Multiple sequence alignment - TraesCS2B01G369500

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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 TraesCS2B01G369500 chr2B 100.000 3173 0 0 1 3173 526775238 526778410 0.000000e+00 5860.0
1 TraesCS2B01G369500 chr2B 77.001 1187 232 29 1008 2173 526763367 526764533 2.670000e-180 641.0
2 TraesCS2B01G369500 chr2B 79.592 539 87 14 1622 2138 632403871 632404408 6.470000e-97 364.0
3 TraesCS2B01G369500 chr2B 88.764 89 9 1 3080 3167 247368625 247368537 1.200000e-19 108.0
4 TraesCS2B01G369500 chr2D 90.417 2108 128 37 1001 3082 446942037 446944096 0.000000e+00 2706.0
5 TraesCS2B01G369500 chr2D 76.535 1189 229 34 1011 2173 446858922 446857758 3.500000e-169 604.0
6 TraesCS2B01G369500 chr2D 81.299 508 53 28 361 839 446940933 446941427 1.070000e-99 374.0
7 TraesCS2B01G369500 chr2D 77.281 537 95 18 1609 2136 447321987 447322505 1.110000e-74 291.0
8 TraesCS2B01G369500 chr2A 93.514 1218 68 8 960 2177 591277973 591279179 0.000000e+00 1801.0
9 TraesCS2B01G369500 chr2A 88.387 775 54 17 2418 3173 591279326 591280083 0.000000e+00 900.0
10 TraesCS2B01G369500 chr2A 86.483 725 39 20 161 872 591277282 591277960 0.000000e+00 741.0
11 TraesCS2B01G369500 chr2A 77.395 1190 219 36 1008 2177 591264528 591265687 0.000000e+00 662.0
12 TraesCS2B01G369500 chr2A 79.667 541 83 19 1622 2138 676984962 676985499 6.470000e-97 364.0
13 TraesCS2B01G369500 chr2A 73.258 1148 238 52 1010 2136 592091405 592092504 3.890000e-94 355.0
14 TraesCS2B01G369500 chr2A 76.482 506 100 13 1012 1514 591607991 591608480 1.130000e-64 257.0
15 TraesCS2B01G369500 chr5D 86.085 1193 134 21 992 2177 463087452 463088619 0.000000e+00 1254.0
16 TraesCS2B01G369500 chr5D 85.326 184 20 3 680 860 463087199 463087378 1.940000e-42 183.0
17 TraesCS2B01G369500 chr5D 90.588 85 6 1 3087 3171 546857355 546857273 9.300000e-21 111.0
18 TraesCS2B01G369500 chr5D 87.778 90 10 1 3078 3166 421531320 421531409 1.560000e-18 104.0
19 TraesCS2B01G369500 chr5A 86.158 1192 130 23 995 2177 582980948 582982113 0.000000e+00 1254.0
20 TraesCS2B01G369500 chr5B 84.958 1190 138 20 995 2177 569825553 569826708 0.000000e+00 1168.0
21 TraesCS2B01G369500 chr6B 89.286 84 7 2 3089 3170 624798187 624798104 1.560000e-18 104.0
22 TraesCS2B01G369500 chr6B 97.436 39 1 0 1 39 506128068 506128030 2.040000e-07 67.6
23 TraesCS2B01G369500 chr6A 87.778 90 9 2 3080 3167 263872797 263872886 1.560000e-18 104.0
24 TraesCS2B01G369500 chr6A 93.443 61 4 0 779 839 154740173 154740113 1.210000e-14 91.6
25 TraesCS2B01G369500 chr4D 88.235 85 9 1 3083 3166 482363719 482363635 2.010000e-17 100.0
26 TraesCS2B01G369500 chr4B 88.235 85 8 2 3083 3166 612214247 612214164 2.010000e-17 100.0
27 TraesCS2B01G369500 chr1A 87.500 88 9 2 3083 3168 546795133 546795220 2.010000e-17 100.0
28 TraesCS2B01G369500 chrUn 97.436 39 1 0 1 39 63181021 63180983 2.040000e-07 67.6
29 TraesCS2B01G369500 chrUn 97.436 39 1 0 1 39 94181956 94181918 2.040000e-07 67.6
30 TraesCS2B01G369500 chrUn 97.368 38 1 0 1 38 92183683 92183720 7.350000e-07 65.8
31 TraesCS2B01G369500 chr7D 97.436 39 1 0 1 39 234551870 234551908 2.040000e-07 67.6
32 TraesCS2B01G369500 chr3D 97.436 39 1 0 1 39 104404852 104404890 2.040000e-07 67.6
33 TraesCS2B01G369500 chr3A 97.436 39 1 0 1 39 362337460 362337498 2.040000e-07 67.6
34 TraesCS2B01G369500 chr1D 97.436 39 1 0 1 39 465596889 465596851 2.040000e-07 67.6
35 TraesCS2B01G369500 chr6D 94.872 39 2 0 1 39 318149839 318149877 9.500000e-06 62.1


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 TraesCS2B01G369500 chr2B 526775238 526778410 3172 False 5860.000000 5860 100.000000 1 3173 1 chr2B.!!$F2 3172
1 TraesCS2B01G369500 chr2B 526763367 526764533 1166 False 641.000000 641 77.001000 1008 2173 1 chr2B.!!$F1 1165
2 TraesCS2B01G369500 chr2B 632403871 632404408 537 False 364.000000 364 79.592000 1622 2138 1 chr2B.!!$F3 516
3 TraesCS2B01G369500 chr2D 446940933 446944096 3163 False 1540.000000 2706 85.858000 361 3082 2 chr2D.!!$F2 2721
4 TraesCS2B01G369500 chr2D 446857758 446858922 1164 True 604.000000 604 76.535000 1011 2173 1 chr2D.!!$R1 1162
5 TraesCS2B01G369500 chr2D 447321987 447322505 518 False 291.000000 291 77.281000 1609 2136 1 chr2D.!!$F1 527
6 TraesCS2B01G369500 chr2A 591277282 591280083 2801 False 1147.333333 1801 89.461333 161 3173 3 chr2A.!!$F5 3012
7 TraesCS2B01G369500 chr2A 591264528 591265687 1159 False 662.000000 662 77.395000 1008 2177 1 chr2A.!!$F1 1169
8 TraesCS2B01G369500 chr2A 676984962 676985499 537 False 364.000000 364 79.667000 1622 2138 1 chr2A.!!$F4 516
9 TraesCS2B01G369500 chr2A 592091405 592092504 1099 False 355.000000 355 73.258000 1010 2136 1 chr2A.!!$F3 1126
10 TraesCS2B01G369500 chr5D 463087199 463088619 1420 False 718.500000 1254 85.705500 680 2177 2 chr5D.!!$F2 1497
11 TraesCS2B01G369500 chr5A 582980948 582982113 1165 False 1254.000000 1254 86.158000 995 2177 1 chr5A.!!$F1 1182
12 TraesCS2B01G369500 chr5B 569825553 569826708 1155 False 1168.000000 1168 84.958000 995 2177 1 chr5B.!!$F1 1182

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 0.034896 GGGAGGAGCGTTGACAAAGA 59.965 55.0 5.22 0.0 0.00 2.52 F
271 272 0.042581 TGAGACCCTACCCAGCATGA 59.957 55.0 0.00 0.0 39.69 3.07 F
1110 1635 0.102481 CGATCCCGTACTGGAAGGTG 59.898 60.0 10.32 0.0 42.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1594 2144 0.933097 CATGTCATGCAGGCGTAGAC 59.067 55.000 0.00 8.27 0.00 2.59 R
1615 2170 2.998670 CGTTGATCAGCATGTTCTCTGT 59.001 45.455 10.36 0.00 35.86 3.41 R
2643 3269 0.251916 CCCGCTAATTCCTCCACACA 59.748 55.000 0.00 0.00 0.00 3.72 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
32 33 6.551385 CAGACAACTGAAAATGAGCTACTT 57.449 37.500 0.00 0.00 46.03 2.24
33 34 6.963796 CAGACAACTGAAAATGAGCTACTTT 58.036 36.000 0.00 0.00 46.03 2.66
34 35 7.074502 CAGACAACTGAAAATGAGCTACTTTC 58.925 38.462 7.41 7.41 46.03 2.62
35 36 6.205658 AGACAACTGAAAATGAGCTACTTTCC 59.794 38.462 10.53 0.00 0.00 3.13
36 37 5.827797 ACAACTGAAAATGAGCTACTTTCCA 59.172 36.000 10.53 0.00 0.00 3.53
37 38 5.948992 ACTGAAAATGAGCTACTTTCCAC 57.051 39.130 10.53 1.31 0.00 4.02
38 39 4.762251 ACTGAAAATGAGCTACTTTCCACC 59.238 41.667 10.53 0.00 0.00 4.61
39 40 3.751175 TGAAAATGAGCTACTTTCCACCG 59.249 43.478 10.53 0.00 0.00 4.94
40 41 3.418684 AAATGAGCTACTTTCCACCGT 57.581 42.857 0.00 0.00 0.00 4.83
41 42 2.674796 ATGAGCTACTTTCCACCGTC 57.325 50.000 0.00 0.00 0.00 4.79
42 43 1.629043 TGAGCTACTTTCCACCGTCT 58.371 50.000 0.00 0.00 0.00 4.18
43 44 1.968493 TGAGCTACTTTCCACCGTCTT 59.032 47.619 0.00 0.00 0.00 3.01
44 45 2.029290 TGAGCTACTTTCCACCGTCTTC 60.029 50.000 0.00 0.00 0.00 2.87
45 46 1.968493 AGCTACTTTCCACCGTCTTCA 59.032 47.619 0.00 0.00 0.00 3.02
46 47 2.367567 AGCTACTTTCCACCGTCTTCAA 59.632 45.455 0.00 0.00 0.00 2.69
47 48 2.737252 GCTACTTTCCACCGTCTTCAAG 59.263 50.000 0.00 0.00 0.00 3.02
48 49 2.256117 ACTTTCCACCGTCTTCAAGG 57.744 50.000 0.00 0.00 0.00 3.61
49 50 0.875059 CTTTCCACCGTCTTCAAGGC 59.125 55.000 0.00 0.00 0.00 4.35
50 51 0.536460 TTTCCACCGTCTTCAAGGCC 60.536 55.000 0.00 0.00 0.00 5.19
51 52 1.415672 TTCCACCGTCTTCAAGGCCT 61.416 55.000 0.00 0.00 0.00 5.19
52 53 1.073199 CCACCGTCTTCAAGGCCTT 59.927 57.895 13.78 13.78 0.00 4.35
53 54 0.323629 CCACCGTCTTCAAGGCCTTA 59.676 55.000 20.00 2.00 0.00 2.69
54 55 1.065418 CCACCGTCTTCAAGGCCTTAT 60.065 52.381 20.00 0.00 0.00 1.73
55 56 2.169769 CCACCGTCTTCAAGGCCTTATA 59.830 50.000 20.00 6.65 0.00 0.98
56 57 3.458189 CACCGTCTTCAAGGCCTTATAG 58.542 50.000 20.00 17.76 0.00 1.31
57 58 3.105283 ACCGTCTTCAAGGCCTTATAGT 58.895 45.455 20.00 6.18 0.00 2.12
58 59 3.118738 ACCGTCTTCAAGGCCTTATAGTG 60.119 47.826 20.00 6.32 0.00 2.74
59 60 3.132289 CCGTCTTCAAGGCCTTATAGTGA 59.868 47.826 20.00 9.11 0.00 3.41
60 61 4.382685 CCGTCTTCAAGGCCTTATAGTGAA 60.383 45.833 20.00 16.74 0.00 3.18
61 62 5.360591 CGTCTTCAAGGCCTTATAGTGAAT 58.639 41.667 20.00 0.00 0.00 2.57
62 63 6.462487 CCGTCTTCAAGGCCTTATAGTGAATA 60.462 42.308 20.00 7.88 0.00 1.75
63 64 6.642950 CGTCTTCAAGGCCTTATAGTGAATAG 59.357 42.308 20.00 7.19 0.00 1.73
64 65 7.470147 CGTCTTCAAGGCCTTATAGTGAATAGA 60.470 40.741 20.00 9.50 0.00 1.98
65 66 7.870445 GTCTTCAAGGCCTTATAGTGAATAGAG 59.130 40.741 20.00 6.10 0.00 2.43
66 67 6.672266 TCAAGGCCTTATAGTGAATAGAGG 57.328 41.667 20.00 0.00 0.00 3.69
67 68 5.544176 TCAAGGCCTTATAGTGAATAGAGGG 59.456 44.000 20.00 0.00 0.00 4.30
68 69 5.355670 AGGCCTTATAGTGAATAGAGGGA 57.644 43.478 0.00 0.00 0.00 4.20
69 70 5.337788 AGGCCTTATAGTGAATAGAGGGAG 58.662 45.833 0.00 0.00 0.00 4.30
70 71 5.088026 GGCCTTATAGTGAATAGAGGGAGT 58.912 45.833 0.00 0.00 0.00 3.85
71 72 5.046950 GGCCTTATAGTGAATAGAGGGAGTG 60.047 48.000 0.00 0.00 0.00 3.51
72 73 5.775701 GCCTTATAGTGAATAGAGGGAGTGA 59.224 44.000 0.00 0.00 0.00 3.41
73 74 6.439058 GCCTTATAGTGAATAGAGGGAGTGAT 59.561 42.308 0.00 0.00 0.00 3.06
74 75 7.616150 GCCTTATAGTGAATAGAGGGAGTGATA 59.384 40.741 0.00 0.00 0.00 2.15
75 76 9.707957 CCTTATAGTGAATAGAGGGAGTGATAT 57.292 37.037 0.00 0.00 0.00 1.63
86 87 7.618019 AGAGGGAGTGATATAAATACTTGCA 57.382 36.000 0.00 0.00 0.00 4.08
87 88 8.212259 AGAGGGAGTGATATAAATACTTGCAT 57.788 34.615 0.00 0.00 0.00 3.96
88 89 9.326489 AGAGGGAGTGATATAAATACTTGCATA 57.674 33.333 0.00 0.00 0.00 3.14
104 105 9.877178 ATACTTGCATATAACTATTGTAGCCTC 57.123 33.333 0.00 0.00 0.00 4.70
105 106 7.162082 ACTTGCATATAACTATTGTAGCCTCC 58.838 38.462 0.00 0.00 0.00 4.30
106 107 6.680148 TGCATATAACTATTGTAGCCTCCA 57.320 37.500 0.00 0.00 0.00 3.86
107 108 6.701340 TGCATATAACTATTGTAGCCTCCAG 58.299 40.000 0.00 0.00 0.00 3.86
108 109 5.582665 GCATATAACTATTGTAGCCTCCAGC 59.417 44.000 0.00 0.00 44.25 4.85
124 125 2.050985 GCAAGTTGCACCGTCTGC 60.051 61.111 22.90 0.00 44.26 4.26
131 132 4.847255 GCACCGTCTGCAATTGAC 57.153 55.556 10.34 1.02 46.29 3.18
132 133 1.948508 GCACCGTCTGCAATTGACA 59.051 52.632 10.34 6.02 46.29 3.58
133 134 0.523072 GCACCGTCTGCAATTGACAT 59.477 50.000 10.34 0.00 46.29 3.06
134 135 1.737236 GCACCGTCTGCAATTGACATA 59.263 47.619 10.34 0.00 46.29 2.29
135 136 2.223112 GCACCGTCTGCAATTGACATAG 60.223 50.000 10.34 1.54 46.29 2.23
136 137 2.009774 ACCGTCTGCAATTGACATAGC 58.990 47.619 10.34 0.00 34.37 2.97
137 138 1.331756 CCGTCTGCAATTGACATAGCC 59.668 52.381 10.34 0.00 34.37 3.93
138 139 2.009051 CGTCTGCAATTGACATAGCCA 58.991 47.619 10.34 0.00 34.37 4.75
139 140 2.615447 CGTCTGCAATTGACATAGCCAT 59.385 45.455 10.34 0.00 34.37 4.40
140 141 3.303593 CGTCTGCAATTGACATAGCCATC 60.304 47.826 10.34 0.00 34.37 3.51
141 142 3.004106 GTCTGCAATTGACATAGCCATCC 59.996 47.826 10.34 0.00 34.80 3.51
142 143 2.295349 CTGCAATTGACATAGCCATCCC 59.705 50.000 10.34 0.00 0.00 3.85
143 144 1.615392 GCAATTGACATAGCCATCCCC 59.385 52.381 10.34 0.00 0.00 4.81
144 145 2.754186 GCAATTGACATAGCCATCCCCT 60.754 50.000 10.34 0.00 0.00 4.79
145 146 2.889045 CAATTGACATAGCCATCCCCTG 59.111 50.000 0.00 0.00 0.00 4.45
146 147 1.891933 TTGACATAGCCATCCCCTGA 58.108 50.000 0.00 0.00 0.00 3.86
147 148 1.131638 TGACATAGCCATCCCCTGAC 58.868 55.000 0.00 0.00 0.00 3.51
148 149 1.131638 GACATAGCCATCCCCTGACA 58.868 55.000 0.00 0.00 0.00 3.58
149 150 0.839946 ACATAGCCATCCCCTGACAC 59.160 55.000 0.00 0.00 0.00 3.67
150 151 0.250038 CATAGCCATCCCCTGACACG 60.250 60.000 0.00 0.00 0.00 4.49
151 152 2.044806 ATAGCCATCCCCTGACACGC 62.045 60.000 0.00 0.00 0.00 5.34
153 154 4.838152 CCATCCCCTGACACGCGG 62.838 72.222 12.47 1.27 0.00 6.46
186 187 0.034896 GGGAGGAGCGTTGACAAAGA 59.965 55.000 5.22 0.00 0.00 2.52
190 191 2.612212 GAGGAGCGTTGACAAAGAAACA 59.388 45.455 5.22 0.00 0.00 2.83
237 238 1.612442 GGTGTGCCCTCCCTAGTCA 60.612 63.158 0.00 0.00 0.00 3.41
251 252 0.618458 TAGTCACCATGGTTCCCAGC 59.382 55.000 16.84 1.87 36.75 4.85
257 258 0.393537 CCATGGTTCCCAGCTGAGAC 60.394 60.000 17.39 10.26 36.75 3.36
261 262 0.617820 GGTTCCCAGCTGAGACCCTA 60.618 60.000 17.39 0.00 0.00 3.53
266 267 1.333636 CCAGCTGAGACCCTACCCAG 61.334 65.000 17.39 0.00 0.00 4.45
267 268 2.904131 GCTGAGACCCTACCCAGC 59.096 66.667 0.00 0.00 44.00 4.85
268 269 4.461119 CTGAGACCCTACCCAGCA 57.539 61.111 0.00 0.00 0.00 4.41
269 270 2.922162 CTGAGACCCTACCCAGCAT 58.078 57.895 0.00 0.00 0.00 3.79
270 271 0.467384 CTGAGACCCTACCCAGCATG 59.533 60.000 0.00 0.00 0.00 4.06
271 272 0.042581 TGAGACCCTACCCAGCATGA 59.957 55.000 0.00 0.00 39.69 3.07
272 273 1.204146 GAGACCCTACCCAGCATGAA 58.796 55.000 0.00 0.00 39.69 2.57
342 350 1.040339 ACTGACAGCCTCCTCGATCC 61.040 60.000 1.25 0.00 0.00 3.36
348 356 3.531207 CCTCCTCGATCCTGCGCA 61.531 66.667 10.98 10.98 0.00 6.09
353 361 3.451556 CTCGATCCTGCGCATGGGT 62.452 63.158 12.24 11.39 0.00 4.51
451 464 4.202441 GGCAACCAGAACATCACAGATAT 58.798 43.478 0.00 0.00 0.00 1.63
452 465 4.641989 GGCAACCAGAACATCACAGATATT 59.358 41.667 0.00 0.00 0.00 1.28
453 466 5.822519 GGCAACCAGAACATCACAGATATTA 59.177 40.000 0.00 0.00 0.00 0.98
455 468 6.540189 GCAACCAGAACATCACAGATATTAGT 59.460 38.462 0.00 0.00 0.00 2.24
457 470 9.035607 CAACCAGAACATCACAGATATTAGTAC 57.964 37.037 0.00 0.00 0.00 2.73
458 471 7.727181 ACCAGAACATCACAGATATTAGTACC 58.273 38.462 0.00 0.00 0.00 3.34
459 472 7.344612 ACCAGAACATCACAGATATTAGTACCA 59.655 37.037 0.00 0.00 0.00 3.25
511 526 3.788766 CGCCGCACCTGCACTAAC 61.789 66.667 0.00 0.00 42.21 2.34
512 527 2.668212 GCCGCACCTGCACTAACA 60.668 61.111 0.00 0.00 42.21 2.41
513 528 2.966309 GCCGCACCTGCACTAACAC 61.966 63.158 0.00 0.00 42.21 3.32
514 529 1.596752 CCGCACCTGCACTAACACA 60.597 57.895 0.00 0.00 42.21 3.72
517 532 1.266718 CGCACCTGCACTAACACATTT 59.733 47.619 0.00 0.00 42.21 2.32
608 652 2.914908 ATTTCGCGGCGCCAAACTT 61.915 52.632 25.82 9.48 0.00 2.66
609 653 3.815569 TTTCGCGGCGCCAAACTTG 62.816 57.895 28.98 10.13 0.00 3.16
695 739 1.139256 ACTCCGTGATCGAGAGCTCTA 59.861 52.381 18.25 1.54 37.65 2.43
844 890 3.316573 GACGGTGAGGGCCTCCAAG 62.317 68.421 30.03 21.55 34.83 3.61
886 1039 4.461431 TCTTCTTACTAACCGCACAGATCA 59.539 41.667 0.00 0.00 0.00 2.92
892 1045 1.656652 AACCGCACAGATCATACTGC 58.343 50.000 0.00 0.00 41.06 4.40
897 1050 1.067669 GCACAGATCATACTGCTCCGA 59.932 52.381 0.00 0.00 41.06 4.55
909 1062 2.076100 CTGCTCCGATTGTGTTAGCAA 58.924 47.619 0.00 0.00 42.21 3.91
910 1063 1.804151 TGCTCCGATTGTGTTAGCAAC 59.196 47.619 0.00 0.00 40.05 4.17
911 1064 2.076863 GCTCCGATTGTGTTAGCAACT 58.923 47.619 0.00 0.00 33.38 3.16
912 1065 2.484264 GCTCCGATTGTGTTAGCAACTT 59.516 45.455 0.00 0.00 33.38 2.66
913 1066 3.682858 GCTCCGATTGTGTTAGCAACTTA 59.317 43.478 0.00 0.00 33.38 2.24
915 1068 3.682858 TCCGATTGTGTTAGCAACTTAGC 59.317 43.478 0.00 0.00 0.00 3.09
916 1069 3.435327 CCGATTGTGTTAGCAACTTAGCA 59.565 43.478 0.00 0.00 36.85 3.49
917 1070 4.094887 CCGATTGTGTTAGCAACTTAGCAT 59.905 41.667 0.00 0.00 36.85 3.79
918 1071 5.391950 CCGATTGTGTTAGCAACTTAGCATT 60.392 40.000 0.00 0.00 36.85 3.56
919 1072 5.734498 CGATTGTGTTAGCAACTTAGCATTC 59.266 40.000 0.00 0.00 36.85 2.67
920 1073 6.573664 ATTGTGTTAGCAACTTAGCATTCA 57.426 33.333 0.00 0.00 36.85 2.57
921 1074 6.573664 TTGTGTTAGCAACTTAGCATTCAT 57.426 33.333 0.00 0.00 36.85 2.57
922 1075 6.182039 TGTGTTAGCAACTTAGCATTCATC 57.818 37.500 0.00 0.00 36.85 2.92
931 1084 6.320171 CAACTTAGCATTCATCAAGGACAAG 58.680 40.000 0.00 0.00 0.00 3.16
933 1086 5.879223 ACTTAGCATTCATCAAGGACAAGAG 59.121 40.000 0.00 0.00 0.00 2.85
940 1093 4.099633 TCATCAAGGACAAGAGGATCACT 58.900 43.478 0.00 0.00 37.82 3.41
942 1095 4.543590 TCAAGGACAAGAGGATCACTTC 57.456 45.455 0.00 0.00 37.82 3.01
951 1104 5.643777 ACAAGAGGATCACTTCGTTTTATGG 59.356 40.000 0.00 0.00 37.82 2.74
952 1105 5.677319 AGAGGATCACTTCGTTTTATGGA 57.323 39.130 0.00 0.00 37.82 3.41
953 1106 5.665459 AGAGGATCACTTCGTTTTATGGAG 58.335 41.667 0.00 0.00 37.82 3.86
954 1107 4.770795 AGGATCACTTCGTTTTATGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
955 1108 4.469945 AGGATCACTTCGTTTTATGGAGGA 59.530 41.667 0.00 0.00 0.00 3.71
956 1109 4.811557 GGATCACTTCGTTTTATGGAGGAG 59.188 45.833 0.00 0.00 0.00 3.69
957 1110 4.884668 TCACTTCGTTTTATGGAGGAGT 57.115 40.909 0.00 0.00 0.00 3.85
958 1111 5.988310 TCACTTCGTTTTATGGAGGAGTA 57.012 39.130 0.00 0.00 0.00 2.59
989 1172 2.473609 TGTCGTTTAATCTGACACGTGC 59.526 45.455 17.22 9.30 37.69 5.34
1110 1635 0.102481 CGATCCCGTACTGGAAGGTG 59.898 60.000 10.32 0.00 42.00 4.00
1111 1636 0.464452 GATCCCGTACTGGAAGGTGG 59.536 60.000 10.32 0.00 42.00 4.61
1251 1776 1.324740 TGACGCGGGGCAAGTACTAT 61.325 55.000 12.47 0.00 0.00 2.12
1502 2033 1.153765 TCGCCATCAGAACGCTCAG 60.154 57.895 0.00 0.00 0.00 3.35
1531 2076 1.298667 GCCACCCACCGTAAGACAT 59.701 57.895 0.00 0.00 43.02 3.06
1534 2079 1.134610 CCACCCACCGTAAGACATACC 60.135 57.143 0.00 0.00 43.02 2.73
1594 2144 5.029014 CACGTTACGGAATTCTCACTCTAG 58.971 45.833 10.20 0.00 0.00 2.43
1615 2170 1.754226 TCTACGCCTGCATGACATGTA 59.246 47.619 16.62 11.47 0.00 2.29
1778 2333 1.138036 TCAAGTACATCGACGCGGG 59.862 57.895 12.47 1.12 0.00 6.13
2303 2895 5.845103 ACTGCTGAGAATGAGATGATAGTG 58.155 41.667 0.00 0.00 0.00 2.74
2358 2973 5.190677 ACAGATTGATCATGATTCACTGCA 58.809 37.500 21.48 9.55 0.00 4.41
2465 3081 2.554142 TCTCTGCGTATGAAATGCTGG 58.446 47.619 0.00 0.00 41.03 4.85
2520 3137 2.352503 AATTCAGTTTGGCATGTCGC 57.647 45.000 0.00 0.00 41.28 5.19
2524 3141 0.311790 CAGTTTGGCATGTCGCTGTT 59.688 50.000 7.81 0.00 41.91 3.16
2525 3142 0.311790 AGTTTGGCATGTCGCTGTTG 59.688 50.000 0.00 0.00 41.91 3.33
2526 3143 0.030638 GTTTGGCATGTCGCTGTTGT 59.969 50.000 0.00 0.00 41.91 3.32
2527 3144 1.265635 GTTTGGCATGTCGCTGTTGTA 59.734 47.619 0.00 0.00 41.91 2.41
2528 3145 1.598882 TTGGCATGTCGCTGTTGTAA 58.401 45.000 0.00 0.00 41.91 2.41
2529 3146 1.155889 TGGCATGTCGCTGTTGTAAG 58.844 50.000 0.00 0.00 41.91 2.34
2530 3147 0.179189 GGCATGTCGCTGTTGTAAGC 60.179 55.000 0.00 0.00 41.91 3.09
2534 3151 1.217001 TGTCGCTGTTGTAAGCTGTG 58.783 50.000 0.00 0.00 41.24 3.66
2544 3161 5.616270 TGTTGTAAGCTGTGACTCCAAATA 58.384 37.500 0.00 0.00 0.00 1.40
2548 3165 7.759489 TGTAAGCTGTGACTCCAAATATTTT 57.241 32.000 0.00 0.00 0.00 1.82
2561 3178 4.562394 CCAAATATTTTACTGTTGCCGCTG 59.438 41.667 0.00 0.00 0.00 5.18
2643 3269 6.644347 CAGTGATTTAGTAGAGGGATTGTGT 58.356 40.000 0.00 0.00 0.00 3.72
2645 3271 6.213600 AGTGATTTAGTAGAGGGATTGTGTGT 59.786 38.462 0.00 0.00 0.00 3.72
2649 3275 2.303022 AGTAGAGGGATTGTGTGTGTGG 59.697 50.000 0.00 0.00 0.00 4.17
2659 3285 2.778299 TGTGTGTGTGGAGGAATTAGC 58.222 47.619 0.00 0.00 0.00 3.09
2667 3293 1.142870 TGGAGGAATTAGCGGGGATTG 59.857 52.381 0.00 0.00 0.00 2.67
2677 3303 4.143301 GGGGATTGGGTGAGGGGC 62.143 72.222 0.00 0.00 0.00 5.80
2696 3323 4.171186 GGATCACCCAACCCCTCT 57.829 61.111 0.00 0.00 34.14 3.69
2705 3332 0.323725 CCAACCCCTCTGTGGATTGG 60.324 60.000 13.71 13.71 41.91 3.16
2716 3343 0.679640 GTGGATTGGATCGCCACCAA 60.680 55.000 12.16 0.00 45.94 3.67
2727 3354 1.807226 GCCACCAACCGAATAAGGC 59.193 57.895 0.00 0.00 33.69 4.35
2731 3358 0.679960 ACCAACCGAATAAGGCCTGC 60.680 55.000 5.69 0.00 33.69 4.85
2732 3359 1.384222 CCAACCGAATAAGGCCTGCC 61.384 60.000 5.69 0.00 33.69 4.85
2844 3480 8.514330 TTGTTTACCTGATGAAACAAACTAGT 57.486 30.769 9.76 0.00 46.91 2.57
2851 3487 8.576442 ACCTGATGAAACAAACTAGTAAAATGG 58.424 33.333 0.00 0.00 0.00 3.16
2938 3574 6.669591 TCCTACAGAAAATTCAGGAGATCAGA 59.330 38.462 0.00 0.00 31.76 3.27
2947 3583 2.768527 TCAGGAGATCAGAATGTGGACC 59.231 50.000 0.00 0.00 37.40 4.46
3070 3707 5.240403 GCCTGTCAAAAGAAAGTCATCTCTT 59.760 40.000 0.00 0.00 33.25 2.85
3085 3722 6.201044 AGTCATCTCTTGTGTTCAAAAGTACG 59.799 38.462 3.14 0.00 32.87 3.67
3109 3749 6.417044 CGACCTCTGTACCAAAATATAAGACG 59.583 42.308 0.00 0.00 0.00 4.18
3113 3753 8.601476 CCTCTGTACCAAAATATAAGACGTTTC 58.399 37.037 0.00 0.00 0.00 2.78
3116 3756 8.836268 TGTACCAAAATATAAGACGTTTCTGT 57.164 30.769 0.00 0.00 29.98 3.41
3120 3760 9.275398 ACCAAAATATAAGACGTTTCTGTAACA 57.725 29.630 0.00 0.00 36.50 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.551385 AAGTAGCTCATTTTCAGTTGTCTG 57.449 37.500 0.00 0.00 42.54 3.51
10 11 6.205658 GGAAAGTAGCTCATTTTCAGTTGTCT 59.794 38.462 15.25 0.00 35.21 3.41
11 12 6.017109 TGGAAAGTAGCTCATTTTCAGTTGTC 60.017 38.462 15.25 2.96 35.21 3.18
12 13 5.827797 TGGAAAGTAGCTCATTTTCAGTTGT 59.172 36.000 15.25 0.00 35.21 3.32
13 14 6.145535 GTGGAAAGTAGCTCATTTTCAGTTG 58.854 40.000 15.25 0.00 35.21 3.16
14 15 5.241728 GGTGGAAAGTAGCTCATTTTCAGTT 59.758 40.000 15.25 0.00 35.21 3.16
15 16 4.762251 GGTGGAAAGTAGCTCATTTTCAGT 59.238 41.667 15.25 0.00 35.21 3.41
16 17 4.142816 CGGTGGAAAGTAGCTCATTTTCAG 60.143 45.833 15.25 0.61 35.21 3.02
17 18 3.751175 CGGTGGAAAGTAGCTCATTTTCA 59.249 43.478 15.25 9.23 35.21 2.69
18 19 3.751698 ACGGTGGAAAGTAGCTCATTTTC 59.248 43.478 0.00 0.00 33.32 2.29
19 20 3.751518 ACGGTGGAAAGTAGCTCATTTT 58.248 40.909 0.00 0.00 0.00 1.82
20 21 3.008049 AGACGGTGGAAAGTAGCTCATTT 59.992 43.478 0.00 0.00 0.00 2.32
21 22 2.567615 AGACGGTGGAAAGTAGCTCATT 59.432 45.455 0.00 0.00 0.00 2.57
22 23 2.180276 AGACGGTGGAAAGTAGCTCAT 58.820 47.619 0.00 0.00 0.00 2.90
23 24 1.629043 AGACGGTGGAAAGTAGCTCA 58.371 50.000 0.00 0.00 0.00 4.26
24 25 2.029290 TGAAGACGGTGGAAAGTAGCTC 60.029 50.000 0.00 0.00 0.00 4.09
25 26 1.968493 TGAAGACGGTGGAAAGTAGCT 59.032 47.619 0.00 0.00 0.00 3.32
26 27 2.450609 TGAAGACGGTGGAAAGTAGC 57.549 50.000 0.00 0.00 0.00 3.58
27 28 3.326747 CCTTGAAGACGGTGGAAAGTAG 58.673 50.000 0.00 0.00 0.00 2.57
28 29 2.549349 GCCTTGAAGACGGTGGAAAGTA 60.549 50.000 0.00 0.00 0.00 2.24
29 30 1.814248 GCCTTGAAGACGGTGGAAAGT 60.814 52.381 0.00 0.00 0.00 2.66
30 31 0.875059 GCCTTGAAGACGGTGGAAAG 59.125 55.000 0.00 0.00 0.00 2.62
31 32 0.536460 GGCCTTGAAGACGGTGGAAA 60.536 55.000 0.00 0.00 0.00 3.13
32 33 1.072505 GGCCTTGAAGACGGTGGAA 59.927 57.895 0.00 0.00 0.00 3.53
33 34 1.415672 AAGGCCTTGAAGACGGTGGA 61.416 55.000 19.73 0.00 0.00 4.02
34 35 0.323629 TAAGGCCTTGAAGACGGTGG 59.676 55.000 28.77 0.00 0.00 4.61
35 36 2.403252 ATAAGGCCTTGAAGACGGTG 57.597 50.000 28.77 0.00 0.00 4.94
36 37 3.105283 ACTATAAGGCCTTGAAGACGGT 58.895 45.455 28.77 13.06 0.00 4.83
37 38 3.132289 TCACTATAAGGCCTTGAAGACGG 59.868 47.826 28.77 17.13 0.00 4.79
38 39 4.386867 TCACTATAAGGCCTTGAAGACG 57.613 45.455 28.77 18.49 0.00 4.18
39 40 7.727181 TCTATTCACTATAAGGCCTTGAAGAC 58.273 38.462 28.77 0.00 30.07 3.01
40 41 7.015682 CCTCTATTCACTATAAGGCCTTGAAGA 59.984 40.741 28.77 18.29 30.07 2.87
41 42 7.158021 CCTCTATTCACTATAAGGCCTTGAAG 58.842 42.308 28.77 24.38 30.07 3.02
42 43 6.043243 CCCTCTATTCACTATAAGGCCTTGAA 59.957 42.308 28.77 22.29 0.00 2.69
43 44 5.544176 CCCTCTATTCACTATAAGGCCTTGA 59.456 44.000 28.77 14.39 0.00 3.02
44 45 5.544176 TCCCTCTATTCACTATAAGGCCTTG 59.456 44.000 28.77 14.05 0.00 3.61
45 46 5.727630 TCCCTCTATTCACTATAAGGCCTT 58.272 41.667 24.18 24.18 0.00 4.35
46 47 5.162815 ACTCCCTCTATTCACTATAAGGCCT 60.163 44.000 0.00 0.00 0.00 5.19
47 48 5.046950 CACTCCCTCTATTCACTATAAGGCC 60.047 48.000 0.00 0.00 0.00 5.19
48 49 5.775701 TCACTCCCTCTATTCACTATAAGGC 59.224 44.000 0.00 0.00 0.00 4.35
49 50 9.707957 ATATCACTCCCTCTATTCACTATAAGG 57.292 37.037 0.00 0.00 0.00 2.69
60 61 9.326489 TGCAAGTATTTATATCACTCCCTCTAT 57.674 33.333 0.00 0.00 0.00 1.98
61 62 8.721133 TGCAAGTATTTATATCACTCCCTCTA 57.279 34.615 0.00 0.00 0.00 2.43
62 63 7.618019 TGCAAGTATTTATATCACTCCCTCT 57.382 36.000 0.00 0.00 0.00 3.69
78 79 9.877178 GAGGCTACAATAGTTATATGCAAGTAT 57.123 33.333 0.00 0.00 0.00 2.12
79 80 8.311836 GGAGGCTACAATAGTTATATGCAAGTA 58.688 37.037 0.00 0.00 0.00 2.24
80 81 7.162082 GGAGGCTACAATAGTTATATGCAAGT 58.838 38.462 0.00 0.00 0.00 3.16
81 82 7.161404 TGGAGGCTACAATAGTTATATGCAAG 58.839 38.462 0.00 0.00 0.00 4.01
82 83 7.073457 TGGAGGCTACAATAGTTATATGCAA 57.927 36.000 0.00 0.00 0.00 4.08
83 84 6.680148 TGGAGGCTACAATAGTTATATGCA 57.320 37.500 0.00 0.00 0.00 3.96
84 85 5.582665 GCTGGAGGCTACAATAGTTATATGC 59.417 44.000 0.00 0.00 38.06 3.14
85 86 6.701340 TGCTGGAGGCTACAATAGTTATATG 58.299 40.000 0.00 0.00 42.39 1.78
86 87 6.935240 TGCTGGAGGCTACAATAGTTATAT 57.065 37.500 0.00 0.00 42.39 0.86
87 88 6.326583 ACTTGCTGGAGGCTACAATAGTTATA 59.673 38.462 0.00 0.00 42.39 0.98
88 89 5.131142 ACTTGCTGGAGGCTACAATAGTTAT 59.869 40.000 0.00 0.00 42.39 1.89
89 90 4.469945 ACTTGCTGGAGGCTACAATAGTTA 59.530 41.667 0.00 0.00 42.39 2.24
90 91 3.264450 ACTTGCTGGAGGCTACAATAGTT 59.736 43.478 0.00 0.00 42.39 2.24
91 92 2.840651 ACTTGCTGGAGGCTACAATAGT 59.159 45.455 0.00 1.42 42.39 2.12
92 93 3.550437 ACTTGCTGGAGGCTACAATAG 57.450 47.619 0.00 0.75 42.39 1.73
93 94 3.609853 CAACTTGCTGGAGGCTACAATA 58.390 45.455 0.00 0.00 42.39 1.90
94 95 2.440409 CAACTTGCTGGAGGCTACAAT 58.560 47.619 0.00 0.00 42.39 2.71
95 96 1.896220 CAACTTGCTGGAGGCTACAA 58.104 50.000 0.00 0.00 42.39 2.41
96 97 0.606401 GCAACTTGCTGGAGGCTACA 60.606 55.000 6.50 0.00 40.96 2.74
97 98 0.606401 TGCAACTTGCTGGAGGCTAC 60.606 55.000 14.78 0.00 45.31 3.58
98 99 0.606401 GTGCAACTTGCTGGAGGCTA 60.606 55.000 14.78 0.00 45.31 3.93
99 100 1.900498 GTGCAACTTGCTGGAGGCT 60.900 57.895 14.78 0.00 45.31 4.58
100 101 2.647297 GTGCAACTTGCTGGAGGC 59.353 61.111 14.78 0.00 45.31 4.70
101 102 2.620112 CGGTGCAACTTGCTGGAGG 61.620 63.158 14.78 0.00 45.31 4.30
102 103 1.845809 GACGGTGCAACTTGCTGGAG 61.846 60.000 14.78 6.46 45.31 3.86
103 104 1.891919 GACGGTGCAACTTGCTGGA 60.892 57.895 14.78 0.00 45.31 3.86
104 105 1.893808 AGACGGTGCAACTTGCTGG 60.894 57.895 14.78 6.53 45.31 4.85
105 106 1.280746 CAGACGGTGCAACTTGCTG 59.719 57.895 14.78 0.18 45.31 4.41
106 107 3.736483 CAGACGGTGCAACTTGCT 58.264 55.556 14.78 0.00 45.31 3.91
115 116 2.223112 GCTATGTCAATTGCAGACGGTG 60.223 50.000 0.00 0.00 38.83 4.94
116 117 2.009774 GCTATGTCAATTGCAGACGGT 58.990 47.619 0.00 0.00 38.83 4.83
117 118 1.331756 GGCTATGTCAATTGCAGACGG 59.668 52.381 0.00 0.00 38.83 4.79
118 119 2.009051 TGGCTATGTCAATTGCAGACG 58.991 47.619 0.00 0.00 38.83 4.18
119 120 3.004106 GGATGGCTATGTCAATTGCAGAC 59.996 47.826 0.00 0.00 36.40 3.51
120 121 3.216800 GGATGGCTATGTCAATTGCAGA 58.783 45.455 0.00 0.00 36.40 4.26
121 122 2.295349 GGGATGGCTATGTCAATTGCAG 59.705 50.000 0.00 0.00 36.40 4.41
122 123 2.309613 GGGATGGCTATGTCAATTGCA 58.690 47.619 0.00 2.71 36.40 4.08
123 124 1.615392 GGGGATGGCTATGTCAATTGC 59.385 52.381 0.00 0.00 34.25 3.56
124 125 2.889045 CAGGGGATGGCTATGTCAATTG 59.111 50.000 0.00 0.00 0.00 2.32
125 126 2.785269 TCAGGGGATGGCTATGTCAATT 59.215 45.455 0.00 0.00 0.00 2.32
126 127 2.107204 GTCAGGGGATGGCTATGTCAAT 59.893 50.000 0.00 0.00 0.00 2.57
127 128 1.490490 GTCAGGGGATGGCTATGTCAA 59.510 52.381 0.00 0.00 0.00 3.18
128 129 1.131638 GTCAGGGGATGGCTATGTCA 58.868 55.000 0.00 0.00 0.00 3.58
129 130 1.131638 TGTCAGGGGATGGCTATGTC 58.868 55.000 0.00 0.00 33.40 3.06
130 131 0.839946 GTGTCAGGGGATGGCTATGT 59.160 55.000 0.00 0.00 33.40 2.29
131 132 0.250038 CGTGTCAGGGGATGGCTATG 60.250 60.000 0.00 0.00 33.40 2.23
132 133 2.044806 GCGTGTCAGGGGATGGCTAT 62.045 60.000 0.00 0.00 33.40 2.97
133 134 2.731571 GCGTGTCAGGGGATGGCTA 61.732 63.158 0.00 0.00 33.40 3.93
134 135 4.101448 GCGTGTCAGGGGATGGCT 62.101 66.667 0.00 0.00 33.40 4.75
136 137 4.838152 CCGCGTGTCAGGGGATGG 62.838 72.222 4.92 0.00 45.92 3.51
167 168 0.034896 TCTTTGTCAACGCTCCTCCC 59.965 55.000 0.00 0.00 0.00 4.30
186 187 1.547372 GCTCACATGGCCATTCTGTTT 59.453 47.619 17.92 0.00 0.00 2.83
190 191 0.622136 TCTGCTCACATGGCCATTCT 59.378 50.000 17.92 0.13 0.00 2.40
251 252 0.467384 CATGCTGGGTAGGGTCTCAG 59.533 60.000 0.00 0.00 0.00 3.35
257 258 3.483954 CAGTTCATGCTGGGTAGGG 57.516 57.895 0.00 0.00 33.11 3.53
267 268 1.349627 GCGACCGATGCAGTTCATG 59.650 57.895 0.00 0.00 35.05 3.07
268 269 1.815421 GGCGACCGATGCAGTTCAT 60.815 57.895 0.00 0.00 38.32 2.57
269 270 2.434185 GGCGACCGATGCAGTTCA 60.434 61.111 0.00 0.00 0.00 3.18
270 271 3.195698 GGGCGACCGATGCAGTTC 61.196 66.667 0.00 0.00 43.64 3.01
314 317 3.720193 GCTGTCAGTGGTGCTGCG 61.720 66.667 0.93 0.00 44.66 5.18
451 464 3.005050 CACGTGGACTTGAGTGGTACTAA 59.995 47.826 7.95 0.00 0.00 2.24
452 465 2.555325 CACGTGGACTTGAGTGGTACTA 59.445 50.000 7.95 0.00 0.00 1.82
453 466 1.340248 CACGTGGACTTGAGTGGTACT 59.660 52.381 7.95 0.00 0.00 2.73
455 468 0.677288 CCACGTGGACTTGAGTGGTA 59.323 55.000 31.31 0.00 46.52 3.25
457 470 4.361253 CCACGTGGACTTGAGTGG 57.639 61.111 31.31 0.00 46.52 4.00
458 471 0.939577 CGACCACGTGGACTTGAGTG 60.940 60.000 40.21 16.42 38.94 3.51
459 472 1.362717 CGACCACGTGGACTTGAGT 59.637 57.895 40.21 16.93 38.94 3.41
501 516 5.633830 AATCTGAAATGTGTTAGTGCAGG 57.366 39.130 0.00 0.00 0.00 4.85
506 521 6.293407 CGTGGTGAAATCTGAAATGTGTTAGT 60.293 38.462 0.00 0.00 0.00 2.24
507 522 6.079763 CGTGGTGAAATCTGAAATGTGTTAG 58.920 40.000 0.00 0.00 0.00 2.34
509 524 4.792704 GCGTGGTGAAATCTGAAATGTGTT 60.793 41.667 0.00 0.00 0.00 3.32
510 525 3.304659 GCGTGGTGAAATCTGAAATGTGT 60.305 43.478 0.00 0.00 0.00 3.72
511 526 3.236816 GCGTGGTGAAATCTGAAATGTG 58.763 45.455 0.00 0.00 0.00 3.21
512 527 2.095768 CGCGTGGTGAAATCTGAAATGT 60.096 45.455 0.00 0.00 0.00 2.71
513 528 2.508867 CGCGTGGTGAAATCTGAAATG 58.491 47.619 0.00 0.00 0.00 2.32
514 529 1.135689 GCGCGTGGTGAAATCTGAAAT 60.136 47.619 8.43 0.00 0.00 2.17
517 532 2.379634 CGCGCGTGGTGAAATCTGA 61.380 57.895 24.19 0.00 0.00 3.27
610 654 3.535629 TTGAGGCGTCTGGCAGTGG 62.536 63.158 15.27 8.71 46.16 4.00
611 655 2.031012 TTGAGGCGTCTGGCAGTG 59.969 61.111 15.27 9.66 46.16 3.66
612 656 2.031163 GTTGAGGCGTCTGGCAGT 59.969 61.111 15.27 0.00 46.16 4.40
613 657 3.114616 CGTTGAGGCGTCTGGCAG 61.115 66.667 8.58 8.58 46.16 4.85
614 658 4.680237 CCGTTGAGGCGTCTGGCA 62.680 66.667 8.06 0.00 46.16 4.92
695 739 1.533711 CTTCGGGGCTGGATGGAAT 59.466 57.895 0.00 0.00 0.00 3.01
777 823 0.941463 CGCAGACGAGCAAGAACAGT 60.941 55.000 0.00 0.00 43.93 3.55
844 890 5.128008 AGAAGATCAAGGAGTAACAGTAGCC 59.872 44.000 0.00 0.00 0.00 3.93
886 1039 3.118775 TGCTAACACAATCGGAGCAGTAT 60.119 43.478 0.00 0.00 38.20 2.12
892 1045 4.201724 GCTAAGTTGCTAACACAATCGGAG 60.202 45.833 0.00 0.00 0.00 4.63
897 1050 6.573664 TGAATGCTAAGTTGCTAACACAAT 57.426 33.333 0.00 0.00 0.00 2.71
909 1062 5.809001 TCTTGTCCTTGATGAATGCTAAGT 58.191 37.500 0.00 0.00 0.00 2.24
910 1063 5.296283 CCTCTTGTCCTTGATGAATGCTAAG 59.704 44.000 0.00 0.00 0.00 2.18
911 1064 5.045651 TCCTCTTGTCCTTGATGAATGCTAA 60.046 40.000 0.00 0.00 0.00 3.09
912 1065 4.471025 TCCTCTTGTCCTTGATGAATGCTA 59.529 41.667 0.00 0.00 0.00 3.49
913 1066 3.265221 TCCTCTTGTCCTTGATGAATGCT 59.735 43.478 0.00 0.00 0.00 3.79
915 1068 5.296283 GTGATCCTCTTGTCCTTGATGAATG 59.704 44.000 0.00 0.00 0.00 2.67
916 1069 5.191323 AGTGATCCTCTTGTCCTTGATGAAT 59.809 40.000 0.00 0.00 0.00 2.57
917 1070 4.533707 AGTGATCCTCTTGTCCTTGATGAA 59.466 41.667 0.00 0.00 0.00 2.57
918 1071 4.099633 AGTGATCCTCTTGTCCTTGATGA 58.900 43.478 0.00 0.00 0.00 2.92
919 1072 4.484537 AGTGATCCTCTTGTCCTTGATG 57.515 45.455 0.00 0.00 0.00 3.07
920 1073 4.382470 CGAAGTGATCCTCTTGTCCTTGAT 60.382 45.833 5.22 0.00 0.00 2.57
921 1074 3.056536 CGAAGTGATCCTCTTGTCCTTGA 60.057 47.826 5.22 0.00 0.00 3.02
922 1075 3.257393 CGAAGTGATCCTCTTGTCCTTG 58.743 50.000 5.22 0.00 0.00 3.61
931 1084 4.811557 CCTCCATAAAACGAAGTGATCCTC 59.188 45.833 0.00 0.00 45.00 3.71
933 1086 4.766375 TCCTCCATAAAACGAAGTGATCC 58.234 43.478 0.00 0.00 45.00 3.36
940 1093 7.611467 TGTAGTAGTACTCCTCCATAAAACGAA 59.389 37.037 5.96 0.00 0.00 3.85
942 1095 7.325660 TGTAGTAGTACTCCTCCATAAAACG 57.674 40.000 5.96 0.00 0.00 3.60
951 1104 6.434018 AACGACAATGTAGTAGTACTCCTC 57.566 41.667 5.96 0.00 0.00 3.71
952 1105 6.830873 AAACGACAATGTAGTAGTACTCCT 57.169 37.500 5.96 0.00 0.00 3.69
953 1106 9.230932 GATTAAACGACAATGTAGTAGTACTCC 57.769 37.037 5.96 0.00 0.00 3.85
955 1108 9.784680 CAGATTAAACGACAATGTAGTAGTACT 57.215 33.333 8.14 8.14 0.00 2.73
956 1109 9.778993 TCAGATTAAACGACAATGTAGTAGTAC 57.221 33.333 0.00 0.37 0.00 2.73
957 1110 9.778993 GTCAGATTAAACGACAATGTAGTAGTA 57.221 33.333 0.00 0.00 0.00 1.82
958 1111 8.301720 TGTCAGATTAAACGACAATGTAGTAGT 58.698 33.333 0.00 0.00 36.75 2.73
1029 1554 1.226101 CGGCGCGTACTCGAAGTTA 60.226 57.895 9.88 0.00 39.71 2.24
1110 1635 3.766691 TACTCCACGAAGCCGGCC 61.767 66.667 26.15 7.92 40.78 6.13
1111 1636 2.508663 GTACTCCACGAAGCCGGC 60.509 66.667 21.89 21.89 40.78 6.13
1155 1680 1.133294 TCCGGCACTATGAGGACCATA 60.133 52.381 0.00 0.00 36.71 2.74
1251 1776 1.741401 CGCGCTGAAGGTGATGGAA 60.741 57.895 5.56 0.00 0.00 3.53
1594 2144 0.933097 CATGTCATGCAGGCGTAGAC 59.067 55.000 0.00 8.27 0.00 2.59
1615 2170 2.998670 CGTTGATCAGCATGTTCTCTGT 59.001 45.455 10.36 0.00 35.86 3.41
1929 2502 3.503363 GCCACCTGCACGCTCATC 61.503 66.667 0.00 0.00 40.77 2.92
2270 2862 5.072055 TCATTCTCAGCAGTCAATTTTCCA 58.928 37.500 0.00 0.00 0.00 3.53
2358 2973 4.870426 CAGCTGATTACGGTGATACTGTTT 59.130 41.667 8.42 0.00 38.84 2.83
2419 3035 9.500785 AAAGTGATTTGAAAAGGAAAGTGAAAA 57.499 25.926 0.00 0.00 0.00 2.29
2421 3037 8.531146 AGAAAGTGATTTGAAAAGGAAAGTGAA 58.469 29.630 0.00 0.00 0.00 3.18
2422 3038 8.066612 AGAAAGTGATTTGAAAAGGAAAGTGA 57.933 30.769 0.00 0.00 0.00 3.41
2424 3040 8.193438 CAGAGAAAGTGATTTGAAAAGGAAAGT 58.807 33.333 0.00 0.00 0.00 2.66
2425 3041 7.168804 GCAGAGAAAGTGATTTGAAAAGGAAAG 59.831 37.037 0.00 0.00 0.00 2.62
2465 3081 1.134491 GTACTGACAGGGGCACATACC 60.134 57.143 7.51 0.00 0.00 2.73
2520 3137 3.111853 TGGAGTCACAGCTTACAACAG 57.888 47.619 0.00 0.00 0.00 3.16
2524 3141 7.759489 AAAATATTTGGAGTCACAGCTTACA 57.241 32.000 0.39 0.00 0.00 2.41
2525 3142 8.947115 AGTAAAATATTTGGAGTCACAGCTTAC 58.053 33.333 0.39 0.00 0.00 2.34
2526 3143 8.946085 CAGTAAAATATTTGGAGTCACAGCTTA 58.054 33.333 0.39 0.00 0.00 3.09
2527 3144 7.448469 ACAGTAAAATATTTGGAGTCACAGCTT 59.552 33.333 0.39 0.00 0.00 3.74
2528 3145 6.942576 ACAGTAAAATATTTGGAGTCACAGCT 59.057 34.615 0.39 0.00 0.00 4.24
2529 3146 7.145932 ACAGTAAAATATTTGGAGTCACAGC 57.854 36.000 0.39 0.00 0.00 4.40
2530 3147 7.538678 GCAACAGTAAAATATTTGGAGTCACAG 59.461 37.037 0.39 0.00 0.00 3.66
2534 3151 6.027749 CGGCAACAGTAAAATATTTGGAGTC 58.972 40.000 0.39 0.00 0.00 3.36
2544 3161 3.792716 GCAGCGGCAACAGTAAAAT 57.207 47.368 3.18 0.00 40.72 1.82
2561 3178 3.763097 TGTGCATAGCTGTTACAATGC 57.237 42.857 12.09 12.09 43.92 3.56
2564 3181 5.956068 TGAATTGTGCATAGCTGTTACAA 57.044 34.783 10.98 10.98 36.62 2.41
2574 3191 3.631686 CGGGGAGATTTGAATTGTGCATA 59.368 43.478 0.00 0.00 0.00 3.14
2643 3269 0.251916 CCCGCTAATTCCTCCACACA 59.748 55.000 0.00 0.00 0.00 3.72
2645 3271 0.619255 TCCCCGCTAATTCCTCCACA 60.619 55.000 0.00 0.00 0.00 4.17
2649 3275 1.545651 CCCAATCCCCGCTAATTCCTC 60.546 57.143 0.00 0.00 0.00 3.71
2659 3285 3.809013 CCCCTCACCCAATCCCCG 61.809 72.222 0.00 0.00 0.00 5.73
2695 3322 4.961637 TGGCGATCCAATCCACAG 57.038 55.556 0.00 0.00 39.99 3.66
2705 3332 1.597663 CTTATTCGGTTGGTGGCGATC 59.402 52.381 0.00 0.00 0.00 3.69
2716 3343 1.906105 TTCGGCAGGCCTTATTCGGT 61.906 55.000 0.00 0.00 0.00 4.69
2718 3345 0.657840 CTTTCGGCAGGCCTTATTCG 59.342 55.000 0.00 4.86 0.00 3.34
2731 3358 2.162681 AGTGGAATTTCCTGCTTTCGG 58.837 47.619 16.25 0.00 37.46 4.30
2732 3359 4.035675 GGATAGTGGAATTTCCTGCTTTCG 59.964 45.833 16.25 0.00 37.46 3.46
2847 3483 8.713971 TGTGAGGTATGTAATGACTTATCCATT 58.286 33.333 0.00 0.00 37.86 3.16
2849 3485 7.669089 TGTGAGGTATGTAATGACTTATCCA 57.331 36.000 0.00 0.00 0.00 3.41
2938 3574 3.070446 TGTTCAGTCTAACGGTCCACATT 59.930 43.478 0.00 0.00 31.76 2.71
3070 3707 4.116961 CAGAGGTCGTACTTTTGAACACA 58.883 43.478 0.00 0.00 0.00 3.72
3085 3722 7.263496 ACGTCTTATATTTTGGTACAGAGGTC 58.737 38.462 0.00 0.00 42.39 3.85
3113 3753 9.879973 CGTTTTTGTAGTTCAATTTTGTTACAG 57.120 29.630 0.00 0.00 35.84 2.74
3116 3756 9.843334 AGACGTTTTTGTAGTTCAATTTTGTTA 57.157 25.926 0.00 0.00 35.84 2.41
3118 3758 8.751302 AAGACGTTTTTGTAGTTCAATTTTGT 57.249 26.923 0.00 0.00 35.84 2.83
3138 3779 4.986659 CCCTCCGTACCAAAATATAAGACG 59.013 45.833 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.