Multiple sequence alignment - TraesCS5D01G092700

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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 TraesCS5D01G092700 chr5D 100.000 6443 0 0 1 6443 101462219 101455777 0.000000e+00 11899.0
1 TraesCS5D01G092700 chr5D 85.428 549 54 11 3695 4229 35871877 35871341 1.220000e-151 547.0
2 TraesCS5D01G092700 chr5D 78.868 265 46 6 1587 1850 101698395 101698650 3.090000e-38 171.0
3 TraesCS5D01G092700 chr5D 94.505 91 5 0 5712 5802 101456327 101456237 2.420000e-29 141.0
4 TraesCS5D01G092700 chr5D 94.505 91 5 0 5893 5983 101456508 101456418 2.420000e-29 141.0
5 TraesCS5D01G092700 chr5A 96.341 5684 145 20 1 5636 98977020 98982688 0.000000e+00 9286.0
6 TraesCS5D01G092700 chr5A 93.488 645 41 1 5800 6443 98982785 98983429 0.000000e+00 957.0
7 TraesCS5D01G092700 chr5A 85.093 322 33 6 3922 4229 324967038 324967358 1.350000e-81 315.0
8 TraesCS5D01G092700 chr5A 92.350 183 13 1 5708 5889 98982784 98982966 6.410000e-65 259.0
9 TraesCS5D01G092700 chr5A 78.491 265 45 6 1587 1850 98453605 98453352 5.170000e-36 163.0
10 TraesCS5D01G092700 chr5A 94.505 91 5 0 5709 5799 98982876 98982966 2.420000e-29 141.0
11 TraesCS5D01G092700 chr5A 92.157 51 2 1 261 311 98454563 98454515 3.220000e-08 71.3
12 TraesCS5D01G092700 chr5B 95.378 4760 121 23 1 4716 109890664 109885960 0.000000e+00 7480.0
13 TraesCS5D01G092700 chr5B 84.814 698 35 15 4999 5660 109885602 109884940 2.530000e-178 636.0
14 TraesCS5D01G092700 chr5B 95.902 244 9 1 4715 4958 109885836 109885594 1.680000e-105 394.0
15 TraesCS5D01G092700 chr5B 87.226 274 29 1 6170 6443 109775231 109774964 2.260000e-79 307.0
16 TraesCS5D01G092700 chr5B 83.439 314 38 6 3700 4012 311042350 311042050 4.920000e-71 279.0
17 TraesCS5D01G092700 chr5B 78.491 265 45 8 1587 1850 110113544 110113797 5.170000e-36 163.0
18 TraesCS5D01G092700 chr5B 90.741 54 3 1 258 311 110112465 110112516 3.220000e-08 71.3
19 TraesCS5D01G092700 chrUn 88.172 93 10 1 504 595 310268353 310268445 6.830000e-20 110.0
20 TraesCS5D01G092700 chrUn 88.172 93 10 1 504 595 347986661 347986753 6.830000e-20 110.0
21 TraesCS5D01G092700 chrUn 88.889 90 9 1 507 595 383981134 383981045 6.830000e-20 110.0
22 TraesCS5D01G092700 chr1B 88.889 90 9 1 507 595 666348853 666348764 6.830000e-20 110.0
23 TraesCS5D01G092700 chr2A 86.076 79 11 0 507 585 621679939 621680017 1.150000e-12 86.1
24 TraesCS5D01G092700 chr6D 92.727 55 3 1 543 596 448785174 448785228 1.930000e-10 78.7
25 TraesCS5D01G092700 chr2D 84.286 70 11 0 6278 6347 158253118 158253049 1.160000e-07 69.4
26 TraesCS5D01G092700 chr1A 77.586 116 23 2 5601 5714 139139131 139139017 4.170000e-07 67.6
27 TraesCS5D01G092700 chr7B 92.308 39 3 0 5609 5647 477425182 477425144 1.000000e-03 56.5


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 TraesCS5D01G092700 chr5D 101455777 101462219 6442 True 11899.000000 11899 100.000000 1 6443 1 chr5D.!!$R2 6442
1 TraesCS5D01G092700 chr5D 35871341 35871877 536 True 547.000000 547 85.428000 3695 4229 1 chr5D.!!$R1 534
2 TraesCS5D01G092700 chr5A 98977020 98983429 6409 False 2660.750000 9286 94.171000 1 6443 4 chr5A.!!$F2 6442
3 TraesCS5D01G092700 chr5B 109884940 109890664 5724 True 2836.666667 7480 92.031333 1 5660 3 chr5B.!!$R3 5659

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
178 193 0.958822 GGTGACGTTTTCCCTGCAAT 59.041 50.000 0.00 0.0 0.00 3.56 F
1542 1602 0.690762 GCTTCTAACCCCTGACCACA 59.309 55.000 0.00 0.0 0.00 4.17 F
1768 1829 0.592637 TCAACAATGCGCTTCACTGG 59.407 50.000 9.73 0.0 0.00 4.00 F
3447 3514 2.621055 TGAAAAATGAACACGAGGTGGG 59.379 45.455 0.42 0.0 37.94 4.61 F
3509 3576 2.159627 GGTGCTACTTCAACACGGAATG 59.840 50.000 0.00 0.0 35.11 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1829 3.862264 GCTTTGCTTTTTCCTCCATGACC 60.862 47.826 0.00 0.00 0.00 4.02 R
2496 2558 0.036732 CCACTTCCCTGCAGTGCTAA 59.963 55.000 17.60 4.79 40.43 3.09 R
3488 3555 1.873698 TTCCGTGTTGAAGTAGCACC 58.126 50.000 0.00 0.00 37.22 5.01 R
5233 5493 2.570302 AGGACAGCTAAAATACGGTGGT 59.430 45.455 0.00 0.00 33.22 4.16 R
5488 5757 1.788308 TCGTCGCGGTCAAAAACTAAG 59.212 47.619 6.13 0.00 0.00 2.18 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
22 23 5.571784 CAGATTTCTGCCTGCATTTCTTA 57.428 39.130 0.00 0.00 37.15 2.10
89 90 2.959465 ACTCCCCTTTCTGTCCTTTG 57.041 50.000 0.00 0.00 0.00 2.77
132 147 2.203470 TGCAGATCTGTTGCATCCAA 57.797 45.000 23.38 0.00 45.89 3.53
133 148 2.730382 TGCAGATCTGTTGCATCCAAT 58.270 42.857 23.38 0.00 45.89 3.16
134 149 3.888583 TGCAGATCTGTTGCATCCAATA 58.111 40.909 23.38 0.00 45.89 1.90
135 150 4.271661 TGCAGATCTGTTGCATCCAATAA 58.728 39.130 23.38 0.00 45.89 1.40
136 151 4.705991 TGCAGATCTGTTGCATCCAATAAA 59.294 37.500 23.38 0.00 45.89 1.40
137 152 5.361571 TGCAGATCTGTTGCATCCAATAAAT 59.638 36.000 23.38 0.00 45.89 1.40
138 153 5.919141 GCAGATCTGTTGCATCCAATAAATC 59.081 40.000 23.38 0.00 41.17 2.17
139 154 6.140786 CAGATCTGTTGCATCCAATAAATCG 58.859 40.000 14.95 0.00 32.75 3.34
140 155 4.898829 TCTGTTGCATCCAATAAATCGG 57.101 40.909 0.00 0.00 32.75 4.18
141 156 4.269183 TCTGTTGCATCCAATAAATCGGT 58.731 39.130 0.00 0.00 32.75 4.69
142 157 4.096231 TCTGTTGCATCCAATAAATCGGTG 59.904 41.667 0.00 0.00 32.75 4.94
143 158 3.115554 GTTGCATCCAATAAATCGGTGC 58.884 45.455 0.00 0.00 32.75 5.01
144 159 2.653726 TGCATCCAATAAATCGGTGCT 58.346 42.857 0.00 0.00 33.32 4.40
145 160 3.814625 TGCATCCAATAAATCGGTGCTA 58.185 40.909 0.00 0.00 33.32 3.49
146 161 3.563808 TGCATCCAATAAATCGGTGCTAC 59.436 43.478 0.00 0.00 33.32 3.58
147 162 3.058224 GCATCCAATAAATCGGTGCTACC 60.058 47.826 0.00 0.00 34.05 3.18
148 163 3.916359 TCCAATAAATCGGTGCTACCA 57.084 42.857 6.21 0.00 38.47 3.25
157 172 1.679898 GGTGCTACCACTCCTGCTT 59.320 57.895 1.01 0.00 41.75 3.91
178 193 0.958822 GGTGACGTTTTCCCTGCAAT 59.041 50.000 0.00 0.00 0.00 3.56
232 252 2.450500 CCATATTTCTGGGATGGGGGAA 59.549 50.000 0.00 0.00 37.13 3.97
235 255 3.801511 ATTTCTGGGATGGGGGAATTT 57.198 42.857 0.00 0.00 0.00 1.82
238 285 2.006873 TCTGGGATGGGGGAATTTTGA 58.993 47.619 0.00 0.00 0.00 2.69
252 299 6.152831 GGGGAATTTTGATGTAAGCTGTAACT 59.847 38.462 0.00 0.00 0.00 2.24
253 300 7.338449 GGGGAATTTTGATGTAAGCTGTAACTA 59.662 37.037 0.00 0.00 0.00 2.24
290 342 8.100508 AGAAGAGGTAAAATAAAGAAGCACAC 57.899 34.615 0.00 0.00 0.00 3.82
320 372 8.795513 GTGTTATCCCTATTCCTCTCTTAGTAC 58.204 40.741 0.00 0.00 0.00 2.73
344 400 7.357303 ACTTGGTACATCAACGTAAACATTTC 58.643 34.615 0.00 0.00 39.30 2.17
361 420 5.543714 ACATTTCCGGGAAACATAAAAACC 58.456 37.500 23.69 0.00 34.23 3.27
434 493 2.519377 ACAGATTCGACACGGAAACA 57.481 45.000 0.00 0.00 0.00 2.83
527 586 1.338674 TGTGGTTACAAGATGCTCCCG 60.339 52.381 0.00 0.00 32.88 5.14
818 878 4.202326 ACCGGTAATGACAGAGTTTTCAGT 60.202 41.667 4.49 0.00 0.00 3.41
916 976 3.066760 CCTAGGTTCCGATTTTCATTGCC 59.933 47.826 0.00 0.00 0.00 4.52
1032 1092 5.764686 TGATCTTTCATGCCCACACATATAC 59.235 40.000 0.00 0.00 0.00 1.47
1033 1093 5.109500 TCTTTCATGCCCACACATATACA 57.891 39.130 0.00 0.00 0.00 2.29
1419 1479 7.222000 TGAACTTGTACCAAAGAAAGTTTGT 57.778 32.000 7.84 0.00 41.62 2.83
1542 1602 0.690762 GCTTCTAACCCCTGACCACA 59.309 55.000 0.00 0.00 0.00 4.17
1768 1829 0.592637 TCAACAATGCGCTTCACTGG 59.407 50.000 9.73 0.00 0.00 4.00
1983 2044 2.770164 AACACAGTACTCCCATCTGC 57.230 50.000 0.00 0.00 33.12 4.26
2026 2087 2.806019 GCATGGACATGGTCTCTGCTAG 60.806 54.545 13.63 0.00 39.16 3.42
2192 2254 8.612619 CAGTTAGAAATGTTTTGACTGTACACT 58.387 33.333 0.00 0.00 0.00 3.55
2218 2280 7.130303 TCTAGGATGTCATCTAATTACGACG 57.870 40.000 12.54 0.00 0.00 5.12
2473 2535 4.421131 TCTCTAAAGGAAGAGCTGGAAGT 58.579 43.478 0.00 0.00 42.36 3.01
2496 2558 3.658725 AGGGAGTCAAGCCATGTACTAT 58.341 45.455 0.00 0.00 0.00 2.12
2573 2635 3.777087 TCCTTGGAGCAATTGGAAATCA 58.223 40.909 7.72 0.00 0.00 2.57
2896 2962 3.126171 GTGTTTGTCAGCGCCATGTAATA 59.874 43.478 2.29 0.00 0.00 0.98
3447 3514 2.621055 TGAAAAATGAACACGAGGTGGG 59.379 45.455 0.42 0.00 37.94 4.61
3509 3576 2.159627 GGTGCTACTTCAACACGGAATG 59.840 50.000 0.00 0.00 35.11 2.67
4619 4724 5.991328 ATTATTTCGTGCAGTACCATGAG 57.009 39.130 0.00 0.00 32.75 2.90
4674 4779 9.289782 GAATAAGTTAATATGAATGAGCCCACT 57.710 33.333 0.00 0.00 0.00 4.00
4863 5093 5.960811 TGTGAGATCCTAGAAATTCTGGACT 59.039 40.000 7.98 10.51 30.44 3.85
4910 5140 8.422973 TTTTCTGAAGGAAAAACATGAACATG 57.577 30.769 12.43 12.43 46.84 3.21
5161 5392 3.959293 TGGCAGAACATTGTCATGATCT 58.041 40.909 0.00 0.00 41.92 2.75
5233 5493 1.391157 AACGCAAGCAGCCCTTTTGA 61.391 50.000 0.00 0.00 45.62 2.69
5237 5497 0.032540 CAAGCAGCCCTTTTGACCAC 59.967 55.000 0.00 0.00 0.00 4.16
5272 5532 5.844004 TGTCCTCTTAGTTTCAGTGTTCTC 58.156 41.667 0.00 0.00 0.00 2.87
5381 5641 3.026311 GTGCTGCACTGCAAACGC 61.026 61.111 24.68 6.00 45.12 4.84
5488 5757 2.683362 GCAACTGGCCTGGTAAATCTAC 59.317 50.000 14.82 0.00 36.11 2.59
5512 5781 0.940519 TTTTTGACCGCGACGACGAT 60.941 50.000 8.23 0.00 42.66 3.73
5520 5789 0.493146 CGCGACGACGATGATGTTAC 59.507 55.000 12.29 0.00 42.66 2.50
5606 5875 2.738846 GAGCAAGCGACTGAGAAAATCA 59.261 45.455 0.00 0.00 36.21 2.57
5649 5985 3.278574 TGAAACTTCCTGTGTCCTTGTG 58.721 45.455 0.00 0.00 31.90 3.33
5661 5997 2.224523 TGTCCTTGTGTGAGATCCAACC 60.225 50.000 0.00 0.00 0.00 3.77
5664 6000 2.224621 CCTTGTGTGAGATCCAACCACT 60.225 50.000 0.00 0.00 0.00 4.00
5665 6001 3.007940 CCTTGTGTGAGATCCAACCACTA 59.992 47.826 0.00 0.00 0.00 2.74
5666 6002 4.323792 CCTTGTGTGAGATCCAACCACTAT 60.324 45.833 0.00 0.00 0.00 2.12
5667 6003 4.206477 TGTGTGAGATCCAACCACTATG 57.794 45.455 0.00 0.00 0.00 2.23
5668 6004 3.837731 TGTGTGAGATCCAACCACTATGA 59.162 43.478 0.00 0.00 0.00 2.15
5669 6005 4.285775 TGTGTGAGATCCAACCACTATGAA 59.714 41.667 0.00 0.00 0.00 2.57
5670 6006 5.045651 TGTGTGAGATCCAACCACTATGAAT 60.046 40.000 0.00 0.00 0.00 2.57
5671 6007 5.525378 GTGTGAGATCCAACCACTATGAATC 59.475 44.000 0.00 0.00 0.00 2.52
5672 6008 5.426509 TGTGAGATCCAACCACTATGAATCT 59.573 40.000 0.00 0.00 0.00 2.40
5673 6009 5.757320 GTGAGATCCAACCACTATGAATCTG 59.243 44.000 0.00 0.00 0.00 2.90
5674 6010 5.662657 TGAGATCCAACCACTATGAATCTGA 59.337 40.000 0.00 0.00 0.00 3.27
5675 6011 6.172136 AGATCCAACCACTATGAATCTGAG 57.828 41.667 0.00 0.00 0.00 3.35
5676 6012 4.760530 TCCAACCACTATGAATCTGAGG 57.239 45.455 0.00 0.00 0.00 3.86
5677 6013 4.104086 TCCAACCACTATGAATCTGAGGT 58.896 43.478 0.00 0.00 0.00 3.85
5678 6014 5.277250 TCCAACCACTATGAATCTGAGGTA 58.723 41.667 0.00 0.00 0.00 3.08
5679 6015 5.724370 TCCAACCACTATGAATCTGAGGTAA 59.276 40.000 0.00 0.00 0.00 2.85
5680 6016 6.214615 TCCAACCACTATGAATCTGAGGTAAA 59.785 38.462 0.00 0.00 0.00 2.01
5681 6017 6.316390 CCAACCACTATGAATCTGAGGTAAAC 59.684 42.308 0.00 0.00 0.00 2.01
5682 6018 5.661458 ACCACTATGAATCTGAGGTAAACG 58.339 41.667 0.00 0.00 0.00 3.60
5683 6019 5.050490 CCACTATGAATCTGAGGTAAACGG 58.950 45.833 0.00 0.00 0.00 4.44
5684 6020 5.050490 CACTATGAATCTGAGGTAAACGGG 58.950 45.833 0.00 0.00 0.00 5.28
5685 6021 4.715297 ACTATGAATCTGAGGTAAACGGGT 59.285 41.667 0.00 0.00 0.00 5.28
5686 6022 3.328382 TGAATCTGAGGTAAACGGGTG 57.672 47.619 0.00 0.00 0.00 4.61
5687 6023 2.027561 TGAATCTGAGGTAAACGGGTGG 60.028 50.000 0.00 0.00 0.00 4.61
5688 6024 0.252197 ATCTGAGGTAAACGGGTGGC 59.748 55.000 0.00 0.00 0.00 5.01
5689 6025 1.122632 TCTGAGGTAAACGGGTGGCA 61.123 55.000 0.00 0.00 0.00 4.92
5690 6026 0.673644 CTGAGGTAAACGGGTGGCAG 60.674 60.000 0.00 0.00 0.00 4.85
5691 6027 1.376812 GAGGTAAACGGGTGGCAGG 60.377 63.158 0.00 0.00 0.00 4.85
5692 6028 2.360726 GGTAAACGGGTGGCAGGG 60.361 66.667 0.00 0.00 0.00 4.45
5693 6029 2.751688 GTAAACGGGTGGCAGGGA 59.248 61.111 0.00 0.00 0.00 4.20
5694 6030 1.073548 GTAAACGGGTGGCAGGGAA 59.926 57.895 0.00 0.00 0.00 3.97
5695 6031 0.958876 GTAAACGGGTGGCAGGGAAG 60.959 60.000 0.00 0.00 0.00 3.46
5696 6032 2.132089 TAAACGGGTGGCAGGGAAGG 62.132 60.000 0.00 0.00 0.00 3.46
5700 6036 4.748144 GGTGGCAGGGAAGGGCTG 62.748 72.222 0.00 0.00 0.00 4.85
5701 6037 4.748144 GTGGCAGGGAAGGGCTGG 62.748 72.222 0.00 0.00 0.00 4.85
5704 6040 3.015145 GCAGGGAAGGGCTGGGTA 61.015 66.667 0.00 0.00 0.00 3.69
5705 6041 3.049080 GCAGGGAAGGGCTGGGTAG 62.049 68.421 0.00 0.00 0.00 3.18
5706 6042 2.042930 AGGGAAGGGCTGGGTAGG 59.957 66.667 0.00 0.00 0.00 3.18
5718 6054 2.264794 GGTAGGTGTGTGCTCCCG 59.735 66.667 0.00 0.00 0.00 5.14
5743 6079 4.160252 ACCTGTGTGCCCATATGAATTTTC 59.840 41.667 3.65 0.00 0.00 2.29
5752 6088 6.826231 TGCCCATATGAATTTTCGAGAACTTA 59.174 34.615 3.65 0.00 0.00 2.24
5759 6095 5.710099 TGAATTTTCGAGAACTTAGGGCAAT 59.290 36.000 0.00 0.00 0.00 3.56
5765 6101 3.129287 CGAGAACTTAGGGCAATTGCAAT 59.871 43.478 30.32 20.14 44.36 3.56
5768 6104 2.181975 ACTTAGGGCAATTGCAATGCT 58.818 42.857 30.32 13.52 43.34 3.79
5769 6105 2.167075 ACTTAGGGCAATTGCAATGCTC 59.833 45.455 30.32 21.83 44.80 4.26
5808 6144 4.385825 TCACTAAATGTTCGTTTGCTCCT 58.614 39.130 0.90 0.00 0.00 3.69
5827 6163 3.424300 CACCTGCGTGCCCATATG 58.576 61.111 0.00 0.00 32.04 1.78
5828 6164 1.153188 CACCTGCGTGCCCATATGA 60.153 57.895 3.65 0.00 32.04 2.15
5829 6165 0.747644 CACCTGCGTGCCCATATGAA 60.748 55.000 3.65 0.00 32.04 2.57
5830 6166 0.183492 ACCTGCGTGCCCATATGAAT 59.817 50.000 3.65 0.00 0.00 2.57
5831 6167 1.321474 CCTGCGTGCCCATATGAATT 58.679 50.000 3.65 0.00 0.00 2.17
5832 6168 1.682854 CCTGCGTGCCCATATGAATTT 59.317 47.619 3.65 0.00 0.00 1.82
5833 6169 2.101249 CCTGCGTGCCCATATGAATTTT 59.899 45.455 3.65 0.00 0.00 1.82
5834 6170 3.430651 CCTGCGTGCCCATATGAATTTTT 60.431 43.478 3.65 0.00 0.00 1.94
5835 6171 3.519579 TGCGTGCCCATATGAATTTTTG 58.480 40.909 3.65 0.00 0.00 2.44
5836 6172 3.194329 TGCGTGCCCATATGAATTTTTGA 59.806 39.130 3.65 0.00 0.00 2.69
5837 6173 3.798337 GCGTGCCCATATGAATTTTTGAG 59.202 43.478 3.65 0.00 0.00 3.02
5838 6174 4.439974 GCGTGCCCATATGAATTTTTGAGA 60.440 41.667 3.65 0.00 0.00 3.27
5839 6175 5.649557 CGTGCCCATATGAATTTTTGAGAA 58.350 37.500 3.65 0.00 0.00 2.87
5840 6176 5.516339 CGTGCCCATATGAATTTTTGAGAAC 59.484 40.000 3.65 0.00 0.00 3.01
5841 6177 6.625740 CGTGCCCATATGAATTTTTGAGAACT 60.626 38.462 3.65 0.00 0.00 3.01
5842 6178 7.099120 GTGCCCATATGAATTTTTGAGAACTT 58.901 34.615 3.65 0.00 0.00 2.66
5843 6179 8.250332 GTGCCCATATGAATTTTTGAGAACTTA 58.750 33.333 3.65 0.00 0.00 2.24
5844 6180 8.469200 TGCCCATATGAATTTTTGAGAACTTAG 58.531 33.333 3.65 0.00 0.00 2.18
5845 6181 7.922811 GCCCATATGAATTTTTGAGAACTTAGG 59.077 37.037 3.65 0.00 0.00 2.69
5846 6182 8.416329 CCCATATGAATTTTTGAGAACTTAGGG 58.584 37.037 3.65 0.00 0.00 3.53
5847 6183 7.922811 CCATATGAATTTTTGAGAACTTAGGGC 59.077 37.037 3.65 0.00 0.00 5.19
5848 6184 6.916360 ATGAATTTTTGAGAACTTAGGGCA 57.084 33.333 0.00 0.00 0.00 5.36
5849 6185 6.723298 TGAATTTTTGAGAACTTAGGGCAA 57.277 33.333 0.00 0.00 0.00 4.52
5850 6186 7.301868 TGAATTTTTGAGAACTTAGGGCAAT 57.698 32.000 0.00 0.00 0.00 3.56
5851 6187 7.734942 TGAATTTTTGAGAACTTAGGGCAATT 58.265 30.769 0.00 0.00 0.00 2.32
5852 6188 7.656948 TGAATTTTTGAGAACTTAGGGCAATTG 59.343 33.333 0.00 0.00 0.00 2.32
5853 6189 4.519540 TTTGAGAACTTAGGGCAATTGC 57.480 40.909 22.47 22.47 41.14 3.56
5854 6190 3.153369 TGAGAACTTAGGGCAATTGCA 57.847 42.857 30.32 8.86 44.36 4.08
5855 6191 3.495331 TGAGAACTTAGGGCAATTGCAA 58.505 40.909 30.32 15.96 44.36 4.08
5856 6192 3.255642 TGAGAACTTAGGGCAATTGCAAC 59.744 43.478 30.32 21.92 44.36 4.17
5857 6193 2.228822 AGAACTTAGGGCAATTGCAACG 59.771 45.455 30.32 15.32 44.36 4.10
5858 6194 0.243636 ACTTAGGGCAATTGCAACGC 59.756 50.000 30.32 13.74 44.36 4.84
5859 6195 0.527565 CTTAGGGCAATTGCAACGCT 59.472 50.000 30.32 17.33 44.36 5.07
5860 6196 1.742831 CTTAGGGCAATTGCAACGCTA 59.257 47.619 30.32 16.39 44.36 4.26
5861 6197 2.051334 TAGGGCAATTGCAACGCTAT 57.949 45.000 30.32 10.20 44.36 2.97
5862 6198 0.740737 AGGGCAATTGCAACGCTATC 59.259 50.000 30.32 11.22 44.36 2.08
5863 6199 0.455410 GGGCAATTGCAACGCTATCA 59.545 50.000 30.32 0.00 44.36 2.15
5864 6200 1.067516 GGGCAATTGCAACGCTATCAT 59.932 47.619 30.32 0.00 44.36 2.45
5865 6201 2.388121 GGCAATTGCAACGCTATCATC 58.612 47.619 30.32 5.99 44.36 2.92
5866 6202 2.223548 GGCAATTGCAACGCTATCATCA 60.224 45.455 30.32 0.00 44.36 3.07
5867 6203 3.437428 GCAATTGCAACGCTATCATCAA 58.563 40.909 25.36 0.00 41.59 2.57
5868 6204 3.858812 GCAATTGCAACGCTATCATCAAA 59.141 39.130 25.36 0.00 41.59 2.69
5869 6205 4.326817 GCAATTGCAACGCTATCATCAAAA 59.673 37.500 25.36 0.00 41.59 2.44
5870 6206 5.005971 GCAATTGCAACGCTATCATCAAAAT 59.994 36.000 25.36 0.00 41.59 1.82
5871 6207 6.198778 GCAATTGCAACGCTATCATCAAAATA 59.801 34.615 25.36 0.00 41.59 1.40
5872 6208 7.566328 GCAATTGCAACGCTATCATCAAAATAG 60.566 37.037 25.36 0.00 41.59 1.73
5873 6209 6.676237 TTGCAACGCTATCATCAAAATAGA 57.324 33.333 0.00 0.00 0.00 1.98
5874 6210 6.866010 TGCAACGCTATCATCAAAATAGAT 57.134 33.333 0.00 0.00 0.00 1.98
5875 6211 7.961325 TGCAACGCTATCATCAAAATAGATA 57.039 32.000 0.00 0.00 0.00 1.98
5876 6212 8.021955 TGCAACGCTATCATCAAAATAGATAG 57.978 34.615 0.00 0.00 42.48 2.08
5890 6226 9.378551 TCAAAATAGATAGCACTAAATGTTCGT 57.621 29.630 0.00 0.00 0.00 3.85
5891 6227 9.988350 CAAAATAGATAGCACTAAATGTTCGTT 57.012 29.630 0.00 0.00 0.00 3.85
5893 6229 9.988350 AAATAGATAGCACTAAATGTTCGTTTG 57.012 29.630 0.90 0.00 0.00 2.93
5894 6230 5.869350 AGATAGCACTAAATGTTCGTTTGC 58.131 37.500 0.90 0.00 0.00 3.68
5895 6231 5.643777 AGATAGCACTAAATGTTCGTTTGCT 59.356 36.000 0.00 0.00 0.00 3.91
5896 6232 4.147219 AGCACTAAATGTTCGTTTGCTC 57.853 40.909 0.00 0.00 0.00 4.26
5897 6233 3.058224 AGCACTAAATGTTCGTTTGCTCC 60.058 43.478 0.00 0.00 0.00 4.70
5898 6234 3.821841 CACTAAATGTTCGTTTGCTCCC 58.178 45.455 0.90 0.00 0.00 4.30
5899 6235 2.482721 ACTAAATGTTCGTTTGCTCCCG 59.517 45.455 0.90 0.00 0.00 5.14
5900 6236 0.039527 AAATGTTCGTTTGCTCCCGC 60.040 50.000 0.00 0.00 0.00 6.13
5901 6237 1.169661 AATGTTCGTTTGCTCCCGCA 61.170 50.000 0.00 0.00 46.24 5.69
5942 6278 5.371115 TTTTCGAGAACTTAGGGCAATTG 57.629 39.130 0.00 0.00 0.00 2.32
5963 6299 3.243334 TGCAACGCTGATCATCAAAACAA 60.243 39.130 0.00 0.00 0.00 2.83
5987 6323 9.773328 CAAATATCACTAAATGTTCGTTGTCAT 57.227 29.630 0.00 0.00 0.00 3.06
5992 6328 0.521291 AATGTTCGTTGTCATGCCCG 59.479 50.000 0.00 0.00 0.00 6.13
6001 6337 2.609299 TCATGCCCGGACTTCCCA 60.609 61.111 0.73 0.00 34.14 4.37
6089 6425 4.308458 CGTTGGCCTCCACGTCCA 62.308 66.667 3.32 0.00 30.78 4.02
6091 6427 1.303317 GTTGGCCTCCACGTCCAAT 60.303 57.895 3.32 0.00 41.35 3.16
6117 6453 3.119096 GAGGTGGTTTCGCTCCGC 61.119 66.667 0.00 0.00 35.03 5.54
6147 6483 0.105964 CGGAACAACCACCTCTCACA 59.894 55.000 0.00 0.00 38.90 3.58
6177 6513 3.564027 GGCGCTGCACACGGTATC 61.564 66.667 7.64 0.00 0.00 2.24
6180 6516 2.224217 CGCTGCACACGGTATCGAG 61.224 63.158 0.34 0.00 40.11 4.04
6211 6547 1.442526 GCTTGTCCATGATGCTCGGG 61.443 60.000 0.00 0.00 0.00 5.14
6237 6573 3.771160 GACCATGGTCCGACGGCT 61.771 66.667 31.37 0.00 39.08 5.52
6273 6609 1.775459 TCCCCTGCGATCTAGTACTCT 59.225 52.381 0.00 0.00 0.00 3.24
6280 6616 1.268352 CGATCTAGTACTCTGCCAGCC 59.732 57.143 0.00 0.00 0.00 4.85
6284 6620 1.135915 CTAGTACTCTGCCAGCCAGTG 59.864 57.143 0.00 0.00 42.38 3.66
6297 6633 4.154347 CAGTGCCCCTCGAGGAGC 62.154 72.222 33.39 31.36 38.24 4.70
6321 6657 1.834263 AGGTTGTATCACTGCTCCTCC 59.166 52.381 0.00 0.00 0.00 4.30
6332 6668 2.362369 GCTCCTCCTGCAGTAGCCA 61.362 63.158 13.81 0.00 41.13 4.75
6360 6696 2.584791 GACACCGACAATGCATGTTTC 58.415 47.619 0.00 0.00 44.12 2.78
6363 6699 1.812571 ACCGACAATGCATGTTTCTCC 59.187 47.619 0.00 0.00 44.12 3.71
6408 6744 4.150980 CGGTTGTAGTGTTATTTCGCTTGA 59.849 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.133221 ACAAAACTGGAATGTAGCTTCAGT 58.867 37.500 0.00 0.00 0.00 3.41
89 90 2.029020 GGGGAAAATCAAGCAGGTCAAC 60.029 50.000 0.00 0.00 0.00 3.18
132 147 3.039011 AGGAGTGGTAGCACCGATTTAT 58.961 45.455 20.99 0.69 42.58 1.40
133 148 2.167693 CAGGAGTGGTAGCACCGATTTA 59.832 50.000 20.99 0.00 42.58 1.40
134 149 1.066143 CAGGAGTGGTAGCACCGATTT 60.066 52.381 20.99 2.25 42.58 2.17
135 150 0.537188 CAGGAGTGGTAGCACCGATT 59.463 55.000 20.99 2.65 42.58 3.34
136 151 1.961180 GCAGGAGTGGTAGCACCGAT 61.961 60.000 20.99 3.05 42.58 4.18
137 152 2.646175 GCAGGAGTGGTAGCACCGA 61.646 63.158 20.99 0.00 42.58 4.69
138 153 2.125512 GCAGGAGTGGTAGCACCG 60.126 66.667 20.99 8.91 42.58 4.94
139 154 0.902531 TAAGCAGGAGTGGTAGCACC 59.097 55.000 20.99 12.38 39.22 5.01
140 155 1.134670 CCTAAGCAGGAGTGGTAGCAC 60.135 57.143 17.29 17.29 45.91 4.40
141 156 1.195115 CCTAAGCAGGAGTGGTAGCA 58.805 55.000 0.00 0.00 45.91 3.49
142 157 1.134670 CACCTAAGCAGGAGTGGTAGC 60.135 57.143 0.00 0.00 45.91 3.58
143 158 2.166664 GTCACCTAAGCAGGAGTGGTAG 59.833 54.545 0.00 0.00 45.91 3.18
144 159 2.176889 GTCACCTAAGCAGGAGTGGTA 58.823 52.381 0.00 0.00 45.91 3.25
145 160 0.977395 GTCACCTAAGCAGGAGTGGT 59.023 55.000 0.00 0.00 45.91 4.16
146 161 0.108615 CGTCACCTAAGCAGGAGTGG 60.109 60.000 0.00 0.00 45.91 4.00
147 162 0.603569 ACGTCACCTAAGCAGGAGTG 59.396 55.000 0.00 0.00 45.91 3.51
148 163 1.339097 AACGTCACCTAAGCAGGAGT 58.661 50.000 0.00 0.00 45.91 3.85
157 172 0.759959 TGCAGGGAAAACGTCACCTA 59.240 50.000 0.00 0.00 0.00 3.08
193 208 9.770097 GAAATATGGTGTTTCTCTGATGATAGA 57.230 33.333 0.00 0.00 33.79 1.98
194 209 9.775854 AGAAATATGGTGTTTCTCTGATGATAG 57.224 33.333 0.00 0.00 40.85 2.08
196 211 7.501559 CCAGAAATATGGTGTTTCTCTGATGAT 59.498 37.037 0.00 0.00 42.38 2.45
232 252 8.960591 AGCAATAGTTACAGCTTACATCAAAAT 58.039 29.630 0.00 0.00 32.52 1.82
235 255 6.878923 ACAGCAATAGTTACAGCTTACATCAA 59.121 34.615 0.00 0.00 34.61 2.57
238 285 7.607991 AGAAACAGCAATAGTTACAGCTTACAT 59.392 33.333 0.00 0.00 34.61 2.29
252 299 9.959721 ATTTTACCTCTTCTAGAAACAGCAATA 57.040 29.630 6.63 0.01 0.00 1.90
253 300 8.870075 ATTTTACCTCTTCTAGAAACAGCAAT 57.130 30.769 6.63 0.00 0.00 3.56
290 342 7.072263 AGAGAGGAATAGGGATAACACAATG 57.928 40.000 0.00 0.00 0.00 2.82
320 372 6.799925 GGAAATGTTTACGTTGATGTACCAAG 59.200 38.462 0.00 0.00 0.00 3.61
344 400 2.560981 AGCAGGTTTTTATGTTTCCCGG 59.439 45.455 0.00 0.00 0.00 5.73
434 493 7.366847 ACCAAGTGCTCTAGTTATATGTGAT 57.633 36.000 0.00 0.00 0.00 3.06
478 537 3.253230 TCGACATGCACACATACTTGAG 58.747 45.455 0.00 0.00 33.67 3.02
488 547 2.877786 ACAAATCAGTTCGACATGCACA 59.122 40.909 0.00 0.00 0.00 4.57
527 586 6.030548 AGCCAAAAGGCTTAAAAGATTCTC 57.969 37.500 0.00 0.00 43.30 2.87
712 772 2.048222 ACATCACACGGTGAGGCG 60.048 61.111 16.29 4.52 46.40 5.52
1156 1216 5.245751 TGTGCACCCAAATAAATGTTCTGAT 59.754 36.000 15.69 0.00 0.00 2.90
1542 1602 5.013704 TGTGGAAACCAGTAACCATACATCT 59.986 40.000 0.00 0.00 32.34 2.90
1768 1829 3.862264 GCTTTGCTTTTTCCTCCATGACC 60.862 47.826 0.00 0.00 0.00 4.02
2026 2087 5.587289 TGTGACAAACATAGAAAAGTTGCC 58.413 37.500 0.00 0.00 32.36 4.52
2152 2214 4.521130 TCTAACTGTGACTCACCATGTC 57.479 45.455 6.72 0.00 32.73 3.06
2192 2254 8.074370 CGTCGTAATTAGATGACATCCTAGAAA 58.926 37.037 11.92 0.39 35.44 2.52
2218 2280 2.382882 AGGTAGTAAACTACTCGCCCC 58.617 52.381 17.40 2.93 46.06 5.80
2329 2391 8.378172 TCACAGTACCAAAAAGAATAGAACAG 57.622 34.615 0.00 0.00 0.00 3.16
2473 2535 3.450904 AGTACATGGCTTGACTCCCTTA 58.549 45.455 7.45 0.00 0.00 2.69
2496 2558 0.036732 CCACTTCCCTGCAGTGCTAA 59.963 55.000 17.60 4.79 40.43 3.09
2573 2635 6.103997 CAGCAAGGATTAGCAATCAAAATGT 58.896 36.000 9.92 0.00 39.71 2.71
2896 2962 4.858850 TGTGCATAAAGATTCATCAGGGT 58.141 39.130 0.00 0.00 0.00 4.34
3310 3376 9.366216 GTAACTTCAACAAGGATTTTCAGTTTT 57.634 29.630 0.00 0.00 33.37 2.43
3447 3514 7.490402 CCTGGAGCACAAGAAATTTTCAATATC 59.510 37.037 11.53 2.33 0.00 1.63
3488 3555 1.873698 TTCCGTGTTGAAGTAGCACC 58.126 50.000 0.00 0.00 37.22 5.01
3509 3576 8.905702 CAATTCGCCTATATTCTTTATTGCAAC 58.094 33.333 0.00 0.00 0.00 4.17
3962 4029 3.604582 CTGTCCTGTCCTCCTTTTGATC 58.395 50.000 0.00 0.00 0.00 2.92
4354 4457 4.772886 ACTCATGGAGGGGTAAATGTAC 57.227 45.455 0.00 0.00 33.35 2.90
4355 4458 5.014755 ACAAACTCATGGAGGGGTAAATGTA 59.985 40.000 0.00 0.00 33.35 2.29
4619 4724 8.958043 GTGTTTGTATCAAAAGATCTCAAACAC 58.042 33.333 30.56 30.56 46.51 3.32
4908 5138 3.965379 TTTTCATGCAACATCAGCCAT 57.035 38.095 0.00 0.00 0.00 4.40
4953 5183 8.777578 TGTACTGTTATAGAGGTTACCATCAT 57.222 34.615 3.51 0.00 0.00 2.45
5161 5392 7.327518 CAGTACTAAACGATCACATAACACACA 59.672 37.037 0.00 0.00 0.00 3.72
5233 5493 2.570302 AGGACAGCTAAAATACGGTGGT 59.430 45.455 0.00 0.00 33.22 4.16
5237 5497 5.903810 ACTAAGAGGACAGCTAAAATACGG 58.096 41.667 0.00 0.00 0.00 4.02
5272 5532 4.154347 GCTGCCGGAGAGTCCAGG 62.154 72.222 5.05 0.00 35.91 4.45
5476 5743 8.440833 CGGTCAAAAACTAAGTAGATTTACCAG 58.559 37.037 10.92 0.00 29.69 4.00
5488 5757 1.788308 TCGTCGCGGTCAAAAACTAAG 59.212 47.619 6.13 0.00 0.00 2.18
5512 5781 0.615850 TGTGGGCCATCGTAACATCA 59.384 50.000 10.70 0.00 0.00 3.07
5520 5789 0.887247 TGTGATTTTGTGGGCCATCG 59.113 50.000 10.70 0.00 0.00 3.84
5636 5972 2.613977 GGATCTCACACAAGGACACAGG 60.614 54.545 0.00 0.00 0.00 4.00
5649 5985 5.757320 CAGATTCATAGTGGTTGGATCTCAC 59.243 44.000 0.00 0.00 37.34 3.51
5661 5997 5.050490 CCCGTTTACCTCAGATTCATAGTG 58.950 45.833 0.00 0.00 0.00 2.74
5664 6000 4.141801 CCACCCGTTTACCTCAGATTCATA 60.142 45.833 0.00 0.00 0.00 2.15
5665 6001 3.370527 CCACCCGTTTACCTCAGATTCAT 60.371 47.826 0.00 0.00 0.00 2.57
5666 6002 2.027561 CCACCCGTTTACCTCAGATTCA 60.028 50.000 0.00 0.00 0.00 2.57
5667 6003 2.629051 CCACCCGTTTACCTCAGATTC 58.371 52.381 0.00 0.00 0.00 2.52
5668 6004 1.339727 GCCACCCGTTTACCTCAGATT 60.340 52.381 0.00 0.00 0.00 2.40
5669 6005 0.252197 GCCACCCGTTTACCTCAGAT 59.748 55.000 0.00 0.00 0.00 2.90
5670 6006 1.122632 TGCCACCCGTTTACCTCAGA 61.123 55.000 0.00 0.00 0.00 3.27
5671 6007 0.673644 CTGCCACCCGTTTACCTCAG 60.674 60.000 0.00 0.00 0.00 3.35
5672 6008 1.373435 CTGCCACCCGTTTACCTCA 59.627 57.895 0.00 0.00 0.00 3.86
5673 6009 1.376812 CCTGCCACCCGTTTACCTC 60.377 63.158 0.00 0.00 0.00 3.85
5674 6010 2.754375 CCTGCCACCCGTTTACCT 59.246 61.111 0.00 0.00 0.00 3.08
5675 6011 2.360726 CCCTGCCACCCGTTTACC 60.361 66.667 0.00 0.00 0.00 2.85
5676 6012 0.958876 CTTCCCTGCCACCCGTTTAC 60.959 60.000 0.00 0.00 0.00 2.01
5677 6013 1.377229 CTTCCCTGCCACCCGTTTA 59.623 57.895 0.00 0.00 0.00 2.01
5678 6014 2.115266 CTTCCCTGCCACCCGTTT 59.885 61.111 0.00 0.00 0.00 3.60
5679 6015 3.966543 CCTTCCCTGCCACCCGTT 61.967 66.667 0.00 0.00 0.00 4.44
5683 6019 4.748144 CAGCCCTTCCCTGCCACC 62.748 72.222 0.00 0.00 0.00 4.61
5684 6020 4.748144 CCAGCCCTTCCCTGCCAC 62.748 72.222 0.00 0.00 0.00 5.01
5687 6023 3.015145 TACCCAGCCCTTCCCTGC 61.015 66.667 0.00 0.00 0.00 4.85
5688 6024 2.378634 CCTACCCAGCCCTTCCCTG 61.379 68.421 0.00 0.00 0.00 4.45
5689 6025 2.042930 CCTACCCAGCCCTTCCCT 59.957 66.667 0.00 0.00 0.00 4.20
5690 6026 2.286197 ACCTACCCAGCCCTTCCC 60.286 66.667 0.00 0.00 0.00 3.97
5691 6027 1.923909 ACACCTACCCAGCCCTTCC 60.924 63.158 0.00 0.00 0.00 3.46
5692 6028 1.299976 CACACCTACCCAGCCCTTC 59.700 63.158 0.00 0.00 0.00 3.46
5693 6029 1.463410 ACACACCTACCCAGCCCTT 60.463 57.895 0.00 0.00 0.00 3.95
5694 6030 2.207189 ACACACCTACCCAGCCCT 59.793 61.111 0.00 0.00 0.00 5.19
5695 6031 2.351276 CACACACCTACCCAGCCC 59.649 66.667 0.00 0.00 0.00 5.19
5696 6032 2.359975 GCACACACCTACCCAGCC 60.360 66.667 0.00 0.00 0.00 4.85
5697 6033 1.376037 GAGCACACACCTACCCAGC 60.376 63.158 0.00 0.00 0.00 4.85
5698 6034 1.296715 GGAGCACACACCTACCCAG 59.703 63.158 0.00 0.00 0.00 4.45
5699 6035 2.221299 GGGAGCACACACCTACCCA 61.221 63.158 0.00 0.00 37.50 4.51
5700 6036 2.669240 GGGAGCACACACCTACCC 59.331 66.667 0.00 0.00 0.00 3.69
5701 6037 2.264794 CGGGAGCACACACCTACC 59.735 66.667 0.00 0.00 0.00 3.18
5725 6061 4.522114 TCTCGAAAATTCATATGGGCACA 58.478 39.130 2.13 0.00 0.00 4.57
5743 6079 2.083774 TGCAATTGCCCTAAGTTCTCG 58.916 47.619 26.94 0.00 41.18 4.04
5752 6088 1.138266 GATGAGCATTGCAATTGCCCT 59.862 47.619 26.94 16.99 41.18 5.19
5759 6095 4.884247 TGTTTTGATGATGAGCATTGCAA 58.116 34.783 11.91 0.00 37.34 4.08
5765 6101 7.052248 AGTGATATCTGTTTTGATGATGAGCA 58.948 34.615 3.98 0.00 0.00 4.26
5822 6158 8.469200 TGCCCTAAGTTCTCAAAAATTCATATG 58.531 33.333 0.00 0.00 0.00 1.78
5823 6159 8.593945 TGCCCTAAGTTCTCAAAAATTCATAT 57.406 30.769 0.00 0.00 0.00 1.78
5824 6160 8.415950 TTGCCCTAAGTTCTCAAAAATTCATA 57.584 30.769 0.00 0.00 0.00 2.15
5825 6161 6.916360 TGCCCTAAGTTCTCAAAAATTCAT 57.084 33.333 0.00 0.00 0.00 2.57
5826 6162 6.723298 TTGCCCTAAGTTCTCAAAAATTCA 57.277 33.333 0.00 0.00 0.00 2.57
5827 6163 7.360353 GCAATTGCCCTAAGTTCTCAAAAATTC 60.360 37.037 20.06 0.00 34.31 2.17
5828 6164 6.427853 GCAATTGCCCTAAGTTCTCAAAAATT 59.572 34.615 20.06 0.00 34.31 1.82
5829 6165 5.934043 GCAATTGCCCTAAGTTCTCAAAAAT 59.066 36.000 20.06 0.00 34.31 1.82
5830 6166 5.163364 TGCAATTGCCCTAAGTTCTCAAAAA 60.163 36.000 26.94 0.00 41.18 1.94
5831 6167 4.343526 TGCAATTGCCCTAAGTTCTCAAAA 59.656 37.500 26.94 0.00 41.18 2.44
5832 6168 3.894427 TGCAATTGCCCTAAGTTCTCAAA 59.106 39.130 26.94 0.40 41.18 2.69
5833 6169 3.495331 TGCAATTGCCCTAAGTTCTCAA 58.505 40.909 26.94 0.87 41.18 3.02
5834 6170 3.153369 TGCAATTGCCCTAAGTTCTCA 57.847 42.857 26.94 1.08 41.18 3.27
5835 6171 3.670627 CGTTGCAATTGCCCTAAGTTCTC 60.671 47.826 26.94 2.76 41.18 2.87
5836 6172 2.228822 CGTTGCAATTGCCCTAAGTTCT 59.771 45.455 26.94 0.00 41.18 3.01
5837 6173 2.595386 CGTTGCAATTGCCCTAAGTTC 58.405 47.619 26.94 7.81 41.18 3.01
5838 6174 1.336795 GCGTTGCAATTGCCCTAAGTT 60.337 47.619 26.94 0.00 41.18 2.66
5839 6175 0.243636 GCGTTGCAATTGCCCTAAGT 59.756 50.000 26.94 0.00 41.18 2.24
5840 6176 0.527565 AGCGTTGCAATTGCCCTAAG 59.472 50.000 26.94 15.06 41.18 2.18
5841 6177 1.827681 TAGCGTTGCAATTGCCCTAA 58.172 45.000 26.94 12.51 41.18 2.69
5842 6178 1.946768 GATAGCGTTGCAATTGCCCTA 59.053 47.619 26.94 19.88 41.18 3.53
5843 6179 0.740737 GATAGCGTTGCAATTGCCCT 59.259 50.000 26.94 18.54 41.18 5.19
5844 6180 0.455410 TGATAGCGTTGCAATTGCCC 59.545 50.000 26.94 16.30 41.18 5.36
5845 6181 2.223548 TGATGATAGCGTTGCAATTGCC 60.224 45.455 26.94 12.00 41.18 4.52
5846 6182 3.069074 TGATGATAGCGTTGCAATTGC 57.931 42.857 23.69 23.69 42.50 3.56
5847 6183 6.578020 ATTTTGATGATAGCGTTGCAATTG 57.422 33.333 0.59 0.00 0.00 2.32
5848 6184 7.706159 TCTATTTTGATGATAGCGTTGCAATT 58.294 30.769 0.59 0.00 0.00 2.32
5849 6185 7.263100 TCTATTTTGATGATAGCGTTGCAAT 57.737 32.000 0.59 0.00 0.00 3.56
5850 6186 6.676237 TCTATTTTGATGATAGCGTTGCAA 57.324 33.333 0.00 0.00 0.00 4.08
5851 6187 6.866010 ATCTATTTTGATGATAGCGTTGCA 57.134 33.333 0.00 0.00 0.00 4.08
5864 6200 9.378551 ACGAACATTTAGTGCTATCTATTTTGA 57.621 29.630 0.00 0.00 0.00 2.69
5865 6201 9.988350 AACGAACATTTAGTGCTATCTATTTTG 57.012 29.630 0.00 0.00 0.00 2.44
5867 6203 9.988350 CAAACGAACATTTAGTGCTATCTATTT 57.012 29.630 0.00 0.00 0.00 1.40
5868 6204 8.122952 GCAAACGAACATTTAGTGCTATCTATT 58.877 33.333 0.00 0.00 0.00 1.73
5869 6205 7.495934 AGCAAACGAACATTTAGTGCTATCTAT 59.504 33.333 0.00 0.00 0.00 1.98
5870 6206 6.816640 AGCAAACGAACATTTAGTGCTATCTA 59.183 34.615 0.00 0.00 0.00 1.98
5871 6207 5.643777 AGCAAACGAACATTTAGTGCTATCT 59.356 36.000 0.00 0.00 0.00 1.98
5872 6208 5.869350 AGCAAACGAACATTTAGTGCTATC 58.131 37.500 0.00 0.00 0.00 2.08
5873 6209 5.163754 GGAGCAAACGAACATTTAGTGCTAT 60.164 40.000 0.00 0.00 0.00 2.97
5874 6210 4.153475 GGAGCAAACGAACATTTAGTGCTA 59.847 41.667 0.00 0.00 0.00 3.49
5875 6211 3.058224 GGAGCAAACGAACATTTAGTGCT 60.058 43.478 0.00 0.00 0.00 4.40
5876 6212 3.234386 GGAGCAAACGAACATTTAGTGC 58.766 45.455 0.00 0.00 0.00 4.40
5877 6213 3.666902 CGGGAGCAAACGAACATTTAGTG 60.667 47.826 0.00 0.00 0.00 2.74
5878 6214 2.482721 CGGGAGCAAACGAACATTTAGT 59.517 45.455 0.00 0.00 0.00 2.24
5879 6215 3.117434 CGGGAGCAAACGAACATTTAG 57.883 47.619 0.00 0.00 0.00 1.85
5898 6234 3.779850 ATATGGGCAGGCAGGTGCG 62.780 63.158 0.00 0.00 45.00 5.34
5899 6235 2.196776 ATATGGGCAGGCAGGTGC 59.803 61.111 0.00 0.00 43.19 5.01
5900 6236 0.106569 TTCATATGGGCAGGCAGGTG 60.107 55.000 2.13 0.00 0.00 4.00
5901 6237 0.855598 ATTCATATGGGCAGGCAGGT 59.144 50.000 2.13 0.00 0.00 4.00
5902 6238 2.005370 AATTCATATGGGCAGGCAGG 57.995 50.000 2.13 0.00 0.00 4.85
5903 6239 3.551454 CGAAAATTCATATGGGCAGGCAG 60.551 47.826 2.13 0.00 0.00 4.85
5904 6240 2.361757 CGAAAATTCATATGGGCAGGCA 59.638 45.455 2.13 0.00 0.00 4.75
5905 6241 2.622942 TCGAAAATTCATATGGGCAGGC 59.377 45.455 2.13 0.00 0.00 4.85
5906 6242 4.136796 TCTCGAAAATTCATATGGGCAGG 58.863 43.478 2.13 0.00 0.00 4.85
5907 6243 5.297776 AGTTCTCGAAAATTCATATGGGCAG 59.702 40.000 2.13 0.00 0.00 4.85
5908 6244 5.192927 AGTTCTCGAAAATTCATATGGGCA 58.807 37.500 2.13 0.00 0.00 5.36
5909 6245 5.757850 AGTTCTCGAAAATTCATATGGGC 57.242 39.130 2.13 0.00 0.00 5.36
5910 6246 7.041098 CCCTAAGTTCTCGAAAATTCATATGGG 60.041 40.741 2.13 0.00 0.00 4.00
5911 6247 7.520614 GCCCTAAGTTCTCGAAAATTCATATGG 60.521 40.741 2.13 0.00 0.00 2.74
5942 6278 2.932498 TGTTTTGATGATCAGCGTTGC 58.068 42.857 6.46 0.00 0.00 4.17
5963 6299 7.910162 GCATGACAACGAACATTTAGTGATATT 59.090 33.333 0.00 0.00 0.00 1.28
5980 6316 1.305930 GGAAGTCCGGGCATGACAAC 61.306 60.000 9.71 0.00 35.15 3.32
5987 6323 3.727258 CCATGGGAAGTCCGGGCA 61.727 66.667 9.71 0.00 38.76 5.36
5992 6328 1.216990 ATCCTGTCCATGGGAAGTCC 58.783 55.000 13.02 0.00 35.08 3.85
6001 6337 0.188587 TCCGCCTCTATCCTGTCCAT 59.811 55.000 0.00 0.00 0.00 3.41
6034 6370 6.040842 AGTGTCTGCTTTTTATTTGGTGACAT 59.959 34.615 0.00 0.00 42.32 3.06
6035 6371 5.359576 AGTGTCTGCTTTTTATTTGGTGACA 59.640 36.000 0.00 0.00 39.83 3.58
6064 6400 4.980805 GAGGCCAACGACGCACCA 62.981 66.667 5.01 0.00 0.00 4.17
6186 6522 0.452987 CATCATGGACAAGCAACGGG 59.547 55.000 0.00 0.00 0.00 5.28
6211 6547 0.462047 GGACCATGGTCACGATGGAC 60.462 60.000 38.83 18.00 46.20 4.02
6253 6589 1.775459 AGAGTACTAGATCGCAGGGGA 59.225 52.381 0.00 0.00 0.00 4.81
6321 6657 0.806868 CCATGTTGTGGCTACTGCAG 59.193 55.000 13.48 13.48 42.12 4.41
6332 6668 1.879380 CATTGTCGGTGTCCATGTTGT 59.121 47.619 0.00 0.00 0.00 3.32
6343 6679 1.812571 GGAGAAACATGCATTGTCGGT 59.187 47.619 0.00 0.00 37.68 4.69
6360 6696 0.907486 TGGAGAATGTGGAGCAGGAG 59.093 55.000 0.00 0.00 0.00 3.69
6363 6699 2.286872 GTGATGGAGAATGTGGAGCAG 58.713 52.381 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.