Multiple sequence alignment - TraesCS1A01G272700

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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 TraesCS1A01G272700 chr1A 100.000 4476 0 0 1 4476 466035875 466040350 0.000000e+00 8266.0
1 TraesCS1A01G272700 chr1A 96.881 3559 79 12 1 3539 466335487 466339033 0.000000e+00 5928.0
2 TraesCS1A01G272700 chr6A 96.715 3562 62 20 1 3539 428667683 428664154 0.000000e+00 5879.0
3 TraesCS1A01G272700 chr1B 95.613 3579 99 19 1 3539 491437600 491441160 0.000000e+00 5686.0
4 TraesCS1A01G272700 chr1B 95.589 3582 97 26 1 3539 491396357 491399920 0.000000e+00 5683.0
5 TraesCS1A01G272700 chr1B 93.590 78 5 0 3932 4009 703460 703383 2.830000e-22 117.0
6 TraesCS1A01G272700 chr1B 98.182 55 1 0 2450 2504 491398777 491398831 3.690000e-16 97.1
7 TraesCS1A01G272700 chr1D 96.232 3503 72 16 59 3539 367147578 367151042 0.000000e+00 5683.0
8 TraesCS1A01G272700 chr1D 96.513 3155 60 11 394 3539 366089254 366092367 0.000000e+00 5171.0
9 TraesCS1A01G272700 chr1D 91.716 338 9 5 1 338 366088932 366089250 6.830000e-123 451.0
10 TraesCS1A01G272700 chr7D 92.797 472 29 3 4008 4476 23080283 23079814 0.000000e+00 678.0
11 TraesCS1A01G272700 chr7D 90.863 197 18 0 3663 3859 23080471 23080275 9.550000e-67 265.0
12 TraesCS1A01G272700 chr7D 94.891 137 2 3 3858 3991 550895997 550895863 4.540000e-50 209.0
13 TraesCS1A01G272700 chr6D 92.797 472 29 3 4008 4476 429317899 429318368 0.000000e+00 678.0
14 TraesCS1A01G272700 chr6D 92.585 472 30 3 4008 4476 291718384 291717915 0.000000e+00 673.0
15 TraesCS1A01G272700 chr6D 90.722 194 18 0 3666 3859 291718569 291718376 4.440000e-65 259.0
16 TraesCS1A01G272700 chr6D 89.848 197 20 0 3663 3859 429317711 429317907 2.070000e-63 254.0
17 TraesCS1A01G272700 chr6D 91.946 149 9 1 3860 4005 108225390 108225538 5.870000e-49 206.0
18 TraesCS1A01G272700 chrUn 92.373 472 29 5 4008 4476 96524959 96525426 0.000000e+00 665.0
19 TraesCS1A01G272700 chrUn 90.355 197 19 0 3663 3859 96524771 96524967 4.440000e-65 259.0
20 TraesCS1A01G272700 chr4D 92.161 472 32 3 4008 4476 215187974 215188443 0.000000e+00 662.0
21 TraesCS1A01G272700 chr5D 92.763 456 28 3 4024 4476 178475496 178475949 0.000000e+00 654.0
22 TraesCS1A01G272700 chr3A 90.972 144 10 1 3860 4000 103020094 103020237 1.640000e-44 191.0
23 TraesCS1A01G272700 chr5B 92.593 81 6 0 3925 4005 176633370 176633290 2.830000e-22 117.0


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 TraesCS1A01G272700 chr1A 466035875 466040350 4475 False 8266.00 8266 100.0000 1 4476 1 chr1A.!!$F1 4475
1 TraesCS1A01G272700 chr1A 466335487 466339033 3546 False 5928.00 5928 96.8810 1 3539 1 chr1A.!!$F2 3538
2 TraesCS1A01G272700 chr6A 428664154 428667683 3529 True 5879.00 5879 96.7150 1 3539 1 chr6A.!!$R1 3538
3 TraesCS1A01G272700 chr1B 491437600 491441160 3560 False 5686.00 5686 95.6130 1 3539 1 chr1B.!!$F1 3538
4 TraesCS1A01G272700 chr1B 491396357 491399920 3563 False 2890.05 5683 96.8855 1 3539 2 chr1B.!!$F2 3538
5 TraesCS1A01G272700 chr1D 367147578 367151042 3464 False 5683.00 5683 96.2320 59 3539 1 chr1D.!!$F1 3480
6 TraesCS1A01G272700 chr1D 366088932 366092367 3435 False 2811.00 5171 94.1145 1 3539 2 chr1D.!!$F2 3538
7 TraesCS1A01G272700 chr7D 23079814 23080471 657 True 471.50 678 91.8300 3663 4476 2 chr7D.!!$R2 813
8 TraesCS1A01G272700 chr6D 291717915 291718569 654 True 466.00 673 91.6535 3666 4476 2 chr6D.!!$R1 810
9 TraesCS1A01G272700 chr6D 429317711 429318368 657 False 466.00 678 91.3225 3663 4476 2 chr6D.!!$F2 813
10 TraesCS1A01G272700 chrUn 96524771 96525426 655 False 462.00 665 91.3640 3663 4476 2 chrUn.!!$F1 813

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
969 1010 1.000396 GGCTGTGGCTTCAATCCCT 60.000 57.895 0.00 0.0 38.73 4.20 F
1545 1599 5.308014 TCATTGCAGCTCTTTCTCTTGTTA 58.692 37.500 0.00 0.0 0.00 2.41 F
2685 2801 4.100653 GGGGAAGTACAAGAGGTATACACC 59.899 50.000 5.01 0.0 46.19 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2097 4.141287 CCTGTGTGGATTGAAACCAGTTA 58.859 43.478 0.00 0.0 38.14 2.24 R
3251 3367 6.941857 TGTGGAGTTTGTACTTGCTATCATA 58.058 36.000 0.00 0.0 33.84 2.15 R
3914 4030 0.033208 TAGCCTTGGCTTTGGATGGG 60.033 55.000 19.93 0.0 0.00 4.00 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
104 108 7.015292 ACGTCTCCTTTGGCATATCTTATTAGA 59.985 37.037 0.00 0.00 34.21 2.10
332 345 5.841957 ATGTTCCTACTCATTTTGATGGC 57.158 39.130 0.00 0.00 0.00 4.40
501 538 1.742308 TTTTGGGTAGGCTCCTCACT 58.258 50.000 0.00 0.00 0.00 3.41
556 593 7.990917 TGTAGTAATTCTCAAAAGTTTGCACA 58.009 30.769 0.00 0.00 38.05 4.57
827 868 2.899900 TCTTAGCTCAGCAGGACAAAGA 59.100 45.455 0.00 0.00 0.00 2.52
883 924 4.887071 CCAGCTGCCTACATTTACCAATAA 59.113 41.667 8.66 0.00 0.00 1.40
969 1010 1.000396 GGCTGTGGCTTCAATCCCT 60.000 57.895 0.00 0.00 38.73 4.20
1209 1259 6.489603 TGGTGATAATATTGTCAGTGGGTTT 58.510 36.000 14.48 0.00 0.00 3.27
1211 1261 6.265577 GTGATAATATTGTCAGTGGGTTTGC 58.734 40.000 14.48 0.00 0.00 3.68
1366 1417 6.992063 TTGTTTGTGCCAAATTACATTTGT 57.008 29.167 8.11 0.00 46.22 2.83
1545 1599 5.308014 TCATTGCAGCTCTTTCTCTTGTTA 58.692 37.500 0.00 0.00 0.00 2.41
1554 1608 6.376018 AGCTCTTTCTCTTGTTAGTCTACGAT 59.624 38.462 0.00 0.00 0.00 3.73
2685 2801 4.100653 GGGGAAGTACAAGAGGTATACACC 59.899 50.000 5.01 0.00 46.19 4.16
3251 3367 2.354303 CCACACATGATTGCATTGCCTT 60.354 45.455 6.12 0.00 30.68 4.35
3255 3371 4.403113 ACACATGATTGCATTGCCTTATGA 59.597 37.500 15.45 0.44 30.68 2.15
3580 3696 9.877178 ACCACAAACTGTGTAAAAATTAATCAA 57.123 25.926 6.08 0.00 46.45 2.57
3601 3717 9.850628 AATCAACACATCATTTCAACATAAGAG 57.149 29.630 0.00 0.00 0.00 2.85
3602 3718 8.620116 TCAACACATCATTTCAACATAAGAGA 57.380 30.769 0.00 0.00 0.00 3.10
3603 3719 9.234827 TCAACACATCATTTCAACATAAGAGAT 57.765 29.630 0.00 0.00 0.00 2.75
3604 3720 9.850628 CAACACATCATTTCAACATAAGAGATT 57.149 29.630 0.00 0.00 0.00 2.40
3605 3721 9.850628 AACACATCATTTCAACATAAGAGATTG 57.149 29.630 0.00 0.00 0.00 2.67
3606 3722 8.464404 ACACATCATTTCAACATAAGAGATTGG 58.536 33.333 0.00 0.00 0.00 3.16
3607 3723 8.464404 CACATCATTTCAACATAAGAGATTGGT 58.536 33.333 0.00 0.00 0.00 3.67
3608 3724 8.464404 ACATCATTTCAACATAAGAGATTGGTG 58.536 33.333 0.00 0.00 31.68 4.17
3609 3725 8.464404 CATCATTTCAACATAAGAGATTGGTGT 58.536 33.333 0.00 0.00 32.33 4.16
3610 3726 8.408043 TCATTTCAACATAAGAGATTGGTGTT 57.592 30.769 0.00 0.00 32.33 3.32
3611 3727 8.859090 TCATTTCAACATAAGAGATTGGTGTTT 58.141 29.630 0.00 0.00 32.33 2.83
3628 3744 5.497474 GGTGTTTACCATCCACTTATCAGT 58.503 41.667 0.00 0.00 46.71 3.41
3629 3745 5.944007 GGTGTTTACCATCCACTTATCAGTT 59.056 40.000 0.00 0.00 46.71 3.16
3630 3746 6.433093 GGTGTTTACCATCCACTTATCAGTTT 59.567 38.462 0.00 0.00 46.71 2.66
3631 3747 7.305474 GTGTTTACCATCCACTTATCAGTTTG 58.695 38.462 0.00 0.00 0.00 2.93
3632 3748 6.072175 TGTTTACCATCCACTTATCAGTTTGC 60.072 38.462 0.00 0.00 0.00 3.68
3633 3749 4.032960 ACCATCCACTTATCAGTTTGCA 57.967 40.909 0.00 0.00 0.00 4.08
3634 3750 4.603131 ACCATCCACTTATCAGTTTGCAT 58.397 39.130 0.00 0.00 0.00 3.96
3635 3751 4.400251 ACCATCCACTTATCAGTTTGCATG 59.600 41.667 0.00 0.00 0.00 4.06
3636 3752 4.641541 CCATCCACTTATCAGTTTGCATGA 59.358 41.667 0.00 0.00 0.00 3.07
3637 3753 5.220989 CCATCCACTTATCAGTTTGCATGAG 60.221 44.000 0.00 0.00 0.00 2.90
3638 3754 5.164620 TCCACTTATCAGTTTGCATGAGA 57.835 39.130 0.00 0.00 0.00 3.27
3639 3755 4.937620 TCCACTTATCAGTTTGCATGAGAC 59.062 41.667 0.00 0.00 0.00 3.36
3640 3756 4.940046 CCACTTATCAGTTTGCATGAGACT 59.060 41.667 0.00 0.00 0.00 3.24
3641 3757 5.064452 CCACTTATCAGTTTGCATGAGACTC 59.936 44.000 0.00 0.00 0.00 3.36
3642 3758 5.640783 CACTTATCAGTTTGCATGAGACTCA 59.359 40.000 7.80 7.80 0.00 3.41
3643 3759 6.148315 CACTTATCAGTTTGCATGAGACTCAA 59.852 38.462 9.70 0.00 0.00 3.02
3644 3760 6.883217 ACTTATCAGTTTGCATGAGACTCAAT 59.117 34.615 9.70 0.00 0.00 2.57
3645 3761 5.814764 ATCAGTTTGCATGAGACTCAATC 57.185 39.130 9.70 4.89 0.00 2.67
3646 3762 4.644498 TCAGTTTGCATGAGACTCAATCA 58.356 39.130 9.70 7.53 0.00 2.57
3647 3763 5.065235 TCAGTTTGCATGAGACTCAATCAA 58.935 37.500 9.70 12.96 0.00 2.57
3648 3764 5.180680 TCAGTTTGCATGAGACTCAATCAAG 59.819 40.000 9.70 5.60 0.00 3.02
3649 3765 5.180680 CAGTTTGCATGAGACTCAATCAAGA 59.819 40.000 9.70 5.41 0.00 3.02
3650 3766 5.180868 AGTTTGCATGAGACTCAATCAAGAC 59.819 40.000 9.70 14.50 0.00 3.01
3651 3767 4.276058 TGCATGAGACTCAATCAAGACA 57.724 40.909 9.70 0.00 0.00 3.41
3652 3768 4.644498 TGCATGAGACTCAATCAAGACAA 58.356 39.130 9.70 0.00 0.00 3.18
3653 3769 4.694037 TGCATGAGACTCAATCAAGACAAG 59.306 41.667 9.70 0.00 0.00 3.16
3654 3770 4.934001 GCATGAGACTCAATCAAGACAAGA 59.066 41.667 9.70 0.00 0.00 3.02
3655 3771 5.410746 GCATGAGACTCAATCAAGACAAGAA 59.589 40.000 9.70 0.00 0.00 2.52
3656 3772 6.620303 GCATGAGACTCAATCAAGACAAGAAC 60.620 42.308 9.70 0.00 0.00 3.01
3657 3773 5.917462 TGAGACTCAATCAAGACAAGAACA 58.083 37.500 1.64 0.00 0.00 3.18
3658 3774 6.348498 TGAGACTCAATCAAGACAAGAACAA 58.652 36.000 1.64 0.00 0.00 2.83
3659 3775 6.823182 TGAGACTCAATCAAGACAAGAACAAA 59.177 34.615 1.64 0.00 0.00 2.83
3660 3776 7.336679 TGAGACTCAATCAAGACAAGAACAAAA 59.663 33.333 1.64 0.00 0.00 2.44
3661 3777 8.230472 AGACTCAATCAAGACAAGAACAAAAT 57.770 30.769 0.00 0.00 0.00 1.82
3684 3800 3.941483 AGCAGTACTGATAAACACCATGC 59.059 43.478 27.08 6.91 0.00 4.06
3687 3803 4.094887 CAGTACTGATAAACACCATGCACC 59.905 45.833 18.45 0.00 0.00 5.01
3691 3807 2.088423 GATAAACACCATGCACCGGAA 58.912 47.619 9.46 0.00 0.00 4.30
3704 3820 0.620556 ACCGGAAGACAATGGCATCT 59.379 50.000 9.46 0.00 0.00 2.90
3728 3844 2.198827 AAACCATTCGCCTCACATGA 57.801 45.000 0.00 0.00 0.00 3.07
3743 3859 1.375140 ATGAGTGCAGTGCAGGACG 60.375 57.895 20.42 0.00 40.08 4.79
3770 3886 2.030805 GCGATTATTCCCCAACATGCTC 60.031 50.000 0.00 0.00 0.00 4.26
3773 3889 3.464720 TTATTCCCCAACATGCTCCAA 57.535 42.857 0.00 0.00 0.00 3.53
3782 3898 0.534877 ACATGCTCCAACGCTCAACA 60.535 50.000 0.00 0.00 0.00 3.33
3784 3900 1.089920 ATGCTCCAACGCTCAACATC 58.910 50.000 0.00 0.00 0.00 3.06
3785 3901 0.035317 TGCTCCAACGCTCAACATCT 59.965 50.000 0.00 0.00 0.00 2.90
3794 3910 2.225019 ACGCTCAACATCTTTTGCTGAG 59.775 45.455 2.44 2.44 46.74 3.35
3797 3913 4.093998 CGCTCAACATCTTTTGCTGAGTAT 59.906 41.667 7.58 0.00 46.06 2.12
3799 3915 6.183360 CGCTCAACATCTTTTGCTGAGTATAA 60.183 38.462 7.58 0.00 46.06 0.98
3862 3978 7.035004 TGCCAATTCTACATTGTAAATTGAGC 58.965 34.615 25.76 24.87 40.07 4.26
3863 3979 7.035004 GCCAATTCTACATTGTAAATTGAGCA 58.965 34.615 25.76 2.97 40.07 4.26
3864 3980 7.009540 GCCAATTCTACATTGTAAATTGAGCAC 59.990 37.037 25.76 16.81 40.07 4.40
3865 3981 8.246180 CCAATTCTACATTGTAAATTGAGCACT 58.754 33.333 25.76 5.70 40.07 4.40
3866 3982 9.069078 CAATTCTACATTGTAAATTGAGCACTG 57.931 33.333 23.01 8.88 40.07 3.66
3867 3983 6.182039 TCTACATTGTAAATTGAGCACTGC 57.818 37.500 0.00 0.00 0.00 4.40
3868 3984 5.939883 TCTACATTGTAAATTGAGCACTGCT 59.060 36.000 2.22 2.22 43.88 4.24
3869 3985 5.458041 ACATTGTAAATTGAGCACTGCTT 57.542 34.783 4.67 0.00 39.88 3.91
3870 3986 5.464168 ACATTGTAAATTGAGCACTGCTTC 58.536 37.500 4.67 0.00 39.88 3.86
3871 3987 5.009911 ACATTGTAAATTGAGCACTGCTTCA 59.990 36.000 4.67 2.23 39.88 3.02
3872 3988 4.488126 TGTAAATTGAGCACTGCTTCAC 57.512 40.909 4.67 0.00 39.88 3.18
3873 3989 3.882288 TGTAAATTGAGCACTGCTTCACA 59.118 39.130 4.67 0.00 39.88 3.58
3874 3990 3.360249 AAATTGAGCACTGCTTCACAC 57.640 42.857 4.67 0.00 39.88 3.82
3875 3991 1.971481 ATTGAGCACTGCTTCACACA 58.029 45.000 4.67 0.00 39.88 3.72
3876 3992 1.016627 TTGAGCACTGCTTCACACAC 58.983 50.000 4.67 0.00 39.88 3.82
3877 3993 1.153597 TGAGCACTGCTTCACACACG 61.154 55.000 4.67 0.00 39.88 4.49
3878 3994 0.875908 GAGCACTGCTTCACACACGA 60.876 55.000 4.67 0.00 39.88 4.35
3879 3995 1.154205 AGCACTGCTTCACACACGAC 61.154 55.000 0.00 0.00 33.89 4.34
3880 3996 1.428370 GCACTGCTTCACACACGACA 61.428 55.000 0.00 0.00 0.00 4.35
3881 3997 0.301687 CACTGCTTCACACACGACAC 59.698 55.000 0.00 0.00 0.00 3.67
3882 3998 0.175760 ACTGCTTCACACACGACACT 59.824 50.000 0.00 0.00 0.00 3.55
3883 3999 1.290203 CTGCTTCACACACGACACTT 58.710 50.000 0.00 0.00 0.00 3.16
3884 4000 1.665679 CTGCTTCACACACGACACTTT 59.334 47.619 0.00 0.00 0.00 2.66
3885 4001 1.663643 TGCTTCACACACGACACTTTC 59.336 47.619 0.00 0.00 0.00 2.62
3886 4002 1.003866 GCTTCACACACGACACTTTCC 60.004 52.381 0.00 0.00 0.00 3.13
3887 4003 2.276201 CTTCACACACGACACTTTCCA 58.724 47.619 0.00 0.00 0.00 3.53
3888 4004 1.647346 TCACACACGACACTTTCCAC 58.353 50.000 0.00 0.00 0.00 4.02
3889 4005 1.066787 TCACACACGACACTTTCCACA 60.067 47.619 0.00 0.00 0.00 4.17
3890 4006 1.062002 CACACACGACACTTTCCACAC 59.938 52.381 0.00 0.00 0.00 3.82
3891 4007 0.300491 CACACGACACTTTCCACACG 59.700 55.000 0.00 0.00 0.00 4.49
3892 4008 0.173935 ACACGACACTTTCCACACGA 59.826 50.000 0.00 0.00 0.00 4.35
3893 4009 1.282817 CACGACACTTTCCACACGAA 58.717 50.000 0.00 0.00 0.00 3.85
3894 4010 1.661617 CACGACACTTTCCACACGAAA 59.338 47.619 0.00 0.00 38.16 3.46
3895 4011 2.286833 CACGACACTTTCCACACGAAAT 59.713 45.455 0.00 0.00 39.73 2.17
3896 4012 3.491639 CACGACACTTTCCACACGAAATA 59.508 43.478 0.00 0.00 39.73 1.40
3897 4013 3.492011 ACGACACTTTCCACACGAAATAC 59.508 43.478 0.00 0.00 39.73 1.89
3898 4014 3.491639 CGACACTTTCCACACGAAATACA 59.508 43.478 0.00 0.00 39.73 2.29
3899 4015 4.376008 CGACACTTTCCACACGAAATACAG 60.376 45.833 0.00 0.00 39.73 2.74
3900 4016 4.699637 ACACTTTCCACACGAAATACAGA 58.300 39.130 0.00 0.00 39.73 3.41
3901 4017 4.510340 ACACTTTCCACACGAAATACAGAC 59.490 41.667 0.00 0.00 39.73 3.51
3902 4018 3.739300 ACTTTCCACACGAAATACAGACG 59.261 43.478 0.00 0.00 39.73 4.18
3903 4019 3.646611 TTCCACACGAAATACAGACGA 57.353 42.857 0.00 0.00 0.00 4.20
3904 4020 2.937591 TCCACACGAAATACAGACGAC 58.062 47.619 0.00 0.00 0.00 4.34
3905 4021 2.293955 TCCACACGAAATACAGACGACA 59.706 45.455 0.00 0.00 0.00 4.35
3906 4022 3.057104 TCCACACGAAATACAGACGACAT 60.057 43.478 0.00 0.00 0.00 3.06
3907 4023 3.060761 CCACACGAAATACAGACGACATG 59.939 47.826 0.00 0.00 0.00 3.21
3908 4024 3.673338 CACACGAAATACAGACGACATGT 59.327 43.478 0.00 0.00 34.62 3.21
3920 4036 2.643551 ACGACATGTCAAATCCCATCC 58.356 47.619 24.93 0.00 0.00 3.51
3921 4037 2.026356 ACGACATGTCAAATCCCATCCA 60.026 45.455 24.93 0.00 0.00 3.41
3922 4038 3.016031 CGACATGTCAAATCCCATCCAA 58.984 45.455 24.93 0.00 0.00 3.53
3923 4039 3.443329 CGACATGTCAAATCCCATCCAAA 59.557 43.478 24.93 0.00 0.00 3.28
3924 4040 4.439153 CGACATGTCAAATCCCATCCAAAG 60.439 45.833 24.93 0.00 0.00 2.77
3925 4041 3.196254 ACATGTCAAATCCCATCCAAAGC 59.804 43.478 0.00 0.00 0.00 3.51
3926 4042 2.178580 TGTCAAATCCCATCCAAAGCC 58.821 47.619 0.00 0.00 0.00 4.35
3927 4043 2.178580 GTCAAATCCCATCCAAAGCCA 58.821 47.619 0.00 0.00 0.00 4.75
3928 4044 2.566724 GTCAAATCCCATCCAAAGCCAA 59.433 45.455 0.00 0.00 0.00 4.52
3929 4045 2.833338 TCAAATCCCATCCAAAGCCAAG 59.167 45.455 0.00 0.00 0.00 3.61
3930 4046 1.870064 AATCCCATCCAAAGCCAAGG 58.130 50.000 0.00 0.00 0.00 3.61
3931 4047 0.688749 ATCCCATCCAAAGCCAAGGC 60.689 55.000 2.02 2.02 42.33 4.35
3943 4059 1.247567 GCCAAGGCTAAACAGCTTCA 58.752 50.000 3.29 0.00 38.26 3.02
3944 4060 1.200948 GCCAAGGCTAAACAGCTTCAG 59.799 52.381 3.29 0.00 38.26 3.02
3945 4061 1.200948 CCAAGGCTAAACAGCTTCAGC 59.799 52.381 0.00 0.00 42.49 4.26
3947 4063 1.796796 GGCTAAACAGCTTCAGCCG 59.203 57.895 8.45 0.00 43.80 5.52
3948 4064 1.648467 GGCTAAACAGCTTCAGCCGG 61.648 60.000 0.00 0.00 43.80 6.13
3949 4065 0.955919 GCTAAACAGCTTCAGCCGGT 60.956 55.000 1.90 0.00 43.38 5.28
3950 4066 1.523758 CTAAACAGCTTCAGCCGGTT 58.476 50.000 1.90 0.00 43.38 4.44
3951 4067 1.197721 CTAAACAGCTTCAGCCGGTTG 59.802 52.381 12.81 12.81 43.38 3.77
3952 4068 1.455383 AAACAGCTTCAGCCGGTTGG 61.455 55.000 18.99 4.24 43.38 3.77
3953 4069 2.032528 CAGCTTCAGCCGGTTGGA 59.967 61.111 18.99 9.11 43.38 3.53
3954 4070 1.377725 CAGCTTCAGCCGGTTGGAT 60.378 57.895 18.99 0.00 43.38 3.41
3955 4071 0.962356 CAGCTTCAGCCGGTTGGATT 60.962 55.000 18.99 0.00 43.38 3.01
3956 4072 0.962356 AGCTTCAGCCGGTTGGATTG 60.962 55.000 18.99 7.33 43.38 2.67
3957 4073 1.937546 GCTTCAGCCGGTTGGATTGG 61.938 60.000 18.99 0.00 37.49 3.16
3958 4074 1.304052 TTCAGCCGGTTGGATTGGG 60.304 57.895 18.99 0.00 37.49 4.12
3959 4075 3.451894 CAGCCGGTTGGATTGGGC 61.452 66.667 10.99 0.00 45.91 5.36
3961 4077 2.759560 GCCGGTTGGATTGGGCAT 60.760 61.111 1.90 0.00 44.91 4.40
3962 4078 2.785425 GCCGGTTGGATTGGGCATC 61.785 63.158 1.90 0.00 44.91 3.91
3963 4079 2.480610 CCGGTTGGATTGGGCATCG 61.481 63.158 0.00 0.00 37.49 3.84
3964 4080 1.748879 CGGTTGGATTGGGCATCGT 60.749 57.895 0.00 0.00 31.73 3.73
3965 4081 1.312371 CGGTTGGATTGGGCATCGTT 61.312 55.000 0.00 0.00 31.73 3.85
3966 4082 0.455815 GGTTGGATTGGGCATCGTTC 59.544 55.000 0.00 0.00 31.73 3.95
3967 4083 0.455815 GTTGGATTGGGCATCGTTCC 59.544 55.000 0.00 0.00 31.73 3.62
3968 4084 0.038890 TTGGATTGGGCATCGTTCCA 59.961 50.000 0.00 0.00 34.74 3.53
3969 4085 0.394216 TGGATTGGGCATCGTTCCAG 60.394 55.000 0.00 0.00 34.17 3.86
3970 4086 0.394352 GGATTGGGCATCGTTCCAGT 60.394 55.000 0.00 0.00 34.17 4.00
3971 4087 1.134220 GGATTGGGCATCGTTCCAGTA 60.134 52.381 0.00 0.00 34.17 2.74
3972 4088 2.487265 GGATTGGGCATCGTTCCAGTAT 60.487 50.000 0.00 0.00 34.17 2.12
3973 4089 2.325583 TTGGGCATCGTTCCAGTATC 57.674 50.000 0.00 0.00 34.17 2.24
3974 4090 0.104120 TGGGCATCGTTCCAGTATCG 59.896 55.000 0.00 0.00 0.00 2.92
3975 4091 0.104304 GGGCATCGTTCCAGTATCGT 59.896 55.000 0.00 0.00 0.00 3.73
3976 4092 1.472728 GGGCATCGTTCCAGTATCGTT 60.473 52.381 0.00 0.00 0.00 3.85
3977 4093 1.859080 GGCATCGTTCCAGTATCGTTC 59.141 52.381 0.00 0.00 0.00 3.95
3978 4094 2.536365 GCATCGTTCCAGTATCGTTCA 58.464 47.619 0.00 0.00 0.00 3.18
3979 4095 2.281762 GCATCGTTCCAGTATCGTTCAC 59.718 50.000 0.00 0.00 0.00 3.18
3980 4096 2.642139 TCGTTCCAGTATCGTTCACC 57.358 50.000 0.00 0.00 0.00 4.02
3981 4097 1.135603 TCGTTCCAGTATCGTTCACCG 60.136 52.381 0.00 0.00 38.13 4.94
3998 4114 3.935133 CGAAGCATCGTGTGTGAAG 57.065 52.632 2.58 0.00 44.06 3.02
3999 4115 1.139989 CGAAGCATCGTGTGTGAAGT 58.860 50.000 2.58 0.00 44.06 3.01
4000 4116 2.324860 CGAAGCATCGTGTGTGAAGTA 58.675 47.619 2.58 0.00 44.06 2.24
4001 4117 2.090658 CGAAGCATCGTGTGTGAAGTAC 59.909 50.000 2.58 0.00 44.06 2.73
4002 4118 3.318017 GAAGCATCGTGTGTGAAGTACT 58.682 45.455 0.00 0.00 0.00 2.73
4003 4119 3.386768 AGCATCGTGTGTGAAGTACTT 57.613 42.857 8.13 8.13 0.00 2.24
4004 4120 3.728845 AGCATCGTGTGTGAAGTACTTT 58.271 40.909 10.02 0.00 0.00 2.66
4005 4121 4.127171 AGCATCGTGTGTGAAGTACTTTT 58.873 39.130 10.02 0.00 0.00 2.27
4006 4122 4.024893 AGCATCGTGTGTGAAGTACTTTTG 60.025 41.667 10.02 0.00 0.00 2.44
4007 4123 4.260620 GCATCGTGTGTGAAGTACTTTTGT 60.261 41.667 10.02 0.00 0.00 2.83
4008 4124 5.729454 GCATCGTGTGTGAAGTACTTTTGTT 60.729 40.000 10.02 0.00 0.00 2.83
4009 4125 5.211266 TCGTGTGTGAAGTACTTTTGTTG 57.789 39.130 10.02 0.00 0.00 3.33
4010 4126 4.691685 TCGTGTGTGAAGTACTTTTGTTGT 59.308 37.500 10.02 0.00 0.00 3.32
4011 4127 5.868258 TCGTGTGTGAAGTACTTTTGTTGTA 59.132 36.000 10.02 0.00 0.00 2.41
4012 4128 6.368243 TCGTGTGTGAAGTACTTTTGTTGTAA 59.632 34.615 10.02 0.00 0.00 2.41
4013 4129 7.016466 CGTGTGTGAAGTACTTTTGTTGTAAA 58.984 34.615 10.02 0.00 0.00 2.01
4014 4130 7.694784 CGTGTGTGAAGTACTTTTGTTGTAAAT 59.305 33.333 10.02 0.00 0.00 1.40
4015 4131 9.349145 GTGTGTGAAGTACTTTTGTTGTAAATT 57.651 29.630 10.02 0.00 0.00 1.82
4045 4161 6.757947 CAGTTCAAGAACAATCAACACCAAAT 59.242 34.615 14.69 0.00 43.47 2.32
4118 4234 1.413077 GATCAACTAACCTCCCTCCCG 59.587 57.143 0.00 0.00 0.00 5.14
4131 4247 0.896019 CCTCCCGCGGACTATCATCT 60.896 60.000 30.73 0.00 0.00 2.90
4145 4261 2.219080 TCATCTGGGCTGCAAATCAA 57.781 45.000 0.50 0.00 0.00 2.57
4147 4263 0.813184 ATCTGGGCTGCAAATCAACG 59.187 50.000 0.50 0.00 0.00 4.10
4170 4286 1.875963 CACGCCATGACCCAAGAAC 59.124 57.895 0.00 0.00 0.00 3.01
4176 4292 2.165030 GCCATGACCCAAGAACATTGAG 59.835 50.000 0.00 0.00 0.00 3.02
4204 4320 8.980481 TGAAGAAGAAAAAGAAGGAACTATGT 57.020 30.769 0.00 0.00 38.49 2.29
4225 4341 5.345702 TGTAACCACGTAATCTAGCATCAC 58.654 41.667 0.00 0.00 0.00 3.06
4227 4343 4.465632 ACCACGTAATCTAGCATCACAA 57.534 40.909 0.00 0.00 0.00 3.33
4244 4360 2.535166 CACAACCAAAAATCACAGCACG 59.465 45.455 0.00 0.00 0.00 5.34
4252 4368 2.395988 AATCACAGCACGGGCAGACA 62.396 55.000 14.57 0.00 44.61 3.41
4298 4417 5.123936 AGTAGTCAAATATCCGAAAAGGGC 58.876 41.667 0.00 0.00 41.52 5.19
4314 4433 3.739613 GCCCCCTTTCCCCACGAT 61.740 66.667 0.00 0.00 0.00 3.73
4329 4448 6.654959 TCCCCACGATTCTGATATAAAACAA 58.345 36.000 0.00 0.00 0.00 2.83
4330 4449 6.540914 TCCCCACGATTCTGATATAAAACAAC 59.459 38.462 0.00 0.00 0.00 3.32
4332 4451 7.148154 CCCCACGATTCTGATATAAAACAACAA 60.148 37.037 0.00 0.00 0.00 2.83
4344 4463 8.691661 ATATAAAACAACAACACCTTCAGACT 57.308 30.769 0.00 0.00 0.00 3.24
4351 4470 4.130118 ACAACACCTTCAGACTGATTGAC 58.870 43.478 18.24 0.00 0.00 3.18
4363 4482 4.588951 AGACTGATTGACTGTTGTGGTCTA 59.411 41.667 0.00 0.00 35.04 2.59
4371 4490 4.404394 TGACTGTTGTGGTCTAAACTCTGA 59.596 41.667 0.00 0.00 35.04 3.27
4405 4524 7.862512 TCAACTCATGTGCAATATGTGATAA 57.137 32.000 16.56 3.76 36.73 1.75
4417 4536 7.980099 TGCAATATGTGATAATGCAACATGAAA 59.020 29.630 10.54 0.00 45.66 2.69
4430 4549 5.523188 TGCAACATGAAAGTTCACAAAATCC 59.477 36.000 0.00 0.00 40.49 3.01
4460 4579 4.439253 AAAAGTGGTAGTGCTCTTCCTT 57.561 40.909 12.00 0.00 33.18 3.36
4466 4585 3.135712 TGGTAGTGCTCTTCCTTGTTGAA 59.864 43.478 12.00 0.00 33.18 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 48 2.679132 AATCCGATTCCGACCTCGCG 62.679 60.000 0.00 0.00 38.22 5.87
104 108 6.894828 ACAAAATAAATCGTTCTGTTAGCGT 58.105 32.000 0.00 0.00 32.98 5.07
332 345 7.798596 AAGACAGATGCATAATAACTTGGAG 57.201 36.000 0.00 0.00 0.00 3.86
405 442 5.624344 TTTAGTCACCACGTTTTTGTTCA 57.376 34.783 0.00 0.00 0.00 3.18
486 523 1.687493 AGCAGTGAGGAGCCTACCC 60.687 63.158 0.00 0.00 0.00 3.69
501 538 1.059098 ATGAGGTGGACAAGACAGCA 58.941 50.000 0.00 0.00 38.72 4.41
556 593 7.094890 GCATTGATACTTCATATGCTACTTGCT 60.095 37.037 0.00 0.00 39.99 3.91
842 883 4.003648 GCTGGCATCAAACTAGTGTAAGT 58.996 43.478 0.00 0.00 0.00 2.24
1366 1417 4.219507 TGCAAGTTTCAGAAGAACAAACCA 59.780 37.500 0.00 0.00 32.39 3.67
1417 1468 9.726438 AGCTGATGTTACTTTTATTCTGTTACT 57.274 29.630 0.00 0.00 0.00 2.24
1420 1471 9.066892 TGAAGCTGATGTTACTTTTATTCTGTT 57.933 29.630 0.00 0.00 0.00 3.16
1421 1472 8.507249 GTGAAGCTGATGTTACTTTTATTCTGT 58.493 33.333 0.00 0.00 0.00 3.41
1422 1473 8.725148 AGTGAAGCTGATGTTACTTTTATTCTG 58.275 33.333 0.00 0.00 0.00 3.02
2007 2062 9.929722 GATAATTACAGTGTATCGCAAAAATGA 57.070 29.630 3.28 0.00 0.00 2.57
2042 2097 4.141287 CCTGTGTGGATTGAAACCAGTTA 58.859 43.478 0.00 0.00 38.14 2.24
2685 2801 9.159364 TGTAGTAGATATAACATACGGTAGCTG 57.841 37.037 0.00 0.00 0.00 4.24
3251 3367 6.941857 TGTGGAGTTTGTACTTGCTATCATA 58.058 36.000 0.00 0.00 33.84 2.15
3255 3371 7.182817 TCTATGTGGAGTTTGTACTTGCTAT 57.817 36.000 0.00 0.00 33.84 2.97
3575 3691 9.850628 CTCTTATGTTGAAATGATGTGTTGATT 57.149 29.630 0.00 0.00 0.00 2.57
3576 3692 9.234827 TCTCTTATGTTGAAATGATGTGTTGAT 57.765 29.630 0.00 0.00 0.00 2.57
3577 3693 8.620116 TCTCTTATGTTGAAATGATGTGTTGA 57.380 30.769 0.00 0.00 0.00 3.18
3578 3694 9.850628 AATCTCTTATGTTGAAATGATGTGTTG 57.149 29.630 0.00 0.00 0.00 3.33
3579 3695 9.850628 CAATCTCTTATGTTGAAATGATGTGTT 57.149 29.630 0.00 0.00 0.00 3.32
3580 3696 8.464404 CCAATCTCTTATGTTGAAATGATGTGT 58.536 33.333 0.00 0.00 0.00 3.72
3581 3697 8.464404 ACCAATCTCTTATGTTGAAATGATGTG 58.536 33.333 0.00 0.00 0.00 3.21
3582 3698 8.464404 CACCAATCTCTTATGTTGAAATGATGT 58.536 33.333 0.00 0.00 0.00 3.06
3583 3699 8.464404 ACACCAATCTCTTATGTTGAAATGATG 58.536 33.333 0.00 0.00 0.00 3.07
3584 3700 8.585471 ACACCAATCTCTTATGTTGAAATGAT 57.415 30.769 0.00 0.00 0.00 2.45
3585 3701 8.408043 AACACCAATCTCTTATGTTGAAATGA 57.592 30.769 0.00 0.00 32.42 2.57
3588 3704 8.573035 GGTAAACACCAATCTCTTATGTTGAAA 58.427 33.333 0.00 0.00 33.88 2.69
3589 3705 7.721842 TGGTAAACACCAATCTCTTATGTTGAA 59.278 33.333 0.00 0.00 36.74 2.69
3590 3706 7.227873 TGGTAAACACCAATCTCTTATGTTGA 58.772 34.615 0.00 0.00 36.74 3.18
3591 3707 7.447374 TGGTAAACACCAATCTCTTATGTTG 57.553 36.000 0.00 0.00 36.74 3.33
3592 3708 7.339466 GGATGGTAAACACCAATCTCTTATGTT 59.661 37.037 0.00 0.00 43.83 2.71
3593 3709 6.828785 GGATGGTAAACACCAATCTCTTATGT 59.171 38.462 0.00 0.00 43.83 2.29
3594 3710 6.828273 TGGATGGTAAACACCAATCTCTTATG 59.172 38.462 0.00 0.00 43.83 1.90
3595 3711 6.828785 GTGGATGGTAAACACCAATCTCTTAT 59.171 38.462 0.00 0.00 43.83 1.73
3596 3712 6.012858 AGTGGATGGTAAACACCAATCTCTTA 60.013 38.462 0.00 0.00 43.83 2.10
3597 3713 5.010282 GTGGATGGTAAACACCAATCTCTT 58.990 41.667 0.00 0.00 43.83 2.85
3598 3714 4.289672 AGTGGATGGTAAACACCAATCTCT 59.710 41.667 0.00 0.69 43.83 3.10
3599 3715 4.589908 AGTGGATGGTAAACACCAATCTC 58.410 43.478 0.00 0.00 43.83 2.75
3600 3716 4.657814 AGTGGATGGTAAACACCAATCT 57.342 40.909 0.00 0.00 43.83 2.40
3601 3717 6.601613 TGATAAGTGGATGGTAAACACCAATC 59.398 38.462 0.00 0.00 43.83 2.67
3602 3718 6.489603 TGATAAGTGGATGGTAAACACCAAT 58.510 36.000 0.00 0.00 43.83 3.16
3603 3719 5.882040 TGATAAGTGGATGGTAAACACCAA 58.118 37.500 0.00 0.00 43.83 3.67
3604 3720 5.013704 ACTGATAAGTGGATGGTAAACACCA 59.986 40.000 0.00 0.00 44.85 4.17
3605 3721 5.497474 ACTGATAAGTGGATGGTAAACACC 58.503 41.667 0.00 0.00 35.79 4.16
3606 3722 7.305474 CAAACTGATAAGTGGATGGTAAACAC 58.695 38.462 0.00 0.00 35.43 3.32
3607 3723 6.072175 GCAAACTGATAAGTGGATGGTAAACA 60.072 38.462 0.00 0.00 0.00 2.83
3608 3724 6.072175 TGCAAACTGATAAGTGGATGGTAAAC 60.072 38.462 0.00 0.00 0.00 2.01
3609 3725 6.007076 TGCAAACTGATAAGTGGATGGTAAA 58.993 36.000 0.00 0.00 0.00 2.01
3610 3726 5.565509 TGCAAACTGATAAGTGGATGGTAA 58.434 37.500 0.00 0.00 0.00 2.85
3611 3727 5.172687 TGCAAACTGATAAGTGGATGGTA 57.827 39.130 0.00 0.00 0.00 3.25
3612 3728 4.032960 TGCAAACTGATAAGTGGATGGT 57.967 40.909 0.00 0.00 0.00 3.55
3613 3729 4.641541 TCATGCAAACTGATAAGTGGATGG 59.358 41.667 0.00 0.00 39.48 3.51
3614 3730 5.587443 TCTCATGCAAACTGATAAGTGGATG 59.413 40.000 0.00 0.00 40.12 3.51
3615 3731 5.587844 GTCTCATGCAAACTGATAAGTGGAT 59.412 40.000 0.00 0.00 0.00 3.41
3616 3732 4.937620 GTCTCATGCAAACTGATAAGTGGA 59.062 41.667 0.00 0.00 0.00 4.02
3617 3733 4.940046 AGTCTCATGCAAACTGATAAGTGG 59.060 41.667 0.00 0.00 0.00 4.00
3618 3734 5.640783 TGAGTCTCATGCAAACTGATAAGTG 59.359 40.000 0.00 0.00 0.00 3.16
3619 3735 5.798132 TGAGTCTCATGCAAACTGATAAGT 58.202 37.500 0.00 0.00 0.00 2.24
3620 3736 6.732531 TTGAGTCTCATGCAAACTGATAAG 57.267 37.500 2.68 0.00 0.00 1.73
3621 3737 6.880529 TGATTGAGTCTCATGCAAACTGATAA 59.119 34.615 2.68 0.00 0.00 1.75
3622 3738 6.408869 TGATTGAGTCTCATGCAAACTGATA 58.591 36.000 2.68 0.00 0.00 2.15
3623 3739 5.250982 TGATTGAGTCTCATGCAAACTGAT 58.749 37.500 2.68 0.00 0.00 2.90
3624 3740 4.644498 TGATTGAGTCTCATGCAAACTGA 58.356 39.130 2.68 0.00 0.00 3.41
3625 3741 5.180680 TCTTGATTGAGTCTCATGCAAACTG 59.819 40.000 2.68 1.13 0.00 3.16
3626 3742 5.180868 GTCTTGATTGAGTCTCATGCAAACT 59.819 40.000 2.68 0.00 0.00 2.66
3627 3743 5.049198 TGTCTTGATTGAGTCTCATGCAAAC 60.049 40.000 2.68 11.32 0.00 2.93
3628 3744 5.065235 TGTCTTGATTGAGTCTCATGCAAA 58.935 37.500 2.68 0.00 0.00 3.68
3629 3745 4.644498 TGTCTTGATTGAGTCTCATGCAA 58.356 39.130 2.68 9.97 0.00 4.08
3630 3746 4.276058 TGTCTTGATTGAGTCTCATGCA 57.724 40.909 2.68 2.31 0.00 3.96
3631 3747 4.934001 TCTTGTCTTGATTGAGTCTCATGC 59.066 41.667 2.68 0.00 0.00 4.06
3632 3748 6.426025 TGTTCTTGTCTTGATTGAGTCTCATG 59.574 38.462 2.68 0.00 0.00 3.07
3633 3749 6.528321 TGTTCTTGTCTTGATTGAGTCTCAT 58.472 36.000 2.68 0.00 0.00 2.90
3634 3750 5.917462 TGTTCTTGTCTTGATTGAGTCTCA 58.083 37.500 0.00 0.00 0.00 3.27
3635 3751 6.851222 TTGTTCTTGTCTTGATTGAGTCTC 57.149 37.500 0.00 0.00 0.00 3.36
3636 3752 7.630242 TTTTGTTCTTGTCTTGATTGAGTCT 57.370 32.000 0.00 0.00 0.00 3.24
3637 3753 9.604626 CTATTTTGTTCTTGTCTTGATTGAGTC 57.395 33.333 0.00 0.00 0.00 3.36
3638 3754 8.078596 GCTATTTTGTTCTTGTCTTGATTGAGT 58.921 33.333 0.00 0.00 0.00 3.41
3639 3755 8.077991 TGCTATTTTGTTCTTGTCTTGATTGAG 58.922 33.333 0.00 0.00 0.00 3.02
3640 3756 7.939782 TGCTATTTTGTTCTTGTCTTGATTGA 58.060 30.769 0.00 0.00 0.00 2.57
3641 3757 7.864379 ACTGCTATTTTGTTCTTGTCTTGATTG 59.136 33.333 0.00 0.00 0.00 2.67
3642 3758 7.945134 ACTGCTATTTTGTTCTTGTCTTGATT 58.055 30.769 0.00 0.00 0.00 2.57
3643 3759 7.516198 ACTGCTATTTTGTTCTTGTCTTGAT 57.484 32.000 0.00 0.00 0.00 2.57
3644 3760 6.942532 ACTGCTATTTTGTTCTTGTCTTGA 57.057 33.333 0.00 0.00 0.00 3.02
3645 3761 7.800380 CAGTACTGCTATTTTGTTCTTGTCTTG 59.200 37.037 10.54 0.00 0.00 3.02
3646 3762 7.715249 TCAGTACTGCTATTTTGTTCTTGTCTT 59.285 33.333 18.45 0.00 0.00 3.01
3647 3763 7.217200 TCAGTACTGCTATTTTGTTCTTGTCT 58.783 34.615 18.45 0.00 0.00 3.41
3648 3764 7.421530 TCAGTACTGCTATTTTGTTCTTGTC 57.578 36.000 18.45 0.00 0.00 3.18
3649 3765 7.986085 ATCAGTACTGCTATTTTGTTCTTGT 57.014 32.000 18.45 0.00 0.00 3.16
3652 3768 9.502091 TGTTTATCAGTACTGCTATTTTGTTCT 57.498 29.630 18.45 0.00 0.00 3.01
3653 3769 9.543018 GTGTTTATCAGTACTGCTATTTTGTTC 57.457 33.333 18.45 2.03 0.00 3.18
3654 3770 8.512138 GGTGTTTATCAGTACTGCTATTTTGTT 58.488 33.333 18.45 0.00 0.00 2.83
3655 3771 7.663905 TGGTGTTTATCAGTACTGCTATTTTGT 59.336 33.333 18.45 0.00 0.00 2.83
3656 3772 8.039603 TGGTGTTTATCAGTACTGCTATTTTG 57.960 34.615 18.45 0.00 0.00 2.44
3657 3773 8.677300 CATGGTGTTTATCAGTACTGCTATTTT 58.323 33.333 18.45 1.43 0.00 1.82
3658 3774 7.201732 GCATGGTGTTTATCAGTACTGCTATTT 60.202 37.037 18.45 3.10 0.00 1.40
3659 3775 6.260936 GCATGGTGTTTATCAGTACTGCTATT 59.739 38.462 18.45 5.47 0.00 1.73
3660 3776 5.760253 GCATGGTGTTTATCAGTACTGCTAT 59.240 40.000 18.45 9.94 0.00 2.97
3661 3777 5.116180 GCATGGTGTTTATCAGTACTGCTA 58.884 41.667 18.45 10.26 0.00 3.49
3684 3800 0.734889 GATGCCATTGTCTTCCGGTG 59.265 55.000 0.00 0.00 0.00 4.94
3687 3803 3.459232 TCTAGATGCCATTGTCTTCCG 57.541 47.619 0.00 0.00 0.00 4.30
3691 3807 5.324409 TGGTTTTTCTAGATGCCATTGTCT 58.676 37.500 0.00 0.00 0.00 3.41
3704 3820 3.745799 TGTGAGGCGAATGGTTTTTCTA 58.254 40.909 0.00 0.00 0.00 2.10
3728 3844 1.006102 GTACGTCCTGCACTGCACT 60.006 57.895 0.00 0.00 33.79 4.40
3743 3859 2.876550 GTTGGGGAATAATCGCAGGTAC 59.123 50.000 0.00 0.00 40.13 3.34
3753 3869 3.096092 GTTGGAGCATGTTGGGGAATAA 58.904 45.455 0.00 0.00 0.00 1.40
3755 3871 1.560505 GTTGGAGCATGTTGGGGAAT 58.439 50.000 0.00 0.00 0.00 3.01
3770 3886 2.053627 GCAAAAGATGTTGAGCGTTGG 58.946 47.619 0.00 0.00 0.00 3.77
3773 3889 2.221169 TCAGCAAAAGATGTTGAGCGT 58.779 42.857 0.00 0.00 43.36 5.07
3782 3898 6.825213 TGCATGTCTTATACTCAGCAAAAGAT 59.175 34.615 0.00 0.00 30.63 2.40
3784 3900 6.426980 TGCATGTCTTATACTCAGCAAAAG 57.573 37.500 0.00 0.00 30.63 2.27
3785 3901 6.430925 AGTTGCATGTCTTATACTCAGCAAAA 59.569 34.615 0.00 0.00 39.59 2.44
3859 3975 0.875908 TCGTGTGTGAAGCAGTGCTC 60.876 55.000 20.03 12.48 38.25 4.26
3860 3976 1.143838 TCGTGTGTGAAGCAGTGCT 59.856 52.632 13.14 13.14 42.56 4.40
3861 3977 1.276844 GTCGTGTGTGAAGCAGTGC 59.723 57.895 7.13 7.13 0.00 4.40
3862 3978 0.301687 GTGTCGTGTGTGAAGCAGTG 59.698 55.000 0.00 0.00 0.00 3.66
3863 3979 0.175760 AGTGTCGTGTGTGAAGCAGT 59.824 50.000 0.00 0.00 0.00 4.40
3864 3980 1.290203 AAGTGTCGTGTGTGAAGCAG 58.710 50.000 0.00 0.00 0.00 4.24
3865 3981 1.663643 GAAAGTGTCGTGTGTGAAGCA 59.336 47.619 0.00 0.00 0.00 3.91
3866 3982 1.003866 GGAAAGTGTCGTGTGTGAAGC 60.004 52.381 0.00 0.00 0.00 3.86
3867 3983 2.030457 GTGGAAAGTGTCGTGTGTGAAG 59.970 50.000 0.00 0.00 0.00 3.02
3868 3984 2.004017 GTGGAAAGTGTCGTGTGTGAA 58.996 47.619 0.00 0.00 0.00 3.18
3869 3985 1.066787 TGTGGAAAGTGTCGTGTGTGA 60.067 47.619 0.00 0.00 0.00 3.58
3870 3986 1.062002 GTGTGGAAAGTGTCGTGTGTG 59.938 52.381 0.00 0.00 0.00 3.82
3871 3987 1.365699 GTGTGGAAAGTGTCGTGTGT 58.634 50.000 0.00 0.00 0.00 3.72
3872 3988 0.300491 CGTGTGGAAAGTGTCGTGTG 59.700 55.000 0.00 0.00 0.00 3.82
3873 3989 0.173935 TCGTGTGGAAAGTGTCGTGT 59.826 50.000 0.00 0.00 0.00 4.49
3874 3990 1.282817 TTCGTGTGGAAAGTGTCGTG 58.717 50.000 0.00 0.00 0.00 4.35
3875 3991 2.012937 TTTCGTGTGGAAAGTGTCGT 57.987 45.000 0.00 0.00 39.67 4.34
3883 3999 3.243468 TGTCGTCTGTATTTCGTGTGGAA 60.243 43.478 0.00 0.00 0.00 3.53
3884 4000 2.293955 TGTCGTCTGTATTTCGTGTGGA 59.706 45.455 0.00 0.00 0.00 4.02
3885 4001 2.668250 TGTCGTCTGTATTTCGTGTGG 58.332 47.619 0.00 0.00 0.00 4.17
3886 4002 3.673338 ACATGTCGTCTGTATTTCGTGTG 59.327 43.478 0.00 0.00 0.00 3.82
3887 4003 3.909430 ACATGTCGTCTGTATTTCGTGT 58.091 40.909 0.00 0.00 0.00 4.49
3888 4004 3.917985 TGACATGTCGTCTGTATTTCGTG 59.082 43.478 20.54 0.00 45.60 4.35
3889 4005 4.168922 TGACATGTCGTCTGTATTTCGT 57.831 40.909 20.54 0.00 45.60 3.85
3890 4006 5.509605 TTTGACATGTCGTCTGTATTTCG 57.490 39.130 20.54 0.00 45.60 3.46
3891 4007 6.456988 GGGATTTGACATGTCGTCTGTATTTC 60.457 42.308 20.54 7.18 45.60 2.17
3892 4008 5.354234 GGGATTTGACATGTCGTCTGTATTT 59.646 40.000 20.54 0.00 45.60 1.40
3893 4009 4.876107 GGGATTTGACATGTCGTCTGTATT 59.124 41.667 20.54 0.05 45.60 1.89
3894 4010 4.081142 TGGGATTTGACATGTCGTCTGTAT 60.081 41.667 20.54 7.46 45.60 2.29
3895 4011 3.259625 TGGGATTTGACATGTCGTCTGTA 59.740 43.478 20.54 0.00 45.60 2.74
3896 4012 2.038426 TGGGATTTGACATGTCGTCTGT 59.962 45.455 20.54 5.18 45.60 3.41
3897 4013 2.698803 TGGGATTTGACATGTCGTCTG 58.301 47.619 20.54 0.00 45.60 3.51
3898 4014 3.535561 GATGGGATTTGACATGTCGTCT 58.464 45.455 20.54 7.41 45.60 4.18
3899 4015 2.614057 GGATGGGATTTGACATGTCGTC 59.386 50.000 20.54 16.83 45.61 4.20
3900 4016 2.026356 TGGATGGGATTTGACATGTCGT 60.026 45.455 20.54 9.43 0.00 4.34
3901 4017 2.642427 TGGATGGGATTTGACATGTCG 58.358 47.619 20.54 0.00 0.00 4.35
3902 4018 4.678840 GCTTTGGATGGGATTTGACATGTC 60.679 45.833 19.27 19.27 0.00 3.06
3903 4019 3.196254 GCTTTGGATGGGATTTGACATGT 59.804 43.478 0.00 0.00 0.00 3.21
3904 4020 3.431207 GGCTTTGGATGGGATTTGACATG 60.431 47.826 0.00 0.00 0.00 3.21
3905 4021 2.767960 GGCTTTGGATGGGATTTGACAT 59.232 45.455 0.00 0.00 0.00 3.06
3906 4022 2.178580 GGCTTTGGATGGGATTTGACA 58.821 47.619 0.00 0.00 0.00 3.58
3907 4023 2.178580 TGGCTTTGGATGGGATTTGAC 58.821 47.619 0.00 0.00 0.00 3.18
3908 4024 2.619697 TGGCTTTGGATGGGATTTGA 57.380 45.000 0.00 0.00 0.00 2.69
3909 4025 2.093341 CCTTGGCTTTGGATGGGATTTG 60.093 50.000 0.00 0.00 0.00 2.32
3910 4026 2.190538 CCTTGGCTTTGGATGGGATTT 58.809 47.619 0.00 0.00 0.00 2.17
3911 4027 1.870064 CCTTGGCTTTGGATGGGATT 58.130 50.000 0.00 0.00 0.00 3.01
3912 4028 0.688749 GCCTTGGCTTTGGATGGGAT 60.689 55.000 4.11 0.00 0.00 3.85
3913 4029 1.305213 GCCTTGGCTTTGGATGGGA 60.305 57.895 4.11 0.00 0.00 4.37
3914 4030 0.033208 TAGCCTTGGCTTTGGATGGG 60.033 55.000 19.93 0.00 0.00 4.00
3915 4031 1.851304 TTAGCCTTGGCTTTGGATGG 58.149 50.000 19.93 0.00 0.00 3.51
3916 4032 2.562298 TGTTTAGCCTTGGCTTTGGATG 59.438 45.455 19.93 0.00 0.00 3.51
3917 4033 2.827921 CTGTTTAGCCTTGGCTTTGGAT 59.172 45.455 19.93 0.00 0.00 3.41
3918 4034 2.238521 CTGTTTAGCCTTGGCTTTGGA 58.761 47.619 19.93 0.00 0.00 3.53
3919 4035 1.337167 GCTGTTTAGCCTTGGCTTTGG 60.337 52.381 19.93 7.31 44.33 3.28
3920 4036 2.070262 GCTGTTTAGCCTTGGCTTTG 57.930 50.000 19.93 7.00 44.33 2.77
3931 4047 1.197721 CAACCGGCTGAAGCTGTTTAG 59.802 52.381 0.00 0.00 45.66 1.85
3932 4048 1.234821 CAACCGGCTGAAGCTGTTTA 58.765 50.000 0.00 0.00 45.66 2.01
3933 4049 1.455383 CCAACCGGCTGAAGCTGTTT 61.455 55.000 6.38 0.00 45.66 2.83
3934 4050 1.898574 CCAACCGGCTGAAGCTGTT 60.899 57.895 6.38 7.48 45.66 3.16
3935 4051 2.129555 ATCCAACCGGCTGAAGCTGT 62.130 55.000 6.38 1.78 45.66 4.40
3936 4052 0.962356 AATCCAACCGGCTGAAGCTG 60.962 55.000 6.38 4.03 46.63 4.24
3937 4053 0.962356 CAATCCAACCGGCTGAAGCT 60.962 55.000 6.38 0.00 41.70 3.74
3938 4054 1.508088 CAATCCAACCGGCTGAAGC 59.492 57.895 6.38 0.00 41.14 3.86
3939 4055 1.315257 CCCAATCCAACCGGCTGAAG 61.315 60.000 6.38 0.00 0.00 3.02
3940 4056 1.304052 CCCAATCCAACCGGCTGAA 60.304 57.895 6.38 0.00 0.00 3.02
3941 4057 2.354729 CCCAATCCAACCGGCTGA 59.645 61.111 6.38 0.00 0.00 4.26
3942 4058 3.451894 GCCCAATCCAACCGGCTG 61.452 66.667 0.00 0.00 38.41 4.85
3943 4059 3.301222 ATGCCCAATCCAACCGGCT 62.301 57.895 0.00 0.00 42.15 5.52
3944 4060 2.759560 ATGCCCAATCCAACCGGC 60.760 61.111 0.00 0.00 41.99 6.13
3945 4061 2.480610 CGATGCCCAATCCAACCGG 61.481 63.158 0.00 0.00 30.80 5.28
3946 4062 1.312371 AACGATGCCCAATCCAACCG 61.312 55.000 0.00 0.00 30.80 4.44
3947 4063 0.455815 GAACGATGCCCAATCCAACC 59.544 55.000 0.00 0.00 30.80 3.77
3948 4064 0.455815 GGAACGATGCCCAATCCAAC 59.544 55.000 0.00 0.00 30.80 3.77
3949 4065 0.038890 TGGAACGATGCCCAATCCAA 59.961 50.000 0.00 0.00 37.24 3.53
3950 4066 0.394216 CTGGAACGATGCCCAATCCA 60.394 55.000 0.00 0.00 37.83 3.41
3951 4067 0.394352 ACTGGAACGATGCCCAATCC 60.394 55.000 0.00 0.00 31.11 3.01
3952 4068 2.325583 TACTGGAACGATGCCCAATC 57.674 50.000 0.00 0.00 31.11 2.67
3953 4069 2.806745 CGATACTGGAACGATGCCCAAT 60.807 50.000 0.00 0.00 31.11 3.16
3954 4070 1.472552 CGATACTGGAACGATGCCCAA 60.473 52.381 0.00 0.00 31.11 4.12
3955 4071 0.104120 CGATACTGGAACGATGCCCA 59.896 55.000 0.00 0.00 0.00 5.36
3956 4072 0.104304 ACGATACTGGAACGATGCCC 59.896 55.000 0.00 0.00 0.00 5.36
3957 4073 1.859080 GAACGATACTGGAACGATGCC 59.141 52.381 0.00 0.00 0.00 4.40
3958 4074 2.281762 GTGAACGATACTGGAACGATGC 59.718 50.000 0.00 0.00 0.00 3.91
3959 4075 2.858344 GGTGAACGATACTGGAACGATG 59.142 50.000 0.00 0.00 0.00 3.84
3960 4076 3.160777 GGTGAACGATACTGGAACGAT 57.839 47.619 0.00 0.00 0.00 3.73
3961 4077 2.642139 GGTGAACGATACTGGAACGA 57.358 50.000 0.00 0.00 0.00 3.85
3981 4097 3.318017 AGTACTTCACACACGATGCTTC 58.682 45.455 0.00 0.00 0.00 3.86
3982 4098 3.386768 AGTACTTCACACACGATGCTT 57.613 42.857 0.00 0.00 0.00 3.91
3983 4099 3.386768 AAGTACTTCACACACGATGCT 57.613 42.857 1.12 0.00 0.00 3.79
3984 4100 4.211389 CAAAAGTACTTCACACACGATGC 58.789 43.478 8.95 0.00 0.00 3.91
3985 4101 5.403897 ACAAAAGTACTTCACACACGATG 57.596 39.130 8.95 0.74 0.00 3.84
3986 4102 5.353123 ACAACAAAAGTACTTCACACACGAT 59.647 36.000 8.95 0.00 0.00 3.73
3987 4103 4.691685 ACAACAAAAGTACTTCACACACGA 59.308 37.500 8.95 0.00 0.00 4.35
3988 4104 4.965062 ACAACAAAAGTACTTCACACACG 58.035 39.130 8.95 0.00 0.00 4.49
3989 4105 8.905103 ATTTACAACAAAAGTACTTCACACAC 57.095 30.769 8.95 0.00 0.00 3.82
3990 4106 9.915629 AAATTTACAACAAAAGTACTTCACACA 57.084 25.926 8.95 0.00 0.00 3.72
4000 4116 9.921637 TGAACTGAAGAAATTTACAACAAAAGT 57.078 25.926 0.00 0.00 0.00 2.66
4005 4121 9.567848 GTTCTTGAACTGAAGAAATTTACAACA 57.432 29.630 6.28 0.00 42.27 3.33
4006 4122 9.567848 TGTTCTTGAACTGAAGAAATTTACAAC 57.432 29.630 13.65 0.00 42.27 3.32
4011 4127 9.874205 TTGATTGTTCTTGAACTGAAGAAATTT 57.126 25.926 13.65 0.00 42.27 1.82
4012 4128 9.305925 GTTGATTGTTCTTGAACTGAAGAAATT 57.694 29.630 13.65 0.00 42.27 1.82
4013 4129 8.469200 TGTTGATTGTTCTTGAACTGAAGAAAT 58.531 29.630 13.65 5.04 42.27 2.17
4014 4130 7.754924 GTGTTGATTGTTCTTGAACTGAAGAAA 59.245 33.333 13.65 0.77 42.27 2.52
4015 4131 7.250569 GTGTTGATTGTTCTTGAACTGAAGAA 58.749 34.615 13.65 0.00 39.20 2.52
4092 4208 4.625963 AGGGAGGTTAGTTGATCTAGCTT 58.374 43.478 0.00 0.00 31.83 3.74
4118 4234 0.320247 CAGCCCAGATGATAGTCCGC 60.320 60.000 0.00 0.00 0.00 5.54
4131 4247 0.821301 TCACGTTGATTTGCAGCCCA 60.821 50.000 0.00 0.00 0.00 5.36
4147 4263 3.127533 GGGTCATGGCGTGCTCAC 61.128 66.667 0.65 0.00 0.00 3.51
4155 4271 2.165030 CTCAATGTTCTTGGGTCATGGC 59.835 50.000 0.00 0.00 0.00 4.40
4170 4286 9.028185 CCTTCTTTTTCTTCTTCAAACTCAATG 57.972 33.333 0.00 0.00 0.00 2.82
4204 4320 5.585820 TGTGATGCTAGATTACGTGGTTA 57.414 39.130 0.00 0.00 0.00 2.85
4225 4341 2.126467 CCGTGCTGTGATTTTTGGTTG 58.874 47.619 0.00 0.00 0.00 3.77
4227 4343 0.673437 CCCGTGCTGTGATTTTTGGT 59.327 50.000 0.00 0.00 0.00 3.67
4298 4417 1.076995 GAATCGTGGGGAAAGGGGG 60.077 63.158 0.00 0.00 0.00 5.40
4303 4422 7.113437 TGTTTTATATCAGAATCGTGGGGAAA 58.887 34.615 0.00 0.00 0.00 3.13
4308 4427 8.233868 TGTTGTTGTTTTATATCAGAATCGTGG 58.766 33.333 0.00 0.00 0.00 4.94
4314 4433 9.126151 TGAAGGTGTTGTTGTTTTATATCAGAA 57.874 29.630 0.00 0.00 0.00 3.02
4329 4448 4.130118 GTCAATCAGTCTGAAGGTGTTGT 58.870 43.478 6.64 0.00 0.00 3.32
4330 4449 4.212847 CAGTCAATCAGTCTGAAGGTGTTG 59.787 45.833 6.64 6.71 35.73 3.33
4332 4451 3.389329 ACAGTCAATCAGTCTGAAGGTGT 59.611 43.478 6.64 7.47 36.94 4.16
4344 4463 5.680619 AGTTTAGACCACAACAGTCAATCA 58.319 37.500 0.00 0.00 36.68 2.57
4351 4470 6.458342 GGTTTTCAGAGTTTAGACCACAACAG 60.458 42.308 0.00 0.00 0.00 3.16
4363 4482 6.603201 TGAGTTGATTCAGGTTTTCAGAGTTT 59.397 34.615 0.00 0.00 0.00 2.66
4371 4490 4.341806 TGCACATGAGTTGATTCAGGTTTT 59.658 37.500 0.00 0.00 39.81 2.43
4405 4524 6.203338 GGATTTTGTGAACTTTCATGTTGCAT 59.797 34.615 0.00 0.00 39.73 3.96
4417 4536 9.101655 CTTTTTCAGAATTGGATTTTGTGAACT 57.898 29.630 0.00 0.00 36.46 3.01
4430 4549 6.016777 AGAGCACTACCACTTTTTCAGAATTG 60.017 38.462 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.