Multiple sequence alignment - TraesCS1D01G194300

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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 TraesCS1D01G194300 chr1D 100.000 6228 0 0 1 6228 270293036 270286809 0.000000e+00 11502.0
1 TraesCS1D01G194300 chr1D 91.304 92 2 3 6132 6223 458393613 458393698 3.050000e-23 121.0
2 TraesCS1D01G194300 chr1A 94.723 5533 165 46 559 6011 343686188 343680703 0.000000e+00 8482.0
3 TraesCS1D01G194300 chr1A 85.592 583 45 14 1 562 343687298 343686734 5.410000e-160 575.0
4 TraesCS1D01G194300 chr1B 94.219 4584 157 41 237 4789 344049343 344044837 0.000000e+00 6898.0
5 TraesCS1D01G194300 chr1B 96.000 1100 38 5 4791 5884 344044767 344043668 0.000000e+00 1783.0
6 TraesCS1D01G194300 chr1B 91.057 246 22 0 1 246 344050080 344049835 3.600000e-87 333.0
7 TraesCS1D01G194300 chr1B 88.538 253 19 6 5880 6129 344011642 344011397 1.310000e-76 298.0
8 TraesCS1D01G194300 chr1B 83.851 161 25 1 1 161 456192159 456192000 1.080000e-32 152.0
9 TraesCS1D01G194300 chr1B 90.426 94 5 1 6130 6223 430344332 430344421 3.050000e-23 121.0
10 TraesCS1D01G194300 chr1B 91.071 56 4 1 3152 3207 118513334 118513388 2.410000e-09 75.0
11 TraesCS1D01G194300 chr7B 80.242 248 32 10 3162 3407 44306935 44306703 2.990000e-38 171.0
12 TraesCS1D01G194300 chr7B 85.484 62 9 0 250 311 244720064 244720125 1.450000e-06 65.8
13 TraesCS1D01G194300 chr7B 100.000 28 0 0 5881 5908 748170773 748170746 1.100000e-02 52.8
14 TraesCS1D01G194300 chr7B 100.000 28 0 0 5881 5908 748175688 748175661 1.100000e-02 52.8
15 TraesCS1D01G194300 chr6B 90.909 99 8 1 6130 6228 262271719 262271622 1.410000e-26 132.0
16 TraesCS1D01G194300 chr5B 91.489 94 6 2 6132 6223 443276935 443277028 1.820000e-25 128.0
17 TraesCS1D01G194300 chr5B 78.818 203 32 10 1269 1465 668187001 668187198 6.550000e-25 126.0
18 TraesCS1D01G194300 chr5B 89.362 94 6 2 6130 6223 692123576 692123487 1.420000e-21 115.0
19 TraesCS1D01G194300 chr5D 78.713 202 34 7 1269 1465 529347510 529347707 6.550000e-25 126.0
20 TraesCS1D01G194300 chr2B 91.304 92 6 2 6132 6223 105899790 105899879 2.360000e-24 124.0
21 TraesCS1D01G194300 chr2B 83.453 139 15 7 1345 1479 786039209 786039075 8.480000e-24 122.0
22 TraesCS1D01G194300 chr2B 88.542 96 11 0 6128 6223 696368920 696369015 3.940000e-22 117.0
23 TraesCS1D01G194300 chr2B 89.130 92 10 0 6132 6223 494378862 494378771 1.420000e-21 115.0
24 TraesCS1D01G194300 chr2A 89.691 97 6 4 6132 6227 101693021 101693114 3.050000e-23 121.0
25 TraesCS1D01G194300 chr7D 94.872 39 2 0 273 311 264389918 264389956 1.870000e-05 62.1


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 TraesCS1D01G194300 chr1D 270286809 270293036 6227 True 11502.000000 11502 100.000000 1 6228 1 chr1D.!!$R1 6227
1 TraesCS1D01G194300 chr1A 343680703 343687298 6595 True 4528.500000 8482 90.157500 1 6011 2 chr1A.!!$R1 6010
2 TraesCS1D01G194300 chr1B 344043668 344050080 6412 True 3004.666667 6898 93.758667 1 5884 3 chr1B.!!$R3 5883

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
234 252 1.153127 TGTTTGTCCGGTTCGCCTT 60.153 52.632 0.0 0.0 34.30 4.35 F
2081 3224 0.036858 GGAGTGTGGTCTGCCTCTTC 60.037 60.000 0.0 0.0 35.27 2.87 F
3810 4961 0.248743 CGCATGTGTTGATGGGCATC 60.249 55.000 0.0 0.0 38.29 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2126 3269 1.954437 CTTGTGCAATGTAGTGTGCG 58.046 50.0 0.0 0.0 43.93 5.34 R
3864 5015 0.810031 CTGTAAGGTCCATTCCGGCG 60.810 60.0 0.0 0.0 33.14 6.46 R
5572 6834 0.179001 AACAAACCCCCTCTGTTCCG 60.179 55.0 0.0 0.0 0.00 4.30 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 1.825090 TGCAGCGAATTCCAAGTCAT 58.175 45.000 0.00 0.00 0.00 3.06
183 201 2.100197 TGTCTTATGGTGCTAGCGACT 58.900 47.619 10.77 0.00 0.00 4.18
206 224 7.960262 ACTTAGTTTAACTAGGTGTAGTTGCT 58.040 34.615 17.14 6.24 46.91 3.91
207 225 8.087136 ACTTAGTTTAACTAGGTGTAGTTGCTC 58.913 37.037 17.14 0.00 46.91 4.26
220 238 3.004752 AGTTGCTCTGTTCAGGTGTTT 57.995 42.857 0.00 0.00 0.00 2.83
222 240 2.418368 TGCTCTGTTCAGGTGTTTGT 57.582 45.000 0.00 0.00 0.00 2.83
229 247 1.332686 GTTCAGGTGTTTGTCCGGTTC 59.667 52.381 0.00 0.00 0.00 3.62
234 252 1.153127 TGTTTGTCCGGTTCGCCTT 60.153 52.632 0.00 0.00 34.30 4.35
246 264 3.121544 GGTTCGCCTTTAATAGACCGAG 58.878 50.000 0.00 0.00 32.05 4.63
272 791 3.067106 CAGTTCTTGCCATCAACGTACT 58.933 45.455 0.00 0.00 0.00 2.73
273 792 3.498397 CAGTTCTTGCCATCAACGTACTT 59.502 43.478 0.00 0.00 0.00 2.24
274 793 4.024048 CAGTTCTTGCCATCAACGTACTTT 60.024 41.667 0.00 0.00 0.00 2.66
314 836 4.532521 AGCAGCTCTCCTCCTAACTTAAAA 59.467 41.667 0.00 0.00 0.00 1.52
315 837 5.013183 AGCAGCTCTCCTCCTAACTTAAAAA 59.987 40.000 0.00 0.00 0.00 1.94
363 885 6.100404 ACAATATTGTGCAAATTCTGGTGT 57.900 33.333 20.19 0.00 40.49 4.16
444 977 2.031682 GCACTGTGGTCAAGTTTAGCTG 60.032 50.000 10.21 0.00 0.00 4.24
445 978 2.549754 CACTGTGGTCAAGTTTAGCTGG 59.450 50.000 0.00 0.00 0.00 4.85
446 979 2.438021 ACTGTGGTCAAGTTTAGCTGGA 59.562 45.455 0.00 0.00 0.00 3.86
447 980 3.073062 ACTGTGGTCAAGTTTAGCTGGAT 59.927 43.478 0.00 0.00 28.28 3.41
448 981 4.286032 ACTGTGGTCAAGTTTAGCTGGATA 59.714 41.667 0.00 0.00 28.28 2.59
449 982 5.221843 ACTGTGGTCAAGTTTAGCTGGATAA 60.222 40.000 0.00 0.00 28.28 1.75
450 983 5.815581 TGTGGTCAAGTTTAGCTGGATAAT 58.184 37.500 0.00 0.00 28.28 1.28
451 984 5.647658 TGTGGTCAAGTTTAGCTGGATAATG 59.352 40.000 0.00 0.00 28.28 1.90
452 985 4.640201 TGGTCAAGTTTAGCTGGATAATGC 59.360 41.667 0.00 0.00 28.28 3.56
529 1062 1.936547 GGCAGCTGGTATTCTCGAAAG 59.063 52.381 17.12 0.00 0.00 2.62
631 1718 8.681486 TCATCATAAACCATCGATTTGATTCT 57.319 30.769 0.00 0.00 34.13 2.40
640 1727 6.649973 ACCATCGATTTGATTCTGATCTGATC 59.350 38.462 10.72 10.72 34.13 2.92
684 1771 5.417580 AGAAGAGCAGATACTTCTTTCGTCT 59.582 40.000 0.00 0.00 46.86 4.18
940 2036 3.151022 CACGCTCTCCCTCCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
941 2037 4.467107 ACGCTCTCCCTCCCTCCC 62.467 72.222 0.00 0.00 0.00 4.30
942 2038 4.150454 CGCTCTCCCTCCCTCCCT 62.150 72.222 0.00 0.00 0.00 4.20
943 2039 2.123033 GCTCTCCCTCCCTCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
952 2056 4.371231 CCCTCCCTCCCCCACCTT 62.371 72.222 0.00 0.00 0.00 3.50
1096 2200 0.532862 CGCAGATCCCGGTAAGCAAT 60.533 55.000 0.00 0.00 0.00 3.56
1204 2316 2.668120 GGCCTGCTCTCTTGCTCCT 61.668 63.158 0.00 0.00 0.00 3.69
1474 2601 2.152699 CAGCAGTTCCTCGTACGCG 61.153 63.158 11.24 3.53 39.92 6.01
1475 2602 3.542742 GCAGTTCCTCGTACGCGC 61.543 66.667 11.24 0.00 38.14 6.86
1476 2603 2.879462 CAGTTCCTCGTACGCGCC 60.879 66.667 11.24 0.00 38.14 6.53
1477 2604 4.125695 AGTTCCTCGTACGCGCCC 62.126 66.667 11.24 0.00 38.14 6.13
1713 2856 0.317479 ACCTCTTCCACTGTACGTGC 59.683 55.000 0.00 0.00 42.42 5.34
1714 2857 0.603569 CCTCTTCCACTGTACGTGCT 59.396 55.000 4.97 0.00 42.42 4.40
1734 2877 7.393515 ACGTGCTACTGTCTATTCATATCCATA 59.606 37.037 0.00 0.00 0.00 2.74
1735 2878 8.244113 CGTGCTACTGTCTATTCATATCCATAA 58.756 37.037 0.00 0.00 0.00 1.90
2081 3224 0.036858 GGAGTGTGGTCTGCCTCTTC 60.037 60.000 0.00 0.00 35.27 2.87
2126 3269 1.313091 GGGAAATGCGGTTGAGGGTC 61.313 60.000 0.00 0.00 0.00 4.46
2353 3496 4.242475 TGCTGTTACTCCTTACATGAACG 58.758 43.478 0.00 0.00 0.00 3.95
2356 3499 4.562082 TGTTACTCCTTACATGAACGTGG 58.438 43.478 0.00 0.00 0.00 4.94
2359 3502 4.553330 ACTCCTTACATGAACGTGGAAT 57.447 40.909 0.00 0.00 0.00 3.01
2480 3623 1.001378 CCTCGCTTGTCAAGTTTTGGG 60.001 52.381 14.03 6.23 0.00 4.12
2583 3726 1.667595 TGACCACATGATCCCTCCAA 58.332 50.000 0.00 0.00 0.00 3.53
2584 3727 1.561076 TGACCACATGATCCCTCCAAG 59.439 52.381 0.00 0.00 0.00 3.61
2629 3779 7.447374 TTGGTGTTATCCATTACAAGTGAAG 57.553 36.000 0.00 0.00 37.33 3.02
2695 3845 6.640518 TCTTATTGTGTCCACAGAGGTAATC 58.359 40.000 0.00 0.00 42.94 1.75
2821 3971 6.773638 TCTCTTTTTATTCCTGAACTGCTCT 58.226 36.000 0.00 0.00 0.00 4.09
2829 3979 2.167808 CTGAACTGCTCTGCACGTGC 62.168 60.000 33.11 33.11 42.50 5.34
2854 4004 6.913170 TCTTTGGACTGCACTGAATAATTTC 58.087 36.000 0.00 0.00 0.00 2.17
2983 4133 8.186163 GTCATGTATGCTTCATTTCAATCTTCA 58.814 33.333 0.00 0.00 0.00 3.02
3011 4161 7.509141 TTCTTGTTATCAGTTTCTTGCATCA 57.491 32.000 0.00 0.00 0.00 3.07
3085 4235 7.955918 AGTTTTGAACCATTAGCTTGAATCTT 58.044 30.769 0.00 0.00 0.00 2.40
3136 4286 1.408683 GCAGGGCACATAACCATCTCA 60.409 52.381 0.00 0.00 0.00 3.27
3232 4382 4.202212 GCTTAAGGTTTTGGTTGTCCATGT 60.202 41.667 4.29 0.00 43.91 3.21
3294 4444 7.660112 AGAGTTGATTAGAGAGCACAGATATG 58.340 38.462 0.00 0.00 0.00 1.78
3410 4561 1.288127 CTTGAAGCCAAGTGCAGCC 59.712 57.895 0.00 0.00 43.60 4.85
3422 4573 3.091633 AGTGCAGCCCAAAGAACATAT 57.908 42.857 0.00 0.00 0.00 1.78
3449 4600 5.299279 GCATTATGCTAGGGTGTTGTATTGT 59.701 40.000 10.27 0.00 40.96 2.71
3454 4605 3.877508 GCTAGGGTGTTGTATTGTCATCC 59.122 47.826 0.00 0.00 33.03 3.51
3581 4732 6.150140 CCTTAGAAGGGCAATATGCTAATGAC 59.850 42.308 0.00 0.00 44.28 3.06
3614 4765 7.964559 TCAAAATTAGTCGATCTTGCATCAAAG 59.035 33.333 0.00 0.00 0.00 2.77
3758 4909 4.152759 GCGTTGCCTACAGTAACACAATTA 59.847 41.667 0.00 0.00 40.79 1.40
3810 4961 0.248743 CGCATGTGTTGATGGGCATC 60.249 55.000 0.00 0.00 38.29 3.91
4027 5179 3.442273 TGTGGTGAACTTTCCTTTGTCAC 59.558 43.478 0.00 0.00 0.00 3.67
4095 5247 5.036117 TGCTAACTTGTTCTTGAAGGTCT 57.964 39.130 0.00 0.00 0.00 3.85
4156 5309 9.969001 ACCTTTCCTATGCTAGTTTACAATTAA 57.031 29.630 0.00 0.00 0.00 1.40
4286 5446 7.882271 AGAGAAGCTGACTTTCATCAATAACTT 59.118 33.333 0.00 0.00 35.82 2.66
4376 5538 5.646360 GGCTTAAACTTAGGATGCTGTTGTA 59.354 40.000 0.00 0.00 0.00 2.41
4753 5915 6.347888 CCAAGTTCATGAATTTTGCAATGTCC 60.348 38.462 21.25 3.80 0.00 4.02
4829 6059 0.465287 CAACAAGCAGTTTGGCCCTT 59.535 50.000 0.00 0.00 41.25 3.95
4842 6072 3.644966 TGGCCCTTAATCTGTTACCTG 57.355 47.619 0.00 0.00 0.00 4.00
4867 6097 3.322514 TGCCAGTAAAGCAGTCACC 57.677 52.632 0.00 0.00 34.69 4.02
4955 6212 6.319911 TCATTTTGTGTGTCCTGTAACATGAA 59.680 34.615 0.00 0.00 0.00 2.57
4956 6213 6.707440 TTTTGTGTGTCCTGTAACATGAAT 57.293 33.333 0.00 0.00 0.00 2.57
5032 6291 2.561373 GCCAGGCGGAGTTTTTCG 59.439 61.111 0.00 0.00 0.00 3.46
5239 6498 0.252197 GTGGTTAGGGACGAAGCCAT 59.748 55.000 0.00 0.00 40.59 4.40
5446 6706 1.200020 GGCTTATGAGTTGCACCACAC 59.800 52.381 0.00 0.00 0.00 3.82
5539 6801 7.097834 ACGATCTCTTAACGATTTCTCCTTTT 58.902 34.615 0.00 0.00 0.00 2.27
5572 6834 1.009829 GATGGCTGGACGATTGTGTC 58.990 55.000 0.00 0.00 38.17 3.67
5734 6996 6.966534 ATGTTAGATCATTTTTAGCCCTGG 57.033 37.500 0.00 0.00 0.00 4.45
5737 6999 4.337264 AGATCATTTTTAGCCCTGGGTT 57.663 40.909 15.56 11.53 0.00 4.11
5745 7007 3.322191 TTAGCCCTGGGTTCTGTTTTT 57.678 42.857 15.56 0.00 0.00 1.94
5801 7063 2.837498 TGGCCACGTCAGATGATATTG 58.163 47.619 0.00 0.00 0.00 1.90
5847 7109 2.540515 ACCTCGATGTATGAACTTGCG 58.459 47.619 0.00 0.00 0.00 4.85
5858 7120 3.006659 TGAACTTGCGTTAACCAATGC 57.993 42.857 0.00 0.00 45.32 3.56
5871 7133 4.584327 AACCAATGCCTTGTTAGTTGAC 57.416 40.909 0.91 0.00 0.00 3.18
5892 7154 5.203060 ACGAAAGAACTTAGAGCAACTCT 57.797 39.130 2.23 2.23 43.83 3.24
5982 7244 3.793144 GGCCTGAGCAGAAACGCG 61.793 66.667 3.53 3.53 42.56 6.01
6006 7268 3.560636 TCTAGCCTGGCCTGTAATTTC 57.439 47.619 16.57 0.00 0.00 2.17
6010 7272 3.510459 AGCCTGGCCTGTAATTTCTTTT 58.490 40.909 16.57 0.00 0.00 2.27
6011 7273 3.903714 AGCCTGGCCTGTAATTTCTTTTT 59.096 39.130 16.57 0.00 0.00 1.94
6012 7274 5.083821 AGCCTGGCCTGTAATTTCTTTTTA 58.916 37.500 16.57 0.00 0.00 1.52
6013 7275 5.047306 AGCCTGGCCTGTAATTTCTTTTTAC 60.047 40.000 16.57 0.00 0.00 2.01
6014 7276 5.279256 GCCTGGCCTGTAATTTCTTTTTACA 60.279 40.000 7.66 0.00 37.25 2.41
6015 7277 6.740122 GCCTGGCCTGTAATTTCTTTTTACAA 60.740 38.462 7.66 0.00 38.65 2.41
6016 7278 6.868339 CCTGGCCTGTAATTTCTTTTTACAAG 59.132 38.462 3.32 0.00 38.65 3.16
6017 7279 7.255801 CCTGGCCTGTAATTTCTTTTTACAAGA 60.256 37.037 3.32 0.00 38.65 3.02
6018 7280 7.657336 TGGCCTGTAATTTCTTTTTACAAGAG 58.343 34.615 3.32 0.00 38.65 2.85
6019 7281 7.090808 GGCCTGTAATTTCTTTTTACAAGAGG 58.909 38.462 0.00 0.00 38.65 3.69
6020 7282 6.586463 GCCTGTAATTTCTTTTTACAAGAGGC 59.414 38.462 0.00 0.00 39.30 4.70
6021 7283 7.090808 CCTGTAATTTCTTTTTACAAGAGGCC 58.909 38.462 0.00 0.00 38.65 5.19
6022 7284 7.039714 CCTGTAATTTCTTTTTACAAGAGGCCT 60.040 37.037 3.86 3.86 38.65 5.19
6023 7285 7.657336 TGTAATTTCTTTTTACAAGAGGCCTG 58.343 34.615 12.00 0.00 36.79 4.85
6024 7286 4.584327 TTTCTTTTTACAAGAGGCCTGC 57.416 40.909 12.00 1.09 0.00 4.85
6025 7287 3.222173 TCTTTTTACAAGAGGCCTGCA 57.778 42.857 12.00 0.00 0.00 4.41
6026 7288 3.766545 TCTTTTTACAAGAGGCCTGCAT 58.233 40.909 12.00 0.00 0.00 3.96
6027 7289 4.917385 TCTTTTTACAAGAGGCCTGCATA 58.083 39.130 12.00 0.00 0.00 3.14
6028 7290 4.700213 TCTTTTTACAAGAGGCCTGCATAC 59.300 41.667 12.00 0.00 0.00 2.39
6029 7291 4.301072 TTTTACAAGAGGCCTGCATACT 57.699 40.909 12.00 0.00 0.00 2.12
6030 7292 2.988010 TACAAGAGGCCTGCATACTG 57.012 50.000 12.00 0.00 0.00 2.74
6031 7293 0.393537 ACAAGAGGCCTGCATACTGC 60.394 55.000 12.00 0.00 45.29 4.40
6032 7294 1.099879 CAAGAGGCCTGCATACTGCC 61.100 60.000 12.00 8.24 44.23 4.85
6033 7295 2.203266 GAGGCCTGCATACTGCCC 60.203 66.667 12.00 0.00 46.55 5.36
6034 7296 3.781605 GAGGCCTGCATACTGCCCC 62.782 68.421 12.00 0.00 46.55 5.80
6035 7297 3.813724 GGCCTGCATACTGCCCCT 61.814 66.667 0.00 0.00 44.23 4.79
6036 7298 2.203266 GCCTGCATACTGCCCCTC 60.203 66.667 0.00 0.00 44.23 4.30
6037 7299 2.512896 CCTGCATACTGCCCCTCC 59.487 66.667 0.00 0.00 44.23 4.30
6038 7300 2.109799 CTGCATACTGCCCCTCCG 59.890 66.667 0.00 0.00 44.23 4.63
6039 7301 4.175337 TGCATACTGCCCCTCCGC 62.175 66.667 0.00 0.00 44.23 5.54
6041 7303 4.609018 CATACTGCCCCTCCGCGG 62.609 72.222 22.12 22.12 41.17 6.46
6047 7309 3.391382 GCCCCTCCGCGGCTATAT 61.391 66.667 23.51 0.00 43.48 0.86
6048 7310 2.893398 CCCCTCCGCGGCTATATC 59.107 66.667 23.51 0.00 0.00 1.63
6049 7311 1.682684 CCCCTCCGCGGCTATATCT 60.683 63.158 23.51 0.00 0.00 1.98
6050 7312 0.395311 CCCCTCCGCGGCTATATCTA 60.395 60.000 23.51 0.00 0.00 1.98
6051 7313 1.693627 CCCTCCGCGGCTATATCTAT 58.306 55.000 23.51 0.00 0.00 1.98
6052 7314 1.338337 CCCTCCGCGGCTATATCTATG 59.662 57.143 23.51 0.00 0.00 2.23
6053 7315 1.338337 CCTCCGCGGCTATATCTATGG 59.662 57.143 23.51 5.32 0.00 2.74
6054 7316 1.338337 CTCCGCGGCTATATCTATGGG 59.662 57.143 23.51 0.00 0.00 4.00
6055 7317 0.389391 CCGCGGCTATATCTATGGGG 59.611 60.000 14.67 0.00 0.00 4.96
6056 7318 1.112113 CGCGGCTATATCTATGGGGT 58.888 55.000 0.00 0.00 0.00 4.95
6057 7319 1.202417 CGCGGCTATATCTATGGGGTG 60.202 57.143 0.00 0.00 0.00 4.61
6058 7320 1.139058 GCGGCTATATCTATGGGGTGG 59.861 57.143 0.00 0.00 0.00 4.61
6059 7321 1.762957 CGGCTATATCTATGGGGTGGG 59.237 57.143 0.00 0.00 0.00 4.61
6060 7322 2.127708 GGCTATATCTATGGGGTGGGG 58.872 57.143 0.00 0.00 0.00 4.96
6061 7323 1.490910 GCTATATCTATGGGGTGGGGC 59.509 57.143 0.00 0.00 0.00 5.80
6062 7324 1.762957 CTATATCTATGGGGTGGGGCG 59.237 57.143 0.00 0.00 0.00 6.13
6063 7325 1.562672 ATATCTATGGGGTGGGGCGC 61.563 60.000 0.00 0.00 0.00 6.53
6070 7332 3.436924 GGGTGGGGCGCGTTTTAG 61.437 66.667 8.43 0.00 0.00 1.85
6071 7333 3.436924 GGTGGGGCGCGTTTTAGG 61.437 66.667 8.43 0.00 0.00 2.69
6072 7334 3.436924 GTGGGGCGCGTTTTAGGG 61.437 66.667 8.43 0.00 0.00 3.53
6073 7335 3.956314 TGGGGCGCGTTTTAGGGT 61.956 61.111 8.43 0.00 0.00 4.34
6074 7336 2.674033 GGGGCGCGTTTTAGGGTT 60.674 61.111 8.43 0.00 0.00 4.11
6075 7337 2.693762 GGGGCGCGTTTTAGGGTTC 61.694 63.158 8.43 0.00 0.00 3.62
6076 7338 2.477396 GGCGCGTTTTAGGGTTCG 59.523 61.111 8.43 0.00 0.00 3.95
6077 7339 2.319841 GGCGCGTTTTAGGGTTCGT 61.320 57.895 8.43 0.00 0.00 3.85
6078 7340 1.570967 GCGCGTTTTAGGGTTCGTT 59.429 52.632 8.43 0.00 0.00 3.85
6079 7341 0.041047 GCGCGTTTTAGGGTTCGTTT 60.041 50.000 8.43 0.00 0.00 3.60
6080 7342 1.665766 CGCGTTTTAGGGTTCGTTTG 58.334 50.000 0.00 0.00 0.00 2.93
6081 7343 1.401530 GCGTTTTAGGGTTCGTTTGC 58.598 50.000 0.00 0.00 0.00 3.68
6082 7344 1.002142 GCGTTTTAGGGTTCGTTTGCT 60.002 47.619 0.00 0.00 0.00 3.91
6083 7345 2.912366 CGTTTTAGGGTTCGTTTGCTC 58.088 47.619 0.00 0.00 0.00 4.26
6084 7346 2.350102 CGTTTTAGGGTTCGTTTGCTCC 60.350 50.000 0.00 0.00 0.00 4.70
6085 7347 2.619646 GTTTTAGGGTTCGTTTGCTCCA 59.380 45.455 0.00 0.00 0.00 3.86
6086 7348 2.871096 TTAGGGTTCGTTTGCTCCAT 57.129 45.000 0.00 0.00 0.00 3.41
6087 7349 3.985019 TTAGGGTTCGTTTGCTCCATA 57.015 42.857 0.00 0.00 0.00 2.74
6088 7350 4.497291 TTAGGGTTCGTTTGCTCCATAT 57.503 40.909 0.00 0.00 0.00 1.78
6089 7351 2.919228 AGGGTTCGTTTGCTCCATATC 58.081 47.619 0.00 0.00 0.00 1.63
6090 7352 1.947456 GGGTTCGTTTGCTCCATATCC 59.053 52.381 0.00 0.00 0.00 2.59
6091 7353 2.421529 GGGTTCGTTTGCTCCATATCCT 60.422 50.000 0.00 0.00 0.00 3.24
6092 7354 2.872858 GGTTCGTTTGCTCCATATCCTC 59.127 50.000 0.00 0.00 0.00 3.71
6093 7355 2.872858 GTTCGTTTGCTCCATATCCTCC 59.127 50.000 0.00 0.00 0.00 4.30
6094 7356 1.068588 TCGTTTGCTCCATATCCTCCG 59.931 52.381 0.00 0.00 0.00 4.63
6095 7357 1.202533 CGTTTGCTCCATATCCTCCGT 60.203 52.381 0.00 0.00 0.00 4.69
6096 7358 2.484889 GTTTGCTCCATATCCTCCGTC 58.515 52.381 0.00 0.00 0.00 4.79
6097 7359 1.788229 TTGCTCCATATCCTCCGTCA 58.212 50.000 0.00 0.00 0.00 4.35
6098 7360 1.040646 TGCTCCATATCCTCCGTCAC 58.959 55.000 0.00 0.00 0.00 3.67
6099 7361 1.040646 GCTCCATATCCTCCGTCACA 58.959 55.000 0.00 0.00 0.00 3.58
6100 7362 1.412710 GCTCCATATCCTCCGTCACAA 59.587 52.381 0.00 0.00 0.00 3.33
6101 7363 2.037772 GCTCCATATCCTCCGTCACAAT 59.962 50.000 0.00 0.00 0.00 2.71
6102 7364 3.862642 GCTCCATATCCTCCGTCACAATC 60.863 52.174 0.00 0.00 0.00 2.67
6103 7365 3.576118 CTCCATATCCTCCGTCACAATCT 59.424 47.826 0.00 0.00 0.00 2.40
6104 7366 3.967326 TCCATATCCTCCGTCACAATCTT 59.033 43.478 0.00 0.00 0.00 2.40
6105 7367 4.039245 TCCATATCCTCCGTCACAATCTTC 59.961 45.833 0.00 0.00 0.00 2.87
6106 7368 2.990066 ATCCTCCGTCACAATCTTCC 57.010 50.000 0.00 0.00 0.00 3.46
6107 7369 0.902531 TCCTCCGTCACAATCTTCCC 59.097 55.000 0.00 0.00 0.00 3.97
6108 7370 0.107654 CCTCCGTCACAATCTTCCCC 60.108 60.000 0.00 0.00 0.00 4.81
6109 7371 0.107654 CTCCGTCACAATCTTCCCCC 60.108 60.000 0.00 0.00 0.00 5.40
6123 7385 4.463043 CCCCCTCTCGTCTCCTTT 57.537 61.111 0.00 0.00 0.00 3.11
6124 7386 1.901085 CCCCCTCTCGTCTCCTTTG 59.099 63.158 0.00 0.00 0.00 2.77
6125 7387 1.219393 CCCCTCTCGTCTCCTTTGC 59.781 63.158 0.00 0.00 0.00 3.68
6126 7388 1.261238 CCCCTCTCGTCTCCTTTGCT 61.261 60.000 0.00 0.00 0.00 3.91
6127 7389 0.174617 CCCTCTCGTCTCCTTTGCTC 59.825 60.000 0.00 0.00 0.00 4.26
6128 7390 1.181786 CCTCTCGTCTCCTTTGCTCT 58.818 55.000 0.00 0.00 0.00 4.09
6129 7391 1.548269 CCTCTCGTCTCCTTTGCTCTT 59.452 52.381 0.00 0.00 0.00 2.85
6130 7392 2.028567 CCTCTCGTCTCCTTTGCTCTTT 60.029 50.000 0.00 0.00 0.00 2.52
6131 7393 3.193691 CCTCTCGTCTCCTTTGCTCTTTA 59.806 47.826 0.00 0.00 0.00 1.85
6132 7394 4.420168 CTCTCGTCTCCTTTGCTCTTTAG 58.580 47.826 0.00 0.00 0.00 1.85
6133 7395 4.079970 TCTCGTCTCCTTTGCTCTTTAGA 58.920 43.478 0.00 0.00 0.00 2.10
6134 7396 4.156922 TCTCGTCTCCTTTGCTCTTTAGAG 59.843 45.833 2.33 2.33 44.75 2.43
6170 7432 3.732849 CAACAGCCCCCTCCCCTC 61.733 72.222 0.00 0.00 0.00 4.30
6183 7445 3.420482 CCCTCCCCCAGGCGATTT 61.420 66.667 0.00 0.00 41.80 2.17
6184 7446 2.683475 CCTCCCCCAGGCGATTTT 59.317 61.111 0.00 0.00 34.56 1.82
6185 7447 1.453928 CCTCCCCCAGGCGATTTTC 60.454 63.158 0.00 0.00 34.56 2.29
6186 7448 1.609783 CTCCCCCAGGCGATTTTCT 59.390 57.895 0.00 0.00 0.00 2.52
6187 7449 0.837272 CTCCCCCAGGCGATTTTCTA 59.163 55.000 0.00 0.00 0.00 2.10
6188 7450 0.837272 TCCCCCAGGCGATTTTCTAG 59.163 55.000 0.00 0.00 0.00 2.43
6189 7451 0.819666 CCCCCAGGCGATTTTCTAGC 60.820 60.000 0.00 0.00 0.00 3.42
6190 7452 1.160329 CCCCAGGCGATTTTCTAGCG 61.160 60.000 0.00 0.00 0.00 4.26
6194 7456 2.626455 GCGATTTTCTAGCGCCGG 59.374 61.111 2.29 0.00 44.55 6.13
6195 7457 2.171725 GCGATTTTCTAGCGCCGGT 61.172 57.895 2.29 0.00 44.55 5.28
6196 7458 1.636340 CGATTTTCTAGCGCCGGTG 59.364 57.895 11.67 11.67 0.00 4.94
6197 7459 1.762222 CGATTTTCTAGCGCCGGTGG 61.762 60.000 18.41 3.39 0.00 4.61
6198 7460 2.048312 GATTTTCTAGCGCCGGTGGC 62.048 60.000 18.41 14.42 46.75 5.01
6216 7478 3.089784 CGAAAATCGGCCCAGTCG 58.910 61.111 0.00 0.00 36.00 4.18
6217 7479 2.791927 GAAAATCGGCCCAGTCGC 59.208 61.111 0.00 0.00 0.00 5.19
6218 7480 3.095898 GAAAATCGGCCCAGTCGCG 62.096 63.158 0.00 0.00 0.00 5.87
6227 7489 4.473520 CCAGTCGCGCCCCAGAAT 62.474 66.667 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.394708 GGTGTCATCGTACATCATCCG 58.605 52.381 0.00 0.00 30.49 4.18
183 201 8.086522 CAGAGCAACTACACCTAGTTAAACTAA 58.913 37.037 0.00 0.00 40.64 2.24
206 224 1.474320 CCGGACAAACACCTGAACAGA 60.474 52.381 0.00 0.00 0.00 3.41
207 225 0.944386 CCGGACAAACACCTGAACAG 59.056 55.000 0.00 0.00 0.00 3.16
220 238 2.496871 TCTATTAAAGGCGAACCGGACA 59.503 45.455 9.46 0.00 42.76 4.02
222 240 2.159057 GGTCTATTAAAGGCGAACCGGA 60.159 50.000 9.46 0.00 42.76 5.14
229 247 2.218953 TGCTCGGTCTATTAAAGGCG 57.781 50.000 0.00 0.00 0.00 5.52
234 252 3.887621 ACTGCTTGCTCGGTCTATTAA 57.112 42.857 0.00 0.00 0.00 1.40
272 791 8.353423 AGCTGCTAAGATTCCATTAAGAAAAA 57.647 30.769 0.00 0.00 0.00 1.94
273 792 7.831193 AGAGCTGCTAAGATTCCATTAAGAAAA 59.169 33.333 0.15 0.00 0.00 2.29
274 793 7.341805 AGAGCTGCTAAGATTCCATTAAGAAA 58.658 34.615 0.15 0.00 0.00 2.52
315 837 9.807649 GTTCATATGTGGCATATCTTTCTTTTT 57.192 29.630 0.00 0.00 0.00 1.94
316 838 8.970020 TGTTCATATGTGGCATATCTTTCTTTT 58.030 29.630 0.00 0.00 0.00 2.27
430 954 4.260784 CGCATTATCCAGCTAAACTTGACC 60.261 45.833 0.00 0.00 0.00 4.02
432 956 3.876914 CCGCATTATCCAGCTAAACTTGA 59.123 43.478 0.00 0.00 0.00 3.02
444 977 6.199937 AGATTTGCATTATCCGCATTATCC 57.800 37.500 5.88 0.00 39.58 2.59
445 978 6.909357 GCTAGATTTGCATTATCCGCATTATC 59.091 38.462 0.00 0.00 39.58 1.75
446 979 6.183360 GGCTAGATTTGCATTATCCGCATTAT 60.183 38.462 16.17 0.00 39.58 1.28
447 980 5.123820 GGCTAGATTTGCATTATCCGCATTA 59.876 40.000 16.17 1.95 39.58 1.90
448 981 4.082571 GGCTAGATTTGCATTATCCGCATT 60.083 41.667 16.17 1.15 39.58 3.56
449 982 3.441572 GGCTAGATTTGCATTATCCGCAT 59.558 43.478 16.17 1.40 39.58 4.73
450 983 2.813754 GGCTAGATTTGCATTATCCGCA 59.186 45.455 16.17 0.00 37.68 5.69
451 984 2.813754 TGGCTAGATTTGCATTATCCGC 59.186 45.455 0.00 8.41 0.00 5.54
452 985 5.437289 TTTGGCTAGATTTGCATTATCCG 57.563 39.130 0.00 0.77 0.00 4.18
497 1030 1.211457 CCAGCTGCCTCTACTTCCATT 59.789 52.381 8.66 0.00 0.00 3.16
499 1032 0.545309 ACCAGCTGCCTCTACTTCCA 60.545 55.000 8.66 0.00 0.00 3.53
500 1033 1.486211 TACCAGCTGCCTCTACTTCC 58.514 55.000 8.66 0.00 0.00 3.46
502 1035 3.379452 AGAATACCAGCTGCCTCTACTT 58.621 45.455 8.66 0.00 0.00 2.24
631 1718 9.415544 CTATTGTGTATTCATTCGATCAGATCA 57.584 33.333 11.12 0.00 0.00 2.92
640 1727 8.634475 TCTTCTGTCTATTGTGTATTCATTCG 57.366 34.615 0.00 0.00 0.00 3.34
707 1794 7.818930 GGAAAAAGGATGCAGAAAACATCATTA 59.181 33.333 4.34 0.00 45.00 1.90
940 2036 2.669240 GAACGAAGGTGGGGGAGG 59.331 66.667 0.00 0.00 0.00 4.30
941 2037 2.221299 TGGAACGAAGGTGGGGGAG 61.221 63.158 0.00 0.00 0.00 4.30
942 2038 2.122324 TGGAACGAAGGTGGGGGA 60.122 61.111 0.00 0.00 0.00 4.81
943 2039 2.033602 GTGGAACGAAGGTGGGGG 59.966 66.667 0.00 0.00 0.00 5.40
1075 2179 2.792947 GCTTACCGGGATCTGCGGA 61.793 63.158 6.32 0.00 0.00 5.54
1204 2316 4.430765 GTTCGCCGCCTCTTCCGA 62.431 66.667 0.00 0.00 0.00 4.55
1735 2878 9.547753 CAACAACAACTATAACTAGCTGGATAT 57.452 33.333 3.17 4.41 0.00 1.63
1736 2879 7.494625 GCAACAACAACTATAACTAGCTGGATA 59.505 37.037 3.17 0.00 0.00 2.59
1737 2880 6.316390 GCAACAACAACTATAACTAGCTGGAT 59.684 38.462 3.17 0.00 0.00 3.41
1743 2886 6.255020 CCCGTAGCAACAACAACTATAACTAG 59.745 42.308 0.00 0.00 0.00 2.57
1747 2890 3.685756 GCCCGTAGCAACAACAACTATAA 59.314 43.478 0.00 0.00 42.97 0.98
2081 3224 2.592861 GGCTGCTTATCCCCTGCG 60.593 66.667 0.00 0.00 0.00 5.18
2126 3269 1.954437 CTTGTGCAATGTAGTGTGCG 58.046 50.000 0.00 0.00 43.93 5.34
2480 3623 0.026803 CGCGGCTGTTCTTCATTAGC 59.973 55.000 0.00 0.00 35.49 3.09
2666 3816 2.744202 CTGTGGACACAATAAGAGCACC 59.256 50.000 6.60 0.00 41.33 5.01
2734 3884 3.381590 TCATCTGATACTGAGGGAACACG 59.618 47.826 0.00 0.00 0.00 4.49
2778 3928 6.279227 AGAGAAAATGCGATCAGTTTATCG 57.721 37.500 7.03 2.02 46.65 2.92
2807 3957 0.601046 CGTGCAGAGCAGTTCAGGAA 60.601 55.000 0.00 0.00 40.08 3.36
2821 3971 1.146041 AGTCCAAAGAGCACGTGCA 59.854 52.632 39.21 16.76 45.16 4.57
2829 3979 6.506500 AATTATTCAGTGCAGTCCAAAGAG 57.493 37.500 0.00 0.00 0.00 2.85
2854 4004 3.128242 CCTGCCATTAAAGAGTCAAGCAG 59.872 47.826 0.00 0.00 44.64 4.24
2955 4105 8.289939 AGATTGAAATGAAGCATACATGACTT 57.710 30.769 0.00 0.00 0.00 3.01
2983 4133 7.771183 TGCAAGAAACTGATAACAAGAAAAGT 58.229 30.769 0.00 0.00 0.00 2.66
3002 4152 5.830799 ATGGTACTATCCATGATGCAAGA 57.169 39.130 0.00 0.00 45.26 3.02
3042 4192 2.157738 ACTCATTTGAGCTTCCAGCAC 58.842 47.619 7.48 0.00 45.56 4.40
3062 4212 8.181904 AGAAGATTCAAGCTAATGGTTCAAAA 57.818 30.769 0.00 0.00 0.00 2.44
3107 4257 5.070001 GGTTATGTGCCCTGCTTATTATCA 58.930 41.667 0.00 0.00 0.00 2.15
3136 4286 3.846588 ACACACCCTAAGACATTCCAGAT 59.153 43.478 0.00 0.00 0.00 2.90
3581 4732 6.279227 AGATCGACTAATTTTGAAGCATCG 57.721 37.500 0.00 0.00 0.00 3.84
3614 4765 2.351157 CCTAGCTTCAAACTGCAAGCAC 60.351 50.000 8.43 0.00 46.37 4.40
3864 5015 0.810031 CTGTAAGGTCCATTCCGGCG 60.810 60.000 0.00 0.00 33.14 6.46
4027 5179 0.865111 TGCCAAGTCGACACAAATCG 59.135 50.000 19.50 0.00 43.63 3.34
4095 5247 9.814899 CCATATGCCAAAACAAATCAAGTATAA 57.185 29.630 0.00 0.00 0.00 0.98
4156 5309 7.039574 TGCAATGCCAACATAGCTAATCATATT 60.040 33.333 1.53 0.00 34.62 1.28
4209 5362 4.142381 GCTTGATCCCCACTGTATTTTCAC 60.142 45.833 0.00 0.00 0.00 3.18
4312 5472 5.841957 ATCCAGTGTAAATGATTGCCTTC 57.158 39.130 0.00 0.00 30.28 3.46
4376 5538 9.830975 AAAAAGGAGTTTAATAAGCAAATGTGT 57.169 25.926 0.00 0.00 0.00 3.72
4446 5608 5.941788 TGGGAATAAGAAAAGGAGATAGGC 58.058 41.667 0.00 0.00 0.00 3.93
4450 5612 6.899631 AGCAAATGGGAATAAGAAAAGGAGAT 59.100 34.615 0.00 0.00 0.00 2.75
4452 5614 6.153340 TGAGCAAATGGGAATAAGAAAAGGAG 59.847 38.462 0.00 0.00 0.00 3.69
4453 5615 6.015918 TGAGCAAATGGGAATAAGAAAAGGA 58.984 36.000 0.00 0.00 0.00 3.36
4454 5616 6.284891 TGAGCAAATGGGAATAAGAAAAGG 57.715 37.500 0.00 0.00 0.00 3.11
4753 5915 4.229876 CAATCATGAAGCAGCAGCATATG 58.770 43.478 3.17 0.00 45.49 1.78
4811 6041 2.080654 TAAGGGCCAAACTGCTTGTT 57.919 45.000 6.18 0.00 41.29 2.83
4813 6043 2.827921 AGATTAAGGGCCAAACTGCTTG 59.172 45.455 6.18 0.00 34.52 4.01
4829 6059 4.253685 GCAGCACTTCAGGTAACAGATTA 58.746 43.478 0.00 0.00 41.41 1.75
4842 6072 1.238439 TGCTTTACTGGCAGCACTTC 58.762 50.000 15.89 1.99 41.20 3.01
4867 6097 9.442047 ACATCAGTTAGAAAGTAGAATTCCTTG 57.558 33.333 0.65 0.00 0.00 3.61
4955 6212 3.449737 AGCTGCAACATGGCAAATTAGAT 59.550 39.130 1.02 0.00 44.40 1.98
4956 6213 2.827322 AGCTGCAACATGGCAAATTAGA 59.173 40.909 1.02 0.00 44.40 2.10
5032 6291 2.731341 CGACTGACCGTTCATCAGGTAC 60.731 54.545 6.92 0.00 46.60 3.34
5239 6498 0.758685 CAACAGTTTGGGGGAAGCCA 60.759 55.000 0.00 0.00 0.00 4.75
5401 6661 2.234143 GCCCATTTAGATCTTCCAGGC 58.766 52.381 0.00 4.10 0.00 4.85
5446 6706 1.135315 CAGCGAAATCTTGCCACCG 59.865 57.895 0.00 0.00 0.00 4.94
5486 6746 6.480320 CCTTAATTACAATCTTCTCTCCCACG 59.520 42.308 0.00 0.00 0.00 4.94
5539 6801 2.036217 CAGCCATCCAGCAGAAACAAAA 59.964 45.455 0.00 0.00 34.23 2.44
5572 6834 0.179001 AACAAACCCCCTCTGTTCCG 60.179 55.000 0.00 0.00 0.00 4.30
5745 7007 0.953727 GCAATGCACTGTCTGTCCAA 59.046 50.000 0.00 0.00 0.00 3.53
5760 7022 5.007921 GCCAAAACAATCAAAGACAAGCAAT 59.992 36.000 0.00 0.00 0.00 3.56
5801 7063 1.373497 CCAGAGGACACGCTGACAC 60.373 63.158 0.00 0.00 46.01 3.67
5847 7109 5.918576 GTCAACTAACAAGGCATTGGTTAAC 59.081 40.000 16.45 2.87 40.97 2.01
5858 7120 5.986004 AGTTCTTTCGTCAACTAACAAGG 57.014 39.130 0.00 0.00 30.80 3.61
5871 7133 5.287513 GCTAGAGTTGCTCTAAGTTCTTTCG 59.712 44.000 7.22 0.00 41.74 3.46
5892 7154 0.744414 GAGGTTTGCGGCATCTGCTA 60.744 55.000 2.28 0.00 41.70 3.49
5913 7175 1.656441 CCAGATTTATGCAGGCCGC 59.344 57.895 11.92 11.92 42.89 6.53
5959 7221 1.412343 GTTTCTGCTCAGGCCCAAAAA 59.588 47.619 0.00 0.00 37.74 1.94
5982 7244 5.428184 AATTACAGGCCAGGCTAGATATC 57.572 43.478 12.43 0.00 0.00 1.63
6006 7268 4.702131 AGTATGCAGGCCTCTTGTAAAAAG 59.298 41.667 0.00 0.00 0.00 2.27
6010 7272 3.266510 CAGTATGCAGGCCTCTTGTAA 57.733 47.619 0.00 0.00 0.00 2.41
6011 7273 2.988010 CAGTATGCAGGCCTCTTGTA 57.012 50.000 0.00 0.00 0.00 2.41
6012 7274 3.869623 CAGTATGCAGGCCTCTTGT 57.130 52.632 0.00 0.00 0.00 3.16
6032 7294 1.338337 CATAGATATAGCCGCGGAGGG 59.662 57.143 33.48 1.43 41.48 4.30
6033 7295 1.338337 CCATAGATATAGCCGCGGAGG 59.662 57.143 33.48 6.61 44.97 4.30
6034 7296 1.338337 CCCATAGATATAGCCGCGGAG 59.662 57.143 33.48 2.86 0.00 4.63
6035 7297 1.399714 CCCATAGATATAGCCGCGGA 58.600 55.000 33.48 9.86 0.00 5.54
6036 7298 0.389391 CCCCATAGATATAGCCGCGG 59.611 60.000 24.05 24.05 0.00 6.46
6037 7299 1.112113 ACCCCATAGATATAGCCGCG 58.888 55.000 0.00 0.00 0.00 6.46
6038 7300 1.139058 CCACCCCATAGATATAGCCGC 59.861 57.143 0.00 0.00 0.00 6.53
6039 7301 1.762957 CCCACCCCATAGATATAGCCG 59.237 57.143 0.00 0.00 0.00 5.52
6040 7302 2.127708 CCCCACCCCATAGATATAGCC 58.872 57.143 0.00 0.00 0.00 3.93
6041 7303 1.490910 GCCCCACCCCATAGATATAGC 59.509 57.143 0.00 0.00 0.00 2.97
6042 7304 1.762957 CGCCCCACCCCATAGATATAG 59.237 57.143 0.00 0.00 0.00 1.31
6043 7305 1.874129 CGCCCCACCCCATAGATATA 58.126 55.000 0.00 0.00 0.00 0.86
6044 7306 1.562672 GCGCCCCACCCCATAGATAT 61.563 60.000 0.00 0.00 0.00 1.63
6045 7307 2.221299 GCGCCCCACCCCATAGATA 61.221 63.158 0.00 0.00 0.00 1.98
6046 7308 3.570212 GCGCCCCACCCCATAGAT 61.570 66.667 0.00 0.00 0.00 1.98
6053 7315 3.436924 CTAAAACGCGCCCCACCC 61.437 66.667 5.73 0.00 0.00 4.61
6054 7316 3.436924 CCTAAAACGCGCCCCACC 61.437 66.667 5.73 0.00 0.00 4.61
6055 7317 3.436924 CCCTAAAACGCGCCCCAC 61.437 66.667 5.73 0.00 0.00 4.61
6056 7318 3.494736 AACCCTAAAACGCGCCCCA 62.495 57.895 5.73 0.00 0.00 4.96
6057 7319 2.674033 AACCCTAAAACGCGCCCC 60.674 61.111 5.73 0.00 0.00 5.80
6058 7320 2.872557 GAACCCTAAAACGCGCCC 59.127 61.111 5.73 0.00 0.00 6.13
6059 7321 1.844771 AACGAACCCTAAAACGCGCC 61.845 55.000 5.73 0.00 0.00 6.53
6060 7322 0.041047 AAACGAACCCTAAAACGCGC 60.041 50.000 5.73 0.00 0.00 6.86
6061 7323 1.665766 CAAACGAACCCTAAAACGCG 58.334 50.000 3.53 3.53 0.00 6.01
6062 7324 1.002142 AGCAAACGAACCCTAAAACGC 60.002 47.619 0.00 0.00 0.00 4.84
6063 7325 2.350102 GGAGCAAACGAACCCTAAAACG 60.350 50.000 0.00 0.00 0.00 3.60
6064 7326 2.619646 TGGAGCAAACGAACCCTAAAAC 59.380 45.455 0.00 0.00 0.00 2.43
6065 7327 2.933573 TGGAGCAAACGAACCCTAAAA 58.066 42.857 0.00 0.00 0.00 1.52
6066 7328 2.642154 TGGAGCAAACGAACCCTAAA 57.358 45.000 0.00 0.00 0.00 1.85
6067 7329 2.871096 ATGGAGCAAACGAACCCTAA 57.129 45.000 0.00 0.00 0.00 2.69
6068 7330 3.181458 GGATATGGAGCAAACGAACCCTA 60.181 47.826 0.00 0.00 0.00 3.53
6069 7331 2.421529 GGATATGGAGCAAACGAACCCT 60.422 50.000 0.00 0.00 0.00 4.34
6070 7332 1.947456 GGATATGGAGCAAACGAACCC 59.053 52.381 0.00 0.00 0.00 4.11
6071 7333 2.872858 GAGGATATGGAGCAAACGAACC 59.127 50.000 0.00 0.00 0.00 3.62
6072 7334 2.872858 GGAGGATATGGAGCAAACGAAC 59.127 50.000 0.00 0.00 0.00 3.95
6073 7335 2.483013 CGGAGGATATGGAGCAAACGAA 60.483 50.000 0.00 0.00 0.00 3.85
6074 7336 1.068588 CGGAGGATATGGAGCAAACGA 59.931 52.381 0.00 0.00 0.00 3.85
6075 7337 1.202533 ACGGAGGATATGGAGCAAACG 60.203 52.381 0.00 0.00 0.00 3.60
6076 7338 2.158957 TGACGGAGGATATGGAGCAAAC 60.159 50.000 0.00 0.00 0.00 2.93
6077 7339 2.115427 TGACGGAGGATATGGAGCAAA 58.885 47.619 0.00 0.00 0.00 3.68
6078 7340 1.412710 GTGACGGAGGATATGGAGCAA 59.587 52.381 0.00 0.00 0.00 3.91
6079 7341 1.040646 GTGACGGAGGATATGGAGCA 58.959 55.000 0.00 0.00 0.00 4.26
6080 7342 1.040646 TGTGACGGAGGATATGGAGC 58.959 55.000 0.00 0.00 0.00 4.70
6081 7343 3.576118 AGATTGTGACGGAGGATATGGAG 59.424 47.826 0.00 0.00 0.00 3.86
6082 7344 3.576861 AGATTGTGACGGAGGATATGGA 58.423 45.455 0.00 0.00 0.00 3.41
6083 7345 4.310769 GAAGATTGTGACGGAGGATATGG 58.689 47.826 0.00 0.00 0.00 2.74
6084 7346 4.310769 GGAAGATTGTGACGGAGGATATG 58.689 47.826 0.00 0.00 0.00 1.78
6085 7347 3.325135 GGGAAGATTGTGACGGAGGATAT 59.675 47.826 0.00 0.00 0.00 1.63
6086 7348 2.698797 GGGAAGATTGTGACGGAGGATA 59.301 50.000 0.00 0.00 0.00 2.59
6087 7349 1.486726 GGGAAGATTGTGACGGAGGAT 59.513 52.381 0.00 0.00 0.00 3.24
6088 7350 0.902531 GGGAAGATTGTGACGGAGGA 59.097 55.000 0.00 0.00 0.00 3.71
6089 7351 0.107654 GGGGAAGATTGTGACGGAGG 60.108 60.000 0.00 0.00 0.00 4.30
6090 7352 0.107654 GGGGGAAGATTGTGACGGAG 60.108 60.000 0.00 0.00 0.00 4.63
6091 7353 1.988015 GGGGGAAGATTGTGACGGA 59.012 57.895 0.00 0.00 0.00 4.69
6092 7354 4.637771 GGGGGAAGATTGTGACGG 57.362 61.111 0.00 0.00 0.00 4.79
6106 7368 1.901085 CAAAGGAGACGAGAGGGGG 59.099 63.158 0.00 0.00 0.00 5.40
6107 7369 1.219393 GCAAAGGAGACGAGAGGGG 59.781 63.158 0.00 0.00 0.00 4.79
6108 7370 0.174617 GAGCAAAGGAGACGAGAGGG 59.825 60.000 0.00 0.00 0.00 4.30
6109 7371 1.181786 AGAGCAAAGGAGACGAGAGG 58.818 55.000 0.00 0.00 0.00 3.69
6110 7372 3.311486 AAAGAGCAAAGGAGACGAGAG 57.689 47.619 0.00 0.00 0.00 3.20
6111 7373 4.079970 TCTAAAGAGCAAAGGAGACGAGA 58.920 43.478 0.00 0.00 0.00 4.04
6112 7374 4.420168 CTCTAAAGAGCAAAGGAGACGAG 58.580 47.826 0.00 0.00 35.13 4.18
6113 7375 4.442375 CTCTAAAGAGCAAAGGAGACGA 57.558 45.455 0.00 0.00 35.13 4.20
6125 7387 2.545532 CGGCTGGAGATGCTCTAAAGAG 60.546 54.545 2.47 2.47 44.75 2.85
6126 7388 1.410517 CGGCTGGAGATGCTCTAAAGA 59.589 52.381 0.00 0.00 0.00 2.52
6127 7389 1.863267 CGGCTGGAGATGCTCTAAAG 58.137 55.000 0.00 0.00 0.00 1.85
6128 7390 0.179073 GCGGCTGGAGATGCTCTAAA 60.179 55.000 0.00 0.00 0.00 1.85
6129 7391 1.443407 GCGGCTGGAGATGCTCTAA 59.557 57.895 0.00 0.00 0.00 2.10
6130 7392 2.849964 CGCGGCTGGAGATGCTCTA 61.850 63.158 0.00 0.00 0.00 2.43
6131 7393 4.218578 CGCGGCTGGAGATGCTCT 62.219 66.667 0.00 0.00 0.00 4.09
6153 7415 3.732849 GAGGGGAGGGGGCTGTTG 61.733 72.222 0.00 0.00 0.00 3.33
6166 7428 2.911221 GAAAATCGCCTGGGGGAGGG 62.911 65.000 11.17 0.00 43.07 4.30
6167 7429 1.453928 GAAAATCGCCTGGGGGAGG 60.454 63.158 11.17 0.00 46.13 4.30
6168 7430 0.837272 TAGAAAATCGCCTGGGGGAG 59.163 55.000 11.17 0.00 40.35 4.30
6169 7431 0.837272 CTAGAAAATCGCCTGGGGGA 59.163 55.000 11.17 8.78 41.24 4.81
6170 7432 0.819666 GCTAGAAAATCGCCTGGGGG 60.820 60.000 11.17 0.78 0.00 5.40
6171 7433 1.160329 CGCTAGAAAATCGCCTGGGG 61.160 60.000 4.03 4.03 0.00 4.96
6172 7434 1.776034 GCGCTAGAAAATCGCCTGGG 61.776 60.000 0.00 0.00 42.71 4.45
6173 7435 1.643832 GCGCTAGAAAATCGCCTGG 59.356 57.895 0.00 0.00 42.71 4.45
6178 7440 1.636340 CACCGGCGCTAGAAAATCG 59.364 57.895 7.64 0.00 0.00 3.34
6179 7441 2.014594 CCACCGGCGCTAGAAAATC 58.985 57.895 7.64 0.00 0.00 2.17
6180 7442 2.112815 GCCACCGGCGCTAGAAAAT 61.113 57.895 7.64 0.00 39.62 1.82
6181 7443 2.744709 GCCACCGGCGCTAGAAAA 60.745 61.111 7.64 0.00 39.62 2.29
6199 7461 3.089784 CGACTGGGCCGATTTTCG 58.910 61.111 0.00 0.00 40.07 3.46
6200 7462 2.791927 GCGACTGGGCCGATTTTC 59.208 61.111 0.00 0.00 0.00 2.29
6201 7463 3.124921 CGCGACTGGGCCGATTTT 61.125 61.111 0.00 0.00 0.00 1.82
6210 7472 4.473520 ATTCTGGGGCGCGACTGG 62.474 66.667 13.91 1.92 0.00 4.00


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

AutoCloner maintained by Alex Coulton.