Multiple sequence alignment - TraesCS2D01G359100

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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 TraesCS2D01G359100 chr2D 100.000 5470 0 0 1 5470 460989031 460983562 0.000000e+00 10102
1 TraesCS2D01G359100 chr2A 93.950 4909 188 58 22 4845 604755094 604750210 0.000000e+00 7319
2 TraesCS2D01G359100 chr2B 93.928 4891 195 32 21 4845 542763944 542759090 0.000000e+00 7293
3 TraesCS2D01G359100 chr2B 83.864 440 44 7 629 1054 134859267 134859693 1.430000e-105 394
4 TraesCS2D01G359100 chr2B 82.927 123 9 5 5348 5470 542758398 542758288 3.490000e-17 100
5 TraesCS2D01G359100 chr4A 82.828 1089 109 31 11 1054 619802896 619801841 0.000000e+00 904
6 TraesCS2D01G359100 chr3D 84.091 528 67 11 4053 4577 598947296 598947809 1.370000e-135 494
7 TraesCS2D01G359100 chr6B 83.902 528 61 12 4053 4576 92344897 92344390 2.960000e-132 483
8 TraesCS2D01G359100 chr5B 83.333 528 64 12 4053 4576 101898772 101898265 2.980000e-127 466
9 TraesCS2D01G359100 chr7A 82.955 528 71 12 4053 4576 33836168 33836680 4.990000e-125 459
10 TraesCS2D01G359100 chr1B 79.913 458 54 18 4053 4498 641635755 641636186 8.900000e-78 302
11 TraesCS2D01G359100 chr3B 86.638 232 29 1 4053 4284 777692744 777692515 7.030000e-64 255


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 TraesCS2D01G359100 chr2D 460983562 460989031 5469 True 10102.0 10102 100.0000 1 5470 1 chr2D.!!$R1 5469
1 TraesCS2D01G359100 chr2A 604750210 604755094 4884 True 7319.0 7319 93.9500 22 4845 1 chr2A.!!$R1 4823
2 TraesCS2D01G359100 chr2B 542758288 542763944 5656 True 3696.5 7293 88.4275 21 5470 2 chr2B.!!$R1 5449
3 TraesCS2D01G359100 chr4A 619801841 619802896 1055 True 904.0 904 82.8280 11 1054 1 chr4A.!!$R1 1043
4 TraesCS2D01G359100 chr3D 598947296 598947809 513 False 494.0 494 84.0910 4053 4577 1 chr3D.!!$F1 524
5 TraesCS2D01G359100 chr6B 92344390 92344897 507 True 483.0 483 83.9020 4053 4576 1 chr6B.!!$R1 523
6 TraesCS2D01G359100 chr5B 101898265 101898772 507 True 466.0 466 83.3330 4053 4576 1 chr5B.!!$R1 523
7 TraesCS2D01G359100 chr7A 33836168 33836680 512 False 459.0 459 82.9550 4053 4576 1 chr7A.!!$F1 523

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
592 681 0.107654 GGGTTCCTCGATTGGTCCTG 60.108 60.0 0.00 0.00 0.00 3.86 F
1044 1170 0.112412 CCTGGGGTTTGCAACTAGGT 59.888 55.0 0.00 0.00 0.00 3.08 F
1777 1906 0.114954 AAATCAGCTTTCTGGCCCCA 59.885 50.0 0.00 0.00 40.69 4.96 F
2478 2607 0.169672 CAACAATTGAGCTGGCTCGG 59.830 55.0 13.59 9.19 45.48 4.63 F
3537 3666 0.178990 ACAGGGAAGGAAGCAACACC 60.179 55.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1571 0.182061 ATTGCATCCGATCAGCAGGT 59.818 50.000 0.00 0.00 39.72 4.00 R
2523 2652 1.086634 GGTTAAGCCTCTGCAGAGCG 61.087 60.000 34.09 26.97 40.75 5.03 R
3726 3855 0.106819 CAGCTGCTCCAAGGGCTATT 60.107 55.000 0.00 0.00 33.43 1.73 R
3738 3867 1.457604 TGAAAGCCCTTCAGCTGCT 59.542 52.632 9.47 0.00 44.11 4.24 R
5372 5726 0.035915 GAGGCCTGGACCTTGAGAAC 60.036 60.000 12.00 0.00 41.32 3.01 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
17 18 4.051932 CTCCTCCCCTACCACCAC 57.948 66.667 0.00 0.00 0.00 4.16
27 28 1.229400 TACCACCACCACCTCTCCC 60.229 63.158 0.00 0.00 0.00 4.30
62 67 0.804156 GCTAGCTCTCTTGCCGTCAC 60.804 60.000 7.70 0.00 35.49 3.67
69 74 2.203139 CTTGCCGTCACCACACCA 60.203 61.111 0.00 0.00 0.00 4.17
71 76 2.940890 CTTGCCGTCACCACACCACT 62.941 60.000 0.00 0.00 0.00 4.00
76 81 0.600255 CGTCACCACACCACTTCCTC 60.600 60.000 0.00 0.00 0.00 3.71
82 88 1.638529 CACACCACTTCCTCCTCTCT 58.361 55.000 0.00 0.00 0.00 3.10
133 149 2.708216 TCGCCCATTCATTGCTCTTA 57.292 45.000 0.00 0.00 0.00 2.10
163 180 3.753434 AGTGAGTCGGCGCCAGAG 61.753 66.667 28.98 10.81 0.00 3.35
227 251 1.161563 GGAAAACGCGGTGAGTTGGA 61.162 55.000 12.47 0.00 31.43 3.53
239 263 1.151810 AGTTGGAAGGCCTCCTCCA 60.152 57.895 20.46 20.46 45.64 3.86
263 291 4.877882 TTGTTGCGTGCGTGCGTG 62.878 61.111 3.11 0.00 37.81 5.34
382 427 3.943034 GCTCGCTCGCTCGCTCTA 61.943 66.667 0.00 0.00 0.00 2.43
489 570 1.375396 CCGCGATTTGAGGGTGTCA 60.375 57.895 8.23 0.00 33.17 3.58
546 634 5.813672 CCATCTTTTTCTGCAAATATGGTGG 59.186 40.000 5.50 4.88 35.43 4.61
592 681 0.107654 GGGTTCCTCGATTGGTCCTG 60.108 60.000 0.00 0.00 0.00 3.86
618 717 4.034048 CGAGTAAGCATTATTTTCAGGCGT 59.966 41.667 0.00 0.00 30.46 5.68
710 809 3.717707 TGCTCCCGAATTCGATTCTTAG 58.282 45.455 28.76 15.55 43.02 2.18
711 810 3.132289 TGCTCCCGAATTCGATTCTTAGT 59.868 43.478 28.76 0.00 43.02 2.24
712 811 4.120589 GCTCCCGAATTCGATTCTTAGTT 58.879 43.478 28.76 0.00 43.02 2.24
713 812 5.163488 TGCTCCCGAATTCGATTCTTAGTTA 60.163 40.000 28.76 7.44 43.02 2.24
714 813 5.927115 GCTCCCGAATTCGATTCTTAGTTAT 59.073 40.000 28.76 0.00 43.02 1.89
715 814 6.128795 GCTCCCGAATTCGATTCTTAGTTATG 60.129 42.308 28.76 7.13 43.02 1.90
716 815 5.694910 TCCCGAATTCGATTCTTAGTTATGC 59.305 40.000 28.76 0.00 43.02 3.14
717 816 5.696724 CCCGAATTCGATTCTTAGTTATGCT 59.303 40.000 28.76 0.00 43.02 3.79
718 817 6.128795 CCCGAATTCGATTCTTAGTTATGCTC 60.129 42.308 28.76 0.00 43.02 4.26
719 818 6.420903 CCGAATTCGATTCTTAGTTATGCTCA 59.579 38.462 28.76 0.00 43.02 4.26
720 819 7.358765 CCGAATTCGATTCTTAGTTATGCTCAG 60.359 40.741 28.76 1.37 43.02 3.35
721 820 7.168302 CGAATTCGATTCTTAGTTATGCTCAGT 59.832 37.037 23.29 0.00 43.02 3.41
722 821 9.464714 GAATTCGATTCTTAGTTATGCTCAGTA 57.535 33.333 0.00 0.00 36.37 2.74
749 848 3.891049 ACCATAGCTTTCATTCCTGTCC 58.109 45.455 0.00 0.00 0.00 4.02
759 858 2.239654 TCATTCCTGTCCTGGATTGTCC 59.760 50.000 0.00 0.00 38.16 4.02
761 860 2.044793 TCCTGTCCTGGATTGTCCTT 57.955 50.000 0.00 0.00 37.46 3.36
788 899 3.253188 CCATTTCTCTGAAAACGAAGGCA 59.747 43.478 0.00 0.00 0.00 4.75
791 902 5.514274 TTTCTCTGAAAACGAAGGCAAAT 57.486 34.783 0.00 0.00 0.00 2.32
796 907 5.040635 TCTGAAAACGAAGGCAAATCAAAC 58.959 37.500 0.00 0.00 0.00 2.93
797 908 4.748892 TGAAAACGAAGGCAAATCAAACA 58.251 34.783 0.00 0.00 0.00 2.83
801 912 4.647424 ACGAAGGCAAATCAAACAAGAA 57.353 36.364 0.00 0.00 0.00 2.52
802 913 4.610945 ACGAAGGCAAATCAAACAAGAAG 58.389 39.130 0.00 0.00 0.00 2.85
810 924 8.154856 AGGCAAATCAAACAAGAAGTACTAGTA 58.845 33.333 0.00 0.00 0.00 1.82
829 954 5.065704 AGTATCCTGCAGATAGTTATGCG 57.934 43.478 17.39 0.00 45.54 4.73
844 969 5.741011 AGTTATGCGGTTAGAATCTTTCCA 58.259 37.500 0.00 0.00 0.00 3.53
847 972 4.280436 TGCGGTTAGAATCTTTCCAGAA 57.720 40.909 0.00 0.00 30.76 3.02
848 973 4.000988 TGCGGTTAGAATCTTTCCAGAAC 58.999 43.478 0.00 0.00 30.76 3.01
860 985 5.132502 TCTTTCCAGAACAGAAGCATTTCA 58.867 37.500 0.00 0.00 35.70 2.69
861 986 5.771666 TCTTTCCAGAACAGAAGCATTTCAT 59.228 36.000 0.00 0.00 35.70 2.57
901 1027 4.698583 ATTCTCTGCTTGCATTCTGTTC 57.301 40.909 0.00 0.00 0.00 3.18
944 1070 4.153835 GGAGATGCACAAGATTATAGCAGC 59.846 45.833 0.00 0.00 41.48 5.25
982 1108 1.674962 GGCTCTGAGCATTGGTTGATC 59.325 52.381 28.95 5.80 44.75 2.92
983 1109 2.641305 GCTCTGAGCATTGGTTGATCT 58.359 47.619 24.02 0.00 41.44 2.75
1041 1167 0.250553 CGTCCTGGGGTTTGCAACTA 60.251 55.000 0.00 0.00 0.00 2.24
1044 1170 0.112412 CCTGGGGTTTGCAACTAGGT 59.888 55.000 0.00 0.00 0.00 3.08
1183 1309 3.030168 AAGGATCCATCGCCGTGCA 62.030 57.895 15.82 0.00 0.00 4.57
1212 1338 0.389166 GTGTCAACTGCTCCTCCTCG 60.389 60.000 0.00 0.00 0.00 4.63
1329 1458 2.427506 AGCCTCGATTTGTCCTTCAAC 58.572 47.619 0.00 0.00 35.61 3.18
1342 1471 3.255149 GTCCTTCAACGAGTTCTCTGGTA 59.745 47.826 0.00 0.00 32.55 3.25
1344 1473 3.256136 CCTTCAACGAGTTCTCTGGTACT 59.744 47.826 0.00 0.00 32.55 2.73
1351 1480 3.566322 CGAGTTCTCTGGTACTATCCCTG 59.434 52.174 0.00 0.00 0.00 4.45
1353 1482 3.052490 AGTTCTCTGGTACTATCCCTGCT 60.052 47.826 0.00 0.00 0.00 4.24
1421 1550 5.067936 ACAACAATTTTGACGGTACAATCCA 59.932 36.000 0.00 0.00 0.00 3.41
1451 1580 1.606531 GGAAGCTGGACCTGCTGAT 59.393 57.895 24.86 11.63 38.59 2.90
1524 1653 3.261580 TGGTAACATGTCATCGCTTCAG 58.738 45.455 0.00 0.00 46.17 3.02
1650 1779 0.394565 GCATTCCTGCCGAGATAGGT 59.605 55.000 0.00 0.00 42.88 3.08
1777 1906 0.114954 AAATCAGCTTTCTGGCCCCA 59.885 50.000 0.00 0.00 40.69 4.96
1791 1920 0.849417 GCCCCATTCCTCCAGAGATT 59.151 55.000 0.00 0.00 0.00 2.40
1908 2037 9.988815 GAGAAGCTATATCTTTACAGGAATTCA 57.011 33.333 7.93 0.00 0.00 2.57
1926 2055 7.014230 AGGAATTCAATAAATGGTACCATTCCG 59.986 37.037 34.67 23.45 44.86 4.30
1950 2079 5.923114 GTCTGAAATTGGGAAGCTTTCTTTC 59.077 40.000 4.35 7.74 31.48 2.62
2115 2244 3.505293 ACTTGAGCAAGCTTGATCTTTCC 59.495 43.478 36.42 17.73 43.58 3.13
2167 2296 4.253685 CGGATTTCAGTACATGACCAAGT 58.746 43.478 0.00 0.00 37.77 3.16
2287 2416 4.130118 CAACATTACAGGGCAGATACCTC 58.870 47.826 0.00 0.00 35.78 3.85
2478 2607 0.169672 CAACAATTGAGCTGGCTCGG 59.830 55.000 13.59 9.19 45.48 4.63
2523 2652 4.133078 CTCCTCAGATAGGGAATTGCAAC 58.867 47.826 0.00 0.00 46.55 4.17
2775 2904 2.983136 CTCGTTCGCTGATAATAGGCTG 59.017 50.000 0.00 0.00 0.00 4.85
2880 3009 3.580604 AAAGGAGCTGGGCCTGCTG 62.581 63.158 38.13 11.88 38.70 4.41
3084 3213 2.363406 ACCGGTACTCTTCCCCCG 60.363 66.667 4.49 0.00 40.12 5.73
3102 3231 0.318614 CGGTGCCGCTTTTTGACAAT 60.319 50.000 0.00 0.00 0.00 2.71
3190 3319 0.545548 GTCACCCTCCTCTTCCCAGT 60.546 60.000 0.00 0.00 0.00 4.00
3413 3542 2.564947 AGGAACTGGTCTCTGCTACAAG 59.435 50.000 0.00 0.00 37.18 3.16
3537 3666 0.178990 ACAGGGAAGGAAGCAACACC 60.179 55.000 0.00 0.00 0.00 4.16
3540 3669 1.235281 GGGAAGGAAGCAACACCGAC 61.235 60.000 0.00 0.00 0.00 4.79
3600 3729 8.771920 AGATAAGACATCGTAACATTGTGAAA 57.228 30.769 0.00 0.00 0.00 2.69
3637 3766 0.467290 TCACCAGGGTGCAAACCTTC 60.467 55.000 13.64 0.00 45.04 3.46
3726 3855 0.396435 ATTGGGAGACACGCTTCACA 59.604 50.000 0.00 0.00 0.00 3.58
3738 3867 1.678728 CGCTTCACAATAGCCCTTGGA 60.679 52.381 1.44 0.00 35.18 3.53
4000 4129 2.286872 GCATGTCACTGCTATCTTGCT 58.713 47.619 0.00 0.00 39.12 3.91
4094 4223 7.325660 TCTTTTCATTTGATCAGAGTATGCC 57.674 36.000 0.00 0.00 0.00 4.40
4409 4538 0.386113 GCGAGTCGAAAGATAGGGCT 59.614 55.000 18.61 0.00 45.19 5.19
4414 4543 0.396695 TCGAAAGATAGGGCTCGGGT 60.397 55.000 0.00 0.00 33.31 5.28
4543 4675 2.291540 CCCTTTCCCCTGTTGCTTATGA 60.292 50.000 0.00 0.00 0.00 2.15
4551 4683 3.152341 CCTGTTGCTTATGATGGGGATC 58.848 50.000 0.00 0.00 0.00 3.36
4662 4797 1.135333 GCCTCTCTGAAGAAGGTACCG 59.865 57.143 6.18 0.00 0.00 4.02
4665 4800 3.082548 CTCTCTGAAGAAGGTACCGTCA 58.917 50.000 26.69 17.37 0.00 4.35
4673 4808 0.974383 AAGGTACCGTCAAGTCCAGG 59.026 55.000 6.18 0.00 0.00 4.45
4737 4873 0.321919 TGCTGTGCCTCTTGCTTAGG 60.322 55.000 0.00 0.00 42.00 2.69
4759 4901 6.607019 AGGTTTGGGTTTAGTATTTCTCACA 58.393 36.000 0.00 0.00 0.00 3.58
4810 4952 6.405842 GGAACAACATGGTCTTTCTGAACTTT 60.406 38.462 0.00 0.00 33.75 2.66
4822 4964 6.878923 TCTTTCTGAACTTTTGACACTCTCAA 59.121 34.615 0.00 0.00 37.08 3.02
4853 5071 9.438228 GTTTTATCTGAGCTTCCTAAACTTAGT 57.562 33.333 0.00 0.00 0.00 2.24
4858 5076 5.560724 TGAGCTTCCTAAACTTAGTGCAAT 58.439 37.500 0.00 0.00 0.00 3.56
4860 5078 6.149474 TGAGCTTCCTAAACTTAGTGCAATTC 59.851 38.462 0.00 0.00 0.00 2.17
4861 5079 6.003950 AGCTTCCTAAACTTAGTGCAATTCA 58.996 36.000 0.00 0.00 0.00 2.57
4886 5123 4.950434 TTTTTATCCGTTTGGGTCGATC 57.050 40.909 0.00 0.00 37.00 3.69
4893 5130 0.672401 GTTTGGGTCGATCGAAGGCA 60.672 55.000 21.31 1.51 0.00 4.75
4894 5131 0.251916 TTTGGGTCGATCGAAGGCAT 59.748 50.000 21.31 0.00 0.00 4.40
4895 5132 0.461870 TTGGGTCGATCGAAGGCATG 60.462 55.000 21.31 0.00 0.00 4.06
4896 5133 2.247437 GGGTCGATCGAAGGCATGC 61.247 63.158 21.31 9.90 0.00 4.06
4913 5150 2.341543 CTGTCCAGCTGCGTCTGT 59.658 61.111 8.66 0.00 32.32 3.41
4924 5161 2.617274 GCGTCTGTCCAAACCTGGC 61.617 63.158 0.00 0.00 43.17 4.85
4925 5162 1.966451 CGTCTGTCCAAACCTGGCC 60.966 63.158 0.00 0.00 43.17 5.36
4948 5255 1.545136 TGCGTCCAACGGTAGTTCATA 59.455 47.619 1.33 0.00 42.82 2.15
4970 5277 3.164028 GCACACTTGCGAACCTTTC 57.836 52.632 0.00 0.00 39.50 2.62
4973 5280 1.264288 CACACTTGCGAACCTTTCTCC 59.736 52.381 0.00 0.00 0.00 3.71
4979 5286 1.302192 CGAACCTTTCTCCGGCCAA 60.302 57.895 2.24 0.00 0.00 4.52
4989 5296 4.016706 CCGGCCAACCCTCTTCGT 62.017 66.667 2.24 0.00 0.00 3.85
4996 5303 0.868406 CAACCCTCTTCGTTGACTGC 59.132 55.000 0.00 0.00 42.63 4.40
5001 5308 1.609061 CCTCTTCGTTGACTGCATGGT 60.609 52.381 0.00 0.00 0.00 3.55
5004 5311 0.107643 TTCGTTGACTGCATGGTCCA 59.892 50.000 0.00 0.00 35.54 4.02
5084 5435 4.760047 GCGTCGGCCATGGTGAGT 62.760 66.667 14.67 0.00 0.00 3.41
5092 5443 2.044650 CATGGTGAGTGGGCAGGG 60.045 66.667 0.00 0.00 0.00 4.45
5093 5444 2.532715 ATGGTGAGTGGGCAGGGT 60.533 61.111 0.00 0.00 0.00 4.34
5094 5445 2.910737 ATGGTGAGTGGGCAGGGTG 61.911 63.158 0.00 0.00 0.00 4.61
5095 5446 4.351054 GGTGAGTGGGCAGGGTGG 62.351 72.222 0.00 0.00 0.00 4.61
5109 5460 2.570284 GGTGGCGAAGGGTTTTGGG 61.570 63.158 0.00 0.00 0.00 4.12
5114 5465 0.036306 GCGAAGGGTTTTGGGAGAGA 59.964 55.000 0.00 0.00 0.00 3.10
5116 5467 1.348036 CGAAGGGTTTTGGGAGAGAGT 59.652 52.381 0.00 0.00 0.00 3.24
5117 5468 2.784347 GAAGGGTTTTGGGAGAGAGTG 58.216 52.381 0.00 0.00 0.00 3.51
5118 5469 1.068121 AGGGTTTTGGGAGAGAGTGG 58.932 55.000 0.00 0.00 0.00 4.00
5127 5478 2.225624 TGGGAGAGAGTGGGAAATGAGA 60.226 50.000 0.00 0.00 0.00 3.27
5130 5481 3.708631 GGAGAGAGTGGGAAATGAGATGA 59.291 47.826 0.00 0.00 0.00 2.92
5145 5496 0.739462 GATGAATGTGCCACCGACGA 60.739 55.000 0.00 0.00 0.00 4.20
5146 5497 0.321210 ATGAATGTGCCACCGACGAA 60.321 50.000 0.00 0.00 0.00 3.85
5147 5498 0.321210 TGAATGTGCCACCGACGAAT 60.321 50.000 0.00 0.00 0.00 3.34
5150 5501 3.124921 GTGCCACCGACGAATGGG 61.125 66.667 16.82 5.28 36.41 4.00
5151 5502 3.632080 TGCCACCGACGAATGGGT 61.632 61.111 16.82 0.00 37.42 4.51
5155 5506 1.447838 CACCGACGAATGGGTCAGG 60.448 63.158 0.00 0.00 34.03 3.86
5157 5508 2.186903 CGACGAATGGGTCAGGGG 59.813 66.667 0.00 0.00 36.73 4.79
5161 5512 0.546747 ACGAATGGGTCAGGGGAGAA 60.547 55.000 0.00 0.00 0.00 2.87
5165 5516 2.059756 ATGGGTCAGGGGAGAAAAGA 57.940 50.000 0.00 0.00 0.00 2.52
5171 5522 1.132527 TCAGGGGAGAAAAGAGTGGGA 60.133 52.381 0.00 0.00 0.00 4.37
5175 5526 1.978580 GGGAGAAAAGAGTGGGAGTCA 59.021 52.381 0.00 0.00 0.00 3.41
5203 5557 4.794439 CATGTCCGCCTCGACGCA 62.794 66.667 7.18 0.00 35.40 5.24
5207 5561 3.896133 TCCGCCTCGACGCATACC 61.896 66.667 7.18 0.00 0.00 2.73
5212 5566 3.900892 CTCGACGCATACCGGGCT 61.901 66.667 6.32 0.00 42.52 5.19
5214 5568 4.201679 CGACGCATACCGGGCTCA 62.202 66.667 6.32 0.00 42.52 4.26
5220 5574 1.944024 CGCATACCGGGCTCAAATTTA 59.056 47.619 6.32 0.00 0.00 1.40
5227 5581 3.184736 GGCTCAAATTTAGGCCGGA 57.815 52.632 5.05 0.00 35.08 5.14
5228 5582 1.025041 GGCTCAAATTTAGGCCGGAG 58.975 55.000 5.05 7.08 35.08 4.63
5229 5583 1.408266 GGCTCAAATTTAGGCCGGAGA 60.408 52.381 5.05 0.00 35.08 3.71
5230 5584 2.576615 GCTCAAATTTAGGCCGGAGAT 58.423 47.619 5.05 0.00 0.00 2.75
5231 5585 3.496160 GGCTCAAATTTAGGCCGGAGATA 60.496 47.826 5.05 0.00 35.08 1.98
5234 5588 3.714798 TCAAATTTAGGCCGGAGATAGGT 59.285 43.478 5.05 0.00 0.00 3.08
5236 5590 1.325355 TTTAGGCCGGAGATAGGTCG 58.675 55.000 5.05 0.00 38.65 4.79
5237 5591 1.177256 TTAGGCCGGAGATAGGTCGC 61.177 60.000 5.05 0.00 38.65 5.19
5238 5592 4.344474 GGCCGGAGATAGGTCGCG 62.344 72.222 5.05 0.00 0.00 5.87
5239 5593 3.285215 GCCGGAGATAGGTCGCGA 61.285 66.667 5.05 3.71 0.00 5.87
5241 5595 1.892862 CCGGAGATAGGTCGCGAGT 60.893 63.158 10.24 1.70 0.00 4.18
5242 5596 1.280142 CGGAGATAGGTCGCGAGTG 59.720 63.158 10.24 0.00 0.00 3.51
5243 5597 1.655329 GGAGATAGGTCGCGAGTGG 59.345 63.158 10.24 0.00 0.00 4.00
5245 5599 1.240256 GAGATAGGTCGCGAGTGGAT 58.760 55.000 10.24 0.00 0.00 3.41
5246 5600 0.955178 AGATAGGTCGCGAGTGGATG 59.045 55.000 10.24 0.00 0.00 3.51
5247 5601 0.952280 GATAGGTCGCGAGTGGATGA 59.048 55.000 10.24 0.00 0.00 2.92
5248 5602 1.337071 GATAGGTCGCGAGTGGATGAA 59.663 52.381 10.24 0.00 0.00 2.57
5249 5603 1.179152 TAGGTCGCGAGTGGATGAAA 58.821 50.000 10.24 0.00 0.00 2.69
5252 5606 0.442699 GTCGCGAGTGGATGAAAACC 59.557 55.000 10.24 0.00 0.00 3.27
5255 5609 0.672401 GCGAGTGGATGAAAACCGGA 60.672 55.000 9.46 0.00 0.00 5.14
5256 5610 2.012051 GCGAGTGGATGAAAACCGGAT 61.012 52.381 9.46 0.00 0.00 4.18
5257 5611 2.740580 GCGAGTGGATGAAAACCGGATA 60.741 50.000 9.46 0.00 0.00 2.59
5258 5612 3.123804 CGAGTGGATGAAAACCGGATAG 58.876 50.000 9.46 0.00 0.00 2.08
5261 5615 2.092592 GTGGATGAAAACCGGATAGGGT 60.093 50.000 9.46 0.00 46.47 4.34
5262 5616 2.171870 TGGATGAAAACCGGATAGGGTC 59.828 50.000 9.46 0.00 40.76 4.46
5263 5617 2.486727 GGATGAAAACCGGATAGGGTCC 60.487 54.545 9.46 5.10 40.76 4.46
5275 5629 5.422214 GGATAGGGTCCATTTATGTCGAT 57.578 43.478 0.00 0.00 46.96 3.59
5277 5631 3.492102 AGGGTCCATTTATGTCGATGG 57.508 47.619 0.00 0.00 43.36 3.51
5285 5639 0.106918 TTATGTCGATGGGTTGGGCC 60.107 55.000 0.00 0.00 0.00 5.80
5295 5649 1.302993 GGTTGGGCCGCAGTTTCTA 60.303 57.895 0.00 0.00 0.00 2.10
5299 5653 1.887707 GGGCCGCAGTTTCTATCCG 60.888 63.158 0.00 0.00 0.00 4.18
5302 5656 1.084289 GCCGCAGTTTCTATCCGTTT 58.916 50.000 0.00 0.00 0.00 3.60
5303 5657 1.467342 GCCGCAGTTTCTATCCGTTTT 59.533 47.619 0.00 0.00 0.00 2.43
5305 5659 2.739913 CCGCAGTTTCTATCCGTTTTGA 59.260 45.455 0.00 0.00 0.00 2.69
5306 5660 3.424433 CCGCAGTTTCTATCCGTTTTGAC 60.424 47.826 0.00 0.00 0.00 3.18
5308 5662 3.119955 GCAGTTTCTATCCGTTTTGACCC 60.120 47.826 0.00 0.00 0.00 4.46
5309 5663 4.069304 CAGTTTCTATCCGTTTTGACCCA 58.931 43.478 0.00 0.00 0.00 4.51
5310 5664 4.517453 CAGTTTCTATCCGTTTTGACCCAA 59.483 41.667 0.00 0.00 0.00 4.12
5311 5665 5.009210 CAGTTTCTATCCGTTTTGACCCAAA 59.991 40.000 0.00 0.00 0.00 3.28
5312 5666 5.595133 AGTTTCTATCCGTTTTGACCCAAAA 59.405 36.000 1.19 1.19 40.41 2.44
5320 5674 2.409152 TTTGACCCAAAACGAATCGC 57.591 45.000 1.15 0.00 29.89 4.58
5322 5676 0.589223 TGACCCAAAACGAATCGCAC 59.411 50.000 1.15 0.00 0.00 5.34
5323 5677 0.452122 GACCCAAAACGAATCGCACG 60.452 55.000 1.15 0.00 0.00 5.34
5326 5680 2.137395 CAAAACGAATCGCACGCGG 61.137 57.895 12.47 0.00 40.25 6.46
5327 5681 2.311701 AAAACGAATCGCACGCGGA 61.312 52.632 12.47 0.00 40.25 5.54
5336 5690 3.641986 GCACGCGGACGGACAAAA 61.642 61.111 12.47 0.00 46.04 2.44
5337 5691 2.961669 GCACGCGGACGGACAAAAT 61.962 57.895 12.47 0.00 46.04 1.82
5339 5693 0.452122 CACGCGGACGGACAAAATTC 60.452 55.000 12.47 0.00 46.04 2.17
5340 5694 1.225637 CGCGGACGGACAAAATTCG 60.226 57.895 0.00 0.00 34.97 3.34
5341 5695 1.864176 GCGGACGGACAAAATTCGT 59.136 52.632 0.00 0.00 39.99 3.85
5344 5698 3.269465 GACGGACAAAATTCGTCGC 57.731 52.632 1.50 0.00 42.60 5.19
5345 5699 0.515717 GACGGACAAAATTCGTCGCG 60.516 55.000 0.00 0.00 42.60 5.87
5346 5700 1.857426 CGGACAAAATTCGTCGCGC 60.857 57.895 0.00 0.00 34.04 6.86
5347 5701 1.857426 GGACAAAATTCGTCGCGCG 60.857 57.895 26.76 26.76 43.01 6.86
5348 5702 1.154727 GACAAAATTCGTCGCGCGT 60.155 52.632 30.98 6.92 42.13 6.01
5349 5703 0.720173 GACAAAATTCGTCGCGCGTT 60.720 50.000 30.98 13.72 42.13 4.84
5350 5704 0.989805 ACAAAATTCGTCGCGCGTTG 60.990 50.000 30.98 25.05 42.13 4.10
5372 5726 1.737793 GAGTTGCCCTTACGAATGTGG 59.262 52.381 0.00 0.00 0.00 4.17
5376 5730 1.349688 TGCCCTTACGAATGTGGTTCT 59.650 47.619 0.00 0.00 34.56 3.01
5384 5738 2.076863 CGAATGTGGTTCTCAAGGTCC 58.923 52.381 0.00 0.00 34.56 4.46
5387 5741 0.764890 TGTGGTTCTCAAGGTCCAGG 59.235 55.000 0.00 0.00 0.00 4.45
5389 5743 1.002011 GGTTCTCAAGGTCCAGGCC 60.002 63.158 0.00 0.00 0.00 5.19
5402 5756 1.306141 CAGGCCTCCAGGGTCACTA 60.306 63.158 0.00 0.00 43.45 2.74
5420 5774 2.159282 ACTATACTCCACCGAACAAGCG 60.159 50.000 0.00 0.00 0.00 4.68
5423 5777 1.300620 CTCCACCGAACAAGCGACA 60.301 57.895 0.00 0.00 0.00 4.35
5428 5782 2.660552 CGAACAAGCGACACCCGT 60.661 61.111 0.00 0.00 41.15 5.28
5429 5783 2.654912 CGAACAAGCGACACCCGTC 61.655 63.158 0.00 0.00 41.15 4.79
5430 5784 1.593209 GAACAAGCGACACCCGTCA 60.593 57.895 0.00 0.00 42.74 4.35
5431 5785 1.557443 GAACAAGCGACACCCGTCAG 61.557 60.000 0.00 0.00 42.74 3.51
5432 5786 2.023414 AACAAGCGACACCCGTCAGA 62.023 55.000 0.00 0.00 42.74 3.27
5433 5787 1.734477 CAAGCGACACCCGTCAGAG 60.734 63.158 0.00 0.00 42.74 3.35
5434 5788 2.932234 AAGCGACACCCGTCAGAGG 61.932 63.158 0.00 0.00 42.74 3.69
5435 5789 3.681835 GCGACACCCGTCAGAGGT 61.682 66.667 0.00 0.00 42.74 3.85
5436 5790 2.567049 CGACACCCGTCAGAGGTC 59.433 66.667 0.00 0.00 42.74 3.85
5437 5791 2.265904 CGACACCCGTCAGAGGTCA 61.266 63.158 0.00 0.00 42.74 4.02
5438 5792 1.587054 GACACCCGTCAGAGGTCAG 59.413 63.158 0.00 0.00 42.13 3.51
5439 5793 0.894184 GACACCCGTCAGAGGTCAGA 60.894 60.000 0.00 0.00 42.13 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.453054 GGTGGTGGTAGGGGAGGA 59.547 66.667 0.00 0.00 0.00 3.71
2 3 2.124085 TGGTGGTGGTAGGGGAGG 59.876 66.667 0.00 0.00 0.00 4.30
4 5 2.204029 GGTGGTGGTGGTAGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
6 7 1.229529 AGAGGTGGTGGTGGTAGGG 60.230 63.158 0.00 0.00 0.00 3.53
7 8 1.265454 GGAGAGGTGGTGGTGGTAGG 61.265 65.000 0.00 0.00 0.00 3.18
8 9 1.265454 GGGAGAGGTGGTGGTGGTAG 61.265 65.000 0.00 0.00 0.00 3.18
9 10 1.229400 GGGAGAGGTGGTGGTGGTA 60.229 63.158 0.00 0.00 0.00 3.25
13 14 3.542602 AGGGGGAGAGGTGGTGGT 61.543 66.667 0.00 0.00 0.00 4.16
17 18 4.825679 GGGGAGGGGGAGAGGTGG 62.826 77.778 0.00 0.00 0.00 4.61
62 67 0.610687 GAGAGGAGGAAGTGGTGTGG 59.389 60.000 0.00 0.00 0.00 4.17
69 74 3.852578 AGAGAGAGAAGAGAGGAGGAAGT 59.147 47.826 0.00 0.00 0.00 3.01
71 76 5.036916 AGTAGAGAGAGAAGAGAGGAGGAA 58.963 45.833 0.00 0.00 0.00 3.36
76 81 3.728845 CGGAGTAGAGAGAGAAGAGAGG 58.271 54.545 0.00 0.00 0.00 3.69
82 88 1.096386 GCCGCGGAGTAGAGAGAGAA 61.096 60.000 33.48 0.00 0.00 2.87
111 123 1.027357 GAGCAATGAATGGGCGATGT 58.973 50.000 0.00 0.00 0.00 3.06
227 251 2.366167 AGCGATGGAGGAGGCCTT 60.366 61.111 6.77 0.00 31.76 4.35
267 295 1.279840 GGCTCAATAATGCGGACGC 59.720 57.895 10.13 10.13 42.35 5.19
268 296 0.813610 TGGGCTCAATAATGCGGACG 60.814 55.000 0.00 0.00 0.00 4.79
269 297 0.663153 GTGGGCTCAATAATGCGGAC 59.337 55.000 0.00 0.00 0.00 4.79
270 298 0.465460 GGTGGGCTCAATAATGCGGA 60.465 55.000 0.00 0.00 0.00 5.54
271 299 1.785041 CGGTGGGCTCAATAATGCGG 61.785 60.000 0.00 0.00 0.00 5.69
272 300 1.648720 CGGTGGGCTCAATAATGCG 59.351 57.895 0.00 0.00 0.00 4.73
273 301 0.751643 ACCGGTGGGCTCAATAATGC 60.752 55.000 6.12 0.00 36.48 3.56
382 427 4.035102 GGGCCTTTCACTCCGCCT 62.035 66.667 0.84 0.00 41.35 5.52
467 548 2.203070 CCCTCAAATCGCGGGAGG 60.203 66.667 21.90 21.90 43.04 4.30
485 566 3.311110 GGAGGGACCGCTGTGACA 61.311 66.667 0.00 0.00 0.00 3.58
546 634 4.773209 GTAGCCGGCTACCAATCC 57.227 61.111 43.81 25.69 42.11 3.01
592 681 5.504173 GCCTGAAAATAATGCTTACTCGGTC 60.504 44.000 0.00 0.00 0.00 4.79
618 717 2.959516 AGCGACAAGAATCGAATCACA 58.040 42.857 2.82 0.00 45.13 3.58
710 809 7.175293 AGCTATGGTAGTACTACTGAGCATAAC 59.825 40.741 32.22 24.31 37.40 1.89
711 810 7.232188 AGCTATGGTAGTACTACTGAGCATAA 58.768 38.462 32.22 17.84 37.40 1.90
712 811 6.780901 AGCTATGGTAGTACTACTGAGCATA 58.219 40.000 32.22 26.41 37.40 3.14
713 812 5.636123 AGCTATGGTAGTACTACTGAGCAT 58.364 41.667 32.22 26.60 37.40 3.79
714 813 5.050126 AGCTATGGTAGTACTACTGAGCA 57.950 43.478 32.22 23.60 37.40 4.26
715 814 6.039493 TGAAAGCTATGGTAGTACTACTGAGC 59.961 42.308 28.24 28.24 36.35 4.26
716 815 7.569639 TGAAAGCTATGGTAGTACTACTGAG 57.430 40.000 27.71 22.03 36.36 3.35
717 816 8.534954 AATGAAAGCTATGGTAGTACTACTGA 57.465 34.615 27.71 17.33 36.36 3.41
718 817 7.868415 GGAATGAAAGCTATGGTAGTACTACTG 59.132 40.741 27.71 17.63 36.36 2.74
719 818 7.785506 AGGAATGAAAGCTATGGTAGTACTACT 59.214 37.037 27.71 14.80 36.36 2.57
720 819 7.868415 CAGGAATGAAAGCTATGGTAGTACTAC 59.132 40.741 22.53 22.53 35.40 2.73
721 820 7.563924 ACAGGAATGAAAGCTATGGTAGTACTA 59.436 37.037 0.00 0.00 0.00 1.82
722 821 6.384305 ACAGGAATGAAAGCTATGGTAGTACT 59.616 38.462 0.00 0.00 0.00 2.73
749 848 2.566833 TGGACACAAGGACAATCCAG 57.433 50.000 0.00 0.00 39.61 3.86
759 858 5.007626 TCGTTTTCAGAGAAATGGACACAAG 59.992 40.000 0.00 0.00 0.00 3.16
761 860 4.447290 TCGTTTTCAGAGAAATGGACACA 58.553 39.130 0.00 0.00 0.00 3.72
810 924 2.634940 ACCGCATAACTATCTGCAGGAT 59.365 45.455 15.13 8.76 38.30 3.24
829 954 6.128145 GCTTCTGTTCTGGAAAGATTCTAACC 60.128 42.308 0.00 0.00 0.00 2.85
844 969 4.232221 CGCAAATGAAATGCTTCTGTTCT 58.768 39.130 0.00 0.00 41.64 3.01
847 972 2.927871 GCCGCAAATGAAATGCTTCTGT 60.928 45.455 0.00 0.00 41.64 3.41
848 973 1.657094 GCCGCAAATGAAATGCTTCTG 59.343 47.619 0.00 0.00 41.64 3.02
860 985 1.246649 TGTGAGAACATGCCGCAAAT 58.753 45.000 0.00 0.00 0.00 2.32
861 986 1.028130 TTGTGAGAACATGCCGCAAA 58.972 45.000 0.00 0.00 0.00 3.68
901 1027 2.037136 CGGCTTGCAGACTTCCTGG 61.037 63.158 0.00 0.00 43.13 4.45
944 1070 1.151668 CCGAACAAGGAGCAGAACAG 58.848 55.000 0.00 0.00 0.00 3.16
982 1108 2.543012 CCATGCTATCTTCACTTCGCAG 59.457 50.000 0.00 0.00 0.00 5.18
983 1109 2.168313 TCCATGCTATCTTCACTTCGCA 59.832 45.455 0.00 0.00 0.00 5.10
1041 1167 0.179018 GAAAGACCAGCACCACACCT 60.179 55.000 0.00 0.00 0.00 4.00
1044 1170 0.819259 GCAGAAAGACCAGCACCACA 60.819 55.000 0.00 0.00 0.00 4.17
1086 1212 1.304713 AAGCCAGCCCTCATGGTTG 60.305 57.895 0.00 0.00 44.51 3.77
1183 1309 0.179084 CAGTTGACACCACTCCACGT 60.179 55.000 0.00 0.00 0.00 4.49
1212 1338 2.023041 GCTAGCCTCGACGACGAC 59.977 66.667 5.75 0.00 43.81 4.34
1318 1447 3.492656 CCAGAGAACTCGTTGAAGGACAA 60.493 47.826 0.00 0.00 33.61 3.18
1329 1458 3.566322 CAGGGATAGTACCAGAGAACTCG 59.434 52.174 0.00 0.00 34.09 4.18
1342 1471 2.053244 CCCAATCTCAGCAGGGATAGT 58.947 52.381 0.00 0.00 44.30 2.12
1344 1473 2.494888 TCCCAATCTCAGCAGGGATA 57.505 50.000 0.00 0.00 45.15 2.59
1351 1480 2.372264 TGAGCAATTCCCAATCTCAGC 58.628 47.619 0.00 0.00 31.07 4.26
1353 1482 4.834496 AGTTTTGAGCAATTCCCAATCTCA 59.166 37.500 0.00 0.00 32.58 3.27
1442 1571 0.182061 ATTGCATCCGATCAGCAGGT 59.818 50.000 0.00 0.00 39.72 4.00
1444 1573 1.531578 CAGATTGCATCCGATCAGCAG 59.468 52.381 0.00 0.00 39.72 4.24
1518 1647 1.303643 CCCCACCAAGTCCTGAAGC 60.304 63.158 0.00 0.00 0.00 3.86
1524 1653 1.648116 TACTGTACCCCACCAAGTCC 58.352 55.000 0.00 0.00 0.00 3.85
1650 1779 0.390603 CGGTCAGGTTACGGCATTCA 60.391 55.000 0.00 0.00 0.00 2.57
1791 1920 5.222027 TGTCCTGAGATTTGTACAATTCCCA 60.222 40.000 21.22 16.79 0.00 4.37
1908 2037 5.996644 TCAGACGGAATGGTACCATTTATT 58.003 37.500 34.93 23.33 45.50 1.40
1926 2055 5.459536 AAGAAAGCTTCCCAATTTCAGAC 57.540 39.130 0.00 0.00 35.79 3.51
1950 2079 4.214119 TCTGAAAAATCAACCTCTTCTGCG 59.786 41.667 0.00 0.00 0.00 5.18
2115 2244 1.747355 GGGCCAGTGAGTGAATTGATG 59.253 52.381 4.39 0.00 0.00 3.07
2167 2296 5.592282 TGTTGAAGAGTTGCAACTGGATTAA 59.408 36.000 35.67 19.61 43.52 1.40
2287 2416 3.510388 TGACTGCCTACAAAGATCTCG 57.490 47.619 0.00 0.00 0.00 4.04
2478 2607 4.142160 GGAATAGGGCCATTGAACTTGTTC 60.142 45.833 6.18 6.56 0.00 3.18
2523 2652 1.086634 GGTTAAGCCTCTGCAGAGCG 61.087 60.000 34.09 26.97 40.75 5.03
3084 3213 2.715737 TATTGTCAAAAAGCGGCACC 57.284 45.000 1.45 0.00 0.00 5.01
3537 3666 2.162921 CTGCACGGAAGCTGTTGTCG 62.163 60.000 0.00 0.00 34.99 4.35
3540 3669 0.601046 TCTCTGCACGGAAGCTGTTG 60.601 55.000 0.00 0.00 35.31 3.33
3600 3729 4.464951 TGGTGATAGATGAAACCGTACAGT 59.535 41.667 0.00 0.00 35.33 3.55
3637 3766 5.178061 TCTTGGCATGTACTCATACAACAG 58.822 41.667 0.00 0.00 44.47 3.16
3726 3855 0.106819 CAGCTGCTCCAAGGGCTATT 60.107 55.000 0.00 0.00 33.43 1.73
3738 3867 1.457604 TGAAAGCCCTTCAGCTGCT 59.542 52.632 9.47 0.00 44.11 4.24
4015 4144 8.586273 TCGCGTAACTTACATATTCAAGTAAAC 58.414 33.333 5.77 2.24 33.92 2.01
4018 4147 8.130469 TCATCGCGTAACTTACATATTCAAGTA 58.870 33.333 5.77 0.00 33.92 2.24
4027 4156 4.439057 ACCATTCATCGCGTAACTTACAT 58.561 39.130 5.77 0.00 0.00 2.29
4031 4160 2.967362 TGACCATTCATCGCGTAACTT 58.033 42.857 5.77 0.00 0.00 2.66
4037 4166 2.095768 ACTTTGTTGACCATTCATCGCG 60.096 45.455 0.00 0.00 0.00 5.87
4409 4538 4.373116 GACGCCAAGCTCACCCGA 62.373 66.667 0.00 0.00 0.00 5.14
4434 4563 5.698545 CCTTCTTCGAAGAACAATCAGAAGT 59.301 40.000 31.62 0.00 45.90 3.01
4543 4675 0.481567 CATGCTCCCAAGATCCCCAT 59.518 55.000 0.00 0.00 0.00 4.00
4551 4683 1.404391 GAATGAGTGCATGCTCCCAAG 59.596 52.381 20.33 0.00 34.26 3.61
4627 4759 5.008712 TCAGAGAGGCTAACATACATACACG 59.991 44.000 0.00 0.00 0.00 4.49
4662 4797 1.610886 GGGTTACTGCCTGGACTTGAC 60.611 57.143 0.00 0.00 0.00 3.18
4665 4800 0.693049 CAGGGTTACTGCCTGGACTT 59.307 55.000 0.00 0.00 40.97 3.01
4673 4808 3.851098 CTGAACTACTCAGGGTTACTGC 58.149 50.000 0.00 0.00 46.89 4.40
4737 4873 7.506328 ACTGTGAGAAATACTAAACCCAAAC 57.494 36.000 0.00 0.00 0.00 2.93
4759 4901 5.870978 GCAAAAGCACATTCATATTCCAACT 59.129 36.000 0.00 0.00 0.00 3.16
4822 4964 5.753721 AGGAAGCTCAGATAAAACTCAGT 57.246 39.130 0.00 0.00 0.00 3.41
4869 5106 1.391577 TCGATCGACCCAAACGGATA 58.608 50.000 15.15 0.00 34.64 2.59
4874 5111 0.672401 TGCCTTCGATCGACCCAAAC 60.672 55.000 19.26 5.12 0.00 2.93
4882 5119 1.493950 GGACAGCATGCCTTCGATCG 61.494 60.000 15.66 9.36 42.53 3.69
4883 5120 0.462581 TGGACAGCATGCCTTCGATC 60.463 55.000 15.66 3.06 42.53 3.69
4884 5121 0.463295 CTGGACAGCATGCCTTCGAT 60.463 55.000 15.66 0.00 42.53 3.59
4885 5122 1.078918 CTGGACAGCATGCCTTCGA 60.079 57.895 15.66 7.37 42.53 3.71
4886 5123 3.494378 CTGGACAGCATGCCTTCG 58.506 61.111 15.66 3.07 42.53 3.79
4896 5133 1.735920 GACAGACGCAGCTGGACAG 60.736 63.158 17.12 5.78 40.20 3.51
4924 5161 4.360964 TACCGTTGGACGCACCGG 62.361 66.667 0.00 0.00 45.72 5.28
4925 5162 2.807895 CTACCGTTGGACGCACCG 60.808 66.667 0.00 0.00 40.91 4.94
4953 5260 1.264288 GGAGAAAGGTTCGCAAGTGTG 59.736 52.381 0.00 0.00 39.48 3.82
4962 5269 1.241990 GGTTGGCCGGAGAAAGGTTC 61.242 60.000 5.05 0.00 0.00 3.62
4969 5276 2.203938 AAGAGGGTTGGCCGGAGA 60.204 61.111 5.05 0.00 34.97 3.71
4970 5277 2.269241 GAAGAGGGTTGGCCGGAG 59.731 66.667 5.05 0.00 34.97 4.63
4973 5280 2.032071 AACGAAGAGGGTTGGCCG 59.968 61.111 0.00 0.00 34.97 6.13
4979 5286 0.687354 ATGCAGTCAACGAAGAGGGT 59.313 50.000 0.00 0.00 0.00 4.34
4989 5296 0.890542 GCAGTGGACCATGCAGTCAA 60.891 55.000 18.43 0.00 42.11 3.18
4996 5303 2.981302 TCCGAGCAGTGGACCATG 59.019 61.111 0.00 0.00 0.00 3.66
5054 5405 3.408851 GACGCGACAAACCCCGTC 61.409 66.667 15.93 0.00 42.39 4.79
5067 5418 4.760047 ACTCACCATGGCCGACGC 62.760 66.667 13.04 0.00 0.00 5.19
5073 5424 2.753043 CTGCCCACTCACCATGGC 60.753 66.667 13.04 0.00 44.27 4.40
5089 5440 1.530655 CAAAACCCTTCGCCACCCT 60.531 57.895 0.00 0.00 0.00 4.34
5092 5443 1.524008 CTCCCAAAACCCTTCGCCAC 61.524 60.000 0.00 0.00 0.00 5.01
5093 5444 1.228429 CTCCCAAAACCCTTCGCCA 60.228 57.895 0.00 0.00 0.00 5.69
5094 5445 0.960861 CTCTCCCAAAACCCTTCGCC 60.961 60.000 0.00 0.00 0.00 5.54
5095 5446 0.036306 TCTCTCCCAAAACCCTTCGC 59.964 55.000 0.00 0.00 0.00 4.70
5096 5447 1.348036 ACTCTCTCCCAAAACCCTTCG 59.652 52.381 0.00 0.00 0.00 3.79
5097 5448 2.553247 CCACTCTCTCCCAAAACCCTTC 60.553 54.545 0.00 0.00 0.00 3.46
5098 5449 1.425448 CCACTCTCTCCCAAAACCCTT 59.575 52.381 0.00 0.00 0.00 3.95
5109 5460 5.350504 TTCATCTCATTTCCCACTCTCTC 57.649 43.478 0.00 0.00 0.00 3.20
5114 5465 3.698040 GCACATTCATCTCATTTCCCACT 59.302 43.478 0.00 0.00 0.00 4.00
5116 5467 3.025978 GGCACATTCATCTCATTTCCCA 58.974 45.455 0.00 0.00 0.00 4.37
5117 5468 3.025978 TGGCACATTCATCTCATTTCCC 58.974 45.455 0.00 0.00 0.00 3.97
5118 5469 3.181483 GGTGGCACATTCATCTCATTTCC 60.181 47.826 20.82 0.00 44.52 3.13
5127 5478 0.321210 TTCGTCGGTGGCACATTCAT 60.321 50.000 20.82 0.00 44.52 2.57
5130 5481 1.305219 CCATTCGTCGGTGGCACATT 61.305 55.000 20.82 0.00 44.52 2.71
5145 5496 2.310052 CTCTTTTCTCCCCTGACCCATT 59.690 50.000 0.00 0.00 0.00 3.16
5146 5497 1.918957 CTCTTTTCTCCCCTGACCCAT 59.081 52.381 0.00 0.00 0.00 4.00
5147 5498 1.362224 CTCTTTTCTCCCCTGACCCA 58.638 55.000 0.00 0.00 0.00 4.51
5150 5501 1.003696 CCCACTCTTTTCTCCCCTGAC 59.996 57.143 0.00 0.00 0.00 3.51
5151 5502 1.132527 TCCCACTCTTTTCTCCCCTGA 60.133 52.381 0.00 0.00 0.00 3.86
5155 5506 1.978580 TGACTCCCACTCTTTTCTCCC 59.021 52.381 0.00 0.00 0.00 4.30
5157 5508 2.678324 CGTGACTCCCACTCTTTTCTC 58.322 52.381 0.00 0.00 43.53 2.87
5161 5512 1.371558 GGCGTGACTCCCACTCTTT 59.628 57.895 0.00 0.00 43.53 2.52
5165 5516 2.665000 CATGGCGTGACTCCCACT 59.335 61.111 0.00 0.00 43.53 4.00
5195 5549 3.825833 GAGCCCGGTATGCGTCGAG 62.826 68.421 0.00 0.00 0.00 4.04
5196 5550 3.896133 GAGCCCGGTATGCGTCGA 61.896 66.667 0.00 0.00 0.00 4.20
5198 5552 0.814010 ATTTGAGCCCGGTATGCGTC 60.814 55.000 0.00 0.00 0.00 5.19
5203 5557 2.583143 GCCTAAATTTGAGCCCGGTAT 58.417 47.619 0.00 0.00 0.00 2.73
5207 5561 1.724582 CCGGCCTAAATTTGAGCCCG 61.725 60.000 21.19 16.45 42.66 6.13
5208 5562 0.395173 TCCGGCCTAAATTTGAGCCC 60.395 55.000 21.19 7.88 42.66 5.19
5212 5566 3.714798 ACCTATCTCCGGCCTAAATTTGA 59.285 43.478 0.00 0.00 0.00 2.69
5214 5568 3.244112 CGACCTATCTCCGGCCTAAATTT 60.244 47.826 0.00 0.00 0.00 1.82
5220 5574 2.913060 GCGACCTATCTCCGGCCT 60.913 66.667 0.00 0.00 0.00 5.19
5225 5579 0.818445 TCCACTCGCGACCTATCTCC 60.818 60.000 3.71 0.00 0.00 3.71
5227 5581 0.955178 CATCCACTCGCGACCTATCT 59.045 55.000 3.71 0.00 0.00 1.98
5228 5582 0.952280 TCATCCACTCGCGACCTATC 59.048 55.000 3.71 0.00 0.00 2.08
5229 5583 1.399714 TTCATCCACTCGCGACCTAT 58.600 50.000 3.71 0.00 0.00 2.57
5230 5584 1.179152 TTTCATCCACTCGCGACCTA 58.821 50.000 3.71 0.00 0.00 3.08
5231 5585 0.320374 TTTTCATCCACTCGCGACCT 59.680 50.000 3.71 0.00 0.00 3.85
5234 5588 1.011968 CGGTTTTCATCCACTCGCGA 61.012 55.000 9.26 9.26 0.00 5.87
5236 5590 0.672401 TCCGGTTTTCATCCACTCGC 60.672 55.000 0.00 0.00 0.00 5.03
5237 5591 2.024176 ATCCGGTTTTCATCCACTCG 57.976 50.000 0.00 0.00 0.00 4.18
5238 5592 3.467803 CCTATCCGGTTTTCATCCACTC 58.532 50.000 0.00 0.00 0.00 3.51
5239 5593 2.172717 CCCTATCCGGTTTTCATCCACT 59.827 50.000 0.00 0.00 0.00 4.00
5241 5595 2.171870 GACCCTATCCGGTTTTCATCCA 59.828 50.000 0.00 0.00 35.79 3.41
5242 5596 2.486727 GGACCCTATCCGGTTTTCATCC 60.487 54.545 0.00 0.00 37.88 3.51
5243 5597 2.847441 GGACCCTATCCGGTTTTCATC 58.153 52.381 0.00 0.00 37.88 2.92
5255 5609 4.019321 CCCATCGACATAAATGGACCCTAT 60.019 45.833 1.99 0.00 44.37 2.57
5256 5610 3.326588 CCCATCGACATAAATGGACCCTA 59.673 47.826 1.99 0.00 44.37 3.53
5257 5611 2.106511 CCCATCGACATAAATGGACCCT 59.893 50.000 1.99 0.00 44.37 4.34
5258 5612 2.158667 ACCCATCGACATAAATGGACCC 60.159 50.000 1.99 0.00 44.37 4.46
5259 5613 3.208747 ACCCATCGACATAAATGGACC 57.791 47.619 1.99 0.00 44.37 4.46
5261 5615 3.550820 CCAACCCATCGACATAAATGGA 58.449 45.455 1.99 0.00 44.37 3.41
5262 5616 2.622942 CCCAACCCATCGACATAAATGG 59.377 50.000 0.00 0.00 41.81 3.16
5263 5617 2.034558 GCCCAACCCATCGACATAAATG 59.965 50.000 0.00 0.00 0.00 2.32
5264 5618 2.306847 GCCCAACCCATCGACATAAAT 58.693 47.619 0.00 0.00 0.00 1.40
5265 5619 1.683629 GGCCCAACCCATCGACATAAA 60.684 52.381 0.00 0.00 0.00 1.40
5268 5622 2.275418 GGCCCAACCCATCGACAT 59.725 61.111 0.00 0.00 0.00 3.06
5269 5623 4.402528 CGGCCCAACCCATCGACA 62.403 66.667 0.00 0.00 33.26 4.35
5275 5629 4.531426 AAACTGCGGCCCAACCCA 62.531 61.111 0.00 0.00 33.26 4.51
5277 5631 0.679960 ATAGAAACTGCGGCCCAACC 60.680 55.000 0.00 0.00 0.00 3.77
5285 5639 3.424433 GGTCAAAACGGATAGAAACTGCG 60.424 47.826 0.00 0.00 0.00 5.18
5288 5642 4.360951 TGGGTCAAAACGGATAGAAACT 57.639 40.909 0.00 0.00 0.00 2.66
5302 5656 1.002251 GTGCGATTCGTTTTGGGTCAA 60.002 47.619 8.03 0.00 0.00 3.18
5303 5657 0.589223 GTGCGATTCGTTTTGGGTCA 59.411 50.000 8.03 0.00 0.00 4.02
5305 5659 1.572447 CGTGCGATTCGTTTTGGGT 59.428 52.632 8.03 0.00 0.00 4.51
5306 5660 1.795962 GCGTGCGATTCGTTTTGGG 60.796 57.895 8.03 0.00 0.00 4.12
5308 5662 2.137395 CCGCGTGCGATTCGTTTTG 61.137 57.895 16.91 0.00 42.83 2.44
5309 5663 2.172419 CCGCGTGCGATTCGTTTT 59.828 55.556 16.91 0.00 42.83 2.43
5310 5664 2.735478 TCCGCGTGCGATTCGTTT 60.735 55.556 16.91 0.00 42.83 3.60
5311 5665 3.475774 GTCCGCGTGCGATTCGTT 61.476 61.111 16.91 0.00 42.83 3.85
5319 5673 2.452366 AATTTTGTCCGTCCGCGTGC 62.452 55.000 4.92 0.00 36.15 5.34
5320 5674 0.452122 GAATTTTGTCCGTCCGCGTG 60.452 55.000 4.92 0.00 36.15 5.34
5322 5676 1.225637 CGAATTTTGTCCGTCCGCG 60.226 57.895 0.00 0.00 37.95 6.46
5323 5677 0.179233 GACGAATTTTGTCCGTCCGC 60.179 55.000 5.58 0.00 44.67 5.54
5326 5680 0.515717 CGCGACGAATTTTGTCCGTC 60.516 55.000 0.00 6.57 46.27 4.79
5327 5681 1.489824 CGCGACGAATTTTGTCCGT 59.510 52.632 0.00 0.00 39.41 4.69
5329 5683 4.036544 GCGCGACGAATTTTGTCC 57.963 55.556 12.10 3.94 32.68 4.02
5340 5694 4.072088 CAACTCCCAACGCGCGAC 62.072 66.667 39.36 0.00 0.00 5.19
5354 5708 1.530323 ACCACATTCGTAAGGGCAAC 58.470 50.000 0.00 0.00 38.47 4.17
5364 5718 2.076863 GGACCTTGAGAACCACATTCG 58.923 52.381 0.00 0.00 42.69 3.34
5372 5726 0.035915 GAGGCCTGGACCTTGAGAAC 60.036 60.000 12.00 0.00 41.32 3.01
5376 5730 1.920325 CTGGAGGCCTGGACCTTGA 60.920 63.158 12.00 0.00 41.32 3.02
5384 5738 0.692419 ATAGTGACCCTGGAGGCCTG 60.692 60.000 12.00 0.00 40.58 4.85
5387 5741 1.964933 GAGTATAGTGACCCTGGAGGC 59.035 57.143 0.00 0.00 40.58 4.70
5389 5743 2.959707 GTGGAGTATAGTGACCCTGGAG 59.040 54.545 0.00 0.00 0.00 3.86
5402 5756 0.892755 TCGCTTGTTCGGTGGAGTAT 59.107 50.000 0.00 0.00 0.00 2.12
5420 5774 0.894184 TCTGACCTCTGACGGGTGTC 60.894 60.000 0.00 0.00 45.71 3.67
5423 5777 0.896019 CTGTCTGACCTCTGACGGGT 60.896 60.000 5.17 0.00 44.54 5.28
5434 5788 2.093973 CCATGGTAGTGGTCTGTCTGAC 60.094 54.545 2.57 0.00 44.63 3.51
5435 5789 2.179427 CCATGGTAGTGGTCTGTCTGA 58.821 52.381 2.57 0.00 34.46 3.27
5436 5790 1.406069 GCCATGGTAGTGGTCTGTCTG 60.406 57.143 14.67 0.00 41.47 3.51
5437 5791 0.905357 GCCATGGTAGTGGTCTGTCT 59.095 55.000 14.67 0.00 41.47 3.41
5438 5792 0.613260 TGCCATGGTAGTGGTCTGTC 59.387 55.000 14.67 0.00 41.47 3.51
5439 5793 0.615331 CTGCCATGGTAGTGGTCTGT 59.385 55.000 20.86 0.00 41.47 3.41


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

AutoCloner maintained by Alex Coulton.