Multiple sequence alignment - TraesCS4B01G363100

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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 TraesCS4B01G363100 chr4B 100.000 3428 0 0 985 4412 651994086 651990659 0.000000e+00 6331
1 TraesCS4B01G363100 chr4B 100.000 594 0 0 1 594 651995070 651994477 0.000000e+00 1098
2 TraesCS4B01G363100 chr4B 92.308 91 7 0 120 210 300550663 300550573 3.580000e-26 130
3 TraesCS4B01G363100 chr5A 92.098 1430 65 20 985 2394 689611927 689610526 0.000000e+00 1971
4 TraesCS4B01G363100 chr5A 92.387 775 46 8 3151 3919 689609742 689608975 0.000000e+00 1092
5 TraesCS4B01G363100 chr5A 91.561 474 38 2 2690 3163 689610238 689609767 0.000000e+00 652
6 TraesCS4B01G363100 chr5A 94.850 233 9 3 3944 4175 689608599 689608369 1.170000e-95 361
7 TraesCS4B01G363100 chr5A 83.714 350 30 11 252 594 689612343 689612014 5.540000e-79 305
8 TraesCS4B01G363100 chr5A 87.833 263 13 9 2394 2647 689610498 689610246 1.550000e-74 291
9 TraesCS4B01G363100 chr5A 90.291 103 9 1 109 210 555212656 555212554 2.770000e-27 134
10 TraesCS4B01G363100 chr4D 91.413 1246 75 13 2690 3924 505331706 505330482 0.000000e+00 1679
11 TraesCS4B01G363100 chr4D 92.903 930 47 11 985 1904 505333372 505332452 0.000000e+00 1334
12 TraesCS4B01G363100 chr4D 94.737 456 24 0 1939 2394 505332448 505331993 0.000000e+00 710
13 TraesCS4B01G363100 chr4D 89.738 497 34 6 3925 4412 505330084 505329596 1.740000e-173 619
14 TraesCS4B01G363100 chr4D 90.585 393 26 8 207 592 505333830 505333442 1.090000e-140 510
15 TraesCS4B01G363100 chr4D 90.377 239 19 3 2394 2632 505331966 505331732 1.190000e-80 311
16 TraesCS4B01G363100 chr4D 80.714 280 52 2 2846 3124 4107054 4107332 2.670000e-52 217
17 TraesCS4B01G363100 chr4D 84.800 125 19 0 1536 1660 4105590 4105714 4.630000e-25 126
18 TraesCS4B01G363100 chr5B 81.622 740 127 9 2719 3455 419243420 419242687 4.880000e-169 604
19 TraesCS4B01G363100 chr5B 85.791 373 50 3 2022 2393 419244095 419243725 4.140000e-105 392
20 TraesCS4B01G363100 chr5B 86.345 249 34 0 1444 1692 419245186 419244938 5.620000e-69 272
21 TraesCS4B01G363100 chr5B 91.781 146 12 0 1771 1916 419244304 419244159 2.080000e-48 204
22 TraesCS4B01G363100 chr5B 88.679 106 12 0 999 1104 419245693 419245588 3.580000e-26 130
23 TraesCS4B01G363100 chr4A 79.715 281 53 3 2846 3124 599845694 599845972 2.690000e-47 200
24 TraesCS4B01G363100 chr7A 90.476 105 8 2 122 225 383096083 383095980 2.140000e-28 137
25 TraesCS4B01G363100 chr6D 90.291 103 9 1 109 210 108977502 108977604 2.770000e-27 134
26 TraesCS4B01G363100 chr1B 90.291 103 9 1 109 210 174112236 174112134 2.770000e-27 134
27 TraesCS4B01G363100 chr2D 92.308 91 7 0 120 210 426473181 426473091 3.580000e-26 130
28 TraesCS4B01G363100 chr3D 89.320 103 10 1 109 210 301067495 301067597 1.290000e-25 128
29 TraesCS4B01G363100 chr3B 86.364 110 13 2 120 229 362576406 362576299 7.750000e-23 119
30 TraesCS4B01G363100 chr3B 86.364 110 13 2 120 229 466816905 466816798 7.750000e-23 119


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 TraesCS4B01G363100 chr4B 651990659 651995070 4411 True 3714.500000 6331 100.000000 1 4412 2 chr4B.!!$R2 4411
1 TraesCS4B01G363100 chr5A 689608369 689612343 3974 True 778.666667 1971 90.407167 252 4175 6 chr5A.!!$R2 3923
2 TraesCS4B01G363100 chr4D 505329596 505333830 4234 True 860.500000 1679 91.625500 207 4412 6 chr4D.!!$R1 4205
3 TraesCS4B01G363100 chr5B 419242687 419245693 3006 True 320.400000 604 86.843600 999 3455 5 chr5B.!!$R1 2456

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
472 477 0.968405 TTGAGCAAAAGATGGGCCAC 59.032 50.000 9.28 2.67 0.0 5.01 F
526 533 2.966050 TCAACTGCCAAACAACAAACC 58.034 42.857 0.00 0.00 0.0 3.27 F
1754 2413 0.172803 GTACGCGGTGAATGGTCTCT 59.827 55.000 12.47 0.00 0.0 3.10 F
2624 3344 0.673437 CCAGGCAATGTTTGGTCGTT 59.327 50.000 0.00 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1313 1392 0.036010 CAGTCTCCACCCGATGCTTT 60.036 55.0 0.00 0.00 0.00 3.51 R
2339 3023 0.106149 GTGGGTCGTTCTGGACACTT 59.894 55.0 0.00 0.00 41.02 3.16 R
2696 3421 0.320771 GATTGCACTCACCACCGACT 60.321 55.0 0.00 0.00 0.00 4.18 R
3771 4543 0.165511 GCACTGAGAAGCGCTTGAAG 59.834 55.0 30.47 22.38 0.00 3.02 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
26 27 9.817809 TGTTCTAATGAGAGAAAAATACGCTAT 57.182 29.630 0.00 0.00 37.20 2.97
28 29 8.299262 TCTAATGAGAGAAAAATACGCTATGC 57.701 34.615 0.00 0.00 0.00 3.14
42 43 3.004024 GCTATGCGTTTCCAATGGATG 57.996 47.619 1.39 0.00 30.65 3.51
57 58 6.576662 CAATGGATGGAGTACGATACTACT 57.423 41.667 8.30 0.00 40.41 2.57
58 59 6.613233 CAATGGATGGAGTACGATACTACTC 58.387 44.000 8.30 5.87 40.41 2.59
59 60 5.563876 TGGATGGAGTACGATACTACTCT 57.436 43.478 9.88 0.00 41.68 3.24
60 61 6.676990 TGGATGGAGTACGATACTACTCTA 57.323 41.667 9.88 5.45 41.68 2.43
61 62 7.255199 TGGATGGAGTACGATACTACTCTAT 57.745 40.000 8.81 8.81 43.78 1.98
66 67 9.820725 ATGGAGTACGATACTACTCTATCATAC 57.179 37.037 9.88 0.00 39.51 2.39
67 68 9.033711 TGGAGTACGATACTACTCTATCATACT 57.966 37.037 9.88 0.00 41.68 2.12
68 69 9.520204 GGAGTACGATACTACTCTATCATACTC 57.480 40.741 11.42 11.42 42.74 2.59
69 70 9.520204 GAGTACGATACTACTCTATCATACTCC 57.480 40.741 9.68 0.00 40.19 3.85
70 71 9.033711 AGTACGATACTACTCTATCATACTCCA 57.966 37.037 0.00 0.00 37.23 3.86
71 72 9.086336 GTACGATACTACTCTATCATACTCCAC 57.914 40.741 0.00 0.00 0.00 4.02
72 73 7.909518 ACGATACTACTCTATCATACTCCACT 58.090 38.462 0.00 0.00 0.00 4.00
73 74 8.036575 ACGATACTACTCTATCATACTCCACTC 58.963 40.741 0.00 0.00 0.00 3.51
74 75 8.035984 CGATACTACTCTATCATACTCCACTCA 58.964 40.741 0.00 0.00 0.00 3.41
75 76 9.899661 GATACTACTCTATCATACTCCACTCAT 57.100 37.037 0.00 0.00 0.00 2.90
76 77 9.899661 ATACTACTCTATCATACTCCACTCATC 57.100 37.037 0.00 0.00 0.00 2.92
77 78 7.750655 ACTACTCTATCATACTCCACTCATCA 58.249 38.462 0.00 0.00 0.00 3.07
78 79 8.221251 ACTACTCTATCATACTCCACTCATCAA 58.779 37.037 0.00 0.00 0.00 2.57
79 80 9.241919 CTACTCTATCATACTCCACTCATCAAT 57.758 37.037 0.00 0.00 0.00 2.57
80 81 8.489676 ACTCTATCATACTCCACTCATCAATT 57.510 34.615 0.00 0.00 0.00 2.32
81 82 8.366401 ACTCTATCATACTCCACTCATCAATTG 58.634 37.037 0.00 0.00 0.00 2.32
82 83 8.255111 TCTATCATACTCCACTCATCAATTGT 57.745 34.615 5.13 0.00 0.00 2.71
83 84 9.367160 TCTATCATACTCCACTCATCAATTGTA 57.633 33.333 5.13 0.00 0.00 2.41
84 85 9.636879 CTATCATACTCCACTCATCAATTGTAG 57.363 37.037 5.13 4.70 0.00 2.74
85 86 6.820335 TCATACTCCACTCATCAATTGTAGG 58.180 40.000 5.13 0.48 0.00 3.18
86 87 6.611236 TCATACTCCACTCATCAATTGTAGGA 59.389 38.462 5.13 4.60 0.00 2.94
87 88 5.350504 ACTCCACTCATCAATTGTAGGAG 57.649 43.478 19.11 19.11 40.87 3.69
88 89 4.780021 ACTCCACTCATCAATTGTAGGAGT 59.220 41.667 19.93 19.93 42.03 3.85
89 90 5.958380 ACTCCACTCATCAATTGTAGGAGTA 59.042 40.000 22.13 12.57 43.43 2.59
90 91 6.127310 ACTCCACTCATCAATTGTAGGAGTAC 60.127 42.308 22.13 0.00 43.43 2.73
91 92 5.128827 TCCACTCATCAATTGTAGGAGTACC 59.871 44.000 20.60 0.00 36.74 3.34
92 93 5.360591 CACTCATCAATTGTAGGAGTACCC 58.639 45.833 20.60 0.00 36.74 3.69
94 95 6.323996 CACTCATCAATTGTAGGAGTACCCTA 59.676 42.308 20.60 6.13 45.48 3.53
107 108 7.138054 AGGAGTACCCTACAATTTCTAATGG 57.862 40.000 1.40 0.00 45.48 3.16
108 109 6.677076 AGGAGTACCCTACAATTTCTAATGGT 59.323 38.462 1.40 0.00 45.48 3.55
109 110 7.847848 AGGAGTACCCTACAATTTCTAATGGTA 59.152 37.037 1.40 0.00 45.48 3.25
110 111 8.657712 GGAGTACCCTACAATTTCTAATGGTAT 58.342 37.037 0.00 0.00 30.51 2.73
126 127 9.875691 TCTAATGGTATAACTATGATGACATGC 57.124 33.333 0.00 0.00 37.87 4.06
127 128 9.657419 CTAATGGTATAACTATGATGACATGCA 57.343 33.333 0.00 0.00 37.87 3.96
128 129 7.912056 ATGGTATAACTATGATGACATGCAC 57.088 36.000 0.00 0.00 37.87 4.57
129 130 7.066307 TGGTATAACTATGATGACATGCACT 57.934 36.000 0.00 0.00 37.87 4.40
130 131 8.189119 TGGTATAACTATGATGACATGCACTA 57.811 34.615 0.00 0.00 37.87 2.74
131 132 8.646900 TGGTATAACTATGATGACATGCACTAA 58.353 33.333 0.00 0.00 37.87 2.24
132 133 9.658799 GGTATAACTATGATGACATGCACTAAT 57.341 33.333 0.00 0.00 37.87 1.73
141 142 8.278729 TGATGACATGCACTAATATTTTGTCA 57.721 30.769 14.34 14.34 44.06 3.58
142 143 8.738106 TGATGACATGCACTAATATTTTGTCAA 58.262 29.630 15.55 1.10 43.42 3.18
143 144 9.229784 GATGACATGCACTAATATTTTGTCAAG 57.770 33.333 15.55 0.69 43.42 3.02
144 145 8.109705 TGACATGCACTAATATTTTGTCAAGT 57.890 30.769 10.64 0.00 39.06 3.16
145 146 9.225436 TGACATGCACTAATATTTTGTCAAGTA 57.775 29.630 10.64 0.00 39.06 2.24
159 160 9.883142 ATTTTGTCAAGTAAATCTTTGGTGAAA 57.117 25.926 0.00 0.00 33.63 2.69
160 161 9.712305 TTTTGTCAAGTAAATCTTTGGTGAAAA 57.288 25.926 0.00 0.00 33.63 2.29
161 162 9.883142 TTTGTCAAGTAAATCTTTGGTGAAAAT 57.117 25.926 0.00 0.00 33.63 1.82
162 163 9.883142 TTGTCAAGTAAATCTTTGGTGAAAATT 57.117 25.926 0.00 0.00 33.63 1.82
163 164 9.883142 TGTCAAGTAAATCTTTGGTGAAAATTT 57.117 25.926 0.00 0.00 33.63 1.82
168 169 9.476202 AGTAAATCTTTGGTGAAAATTTAGCAC 57.524 29.630 13.05 13.05 0.00 4.40
169 170 9.255304 GTAAATCTTTGGTGAAAATTTAGCACA 57.745 29.630 19.58 3.57 34.33 4.57
170 171 8.729805 AAATCTTTGGTGAAAATTTAGCACAA 57.270 26.923 19.58 10.39 34.33 3.33
171 172 8.729805 AATCTTTGGTGAAAATTTAGCACAAA 57.270 26.923 19.58 14.49 34.33 2.83
172 173 8.907222 ATCTTTGGTGAAAATTTAGCACAAAT 57.093 26.923 19.58 4.27 34.33 2.32
173 174 8.729805 TCTTTGGTGAAAATTTAGCACAAATT 57.270 26.923 19.58 3.84 34.33 1.82
174 175 9.823647 TCTTTGGTGAAAATTTAGCACAAATTA 57.176 25.926 19.58 8.25 34.33 1.40
175 176 9.862585 CTTTGGTGAAAATTTAGCACAAATTAC 57.137 29.630 19.58 5.06 34.33 1.89
176 177 8.948631 TTGGTGAAAATTTAGCACAAATTACA 57.051 26.923 19.58 9.39 34.33 2.41
177 178 8.948631 TGGTGAAAATTTAGCACAAATTACAA 57.051 26.923 19.58 0.00 34.33 2.41
178 179 9.553064 TGGTGAAAATTTAGCACAAATTACAAT 57.447 25.926 19.58 0.00 34.33 2.71
179 180 9.810231 GGTGAAAATTTAGCACAAATTACAATG 57.190 29.630 19.58 0.00 34.33 2.82
198 199 7.923414 ACAATGAAGACTAATAAACCAGGAC 57.077 36.000 0.00 0.00 0.00 3.85
199 200 6.594159 ACAATGAAGACTAATAAACCAGGACG 59.406 38.462 0.00 0.00 0.00 4.79
200 201 5.080969 TGAAGACTAATAAACCAGGACGG 57.919 43.478 0.00 0.00 42.50 4.79
201 202 4.773674 TGAAGACTAATAAACCAGGACGGA 59.226 41.667 0.00 0.00 38.63 4.69
202 203 5.105473 TGAAGACTAATAAACCAGGACGGAG 60.105 44.000 0.00 0.00 38.63 4.63
203 204 3.705072 AGACTAATAAACCAGGACGGAGG 59.295 47.826 0.00 0.00 38.63 4.30
204 205 3.447950 ACTAATAAACCAGGACGGAGGT 58.552 45.455 0.00 0.00 40.61 3.85
205 206 4.613437 ACTAATAAACCAGGACGGAGGTA 58.387 43.478 0.00 0.00 37.07 3.08
227 228 9.069082 AGGTAGTAGCAATAATACTGAGTACTG 57.931 37.037 0.00 0.00 35.20 2.74
229 230 7.589958 AGTAGCAATAATACTGAGTACTGCT 57.410 36.000 18.28 18.28 32.27 4.24
247 248 4.065110 GGTTGTCCACCTGAGCAC 57.935 61.111 0.00 0.00 43.29 4.40
248 249 1.148273 GGTTGTCCACCTGAGCACA 59.852 57.895 0.00 0.00 43.29 4.57
255 256 5.172687 TGTCCACCTGAGCACAATTAATA 57.827 39.130 0.00 0.00 0.00 0.98
274 276 2.240493 ATGATGGCTAGCAACGTACC 57.760 50.000 18.24 0.00 0.00 3.34
279 281 1.293267 GGCTAGCAACGTACCGCAAA 61.293 55.000 18.24 0.00 0.00 3.68
333 335 4.916099 ACTTCTACGCGTTATTTTGACC 57.084 40.909 20.78 0.00 0.00 4.02
349 351 1.293924 GACCGCATGTGATTCCTCTG 58.706 55.000 8.11 0.00 0.00 3.35
376 378 3.053544 TCACTGGGTCCTTGTTTTGGTTA 60.054 43.478 0.00 0.00 0.00 2.85
378 380 2.890945 CTGGGTCCTTGTTTTGGTTAGG 59.109 50.000 0.00 0.00 0.00 2.69
442 444 2.384375 TCCCCTCTCCTACCTACAACAA 59.616 50.000 0.00 0.00 0.00 2.83
445 447 4.565028 CCCCTCTCCTACCTACAACAAAAC 60.565 50.000 0.00 0.00 0.00 2.43
447 449 4.995487 CCTCTCCTACCTACAACAAAACAC 59.005 45.833 0.00 0.00 0.00 3.32
448 450 4.964593 TCTCCTACCTACAACAAAACACC 58.035 43.478 0.00 0.00 0.00 4.16
471 476 1.714541 TTTGAGCAAAAGATGGGCCA 58.285 45.000 9.61 9.61 0.00 5.36
472 477 0.968405 TTGAGCAAAAGATGGGCCAC 59.032 50.000 9.28 2.67 0.00 5.01
526 533 2.966050 TCAACTGCCAAACAACAAACC 58.034 42.857 0.00 0.00 0.00 3.27
1153 1171 8.559222 TGCATATACTATTTGTTGCAAATTCG 57.441 30.769 0.00 7.06 37.10 3.34
1195 1274 4.254402 TCATATCTGCTGTGCTCATCTC 57.746 45.455 0.00 0.00 0.00 2.75
1201 1280 4.439968 TCTGCTGTGCTCATCTCTTAATG 58.560 43.478 0.00 0.00 0.00 1.90
1347 1426 1.887198 AGACTGAGGTAGTGTTGTCCG 59.113 52.381 0.00 0.00 40.53 4.79
1377 1456 6.547880 GGTTCTTCATGATCTAGACCTCTACA 59.452 42.308 0.00 0.00 0.00 2.74
1382 1467 4.779993 TGATCTAGACCTCTACAGCTCA 57.220 45.455 0.00 0.00 0.00 4.26
1383 1468 5.317600 TGATCTAGACCTCTACAGCTCAT 57.682 43.478 0.00 0.00 0.00 2.90
1384 1469 5.312895 TGATCTAGACCTCTACAGCTCATC 58.687 45.833 0.00 0.00 0.00 2.92
1410 1495 5.649782 TGATTCTTTTGATCCCTTTGCTC 57.350 39.130 0.00 0.00 0.00 4.26
1431 1516 3.932710 TCGAGTGTTGGTGCTGAATAATC 59.067 43.478 0.00 0.00 0.00 1.75
1498 1613 3.319198 GGGAGAAGCACGGGGACA 61.319 66.667 0.00 0.00 0.00 4.02
1518 1633 5.105997 GGACAGGTTTCAATCTTTCATCTGG 60.106 44.000 0.00 0.00 0.00 3.86
1741 1856 2.730672 GGTGCAGCAAGAGTACGCG 61.731 63.158 11.86 3.53 0.00 6.01
1754 2413 0.172803 GTACGCGGTGAATGGTCTCT 59.827 55.000 12.47 0.00 0.00 3.10
1758 2417 1.808411 GCGGTGAATGGTCTCTGAAA 58.192 50.000 0.00 0.00 0.00 2.69
1763 2422 4.319766 CGGTGAATGGTCTCTGAAAAACAG 60.320 45.833 0.00 0.00 46.97 3.16
1793 2470 2.103094 GTGCAGGTATGATGTGGCTCTA 59.897 50.000 0.00 0.00 0.00 2.43
1910 2587 5.995282 CACCAACTCTACAAGTAACCATTGA 59.005 40.000 0.00 0.00 37.17 2.57
1911 2588 5.995897 ACCAACTCTACAAGTAACCATTGAC 59.004 40.000 0.00 0.00 37.17 3.18
1917 2594 8.470805 ACTCTACAAGTAACCATTGACTATGAG 58.529 37.037 0.00 0.00 36.07 2.90
1935 2612 7.341805 ACTATGAGTATGAACTTGGATGCTTT 58.658 34.615 0.00 0.00 35.56 3.51
1936 2613 5.885230 TGAGTATGAACTTGGATGCTTTG 57.115 39.130 0.00 0.00 35.56 2.77
2171 2855 1.741770 GCTTGAGGCCGACGTTGAT 60.742 57.895 3.74 0.00 34.27 2.57
2285 2969 1.121407 CGATGGGGGAGATGGTGCTA 61.121 60.000 0.00 0.00 0.00 3.49
2286 2970 1.140312 GATGGGGGAGATGGTGCTAA 58.860 55.000 0.00 0.00 0.00 3.09
2339 3023 1.221566 CCGTCCCAGCATCATCACA 59.778 57.895 0.00 0.00 0.00 3.58
2424 3136 4.723862 GTGCAGTCGTTTTAATCTATTGCG 59.276 41.667 0.00 0.00 32.03 4.85
2465 3177 8.333235 AGGGATAAATGGTACTTGTTCAATGTA 58.667 33.333 0.00 0.00 0.00 2.29
2466 3178 8.962679 GGGATAAATGGTACTTGTTCAATGTAA 58.037 33.333 0.00 0.00 0.00 2.41
2615 3335 7.175641 GCAGTTAAGATATATTCCAGGCAATGT 59.824 37.037 0.00 0.00 0.00 2.71
2621 3341 6.491403 AGATATATTCCAGGCAATGTTTGGTC 59.509 38.462 5.37 0.00 33.65 4.02
2624 3344 0.673437 CCAGGCAATGTTTGGTCGTT 59.327 50.000 0.00 0.00 0.00 3.85
2629 3349 2.812011 GGCAATGTTTGGTCGTTAGTCT 59.188 45.455 0.00 0.00 0.00 3.24
2636 3361 6.105397 TGTTTGGTCGTTAGTCTAGGAATT 57.895 37.500 0.00 0.00 0.00 2.17
2647 3372 8.848182 CGTTAGTCTAGGAATTCCTACAGTAAT 58.152 37.037 26.82 17.09 46.48 1.89
2685 3410 7.713750 GGTTTCCCCACTTAAGATTATAAAGC 58.286 38.462 10.09 9.48 0.00 3.51
2686 3411 7.340999 GGTTTCCCCACTTAAGATTATAAAGCA 59.659 37.037 10.09 0.00 0.00 3.91
2687 3412 8.745590 GTTTCCCCACTTAAGATTATAAAGCAA 58.254 33.333 10.09 0.00 0.00 3.91
2708 3433 2.878406 ACATTTCAAAGTCGGTGGTGAG 59.122 45.455 0.00 0.00 0.00 3.51
2716 3441 0.602638 GTCGGTGGTGAGTGCAATCA 60.603 55.000 13.76 13.76 0.00 2.57
2731 3456 5.127031 AGTGCAATCATTTGGTTGGGTATAC 59.873 40.000 5.75 0.00 33.22 1.47
2732 3457 5.019470 TGCAATCATTTGGTTGGGTATACA 58.981 37.500 5.01 0.00 33.22 2.29
2777 3502 1.280746 GGTGAATGCGATGATGGCG 59.719 57.895 0.00 0.00 0.00 5.69
2780 3505 2.516695 AATGCGATGATGGCGGCA 60.517 55.556 16.34 16.34 40.06 5.69
2783 3508 0.606130 ATGCGATGATGGCGGCAATA 60.606 50.000 18.31 8.55 39.09 1.90
2833 3558 2.158623 AGACAAAGTCACATCCCAAGCA 60.159 45.455 0.00 0.00 34.60 3.91
2837 3562 2.592102 AGTCACATCCCAAGCAACAT 57.408 45.000 0.00 0.00 0.00 2.71
2936 3661 4.373116 TTCACGGAGCACCCTCGC 62.373 66.667 0.00 0.00 39.06 5.03
3008 3733 0.255890 GCATGGCTTCCTTCCACCTA 59.744 55.000 0.00 0.00 36.26 3.08
3144 3873 7.093509 ACAGGTTAGTTGGTTGAAATCTTTTGT 60.094 33.333 0.00 0.00 0.00 2.83
3147 3876 5.675684 AGTTGGTTGAAATCTTTTGTGGT 57.324 34.783 0.00 0.00 0.00 4.16
3187 3954 1.470805 CGGCACATAAGATGACACGGA 60.471 52.381 0.00 0.00 0.00 4.69
3246 4013 0.912487 TGGATCTGTACGGGCCCTTT 60.912 55.000 22.43 9.37 0.00 3.11
3351 4118 1.191535 TCGACCCGAAGACCATTGAT 58.808 50.000 0.00 0.00 31.06 2.57
3419 4186 5.755375 AGTACATGCTCAAGTGAAATATCCG 59.245 40.000 0.00 0.00 0.00 4.18
3561 4329 2.229675 TGATAGAGCAGGCATCAACG 57.770 50.000 0.00 0.00 0.00 4.10
3569 4337 1.135431 GCAGGCATCAACGTTGCATAA 60.135 47.619 23.47 6.64 41.95 1.90
3571 4339 2.162208 CAGGCATCAACGTTGCATAAGT 59.838 45.455 23.47 3.40 41.95 2.24
3615 4384 5.975988 ACATTATGTAGTCCCATTCTGGT 57.024 39.130 0.00 0.00 35.17 4.00
3621 4390 3.587061 TGTAGTCCCATTCTGGTTCATGT 59.413 43.478 0.00 0.00 35.17 3.21
3622 4391 4.780554 TGTAGTCCCATTCTGGTTCATGTA 59.219 41.667 0.00 0.00 35.17 2.29
3632 4401 7.201848 CCATTCTGGTTCATGTATTGTATTGCT 60.202 37.037 0.00 0.00 31.35 3.91
3684 4453 7.596494 ACCAATTTCTTGTTCAGTCACATATG 58.404 34.615 0.00 0.00 0.00 1.78
3698 4467 5.069251 AGTCACATATGGTACCTTGACTAGC 59.931 44.000 21.71 7.16 41.41 3.42
3789 4561 1.725706 CTCTTCAAGCGCTTCTCAGTG 59.274 52.381 22.21 9.19 0.00 3.66
3803 4575 5.803967 GCTTCTCAGTGCAAAATGAATAAGG 59.196 40.000 14.73 1.13 0.00 2.69
3921 4694 5.097529 GCATACACATCTCACCAAAACATG 58.902 41.667 0.00 0.00 0.00 3.21
4094 5272 7.807907 ACGTCAAGAAATCACAATAAATTGGTC 59.192 33.333 7.56 0.00 41.96 4.02
4160 5338 8.049117 TCAGCATACAAGATAGGAAAAGAACAT 58.951 33.333 0.00 0.00 0.00 2.71
4256 5442 5.824904 ACATCACTTGATACATTTGGAGC 57.175 39.130 0.00 0.00 32.63 4.70
4273 5459 7.441890 TTTGGAGCAACGTTTATTATTCTGA 57.558 32.000 0.00 0.00 0.00 3.27
4276 5462 7.877003 TGGAGCAACGTTTATTATTCTGAAAA 58.123 30.769 0.00 0.00 0.00 2.29
4277 5463 8.353684 TGGAGCAACGTTTATTATTCTGAAAAA 58.646 29.630 0.00 0.00 0.00 1.94
4325 5511 2.158623 TGTGCCATGTTCAGGAACTCTT 60.159 45.455 12.86 0.00 41.67 2.85
4326 5512 2.887152 GTGCCATGTTCAGGAACTCTTT 59.113 45.455 12.86 0.00 41.67 2.52
4335 5521 3.169099 TCAGGAACTCTTTCTAGCTGCT 58.831 45.455 7.57 7.57 34.60 4.24
4350 5536 0.609957 CTGCTCAGCCCAATTGACCA 60.610 55.000 7.12 0.00 0.00 4.02
4358 5544 2.305635 AGCCCAATTGACCATTTTTCCC 59.694 45.455 7.12 0.00 0.00 3.97
4360 5546 3.497584 GCCCAATTGACCATTTTTCCCAA 60.498 43.478 7.12 0.00 0.00 4.12
4361 5547 4.325972 CCCAATTGACCATTTTTCCCAAG 58.674 43.478 7.12 0.00 0.00 3.61
4362 5548 4.041444 CCCAATTGACCATTTTTCCCAAGA 59.959 41.667 7.12 0.00 0.00 3.02
4363 5549 5.280624 CCCAATTGACCATTTTTCCCAAGAT 60.281 40.000 7.12 0.00 0.00 2.40
4365 5551 5.682234 ATTGACCATTTTTCCCAAGATCC 57.318 39.130 0.00 0.00 0.00 3.36
4366 5552 4.402616 TGACCATTTTTCCCAAGATCCT 57.597 40.909 0.00 0.00 0.00 3.24
4367 5553 5.528600 TGACCATTTTTCCCAAGATCCTA 57.471 39.130 0.00 0.00 0.00 2.94
4370 5556 6.607198 TGACCATTTTTCCCAAGATCCTATTC 59.393 38.462 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.817809 ATAGCGTATTTTTCTCTCATTAGAACA 57.182 29.630 0.00 0.00 35.25 3.18
2 3 8.765219 GCATAGCGTATTTTTCTCTCATTAGAA 58.235 33.333 0.00 0.00 33.69 2.10
3 4 8.299262 GCATAGCGTATTTTTCTCTCATTAGA 57.701 34.615 0.00 0.00 0.00 2.10
21 22 1.603802 ATCCATTGGAAACGCATAGCG 59.396 47.619 9.98 10.11 46.74 4.26
22 23 3.004024 CATCCATTGGAAACGCATAGC 57.996 47.619 9.98 0.00 34.34 2.97
34 35 6.576662 AGTAGTATCGTACTCCATCCATTG 57.423 41.667 1.69 0.00 40.14 2.82
35 36 6.821031 GAGTAGTATCGTACTCCATCCATT 57.179 41.667 0.34 0.00 42.16 3.16
45 46 9.086336 GTGGAGTATGATAGAGTAGTATCGTAC 57.914 40.741 12.42 12.42 44.97 3.67
46 47 9.033711 AGTGGAGTATGATAGAGTAGTATCGTA 57.966 37.037 0.00 0.00 32.79 3.43
47 48 7.909518 AGTGGAGTATGATAGAGTAGTATCGT 58.090 38.462 0.00 0.00 32.79 3.73
48 49 8.035984 TGAGTGGAGTATGATAGAGTAGTATCG 58.964 40.741 0.00 0.00 32.79 2.92
49 50 9.899661 ATGAGTGGAGTATGATAGAGTAGTATC 57.100 37.037 0.00 0.00 0.00 2.24
50 51 9.899661 GATGAGTGGAGTATGATAGAGTAGTAT 57.100 37.037 0.00 0.00 0.00 2.12
51 52 8.881262 TGATGAGTGGAGTATGATAGAGTAGTA 58.119 37.037 0.00 0.00 0.00 1.82
52 53 7.750655 TGATGAGTGGAGTATGATAGAGTAGT 58.249 38.462 0.00 0.00 0.00 2.73
53 54 8.628630 TTGATGAGTGGAGTATGATAGAGTAG 57.371 38.462 0.00 0.00 0.00 2.57
54 55 9.593565 AATTGATGAGTGGAGTATGATAGAGTA 57.406 33.333 0.00 0.00 0.00 2.59
55 56 8.366401 CAATTGATGAGTGGAGTATGATAGAGT 58.634 37.037 0.00 0.00 0.00 3.24
56 57 8.366401 ACAATTGATGAGTGGAGTATGATAGAG 58.634 37.037 13.59 0.00 0.00 2.43
57 58 8.255111 ACAATTGATGAGTGGAGTATGATAGA 57.745 34.615 13.59 0.00 0.00 1.98
58 59 9.636879 CTACAATTGATGAGTGGAGTATGATAG 57.363 37.037 13.59 0.00 29.57 2.08
59 60 8.588472 CCTACAATTGATGAGTGGAGTATGATA 58.412 37.037 13.59 0.00 32.28 2.15
60 61 7.290948 TCCTACAATTGATGAGTGGAGTATGAT 59.709 37.037 13.59 0.00 32.28 2.45
61 62 6.611236 TCCTACAATTGATGAGTGGAGTATGA 59.389 38.462 13.59 0.00 32.28 2.15
62 63 6.820335 TCCTACAATTGATGAGTGGAGTATG 58.180 40.000 13.59 0.00 32.28 2.39
63 64 6.613271 ACTCCTACAATTGATGAGTGGAGTAT 59.387 38.462 22.98 10.63 45.20 2.12
64 65 5.958380 ACTCCTACAATTGATGAGTGGAGTA 59.042 40.000 22.98 2.60 45.20 2.59
65 66 4.780021 ACTCCTACAATTGATGAGTGGAGT 59.220 41.667 20.41 20.65 43.88 3.85
66 67 5.350504 ACTCCTACAATTGATGAGTGGAG 57.649 43.478 20.41 20.22 42.77 3.86
67 68 5.128827 GGTACTCCTACAATTGATGAGTGGA 59.871 44.000 25.38 16.20 36.95 4.02
68 69 5.360591 GGTACTCCTACAATTGATGAGTGG 58.639 45.833 25.38 13.87 36.95 4.00
69 70 5.129485 AGGGTACTCCTACAATTGATGAGTG 59.871 44.000 25.38 11.80 45.98 3.51
70 71 5.281314 AGGGTACTCCTACAATTGATGAGT 58.719 41.667 22.80 22.80 45.98 3.41
71 72 5.878406 AGGGTACTCCTACAATTGATGAG 57.122 43.478 13.59 15.50 45.98 2.90
82 83 7.847848 ACCATTAGAAATTGTAGGGTACTCCTA 59.152 37.037 6.13 6.13 45.98 2.94
84 85 6.896883 ACCATTAGAAATTGTAGGGTACTCC 58.103 40.000 0.00 0.00 0.00 3.85
100 101 9.875691 GCATGTCATCATAGTTATACCATTAGA 57.124 33.333 0.00 0.00 32.47 2.10
101 102 9.657419 TGCATGTCATCATAGTTATACCATTAG 57.343 33.333 0.00 0.00 32.47 1.73
102 103 9.435688 GTGCATGTCATCATAGTTATACCATTA 57.564 33.333 0.00 0.00 32.47 1.90
103 104 8.159447 AGTGCATGTCATCATAGTTATACCATT 58.841 33.333 0.00 0.00 32.47 3.16
104 105 7.683578 AGTGCATGTCATCATAGTTATACCAT 58.316 34.615 0.00 0.00 32.47 3.55
105 106 7.066307 AGTGCATGTCATCATAGTTATACCA 57.934 36.000 0.00 0.00 32.47 3.25
106 107 9.658799 ATTAGTGCATGTCATCATAGTTATACC 57.341 33.333 0.00 0.00 32.47 2.73
115 116 8.905850 TGACAAAATATTAGTGCATGTCATCAT 58.094 29.630 9.32 0.00 40.31 2.45
116 117 8.278729 TGACAAAATATTAGTGCATGTCATCA 57.721 30.769 9.32 0.00 40.31 3.07
117 118 9.229784 CTTGACAAAATATTAGTGCATGTCATC 57.770 33.333 13.10 0.00 43.42 2.92
118 119 8.742777 ACTTGACAAAATATTAGTGCATGTCAT 58.257 29.630 13.10 0.00 43.42 3.06
119 120 8.109705 ACTTGACAAAATATTAGTGCATGTCA 57.890 30.769 9.32 9.32 42.60 3.58
133 134 9.883142 TTTCACCAAAGATTTACTTGACAAAAT 57.117 25.926 0.00 0.00 38.98 1.82
134 135 9.712305 TTTTCACCAAAGATTTACTTGACAAAA 57.288 25.926 0.00 0.00 38.98 2.44
135 136 9.883142 ATTTTCACCAAAGATTTACTTGACAAA 57.117 25.926 0.00 0.00 38.98 2.83
136 137 9.883142 AATTTTCACCAAAGATTTACTTGACAA 57.117 25.926 0.00 0.00 38.98 3.18
137 138 9.883142 AAATTTTCACCAAAGATTTACTTGACA 57.117 25.926 0.00 0.00 38.98 3.58
142 143 9.476202 GTGCTAAATTTTCACCAAAGATTTACT 57.524 29.630 0.00 0.00 0.00 2.24
143 144 9.255304 TGTGCTAAATTTTCACCAAAGATTTAC 57.745 29.630 15.96 0.00 0.00 2.01
144 145 9.823647 TTGTGCTAAATTTTCACCAAAGATTTA 57.176 25.926 15.96 0.00 0.00 1.40
145 146 8.729805 TTGTGCTAAATTTTCACCAAAGATTT 57.270 26.923 15.96 0.00 0.00 2.17
146 147 8.729805 TTTGTGCTAAATTTTCACCAAAGATT 57.270 26.923 15.96 0.00 0.00 2.40
147 148 8.907222 ATTTGTGCTAAATTTTCACCAAAGAT 57.093 26.923 15.96 5.30 0.00 2.40
148 149 8.729805 AATTTGTGCTAAATTTTCACCAAAGA 57.270 26.923 15.96 0.87 0.00 2.52
149 150 9.862585 GTAATTTGTGCTAAATTTTCACCAAAG 57.137 29.630 14.43 0.56 32.64 2.77
150 151 9.383519 TGTAATTTGTGCTAAATTTTCACCAAA 57.616 25.926 14.43 15.30 32.64 3.28
151 152 8.948631 TGTAATTTGTGCTAAATTTTCACCAA 57.051 26.923 14.43 13.02 32.64 3.67
152 153 8.948631 TTGTAATTTGTGCTAAATTTTCACCA 57.051 26.923 14.43 6.80 32.64 4.17
153 154 9.810231 CATTGTAATTTGTGCTAAATTTTCACC 57.190 29.630 14.43 5.18 32.64 4.02
172 173 9.444600 GTCCTGGTTTATTAGTCTTCATTGTAA 57.555 33.333 0.00 0.00 0.00 2.41
173 174 7.762615 CGTCCTGGTTTATTAGTCTTCATTGTA 59.237 37.037 0.00 0.00 0.00 2.41
174 175 6.594159 CGTCCTGGTTTATTAGTCTTCATTGT 59.406 38.462 0.00 0.00 0.00 2.71
175 176 6.037172 CCGTCCTGGTTTATTAGTCTTCATTG 59.963 42.308 0.00 0.00 0.00 2.82
176 177 6.070424 TCCGTCCTGGTTTATTAGTCTTCATT 60.070 38.462 0.00 0.00 39.52 2.57
177 178 5.424252 TCCGTCCTGGTTTATTAGTCTTCAT 59.576 40.000 0.00 0.00 39.52 2.57
178 179 4.773674 TCCGTCCTGGTTTATTAGTCTTCA 59.226 41.667 0.00 0.00 39.52 3.02
179 180 5.334724 TCCGTCCTGGTTTATTAGTCTTC 57.665 43.478 0.00 0.00 39.52 2.87
180 181 4.161754 CCTCCGTCCTGGTTTATTAGTCTT 59.838 45.833 0.00 0.00 39.52 3.01
181 182 3.705072 CCTCCGTCCTGGTTTATTAGTCT 59.295 47.826 0.00 0.00 39.52 3.24
182 183 3.450096 ACCTCCGTCCTGGTTTATTAGTC 59.550 47.826 0.00 0.00 39.52 2.59
183 184 3.447950 ACCTCCGTCCTGGTTTATTAGT 58.552 45.455 0.00 0.00 39.52 2.24
184 185 4.648307 ACTACCTCCGTCCTGGTTTATTAG 59.352 45.833 0.00 0.00 39.52 1.73
185 186 4.613437 ACTACCTCCGTCCTGGTTTATTA 58.387 43.478 0.00 0.00 39.52 0.98
186 187 3.447950 ACTACCTCCGTCCTGGTTTATT 58.552 45.455 0.00 0.00 39.52 1.40
187 188 3.111741 ACTACCTCCGTCCTGGTTTAT 57.888 47.619 0.00 0.00 39.52 1.40
188 189 2.610438 ACTACCTCCGTCCTGGTTTA 57.390 50.000 0.00 0.00 39.52 2.01
189 190 2.454538 CTACTACCTCCGTCCTGGTTT 58.545 52.381 0.00 0.00 39.52 3.27
190 191 1.959028 GCTACTACCTCCGTCCTGGTT 60.959 57.143 0.00 0.00 39.52 3.67
191 192 0.395448 GCTACTACCTCCGTCCTGGT 60.395 60.000 0.00 0.00 39.52 4.00
192 193 0.395311 TGCTACTACCTCCGTCCTGG 60.395 60.000 0.00 0.00 40.09 4.45
193 194 1.471119 TTGCTACTACCTCCGTCCTG 58.529 55.000 0.00 0.00 0.00 3.86
194 195 2.456073 ATTGCTACTACCTCCGTCCT 57.544 50.000 0.00 0.00 0.00 3.85
195 196 4.868314 ATTATTGCTACTACCTCCGTCC 57.132 45.455 0.00 0.00 0.00 4.79
196 197 6.206243 TCAGTATTATTGCTACTACCTCCGTC 59.794 42.308 0.00 0.00 0.00 4.79
197 198 6.066690 TCAGTATTATTGCTACTACCTCCGT 58.933 40.000 0.00 0.00 0.00 4.69
198 199 6.207025 ACTCAGTATTATTGCTACTACCTCCG 59.793 42.308 0.00 0.00 0.00 4.63
199 200 7.527568 ACTCAGTATTATTGCTACTACCTCC 57.472 40.000 0.00 0.00 0.00 4.30
200 201 9.287373 AGTACTCAGTATTATTGCTACTACCTC 57.713 37.037 0.00 0.00 0.00 3.85
201 202 9.069082 CAGTACTCAGTATTATTGCTACTACCT 57.931 37.037 0.00 0.00 0.00 3.08
202 203 7.808856 GCAGTACTCAGTATTATTGCTACTACC 59.191 40.741 0.00 0.00 0.00 3.18
203 204 8.569641 AGCAGTACTCAGTATTATTGCTACTAC 58.430 37.037 11.95 0.00 0.00 2.73
204 205 8.568794 CAGCAGTACTCAGTATTATTGCTACTA 58.431 37.037 12.78 0.00 0.00 1.82
205 206 7.429633 CAGCAGTACTCAGTATTATTGCTACT 58.570 38.462 12.78 0.00 0.00 2.57
240 241 6.570672 AGCCATCATATTAATTGTGCTCAG 57.429 37.500 0.00 0.00 0.00 3.35
246 247 6.486657 ACGTTGCTAGCCATCATATTAATTGT 59.513 34.615 13.29 0.00 0.00 2.71
247 248 6.902341 ACGTTGCTAGCCATCATATTAATTG 58.098 36.000 13.29 0.00 0.00 2.32
248 249 7.119262 GGTACGTTGCTAGCCATCATATTAATT 59.881 37.037 13.29 0.00 0.00 1.40
255 256 2.240493 GGTACGTTGCTAGCCATCAT 57.760 50.000 13.29 0.00 0.00 2.45
274 276 3.445805 ACAGGGTTATTATTGGGTTTGCG 59.554 43.478 0.00 0.00 0.00 4.85
279 281 7.619512 TTTTCAAACAGGGTTATTATTGGGT 57.380 32.000 0.00 0.00 0.00 4.51
333 335 2.830104 TCATCAGAGGAATCACATGCG 58.170 47.619 0.00 0.00 0.00 4.73
349 351 3.356529 AACAAGGACCCAGTGATCATC 57.643 47.619 0.00 0.00 0.00 2.92
392 394 0.390340 TGAGGCACTTAAGAGCGCAG 60.390 55.000 17.08 0.00 41.55 5.18
400 402 5.944007 GGGAGTCTTAATTTGAGGCACTTAA 59.056 40.000 0.00 0.00 41.55 1.85
401 403 5.497474 GGGAGTCTTAATTTGAGGCACTTA 58.503 41.667 0.00 0.00 41.55 2.24
455 460 1.607801 GGGTGGCCCATCTTTTGCTC 61.608 60.000 0.00 0.00 44.65 4.26
468 473 2.822701 GAAATCGGACGGGGTGGC 60.823 66.667 0.00 0.00 0.00 5.01
469 474 0.466543 TATGAAATCGGACGGGGTGG 59.533 55.000 0.00 0.00 0.00 4.61
471 476 4.285003 TCATTATATGAAATCGGACGGGGT 59.715 41.667 0.00 0.00 36.11 4.95
472 477 4.827692 TCATTATATGAAATCGGACGGGG 58.172 43.478 0.00 0.00 36.11 5.73
498 504 1.677052 GTTTGGCAGTTGAACCGGTTA 59.323 47.619 22.33 1.82 0.00 2.85
502 508 1.135257 TGTTGTTTGGCAGTTGAACCG 60.135 47.619 0.00 0.00 0.00 4.44
526 533 4.362279 CCATCAAGGTGTTTTGTCTTGTG 58.638 43.478 0.00 0.00 38.99 3.33
992 1001 4.756642 TCAGTGTGTCAACCATCTTGATTC 59.243 41.667 0.00 0.00 0.00 2.52
1026 1035 8.272545 TCTTGTTCTTGAAGTATCCAATGATG 57.727 34.615 0.00 0.00 32.18 3.07
1180 1201 4.439968 TCATTAAGAGATGAGCACAGCAG 58.560 43.478 1.47 0.00 34.60 4.24
1195 1274 6.347725 GCACACCAACAGTAGAACTCATTAAG 60.348 42.308 0.00 0.00 0.00 1.85
1201 1280 1.792949 CGCACACCAACAGTAGAACTC 59.207 52.381 0.00 0.00 0.00 3.01
1313 1392 0.036010 CAGTCTCCACCCGATGCTTT 60.036 55.000 0.00 0.00 0.00 3.51
1377 1456 6.487331 GGATCAAAAGAATCATGAGATGAGCT 59.513 38.462 0.09 0.00 43.53 4.09
1382 1467 7.417570 GCAAAGGGATCAAAAGAATCATGAGAT 60.418 37.037 0.09 0.00 35.53 2.75
1383 1468 6.127535 GCAAAGGGATCAAAAGAATCATGAGA 60.128 38.462 0.09 0.00 0.00 3.27
1384 1469 6.040878 GCAAAGGGATCAAAAGAATCATGAG 58.959 40.000 0.09 0.00 0.00 2.90
1410 1495 3.935203 AGATTATTCAGCACCAACACTCG 59.065 43.478 0.00 0.00 0.00 4.18
1431 1516 3.012518 CACCTGGGCACATAGAAAAGAG 58.987 50.000 0.00 0.00 0.00 2.85
1498 1613 5.261040 TCCCAGATGAAAGATTGAAACCT 57.739 39.130 0.00 0.00 0.00 3.50
1518 1633 1.405463 GCCAATGGGACGATCTTTTCC 59.595 52.381 0.00 0.00 35.59 3.13
1700 1815 5.592282 CCTACTCTCAAGTTCTCTGCTGATA 59.408 44.000 0.00 0.00 36.92 2.15
1716 1831 1.548269 ACTCTTGCTGCACCTACTCTC 59.452 52.381 0.00 0.00 0.00 3.20
1717 1832 1.638529 ACTCTTGCTGCACCTACTCT 58.361 50.000 0.00 0.00 0.00 3.24
1741 1856 4.580580 ACTGTTTTTCAGAGACCATTCACC 59.419 41.667 1.79 0.00 46.27 4.02
1754 2413 2.590073 CACGCACACAACTGTTTTTCA 58.410 42.857 0.00 0.00 0.00 2.69
1758 2417 0.179166 CTGCACGCACACAACTGTTT 60.179 50.000 0.00 0.00 0.00 2.83
1763 2422 0.110238 CATACCTGCACGCACACAAC 60.110 55.000 0.00 0.00 0.00 3.32
1910 2587 6.491714 AGCATCCAAGTTCATACTCATAGT 57.508 37.500 0.00 0.00 31.99 2.12
1911 2588 7.255035 CCAAAGCATCCAAGTTCATACTCATAG 60.255 40.741 0.00 0.00 31.99 2.23
1917 2594 3.193267 TGCCAAAGCATCCAAGTTCATAC 59.807 43.478 0.00 0.00 46.52 2.39
1944 2628 8.721133 ACTTTAATTAACATCCAAGAACCCTT 57.279 30.769 0.00 0.00 0.00 3.95
1946 2630 9.016438 TGTACTTTAATTAACATCCAAGAACCC 57.984 33.333 0.00 0.00 0.00 4.11
1947 2631 9.836076 GTGTACTTTAATTAACATCCAAGAACC 57.164 33.333 0.00 0.00 0.00 3.62
2006 2690 1.402968 GCTGCACCAACTCATGTATGG 59.597 52.381 11.07 11.07 40.16 2.74
2235 2919 0.109723 ACGTATGTGTTTGGCCACCT 59.890 50.000 3.88 0.00 34.35 4.00
2285 2969 0.956633 CATCACACTGCAACTGGCTT 59.043 50.000 0.00 0.00 45.15 4.35
2286 2970 0.179009 ACATCACACTGCAACTGGCT 60.179 50.000 0.00 0.00 45.15 4.75
2339 3023 0.106149 GTGGGTCGTTCTGGACACTT 59.894 55.000 0.00 0.00 41.02 3.16
2574 3286 6.169800 TCTTAACTGCATGCATAGTACAACA 58.830 36.000 22.97 0.20 0.00 3.33
2615 3335 5.482878 AGGAATTCCTAGACTAACGACCAAA 59.517 40.000 25.99 0.00 46.48 3.28
2661 3386 8.288689 TGCTTTATAATCTTAAGTGGGGAAAC 57.711 34.615 1.63 0.00 0.00 2.78
2662 3387 8.745590 GTTGCTTTATAATCTTAAGTGGGGAAA 58.254 33.333 1.63 0.00 0.00 3.13
2663 3388 7.891183 TGTTGCTTTATAATCTTAAGTGGGGAA 59.109 33.333 1.63 0.00 0.00 3.97
2664 3389 7.406916 TGTTGCTTTATAATCTTAAGTGGGGA 58.593 34.615 1.63 0.00 0.00 4.81
2665 3390 7.639113 TGTTGCTTTATAATCTTAAGTGGGG 57.361 36.000 1.63 0.00 0.00 4.96
2674 3399 9.559958 CGACTTTGAAATGTTGCTTTATAATCT 57.440 29.630 0.00 0.00 0.00 2.40
2675 3400 8.798153 CCGACTTTGAAATGTTGCTTTATAATC 58.202 33.333 0.00 0.00 0.00 1.75
2676 3401 8.303876 ACCGACTTTGAAATGTTGCTTTATAAT 58.696 29.630 0.00 0.00 0.00 1.28
2677 3402 7.593273 CACCGACTTTGAAATGTTGCTTTATAA 59.407 33.333 0.00 0.00 0.00 0.98
2678 3403 7.081349 CACCGACTTTGAAATGTTGCTTTATA 58.919 34.615 0.00 0.00 0.00 0.98
2679 3404 5.920273 CACCGACTTTGAAATGTTGCTTTAT 59.080 36.000 0.00 0.00 0.00 1.40
2680 3405 5.277825 CACCGACTTTGAAATGTTGCTTTA 58.722 37.500 0.00 0.00 0.00 1.85
2681 3406 4.111916 CACCGACTTTGAAATGTTGCTTT 58.888 39.130 0.00 0.00 0.00 3.51
2682 3407 3.490761 CCACCGACTTTGAAATGTTGCTT 60.491 43.478 0.00 0.00 0.00 3.91
2683 3408 2.034558 CCACCGACTTTGAAATGTTGCT 59.965 45.455 0.00 0.00 0.00 3.91
2684 3409 2.223711 ACCACCGACTTTGAAATGTTGC 60.224 45.455 0.00 0.00 0.00 4.17
2685 3410 3.066064 TCACCACCGACTTTGAAATGTTG 59.934 43.478 0.00 0.00 0.00 3.33
2686 3411 3.283751 TCACCACCGACTTTGAAATGTT 58.716 40.909 0.00 0.00 0.00 2.71
2687 3412 2.878406 CTCACCACCGACTTTGAAATGT 59.122 45.455 0.00 0.00 0.00 2.71
2696 3421 0.320771 GATTGCACTCACCACCGACT 60.321 55.000 0.00 0.00 0.00 4.18
2698 3423 0.324614 ATGATTGCACTCACCACCGA 59.675 50.000 9.14 0.00 0.00 4.69
2708 3433 2.837532 ACCCAACCAAATGATTGCAC 57.162 45.000 0.00 0.00 35.10 4.57
2716 3441 4.161377 GCACCAATGTATACCCAACCAAAT 59.839 41.667 0.00 0.00 0.00 2.32
2731 3456 2.777972 CCCGGCATCTGCACCAATG 61.778 63.158 0.00 0.00 44.36 2.82
2732 3457 2.440796 CCCGGCATCTGCACCAAT 60.441 61.111 0.00 0.00 44.36 3.16
2777 3502 0.962356 AGCTGTGTGCCACTATTGCC 60.962 55.000 0.00 0.00 44.23 4.52
2780 3505 0.321671 ACGAGCTGTGTGCCACTATT 59.678 50.000 0.00 0.00 44.23 1.73
2783 3508 2.029666 GACGAGCTGTGTGCCACT 59.970 61.111 0.00 0.00 44.23 4.00
3144 3873 3.689161 CGCCATCAAGAAGATACAAACCA 59.311 43.478 0.00 0.00 34.43 3.67
3147 3876 2.351418 CGCGCCATCAAGAAGATACAAA 59.649 45.455 0.00 0.00 34.43 2.83
3246 4013 2.594303 CACCCCTTGAACAGCGCA 60.594 61.111 11.47 0.00 0.00 6.09
3318 4085 2.418197 CGGGTCGAAATTGAAGAGGCTA 60.418 50.000 0.00 0.00 0.00 3.93
3351 4118 3.087031 CCTGTAGAAGTACTCGTCCCAA 58.913 50.000 0.00 0.00 0.00 4.12
3360 4127 3.132467 GGATGTGGACCCTGTAGAAGTAC 59.868 52.174 0.00 0.00 0.00 2.73
3419 4186 1.154225 CGCCTGAATTTCGGTGCAC 60.154 57.895 8.80 8.80 0.00 4.57
3465 4233 7.310609 CCAATTTGGGAGGACATTTCTTACAAT 60.311 37.037 7.60 0.00 32.67 2.71
3608 4377 7.886629 AGCAATACAATACATGAACCAGAAT 57.113 32.000 0.00 0.00 0.00 2.40
3657 4426 7.581213 ATGTGACTGAACAAGAAATTGGTAA 57.419 32.000 0.00 0.00 32.81 2.85
3660 4429 7.031372 CCATATGTGACTGAACAAGAAATTGG 58.969 38.462 1.24 0.00 32.81 3.16
3684 4453 5.186198 ACAATCAATGCTAGTCAAGGTACC 58.814 41.667 2.73 2.73 0.00 3.34
3720 4492 9.770097 TGGAGCACTATATTTATTTCTCTTGAG 57.230 33.333 0.00 0.00 0.00 3.02
3771 4543 0.165511 GCACTGAGAAGCGCTTGAAG 59.834 55.000 30.47 22.38 0.00 3.02
3789 4561 6.833342 AATCGATTGCCTTATTCATTTTGC 57.167 33.333 10.50 0.00 0.00 3.68
3795 4567 9.337396 ACAACTATTAATCGATTGCCTTATTCA 57.663 29.630 20.87 0.00 0.00 2.57
4011 5188 9.878599 CAACTTTGATTAGTACACTTTTACTGG 57.121 33.333 0.00 0.00 34.10 4.00
4019 5196 6.509656 TCGTGTCAACTTTGATTAGTACACT 58.490 36.000 0.00 0.00 39.73 3.55
4021 5198 7.956420 ATTCGTGTCAACTTTGATTAGTACA 57.044 32.000 0.00 0.00 39.73 2.90
4160 5338 4.581868 TCTGTTGATGATGCTGATGACAA 58.418 39.130 0.00 0.00 0.00 3.18
4310 5496 5.486526 CAGCTAGAAAGAGTTCCTGAACAT 58.513 41.667 12.21 0.00 43.47 2.71
4335 5521 3.007831 GGAAAAATGGTCAATTGGGCTGA 59.992 43.478 5.42 0.00 0.00 4.26
4340 5526 5.226194 TCTTGGGAAAAATGGTCAATTGG 57.774 39.130 5.42 0.00 0.00 3.16
4341 5527 5.876460 GGATCTTGGGAAAAATGGTCAATTG 59.124 40.000 0.00 0.00 0.00 2.32
4342 5528 5.786975 AGGATCTTGGGAAAAATGGTCAATT 59.213 36.000 0.00 0.00 0.00 2.32
4344 5530 4.750941 AGGATCTTGGGAAAAATGGTCAA 58.249 39.130 0.00 0.00 0.00 3.18
4350 5536 6.491403 CCATCGAATAGGATCTTGGGAAAAAT 59.509 38.462 0.00 0.00 0.00 1.82
4358 5544 7.710907 TCTTGTTTACCATCGAATAGGATCTTG 59.289 37.037 8.68 0.00 0.00 3.02
4360 5546 7.287927 TCTCTTGTTTACCATCGAATAGGATCT 59.712 37.037 8.68 0.00 0.00 2.75
4361 5547 7.434492 TCTCTTGTTTACCATCGAATAGGATC 58.566 38.462 8.68 0.00 0.00 3.36
4362 5548 7.361457 TCTCTTGTTTACCATCGAATAGGAT 57.639 36.000 8.68 0.00 0.00 3.24
4363 5549 6.785337 TCTCTTGTTTACCATCGAATAGGA 57.215 37.500 8.68 0.00 0.00 2.94
4365 5551 7.852945 GCAATTCTCTTGTTTACCATCGAATAG 59.147 37.037 0.00 0.00 0.00 1.73
4366 5552 7.335673 TGCAATTCTCTTGTTTACCATCGAATA 59.664 33.333 0.00 0.00 0.00 1.75
4367 5553 6.150976 TGCAATTCTCTTGTTTACCATCGAAT 59.849 34.615 0.00 0.00 0.00 3.34
4370 5556 5.088739 GTGCAATTCTCTTGTTTACCATCG 58.911 41.667 0.00 0.00 0.00 3.84


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

AutoCloner maintained by Alex Coulton.