Multiple sequence alignment - TraesCS4A01G106800

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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 TraesCS4A01G106800 chr4A 100.000 3047 0 0 943 3989 121506215 121503169 0.000000e+00 5627.0
1 TraesCS4A01G106800 chr4A 100.000 738 0 0 1 738 121507157 121506420 0.000000e+00 1363.0
2 TraesCS4A01G106800 chr4D 94.199 1810 57 24 943 2737 344109820 344111596 0.000000e+00 2717.0
3 TraesCS4A01G106800 chr4D 89.158 701 32 24 2690 3365 344111598 344112279 0.000000e+00 833.0
4 TraesCS4A01G106800 chr4D 88.273 469 23 17 1 447 344108758 344109216 2.110000e-147 532.0
5 TraesCS4A01G106800 chr4D 87.466 367 38 5 3547 3909 344112425 344112787 2.220000e-112 416.0
6 TraesCS4A01G106800 chr4D 96.089 179 6 1 445 622 344109251 344109429 1.400000e-74 291.0
7 TraesCS4A01G106800 chr4D 92.727 110 7 1 3472 3580 344112314 344112423 1.480000e-34 158.0
8 TraesCS4A01G106800 chr4B 94.113 1274 42 13 997 2266 426104727 426105971 0.000000e+00 1906.0
9 TraesCS4A01G106800 chr4B 92.333 600 19 13 2775 3355 426108998 426109589 0.000000e+00 828.0
10 TraesCS4A01G106800 chr4B 92.929 495 13 12 2258 2736 426108413 426108901 0.000000e+00 701.0
11 TraesCS4A01G106800 chr4B 89.347 291 8 10 443 732 426104294 426104562 1.060000e-90 344.0
12 TraesCS4A01G106800 chr4B 95.431 197 9 0 259 455 426104072 426104268 8.320000e-82 315.0
13 TraesCS4A01G106800 chr3D 87.500 256 25 4 3601 3852 336825929 336826181 5.040000e-74 289.0
14 TraesCS4A01G106800 chr3D 83.226 155 23 3 1039 1191 496733042 496733195 5.380000e-29 139.0
15 TraesCS4A01G106800 chr2D 86.831 243 27 2 3603 3842 481662838 481663078 2.360000e-67 267.0
16 TraesCS4A01G106800 chr2A 86.345 249 27 4 3602 3847 32775341 32775097 8.500000e-67 265.0
17 TraesCS4A01G106800 chr2A 85.259 251 30 4 3602 3849 81461832 81461586 6.620000e-63 252.0
18 TraesCS4A01G106800 chr7A 86.000 250 27 5 3602 3847 287009181 287008936 1.100000e-65 261.0
19 TraesCS4A01G106800 chr7A 85.887 248 28 3 3594 3836 701288247 701288492 1.420000e-64 257.0
20 TraesCS4A01G106800 chr7A 83.648 159 26 0 1042 1200 133058859 133058701 2.480000e-32 150.0
21 TraesCS4A01G106800 chr1A 85.714 252 30 3 3602 3850 10585460 10585708 1.100000e-65 261.0
22 TraesCS4A01G106800 chr7B 85.542 249 30 3 3602 3846 570102935 570103181 5.120000e-64 255.0
23 TraesCS4A01G106800 chr7B 84.906 159 24 0 1042 1200 96281871 96281713 1.150000e-35 161.0
24 TraesCS4A01G106800 chr7D 84.906 159 24 0 1042 1200 134178575 134178417 1.150000e-35 161.0
25 TraesCS4A01G106800 chr3A 83.537 164 24 3 1039 1200 638074547 638074385 2.480000e-32 150.0
26 TraesCS4A01G106800 chr6D 78.857 175 26 8 1042 1210 408222352 408222183 1.520000e-19 108.0
27 TraesCS4A01G106800 chr6D 89.062 64 4 3 3847 3907 395332244 395332307 4.270000e-10 76.8


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 TraesCS4A01G106800 chr4A 121503169 121507157 3988 True 3495.0 5627 100.000000 1 3989 2 chr4A.!!$R1 3988
1 TraesCS4A01G106800 chr4D 344108758 344112787 4029 False 824.5 2717 91.318667 1 3909 6 chr4D.!!$F1 3908
2 TraesCS4A01G106800 chr4B 426104072 426109589 5517 False 818.8 1906 92.830600 259 3355 5 chr4B.!!$F1 3096

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
231 259 0.101399 CGTTCCATGTAGAGCGAGCT 59.899 55.0 0.00 0.0 42.32 4.09 F
485 553 0.321671 ATATCTTGCGTCCCATCGGG 59.678 55.0 0.00 0.0 46.11 5.14 F
1529 1673 0.370273 CGCGCTAAGCCAGTTGTTAG 59.630 55.0 5.56 0.0 44.76 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1216 1359 0.031917 ATGCATGGCAATGGAGGGAA 60.032 50.0 2.54 0.0 43.62 3.97 R
1800 1947 0.099791 GTCGCGAGGAGGAAGAAGAG 59.900 60.0 10.24 0.0 0.00 2.85 R
3374 6141 0.036590 TGAACAGCAGCATACAGGCA 59.963 50.0 0.00 0.0 35.83 4.75 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
67 68 5.877012 ACTTGCATGAAACTGTATTCGATCT 59.123 36.000 6.60 0.00 31.80 2.75
102 129 8.626526 TCAAATACCAAGAAAGTTACCTGAAAC 58.373 33.333 0.00 0.00 0.00 2.78
103 130 8.630037 CAAATACCAAGAAAGTTACCTGAAACT 58.370 33.333 0.00 0.00 41.46 2.66
104 131 7.745620 ATACCAAGAAAGTTACCTGAAACTG 57.254 36.000 0.00 0.00 39.62 3.16
105 132 5.751586 ACCAAGAAAGTTACCTGAAACTGA 58.248 37.500 0.00 0.00 39.62 3.41
106 133 6.184789 ACCAAGAAAGTTACCTGAAACTGAA 58.815 36.000 0.00 0.00 39.62 3.02
107 134 6.661805 ACCAAGAAAGTTACCTGAAACTGAAA 59.338 34.615 0.00 0.00 39.62 2.69
118 145 4.340950 CCTGAAACTGAAAAGCCACCTTTA 59.659 41.667 0.00 0.00 40.30 1.85
123 150 3.889538 ACTGAAAAGCCACCTTTAGGAAC 59.110 43.478 2.06 0.00 40.30 3.62
127 154 0.404426 AGCCACCTTTAGGAACCACC 59.596 55.000 2.06 0.00 38.94 4.61
129 156 1.886655 GCCACCTTTAGGAACCACCAG 60.887 57.143 2.06 0.00 42.04 4.00
131 158 2.640826 CCACCTTTAGGAACCACCAGTA 59.359 50.000 2.06 0.00 42.04 2.74
144 171 6.128090 GGAACCACCAGTAGTAAAAATGCTAC 60.128 42.308 0.00 0.00 38.20 3.58
145 172 6.123045 ACCACCAGTAGTAAAAATGCTACT 57.877 37.500 1.44 1.44 46.05 2.57
214 242 1.194781 AGACAGTGCAAGGGGATCGT 61.195 55.000 0.00 0.00 0.00 3.73
231 259 0.101399 CGTTCCATGTAGAGCGAGCT 59.899 55.000 0.00 0.00 42.32 4.09
232 260 1.333931 CGTTCCATGTAGAGCGAGCTA 59.666 52.381 0.00 0.00 42.32 3.32
233 261 2.733517 GTTCCATGTAGAGCGAGCTAC 58.266 52.381 0.00 7.84 40.85 3.58
234 262 0.945099 TCCATGTAGAGCGAGCTACG 59.055 55.000 0.00 0.00 42.84 3.51
301 330 3.482232 AACTGCGAGGCCAGCTGTT 62.482 57.895 29.18 29.18 46.72 3.16
362 391 1.654105 CCGTTTTACTACTGCGAGCTG 59.346 52.381 0.00 0.37 0.00 4.24
439 468 3.146066 AGACTGCGCATTTTTCACCTAA 58.854 40.909 12.24 0.00 0.00 2.69
485 553 0.321671 ATATCTTGCGTCCCATCGGG 59.678 55.000 0.00 0.00 46.11 5.14
525 593 1.402968 CAACCTTCATCGCCCTCAATG 59.597 52.381 0.00 0.00 0.00 2.82
569 637 1.934849 GCCAGGCCATTTTTGTTCGTC 60.935 52.381 5.01 0.00 0.00 4.20
622 690 2.378038 GTGAGTGGCATCTCTCTCTCT 58.622 52.381 14.98 0.00 35.28 3.10
624 692 2.241941 TGAGTGGCATCTCTCTCTCTCT 59.758 50.000 14.98 0.00 35.28 3.10
732 800 2.553466 CCTGTTTCCGTTATCCACCCAA 60.553 50.000 0.00 0.00 0.00 4.12
735 803 1.065647 TTCCGTTATCCACCCAACCA 58.934 50.000 0.00 0.00 0.00 3.67
736 804 1.065647 TCCGTTATCCACCCAACCAA 58.934 50.000 0.00 0.00 0.00 3.67
1201 1344 3.352338 AAGGGCTACGGCTTCGTCG 62.352 63.158 0.00 0.00 44.73 5.12
1216 1359 1.985116 GTCGGTCCCCTCTGCTTCT 60.985 63.158 0.00 0.00 0.00 2.85
1264 1407 0.526524 ATGCTAGCTTCTGACGCGTC 60.527 55.000 31.66 31.66 0.00 5.19
1363 1507 4.688419 CGCGCCAACTGCAACCTG 62.688 66.667 0.00 0.00 41.33 4.00
1527 1671 2.966309 GCGCGCTAAGCCAGTTGTT 61.966 57.895 26.67 0.00 44.76 2.83
1528 1672 1.632046 GCGCGCTAAGCCAGTTGTTA 61.632 55.000 26.67 0.00 44.76 2.41
1529 1673 0.370273 CGCGCTAAGCCAGTTGTTAG 59.630 55.000 5.56 0.00 44.76 2.34
1530 1674 1.439679 GCGCTAAGCCAGTTGTTAGT 58.560 50.000 0.00 0.00 40.81 2.24
1736 1880 4.700448 TCCCGTTCTACCCCGCCA 62.700 66.667 0.00 0.00 0.00 5.69
1800 1947 2.029828 CCTCCTCCTGCATCACGTATAC 60.030 54.545 0.00 0.00 0.00 1.47
1840 1987 0.319405 GCAATGCTTTTGGACTGCCT 59.681 50.000 0.00 0.00 34.31 4.75
2188 2337 8.981724 AAGGAAAAGAAAATTATTAACCTCGC 57.018 30.769 0.00 0.00 0.00 5.03
2189 2338 7.544622 AGGAAAAGAAAATTATTAACCTCGCC 58.455 34.615 0.00 0.00 0.00 5.54
2208 2357 2.779506 CCTTAATTACCCGATCTGCCC 58.220 52.381 0.00 0.00 0.00 5.36
2209 2358 2.413837 CTTAATTACCCGATCTGCCCG 58.586 52.381 0.00 0.00 0.00 6.13
2231 2385 3.795488 GCCTTGTCCTGTTTTTACAGCAC 60.795 47.826 0.00 0.00 36.46 4.40
2299 4903 4.201950 ACTGATTTGTCTGCTTTGTGTGTC 60.202 41.667 0.00 0.00 0.00 3.67
2365 4976 3.934579 CGCGGTAAGTTACCTACCAAAAT 59.065 43.478 25.91 0.00 46.81 1.82
2366 4977 4.201744 CGCGGTAAGTTACCTACCAAAATG 60.202 45.833 25.91 10.93 46.81 2.32
2367 4978 4.696877 GCGGTAAGTTACCTACCAAAATGT 59.303 41.667 25.91 0.00 46.81 2.71
2369 4980 6.371271 GCGGTAAGTTACCTACCAAAATGTTA 59.629 38.462 25.91 0.00 46.81 2.41
2370 4981 7.624134 GCGGTAAGTTACCTACCAAAATGTTAC 60.624 40.741 25.91 0.00 46.81 2.50
2371 4982 7.603784 CGGTAAGTTACCTACCAAAATGTTACT 59.396 37.037 25.91 0.00 46.81 2.24
2372 4983 8.939929 GGTAAGTTACCTACCAAAATGTTACTC 58.060 37.037 22.62 0.00 45.52 2.59
2373 4984 7.991084 AAGTTACCTACCAAAATGTTACTCC 57.009 36.000 0.00 0.00 0.00 3.85
2418 5035 4.856664 TGGTAGATCGAGAATTAACGAGC 58.143 43.478 12.04 12.04 43.61 5.03
2422 5039 2.184385 TCGAGAATTAACGAGCGTCC 57.816 50.000 0.00 0.00 34.49 4.79
2423 5040 1.469703 TCGAGAATTAACGAGCGTCCA 59.530 47.619 0.00 0.00 34.49 4.02
2435 5052 0.607489 AGCGTCCATTTGCTGCTTCT 60.607 50.000 0.00 0.00 40.62 2.85
2597 5217 3.435601 CCGTGTACCCCTACTACCACTAT 60.436 52.174 0.00 0.00 0.00 2.12
2600 5220 5.392125 GTGTACCCCTACTACCACTATCAT 58.608 45.833 0.00 0.00 0.00 2.45
2601 5221 5.476254 GTGTACCCCTACTACCACTATCATC 59.524 48.000 0.00 0.00 0.00 2.92
2602 5222 4.827036 ACCCCTACTACCACTATCATCA 57.173 45.455 0.00 0.00 0.00 3.07
2603 5223 4.481072 ACCCCTACTACCACTATCATCAC 58.519 47.826 0.00 0.00 0.00 3.06
2604 5224 4.170251 ACCCCTACTACCACTATCATCACT 59.830 45.833 0.00 0.00 0.00 3.41
2605 5225 5.374753 ACCCCTACTACCACTATCATCACTA 59.625 44.000 0.00 0.00 0.00 2.74
2606 5226 5.711036 CCCCTACTACCACTATCATCACTAC 59.289 48.000 0.00 0.00 0.00 2.73
2607 5227 5.711036 CCCTACTACCACTATCATCACTACC 59.289 48.000 0.00 0.00 0.00 3.18
2696 5316 2.592861 GTGCCCGCCATCATCTCC 60.593 66.667 0.00 0.00 0.00 3.71
2705 5374 0.466922 CCATCATCTCCAAGCCCACC 60.467 60.000 0.00 0.00 0.00 4.61
2737 5406 2.296190 CTCCCAAAGGTAACCAACTTGC 59.704 50.000 0.00 0.00 37.17 4.01
2740 5409 3.222603 CCAAAGGTAACCAACTTGCTCT 58.777 45.455 0.00 0.00 37.17 4.09
2741 5410 4.394729 CCAAAGGTAACCAACTTGCTCTA 58.605 43.478 0.00 0.00 37.17 2.43
2742 5411 4.215613 CCAAAGGTAACCAACTTGCTCTAC 59.784 45.833 0.00 0.00 37.17 2.59
2743 5412 4.699925 AAGGTAACCAACTTGCTCTACA 57.300 40.909 0.00 0.00 37.17 2.74
2744 5413 4.699925 AGGTAACCAACTTGCTCTACAA 57.300 40.909 0.00 0.00 34.69 2.41
2745 5414 4.386711 AGGTAACCAACTTGCTCTACAAC 58.613 43.478 0.00 0.00 32.63 3.32
2746 5415 4.102681 AGGTAACCAACTTGCTCTACAACT 59.897 41.667 0.00 0.00 32.63 3.16
2747 5416 4.213482 GGTAACCAACTTGCTCTACAACTG 59.787 45.833 0.00 0.00 33.68 3.16
2748 5417 3.560636 ACCAACTTGCTCTACAACTGT 57.439 42.857 0.00 0.00 33.68 3.55
2749 5418 3.886123 ACCAACTTGCTCTACAACTGTT 58.114 40.909 0.00 0.00 33.68 3.16
2750 5419 5.031066 ACCAACTTGCTCTACAACTGTTA 57.969 39.130 0.00 0.00 33.68 2.41
2754 5423 4.884247 ACTTGCTCTACAACTGTTACTCC 58.116 43.478 0.00 0.00 33.68 3.85
2755 5424 4.589374 ACTTGCTCTACAACTGTTACTCCT 59.411 41.667 0.00 0.00 33.68 3.69
2766 5435 6.663953 ACAACTGTTACTCCTAGCTAGATTGA 59.336 38.462 22.70 9.92 0.00 2.57
2818 5557 2.993899 AGATGAACGAAAACCAGTAGCG 59.006 45.455 0.00 0.00 0.00 4.26
2822 5561 3.256558 GAACGAAAACCAGTAGCGGTAT 58.743 45.455 0.00 0.00 38.76 2.73
2827 5566 3.899052 AAACCAGTAGCGGTATTGCTA 57.101 42.857 11.27 0.00 45.14 3.49
2840 5579 5.197549 CGGTATTGCTAAAACATCATGTCG 58.802 41.667 0.00 0.00 0.00 4.35
2841 5580 4.970003 GGTATTGCTAAAACATCATGTCGC 59.030 41.667 0.00 0.00 0.00 5.19
2842 5581 4.700268 ATTGCTAAAACATCATGTCGCA 57.300 36.364 0.00 0.00 0.00 5.10
2843 5582 3.745332 TGCTAAAACATCATGTCGCAG 57.255 42.857 0.00 0.00 0.00 5.18
2872 5611 1.244697 ACCACCAACGTGCAACACAA 61.245 50.000 0.00 0.00 38.79 3.33
2874 5613 0.109551 CACCAACGTGCAACACAACA 60.110 50.000 0.00 0.00 35.74 3.33
2875 5614 0.170116 ACCAACGTGCAACACAACAG 59.830 50.000 0.00 0.00 35.74 3.16
2876 5615 1.139226 CCAACGTGCAACACAACAGC 61.139 55.000 0.00 0.00 35.74 4.40
2877 5616 0.179166 CAACGTGCAACACAACAGCT 60.179 50.000 0.00 0.00 35.74 4.24
2879 5618 0.525761 ACGTGCAACACAACAGCTTT 59.474 45.000 0.00 0.00 35.74 3.51
2880 5619 0.915904 CGTGCAACACAACAGCTTTG 59.084 50.000 0.00 6.98 35.74 2.77
2881 5620 1.732077 CGTGCAACACAACAGCTTTGT 60.732 47.619 8.03 8.03 35.74 2.83
2884 5623 3.730715 GTGCAACACAACAGCTTTGTATC 59.269 43.478 12.06 5.18 36.32 2.24
2938 5688 2.543430 GCTGGCGAGATCTGATCTTTTC 59.457 50.000 20.40 12.94 40.38 2.29
2947 5698 4.936411 AGATCTGATCTTTTCTGCACTGTG 59.064 41.667 14.31 2.76 35.76 3.66
3015 5766 1.278238 GTGACGGTGCGAGGAATTAG 58.722 55.000 0.00 0.00 0.00 1.73
3026 5777 2.224161 CGAGGAATTAGAAGGAGGCCAG 60.224 54.545 5.01 0.00 0.00 4.85
3041 5797 3.842923 CAGAGGTGCTCGCCCGAT 61.843 66.667 0.00 0.00 35.36 4.18
3042 5798 3.532155 AGAGGTGCTCGCCCGATC 61.532 66.667 0.00 0.00 35.36 3.69
3043 5799 4.933064 GAGGTGCTCGCCCGATCG 62.933 72.222 8.51 8.51 0.00 3.69
3295 6062 7.497909 TGAACCTGAATAAAATCCTCGTAATCC 59.502 37.037 0.00 0.00 0.00 3.01
3319 6086 1.925847 GTCATTCTCTTGAGCTCGCAG 59.074 52.381 9.64 7.82 0.00 5.18
3355 6122 2.213499 CTCGCTGAGTTGGTGAACTTT 58.787 47.619 0.00 0.00 42.80 2.66
3356 6123 3.390135 CTCGCTGAGTTGGTGAACTTTA 58.610 45.455 0.00 0.00 42.80 1.85
3357 6124 3.390135 TCGCTGAGTTGGTGAACTTTAG 58.610 45.455 0.00 0.00 42.80 1.85
3358 6125 2.096218 CGCTGAGTTGGTGAACTTTAGC 60.096 50.000 0.00 0.00 42.80 3.09
3359 6126 2.878406 GCTGAGTTGGTGAACTTTAGCA 59.122 45.455 14.88 0.00 44.27 3.49
3360 6127 3.503748 GCTGAGTTGGTGAACTTTAGCAT 59.496 43.478 14.88 0.00 44.27 3.79
3361 6128 4.378874 GCTGAGTTGGTGAACTTTAGCATC 60.379 45.833 14.88 0.00 44.27 3.91
3362 6129 4.713553 TGAGTTGGTGAACTTTAGCATCA 58.286 39.130 0.00 0.00 42.80 3.07
3363 6130 4.515191 TGAGTTGGTGAACTTTAGCATCAC 59.485 41.667 7.41 7.41 42.80 3.06
3364 6131 4.460263 AGTTGGTGAACTTTAGCATCACA 58.540 39.130 14.43 3.27 44.05 3.58
3365 6132 4.275936 AGTTGGTGAACTTTAGCATCACAC 59.724 41.667 14.43 0.00 44.05 3.82
3366 6133 4.085357 TGGTGAACTTTAGCATCACACT 57.915 40.909 14.43 0.00 44.05 3.55
3367 6134 3.814842 TGGTGAACTTTAGCATCACACTG 59.185 43.478 14.43 0.00 44.05 3.66
3368 6135 3.815401 GGTGAACTTTAGCATCACACTGT 59.185 43.478 14.43 0.00 44.05 3.55
3369 6136 4.275936 GGTGAACTTTAGCATCACACTGTT 59.724 41.667 14.43 0.00 44.05 3.16
3370 6137 5.468746 GGTGAACTTTAGCATCACACTGTTA 59.531 40.000 14.43 0.00 44.05 2.41
3371 6138 6.017440 GGTGAACTTTAGCATCACACTGTTAA 60.017 38.462 14.43 0.00 44.05 2.01
3372 6139 7.414436 GTGAACTTTAGCATCACACTGTTAAA 58.586 34.615 9.93 0.00 42.31 1.52
3373 6140 7.376072 GTGAACTTTAGCATCACACTGTTAAAC 59.624 37.037 9.93 0.00 42.31 2.01
3374 6141 7.282224 TGAACTTTAGCATCACACTGTTAAACT 59.718 33.333 0.00 0.00 31.32 2.66
3375 6142 6.959361 ACTTTAGCATCACACTGTTAAACTG 58.041 36.000 0.00 0.00 31.32 3.16
3376 6143 3.904136 AGCATCACACTGTTAAACTGC 57.096 42.857 0.00 0.00 0.00 4.40
3377 6144 2.554032 AGCATCACACTGTTAAACTGCC 59.446 45.455 0.00 0.00 0.00 4.85
3378 6145 2.554032 GCATCACACTGTTAAACTGCCT 59.446 45.455 0.00 0.00 0.00 4.75
3379 6146 3.610114 GCATCACACTGTTAAACTGCCTG 60.610 47.826 0.00 0.00 0.00 4.85
3380 6147 3.275617 TCACACTGTTAAACTGCCTGT 57.724 42.857 0.00 0.00 0.00 4.00
3381 6148 4.409718 TCACACTGTTAAACTGCCTGTA 57.590 40.909 0.00 0.00 0.00 2.74
3382 6149 4.968259 TCACACTGTTAAACTGCCTGTAT 58.032 39.130 0.00 0.00 0.00 2.29
3383 6150 4.754618 TCACACTGTTAAACTGCCTGTATG 59.245 41.667 0.00 0.00 0.00 2.39
3384 6151 3.502211 ACACTGTTAAACTGCCTGTATGC 59.498 43.478 0.00 0.00 0.00 3.14
3385 6152 3.753272 CACTGTTAAACTGCCTGTATGCT 59.247 43.478 0.00 0.00 0.00 3.79
3386 6153 3.753272 ACTGTTAAACTGCCTGTATGCTG 59.247 43.478 0.00 0.00 36.39 4.41
3387 6154 2.487762 TGTTAAACTGCCTGTATGCTGC 59.512 45.455 0.00 0.00 33.92 5.25
3388 6155 2.749621 GTTAAACTGCCTGTATGCTGCT 59.250 45.455 0.00 0.00 33.92 4.24
3389 6156 1.171308 AAACTGCCTGTATGCTGCTG 58.829 50.000 0.00 0.00 33.92 4.41
3390 6157 0.037303 AACTGCCTGTATGCTGCTGT 59.963 50.000 0.00 3.58 38.57 4.40
3391 6158 0.037303 ACTGCCTGTATGCTGCTGTT 59.963 50.000 0.00 0.00 34.10 3.16
3392 6159 0.731417 CTGCCTGTATGCTGCTGTTC 59.269 55.000 0.00 0.00 0.00 3.18
3393 6160 0.036590 TGCCTGTATGCTGCTGTTCA 59.963 50.000 0.00 0.00 0.00 3.18
3394 6161 1.167851 GCCTGTATGCTGCTGTTCAA 58.832 50.000 0.00 0.00 0.00 2.69
3395 6162 1.131883 GCCTGTATGCTGCTGTTCAAG 59.868 52.381 0.00 0.00 0.00 3.02
3410 6177 2.945668 GTTCAAGCTGTGTCTCCACTTT 59.054 45.455 0.00 0.00 42.34 2.66
3430 6197 7.362056 CCACTTTGAAAACAGAACTTTGAGAGA 60.362 37.037 0.00 0.00 0.00 3.10
3431 6198 7.695618 CACTTTGAAAACAGAACTTTGAGAGAG 59.304 37.037 0.00 0.00 0.00 3.20
3432 6199 7.607991 ACTTTGAAAACAGAACTTTGAGAGAGA 59.392 33.333 0.00 0.00 0.00 3.10
3433 6200 8.511604 TTTGAAAACAGAACTTTGAGAGAGAT 57.488 30.769 0.00 0.00 0.00 2.75
3434 6201 7.721286 TGAAAACAGAACTTTGAGAGAGATC 57.279 36.000 0.00 0.00 0.00 2.75
3435 6202 6.708054 TGAAAACAGAACTTTGAGAGAGATCC 59.292 38.462 0.00 0.00 0.00 3.36
3436 6203 6.432403 AAACAGAACTTTGAGAGAGATCCT 57.568 37.500 0.00 0.00 0.00 3.24
3437 6204 5.659440 ACAGAACTTTGAGAGAGATCCTC 57.341 43.478 3.70 3.70 42.28 3.71
3447 6214 3.593442 GAGAGATCCTCTGAGGGAGAA 57.407 52.381 23.00 4.53 41.35 2.87
3448 6215 3.909732 GAGAGATCCTCTGAGGGAGAAA 58.090 50.000 23.00 4.14 41.35 2.52
3449 6216 4.285863 GAGAGATCCTCTGAGGGAGAAAA 58.714 47.826 23.00 3.37 41.35 2.29
3450 6217 4.693420 AGAGATCCTCTGAGGGAGAAAAA 58.307 43.478 23.00 2.61 44.45 1.94
3469 6236 3.605946 ACCTGCTGGTGACCAAAAA 57.394 47.368 15.36 0.00 46.51 1.94
3503 6270 2.355197 TGTCGGTAATGCAAGACCATG 58.645 47.619 17.82 5.40 35.26 3.66
3508 6275 5.065988 GTCGGTAATGCAAGACCATGTTAAT 59.934 40.000 17.82 0.00 35.26 1.40
3523 6290 5.294306 CCATGTTAATGTGAGCGTCATTACT 59.706 40.000 9.52 0.00 37.45 2.24
3527 6294 0.391130 TGTGAGCGTCATTACTGGCC 60.391 55.000 0.00 0.00 0.00 5.36
3583 6386 1.821216 TCACAAAGAAATCGGCTCCC 58.179 50.000 0.00 0.00 0.00 4.30
3597 6400 1.376037 CTCCCAAACCGGCTCTCAC 60.376 63.158 0.00 0.00 0.00 3.51
3635 6438 1.078709 TTTGGAGCGAGAGAAATGCG 58.921 50.000 0.00 0.00 0.00 4.73
3643 6446 1.346365 GAGAGAAATGCGCACGTGTA 58.654 50.000 14.90 4.54 0.00 2.90
3681 6484 2.106166 TCGGTAGGGGTTTTTGTTGCTA 59.894 45.455 0.00 0.00 0.00 3.49
3682 6485 2.227149 CGGTAGGGGTTTTTGTTGCTAC 59.773 50.000 0.00 0.00 0.00 3.58
3693 6496 7.307337 GGGTTTTTGTTGCTACAATCAAAGATG 60.307 37.037 14.40 0.00 43.43 2.90
3701 6504 7.558161 TGCTACAATCAAAGATGTATCCAAG 57.442 36.000 0.00 0.00 32.02 3.61
3730 6536 3.708403 TGCTGGGGCAAGATATATGAG 57.292 47.619 0.00 0.00 46.36 2.90
3739 6545 7.457852 TGGGGCAAGATATATGAGTAATGTAGT 59.542 37.037 0.00 0.00 0.00 2.73
3741 6547 8.314751 GGGCAAGATATATGAGTAATGTAGTGT 58.685 37.037 0.00 0.00 0.00 3.55
3750 6556 3.008330 AGTAATGTAGTGTCGCGAGAGT 58.992 45.455 18.29 18.29 43.49 3.24
3804 6610 6.455690 AAACCTCTGACCCTTCTTCTTAAT 57.544 37.500 0.00 0.00 0.00 1.40
3806 6612 4.160626 ACCTCTGACCCTTCTTCTTAATCG 59.839 45.833 0.00 0.00 0.00 3.34
3820 6626 6.429692 TCTTCTTAATCGATGAAAGTGGCAAA 59.570 34.615 16.28 6.31 0.00 3.68
3838 6644 5.038247 GCAAATCTTTTGCCCAATTTCAG 57.962 39.130 12.74 0.00 39.38 3.02
3842 6648 7.357303 CAAATCTTTTGCCCAATTTCAGAAAG 58.643 34.615 1.28 0.00 0.00 2.62
3844 6650 6.232581 TCTTTTGCCCAATTTCAGAAAGAA 57.767 33.333 1.28 0.00 31.10 2.52
3873 6679 2.486966 GAGCGACATTTGCTGGCC 59.513 61.111 0.00 0.00 44.18 5.36
3874 6680 2.282391 AGCGACATTTGCTGGCCA 60.282 55.556 4.71 4.71 42.14 5.36
3909 6715 2.614057 GGAGGTTTCAATGGTGCTATCG 59.386 50.000 0.00 0.00 0.00 2.92
3910 6716 2.017049 AGGTTTCAATGGTGCTATCGC 58.983 47.619 0.00 0.00 0.00 4.58
3911 6717 2.017049 GGTTTCAATGGTGCTATCGCT 58.983 47.619 0.00 0.00 36.97 4.93
3912 6718 2.423538 GGTTTCAATGGTGCTATCGCTT 59.576 45.455 0.00 0.00 36.97 4.68
3913 6719 3.487544 GGTTTCAATGGTGCTATCGCTTC 60.488 47.826 0.00 0.00 36.97 3.86
3914 6720 2.689553 TCAATGGTGCTATCGCTTCA 57.310 45.000 0.00 0.00 36.97 3.02
3915 6721 2.984562 TCAATGGTGCTATCGCTTCAA 58.015 42.857 0.00 0.00 36.97 2.69
3916 6722 3.342719 TCAATGGTGCTATCGCTTCAAA 58.657 40.909 0.00 0.00 36.97 2.69
3917 6723 3.755905 TCAATGGTGCTATCGCTTCAAAA 59.244 39.130 0.00 0.00 36.97 2.44
3918 6724 4.217334 TCAATGGTGCTATCGCTTCAAAAA 59.783 37.500 0.00 0.00 36.97 1.94
3919 6725 4.989279 ATGGTGCTATCGCTTCAAAAAT 57.011 36.364 0.00 0.00 36.97 1.82
3920 6726 6.094742 TCAATGGTGCTATCGCTTCAAAAATA 59.905 34.615 0.00 0.00 36.97 1.40
3921 6727 5.484173 TGGTGCTATCGCTTCAAAAATAG 57.516 39.130 0.00 0.00 36.97 1.73
3922 6728 4.941263 TGGTGCTATCGCTTCAAAAATAGT 59.059 37.500 0.00 0.00 36.97 2.12
3923 6729 5.064707 TGGTGCTATCGCTTCAAAAATAGTC 59.935 40.000 0.00 0.00 36.97 2.59
3924 6730 5.502606 GTGCTATCGCTTCAAAAATAGTCC 58.497 41.667 0.00 0.00 36.97 3.85
3925 6731 5.064707 GTGCTATCGCTTCAAAAATAGTCCA 59.935 40.000 0.00 0.00 36.97 4.02
3926 6732 5.294306 TGCTATCGCTTCAAAAATAGTCCAG 59.706 40.000 0.00 0.00 36.97 3.86
3927 6733 5.523916 GCTATCGCTTCAAAAATAGTCCAGA 59.476 40.000 0.00 0.00 0.00 3.86
3928 6734 5.803020 ATCGCTTCAAAAATAGTCCAGAC 57.197 39.130 0.00 0.00 0.00 3.51
3929 6735 4.000988 TCGCTTCAAAAATAGTCCAGACC 58.999 43.478 0.00 0.00 0.00 3.85
3930 6736 3.181520 CGCTTCAAAAATAGTCCAGACCG 60.182 47.826 0.00 0.00 0.00 4.79
3931 6737 3.751698 GCTTCAAAAATAGTCCAGACCGT 59.248 43.478 0.00 0.00 0.00 4.83
3932 6738 4.378459 GCTTCAAAAATAGTCCAGACCGTG 60.378 45.833 0.00 0.00 0.00 4.94
3933 6739 4.345859 TCAAAAATAGTCCAGACCGTGT 57.654 40.909 0.00 0.00 0.00 4.49
3934 6740 4.312443 TCAAAAATAGTCCAGACCGTGTC 58.688 43.478 0.00 0.00 0.00 3.67
3935 6741 2.649331 AAATAGTCCAGACCGTGTCG 57.351 50.000 0.00 0.00 37.67 4.35
3936 6742 1.542492 AATAGTCCAGACCGTGTCGT 58.458 50.000 0.00 0.00 37.67 4.34
3937 6743 0.809385 ATAGTCCAGACCGTGTCGTG 59.191 55.000 0.00 0.00 37.67 4.35
3938 6744 0.535780 TAGTCCAGACCGTGTCGTGT 60.536 55.000 0.00 0.00 37.67 4.49
3939 6745 1.660575 GTCCAGACCGTGTCGTGTG 60.661 63.158 0.00 0.00 37.67 3.82
3940 6746 2.122797 TCCAGACCGTGTCGTGTGT 61.123 57.895 0.00 0.00 37.67 3.72
3941 6747 1.949133 CCAGACCGTGTCGTGTGTG 60.949 63.158 0.00 0.00 37.67 3.82
3942 6748 1.226859 CAGACCGTGTCGTGTGTGT 60.227 57.895 0.00 0.00 37.67 3.72
3943 6749 0.029700 CAGACCGTGTCGTGTGTGTA 59.970 55.000 0.00 0.00 37.67 2.90
3944 6750 0.309922 AGACCGTGTCGTGTGTGTAG 59.690 55.000 0.00 0.00 37.67 2.74
3945 6751 1.273455 GACCGTGTCGTGTGTGTAGC 61.273 60.000 0.00 0.00 0.00 3.58
3946 6752 1.299544 CCGTGTCGTGTGTGTAGCA 60.300 57.895 0.00 0.00 0.00 3.49
3947 6753 1.275471 CCGTGTCGTGTGTGTAGCAG 61.275 60.000 0.00 0.00 0.00 4.24
3948 6754 1.853319 GTGTCGTGTGTGTAGCAGC 59.147 57.895 0.00 0.00 0.00 5.25
3949 6755 1.660264 TGTCGTGTGTGTAGCAGCG 60.660 57.895 0.00 0.00 0.00 5.18
3950 6756 1.660575 GTCGTGTGTGTAGCAGCGT 60.661 57.895 0.00 0.00 0.00 5.07
3951 6757 1.066752 TCGTGTGTGTAGCAGCGTT 59.933 52.632 0.00 0.00 0.00 4.84
3952 6758 0.937699 TCGTGTGTGTAGCAGCGTTC 60.938 55.000 0.00 0.00 0.00 3.95
3953 6759 1.212455 CGTGTGTGTAGCAGCGTTCA 61.212 55.000 0.00 0.00 0.00 3.18
3954 6760 0.934496 GTGTGTGTAGCAGCGTTCAA 59.066 50.000 0.00 0.00 0.00 2.69
3955 6761 1.531149 GTGTGTGTAGCAGCGTTCAAT 59.469 47.619 0.00 0.00 0.00 2.57
3956 6762 1.798223 TGTGTGTAGCAGCGTTCAATC 59.202 47.619 0.00 0.00 0.00 2.67
3957 6763 1.798223 GTGTGTAGCAGCGTTCAATCA 59.202 47.619 0.00 0.00 0.00 2.57
3958 6764 2.068519 TGTGTAGCAGCGTTCAATCAG 58.931 47.619 0.00 0.00 0.00 2.90
3959 6765 2.288763 TGTGTAGCAGCGTTCAATCAGA 60.289 45.455 0.00 0.00 0.00 3.27
3960 6766 2.932614 GTGTAGCAGCGTTCAATCAGAT 59.067 45.455 0.00 0.00 0.00 2.90
3961 6767 3.000724 GTGTAGCAGCGTTCAATCAGATC 59.999 47.826 0.00 0.00 0.00 2.75
3962 6768 2.391616 AGCAGCGTTCAATCAGATCA 57.608 45.000 0.00 0.00 0.00 2.92
3963 6769 2.703416 AGCAGCGTTCAATCAGATCAA 58.297 42.857 0.00 0.00 0.00 2.57
3964 6770 2.417933 AGCAGCGTTCAATCAGATCAAC 59.582 45.455 0.00 0.00 0.00 3.18
3965 6771 2.417933 GCAGCGTTCAATCAGATCAACT 59.582 45.455 0.00 0.00 0.00 3.16
3966 6772 3.484886 GCAGCGTTCAATCAGATCAACTC 60.485 47.826 0.00 0.00 0.00 3.01
3967 6773 3.931468 CAGCGTTCAATCAGATCAACTCT 59.069 43.478 0.00 0.00 33.14 3.24
3968 6774 5.105063 CAGCGTTCAATCAGATCAACTCTA 58.895 41.667 0.00 0.00 31.13 2.43
3969 6775 5.005203 CAGCGTTCAATCAGATCAACTCTAC 59.995 44.000 0.00 0.00 31.13 2.59
3970 6776 4.268884 GCGTTCAATCAGATCAACTCTACC 59.731 45.833 0.00 0.00 31.13 3.18
3971 6777 4.500837 CGTTCAATCAGATCAACTCTACCG 59.499 45.833 0.00 0.00 31.13 4.02
3972 6778 5.411781 GTTCAATCAGATCAACTCTACCGT 58.588 41.667 0.00 0.00 31.13 4.83
3973 6779 5.661056 TCAATCAGATCAACTCTACCGTT 57.339 39.130 0.00 0.00 31.13 4.44
3974 6780 5.410924 TCAATCAGATCAACTCTACCGTTG 58.589 41.667 0.00 0.00 44.26 4.10
3975 6781 5.047306 TCAATCAGATCAACTCTACCGTTGT 60.047 40.000 0.00 0.00 43.55 3.32
3976 6782 4.436242 TCAGATCAACTCTACCGTTGTC 57.564 45.455 0.00 2.26 43.55 3.18
3977 6783 3.824443 TCAGATCAACTCTACCGTTGTCA 59.176 43.478 0.00 0.00 43.55 3.58
3978 6784 4.279922 TCAGATCAACTCTACCGTTGTCAA 59.720 41.667 0.00 0.00 43.55 3.18
3979 6785 4.988540 CAGATCAACTCTACCGTTGTCAAA 59.011 41.667 0.00 0.00 43.55 2.69
3980 6786 5.639506 CAGATCAACTCTACCGTTGTCAAAT 59.360 40.000 0.00 0.00 43.55 2.32
3981 6787 6.811665 CAGATCAACTCTACCGTTGTCAAATA 59.188 38.462 0.00 0.00 43.55 1.40
3982 6788 7.330946 CAGATCAACTCTACCGTTGTCAAATAA 59.669 37.037 0.00 0.00 43.55 1.40
3983 6789 7.545965 AGATCAACTCTACCGTTGTCAAATAAG 59.454 37.037 0.00 0.00 43.55 1.73
3984 6790 6.751157 TCAACTCTACCGTTGTCAAATAAGA 58.249 36.000 3.92 0.00 43.55 2.10
3985 6791 7.211573 TCAACTCTACCGTTGTCAAATAAGAA 58.788 34.615 3.92 0.00 43.55 2.52
3986 6792 7.876068 TCAACTCTACCGTTGTCAAATAAGAAT 59.124 33.333 3.92 0.00 43.55 2.40
3987 6793 9.146984 CAACTCTACCGTTGTCAAATAAGAATA 57.853 33.333 0.00 0.00 39.45 1.75
3988 6794 8.699283 ACTCTACCGTTGTCAAATAAGAATAC 57.301 34.615 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 129 3.255888 GGTTCCTAAAGGTGGCTTTTCAG 59.744 47.826 0.00 0.00 36.34 3.02
103 130 3.227614 GGTTCCTAAAGGTGGCTTTTCA 58.772 45.455 0.00 0.00 36.34 2.69
104 131 3.005472 GTGGTTCCTAAAGGTGGCTTTTC 59.995 47.826 0.00 0.00 36.34 2.29
105 132 2.963101 GTGGTTCCTAAAGGTGGCTTTT 59.037 45.455 0.00 0.00 36.34 2.27
106 133 2.594131 GTGGTTCCTAAAGGTGGCTTT 58.406 47.619 0.00 0.00 36.34 3.51
107 134 1.203013 GGTGGTTCCTAAAGGTGGCTT 60.203 52.381 0.00 0.00 36.34 4.35
118 145 4.765339 GCATTTTTACTACTGGTGGTTCCT 59.235 41.667 0.00 0.00 37.07 3.36
129 156 7.168804 GGATCGGTACAGTAGCATTTTTACTAC 59.831 40.741 10.37 0.00 39.25 2.73
131 158 6.047231 GGATCGGTACAGTAGCATTTTTACT 58.953 40.000 10.37 0.00 0.00 2.24
144 171 8.657074 TTAATTAACATTCAGGATCGGTACAG 57.343 34.615 0.00 0.00 0.00 2.74
145 172 9.268268 GATTAATTAACATTCAGGATCGGTACA 57.732 33.333 0.00 0.00 0.00 2.90
146 173 9.490379 AGATTAATTAACATTCAGGATCGGTAC 57.510 33.333 0.00 0.00 0.00 3.34
147 174 9.706691 GAGATTAATTAACATTCAGGATCGGTA 57.293 33.333 0.00 0.00 0.00 4.02
148 175 7.661847 GGAGATTAATTAACATTCAGGATCGGT 59.338 37.037 0.00 0.00 0.00 4.69
149 176 7.880195 AGGAGATTAATTAACATTCAGGATCGG 59.120 37.037 0.00 0.00 0.00 4.18
207 235 1.603172 CGCTCTACATGGAACGATCCC 60.603 57.143 9.50 0.00 45.95 3.85
214 242 1.333931 CGTAGCTCGCTCTACATGGAA 59.666 52.381 12.27 0.00 39.01 3.53
231 259 2.449464 TCTTGGCCAACTAGCTACGTA 58.551 47.619 16.05 0.00 0.00 3.57
232 260 1.263356 TCTTGGCCAACTAGCTACGT 58.737 50.000 16.05 0.00 0.00 3.57
233 261 2.380084 TTCTTGGCCAACTAGCTACG 57.620 50.000 16.05 1.92 0.00 3.51
234 262 3.440522 CCTTTTCTTGGCCAACTAGCTAC 59.559 47.826 16.05 0.00 0.00 3.58
301 330 0.193574 ACTGGGAGGAGAAGGTGGAA 59.806 55.000 0.00 0.00 0.00 3.53
439 468 4.584325 CCATTATGTGGGAATGAACCGATT 59.416 41.667 0.00 0.00 44.79 3.34
485 553 2.561419 TGTAGACACTGACAGGTAAGGC 59.439 50.000 7.51 0.00 0.00 4.35
525 593 2.415512 GCTGTGTAGATCCGGTGTTTTC 59.584 50.000 0.00 0.00 0.00 2.29
569 637 1.300931 CGGTGTCCTGTCCAGTGTG 60.301 63.158 0.00 0.00 0.00 3.82
651 719 2.107953 CTAGCCTGGCGCCTCTTC 59.892 66.667 29.70 13.89 38.78 2.87
652 720 2.364317 TCTAGCCTGGCGCCTCTT 60.364 61.111 29.70 13.03 38.78 2.85
696 764 2.713863 ACAGGAGCGCTACTACTACT 57.286 50.000 24.75 0.00 37.53 2.57
697 765 3.488890 GGAAACAGGAGCGCTACTACTAC 60.489 52.174 24.75 14.09 37.53 2.73
698 766 2.686915 GGAAACAGGAGCGCTACTACTA 59.313 50.000 24.75 0.00 37.53 1.82
965 1108 1.298859 CGCTCTGCCACCCAACTAAC 61.299 60.000 0.00 0.00 0.00 2.34
1047 1190 2.279851 TTGGTCAGCGTGGTGTCG 60.280 61.111 0.00 0.00 0.00 4.35
1216 1359 0.031917 ATGCATGGCAATGGAGGGAA 60.032 50.000 2.54 0.00 43.62 3.97
1264 1407 1.208358 CGTCACCTGTTGCATGCAG 59.792 57.895 21.50 11.84 0.00 4.41
1491 1635 1.136565 CGCGGATTTGGATTTGCGT 59.863 52.632 0.00 0.00 40.61 5.24
1527 1671 0.668096 CACGTTGGCGGCAGTAACTA 60.668 55.000 12.87 0.00 43.45 2.24
1528 1672 1.959226 CACGTTGGCGGCAGTAACT 60.959 57.895 12.87 0.00 43.45 2.24
1529 1673 2.554272 CACGTTGGCGGCAGTAAC 59.446 61.111 12.87 7.02 43.45 2.50
1530 1674 3.350612 GCACGTTGGCGGCAGTAA 61.351 61.111 12.87 0.00 43.45 2.24
1775 1919 2.202987 GATGCAGGAGGAGGTGCG 60.203 66.667 0.00 0.00 42.96 5.34
1779 1923 1.043816 ATACGTGATGCAGGAGGAGG 58.956 55.000 0.00 0.00 0.00 4.30
1780 1924 2.887783 AGTATACGTGATGCAGGAGGAG 59.112 50.000 0.00 0.00 0.00 3.69
1781 1925 2.885266 GAGTATACGTGATGCAGGAGGA 59.115 50.000 0.00 0.00 0.00 3.71
1800 1947 0.099791 GTCGCGAGGAGGAAGAAGAG 59.900 60.000 10.24 0.00 0.00 2.85
2165 2314 7.544622 AGGCGAGGTTAATAATTTTCTTTTCC 58.455 34.615 0.00 0.00 0.00 3.13
2176 2325 5.990996 CGGGTAATTAAGGCGAGGTTAATAA 59.009 40.000 0.00 0.00 31.27 1.40
2177 2326 5.304101 TCGGGTAATTAAGGCGAGGTTAATA 59.696 40.000 0.00 0.00 31.27 0.98
2179 2328 3.450457 TCGGGTAATTAAGGCGAGGTTAA 59.550 43.478 0.00 0.00 0.00 2.01
2180 2329 3.030291 TCGGGTAATTAAGGCGAGGTTA 58.970 45.455 0.00 0.00 0.00 2.85
2181 2330 1.832998 TCGGGTAATTAAGGCGAGGTT 59.167 47.619 0.00 0.00 0.00 3.50
2182 2331 1.488390 TCGGGTAATTAAGGCGAGGT 58.512 50.000 0.00 0.00 0.00 3.85
2183 2332 2.299297 AGATCGGGTAATTAAGGCGAGG 59.701 50.000 0.00 0.00 0.00 4.63
2184 2333 3.318017 CAGATCGGGTAATTAAGGCGAG 58.682 50.000 0.00 0.00 0.00 5.03
2185 2334 2.547218 GCAGATCGGGTAATTAAGGCGA 60.547 50.000 0.00 0.00 0.00 5.54
2186 2335 1.798813 GCAGATCGGGTAATTAAGGCG 59.201 52.381 0.00 0.00 0.00 5.52
2187 2336 2.152016 GGCAGATCGGGTAATTAAGGC 58.848 52.381 0.00 0.00 0.00 4.35
2188 2337 2.779506 GGGCAGATCGGGTAATTAAGG 58.220 52.381 0.00 0.00 0.00 2.69
2189 2338 2.413837 CGGGCAGATCGGGTAATTAAG 58.586 52.381 0.00 0.00 0.00 1.85
2208 2357 2.604614 GCTGTAAAAACAGGACAAGGCG 60.605 50.000 7.57 0.00 38.14 5.52
2209 2358 2.360801 TGCTGTAAAAACAGGACAAGGC 59.639 45.455 7.57 0.00 38.14 4.35
2231 2385 7.558161 TGAGATGCAGTCAGTTTAATATTGG 57.442 36.000 0.00 0.00 0.00 3.16
2299 4903 2.025887 AGTTTGGGGAGTAGCTGAATGG 60.026 50.000 0.00 0.00 0.00 3.16
2365 4976 2.315925 GCAGCAGCATAGGAGTAACA 57.684 50.000 0.00 0.00 41.58 2.41
2418 5035 0.877071 ACAGAAGCAGCAAATGGACG 59.123 50.000 0.00 0.00 0.00 4.79
2422 5039 1.265095 ACGTCACAGAAGCAGCAAATG 59.735 47.619 0.00 0.00 0.00 2.32
2423 5040 1.265095 CACGTCACAGAAGCAGCAAAT 59.735 47.619 0.00 0.00 0.00 2.32
2435 5052 0.875908 GCTTCTGCTGTCACGTCACA 60.876 55.000 0.00 0.00 36.03 3.58
2597 5217 0.902984 AGCCGTGGTGGTAGTGATGA 60.903 55.000 0.00 0.00 41.21 2.92
2600 5220 2.632544 CGAGCCGTGGTGGTAGTGA 61.633 63.158 0.00 0.00 41.21 3.41
2601 5221 2.126071 CGAGCCGTGGTGGTAGTG 60.126 66.667 0.00 0.00 41.21 2.74
2602 5222 4.065281 GCGAGCCGTGGTGGTAGT 62.065 66.667 0.00 0.00 41.21 2.73
2603 5223 3.989698 CTGCGAGCCGTGGTGGTAG 62.990 68.421 0.00 0.00 41.21 3.18
2604 5224 4.063967 CTGCGAGCCGTGGTGGTA 62.064 66.667 0.00 0.00 41.21 3.25
2644 5264 4.083862 AGACCGGCGGGAAGAAGC 62.084 66.667 31.78 9.83 36.97 3.86
2705 5374 1.303236 TTTGGGAGGCACCATGACG 60.303 57.895 2.69 0.00 40.91 4.35
2737 5406 7.049133 TCTAGCTAGGAGTAACAGTTGTAGAG 58.951 42.308 20.58 0.00 0.00 2.43
2740 5409 7.832685 TCAATCTAGCTAGGAGTAACAGTTGTA 59.167 37.037 20.58 0.00 0.00 2.41
2741 5410 6.663953 TCAATCTAGCTAGGAGTAACAGTTGT 59.336 38.462 20.58 0.00 0.00 3.32
2742 5411 7.101652 TCAATCTAGCTAGGAGTAACAGTTG 57.898 40.000 20.58 10.99 0.00 3.16
2743 5412 7.906199 ATCAATCTAGCTAGGAGTAACAGTT 57.094 36.000 20.58 0.00 0.00 3.16
2744 5413 8.221944 AGTATCAATCTAGCTAGGAGTAACAGT 58.778 37.037 20.58 0.00 0.00 3.55
2745 5414 8.511321 CAGTATCAATCTAGCTAGGAGTAACAG 58.489 40.741 20.58 6.11 0.00 3.16
2746 5415 7.999545 ACAGTATCAATCTAGCTAGGAGTAACA 59.000 37.037 20.58 0.00 0.00 2.41
2747 5416 8.398878 ACAGTATCAATCTAGCTAGGAGTAAC 57.601 38.462 20.58 11.71 0.00 2.50
2748 5417 9.727859 CTACAGTATCAATCTAGCTAGGAGTAA 57.272 37.037 20.58 0.96 0.00 2.24
2749 5418 8.882282 ACTACAGTATCAATCTAGCTAGGAGTA 58.118 37.037 20.58 1.36 0.00 2.59
2750 5419 7.751646 ACTACAGTATCAATCTAGCTAGGAGT 58.248 38.462 20.58 4.30 0.00 3.85
2754 5423 9.899661 ATCCTACTACAGTATCAATCTAGCTAG 57.100 37.037 15.01 15.01 0.00 3.42
2798 5537 2.093783 CCGCTACTGGTTTTCGTTCATC 59.906 50.000 0.00 0.00 0.00 2.92
2800 5539 1.202557 ACCGCTACTGGTTTTCGTTCA 60.203 47.619 0.00 0.00 39.99 3.18
2818 5557 4.970003 GCGACATGATGTTTTAGCAATACC 59.030 41.667 0.00 0.00 0.00 2.73
2822 5561 3.670359 GCTGCGACATGATGTTTTAGCAA 60.670 43.478 17.80 6.31 33.17 3.91
2827 5566 1.401931 GCTGCTGCGACATGATGTTTT 60.402 47.619 0.00 0.00 0.00 2.43
2836 5575 2.029288 GTTGCTAGCTGCTGCGACA 61.029 57.895 25.84 12.91 45.42 4.35
2840 5579 2.694760 GGTGGTTGCTAGCTGCTGC 61.695 63.158 17.23 14.04 43.37 5.25
2841 5580 0.890542 TTGGTGGTTGCTAGCTGCTG 60.891 55.000 17.23 3.55 43.37 4.41
2842 5581 0.890996 GTTGGTGGTTGCTAGCTGCT 60.891 55.000 17.23 7.57 43.37 4.24
2843 5582 1.581447 GTTGGTGGTTGCTAGCTGC 59.419 57.895 17.23 8.37 43.25 5.25
2872 5611 2.561569 GCCCATACGATACAAAGCTGT 58.438 47.619 0.00 0.00 39.75 4.40
2874 5613 1.865865 CGCCCATACGATACAAAGCT 58.134 50.000 0.00 0.00 34.06 3.74
2875 5614 0.234884 GCGCCCATACGATACAAAGC 59.765 55.000 0.00 0.00 34.06 3.51
2876 5615 0.865769 GGCGCCCATACGATACAAAG 59.134 55.000 18.11 0.00 34.06 2.77
2877 5616 0.178301 TGGCGCCCATACGATACAAA 59.822 50.000 26.77 0.00 34.06 2.83
2879 5618 0.037697 GATGGCGCCCATACGATACA 60.038 55.000 26.77 0.00 45.26 2.29
2880 5619 0.246635 AGATGGCGCCCATACGATAC 59.753 55.000 26.77 4.59 45.26 2.24
2881 5620 0.973632 AAGATGGCGCCCATACGATA 59.026 50.000 26.77 1.65 45.26 2.92
2884 5623 1.808411 ATTAAGATGGCGCCCATACG 58.192 50.000 26.77 0.00 45.26 3.06
2938 5688 1.949133 ACACGTACGCACAGTGCAG 60.949 57.895 25.19 18.81 45.36 4.41
3011 5762 2.122768 CACCTCTGGCCTCCTTCTAAT 58.877 52.381 3.32 0.00 0.00 1.73
3015 5766 2.250741 GAGCACCTCTGGCCTCCTTC 62.251 65.000 3.32 0.00 0.00 3.46
3026 5777 4.933064 CGATCGGGCGAGCACCTC 62.933 72.222 7.38 0.00 0.00 3.85
3041 5797 7.013750 AGCTTGTTATAATCAGACAGATCTCGA 59.986 37.037 0.00 0.00 35.39 4.04
3042 5798 7.114670 CAGCTTGTTATAATCAGACAGATCTCG 59.885 40.741 0.00 0.00 35.39 4.04
3043 5799 7.095691 GCAGCTTGTTATAATCAGACAGATCTC 60.096 40.741 0.00 0.00 35.39 2.75
3044 5800 6.705381 GCAGCTTGTTATAATCAGACAGATCT 59.295 38.462 0.00 0.00 35.39 2.75
3045 5801 6.705381 AGCAGCTTGTTATAATCAGACAGATC 59.295 38.462 0.00 0.00 35.39 2.75
3046 5802 6.482641 CAGCAGCTTGTTATAATCAGACAGAT 59.517 38.462 0.00 0.00 39.09 2.90
3295 6062 2.794282 CGAGCTCAAGAGAATGACCGAG 60.794 54.545 15.40 0.00 0.00 4.63
3319 6086 0.941463 CGAGCTCAGACACACACCAC 60.941 60.000 15.40 0.00 0.00 4.16
3355 6122 3.751175 GGCAGTTTAACAGTGTGATGCTA 59.249 43.478 0.00 0.00 33.09 3.49
3356 6123 2.554032 GGCAGTTTAACAGTGTGATGCT 59.446 45.455 0.00 0.00 33.09 3.79
3357 6124 2.554032 AGGCAGTTTAACAGTGTGATGC 59.446 45.455 0.00 3.30 0.00 3.91
3358 6125 3.565482 ACAGGCAGTTTAACAGTGTGATG 59.435 43.478 0.00 0.00 0.00 3.07
3359 6126 3.820557 ACAGGCAGTTTAACAGTGTGAT 58.179 40.909 0.00 0.00 0.00 3.06
3360 6127 3.275617 ACAGGCAGTTTAACAGTGTGA 57.724 42.857 0.00 0.00 0.00 3.58
3361 6128 4.613622 GCATACAGGCAGTTTAACAGTGTG 60.614 45.833 0.00 0.00 0.00 3.82
3362 6129 3.502211 GCATACAGGCAGTTTAACAGTGT 59.498 43.478 0.00 0.00 0.00 3.55
3363 6130 3.753272 AGCATACAGGCAGTTTAACAGTG 59.247 43.478 0.00 0.00 35.83 3.66
3364 6131 3.753272 CAGCATACAGGCAGTTTAACAGT 59.247 43.478 0.00 0.00 35.83 3.55
3365 6132 3.426695 GCAGCATACAGGCAGTTTAACAG 60.427 47.826 0.00 0.00 35.83 3.16
3366 6133 2.487762 GCAGCATACAGGCAGTTTAACA 59.512 45.455 0.00 0.00 35.83 2.41
3367 6134 2.749621 AGCAGCATACAGGCAGTTTAAC 59.250 45.455 0.00 0.00 35.83 2.01
3368 6135 2.749076 CAGCAGCATACAGGCAGTTTAA 59.251 45.455 0.00 0.00 35.83 1.52
3369 6136 2.290260 ACAGCAGCATACAGGCAGTTTA 60.290 45.455 0.00 0.00 35.83 2.01
3370 6137 1.171308 CAGCAGCATACAGGCAGTTT 58.829 50.000 0.00 0.00 35.83 2.66
3371 6138 0.037303 ACAGCAGCATACAGGCAGTT 59.963 50.000 0.00 0.00 35.83 3.16
3372 6139 0.037303 AACAGCAGCATACAGGCAGT 59.963 50.000 0.00 0.00 35.83 4.40
3373 6140 0.731417 GAACAGCAGCATACAGGCAG 59.269 55.000 0.00 0.00 35.83 4.85
3374 6141 0.036590 TGAACAGCAGCATACAGGCA 59.963 50.000 0.00 0.00 35.83 4.75
3375 6142 1.131883 CTTGAACAGCAGCATACAGGC 59.868 52.381 0.00 0.00 0.00 4.85
3385 6152 4.385320 TGGAGACACAGCTTGAACAGCA 62.385 50.000 0.00 0.00 44.04 4.41
3386 6153 1.811558 TGGAGACACAGCTTGAACAGC 60.812 52.381 3.37 0.00 42.49 4.40
3387 6154 2.245159 TGGAGACACAGCTTGAACAG 57.755 50.000 3.37 0.00 33.40 3.16
3399 6166 5.253330 AGTTCTGTTTTCAAAGTGGAGACA 58.747 37.500 0.00 0.00 38.70 3.41
3405 6172 7.530010 TCTCTCAAAGTTCTGTTTTCAAAGTG 58.470 34.615 0.00 0.00 0.00 3.16
3410 6177 6.708054 GGATCTCTCTCAAAGTTCTGTTTTCA 59.292 38.462 0.00 0.00 0.00 2.69
3467 6234 5.514274 ACCGACAATCTGTGATTGTTTTT 57.486 34.783 21.80 10.07 41.76 1.94
3468 6235 6.627395 TTACCGACAATCTGTGATTGTTTT 57.373 33.333 21.80 13.77 41.76 2.43
3469 6236 6.611381 CATTACCGACAATCTGTGATTGTTT 58.389 36.000 21.80 14.03 41.76 2.83
3470 6237 5.391950 GCATTACCGACAATCTGTGATTGTT 60.392 40.000 21.80 12.16 41.76 2.83
3503 6270 4.494199 GCCAGTAATGACGCTCACATTAAC 60.494 45.833 0.00 0.00 40.36 2.01
3508 6275 0.391130 GGCCAGTAATGACGCTCACA 60.391 55.000 0.00 0.00 0.00 3.58
3542 6309 6.823689 GTGATACAAATCTGGTATCCTGTGTT 59.176 38.462 9.36 0.00 44.08 3.32
3544 6311 6.348498 TGTGATACAAATCTGGTATCCTGTG 58.652 40.000 9.36 0.00 44.08 3.66
3545 6312 6.560003 TGTGATACAAATCTGGTATCCTGT 57.440 37.500 9.36 0.00 44.08 4.00
3561 6364 3.312697 GGGAGCCGATTTCTTTGTGATAC 59.687 47.826 0.00 0.00 0.00 2.24
3653 6456 1.955451 AAACCCCTACCGACACCATA 58.045 50.000 0.00 0.00 0.00 2.74
3654 6457 1.069775 AAAACCCCTACCGACACCAT 58.930 50.000 0.00 0.00 0.00 3.55
3655 6458 0.845337 AAAAACCCCTACCGACACCA 59.155 50.000 0.00 0.00 0.00 4.17
3660 6463 1.133730 AGCAACAAAAACCCCTACCGA 60.134 47.619 0.00 0.00 0.00 4.69
3701 6504 2.830370 GCCCCAGCACACCATAGC 60.830 66.667 0.00 0.00 39.53 2.97
3713 6519 6.702449 ACATTACTCATATATCTTGCCCCA 57.298 37.500 0.00 0.00 0.00 4.96
3721 6527 7.461918 TCGCGACACTACATTACTCATATATC 58.538 38.462 3.71 0.00 0.00 1.63
3722 6528 7.333672 TCTCGCGACACTACATTACTCATATAT 59.666 37.037 3.71 0.00 0.00 0.86
3726 6532 3.626217 TCTCGCGACACTACATTACTCAT 59.374 43.478 3.71 0.00 0.00 2.90
3730 6536 3.402058 ACTCTCGCGACACTACATTAC 57.598 47.619 3.71 0.00 0.00 1.89
3739 6545 2.287970 ACAACACATTACTCTCGCGACA 60.288 45.455 3.71 0.00 0.00 4.35
3741 6547 2.717580 ACAACACATTACTCTCGCGA 57.282 45.000 9.26 9.26 0.00 5.87
3750 6556 6.970043 GCAAATAGCCGAATTACAACACATTA 59.030 34.615 0.00 0.00 37.23 1.90
3782 6588 5.337652 CGATTAAGAAGAAGGGTCAGAGGTT 60.338 44.000 0.00 0.00 0.00 3.50
3783 6589 4.160626 CGATTAAGAAGAAGGGTCAGAGGT 59.839 45.833 0.00 0.00 0.00 3.85
3784 6590 4.402793 TCGATTAAGAAGAAGGGTCAGAGG 59.597 45.833 0.00 0.00 0.00 3.69
3787 6593 5.907207 TCATCGATTAAGAAGAAGGGTCAG 58.093 41.667 0.00 0.00 0.00 3.51
3788 6594 5.932619 TCATCGATTAAGAAGAAGGGTCA 57.067 39.130 0.00 0.00 0.00 4.02
3789 6595 6.819146 ACTTTCATCGATTAAGAAGAAGGGTC 59.181 38.462 18.97 0.00 31.92 4.46
3804 6610 5.221880 CAAAAGATTTGCCACTTTCATCGA 58.778 37.500 0.00 0.00 35.66 3.59
3806 6612 5.273523 GCAAAAGATTTGCCACTTTCATC 57.726 39.130 15.12 0.00 39.38 2.92
3820 6626 6.423776 TCTTTCTGAAATTGGGCAAAAGAT 57.576 33.333 2.88 0.00 0.00 2.40
3850 6656 1.059692 CAGCAAATGTCGCTCGTGTAG 59.940 52.381 0.00 0.00 37.72 2.74
3853 6659 1.133253 CCAGCAAATGTCGCTCGTG 59.867 57.895 0.00 0.00 37.72 4.35
3854 6660 2.680913 GCCAGCAAATGTCGCTCGT 61.681 57.895 0.00 0.00 37.72 4.18
3855 6661 2.099062 GCCAGCAAATGTCGCTCG 59.901 61.111 0.00 0.00 37.72 5.03
3858 6664 1.006337 TTTGGCCAGCAAATGTCGC 60.006 52.632 5.11 0.00 0.00 5.19
3864 6670 0.685785 TGTGGAGTTTGGCCAGCAAA 60.686 50.000 5.11 0.00 35.77 3.68
3909 6715 3.751698 ACGGTCTGGACTATTTTTGAAGC 59.248 43.478 0.67 0.00 0.00 3.86
3910 6716 4.755123 ACACGGTCTGGACTATTTTTGAAG 59.245 41.667 0.67 0.00 0.00 3.02
3911 6717 4.710324 ACACGGTCTGGACTATTTTTGAA 58.290 39.130 0.67 0.00 0.00 2.69
3912 6718 4.312443 GACACGGTCTGGACTATTTTTGA 58.688 43.478 0.67 0.00 0.00 2.69
3913 6719 3.122948 CGACACGGTCTGGACTATTTTTG 59.877 47.826 0.67 0.00 0.00 2.44
3914 6720 3.243975 ACGACACGGTCTGGACTATTTTT 60.244 43.478 0.00 0.00 0.00 1.94
3915 6721 2.298163 ACGACACGGTCTGGACTATTTT 59.702 45.455 0.00 0.00 0.00 1.82
3916 6722 1.891150 ACGACACGGTCTGGACTATTT 59.109 47.619 0.00 0.00 0.00 1.40
3917 6723 1.201647 CACGACACGGTCTGGACTATT 59.798 52.381 0.00 0.00 0.00 1.73
3918 6724 0.809385 CACGACACGGTCTGGACTAT 59.191 55.000 0.00 0.00 0.00 2.12
3919 6725 0.535780 ACACGACACGGTCTGGACTA 60.536 55.000 0.00 0.00 0.00 2.59
3920 6726 1.826921 ACACGACACGGTCTGGACT 60.827 57.895 0.00 0.00 0.00 3.85
3921 6727 1.660575 CACACGACACGGTCTGGAC 60.661 63.158 0.00 0.00 0.00 4.02
3922 6728 2.122797 ACACACGACACGGTCTGGA 61.123 57.895 0.00 0.00 0.00 3.86
3923 6729 1.949133 CACACACGACACGGTCTGG 60.949 63.158 0.00 0.00 0.00 3.86
3924 6730 0.029700 TACACACACGACACGGTCTG 59.970 55.000 0.00 3.47 0.00 3.51
3925 6731 0.309922 CTACACACACGACACGGTCT 59.690 55.000 0.00 0.00 0.00 3.85
3926 6732 1.273455 GCTACACACACGACACGGTC 61.273 60.000 0.00 0.00 0.00 4.79
3927 6733 1.299620 GCTACACACACGACACGGT 60.300 57.895 0.00 0.00 0.00 4.83
3928 6734 1.275471 CTGCTACACACACGACACGG 61.275 60.000 0.00 0.00 0.00 4.94
3929 6735 1.876453 GCTGCTACACACACGACACG 61.876 60.000 0.00 0.00 0.00 4.49
3930 6736 1.853319 GCTGCTACACACACGACAC 59.147 57.895 0.00 0.00 0.00 3.67
3931 6737 1.660264 CGCTGCTACACACACGACA 60.660 57.895 0.00 0.00 0.00 4.35
3932 6738 1.213094 AACGCTGCTACACACACGAC 61.213 55.000 0.00 0.00 0.00 4.34
3933 6739 0.937699 GAACGCTGCTACACACACGA 60.938 55.000 0.00 0.00 0.00 4.35
3934 6740 1.212455 TGAACGCTGCTACACACACG 61.212 55.000 0.00 0.00 0.00 4.49
3935 6741 0.934496 TTGAACGCTGCTACACACAC 59.066 50.000 0.00 0.00 0.00 3.82
3936 6742 1.798223 GATTGAACGCTGCTACACACA 59.202 47.619 0.00 0.00 0.00 3.72
3937 6743 1.798223 TGATTGAACGCTGCTACACAC 59.202 47.619 0.00 0.00 0.00 3.82
3938 6744 2.068519 CTGATTGAACGCTGCTACACA 58.931 47.619 0.00 0.00 0.00 3.72
3939 6745 2.337583 TCTGATTGAACGCTGCTACAC 58.662 47.619 0.00 0.00 0.00 2.90
3940 6746 2.741759 TCTGATTGAACGCTGCTACA 57.258 45.000 0.00 0.00 0.00 2.74
3941 6747 3.190079 TGATCTGATTGAACGCTGCTAC 58.810 45.455 0.00 0.00 0.00 3.58
3942 6748 3.525268 TGATCTGATTGAACGCTGCTA 57.475 42.857 0.00 0.00 0.00 3.49
3943 6749 2.391616 TGATCTGATTGAACGCTGCT 57.608 45.000 0.00 0.00 0.00 4.24
3944 6750 2.417933 AGTTGATCTGATTGAACGCTGC 59.582 45.455 0.00 0.00 0.00 5.25
3945 6751 3.931468 AGAGTTGATCTGATTGAACGCTG 59.069 43.478 14.50 0.00 36.69 5.18
3946 6752 4.199432 AGAGTTGATCTGATTGAACGCT 57.801 40.909 11.38 11.38 36.69 5.07
3947 6753 4.268884 GGTAGAGTTGATCTGATTGAACGC 59.731 45.833 0.00 8.29 39.20 4.84
3948 6754 4.500837 CGGTAGAGTTGATCTGATTGAACG 59.499 45.833 0.00 0.00 39.20 3.95
3949 6755 5.411781 ACGGTAGAGTTGATCTGATTGAAC 58.588 41.667 0.00 0.00 39.20 3.18
3950 6756 5.661056 ACGGTAGAGTTGATCTGATTGAA 57.339 39.130 0.00 0.00 39.20 2.69
3951 6757 5.661056 AACGGTAGAGTTGATCTGATTGA 57.339 39.130 0.00 0.00 39.20 2.57
3962 6768 9.148104 GTATTCTTATTTGACAACGGTAGAGTT 57.852 33.333 0.00 0.00 34.15 3.01
3963 6769 8.699283 GTATTCTTATTTGACAACGGTAGAGT 57.301 34.615 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.