Multiple sequence alignment - TraesCS1D01G193800

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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 TraesCS1D01G193800 chr1D 100.000 6129 0 0 1 6129 269730983 269724855 0.000000e+00 11319.0
1 TraesCS1D01G193800 chr1A 90.681 6106 274 120 1 5951 333140177 333134212 0.000000e+00 7851.0
2 TraesCS1D01G193800 chr1B 93.812 3038 96 29 1 3011 342977818 342974846 0.000000e+00 4484.0
3 TraesCS1D01G193800 chr1B 90.721 2996 126 71 3010 5943 342974742 342971837 0.000000e+00 3853.0
4 TraesCS1D01G193800 chr4D 81.327 407 57 10 2489 2884 497897051 497896653 4.610000e-81 313.0
5 TraesCS1D01G193800 chr4D 86.607 112 10 4 4498 4605 93070612 93070722 1.080000e-22 119.0
6 TraesCS1D01G193800 chr4A 86.726 113 10 4 4497 4605 489433340 489433229 3.000000e-23 121.0
7 TraesCS1D01G193800 chr4B 85.714 112 11 4 4498 4605 130625845 130625955 5.020000e-21 113.0
8 TraesCS1D01G193800 chr3D 95.312 64 3 0 4495 4558 470487154 470487091 1.090000e-17 102.0
9 TraesCS1D01G193800 chr3D 87.805 82 10 0 2803 2884 470488886 470488805 5.060000e-16 97.1
10 TraesCS1D01G193800 chr3A 86.585 82 11 0 2803 2884 612526052 612525971 2.350000e-14 91.6
11 TraesCS1D01G193800 chr7B 83.333 84 14 0 2801 2884 494217915 494217998 1.830000e-10 78.7


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 TraesCS1D01G193800 chr1D 269724855 269730983 6128 True 11319.0 11319 100.0000 1 6129 1 chr1D.!!$R1 6128
1 TraesCS1D01G193800 chr1A 333134212 333140177 5965 True 7851.0 7851 90.6810 1 5951 1 chr1A.!!$R1 5950
2 TraesCS1D01G193800 chr1B 342971837 342977818 5981 True 4168.5 4484 92.2665 1 5943 2 chr1B.!!$R1 5942

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
819 851 0.106967 GTCTCCATCCCTTTGGCCTC 60.107 60.0 3.32 0.0 36.66 4.70 F
1122 1166 0.604780 AGCATCAGATGTATGGCGGC 60.605 55.0 12.18 0.0 0.00 6.53 F
2224 2315 0.096976 CATTTACTGCCTCCGTTGCG 59.903 55.0 0.00 0.0 0.00 4.85 F
2887 2986 0.606604 TTCCTGCACCCGTAAGAGAC 59.393 55.0 0.00 0.0 43.02 3.36 F
3974 4248 0.759346 GATCCAGGTACCCAAGCGAT 59.241 55.0 8.74 2.4 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2014 2078 0.253630 AAAGATAGGGGGAGTGGGCA 60.254 55.0 0.00 0.00 0.00 5.36 R
2474 2573 1.158484 CCTGCATGCCATCGAGTCAG 61.158 60.0 16.68 1.79 0.00 3.51 R
3944 4218 0.994247 ACCTGGATCAGAACATGCCA 59.006 50.0 0.00 0.00 32.44 4.92 R
4327 4605 0.858583 CGTGTCATGTCGAGTGCAAA 59.141 50.0 0.00 0.00 0.00 3.68 R
5314 5622 0.033796 AGCTACCAACCATGCATGCT 60.034 50.0 21.69 9.60 0.00 3.79 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
26 27 1.139455 ACGAGAAAACAACGGAGGGAA 59.861 47.619 0.00 0.00 0.00 3.97
27 28 1.798813 CGAGAAAACAACGGAGGGAAG 59.201 52.381 0.00 0.00 0.00 3.46
28 29 2.152016 GAGAAAACAACGGAGGGAAGG 58.848 52.381 0.00 0.00 0.00 3.46
56 57 4.543590 AAATACATAGCCCAGGAGATCG 57.456 45.455 0.00 0.00 0.00 3.69
57 58 2.971901 TACATAGCCCAGGAGATCGA 57.028 50.000 0.00 0.00 0.00 3.59
58 59 2.317371 ACATAGCCCAGGAGATCGAT 57.683 50.000 0.00 0.00 0.00 3.59
59 60 2.175202 ACATAGCCCAGGAGATCGATC 58.825 52.381 17.91 17.91 0.00 3.69
94 95 3.181445 ACACAAAATCCACCAGACTAGCA 60.181 43.478 0.00 0.00 0.00 3.49
100 101 1.419762 TCCACCAGACTAGCAAGCAAA 59.580 47.619 0.00 0.00 0.00 3.68
388 406 1.679153 ACCACCGCGTTTTTCATTTCT 59.321 42.857 4.92 0.00 0.00 2.52
502 525 0.108945 TCGACTCGACTCAGCTCGTA 60.109 55.000 0.00 0.00 35.10 3.43
531 554 2.923035 CCACCGTCCTCCCTGTGT 60.923 66.667 0.00 0.00 0.00 3.72
532 555 1.608336 CCACCGTCCTCCCTGTGTA 60.608 63.158 0.00 0.00 0.00 2.90
600 627 1.411041 GCTGGTAGTGGTAGGTAGGG 58.589 60.000 0.00 0.00 0.00 3.53
742 774 2.105128 CCATCGCACGTCTCCTCC 59.895 66.667 0.00 0.00 0.00 4.30
743 775 2.105128 CATCGCACGTCTCCTCCC 59.895 66.667 0.00 0.00 0.00 4.30
745 777 3.663815 ATCGCACGTCTCCTCCCCT 62.664 63.158 0.00 0.00 0.00 4.79
746 778 3.827898 CGCACGTCTCCTCCCCTC 61.828 72.222 0.00 0.00 0.00 4.30
747 779 3.462678 GCACGTCTCCTCCCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
748 780 2.760385 CACGTCTCCTCCCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
749 781 4.077180 ACGTCTCCTCCCCTCCCC 62.077 72.222 0.00 0.00 0.00 4.81
750 782 3.756783 CGTCTCCTCCCCTCCCCT 61.757 72.222 0.00 0.00 0.00 4.79
751 783 2.284151 GTCTCCTCCCCTCCCCTC 59.716 72.222 0.00 0.00 0.00 4.30
752 784 3.036959 TCTCCTCCCCTCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
814 846 1.026718 GGTGCGTCTCCATCCCTTTG 61.027 60.000 0.00 0.00 0.00 2.77
815 847 1.026718 GTGCGTCTCCATCCCTTTGG 61.027 60.000 0.00 0.00 38.18 3.28
816 848 2.115291 GCGTCTCCATCCCTTTGGC 61.115 63.158 0.00 0.00 36.66 4.52
817 849 1.452108 CGTCTCCATCCCTTTGGCC 60.452 63.158 0.00 0.00 36.66 5.36
818 850 1.915078 CGTCTCCATCCCTTTGGCCT 61.915 60.000 3.32 0.00 36.66 5.19
819 851 0.106967 GTCTCCATCCCTTTGGCCTC 60.107 60.000 3.32 0.00 36.66 4.70
820 852 1.153086 CTCCATCCCTTTGGCCTCG 60.153 63.158 3.32 0.00 36.66 4.63
1032 1076 1.653115 CAGCCTAGTAGGGTACGCG 59.347 63.158 20.36 3.53 45.88 6.01
1050 1094 2.578981 GACTACTTCGCGGCGACC 60.579 66.667 26.40 6.46 34.89 4.79
1122 1166 0.604780 AGCATCAGATGTATGGCGGC 60.605 55.000 12.18 0.00 0.00 6.53
1123 1167 1.904852 GCATCAGATGTATGGCGGCG 61.905 60.000 12.18 0.51 0.00 6.46
1124 1168 1.004560 ATCAGATGTATGGCGGCGG 60.005 57.895 9.78 0.00 0.00 6.13
1154 1198 2.746375 ATCATCACCACTCCGGGGC 61.746 63.158 0.00 0.00 38.54 5.80
1296 1340 2.338015 GCAGCATCACCACCACCAG 61.338 63.158 0.00 0.00 0.00 4.00
1386 1430 1.286880 GTTCATGCTGCACCACCAC 59.713 57.895 3.57 0.00 0.00 4.16
1704 1748 2.024176 TCGAAGAGGTTTGCATAGCC 57.976 50.000 2.56 0.00 0.00 3.93
1709 1761 4.380867 CGAAGAGGTTTGCATAGCCAATTT 60.381 41.667 2.56 0.00 0.00 1.82
1725 1777 4.380023 GCCAATTTACACGCTGATTAACCA 60.380 41.667 0.00 0.00 0.00 3.67
1732 1784 0.719465 CGCTGATTAACCACCACGTC 59.281 55.000 0.00 0.00 0.00 4.34
1747 1799 2.960170 GTCCTACACCGCTCACGT 59.040 61.111 0.00 0.00 37.70 4.49
1758 1810 3.121019 CTCACGTCGGATCCCTCC 58.879 66.667 6.06 0.00 38.29 4.30
2041 2110 3.797269 ACTCCCCCTATCTTTCTCTCTCT 59.203 47.826 0.00 0.00 0.00 3.10
2042 2111 4.141018 ACTCCCCCTATCTTTCTCTCTCTC 60.141 50.000 0.00 0.00 0.00 3.20
2043 2112 4.058731 TCCCCCTATCTTTCTCTCTCTCT 58.941 47.826 0.00 0.00 0.00 3.10
2044 2113 4.105697 TCCCCCTATCTTTCTCTCTCTCTC 59.894 50.000 0.00 0.00 0.00 3.20
2045 2114 4.407365 CCCCTATCTTTCTCTCTCTCTCC 58.593 52.174 0.00 0.00 0.00 3.71
2046 2115 4.141041 CCCCTATCTTTCTCTCTCTCTCCA 60.141 50.000 0.00 0.00 0.00 3.86
2047 2116 5.459536 CCCCTATCTTTCTCTCTCTCTCCAT 60.460 48.000 0.00 0.00 0.00 3.41
2048 2117 5.477984 CCCTATCTTTCTCTCTCTCTCCATG 59.522 48.000 0.00 0.00 0.00 3.66
2049 2118 6.306199 CCTATCTTTCTCTCTCTCTCCATGA 58.694 44.000 0.00 0.00 0.00 3.07
2050 2119 6.432162 CCTATCTTTCTCTCTCTCTCCATGAG 59.568 46.154 0.00 0.00 43.96 2.90
2052 2121 5.192927 TCTTTCTCTCTCTCTCCATGAGAC 58.807 45.833 0.00 0.00 46.03 3.36
2084 2158 0.818445 CCTCTGCATGCATGGACTCC 60.818 60.000 27.34 11.23 0.00 3.85
2144 2220 2.203523 TGCACTTGTGCAGGCCAT 60.204 55.556 22.47 0.00 40.23 4.40
2215 2306 2.778299 TCCACTCACACATTTACTGCC 58.222 47.619 0.00 0.00 0.00 4.85
2217 2308 2.744202 CCACTCACACATTTACTGCCTC 59.256 50.000 0.00 0.00 0.00 4.70
2224 2315 0.096976 CATTTACTGCCTCCGTTGCG 59.903 55.000 0.00 0.00 0.00 4.85
2250 2341 4.921515 TCTTATGTTACTGCACACTTCGAC 59.078 41.667 0.00 0.00 0.00 4.20
2378 2473 6.945218 AGCTAGTCAAGATCAAGAGTCAAAT 58.055 36.000 0.00 0.00 0.00 2.32
2429 2528 4.112634 CGATCAGAATTTCCTCGCAACTA 58.887 43.478 0.00 0.00 0.00 2.24
2437 2536 4.921470 TTTCCTCGCAACTATTTCTTCG 57.079 40.909 0.00 0.00 0.00 3.79
2439 2538 1.327764 CCTCGCAACTATTTCTTCGCC 59.672 52.381 0.00 0.00 0.00 5.54
2499 2598 2.043652 ATGGCATGCAGGTGGACC 60.044 61.111 21.36 0.00 0.00 4.46
2614 2713 2.577059 GTCGCGGACCATCTCCAA 59.423 61.111 6.13 0.00 39.39 3.53
2690 2789 3.787001 CTGGGGGAGAAGGACGCC 61.787 72.222 0.00 0.00 39.88 5.68
2716 2815 4.838152 CGTGCCCGGGATGACCAG 62.838 72.222 29.31 3.12 40.22 4.00
2887 2986 0.606604 TTCCTGCACCCGTAAGAGAC 59.393 55.000 0.00 0.00 43.02 3.36
2907 3006 6.380274 AGAGACGATCCTTCTTACATAAACCA 59.620 38.462 0.00 0.00 0.00 3.67
2959 3064 1.064463 TGTCTTTCCCTCCCATGCATC 60.064 52.381 0.00 0.00 0.00 3.91
2974 3079 2.431454 TGCATCTCGTGGCATGTTAAA 58.569 42.857 6.60 0.00 34.58 1.52
2983 3088 7.877003 TCTCGTGGCATGTTAAAAAGATTAAA 58.123 30.769 6.60 0.00 0.00 1.52
3044 3254 4.787598 ACGTGCATTGTCAGAAAGATTTC 58.212 39.130 0.00 0.00 37.45 2.17
3089 3299 9.695884 GAATTTAGTTGATCGCTTAGAAAGAAG 57.304 33.333 0.00 0.00 0.00 2.85
3133 3343 5.422331 AGCTAGCACATCCAAAGAAGTACTA 59.578 40.000 18.83 0.00 0.00 1.82
3288 3508 7.425595 GCTAACGAACTAAATCTACATGTTTGC 59.574 37.037 2.30 0.00 0.00 3.68
3395 3618 6.199531 GTGCCATATTTGTCTTGCATTACATG 59.800 38.462 2.79 0.00 0.00 3.21
3401 3628 4.747540 TGTCTTGCATTACATGTGTGAC 57.252 40.909 9.11 6.65 0.00 3.67
3439 3670 7.984617 AGCTGTTTTGGCTTGATTTAACTTTAA 59.015 29.630 0.00 0.00 36.56 1.52
3527 3766 1.421268 TGTCCCCATCTATGTGCCATC 59.579 52.381 0.00 0.00 0.00 3.51
3554 3793 9.733556 TTGCTTATGTTCACTCTCCTAATTTTA 57.266 29.630 0.00 0.00 0.00 1.52
3815 4069 5.983333 AAACAATCCCTACATCTCCATCT 57.017 39.130 0.00 0.00 0.00 2.90
3816 4070 7.789831 ACTAAACAATCCCTACATCTCCATCTA 59.210 37.037 0.00 0.00 0.00 1.98
3922 4196 3.130340 CGCAGGTTACCTTAAATTGGCAT 59.870 43.478 0.00 0.00 0.00 4.40
3923 4197 4.432712 GCAGGTTACCTTAAATTGGCATG 58.567 43.478 0.00 0.00 0.00 4.06
3924 4198 4.081697 GCAGGTTACCTTAAATTGGCATGT 60.082 41.667 0.00 0.00 0.00 3.21
3925 4199 5.568624 GCAGGTTACCTTAAATTGGCATGTT 60.569 40.000 0.00 0.00 0.00 2.71
3926 4200 6.099341 CAGGTTACCTTAAATTGGCATGTTC 58.901 40.000 0.00 0.00 0.00 3.18
3927 4201 6.016555 AGGTTACCTTAAATTGGCATGTTCT 58.983 36.000 0.00 0.00 0.00 3.01
3928 4202 7.122055 CAGGTTACCTTAAATTGGCATGTTCTA 59.878 37.037 0.00 0.00 0.00 2.10
3929 4203 7.672239 AGGTTACCTTAAATTGGCATGTTCTAA 59.328 33.333 0.00 0.00 0.00 2.10
3930 4204 7.758076 GGTTACCTTAAATTGGCATGTTCTAAC 59.242 37.037 0.00 0.00 0.00 2.34
3931 4205 5.949735 ACCTTAAATTGGCATGTTCTAACG 58.050 37.500 0.00 0.00 0.00 3.18
3932 4206 4.798387 CCTTAAATTGGCATGTTCTAACGC 59.202 41.667 0.00 0.00 0.00 4.84
3933 4207 5.393027 CCTTAAATTGGCATGTTCTAACGCT 60.393 40.000 0.00 0.00 0.00 5.07
3934 4208 3.764885 AATTGGCATGTTCTAACGCTC 57.235 42.857 0.00 0.00 0.00 5.03
3935 4209 2.177394 TTGGCATGTTCTAACGCTCA 57.823 45.000 0.00 0.00 0.00 4.26
3936 4210 2.177394 TGGCATGTTCTAACGCTCAA 57.823 45.000 0.00 0.00 0.00 3.02
3937 4211 2.499197 TGGCATGTTCTAACGCTCAAA 58.501 42.857 0.00 0.00 0.00 2.69
3938 4212 3.081061 TGGCATGTTCTAACGCTCAAAT 58.919 40.909 0.00 0.00 0.00 2.32
3939 4213 3.505680 TGGCATGTTCTAACGCTCAAATT 59.494 39.130 0.00 0.00 0.00 1.82
3940 4214 4.022416 TGGCATGTTCTAACGCTCAAATTT 60.022 37.500 0.00 0.00 0.00 1.82
3941 4215 4.923281 GGCATGTTCTAACGCTCAAATTTT 59.077 37.500 0.00 0.00 0.00 1.82
3942 4216 5.405269 GGCATGTTCTAACGCTCAAATTTTT 59.595 36.000 0.00 0.00 0.00 1.94
3968 4242 2.335681 TGTTCTGATCCAGGTACCCA 57.664 50.000 8.74 0.00 31.51 4.51
3974 4248 0.759346 GATCCAGGTACCCAAGCGAT 59.241 55.000 8.74 2.40 0.00 4.58
4048 4326 2.088104 ACTCACTCACTCCTCCACAA 57.912 50.000 0.00 0.00 0.00 3.33
4055 4333 2.746362 CTCACTCCTCCACAAAATCAGC 59.254 50.000 0.00 0.00 0.00 4.26
4094 4372 2.011947 TCGATGGATCAGCTGCAAAAG 58.988 47.619 9.47 0.00 0.00 2.27
4234 4512 3.047280 GTGTCGATTGGCCACGCA 61.047 61.111 3.88 6.86 0.00 5.24
4235 4513 2.046411 TGTCGATTGGCCACGCAT 60.046 55.556 3.88 0.00 0.00 4.73
4453 4744 2.616376 TCTAATTGTGTGTGTGGTGTGC 59.384 45.455 0.00 0.00 0.00 4.57
4656 4955 3.709633 GGCGAACCCTAACCCGGT 61.710 66.667 0.00 0.00 34.07 5.28
4897 5196 4.039357 CACCAGCAGCAGCAGCAC 62.039 66.667 12.92 0.00 45.49 4.40
4900 5199 3.738246 CAGCAGCAGCAGCACCAG 61.738 66.667 12.92 0.00 45.49 4.00
4903 5202 4.039357 CAGCAGCAGCACCAGCAC 62.039 66.667 3.17 0.00 45.49 4.40
4927 5226 3.698463 CACGGTGGCGTGAACGTC 61.698 66.667 0.00 0.00 45.40 4.34
5005 5304 0.610232 AGTTCCTGTTCATGGCTGGC 60.610 55.000 0.00 0.00 0.00 4.85
5116 5415 3.390521 TTCCACCTCCTGCGCGAT 61.391 61.111 12.10 0.00 0.00 4.58
5203 5510 0.744874 ACGTACGTCCAGGGATCATG 59.255 55.000 16.72 0.00 0.00 3.07
5408 5716 5.934043 TGTAGCGCGTAGATACCTCTATTTA 59.066 40.000 8.43 0.00 40.79 1.40
5533 5845 4.794439 CGGCCGTGTGATCGAGCA 62.794 66.667 19.50 0.00 0.00 4.26
5535 5847 2.125912 GCCGTGTGATCGAGCAGT 60.126 61.111 2.20 0.00 0.00 4.40
5562 5878 1.270907 CCAGAGGTGCTCTTACTGGT 58.729 55.000 0.00 0.00 38.99 4.00
5587 5903 0.179097 GTCCGGAACTCAGCAGGATC 60.179 60.000 5.23 0.00 33.15 3.36
5726 6046 1.135199 TCGTATCTTGGTCTTGGCGTC 60.135 52.381 0.00 0.00 0.00 5.19
5840 6161 2.239907 GGGGAAGAGAACTAGCCAACAT 59.760 50.000 0.00 0.00 0.00 2.71
5848 6169 8.443953 AAGAGAACTAGCCAACATATTTGATC 57.556 34.615 0.00 0.00 0.00 2.92
5907 6228 8.686418 TGAACGTTATTCATGAAAAATCAAACG 58.314 29.630 23.01 23.01 41.94 3.60
5912 6233 8.424731 GTTATTCATGAAAAATCAAACGTGTCC 58.575 33.333 13.09 0.00 0.00 4.02
5930 6252 6.158598 CGTGTCCAAATCAAAGATGGATTTT 58.841 36.000 0.00 0.00 44.55 1.82
5944 6266 9.903682 AAAGATGGATTTTATAATGATCTTGCG 57.096 29.630 0.00 0.00 33.69 4.85
5945 6267 8.627208 AGATGGATTTTATAATGATCTTGCGT 57.373 30.769 0.00 0.00 0.00 5.24
5946 6268 8.725148 AGATGGATTTTATAATGATCTTGCGTC 58.275 33.333 0.00 4.87 0.00 5.19
5947 6269 7.800155 TGGATTTTATAATGATCTTGCGTCA 57.200 32.000 0.00 0.00 0.00 4.35
5948 6270 8.394971 TGGATTTTATAATGATCTTGCGTCAT 57.605 30.769 0.00 0.00 37.91 3.06
5949 6271 8.506437 TGGATTTTATAATGATCTTGCGTCATC 58.494 33.333 0.00 0.00 35.35 2.92
5950 6272 7.689812 GGATTTTATAATGATCTTGCGTCATCG 59.310 37.037 0.00 0.00 35.35 3.84
5951 6273 6.466308 TTTATAATGATCTTGCGTCATCGG 57.534 37.500 0.00 0.00 35.35 4.18
5952 6274 2.602257 AATGATCTTGCGTCATCGGA 57.398 45.000 0.00 0.00 35.35 4.55
5953 6275 2.145958 ATGATCTTGCGTCATCGGAG 57.854 50.000 0.00 0.00 38.80 4.63
5954 6276 0.103026 TGATCTTGCGTCATCGGAGG 59.897 55.000 0.00 0.00 38.80 4.30
5955 6277 0.598680 GATCTTGCGTCATCGGAGGG 60.599 60.000 0.00 0.00 38.80 4.30
5956 6278 2.650813 ATCTTGCGTCATCGGAGGGC 62.651 60.000 0.00 0.00 38.80 5.19
5957 6279 4.467084 TTGCGTCATCGGAGGGCC 62.467 66.667 0.00 0.00 38.80 5.80
5960 6282 3.550431 CGTCATCGGAGGGCCCAT 61.550 66.667 27.56 9.36 34.14 4.00
5961 6283 2.427753 GTCATCGGAGGGCCCATC 59.572 66.667 27.56 18.23 34.14 3.51
5962 6284 3.233980 TCATCGGAGGGCCCATCG 61.234 66.667 27.56 26.07 34.14 3.84
5963 6285 3.233980 CATCGGAGGGCCCATCGA 61.234 66.667 31.90 31.90 36.07 3.59
5964 6286 2.445845 ATCGGAGGGCCCATCGAA 60.446 61.111 32.89 20.94 35.25 3.71
5965 6287 1.843376 ATCGGAGGGCCCATCGAAT 60.843 57.895 32.89 21.89 35.25 3.34
5966 6288 2.116983 ATCGGAGGGCCCATCGAATG 62.117 60.000 32.89 13.97 35.25 2.67
5974 6296 3.846180 CCATCGAATGGGCCTTGG 58.154 61.111 4.53 0.00 46.86 3.61
5975 6297 2.492773 CCATCGAATGGGCCTTGGC 61.493 63.158 4.53 2.49 46.86 4.52
5987 6309 4.424711 CTTGGCCCGCCCAGCTTA 62.425 66.667 0.00 0.00 46.39 3.09
5988 6310 3.721370 CTTGGCCCGCCCAGCTTAT 62.721 63.158 0.00 0.00 46.39 1.73
5989 6311 4.504596 TGGCCCGCCCAGCTTATG 62.505 66.667 0.00 0.00 39.18 1.90
5990 6312 4.189580 GGCCCGCCCAGCTTATGA 62.190 66.667 0.00 0.00 0.00 2.15
5991 6313 2.124320 GCCCGCCCAGCTTATGAA 60.124 61.111 0.00 0.00 0.00 2.57
5992 6314 1.752694 GCCCGCCCAGCTTATGAAA 60.753 57.895 0.00 0.00 0.00 2.69
5993 6315 1.109323 GCCCGCCCAGCTTATGAAAT 61.109 55.000 0.00 0.00 0.00 2.17
5994 6316 1.402787 CCCGCCCAGCTTATGAAATT 58.597 50.000 0.00 0.00 0.00 1.82
5995 6317 1.756538 CCCGCCCAGCTTATGAAATTT 59.243 47.619 0.00 0.00 0.00 1.82
5996 6318 2.168313 CCCGCCCAGCTTATGAAATTTT 59.832 45.455 0.00 0.00 0.00 1.82
5997 6319 3.189285 CCGCCCAGCTTATGAAATTTTG 58.811 45.455 0.00 0.00 0.00 2.44
5998 6320 3.368323 CCGCCCAGCTTATGAAATTTTGT 60.368 43.478 0.00 0.00 0.00 2.83
5999 6321 4.142271 CCGCCCAGCTTATGAAATTTTGTA 60.142 41.667 0.00 0.00 0.00 2.41
6000 6322 5.451798 CCGCCCAGCTTATGAAATTTTGTAT 60.452 40.000 0.00 0.00 0.00 2.29
6001 6323 6.238897 CCGCCCAGCTTATGAAATTTTGTATA 60.239 38.462 0.00 0.00 0.00 1.47
6002 6324 6.636850 CGCCCAGCTTATGAAATTTTGTATAC 59.363 38.462 0.00 0.00 0.00 1.47
6003 6325 6.923508 GCCCAGCTTATGAAATTTTGTATACC 59.076 38.462 0.00 0.00 0.00 2.73
6004 6326 7.417342 GCCCAGCTTATGAAATTTTGTATACCA 60.417 37.037 0.00 0.00 0.00 3.25
6005 6327 8.641541 CCCAGCTTATGAAATTTTGTATACCAT 58.358 33.333 0.00 0.00 0.00 3.55
6020 6342 7.776618 TGTATACCATACATCTACTCTTGGG 57.223 40.000 0.00 0.00 0.00 4.12
6021 6343 5.746990 ATACCATACATCTACTCTTGGGC 57.253 43.478 0.00 0.00 0.00 5.36
6022 6344 2.706190 ACCATACATCTACTCTTGGGCC 59.294 50.000 0.00 0.00 0.00 5.80
6023 6345 2.975489 CCATACATCTACTCTTGGGCCT 59.025 50.000 4.53 0.00 0.00 5.19
6024 6346 3.392616 CCATACATCTACTCTTGGGCCTT 59.607 47.826 4.53 0.00 0.00 4.35
6025 6347 4.384056 CATACATCTACTCTTGGGCCTTG 58.616 47.826 4.53 0.00 0.00 3.61
6026 6348 2.551270 ACATCTACTCTTGGGCCTTGA 58.449 47.619 4.53 1.62 0.00 3.02
6027 6349 2.912956 ACATCTACTCTTGGGCCTTGAA 59.087 45.455 4.53 0.00 0.00 2.69
6028 6350 3.330701 ACATCTACTCTTGGGCCTTGAAA 59.669 43.478 4.53 0.00 0.00 2.69
6029 6351 3.418684 TCTACTCTTGGGCCTTGAAAC 57.581 47.619 4.53 0.00 0.00 2.78
6030 6352 2.708861 TCTACTCTTGGGCCTTGAAACA 59.291 45.455 4.53 0.00 0.00 2.83
6031 6353 2.452600 ACTCTTGGGCCTTGAAACAA 57.547 45.000 4.53 0.00 0.00 2.83
6032 6354 2.031870 ACTCTTGGGCCTTGAAACAAC 58.968 47.619 4.53 0.00 0.00 3.32
6033 6355 2.031120 CTCTTGGGCCTTGAAACAACA 58.969 47.619 4.53 0.00 0.00 3.33
6034 6356 2.430332 CTCTTGGGCCTTGAAACAACAA 59.570 45.455 4.53 0.00 0.00 2.83
6035 6357 2.167487 TCTTGGGCCTTGAAACAACAAC 59.833 45.455 4.53 0.00 0.00 3.32
6036 6358 0.827368 TGGGCCTTGAAACAACAACC 59.173 50.000 4.53 0.00 0.00 3.77
6037 6359 0.105964 GGGCCTTGAAACAACAACCC 59.894 55.000 0.84 0.00 31.96 4.11
6038 6360 0.827368 GGCCTTGAAACAACAACCCA 59.173 50.000 0.00 0.00 0.00 4.51
6039 6361 1.472552 GGCCTTGAAACAACAACCCAC 60.473 52.381 0.00 0.00 0.00 4.61
6040 6362 1.205893 GCCTTGAAACAACAACCCACA 59.794 47.619 0.00 0.00 0.00 4.17
6041 6363 2.354203 GCCTTGAAACAACAACCCACAA 60.354 45.455 0.00 0.00 0.00 3.33
6042 6364 3.258228 CCTTGAAACAACAACCCACAAC 58.742 45.455 0.00 0.00 0.00 3.32
6043 6365 3.258228 CTTGAAACAACAACCCACAACC 58.742 45.455 0.00 0.00 0.00 3.77
6044 6366 2.530701 TGAAACAACAACCCACAACCT 58.469 42.857 0.00 0.00 0.00 3.50
6045 6367 3.698289 TGAAACAACAACCCACAACCTA 58.302 40.909 0.00 0.00 0.00 3.08
6046 6368 4.282496 TGAAACAACAACCCACAACCTAT 58.718 39.130 0.00 0.00 0.00 2.57
6047 6369 4.712337 TGAAACAACAACCCACAACCTATT 59.288 37.500 0.00 0.00 0.00 1.73
6048 6370 5.187967 TGAAACAACAACCCACAACCTATTT 59.812 36.000 0.00 0.00 0.00 1.40
6049 6371 4.664150 ACAACAACCCACAACCTATTTG 57.336 40.909 0.00 0.00 41.49 2.32
6050 6372 3.181470 ACAACAACCCACAACCTATTTGC 60.181 43.478 0.00 0.00 39.01 3.68
6051 6373 2.957474 ACAACCCACAACCTATTTGCT 58.043 42.857 0.00 0.00 39.01 3.91
6052 6374 3.304829 ACAACCCACAACCTATTTGCTT 58.695 40.909 0.00 0.00 39.01 3.91
6053 6375 3.320826 ACAACCCACAACCTATTTGCTTC 59.679 43.478 0.00 0.00 39.01 3.86
6054 6376 2.525368 ACCCACAACCTATTTGCTTCC 58.475 47.619 0.00 0.00 39.01 3.46
6055 6377 1.472480 CCCACAACCTATTTGCTTCCG 59.528 52.381 0.00 0.00 39.01 4.30
6056 6378 2.159382 CCACAACCTATTTGCTTCCGT 58.841 47.619 0.00 0.00 39.01 4.69
6057 6379 2.556622 CCACAACCTATTTGCTTCCGTT 59.443 45.455 0.00 0.00 39.01 4.44
6058 6380 3.005367 CCACAACCTATTTGCTTCCGTTT 59.995 43.478 0.00 0.00 39.01 3.60
6059 6381 4.226761 CACAACCTATTTGCTTCCGTTTC 58.773 43.478 0.00 0.00 39.01 2.78
6060 6382 3.058501 ACAACCTATTTGCTTCCGTTTCG 60.059 43.478 0.00 0.00 39.01 3.46
6061 6383 1.467342 ACCTATTTGCTTCCGTTTCGC 59.533 47.619 0.00 0.00 0.00 4.70
6062 6384 1.202143 CCTATTTGCTTCCGTTTCGCC 60.202 52.381 0.00 0.00 0.00 5.54
6063 6385 0.806241 TATTTGCTTCCGTTTCGCCC 59.194 50.000 0.00 0.00 0.00 6.13
6064 6386 0.893727 ATTTGCTTCCGTTTCGCCCT 60.894 50.000 0.00 0.00 0.00 5.19
6065 6387 1.104577 TTTGCTTCCGTTTCGCCCTT 61.105 50.000 0.00 0.00 0.00 3.95
6066 6388 1.512156 TTGCTTCCGTTTCGCCCTTC 61.512 55.000 0.00 0.00 0.00 3.46
6067 6389 1.964373 GCTTCCGTTTCGCCCTTCA 60.964 57.895 0.00 0.00 0.00 3.02
6068 6390 1.305930 GCTTCCGTTTCGCCCTTCAT 61.306 55.000 0.00 0.00 0.00 2.57
6069 6391 0.447801 CTTCCGTTTCGCCCTTCATG 59.552 55.000 0.00 0.00 0.00 3.07
6070 6392 1.582610 TTCCGTTTCGCCCTTCATGC 61.583 55.000 0.00 0.00 0.00 4.06
6071 6393 2.040544 CCGTTTCGCCCTTCATGCT 61.041 57.895 0.00 0.00 0.00 3.79
6072 6394 1.586154 CCGTTTCGCCCTTCATGCTT 61.586 55.000 0.00 0.00 0.00 3.91
6073 6395 0.240945 CGTTTCGCCCTTCATGCTTT 59.759 50.000 0.00 0.00 0.00 3.51
6074 6396 1.701704 GTTTCGCCCTTCATGCTTTG 58.298 50.000 0.00 0.00 0.00 2.77
6075 6397 1.000274 GTTTCGCCCTTCATGCTTTGT 60.000 47.619 0.00 0.00 0.00 2.83
6076 6398 2.192664 TTCGCCCTTCATGCTTTGTA 57.807 45.000 0.00 0.00 0.00 2.41
6077 6399 1.737838 TCGCCCTTCATGCTTTGTAG 58.262 50.000 0.00 0.00 0.00 2.74
6078 6400 0.734889 CGCCCTTCATGCTTTGTAGG 59.265 55.000 6.09 6.09 41.38 3.18
6079 6401 1.678728 CGCCCTTCATGCTTTGTAGGA 60.679 52.381 12.35 0.00 43.71 2.94
6080 6402 2.659428 GCCCTTCATGCTTTGTAGGAT 58.341 47.619 12.35 0.00 43.71 3.24
6081 6403 2.620585 GCCCTTCATGCTTTGTAGGATC 59.379 50.000 12.35 0.00 43.71 3.36
6082 6404 3.686691 GCCCTTCATGCTTTGTAGGATCT 60.687 47.826 12.35 0.00 43.71 2.75
6083 6405 4.530875 CCCTTCATGCTTTGTAGGATCTT 58.469 43.478 12.35 0.00 43.71 2.40
6084 6406 4.337555 CCCTTCATGCTTTGTAGGATCTTG 59.662 45.833 12.35 0.00 43.71 3.02
6085 6407 4.946157 CCTTCATGCTTTGTAGGATCTTGT 59.054 41.667 6.96 0.00 43.71 3.16
6086 6408 5.065731 CCTTCATGCTTTGTAGGATCTTGTC 59.934 44.000 6.96 0.00 43.71 3.18
6087 6409 5.426689 TCATGCTTTGTAGGATCTTGTCT 57.573 39.130 0.00 0.00 28.79 3.41
6088 6410 5.423015 TCATGCTTTGTAGGATCTTGTCTC 58.577 41.667 0.00 0.00 28.79 3.36
6089 6411 4.890158 TGCTTTGTAGGATCTTGTCTCA 57.110 40.909 0.00 0.00 0.00 3.27
6090 6412 5.227569 TGCTTTGTAGGATCTTGTCTCAA 57.772 39.130 0.00 0.00 0.00 3.02
6091 6413 5.620206 TGCTTTGTAGGATCTTGTCTCAAA 58.380 37.500 0.00 0.00 0.00 2.69
6092 6414 6.061441 TGCTTTGTAGGATCTTGTCTCAAAA 58.939 36.000 0.00 0.00 0.00 2.44
6093 6415 6.545666 TGCTTTGTAGGATCTTGTCTCAAAAA 59.454 34.615 0.00 0.00 0.00 1.94
6094 6416 7.231317 TGCTTTGTAGGATCTTGTCTCAAAAAT 59.769 33.333 0.00 0.00 0.00 1.82
6095 6417 8.084684 GCTTTGTAGGATCTTGTCTCAAAAATT 58.915 33.333 0.00 0.00 0.00 1.82
6096 6418 9.971922 CTTTGTAGGATCTTGTCTCAAAAATTT 57.028 29.630 0.00 0.00 0.00 1.82
6118 6440 4.336889 TTTTGTCTCTGTTGGATCTCGT 57.663 40.909 0.00 0.00 0.00 4.18
6119 6441 3.303881 TTGTCTCTGTTGGATCTCGTG 57.696 47.619 0.00 0.00 0.00 4.35
6120 6442 2.514803 TGTCTCTGTTGGATCTCGTGA 58.485 47.619 0.00 0.00 0.00 4.35
6121 6443 2.489722 TGTCTCTGTTGGATCTCGTGAG 59.510 50.000 0.00 0.00 0.00 3.51
6122 6444 2.750166 GTCTCTGTTGGATCTCGTGAGA 59.250 50.000 1.43 1.43 42.37 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.309806 CCTGGGCTATGTATTTTACTACCCT 59.690 44.000 0.00 0.00 35.76 4.34
27 28 5.308759 TCCTGGGCTATGTATTTTACTACCC 59.691 44.000 0.00 0.00 35.29 3.69
28 29 6.269307 TCTCCTGGGCTATGTATTTTACTACC 59.731 42.308 0.00 0.00 0.00 3.18
56 57 1.895798 TGTGTGTGTGAGAGGGAGATC 59.104 52.381 0.00 0.00 0.00 2.75
57 58 2.015456 TGTGTGTGTGAGAGGGAGAT 57.985 50.000 0.00 0.00 0.00 2.75
58 59 1.788229 TTGTGTGTGTGAGAGGGAGA 58.212 50.000 0.00 0.00 0.00 3.71
59 60 2.620251 TTTGTGTGTGTGAGAGGGAG 57.380 50.000 0.00 0.00 0.00 4.30
94 95 0.112412 ATCTCCCGGGTTGTTTGCTT 59.888 50.000 22.86 0.00 0.00 3.91
100 101 4.778143 GCGCATCTCCCGGGTTGT 62.778 66.667 22.86 4.19 0.00 3.32
287 301 2.876368 CTAGCTGCAAACCTCCGGGG 62.876 65.000 0.00 0.00 41.89 5.73
431 453 1.949257 CAAAAGTGTGACGGAGGCC 59.051 57.895 0.00 0.00 0.00 5.19
432 454 1.282875 GCAAAAGTGTGACGGAGGC 59.717 57.895 0.00 0.00 0.00 4.70
433 455 1.515521 GGGCAAAAGTGTGACGGAGG 61.516 60.000 0.00 0.00 0.00 4.30
434 456 1.515521 GGGGCAAAAGTGTGACGGAG 61.516 60.000 0.00 0.00 0.00 4.63
531 554 7.002276 TGCTATAGCTCCACTACAAGTACATA 58.998 38.462 24.61 0.00 42.66 2.29
532 555 5.833667 TGCTATAGCTCCACTACAAGTACAT 59.166 40.000 24.61 0.00 42.66 2.29
600 627 1.542547 CCGCCCATACCAATACCAGTC 60.543 57.143 0.00 0.00 0.00 3.51
746 778 3.596459 TTTCTGGGGAGGGGAGGGG 62.596 68.421 0.00 0.00 0.00 4.79
747 779 2.003548 CTTTCTGGGGAGGGGAGGG 61.004 68.421 0.00 0.00 0.00 4.30
748 780 0.327964 ATCTTTCTGGGGAGGGGAGG 60.328 60.000 0.00 0.00 0.00 4.30
749 781 2.496679 TATCTTTCTGGGGAGGGGAG 57.503 55.000 0.00 0.00 0.00 4.30
750 782 2.700225 CCATATCTTTCTGGGGAGGGGA 60.700 54.545 0.00 0.00 0.00 4.81
751 783 1.707427 CCATATCTTTCTGGGGAGGGG 59.293 57.143 0.00 0.00 0.00 4.79
752 784 1.074566 GCCATATCTTTCTGGGGAGGG 59.925 57.143 0.00 0.00 32.90 4.30
814 846 1.676529 GAAGGGAAATAAAGCGAGGCC 59.323 52.381 0.00 0.00 0.00 5.19
815 847 1.676529 GGAAGGGAAATAAAGCGAGGC 59.323 52.381 0.00 0.00 0.00 4.70
816 848 2.298610 GGGAAGGGAAATAAAGCGAGG 58.701 52.381 0.00 0.00 0.00 4.63
817 849 2.092375 AGGGGAAGGGAAATAAAGCGAG 60.092 50.000 0.00 0.00 0.00 5.03
818 850 1.920351 AGGGGAAGGGAAATAAAGCGA 59.080 47.619 0.00 0.00 0.00 4.93
819 851 2.298610 GAGGGGAAGGGAAATAAAGCG 58.701 52.381 0.00 0.00 0.00 4.68
820 852 2.667470 GGAGGGGAAGGGAAATAAAGC 58.333 52.381 0.00 0.00 0.00 3.51
1032 1076 2.578981 GTCGCCGCGAAGTAGTCC 60.579 66.667 18.71 0.00 37.72 3.85
1123 1167 1.102809 TGATGATGGTGCAATCCGCC 61.103 55.000 0.00 0.00 44.67 6.13
1124 1168 0.029834 GTGATGATGGTGCAATCCGC 59.970 55.000 0.00 0.00 42.89 5.54
1154 1198 4.402528 TGGCCCCGAACATGTCCG 62.403 66.667 0.00 0.00 0.00 4.79
1362 1406 1.859398 GTGCAGCATGAACGACGAA 59.141 52.632 0.00 0.00 32.99 3.85
1486 1530 4.379243 CGTCGGCAGCAGGAACCT 62.379 66.667 0.00 0.00 0.00 3.50
1704 1748 5.092781 GGTGGTTAATCAGCGTGTAAATTG 58.907 41.667 1.50 0.00 0.00 2.32
1709 1761 2.690786 GTGGTGGTTAATCAGCGTGTA 58.309 47.619 12.95 0.00 37.91 2.90
1725 1777 2.599578 AGCGGTGTAGGACGTGGT 60.600 61.111 0.00 0.00 0.00 4.16
1732 1784 2.202440 CGACGTGAGCGGTGTAGG 60.202 66.667 0.00 0.00 43.45 3.18
1758 1810 0.664466 CCCGTGATCGATGATCGGTG 60.664 60.000 15.48 14.21 41.51 4.94
1894 1946 3.925630 AATCGCCCCCACTGTGCTG 62.926 63.158 1.29 0.00 0.00 4.41
2014 2078 0.253630 AAAGATAGGGGGAGTGGGCA 60.254 55.000 0.00 0.00 0.00 5.36
2046 2115 4.107798 AGAGGGATAGAGTCATGGTCTCAT 59.892 45.833 16.72 10.33 34.73 2.90
2047 2116 3.465210 AGAGGGATAGAGTCATGGTCTCA 59.535 47.826 16.72 7.20 34.73 3.27
2048 2117 3.826157 CAGAGGGATAGAGTCATGGTCTC 59.174 52.174 9.67 9.67 0.00 3.36
2049 2118 3.843422 CAGAGGGATAGAGTCATGGTCT 58.157 50.000 0.00 0.00 0.00 3.85
2050 2119 2.298729 GCAGAGGGATAGAGTCATGGTC 59.701 54.545 0.00 0.00 0.00 4.02
2051 2120 2.324541 GCAGAGGGATAGAGTCATGGT 58.675 52.381 0.00 0.00 0.00 3.55
2052 2121 2.323599 TGCAGAGGGATAGAGTCATGG 58.676 52.381 0.00 0.00 0.00 3.66
2084 2158 1.271001 TGCAATGGTCTGTGAGACTGG 60.271 52.381 3.85 0.00 44.46 4.00
2183 2274 3.324846 GTGTGAGTGGATAGATGGCCATA 59.675 47.826 20.84 3.94 36.41 2.74
2215 2306 3.806316 AACATAAGAAACGCAACGGAG 57.194 42.857 0.00 0.00 0.00 4.63
2217 2308 4.391358 CAGTAACATAAGAAACGCAACGG 58.609 43.478 0.00 0.00 0.00 4.44
2224 2315 6.071463 CGAAGTGTGCAGTAACATAAGAAAC 58.929 40.000 0.00 0.00 31.49 2.78
2250 2341 5.602978 ACCTACCTATGAATTGGACTGTAGG 59.397 44.000 14.18 14.18 46.04 3.18
2378 2473 4.142359 GCTAGCTTCTCTAGTGCAACAGTA 60.142 45.833 7.70 0.00 45.22 2.74
2389 2484 3.195471 TCGCTGTAGCTAGCTTCTCTA 57.805 47.619 24.88 0.15 41.51 2.43
2426 2525 2.993899 CAAGTCACGGCGAAGAAATAGT 59.006 45.455 16.62 0.00 0.00 2.12
2429 2528 1.531149 CACAAGTCACGGCGAAGAAAT 59.469 47.619 16.62 0.54 0.00 2.17
2437 2536 1.508632 TTAAGCTCACAAGTCACGGC 58.491 50.000 0.00 0.00 0.00 5.68
2439 2538 4.950926 CTTCATTAAGCTCACAAGTCACG 58.049 43.478 0.00 0.00 0.00 4.35
2474 2573 1.158484 CCTGCATGCCATCGAGTCAG 61.158 60.000 16.68 1.79 0.00 3.51
2614 2713 3.288308 CTCACGCTCCGGAAGTGCT 62.288 63.158 26.26 7.36 39.21 4.40
2887 2986 5.701290 GGGATGGTTTATGTAAGAAGGATCG 59.299 44.000 0.00 0.00 0.00 3.69
2894 2993 6.317642 CACGAAATGGGATGGTTTATGTAAGA 59.682 38.462 0.00 0.00 0.00 2.10
2959 3064 8.586273 CATTTAATCTTTTTAACATGCCACGAG 58.414 33.333 0.00 0.00 0.00 4.18
2974 3079 7.121315 GGTGCTGTAGGAAGACATTTAATCTTT 59.879 37.037 0.00 0.00 36.53 2.52
2983 3088 1.267121 ACGGTGCTGTAGGAAGACAT 58.733 50.000 0.00 0.00 0.00 3.06
3044 3254 7.642071 AAATTCACCTGTTCAATTCGAATTG 57.358 32.000 34.80 34.80 45.49 2.32
3100 3310 7.775093 TCTTTGGATGTGCTAGCTGTTAATTAT 59.225 33.333 17.23 0.00 0.00 1.28
3133 3343 8.039603 TCATTTCGTGCAAACTAATCAATACT 57.960 30.769 0.00 0.00 0.00 2.12
3202 3422 6.620877 TGTCTATGGTACTTGTCCTTCATT 57.379 37.500 0.00 0.00 0.00 2.57
3203 3423 6.814954 ATGTCTATGGTACTTGTCCTTCAT 57.185 37.500 0.00 0.00 0.00 2.57
3204 3424 7.553334 GTTATGTCTATGGTACTTGTCCTTCA 58.447 38.462 0.00 0.00 0.00 3.02
3205 3425 6.696148 CGTTATGTCTATGGTACTTGTCCTTC 59.304 42.308 0.00 0.00 0.00 3.46
3206 3426 6.154021 ACGTTATGTCTATGGTACTTGTCCTT 59.846 38.462 0.00 0.00 0.00 3.36
3238 3458 2.284263 TCTGCAAGCAGATGACGTAG 57.716 50.000 20.00 0.00 46.80 3.51
3240 3460 2.354503 ATCTTCTGCAAGCAGATGACGT 60.355 45.455 30.63 19.44 45.27 4.34
3395 3618 6.300354 ACAGCTATTGTTTGTTAGTCACAC 57.700 37.500 0.00 0.00 36.31 3.82
3411 3638 7.232118 AGTTAAATCAAGCCAAAACAGCTAT 57.768 32.000 0.00 0.00 40.49 2.97
3527 3766 7.856145 AATTAGGAGAGTGAACATAAGCAAG 57.144 36.000 0.00 0.00 0.00 4.01
3554 3793 9.646522 AGGTGAATAATTAGGACAGCAAATTAT 57.353 29.630 15.49 0.00 37.38 1.28
3558 3804 8.736244 GTTTAGGTGAATAATTAGGACAGCAAA 58.264 33.333 15.49 12.02 0.00 3.68
3771 4025 4.625607 AGTACAAGGGCATATCTAAGGC 57.374 45.455 0.00 0.00 0.00 4.35
3834 4088 5.172934 CGGCAAACCTAACTTGTATGTAGA 58.827 41.667 0.00 0.00 0.00 2.59
3835 4089 4.933400 ACGGCAAACCTAACTTGTATGTAG 59.067 41.667 0.00 0.00 0.00 2.74
3838 4098 4.023536 ACAACGGCAAACCTAACTTGTATG 60.024 41.667 0.00 0.00 0.00 2.39
3940 4214 3.258872 CCTGGATCAGAACATGCCAAAAA 59.741 43.478 0.00 0.00 32.44 1.94
3941 4215 2.827322 CCTGGATCAGAACATGCCAAAA 59.173 45.455 0.00 0.00 32.44 2.44
3942 4216 2.225091 ACCTGGATCAGAACATGCCAAA 60.225 45.455 0.00 0.00 32.44 3.28
3943 4217 1.355381 ACCTGGATCAGAACATGCCAA 59.645 47.619 0.00 0.00 32.44 4.52
3944 4218 0.994247 ACCTGGATCAGAACATGCCA 59.006 50.000 0.00 0.00 32.44 4.92
3945 4219 2.565841 GTACCTGGATCAGAACATGCC 58.434 52.381 0.00 0.00 32.44 4.40
3946 4220 2.565841 GGTACCTGGATCAGAACATGC 58.434 52.381 4.06 0.00 32.44 4.06
3968 4242 2.401583 TGTGCTTATCCACATCGCTT 57.598 45.000 0.00 0.00 40.55 4.68
4026 4300 2.158519 TGTGGAGGAGTGAGTGAGTACA 60.159 50.000 0.00 0.00 0.00 2.90
4111 4389 8.038492 ACATTTTTCTTTTTGCAAGTGCTAAA 57.962 26.923 8.50 8.50 42.22 1.85
4112 4390 7.608308 ACATTTTTCTTTTTGCAAGTGCTAA 57.392 28.000 0.00 0.08 42.66 3.09
4113 4391 7.608308 AACATTTTTCTTTTTGCAAGTGCTA 57.392 28.000 0.00 0.00 42.66 3.49
4234 4512 9.875691 CGGCCAGCATTATGTGTATATATATAT 57.124 33.333 2.24 10.10 0.00 0.86
4235 4513 8.311109 CCGGCCAGCATTATGTGTATATATATA 58.689 37.037 2.24 0.00 0.00 0.86
4327 4605 0.858583 CGTGTCATGTCGAGTGCAAA 59.141 50.000 0.00 0.00 0.00 3.68
4425 4716 5.473504 ACCACACACACAATTAGATTCTTCC 59.526 40.000 0.00 0.00 0.00 3.46
4468 4759 6.870965 TGCGTTGCACAATTTAATATTTTCCT 59.129 30.769 0.00 0.00 31.71 3.36
4898 5197 4.935495 ACCGTGGTGCTGGTGCTG 62.935 66.667 0.00 0.00 37.02 4.41
5116 5415 3.572447 TACAGGTCACCCGGCGAGA 62.572 63.158 9.30 0.00 35.12 4.04
5131 5430 0.250424 TCCAGACTGACCGACGTACA 60.250 55.000 3.32 0.00 0.00 2.90
5314 5622 0.033796 AGCTACCAACCATGCATGCT 60.034 50.000 21.69 9.60 0.00 3.79
5408 5716 1.094785 CGACATCCCGCCAAGAATTT 58.905 50.000 0.00 0.00 0.00 1.82
5517 5829 2.887568 CTGCTCGATCACACGGCC 60.888 66.667 0.00 0.00 0.00 6.13
5533 5845 2.526873 ACCTCTGGCCGTTGGACT 60.527 61.111 13.63 0.00 0.00 3.85
5535 5847 4.329545 GCACCTCTGGCCGTTGGA 62.330 66.667 13.63 1.62 0.00 3.53
5562 5878 1.816863 GCTGAGTTCCGGACCTGTCA 61.817 60.000 6.11 5.15 0.00 3.58
5587 5903 2.880268 TCTGATACGTACCATGTACCCG 59.120 50.000 0.00 0.00 0.00 5.28
5726 6046 0.532862 CATCTCCCGATGGAAACCCG 60.533 60.000 0.00 0.00 42.66 5.28
5759 6079 2.778679 CTCGCCGTTGCAAGTAGC 59.221 61.111 0.00 1.85 45.96 3.58
5760 6080 2.778679 GCTCGCCGTTGCAAGTAG 59.221 61.111 0.00 0.00 37.32 2.57
5761 6081 3.109547 CGCTCGCCGTTGCAAGTA 61.110 61.111 0.00 0.00 37.32 2.24
5791 6111 0.182299 GGGAATCCCTCTTGCCTCAG 59.818 60.000 11.95 0.00 41.34 3.35
5840 6161 5.914898 TCACGAGGAGACAAGATCAAATA 57.085 39.130 0.00 0.00 0.00 1.40
5868 6189 8.155821 TGAATAACGTTCACATCTTTGGTTTA 57.844 30.769 2.82 0.00 0.00 2.01
5882 6203 8.687301 ACGTTTGATTTTTCATGAATAACGTTC 58.313 29.630 22.09 14.61 44.24 3.95
5886 6207 8.424731 GGACACGTTTGATTTTTCATGAATAAC 58.575 33.333 9.40 6.62 0.00 1.89
5930 6252 5.385509 TCCGATGACGCAAGATCATTATA 57.614 39.130 0.00 0.00 37.92 0.98
5934 6256 1.269988 CCTCCGATGACGCAAGATCAT 60.270 52.381 0.00 0.00 39.58 2.45
5937 6259 1.443407 CCCTCCGATGACGCAAGAT 59.557 57.895 0.00 0.00 43.62 2.40
5938 6260 2.892640 CCCTCCGATGACGCAAGA 59.107 61.111 0.00 0.00 43.62 3.02
5940 6262 4.467084 GGCCCTCCGATGACGCAA 62.467 66.667 0.00 0.00 38.29 4.85
5943 6265 3.521529 GATGGGCCCTCCGATGACG 62.522 68.421 25.70 0.00 38.76 4.35
5944 6266 2.427753 GATGGGCCCTCCGATGAC 59.572 66.667 25.70 1.42 38.76 3.06
5945 6267 3.233980 CGATGGGCCCTCCGATGA 61.234 66.667 25.70 0.00 38.76 2.92
5946 6268 2.116983 ATTCGATGGGCCCTCCGATG 62.117 60.000 30.02 13.48 38.76 3.84
5947 6269 1.843376 ATTCGATGGGCCCTCCGAT 60.843 57.895 30.02 20.32 38.76 4.18
5948 6270 2.445845 ATTCGATGGGCCCTCCGA 60.446 61.111 27.36 27.36 38.76 4.55
5949 6271 2.281070 CATTCGATGGGCCCTCCG 60.281 66.667 25.70 24.86 38.76 4.63
5950 6272 2.113986 CCATTCGATGGGCCCTCC 59.886 66.667 25.70 13.72 46.86 4.30
5958 6280 3.122850 GCCAAGGCCCATTCGATG 58.877 61.111 0.00 0.00 34.56 3.84
5970 6292 3.721370 ATAAGCTGGGCGGGCCAAG 62.721 63.158 24.45 18.02 40.15 3.61
5971 6293 3.738481 ATAAGCTGGGCGGGCCAA 61.738 61.111 24.45 10.03 37.98 4.52
5972 6294 4.504596 CATAAGCTGGGCGGGCCA 62.505 66.667 22.99 22.99 37.98 5.36
5973 6295 3.714487 TTCATAAGCTGGGCGGGCC 62.714 63.158 14.65 14.65 0.00 5.80
5974 6296 1.109323 ATTTCATAAGCTGGGCGGGC 61.109 55.000 0.00 0.00 0.00 6.13
5975 6297 1.402787 AATTTCATAAGCTGGGCGGG 58.597 50.000 0.00 0.00 0.00 6.13
5976 6298 3.189285 CAAAATTTCATAAGCTGGGCGG 58.811 45.455 0.00 0.00 0.00 6.13
5977 6299 3.848726 ACAAAATTTCATAAGCTGGGCG 58.151 40.909 0.00 0.00 0.00 6.13
5978 6300 6.923508 GGTATACAAAATTTCATAAGCTGGGC 59.076 38.462 5.01 0.00 0.00 5.36
5979 6301 8.006298 TGGTATACAAAATTTCATAAGCTGGG 57.994 34.615 5.01 0.00 0.00 4.45
5994 6316 8.647796 CCCAAGAGTAGATGTATGGTATACAAA 58.352 37.037 5.01 0.00 0.00 2.83
5995 6317 7.256190 GCCCAAGAGTAGATGTATGGTATACAA 60.256 40.741 5.01 0.00 0.00 2.41
5996 6318 6.210784 GCCCAAGAGTAGATGTATGGTATACA 59.789 42.308 5.01 4.33 0.00 2.29
5997 6319 6.351117 GGCCCAAGAGTAGATGTATGGTATAC 60.351 46.154 0.00 0.00 0.00 1.47
5998 6320 5.720041 GGCCCAAGAGTAGATGTATGGTATA 59.280 44.000 0.00 0.00 0.00 1.47
5999 6321 4.532521 GGCCCAAGAGTAGATGTATGGTAT 59.467 45.833 0.00 0.00 0.00 2.73
6000 6322 3.901844 GGCCCAAGAGTAGATGTATGGTA 59.098 47.826 0.00 0.00 0.00 3.25
6001 6323 2.706190 GGCCCAAGAGTAGATGTATGGT 59.294 50.000 0.00 0.00 0.00 3.55
6002 6324 2.975489 AGGCCCAAGAGTAGATGTATGG 59.025 50.000 0.00 0.00 0.00 2.74
6003 6325 4.101585 TCAAGGCCCAAGAGTAGATGTATG 59.898 45.833 0.00 0.00 0.00 2.39
6004 6326 4.298626 TCAAGGCCCAAGAGTAGATGTAT 58.701 43.478 0.00 0.00 0.00 2.29
6005 6327 3.719871 TCAAGGCCCAAGAGTAGATGTA 58.280 45.455 0.00 0.00 0.00 2.29
6006 6328 2.551270 TCAAGGCCCAAGAGTAGATGT 58.449 47.619 0.00 0.00 0.00 3.06
6007 6329 3.634397 TTCAAGGCCCAAGAGTAGATG 57.366 47.619 0.00 0.00 0.00 2.90
6008 6330 3.330701 TGTTTCAAGGCCCAAGAGTAGAT 59.669 43.478 0.00 0.00 0.00 1.98
6009 6331 2.708861 TGTTTCAAGGCCCAAGAGTAGA 59.291 45.455 0.00 0.00 0.00 2.59
6010 6332 3.140325 TGTTTCAAGGCCCAAGAGTAG 57.860 47.619 0.00 0.00 0.00 2.57
6011 6333 3.219281 GTTGTTTCAAGGCCCAAGAGTA 58.781 45.455 0.00 0.00 0.00 2.59
6012 6334 2.031870 GTTGTTTCAAGGCCCAAGAGT 58.968 47.619 0.00 0.00 0.00 3.24
6013 6335 2.031120 TGTTGTTTCAAGGCCCAAGAG 58.969 47.619 0.00 0.00 0.00 2.85
6014 6336 2.151502 TGTTGTTTCAAGGCCCAAGA 57.848 45.000 0.00 0.00 0.00 3.02
6015 6337 2.549926 GTTGTTGTTTCAAGGCCCAAG 58.450 47.619 0.00 0.00 0.00 3.61
6016 6338 1.208293 GGTTGTTGTTTCAAGGCCCAA 59.792 47.619 0.00 0.00 0.00 4.12
6017 6339 0.827368 GGTTGTTGTTTCAAGGCCCA 59.173 50.000 0.00 0.00 0.00 5.36
6018 6340 0.105964 GGGTTGTTGTTTCAAGGCCC 59.894 55.000 0.00 0.00 0.00 5.80
6019 6341 0.827368 TGGGTTGTTGTTTCAAGGCC 59.173 50.000 0.00 0.00 0.00 5.19
6020 6342 1.205893 TGTGGGTTGTTGTTTCAAGGC 59.794 47.619 0.00 0.00 0.00 4.35
6021 6343 3.258228 GTTGTGGGTTGTTGTTTCAAGG 58.742 45.455 0.00 0.00 0.00 3.61
6022 6344 3.056179 AGGTTGTGGGTTGTTGTTTCAAG 60.056 43.478 0.00 0.00 0.00 3.02
6023 6345 2.900546 AGGTTGTGGGTTGTTGTTTCAA 59.099 40.909 0.00 0.00 0.00 2.69
6024 6346 2.530701 AGGTTGTGGGTTGTTGTTTCA 58.469 42.857 0.00 0.00 0.00 2.69
6025 6347 4.929819 ATAGGTTGTGGGTTGTTGTTTC 57.070 40.909 0.00 0.00 0.00 2.78
6026 6348 5.423886 CAAATAGGTTGTGGGTTGTTGTTT 58.576 37.500 0.00 0.00 32.08 2.83
6027 6349 4.682050 GCAAATAGGTTGTGGGTTGTTGTT 60.682 41.667 0.00 0.00 39.63 2.83
6028 6350 3.181470 GCAAATAGGTTGTGGGTTGTTGT 60.181 43.478 0.00 0.00 39.63 3.32
6029 6351 3.069443 AGCAAATAGGTTGTGGGTTGTTG 59.931 43.478 0.00 0.00 39.63 3.33
6030 6352 3.304829 AGCAAATAGGTTGTGGGTTGTT 58.695 40.909 0.00 0.00 39.63 2.83
6031 6353 2.957474 AGCAAATAGGTTGTGGGTTGT 58.043 42.857 0.00 0.00 39.63 3.32
6032 6354 3.306019 GGAAGCAAATAGGTTGTGGGTTG 60.306 47.826 0.00 0.00 39.63 3.77
6033 6355 2.897326 GGAAGCAAATAGGTTGTGGGTT 59.103 45.455 0.00 0.00 39.63 4.11
6034 6356 2.525368 GGAAGCAAATAGGTTGTGGGT 58.475 47.619 0.00 0.00 39.63 4.51
6035 6357 1.472480 CGGAAGCAAATAGGTTGTGGG 59.528 52.381 0.00 0.00 39.63 4.61
6036 6358 2.159382 ACGGAAGCAAATAGGTTGTGG 58.841 47.619 0.00 0.00 39.63 4.17
6037 6359 3.915437 AACGGAAGCAAATAGGTTGTG 57.085 42.857 0.00 0.00 39.63 3.33
6038 6360 3.058501 CGAAACGGAAGCAAATAGGTTGT 60.059 43.478 0.00 0.00 39.63 3.32
6039 6361 3.488489 CGAAACGGAAGCAAATAGGTTG 58.512 45.455 0.00 0.00 38.24 3.77
6040 6362 2.095415 GCGAAACGGAAGCAAATAGGTT 60.095 45.455 0.00 0.00 41.46 3.50
6041 6363 1.467342 GCGAAACGGAAGCAAATAGGT 59.533 47.619 0.00 0.00 0.00 3.08
6042 6364 1.202143 GGCGAAACGGAAGCAAATAGG 60.202 52.381 0.00 0.00 0.00 2.57
6043 6365 1.202143 GGGCGAAACGGAAGCAAATAG 60.202 52.381 0.00 0.00 0.00 1.73
6044 6366 0.806241 GGGCGAAACGGAAGCAAATA 59.194 50.000 0.00 0.00 0.00 1.40
6045 6367 0.893727 AGGGCGAAACGGAAGCAAAT 60.894 50.000 0.00 0.00 0.00 2.32
6046 6368 1.104577 AAGGGCGAAACGGAAGCAAA 61.105 50.000 0.00 0.00 0.00 3.68
6047 6369 1.512156 GAAGGGCGAAACGGAAGCAA 61.512 55.000 0.00 0.00 0.00 3.91
6048 6370 1.964373 GAAGGGCGAAACGGAAGCA 60.964 57.895 0.00 0.00 0.00 3.91
6049 6371 1.305930 ATGAAGGGCGAAACGGAAGC 61.306 55.000 0.00 0.00 0.00 3.86
6050 6372 0.447801 CATGAAGGGCGAAACGGAAG 59.552 55.000 0.00 0.00 0.00 3.46
6051 6373 1.582610 GCATGAAGGGCGAAACGGAA 61.583 55.000 0.00 0.00 0.00 4.30
6052 6374 2.038269 GCATGAAGGGCGAAACGGA 61.038 57.895 0.00 0.00 0.00 4.69
6053 6375 1.586154 AAGCATGAAGGGCGAAACGG 61.586 55.000 0.00 0.00 36.08 4.44
6054 6376 0.240945 AAAGCATGAAGGGCGAAACG 59.759 50.000 0.00 0.00 36.08 3.60
6055 6377 1.000274 ACAAAGCATGAAGGGCGAAAC 60.000 47.619 0.00 0.00 36.08 2.78
6056 6378 1.327303 ACAAAGCATGAAGGGCGAAA 58.673 45.000 0.00 0.00 36.08 3.46
6057 6379 2.083774 CTACAAAGCATGAAGGGCGAA 58.916 47.619 0.00 0.00 36.08 4.70
6058 6380 1.678728 CCTACAAAGCATGAAGGGCGA 60.679 52.381 0.00 0.00 36.08 5.54
6059 6381 0.734889 CCTACAAAGCATGAAGGGCG 59.265 55.000 0.00 0.00 36.08 6.13
6060 6382 2.128771 TCCTACAAAGCATGAAGGGC 57.871 50.000 0.00 0.00 0.00 5.19
6061 6383 4.162040 AGATCCTACAAAGCATGAAGGG 57.838 45.455 0.00 0.00 0.00 3.95
6062 6384 4.946157 ACAAGATCCTACAAAGCATGAAGG 59.054 41.667 0.00 0.00 0.00 3.46
6063 6385 5.879223 AGACAAGATCCTACAAAGCATGAAG 59.121 40.000 0.00 0.00 0.00 3.02
6064 6386 5.809001 AGACAAGATCCTACAAAGCATGAA 58.191 37.500 0.00 0.00 0.00 2.57
6065 6387 5.046376 TGAGACAAGATCCTACAAAGCATGA 60.046 40.000 0.00 0.00 0.00 3.07
6066 6388 5.181009 TGAGACAAGATCCTACAAAGCATG 58.819 41.667 0.00 0.00 0.00 4.06
6067 6389 5.426689 TGAGACAAGATCCTACAAAGCAT 57.573 39.130 0.00 0.00 0.00 3.79
6068 6390 4.890158 TGAGACAAGATCCTACAAAGCA 57.110 40.909 0.00 0.00 0.00 3.91
6069 6391 6.560253 TTTTGAGACAAGATCCTACAAAGC 57.440 37.500 0.00 0.00 31.68 3.51
6070 6392 9.971922 AAATTTTTGAGACAAGATCCTACAAAG 57.028 29.630 0.00 0.00 31.68 2.77
6096 6418 4.511454 CACGAGATCCAACAGAGACAAAAA 59.489 41.667 0.00 0.00 0.00 1.94
6097 6419 4.058124 CACGAGATCCAACAGAGACAAAA 58.942 43.478 0.00 0.00 0.00 2.44
6098 6420 3.320826 TCACGAGATCCAACAGAGACAAA 59.679 43.478 0.00 0.00 0.00 2.83
6099 6421 2.890945 TCACGAGATCCAACAGAGACAA 59.109 45.455 0.00 0.00 0.00 3.18
6100 6422 2.489722 CTCACGAGATCCAACAGAGACA 59.510 50.000 0.00 0.00 0.00 3.41
6101 6423 2.750166 TCTCACGAGATCCAACAGAGAC 59.250 50.000 0.00 0.00 31.41 3.36
6102 6424 3.073274 TCTCACGAGATCCAACAGAGA 57.927 47.619 0.00 0.00 31.41 3.10
6103 6425 4.111198 CAATCTCACGAGATCCAACAGAG 58.889 47.826 9.92 0.00 46.75 3.35
6104 6426 3.763897 TCAATCTCACGAGATCCAACAGA 59.236 43.478 9.92 0.63 46.75 3.41
6105 6427 4.115401 TCAATCTCACGAGATCCAACAG 57.885 45.455 9.92 0.00 46.75 3.16
6106 6428 4.686972 GATCAATCTCACGAGATCCAACA 58.313 43.478 9.92 0.00 46.75 3.33


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

AutoCloner maintained by Alex Coulton.