Multiple sequence alignment - TraesCS6D01G180200

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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 TraesCS6D01G180200 chr6D 100.000 4862 0 0 1 4862 199146663 199141802 0.000000e+00 8979.0
1 TraesCS6D01G180200 chr6D 93.594 281 15 2 4585 4862 412145409 412145129 2.710000e-112 416.0
2 TraesCS6D01G180200 chr6D 92.381 105 6 2 1720 1823 246435969 246436072 1.090000e-31 148.0
3 TraesCS6D01G180200 chr6B 96.990 3422 87 8 911 4324 320551938 320548525 0.000000e+00 5734.0
4 TraesCS6D01G180200 chr6B 94.680 921 13 13 1 912 320552860 320551967 0.000000e+00 1397.0
5 TraesCS6D01G180200 chr6B 93.103 116 6 1 4308 4423 320517551 320517438 8.370000e-38 169.0
6 TraesCS6D01G180200 chr6A 98.115 2705 44 5 1892 4590 255325234 255327937 0.000000e+00 4706.0
7 TraesCS6D01G180200 chr6A 97.772 1481 30 2 1 1478 255323276 255324756 0.000000e+00 2549.0
8 TraesCS6D01G180200 chr6A 98.423 444 7 0 1462 1905 255324772 255325215 0.000000e+00 782.0
9 TraesCS6D01G180200 chr6A 92.453 106 6 2 1720 1824 362228911 362228807 3.030000e-32 150.0
10 TraesCS6D01G180200 chr1D 93.950 281 14 2 4585 4862 136367605 136367885 5.820000e-114 422.0
11 TraesCS6D01G180200 chr1D 93.056 288 17 2 4578 4862 300071069 300071356 7.530000e-113 418.0
12 TraesCS6D01G180200 chr1D 95.833 96 4 0 1728 1823 485967757 485967852 6.520000e-34 156.0
13 TraesCS6D01G180200 chr5D 93.929 280 14 2 4585 4861 166728464 166728743 2.090000e-113 420.0
14 TraesCS6D01G180200 chr5D 93.929 280 14 2 4585 4861 399682697 399682418 2.090000e-113 420.0
15 TraesCS6D01G180200 chr5D 93.594 281 15 2 4585 4862 338832862 338833142 2.710000e-112 416.0
16 TraesCS6D01G180200 chr5D 92.708 288 18 2 4578 4862 68081792 68081505 3.500000e-111 412.0
17 TraesCS6D01G180200 chr4D 93.594 281 14 3 4585 4862 158680924 158680645 2.710000e-112 416.0
18 TraesCS6D01G180200 chr4D 93.594 281 15 2 4585 4862 409546337 409546617 2.710000e-112 416.0
19 TraesCS6D01G180200 chr4D 91.228 57 5 0 4477 4533 409472152 409472208 1.450000e-10 78.7
20 TraesCS6D01G180200 chr1B 92.241 116 9 0 4465 4580 18383408 18383293 1.080000e-36 165.0
21 TraesCS6D01G180200 chr1B 96.774 93 3 0 1737 1829 234252675 234252583 6.520000e-34 156.0
22 TraesCS6D01G180200 chr7A 91.379 116 10 0 4465 4580 105247712 105247827 5.040000e-35 159.0
23 TraesCS6D01G180200 chr7A 89.157 83 9 0 4475 4557 671362378 671362296 2.390000e-18 104.0
24 TraesCS6D01G180200 chr7B 95.789 95 4 0 1729 1823 458527873 458527967 2.340000e-33 154.0
25 TraesCS6D01G180200 chr3D 94.059 101 6 0 1729 1829 263991631 263991731 2.340000e-33 154.0
26 TraesCS6D01G180200 chr3D 89.474 57 6 0 4477 4533 323773689 323773633 6.750000e-09 73.1
27 TraesCS6D01G180200 chr3D 93.182 44 3 0 4465 4508 141401036 141400993 1.130000e-06 65.8
28 TraesCS6D01G180200 chr2D 93.269 104 6 1 1720 1823 366499485 366499383 8.430000e-33 152.0
29 TraesCS6D01G180200 chr7D 90.099 101 10 0 4490 4590 631675246 631675146 1.100000e-26 132.0
30 TraesCS6D01G180200 chr5B 90.909 77 7 0 4465 4541 6596585 6596509 2.390000e-18 104.0
31 TraesCS6D01G180200 chr5B 100.000 28 0 0 127 154 378513264 378513237 9.000000e-03 52.8
32 TraesCS6D01G180200 chr4A 90.909 55 5 0 4477 4531 713271342 713271288 1.880000e-09 75.0
33 TraesCS6D01G180200 chr5A 100.000 28 0 0 127 154 430505759 430505786 9.000000e-03 52.8


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 TraesCS6D01G180200 chr6D 199141802 199146663 4861 True 8979.0 8979 100.000000 1 4862 1 chr6D.!!$R1 4861
1 TraesCS6D01G180200 chr6B 320548525 320552860 4335 True 3565.5 5734 95.835000 1 4324 2 chr6B.!!$R2 4323
2 TraesCS6D01G180200 chr6A 255323276 255327937 4661 False 2679.0 4706 98.103333 1 4590 3 chr6A.!!$F1 4589

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
668 680 1.201424 GGGGGTCGATCACTTACCTT 58.799 55.000 0.00 0.0 33.59 3.50 F
1032 1074 0.391263 AAGGCACCGGAGATTCGAAC 60.391 55.000 9.46 0.0 0.00 3.95 F
1608 1684 3.065925 GCAAAACTGAGAGTGTTTCTGCT 59.934 43.478 1.32 0.0 37.80 4.24 F
3111 3223 4.439700 GCATCATAATGGCACCATCATAGC 60.440 45.833 1.88 0.0 35.31 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2151 0.108585 GCTGGCATCGGGGATCTTTA 59.891 55.000 0.0 0.00 0.00 1.85 R
2783 2891 7.575720 GCTTAGGATATTTGGATCAATTTCCCG 60.576 40.741 10.0 3.75 34.67 5.14 R
3291 3403 2.498167 CACAGGAAAACACCCAGAGAG 58.502 52.381 0.0 0.00 0.00 3.20 R
4761 4879 0.036875 CCAGGAGGCGAGGAAAGTTT 59.963 55.000 0.0 0.00 0.00 2.66 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
37 39 5.708948 TGTAAACATGCTGATAACAAAGCC 58.291 37.500 0.00 0.00 38.71 4.35
601 613 2.322081 CCTGTACCACGCAAACCCG 61.322 63.158 0.00 0.00 0.00 5.28
668 680 1.201424 GGGGGTCGATCACTTACCTT 58.799 55.000 0.00 0.00 33.59 3.50
863 875 2.554032 CCTTGCGATTTGAGACCAAGTT 59.446 45.455 0.00 0.00 32.99 2.66
1032 1074 0.391263 AAGGCACCGGAGATTCGAAC 60.391 55.000 9.46 0.00 0.00 3.95
1420 1464 5.238650 GCACTTTCTTTCCTAGTACAGCAAA 59.761 40.000 0.00 0.00 0.00 3.68
1422 1466 7.681065 GCACTTTCTTTCCTAGTACAGCAAAAA 60.681 37.037 0.00 0.00 0.00 1.94
1530 1606 6.158598 ACATGTGTATGCAGGAAAATTGAAC 58.841 36.000 0.00 0.00 37.85 3.18
1608 1684 3.065925 GCAAAACTGAGAGTGTTTCTGCT 59.934 43.478 1.32 0.00 37.80 4.24
2783 2891 5.195001 TCCTTGGTGCACAAAAATAAGTC 57.805 39.130 20.43 0.00 38.91 3.01
3111 3223 4.439700 GCATCATAATGGCACCATCATAGC 60.440 45.833 1.88 0.00 35.31 2.97
3199 3311 7.572523 TTGTGTATGGAATTCTGGATGAATC 57.427 36.000 5.23 0.00 43.99 2.52
3338 3451 9.058174 CCACGTTTGATTTACCATACCATTATA 57.942 33.333 0.00 0.00 0.00 0.98
3819 3933 8.004087 ACTATTCATCCACATTGAAGGAAATG 57.996 34.615 6.68 0.00 42.21 2.32
4131 4245 3.190849 CTCCATGCTCGTGCCACG 61.191 66.667 11.80 11.80 44.19 4.94
4243 4360 2.017559 GACGCTGGCCGGACTAATCT 62.018 60.000 18.31 0.00 42.52 2.40
4445 4563 4.678509 TGCTTTATTCCACGTTGCTAAG 57.321 40.909 0.00 0.00 0.00 2.18
4446 4564 3.438781 TGCTTTATTCCACGTTGCTAAGG 59.561 43.478 0.00 0.00 0.00 2.69
4447 4565 3.181500 GCTTTATTCCACGTTGCTAAGGG 60.181 47.826 0.00 0.00 0.00 3.95
4451 4569 0.109723 TCCACGTTGCTAAGGGCTTT 59.890 50.000 0.00 0.00 42.39 3.51
4471 4589 5.106712 GCTTTCACGGTTTCATAAGATGACA 60.107 40.000 0.00 0.00 39.39 3.58
4602 4720 5.019907 CGTGATAGACGGTACATAGACAG 57.980 47.826 0.00 0.00 44.85 3.51
4603 4721 4.748600 CGTGATAGACGGTACATAGACAGA 59.251 45.833 0.00 0.00 44.85 3.41
4604 4722 5.408909 CGTGATAGACGGTACATAGACAGAT 59.591 44.000 0.00 0.00 44.85 2.90
4605 4723 6.604012 GTGATAGACGGTACATAGACAGATG 58.396 44.000 0.00 0.00 0.00 2.90
4606 4724 3.992260 AGACGGTACATAGACAGATGC 57.008 47.619 0.00 0.00 0.00 3.91
4607 4725 3.288092 AGACGGTACATAGACAGATGCA 58.712 45.455 0.00 0.00 0.00 3.96
4608 4726 3.891977 AGACGGTACATAGACAGATGCAT 59.108 43.478 0.00 0.00 0.00 3.96
4609 4727 4.022762 AGACGGTACATAGACAGATGCATC 60.023 45.833 19.37 19.37 0.00 3.91
4610 4728 3.891977 ACGGTACATAGACAGATGCATCT 59.108 43.478 23.75 23.75 37.72 2.90
4611 4729 4.022762 ACGGTACATAGACAGATGCATCTC 60.023 45.833 26.44 16.32 34.22 2.75
4612 4730 4.022849 CGGTACATAGACAGATGCATCTCA 60.023 45.833 26.44 12.12 34.22 3.27
4613 4731 5.336293 CGGTACATAGACAGATGCATCTCAT 60.336 44.000 26.44 17.29 38.32 2.90
4624 4742 5.171147 GATGCATCTCATCTGGAAAACTG 57.829 43.478 19.70 0.00 46.29 3.16
4625 4743 2.751259 TGCATCTCATCTGGAAAACTGC 59.249 45.455 0.00 0.00 0.00 4.40
4626 4744 3.015327 GCATCTCATCTGGAAAACTGCT 58.985 45.455 0.00 0.00 0.00 4.24
4627 4745 3.181499 GCATCTCATCTGGAAAACTGCTG 60.181 47.826 0.00 0.00 0.00 4.41
4628 4746 4.259356 CATCTCATCTGGAAAACTGCTGA 58.741 43.478 0.00 0.00 0.00 4.26
4629 4747 4.356405 TCTCATCTGGAAAACTGCTGAA 57.644 40.909 0.00 0.00 0.00 3.02
4630 4748 4.321718 TCTCATCTGGAAAACTGCTGAAG 58.678 43.478 0.00 0.00 0.00 3.02
4631 4749 2.816087 TCATCTGGAAAACTGCTGAAGC 59.184 45.455 0.00 0.00 42.50 3.86
4632 4750 1.229428 TCTGGAAAACTGCTGAAGCG 58.771 50.000 0.00 0.00 45.83 4.68
4649 4767 0.235926 GCGGAAGGCGAATATTGAGC 59.764 55.000 0.00 0.00 0.00 4.26
4657 4775 4.152607 GGCGAATATTGAGCCTTCATTC 57.847 45.455 19.13 0.00 46.83 2.67
4658 4776 3.565482 GGCGAATATTGAGCCTTCATTCA 59.435 43.478 19.13 0.00 46.83 2.57
4659 4777 4.217118 GGCGAATATTGAGCCTTCATTCAT 59.783 41.667 19.13 0.00 46.83 2.57
4660 4778 5.152097 GCGAATATTGAGCCTTCATTCATG 58.848 41.667 0.00 0.00 32.27 3.07
4661 4779 5.278169 GCGAATATTGAGCCTTCATTCATGT 60.278 40.000 0.00 0.00 32.27 3.21
4662 4780 6.732154 CGAATATTGAGCCTTCATTCATGTT 58.268 36.000 0.00 0.00 32.27 2.71
4663 4781 6.635641 CGAATATTGAGCCTTCATTCATGTTG 59.364 38.462 0.00 0.00 32.27 3.33
4664 4782 7.467675 CGAATATTGAGCCTTCATTCATGTTGA 60.468 37.037 0.00 0.00 32.27 3.18
4665 4783 5.988310 ATTGAGCCTTCATTCATGTTGAA 57.012 34.783 11.52 11.52 41.09 2.69
4666 4784 5.381174 TTGAGCCTTCATTCATGTTGAAG 57.619 39.130 23.06 23.06 46.23 3.02
4674 4792 5.125100 TCATTCATGTTGAAGGTCTTTGC 57.875 39.130 2.34 0.00 40.05 3.68
4675 4793 4.583907 TCATTCATGTTGAAGGTCTTTGCA 59.416 37.500 2.34 0.00 40.05 4.08
4676 4794 4.998671 TTCATGTTGAAGGTCTTTGCAA 57.001 36.364 0.00 0.00 31.83 4.08
4677 4795 5.534207 TTCATGTTGAAGGTCTTTGCAAT 57.466 34.783 0.00 0.00 31.83 3.56
4678 4796 4.873817 TCATGTTGAAGGTCTTTGCAATG 58.126 39.130 0.00 2.27 0.00 2.82
4679 4797 3.731652 TGTTGAAGGTCTTTGCAATGG 57.268 42.857 11.99 3.33 0.00 3.16
4680 4798 2.364970 TGTTGAAGGTCTTTGCAATGGG 59.635 45.455 11.99 0.92 0.00 4.00
4681 4799 0.968405 TGAAGGTCTTTGCAATGGGC 59.032 50.000 11.99 4.45 45.13 5.36
4682 4800 0.247460 GAAGGTCTTTGCAATGGGCC 59.753 55.000 13.58 13.58 43.89 5.80
4683 4801 0.471591 AAGGTCTTTGCAATGGGCCA 60.472 50.000 20.60 9.61 43.89 5.36
4684 4802 0.901580 AGGTCTTTGCAATGGGCCAG 60.902 55.000 20.60 0.00 43.89 4.85
4685 4803 1.187567 GGTCTTTGCAATGGGCCAGT 61.188 55.000 13.78 6.48 43.89 4.00
4686 4804 0.037975 GTCTTTGCAATGGGCCAGTG 60.038 55.000 28.57 28.57 43.89 3.66
4691 4809 3.781760 CAATGGGCCAGTGCTTGT 58.218 55.556 22.13 0.00 37.74 3.16
4692 4810 1.290955 CAATGGGCCAGTGCTTGTG 59.709 57.895 22.13 0.00 37.74 3.33
4693 4811 1.909781 AATGGGCCAGTGCTTGTGG 60.910 57.895 13.78 0.00 38.21 4.17
4694 4812 2.370459 AATGGGCCAGTGCTTGTGGA 62.370 55.000 13.78 0.00 37.23 4.02
4695 4813 2.036256 GGGCCAGTGCTTGTGGAT 59.964 61.111 4.39 0.00 37.23 3.41
4696 4814 1.302949 GGGCCAGTGCTTGTGGATA 59.697 57.895 4.39 0.00 37.23 2.59
4697 4815 0.323360 GGGCCAGTGCTTGTGGATAA 60.323 55.000 4.39 0.00 37.23 1.75
4698 4816 1.686115 GGGCCAGTGCTTGTGGATAAT 60.686 52.381 4.39 0.00 37.23 1.28
4699 4817 2.102578 GGCCAGTGCTTGTGGATAATT 58.897 47.619 0.00 0.00 37.23 1.40
4700 4818 3.287222 GGCCAGTGCTTGTGGATAATTA 58.713 45.455 0.00 0.00 37.23 1.40
4701 4819 3.699038 GGCCAGTGCTTGTGGATAATTAA 59.301 43.478 0.00 0.00 37.23 1.40
4702 4820 4.342092 GGCCAGTGCTTGTGGATAATTAAT 59.658 41.667 0.00 0.00 37.23 1.40
4703 4821 5.507985 GGCCAGTGCTTGTGGATAATTAATC 60.508 44.000 0.00 0.00 37.23 1.75
4704 4822 5.751680 CCAGTGCTTGTGGATAATTAATCG 58.248 41.667 0.00 0.00 37.23 3.34
4705 4823 5.296780 CCAGTGCTTGTGGATAATTAATCGT 59.703 40.000 0.00 0.00 37.23 3.73
4706 4824 6.422223 CAGTGCTTGTGGATAATTAATCGTC 58.578 40.000 0.00 0.00 35.21 4.20
4707 4825 5.527582 AGTGCTTGTGGATAATTAATCGTCC 59.472 40.000 10.63 10.63 35.21 4.79
4708 4826 5.295787 GTGCTTGTGGATAATTAATCGTCCA 59.704 40.000 14.55 14.55 38.37 4.02
4709 4827 6.017109 GTGCTTGTGGATAATTAATCGTCCAT 60.017 38.462 19.13 0.00 42.27 3.41
4710 4828 6.204688 TGCTTGTGGATAATTAATCGTCCATC 59.795 38.462 19.13 14.54 42.27 3.51
4711 4829 6.348540 GCTTGTGGATAATTAATCGTCCATCC 60.349 42.308 19.13 12.47 42.27 3.51
4712 4830 6.433847 TGTGGATAATTAATCGTCCATCCT 57.566 37.500 19.13 0.00 42.27 3.24
4713 4831 6.837312 TGTGGATAATTAATCGTCCATCCTT 58.163 36.000 19.13 0.00 42.27 3.36
4714 4832 6.934645 TGTGGATAATTAATCGTCCATCCTTC 59.065 38.462 19.13 10.35 42.27 3.46
4715 4833 6.090898 GTGGATAATTAATCGTCCATCCTTCG 59.909 42.308 19.13 0.00 42.27 3.79
4716 4834 6.014925 TGGATAATTAATCGTCCATCCTTCGA 60.015 38.462 14.55 0.00 35.91 3.71
4717 4835 6.310711 GGATAATTAATCGTCCATCCTTCGAC 59.689 42.308 12.06 0.00 36.46 4.20
4718 4836 3.447918 TTAATCGTCCATCCTTCGACC 57.552 47.619 0.00 0.00 36.46 4.79
4719 4837 1.486211 AATCGTCCATCCTTCGACCT 58.514 50.000 0.00 0.00 36.46 3.85
4720 4838 1.486211 ATCGTCCATCCTTCGACCTT 58.514 50.000 0.00 0.00 36.46 3.50
4721 4839 1.263356 TCGTCCATCCTTCGACCTTT 58.737 50.000 0.00 0.00 0.00 3.11
4722 4840 1.621814 TCGTCCATCCTTCGACCTTTT 59.378 47.619 0.00 0.00 0.00 2.27
4723 4841 2.000447 CGTCCATCCTTCGACCTTTTC 59.000 52.381 0.00 0.00 0.00 2.29
4724 4842 2.611971 CGTCCATCCTTCGACCTTTTCA 60.612 50.000 0.00 0.00 0.00 2.69
4725 4843 3.003480 GTCCATCCTTCGACCTTTTCAG 58.997 50.000 0.00 0.00 0.00 3.02
4727 4845 2.027192 CCATCCTTCGACCTTTTCAGGA 60.027 50.000 2.37 2.37 44.19 3.86
4728 4846 3.559171 CCATCCTTCGACCTTTTCAGGAA 60.559 47.826 3.97 0.00 44.19 3.36
4729 4847 3.121738 TCCTTCGACCTTTTCAGGAAC 57.878 47.619 0.00 0.00 44.19 3.62
4730 4848 2.436542 TCCTTCGACCTTTTCAGGAACA 59.563 45.455 0.00 0.00 44.19 3.18
4731 4849 2.548480 CCTTCGACCTTTTCAGGAACAC 59.452 50.000 0.00 0.00 44.19 3.32
4732 4850 3.467803 CTTCGACCTTTTCAGGAACACT 58.532 45.455 0.00 0.00 44.19 3.55
4733 4851 3.553828 TCGACCTTTTCAGGAACACTT 57.446 42.857 0.00 0.00 44.19 3.16
4734 4852 3.881220 TCGACCTTTTCAGGAACACTTT 58.119 40.909 0.00 0.00 44.19 2.66
4735 4853 5.026038 TCGACCTTTTCAGGAACACTTTA 57.974 39.130 0.00 0.00 44.19 1.85
4736 4854 5.430007 TCGACCTTTTCAGGAACACTTTAA 58.570 37.500 0.00 0.00 44.19 1.52
4737 4855 6.059484 TCGACCTTTTCAGGAACACTTTAAT 58.941 36.000 0.00 0.00 44.19 1.40
4738 4856 7.218614 TCGACCTTTTCAGGAACACTTTAATA 58.781 34.615 0.00 0.00 44.19 0.98
4739 4857 7.881232 TCGACCTTTTCAGGAACACTTTAATAT 59.119 33.333 0.00 0.00 44.19 1.28
4740 4858 8.512138 CGACCTTTTCAGGAACACTTTAATATT 58.488 33.333 0.00 0.00 44.19 1.28
4741 4859 9.626045 GACCTTTTCAGGAACACTTTAATATTG 57.374 33.333 0.00 0.00 44.19 1.90
4742 4860 9.362151 ACCTTTTCAGGAACACTTTAATATTGA 57.638 29.630 0.00 0.00 44.19 2.57
4745 4863 9.974980 TTTTCAGGAACACTTTAATATTGAACC 57.025 29.630 0.00 0.00 0.00 3.62
4746 4864 7.372451 TCAGGAACACTTTAATATTGAACCG 57.628 36.000 0.00 0.00 0.00 4.44
4747 4865 6.938030 TCAGGAACACTTTAATATTGAACCGT 59.062 34.615 0.00 0.00 0.00 4.83
4748 4866 7.021196 CAGGAACACTTTAATATTGAACCGTG 58.979 38.462 9.47 9.47 0.00 4.94
4749 4867 6.150474 AGGAACACTTTAATATTGAACCGTGG 59.850 38.462 13.46 0.00 0.00 4.94
4750 4868 5.890424 ACACTTTAATATTGAACCGTGGG 57.110 39.130 13.46 0.00 0.00 4.61
4751 4869 5.318630 ACACTTTAATATTGAACCGTGGGT 58.681 37.500 13.46 0.19 37.65 4.51
4752 4870 5.182380 ACACTTTAATATTGAACCGTGGGTG 59.818 40.000 13.46 10.00 35.34 4.61
4753 4871 5.182380 CACTTTAATATTGAACCGTGGGTGT 59.818 40.000 0.00 0.00 35.34 4.16
4754 4872 5.771165 ACTTTAATATTGAACCGTGGGTGTT 59.229 36.000 0.00 0.00 35.34 3.32
4755 4873 5.630661 TTAATATTGAACCGTGGGTGTTG 57.369 39.130 0.00 0.00 35.34 3.33
4756 4874 2.642154 TATTGAACCGTGGGTGTTGT 57.358 45.000 0.00 0.00 35.34 3.32
4757 4875 2.642154 ATTGAACCGTGGGTGTTGTA 57.358 45.000 0.00 0.00 35.34 2.41
4758 4876 2.642154 TTGAACCGTGGGTGTTGTAT 57.358 45.000 0.00 0.00 35.34 2.29
4759 4877 1.885560 TGAACCGTGGGTGTTGTATG 58.114 50.000 0.00 0.00 35.34 2.39
4760 4878 1.416772 TGAACCGTGGGTGTTGTATGA 59.583 47.619 0.00 0.00 35.34 2.15
4761 4879 2.158798 TGAACCGTGGGTGTTGTATGAA 60.159 45.455 0.00 0.00 35.34 2.57
4762 4880 2.642154 ACCGTGGGTGTTGTATGAAA 57.358 45.000 0.00 0.00 32.98 2.69
4763 4881 2.933573 ACCGTGGGTGTTGTATGAAAA 58.066 42.857 0.00 0.00 32.98 2.29
4764 4882 2.619646 ACCGTGGGTGTTGTATGAAAAC 59.380 45.455 0.00 0.00 32.98 2.43
4765 4883 2.882137 CCGTGGGTGTTGTATGAAAACT 59.118 45.455 0.00 0.00 0.00 2.66
4766 4884 3.316868 CCGTGGGTGTTGTATGAAAACTT 59.683 43.478 0.00 0.00 0.00 2.66
4767 4885 4.202070 CCGTGGGTGTTGTATGAAAACTTT 60.202 41.667 0.00 0.00 0.00 2.66
4768 4886 4.973663 CGTGGGTGTTGTATGAAAACTTTC 59.026 41.667 0.00 0.00 37.69 2.62
4769 4887 5.286438 GTGGGTGTTGTATGAAAACTTTCC 58.714 41.667 0.00 0.00 36.36 3.13
4770 4888 5.068591 GTGGGTGTTGTATGAAAACTTTCCT 59.931 40.000 0.00 0.00 36.36 3.36
4771 4889 5.300792 TGGGTGTTGTATGAAAACTTTCCTC 59.699 40.000 0.00 0.00 36.36 3.71
4772 4890 5.449304 GGTGTTGTATGAAAACTTTCCTCG 58.551 41.667 0.00 0.00 36.36 4.63
4773 4891 4.909880 GTGTTGTATGAAAACTTTCCTCGC 59.090 41.667 0.00 0.00 36.36 5.03
4774 4892 4.023536 TGTTGTATGAAAACTTTCCTCGCC 60.024 41.667 0.00 0.00 36.36 5.54
4775 4893 4.015872 TGTATGAAAACTTTCCTCGCCT 57.984 40.909 0.00 0.00 36.36 5.52
4776 4894 4.000988 TGTATGAAAACTTTCCTCGCCTC 58.999 43.478 0.00 0.00 36.36 4.70
4777 4895 1.892209 TGAAAACTTTCCTCGCCTCC 58.108 50.000 0.00 0.00 36.36 4.30
4778 4896 1.420138 TGAAAACTTTCCTCGCCTCCT 59.580 47.619 0.00 0.00 36.36 3.69
4779 4897 1.807142 GAAAACTTTCCTCGCCTCCTG 59.193 52.381 0.00 0.00 0.00 3.86
4780 4898 0.036875 AAACTTTCCTCGCCTCCTGG 59.963 55.000 0.00 0.00 0.00 4.45
4801 4919 2.175878 CACAGAGGTGGTTTGAGAGG 57.824 55.000 0.00 0.00 41.45 3.69
4802 4920 1.417890 CACAGAGGTGGTTTGAGAGGT 59.582 52.381 0.00 0.00 41.45 3.85
4803 4921 2.632996 CACAGAGGTGGTTTGAGAGGTA 59.367 50.000 0.00 0.00 41.45 3.08
4804 4922 3.071023 CACAGAGGTGGTTTGAGAGGTAA 59.929 47.826 0.00 0.00 41.45 2.85
4805 4923 3.910627 ACAGAGGTGGTTTGAGAGGTAAT 59.089 43.478 0.00 0.00 0.00 1.89
4806 4924 4.020128 ACAGAGGTGGTTTGAGAGGTAATC 60.020 45.833 0.00 0.00 0.00 1.75
4807 4925 4.020218 CAGAGGTGGTTTGAGAGGTAATCA 60.020 45.833 0.00 0.00 0.00 2.57
4808 4926 4.785376 AGAGGTGGTTTGAGAGGTAATCAT 59.215 41.667 0.00 0.00 0.00 2.45
4809 4927 5.251700 AGAGGTGGTTTGAGAGGTAATCATT 59.748 40.000 0.00 0.00 0.00 2.57
4810 4928 6.443849 AGAGGTGGTTTGAGAGGTAATCATTA 59.556 38.462 0.00 0.00 0.00 1.90
4811 4929 6.653989 AGGTGGTTTGAGAGGTAATCATTAG 58.346 40.000 0.00 0.00 0.00 1.73
4812 4930 6.215636 AGGTGGTTTGAGAGGTAATCATTAGT 59.784 38.462 0.00 0.00 0.00 2.24
4813 4931 6.316390 GGTGGTTTGAGAGGTAATCATTAGTG 59.684 42.308 0.00 0.00 0.00 2.74
4814 4932 7.103641 GTGGTTTGAGAGGTAATCATTAGTGA 58.896 38.462 0.00 0.00 39.04 3.41
4815 4933 7.606456 GTGGTTTGAGAGGTAATCATTAGTGAA 59.394 37.037 0.00 0.00 38.01 3.18
4816 4934 7.606456 TGGTTTGAGAGGTAATCATTAGTGAAC 59.394 37.037 0.00 0.00 38.01 3.18
4817 4935 7.065923 GGTTTGAGAGGTAATCATTAGTGAACC 59.934 40.741 1.73 1.73 38.01 3.62
4818 4936 6.235231 TGAGAGGTAATCATTAGTGAACCC 57.765 41.667 5.68 0.65 36.36 4.11
4819 4937 5.964477 TGAGAGGTAATCATTAGTGAACCCT 59.036 40.000 5.68 4.89 36.36 4.34
4820 4938 7.130099 TGAGAGGTAATCATTAGTGAACCCTA 58.870 38.462 5.68 0.00 36.36 3.53
4821 4939 7.622081 TGAGAGGTAATCATTAGTGAACCCTAA 59.378 37.037 5.68 0.00 36.36 2.69
4822 4940 8.388656 AGAGGTAATCATTAGTGAACCCTAAA 57.611 34.615 5.68 0.00 36.36 1.85
4823 4941 8.832735 AGAGGTAATCATTAGTGAACCCTAAAA 58.167 33.333 5.68 0.00 36.36 1.52
4824 4942 9.457436 GAGGTAATCATTAGTGAACCCTAAAAA 57.543 33.333 5.68 0.00 36.36 1.94
4825 4943 9.990868 AGGTAATCATTAGTGAACCCTAAAAAT 57.009 29.630 5.68 0.00 36.36 1.82
4833 4951 9.990868 ATTAGTGAACCCTAAAAATAAGGATGT 57.009 29.630 0.00 0.00 36.08 3.06
4834 4952 7.703058 AGTGAACCCTAAAAATAAGGATGTG 57.297 36.000 0.00 0.00 36.08 3.21
4835 4953 6.152831 AGTGAACCCTAAAAATAAGGATGTGC 59.847 38.462 0.00 0.00 36.08 4.57
4836 4954 6.013379 TGAACCCTAAAAATAAGGATGTGCA 58.987 36.000 0.00 0.00 36.08 4.57
4837 4955 6.667414 TGAACCCTAAAAATAAGGATGTGCAT 59.333 34.615 0.00 0.00 36.08 3.96
4838 4956 7.836685 TGAACCCTAAAAATAAGGATGTGCATA 59.163 33.333 0.00 0.00 36.08 3.14
4839 4957 8.602472 AACCCTAAAAATAAGGATGTGCATAA 57.398 30.769 0.00 0.00 36.08 1.90
4840 4958 8.007405 ACCCTAAAAATAAGGATGTGCATAAC 57.993 34.615 0.00 0.00 36.08 1.89
4841 4959 7.839200 ACCCTAAAAATAAGGATGTGCATAACT 59.161 33.333 0.00 0.00 36.08 2.24
4842 4960 9.349713 CCCTAAAAATAAGGATGTGCATAACTA 57.650 33.333 0.00 0.00 36.08 2.24
4849 4967 9.717942 AATAAGGATGTGCATAACTATCTTCTC 57.282 33.333 0.00 0.00 0.00 2.87
4850 4968 6.992664 AGGATGTGCATAACTATCTTCTCT 57.007 37.500 0.00 0.00 0.00 3.10
4851 4969 7.372260 AGGATGTGCATAACTATCTTCTCTT 57.628 36.000 0.00 0.00 0.00 2.85
4852 4970 7.800092 AGGATGTGCATAACTATCTTCTCTTT 58.200 34.615 0.00 0.00 0.00 2.52
4853 4971 8.928448 AGGATGTGCATAACTATCTTCTCTTTA 58.072 33.333 0.00 0.00 0.00 1.85
4854 4972 9.717942 GGATGTGCATAACTATCTTCTCTTTAT 57.282 33.333 0.00 0.00 0.00 1.40
4857 4975 9.330063 TGTGCATAACTATCTTCTCTTTATTGG 57.670 33.333 0.00 0.00 0.00 3.16
4858 4976 9.547753 GTGCATAACTATCTTCTCTTTATTGGA 57.452 33.333 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 39 1.444895 GGCATGCCACAAGAAAGCG 60.445 57.895 32.08 0.00 35.81 4.68
51 53 1.398958 GCGAGAGGAGAGGAAGGCAT 61.399 60.000 0.00 0.00 0.00 4.40
668 680 3.706373 GCTCTCGCTCCAACCCCA 61.706 66.667 0.00 0.00 0.00 4.96
793 805 2.042843 TCCCCTCTCTCCTTCCGC 60.043 66.667 0.00 0.00 0.00 5.54
863 875 3.023119 CCATTAAAGCCCATGTACAGCA 58.977 45.455 0.33 0.00 0.00 4.41
1422 1466 6.729690 TCTTGTGATGGTGGAAGAATTTTT 57.270 33.333 0.00 0.00 0.00 1.94
1423 1467 6.923199 ATCTTGTGATGGTGGAAGAATTTT 57.077 33.333 0.00 0.00 0.00 1.82
1424 1468 6.923199 AATCTTGTGATGGTGGAAGAATTT 57.077 33.333 0.00 0.00 32.44 1.82
1425 1469 6.923199 AAATCTTGTGATGGTGGAAGAATT 57.077 33.333 0.00 0.00 32.44 2.17
1426 1470 6.268387 ACAAAATCTTGTGATGGTGGAAGAAT 59.732 34.615 0.00 0.00 44.28 2.40
1608 1684 5.981088 AAGTGATGTGCATAACCATTTCA 57.019 34.783 0.00 0.00 0.00 2.69
2043 2151 0.108585 GCTGGCATCGGGGATCTTTA 59.891 55.000 0.00 0.00 0.00 1.85
2783 2891 7.575720 GCTTAGGATATTTGGATCAATTTCCCG 60.576 40.741 10.00 3.75 34.67 5.14
3111 3223 8.495949 ACATAAAACGTGAGATTGAGTTTACTG 58.504 33.333 0.00 0.00 35.99 2.74
3199 3311 4.516698 AGCACTTTGGATGTCACACTTAAG 59.483 41.667 0.00 0.00 0.00 1.85
3291 3403 2.498167 CACAGGAAAACACCCAGAGAG 58.502 52.381 0.00 0.00 0.00 3.20
3338 3451 7.771927 AGAAAATCTGATGTCCATTTCAGTT 57.228 32.000 11.99 0.00 40.22 3.16
3341 3454 8.180706 TCAAAGAAAATCTGATGTCCATTTCA 57.819 30.769 11.99 0.00 31.06 2.69
3481 3595 3.256631 GTGAAACTTCCAGATTGCACCAT 59.743 43.478 0.00 0.00 0.00 3.55
3666 3780 3.282021 AGTAGGCCAGTTGCACAATATG 58.718 45.455 5.01 0.00 43.89 1.78
3819 3933 7.662604 ATCAATTTGCTCAAGATTTGGAAAC 57.337 32.000 0.00 0.00 0.00 2.78
4131 4245 5.329035 ACAAATACATCATCCCTTGCAAC 57.671 39.130 0.00 0.00 0.00 4.17
4210 4324 1.937223 CAGCGTCTAACACCACAAACA 59.063 47.619 0.00 0.00 0.00 2.83
4424 4542 3.438781 CCTTAGCAACGTGGAATAAAGCA 59.561 43.478 0.00 0.00 0.00 3.91
4445 4563 3.078837 TCTTATGAAACCGTGAAAGCCC 58.921 45.455 0.00 0.00 0.00 5.19
4446 4564 4.394920 TCATCTTATGAAACCGTGAAAGCC 59.605 41.667 0.00 0.00 36.11 4.35
4447 4565 5.106712 TGTCATCTTATGAAACCGTGAAAGC 60.107 40.000 0.00 0.00 41.69 3.51
4451 4569 3.924073 CGTGTCATCTTATGAAACCGTGA 59.076 43.478 4.94 0.00 43.19 4.35
4488 4606 1.133458 GGCTCGCTCTCGCTTTTTG 59.867 57.895 0.00 0.00 35.26 2.44
4496 4614 2.586258 TGAATACTTGGCTCGCTCTC 57.414 50.000 0.00 0.00 0.00 3.20
4581 4699 6.604012 CATCTGTCTATGTACCGTCTATCAC 58.396 44.000 0.00 0.00 0.00 3.06
4590 4708 5.459536 TGAGATGCATCTGTCTATGTACC 57.540 43.478 33.33 14.86 37.25 3.34
4603 4721 3.380637 GCAGTTTTCCAGATGAGATGCAT 59.619 43.478 0.00 0.00 40.77 3.96
4604 4722 2.751259 GCAGTTTTCCAGATGAGATGCA 59.249 45.455 0.00 0.00 0.00 3.96
4605 4723 3.015327 AGCAGTTTTCCAGATGAGATGC 58.985 45.455 0.00 0.00 0.00 3.91
4606 4724 4.259356 TCAGCAGTTTTCCAGATGAGATG 58.741 43.478 0.00 0.00 0.00 2.90
4607 4725 4.564782 TCAGCAGTTTTCCAGATGAGAT 57.435 40.909 0.00 0.00 0.00 2.75
4608 4726 4.321718 CTTCAGCAGTTTTCCAGATGAGA 58.678 43.478 0.00 0.00 0.00 3.27
4609 4727 3.119919 GCTTCAGCAGTTTTCCAGATGAG 60.120 47.826 0.00 0.00 41.59 2.90
4610 4728 2.816087 GCTTCAGCAGTTTTCCAGATGA 59.184 45.455 0.00 0.00 41.59 2.92
4611 4729 2.413765 CGCTTCAGCAGTTTTCCAGATG 60.414 50.000 0.00 0.00 42.21 2.90
4612 4730 1.808945 CGCTTCAGCAGTTTTCCAGAT 59.191 47.619 0.00 0.00 42.21 2.90
4613 4731 1.229428 CGCTTCAGCAGTTTTCCAGA 58.771 50.000 0.00 0.00 42.21 3.86
4614 4732 0.239347 CCGCTTCAGCAGTTTTCCAG 59.761 55.000 0.00 0.00 42.21 3.86
4615 4733 0.179032 TCCGCTTCAGCAGTTTTCCA 60.179 50.000 0.00 0.00 42.21 3.53
4616 4734 0.951558 TTCCGCTTCAGCAGTTTTCC 59.048 50.000 0.00 0.00 42.21 3.13
4617 4735 1.068954 CCTTCCGCTTCAGCAGTTTTC 60.069 52.381 0.00 0.00 42.21 2.29
4618 4736 0.954452 CCTTCCGCTTCAGCAGTTTT 59.046 50.000 0.00 0.00 42.21 2.43
4619 4737 1.518903 GCCTTCCGCTTCAGCAGTTT 61.519 55.000 0.00 0.00 42.21 2.66
4620 4738 1.968540 GCCTTCCGCTTCAGCAGTT 60.969 57.895 0.00 0.00 42.21 3.16
4621 4739 2.359230 GCCTTCCGCTTCAGCAGT 60.359 61.111 0.00 0.00 42.21 4.40
4622 4740 3.494336 CGCCTTCCGCTTCAGCAG 61.494 66.667 0.00 0.00 42.21 4.24
4623 4741 2.803155 ATTCGCCTTCCGCTTCAGCA 62.803 55.000 0.00 0.00 42.21 4.41
4624 4742 0.810031 TATTCGCCTTCCGCTTCAGC 60.810 55.000 0.00 0.00 36.73 4.26
4625 4743 1.871080 ATATTCGCCTTCCGCTTCAG 58.129 50.000 0.00 0.00 36.73 3.02
4626 4744 1.939934 CAATATTCGCCTTCCGCTTCA 59.060 47.619 0.00 0.00 36.73 3.02
4627 4745 2.210116 TCAATATTCGCCTTCCGCTTC 58.790 47.619 0.00 0.00 36.73 3.86
4628 4746 2.213499 CTCAATATTCGCCTTCCGCTT 58.787 47.619 0.00 0.00 36.73 4.68
4629 4747 1.871080 CTCAATATTCGCCTTCCGCT 58.129 50.000 0.00 0.00 36.73 5.52
4630 4748 0.235926 GCTCAATATTCGCCTTCCGC 59.764 55.000 0.00 0.00 36.73 5.54
4631 4749 0.868406 GGCTCAATATTCGCCTTCCG 59.132 55.000 15.02 0.00 40.62 4.30
4636 4754 3.565482 TGAATGAAGGCTCAATATTCGCC 59.435 43.478 14.64 14.64 44.09 5.54
4637 4755 4.818534 TGAATGAAGGCTCAATATTCGC 57.181 40.909 0.00 0.00 34.49 4.70
4638 4756 6.309712 ACATGAATGAAGGCTCAATATTCG 57.690 37.500 0.00 0.00 34.49 3.34
4639 4757 7.709947 TCAACATGAATGAAGGCTCAATATTC 58.290 34.615 0.00 0.00 34.49 1.75
4640 4758 7.649533 TCAACATGAATGAAGGCTCAATATT 57.350 32.000 0.00 0.00 34.49 1.28
4641 4759 7.649533 TTCAACATGAATGAAGGCTCAATAT 57.350 32.000 12.53 0.00 34.49 1.28
4642 4760 7.092137 CTTCAACATGAATGAAGGCTCAATA 57.908 36.000 25.29 4.31 46.39 1.90
4643 4761 5.962433 CTTCAACATGAATGAAGGCTCAAT 58.038 37.500 25.29 0.00 46.39 2.57
4644 4762 5.381174 CTTCAACATGAATGAAGGCTCAA 57.619 39.130 25.29 5.34 46.39 3.02
4651 4769 5.068855 TGCAAAGACCTTCAACATGAATGAA 59.931 36.000 14.77 14.77 35.59 2.57
4652 4770 4.583907 TGCAAAGACCTTCAACATGAATGA 59.416 37.500 0.00 0.13 35.59 2.57
4653 4771 4.873817 TGCAAAGACCTTCAACATGAATG 58.126 39.130 0.00 0.00 35.59 2.67
4654 4772 5.534207 TTGCAAAGACCTTCAACATGAAT 57.466 34.783 0.00 0.00 35.59 2.57
4655 4773 4.998671 TTGCAAAGACCTTCAACATGAA 57.001 36.364 0.00 0.00 34.79 2.57
4656 4774 4.262121 CCATTGCAAAGACCTTCAACATGA 60.262 41.667 1.71 0.00 0.00 3.07
4657 4775 3.991773 CCATTGCAAAGACCTTCAACATG 59.008 43.478 1.71 0.00 0.00 3.21
4658 4776 3.007182 CCCATTGCAAAGACCTTCAACAT 59.993 43.478 1.71 0.00 0.00 2.71
4659 4777 2.364970 CCCATTGCAAAGACCTTCAACA 59.635 45.455 1.71 0.00 0.00 3.33
4660 4778 2.867647 GCCCATTGCAAAGACCTTCAAC 60.868 50.000 1.71 0.00 40.77 3.18
4661 4779 1.344114 GCCCATTGCAAAGACCTTCAA 59.656 47.619 1.71 0.00 40.77 2.69
4662 4780 0.968405 GCCCATTGCAAAGACCTTCA 59.032 50.000 1.71 0.00 40.77 3.02
4663 4781 0.247460 GGCCCATTGCAAAGACCTTC 59.753 55.000 1.71 0.00 43.89 3.46
4664 4782 0.471591 TGGCCCATTGCAAAGACCTT 60.472 50.000 1.71 0.00 43.89 3.50
4665 4783 0.901580 CTGGCCCATTGCAAAGACCT 60.902 55.000 1.71 0.00 43.89 3.85
4666 4784 1.187567 ACTGGCCCATTGCAAAGACC 61.188 55.000 1.71 4.96 43.89 3.85
4667 4785 0.037975 CACTGGCCCATTGCAAAGAC 60.038 55.000 1.71 0.00 43.89 3.01
4668 4786 1.818959 GCACTGGCCCATTGCAAAGA 61.819 55.000 20.07 0.00 43.89 2.52
4669 4787 1.375013 GCACTGGCCCATTGCAAAG 60.375 57.895 20.07 0.00 43.89 2.77
4670 4788 1.409251 AAGCACTGGCCCATTGCAAA 61.409 50.000 25.63 0.00 41.46 3.68
4671 4789 1.837947 AAGCACTGGCCCATTGCAA 60.838 52.632 25.63 0.00 41.46 4.08
4672 4790 2.203669 AAGCACTGGCCCATTGCA 60.204 55.556 25.63 0.00 41.46 4.08
4673 4791 2.263540 CAAGCACTGGCCCATTGC 59.736 61.111 17.64 17.64 42.56 3.56
4674 4792 1.290955 CACAAGCACTGGCCCATTG 59.709 57.895 0.00 0.00 42.56 2.82
4675 4793 1.909781 CCACAAGCACTGGCCCATT 60.910 57.895 0.00 0.00 42.56 3.16
4676 4794 2.159101 ATCCACAAGCACTGGCCCAT 62.159 55.000 0.00 0.00 42.56 4.00
4677 4795 1.496444 TATCCACAAGCACTGGCCCA 61.496 55.000 0.00 0.00 42.56 5.36
4678 4796 0.323360 TTATCCACAAGCACTGGCCC 60.323 55.000 0.00 0.00 42.56 5.80
4679 4797 1.767759 ATTATCCACAAGCACTGGCC 58.232 50.000 0.00 0.00 42.56 5.36
4680 4798 4.981806 TTAATTATCCACAAGCACTGGC 57.018 40.909 0.00 0.00 41.61 4.85
4681 4799 5.296780 ACGATTAATTATCCACAAGCACTGG 59.703 40.000 0.00 0.00 0.00 4.00
4682 4800 6.363577 ACGATTAATTATCCACAAGCACTG 57.636 37.500 0.00 0.00 0.00 3.66
4683 4801 5.527582 GGACGATTAATTATCCACAAGCACT 59.472 40.000 12.05 0.00 0.00 4.40
4684 4802 5.295787 TGGACGATTAATTATCCACAAGCAC 59.704 40.000 14.58 0.00 36.30 4.40
4685 4803 5.432645 TGGACGATTAATTATCCACAAGCA 58.567 37.500 14.58 0.00 36.30 3.91
4686 4804 6.348540 GGATGGACGATTAATTATCCACAAGC 60.349 42.308 18.86 11.29 43.88 4.01
4687 4805 6.936900 AGGATGGACGATTAATTATCCACAAG 59.063 38.462 18.86 0.00 43.88 3.16
4688 4806 6.837312 AGGATGGACGATTAATTATCCACAA 58.163 36.000 18.86 3.04 43.88 3.33
4689 4807 6.433847 AGGATGGACGATTAATTATCCACA 57.566 37.500 18.86 3.60 43.88 4.17
4690 4808 6.090898 CGAAGGATGGACGATTAATTATCCAC 59.909 42.308 18.86 13.90 43.88 4.02
4691 4809 6.014925 TCGAAGGATGGACGATTAATTATCCA 60.015 38.462 18.80 18.80 45.12 3.41
4692 4810 6.310711 GTCGAAGGATGGACGATTAATTATCC 59.689 42.308 10.60 10.60 38.27 2.59
4693 4811 6.310711 GGTCGAAGGATGGACGATTAATTATC 59.689 42.308 0.00 0.00 38.27 1.75
4694 4812 6.014499 AGGTCGAAGGATGGACGATTAATTAT 60.014 38.462 0.00 0.00 38.27 1.28
4695 4813 5.303589 AGGTCGAAGGATGGACGATTAATTA 59.696 40.000 0.00 0.00 38.27 1.40
4696 4814 4.101119 AGGTCGAAGGATGGACGATTAATT 59.899 41.667 0.00 0.00 38.27 1.40
4697 4815 3.641906 AGGTCGAAGGATGGACGATTAAT 59.358 43.478 0.00 0.00 38.27 1.40
4698 4816 3.028850 AGGTCGAAGGATGGACGATTAA 58.971 45.455 0.00 0.00 38.27 1.40
4699 4817 2.662866 AGGTCGAAGGATGGACGATTA 58.337 47.619 0.00 0.00 38.27 1.75
4700 4818 1.486211 AGGTCGAAGGATGGACGATT 58.514 50.000 0.00 0.00 38.27 3.34
4701 4819 1.486211 AAGGTCGAAGGATGGACGAT 58.514 50.000 0.00 0.00 38.27 3.73
4702 4820 1.263356 AAAGGTCGAAGGATGGACGA 58.737 50.000 0.00 0.00 35.33 4.20
4703 4821 2.000447 GAAAAGGTCGAAGGATGGACG 59.000 52.381 0.00 0.00 35.33 4.79
4704 4822 3.003480 CTGAAAAGGTCGAAGGATGGAC 58.997 50.000 0.00 0.00 33.89 4.02
4705 4823 2.027192 CCTGAAAAGGTCGAAGGATGGA 60.027 50.000 0.00 0.00 0.00 3.41
4706 4824 2.027192 TCCTGAAAAGGTCGAAGGATGG 60.027 50.000 0.00 0.00 0.00 3.51
4707 4825 3.334583 TCCTGAAAAGGTCGAAGGATG 57.665 47.619 0.00 0.00 0.00 3.51
4708 4826 3.072476 TGTTCCTGAAAAGGTCGAAGGAT 59.928 43.478 0.75 0.00 0.00 3.24
4709 4827 2.436542 TGTTCCTGAAAAGGTCGAAGGA 59.563 45.455 0.00 0.00 0.00 3.36
4710 4828 2.548480 GTGTTCCTGAAAAGGTCGAAGG 59.452 50.000 0.00 0.00 0.00 3.46
4711 4829 3.467803 AGTGTTCCTGAAAAGGTCGAAG 58.532 45.455 0.00 0.00 0.00 3.79
4712 4830 3.553828 AGTGTTCCTGAAAAGGTCGAA 57.446 42.857 0.00 0.00 0.00 3.71
4713 4831 3.553828 AAGTGTTCCTGAAAAGGTCGA 57.446 42.857 0.00 0.00 0.00 4.20
4714 4832 5.744666 TTAAAGTGTTCCTGAAAAGGTCG 57.255 39.130 0.00 0.00 0.00 4.79
4715 4833 9.626045 CAATATTAAAGTGTTCCTGAAAAGGTC 57.374 33.333 0.00 0.00 0.00 3.85
4716 4834 9.362151 TCAATATTAAAGTGTTCCTGAAAAGGT 57.638 29.630 0.00 0.00 0.00 3.50
4719 4837 9.974980 GGTTCAATATTAAAGTGTTCCTGAAAA 57.025 29.630 0.00 0.00 0.00 2.29
4720 4838 8.293867 CGGTTCAATATTAAAGTGTTCCTGAAA 58.706 33.333 0.00 0.00 0.00 2.69
4721 4839 7.446013 ACGGTTCAATATTAAAGTGTTCCTGAA 59.554 33.333 0.00 0.00 0.00 3.02
4722 4840 6.938030 ACGGTTCAATATTAAAGTGTTCCTGA 59.062 34.615 0.00 0.00 0.00 3.86
4723 4841 7.021196 CACGGTTCAATATTAAAGTGTTCCTG 58.979 38.462 0.00 0.00 0.00 3.86
4724 4842 6.150474 CCACGGTTCAATATTAAAGTGTTCCT 59.850 38.462 0.00 0.00 0.00 3.36
4725 4843 6.319399 CCACGGTTCAATATTAAAGTGTTCC 58.681 40.000 0.00 0.00 0.00 3.62
4726 4844 6.072342 ACCCACGGTTCAATATTAAAGTGTTC 60.072 38.462 0.00 0.00 27.29 3.18
4727 4845 5.771165 ACCCACGGTTCAATATTAAAGTGTT 59.229 36.000 0.00 0.00 27.29 3.32
4728 4846 5.182380 CACCCACGGTTCAATATTAAAGTGT 59.818 40.000 0.00 0.00 31.02 3.55
4729 4847 5.182380 ACACCCACGGTTCAATATTAAAGTG 59.818 40.000 0.00 0.00 31.02 3.16
4730 4848 5.318630 ACACCCACGGTTCAATATTAAAGT 58.681 37.500 0.00 0.00 31.02 2.66
4731 4849 5.890424 ACACCCACGGTTCAATATTAAAG 57.110 39.130 0.00 0.00 31.02 1.85
4732 4850 5.535406 ACAACACCCACGGTTCAATATTAAA 59.465 36.000 0.00 0.00 31.02 1.52
4733 4851 5.071370 ACAACACCCACGGTTCAATATTAA 58.929 37.500 0.00 0.00 31.02 1.40
4734 4852 4.653868 ACAACACCCACGGTTCAATATTA 58.346 39.130 0.00 0.00 31.02 0.98
4735 4853 3.492337 ACAACACCCACGGTTCAATATT 58.508 40.909 0.00 0.00 31.02 1.28
4736 4854 3.149005 ACAACACCCACGGTTCAATAT 57.851 42.857 0.00 0.00 31.02 1.28
4737 4855 2.642154 ACAACACCCACGGTTCAATA 57.358 45.000 0.00 0.00 31.02 1.90
4738 4856 2.642154 TACAACACCCACGGTTCAAT 57.358 45.000 0.00 0.00 31.02 2.57
4739 4857 2.158798 TCATACAACACCCACGGTTCAA 60.159 45.455 0.00 0.00 31.02 2.69
4740 4858 1.416772 TCATACAACACCCACGGTTCA 59.583 47.619 0.00 0.00 31.02 3.18
4741 4859 2.172851 TCATACAACACCCACGGTTC 57.827 50.000 0.00 0.00 31.02 3.62
4742 4860 2.642154 TTCATACAACACCCACGGTT 57.358 45.000 0.00 0.00 31.02 4.44
4743 4861 2.619646 GTTTTCATACAACACCCACGGT 59.380 45.455 0.00 0.00 35.62 4.83
4744 4862 2.882137 AGTTTTCATACAACACCCACGG 59.118 45.455 0.00 0.00 0.00 4.94
4745 4863 4.561735 AAGTTTTCATACAACACCCACG 57.438 40.909 0.00 0.00 0.00 4.94
4746 4864 5.068591 AGGAAAGTTTTCATACAACACCCAC 59.931 40.000 6.90 0.00 38.92 4.61
4747 4865 5.205056 AGGAAAGTTTTCATACAACACCCA 58.795 37.500 6.90 0.00 38.92 4.51
4748 4866 5.562113 CGAGGAAAGTTTTCATACAACACCC 60.562 44.000 6.90 0.00 38.92 4.61
4749 4867 5.449304 CGAGGAAAGTTTTCATACAACACC 58.551 41.667 6.90 0.00 38.92 4.16
4750 4868 4.909880 GCGAGGAAAGTTTTCATACAACAC 59.090 41.667 6.90 0.00 38.92 3.32
4751 4869 4.023536 GGCGAGGAAAGTTTTCATACAACA 60.024 41.667 6.90 0.00 38.92 3.33
4752 4870 4.215613 AGGCGAGGAAAGTTTTCATACAAC 59.784 41.667 6.90 0.00 38.92 3.32
4753 4871 4.394729 AGGCGAGGAAAGTTTTCATACAA 58.605 39.130 6.90 0.00 38.92 2.41
4754 4872 4.000988 GAGGCGAGGAAAGTTTTCATACA 58.999 43.478 6.90 0.00 38.92 2.29
4755 4873 3.374367 GGAGGCGAGGAAAGTTTTCATAC 59.626 47.826 6.90 0.00 38.92 2.39
4756 4874 3.263425 AGGAGGCGAGGAAAGTTTTCATA 59.737 43.478 6.90 0.00 38.92 2.15
4757 4875 2.040412 AGGAGGCGAGGAAAGTTTTCAT 59.960 45.455 6.90 0.00 38.92 2.57
4758 4876 1.420138 AGGAGGCGAGGAAAGTTTTCA 59.580 47.619 6.90 0.00 38.92 2.69
4759 4877 1.807142 CAGGAGGCGAGGAAAGTTTTC 59.193 52.381 0.00 0.00 36.46 2.29
4760 4878 1.545651 CCAGGAGGCGAGGAAAGTTTT 60.546 52.381 0.00 0.00 0.00 2.43
4761 4879 0.036875 CCAGGAGGCGAGGAAAGTTT 59.963 55.000 0.00 0.00 0.00 2.66
4762 4880 1.679898 CCAGGAGGCGAGGAAAGTT 59.320 57.895 0.00 0.00 0.00 2.66
4763 4881 3.393360 CCAGGAGGCGAGGAAAGT 58.607 61.111 0.00 0.00 0.00 2.66
4773 4891 2.608988 ACCTCTGTGGCCAGGAGG 60.609 66.667 35.17 35.17 39.72 4.30
4774 4892 2.667418 CACCTCTGTGGCCAGGAG 59.333 66.667 22.18 22.18 39.31 3.69
4782 4900 1.417890 ACCTCTCAAACCACCTCTGTG 59.582 52.381 0.00 0.00 42.39 3.66
4783 4901 1.807814 ACCTCTCAAACCACCTCTGT 58.192 50.000 0.00 0.00 0.00 3.41
4784 4902 4.020218 TGATTACCTCTCAAACCACCTCTG 60.020 45.833 0.00 0.00 0.00 3.35
4785 4903 4.168101 TGATTACCTCTCAAACCACCTCT 58.832 43.478 0.00 0.00 0.00 3.69
4786 4904 4.553330 TGATTACCTCTCAAACCACCTC 57.447 45.455 0.00 0.00 0.00 3.85
4787 4905 5.520748 AATGATTACCTCTCAAACCACCT 57.479 39.130 0.00 0.00 0.00 4.00
4788 4906 6.316390 CACTAATGATTACCTCTCAAACCACC 59.684 42.308 0.00 0.00 0.00 4.61
4789 4907 7.103641 TCACTAATGATTACCTCTCAAACCAC 58.896 38.462 0.00 0.00 0.00 4.16
4790 4908 7.252612 TCACTAATGATTACCTCTCAAACCA 57.747 36.000 0.00 0.00 0.00 3.67
4791 4909 7.065923 GGTTCACTAATGATTACCTCTCAAACC 59.934 40.741 0.00 0.00 34.19 3.27
4792 4910 7.065923 GGGTTCACTAATGATTACCTCTCAAAC 59.934 40.741 0.00 0.00 36.38 2.93
4793 4911 7.037586 AGGGTTCACTAATGATTACCTCTCAAA 60.038 37.037 0.00 0.00 36.38 2.69
4794 4912 6.443849 AGGGTTCACTAATGATTACCTCTCAA 59.556 38.462 0.00 0.00 36.38 3.02
4795 4913 5.964477 AGGGTTCACTAATGATTACCTCTCA 59.036 40.000 0.00 0.00 36.38 3.27
4796 4914 6.487299 AGGGTTCACTAATGATTACCTCTC 57.513 41.667 0.00 0.00 36.38 3.20
4797 4915 7.989947 TTAGGGTTCACTAATGATTACCTCT 57.010 36.000 0.00 0.00 36.38 3.69
4798 4916 9.457436 TTTTTAGGGTTCACTAATGATTACCTC 57.543 33.333 0.00 0.00 36.38 3.85
4799 4917 9.990868 ATTTTTAGGGTTCACTAATGATTACCT 57.009 29.630 0.00 0.00 36.38 3.08
4807 4925 9.990868 ACATCCTTATTTTTAGGGTTCACTAAT 57.009 29.630 0.00 0.00 33.31 1.73
4808 4926 9.238368 CACATCCTTATTTTTAGGGTTCACTAA 57.762 33.333 0.00 0.00 33.41 2.24
4809 4927 7.338449 GCACATCCTTATTTTTAGGGTTCACTA 59.662 37.037 0.00 0.00 33.41 2.74
4810 4928 6.152831 GCACATCCTTATTTTTAGGGTTCACT 59.847 38.462 0.00 0.00 33.41 3.41
4811 4929 6.071616 TGCACATCCTTATTTTTAGGGTTCAC 60.072 38.462 0.00 0.00 33.41 3.18
4812 4930 6.013379 TGCACATCCTTATTTTTAGGGTTCA 58.987 36.000 0.00 0.00 33.41 3.18
4813 4931 6.524101 TGCACATCCTTATTTTTAGGGTTC 57.476 37.500 0.00 0.00 33.41 3.62
4814 4932 8.474831 GTTATGCACATCCTTATTTTTAGGGTT 58.525 33.333 0.00 0.00 33.41 4.11
4815 4933 7.839200 AGTTATGCACATCCTTATTTTTAGGGT 59.161 33.333 0.00 0.00 33.41 4.34
4816 4934 8.237811 AGTTATGCACATCCTTATTTTTAGGG 57.762 34.615 0.00 0.00 33.41 3.53
4823 4941 9.717942 GAGAAGATAGTTATGCACATCCTTATT 57.282 33.333 0.00 0.00 0.00 1.40
4824 4942 9.099071 AGAGAAGATAGTTATGCACATCCTTAT 57.901 33.333 0.00 0.00 0.00 1.73
4825 4943 8.484214 AGAGAAGATAGTTATGCACATCCTTA 57.516 34.615 0.00 0.00 0.00 2.69
4826 4944 7.372260 AGAGAAGATAGTTATGCACATCCTT 57.628 36.000 0.00 0.00 0.00 3.36
4827 4945 6.992664 AGAGAAGATAGTTATGCACATCCT 57.007 37.500 0.00 0.00 0.00 3.24
4828 4946 9.717942 ATAAAGAGAAGATAGTTATGCACATCC 57.282 33.333 0.00 0.00 0.00 3.51
4831 4949 9.330063 CCAATAAAGAGAAGATAGTTATGCACA 57.670 33.333 0.00 0.00 0.00 4.57
4832 4950 9.547753 TCCAATAAAGAGAAGATAGTTATGCAC 57.452 33.333 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.