGATAACTAGCCAAGC 58.944 40.000 13.35 0.00 42.32 4.01
3135 3727 8.153550 AGATCCTGTTATTGATAACTAGCCAAG 58.846 37.037 13.35 3.62 42.32 3.61
3136 3728 7.933577 CAGATCCTGTTATTGATAACTAGCCAA 59.066 37.037 13.35 0.00 42.32 4.52
3137 3729 7.445121 CAGATCCTGTTATTGATAACTAGCCA 58.555 38.462 13.35 0.00 42.32 4.75
3138 3730 6.876257 CCAGATCCTGTTATTGATAACTAGCC 59.124 42.308 13.35 2.42 42.32 3.93
3139 3731 7.600752 GTCCAGATCCTGTTATTGATAACTAGC 59.399 40.741 13.35 4.41 42.32 3.42
3140 3732 7.810282 CGTCCAGATCCTGTTATTGATAACTAG 59.190 40.741 13.35 9.49 42.32 2.57
3141 3733 7.255836 CCGTCCAGATCCTGTTATTGATAACTA 60.256 40.741 13.35 2.47 42.32 2.24
3142 3734 6.463049 CCGTCCAGATCCTGTTATTGATAACT 60.463 42.308 13.35 0.00 42.32 2.24
3143 3735 5.696724 CCGTCCAGATCCTGTTATTGATAAC 59.303 44.000 6.88 6.88 42.21 1.89
3144 3736 5.741964 GCCGTCCAGATCCTGTTATTGATAA 60.742 44.000 0.00 0.00 0.00 1.75
3145 3737 4.262463 GCCGTCCAGATCCTGTTATTGATA 60.262 45.833 0.00 0.00 0.00 2.15
3146 3738 3.495100 GCCGTCCAGATCCTGTTATTGAT 60.495 47.826 0.00 0.00 0.00 2.57
3147 3739 2.158957 GCCGTCCAGATCCTGTTATTGA 60.159 50.000 0.00 0.00 0.00 2.57
3148 3740 2.213499 GCCGTCCAGATCCTGTTATTG 58.787 52.381 0.00 0.00 0.00 1.90
3149 3741 1.141053 GGCCGTCCAGATCCTGTTATT 59.859 52.381 0.00 0.00 0.00 1.40
3150 3742 0.759346 GGCCGTCCAGATCCTGTTAT 59.241 55.000 0.00 0.00 0.00 1.89
3151 3743 1.672854 CGGCCGTCCAGATCCTGTTA 61.673 60.000 19.50 0.00 0.00 2.41
3152 3744 2.990479 GGCCGTCCAGATCCTGTT 59.010 61.111 0.00 0.00 0.00 3.16
3153 3745 3.461773 CGGCCGTCCAGATCCTGT 61.462 66.667 19.50 0.00 0.00 4.00
3154 3746 3.147595 TCGGCCGTCCAGATCCTG 61.148 66.667 27.15 0.00 0.00 3.86
3155 3747 3.148279 GTCGGCCGTCCAGATCCT 61.148 66.667 27.15 0.00 0.00 3.24
3156 3748 3.432051 CTGTCGGCCGTCCAGATCC 62.432 68.421 30.75 11.19 0.00 3.36
3157 3749 2.105128 CTGTCGGCCGTCCAGATC 59.895 66.667 30.75 14.07 0.00 2.75
3158 3750 3.461773 CCTGTCGGCCGTCCAGAT 61.462 66.667 33.84 0.00 0.00 2.90
3175 3767 4.038080 CAACCCCGGCGTTGAAGC 62.038 66.667 24.67 0.00 44.88 3.86
3176 3768 3.361977 CCAACCCCGGCGTTGAAG 61.362 66.667 29.29 12.72 44.88 3.02
3184 3776 2.045340 CAGTTAGGCCAACCCCGG 60.045 66.667 5.01 0.00 37.93 5.73
3185 3777 2.750237 GCAGTTAGGCCAACCCCG 60.750 66.667 5.01 0.94 37.93 5.73
3186 3778 2.750237 CGCAGTTAGGCCAACCCC 60.750 66.667 5.01 1.01 37.93 4.95
3187 3779 2.038837 GTCGCAGTTAGGCCAACCC 61.039 63.158 5.01 1.36 37.93 4.11
3188 3780 2.038837 GGTCGCAGTTAGGCCAACC 61.039 63.158 5.01 0.00 37.93 3.77
3189 3781 0.676782 ATGGTCGCAGTTAGGCCAAC 60.677 55.000 5.01 7.78 37.41 3.77
3190 3782 0.037590 AATGGTCGCAGTTAGGCCAA 59.962 50.000 5.01 0.00 32.54 4.52
3191 3783 0.676466 CAATGGTCGCAGTTAGGCCA 60.676 55.000 5.01 0.00 0.00 5.36
3192 3784 1.993369 GCAATGGTCGCAGTTAGGCC 61.993 60.000 0.00 0.00 0.00 5.19
3193 3785 1.429423 GCAATGGTCGCAGTTAGGC 59.571 57.895 0.00 0.00 0.00 3.93
3194 3786 1.376609 GGGCAATGGTCGCAGTTAGG 61.377 60.000 0.00 0.00 0.00 2.69
3195 3787 0.676466 TGGGCAATGGTCGCAGTTAG 60.676 55.000 0.00 0.00 0.00 2.34
3196 3788 0.958382 GTGGGCAATGGTCGCAGTTA 60.958 55.000 0.00 0.00 0.00 2.24
3197 3789 2.115052 TGGGCAATGGTCGCAGTT 59.885 55.556 0.00 0.00 0.00 3.16
3198 3790 1.836999 TAGTGGGCAATGGTCGCAGT 61.837 55.000 0.00 0.00 34.89 4.40
3199 3791 0.464373 ATAGTGGGCAATGGTCGCAG 60.464 55.000 0.00 0.00 0.00 5.18
3200 3792 0.747644 CATAGTGGGCAATGGTCGCA 60.748 55.000 0.00 0.00 0.00 5.10
3201 3793 2.024918 CATAGTGGGCAATGGTCGC 58.975 57.895 0.00 0.00 0.00 5.19
3202 3794 0.747644 TGCATAGTGGGCAATGGTCG 60.748 55.000 0.00 0.00 38.54 4.79
3203 3795 1.473258 TTGCATAGTGGGCAATGGTC 58.527 50.000 0.00 0.00 45.57 4.02
3204 3796 3.687847 TTGCATAGTGGGCAATGGT 57.312 47.368 0.00 0.00 45.57 3.55
3209 3801 1.993956 ACTTGTTTGCATAGTGGGCA 58.006 45.000 0.00 0.00 40.00 5.36
3210 3802 2.295909 TGAACTTGTTTGCATAGTGGGC 59.704 45.455 0.00 0.00 0.00 5.36
3211 3803 4.278170 TCTTGAACTTGTTTGCATAGTGGG 59.722 41.667 0.00 0.00 0.00 4.61
3212 3804 5.437289 TCTTGAACTTGTTTGCATAGTGG 57.563 39.130 0.00 0.00 0.00 4.00
3213 3805 6.583806 GGATTCTTGAACTTGTTTGCATAGTG 59.416 38.462 0.00 0.00 0.00 2.74
3214 3806 6.568462 CGGATTCTTGAACTTGTTTGCATAGT 60.568 38.462 0.00 0.00 0.00 2.12
3215 3807 5.796935 CGGATTCTTGAACTTGTTTGCATAG 59.203 40.000 0.00 0.00 0.00 2.23
3216 3808 5.698832 CGGATTCTTGAACTTGTTTGCATA 58.301 37.500 0.00 0.00 0.00 3.14
3217 3809 4.549458 CGGATTCTTGAACTTGTTTGCAT 58.451 39.130 0.00 0.00 0.00 3.96
3218 3810 3.795150 GCGGATTCTTGAACTTGTTTGCA 60.795 43.478 0.00 0.00 0.00 4.08
3219 3811 2.726241 GCGGATTCTTGAACTTGTTTGC 59.274 45.455 0.00 0.00 0.00 3.68
3220 3812 2.973224 CGCGGATTCTTGAACTTGTTTG 59.027 45.455 0.00 0.00 0.00 2.93
3221 3813 2.031157 CCGCGGATTCTTGAACTTGTTT 60.031 45.455 24.07 0.00 0.00 2.83
3222 3814 1.535462 CCGCGGATTCTTGAACTTGTT 59.465 47.619 24.07 0.00 0.00 2.83
3223 3815 1.156736 CCGCGGATTCTTGAACTTGT 58.843 50.000 24.07 0.00 0.00 3.16
3224 3816 0.179189 GCCGCGGATTCTTGAACTTG 60.179 55.000 33.48 0.00 0.00 3.16
3225 3817 1.305930 GGCCGCGGATTCTTGAACTT 61.306 55.000 33.48 0.00 0.00 2.66
3226 3818 1.745489 GGCCGCGGATTCTTGAACT 60.745 57.895 33.48 0.00 0.00 3.01
3227 3819 2.761195 GGGCCGCGGATTCTTGAAC 61.761 63.158 33.48 7.28 0.00 3.18
3228 3820 2.437716 GGGCCGCGGATTCTTGAA 60.438 61.111 33.48 0.00 0.00 2.69
3229 3821 3.711814 TGGGCCGCGGATTCTTGA 61.712 61.111 33.48 0.65 0.00 3.02
3230 3822 3.508840 GTGGGCCGCGGATTCTTG 61.509 66.667 33.48 0.00 0.00 3.02
3231 3823 4.796495 GGTGGGCCGCGGATTCTT 62.796 66.667 33.48 0.00 0.00 2.52
3233 3825 3.857038 TAGGTGGGCCGCGGATTC 61.857 66.667 33.48 17.55 40.50 2.52
3234 3826 4.171103 GTAGGTGGGCCGCGGATT 62.171 66.667 33.48 9.04 40.50 3.01
3238 3830 3.894547 AAACAGTAGGTGGGCCGCG 62.895 63.158 11.61 0.00 40.50 6.46
3239 3831 2.033602 AAACAGTAGGTGGGCCGC 59.966 61.111 9.05 9.05 40.50 6.53
3240 3832 0.250553 TTGAAACAGTAGGTGGGCCG 60.251 55.000 0.00 0.00 40.50 6.13
3241 3833 1.818674 CATTGAAACAGTAGGTGGGCC 59.181 52.381 0.00 0.00 0.00 5.80
3242 3834 1.202348 GCATTGAAACAGTAGGTGGGC 59.798 52.381 0.00 0.00 0.00 5.36
3243 3835 1.818674 GGCATTGAAACAGTAGGTGGG 59.181 52.381 0.00 0.00 0.00 4.61
3244 3836 2.228822 GTGGCATTGAAACAGTAGGTGG 59.771 50.000 0.00 0.00 0.00 4.61
3245 3837 3.149196 AGTGGCATTGAAACAGTAGGTG 58.851 45.455 0.00 0.00 0.00 4.00
3246 3838 3.508845 AGTGGCATTGAAACAGTAGGT 57.491 42.857 0.00 0.00 0.00 3.08
3247 3839 4.154195 GTGTAGTGGCATTGAAACAGTAGG 59.846 45.833 0.00 0.00 0.00 3.18
3248 3840 4.143115 CGTGTAGTGGCATTGAAACAGTAG 60.143 45.833 0.00 0.00 0.00 2.57
3249 3841 3.743911 CGTGTAGTGGCATTGAAACAGTA 59.256 43.478 0.00 0.00 0.00 2.74
3250 3842 2.548057 CGTGTAGTGGCATTGAAACAGT 59.452 45.455 0.00 0.00 0.00 3.55
3251 3843 2.095768 CCGTGTAGTGGCATTGAAACAG 60.096 50.000 0.00 0.00 0.00 3.16
3252 3844 1.876799 CCGTGTAGTGGCATTGAAACA 59.123 47.619 0.00 0.00 0.00 2.83
3253 3845 1.877443 ACCGTGTAGTGGCATTGAAAC 59.123 47.619 0.00 0.00 0.00 2.78
3254 3846 2.264005 ACCGTGTAGTGGCATTGAAA 57.736 45.000 0.00 0.00 0.00 2.69
3255 3847 2.147958 GAACCGTGTAGTGGCATTGAA 58.852 47.619 0.00 0.00 0.00 2.69
3256 3848 1.803334 GAACCGTGTAGTGGCATTGA 58.197 50.000 0.00 0.00 0.00 2.57
3257 3849 0.442310 CGAACCGTGTAGTGGCATTG 59.558 55.000 0.00 0.00 0.00 2.82
3258 3850 0.319083 TCGAACCGTGTAGTGGCATT 59.681 50.000 0.00 0.00 0.00 3.56
3259 3851 0.108804 CTCGAACCGTGTAGTGGCAT 60.109 55.000 0.00 0.00 0.00 4.40
3260 3852 1.287815 CTCGAACCGTGTAGTGGCA 59.712 57.895 0.00 0.00 0.00 4.92
3261 3853 0.319297 AACTCGAACCGTGTAGTGGC 60.319 55.000 0.00 0.00 33.29 5.01
3262 3854 1.790623 CAAACTCGAACCGTGTAGTGG 59.209 52.381 0.00 0.00 33.29 4.00
3263 3855 1.790623 CCAAACTCGAACCGTGTAGTG 59.209 52.381 0.00 0.00 33.29 2.74
3264 3856 1.269936 CCCAAACTCGAACCGTGTAGT 60.270 52.381 0.00 0.00 33.29 2.73
3265 3857 1.425412 CCCAAACTCGAACCGTGTAG 58.575 55.000 0.00 0.00 33.29 2.74
3266 3858 0.033781 CCCCAAACTCGAACCGTGTA 59.966 55.000 0.00 0.00 33.29 2.90
3267 3859 1.227734 CCCCAAACTCGAACCGTGT 60.228 57.895 0.00 0.00 35.09 4.49
3268 3860 0.533308 TTCCCCAAACTCGAACCGTG 60.533 55.000 0.00 0.00 0.00 4.94
3269 3861 0.399075 ATTCCCCAAACTCGAACCGT 59.601 50.000 0.00 0.00 0.00 4.83
3270 3862 0.802494 CATTCCCCAAACTCGAACCG 59.198 55.000 0.00 0.00 0.00 4.44
3271 3863 2.194201 TCATTCCCCAAACTCGAACC 57.806 50.000 0.00 0.00 0.00 3.62
3272 3864 3.343617 TGATCATTCCCCAAACTCGAAC 58.656 45.455 0.00 0.00 0.00 3.95
3273 3865 3.712016 TGATCATTCCCCAAACTCGAA 57.288 42.857 0.00 0.00 0.00 3.71
3274 3866 3.009033 ACTTGATCATTCCCCAAACTCGA 59.991 43.478 0.00 0.00 0.00 4.04
3275 3867 3.347216 ACTTGATCATTCCCCAAACTCG 58.653 45.455 0.00 0.00 0.00 4.18
3276 3868 4.593956 AGACTTGATCATTCCCCAAACTC 58.406 43.478 0.00 0.00 0.00 3.01
3277 3869 4.664688 AGACTTGATCATTCCCCAAACT 57.335 40.909 0.00 0.00 0.00 2.66
3278 3870 4.082026 CCAAGACTTGATCATTCCCCAAAC 60.082 45.833 16.99 0.00 0.00 2.93
3279 3871 4.088634 CCAAGACTTGATCATTCCCCAAA 58.911 43.478 16.99 0.00 0.00 3.28
3280 3872 3.700538 CCAAGACTTGATCATTCCCCAA 58.299 45.455 16.99 0.00 0.00 4.12
3281 3873 2.621407 GCCAAGACTTGATCATTCCCCA 60.621 50.000 16.99 0.00 0.00 4.96
3282 3874 2.027385 GCCAAGACTTGATCATTCCCC 58.973 52.381 16.99 0.00 0.00 4.81
3283 3875 3.010200 AGCCAAGACTTGATCATTCCC 57.990 47.619 16.99 0.00 0.00 3.97
3292 3884 0.316204 CCAAGCCAAGCCAAGACTTG 59.684 55.000 8.31 8.31 45.42 3.16
3293 3885 0.106015 ACCAAGCCAAGCCAAGACTT 60.106 50.000 0.00 0.00 0.00 3.01
3294 3886 0.825010 CACCAAGCCAAGCCAAGACT 60.825 55.000 0.00 0.00 0.00 3.24
3295 3887 1.662044 CACCAAGCCAAGCCAAGAC 59.338 57.895 0.00 0.00 0.00 3.01
3296 3888 1.531365 CCACCAAGCCAAGCCAAGA 60.531 57.895 0.00 0.00 0.00 3.02
3297 3889 0.901580 ATCCACCAAGCCAAGCCAAG 60.902 55.000 0.00 0.00 0.00 3.61
3298 3890 1.155859 ATCCACCAAGCCAAGCCAA 59.844 52.632 0.00 0.00 0.00 4.52
3299 3891 1.607178 CATCCACCAAGCCAAGCCA 60.607 57.895 0.00 0.00 0.00 4.75
3300 3892 1.607467 ACATCCACCAAGCCAAGCC 60.607 57.895 0.00 0.00 0.00 4.35
3301 3893 1.588082 CACATCCACCAAGCCAAGC 59.412 57.895 0.00 0.00 0.00 4.01
3302 3894 1.180456 TGCACATCCACCAAGCCAAG 61.180 55.000 0.00 0.00 0.00 3.61
3303 3895 1.152589 TGCACATCCACCAAGCCAA 60.153 52.632 0.00 0.00 0.00 4.52
3304 3896 1.902918 GTGCACATCCACCAAGCCA 60.903 57.895 13.17 0.00 0.00 4.75
3305 3897 2.964978 GTGCACATCCACCAAGCC 59.035 61.111 13.17 0.00 0.00 4.35
3311 3903 1.589716 GCAGAAGGGTGCACATCCAC 61.590 60.000 20.43 9.72 43.41 4.02
3312 3904 1.303561 GCAGAAGGGTGCACATCCA 60.304 57.895 20.43 0.00 43.41 3.41
3313 3905 0.610232 AAGCAGAAGGGTGCACATCC 60.610 55.000 20.43 11.78 46.60 3.51
3314 3906 0.524862 CAAGCAGAAGGGTGCACATC 59.475 55.000 20.43 13.35 46.60 3.06
3315 3907 0.896940 CCAAGCAGAAGGGTGCACAT 60.897 55.000 20.43 3.17 46.60 3.21
3316 3908 1.529010 CCAAGCAGAAGGGTGCACA 60.529 57.895 20.43 0.00 46.60 4.57
3317 3909 0.610232 ATCCAAGCAGAAGGGTGCAC 60.610 55.000 8.80 8.80 46.60 4.57
3318 3910 0.609957 CATCCAAGCAGAAGGGTGCA 60.610 55.000 0.00 0.00 46.60 4.57
3319 3911 1.318158 CCATCCAAGCAGAAGGGTGC 61.318 60.000 0.00 0.00 44.35 5.01
3320 3912 1.318158 GCCATCCAAGCAGAAGGGTG 61.318 60.000 0.00 0.00 35.74 4.61
3321 3913 1.000396 GCCATCCAAGCAGAAGGGT 60.000 57.895 0.00 0.00 0.00 4.34
3322 3914 0.548031 TAGCCATCCAAGCAGAAGGG 59.452 55.000 0.00 0.00 0.00 3.95
3323 3915 2.502295 GATAGCCATCCAAGCAGAAGG 58.498 52.381 0.00 0.00 0.00 3.46
3337 3929 2.628178 GGCCTTTACCAAATGGATAGCC 59.372 50.000 6.42 7.14 38.94 3.93
3338 3930 3.319122 CAGGCCTTTACCAAATGGATAGC 59.681 47.826 0.00 1.81 38.94 2.97
3339 3931 3.891366 CCAGGCCTTTACCAAATGGATAG 59.109 47.826 0.00 0.44 38.94 2.08
3340 3932 3.270960 ACCAGGCCTTTACCAAATGGATA 59.729 43.478 0.00 0.00 38.94 2.59
3341 3933 2.044353 ACCAGGCCTTTACCAAATGGAT 59.956 45.455 0.00 0.00 38.94 3.41
3342 3934 1.431243 ACCAGGCCTTTACCAAATGGA 59.569 47.619 0.00 0.00 38.94 3.41
3343 3935 1.550072 CACCAGGCCTTTACCAAATGG 59.450 52.381 0.00 0.24 42.17 3.16
3344 3936 1.550072 CCACCAGGCCTTTACCAAATG 59.450 52.381 0.00 0.00 0.00 2.32
3345 3937 1.431243 TCCACCAGGCCTTTACCAAAT 59.569 47.619 0.00 0.00 33.74 2.32
3346 3938 0.854218 TCCACCAGGCCTTTACCAAA 59.146 50.000 0.00 0.00 33.74 3.28
3347 3939 0.854218 TTCCACCAGGCCTTTACCAA 59.146 50.000 0.00 0.00 33.74 3.67
3348 3940 0.111639 GTTCCACCAGGCCTTTACCA 59.888 55.000 0.00 0.00 33.74 3.25
3349 3941 2.957060 GTTCCACCAGGCCTTTACC 58.043 57.895 0.00 0.00 33.74 2.85


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

AutoCloner maintained by Alex Coulton.