Multiple sequence alignment - TraesCS4B01G258700

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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 TraesCS4B01G258700 chr4B 100.000 5683 0 0 1 5683 525272268 525266586 0.000000e+00 10495.0
1 TraesCS4B01G258700 chr4B 97.395 3531 20 13 1563 5025 525302208 525305734 0.000000e+00 5945.0
2 TraesCS4B01G258700 chr4B 96.267 3509 37 20 1605 5025 525392442 525388940 0.000000e+00 5668.0
3 TraesCS4B01G258700 chr4B 94.409 1574 40 14 1 1529 525300637 525302207 0.000000e+00 2375.0
4 TraesCS4B01G258700 chr4B 94.193 1257 28 15 1 1237 525394320 525393089 0.000000e+00 1875.0
5 TraesCS4B01G258700 chr4B 97.354 378 9 1 1236 1612 525393007 525392630 4.800000e-180 641.0
6 TraesCS4B01G258700 chr4B 91.304 414 17 2 5289 5683 525388938 525388525 1.080000e-151 547.0
7 TraesCS4B01G258700 chr4B 91.316 380 15 2 5322 5683 525305749 525306128 2.360000e-138 503.0
8 TraesCS4B01G258700 chr4B 98.864 264 3 0 5025 5288 209151035 209151298 6.660000e-129 472.0
9 TraesCS4B01G258700 chr4B 94.783 115 6 0 3793 3907 525268176 525268290 4.520000e-41 180.0
10 TraesCS4B01G258700 chr4B 93.913 115 7 0 3793 3907 525304753 525304639 2.100000e-39 174.0
11 TraesCS4B01G258700 chr4B 93.913 115 7 0 3793 3907 525389930 525390044 2.100000e-39 174.0
12 TraesCS4B01G258700 chr4B 93.750 112 7 0 5289 5400 525389007 525388896 9.790000e-38 169.0
13 TraesCS4B01G258700 chr4B 96.078 51 2 0 4677 4727 525267541 525267491 3.650000e-12 84.2
14 TraesCS4B01G258700 chr4B 96.078 51 2 0 4728 4778 525267592 525267542 3.650000e-12 84.2
15 TraesCS4B01G258700 chr4B 96.078 51 2 0 4728 4778 525305386 525305436 3.650000e-12 84.2
16 TraesCS4B01G258700 chr4B 94.118 51 3 0 4677 4727 525305437 525305487 1.700000e-10 78.7
17 TraesCS4B01G258700 chr4B 94.118 51 3 0 4677 4727 525389249 525389199 1.700000e-10 78.7
18 TraesCS4B01G258700 chr2A 86.398 2132 200 44 1639 3704 695299648 695301755 0.000000e+00 2248.0
19 TraesCS4B01G258700 chr2A 99.242 264 2 0 5025 5288 563291223 563290960 1.430000e-130 477.0
20 TraesCS4B01G258700 chr2A 84.807 362 44 10 4324 4683 695305475 695305827 2.520000e-93 353.0
21 TraesCS4B01G258700 chr2A 83.628 226 21 6 952 1164 695299321 695299543 1.250000e-46 198.0
22 TraesCS4B01G258700 chr2A 90.909 66 5 1 188 253 778068390 778068326 2.820000e-13 87.9
23 TraesCS4B01G258700 chr2A 89.231 65 7 0 190 254 773068548 773068612 1.310000e-11 82.4
24 TraesCS4B01G258700 chr2A 88.235 68 7 1 189 255 374084122 374084189 4.720000e-11 80.5
25 TraesCS4B01G258700 chr2D 85.187 2059 208 44 1708 3705 555908422 555910444 0.000000e+00 2023.0
26 TraesCS4B01G258700 chr2D 85.965 399 49 5 4290 4683 555911114 555911510 2.450000e-113 420.0
27 TraesCS4B01G258700 chr2D 86.755 302 11 10 5411 5683 26447301 26447602 5.530000e-80 309.0
28 TraesCS4B01G258700 chr2D 90.547 201 17 2 3907 4106 325325588 325325389 1.210000e-66 265.0
29 TraesCS4B01G258700 chr2D 85.714 266 20 2 5436 5683 562463781 562464046 1.210000e-66 265.0
30 TraesCS4B01G258700 chr2D 83.113 302 20 19 5412 5683 114668393 114668093 4.400000e-61 246.0
31 TraesCS4B01G258700 chr2D 93.043 115 8 0 3792 3906 26528254 26528368 9.790000e-38 169.0
32 TraesCS4B01G258700 chr2D 80.282 142 13 8 168 294 14459695 14459554 6.060000e-15 93.5
33 TraesCS4B01G258700 chr2D 94.595 37 2 0 258 294 607998639 607998675 2.210000e-04 58.4
34 TraesCS4B01G258700 chr2B 87.560 1680 161 27 1639 3281 662680522 662682190 0.000000e+00 1901.0
35 TraesCS4B01G258700 chr2B 89.820 334 34 0 3371 3704 662682239 662682572 4.070000e-116 429.0
36 TraesCS4B01G258700 chr2B 81.481 216 13 12 4091 4283 662682696 662682907 9.860000e-33 152.0
37 TraesCS4B01G258700 chr7B 99.242 264 2 0 5025 5288 743064875 743064612 1.430000e-130 477.0
38 TraesCS4B01G258700 chr7A 99.242 264 2 0 5025 5288 120830278 120830541 1.430000e-130 477.0
39 TraesCS4B01G258700 chr7A 99.242 264 2 0 5025 5288 672003744 672003481 1.430000e-130 477.0
40 TraesCS4B01G258700 chr7A 91.371 197 16 1 3898 4093 293302436 293302632 9.390000e-68 268.0
41 TraesCS4B01G258700 chr7A 92.174 115 9 0 3793 3907 251840838 251840724 4.560000e-36 163.0
42 TraesCS4B01G258700 chr7A 90.123 81 8 0 175 255 11577409 11577329 7.790000e-19 106.0
43 TraesCS4B01G258700 chr7A 76.056 142 17 8 179 304 29056345 29056485 2.210000e-04 58.4
44 TraesCS4B01G258700 chr5A 99.242 264 2 0 5025 5288 300047136 300046873 1.430000e-130 477.0
45 TraesCS4B01G258700 chr5A 86.379 301 12 12 5412 5683 573662629 573662329 9.250000e-78 302.0
46 TraesCS4B01G258700 chr5A 86.517 267 17 8 5436 5683 524633033 524632767 5.610000e-70 276.0
47 TraesCS4B01G258700 chr5A 84.244 311 18 15 5403 5683 673402125 673401816 2.020000e-69 274.0
48 TraesCS4B01G258700 chr4A 99.242 264 2 0 5025 5288 73804863 73805126 1.430000e-130 477.0
49 TraesCS4B01G258700 chr4A 91.534 189 15 1 3907 4094 89430988 89430800 5.650000e-65 259.0
50 TraesCS4B01G258700 chr4A 91.176 68 6 0 188 255 622973183 622973250 6.060000e-15 93.5
51 TraesCS4B01G258700 chr4A 88.235 68 8 0 188 255 568376122 568376055 1.310000e-11 82.4
52 TraesCS4B01G258700 chr4A 100.000 34 0 0 260 293 639375558 639375591 4.750000e-06 63.9
53 TraesCS4B01G258700 chr1B 98.864 264 3 0 5025 5288 338927011 338926748 6.660000e-129 472.0
54 TraesCS4B01G258700 chr1B 98.864 264 3 0 5025 5288 461450792 461450529 6.660000e-129 472.0
55 TraesCS4B01G258700 chr5D 88.312 308 36 0 4376 4683 472384556 472384863 2.500000e-98 370.0
56 TraesCS4B01G258700 chr5D 86.333 300 12 13 5413 5683 363005420 363005719 3.330000e-77 300.0
57 TraesCS4B01G258700 chr5D 87.640 267 14 3 5436 5683 320660573 320660839 5.570000e-75 292.0
58 TraesCS4B01G258700 chr5D 85.424 295 22 6 5410 5683 350369590 350369296 2.590000e-73 287.0
59 TraesCS4B01G258700 chr5D 84.488 303 17 14 5410 5683 530733134 530733435 7.260000e-69 272.0
60 TraesCS4B01G258700 chr3D 88.015 267 13 9 5436 5683 68839754 68840020 1.200000e-76 298.0
61 TraesCS4B01G258700 chr3D 87.594 266 14 9 5436 5683 380493501 380493765 2.000000e-74 291.0
62 TraesCS4B01G258700 chr3D 85.149 303 16 9 5410 5683 579163245 579163547 3.350000e-72 283.0
63 TraesCS4B01G258700 chr3D 88.945 199 20 2 3898 4094 124059579 124059381 1.580000e-60 244.0
64 TraesCS4B01G258700 chr3D 84.259 108 15 1 148 255 604601320 604601215 2.800000e-18 104.0
65 TraesCS4B01G258700 chr1D 86.093 302 13 13 5410 5682 377957580 377957881 1.200000e-76 298.0
66 TraesCS4B01G258700 chr1D 85.479 303 15 10 5410 5683 447756394 447756092 7.200000e-74 289.0
67 TraesCS4B01G258700 chr1D 89.744 195 17 2 3904 4097 486144675 486144867 4.400000e-61 246.0
68 TraesCS4B01G258700 chr7D 85.099 302 16 13 5411 5683 604446403 604446704 1.210000e-71 281.0
69 TraesCS4B01G258700 chr7D 79.487 117 8 5 192 293 65725386 65725501 1.020000e-07 69.4
70 TraesCS4B01G258700 chr1A 86.142 267 18 6 5436 5683 522238395 522238129 2.610000e-68 270.0
71 TraesCS4B01G258700 chr6D 90.909 187 16 1 3913 4098 464536720 464536534 3.400000e-62 250.0
72 TraesCS4B01G258700 chr6D 91.057 123 9 1 3785 3907 418956981 418957101 1.270000e-36 165.0
73 TraesCS4B01G258700 chr4D 88.350 206 20 4 3898 4101 375175232 375175029 1.580000e-60 244.0
74 TraesCS4B01G258700 chr6A 93.966 116 6 1 3793 3907 596548467 596548582 2.100000e-39 174.0
75 TraesCS4B01G258700 chr6A 97.222 36 1 0 260 295 21763107 21763142 1.710000e-05 62.1
76 TraesCS4B01G258700 chr3A 93.333 45 2 1 1777 1821 693109809 693109852 1.320000e-06 65.8
77 TraesCS4B01G258700 chr5B 97.297 37 1 0 258 294 75901983 75902019 4.750000e-06 63.9


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 TraesCS4B01G258700 chr4B 525266586 525272268 5682 True 10495.000000 10495 100.000000 1 5683 1 chr4B.!!$R1 5682
1 TraesCS4B01G258700 chr4B 525300637 525306128 5491 False 1797.180000 5945 94.663200 1 5683 5 chr4B.!!$F4 5682
2 TraesCS4B01G258700 chr4B 525388525 525394320 5795 True 1496.450000 5668 94.497667 1 5683 6 chr4B.!!$R4 5682
3 TraesCS4B01G258700 chr2A 695299321 695305827 6506 False 933.000000 2248 84.944333 952 4683 3 chr2A.!!$F3 3731
4 TraesCS4B01G258700 chr2D 555908422 555911510 3088 False 1221.500000 2023 85.576000 1708 4683 2 chr2D.!!$F5 2975
5 TraesCS4B01G258700 chr2B 662680522 662682907 2385 False 827.333333 1901 86.287000 1639 4283 3 chr2B.!!$F1 2644

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
521 543 0.254178 GCACTCCATCACCACTCCAT 59.746 55.000 0.00 0.00 0.0 3.41 F
1311 1433 0.109723 TCCACAGAAAACGGAAGGGG 59.890 55.000 0.00 0.00 0.0 4.79 F
1350 1472 2.590092 GCAGTAATGGAGGGCGGT 59.410 61.111 0.00 0.00 0.0 5.68 F
3057 3468 0.470766 ACTACTTCCCAACCGTTGCA 59.529 50.000 5.68 0.00 0.0 4.08 F
3879 4410 3.898627 AACGAGACTGACTGCGGCG 62.899 63.158 0.51 0.51 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1459 0.692756 TCATCCACCGCCCTCCATTA 60.693 55.0 0.00 0.00 0.00 1.90 R
3057 3468 0.685097 ACACAGGTATCGCAACTGGT 59.315 50.0 6.81 0.25 36.57 4.00 R
3145 3556 0.909610 CTGGGTGGGTCTCCAAGCTA 60.910 60.0 0.00 0.00 46.04 3.32 R
4460 8736 0.029567 CGTAGACTCCGGTCATCTGC 59.970 60.0 0.00 5.90 44.36 4.26 R
5286 9574 0.179076 CAGCATGACCCATCGCAGTA 60.179 55.0 0.00 0.00 39.69 2.74 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
140 141 1.082756 GTGCAGACTTTGTTCCGCG 60.083 57.895 0.00 0.00 0.00 6.46
255 256 5.367352 TGGATATAAAAGGGTGACGTATGGT 59.633 40.000 0.00 0.00 0.00 3.55
256 257 6.554228 TGGATATAAAAGGGTGACGTATGGTA 59.446 38.462 0.00 0.00 0.00 3.25
257 258 6.870439 GGATATAAAAGGGTGACGTATGGTAC 59.130 42.308 0.00 0.00 0.00 3.34
258 259 5.945144 ATAAAAGGGTGACGTATGGTACT 57.055 39.130 0.00 0.00 0.00 2.73
322 339 9.014297 CATCTTTTCACTAAATGGTACTTCCTT 57.986 33.333 0.00 0.00 37.07 3.36
329 346 8.149647 TCACTAAATGGTACTTCCTTCGTAAAA 58.850 33.333 0.00 0.00 37.07 1.52
381 402 7.658261 CATATAAGAGCGTATAAGAGCGTTTG 58.342 38.462 0.00 0.00 38.61 2.93
427 449 9.387397 TGAGTATGTTGTAATGATATCCCCTTA 57.613 33.333 0.00 0.00 0.00 2.69
518 540 2.846371 GTGCACTCCATCACCACTC 58.154 57.895 10.32 0.00 0.00 3.51
519 541 0.674895 GTGCACTCCATCACCACTCC 60.675 60.000 10.32 0.00 0.00 3.85
521 543 0.254178 GCACTCCATCACCACTCCAT 59.746 55.000 0.00 0.00 0.00 3.41
523 545 1.556451 CACTCCATCACCACTCCATCA 59.444 52.381 0.00 0.00 0.00 3.07
524 546 1.556911 ACTCCATCACCACTCCATCAC 59.443 52.381 0.00 0.00 0.00 3.06
525 547 0.911769 TCCATCACCACTCCATCACC 59.088 55.000 0.00 0.00 0.00 4.02
1311 1433 0.109723 TCCACAGAAAACGGAAGGGG 59.890 55.000 0.00 0.00 0.00 4.79
1337 1459 3.984732 GCCTTCCCTTGGGGCAGT 61.985 66.667 5.78 0.00 43.94 4.40
1350 1472 2.590092 GCAGTAATGGAGGGCGGT 59.410 61.111 0.00 0.00 0.00 5.68
3057 3468 0.470766 ACTACTTCCCAACCGTTGCA 59.529 50.000 5.68 0.00 0.00 4.08
3145 3556 7.563556 CCCAACCTTAATACCTTCATATTTGGT 59.436 37.037 0.00 0.00 34.45 3.67
3797 4328 5.356470 CCTAGTTACTGTTAAGCGGTACTCT 59.644 44.000 0.00 0.00 38.57 3.24
3879 4410 3.898627 AACGAGACTGACTGCGGCG 62.899 63.158 0.51 0.51 0.00 6.46
4328 4997 6.006449 AGAGGTGCTTTTATGAAACAGTGAT 58.994 36.000 0.00 0.00 0.00 3.06
4460 8736 6.262496 AGCCACATTATCATCTGAAGACATTG 59.738 38.462 0.00 0.00 0.00 2.82
4946 9234 0.896940 CTGTTGACCCATGCTTGCCT 60.897 55.000 0.00 0.00 0.00 4.75
5018 9306 1.686355 CGTCTGCCTCTCCTACTCAT 58.314 55.000 0.00 0.00 0.00 2.90
5025 9313 3.840666 TGCCTCTCCTACTCATTCACTTT 59.159 43.478 0.00 0.00 0.00 2.66
5026 9314 4.081420 TGCCTCTCCTACTCATTCACTTTC 60.081 45.833 0.00 0.00 0.00 2.62
5027 9315 4.081420 GCCTCTCCTACTCATTCACTTTCA 60.081 45.833 0.00 0.00 0.00 2.69
5028 9316 5.569630 GCCTCTCCTACTCATTCACTTTCAA 60.570 44.000 0.00 0.00 0.00 2.69
5029 9317 6.648192 CCTCTCCTACTCATTCACTTTCAAT 58.352 40.000 0.00 0.00 0.00 2.57
5030 9318 7.633772 GCCTCTCCTACTCATTCACTTTCAATA 60.634 40.741 0.00 0.00 0.00 1.90
5031 9319 8.428063 CCTCTCCTACTCATTCACTTTCAATAT 58.572 37.037 0.00 0.00 0.00 1.28
5032 9320 9.829507 CTCTCCTACTCATTCACTTTCAATATT 57.170 33.333 0.00 0.00 0.00 1.28
5033 9321 9.823647 TCTCCTACTCATTCACTTTCAATATTC 57.176 33.333 0.00 0.00 0.00 1.75
5034 9322 8.964476 TCCTACTCATTCACTTTCAATATTCC 57.036 34.615 0.00 0.00 0.00 3.01
5035 9323 8.548025 TCCTACTCATTCACTTTCAATATTCCA 58.452 33.333 0.00 0.00 0.00 3.53
5036 9324 8.834465 CCTACTCATTCACTTTCAATATTCCAG 58.166 37.037 0.00 0.00 0.00 3.86
5037 9325 9.388506 CTACTCATTCACTTTCAATATTCCAGT 57.611 33.333 0.00 0.00 0.00 4.00
5038 9326 8.273780 ACTCATTCACTTTCAATATTCCAGTC 57.726 34.615 0.00 0.00 0.00 3.51
5039 9327 7.884877 ACTCATTCACTTTCAATATTCCAGTCA 59.115 33.333 0.00 0.00 0.00 3.41
5040 9328 8.812513 TCATTCACTTTCAATATTCCAGTCAT 57.187 30.769 0.00 0.00 0.00 3.06
5041 9329 9.246670 TCATTCACTTTCAATATTCCAGTCATT 57.753 29.630 0.00 0.00 0.00 2.57
5042 9330 9.297586 CATTCACTTTCAATATTCCAGTCATTG 57.702 33.333 0.00 0.00 0.00 2.82
5043 9331 8.634335 TTCACTTTCAATATTCCAGTCATTGA 57.366 30.769 0.00 0.00 37.00 2.57
5044 9332 8.272545 TCACTTTCAATATTCCAGTCATTGAG 57.727 34.615 0.00 0.00 39.23 3.02
5045 9333 7.337689 TCACTTTCAATATTCCAGTCATTGAGG 59.662 37.037 0.00 0.00 39.23 3.86
5046 9334 7.337689 CACTTTCAATATTCCAGTCATTGAGGA 59.662 37.037 0.00 0.00 39.23 3.71
5047 9335 8.057623 ACTTTCAATATTCCAGTCATTGAGGAT 58.942 33.333 0.00 0.00 39.23 3.24
5048 9336 8.455903 TTTCAATATTCCAGTCATTGAGGATC 57.544 34.615 0.00 0.00 39.23 3.36
5049 9337 7.384524 TCAATATTCCAGTCATTGAGGATCT 57.615 36.000 0.00 0.00 34.58 2.75
5050 9338 8.496534 TCAATATTCCAGTCATTGAGGATCTA 57.503 34.615 0.00 0.00 34.58 1.98
5051 9339 9.109246 TCAATATTCCAGTCATTGAGGATCTAT 57.891 33.333 0.00 0.00 34.58 1.98
5052 9340 9.736414 CAATATTCCAGTCATTGAGGATCTATT 57.264 33.333 0.00 1.91 34.92 1.73
5055 9343 8.733092 ATTCCAGTCATTGAGGATCTATTAGA 57.267 34.615 0.00 0.00 34.92 2.10
5056 9344 8.733092 TTCCAGTCATTGAGGATCTATTAGAT 57.267 34.615 5.88 5.88 37.73 1.98
5057 9345 8.131847 TCCAGTCATTGAGGATCTATTAGATG 57.868 38.462 10.93 0.00 34.53 2.90
5058 9346 7.952368 TCCAGTCATTGAGGATCTATTAGATGA 59.048 37.037 10.93 0.00 34.53 2.92
5059 9347 8.252417 CCAGTCATTGAGGATCTATTAGATGAG 58.748 40.741 10.93 0.00 34.53 2.90
5060 9348 7.760794 CAGTCATTGAGGATCTATTAGATGAGC 59.239 40.741 10.93 0.00 34.53 4.26
5061 9349 7.675195 AGTCATTGAGGATCTATTAGATGAGCT 59.325 37.037 10.93 0.00 34.53 4.09
5062 9350 8.965819 GTCATTGAGGATCTATTAGATGAGCTA 58.034 37.037 10.93 0.00 34.53 3.32
5063 9351 8.965819 TCATTGAGGATCTATTAGATGAGCTAC 58.034 37.037 10.93 0.00 34.53 3.58
5064 9352 8.747471 CATTGAGGATCTATTAGATGAGCTACA 58.253 37.037 10.93 1.15 34.53 2.74
5065 9353 8.891985 TTGAGGATCTATTAGATGAGCTACAT 57.108 34.615 10.93 0.00 34.53 2.29
5066 9354 8.291191 TGAGGATCTATTAGATGAGCTACATG 57.709 38.462 10.93 0.00 34.53 3.21
5067 9355 7.341512 TGAGGATCTATTAGATGAGCTACATGG 59.658 40.741 10.93 0.00 34.53 3.66
5068 9356 7.188381 AGGATCTATTAGATGAGCTACATGGT 58.812 38.462 10.93 0.00 39.56 3.55
5069 9357 7.123997 AGGATCTATTAGATGAGCTACATGGTG 59.876 40.741 10.93 0.00 39.56 4.17
5070 9358 6.030548 TCTATTAGATGAGCTACATGGTGC 57.969 41.667 0.00 0.27 39.56 5.01
5071 9359 4.694760 ATTAGATGAGCTACATGGTGCA 57.305 40.909 13.32 0.00 39.56 4.57
5072 9360 2.322355 AGATGAGCTACATGGTGCAC 57.678 50.000 8.80 8.80 39.56 4.57
5073 9361 1.556451 AGATGAGCTACATGGTGCACA 59.444 47.619 20.43 12.67 39.56 4.57
5074 9362 2.026915 AGATGAGCTACATGGTGCACAA 60.027 45.455 20.43 8.12 39.56 3.33
5075 9363 1.522668 TGAGCTACATGGTGCACAAC 58.477 50.000 20.43 2.20 0.00 3.32
5076 9364 1.072173 TGAGCTACATGGTGCACAACT 59.928 47.619 20.43 0.00 0.00 3.16
5077 9365 1.466167 GAGCTACATGGTGCACAACTG 59.534 52.381 20.43 14.36 0.00 3.16
5078 9366 1.202806 AGCTACATGGTGCACAACTGT 60.203 47.619 20.43 19.12 0.00 3.55
5079 9367 1.608590 GCTACATGGTGCACAACTGTT 59.391 47.619 20.43 6.13 0.00 3.16
5080 9368 2.034558 GCTACATGGTGCACAACTGTTT 59.965 45.455 20.43 0.57 0.00 2.83
5081 9369 3.490761 GCTACATGGTGCACAACTGTTTT 60.491 43.478 20.43 0.00 0.00 2.43
5082 9370 3.163630 ACATGGTGCACAACTGTTTTC 57.836 42.857 20.43 0.00 0.00 2.29
5083 9371 2.760092 ACATGGTGCACAACTGTTTTCT 59.240 40.909 20.43 0.00 0.00 2.52
5084 9372 3.951037 ACATGGTGCACAACTGTTTTCTA 59.049 39.130 20.43 0.00 0.00 2.10
5085 9373 4.400884 ACATGGTGCACAACTGTTTTCTAA 59.599 37.500 20.43 0.00 0.00 2.10
5086 9374 5.105554 ACATGGTGCACAACTGTTTTCTAAA 60.106 36.000 20.43 0.00 0.00 1.85
5087 9375 4.739195 TGGTGCACAACTGTTTTCTAAAC 58.261 39.130 20.43 0.00 0.00 2.01
5088 9376 4.461081 TGGTGCACAACTGTTTTCTAAACT 59.539 37.500 20.43 0.00 0.00 2.66
5089 9377 5.047660 TGGTGCACAACTGTTTTCTAAACTT 60.048 36.000 20.43 0.00 0.00 2.66
5090 9378 5.288472 GGTGCACAACTGTTTTCTAAACTTG 59.712 40.000 20.43 4.06 0.00 3.16
5091 9379 6.090129 GTGCACAACTGTTTTCTAAACTTGA 58.910 36.000 13.17 0.00 0.00 3.02
5092 9380 6.751888 GTGCACAACTGTTTTCTAAACTTGAT 59.248 34.615 13.17 0.00 0.00 2.57
5093 9381 7.275560 GTGCACAACTGTTTTCTAAACTTGATT 59.724 33.333 13.17 0.00 0.00 2.57
5094 9382 7.816995 TGCACAACTGTTTTCTAAACTTGATTT 59.183 29.630 9.73 0.00 0.00 2.17
5095 9383 8.110002 GCACAACTGTTTTCTAAACTTGATTTG 58.890 33.333 9.73 6.12 0.00 2.32
5096 9384 9.352784 CACAACTGTTTTCTAAACTTGATTTGA 57.647 29.630 9.73 0.00 0.00 2.69
5097 9385 9.573133 ACAACTGTTTTCTAAACTTGATTTGAG 57.427 29.630 9.73 0.00 0.00 3.02
5098 9386 9.787532 CAACTGTTTTCTAAACTTGATTTGAGA 57.212 29.630 4.19 0.00 0.00 3.27
5103 9391 9.617975 GTTTTCTAAACTTGATTTGAGATCAGG 57.382 33.333 0.00 0.00 0.00 3.86
5104 9392 8.924511 TTTCTAAACTTGATTTGAGATCAGGT 57.075 30.769 0.00 0.00 39.56 4.00
5105 9393 8.924511 TTCTAAACTTGATTTGAGATCAGGTT 57.075 30.769 7.50 7.50 45.96 3.50
5109 9397 8.868522 AAACTTGATTTGAGATCAGGTTATCA 57.131 30.769 12.62 0.00 44.15 2.15
5110 9398 9.471702 AAACTTGATTTGAGATCAGGTTATCAT 57.528 29.630 12.62 0.00 44.15 2.45
5111 9399 8.674263 ACTTGATTTGAGATCAGGTTATCATC 57.326 34.615 0.00 0.00 35.24 2.92
5112 9400 8.270030 ACTTGATTTGAGATCAGGTTATCATCA 58.730 33.333 0.00 0.00 35.24 3.07
5113 9401 8.672823 TTGATTTGAGATCAGGTTATCATCAG 57.327 34.615 0.00 0.00 0.00 2.90
5114 9402 8.026396 TGATTTGAGATCAGGTTATCATCAGA 57.974 34.615 0.00 0.00 0.00 3.27
5115 9403 8.657712 TGATTTGAGATCAGGTTATCATCAGAT 58.342 33.333 0.00 0.00 38.29 2.90
5118 9406 9.993454 TTTGAGATCAGGTTATCATCAGATAAG 57.007 33.333 0.00 0.00 44.95 1.73
5119 9407 8.946797 TGAGATCAGGTTATCATCAGATAAGA 57.053 34.615 0.00 0.00 44.95 2.10
5120 9408 9.372189 TGAGATCAGGTTATCATCAGATAAGAA 57.628 33.333 0.00 0.00 44.95 2.52
5125 9413 9.372189 TCAGGTTATCATCAGATAAGAATGAGA 57.628 33.333 0.00 0.00 44.95 3.27
5126 9414 9.993454 CAGGTTATCATCAGATAAGAATGAGAA 57.007 33.333 0.00 0.00 44.95 2.87
5133 9421 9.418839 TCATCAGATAAGAATGAGAAGAGAAGA 57.581 33.333 0.00 0.00 0.00 2.87
5134 9422 9.467258 CATCAGATAAGAATGAGAAGAGAAGAC 57.533 37.037 0.00 0.00 0.00 3.01
5135 9423 8.586879 TCAGATAAGAATGAGAAGAGAAGACA 57.413 34.615 0.00 0.00 0.00 3.41
5136 9424 9.199645 TCAGATAAGAATGAGAAGAGAAGACAT 57.800 33.333 0.00 0.00 0.00 3.06
5137 9425 9.820725 CAGATAAGAATGAGAAGAGAAGACATT 57.179 33.333 0.00 0.00 34.55 2.71
5139 9427 9.260002 GATAAGAATGAGAAGAGAAGACATTCC 57.740 37.037 0.00 0.00 44.13 3.01
5140 9428 6.617782 AGAATGAGAAGAGAAGACATTCCA 57.382 37.500 0.00 0.00 44.13 3.53
5141 9429 7.013823 AGAATGAGAAGAGAAGACATTCCAA 57.986 36.000 0.00 0.00 44.13 3.53
5142 9430 7.456725 AGAATGAGAAGAGAAGACATTCCAAA 58.543 34.615 0.00 0.00 44.13 3.28
5143 9431 7.941238 AGAATGAGAAGAGAAGACATTCCAAAA 59.059 33.333 0.00 0.00 44.13 2.44
5144 9432 8.647256 AATGAGAAGAGAAGACATTCCAAAAT 57.353 30.769 0.00 0.00 35.94 1.82
5145 9433 8.647256 ATGAGAAGAGAAGACATTCCAAAATT 57.353 30.769 0.00 0.00 35.94 1.82
5146 9434 8.469309 TGAGAAGAGAAGACATTCCAAAATTT 57.531 30.769 0.00 0.00 35.94 1.82
5147 9435 8.917088 TGAGAAGAGAAGACATTCCAAAATTTT 58.083 29.630 0.00 0.00 35.94 1.82
5150 9438 9.631452 GAAGAGAAGACATTCCAAAATTTTAGG 57.369 33.333 2.44 7.91 35.94 2.69
5151 9439 8.940397 AGAGAAGACATTCCAAAATTTTAGGA 57.060 30.769 14.39 14.39 35.94 2.94
5152 9440 8.797438 AGAGAAGACATTCCAAAATTTTAGGAC 58.203 33.333 16.74 9.17 35.94 3.85
5153 9441 8.477419 AGAAGACATTCCAAAATTTTAGGACA 57.523 30.769 16.74 11.17 35.94 4.02
5154 9442 9.093458 AGAAGACATTCCAAAATTTTAGGACAT 57.907 29.630 16.74 12.34 35.94 3.06
5185 9473 8.607441 TGTCATTATGAATACTTAGTGATGCC 57.393 34.615 0.00 0.00 30.12 4.40
5186 9474 8.210265 TGTCATTATGAATACTTAGTGATGCCA 58.790 33.333 0.00 0.00 30.12 4.92
5187 9475 9.224267 GTCATTATGAATACTTAGTGATGCCAT 57.776 33.333 0.00 0.00 30.12 4.40
5188 9476 9.797642 TCATTATGAATACTTAGTGATGCCATT 57.202 29.630 0.00 0.00 0.00 3.16
5191 9479 6.698008 TGAATACTTAGTGATGCCATTTGG 57.302 37.500 0.00 0.00 38.53 3.28
5192 9480 6.422333 TGAATACTTAGTGATGCCATTTGGA 58.578 36.000 0.00 0.00 37.39 3.53
5193 9481 6.318648 TGAATACTTAGTGATGCCATTTGGAC 59.681 38.462 0.00 0.00 37.39 4.02
5194 9482 4.307032 ACTTAGTGATGCCATTTGGACT 57.693 40.909 0.00 0.00 37.39 3.85
5195 9483 4.265073 ACTTAGTGATGCCATTTGGACTC 58.735 43.478 0.00 0.00 37.39 3.36
5196 9484 2.885135 AGTGATGCCATTTGGACTCA 57.115 45.000 0.00 0.00 37.39 3.41
5197 9485 2.440409 AGTGATGCCATTTGGACTCAC 58.560 47.619 17.53 17.53 43.02 3.51
5198 9486 2.040813 AGTGATGCCATTTGGACTCACT 59.959 45.455 20.22 20.22 45.47 3.41
5199 9487 3.264193 AGTGATGCCATTTGGACTCACTA 59.736 43.478 22.65 0.00 46.90 2.74
5200 9488 4.009675 GTGATGCCATTTGGACTCACTAA 58.990 43.478 17.78 0.00 41.23 2.24
5201 9489 4.641989 GTGATGCCATTTGGACTCACTAAT 59.358 41.667 17.78 0.00 41.23 1.73
5202 9490 4.641541 TGATGCCATTTGGACTCACTAATG 59.358 41.667 0.00 0.00 37.39 1.90
5203 9491 2.754552 TGCCATTTGGACTCACTAATGC 59.245 45.455 0.00 0.00 37.39 3.56
5204 9492 2.754552 GCCATTTGGACTCACTAATGCA 59.245 45.455 0.00 0.00 37.39 3.96
5205 9493 3.428045 GCCATTTGGACTCACTAATGCAC 60.428 47.826 0.00 0.00 37.39 4.57
5206 9494 3.129287 CCATTTGGACTCACTAATGCACC 59.871 47.826 0.00 0.00 37.39 5.01
5207 9495 3.788227 TTTGGACTCACTAATGCACCT 57.212 42.857 0.00 0.00 0.00 4.00
5208 9496 2.768253 TGGACTCACTAATGCACCTG 57.232 50.000 0.00 0.00 0.00 4.00
5209 9497 1.339055 TGGACTCACTAATGCACCTGC 60.339 52.381 0.00 0.00 42.50 4.85
5210 9498 1.065854 GGACTCACTAATGCACCTGCT 60.066 52.381 0.00 0.00 42.66 4.24
5211 9499 2.168521 GGACTCACTAATGCACCTGCTA 59.831 50.000 0.00 0.00 42.66 3.49
5212 9500 3.190874 GACTCACTAATGCACCTGCTAC 58.809 50.000 0.00 0.00 42.66 3.58
5213 9501 2.093447 ACTCACTAATGCACCTGCTACC 60.093 50.000 0.00 0.00 42.66 3.18
5214 9502 2.169352 CTCACTAATGCACCTGCTACCT 59.831 50.000 0.00 0.00 42.66 3.08
5215 9503 2.571653 TCACTAATGCACCTGCTACCTT 59.428 45.455 0.00 0.00 42.66 3.50
5216 9504 2.939103 CACTAATGCACCTGCTACCTTC 59.061 50.000 0.00 0.00 42.66 3.46
5217 9505 2.092914 ACTAATGCACCTGCTACCTTCC 60.093 50.000 0.00 0.00 42.66 3.46
5218 9506 0.698238 AATGCACCTGCTACCTTCCA 59.302 50.000 0.00 0.00 42.66 3.53
5219 9507 0.698238 ATGCACCTGCTACCTTCCAA 59.302 50.000 0.00 0.00 42.66 3.53
5220 9508 0.698238 TGCACCTGCTACCTTCCAAT 59.302 50.000 0.00 0.00 42.66 3.16
5221 9509 1.340017 TGCACCTGCTACCTTCCAATC 60.340 52.381 0.00 0.00 42.66 2.67
5222 9510 1.065126 GCACCTGCTACCTTCCAATCT 60.065 52.381 0.00 0.00 38.21 2.40
5223 9511 2.619074 GCACCTGCTACCTTCCAATCTT 60.619 50.000 0.00 0.00 38.21 2.40
5224 9512 3.690460 CACCTGCTACCTTCCAATCTTT 58.310 45.455 0.00 0.00 0.00 2.52
5225 9513 4.843728 CACCTGCTACCTTCCAATCTTTA 58.156 43.478 0.00 0.00 0.00 1.85
5226 9514 5.253330 CACCTGCTACCTTCCAATCTTTAA 58.747 41.667 0.00 0.00 0.00 1.52
5227 9515 5.888161 CACCTGCTACCTTCCAATCTTTAAT 59.112 40.000 0.00 0.00 0.00 1.40
5228 9516 5.888161 ACCTGCTACCTTCCAATCTTTAATG 59.112 40.000 0.00 0.00 0.00 1.90
5229 9517 6.122277 CCTGCTACCTTCCAATCTTTAATGA 58.878 40.000 0.00 0.00 0.00 2.57
5230 9518 6.603201 CCTGCTACCTTCCAATCTTTAATGAA 59.397 38.462 0.00 0.00 0.00 2.57
5231 9519 7.286316 CCTGCTACCTTCCAATCTTTAATGAAT 59.714 37.037 0.00 0.00 0.00 2.57
5232 9520 8.225603 TGCTACCTTCCAATCTTTAATGAATC 57.774 34.615 0.00 0.00 0.00 2.52
5233 9521 7.833682 TGCTACCTTCCAATCTTTAATGAATCA 59.166 33.333 0.00 0.00 0.00 2.57
5234 9522 8.854117 GCTACCTTCCAATCTTTAATGAATCAT 58.146 33.333 0.00 0.00 0.00 2.45
5236 9524 8.599624 ACCTTCCAATCTTTAATGAATCATGT 57.400 30.769 0.00 0.00 0.00 3.21
5237 9525 9.039165 ACCTTCCAATCTTTAATGAATCATGTT 57.961 29.630 0.00 0.00 0.00 2.71
5238 9526 9.880157 CCTTCCAATCTTTAATGAATCATGTTT 57.120 29.630 0.00 0.00 0.00 2.83
5242 9530 9.763465 CCAATCTTTAATGAATCATGTTTTTGC 57.237 29.630 0.00 0.00 0.00 3.68
5245 9533 8.761575 TCTTTAATGAATCATGTTTTTGCTCC 57.238 30.769 0.00 0.00 0.00 4.70
5246 9534 7.541783 TCTTTAATGAATCATGTTTTTGCTCCG 59.458 33.333 0.00 0.00 0.00 4.63
5247 9535 3.574284 TGAATCATGTTTTTGCTCCGG 57.426 42.857 0.00 0.00 0.00 5.14
5248 9536 3.153130 TGAATCATGTTTTTGCTCCGGA 58.847 40.909 2.93 2.93 0.00 5.14
5249 9537 3.571828 TGAATCATGTTTTTGCTCCGGAA 59.428 39.130 5.23 0.00 0.00 4.30
5250 9538 4.038522 TGAATCATGTTTTTGCTCCGGAAA 59.961 37.500 5.23 0.00 0.00 3.13
5251 9539 4.806640 ATCATGTTTTTGCTCCGGAAAT 57.193 36.364 5.23 0.00 0.00 2.17
5252 9540 5.913137 ATCATGTTTTTGCTCCGGAAATA 57.087 34.783 5.23 0.00 0.00 1.40
5253 9541 5.054390 TCATGTTTTTGCTCCGGAAATAC 57.946 39.130 5.23 3.27 0.00 1.89
5254 9542 3.926821 TGTTTTTGCTCCGGAAATACC 57.073 42.857 5.23 0.00 0.00 2.73
5255 9543 3.492337 TGTTTTTGCTCCGGAAATACCT 58.508 40.909 5.23 0.00 36.31 3.08
5256 9544 3.892588 TGTTTTTGCTCCGGAAATACCTT 59.107 39.130 5.23 0.00 36.31 3.50
5257 9545 4.342665 TGTTTTTGCTCCGGAAATACCTTT 59.657 37.500 5.23 0.00 36.31 3.11
5258 9546 5.163395 TGTTTTTGCTCCGGAAATACCTTTT 60.163 36.000 5.23 0.00 36.31 2.27
5259 9547 4.513198 TTTGCTCCGGAAATACCTTTTG 57.487 40.909 5.23 0.00 36.31 2.44
5304 9592 0.761187 ATACTGCGATGGGTCATGCT 59.239 50.000 0.00 0.00 0.00 3.79
5313 9601 1.131638 TGGGTCATGCTGTATCCCTC 58.868 55.000 4.55 0.00 38.95 4.30
5459 9747 1.682344 GGCGGGAAGAATTTGGCCT 60.682 57.895 3.32 0.00 35.81 5.19
5464 9752 2.037121 CGGGAAGAATTTGGCCTGTTTT 59.963 45.455 3.32 0.00 0.00 2.43
5465 9753 3.402110 GGGAAGAATTTGGCCTGTTTTG 58.598 45.455 3.32 0.00 0.00 2.44
5680 9986 1.834301 GCCGCTCCACCCCTATTTA 59.166 57.895 0.00 0.00 0.00 1.40
5681 9987 0.250338 GCCGCTCCACCCCTATTTAG 60.250 60.000 0.00 0.00 0.00 1.85
5682 9988 0.250338 CCGCTCCACCCCTATTTAGC 60.250 60.000 0.00 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 7.095439 ACGCTTGATGAAAAACAAAGAAAAACA 60.095 29.630 0.00 0.00 0.00 2.83
106 107 1.009829 GCACGTTTGGCTAGATGAGG 58.990 55.000 0.00 0.00 0.00 3.86
231 232 5.367352 ACCATACGTCACCCTTTTATATCCA 59.633 40.000 0.00 0.00 0.00 3.41
301 318 6.527423 ACGAAGGAAGTACCATTTAGTGAAA 58.473 36.000 0.00 0.00 42.04 2.69
329 346 9.408069 CGTTTAGGAGATACGCTCTTATATTTT 57.592 33.333 0.00 0.00 43.43 1.82
381 402 6.342111 ACTCATCCGTAAAGAAAAGAGATCC 58.658 40.000 0.00 0.00 0.00 3.36
427 449 1.787012 ACCGTATTTCGAACGCAAGT 58.213 45.000 0.00 0.00 45.57 3.16
517 539 1.987306 TAGCTGCCGTGGTGATGGA 60.987 57.895 0.00 0.00 0.00 3.41
518 540 1.815421 GTAGCTGCCGTGGTGATGG 60.815 63.158 0.00 0.00 0.00 3.51
519 541 2.167219 CGTAGCTGCCGTGGTGATG 61.167 63.158 0.00 0.00 0.00 3.07
521 543 1.033202 TATCGTAGCTGCCGTGGTGA 61.033 55.000 0.00 0.00 0.00 4.02
523 545 1.436336 GTATCGTAGCTGCCGTGGT 59.564 57.895 0.00 0.00 0.00 4.16
524 546 1.657487 CGTATCGTAGCTGCCGTGG 60.657 63.158 0.00 0.00 0.00 4.94
525 547 2.293627 GCGTATCGTAGCTGCCGTG 61.294 63.158 0.00 0.00 0.00 4.94
781 808 2.852495 ATTCGTCCGAAGTGCCGCAT 62.852 55.000 8.22 0.00 37.56 4.73
1024 1052 1.416243 ATTGCTATGCCCCCACAATG 58.584 50.000 0.00 0.00 30.14 2.82
1132 1169 7.065120 AGAATATAGCAAGATGAAGAGCAGT 57.935 36.000 0.00 0.00 0.00 4.40
1311 1433 0.679321 CAAGGGAAGGCAAGCTCCTC 60.679 60.000 0.00 0.00 34.82 3.71
1337 1459 0.692756 TCATCCACCGCCCTCCATTA 60.693 55.000 0.00 0.00 0.00 1.90
1350 1472 2.245379 CCCCCAAACCCCTCATCCA 61.245 63.158 0.00 0.00 0.00 3.41
1538 1679 5.062308 GCGTTGTTATCTCTTCAGTTACCTG 59.938 44.000 0.00 0.00 40.25 4.00
3057 3468 0.685097 ACACAGGTATCGCAACTGGT 59.315 50.000 6.81 0.25 36.57 4.00
3145 3556 0.909610 CTGGGTGGGTCTCCAAGCTA 60.910 60.000 0.00 0.00 46.04 3.32
3879 4410 8.962884 AATTCAATGGTATAATTTTTGCTCCC 57.037 30.769 0.00 0.00 0.00 4.30
4371 8622 3.243101 CCTGTTCTGAGTACGCATACGAT 60.243 47.826 0.00 0.00 43.93 3.73
4374 8625 3.377485 TCTCCTGTTCTGAGTACGCATAC 59.623 47.826 0.00 2.64 0.00 2.39
4460 8736 0.029567 CGTAGACTCCGGTCATCTGC 59.970 60.000 0.00 5.90 44.36 4.26
4946 9234 3.763356 ATCGCAGCAGCACGGAGA 61.763 61.111 0.82 0.00 42.27 3.71
4999 9287 1.686355 ATGAGTAGGAGAGGCAGACG 58.314 55.000 0.00 0.00 0.00 4.18
5018 9306 8.634335 TCAATGACTGGAATATTGAAAGTGAA 57.366 30.769 0.00 0.00 37.74 3.18
5025 9313 7.384524 AGATCCTCAATGACTGGAATATTGA 57.615 36.000 0.00 0.00 38.20 2.57
5026 9314 9.736414 AATAGATCCTCAATGACTGGAATATTG 57.264 33.333 0.00 0.00 33.20 1.90
5029 9317 9.828691 TCTAATAGATCCTCAATGACTGGAATA 57.171 33.333 0.00 0.00 33.20 1.75
5030 9318 8.733092 TCTAATAGATCCTCAATGACTGGAAT 57.267 34.615 0.00 0.00 33.20 3.01
5031 9319 8.591940 CATCTAATAGATCCTCAATGACTGGAA 58.408 37.037 0.00 0.00 31.32 3.53
5032 9320 7.952368 TCATCTAATAGATCCTCAATGACTGGA 59.048 37.037 0.00 0.00 31.32 3.86
5033 9321 8.131847 TCATCTAATAGATCCTCAATGACTGG 57.868 38.462 0.00 0.00 31.32 4.00
5034 9322 7.760794 GCTCATCTAATAGATCCTCAATGACTG 59.239 40.741 0.00 0.00 31.32 3.51
5035 9323 7.675195 AGCTCATCTAATAGATCCTCAATGACT 59.325 37.037 0.00 0.00 31.32 3.41
5036 9324 7.839907 AGCTCATCTAATAGATCCTCAATGAC 58.160 38.462 0.00 0.00 31.32 3.06
5037 9325 8.965819 GTAGCTCATCTAATAGATCCTCAATGA 58.034 37.037 0.00 0.00 31.32 2.57
5038 9326 8.747471 TGTAGCTCATCTAATAGATCCTCAATG 58.253 37.037 0.00 0.00 31.32 2.82
5039 9327 8.891985 TGTAGCTCATCTAATAGATCCTCAAT 57.108 34.615 0.00 0.00 31.32 2.57
5040 9328 8.747471 CATGTAGCTCATCTAATAGATCCTCAA 58.253 37.037 0.00 0.00 31.32 3.02
5041 9329 7.341512 CCATGTAGCTCATCTAATAGATCCTCA 59.658 40.741 0.00 0.00 31.32 3.86
5042 9330 7.341769 ACCATGTAGCTCATCTAATAGATCCTC 59.658 40.741 0.00 0.00 31.32 3.71
5043 9331 7.123997 CACCATGTAGCTCATCTAATAGATCCT 59.876 40.741 0.00 0.67 31.32 3.24
5044 9332 7.264221 CACCATGTAGCTCATCTAATAGATCC 58.736 42.308 0.00 0.00 31.32 3.36
5045 9333 6.756074 GCACCATGTAGCTCATCTAATAGATC 59.244 42.308 0.00 0.00 31.32 2.75
5046 9334 6.212187 TGCACCATGTAGCTCATCTAATAGAT 59.788 38.462 0.00 0.00 34.74 1.98
5047 9335 5.539955 TGCACCATGTAGCTCATCTAATAGA 59.460 40.000 0.00 0.00 34.09 1.98
5048 9336 5.636965 GTGCACCATGTAGCTCATCTAATAG 59.363 44.000 5.22 0.00 34.09 1.73
5049 9337 5.070313 TGTGCACCATGTAGCTCATCTAATA 59.930 40.000 15.69 0.00 34.09 0.98
5050 9338 4.141642 TGTGCACCATGTAGCTCATCTAAT 60.142 41.667 15.69 0.00 34.09 1.73
5051 9339 3.197549 TGTGCACCATGTAGCTCATCTAA 59.802 43.478 15.69 0.00 34.09 2.10
5052 9340 2.765699 TGTGCACCATGTAGCTCATCTA 59.234 45.455 15.69 0.00 34.09 1.98
5053 9341 1.556451 TGTGCACCATGTAGCTCATCT 59.444 47.619 15.69 0.00 34.09 2.90
5054 9342 2.028420 TGTGCACCATGTAGCTCATC 57.972 50.000 15.69 0.00 34.09 2.92
5055 9343 2.086869 GTTGTGCACCATGTAGCTCAT 58.913 47.619 15.69 0.00 34.68 2.90
5056 9344 1.072173 AGTTGTGCACCATGTAGCTCA 59.928 47.619 15.69 7.51 33.05 4.26
5057 9345 1.466167 CAGTTGTGCACCATGTAGCTC 59.534 52.381 15.69 5.26 0.00 4.09
5058 9346 1.202806 ACAGTTGTGCACCATGTAGCT 60.203 47.619 15.69 0.00 0.00 3.32
5059 9347 1.238439 ACAGTTGTGCACCATGTAGC 58.762 50.000 15.69 0.00 0.00 3.58
5060 9348 3.988379 AAACAGTTGTGCACCATGTAG 57.012 42.857 15.69 1.96 0.00 2.74
5061 9349 3.951037 AGAAAACAGTTGTGCACCATGTA 59.049 39.130 15.69 0.00 0.00 2.29
5062 9350 2.760092 AGAAAACAGTTGTGCACCATGT 59.240 40.909 15.69 13.26 0.00 3.21
5063 9351 3.441496 AGAAAACAGTTGTGCACCATG 57.559 42.857 15.69 12.59 0.00 3.66
5064 9352 5.127031 AGTTTAGAAAACAGTTGTGCACCAT 59.873 36.000 15.69 0.00 0.00 3.55
5065 9353 4.461081 AGTTTAGAAAACAGTTGTGCACCA 59.539 37.500 15.69 0.00 0.00 4.17
5066 9354 4.993905 AGTTTAGAAAACAGTTGTGCACC 58.006 39.130 15.69 0.00 0.00 5.01
5067 9355 6.090129 TCAAGTTTAGAAAACAGTTGTGCAC 58.910 36.000 10.75 10.75 0.00 4.57
5068 9356 6.260870 TCAAGTTTAGAAAACAGTTGTGCA 57.739 33.333 5.42 0.00 0.00 4.57
5069 9357 7.755582 AATCAAGTTTAGAAAACAGTTGTGC 57.244 32.000 5.42 0.00 0.00 4.57
5070 9358 9.352784 TCAAATCAAGTTTAGAAAACAGTTGTG 57.647 29.630 5.42 0.00 0.00 3.33
5071 9359 9.573133 CTCAAATCAAGTTTAGAAAACAGTTGT 57.427 29.630 5.42 0.00 0.00 3.32
5072 9360 9.787532 TCTCAAATCAAGTTTAGAAAACAGTTG 57.212 29.630 5.42 2.69 0.00 3.16
5077 9365 9.617975 CCTGATCTCAAATCAAGTTTAGAAAAC 57.382 33.333 0.00 0.00 0.00 2.43
5078 9366 9.354673 ACCTGATCTCAAATCAAGTTTAGAAAA 57.645 29.630 0.00 0.00 0.00 2.29
5079 9367 8.924511 ACCTGATCTCAAATCAAGTTTAGAAA 57.075 30.769 0.00 0.00 0.00 2.52
5080 9368 8.924511 AACCTGATCTCAAATCAAGTTTAGAA 57.075 30.769 0.00 0.00 30.90 2.10
5083 9371 9.958180 TGATAACCTGATCTCAAATCAAGTTTA 57.042 29.630 7.18 0.00 35.21 2.01
5084 9372 8.868522 TGATAACCTGATCTCAAATCAAGTTT 57.131 30.769 7.18 0.00 35.21 2.66
5085 9373 9.118300 GATGATAACCTGATCTCAAATCAAGTT 57.882 33.333 7.08 7.08 36.81 2.66
5086 9374 8.270030 TGATGATAACCTGATCTCAAATCAAGT 58.730 33.333 0.00 0.00 0.00 3.16
5087 9375 8.672823 TGATGATAACCTGATCTCAAATCAAG 57.327 34.615 0.00 0.00 0.00 3.02
5088 9376 8.488668 TCTGATGATAACCTGATCTCAAATCAA 58.511 33.333 0.00 0.00 0.00 2.57
5089 9377 8.026396 TCTGATGATAACCTGATCTCAAATCA 57.974 34.615 0.00 0.00 0.00 2.57
5092 9380 9.993454 CTTATCTGATGATAACCTGATCTCAAA 57.007 33.333 0.00 0.00 39.46 2.69
5093 9381 9.372189 TCTTATCTGATGATAACCTGATCTCAA 57.628 33.333 0.00 0.00 39.46 3.02
5094 9382 8.946797 TCTTATCTGATGATAACCTGATCTCA 57.053 34.615 0.00 0.00 39.46 3.27
5099 9387 9.372189 TCTCATTCTTATCTGATGATAACCTGA 57.628 33.333 0.00 0.00 39.46 3.86
5100 9388 9.993454 TTCTCATTCTTATCTGATGATAACCTG 57.007 33.333 0.00 0.00 39.46 4.00
5107 9395 9.418839 TCTTCTCTTCTCATTCTTATCTGATGA 57.581 33.333 0.00 0.00 0.00 2.92
5108 9396 9.467258 GTCTTCTCTTCTCATTCTTATCTGATG 57.533 37.037 0.00 0.00 0.00 3.07
5109 9397 9.199645 TGTCTTCTCTTCTCATTCTTATCTGAT 57.800 33.333 0.00 0.00 0.00 2.90
5110 9398 8.586879 TGTCTTCTCTTCTCATTCTTATCTGA 57.413 34.615 0.00 0.00 0.00 3.27
5111 9399 9.820725 AATGTCTTCTCTTCTCATTCTTATCTG 57.179 33.333 0.00 0.00 0.00 2.90
5113 9401 9.260002 GGAATGTCTTCTCTTCTCATTCTTATC 57.740 37.037 13.30 0.00 41.95 1.75
5114 9402 8.766476 TGGAATGTCTTCTCTTCTCATTCTTAT 58.234 33.333 13.30 0.00 41.95 1.73
5115 9403 8.138928 TGGAATGTCTTCTCTTCTCATTCTTA 57.861 34.615 13.30 4.05 41.95 2.10
5116 9404 7.013823 TGGAATGTCTTCTCTTCTCATTCTT 57.986 36.000 13.30 0.00 41.95 2.52
5117 9405 6.617782 TGGAATGTCTTCTCTTCTCATTCT 57.382 37.500 13.30 0.00 41.95 2.40
5118 9406 7.678947 TTTGGAATGTCTTCTCTTCTCATTC 57.321 36.000 0.00 0.00 41.71 2.67
5119 9407 8.647256 ATTTTGGAATGTCTTCTCTTCTCATT 57.353 30.769 0.00 0.00 0.00 2.57
5120 9408 8.647256 AATTTTGGAATGTCTTCTCTTCTCAT 57.353 30.769 0.00 0.00 0.00 2.90
5121 9409 8.469309 AAATTTTGGAATGTCTTCTCTTCTCA 57.531 30.769 0.00 0.00 0.00 3.27
5124 9412 9.631452 CCTAAAATTTTGGAATGTCTTCTCTTC 57.369 33.333 15.21 0.00 0.00 2.87
5125 9413 9.367160 TCCTAAAATTTTGGAATGTCTTCTCTT 57.633 29.630 15.21 0.00 0.00 2.85
5126 9414 8.797438 GTCCTAAAATTTTGGAATGTCTTCTCT 58.203 33.333 15.21 0.00 0.00 3.10
5127 9415 8.576442 TGTCCTAAAATTTTGGAATGTCTTCTC 58.424 33.333 15.21 5.37 0.00 2.87
5128 9416 8.477419 TGTCCTAAAATTTTGGAATGTCTTCT 57.523 30.769 15.21 0.00 0.00 2.85
5159 9447 9.056005 GGCATCACTAAGTATTCATAATGACAA 57.944 33.333 0.00 0.00 0.00 3.18
5160 9448 8.210265 TGGCATCACTAAGTATTCATAATGACA 58.790 33.333 0.00 0.00 0.00 3.58
5161 9449 8.607441 TGGCATCACTAAGTATTCATAATGAC 57.393 34.615 0.00 0.00 0.00 3.06
5162 9450 9.797642 AATGGCATCACTAAGTATTCATAATGA 57.202 29.630 0.00 0.00 0.00 2.57
5165 9453 8.849168 CCAAATGGCATCACTAAGTATTCATAA 58.151 33.333 0.00 0.00 0.00 1.90
5166 9454 8.217111 TCCAAATGGCATCACTAAGTATTCATA 58.783 33.333 0.00 0.00 34.44 2.15
5167 9455 7.013655 GTCCAAATGGCATCACTAAGTATTCAT 59.986 37.037 0.00 0.00 34.44 2.57
5168 9456 6.318648 GTCCAAATGGCATCACTAAGTATTCA 59.681 38.462 0.00 0.00 34.44 2.57
5169 9457 6.543831 AGTCCAAATGGCATCACTAAGTATTC 59.456 38.462 0.00 0.00 34.44 1.75
5170 9458 6.426587 AGTCCAAATGGCATCACTAAGTATT 58.573 36.000 0.00 0.00 34.44 1.89
5171 9459 6.006275 AGTCCAAATGGCATCACTAAGTAT 57.994 37.500 0.00 0.00 34.44 2.12
5172 9460 5.045942 TGAGTCCAAATGGCATCACTAAGTA 60.046 40.000 0.00 0.00 34.44 2.24
5173 9461 4.263462 TGAGTCCAAATGGCATCACTAAGT 60.263 41.667 0.00 0.00 34.44 2.24
5174 9462 4.095483 GTGAGTCCAAATGGCATCACTAAG 59.905 45.833 20.55 0.00 42.27 2.18
5175 9463 4.009675 GTGAGTCCAAATGGCATCACTAA 58.990 43.478 20.55 2.15 42.27 2.24
5176 9464 3.609853 GTGAGTCCAAATGGCATCACTA 58.390 45.455 20.55 0.00 42.27 2.74
5177 9465 2.040813 AGTGAGTCCAAATGGCATCACT 59.959 45.455 22.96 22.96 46.47 3.41
5178 9466 2.440409 AGTGAGTCCAAATGGCATCAC 58.560 47.619 20.38 20.38 44.08 3.06
5179 9467 2.885135 AGTGAGTCCAAATGGCATCA 57.115 45.000 0.00 0.00 34.44 3.07
5180 9468 4.498682 GCATTAGTGAGTCCAAATGGCATC 60.499 45.833 0.00 0.00 34.44 3.91
5181 9469 3.382546 GCATTAGTGAGTCCAAATGGCAT 59.617 43.478 0.00 0.00 34.44 4.40
5182 9470 2.754552 GCATTAGTGAGTCCAAATGGCA 59.245 45.455 0.00 0.00 34.44 4.92
5183 9471 2.754552 TGCATTAGTGAGTCCAAATGGC 59.245 45.455 9.79 0.00 34.44 4.40
5184 9472 3.129287 GGTGCATTAGTGAGTCCAAATGG 59.871 47.826 0.00 0.00 31.46 3.16
5185 9473 4.012374 AGGTGCATTAGTGAGTCCAAATG 58.988 43.478 0.00 5.32 33.45 2.32
5186 9474 4.012374 CAGGTGCATTAGTGAGTCCAAAT 58.988 43.478 0.00 0.00 0.00 2.32
5187 9475 3.411446 CAGGTGCATTAGTGAGTCCAAA 58.589 45.455 0.00 0.00 0.00 3.28
5188 9476 2.875672 GCAGGTGCATTAGTGAGTCCAA 60.876 50.000 0.00 0.00 41.59 3.53
5189 9477 1.339055 GCAGGTGCATTAGTGAGTCCA 60.339 52.381 0.00 0.00 41.59 4.02
5190 9478 1.065854 AGCAGGTGCATTAGTGAGTCC 60.066 52.381 4.48 0.00 45.16 3.85
5191 9479 2.393271 AGCAGGTGCATTAGTGAGTC 57.607 50.000 4.48 0.00 45.16 3.36
5192 9480 2.093447 GGTAGCAGGTGCATTAGTGAGT 60.093 50.000 4.48 0.00 45.16 3.41
5193 9481 2.169352 AGGTAGCAGGTGCATTAGTGAG 59.831 50.000 4.48 0.00 45.16 3.51
5194 9482 2.187958 AGGTAGCAGGTGCATTAGTGA 58.812 47.619 4.48 0.00 45.16 3.41
5195 9483 2.698855 AGGTAGCAGGTGCATTAGTG 57.301 50.000 4.48 0.00 45.16 2.74
5196 9484 2.092914 GGAAGGTAGCAGGTGCATTAGT 60.093 50.000 4.48 0.00 45.16 2.24
5197 9485 2.092968 TGGAAGGTAGCAGGTGCATTAG 60.093 50.000 4.48 0.00 45.16 1.73
5198 9486 1.912731 TGGAAGGTAGCAGGTGCATTA 59.087 47.619 4.48 0.00 45.16 1.90
5199 9487 0.698238 TGGAAGGTAGCAGGTGCATT 59.302 50.000 4.48 0.00 45.16 3.56
5200 9488 0.698238 TTGGAAGGTAGCAGGTGCAT 59.302 50.000 4.48 0.00 45.16 3.96
5201 9489 0.698238 ATTGGAAGGTAGCAGGTGCA 59.302 50.000 4.48 0.00 45.16 4.57
5202 9490 1.065126 AGATTGGAAGGTAGCAGGTGC 60.065 52.381 0.00 0.00 42.49 5.01
5203 9491 3.356529 AAGATTGGAAGGTAGCAGGTG 57.643 47.619 0.00 0.00 0.00 4.00
5204 9492 5.514500 TTAAAGATTGGAAGGTAGCAGGT 57.486 39.130 0.00 0.00 0.00 4.00
5205 9493 6.122277 TCATTAAAGATTGGAAGGTAGCAGG 58.878 40.000 0.00 0.00 0.00 4.85
5206 9494 7.630242 TTCATTAAAGATTGGAAGGTAGCAG 57.370 36.000 0.00 0.00 0.00 4.24
5207 9495 7.833682 TGATTCATTAAAGATTGGAAGGTAGCA 59.166 33.333 0.00 0.00 0.00 3.49
5208 9496 8.225603 TGATTCATTAAAGATTGGAAGGTAGC 57.774 34.615 0.00 0.00 0.00 3.58
5210 9498 9.699410 ACATGATTCATTAAAGATTGGAAGGTA 57.301 29.630 0.00 0.00 0.00 3.08
5211 9499 8.599624 ACATGATTCATTAAAGATTGGAAGGT 57.400 30.769 0.00 0.00 0.00 3.50
5212 9500 9.880157 AAACATGATTCATTAAAGATTGGAAGG 57.120 29.630 0.00 0.00 0.00 3.46
5216 9504 9.763465 GCAAAAACATGATTCATTAAAGATTGG 57.237 29.630 0.00 0.00 0.00 3.16
5219 9507 9.374838 GGAGCAAAAACATGATTCATTAAAGAT 57.625 29.630 0.00 0.00 0.00 2.40
5220 9508 7.541783 CGGAGCAAAAACATGATTCATTAAAGA 59.458 33.333 0.00 0.00 0.00 2.52
5221 9509 7.201461 CCGGAGCAAAAACATGATTCATTAAAG 60.201 37.037 0.00 0.00 0.00 1.85
5222 9510 6.589523 CCGGAGCAAAAACATGATTCATTAAA 59.410 34.615 0.00 0.00 0.00 1.52
5223 9511 6.071672 TCCGGAGCAAAAACATGATTCATTAA 60.072 34.615 0.00 0.00 0.00 1.40
5224 9512 5.417266 TCCGGAGCAAAAACATGATTCATTA 59.583 36.000 0.00 0.00 0.00 1.90
5225 9513 4.220382 TCCGGAGCAAAAACATGATTCATT 59.780 37.500 0.00 0.00 0.00 2.57
5226 9514 3.763360 TCCGGAGCAAAAACATGATTCAT 59.237 39.130 0.00 0.00 0.00 2.57
5227 9515 3.153130 TCCGGAGCAAAAACATGATTCA 58.847 40.909 0.00 0.00 0.00 2.57
5228 9516 3.848272 TCCGGAGCAAAAACATGATTC 57.152 42.857 0.00 0.00 0.00 2.52
5229 9517 4.599047 TTTCCGGAGCAAAAACATGATT 57.401 36.364 3.34 0.00 0.00 2.57
5230 9518 4.806640 ATTTCCGGAGCAAAAACATGAT 57.193 36.364 3.34 0.00 0.00 2.45
5231 9519 4.082463 GGTATTTCCGGAGCAAAAACATGA 60.082 41.667 3.34 0.00 0.00 3.07
5232 9520 4.082245 AGGTATTTCCGGAGCAAAAACATG 60.082 41.667 3.34 0.00 41.99 3.21
5233 9521 4.086457 AGGTATTTCCGGAGCAAAAACAT 58.914 39.130 3.34 0.00 41.99 2.71
5234 9522 3.492337 AGGTATTTCCGGAGCAAAAACA 58.508 40.909 3.34 0.00 41.99 2.83
5235 9523 4.514781 AAGGTATTTCCGGAGCAAAAAC 57.485 40.909 3.34 0.39 41.99 2.43
5236 9524 5.293560 CAAAAGGTATTTCCGGAGCAAAAA 58.706 37.500 3.34 0.00 41.99 1.94
5237 9525 4.262249 CCAAAAGGTATTTCCGGAGCAAAA 60.262 41.667 3.34 0.00 41.99 2.44
5238 9526 3.257127 CCAAAAGGTATTTCCGGAGCAAA 59.743 43.478 3.34 0.00 41.99 3.68
5239 9527 2.823154 CCAAAAGGTATTTCCGGAGCAA 59.177 45.455 3.34 0.00 41.99 3.91
5240 9528 2.224917 ACCAAAAGGTATTTCCGGAGCA 60.225 45.455 3.34 0.00 41.99 4.26
5241 9529 2.443416 ACCAAAAGGTATTTCCGGAGC 58.557 47.619 3.34 0.00 41.99 4.70
5242 9530 6.120220 AGAATACCAAAAGGTATTTCCGGAG 58.880 40.000 18.05 0.00 42.77 4.63
5243 9531 6.069705 AGAATACCAAAAGGTATTTCCGGA 57.930 37.500 18.05 0.00 42.77 5.14
5244 9532 6.769134 AAGAATACCAAAAGGTATTTCCGG 57.231 37.500 18.05 0.00 42.77 5.14
5245 9533 7.822658 TCAAAGAATACCAAAAGGTATTTCCG 58.177 34.615 18.05 9.65 42.77 4.30
5246 9534 9.586435 CATCAAAGAATACCAAAAGGTATTTCC 57.414 33.333 18.05 8.91 42.77 3.13
5271 9559 8.579863 CCCATCGCAGTATATATCAGAATATCA 58.420 37.037 0.00 0.00 30.59 2.15
5272 9560 8.580720 ACCCATCGCAGTATATATCAGAATATC 58.419 37.037 0.00 0.00 30.59 1.63
5273 9561 8.484214 ACCCATCGCAGTATATATCAGAATAT 57.516 34.615 0.00 0.00 32.72 1.28
5274 9562 7.559897 TGACCCATCGCAGTATATATCAGAATA 59.440 37.037 0.00 0.00 0.00 1.75
5275 9563 6.381133 TGACCCATCGCAGTATATATCAGAAT 59.619 38.462 0.00 0.00 0.00 2.40
5276 9564 5.714806 TGACCCATCGCAGTATATATCAGAA 59.285 40.000 0.00 0.00 0.00 3.02
5277 9565 5.261216 TGACCCATCGCAGTATATATCAGA 58.739 41.667 0.00 0.00 0.00 3.27
5278 9566 5.582689 TGACCCATCGCAGTATATATCAG 57.417 43.478 0.00 0.00 0.00 2.90
5279 9567 5.682212 GCATGACCCATCGCAGTATATATCA 60.682 44.000 0.00 0.00 0.00 2.15
5280 9568 4.747108 GCATGACCCATCGCAGTATATATC 59.253 45.833 0.00 0.00 0.00 1.63
5281 9569 4.406972 AGCATGACCCATCGCAGTATATAT 59.593 41.667 0.00 0.00 0.00 0.86
5282 9570 3.769300 AGCATGACCCATCGCAGTATATA 59.231 43.478 0.00 0.00 0.00 0.86
5283 9571 2.568956 AGCATGACCCATCGCAGTATAT 59.431 45.455 0.00 0.00 0.00 0.86
5284 9572 1.970640 AGCATGACCCATCGCAGTATA 59.029 47.619 0.00 0.00 0.00 1.47
5285 9573 0.761187 AGCATGACCCATCGCAGTAT 59.239 50.000 0.00 0.00 0.00 2.12
5286 9574 0.179076 CAGCATGACCCATCGCAGTA 60.179 55.000 0.00 0.00 39.69 2.74
5287 9575 1.450848 CAGCATGACCCATCGCAGT 60.451 57.895 0.00 0.00 39.69 4.40
5304 9592 0.686441 CCACAGGGACGAGGGATACA 60.686 60.000 0.00 0.00 35.59 2.29
5459 9747 4.081752 ACAGTGAATGCAGGAAACAAAACA 60.082 37.500 0.00 0.00 0.00 2.83
5464 9752 1.337703 GCACAGTGAATGCAGGAAACA 59.662 47.619 4.15 0.00 42.88 2.83
5465 9753 1.664016 CGCACAGTGAATGCAGGAAAC 60.664 52.381 4.15 0.00 43.57 2.78
5518 9806 3.720601 CTACTGCTGGGCCAGGCA 61.721 66.667 33.43 27.58 37.16 4.75
5622 9928 1.081108 CCGCCAATTTTTCGCCGAA 60.081 52.632 0.00 0.00 0.00 4.30
5626 9932 1.153842 CCTCCCGCCAATTTTTCGC 60.154 57.895 0.00 0.00 0.00 4.70
5635 9941 4.483243 GCCGAAATCCTCCCGCCA 62.483 66.667 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.