Multiple sequence alignment - TraesCS1D01G159300

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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 TraesCS1D01G159300 chr1D 100.000 4577 0 0 1 4577 225058269 225062845 0.000000e+00 8453.0
1 TraesCS1D01G159300 chr1D 98.305 472 6 2 239 709 225052420 225051950 0.000000e+00 826.0
2 TraesCS1D01G159300 chr1A 95.536 2173 80 7 831 2991 292881907 292879740 0.000000e+00 3459.0
3 TraesCS1D01G159300 chr1A 92.909 959 47 9 2991 3932 292879701 292878747 0.000000e+00 1375.0
4 TraesCS1D01G159300 chr1A 95.035 423 20 1 4155 4577 292878723 292878302 0.000000e+00 664.0
5 TraesCS1D01G159300 chr1B 95.190 2162 95 7 831 2991 324778553 324780706 0.000000e+00 3408.0
6 TraesCS1D01G159300 chr1B 90.899 945 57 10 2991 3924 324780745 324781671 0.000000e+00 1242.0
7 TraesCS1D01G159300 chr1B 92.676 710 49 3 1 709 86777051 86776344 0.000000e+00 1020.0
8 TraesCS1D01G159300 chr1B 96.691 272 8 1 4162 4432 324789701 324789972 6.980000e-123 451.0
9 TraesCS1D01G159300 chr1B 95.050 101 5 0 4477 4577 324790283 324790383 4.740000e-35 159.0
10 TraesCS1D01G159300 chr4D 98.592 710 8 2 1 709 92071391 92070683 0.000000e+00 1254.0
11 TraesCS1D01G159300 chr4D 98.837 86 1 0 745 830 92069174 92069089 2.210000e-33 154.0
12 TraesCS1D01G159300 chr4D 96.078 51 2 0 831 881 18734092 18734142 2.930000e-12 84.2
13 TraesCS1D01G159300 chr7D 85.079 315 36 9 55 359 579631630 579631943 1.240000e-80 311.0
14 TraesCS1D01G159300 chr5A 91.503 153 13 0 1 153 409336902 409336750 1.290000e-50 211.0
15 TraesCS1D01G159300 chr5A 94.545 55 3 0 831 885 510463933 510463987 8.160000e-13 86.1
16 TraesCS1D01G159300 chrUn 90.850 153 14 0 1 153 108530420 108530572 6.000000e-49 206.0
17 TraesCS1D01G159300 chr6B 87.730 163 19 1 1 162 345632869 345632707 6.040000e-44 189.0
18 TraesCS1D01G159300 chr6B 94.444 54 2 1 831 884 473067473 473067525 1.060000e-11 82.4
19 TraesCS1D01G159300 chr6D 89.256 121 13 0 2 122 17455667 17455787 7.930000e-33 152.0
20 TraesCS1D01G159300 chr6D 86.179 123 17 0 1 123 193213955 193213833 2.870000e-27 134.0
21 TraesCS1D01G159300 chr6D 94.444 54 2 1 831 884 306137346 306137398 1.060000e-11 82.4
22 TraesCS1D01G159300 chr6A 87.603 121 15 0 2 122 18346589 18346709 1.720000e-29 141.0
23 TraesCS1D01G159300 chr2D 85.088 114 16 1 400 512 21302317 21302204 1.040000e-21 115.0
24 TraesCS1D01G159300 chr7B 87.640 89 9 2 298 385 130135927 130136014 8.100000e-18 102.0
25 TraesCS1D01G159300 chr4B 98.077 52 1 0 831 882 30841062 30841113 1.750000e-14 91.6
26 TraesCS1D01G159300 chr4B 96.364 55 2 0 831 885 30842693 30842747 1.750000e-14 91.6
27 TraesCS1D01G159300 chr4A 96.364 55 2 0 831 885 582505919 582505865 1.750000e-14 91.6


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 TraesCS1D01G159300 chr1D 225058269 225062845 4576 False 8453.000000 8453 100.000000 1 4577 1 chr1D.!!$F1 4576
1 TraesCS1D01G159300 chr1A 292878302 292881907 3605 True 1832.666667 3459 94.493333 831 4577 3 chr1A.!!$R1 3746
2 TraesCS1D01G159300 chr1B 324778553 324781671 3118 False 2325.000000 3408 93.044500 831 3924 2 chr1B.!!$F1 3093
3 TraesCS1D01G159300 chr1B 86776344 86777051 707 True 1020.000000 1020 92.676000 1 709 1 chr1B.!!$R1 708
4 TraesCS1D01G159300 chr1B 324789701 324790383 682 False 305.000000 451 95.870500 4162 4577 2 chr1B.!!$F2 415
5 TraesCS1D01G159300 chr4D 92069089 92071391 2302 True 704.000000 1254 98.714500 1 830 2 chr4D.!!$R1 829

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
588 592 2.427812 GTGAGCAACTCCTACTACCCTC 59.572 54.545 0.0 0.0 0.00 4.30 F
1290 2775 1.347707 TCCACAGCGTTCCATCTTCTT 59.652 47.619 0.0 0.0 0.00 2.52 F
1813 3301 0.819582 CCAGTGATTTGTGGCCCATC 59.180 55.000 0.0 0.0 0.00 3.51 F
2457 3947 0.178981 ATCTGTGTTGCCAGTTGCCT 60.179 50.000 0.0 0.0 40.16 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 3119 0.031449 TTGTGTCGCTGATCGTGTGA 59.969 50.000 0.0 0.0 39.67 3.58 R
2438 3928 2.344535 GGCAACTGGCAACACAGAT 58.655 52.632 0.0 0.0 46.17 2.90 R
3502 5041 1.156736 CATCCAAGACCCACACGTTC 58.843 55.000 0.0 0.0 0.00 3.95 R
3976 5527 0.042013 CTCGCTATCGACGGAGACAC 60.042 60.000 0.0 0.0 40.21 3.67 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
531 534 7.951530 AATTGTGCAAAGAAAAATCCTACTG 57.048 32.000 0.00 0.00 0.00 2.74
535 538 3.258123 GCAAAGAAAAATCCTACTGCCCA 59.742 43.478 0.00 0.00 0.00 5.36
588 592 2.427812 GTGAGCAACTCCTACTACCCTC 59.572 54.545 0.00 0.00 0.00 4.30
662 666 6.072783 GCAACTGTCTCTAGCAAAAGAAATCT 60.073 38.462 0.00 0.00 0.00 2.40
709 713 5.778862 TGCAAAACTATTCTAGCAAAACCC 58.221 37.500 0.00 0.00 0.00 4.11
725 2131 2.444706 CCCTCCTCTGATCCGCCA 60.445 66.667 0.00 0.00 0.00 5.69
738 2144 2.501128 CGCCACCTCCACATCGAT 59.499 61.111 0.00 0.00 0.00 3.59
903 2380 8.761575 AATTTGCCAGTATTACATGAAAAGTG 57.238 30.769 0.00 0.00 0.00 3.16
909 2386 9.289303 GCCAGTATTACATGAAAAGTGTATTTG 57.711 33.333 0.00 0.00 32.56 2.32
1254 2739 3.210012 AAGGCACGGCTCACCCAAT 62.210 57.895 0.00 0.00 0.00 3.16
1290 2775 1.347707 TCCACAGCGTTCCATCTTCTT 59.652 47.619 0.00 0.00 0.00 2.52
1292 2777 1.466167 CACAGCGTTCCATCTTCTTGG 59.534 52.381 0.00 0.00 38.18 3.61
1462 2947 6.051717 ACTACATTGAGGTATCTTGCACATC 58.948 40.000 0.00 0.00 0.00 3.06
1488 2973 6.563222 TGGGTTTGTAATAGTTTACAGCAC 57.437 37.500 0.00 1.82 46.22 4.40
1499 2987 5.399604 AGTTTACAGCACGTTAGTTTGTC 57.600 39.130 0.00 0.00 30.92 3.18
1621 3109 6.964934 GTCGGTTATTGGTGACATTTTGATAC 59.035 38.462 0.00 0.00 42.32 2.24
1622 3110 6.655425 TCGGTTATTGGTGACATTTTGATACA 59.345 34.615 0.00 0.00 42.32 2.29
1623 3111 6.966632 CGGTTATTGGTGACATTTTGATACAG 59.033 38.462 0.00 0.00 42.32 2.74
1630 3118 6.206634 TGGTGACATTTTGATACAGAGGAAAC 59.793 38.462 0.00 0.00 33.40 2.78
1631 3119 7.908862 TGGTGACATTTTGATACAGAGGAAACT 60.909 37.037 0.00 0.00 38.91 2.66
1644 3132 1.670087 AGGAAACTCACACGATCAGCG 60.670 52.381 0.00 0.00 41.69 5.18
1652 3140 1.275471 ACACGATCAGCGACACAACG 61.275 55.000 0.00 0.00 44.57 4.10
1678 3166 4.074970 AGTTGCCATGAAAGTTCCACTAG 58.925 43.478 0.00 0.00 0.00 2.57
1739 3227 5.239525 GTCTTGTTCCATGTAAAGTTCAGCT 59.760 40.000 0.00 0.00 0.00 4.24
1752 3240 3.356290 AGTTCAGCTTTGTTTGGTGAGT 58.644 40.909 0.00 0.00 41.87 3.41
1813 3301 0.819582 CCAGTGATTTGTGGCCCATC 59.180 55.000 0.00 0.00 0.00 3.51
1871 3359 4.377897 CTCTGTTGCTCATGAGATGCATA 58.622 43.478 27.04 11.59 36.55 3.14
1900 3388 3.054655 TGGCCTGTAATTTAGGTCACTCC 60.055 47.826 3.32 4.22 44.54 3.85
2118 3606 6.644347 ACTTGAGGTAATATTGACTGACTGG 58.356 40.000 0.00 0.00 0.00 4.00
2164 3652 1.336240 GCACAACTGGAGGACAAATGC 60.336 52.381 0.00 0.00 0.00 3.56
2165 3653 2.233271 CACAACTGGAGGACAAATGCT 58.767 47.619 0.00 0.00 0.00 3.79
2261 3751 7.148171 GCCATTTTGAGCTTGAGTAACTTCTAT 60.148 37.037 0.00 0.00 0.00 1.98
2276 3766 8.741841 AGTAACTTCTATTTGAGTGAGGTAGAC 58.258 37.037 0.00 0.00 0.00 2.59
2283 3773 2.457598 TGAGTGAGGTAGACATGGTCC 58.542 52.381 0.00 0.00 32.18 4.46
2331 3821 6.094719 TGTTTTCATTCATCTATGCTTGTGC 58.905 36.000 0.00 0.00 40.20 4.57
2427 3917 5.079689 TGACATACCGACAGCATTCTTTA 57.920 39.130 0.00 0.00 0.00 1.85
2438 3928 9.834628 CCGACAGCATTCTTTATAAAAGTTAAA 57.165 29.630 0.00 0.00 0.00 1.52
2457 3947 0.178981 ATCTGTGTTGCCAGTTGCCT 60.179 50.000 0.00 0.00 40.16 4.75
2477 3967 3.456277 CCTCCAGATTAACCTTAGGCACT 59.544 47.826 0.00 0.00 46.37 4.40
2623 4114 0.674895 CAGGGCTTCGGGTTTCTCTG 60.675 60.000 0.00 0.00 0.00 3.35
2706 4197 4.018415 ACCTGGTCACAATAGGTAGCATTT 60.018 41.667 0.00 0.00 42.78 2.32
2736 4227 6.368516 TGCTTTGTTATTCCTTTTAAGCATGC 59.631 34.615 10.51 10.51 40.86 4.06
2740 4231 6.781138 TGTTATTCCTTTTAAGCATGCTACG 58.219 36.000 23.00 2.77 0.00 3.51
2873 4364 3.184986 GCACAAAGCACCAATGTCATTTC 59.815 43.478 0.00 0.00 44.79 2.17
2944 4435 6.989759 ACTCCTTTTTATTGTGGCGAATTTTT 59.010 30.769 0.00 0.00 0.00 1.94
3014 4544 8.503196 CGTAATGATAGCCACATAAATTGCTAA 58.497 33.333 0.00 0.00 39.53 3.09
3018 4548 8.378172 TGATAGCCACATAAATTGCTAACTAC 57.622 34.615 0.00 0.00 39.53 2.73
3090 4621 1.985895 CCCCCTCCACTGAACTTAACT 59.014 52.381 0.00 0.00 0.00 2.24
3173 4704 3.523564 AGGCACATACCTAACCTGAATGT 59.476 43.478 0.00 0.00 38.67 2.71
3316 4847 0.800012 GAGCTCGAGTTCGTGAGAGT 59.200 55.000 13.75 0.00 43.69 3.24
3323 4854 1.609555 GAGTTCGTGAGAGTGGAGTGT 59.390 52.381 0.00 0.00 43.69 3.55
3353 4892 1.656441 CTTGCTTTGTTGGAGCGCT 59.344 52.632 11.27 11.27 43.02 5.92
3372 4911 4.070552 GGGTGGTTCGCTCGCTCT 62.071 66.667 0.00 0.00 0.00 4.09
3411 4950 7.156673 ACATAGGACGTTCTTTAGCTGTTTTA 58.843 34.615 0.00 0.00 0.00 1.52
3502 5041 5.885020 GAGTAATTTGGAACTCGGTATCG 57.115 43.478 0.00 0.00 33.38 2.92
3511 5050 0.169672 ACTCGGTATCGAACGTGTGG 59.830 55.000 0.00 0.00 45.47 4.17
3561 5101 9.585099 TTAATGGCTTTGACAATCAATTATGAC 57.415 29.630 0.00 0.00 38.69 3.06
3577 5119 8.305317 TCAATTATGACTGTTGCATTTTGATGA 58.695 29.630 0.00 0.00 29.48 2.92
3595 5137 1.340889 TGACTGGATGCTTGGTTTTGC 59.659 47.619 0.00 0.00 0.00 3.68
3614 5156 2.875317 TGCTTTCGCATACTGTTGTTGA 59.125 40.909 0.00 0.00 42.25 3.18
3681 5225 0.096802 TACTCGTGCATGCATTTGCG 59.903 50.000 25.64 21.85 45.77 4.85
3731 5275 7.309770 TGTTAAAGCAAAAATCCCTGGTTAT 57.690 32.000 0.00 0.00 33.14 1.89
3790 5334 5.123820 TCGACACAAATTCTTTCCATGGATC 59.876 40.000 17.06 4.35 0.00 3.36
3792 5336 4.766891 ACACAAATTCTTTCCATGGATCGT 59.233 37.500 17.06 1.40 0.00 3.73
3814 5364 5.452776 CGTCTATAGGGGCAGATTAAACACA 60.453 44.000 0.00 0.00 0.00 3.72
3905 5456 0.465097 ATCCCCGCAGAAATGCTCAG 60.465 55.000 0.00 0.00 0.00 3.35
3918 5469 2.957402 TGCTCAGTGGTTTTGAGGAT 57.043 45.000 4.62 0.00 41.82 3.24
3924 5475 5.009610 GCTCAGTGGTTTTGAGGATGTTAAA 59.990 40.000 4.62 0.00 41.82 1.52
3925 5476 6.294731 GCTCAGTGGTTTTGAGGATGTTAAAT 60.295 38.462 4.62 0.00 41.82 1.40
3926 5477 6.980593 TCAGTGGTTTTGAGGATGTTAAATG 58.019 36.000 0.00 0.00 0.00 2.32
3927 5478 6.549364 TCAGTGGTTTTGAGGATGTTAAATGT 59.451 34.615 0.00 0.00 0.00 2.71
3928 5479 6.863126 CAGTGGTTTTGAGGATGTTAAATGTC 59.137 38.462 0.00 0.00 0.00 3.06
3929 5480 6.015434 AGTGGTTTTGAGGATGTTAAATGTCC 60.015 38.462 0.00 0.00 0.00 4.02
3930 5481 5.835819 TGGTTTTGAGGATGTTAAATGTCCA 59.164 36.000 5.22 0.00 34.42 4.02
3931 5482 6.496565 TGGTTTTGAGGATGTTAAATGTCCAT 59.503 34.615 5.22 0.00 34.42 3.41
3932 5483 7.016072 TGGTTTTGAGGATGTTAAATGTCCATT 59.984 33.333 5.22 0.00 34.42 3.16
3933 5484 7.331687 GGTTTTGAGGATGTTAAATGTCCATTG 59.668 37.037 0.00 0.00 34.42 2.82
3935 5486 6.513806 TGAGGATGTTAAATGTCCATTGTG 57.486 37.500 0.00 0.00 34.42 3.33
3948 5499 1.402787 CATTGTGGATGGTTAGGCCC 58.597 55.000 0.00 0.00 36.04 5.80
3949 5500 0.261696 ATTGTGGATGGTTAGGCCCC 59.738 55.000 0.00 0.00 36.04 5.80
3950 5501 1.869824 TTGTGGATGGTTAGGCCCCC 61.870 60.000 0.00 0.00 36.04 5.40
3952 5503 2.006415 TGGATGGTTAGGCCCCCAG 61.006 63.158 11.62 0.00 35.12 4.45
3964 5515 3.350163 CCCCAGCCCACCAAGGAT 61.350 66.667 0.00 0.00 41.22 3.24
3965 5516 2.772924 CCCAGCCCACCAAGGATT 59.227 61.111 0.00 0.00 41.22 3.01
3966 5517 1.079073 CCCAGCCCACCAAGGATTT 59.921 57.895 0.00 0.00 41.22 2.17
3967 5518 1.259840 CCCAGCCCACCAAGGATTTG 61.260 60.000 0.00 0.00 41.22 2.32
3968 5519 0.251742 CCAGCCCACCAAGGATTTGA 60.252 55.000 0.00 0.00 41.22 2.69
3969 5520 0.890683 CAGCCCACCAAGGATTTGAC 59.109 55.000 0.00 0.00 41.22 3.18
3970 5521 0.609131 AGCCCACCAAGGATTTGACG 60.609 55.000 0.00 0.00 41.22 4.35
3971 5522 1.883021 CCCACCAAGGATTTGACGC 59.117 57.895 0.00 0.00 41.22 5.19
3972 5523 0.609131 CCCACCAAGGATTTGACGCT 60.609 55.000 0.00 0.00 41.22 5.07
3973 5524 1.247567 CCACCAAGGATTTGACGCTT 58.752 50.000 0.00 0.00 41.22 4.68
3974 5525 1.613437 CCACCAAGGATTTGACGCTTT 59.387 47.619 0.00 0.00 41.22 3.51
3975 5526 2.607771 CCACCAAGGATTTGACGCTTTG 60.608 50.000 0.00 0.00 41.22 2.77
3976 5527 1.613437 ACCAAGGATTTGACGCTTTGG 59.387 47.619 0.00 0.00 40.59 3.28
3977 5528 1.613437 CCAAGGATTTGACGCTTTGGT 59.387 47.619 0.00 0.00 36.36 3.67
3978 5529 2.607771 CCAAGGATTTGACGCTTTGGTG 60.608 50.000 0.00 0.00 36.36 4.17
3979 5530 1.981256 AGGATTTGACGCTTTGGTGT 58.019 45.000 0.00 0.00 39.06 4.16
3984 5535 3.550656 GACGCTTTGGTGTCTCCG 58.449 61.111 2.93 0.00 46.12 4.63
3985 5536 1.300697 GACGCTTTGGTGTCTCCGT 60.301 57.895 2.93 0.00 46.12 4.69
3986 5537 1.282930 GACGCTTTGGTGTCTCCGTC 61.283 60.000 0.00 0.00 46.12 4.79
3987 5538 2.372690 CGCTTTGGTGTCTCCGTCG 61.373 63.158 0.00 0.00 39.52 5.12
3988 5539 1.006571 GCTTTGGTGTCTCCGTCGA 60.007 57.895 0.00 0.00 39.52 4.20
3989 5540 0.389948 GCTTTGGTGTCTCCGTCGAT 60.390 55.000 0.00 0.00 39.52 3.59
3990 5541 1.135199 GCTTTGGTGTCTCCGTCGATA 60.135 52.381 0.00 0.00 39.52 2.92
3991 5542 2.798680 CTTTGGTGTCTCCGTCGATAG 58.201 52.381 0.00 0.00 39.52 2.08
3992 5543 0.454600 TTGGTGTCTCCGTCGATAGC 59.545 55.000 0.00 0.00 39.52 2.97
3993 5544 1.009900 GGTGTCTCCGTCGATAGCG 60.010 63.158 0.00 0.00 39.35 4.26
3994 5545 1.434622 GGTGTCTCCGTCGATAGCGA 61.435 60.000 0.00 0.00 45.71 4.93
4009 5560 2.969238 CGAGGCGCCATGATGACC 60.969 66.667 31.54 5.67 0.00 4.02
4010 5561 2.507944 GAGGCGCCATGATGACCT 59.492 61.111 31.54 3.33 0.00 3.85
4011 5562 1.596477 GAGGCGCCATGATGACCTC 60.596 63.158 31.54 10.29 40.14 3.85
4012 5563 2.969238 GGCGCCATGATGACCTCG 60.969 66.667 24.80 0.00 0.00 4.63
4013 5564 3.643978 GCGCCATGATGACCTCGC 61.644 66.667 0.00 0.00 35.82 5.03
4014 5565 2.969238 CGCCATGATGACCTCGCC 60.969 66.667 0.00 0.00 0.00 5.54
4015 5566 2.507944 GCCATGATGACCTCGCCT 59.492 61.111 0.00 0.00 0.00 5.52
4016 5567 1.890979 GCCATGATGACCTCGCCTG 60.891 63.158 0.00 0.00 0.00 4.85
4017 5568 1.524002 CCATGATGACCTCGCCTGT 59.476 57.895 0.00 0.00 0.00 4.00
4018 5569 0.812811 CCATGATGACCTCGCCTGTG 60.813 60.000 0.00 0.00 0.00 3.66
4019 5570 0.107993 CATGATGACCTCGCCTGTGT 60.108 55.000 0.00 0.00 0.00 3.72
4020 5571 0.176680 ATGATGACCTCGCCTGTGTC 59.823 55.000 0.00 0.00 0.00 3.67
4021 5572 0.900182 TGATGACCTCGCCTGTGTCT 60.900 55.000 0.00 0.00 0.00 3.41
4022 5573 0.459237 GATGACCTCGCCTGTGTCTG 60.459 60.000 0.00 0.00 0.00 3.51
4023 5574 1.188219 ATGACCTCGCCTGTGTCTGT 61.188 55.000 0.00 0.00 0.00 3.41
4024 5575 1.373497 GACCTCGCCTGTGTCTGTG 60.373 63.158 0.00 0.00 0.00 3.66
4025 5576 2.088674 GACCTCGCCTGTGTCTGTGT 62.089 60.000 0.00 0.00 0.00 3.72
4026 5577 1.665916 CCTCGCCTGTGTCTGTGTG 60.666 63.158 0.00 0.00 0.00 3.82
4027 5578 1.068083 CTCGCCTGTGTCTGTGTGT 59.932 57.895 0.00 0.00 0.00 3.72
4028 5579 0.530650 CTCGCCTGTGTCTGTGTGTT 60.531 55.000 0.00 0.00 0.00 3.32
4029 5580 0.529773 TCGCCTGTGTCTGTGTGTTC 60.530 55.000 0.00 0.00 0.00 3.18
4030 5581 0.530650 CGCCTGTGTCTGTGTGTTCT 60.531 55.000 0.00 0.00 0.00 3.01
4031 5582 1.221414 GCCTGTGTCTGTGTGTTCTC 58.779 55.000 0.00 0.00 0.00 2.87
4032 5583 1.473257 GCCTGTGTCTGTGTGTTCTCA 60.473 52.381 0.00 0.00 0.00 3.27
4033 5584 2.905075 CCTGTGTCTGTGTGTTCTCAA 58.095 47.619 0.00 0.00 0.00 3.02
4034 5585 3.270027 CCTGTGTCTGTGTGTTCTCAAA 58.730 45.455 0.00 0.00 0.00 2.69
4035 5586 3.689161 CCTGTGTCTGTGTGTTCTCAAAA 59.311 43.478 0.00 0.00 0.00 2.44
4036 5587 4.155826 CCTGTGTCTGTGTGTTCTCAAAAA 59.844 41.667 0.00 0.00 0.00 1.94
4055 5606 4.639135 AAAAGAACTCCAGTCAAGCAAC 57.361 40.909 0.00 0.00 0.00 4.17
4056 5607 3.281727 AAGAACTCCAGTCAAGCAACA 57.718 42.857 0.00 0.00 0.00 3.33
4057 5608 2.843701 AGAACTCCAGTCAAGCAACAG 58.156 47.619 0.00 0.00 0.00 3.16
4058 5609 2.171448 AGAACTCCAGTCAAGCAACAGT 59.829 45.455 0.00 0.00 0.00 3.55
4059 5610 3.388024 AGAACTCCAGTCAAGCAACAGTA 59.612 43.478 0.00 0.00 0.00 2.74
4060 5611 3.838244 ACTCCAGTCAAGCAACAGTAA 57.162 42.857 0.00 0.00 0.00 2.24
4061 5612 4.150897 ACTCCAGTCAAGCAACAGTAAA 57.849 40.909 0.00 0.00 0.00 2.01
4062 5613 3.877508 ACTCCAGTCAAGCAACAGTAAAC 59.122 43.478 0.00 0.00 0.00 2.01
4063 5614 3.876914 CTCCAGTCAAGCAACAGTAAACA 59.123 43.478 0.00 0.00 0.00 2.83
4064 5615 4.265893 TCCAGTCAAGCAACAGTAAACAA 58.734 39.130 0.00 0.00 0.00 2.83
4065 5616 4.335315 TCCAGTCAAGCAACAGTAAACAAG 59.665 41.667 0.00 0.00 0.00 3.16
4066 5617 4.335315 CCAGTCAAGCAACAGTAAACAAGA 59.665 41.667 0.00 0.00 0.00 3.02
4067 5618 5.163663 CCAGTCAAGCAACAGTAAACAAGAA 60.164 40.000 0.00 0.00 0.00 2.52
4068 5619 5.967674 CAGTCAAGCAACAGTAAACAAGAAG 59.032 40.000 0.00 0.00 0.00 2.85
4069 5620 5.066505 AGTCAAGCAACAGTAAACAAGAAGG 59.933 40.000 0.00 0.00 0.00 3.46
4070 5621 5.065988 GTCAAGCAACAGTAAACAAGAAGGA 59.934 40.000 0.00 0.00 0.00 3.36
4071 5622 5.827797 TCAAGCAACAGTAAACAAGAAGGAT 59.172 36.000 0.00 0.00 0.00 3.24
4072 5623 5.948992 AGCAACAGTAAACAAGAAGGATC 57.051 39.130 0.00 0.00 0.00 3.36
4073 5624 4.762251 AGCAACAGTAAACAAGAAGGATCC 59.238 41.667 2.48 2.48 0.00 3.36
4074 5625 4.762251 GCAACAGTAAACAAGAAGGATCCT 59.238 41.667 9.02 9.02 0.00 3.24
4075 5626 5.106515 GCAACAGTAAACAAGAAGGATCCTC 60.107 44.000 16.52 8.89 0.00 3.71
4076 5627 5.167303 ACAGTAAACAAGAAGGATCCTCC 57.833 43.478 16.52 0.62 36.58 4.30
4077 5628 4.019231 ACAGTAAACAAGAAGGATCCTCCC 60.019 45.833 16.52 10.37 37.19 4.30
4078 5629 3.523972 AGTAAACAAGAAGGATCCTCCCC 59.476 47.826 16.52 7.68 37.19 4.81
4079 5630 2.059756 AACAAGAAGGATCCTCCCCA 57.940 50.000 16.52 0.00 37.19 4.96
4080 5631 2.059756 ACAAGAAGGATCCTCCCCAA 57.940 50.000 16.52 0.00 37.19 4.12
4081 5632 2.577970 ACAAGAAGGATCCTCCCCAAT 58.422 47.619 16.52 0.00 37.19 3.16
4082 5633 2.929043 ACAAGAAGGATCCTCCCCAATT 59.071 45.455 16.52 0.00 37.19 2.32
4083 5634 3.337909 ACAAGAAGGATCCTCCCCAATTT 59.662 43.478 16.52 0.00 37.19 1.82
4084 5635 3.677156 AGAAGGATCCTCCCCAATTTG 57.323 47.619 16.52 0.00 37.19 2.32
4085 5636 2.034878 GAAGGATCCTCCCCAATTTGC 58.965 52.381 16.52 0.00 37.19 3.68
4086 5637 1.312884 AGGATCCTCCCCAATTTGCT 58.687 50.000 9.02 0.00 37.19 3.91
4087 5638 1.648037 AGGATCCTCCCCAATTTGCTT 59.352 47.619 9.02 0.00 37.19 3.91
4088 5639 2.044908 AGGATCCTCCCCAATTTGCTTT 59.955 45.455 9.02 0.00 37.19 3.51
4089 5640 2.169144 GGATCCTCCCCAATTTGCTTTG 59.831 50.000 3.84 0.00 0.00 2.77
4090 5641 2.397044 TCCTCCCCAATTTGCTTTGT 57.603 45.000 0.00 0.00 0.00 2.83
4091 5642 3.534357 TCCTCCCCAATTTGCTTTGTA 57.466 42.857 0.00 0.00 0.00 2.41
4092 5643 3.430453 TCCTCCCCAATTTGCTTTGTAG 58.570 45.455 0.00 0.00 0.00 2.74
4102 5653 3.080647 GCTTTGTAGCATACGCCCT 57.919 52.632 0.00 0.00 46.99 5.19
4103 5654 1.379527 GCTTTGTAGCATACGCCCTT 58.620 50.000 0.00 0.00 46.99 3.95
4104 5655 2.557317 GCTTTGTAGCATACGCCCTTA 58.443 47.619 0.00 0.00 46.99 2.69
4105 5656 2.940410 GCTTTGTAGCATACGCCCTTAA 59.060 45.455 0.00 0.00 46.99 1.85
4106 5657 3.375922 GCTTTGTAGCATACGCCCTTAAA 59.624 43.478 0.00 0.00 46.99 1.52
4107 5658 4.036380 GCTTTGTAGCATACGCCCTTAAAT 59.964 41.667 0.00 0.00 46.99 1.40
4108 5659 5.449999 GCTTTGTAGCATACGCCCTTAAATT 60.450 40.000 0.00 0.00 46.99 1.82
4109 5660 6.518208 TTTGTAGCATACGCCCTTAAATTT 57.482 33.333 0.00 0.00 46.99 1.82
4110 5661 6.518208 TTGTAGCATACGCCCTTAAATTTT 57.482 33.333 0.00 0.00 46.99 1.82
4111 5662 5.885881 TGTAGCATACGCCCTTAAATTTTG 58.114 37.500 0.00 0.00 46.99 2.44
4112 5663 4.385358 AGCATACGCCCTTAAATTTTGG 57.615 40.909 0.00 0.00 39.83 3.28
4113 5664 2.863740 GCATACGCCCTTAAATTTTGGC 59.136 45.455 13.29 13.29 40.54 4.52
4114 5665 3.677424 GCATACGCCCTTAAATTTTGGCA 60.677 43.478 19.73 7.38 44.22 4.92
4115 5666 4.692228 CATACGCCCTTAAATTTTGGCAT 58.308 39.130 19.73 11.43 44.22 4.40
4116 5667 2.971307 ACGCCCTTAAATTTTGGCATG 58.029 42.857 19.73 10.86 44.22 4.06
4117 5668 1.665169 CGCCCTTAAATTTTGGCATGC 59.335 47.619 9.90 9.90 44.22 4.06
4118 5669 2.677613 CGCCCTTAAATTTTGGCATGCT 60.678 45.455 18.92 0.00 44.22 3.79
4119 5670 2.938451 GCCCTTAAATTTTGGCATGCTC 59.062 45.455 18.92 8.46 43.46 4.26
4120 5671 3.189285 CCCTTAAATTTTGGCATGCTCG 58.811 45.455 18.92 0.00 0.00 5.03
4121 5672 2.604462 CCTTAAATTTTGGCATGCTCGC 59.396 45.455 18.92 0.95 0.00 5.03
4122 5673 3.252400 CTTAAATTTTGGCATGCTCGCA 58.748 40.909 18.92 4.09 0.00 5.10
4123 5674 1.717194 AAATTTTGGCATGCTCGCAG 58.283 45.000 18.92 0.00 0.00 5.18
4124 5675 0.738412 AATTTTGGCATGCTCGCAGC 60.738 50.000 18.92 0.00 42.82 5.25
4125 5676 1.601419 ATTTTGGCATGCTCGCAGCT 61.601 50.000 18.92 0.00 42.97 4.24
4126 5677 2.203972 TTTTGGCATGCTCGCAGCTC 62.204 55.000 18.92 0.00 42.97 4.09
4130 5681 3.493440 CATGCTCGCAGCTCGCAA 61.493 61.111 9.21 0.00 42.97 4.85
4131 5682 2.513204 ATGCTCGCAGCTCGCAAT 60.513 55.556 9.21 0.00 42.97 3.56
4132 5683 2.820619 ATGCTCGCAGCTCGCAATG 61.821 57.895 9.21 0.34 42.97 2.82
4133 5684 4.233635 GCTCGCAGCTCGCAATGG 62.234 66.667 8.52 0.00 42.60 3.16
4134 5685 4.233635 CTCGCAGCTCGCAATGGC 62.234 66.667 8.52 0.00 42.60 4.40
4136 5687 4.105733 CGCAGCTCGCAATGGCAA 62.106 61.111 0.00 0.00 42.60 4.52
4137 5688 2.202570 GCAGCTCGCAATGGCAAG 60.203 61.111 0.00 0.00 41.79 4.01
4138 5689 2.693762 GCAGCTCGCAATGGCAAGA 61.694 57.895 0.00 0.00 41.79 3.02
4139 5690 2.001361 GCAGCTCGCAATGGCAAGAT 62.001 55.000 0.00 0.00 41.79 2.40
4140 5691 1.302366 CAGCTCGCAATGGCAAGATA 58.698 50.000 0.00 0.00 41.24 1.98
4141 5692 1.878088 CAGCTCGCAATGGCAAGATAT 59.122 47.619 0.00 0.00 41.24 1.63
4142 5693 2.292569 CAGCTCGCAATGGCAAGATATT 59.707 45.455 0.00 0.00 41.24 1.28
4143 5694 2.292569 AGCTCGCAATGGCAAGATATTG 59.707 45.455 0.00 0.00 41.24 1.90
4144 5695 2.291465 GCTCGCAATGGCAAGATATTGA 59.709 45.455 3.77 0.00 41.24 2.57
4145 5696 3.608707 GCTCGCAATGGCAAGATATTGAG 60.609 47.826 3.77 0.00 41.24 3.02
4146 5697 3.544684 TCGCAATGGCAAGATATTGAGT 58.455 40.909 3.77 0.00 41.24 3.41
4147 5698 3.313249 TCGCAATGGCAAGATATTGAGTG 59.687 43.478 3.77 0.00 41.24 3.51
4148 5699 3.313249 CGCAATGGCAAGATATTGAGTGA 59.687 43.478 3.77 0.00 41.24 3.41
4149 5700 4.604976 GCAATGGCAAGATATTGAGTGAC 58.395 43.478 3.77 0.00 40.72 3.67
4150 5701 4.096833 GCAATGGCAAGATATTGAGTGACA 59.903 41.667 3.77 0.00 40.72 3.58
4151 5702 5.575957 CAATGGCAAGATATTGAGTGACAC 58.424 41.667 3.77 0.00 36.61 3.67
4152 5703 4.558226 TGGCAAGATATTGAGTGACACT 57.442 40.909 8.12 8.12 0.00 3.55
4153 5704 5.675684 TGGCAAGATATTGAGTGACACTA 57.324 39.130 8.41 0.00 0.00 2.74
4154 5705 6.048732 TGGCAAGATATTGAGTGACACTAA 57.951 37.500 8.41 0.00 0.00 2.24
4155 5706 6.653020 TGGCAAGATATTGAGTGACACTAAT 58.347 36.000 8.41 10.87 0.00 1.73
4156 5707 6.539826 TGGCAAGATATTGAGTGACACTAATG 59.460 38.462 8.41 0.00 0.00 1.90
4157 5708 6.425504 GCAAGATATTGAGTGACACTAATGC 58.574 40.000 8.41 3.13 0.00 3.56
4311 5862 7.449247 ACATTCCTCTGCTTCTATATCCTTTC 58.551 38.462 0.00 0.00 0.00 2.62
4338 5890 2.027745 TCCTCTTACCAGCAAGCTTCAG 60.028 50.000 0.00 0.00 0.00 3.02
4458 6116 9.404348 TGATACGTTACATTCTAAAACACGTAA 57.596 29.630 0.00 0.00 42.83 3.18
4564 6382 1.813513 ACATGAAGGTTCAAGGCTCG 58.186 50.000 0.00 0.00 41.13 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 193 7.041780 ACACAACAAAAGCAACAAAAATACACA 60.042 29.630 0.00 0.00 0.00 3.72
192 194 7.268023 CACACAACAAAAGCAACAAAAATACAC 59.732 33.333 0.00 0.00 0.00 2.90
662 666 9.549509 GCATTGTTTGTTTTCGTAATATAGTGA 57.450 29.630 0.00 0.00 0.00 3.41
709 713 2.801631 GGTGGCGGATCAGAGGAGG 61.802 68.421 0.00 0.00 0.00 4.30
725 2131 1.826024 GGAGCATCGATGTGGAGGT 59.174 57.895 25.47 5.67 34.37 3.85
805 2282 0.375454 CCGACAAACTGCAAACGTCA 59.625 50.000 0.00 0.00 0.00 4.35
1254 2739 2.382305 TGTGGAGAAGAGGGAGTTAGGA 59.618 50.000 0.00 0.00 0.00 2.94
1292 2777 2.203582 AAACCCCCGTGGAAAGGC 60.204 61.111 0.00 0.00 38.00 4.35
1488 2973 4.150098 GCTGAAGTAGTGGACAAACTAACG 59.850 45.833 0.00 0.00 34.50 3.18
1499 2987 3.129462 TGAGAGATTCGCTGAAGTAGTGG 59.871 47.826 0.00 0.00 37.51 4.00
1572 3060 7.396418 ACCAATACTATGTTCCTTTTTCCGTA 58.604 34.615 0.00 0.00 0.00 4.02
1573 3061 6.243148 ACCAATACTATGTTCCTTTTTCCGT 58.757 36.000 0.00 0.00 0.00 4.69
1583 3071 6.764560 ACCAATAACCGACCAATACTATGTTC 59.235 38.462 0.00 0.00 0.00 3.18
1621 3109 3.249091 CTGATCGTGTGAGTTTCCTCTG 58.751 50.000 0.00 0.00 38.61 3.35
1622 3110 2.353208 GCTGATCGTGTGAGTTTCCTCT 60.353 50.000 0.00 0.00 38.61 3.69
1623 3111 1.996191 GCTGATCGTGTGAGTTTCCTC 59.004 52.381 0.00 0.00 38.27 3.71
1630 3118 0.387239 TGTGTCGCTGATCGTGTGAG 60.387 55.000 2.60 0.00 39.67 3.51
1631 3119 0.031449 TTGTGTCGCTGATCGTGTGA 59.969 50.000 0.00 0.00 39.67 3.58
1678 3166 4.630894 TGGATGATTTCGGTGCAATAAC 57.369 40.909 0.00 0.00 0.00 1.89
1739 3227 7.496591 ACGATTAACTTCTACTCACCAAACAAA 59.503 33.333 0.00 0.00 0.00 2.83
1752 3240 6.205101 GGAGACCTTCACGATTAACTTCTA 57.795 41.667 0.00 0.00 0.00 2.10
1813 3301 0.321564 TCTCATTCACCAAGCACCCG 60.322 55.000 0.00 0.00 0.00 5.28
1871 3359 5.589831 ACCTAAATTACAGGCCAGGAAAAT 58.410 37.500 5.01 0.00 36.57 1.82
1900 3388 1.464997 GCCGCTCACTTGGTTCTAAAG 59.535 52.381 0.00 0.00 0.00 1.85
2261 3751 3.260884 GGACCATGTCTACCTCACTCAAA 59.739 47.826 0.00 0.00 32.47 2.69
2283 3773 8.526147 ACATTTCTCCTAAAAGTTTCATCATGG 58.474 33.333 0.00 0.00 0.00 3.66
2427 3917 7.951591 ACTGGCAACACAGATTTAACTTTTAT 58.048 30.769 0.00 0.00 46.17 1.40
2438 3928 2.344535 GGCAACTGGCAACACAGAT 58.655 52.632 0.00 0.00 46.17 2.90
2457 3947 5.665812 ACATAGTGCCTAAGGTTAATCTGGA 59.334 40.000 0.00 0.00 0.00 3.86
2477 3967 4.565444 CCCATCAACTTGGTCAGTGACATA 60.565 45.833 24.20 10.23 35.12 2.29
2623 4114 9.109393 TGCTCCATGTATTCTACAACTTAAATC 57.891 33.333 0.00 0.00 42.76 2.17
2706 4197 7.602265 GCTTAAAAGGAATAACAAAGCATTGGA 59.398 33.333 6.62 0.00 41.01 3.53
2736 4227 7.426410 ACTGGTAGACAATGTCATATTCGTAG 58.574 38.462 16.38 5.33 34.60 3.51
2740 4231 9.378551 TGTAAACTGGTAGACAATGTCATATTC 57.621 33.333 16.38 1.32 34.60 1.75
2944 4435 4.788679 TCGTACCAGAGAATCACCAGATA 58.211 43.478 0.00 0.00 37.82 1.98
3014 4544 4.721776 TGCCTTCCAAATAGAGATGGTAGT 59.278 41.667 0.00 0.00 37.94 2.73
3018 4548 3.889815 TGTGCCTTCCAAATAGAGATGG 58.110 45.455 0.00 0.00 38.09 3.51
3090 4621 5.576774 CACATAATCATATTTAGCGCCGAGA 59.423 40.000 2.29 0.00 0.00 4.04
3316 4847 2.818169 GGACAGGGCACACACTCCA 61.818 63.158 0.00 0.00 0.00 3.86
3323 4854 2.296945 AAAGCAAGGGACAGGGCACA 62.297 55.000 0.00 0.00 0.00 4.57
3372 4911 1.500474 CTATGTTCCCTGAGGGCTGA 58.500 55.000 14.20 0.00 43.94 4.26
3411 4950 2.124320 AACCTTGCACACACGGCT 60.124 55.556 0.00 0.00 38.79 5.52
3502 5041 1.156736 CATCCAAGACCCACACGTTC 58.843 55.000 0.00 0.00 0.00 3.95
3561 5101 4.508461 TCCAGTCATCAAAATGCAACAG 57.492 40.909 0.00 0.00 32.58 3.16
3577 5119 1.708341 AGCAAAACCAAGCATCCAGT 58.292 45.000 0.00 0.00 0.00 4.00
3595 5137 5.536554 AGATCAACAACAGTATGCGAAAG 57.463 39.130 0.00 0.00 42.53 2.62
3604 5146 3.864789 ACCAGGAAGATCAACAACAGT 57.135 42.857 0.00 0.00 0.00 3.55
3614 5156 4.327680 GCTTCAACAAGTACCAGGAAGAT 58.672 43.478 11.99 0.00 35.04 2.40
3666 5210 2.153945 GGTCGCAAATGCATGCACG 61.154 57.895 25.37 21.66 46.76 5.34
3731 5275 9.562408 TTCCTCACACTGTATTTGTAAACATAA 57.438 29.630 0.00 0.00 0.00 1.90
3750 5294 2.288825 TGTCGATGTGGTTCTTCCTCAC 60.289 50.000 0.00 0.00 41.60 3.51
3790 5334 4.989168 GTGTTTAATCTGCCCCTATAGACG 59.011 45.833 0.00 0.00 0.00 4.18
3792 5336 6.569127 TTGTGTTTAATCTGCCCCTATAGA 57.431 37.500 0.00 0.00 0.00 1.98
3814 5364 8.706322 AGGTTTTAGTTGTCATATTGTCCTTT 57.294 30.769 0.00 0.00 0.00 3.11
3905 5456 6.156519 GGACATTTAACATCCTCAAAACCAC 58.843 40.000 0.00 0.00 0.00 4.16
3929 5480 1.402787 GGGCCTAACCATCCACAATG 58.597 55.000 0.84 0.00 42.05 2.82
3930 5481 0.261696 GGGGCCTAACCATCCACAAT 59.738 55.000 0.84 0.00 42.05 2.71
3931 5482 1.694856 GGGGCCTAACCATCCACAA 59.305 57.895 0.84 0.00 42.05 3.33
3932 5483 2.313427 GGGGGCCTAACCATCCACA 61.313 63.158 0.84 0.00 42.05 4.17
3933 5484 2.284515 CTGGGGGCCTAACCATCCAC 62.285 65.000 13.45 0.00 42.05 4.02
3935 5486 2.927056 CTGGGGGCCTAACCATCC 59.073 66.667 13.45 0.00 42.05 3.51
3948 5499 1.079073 AAATCCTTGGTGGGCTGGG 59.921 57.895 0.00 0.00 36.20 4.45
3949 5500 0.251742 TCAAATCCTTGGTGGGCTGG 60.252 55.000 0.00 0.00 36.20 4.85
3950 5501 0.890683 GTCAAATCCTTGGTGGGCTG 59.109 55.000 0.00 0.00 36.20 4.85
3952 5503 1.883021 CGTCAAATCCTTGGTGGGC 59.117 57.895 0.00 0.00 36.20 5.36
3955 5506 2.607771 CCAAAGCGTCAAATCCTTGGTG 60.608 50.000 0.00 0.00 33.01 4.17
3958 5509 2.034558 ACACCAAAGCGTCAAATCCTTG 59.965 45.455 0.00 0.00 0.00 3.61
3959 5510 2.293399 GACACCAAAGCGTCAAATCCTT 59.707 45.455 0.00 0.00 32.24 3.36
3960 5511 1.880027 GACACCAAAGCGTCAAATCCT 59.120 47.619 0.00 0.00 32.24 3.24
3961 5512 1.880027 AGACACCAAAGCGTCAAATCC 59.120 47.619 0.00 0.00 34.48 3.01
3962 5513 2.095718 GGAGACACCAAAGCGTCAAATC 60.096 50.000 0.00 0.00 38.79 2.17
3963 5514 1.880027 GGAGACACCAAAGCGTCAAAT 59.120 47.619 0.00 0.00 38.79 2.32
3964 5515 1.305201 GGAGACACCAAAGCGTCAAA 58.695 50.000 0.00 0.00 38.79 2.69
3965 5516 0.878523 CGGAGACACCAAAGCGTCAA 60.879 55.000 0.00 0.00 38.90 3.18
3966 5517 1.300620 CGGAGACACCAAAGCGTCA 60.301 57.895 0.00 0.00 38.90 4.35
3967 5518 1.282930 GACGGAGACACCAAAGCGTC 61.283 60.000 0.00 0.00 38.90 5.19
3968 5519 1.300697 GACGGAGACACCAAAGCGT 60.301 57.895 0.00 0.00 38.90 5.07
3969 5520 2.372690 CGACGGAGACACCAAAGCG 61.373 63.158 0.00 0.00 38.90 4.68
3970 5521 0.389948 ATCGACGGAGACACCAAAGC 60.390 55.000 0.00 0.00 38.90 3.51
3971 5522 2.798680 CTATCGACGGAGACACCAAAG 58.201 52.381 0.00 0.00 38.90 2.77
3972 5523 1.135199 GCTATCGACGGAGACACCAAA 60.135 52.381 0.00 0.00 38.90 3.28
3973 5524 0.454600 GCTATCGACGGAGACACCAA 59.545 55.000 0.00 0.00 38.90 3.67
3974 5525 1.712018 CGCTATCGACGGAGACACCA 61.712 60.000 0.00 0.00 36.74 4.17
3975 5526 1.009900 CGCTATCGACGGAGACACC 60.010 63.158 0.00 0.00 38.10 4.16
3976 5527 0.042013 CTCGCTATCGACGGAGACAC 60.042 60.000 0.00 0.00 40.21 3.67
3977 5528 1.158484 CCTCGCTATCGACGGAGACA 61.158 60.000 0.00 0.00 40.21 3.41
3978 5529 1.570475 CCTCGCTATCGACGGAGAC 59.430 63.158 0.00 0.00 40.21 3.36
3979 5530 2.252346 GCCTCGCTATCGACGGAGA 61.252 63.158 8.14 0.00 40.21 3.71
3980 5531 2.252855 GCCTCGCTATCGACGGAG 59.747 66.667 8.14 0.00 40.21 4.63
3981 5532 3.646976 CGCCTCGCTATCGACGGA 61.647 66.667 8.14 0.00 40.21 4.69
3992 5543 2.969238 GGTCATCATGGCGCCTCG 60.969 66.667 29.70 18.68 0.00 4.63
3993 5544 1.596477 GAGGTCATCATGGCGCCTC 60.596 63.158 29.70 9.60 38.89 4.70
3994 5545 2.507944 GAGGTCATCATGGCGCCT 59.492 61.111 29.70 10.60 0.00 5.52
3995 5546 2.969238 CGAGGTCATCATGGCGCC 60.969 66.667 22.73 22.73 0.00 6.53
3996 5547 3.643978 GCGAGGTCATCATGGCGC 61.644 66.667 0.00 0.00 37.60 6.53
3997 5548 2.969238 GGCGAGGTCATCATGGCG 60.969 66.667 0.00 0.00 30.36 5.69
3998 5549 1.890979 CAGGCGAGGTCATCATGGC 60.891 63.158 0.00 0.00 0.00 4.40
3999 5550 0.812811 CACAGGCGAGGTCATCATGG 60.813 60.000 0.00 0.00 0.00 3.66
4000 5551 0.107993 ACACAGGCGAGGTCATCATG 60.108 55.000 0.00 0.00 0.00 3.07
4001 5552 0.176680 GACACAGGCGAGGTCATCAT 59.823 55.000 0.00 0.00 0.00 2.45
4002 5553 0.900182 AGACACAGGCGAGGTCATCA 60.900 55.000 7.90 0.00 34.04 3.07
4003 5554 0.459237 CAGACACAGGCGAGGTCATC 60.459 60.000 7.90 0.00 34.04 2.92
4004 5555 1.188219 ACAGACACAGGCGAGGTCAT 61.188 55.000 7.90 0.00 34.04 3.06
4005 5556 1.832608 ACAGACACAGGCGAGGTCA 60.833 57.895 7.90 0.00 34.04 4.02
4006 5557 1.373497 CACAGACACAGGCGAGGTC 60.373 63.158 0.00 0.00 0.00 3.85
4007 5558 2.134287 ACACAGACACAGGCGAGGT 61.134 57.895 0.00 0.00 0.00 3.85
4008 5559 1.665916 CACACAGACACAGGCGAGG 60.666 63.158 0.00 0.00 0.00 4.63
4009 5560 0.530650 AACACACAGACACAGGCGAG 60.531 55.000 0.00 0.00 0.00 5.03
4010 5561 0.529773 GAACACACAGACACAGGCGA 60.530 55.000 0.00 0.00 0.00 5.54
4011 5562 0.530650 AGAACACACAGACACAGGCG 60.531 55.000 0.00 0.00 0.00 5.52
4012 5563 1.221414 GAGAACACACAGACACAGGC 58.779 55.000 0.00 0.00 0.00 4.85
4013 5564 2.602257 TGAGAACACACAGACACAGG 57.398 50.000 0.00 0.00 0.00 4.00
4014 5565 4.944962 TTTTGAGAACACACAGACACAG 57.055 40.909 0.00 0.00 0.00 3.66
4033 5584 4.462483 TGTTGCTTGACTGGAGTTCTTTTT 59.538 37.500 0.00 0.00 0.00 1.94
4034 5585 4.016444 TGTTGCTTGACTGGAGTTCTTTT 58.984 39.130 0.00 0.00 0.00 2.27
4035 5586 3.620488 TGTTGCTTGACTGGAGTTCTTT 58.380 40.909 0.00 0.00 0.00 2.52
4036 5587 3.209410 CTGTTGCTTGACTGGAGTTCTT 58.791 45.455 0.00 0.00 0.00 2.52
4037 5588 2.171448 ACTGTTGCTTGACTGGAGTTCT 59.829 45.455 0.00 0.00 0.00 3.01
4038 5589 2.565841 ACTGTTGCTTGACTGGAGTTC 58.434 47.619 0.00 0.00 0.00 3.01
4039 5590 2.717639 ACTGTTGCTTGACTGGAGTT 57.282 45.000 0.00 0.00 0.00 3.01
4040 5591 3.838244 TTACTGTTGCTTGACTGGAGT 57.162 42.857 0.00 0.00 0.00 3.85
4041 5592 3.876914 TGTTTACTGTTGCTTGACTGGAG 59.123 43.478 0.00 0.00 0.00 3.86
4042 5593 3.879998 TGTTTACTGTTGCTTGACTGGA 58.120 40.909 0.00 0.00 0.00 3.86
4043 5594 4.335315 TCTTGTTTACTGTTGCTTGACTGG 59.665 41.667 0.00 0.00 0.00 4.00
4044 5595 5.484173 TCTTGTTTACTGTTGCTTGACTG 57.516 39.130 0.00 0.00 0.00 3.51
4045 5596 5.066505 CCTTCTTGTTTACTGTTGCTTGACT 59.933 40.000 0.00 0.00 0.00 3.41
4046 5597 5.065988 TCCTTCTTGTTTACTGTTGCTTGAC 59.934 40.000 0.00 0.00 0.00 3.18
4047 5598 5.189928 TCCTTCTTGTTTACTGTTGCTTGA 58.810 37.500 0.00 0.00 0.00 3.02
4048 5599 5.499139 TCCTTCTTGTTTACTGTTGCTTG 57.501 39.130 0.00 0.00 0.00 4.01
4049 5600 5.241728 GGATCCTTCTTGTTTACTGTTGCTT 59.758 40.000 3.84 0.00 0.00 3.91
4050 5601 4.762251 GGATCCTTCTTGTTTACTGTTGCT 59.238 41.667 3.84 0.00 0.00 3.91
4051 5602 4.762251 AGGATCCTTCTTGTTTACTGTTGC 59.238 41.667 9.02 0.00 0.00 4.17
4052 5603 6.487689 GAGGATCCTTCTTGTTTACTGTTG 57.512 41.667 17.42 0.00 0.00 3.33
4066 5617 8.695207 TACAAAGCAAATTGGGGAGGATCCTT 62.695 42.308 17.42 0.00 43.65 3.36
4067 5618 6.614294 ACAAAGCAAATTGGGGAGGATCCT 62.614 45.833 16.13 16.13 43.65 3.24
4068 5619 4.389393 ACAAAGCAAATTGGGGAGGATCC 61.389 47.826 2.48 2.48 43.53 3.36
4069 5620 2.833943 ACAAAGCAAATTGGGGAGGATC 59.166 45.455 0.00 0.00 34.56 3.36
4070 5621 2.906568 ACAAAGCAAATTGGGGAGGAT 58.093 42.857 0.00 0.00 34.56 3.24
4071 5622 2.397044 ACAAAGCAAATTGGGGAGGA 57.603 45.000 0.00 0.00 34.56 3.71
4072 5623 3.874392 CTACAAAGCAAATTGGGGAGG 57.126 47.619 0.00 0.00 34.56 4.30
4085 5636 5.751243 ATTTAAGGGCGTATGCTACAAAG 57.249 39.130 6.92 0.00 42.25 2.77
4086 5637 6.518208 AAATTTAAGGGCGTATGCTACAAA 57.482 33.333 6.92 3.38 42.25 2.83
4087 5638 6.326375 CAAAATTTAAGGGCGTATGCTACAA 58.674 36.000 6.92 0.00 42.25 2.41
4088 5639 5.163602 CCAAAATTTAAGGGCGTATGCTACA 60.164 40.000 6.92 0.00 42.25 2.74
4089 5640 5.278604 CCAAAATTTAAGGGCGTATGCTAC 58.721 41.667 6.92 0.40 42.25 3.58
4090 5641 4.202070 GCCAAAATTTAAGGGCGTATGCTA 60.202 41.667 6.92 0.00 42.25 3.49
4091 5642 3.430236 GCCAAAATTTAAGGGCGTATGCT 60.430 43.478 6.92 0.00 42.25 3.79
4092 5643 2.863740 GCCAAAATTTAAGGGCGTATGC 59.136 45.455 11.30 0.00 36.58 3.14
4098 5649 2.938451 GAGCATGCCAAAATTTAAGGGC 59.062 45.455 15.66 17.15 46.58 5.19
4099 5650 3.189285 CGAGCATGCCAAAATTTAAGGG 58.811 45.455 15.66 5.64 0.00 3.95
4100 5651 2.604462 GCGAGCATGCCAAAATTTAAGG 59.396 45.455 15.66 5.45 0.00 2.69
4101 5652 3.252400 TGCGAGCATGCCAAAATTTAAG 58.748 40.909 15.66 0.00 0.00 1.85
4102 5653 3.252400 CTGCGAGCATGCCAAAATTTAA 58.748 40.909 15.66 0.00 0.00 1.52
4103 5654 2.878580 CTGCGAGCATGCCAAAATTTA 58.121 42.857 15.66 0.00 0.00 1.40
4104 5655 1.717194 CTGCGAGCATGCCAAAATTT 58.283 45.000 15.66 0.00 0.00 1.82
4105 5656 0.738412 GCTGCGAGCATGCCAAAATT 60.738 50.000 15.66 0.00 41.89 1.82
4106 5657 1.153706 GCTGCGAGCATGCCAAAAT 60.154 52.632 15.66 0.00 41.89 1.82
4107 5658 2.203972 GAGCTGCGAGCATGCCAAAA 62.204 55.000 15.66 0.00 45.56 2.44
4108 5659 2.674033 AGCTGCGAGCATGCCAAA 60.674 55.556 15.66 0.00 45.56 3.28
4109 5660 3.129502 GAGCTGCGAGCATGCCAA 61.130 61.111 15.66 0.00 45.56 4.52
4120 5671 2.001361 ATCTTGCCATTGCGAGCTGC 62.001 55.000 0.00 0.00 46.88 5.25
4121 5672 1.302366 TATCTTGCCATTGCGAGCTG 58.698 50.000 0.00 0.00 46.88 4.24
4122 5673 2.267174 ATATCTTGCCATTGCGAGCT 57.733 45.000 0.95 0.00 46.88 4.09
4123 5674 2.291465 TCAATATCTTGCCATTGCGAGC 59.709 45.455 0.95 0.00 46.88 5.03
4125 5676 3.313249 CACTCAATATCTTGCCATTGCGA 59.687 43.478 0.00 0.00 41.78 5.10
4126 5677 3.313249 TCACTCAATATCTTGCCATTGCG 59.687 43.478 0.00 0.00 41.78 4.85
4127 5678 4.096833 TGTCACTCAATATCTTGCCATTGC 59.903 41.667 0.00 0.00 33.14 3.56
4128 5679 5.356190 AGTGTCACTCAATATCTTGCCATTG 59.644 40.000 0.00 0.00 34.17 2.82
4129 5680 5.503927 AGTGTCACTCAATATCTTGCCATT 58.496 37.500 0.00 0.00 32.11 3.16
4130 5681 5.108187 AGTGTCACTCAATATCTTGCCAT 57.892 39.130 0.00 0.00 32.11 4.40
4131 5682 4.558226 AGTGTCACTCAATATCTTGCCA 57.442 40.909 0.00 0.00 32.11 4.92
4132 5683 6.512415 GCATTAGTGTCACTCAATATCTTGCC 60.512 42.308 9.26 0.00 32.11 4.52
4133 5684 6.259608 AGCATTAGTGTCACTCAATATCTTGC 59.740 38.462 9.26 4.53 32.70 4.01
4134 5685 7.628235 CAGCATTAGTGTCACTCAATATCTTG 58.372 38.462 9.26 0.00 0.00 3.02
4135 5686 6.259608 GCAGCATTAGTGTCACTCAATATCTT 59.740 38.462 9.26 0.00 0.00 2.40
4136 5687 5.757320 GCAGCATTAGTGTCACTCAATATCT 59.243 40.000 9.26 6.18 0.00 1.98
4137 5688 5.525012 TGCAGCATTAGTGTCACTCAATATC 59.475 40.000 9.26 4.37 0.00 1.63
4138 5689 5.295292 GTGCAGCATTAGTGTCACTCAATAT 59.705 40.000 9.26 0.00 0.00 1.28
4139 5690 4.631377 GTGCAGCATTAGTGTCACTCAATA 59.369 41.667 9.26 0.00 0.00 1.90
4140 5691 3.438087 GTGCAGCATTAGTGTCACTCAAT 59.562 43.478 9.26 5.46 0.00 2.57
4141 5692 2.807967 GTGCAGCATTAGTGTCACTCAA 59.192 45.455 9.26 3.28 0.00 3.02
4142 5693 2.416747 GTGCAGCATTAGTGTCACTCA 58.583 47.619 9.26 0.00 0.00 3.41
4143 5694 1.391485 CGTGCAGCATTAGTGTCACTC 59.609 52.381 9.26 0.00 0.00 3.51
4144 5695 1.432514 CGTGCAGCATTAGTGTCACT 58.567 50.000 10.99 10.99 0.00 3.41
4145 5696 3.955429 CGTGCAGCATTAGTGTCAC 57.045 52.632 0.00 0.00 0.00 3.67
4157 5708 1.808799 AGCAGATTCGAGCGTGCAG 60.809 57.895 14.90 0.00 38.44 4.41
4311 5862 3.594134 CTTGCTGGTAAGAGGAAGACAG 58.406 50.000 0.00 0.00 42.42 3.51
4338 5890 3.751479 AGGTTTGTTTCCAATCAAGCC 57.249 42.857 7.55 7.55 42.45 4.35


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

AutoCloner maintained by Alex Coulton.