Multiple sequence alignment - TraesCS5B01G442300

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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 TraesCS5B01G442300 chr5B 100.000 3656 0 0 1 3656 615698045 615694390 0.000000e+00 6752
1 TraesCS5B01G442300 chr5A 91.543 2625 154 15 551 3151 620996245 620993665 0.000000e+00 3555
2 TraesCS5B01G442300 chr5A 92.950 539 34 4 15 551 620996823 620996287 0.000000e+00 782
3 TraesCS5B01G442300 chr5A 96.023 176 5 2 3271 3444 651496811 651496986 5.980000e-73 285
4 TraesCS5B01G442300 chr5A 95.977 174 6 1 3271 3444 290391869 290391697 7.730000e-72 281
5 TraesCS5B01G442300 chr5A 95.833 72 3 0 3442 3513 620993565 620993494 2.310000e-22 117
6 TraesCS5B01G442300 chr5D 95.086 2198 82 12 601 2795 496910645 496908471 0.000000e+00 3437
7 TraesCS5B01G442300 chr5D 91.337 531 40 6 15 540 496911271 496910742 0.000000e+00 721
8 TraesCS5B01G442300 chr5D 96.532 173 4 2 3273 3444 321901907 321902078 5.980000e-73 285
9 TraesCS5B01G442300 chr5D 79.669 423 37 20 2830 3251 496907235 496906861 3.620000e-65 259
10 TraesCS5B01G442300 chr5D 94.872 117 5 1 3541 3656 496906700 496906584 8.060000e-42 182
11 TraesCS5B01G442300 chr2B 84.326 1595 199 30 1183 2739 182008351 182009932 0.000000e+00 1513
12 TraesCS5B01G442300 chr2A 83.647 1382 172 26 1467 2811 135199792 135198428 0.000000e+00 1251
13 TraesCS5B01G442300 chr2D 83.158 950 117 18 1872 2814 128402145 128401232 0.000000e+00 828
14 TraesCS5B01G442300 chr2D 96.532 173 6 0 3280 3452 516708476 516708304 1.660000e-73 287
15 TraesCS5B01G442300 chr2D 95.000 180 6 3 3266 3444 309971406 309971583 2.780000e-71 279
16 TraesCS5B01G442300 chr7D 95.531 179 6 2 3267 3444 39001272 39001449 5.980000e-73 285
17 TraesCS5B01G442300 chr3B 95.531 179 6 2 3272 3449 550322767 550322944 5.980000e-73 285
18 TraesCS5B01G442300 chr4B 95.506 178 5 3 3268 3444 585609113 585609288 7.730000e-72 281
19 TraesCS5B01G442300 chr3D 94.536 183 9 1 3269 3451 4171291 4171110 7.730000e-72 281


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 TraesCS5B01G442300 chr5B 615694390 615698045 3655 True 6752.000000 6752 100.000 1 3656 1 chr5B.!!$R1 3655
1 TraesCS5B01G442300 chr5A 620993494 620996823 3329 True 1484.666667 3555 93.442 15 3513 3 chr5A.!!$R2 3498
2 TraesCS5B01G442300 chr5D 496906584 496911271 4687 True 1149.750000 3437 90.241 15 3656 4 chr5D.!!$R1 3641
3 TraesCS5B01G442300 chr2B 182008351 182009932 1581 False 1513.000000 1513 84.326 1183 2739 1 chr2B.!!$F1 1556
4 TraesCS5B01G442300 chr2A 135198428 135199792 1364 True 1251.000000 1251 83.647 1467 2811 1 chr2A.!!$R1 1344
5 TraesCS5B01G442300 chr2D 128401232 128402145 913 True 828.000000 828 83.158 1872 2814 1 chr2D.!!$R1 942

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
865 932 0.79325 GAAGCTCGCTGTCCTGTTTC 59.207 55.0 0.0 0.0 0.0 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2827 4178 0.0293 CACTCAAACAACGGGCACAG 59.971 55.0 0.0 0.0 0.0 3.66 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
38 39 7.261325 CAGTACAGCACTACAATCTACAAGAT 58.739 38.462 0.00 0.00 33.88 2.40
60 61 3.882888 TGTCAGTGAAGAAAACATGTCCC 59.117 43.478 0.00 0.00 0.00 4.46
72 73 6.553100 AGAAAACATGTCCCAAATACTCCAAA 59.447 34.615 0.00 0.00 0.00 3.28
116 117 7.475771 AATTTGCACATAACAACGAAACAAT 57.524 28.000 0.00 0.00 0.00 2.71
154 155 3.005472 GGAACGATGATCTTGACGGGATA 59.995 47.826 0.00 0.00 0.00 2.59
163 164 7.303182 TGATCTTGACGGGATAATTATCTGT 57.697 36.000 21.80 19.66 33.28 3.41
198 199 1.432270 GCGATCTAGCACTTGGGCAC 61.432 60.000 0.00 0.00 37.05 5.01
235 237 3.534704 AACTCCCCCGTCCTCCGAA 62.535 63.158 0.00 0.00 39.56 4.30
237 239 3.657038 CTCCCCCGTCCTCCGAAGA 62.657 68.421 0.00 0.00 39.56 2.87
238 240 2.682494 CCCCCGTCCTCCGAAGAA 60.682 66.667 0.00 0.00 39.56 2.52
252 255 1.078001 AAGAACGGCCGTATTGGGG 60.078 57.895 34.44 0.00 38.63 4.96
263 266 1.512735 GTATTGGGGGAGGAGAAGCT 58.487 55.000 0.00 0.00 0.00 3.74
299 302 3.260380 CAGATGATAGGGGACTCACCATC 59.740 52.174 0.00 1.90 43.67 3.51
564 607 3.619900 TCCCTATGGAGTAGTGCTCAT 57.380 47.619 10.59 4.80 45.88 2.90
747 814 2.109387 CACCGTCGACACCCCAAA 59.891 61.111 17.16 0.00 0.00 3.28
856 923 4.386245 GAGGTACGAAGCTCGCTG 57.614 61.111 5.63 0.00 45.12 5.18
865 932 0.793250 GAAGCTCGCTGTCCTGTTTC 59.207 55.000 0.00 0.00 0.00 2.78
881 948 2.293122 TGTTTCCTTCCAGCGATTTGTG 59.707 45.455 0.00 0.00 0.00 3.33
885 952 1.666888 CCTTCCAGCGATTTGTGCAAC 60.667 52.381 0.00 0.00 33.85 4.17
893 960 1.805428 GATTTGTGCAACCCCGCTGT 61.805 55.000 0.00 0.00 34.36 4.40
926 993 2.150051 GGATCCGCCCCCTGATTCT 61.150 63.158 0.00 0.00 0.00 2.40
934 1001 1.340991 GCCCCCTGATTCTAAACTGCA 60.341 52.381 0.00 0.00 0.00 4.41
980 1047 1.140161 TCTAATCCGCCGGTGTTCG 59.860 57.895 15.14 2.87 38.88 3.95
1031 1098 1.399744 ATATCCCAGAACGCGCTCCA 61.400 55.000 5.73 0.00 0.00 3.86
1098 1165 2.768344 ATGGATTCCCCCGTCGCT 60.768 61.111 0.00 0.00 0.00 4.93
1154 1221 1.956629 GATCGCAGGAAGGACCGGAA 61.957 60.000 9.46 0.00 44.74 4.30
1365 1441 2.441001 CCTGCCTGTTTATGAGGAGGAT 59.559 50.000 0.00 0.00 33.21 3.24
1452 1537 1.219124 CACCGAGGTGGACATCCTG 59.781 63.158 14.19 0.00 42.00 3.86
1461 1546 0.038166 TGGACATCCTGAAGGTTGCC 59.962 55.000 7.24 9.52 38.21 4.52
1525 1610 0.107643 GGGCAAGGAGTATGAGGCTC 59.892 60.000 7.79 7.79 0.00 4.70
1551 1636 2.594592 GGTCACCACGCCAAGCTT 60.595 61.111 0.00 0.00 0.00 3.74
1649 1743 3.046390 GAGTCGACAATATGCTTCGGAG 58.954 50.000 19.50 0.00 33.50 4.63
1724 1819 4.319177 GACTACTCAAGGCTTGTTGATGT 58.681 43.478 25.39 17.86 35.88 3.06
1786 1881 4.263462 TGCAGTTTCATAGGAATGGTCAGT 60.263 41.667 0.00 0.00 33.61 3.41
1896 1999 1.734465 GACTGTCCAATTCAGAAGGCG 59.266 52.381 0.00 0.00 36.81 5.52
2040 2146 3.556843 GCCTGGAGAGCTTTGAGATATCC 60.557 52.174 0.00 0.21 42.01 2.59
2088 2202 3.175109 GGTAACGAGGGGTACATTCTG 57.825 52.381 0.00 0.00 0.00 3.02
2141 2255 4.080356 TGGAACCCTCAAGATGAATGGTAG 60.080 45.833 2.69 0.00 32.40 3.18
2596 2710 3.706373 GCAGCGGGTTCCTCTCCA 61.706 66.667 0.00 0.00 0.00 3.86
2666 2787 3.889044 CGCTTAGGGCTCTCGCGA 61.889 66.667 21.67 9.26 42.04 5.87
2669 2790 2.033793 CTTAGGGCTCTCGCGATCA 58.966 57.895 10.36 0.00 36.88 2.92
2677 2798 1.788344 GCTCTCGCGATCAAGTTTTGC 60.788 52.381 10.36 0.05 0.00 3.68
2802 4153 2.575532 GCTCAATGCAATACCCTGCTA 58.424 47.619 0.00 0.00 43.07 3.49
2803 4154 2.551459 GCTCAATGCAATACCCTGCTAG 59.449 50.000 0.00 0.00 43.07 3.42
2804 4155 2.551459 CTCAATGCAATACCCTGCTAGC 59.449 50.000 8.10 8.10 43.07 3.42
2805 4156 2.173356 TCAATGCAATACCCTGCTAGCT 59.827 45.455 17.23 0.00 43.07 3.32
2806 4157 2.551459 CAATGCAATACCCTGCTAGCTC 59.449 50.000 17.23 0.00 43.07 4.09
2807 4158 1.500474 TGCAATACCCTGCTAGCTCT 58.500 50.000 17.23 0.00 43.07 4.09
2808 4159 1.839994 TGCAATACCCTGCTAGCTCTT 59.160 47.619 17.23 0.06 43.07 2.85
2809 4160 2.239654 TGCAATACCCTGCTAGCTCTTT 59.760 45.455 17.23 0.44 43.07 2.52
2810 4161 3.282885 GCAATACCCTGCTAGCTCTTTT 58.717 45.455 17.23 0.00 39.34 2.27
2811 4162 3.313803 GCAATACCCTGCTAGCTCTTTTC 59.686 47.826 17.23 0.00 39.34 2.29
2812 4163 4.775236 CAATACCCTGCTAGCTCTTTTCT 58.225 43.478 17.23 0.00 0.00 2.52
2813 4164 2.777832 ACCCTGCTAGCTCTTTTCTG 57.222 50.000 17.23 0.00 0.00 3.02
2814 4165 1.280421 ACCCTGCTAGCTCTTTTCTGG 59.720 52.381 17.23 7.01 0.00 3.86
2815 4166 1.280421 CCCTGCTAGCTCTTTTCTGGT 59.720 52.381 17.23 0.00 0.00 4.00
2816 4167 2.501723 CCCTGCTAGCTCTTTTCTGGTA 59.498 50.000 17.23 0.00 0.00 3.25
2817 4168 3.526534 CCTGCTAGCTCTTTTCTGGTAC 58.473 50.000 17.23 0.00 0.00 3.34
2818 4169 3.196685 CCTGCTAGCTCTTTTCTGGTACT 59.803 47.826 17.23 0.00 0.00 2.73
2819 4170 4.429108 CTGCTAGCTCTTTTCTGGTACTC 58.571 47.826 17.23 0.00 0.00 2.59
2820 4171 3.832490 TGCTAGCTCTTTTCTGGTACTCA 59.168 43.478 17.23 0.00 0.00 3.41
2821 4172 4.467795 TGCTAGCTCTTTTCTGGTACTCAT 59.532 41.667 17.23 0.00 0.00 2.90
2822 4173 4.808364 GCTAGCTCTTTTCTGGTACTCATG 59.192 45.833 7.70 0.00 0.00 3.07
2823 4174 4.899352 AGCTCTTTTCTGGTACTCATGT 57.101 40.909 0.00 0.00 0.00 3.21
2824 4175 5.234466 AGCTCTTTTCTGGTACTCATGTT 57.766 39.130 0.00 0.00 0.00 2.71
2825 4176 4.999950 AGCTCTTTTCTGGTACTCATGTTG 59.000 41.667 0.00 0.00 0.00 3.33
2826 4177 4.378874 GCTCTTTTCTGGTACTCATGTTGC 60.379 45.833 0.00 0.00 0.00 4.17
2827 4178 4.072131 TCTTTTCTGGTACTCATGTTGCC 58.928 43.478 0.00 0.00 0.00 4.52
2828 4179 3.788227 TTTCTGGTACTCATGTTGCCT 57.212 42.857 0.00 0.00 0.00 4.75
2889 4240 0.385390 GAAGTTTGGTGGTGTGGCTG 59.615 55.000 0.00 0.00 0.00 4.85
2890 4241 1.042559 AAGTTTGGTGGTGTGGCTGG 61.043 55.000 0.00 0.00 0.00 4.85
2898 4249 0.843309 TGGTGTGGCTGGAGAAAAGA 59.157 50.000 0.00 0.00 0.00 2.52
2899 4250 1.214175 TGGTGTGGCTGGAGAAAAGAA 59.786 47.619 0.00 0.00 0.00 2.52
2905 4256 1.004161 GGCTGGAGAAAAGAAGGAGCT 59.996 52.381 0.00 0.00 0.00 4.09
2913 4264 6.486993 TGGAGAAAAGAAGGAGCTTTTAGAAC 59.513 38.462 0.00 0.00 45.34 3.01
2919 4270 4.515567 AGAAGGAGCTTTTAGAACGTTTGG 59.484 41.667 0.46 0.00 0.00 3.28
2933 4284 2.032924 ACGTTTGGTTGCAGCTCTAAAC 59.967 45.455 14.90 14.90 33.73 2.01
2935 4286 1.234821 TTGGTTGCAGCTCTAAACGG 58.765 50.000 0.00 0.00 0.00 4.44
2944 4295 3.058224 GCAGCTCTAAACGGTTGTTTCAT 60.058 43.478 0.00 0.00 44.94 2.57
2951 4311 1.604604 ACGGTTGTTTCATCAGGTGG 58.395 50.000 0.00 0.00 0.00 4.61
2953 4313 1.620822 GGTTGTTTCATCAGGTGGCT 58.379 50.000 0.00 0.00 0.00 4.75
2955 4315 2.229792 GTTGTTTCATCAGGTGGCTGA 58.770 47.619 0.00 0.00 37.79 4.26
2964 4324 1.980765 TCAGGTGGCTGAGATTCTGTT 59.019 47.619 0.00 0.00 0.00 3.16
2966 4326 2.486982 CAGGTGGCTGAGATTCTGTTTG 59.513 50.000 0.00 0.00 0.00 2.93
3027 4401 1.141657 AGCATATGACATCGGCCAAGT 59.858 47.619 6.97 0.00 0.00 3.16
3049 4424 6.176183 AGTAATGTAAGCATGCAACTCTTCT 58.824 36.000 21.98 11.59 35.15 2.85
3078 4469 7.530426 AGGATGCTTTCTGTTGTAGAATTTT 57.470 32.000 0.00 0.00 44.54 1.82
3079 4470 7.373493 AGGATGCTTTCTGTTGTAGAATTTTG 58.627 34.615 0.00 0.00 44.54 2.44
3080 4471 7.231317 AGGATGCTTTCTGTTGTAGAATTTTGA 59.769 33.333 0.00 0.00 44.54 2.69
3081 4472 7.867403 GGATGCTTTCTGTTGTAGAATTTTGAA 59.133 33.333 0.00 0.00 44.54 2.69
3082 4473 9.248291 GATGCTTTCTGTTGTAGAATTTTGAAA 57.752 29.630 0.00 0.00 44.54 2.69
3083 4474 8.406172 TGCTTTCTGTTGTAGAATTTTGAAAC 57.594 30.769 0.00 0.00 44.54 2.78
3084 4475 7.219917 TGCTTTCTGTTGTAGAATTTTGAAACG 59.780 33.333 0.00 0.00 44.54 3.60
3085 4476 7.220108 GCTTTCTGTTGTAGAATTTTGAAACGT 59.780 33.333 0.00 0.00 44.54 3.99
3086 4477 7.962934 TTCTGTTGTAGAATTTTGAAACGTG 57.037 32.000 0.00 0.00 40.43 4.49
3087 4478 6.491394 TCTGTTGTAGAATTTTGAAACGTGG 58.509 36.000 0.00 0.00 30.84 4.94
3088 4479 6.316640 TCTGTTGTAGAATTTTGAAACGTGGA 59.683 34.615 0.00 0.00 30.84 4.02
3089 4480 6.853720 TGTTGTAGAATTTTGAAACGTGGAA 58.146 32.000 0.00 0.00 0.00 3.53
3090 4481 7.484975 TGTTGTAGAATTTTGAAACGTGGAAT 58.515 30.769 0.00 0.00 0.00 3.01
3091 4482 7.976734 TGTTGTAGAATTTTGAAACGTGGAATT 59.023 29.630 0.00 0.00 0.00 2.17
3092 4483 8.813282 GTTGTAGAATTTTGAAACGTGGAATTT 58.187 29.630 0.00 0.00 0.00 1.82
3101 4492 9.974750 TTTTGAAACGTGGAATTTATTTTCAAC 57.025 25.926 6.77 0.00 40.70 3.18
3151 4542 3.365264 GCATCGCTGAAACATCAACTTGA 60.365 43.478 0.00 0.00 0.00 3.02
3153 4544 3.202097 TCGCTGAAACATCAACTTGACA 58.798 40.909 0.00 0.00 0.00 3.58
3155 4546 4.083855 TCGCTGAAACATCAACTTGACATC 60.084 41.667 0.00 0.00 0.00 3.06
3166 4557 7.445096 ACATCAACTTGACATCATCAGTTTACA 59.555 33.333 0.00 0.00 38.99 2.41
3171 4562 6.992123 ACTTGACATCATCAGTTTACAAGTCA 59.008 34.615 0.00 0.00 41.37 3.41
3176 4567 5.290493 TCATCAGTTTACAAGTCACCACT 57.710 39.130 0.00 0.00 0.00 4.00
3182 4573 7.152645 TCAGTTTACAAGTCACCACTAATCTC 58.847 38.462 0.00 0.00 30.14 2.75
3208 4599 4.273235 TGGAACATGTCTGCTATTTATGCG 59.727 41.667 0.00 0.00 0.00 4.73
3239 4630 1.273986 TTCCTAGCATGCAGGAGCCA 61.274 55.000 26.93 16.70 43.05 4.75
3265 4665 3.896272 GGTTCCGTCCTATCCAGAATAGT 59.104 47.826 0.00 0.00 36.38 2.12
3288 4688 7.852263 AGTTATGCATAATATGTACTCCCTCC 58.148 38.462 21.52 4.41 0.00 4.30
3289 4689 4.801330 TGCATAATATGTACTCCCTCCG 57.199 45.455 1.92 0.00 0.00 4.63
3291 4691 4.591498 TGCATAATATGTACTCCCTCCGTT 59.409 41.667 1.92 0.00 0.00 4.44
3292 4692 5.169295 GCATAATATGTACTCCCTCCGTTC 58.831 45.833 1.92 0.00 0.00 3.95
3293 4693 5.721232 CATAATATGTACTCCCTCCGTTCC 58.279 45.833 0.00 0.00 0.00 3.62
3294 4694 3.614568 ATATGTACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
3295 4695 4.736611 ATATGTACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
3296 4696 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3299 4699 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3301 4701 5.901276 TGTACTCCCTCCGTTCCTAAATATT 59.099 40.000 0.00 0.00 0.00 1.28
3303 4703 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3304 4704 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3306 4706 6.486941 TCCCTCCGTTCCTAAATATTTGTTT 58.513 36.000 11.05 0.00 0.00 2.83
3308 4708 7.452189 TCCCTCCGTTCCTAAATATTTGTTTTT 59.548 33.333 11.05 0.00 0.00 1.94
3334 4734 9.582431 TTTAGAGATTTCAAATAGACTACCACG 57.418 33.333 0.00 0.00 0.00 4.94
3335 4735 7.171630 AGAGATTTCAAATAGACTACCACGT 57.828 36.000 0.00 0.00 0.00 4.49
3336 4736 8.289939 AGAGATTTCAAATAGACTACCACGTA 57.710 34.615 0.00 0.00 0.00 3.57
3338 4738 6.971184 AGATTTCAAATAGACTACCACGTACG 59.029 38.462 15.01 15.01 0.00 3.67
3339 4739 4.621068 TCAAATAGACTACCACGTACGG 57.379 45.455 21.06 8.46 0.00 4.02
3340 4740 4.260985 TCAAATAGACTACCACGTACGGA 58.739 43.478 21.06 0.65 0.00 4.69
3341 4741 4.883585 TCAAATAGACTACCACGTACGGAT 59.116 41.667 21.06 6.82 0.00 4.18
3342 4742 4.825546 AATAGACTACCACGTACGGATG 57.174 45.455 21.06 9.60 0.00 3.51
3343 4743 2.119801 AGACTACCACGTACGGATGT 57.880 50.000 21.06 15.02 0.00 3.06
3345 4745 3.813443 AGACTACCACGTACGGATGTAT 58.187 45.455 21.06 5.45 32.11 2.29
3346 4746 4.960938 AGACTACCACGTACGGATGTATA 58.039 43.478 21.06 3.97 32.11 1.47
3347 4747 5.555017 AGACTACCACGTACGGATGTATAT 58.445 41.667 21.06 8.53 32.11 0.86
3349 4749 6.815641 AGACTACCACGTACGGATGTATATAG 59.184 42.308 21.06 11.06 32.11 1.31
3351 4751 5.869753 ACCACGTACGGATGTATATAGAC 57.130 43.478 21.06 0.00 32.11 2.59
3353 4753 5.180117 ACCACGTACGGATGTATATAGACAC 59.820 44.000 21.06 0.00 32.11 3.67
3354 4754 5.179929 CCACGTACGGATGTATATAGACACA 59.820 44.000 21.06 0.00 32.11 3.72
3355 4755 6.128090 CCACGTACGGATGTATATAGACACAT 60.128 42.308 21.06 0.00 38.08 3.21
3356 4756 7.303261 CACGTACGGATGTATATAGACACATT 58.697 38.462 21.06 0.00 35.55 2.71
3357 4757 7.806487 CACGTACGGATGTATATAGACACATTT 59.194 37.037 21.06 0.00 35.55 2.32
3358 4758 8.355169 ACGTACGGATGTATATAGACACATTTT 58.645 33.333 21.06 0.00 35.55 1.82
3359 4759 9.830294 CGTACGGATGTATATAGACACATTTTA 57.170 33.333 7.57 0.00 35.55 1.52
3385 4785 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3386 4786 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
3388 4788 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
3390 4790 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
3393 4793 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
3394 4794 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3395 4795 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
3397 4797 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
3398 4798 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
3399 4799 6.649141 TCATTTTGCTTCGTATGTAGTCACTT 59.351 34.615 0.00 0.00 0.00 3.16
3400 4800 5.839262 TTTGCTTCGTATGTAGTCACTTG 57.161 39.130 0.00 0.00 0.00 3.16
3401 4801 4.514781 TGCTTCGTATGTAGTCACTTGT 57.485 40.909 0.00 0.00 0.00 3.16
3402 4802 4.878439 TGCTTCGTATGTAGTCACTTGTT 58.122 39.130 0.00 0.00 0.00 2.83
3403 4803 4.684242 TGCTTCGTATGTAGTCACTTGTTG 59.316 41.667 0.00 0.00 0.00 3.33
3404 4804 4.921515 GCTTCGTATGTAGTCACTTGTTGA 59.078 41.667 0.00 0.00 0.00 3.18
3405 4805 5.404366 GCTTCGTATGTAGTCACTTGTTGAA 59.596 40.000 0.00 0.00 35.39 2.69
3406 4806 6.073980 GCTTCGTATGTAGTCACTTGTTGAAA 60.074 38.462 0.00 0.00 35.39 2.69
3407 4807 7.360101 GCTTCGTATGTAGTCACTTGTTGAAAT 60.360 37.037 0.00 0.00 35.39 2.17
3408 4808 7.576750 TCGTATGTAGTCACTTGTTGAAATC 57.423 36.000 0.00 0.00 35.39 2.17
3409 4809 7.375834 TCGTATGTAGTCACTTGTTGAAATCT 58.624 34.615 0.00 0.00 35.39 2.40
3410 4810 7.541091 TCGTATGTAGTCACTTGTTGAAATCTC 59.459 37.037 0.00 0.00 35.39 2.75
3411 4811 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
3412 4812 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
3413 4813 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
3414 4814 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
3415 4815 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
3416 4816 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
3417 4817 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
3418 4818 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
3419 4819 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
3420 4820 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
3421 4821 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
3422 4822 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
3435 4835 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3436 4836 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3437 4837 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3438 4838 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3439 4839 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3440 4840 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3454 4854 5.340439 ACGGAGGGAGTAAAAGACTATTG 57.660 43.478 0.00 0.00 39.06 1.90
3469 4869 0.582960 TATTGCTGCGCGTGATCATG 59.417 50.000 8.43 10.76 0.00 3.07
3477 4877 1.193203 GCGCGTGATCATGTCTTATGG 59.807 52.381 16.18 0.00 0.00 2.74
3513 4913 8.650143 AGCTTTTATGACCAATAAGGAAAAGA 57.350 30.769 8.06 0.00 38.67 2.52
3514 4914 8.523658 AGCTTTTATGACCAATAAGGAAAAGAC 58.476 33.333 8.06 1.31 38.67 3.01
3515 4915 8.303876 GCTTTTATGACCAATAAGGAAAAGACA 58.696 33.333 8.06 0.00 38.67 3.41
3530 4930 8.857694 AGGAAAAGACATAAATTTAGGAACGA 57.142 30.769 16.26 0.00 0.00 3.85
3531 4931 9.292195 AGGAAAAGACATAAATTTAGGAACGAA 57.708 29.630 16.26 0.00 0.00 3.85
3532 4932 9.556030 GGAAAAGACATAAATTTAGGAACGAAG 57.444 33.333 16.26 0.00 0.00 3.79
3533 4933 9.556030 GAAAAGACATAAATTTAGGAACGAAGG 57.444 33.333 16.26 0.00 0.00 3.46
3534 4934 7.625828 AAGACATAAATTTAGGAACGAAGGG 57.374 36.000 16.26 0.00 0.00 3.95
3535 4935 6.954232 AGACATAAATTTAGGAACGAAGGGA 58.046 36.000 16.26 0.00 0.00 4.20
3536 4936 7.048512 AGACATAAATTTAGGAACGAAGGGAG 58.951 38.462 16.26 0.00 0.00 4.30
3537 4937 6.718294 ACATAAATTTAGGAACGAAGGGAGT 58.282 36.000 16.26 0.00 0.00 3.85
3538 4938 7.854337 ACATAAATTTAGGAACGAAGGGAGTA 58.146 34.615 16.26 0.00 0.00 2.59
3539 4939 7.767659 ACATAAATTTAGGAACGAAGGGAGTAC 59.232 37.037 16.26 0.00 0.00 2.73
3545 4945 4.414677 AGGAACGAAGGGAGTACTAGTTT 58.585 43.478 0.00 0.00 0.00 2.66
3553 4953 6.571925 CGAAGGGAGTACTAGTTTGTAGCTTT 60.572 42.308 0.00 0.00 0.00 3.51
3562 4962 9.859692 GTACTAGTTTGTAGCTTTAAAACACAG 57.140 33.333 16.30 14.52 36.48 3.66
3574 4974 6.640907 GCTTTAAAACACAGAGGGTTTACATG 59.359 38.462 0.00 0.00 37.47 3.21
3576 4976 8.749026 TTTAAAACACAGAGGGTTTACATGTA 57.251 30.769 0.08 0.08 37.47 2.29
3577 4977 8.927675 TTAAAACACAGAGGGTTTACATGTAT 57.072 30.769 6.36 0.00 37.47 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.570926 TGTAGTGCTGTACTGCTGTAC 57.429 47.619 22.87 22.87 46.74 2.90
8 9 4.462834 AGATTGTAGTGCTGTACTGCTGTA 59.537 41.667 23.07 12.75 41.93 2.74
10 11 3.854666 AGATTGTAGTGCTGTACTGCTG 58.145 45.455 23.07 0.00 41.93 4.41
11 12 4.462834 TGTAGATTGTAGTGCTGTACTGCT 59.537 41.667 23.07 8.71 41.93 4.24
12 13 4.744570 TGTAGATTGTAGTGCTGTACTGC 58.255 43.478 17.07 17.07 40.65 4.40
13 14 6.621613 TCTTGTAGATTGTAGTGCTGTACTG 58.378 40.000 8.75 0.00 40.65 2.74
21 22 7.315890 TCACTGACATCTTGTAGATTGTAGTG 58.684 38.462 12.85 12.85 31.32 2.74
38 39 3.882888 GGGACATGTTTTCTTCACTGACA 59.117 43.478 0.00 0.00 0.00 3.58
72 73 6.544928 AATTTTCTGTTGGAAGTTGGAACT 57.455 33.333 0.00 0.00 42.04 3.01
91 92 6.893958 TGTTTCGTTGTTATGTGCAAATTT 57.106 29.167 0.00 0.00 0.00 1.82
116 117 6.428465 TCATCGTTCCTTTTGCAATTGTACTA 59.572 34.615 7.40 0.00 0.00 1.82
154 155 7.977853 GCACTTCATCAAATTCCACAGATAATT 59.022 33.333 0.00 0.00 0.00 1.40
163 164 4.264253 AGATCGCACTTCATCAAATTCCA 58.736 39.130 0.00 0.00 0.00 3.53
198 199 2.078849 TGCGGCGTTATATGATCCAG 57.921 50.000 9.37 0.00 0.00 3.86
235 237 2.587889 CCCCAATACGGCCGTTCT 59.412 61.111 38.94 21.87 0.00 3.01
237 239 3.010314 TCCCCCAATACGGCCGTT 61.010 61.111 38.94 21.29 0.00 4.44
238 240 3.476419 CTCCCCCAATACGGCCGT 61.476 66.667 36.01 36.01 0.00 5.68
244 246 1.512735 AGCTTCTCCTCCCCCAATAC 58.487 55.000 0.00 0.00 0.00 1.89
247 249 0.475632 TCAAGCTTCTCCTCCCCCAA 60.476 55.000 0.00 0.00 0.00 4.12
248 250 0.253347 ATCAAGCTTCTCCTCCCCCA 60.253 55.000 0.00 0.00 0.00 4.96
249 251 0.182299 CATCAAGCTTCTCCTCCCCC 59.818 60.000 0.00 0.00 0.00 5.40
252 255 3.269178 CTTCACATCAAGCTTCTCCTCC 58.731 50.000 0.00 0.00 0.00 4.30
263 266 5.587443 CCTATCATCTGTTGCTTCACATCAA 59.413 40.000 0.00 0.00 0.00 2.57
387 390 2.663852 AACCTTCACCGGCGTTCG 60.664 61.111 6.01 0.00 38.88 3.95
546 589 7.675062 AGAATAAATGAGCACTACTCCATAGG 58.325 38.462 0.00 0.00 45.61 2.57
547 590 9.553064 AAAGAATAAATGAGCACTACTCCATAG 57.447 33.333 0.00 0.00 45.61 2.23
549 592 8.814038 AAAAGAATAAATGAGCACTACTCCAT 57.186 30.769 0.00 0.00 45.61 3.41
809 876 4.003788 CCAAGGACTGCGGACGGT 62.004 66.667 0.00 0.00 38.42 4.83
822 889 3.121030 CGGAAGTCAGCGGCCAAG 61.121 66.667 2.24 0.00 0.00 3.61
856 923 0.034896 TCGCTGGAAGGAAACAGGAC 59.965 55.000 0.00 0.00 35.30 3.85
865 932 0.597568 TTGCACAAATCGCTGGAAGG 59.402 50.000 0.00 0.00 0.00 3.46
881 948 3.056328 GAAGGACAGCGGGGTTGC 61.056 66.667 0.00 0.00 0.00 4.17
885 952 2.046892 CTGTGAAGGACAGCGGGG 60.047 66.667 0.00 0.00 45.72 5.73
893 960 2.284798 GATCCGCGAGCTGTGAAGGA 62.285 60.000 8.23 0.00 0.00 3.36
919 986 5.860182 CCACAAATGTGCAGTTTAGAATCAG 59.140 40.000 8.03 0.00 44.34 2.90
922 989 4.281688 AGCCACAAATGTGCAGTTTAGAAT 59.718 37.500 8.03 0.00 44.34 2.40
926 993 2.035704 CCAGCCACAAATGTGCAGTTTA 59.964 45.455 8.03 0.00 44.34 2.01
934 1001 1.269012 CCAATCCCAGCCACAAATGT 58.731 50.000 0.00 0.00 0.00 2.71
1057 1124 0.738762 TCTTCATCGCTGCTGCTGTC 60.739 55.000 14.03 0.42 36.97 3.51
1058 1125 0.740164 CTCTTCATCGCTGCTGCTGT 60.740 55.000 14.03 0.00 36.97 4.40
1098 1165 4.161295 CCGGCCTCTGCATCCGAA 62.161 66.667 15.42 0.00 45.53 4.30
1154 1221 0.248843 CAGCGCCTTCTTCTTCCTCT 59.751 55.000 2.29 0.00 0.00 3.69
1365 1441 0.979709 CCTCATCCTCACTGCCCAGA 60.980 60.000 1.69 0.00 0.00 3.86
1452 1537 1.676967 CCTCAGCCTGGCAACCTTC 60.677 63.158 22.65 0.00 0.00 3.46
1551 1636 1.497309 CCCAGCCAGTGAAGGGGTTA 61.497 60.000 6.61 0.00 37.66 2.85
1612 1706 2.234908 CGACTCCACCTTCTTCCTCATT 59.765 50.000 0.00 0.00 0.00 2.57
1649 1743 3.811722 TGACGACAAGTTCATCATTGC 57.188 42.857 0.00 0.00 0.00 3.56
1724 1819 2.172082 CTGGAAGGATCCTGAGCATTCA 59.828 50.000 17.02 2.77 46.70 2.57
1896 1999 0.548510 AGCCATCAGGTAGAAAGGCC 59.451 55.000 0.00 0.00 46.77 5.19
2040 2146 2.159338 CGCAATGGTTCTTGAATCAGGG 60.159 50.000 2.71 0.00 0.00 4.45
2088 2202 5.713025 TGCTTTGTTTTGGAAGATATCAGC 58.287 37.500 5.32 1.15 0.00 4.26
2181 2295 4.096003 TCCCCACCGCTGCTTAGC 62.096 66.667 0.00 0.00 0.00 3.09
2454 2568 2.223923 CCTGTCCTTCCTCGAGCTTATG 60.224 54.545 6.99 0.00 0.00 1.90
2596 2710 2.535485 TTTCCGCCAGCATGTCCGAT 62.535 55.000 0.00 0.00 31.79 4.18
2666 2787 7.439056 CAGAAAAATACAGTGGCAAAACTTGAT 59.561 33.333 0.00 0.00 0.00 2.57
2669 2790 5.523552 GCAGAAAAATACAGTGGCAAAACTT 59.476 36.000 0.00 0.00 0.00 2.66
2677 2798 4.761739 TCTGGAAGCAGAAAAATACAGTGG 59.238 41.667 0.00 0.00 0.00 4.00
2799 4150 4.457834 TGAGTACCAGAAAAGAGCTAGC 57.542 45.455 6.62 6.62 0.00 3.42
2802 4153 4.899352 ACATGAGTACCAGAAAAGAGCT 57.101 40.909 0.00 0.00 0.00 4.09
2803 4154 4.378874 GCAACATGAGTACCAGAAAAGAGC 60.379 45.833 0.00 0.00 0.00 4.09
2804 4155 4.154918 GGCAACATGAGTACCAGAAAAGAG 59.845 45.833 0.00 0.00 0.00 2.85
2805 4156 4.072131 GGCAACATGAGTACCAGAAAAGA 58.928 43.478 0.00 0.00 0.00 2.52
2806 4157 4.074970 AGGCAACATGAGTACCAGAAAAG 58.925 43.478 0.00 0.00 41.41 2.27
2807 4158 3.820467 CAGGCAACATGAGTACCAGAAAA 59.180 43.478 0.00 0.00 41.41 2.29
2808 4159 3.181445 ACAGGCAACATGAGTACCAGAAA 60.181 43.478 0.00 0.00 41.41 2.52
2809 4160 2.371841 ACAGGCAACATGAGTACCAGAA 59.628 45.455 0.00 0.00 41.41 3.02
2810 4161 1.977854 ACAGGCAACATGAGTACCAGA 59.022 47.619 0.00 0.00 41.41 3.86
2811 4162 2.079158 CACAGGCAACATGAGTACCAG 58.921 52.381 0.00 0.00 41.41 4.00
2812 4163 1.881925 GCACAGGCAACATGAGTACCA 60.882 52.381 0.00 0.00 40.72 3.25
2813 4164 0.804989 GCACAGGCAACATGAGTACC 59.195 55.000 0.00 0.00 40.72 3.34
2814 4165 0.804989 GGCACAGGCAACATGAGTAC 59.195 55.000 0.00 0.00 43.71 2.73
2815 4166 0.322456 GGGCACAGGCAACATGAGTA 60.322 55.000 0.00 0.00 43.71 2.59
2816 4167 1.604593 GGGCACAGGCAACATGAGT 60.605 57.895 0.00 0.00 43.71 3.41
2817 4168 2.693762 CGGGCACAGGCAACATGAG 61.694 63.158 0.00 0.00 43.71 2.90
2818 4169 2.672651 CGGGCACAGGCAACATGA 60.673 61.111 0.00 0.00 43.71 3.07
2819 4170 2.563798 AACGGGCACAGGCAACATG 61.564 57.895 0.00 0.00 43.71 3.21
2820 4171 2.203480 AACGGGCACAGGCAACAT 60.203 55.556 0.00 0.00 43.71 2.71
2821 4172 3.215568 CAACGGGCACAGGCAACA 61.216 61.111 0.00 0.00 43.71 3.33
2822 4173 2.291457 AAACAACGGGCACAGGCAAC 62.291 55.000 0.00 0.00 43.71 4.17
2823 4174 2.055042 AAACAACGGGCACAGGCAA 61.055 52.632 0.00 0.00 43.71 4.52
2824 4175 2.441164 AAACAACGGGCACAGGCA 60.441 55.556 0.00 0.00 43.71 4.75
2825 4176 2.027460 CAAACAACGGGCACAGGC 59.973 61.111 0.00 0.00 40.13 4.85
2826 4177 1.101049 ACTCAAACAACGGGCACAGG 61.101 55.000 0.00 0.00 0.00 4.00
2827 4178 0.029300 CACTCAAACAACGGGCACAG 59.971 55.000 0.00 0.00 0.00 3.66
2828 4179 0.393132 TCACTCAAACAACGGGCACA 60.393 50.000 0.00 0.00 0.00 4.57
2876 4227 1.640593 TTTCTCCAGCCACACCACCA 61.641 55.000 0.00 0.00 0.00 4.17
2889 4240 6.347806 CGTTCTAAAAGCTCCTTCTTTTCTCC 60.348 42.308 4.95 0.00 43.09 3.71
2890 4241 6.203145 ACGTTCTAAAAGCTCCTTCTTTTCTC 59.797 38.462 4.95 0.00 43.09 2.87
2898 4249 4.204799 ACCAAACGTTCTAAAAGCTCCTT 58.795 39.130 0.00 0.00 0.00 3.36
2899 4250 3.816994 ACCAAACGTTCTAAAAGCTCCT 58.183 40.909 0.00 0.00 0.00 3.69
2905 4256 3.129638 AGCTGCAACCAAACGTTCTAAAA 59.870 39.130 0.00 0.00 29.93 1.52
2913 4264 2.650608 GTTTAGAGCTGCAACCAAACG 58.349 47.619 1.02 0.00 0.00 3.60
2919 4270 1.602377 ACAACCGTTTAGAGCTGCAAC 59.398 47.619 1.02 0.00 0.00 4.17
2933 4284 0.240945 GCCACCTGATGAAACAACCG 59.759 55.000 0.00 0.00 0.00 4.44
2935 4286 2.227388 CTCAGCCACCTGATGAAACAAC 59.773 50.000 0.00 0.00 46.44 3.32
2944 4295 1.649321 ACAGAATCTCAGCCACCTGA 58.351 50.000 0.00 0.00 45.54 3.86
2951 4311 4.094590 CCAGATCACAAACAGAATCTCAGC 59.905 45.833 0.00 0.00 0.00 4.26
2953 4313 4.999311 CACCAGATCACAAACAGAATCTCA 59.001 41.667 0.00 0.00 0.00 3.27
2955 4315 5.221803 ACTCACCAGATCACAAACAGAATCT 60.222 40.000 0.00 0.00 0.00 2.40
2964 4324 2.636647 TGCAACTCACCAGATCACAA 57.363 45.000 0.00 0.00 0.00 3.33
2966 4326 2.012673 GGATGCAACTCACCAGATCAC 58.987 52.381 0.00 0.00 0.00 3.06
3013 4373 2.779755 ACATTACTTGGCCGATGTCA 57.220 45.000 0.00 0.00 0.00 3.58
3020 4380 2.426738 TGCATGCTTACATTACTTGGCC 59.573 45.455 20.33 0.00 32.87 5.36
3027 4401 5.355071 CCAGAAGAGTTGCATGCTTACATTA 59.645 40.000 20.33 0.00 32.87 1.90
3078 4469 8.879342 ATGTTGAAAATAAATTCCACGTTTCA 57.121 26.923 0.00 0.00 34.20 2.69
3099 4490 6.493458 AGCTCCCAAACTGTTTGTATAATGTT 59.507 34.615 26.35 9.71 38.98 2.71
3101 4492 6.515272 AGCTCCCAAACTGTTTGTATAATG 57.485 37.500 26.35 13.21 38.98 1.90
3151 4542 5.470098 GTGGTGACTTGTAAACTGATGATGT 59.530 40.000 0.00 0.00 0.00 3.06
3153 4544 5.869579 AGTGGTGACTTGTAAACTGATGAT 58.130 37.500 0.00 0.00 0.00 2.45
3155 4546 7.604164 AGATTAGTGGTGACTTGTAAACTGATG 59.396 37.037 0.00 0.00 33.21 3.07
3166 4557 4.678256 TCCAGAGAGATTAGTGGTGACTT 58.322 43.478 0.00 0.00 33.21 3.01
3171 4562 4.780021 ACATGTTCCAGAGAGATTAGTGGT 59.220 41.667 0.00 0.00 0.00 4.16
3176 4567 4.713814 AGCAGACATGTTCCAGAGAGATTA 59.286 41.667 0.00 0.00 0.00 1.75
3182 4573 6.293298 GCATAAATAGCAGACATGTTCCAGAG 60.293 42.308 0.00 0.00 0.00 3.35
3208 4599 5.991606 TGCATGCTAGGAACATAATACTGTC 59.008 40.000 20.33 0.00 0.00 3.51
3239 4630 2.091278 TCTGGATAGGACGGAACCATCT 60.091 50.000 0.00 0.00 0.00 2.90
3265 4665 6.439375 ACGGAGGGAGTACATATTATGCATAA 59.561 38.462 20.95 20.95 0.00 1.90
3278 4678 6.416631 AATATTTAGGAACGGAGGGAGTAC 57.583 41.667 0.00 0.00 0.00 2.73
3279 4679 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3280 4680 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3281 4681 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3282 4682 5.703730 ACAAATATTTAGGAACGGAGGGA 57.296 39.130 0.00 0.00 0.00 4.20
3283 4683 6.769134 AAACAAATATTTAGGAACGGAGGG 57.231 37.500 0.00 0.00 0.00 4.30
3308 4708 9.582431 CGTGGTAGTCTATTTGAAATCTCTAAA 57.418 33.333 0.00 0.00 0.00 1.85
3309 4709 8.746530 ACGTGGTAGTCTATTTGAAATCTCTAA 58.253 33.333 0.00 0.00 0.00 2.10
3310 4710 8.289939 ACGTGGTAGTCTATTTGAAATCTCTA 57.710 34.615 0.00 0.00 0.00 2.43
3311 4711 7.171630 ACGTGGTAGTCTATTTGAAATCTCT 57.828 36.000 0.00 0.00 0.00 3.10
3312 4712 7.165483 CGTACGTGGTAGTCTATTTGAAATCTC 59.835 40.741 7.22 0.00 0.00 2.75
3317 4717 4.699735 TCCGTACGTGGTAGTCTATTTGAA 59.300 41.667 15.21 0.00 0.00 2.69
3319 4719 4.621068 TCCGTACGTGGTAGTCTATTTG 57.379 45.455 15.21 0.00 0.00 2.32
3321 4721 4.202441 ACATCCGTACGTGGTAGTCTATT 58.798 43.478 15.21 0.00 0.00 1.73
3324 4724 2.119801 ACATCCGTACGTGGTAGTCT 57.880 50.000 15.21 0.00 0.00 3.24
3325 4725 5.869753 ATATACATCCGTACGTGGTAGTC 57.130 43.478 15.21 0.00 0.00 2.59
3326 4726 6.591834 GTCTATATACATCCGTACGTGGTAGT 59.408 42.308 15.21 7.78 0.00 2.73
3329 4729 5.180117 GTGTCTATATACATCCGTACGTGGT 59.820 44.000 15.21 11.27 0.00 4.16
3330 4730 5.179929 TGTGTCTATATACATCCGTACGTGG 59.820 44.000 15.21 5.54 0.00 4.94
3331 4731 6.232139 TGTGTCTATATACATCCGTACGTG 57.768 41.667 15.21 9.44 0.00 4.49
3347 4747 9.856488 GTGAATCTACACTCTAAAATGTGTCTA 57.144 33.333 1.91 0.00 44.94 2.59
3349 4749 8.764524 AGTGAATCTACACTCTAAAATGTGTC 57.235 34.615 1.91 0.00 46.36 3.67
3362 4762 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
3363 4763 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
3364 4764 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
3366 4766 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
3367 4767 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3368 4768 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3370 4770 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3371 4771 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3373 4773 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
3374 4774 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
3376 4776 6.426937 ACAAGTGACTACATACGAAGCAAAAT 59.573 34.615 0.00 0.00 0.00 1.82
3377 4777 5.756347 ACAAGTGACTACATACGAAGCAAAA 59.244 36.000 0.00 0.00 0.00 2.44
3379 4779 4.878439 ACAAGTGACTACATACGAAGCAA 58.122 39.130 0.00 0.00 0.00 3.91
3381 4781 4.921515 TCAACAAGTGACTACATACGAAGC 59.078 41.667 0.00 0.00 0.00 3.86
3382 4782 7.402811 TTTCAACAAGTGACTACATACGAAG 57.597 36.000 0.00 0.00 35.39 3.79
3384 4784 7.375834 AGATTTCAACAAGTGACTACATACGA 58.624 34.615 0.00 0.00 35.39 3.43
3385 4785 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
3386 4786 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
3388 4788 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
3390 4790 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
3393 4793 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
3394 4794 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
3395 4795 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
3409 4809 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3410 4810 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3411 4811 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3412 4812 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3413 4813 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3414 4814 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3415 4815 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3416 4816 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3417 4817 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3418 4818 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3419 4819 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3420 4820 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3421 4821 7.441903 TTTACTCCCTCCGTTCCTAAATATT 57.558 36.000 0.00 0.00 0.00 1.28
3422 4822 7.346436 TCTTTTACTCCCTCCGTTCCTAAATAT 59.654 37.037 0.00 0.00 0.00 1.28
3423 4823 6.669154 TCTTTTACTCCCTCCGTTCCTAAATA 59.331 38.462 0.00 0.00 0.00 1.40
3424 4824 5.486419 TCTTTTACTCCCTCCGTTCCTAAAT 59.514 40.000 0.00 0.00 0.00 1.40
3425 4825 4.840115 TCTTTTACTCCCTCCGTTCCTAAA 59.160 41.667 0.00 0.00 0.00 1.85
3426 4826 4.221482 GTCTTTTACTCCCTCCGTTCCTAA 59.779 45.833 0.00 0.00 0.00 2.69
3427 4827 3.766051 GTCTTTTACTCCCTCCGTTCCTA 59.234 47.826 0.00 0.00 0.00 2.94
3428 4828 2.566279 GTCTTTTACTCCCTCCGTTCCT 59.434 50.000 0.00 0.00 0.00 3.36
3429 4829 2.566279 AGTCTTTTACTCCCTCCGTTCC 59.434 50.000 0.00 0.00 30.33 3.62
3430 4830 3.957591 AGTCTTTTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 30.33 3.95
3431 4831 5.731591 CAATAGTCTTTTACTCCCTCCGTT 58.268 41.667 0.00 0.00 39.80 4.44
3432 4832 4.382793 GCAATAGTCTTTTACTCCCTCCGT 60.383 45.833 0.00 0.00 39.80 4.69
3433 4833 4.120589 GCAATAGTCTTTTACTCCCTCCG 58.879 47.826 0.00 0.00 39.80 4.63
3434 4834 5.119694 CAGCAATAGTCTTTTACTCCCTCC 58.880 45.833 0.00 0.00 39.80 4.30
3435 4835 4.572795 GCAGCAATAGTCTTTTACTCCCTC 59.427 45.833 0.00 0.00 39.80 4.30
3436 4836 4.518249 GCAGCAATAGTCTTTTACTCCCT 58.482 43.478 0.00 0.00 39.80 4.20
3437 4837 3.309954 CGCAGCAATAGTCTTTTACTCCC 59.690 47.826 0.00 0.00 39.80 4.30
3438 4838 4.522297 CGCAGCAATAGTCTTTTACTCC 57.478 45.455 0.00 0.00 39.80 3.85
3469 4869 6.759497 AAGCTATGGTTTGTTCCATAAGAC 57.241 37.500 6.84 1.28 45.93 3.01
3477 4877 6.919721 TGGTCATAAAAGCTATGGTTTGTTC 58.080 36.000 0.00 0.00 33.41 3.18
3513 4913 6.718294 ACTCCCTTCGTTCCTAAATTTATGT 58.282 36.000 0.00 0.00 0.00 2.29
3514 4914 7.985752 AGTACTCCCTTCGTTCCTAAATTTATG 59.014 37.037 0.00 0.00 0.00 1.90
3515 4915 8.087303 AGTACTCCCTTCGTTCCTAAATTTAT 57.913 34.615 0.00 0.00 0.00 1.40
3516 4916 7.486407 AGTACTCCCTTCGTTCCTAAATTTA 57.514 36.000 0.00 0.00 0.00 1.40
3517 4917 6.370186 AGTACTCCCTTCGTTCCTAAATTT 57.630 37.500 0.00 0.00 0.00 1.82
3518 4918 6.666980 ACTAGTACTCCCTTCGTTCCTAAATT 59.333 38.462 0.00 0.00 0.00 1.82
3519 4919 6.193504 ACTAGTACTCCCTTCGTTCCTAAAT 58.806 40.000 0.00 0.00 0.00 1.40
3520 4920 5.574188 ACTAGTACTCCCTTCGTTCCTAAA 58.426 41.667 0.00 0.00 0.00 1.85
3521 4921 5.184892 ACTAGTACTCCCTTCGTTCCTAA 57.815 43.478 0.00 0.00 0.00 2.69
3522 4922 4.851639 ACTAGTACTCCCTTCGTTCCTA 57.148 45.455 0.00 0.00 0.00 2.94
3523 4923 3.735720 ACTAGTACTCCCTTCGTTCCT 57.264 47.619 0.00 0.00 0.00 3.36
3524 4924 4.021632 ACAAACTAGTACTCCCTTCGTTCC 60.022 45.833 0.00 0.00 0.00 3.62
3525 4925 5.131594 ACAAACTAGTACTCCCTTCGTTC 57.868 43.478 0.00 0.00 0.00 3.95
3526 4926 5.336293 GCTACAAACTAGTACTCCCTTCGTT 60.336 44.000 0.00 0.00 0.00 3.85
3527 4927 4.157472 GCTACAAACTAGTACTCCCTTCGT 59.843 45.833 0.00 0.00 0.00 3.85
3528 4928 4.398673 AGCTACAAACTAGTACTCCCTTCG 59.601 45.833 0.00 0.00 0.00 3.79
3529 4929 5.918426 AGCTACAAACTAGTACTCCCTTC 57.082 43.478 0.00 0.00 0.00 3.46
3530 4930 6.683312 AAAGCTACAAACTAGTACTCCCTT 57.317 37.500 0.00 0.00 0.00 3.95
3531 4931 7.787623 TTAAAGCTACAAACTAGTACTCCCT 57.212 36.000 0.00 0.00 0.00 4.20
3532 4932 8.715998 GTTTTAAAGCTACAAACTAGTACTCCC 58.284 37.037 0.00 0.00 0.00 4.30
3533 4933 9.264719 TGTTTTAAAGCTACAAACTAGTACTCC 57.735 33.333 0.00 0.00 32.58 3.85
3535 4935 9.603921 TGTGTTTTAAAGCTACAAACTAGTACT 57.396 29.630 0.00 0.00 32.58 2.73
3536 4936 9.859692 CTGTGTTTTAAAGCTACAAACTAGTAC 57.140 33.333 13.55 6.69 32.58 2.73
3537 4937 9.820725 TCTGTGTTTTAAAGCTACAAACTAGTA 57.179 29.630 13.55 0.00 32.58 1.82
3538 4938 8.726870 TCTGTGTTTTAAAGCTACAAACTAGT 57.273 30.769 13.55 0.00 32.58 2.57
3539 4939 8.283291 CCTCTGTGTTTTAAAGCTACAAACTAG 58.717 37.037 13.55 11.87 32.58 2.57
3545 4945 5.043737 ACCCTCTGTGTTTTAAAGCTACA 57.956 39.130 3.62 5.63 0.00 2.74
3553 4953 7.608761 GGATACATGTAAACCCTCTGTGTTTTA 59.391 37.037 10.14 0.00 37.18 1.52
3574 4974 7.924412 TCCTATAAACTGAACACGATTGGATAC 59.076 37.037 0.00 0.00 0.00 2.24
3576 4976 6.884832 TCCTATAAACTGAACACGATTGGAT 58.115 36.000 0.00 0.00 0.00 3.41
3577 4977 6.288941 TCCTATAAACTGAACACGATTGGA 57.711 37.500 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.