Multiple sequence alignment - TraesCS4A01G087600

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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 TraesCS4A01G087600 chr4A 100.000 5115 0 0 1 5115 92210998 92216112 0.000000e+00 9446
1 TraesCS4A01G087600 chr4D 94.852 3807 128 29 861 4631 371798772 371794998 0.000000e+00 5882
2 TraesCS4A01G087600 chr4D 83.214 280 15 14 4663 4913 371794993 371794717 1.430000e-55 228
3 TraesCS4A01G087600 chr4B 93.758 3829 158 31 858 4635 456609369 456605571 0.000000e+00 5672
4 TraesCS4A01G087600 chr4B 98.487 859 11 2 1 858 468284352 468285209 0.000000e+00 1513
5 TraesCS4A01G087600 chr4B 92.683 123 8 1 4663 4785 456605570 456605449 5.260000e-40 176
6 TraesCS4A01G087600 chr4B 91.837 98 6 1 4816 4913 456599457 456599362 8.930000e-28 135
7 TraesCS4A01G087600 chr7A 98.721 860 11 0 1 860 657506476 657505617 0.000000e+00 1528
8 TraesCS4A01G087600 chr5A 98.721 860 11 0 1 860 22288131 22288990 0.000000e+00 1528
9 TraesCS4A01G087600 chr5A 98.485 858 13 0 1 858 549963653 549962796 0.000000e+00 1513
10 TraesCS4A01G087600 chr6B 98.605 860 12 0 1 860 135852752 135851893 0.000000e+00 1522
11 TraesCS4A01G087600 chr7B 98.492 862 13 0 1 862 253904352 253903491 0.000000e+00 1520
12 TraesCS4A01G087600 chr3A 98.601 858 12 0 1 858 604310113 604309256 0.000000e+00 1519
13 TraesCS4A01G087600 chr2A 98.487 859 13 0 1 859 608889398 608890256 0.000000e+00 1515
14 TraesCS4A01G087600 chr2B 98.260 862 15 0 1 862 689373872 689374733 0.000000e+00 1509


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 TraesCS4A01G087600 chr4A 92210998 92216112 5114 False 9446 9446 100.0000 1 5115 1 chr4A.!!$F1 5114
1 TraesCS4A01G087600 chr4D 371794717 371798772 4055 True 3055 5882 89.0330 861 4913 2 chr4D.!!$R1 4052
2 TraesCS4A01G087600 chr4B 456605449 456609369 3920 True 2924 5672 93.2205 858 4785 2 chr4B.!!$R2 3927
3 TraesCS4A01G087600 chr4B 468284352 468285209 857 False 1513 1513 98.4870 1 858 1 chr4B.!!$F1 857
4 TraesCS4A01G087600 chr7A 657505617 657506476 859 True 1528 1528 98.7210 1 860 1 chr7A.!!$R1 859
5 TraesCS4A01G087600 chr5A 22288131 22288990 859 False 1528 1528 98.7210 1 860 1 chr5A.!!$F1 859
6 TraesCS4A01G087600 chr5A 549962796 549963653 857 True 1513 1513 98.4850 1 858 1 chr5A.!!$R1 857
7 TraesCS4A01G087600 chr6B 135851893 135852752 859 True 1522 1522 98.6050 1 860 1 chr6B.!!$R1 859
8 TraesCS4A01G087600 chr7B 253903491 253904352 861 True 1520 1520 98.4920 1 862 1 chr7B.!!$R1 861
9 TraesCS4A01G087600 chr3A 604309256 604310113 857 True 1519 1519 98.6010 1 858 1 chr3A.!!$R1 857
10 TraesCS4A01G087600 chr2A 608889398 608890256 858 False 1515 1515 98.4870 1 859 1 chr2A.!!$F1 858
11 TraesCS4A01G087600 chr2B 689373872 689374733 861 False 1509 1509 98.2600 1 862 1 chr2B.!!$F1 861

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
723 725 1.153628 GATGTGCGACGCCTAAGGT 60.154 57.895 18.69 0.0 0.00 3.50 F
1419 1426 0.103390 GGTAGGCCTTCTTCTCTCGC 59.897 60.000 12.58 0.0 0.00 5.03 F
2912 2941 0.106149 GGACCTGACAAACACGTCCT 59.894 55.000 0.00 0.0 45.01 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2629 2658 0.826672 AGGGAACGAACAGACCGAGT 60.827 55.0 0.00 0.00 0.0 4.18 R
3129 3196 0.035820 GGGATGAGTAAACCACGCCA 60.036 55.0 0.00 0.00 0.0 5.69 R
4813 4912 0.044092 TCCTACATTCTGGGGCCTCA 59.956 55.0 4.49 4.49 0.0 3.86 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
487 488 4.408270 TCAAATCTTCAGATCTGAGAGGGG 59.592 45.833 23.92 13.86 41.13 4.79
660 662 1.817099 GCTCTTAGGCGCTGCACAT 60.817 57.895 7.64 0.00 0.00 3.21
723 725 1.153628 GATGTGCGACGCCTAAGGT 60.154 57.895 18.69 0.00 0.00 3.50
875 877 2.122769 TCACCCGACCCAACCTCA 60.123 61.111 0.00 0.00 0.00 3.86
969 974 3.732849 CAGCCTTCCACCCCCTCC 61.733 72.222 0.00 0.00 0.00 4.30
1397 1404 2.690778 GCGCAAGGAGAAACGGCAT 61.691 57.895 0.30 0.00 38.28 4.40
1419 1426 0.103390 GGTAGGCCTTCTTCTCTCGC 59.897 60.000 12.58 0.00 0.00 5.03
1423 1430 2.393646 AGGCCTTCTTCTCTCGCTAAT 58.606 47.619 0.00 0.00 0.00 1.73
1429 1436 3.406728 TCTTCTCTCGCTAATGTGTCG 57.593 47.619 0.00 0.00 0.00 4.35
1451 1458 3.243301 GCCATTGTCCATTGATGCTACAG 60.243 47.826 0.00 0.00 0.00 2.74
1459 1466 4.883585 TCCATTGATGCTACAGGAACATTC 59.116 41.667 0.00 0.00 0.00 2.67
1470 1477 5.160607 ACAGGAACATTCTGATTCGGTTA 57.839 39.130 0.00 0.00 36.22 2.85
1509 1516 1.093496 GGGTTTATTGTCCGAGGGCG 61.093 60.000 0.00 0.00 37.24 6.13
1510 1517 0.392060 GGTTTATTGTCCGAGGGCGT 60.392 55.000 0.00 0.00 35.23 5.68
1522 1529 3.905249 GGGCGTCATTGACCTTCC 58.095 61.111 11.12 9.43 32.64 3.46
1590 1609 4.948847 ACGATGCTGTCATTGCTAAGATA 58.051 39.130 0.00 0.00 37.56 1.98
1612 1631 7.767198 AGATAATTTGATTTGGTGCTCAATTGG 59.233 33.333 5.42 0.00 34.98 3.16
1655 1674 5.597806 ACGTATTCTGCCGAAGATATTTGA 58.402 37.500 0.00 0.00 33.93 2.69
1731 1750 3.784338 ACTTCATTTTGCTGTGTTGGTG 58.216 40.909 0.00 0.00 0.00 4.17
1798 1817 4.806892 TCCATGCCATATTCTCCACAAAT 58.193 39.130 0.00 0.00 0.00 2.32
1813 1832 3.372822 CCACAAATTCATGAGCAATTGGC 59.627 43.478 7.72 0.00 45.30 4.52
1839 1858 2.742053 GCACAATGTTGTATCACGGACT 59.258 45.455 0.00 0.00 39.91 3.85
2022 2041 2.923655 CACGTTTAGACAGATCGCATGT 59.076 45.455 0.00 0.00 0.00 3.21
2027 2046 5.504755 CGTTTAGACAGATCGCATGTTTTTC 59.495 40.000 0.00 0.00 0.00 2.29
2028 2047 6.370593 GTTTAGACAGATCGCATGTTTTTCA 58.629 36.000 0.00 0.00 0.00 2.69
2029 2048 6.552859 TTAGACAGATCGCATGTTTTTCAA 57.447 33.333 0.00 0.00 0.00 2.69
2040 2059 8.984891 TCGCATGTTTTTCAAATCTTAATCAT 57.015 26.923 0.00 0.00 0.00 2.45
2068 2087 2.939103 ACACCATCTTCAGCGAATTAGC 59.061 45.455 1.81 1.81 37.41 3.09
2280 2302 0.804364 TGCAGTATGGAGCTTTTGCG 59.196 50.000 0.00 0.00 44.42 4.85
2442 2464 6.458210 CCAAGTAGCAAATGGTTCAAGAAAT 58.542 36.000 0.00 0.00 0.00 2.17
2468 2490 5.183228 CCACCCAAACATTACTCGATTACT 58.817 41.667 0.00 0.00 0.00 2.24
2629 2658 3.758755 ACTCTTTGATCTCTGCACACA 57.241 42.857 0.00 0.00 0.00 3.72
2699 2728 1.475034 GCCCCACGTGATGTACATGAT 60.475 52.381 19.30 0.00 38.72 2.45
2733 2762 1.522668 TGAACAATCTGAGCAACCGG 58.477 50.000 0.00 0.00 0.00 5.28
2804 2833 3.061697 CCAAGGACGCGTAATTGTTAGAC 59.938 47.826 25.41 6.88 0.00 2.59
2877 2906 4.695455 CCAGTTAAACGTGACTTCATCCAT 59.305 41.667 0.00 0.00 0.00 3.41
2912 2941 0.106149 GGACCTGACAAACACGTCCT 59.894 55.000 0.00 0.00 45.01 3.85
2929 2958 1.531365 CTTGGCCACCACACCATGT 60.531 57.895 3.88 0.00 35.42 3.21
2944 2973 1.302511 ATGTGTGGCCTTGTCGTCC 60.303 57.895 3.32 0.00 0.00 4.79
2945 2974 1.768684 ATGTGTGGCCTTGTCGTCCT 61.769 55.000 3.32 0.00 0.00 3.85
2946 2975 1.227853 GTGTGGCCTTGTCGTCCTT 60.228 57.895 3.32 0.00 0.00 3.36
2947 2976 1.227823 TGTGGCCTTGTCGTCCTTG 60.228 57.895 3.32 0.00 0.00 3.61
2948 2977 1.070786 GTGGCCTTGTCGTCCTTGA 59.929 57.895 3.32 0.00 0.00 3.02
2949 2978 0.951040 GTGGCCTTGTCGTCCTTGAG 60.951 60.000 3.32 0.00 0.00 3.02
2950 2979 2.035442 GGCCTTGTCGTCCTTGAGC 61.035 63.158 0.00 0.00 0.00 4.26
2963 2992 3.679389 TCCTTGAGCTTGAGGACATTTC 58.321 45.455 13.37 0.00 37.15 2.17
3075 3142 4.093115 CGACAGTGTCTTGTCTACTACGAT 59.907 45.833 20.64 0.00 44.13 3.73
3129 3196 2.472607 AAAGGAGGTAGGAGGGGCGT 62.473 60.000 0.00 0.00 0.00 5.68
3192 3259 1.490490 AGAGAATTAAGCGGGGCATGA 59.510 47.619 0.00 0.00 0.00 3.07
3258 3325 2.163613 GCCTCCTGTTTTCCGGTATTTG 59.836 50.000 0.00 0.00 0.00 2.32
3262 3329 5.189659 TCCTGTTTTCCGGTATTTGTTTG 57.810 39.130 0.00 0.00 0.00 2.93
3263 3330 4.038162 TCCTGTTTTCCGGTATTTGTTTGG 59.962 41.667 0.00 0.00 0.00 3.28
3584 3654 2.355756 ACTATGTGATTTGTGCGATGGC 59.644 45.455 0.00 0.00 40.52 4.40
3782 3852 5.129320 TGCTATTTCTGAATCTCCAGCTACA 59.871 40.000 0.00 0.00 34.28 2.74
3803 3873 0.321346 CAACCCCTTCCACAAATGCC 59.679 55.000 0.00 0.00 0.00 4.40
3860 3930 6.526325 CAGAGATAGATAAGAAAATCCGAGCG 59.474 42.308 0.00 0.00 0.00 5.03
3917 3987 0.453782 CATCTGTGCATGCGTGTGTG 60.454 55.000 14.09 5.53 0.00 3.82
3918 3988 2.191354 ATCTGTGCATGCGTGTGTGC 62.191 55.000 14.09 0.00 41.61 4.57
3970 4042 4.614555 TGTGTGCTATCGCCTTAATTTG 57.385 40.909 0.00 0.00 34.43 2.32
4034 4106 5.993441 CCAGAAAAATTGAAACCTGAGCAAT 59.007 36.000 0.00 0.00 33.96 3.56
4045 4117 2.554032 ACCTGAGCAATTGGAGAAAACG 59.446 45.455 7.72 0.00 0.00 3.60
4153 4225 4.511527 CCTGATGTAAACTGAGCTGTCAT 58.488 43.478 0.00 0.00 30.18 3.06
4166 4238 1.228094 TGTCATTTCTGCACGCCCA 60.228 52.632 0.00 0.00 0.00 5.36
4207 4279 4.216731 CCGAAATTCAATCGATCATGCTG 58.783 43.478 0.00 0.00 42.76 4.41
4215 4287 2.391616 TCGATCATGCTGTGCTTCTT 57.608 45.000 0.00 0.00 0.00 2.52
4360 4432 8.715998 GCAATATCTGTTTGTCGAAGATCATAT 58.284 33.333 0.00 0.00 40.67 1.78
4438 4510 1.133606 ACTTTGGGGTCCATTTGACGT 60.134 47.619 0.00 0.00 45.46 4.34
4440 4512 2.074729 TTGGGGTCCATTTGACGTTT 57.925 45.000 0.00 0.00 45.46 3.60
4525 4603 4.697352 CACCTTGAGTGGAGGAATAACAAG 59.303 45.833 0.00 0.00 43.26 3.16
4536 4614 6.655003 TGGAGGAATAACAAGACAAAGTGATC 59.345 38.462 0.00 0.00 0.00 2.92
4568 4646 8.928448 AGCAGAGGAATTGACTATAATGTCTTA 58.072 33.333 0.00 0.00 37.79 2.10
4592 4670 9.859427 TTATGCAATCTTAGAATTTCACAAAGG 57.141 29.630 0.00 0.00 0.00 3.11
4611 4689 1.885887 GGTGTTTGTATGCCTTGCAGA 59.114 47.619 0.00 0.00 43.65 4.26
4613 4691 3.056607 GGTGTTTGTATGCCTTGCAGAAT 60.057 43.478 0.00 0.00 43.65 2.40
4631 4709 5.049474 GCAGAATTTTTGTGGGAAATTGGTC 60.049 40.000 0.08 0.00 36.96 4.02
4635 4713 4.414337 TTTTGTGGGAAATTGGTCCTTG 57.586 40.909 0.00 0.00 37.85 3.61
4636 4714 3.320610 TTGTGGGAAATTGGTCCTTGA 57.679 42.857 0.00 0.00 37.85 3.02
4637 4715 3.541242 TGTGGGAAATTGGTCCTTGAT 57.459 42.857 0.00 0.00 37.85 2.57
4638 4716 3.855668 TGTGGGAAATTGGTCCTTGATT 58.144 40.909 0.00 0.00 37.85 2.57
4639 4717 3.577848 TGTGGGAAATTGGTCCTTGATTG 59.422 43.478 0.00 0.00 37.85 2.67
4640 4718 3.055891 GTGGGAAATTGGTCCTTGATTGG 60.056 47.826 0.00 0.00 37.85 3.16
4641 4719 3.181413 TGGGAAATTGGTCCTTGATTGGA 60.181 43.478 0.00 0.00 37.85 3.53
4650 4728 2.517959 TCCTTGATTGGACAGCAAAGG 58.482 47.619 0.00 0.00 0.00 3.11
4651 4729 1.547372 CCTTGATTGGACAGCAAAGGG 59.453 52.381 0.00 0.00 0.00 3.95
4652 4730 2.517959 CTTGATTGGACAGCAAAGGGA 58.482 47.619 0.00 0.00 0.00 4.20
4653 4731 2.205022 TGATTGGACAGCAAAGGGAG 57.795 50.000 0.00 0.00 0.00 4.30
4654 4732 1.704628 TGATTGGACAGCAAAGGGAGA 59.295 47.619 0.00 0.00 0.00 3.71
4655 4733 2.087646 GATTGGACAGCAAAGGGAGAC 58.912 52.381 0.00 0.00 0.00 3.36
4667 4745 4.234673 GGAGACCCCACCTTGACT 57.765 61.111 0.00 0.00 34.14 3.41
4668 4746 1.984020 GGAGACCCCACCTTGACTC 59.016 63.158 0.00 0.00 34.14 3.36
4669 4747 0.836400 GGAGACCCCACCTTGACTCA 60.836 60.000 0.00 0.00 34.14 3.41
4700 4778 4.274950 TCAAAGGAATTTCAACACGAGGTC 59.725 41.667 0.00 0.00 0.00 3.85
4795 4873 4.256920 TCTGAGAAGCCAGATTTAAGCAC 58.743 43.478 0.00 0.00 38.18 4.40
4799 4877 1.739067 AGCCAGATTTAAGCACGACC 58.261 50.000 0.00 0.00 0.00 4.79
4800 4878 1.003118 AGCCAGATTTAAGCACGACCA 59.997 47.619 0.00 0.00 0.00 4.02
4801 4879 2.017049 GCCAGATTTAAGCACGACCAT 58.983 47.619 0.00 0.00 0.00 3.55
4803 4881 3.270027 CCAGATTTAAGCACGACCATGA 58.730 45.455 0.00 0.00 0.00 3.07
4804 4882 3.879295 CCAGATTTAAGCACGACCATGAT 59.121 43.478 0.00 0.00 0.00 2.45
4813 4912 3.059884 GCACGACCATGATCGATACAAT 58.940 45.455 18.44 0.00 45.13 2.71
4814 4913 3.120889 GCACGACCATGATCGATACAATG 60.121 47.826 18.44 3.58 45.13 2.82
4819 4918 3.005554 CCATGATCGATACAATGAGGCC 58.994 50.000 13.91 0.00 0.00 5.19
4821 4920 1.347707 TGATCGATACAATGAGGCCCC 59.652 52.381 0.00 0.00 0.00 5.80
4839 4938 4.137543 GCCCCAGAATGTAGGAATAACAG 58.862 47.826 0.00 0.00 29.59 3.16
4852 4959 5.500234 AGGAATAACAGCATAGTTTGAGCA 58.500 37.500 0.00 0.00 33.07 4.26
4868 4975 2.012673 GAGCACCATGTCTTGTGGATC 58.987 52.381 0.00 0.00 39.12 3.36
4875 4982 2.642171 TGTCTTGTGGATCCCTAGGT 57.358 50.000 9.90 0.00 0.00 3.08
4876 4983 2.187958 TGTCTTGTGGATCCCTAGGTG 58.812 52.381 9.90 0.00 0.00 4.00
4896 5003 1.126846 GATTTCACACCTCAAGCGTCG 59.873 52.381 0.00 0.00 0.00 5.12
4913 5020 3.363673 GCGTCGGAGTAAGAAAACAAAGG 60.364 47.826 0.00 0.00 0.00 3.11
4914 5021 4.053295 CGTCGGAGTAAGAAAACAAAGGA 58.947 43.478 0.00 0.00 0.00 3.36
4915 5022 4.508861 CGTCGGAGTAAGAAAACAAAGGAA 59.491 41.667 0.00 0.00 0.00 3.36
4916 5023 5.178809 CGTCGGAGTAAGAAAACAAAGGAAT 59.821 40.000 0.00 0.00 0.00 3.01
4917 5024 6.371389 GTCGGAGTAAGAAAACAAAGGAATG 58.629 40.000 0.00 0.00 0.00 2.67
4918 5025 5.048991 TCGGAGTAAGAAAACAAAGGAATGC 60.049 40.000 0.00 0.00 0.00 3.56
4919 5026 5.154222 GGAGTAAGAAAACAAAGGAATGCG 58.846 41.667 0.00 0.00 0.00 4.73
4920 5027 5.048991 GGAGTAAGAAAACAAAGGAATGCGA 60.049 40.000 0.00 0.00 0.00 5.10
4921 5028 6.385649 AGTAAGAAAACAAAGGAATGCGAA 57.614 33.333 0.00 0.00 0.00 4.70
4922 5029 6.801575 AGTAAGAAAACAAAGGAATGCGAAA 58.198 32.000 0.00 0.00 0.00 3.46
4923 5030 7.262048 AGTAAGAAAACAAAGGAATGCGAAAA 58.738 30.769 0.00 0.00 0.00 2.29
4924 5031 6.976636 AAGAAAACAAAGGAATGCGAAAAA 57.023 29.167 0.00 0.00 0.00 1.94
4925 5032 6.588348 AGAAAACAAAGGAATGCGAAAAAG 57.412 33.333 0.00 0.00 0.00 2.27
4926 5033 5.523552 AGAAAACAAAGGAATGCGAAAAAGG 59.476 36.000 0.00 0.00 0.00 3.11
4927 5034 2.754472 ACAAAGGAATGCGAAAAAGGC 58.246 42.857 0.00 0.00 0.00 4.35
4928 5035 2.102252 ACAAAGGAATGCGAAAAAGGCA 59.898 40.909 0.00 0.00 45.71 4.75
4938 5045 3.925913 TGCGAAAAAGGCATAATTTGAGC 59.074 39.130 0.00 0.00 35.04 4.26
4939 5046 3.925913 GCGAAAAAGGCATAATTTGAGCA 59.074 39.130 0.00 0.00 0.00 4.26
4940 5047 4.201618 GCGAAAAAGGCATAATTTGAGCAC 60.202 41.667 0.00 0.00 0.00 4.40
4941 5048 4.327087 CGAAAAAGGCATAATTTGAGCACC 59.673 41.667 0.00 0.00 0.00 5.01
4942 5049 4.888326 AAAAGGCATAATTTGAGCACCA 57.112 36.364 0.00 0.00 0.00 4.17
4943 5050 5.425196 AAAAGGCATAATTTGAGCACCAT 57.575 34.783 0.00 0.00 0.00 3.55
4944 5051 4.395959 AAGGCATAATTTGAGCACCATG 57.604 40.909 0.00 0.00 0.00 3.66
4945 5052 2.101917 AGGCATAATTTGAGCACCATGC 59.898 45.455 0.00 0.00 45.46 4.06
4946 5053 2.476821 GCATAATTTGAGCACCATGCC 58.523 47.619 0.00 0.00 46.52 4.40
4947 5054 2.101917 GCATAATTTGAGCACCATGCCT 59.898 45.455 0.00 0.00 46.52 4.75
4948 5055 3.431207 GCATAATTTGAGCACCATGCCTT 60.431 43.478 0.00 0.00 46.52 4.35
4949 5056 2.754946 AATTTGAGCACCATGCCTTG 57.245 45.000 0.00 0.00 46.52 3.61
4950 5057 1.636148 ATTTGAGCACCATGCCTTGT 58.364 45.000 0.00 0.00 46.52 3.16
4951 5058 0.675083 TTTGAGCACCATGCCTTGTG 59.325 50.000 0.00 0.00 46.52 3.33
4952 5059 1.180456 TTGAGCACCATGCCTTGTGG 61.180 55.000 0.00 0.00 46.52 4.17
4953 5060 1.303561 GAGCACCATGCCTTGTGGA 60.304 57.895 0.00 0.00 46.52 4.02
4954 5061 0.682209 GAGCACCATGCCTTGTGGAT 60.682 55.000 0.00 0.00 46.52 3.41
4955 5062 0.251922 AGCACCATGCCTTGTGGATT 60.252 50.000 0.00 0.00 46.52 3.01
4956 5063 0.174162 GCACCATGCCTTGTGGATTC 59.826 55.000 0.00 0.00 39.12 2.52
4957 5064 0.819582 CACCATGCCTTGTGGATTCC 59.180 55.000 0.00 0.00 39.12 3.01
4958 5065 0.706433 ACCATGCCTTGTGGATTCCT 59.294 50.000 3.95 0.00 39.12 3.36
4959 5066 1.922447 ACCATGCCTTGTGGATTCCTA 59.078 47.619 3.95 0.00 39.12 2.94
4960 5067 2.092212 ACCATGCCTTGTGGATTCCTAG 60.092 50.000 3.95 0.00 39.12 3.02
4961 5068 2.173356 CCATGCCTTGTGGATTCCTAGA 59.827 50.000 3.95 0.00 39.12 2.43
4962 5069 3.371917 CCATGCCTTGTGGATTCCTAGAA 60.372 47.826 3.95 0.00 39.12 2.10
4963 5070 4.467769 CATGCCTTGTGGATTCCTAGAAT 58.532 43.478 3.95 0.00 34.57 2.40
4964 5071 4.591321 TGCCTTGTGGATTCCTAGAATT 57.409 40.909 3.95 0.00 34.57 2.17
4965 5072 4.526970 TGCCTTGTGGATTCCTAGAATTC 58.473 43.478 3.95 0.00 34.57 2.17
4966 5073 4.018506 TGCCTTGTGGATTCCTAGAATTCA 60.019 41.667 8.44 0.00 34.57 2.57
4967 5074 4.949856 GCCTTGTGGATTCCTAGAATTCAA 59.050 41.667 8.44 0.00 34.57 2.69
4968 5075 5.418840 GCCTTGTGGATTCCTAGAATTCAAA 59.581 40.000 8.44 0.00 34.57 2.69
4969 5076 6.071391 GCCTTGTGGATTCCTAGAATTCAAAA 60.071 38.462 8.44 1.07 34.57 2.44
4970 5077 7.364144 GCCTTGTGGATTCCTAGAATTCAAAAT 60.364 37.037 8.44 1.65 34.57 1.82
4971 5078 9.189156 CCTTGTGGATTCCTAGAATTCAAAATA 57.811 33.333 8.44 0.00 34.57 1.40
4986 5093 9.986833 GAATTCAAAATATTGTTGTTTATGCCC 57.013 29.630 0.00 0.00 37.79 5.36
4987 5094 9.512588 AATTCAAAATATTGTTGTTTATGCCCA 57.487 25.926 0.00 0.00 37.79 5.36
4988 5095 9.683870 ATTCAAAATATTGTTGTTTATGCCCAT 57.316 25.926 0.00 0.00 37.79 4.00
4989 5096 9.512588 TTCAAAATATTGTTGTTTATGCCCATT 57.487 25.926 0.00 0.00 37.79 3.16
4997 5104 9.737844 ATTGTTGTTTATGCCCATTAGAAATTT 57.262 25.926 0.00 0.00 0.00 1.82
4998 5105 9.566432 TTGTTGTTTATGCCCATTAGAAATTTT 57.434 25.926 0.00 0.00 0.00 1.82
4999 5106 8.997323 TGTTGTTTATGCCCATTAGAAATTTTG 58.003 29.630 0.00 0.00 0.00 2.44
5000 5107 8.998377 GTTGTTTATGCCCATTAGAAATTTTGT 58.002 29.630 0.00 0.00 0.00 2.83
5001 5108 8.545229 TGTTTATGCCCATTAGAAATTTTGTG 57.455 30.769 0.00 0.00 0.00 3.33
5002 5109 7.605691 TGTTTATGCCCATTAGAAATTTTGTGG 59.394 33.333 0.00 0.00 0.00 4.17
5003 5110 7.487822 TTATGCCCATTAGAAATTTTGTGGA 57.512 32.000 11.40 0.00 0.00 4.02
5004 5111 5.404466 TGCCCATTAGAAATTTTGTGGAG 57.596 39.130 11.40 5.56 0.00 3.86
5005 5112 5.083122 TGCCCATTAGAAATTTTGTGGAGA 58.917 37.500 11.40 0.00 0.00 3.71
5006 5113 5.541868 TGCCCATTAGAAATTTTGTGGAGAA 59.458 36.000 11.40 0.00 0.00 2.87
5007 5114 5.869344 GCCCATTAGAAATTTTGTGGAGAAC 59.131 40.000 11.40 0.00 0.00 3.01
5008 5115 6.295292 GCCCATTAGAAATTTTGTGGAGAACT 60.295 38.462 11.40 0.00 0.00 3.01
5009 5116 7.093945 GCCCATTAGAAATTTTGTGGAGAACTA 60.094 37.037 11.40 0.00 0.00 2.24
5010 5117 8.462016 CCCATTAGAAATTTTGTGGAGAACTAG 58.538 37.037 11.40 0.00 0.00 2.57
5011 5118 9.014297 CCATTAGAAATTTTGTGGAGAACTAGT 57.986 33.333 0.00 0.00 0.00 2.57
5025 5132 5.975693 AGAACTAGTTCTTGACTGGAGAG 57.024 43.478 28.73 0.00 46.95 3.20
5026 5133 5.636123 AGAACTAGTTCTTGACTGGAGAGA 58.364 41.667 28.73 0.00 46.95 3.10
5027 5134 5.710099 AGAACTAGTTCTTGACTGGAGAGAG 59.290 44.000 28.73 0.00 46.95 3.20
5028 5135 3.761752 ACTAGTTCTTGACTGGAGAGAGC 59.238 47.826 0.00 0.00 39.05 4.09
5029 5136 2.603021 AGTTCTTGACTGGAGAGAGCA 58.397 47.619 0.00 0.00 37.17 4.26
5030 5137 3.172339 AGTTCTTGACTGGAGAGAGCAT 58.828 45.455 0.00 0.00 37.17 3.79
5031 5138 4.348486 AGTTCTTGACTGGAGAGAGCATA 58.652 43.478 0.00 0.00 37.17 3.14
5032 5139 4.402155 AGTTCTTGACTGGAGAGAGCATAG 59.598 45.833 0.00 0.00 37.17 2.23
5033 5140 3.295093 TCTTGACTGGAGAGAGCATAGG 58.705 50.000 0.00 0.00 0.00 2.57
5034 5141 3.053320 TCTTGACTGGAGAGAGCATAGGA 60.053 47.826 0.00 0.00 0.00 2.94
5035 5142 2.942804 TGACTGGAGAGAGCATAGGAG 58.057 52.381 0.00 0.00 0.00 3.69
5036 5143 2.243478 TGACTGGAGAGAGCATAGGAGT 59.757 50.000 0.00 0.00 0.00 3.85
5037 5144 2.622942 GACTGGAGAGAGCATAGGAGTG 59.377 54.545 0.00 0.00 0.00 3.51
5038 5145 2.243478 ACTGGAGAGAGCATAGGAGTGA 59.757 50.000 0.00 0.00 0.00 3.41
5039 5146 3.295093 CTGGAGAGAGCATAGGAGTGAA 58.705 50.000 0.00 0.00 0.00 3.18
5040 5147 3.703556 CTGGAGAGAGCATAGGAGTGAAA 59.296 47.826 0.00 0.00 0.00 2.69
5041 5148 3.703556 TGGAGAGAGCATAGGAGTGAAAG 59.296 47.826 0.00 0.00 0.00 2.62
5042 5149 3.957497 GGAGAGAGCATAGGAGTGAAAGA 59.043 47.826 0.00 0.00 0.00 2.52
5043 5150 4.404073 GGAGAGAGCATAGGAGTGAAAGAA 59.596 45.833 0.00 0.00 0.00 2.52
5044 5151 5.451798 GGAGAGAGCATAGGAGTGAAAGAAG 60.452 48.000 0.00 0.00 0.00 2.85
5045 5152 4.119136 GAGAGCATAGGAGTGAAAGAAGC 58.881 47.826 0.00 0.00 0.00 3.86
5046 5153 3.517100 AGAGCATAGGAGTGAAAGAAGCA 59.483 43.478 0.00 0.00 0.00 3.91
5047 5154 4.163839 AGAGCATAGGAGTGAAAGAAGCAT 59.836 41.667 0.00 0.00 0.00 3.79
5048 5155 4.450053 AGCATAGGAGTGAAAGAAGCATC 58.550 43.478 0.00 0.00 0.00 3.91
5049 5156 4.163839 AGCATAGGAGTGAAAGAAGCATCT 59.836 41.667 0.00 0.00 37.57 2.90
5051 5158 5.220815 GCATAGGAGTGAAAGAAGCATCTTG 60.221 44.000 4.72 0.00 45.19 3.02
5052 5159 3.080319 AGGAGTGAAAGAAGCATCTTGC 58.920 45.455 4.72 3.57 45.19 4.01
5053 5160 2.163211 GGAGTGAAAGAAGCATCTTGCC 59.837 50.000 4.72 1.53 46.52 4.52
5054 5161 3.080319 GAGTGAAAGAAGCATCTTGCCT 58.920 45.455 4.72 2.90 46.52 4.75
5055 5162 3.494332 AGTGAAAGAAGCATCTTGCCTT 58.506 40.909 4.72 0.00 46.52 4.35
5056 5163 3.893813 AGTGAAAGAAGCATCTTGCCTTT 59.106 39.130 4.72 4.20 46.52 3.11
5057 5164 5.072741 AGTGAAAGAAGCATCTTGCCTTTA 58.927 37.500 4.72 0.00 46.52 1.85
5058 5165 5.536161 AGTGAAAGAAGCATCTTGCCTTTAA 59.464 36.000 4.72 0.00 46.52 1.52
5059 5166 5.631096 GTGAAAGAAGCATCTTGCCTTTAAC 59.369 40.000 4.72 0.00 46.52 2.01
5060 5167 5.536161 TGAAAGAAGCATCTTGCCTTTAACT 59.464 36.000 4.72 0.00 46.52 2.24
5061 5168 6.040842 TGAAAGAAGCATCTTGCCTTTAACTT 59.959 34.615 4.72 0.00 46.52 2.66
5062 5169 5.635417 AGAAGCATCTTGCCTTTAACTTC 57.365 39.130 0.00 0.00 46.52 3.01
5063 5170 5.320277 AGAAGCATCTTGCCTTTAACTTCT 58.680 37.500 0.00 0.00 46.52 2.85
5064 5171 5.414144 AGAAGCATCTTGCCTTTAACTTCTC 59.586 40.000 0.00 0.00 46.52 2.87
5065 5172 4.655963 AGCATCTTGCCTTTAACTTCTCA 58.344 39.130 0.00 0.00 46.52 3.27
5066 5173 5.072741 AGCATCTTGCCTTTAACTTCTCAA 58.927 37.500 0.00 0.00 46.52 3.02
5067 5174 5.536161 AGCATCTTGCCTTTAACTTCTCAAA 59.464 36.000 0.00 0.00 46.52 2.69
5068 5175 5.860716 GCATCTTGCCTTTAACTTCTCAAAG 59.139 40.000 0.00 0.00 37.42 2.77
5083 5190 9.971922 AACTTCTCAAAGGAATTTTAACATGAG 57.028 29.630 0.00 0.00 36.78 2.90
5084 5191 9.354673 ACTTCTCAAAGGAATTTTAACATGAGA 57.645 29.630 0.00 0.00 36.78 3.27
5088 5195 9.362539 CTCAAAGGAATTTTAACATGAGATTGG 57.637 33.333 0.00 0.00 0.00 3.16
5089 5196 9.087871 TCAAAGGAATTTTAACATGAGATTGGA 57.912 29.630 0.00 0.00 0.00 3.53
5090 5197 9.362539 CAAAGGAATTTTAACATGAGATTGGAG 57.637 33.333 0.00 0.00 0.00 3.86
5091 5198 7.105241 AGGAATTTTAACATGAGATTGGAGC 57.895 36.000 0.00 0.00 0.00 4.70
5092 5199 6.894103 AGGAATTTTAACATGAGATTGGAGCT 59.106 34.615 0.00 0.00 0.00 4.09
5093 5200 7.067981 AGGAATTTTAACATGAGATTGGAGCTC 59.932 37.037 4.71 4.71 0.00 4.09
5094 5201 7.148018 GGAATTTTAACATGAGATTGGAGCTCA 60.148 37.037 17.19 0.00 45.52 4.26
5103 5210 6.550938 TGAGATTGGAGCTCATCTTTAGAA 57.449 37.500 17.19 0.00 37.46 2.10
5104 5211 7.134362 TGAGATTGGAGCTCATCTTTAGAAT 57.866 36.000 17.19 0.20 37.46 2.40
5105 5212 7.215789 TGAGATTGGAGCTCATCTTTAGAATC 58.784 38.462 17.19 8.88 37.46 2.52
5106 5213 6.532826 AGATTGGAGCTCATCTTTAGAATCC 58.467 40.000 17.19 0.00 0.00 3.01
5107 5214 5.965033 TTGGAGCTCATCTTTAGAATCCT 57.035 39.130 17.19 0.00 0.00 3.24
5108 5215 5.543507 TGGAGCTCATCTTTAGAATCCTC 57.456 43.478 17.19 0.00 0.00 3.71
5109 5216 4.346418 TGGAGCTCATCTTTAGAATCCTCC 59.654 45.833 17.19 0.00 37.45 4.30
5110 5217 4.346418 GGAGCTCATCTTTAGAATCCTCCA 59.654 45.833 17.19 0.00 37.04 3.86
5111 5218 5.163258 GGAGCTCATCTTTAGAATCCTCCAA 60.163 44.000 17.19 0.00 37.04 3.53
5112 5219 6.319048 AGCTCATCTTTAGAATCCTCCAAA 57.681 37.500 0.00 0.00 0.00 3.28
5113 5220 6.725364 AGCTCATCTTTAGAATCCTCCAAAA 58.275 36.000 0.00 0.00 0.00 2.44
5114 5221 6.601217 AGCTCATCTTTAGAATCCTCCAAAAC 59.399 38.462 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
723 725 0.391130 CCTACTGTGCAGCGCCTTTA 60.391 55.000 2.29 0.00 0.00 1.85
808 810 6.014840 AGGCAGAAATCAAATCACAAACTGAT 60.015 34.615 0.00 0.00 41.85 2.90
875 877 0.412640 AGTTAAGACCGGAGACCCCT 59.587 55.000 9.46 0.00 0.00 4.79
969 974 4.084147 TACGGGGTCTGGAGGGGG 62.084 72.222 0.00 0.00 0.00 5.40
1411 1418 1.469251 GGCGACACATTAGCGAGAGAA 60.469 52.381 0.00 0.00 0.00 2.87
1412 1419 0.100682 GGCGACACATTAGCGAGAGA 59.899 55.000 0.00 0.00 0.00 3.10
1429 1436 2.689471 TGTAGCATCAATGGACAATGGC 59.311 45.455 0.00 0.00 0.00 4.40
1451 1458 6.751888 CCAATTTAACCGAATCAGAATGTTCC 59.248 38.462 0.00 0.00 37.40 3.62
1459 1466 4.142182 ACCATGCCAATTTAACCGAATCAG 60.142 41.667 0.00 0.00 0.00 2.90
1470 1477 4.968080 ACCCACATATAACCATGCCAATTT 59.032 37.500 0.00 0.00 0.00 1.82
1509 1516 2.412089 CGAACGAAGGAAGGTCAATGAC 59.588 50.000 4.51 4.51 0.00 3.06
1510 1517 2.036733 ACGAACGAAGGAAGGTCAATGA 59.963 45.455 0.14 0.00 0.00 2.57
1590 1609 5.005094 CCCAATTGAGCACCAAATCAAATT 58.995 37.500 7.12 0.00 38.80 1.82
1612 1631 6.436843 ACGTTGATGTTTATCCATTCTTCC 57.563 37.500 0.00 0.00 32.09 3.46
1655 1674 6.535963 TCAGTGATATCAGTGTTCATCTGT 57.464 37.500 30.62 0.00 45.17 3.41
1674 1693 6.095440 GGCAACACCATAGAAAACATATCAGT 59.905 38.462 0.00 0.00 38.86 3.41
1731 1750 5.046087 ACAACCTAAACTACCAGGTATCACC 60.046 44.000 0.00 0.00 44.55 4.02
1798 1817 3.306917 CAAGTGCCAATTGCTCATGAA 57.693 42.857 0.00 0.00 42.00 2.57
1813 1832 3.907788 CGTGATACAACATTGTGCAAGTG 59.092 43.478 7.53 0.00 42.31 3.16
1814 1833 3.058293 CCGTGATACAACATTGTGCAAGT 60.058 43.478 7.53 0.00 42.31 3.16
2005 2024 6.552859 TGAAAAACATGCGATCTGTCTAAA 57.447 33.333 0.00 0.00 0.00 1.85
2022 2041 9.153721 GTCATGGCATGATTAAGATTTGAAAAA 57.846 29.630 30.94 1.49 42.04 1.94
2027 2046 5.981315 GGTGTCATGGCATGATTAAGATTTG 59.019 40.000 30.94 1.50 42.04 2.32
2028 2047 5.657745 TGGTGTCATGGCATGATTAAGATTT 59.342 36.000 30.94 0.00 42.04 2.17
2029 2048 5.202765 TGGTGTCATGGCATGATTAAGATT 58.797 37.500 30.94 0.00 42.04 2.40
2040 2059 1.951895 GCTGAAGATGGTGTCATGGCA 60.952 52.381 0.00 0.00 32.98 4.92
2068 2087 4.631377 TGCTGAAACTTGAGTAATGGATCG 59.369 41.667 0.00 0.00 0.00 3.69
2280 2302 9.503427 GGTCAGTTCACAGCAATATATTTTTAC 57.497 33.333 0.00 0.00 0.00 2.01
2442 2464 4.620589 TCGAGTAATGTTTGGGTGGTTA 57.379 40.909 0.00 0.00 0.00 2.85
2468 2490 5.964477 ACACCATCCTTATAAGAACTGAGGA 59.036 40.000 14.28 1.72 40.52 3.71
2629 2658 0.826672 AGGGAACGAACAGACCGAGT 60.827 55.000 0.00 0.00 0.00 4.18
2661 2690 2.034879 CGATGCTGAAAGTGCGGGT 61.035 57.895 0.00 0.00 35.30 5.28
2733 2762 0.740149 TCGCCATCACCAATTCATGC 59.260 50.000 0.00 0.00 0.00 4.06
2804 2833 7.167302 TGCAGTTTCTTGTTACAATTTCAATCG 59.833 33.333 0.00 0.00 0.00 3.34
2912 2941 1.831726 CACATGGTGTGGTGGCCAA 60.832 57.895 7.24 0.00 44.27 4.52
2944 2973 2.159599 GCGAAATGTCCTCAAGCTCAAG 60.160 50.000 0.00 0.00 0.00 3.02
2945 2974 1.806542 GCGAAATGTCCTCAAGCTCAA 59.193 47.619 0.00 0.00 0.00 3.02
2946 2975 1.270785 TGCGAAATGTCCTCAAGCTCA 60.271 47.619 0.00 0.00 0.00 4.26
2947 2976 1.396301 CTGCGAAATGTCCTCAAGCTC 59.604 52.381 0.00 0.00 0.00 4.09
2948 2977 1.446907 CTGCGAAATGTCCTCAAGCT 58.553 50.000 0.00 0.00 0.00 3.74
2949 2978 0.179179 GCTGCGAAATGTCCTCAAGC 60.179 55.000 0.00 0.00 0.00 4.01
2950 2979 1.159285 TGCTGCGAAATGTCCTCAAG 58.841 50.000 0.00 0.00 0.00 3.02
2963 2992 0.867753 GTGGTAGACGAGATGCTGCG 60.868 60.000 0.00 0.00 0.00 5.18
3029 3096 1.734477 CCGTTGACTGCGAGGACAG 60.734 63.158 0.00 0.00 43.59 3.51
3075 3142 0.613292 GAGGGAGAGAGAGTGTGCCA 60.613 60.000 0.00 0.00 31.09 4.92
3129 3196 0.035820 GGGATGAGTAAACCACGCCA 60.036 55.000 0.00 0.00 0.00 5.69
3192 3259 5.975988 TCTCCCAAAAATACCTATCAGCT 57.024 39.130 0.00 0.00 0.00 4.24
3263 3330 2.604912 AAAGAGTGTGGATTTCCCCC 57.395 50.000 0.00 0.00 34.29 5.40
3267 3334 9.956720 CATTCCATATTAAAGAGTGTGGATTTC 57.043 33.333 0.00 0.00 35.82 2.17
3558 3628 6.403092 CCATCGCACAAATCACATAGTTGTTA 60.403 38.462 0.00 0.00 43.55 2.41
3782 3852 1.341080 CATTTGTGGAAGGGGTTGCT 58.659 50.000 0.00 0.00 0.00 3.91
3803 3873 3.064820 ACTCTGTTTGTAAGTTGTTGGCG 59.935 43.478 0.00 0.00 0.00 5.69
3860 3930 3.924918 GGGAGAACCTTTTTCTTCAGC 57.075 47.619 0.00 0.00 35.85 4.26
3917 3987 2.468777 CACGCTGACACATTTTTCAAGC 59.531 45.455 0.00 0.00 0.00 4.01
3918 3988 3.694734 ACACGCTGACACATTTTTCAAG 58.305 40.909 0.00 0.00 0.00 3.02
3970 4042 3.422417 TCAGCTAAGCGTATCTGTGAC 57.578 47.619 9.76 0.00 0.00 3.67
4034 4106 6.978080 CCTTCAATCTTTTTCGTTTTCTCCAA 59.022 34.615 0.00 0.00 0.00 3.53
4045 4117 4.082787 TCACGCCATCCTTCAATCTTTTTC 60.083 41.667 0.00 0.00 0.00 2.29
4153 4225 2.192861 CCAAGTGGGCGTGCAGAAA 61.193 57.895 0.00 0.00 0.00 2.52
4166 4238 1.724582 GGTCAGCAACAACGCCAAGT 61.725 55.000 0.00 0.00 0.00 3.16
4252 4324 0.681564 TTCTGTGCAAACCCCACGTT 60.682 50.000 0.00 0.00 36.01 3.99
4342 4414 7.107639 TCCACTATATGATCTTCGACAAACA 57.892 36.000 0.00 0.00 0.00 2.83
4350 4422 5.590530 ATCGCCTCCACTATATGATCTTC 57.409 43.478 0.00 0.00 0.00 2.87
4360 4432 4.693283 CAAATCAGTTATCGCCTCCACTA 58.307 43.478 0.00 0.00 0.00 2.74
4428 4500 7.590279 AGGTAAATTAGTCAAACGTCAAATGG 58.410 34.615 0.00 0.00 0.00 3.16
4490 4568 4.378770 CCACTCAAGGTGTGAAATCAATCG 60.379 45.833 0.00 0.00 43.94 3.34
4525 4603 5.006165 CCTCTGCTTATTCGATCACTTTGTC 59.994 44.000 0.00 0.00 0.00 3.18
4536 4614 8.818141 TTATAGTCAATTCCTCTGCTTATTCG 57.182 34.615 0.00 0.00 0.00 3.34
4568 4646 7.816031 CACCTTTGTGAAATTCTAAGATTGCAT 59.184 33.333 0.00 0.00 45.76 3.96
4592 4670 3.641437 TTCTGCAAGGCATACAAACAC 57.359 42.857 0.00 0.00 38.13 3.32
4611 4689 5.645056 AGGACCAATTTCCCACAAAAATT 57.355 34.783 0.00 0.00 36.91 1.82
4613 4691 4.471386 TCAAGGACCAATTTCCCACAAAAA 59.529 37.500 0.00 0.00 36.12 1.94
4631 4709 1.547372 CCCTTTGCTGTCCAATCAAGG 59.453 52.381 0.00 0.00 32.49 3.61
4635 4713 2.087646 GTCTCCCTTTGCTGTCCAATC 58.912 52.381 0.00 0.00 32.49 2.67
4636 4714 1.272147 GGTCTCCCTTTGCTGTCCAAT 60.272 52.381 0.00 0.00 32.49 3.16
4637 4715 0.110486 GGTCTCCCTTTGCTGTCCAA 59.890 55.000 0.00 0.00 0.00 3.53
4638 4716 1.761174 GGTCTCCCTTTGCTGTCCA 59.239 57.895 0.00 0.00 0.00 4.02
4639 4717 1.002011 GGGTCTCCCTTTGCTGTCC 60.002 63.158 0.00 0.00 41.34 4.02
4640 4718 4.724262 GGGTCTCCCTTTGCTGTC 57.276 61.111 0.00 0.00 41.34 3.51
4650 4728 0.836400 TGAGTCAAGGTGGGGTCTCC 60.836 60.000 0.00 0.00 0.00 3.71
4651 4729 1.056660 TTGAGTCAAGGTGGGGTCTC 58.943 55.000 0.08 0.00 0.00 3.36
4652 4730 1.518367 TTTGAGTCAAGGTGGGGTCT 58.482 50.000 5.56 0.00 0.00 3.85
4653 4731 1.954382 GTTTTGAGTCAAGGTGGGGTC 59.046 52.381 5.56 0.00 0.00 4.46
4654 4732 1.569072 AGTTTTGAGTCAAGGTGGGGT 59.431 47.619 5.56 0.00 0.00 4.95
4655 4733 2.364972 AGTTTTGAGTCAAGGTGGGG 57.635 50.000 5.56 0.00 0.00 4.96
4656 4734 4.159506 TGAAAAGTTTTGAGTCAAGGTGGG 59.840 41.667 5.36 0.00 0.00 4.61
4657 4735 5.323371 TGAAAAGTTTTGAGTCAAGGTGG 57.677 39.130 5.36 0.00 0.00 4.61
4658 4736 6.311200 CCTTTGAAAAGTTTTGAGTCAAGGTG 59.689 38.462 5.36 0.00 34.20 4.00
4659 4737 6.210584 TCCTTTGAAAAGTTTTGAGTCAAGGT 59.789 34.615 5.36 0.00 34.20 3.50
4660 4738 6.630071 TCCTTTGAAAAGTTTTGAGTCAAGG 58.370 36.000 5.36 7.86 34.20 3.61
4661 4739 8.707938 ATTCCTTTGAAAAGTTTTGAGTCAAG 57.292 30.769 5.36 0.00 33.32 3.02
4662 4740 9.500785 AAATTCCTTTGAAAAGTTTTGAGTCAA 57.499 25.926 5.36 0.08 33.32 3.18
4663 4741 9.150348 GAAATTCCTTTGAAAAGTTTTGAGTCA 57.850 29.630 5.36 0.00 33.32 3.41
4664 4742 9.150348 TGAAATTCCTTTGAAAAGTTTTGAGTC 57.850 29.630 5.36 0.00 33.32 3.36
4665 4743 9.500785 TTGAAATTCCTTTGAAAAGTTTTGAGT 57.499 25.926 5.36 0.00 33.32 3.41
4666 4744 9.759259 GTTGAAATTCCTTTGAAAAGTTTTGAG 57.241 29.630 5.36 1.28 33.32 3.02
4667 4745 9.277783 TGTTGAAATTCCTTTGAAAAGTTTTGA 57.722 25.926 5.36 0.00 33.32 2.69
4668 4746 9.328721 GTGTTGAAATTCCTTTGAAAAGTTTTG 57.671 29.630 5.36 0.00 33.32 2.44
4669 4747 8.227119 CGTGTTGAAATTCCTTTGAAAAGTTTT 58.773 29.630 0.00 0.00 33.32 2.43
4700 4778 3.810310 AGAACCTAAATGAGCTCTCCG 57.190 47.619 16.19 0.00 0.00 4.63
4755 4833 6.475504 TCTCAGATTCTTATGGCTTGTTTGA 58.524 36.000 0.00 0.00 0.00 2.69
4795 4873 3.922850 CCTCATTGTATCGATCATGGTCG 59.077 47.826 22.43 22.43 42.74 4.79
4799 4877 3.005554 GGGCCTCATTGTATCGATCATG 58.994 50.000 0.00 3.46 0.00 3.07
4800 4878 2.026822 GGGGCCTCATTGTATCGATCAT 60.027 50.000 0.00 0.00 0.00 2.45
4801 4879 1.347707 GGGGCCTCATTGTATCGATCA 59.652 52.381 0.00 0.00 0.00 2.92
4803 4881 1.349026 CTGGGGCCTCATTGTATCGAT 59.651 52.381 5.29 2.16 0.00 3.59
4804 4882 0.758734 CTGGGGCCTCATTGTATCGA 59.241 55.000 5.29 0.00 0.00 3.59
4813 4912 0.044092 TCCTACATTCTGGGGCCTCA 59.956 55.000 4.49 4.49 0.00 3.86
4814 4913 1.213296 TTCCTACATTCTGGGGCCTC 58.787 55.000 0.84 0.00 0.00 4.70
4819 4918 4.780815 TGCTGTTATTCCTACATTCTGGG 58.219 43.478 0.00 0.00 0.00 4.45
4821 4920 8.668510 AACTATGCTGTTATTCCTACATTCTG 57.331 34.615 0.00 0.00 0.00 3.02
4839 4938 3.012518 AGACATGGTGCTCAAACTATGC 58.987 45.455 0.00 0.00 41.36 3.14
4852 4959 1.673767 AGGGATCCACAAGACATGGT 58.326 50.000 15.23 0.00 38.47 3.55
4875 4982 2.143122 GACGCTTGAGGTGTGAAATCA 58.857 47.619 0.00 0.00 38.95 2.57
4876 4983 1.126846 CGACGCTTGAGGTGTGAAATC 59.873 52.381 0.00 0.00 38.95 2.17
4889 4996 3.102052 TGTTTTCTTACTCCGACGCTT 57.898 42.857 0.00 0.00 0.00 4.68
4890 4997 2.806608 TGTTTTCTTACTCCGACGCT 57.193 45.000 0.00 0.00 0.00 5.07
4892 4999 4.053295 TCCTTTGTTTTCTTACTCCGACG 58.947 43.478 0.00 0.00 0.00 5.12
4896 5003 5.048991 TCGCATTCCTTTGTTTTCTTACTCC 60.049 40.000 0.00 0.00 0.00 3.85
4913 5020 6.645700 TCAAATTATGCCTTTTTCGCATTC 57.354 33.333 0.00 0.00 44.48 2.67
4914 5021 5.063817 GCTCAAATTATGCCTTTTTCGCATT 59.936 36.000 0.00 0.00 44.48 3.56
4916 5023 3.925913 GCTCAAATTATGCCTTTTTCGCA 59.074 39.130 0.00 0.00 41.28 5.10
4917 5024 3.925913 TGCTCAAATTATGCCTTTTTCGC 59.074 39.130 0.00 0.00 0.00 4.70
4918 5025 4.327087 GGTGCTCAAATTATGCCTTTTTCG 59.673 41.667 0.00 0.00 0.00 3.46
4919 5026 5.237048 TGGTGCTCAAATTATGCCTTTTTC 58.763 37.500 0.00 0.00 0.00 2.29
4920 5027 5.226194 TGGTGCTCAAATTATGCCTTTTT 57.774 34.783 0.00 0.00 0.00 1.94
4921 5028 4.888326 TGGTGCTCAAATTATGCCTTTT 57.112 36.364 0.00 0.00 0.00 2.27
4922 5029 4.761975 CATGGTGCTCAAATTATGCCTTT 58.238 39.130 0.00 0.00 0.00 3.11
4923 5030 3.431207 GCATGGTGCTCAAATTATGCCTT 60.431 43.478 0.00 0.00 40.96 4.35
4924 5031 2.101917 GCATGGTGCTCAAATTATGCCT 59.898 45.455 0.00 0.00 40.96 4.75
4925 5032 2.476821 GCATGGTGCTCAAATTATGCC 58.523 47.619 0.00 0.00 40.96 4.40
4926 5033 2.101917 AGGCATGGTGCTCAAATTATGC 59.898 45.455 1.64 0.00 44.28 3.14
4927 5034 4.116961 CAAGGCATGGTGCTCAAATTATG 58.883 43.478 1.64 0.00 44.28 1.90
4928 5035 3.770933 ACAAGGCATGGTGCTCAAATTAT 59.229 39.130 1.64 0.00 44.28 1.28
4929 5036 3.056678 CACAAGGCATGGTGCTCAAATTA 60.057 43.478 0.00 0.00 44.28 1.40
4930 5037 1.972795 ACAAGGCATGGTGCTCAAATT 59.027 42.857 1.64 0.00 44.28 1.82
4931 5038 1.274167 CACAAGGCATGGTGCTCAAAT 59.726 47.619 0.00 0.00 44.28 2.32
4932 5039 0.675083 CACAAGGCATGGTGCTCAAA 59.325 50.000 0.00 0.00 44.28 2.69
4933 5040 1.180456 CCACAAGGCATGGTGCTCAA 61.180 55.000 0.00 0.00 44.28 3.02
4934 5041 1.604308 CCACAAGGCATGGTGCTCA 60.604 57.895 0.00 0.00 44.28 4.26
4935 5042 0.682209 ATCCACAAGGCATGGTGCTC 60.682 55.000 0.00 0.00 44.28 4.26
4936 5043 0.251922 AATCCACAAGGCATGGTGCT 60.252 50.000 0.00 0.00 44.28 4.40
4937 5044 0.174162 GAATCCACAAGGCATGGTGC 59.826 55.000 0.00 0.00 44.08 5.01
4938 5045 0.819582 GGAATCCACAAGGCATGGTG 59.180 55.000 0.00 0.00 38.47 4.17
4939 5046 0.706433 AGGAATCCACAAGGCATGGT 59.294 50.000 0.61 0.00 38.47 3.55
4940 5047 2.173356 TCTAGGAATCCACAAGGCATGG 59.827 50.000 0.61 0.00 38.71 3.66
4941 5048 3.565764 TCTAGGAATCCACAAGGCATG 57.434 47.619 0.61 0.00 33.74 4.06
4942 5049 4.803329 ATTCTAGGAATCCACAAGGCAT 57.197 40.909 0.61 0.00 33.74 4.40
4943 5050 4.018506 TGAATTCTAGGAATCCACAAGGCA 60.019 41.667 7.05 0.00 33.74 4.75
4944 5051 4.526970 TGAATTCTAGGAATCCACAAGGC 58.473 43.478 7.05 0.00 33.74 4.35
4945 5052 7.466746 TTTTGAATTCTAGGAATCCACAAGG 57.533 36.000 7.05 0.00 0.00 3.61
4960 5067 9.986833 GGGCATAAACAACAATATTTTGAATTC 57.013 29.630 13.71 0.00 36.64 2.17
4961 5068 9.512588 TGGGCATAAACAACAATATTTTGAATT 57.487 25.926 13.71 11.03 36.64 2.17
4962 5069 9.683870 ATGGGCATAAACAACAATATTTTGAAT 57.316 25.926 13.71 7.23 36.64 2.57
4963 5070 9.512588 AATGGGCATAAACAACAATATTTTGAA 57.487 25.926 13.71 3.95 36.64 2.69
4971 5078 9.737844 AAATTTCTAATGGGCATAAACAACAAT 57.262 25.926 0.00 0.00 0.00 2.71
4972 5079 9.566432 AAAATTTCTAATGGGCATAAACAACAA 57.434 25.926 0.00 0.00 0.00 2.83
4973 5080 8.997323 CAAAATTTCTAATGGGCATAAACAACA 58.003 29.630 0.00 0.00 0.00 3.33
4974 5081 8.998377 ACAAAATTTCTAATGGGCATAAACAAC 58.002 29.630 0.00 0.00 0.00 3.32
4975 5082 8.997323 CACAAAATTTCTAATGGGCATAAACAA 58.003 29.630 0.00 0.00 0.00 2.83
4976 5083 7.605691 CCACAAAATTTCTAATGGGCATAAACA 59.394 33.333 0.00 0.00 0.00 2.83
4977 5084 7.821846 TCCACAAAATTTCTAATGGGCATAAAC 59.178 33.333 9.04 0.00 0.00 2.01
4978 5085 7.911651 TCCACAAAATTTCTAATGGGCATAAA 58.088 30.769 9.04 0.00 0.00 1.40
4979 5086 7.398618 TCTCCACAAAATTTCTAATGGGCATAA 59.601 33.333 9.04 0.00 0.00 1.90
4980 5087 6.894654 TCTCCACAAAATTTCTAATGGGCATA 59.105 34.615 9.04 0.00 0.00 3.14
4981 5088 5.721000 TCTCCACAAAATTTCTAATGGGCAT 59.279 36.000 9.04 0.00 0.00 4.40
4982 5089 5.083122 TCTCCACAAAATTTCTAATGGGCA 58.917 37.500 9.04 0.00 0.00 5.36
4983 5090 5.659440 TCTCCACAAAATTTCTAATGGGC 57.341 39.130 9.04 0.00 0.00 5.36
4984 5091 7.232118 AGTTCTCCACAAAATTTCTAATGGG 57.768 36.000 9.04 0.00 0.00 4.00
4985 5092 9.014297 ACTAGTTCTCCACAAAATTTCTAATGG 57.986 33.333 0.00 0.00 0.00 3.16
4988 5095 9.847224 AGAACTAGTTCTCCACAAAATTTCTAA 57.153 29.630 28.73 0.00 46.13 2.10
5004 5111 5.621329 GCTCTCTCCAGTCAAGAACTAGTTC 60.621 48.000 25.24 25.24 36.07 3.01
5005 5112 4.219725 GCTCTCTCCAGTCAAGAACTAGTT 59.780 45.833 8.13 8.13 36.07 2.24
5006 5113 3.761752 GCTCTCTCCAGTCAAGAACTAGT 59.238 47.826 0.00 0.00 36.07 2.57
5007 5114 3.761218 TGCTCTCTCCAGTCAAGAACTAG 59.239 47.826 0.00 0.00 36.07 2.57
5008 5115 3.767711 TGCTCTCTCCAGTCAAGAACTA 58.232 45.455 0.00 0.00 36.07 2.24
5009 5116 2.603021 TGCTCTCTCCAGTCAAGAACT 58.397 47.619 0.00 0.00 39.44 3.01
5010 5117 3.608316 ATGCTCTCTCCAGTCAAGAAC 57.392 47.619 0.00 0.00 0.00 3.01
5011 5118 3.703556 CCTATGCTCTCTCCAGTCAAGAA 59.296 47.826 0.00 0.00 0.00 2.52
5012 5119 3.053320 TCCTATGCTCTCTCCAGTCAAGA 60.053 47.826 0.00 0.00 0.00 3.02
5013 5120 3.295093 TCCTATGCTCTCTCCAGTCAAG 58.705 50.000 0.00 0.00 0.00 3.02
5014 5121 3.295093 CTCCTATGCTCTCTCCAGTCAA 58.705 50.000 0.00 0.00 0.00 3.18
5015 5122 2.243478 ACTCCTATGCTCTCTCCAGTCA 59.757 50.000 0.00 0.00 0.00 3.41
5016 5123 2.622942 CACTCCTATGCTCTCTCCAGTC 59.377 54.545 0.00 0.00 0.00 3.51
5017 5124 2.243478 TCACTCCTATGCTCTCTCCAGT 59.757 50.000 0.00 0.00 0.00 4.00
5018 5125 2.942804 TCACTCCTATGCTCTCTCCAG 58.057 52.381 0.00 0.00 0.00 3.86
5019 5126 3.388552 TTCACTCCTATGCTCTCTCCA 57.611 47.619 0.00 0.00 0.00 3.86
5020 5127 3.957497 TCTTTCACTCCTATGCTCTCTCC 59.043 47.826 0.00 0.00 0.00 3.71
5021 5128 5.590530 TTCTTTCACTCCTATGCTCTCTC 57.409 43.478 0.00 0.00 0.00 3.20
5022 5129 4.141959 GCTTCTTTCACTCCTATGCTCTCT 60.142 45.833 0.00 0.00 0.00 3.10
5023 5130 4.119136 GCTTCTTTCACTCCTATGCTCTC 58.881 47.826 0.00 0.00 0.00 3.20
5024 5131 3.517100 TGCTTCTTTCACTCCTATGCTCT 59.483 43.478 0.00 0.00 0.00 4.09
5025 5132 3.866651 TGCTTCTTTCACTCCTATGCTC 58.133 45.455 0.00 0.00 0.00 4.26
5026 5133 3.988976 TGCTTCTTTCACTCCTATGCT 57.011 42.857 0.00 0.00 0.00 3.79
5027 5134 4.450053 AGATGCTTCTTTCACTCCTATGC 58.550 43.478 0.00 0.00 0.00 3.14
5028 5135 5.220815 GCAAGATGCTTCTTTCACTCCTATG 60.221 44.000 11.92 0.01 40.28 2.23
5029 5136 4.880696 GCAAGATGCTTCTTTCACTCCTAT 59.119 41.667 11.92 0.00 40.28 2.57
5030 5137 4.256920 GCAAGATGCTTCTTTCACTCCTA 58.743 43.478 11.92 0.00 40.28 2.94
5031 5138 3.080319 GCAAGATGCTTCTTTCACTCCT 58.920 45.455 11.92 0.00 40.28 3.69
5032 5139 2.163211 GGCAAGATGCTTCTTTCACTCC 59.837 50.000 11.92 5.64 44.28 3.85
5033 5140 3.080319 AGGCAAGATGCTTCTTTCACTC 58.920 45.455 11.92 1.80 44.28 3.51
5034 5141 3.151912 AGGCAAGATGCTTCTTTCACT 57.848 42.857 11.92 7.93 44.28 3.41
5035 5142 3.930634 AAGGCAAGATGCTTCTTTCAC 57.069 42.857 11.92 5.98 44.28 3.18
5036 5143 5.536161 AGTTAAAGGCAAGATGCTTCTTTCA 59.464 36.000 11.92 0.00 44.28 2.69
5037 5144 6.018589 AGTTAAAGGCAAGATGCTTCTTTC 57.981 37.500 11.92 7.69 44.28 2.62
5038 5145 6.266330 AGAAGTTAAAGGCAAGATGCTTCTTT 59.734 34.615 11.92 6.98 44.28 2.52
5039 5146 5.772169 AGAAGTTAAAGGCAAGATGCTTCTT 59.228 36.000 8.97 8.97 44.28 2.52
5040 5147 5.320277 AGAAGTTAAAGGCAAGATGCTTCT 58.680 37.500 2.00 0.00 44.28 2.85
5041 5148 5.182001 TGAGAAGTTAAAGGCAAGATGCTTC 59.818 40.000 2.00 0.00 44.28 3.86
5042 5149 5.072741 TGAGAAGTTAAAGGCAAGATGCTT 58.927 37.500 2.00 0.00 44.28 3.91
5043 5150 4.655963 TGAGAAGTTAAAGGCAAGATGCT 58.344 39.130 2.00 0.00 44.28 3.79
5044 5151 5.376854 TTGAGAAGTTAAAGGCAAGATGC 57.623 39.130 0.00 0.00 44.08 3.91
5045 5152 6.385033 CCTTTGAGAAGTTAAAGGCAAGATG 58.615 40.000 3.29 0.00 44.40 2.90
5046 5153 6.581171 CCTTTGAGAAGTTAAAGGCAAGAT 57.419 37.500 3.29 0.00 44.40 2.40
5057 5164 9.971922 CTCATGTTAAAATTCCTTTGAGAAGTT 57.028 29.630 0.00 0.00 35.70 2.66
5058 5165 9.354673 TCTCATGTTAAAATTCCTTTGAGAAGT 57.645 29.630 0.00 0.00 0.00 3.01
5062 5169 9.362539 CCAATCTCATGTTAAAATTCCTTTGAG 57.637 33.333 0.00 0.00 0.00 3.02
5063 5170 9.087871 TCCAATCTCATGTTAAAATTCCTTTGA 57.912 29.630 0.00 0.00 0.00 2.69
5064 5171 9.362539 CTCCAATCTCATGTTAAAATTCCTTTG 57.637 33.333 0.00 0.00 0.00 2.77
5065 5172 8.037166 GCTCCAATCTCATGTTAAAATTCCTTT 58.963 33.333 0.00 0.00 0.00 3.11
5066 5173 7.398332 AGCTCCAATCTCATGTTAAAATTCCTT 59.602 33.333 0.00 0.00 0.00 3.36
5067 5174 6.894103 AGCTCCAATCTCATGTTAAAATTCCT 59.106 34.615 0.00 0.00 0.00 3.36
5068 5175 7.105241 AGCTCCAATCTCATGTTAAAATTCC 57.895 36.000 0.00 0.00 0.00 3.01
5069 5176 7.765307 TGAGCTCCAATCTCATGTTAAAATTC 58.235 34.615 12.15 0.00 35.81 2.17
5070 5177 7.707624 TGAGCTCCAATCTCATGTTAAAATT 57.292 32.000 12.15 0.00 35.81 1.82
5071 5178 7.893124 ATGAGCTCCAATCTCATGTTAAAAT 57.107 32.000 12.15 0.00 46.27 1.82
5072 5179 7.613022 AAGATGAGCTCCAATCTCATGTTAAAA 59.387 33.333 14.98 0.00 46.23 1.52
5073 5180 7.114754 AAGATGAGCTCCAATCTCATGTTAAA 58.885 34.615 14.98 0.00 46.23 1.52
5074 5181 6.656902 AAGATGAGCTCCAATCTCATGTTAA 58.343 36.000 14.98 0.00 46.23 2.01
5075 5182 6.244552 AAGATGAGCTCCAATCTCATGTTA 57.755 37.500 14.98 0.00 46.23 2.41
5080 5187 6.550938 TTCTAAAGATGAGCTCCAATCTCA 57.449 37.500 14.98 7.32 43.79 3.27
5081 5188 6.650390 GGATTCTAAAGATGAGCTCCAATCTC 59.350 42.308 14.98 3.78 0.00 2.75
5082 5189 6.329723 AGGATTCTAAAGATGAGCTCCAATCT 59.670 38.462 12.15 10.95 0.00 2.40
5083 5190 6.532826 AGGATTCTAAAGATGAGCTCCAATC 58.467 40.000 12.15 8.62 0.00 2.67
5084 5191 6.465607 GGAGGATTCTAAAGATGAGCTCCAAT 60.466 42.308 12.15 0.00 0.00 3.16
5085 5192 5.163258 GGAGGATTCTAAAGATGAGCTCCAA 60.163 44.000 12.15 0.00 0.00 3.53
5086 5193 4.346418 GGAGGATTCTAAAGATGAGCTCCA 59.654 45.833 12.15 0.00 0.00 3.86
5087 5194 4.346418 TGGAGGATTCTAAAGATGAGCTCC 59.654 45.833 12.15 0.00 0.00 4.70
5088 5195 5.543507 TGGAGGATTCTAAAGATGAGCTC 57.456 43.478 6.82 6.82 0.00 4.09
5089 5196 5.965033 TTGGAGGATTCTAAAGATGAGCT 57.035 39.130 0.00 0.00 0.00 4.09
5090 5197 6.790282 GTTTTGGAGGATTCTAAAGATGAGC 58.210 40.000 0.00 0.00 35.56 4.26


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

AutoCloner maintained by Alex Coulton.