Multiple sequence alignment - TraesCS2A01G073400

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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 TraesCS2A01G073400 chr2A 100.000 3231 0 0 1 3231 32430969 32427739 0.000000e+00 5967
1 TraesCS2A01G073400 chr2A 96.230 2944 81 12 315 3231 772274208 772277148 0.000000e+00 4795
2 TraesCS2A01G073400 chr2A 96.135 2484 55 8 758 3231 669669733 669667281 0.000000e+00 4017
3 TraesCS2A01G073400 chr1A 97.096 2927 72 7 315 3231 1567906 1564983 0.000000e+00 4922
4 TraesCS2A01G073400 chr1A 96.755 2928 82 7 314 3231 1618845 1615921 0.000000e+00 4868
5 TraesCS2A01G073400 chr1A 96.376 2511 61 7 731 3231 12275676 12278166 0.000000e+00 4106
6 TraesCS2A01G073400 chrUn 97.003 2936 67 8 315 3231 264694584 264697517 0.000000e+00 4915
7 TraesCS2A01G073400 chrUn 98.476 328 3 2 1 326 440716191 440716518 7.770000e-161 577
8 TraesCS2A01G073400 chrUn 92.621 393 11 8 2841 3231 197743885 197743509 1.690000e-152 549
9 TraesCS2A01G073400 chr4A 96.691 2931 72 10 315 3231 631535231 631532312 0.000000e+00 4852
10 TraesCS2A01G073400 chr4A 96.587 2930 73 13 315 3231 17861347 17864262 0.000000e+00 4831
11 TraesCS2A01G073400 chr4A 97.464 2484 53 2 758 3231 618493194 618490711 0.000000e+00 4229
12 TraesCS2A01G073400 chr7B 96.449 2929 78 7 315 3231 643692431 643689517 0.000000e+00 4809
13 TraesCS2A01G073400 chr7B 99.682 314 1 0 1 314 270376788 270377101 2.800000e-160 575
14 TraesCS2A01G073400 chr6B 96.193 2942 72 17 315 3231 70703496 70706422 0.000000e+00 4776
15 TraesCS2A01G073400 chr6B 94.944 2393 75 16 853 3231 689052882 689050522 0.000000e+00 3707
16 TraesCS2A01G073400 chr6B 99.068 322 3 0 1 322 370840018 370839697 2.160000e-161 579
17 TraesCS2A01G073400 chr1B 96.221 2937 73 10 315 3231 560203702 560200784 0.000000e+00 4774
18 TraesCS2A01G073400 chr4B 96.026 2944 78 13 315 3231 664138595 664141526 0.000000e+00 4752
19 TraesCS2A01G073400 chr4B 96.024 2943 77 10 315 3231 664113667 664116595 0.000000e+00 4750
20 TraesCS2A01G073400 chr4B 98.476 328 3 2 1 326 479482 479155 7.770000e-161 577
21 TraesCS2A01G073400 chr5B 95.992 2944 77 10 315 3231 127790826 127787897 0.000000e+00 4745
22 TraesCS2A01G073400 chr5B 95.887 2942 77 11 315 3231 689154101 689157023 0.000000e+00 4723
23 TraesCS2A01G073400 chr5B 96.025 2742 69 11 517 3231 688512055 688509327 0.000000e+00 4423
24 TraesCS2A01G073400 chr5B 98.471 327 3 2 1 326 103692902 103692577 2.800000e-160 575
25 TraesCS2A01G073400 chr3A 96.176 2929 63 11 315 3231 701724813 701721922 0.000000e+00 4743
26 TraesCS2A01G073400 chr5A 99.686 318 1 0 1 318 569747275 569746958 1.670000e-162 582
27 TraesCS2A01G073400 chr7A 99.068 322 3 0 1 322 479169884 479169563 2.160000e-161 579
28 TraesCS2A01G073400 chr7A 98.476 328 3 2 1 326 279541004 279540677 7.770000e-161 577
29 TraesCS2A01G073400 chr6A 97.898 333 6 1 1 333 353837974 353837643 2.800000e-160 575


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 TraesCS2A01G073400 chr2A 32427739 32430969 3230 True 5967 5967 100.000 1 3231 1 chr2A.!!$R1 3230
1 TraesCS2A01G073400 chr2A 772274208 772277148 2940 False 4795 4795 96.230 315 3231 1 chr2A.!!$F1 2916
2 TraesCS2A01G073400 chr2A 669667281 669669733 2452 True 4017 4017 96.135 758 3231 1 chr2A.!!$R2 2473
3 TraesCS2A01G073400 chr1A 1564983 1567906 2923 True 4922 4922 97.096 315 3231 1 chr1A.!!$R1 2916
4 TraesCS2A01G073400 chr1A 1615921 1618845 2924 True 4868 4868 96.755 314 3231 1 chr1A.!!$R2 2917
5 TraesCS2A01G073400 chr1A 12275676 12278166 2490 False 4106 4106 96.376 731 3231 1 chr1A.!!$F1 2500
6 TraesCS2A01G073400 chrUn 264694584 264697517 2933 False 4915 4915 97.003 315 3231 1 chrUn.!!$F1 2916
7 TraesCS2A01G073400 chr4A 631532312 631535231 2919 True 4852 4852 96.691 315 3231 1 chr4A.!!$R2 2916
8 TraesCS2A01G073400 chr4A 17861347 17864262 2915 False 4831 4831 96.587 315 3231 1 chr4A.!!$F1 2916
9 TraesCS2A01G073400 chr4A 618490711 618493194 2483 True 4229 4229 97.464 758 3231 1 chr4A.!!$R1 2473
10 TraesCS2A01G073400 chr7B 643689517 643692431 2914 True 4809 4809 96.449 315 3231 1 chr7B.!!$R1 2916
11 TraesCS2A01G073400 chr6B 70703496 70706422 2926 False 4776 4776 96.193 315 3231 1 chr6B.!!$F1 2916
12 TraesCS2A01G073400 chr6B 689050522 689052882 2360 True 3707 3707 94.944 853 3231 1 chr6B.!!$R2 2378
13 TraesCS2A01G073400 chr1B 560200784 560203702 2918 True 4774 4774 96.221 315 3231 1 chr1B.!!$R1 2916
14 TraesCS2A01G073400 chr4B 664138595 664141526 2931 False 4752 4752 96.026 315 3231 1 chr4B.!!$F2 2916
15 TraesCS2A01G073400 chr4B 664113667 664116595 2928 False 4750 4750 96.024 315 3231 1 chr4B.!!$F1 2916
16 TraesCS2A01G073400 chr5B 127787897 127790826 2929 True 4745 4745 95.992 315 3231 1 chr5B.!!$R2 2916
17 TraesCS2A01G073400 chr5B 689154101 689157023 2922 False 4723 4723 95.887 315 3231 1 chr5B.!!$F1 2916
18 TraesCS2A01G073400 chr5B 688509327 688512055 2728 True 4423 4423 96.025 517 3231 1 chr5B.!!$R3 2714
19 TraesCS2A01G073400 chr3A 701721922 701724813 2891 True 4743 4743 96.176 315 3231 1 chr3A.!!$R1 2916

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
86 87 0.036388 GTTCGAAGCTGGGTCATGGA 60.036 55.0 0.00 0.00 0.00 3.41 F
143 144 0.103208 GACTAGTCATGTCAGCCCGG 59.897 60.0 18.20 0.00 34.80 5.73 F
221 222 0.392060 CGGTCCCGGGAAAAGGTAAG 60.392 60.0 28.84 6.57 35.56 2.34 F
1952 2039 0.036765 TTTGGAGATCAACCCCGACG 60.037 55.0 0.00 0.00 34.67 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1195 1229 0.108138 CGGATCCTCTTGTCGGCTTT 60.108 55.000 10.75 0.0 0.00 3.51 R
1952 2039 1.464429 CGCTGCATGTCGACGTACTC 61.464 60.000 10.54 3.6 0.00 2.59 R
2071 2158 5.205056 AGTTTGTGGTCCAATTCCTTGTTA 58.795 37.500 0.00 0.0 31.81 2.41 R
3056 3167 4.335647 CGCACTGTGGCCTCCCTT 62.336 66.667 10.21 0.0 0.00 3.95 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
22 23 4.611961 GGTTTACCGGAGTCCTGC 57.388 61.111 9.46 0.00 0.00 4.85
23 24 1.980844 GGTTTACCGGAGTCCTGCT 59.019 57.895 9.46 0.00 0.00 4.24
24 25 1.188863 GGTTTACCGGAGTCCTGCTA 58.811 55.000 9.46 0.00 0.00 3.49
25 26 1.136500 GGTTTACCGGAGTCCTGCTAG 59.864 57.143 9.46 0.00 0.00 3.42
26 27 0.822164 TTTACCGGAGTCCTGCTAGC 59.178 55.000 9.46 8.10 0.00 3.42
27 28 1.041447 TTACCGGAGTCCTGCTAGCC 61.041 60.000 9.46 0.00 0.00 3.93
28 29 2.923634 TACCGGAGTCCTGCTAGCCC 62.924 65.000 9.46 3.65 0.00 5.19
29 30 2.759973 CGGAGTCCTGCTAGCCCA 60.760 66.667 13.29 0.00 0.00 5.36
30 31 2.790791 CGGAGTCCTGCTAGCCCAG 61.791 68.421 13.29 3.40 0.00 4.45
31 32 1.687493 GGAGTCCTGCTAGCCCAGT 60.687 63.158 13.29 0.00 0.00 4.00
32 33 1.519719 GAGTCCTGCTAGCCCAGTG 59.480 63.158 13.29 0.00 0.00 3.66
33 34 2.124942 GTCCTGCTAGCCCAGTGC 60.125 66.667 13.29 0.00 41.71 4.40
43 44 4.473520 CCCAGTGCTACAGCCCGG 62.474 72.222 0.00 0.00 41.18 5.73
44 45 3.390521 CCAGTGCTACAGCCCGGA 61.391 66.667 0.73 0.00 41.18 5.14
45 46 2.125512 CAGTGCTACAGCCCGGAC 60.126 66.667 0.73 0.00 41.18 4.79
46 47 3.391382 AGTGCTACAGCCCGGACC 61.391 66.667 0.73 0.00 41.18 4.46
47 48 4.468689 GTGCTACAGCCCGGACCC 62.469 72.222 0.73 0.00 41.18 4.46
49 50 4.468689 GCTACAGCCCGGACCCAC 62.469 72.222 0.73 0.00 34.31 4.61
50 51 2.683933 CTACAGCCCGGACCCACT 60.684 66.667 0.73 0.00 0.00 4.00
51 52 2.203877 TACAGCCCGGACCCACTT 60.204 61.111 0.73 0.00 0.00 3.16
52 53 2.521958 CTACAGCCCGGACCCACTTG 62.522 65.000 0.73 0.00 0.00 3.16
56 57 3.636231 CCCGGACCCACTTGCTGA 61.636 66.667 0.73 0.00 0.00 4.26
57 58 2.671070 CCGGACCCACTTGCTGAT 59.329 61.111 0.00 0.00 0.00 2.90
58 59 1.746615 CCGGACCCACTTGCTGATG 60.747 63.158 0.00 0.00 0.00 3.07
59 60 1.296392 CGGACCCACTTGCTGATGA 59.704 57.895 0.00 0.00 0.00 2.92
60 61 1.021390 CGGACCCACTTGCTGATGAC 61.021 60.000 0.00 0.00 0.00 3.06
61 62 0.678048 GGACCCACTTGCTGATGACC 60.678 60.000 0.00 0.00 0.00 4.02
62 63 1.003355 ACCCACTTGCTGATGACCG 60.003 57.895 0.00 0.00 0.00 4.79
63 64 1.296392 CCCACTTGCTGATGACCGA 59.704 57.895 0.00 0.00 0.00 4.69
64 65 1.021390 CCCACTTGCTGATGACCGAC 61.021 60.000 0.00 0.00 0.00 4.79
65 66 0.320683 CCACTTGCTGATGACCGACA 60.321 55.000 0.00 0.00 0.00 4.35
66 67 0.792640 CACTTGCTGATGACCGACAC 59.207 55.000 0.00 0.00 0.00 3.67
67 68 0.667487 ACTTGCTGATGACCGACACG 60.667 55.000 0.00 0.00 0.00 4.49
68 69 0.667487 CTTGCTGATGACCGACACGT 60.667 55.000 0.00 0.00 0.00 4.49
69 70 0.249699 TTGCTGATGACCGACACGTT 60.250 50.000 0.00 0.00 0.00 3.99
70 71 0.666274 TGCTGATGACCGACACGTTC 60.666 55.000 0.00 0.00 0.00 3.95
79 80 3.550656 GACACGTTCGAAGCTGGG 58.449 61.111 0.00 0.00 0.00 4.45
80 81 1.300697 GACACGTTCGAAGCTGGGT 60.301 57.895 0.00 0.00 0.00 4.51
81 82 1.282930 GACACGTTCGAAGCTGGGTC 61.283 60.000 10.51 10.51 0.00 4.46
82 83 1.300620 CACGTTCGAAGCTGGGTCA 60.301 57.895 0.00 0.00 0.00 4.02
83 84 0.670546 CACGTTCGAAGCTGGGTCAT 60.671 55.000 0.00 0.00 0.00 3.06
84 85 0.670546 ACGTTCGAAGCTGGGTCATG 60.671 55.000 0.00 0.00 0.00 3.07
85 86 1.361668 CGTTCGAAGCTGGGTCATGG 61.362 60.000 0.00 0.00 0.00 3.66
86 87 0.036388 GTTCGAAGCTGGGTCATGGA 60.036 55.000 0.00 0.00 0.00 3.41
87 88 0.911769 TTCGAAGCTGGGTCATGGAT 59.088 50.000 0.00 0.00 0.00 3.41
88 89 0.178767 TCGAAGCTGGGTCATGGATG 59.821 55.000 0.00 0.00 0.00 3.51
89 90 1.442526 CGAAGCTGGGTCATGGATGC 61.443 60.000 0.00 0.00 0.00 3.91
90 91 1.076485 AAGCTGGGTCATGGATGCC 60.076 57.895 0.00 0.00 0.00 4.40
91 92 1.578215 AAGCTGGGTCATGGATGCCT 61.578 55.000 0.00 0.00 0.00 4.75
92 93 1.826921 GCTGGGTCATGGATGCCTG 60.827 63.158 0.00 0.00 0.00 4.85
93 94 1.611419 CTGGGTCATGGATGCCTGT 59.389 57.895 0.00 0.00 0.00 4.00
94 95 0.465097 CTGGGTCATGGATGCCTGTC 60.465 60.000 0.00 0.00 0.00 3.51
95 96 1.152881 GGGTCATGGATGCCTGTCC 60.153 63.158 0.00 0.00 38.81 4.02
96 97 1.152881 GGTCATGGATGCCTGTCCC 60.153 63.158 0.00 0.00 37.48 4.46
97 98 1.639635 GGTCATGGATGCCTGTCCCT 61.640 60.000 0.00 0.00 37.48 4.20
98 99 0.465097 GTCATGGATGCCTGTCCCTG 60.465 60.000 0.00 0.00 37.48 4.45
99 100 0.915872 TCATGGATGCCTGTCCCTGT 60.916 55.000 0.00 0.00 37.48 4.00
100 101 0.839277 CATGGATGCCTGTCCCTGTA 59.161 55.000 0.00 0.00 37.48 2.74
101 102 1.212688 CATGGATGCCTGTCCCTGTAA 59.787 52.381 0.00 0.00 37.48 2.41
102 103 0.911769 TGGATGCCTGTCCCTGTAAG 59.088 55.000 0.00 0.00 37.48 2.34
103 104 0.912486 GGATGCCTGTCCCTGTAAGT 59.088 55.000 0.00 0.00 31.82 2.24
104 105 1.134371 GGATGCCTGTCCCTGTAAGTC 60.134 57.143 0.00 0.00 31.82 3.01
105 106 1.834263 GATGCCTGTCCCTGTAAGTCT 59.166 52.381 0.00 0.00 0.00 3.24
106 107 0.976641 TGCCTGTCCCTGTAAGTCTG 59.023 55.000 0.00 0.00 0.00 3.51
107 108 0.977395 GCCTGTCCCTGTAAGTCTGT 59.023 55.000 0.00 0.00 0.00 3.41
108 109 1.338200 GCCTGTCCCTGTAAGTCTGTG 60.338 57.143 0.00 0.00 0.00 3.66
109 110 1.338200 CCTGTCCCTGTAAGTCTGTGC 60.338 57.143 0.00 0.00 0.00 4.57
110 111 0.685097 TGTCCCTGTAAGTCTGTGCC 59.315 55.000 0.00 0.00 0.00 5.01
111 112 0.685097 GTCCCTGTAAGTCTGTGCCA 59.315 55.000 0.00 0.00 0.00 4.92
112 113 0.685097 TCCCTGTAAGTCTGTGCCAC 59.315 55.000 0.00 0.00 0.00 5.01
113 114 0.687354 CCCTGTAAGTCTGTGCCACT 59.313 55.000 0.00 0.00 0.00 4.00
114 115 1.072331 CCCTGTAAGTCTGTGCCACTT 59.928 52.381 0.00 0.00 37.80 3.16
115 116 2.487265 CCCTGTAAGTCTGTGCCACTTT 60.487 50.000 0.00 0.00 35.63 2.66
116 117 2.549754 CCTGTAAGTCTGTGCCACTTTG 59.450 50.000 0.00 0.00 35.63 2.77
117 118 2.549754 CTGTAAGTCTGTGCCACTTTGG 59.450 50.000 0.00 0.00 41.55 3.28
118 119 1.880027 GTAAGTCTGTGCCACTTTGGG 59.120 52.381 0.00 0.00 38.19 4.12
119 120 0.258774 AAGTCTGTGCCACTTTGGGT 59.741 50.000 0.00 0.00 38.19 4.51
120 121 0.258774 AGTCTGTGCCACTTTGGGTT 59.741 50.000 0.00 0.00 38.19 4.11
121 122 1.111277 GTCTGTGCCACTTTGGGTTT 58.889 50.000 0.00 0.00 38.19 3.27
122 123 2.092103 AGTCTGTGCCACTTTGGGTTTA 60.092 45.455 0.00 0.00 38.19 2.01
123 124 2.034179 GTCTGTGCCACTTTGGGTTTAC 59.966 50.000 0.00 0.00 38.19 2.01
124 125 1.001815 CTGTGCCACTTTGGGTTTACG 60.002 52.381 0.00 0.00 38.19 3.18
125 126 1.310904 GTGCCACTTTGGGTTTACGA 58.689 50.000 0.00 0.00 38.19 3.43
126 127 1.002142 GTGCCACTTTGGGTTTACGAC 60.002 52.381 0.00 0.00 38.19 4.34
127 128 1.134037 TGCCACTTTGGGTTTACGACT 60.134 47.619 0.00 0.00 38.19 4.18
128 129 2.104451 TGCCACTTTGGGTTTACGACTA 59.896 45.455 0.00 0.00 38.19 2.59
129 130 2.740447 GCCACTTTGGGTTTACGACTAG 59.260 50.000 0.00 0.00 38.19 2.57
130 131 3.804759 GCCACTTTGGGTTTACGACTAGT 60.805 47.826 0.00 0.00 38.19 2.57
131 132 3.992427 CCACTTTGGGTTTACGACTAGTC 59.008 47.826 13.18 13.18 32.67 2.59
132 133 4.501915 CCACTTTGGGTTTACGACTAGTCA 60.502 45.833 22.37 0.95 32.67 3.41
133 134 5.235516 CACTTTGGGTTTACGACTAGTCAT 58.764 41.667 22.37 10.40 0.00 3.06
134 135 5.120208 CACTTTGGGTTTACGACTAGTCATG 59.880 44.000 22.37 9.72 0.00 3.07
135 136 4.877378 TTGGGTTTACGACTAGTCATGT 57.123 40.909 22.37 14.86 0.00 3.21
136 137 4.445452 TGGGTTTACGACTAGTCATGTC 57.555 45.455 22.37 8.28 0.00 3.06
137 138 3.827876 TGGGTTTACGACTAGTCATGTCA 59.172 43.478 22.37 8.10 34.37 3.58
138 139 4.082408 TGGGTTTACGACTAGTCATGTCAG 60.082 45.833 22.37 7.59 34.37 3.51
139 140 3.858238 GGTTTACGACTAGTCATGTCAGC 59.142 47.826 22.37 9.28 34.37 4.26
140 141 3.777465 TTACGACTAGTCATGTCAGCC 57.223 47.619 22.37 0.00 34.37 4.85
141 142 0.818296 ACGACTAGTCATGTCAGCCC 59.182 55.000 22.37 0.00 34.37 5.19
142 143 0.248661 CGACTAGTCATGTCAGCCCG 60.249 60.000 22.37 1.38 34.37 6.13
143 144 0.103208 GACTAGTCATGTCAGCCCGG 59.897 60.000 18.20 0.00 34.80 5.73
144 145 1.330655 ACTAGTCATGTCAGCCCGGG 61.331 60.000 19.09 19.09 0.00 5.73
145 146 2.650813 CTAGTCATGTCAGCCCGGGC 62.651 65.000 39.29 39.29 42.33 6.13
157 158 2.789409 GCCCGGGCTCTTTATCATAT 57.211 50.000 38.76 0.00 38.26 1.78
158 159 2.359900 GCCCGGGCTCTTTATCATATG 58.640 52.381 38.76 0.00 38.26 1.78
159 160 2.941415 GCCCGGGCTCTTTATCATATGG 60.941 54.545 38.76 0.00 38.26 2.74
160 161 2.571653 CCCGGGCTCTTTATCATATGGA 59.428 50.000 8.08 0.00 0.00 3.41
161 162 3.200825 CCCGGGCTCTTTATCATATGGAT 59.799 47.826 8.08 0.00 40.14 3.41
162 163 4.194640 CCGGGCTCTTTATCATATGGATG 58.805 47.826 2.13 0.00 36.72 3.51
163 164 3.624861 CGGGCTCTTTATCATATGGATGC 59.375 47.826 2.13 0.00 36.72 3.91
164 165 4.624843 CGGGCTCTTTATCATATGGATGCT 60.625 45.833 2.13 0.00 36.72 3.79
165 166 5.395657 CGGGCTCTTTATCATATGGATGCTA 60.396 44.000 2.13 0.00 36.72 3.49
166 167 6.054295 GGGCTCTTTATCATATGGATGCTAG 58.946 44.000 2.13 0.00 36.72 3.42
167 168 5.526846 GGCTCTTTATCATATGGATGCTAGC 59.473 44.000 8.10 8.10 36.72 3.42
168 169 5.233902 GCTCTTTATCATATGGATGCTAGCG 59.766 44.000 10.77 0.00 36.72 4.26
169 170 6.530019 TCTTTATCATATGGATGCTAGCGA 57.470 37.500 10.77 0.00 36.72 4.93
170 171 6.333416 TCTTTATCATATGGATGCTAGCGAC 58.667 40.000 10.77 6.33 36.72 5.19
171 172 5.659440 TTATCATATGGATGCTAGCGACA 57.341 39.130 10.77 9.20 36.72 4.35
172 173 3.303881 TCATATGGATGCTAGCGACAC 57.696 47.619 10.77 0.81 32.62 3.67
173 174 2.893489 TCATATGGATGCTAGCGACACT 59.107 45.455 10.77 0.00 32.62 3.55
174 175 4.079253 TCATATGGATGCTAGCGACACTA 58.921 43.478 10.77 0.00 32.62 2.74
175 176 4.706962 TCATATGGATGCTAGCGACACTAT 59.293 41.667 10.77 7.20 32.62 2.12
176 177 3.584406 ATGGATGCTAGCGACACTATC 57.416 47.619 10.77 6.09 0.00 2.08
177 178 2.306847 TGGATGCTAGCGACACTATCA 58.693 47.619 10.77 0.00 31.82 2.15
178 179 2.893489 TGGATGCTAGCGACACTATCAT 59.107 45.455 10.77 0.00 39.77 2.45
179 180 4.079253 TGGATGCTAGCGACACTATCATA 58.921 43.478 10.77 0.00 37.73 2.15
180 181 4.706962 TGGATGCTAGCGACACTATCATAT 59.293 41.667 10.77 0.00 37.73 1.78
181 182 5.885912 TGGATGCTAGCGACACTATCATATA 59.114 40.000 10.77 0.00 37.73 0.86
182 183 6.183360 TGGATGCTAGCGACACTATCATATAC 60.183 42.308 10.77 0.00 37.73 1.47
183 184 5.217895 TGCTAGCGACACTATCATATACG 57.782 43.478 10.77 0.00 0.00 3.06
184 185 4.694037 TGCTAGCGACACTATCATATACGT 59.306 41.667 10.77 0.00 0.00 3.57
185 186 5.022653 GCTAGCGACACTATCATATACGTG 58.977 45.833 0.00 0.00 0.00 4.49
186 187 5.163884 GCTAGCGACACTATCATATACGTGA 60.164 44.000 0.00 0.00 0.00 4.35
187 188 5.284428 AGCGACACTATCATATACGTGAG 57.716 43.478 0.00 0.00 0.00 3.51
188 189 3.846896 GCGACACTATCATATACGTGAGC 59.153 47.826 0.00 0.00 0.00 4.26
189 190 4.404324 CGACACTATCATATACGTGAGCC 58.596 47.826 0.00 0.00 0.00 4.70
190 191 4.083484 CGACACTATCATATACGTGAGCCA 60.083 45.833 0.00 0.00 0.00 4.75
191 192 5.562113 CGACACTATCATATACGTGAGCCAA 60.562 44.000 0.00 0.00 0.00 4.52
192 193 5.529791 ACACTATCATATACGTGAGCCAAC 58.470 41.667 0.00 0.00 0.00 3.77
193 194 5.068591 ACACTATCATATACGTGAGCCAACA 59.931 40.000 0.00 0.00 0.00 3.33
194 195 5.631096 CACTATCATATACGTGAGCCAACAG 59.369 44.000 0.00 0.00 0.00 3.16
195 196 3.452755 TCATATACGTGAGCCAACAGG 57.547 47.619 0.00 0.00 0.00 4.00
204 205 4.999939 GCCAACAGGCGCAAACGG 63.000 66.667 10.83 3.45 38.93 4.44
205 206 3.591835 CCAACAGGCGCAAACGGT 61.592 61.111 10.83 0.00 40.57 4.83
206 207 2.051345 CAACAGGCGCAAACGGTC 60.051 61.111 10.83 0.00 40.57 4.79
207 208 3.284449 AACAGGCGCAAACGGTCC 61.284 61.111 10.83 0.00 40.57 4.46
213 214 4.992511 CGCAAACGGTCCCGGGAA 62.993 66.667 28.84 6.65 44.69 3.97
214 215 2.595172 GCAAACGGTCCCGGGAAA 60.595 61.111 28.84 0.00 44.69 3.13
215 216 2.194889 GCAAACGGTCCCGGGAAAA 61.195 57.895 28.84 0.00 44.69 2.29
216 217 1.953772 CAAACGGTCCCGGGAAAAG 59.046 57.895 28.84 21.49 44.69 2.27
217 218 1.228337 AAACGGTCCCGGGAAAAGG 60.228 57.895 28.84 16.97 44.69 3.11
218 219 1.998444 AAACGGTCCCGGGAAAAGGT 61.998 55.000 28.84 17.68 44.69 3.50
219 220 1.126948 AACGGTCCCGGGAAAAGGTA 61.127 55.000 28.84 0.00 44.69 3.08
220 221 1.126948 ACGGTCCCGGGAAAAGGTAA 61.127 55.000 28.84 0.00 44.69 2.85
221 222 0.392060 CGGTCCCGGGAAAAGGTAAG 60.392 60.000 28.84 6.57 35.56 2.34
222 223 0.986527 GGTCCCGGGAAAAGGTAAGA 59.013 55.000 28.84 0.00 0.00 2.10
223 224 1.339438 GGTCCCGGGAAAAGGTAAGAC 60.339 57.143 28.84 9.16 0.00 3.01
224 225 0.609662 TCCCGGGAAAAGGTAAGACG 59.390 55.000 24.50 0.00 0.00 4.18
225 226 0.609662 CCCGGGAAAAGGTAAGACGA 59.390 55.000 18.48 0.00 0.00 4.20
226 227 1.673923 CCCGGGAAAAGGTAAGACGAC 60.674 57.143 18.48 0.00 0.00 4.34
227 228 1.001181 CCGGGAAAAGGTAAGACGACA 59.999 52.381 0.00 0.00 0.00 4.35
228 229 2.064014 CGGGAAAAGGTAAGACGACAC 58.936 52.381 0.00 0.00 0.00 3.67
229 230 2.420642 GGGAAAAGGTAAGACGACACC 58.579 52.381 0.00 0.00 34.86 4.16
230 231 2.420642 GGAAAAGGTAAGACGACACCC 58.579 52.381 0.00 0.00 35.25 4.61
231 232 2.064014 GAAAAGGTAAGACGACACCCG 58.936 52.381 0.00 0.00 45.44 5.28
252 253 2.585247 GGATACCGTGCGTGAGGC 60.585 66.667 0.00 0.00 43.96 4.70
253 254 2.585247 GATACCGTGCGTGAGGCC 60.585 66.667 0.00 0.00 42.61 5.19
254 255 4.508128 ATACCGTGCGTGAGGCCG 62.508 66.667 0.00 0.00 42.61 6.13
262 263 2.664851 CGTGAGGCCGCAAAGTGA 60.665 61.111 12.05 0.00 0.00 3.41
263 264 2.034879 CGTGAGGCCGCAAAGTGAT 61.035 57.895 12.05 0.00 0.00 3.06
264 265 0.739462 CGTGAGGCCGCAAAGTGATA 60.739 55.000 12.05 0.00 0.00 2.15
265 266 1.668419 GTGAGGCCGCAAAGTGATAT 58.332 50.000 12.05 0.00 0.00 1.63
266 267 1.331756 GTGAGGCCGCAAAGTGATATG 59.668 52.381 12.05 0.00 0.00 1.78
267 268 1.209261 TGAGGCCGCAAAGTGATATGA 59.791 47.619 6.75 0.00 0.00 2.15
268 269 1.869767 GAGGCCGCAAAGTGATATGAG 59.130 52.381 0.00 0.00 0.00 2.90
269 270 0.947244 GGCCGCAAAGTGATATGAGG 59.053 55.000 0.00 0.00 39.25 3.86
270 271 1.668419 GCCGCAAAGTGATATGAGGT 58.332 50.000 0.00 0.00 38.58 3.85
271 272 1.331756 GCCGCAAAGTGATATGAGGTG 59.668 52.381 0.00 0.00 38.58 4.00
272 273 2.632377 CCGCAAAGTGATATGAGGTGT 58.368 47.619 0.00 0.00 32.55 4.16
273 274 3.009723 CCGCAAAGTGATATGAGGTGTT 58.990 45.455 0.00 0.00 32.55 3.32
274 275 4.188462 CCGCAAAGTGATATGAGGTGTTA 58.812 43.478 0.00 0.00 32.55 2.41
275 276 4.034048 CCGCAAAGTGATATGAGGTGTTAC 59.966 45.833 0.00 0.00 32.55 2.50
276 277 4.034048 CGCAAAGTGATATGAGGTGTTACC 59.966 45.833 0.00 0.00 38.99 2.85
277 278 4.941263 GCAAAGTGATATGAGGTGTTACCA 59.059 41.667 0.28 0.00 41.95 3.25
278 279 5.065218 GCAAAGTGATATGAGGTGTTACCAG 59.935 44.000 0.28 0.00 41.95 4.00
279 280 4.408182 AGTGATATGAGGTGTTACCAGC 57.592 45.455 0.28 0.00 41.95 4.85
289 290 3.643763 GGTGTTACCAGCTAGATCGATG 58.356 50.000 0.54 0.00 38.42 3.84
290 291 3.068307 GGTGTTACCAGCTAGATCGATGT 59.932 47.826 0.54 0.00 38.42 3.06
291 292 4.045104 GTGTTACCAGCTAGATCGATGTG 58.955 47.826 0.54 0.00 0.00 3.21
292 293 3.951680 TGTTACCAGCTAGATCGATGTGA 59.048 43.478 0.54 0.00 0.00 3.58
293 294 4.202020 TGTTACCAGCTAGATCGATGTGAC 60.202 45.833 0.54 0.01 0.00 3.67
294 295 2.379005 ACCAGCTAGATCGATGTGACA 58.621 47.619 0.54 0.00 0.00 3.58
295 296 2.961741 ACCAGCTAGATCGATGTGACAT 59.038 45.455 0.54 0.00 0.00 3.06
296 297 3.005261 ACCAGCTAGATCGATGTGACATC 59.995 47.826 15.36 15.36 0.00 3.06
297 298 3.232771 CAGCTAGATCGATGTGACATCG 58.767 50.000 34.77 34.77 42.38 3.84
308 309 2.806237 GACATCGAGTCGGGGTCC 59.194 66.667 20.03 8.02 37.53 4.46
309 310 1.753463 GACATCGAGTCGGGGTCCT 60.753 63.158 20.03 0.00 37.53 3.85
310 311 2.005960 GACATCGAGTCGGGGTCCTG 62.006 65.000 20.03 9.27 37.53 3.86
311 312 1.753078 CATCGAGTCGGGGTCCTGA 60.753 63.158 13.54 0.00 0.00 3.86
326 327 4.074970 GGTCCTGACACAATGTTTCAGAT 58.925 43.478 25.87 0.00 41.27 2.90
445 446 1.790755 CCTGCACTTGTAGCGTTGTA 58.209 50.000 0.00 0.00 33.85 2.41
511 512 4.214980 ACGATCGATGGATGCATTTTTC 57.785 40.909 24.34 0.00 31.51 2.29
1195 1229 4.402851 GCACCAGCAATCCAGACA 57.597 55.556 0.00 0.00 41.58 3.41
1505 1548 7.815068 GCAATACTAGTTCTGAAGTTCTGAAGA 59.185 37.037 21.45 13.45 35.48 2.87
1512 1555 8.286191 AGTTCTGAAGTTCTGAAGATTTTGTT 57.714 30.769 21.45 2.72 35.48 2.83
1581 1624 7.064016 GCAATAGTTCTGAAGTTCTGAAGTAGG 59.936 40.741 28.86 25.18 40.82 3.18
1658 1709 8.485976 AAGTTTCTCAAGTAGATGCAATAGTC 57.514 34.615 0.00 0.00 33.05 2.59
1921 2008 1.349357 GGAGGTGACAAGGAGAAGCTT 59.651 52.381 0.00 0.00 0.00 3.74
1952 2039 0.036765 TTTGGAGATCAACCCCGACG 60.037 55.000 0.00 0.00 34.67 5.12
2071 2158 6.128172 CGTACAAGGAAATGAAGCAGAAGATT 60.128 38.462 0.00 0.00 0.00 2.40
2230 2317 1.139654 CAAGAGGCGGAGGATCATTGA 59.860 52.381 0.00 0.00 36.25 2.57
3056 3167 1.838846 GGGATCTGGCGATGGAGGA 60.839 63.158 0.00 0.00 0.00 3.71
3202 3360 2.903547 GCGACGTGGGTTTGCATGT 61.904 57.895 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.136500 CTAGCAGGACTCCGGTAAACC 59.864 57.143 0.00 1.24 0.00 3.27
6 7 1.471153 GCTAGCAGGACTCCGGTAAAC 60.471 57.143 10.63 0.00 0.00 2.01
7 8 0.822164 GCTAGCAGGACTCCGGTAAA 59.178 55.000 10.63 0.00 0.00 2.01
8 9 1.041447 GGCTAGCAGGACTCCGGTAA 61.041 60.000 18.24 0.00 0.00 2.85
9 10 1.455217 GGCTAGCAGGACTCCGGTA 60.455 63.158 18.24 0.00 0.00 4.02
10 11 2.760385 GGCTAGCAGGACTCCGGT 60.760 66.667 18.24 0.00 0.00 5.28
11 12 3.541713 GGGCTAGCAGGACTCCGG 61.542 72.222 18.24 0.00 0.00 5.14
12 13 2.759973 TGGGCTAGCAGGACTCCG 60.760 66.667 18.24 0.00 0.00 4.63
13 14 1.687493 ACTGGGCTAGCAGGACTCC 60.687 63.158 18.24 7.80 0.00 3.85
14 15 1.519719 CACTGGGCTAGCAGGACTC 59.480 63.158 18.24 0.00 0.00 3.36
15 16 2.664081 GCACTGGGCTAGCAGGACT 61.664 63.158 18.24 0.00 40.25 3.85
16 17 2.124942 GCACTGGGCTAGCAGGAC 60.125 66.667 18.24 4.03 40.25 3.85
26 27 4.473520 CCGGGCTGTAGCACTGGG 62.474 72.222 4.43 0.00 43.67 4.45
27 28 3.390521 TCCGGGCTGTAGCACTGG 61.391 66.667 0.00 7.49 43.67 4.00
28 29 2.125512 GTCCGGGCTGTAGCACTG 60.126 66.667 0.00 0.00 43.67 3.66
29 30 3.391382 GGTCCGGGCTGTAGCACT 61.391 66.667 5.77 0.00 43.67 4.40
30 31 4.468689 GGGTCCGGGCTGTAGCAC 62.469 72.222 5.77 0.38 44.36 4.40
32 33 4.468689 GTGGGTCCGGGCTGTAGC 62.469 72.222 5.77 0.00 41.14 3.58
33 34 2.291043 AAGTGGGTCCGGGCTGTAG 61.291 63.158 5.77 0.00 0.00 2.74
34 35 2.203877 AAGTGGGTCCGGGCTGTA 60.204 61.111 5.77 0.00 0.00 2.74
35 36 3.953775 CAAGTGGGTCCGGGCTGT 61.954 66.667 5.77 0.00 0.00 4.40
39 40 2.971598 ATCAGCAAGTGGGTCCGGG 61.972 63.158 0.00 0.00 0.00 5.73
40 41 1.746615 CATCAGCAAGTGGGTCCGG 60.747 63.158 0.00 0.00 0.00 5.14
41 42 1.021390 GTCATCAGCAAGTGGGTCCG 61.021 60.000 0.00 0.00 0.00 4.79
42 43 0.678048 GGTCATCAGCAAGTGGGTCC 60.678 60.000 0.00 0.00 0.00 4.46
43 44 1.021390 CGGTCATCAGCAAGTGGGTC 61.021 60.000 0.00 0.00 0.00 4.46
44 45 1.003355 CGGTCATCAGCAAGTGGGT 60.003 57.895 0.00 0.00 0.00 4.51
45 46 1.021390 GTCGGTCATCAGCAAGTGGG 61.021 60.000 0.00 0.00 0.00 4.61
46 47 0.320683 TGTCGGTCATCAGCAAGTGG 60.321 55.000 0.00 0.00 0.00 4.00
47 48 0.792640 GTGTCGGTCATCAGCAAGTG 59.207 55.000 0.00 0.00 0.00 3.16
48 49 0.667487 CGTGTCGGTCATCAGCAAGT 60.667 55.000 0.00 0.00 0.00 3.16
49 50 0.667487 ACGTGTCGGTCATCAGCAAG 60.667 55.000 0.00 0.00 0.00 4.01
50 51 0.249699 AACGTGTCGGTCATCAGCAA 60.250 50.000 0.00 0.00 0.00 3.91
51 52 0.666274 GAACGTGTCGGTCATCAGCA 60.666 55.000 2.27 0.00 43.67 4.41
52 53 1.674611 CGAACGTGTCGGTCATCAGC 61.675 60.000 7.89 0.00 44.54 4.26
53 54 2.349843 CGAACGTGTCGGTCATCAG 58.650 57.895 7.89 0.00 44.54 2.90
54 55 4.544762 CGAACGTGTCGGTCATCA 57.455 55.556 7.89 0.00 44.54 3.07
62 63 1.282930 GACCCAGCTTCGAACGTGTC 61.283 60.000 0.00 0.00 0.00 3.67
63 64 1.300697 GACCCAGCTTCGAACGTGT 60.301 57.895 0.00 0.00 0.00 4.49
64 65 0.670546 ATGACCCAGCTTCGAACGTG 60.671 55.000 0.00 0.00 0.00 4.49
65 66 0.670546 CATGACCCAGCTTCGAACGT 60.671 55.000 0.00 0.00 0.00 3.99
66 67 1.361668 CCATGACCCAGCTTCGAACG 61.362 60.000 0.00 0.00 0.00 3.95
67 68 0.036388 TCCATGACCCAGCTTCGAAC 60.036 55.000 0.00 0.00 0.00 3.95
68 69 0.911769 ATCCATGACCCAGCTTCGAA 59.088 50.000 0.00 0.00 0.00 3.71
69 70 0.178767 CATCCATGACCCAGCTTCGA 59.821 55.000 0.00 0.00 0.00 3.71
70 71 1.442526 GCATCCATGACCCAGCTTCG 61.443 60.000 0.00 0.00 0.00 3.79
71 72 1.105759 GGCATCCATGACCCAGCTTC 61.106 60.000 0.00 0.00 0.00 3.86
72 73 1.076485 GGCATCCATGACCCAGCTT 60.076 57.895 0.00 0.00 0.00 3.74
73 74 2.005266 AGGCATCCATGACCCAGCT 61.005 57.895 0.00 0.00 36.08 4.24
74 75 1.826921 CAGGCATCCATGACCCAGC 60.827 63.158 0.00 0.00 36.08 4.85
75 76 0.465097 GACAGGCATCCATGACCCAG 60.465 60.000 0.00 0.00 36.08 4.45
76 77 1.609239 GACAGGCATCCATGACCCA 59.391 57.895 0.00 0.00 36.08 4.51
77 78 1.152881 GGACAGGCATCCATGACCC 60.153 63.158 0.00 0.00 38.77 4.46
78 79 1.152881 GGGACAGGCATCCATGACC 60.153 63.158 9.72 0.00 40.96 4.02
79 80 1.918253 AGGGACAGGCATCCATGAC 59.082 57.895 9.72 0.00 40.96 3.06
80 81 4.506076 AGGGACAGGCATCCATGA 57.494 55.556 9.72 0.00 40.96 3.07
81 82 4.573210 CAGGGACAGGCATCCATG 57.427 61.111 7.89 7.89 43.58 3.66
82 83 1.492176 CTTACAGGGACAGGCATCCAT 59.508 52.381 9.72 0.00 40.96 3.41
83 84 0.911769 CTTACAGGGACAGGCATCCA 59.088 55.000 9.72 0.00 40.96 3.41
84 85 0.912486 ACTTACAGGGACAGGCATCC 59.088 55.000 0.00 0.00 38.13 3.51
85 86 1.834263 AGACTTACAGGGACAGGCATC 59.166 52.381 0.00 0.00 0.00 3.91
86 87 1.556911 CAGACTTACAGGGACAGGCAT 59.443 52.381 0.00 0.00 0.00 4.40
87 88 0.976641 CAGACTTACAGGGACAGGCA 59.023 55.000 0.00 0.00 0.00 4.75
88 89 0.977395 ACAGACTTACAGGGACAGGC 59.023 55.000 0.00 0.00 0.00 4.85
89 90 1.338200 GCACAGACTTACAGGGACAGG 60.338 57.143 0.00 0.00 0.00 4.00
90 91 1.338200 GGCACAGACTTACAGGGACAG 60.338 57.143 0.00 0.00 0.00 3.51
91 92 0.685097 GGCACAGACTTACAGGGACA 59.315 55.000 0.00 0.00 0.00 4.02
92 93 0.685097 TGGCACAGACTTACAGGGAC 59.315 55.000 0.00 0.00 0.00 4.46
93 94 0.685097 GTGGCACAGACTTACAGGGA 59.315 55.000 13.86 0.00 41.80 4.20
94 95 0.687354 AGTGGCACAGACTTACAGGG 59.313 55.000 21.41 0.00 41.80 4.45
95 96 2.549754 CAAAGTGGCACAGACTTACAGG 59.450 50.000 21.41 0.00 41.80 4.00
96 97 2.549754 CCAAAGTGGCACAGACTTACAG 59.450 50.000 21.41 0.00 41.80 2.74
97 98 2.571212 CCAAAGTGGCACAGACTTACA 58.429 47.619 21.41 0.00 41.80 2.41
98 99 1.880027 CCCAAAGTGGCACAGACTTAC 59.120 52.381 21.41 0.00 41.80 2.34
99 100 1.493022 ACCCAAAGTGGCACAGACTTA 59.507 47.619 21.41 0.00 41.80 2.24
100 101 0.258774 ACCCAAAGTGGCACAGACTT 59.741 50.000 21.41 1.75 41.80 3.01
101 102 0.258774 AACCCAAAGTGGCACAGACT 59.741 50.000 21.41 0.00 41.80 3.24
102 103 1.111277 AAACCCAAAGTGGCACAGAC 58.889 50.000 21.41 0.00 41.80 3.51
103 104 2.303175 GTAAACCCAAAGTGGCACAGA 58.697 47.619 21.41 0.00 41.80 3.41
104 105 1.001815 CGTAAACCCAAAGTGGCACAG 60.002 52.381 21.41 9.03 41.80 3.66
105 106 1.025812 CGTAAACCCAAAGTGGCACA 58.974 50.000 21.41 0.00 35.79 4.57
106 107 1.002142 GTCGTAAACCCAAAGTGGCAC 60.002 52.381 10.29 10.29 35.79 5.01
107 108 1.134037 AGTCGTAAACCCAAAGTGGCA 60.134 47.619 0.00 0.00 35.79 4.92
108 109 1.601166 AGTCGTAAACCCAAAGTGGC 58.399 50.000 0.00 0.00 35.79 5.01
109 110 3.992427 GACTAGTCGTAAACCCAAAGTGG 59.008 47.826 7.22 0.00 37.25 4.00
110 111 4.624015 TGACTAGTCGTAAACCCAAAGTG 58.376 43.478 17.85 0.00 0.00 3.16
111 112 4.942761 TGACTAGTCGTAAACCCAAAGT 57.057 40.909 17.85 0.00 0.00 2.66
112 113 5.235516 ACATGACTAGTCGTAAACCCAAAG 58.764 41.667 17.18 4.72 0.00 2.77
113 114 5.217978 ACATGACTAGTCGTAAACCCAAA 57.782 39.130 17.18 0.00 0.00 3.28
114 115 4.281435 TGACATGACTAGTCGTAAACCCAA 59.719 41.667 17.18 0.00 38.83 4.12
115 116 3.827876 TGACATGACTAGTCGTAAACCCA 59.172 43.478 17.18 8.22 38.83 4.51
116 117 4.421948 CTGACATGACTAGTCGTAAACCC 58.578 47.826 17.18 5.99 38.83 4.11
117 118 3.858238 GCTGACATGACTAGTCGTAAACC 59.142 47.826 17.18 7.55 38.83 3.27
118 119 3.858238 GGCTGACATGACTAGTCGTAAAC 59.142 47.826 17.18 11.57 38.83 2.01
119 120 3.119245 GGGCTGACATGACTAGTCGTAAA 60.119 47.826 17.18 0.00 38.83 2.01
120 121 2.426024 GGGCTGACATGACTAGTCGTAA 59.574 50.000 17.18 2.77 38.83 3.18
121 122 2.022195 GGGCTGACATGACTAGTCGTA 58.978 52.381 17.18 1.00 38.83 3.43
122 123 0.818296 GGGCTGACATGACTAGTCGT 59.182 55.000 17.85 15.05 38.83 4.34
123 124 0.248661 CGGGCTGACATGACTAGTCG 60.249 60.000 17.85 7.27 38.83 4.18
124 125 0.103208 CCGGGCTGACATGACTAGTC 59.897 60.000 16.32 16.32 36.55 2.59
125 126 1.330655 CCCGGGCTGACATGACTAGT 61.331 60.000 8.08 0.00 0.00 2.57
126 127 1.443407 CCCGGGCTGACATGACTAG 59.557 63.158 8.08 0.00 0.00 2.57
127 128 2.731571 GCCCGGGCTGACATGACTA 61.732 63.158 38.76 0.00 38.26 2.59
128 129 4.101448 GCCCGGGCTGACATGACT 62.101 66.667 38.76 0.00 38.26 3.41
138 139 2.359900 CATATGATAAAGAGCCCGGGC 58.640 52.381 39.29 39.29 42.33 6.13
139 140 2.571653 TCCATATGATAAAGAGCCCGGG 59.428 50.000 19.09 19.09 0.00 5.73
140 141 3.981071 TCCATATGATAAAGAGCCCGG 57.019 47.619 3.65 0.00 0.00 5.73
141 142 3.624861 GCATCCATATGATAAAGAGCCCG 59.375 47.826 3.65 0.00 34.84 6.13
142 143 4.853007 AGCATCCATATGATAAAGAGCCC 58.147 43.478 3.65 0.00 34.84 5.19
143 144 5.526846 GCTAGCATCCATATGATAAAGAGCC 59.473 44.000 10.63 0.00 33.75 4.70
144 145 5.233902 CGCTAGCATCCATATGATAAAGAGC 59.766 44.000 16.45 5.53 33.75 4.09
145 146 6.475076 GTCGCTAGCATCCATATGATAAAGAG 59.525 42.308 16.45 0.00 33.75 2.85
146 147 6.071391 TGTCGCTAGCATCCATATGATAAAGA 60.071 38.462 16.45 0.00 33.75 2.52
147 148 6.035435 GTGTCGCTAGCATCCATATGATAAAG 59.965 42.308 16.45 0.00 33.75 1.85
148 149 5.869344 GTGTCGCTAGCATCCATATGATAAA 59.131 40.000 16.45 0.00 33.75 1.40
149 150 5.185828 AGTGTCGCTAGCATCCATATGATAA 59.814 40.000 16.45 0.00 33.75 1.75
150 151 4.706962 AGTGTCGCTAGCATCCATATGATA 59.293 41.667 16.45 0.00 34.84 2.15
151 152 3.513119 AGTGTCGCTAGCATCCATATGAT 59.487 43.478 16.45 0.00 34.84 2.45
152 153 2.893489 AGTGTCGCTAGCATCCATATGA 59.107 45.455 16.45 0.00 34.84 2.15
153 154 3.309961 AGTGTCGCTAGCATCCATATG 57.690 47.619 16.45 0.00 36.09 1.78
154 155 4.706962 TGATAGTGTCGCTAGCATCCATAT 59.293 41.667 16.45 6.97 40.72 1.78
155 156 4.079253 TGATAGTGTCGCTAGCATCCATA 58.921 43.478 16.45 1.98 40.72 2.74
156 157 2.893489 TGATAGTGTCGCTAGCATCCAT 59.107 45.455 16.45 0.00 40.72 3.41
157 158 2.306847 TGATAGTGTCGCTAGCATCCA 58.693 47.619 16.45 4.65 40.72 3.41
162 163 5.022653 CACGTATATGATAGTGTCGCTAGC 58.977 45.833 4.06 4.06 36.67 3.42
163 164 6.404712 TCACGTATATGATAGTGTCGCTAG 57.595 41.667 0.00 0.00 36.16 3.42
164 165 5.163884 GCTCACGTATATGATAGTGTCGCTA 60.164 44.000 0.00 0.00 36.16 4.26
165 166 4.378563 GCTCACGTATATGATAGTGTCGCT 60.379 45.833 0.00 0.00 36.16 4.93
166 167 3.846896 GCTCACGTATATGATAGTGTCGC 59.153 47.826 0.00 0.00 36.16 5.19
167 168 4.083484 TGGCTCACGTATATGATAGTGTCG 60.083 45.833 0.00 0.00 36.16 4.35
168 169 5.372547 TGGCTCACGTATATGATAGTGTC 57.627 43.478 0.00 0.00 36.16 3.67
169 170 5.068591 TGTTGGCTCACGTATATGATAGTGT 59.931 40.000 0.00 0.00 36.16 3.55
170 171 5.528870 TGTTGGCTCACGTATATGATAGTG 58.471 41.667 0.00 0.00 36.06 2.74
171 172 5.279006 CCTGTTGGCTCACGTATATGATAGT 60.279 44.000 0.00 0.00 0.00 2.12
172 173 5.164233 CCTGTTGGCTCACGTATATGATAG 58.836 45.833 0.00 0.00 0.00 2.08
173 174 5.134202 CCTGTTGGCTCACGTATATGATA 57.866 43.478 0.00 0.00 0.00 2.15
174 175 3.995199 CCTGTTGGCTCACGTATATGAT 58.005 45.455 0.00 0.00 0.00 2.45
175 176 3.452755 CCTGTTGGCTCACGTATATGA 57.547 47.619 0.00 0.00 0.00 2.15
188 189 3.536498 GACCGTTTGCGCCTGTTGG 62.536 63.158 4.18 2.72 36.67 3.77
189 190 2.051345 GACCGTTTGCGCCTGTTG 60.051 61.111 4.18 0.00 36.67 3.33
190 191 3.284449 GGACCGTTTGCGCCTGTT 61.284 61.111 4.18 0.00 36.67 3.16
196 197 4.992511 TTCCCGGGACCGTTTGCG 62.993 66.667 26.87 0.00 37.81 4.85
197 198 2.137425 CTTTTCCCGGGACCGTTTGC 62.137 60.000 26.87 0.00 37.81 3.68
198 199 1.520600 CCTTTTCCCGGGACCGTTTG 61.521 60.000 26.87 10.30 37.81 2.93
199 200 1.228337 CCTTTTCCCGGGACCGTTT 60.228 57.895 26.87 0.00 37.81 3.60
200 201 1.126948 TACCTTTTCCCGGGACCGTT 61.127 55.000 26.87 9.48 37.81 4.44
201 202 1.126948 TTACCTTTTCCCGGGACCGT 61.127 55.000 26.87 18.60 37.81 4.83
202 203 0.392060 CTTACCTTTTCCCGGGACCG 60.392 60.000 26.87 14.42 39.44 4.79
203 204 0.986527 TCTTACCTTTTCCCGGGACC 59.013 55.000 26.87 0.00 0.00 4.46
204 205 1.673923 CGTCTTACCTTTTCCCGGGAC 60.674 57.143 26.87 7.18 0.00 4.46
205 206 0.609662 CGTCTTACCTTTTCCCGGGA 59.390 55.000 22.63 22.63 0.00 5.14
206 207 0.609662 TCGTCTTACCTTTTCCCGGG 59.390 55.000 16.85 16.85 0.00 5.73
207 208 1.001181 TGTCGTCTTACCTTTTCCCGG 59.999 52.381 0.00 0.00 0.00 5.73
208 209 2.064014 GTGTCGTCTTACCTTTTCCCG 58.936 52.381 0.00 0.00 0.00 5.14
209 210 2.420642 GGTGTCGTCTTACCTTTTCCC 58.579 52.381 0.00 0.00 34.11 3.97
210 211 2.420642 GGGTGTCGTCTTACCTTTTCC 58.579 52.381 0.00 0.00 37.15 3.13
211 212 2.064014 CGGGTGTCGTCTTACCTTTTC 58.936 52.381 0.00 0.00 37.15 2.29
212 213 2.159327 CGGGTGTCGTCTTACCTTTT 57.841 50.000 0.00 0.00 37.15 2.27
213 214 3.900446 CGGGTGTCGTCTTACCTTT 57.100 52.632 0.00 0.00 37.15 3.11
223 224 2.497770 GTATCCCCACGGGTGTCG 59.502 66.667 0.41 0.00 44.74 4.35
224 225 2.905681 GGTATCCCCACGGGTGTC 59.094 66.667 0.41 0.00 44.74 3.67
225 226 3.078836 CGGTATCCCCACGGGTGT 61.079 66.667 0.41 0.00 44.74 4.16
226 227 3.078836 ACGGTATCCCCACGGGTG 61.079 66.667 0.41 0.00 44.74 4.61
227 228 3.078836 CACGGTATCCCCACGGGT 61.079 66.667 0.41 0.00 44.74 5.28
228 229 4.540735 GCACGGTATCCCCACGGG 62.541 72.222 0.00 0.00 46.11 5.28
229 230 4.884257 CGCACGGTATCCCCACGG 62.884 72.222 0.00 0.00 0.00 4.94
230 231 4.137872 ACGCACGGTATCCCCACG 62.138 66.667 0.00 0.00 0.00 4.94
231 232 2.510691 CACGCACGGTATCCCCAC 60.511 66.667 0.00 0.00 0.00 4.61
232 233 2.680707 TCACGCACGGTATCCCCA 60.681 61.111 0.00 0.00 0.00 4.96
233 234 2.106332 CTCACGCACGGTATCCCC 59.894 66.667 0.00 0.00 0.00 4.81
234 235 2.106332 CCTCACGCACGGTATCCC 59.894 66.667 0.00 0.00 0.00 3.85
235 236 2.585247 GCCTCACGCACGGTATCC 60.585 66.667 0.00 0.00 37.47 2.59
236 237 2.585247 GGCCTCACGCACGGTATC 60.585 66.667 0.00 0.00 40.31 2.24
237 238 4.508128 CGGCCTCACGCACGGTAT 62.508 66.667 0.00 0.00 40.31 2.73
245 246 0.739462 TATCACTTTGCGGCCTCACG 60.739 55.000 0.00 0.00 0.00 4.35
246 247 1.331756 CATATCACTTTGCGGCCTCAC 59.668 52.381 0.00 0.00 0.00 3.51
247 248 1.209261 TCATATCACTTTGCGGCCTCA 59.791 47.619 0.00 0.00 0.00 3.86
248 249 1.869767 CTCATATCACTTTGCGGCCTC 59.130 52.381 0.00 0.00 0.00 4.70
249 250 1.475751 CCTCATATCACTTTGCGGCCT 60.476 52.381 0.00 0.00 0.00 5.19
250 251 0.947244 CCTCATATCACTTTGCGGCC 59.053 55.000 0.00 0.00 0.00 6.13
251 252 1.331756 CACCTCATATCACTTTGCGGC 59.668 52.381 0.00 0.00 0.00 6.53
252 253 2.632377 ACACCTCATATCACTTTGCGG 58.368 47.619 0.00 0.00 0.00 5.69
253 254 4.034048 GGTAACACCTCATATCACTTTGCG 59.966 45.833 0.00 0.00 34.73 4.85
254 255 4.941263 TGGTAACACCTCATATCACTTTGC 59.059 41.667 0.00 0.00 46.17 3.68
255 256 5.065218 GCTGGTAACACCTCATATCACTTTG 59.935 44.000 0.00 0.00 46.17 2.77
256 257 5.045578 AGCTGGTAACACCTCATATCACTTT 60.046 40.000 0.00 0.00 46.17 2.66
257 258 4.471386 AGCTGGTAACACCTCATATCACTT 59.529 41.667 0.00 0.00 46.17 3.16
258 259 4.033709 AGCTGGTAACACCTCATATCACT 58.966 43.478 0.00 0.00 46.17 3.41
259 260 4.408182 AGCTGGTAACACCTCATATCAC 57.592 45.455 0.00 0.00 46.17 3.06
260 261 5.454966 TCTAGCTGGTAACACCTCATATCA 58.545 41.667 0.00 0.00 46.17 2.15
261 262 6.597832 ATCTAGCTGGTAACACCTCATATC 57.402 41.667 0.00 0.00 46.17 1.63
262 263 5.184096 CGATCTAGCTGGTAACACCTCATAT 59.816 44.000 0.00 0.00 46.17 1.78
263 264 4.519350 CGATCTAGCTGGTAACACCTCATA 59.481 45.833 0.00 0.00 46.17 2.15
264 265 3.319405 CGATCTAGCTGGTAACACCTCAT 59.681 47.826 0.00 0.00 46.17 2.90
265 266 2.688446 CGATCTAGCTGGTAACACCTCA 59.312 50.000 0.00 0.00 46.17 3.86
266 267 2.950309 TCGATCTAGCTGGTAACACCTC 59.050 50.000 0.00 0.00 46.17 3.85
267 268 3.014304 TCGATCTAGCTGGTAACACCT 57.986 47.619 0.00 0.00 46.17 4.00
268 269 3.068307 ACATCGATCTAGCTGGTAACACC 59.932 47.826 0.00 0.00 46.17 4.16
269 270 4.045104 CACATCGATCTAGCTGGTAACAC 58.955 47.826 0.00 0.00 46.17 3.32
271 272 4.202020 TGTCACATCGATCTAGCTGGTAAC 60.202 45.833 0.00 0.00 0.00 2.50
272 273 3.951680 TGTCACATCGATCTAGCTGGTAA 59.048 43.478 0.00 0.00 0.00 2.85
273 274 3.551846 TGTCACATCGATCTAGCTGGTA 58.448 45.455 0.00 0.00 0.00 3.25
274 275 2.379005 TGTCACATCGATCTAGCTGGT 58.621 47.619 0.00 0.00 0.00 4.00
275 276 3.573598 GATGTCACATCGATCTAGCTGG 58.426 50.000 0.93 0.00 0.00 4.85
276 277 3.058639 TCGATGTCACATCGATCTAGCTG 60.059 47.826 33.92 7.87 44.42 4.24
277 278 3.142174 TCGATGTCACATCGATCTAGCT 58.858 45.455 33.92 0.00 44.42 3.32
278 279 3.544356 TCGATGTCACATCGATCTAGC 57.456 47.619 33.92 0.00 44.42 3.42
284 285 0.377203 CCGACTCGATGTCACATCGA 59.623 55.000 34.63 34.63 46.69 3.59
285 286 0.592500 CCCGACTCGATGTCACATCG 60.593 60.000 30.60 30.60 45.60 3.84
286 287 0.249073 CCCCGACTCGATGTCACATC 60.249 60.000 7.83 7.83 45.60 3.06
287 288 0.970937 ACCCCGACTCGATGTCACAT 60.971 55.000 13.14 0.00 45.60 3.21
288 289 1.592400 GACCCCGACTCGATGTCACA 61.592 60.000 13.14 0.00 45.60 3.58
289 290 1.139095 GACCCCGACTCGATGTCAC 59.861 63.158 13.14 0.00 45.60 3.67
290 291 2.050350 GGACCCCGACTCGATGTCA 61.050 63.158 16.91 0.00 45.60 3.58
291 292 1.753463 AGGACCCCGACTCGATGTC 60.753 63.158 0.00 5.96 42.06 3.06
292 293 2.052690 CAGGACCCCGACTCGATGT 61.053 63.158 0.00 0.00 0.00 3.06
293 294 1.753078 TCAGGACCCCGACTCGATG 60.753 63.158 0.00 0.00 0.00 3.84
294 295 1.753463 GTCAGGACCCCGACTCGAT 60.753 63.158 0.00 0.00 0.00 3.59
295 296 2.360852 GTCAGGACCCCGACTCGA 60.361 66.667 0.00 0.00 0.00 4.04
296 297 2.675423 TGTCAGGACCCCGACTCG 60.675 66.667 11.80 0.00 31.80 4.18
297 298 1.469335 TTGTGTCAGGACCCCGACTC 61.469 60.000 11.80 9.18 31.80 3.36
298 299 0.836400 ATTGTGTCAGGACCCCGACT 60.836 55.000 11.80 0.00 31.80 4.18
299 300 0.673644 CATTGTGTCAGGACCCCGAC 60.674 60.000 4.95 4.95 0.00 4.79
300 301 1.125093 ACATTGTGTCAGGACCCCGA 61.125 55.000 0.00 0.00 0.00 5.14
301 302 0.250727 AACATTGTGTCAGGACCCCG 60.251 55.000 0.00 0.00 0.00 5.73
302 303 1.886542 GAAACATTGTGTCAGGACCCC 59.113 52.381 1.92 0.00 0.00 4.95
303 304 2.554032 CTGAAACATTGTGTCAGGACCC 59.446 50.000 23.93 0.00 42.42 4.46
304 305 3.476552 TCTGAAACATTGTGTCAGGACC 58.523 45.455 28.57 0.00 45.21 4.46
305 306 4.999950 AGATCTGAAACATTGTGTCAGGAC 59.000 41.667 28.57 22.75 45.21 3.85
306 307 5.233083 AGATCTGAAACATTGTGTCAGGA 57.767 39.130 28.57 18.85 45.21 3.86
307 308 5.934043 TGTAGATCTGAAACATTGTGTCAGG 59.066 40.000 28.57 15.20 45.21 3.86
308 309 6.424812 TGTGTAGATCTGAAACATTGTGTCAG 59.575 38.462 25.17 25.17 46.17 3.51
309 310 6.287525 TGTGTAGATCTGAAACATTGTGTCA 58.712 36.000 9.30 9.30 0.00 3.58
310 311 6.785488 TGTGTAGATCTGAAACATTGTGTC 57.215 37.500 5.18 0.00 0.00 3.67
311 312 7.065085 GCTATGTGTAGATCTGAAACATTGTGT 59.935 37.037 18.92 4.67 33.67 3.72
312 313 7.064966 TGCTATGTGTAGATCTGAAACATTGTG 59.935 37.037 18.92 13.04 33.67 3.33
326 327 6.317893 TCGAAAGTAGTGATGCTATGTGTAGA 59.682 38.462 0.00 0.00 31.50 2.59
388 389 4.849813 TTTCATGACCATCAGGACAGAT 57.150 40.909 0.00 0.00 42.66 2.90
432 433 6.634837 CAGTGAGATAGATACAACGCTACAAG 59.365 42.308 0.00 0.00 0.00 3.16
445 446 4.676459 CGTGTTCTGTGCAGTGAGATAGAT 60.676 45.833 0.00 0.00 0.00 1.98
488 489 4.637483 AAAATGCATCCATCGATCGTTT 57.363 36.364 15.94 1.83 0.00 3.60
511 512 1.269206 ACAACATCAGCCAAAACAGCG 60.269 47.619 0.00 0.00 34.64 5.18
578 579 7.014518 CCATATTAAGAGATCAAAATGGCACCA 59.985 37.037 0.00 0.00 0.00 4.17
580 581 7.945134 ACCATATTAAGAGATCAAAATGGCAC 58.055 34.615 0.00 0.00 36.86 5.01
581 582 8.415553 CAACCATATTAAGAGATCAAAATGGCA 58.584 33.333 0.00 0.00 36.86 4.92
582 583 7.383300 GCAACCATATTAAGAGATCAAAATGGC 59.617 37.037 0.00 0.00 36.86 4.40
584 585 9.459640 CTGCAACCATATTAAGAGATCAAAATG 57.540 33.333 0.00 0.00 0.00 2.32
585 586 9.193806 ACTGCAACCATATTAAGAGATCAAAAT 57.806 29.630 0.00 0.00 0.00 1.82
1161 1195 2.009774 GTGCATACGACATCCAGCTTT 58.990 47.619 0.00 0.00 0.00 3.51
1195 1229 0.108138 CGGATCCTCTTGTCGGCTTT 60.108 55.000 10.75 0.00 0.00 3.51
1537 1580 8.854614 ACTATTGCATCTACTTCAGAAACTTT 57.145 30.769 0.00 0.00 36.67 2.66
1581 1624 7.861630 TCAGAACTTCAAAACTAGTATTGCAC 58.138 34.615 0.00 0.00 0.00 4.57
1658 1709 6.317391 ACTTGAGAAACTTCAGAAACTTCAGG 59.683 38.462 6.64 0.94 0.00 3.86
1921 2008 6.208599 GGTTGATCTCCAAACCAGACAATTTA 59.791 38.462 7.61 0.00 36.47 1.40
1952 2039 1.464429 CGCTGCATGTCGACGTACTC 61.464 60.000 10.54 3.60 0.00 2.59
2071 2158 5.205056 AGTTTGTGGTCCAATTCCTTGTTA 58.795 37.500 0.00 0.00 31.81 2.41
2230 2317 2.777459 CCCAGTAGTAGGGGTCATCT 57.223 55.000 0.00 0.00 42.90 2.90
3056 3167 4.335647 CGCACTGTGGCCTCCCTT 62.336 66.667 10.21 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.