Multiple sequence alignment - TraesCS5A01G181500

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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 TraesCS5A01G181500 chr5A 100.000 3371 0 0 1 3371 380226819 380223449 0.000000e+00 6226.0
1 TraesCS5A01G181500 chr5B 93.680 3054 98 26 1 3000 326919267 326916255 0.000000e+00 4482.0
2 TraesCS5A01G181500 chr5D 94.383 2368 82 26 657 3000 287809216 287806876 0.000000e+00 3589.0
3 TraesCS5A01G181500 chr5D 87.108 574 34 20 7 573 287809760 287809220 6.180000e-172 614.0
4 TraesCS5A01G181500 chr5D 85.714 161 14 5 2844 3000 270200643 270200798 9.680000e-36 161.0
5 TraesCS5A01G181500 chr5D 96.875 32 1 0 2994 3025 353691713 353691744 2.000000e-03 54.7
6 TraesCS5A01G181500 chr1B 90.102 394 21 2 2996 3371 612933321 612933714 2.340000e-136 496.0
7 TraesCS5A01G181500 chr4A 89.340 394 24 4 2996 3371 655628673 655629066 2.350000e-131 479.0
8 TraesCS5A01G181500 chr3D 90.133 375 25 4 3007 3371 599168197 599167825 8.460000e-131 477.0
9 TraesCS5A01G181500 chr1D 85.535 159 17 5 2843 3000 443815793 443815640 9.680000e-36 161.0
10 TraesCS5A01G181500 chr1D 100.000 28 0 0 2998 3025 229408622 229408595 6.000000e-03 52.8
11 TraesCS5A01G181500 chr7D 85.276 163 14 6 2841 3000 544656442 544656597 3.480000e-35 159.0
12 TraesCS5A01G181500 chr4B 88.281 128 8 3 2855 2980 581308322 581308444 2.710000e-31 147.0
13 TraesCS5A01G181500 chr2D 85.517 145 15 3 2855 2998 579765615 579765476 2.710000e-31 147.0
14 TraesCS5A01G181500 chr7A 83.230 161 21 2 2841 3000 626415124 626415279 3.510000e-30 143.0
15 TraesCS5A01G181500 chr2A 83.448 145 18 2 2855 2998 717391896 717391757 2.730000e-26 130.0
16 TraesCS5A01G181500 chr2B 100.000 28 0 0 2996 3023 261968327 261968300 6.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G181500 chr5A 380223449 380226819 3370 True 6226.0 6226 100.0000 1 3371 1 chr5A.!!$R1 3370
1 TraesCS5A01G181500 chr5B 326916255 326919267 3012 True 4482.0 4482 93.6800 1 3000 1 chr5B.!!$R1 2999
2 TraesCS5A01G181500 chr5D 287806876 287809760 2884 True 2101.5 3589 90.7455 7 3000 2 chr5D.!!$R1 2993

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
144 148 0.739112 GAGAAGCCAAGACCTCGCAG 60.739 60.0 0.00 0.0 0.00 5.18 F
2030 2077 1.327303 TTGGTTTGGTTAGCCTGCTG 58.673 50.0 0.97 0.0 35.27 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2148 0.251916 TTCCTCCGATGCCGTTTCAT 59.748 50.0 0.00 0.0 0.0 2.57 R
3198 3270 0.033228 CTTGGCAGGCTATCTCGAGG 59.967 60.0 13.56 0.0 0.0 4.63 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
30 31 1.884235 AATCCGCATCCGAGAAATCC 58.116 50.000 0.00 0.00 36.29 3.01
39 40 1.520787 CGAGAAATCCCGGGGAACG 60.521 63.158 23.50 15.98 43.80 3.95
103 104 3.512516 GCTCGCCCTTGATGTGGC 61.513 66.667 0.00 0.00 44.41 5.01
122 126 2.805099 GGCGAATAGATTCTTGGCTCAG 59.195 50.000 0.00 0.00 34.69 3.35
127 131 2.695127 AGATTCTTGGCTCAGCTGAG 57.305 50.000 34.82 34.82 44.75 3.35
144 148 0.739112 GAGAAGCCAAGACCTCGCAG 60.739 60.000 0.00 0.00 0.00 5.18
169 173 8.314021 AGAAAGAAAGAAAAGCCAAGAGAAAAA 58.686 29.630 0.00 0.00 0.00 1.94
170 174 8.484641 AAAGAAAGAAAAGCCAAGAGAAAAAG 57.515 30.769 0.00 0.00 0.00 2.27
175 179 8.846943 AAGAAAAGCCAAGAGAAAAAGAAAAA 57.153 26.923 0.00 0.00 0.00 1.94
176 180 9.453572 AAGAAAAGCCAAGAGAAAAAGAAAAAT 57.546 25.926 0.00 0.00 0.00 1.82
177 181 9.102757 AGAAAAGCCAAGAGAAAAAGAAAAATC 57.897 29.630 0.00 0.00 0.00 2.17
179 183 9.453572 AAAAGCCAAGAGAAAAAGAAAAATCTT 57.546 25.926 0.00 0.00 0.00 2.40
180 184 8.429493 AAGCCAAGAGAAAAAGAAAAATCTTG 57.571 30.769 5.90 5.90 41.96 3.02
198 202 3.840078 TCTTGGGGGTTACTGTTACTACC 59.160 47.826 0.00 1.14 0.00 3.18
206 214 5.186409 GGGTTACTGTTACTACCATGACTCA 59.814 44.000 0.00 0.00 32.20 3.41
292 300 3.438434 GGAAGCTGATGGTTTCTTGTCTC 59.562 47.826 0.00 0.00 35.82 3.36
317 325 8.043710 TCCATTCCTTTTGTTATTTGTTTGTGT 58.956 29.630 0.00 0.00 0.00 3.72
318 326 8.121708 CCATTCCTTTTGTTATTTGTTTGTGTG 58.878 33.333 0.00 0.00 0.00 3.82
328 336 1.588667 GTTTGTGTGCAGCCAACCG 60.589 57.895 0.00 0.00 0.00 4.44
437 453 3.866651 TCATCTTAGGAGCTTCTTGCAC 58.133 45.455 0.00 0.00 45.94 4.57
468 484 5.763355 ACTAGTAGTAGTACCCATTCTGCA 58.237 41.667 8.55 0.00 37.76 4.41
469 485 5.828859 ACTAGTAGTAGTACCCATTCTGCAG 59.171 44.000 7.63 7.63 37.76 4.41
470 486 4.611367 AGTAGTAGTACCCATTCTGCAGT 58.389 43.478 14.67 0.00 0.00 4.40
471 487 5.763355 AGTAGTAGTACCCATTCTGCAGTA 58.237 41.667 14.67 4.08 0.00 2.74
472 488 6.374588 AGTAGTAGTACCCATTCTGCAGTAT 58.625 40.000 14.67 6.84 0.00 2.12
473 489 7.524290 AGTAGTAGTACCCATTCTGCAGTATA 58.476 38.462 14.67 0.76 0.00 1.47
474 490 6.651975 AGTAGTACCCATTCTGCAGTATAC 57.348 41.667 14.67 4.78 0.00 1.47
475 491 6.374588 AGTAGTACCCATTCTGCAGTATACT 58.625 40.000 14.67 11.95 0.00 2.12
476 492 7.524290 AGTAGTACCCATTCTGCAGTATACTA 58.476 38.462 14.67 10.98 0.00 1.82
477 493 6.902771 AGTACCCATTCTGCAGTATACTAG 57.097 41.667 14.67 0.38 0.00 2.57
555 579 3.253432 GCAGTAATTAATGCCTAGCCCAC 59.747 47.826 23.81 0.00 41.02 4.61
607 632 2.006888 GGCTGTGCAAAGACGCTTATA 58.993 47.619 8.49 0.00 0.00 0.98
608 633 2.614057 GGCTGTGCAAAGACGCTTATAT 59.386 45.455 8.49 0.00 0.00 0.86
609 634 3.546815 GGCTGTGCAAAGACGCTTATATG 60.547 47.826 8.49 0.00 0.00 1.78
610 635 3.309682 GCTGTGCAAAGACGCTTATATGA 59.690 43.478 8.49 0.00 0.00 2.15
611 636 4.201812 GCTGTGCAAAGACGCTTATATGAA 60.202 41.667 8.49 0.00 0.00 2.57
621 646 9.680315 AAAGACGCTTATATGAACTCATACTAC 57.320 33.333 1.53 0.00 41.15 2.73
623 648 8.291032 AGACGCTTATATGAACTCATACTACAC 58.709 37.037 1.53 0.00 41.15 2.90
624 649 7.937649 ACGCTTATATGAACTCATACTACACA 58.062 34.615 1.53 0.00 41.15 3.72
625 650 7.861372 ACGCTTATATGAACTCATACTACACAC 59.139 37.037 1.53 0.00 41.15 3.82
633 658 5.190992 ACTCATACTACACACGTGTTGAA 57.809 39.130 20.79 6.33 41.83 2.69
637 662 5.631929 TCATACTACACACGTGTTGAATCAC 59.368 40.000 20.79 0.00 41.83 3.06
652 677 4.635223 TGAATCACTTGTCCTCAACTGAG 58.365 43.478 0.00 0.00 41.71 3.35
706 731 4.335416 AGCAGAGCACCATTTTAGCTTTA 58.665 39.130 0.00 0.00 39.02 1.85
712 737 3.676049 GCACCATTTTAGCTTTAGTGCCC 60.676 47.826 0.00 0.00 42.44 5.36
720 745 3.283259 AGCTTTAGTGCCCTGGTATTC 57.717 47.619 0.00 0.00 0.00 1.75
744 772 8.560355 TCTCTAGCTATACTCTCATGATTCAC 57.440 38.462 0.00 0.00 0.00 3.18
800 828 4.701171 TGCTGACAAATGTGATCATAAGCA 59.299 37.500 9.41 9.41 33.49 3.91
806 834 7.175467 TGACAAATGTGATCATAAGCAAGAACT 59.825 33.333 0.00 0.00 33.49 3.01
820 848 3.119708 GCAAGAACTGCCAAGACATTAGG 60.120 47.826 0.00 0.00 46.13 2.69
822 850 2.025887 AGAACTGCCAAGACATTAGGGG 60.026 50.000 0.00 0.00 0.00 4.79
847 886 8.772705 GGAGAAAATTGTCTAAGATCATGCTAG 58.227 37.037 0.00 0.00 0.00 3.42
948 994 6.537660 GTGGCCAGGTAGTACTAATTTAACAG 59.462 42.308 5.11 0.00 0.00 3.16
1016 1062 8.316214 TGGGGACATCCGATAAAAATATACTAC 58.684 37.037 0.00 0.00 36.71 2.73
1064 1110 9.308318 CTAGTTCTCTTAGAGGCAAAATAAGTC 57.692 37.037 9.58 0.00 0.00 3.01
1133 1180 4.323417 TGGTTTGGTATCTCATGTGTGTC 58.677 43.478 0.00 0.00 0.00 3.67
1277 1324 3.057806 CCGTCACAAAGTTCAATTACCCC 60.058 47.826 0.00 0.00 0.00 4.95
1343 1390 1.754621 GGCCCTTGGAAAGCTAGGC 60.755 63.158 0.00 0.00 44.78 3.93
1394 1441 2.036346 GACTGCCAAGAAATTTGCACCT 59.964 45.455 0.00 0.00 0.00 4.00
1967 2014 2.031683 GGTTGTGAACAAGTTCCTCACG 59.968 50.000 10.19 0.00 41.94 4.35
2030 2077 1.327303 TTGGTTTGGTTAGCCTGCTG 58.673 50.000 0.97 0.00 35.27 4.41
2101 2148 3.317149 GGAAATATTGCATCAGCTCAGCA 59.683 43.478 0.00 0.42 42.74 4.41
2189 2236 3.950395 AGCTTATTTCATCTTGAGTGCCC 59.050 43.478 0.00 0.00 0.00 5.36
2226 2273 4.141711 TGCCATTCTTAGCTTTAGGTCGAT 60.142 41.667 0.00 0.00 0.00 3.59
2361 2408 7.656137 GTCTGTGTTACTCATTTCTACTGGAAA 59.344 37.037 0.00 0.00 46.33 3.13
2668 2740 1.867363 ATCCAGGTAAGGCGAAGAGT 58.133 50.000 0.00 0.00 0.00 3.24
2678 2750 1.066787 AGGCGAAGAGTCCAAGCTTAC 60.067 52.381 0.00 0.00 0.00 2.34
3039 3111 8.918202 AGTATACCAGTTTTGAATTGAACTCA 57.082 30.769 0.00 0.00 34.04 3.41
3040 3112 9.349713 AGTATACCAGTTTTGAATTGAACTCAA 57.650 29.630 0.00 0.00 40.51 3.02
3041 3113 9.959749 GTATACCAGTTTTGAATTGAACTCAAA 57.040 29.630 0.00 0.00 40.21 2.69
3043 3115 5.812127 ACCAGTTTTGAATTGAACTCAAAGC 59.188 36.000 7.68 7.68 42.21 3.51
3044 3116 5.234972 CCAGTTTTGAATTGAACTCAAAGCC 59.765 40.000 11.32 3.37 41.98 4.35
3045 3117 6.044682 CAGTTTTGAATTGAACTCAAAGCCT 58.955 36.000 11.32 5.30 41.98 4.58
3046 3118 6.536224 CAGTTTTGAATTGAACTCAAAGCCTT 59.464 34.615 11.32 0.00 41.98 4.35
3047 3119 6.536224 AGTTTTGAATTGAACTCAAAGCCTTG 59.464 34.615 11.32 0.00 41.98 3.61
3048 3120 5.850557 TTGAATTGAACTCAAAGCCTTGA 57.149 34.783 0.00 0.00 39.55 3.02
3049 3121 6.409524 TTGAATTGAACTCAAAGCCTTGAT 57.590 33.333 0.00 0.00 40.78 2.57
3050 3122 6.017400 TGAATTGAACTCAAAGCCTTGATC 57.983 37.500 0.00 0.00 40.78 2.92
3051 3123 4.691860 ATTGAACTCAAAGCCTTGATCG 57.308 40.909 0.00 0.00 40.78 3.69
3052 3124 2.426522 TGAACTCAAAGCCTTGATCGG 58.573 47.619 0.00 0.00 40.78 4.18
3053 3125 2.038426 TGAACTCAAAGCCTTGATCGGA 59.962 45.455 0.00 0.00 40.78 4.55
3054 3126 2.859165 ACTCAAAGCCTTGATCGGAA 57.141 45.000 0.00 0.00 40.78 4.30
3055 3127 2.427506 ACTCAAAGCCTTGATCGGAAC 58.572 47.619 0.00 0.00 40.78 3.62
3056 3128 1.740025 CTCAAAGCCTTGATCGGAACC 59.260 52.381 0.00 0.00 40.78 3.62
3057 3129 0.447801 CAAAGCCTTGATCGGAACCG 59.552 55.000 6.94 6.94 36.30 4.44
3058 3130 0.036306 AAAGCCTTGATCGGAACCGT 59.964 50.000 12.93 0.94 40.74 4.83
3059 3131 0.036306 AAGCCTTGATCGGAACCGTT 59.964 50.000 12.93 4.82 40.74 4.44
3060 3132 0.673644 AGCCTTGATCGGAACCGTTG 60.674 55.000 12.93 1.16 40.74 4.10
3061 3133 0.672401 GCCTTGATCGGAACCGTTGA 60.672 55.000 12.93 0.00 40.74 3.18
3062 3134 2.012051 GCCTTGATCGGAACCGTTGAT 61.012 52.381 12.93 0.00 40.74 2.57
3063 3135 2.356135 CCTTGATCGGAACCGTTGATT 58.644 47.619 12.93 0.00 40.74 2.57
3064 3136 2.747446 CCTTGATCGGAACCGTTGATTT 59.253 45.455 12.93 0.00 40.74 2.17
3065 3137 3.190535 CCTTGATCGGAACCGTTGATTTT 59.809 43.478 12.93 0.00 40.74 1.82
3066 3138 4.403453 CTTGATCGGAACCGTTGATTTTC 58.597 43.478 12.93 2.07 40.74 2.29
3067 3139 3.670625 TGATCGGAACCGTTGATTTTCT 58.329 40.909 12.93 0.00 40.74 2.52
3068 3140 4.823157 TGATCGGAACCGTTGATTTTCTA 58.177 39.130 12.93 0.00 40.74 2.10
3069 3141 5.239351 TGATCGGAACCGTTGATTTTCTAA 58.761 37.500 12.93 0.00 40.74 2.10
3070 3142 5.701750 TGATCGGAACCGTTGATTTTCTAAA 59.298 36.000 12.93 0.00 40.74 1.85
3071 3143 6.373216 TGATCGGAACCGTTGATTTTCTAAAT 59.627 34.615 12.93 0.00 40.74 1.40
3072 3144 6.173191 TCGGAACCGTTGATTTTCTAAATC 57.827 37.500 12.93 5.42 40.74 2.17
3073 3145 5.935789 TCGGAACCGTTGATTTTCTAAATCT 59.064 36.000 12.93 0.00 40.74 2.40
3074 3146 7.098477 TCGGAACCGTTGATTTTCTAAATCTA 58.902 34.615 12.93 3.66 40.74 1.98
3075 3147 7.277098 TCGGAACCGTTGATTTTCTAAATCTAG 59.723 37.037 12.93 0.00 40.74 2.43
3076 3148 7.187480 GGAACCGTTGATTTTCTAAATCTAGC 58.813 38.462 11.98 3.71 0.00 3.42
3077 3149 6.345920 ACCGTTGATTTTCTAAATCTAGCG 57.654 37.500 11.98 12.05 0.00 4.26
3078 3150 5.293569 ACCGTTGATTTTCTAAATCTAGCGG 59.706 40.000 23.55 23.55 39.35 5.52
3079 3151 5.198274 CGTTGATTTTCTAAATCTAGCGGC 58.802 41.667 11.98 0.00 0.00 6.53
3080 3152 5.006746 CGTTGATTTTCTAAATCTAGCGGCT 59.993 40.000 7.98 7.98 0.00 5.52
3081 3153 5.991328 TGATTTTCTAAATCTAGCGGCTG 57.009 39.130 13.86 2.84 0.00 4.85
3082 3154 5.670485 TGATTTTCTAAATCTAGCGGCTGA 58.330 37.500 13.86 8.61 0.00 4.26
3083 3155 5.755375 TGATTTTCTAAATCTAGCGGCTGAG 59.245 40.000 13.86 6.45 0.00 3.35
3084 3156 5.339008 TTTTCTAAATCTAGCGGCTGAGA 57.661 39.130 13.86 11.61 0.00 3.27
3085 3157 5.537300 TTTCTAAATCTAGCGGCTGAGAT 57.463 39.130 13.86 13.29 33.75 2.75
3086 3158 4.511617 TCTAAATCTAGCGGCTGAGATG 57.488 45.455 13.86 6.01 32.66 2.90
3087 3159 4.145052 TCTAAATCTAGCGGCTGAGATGA 58.855 43.478 13.86 7.94 32.66 2.92
3088 3160 4.769488 TCTAAATCTAGCGGCTGAGATGAT 59.231 41.667 13.86 11.29 32.66 2.45
3089 3161 3.591196 AATCTAGCGGCTGAGATGATC 57.409 47.619 13.86 0.00 32.66 2.92
3090 3162 1.986882 TCTAGCGGCTGAGATGATCA 58.013 50.000 13.86 0.00 36.21 2.92
3100 3172 3.382048 TGAGATGATCAGGATTCGCAG 57.618 47.619 0.09 0.00 32.77 5.18
3101 3173 2.697229 TGAGATGATCAGGATTCGCAGT 59.303 45.455 0.09 0.00 32.77 4.40
3102 3174 3.058450 GAGATGATCAGGATTCGCAGTG 58.942 50.000 0.09 0.00 0.00 3.66
3103 3175 1.530293 GATGATCAGGATTCGCAGTGC 59.470 52.381 4.58 4.58 0.00 4.40
3104 3176 0.249955 TGATCAGGATTCGCAGTGCA 59.750 50.000 16.83 0.00 0.00 4.57
3105 3177 0.654683 GATCAGGATTCGCAGTGCAC 59.345 55.000 16.83 9.40 0.00 4.57
3106 3178 0.036105 ATCAGGATTCGCAGTGCACA 60.036 50.000 21.04 0.00 0.00 4.57
3107 3179 0.671472 TCAGGATTCGCAGTGCACAG 60.671 55.000 21.04 12.97 0.00 3.66
3108 3180 0.952497 CAGGATTCGCAGTGCACAGT 60.952 55.000 21.04 0.00 0.00 3.55
3109 3181 0.608130 AGGATTCGCAGTGCACAGTA 59.392 50.000 21.04 4.21 0.00 2.74
3110 3182 1.002366 GGATTCGCAGTGCACAGTAG 58.998 55.000 21.04 9.88 0.00 2.57
3111 3183 0.371645 GATTCGCAGTGCACAGTAGC 59.628 55.000 21.04 15.61 0.00 3.58
3112 3184 0.320683 ATTCGCAGTGCACAGTAGCA 60.321 50.000 21.04 0.59 43.35 3.49
3135 3207 1.960417 GCTTACTCCAGAAGCATCCC 58.040 55.000 2.59 0.00 46.97 3.85
3136 3208 1.808133 GCTTACTCCAGAAGCATCCCG 60.808 57.143 2.59 0.00 46.97 5.14
3137 3209 0.178068 TTACTCCAGAAGCATCCCGC 59.822 55.000 0.00 0.00 42.91 6.13
3146 3218 3.934962 GCATCCCGCTCTCCCTCC 61.935 72.222 0.00 0.00 37.77 4.30
3147 3219 2.123077 CATCCCGCTCTCCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
3148 3220 2.123077 ATCCCGCTCTCCCTCCTG 60.123 66.667 0.00 0.00 0.00 3.86
3149 3221 2.705487 ATCCCGCTCTCCCTCCTGA 61.705 63.158 0.00 0.00 0.00 3.86
3150 3222 2.243774 ATCCCGCTCTCCCTCCTGAA 62.244 60.000 0.00 0.00 0.00 3.02
3151 3223 1.990060 CCCGCTCTCCCTCCTGAAA 60.990 63.158 0.00 0.00 0.00 2.69
3152 3224 1.553690 CCCGCTCTCCCTCCTGAAAA 61.554 60.000 0.00 0.00 0.00 2.29
3153 3225 0.324943 CCGCTCTCCCTCCTGAAAAA 59.675 55.000 0.00 0.00 0.00 1.94
3167 3239 4.585474 AAAAAGGGCCCCATGCAT 57.415 50.000 21.43 0.00 43.89 3.96
3168 3240 2.299975 AAAAAGGGCCCCATGCATC 58.700 52.632 21.43 0.00 43.89 3.91
3169 3241 1.616091 AAAAAGGGCCCCATGCATCG 61.616 55.000 21.43 0.00 43.89 3.84
3170 3242 2.803593 AAAAGGGCCCCATGCATCGT 62.804 55.000 21.43 0.00 43.89 3.73
3171 3243 4.511246 AGGGCCCCATGCATCGTG 62.511 66.667 21.43 0.00 43.89 4.35
3172 3244 4.820744 GGGCCCCATGCATCGTGT 62.821 66.667 12.23 0.00 43.89 4.49
3173 3245 3.520862 GGCCCCATGCATCGTGTG 61.521 66.667 0.00 0.00 43.89 3.82
3182 3254 3.463505 CATCGTGTGCTCGTGACC 58.536 61.111 0.00 0.00 0.00 4.02
3183 3255 1.080501 CATCGTGTGCTCGTGACCT 60.081 57.895 0.00 0.00 0.00 3.85
3184 3256 1.080501 ATCGTGTGCTCGTGACCTG 60.081 57.895 0.00 0.00 0.00 4.00
3185 3257 2.492449 ATCGTGTGCTCGTGACCTGG 62.492 60.000 0.00 0.00 0.00 4.45
3186 3258 2.421739 GTGTGCTCGTGACCTGGT 59.578 61.111 0.00 0.00 0.00 4.00
3187 3259 1.663739 GTGTGCTCGTGACCTGGTA 59.336 57.895 0.00 0.00 0.00 3.25
3188 3260 0.666577 GTGTGCTCGTGACCTGGTAC 60.667 60.000 0.00 0.00 0.00 3.34
3189 3261 1.443872 GTGCTCGTGACCTGGTACG 60.444 63.158 17.18 17.18 41.38 3.67
3190 3262 2.181021 GCTCGTGACCTGGTACGG 59.819 66.667 20.62 15.03 40.48 4.02
3191 3263 2.338015 GCTCGTGACCTGGTACGGA 61.338 63.158 20.62 9.78 40.48 4.69
3192 3264 1.505353 CTCGTGACCTGGTACGGAC 59.495 63.158 20.62 0.00 40.48 4.79
3193 3265 2.177531 CGTGACCTGGTACGGACG 59.822 66.667 16.13 11.39 36.31 4.79
3194 3266 2.327343 CGTGACCTGGTACGGACGA 61.327 63.158 16.13 0.00 36.31 4.20
3195 3267 1.505353 GTGACCTGGTACGGACGAG 59.495 63.158 2.20 2.20 36.31 4.18
3196 3268 2.338015 TGACCTGGTACGGACGAGC 61.338 63.158 3.90 0.00 36.31 5.03
3197 3269 3.061260 GACCTGGTACGGACGAGCC 62.061 68.421 3.90 0.62 36.31 4.70
3198 3270 3.834799 CCTGGTACGGACGAGCCC 61.835 72.222 3.90 0.00 36.31 5.19
3199 3271 3.834799 CTGGTACGGACGAGCCCC 61.835 72.222 0.00 0.00 36.31 5.80
3200 3272 4.371417 TGGTACGGACGAGCCCCT 62.371 66.667 0.00 0.00 0.00 4.79
3201 3273 3.525545 GGTACGGACGAGCCCCTC 61.526 72.222 0.00 0.00 0.00 4.30
3210 3282 3.372123 GAGCCCCTCGAGATAGCC 58.628 66.667 15.71 4.32 0.00 3.93
3211 3283 1.228737 GAGCCCCTCGAGATAGCCT 60.229 63.158 15.71 2.34 0.00 4.58
3212 3284 1.531739 GAGCCCCTCGAGATAGCCTG 61.532 65.000 15.71 0.00 0.00 4.85
3213 3285 3.055580 CCCCTCGAGATAGCCTGC 58.944 66.667 15.71 0.00 0.00 4.85
3214 3286 2.578714 CCCCTCGAGATAGCCTGCC 61.579 68.421 15.71 0.00 0.00 4.85
3215 3287 1.834378 CCCTCGAGATAGCCTGCCA 60.834 63.158 15.71 0.00 0.00 4.92
3216 3288 1.402896 CCCTCGAGATAGCCTGCCAA 61.403 60.000 15.71 0.00 0.00 4.52
3217 3289 0.033228 CCTCGAGATAGCCTGCCAAG 59.967 60.000 15.71 0.00 0.00 3.61
3218 3290 1.035923 CTCGAGATAGCCTGCCAAGA 58.964 55.000 6.58 0.00 0.00 3.02
3219 3291 1.410517 CTCGAGATAGCCTGCCAAGAA 59.589 52.381 6.58 0.00 0.00 2.52
3220 3292 1.831106 TCGAGATAGCCTGCCAAGAAA 59.169 47.619 0.00 0.00 0.00 2.52
3221 3293 2.236146 TCGAGATAGCCTGCCAAGAAAA 59.764 45.455 0.00 0.00 0.00 2.29
3222 3294 2.352960 CGAGATAGCCTGCCAAGAAAAC 59.647 50.000 0.00 0.00 0.00 2.43
3223 3295 3.347216 GAGATAGCCTGCCAAGAAAACA 58.653 45.455 0.00 0.00 0.00 2.83
3224 3296 3.350833 AGATAGCCTGCCAAGAAAACAG 58.649 45.455 0.00 0.00 0.00 3.16
3227 3299 3.437642 CCTGCCAAGAAAACAGGGA 57.562 52.632 0.19 0.00 45.97 4.20
3228 3300 1.251251 CCTGCCAAGAAAACAGGGAG 58.749 55.000 0.19 0.00 45.97 4.30
3229 3301 1.202927 CCTGCCAAGAAAACAGGGAGA 60.203 52.381 0.00 0.00 45.97 3.71
3230 3302 1.882623 CTGCCAAGAAAACAGGGAGAC 59.117 52.381 0.00 0.00 42.78 3.36
3231 3303 1.214175 TGCCAAGAAAACAGGGAGACA 59.786 47.619 0.00 0.00 0.00 3.41
3232 3304 1.882623 GCCAAGAAAACAGGGAGACAG 59.117 52.381 0.00 0.00 0.00 3.51
3233 3305 2.508526 CCAAGAAAACAGGGAGACAGG 58.491 52.381 0.00 0.00 0.00 4.00
3234 3306 2.106511 CCAAGAAAACAGGGAGACAGGA 59.893 50.000 0.00 0.00 0.00 3.86
3235 3307 3.435026 CCAAGAAAACAGGGAGACAGGAA 60.435 47.826 0.00 0.00 0.00 3.36
3236 3308 4.207165 CAAGAAAACAGGGAGACAGGAAA 58.793 43.478 0.00 0.00 0.00 3.13
3237 3309 4.731313 AGAAAACAGGGAGACAGGAAAT 57.269 40.909 0.00 0.00 0.00 2.17
3238 3310 5.066913 AGAAAACAGGGAGACAGGAAATT 57.933 39.130 0.00 0.00 0.00 1.82
3239 3311 6.200878 AGAAAACAGGGAGACAGGAAATTA 57.799 37.500 0.00 0.00 0.00 1.40
3240 3312 6.610830 AGAAAACAGGGAGACAGGAAATTAA 58.389 36.000 0.00 0.00 0.00 1.40
3241 3313 7.241628 AGAAAACAGGGAGACAGGAAATTAAT 58.758 34.615 0.00 0.00 0.00 1.40
3242 3314 8.390921 AGAAAACAGGGAGACAGGAAATTAATA 58.609 33.333 0.00 0.00 0.00 0.98
3243 3315 9.190317 GAAAACAGGGAGACAGGAAATTAATAT 57.810 33.333 0.00 0.00 0.00 1.28
3244 3316 9.547279 AAAACAGGGAGACAGGAAATTAATATT 57.453 29.630 0.00 0.00 0.00 1.28
3245 3317 9.547279 AAACAGGGAGACAGGAAATTAATATTT 57.453 29.630 0.00 0.00 36.68 1.40
3246 3318 9.547279 AACAGGGAGACAGGAAATTAATATTTT 57.453 29.630 0.00 0.00 34.16 1.82
3282 3354 9.665719 ATGGGTTTGTACATGGATAAAATTTTC 57.334 29.630 6.72 0.00 0.00 2.29
3283 3355 8.875168 TGGGTTTGTACATGGATAAAATTTTCT 58.125 29.630 6.72 0.00 0.00 2.52
3284 3356 9.150348 GGGTTTGTACATGGATAAAATTTTCTG 57.850 33.333 6.72 1.93 0.00 3.02
3285 3357 9.705290 GGTTTGTACATGGATAAAATTTTCTGT 57.295 29.630 6.72 7.31 0.00 3.41
3303 3375 7.464830 TTTCTGTATCTATGTTTAGCTTCGC 57.535 36.000 0.00 0.00 0.00 4.70
3304 3376 6.392625 TCTGTATCTATGTTTAGCTTCGCT 57.607 37.500 0.00 0.00 43.41 4.93
3305 3377 6.439599 TCTGTATCTATGTTTAGCTTCGCTC 58.560 40.000 0.00 0.00 40.44 5.03
3306 3378 6.263392 TCTGTATCTATGTTTAGCTTCGCTCT 59.737 38.462 0.00 0.00 40.44 4.09
3307 3379 6.806751 TGTATCTATGTTTAGCTTCGCTCTT 58.193 36.000 0.00 0.00 40.44 2.85
3308 3380 7.265673 TGTATCTATGTTTAGCTTCGCTCTTT 58.734 34.615 0.00 0.00 40.44 2.52
3309 3381 6.595772 ATCTATGTTTAGCTTCGCTCTTTG 57.404 37.500 0.00 0.00 40.44 2.77
3310 3382 5.479306 TCTATGTTTAGCTTCGCTCTTTGT 58.521 37.500 0.00 0.00 40.44 2.83
3311 3383 4.670227 ATGTTTAGCTTCGCTCTTTGTC 57.330 40.909 0.00 0.00 40.44 3.18
3312 3384 2.475111 TGTTTAGCTTCGCTCTTTGTCG 59.525 45.455 0.00 0.00 40.44 4.35
3313 3385 1.068474 TTAGCTTCGCTCTTTGTCGC 58.932 50.000 0.00 0.00 40.44 5.19
3314 3386 0.736325 TAGCTTCGCTCTTTGTCGCC 60.736 55.000 0.00 0.00 40.44 5.54
3315 3387 2.317609 GCTTCGCTCTTTGTCGCCA 61.318 57.895 0.00 0.00 0.00 5.69
3316 3388 1.841663 GCTTCGCTCTTTGTCGCCAA 61.842 55.000 0.00 0.00 0.00 4.52
3317 3389 0.164647 CTTCGCTCTTTGTCGCCAAG 59.835 55.000 0.00 0.00 0.00 3.61
3318 3390 0.531974 TTCGCTCTTTGTCGCCAAGT 60.532 50.000 0.00 0.00 0.00 3.16
3319 3391 0.315886 TCGCTCTTTGTCGCCAAGTA 59.684 50.000 0.00 0.00 0.00 2.24
3320 3392 1.144969 CGCTCTTTGTCGCCAAGTAA 58.855 50.000 0.00 0.00 0.00 2.24
3321 3393 1.732259 CGCTCTTTGTCGCCAAGTAAT 59.268 47.619 0.00 0.00 0.00 1.89
3322 3394 2.927477 CGCTCTTTGTCGCCAAGTAATA 59.073 45.455 0.00 0.00 0.00 0.98
3323 3395 3.369756 CGCTCTTTGTCGCCAAGTAATAA 59.630 43.478 0.00 0.00 0.00 1.40
3324 3396 4.492570 CGCTCTTTGTCGCCAAGTAATAAG 60.493 45.833 0.00 0.00 0.00 1.73
3325 3397 4.630069 GCTCTTTGTCGCCAAGTAATAAGA 59.370 41.667 0.00 0.00 0.00 2.10
3326 3398 5.121768 GCTCTTTGTCGCCAAGTAATAAGAA 59.878 40.000 0.00 0.00 0.00 2.52
3327 3399 6.183360 GCTCTTTGTCGCCAAGTAATAAGAAT 60.183 38.462 0.00 0.00 0.00 2.40
3328 3400 7.626452 GCTCTTTGTCGCCAAGTAATAAGAATT 60.626 37.037 0.00 0.00 0.00 2.17
3329 3401 8.780846 TCTTTGTCGCCAAGTAATAAGAATTA 57.219 30.769 0.00 0.00 33.48 1.40
3330 3402 8.662141 TCTTTGTCGCCAAGTAATAAGAATTAC 58.338 33.333 0.94 0.94 45.29 1.89
3365 3437 9.490379 AACACGGATCTATTATCATAAAGGTTC 57.510 33.333 0.00 0.00 0.00 3.62
3366 3438 8.647796 ACACGGATCTATTATCATAAAGGTTCA 58.352 33.333 0.00 0.00 0.00 3.18
3367 3439 9.658799 CACGGATCTATTATCATAAAGGTTCAT 57.341 33.333 0.00 0.00 0.00 2.57
3368 3440 9.877178 ACGGATCTATTATCATAAAGGTTCATC 57.123 33.333 0.00 0.00 0.00 2.92
3369 3441 9.319143 CGGATCTATTATCATAAAGGTTCATCC 57.681 37.037 0.00 0.00 0.00 3.51
3370 3442 9.319143 GGATCTATTATCATAAAGGTTCATCCG 57.681 37.037 0.00 0.00 41.99 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.759346 ATTATCTCACGGCCAGGTCC 59.241 55.000 2.24 0.00 0.00 4.46
48 49 3.321111 TCTTATTATCTCACGGCCAGGTC 59.679 47.826 2.24 0.00 0.00 3.85
49 50 3.305720 TCTTATTATCTCACGGCCAGGT 58.694 45.455 2.24 0.00 0.00 4.00
50 51 4.499183 GATCTTATTATCTCACGGCCAGG 58.501 47.826 2.24 0.00 0.00 4.45
51 52 4.169508 CGATCTTATTATCTCACGGCCAG 58.830 47.826 2.24 0.00 0.00 4.85
103 104 3.493877 CAGCTGAGCCAAGAATCTATTCG 59.506 47.826 8.42 0.00 41.56 3.34
122 126 0.739112 CGAGGTCTTGGCTTCTCAGC 60.739 60.000 0.00 0.00 46.52 4.26
127 131 0.320771 TTCTGCGAGGTCTTGGCTTC 60.321 55.000 0.00 0.00 0.00 3.86
144 148 8.479313 TTTTTCTCTTGGCTTTTCTTTCTTTC 57.521 30.769 0.00 0.00 0.00 2.62
169 173 5.074746 ACAGTAACCCCCAAGATTTTTCT 57.925 39.130 0.00 0.00 0.00 2.52
170 174 5.801531 AACAGTAACCCCCAAGATTTTTC 57.198 39.130 0.00 0.00 0.00 2.29
175 179 4.472470 GGTAGTAACAGTAACCCCCAAGAT 59.528 45.833 0.00 0.00 0.00 2.40
176 180 3.840078 GGTAGTAACAGTAACCCCCAAGA 59.160 47.826 0.00 0.00 0.00 3.02
177 181 3.583966 TGGTAGTAACAGTAACCCCCAAG 59.416 47.826 0.00 0.00 0.00 3.61
179 183 3.272716 TGGTAGTAACAGTAACCCCCA 57.727 47.619 0.00 0.00 0.00 4.96
180 184 3.776417 TCATGGTAGTAACAGTAACCCCC 59.224 47.826 0.00 0.00 0.00 5.40
198 202 2.429478 TCACACAGGCAATGAGTCATG 58.571 47.619 6.34 2.46 29.35 3.07
206 214 2.283298 CGCTAAGATCACACAGGCAAT 58.717 47.619 0.00 0.00 0.00 3.56
292 300 8.121708 CACACAAACAAATAACAAAAGGAATGG 58.878 33.333 0.00 0.00 0.00 3.16
317 325 2.268920 GATCTCCGGTTGGCTGCA 59.731 61.111 0.00 0.00 34.14 4.41
318 326 2.892425 CGATCTCCGGTTGGCTGC 60.892 66.667 0.00 0.00 34.14 5.25
328 336 0.249657 GGATCTGCCACACGATCTCC 60.250 60.000 0.00 0.00 36.97 3.71
352 368 1.062294 ACAAAACAGCGCGTTCGTTTA 59.938 42.857 18.33 0.00 36.59 2.01
465 481 5.437946 ACTGACTACTGCTAGTATACTGCA 58.562 41.667 21.11 21.11 32.96 4.41
466 482 6.073112 GGTACTGACTACTGCTAGTATACTGC 60.073 46.154 15.90 15.94 32.96 4.40
467 483 6.990939 TGGTACTGACTACTGCTAGTATACTG 59.009 42.308 15.90 6.78 32.96 2.74
468 484 7.134362 TGGTACTGACTACTGCTAGTATACT 57.866 40.000 10.87 10.87 32.96 2.12
469 485 6.991531 ACTGGTACTGACTACTGCTAGTATAC 59.008 42.308 0.00 0.00 32.96 1.47
470 486 7.134362 ACTGGTACTGACTACTGCTAGTATA 57.866 40.000 0.00 0.00 32.96 1.47
471 487 6.003859 ACTGGTACTGACTACTGCTAGTAT 57.996 41.667 0.00 0.00 32.96 2.12
472 488 5.432680 ACTGGTACTGACTACTGCTAGTA 57.567 43.478 0.00 0.00 32.96 1.82
473 489 4.304048 ACTGGTACTGACTACTGCTAGT 57.696 45.455 0.00 0.00 35.77 2.57
474 490 4.273969 GCTACTGGTACTGACTACTGCTAG 59.726 50.000 0.00 0.00 0.00 3.42
475 491 4.197750 GCTACTGGTACTGACTACTGCTA 58.802 47.826 0.00 0.00 0.00 3.49
476 492 3.018149 GCTACTGGTACTGACTACTGCT 58.982 50.000 0.00 0.00 0.00 4.24
477 493 2.753452 TGCTACTGGTACTGACTACTGC 59.247 50.000 0.00 0.00 0.00 4.40
524 548 4.275936 GGCATTAATTACTGCAGAATCGGT 59.724 41.667 23.35 0.00 40.18 4.69
555 579 7.000472 CCCATATGCCTATGTATCCCAATTAG 59.000 42.308 8.02 0.00 34.12 1.73
596 621 8.847196 TGTAGTATGAGTTCATATAAGCGTCTT 58.153 33.333 5.22 0.00 40.53 3.01
607 632 5.386958 ACACGTGTGTAGTATGAGTTCAT 57.613 39.130 22.71 0.00 42.90 2.57
608 633 4.841443 ACACGTGTGTAGTATGAGTTCA 57.159 40.909 22.71 0.00 42.90 3.18
609 634 5.217393 TCAACACGTGTGTAGTATGAGTTC 58.783 41.667 24.16 0.00 44.13 3.01
610 635 5.190992 TCAACACGTGTGTAGTATGAGTT 57.809 39.130 24.16 0.00 44.13 3.01
611 636 4.841443 TCAACACGTGTGTAGTATGAGT 57.159 40.909 24.16 0.00 44.13 3.41
624 649 3.131396 GAGGACAAGTGATTCAACACGT 58.869 45.455 0.00 0.00 44.35 4.49
625 650 3.130633 TGAGGACAAGTGATTCAACACG 58.869 45.455 0.00 0.00 44.35 4.49
637 662 6.638610 ACAGAATATCTCAGTTGAGGACAAG 58.361 40.000 9.13 0.00 42.30 3.16
652 677 4.039245 TCTGATCCGGACCAACAGAATATC 59.961 45.833 21.69 7.84 35.20 1.63
696 721 3.518992 ACCAGGGCACTAAAGCTAAAA 57.481 42.857 0.00 0.00 34.17 1.52
699 724 4.037927 AGAATACCAGGGCACTAAAGCTA 58.962 43.478 0.00 0.00 34.17 3.32
706 731 2.043227 GCTAGAGAATACCAGGGCACT 58.957 52.381 0.00 0.00 0.00 4.40
712 737 8.892723 CATGAGAGTATAGCTAGAGAATACCAG 58.107 40.741 0.00 0.00 0.00 4.00
720 745 7.463544 CGTGAATCATGAGAGTATAGCTAGAG 58.536 42.308 0.09 0.00 0.00 2.43
744 772 3.888221 GTGTGTTTCACTTGCGCG 58.112 55.556 0.00 0.00 43.13 6.86
800 828 3.562176 CCCCTAATGTCTTGGCAGTTCTT 60.562 47.826 0.00 0.00 0.00 2.52
806 834 1.965414 TCTCCCCTAATGTCTTGGCA 58.035 50.000 0.00 0.00 0.00 4.92
820 848 6.545298 AGCATGATCTTAGACAATTTTCTCCC 59.455 38.462 0.00 0.00 0.00 4.30
822 850 8.772705 CCTAGCATGATCTTAGACAATTTTCTC 58.227 37.037 0.00 0.00 0.00 2.87
847 886 0.169009 CAGCAAGAGTTTAAGGCGCC 59.831 55.000 21.89 21.89 0.00 6.53
1016 1062 9.737427 ACTAGTTAGATATTTTGACATGACTCG 57.263 33.333 0.00 0.00 0.00 4.18
1064 1110 5.991606 TGCAAGATATCCCAAGTATTCTTCG 59.008 40.000 0.00 0.00 0.00 3.79
1106 1152 6.543465 CACACATGAGATACCAAACCATACAT 59.457 38.462 0.00 0.00 0.00 2.29
1120 1167 5.877012 GGTTCAGTAATGACACACATGAGAT 59.123 40.000 0.00 0.00 39.39 2.75
1277 1324 3.001902 TAGCGTTGTCAGGAGGCCG 62.002 63.158 0.00 0.00 0.00 6.13
1343 1390 0.622665 AGGGGTCATGGCAGAGAAAG 59.377 55.000 0.00 0.00 0.00 2.62
1394 1441 3.181486 CGAGGTAGAAGACAATAGCAGCA 60.181 47.826 0.00 0.00 0.00 4.41
1967 2014 1.164411 TCGTCACATTGATTGCCACC 58.836 50.000 0.00 0.00 0.00 4.61
2030 2077 1.202698 ACTCCACCAGCAAGAGTGAAC 60.203 52.381 0.00 0.00 39.36 3.18
2101 2148 0.251916 TTCCTCCGATGCCGTTTCAT 59.748 50.000 0.00 0.00 0.00 2.57
2189 2236 1.460504 ATGGCACTCTTCATGCACTG 58.539 50.000 0.00 0.00 45.27 3.66
2316 2363 4.223032 CAGACAGAAAGGGCCTTCTAGTTA 59.777 45.833 21.20 0.00 33.81 2.24
2382 2429 4.532834 GGGCATCACTCCTACCATAAAAA 58.467 43.478 0.00 0.00 0.00 1.94
2484 2532 4.556699 GCATCTGGACTTTGTTACCACAAC 60.557 45.833 0.00 0.00 42.87 3.32
2558 2630 2.354704 CCACAGCTTGTTCCGAGGATAA 60.355 50.000 0.00 0.00 0.00 1.75
2668 2740 1.066430 GGACATGGTCGTAAGCTTGGA 60.066 52.381 9.86 3.37 33.60 3.53
2678 2750 3.387091 TCACCGGGGACATGGTCG 61.387 66.667 0.00 0.00 36.47 4.79
2700 2772 5.050490 CGACTATCCGAAAGACCAATTGAT 58.950 41.667 7.12 0.00 0.00 2.57
3014 3086 8.918202 TGAGTTCAATTCAAAACTGGTATACT 57.082 30.769 2.25 0.00 35.90 2.12
3015 3087 9.959749 TTTGAGTTCAATTCAAAACTGGTATAC 57.040 29.630 5.63 0.00 40.50 1.47
3017 3089 7.653311 GCTTTGAGTTCAATTCAAAACTGGTAT 59.347 33.333 9.16 0.00 42.21 2.73
3018 3090 6.978080 GCTTTGAGTTCAATTCAAAACTGGTA 59.022 34.615 9.16 0.00 42.21 3.25
3019 3091 5.812127 GCTTTGAGTTCAATTCAAAACTGGT 59.188 36.000 9.16 0.00 42.21 4.00
3020 3092 5.234972 GGCTTTGAGTTCAATTCAAAACTGG 59.765 40.000 9.16 0.01 42.21 4.00
3021 3093 6.044682 AGGCTTTGAGTTCAATTCAAAACTG 58.955 36.000 9.16 0.32 42.21 3.16
3022 3094 6.225981 AGGCTTTGAGTTCAATTCAAAACT 57.774 33.333 9.16 7.67 42.21 2.66
3023 3095 6.534793 TCAAGGCTTTGAGTTCAATTCAAAAC 59.465 34.615 7.24 5.11 42.21 2.43
3024 3096 6.638610 TCAAGGCTTTGAGTTCAATTCAAAA 58.361 32.000 7.24 0.00 42.21 2.44
3025 3097 6.219417 TCAAGGCTTTGAGTTCAATTCAAA 57.781 33.333 7.24 7.74 41.00 2.69
3026 3098 5.850557 TCAAGGCTTTGAGTTCAATTCAA 57.149 34.783 7.24 0.00 38.37 2.69
3027 3099 5.335113 CGATCAAGGCTTTGAGTTCAATTCA 60.335 40.000 16.88 0.00 45.89 2.57
3028 3100 5.091431 CGATCAAGGCTTTGAGTTCAATTC 58.909 41.667 16.88 6.70 45.89 2.17
3029 3101 4.082571 CCGATCAAGGCTTTGAGTTCAATT 60.083 41.667 16.88 0.00 45.89 2.32
3030 3102 3.441572 CCGATCAAGGCTTTGAGTTCAAT 59.558 43.478 16.88 0.00 45.89 2.57
3031 3103 2.813754 CCGATCAAGGCTTTGAGTTCAA 59.186 45.455 16.88 0.00 45.89 2.69
3032 3104 2.038426 TCCGATCAAGGCTTTGAGTTCA 59.962 45.455 16.88 0.00 45.89 3.18
3033 3105 2.699954 TCCGATCAAGGCTTTGAGTTC 58.300 47.619 16.88 9.41 45.89 3.01
3034 3106 2.814336 GTTCCGATCAAGGCTTTGAGTT 59.186 45.455 16.88 0.62 45.89 3.01
3035 3107 2.427506 GTTCCGATCAAGGCTTTGAGT 58.572 47.619 16.88 5.44 45.89 3.41
3036 3108 1.740025 GGTTCCGATCAAGGCTTTGAG 59.260 52.381 16.88 4.26 45.89 3.02
3037 3109 1.821216 GGTTCCGATCAAGGCTTTGA 58.179 50.000 14.17 14.17 46.67 2.69
3038 3110 0.447801 CGGTTCCGATCAAGGCTTTG 59.552 55.000 5.19 1.35 35.57 2.77
3039 3111 0.036306 ACGGTTCCGATCAAGGCTTT 59.964 50.000 18.28 0.00 0.00 3.51
3040 3112 0.036306 AACGGTTCCGATCAAGGCTT 59.964 50.000 18.28 0.00 0.00 4.35
3041 3113 0.673644 CAACGGTTCCGATCAAGGCT 60.674 55.000 18.28 0.00 0.00 4.58
3042 3114 0.672401 TCAACGGTTCCGATCAAGGC 60.672 55.000 18.28 0.00 0.00 4.35
3043 3115 2.024176 ATCAACGGTTCCGATCAAGG 57.976 50.000 18.28 1.19 0.00 3.61
3044 3116 4.154195 AGAAAATCAACGGTTCCGATCAAG 59.846 41.667 18.28 3.14 0.00 3.02
3045 3117 4.069304 AGAAAATCAACGGTTCCGATCAA 58.931 39.130 18.28 1.12 0.00 2.57
3046 3118 3.670625 AGAAAATCAACGGTTCCGATCA 58.329 40.909 18.28 0.00 0.00 2.92
3047 3119 5.789710 TTAGAAAATCAACGGTTCCGATC 57.210 39.130 18.28 4.65 0.00 3.69
3048 3120 6.598064 AGATTTAGAAAATCAACGGTTCCGAT 59.402 34.615 18.28 2.91 0.00 4.18
3049 3121 5.935789 AGATTTAGAAAATCAACGGTTCCGA 59.064 36.000 18.28 0.00 0.00 4.55
3050 3122 6.178239 AGATTTAGAAAATCAACGGTTCCG 57.822 37.500 9.81 9.81 0.00 4.30
3051 3123 7.187480 GCTAGATTTAGAAAATCAACGGTTCC 58.813 38.462 13.29 0.00 0.00 3.62
3052 3124 6.900299 CGCTAGATTTAGAAAATCAACGGTTC 59.100 38.462 13.29 0.00 0.00 3.62
3053 3125 6.183360 CCGCTAGATTTAGAAAATCAACGGTT 60.183 38.462 20.66 0.00 35.66 4.44
3054 3126 5.293569 CCGCTAGATTTAGAAAATCAACGGT 59.706 40.000 20.66 5.19 35.66 4.83
3055 3127 5.738370 CCGCTAGATTTAGAAAATCAACGG 58.262 41.667 17.97 17.97 34.67 4.44
3056 3128 5.006746 AGCCGCTAGATTTAGAAAATCAACG 59.993 40.000 13.29 12.26 0.00 4.10
3057 3129 6.037172 TCAGCCGCTAGATTTAGAAAATCAAC 59.963 38.462 13.29 3.34 0.00 3.18
3058 3130 6.112734 TCAGCCGCTAGATTTAGAAAATCAA 58.887 36.000 13.29 0.00 0.00 2.57
3059 3131 5.670485 TCAGCCGCTAGATTTAGAAAATCA 58.330 37.500 13.29 1.51 0.00 2.57
3060 3132 5.986135 TCTCAGCCGCTAGATTTAGAAAATC 59.014 40.000 0.00 4.55 0.00 2.17
3061 3133 5.918608 TCTCAGCCGCTAGATTTAGAAAAT 58.081 37.500 0.00 0.00 0.00 1.82
3062 3134 5.339008 TCTCAGCCGCTAGATTTAGAAAA 57.661 39.130 0.00 0.00 0.00 2.29
3063 3135 5.069119 TCATCTCAGCCGCTAGATTTAGAAA 59.931 40.000 0.00 0.00 29.93 2.52
3064 3136 4.584743 TCATCTCAGCCGCTAGATTTAGAA 59.415 41.667 0.00 0.00 29.93 2.10
3065 3137 4.145052 TCATCTCAGCCGCTAGATTTAGA 58.855 43.478 0.00 0.00 29.93 2.10
3066 3138 4.511617 TCATCTCAGCCGCTAGATTTAG 57.488 45.455 0.00 0.00 29.93 1.85
3067 3139 4.524328 TGATCATCTCAGCCGCTAGATTTA 59.476 41.667 0.00 0.00 29.93 1.40
3068 3140 3.323115 TGATCATCTCAGCCGCTAGATTT 59.677 43.478 0.00 0.00 29.93 2.17
3069 3141 2.896044 TGATCATCTCAGCCGCTAGATT 59.104 45.455 0.00 0.00 29.93 2.40
3070 3142 2.492881 CTGATCATCTCAGCCGCTAGAT 59.507 50.000 0.00 0.00 44.73 1.98
3071 3143 1.885233 CTGATCATCTCAGCCGCTAGA 59.115 52.381 0.00 0.00 44.73 2.43
3072 3144 2.350899 CTGATCATCTCAGCCGCTAG 57.649 55.000 0.00 0.00 44.73 3.42
3080 3152 2.697229 ACTGCGAATCCTGATCATCTCA 59.303 45.455 0.00 0.00 0.00 3.27
3081 3153 3.058450 CACTGCGAATCCTGATCATCTC 58.942 50.000 0.00 0.00 0.00 2.75
3082 3154 2.806019 GCACTGCGAATCCTGATCATCT 60.806 50.000 0.00 0.00 0.00 2.90
3083 3155 1.530293 GCACTGCGAATCCTGATCATC 59.470 52.381 0.00 0.00 0.00 2.92
3084 3156 1.134310 TGCACTGCGAATCCTGATCAT 60.134 47.619 0.00 0.00 0.00 2.45
3085 3157 0.249955 TGCACTGCGAATCCTGATCA 59.750 50.000 0.00 0.00 0.00 2.92
3086 3158 0.654683 GTGCACTGCGAATCCTGATC 59.345 55.000 10.32 0.00 0.00 2.92
3087 3159 0.036105 TGTGCACTGCGAATCCTGAT 60.036 50.000 19.41 0.00 0.00 2.90
3088 3160 0.671472 CTGTGCACTGCGAATCCTGA 60.671 55.000 19.41 0.00 0.00 3.86
3089 3161 0.952497 ACTGTGCACTGCGAATCCTG 60.952 55.000 22.15 0.00 0.00 3.86
3090 3162 0.608130 TACTGTGCACTGCGAATCCT 59.392 50.000 22.15 4.98 0.00 3.24
3091 3163 1.002366 CTACTGTGCACTGCGAATCC 58.998 55.000 22.15 0.00 0.00 3.01
3092 3164 0.371645 GCTACTGTGCACTGCGAATC 59.628 55.000 22.15 5.23 0.00 2.52
3093 3165 0.320683 TGCTACTGTGCACTGCGAAT 60.321 50.000 22.15 6.71 38.12 3.34
3094 3166 0.320683 ATGCTACTGTGCACTGCGAA 60.321 50.000 22.15 9.79 46.33 4.70
3095 3167 0.737367 GATGCTACTGTGCACTGCGA 60.737 55.000 22.15 10.60 46.33 5.10
3096 3168 1.015607 TGATGCTACTGTGCACTGCG 61.016 55.000 22.15 14.75 46.33 5.18
3097 3169 0.725686 CTGATGCTACTGTGCACTGC 59.274 55.000 22.15 17.75 46.33 4.40
3098 3170 0.725686 GCTGATGCTACTGTGCACTG 59.274 55.000 20.83 20.83 46.33 3.66
3099 3171 3.149899 GCTGATGCTACTGTGCACT 57.850 52.632 19.41 0.28 46.33 4.40
3110 3182 1.939255 GCTTCTGGAGTAAGCTGATGC 59.061 52.381 0.00 0.00 44.75 3.91
3117 3189 1.808133 GCGGGATGCTTCTGGAGTAAG 60.808 57.143 0.00 0.00 41.73 2.34
3118 3190 0.178068 GCGGGATGCTTCTGGAGTAA 59.822 55.000 0.00 0.00 41.73 2.24
3119 3191 1.823295 GCGGGATGCTTCTGGAGTA 59.177 57.895 0.00 0.00 41.73 2.59
3120 3192 2.586792 GCGGGATGCTTCTGGAGT 59.413 61.111 0.00 0.00 41.73 3.85
3129 3201 3.934962 GGAGGGAGAGCGGGATGC 61.935 72.222 0.00 0.00 46.98 3.91
3130 3202 2.123077 AGGAGGGAGAGCGGGATG 60.123 66.667 0.00 0.00 0.00 3.51
3131 3203 2.123077 CAGGAGGGAGAGCGGGAT 60.123 66.667 0.00 0.00 0.00 3.85
3132 3204 2.455960 TTTCAGGAGGGAGAGCGGGA 62.456 60.000 0.00 0.00 0.00 5.14
3133 3205 1.553690 TTTTCAGGAGGGAGAGCGGG 61.554 60.000 0.00 0.00 0.00 6.13
3134 3206 0.324943 TTTTTCAGGAGGGAGAGCGG 59.675 55.000 0.00 0.00 0.00 5.52
3135 3207 3.935993 TTTTTCAGGAGGGAGAGCG 57.064 52.632 0.00 0.00 0.00 5.03
3150 3222 1.616091 CGATGCATGGGGCCCTTTTT 61.616 55.000 25.93 4.59 43.89 1.94
3151 3223 2.059786 CGATGCATGGGGCCCTTTT 61.060 57.895 25.93 5.69 43.89 2.27
3152 3224 2.442643 CGATGCATGGGGCCCTTT 60.443 61.111 25.93 8.64 43.89 3.11
3153 3225 3.743017 ACGATGCATGGGGCCCTT 61.743 61.111 25.93 15.82 43.89 3.95
3154 3226 4.511246 CACGATGCATGGGGCCCT 62.511 66.667 25.93 6.39 43.89 5.19
3155 3227 4.820744 ACACGATGCATGGGGCCC 62.821 66.667 18.17 18.17 43.89 5.80
3156 3228 3.520862 CACACGATGCATGGGGCC 61.521 66.667 11.29 0.00 43.89 5.80
3165 3237 1.080501 AGGTCACGAGCACACGATG 60.081 57.895 5.12 0.00 37.03 3.84
3166 3238 1.080501 CAGGTCACGAGCACACGAT 60.081 57.895 5.12 0.00 37.03 3.73
3167 3239 2.335011 CAGGTCACGAGCACACGA 59.665 61.111 5.12 0.00 37.03 4.35
3168 3240 2.137425 TACCAGGTCACGAGCACACG 62.137 60.000 0.00 0.00 39.31 4.49
3169 3241 0.666577 GTACCAGGTCACGAGCACAC 60.667 60.000 0.00 0.00 0.00 3.82
3170 3242 1.663739 GTACCAGGTCACGAGCACA 59.336 57.895 0.00 0.00 0.00 4.57
3171 3243 1.443872 CGTACCAGGTCACGAGCAC 60.444 63.158 13.41 0.00 40.56 4.40
3172 3244 2.632544 CCGTACCAGGTCACGAGCA 61.633 63.158 18.01 0.00 40.56 4.26
3173 3245 2.181021 CCGTACCAGGTCACGAGC 59.819 66.667 18.01 0.00 40.56 5.03
3174 3246 1.505353 GTCCGTACCAGGTCACGAG 59.495 63.158 18.01 10.97 40.56 4.18
3175 3247 2.327343 CGTCCGTACCAGGTCACGA 61.327 63.158 18.01 1.71 40.56 4.35
3176 3248 2.177531 CGTCCGTACCAGGTCACG 59.822 66.667 0.00 4.99 37.89 4.35
3177 3249 1.505353 CTCGTCCGTACCAGGTCAC 59.495 63.158 0.00 0.00 0.00 3.67
3178 3250 2.338015 GCTCGTCCGTACCAGGTCA 61.338 63.158 0.00 0.00 0.00 4.02
3179 3251 2.488820 GCTCGTCCGTACCAGGTC 59.511 66.667 0.00 0.00 0.00 3.85
3180 3252 3.066814 GGCTCGTCCGTACCAGGT 61.067 66.667 0.00 0.00 0.00 4.00
3181 3253 3.834799 GGGCTCGTCCGTACCAGG 61.835 72.222 0.00 0.00 34.94 4.45
3182 3254 3.834799 GGGGCTCGTCCGTACCAG 61.835 72.222 0.00 0.00 34.94 4.00
3183 3255 4.371417 AGGGGCTCGTCCGTACCA 62.371 66.667 0.00 0.00 34.94 3.25
3184 3256 3.525545 GAGGGGCTCGTCCGTACC 61.526 72.222 0.00 0.00 34.94 3.34
3193 3265 1.228737 AGGCTATCTCGAGGGGCTC 60.229 63.158 13.56 8.56 0.00 4.70
3194 3266 1.532794 CAGGCTATCTCGAGGGGCT 60.533 63.158 13.56 16.67 34.96 5.19
3195 3267 3.055580 CAGGCTATCTCGAGGGGC 58.944 66.667 13.56 14.76 0.00 5.80
3196 3268 2.578714 GGCAGGCTATCTCGAGGGG 61.579 68.421 13.56 4.29 0.00 4.79
3197 3269 1.402896 TTGGCAGGCTATCTCGAGGG 61.403 60.000 13.56 4.66 0.00 4.30
3198 3270 0.033228 CTTGGCAGGCTATCTCGAGG 59.967 60.000 13.56 0.00 0.00 4.63
3199 3271 1.035923 TCTTGGCAGGCTATCTCGAG 58.964 55.000 5.93 5.93 0.00 4.04
3200 3272 1.485124 TTCTTGGCAGGCTATCTCGA 58.515 50.000 0.00 0.00 0.00 4.04
3201 3273 2.315925 TTTCTTGGCAGGCTATCTCG 57.684 50.000 0.00 0.00 0.00 4.04
3202 3274 3.347216 TGTTTTCTTGGCAGGCTATCTC 58.653 45.455 0.00 0.00 0.00 2.75
3203 3275 3.350833 CTGTTTTCTTGGCAGGCTATCT 58.649 45.455 0.00 0.00 0.00 1.98
3204 3276 2.424956 CCTGTTTTCTTGGCAGGCTATC 59.575 50.000 0.00 0.00 42.54 2.08
3205 3277 2.450476 CCTGTTTTCTTGGCAGGCTAT 58.550 47.619 0.00 0.00 42.54 2.97
3206 3278 1.547675 CCCTGTTTTCTTGGCAGGCTA 60.548 52.381 4.43 0.00 46.15 3.93
3207 3279 0.829182 CCCTGTTTTCTTGGCAGGCT 60.829 55.000 4.43 0.00 46.15 4.58
3208 3280 0.827507 TCCCTGTTTTCTTGGCAGGC 60.828 55.000 4.43 0.00 46.15 4.85
3209 3281 1.202927 TCTCCCTGTTTTCTTGGCAGG 60.203 52.381 0.00 0.00 46.83 4.85
3210 3282 1.882623 GTCTCCCTGTTTTCTTGGCAG 59.117 52.381 0.00 0.00 0.00 4.85
3211 3283 1.214175 TGTCTCCCTGTTTTCTTGGCA 59.786 47.619 0.00 0.00 0.00 4.92
3212 3284 1.882623 CTGTCTCCCTGTTTTCTTGGC 59.117 52.381 0.00 0.00 0.00 4.52
3213 3285 2.106511 TCCTGTCTCCCTGTTTTCTTGG 59.893 50.000 0.00 0.00 0.00 3.61
3214 3286 3.492102 TCCTGTCTCCCTGTTTTCTTG 57.508 47.619 0.00 0.00 0.00 3.02
3215 3287 4.519906 TTTCCTGTCTCCCTGTTTTCTT 57.480 40.909 0.00 0.00 0.00 2.52
3216 3288 4.731313 ATTTCCTGTCTCCCTGTTTTCT 57.269 40.909 0.00 0.00 0.00 2.52
3217 3289 6.894339 TTAATTTCCTGTCTCCCTGTTTTC 57.106 37.500 0.00 0.00 0.00 2.29
3218 3290 9.547279 AATATTAATTTCCTGTCTCCCTGTTTT 57.453 29.630 0.00 0.00 0.00 2.43
3219 3291 9.547279 AAATATTAATTTCCTGTCTCCCTGTTT 57.453 29.630 0.00 0.00 28.88 2.83
3220 3292 9.547279 AAAATATTAATTTCCTGTCTCCCTGTT 57.453 29.630 0.00 0.00 34.12 3.16
3256 3328 9.665719 GAAAATTTTATCCATGTACAAACCCAT 57.334 29.630 2.75 0.00 0.00 4.00
3257 3329 8.875168 AGAAAATTTTATCCATGTACAAACCCA 58.125 29.630 2.75 0.00 0.00 4.51
3258 3330 9.150348 CAGAAAATTTTATCCATGTACAAACCC 57.850 33.333 2.75 0.00 0.00 4.11
3259 3331 9.705290 ACAGAAAATTTTATCCATGTACAAACC 57.295 29.630 2.75 0.00 0.00 3.27
3298 3370 3.951332 TGGCGACAAAGAGCGAAG 58.049 55.556 0.00 0.00 37.44 3.79
3339 3411 9.490379 GAACCTTTATGATAATAGATCCGTGTT 57.510 33.333 0.00 0.00 0.00 3.32
3340 3412 8.647796 TGAACCTTTATGATAATAGATCCGTGT 58.352 33.333 0.00 0.00 0.00 4.49
3341 3413 9.658799 ATGAACCTTTATGATAATAGATCCGTG 57.341 33.333 0.00 0.00 0.00 4.94
3342 3414 9.877178 GATGAACCTTTATGATAATAGATCCGT 57.123 33.333 0.00 0.00 0.00 4.69
3343 3415 9.319143 GGATGAACCTTTATGATAATAGATCCG 57.681 37.037 0.00 0.00 35.41 4.18
3344 3416 9.319143 CGGATGAACCTTTATGATAATAGATCC 57.681 37.037 0.00 0.00 36.31 3.36


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

AutoCloner maintained by Alex Coulton.