Multiple sequence alignment - TraesCS1B01G202200

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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 TraesCS1B01G202200 chr1B 100.000 4197 0 0 3540 7736 363152042 363156238 0.000000e+00 7751.0
1 TraesCS1B01G202200 chr1B 100.000 3263 0 0 1 3263 363148503 363151765 0.000000e+00 6026.0
2 TraesCS1B01G202200 chr1B 98.969 97 0 1 3168 3263 245935489 245935393 1.030000e-38 172.0
3 TraesCS1B01G202200 chr1B 97.959 98 0 2 3161 3256 679654852 679654949 1.340000e-37 169.0
4 TraesCS1B01G202200 chr1B 100.000 31 0 0 3540 3570 611521414 611521384 3.020000e-04 58.4
5 TraesCS1B01G202200 chr1A 95.918 4189 99 27 3560 7736 321409746 321405618 0.000000e+00 6722.0
6 TraesCS1B01G202200 chr1A 93.937 2936 76 17 287 3166 321412631 321409742 0.000000e+00 4342.0
7 TraesCS1B01G202200 chr1A 91.096 146 13 0 113 258 321412773 321412628 1.700000e-46 198.0
8 TraesCS1B01G202200 chr1A 100.000 28 0 0 3540 3567 461203869 461203896 1.400000e-02 52.8
9 TraesCS1B01G202200 chr1D 96.358 3734 92 17 3560 7266 251312815 251309099 0.000000e+00 6102.0
10 TraesCS1B01G202200 chr1D 93.925 3111 93 25 113 3166 251315882 251312811 0.000000e+00 4610.0
11 TraesCS1B01G202200 chr1D 96.706 425 13 1 7313 7736 251309100 251308676 0.000000e+00 706.0
12 TraesCS1B01G202200 chrUn 97.975 395 7 1 1830 2223 479376455 479376849 0.000000e+00 684.0
13 TraesCS1B01G202200 chr6B 100.000 96 0 0 3168 3263 217172080 217172175 2.220000e-40 178.0
14 TraesCS1B01G202200 chr6B 98.947 95 0 1 3166 3260 359815018 359814925 1.340000e-37 169.0
15 TraesCS1B01G202200 chr2A 98.058 103 1 1 3161 3263 498099280 498099179 2.220000e-40 178.0
16 TraesCS1B01G202200 chr2A 100.000 29 0 0 3540 3568 498099147 498099119 4.000000e-03 54.7
17 TraesCS1B01G202200 chr2A 100.000 28 0 0 3540 3567 260536012 260536039 1.400000e-02 52.8
18 TraesCS1B01G202200 chr7A 98.969 97 0 1 3168 3263 539312392 539312488 1.030000e-38 172.0
19 TraesCS1B01G202200 chr7A 96.970 99 3 0 3165 3263 384425329 384425427 4.800000e-37 167.0
20 TraesCS1B01G202200 chr7A 100.000 31 0 0 3540 3570 539312540 539312570 3.020000e-04 58.4
21 TraesCS1B01G202200 chr4B 98.958 96 1 0 3168 3263 31525675 31525770 1.030000e-38 172.0
22 TraesCS1B01G202200 chr5B 98.925 93 1 0 3171 3263 124768697 124768789 4.800000e-37 167.0
23 TraesCS1B01G202200 chr5B 100.000 28 0 0 3540 3567 123212640 123212667 1.400000e-02 52.8
24 TraesCS1B01G202200 chr5B 100.000 28 0 0 3540 3567 123430159 123430186 1.400000e-02 52.8
25 TraesCS1B01G202200 chr7B 78.351 97 20 1 2744 2839 109921622 109921718 2.330000e-05 62.1
26 TraesCS1B01G202200 chr5A 100.000 29 0 0 3540 3568 344545909 344545881 4.000000e-03 54.7
27 TraesCS1B01G202200 chr2B 100.000 29 0 0 3540 3568 779110998 779111026 4.000000e-03 54.7


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 TraesCS1B01G202200 chr1B 363148503 363156238 7735 False 6888.5 7751 100.000000 1 7736 2 chr1B.!!$F2 7735
1 TraesCS1B01G202200 chr1A 321405618 321412773 7155 True 3754.0 6722 93.650333 113 7736 3 chr1A.!!$R1 7623
2 TraesCS1B01G202200 chr1D 251308676 251315882 7206 True 3806.0 6102 95.663000 113 7736 3 chr1D.!!$R1 7623

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
158 159 0.255890 GAGCCCAATAACTGCCTCCA 59.744 55.000 0.00 0.00 0.00 3.86 F
935 976 1.551452 CGGTGAAGAGGAAGAGAGGT 58.449 55.000 0.00 0.00 0.00 3.85 F
2323 2389 0.250234 ATCATGAGGGTGACACGTGG 59.750 55.000 21.57 1.66 0.00 4.94 F
2976 3044 0.295470 CGCTGCATGTTTTATTGCGC 59.705 50.000 0.00 0.00 41.80 6.09 F
3240 3308 0.040425 GCGCCTTACAAATATGCCCG 60.040 55.000 0.00 0.00 0.00 6.13 F
3242 3310 0.313987 GCCTTACAAATATGCCCGCC 59.686 55.000 0.00 0.00 0.00 6.13 F
4005 4097 1.401931 CCTTTGCAGTGCGGAAATCTG 60.402 52.381 11.20 0.00 34.08 2.90 F
4656 4754 0.896923 TTGGGCACATGAGAAATGGC 59.103 50.000 0.00 0.00 38.14 4.40 F
5766 5873 1.266718 CACACGACCATCAAAGGTTGG 59.733 52.381 5.44 0.00 45.69 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1184 0.784778 GTCGAAGCAACGAGTCCAAG 59.215 55.000 5.56 0.0 42.88 3.61 R
2325 2391 0.244994 AGTGTGACGATGACCTGAGC 59.755 55.000 0.00 0.0 0.00 4.26 R
3221 3289 0.040425 CGGGCATATTTGTAAGGCGC 60.040 55.000 0.00 0.0 0.00 6.53 R
3986 4078 1.973138 CAGATTTCCGCACTGCAAAG 58.027 50.000 1.11 0.0 0.00 2.77 R
4543 4641 2.082231 GGGTAAGCTTTCGGAACCTTC 58.918 52.381 3.20 0.0 0.00 3.46 R
4656 4754 2.166829 TGGGAAATTTGGGACACATCG 58.833 47.619 0.00 0.0 39.29 3.84 R
5766 5873 1.734465 GGCAGTATTGAGACACAGCAC 59.266 52.381 0.00 0.0 0.00 4.40 R
6632 6749 0.171455 GAAACACCAACACCAACGCA 59.829 50.000 0.00 0.0 0.00 5.24 R
7700 7820 1.015109 GAGTGACGACTAGCATCGGA 58.985 55.000 7.56 0.0 46.56 4.55 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
17 18 4.306245 TTGTTCCCCGTGGTCTCT 57.694 55.556 0.00 0.00 0.00 3.10
18 19 3.461214 TTGTTCCCCGTGGTCTCTA 57.539 52.632 0.00 0.00 0.00 2.43
19 20 1.946984 TTGTTCCCCGTGGTCTCTAT 58.053 50.000 0.00 0.00 0.00 1.98
20 21 1.946984 TGTTCCCCGTGGTCTCTATT 58.053 50.000 0.00 0.00 0.00 1.73
21 22 1.553248 TGTTCCCCGTGGTCTCTATTG 59.447 52.381 0.00 0.00 0.00 1.90
22 23 1.829222 GTTCCCCGTGGTCTCTATTGA 59.171 52.381 0.00 0.00 0.00 2.57
23 24 1.481871 TCCCCGTGGTCTCTATTGAC 58.518 55.000 0.00 0.00 36.31 3.18
32 33 1.338655 GTCTCTATTGACCTCGAGGGC 59.661 57.143 34.04 32.90 45.93 5.19
33 34 1.215673 TCTCTATTGACCTCGAGGGCT 59.784 52.381 36.53 21.22 45.91 5.19
34 35 1.611491 CTCTATTGACCTCGAGGGCTC 59.389 57.143 36.53 24.64 45.91 4.70
35 36 1.063942 TCTATTGACCTCGAGGGCTCA 60.064 52.381 36.53 26.89 45.91 4.26
36 37 1.339610 CTATTGACCTCGAGGGCTCAG 59.660 57.143 36.53 25.12 45.91 3.35
37 38 1.333636 ATTGACCTCGAGGGCTCAGG 61.334 60.000 36.53 11.12 45.91 3.86
38 39 2.043852 GACCTCGAGGGCTCAGGA 60.044 66.667 34.04 0.00 41.12 3.86
39 40 2.363147 ACCTCGAGGGCTCAGGAC 60.363 66.667 34.04 0.00 40.27 3.85
40 41 2.043450 CCTCGAGGGCTCAGGACT 60.043 66.667 24.62 0.00 32.96 3.85
41 42 2.124693 CCTCGAGGGCTCAGGACTC 61.125 68.421 24.62 0.00 32.96 3.36
42 43 1.379176 CTCGAGGGCTCAGGACTCA 60.379 63.158 3.91 0.00 0.00 3.41
43 44 1.379176 TCGAGGGCTCAGGACTCAG 60.379 63.158 0.00 0.00 0.00 3.35
44 45 2.422231 CGAGGGCTCAGGACTCAGG 61.422 68.421 0.00 0.00 0.00 3.86
45 46 1.305718 GAGGGCTCAGGACTCAGGT 60.306 63.158 0.00 0.00 0.00 4.00
46 47 1.305718 AGGGCTCAGGACTCAGGTC 60.306 63.158 0.00 0.00 41.43 3.85
47 48 1.610673 GGGCTCAGGACTCAGGTCA 60.611 63.158 0.00 0.00 43.77 4.02
48 49 1.194781 GGGCTCAGGACTCAGGTCAA 61.195 60.000 0.00 0.00 43.77 3.18
49 50 0.908198 GGCTCAGGACTCAGGTCAAT 59.092 55.000 0.00 0.00 43.77 2.57
50 51 1.134551 GGCTCAGGACTCAGGTCAATC 60.135 57.143 0.00 0.00 43.77 2.67
51 52 1.830477 GCTCAGGACTCAGGTCAATCT 59.170 52.381 0.00 0.00 43.77 2.40
52 53 2.418471 GCTCAGGACTCAGGTCAATCTG 60.418 54.545 0.00 0.00 43.77 2.90
53 54 3.095332 CTCAGGACTCAGGTCAATCTGA 58.905 50.000 0.00 0.00 43.77 3.27
54 55 3.705579 CTCAGGACTCAGGTCAATCTGAT 59.294 47.826 0.00 0.00 42.19 2.90
55 56 3.703556 TCAGGACTCAGGTCAATCTGATC 59.296 47.826 0.00 0.00 42.19 2.92
56 57 2.692557 AGGACTCAGGTCAATCTGATCG 59.307 50.000 0.00 0.00 42.19 3.69
57 58 2.223923 GGACTCAGGTCAATCTGATCGG 60.224 54.545 0.00 0.00 42.19 4.18
58 59 1.137872 ACTCAGGTCAATCTGATCGGC 59.862 52.381 0.00 0.00 42.19 5.54
59 60 1.137675 CTCAGGTCAATCTGATCGGCA 59.862 52.381 0.00 0.00 42.19 5.69
60 61 1.554617 TCAGGTCAATCTGATCGGCAA 59.445 47.619 0.00 0.00 38.70 4.52
61 62 1.667724 CAGGTCAATCTGATCGGCAAC 59.332 52.381 0.00 0.00 36.93 4.17
73 74 2.559330 GGCAACGGCAGGTAAACG 59.441 61.111 0.00 0.00 43.71 3.60
74 75 2.559330 GCAACGGCAGGTAAACGG 59.441 61.111 0.00 0.00 40.72 4.44
75 76 2.559330 CAACGGCAGGTAAACGGC 59.441 61.111 0.00 0.00 39.75 5.68
79 80 3.799755 GGCAGGTAAACGGCGCAG 61.800 66.667 10.83 8.25 41.53 5.18
80 81 3.799755 GCAGGTAAACGGCGCAGG 61.800 66.667 13.26 4.07 0.00 4.85
81 82 2.047655 CAGGTAAACGGCGCAGGA 60.048 61.111 13.26 0.00 0.00 3.86
82 83 2.100631 CAGGTAAACGGCGCAGGAG 61.101 63.158 13.26 0.86 0.00 3.69
83 84 2.263540 GGTAAACGGCGCAGGAGA 59.736 61.111 13.26 0.00 0.00 3.71
84 85 1.810030 GGTAAACGGCGCAGGAGAG 60.810 63.158 13.26 0.00 0.00 3.20
85 86 1.214589 GTAAACGGCGCAGGAGAGA 59.785 57.895 13.26 0.00 0.00 3.10
86 87 0.389426 GTAAACGGCGCAGGAGAGAA 60.389 55.000 13.26 0.00 0.00 2.87
87 88 0.319083 TAAACGGCGCAGGAGAGAAA 59.681 50.000 13.26 0.00 0.00 2.52
88 89 0.534203 AAACGGCGCAGGAGAGAAAA 60.534 50.000 13.26 0.00 0.00 2.29
89 90 1.228657 AACGGCGCAGGAGAGAAAAC 61.229 55.000 13.26 0.00 0.00 2.43
90 91 1.667830 CGGCGCAGGAGAGAAAACA 60.668 57.895 10.83 0.00 0.00 2.83
91 92 1.869690 GGCGCAGGAGAGAAAACAC 59.130 57.895 10.83 0.00 0.00 3.32
92 93 1.493311 GCGCAGGAGAGAAAACACG 59.507 57.895 0.30 0.00 0.00 4.49
93 94 0.944311 GCGCAGGAGAGAAAACACGA 60.944 55.000 0.30 0.00 0.00 4.35
94 95 0.784778 CGCAGGAGAGAAAACACGAC 59.215 55.000 0.00 0.00 0.00 4.34
95 96 0.784778 GCAGGAGAGAAAACACGACG 59.215 55.000 0.00 0.00 0.00 5.12
96 97 1.602165 GCAGGAGAGAAAACACGACGA 60.602 52.381 0.00 0.00 0.00 4.20
97 98 2.052157 CAGGAGAGAAAACACGACGAC 58.948 52.381 0.00 0.00 0.00 4.34
98 99 1.679680 AGGAGAGAAAACACGACGACA 59.320 47.619 0.00 0.00 0.00 4.35
99 100 2.100252 AGGAGAGAAAACACGACGACAA 59.900 45.455 0.00 0.00 0.00 3.18
100 101 2.218075 GGAGAGAAAACACGACGACAAC 59.782 50.000 0.00 0.00 0.00 3.32
101 102 1.850441 AGAGAAAACACGACGACAACG 59.150 47.619 0.00 0.00 45.75 4.10
102 103 0.925466 AGAAAACACGACGACAACGG 59.075 50.000 0.00 0.00 44.46 4.44
103 104 0.652465 GAAAACACGACGACAACGGC 60.652 55.000 0.00 0.00 45.02 5.68
104 105 2.039062 AAAACACGACGACAACGGCC 62.039 55.000 0.00 0.00 45.81 6.13
105 106 3.719883 AACACGACGACAACGGCCA 62.720 57.895 2.24 0.00 45.81 5.36
106 107 3.698463 CACGACGACAACGGCCAC 61.698 66.667 2.24 0.00 45.81 5.01
158 159 0.255890 GAGCCCAATAACTGCCTCCA 59.744 55.000 0.00 0.00 0.00 3.86
257 258 4.394712 CACCACGCCTCCCACCTC 62.395 72.222 0.00 0.00 0.00 3.85
900 941 1.900016 CAGCAGCAGCAGGAACCAA 60.900 57.895 3.17 0.00 45.49 3.67
935 976 1.551452 CGGTGAAGAGGAAGAGAGGT 58.449 55.000 0.00 0.00 0.00 3.85
1176 1237 4.666253 TTCTGTGGCTGCAGGGGC 62.666 66.667 17.12 3.90 37.12 5.80
1256 1317 2.030274 GTGGCAAGTGGAATTGTGGTAC 60.030 50.000 0.00 0.00 32.56 3.34
1311 1372 9.282247 GTATAATTACAATATCAATGCTGCAGC 57.718 33.333 31.89 31.89 42.50 5.25
1319 1380 2.922950 AATGCTGCAGCGTGTTGGG 61.923 57.895 33.04 0.00 45.83 4.12
1390 1451 8.641541 ACAAAAGCTCTATTGAAAGAAATTGGA 58.358 29.630 12.26 0.00 0.00 3.53
1416 1477 7.595819 ACATTTGAAAGAACCTGATTTACCA 57.404 32.000 0.00 0.00 0.00 3.25
1426 1487 3.084039 CCTGATTTACCAAAGAGCAGCA 58.916 45.455 0.00 0.00 0.00 4.41
1449 1510 5.796502 TTGATCTTCTTCCATACCCCTTT 57.203 39.130 0.00 0.00 0.00 3.11
1486 1547 0.541863 ATGTAGTCTTGCCTTCCCGG 59.458 55.000 0.00 0.00 0.00 5.73
1515 1576 3.720949 CATGAATGCCCGATCACATTT 57.279 42.857 6.96 0.00 36.65 2.32
1516 1577 4.049546 CATGAATGCCCGATCACATTTT 57.950 40.909 6.96 0.00 36.65 1.82
1569 1630 5.183331 AGACGTAGAGTTTGTAGAAGATGCA 59.817 40.000 0.00 0.00 0.00 3.96
1679 1740 3.605634 TGATGTGTACATGCCCTGTTAC 58.394 45.455 0.00 0.00 39.39 2.50
1688 1749 2.556286 GCCCTGTTACAAGGCTGTC 58.444 57.895 16.99 0.00 43.62 3.51
2010 2074 1.971167 GGCATGCGTCAAACAGGGA 60.971 57.895 12.44 0.00 0.00 4.20
2021 2085 4.209080 CGTCAAACAGGGAAAATTCTTTGC 59.791 41.667 0.00 0.00 32.40 3.68
2076 2140 7.503566 ACTTGCTATGCCACTATATTGTTGATT 59.496 33.333 0.00 0.00 0.00 2.57
2089 2153 9.166173 CTATATTGTTGATTGAGTCCAAAGACA 57.834 33.333 0.00 0.00 46.15 3.41
2117 2181 8.537016 AGATGCTACAAAGGTATTGTACTGTTA 58.463 33.333 0.00 0.00 34.11 2.41
2323 2389 0.250234 ATCATGAGGGTGACACGTGG 59.750 55.000 21.57 1.66 0.00 4.94
2325 2391 2.592993 ATGAGGGTGACACGTGGGG 61.593 63.158 21.57 0.00 0.00 4.96
2372 2438 7.552687 ACATTTTCCTAACTATGCATCTTCGAA 59.447 33.333 0.19 0.00 0.00 3.71
2373 2439 7.539712 TTTTCCTAACTATGCATCTTCGAAG 57.460 36.000 19.35 19.35 0.00 3.79
2536 2602 7.977293 AGAAAAATAACGTGGCACTAAAAAGTT 59.023 29.630 16.72 13.03 0.00 2.66
2572 2638 1.196354 GTCATGAGTCAGCAAGTGCAC 59.804 52.381 9.40 9.40 45.16 4.57
2607 2673 4.215399 TCGGTTTCTGTAAGGAAAATGCTG 59.785 41.667 0.00 0.00 29.40 4.41
2626 2692 2.276201 TGCTCCATTCCAACGAATACG 58.724 47.619 0.00 0.00 45.75 3.06
2633 2699 0.319083 TCCAACGAATACGGCACACT 59.681 50.000 0.00 0.00 44.46 3.55
2658 2724 4.890158 ATCCCAAAATTGAACTTGGACC 57.110 40.909 8.00 0.00 44.16 4.46
2861 2927 7.316544 AGGTAGTAATAAGTTTTGAATGCCG 57.683 36.000 0.00 0.00 0.00 5.69
2959 3027 3.881688 TGTACTAGGTCTCCTGATTACGC 59.118 47.826 0.00 0.00 34.61 4.42
2976 3044 0.295470 CGCTGCATGTTTTATTGCGC 59.705 50.000 0.00 0.00 41.80 6.09
3070 3138 3.007940 TCTGTGCATGCTAAGTTGGTAGT 59.992 43.478 20.33 0.00 0.00 2.73
3084 3152 4.576463 AGTTGGTAGTTTTTGCTGAGTCAG 59.424 41.667 16.21 16.21 34.12 3.51
3130 3198 2.566833 TAGCCACATGTGTCTTTGCT 57.433 45.000 23.84 23.84 0.00 3.91
3167 3235 9.474920 TTGCATTATAAAATTATGCTACAAGGC 57.525 29.630 10.60 2.13 43.80 4.35
3168 3236 8.637099 TGCATTATAAAATTATGCTACAAGGCA 58.363 29.630 10.60 4.16 43.80 4.75
3183 3251 3.389221 CAAGGCATTGTTTTTAAGGCGT 58.611 40.909 2.19 0.00 38.16 5.68
3184 3252 3.297830 AGGCATTGTTTTTAAGGCGTC 57.702 42.857 0.00 0.00 38.16 5.19
3185 3253 2.029380 AGGCATTGTTTTTAAGGCGTCC 60.029 45.455 0.00 0.00 38.16 4.79
3186 3254 2.333926 GCATTGTTTTTAAGGCGTCCC 58.666 47.619 0.00 0.00 0.00 4.46
3187 3255 2.591133 CATTGTTTTTAAGGCGTCCCG 58.409 47.619 0.00 0.00 35.76 5.14
3199 3267 4.699522 GTCCCGCCTTGGACGCTT 62.700 66.667 0.00 0.00 44.98 4.68
3200 3268 2.998480 TCCCGCCTTGGACGCTTA 60.998 61.111 0.00 0.00 42.00 3.09
3201 3269 2.511600 CCCGCCTTGGACGCTTAG 60.512 66.667 0.00 0.00 42.00 2.18
3202 3270 2.511600 CCGCCTTGGACGCTTAGG 60.512 66.667 0.00 0.00 42.00 2.69
3232 3300 2.034999 CCCCCAGCGCCTTACAAA 59.965 61.111 2.29 0.00 0.00 2.83
3233 3301 1.379843 CCCCCAGCGCCTTACAAAT 60.380 57.895 2.29 0.00 0.00 2.32
3234 3302 0.106918 CCCCCAGCGCCTTACAAATA 60.107 55.000 2.29 0.00 0.00 1.40
3235 3303 1.478654 CCCCCAGCGCCTTACAAATAT 60.479 52.381 2.29 0.00 0.00 1.28
3236 3304 1.608590 CCCCAGCGCCTTACAAATATG 59.391 52.381 2.29 0.00 0.00 1.78
3237 3305 1.001378 CCCAGCGCCTTACAAATATGC 60.001 52.381 2.29 0.00 0.00 3.14
3238 3306 1.001378 CCAGCGCCTTACAAATATGCC 60.001 52.381 2.29 0.00 0.00 4.40
3239 3307 1.001378 CAGCGCCTTACAAATATGCCC 60.001 52.381 2.29 0.00 0.00 5.36
3240 3308 0.040425 GCGCCTTACAAATATGCCCG 60.040 55.000 0.00 0.00 0.00 6.13
3241 3309 0.040425 CGCCTTACAAATATGCCCGC 60.040 55.000 0.00 0.00 0.00 6.13
3242 3310 0.313987 GCCTTACAAATATGCCCGCC 59.686 55.000 0.00 0.00 0.00 6.13
3243 3311 1.981256 CCTTACAAATATGCCCGCCT 58.019 50.000 0.00 0.00 0.00 5.52
3244 3312 2.306847 CCTTACAAATATGCCCGCCTT 58.693 47.619 0.00 0.00 0.00 4.35
3245 3313 3.482436 CCTTACAAATATGCCCGCCTTA 58.518 45.455 0.00 0.00 0.00 2.69
3246 3314 3.502211 CCTTACAAATATGCCCGCCTTAG 59.498 47.826 0.00 0.00 0.00 2.18
3247 3315 1.981256 ACAAATATGCCCGCCTTAGG 58.019 50.000 0.00 0.00 0.00 2.69
3556 3624 4.917474 GTCGCCTTACCGCCTTAA 57.083 55.556 0.00 0.00 0.00 1.85
3557 3625 3.142124 GTCGCCTTACCGCCTTAAA 57.858 52.632 0.00 0.00 0.00 1.52
3558 3626 1.441738 GTCGCCTTACCGCCTTAAAA 58.558 50.000 0.00 0.00 0.00 1.52
3559 3627 1.805943 GTCGCCTTACCGCCTTAAAAA 59.194 47.619 0.00 0.00 0.00 1.94
3560 3628 1.805943 TCGCCTTACCGCCTTAAAAAC 59.194 47.619 0.00 0.00 0.00 2.43
3561 3629 1.808343 CGCCTTACCGCCTTAAAAACT 59.192 47.619 0.00 0.00 0.00 2.66
3562 3630 3.002102 CGCCTTACCGCCTTAAAAACTA 58.998 45.455 0.00 0.00 0.00 2.24
3563 3631 3.624410 CGCCTTACCGCCTTAAAAACTAT 59.376 43.478 0.00 0.00 0.00 2.12
3564 3632 4.495184 CGCCTTACCGCCTTAAAAACTATG 60.495 45.833 0.00 0.00 0.00 2.23
3565 3633 4.201980 GCCTTACCGCCTTAAAAACTATGG 60.202 45.833 0.00 0.00 0.00 2.74
3629 3697 9.590451 CTTCAAAAGGCACAATACATAATGATT 57.410 29.630 0.00 0.00 0.00 2.57
3749 3817 7.809665 CATCGTCATATGATGGCTAAATTTGA 58.190 34.615 21.97 2.22 37.83 2.69
3759 3827 4.808558 TGGCTAAATTTGATTGTGCTCAC 58.191 39.130 0.00 0.00 0.00 3.51
3783 3851 8.559536 CACTCATTATCCGTTTTAGTATGCAAT 58.440 33.333 0.00 0.00 0.00 3.56
3802 3870 5.799681 CAATTTTGCTTGGACTGTTGTTT 57.200 34.783 0.00 0.00 0.00 2.83
3803 3871 5.561993 CAATTTTGCTTGGACTGTTGTTTG 58.438 37.500 0.00 0.00 0.00 2.93
3804 3872 3.951775 TTTGCTTGGACTGTTGTTTGT 57.048 38.095 0.00 0.00 0.00 2.83
3805 3873 5.392767 TTTTGCTTGGACTGTTGTTTGTA 57.607 34.783 0.00 0.00 0.00 2.41
3806 3874 5.392767 TTTGCTTGGACTGTTGTTTGTAA 57.607 34.783 0.00 0.00 0.00 2.41
3807 3875 5.590530 TTGCTTGGACTGTTGTTTGTAAT 57.409 34.783 0.00 0.00 0.00 1.89
3808 3876 6.701145 TTGCTTGGACTGTTGTTTGTAATA 57.299 33.333 0.00 0.00 0.00 0.98
3809 3877 6.892658 TGCTTGGACTGTTGTTTGTAATAT 57.107 33.333 0.00 0.00 0.00 1.28
3810 3878 6.908825 TGCTTGGACTGTTGTTTGTAATATC 58.091 36.000 0.00 0.00 0.00 1.63
3811 3879 6.714810 TGCTTGGACTGTTGTTTGTAATATCT 59.285 34.615 0.00 0.00 0.00 1.98
3812 3880 7.880713 TGCTTGGACTGTTGTTTGTAATATCTA 59.119 33.333 0.00 0.00 0.00 1.98
3813 3881 8.175716 GCTTGGACTGTTGTTTGTAATATCTAC 58.824 37.037 0.00 0.00 0.00 2.59
3814 3882 9.214957 CTTGGACTGTTGTTTGTAATATCTACA 57.785 33.333 0.00 0.00 0.00 2.74
3815 3883 8.542497 TGGACTGTTGTTTGTAATATCTACAC 57.458 34.615 0.00 0.00 0.00 2.90
3816 3884 8.372459 TGGACTGTTGTTTGTAATATCTACACT 58.628 33.333 0.00 0.00 0.00 3.55
3817 3885 9.216117 GGACTGTTGTTTGTAATATCTACACTT 57.784 33.333 0.00 0.00 0.00 3.16
3885 3977 6.536582 GCTTAGATGACTGAGATTTACTGCAA 59.463 38.462 0.00 0.00 32.45 4.08
3986 4078 2.213499 CATTTGGCCATCGTCTAGTCC 58.787 52.381 6.09 0.00 0.00 3.85
4005 4097 1.401931 CCTTTGCAGTGCGGAAATCTG 60.402 52.381 11.20 0.00 34.08 2.90
4073 4171 3.703556 TGAAATCTGCTTTGTTTGGGACA 59.296 39.130 0.00 0.00 36.19 4.02
4155 4253 8.579006 TGCATAAATCATGAAATGGTCTATTCC 58.421 33.333 0.00 0.00 46.73 3.01
4185 4283 5.292589 CCTTTTTGATTGATTATGTGCCTGC 59.707 40.000 0.00 0.00 0.00 4.85
4543 4641 6.258287 TGCAAGGAACTGTGAAATTTCAATTG 59.742 34.615 22.07 16.14 40.86 2.32
4656 4754 0.896923 TTGGGCACATGAGAAATGGC 59.103 50.000 0.00 0.00 38.14 4.40
4665 4763 1.737838 TGAGAAATGGCGATGTGTCC 58.262 50.000 0.00 0.00 0.00 4.02
4830 4928 9.965824 TTTGAGATGTTAAAACTTTTGGAGATC 57.034 29.630 0.00 0.00 0.00 2.75
4858 4956 3.071457 TCATGTGAAAGAGACTCCAGCAA 59.929 43.478 0.00 0.00 0.00 3.91
5001 5099 7.048629 TGAAAGAGATCTACCAGCTAATCTG 57.951 40.000 0.00 0.00 42.49 2.90
5031 5129 2.159212 TGCAGCCATTGACATGCATAAC 60.159 45.455 0.00 0.00 43.34 1.89
5089 5187 7.108194 GGAGGATATCATTGATGATGTTGCTA 58.892 38.462 15.03 0.00 46.34 3.49
5212 5310 8.606830 AGATTTTTACTCCTGACTGATTTACCT 58.393 33.333 0.00 0.00 0.00 3.08
5213 5311 9.886132 GATTTTTACTCCTGACTGATTTACCTA 57.114 33.333 0.00 0.00 0.00 3.08
5214 5312 9.668497 ATTTTTACTCCTGACTGATTTACCTAC 57.332 33.333 0.00 0.00 0.00 3.18
5215 5313 6.786967 TTACTCCTGACTGATTTACCTACC 57.213 41.667 0.00 0.00 0.00 3.18
5216 5314 4.684724 ACTCCTGACTGATTTACCTACCA 58.315 43.478 0.00 0.00 0.00 3.25
5594 5701 9.995003 TTGGCAACTATTTTCACATTTTAGATT 57.005 25.926 0.00 0.00 37.61 2.40
5607 5714 9.571810 TCACATTTTAGATTATCAATGCACAAC 57.428 29.630 0.00 0.00 30.96 3.32
5712 5819 7.255569 TCACGAGAAACGACTATTCATAATGT 58.744 34.615 0.00 0.00 45.77 2.71
5715 5822 9.745880 ACGAGAAACGACTATTCATAATGTATT 57.254 29.630 0.00 0.00 45.77 1.89
5766 5873 1.266718 CACACGACCATCAAAGGTTGG 59.733 52.381 5.44 0.00 45.69 3.77
5790 5897 3.265791 CTGTGTCTCAATACTGCCTTCC 58.734 50.000 0.00 0.00 0.00 3.46
5791 5898 2.906389 TGTGTCTCAATACTGCCTTCCT 59.094 45.455 0.00 0.00 0.00 3.36
5805 5912 3.826157 TGCCTTCCTGAATTTGTTAGTGG 59.174 43.478 0.00 0.00 0.00 4.00
5823 5930 8.714179 TGTTAGTGGTTATGTCTAATTTTGACG 58.286 33.333 6.52 0.00 37.26 4.35
5898 6005 5.365403 TTGTCGATCATTTACAAACCCAC 57.635 39.130 0.00 0.00 30.54 4.61
6102 6218 8.858003 TCACTAGCTCTTAGATGTAATTTTCG 57.142 34.615 0.00 0.00 33.39 3.46
6130 6246 2.574369 TGAATGTGGGGGTAGTGTTAGG 59.426 50.000 0.00 0.00 0.00 2.69
6144 6260 6.377712 GGTAGTGTTAGGTGAGTGTCTCTTAT 59.622 42.308 0.00 0.00 0.00 1.73
6153 6269 6.483640 AGGTGAGTGTCTCTTATGTTTTGTTC 59.516 38.462 0.00 0.00 0.00 3.18
6429 6545 6.092748 CACTAACAAATAAAAGCTGGCGATT 58.907 36.000 0.00 0.00 0.00 3.34
6698 6815 6.105333 TCTTGTTTTGGTCCTTGATTGTTTG 58.895 36.000 0.00 0.00 0.00 2.93
6703 6820 2.955660 TGGTCCTTGATTGTTTGGTCAC 59.044 45.455 0.00 0.00 0.00 3.67
6709 6826 2.028130 TGATTGTTTGGTCACGGCTTT 58.972 42.857 0.00 0.00 0.00 3.51
6732 6849 2.189594 TGCATATGCTCACCATAGCC 57.810 50.000 27.13 0.00 42.05 3.93
6817 6934 9.260002 CACATTTATTCTGGCAAACTTTAACTT 57.740 29.630 0.00 0.00 0.00 2.66
6928 7045 5.871396 ACGAAGATACTACATGGGATTGT 57.129 39.130 0.00 0.00 0.00 2.71
6963 7080 1.576421 CTCACAACCTCTTTGGCGC 59.424 57.895 0.00 0.00 39.84 6.53
6972 7089 3.913089 ACCTCTTTGGCGCTTATTTTTG 58.087 40.909 7.64 0.00 40.22 2.44
6973 7090 3.320826 ACCTCTTTGGCGCTTATTTTTGT 59.679 39.130 7.64 0.00 40.22 2.83
6976 7094 5.107491 CCTCTTTGGCGCTTATTTTTGTTTC 60.107 40.000 7.64 0.00 0.00 2.78
7020 7138 5.968254 GGAGTTTCTTATCTCCGAACTTCT 58.032 41.667 0.00 0.00 40.36 2.85
7114 7232 7.773224 TGTGACCGTCATTTAATGGAGATAAAT 59.227 33.333 4.13 0.00 34.20 1.40
7216 7335 4.047822 CCGAGCTATCATTCAGTGTTCTC 58.952 47.826 0.00 0.00 0.00 2.87
7257 7376 9.531942 GCATCTATCCTGTCATATAATCTCAAG 57.468 37.037 0.00 0.00 0.00 3.02
7258 7377 9.531942 CATCTATCCTGTCATATAATCTCAAGC 57.468 37.037 0.00 0.00 0.00 4.01
7522 7641 7.094205 GGAATGATGAAACAACTGGTACTTCAT 60.094 37.037 4.46 4.46 38.97 2.57
7635 7755 5.163099 TGACCATAAATAGGAATGGACCAGG 60.163 44.000 8.29 0.00 44.62 4.45
7700 7820 4.400884 TGCAGTACCTGTCACAAAAATGTT 59.599 37.500 0.00 0.00 33.43 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.946984 ATAGAGACCACGGGGAACAA 58.053 50.000 12.96 0.00 38.05 2.83
1 2 1.553248 CAATAGAGACCACGGGGAACA 59.447 52.381 12.96 0.00 38.05 3.18
2 3 1.829222 TCAATAGAGACCACGGGGAAC 59.171 52.381 12.96 3.66 38.05 3.62
3 4 1.829222 GTCAATAGAGACCACGGGGAA 59.171 52.381 12.96 0.00 38.05 3.97
4 5 1.481871 GTCAATAGAGACCACGGGGA 58.518 55.000 12.96 0.00 38.05 4.81
12 13 1.338655 GCCCTCGAGGTCAATAGAGAC 59.661 57.143 29.25 5.02 38.26 3.36
13 14 1.215673 AGCCCTCGAGGTCAATAGAGA 59.784 52.381 29.25 0.00 38.26 3.10
14 15 1.611491 GAGCCCTCGAGGTCAATAGAG 59.389 57.143 29.25 12.78 38.26 2.43
15 16 1.063942 TGAGCCCTCGAGGTCAATAGA 60.064 52.381 29.25 3.03 41.08 1.98
16 17 1.339610 CTGAGCCCTCGAGGTCAATAG 59.660 57.143 29.25 16.24 43.22 1.73
17 18 1.403814 CTGAGCCCTCGAGGTCAATA 58.596 55.000 29.25 11.02 43.22 1.90
18 19 1.333636 CCTGAGCCCTCGAGGTCAAT 61.334 60.000 29.25 12.33 43.22 2.57
19 20 1.984570 CCTGAGCCCTCGAGGTCAA 60.985 63.158 29.25 9.16 43.22 3.18
20 21 2.363018 CCTGAGCCCTCGAGGTCA 60.363 66.667 29.25 24.29 41.74 4.02
21 22 2.043852 TCCTGAGCCCTCGAGGTC 60.044 66.667 29.25 21.12 38.26 3.85
22 23 2.363147 GTCCTGAGCCCTCGAGGT 60.363 66.667 29.25 12.84 38.26 3.85
23 24 2.043450 AGTCCTGAGCCCTCGAGG 60.043 66.667 25.36 25.36 39.47 4.63
24 25 1.379176 TGAGTCCTGAGCCCTCGAG 60.379 63.158 5.13 5.13 0.00 4.04
25 26 1.379176 CTGAGTCCTGAGCCCTCGA 60.379 63.158 0.00 0.00 0.00 4.04
26 27 2.422231 CCTGAGTCCTGAGCCCTCG 61.422 68.421 0.00 0.00 0.00 4.63
27 28 1.305718 ACCTGAGTCCTGAGCCCTC 60.306 63.158 0.00 0.00 0.00 4.30
28 29 1.305718 GACCTGAGTCCTGAGCCCT 60.306 63.158 0.00 0.00 37.00 5.19
29 30 1.194781 TTGACCTGAGTCCTGAGCCC 61.195 60.000 0.00 0.00 42.81 5.19
30 31 0.908198 ATTGACCTGAGTCCTGAGCC 59.092 55.000 0.00 0.00 42.81 4.70
31 32 1.830477 AGATTGACCTGAGTCCTGAGC 59.170 52.381 0.00 0.00 42.81 4.26
32 33 3.095332 TCAGATTGACCTGAGTCCTGAG 58.905 50.000 0.00 0.00 42.81 3.35
33 34 3.175438 TCAGATTGACCTGAGTCCTGA 57.825 47.619 0.00 0.00 42.81 3.86
34 35 3.490590 CGATCAGATTGACCTGAGTCCTG 60.491 52.174 0.00 0.00 45.27 3.86
35 36 2.692557 CGATCAGATTGACCTGAGTCCT 59.307 50.000 0.00 0.00 45.27 3.85
36 37 2.223923 CCGATCAGATTGACCTGAGTCC 60.224 54.545 0.00 0.00 45.27 3.85
37 38 2.801342 GCCGATCAGATTGACCTGAGTC 60.801 54.545 0.00 0.00 45.27 3.36
38 39 1.137872 GCCGATCAGATTGACCTGAGT 59.862 52.381 0.00 0.00 45.27 3.41
39 40 1.137675 TGCCGATCAGATTGACCTGAG 59.862 52.381 0.00 0.00 45.27 3.35
40 41 1.194218 TGCCGATCAGATTGACCTGA 58.806 50.000 0.00 0.00 46.02 3.86
41 42 1.667724 GTTGCCGATCAGATTGACCTG 59.332 52.381 0.00 0.00 35.55 4.00
42 43 1.740380 CGTTGCCGATCAGATTGACCT 60.740 52.381 0.00 0.00 35.63 3.85
43 44 0.652592 CGTTGCCGATCAGATTGACC 59.347 55.000 0.00 0.00 35.63 4.02
44 45 0.652592 CCGTTGCCGATCAGATTGAC 59.347 55.000 0.00 0.00 35.63 3.18
45 46 1.089481 GCCGTTGCCGATCAGATTGA 61.089 55.000 0.00 0.00 35.63 2.57
46 47 1.353103 GCCGTTGCCGATCAGATTG 59.647 57.895 0.00 0.00 35.63 2.67
47 48 1.078497 TGCCGTTGCCGATCAGATT 60.078 52.632 0.00 0.00 36.33 2.40
48 49 1.522355 CTGCCGTTGCCGATCAGAT 60.522 57.895 0.00 0.00 36.94 2.90
49 50 2.125552 CTGCCGTTGCCGATCAGA 60.126 61.111 0.00 0.00 36.94 3.27
50 51 2.572095 TACCTGCCGTTGCCGATCAG 62.572 60.000 0.00 0.00 36.33 2.90
51 52 2.173758 TTACCTGCCGTTGCCGATCA 62.174 55.000 0.00 0.00 36.33 2.92
52 53 1.022451 TTTACCTGCCGTTGCCGATC 61.022 55.000 0.00 0.00 36.33 3.69
53 54 1.003112 TTTACCTGCCGTTGCCGAT 60.003 52.632 0.00 0.00 36.33 4.18
54 55 1.962306 GTTTACCTGCCGTTGCCGA 60.962 57.895 0.00 0.00 36.33 5.54
55 56 2.559330 GTTTACCTGCCGTTGCCG 59.441 61.111 0.00 0.00 36.33 5.69
56 57 2.559330 CGTTTACCTGCCGTTGCC 59.441 61.111 0.00 0.00 36.33 4.52
57 58 2.559330 CCGTTTACCTGCCGTTGC 59.441 61.111 0.00 0.00 38.26 4.17
58 59 2.559330 GCCGTTTACCTGCCGTTG 59.441 61.111 0.00 0.00 0.00 4.10
59 60 3.045492 CGCCGTTTACCTGCCGTT 61.045 61.111 0.00 0.00 0.00 4.44
62 63 3.799755 CTGCGCCGTTTACCTGCC 61.800 66.667 4.18 0.00 0.00 4.85
63 64 3.799755 CCTGCGCCGTTTACCTGC 61.800 66.667 4.18 0.00 0.00 4.85
64 65 2.047655 TCCTGCGCCGTTTACCTG 60.048 61.111 4.18 0.00 0.00 4.00
65 66 2.227089 CTCTCCTGCGCCGTTTACCT 62.227 60.000 4.18 0.00 0.00 3.08
66 67 1.810030 CTCTCCTGCGCCGTTTACC 60.810 63.158 4.18 0.00 0.00 2.85
67 68 0.389426 TTCTCTCCTGCGCCGTTTAC 60.389 55.000 4.18 0.00 0.00 2.01
68 69 0.319083 TTTCTCTCCTGCGCCGTTTA 59.681 50.000 4.18 0.00 0.00 2.01
69 70 0.534203 TTTTCTCTCCTGCGCCGTTT 60.534 50.000 4.18 0.00 0.00 3.60
70 71 1.070786 TTTTCTCTCCTGCGCCGTT 59.929 52.632 4.18 0.00 0.00 4.44
71 72 1.668151 GTTTTCTCTCCTGCGCCGT 60.668 57.895 4.18 0.00 0.00 5.68
72 73 1.667830 TGTTTTCTCTCCTGCGCCG 60.668 57.895 4.18 0.00 0.00 6.46
73 74 1.869690 GTGTTTTCTCTCCTGCGCC 59.130 57.895 4.18 0.00 0.00 6.53
74 75 0.944311 TCGTGTTTTCTCTCCTGCGC 60.944 55.000 0.00 0.00 0.00 6.09
75 76 0.784778 GTCGTGTTTTCTCTCCTGCG 59.215 55.000 0.00 0.00 0.00 5.18
76 77 0.784778 CGTCGTGTTTTCTCTCCTGC 59.215 55.000 0.00 0.00 0.00 4.85
77 78 2.052157 GTCGTCGTGTTTTCTCTCCTG 58.948 52.381 0.00 0.00 0.00 3.86
78 79 1.679680 TGTCGTCGTGTTTTCTCTCCT 59.320 47.619 0.00 0.00 0.00 3.69
79 80 2.129823 TGTCGTCGTGTTTTCTCTCC 57.870 50.000 0.00 0.00 0.00 3.71
80 81 2.098021 CGTTGTCGTCGTGTTTTCTCTC 60.098 50.000 0.00 0.00 0.00 3.20
81 82 1.850441 CGTTGTCGTCGTGTTTTCTCT 59.150 47.619 0.00 0.00 0.00 3.10
82 83 1.071698 CCGTTGTCGTCGTGTTTTCTC 60.072 52.381 0.00 0.00 35.01 2.87
83 84 0.925466 CCGTTGTCGTCGTGTTTTCT 59.075 50.000 0.00 0.00 35.01 2.52
84 85 0.652465 GCCGTTGTCGTCGTGTTTTC 60.652 55.000 0.00 0.00 35.01 2.29
85 86 1.349282 GCCGTTGTCGTCGTGTTTT 59.651 52.632 0.00 0.00 35.01 2.43
86 87 2.527867 GGCCGTTGTCGTCGTGTTT 61.528 57.895 0.00 0.00 35.01 2.83
87 88 2.963320 GGCCGTTGTCGTCGTGTT 60.963 61.111 0.00 0.00 35.01 3.32
88 89 4.210093 TGGCCGTTGTCGTCGTGT 62.210 61.111 0.00 0.00 35.01 4.49
89 90 3.698463 GTGGCCGTTGTCGTCGTG 61.698 66.667 0.00 0.00 35.01 4.35
249 250 1.267121 CGGAAAAGAGAGAGGTGGGA 58.733 55.000 0.00 0.00 0.00 4.37
325 326 1.985662 AACGATCGGGGCCACAGTA 60.986 57.895 20.98 0.00 0.00 2.74
386 388 1.344226 GAAATGCAAAAGGACGGCGC 61.344 55.000 6.90 0.00 0.00 6.53
388 390 0.239879 TCGAAATGCAAAAGGACGGC 59.760 50.000 0.00 0.00 0.00 5.68
935 976 2.577059 CTGTTCTTCCGCGGCCTA 59.423 61.111 23.51 7.32 0.00 3.93
1083 1134 9.605275 CACAGAATACAGAGGAAGATGATAAAA 57.395 33.333 0.00 0.00 0.00 1.52
1089 1140 4.569966 GCACACAGAATACAGAGGAAGATG 59.430 45.833 0.00 0.00 0.00 2.90
1123 1184 0.784778 GTCGAAGCAACGAGTCCAAG 59.215 55.000 5.56 0.00 42.88 3.61
1176 1237 1.407437 GGATGGTACACCTTGGAGCAG 60.407 57.143 0.00 0.00 42.60 4.24
1256 1317 5.580691 TGCAAATACTAGAATGACCAAGACG 59.419 40.000 0.00 0.00 0.00 4.18
1311 1372 8.717821 CCAAATACTATATGAATACCCAACACG 58.282 37.037 0.00 0.00 0.00 4.49
1390 1451 8.482128 TGGTAAATCAGGTTCTTTCAAATGTTT 58.518 29.630 0.00 0.00 0.00 2.83
1416 1477 4.398673 GGAAGAAGATCAATGCTGCTCTTT 59.601 41.667 0.00 0.00 37.98 2.52
1426 1487 6.347061 AAAGGGGTATGGAAGAAGATCAAT 57.653 37.500 0.00 0.00 0.00 2.57
1521 1582 9.889128 TCTATAATGAATGTGATCACTGTTCAA 57.111 29.630 31.76 23.54 38.79 2.69
1522 1583 9.317936 GTCTATAATGAATGTGATCACTGTTCA 57.682 33.333 30.97 30.97 39.23 3.18
1523 1584 8.483218 CGTCTATAATGAATGTGATCACTGTTC 58.517 37.037 25.55 25.24 30.82 3.18
1524 1585 7.981789 ACGTCTATAATGAATGTGATCACTGTT 59.018 33.333 25.55 19.37 30.82 3.16
1525 1586 7.492524 ACGTCTATAATGAATGTGATCACTGT 58.507 34.615 25.55 13.79 30.82 3.55
1526 1587 7.936950 ACGTCTATAATGAATGTGATCACTG 57.063 36.000 25.55 4.58 30.82 3.66
1527 1588 9.067986 TCTACGTCTATAATGAATGTGATCACT 57.932 33.333 25.55 7.38 30.82 3.41
1528 1589 9.335891 CTCTACGTCTATAATGAATGTGATCAC 57.664 37.037 19.27 19.27 30.82 3.06
1529 1590 9.067986 ACTCTACGTCTATAATGAATGTGATCA 57.932 33.333 0.00 0.00 0.00 2.92
1569 1630 6.389906 GGCATAAGCTATATTGCGGAAAAAT 58.610 36.000 3.46 0.00 41.70 1.82
1679 1740 6.017026 TCGACTTCACTATATAGACAGCCTTG 60.017 42.308 16.79 2.65 0.00 3.61
1937 2001 3.493028 TGTGCTGCCTTTTCACAGA 57.507 47.368 0.00 0.00 35.99 3.41
2010 2074 6.323739 TGTTCCCTCTAACAGCAAAGAATTTT 59.676 34.615 0.00 0.00 33.00 1.82
2021 2085 1.630878 AGCCCTTGTTCCCTCTAACAG 59.369 52.381 0.00 0.00 40.29 3.16
2076 2140 4.090761 AGCATCTTTGTCTTTGGACTCA 57.909 40.909 0.00 0.00 42.54 3.41
2089 2153 7.883311 ACAGTACAATACCTTTGTAGCATCTTT 59.117 33.333 0.00 0.00 35.77 2.52
2117 2181 7.415086 TGGAACATGGTATACAATTTAAGGGT 58.585 34.615 5.01 0.00 0.00 4.34
2136 2201 4.935702 CTGTGCTTCAGAAAAATGGAACA 58.064 39.130 3.96 0.00 46.27 3.18
2323 2389 1.153549 GTGACGATGACCTGAGCCC 60.154 63.158 0.00 0.00 0.00 5.19
2325 2391 0.244994 AGTGTGACGATGACCTGAGC 59.755 55.000 0.00 0.00 0.00 4.26
2437 2503 9.747898 AACTGGAAAAATTAGGATGTATGTGTA 57.252 29.630 0.00 0.00 0.00 2.90
2520 2586 3.963383 ACTCAACTTTTTAGTGCCACG 57.037 42.857 0.00 0.00 0.00 4.94
2536 2602 2.908688 TGACTTGCAGTGCTAACTCA 57.091 45.000 17.60 9.30 32.98 3.41
2572 2638 4.307432 ACAGAAACCGAGTACACAATCTG 58.693 43.478 0.00 4.00 39.09 2.90
2582 2648 4.215613 GCATTTTCCTTACAGAAACCGAGT 59.784 41.667 0.00 0.00 35.53 4.18
2607 2673 1.597663 CCGTATTCGTTGGAATGGAGC 59.402 52.381 0.00 0.00 42.72 4.70
2626 2692 1.816074 TTTTGGGATACGAGTGTGCC 58.184 50.000 3.71 3.71 32.96 5.01
2633 2699 5.182380 GTCCAAGTTCAATTTTGGGATACGA 59.818 40.000 6.76 0.00 43.22 3.43
2639 2705 4.040217 TGATGGTCCAAGTTCAATTTTGGG 59.960 41.667 0.00 0.00 43.22 4.12
2658 2724 8.934825 CCCCACATTTAGTTGTTTAAATTGATG 58.065 33.333 0.00 0.00 32.38 3.07
2861 2927 7.381323 GGAAATGTTCCCATATTCCATGAATC 58.619 38.462 0.00 0.00 44.30 2.52
2941 3009 2.287909 GCAGCGTAATCAGGAGACCTAG 60.288 54.545 0.00 0.00 29.64 3.02
2959 3027 1.893759 TCGCGCAATAAAACATGCAG 58.106 45.000 8.75 0.00 42.68 4.41
2976 3044 5.105675 GGTAGAAGGGCTAGGATTTAGATCG 60.106 48.000 0.00 0.00 32.84 3.69
3070 3138 5.827797 AGTGGATAAACTGACTCAGCAAAAA 59.172 36.000 5.92 0.00 34.37 1.94
3084 3152 8.051901 ACTTAAAGGCAATACAGTGGATAAAC 57.948 34.615 0.00 0.00 0.00 2.01
3163 3231 3.554129 GGACGCCTTAAAAACAATGCCTT 60.554 43.478 0.00 0.00 0.00 4.35
3166 3234 2.333926 GGGACGCCTTAAAAACAATGC 58.666 47.619 0.00 0.00 0.00 3.56
3183 3251 2.998480 TAAGCGTCCAAGGCGGGA 60.998 61.111 0.00 0.00 33.62 5.14
3184 3252 2.511600 CTAAGCGTCCAAGGCGGG 60.512 66.667 5.39 0.00 33.62 6.13
3185 3253 2.511600 CCTAAGCGTCCAAGGCGG 60.512 66.667 5.39 0.00 33.62 6.13
3186 3254 3.195698 GCCTAAGCGTCCAAGGCG 61.196 66.667 0.00 0.00 45.82 5.52
3215 3283 0.106918 TATTTGTAAGGCGCTGGGGG 60.107 55.000 7.64 0.00 0.00 5.40
3216 3284 1.608590 CATATTTGTAAGGCGCTGGGG 59.391 52.381 7.64 0.00 0.00 4.96
3217 3285 1.001378 GCATATTTGTAAGGCGCTGGG 60.001 52.381 7.64 0.00 0.00 4.45
3218 3286 1.001378 GGCATATTTGTAAGGCGCTGG 60.001 52.381 7.64 0.00 0.00 4.85
3219 3287 1.001378 GGGCATATTTGTAAGGCGCTG 60.001 52.381 7.64 0.00 34.95 5.18
3220 3288 1.318576 GGGCATATTTGTAAGGCGCT 58.681 50.000 7.64 0.00 34.95 5.92
3221 3289 0.040425 CGGGCATATTTGTAAGGCGC 60.040 55.000 0.00 0.00 0.00 6.53
3222 3290 0.040425 GCGGGCATATTTGTAAGGCG 60.040 55.000 0.00 0.00 0.00 5.52
3223 3291 0.313987 GGCGGGCATATTTGTAAGGC 59.686 55.000 0.00 0.00 0.00 4.35
3224 3292 1.981256 AGGCGGGCATATTTGTAAGG 58.019 50.000 3.78 0.00 0.00 2.69
3225 3293 3.502211 CCTAAGGCGGGCATATTTGTAAG 59.498 47.826 3.78 0.00 0.00 2.34
3226 3294 3.482436 CCTAAGGCGGGCATATTTGTAA 58.518 45.455 3.78 0.00 0.00 2.41
3227 3295 3.134574 CCTAAGGCGGGCATATTTGTA 57.865 47.619 3.78 0.00 0.00 2.41
3228 3296 1.981256 CCTAAGGCGGGCATATTTGT 58.019 50.000 3.78 0.00 0.00 2.83
3542 3610 8.017611 AACCATAGTTTTTAAGGCGGTAAGGC 62.018 42.308 0.00 0.00 38.26 4.35
3543 3611 4.945543 ACCATAGTTTTTAAGGCGGTAAGG 59.054 41.667 0.00 0.00 0.00 2.69
3544 3612 6.149807 TCAACCATAGTTTTTAAGGCGGTAAG 59.850 38.462 0.00 0.00 32.45 2.34
3545 3613 6.002704 TCAACCATAGTTTTTAAGGCGGTAA 58.997 36.000 0.00 0.00 32.45 2.85
3546 3614 5.558818 TCAACCATAGTTTTTAAGGCGGTA 58.441 37.500 0.00 0.00 32.45 4.02
3547 3615 4.400120 TCAACCATAGTTTTTAAGGCGGT 58.600 39.130 0.00 0.00 32.45 5.68
3548 3616 5.379732 TTCAACCATAGTTTTTAAGGCGG 57.620 39.130 0.00 0.00 32.45 6.13
3549 3617 6.616947 TGATTCAACCATAGTTTTTAAGGCG 58.383 36.000 0.00 0.00 32.45 5.52
3550 3618 7.826690 TCTGATTCAACCATAGTTTTTAAGGC 58.173 34.615 0.00 0.00 32.45 4.35
3555 3623 8.970020 TGCATATCTGATTCAACCATAGTTTTT 58.030 29.630 0.00 0.00 32.45 1.94
3556 3624 8.523915 TGCATATCTGATTCAACCATAGTTTT 57.476 30.769 0.00 0.00 32.45 2.43
3557 3625 8.408601 GTTGCATATCTGATTCAACCATAGTTT 58.591 33.333 14.05 0.00 32.45 2.66
3558 3626 7.934457 GTTGCATATCTGATTCAACCATAGTT 58.066 34.615 14.05 0.00 36.33 2.24
3559 3627 7.502120 GTTGCATATCTGATTCAACCATAGT 57.498 36.000 14.05 0.00 33.05 2.12
3565 3633 4.496341 CCGTGGTTGCATATCTGATTCAAC 60.496 45.833 15.54 15.54 37.04 3.18
3629 3697 5.875224 TCAGAATGGAAATTAGGTCACACA 58.125 37.500 0.00 0.00 36.16 3.72
3749 3817 4.142609 ACGGATAATGAGTGAGCACAAT 57.857 40.909 3.19 0.00 0.00 2.71
3759 3827 9.950680 AAATTGCATACTAAAACGGATAATGAG 57.049 29.630 0.00 0.00 0.00 2.90
3783 3851 4.264460 ACAAACAACAGTCCAAGCAAAA 57.736 36.364 0.00 0.00 0.00 2.44
3790 3858 8.372459 AGTGTAGATATTACAAACAACAGTCCA 58.628 33.333 1.05 0.00 0.00 4.02
3798 3866 9.672086 GCAAACAAAGTGTAGATATTACAAACA 57.328 29.630 1.05 0.00 0.00 2.83
3799 3867 9.893305 AGCAAACAAAGTGTAGATATTACAAAC 57.107 29.630 0.00 0.00 0.00 2.93
3800 3868 9.891828 CAGCAAACAAAGTGTAGATATTACAAA 57.108 29.630 0.00 0.00 0.00 2.83
3801 3869 9.278978 TCAGCAAACAAAGTGTAGATATTACAA 57.721 29.630 0.00 0.00 0.00 2.41
3802 3870 8.840833 TCAGCAAACAAAGTGTAGATATTACA 57.159 30.769 0.00 0.00 0.00 2.41
3807 3875 9.317936 CAGATATCAGCAAACAAAGTGTAGATA 57.682 33.333 5.32 0.00 0.00 1.98
3808 3876 8.043113 TCAGATATCAGCAAACAAAGTGTAGAT 58.957 33.333 5.32 0.00 0.00 1.98
3809 3877 7.386059 TCAGATATCAGCAAACAAAGTGTAGA 58.614 34.615 5.32 0.00 0.00 2.59
3810 3878 7.601073 TCAGATATCAGCAAACAAAGTGTAG 57.399 36.000 5.32 0.00 0.00 2.74
3811 3879 7.443879 TGTTCAGATATCAGCAAACAAAGTGTA 59.556 33.333 5.32 0.00 0.00 2.90
3812 3880 6.262944 TGTTCAGATATCAGCAAACAAAGTGT 59.737 34.615 5.32 0.00 0.00 3.55
3813 3881 6.671190 TGTTCAGATATCAGCAAACAAAGTG 58.329 36.000 5.32 0.00 0.00 3.16
3814 3882 6.882610 TGTTCAGATATCAGCAAACAAAGT 57.117 33.333 5.32 0.00 0.00 2.66
3815 3883 9.447040 CATATGTTCAGATATCAGCAAACAAAG 57.553 33.333 5.32 1.78 31.19 2.77
3816 3884 8.407832 CCATATGTTCAGATATCAGCAAACAAA 58.592 33.333 5.32 0.00 31.19 2.83
3817 3885 7.557358 ACCATATGTTCAGATATCAGCAAACAA 59.443 33.333 5.32 2.58 31.19 2.83
3885 3977 8.935614 AACTTCTTAAGGGCATTAAAGTTAGT 57.064 30.769 15.99 9.52 34.71 2.24
3986 4078 1.973138 CAGATTTCCGCACTGCAAAG 58.027 50.000 1.11 0.00 0.00 2.77
4155 4253 8.437742 GCACATAATCAATCAAAAAGGAAACAG 58.562 33.333 0.00 0.00 0.00 3.16
4219 4317 3.173540 CCATCACCTGGCATCGAAA 57.826 52.632 0.00 0.00 38.47 3.46
4220 4318 4.961637 CCATCACCTGGCATCGAA 57.038 55.556 0.00 0.00 38.47 3.71
4278 4376 7.534852 TCCCTTTTACATCCAGCCAATATAAT 58.465 34.615 0.00 0.00 0.00 1.28
4543 4641 2.082231 GGGTAAGCTTTCGGAACCTTC 58.918 52.381 3.20 0.00 0.00 3.46
4656 4754 2.166829 TGGGAAATTTGGGACACATCG 58.833 47.619 0.00 0.00 39.29 3.84
4665 4763 6.149807 CCTGAACATCAAATTGGGAAATTTGG 59.850 38.462 18.74 9.86 45.45 3.28
4806 4904 7.723616 TGGATCTCCAAAAGTTTTAACATCTCA 59.276 33.333 0.00 0.29 44.35 3.27
4830 4928 4.874966 GGAGTCTCTTTCACATGAAGATGG 59.125 45.833 0.00 0.00 35.21 3.51
4858 4956 6.016555 GGGCTAATTGGGTATCACCATTTAT 58.983 40.000 0.00 0.00 41.02 1.40
5001 5099 2.555757 GTCAATGGCTGCATAATCCTCC 59.444 50.000 0.50 0.00 0.00 4.30
5031 5129 7.514805 TGCGGCGTAAGTATATTAAATTGATG 58.485 34.615 9.37 0.00 41.68 3.07
5049 5147 4.393155 TCCATCAAGCTGCGGCGT 62.393 61.111 12.87 5.85 44.37 5.68
5089 5187 6.638610 CACCAGTAATCTTCTCAGAGAATGT 58.361 40.000 13.49 2.73 33.13 2.71
5438 5544 3.364277 GTGAAGGCTCACCCGATAC 57.636 57.895 5.98 0.00 45.41 2.24
5462 5568 2.668279 GCCAACACCTAACAGCATTTCG 60.668 50.000 0.00 0.00 0.00 3.46
5607 5714 9.058424 GCTTAACGCCTTAACTAAACATTAAAG 57.942 33.333 0.00 0.00 0.00 1.85
5766 5873 1.734465 GGCAGTATTGAGACACAGCAC 59.266 52.381 0.00 0.00 0.00 4.40
5805 5912 6.417191 TCCAGCGTCAAAATTAGACATAAC 57.583 37.500 10.47 0.00 35.77 1.89
5823 5930 7.322664 TCAAATAAAAGATGTCCAAATCCAGC 58.677 34.615 0.00 0.00 0.00 4.85
5898 6005 6.472163 TGTTAAAAGCTTGCGAAAAAGAGAAG 59.528 34.615 0.00 0.00 0.00 2.85
6102 6218 1.379044 CCCCCACATTCAGCAGTCC 60.379 63.158 0.00 0.00 0.00 3.85
6130 6246 7.484035 AGAACAAAACATAAGAGACACTCAC 57.516 36.000 0.00 0.00 32.06 3.51
6144 6260 6.770785 ACAAGCCAGTTAGATAGAACAAAACA 59.229 34.615 0.00 0.00 0.00 2.83
6153 6269 5.182001 ACAAGCAAACAAGCCAGTTAGATAG 59.818 40.000 0.00 0.00 34.23 2.08
6429 6545 7.716799 ATTACCAAATAAGCAACCTCATCAA 57.283 32.000 0.00 0.00 0.00 2.57
6632 6749 0.171455 GAAACACCAACACCAACGCA 59.829 50.000 0.00 0.00 0.00 5.24
6698 6815 2.126346 GCATGCAAAGCCGTGACC 60.126 61.111 14.21 0.00 0.00 4.02
6817 6934 3.562141 CGTCCTTGGTCACAAATGTTACA 59.438 43.478 0.84 0.00 35.89 2.41
6877 6994 8.185953 TCCAGAGAGGTTATGAGAAACTCTCAA 61.186 40.741 29.78 15.97 46.60 3.02
6928 7045 2.497273 GTGAGCTAAACCCGGTACCTAA 59.503 50.000 10.90 0.00 0.00 2.69
6972 7089 7.904461 CCAATTGAAGACAAAACAACATGAAAC 59.096 33.333 7.12 0.00 39.54 2.78
6973 7090 7.821359 TCCAATTGAAGACAAAACAACATGAAA 59.179 29.630 7.12 0.00 39.54 2.69
6976 7094 6.757947 ACTCCAATTGAAGACAAAACAACATG 59.242 34.615 7.12 0.00 39.54 3.21
7019 7137 4.863131 ACTATTCGGTAAGTGCGAGAAAAG 59.137 41.667 0.00 0.00 0.00 2.27
7020 7138 4.813027 ACTATTCGGTAAGTGCGAGAAAA 58.187 39.130 0.00 0.00 0.00 2.29
7114 7232 8.826765 AGGAAGGATGAGAACAATAAGAAGTTA 58.173 33.333 0.00 0.00 0.00 2.24
7257 7376 7.096518 GCAAAAAGAAAGCCAAACATAAATTGC 60.097 33.333 0.00 0.00 0.00 3.56
7258 7377 7.914346 TGCAAAAAGAAAGCCAAACATAAATTG 59.086 29.630 0.00 0.00 0.00 2.32
7597 7717 9.669353 CTATTTATGGTCAAATCAACTGCATAC 57.331 33.333 0.00 0.00 30.84 2.39
7635 7755 4.608948 TCTCTTCCAGGAAACAGAAGAC 57.391 45.455 2.72 0.00 43.14 3.01
7700 7820 1.015109 GAGTGACGACTAGCATCGGA 58.985 55.000 7.56 0.00 46.56 4.55


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

AutoCloner maintained by Alex Coulton.