Multiple sequence alignment - TraesCS5B01G190700

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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 TraesCS5B01G190700 chr5B 100.000 5085 0 0 1 5085 344611934 344617018 0.000000e+00 9391
1 TraesCS5B01G190700 chr5B 100.000 2562 0 0 5438 7999 344617371 344619932 0.000000e+00 4732
2 TraesCS5B01G190700 chr5B 90.164 122 6 4 3882 4000 344615933 344615815 3.870000e-33 154
3 TraesCS5B01G190700 chr5A 93.581 3957 159 38 1 3889 395920595 395916666 0.000000e+00 5812
4 TraesCS5B01G190700 chr5A 95.248 2483 92 11 5536 7999 395914779 395912304 0.000000e+00 3908
5 TraesCS5B01G190700 chr5A 94.159 565 28 4 3995 4555 395916669 395916106 0.000000e+00 856
6 TraesCS5B01G190700 chr5A 89.066 503 20 4 4583 5085 395915484 395915017 6.910000e-165 592
7 TraesCS5B01G190700 chr5D 94.821 3109 105 23 815 3889 301571856 301574942 0.000000e+00 4798
8 TraesCS5B01G190700 chr5D 95.382 2490 94 10 5528 7999 301576849 301579335 0.000000e+00 3941
9 TraesCS5B01G190700 chr5D 87.799 836 46 22 1 798 301570949 301571766 0.000000e+00 928
10 TraesCS5B01G190700 chr5D 94.286 560 27 1 3996 4555 301574940 301575494 0.000000e+00 852
11 TraesCS5B01G190700 chr5D 96.419 391 9 3 4580 4970 301576141 301576526 2.430000e-179 640
12 TraesCS5B01G190700 chrUn 91.379 232 8 1 1 220 476731906 476732137 2.800000e-79 307
13 TraesCS5B01G190700 chr1A 75.137 366 74 11 4041 4404 528058209 528057859 1.070000e-33 156
14 TraesCS5B01G190700 chr1B 90.179 112 7 4 3886 3996 131502770 131502662 8.370000e-30 143
15 TraesCS5B01G190700 chr1B 92.941 85 3 2 3929 4013 428810790 428810871 3.920000e-23 121
16 TraesCS5B01G190700 chr1B 88.660 97 7 4 3929 4025 325812613 325812521 1.820000e-21 115
17 TraesCS5B01G190700 chr7D 89.076 119 6 4 3886 3997 613870636 613870754 3.010000e-29 141
18 TraesCS5B01G190700 chr6D 88.430 121 9 4 3881 3996 382346860 382346980 3.010000e-29 141
19 TraesCS5B01G190700 chr6D 87.931 116 10 4 3886 3997 462028367 462028482 5.040000e-27 134
20 TraesCS5B01G190700 chr2D 89.474 114 7 4 3886 3994 627911300 627911187 1.080000e-28 139
21 TraesCS5B01G190700 chr2D 88.136 118 9 4 3884 3996 627911183 627911300 1.400000e-27 135
22 TraesCS5B01G190700 chr1D 89.189 111 8 3 3886 3996 23007776 23007882 1.400000e-27 135
23 TraesCS5B01G190700 chr1D 87.629 97 8 4 3929 4025 225704852 225704760 8.490000e-20 110
24 TraesCS5B01G190700 chr6A 89.189 111 7 4 3886 3996 83356701 83356596 5.040000e-27 134
25 TraesCS5B01G190700 chr4D 97.183 71 2 0 3929 3999 334164485 334164555 3.920000e-23 121
26 TraesCS5B01G190700 chr4D 94.737 76 3 1 3929 4004 435010436 435010362 5.070000e-22 117
27 TraesCS5B01G190700 chr3B 83.478 115 14 3 3886 3996 5745675 5745788 1.420000e-17 102


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 TraesCS5B01G190700 chr5B 344611934 344619932 7998 False 7061.5 9391 100.0000 1 7999 2 chr5B.!!$F1 7998
1 TraesCS5B01G190700 chr5A 395912304 395920595 8291 True 2792.0 5812 93.0135 1 7999 4 chr5A.!!$R1 7998
2 TraesCS5B01G190700 chr5D 301570949 301579335 8386 False 2231.8 4798 93.7414 1 7999 5 chr5D.!!$F1 7998

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
426 457 0.109153 TTCATCGGCTGATCCCATGG 59.891 55.000 4.63 4.14 32.72 3.66 F
1461 1578 0.105862 CCCGTATGACCCTCCACCTA 60.106 60.000 0.00 0.00 0.00 3.08 F
2235 2381 0.690762 AACCCATCGTACTTGTGGCT 59.309 50.000 0.00 0.00 0.00 4.75 F
2617 2767 2.129607 GGTGCTGCAGTTTCAACATTG 58.870 47.619 16.64 0.00 0.00 2.82 F
4069 4229 3.059097 AGATTAGGGCATGGGATCTGTT 58.941 45.455 0.00 0.00 0.00 3.16 F
4338 4498 0.850100 CCATGCCCCCTAACCATACA 59.150 55.000 0.00 0.00 0.00 2.29 F
5848 6721 0.901124 CTCCAGCTGCTTGTCCTAGT 59.099 55.000 8.66 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1660 1778 1.153765 CTTGCCAGCGTCGATGAGA 60.154 57.895 12.96 0.00 0.00 3.27 R
2525 2675 3.181434 ACCTGATACAAACCAGCAAAGGA 60.181 43.478 0.00 0.00 0.00 3.36 R
3591 3747 4.081752 ACTCAAGAGAGATGCACAAGTAGG 60.082 45.833 3.73 0.00 44.98 3.18 R
4235 4395 1.933812 GGGGTGGGAATTGGGAGGA 60.934 63.158 0.00 0.00 0.00 3.71 R
5606 6467 0.313043 CAGCCCAGTTGAACTGCTTG 59.687 55.000 19.45 12.42 44.63 4.01 R
6095 6968 0.616371 GCACTACCATGGTGGGTGTA 59.384 55.000 33.23 15.60 43.37 2.90 R
7219 8101 0.325296 TGAGACCAAGGGCTATCGGT 60.325 55.000 0.00 0.00 0.00 4.69 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
37 38 5.067674 GTGGATGCTGCCTTTGTTCATTATA 59.932 40.000 0.00 0.00 0.00 0.98
101 102 5.175856 GTCAGTAGTAGTGCACAAGAAACTG 59.824 44.000 21.04 22.14 34.54 3.16
141 142 2.922335 GCACTCGACCAAAAATGCCTTC 60.922 50.000 0.00 0.00 0.00 3.46
171 184 0.678366 TTGGAACAGCAACACGTGGT 60.678 50.000 21.57 11.47 42.39 4.16
196 209 2.043625 CTTGCTTTGCAGGAAGGCA 58.956 52.632 7.41 7.41 44.41 4.75
209 222 4.384868 GCAGGAAGGCATAAGGGTTAACTA 60.385 45.833 5.42 0.00 0.00 2.24
210 223 5.751586 CAGGAAGGCATAAGGGTTAACTAA 58.248 41.667 5.42 0.00 0.00 2.24
253 266 6.461648 CCGAGATCAAGAGGTTAAGCATCTAA 60.462 42.308 7.52 0.89 37.23 2.10
257 270 7.768120 AGATCAAGAGGTTAAGCATCTAAAGTG 59.232 37.037 7.52 3.21 37.23 3.16
285 298 8.398878 TCGGTAACAAACAGGAAATTTCTAAT 57.601 30.769 17.42 2.13 0.00 1.73
286 299 9.504708 TCGGTAACAAACAGGAAATTTCTAATA 57.495 29.630 17.42 0.00 0.00 0.98
295 308 8.040716 ACAGGAAATTTCTAATAAACTGGTCG 57.959 34.615 17.42 0.00 0.00 4.79
296 309 6.967199 CAGGAAATTTCTAATAAACTGGTCGC 59.033 38.462 17.42 0.00 0.00 5.19
303 322 5.413499 TCTAATAAACTGGTCGCCTACAAC 58.587 41.667 0.00 0.00 0.00 3.32
313 332 3.751698 GGTCGCCTACAACTTCAGAAAAT 59.248 43.478 0.00 0.00 0.00 1.82
339 358 4.406069 CACAAATCGACATGGTTAGCTTG 58.594 43.478 0.00 0.00 0.00 4.01
361 380 2.280186 GATCCCAGCTAACCGCGG 60.280 66.667 26.86 26.86 45.59 6.46
369 388 2.433664 CTAACCGCGGCGAACCTT 60.434 61.111 28.58 13.78 0.00 3.50
370 389 2.030862 TAACCGCGGCGAACCTTT 59.969 55.556 28.58 12.96 0.00 3.11
371 390 1.571215 CTAACCGCGGCGAACCTTTT 61.571 55.000 28.58 12.13 0.00 2.27
372 391 1.843734 TAACCGCGGCGAACCTTTTG 61.844 55.000 28.58 6.71 0.00 2.44
426 457 0.109153 TTCATCGGCTGATCCCATGG 59.891 55.000 4.63 4.14 32.72 3.66
525 556 2.124693 CAGAGCGGGAGAGGGAGAC 61.125 68.421 0.00 0.00 0.00 3.36
537 568 2.774234 AGAGGGAGACAGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
538 569 2.771943 GAGGGAGACAGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
539 570 2.774234 AGGGAGACAGAGAGAGAGAGAG 59.226 54.545 0.00 0.00 0.00 3.20
540 571 2.771943 GGGAGACAGAGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
541 572 3.181461 GGGAGACAGAGAGAGAGAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
542 573 3.706594 GGAGACAGAGAGAGAGAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
543 574 4.346418 GGAGACAGAGAGAGAGAGAGAGAT 59.654 50.000 0.00 0.00 0.00 2.75
544 575 5.540337 GGAGACAGAGAGAGAGAGAGAGATA 59.460 48.000 0.00 0.00 0.00 1.98
545 576 6.295011 GGAGACAGAGAGAGAGAGAGAGATAG 60.295 50.000 0.00 0.00 0.00 2.08
546 577 5.541868 AGACAGAGAGAGAGAGAGAGATAGG 59.458 48.000 0.00 0.00 0.00 2.57
564 595 3.948719 TTCGTGCCTGTGGGGGTC 61.949 66.667 0.00 0.00 35.12 4.46
572 603 1.908793 CTGTGGGGGTCTGTCGTCT 60.909 63.158 0.00 0.00 0.00 4.18
636 667 1.379977 TCCGGGAGCACGAGAGATT 60.380 57.895 0.00 0.00 35.47 2.40
678 717 2.510382 AGGAGACGATAGGACAGGAAGA 59.490 50.000 0.00 0.00 43.77 2.87
751 790 4.385865 CCCATGTAAAGCCCACTTATGGTA 60.386 45.833 0.00 0.00 45.66 3.25
782 821 1.059098 ATGTCAGTGAACAGGGCTCA 58.941 50.000 0.00 0.00 31.50 4.26
827 939 4.148825 CAGGGCCGTCGGAAGAGG 62.149 72.222 17.49 0.00 43.49 3.69
1302 1419 0.744281 CGCTTCTTCTCCTCCTCCTC 59.256 60.000 0.00 0.00 0.00 3.71
1304 1421 1.342975 GCTTCTTCTCCTCCTCCTCCT 60.343 57.143 0.00 0.00 0.00 3.69
1461 1578 0.105862 CCCGTATGACCCTCCACCTA 60.106 60.000 0.00 0.00 0.00 3.08
1519 1637 0.948141 GCTTTCTCACAGTGCTCGCT 60.948 55.000 0.00 0.00 0.00 4.93
1660 1778 1.135083 CCGTCTCGCACCTCTAACATT 60.135 52.381 0.00 0.00 0.00 2.71
1718 1836 0.739112 GCCAGTTGCTTCTCCTCTCG 60.739 60.000 0.00 0.00 36.87 4.04
1720 1838 1.001406 CCAGTTGCTTCTCCTCTCGTT 59.999 52.381 0.00 0.00 0.00 3.85
1726 1868 2.029828 TGCTTCTCCTCTCGTTCTTGAC 60.030 50.000 0.00 0.00 0.00 3.18
1789 1933 5.466728 GTGTATCACTGTTTTGAAGCAGAGA 59.533 40.000 13.44 11.26 39.97 3.10
1925 2071 6.187727 TCTGTCAGGTTTTTCTACCATTCT 57.812 37.500 0.00 0.00 40.82 2.40
1985 2131 9.823647 ACTGTTCACATCCTCTATTAGTATTTG 57.176 33.333 0.00 0.00 0.00 2.32
1986 2132 8.662781 TGTTCACATCCTCTATTAGTATTTGC 57.337 34.615 0.00 0.00 0.00 3.68
2020 2166 4.787083 CGCAAGTGTTGTTAACGTTTTGTA 59.213 37.500 5.91 0.00 0.00 2.41
2141 2287 9.013229 CCTATGCACCTTATAATTGAATGCTTA 57.987 33.333 0.00 0.00 32.81 3.09
2145 2291 8.503196 TGCACCTTATAATTGAATGCTTATACG 58.497 33.333 0.00 0.00 32.81 3.06
2224 2370 2.363788 TCAAGACGAGAAACCCATCG 57.636 50.000 0.00 0.00 44.36 3.84
2235 2381 0.690762 AACCCATCGTACTTGTGGCT 59.309 50.000 0.00 0.00 0.00 4.75
2239 2385 2.161609 CCCATCGTACTTGTGGCTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
2424 2570 6.916360 ACAGCCTCAGAAAATTTTATGGAA 57.084 33.333 21.86 6.30 30.74 3.53
2425 2571 7.486407 ACAGCCTCAGAAAATTTTATGGAAT 57.514 32.000 21.86 6.66 30.74 3.01
2525 2675 3.891977 GGCTCAGTTTTCTTTCCTTTCCT 59.108 43.478 0.00 0.00 0.00 3.36
2617 2767 2.129607 GGTGCTGCAGTTTCAACATTG 58.870 47.619 16.64 0.00 0.00 2.82
2669 2819 4.013267 ACTGTTCAGGATCTTGAGGTTG 57.987 45.455 7.65 3.29 0.00 3.77
2699 2849 4.928615 TGAAACAACAACTTCAAAGCAAGG 59.071 37.500 0.00 0.00 0.00 3.61
2704 2854 3.356290 ACAACTTCAAAGCAAGGAGTGT 58.644 40.909 0.00 0.00 0.00 3.55
2725 2875 9.857957 GAGTGTACTTATACTTCTAAGCTGTTT 57.142 33.333 0.00 0.00 32.93 2.83
2812 2962 7.047891 CCATGTAGTCAGGTATACAAATGTGT 58.952 38.462 5.01 0.00 42.09 3.72
3053 3203 4.192317 GGAGCTAAGTAAACCTGTCATGG 58.808 47.826 0.00 0.00 0.00 3.66
3099 3249 9.486497 TGCTCAAATGCAAAATTACTTATTCAA 57.514 25.926 0.00 0.00 40.29 2.69
3135 3285 6.823182 TGTGTTGAGTATACTTGGGATTCATG 59.177 38.462 6.88 0.00 0.00 3.07
3288 3438 4.020128 GGTAGATTGAGTTCACTGGAAGGT 60.020 45.833 0.00 0.00 39.30 3.50
3458 3614 9.853921 CTTTTCTTGCATTTCTGATTGTTAAAC 57.146 29.630 0.00 0.00 0.00 2.01
3487 3643 8.420222 TGAAATTGTTTCATTGGACTGTTGTAT 58.580 29.630 1.24 0.00 44.21 2.29
3490 3646 4.826733 TGTTTCATTGGACTGTTGTATGCT 59.173 37.500 0.00 0.00 0.00 3.79
3591 3747 8.450964 TCTTATGCTGCTAACTTTTGTATTGAC 58.549 33.333 0.00 0.00 0.00 3.18
3893 4049 9.744468 TTTTGTTGCTTCTTTTTATACTTCCTC 57.256 29.630 0.00 0.00 0.00 3.71
3894 4050 7.448748 TGTTGCTTCTTTTTATACTTCCTCC 57.551 36.000 0.00 0.00 0.00 4.30
3895 4051 6.148811 TGTTGCTTCTTTTTATACTTCCTCCG 59.851 38.462 0.00 0.00 0.00 4.63
3896 4052 5.801380 TGCTTCTTTTTATACTTCCTCCGT 58.199 37.500 0.00 0.00 0.00 4.69
3897 4053 6.235664 TGCTTCTTTTTATACTTCCTCCGTT 58.764 36.000 0.00 0.00 0.00 4.44
3898 4054 6.370718 TGCTTCTTTTTATACTTCCTCCGTTC 59.629 38.462 0.00 0.00 0.00 3.95
3899 4055 6.183360 GCTTCTTTTTATACTTCCTCCGTTCC 60.183 42.308 0.00 0.00 0.00 3.62
3900 4056 6.616237 TCTTTTTATACTTCCTCCGTTCCT 57.384 37.500 0.00 0.00 0.00 3.36
3901 4057 7.722949 TCTTTTTATACTTCCTCCGTTCCTA 57.277 36.000 0.00 0.00 0.00 2.94
3902 4058 8.137745 TCTTTTTATACTTCCTCCGTTCCTAA 57.862 34.615 0.00 0.00 0.00 2.69
3903 4059 8.596293 TCTTTTTATACTTCCTCCGTTCCTAAA 58.404 33.333 0.00 0.00 0.00 1.85
3904 4060 9.392259 CTTTTTATACTTCCTCCGTTCCTAAAT 57.608 33.333 0.00 0.00 0.00 1.40
3910 4066 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3911 4067 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3912 4068 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3913 4069 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
3914 4070 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
3915 4071 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
3916 4072 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3957 4113 7.297936 ACATCCGTATGTAGTTCATATTGGA 57.702 36.000 12.80 12.80 44.66 3.53
3958 4114 7.732025 ACATCCGTATGTAGTTCATATTGGAA 58.268 34.615 13.81 3.55 44.66 3.53
3959 4115 8.375506 ACATCCGTATGTAGTTCATATTGGAAT 58.624 33.333 13.81 6.58 44.66 3.01
3960 4116 8.873830 CATCCGTATGTAGTTCATATTGGAATC 58.126 37.037 13.81 0.00 43.20 2.52
3961 4117 8.190326 TCCGTATGTAGTTCATATTGGAATCT 57.810 34.615 9.72 0.00 40.31 2.40
3962 4118 8.304596 TCCGTATGTAGTTCATATTGGAATCTC 58.695 37.037 9.72 0.00 40.31 2.75
3963 4119 8.307483 CCGTATGTAGTTCATATTGGAATCTCT 58.693 37.037 5.56 0.00 40.54 3.10
3990 4146 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3991 4147 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
3992 4148 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
3993 4149 7.953752 AGACTTATATTTAGGAACGGAGGAAG 58.046 38.462 0.00 0.00 0.00 3.46
3994 4150 7.564292 AGACTTATATTTAGGAACGGAGGAAGT 59.436 37.037 0.00 0.00 0.00 3.01
3997 4153 8.537728 TTATATTTAGGAACGGAGGAAGTACA 57.462 34.615 0.00 0.00 0.00 2.90
4008 4164 9.159364 GAACGGAGGAAGTACAAATTTATAGTT 57.841 33.333 0.00 0.00 0.00 2.24
4069 4229 3.059097 AGATTAGGGCATGGGATCTGTT 58.941 45.455 0.00 0.00 0.00 3.16
4141 4301 7.944554 TGGGAAATTGACAGAGAAGTTTATTCT 59.055 33.333 0.00 0.00 0.00 2.40
4184 4344 4.569943 TGGTGCAAGATTAGACAAGAGAC 58.430 43.478 0.00 0.00 0.00 3.36
4185 4345 4.040339 TGGTGCAAGATTAGACAAGAGACA 59.960 41.667 0.00 0.00 0.00 3.41
4254 4414 1.935931 CCTCCCAATTCCCACCCCT 60.936 63.158 0.00 0.00 0.00 4.79
4278 4438 3.193903 CCCTTGTTAATAAAACGGTGGGG 59.806 47.826 0.00 0.00 0.00 4.96
4300 4460 3.495100 GGTTGGACTCTCAACTGTCATGT 60.495 47.826 7.51 0.00 44.52 3.21
4338 4498 0.850100 CCATGCCCCCTAACCATACA 59.150 55.000 0.00 0.00 0.00 2.29
4342 4502 1.926665 TGCCCCCTAACCATACAATGT 59.073 47.619 0.00 0.00 0.00 2.71
4388 4548 2.158295 TCCTCACCCCCTAGCTCTAATC 60.158 54.545 0.00 0.00 0.00 1.75
4406 4566 2.443958 TCACACCCAACCAAACATGA 57.556 45.000 0.00 0.00 0.00 3.07
4464 4624 5.875224 TCTCTGGATCCACAAAACATAACA 58.125 37.500 11.44 0.00 0.00 2.41
4484 4644 4.122776 ACACACTCTTAAACAGACTGCAG 58.877 43.478 13.48 13.48 0.00 4.41
4702 5489 4.829492 AGGAATGGAGTCTTGGAAACTTTG 59.171 41.667 0.00 0.00 0.00 2.77
4710 5497 3.975035 GTCTTGGAAACTTTGTCGCAATC 59.025 43.478 0.00 0.00 0.00 2.67
4770 5557 5.818857 GCCTTATTTGATCAAATGGCATGTT 59.181 36.000 35.33 19.01 43.62 2.71
4771 5558 6.316890 GCCTTATTTGATCAAATGGCATGTTT 59.683 34.615 35.33 18.47 43.62 2.83
4772 5559 7.148205 GCCTTATTTGATCAAATGGCATGTTTT 60.148 33.333 35.33 17.92 43.62 2.43
4972 5759 4.106197 GCTCTAGAACTATTGGACACACG 58.894 47.826 0.00 0.00 0.00 4.49
4973 5760 4.380655 GCTCTAGAACTATTGGACACACGT 60.381 45.833 0.00 0.00 0.00 4.49
4975 5762 2.413837 AGAACTATTGGACACACGTGC 58.586 47.619 17.22 0.00 0.00 5.34
4978 5765 2.955614 ACTATTGGACACACGTGCTAC 58.044 47.619 17.22 6.69 33.94 3.58
5002 5789 5.812642 CGTTATCTCTTAGGCACTGTTGAAT 59.187 40.000 0.00 0.00 41.52 2.57
5004 5791 4.890158 TCTCTTAGGCACTGTTGAATGA 57.110 40.909 0.00 0.00 41.52 2.57
5067 5854 6.374053 TGATCACAACATGTAATCCGTTGAAT 59.626 34.615 0.00 2.18 42.03 2.57
5072 5859 6.208599 ACAACATGTAATCCGTTGAATTCCTT 59.791 34.615 0.00 0.00 42.03 3.36
5073 5860 6.194796 ACATGTAATCCGTTGAATTCCTTG 57.805 37.500 0.00 0.00 0.00 3.61
5075 5862 4.075682 TGTAATCCGTTGAATTCCTTGCA 58.924 39.130 2.27 0.00 0.00 4.08
5470 6257 6.647334 TGATGGAATAAAGTTTCAGCACAA 57.353 33.333 0.00 0.00 0.00 3.33
5478 6265 2.825205 AGTTTCAGCACAATGGTTTGC 58.175 42.857 0.00 0.00 36.22 3.68
5492 6279 9.421806 CACAATGGTTTGCTTTATATTTTCTGA 57.578 29.630 0.00 0.00 36.22 3.27
5493 6280 9.643693 ACAATGGTTTGCTTTATATTTTCTGAG 57.356 29.630 0.00 0.00 36.22 3.35
5494 6281 9.643693 CAATGGTTTGCTTTATATTTTCTGAGT 57.356 29.630 0.00 0.00 0.00 3.41
5496 6283 9.643693 ATGGTTTGCTTTATATTTTCTGAGTTG 57.356 29.630 0.00 0.00 0.00 3.16
5497 6284 8.855110 TGGTTTGCTTTATATTTTCTGAGTTGA 58.145 29.630 0.00 0.00 0.00 3.18
5498 6285 9.860898 GGTTTGCTTTATATTTTCTGAGTTGAT 57.139 29.630 0.00 0.00 0.00 2.57
5534 6321 9.598517 CTTTTTGGTATATTGTATTTGCACCAT 57.401 29.630 0.00 0.00 34.73 3.55
5580 6441 8.055279 TCTGGAAGATGTTTTATCAAACCATC 57.945 34.615 0.20 2.07 38.67 3.51
5583 6444 7.399765 TGGAAGATGTTTTATCAAACCATCCAT 59.600 33.333 5.79 0.00 41.60 3.41
5595 6456 5.827797 TCAAACCATCCATGTAAGATTAGGC 59.172 40.000 0.00 0.00 0.00 3.93
5596 6457 4.373156 ACCATCCATGTAAGATTAGGCC 57.627 45.455 0.00 0.00 0.00 5.19
5597 6458 3.721575 ACCATCCATGTAAGATTAGGCCA 59.278 43.478 5.01 0.00 0.00 5.36
5605 6466 6.823689 CCATGTAAGATTAGGCCACATATACC 59.176 42.308 5.01 0.00 0.00 2.73
5606 6467 6.368779 TGTAAGATTAGGCCACATATACCC 57.631 41.667 5.01 0.00 0.00 3.69
5612 6473 1.143684 AGGCCACATATACCCAAGCAG 59.856 52.381 5.01 0.00 0.00 4.24
5617 6478 4.269183 CCACATATACCCAAGCAGTTCAA 58.731 43.478 0.00 0.00 0.00 2.69
5619 6480 4.943705 CACATATACCCAAGCAGTTCAACT 59.056 41.667 0.00 0.00 0.00 3.16
5628 6490 1.656441 CAGTTCAACTGGGCTGTGC 59.344 57.895 9.96 0.00 42.35 4.57
5705 6578 7.634671 TCATACGAGACAAATAGTTACTGGA 57.365 36.000 0.00 0.00 0.00 3.86
5840 6713 2.808919 TCTACTACACTCCAGCTGCTT 58.191 47.619 8.66 0.00 0.00 3.91
5848 6721 0.901124 CTCCAGCTGCTTGTCCTAGT 59.099 55.000 8.66 0.00 0.00 2.57
6095 6968 1.553704 GTCGACCACCTTCCCTACATT 59.446 52.381 3.51 0.00 0.00 2.71
6240 7116 3.254166 CCCTTTCCATTTCATATCCAGCG 59.746 47.826 0.00 0.00 0.00 5.18
6261 7137 2.743553 TCATCAGGAGTCAGATGAGCA 58.256 47.619 18.33 3.20 44.04 4.26
6569 7445 5.853936 TGATAGGAATGTAGTATGGTGCAC 58.146 41.667 8.80 8.80 0.00 4.57
6738 7616 7.328277 TCAATAACTTATGTTGCATACCCAC 57.672 36.000 4.33 0.00 37.59 4.61
6937 7819 1.003839 GGCCTCGATGAACACACCA 60.004 57.895 0.00 0.00 0.00 4.17
7108 7990 2.440980 GGCCCAATCCCACTGAGC 60.441 66.667 0.00 0.00 0.00 4.26
7111 7993 1.751927 CCCAATCCCACTGAGCAGC 60.752 63.158 0.00 0.00 0.00 5.25
7146 8028 0.804989 CCAATTGCACCCGAAGAGAC 59.195 55.000 0.00 0.00 0.00 3.36
7150 8032 0.389817 TTGCACCCGAAGAGACGATG 60.390 55.000 0.00 0.00 35.09 3.84
7153 8035 1.866063 GCACCCGAAGAGACGATGATC 60.866 57.143 0.00 0.00 35.09 2.92
7156 8038 1.950216 CCCGAAGAGACGATGATCTCA 59.050 52.381 5.63 0.00 46.51 3.27
7162 8044 5.390461 CGAAGAGACGATGATCTCACTATCC 60.390 48.000 5.63 0.00 46.51 2.59
7163 8045 5.241403 AGAGACGATGATCTCACTATCCT 57.759 43.478 5.63 0.00 46.51 3.24
7198 8080 2.607750 GCCTGGTGGAGTCTCCCA 60.608 66.667 16.60 7.02 35.03 4.37
7201 8083 0.326048 CCTGGTGGAGTCTCCCATCT 60.326 60.000 16.60 0.00 38.16 2.90
7210 8092 0.598680 GTCTCCCATCTTCATCGGCG 60.599 60.000 0.00 0.00 0.00 6.46
7213 8095 0.179084 TCCCATCTTCATCGGCGAAC 60.179 55.000 15.93 0.00 0.00 3.95
7219 8101 1.542472 TCTTCATCGGCGAACTGTACA 59.458 47.619 15.93 0.00 0.00 2.90
7247 8129 1.616187 CCCTTGGTCTCAGTCGTCCTA 60.616 57.143 0.00 0.00 0.00 2.94
7251 8133 2.366533 TGGTCTCAGTCGTCCTACATC 58.633 52.381 0.00 0.00 0.00 3.06
7286 8168 7.453126 TGTTATTGAAAAAGGGTACATGATGGT 59.547 33.333 0.00 0.00 0.00 3.55
7291 8173 7.054124 TGAAAAAGGGTACATGATGGTCTATC 58.946 38.462 0.00 0.00 36.29 2.08
7292 8174 4.873746 AAGGGTACATGATGGTCTATCG 57.126 45.455 0.00 0.00 38.71 2.92
7348 8231 7.971183 ATTCTAGACTGTTTTGGAAGAGAAC 57.029 36.000 0.00 0.00 31.04 3.01
7349 8232 6.479972 TCTAGACTGTTTTGGAAGAGAACA 57.520 37.500 0.00 0.00 31.04 3.18
7385 8268 0.938008 GGCTATACCTTGTTGCGAGC 59.062 55.000 0.00 0.00 34.51 5.03
7428 8311 1.599047 CGTGAAGCAGGACCCTCAT 59.401 57.895 0.00 0.00 0.00 2.90
7450 8333 0.835971 TGTTAGGGTCTCCAGCTGCA 60.836 55.000 8.66 0.00 34.83 4.41
7700 8583 1.001378 GCACGAAGCTGTTGTTCCAAT 60.001 47.619 0.00 0.00 41.15 3.16
7737 8620 7.864108 TGTAAGTATCAGGTTTGATGGAATG 57.136 36.000 0.48 0.00 43.76 2.67
7865 8748 2.288518 GGGTTTGGTTTTGCTAATGCGA 60.289 45.455 0.00 0.00 43.34 5.10
7866 8749 3.584834 GGTTTGGTTTTGCTAATGCGAT 58.415 40.909 0.00 0.00 43.34 4.58
7922 8807 0.531753 TTGCGCTGAACTGTACTGCA 60.532 50.000 9.73 0.00 33.57 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.523711 CAACAGAGTGGTGGTGCGT 60.524 57.895 0.00 0.00 29.70 5.24
101 102 6.087291 CGAGTGCAAATCTCTTGTTTCATTTC 59.913 38.462 0.00 0.00 0.00 2.17
141 142 6.089820 GTGTTGCTGTTCCAATTCATTGTATG 59.910 38.462 0.00 0.00 36.06 2.39
253 266 2.616842 CCTGTTTGTTACCGAAGCACTT 59.383 45.455 0.00 0.00 0.00 3.16
257 270 3.974871 TTTCCTGTTTGTTACCGAAGC 57.025 42.857 0.00 0.00 0.00 3.86
285 298 3.069872 TGAAGTTGTAGGCGACCAGTTTA 59.930 43.478 0.00 0.00 0.00 2.01
286 299 2.158871 TGAAGTTGTAGGCGACCAGTTT 60.159 45.455 0.00 0.00 0.00 2.66
313 332 2.183478 ACCATGTCGATTTGTGCAGA 57.817 45.000 0.00 0.00 0.00 4.26
339 358 1.889573 GGTTAGCTGGGATCGCAGC 60.890 63.158 42.15 42.15 44.20 5.25
345 364 4.547367 GCCGCGGTTAGCTGGGAT 62.547 66.667 28.70 0.00 45.59 3.85
361 380 1.285950 GGAGTGCCAAAAGGTTCGC 59.714 57.895 0.00 0.00 0.00 4.70
371 390 0.965866 CCGTCTCTAGTGGAGTGCCA 60.966 60.000 3.16 0.00 43.47 4.92
372 391 1.810532 CCGTCTCTAGTGGAGTGCC 59.189 63.158 3.16 0.00 42.40 5.01
373 392 1.139947 GCCGTCTCTAGTGGAGTGC 59.860 63.158 3.16 2.07 42.40 4.40
374 393 0.888619 TTGCCGTCTCTAGTGGAGTG 59.111 55.000 3.16 0.00 42.40 3.51
426 457 1.399089 GGATAGGCTAGATCGCTCGTC 59.601 57.143 0.00 0.00 0.00 4.20
525 556 5.815233 ACCTATCTCTCTCTCTCTCTCTG 57.185 47.826 0.00 0.00 0.00 3.35
537 568 1.751924 ACAGGCACGAACCTATCTCTC 59.248 52.381 0.67 0.00 38.26 3.20
538 569 1.478510 CACAGGCACGAACCTATCTCT 59.521 52.381 0.67 0.00 38.26 3.10
539 570 1.471676 CCACAGGCACGAACCTATCTC 60.472 57.143 0.67 0.00 38.26 2.75
540 571 0.537188 CCACAGGCACGAACCTATCT 59.463 55.000 0.67 0.00 38.26 1.98
541 572 0.462047 CCCACAGGCACGAACCTATC 60.462 60.000 0.67 0.00 38.26 2.08
542 573 1.602237 CCCACAGGCACGAACCTAT 59.398 57.895 0.67 0.00 38.26 2.57
543 574 2.589157 CCCCACAGGCACGAACCTA 61.589 63.158 0.67 0.00 38.26 3.08
544 575 3.953775 CCCCACAGGCACGAACCT 61.954 66.667 0.00 0.00 42.30 3.50
546 577 4.265056 ACCCCCACAGGCACGAAC 62.265 66.667 0.00 0.00 0.00 3.95
594 625 1.139734 GAGCACGCAGGAGATCGAA 59.860 57.895 0.00 0.00 0.00 3.71
626 657 1.064803 CCAGAGTCCGAATCTCTCGTG 59.935 57.143 0.00 0.00 46.65 4.35
627 658 1.384525 CCAGAGTCCGAATCTCTCGT 58.615 55.000 0.00 0.00 46.65 4.18
636 667 1.198094 TCCCAATTGCCAGAGTCCGA 61.198 55.000 0.00 0.00 0.00 4.55
643 674 0.914644 TCTCCTCTCCCAATTGCCAG 59.085 55.000 0.00 0.00 0.00 4.85
678 717 3.257127 CGTCTCTTTCTTCTCCCACTTCT 59.743 47.826 0.00 0.00 0.00 2.85
751 790 2.106338 TCACTGACATGTGGGTCAACAT 59.894 45.455 1.15 0.00 46.36 2.71
782 821 2.912956 ACATGTGGGTCAATAGTCCAGT 59.087 45.455 0.00 0.00 0.00 4.00
827 939 4.103103 GTCAAGAAAGCCCCGCGC 62.103 66.667 0.00 0.00 37.98 6.86
832 944 0.955919 CCTGACGGTCAAGAAAGCCC 60.956 60.000 12.54 0.00 0.00 5.19
1194 1307 7.384358 TGCAATTACGATTGTATACGTACAG 57.616 36.000 0.00 0.00 43.67 2.74
1195 1308 7.933728 ATGCAATTACGATTGTATACGTACA 57.066 32.000 0.00 0.00 43.78 2.90
1356 1473 1.535015 GGAAGATGAGCTCCGACTTCG 60.535 57.143 24.42 0.00 38.13 3.79
1461 1578 1.801395 CGGCGGTTGATAACGAGATGT 60.801 52.381 0.00 0.00 0.00 3.06
1484 1601 1.953559 AAGCAGAACAAAGCGAGTCA 58.046 45.000 0.00 0.00 35.48 3.41
1490 1607 3.065925 ACTGTGAGAAAGCAGAACAAAGC 59.934 43.478 0.00 0.00 36.62 3.51
1519 1637 1.965930 GCCAACATCACACCGAGCA 60.966 57.895 0.00 0.00 0.00 4.26
1660 1778 1.153765 CTTGCCAGCGTCGATGAGA 60.154 57.895 12.96 0.00 0.00 3.27
1767 1911 6.366630 GTTCTCTGCTTCAAAACAGTGATAC 58.633 40.000 0.00 0.00 36.59 2.24
1768 1912 5.470098 GGTTCTCTGCTTCAAAACAGTGATA 59.530 40.000 0.00 0.00 36.59 2.15
1789 1933 8.655935 ACTATGAATGGAAGAAATTTCAGGTT 57.344 30.769 19.99 5.95 32.13 3.50
1827 1971 5.226396 TGCGCATTATTTACAAAAACAGCT 58.774 33.333 5.66 0.00 0.00 4.24
1870 2015 6.525629 AGCATCAGGGTGTGATAACTATTAC 58.474 40.000 0.00 0.00 44.73 1.89
1985 2131 4.561213 ACAACACTTGCGTTTCTTTAAAGC 59.439 37.500 10.51 0.00 40.99 3.51
1986 2132 6.626199 AACAACACTTGCGTTTCTTTAAAG 57.374 33.333 9.04 9.04 0.00 1.85
1999 2145 7.016466 TCAGTACAAAACGTTAACAACACTTG 58.984 34.615 0.00 2.15 0.00 3.16
2017 2163 3.515502 CCCTCAACCTGAAGATCAGTACA 59.484 47.826 6.62 0.00 42.80 2.90
2020 2166 2.836981 CTCCCTCAACCTGAAGATCAGT 59.163 50.000 6.62 0.00 42.80 3.41
2141 2287 8.037166 ACTAGACGGGACTTTTAAAAATCGTAT 58.963 33.333 13.53 13.18 0.00 3.06
2145 2291 7.430992 ACACTAGACGGGACTTTTAAAAATC 57.569 36.000 0.73 0.73 0.00 2.17
2207 2353 2.824341 AGTACGATGGGTTTCTCGTCTT 59.176 45.455 0.37 0.00 44.21 3.01
2224 2370 3.005472 GGAAAGGGAAAAGCCACAAGTAC 59.995 47.826 0.00 0.00 38.95 2.73
2226 2372 2.039418 GGAAAGGGAAAAGCCACAAGT 58.961 47.619 0.00 0.00 38.95 3.16
2235 2381 6.989759 GCTGTTATCTTTTTGGAAAGGGAAAA 59.010 34.615 0.00 0.00 42.05 2.29
2239 2385 5.467035 TGCTGTTATCTTTTTGGAAAGGG 57.533 39.130 0.00 0.00 42.05 3.95
2275 2421 4.690748 GTCCAATCACGAAGACAATCAAGA 59.309 41.667 0.00 0.00 0.00 3.02
2525 2675 3.181434 ACCTGATACAAACCAGCAAAGGA 60.181 43.478 0.00 0.00 0.00 3.36
2617 2767 7.276438 GGTTCCTCTTTCATAATGTTGAATTGC 59.724 37.037 0.00 0.00 35.64 3.56
2669 2819 7.043391 GCTTTGAAGTTGTTGTTTCAGATTACC 60.043 37.037 0.00 0.00 35.01 2.85
2699 2849 9.857957 AAACAGCTTAGAAGTATAAGTACACTC 57.142 33.333 0.00 0.00 35.57 3.51
2741 2891 9.035890 TCACTGAGTCTAAAAGGAGAATATCAA 57.964 33.333 0.00 0.00 0.00 2.57
2753 2903 8.740906 CCTTACTACATCTCACTGAGTCTAAAA 58.259 37.037 5.94 0.00 0.00 1.52
2837 2987 9.705103 CAATTAAGTGATCCCATCCCATTATAT 57.295 33.333 0.00 0.00 0.00 0.86
2898 3048 3.505680 TGTCTGAATTGCGCTGGTAAATT 59.494 39.130 9.73 5.56 0.00 1.82
3053 3203 6.039717 TGAGCAGGATACATAAAAATTGAGCC 59.960 38.462 0.00 0.00 41.41 4.70
3099 3249 8.405418 AGTATACTCAACACATACGGACATAT 57.595 34.615 0.00 0.00 31.76 1.78
3102 3252 6.327154 CAAGTATACTCAACACATACGGACA 58.673 40.000 5.70 0.00 31.76 4.02
3135 3285 7.913674 AATAAATTGAACAGGAGACTCTGTC 57.086 36.000 1.74 0.00 46.17 3.51
3288 3438 8.500753 ACAACACAAGTCTTACAATAAACAGA 57.499 30.769 0.00 0.00 0.00 3.41
3487 3643 4.111916 GCAAGAAAACAAAGTTAGCAGCA 58.888 39.130 0.00 0.00 0.00 4.41
3490 3646 4.364415 ACGCAAGAAAACAAAGTTAGCA 57.636 36.364 0.00 0.00 43.62 3.49
3591 3747 4.081752 ACTCAAGAGAGATGCACAAGTAGG 60.082 45.833 3.73 0.00 44.98 3.18
3888 4044 7.909485 AGACTTATATTTAGGAACGGAGGAA 57.091 36.000 0.00 0.00 0.00 3.36
3889 4045 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
3890 4046 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
3931 4087 9.031537 TCCAATATGAACTACATACGGATGTAT 57.968 33.333 20.64 7.28 45.42 2.29
3932 4088 8.411991 TCCAATATGAACTACATACGGATGTA 57.588 34.615 19.32 19.32 44.77 2.29
3934 4090 8.777865 ATTCCAATATGAACTACATACGGATG 57.222 34.615 5.94 5.94 43.12 3.51
3935 4091 8.816894 AGATTCCAATATGAACTACATACGGAT 58.183 33.333 0.00 0.00 43.12 4.18
3936 4092 8.190326 AGATTCCAATATGAACTACATACGGA 57.810 34.615 0.00 0.00 43.12 4.69
3937 4093 8.307483 AGAGATTCCAATATGAACTACATACGG 58.693 37.037 0.00 0.00 43.12 4.02
3964 4120 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3965 4121 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
3966 4122 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
3967 4123 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
3968 4124 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3969 4125 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3970 4126 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3971 4127 8.636213 TGTACTTCCTCCGTTCCTAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
3972 4128 8.537728 TGTACTTCCTCCGTTCCTAAATATAA 57.462 34.615 0.00 0.00 0.00 0.98
3973 4129 8.537728 TTGTACTTCCTCCGTTCCTAAATATA 57.462 34.615 0.00 0.00 0.00 0.86
3974 4130 7.427989 TTGTACTTCCTCCGTTCCTAAATAT 57.572 36.000 0.00 0.00 0.00 1.28
3975 4131 6.855763 TTGTACTTCCTCCGTTCCTAAATA 57.144 37.500 0.00 0.00 0.00 1.40
3976 4132 5.750352 TTGTACTTCCTCCGTTCCTAAAT 57.250 39.130 0.00 0.00 0.00 1.40
3977 4133 5.549742 TTTGTACTTCCTCCGTTCCTAAA 57.450 39.130 0.00 0.00 0.00 1.85
3978 4134 5.750352 ATTTGTACTTCCTCCGTTCCTAA 57.250 39.130 0.00 0.00 0.00 2.69
3979 4135 5.750352 AATTTGTACTTCCTCCGTTCCTA 57.250 39.130 0.00 0.00 0.00 2.94
3980 4136 4.635699 AATTTGTACTTCCTCCGTTCCT 57.364 40.909 0.00 0.00 0.00 3.36
3981 4137 6.997239 ATAAATTTGTACTTCCTCCGTTCC 57.003 37.500 0.00 0.00 0.00 3.62
3982 4138 8.713737 ACTATAAATTTGTACTTCCTCCGTTC 57.286 34.615 0.00 0.00 0.00 3.95
4069 4229 7.044798 CCAAACAAAGGAGTTGGAATAAAACA 58.955 34.615 0.00 0.00 41.97 2.83
4141 4301 7.147983 GCACCAATTCCCACTATACAAATAACA 60.148 37.037 0.00 0.00 0.00 2.41
4235 4395 1.933812 GGGGTGGGAATTGGGAGGA 60.934 63.158 0.00 0.00 0.00 3.71
4254 4414 4.523558 CCCACCGTTTTATTAACAAGGGAA 59.476 41.667 8.77 0.00 34.49 3.97
4278 4438 2.910688 TGACAGTTGAGAGTCCAACC 57.089 50.000 16.29 6.59 45.52 3.77
4300 4460 5.305128 GCATGGGAATTGATGAGGGATTAAA 59.695 40.000 0.00 0.00 0.00 1.52
4338 4498 9.628500 GAAGGGGTATGAGACTTTAAATACATT 57.372 33.333 0.00 0.00 0.00 2.71
4342 4502 9.847224 GATTGAAGGGGTATGAGACTTTAAATA 57.153 33.333 0.00 0.00 0.00 1.40
4388 4548 2.364970 ACATCATGTTTGGTTGGGTGTG 59.635 45.455 0.00 0.00 0.00 3.82
4406 4566 4.564041 CACTTAAGAGCTGACACTGACAT 58.436 43.478 10.09 0.00 0.00 3.06
4559 4731 8.567948 GTGAAATCATCTCCTTGTTACTTTTCA 58.432 33.333 0.00 0.00 0.00 2.69
4575 4747 8.273780 ACAAGTATTTGAGAGGTGAAATCATC 57.726 34.615 4.81 0.00 37.73 2.92
4577 4749 6.655003 GGACAAGTATTTGAGAGGTGAAATCA 59.345 38.462 4.81 0.00 37.73 2.57
4578 4750 6.655003 TGGACAAGTATTTGAGAGGTGAAATC 59.345 38.462 4.81 0.00 37.73 2.17
4579 4751 6.542821 TGGACAAGTATTTGAGAGGTGAAAT 58.457 36.000 4.81 0.00 37.73 2.17
4580 4752 5.935945 TGGACAAGTATTTGAGAGGTGAAA 58.064 37.500 4.81 0.00 37.73 2.69
4702 5489 5.095691 TGTCAAGAAGAAAAGATTGCGAC 57.904 39.130 0.00 0.00 0.00 5.19
4710 5497 7.362401 CCCATAGTTCCATGTCAAGAAGAAAAG 60.362 40.741 0.00 0.00 0.00 2.27
4770 5557 7.479352 TCAAAATAATGGAAGATGAGGCAAA 57.521 32.000 0.00 0.00 0.00 3.68
4771 5558 7.664552 ATCAAAATAATGGAAGATGAGGCAA 57.335 32.000 0.00 0.00 0.00 4.52
4772 5559 7.664552 AATCAAAATAATGGAAGATGAGGCA 57.335 32.000 0.00 0.00 0.00 4.75
4972 5759 4.043073 GTGCCTAAGAGATAACGTAGCAC 58.957 47.826 0.00 0.00 0.00 4.40
4973 5760 3.952323 AGTGCCTAAGAGATAACGTAGCA 59.048 43.478 0.00 0.00 0.00 3.49
4975 5762 5.502153 ACAGTGCCTAAGAGATAACGTAG 57.498 43.478 0.00 0.00 0.00 3.51
4978 5765 4.744570 TCAACAGTGCCTAAGAGATAACG 58.255 43.478 0.00 0.00 0.00 3.18
4986 5773 4.012374 ACCATCATTCAACAGTGCCTAAG 58.988 43.478 0.00 0.00 0.00 2.18
4989 5776 2.592102 ACCATCATTCAACAGTGCCT 57.408 45.000 0.00 0.00 0.00 4.75
5027 5814 8.815141 TGTTGTGATCATTTTTACTGAAATGG 57.185 30.769 0.00 0.00 43.74 3.16
5442 6229 5.728898 GCTGAAACTTTATTCCATCAGCGAG 60.729 44.000 9.48 0.00 46.83 5.03
5446 6233 6.258230 TGTGCTGAAACTTTATTCCATCAG 57.742 37.500 0.00 0.00 37.83 2.90
5452 6239 7.566709 CAAACCATTGTGCTGAAACTTTATTC 58.433 34.615 0.00 0.00 0.00 1.75
5470 6257 9.643693 CAACTCAGAAAATATAAAGCAAACCAT 57.356 29.630 0.00 0.00 0.00 3.55
5506 6293 9.816354 GGTGCAAATACAATATACCAAAAAGAT 57.184 29.630 0.00 0.00 0.00 2.40
5508 6295 8.994429 TGGTGCAAATACAATATACCAAAAAG 57.006 30.769 0.00 0.00 34.12 2.27
5551 6338 7.809806 GGTTTGATAAAACATCTTCCAGAACTG 59.190 37.037 7.99 0.00 34.46 3.16
5580 6441 6.823689 GGTATATGTGGCCTAATCTTACATGG 59.176 42.308 3.32 0.00 34.22 3.66
5583 6444 5.847265 TGGGTATATGTGGCCTAATCTTACA 59.153 40.000 3.32 0.00 0.00 2.41
5595 6456 3.884895 TGAACTGCTTGGGTATATGTGG 58.115 45.455 0.00 0.00 0.00 4.17
5596 6457 4.943705 AGTTGAACTGCTTGGGTATATGTG 59.056 41.667 0.00 0.00 0.00 3.21
5597 6458 4.943705 CAGTTGAACTGCTTGGGTATATGT 59.056 41.667 12.89 0.00 39.62 2.29
5605 6466 0.825010 AGCCCAGTTGAACTGCTTGG 60.825 55.000 19.45 15.76 44.63 3.61
5606 6467 0.313043 CAGCCCAGTTGAACTGCTTG 59.687 55.000 19.45 12.42 44.63 4.01
5612 6473 3.042560 GGCACAGCCCAGTTGAAC 58.957 61.111 0.00 0.00 44.06 3.18
5628 6490 9.672086 CATCTTTCTTATAAGTAGAGTTCGAGG 57.328 37.037 12.19 0.00 0.00 4.63
5688 6561 9.201989 TCATCTGTATCCAGTAACTATTTGTCT 57.798 33.333 0.00 0.00 39.82 3.41
5705 6578 8.546083 AGACATTCTAGGAGTTTCATCTGTAT 57.454 34.615 0.00 0.00 0.00 2.29
5840 6713 4.038271 TCTTAAGGGAACGACTAGGACA 57.962 45.455 1.85 0.00 0.00 4.02
5848 6721 4.159879 GGAGTGAAGATCTTAAGGGAACGA 59.840 45.833 8.25 0.00 0.00 3.85
5930 6803 9.696917 AGAACATAACTTTCTTATTTGGCAAAG 57.303 29.630 18.61 4.92 28.36 2.77
6095 6968 0.616371 GCACTACCATGGTGGGTGTA 59.384 55.000 33.23 15.60 43.37 2.90
6216 7089 4.651045 GCTGGATATGAAATGGAAAGGGTT 59.349 41.667 0.00 0.00 0.00 4.11
6240 7116 2.429971 TGCTCATCTGACTCCTGATGAC 59.570 50.000 9.81 8.39 46.18 3.06
6569 7445 0.597568 TTTTGCCGTTGCTGATCCAG 59.402 50.000 0.00 0.00 38.71 3.86
6777 7655 6.127814 CCACAAGATTCAGATTGCACTGTATT 60.128 38.462 4.42 0.00 38.79 1.89
6892 7774 2.306847 GGTTTTGGCCAGTCTGAAGAA 58.693 47.619 5.11 0.00 0.00 2.52
6937 7819 3.511934 AGACTGTCGGAATAACTGAAGCT 59.488 43.478 1.52 0.00 35.49 3.74
7138 8020 3.961477 AGTGAGATCATCGTCTCTTCG 57.039 47.619 0.00 0.00 43.96 3.79
7146 8028 5.595885 ACAACAAGGATAGTGAGATCATCG 58.404 41.667 0.00 0.00 0.00 3.84
7150 8032 6.650807 TCAACAACAACAAGGATAGTGAGATC 59.349 38.462 0.00 0.00 0.00 2.75
7153 8035 5.180117 CCTCAACAACAACAAGGATAGTGAG 59.820 44.000 0.00 0.00 0.00 3.51
7156 8038 5.163195 ACTCCTCAACAACAACAAGGATAGT 60.163 40.000 0.00 0.00 35.65 2.12
7162 8044 2.223572 GGCACTCCTCAACAACAACAAG 60.224 50.000 0.00 0.00 0.00 3.16
7163 8045 1.748493 GGCACTCCTCAACAACAACAA 59.252 47.619 0.00 0.00 0.00 2.83
7198 8080 2.165641 TGTACAGTTCGCCGATGAAGAT 59.834 45.455 0.00 0.00 0.00 2.40
7201 8083 1.670674 GGTGTACAGTTCGCCGATGAA 60.671 52.381 0.00 0.00 0.00 2.57
7210 8092 1.755380 AGGGCTATCGGTGTACAGTTC 59.245 52.381 0.00 0.00 0.00 3.01
7213 8095 1.202533 CCAAGGGCTATCGGTGTACAG 60.203 57.143 0.00 0.00 0.00 2.74
7219 8101 0.325296 TGAGACCAAGGGCTATCGGT 60.325 55.000 0.00 0.00 0.00 4.69
7247 8129 7.447374 TTTTCAATAACATGAACTCCGATGT 57.553 32.000 0.00 0.00 38.95 3.06
7251 8133 6.092748 CCCTTTTTCAATAACATGAACTCCG 58.907 40.000 0.00 0.00 38.95 4.63
7286 8168 6.782298 GTGTAGATACTACACAGCGATAGA 57.218 41.667 26.60 0.00 45.13 1.98
7368 8251 3.165058 TCAGCTCGCAACAAGGTATAG 57.835 47.619 0.00 0.00 0.00 1.31
7370 8253 2.076863 GTTCAGCTCGCAACAAGGTAT 58.923 47.619 0.00 0.00 0.00 2.73
7385 8268 4.060900 AGTGTGCACAAGATAGTGTTCAG 58.939 43.478 23.59 0.00 41.52 3.02
7428 8311 1.347707 CAGCTGGAGACCCTAACAACA 59.652 52.381 5.57 0.00 0.00 3.33
7700 8583 8.818860 ACCTGATACTTACATACCTTGTGTTTA 58.181 33.333 0.00 0.00 39.48 2.01
7922 8807 3.105283 AGCCCAAGAGATAACCGTAACT 58.895 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.