Multiple sequence alignment - TraesCS3B01G036800

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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 TraesCS3B01G036800 chr3B 100.000 3810 0 0 1 3810 17987264 17991073 0.000000e+00 7036
1 TraesCS3B01G036800 chr3B 87.680 1802 173 29 1347 3129 17783913 17782142 0.000000e+00 2052
2 TraesCS3B01G036800 chr3B 86.236 1562 140 42 1346 2871 17689080 17687558 0.000000e+00 1624
3 TraesCS3B01G036800 chr3B 83.153 926 120 21 2187 3109 17903551 17902659 0.000000e+00 813
4 TraesCS3B01G036800 chr3B 91.021 568 28 17 3252 3810 684511129 684510576 0.000000e+00 745
5 TraesCS3B01G036800 chr3B 90.467 493 25 10 419 895 17784548 17784062 6.950000e-177 630
6 TraesCS3B01G036800 chr3B 89.776 313 21 6 400 708 17691969 17691664 1.280000e-104 390
7 TraesCS3B01G036800 chr3B 89.316 234 17 2 1612 1838 17904156 17903924 1.730000e-73 287
8 TraesCS3B01G036800 chr3B 84.436 257 32 4 986 1238 17689329 17689077 2.940000e-61 246
9 TraesCS3B01G036800 chr3B 82.090 268 33 10 965 1224 17905922 17905662 8.290000e-52 215
10 TraesCS3B01G036800 chr3B 81.250 208 31 5 2905 3109 17687565 17687363 1.100000e-35 161
11 TraesCS3B01G036800 chr3A 90.205 2389 171 35 704 3064 24781939 24779586 0.000000e+00 3057
12 TraesCS3B01G036800 chr3A 86.131 274 23 8 251 515 24782381 24782114 8.060000e-72 281
13 TraesCS3B01G036800 chr3A 88.119 101 9 2 139 238 24782529 24782431 2.400000e-22 117
14 TraesCS3B01G036800 chr3D 90.405 1730 130 21 1347 3065 12300250 12298546 0.000000e+00 2242
15 TraesCS3B01G036800 chr3D 90.405 1730 130 21 1347 3065 12374585 12376289 0.000000e+00 2242
16 TraesCS3B01G036800 chr3D 84.536 873 60 26 400 1238 12301079 12300248 0.000000e+00 795
17 TraesCS3B01G036800 chr3D 83.702 859 112 20 2187 3042 12385758 12386591 0.000000e+00 785
18 TraesCS3B01G036800 chr3D 84.660 854 56 26 419 1238 12373775 12374587 0.000000e+00 782
19 TraesCS3B01G036800 chr3D 89.316 234 17 5 1612 1838 12385167 12385399 1.730000e-73 287
20 TraesCS3B01G036800 chrUn 96.802 688 20 2 3124 3810 224666270 224665584 0.000000e+00 1147
21 TraesCS3B01G036800 chrUn 96.899 258 8 0 3130 3387 224661350 224661093 2.100000e-117 433
22 TraesCS3B01G036800 chr5B 91.549 568 31 16 3252 3810 546826119 546825560 0.000000e+00 767
23 TraesCS3B01G036800 chr7D 91.037 569 32 18 3252 3810 632053285 632053844 0.000000e+00 750
24 TraesCS3B01G036800 chr7A 90.586 563 36 16 3257 3810 685855061 685855615 0.000000e+00 730
25 TraesCS3B01G036800 chr7A 95.960 99 4 0 1141 1239 692523274 692523176 1.100000e-35 161
26 TraesCS3B01G036800 chr7A 82.635 167 22 5 1625 1786 692800073 692800237 1.430000e-29 141
27 TraesCS3B01G036800 chr5A 90.631 555 36 15 3264 3810 35042316 35041770 0.000000e+00 723
28 TraesCS3B01G036800 chr1D 89.649 570 40 18 3252 3810 395889329 395889890 0.000000e+00 708
29 TraesCS3B01G036800 chr1D 88.566 516 47 12 3302 3810 5123688 5124198 1.940000e-172 616
30 TraesCS3B01G036800 chr2B 89.142 571 44 13 3252 3810 771858725 771859289 0.000000e+00 695
31 TraesCS3B01G036800 chr4A 85.240 542 77 3 2260 2798 715915230 715915771 4.300000e-154 555
32 TraesCS3B01G036800 chr4A 85.055 542 78 3 2260 2798 715639161 715638620 2.000000e-152 549
33 TraesCS3B01G036800 chr4A 84.571 175 27 0 1347 1521 11678106 11677932 1.410000e-39 174
34 TraesCS3B01G036800 chr4A 92.562 121 8 1 1119 1239 11678312 11678193 5.060000e-39 172
35 TraesCS3B01G036800 chr4D 79.259 405 57 20 1119 1522 456047117 456047495 1.360000e-64 257
36 TraesCS3B01G036800 chr4B 79.259 405 57 20 1119 1522 570138565 570138943 1.360000e-64 257
37 TraesCS3B01G036800 chr7B 76.364 440 77 19 1625 2060 680096402 680096818 1.070000e-50 211
38 TraesCS3B01G036800 chr1A 75.362 414 67 28 1130 1534 497083336 497083723 2.350000e-37 167
39 TraesCS3B01G036800 chr6D 83.051 177 30 0 1347 1523 97914623 97914447 1.100000e-35 161
40 TraesCS3B01G036800 chr6B 82.778 180 25 6 1347 1523 182585980 182585804 5.100000e-34 156


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 TraesCS3B01G036800 chr3B 17987264 17991073 3809 False 7036.000000 7036 100.000000 1 3810 1 chr3B.!!$F1 3809
1 TraesCS3B01G036800 chr3B 17782142 17784548 2406 True 1341.000000 2052 89.073500 419 3129 2 chr3B.!!$R3 2710
2 TraesCS3B01G036800 chr3B 684510576 684511129 553 True 745.000000 745 91.021000 3252 3810 1 chr3B.!!$R1 558
3 TraesCS3B01G036800 chr3B 17687363 17691969 4606 True 605.250000 1624 85.424500 400 3109 4 chr3B.!!$R2 2709
4 TraesCS3B01G036800 chr3B 17902659 17905922 3263 True 438.333333 813 84.853000 965 3109 3 chr3B.!!$R4 2144
5 TraesCS3B01G036800 chr3A 24779586 24782529 2943 True 1151.666667 3057 88.151667 139 3064 3 chr3A.!!$R1 2925
6 TraesCS3B01G036800 chr3D 12298546 12301079 2533 True 1518.500000 2242 87.470500 400 3065 2 chr3D.!!$R1 2665
7 TraesCS3B01G036800 chr3D 12373775 12376289 2514 False 1512.000000 2242 87.532500 419 3065 2 chr3D.!!$F1 2646
8 TraesCS3B01G036800 chr3D 12385167 12386591 1424 False 536.000000 785 86.509000 1612 3042 2 chr3D.!!$F2 1430
9 TraesCS3B01G036800 chrUn 224665584 224666270 686 True 1147.000000 1147 96.802000 3124 3810 1 chrUn.!!$R2 686
10 TraesCS3B01G036800 chr5B 546825560 546826119 559 True 767.000000 767 91.549000 3252 3810 1 chr5B.!!$R1 558
11 TraesCS3B01G036800 chr7D 632053285 632053844 559 False 750.000000 750 91.037000 3252 3810 1 chr7D.!!$F1 558
12 TraesCS3B01G036800 chr7A 685855061 685855615 554 False 730.000000 730 90.586000 3257 3810 1 chr7A.!!$F1 553
13 TraesCS3B01G036800 chr5A 35041770 35042316 546 True 723.000000 723 90.631000 3264 3810 1 chr5A.!!$R1 546
14 TraesCS3B01G036800 chr1D 395889329 395889890 561 False 708.000000 708 89.649000 3252 3810 1 chr1D.!!$F2 558
15 TraesCS3B01G036800 chr1D 5123688 5124198 510 False 616.000000 616 88.566000 3302 3810 1 chr1D.!!$F1 508
16 TraesCS3B01G036800 chr2B 771858725 771859289 564 False 695.000000 695 89.142000 3252 3810 1 chr2B.!!$F1 558
17 TraesCS3B01G036800 chr4A 715915230 715915771 541 False 555.000000 555 85.240000 2260 2798 1 chr4A.!!$F1 538
18 TraesCS3B01G036800 chr4A 715638620 715639161 541 True 549.000000 549 85.055000 2260 2798 1 chr4A.!!$R1 538

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
128 129 0.325203 AATTGGGCCGGCCAAATAGT 60.325 50.0 41.94 28.15 38.73 2.12 F
1285 3469 0.110056 CACTGATGCACGCACCTTTC 60.110 55.0 0.00 0.00 0.00 2.62 F
1544 4410 0.168128 GCCAGGTACACAAATCGCAC 59.832 55.0 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 4430 0.107312 GACCATGCATGCAGGAGACT 60.107 55.0 32.39 13.90 46.44 3.24 R
2256 5796 0.253044 TGCCAGCAGGGTCTGTAATC 59.747 55.0 0.00 0.00 39.65 1.75 R
3088 6646 0.320073 TGTCCAAACTCCGCGGTTAG 60.320 55.0 27.15 19.01 0.00 2.34 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
85 86 9.899661 ATTTTAACTTTTTACTGGAGCCTTTTT 57.100 25.926 0.00 0.00 0.00 1.94
89 90 7.833285 ACTTTTTACTGGAGCCTTTTTATCA 57.167 32.000 0.00 0.00 0.00 2.15
90 91 8.422577 ACTTTTTACTGGAGCCTTTTTATCAT 57.577 30.769 0.00 0.00 0.00 2.45
91 92 8.523658 ACTTTTTACTGGAGCCTTTTTATCATC 58.476 33.333 0.00 0.00 0.00 2.92
92 93 7.404671 TTTTACTGGAGCCTTTTTATCATCC 57.595 36.000 0.00 0.00 0.00 3.51
93 94 3.903467 ACTGGAGCCTTTTTATCATCCC 58.097 45.455 0.00 0.00 0.00 3.85
94 95 3.529319 ACTGGAGCCTTTTTATCATCCCT 59.471 43.478 0.00 0.00 0.00 4.20
95 96 4.017130 ACTGGAGCCTTTTTATCATCCCTT 60.017 41.667 0.00 0.00 0.00 3.95
96 97 4.946646 TGGAGCCTTTTTATCATCCCTTT 58.053 39.130 0.00 0.00 0.00 3.11
97 98 5.341169 TGGAGCCTTTTTATCATCCCTTTT 58.659 37.500 0.00 0.00 0.00 2.27
98 99 5.422012 TGGAGCCTTTTTATCATCCCTTTTC 59.578 40.000 0.00 0.00 0.00 2.29
99 100 5.658634 GGAGCCTTTTTATCATCCCTTTTCT 59.341 40.000 0.00 0.00 0.00 2.52
100 101 6.183360 GGAGCCTTTTTATCATCCCTTTTCTC 60.183 42.308 0.00 0.00 0.00 2.87
101 102 5.358160 AGCCTTTTTATCATCCCTTTTCTCG 59.642 40.000 0.00 0.00 0.00 4.04
102 103 5.357032 GCCTTTTTATCATCCCTTTTCTCGA 59.643 40.000 0.00 0.00 0.00 4.04
103 104 6.039829 GCCTTTTTATCATCCCTTTTCTCGAT 59.960 38.462 0.00 0.00 0.00 3.59
104 105 7.643579 CCTTTTTATCATCCCTTTTCTCGATC 58.356 38.462 0.00 0.00 0.00 3.69
105 106 6.844696 TTTTATCATCCCTTTTCTCGATCG 57.155 37.500 9.36 9.36 0.00 3.69
106 107 2.890808 TCATCCCTTTTCTCGATCGG 57.109 50.000 16.41 6.26 0.00 4.18
107 108 2.108168 TCATCCCTTTTCTCGATCGGT 58.892 47.619 16.41 0.00 0.00 4.69
108 109 3.293337 TCATCCCTTTTCTCGATCGGTA 58.707 45.455 16.41 0.14 0.00 4.02
109 110 3.702548 TCATCCCTTTTCTCGATCGGTAA 59.297 43.478 16.41 7.11 0.00 2.85
110 111 4.160814 TCATCCCTTTTCTCGATCGGTAAA 59.839 41.667 16.41 12.85 0.00 2.01
111 112 4.748277 TCCCTTTTCTCGATCGGTAAAT 57.252 40.909 16.41 0.00 0.00 1.40
112 113 5.093849 TCCCTTTTCTCGATCGGTAAATT 57.906 39.130 16.41 0.00 0.00 1.82
113 114 4.873827 TCCCTTTTCTCGATCGGTAAATTG 59.126 41.667 16.41 10.99 0.00 2.32
114 115 4.035208 CCCTTTTCTCGATCGGTAAATTGG 59.965 45.833 16.41 17.43 0.00 3.16
115 116 4.035208 CCTTTTCTCGATCGGTAAATTGGG 59.965 45.833 16.41 13.09 0.00 4.12
116 117 2.234300 TCTCGATCGGTAAATTGGGC 57.766 50.000 16.41 0.00 0.00 5.36
117 118 1.202604 TCTCGATCGGTAAATTGGGCC 60.203 52.381 16.41 0.00 0.00 5.80
118 119 0.531090 TCGATCGGTAAATTGGGCCG 60.531 55.000 16.41 8.69 46.12 6.13
119 120 1.503818 CGATCGGTAAATTGGGCCGG 61.504 60.000 7.38 0.00 44.97 6.13
120 121 1.792118 GATCGGTAAATTGGGCCGGC 61.792 60.000 21.18 21.18 44.97 6.13
121 122 3.523668 CGGTAAATTGGGCCGGCC 61.524 66.667 38.57 38.57 41.60 6.13
122 123 2.363147 GGTAAATTGGGCCGGCCA 60.363 61.111 44.46 28.13 37.98 5.36
123 124 1.985116 GGTAAATTGGGCCGGCCAA 60.985 57.895 44.46 35.30 37.98 4.52
124 125 1.545706 GGTAAATTGGGCCGGCCAAA 61.546 55.000 44.46 40.94 37.98 3.28
125 126 0.539518 GTAAATTGGGCCGGCCAAAT 59.460 50.000 44.46 41.21 41.30 2.32
126 127 1.757699 GTAAATTGGGCCGGCCAAATA 59.242 47.619 41.94 28.15 38.73 1.40
127 128 0.829990 AAATTGGGCCGGCCAAATAG 59.170 50.000 41.94 0.00 38.73 1.73
128 129 0.325203 AATTGGGCCGGCCAAATAGT 60.325 50.000 41.94 28.15 38.73 2.12
129 130 0.325203 ATTGGGCCGGCCAAATAGTT 60.325 50.000 41.45 22.89 37.94 2.24
130 131 1.254284 TTGGGCCGGCCAAATAGTTG 61.254 55.000 44.46 0.00 37.98 3.16
131 132 2.494445 GGCCGGCCAAATAGTTGC 59.506 61.111 40.73 8.62 35.81 4.17
132 133 2.052104 GGCCGGCCAAATAGTTGCT 61.052 57.895 40.73 0.00 35.81 3.91
133 134 1.433471 GCCGGCCAAATAGTTGCTC 59.567 57.895 18.11 0.00 33.01 4.26
134 135 1.032114 GCCGGCCAAATAGTTGCTCT 61.032 55.000 18.11 0.00 33.01 4.09
135 136 0.734889 CCGGCCAAATAGTTGCTCTG 59.265 55.000 2.24 0.00 33.01 3.35
136 137 1.453155 CGGCCAAATAGTTGCTCTGT 58.547 50.000 2.24 0.00 33.01 3.41
137 138 1.131126 CGGCCAAATAGTTGCTCTGTG 59.869 52.381 2.24 0.00 33.01 3.66
146 147 7.119699 CCAAATAGTTGCTCTGTGTGATTTCTA 59.880 37.037 0.00 0.00 33.01 2.10
147 148 8.671921 CAAATAGTTGCTCTGTGTGATTTCTAT 58.328 33.333 0.00 0.00 0.00 1.98
154 155 5.970023 GCTCTGTGTGATTTCTATGCAATTC 59.030 40.000 0.00 0.00 0.00 2.17
155 156 6.183360 GCTCTGTGTGATTTCTATGCAATTCT 60.183 38.462 0.00 0.00 0.00 2.40
160 161 6.257849 GTGTGATTTCTATGCAATTCTCCGTA 59.742 38.462 0.00 0.00 0.00 4.02
161 162 6.479990 TGTGATTTCTATGCAATTCTCCGTAG 59.520 38.462 0.00 0.00 0.00 3.51
191 192 4.759693 TCAAATAGGAATTTCTGCGTGTGT 59.240 37.500 0.00 0.00 32.87 3.72
192 193 4.946784 AATAGGAATTTCTGCGTGTGTC 57.053 40.909 0.00 0.00 0.00 3.67
219 220 7.339466 TCAGCTTGAACTAGTCTATGTGATGTA 59.661 37.037 0.00 0.00 0.00 2.29
245 246 7.420184 AAAAAGGAAAAAGTTGACAAGTGTG 57.580 32.000 0.00 0.00 0.00 3.82
246 247 5.722021 AAGGAAAAAGTTGACAAGTGTGT 57.278 34.783 0.00 0.00 42.10 3.72
255 256 3.694364 ACAAGTGTGTCTCAGCCAG 57.306 52.632 0.00 0.00 29.49 4.85
256 257 0.833287 ACAAGTGTGTCTCAGCCAGT 59.167 50.000 0.00 0.00 29.49 4.00
257 258 2.039418 ACAAGTGTGTCTCAGCCAGTA 58.961 47.619 0.00 0.00 29.49 2.74
258 259 2.224066 ACAAGTGTGTCTCAGCCAGTAC 60.224 50.000 0.00 0.00 29.49 2.73
259 260 2.002505 AGTGTGTCTCAGCCAGTACT 57.997 50.000 0.00 0.00 0.00 2.73
260 261 1.889829 AGTGTGTCTCAGCCAGTACTC 59.110 52.381 0.00 0.00 0.00 2.59
261 262 1.067495 GTGTGTCTCAGCCAGTACTCC 60.067 57.143 0.00 0.00 0.00 3.85
263 264 1.827969 GTGTCTCAGCCAGTACTCCAT 59.172 52.381 0.00 0.00 0.00 3.41
318 359 6.016276 CCAGTAGTTTCACCTGCAAGTAATTT 60.016 38.462 0.00 0.00 0.00 1.82
322 363 9.908152 GTAGTTTCACCTGCAAGTAATTTAATT 57.092 29.630 0.00 0.00 0.00 1.40
328 369 7.448777 TCACCTGCAAGTAATTTAATTACCACA 59.551 33.333 20.29 15.50 44.77 4.17
329 370 7.754924 CACCTGCAAGTAATTTAATTACCACAG 59.245 37.037 20.29 21.33 44.77 3.66
343 384 9.607988 TTAATTACCACAGTAATATCTGGTGTG 57.392 33.333 0.00 0.00 46.30 3.82
345 386 2.866156 CCACAGTAATATCTGGTGTGCG 59.134 50.000 0.00 0.00 37.73 5.34
346 387 3.521560 CACAGTAATATCTGGTGTGCGT 58.478 45.455 0.00 0.00 39.48 5.24
347 388 3.306973 CACAGTAATATCTGGTGTGCGTG 59.693 47.826 0.00 0.00 39.48 5.34
348 389 2.285220 CAGTAATATCTGGTGTGCGTGC 59.715 50.000 0.00 0.00 0.00 5.34
349 390 2.093711 AGTAATATCTGGTGTGCGTGCA 60.094 45.455 0.00 0.00 0.00 4.57
351 392 0.462581 ATATCTGGTGTGCGTGCAGG 60.463 55.000 1.01 1.01 0.00 4.85
352 393 2.520465 TATCTGGTGTGCGTGCAGGG 62.520 60.000 8.72 0.00 0.00 4.45
353 394 4.624364 CTGGTGTGCGTGCAGGGA 62.624 66.667 8.72 1.68 0.00 4.20
354 395 3.907260 CTGGTGTGCGTGCAGGGAT 62.907 63.158 8.72 0.00 0.00 3.85
355 396 2.267642 GGTGTGCGTGCAGGGATA 59.732 61.111 8.72 0.08 0.00 2.59
356 397 1.376683 GGTGTGCGTGCAGGGATAA 60.377 57.895 8.72 0.00 0.00 1.75
357 398 1.369091 GGTGTGCGTGCAGGGATAAG 61.369 60.000 8.72 0.00 0.00 1.73
358 399 0.391130 GTGTGCGTGCAGGGATAAGA 60.391 55.000 8.72 0.00 0.00 2.10
359 400 0.541392 TGTGCGTGCAGGGATAAGAT 59.459 50.000 8.72 0.00 0.00 2.40
360 401 1.760029 TGTGCGTGCAGGGATAAGATA 59.240 47.619 8.72 0.00 0.00 1.98
361 402 2.368548 TGTGCGTGCAGGGATAAGATAT 59.631 45.455 8.72 0.00 0.00 1.63
362 403 2.996621 GTGCGTGCAGGGATAAGATATC 59.003 50.000 8.72 0.00 0.00 1.63
372 413 6.380846 GCAGGGATAAGATATCTCTCTCACAT 59.619 42.308 5.51 0.00 0.00 3.21
373 414 7.631161 GCAGGGATAAGATATCTCTCTCACATG 60.631 44.444 5.51 4.40 0.00 3.21
389 439 6.946340 TCTCACATGGAAGCTACTAATTTGA 58.054 36.000 0.00 0.00 0.00 2.69
413 463 1.881903 CTCGACTGCAGGAGCCTTCA 61.882 60.000 19.93 0.00 41.13 3.02
417 467 0.694771 ACTGCAGGAGCCTTCATCAA 59.305 50.000 19.93 0.00 41.13 2.57
515 566 6.204108 AGGTAAACAACAAAGAATGAGTACCG 59.796 38.462 0.00 0.00 36.01 4.02
516 567 6.203338 GGTAAACAACAAAGAATGAGTACCGA 59.797 38.462 0.00 0.00 0.00 4.69
517 568 5.668558 AACAACAAAGAATGAGTACCGAC 57.331 39.130 0.00 0.00 0.00 4.79
518 569 4.062991 ACAACAAAGAATGAGTACCGACC 58.937 43.478 0.00 0.00 0.00 4.79
568 622 0.453793 CACTCACTCTGGACGCTAGG 59.546 60.000 0.00 0.00 0.00 3.02
618 672 2.159085 CCCTATTGGACGAGGAGTTCAC 60.159 54.545 0.00 0.00 38.27 3.18
745 818 2.297033 TGGCTCCTTCAATTCAACTTGC 59.703 45.455 0.00 0.00 0.00 4.01
762 835 1.863880 GCTGACTCGTCGCACGTAG 60.864 63.158 8.22 7.29 43.14 3.51
891 3052 3.315796 CGCCGTCGTCACAAAAGT 58.684 55.556 0.00 0.00 0.00 2.66
892 3053 1.083657 CGCCGTCGTCACAAAAGTG 60.084 57.895 0.00 0.00 0.00 3.16
893 3054 1.368850 GCCGTCGTCACAAAAGTGC 60.369 57.895 0.00 0.00 0.00 4.40
894 3055 1.278637 CCGTCGTCACAAAAGTGCC 59.721 57.895 0.00 0.00 0.00 5.01
896 3057 0.375454 CGTCGTCACAAAAGTGCCAA 59.625 50.000 0.00 0.00 0.00 4.52
897 3058 1.202087 CGTCGTCACAAAAGTGCCAAA 60.202 47.619 0.00 0.00 0.00 3.28
898 3059 2.450160 GTCGTCACAAAAGTGCCAAAG 58.550 47.619 0.00 0.00 0.00 2.77
975 3149 5.244178 TCTCTTCTCAGGTGGTCTTAGTTTC 59.756 44.000 0.00 0.00 0.00 2.78
981 3155 4.903049 TCAGGTGGTCTTAGTTTCAGGTTA 59.097 41.667 0.00 0.00 0.00 2.85
982 3156 5.367352 TCAGGTGGTCTTAGTTTCAGGTTAA 59.633 40.000 0.00 0.00 0.00 2.01
1122 3306 2.284331 TTGTCGCTAGGGAGCCCA 60.284 61.111 10.19 2.04 46.86 5.36
1257 3441 3.326880 AGGTACGTTCCCAATTGAAGACT 59.673 43.478 7.12 0.00 0.00 3.24
1269 3453 5.413833 CCAATTGAAGACTCTTACATGCACT 59.586 40.000 7.12 0.00 0.00 4.40
1270 3454 6.312487 CAATTGAAGACTCTTACATGCACTG 58.688 40.000 0.00 0.00 0.00 3.66
1271 3455 4.871933 TGAAGACTCTTACATGCACTGA 57.128 40.909 0.00 0.00 0.00 3.41
1272 3456 5.411831 TGAAGACTCTTACATGCACTGAT 57.588 39.130 0.00 0.00 0.00 2.90
1273 3457 5.173664 TGAAGACTCTTACATGCACTGATG 58.826 41.667 0.00 0.00 0.00 3.07
1285 3469 0.110056 CACTGATGCACGCACCTTTC 60.110 55.000 0.00 0.00 0.00 2.62
1294 3478 1.355210 CGCACCTTTCGCTTTGTGT 59.645 52.632 0.00 0.00 0.00 3.72
1298 3482 2.918131 GCACCTTTCGCTTTGTGTGATC 60.918 50.000 0.00 0.00 34.87 2.92
1303 3487 5.106555 ACCTTTCGCTTTGTGTGATCTAATG 60.107 40.000 0.00 0.00 34.87 1.90
1308 3492 4.437794 CGCTTTGTGTGATCTAATGCACAT 60.438 41.667 0.00 0.00 45.59 3.21
1310 3494 6.554419 GCTTTGTGTGATCTAATGCACATTA 58.446 36.000 0.00 3.24 45.59 1.90
1312 3496 6.435430 TTGTGTGATCTAATGCACATTACC 57.565 37.500 0.00 0.00 45.59 2.85
1315 3499 4.576053 TGTGATCTAATGCACATTACCAGC 59.424 41.667 0.00 0.00 39.86 4.85
1316 3500 4.576053 GTGATCTAATGCACATTACCAGCA 59.424 41.667 0.00 0.00 43.14 4.41
1339 3523 7.886970 AGCACTAATGAGTTGCCATGAATATAT 59.113 33.333 0.00 0.00 31.73 0.86
1359 3543 3.728076 TGTATGTAGGATCTTGACGGC 57.272 47.619 0.00 0.00 0.00 5.68
1497 3906 3.910627 AGGACATCAACCAGTTCTACCTT 59.089 43.478 0.00 0.00 0.00 3.50
1541 4407 2.416547 CTCAAGCCAGGTACACAAATCG 59.583 50.000 0.00 0.00 0.00 3.34
1544 4410 0.168128 GCCAGGTACACAAATCGCAC 59.832 55.000 0.00 0.00 0.00 5.34
1549 4415 2.060284 GGTACACAAATCGCACGTACA 58.940 47.619 0.00 0.00 35.28 2.90
1550 4416 2.669434 GGTACACAAATCGCACGTACAT 59.331 45.455 0.00 0.00 35.28 2.29
1551 4417 3.858812 GGTACACAAATCGCACGTACATA 59.141 43.478 0.00 0.00 35.28 2.29
1553 4419 4.772046 ACACAAATCGCACGTACATATC 57.228 40.909 0.00 0.00 0.00 1.63
1554 4420 4.430007 ACACAAATCGCACGTACATATCT 58.570 39.130 0.00 0.00 0.00 1.98
1556 4422 5.457799 ACACAAATCGCACGTACATATCTAC 59.542 40.000 0.00 0.00 0.00 2.59
1557 4423 4.980434 ACAAATCGCACGTACATATCTACC 59.020 41.667 0.00 0.00 0.00 3.18
1560 4426 6.564709 AATCGCACGTACATATCTACCTAA 57.435 37.500 0.00 0.00 0.00 2.69
1561 4427 6.564709 ATCGCACGTACATATCTACCTAAA 57.435 37.500 0.00 0.00 0.00 1.85
1562 4428 6.375945 TCGCACGTACATATCTACCTAAAA 57.624 37.500 0.00 0.00 0.00 1.52
1563 4429 6.201517 TCGCACGTACATATCTACCTAAAAC 58.798 40.000 0.00 0.00 0.00 2.43
1564 4430 5.972973 CGCACGTACATATCTACCTAAAACA 59.027 40.000 0.00 0.00 0.00 2.83
1581 4447 0.393944 ACAGTCTCCTGCATGCATGG 60.394 55.000 27.34 22.87 42.81 3.66
1597 4463 1.589630 TGGTCGACCATCTTGACGG 59.410 57.895 33.23 0.00 42.01 4.79
1722 5155 4.521062 GGAGCTGCTCGGCGACAT 62.521 66.667 22.25 0.00 37.29 3.06
1876 5381 0.447801 CACCACGCCTGCTGATTTAC 59.552 55.000 0.00 0.00 0.00 2.01
2118 5649 8.723942 ATTAGTGAGACTTGCTAACCTAATTG 57.276 34.615 0.00 0.00 0.00 2.32
2256 5796 5.934043 TCTGTTTGACAACTGACATGGATAG 59.066 40.000 0.00 0.00 36.29 2.08
2302 5842 1.135139 GACGTCAGCAAGCAGATCCTA 59.865 52.381 11.55 0.00 0.00 2.94
2395 5935 1.134907 GGTACCGCCAAGATCGAAGAA 60.135 52.381 0.00 0.00 37.35 2.52
2434 5974 3.655211 AGCAAGTGGGGCCTCCTG 61.655 66.667 0.00 0.00 36.20 3.86
2476 6016 1.153568 CACGCCCATCATCGACAGT 60.154 57.895 0.00 0.00 0.00 3.55
2479 6019 1.086696 CGCCCATCATCGACAGTTTT 58.913 50.000 0.00 0.00 0.00 2.43
2719 6262 1.305287 GCCCGACCAAAATAGGGGT 59.695 57.895 1.26 0.00 43.95 4.95
2809 6352 4.934356 AGGAGGGCAATGTTGATTTCTAA 58.066 39.130 0.00 0.00 0.00 2.10
2844 6387 7.649306 GGCATTGCTTACTATTCGAATTTGATT 59.351 33.333 17.19 0.00 0.00 2.57
2851 6394 8.583810 TTACTATTCGAATTTGATTAGACCGG 57.416 34.615 22.85 0.00 0.00 5.28
2852 6395 6.812998 ACTATTCGAATTTGATTAGACCGGA 58.187 36.000 22.85 0.00 0.00 5.14
2873 6416 6.462487 CCGGAGAGCACTACCTAAATTATTCA 60.462 42.308 0.00 0.00 0.00 2.57
2935 6482 8.568794 TCTCTGATAGTCGTGTATATCTTTTGG 58.431 37.037 0.00 0.00 31.07 3.28
2946 6493 8.166706 CGTGTATATCTTTTGGTTTGTGTAGAC 58.833 37.037 0.00 0.00 0.00 2.59
2970 6528 9.806203 GACATTCATTCATTTGTCCAATATTCA 57.194 29.630 0.00 0.00 33.91 2.57
3018 6576 5.233476 GCATGGATGTGCTAATTTGTGAATG 59.767 40.000 0.00 0.00 41.82 2.67
3057 6615 4.041567 ACATGATGGGTAACTGTCACTTGA 59.958 41.667 0.00 0.00 33.88 3.02
3060 6618 5.245531 TGATGGGTAACTGTCACTTGATTC 58.754 41.667 0.00 0.00 0.00 2.52
3064 6622 6.126409 TGGGTAACTGTCACTTGATTCTTTT 58.874 36.000 0.00 0.00 0.00 2.27
3065 6623 6.605594 TGGGTAACTGTCACTTGATTCTTTTT 59.394 34.615 0.00 0.00 0.00 1.94
3094 6652 8.738199 TCGTTCTTGATTAATATAGCTAACCG 57.262 34.615 0.00 0.00 0.00 4.44
3113 6671 1.227734 CGGAGTTTGGACAACCCGT 60.228 57.895 9.92 0.00 37.93 5.28
3121 6679 1.597027 GGACAACCCGTGTGGACAG 60.597 63.158 0.00 0.00 41.96 3.51
3209 6767 7.120873 GTCGTTGGATAGATAGATAGTTAGGCA 59.879 40.741 0.00 0.00 0.00 4.75
3278 6837 6.200878 TCTTCCCTTCCAAGTTGTAATCTT 57.799 37.500 1.45 0.00 0.00 2.40
3319 6879 1.470979 CCTGTACGCGCTATCAGGTTT 60.471 52.381 23.71 0.00 41.51 3.27
3744 7314 4.988716 AGGAGGTGCCCGTCACGA 62.989 66.667 0.00 0.00 46.56 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 9.899661 AAAAAGGCTCCAGTAAAAAGTTAAAAT 57.100 25.926 0.00 0.00 0.00 1.82
63 64 9.357161 TGATAAAAAGGCTCCAGTAAAAAGTTA 57.643 29.630 0.00 0.00 0.00 2.24
64 65 8.245195 TGATAAAAAGGCTCCAGTAAAAAGTT 57.755 30.769 0.00 0.00 0.00 2.66
65 66 7.833285 TGATAAAAAGGCTCCAGTAAAAAGT 57.167 32.000 0.00 0.00 0.00 2.66
66 67 7.976175 GGATGATAAAAAGGCTCCAGTAAAAAG 59.024 37.037 0.00 0.00 0.00 2.27
67 68 7.093509 GGGATGATAAAAAGGCTCCAGTAAAAA 60.094 37.037 0.00 0.00 0.00 1.94
68 69 6.379988 GGGATGATAAAAAGGCTCCAGTAAAA 59.620 38.462 0.00 0.00 0.00 1.52
69 70 5.891551 GGGATGATAAAAAGGCTCCAGTAAA 59.108 40.000 0.00 0.00 0.00 2.01
70 71 5.193728 AGGGATGATAAAAAGGCTCCAGTAA 59.806 40.000 0.00 0.00 0.00 2.24
71 72 4.726825 AGGGATGATAAAAAGGCTCCAGTA 59.273 41.667 0.00 0.00 0.00 2.74
72 73 3.529319 AGGGATGATAAAAAGGCTCCAGT 59.471 43.478 0.00 0.00 0.00 4.00
73 74 4.176120 AGGGATGATAAAAAGGCTCCAG 57.824 45.455 0.00 0.00 0.00 3.86
74 75 4.608170 AAGGGATGATAAAAAGGCTCCA 57.392 40.909 0.00 0.00 0.00 3.86
75 76 5.658634 AGAAAAGGGATGATAAAAAGGCTCC 59.341 40.000 0.00 0.00 0.00 4.70
76 77 6.458888 CGAGAAAAGGGATGATAAAAAGGCTC 60.459 42.308 0.00 0.00 0.00 4.70
77 78 5.358160 CGAGAAAAGGGATGATAAAAAGGCT 59.642 40.000 0.00 0.00 0.00 4.58
78 79 5.357032 TCGAGAAAAGGGATGATAAAAAGGC 59.643 40.000 0.00 0.00 0.00 4.35
79 80 7.519008 CGATCGAGAAAAGGGATGATAAAAAGG 60.519 40.741 10.26 0.00 0.00 3.11
80 81 7.348201 CGATCGAGAAAAGGGATGATAAAAAG 58.652 38.462 10.26 0.00 0.00 2.27
81 82 6.260050 CCGATCGAGAAAAGGGATGATAAAAA 59.740 38.462 18.66 0.00 0.00 1.94
82 83 5.758296 CCGATCGAGAAAAGGGATGATAAAA 59.242 40.000 18.66 0.00 0.00 1.52
83 84 5.163343 ACCGATCGAGAAAAGGGATGATAAA 60.163 40.000 18.66 0.00 0.00 1.40
84 85 4.344102 ACCGATCGAGAAAAGGGATGATAA 59.656 41.667 18.66 0.00 0.00 1.75
85 86 3.895656 ACCGATCGAGAAAAGGGATGATA 59.104 43.478 18.66 0.00 0.00 2.15
86 87 2.700897 ACCGATCGAGAAAAGGGATGAT 59.299 45.455 18.66 0.00 0.00 2.45
87 88 2.108168 ACCGATCGAGAAAAGGGATGA 58.892 47.619 18.66 0.00 0.00 2.92
88 89 2.604046 ACCGATCGAGAAAAGGGATG 57.396 50.000 18.66 0.00 0.00 3.51
89 90 4.748277 TTTACCGATCGAGAAAAGGGAT 57.252 40.909 18.66 0.00 0.00 3.85
90 91 4.748277 ATTTACCGATCGAGAAAAGGGA 57.252 40.909 18.66 0.00 0.00 4.20
91 92 4.035208 CCAATTTACCGATCGAGAAAAGGG 59.965 45.833 18.66 15.84 0.00 3.95
92 93 4.035208 CCCAATTTACCGATCGAGAAAAGG 59.965 45.833 18.66 18.75 0.00 3.11
93 94 4.495844 GCCCAATTTACCGATCGAGAAAAG 60.496 45.833 18.66 12.11 0.00 2.27
94 95 3.375922 GCCCAATTTACCGATCGAGAAAA 59.624 43.478 18.66 13.55 0.00 2.29
95 96 2.940410 GCCCAATTTACCGATCGAGAAA 59.060 45.455 18.66 15.90 0.00 2.52
96 97 2.557317 GCCCAATTTACCGATCGAGAA 58.443 47.619 18.66 7.14 0.00 2.87
97 98 1.202604 GGCCCAATTTACCGATCGAGA 60.203 52.381 18.66 0.00 0.00 4.04
98 99 1.226746 GGCCCAATTTACCGATCGAG 58.773 55.000 18.66 9.42 0.00 4.04
99 100 3.390003 GGCCCAATTTACCGATCGA 57.610 52.632 18.66 0.00 0.00 3.59
104 105 3.523668 GGCCGGCCCAATTTACCG 61.524 66.667 36.64 4.02 46.50 4.02
105 106 2.363147 TGGCCGGCCCAATTTACC 60.363 61.111 41.75 15.00 41.82 2.85
112 113 1.680651 CAACTATTTGGCCGGCCCA 60.681 57.895 41.75 30.62 43.51 5.36
113 114 3.076258 GCAACTATTTGGCCGGCCC 62.076 63.158 41.75 24.44 32.81 5.80
114 115 2.004808 GAGCAACTATTTGGCCGGCC 62.005 60.000 39.40 39.40 32.81 6.13
115 116 1.032114 AGAGCAACTATTTGGCCGGC 61.032 55.000 21.18 21.18 32.81 6.13
116 117 0.734889 CAGAGCAACTATTTGGCCGG 59.265 55.000 0.00 0.00 32.81 6.13
117 118 1.131126 CACAGAGCAACTATTTGGCCG 59.869 52.381 0.00 0.00 32.81 6.13
118 119 2.095059 CACACAGAGCAACTATTTGGCC 60.095 50.000 0.00 0.00 32.81 5.36
119 120 2.813754 TCACACAGAGCAACTATTTGGC 59.186 45.455 0.00 0.00 32.81 4.52
120 121 5.633830 AATCACACAGAGCAACTATTTGG 57.366 39.130 0.00 0.00 32.81 3.28
121 122 6.906659 AGAAATCACACAGAGCAACTATTTG 58.093 36.000 0.00 0.00 35.62 2.32
122 123 8.671921 CATAGAAATCACACAGAGCAACTATTT 58.328 33.333 0.00 0.00 0.00 1.40
123 124 7.201679 GCATAGAAATCACACAGAGCAACTATT 60.202 37.037 0.00 0.00 0.00 1.73
124 125 6.259608 GCATAGAAATCACACAGAGCAACTAT 59.740 38.462 0.00 0.00 0.00 2.12
125 126 5.582269 GCATAGAAATCACACAGAGCAACTA 59.418 40.000 0.00 0.00 0.00 2.24
126 127 4.394300 GCATAGAAATCACACAGAGCAACT 59.606 41.667 0.00 0.00 0.00 3.16
127 128 4.154737 TGCATAGAAATCACACAGAGCAAC 59.845 41.667 0.00 0.00 0.00 4.17
128 129 4.325972 TGCATAGAAATCACACAGAGCAA 58.674 39.130 0.00 0.00 0.00 3.91
129 130 3.941573 TGCATAGAAATCACACAGAGCA 58.058 40.909 0.00 0.00 0.00 4.26
130 131 4.952262 TTGCATAGAAATCACACAGAGC 57.048 40.909 0.00 0.00 0.00 4.09
131 132 7.317842 AGAATTGCATAGAAATCACACAGAG 57.682 36.000 0.00 0.00 0.00 3.35
132 133 6.317140 GGAGAATTGCATAGAAATCACACAGA 59.683 38.462 0.00 0.00 0.00 3.41
133 134 6.493116 GGAGAATTGCATAGAAATCACACAG 58.507 40.000 0.00 0.00 0.00 3.66
134 135 5.065090 CGGAGAATTGCATAGAAATCACACA 59.935 40.000 0.00 0.00 0.00 3.72
135 136 5.065218 ACGGAGAATTGCATAGAAATCACAC 59.935 40.000 0.00 0.00 0.00 3.82
136 137 5.185454 ACGGAGAATTGCATAGAAATCACA 58.815 37.500 0.00 0.00 0.00 3.58
137 138 5.741388 ACGGAGAATTGCATAGAAATCAC 57.259 39.130 0.00 0.00 0.00 3.06
146 147 2.697751 AGCTCTCTACGGAGAATTGCAT 59.302 45.455 15.54 2.31 46.50 3.96
147 148 2.103373 AGCTCTCTACGGAGAATTGCA 58.897 47.619 15.54 0.00 46.50 4.08
154 155 4.580995 TCCTATTTGAAGCTCTCTACGGAG 59.419 45.833 0.00 0.00 40.73 4.63
155 156 4.533815 TCCTATTTGAAGCTCTCTACGGA 58.466 43.478 0.00 0.00 0.00 4.69
160 161 6.318396 GCAGAAATTCCTATTTGAAGCTCTCT 59.682 38.462 0.00 0.00 34.16 3.10
161 162 6.493978 GCAGAAATTCCTATTTGAAGCTCTC 58.506 40.000 0.00 0.00 34.16 3.20
191 192 5.946377 TCACATAGACTAGTTCAAGCTGAGA 59.054 40.000 0.00 0.00 0.00 3.27
192 193 6.201226 TCACATAGACTAGTTCAAGCTGAG 57.799 41.667 0.00 0.00 0.00 3.35
238 239 2.036475 AGTACTGGCTGAGACACACTTG 59.964 50.000 0.00 0.00 0.00 3.16
242 243 1.257743 GGAGTACTGGCTGAGACACA 58.742 55.000 0.00 0.00 0.00 3.72
243 244 1.257743 TGGAGTACTGGCTGAGACAC 58.742 55.000 0.00 0.00 0.00 3.67
245 246 2.497675 TGAATGGAGTACTGGCTGAGAC 59.502 50.000 0.00 0.00 0.00 3.36
246 247 2.497675 GTGAATGGAGTACTGGCTGAGA 59.502 50.000 0.00 0.00 0.00 3.27
248 249 2.540383 AGTGAATGGAGTACTGGCTGA 58.460 47.619 0.00 0.00 0.00 4.26
249 250 3.005554 CAAGTGAATGGAGTACTGGCTG 58.994 50.000 0.00 0.00 0.00 4.85
250 251 2.639839 ACAAGTGAATGGAGTACTGGCT 59.360 45.455 0.00 0.00 0.00 4.75
251 252 2.744202 CACAAGTGAATGGAGTACTGGC 59.256 50.000 0.00 0.00 0.00 4.85
252 253 4.271696 TCACAAGTGAATGGAGTACTGG 57.728 45.455 0.00 0.00 36.53 4.00
253 254 6.808008 AAATCACAAGTGAATGGAGTACTG 57.192 37.500 0.00 0.00 43.58 2.74
254 255 6.772716 ACAAAATCACAAGTGAATGGAGTACT 59.227 34.615 7.02 0.00 43.58 2.73
255 256 6.970484 ACAAAATCACAAGTGAATGGAGTAC 58.030 36.000 7.02 0.00 43.58 2.73
256 257 7.581213 AACAAAATCACAAGTGAATGGAGTA 57.419 32.000 7.02 0.00 43.58 2.59
257 258 6.469782 AACAAAATCACAAGTGAATGGAGT 57.530 33.333 7.02 0.72 43.58 3.85
258 259 7.168637 CAGAAACAAAATCACAAGTGAATGGAG 59.831 37.037 7.02 0.14 43.58 3.86
259 260 6.979817 CAGAAACAAAATCACAAGTGAATGGA 59.020 34.615 7.02 0.00 43.58 3.41
260 261 6.979817 TCAGAAACAAAATCACAAGTGAATGG 59.020 34.615 7.02 0.15 43.58 3.16
261 262 7.990541 TCAGAAACAAAATCACAAGTGAATG 57.009 32.000 7.02 9.18 43.58 2.67
263 264 7.701924 GTCATCAGAAACAAAATCACAAGTGAA 59.298 33.333 7.02 0.00 43.58 3.18
318 359 7.713507 GCACACCAGATATTACTGTGGTAATTA 59.286 37.037 6.70 0.00 43.65 1.40
322 363 4.440940 CGCACACCAGATATTACTGTGGTA 60.441 45.833 0.00 0.00 41.52 3.25
328 369 2.093711 TGCACGCACACCAGATATTACT 60.094 45.455 0.00 0.00 0.00 2.24
329 370 2.276201 TGCACGCACACCAGATATTAC 58.724 47.619 0.00 0.00 0.00 1.89
333 374 1.079197 CCTGCACGCACACCAGATA 60.079 57.895 0.00 0.00 0.00 1.98
343 384 3.194542 AGAGATATCTTATCCCTGCACGC 59.805 47.826 6.70 0.00 0.00 5.34
345 386 5.714333 TGAGAGAGATATCTTATCCCTGCAC 59.286 44.000 6.70 0.00 0.00 4.57
346 387 5.714333 GTGAGAGAGATATCTTATCCCTGCA 59.286 44.000 6.70 2.94 0.00 4.41
347 388 5.714333 TGTGAGAGAGATATCTTATCCCTGC 59.286 44.000 6.70 0.00 0.00 4.85
348 389 7.147863 CCATGTGAGAGAGATATCTTATCCCTG 60.148 44.444 6.70 3.93 0.00 4.45
349 390 6.896860 CCATGTGAGAGAGATATCTTATCCCT 59.103 42.308 6.70 0.00 0.00 4.20
351 392 7.953005 TCCATGTGAGAGAGATATCTTATCC 57.047 40.000 6.70 4.17 0.00 2.59
352 393 7.975616 GCTTCCATGTGAGAGAGATATCTTATC 59.024 40.741 6.70 8.55 0.00 1.75
353 394 7.675195 AGCTTCCATGTGAGAGAGATATCTTAT 59.325 37.037 6.70 0.00 0.00 1.73
354 395 7.009550 AGCTTCCATGTGAGAGAGATATCTTA 58.990 38.462 6.70 0.00 0.00 2.10
355 396 5.840149 AGCTTCCATGTGAGAGAGATATCTT 59.160 40.000 6.70 0.00 0.00 2.40
356 397 5.396485 AGCTTCCATGTGAGAGAGATATCT 58.604 41.667 4.47 4.47 0.00 1.98
357 398 5.726980 AGCTTCCATGTGAGAGAGATATC 57.273 43.478 0.00 0.00 0.00 1.63
358 399 6.314120 AGTAGCTTCCATGTGAGAGAGATAT 58.686 40.000 0.00 0.00 0.00 1.63
359 400 5.700183 AGTAGCTTCCATGTGAGAGAGATA 58.300 41.667 0.00 0.00 0.00 1.98
360 401 4.545678 AGTAGCTTCCATGTGAGAGAGAT 58.454 43.478 0.00 0.00 0.00 2.75
361 402 3.974719 AGTAGCTTCCATGTGAGAGAGA 58.025 45.455 0.00 0.00 0.00 3.10
362 403 5.843673 TTAGTAGCTTCCATGTGAGAGAG 57.156 43.478 0.00 0.00 0.00 3.20
372 413 4.081642 AGAGCGTCAAATTAGTAGCTTCCA 60.082 41.667 0.00 0.00 34.85 3.53
373 414 4.434520 AGAGCGTCAAATTAGTAGCTTCC 58.565 43.478 0.00 0.00 34.85 3.46
389 439 2.673341 TCCTGCAGTCGAGAGCGT 60.673 61.111 13.81 0.00 38.98 5.07
413 463 5.010012 AGTTTCTCCTGCACGAAAATTTGAT 59.990 36.000 0.00 0.00 31.63 2.57
417 467 4.580580 AGAAGTTTCTCCTGCACGAAAATT 59.419 37.500 11.48 11.48 39.29 1.82
461 511 5.560183 CGTTTACTCTTGTGGAATGTTGGAC 60.560 44.000 0.00 0.00 0.00 4.02
518 569 4.565531 GGGACACGTACCGACAAG 57.434 61.111 0.00 0.00 0.00 3.16
540 591 1.531840 AGAGTGAGTGGTGCTCCGT 60.532 57.895 0.00 0.00 43.48 4.69
568 622 2.159085 ACTCTATTTCGTGTGGCTAGCC 60.159 50.000 27.71 27.71 0.00 3.93
745 818 0.789753 CACTACGTGCGACGAGTCAG 60.790 60.000 14.18 8.41 46.05 3.51
762 835 3.022287 CATATGCCGGCGGTTCAC 58.978 61.111 28.82 11.33 0.00 3.18
765 838 3.209097 GTGCATATGCCGGCGGTT 61.209 61.111 28.82 17.82 41.18 4.44
857 3018 2.029743 CGTTGTTGGTGGTTGAGGG 58.970 57.895 0.00 0.00 0.00 4.30
885 3046 1.854126 CGCTTGTCTTTGGCACTTTTG 59.146 47.619 0.00 0.00 0.00 2.44
886 3047 1.748493 TCGCTTGTCTTTGGCACTTTT 59.252 42.857 0.00 0.00 0.00 2.27
887 3048 1.388547 TCGCTTGTCTTTGGCACTTT 58.611 45.000 0.00 0.00 0.00 2.66
888 3049 1.065551 GTTCGCTTGTCTTTGGCACTT 59.934 47.619 0.00 0.00 0.00 3.16
889 3050 0.663153 GTTCGCTTGTCTTTGGCACT 59.337 50.000 0.00 0.00 0.00 4.40
890 3051 0.317854 GGTTCGCTTGTCTTTGGCAC 60.318 55.000 0.00 0.00 0.00 5.01
891 3052 0.749818 TGGTTCGCTTGTCTTTGGCA 60.750 50.000 0.00 0.00 0.00 4.92
892 3053 0.040067 CTGGTTCGCTTGTCTTTGGC 60.040 55.000 0.00 0.00 0.00 4.52
893 3054 0.040067 GCTGGTTCGCTTGTCTTTGG 60.040 55.000 0.00 0.00 0.00 3.28
894 3055 0.384725 CGCTGGTTCGCTTGTCTTTG 60.385 55.000 0.00 0.00 0.00 2.77
896 3057 0.946221 CTCGCTGGTTCGCTTGTCTT 60.946 55.000 0.00 0.00 0.00 3.01
897 3058 1.373497 CTCGCTGGTTCGCTTGTCT 60.373 57.895 0.00 0.00 0.00 3.41
898 3059 3.016474 GCTCGCTGGTTCGCTTGTC 62.016 63.158 0.00 0.00 0.00 3.18
943 3117 3.132646 CCACCTGAGAAGAGATTCCTGAG 59.867 52.174 0.00 0.00 0.00 3.35
975 3149 3.053831 ACGATGGACCTTGTTAACCTG 57.946 47.619 2.48 0.00 0.00 4.00
981 3155 3.343617 CATGGTTACGATGGACCTTGTT 58.656 45.455 0.00 0.00 36.72 2.83
982 3156 2.939640 GCATGGTTACGATGGACCTTGT 60.940 50.000 9.26 0.00 40.98 3.16
1269 3453 2.965147 GCGAAAGGTGCGTGCATCA 61.965 57.895 7.97 0.00 0.00 3.07
1270 3454 2.187599 AAGCGAAAGGTGCGTGCATC 62.188 55.000 0.00 0.00 43.76 3.91
1271 3455 1.795170 AAAGCGAAAGGTGCGTGCAT 61.795 50.000 0.00 0.00 43.76 3.96
1272 3456 2.477176 AAAGCGAAAGGTGCGTGCA 61.477 52.632 0.00 0.00 43.76 4.57
1273 3457 2.010817 CAAAGCGAAAGGTGCGTGC 61.011 57.895 0.00 0.00 43.76 5.34
1274 3458 0.929824 CACAAAGCGAAAGGTGCGTG 60.930 55.000 0.00 0.00 43.76 5.34
1275 3459 1.355210 CACAAAGCGAAAGGTGCGT 59.645 52.632 0.00 0.00 43.76 5.24
1276 3460 0.929824 CACACAAAGCGAAAGGTGCG 60.930 55.000 0.00 0.00 43.76 5.34
1285 3469 3.120234 TGTGCATTAGATCACACAAAGCG 60.120 43.478 0.00 0.00 39.91 4.68
1294 3478 4.576053 GTGCTGGTAATGTGCATTAGATCA 59.424 41.667 5.01 4.42 39.00 2.92
1298 3482 6.260714 TCATTAGTGCTGGTAATGTGCATTAG 59.739 38.462 5.01 0.00 38.50 1.73
1303 3487 3.941483 ACTCATTAGTGCTGGTAATGTGC 59.059 43.478 10.90 0.00 38.50 4.57
1308 3492 3.244735 TGGCAACTCATTAGTGCTGGTAA 60.245 43.478 0.00 0.00 35.62 2.85
1310 3494 1.073763 TGGCAACTCATTAGTGCTGGT 59.926 47.619 0.00 0.00 35.62 4.00
1312 3496 3.011818 TCATGGCAACTCATTAGTGCTG 58.988 45.455 0.00 0.00 35.62 4.41
1315 3499 9.006839 ACATATATTCATGGCAACTCATTAGTG 57.993 33.333 0.00 0.00 35.62 2.74
1339 3523 2.364324 GGCCGTCAAGATCCTACATACA 59.636 50.000 0.00 0.00 0.00 2.29
1344 3528 1.067582 CGGGCCGTCAAGATCCTAC 59.932 63.158 19.97 0.00 0.00 3.18
1359 3543 3.299190 GAGATCCTCGCCTCCGGG 61.299 72.222 0.00 0.00 34.56 5.73
1497 3906 1.595311 AGATATTGGGGCAGTGGTCA 58.405 50.000 0.00 0.00 0.00 4.02
1541 4407 6.976925 ACTGTTTTAGGTAGATATGTACGTGC 59.023 38.462 13.75 0.00 0.00 5.34
1544 4410 8.074972 GGAGACTGTTTTAGGTAGATATGTACG 58.925 40.741 4.11 0.00 0.00 3.67
1564 4430 0.107312 GACCATGCATGCAGGAGACT 60.107 55.000 32.39 13.90 46.44 3.24
1581 4447 1.405821 AGATCCGTCAAGATGGTCGAC 59.594 52.381 7.13 7.13 38.61 4.20
1597 4463 7.116948 GCACCACAGAACATACATACATAGATC 59.883 40.741 0.00 0.00 0.00 2.75
1838 5271 3.271142 CAACCGTGCAAGCACATTT 57.729 47.368 23.23 12.97 46.47 2.32
1876 5381 7.391275 TCATGGCCTACATACATGTTTCATATG 59.609 37.037 2.30 3.60 41.91 1.78
1961 5473 4.342086 TGGCCGGGGAGGTAGGTT 62.342 66.667 2.18 0.00 43.70 3.50
2256 5796 0.253044 TGCCAGCAGGGTCTGTAATC 59.747 55.000 0.00 0.00 39.65 1.75
2395 5935 1.267806 CACTCGGCAGCATCAAACTTT 59.732 47.619 0.00 0.00 0.00 2.66
2434 5974 1.299976 CCTGTTGTAGAGCCACCCC 59.700 63.158 0.00 0.00 0.00 4.95
2476 6016 4.095590 GCACTGGCCTGGCTAAAA 57.904 55.556 19.68 1.24 0.00 1.52
2677 6217 2.676121 TTCCCCGTCTCGGCGTTA 60.676 61.111 6.85 0.00 46.86 3.18
2719 6262 3.907474 TGACCAACTCCTCCTCATTTGTA 59.093 43.478 0.00 0.00 0.00 2.41
2809 6352 2.171003 GTAAGCAATGCCCCAAGTCTT 58.829 47.619 0.00 0.00 0.00 3.01
2844 6387 0.917533 AGGTAGTGCTCTCCGGTCTA 59.082 55.000 0.00 0.00 0.00 2.59
2910 6456 8.353684 ACCAAAAGATATACACGACTATCAGAG 58.646 37.037 0.00 0.00 0.00 3.35
2935 6482 8.801715 ACAAATGAATGAATGTCTACACAAAC 57.198 30.769 0.00 0.00 35.64 2.93
3018 6576 6.183360 CCCATCATGTAGGAACAATGAAAGAC 60.183 42.308 7.61 0.00 39.58 3.01
3067 6625 9.909644 GGTTAGCTATATTAATCAAGAACGAGA 57.090 33.333 0.00 0.00 0.00 4.04
3072 6630 6.588756 CCGCGGTTAGCTATATTAATCAAGAA 59.411 38.462 19.50 0.00 45.59 2.52
3088 6646 0.320073 TGTCCAAACTCCGCGGTTAG 60.320 55.000 27.15 19.01 0.00 2.34
3094 6652 2.613506 CGGGTTGTCCAAACTCCGC 61.614 63.158 0.00 0.00 34.36 5.54
3121 6679 7.577979 TGAATAACGTGTTTAACAGTGGAATC 58.422 34.615 0.00 0.00 0.00 2.52
3278 6837 5.939883 CAGGAGTTTGTTGGAGATTACATGA 59.060 40.000 0.00 0.00 0.00 3.07
3319 6879 3.491964 GCGTGTTATATAGACAGGGTGCA 60.492 47.826 14.15 0.00 34.44 4.57
3785 7355 2.954868 GACGAGTACATGCCCGCG 60.955 66.667 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.