Multiple sequence alignment - TraesCS4D01G039700

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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 TraesCS4D01G039700 chr4D 100.000 5598 0 0 1 5598 17254048 17248451 0.000000e+00 10338.0
1 TraesCS4D01G039700 chr4B 92.443 4896 186 83 244 5056 29271483 29266689 0.000000e+00 6822.0
2 TraesCS4D01G039700 chr4B 82.988 482 30 25 5137 5598 29266380 29265931 6.800000e-104 388.0
3 TraesCS4D01G039700 chr4B 100.000 28 0 0 117 144 25710937 25710910 1.000000e-02 52.8
4 TraesCS4D01G039700 chr4A 91.967 3797 182 45 87 3804 583418373 583422125 0.000000e+00 5208.0
5 TraesCS4D01G039700 chr4A 86.714 1829 85 75 3840 5598 583422129 583423869 0.000000e+00 1886.0
6 TraesCS4D01G039700 chr4A 93.023 43 3 0 101 143 183620158 183620116 4.680000e-06 63.9
7 TraesCS4D01G039700 chr5D 84.192 291 29 12 383 671 312151949 312152224 3.320000e-67 267.0
8 TraesCS4D01G039700 chr2B 75.610 533 115 14 1093 1617 119633722 119633197 3.350000e-62 250.0
9 TraesCS4D01G039700 chr2B 88.889 54 4 2 104 155 139573636 139573583 1.300000e-06 65.8
10 TraesCS4D01G039700 chr2D 75.330 531 120 11 1093 1617 77383217 77382692 1.560000e-60 244.0
11 TraesCS4D01G039700 chr2A 84.507 142 14 7 1130 1267 465364064 465363927 3.520000e-27 134.0
12 TraesCS4D01G039700 chr7B 83.571 140 18 5 1130 1267 197406610 197406474 5.890000e-25 126.0


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 TraesCS4D01G039700 chr4D 17248451 17254048 5597 True 10338 10338 100.0000 1 5598 1 chr4D.!!$R1 5597
1 TraesCS4D01G039700 chr4B 29265931 29271483 5552 True 3605 6822 87.7155 244 5598 2 chr4B.!!$R2 5354
2 TraesCS4D01G039700 chr4A 583418373 583423869 5496 False 3547 5208 89.3405 87 5598 2 chr4A.!!$F1 5511
3 TraesCS4D01G039700 chr2B 119633197 119633722 525 True 250 250 75.6100 1093 1617 1 chr2B.!!$R1 524
4 TraesCS4D01G039700 chr2D 77382692 77383217 525 True 244 244 75.3300 1093 1617 1 chr2D.!!$R1 524

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
91 92 0.037734 CCCTCCGCCCAAACTACTTT 59.962 55.0 0.00 0.0 0.00 2.66 F
833 908 0.676736 CTACTACTAGCCAGCCAGCC 59.323 60.0 0.00 0.0 0.00 4.85 F
2021 2145 0.465705 GGCATCAGGTGATTCCTCGA 59.534 55.0 1.75 0.0 46.24 4.04 F
2680 2819 0.740149 TGCATCGTGGAAATGGCATC 59.260 50.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1563 1687 2.663196 CAGGTGAAGACCCCGGTC 59.337 66.667 5.7 5.7 44.40 4.79 R
2145 2270 1.030488 CCAGTGCAAGCTCCCTCATG 61.030 60.000 0.0 0.0 0.00 3.07 R
3718 3859 1.275856 GGCTTGTTTGGAATGCATGGA 59.724 47.619 0.0 0.0 0.00 3.41 R
4658 4831 0.026803 GAATCAATCGTCGCAGGTGC 59.973 55.000 0.0 0.0 37.78 5.01 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
25 26 7.996098 ATAGCAAACTATAACCACAACAAGT 57.004 32.000 0.00 0.00 37.33 3.16
26 27 9.158233 GATAGCAAACTATAACCACAACAAGTA 57.842 33.333 0.00 0.00 39.28 2.24
27 28 7.811117 AGCAAACTATAACCACAACAAGTAA 57.189 32.000 0.00 0.00 0.00 2.24
28 29 7.871853 AGCAAACTATAACCACAACAAGTAAG 58.128 34.615 0.00 0.00 0.00 2.34
29 30 7.717875 AGCAAACTATAACCACAACAAGTAAGA 59.282 33.333 0.00 0.00 0.00 2.10
30 31 8.347035 GCAAACTATAACCACAACAAGTAAGAA 58.653 33.333 0.00 0.00 0.00 2.52
31 32 9.878599 CAAACTATAACCACAACAAGTAAGAAG 57.121 33.333 0.00 0.00 0.00 2.85
32 33 9.841295 AAACTATAACCACAACAAGTAAGAAGA 57.159 29.630 0.00 0.00 0.00 2.87
33 34 9.841295 AACTATAACCACAACAAGTAAGAAGAA 57.159 29.630 0.00 0.00 0.00 2.52
34 35 9.841295 ACTATAACCACAACAAGTAAGAAGAAA 57.159 29.630 0.00 0.00 0.00 2.52
38 39 6.330278 ACCACAACAAGTAAGAAGAAAAAGC 58.670 36.000 0.00 0.00 0.00 3.51
39 40 6.152831 ACCACAACAAGTAAGAAGAAAAAGCT 59.847 34.615 0.00 0.00 0.00 3.74
40 41 7.338449 ACCACAACAAGTAAGAAGAAAAAGCTA 59.662 33.333 0.00 0.00 0.00 3.32
41 42 8.188139 CCACAACAAGTAAGAAGAAAAAGCTAA 58.812 33.333 0.00 0.00 0.00 3.09
42 43 9.567848 CACAACAAGTAAGAAGAAAAAGCTAAA 57.432 29.630 0.00 0.00 0.00 1.85
43 44 9.788960 ACAACAAGTAAGAAGAAAAAGCTAAAG 57.211 29.630 0.00 0.00 0.00 1.85
46 47 9.174166 ACAAGTAAGAAGAAAAAGCTAAAGACA 57.826 29.630 0.00 0.00 0.00 3.41
49 50 9.561069 AGTAAGAAGAAAAAGCTAAAGACATCA 57.439 29.630 0.00 0.00 0.00 3.07
52 53 8.457238 AGAAGAAAAAGCTAAAGACATCAACT 57.543 30.769 0.00 0.00 0.00 3.16
53 54 8.907885 AGAAGAAAAAGCTAAAGACATCAACTT 58.092 29.630 0.00 0.00 0.00 2.66
54 55 9.521503 GAAGAAAAAGCTAAAGACATCAACTTT 57.478 29.630 0.00 0.00 40.13 2.66
77 78 9.798994 CTTTATGTCGTATATAATACACCCTCC 57.201 37.037 1.56 0.00 0.00 4.30
78 79 5.885230 TGTCGTATATAATACACCCTCCG 57.115 43.478 0.00 0.00 0.00 4.63
79 80 4.156556 TGTCGTATATAATACACCCTCCGC 59.843 45.833 0.00 0.00 0.00 5.54
80 81 3.696051 TCGTATATAATACACCCTCCGCC 59.304 47.826 0.00 0.00 0.00 6.13
81 82 3.181483 CGTATATAATACACCCTCCGCCC 60.181 52.174 0.00 0.00 0.00 6.13
82 83 2.402182 TATAATACACCCTCCGCCCA 57.598 50.000 0.00 0.00 0.00 5.36
83 84 1.513858 ATAATACACCCTCCGCCCAA 58.486 50.000 0.00 0.00 0.00 4.12
84 85 1.287217 TAATACACCCTCCGCCCAAA 58.713 50.000 0.00 0.00 0.00 3.28
85 86 0.323087 AATACACCCTCCGCCCAAAC 60.323 55.000 0.00 0.00 0.00 2.93
91 92 0.037734 CCCTCCGCCCAAACTACTTT 59.962 55.000 0.00 0.00 0.00 2.66
97 98 1.197721 CGCCCAAACTACTTTCTGCAG 59.802 52.381 7.63 7.63 0.00 4.41
148 149 1.339824 GGGACGGAGAGAGTACAGTGA 60.340 57.143 0.00 0.00 0.00 3.41
153 154 4.810790 ACGGAGAGAGTACAGTGAAAATG 58.189 43.478 0.00 0.00 38.30 2.32
155 156 4.859798 CGGAGAGAGTACAGTGAAAATGTC 59.140 45.833 0.00 0.00 44.85 3.06
156 157 5.172205 GGAGAGAGTACAGTGAAAATGTCC 58.828 45.833 0.00 0.00 44.85 4.02
188 192 8.586570 TTATGTGCAAGTCATTTTAAAACAGG 57.413 30.769 1.97 0.00 0.00 4.00
212 216 4.131596 GGGCGTACACATAAACCATGTAT 58.868 43.478 0.00 0.00 46.47 2.29
213 217 5.070714 AGGGCGTACACATAAACCATGTATA 59.929 40.000 0.00 0.00 46.47 1.47
214 218 5.935789 GGGCGTACACATAAACCATGTATAT 59.064 40.000 0.00 0.00 46.47 0.86
215 219 6.428771 GGGCGTACACATAAACCATGTATATT 59.571 38.462 0.00 0.00 46.47 1.28
216 220 7.360607 GGGCGTACACATAAACCATGTATATTC 60.361 40.741 0.00 0.00 46.47 1.75
217 221 7.360607 GGCGTACACATAAACCATGTATATTCC 60.361 40.741 0.00 0.00 46.47 3.01
218 222 7.386848 GCGTACACATAAACCATGTATATTCCT 59.613 37.037 0.00 0.00 46.47 3.36
347 362 2.092882 CCTTTCCTTCGTCGTCGCC 61.093 63.158 0.00 0.00 36.96 5.54
394 409 2.486982 CCAAGGAAGTCAGCAGTGAATG 59.513 50.000 0.00 0.00 33.27 2.67
761 817 1.017701 GCAGTACGGTAAAAGCGCCT 61.018 55.000 2.29 0.00 43.79 5.52
830 905 3.053842 ACAGTACTACTACTAGCCAGCCA 60.054 47.826 0.00 0.00 31.46 4.75
831 906 3.566322 CAGTACTACTACTAGCCAGCCAG 59.434 52.174 0.00 0.00 31.46 4.85
832 907 1.404843 ACTACTACTAGCCAGCCAGC 58.595 55.000 0.00 0.00 0.00 4.85
833 908 0.676736 CTACTACTAGCCAGCCAGCC 59.323 60.000 0.00 0.00 0.00 4.85
850 925 4.202574 CCAGTGCCACCACCACCA 62.203 66.667 0.00 0.00 43.09 4.17
946 1023 2.562973 TTTAGGAGGGGAGGGAGGCC 62.563 65.000 0.00 0.00 0.00 5.19
1725 1849 4.489771 ATTGGGGAGAAGGCGGCG 62.490 66.667 0.51 0.51 0.00 6.46
2021 2145 0.465705 GGCATCAGGTGATTCCTCGA 59.534 55.000 1.75 0.00 46.24 4.04
2103 2228 4.651503 TGGATTTGTGGGTGTTTATTGTGT 59.348 37.500 0.00 0.00 0.00 3.72
2271 2396 1.218316 GTGGAAGGACTACTGCCCG 59.782 63.158 0.00 0.00 45.47 6.13
2281 2406 0.806102 CTACTGCCCGATGGTGTTCG 60.806 60.000 0.00 0.00 38.83 3.95
2295 2420 3.659092 TTCGGGTGCTTGCTTGCG 61.659 61.111 0.00 0.00 35.36 4.85
2307 2432 3.486542 GCTTGCTTGCGATTCCTTCTAAG 60.487 47.826 0.00 0.00 0.00 2.18
2327 2452 3.146618 GCAATGTTCTCTGGATTGCTG 57.853 47.619 0.00 0.00 45.57 4.41
2334 2459 4.036734 TGTTCTCTGGATTGCTGTGTTTTC 59.963 41.667 0.00 0.00 0.00 2.29
2337 2462 4.276678 TCTCTGGATTGCTGTGTTTTCTTG 59.723 41.667 0.00 0.00 0.00 3.02
2338 2463 3.054878 CTGGATTGCTGTGTTTTCTTGC 58.945 45.455 0.00 0.00 0.00 4.01
2340 2465 3.888323 TGGATTGCTGTGTTTTCTTGCTA 59.112 39.130 0.00 0.00 0.00 3.49
2343 2476 3.969117 TGCTGTGTTTTCTTGCTACTG 57.031 42.857 0.00 0.00 0.00 2.74
2349 2482 7.015877 GCTGTGTTTTCTTGCTACTGTATTAC 58.984 38.462 0.00 0.00 0.00 1.89
2360 2493 6.370453 TGCTACTGTATTACTGACTGGGATA 58.630 40.000 7.61 0.00 0.00 2.59
2648 2781 6.238731 GGTTCTGTCACTTGTGAAATGATTGA 60.239 38.462 4.93 0.00 0.00 2.57
2680 2819 0.740149 TGCATCGTGGAAATGGCATC 59.260 50.000 0.00 0.00 0.00 3.91
2686 2825 4.533919 TCGTGGAAATGGCATCAAATTT 57.466 36.364 0.00 0.00 0.00 1.82
2734 2873 2.260869 AAGCCTTGCGAATGTGCGT 61.261 52.632 0.00 0.00 37.81 5.24
2872 3011 1.176527 TCACCTTGCTATTTGCCTGC 58.823 50.000 0.00 0.00 42.00 4.85
2895 3034 3.119849 GCAGTTGCTTATTCGGATGTTGT 60.120 43.478 0.00 0.00 38.21 3.32
3173 3313 6.320944 GGCAGACAAATTTGAAGAAGAGATC 58.679 40.000 24.64 8.19 0.00 2.75
3188 3328 5.883115 AGAAGAGATCGATGAGACAACTACA 59.117 40.000 0.54 0.00 0.00 2.74
3264 3404 7.673641 AGAGATCTCCATGAGTAAGTTCAAT 57.326 36.000 19.30 0.00 0.00 2.57
3271 3411 6.650120 TCCATGAGTAAGTTCAATCCCTTAC 58.350 40.000 0.00 0.00 42.05 2.34
3288 3428 4.119862 CCTTACGATATCTGTGGTGTTGG 58.880 47.826 0.34 0.00 0.00 3.77
3302 3442 4.982295 GTGGTGTTGGAATTACTTTCAAGC 59.018 41.667 0.00 0.00 35.94 4.01
3303 3443 4.038642 TGGTGTTGGAATTACTTTCAAGCC 59.961 41.667 0.00 0.00 35.94 4.35
3311 3451 7.826690 TGGAATTACTTTCAAGCCAATAACTC 58.173 34.615 0.00 0.00 35.94 3.01
3370 3510 1.377536 GGCAACTCCAGAGAGATTGC 58.622 55.000 15.70 15.70 45.87 3.56
3463 3603 1.139853 GCCTCGAAGATGGGATTGTCT 59.860 52.381 0.00 0.00 33.89 3.41
3472 3612 6.019801 CGAAGATGGGATTGTCTACTTTTACG 60.020 42.308 0.00 0.00 0.00 3.18
3494 3634 4.004314 GGCTTCTCCAAGTAAGTTCCTTC 58.996 47.826 0.00 0.00 34.01 3.46
3550 3691 7.334421 CCATATGTGCTAACCTAAGCGATTATT 59.666 37.037 1.24 0.00 45.85 1.40
3576 3717 4.484537 AGCAGAGCTATCAATGAAGTGT 57.515 40.909 0.00 0.00 36.99 3.55
3630 3771 3.864583 CAGAGCTGTGCTTCTCAGATAAC 59.135 47.826 0.00 0.00 39.88 1.89
3745 3887 2.757894 TTCCAAACAAGCCTGGGTTA 57.242 45.000 11.32 0.00 33.19 2.85
3793 3935 6.462552 TTCTCAAAATGACCACATGAAACA 57.537 33.333 0.00 0.00 36.79 2.83
3800 3942 6.808008 AATGACCACATGAAACAGAAGTAG 57.192 37.500 0.00 0.00 36.79 2.57
3820 3962 4.228912 AGTTCTTTGCATCCTTTCAACG 57.771 40.909 0.00 0.00 0.00 4.10
3837 3979 6.680874 TTCAACGTTATGTACCTTGTGTTT 57.319 33.333 0.00 0.00 0.00 2.83
3839 3981 7.410800 TCAACGTTATGTACCTTGTGTTTAG 57.589 36.000 0.00 0.00 0.00 1.85
3840 3982 7.208777 TCAACGTTATGTACCTTGTGTTTAGA 58.791 34.615 0.00 0.00 0.00 2.10
3841 3983 7.874016 TCAACGTTATGTACCTTGTGTTTAGAT 59.126 33.333 0.00 0.00 0.00 1.98
3843 3985 8.248117 ACGTTATGTACCTTGTGTTTAGATTC 57.752 34.615 0.00 0.00 0.00 2.52
3848 3990 7.739498 TGTACCTTGTGTTTAGATTCCTTTC 57.261 36.000 0.00 0.00 0.00 2.62
3849 3991 7.284074 TGTACCTTGTGTTTAGATTCCTTTCA 58.716 34.615 0.00 0.00 0.00 2.69
3885 4027 7.169645 TGTTTGCTGAAGATAAAATTGCAAGAC 59.830 33.333 4.94 0.00 39.53 3.01
3887 4029 6.384224 TGCTGAAGATAAAATTGCAAGACTG 58.616 36.000 4.94 0.00 0.00 3.51
3950 4092 6.872920 TCAACAACCTGAAAGCAATTAGTTT 58.127 32.000 0.00 0.00 0.00 2.66
3952 4094 8.134895 TCAACAACCTGAAAGCAATTAGTTTAG 58.865 33.333 0.00 0.00 0.00 1.85
3957 4099 9.961265 AACCTGAAAGCAATTAGTTTAGTTTAC 57.039 29.630 0.00 0.00 0.00 2.01
4029 4181 2.805657 GCTTTGTCACGGGTTCTACACT 60.806 50.000 0.00 0.00 0.00 3.55
4081 4243 3.265791 CTCAGTGCCCATCTTAGTTGAC 58.734 50.000 0.00 0.00 0.00 3.18
4128 4290 6.453092 CAAAATCTTCATTGCTCTCCACTTT 58.547 36.000 0.00 0.00 0.00 2.66
4196 4368 5.454471 GCATTAGAGATGATTGTCCTGTCCT 60.454 44.000 0.00 0.00 0.00 3.85
4210 4382 3.135712 TCCTGTCCTGTTTAAGAGCAACA 59.864 43.478 0.00 0.00 33.09 3.33
4263 4435 7.230108 CCATTAATCTGTGTTCTCTAATGCCAT 59.770 37.037 0.00 0.00 0.00 4.40
4264 4436 9.276590 CATTAATCTGTGTTCTCTAATGCCATA 57.723 33.333 0.00 0.00 0.00 2.74
4266 4438 9.851686 TTAATCTGTGTTCTCTAATGCCATATT 57.148 29.630 0.00 0.00 0.00 1.28
4267 4439 7.976135 ATCTGTGTTCTCTAATGCCATATTC 57.024 36.000 0.00 0.00 0.00 1.75
4268 4440 6.291377 TCTGTGTTCTCTAATGCCATATTCC 58.709 40.000 0.00 0.00 0.00 3.01
4269 4441 6.100279 TCTGTGTTCTCTAATGCCATATTCCT 59.900 38.462 0.00 0.00 0.00 3.36
4456 4628 3.639561 TCGGGATAATCGACATTCTCCAA 59.360 43.478 5.77 0.00 37.11 3.53
4546 4718 2.517609 GGTGGACCCGAAGCTCTAT 58.482 57.895 0.00 0.00 0.00 1.98
4615 4788 5.044476 TGGCTAAGAATTGGGGTCAAAGATA 60.044 40.000 0.00 0.00 36.36 1.98
4616 4789 6.071320 GGCTAAGAATTGGGGTCAAAGATAT 58.929 40.000 0.00 0.00 36.36 1.63
4637 4810 3.363627 TGCATGCAACAGGAATTCCATA 58.636 40.909 26.22 6.09 38.89 2.74
4650 4823 3.821421 ATTCCATACGAAGTCCAGTCC 57.179 47.619 0.00 0.00 43.93 3.85
4653 4826 2.100197 CCATACGAAGTCCAGTCCAGA 58.900 52.381 0.00 0.00 43.93 3.86
4654 4827 2.099921 CCATACGAAGTCCAGTCCAGAG 59.900 54.545 0.00 0.00 43.93 3.35
4655 4828 1.174783 TACGAAGTCCAGTCCAGAGC 58.825 55.000 0.00 0.00 43.93 4.09
4656 4829 1.153939 CGAAGTCCAGTCCAGAGCG 60.154 63.158 0.00 0.00 0.00 5.03
4657 4830 1.587043 CGAAGTCCAGTCCAGAGCGA 61.587 60.000 0.00 0.00 0.00 4.93
4658 4831 0.172352 GAAGTCCAGTCCAGAGCGAG 59.828 60.000 0.00 0.00 0.00 5.03
4659 4832 1.882989 AAGTCCAGTCCAGAGCGAGC 61.883 60.000 0.00 0.00 0.00 5.03
4661 4834 2.125753 CCAGTCCAGAGCGAGCAC 60.126 66.667 0.00 0.00 0.00 4.40
4662 4835 2.125753 CAGTCCAGAGCGAGCACC 60.126 66.667 0.00 0.00 0.00 5.01
4663 4836 2.283532 AGTCCAGAGCGAGCACCT 60.284 61.111 0.00 0.00 0.00 4.00
4664 4837 2.125753 GTCCAGAGCGAGCACCTG 60.126 66.667 9.47 9.47 0.00 4.00
4665 4838 4.074526 TCCAGAGCGAGCACCTGC 62.075 66.667 10.53 0.00 42.49 4.85
4675 4848 3.799753 GCACCTGCGACGATTGAT 58.200 55.556 0.00 0.00 0.00 2.57
4676 4849 2.089854 GCACCTGCGACGATTGATT 58.910 52.632 0.00 0.00 0.00 2.57
4677 4850 0.026803 GCACCTGCGACGATTGATTC 59.973 55.000 0.00 0.00 0.00 2.52
4678 4851 0.652592 CACCTGCGACGATTGATTCC 59.347 55.000 0.00 0.00 0.00 3.01
4679 4852 0.249120 ACCTGCGACGATTGATTCCA 59.751 50.000 0.00 0.00 0.00 3.53
4680 4853 1.134401 ACCTGCGACGATTGATTCCAT 60.134 47.619 0.00 0.00 0.00 3.41
4693 4867 4.119556 TGATTCCATGGTGGTTTTGGTA 57.880 40.909 12.58 0.00 39.03 3.25
4723 4897 3.010027 TGCATGGTCAAAGGAACTCCATA 59.990 43.478 0.00 0.00 38.49 2.74
4724 4898 4.210331 GCATGGTCAAAGGAACTCCATAT 58.790 43.478 0.00 0.00 38.49 1.78
4725 4899 5.104151 TGCATGGTCAAAGGAACTCCATATA 60.104 40.000 0.00 0.00 38.49 0.86
4727 4901 6.491403 GCATGGTCAAAGGAACTCCATATATT 59.509 38.462 0.00 0.00 38.49 1.28
4728 4902 7.014615 GCATGGTCAAAGGAACTCCATATATTT 59.985 37.037 0.00 0.00 38.49 1.40
4763 4937 0.471191 ATCATCAGCCGCTGGAATCA 59.529 50.000 20.23 0.56 31.51 2.57
4796 4970 0.677731 TCGTCGACCGGGTAATCACT 60.678 55.000 10.58 0.00 37.11 3.41
4804 4978 2.370849 ACCGGGTAATCACTGTTGAACT 59.629 45.455 6.32 0.00 34.61 3.01
4805 4979 3.000727 CCGGGTAATCACTGTTGAACTC 58.999 50.000 0.00 0.00 34.61 3.01
4806 4980 3.306780 CCGGGTAATCACTGTTGAACTCT 60.307 47.826 0.00 0.00 34.61 3.24
4808 4982 3.927142 GGGTAATCACTGTTGAACTCTCG 59.073 47.826 0.00 0.00 34.61 4.04
4809 4983 4.321750 GGGTAATCACTGTTGAACTCTCGA 60.322 45.833 0.00 0.00 34.61 4.04
4810 4984 5.411781 GGTAATCACTGTTGAACTCTCGAT 58.588 41.667 0.00 0.00 34.61 3.59
4877 5054 1.677217 GGAGAATGTGGACTGTGGCTC 60.677 57.143 0.00 0.00 0.00 4.70
4888 5066 2.552315 GACTGTGGCTCGATTTTGGAAA 59.448 45.455 0.00 0.00 0.00 3.13
4983 5166 0.465097 CAGCTCCCTTGGTAGCATGG 60.465 60.000 17.65 17.65 41.32 3.66
4991 5174 0.253044 TTGGTAGCATGGCAGTCCTC 59.747 55.000 0.00 0.00 0.00 3.71
4996 5179 2.299326 AGCATGGCAGTCCTCTTTTT 57.701 45.000 0.00 0.00 0.00 1.94
5113 5297 5.249622 GGGGATAGGGAATTTTTGTTTCCAA 59.750 40.000 4.96 0.00 43.72 3.53
5133 5317 4.775253 CCAAAAGGAGGGTAATTTAAGGCA 59.225 41.667 0.00 0.00 0.00 4.75
5135 5319 4.948062 AAGGAGGGTAATTTAAGGCAGT 57.052 40.909 0.00 0.00 0.00 4.40
5137 5321 3.850173 AGGAGGGTAATTTAAGGCAGTGA 59.150 43.478 0.00 0.00 0.00 3.41
5138 5322 4.291249 AGGAGGGTAATTTAAGGCAGTGAA 59.709 41.667 0.00 0.00 0.00 3.18
5139 5323 5.044105 AGGAGGGTAATTTAAGGCAGTGAAT 60.044 40.000 0.00 0.00 0.00 2.57
5141 5325 6.831868 GGAGGGTAATTTAAGGCAGTGAATAA 59.168 38.462 0.00 0.00 0.00 1.40
5142 5326 7.013369 GGAGGGTAATTTAAGGCAGTGAATAAG 59.987 40.741 0.00 0.00 0.00 1.73
5163 5575 6.653526 AAGGAGAGAGATCATGTACAGATG 57.346 41.667 0.33 0.00 0.00 2.90
5229 5643 2.010145 TTCGGCATCTTCTTCCTTCG 57.990 50.000 0.00 0.00 0.00 3.79
5241 5655 1.230635 TTCCTTCGCTGCACTGCTTC 61.231 55.000 1.98 0.00 0.00 3.86
5250 5664 1.220477 GCACTGCTTCTCCCTCTCC 59.780 63.158 0.00 0.00 0.00 3.71
5251 5665 1.904032 CACTGCTTCTCCCTCTCCC 59.096 63.158 0.00 0.00 0.00 4.30
5252 5666 0.617249 CACTGCTTCTCCCTCTCCCT 60.617 60.000 0.00 0.00 0.00 4.20
5253 5667 0.325203 ACTGCTTCTCCCTCTCCCTC 60.325 60.000 0.00 0.00 0.00 4.30
5254 5668 0.032217 CTGCTTCTCCCTCTCCCTCT 60.032 60.000 0.00 0.00 0.00 3.69
5255 5669 0.032615 TGCTTCTCCCTCTCCCTCTC 60.033 60.000 0.00 0.00 0.00 3.20
5259 5673 2.838637 TCTCCCTCTCCCTCTCTTTC 57.161 55.000 0.00 0.00 0.00 2.62
5261 5675 0.705253 TCCCTCTCCCTCTCTTTCGT 59.295 55.000 0.00 0.00 0.00 3.85
5264 5678 1.896465 CCTCTCCCTCTCTTTCGTGTT 59.104 52.381 0.00 0.00 0.00 3.32
5289 5707 4.108570 TGGCTTCTTCCTTTCCCAGTATA 58.891 43.478 0.00 0.00 0.00 1.47
5321 5747 1.184970 GGGTAGCTTTTTGCAGGCCA 61.185 55.000 5.01 0.00 45.94 5.36
5385 5813 3.941657 GACCTGCTGTGACCGAGGC 62.942 68.421 0.00 0.00 0.00 4.70
5386 5814 4.767255 CCTGCTGTGACCGAGGCC 62.767 72.222 0.00 0.00 0.00 5.19
5418 5846 3.138798 CCTGCCTGCCTGTGATGC 61.139 66.667 0.00 0.00 0.00 3.91
5460 5898 2.846827 AGTGGGGAAAAGTGATAGGAGG 59.153 50.000 0.00 0.00 0.00 4.30
5462 5900 1.495148 GGGGAAAAGTGATAGGAGGGG 59.505 57.143 0.00 0.00 0.00 4.79
5463 5901 2.488836 GGGAAAAGTGATAGGAGGGGA 58.511 52.381 0.00 0.00 0.00 4.81
5464 5902 2.439880 GGGAAAAGTGATAGGAGGGGAG 59.560 54.545 0.00 0.00 0.00 4.30
5465 5903 2.439880 GGAAAAGTGATAGGAGGGGAGG 59.560 54.545 0.00 0.00 0.00 4.30
5466 5904 2.972153 AAAGTGATAGGAGGGGAGGT 57.028 50.000 0.00 0.00 0.00 3.85
5507 5950 3.279116 GCACAGCACGGAACAGCA 61.279 61.111 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.996098 ACTTGTTGTGGTTATAGTTTGCTAT 57.004 32.000 0.00 0.00 40.69 2.97
2 3 8.905660 TTACTTGTTGTGGTTATAGTTTGCTA 57.094 30.769 0.00 0.00 0.00 3.49
3 4 7.717875 TCTTACTTGTTGTGGTTATAGTTTGCT 59.282 33.333 0.00 0.00 0.00 3.91
4 5 7.867752 TCTTACTTGTTGTGGTTATAGTTTGC 58.132 34.615 0.00 0.00 0.00 3.68
6 7 9.841295 TCTTCTTACTTGTTGTGGTTATAGTTT 57.159 29.630 0.00 0.00 0.00 2.66
7 8 9.841295 TTCTTCTTACTTGTTGTGGTTATAGTT 57.159 29.630 0.00 0.00 0.00 2.24
8 9 9.841295 TTTCTTCTTACTTGTTGTGGTTATAGT 57.159 29.630 0.00 0.00 0.00 2.12
12 13 7.971722 GCTTTTTCTTCTTACTTGTTGTGGTTA 59.028 33.333 0.00 0.00 0.00 2.85
13 14 6.811665 GCTTTTTCTTCTTACTTGTTGTGGTT 59.188 34.615 0.00 0.00 0.00 3.67
14 15 6.152831 AGCTTTTTCTTCTTACTTGTTGTGGT 59.847 34.615 0.00 0.00 0.00 4.16
15 16 6.564328 AGCTTTTTCTTCTTACTTGTTGTGG 58.436 36.000 0.00 0.00 0.00 4.17
16 17 9.567848 TTTAGCTTTTTCTTCTTACTTGTTGTG 57.432 29.630 0.00 0.00 0.00 3.33
17 18 9.788960 CTTTAGCTTTTTCTTCTTACTTGTTGT 57.211 29.630 0.00 0.00 0.00 3.32
20 21 9.174166 TGTCTTTAGCTTTTTCTTCTTACTTGT 57.826 29.630 0.00 0.00 0.00 3.16
23 24 9.561069 TGATGTCTTTAGCTTTTTCTTCTTACT 57.439 29.630 0.00 0.00 0.00 2.24
26 27 8.907885 AGTTGATGTCTTTAGCTTTTTCTTCTT 58.092 29.630 0.00 0.00 0.00 2.52
27 28 8.457238 AGTTGATGTCTTTAGCTTTTTCTTCT 57.543 30.769 0.00 0.00 0.00 2.85
28 29 9.521503 AAAGTTGATGTCTTTAGCTTTTTCTTC 57.478 29.630 0.00 0.00 34.02 2.87
33 34 9.899226 GACATAAAGTTGATGTCTTTAGCTTTT 57.101 29.630 21.79 0.00 46.42 2.27
51 52 9.798994 GGAGGGTGTATTATATACGACATAAAG 57.201 37.037 0.00 0.00 0.00 1.85
52 53 8.461222 CGGAGGGTGTATTATATACGACATAAA 58.539 37.037 0.00 0.00 0.00 1.40
53 54 7.415541 GCGGAGGGTGTATTATATACGACATAA 60.416 40.741 0.00 0.00 0.00 1.90
54 55 6.038603 GCGGAGGGTGTATTATATACGACATA 59.961 42.308 0.00 0.00 0.00 2.29
55 56 5.163581 GCGGAGGGTGTATTATATACGACAT 60.164 44.000 0.00 0.00 0.00 3.06
56 57 4.156556 GCGGAGGGTGTATTATATACGACA 59.843 45.833 0.00 0.00 0.00 4.35
57 58 4.439289 GGCGGAGGGTGTATTATATACGAC 60.439 50.000 0.00 0.00 0.00 4.34
58 59 3.696051 GGCGGAGGGTGTATTATATACGA 59.304 47.826 0.00 0.00 0.00 3.43
59 60 3.181483 GGGCGGAGGGTGTATTATATACG 60.181 52.174 0.00 0.00 0.00 3.06
60 61 3.770933 TGGGCGGAGGGTGTATTATATAC 59.229 47.826 0.00 0.00 0.00 1.47
61 62 4.063851 TGGGCGGAGGGTGTATTATATA 57.936 45.455 0.00 0.00 0.00 0.86
62 63 2.910544 TGGGCGGAGGGTGTATTATAT 58.089 47.619 0.00 0.00 0.00 0.86
63 64 2.402182 TGGGCGGAGGGTGTATTATA 57.598 50.000 0.00 0.00 0.00 0.98
64 65 1.513858 TTGGGCGGAGGGTGTATTAT 58.486 50.000 0.00 0.00 0.00 1.28
65 66 1.065272 GTTTGGGCGGAGGGTGTATTA 60.065 52.381 0.00 0.00 0.00 0.98
66 67 0.323087 GTTTGGGCGGAGGGTGTATT 60.323 55.000 0.00 0.00 0.00 1.89
67 68 1.205460 AGTTTGGGCGGAGGGTGTAT 61.205 55.000 0.00 0.00 0.00 2.29
68 69 0.544833 TAGTTTGGGCGGAGGGTGTA 60.545 55.000 0.00 0.00 0.00 2.90
69 70 1.844289 TAGTTTGGGCGGAGGGTGT 60.844 57.895 0.00 0.00 0.00 4.16
70 71 1.376812 GTAGTTTGGGCGGAGGGTG 60.377 63.158 0.00 0.00 0.00 4.61
71 72 1.131928 AAGTAGTTTGGGCGGAGGGT 61.132 55.000 0.00 0.00 0.00 4.34
72 73 0.037734 AAAGTAGTTTGGGCGGAGGG 59.962 55.000 0.00 0.00 0.00 4.30
73 74 1.003233 AGAAAGTAGTTTGGGCGGAGG 59.997 52.381 0.00 0.00 0.00 4.30
74 75 2.076863 CAGAAAGTAGTTTGGGCGGAG 58.923 52.381 0.00 0.00 0.00 4.63
75 76 1.880646 GCAGAAAGTAGTTTGGGCGGA 60.881 52.381 0.00 0.00 0.00 5.54
76 77 0.521735 GCAGAAAGTAGTTTGGGCGG 59.478 55.000 0.00 0.00 0.00 6.13
77 78 1.197721 CTGCAGAAAGTAGTTTGGGCG 59.802 52.381 8.42 0.00 0.00 6.13
78 79 2.504367 TCTGCAGAAAGTAGTTTGGGC 58.496 47.619 15.67 4.59 0.00 5.36
79 80 5.712152 ATTTCTGCAGAAAGTAGTTTGGG 57.288 39.130 37.00 0.79 45.87 4.12
107 108 4.096382 CCCGAATTACTTGTCCCAGAAATG 59.904 45.833 0.00 0.00 0.00 2.32
115 116 1.205417 TCCGTCCCGAATTACTTGTCC 59.795 52.381 0.00 0.00 0.00 4.02
116 117 2.165030 TCTCCGTCCCGAATTACTTGTC 59.835 50.000 0.00 0.00 0.00 3.18
118 119 2.426024 TCTCTCCGTCCCGAATTACTTG 59.574 50.000 0.00 0.00 0.00 3.16
142 143 4.170468 AGGAAGTGGACATTTTCACTGT 57.830 40.909 0.00 0.00 42.67 3.55
145 146 6.381801 CACATAAGGAAGTGGACATTTTCAC 58.618 40.000 0.00 0.00 32.24 3.18
148 149 4.832266 TGCACATAAGGAAGTGGACATTTT 59.168 37.500 0.00 0.00 36.29 1.82
153 154 3.412386 ACTTGCACATAAGGAAGTGGAC 58.588 45.455 0.03 0.00 46.44 4.02
188 192 2.389962 TGGTTTATGTGTACGCCCTC 57.610 50.000 3.51 0.00 0.00 4.30
212 216 4.016444 GCCACATTCTGTTTGGAGGAATA 58.984 43.478 0.00 0.00 31.39 1.75
213 217 2.827921 GCCACATTCTGTTTGGAGGAAT 59.172 45.455 0.00 0.00 31.39 3.01
214 218 2.158475 AGCCACATTCTGTTTGGAGGAA 60.158 45.455 0.00 0.00 31.39 3.36
215 219 1.425066 AGCCACATTCTGTTTGGAGGA 59.575 47.619 0.00 0.00 31.39 3.71
216 220 1.815003 GAGCCACATTCTGTTTGGAGG 59.185 52.381 0.00 0.00 31.39 4.30
217 221 2.787994 AGAGCCACATTCTGTTTGGAG 58.212 47.619 0.00 0.00 31.39 3.86
218 222 2.957402 AGAGCCACATTCTGTTTGGA 57.043 45.000 0.00 0.00 31.39 3.53
240 254 3.009723 CTGGCGTGGTCAGTAAAATCAT 58.990 45.455 0.00 0.00 29.72 2.45
241 255 2.422597 CTGGCGTGGTCAGTAAAATCA 58.577 47.619 0.00 0.00 29.72 2.57
266 280 4.683334 GGCGACGTGCTGTTTGCC 62.683 66.667 0.00 9.73 45.43 4.52
267 281 4.683334 GGGCGACGTGCTGTTTGC 62.683 66.667 0.00 0.00 45.43 3.68
268 282 2.329678 TTTGGGCGACGTGCTGTTTG 62.330 55.000 0.00 0.00 45.43 2.93
365 380 3.553095 GACTTCCTTGGGCCAGCGT 62.553 63.158 6.23 0.32 0.00 5.07
394 409 2.132740 TTGTTTTTCACGAGCATGCC 57.867 45.000 15.66 4.99 0.00 4.40
459 475 3.636231 CTGAGGTGGTTGGGGCGA 61.636 66.667 0.00 0.00 0.00 5.54
463 479 4.366684 GCCCCTGAGGTGGTTGGG 62.367 72.222 0.00 0.00 38.26 4.12
590 619 0.252467 CCTCTTCTGGGTCTGGGTCT 60.252 60.000 0.00 0.00 0.00 3.85
761 817 0.252284 GAAGAGGAGTGAGGGGGACA 60.252 60.000 0.00 0.00 0.00 4.02
832 907 4.974721 GGTGGTGGTGGCACTGGG 62.975 72.222 18.45 0.00 0.00 4.45
833 908 4.202574 TGGTGGTGGTGGCACTGG 62.203 66.667 18.45 0.00 0.00 4.00
850 925 4.109675 ATTTGGGCTAGCGGCGGT 62.110 61.111 18.21 18.21 42.94 5.68
946 1023 4.174129 GGTTTGCGATTCGGGGCG 62.174 66.667 8.34 0.00 0.00 6.13
1563 1687 2.663196 CAGGTGAAGACCCCGGTC 59.337 66.667 5.70 5.70 44.40 4.79
1566 1690 4.410400 GGCCAGGTGAAGACCCCG 62.410 72.222 0.00 0.00 44.40 5.73
2103 2228 1.097232 CCGAATGCCTGAAAGATGCA 58.903 50.000 0.00 0.00 35.63 3.96
2145 2270 1.030488 CCAGTGCAAGCTCCCTCATG 61.030 60.000 0.00 0.00 0.00 3.07
2149 2274 3.573229 TGCCAGTGCAAGCTCCCT 61.573 61.111 6.24 0.00 46.66 4.20
2271 2396 1.875963 CAAGCACCCGAACACCATC 59.124 57.895 0.00 0.00 0.00 3.51
2281 2406 1.153958 GAATCGCAAGCAAGCACCC 60.154 57.895 1.32 0.00 37.18 4.61
2295 2420 6.038050 CCAGAGAACATTGCTTAGAAGGAATC 59.962 42.308 6.08 0.00 43.91 2.52
2327 2452 8.221766 GTCAGTAATACAGTAGCAAGAAAACAC 58.778 37.037 0.00 0.00 0.00 3.32
2334 2459 5.127194 TCCCAGTCAGTAATACAGTAGCAAG 59.873 44.000 0.00 0.00 0.00 4.01
2337 2462 5.793030 ATCCCAGTCAGTAATACAGTAGC 57.207 43.478 0.00 0.00 0.00 3.58
2338 2463 7.040340 CCAGTATCCCAGTCAGTAATACAGTAG 60.040 44.444 0.00 0.00 0.00 2.57
2340 2465 5.598830 CCAGTATCCCAGTCAGTAATACAGT 59.401 44.000 0.00 0.00 0.00 3.55
2343 2476 6.919775 ATCCAGTATCCCAGTCAGTAATAC 57.080 41.667 0.00 0.00 0.00 1.89
2349 2482 4.040829 TGCATAATCCAGTATCCCAGTCAG 59.959 45.833 0.00 0.00 0.00 3.51
2360 2493 4.885907 CCTCAAATGTCTGCATAATCCAGT 59.114 41.667 0.00 0.00 34.39 4.00
2648 2781 3.989167 CCACGATGCAATTCAAACAATGT 59.011 39.130 0.00 0.00 0.00 2.71
2680 2819 8.881743 TGTGAGAAACAAGATTTTCCAAATTTG 58.118 29.630 11.40 11.40 36.31 2.32
2686 2825 6.434028 CCCTATGTGAGAAACAAGATTTTCCA 59.566 38.462 0.00 0.00 43.61 3.53
2734 2873 5.534207 AGAAGACAATGCCAAAACAATGA 57.466 34.783 0.00 0.00 0.00 2.57
3052 3192 3.933332 GACAATAAAACGGACCTGGAGAG 59.067 47.826 0.00 0.00 0.00 3.20
3173 3313 7.085116 AGTCTTTAAGTGTAGTTGTCTCATCG 58.915 38.462 0.00 0.00 0.00 3.84
3188 3328 5.632034 AGTTGAGGTCCAAGTCTTTAAGT 57.368 39.130 0.00 0.00 33.25 2.24
3264 3404 3.638860 ACACCACAGATATCGTAAGGGA 58.361 45.455 0.00 0.00 38.47 4.20
3271 3411 6.049149 AGTAATTCCAACACCACAGATATCG 58.951 40.000 0.00 0.00 0.00 2.92
3288 3428 9.860898 ATTGAGTTATTGGCTTGAAAGTAATTC 57.139 29.630 0.00 0.00 38.60 2.17
3302 3442 9.760077 AGTTAGTATTACCGATTGAGTTATTGG 57.240 33.333 0.00 0.00 35.50 3.16
3311 3451 8.328146 CACACATCAAGTTAGTATTACCGATTG 58.672 37.037 0.00 0.00 0.00 2.67
3370 3510 6.743575 ATACCTTCAGACTCCAAAAATTCG 57.256 37.500 0.00 0.00 0.00 3.34
3463 3603 4.612264 ACTTGGAGAAGCCGTAAAAGTA 57.388 40.909 0.00 0.00 40.66 2.24
3472 3612 3.704800 AGGAACTTACTTGGAGAAGCC 57.295 47.619 0.00 0.00 27.25 4.35
3550 3691 6.760298 CACTTCATTGATAGCTCTGCTTAAGA 59.240 38.462 6.67 0.00 40.44 2.10
3576 3717 3.631686 CACCACCAACTTGAAATGTCTCA 59.368 43.478 0.00 0.00 0.00 3.27
3630 3771 6.269315 GCAGTCAGGTATCCTATCATAATCG 58.731 44.000 0.00 0.00 29.64 3.34
3718 3859 1.275856 GGCTTGTTTGGAATGCATGGA 59.724 47.619 0.00 0.00 0.00 3.41
3719 3860 1.276989 AGGCTTGTTTGGAATGCATGG 59.723 47.619 0.00 0.00 0.00 3.66
3793 3935 6.299141 TGAAAGGATGCAAAGAACTACTTCT 58.701 36.000 0.00 0.00 38.49 2.85
3800 3942 3.964909 ACGTTGAAAGGATGCAAAGAAC 58.035 40.909 0.00 0.00 0.00 3.01
3820 3962 8.788325 AGGAATCTAAACACAAGGTACATAAC 57.212 34.615 0.00 0.00 0.00 1.89
3837 3979 8.463930 AACAACAAATGTCTGAAAGGAATCTA 57.536 30.769 0.00 0.00 42.99 1.98
3839 3981 7.517259 GCAAACAACAAATGTCTGAAAGGAATC 60.517 37.037 0.00 0.00 42.99 2.52
3840 3982 6.258507 GCAAACAACAAATGTCTGAAAGGAAT 59.741 34.615 0.00 0.00 42.99 3.01
3841 3983 5.580297 GCAAACAACAAATGTCTGAAAGGAA 59.420 36.000 0.00 0.00 42.99 3.36
3843 3985 5.005971 CAGCAAACAACAAATGTCTGAAAGG 59.994 40.000 0.00 0.00 42.99 3.11
3848 3990 5.342433 TCTTCAGCAAACAACAAATGTCTG 58.658 37.500 0.00 0.00 42.99 3.51
3849 3991 5.581126 TCTTCAGCAAACAACAAATGTCT 57.419 34.783 0.00 0.00 42.99 3.41
3887 4029 9.316730 TGCTTCCATTTTCTAATATGAAATTGC 57.683 29.630 0.00 0.00 36.65 3.56
3897 4039 7.269477 GCACTATCTGCTTCCATTTTCTAAT 57.731 36.000 0.00 0.00 43.33 1.73
3950 4092 5.785123 AGGATGGGCTAGTAAGGTAAACTA 58.215 41.667 0.00 0.00 0.00 2.24
3952 4094 5.123936 CAAGGATGGGCTAGTAAGGTAAAC 58.876 45.833 0.00 0.00 0.00 2.01
3957 4099 3.199880 CACAAGGATGGGCTAGTAAGG 57.800 52.381 0.00 0.00 0.00 2.69
4041 4193 3.772572 TGAGCCAGGTACAGCTTGTATAA 59.227 43.478 5.84 0.00 40.29 0.98
4081 4243 3.064958 CAGTATGATGGCTGCTCAAAGTG 59.935 47.826 0.00 0.00 39.69 3.16
4128 4290 5.244851 ACCCAACAATGCATATGTGTTAACA 59.755 36.000 13.47 3.59 41.58 2.41
4264 4436 8.940397 TCCTGAAATCAAGAAAAAGTAGGAAT 57.060 30.769 0.00 0.00 0.00 3.01
4265 4437 8.760980 TTCCTGAAATCAAGAAAAAGTAGGAA 57.239 30.769 0.00 0.00 38.03 3.36
4266 4438 7.040409 GCTTCCTGAAATCAAGAAAAAGTAGGA 60.040 37.037 0.00 0.00 0.00 2.94
4267 4439 7.087007 GCTTCCTGAAATCAAGAAAAAGTAGG 58.913 38.462 0.00 0.00 0.00 3.18
4268 4440 7.087007 GGCTTCCTGAAATCAAGAAAAAGTAG 58.913 38.462 0.00 0.00 0.00 2.57
4269 4441 6.549364 TGGCTTCCTGAAATCAAGAAAAAGTA 59.451 34.615 0.00 0.00 0.00 2.24
4327 4499 0.327259 TTCTGGATGCTTGCTCTGCT 59.673 50.000 0.00 0.00 0.00 4.24
4456 4628 4.018960 AGCCTTTTGGTGATGTCATAGTCT 60.019 41.667 0.00 0.00 42.99 3.24
4507 4679 2.547855 CGCAGATATCGAATTGGGGTCA 60.548 50.000 0.00 0.00 0.00 4.02
4546 4718 5.060427 TGAAATCCTGAAACCTCTTGGAA 57.940 39.130 0.00 0.00 37.04 3.53
4615 4788 2.181125 TGGAATTCCTGTTGCATGCAT 58.819 42.857 23.37 2.99 36.82 3.96
4616 4789 1.630223 TGGAATTCCTGTTGCATGCA 58.370 45.000 24.73 18.46 36.82 3.96
4637 4810 1.867919 CGCTCTGGACTGGACTTCGT 61.868 60.000 0.00 0.00 0.00 3.85
4648 4821 4.074526 GCAGGTGCTCGCTCTGGA 62.075 66.667 12.16 0.00 38.21 3.86
4650 4823 4.426112 TCGCAGGTGCTCGCTCTG 62.426 66.667 0.00 7.92 39.32 3.35
4655 4828 2.507102 AATCGTCGCAGGTGCTCG 60.507 61.111 0.00 5.38 39.32 5.03
4656 4829 0.807667 ATCAATCGTCGCAGGTGCTC 60.808 55.000 0.00 0.00 39.32 4.26
4657 4830 0.391661 AATCAATCGTCGCAGGTGCT 60.392 50.000 0.00 0.00 39.32 4.40
4658 4831 0.026803 GAATCAATCGTCGCAGGTGC 59.973 55.000 0.00 0.00 37.78 5.01
4659 4832 0.652592 GGAATCAATCGTCGCAGGTG 59.347 55.000 0.00 0.00 0.00 4.00
4661 4834 1.262417 CATGGAATCAATCGTCGCAGG 59.738 52.381 0.00 0.00 0.00 4.85
4662 4835 1.262417 CCATGGAATCAATCGTCGCAG 59.738 52.381 5.56 0.00 0.00 5.18
4663 4836 1.298602 CCATGGAATCAATCGTCGCA 58.701 50.000 5.56 0.00 0.00 5.10
4664 4837 1.003545 CACCATGGAATCAATCGTCGC 60.004 52.381 21.47 0.00 0.00 5.19
4665 4838 1.599071 CCACCATGGAATCAATCGTCG 59.401 52.381 21.47 0.00 40.96 5.12
4666 4839 2.643551 ACCACCATGGAATCAATCGTC 58.356 47.619 21.47 0.00 40.96 4.20
4667 4840 2.806945 ACCACCATGGAATCAATCGT 57.193 45.000 21.47 0.00 40.96 3.73
4668 4841 4.175516 CAAAACCACCATGGAATCAATCG 58.824 43.478 21.47 0.00 40.96 3.34
4669 4842 4.020307 ACCAAAACCACCATGGAATCAATC 60.020 41.667 21.47 0.00 40.96 2.67
4670 4843 3.909364 ACCAAAACCACCATGGAATCAAT 59.091 39.130 21.47 0.00 40.96 2.57
4671 4844 3.312890 ACCAAAACCACCATGGAATCAA 58.687 40.909 21.47 0.00 40.96 2.57
4672 4845 2.969628 ACCAAAACCACCATGGAATCA 58.030 42.857 21.47 0.00 40.96 2.57
4673 4846 4.340617 TCTACCAAAACCACCATGGAATC 58.659 43.478 21.47 0.00 40.96 2.52
4674 4847 4.396357 TCTACCAAAACCACCATGGAAT 57.604 40.909 21.47 0.00 40.96 3.01
4675 4848 3.885976 TCTACCAAAACCACCATGGAA 57.114 42.857 21.47 0.00 40.96 3.53
4676 4849 4.396357 AATCTACCAAAACCACCATGGA 57.604 40.909 21.47 0.00 40.96 3.41
4677 4850 5.245977 AGAAAATCTACCAAAACCACCATGG 59.754 40.000 11.19 11.19 45.02 3.66
4678 4851 6.158598 CAGAAAATCTACCAAAACCACCATG 58.841 40.000 0.00 0.00 0.00 3.66
4679 4852 5.279456 GCAGAAAATCTACCAAAACCACCAT 60.279 40.000 0.00 0.00 0.00 3.55
4680 4853 4.038642 GCAGAAAATCTACCAAAACCACCA 59.961 41.667 0.00 0.00 0.00 4.17
4693 4867 4.410099 TCCTTTGACCATGCAGAAAATCT 58.590 39.130 0.00 0.00 0.00 2.40
4733 4907 0.528924 GCTGATGATGCTTGTTGGCA 59.471 50.000 0.00 0.00 46.63 4.92
4734 4908 0.179119 GGCTGATGATGCTTGTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
4740 4914 1.822613 CCAGCGGCTGATGATGCTT 60.823 57.895 30.52 0.00 34.99 3.91
4742 4916 1.170919 ATTCCAGCGGCTGATGATGC 61.171 55.000 30.52 0.00 31.64 3.91
4763 4937 3.251571 GTCGACGAGCTGATTTTTACCT 58.748 45.455 0.00 0.00 0.00 3.08
4796 4970 3.243873 ACTGCTGAATCGAGAGTTCAACA 60.244 43.478 0.00 3.01 35.36 3.33
4804 4978 1.205655 CCCTTCACTGCTGAATCGAGA 59.794 52.381 0.00 0.00 35.78 4.04
4805 4979 1.205655 TCCCTTCACTGCTGAATCGAG 59.794 52.381 0.00 0.00 35.78 4.04
4806 4980 1.205655 CTCCCTTCACTGCTGAATCGA 59.794 52.381 0.00 0.00 35.78 3.59
4808 4982 2.626840 GTCTCCCTTCACTGCTGAATC 58.373 52.381 0.00 0.00 35.78 2.52
4809 4983 1.066573 CGTCTCCCTTCACTGCTGAAT 60.067 52.381 0.00 0.00 35.78 2.57
4810 4984 0.318441 CGTCTCCCTTCACTGCTGAA 59.682 55.000 0.00 0.00 35.04 3.02
4877 5054 1.799916 GGCCGCGTTTCCAAAATCG 60.800 57.895 4.92 0.00 0.00 3.34
5021 5204 5.134725 ACCAGCCATGAAAAGAATCCTAT 57.865 39.130 0.00 0.00 0.00 2.57
5035 5218 5.970021 AGGGGAAATAAATTAAACCAGCCAT 59.030 36.000 0.00 0.00 0.00 4.40
5113 5297 5.016831 CACTGCCTTAAATTACCCTCCTTT 58.983 41.667 0.00 0.00 0.00 3.11
5116 5300 4.230745 TCACTGCCTTAAATTACCCTCC 57.769 45.455 0.00 0.00 0.00 4.30
5133 5317 7.782168 TGTACATGATCTCTCTCCTTATTCACT 59.218 37.037 0.00 0.00 0.00 3.41
5135 5319 8.001292 TCTGTACATGATCTCTCTCCTTATTCA 58.999 37.037 0.00 0.00 0.00 2.57
5137 5321 8.805175 CATCTGTACATGATCTCTCTCCTTATT 58.195 37.037 0.00 0.00 0.00 1.40
5138 5322 7.093814 GCATCTGTACATGATCTCTCTCCTTAT 60.094 40.741 0.00 0.00 0.00 1.73
5139 5323 6.208402 GCATCTGTACATGATCTCTCTCCTTA 59.792 42.308 0.00 0.00 0.00 2.69
5141 5325 4.523943 GCATCTGTACATGATCTCTCTCCT 59.476 45.833 0.00 0.00 0.00 3.69
5142 5326 4.280425 TGCATCTGTACATGATCTCTCTCC 59.720 45.833 0.00 0.00 0.00 3.71
5163 5575 3.829886 TCACTGGATCGAAAATGTTGC 57.170 42.857 0.00 0.00 0.00 4.17
5192 5604 3.947196 CCGAATTCAATTCTGATCCACCA 59.053 43.478 8.50 0.00 37.13 4.17
5229 5643 1.744741 GAGGGAGAAGCAGTGCAGC 60.745 63.158 19.20 8.56 0.00 5.25
5241 5655 1.341581 ACGAAAGAGAGGGAGAGGGAG 60.342 57.143 0.00 0.00 0.00 4.30
5250 5664 1.264288 GCCAACAACACGAAAGAGAGG 59.736 52.381 0.00 0.00 0.00 3.69
5251 5665 2.213499 AGCCAACAACACGAAAGAGAG 58.787 47.619 0.00 0.00 0.00 3.20
5252 5666 2.325583 AGCCAACAACACGAAAGAGA 57.674 45.000 0.00 0.00 0.00 3.10
5253 5667 2.614057 AGAAGCCAACAACACGAAAGAG 59.386 45.455 0.00 0.00 0.00 2.85
5254 5668 2.639065 AGAAGCCAACAACACGAAAGA 58.361 42.857 0.00 0.00 0.00 2.52
5255 5669 3.363178 GAAGAAGCCAACAACACGAAAG 58.637 45.455 0.00 0.00 0.00 2.62
5259 5673 1.308998 AGGAAGAAGCCAACAACACG 58.691 50.000 0.00 0.00 0.00 4.49
5261 5675 2.693074 GGAAAGGAAGAAGCCAACAACA 59.307 45.455 0.00 0.00 0.00 3.33
5264 5678 1.216678 TGGGAAAGGAAGAAGCCAACA 59.783 47.619 0.00 0.00 0.00 3.33
5304 5730 1.200948 CTCTGGCCTGCAAAAAGCTAC 59.799 52.381 3.32 0.00 45.94 3.58
5321 5747 3.137728 GCTCTACCCTACCTTCTCTCTCT 59.862 52.174 0.00 0.00 0.00 3.10
5460 5898 1.004745 TCTTCTTTCCATGCACCTCCC 59.995 52.381 0.00 0.00 0.00 4.30
5462 5900 3.340814 TCTCTTCTTTCCATGCACCTC 57.659 47.619 0.00 0.00 0.00 3.85
5463 5901 3.795688 TTCTCTTCTTTCCATGCACCT 57.204 42.857 0.00 0.00 0.00 4.00
5464 5902 3.192212 CCTTTCTCTTCTTTCCATGCACC 59.808 47.826 0.00 0.00 0.00 5.01
5465 5903 4.074970 TCCTTTCTCTTCTTTCCATGCAC 58.925 43.478 0.00 0.00 0.00 4.57
5466 5904 4.371624 TCCTTTCTCTTCTTTCCATGCA 57.628 40.909 0.00 0.00 0.00 3.96
5507 5950 6.256819 TCCGATCTTAACCATCTATCCATCT 58.743 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.