Multiple sequence alignment - TraesCS3B01G245800

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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 TraesCS3B01G245800 chr3B 100.000 5966 0 0 1 5966 389789606 389795571 0.000000e+00 11018
1 TraesCS3B01G245800 chr3A 98.733 1973 21 2 1730 3699 393910261 393912232 0.000000e+00 3502
2 TraesCS3B01G245800 chr3A 95.558 1801 44 17 3861 5651 393912231 393914005 0.000000e+00 2850
3 TraesCS3B01G245800 chr3A 96.214 1717 36 13 2 1713 393908583 393910275 0.000000e+00 2784
4 TraesCS3B01G245800 chr3A 90.970 299 22 5 5649 5946 393917271 393917565 1.200000e-106 398
5 TraesCS3B01G245800 chr3D 97.065 1976 39 3 1730 3699 295556157 295558119 0.000000e+00 3310
6 TraesCS3B01G245800 chr3D 95.821 1723 32 14 2 1713 295554478 295556171 0.000000e+00 2747
7 TraesCS3B01G245800 chr3D 95.000 1760 48 13 3861 5608 295558118 295559849 0.000000e+00 2726
8 TraesCS3B01G245800 chr3D 90.572 297 18 6 5671 5966 295559844 295560131 9.380000e-103 385
9 TraesCS3B01G245800 chr2D 95.506 178 8 0 3688 3865 516708302 516708479 9.790000e-73 285
10 TraesCS3B01G245800 chr1D 96.512 172 6 0 3695 3866 238940383 238940212 9.790000e-73 285
11 TraesCS3B01G245800 chr1D 95.429 175 7 1 3696 3869 178466472 178466298 1.640000e-70 278
12 TraesCS3B01G245800 chr1D 94.944 178 8 1 3698 3875 331539429 331539253 1.640000e-70 278
13 TraesCS3B01G245800 chr6D 96.491 171 6 0 3697 3867 392896974 392897144 3.520000e-72 283
14 TraesCS3B01G245800 chr4B 95.429 175 8 0 3697 3871 389466944 389466770 4.550000e-71 279
15 TraesCS3B01G245800 chr4D 94.886 176 9 0 3695 3870 477898792 477898967 5.890000e-70 276
16 TraesCS3B01G245800 chr7A 94.857 175 9 0 3696 3870 115807521 115807695 2.120000e-69 274
17 TraesCS3B01G245800 chr5D 92.973 185 13 0 3698 3882 391500294 391500478 2.740000e-68 270


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 TraesCS3B01G245800 chr3B 389789606 389795571 5965 False 11018.0 11018 100.00000 1 5966 1 chr3B.!!$F1 5965
1 TraesCS3B01G245800 chr3A 393908583 393917565 8982 False 2383.5 3502 95.36875 2 5946 4 chr3A.!!$F1 5944
2 TraesCS3B01G245800 chr3D 295554478 295560131 5653 False 2292.0 3310 94.61450 2 5966 4 chr3D.!!$F1 5964

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
887 904 0.644843 CTGGTTGTTGCGTTGTTTGC 59.355 50.0 0.0 0.0 0.00 3.68 F
1005 1022 0.690411 CTGGAGAGGAGGTGATGGCT 60.690 60.0 0.0 0.0 0.00 4.75 F
1709 1726 0.539438 TGCGGTGAAAATGGGAGCTT 60.539 50.0 0.0 0.0 0.00 3.74 F
1710 1727 0.603065 GCGGTGAAAATGGGAGCTTT 59.397 50.0 0.0 0.0 0.00 3.51 F
3435 3455 0.537188 AACCTCTGGTATGGACTGCG 59.463 55.0 0.0 0.0 33.12 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1707 0.539438 AAGCTCCCATTTTCACCGCA 60.539 50.000 0.00 0.00 0.00 5.69 R
2805 2822 2.035783 GCCTGGGAGAAACCACCC 59.964 66.667 0.00 0.00 45.74 4.61 R
3342 3362 2.544685 CAGCCAACTCTACATTCCTCG 58.455 52.381 0.00 0.00 0.00 4.63 R
3684 3708 5.163012 ACGGAGGGAGTATAAGACTGGATAA 60.163 44.000 0.00 0.00 39.06 1.75 R
5216 5252 0.591659 CATGGCTGCCATTCTCATCG 59.408 55.000 30.74 14.38 42.23 3.84 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
289 297 2.549563 CGGAGATCTGCTTGCATATGGT 60.550 50.000 12.78 0.00 0.00 3.55
290 298 2.812591 GGAGATCTGCTTGCATATGGTG 59.187 50.000 7.03 0.00 0.00 4.17
291 299 2.812591 GAGATCTGCTTGCATATGGTGG 59.187 50.000 0.00 0.00 0.00 4.61
594 607 1.410004 CCTATTCCGGCTACAGTGGA 58.590 55.000 0.00 0.00 0.00 4.02
675 692 1.276138 TCTTTCTCTCAATCCGCAGCA 59.724 47.619 0.00 0.00 0.00 4.41
676 693 1.664659 CTTTCTCTCAATCCGCAGCAG 59.335 52.381 0.00 0.00 0.00 4.24
677 694 0.742281 TTCTCTCAATCCGCAGCAGC 60.742 55.000 0.00 0.00 37.42 5.25
678 695 1.153409 CTCTCAATCCGCAGCAGCT 60.153 57.895 0.00 0.00 39.10 4.24
679 696 0.743701 CTCTCAATCCGCAGCAGCTT 60.744 55.000 0.00 0.00 39.10 3.74
680 697 1.022982 TCTCAATCCGCAGCAGCTTG 61.023 55.000 0.00 0.00 39.10 4.01
784 801 1.039856 TTGGCTGCCTTTTGGTTCTC 58.960 50.000 21.03 0.00 42.99 2.87
786 803 0.884514 GGCTGCCTTTTGGTTCTCTC 59.115 55.000 12.43 0.00 42.99 3.20
828 845 4.709840 CTGGCAACTGTCAGGGAG 57.290 61.111 4.53 0.00 43.64 4.30
829 846 1.002868 CTGGCAACTGTCAGGGAGG 60.003 63.158 4.53 0.00 43.64 4.30
848 865 4.316025 AGGTAGCTCCTCCTATCTCATC 57.684 50.000 0.00 0.00 44.42 2.92
887 904 0.644843 CTGGTTGTTGCGTTGTTTGC 59.355 50.000 0.00 0.00 0.00 3.68
906 923 3.388345 GCACTAGGCATTACTACTCCC 57.612 52.381 0.00 0.00 43.97 4.30
959 976 1.156736 CCGTGGTTCAGCTGTTTAGG 58.843 55.000 14.67 7.39 0.00 2.69
987 1004 3.266510 TCTTGATTTGTAGGCATCGCT 57.733 42.857 0.00 0.00 0.00 4.93
1005 1022 0.690411 CTGGAGAGGAGGTGATGGCT 60.690 60.000 0.00 0.00 0.00 4.75
1026 1043 1.065636 AGCTCTATCAAGCAGCAGCAA 60.066 47.619 3.17 0.00 45.00 3.91
1275 1292 1.154225 CCGTCCTTCGCAAATGCAC 60.154 57.895 6.18 0.00 42.21 4.57
1284 1301 4.320494 CCTTCGCAAATGCACTTTTCTACT 60.320 41.667 6.18 0.00 42.21 2.57
1299 1316 7.220108 CACTTTTCTACTTTTTGTTGTACTGCC 59.780 37.037 0.00 0.00 0.00 4.85
1613 1630 2.233431 AGATGTCTCAGAGCTGTGTTCC 59.767 50.000 11.09 0.52 0.00 3.62
1704 1721 2.231215 TTTTGTGCGGTGAAAATGGG 57.769 45.000 0.00 0.00 0.00 4.00
1705 1722 1.403814 TTTGTGCGGTGAAAATGGGA 58.596 45.000 0.00 0.00 0.00 4.37
1706 1723 0.958091 TTGTGCGGTGAAAATGGGAG 59.042 50.000 0.00 0.00 0.00 4.30
1707 1724 1.212751 GTGCGGTGAAAATGGGAGC 59.787 57.895 0.00 0.00 0.00 4.70
1708 1725 1.074775 TGCGGTGAAAATGGGAGCT 59.925 52.632 0.00 0.00 0.00 4.09
1709 1726 0.539438 TGCGGTGAAAATGGGAGCTT 60.539 50.000 0.00 0.00 0.00 3.74
1710 1727 0.603065 GCGGTGAAAATGGGAGCTTT 59.397 50.000 0.00 0.00 0.00 3.51
1711 1728 1.816224 GCGGTGAAAATGGGAGCTTTA 59.184 47.619 0.00 0.00 0.00 1.85
1712 1729 2.427095 GCGGTGAAAATGGGAGCTTTAT 59.573 45.455 0.00 0.00 0.00 1.40
1713 1730 3.630312 GCGGTGAAAATGGGAGCTTTATA 59.370 43.478 0.00 0.00 0.00 0.98
1714 1731 4.278419 GCGGTGAAAATGGGAGCTTTATAT 59.722 41.667 0.00 0.00 0.00 0.86
1715 1732 5.221244 GCGGTGAAAATGGGAGCTTTATATT 60.221 40.000 0.00 0.00 0.00 1.28
1716 1733 6.682861 GCGGTGAAAATGGGAGCTTTATATTT 60.683 38.462 0.00 0.00 0.00 1.40
1717 1734 7.264947 CGGTGAAAATGGGAGCTTTATATTTT 58.735 34.615 9.96 9.96 34.65 1.82
1718 1735 7.763985 CGGTGAAAATGGGAGCTTTATATTTTT 59.236 33.333 10.93 4.12 32.79 1.94
1748 1765 5.894807 ACGAAAATGGGAGCTTTATTGATG 58.105 37.500 0.00 0.00 0.00 3.07
2370 2387 3.197927 AGTTCAGATCCAGGGACTTCT 57.802 47.619 0.00 0.00 34.60 2.85
2553 2570 1.672881 GGATCTGCATCCTCAAAACCG 59.327 52.381 0.00 0.00 45.06 4.44
2805 2822 2.111756 GCTGAACTTGAACTTGCAACG 58.888 47.619 0.00 0.00 0.00 4.10
3025 3042 2.467566 TGAGGAAAGGAGGCGTTTAC 57.532 50.000 0.00 0.00 0.00 2.01
3135 3155 1.472904 CCAGTCTGCAGGCTCACTATG 60.473 57.143 20.28 6.96 0.00 2.23
3342 3362 1.535437 CGAGGGTTGCGGTATCTACAC 60.535 57.143 0.00 0.00 0.00 2.90
3435 3455 0.537188 AACCTCTGGTATGGACTGCG 59.463 55.000 0.00 0.00 33.12 5.18
3569 3593 3.279434 GGGTTGGCCTATCTTGTAACTG 58.721 50.000 3.32 0.00 34.45 3.16
3662 3686 8.568617 AACTTCCCCAGTATTATCTTACAGAT 57.431 34.615 0.00 0.00 35.02 2.90
3702 3726 6.360370 TGCCATTATCCAGTCTTATACTCC 57.640 41.667 0.00 0.00 35.76 3.85
3703 3727 5.248477 TGCCATTATCCAGTCTTATACTCCC 59.752 44.000 0.00 0.00 35.76 4.30
3704 3728 5.485708 GCCATTATCCAGTCTTATACTCCCT 59.514 44.000 0.00 0.00 35.76 4.20
3705 3729 6.351456 GCCATTATCCAGTCTTATACTCCCTC 60.351 46.154 0.00 0.00 35.76 4.30
3706 3730 6.155393 CCATTATCCAGTCTTATACTCCCTCC 59.845 46.154 0.00 0.00 35.76 4.30
3708 3732 2.512896 TCCAGTCTTATACTCCCTCCGT 59.487 50.000 0.00 0.00 35.76 4.69
3709 3733 2.885894 CCAGTCTTATACTCCCTCCGTC 59.114 54.545 0.00 0.00 35.76 4.79
3710 3734 3.435313 CCAGTCTTATACTCCCTCCGTCT 60.435 52.174 0.00 0.00 35.76 4.18
3711 3735 3.816523 CAGTCTTATACTCCCTCCGTCTC 59.183 52.174 0.00 0.00 35.76 3.36
3712 3736 3.717913 AGTCTTATACTCCCTCCGTCTCT 59.282 47.826 0.00 0.00 30.33 3.10
3713 3737 4.906664 AGTCTTATACTCCCTCCGTCTCTA 59.093 45.833 0.00 0.00 30.33 2.43
3714 3738 5.369110 AGTCTTATACTCCCTCCGTCTCTAA 59.631 44.000 0.00 0.00 30.33 2.10
3715 3739 6.060788 GTCTTATACTCCCTCCGTCTCTAAA 58.939 44.000 0.00 0.00 0.00 1.85
3716 3740 6.716173 GTCTTATACTCCCTCCGTCTCTAAAT 59.284 42.308 0.00 0.00 0.00 1.40
3717 3741 7.882271 GTCTTATACTCCCTCCGTCTCTAAATA 59.118 40.741 0.00 0.00 0.00 1.40
3718 3742 8.613034 TCTTATACTCCCTCCGTCTCTAAATAT 58.387 37.037 0.00 0.00 0.00 1.28
3719 3743 9.245481 CTTATACTCCCTCCGTCTCTAAATATT 57.755 37.037 0.00 0.00 0.00 1.28
3720 3744 9.597681 TTATACTCCCTCCGTCTCTAAATATTT 57.402 33.333 5.89 5.89 0.00 1.40
3721 3745 6.163135 ACTCCCTCCGTCTCTAAATATTTG 57.837 41.667 11.05 1.65 0.00 2.32
3722 3746 5.661759 ACTCCCTCCGTCTCTAAATATTTGT 59.338 40.000 11.05 0.00 0.00 2.83
3723 3747 6.158023 TCCCTCCGTCTCTAAATATTTGTC 57.842 41.667 11.05 0.00 0.00 3.18
3724 3748 5.897824 TCCCTCCGTCTCTAAATATTTGTCT 59.102 40.000 11.05 0.00 0.00 3.41
3725 3749 6.383147 TCCCTCCGTCTCTAAATATTTGTCTT 59.617 38.462 11.05 0.00 0.00 3.01
3726 3750 7.048512 CCCTCCGTCTCTAAATATTTGTCTTT 58.951 38.462 11.05 0.00 0.00 2.52
3727 3751 7.224949 CCCTCCGTCTCTAAATATTTGTCTTTC 59.775 40.741 11.05 0.00 0.00 2.62
3728 3752 7.982354 CCTCCGTCTCTAAATATTTGTCTTTCT 59.018 37.037 11.05 0.00 0.00 2.52
3742 3766 8.924511 ATTTGTCTTTCTAGAGATTCCAACAA 57.075 30.769 0.00 0.00 0.00 2.83
3743 3767 7.969536 TTGTCTTTCTAGAGATTCCAACAAG 57.030 36.000 0.00 0.00 0.00 3.16
3744 3768 7.067496 TGTCTTTCTAGAGATTCCAACAAGT 57.933 36.000 0.00 0.00 0.00 3.16
3745 3769 6.931281 TGTCTTTCTAGAGATTCCAACAAGTG 59.069 38.462 0.00 0.00 0.00 3.16
3746 3770 7.155328 GTCTTTCTAGAGATTCCAACAAGTGA 58.845 38.462 0.00 0.00 0.00 3.41
3747 3771 7.117092 GTCTTTCTAGAGATTCCAACAAGTGAC 59.883 40.741 0.00 0.00 0.00 3.67
3748 3772 6.672266 TTCTAGAGATTCCAACAAGTGACT 57.328 37.500 0.00 0.00 0.00 3.41
3749 3773 7.776618 TTCTAGAGATTCCAACAAGTGACTA 57.223 36.000 0.00 0.00 0.00 2.59
3750 3774 7.159322 TCTAGAGATTCCAACAAGTGACTAC 57.841 40.000 0.00 0.00 0.00 2.73
3751 3775 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
3752 3776 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
3753 3777 6.169094 AGAGATTCCAACAAGTGACTACATG 58.831 40.000 0.00 0.00 0.00 3.21
3754 3778 4.697352 AGATTCCAACAAGTGACTACATGC 59.303 41.667 0.00 0.00 0.00 4.06
3755 3779 2.412870 TCCAACAAGTGACTACATGCG 58.587 47.619 0.00 0.00 0.00 4.73
3756 3780 2.036604 TCCAACAAGTGACTACATGCGA 59.963 45.455 0.00 0.00 0.00 5.10
3757 3781 2.805671 CCAACAAGTGACTACATGCGAA 59.194 45.455 0.00 0.00 0.00 4.70
3758 3782 3.120546 CCAACAAGTGACTACATGCGAAG 60.121 47.826 0.00 0.00 0.00 3.79
3777 3801 6.169419 CGAAGCAAAATGAGTGAATCTACA 57.831 37.500 0.00 0.00 0.00 2.74
3778 3802 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
3811 3835 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
3813 3837 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
3814 3838 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
3815 3839 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
3816 3840 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
3817 3841 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
3818 3842 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
3819 3843 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
3820 3844 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
3821 3845 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
3822 3846 2.612212 CCGTATGTGGTAGTCCATTTGC 59.388 50.000 0.00 0.00 46.20 3.68
3823 3847 3.266636 CGTATGTGGTAGTCCATTTGCA 58.733 45.455 0.00 0.00 46.20 4.08
3824 3848 3.687212 CGTATGTGGTAGTCCATTTGCAA 59.313 43.478 0.00 0.00 46.20 4.08
3825 3849 4.335315 CGTATGTGGTAGTCCATTTGCAAT 59.665 41.667 0.00 0.00 46.20 3.56
3826 3850 4.989279 ATGTGGTAGTCCATTTGCAATC 57.011 40.909 0.00 0.00 46.20 2.67
3827 3851 4.032960 TGTGGTAGTCCATTTGCAATCT 57.967 40.909 0.00 0.00 46.20 2.40
3828 3852 4.009675 TGTGGTAGTCCATTTGCAATCTC 58.990 43.478 0.00 0.00 46.20 2.75
3829 3853 4.263462 TGTGGTAGTCCATTTGCAATCTCT 60.263 41.667 0.00 0.00 46.20 3.10
3830 3854 5.045942 TGTGGTAGTCCATTTGCAATCTCTA 60.046 40.000 0.00 0.00 46.20 2.43
3831 3855 5.880332 GTGGTAGTCCATTTGCAATCTCTAA 59.120 40.000 0.00 0.00 46.20 2.10
3832 3856 6.374333 GTGGTAGTCCATTTGCAATCTCTAAA 59.626 38.462 0.00 0.00 46.20 1.85
3833 3857 6.945435 TGGTAGTCCATTTGCAATCTCTAAAA 59.055 34.615 0.00 0.00 39.03 1.52
3834 3858 7.450014 TGGTAGTCCATTTGCAATCTCTAAAAA 59.550 33.333 0.00 0.00 39.03 1.94
3835 3859 7.970614 GGTAGTCCATTTGCAATCTCTAAAAAG 59.029 37.037 0.00 0.00 0.00 2.27
3836 3860 7.765695 AGTCCATTTGCAATCTCTAAAAAGA 57.234 32.000 0.00 0.00 0.00 2.52
3837 3861 7.597386 AGTCCATTTGCAATCTCTAAAAAGAC 58.403 34.615 0.00 0.00 0.00 3.01
3838 3862 7.231317 AGTCCATTTGCAATCTCTAAAAAGACA 59.769 33.333 0.00 0.00 0.00 3.41
3839 3863 7.867403 GTCCATTTGCAATCTCTAAAAAGACAA 59.133 33.333 0.00 0.00 0.00 3.18
3840 3864 8.420222 TCCATTTGCAATCTCTAAAAAGACAAA 58.580 29.630 0.00 0.00 0.00 2.83
3841 3865 9.211485 CCATTTGCAATCTCTAAAAAGACAAAT 57.789 29.630 0.00 0.00 33.34 2.32
3856 3880 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3857 3881 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3858 3882 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3859 3883 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3860 3884 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3861 3885 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3862 3886 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
3863 3887 7.628501 AATATTTAGGAACGGAGGGAGTATT 57.371 36.000 0.00 0.00 0.00 1.89
3864 3888 8.731591 AATATTTAGGAACGGAGGGAGTATTA 57.268 34.615 0.00 0.00 0.00 0.98
3865 3889 8.912614 ATATTTAGGAACGGAGGGAGTATTAT 57.087 34.615 0.00 0.00 0.00 1.28
3866 3890 6.415206 TTTAGGAACGGAGGGAGTATTATG 57.585 41.667 0.00 0.00 0.00 1.90
3867 3891 2.633481 AGGAACGGAGGGAGTATTATGC 59.367 50.000 0.00 0.00 0.00 3.14
3868 3892 2.367567 GGAACGGAGGGAGTATTATGCA 59.632 50.000 0.00 0.00 0.00 3.96
3869 3893 3.008049 GGAACGGAGGGAGTATTATGCAT 59.992 47.826 3.79 3.79 0.00 3.96
3870 3894 3.685139 ACGGAGGGAGTATTATGCATG 57.315 47.619 10.16 0.00 0.00 4.06
3871 3895 3.239449 ACGGAGGGAGTATTATGCATGA 58.761 45.455 10.16 0.00 0.00 3.07
4074 4098 4.331168 GCACTCAATGATTCTTAGCGACTT 59.669 41.667 0.00 0.00 0.00 3.01
4194 4219 1.466360 GCGCAAGGCTGTTGACATTAG 60.466 52.381 0.30 0.00 39.11 1.73
4434 4460 2.227388 AGTGCTGCTATGTCAAAACTGC 59.773 45.455 0.00 0.00 0.00 4.40
4651 4687 2.289444 TGTAAGTTCTTTCTGGGCTCGG 60.289 50.000 0.00 0.00 0.00 4.63
4697 4733 4.754618 GCCTGTTGGGAAACTAAATTTTGG 59.245 41.667 0.00 0.00 37.23 3.28
4709 4745 6.472686 ACTAAATTTTGGCAACTTGTACCA 57.527 33.333 0.00 0.00 37.61 3.25
5010 5046 8.230486 GCAACTCAATTATGTATTATTCCCTCG 58.770 37.037 0.00 0.00 0.00 4.63
5035 5071 5.394224 CCCTCTGCTTTTGAGTAATCGTAGA 60.394 44.000 0.00 0.00 45.75 2.59
5081 5117 5.525484 TGTCCTGGTGTATAGTAGGAATGT 58.475 41.667 0.00 0.00 40.75 2.71
5141 5177 2.333926 TCTTTTGTGTATCAGCCGACG 58.666 47.619 0.00 0.00 0.00 5.12
5142 5178 2.029739 TCTTTTGTGTATCAGCCGACGA 60.030 45.455 0.00 0.00 0.00 4.20
5143 5179 2.442212 TTTGTGTATCAGCCGACGAA 57.558 45.000 0.00 0.00 0.00 3.85
5144 5180 2.442212 TTGTGTATCAGCCGACGAAA 57.558 45.000 0.00 0.00 0.00 3.46
5145 5181 2.665649 TGTGTATCAGCCGACGAAAT 57.334 45.000 0.00 0.00 0.00 2.17
5146 5182 2.267426 TGTGTATCAGCCGACGAAATG 58.733 47.619 0.00 0.00 0.00 2.32
5147 5183 2.268298 GTGTATCAGCCGACGAAATGT 58.732 47.619 0.00 0.00 0.00 2.71
5148 5184 2.029244 GTGTATCAGCCGACGAAATGTG 59.971 50.000 0.00 0.00 0.00 3.21
5149 5185 2.094442 TGTATCAGCCGACGAAATGTGA 60.094 45.455 0.00 0.00 0.00 3.58
5150 5186 1.359848 ATCAGCCGACGAAATGTGAC 58.640 50.000 0.00 0.00 0.00 3.67
5151 5187 0.669318 TCAGCCGACGAAATGTGACC 60.669 55.000 0.00 0.00 0.00 4.02
5152 5188 0.670546 CAGCCGACGAAATGTGACCT 60.671 55.000 0.00 0.00 0.00 3.85
5163 5199 5.241506 ACGAAATGTGACCTGAAATGACATT 59.758 36.000 0.00 0.00 38.57 2.71
5181 5217 5.348724 TGACATTTAGTTGTGCGAAGATCTC 59.651 40.000 0.00 0.00 0.00 2.75
5208 5244 6.031549 TGTGATAACTATTTGCAATCGTCG 57.968 37.500 0.00 0.00 0.00 5.12
5213 5249 3.531538 ACTATTTGCAATCGTCGGTCAT 58.468 40.909 0.00 0.00 0.00 3.06
5216 5252 0.742990 TTGCAATCGTCGGTCATCCC 60.743 55.000 0.00 0.00 0.00 3.85
5513 5554 4.933330 TCGAAAATCTTGGACGGAGATAG 58.067 43.478 0.00 0.00 33.63 2.08
5514 5555 4.401519 TCGAAAATCTTGGACGGAGATAGT 59.598 41.667 0.00 0.00 33.63 2.12
5515 5556 5.591472 TCGAAAATCTTGGACGGAGATAGTA 59.409 40.000 0.00 0.00 33.63 1.82
5516 5557 5.686397 CGAAAATCTTGGACGGAGATAGTAC 59.314 44.000 0.00 0.00 33.63 2.73
5518 5559 1.945394 TCTTGGACGGAGATAGTACGC 59.055 52.381 0.00 0.00 0.00 4.42
5519 5560 1.674441 CTTGGACGGAGATAGTACGCA 59.326 52.381 0.00 0.00 0.00 5.24
5520 5561 1.306148 TGGACGGAGATAGTACGCAG 58.694 55.000 0.00 0.00 0.00 5.18
5521 5562 0.040246 GGACGGAGATAGTACGCAGC 60.040 60.000 0.00 0.00 0.00 5.25
5522 5563 0.661552 GACGGAGATAGTACGCAGCA 59.338 55.000 0.00 0.00 0.00 4.41
5523 5564 0.663688 ACGGAGATAGTACGCAGCAG 59.336 55.000 0.00 0.00 0.00 4.24
5524 5565 0.663688 CGGAGATAGTACGCAGCAGT 59.336 55.000 0.00 0.00 0.00 4.40
5525 5566 1.598183 CGGAGATAGTACGCAGCAGTG 60.598 57.143 0.00 0.00 0.00 3.66
5526 5567 1.405821 GGAGATAGTACGCAGCAGTGT 59.594 52.381 0.00 0.00 42.14 3.55
5651 5692 3.664107 TCTTGATCCTCCACTTTCAACG 58.336 45.455 0.00 0.00 0.00 4.10
5654 5695 4.610605 TGATCCTCCACTTTCAACGTAA 57.389 40.909 0.00 0.00 0.00 3.18
5790 9099 2.846371 GCTTCTGGCTTCGTGATGT 58.154 52.632 0.00 0.00 38.06 3.06
5791 9100 1.160137 GCTTCTGGCTTCGTGATGTT 58.840 50.000 0.00 0.00 38.06 2.71
5802 9111 1.542472 TCGTGATGTTAAGTCTCGCCA 59.458 47.619 7.15 0.00 33.89 5.69
5839 9149 7.624549 TCCTCTATCAGCCATCCATTAAATAC 58.375 38.462 0.00 0.00 0.00 1.89
5841 9151 7.311549 CCTCTATCAGCCATCCATTAAATACCT 60.312 40.741 0.00 0.00 0.00 3.08
5871 9181 4.563374 CCAGATTGACCCATTTTCCAAACC 60.563 45.833 0.00 0.00 0.00 3.27
5872 9182 4.284234 CAGATTGACCCATTTTCCAAACCT 59.716 41.667 0.00 0.00 0.00 3.50
5873 9183 4.284234 AGATTGACCCATTTTCCAAACCTG 59.716 41.667 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.493747 CCGCCGGAGAAGACGACC 62.494 72.222 5.05 0.00 0.00 4.79
289 297 2.614134 ACGGAAATTTCCCCATTCCA 57.386 45.000 27.72 0.00 44.67 3.53
290 298 3.893521 TCTACGGAAATTTCCCCATTCC 58.106 45.455 27.72 5.87 44.67 3.01
291 299 5.417894 AGTTTCTACGGAAATTTCCCCATTC 59.582 40.000 27.72 14.00 44.67 2.67
314 322 3.077359 GAGTGGGACAAAATGGAGTCAG 58.923 50.000 0.00 0.00 44.16 3.51
594 607 1.599047 CCTGTGAATGTCCTCGCCT 59.401 57.895 0.00 0.00 0.00 5.52
676 693 1.347817 CTCGACGACCAAGCTCAAGC 61.348 60.000 0.00 0.00 42.49 4.01
677 694 0.241213 TCTCGACGACCAAGCTCAAG 59.759 55.000 0.00 0.00 0.00 3.02
678 695 0.671796 TTCTCGACGACCAAGCTCAA 59.328 50.000 0.00 0.00 0.00 3.02
679 696 0.888619 ATTCTCGACGACCAAGCTCA 59.111 50.000 0.00 0.00 0.00 4.26
680 697 1.551145 GATTCTCGACGACCAAGCTC 58.449 55.000 0.00 0.00 0.00 4.09
784 801 1.068588 TGGACACCGAACTCTGTTGAG 59.931 52.381 0.00 0.00 45.43 3.02
786 803 1.597663 GTTGGACACCGAACTCTGTTG 59.402 52.381 0.00 0.00 0.00 3.33
828 845 4.016444 CAGATGAGATAGGAGGAGCTACC 58.984 52.174 0.00 0.00 39.35 3.18
829 846 3.443681 GCAGATGAGATAGGAGGAGCTAC 59.556 52.174 0.00 0.00 0.00 3.58
848 865 1.404583 GCCCCAAGTGCTTAAATGCAG 60.405 52.381 0.00 0.00 44.20 4.41
887 904 5.386924 AGTAGGGAGTAGTAATGCCTAGTG 58.613 45.833 20.73 0.00 41.38 2.74
906 923 4.918810 AACCCAAGAAGCAAACAAGTAG 57.081 40.909 0.00 0.00 0.00 2.57
959 976 3.282885 CCTACAAATCAAGAAGCTCCCC 58.717 50.000 0.00 0.00 0.00 4.81
987 1004 0.636647 TAGCCATCACCTCCTCTCCA 59.363 55.000 0.00 0.00 0.00 3.86
1005 1022 1.758862 TGCTGCTGCTTGATAGAGCTA 59.241 47.619 17.00 0.00 43.11 3.32
1079 1096 3.128188 CCTCAGCAGCAGCAGCAG 61.128 66.667 12.92 3.97 45.49 4.24
1080 1097 3.607370 CTCCTCAGCAGCAGCAGCA 62.607 63.158 12.92 0.00 45.49 4.41
1092 1109 1.127567 CCACCACCACCTTCTCCTCA 61.128 60.000 0.00 0.00 0.00 3.86
1275 1292 6.413818 CGGCAGTACAACAAAAAGTAGAAAAG 59.586 38.462 0.00 0.00 0.00 2.27
1284 1301 3.057456 ACAACACGGCAGTACAACAAAAA 60.057 39.130 0.00 0.00 0.00 1.94
1299 1316 1.000717 CTAAGCCCCCAAAACAACACG 60.001 52.381 0.00 0.00 0.00 4.49
1688 1705 1.523154 GCTCCCATTTTCACCGCACA 61.523 55.000 0.00 0.00 0.00 4.57
1689 1706 1.212751 GCTCCCATTTTCACCGCAC 59.787 57.895 0.00 0.00 0.00 5.34
1690 1707 0.539438 AAGCTCCCATTTTCACCGCA 60.539 50.000 0.00 0.00 0.00 5.69
1691 1708 0.603065 AAAGCTCCCATTTTCACCGC 59.397 50.000 0.00 0.00 0.00 5.68
1692 1709 6.391227 AATATAAAGCTCCCATTTTCACCG 57.609 37.500 0.00 0.00 0.00 4.94
1719 1736 2.500229 AGCTCCCATTTTCGTTTCGAA 58.500 42.857 0.00 0.00 44.28 3.71
1720 1737 2.178912 AGCTCCCATTTTCGTTTCGA 57.821 45.000 0.00 0.00 0.00 3.71
1721 1738 2.989422 AAGCTCCCATTTTCGTTTCG 57.011 45.000 0.00 0.00 0.00 3.46
1722 1739 6.386654 TCAATAAAGCTCCCATTTTCGTTTC 58.613 36.000 0.00 0.00 0.00 2.78
1723 1740 6.339587 TCAATAAAGCTCCCATTTTCGTTT 57.660 33.333 0.00 0.00 0.00 3.60
1724 1741 5.975693 TCAATAAAGCTCCCATTTTCGTT 57.024 34.783 0.00 0.00 0.00 3.85
1725 1742 5.652014 TCATCAATAAAGCTCCCATTTTCGT 59.348 36.000 0.00 0.00 0.00 3.85
1726 1743 6.135290 TCATCAATAAAGCTCCCATTTTCG 57.865 37.500 0.00 0.00 0.00 3.46
1727 1744 7.490402 CACTTCATCAATAAAGCTCCCATTTTC 59.510 37.037 0.00 0.00 0.00 2.29
1728 1745 7.178983 TCACTTCATCAATAAAGCTCCCATTTT 59.821 33.333 0.00 0.00 0.00 1.82
1748 1765 6.237861 GCTACCGATTGTTATTCTGTCACTTC 60.238 42.308 0.00 0.00 0.00 3.01
2370 2387 4.998671 TGTTTCAGAAGCACAAAATGGA 57.001 36.364 0.00 0.00 0.00 3.41
2523 2540 4.363991 GGATGCAGATCCCTGTAGAATT 57.636 45.455 0.00 0.00 42.42 2.17
2805 2822 2.035783 GCCTGGGAGAAACCACCC 59.964 66.667 0.00 0.00 45.74 4.61
3025 3042 6.238566 CCATTGCAGATGTACTCATAAACCAG 60.239 42.308 0.00 0.00 34.06 4.00
3342 3362 2.544685 CAGCCAACTCTACATTCCTCG 58.455 52.381 0.00 0.00 0.00 4.63
3435 3455 9.546428 AAATGCCAATTAGTAAATTCCAATAGC 57.454 29.630 0.00 0.00 32.87 2.97
3569 3593 5.753921 ACGCTATTATGGTCTAGAAAAGTGC 59.246 40.000 0.00 0.00 0.00 4.40
3684 3708 5.163012 ACGGAGGGAGTATAAGACTGGATAA 60.163 44.000 0.00 0.00 39.06 1.75
3699 3723 6.041069 AGACAAATATTTAGAGACGGAGGGAG 59.959 42.308 0.00 0.00 0.00 4.30
3701 3725 6.163135 AGACAAATATTTAGAGACGGAGGG 57.837 41.667 0.00 0.00 0.00 4.30
3702 3726 7.982354 AGAAAGACAAATATTTAGAGACGGAGG 59.018 37.037 0.00 0.00 0.00 4.30
3703 3727 8.934507 AGAAAGACAAATATTTAGAGACGGAG 57.065 34.615 0.00 0.00 0.00 4.63
3717 3741 8.924511 TTGTTGGAATCTCTAGAAAGACAAAT 57.075 30.769 0.00 0.00 0.00 2.32
3718 3742 7.993183 ACTTGTTGGAATCTCTAGAAAGACAAA 59.007 33.333 0.00 0.00 0.00 2.83
3719 3743 7.442364 CACTTGTTGGAATCTCTAGAAAGACAA 59.558 37.037 0.00 0.00 0.00 3.18
3720 3744 6.931281 CACTTGTTGGAATCTCTAGAAAGACA 59.069 38.462 0.00 0.00 0.00 3.41
3721 3745 7.117092 GTCACTTGTTGGAATCTCTAGAAAGAC 59.883 40.741 0.00 0.00 0.00 3.01
3722 3746 7.015682 AGTCACTTGTTGGAATCTCTAGAAAGA 59.984 37.037 0.00 0.00 0.00 2.52
3723 3747 7.158021 AGTCACTTGTTGGAATCTCTAGAAAG 58.842 38.462 0.00 0.00 0.00 2.62
3724 3748 7.067496 AGTCACTTGTTGGAATCTCTAGAAA 57.933 36.000 0.00 0.00 0.00 2.52
3725 3749 6.672266 AGTCACTTGTTGGAATCTCTAGAA 57.328 37.500 0.00 0.00 0.00 2.10
3726 3750 6.719829 TGTAGTCACTTGTTGGAATCTCTAGA 59.280 38.462 0.00 0.00 0.00 2.43
3727 3751 6.925211 TGTAGTCACTTGTTGGAATCTCTAG 58.075 40.000 0.00 0.00 0.00 2.43
3728 3752 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
3729 3753 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
3730 3754 5.163814 GCATGTAGTCACTTGTTGGAATCTC 60.164 44.000 0.00 0.00 33.46 2.75
3731 3755 4.697352 GCATGTAGTCACTTGTTGGAATCT 59.303 41.667 0.00 0.00 33.46 2.40
3732 3756 4.436050 CGCATGTAGTCACTTGTTGGAATC 60.436 45.833 0.00 0.00 33.46 2.52
3733 3757 3.436704 CGCATGTAGTCACTTGTTGGAAT 59.563 43.478 0.00 0.00 33.46 3.01
3734 3758 2.805671 CGCATGTAGTCACTTGTTGGAA 59.194 45.455 0.00 0.00 33.46 3.53
3735 3759 2.036604 TCGCATGTAGTCACTTGTTGGA 59.963 45.455 0.00 0.00 33.46 3.53
3736 3760 2.412870 TCGCATGTAGTCACTTGTTGG 58.587 47.619 0.00 0.00 33.46 3.77
3737 3761 3.665323 GCTTCGCATGTAGTCACTTGTTG 60.665 47.826 0.00 0.00 33.46 3.33
3738 3762 2.480419 GCTTCGCATGTAGTCACTTGTT 59.520 45.455 0.00 0.00 33.46 2.83
3739 3763 2.069273 GCTTCGCATGTAGTCACTTGT 58.931 47.619 0.00 0.00 33.46 3.16
3740 3764 2.068519 TGCTTCGCATGTAGTCACTTG 58.931 47.619 0.00 0.00 31.71 3.16
3741 3765 2.455674 TGCTTCGCATGTAGTCACTT 57.544 45.000 0.00 0.00 31.71 3.16
3742 3766 2.455674 TTGCTTCGCATGTAGTCACT 57.544 45.000 0.00 0.00 38.76 3.41
3743 3767 3.536158 TTTTGCTTCGCATGTAGTCAC 57.464 42.857 0.00 0.00 38.76 3.67
3744 3768 3.750652 TCATTTTGCTTCGCATGTAGTCA 59.249 39.130 0.00 0.00 38.76 3.41
3745 3769 4.142816 ACTCATTTTGCTTCGCATGTAGTC 60.143 41.667 0.00 0.00 38.76 2.59
3746 3770 3.753272 ACTCATTTTGCTTCGCATGTAGT 59.247 39.130 0.00 0.00 38.76 2.73
3747 3771 4.093514 CACTCATTTTGCTTCGCATGTAG 58.906 43.478 0.00 0.00 38.76 2.74
3748 3772 3.750652 TCACTCATTTTGCTTCGCATGTA 59.249 39.130 0.00 0.00 38.76 2.29
3749 3773 2.553602 TCACTCATTTTGCTTCGCATGT 59.446 40.909 0.00 0.00 38.76 3.21
3750 3774 3.206034 TCACTCATTTTGCTTCGCATG 57.794 42.857 0.00 0.00 38.76 4.06
3751 3775 3.921119 TTCACTCATTTTGCTTCGCAT 57.079 38.095 0.00 0.00 38.76 4.73
3752 3776 3.503363 AGATTCACTCATTTTGCTTCGCA 59.497 39.130 0.00 0.00 36.47 5.10
3753 3777 4.088823 AGATTCACTCATTTTGCTTCGC 57.911 40.909 0.00 0.00 0.00 4.70
3754 3778 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
3755 3779 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3785 3809 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
3787 3811 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
3788 3812 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
3789 3813 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
3790 3814 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
3791 3815 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
3792 3816 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
3793 3817 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
3794 3818 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
3795 3819 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
3796 3820 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
3809 3833 7.391148 TTTTAGAGATTGCAAATGGACTACC 57.609 36.000 1.71 0.00 0.00 3.18
3810 3834 8.730680 TCTTTTTAGAGATTGCAAATGGACTAC 58.269 33.333 1.71 0.00 0.00 2.73
3811 3835 8.730680 GTCTTTTTAGAGATTGCAAATGGACTA 58.269 33.333 1.71 0.91 0.00 2.59
3812 3836 7.231317 TGTCTTTTTAGAGATTGCAAATGGACT 59.769 33.333 1.71 1.89 0.00 3.85
3813 3837 7.370383 TGTCTTTTTAGAGATTGCAAATGGAC 58.630 34.615 1.71 1.84 0.00 4.02
3814 3838 7.523293 TGTCTTTTTAGAGATTGCAAATGGA 57.477 32.000 1.71 0.00 0.00 3.41
3815 3839 8.592105 TTTGTCTTTTTAGAGATTGCAAATGG 57.408 30.769 1.71 0.00 0.00 3.16
3830 3854 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3831 3855 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3832 3856 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3833 3857 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3834 3858 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3835 3859 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3836 3860 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3837 3861 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3838 3862 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3839 3863 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3840 3864 8.759782 CATAATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
3841 3865 7.310237 GCATAATACTCCCTCCGTTCCTAAATA 60.310 40.741 0.00 0.00 0.00 1.40
3842 3866 6.520231 GCATAATACTCCCTCCGTTCCTAAAT 60.520 42.308 0.00 0.00 0.00 1.40
3843 3867 5.221581 GCATAATACTCCCTCCGTTCCTAAA 60.222 44.000 0.00 0.00 0.00 1.85
3844 3868 4.282703 GCATAATACTCCCTCCGTTCCTAA 59.717 45.833 0.00 0.00 0.00 2.69
3845 3869 3.830755 GCATAATACTCCCTCCGTTCCTA 59.169 47.826 0.00 0.00 0.00 2.94
3846 3870 2.633481 GCATAATACTCCCTCCGTTCCT 59.367 50.000 0.00 0.00 0.00 3.36
3847 3871 2.367567 TGCATAATACTCCCTCCGTTCC 59.632 50.000 0.00 0.00 0.00 3.62
3848 3872 3.746045 TGCATAATACTCCCTCCGTTC 57.254 47.619 0.00 0.00 0.00 3.95
3849 3873 3.646162 TCATGCATAATACTCCCTCCGTT 59.354 43.478 0.00 0.00 0.00 4.44
3850 3874 3.006967 GTCATGCATAATACTCCCTCCGT 59.993 47.826 0.00 0.00 0.00 4.69
3851 3875 3.589988 GTCATGCATAATACTCCCTCCG 58.410 50.000 0.00 0.00 0.00 4.63
3852 3876 3.327757 TGGTCATGCATAATACTCCCTCC 59.672 47.826 0.00 0.00 0.00 4.30
3853 3877 4.319177 GTGGTCATGCATAATACTCCCTC 58.681 47.826 0.00 0.00 0.00 4.30
3854 3878 3.073062 GGTGGTCATGCATAATACTCCCT 59.927 47.826 0.00 0.00 0.00 4.20
3855 3879 3.181445 TGGTGGTCATGCATAATACTCCC 60.181 47.826 0.00 3.72 0.00 4.30
3856 3880 4.085357 TGGTGGTCATGCATAATACTCC 57.915 45.455 0.00 6.40 0.00 3.85
3857 3881 4.023707 GCTTGGTGGTCATGCATAATACTC 60.024 45.833 0.00 0.00 43.52 2.59
3858 3882 3.885297 GCTTGGTGGTCATGCATAATACT 59.115 43.478 0.00 0.00 43.52 2.12
3859 3883 3.631686 TGCTTGGTGGTCATGCATAATAC 59.368 43.478 0.00 0.00 46.98 1.89
3860 3884 3.895998 TGCTTGGTGGTCATGCATAATA 58.104 40.909 0.00 0.00 46.98 0.98
3861 3885 2.737544 TGCTTGGTGGTCATGCATAAT 58.262 42.857 0.00 0.00 46.98 1.28
3862 3886 2.212812 TGCTTGGTGGTCATGCATAA 57.787 45.000 0.00 0.00 46.98 1.90
3863 3887 3.974535 TGCTTGGTGGTCATGCATA 57.025 47.368 0.00 0.00 46.98 3.14
3864 3888 4.848000 TGCTTGGTGGTCATGCAT 57.152 50.000 0.00 0.00 46.98 3.96
3866 3890 5.458041 AATTATATGCTTGGTGGTCATGC 57.542 39.130 0.00 0.00 44.09 4.06
3867 3891 6.266103 AGGAAATTATATGCTTGGTGGTCATG 59.734 38.462 0.00 0.00 0.00 3.07
3868 3892 6.266103 CAGGAAATTATATGCTTGGTGGTCAT 59.734 38.462 0.00 0.00 0.00 3.06
3869 3893 5.593909 CAGGAAATTATATGCTTGGTGGTCA 59.406 40.000 0.00 0.00 0.00 4.02
3870 3894 5.827797 TCAGGAAATTATATGCTTGGTGGTC 59.172 40.000 0.00 0.00 0.00 4.02
3871 3895 5.594317 GTCAGGAAATTATATGCTTGGTGGT 59.406 40.000 0.00 0.00 0.00 4.16
4074 4098 2.161855 CTGGTGCCAGATAACTGCAAA 58.838 47.619 12.66 0.00 46.30 3.68
4194 4219 2.437895 GTTGGCCCTTAGGTCGGC 60.438 66.667 0.00 0.00 42.57 5.54
4305 4331 1.074405 ACTTGCAAGAAGATGGAGGCA 59.926 47.619 32.50 0.00 0.00 4.75
4384 4410 2.800250 AGCCAACTCTGAAATCCTTGG 58.200 47.619 0.00 0.00 35.44 3.61
4434 4460 1.900585 CTCCAATCACACCGTGCACG 61.901 60.000 31.77 31.77 39.44 5.34
4651 4687 6.090763 GGCATTTACACAAAATAACTCAAGGC 59.909 38.462 0.00 0.00 35.54 4.35
4656 4692 7.116233 CCAACAGGCATTTACACAAAATAACTC 59.884 37.037 0.00 0.00 35.54 3.01
5010 5046 2.352960 CGATTACTCAAAAGCAGAGGGC 59.647 50.000 0.00 0.00 45.30 5.19
5035 5071 1.341209 GTAGCAGCAAAAGCTTTGGGT 59.659 47.619 13.54 13.02 43.25 4.51
5141 5177 8.299570 ACTAAATGTCATTTCAGGTCACATTTC 58.700 33.333 14.07 0.00 43.37 2.17
5142 5178 8.181904 ACTAAATGTCATTTCAGGTCACATTT 57.818 30.769 14.07 11.79 45.30 2.32
5143 5179 7.765695 ACTAAATGTCATTTCAGGTCACATT 57.234 32.000 14.07 0.00 38.94 2.71
5144 5180 7.231317 ACAACTAAATGTCATTTCAGGTCACAT 59.769 33.333 14.07 0.00 33.82 3.21
5145 5181 6.545666 ACAACTAAATGTCATTTCAGGTCACA 59.454 34.615 14.07 0.00 33.82 3.58
5146 5182 6.857964 CACAACTAAATGTCATTTCAGGTCAC 59.142 38.462 14.07 0.00 33.82 3.67
5147 5183 6.514870 GCACAACTAAATGTCATTTCAGGTCA 60.515 38.462 14.07 0.00 33.82 4.02
5148 5184 5.858581 GCACAACTAAATGTCATTTCAGGTC 59.141 40.000 14.07 0.00 33.82 3.85
5149 5185 5.562696 CGCACAACTAAATGTCATTTCAGGT 60.563 40.000 14.07 9.23 33.82 4.00
5150 5186 4.853196 CGCACAACTAAATGTCATTTCAGG 59.147 41.667 14.07 8.68 33.82 3.86
5151 5187 5.688823 TCGCACAACTAAATGTCATTTCAG 58.311 37.500 14.07 11.95 33.82 3.02
5152 5188 5.681337 TCGCACAACTAAATGTCATTTCA 57.319 34.783 14.07 1.59 33.82 2.69
5163 5199 4.521130 ACTGAGATCTTCGCACAACTAA 57.479 40.909 0.00 0.00 0.00 2.24
5181 5217 7.243487 ACGATTGCAAATAGTTATCACAACTG 58.757 34.615 1.71 0.00 0.00 3.16
5208 5244 1.879796 GCCATTCTCATCGGGATGACC 60.880 57.143 7.26 0.00 42.42 4.02
5213 5249 1.146930 GCTGCCATTCTCATCGGGA 59.853 57.895 0.00 0.00 0.00 5.14
5216 5252 0.591659 CATGGCTGCCATTCTCATCG 59.408 55.000 30.74 14.38 42.23 3.84
5238 5274 3.262420 GAGATCTACAAACGGCACACAT 58.738 45.455 0.00 0.00 0.00 3.21
5513 5554 0.597637 ACACTGACACTGCTGCGTAC 60.598 55.000 0.00 0.00 0.00 3.67
5514 5555 0.597377 CACACTGACACTGCTGCGTA 60.597 55.000 0.00 0.00 0.00 4.42
5515 5556 1.884464 CACACTGACACTGCTGCGT 60.884 57.895 0.00 0.00 0.00 5.24
5516 5557 2.601398 CCACACTGACACTGCTGCG 61.601 63.158 0.00 0.00 0.00 5.18
5518 5559 2.256591 GGCCACACTGACACTGCTG 61.257 63.158 0.00 0.00 0.00 4.41
5519 5560 2.111878 GGCCACACTGACACTGCT 59.888 61.111 0.00 0.00 0.00 4.24
5520 5561 3.349006 CGGCCACACTGACACTGC 61.349 66.667 2.24 0.00 0.00 4.40
5521 5562 2.666190 CCGGCCACACTGACACTG 60.666 66.667 2.24 0.00 0.00 3.66
5522 5563 3.161450 ACCGGCCACACTGACACT 61.161 61.111 0.00 0.00 0.00 3.55
5523 5564 2.972505 CACCGGCCACACTGACAC 60.973 66.667 0.00 0.00 0.00 3.67
5524 5565 4.248842 CCACCGGCCACACTGACA 62.249 66.667 0.00 0.00 0.00 3.58
5597 5638 2.114616 AGAAGGTCCCTCAGCATACTG 58.885 52.381 0.00 0.00 45.95 2.74
5802 9111 5.279056 GGCTGATAGAGGAACGCTAAGTTAT 60.279 44.000 0.00 0.00 45.20 1.89
5812 9121 4.363991 AATGGATGGCTGATAGAGGAAC 57.636 45.455 0.00 0.00 0.00 3.62
5813 9122 6.514012 TTTAATGGATGGCTGATAGAGGAA 57.486 37.500 0.00 0.00 0.00 3.36
5839 9149 1.134788 GGGTCAATCTGGTACGTCAGG 60.135 57.143 0.00 0.00 35.58 3.86
5841 9151 1.634960 TGGGTCAATCTGGTACGTCA 58.365 50.000 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.