Multiple sequence alignment - TraesCS7D01G398100

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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 TraesCS7D01G398100 chr7D 100.000 3662 0 0 1 3662 514073452 514077113 0.000000e+00 6763.0
1 TraesCS7D01G398100 chr7D 80.000 155 28 3 3083 3237 29257567 29257718 1.070000e-20 111.0
2 TraesCS7D01G398100 chr7D 84.783 92 11 2 204 294 29888895 29888806 5.040000e-14 89.8
3 TraesCS7D01G398100 chr7B 96.581 2983 69 13 642 3594 544910982 544913961 0.000000e+00 4913.0
4 TraesCS7D01G398100 chr7B 93.396 424 25 2 202 624 544909507 544909928 3.100000e-175 625.0
5 TraesCS7D01G398100 chr7B 87.317 205 24 2 1 203 637030612 637030408 2.200000e-57 233.0
6 TraesCS7D01G398100 chr7B 91.262 103 8 1 198 299 581388278 581388176 4.930000e-29 139.0
7 TraesCS7D01G398100 chr7B 84.524 84 13 0 3121 3204 296354851 296354934 2.340000e-12 84.2
8 TraesCS7D01G398100 chr7A 94.287 2678 116 19 198 2859 587363754 587366410 0.000000e+00 4063.0
9 TraesCS7D01G398100 chr7A 94.401 768 43 0 2864 3631 587367753 587368520 0.000000e+00 1181.0
10 TraesCS7D01G398100 chr7A 78.082 219 41 6 3088 3305 6857323 6857535 8.250000e-27 132.0
11 TraesCS7D01G398100 chr7A 84.158 101 13 2 198 298 221109116 221109213 1.080000e-15 95.3
12 TraesCS7D01G398100 chr7A 85.714 84 12 0 3121 3204 375911748 375911831 5.040000e-14 89.8
13 TraesCS7D01G398100 chr6D 95.522 201 9 0 3 203 203756063 203755863 4.560000e-84 322.0
14 TraesCS7D01G398100 chr6D 85.556 180 20 5 28 203 409369267 409369444 2.250000e-42 183.0
15 TraesCS7D01G398100 chr6D 84.043 188 22 7 28 211 409435960 409436143 1.350000e-39 174.0
16 TraesCS7D01G398100 chr6D 84.239 184 22 6 28 207 409455325 409455505 4.860000e-39 172.0
17 TraesCS7D01G398100 chr6D 82.447 188 25 7 28 211 409362463 409362646 1.360000e-34 158.0
18 TraesCS7D01G398100 chr6D 73.741 278 53 17 1937 2204 127379947 127379680 1.400000e-14 91.6
19 TraesCS7D01G398100 chr5D 73.042 779 170 33 2763 3524 250585051 250584296 4.730000e-59 239.0
20 TraesCS7D01G398100 chr5D 76.087 276 60 6 1938 2210 519545937 519546209 4.930000e-29 139.0
21 TraesCS7D01G398100 chr2B 76.093 389 77 13 3087 3470 82027008 82026631 4.830000e-44 189.0
22 TraesCS7D01G398100 chr2B 89.000 100 9 2 205 303 682223619 682223717 4.970000e-24 122.0
23 TraesCS7D01G398100 chr2B 85.849 106 12 3 201 304 199010451 199010555 3.870000e-20 110.0
24 TraesCS7D01G398100 chr2D 84.783 184 27 1 21 203 262587425 262587242 2.250000e-42 183.0
25 TraesCS7D01G398100 chr5A 82.703 185 29 3 20 203 401663422 401663240 1.050000e-35 161.0
26 TraesCS7D01G398100 chr5A 75.090 277 51 11 3020 3286 680271141 680271409 2.990000e-21 113.0
27 TraesCS7D01G398100 chr5A 73.222 239 55 8 3072 3308 546102420 546102651 1.090000e-10 78.7
28 TraesCS7D01G398100 chr4A 81.481 189 28 6 21 207 599314572 599314755 8.190000e-32 148.0
29 TraesCS7D01G398100 chr4A 86.275 102 12 2 204 304 448734225 448734125 3.870000e-20 110.0
30 TraesCS7D01G398100 chr5B 78.469 209 41 4 1938 2144 654366560 654366766 2.290000e-27 134.0
31 TraesCS7D01G398100 chr4B 89.024 82 8 1 217 297 667980204 667980123 2.330000e-17 100.0
32 TraesCS7D01G398100 chr6A 81.897 116 15 6 3136 3249 447347127 447347016 3.890000e-15 93.5
33 TraesCS7D01G398100 chr4D 100.000 29 0 0 3497 3525 105144534 105144506 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G398100 chr7D 514073452 514077113 3661 False 6763 6763 100.0000 1 3662 1 chr7D.!!$F2 3661
1 TraesCS7D01G398100 chr7B 544909507 544913961 4454 False 2769 4913 94.9885 202 3594 2 chr7B.!!$F2 3392
2 TraesCS7D01G398100 chr7A 587363754 587368520 4766 False 2622 4063 94.3440 198 3631 2 chr7A.!!$F4 3433
3 TraesCS7D01G398100 chr5D 250584296 250585051 755 True 239 239 73.0420 2763 3524 1 chr5D.!!$R1 761

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
94 95 0.034337 TTGTTGTAGTGCTCGGACCC 59.966 55.0 0.0 0.00 0.00 4.46 F
604 619 0.036875 GCTCTACCAGGCAACCACTT 59.963 55.0 0.0 0.00 37.17 3.16 F
1907 2972 0.034476 GATCATCATCGGCAGCCAGA 59.966 55.0 13.3 10.36 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 2972 1.809619 CGCGATGGATGGACACGTT 60.810 57.895 0.0 0.0 0.00 3.99 R
2502 3567 4.032356 CTGCACGACAGCTTCACA 57.968 55.556 0.0 0.0 40.19 3.58 R
3642 6065 0.861837 GTGATAGCTTTCCCGATGCG 59.138 55.000 0.0 0.0 33.86 4.73 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 4.873746 ATGAGAGAAAAGAGGACGTTGA 57.126 40.909 0.00 0.00 0.00 3.18
23 24 4.873746 TGAGAGAAAAGAGGACGTTGAT 57.126 40.909 0.00 0.00 0.00 2.57
24 25 4.560128 TGAGAGAAAAGAGGACGTTGATG 58.440 43.478 0.00 0.00 0.00 3.07
25 26 3.929610 GAGAGAAAAGAGGACGTTGATGG 59.070 47.826 0.00 0.00 0.00 3.51
26 27 3.003480 GAGAAAAGAGGACGTTGATGGG 58.997 50.000 0.00 0.00 0.00 4.00
27 28 2.637872 AGAAAAGAGGACGTTGATGGGA 59.362 45.455 0.00 0.00 0.00 4.37
28 29 2.770164 AAAGAGGACGTTGATGGGAG 57.230 50.000 0.00 0.00 0.00 4.30
29 30 0.905357 AAGAGGACGTTGATGGGAGG 59.095 55.000 0.00 0.00 0.00 4.30
30 31 0.252284 AGAGGACGTTGATGGGAGGT 60.252 55.000 0.00 0.00 0.00 3.85
31 32 0.175989 GAGGACGTTGATGGGAGGTC 59.824 60.000 0.00 0.00 0.00 3.85
32 33 1.153628 GGACGTTGATGGGAGGTCG 60.154 63.158 0.00 0.00 33.84 4.79
33 34 1.590147 GACGTTGATGGGAGGTCGT 59.410 57.895 0.00 0.00 0.00 4.34
34 35 0.736325 GACGTTGATGGGAGGTCGTG 60.736 60.000 0.00 0.00 0.00 4.35
35 36 1.447838 CGTTGATGGGAGGTCGTGG 60.448 63.158 0.00 0.00 0.00 4.94
36 37 1.677552 GTTGATGGGAGGTCGTGGT 59.322 57.895 0.00 0.00 0.00 4.16
37 38 0.673644 GTTGATGGGAGGTCGTGGTG 60.674 60.000 0.00 0.00 0.00 4.17
38 39 1.836999 TTGATGGGAGGTCGTGGTGG 61.837 60.000 0.00 0.00 0.00 4.61
39 40 3.682292 GATGGGAGGTCGTGGTGGC 62.682 68.421 0.00 0.00 0.00 5.01
45 46 3.324108 GGTCGTGGTGGCCCCTTA 61.324 66.667 0.00 0.00 0.00 2.69
46 47 2.751688 GTCGTGGTGGCCCCTTAA 59.248 61.111 0.00 0.00 0.00 1.85
47 48 1.073548 GTCGTGGTGGCCCCTTAAA 59.926 57.895 0.00 0.00 0.00 1.52
48 49 1.073548 TCGTGGTGGCCCCTTAAAC 59.926 57.895 0.00 0.00 0.00 2.01
49 50 1.228306 CGTGGTGGCCCCTTAAACA 60.228 57.895 0.00 0.00 0.00 2.83
50 51 1.241315 CGTGGTGGCCCCTTAAACAG 61.241 60.000 0.00 0.00 0.00 3.16
51 52 0.178973 GTGGTGGCCCCTTAAACAGT 60.179 55.000 0.00 0.00 0.00 3.55
52 53 1.074244 GTGGTGGCCCCTTAAACAGTA 59.926 52.381 0.00 0.00 0.00 2.74
53 54 1.781529 TGGTGGCCCCTTAAACAGTAA 59.218 47.619 0.00 0.00 0.00 2.24
54 55 2.165167 GGTGGCCCCTTAAACAGTAAC 58.835 52.381 0.00 0.00 0.00 2.50
55 56 2.224942 GGTGGCCCCTTAAACAGTAACT 60.225 50.000 0.00 0.00 0.00 2.24
56 57 2.817844 GTGGCCCCTTAAACAGTAACTG 59.182 50.000 0.00 0.00 37.52 3.16
57 58 2.712087 TGGCCCCTTAAACAGTAACTGA 59.288 45.455 0.00 0.00 35.18 3.41
58 59 3.138653 TGGCCCCTTAAACAGTAACTGAA 59.861 43.478 0.00 0.00 35.18 3.02
59 60 3.756963 GGCCCCTTAAACAGTAACTGAAG 59.243 47.826 0.00 0.00 35.18 3.02
60 61 3.756963 GCCCCTTAAACAGTAACTGAAGG 59.243 47.826 0.00 0.00 34.66 3.46
61 62 3.756963 CCCCTTAAACAGTAACTGAAGGC 59.243 47.826 0.00 0.00 34.00 4.35
62 63 4.506802 CCCCTTAAACAGTAACTGAAGGCT 60.507 45.833 0.00 0.00 34.00 4.58
63 64 5.070685 CCCTTAAACAGTAACTGAAGGCTT 58.929 41.667 0.00 0.00 34.00 4.35
64 65 6.235664 CCCTTAAACAGTAACTGAAGGCTTA 58.764 40.000 0.00 0.00 34.00 3.09
65 66 6.884836 CCCTTAAACAGTAACTGAAGGCTTAT 59.115 38.462 0.00 0.00 34.00 1.73
66 67 7.148239 CCCTTAAACAGTAACTGAAGGCTTATG 60.148 40.741 0.00 0.00 34.00 1.90
67 68 7.390718 CCTTAAACAGTAACTGAAGGCTTATGT 59.609 37.037 0.00 0.00 35.18 2.29
68 69 6.560253 AAACAGTAACTGAAGGCTTATGTG 57.440 37.500 0.00 0.00 35.18 3.21
69 70 4.579869 ACAGTAACTGAAGGCTTATGTGG 58.420 43.478 0.00 0.00 35.18 4.17
70 71 3.375299 CAGTAACTGAAGGCTTATGTGGC 59.625 47.826 0.00 0.00 32.44 5.01
71 72 2.584835 AACTGAAGGCTTATGTGGCA 57.415 45.000 0.00 0.00 34.73 4.92
72 73 2.119801 ACTGAAGGCTTATGTGGCAG 57.880 50.000 0.00 4.72 34.73 4.85
73 74 1.340405 ACTGAAGGCTTATGTGGCAGG 60.340 52.381 13.77 0.14 34.73 4.85
74 75 0.991146 TGAAGGCTTATGTGGCAGGA 59.009 50.000 0.00 0.00 34.73 3.86
75 76 1.565759 TGAAGGCTTATGTGGCAGGAT 59.434 47.619 0.00 0.00 34.73 3.24
76 77 2.025037 TGAAGGCTTATGTGGCAGGATT 60.025 45.455 0.00 0.00 34.73 3.01
77 78 2.062971 AGGCTTATGTGGCAGGATTG 57.937 50.000 0.00 0.00 34.73 2.67
78 79 1.285962 AGGCTTATGTGGCAGGATTGT 59.714 47.619 0.00 0.00 34.73 2.71
79 80 2.102578 GGCTTATGTGGCAGGATTGTT 58.897 47.619 0.00 0.00 0.00 2.83
80 81 2.159198 GGCTTATGTGGCAGGATTGTTG 60.159 50.000 0.00 0.00 0.00 3.33
81 82 2.493278 GCTTATGTGGCAGGATTGTTGT 59.507 45.455 0.00 0.00 0.00 3.32
82 83 3.694072 GCTTATGTGGCAGGATTGTTGTA 59.306 43.478 0.00 0.00 0.00 2.41
83 84 4.201950 GCTTATGTGGCAGGATTGTTGTAG 60.202 45.833 0.00 0.00 0.00 2.74
84 85 2.949177 TGTGGCAGGATTGTTGTAGT 57.051 45.000 0.00 0.00 0.00 2.73
85 86 2.503331 TGTGGCAGGATTGTTGTAGTG 58.497 47.619 0.00 0.00 0.00 2.74
86 87 1.200020 GTGGCAGGATTGTTGTAGTGC 59.800 52.381 0.00 0.00 0.00 4.40
87 88 1.073763 TGGCAGGATTGTTGTAGTGCT 59.926 47.619 0.00 0.00 0.00 4.40
88 89 1.740025 GGCAGGATTGTTGTAGTGCTC 59.260 52.381 0.00 0.00 0.00 4.26
89 90 1.394917 GCAGGATTGTTGTAGTGCTCG 59.605 52.381 0.00 0.00 0.00 5.03
90 91 2.002586 CAGGATTGTTGTAGTGCTCGG 58.997 52.381 0.00 0.00 0.00 4.63
91 92 1.899814 AGGATTGTTGTAGTGCTCGGA 59.100 47.619 0.00 0.00 0.00 4.55
92 93 2.000447 GGATTGTTGTAGTGCTCGGAC 59.000 52.381 0.00 0.00 0.00 4.79
93 94 2.000447 GATTGTTGTAGTGCTCGGACC 59.000 52.381 0.00 0.00 0.00 4.46
94 95 0.034337 TTGTTGTAGTGCTCGGACCC 59.966 55.000 0.00 0.00 0.00 4.46
95 96 1.116536 TGTTGTAGTGCTCGGACCCA 61.117 55.000 0.00 0.00 0.00 4.51
96 97 0.249398 GTTGTAGTGCTCGGACCCAT 59.751 55.000 0.00 0.00 0.00 4.00
97 98 0.535335 TTGTAGTGCTCGGACCCATC 59.465 55.000 0.00 0.00 0.00 3.51
98 99 0.324368 TGTAGTGCTCGGACCCATCT 60.324 55.000 0.00 0.00 0.00 2.90
99 100 0.103208 GTAGTGCTCGGACCCATCTG 59.897 60.000 0.00 0.00 0.00 2.90
100 101 0.324368 TAGTGCTCGGACCCATCTGT 60.324 55.000 0.00 0.00 32.47 3.41
101 102 0.324368 AGTGCTCGGACCCATCTGTA 60.324 55.000 0.00 0.00 32.47 2.74
102 103 0.535335 GTGCTCGGACCCATCTGTAA 59.465 55.000 0.00 0.00 32.47 2.41
103 104 0.824109 TGCTCGGACCCATCTGTAAG 59.176 55.000 0.00 0.00 32.47 2.34
104 105 0.824759 GCTCGGACCCATCTGTAAGT 59.175 55.000 0.00 0.00 33.76 2.24
105 106 1.207329 GCTCGGACCCATCTGTAAGTT 59.793 52.381 0.00 0.00 33.76 2.66
106 107 2.429610 GCTCGGACCCATCTGTAAGTTA 59.570 50.000 0.00 0.00 33.76 2.24
107 108 3.491104 GCTCGGACCCATCTGTAAGTTAG 60.491 52.174 0.00 0.00 33.76 2.34
108 109 3.700038 CTCGGACCCATCTGTAAGTTAGT 59.300 47.826 0.00 0.00 33.76 2.24
109 110 4.858850 TCGGACCCATCTGTAAGTTAGTA 58.141 43.478 0.00 0.00 33.76 1.82
110 111 4.885907 TCGGACCCATCTGTAAGTTAGTAG 59.114 45.833 0.00 0.00 33.76 2.57
111 112 4.643784 CGGACCCATCTGTAAGTTAGTAGT 59.356 45.833 0.00 0.00 33.76 2.73
112 113 5.824624 CGGACCCATCTGTAAGTTAGTAGTA 59.175 44.000 0.00 0.00 33.76 1.82
113 114 6.489361 CGGACCCATCTGTAAGTTAGTAGTAT 59.511 42.308 0.00 0.00 33.76 2.12
114 115 7.663081 CGGACCCATCTGTAAGTTAGTAGTATA 59.337 40.741 0.00 0.00 33.76 1.47
115 116 9.359653 GGACCCATCTGTAAGTTAGTAGTATAA 57.640 37.037 0.00 0.00 33.76 0.98
132 133 9.959721 AGTAGTATAATGTTGATGTGAAAAGGT 57.040 29.630 0.00 0.00 0.00 3.50
135 136 9.295825 AGTATAATGTTGATGTGAAAAGGTTGA 57.704 29.630 0.00 0.00 0.00 3.18
137 138 8.991243 ATAATGTTGATGTGAAAAGGTTGATG 57.009 30.769 0.00 0.00 0.00 3.07
138 139 6.653526 ATGTTGATGTGAAAAGGTTGATGA 57.346 33.333 0.00 0.00 0.00 2.92
139 140 6.075762 TGTTGATGTGAAAAGGTTGATGAG 57.924 37.500 0.00 0.00 0.00 2.90
140 141 5.009911 TGTTGATGTGAAAAGGTTGATGAGG 59.990 40.000 0.00 0.00 0.00 3.86
141 142 4.728772 TGATGTGAAAAGGTTGATGAGGT 58.271 39.130 0.00 0.00 0.00 3.85
142 143 4.520111 TGATGTGAAAAGGTTGATGAGGTG 59.480 41.667 0.00 0.00 0.00 4.00
143 144 3.221771 TGTGAAAAGGTTGATGAGGTGG 58.778 45.455 0.00 0.00 0.00 4.61
144 145 3.117701 TGTGAAAAGGTTGATGAGGTGGA 60.118 43.478 0.00 0.00 0.00 4.02
145 146 4.082125 GTGAAAAGGTTGATGAGGTGGAT 58.918 43.478 0.00 0.00 0.00 3.41
146 147 5.222027 TGTGAAAAGGTTGATGAGGTGGATA 60.222 40.000 0.00 0.00 0.00 2.59
147 148 5.355350 GTGAAAAGGTTGATGAGGTGGATAG 59.645 44.000 0.00 0.00 0.00 2.08
148 149 4.510167 AAAGGTTGATGAGGTGGATAGG 57.490 45.455 0.00 0.00 0.00 2.57
149 150 1.771255 AGGTTGATGAGGTGGATAGGC 59.229 52.381 0.00 0.00 0.00 3.93
150 151 1.771255 GGTTGATGAGGTGGATAGGCT 59.229 52.381 0.00 0.00 0.00 4.58
151 152 2.486191 GGTTGATGAGGTGGATAGGCTG 60.486 54.545 0.00 0.00 0.00 4.85
152 153 0.761187 TGATGAGGTGGATAGGCTGC 59.239 55.000 0.00 0.00 0.00 5.25
153 154 0.761187 GATGAGGTGGATAGGCTGCA 59.239 55.000 0.50 0.00 0.00 4.41
154 155 1.350351 GATGAGGTGGATAGGCTGCAT 59.650 52.381 0.50 0.00 0.00 3.96
155 156 0.471191 TGAGGTGGATAGGCTGCATG 59.529 55.000 0.50 0.00 0.00 4.06
156 157 0.471617 GAGGTGGATAGGCTGCATGT 59.528 55.000 0.50 0.00 0.00 3.21
157 158 0.471617 AGGTGGATAGGCTGCATGTC 59.528 55.000 2.28 2.28 0.00 3.06
158 159 0.181114 GGTGGATAGGCTGCATGTCA 59.819 55.000 12.84 0.00 0.00 3.58
159 160 1.408683 GGTGGATAGGCTGCATGTCAA 60.409 52.381 12.84 0.00 0.00 3.18
160 161 1.945394 GTGGATAGGCTGCATGTCAAG 59.055 52.381 12.84 0.00 0.00 3.02
161 162 1.839354 TGGATAGGCTGCATGTCAAGA 59.161 47.619 12.84 0.00 0.00 3.02
162 163 2.158856 TGGATAGGCTGCATGTCAAGAG 60.159 50.000 12.84 0.00 0.00 2.85
163 164 2.103771 GGATAGGCTGCATGTCAAGAGA 59.896 50.000 12.84 0.00 0.00 3.10
164 165 3.432749 GGATAGGCTGCATGTCAAGAGAA 60.433 47.826 12.84 0.00 0.00 2.87
165 166 2.574006 AGGCTGCATGTCAAGAGAAA 57.426 45.000 0.50 0.00 0.00 2.52
166 167 3.083122 AGGCTGCATGTCAAGAGAAAT 57.917 42.857 0.50 0.00 0.00 2.17
167 168 4.226427 AGGCTGCATGTCAAGAGAAATA 57.774 40.909 0.50 0.00 0.00 1.40
168 169 4.197750 AGGCTGCATGTCAAGAGAAATAG 58.802 43.478 0.50 0.00 0.00 1.73
169 170 3.314635 GGCTGCATGTCAAGAGAAATAGG 59.685 47.826 0.50 0.00 0.00 2.57
170 171 4.194640 GCTGCATGTCAAGAGAAATAGGA 58.805 43.478 0.00 0.00 0.00 2.94
171 172 4.820716 GCTGCATGTCAAGAGAAATAGGAT 59.179 41.667 0.00 0.00 0.00 3.24
172 173 5.994054 GCTGCATGTCAAGAGAAATAGGATA 59.006 40.000 0.00 0.00 0.00 2.59
173 174 6.147492 GCTGCATGTCAAGAGAAATAGGATAG 59.853 42.308 0.00 0.00 0.00 2.08
174 175 7.129457 TGCATGTCAAGAGAAATAGGATAGT 57.871 36.000 0.00 0.00 0.00 2.12
175 176 6.988580 TGCATGTCAAGAGAAATAGGATAGTG 59.011 38.462 0.00 0.00 0.00 2.74
176 177 6.426328 GCATGTCAAGAGAAATAGGATAGTGG 59.574 42.308 0.00 0.00 0.00 4.00
177 178 6.485830 TGTCAAGAGAAATAGGATAGTGGG 57.514 41.667 0.00 0.00 0.00 4.61
178 179 5.366768 TGTCAAGAGAAATAGGATAGTGGGG 59.633 44.000 0.00 0.00 0.00 4.96
179 180 5.602978 GTCAAGAGAAATAGGATAGTGGGGA 59.397 44.000 0.00 0.00 0.00 4.81
180 181 6.271159 GTCAAGAGAAATAGGATAGTGGGGAT 59.729 42.308 0.00 0.00 0.00 3.85
181 182 6.498651 TCAAGAGAAATAGGATAGTGGGGATC 59.501 42.308 0.00 0.00 0.00 3.36
182 183 5.982391 AGAGAAATAGGATAGTGGGGATCA 58.018 41.667 0.00 0.00 0.00 2.92
183 184 6.393897 AGAGAAATAGGATAGTGGGGATCAA 58.606 40.000 0.00 0.00 0.00 2.57
184 185 6.271159 AGAGAAATAGGATAGTGGGGATCAAC 59.729 42.308 0.00 0.00 0.00 3.18
185 186 6.153924 AGAAATAGGATAGTGGGGATCAACT 58.846 40.000 0.00 0.00 0.00 3.16
186 187 7.313731 AGAAATAGGATAGTGGGGATCAACTA 58.686 38.462 0.00 0.00 0.00 2.24
187 188 7.964293 AGAAATAGGATAGTGGGGATCAACTAT 59.036 37.037 12.32 12.32 0.00 2.12
188 189 8.525729 AAATAGGATAGTGGGGATCAACTATT 57.474 34.615 13.23 0.00 31.95 1.73
189 190 8.525729 AATAGGATAGTGGGGATCAACTATTT 57.474 34.615 13.23 9.28 0.00 1.40
190 191 9.629649 AATAGGATAGTGGGGATCAACTATTTA 57.370 33.333 13.23 10.53 0.00 1.40
191 192 7.560796 AGGATAGTGGGGATCAACTATTTAG 57.439 40.000 13.23 0.00 0.00 1.85
192 193 6.502158 AGGATAGTGGGGATCAACTATTTAGG 59.498 42.308 13.23 0.00 0.00 2.69
193 194 6.272558 GGATAGTGGGGATCAACTATTTAGGT 59.727 42.308 13.23 0.00 0.00 3.08
194 195 7.456902 GGATAGTGGGGATCAACTATTTAGGTA 59.543 40.741 13.23 0.00 0.00 3.08
195 196 8.990693 ATAGTGGGGATCAACTATTTAGGTAT 57.009 34.615 8.42 0.00 0.00 2.73
196 197 7.707467 AGTGGGGATCAACTATTTAGGTATT 57.293 36.000 0.00 0.00 0.00 1.89
281 283 1.121378 TTCCTCCCGTACAACACACA 58.879 50.000 0.00 0.00 0.00 3.72
282 284 1.344065 TCCTCCCGTACAACACACAT 58.656 50.000 0.00 0.00 0.00 3.21
287 289 0.438445 CCGTACAACACACATGCTCG 59.562 55.000 0.00 0.00 0.00 5.03
340 342 2.567985 GTCCGAACCCAAAACTTCTCA 58.432 47.619 0.00 0.00 0.00 3.27
352 354 5.128919 CAAAACTTCTCATATCCTCTGGGG 58.871 45.833 0.00 0.00 0.00 4.96
433 435 0.180642 ATCCTCGTACCTGCTCTCGA 59.819 55.000 0.00 0.00 0.00 4.04
451 453 6.183360 GCTCTCGAATGTCTGCTATTTTTCTT 60.183 38.462 0.00 0.00 0.00 2.52
472 474 5.734140 TCTTGAAAGGAAGGATAACCCCATA 59.266 40.000 0.00 0.00 36.73 2.74
581 592 4.409218 GGCACGTACCTCGCGACA 62.409 66.667 3.71 0.00 44.19 4.35
604 619 0.036875 GCTCTACCAGGCAACCACTT 59.963 55.000 0.00 0.00 37.17 3.16
729 1781 4.024048 CCATAGATCGGTTTCGGGATTTTG 60.024 45.833 0.00 0.00 36.95 2.44
801 1853 3.126073 ACGCGTGTCGACATATAGTCTA 58.874 45.455 23.12 0.00 45.32 2.59
831 1883 2.169769 TCTTGTGTTTCCTCCGAAGTGT 59.830 45.455 0.00 0.00 0.00 3.55
834 1886 2.224113 TGTGTTTCCTCCGAAGTGTACC 60.224 50.000 0.00 0.00 0.00 3.34
943 1999 6.147328 CCTAACTAACAGCACCACTTCTTTAC 59.853 42.308 0.00 0.00 0.00 2.01
976 2032 6.734137 TCAGTAATTGCCTAACAAACAACAG 58.266 36.000 0.00 0.00 42.86 3.16
1200 2256 0.955919 CGTTTCCCCTGGTTGCTCTC 60.956 60.000 0.00 0.00 0.00 3.20
1239 2295 4.284550 TGGTGCCTGGAGGTTGCC 62.285 66.667 0.00 0.00 37.57 4.52
1348 2404 1.133025 GCTTAACCATGCATTCGTGCT 59.867 47.619 0.00 0.00 35.49 4.40
1373 2429 1.490910 GGAGTATGCAAGTTAGGGGCT 59.509 52.381 0.00 0.00 0.00 5.19
1907 2972 0.034476 GATCATCATCGGCAGCCAGA 59.966 55.000 13.30 10.36 0.00 3.86
2625 3690 1.293267 AAAACGTCGCCGGTGGTATG 61.293 55.000 16.49 4.66 38.78 2.39
2717 3782 8.993404 ATCGGATAGTAGTAGGACTAAAAAGT 57.007 34.615 0.00 0.00 35.58 2.66
2734 3799 6.811253 AAAAAGTATGACACGCCAAAGATA 57.189 33.333 0.00 0.00 0.00 1.98
2845 3910 2.561419 AGAACGAGCAAGCACTTACCTA 59.439 45.455 0.00 0.00 0.00 3.08
2872 5275 7.554118 GCCTTTGTATATATAGGATGCACACAT 59.446 37.037 9.66 0.00 39.98 3.21
2908 5311 9.120538 ACATGTCGGTAAAGAGCAAAATTATAT 57.879 29.630 0.00 0.00 0.00 0.86
2953 5356 6.883756 AGCCAGGAAAAAGAAAAATCAAACAA 59.116 30.769 0.00 0.00 0.00 2.83
3003 5420 3.502211 GCATTAACCATATCTTGACCCCG 59.498 47.826 0.00 0.00 0.00 5.73
3185 5607 5.894298 TCTGATTGCCAGGTATAACTCAT 57.106 39.130 0.00 0.00 43.12 2.90
3196 5618 6.042552 CCAGGTATAACTCATTCAGGTCAGAT 59.957 42.308 0.00 0.00 0.00 2.90
3313 5735 1.134310 CCATCAGCTACATGCACTGGA 60.134 52.381 9.56 0.00 45.94 3.86
3552 5975 2.824041 GCCACCACGATCCGCAAT 60.824 61.111 0.00 0.00 0.00 3.56
3610 6033 0.321298 AACGCCATACCACCACTCAC 60.321 55.000 0.00 0.00 0.00 3.51
3623 6046 1.016130 CACTCACATCTGTGGCGACC 61.016 60.000 10.26 0.00 45.65 4.79
3637 6060 3.188786 GACCAGCATGTCGCCGAC 61.189 66.667 10.96 10.96 44.04 4.79
3638 6061 3.649277 GACCAGCATGTCGCCGACT 62.649 63.158 19.12 0.92 44.04 4.18
3639 6062 2.887568 CCAGCATGTCGCCGACTC 60.888 66.667 19.12 7.62 44.04 3.36
3640 6063 2.887568 CAGCATGTCGCCGACTCC 60.888 66.667 19.12 6.53 44.04 3.85
3641 6064 4.148825 AGCATGTCGCCGACTCCC 62.149 66.667 19.12 6.18 44.04 4.30
3643 6066 4.873129 CATGTCGCCGACTCCCCG 62.873 72.222 19.12 0.00 33.15 5.73
3658 6081 4.779475 CCGCATCGGGAAAGCTAT 57.221 55.556 0.00 0.00 44.15 2.97
3659 6082 2.533318 CCGCATCGGGAAAGCTATC 58.467 57.895 0.00 0.00 44.15 2.08
3660 6083 0.249868 CCGCATCGGGAAAGCTATCA 60.250 55.000 0.00 0.00 44.15 2.15
3661 6084 0.861837 CGCATCGGGAAAGCTATCAC 59.138 55.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.215252 TCAACGTCCTCTTTTCTCTCATT 57.785 39.130 0.00 0.00 0.00 2.57
1 2 4.873746 TCAACGTCCTCTTTTCTCTCAT 57.126 40.909 0.00 0.00 0.00 2.90
3 4 3.929610 CCATCAACGTCCTCTTTTCTCTC 59.070 47.826 0.00 0.00 0.00 3.20
4 5 3.307059 CCCATCAACGTCCTCTTTTCTCT 60.307 47.826 0.00 0.00 0.00 3.10
5 6 3.003480 CCCATCAACGTCCTCTTTTCTC 58.997 50.000 0.00 0.00 0.00 2.87
6 7 2.637872 TCCCATCAACGTCCTCTTTTCT 59.362 45.455 0.00 0.00 0.00 2.52
9 10 1.279271 CCTCCCATCAACGTCCTCTTT 59.721 52.381 0.00 0.00 0.00 2.52
12 13 0.175989 GACCTCCCATCAACGTCCTC 59.824 60.000 0.00 0.00 0.00 3.71
13 14 1.605058 CGACCTCCCATCAACGTCCT 61.605 60.000 0.00 0.00 0.00 3.85
14 15 1.153628 CGACCTCCCATCAACGTCC 60.154 63.158 0.00 0.00 0.00 4.79
15 16 0.736325 CACGACCTCCCATCAACGTC 60.736 60.000 0.00 0.00 31.82 4.34
16 17 1.292223 CACGACCTCCCATCAACGT 59.708 57.895 0.00 0.00 34.40 3.99
17 18 1.447838 CCACGACCTCCCATCAACG 60.448 63.158 0.00 0.00 0.00 4.10
18 19 0.673644 CACCACGACCTCCCATCAAC 60.674 60.000 0.00 0.00 0.00 3.18
19 20 1.676968 CACCACGACCTCCCATCAA 59.323 57.895 0.00 0.00 0.00 2.57
20 21 2.290287 CCACCACGACCTCCCATCA 61.290 63.158 0.00 0.00 0.00 3.07
21 22 2.584608 CCACCACGACCTCCCATC 59.415 66.667 0.00 0.00 0.00 3.51
22 23 3.717294 GCCACCACGACCTCCCAT 61.717 66.667 0.00 0.00 0.00 4.00
27 28 3.857521 TAAGGGGCCACCACGACCT 62.858 63.158 0.00 0.00 43.89 3.85
28 29 2.414658 TTTAAGGGGCCACCACGACC 62.415 60.000 0.00 0.00 43.89 4.79
29 30 1.073548 TTTAAGGGGCCACCACGAC 59.926 57.895 0.00 0.00 43.89 4.34
30 31 1.073548 GTTTAAGGGGCCACCACGA 59.926 57.895 0.00 0.00 43.89 4.35
31 32 1.228306 TGTTTAAGGGGCCACCACG 60.228 57.895 0.00 0.00 43.89 4.94
32 33 0.178973 ACTGTTTAAGGGGCCACCAC 60.179 55.000 0.00 0.00 43.89 4.16
33 34 1.447099 TACTGTTTAAGGGGCCACCA 58.553 50.000 0.00 0.00 43.89 4.17
34 35 2.165167 GTTACTGTTTAAGGGGCCACC 58.835 52.381 0.00 0.57 40.67 4.61
35 36 2.817844 CAGTTACTGTTTAAGGGGCCAC 59.182 50.000 4.39 0.00 0.00 5.01
36 37 2.712087 TCAGTTACTGTTTAAGGGGCCA 59.288 45.455 12.41 0.00 32.61 5.36
37 38 3.428413 TCAGTTACTGTTTAAGGGGCC 57.572 47.619 12.41 0.00 32.61 5.80
38 39 3.756963 CCTTCAGTTACTGTTTAAGGGGC 59.243 47.826 18.23 0.00 32.65 5.80
39 40 3.756963 GCCTTCAGTTACTGTTTAAGGGG 59.243 47.826 23.75 13.23 35.12 4.79
40 41 4.652822 AGCCTTCAGTTACTGTTTAAGGG 58.347 43.478 23.75 12.40 35.12 3.95
41 42 7.390718 ACATAAGCCTTCAGTTACTGTTTAAGG 59.609 37.037 20.44 20.44 36.60 2.69
42 43 8.230486 CACATAAGCCTTCAGTTACTGTTTAAG 58.770 37.037 12.41 8.54 32.61 1.85
43 44 7.174253 CCACATAAGCCTTCAGTTACTGTTTAA 59.826 37.037 12.41 0.00 32.61 1.52
44 45 6.653320 CCACATAAGCCTTCAGTTACTGTTTA 59.347 38.462 12.41 5.64 32.61 2.01
45 46 5.473504 CCACATAAGCCTTCAGTTACTGTTT 59.526 40.000 12.41 3.80 32.61 2.83
46 47 5.003804 CCACATAAGCCTTCAGTTACTGTT 58.996 41.667 12.41 1.54 32.61 3.16
47 48 4.579869 CCACATAAGCCTTCAGTTACTGT 58.420 43.478 12.41 0.00 32.61 3.55
48 49 3.375299 GCCACATAAGCCTTCAGTTACTG 59.625 47.826 5.94 5.94 0.00 2.74
49 50 3.009033 TGCCACATAAGCCTTCAGTTACT 59.991 43.478 0.00 0.00 0.00 2.24
50 51 3.343617 TGCCACATAAGCCTTCAGTTAC 58.656 45.455 0.00 0.00 0.00 2.50
51 52 3.609853 CTGCCACATAAGCCTTCAGTTA 58.390 45.455 0.00 0.00 0.00 2.24
52 53 2.440409 CTGCCACATAAGCCTTCAGTT 58.560 47.619 0.00 0.00 0.00 3.16
53 54 1.340405 CCTGCCACATAAGCCTTCAGT 60.340 52.381 0.00 0.00 0.00 3.41
54 55 1.065199 TCCTGCCACATAAGCCTTCAG 60.065 52.381 0.00 0.00 0.00 3.02
55 56 0.991146 TCCTGCCACATAAGCCTTCA 59.009 50.000 0.00 0.00 0.00 3.02
56 57 2.355010 ATCCTGCCACATAAGCCTTC 57.645 50.000 0.00 0.00 0.00 3.46
57 58 2.291800 ACAATCCTGCCACATAAGCCTT 60.292 45.455 0.00 0.00 0.00 4.35
58 59 1.285962 ACAATCCTGCCACATAAGCCT 59.714 47.619 0.00 0.00 0.00 4.58
59 60 1.767759 ACAATCCTGCCACATAAGCC 58.232 50.000 0.00 0.00 0.00 4.35
60 61 2.493278 ACAACAATCCTGCCACATAAGC 59.507 45.455 0.00 0.00 0.00 3.09
61 62 4.943705 ACTACAACAATCCTGCCACATAAG 59.056 41.667 0.00 0.00 0.00 1.73
62 63 4.699735 CACTACAACAATCCTGCCACATAA 59.300 41.667 0.00 0.00 0.00 1.90
63 64 4.260985 CACTACAACAATCCTGCCACATA 58.739 43.478 0.00 0.00 0.00 2.29
64 65 3.084039 CACTACAACAATCCTGCCACAT 58.916 45.455 0.00 0.00 0.00 3.21
65 66 2.503331 CACTACAACAATCCTGCCACA 58.497 47.619 0.00 0.00 0.00 4.17
66 67 1.200020 GCACTACAACAATCCTGCCAC 59.800 52.381 0.00 0.00 0.00 5.01
67 68 1.073763 AGCACTACAACAATCCTGCCA 59.926 47.619 0.00 0.00 0.00 4.92
68 69 1.740025 GAGCACTACAACAATCCTGCC 59.260 52.381 0.00 0.00 0.00 4.85
69 70 1.394917 CGAGCACTACAACAATCCTGC 59.605 52.381 0.00 0.00 0.00 4.85
70 71 2.002586 CCGAGCACTACAACAATCCTG 58.997 52.381 0.00 0.00 0.00 3.86
71 72 1.899814 TCCGAGCACTACAACAATCCT 59.100 47.619 0.00 0.00 0.00 3.24
72 73 2.000447 GTCCGAGCACTACAACAATCC 59.000 52.381 0.00 0.00 0.00 3.01
73 74 2.000447 GGTCCGAGCACTACAACAATC 59.000 52.381 0.00 0.00 0.00 2.67
74 75 1.338769 GGGTCCGAGCACTACAACAAT 60.339 52.381 0.00 0.00 0.00 2.71
75 76 0.034337 GGGTCCGAGCACTACAACAA 59.966 55.000 0.00 0.00 0.00 2.83
76 77 1.116536 TGGGTCCGAGCACTACAACA 61.117 55.000 0.00 0.00 0.00 3.33
77 78 0.249398 ATGGGTCCGAGCACTACAAC 59.751 55.000 0.00 0.00 0.00 3.32
78 79 0.535335 GATGGGTCCGAGCACTACAA 59.465 55.000 0.00 0.00 0.00 2.41
79 80 0.324368 AGATGGGTCCGAGCACTACA 60.324 55.000 0.00 0.00 0.00 2.74
80 81 0.103208 CAGATGGGTCCGAGCACTAC 59.897 60.000 0.00 0.00 0.00 2.73
81 82 0.324368 ACAGATGGGTCCGAGCACTA 60.324 55.000 0.00 0.00 0.00 2.74
82 83 0.324368 TACAGATGGGTCCGAGCACT 60.324 55.000 0.00 0.00 0.00 4.40
83 84 0.535335 TTACAGATGGGTCCGAGCAC 59.465 55.000 0.00 0.00 0.00 4.40
84 85 0.824109 CTTACAGATGGGTCCGAGCA 59.176 55.000 0.00 0.00 0.00 4.26
85 86 0.824759 ACTTACAGATGGGTCCGAGC 59.175 55.000 0.00 0.00 0.00 5.03
86 87 3.700038 ACTAACTTACAGATGGGTCCGAG 59.300 47.826 0.00 0.00 0.00 4.63
87 88 3.705051 ACTAACTTACAGATGGGTCCGA 58.295 45.455 0.00 0.00 0.00 4.55
88 89 4.643784 ACTACTAACTTACAGATGGGTCCG 59.356 45.833 0.00 0.00 0.00 4.79
89 90 7.836479 ATACTACTAACTTACAGATGGGTCC 57.164 40.000 0.00 0.00 0.00 4.46
106 107 9.959721 ACCTTTTCACATCAACATTATACTACT 57.040 29.630 0.00 0.00 0.00 2.57
109 110 9.295825 TCAACCTTTTCACATCAACATTATACT 57.704 29.630 0.00 0.00 0.00 2.12
112 113 8.805175 TCATCAACCTTTTCACATCAACATTAT 58.195 29.630 0.00 0.00 0.00 1.28
113 114 8.175925 TCATCAACCTTTTCACATCAACATTA 57.824 30.769 0.00 0.00 0.00 1.90
114 115 7.053316 TCATCAACCTTTTCACATCAACATT 57.947 32.000 0.00 0.00 0.00 2.71
115 116 6.294899 CCTCATCAACCTTTTCACATCAACAT 60.295 38.462 0.00 0.00 0.00 2.71
116 117 5.009911 CCTCATCAACCTTTTCACATCAACA 59.990 40.000 0.00 0.00 0.00 3.33
117 118 5.010012 ACCTCATCAACCTTTTCACATCAAC 59.990 40.000 0.00 0.00 0.00 3.18
118 119 5.009911 CACCTCATCAACCTTTTCACATCAA 59.990 40.000 0.00 0.00 0.00 2.57
119 120 4.520111 CACCTCATCAACCTTTTCACATCA 59.480 41.667 0.00 0.00 0.00 3.07
120 121 4.082571 CCACCTCATCAACCTTTTCACATC 60.083 45.833 0.00 0.00 0.00 3.06
121 122 3.828451 CCACCTCATCAACCTTTTCACAT 59.172 43.478 0.00 0.00 0.00 3.21
122 123 3.117701 TCCACCTCATCAACCTTTTCACA 60.118 43.478 0.00 0.00 0.00 3.58
123 124 3.486383 TCCACCTCATCAACCTTTTCAC 58.514 45.455 0.00 0.00 0.00 3.18
124 125 3.874383 TCCACCTCATCAACCTTTTCA 57.126 42.857 0.00 0.00 0.00 2.69
125 126 4.884164 CCTATCCACCTCATCAACCTTTTC 59.116 45.833 0.00 0.00 0.00 2.29
126 127 4.860022 CCTATCCACCTCATCAACCTTTT 58.140 43.478 0.00 0.00 0.00 2.27
127 128 3.372025 GCCTATCCACCTCATCAACCTTT 60.372 47.826 0.00 0.00 0.00 3.11
128 129 2.173569 GCCTATCCACCTCATCAACCTT 59.826 50.000 0.00 0.00 0.00 3.50
129 130 1.771255 GCCTATCCACCTCATCAACCT 59.229 52.381 0.00 0.00 0.00 3.50
130 131 1.771255 AGCCTATCCACCTCATCAACC 59.229 52.381 0.00 0.00 0.00 3.77
131 132 2.843701 CAGCCTATCCACCTCATCAAC 58.156 52.381 0.00 0.00 0.00 3.18
132 133 1.141657 GCAGCCTATCCACCTCATCAA 59.858 52.381 0.00 0.00 0.00 2.57
133 134 0.761187 GCAGCCTATCCACCTCATCA 59.239 55.000 0.00 0.00 0.00 3.07
134 135 0.761187 TGCAGCCTATCCACCTCATC 59.239 55.000 0.00 0.00 0.00 2.92
135 136 1.073444 CATGCAGCCTATCCACCTCAT 59.927 52.381 0.00 0.00 0.00 2.90
136 137 0.471191 CATGCAGCCTATCCACCTCA 59.529 55.000 0.00 0.00 0.00 3.86
137 138 0.471617 ACATGCAGCCTATCCACCTC 59.528 55.000 0.00 0.00 0.00 3.85
138 139 0.471617 GACATGCAGCCTATCCACCT 59.528 55.000 0.00 0.00 0.00 4.00
139 140 0.181114 TGACATGCAGCCTATCCACC 59.819 55.000 0.00 0.00 0.00 4.61
140 141 1.945394 CTTGACATGCAGCCTATCCAC 59.055 52.381 0.00 0.00 0.00 4.02
141 142 1.839354 TCTTGACATGCAGCCTATCCA 59.161 47.619 0.00 0.00 0.00 3.41
142 143 2.103771 TCTCTTGACATGCAGCCTATCC 59.896 50.000 0.00 0.00 0.00 2.59
143 144 3.465742 TCTCTTGACATGCAGCCTATC 57.534 47.619 0.00 0.00 0.00 2.08
144 145 3.920231 TTCTCTTGACATGCAGCCTAT 57.080 42.857 0.00 0.00 0.00 2.57
145 146 3.701205 TTTCTCTTGACATGCAGCCTA 57.299 42.857 0.00 0.00 0.00 3.93
146 147 2.574006 TTTCTCTTGACATGCAGCCT 57.426 45.000 0.00 0.00 0.00 4.58
147 148 3.314635 CCTATTTCTCTTGACATGCAGCC 59.685 47.826 0.00 0.00 0.00 4.85
148 149 4.194640 TCCTATTTCTCTTGACATGCAGC 58.805 43.478 0.00 0.00 0.00 5.25
149 150 7.171167 CACTATCCTATTTCTCTTGACATGCAG 59.829 40.741 0.00 0.00 0.00 4.41
150 151 6.988580 CACTATCCTATTTCTCTTGACATGCA 59.011 38.462 0.00 0.00 0.00 3.96
151 152 6.426328 CCACTATCCTATTTCTCTTGACATGC 59.574 42.308 0.00 0.00 0.00 4.06
152 153 6.933521 CCCACTATCCTATTTCTCTTGACATG 59.066 42.308 0.00 0.00 0.00 3.21
153 154 6.043706 CCCCACTATCCTATTTCTCTTGACAT 59.956 42.308 0.00 0.00 0.00 3.06
154 155 5.366768 CCCCACTATCCTATTTCTCTTGACA 59.633 44.000 0.00 0.00 0.00 3.58
155 156 5.602978 TCCCCACTATCCTATTTCTCTTGAC 59.397 44.000 0.00 0.00 0.00 3.18
156 157 5.788430 TCCCCACTATCCTATTTCTCTTGA 58.212 41.667 0.00 0.00 0.00 3.02
157 158 6.270927 TGATCCCCACTATCCTATTTCTCTTG 59.729 42.308 0.00 0.00 0.00 3.02
158 159 6.393897 TGATCCCCACTATCCTATTTCTCTT 58.606 40.000 0.00 0.00 0.00 2.85
159 160 5.982391 TGATCCCCACTATCCTATTTCTCT 58.018 41.667 0.00 0.00 0.00 3.10
160 161 6.271159 AGTTGATCCCCACTATCCTATTTCTC 59.729 42.308 0.00 0.00 0.00 2.87
161 162 6.153924 AGTTGATCCCCACTATCCTATTTCT 58.846 40.000 0.00 0.00 0.00 2.52
162 163 6.441088 AGTTGATCCCCACTATCCTATTTC 57.559 41.667 0.00 0.00 0.00 2.17
163 164 8.525729 AATAGTTGATCCCCACTATCCTATTT 57.474 34.615 8.87 0.00 0.00 1.40
164 165 8.525729 AAATAGTTGATCCCCACTATCCTATT 57.474 34.615 8.87 0.00 0.00 1.73
165 166 9.273137 CTAAATAGTTGATCCCCACTATCCTAT 57.727 37.037 8.87 0.00 0.00 2.57
166 167 7.678598 CCTAAATAGTTGATCCCCACTATCCTA 59.321 40.741 8.87 5.05 0.00 2.94
167 168 6.502158 CCTAAATAGTTGATCCCCACTATCCT 59.498 42.308 8.87 4.41 0.00 3.24
168 169 6.272558 ACCTAAATAGTTGATCCCCACTATCC 59.727 42.308 8.87 0.00 0.00 2.59
169 170 7.317722 ACCTAAATAGTTGATCCCCACTATC 57.682 40.000 8.87 0.00 0.00 2.08
170 171 8.990693 ATACCTAAATAGTTGATCCCCACTAT 57.009 34.615 4.29 4.29 0.00 2.12
171 172 8.808240 AATACCTAAATAGTTGATCCCCACTA 57.192 34.615 0.00 0.00 0.00 2.74
172 173 7.707467 AATACCTAAATAGTTGATCCCCACT 57.293 36.000 0.00 0.00 0.00 4.00
194 195 8.721479 CCCCAATAGATCCATGTCATCTATAAT 58.279 37.037 18.31 7.24 41.02 1.28
195 196 7.684186 ACCCCAATAGATCCATGTCATCTATAA 59.316 37.037 18.31 1.84 41.02 0.98
196 197 7.199048 ACCCCAATAGATCCATGTCATCTATA 58.801 38.462 18.31 2.38 41.02 1.31
200 201 4.288105 AGACCCCAATAGATCCATGTCATC 59.712 45.833 0.00 0.00 0.00 2.92
281 283 7.786178 TCATATTTTACTAGCAAACGAGCAT 57.214 32.000 0.00 0.00 36.85 3.79
282 284 7.786178 ATCATATTTTACTAGCAAACGAGCA 57.214 32.000 0.00 0.00 36.85 4.26
287 289 8.761497 TGCTCGTATCATATTTTACTAGCAAAC 58.239 33.333 14.10 0.00 41.39 2.93
319 321 1.529865 GAGAAGTTTTGGGTTCGGACG 59.470 52.381 0.00 0.00 0.00 4.79
340 342 6.013293 GCTATGTACTTTTCCCCAGAGGATAT 60.013 42.308 0.00 0.00 46.94 1.63
352 354 7.173390 AGGAAGTGTTTCAGCTATGTACTTTTC 59.827 37.037 0.00 0.00 34.90 2.29
433 435 8.181904 TCCTTTCAAGAAAAATAGCAGACATT 57.818 30.769 0.00 0.00 0.00 2.71
451 453 5.043762 AGTATGGGGTTATCCTTCCTTTCA 58.956 41.667 0.00 0.00 35.33 2.69
526 536 0.871722 CGAATTTGTTCGGTGGCTGA 59.128 50.000 2.83 0.00 40.48 4.26
578 589 1.475403 TGCCTGGTAGAGCTACTGTC 58.525 55.000 7.51 0.00 36.36 3.51
579 590 1.550976 GTTGCCTGGTAGAGCTACTGT 59.449 52.381 7.51 0.00 36.36 3.55
580 591 1.134670 GGTTGCCTGGTAGAGCTACTG 60.135 57.143 7.51 2.07 35.48 2.74
581 592 1.196012 GGTTGCCTGGTAGAGCTACT 58.804 55.000 7.51 0.00 35.48 2.57
622 637 9.292846 GAGTTGTATACTTTTCGGTTTGTTTTT 57.707 29.630 4.17 0.00 37.17 1.94
729 1781 5.048434 GGATCGAATCTTGATTTTGGGGATC 60.048 44.000 0.00 5.86 0.00 3.36
739 1791 4.694760 TGGTGATGGATCGAATCTTGAT 57.305 40.909 8.11 0.00 0.00 2.57
801 1853 3.699538 GAGGAAACACAAGACCTTTGGTT 59.300 43.478 0.00 0.00 35.25 3.67
831 1883 0.306228 TCAACGACGAAACGACGGTA 59.694 50.000 17.53 3.11 43.08 4.02
943 1999 8.099364 TGTTAGGCAATTACTGAAGAAAGAAG 57.901 34.615 0.00 0.00 0.00 2.85
976 2032 9.979270 CATTCTTGAAAGTGTATGATTGAGTAC 57.021 33.333 0.00 0.00 0.00 2.73
1200 2256 4.272018 CACCTAGCCGAGATCATGAAAAAG 59.728 45.833 0.00 0.00 0.00 2.27
1348 2404 3.635373 CCCTAACTTGCATACTCCTCGTA 59.365 47.826 0.00 0.00 0.00 3.43
1356 2412 2.092375 AGGAAGCCCCTAACTTGCATAC 60.092 50.000 0.00 0.00 45.48 2.39
1373 2429 2.664402 AAAAGCCTGCAGAGAAGGAA 57.336 45.000 17.39 0.00 36.91 3.36
1907 2972 1.809619 CGCGATGGATGGACACGTT 60.810 57.895 0.00 0.00 0.00 3.99
2502 3567 4.032356 CTGCACGACAGCTTCACA 57.968 55.556 0.00 0.00 40.19 3.58
2717 3782 4.450976 AGCAATATCTTTGGCGTGTCATA 58.549 39.130 0.00 0.00 0.00 2.15
2734 3799 4.537135 TCGTACAGAGGAAAGAAGCAAT 57.463 40.909 0.00 0.00 0.00 3.56
2845 3910 7.106239 GTGTGCATCCTATATATACAAAGGCT 58.894 38.462 0.00 0.00 0.00 4.58
2882 5285 5.705609 AATTTTGCTCTTTACCGACATGT 57.294 34.783 0.00 0.00 0.00 3.21
2953 5356 5.940192 TGATCGCTGATGTAGTTTGTTTT 57.060 34.783 0.00 0.00 0.00 2.43
2985 5402 1.069513 CGCGGGGTCAAGATATGGTTA 59.930 52.381 0.00 0.00 0.00 2.85
3003 5420 2.682856 TGAAGACCATTATTGCCTTCGC 59.317 45.455 0.00 0.00 35.52 4.70
3066 5483 4.950475 AGAATCTGATCTCTGGTCGTTACA 59.050 41.667 0.00 0.00 0.00 2.41
3185 5607 4.844085 TGAAAACCCTAGATCTGACCTGAA 59.156 41.667 5.18 0.00 0.00 3.02
3286 5708 2.578786 CATGTAGCTGATGGGATTGCA 58.421 47.619 0.00 0.00 0.00 4.08
3313 5735 5.123502 GCATCAGTGACAGTGAGATTTCATT 59.876 40.000 17.62 0.00 35.39 2.57
3610 6033 1.450848 ATGCTGGTCGCCACAGATG 60.451 57.895 5.24 0.00 38.20 2.90
3642 6065 0.861837 GTGATAGCTTTCCCGATGCG 59.138 55.000 0.00 0.00 33.86 4.73


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

AutoCloner maintained by Alex Coulton.