Multiple sequence alignment - TraesCS1A01G072300

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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 TraesCS1A01G072300 chr1A 100.000 4121 0 0 1 4121 56336402 56340522 0.000000e+00 7611.0
1 TraesCS1A01G072300 chr1A 93.060 1513 85 9 296 1801 54458236 54459735 0.000000e+00 2194.0
2 TraesCS1A01G072300 chr1A 93.191 1263 66 12 1943 3196 54459843 54461094 0.000000e+00 1838.0
3 TraesCS1A01G072300 chr1A 95.349 1118 40 6 2069 3181 56370412 56371522 0.000000e+00 1766.0
4 TraesCS1A01G072300 chr1A 87.052 1089 77 18 1007 2043 56369273 56370349 0.000000e+00 1171.0
5 TraesCS1A01G072300 chr1A 90.559 752 33 14 296 1011 56367967 56368716 0.000000e+00 961.0
6 TraesCS1A01G072300 chr1A 95.814 215 9 0 3907 4121 54461093 54461307 8.480000e-92 348.0
7 TraesCS1A01G072300 chr1A 87.678 211 14 7 3922 4121 56371524 56371733 6.890000e-58 235.0
8 TraesCS1A01G072300 chr1D 88.146 1780 119 45 303 2054 56430701 56428986 0.000000e+00 2034.0
9 TraesCS1A01G072300 chr1D 91.257 1464 83 16 296 1750 56531517 56530090 0.000000e+00 1953.0
10 TraesCS1A01G072300 chr1D 94.278 1136 50 7 2069 3196 56428940 56427812 0.000000e+00 1724.0
11 TraesCS1A01G072300 chr1D 93.548 1116 55 8 2069 3178 56609361 56608257 0.000000e+00 1646.0
12 TraesCS1A01G072300 chr1D 93.116 1133 59 12 2069 3196 56874172 56873054 0.000000e+00 1642.0
13 TraesCS1A01G072300 chr1D 88.453 1403 102 32 366 1750 56610981 56609621 0.000000e+00 1639.0
14 TraesCS1A01G072300 chr1D 92.344 836 48 6 2369 3196 56529582 56528755 0.000000e+00 1175.0
15 TraesCS1A01G072300 chr1D 90.818 795 47 14 966 1750 56875272 56874494 0.000000e+00 1040.0
16 TraesCS1A01G072300 chr1D 91.840 674 41 8 258 922 56875940 56875272 0.000000e+00 928.0
17 TraesCS1A01G072300 chr1D 86.573 715 87 7 3195 3904 437003492 437002782 0.000000e+00 780.0
18 TraesCS1A01G072300 chr1D 91.800 439 26 5 1867 2297 56530010 56529574 1.640000e-168 603.0
19 TraesCS1A01G072300 chr1D 86.041 437 36 6 339 774 56618430 56618018 2.920000e-121 446.0
20 TraesCS1A01G072300 chr1D 94.884 215 11 0 3907 4121 56427813 56427599 1.840000e-88 337.0
21 TraesCS1A01G072300 chr1D 82.776 389 35 14 1442 1827 57200749 57200390 6.650000e-83 318.0
22 TraesCS1A01G072300 chr1D 84.642 293 35 6 296 582 56612630 56612342 2.430000e-72 283.0
23 TraesCS1A01G072300 chr1D 90.355 197 19 0 1248 1444 57212907 57212711 4.090000e-65 259.0
24 TraesCS1A01G072300 chr1D 90.811 185 17 0 1859 2043 56874417 56874233 8.850000e-62 248.0
25 TraesCS1A01G072300 chr1D 85.217 230 19 4 3907 4121 56528756 56528527 5.360000e-54 222.0
26 TraesCS1A01G072300 chr1D 92.199 141 11 0 3907 4047 56873055 56872915 2.510000e-47 200.0
27 TraesCS1A01G072300 chr1D 75.442 509 54 24 1916 2369 57073748 57073256 9.100000e-42 182.0
28 TraesCS1A01G072300 chr1D 97.297 74 2 0 4048 4121 56869542 56869469 4.320000e-25 126.0
29 TraesCS1A01G072300 chr1B 91.385 1300 86 15 1913 3196 91881289 91880000 0.000000e+00 1757.0
30 TraesCS1A01G072300 chr1B 88.901 883 63 22 966 1841 91882373 91881519 0.000000e+00 1055.0
31 TraesCS1A01G072300 chr1B 91.250 560 35 3 258 816 91882981 91882435 0.000000e+00 750.0
32 TraesCS1A01G072300 chr1B 84.783 230 20 4 3907 4121 91880001 91879772 2.490000e-52 217.0
33 TraesCS1A01G072300 chr1B 82.479 234 35 5 27 257 407906405 407906175 2.510000e-47 200.0
34 TraesCS1A01G072300 chr1B 78.750 160 26 7 1319 1474 119774448 119774293 2.620000e-17 100.0
35 TraesCS1A01G072300 chr7D 90.909 715 57 8 3194 3902 272929369 272930081 0.000000e+00 953.0
36 TraesCS1A01G072300 chr7D 86.611 717 88 7 3193 3904 633405275 633405988 0.000000e+00 785.0
37 TraesCS1A01G072300 chr2D 89.525 716 67 8 3195 3904 425758117 425758830 0.000000e+00 900.0
38 TraesCS1A01G072300 chr2A 89.093 706 69 7 3204 3904 562599318 562598616 0.000000e+00 870.0
39 TraesCS1A01G072300 chr5B 88.219 713 77 7 3196 3904 12666416 12665707 0.000000e+00 845.0
40 TraesCS1A01G072300 chr5B 88.079 713 78 7 3196 3904 662076257 662075548 0.000000e+00 839.0
41 TraesCS1A01G072300 chr5B 88.406 69 6 2 1094 1161 363669759 363669692 9.490000e-12 82.4
42 TraesCS1A01G072300 chr4D 86.154 715 86 11 3196 3904 324258068 324258775 0.000000e+00 760.0
43 TraesCS1A01G072300 chr4D 82.297 209 32 5 49 257 14430697 14430494 4.230000e-40 176.0
44 TraesCS1A01G072300 chr7B 85.654 711 95 7 3197 3903 64006349 64007056 0.000000e+00 741.0
45 TraesCS1A01G072300 chr7B 76.075 372 72 13 1298 1662 409712036 409711675 1.180000e-40 178.0
46 TraesCS1A01G072300 chr7B 87.162 148 17 1 110 255 646039048 646038901 2.550000e-37 167.0
47 TraesCS1A01G072300 chr7B 87.162 148 17 1 110 255 646039892 646039745 2.550000e-37 167.0
48 TraesCS1A01G072300 chr4A 84.746 236 29 7 27 259 730694186 730693955 3.200000e-56 230.0
49 TraesCS1A01G072300 chr2B 83.401 247 31 6 17 260 563319635 563319874 1.930000e-53 220.0
50 TraesCS1A01G072300 chr2B 86.957 184 20 4 73 254 495712475 495712656 1.940000e-48 204.0
51 TraesCS1A01G072300 chr2B 85.119 168 23 2 94 260 563319909 563320075 1.970000e-38 171.0
52 TraesCS1A01G072300 chr3D 79.592 245 44 6 19 260 320761828 320761587 1.970000e-38 171.0
53 TraesCS1A01G072300 chr5D 85.393 89 11 2 1094 1181 315485486 315485399 1.580000e-14 91.6


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 TraesCS1A01G072300 chr1A 56336402 56340522 4120 False 7611.000000 7611 100.000000 1 4121 1 chr1A.!!$F1 4120
1 TraesCS1A01G072300 chr1A 54458236 54461307 3071 False 1460.000000 2194 94.021667 296 4121 3 chr1A.!!$F2 3825
2 TraesCS1A01G072300 chr1A 56367967 56371733 3766 False 1033.250000 1766 90.159500 296 4121 4 chr1A.!!$F3 3825
3 TraesCS1A01G072300 chr1D 56427599 56430701 3102 True 1365.000000 2034 92.436000 303 4121 3 chr1D.!!$R6 3818
4 TraesCS1A01G072300 chr1D 56608257 56612630 4373 True 1189.333333 1646 88.881000 296 3178 3 chr1D.!!$R8 2882
5 TraesCS1A01G072300 chr1D 56528527 56531517 2990 True 988.250000 1953 90.154500 296 4121 4 chr1D.!!$R7 3825
6 TraesCS1A01G072300 chr1D 437002782 437003492 710 True 780.000000 780 86.573000 3195 3904 1 chr1D.!!$R5 709
7 TraesCS1A01G072300 chr1D 56869469 56875940 6471 True 697.333333 1642 92.680167 258 4121 6 chr1D.!!$R9 3863
8 TraesCS1A01G072300 chr1B 91879772 91882981 3209 True 944.750000 1757 89.079750 258 4121 4 chr1B.!!$R3 3863
9 TraesCS1A01G072300 chr7D 272929369 272930081 712 False 953.000000 953 90.909000 3194 3902 1 chr7D.!!$F1 708
10 TraesCS1A01G072300 chr7D 633405275 633405988 713 False 785.000000 785 86.611000 3193 3904 1 chr7D.!!$F2 711
11 TraesCS1A01G072300 chr2D 425758117 425758830 713 False 900.000000 900 89.525000 3195 3904 1 chr2D.!!$F1 709
12 TraesCS1A01G072300 chr2A 562598616 562599318 702 True 870.000000 870 89.093000 3204 3904 1 chr2A.!!$R1 700
13 TraesCS1A01G072300 chr5B 12665707 12666416 709 True 845.000000 845 88.219000 3196 3904 1 chr5B.!!$R1 708
14 TraesCS1A01G072300 chr5B 662075548 662076257 709 True 839.000000 839 88.079000 3196 3904 1 chr5B.!!$R3 708
15 TraesCS1A01G072300 chr4D 324258068 324258775 707 False 760.000000 760 86.154000 3196 3904 1 chr4D.!!$F1 708
16 TraesCS1A01G072300 chr7B 64006349 64007056 707 False 741.000000 741 85.654000 3197 3903 1 chr7B.!!$F1 706

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
125 126 0.517316 GTCTGCCACGTCAACAATCC 59.483 55.0 0.0 0.0 0.00 3.01 F
126 127 0.605319 TCTGCCACGTCAACAATCCC 60.605 55.0 0.0 0.0 0.00 3.85 F
129 130 0.893727 GCCACGTCAACAATCCCCTT 60.894 55.0 0.0 0.0 0.00 3.95 F
1267 3508 0.931702 TACGTGTTTGGTTCGTGCAG 59.068 50.0 0.0 0.0 38.27 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1107 3305 1.064946 CGCCTCGAAGTAGAGCAGG 59.935 63.158 0.00 0.0 36.95 4.85 R
2125 4683 0.541063 TGTTCTGGTAGAGGCCACGA 60.541 55.000 5.01 0.0 34.36 4.35 R
2158 4717 4.486090 CGCTGCTTCTGTAGAAACTTCTA 58.514 43.478 0.00 0.0 38.70 2.10 R
3200 5781 0.486879 AGGGCAATCCACCTTTTCCA 59.513 50.000 0.00 0.0 38.24 3.53 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
49 50 8.527567 GCATTTTTAGTTGCCTGTTACAATAA 57.472 30.769 0.00 0.00 32.66 1.40
50 51 8.983724 GCATTTTTAGTTGCCTGTTACAATAAA 58.016 29.630 0.00 0.00 32.66 1.40
57 58 8.642908 AGTTGCCTGTTACAATAAAGAAAAAC 57.357 30.769 0.00 0.00 0.00 2.43
58 59 8.254508 AGTTGCCTGTTACAATAAAGAAAAACA 58.745 29.630 0.00 0.00 0.00 2.83
59 60 7.995463 TGCCTGTTACAATAAAGAAAAACAC 57.005 32.000 0.00 0.00 0.00 3.32
60 61 6.693545 TGCCTGTTACAATAAAGAAAAACACG 59.306 34.615 0.00 0.00 0.00 4.49
61 62 6.345487 GCCTGTTACAATAAAGAAAAACACGC 60.345 38.462 0.00 0.00 0.00 5.34
62 63 6.915843 CCTGTTACAATAAAGAAAAACACGCT 59.084 34.615 0.00 0.00 0.00 5.07
63 64 7.434013 CCTGTTACAATAAAGAAAAACACGCTT 59.566 33.333 0.00 0.00 0.00 4.68
64 65 8.330302 TGTTACAATAAAGAAAAACACGCTTC 57.670 30.769 0.00 0.00 0.00 3.86
65 66 7.164498 TGTTACAATAAAGAAAAACACGCTTCG 59.836 33.333 0.00 0.00 0.00 3.79
66 67 4.439776 ACAATAAAGAAAAACACGCTTCGC 59.560 37.500 0.00 0.00 0.00 4.70
105 106 3.771160 CGTCCCCGCTACAGCCTT 61.771 66.667 0.00 0.00 37.91 4.35
106 107 2.125106 GTCCCCGCTACAGCCTTG 60.125 66.667 0.00 0.00 37.91 3.61
107 108 2.606519 TCCCCGCTACAGCCTTGT 60.607 61.111 0.00 0.00 41.39 3.16
108 109 2.125106 CCCCGCTACAGCCTTGTC 60.125 66.667 0.00 0.00 38.76 3.18
109 110 2.660064 CCCCGCTACAGCCTTGTCT 61.660 63.158 0.00 0.00 38.76 3.41
110 111 1.448540 CCCGCTACAGCCTTGTCTG 60.449 63.158 0.00 0.00 38.76 3.51
111 112 2.103042 CCGCTACAGCCTTGTCTGC 61.103 63.158 0.00 0.00 38.76 4.26
112 113 2.103042 CGCTACAGCCTTGTCTGCC 61.103 63.158 0.00 0.00 38.76 4.85
113 114 1.003355 GCTACAGCCTTGTCTGCCA 60.003 57.895 0.00 0.00 38.76 4.92
114 115 1.301677 GCTACAGCCTTGTCTGCCAC 61.302 60.000 0.00 0.00 38.76 5.01
115 116 1.005037 TACAGCCTTGTCTGCCACG 60.005 57.895 0.00 0.00 38.76 4.94
116 117 1.754380 TACAGCCTTGTCTGCCACGT 61.754 55.000 0.00 0.00 38.76 4.49
117 118 2.031163 AGCCTTGTCTGCCACGTC 59.969 61.111 0.00 0.00 0.00 4.34
118 119 2.280797 GCCTTGTCTGCCACGTCA 60.281 61.111 0.00 0.00 0.00 4.35
119 120 1.891919 GCCTTGTCTGCCACGTCAA 60.892 57.895 0.00 0.00 0.00 3.18
120 121 1.941812 CCTTGTCTGCCACGTCAAC 59.058 57.895 0.00 0.00 0.00 3.18
121 122 0.813610 CCTTGTCTGCCACGTCAACA 60.814 55.000 0.00 0.00 0.00 3.33
122 123 1.013596 CTTGTCTGCCACGTCAACAA 58.986 50.000 0.00 0.00 0.00 2.83
123 124 1.603802 CTTGTCTGCCACGTCAACAAT 59.396 47.619 0.00 0.00 0.00 2.71
124 125 1.225855 TGTCTGCCACGTCAACAATC 58.774 50.000 0.00 0.00 0.00 2.67
125 126 0.517316 GTCTGCCACGTCAACAATCC 59.483 55.000 0.00 0.00 0.00 3.01
126 127 0.605319 TCTGCCACGTCAACAATCCC 60.605 55.000 0.00 0.00 0.00 3.85
127 128 1.586154 CTGCCACGTCAACAATCCCC 61.586 60.000 0.00 0.00 0.00 4.81
128 129 1.303317 GCCACGTCAACAATCCCCT 60.303 57.895 0.00 0.00 0.00 4.79
129 130 0.893727 GCCACGTCAACAATCCCCTT 60.894 55.000 0.00 0.00 0.00 3.95
130 131 1.165270 CCACGTCAACAATCCCCTTC 58.835 55.000 0.00 0.00 0.00 3.46
131 132 1.544537 CCACGTCAACAATCCCCTTCA 60.545 52.381 0.00 0.00 0.00 3.02
132 133 2.436417 CACGTCAACAATCCCCTTCAT 58.564 47.619 0.00 0.00 0.00 2.57
133 134 3.605634 CACGTCAACAATCCCCTTCATA 58.394 45.455 0.00 0.00 0.00 2.15
134 135 4.006989 CACGTCAACAATCCCCTTCATAA 58.993 43.478 0.00 0.00 0.00 1.90
135 136 4.007659 ACGTCAACAATCCCCTTCATAAC 58.992 43.478 0.00 0.00 0.00 1.89
136 137 4.006989 CGTCAACAATCCCCTTCATAACA 58.993 43.478 0.00 0.00 0.00 2.41
137 138 4.142687 CGTCAACAATCCCCTTCATAACAC 60.143 45.833 0.00 0.00 0.00 3.32
138 139 4.006989 TCAACAATCCCCTTCATAACACG 58.993 43.478 0.00 0.00 0.00 4.49
139 140 2.365582 ACAATCCCCTTCATAACACGC 58.634 47.619 0.00 0.00 0.00 5.34
140 141 2.026262 ACAATCCCCTTCATAACACGCT 60.026 45.455 0.00 0.00 0.00 5.07
141 142 2.614057 CAATCCCCTTCATAACACGCTC 59.386 50.000 0.00 0.00 0.00 5.03
142 143 1.271856 TCCCCTTCATAACACGCTCA 58.728 50.000 0.00 0.00 0.00 4.26
143 144 1.626321 TCCCCTTCATAACACGCTCAA 59.374 47.619 0.00 0.00 0.00 3.02
144 145 2.009774 CCCCTTCATAACACGCTCAAG 58.990 52.381 0.00 0.00 0.00 3.02
145 146 2.009774 CCCTTCATAACACGCTCAAGG 58.990 52.381 0.00 0.00 0.00 3.61
146 147 2.615493 CCCTTCATAACACGCTCAAGGT 60.615 50.000 0.00 0.00 30.23 3.50
147 148 3.074412 CCTTCATAACACGCTCAAGGTT 58.926 45.455 0.00 0.00 0.00 3.50
148 149 3.502211 CCTTCATAACACGCTCAAGGTTT 59.498 43.478 0.00 0.00 0.00 3.27
149 150 4.693566 CCTTCATAACACGCTCAAGGTTTA 59.306 41.667 0.00 0.00 0.00 2.01
150 151 5.180492 CCTTCATAACACGCTCAAGGTTTAA 59.820 40.000 0.00 0.00 0.00 1.52
151 152 6.293735 CCTTCATAACACGCTCAAGGTTTAAA 60.294 38.462 0.00 0.00 0.00 1.52
152 153 6.621316 TCATAACACGCTCAAGGTTTAAAA 57.379 33.333 0.00 0.00 0.00 1.52
153 154 7.209471 TCATAACACGCTCAAGGTTTAAAAT 57.791 32.000 0.00 0.00 0.00 1.82
154 155 8.325421 TCATAACACGCTCAAGGTTTAAAATA 57.675 30.769 0.00 0.00 0.00 1.40
155 156 8.447833 TCATAACACGCTCAAGGTTTAAAATAG 58.552 33.333 0.00 0.00 0.00 1.73
156 157 6.870971 AACACGCTCAAGGTTTAAAATAGA 57.129 33.333 0.00 0.00 0.00 1.98
157 158 6.237313 ACACGCTCAAGGTTTAAAATAGAC 57.763 37.500 0.00 0.00 0.00 2.59
158 159 5.180680 ACACGCTCAAGGTTTAAAATAGACC 59.819 40.000 0.00 0.00 0.00 3.85
159 160 4.390909 ACGCTCAAGGTTTAAAATAGACCG 59.609 41.667 0.00 0.00 38.48 4.79
160 161 4.201783 CGCTCAAGGTTTAAAATAGACCGG 60.202 45.833 0.00 0.00 38.48 5.28
161 162 4.095932 GCTCAAGGTTTAAAATAGACCGGG 59.904 45.833 6.32 0.00 38.48 5.73
162 163 5.493809 CTCAAGGTTTAAAATAGACCGGGA 58.506 41.667 6.32 0.00 38.48 5.14
163 164 6.069705 TCAAGGTTTAAAATAGACCGGGAT 57.930 37.500 6.32 0.00 38.48 3.85
164 165 6.117488 TCAAGGTTTAAAATAGACCGGGATC 58.883 40.000 6.32 0.00 38.48 3.36
165 166 5.703730 AGGTTTAAAATAGACCGGGATCA 57.296 39.130 6.32 0.00 38.48 2.92
166 167 6.069705 AGGTTTAAAATAGACCGGGATCAA 57.930 37.500 6.32 0.00 38.48 2.57
167 168 6.486941 AGGTTTAAAATAGACCGGGATCAAA 58.513 36.000 6.32 0.00 38.48 2.69
168 169 7.123383 AGGTTTAAAATAGACCGGGATCAAAT 58.877 34.615 6.32 0.00 38.48 2.32
169 170 8.276477 AGGTTTAAAATAGACCGGGATCAAATA 58.724 33.333 6.32 0.00 38.48 1.40
170 171 8.565416 GGTTTAAAATAGACCGGGATCAAATAG 58.435 37.037 6.32 0.00 0.00 1.73
171 172 9.117183 GTTTAAAATAGACCGGGATCAAATAGT 57.883 33.333 6.32 0.00 0.00 2.12
172 173 9.689501 TTTAAAATAGACCGGGATCAAATAGTT 57.310 29.630 6.32 0.00 0.00 2.24
173 174 9.689501 TTAAAATAGACCGGGATCAAATAGTTT 57.310 29.630 6.32 2.42 0.00 2.66
175 176 8.904099 AAATAGACCGGGATCAAATAGTTTAG 57.096 34.615 6.32 0.00 0.00 1.85
176 177 5.952347 AGACCGGGATCAAATAGTTTAGT 57.048 39.130 6.32 0.00 0.00 2.24
177 178 5.671493 AGACCGGGATCAAATAGTTTAGTG 58.329 41.667 6.32 0.00 0.00 2.74
178 179 5.189145 AGACCGGGATCAAATAGTTTAGTGT 59.811 40.000 6.32 0.00 0.00 3.55
179 180 5.183228 ACCGGGATCAAATAGTTTAGTGTG 58.817 41.667 6.32 0.00 0.00 3.82
180 181 4.035208 CCGGGATCAAATAGTTTAGTGTGC 59.965 45.833 0.00 0.00 0.00 4.57
181 182 4.876107 CGGGATCAAATAGTTTAGTGTGCT 59.124 41.667 0.00 0.00 0.00 4.40
182 183 5.220662 CGGGATCAAATAGTTTAGTGTGCTG 60.221 44.000 0.00 0.00 0.00 4.41
183 184 5.880332 GGGATCAAATAGTTTAGTGTGCTGA 59.120 40.000 0.00 0.00 0.00 4.26
184 185 6.543831 GGGATCAAATAGTTTAGTGTGCTGAT 59.456 38.462 0.00 0.00 0.00 2.90
185 186 7.067494 GGGATCAAATAGTTTAGTGTGCTGATT 59.933 37.037 0.00 0.00 0.00 2.57
186 187 8.462016 GGATCAAATAGTTTAGTGTGCTGATTT 58.538 33.333 0.00 0.00 0.00 2.17
187 188 9.495754 GATCAAATAGTTTAGTGTGCTGATTTC 57.504 33.333 0.00 0.00 0.00 2.17
188 189 8.389779 TCAAATAGTTTAGTGTGCTGATTTCA 57.610 30.769 0.00 0.00 0.00 2.69
189 190 8.506437 TCAAATAGTTTAGTGTGCTGATTTCAG 58.494 33.333 3.13 3.13 46.40 3.02
190 191 6.992063 ATAGTTTAGTGTGCTGATTTCAGG 57.008 37.500 9.49 0.00 43.94 3.86
191 192 4.074970 AGTTTAGTGTGCTGATTTCAGGG 58.925 43.478 9.49 0.00 43.94 4.45
192 193 4.072131 GTTTAGTGTGCTGATTTCAGGGA 58.928 43.478 9.49 0.00 43.94 4.20
193 194 4.574674 TTAGTGTGCTGATTTCAGGGAT 57.425 40.909 9.49 0.00 43.94 3.85
194 195 3.446442 AGTGTGCTGATTTCAGGGATT 57.554 42.857 9.49 0.00 43.94 3.01
195 196 3.771216 AGTGTGCTGATTTCAGGGATTT 58.229 40.909 9.49 0.00 43.94 2.17
196 197 4.922206 AGTGTGCTGATTTCAGGGATTTA 58.078 39.130 9.49 0.00 43.94 1.40
197 198 5.324409 AGTGTGCTGATTTCAGGGATTTAA 58.676 37.500 9.49 0.00 43.94 1.52
198 199 5.774690 AGTGTGCTGATTTCAGGGATTTAAA 59.225 36.000 9.49 0.00 43.94 1.52
199 200 5.863935 GTGTGCTGATTTCAGGGATTTAAAC 59.136 40.000 9.49 0.00 43.94 2.01
200 201 5.774690 TGTGCTGATTTCAGGGATTTAAACT 59.225 36.000 9.49 0.00 43.94 2.66
201 202 6.267471 TGTGCTGATTTCAGGGATTTAAACTT 59.733 34.615 9.49 0.00 43.94 2.66
202 203 6.808704 GTGCTGATTTCAGGGATTTAAACTTC 59.191 38.462 9.49 0.00 43.94 3.01
203 204 6.493115 TGCTGATTTCAGGGATTTAAACTTCA 59.507 34.615 9.49 0.00 43.94 3.02
204 205 7.031975 GCTGATTTCAGGGATTTAAACTTCAG 58.968 38.462 9.49 0.00 43.94 3.02
205 206 7.466746 TGATTTCAGGGATTTAAACTTCAGG 57.533 36.000 0.00 0.00 0.00 3.86
206 207 7.237982 TGATTTCAGGGATTTAAACTTCAGGA 58.762 34.615 0.00 0.00 0.00 3.86
207 208 7.895429 TGATTTCAGGGATTTAAACTTCAGGAT 59.105 33.333 0.00 0.00 0.00 3.24
208 209 8.670521 ATTTCAGGGATTTAAACTTCAGGATT 57.329 30.769 0.00 0.00 0.00 3.01
209 210 8.491045 TTTCAGGGATTTAAACTTCAGGATTT 57.509 30.769 0.00 0.00 0.00 2.17
210 211 7.466746 TCAGGGATTTAAACTTCAGGATTTG 57.533 36.000 0.00 0.00 0.00 2.32
211 212 7.237982 TCAGGGATTTAAACTTCAGGATTTGA 58.762 34.615 0.00 0.00 0.00 2.69
212 213 7.895429 TCAGGGATTTAAACTTCAGGATTTGAT 59.105 33.333 0.00 0.00 35.27 2.57
213 214 8.534496 CAGGGATTTAAACTTCAGGATTTGATT 58.466 33.333 0.00 0.00 35.27 2.57
214 215 9.104713 AGGGATTTAAACTTCAGGATTTGATTT 57.895 29.630 0.00 0.00 35.27 2.17
222 223 6.846350 ACTTCAGGATTTGATTTAGCTTTCG 58.154 36.000 0.00 0.00 35.27 3.46
223 224 6.431234 ACTTCAGGATTTGATTTAGCTTTCGT 59.569 34.615 0.00 0.00 35.27 3.85
224 225 6.422776 TCAGGATTTGATTTAGCTTTCGTC 57.577 37.500 0.00 0.00 0.00 4.20
225 226 6.173339 TCAGGATTTGATTTAGCTTTCGTCT 58.827 36.000 0.00 0.00 0.00 4.18
226 227 7.327975 TCAGGATTTGATTTAGCTTTCGTCTA 58.672 34.615 0.00 0.00 0.00 2.59
227 228 7.277981 TCAGGATTTGATTTAGCTTTCGTCTAC 59.722 37.037 0.00 0.00 0.00 2.59
228 229 7.064609 CAGGATTTGATTTAGCTTTCGTCTACA 59.935 37.037 0.00 0.00 0.00 2.74
229 230 7.606456 AGGATTTGATTTAGCTTTCGTCTACAA 59.394 33.333 0.00 0.00 0.00 2.41
230 231 7.905493 GGATTTGATTTAGCTTTCGTCTACAAG 59.095 37.037 0.00 0.00 0.00 3.16
231 232 7.724305 TTTGATTTAGCTTTCGTCTACAAGT 57.276 32.000 0.00 0.00 0.00 3.16
232 233 7.724305 TTGATTTAGCTTTCGTCTACAAGTT 57.276 32.000 0.00 0.00 0.00 2.66
233 234 7.724305 TGATTTAGCTTTCGTCTACAAGTTT 57.276 32.000 0.00 0.00 0.00 2.66
234 235 8.821147 TGATTTAGCTTTCGTCTACAAGTTTA 57.179 30.769 0.00 0.00 0.00 2.01
235 236 9.263538 TGATTTAGCTTTCGTCTACAAGTTTAA 57.736 29.630 0.00 0.00 0.00 1.52
236 237 9.742552 GATTTAGCTTTCGTCTACAAGTTTAAG 57.257 33.333 0.00 0.00 0.00 1.85
237 238 7.647907 TTAGCTTTCGTCTACAAGTTTAAGG 57.352 36.000 0.00 0.00 0.00 2.69
238 239 5.608449 AGCTTTCGTCTACAAGTTTAAGGT 58.392 37.500 0.00 0.00 0.00 3.50
239 240 6.053650 AGCTTTCGTCTACAAGTTTAAGGTT 58.946 36.000 0.00 0.00 0.00 3.50
240 241 6.202379 AGCTTTCGTCTACAAGTTTAAGGTTC 59.798 38.462 0.00 0.00 0.00 3.62
241 242 6.018507 GCTTTCGTCTACAAGTTTAAGGTTCA 60.019 38.462 0.00 0.00 0.00 3.18
242 243 7.307811 GCTTTCGTCTACAAGTTTAAGGTTCAT 60.308 37.037 0.00 0.00 0.00 2.57
243 244 8.441312 TTTCGTCTACAAGTTTAAGGTTCATT 57.559 30.769 0.00 0.00 0.00 2.57
244 245 8.441312 TTCGTCTACAAGTTTAAGGTTCATTT 57.559 30.769 0.00 0.00 0.00 2.32
245 246 8.441312 TCGTCTACAAGTTTAAGGTTCATTTT 57.559 30.769 0.00 0.00 0.00 1.82
246 247 8.339714 TCGTCTACAAGTTTAAGGTTCATTTTG 58.660 33.333 0.00 0.00 0.00 2.44
247 248 7.589954 CGTCTACAAGTTTAAGGTTCATTTTGG 59.410 37.037 0.00 0.00 0.00 3.28
248 249 8.626526 GTCTACAAGTTTAAGGTTCATTTTGGA 58.373 33.333 0.00 0.00 0.00 3.53
249 250 8.626526 TCTACAAGTTTAAGGTTCATTTTGGAC 58.373 33.333 0.00 0.00 0.00 4.02
250 251 7.418337 ACAAGTTTAAGGTTCATTTTGGACT 57.582 32.000 0.00 0.00 0.00 3.85
251 252 7.847096 ACAAGTTTAAGGTTCATTTTGGACTT 58.153 30.769 0.00 0.00 0.00 3.01
252 253 8.318412 ACAAGTTTAAGGTTCATTTTGGACTTT 58.682 29.630 0.00 0.00 0.00 2.66
253 254 9.161629 CAAGTTTAAGGTTCATTTTGGACTTTT 57.838 29.630 0.00 0.00 0.00 2.27
254 255 9.733556 AAGTTTAAGGTTCATTTTGGACTTTTT 57.266 25.926 0.00 0.00 0.00 1.94
255 256 9.378551 AGTTTAAGGTTCATTTTGGACTTTTTC 57.621 29.630 0.00 0.00 0.00 2.29
256 257 8.609176 GTTTAAGGTTCATTTTGGACTTTTTCC 58.391 33.333 0.00 0.00 46.13 3.13
463 2058 7.169982 CCATCTTGTATGTTAACTCTTCGATCC 59.830 40.741 7.22 0.00 0.00 3.36
696 2292 2.393271 AGGTCGCAAAATCTCCTCAG 57.607 50.000 0.00 0.00 0.00 3.35
1027 3224 3.402681 GGGCTAGGGTGCTGCTCA 61.403 66.667 0.00 0.00 0.00 4.26
1107 3305 4.681978 ACCGCGCTCACCAAGTCC 62.682 66.667 5.56 0.00 0.00 3.85
1267 3508 0.931702 TACGTGTTTGGTTCGTGCAG 59.068 50.000 0.00 0.00 38.27 4.41
1776 4041 1.204231 TCAGAGAGACTGCTGCATGTC 59.796 52.381 18.36 18.36 45.38 3.06
1840 4125 5.012239 AGCACACAGATTACACAATGGATT 58.988 37.500 0.00 0.00 0.00 3.01
1890 4213 4.516698 AGAGAGCCGCACATATTAATTTGG 59.483 41.667 10.17 1.75 0.00 3.28
1940 4391 2.167487 ACAGCACAAATTGGACGGTTTT 59.833 40.909 0.00 0.00 0.00 2.43
1953 4404 3.243602 GGACGGTTTTTGTGGCTACAATT 60.244 43.478 16.93 0.00 45.56 2.32
1971 4423 9.670180 GCTACAATTAATTTGAAAATAACGTGC 57.330 29.630 0.00 0.00 38.76 5.34
2029 4544 6.260050 CGTGGTCATATAGTGGCTAAAAATGT 59.740 38.462 0.00 0.00 31.47 2.71
2158 4717 0.254178 AGAACAGCATTCCATCGGCT 59.746 50.000 0.00 0.00 38.70 5.52
2173 4732 4.098044 CCATCGGCTAGAAGTTTCTACAGA 59.902 45.833 0.00 3.30 38.70 3.41
2257 4828 7.978982 AGCAGTATTGTAAAGCAAATACTGAG 58.021 34.615 27.41 11.66 42.94 3.35
2264 4835 8.896320 TTGTAAAGCAAATACTGAGACTTGTA 57.104 30.769 0.00 0.00 33.53 2.41
2473 5047 2.030457 GTCTGGTGAAGTGACAACAACG 59.970 50.000 0.00 0.00 37.03 4.10
2478 5052 4.142859 TGGTGAAGTGACAACAACGTTTAC 60.143 41.667 0.00 0.00 34.39 2.01
2495 5069 6.698380 ACGTTTACCTTCAGTAACTGATGAT 58.302 36.000 0.00 0.00 40.70 2.45
2524 5098 1.415289 CCATACTGCAGCTCATCCTCA 59.585 52.381 15.27 0.00 0.00 3.86
2535 5109 2.171448 GCTCATCCTCAAAGGGAAGCTA 59.829 50.000 0.00 0.00 39.02 3.32
3087 5668 1.435925 CTACACTGTCGCGCCCATA 59.564 57.895 0.00 0.00 0.00 2.74
3111 5692 2.737039 CGGAGTTCTTGCTAGGCTTCTC 60.737 54.545 0.00 0.00 0.00 2.87
3129 5710 5.627735 GCTTCTCCATAACTGATGTTCCTGA 60.628 44.000 0.00 0.00 37.59 3.86
3130 5711 5.344743 TCTCCATAACTGATGTTCCTGAC 57.655 43.478 0.00 0.00 37.59 3.51
3131 5712 5.026121 TCTCCATAACTGATGTTCCTGACT 58.974 41.667 0.00 0.00 37.59 3.41
3132 5713 5.485353 TCTCCATAACTGATGTTCCTGACTT 59.515 40.000 0.00 0.00 37.59 3.01
3133 5714 5.734720 TCCATAACTGATGTTCCTGACTTC 58.265 41.667 0.00 0.00 37.59 3.01
3134 5715 4.878397 CCATAACTGATGTTCCTGACTTCC 59.122 45.833 0.00 0.00 37.59 3.46
3135 5716 5.338708 CCATAACTGATGTTCCTGACTTCCT 60.339 44.000 0.00 0.00 37.59 3.36
3136 5717 3.692257 ACTGATGTTCCTGACTTCCTG 57.308 47.619 0.00 0.00 32.84 3.86
3140 5721 4.792068 TGATGTTCCTGACTTCCTGTTTT 58.208 39.130 0.00 0.00 32.84 2.43
3141 5722 4.821805 TGATGTTCCTGACTTCCTGTTTTC 59.178 41.667 0.00 0.00 32.84 2.29
3183 5764 5.979517 GTCAATGCCATCCTTGTAATTTAGC 59.020 40.000 0.00 0.00 0.00 3.09
3223 5804 1.789576 AAAGGTGGATTGCCCTCGGT 61.790 55.000 0.00 0.00 35.38 4.69
3226 5807 1.335132 GGTGGATTGCCCTCGGTCTA 61.335 60.000 0.00 0.00 35.38 2.59
3233 5814 0.760567 TGCCCTCGGTCTATGCATCT 60.761 55.000 0.19 0.00 0.00 2.90
3251 5832 2.060004 CTGGAAGATGCATGCAGCCG 62.060 60.000 30.96 16.93 38.55 5.52
3264 5847 6.511416 TGCATGCAGCCGTATTATTAAAAAT 58.489 32.000 18.46 0.00 44.83 1.82
3309 5893 8.633561 TCTGGTATCTGAAGTATAACTCACATG 58.366 37.037 0.00 0.00 0.00 3.21
3319 5903 2.469274 AACTCACATGAGGAGCACAG 57.531 50.000 13.33 0.00 46.13 3.66
3325 5909 3.565482 TCACATGAGGAGCACAGAAAAAC 59.435 43.478 0.00 0.00 0.00 2.43
3330 5914 4.269183 TGAGGAGCACAGAAAAACAAAGA 58.731 39.130 0.00 0.00 0.00 2.52
3331 5915 4.889409 TGAGGAGCACAGAAAAACAAAGAT 59.111 37.500 0.00 0.00 0.00 2.40
3332 5916 6.061441 TGAGGAGCACAGAAAAACAAAGATA 58.939 36.000 0.00 0.00 0.00 1.98
3333 5917 6.545666 TGAGGAGCACAGAAAAACAAAGATAA 59.454 34.615 0.00 0.00 0.00 1.75
3335 5919 7.428826 AGGAGCACAGAAAAACAAAGATAAAG 58.571 34.615 0.00 0.00 0.00 1.85
3336 5920 6.642540 GGAGCACAGAAAAACAAAGATAAAGG 59.357 38.462 0.00 0.00 0.00 3.11
3386 5978 3.452264 CAGTGGACATCAAGGACCTATCA 59.548 47.826 0.00 0.00 0.00 2.15
3404 5996 7.568349 ACCTATCATATTATGCGACCATCATT 58.432 34.615 0.00 0.00 32.85 2.57
3405 5997 8.049117 ACCTATCATATTATGCGACCATCATTT 58.951 33.333 0.00 0.00 32.85 2.32
3445 6037 1.040646 GTGCTACCATCTCCCATCGA 58.959 55.000 0.00 0.00 0.00 3.59
3472 6064 0.324645 CAGTAGCCAAATGCCCCCTT 60.325 55.000 0.00 0.00 42.71 3.95
3474 6066 1.001503 TAGCCAAATGCCCCCTTGG 59.998 57.895 0.00 0.00 44.23 3.61
3499 6091 2.159366 CGTAGGAGTGAGTAGCAACCAG 60.159 54.545 0.00 0.00 0.00 4.00
3515 6108 1.695114 CCAGGTACGGATCCATGCCA 61.695 60.000 17.63 0.00 0.00 4.92
3532 6125 5.512749 CCATGCCATAGCTCTGAAGATAACT 60.513 44.000 0.00 0.00 40.80 2.24
3596 6189 4.516698 CGTTTCTGCAATTCCATATAGCCT 59.483 41.667 0.00 0.00 0.00 4.58
3733 6326 7.094805 GCTATATGGATTGATCGCCAAAGTAAA 60.095 37.037 5.95 0.00 38.43 2.01
3796 6390 6.012658 TCATCCTGAATACAAAAGCAACAC 57.987 37.500 0.00 0.00 0.00 3.32
3852 6447 6.215636 AGTTATCCTTGGTAAGAATGACCTGT 59.784 38.462 0.00 0.00 41.76 4.00
3904 6500 3.181480 GCACAAAGGCACCTTAACTTTCA 60.181 43.478 1.53 0.00 34.84 2.69
3905 6501 4.501400 GCACAAAGGCACCTTAACTTTCAT 60.501 41.667 1.53 0.00 34.84 2.57
3906 6502 5.600696 CACAAAGGCACCTTAACTTTCATT 58.399 37.500 1.53 0.00 34.84 2.57
3907 6503 6.048509 CACAAAGGCACCTTAACTTTCATTT 58.951 36.000 1.53 0.00 34.84 2.32
3941 6538 4.445452 ACTTACACCGACAACGATACAT 57.555 40.909 0.00 0.00 42.66 2.29
3969 6566 7.428282 TTGTTTCCTTCCAAACTTTGAAAAC 57.572 32.000 2.87 6.37 37.20 2.43
4077 10049 9.482175 AGATCTTGTTTACACTAAGAGGTAGAT 57.518 33.333 0.00 0.00 34.30 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.325282 GTGTTTTTCTTTATTGTAACAGGCAAC 58.675 33.333 0.00 0.00 0.00 4.17
34 35 7.221067 CGTGTTTTTCTTTATTGTAACAGGCAA 59.779 33.333 0.00 0.00 0.00 4.52
35 36 6.693545 CGTGTTTTTCTTTATTGTAACAGGCA 59.306 34.615 0.00 0.00 0.00 4.75
36 37 6.345487 GCGTGTTTTTCTTTATTGTAACAGGC 60.345 38.462 12.58 12.58 44.50 4.85
37 38 6.915843 AGCGTGTTTTTCTTTATTGTAACAGG 59.084 34.615 0.00 0.00 35.60 4.00
38 39 7.908193 AGCGTGTTTTTCTTTATTGTAACAG 57.092 32.000 0.00 0.00 0.00 3.16
39 40 7.164498 CGAAGCGTGTTTTTCTTTATTGTAACA 59.836 33.333 0.00 0.00 0.00 2.41
40 41 7.479553 CGAAGCGTGTTTTTCTTTATTGTAAC 58.520 34.615 0.00 0.00 0.00 2.50
41 42 7.597643 CGAAGCGTGTTTTTCTTTATTGTAA 57.402 32.000 0.00 0.00 0.00 2.41
89 90 2.125106 CAAGGCTGTAGCGGGGAC 60.125 66.667 0.00 0.00 43.26 4.46
90 91 2.606519 ACAAGGCTGTAGCGGGGA 60.607 61.111 0.00 0.00 43.26 4.81
91 92 2.125106 GACAAGGCTGTAGCGGGG 60.125 66.667 0.00 0.00 43.26 5.73
92 93 1.448540 CAGACAAGGCTGTAGCGGG 60.449 63.158 0.00 0.00 43.26 6.13
93 94 2.103042 GCAGACAAGGCTGTAGCGG 61.103 63.158 4.63 0.00 43.26 5.52
94 95 2.103042 GGCAGACAAGGCTGTAGCG 61.103 63.158 4.63 0.00 43.26 4.26
95 96 1.003355 TGGCAGACAAGGCTGTAGC 60.003 57.895 4.63 0.00 38.17 3.58
96 97 1.016130 CGTGGCAGACAAGGCTGTAG 61.016 60.000 4.63 0.00 38.17 2.74
97 98 1.005037 CGTGGCAGACAAGGCTGTA 60.005 57.895 4.63 0.00 38.17 2.74
98 99 2.281070 CGTGGCAGACAAGGCTGT 60.281 61.111 4.63 0.00 38.17 4.40
99 100 2.281070 ACGTGGCAGACAAGGCTG 60.281 61.111 0.00 0.00 38.91 4.85
100 101 2.031163 GACGTGGCAGACAAGGCT 59.969 61.111 0.00 0.00 33.37 4.58
101 102 1.891919 TTGACGTGGCAGACAAGGC 60.892 57.895 0.00 0.00 37.08 4.35
102 103 0.813610 TGTTGACGTGGCAGACAAGG 60.814 55.000 0.00 0.00 32.45 3.61
103 104 1.013596 TTGTTGACGTGGCAGACAAG 58.986 50.000 0.00 0.00 34.52 3.16
104 105 1.601903 GATTGTTGACGTGGCAGACAA 59.398 47.619 0.00 0.40 35.04 3.18
105 106 1.225855 GATTGTTGACGTGGCAGACA 58.774 50.000 0.00 0.00 0.00 3.41
106 107 0.517316 GGATTGTTGACGTGGCAGAC 59.483 55.000 0.00 0.00 0.00 3.51
107 108 0.605319 GGGATTGTTGACGTGGCAGA 60.605 55.000 0.00 0.00 0.00 4.26
108 109 1.586154 GGGGATTGTTGACGTGGCAG 61.586 60.000 0.00 0.00 0.00 4.85
109 110 1.602323 GGGGATTGTTGACGTGGCA 60.602 57.895 0.00 0.00 0.00 4.92
110 111 0.893727 AAGGGGATTGTTGACGTGGC 60.894 55.000 0.00 0.00 0.00 5.01
111 112 1.165270 GAAGGGGATTGTTGACGTGG 58.835 55.000 0.00 0.00 0.00 4.94
112 113 1.890876 TGAAGGGGATTGTTGACGTG 58.109 50.000 0.00 0.00 0.00 4.49
113 114 2.879103 ATGAAGGGGATTGTTGACGT 57.121 45.000 0.00 0.00 0.00 4.34
114 115 4.006989 TGTTATGAAGGGGATTGTTGACG 58.993 43.478 0.00 0.00 0.00 4.35
115 116 4.142687 CGTGTTATGAAGGGGATTGTTGAC 60.143 45.833 0.00 0.00 0.00 3.18
116 117 4.006989 CGTGTTATGAAGGGGATTGTTGA 58.993 43.478 0.00 0.00 0.00 3.18
117 118 3.427503 GCGTGTTATGAAGGGGATTGTTG 60.428 47.826 0.00 0.00 0.00 3.33
118 119 2.752903 GCGTGTTATGAAGGGGATTGTT 59.247 45.455 0.00 0.00 0.00 2.83
119 120 2.026262 AGCGTGTTATGAAGGGGATTGT 60.026 45.455 0.00 0.00 0.00 2.71
120 121 2.614057 GAGCGTGTTATGAAGGGGATTG 59.386 50.000 0.00 0.00 0.00 2.67
121 122 2.238646 TGAGCGTGTTATGAAGGGGATT 59.761 45.455 0.00 0.00 0.00 3.01
122 123 1.837439 TGAGCGTGTTATGAAGGGGAT 59.163 47.619 0.00 0.00 0.00 3.85
123 124 1.271856 TGAGCGTGTTATGAAGGGGA 58.728 50.000 0.00 0.00 0.00 4.81
124 125 2.009774 CTTGAGCGTGTTATGAAGGGG 58.990 52.381 0.00 0.00 0.00 4.79
125 126 2.009774 CCTTGAGCGTGTTATGAAGGG 58.990 52.381 0.00 0.00 0.00 3.95
126 127 2.699954 ACCTTGAGCGTGTTATGAAGG 58.300 47.619 0.00 0.00 36.76 3.46
127 128 4.749245 AAACCTTGAGCGTGTTATGAAG 57.251 40.909 0.00 0.00 0.00 3.02
128 129 6.621316 TTTAAACCTTGAGCGTGTTATGAA 57.379 33.333 0.00 0.00 0.00 2.57
129 130 6.621316 TTTTAAACCTTGAGCGTGTTATGA 57.379 33.333 0.00 0.00 0.00 2.15
130 131 8.447833 TCTATTTTAAACCTTGAGCGTGTTATG 58.552 33.333 0.00 0.00 0.00 1.90
131 132 8.448615 GTCTATTTTAAACCTTGAGCGTGTTAT 58.551 33.333 0.00 0.00 0.00 1.89
132 133 7.095102 GGTCTATTTTAAACCTTGAGCGTGTTA 60.095 37.037 0.00 0.00 0.00 2.41
133 134 6.293790 GGTCTATTTTAAACCTTGAGCGTGTT 60.294 38.462 0.00 0.00 0.00 3.32
134 135 5.180680 GGTCTATTTTAAACCTTGAGCGTGT 59.819 40.000 0.00 0.00 0.00 4.49
135 136 5.628134 GGTCTATTTTAAACCTTGAGCGTG 58.372 41.667 0.00 0.00 0.00 5.34
136 137 4.390909 CGGTCTATTTTAAACCTTGAGCGT 59.609 41.667 17.09 0.00 38.55 5.07
137 138 4.201783 CCGGTCTATTTTAAACCTTGAGCG 60.202 45.833 17.79 17.79 41.52 5.03
138 139 4.095932 CCCGGTCTATTTTAAACCTTGAGC 59.904 45.833 0.00 0.00 0.00 4.26
139 140 5.493809 TCCCGGTCTATTTTAAACCTTGAG 58.506 41.667 0.00 0.00 0.00 3.02
140 141 5.502089 TCCCGGTCTATTTTAAACCTTGA 57.498 39.130 0.00 0.00 0.00 3.02
141 142 5.883673 TGATCCCGGTCTATTTTAAACCTTG 59.116 40.000 0.00 0.00 0.00 3.61
142 143 6.069705 TGATCCCGGTCTATTTTAAACCTT 57.930 37.500 0.00 0.00 0.00 3.50
143 144 5.703730 TGATCCCGGTCTATTTTAAACCT 57.296 39.130 0.00 0.00 0.00 3.50
144 145 6.762702 TTTGATCCCGGTCTATTTTAAACC 57.237 37.500 0.00 0.00 0.00 3.27
145 146 9.117183 ACTATTTGATCCCGGTCTATTTTAAAC 57.883 33.333 0.00 0.00 0.00 2.01
146 147 9.689501 AACTATTTGATCCCGGTCTATTTTAAA 57.310 29.630 0.00 0.00 0.00 1.52
147 148 9.689501 AAACTATTTGATCCCGGTCTATTTTAA 57.310 29.630 0.00 0.00 0.00 1.52
149 150 9.338622 CTAAACTATTTGATCCCGGTCTATTTT 57.661 33.333 0.00 0.00 0.00 1.82
150 151 8.491958 ACTAAACTATTTGATCCCGGTCTATTT 58.508 33.333 0.00 0.00 0.00 1.40
151 152 7.931948 CACTAAACTATTTGATCCCGGTCTATT 59.068 37.037 0.00 0.00 0.00 1.73
152 153 7.070821 ACACTAAACTATTTGATCCCGGTCTAT 59.929 37.037 0.00 0.00 0.00 1.98
153 154 6.381994 ACACTAAACTATTTGATCCCGGTCTA 59.618 38.462 0.00 0.00 0.00 2.59
154 155 5.189145 ACACTAAACTATTTGATCCCGGTCT 59.811 40.000 0.00 0.00 0.00 3.85
155 156 5.293569 CACACTAAACTATTTGATCCCGGTC 59.706 44.000 0.00 0.00 0.00 4.79
156 157 5.183228 CACACTAAACTATTTGATCCCGGT 58.817 41.667 0.00 0.00 0.00 5.28
157 158 4.035208 GCACACTAAACTATTTGATCCCGG 59.965 45.833 0.00 0.00 0.00 5.73
158 159 4.876107 AGCACACTAAACTATTTGATCCCG 59.124 41.667 0.00 0.00 0.00 5.14
159 160 5.880332 TCAGCACACTAAACTATTTGATCCC 59.120 40.000 0.00 0.00 0.00 3.85
160 161 6.985188 TCAGCACACTAAACTATTTGATCC 57.015 37.500 0.00 0.00 0.00 3.36
161 162 9.495754 GAAATCAGCACACTAAACTATTTGATC 57.504 33.333 0.00 0.00 0.00 2.92
162 163 9.013229 TGAAATCAGCACACTAAACTATTTGAT 57.987 29.630 0.00 0.00 0.00 2.57
163 164 8.389779 TGAAATCAGCACACTAAACTATTTGA 57.610 30.769 0.00 0.00 0.00 2.69
164 165 7.752239 CCTGAAATCAGCACACTAAACTATTTG 59.248 37.037 4.87 0.00 42.47 2.32
165 166 7.094205 CCCTGAAATCAGCACACTAAACTATTT 60.094 37.037 4.87 0.00 42.47 1.40
166 167 6.375455 CCCTGAAATCAGCACACTAAACTATT 59.625 38.462 4.87 0.00 42.47 1.73
167 168 5.882557 CCCTGAAATCAGCACACTAAACTAT 59.117 40.000 4.87 0.00 42.47 2.12
168 169 5.012664 TCCCTGAAATCAGCACACTAAACTA 59.987 40.000 4.87 0.00 42.47 2.24
169 170 4.074970 CCCTGAAATCAGCACACTAAACT 58.925 43.478 4.87 0.00 42.47 2.66
170 171 4.072131 TCCCTGAAATCAGCACACTAAAC 58.928 43.478 4.87 0.00 42.47 2.01
171 172 4.365514 TCCCTGAAATCAGCACACTAAA 57.634 40.909 4.87 0.00 42.47 1.85
172 173 4.574674 ATCCCTGAAATCAGCACACTAA 57.425 40.909 4.87 0.00 42.47 2.24
173 174 4.574674 AATCCCTGAAATCAGCACACTA 57.425 40.909 4.87 0.00 42.47 2.74
174 175 3.446442 AATCCCTGAAATCAGCACACT 57.554 42.857 4.87 0.00 42.47 3.55
175 176 5.643379 TTAAATCCCTGAAATCAGCACAC 57.357 39.130 4.87 0.00 42.47 3.82
176 177 5.774690 AGTTTAAATCCCTGAAATCAGCACA 59.225 36.000 4.87 0.00 42.47 4.57
177 178 6.272822 AGTTTAAATCCCTGAAATCAGCAC 57.727 37.500 4.87 0.00 42.47 4.40
178 179 6.493115 TGAAGTTTAAATCCCTGAAATCAGCA 59.507 34.615 4.87 0.00 42.47 4.41
179 180 6.924111 TGAAGTTTAAATCCCTGAAATCAGC 58.076 36.000 4.87 0.00 42.47 4.26
180 181 7.394359 TCCTGAAGTTTAAATCCCTGAAATCAG 59.606 37.037 3.37 3.37 43.40 2.90
181 182 7.237982 TCCTGAAGTTTAAATCCCTGAAATCA 58.762 34.615 0.00 0.00 0.00 2.57
182 183 7.703058 TCCTGAAGTTTAAATCCCTGAAATC 57.297 36.000 0.00 0.00 0.00 2.17
183 184 8.670521 AATCCTGAAGTTTAAATCCCTGAAAT 57.329 30.769 0.00 0.00 0.00 2.17
184 185 8.367156 CAAATCCTGAAGTTTAAATCCCTGAAA 58.633 33.333 0.00 0.00 0.00 2.69
185 186 7.728083 TCAAATCCTGAAGTTTAAATCCCTGAA 59.272 33.333 0.00 0.00 0.00 3.02
186 187 7.237982 TCAAATCCTGAAGTTTAAATCCCTGA 58.762 34.615 0.00 0.00 0.00 3.86
187 188 7.466746 TCAAATCCTGAAGTTTAAATCCCTG 57.533 36.000 0.00 0.00 0.00 4.45
188 189 8.670521 AATCAAATCCTGAAGTTTAAATCCCT 57.329 30.769 0.00 0.00 37.67 4.20
196 197 7.809806 CGAAAGCTAAATCAAATCCTGAAGTTT 59.190 33.333 0.00 0.00 37.67 2.66
197 198 7.040409 ACGAAAGCTAAATCAAATCCTGAAGTT 60.040 33.333 0.00 0.00 37.67 2.66
198 199 6.431234 ACGAAAGCTAAATCAAATCCTGAAGT 59.569 34.615 0.00 0.00 37.67 3.01
199 200 6.846350 ACGAAAGCTAAATCAAATCCTGAAG 58.154 36.000 0.00 0.00 37.67 3.02
200 201 6.655003 AGACGAAAGCTAAATCAAATCCTGAA 59.345 34.615 0.00 0.00 37.67 3.02
201 202 6.173339 AGACGAAAGCTAAATCAAATCCTGA 58.827 36.000 0.00 0.00 38.81 3.86
202 203 6.428385 AGACGAAAGCTAAATCAAATCCTG 57.572 37.500 0.00 0.00 0.00 3.86
203 204 7.103641 TGTAGACGAAAGCTAAATCAAATCCT 58.896 34.615 0.00 0.00 0.00 3.24
204 205 7.303634 TGTAGACGAAAGCTAAATCAAATCC 57.696 36.000 0.00 0.00 0.00 3.01
205 206 8.443937 ACTTGTAGACGAAAGCTAAATCAAATC 58.556 33.333 0.00 0.00 0.00 2.17
206 207 8.324163 ACTTGTAGACGAAAGCTAAATCAAAT 57.676 30.769 0.00 0.00 0.00 2.32
207 208 7.724305 ACTTGTAGACGAAAGCTAAATCAAA 57.276 32.000 0.00 0.00 0.00 2.69
208 209 7.724305 AACTTGTAGACGAAAGCTAAATCAA 57.276 32.000 0.00 0.00 0.00 2.57
209 210 7.724305 AAACTTGTAGACGAAAGCTAAATCA 57.276 32.000 0.00 0.00 0.00 2.57
210 211 9.742552 CTTAAACTTGTAGACGAAAGCTAAATC 57.257 33.333 0.00 0.00 0.00 2.17
211 212 8.718734 CCTTAAACTTGTAGACGAAAGCTAAAT 58.281 33.333 0.00 0.00 0.00 1.40
212 213 7.712205 ACCTTAAACTTGTAGACGAAAGCTAAA 59.288 33.333 0.00 0.00 0.00 1.85
213 214 7.212274 ACCTTAAACTTGTAGACGAAAGCTAA 58.788 34.615 0.00 0.00 0.00 3.09
214 215 6.752168 ACCTTAAACTTGTAGACGAAAGCTA 58.248 36.000 0.00 0.00 0.00 3.32
215 216 5.608449 ACCTTAAACTTGTAGACGAAAGCT 58.392 37.500 0.00 0.00 0.00 3.74
216 217 5.919272 ACCTTAAACTTGTAGACGAAAGC 57.081 39.130 0.00 0.00 0.00 3.51
217 218 7.473027 TGAACCTTAAACTTGTAGACGAAAG 57.527 36.000 0.00 0.00 0.00 2.62
218 219 8.441312 AATGAACCTTAAACTTGTAGACGAAA 57.559 30.769 0.00 0.00 0.00 3.46
219 220 8.441312 AAATGAACCTTAAACTTGTAGACGAA 57.559 30.769 0.00 0.00 0.00 3.85
220 221 8.339714 CAAAATGAACCTTAAACTTGTAGACGA 58.660 33.333 0.00 0.00 0.00 4.20
221 222 7.589954 CCAAAATGAACCTTAAACTTGTAGACG 59.410 37.037 0.00 0.00 0.00 4.18
222 223 8.626526 TCCAAAATGAACCTTAAACTTGTAGAC 58.373 33.333 0.00 0.00 0.00 2.59
223 224 8.626526 GTCCAAAATGAACCTTAAACTTGTAGA 58.373 33.333 0.00 0.00 0.00 2.59
224 225 8.630037 AGTCCAAAATGAACCTTAAACTTGTAG 58.370 33.333 0.00 0.00 0.00 2.74
225 226 8.528044 AGTCCAAAATGAACCTTAAACTTGTA 57.472 30.769 0.00 0.00 0.00 2.41
226 227 7.418337 AGTCCAAAATGAACCTTAAACTTGT 57.582 32.000 0.00 0.00 0.00 3.16
227 228 8.716646 AAAGTCCAAAATGAACCTTAAACTTG 57.283 30.769 0.00 0.00 0.00 3.16
228 229 9.733556 AAAAAGTCCAAAATGAACCTTAAACTT 57.266 25.926 0.00 0.00 0.00 2.66
229 230 9.378551 GAAAAAGTCCAAAATGAACCTTAAACT 57.621 29.630 0.00 0.00 0.00 2.66
230 231 8.609176 GGAAAAAGTCCAAAATGAACCTTAAAC 58.391 33.333 0.00 0.00 46.97 2.01
231 232 8.725405 GGAAAAAGTCCAAAATGAACCTTAAA 57.275 30.769 0.00 0.00 46.97 1.52
357 378 6.012683 AGAGAAAGGATGGATATCTGGGAATG 60.013 42.308 2.05 0.00 33.68 2.67
463 2058 9.270640 CTCTGAGATTTGAATACTATCTTTGGG 57.729 37.037 0.00 0.00 0.00 4.12
561 2157 8.902806 CCTACAGCCAGTTCATATATTTTTCAA 58.097 33.333 0.00 0.00 0.00 2.69
562 2158 8.271458 TCCTACAGCCAGTTCATATATTTTTCA 58.729 33.333 0.00 0.00 0.00 2.69
696 2292 8.728088 ACGAGTATTGATTTGTTTTGACAATC 57.272 30.769 0.00 0.00 33.99 2.67
699 2295 7.698628 TGAACGAGTATTGATTTGTTTTGACA 58.301 30.769 0.00 0.00 0.00 3.58
1027 3224 2.515991 CCATACCACGGCGGCAAT 60.516 61.111 13.24 0.00 39.03 3.56
1071 3269 4.382320 GCGTAGTCCCGTTGGGCA 62.382 66.667 0.00 0.00 43.94 5.36
1107 3305 1.064946 CGCCTCGAAGTAGAGCAGG 59.935 63.158 0.00 0.00 36.95 4.85
1149 3347 3.055719 CATTGGACGCGCTGGGTT 61.056 61.111 5.73 0.00 0.00 4.11
1267 3508 2.686405 TCAATCAAGCATGTCAGCATCC 59.314 45.455 0.00 0.00 36.85 3.51
1286 3527 1.604147 ATCCACCTGCACGTCGATCA 61.604 55.000 0.00 0.00 0.00 2.92
1566 3815 4.828296 TAGGACCTCCGGGGCGTC 62.828 72.222 13.00 13.00 43.03 5.19
1689 3938 3.069946 AACGCGTATCGGGGGTCA 61.070 61.111 14.46 0.00 43.94 4.02
1776 4041 3.554524 CATACGTGTGCCAAAACTCAAG 58.445 45.455 0.00 0.00 0.00 3.02
1851 4136 6.432107 CGGCTCTCTAGTTTCTTATCTACAC 58.568 44.000 0.00 0.00 0.00 2.90
1852 4137 5.008811 GCGGCTCTCTAGTTTCTTATCTACA 59.991 44.000 0.00 0.00 0.00 2.74
1853 4138 5.008811 TGCGGCTCTCTAGTTTCTTATCTAC 59.991 44.000 0.00 0.00 0.00 2.59
1865 4188 6.128445 CCAAATTAATATGTGCGGCTCTCTAG 60.128 42.308 0.00 0.00 0.00 2.43
1871 4194 2.035832 GGCCAAATTAATATGTGCGGCT 59.964 45.455 0.00 0.00 38.37 5.52
1890 4213 5.220024 GCATATAATTGCGCGATTAAAAGGC 60.220 40.000 29.00 26.42 32.06 4.35
1953 4404 5.624344 TCCCGCACGTTATTTTCAAATTA 57.376 34.783 0.00 0.00 0.00 1.40
1967 4419 3.684103 TGCTAAATAAATTCCCGCACG 57.316 42.857 0.00 0.00 0.00 5.34
1971 4423 7.547370 TGAAATGGTTTGCTAAATAAATTCCCG 59.453 33.333 0.00 0.00 0.00 5.14
2125 4683 0.541063 TGTTCTGGTAGAGGCCACGA 60.541 55.000 5.01 0.00 34.36 4.35
2158 4717 4.486090 CGCTGCTTCTGTAGAAACTTCTA 58.514 43.478 0.00 0.00 38.70 2.10
2225 4788 9.927668 ATTTGCTTTACAATACTGCTATGTTTT 57.072 25.926 0.00 0.00 38.31 2.43
2257 4828 3.512680 CTCGTCCTGTTCCATACAAGTC 58.487 50.000 0.00 0.00 36.02 3.01
2264 4835 1.078848 GCAGCTCGTCCTGTTCCAT 60.079 57.895 6.87 0.00 35.28 3.41
2374 4945 2.285368 TCGTCCCAGCCCAAGGAT 60.285 61.111 0.00 0.00 33.88 3.24
2448 5020 3.646162 TGTTGTCACTTCACCAGACCTAT 59.354 43.478 0.00 0.00 0.00 2.57
2478 5052 5.178252 CGGCATAATCATCAGTTACTGAAGG 59.822 44.000 19.42 14.05 44.04 3.46
2495 5069 0.534877 CTGCAGTATGGCCGGCATAA 60.535 55.000 30.85 14.01 35.45 1.90
2634 5208 2.765807 AGGTAGAGCATGCCGCCT 60.766 61.111 15.66 13.64 44.04 5.52
3087 5668 0.533032 GCCTAGCAAGAACTCCGACT 59.467 55.000 0.00 0.00 0.00 4.18
3111 5692 4.878397 GGAAGTCAGGAACATCAGTTATGG 59.122 45.833 0.00 0.00 40.16 2.74
3129 5710 4.402056 TCTCTTGACGAAAACAGGAAGT 57.598 40.909 0.00 0.00 0.00 3.01
3130 5711 4.752101 ACATCTCTTGACGAAAACAGGAAG 59.248 41.667 0.00 0.00 0.00 3.46
3131 5712 4.511454 CACATCTCTTGACGAAAACAGGAA 59.489 41.667 0.00 0.00 0.00 3.36
3132 5713 4.058124 CACATCTCTTGACGAAAACAGGA 58.942 43.478 0.00 0.00 0.00 3.86
3133 5714 3.364366 GCACATCTCTTGACGAAAACAGG 60.364 47.826 0.00 0.00 0.00 4.00
3134 5715 3.248363 TGCACATCTCTTGACGAAAACAG 59.752 43.478 0.00 0.00 0.00 3.16
3135 5716 3.202097 TGCACATCTCTTGACGAAAACA 58.798 40.909 0.00 0.00 0.00 2.83
3136 5717 3.878086 TGCACATCTCTTGACGAAAAC 57.122 42.857 0.00 0.00 0.00 2.43
3140 5721 2.995939 GACATTGCACATCTCTTGACGA 59.004 45.455 0.00 0.00 0.00 4.20
3141 5722 2.738314 TGACATTGCACATCTCTTGACG 59.262 45.455 0.00 0.00 0.00 4.35
3196 5777 3.434310 GGGCAATCCACCTTTTCCAAAAA 60.434 43.478 0.00 0.00 35.00 1.94
3197 5778 2.105649 GGGCAATCCACCTTTTCCAAAA 59.894 45.455 0.00 0.00 35.00 2.44
3198 5779 1.696884 GGGCAATCCACCTTTTCCAAA 59.303 47.619 0.00 0.00 35.00 3.28
3199 5780 1.132881 AGGGCAATCCACCTTTTCCAA 60.133 47.619 0.00 0.00 38.24 3.53
3200 5781 0.486879 AGGGCAATCCACCTTTTCCA 59.513 50.000 0.00 0.00 38.24 3.53
3201 5782 1.186200 GAGGGCAATCCACCTTTTCC 58.814 55.000 0.00 0.00 37.18 3.13
3209 5790 0.758734 CATAGACCGAGGGCAATCCA 59.241 55.000 0.00 0.00 38.24 3.41
3233 5814 2.116533 CGGCTGCATGCATCTTCCA 61.117 57.895 22.97 0.00 45.15 3.53
3251 5832 9.757859 TGTTCGACGAACCATTTTTAATAATAC 57.242 29.630 31.70 7.69 41.35 1.89
3264 5847 1.928503 GACTTTGTGTTCGACGAACCA 59.071 47.619 31.70 25.71 41.35 3.67
3309 5893 4.900635 TCTTTGTTTTTCTGTGCTCCTC 57.099 40.909 0.00 0.00 0.00 3.71
3325 5909 7.279758 TGTGGCTTTGTTTTTCCTTTATCTTTG 59.720 33.333 0.00 0.00 0.00 2.77
3330 5914 5.820423 GGTTGTGGCTTTGTTTTTCCTTTAT 59.180 36.000 0.00 0.00 0.00 1.40
3331 5915 5.179533 GGTTGTGGCTTTGTTTTTCCTTTA 58.820 37.500 0.00 0.00 0.00 1.85
3332 5916 4.006989 GGTTGTGGCTTTGTTTTTCCTTT 58.993 39.130 0.00 0.00 0.00 3.11
3333 5917 3.605634 GGTTGTGGCTTTGTTTTTCCTT 58.394 40.909 0.00 0.00 0.00 3.36
3335 5919 1.930503 CGGTTGTGGCTTTGTTTTTCC 59.069 47.619 0.00 0.00 0.00 3.13
3336 5920 1.930503 CCGGTTGTGGCTTTGTTTTTC 59.069 47.619 0.00 0.00 0.00 2.29
3386 5978 7.361713 CCGGTTTAAATGATGGTCGCATAATAT 60.362 37.037 0.00 0.00 0.00 1.28
3404 5996 3.190953 CGGGCTATTTTCAACCGGTTTAA 59.809 43.478 19.55 14.24 40.79 1.52
3405 5997 2.748532 CGGGCTATTTTCAACCGGTTTA 59.251 45.455 19.55 7.23 40.79 2.01
3445 6037 1.826720 CATTTGGCTACTGGGTGCAAT 59.173 47.619 0.00 0.00 0.00 3.56
3472 6064 0.622136 TACTCACTCCTACGGCTCCA 59.378 55.000 0.00 0.00 0.00 3.86
3474 6066 0.664224 GCTACTCACTCCTACGGCTC 59.336 60.000 0.00 0.00 0.00 4.70
3499 6091 1.676014 GCTATGGCATGGATCCGTACC 60.676 57.143 15.63 15.63 38.54 3.34
3515 6108 6.882656 TCTTGCAAGTTATCTTCAGAGCTAT 58.117 36.000 25.19 0.00 0.00 2.97
3577 6170 6.902974 TCCTATAGGCTATATGGAATTGCAGA 59.097 38.462 20.86 0.24 34.44 4.26
3596 6189 4.882842 TTGGAATATGCGCACTCCTATA 57.117 40.909 26.52 11.62 0.00 1.31
3733 6326 4.346730 TCATTGATTGCCCTCTCACAAAT 58.653 39.130 0.00 0.00 0.00 2.32
3775 6369 4.082787 CGGTGTTGCTTTTGTATTCAGGAT 60.083 41.667 0.00 0.00 0.00 3.24
3778 6372 3.974401 CACGGTGTTGCTTTTGTATTCAG 59.026 43.478 0.00 0.00 0.00 3.02
3796 6390 1.747355 ACGATGGTAGGTAGTTCACGG 59.253 52.381 0.00 0.00 0.00 4.94
3852 6447 7.798596 AATTTTCATGTGGTTTGTGCATAAA 57.201 28.000 4.30 4.30 0.00 1.40
3919 6515 4.241590 TGTATCGTTGTCGGTGTAAGTT 57.758 40.909 0.00 0.00 37.69 2.66
3925 6522 1.355005 TGCATGTATCGTTGTCGGTG 58.645 50.000 0.00 0.00 37.69 4.94
3935 6532 5.581126 TGGAAGGAAACAATGCATGTATC 57.419 39.130 0.00 0.00 42.99 2.24
3937 6534 5.304101 AGTTTGGAAGGAAACAATGCATGTA 59.696 36.000 0.00 0.00 42.99 2.29
3941 6538 4.751767 AAGTTTGGAAGGAAACAATGCA 57.248 36.364 0.00 0.00 38.14 3.96
3969 6566 6.558771 TGGACTATTGTGATGTTGAAGTTG 57.441 37.500 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.