Multiple sequence alignment - TraesCS6B01G348700

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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 TraesCS6B01G348700 chr6B 100.000 4385 0 0 1 4385 613290665 613295049 0.000000e+00 8098
1 TraesCS6B01G348700 chr6B 100.000 2944 0 0 4660 7603 613295324 613298267 0.000000e+00 5437
2 TraesCS6B01G348700 chr6B 90.341 176 8 4 5699 5872 112745689 112745521 9.930000e-54 222
3 TraesCS6B01G348700 chr6D 95.046 4239 116 36 197 4385 408664900 408669094 0.000000e+00 6578
4 TraesCS6B01G348700 chr6D 96.871 2109 49 11 4667 6770 408669396 408671492 0.000000e+00 3513
5 TraesCS6B01G348700 chr6D 91.778 900 47 9 6725 7603 408671492 408672385 0.000000e+00 1227
6 TraesCS6B01G348700 chr6D 89.773 176 10 3 5703 5876 406204899 406204730 1.280000e-52 219
7 TraesCS6B01G348700 chr6A 89.684 1900 104 29 260 2112 554507933 554509787 0.000000e+00 2338
8 TraesCS6B01G348700 chr6A 94.461 1336 55 11 5871 7191 554513538 554514869 0.000000e+00 2039
9 TraesCS6B01G348700 chr6A 91.317 1336 88 11 2343 3658 554510067 554511394 0.000000e+00 1799
10 TraesCS6B01G348700 chr6A 95.046 646 30 2 3738 4382 554511435 554512079 0.000000e+00 1014
11 TraesCS6B01G348700 chr6A 90.514 759 43 12 4965 5707 554512794 554513539 0.000000e+00 976
12 TraesCS6B01G348700 chr6A 90.951 431 32 5 7177 7603 554514899 554515326 2.380000e-159 573
13 TraesCS6B01G348700 chr6A 93.182 176 12 0 4687 4862 381088708 381088883 7.570000e-65 259
14 TraesCS6B01G348700 chr6A 88.587 184 13 3 5706 5887 73573911 73573734 4.620000e-52 217
15 TraesCS6B01G348700 chr6A 90.090 111 10 1 4858 4967 554512435 554512545 7.950000e-30 143
16 TraesCS6B01G348700 chr6A 85.612 139 10 6 2203 2339 554509901 554510031 3.700000e-28 137
17 TraesCS6B01G348700 chr5D 93.714 175 11 0 4688 4862 152754107 152753933 5.850000e-66 263
18 TraesCS6B01G348700 chr5D 90.341 176 14 3 5705 5879 82315849 82315676 2.130000e-55 228
19 TraesCS6B01G348700 chr2D 93.750 176 10 1 4687 4862 380416531 380416705 5.850000e-66 263
20 TraesCS6B01G348700 chr2A 92.350 183 13 1 4680 4862 515951638 515951819 7.570000e-65 259
21 TraesCS6B01G348700 chr1D 92.655 177 13 0 4686 4862 107622214 107622038 9.790000e-64 255
22 TraesCS6B01G348700 chr1D 91.228 171 7 3 5705 5874 73732255 73732418 7.680000e-55 226
23 TraesCS6B01G348700 chr1D 87.435 191 13 5 5690 5877 436432530 436432712 7.730000e-50 209
24 TraesCS6B01G348700 chr4D 92.614 176 13 0 4687 4862 108856765 108856590 3.520000e-63 254
25 TraesCS6B01G348700 chr4D 92.614 176 13 0 4687 4862 242938959 242938784 3.520000e-63 254
26 TraesCS6B01G348700 chr4D 90.426 188 17 1 4676 4862 248930101 248930288 5.890000e-61 246
27 TraesCS6B01G348700 chr4D 89.205 176 12 2 5698 5872 460624 460793 5.980000e-51 213
28 TraesCS6B01G348700 chr3D 91.279 172 7 3 5706 5876 397162706 397162542 2.130000e-55 228
29 TraesCS6B01G348700 chr1B 91.716 169 7 2 5706 5873 183877361 183877199 2.130000e-55 228
30 TraesCS6B01G348700 chr4B 90.805 174 8 3 5701 5872 483266546 483266379 7.680000e-55 226
31 TraesCS6B01G348700 chr4B 90.173 173 9 3 5702 5872 659784199 659784365 1.280000e-52 219
32 TraesCS6B01G348700 chr3B 91.667 168 7 2 5706 5872 540174929 540175090 7.680000e-55 226
33 TraesCS6B01G348700 chr7A 90.173 173 9 3 5703 5873 105168192 105168358 1.280000e-52 219
34 TraesCS6B01G348700 chr7D 89.714 175 8 4 5701 5872 235502401 235502568 1.660000e-51 215


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 TraesCS6B01G348700 chr6B 613290665 613298267 7602 False 6767.500000 8098 100.000000 1 7603 2 chr6B.!!$F1 7602
1 TraesCS6B01G348700 chr6D 408664900 408672385 7485 False 3772.666667 6578 94.565000 197 7603 3 chr6D.!!$F1 7406
2 TraesCS6B01G348700 chr6A 554507933 554515326 7393 False 1127.375000 2338 90.959375 260 7603 8 chr6A.!!$F2 7343

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
186 187 0.037790 TGATTGTCGTGCGGTGATGA 60.038 50.000 0.00 0.0 0.00 2.92 F
1480 1556 0.678684 TCACCGACCTGCTCGACATA 60.679 55.000 0.00 0.0 46.14 2.29 F
2566 2744 1.593196 GTTTCCTGTACTGTGCTGCA 58.407 50.000 0.00 0.0 0.00 4.41 F
3313 3504 1.999735 CACTACCAACAGGCATACACG 59.000 52.381 0.00 0.0 0.00 4.49 F
3895 4108 1.133823 TGGATCCCCATTGAACATCGG 60.134 52.381 9.90 0.0 37.58 4.18 F
4731 5017 1.613437 CAAACAAGTTGGGGTAGGCTG 59.387 52.381 7.96 0.0 33.18 4.85 F
5186 5722 2.223758 GCATCCTACGACCAGAGGTAAC 60.224 54.545 0.00 0.0 35.25 2.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1828 1904 2.038557 ACAACCAATAGACGAAGCCACT 59.961 45.455 0.00 0.0 0.00 4.00 R
2589 2775 0.324368 TGGATCGTAGTGGCTGTCCT 60.324 55.000 0.00 0.0 0.00 3.85 R
3895 4108 1.457346 CCTGAGAAGGCCATGTTGTC 58.543 55.000 5.01 0.0 0.00 3.18 R
4773 5059 2.421619 GAAGCTAGCTATCCATGTGCC 58.578 52.381 19.70 0.0 0.00 5.01 R
5444 5981 3.119352 GCCAAACAATGAAGGATGGAGTC 60.119 47.826 0.00 0.0 0.00 3.36 R
6302 6859 0.038251 GCAGTAAAACCTTGGCCTGC 60.038 55.000 3.32 0.0 38.58 4.85 R
7162 7786 1.596954 CGGTTTCAACTTTCAGCCACG 60.597 52.381 0.00 0.0 0.00 4.94 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
20 21 2.489938 TAAAAAGAGGCCGCATCAGT 57.510 45.000 9.88 0.00 0.00 3.41
21 22 2.489938 AAAAAGAGGCCGCATCAGTA 57.510 45.000 9.88 0.00 0.00 2.74
22 23 2.489938 AAAAGAGGCCGCATCAGTAA 57.510 45.000 9.88 0.00 0.00 2.24
23 24 2.717639 AAAGAGGCCGCATCAGTAAT 57.282 45.000 9.88 0.00 0.00 1.89
24 25 3.838244 AAAGAGGCCGCATCAGTAATA 57.162 42.857 9.88 0.00 0.00 0.98
25 26 4.357918 AAAGAGGCCGCATCAGTAATAT 57.642 40.909 9.88 0.00 0.00 1.28
26 27 4.357918 AAGAGGCCGCATCAGTAATATT 57.642 40.909 9.88 0.00 0.00 1.28
27 28 5.483685 AAGAGGCCGCATCAGTAATATTA 57.516 39.130 9.88 0.00 0.00 0.98
28 29 5.078411 AGAGGCCGCATCAGTAATATTAG 57.922 43.478 9.88 0.00 0.00 1.73
29 30 3.600388 AGGCCGCATCAGTAATATTAGC 58.400 45.455 0.00 0.00 0.00 3.09
30 31 2.678336 GGCCGCATCAGTAATATTAGCC 59.322 50.000 0.00 0.00 0.00 3.93
31 32 3.334691 GCCGCATCAGTAATATTAGCCA 58.665 45.455 0.00 0.00 0.00 4.75
32 33 3.941483 GCCGCATCAGTAATATTAGCCAT 59.059 43.478 0.00 0.00 0.00 4.40
33 34 4.396166 GCCGCATCAGTAATATTAGCCATT 59.604 41.667 0.00 0.00 0.00 3.16
34 35 5.674569 GCCGCATCAGTAATATTAGCCATTG 60.675 44.000 0.00 0.00 0.00 2.82
35 36 5.643348 CCGCATCAGTAATATTAGCCATTGA 59.357 40.000 0.00 0.00 0.00 2.57
36 37 6.183360 CCGCATCAGTAATATTAGCCATTGAG 60.183 42.308 0.00 0.00 0.00 3.02
37 38 6.369890 CGCATCAGTAATATTAGCCATTGAGT 59.630 38.462 0.00 0.00 0.00 3.41
38 39 7.412346 CGCATCAGTAATATTAGCCATTGAGTC 60.412 40.741 0.00 0.00 0.00 3.36
39 40 7.388776 GCATCAGTAATATTAGCCATTGAGTCA 59.611 37.037 0.00 0.00 0.00 3.41
40 41 9.445878 CATCAGTAATATTAGCCATTGAGTCAT 57.554 33.333 0.00 0.00 0.00 3.06
41 42 9.664332 ATCAGTAATATTAGCCATTGAGTCATC 57.336 33.333 0.00 0.00 0.00 2.92
42 43 8.097038 TCAGTAATATTAGCCATTGAGTCATCC 58.903 37.037 0.00 0.00 0.00 3.51
43 44 7.879677 CAGTAATATTAGCCATTGAGTCATCCA 59.120 37.037 0.00 0.00 0.00 3.41
44 45 8.609483 AGTAATATTAGCCATTGAGTCATCCAT 58.391 33.333 0.00 0.00 0.00 3.41
45 46 7.698506 AATATTAGCCATTGAGTCATCCATG 57.301 36.000 0.00 0.00 0.00 3.66
46 47 4.776435 TTAGCCATTGAGTCATCCATGA 57.224 40.909 5.08 0.00 31.67 3.07
58 59 4.662468 TCATCCATGACTAACAGCTCTC 57.338 45.455 0.00 0.00 0.00 3.20
59 60 4.026052 TCATCCATGACTAACAGCTCTCA 58.974 43.478 0.00 0.00 0.00 3.27
60 61 3.876274 TCCATGACTAACAGCTCTCAC 57.124 47.619 0.00 0.00 0.00 3.51
61 62 2.164422 TCCATGACTAACAGCTCTCACG 59.836 50.000 0.00 0.00 0.00 4.35
62 63 2.094494 CCATGACTAACAGCTCTCACGT 60.094 50.000 0.00 0.00 0.00 4.49
63 64 2.991434 TGACTAACAGCTCTCACGTC 57.009 50.000 0.00 0.00 0.00 4.34
64 65 2.505405 TGACTAACAGCTCTCACGTCT 58.495 47.619 0.00 0.00 0.00 4.18
65 66 3.671716 TGACTAACAGCTCTCACGTCTA 58.328 45.455 0.00 0.00 0.00 2.59
66 67 3.685272 TGACTAACAGCTCTCACGTCTAG 59.315 47.826 0.00 0.00 0.00 2.43
67 68 2.420722 ACTAACAGCTCTCACGTCTAGC 59.579 50.000 5.39 5.39 36.48 3.42
80 81 1.838943 CGTCTAGCGTCGTTAAAGAGC 59.161 52.381 0.00 0.00 35.54 4.09
81 82 2.726989 CGTCTAGCGTCGTTAAAGAGCA 60.727 50.000 12.51 2.59 35.54 4.26
82 83 2.593336 GTCTAGCGTCGTTAAAGAGCAC 59.407 50.000 12.51 0.00 0.00 4.40
83 84 1.578023 CTAGCGTCGTTAAAGAGCACG 59.422 52.381 12.51 6.29 37.77 5.34
84 85 0.318445 AGCGTCGTTAAAGAGCACGT 60.318 50.000 12.51 0.00 37.66 4.49
85 86 0.179282 GCGTCGTTAAAGAGCACGTG 60.179 55.000 12.28 12.28 37.66 4.49
86 87 0.433492 CGTCGTTAAAGAGCACGTGG 59.567 55.000 18.88 0.00 37.66 4.94
87 88 1.774639 GTCGTTAAAGAGCACGTGGA 58.225 50.000 18.88 0.00 37.66 4.02
88 89 1.719780 GTCGTTAAAGAGCACGTGGAG 59.280 52.381 18.88 0.00 37.66 3.86
89 90 1.068474 CGTTAAAGAGCACGTGGAGG 58.932 55.000 18.88 0.00 0.00 4.30
90 91 1.604693 CGTTAAAGAGCACGTGGAGGT 60.605 52.381 18.88 0.00 0.00 3.85
91 92 1.798813 GTTAAAGAGCACGTGGAGGTG 59.201 52.381 18.88 0.00 40.89 4.00
92 93 1.045407 TAAAGAGCACGTGGAGGTGT 58.955 50.000 18.88 0.00 40.08 4.16
93 94 0.532862 AAAGAGCACGTGGAGGTGTG 60.533 55.000 18.88 0.00 40.08 3.82
94 95 1.686325 AAGAGCACGTGGAGGTGTGT 61.686 55.000 18.88 0.00 40.08 3.72
95 96 1.956170 GAGCACGTGGAGGTGTGTG 60.956 63.158 18.88 0.00 40.08 3.82
96 97 2.203015 GCACGTGGAGGTGTGTGT 60.203 61.111 18.88 0.00 40.08 3.72
97 98 1.817941 GCACGTGGAGGTGTGTGTT 60.818 57.895 18.88 0.00 40.08 3.32
98 99 1.373590 GCACGTGGAGGTGTGTGTTT 61.374 55.000 18.88 0.00 40.08 2.83
99 100 0.376852 CACGTGGAGGTGTGTGTTTG 59.623 55.000 7.95 0.00 33.24 2.93
100 101 0.250793 ACGTGGAGGTGTGTGTTTGA 59.749 50.000 0.00 0.00 0.00 2.69
101 102 1.134220 ACGTGGAGGTGTGTGTTTGAT 60.134 47.619 0.00 0.00 0.00 2.57
102 103 2.103432 ACGTGGAGGTGTGTGTTTGATA 59.897 45.455 0.00 0.00 0.00 2.15
103 104 3.244422 ACGTGGAGGTGTGTGTTTGATAT 60.244 43.478 0.00 0.00 0.00 1.63
104 105 3.125146 CGTGGAGGTGTGTGTTTGATATG 59.875 47.826 0.00 0.00 0.00 1.78
105 106 4.323417 GTGGAGGTGTGTGTTTGATATGA 58.677 43.478 0.00 0.00 0.00 2.15
106 107 4.154195 GTGGAGGTGTGTGTTTGATATGAC 59.846 45.833 0.00 0.00 0.00 3.06
107 108 4.041567 TGGAGGTGTGTGTTTGATATGACT 59.958 41.667 0.00 0.00 0.00 3.41
108 109 5.247337 TGGAGGTGTGTGTTTGATATGACTA 59.753 40.000 0.00 0.00 0.00 2.59
109 110 6.170506 GGAGGTGTGTGTTTGATATGACTAA 58.829 40.000 0.00 0.00 0.00 2.24
110 111 6.823689 GGAGGTGTGTGTTTGATATGACTAAT 59.176 38.462 0.00 0.00 0.00 1.73
111 112 7.201644 GGAGGTGTGTGTTTGATATGACTAATG 60.202 40.741 0.00 0.00 0.00 1.90
112 113 7.168219 AGGTGTGTGTTTGATATGACTAATGT 58.832 34.615 0.00 0.00 0.00 2.71
113 114 8.318412 AGGTGTGTGTTTGATATGACTAATGTA 58.682 33.333 0.00 0.00 0.00 2.29
114 115 8.388103 GGTGTGTGTTTGATATGACTAATGTAC 58.612 37.037 0.00 0.00 0.00 2.90
115 116 8.388103 GTGTGTGTTTGATATGACTAATGTACC 58.612 37.037 0.00 0.00 0.00 3.34
116 117 8.097662 TGTGTGTTTGATATGACTAATGTACCA 58.902 33.333 0.00 0.00 0.00 3.25
117 118 8.941977 GTGTGTTTGATATGACTAATGTACCAA 58.058 33.333 0.00 0.00 0.00 3.67
118 119 9.161629 TGTGTTTGATATGACTAATGTACCAAG 57.838 33.333 0.00 0.00 0.00 3.61
119 120 9.378551 GTGTTTGATATGACTAATGTACCAAGA 57.621 33.333 0.00 0.00 0.00 3.02
120 121 9.952030 TGTTTGATATGACTAATGTACCAAGAA 57.048 29.630 0.00 0.00 0.00 2.52
122 123 9.952030 TTTGATATGACTAATGTACCAAGAACA 57.048 29.630 0.00 0.00 0.00 3.18
123 124 9.952030 TTGATATGACTAATGTACCAAGAACAA 57.048 29.630 0.00 0.00 0.00 2.83
124 125 9.952030 TGATATGACTAATGTACCAAGAACAAA 57.048 29.630 0.00 0.00 0.00 2.83
128 129 7.936584 TGACTAATGTACCAAGAACAAAAAGG 58.063 34.615 0.00 0.00 0.00 3.11
129 130 6.745116 ACTAATGTACCAAGAACAAAAAGGC 58.255 36.000 0.00 0.00 0.00 4.35
130 131 3.701532 TGTACCAAGAACAAAAAGGCG 57.298 42.857 0.00 0.00 0.00 5.52
131 132 3.018149 TGTACCAAGAACAAAAAGGCGT 58.982 40.909 0.00 0.00 0.00 5.68
132 133 3.444388 TGTACCAAGAACAAAAAGGCGTT 59.556 39.130 0.00 0.00 0.00 4.84
133 134 2.887337 ACCAAGAACAAAAAGGCGTTG 58.113 42.857 0.00 0.00 0.00 4.10
134 135 2.494073 ACCAAGAACAAAAAGGCGTTGA 59.506 40.909 5.76 0.00 0.00 3.18
135 136 2.857748 CCAAGAACAAAAAGGCGTTGAC 59.142 45.455 5.76 1.07 0.00 3.18
136 137 2.468532 AGAACAAAAAGGCGTTGACG 57.531 45.000 0.00 0.00 43.27 4.35
137 138 1.741145 AGAACAAAAAGGCGTTGACGT 59.259 42.857 5.36 0.00 42.22 4.34
138 139 2.106418 GAACAAAAAGGCGTTGACGTC 58.894 47.619 9.11 9.11 45.56 4.34
146 147 4.657824 CGTTGACGTCGGTGGCCT 62.658 66.667 11.62 0.00 34.11 5.19
147 148 2.737376 GTTGACGTCGGTGGCCTC 60.737 66.667 11.62 0.00 0.00 4.70
148 149 3.998672 TTGACGTCGGTGGCCTCC 61.999 66.667 14.20 14.20 0.00 4.30
160 161 4.760047 GCCTCCGCCTCGCTTCAA 62.760 66.667 0.00 0.00 0.00 2.69
161 162 2.187946 CCTCCGCCTCGCTTCAAT 59.812 61.111 0.00 0.00 0.00 2.57
162 163 2.176273 CCTCCGCCTCGCTTCAATG 61.176 63.158 0.00 0.00 0.00 2.82
163 164 1.448540 CTCCGCCTCGCTTCAATGT 60.449 57.895 0.00 0.00 0.00 2.71
164 165 1.003839 TCCGCCTCGCTTCAATGTT 60.004 52.632 0.00 0.00 0.00 2.71
165 166 0.605319 TCCGCCTCGCTTCAATGTTT 60.605 50.000 0.00 0.00 0.00 2.83
166 167 0.454957 CCGCCTCGCTTCAATGTTTG 60.455 55.000 0.00 0.00 0.00 2.93
167 168 0.238289 CGCCTCGCTTCAATGTTTGT 59.762 50.000 0.00 0.00 0.00 2.83
168 169 1.689959 GCCTCGCTTCAATGTTTGTG 58.310 50.000 0.00 0.00 0.00 3.33
169 170 1.266718 GCCTCGCTTCAATGTTTGTGA 59.733 47.619 0.00 0.00 0.00 3.58
170 171 2.095059 GCCTCGCTTCAATGTTTGTGAT 60.095 45.455 0.00 0.00 0.00 3.06
171 172 3.612479 GCCTCGCTTCAATGTTTGTGATT 60.612 43.478 0.00 0.00 0.00 2.57
172 173 3.916172 CCTCGCTTCAATGTTTGTGATTG 59.084 43.478 0.00 0.00 32.91 2.67
173 174 4.539870 CTCGCTTCAATGTTTGTGATTGT 58.460 39.130 0.00 0.00 33.33 2.71
174 175 4.536065 TCGCTTCAATGTTTGTGATTGTC 58.464 39.130 0.00 0.00 33.33 3.18
175 176 3.358700 CGCTTCAATGTTTGTGATTGTCG 59.641 43.478 0.00 0.00 33.33 4.35
176 177 4.290155 GCTTCAATGTTTGTGATTGTCGT 58.710 39.130 0.00 0.00 33.33 4.34
177 178 4.146961 GCTTCAATGTTTGTGATTGTCGTG 59.853 41.667 0.00 0.00 33.33 4.35
178 179 3.626977 TCAATGTTTGTGATTGTCGTGC 58.373 40.909 0.00 0.00 33.33 5.34
179 180 2.314561 ATGTTTGTGATTGTCGTGCG 57.685 45.000 0.00 0.00 0.00 5.34
180 181 0.306228 TGTTTGTGATTGTCGTGCGG 59.694 50.000 0.00 0.00 0.00 5.69
181 182 0.306533 GTTTGTGATTGTCGTGCGGT 59.693 50.000 0.00 0.00 0.00 5.68
182 183 0.306228 TTTGTGATTGTCGTGCGGTG 59.694 50.000 0.00 0.00 0.00 4.94
183 184 0.530870 TTGTGATTGTCGTGCGGTGA 60.531 50.000 0.00 0.00 0.00 4.02
184 185 0.320334 TGTGATTGTCGTGCGGTGAT 60.320 50.000 0.00 0.00 0.00 3.06
185 186 0.095245 GTGATTGTCGTGCGGTGATG 59.905 55.000 0.00 0.00 0.00 3.07
186 187 0.037790 TGATTGTCGTGCGGTGATGA 60.038 50.000 0.00 0.00 0.00 2.92
187 188 1.075542 GATTGTCGTGCGGTGATGAA 58.924 50.000 0.00 0.00 0.00 2.57
188 189 1.665679 GATTGTCGTGCGGTGATGAAT 59.334 47.619 0.00 0.00 0.00 2.57
189 190 2.371910 TTGTCGTGCGGTGATGAATA 57.628 45.000 0.00 0.00 0.00 1.75
190 191 1.921243 TGTCGTGCGGTGATGAATAG 58.079 50.000 0.00 0.00 0.00 1.73
191 192 1.474879 TGTCGTGCGGTGATGAATAGA 59.525 47.619 0.00 0.00 0.00 1.98
192 193 2.100749 TGTCGTGCGGTGATGAATAGAT 59.899 45.455 0.00 0.00 0.00 1.98
193 194 3.316868 TGTCGTGCGGTGATGAATAGATA 59.683 43.478 0.00 0.00 0.00 1.98
194 195 3.914966 GTCGTGCGGTGATGAATAGATAG 59.085 47.826 0.00 0.00 0.00 2.08
195 196 3.818773 TCGTGCGGTGATGAATAGATAGA 59.181 43.478 0.00 0.00 0.00 1.98
196 197 4.459337 TCGTGCGGTGATGAATAGATAGAT 59.541 41.667 0.00 0.00 0.00 1.98
197 198 5.048013 TCGTGCGGTGATGAATAGATAGATT 60.048 40.000 0.00 0.00 0.00 2.40
198 199 5.635280 CGTGCGGTGATGAATAGATAGATTT 59.365 40.000 0.00 0.00 0.00 2.17
199 200 6.146184 CGTGCGGTGATGAATAGATAGATTTT 59.854 38.462 0.00 0.00 0.00 1.82
200 201 7.307396 CGTGCGGTGATGAATAGATAGATTTTT 60.307 37.037 0.00 0.00 0.00 1.94
241 242 4.761975 TGACTAATAACGGTTGGGCTTAG 58.238 43.478 3.07 7.88 0.00 2.18
242 243 4.223477 TGACTAATAACGGTTGGGCTTAGT 59.777 41.667 3.07 10.60 33.40 2.24
243 244 5.421693 TGACTAATAACGGTTGGGCTTAGTA 59.578 40.000 3.07 0.56 31.49 1.82
245 246 6.892485 ACTAATAACGGTTGGGCTTAGTATT 58.108 36.000 3.07 0.00 30.02 1.89
246 247 6.764560 ACTAATAACGGTTGGGCTTAGTATTG 59.235 38.462 3.07 0.00 30.02 1.90
247 248 3.706600 AACGGTTGGGCTTAGTATTGA 57.293 42.857 0.00 0.00 0.00 2.57
248 249 3.261981 ACGGTTGGGCTTAGTATTGAG 57.738 47.619 0.00 0.00 0.00 3.02
255 256 5.871396 TGGGCTTAGTATTGAGTTAGGAG 57.129 43.478 0.00 0.00 0.00 3.69
300 301 5.930837 ACATTTCTCCAACCAAAGAACAA 57.069 34.783 0.00 0.00 31.46 2.83
324 325 3.307242 CGTTAGAACAATGCAGAGTAGCC 59.693 47.826 0.00 0.00 0.00 3.93
328 329 1.021390 ACAATGCAGAGTAGCCGCAC 61.021 55.000 0.00 0.00 38.73 5.34
368 378 1.450312 CTCTCCGGCGCCATCTTTT 60.450 57.895 28.98 0.00 0.00 2.27
465 476 3.308053 CCAGCACGATCATCACTAACTTG 59.692 47.826 0.00 0.00 0.00 3.16
482 493 2.296471 ACTTGTTCGACCCAGAGTACTG 59.704 50.000 0.00 0.00 43.12 2.74
533 550 7.763071 GCAAATCCAGCAGAAATAGAAGAAAAT 59.237 33.333 0.00 0.00 0.00 1.82
570 587 4.131088 GAGACTGTCGACCGGGGC 62.131 72.222 14.12 5.54 0.00 5.80
606 623 3.119779 ACGGACACACGTCAAACAAAAAT 60.120 39.130 0.00 0.00 45.08 1.82
631 651 2.443632 TCATCCGGTACATCTCCTCTCT 59.556 50.000 0.00 0.00 0.00 3.10
683 705 1.153539 TTTCAGTTCCATCCCCACCA 58.846 50.000 0.00 0.00 0.00 4.17
784 806 3.132925 GACCGCGCCTTTATTTATACCA 58.867 45.455 0.00 0.00 0.00 3.25
788 810 3.558418 CGCGCCTTTATTTATACCAGTGT 59.442 43.478 0.00 0.00 0.00 3.55
790 812 4.573201 GCGCCTTTATTTATACCAGTGTCA 59.427 41.667 0.00 0.00 0.00 3.58
844 866 5.925506 TGGTAACAGAAGATACGGATTGA 57.074 39.130 0.00 0.00 46.17 2.57
858 880 3.300934 ATTGAGAGCGCGCAGTCCA 62.301 57.895 35.10 20.45 0.00 4.02
904 950 4.373116 GCCGAACAGCCGAGGACA 62.373 66.667 0.00 0.00 0.00 4.02
944 995 1.297664 ACGCTCGCTGGTAGTAGTAG 58.702 55.000 0.00 0.00 0.00 2.57
945 996 1.297664 CGCTCGCTGGTAGTAGTAGT 58.702 55.000 0.00 0.00 0.00 2.73
952 1003 1.869767 CTGGTAGTAGTAGTACCGCCG 59.130 57.143 23.41 13.69 45.17 6.46
1247 1314 3.248248 TACGACCCCAAGGAGCCCT 62.248 63.158 0.00 0.00 36.73 5.19
1480 1556 0.678684 TCACCGACCTGCTCGACATA 60.679 55.000 0.00 0.00 46.14 2.29
1783 1859 1.628846 GGGAGCCTGTTCAAGAGGTAA 59.371 52.381 1.88 0.00 32.60 2.85
1788 1864 4.583871 AGCCTGTTCAAGAGGTAAATGAG 58.416 43.478 1.88 0.00 32.60 2.90
1817 1893 7.968405 GCAATTTGTTACTACTGTATTTGGGAG 59.032 37.037 0.00 0.00 0.00 4.30
1828 1904 7.016153 ACTGTATTTGGGAGATGTTGAGTTA 57.984 36.000 0.00 0.00 0.00 2.24
2062 2143 5.880054 ATAATGGTTTGTAGTGTCACAGC 57.120 39.130 5.62 0.00 0.00 4.40
2101 2188 7.241042 AGCTAGTAGAAATAAACCAGTGACA 57.759 36.000 0.00 0.00 0.00 3.58
2149 2250 5.050837 AGCGACATTTTTGTCTTTGCAAATC 60.051 36.000 13.23 9.67 38.05 2.17
2158 2259 7.467557 TTTGTCTTTGCAAATCACTGAATTC 57.532 32.000 13.23 0.00 33.91 2.17
2251 2391 8.949177 GCCAAAATTTCCATCTGATTTTATTGT 58.051 29.630 0.00 0.00 33.15 2.71
2273 2413 6.978261 TGTACCTAGGTATCAGTAGAGGTTT 58.022 40.000 24.36 0.00 38.29 3.27
2351 2526 6.319141 AGTACAAAAATGCCTCTTCAGTTC 57.681 37.500 0.00 0.00 0.00 3.01
2356 2531 6.536224 ACAAAAATGCCTCTTCAGTTCTTTTG 59.464 34.615 0.00 0.00 37.30 2.44
2361 2536 4.758674 TGCCTCTTCAGTTCTTTTGAGATG 59.241 41.667 0.00 0.00 0.00 2.90
2369 2544 5.048504 TCAGTTCTTTTGAGATGATTGCACC 60.049 40.000 0.00 0.00 0.00 5.01
2376 2551 3.753815 TGAGATGATTGCACCAACTGAA 58.246 40.909 3.30 0.00 0.00 3.02
2526 2704 8.522830 CCTTTGAAAACCATGTATAGTCAATGT 58.477 33.333 0.00 0.00 0.00 2.71
2566 2744 1.593196 GTTTCCTGTACTGTGCTGCA 58.407 50.000 0.00 0.00 0.00 4.41
2583 2769 4.510711 TGCTGCAAATGTTTTGTTGGTATG 59.489 37.500 0.00 0.00 0.00 2.39
2584 2770 4.749099 GCTGCAAATGTTTTGTTGGTATGA 59.251 37.500 0.00 0.00 0.00 2.15
2585 2771 5.333263 GCTGCAAATGTTTTGTTGGTATGAC 60.333 40.000 0.00 0.00 0.00 3.06
2586 2772 5.664457 TGCAAATGTTTTGTTGGTATGACA 58.336 33.333 2.32 0.00 0.00 3.58
2587 2773 5.752472 TGCAAATGTTTTGTTGGTATGACAG 59.248 36.000 2.32 0.00 0.00 3.51
2588 2774 5.752955 GCAAATGTTTTGTTGGTATGACAGT 59.247 36.000 2.32 0.00 0.00 3.55
2589 2775 6.920758 GCAAATGTTTTGTTGGTATGACAGTA 59.079 34.615 2.32 0.00 0.00 2.74
2590 2776 7.114811 GCAAATGTTTTGTTGGTATGACAGTAG 59.885 37.037 2.32 0.00 0.00 2.57
2661 2847 4.545823 TGTACTTTTCTTGGCAAGTTCG 57.454 40.909 25.39 14.87 34.92 3.95
2727 2913 6.210385 AGTTCATCTGCTAGTCCGATATCATT 59.790 38.462 3.12 0.00 0.00 2.57
3060 3248 5.571285 GGAGTATTCCCTTGGTTCTTTTCT 58.429 41.667 0.00 0.00 37.53 2.52
3096 3285 8.768019 TCTCATTGATCGAAATTATGTTAGCTG 58.232 33.333 0.00 0.00 0.00 4.24
3313 3504 1.999735 CACTACCAACAGGCATACACG 59.000 52.381 0.00 0.00 0.00 4.49
3820 4033 2.625314 TGCTAGAAGTCATGATCCGGAG 59.375 50.000 11.34 0.00 0.00 4.63
3895 4108 1.133823 TGGATCCCCATTGAACATCGG 60.134 52.381 9.90 0.00 37.58 4.18
3964 4177 9.452065 GATATACATGGTAAGTATCTGCATACG 57.548 37.037 0.00 0.00 40.09 3.06
3997 4211 8.273780 AGTAGAAATTCACAAACAGATGGATC 57.726 34.615 0.00 0.00 0.00 3.36
4317 4531 6.808212 GTGATGAATGTTGTTCCTACAAATGG 59.192 38.462 0.00 0.00 45.33 3.16
4731 5017 1.613437 CAAACAAGTTGGGGTAGGCTG 59.387 52.381 7.96 0.00 33.18 4.85
4853 5139 4.277476 TCCAGTCCTTCAGATCTCTCTTC 58.723 47.826 0.00 0.00 0.00 2.87
5186 5722 2.223758 GCATCCTACGACCAGAGGTAAC 60.224 54.545 0.00 0.00 35.25 2.50
5197 5734 2.955660 CCAGAGGTAACCAAGTTTTGCA 59.044 45.455 0.00 0.00 37.17 4.08
5206 5743 7.810759 AGGTAACCAAGTTTTGCAAATATTACG 59.189 33.333 13.65 7.05 37.17 3.18
5528 6078 9.534565 GCAATGTGAACTCTACTATTGAAGATA 57.465 33.333 0.00 0.00 0.00 1.98
5778 6331 6.379988 ACCACATACGGATGTATATAGATGCA 59.620 38.462 14.23 0.00 44.82 3.96
5816 6369 2.512485 TTCGTTTTGCTCCGTCTGTA 57.488 45.000 0.00 0.00 0.00 2.74
5893 6446 4.012374 AGATGATGGGTGTTCAATGTGTC 58.988 43.478 0.00 0.00 0.00 3.67
5941 6494 2.551721 CCTGTGCAGGGCTGGATTATAG 60.552 54.545 10.28 0.00 44.87 1.31
6095 6648 7.944729 AAAAATAATGAGCATACCAGACACT 57.055 32.000 0.00 0.00 0.00 3.55
6141 6694 9.736819 TGGAATTATTCTTTACCCCCAAAATAT 57.263 29.630 4.87 0.00 0.00 1.28
6180 6734 4.537015 CGAGAACAACTGGGAACAAATTC 58.463 43.478 0.00 0.00 42.06 2.17
6283 6837 4.237445 GCATGCTGCAGAGGACAT 57.763 55.556 20.43 8.41 44.26 3.06
6302 6859 1.153958 GCTTGGCGGCTAAGCTTTG 60.154 57.895 34.66 10.33 45.34 2.77
6326 6885 1.821666 GCCAAGGTTTTACTGCCAGGA 60.822 52.381 0.00 0.00 0.00 3.86
6327 6886 1.886542 CCAAGGTTTTACTGCCAGGAC 59.113 52.381 0.00 0.00 0.00 3.85
6421 6980 2.248280 ACATAATCGCGGCCAATGTA 57.752 45.000 6.13 0.00 0.00 2.29
6459 7018 2.420687 CCATTTTTCTCCCTCTCCCTCG 60.421 54.545 0.00 0.00 0.00 4.63
6496 7055 5.359009 CCTCTGTAATGGTGCTCATTCATTT 59.641 40.000 8.68 0.00 44.32 2.32
6555 7114 2.771943 TGGTCATCCCCAGATTACAGTC 59.228 50.000 0.00 0.00 29.61 3.51
6576 7136 6.600822 CAGTCCTGTGAAATGAAGGTCAATAT 59.399 38.462 0.00 0.00 32.59 1.28
6577 7137 7.121759 CAGTCCTGTGAAATGAAGGTCAATATT 59.878 37.037 0.00 0.00 32.59 1.28
6613 7174 7.915293 TGATAGGAAAGAGCAAACGAAATTA 57.085 32.000 0.00 0.00 0.00 1.40
6645 7212 8.697846 TTAGATGTTTACACCTACATTTCTCG 57.302 34.615 0.00 0.00 35.24 4.04
6691 7258 6.245115 CCACAGCATGGTATGTGTATTATG 57.755 41.667 12.67 0.00 44.24 1.90
6808 7421 1.518325 TGTGTGTGATTAGTTGCCCG 58.482 50.000 0.00 0.00 0.00 6.13
6962 7581 4.491676 GCACATCATCAGCAAAGACAAAT 58.508 39.130 0.00 0.00 0.00 2.32
7003 7622 4.990426 CACAAATCCAAAGGAATTGACACC 59.010 41.667 18.04 0.00 43.18 4.16
7007 7626 0.958091 CAAAGGAATTGACACCGCCA 59.042 50.000 0.00 0.00 41.85 5.69
7035 7654 1.342275 TGGCCCTTGATTCCATCCAAG 60.342 52.381 0.00 0.00 39.43 3.61
7043 7662 5.958955 CTTGATTCCATCCAAGGTTTCTTC 58.041 41.667 0.00 0.00 36.90 2.87
7162 7786 1.363807 GGTTGCAGCTGTTTGTCCC 59.636 57.895 16.64 3.56 0.00 4.46
7184 7808 0.383949 GGCTGAAAGTTGAAACCGCA 59.616 50.000 0.00 0.00 35.30 5.69
7205 7873 5.041287 GCAGGTGTTAACAAAAGAAAGACC 58.959 41.667 10.51 3.95 36.94 3.85
7207 7875 5.126384 CAGGTGTTAACAAAAGAAAGACCCA 59.874 40.000 10.51 0.00 37.28 4.51
7239 7907 0.957395 CTTGAACGCACATCTGGGCT 60.957 55.000 2.53 0.00 43.67 5.19
7292 7971 2.430080 CTTGTTCGCGAGTGTGGTGC 62.430 60.000 9.59 0.00 0.00 5.01
7294 7973 4.980805 TTCGCGAGTGTGGTGCCC 62.981 66.667 9.59 0.00 0.00 5.36
7405 8086 0.801872 CGCAACGAACCATTCCATCA 59.198 50.000 0.00 0.00 0.00 3.07
7413 8094 3.313526 CGAACCATTCCATCAACCATCTC 59.686 47.826 0.00 0.00 0.00 2.75
7416 8097 1.262417 CATTCCATCAACCATCTCGCG 59.738 52.381 0.00 0.00 0.00 5.87
7561 8243 6.347696 AGCAAATCAAATTTTGTTCTCCACA 58.652 32.000 8.89 0.00 38.55 4.17
7562 8244 6.258507 AGCAAATCAAATTTTGTTCTCCACAC 59.741 34.615 8.89 0.00 38.55 3.82
7585 8267 3.003480 AGTTTTGCCATAAGACGAGAGC 58.997 45.455 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.489938 TACTGATGCGGCCTCTTTTT 57.510 45.000 0.00 0.00 0.00 1.94
3 4 2.489938 TTACTGATGCGGCCTCTTTT 57.510 45.000 0.00 0.00 0.00 2.27
4 5 2.717639 ATTACTGATGCGGCCTCTTT 57.282 45.000 0.00 0.00 0.00 2.52
5 6 4.357918 AATATTACTGATGCGGCCTCTT 57.642 40.909 0.00 0.00 0.00 2.85
6 7 4.621747 GCTAATATTACTGATGCGGCCTCT 60.622 45.833 0.00 0.00 0.00 3.69
7 8 3.619038 GCTAATATTACTGATGCGGCCTC 59.381 47.826 0.00 0.00 0.00 4.70
8 9 3.600388 GCTAATATTACTGATGCGGCCT 58.400 45.455 0.00 0.00 0.00 5.19
9 10 2.678336 GGCTAATATTACTGATGCGGCC 59.322 50.000 0.00 0.00 0.00 6.13
10 11 3.334691 TGGCTAATATTACTGATGCGGC 58.665 45.455 0.00 0.00 0.00 6.53
11 12 5.643348 TCAATGGCTAATATTACTGATGCGG 59.357 40.000 0.00 0.00 0.00 5.69
12 13 6.369890 ACTCAATGGCTAATATTACTGATGCG 59.630 38.462 0.00 0.00 0.00 4.73
13 14 7.388776 TGACTCAATGGCTAATATTACTGATGC 59.611 37.037 0.00 0.00 0.00 3.91
14 15 8.837788 TGACTCAATGGCTAATATTACTGATG 57.162 34.615 0.00 0.00 0.00 3.07
15 16 9.664332 GATGACTCAATGGCTAATATTACTGAT 57.336 33.333 0.00 0.00 0.00 2.90
16 17 8.097038 GGATGACTCAATGGCTAATATTACTGA 58.903 37.037 0.00 0.00 0.00 3.41
17 18 7.879677 TGGATGACTCAATGGCTAATATTACTG 59.120 37.037 0.00 0.00 0.00 2.74
18 19 7.977818 TGGATGACTCAATGGCTAATATTACT 58.022 34.615 0.00 0.00 0.00 2.24
19 20 8.671921 CATGGATGACTCAATGGCTAATATTAC 58.328 37.037 0.00 0.00 0.00 1.89
20 21 8.605065 TCATGGATGACTCAATGGCTAATATTA 58.395 33.333 0.00 0.00 0.00 0.98
21 22 7.464273 TCATGGATGACTCAATGGCTAATATT 58.536 34.615 0.00 0.00 0.00 1.28
22 23 7.024345 TCATGGATGACTCAATGGCTAATAT 57.976 36.000 0.00 0.00 0.00 1.28
23 24 6.438186 TCATGGATGACTCAATGGCTAATA 57.562 37.500 0.00 0.00 0.00 0.98
24 25 5.314718 TCATGGATGACTCAATGGCTAAT 57.685 39.130 0.00 0.00 0.00 1.73
25 26 4.776435 TCATGGATGACTCAATGGCTAA 57.224 40.909 0.00 0.00 0.00 3.09
37 38 4.026052 TGAGAGCTGTTAGTCATGGATGA 58.974 43.478 0.00 0.00 0.00 2.92
38 39 4.118410 GTGAGAGCTGTTAGTCATGGATG 58.882 47.826 0.00 0.00 0.00 3.51
39 40 3.181482 CGTGAGAGCTGTTAGTCATGGAT 60.181 47.826 0.00 0.00 0.00 3.41
40 41 2.164422 CGTGAGAGCTGTTAGTCATGGA 59.836 50.000 0.00 0.00 0.00 3.41
41 42 2.094494 ACGTGAGAGCTGTTAGTCATGG 60.094 50.000 0.00 0.00 31.39 3.66
42 43 3.119673 AGACGTGAGAGCTGTTAGTCATG 60.120 47.826 13.71 7.01 33.05 3.07
43 44 3.085533 AGACGTGAGAGCTGTTAGTCAT 58.914 45.455 13.71 1.31 0.00 3.06
44 45 2.505405 AGACGTGAGAGCTGTTAGTCA 58.495 47.619 13.71 0.00 0.00 3.41
45 46 3.486209 GCTAGACGTGAGAGCTGTTAGTC 60.486 52.174 0.00 0.00 33.28 2.59
46 47 2.420722 GCTAGACGTGAGAGCTGTTAGT 59.579 50.000 0.00 0.00 33.28 2.24
47 48 2.537931 CGCTAGACGTGAGAGCTGTTAG 60.538 54.545 0.00 0.00 36.87 2.34
48 49 1.397343 CGCTAGACGTGAGAGCTGTTA 59.603 52.381 0.00 0.00 36.87 2.41
49 50 0.169230 CGCTAGACGTGAGAGCTGTT 59.831 55.000 0.00 0.00 36.87 3.16
50 51 1.797441 CGCTAGACGTGAGAGCTGT 59.203 57.895 0.00 0.00 36.87 4.40
51 52 4.680349 CGCTAGACGTGAGAGCTG 57.320 61.111 0.00 0.00 36.87 4.24
61 62 2.593336 GTGCTCTTTAACGACGCTAGAC 59.407 50.000 0.00 0.00 0.00 2.59
62 63 2.726989 CGTGCTCTTTAACGACGCTAGA 60.727 50.000 0.00 0.00 42.32 2.43
63 64 1.578023 CGTGCTCTTTAACGACGCTAG 59.422 52.381 0.00 0.00 42.32 3.42
64 65 1.069022 ACGTGCTCTTTAACGACGCTA 60.069 47.619 1.80 0.00 42.32 4.26
65 66 0.318445 ACGTGCTCTTTAACGACGCT 60.318 50.000 1.80 0.00 42.32 5.07
66 67 0.179282 CACGTGCTCTTTAACGACGC 60.179 55.000 0.82 0.00 42.32 5.19
67 68 0.433492 CCACGTGCTCTTTAACGACG 59.567 55.000 10.91 0.00 42.32 5.12
68 69 1.719780 CTCCACGTGCTCTTTAACGAC 59.280 52.381 10.91 0.00 42.32 4.34
69 70 1.336517 CCTCCACGTGCTCTTTAACGA 60.337 52.381 10.91 0.00 42.32 3.85
70 71 1.068474 CCTCCACGTGCTCTTTAACG 58.932 55.000 10.91 0.00 45.15 3.18
71 72 1.798813 CACCTCCACGTGCTCTTTAAC 59.201 52.381 10.91 0.00 0.00 2.01
72 73 1.414919 ACACCTCCACGTGCTCTTTAA 59.585 47.619 10.91 0.00 37.25 1.52
73 74 1.045407 ACACCTCCACGTGCTCTTTA 58.955 50.000 10.91 0.00 37.25 1.85
74 75 0.532862 CACACCTCCACGTGCTCTTT 60.533 55.000 10.91 0.00 37.25 2.52
75 76 1.069765 CACACCTCCACGTGCTCTT 59.930 57.895 10.91 0.00 37.25 2.85
76 77 2.134287 ACACACCTCCACGTGCTCT 61.134 57.895 10.91 0.00 37.25 4.09
77 78 1.956170 CACACACCTCCACGTGCTC 60.956 63.158 10.91 0.00 37.25 4.26
78 79 2.108976 CACACACCTCCACGTGCT 59.891 61.111 10.91 0.00 37.25 4.40
79 80 1.373590 AAACACACACCTCCACGTGC 61.374 55.000 10.91 0.00 37.25 5.34
80 81 0.376852 CAAACACACACCTCCACGTG 59.623 55.000 9.08 9.08 39.75 4.49
81 82 0.250793 TCAAACACACACCTCCACGT 59.749 50.000 0.00 0.00 0.00 4.49
82 83 1.593196 ATCAAACACACACCTCCACG 58.407 50.000 0.00 0.00 0.00 4.94
83 84 4.154195 GTCATATCAAACACACACCTCCAC 59.846 45.833 0.00 0.00 0.00 4.02
84 85 4.041567 AGTCATATCAAACACACACCTCCA 59.958 41.667 0.00 0.00 0.00 3.86
85 86 4.579869 AGTCATATCAAACACACACCTCC 58.420 43.478 0.00 0.00 0.00 4.30
86 87 7.334421 ACATTAGTCATATCAAACACACACCTC 59.666 37.037 0.00 0.00 0.00 3.85
87 88 7.168219 ACATTAGTCATATCAAACACACACCT 58.832 34.615 0.00 0.00 0.00 4.00
88 89 7.377766 ACATTAGTCATATCAAACACACACC 57.622 36.000 0.00 0.00 0.00 4.16
89 90 8.388103 GGTACATTAGTCATATCAAACACACAC 58.612 37.037 0.00 0.00 0.00 3.82
90 91 8.097662 TGGTACATTAGTCATATCAAACACACA 58.902 33.333 0.00 0.00 0.00 3.72
91 92 8.487313 TGGTACATTAGTCATATCAAACACAC 57.513 34.615 0.00 0.00 0.00 3.82
92 93 9.161629 CTTGGTACATTAGTCATATCAAACACA 57.838 33.333 0.00 0.00 39.30 3.72
93 94 9.378551 TCTTGGTACATTAGTCATATCAAACAC 57.621 33.333 0.00 0.00 39.30 3.32
94 95 9.952030 TTCTTGGTACATTAGTCATATCAAACA 57.048 29.630 0.00 0.00 39.30 2.83
96 97 9.952030 TGTTCTTGGTACATTAGTCATATCAAA 57.048 29.630 0.00 0.00 39.30 2.69
97 98 9.952030 TTGTTCTTGGTACATTAGTCATATCAA 57.048 29.630 0.00 0.00 39.30 2.57
98 99 9.952030 TTTGTTCTTGGTACATTAGTCATATCA 57.048 29.630 0.00 0.00 39.30 2.15
102 103 8.576442 CCTTTTTGTTCTTGGTACATTAGTCAT 58.424 33.333 0.00 0.00 39.30 3.06
103 104 7.469456 GCCTTTTTGTTCTTGGTACATTAGTCA 60.469 37.037 0.00 0.00 39.30 3.41
104 105 6.861572 GCCTTTTTGTTCTTGGTACATTAGTC 59.138 38.462 0.00 0.00 39.30 2.59
105 106 6.514376 CGCCTTTTTGTTCTTGGTACATTAGT 60.514 38.462 0.00 0.00 39.30 2.24
106 107 5.856455 CGCCTTTTTGTTCTTGGTACATTAG 59.144 40.000 0.00 0.00 39.30 1.73
107 108 5.299782 ACGCCTTTTTGTTCTTGGTACATTA 59.700 36.000 0.00 0.00 39.30 1.90
108 109 4.098807 ACGCCTTTTTGTTCTTGGTACATT 59.901 37.500 0.00 0.00 39.30 2.71
109 110 3.634910 ACGCCTTTTTGTTCTTGGTACAT 59.365 39.130 0.00 0.00 39.30 2.29
110 111 3.018149 ACGCCTTTTTGTTCTTGGTACA 58.982 40.909 0.00 0.00 0.00 2.90
111 112 3.703286 ACGCCTTTTTGTTCTTGGTAC 57.297 42.857 0.00 0.00 0.00 3.34
112 113 3.695060 TCAACGCCTTTTTGTTCTTGGTA 59.305 39.130 0.00 0.00 0.00 3.25
113 114 2.494073 TCAACGCCTTTTTGTTCTTGGT 59.506 40.909 0.00 0.00 0.00 3.67
114 115 2.857748 GTCAACGCCTTTTTGTTCTTGG 59.142 45.455 0.00 0.00 0.00 3.61
115 116 2.529894 CGTCAACGCCTTTTTGTTCTTG 59.470 45.455 0.00 0.00 0.00 3.02
116 117 2.162809 ACGTCAACGCCTTTTTGTTCTT 59.837 40.909 1.81 0.00 44.43 2.52
117 118 1.741145 ACGTCAACGCCTTTTTGTTCT 59.259 42.857 1.81 0.00 44.43 3.01
118 119 2.106418 GACGTCAACGCCTTTTTGTTC 58.894 47.619 11.55 0.00 44.43 3.18
119 120 1.530236 CGACGTCAACGCCTTTTTGTT 60.530 47.619 17.16 0.00 44.43 2.83
120 121 0.027063 CGACGTCAACGCCTTTTTGT 59.973 50.000 17.16 0.00 44.43 2.83
121 122 0.656205 CCGACGTCAACGCCTTTTTG 60.656 55.000 17.16 0.00 44.43 2.44
122 123 1.091197 ACCGACGTCAACGCCTTTTT 61.091 50.000 17.16 0.00 44.43 1.94
123 124 1.522130 ACCGACGTCAACGCCTTTT 60.522 52.632 17.16 0.00 44.43 2.27
124 125 2.107546 ACCGACGTCAACGCCTTT 59.892 55.556 17.16 0.00 44.43 3.11
125 126 2.660552 CACCGACGTCAACGCCTT 60.661 61.111 17.16 0.00 44.43 4.35
126 127 4.657824 CCACCGACGTCAACGCCT 62.658 66.667 17.16 0.00 44.43 5.52
129 130 4.657824 AGGCCACCGACGTCAACG 62.658 66.667 17.16 1.75 46.33 4.10
130 131 2.737376 GAGGCCACCGACGTCAAC 60.737 66.667 17.16 0.00 0.00 3.18
131 132 3.998672 GGAGGCCACCGACGTCAA 61.999 66.667 17.16 0.00 0.00 3.18
144 145 2.176273 CATTGAAGCGAGGCGGAGG 61.176 63.158 0.00 0.00 0.00 4.30
145 146 1.021390 AACATTGAAGCGAGGCGGAG 61.021 55.000 0.00 0.00 0.00 4.63
146 147 0.605319 AAACATTGAAGCGAGGCGGA 60.605 50.000 0.00 0.00 0.00 5.54
147 148 0.454957 CAAACATTGAAGCGAGGCGG 60.455 55.000 0.00 0.00 0.00 6.13
148 149 0.238289 ACAAACATTGAAGCGAGGCG 59.762 50.000 0.00 0.00 0.00 5.52
149 150 1.266718 TCACAAACATTGAAGCGAGGC 59.733 47.619 0.00 0.00 0.00 4.70
150 151 3.837213 ATCACAAACATTGAAGCGAGG 57.163 42.857 0.00 0.00 0.00 4.63
151 152 4.539870 ACAATCACAAACATTGAAGCGAG 58.460 39.130 0.00 0.00 35.54 5.03
152 153 4.536065 GACAATCACAAACATTGAAGCGA 58.464 39.130 0.00 0.00 35.54 4.93
153 154 3.358700 CGACAATCACAAACATTGAAGCG 59.641 43.478 0.00 0.00 35.54 4.68
154 155 4.146961 CACGACAATCACAAACATTGAAGC 59.853 41.667 0.00 0.00 35.54 3.86
155 156 4.146961 GCACGACAATCACAAACATTGAAG 59.853 41.667 0.00 0.00 35.54 3.02
156 157 4.041049 GCACGACAATCACAAACATTGAA 58.959 39.130 0.00 0.00 35.54 2.69
157 158 3.626977 GCACGACAATCACAAACATTGA 58.373 40.909 0.00 0.00 35.54 2.57
158 159 2.401391 CGCACGACAATCACAAACATTG 59.599 45.455 0.00 0.00 37.29 2.82
159 160 2.604373 CCGCACGACAATCACAAACATT 60.604 45.455 0.00 0.00 0.00 2.71
160 161 1.069296 CCGCACGACAATCACAAACAT 60.069 47.619 0.00 0.00 0.00 2.71
161 162 0.306228 CCGCACGACAATCACAAACA 59.694 50.000 0.00 0.00 0.00 2.83
162 163 0.306533 ACCGCACGACAATCACAAAC 59.693 50.000 0.00 0.00 0.00 2.93
163 164 0.306228 CACCGCACGACAATCACAAA 59.694 50.000 0.00 0.00 0.00 2.83
164 165 0.530870 TCACCGCACGACAATCACAA 60.531 50.000 0.00 0.00 0.00 3.33
165 166 0.320334 ATCACCGCACGACAATCACA 60.320 50.000 0.00 0.00 0.00 3.58
166 167 0.095245 CATCACCGCACGACAATCAC 59.905 55.000 0.00 0.00 0.00 3.06
167 168 0.037790 TCATCACCGCACGACAATCA 60.038 50.000 0.00 0.00 0.00 2.57
168 169 1.075542 TTCATCACCGCACGACAATC 58.924 50.000 0.00 0.00 0.00 2.67
169 170 1.737838 ATTCATCACCGCACGACAAT 58.262 45.000 0.00 0.00 0.00 2.71
170 171 2.094442 TCTATTCATCACCGCACGACAA 60.094 45.455 0.00 0.00 0.00 3.18
171 172 1.474879 TCTATTCATCACCGCACGACA 59.525 47.619 0.00 0.00 0.00 4.35
172 173 2.203800 TCTATTCATCACCGCACGAC 57.796 50.000 0.00 0.00 0.00 4.34
173 174 3.818773 TCTATCTATTCATCACCGCACGA 59.181 43.478 0.00 0.00 0.00 4.35
174 175 4.160736 TCTATCTATTCATCACCGCACG 57.839 45.455 0.00 0.00 0.00 5.34
175 176 7.426929 AAAATCTATCTATTCATCACCGCAC 57.573 36.000 0.00 0.00 0.00 5.34
207 208 9.793259 AACCGTTATTAGTCATGGATGATATTT 57.207 29.630 0.00 0.00 39.30 1.40
210 211 7.158697 CCAACCGTTATTAGTCATGGATGATA 58.841 38.462 0.00 0.00 39.30 2.15
226 227 4.223477 ACTCAATACTAAGCCCAACCGTTA 59.777 41.667 0.00 0.00 0.00 3.18
241 242 6.422400 GCTGTAAGATGCTCCTAACTCAATAC 59.578 42.308 0.00 0.00 34.07 1.89
242 243 6.325028 AGCTGTAAGATGCTCCTAACTCAATA 59.675 38.462 0.00 0.00 33.90 1.90
243 244 5.130145 AGCTGTAAGATGCTCCTAACTCAAT 59.870 40.000 0.00 0.00 33.90 2.57
245 246 4.026744 AGCTGTAAGATGCTCCTAACTCA 58.973 43.478 0.00 0.00 33.90 3.41
246 247 4.664150 AGCTGTAAGATGCTCCTAACTC 57.336 45.455 0.00 0.00 33.90 3.01
255 256 8.370493 TGTAAATATGAAGAGCTGTAAGATGC 57.630 34.615 0.00 0.00 34.07 3.91
294 295 5.295787 TCTGCATTGTTCTAACGTTTGTTCT 59.704 36.000 5.91 0.00 39.54 3.01
295 296 5.507077 TCTGCATTGTTCTAACGTTTGTTC 58.493 37.500 5.91 3.25 39.54 3.18
297 298 4.574828 ACTCTGCATTGTTCTAACGTTTGT 59.425 37.500 5.91 0.00 0.00 2.83
298 299 5.095691 ACTCTGCATTGTTCTAACGTTTG 57.904 39.130 5.91 4.35 0.00 2.93
300 301 4.389077 GCTACTCTGCATTGTTCTAACGTT 59.611 41.667 5.88 5.88 0.00 3.99
324 325 1.497278 CGAGGGAAACATGTGTGCG 59.503 57.895 0.00 0.00 0.00 5.34
328 329 2.046285 GGGCCGAGGGAAACATGTG 61.046 63.158 0.00 0.00 0.00 3.21
368 378 4.558715 GGGGCCTGGGGTTTATATTTTAA 58.441 43.478 0.84 0.00 0.00 1.52
465 476 0.889306 AGCAGTACTCTGGGTCGAAC 59.111 55.000 0.00 0.00 41.57 3.95
482 493 8.297426 GCTGGGGTTTATTATAAGATTTGTAGC 58.703 37.037 0.00 0.00 0.00 3.58
584 601 1.440708 TTTGTTTGACGTGTGTCCGT 58.559 45.000 0.00 0.00 44.86 4.69
606 623 3.574396 GAGGAGATGTACCGGATGATGAA 59.426 47.826 9.46 0.00 0.00 2.57
652 674 3.571828 TGGAACTGAAAAATGAATGCGGA 59.428 39.130 0.00 0.00 0.00 5.54
784 806 0.388649 GTTGCTCCGTCGATGACACT 60.389 55.000 6.11 0.00 32.09 3.55
823 845 6.145338 TCTCAATCCGTATCTTCTGTTACC 57.855 41.667 0.00 0.00 0.00 2.85
844 866 4.427661 GACTGGACTGCGCGCTCT 62.428 66.667 33.29 17.17 0.00 4.09
889 935 2.805353 CGTGTCCTCGGCTGTTCG 60.805 66.667 0.00 0.00 0.00 3.95
963 1014 1.341531 CGAGTAAATGGGGCGAGAGAT 59.658 52.381 0.00 0.00 0.00 2.75
1247 1314 3.430862 GCCAATGCCGTTCTCGCA 61.431 61.111 0.00 0.00 35.54 5.10
1582 1658 2.494918 CCCAGATCCGACACGTCC 59.505 66.667 0.00 0.00 0.00 4.79
1615 1691 2.125912 CACTGGCGCTCGTAGCTT 60.126 61.111 7.64 0.00 39.60 3.74
1771 1847 2.096013 GCGGCTCATTTACCTCTTGAAC 59.904 50.000 0.00 0.00 0.00 3.18
1783 1859 4.700213 AGTAGTAACAAATTGCGGCTCATT 59.300 37.500 0.00 0.00 0.00 2.57
1788 1864 3.824414 ACAGTAGTAACAAATTGCGGC 57.176 42.857 0.00 0.00 0.00 6.53
1817 1893 3.326747 ACGAAGCCACTAACTCAACATC 58.673 45.455 0.00 0.00 0.00 3.06
1828 1904 2.038557 ACAACCAATAGACGAAGCCACT 59.961 45.455 0.00 0.00 0.00 4.00
2062 2143 4.162690 GCTAGCCCCCGTCACCAG 62.163 72.222 2.29 0.00 0.00 4.00
2070 2151 5.512749 GGTTTATTTCTACTAGCTAGCCCCC 60.513 48.000 20.91 3.08 0.00 5.40
2073 2154 6.702282 CACTGGTTTATTTCTACTAGCTAGCC 59.298 42.308 20.91 9.84 0.00 3.93
2149 2250 9.352784 TGTCTTTTTAACAAAGTGAATTCAGTG 57.647 29.630 16.46 13.12 0.00 3.66
2158 2259 7.962917 AGCAATTGTGTCTTTTTAACAAAGTG 58.037 30.769 7.40 0.00 37.36 3.16
2251 2391 7.217028 TGAAACCTCTACTGATACCTAGGTA 57.783 40.000 23.82 23.82 36.34 3.08
2304 2445 1.674962 GCTTGCTCCATGATTCCAGAC 59.325 52.381 0.00 0.00 0.00 3.51
2351 2526 4.921515 CAGTTGGTGCAATCATCTCAAAAG 59.078 41.667 0.00 0.00 0.00 2.27
2356 2531 4.978083 ATTCAGTTGGTGCAATCATCTC 57.022 40.909 0.00 0.00 0.00 2.75
2388 2566 1.202855 AGTGCTGCTGGACACAAATCT 60.203 47.619 17.11 0.00 39.30 2.40
2526 2704 5.670792 ACCCTGATATACACTTTCGAACA 57.329 39.130 0.00 0.00 0.00 3.18
2566 2744 7.504238 TCCTACTGTCATACCAACAAAACATTT 59.496 33.333 0.00 0.00 0.00 2.32
2583 2769 1.132643 CGTAGTGGCTGTCCTACTGTC 59.867 57.143 6.42 0.00 33.04 3.51
2584 2770 1.174783 CGTAGTGGCTGTCCTACTGT 58.825 55.000 6.42 0.00 33.04 3.55
2585 2771 1.460504 TCGTAGTGGCTGTCCTACTG 58.539 55.000 6.42 0.00 33.04 2.74
2586 2772 2.299521 GATCGTAGTGGCTGTCCTACT 58.700 52.381 6.42 0.00 33.04 2.57
2587 2773 1.337387 GGATCGTAGTGGCTGTCCTAC 59.663 57.143 0.00 0.00 0.00 3.18
2588 2774 1.064240 TGGATCGTAGTGGCTGTCCTA 60.064 52.381 0.00 0.00 0.00 2.94
2589 2775 0.324368 TGGATCGTAGTGGCTGTCCT 60.324 55.000 0.00 0.00 0.00 3.85
2590 2776 0.753262 ATGGATCGTAGTGGCTGTCC 59.247 55.000 0.00 0.00 0.00 4.02
2661 2847 6.683974 ATAGCAACAGTGGAAACATCATAC 57.316 37.500 0.00 0.00 46.14 2.39
2727 2913 9.624697 GCATAAACTCAACAATATCTTGAAACA 57.375 29.630 0.00 0.00 36.20 2.83
3060 3248 7.722795 TTTCGATCAATGAGAGTTAAACACA 57.277 32.000 0.00 0.00 0.00 3.72
3096 3285 2.152016 GGTTAGCTTGAACTGGTGACC 58.848 52.381 0.00 0.00 35.15 4.02
3252 3443 5.643421 AGATAGGGCAGAATTCATTCACT 57.357 39.130 8.44 5.04 39.23 3.41
3313 3504 8.379902 CGCATGGATTTTTGTTAACTTAATTCC 58.620 33.333 17.77 17.77 0.00 3.01
3820 4033 6.563222 TTTAGTGGTTTGTAGTATGGCAAC 57.437 37.500 0.00 0.00 0.00 4.17
3895 4108 1.457346 CCTGAGAAGGCCATGTTGTC 58.543 55.000 5.01 0.00 0.00 3.18
3964 4177 6.200665 TGTTTGTGAATTTCTACTTGCATTGC 59.799 34.615 0.46 0.46 0.00 3.56
3980 4193 4.516321 CAGTGTGATCCATCTGTTTGTGAA 59.484 41.667 0.00 0.00 0.00 3.18
3997 4211 5.618056 AATGCTCACATCTAAACAGTGTG 57.382 39.130 0.00 0.00 43.41 3.82
4317 4531 2.925162 AAGCGGCAGATAGTTCGGGC 62.925 60.000 1.45 0.00 38.88 6.13
4731 5017 3.425659 AGATCTTTTGGGTTTCAGCTCC 58.574 45.455 0.00 0.00 0.00 4.70
4773 5059 2.421619 GAAGCTAGCTATCCATGTGCC 58.578 52.381 19.70 0.00 0.00 5.01
4853 5139 6.368213 GTTTGGTAAAAGTTATGAGTCCGTG 58.632 40.000 0.00 0.00 0.00 4.94
5444 5981 3.119352 GCCAAACAATGAAGGATGGAGTC 60.119 47.826 0.00 0.00 0.00 3.36
5497 6047 7.342026 TCAATAGTAGAGTTCACATTGCCTCTA 59.658 37.037 0.00 0.00 35.89 2.43
5528 6078 4.110482 GTTTACGAGATACTGAATGCCGT 58.890 43.478 0.00 0.00 0.00 5.68
5755 6308 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
5778 6331 7.687941 AACGAATGAATCCACACTCTAAAAT 57.312 32.000 0.00 0.00 0.00 1.82
5816 6369 7.617723 AGTCTTGTAGAGATTTCACTATGGACT 59.382 37.037 0.00 0.00 36.61 3.85
5941 6494 3.637926 GAGGGGCGGTGTCACGTAC 62.638 68.421 0.00 0.00 35.98 3.67
6095 6648 4.819088 TCCAATTTCTGAATCGTGTGTCAA 59.181 37.500 0.00 0.00 0.00 3.18
6141 6694 4.502171 TCTCGGACAATACGTGTAACAA 57.498 40.909 0.00 0.00 41.96 2.83
6302 6859 0.038251 GCAGTAAAACCTTGGCCTGC 60.038 55.000 3.32 0.00 38.58 4.85
6326 6885 1.667830 CGCCTTCATCACCGTGTGT 60.668 57.895 0.00 0.00 34.79 3.72
6327 6886 2.390599 CCGCCTTCATCACCGTGTG 61.391 63.158 0.00 0.00 34.45 3.82
6459 7018 6.127026 ACCATTACAGAGGAGGAGAATGTAAC 60.127 42.308 0.00 0.00 38.69 2.50
6555 7114 9.143631 GAAAAATATTGACCTTCATTTCACAGG 57.856 33.333 0.00 0.00 0.00 4.00
6576 7136 8.680903 GCTCTTTCCTATCATTCATCTGAAAAA 58.319 33.333 0.00 0.00 37.61 1.94
6577 7137 7.830697 TGCTCTTTCCTATCATTCATCTGAAAA 59.169 33.333 0.00 0.00 37.61 2.29
6630 7191 4.056050 GACACAACGAGAAATGTAGGTGT 58.944 43.478 0.00 0.00 39.30 4.16
6645 7212 3.371168 ACATGCACAAAATCGACACAAC 58.629 40.909 0.00 0.00 0.00 3.32
6780 7393 2.949451 AATCACACACAAAAACGGCA 57.051 40.000 0.00 0.00 0.00 5.69
6982 7601 4.236935 CGGTGTCAATTCCTTTGGATTTG 58.763 43.478 12.42 12.42 41.59 2.32
7071 7695 2.754946 TAATTTGTCCGTCCTTCGCT 57.245 45.000 0.00 0.00 38.35 4.93
7150 7774 2.594592 GCCACGGGACAAACAGCT 60.595 61.111 0.00 0.00 0.00 4.24
7162 7786 1.596954 CGGTTTCAACTTTCAGCCACG 60.597 52.381 0.00 0.00 0.00 4.94
7184 7808 5.265989 TGGGTCTTTCTTTTGTTAACACCT 58.734 37.500 8.07 0.00 0.00 4.00
7239 7907 2.235016 ACTGGCCGATAAAAACAAGCA 58.765 42.857 0.00 0.00 0.00 3.91
7294 7973 2.815211 CTCACATGGCCCGTCACG 60.815 66.667 0.00 0.00 0.00 4.35
7307 7986 1.211457 ACCAATCATCTCTGGCCTCAC 59.789 52.381 3.32 0.00 36.03 3.51
7315 7994 0.747255 CGGACGGACCAATCATCTCT 59.253 55.000 0.00 0.00 38.90 3.10
7416 8097 1.930567 TAAGATTTCGTACGGCCAGC 58.069 50.000 16.52 2.37 0.00 4.85
7422 8103 7.891782 TGACTTGCTTATTAAGATTTCGTACG 58.108 34.615 9.53 9.53 0.00 3.67
7561 8243 4.385825 TCTCGTCTTATGGCAAAACTTGT 58.614 39.130 0.00 0.00 0.00 3.16
7562 8244 4.670221 GCTCTCGTCTTATGGCAAAACTTG 60.670 45.833 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.