Multiple sequence alignment - TraesCS5D01G144300

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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 TraesCS5D01G144300 chr5D 100.000 4158 0 0 1 4158 230504037 230508194 0.000000e+00 7679.0
1 TraesCS5D01G144300 chr5D 95.429 175 8 0 3983 4157 430156909 430157083 3.170000e-71 279.0
2 TraesCS5D01G144300 chr5D 77.947 263 45 10 167 420 557048896 557049154 7.200000e-33 152.0
3 TraesCS5D01G144300 chr5A 94.334 1359 37 16 519 1853 326058891 326057549 0.000000e+00 2047.0
4 TraesCS5D01G144300 chr5A 95.284 721 23 4 2695 3407 326056595 326055878 0.000000e+00 1133.0
5 TraesCS5D01G144300 chr5A 91.275 447 29 4 1941 2381 326057408 326056966 5.950000e-168 601.0
6 TraesCS5D01G144300 chr5A 86.667 540 53 8 3450 3983 326055879 326055353 7.750000e-162 580.0
7 TraesCS5D01G144300 chr5A 95.480 177 7 1 3983 4158 74706918 74706742 8.800000e-72 281.0
8 TraesCS5D01G144300 chr5A 90.419 167 15 1 1 166 326059506 326059340 7.000000e-53 219.0
9 TraesCS5D01G144300 chr5A 81.043 211 36 4 206 414 402128138 402128346 9.250000e-37 165.0
10 TraesCS5D01G144300 chr5B 96.429 1008 35 1 2695 3701 275267022 275266015 0.000000e+00 1661.0
11 TraesCS5D01G144300 chr5B 91.057 1107 33 16 480 1549 275269263 275268186 0.000000e+00 1435.0
12 TraesCS5D01G144300 chr5B 93.216 796 31 11 1591 2381 275268181 275267404 0.000000e+00 1149.0
13 TraesCS5D01G144300 chr5B 91.019 412 32 3 3751 4158 275266019 275265609 6.080000e-153 551.0
14 TraesCS5D01G144300 chr5B 93.403 288 16 3 2382 2666 275267306 275267019 1.380000e-114 424.0
15 TraesCS5D01G144300 chr5B 78.062 547 100 16 3427 3962 542933685 542933148 1.110000e-85 327.0
16 TraesCS5D01G144300 chr5B 90.184 163 13 3 573 735 275296374 275296215 4.210000e-50 209.0
17 TraesCS5D01G144300 chr2D 79.138 580 111 8 3413 3985 317879268 317878692 3.900000e-105 392.0
18 TraesCS5D01G144300 chr2D 74.890 227 51 5 1279 1501 95645020 95645244 9.510000e-17 99.0
19 TraesCS5D01G144300 chr6B 77.909 593 103 21 3413 3986 612855165 612855748 1.110000e-90 344.0
20 TraesCS5D01G144300 chr6B 79.343 213 35 8 229 438 17096078 17095872 1.560000e-29 141.0
21 TraesCS5D01G144300 chr7D 80.084 477 80 10 3512 3977 509561122 509561594 1.430000e-89 340.0
22 TraesCS5D01G144300 chr7D 77.352 574 116 12 3422 3985 5318336 5318905 1.110000e-85 327.0
23 TraesCS5D01G144300 chr7D 95.455 176 8 0 3983 4158 600948514 600948339 8.800000e-72 281.0
24 TraesCS5D01G144300 chr7D 74.413 426 80 18 28 434 31427909 31427494 5.570000e-34 156.0
25 TraesCS5D01G144300 chr3B 77.504 569 115 10 3419 3978 576046508 576047072 3.100000e-86 329.0
26 TraesCS5D01G144300 chr3B 77.823 487 100 5 3506 3985 556520311 556519826 1.130000e-75 294.0
27 TraesCS5D01G144300 chr3B 96.023 176 7 0 3983 4158 263803335 263803160 1.890000e-73 287.0
28 TraesCS5D01G144300 chr3B 75.085 293 66 4 148 434 10914088 10914379 3.370000e-26 130.0
29 TraesCS5D01G144300 chr4D 77.083 576 117 12 3417 3985 30143122 30143689 6.710000e-83 318.0
30 TraesCS5D01G144300 chr4D 80.966 352 59 8 1157 1504 97957977 97958324 5.300000e-69 272.0
31 TraesCS5D01G144300 chr4D 78.515 377 77 4 1141 1515 97508655 97509029 1.150000e-60 244.0
32 TraesCS5D01G144300 chr4D 79.598 348 65 5 1159 1502 97720684 97721029 1.150000e-60 244.0
33 TraesCS5D01G144300 chr4D 76.568 303 52 10 39 330 351739171 351738877 9.310000e-32 148.0
34 TraesCS5D01G144300 chrUn 96.591 176 6 0 3983 4158 108422477 108422652 4.070000e-75 292.0
35 TraesCS5D01G144300 chr1D 96.023 176 7 0 3983 4158 270277107 270277282 1.890000e-73 287.0
36 TraesCS5D01G144300 chr1D 100.000 28 0 0 512 539 416299505 416299478 8.000000e-03 52.8
37 TraesCS5D01G144300 chr4A 81.481 351 59 6 1157 1504 478219654 478219307 2.450000e-72 283.0
38 TraesCS5D01G144300 chr4A 79.387 359 70 4 1159 1515 478302678 478302322 2.480000e-62 250.0
39 TraesCS5D01G144300 chr4A 79.109 359 71 4 1159 1515 478339981 478339625 1.150000e-60 244.0
40 TraesCS5D01G144300 chr3D 95.480 177 7 1 3983 4158 251690061 251689885 8.800000e-72 281.0
41 TraesCS5D01G144300 chr3D 75.336 446 71 24 1 414 499955694 499955256 1.190000e-40 178.0
42 TraesCS5D01G144300 chr3D 77.612 134 23 5 1358 1489 177778983 177779111 1.600000e-09 75.0
43 TraesCS5D01G144300 chr3A 95.455 176 8 0 3983 4158 737582678 737582503 8.800000e-72 281.0
44 TraesCS5D01G144300 chr3A 72.172 442 94 22 11 438 125807097 125806671 1.580000e-19 108.0
45 TraesCS5D01G144300 chr3A 84.337 83 11 2 1408 1489 218729442 218729523 3.450000e-11 80.5
46 TraesCS5D01G144300 chr3A 88.235 51 6 0 488 538 34039456 34039406 1.250000e-05 62.1
47 TraesCS5D01G144300 chr4B 79.894 378 70 6 1141 1515 139399173 139399547 5.300000e-69 272.0
48 TraesCS5D01G144300 chr4B 86.740 181 24 0 1627 1807 139399603 139399783 7.050000e-48 202.0
49 TraesCS5D01G144300 chr4B 86.740 181 24 0 1627 1807 139472747 139472927 7.050000e-48 202.0
50 TraesCS5D01G144300 chr4B 86.740 181 24 0 1627 1807 139511195 139511375 7.050000e-48 202.0
51 TraesCS5D01G144300 chr4B 75.831 451 79 20 1 438 369480424 369479991 7.050000e-48 202.0
52 TraesCS5D01G144300 chr4B 81.974 233 37 5 1286 1515 139511506 139511736 4.240000e-45 193.0
53 TraesCS5D01G144300 chr1A 82.278 316 51 5 119 431 501998587 501998900 6.850000e-68 268.0
54 TraesCS5D01G144300 chr1A 90.196 51 5 0 488 538 14852730 14852680 2.680000e-07 67.6
55 TraesCS5D01G144300 chr6A 79.012 243 42 6 101 337 447623218 447623457 1.550000e-34 158.0
56 TraesCS5D01G144300 chr6A 100.000 29 0 0 510 538 121746431 121746459 2.000000e-03 54.7
57 TraesCS5D01G144300 chr2B 75.771 227 49 5 1279 1501 146992809 146993033 4.390000e-20 110.0
58 TraesCS5D01G144300 chr2B 90.196 51 5 0 488 538 720796355 720796405 2.680000e-07 67.6
59 TraesCS5D01G144300 chr7A 72.965 344 77 14 2811 3146 80133717 80134052 5.690000e-19 106.0
60 TraesCS5D01G144300 chr7A 77.778 180 31 8 2972 3146 80086692 80086867 7.350000e-18 102.0
61 TraesCS5D01G144300 chr7B 72.622 347 73 18 2811 3146 22261273 22261608 1.230000e-15 95.3
62 TraesCS5D01G144300 chr7B 89.796 49 4 1 496 544 440447186 440447233 1.250000e-05 62.1
63 TraesCS5D01G144300 chr6D 75.974 154 25 7 2945 3092 25826644 25826497 7.460000e-08 69.4
64 TraesCS5D01G144300 chr2A 87.719 57 6 1 382 438 31875083 31875138 9.650000e-07 65.8
65 TraesCS5D01G144300 chr2A 88.235 51 6 0 488 538 261665681 261665731 1.250000e-05 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G144300 chr5D 230504037 230508194 4157 False 7679 7679 100.0000 1 4158 1 chr5D.!!$F1 4157
1 TraesCS5D01G144300 chr5A 326055353 326059506 4153 True 916 2047 91.5958 1 3983 5 chr5A.!!$R2 3982
2 TraesCS5D01G144300 chr5B 275265609 275269263 3654 True 1044 1661 93.0248 480 4158 5 chr5B.!!$R3 3678
3 TraesCS5D01G144300 chr5B 542933148 542933685 537 True 327 327 78.0620 3427 3962 1 chr5B.!!$R2 535
4 TraesCS5D01G144300 chr2D 317878692 317879268 576 True 392 392 79.1380 3413 3985 1 chr2D.!!$R1 572
5 TraesCS5D01G144300 chr6B 612855165 612855748 583 False 344 344 77.9090 3413 3986 1 chr6B.!!$F1 573
6 TraesCS5D01G144300 chr7D 5318336 5318905 569 False 327 327 77.3520 3422 3985 1 chr7D.!!$F1 563
7 TraesCS5D01G144300 chr3B 576046508 576047072 564 False 329 329 77.5040 3419 3978 1 chr3B.!!$F2 559
8 TraesCS5D01G144300 chr4D 30143122 30143689 567 False 318 318 77.0830 3417 3985 1 chr4D.!!$F1 568
9 TraesCS5D01G144300 chr4B 139399173 139399783 610 False 237 272 83.3170 1141 1807 2 chr4B.!!$F2 666

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
385 683 0.030235 CCGTCAATGCCATGCTCATG 59.970 55.0 2.97 2.97 38.51 3.07 F
753 1066 0.177373 AAGCTTTATCGTCGTCCCCC 59.823 55.0 0.00 0.00 0.00 5.40 F
1077 1393 0.318441 ATAGTCTGCACTGCACACGT 59.682 50.0 0.00 0.00 32.91 4.49 F
2365 2781 0.179062 CTAGCAGCCAGGCCACTTAG 60.179 60.0 8.22 1.61 0.00 2.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2171 0.038343 TTTTGCTTTGAGCGATGGGC 60.038 50.000 0.0 0.0 46.26 5.36 R
2065 2471 1.469940 GCTGTATCGTGCAGTGTAGCT 60.470 52.381 0.0 0.0 36.42 3.32 R
2827 3345 1.153745 GAAGCCGCTGTCGATGTCT 60.154 57.895 0.0 0.0 38.10 3.41 R
3930 4477 0.032952 TTTCCAGACCACCGAACGAG 59.967 55.000 0.0 0.0 0.00 4.18 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
18 19 3.373565 CAGGCCTCCAAAACCCGC 61.374 66.667 0.00 0.00 0.00 6.13
19 20 4.678743 AGGCCTCCAAAACCCGCC 62.679 66.667 0.00 0.00 40.03 6.13
23 24 2.596338 CTCCAAAACCCGCCCGTT 60.596 61.111 0.00 0.00 0.00 4.44
26 27 2.272447 CCAAAACCCGCCCGTTGAT 61.272 57.895 0.00 0.00 0.00 2.57
42 43 3.058155 CGTTGATATCCTGTACGGGAGAG 60.058 52.174 27.05 8.22 38.92 3.20
45 46 3.654321 TGATATCCTGTACGGGAGAGGTA 59.346 47.826 27.05 15.57 39.73 3.08
58 59 4.439968 GGGAGAGGTACGATTAGGTTTTG 58.560 47.826 0.00 0.00 0.00 2.44
60 61 4.081254 GGAGAGGTACGATTAGGTTTTGGT 60.081 45.833 0.00 0.00 0.00 3.67
88 90 1.081641 CTACGCGACTGTTCACCGT 60.082 57.895 15.93 0.00 34.71 4.83
132 134 2.203070 ATCGCCTTCGCCATCACC 60.203 61.111 0.00 0.00 35.26 4.02
148 150 1.012086 CACCATGAGTCAGCAATCCG 58.988 55.000 0.00 0.00 0.00 4.18
174 176 2.736995 CGACTCGCCGCCAAGAAA 60.737 61.111 0.00 0.00 0.00 2.52
175 177 2.861006 GACTCGCCGCCAAGAAAC 59.139 61.111 0.00 0.00 0.00 2.78
176 178 1.668151 GACTCGCCGCCAAGAAACT 60.668 57.895 0.00 0.00 0.00 2.66
177 179 1.227853 ACTCGCCGCCAAGAAACTT 60.228 52.632 0.00 0.00 0.00 2.66
179 181 1.227704 TCGCCGCCAAGAAACTTGA 60.228 52.632 12.25 0.00 0.00 3.02
181 183 0.385974 CGCCGCCAAGAAACTTGAAG 60.386 55.000 12.25 0.00 0.00 3.02
183 185 0.039165 CCGCCAAGAAACTTGAAGCC 60.039 55.000 12.25 0.00 0.00 4.35
184 186 0.385974 CGCCAAGAAACTTGAAGCCG 60.386 55.000 12.25 6.35 0.00 5.52
185 187 0.951558 GCCAAGAAACTTGAAGCCGA 59.048 50.000 12.25 0.00 0.00 5.54
189 191 3.058639 CCAAGAAACTTGAAGCCGAGAAG 60.059 47.826 12.25 0.00 0.00 2.85
190 192 3.753294 AGAAACTTGAAGCCGAGAAGA 57.247 42.857 0.00 0.00 0.00 2.87
192 194 4.061596 AGAAACTTGAAGCCGAGAAGAAG 58.938 43.478 0.00 0.00 0.00 2.85
200 498 4.129737 CGAGAAGAAGGCCGCCGA 62.130 66.667 3.05 0.00 0.00 5.54
201 499 2.264794 GAGAAGAAGGCCGCCGAA 59.735 61.111 3.05 0.00 0.00 4.30
203 501 0.953960 GAGAAGAAGGCCGCCGAAAA 60.954 55.000 3.05 0.00 0.00 2.29
242 540 2.689034 GGCCTGGCCTACTGGAGT 60.689 66.667 30.42 0.00 46.69 3.85
243 541 2.586792 GCCTGGCCTACTGGAGTG 59.413 66.667 7.66 0.00 40.42 3.51
244 542 2.294078 GCCTGGCCTACTGGAGTGT 61.294 63.158 7.66 0.00 40.42 3.55
245 543 0.976073 GCCTGGCCTACTGGAGTGTA 60.976 60.000 7.66 0.00 40.42 2.90
246 544 1.794714 CCTGGCCTACTGGAGTGTAT 58.205 55.000 3.32 0.00 40.42 2.29
247 545 2.958818 CCTGGCCTACTGGAGTGTATA 58.041 52.381 3.32 0.00 40.42 1.47
248 546 3.305720 CCTGGCCTACTGGAGTGTATAA 58.694 50.000 3.32 0.00 40.42 0.98
249 547 3.069729 CCTGGCCTACTGGAGTGTATAAC 59.930 52.174 3.32 0.00 40.42 1.89
250 548 3.961408 CTGGCCTACTGGAGTGTATAACT 59.039 47.826 3.32 0.00 43.85 2.24
265 563 0.465287 TAACTCGTTTATCCCGCCCC 59.535 55.000 0.00 0.00 0.00 5.80
266 564 1.269703 AACTCGTTTATCCCGCCCCT 61.270 55.000 0.00 0.00 0.00 4.79
267 565 1.227556 CTCGTTTATCCCGCCCCTG 60.228 63.158 0.00 0.00 0.00 4.45
268 566 1.968050 CTCGTTTATCCCGCCCCTGT 61.968 60.000 0.00 0.00 0.00 4.00
269 567 1.078001 CGTTTATCCCGCCCCTGTT 60.078 57.895 0.00 0.00 0.00 3.16
270 568 0.678684 CGTTTATCCCGCCCCTGTTT 60.679 55.000 0.00 0.00 0.00 2.83
271 569 1.552578 GTTTATCCCGCCCCTGTTTT 58.447 50.000 0.00 0.00 0.00 2.43
272 570 2.725637 GTTTATCCCGCCCCTGTTTTA 58.274 47.619 0.00 0.00 0.00 1.52
273 571 3.293337 GTTTATCCCGCCCCTGTTTTAT 58.707 45.455 0.00 0.00 0.00 1.40
274 572 3.673543 TTATCCCGCCCCTGTTTTATT 57.326 42.857 0.00 0.00 0.00 1.40
275 573 2.543037 ATCCCGCCCCTGTTTTATTT 57.457 45.000 0.00 0.00 0.00 1.40
277 575 1.356398 TCCCGCCCCTGTTTTATTTCT 59.644 47.619 0.00 0.00 0.00 2.52
279 577 2.167662 CCGCCCCTGTTTTATTTCTGT 58.832 47.619 0.00 0.00 0.00 3.41
280 578 2.163613 CCGCCCCTGTTTTATTTCTGTC 59.836 50.000 0.00 0.00 0.00 3.51
281 579 3.081804 CGCCCCTGTTTTATTTCTGTCT 58.918 45.455 0.00 0.00 0.00 3.41
283 581 4.698304 CGCCCCTGTTTTATTTCTGTCTTA 59.302 41.667 0.00 0.00 0.00 2.10
284 582 5.163754 CGCCCCTGTTTTATTTCTGTCTTAG 60.164 44.000 0.00 0.00 0.00 2.18
285 583 5.393135 GCCCCTGTTTTATTTCTGTCTTAGC 60.393 44.000 0.00 0.00 0.00 3.09
286 584 5.710099 CCCCTGTTTTATTTCTGTCTTAGCA 59.290 40.000 0.00 0.00 0.00 3.49
287 585 6.127897 CCCCTGTTTTATTTCTGTCTTAGCAG 60.128 42.308 0.00 0.00 37.81 4.24
289 587 7.606456 CCCTGTTTTATTTCTGTCTTAGCAGTA 59.394 37.037 4.23 0.00 37.70 2.74
291 589 9.209175 CTGTTTTATTTCTGTCTTAGCAGTACT 57.791 33.333 0.00 0.00 37.70 2.73
294 592 8.928270 TTTATTTCTGTCTTAGCAGTACTAGC 57.072 34.615 0.00 1.88 37.70 3.42
295 593 6.783708 ATTTCTGTCTTAGCAGTACTAGCT 57.216 37.500 19.21 19.21 45.77 3.32
296 594 7.883391 ATTTCTGTCTTAGCAGTACTAGCTA 57.117 36.000 17.64 17.64 43.25 3.32
297 595 7.883391 TTTCTGTCTTAGCAGTACTAGCTAT 57.117 36.000 20.45 6.23 43.48 2.97
299 597 9.575868 TTTCTGTCTTAGCAGTACTAGCTATAT 57.424 33.333 20.45 5.44 43.48 0.86
300 598 8.554835 TCTGTCTTAGCAGTACTAGCTATATG 57.445 38.462 20.45 15.45 43.48 1.78
301 599 8.158132 TCTGTCTTAGCAGTACTAGCTATATGT 58.842 37.037 20.45 0.00 43.48 2.29
302 600 8.100508 TGTCTTAGCAGTACTAGCTATATGTG 57.899 38.462 20.45 12.32 43.48 3.21
303 601 7.720074 TGTCTTAGCAGTACTAGCTATATGTGT 59.280 37.037 20.45 0.00 43.48 3.72
304 602 9.217278 GTCTTAGCAGTACTAGCTATATGTGTA 57.783 37.037 20.45 8.89 43.48 2.90
305 603 9.961264 TCTTAGCAGTACTAGCTATATGTGTAT 57.039 33.333 20.45 2.53 43.48 2.29
309 607 9.688091 AGCAGTACTAGCTATATGTGTATATGT 57.312 33.333 15.39 0.00 41.32 2.29
324 622 9.964354 ATGTGTATATGTTTCCACTATATGCAT 57.036 29.630 3.79 3.79 33.88 3.96
332 630 8.831715 TGTTTCCACTATATGCATAGTACATG 57.168 34.615 12.79 6.01 44.55 3.21
333 631 7.387673 TGTTTCCACTATATGCATAGTACATGC 59.612 37.037 12.79 17.91 44.55 4.06
334 632 6.857437 TCCACTATATGCATAGTACATGCT 57.143 37.500 22.31 14.34 44.55 3.79
335 633 7.244886 TCCACTATATGCATAGTACATGCTT 57.755 36.000 22.31 19.45 44.55 3.91
336 634 7.099120 TCCACTATATGCATAGTACATGCTTG 58.901 38.462 22.31 0.00 44.55 4.01
337 635 6.183360 CCACTATATGCATAGTACATGCTTGC 60.183 42.308 22.31 12.53 44.55 4.01
338 636 6.592994 CACTATATGCATAGTACATGCTTGCT 59.407 38.462 22.31 14.18 44.55 3.91
339 637 7.118825 CACTATATGCATAGTACATGCTTGCTT 59.881 37.037 22.31 12.29 44.55 3.91
340 638 4.563337 ATGCATAGTACATGCTTGCTTG 57.437 40.909 22.31 6.90 44.79 4.01
341 639 2.684374 TGCATAGTACATGCTTGCTTGG 59.316 45.455 22.31 0.00 44.79 3.61
342 640 2.684881 GCATAGTACATGCTTGCTTGGT 59.315 45.455 17.63 2.53 41.52 3.67
343 641 3.129287 GCATAGTACATGCTTGCTTGGTT 59.871 43.478 17.63 1.79 41.52 3.67
344 642 4.731773 GCATAGTACATGCTTGCTTGGTTC 60.732 45.833 17.63 3.68 41.52 3.62
345 643 1.806542 AGTACATGCTTGCTTGGTTCG 59.193 47.619 12.06 0.00 0.00 3.95
346 644 1.535462 GTACATGCTTGCTTGGTTCGT 59.465 47.619 12.06 0.00 0.00 3.85
347 645 1.890876 ACATGCTTGCTTGGTTCGTA 58.109 45.000 12.06 0.00 0.00 3.43
348 646 2.226330 ACATGCTTGCTTGGTTCGTAA 58.774 42.857 12.06 0.00 0.00 3.18
349 647 2.819608 ACATGCTTGCTTGGTTCGTAAT 59.180 40.909 12.06 0.00 0.00 1.89
350 648 3.119849 ACATGCTTGCTTGGTTCGTAATC 60.120 43.478 12.06 0.00 0.00 1.75
351 649 2.499197 TGCTTGCTTGGTTCGTAATCA 58.501 42.857 0.00 0.00 0.00 2.57
352 650 2.881513 TGCTTGCTTGGTTCGTAATCAA 59.118 40.909 0.00 0.00 0.00 2.57
353 651 3.505680 TGCTTGCTTGGTTCGTAATCAAT 59.494 39.130 0.00 0.00 0.00 2.57
354 652 3.853671 GCTTGCTTGGTTCGTAATCAATG 59.146 43.478 0.00 0.00 0.00 2.82
355 653 4.615912 GCTTGCTTGGTTCGTAATCAATGT 60.616 41.667 0.00 0.00 0.00 2.71
356 654 4.418013 TGCTTGGTTCGTAATCAATGTG 57.582 40.909 0.00 0.00 0.00 3.21
357 655 3.818210 TGCTTGGTTCGTAATCAATGTGT 59.182 39.130 0.00 0.00 0.00 3.72
358 656 4.158384 GCTTGGTTCGTAATCAATGTGTG 58.842 43.478 0.00 0.00 0.00 3.82
359 657 4.083537 GCTTGGTTCGTAATCAATGTGTGA 60.084 41.667 0.00 0.00 41.67 3.58
361 659 6.183360 GCTTGGTTCGTAATCAATGTGTGATA 60.183 38.462 0.00 0.00 46.80 2.15
362 660 7.467267 GCTTGGTTCGTAATCAATGTGTGATAT 60.467 37.037 0.00 0.00 46.80 1.63
363 661 8.950208 TTGGTTCGTAATCAATGTGTGATATA 57.050 30.769 0.00 0.00 46.80 0.86
364 662 9.554395 TTGGTTCGTAATCAATGTGTGATATAT 57.446 29.630 0.00 0.00 46.80 0.86
365 663 9.554395 TGGTTCGTAATCAATGTGTGATATATT 57.446 29.630 0.00 0.00 46.80 1.28
368 666 8.460831 TCGTAATCAATGTGTGATATATTCCG 57.539 34.615 0.00 0.00 46.80 4.30
369 667 8.085909 TCGTAATCAATGTGTGATATATTCCGT 58.914 33.333 0.00 0.00 46.80 4.69
370 668 8.373256 CGTAATCAATGTGTGATATATTCCGTC 58.627 37.037 0.00 0.00 46.80 4.79
371 669 9.203421 GTAATCAATGTGTGATATATTCCGTCA 57.797 33.333 0.00 0.00 46.80 4.35
372 670 8.675705 AATCAATGTGTGATATATTCCGTCAA 57.324 30.769 0.00 0.00 46.80 3.18
373 671 8.853077 ATCAATGTGTGATATATTCCGTCAAT 57.147 30.769 0.00 0.00 45.59 2.57
374 672 8.086851 TCAATGTGTGATATATTCCGTCAATG 57.913 34.615 0.00 0.00 0.00 2.82
375 673 5.922739 TGTGTGATATATTCCGTCAATGC 57.077 39.130 0.00 0.00 0.00 3.56
376 674 4.754618 TGTGTGATATATTCCGTCAATGCC 59.245 41.667 0.00 0.00 0.00 4.40
377 675 4.754618 GTGTGATATATTCCGTCAATGCCA 59.245 41.667 0.00 0.00 0.00 4.92
378 676 5.412594 GTGTGATATATTCCGTCAATGCCAT 59.587 40.000 0.00 0.00 0.00 4.40
379 677 5.412286 TGTGATATATTCCGTCAATGCCATG 59.588 40.000 0.00 0.00 0.00 3.66
380 678 4.395854 TGATATATTCCGTCAATGCCATGC 59.604 41.667 0.00 0.00 0.00 4.06
381 679 2.346766 TATTCCGTCAATGCCATGCT 57.653 45.000 0.00 0.00 0.00 3.79
382 680 1.027357 ATTCCGTCAATGCCATGCTC 58.973 50.000 0.00 0.00 0.00 4.26
383 681 0.322366 TTCCGTCAATGCCATGCTCA 60.322 50.000 0.00 0.00 0.00 4.26
384 682 0.107066 TCCGTCAATGCCATGCTCAT 60.107 50.000 0.00 0.00 0.00 2.90
385 683 0.030235 CCGTCAATGCCATGCTCATG 59.970 55.000 2.97 2.97 38.51 3.07
386 684 1.018910 CGTCAATGCCATGCTCATGA 58.981 50.000 11.17 0.00 41.20 3.07
387 685 1.607148 CGTCAATGCCATGCTCATGAT 59.393 47.619 11.17 0.00 41.20 2.45
388 686 2.034179 CGTCAATGCCATGCTCATGATT 59.966 45.455 11.17 1.94 41.20 2.57
389 687 3.490249 CGTCAATGCCATGCTCATGATTT 60.490 43.478 11.17 0.08 41.20 2.17
390 688 4.261280 CGTCAATGCCATGCTCATGATTTA 60.261 41.667 11.17 0.00 41.20 1.40
391 689 5.564063 CGTCAATGCCATGCTCATGATTTAT 60.564 40.000 11.17 0.00 41.20 1.40
392 690 6.220930 GTCAATGCCATGCTCATGATTTATT 58.779 36.000 11.17 4.04 41.20 1.40
393 691 6.365247 GTCAATGCCATGCTCATGATTTATTC 59.635 38.462 11.17 0.00 41.20 1.75
394 692 6.041069 TCAATGCCATGCTCATGATTTATTCA 59.959 34.615 11.17 0.00 41.20 2.57
395 693 6.605471 ATGCCATGCTCATGATTTATTCAT 57.395 33.333 11.17 0.00 46.27 2.57
419 717 9.771915 CATGGGTTAAATTAATCAAAACATTGC 57.228 29.630 0.00 0.00 0.00 3.56
420 718 9.737844 ATGGGTTAAATTAATCAAAACATTGCT 57.262 25.926 0.00 0.00 0.00 3.91
439 737 8.556517 CATTGCTAATGTATTCAACACATCTG 57.443 34.615 0.00 0.00 42.09 2.90
440 738 7.920160 TTGCTAATGTATTCAACACATCTGA 57.080 32.000 0.00 0.00 42.09 3.27
441 739 8.510243 TTGCTAATGTATTCAACACATCTGAT 57.490 30.769 0.00 0.00 42.09 2.90
442 740 8.510243 TGCTAATGTATTCAACACATCTGATT 57.490 30.769 0.00 0.00 42.09 2.57
443 741 8.615211 TGCTAATGTATTCAACACATCTGATTC 58.385 33.333 0.00 0.00 42.09 2.52
444 742 8.615211 GCTAATGTATTCAACACATCTGATTCA 58.385 33.333 0.00 0.00 42.09 2.57
446 744 8.797350 AATGTATTCAACACATCTGATTCAGA 57.203 30.769 18.29 18.29 42.23 3.27
447 745 8.797350 ATGTATTCAACACATCTGATTCAGAA 57.203 30.769 19.73 4.58 41.71 3.02
448 746 8.620116 TGTATTCAACACATCTGATTCAGAAA 57.380 30.769 19.73 8.54 37.31 2.52
449 747 9.065798 TGTATTCAACACATCTGATTCAGAAAA 57.934 29.630 19.73 6.94 37.31 2.29
450 748 9.897744 GTATTCAACACATCTGATTCAGAAAAA 57.102 29.630 19.73 7.53 44.04 1.94
472 770 4.937696 ATGCGAACATCGTATTTGTGAA 57.062 36.364 1.45 0.00 42.31 3.18
473 771 4.060288 TGCGAACATCGTATTTGTGAAC 57.940 40.909 1.45 0.00 42.81 3.18
474 772 3.495001 TGCGAACATCGTATTTGTGAACA 59.505 39.130 1.45 0.00 42.81 3.18
475 773 4.024809 TGCGAACATCGTATTTGTGAACAA 60.025 37.500 1.45 0.00 42.81 2.83
476 774 4.907010 GCGAACATCGTATTTGTGAACAAA 59.093 37.500 10.80 10.80 44.57 2.83
477 775 5.058008 GCGAACATCGTATTTGTGAACAAAG 59.942 40.000 13.54 1.89 44.14 2.77
478 776 6.133392 CGAACATCGTATTTGTGAACAAAGT 58.867 36.000 13.54 3.28 40.81 2.66
503 801 8.403236 GTGAGTATTTGAAAGGTGTAACAGTTT 58.597 33.333 0.00 0.00 39.98 2.66
506 804 6.783708 ATTTGAAAGGTGTAACAGTTTCCA 57.216 33.333 0.00 0.00 39.34 3.53
508 806 5.105567 TGAAAGGTGTAACAGTTTCCAGA 57.894 39.130 0.00 0.00 39.34 3.86
523 821 1.281925 CCAGATGCCCCTACACCCTT 61.282 60.000 0.00 0.00 0.00 3.95
612 918 9.292195 TCTTCCGTAAAAGAAACCATTAATCTT 57.708 29.630 0.00 0.00 35.00 2.40
748 1061 3.379372 TGGTAGCTAAGCTTTATCGTCGT 59.621 43.478 3.20 0.00 40.44 4.34
750 1063 3.081329 AGCTAAGCTTTATCGTCGTCC 57.919 47.619 3.20 0.00 33.89 4.79
751 1064 2.125685 GCTAAGCTTTATCGTCGTCCC 58.874 52.381 3.20 0.00 0.00 4.46
752 1065 2.740452 CTAAGCTTTATCGTCGTCCCC 58.260 52.381 3.20 0.00 0.00 4.81
753 1066 0.177373 AAGCTTTATCGTCGTCCCCC 59.823 55.000 0.00 0.00 0.00 5.40
888 1201 2.028748 GCCCTAGACAACGGTACTTCAA 60.029 50.000 0.00 0.00 0.00 2.69
890 1203 4.430908 CCCTAGACAACGGTACTTCAATC 58.569 47.826 0.00 0.00 0.00 2.67
971 1287 4.370364 TTCTTTCTTTCAAGCACCACAC 57.630 40.909 0.00 0.00 0.00 3.82
991 1307 4.343526 ACACTGCCACCACAAATAATTCAA 59.656 37.500 0.00 0.00 0.00 2.69
1057 1373 3.640000 GCAACACACGCACGCTCT 61.640 61.111 0.00 0.00 0.00 4.09
1077 1393 0.318441 ATAGTCTGCACTGCACACGT 59.682 50.000 0.00 0.00 32.91 4.49
1078 1394 0.597377 TAGTCTGCACTGCACACGTG 60.597 55.000 15.48 15.48 32.91 4.49
1245 1595 4.961511 GCGTCGGTGGTGCAGTCA 62.962 66.667 0.00 0.00 0.00 3.41
1522 1872 1.583477 GCCGTACGTATAGGAGCCC 59.417 63.158 20.01 2.98 0.00 5.19
1571 1921 6.517374 GCATACGTTAACGGACTTTTTAGTTG 59.483 38.462 29.81 15.25 44.95 3.16
1834 2188 2.689785 CGCCCATCGCTCAAAGCAA 61.690 57.895 0.00 0.00 42.58 3.91
1905 2301 2.104111 ACTTTTGGACGATCACTGGTGA 59.896 45.455 5.87 5.87 44.59 4.02
1935 2331 5.344743 TGTAGACCTAATTTCTGGCAGAG 57.655 43.478 17.91 7.46 0.00 3.35
1939 2335 4.081198 AGACCTAATTTCTGGCAGAGTGAG 60.081 45.833 17.91 12.41 0.00 3.51
2050 2456 4.156922 TCACACTCTGCTTCTACTAGCTTC 59.843 45.833 0.00 0.00 41.76 3.86
2053 2459 3.127895 ACTCTGCTTCTACTAGCTTCACG 59.872 47.826 0.00 0.00 41.76 4.35
2152 2562 4.278419 ACTTGAAAGCCTGGACATTGTTAC 59.722 41.667 0.00 0.00 0.00 2.50
2158 2568 4.980573 AGCCTGGACATTGTTACTTTACA 58.019 39.130 0.00 0.00 0.00 2.41
2223 2639 5.002464 TCGTACTACCAATTGGAAGTAGC 57.998 43.478 31.22 14.00 37.57 3.58
2334 2750 4.521943 GCATTTTGCACGTCATAGATCTC 58.478 43.478 0.00 0.00 44.26 2.75
2336 2752 5.277683 GCATTTTGCACGTCATAGATCTCAT 60.278 40.000 0.00 0.00 44.26 2.90
2365 2781 0.179062 CTAGCAGCCAGGCCACTTAG 60.179 60.000 8.22 1.61 0.00 2.18
2425 2939 6.909550 ATCTATAAAGCGGAATGAGAGTCT 57.090 37.500 0.00 0.00 0.00 3.24
2456 2973 2.371658 AGAATAAAGCTGGCATCCCC 57.628 50.000 0.00 0.00 0.00 4.81
2457 2974 0.954452 GAATAAAGCTGGCATCCCCG 59.046 55.000 0.00 0.00 35.87 5.73
2563 3080 9.996554 TCCCTTTTTCTTTCTTCCATTATTTTC 57.003 29.630 0.00 0.00 0.00 2.29
2583 3100 8.594881 ATTTTCAGAGAATATACGCACTTAGG 57.405 34.615 0.00 0.00 0.00 2.69
2584 3101 5.707242 TCAGAGAATATACGCACTTAGGG 57.293 43.478 0.00 0.00 0.00 3.53
2597 3114 2.488153 CACTTAGGGGCAAAGTAAGTGC 59.512 50.000 11.98 0.00 43.91 4.40
2666 3184 9.958180 CCCAAATGTTCCCTTTTTATTCTAAAT 57.042 29.630 0.00 0.00 0.00 1.40
2690 3208 4.586306 TTTAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
2691 3209 2.059756 AGAAAAGGAGGATGACCCCA 57.940 50.000 0.00 0.00 36.73 4.96
2692 3210 2.358258 AGAAAAGGAGGATGACCCCAA 58.642 47.619 0.00 0.00 36.73 4.12
2693 3211 2.721906 AGAAAAGGAGGATGACCCCAAA 59.278 45.455 0.00 0.00 36.73 3.28
2694 3212 3.337909 AGAAAAGGAGGATGACCCCAAAT 59.662 43.478 0.00 0.00 36.73 2.32
2695 3213 4.544152 AGAAAAGGAGGATGACCCCAAATA 59.456 41.667 0.00 0.00 36.73 1.40
2728 3246 3.057969 TGAAGCGTTCCTCATCACAAT 57.942 42.857 0.00 0.00 0.00 2.71
2731 3249 5.000591 TGAAGCGTTCCTCATCACAATTTA 58.999 37.500 0.00 0.00 0.00 1.40
2803 3321 0.740737 AAGCTCGCTGCACAAACTTT 59.259 45.000 0.00 0.00 45.94 2.66
2827 3345 2.296190 AGCACACATCTACAACGAGACA 59.704 45.455 0.00 0.00 0.00 3.41
3103 3621 6.351966 GCATGATCAAGATGGGAGATATCTCA 60.352 42.308 29.33 14.59 44.60 3.27
3599 4131 3.555324 TCCTTGCAGGTGCGGTGA 61.555 61.111 0.00 0.00 45.83 4.02
3807 4342 2.371910 TAACGACGATCAATGTGGCA 57.628 45.000 0.00 0.00 0.00 4.92
3821 4356 2.964978 GGCATCAAGGCGCTTGTT 59.035 55.556 7.64 2.41 41.66 2.83
3885 4424 2.735237 CCGGCTCCGATTAGGGAC 59.265 66.667 10.28 0.00 42.83 4.46
3945 4492 2.022129 GTGCTCGTTCGGTGGTCTG 61.022 63.158 0.00 0.00 0.00 3.51
3998 4545 3.892588 AGTTGGTTTTTCGATAAAGGGCA 59.107 39.130 0.98 0.00 0.00 5.36
4017 4564 7.775053 AGGGCATCTTTATTAACTCAAAACA 57.225 32.000 0.00 0.00 0.00 2.83
4019 4566 8.815912 AGGGCATCTTTATTAACTCAAAACATT 58.184 29.630 0.00 0.00 0.00 2.71
4055 4602 8.489489 AGATACAAATCATGATGAGTAACACCT 58.511 33.333 18.78 12.79 34.28 4.00
4068 4615 0.254178 AACACCTGGCCTCTGCATAG 59.746 55.000 3.32 0.00 40.13 2.23
4072 4619 1.765314 ACCTGGCCTCTGCATAGTTAG 59.235 52.381 3.32 0.00 40.13 2.34
4129 4676 9.736023 AAGAAAATAAAAAGATGACATATCGGC 57.264 29.630 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.385528 GATATCAACGGGCGGGTTTT 58.614 50.000 0.00 0.00 0.00 2.43
20 21 2.882761 TCTCCCGTACAGGATATCAACG 59.117 50.000 4.83 8.33 45.00 4.10
23 24 2.445905 ACCTCTCCCGTACAGGATATCA 59.554 50.000 4.83 0.00 45.00 2.15
26 27 2.224378 CGTACCTCTCCCGTACAGGATA 60.224 54.545 0.00 0.00 45.00 2.59
42 43 3.373130 GCTCACCAAAACCTAATCGTACC 59.627 47.826 0.00 0.00 0.00 3.34
45 46 2.073816 CGCTCACCAAAACCTAATCGT 58.926 47.619 0.00 0.00 0.00 3.73
76 78 2.676342 AGACAAACAACGGTGAACAGTC 59.324 45.455 7.88 9.64 0.00 3.51
88 90 8.902540 ACAATGTAGATGAAGTAGACAAACAA 57.097 30.769 0.00 0.00 0.00 2.83
132 134 1.329906 GCTTCGGATTGCTGACTCATG 59.670 52.381 0.00 0.00 0.00 3.07
166 168 0.951558 TCGGCTTCAAGTTTCTTGGC 59.048 50.000 9.18 6.07 0.00 4.52
167 169 2.494059 TCTCGGCTTCAAGTTTCTTGG 58.506 47.619 9.18 0.00 0.00 3.61
168 170 3.809832 TCTTCTCGGCTTCAAGTTTCTTG 59.190 43.478 3.44 3.44 0.00 3.02
169 171 4.073293 TCTTCTCGGCTTCAAGTTTCTT 57.927 40.909 0.00 0.00 0.00 2.52
170 172 3.753294 TCTTCTCGGCTTCAAGTTTCT 57.247 42.857 0.00 0.00 0.00 2.52
174 176 1.609320 GCCTTCTTCTCGGCTTCAAGT 60.609 52.381 0.00 0.00 42.98 3.16
175 177 1.082690 GCCTTCTTCTCGGCTTCAAG 58.917 55.000 0.00 0.00 42.98 3.02
176 178 0.321653 GGCCTTCTTCTCGGCTTCAA 60.322 55.000 0.00 0.00 45.57 2.69
177 179 1.296715 GGCCTTCTTCTCGGCTTCA 59.703 57.895 0.00 0.00 45.57 3.02
179 181 2.266055 CGGCCTTCTTCTCGGCTT 59.734 61.111 0.00 0.00 45.57 4.35
183 185 3.642778 TTCGGCGGCCTTCTTCTCG 62.643 63.158 18.34 0.73 0.00 4.04
184 186 0.953960 TTTTCGGCGGCCTTCTTCTC 60.954 55.000 18.34 0.00 0.00 2.87
185 187 1.072505 TTTTCGGCGGCCTTCTTCT 59.927 52.632 18.34 0.00 0.00 2.85
189 191 2.254350 GTGTTTTCGGCGGCCTTC 59.746 61.111 18.34 3.40 0.00 3.46
190 192 3.292159 GGTGTTTTCGGCGGCCTT 61.292 61.111 18.34 0.00 0.00 4.35
226 524 0.976073 TACACTCCAGTAGGCCAGGC 60.976 60.000 5.01 1.26 33.74 4.85
227 525 1.794714 ATACACTCCAGTAGGCCAGG 58.205 55.000 5.01 0.54 33.74 4.45
229 527 3.958798 GAGTTATACACTCCAGTAGGCCA 59.041 47.826 5.01 0.00 45.84 5.36
230 528 4.587584 GAGTTATACACTCCAGTAGGCC 57.412 50.000 0.00 0.00 45.84 5.19
240 538 4.500375 GGCGGGATAAACGAGTTATACACT 60.500 45.833 0.00 0.00 34.97 3.55
241 539 3.737774 GGCGGGATAAACGAGTTATACAC 59.262 47.826 0.00 0.00 34.97 2.90
242 540 3.243839 GGGCGGGATAAACGAGTTATACA 60.244 47.826 0.00 0.00 34.97 2.29
243 541 3.320626 GGGCGGGATAAACGAGTTATAC 58.679 50.000 0.00 0.00 32.26 1.47
244 542 2.299867 GGGGCGGGATAAACGAGTTATA 59.700 50.000 0.00 0.00 32.26 0.98
245 543 1.071228 GGGGCGGGATAAACGAGTTAT 59.929 52.381 0.00 0.00 34.97 1.89
246 544 0.465287 GGGGCGGGATAAACGAGTTA 59.535 55.000 0.00 0.00 0.00 2.24
247 545 1.222661 GGGGCGGGATAAACGAGTT 59.777 57.895 0.00 0.00 0.00 3.01
248 546 1.688187 AGGGGCGGGATAAACGAGT 60.688 57.895 0.00 0.00 0.00 4.18
249 547 1.227556 CAGGGGCGGGATAAACGAG 60.228 63.158 0.00 0.00 0.00 4.18
250 548 1.555477 AACAGGGGCGGGATAAACGA 61.555 55.000 0.00 0.00 0.00 3.85
251 549 0.678684 AAACAGGGGCGGGATAAACG 60.679 55.000 0.00 0.00 0.00 3.60
252 550 1.552578 AAAACAGGGGCGGGATAAAC 58.447 50.000 0.00 0.00 0.00 2.01
253 551 3.673543 ATAAAACAGGGGCGGGATAAA 57.326 42.857 0.00 0.00 0.00 1.40
254 552 3.673543 AATAAAACAGGGGCGGGATAA 57.326 42.857 0.00 0.00 0.00 1.75
256 554 2.024369 AGAAATAAAACAGGGGCGGGAT 60.024 45.455 0.00 0.00 0.00 3.85
257 555 1.356398 AGAAATAAAACAGGGGCGGGA 59.644 47.619 0.00 0.00 0.00 5.14
259 557 2.163613 GACAGAAATAAAACAGGGGCGG 59.836 50.000 0.00 0.00 0.00 6.13
260 558 3.081804 AGACAGAAATAAAACAGGGGCG 58.918 45.455 0.00 0.00 0.00 6.13
261 559 5.393135 GCTAAGACAGAAATAAAACAGGGGC 60.393 44.000 0.00 0.00 0.00 5.80
265 563 9.209175 AGTACTGCTAAGACAGAAATAAAACAG 57.791 33.333 0.00 0.00 40.25 3.16
268 566 9.367444 GCTAGTACTGCTAAGACAGAAATAAAA 57.633 33.333 5.39 0.00 40.25 1.52
269 567 8.750298 AGCTAGTACTGCTAAGACAGAAATAAA 58.250 33.333 15.39 0.00 40.25 1.40
270 568 8.294954 AGCTAGTACTGCTAAGACAGAAATAA 57.705 34.615 15.39 0.00 40.25 1.40
271 569 7.883391 AGCTAGTACTGCTAAGACAGAAATA 57.117 36.000 15.39 0.00 40.25 1.40
272 570 6.783708 AGCTAGTACTGCTAAGACAGAAAT 57.216 37.500 15.39 0.00 40.25 2.17
273 571 7.883391 ATAGCTAGTACTGCTAAGACAGAAA 57.117 36.000 22.38 6.95 44.73 2.52
274 572 9.004717 CATATAGCTAGTACTGCTAAGACAGAA 57.995 37.037 22.38 7.47 44.73 3.02
275 573 8.158132 ACATATAGCTAGTACTGCTAAGACAGA 58.842 37.037 22.38 8.00 44.73 3.41
277 575 7.720074 ACACATATAGCTAGTACTGCTAAGACA 59.280 37.037 22.38 13.07 44.73 3.41
279 577 9.961264 ATACACATATAGCTAGTACTGCTAAGA 57.039 33.333 22.38 16.49 44.73 2.10
283 581 9.688091 ACATATACACATATAGCTAGTACTGCT 57.312 33.333 19.21 19.21 43.79 4.24
306 604 9.440773 CATGTACTATGCATATAGTGGAAACAT 57.559 33.333 6.92 8.14 46.80 2.71
307 605 7.387673 GCATGTACTATGCATATAGTGGAAACA 59.612 37.037 19.12 6.18 46.80 2.83
309 607 7.679783 AGCATGTACTATGCATATAGTGGAAA 58.320 34.615 23.27 0.00 46.80 3.13
310 608 7.244886 AGCATGTACTATGCATATAGTGGAA 57.755 36.000 23.27 0.00 46.80 3.53
311 609 6.857437 AGCATGTACTATGCATATAGTGGA 57.143 37.500 23.27 0.00 46.80 4.02
313 611 6.592994 AGCAAGCATGTACTATGCATATAGTG 59.407 38.462 23.27 14.90 46.80 2.74
317 615 5.182570 CCAAGCAAGCATGTACTATGCATAT 59.817 40.000 23.27 12.06 46.77 1.78
318 616 4.516321 CCAAGCAAGCATGTACTATGCATA 59.484 41.667 23.27 6.20 46.77 3.14
319 617 3.317149 CCAAGCAAGCATGTACTATGCAT 59.683 43.478 23.27 3.79 46.77 3.96
320 618 2.684374 CCAAGCAAGCATGTACTATGCA 59.316 45.455 23.27 0.00 46.77 3.96
321 619 2.684881 ACCAAGCAAGCATGTACTATGC 59.315 45.455 17.36 17.36 44.85 3.14
322 620 4.494690 CGAACCAAGCAAGCATGTACTATG 60.495 45.833 0.00 0.00 0.00 2.23
323 621 3.623060 CGAACCAAGCAAGCATGTACTAT 59.377 43.478 0.00 0.00 0.00 2.12
324 622 3.000041 CGAACCAAGCAAGCATGTACTA 59.000 45.455 0.00 0.00 0.00 1.82
325 623 1.806542 CGAACCAAGCAAGCATGTACT 59.193 47.619 0.00 0.00 0.00 2.73
326 624 1.535462 ACGAACCAAGCAAGCATGTAC 59.465 47.619 0.00 0.00 0.00 2.90
327 625 1.890876 ACGAACCAAGCAAGCATGTA 58.109 45.000 0.00 0.00 0.00 2.29
328 626 1.890876 TACGAACCAAGCAAGCATGT 58.109 45.000 0.00 0.00 0.00 3.21
329 627 2.987413 TTACGAACCAAGCAAGCATG 57.013 45.000 0.00 0.00 0.00 4.06
330 628 3.081061 TGATTACGAACCAAGCAAGCAT 58.919 40.909 0.00 0.00 0.00 3.79
331 629 2.499197 TGATTACGAACCAAGCAAGCA 58.501 42.857 0.00 0.00 0.00 3.91
332 630 3.552604 TTGATTACGAACCAAGCAAGC 57.447 42.857 0.00 0.00 28.77 4.01
333 631 4.853196 CACATTGATTACGAACCAAGCAAG 59.147 41.667 0.00 0.00 35.04 4.01
334 632 4.277174 ACACATTGATTACGAACCAAGCAA 59.723 37.500 0.00 0.00 35.92 3.91
335 633 3.818210 ACACATTGATTACGAACCAAGCA 59.182 39.130 0.00 0.00 0.00 3.91
336 634 4.083537 TCACACATTGATTACGAACCAAGC 60.084 41.667 0.00 0.00 0.00 4.01
337 635 5.605564 TCACACATTGATTACGAACCAAG 57.394 39.130 0.00 0.00 0.00 3.61
338 636 7.857734 ATATCACACATTGATTACGAACCAA 57.142 32.000 0.00 0.00 42.87 3.67
339 637 9.554395 AATATATCACACATTGATTACGAACCA 57.446 29.630 0.00 0.00 42.87 3.67
342 640 8.921670 CGGAATATATCACACATTGATTACGAA 58.078 33.333 0.00 0.00 42.87 3.85
343 641 8.085909 ACGGAATATATCACACATTGATTACGA 58.914 33.333 3.53 0.00 42.87 3.43
344 642 8.239681 ACGGAATATATCACACATTGATTACG 57.760 34.615 0.00 0.00 42.87 3.18
345 643 9.203421 TGACGGAATATATCACACATTGATTAC 57.797 33.333 0.00 0.00 42.87 1.89
346 644 9.771534 TTGACGGAATATATCACACATTGATTA 57.228 29.630 0.00 0.00 42.87 1.75
347 645 8.675705 TTGACGGAATATATCACACATTGATT 57.324 30.769 0.00 0.00 42.87 2.57
349 647 7.307930 GCATTGACGGAATATATCACACATTGA 60.308 37.037 0.00 0.00 39.11 2.57
350 648 6.798476 GCATTGACGGAATATATCACACATTG 59.202 38.462 0.00 0.00 0.00 2.82
351 649 6.072508 GGCATTGACGGAATATATCACACATT 60.073 38.462 0.00 0.00 0.00 2.71
352 650 5.412594 GGCATTGACGGAATATATCACACAT 59.587 40.000 0.00 0.00 0.00 3.21
353 651 4.754618 GGCATTGACGGAATATATCACACA 59.245 41.667 0.00 0.00 0.00 3.72
354 652 4.754618 TGGCATTGACGGAATATATCACAC 59.245 41.667 0.00 0.00 0.00 3.82
355 653 4.967036 TGGCATTGACGGAATATATCACA 58.033 39.130 0.00 0.00 0.00 3.58
356 654 5.674569 GCATGGCATTGACGGAATATATCAC 60.675 44.000 0.00 0.00 0.00 3.06
357 655 4.395854 GCATGGCATTGACGGAATATATCA 59.604 41.667 0.00 0.00 0.00 2.15
358 656 4.637534 AGCATGGCATTGACGGAATATATC 59.362 41.667 0.00 0.00 0.00 1.63
359 657 4.592942 AGCATGGCATTGACGGAATATAT 58.407 39.130 0.00 0.00 0.00 0.86
360 658 4.002982 GAGCATGGCATTGACGGAATATA 58.997 43.478 0.00 0.00 0.00 0.86
361 659 2.816087 GAGCATGGCATTGACGGAATAT 59.184 45.455 0.00 0.00 0.00 1.28
362 660 2.221169 GAGCATGGCATTGACGGAATA 58.779 47.619 0.00 0.00 0.00 1.75
363 661 1.027357 GAGCATGGCATTGACGGAAT 58.973 50.000 0.00 0.00 0.00 3.01
364 662 0.322366 TGAGCATGGCATTGACGGAA 60.322 50.000 0.00 0.00 0.00 4.30
365 663 0.107066 ATGAGCATGGCATTGACGGA 60.107 50.000 0.00 0.00 0.00 4.69
366 664 0.030235 CATGAGCATGGCATTGACGG 59.970 55.000 0.00 0.00 35.24 4.79
367 665 1.018910 TCATGAGCATGGCATTGACG 58.981 50.000 10.31 0.00 39.24 4.35
368 666 3.728076 AATCATGAGCATGGCATTGAC 57.272 42.857 10.31 0.00 39.24 3.18
369 667 6.041069 TGAATAAATCATGAGCATGGCATTGA 59.959 34.615 10.31 0.00 39.24 2.57
370 668 6.220201 TGAATAAATCATGAGCATGGCATTG 58.780 36.000 10.31 0.00 39.24 2.82
371 669 6.413783 TGAATAAATCATGAGCATGGCATT 57.586 33.333 10.31 1.86 39.24 3.56
393 691 9.771915 GCAATGTTTTGATTAATTTAACCCATG 57.228 29.630 0.00 0.00 34.60 3.66
394 692 9.737844 AGCAATGTTTTGATTAATTTAACCCAT 57.262 25.926 0.00 0.00 34.60 4.00
414 712 8.400186 TCAGATGTGTTGAATACATTAGCAATG 58.600 33.333 8.94 7.16 44.48 2.82
415 713 8.510243 TCAGATGTGTTGAATACATTAGCAAT 57.490 30.769 8.94 0.00 38.78 3.56
416 714 7.920160 TCAGATGTGTTGAATACATTAGCAA 57.080 32.000 8.94 0.00 38.78 3.91
417 715 8.510243 AATCAGATGTGTTGAATACATTAGCA 57.490 30.769 8.94 0.00 38.78 3.49
418 716 8.615211 TGAATCAGATGTGTTGAATACATTAGC 58.385 33.333 8.94 0.00 38.78 3.09
420 718 9.889128 TCTGAATCAGATGTGTTGAATACATTA 57.111 29.630 9.18 0.00 38.78 1.90
421 719 8.797350 TCTGAATCAGATGTGTTGAATACATT 57.203 30.769 9.18 0.00 38.78 2.71
422 720 8.797350 TTCTGAATCAGATGTGTTGAATACAT 57.203 30.769 14.31 7.29 40.39 2.29
423 721 8.620116 TTTCTGAATCAGATGTGTTGAATACA 57.380 30.769 14.31 0.00 40.39 2.29
424 722 9.897744 TTTTTCTGAATCAGATGTGTTGAATAC 57.102 29.630 14.31 0.00 40.39 1.89
447 745 6.146216 TCACAAATACGATGTTCGCATTTTT 58.854 32.000 5.58 0.00 41.47 1.94
448 746 5.694816 TCACAAATACGATGTTCGCATTTT 58.305 33.333 5.58 0.00 41.47 1.82
449 747 5.289917 TCACAAATACGATGTTCGCATTT 57.710 34.783 3.01 3.01 44.03 2.32
450 748 4.937696 TCACAAATACGATGTTCGCATT 57.062 36.364 0.00 0.00 45.12 3.56
451 749 4.153296 TGTTCACAAATACGATGTTCGCAT 59.847 37.500 0.00 0.00 45.12 4.73
452 750 3.495001 TGTTCACAAATACGATGTTCGCA 59.505 39.130 0.00 0.00 45.12 5.10
453 751 4.060288 TGTTCACAAATACGATGTTCGC 57.940 40.909 0.00 0.00 45.12 4.70
454 752 6.084939 CACTTTGTTCACAAATACGATGTTCG 59.915 38.462 5.59 0.00 43.92 3.95
455 753 7.129622 TCACTTTGTTCACAAATACGATGTTC 58.870 34.615 5.59 0.00 43.92 3.18
456 754 7.022055 TCACTTTGTTCACAAATACGATGTT 57.978 32.000 5.59 0.00 43.92 2.71
457 755 6.260050 ACTCACTTTGTTCACAAATACGATGT 59.740 34.615 5.59 0.00 43.92 3.06
458 756 6.658831 ACTCACTTTGTTCACAAATACGATG 58.341 36.000 5.59 1.47 43.92 3.84
459 757 6.861065 ACTCACTTTGTTCACAAATACGAT 57.139 33.333 5.59 0.00 43.92 3.73
460 758 7.956420 ATACTCACTTTGTTCACAAATACGA 57.044 32.000 5.59 2.92 43.92 3.43
461 759 8.891928 CAAATACTCACTTTGTTCACAAATACG 58.108 33.333 5.59 0.00 43.92 3.06
462 760 9.944663 TCAAATACTCACTTTGTTCACAAATAC 57.055 29.630 5.59 0.00 43.92 1.89
464 762 9.868277 TTTCAAATACTCACTTTGTTCACAAAT 57.132 25.926 5.59 0.00 43.92 2.32
465 763 9.352784 CTTTCAAATACTCACTTTGTTCACAAA 57.647 29.630 5.05 5.05 42.90 2.83
466 764 7.973388 CCTTTCAAATACTCACTTTGTTCACAA 59.027 33.333 0.00 0.00 35.56 3.33
467 765 7.122055 ACCTTTCAAATACTCACTTTGTTCACA 59.878 33.333 0.00 0.00 35.56 3.58
468 766 7.432252 CACCTTTCAAATACTCACTTTGTTCAC 59.568 37.037 0.00 0.00 35.56 3.18
469 767 7.122055 ACACCTTTCAAATACTCACTTTGTTCA 59.878 33.333 0.00 0.00 35.56 3.18
470 768 7.480810 ACACCTTTCAAATACTCACTTTGTTC 58.519 34.615 0.00 0.00 35.56 3.18
471 769 7.404671 ACACCTTTCAAATACTCACTTTGTT 57.595 32.000 0.00 0.00 35.56 2.83
472 770 8.403236 GTTACACCTTTCAAATACTCACTTTGT 58.597 33.333 0.00 0.00 35.56 2.83
473 771 8.402472 TGTTACACCTTTCAAATACTCACTTTG 58.598 33.333 0.00 0.00 35.41 2.77
474 772 8.514330 TGTTACACCTTTCAAATACTCACTTT 57.486 30.769 0.00 0.00 0.00 2.66
475 773 7.773690 ACTGTTACACCTTTCAAATACTCACTT 59.226 33.333 0.00 0.00 0.00 3.16
476 774 7.280356 ACTGTTACACCTTTCAAATACTCACT 58.720 34.615 0.00 0.00 0.00 3.41
477 775 7.492352 ACTGTTACACCTTTCAAATACTCAC 57.508 36.000 0.00 0.00 0.00 3.51
478 776 8.514330 AAACTGTTACACCTTTCAAATACTCA 57.486 30.769 0.00 0.00 0.00 3.41
486 784 5.105567 TCTGGAAACTGTTACACCTTTCA 57.894 39.130 10.90 0.00 0.00 2.69
503 801 1.692749 GGGTGTAGGGGCATCTGGA 60.693 63.158 0.00 0.00 0.00 3.86
506 804 2.057922 CATAAGGGTGTAGGGGCATCT 58.942 52.381 0.00 0.00 0.00 2.90
508 806 2.174854 GTTCATAAGGGTGTAGGGGCAT 59.825 50.000 0.00 0.00 0.00 4.40
612 918 4.411869 TCCATCAAGATGCCATAACACCTA 59.588 41.667 4.53 0.00 37.49 3.08
696 1006 5.069516 TGCTGACTGCTCATCATCTGTTATA 59.930 40.000 5.87 0.00 43.37 0.98
701 1011 2.311124 TGCTGACTGCTCATCATCTG 57.689 50.000 5.87 0.00 43.37 2.90
748 1061 1.921869 GCCTTTTCTCCATCGGGGGA 61.922 60.000 0.00 0.00 43.90 4.81
750 1063 1.819632 CGCCTTTTCTCCATCGGGG 60.820 63.158 0.00 0.00 38.37 5.73
751 1064 1.090052 GTCGCCTTTTCTCCATCGGG 61.090 60.000 0.00 0.00 0.00 5.14
752 1065 1.421410 CGTCGCCTTTTCTCCATCGG 61.421 60.000 0.00 0.00 0.00 4.18
753 1066 0.457853 TCGTCGCCTTTTCTCCATCG 60.458 55.000 0.00 0.00 0.00 3.84
757 1070 3.460144 CGTCGTCGCCTTTTCTCC 58.540 61.111 0.00 0.00 0.00 3.71
888 1201 3.326006 TCTGCTGGACTTTGAGTTGAGAT 59.674 43.478 0.00 0.00 0.00 2.75
890 1203 3.065655 CTCTGCTGGACTTTGAGTTGAG 58.934 50.000 0.00 0.00 0.00 3.02
971 1287 4.925054 CAGTTGAATTATTTGTGGTGGCAG 59.075 41.667 0.00 0.00 0.00 4.85
1031 1347 1.571460 CGTGTGTTGCCTTGAGCTC 59.429 57.895 6.82 6.82 44.23 4.09
1081 1397 3.490759 GCTCGATGCACCCGTGTG 61.491 66.667 9.70 0.00 45.65 3.82
1522 1872 0.745468 GAAGTAGGAGTAGGTGGGCG 59.255 60.000 0.00 0.00 0.00 6.13
1589 1939 2.847717 TGTCGTTCGTTGCACGTATATC 59.152 45.455 8.22 1.14 43.14 1.63
1590 1940 2.866198 TGTCGTTCGTTGCACGTATAT 58.134 42.857 8.22 0.00 43.14 0.86
1817 2171 0.038343 TTTTGCTTTGAGCGATGGGC 60.038 50.000 0.00 0.00 46.26 5.36
1856 2236 7.581213 TGGGATTAGTTGGTTATAATGCAAG 57.419 36.000 0.00 0.00 32.98 4.01
1905 2301 9.343539 GCCAGAAATTAGGTCTACATTCTTAAT 57.656 33.333 0.00 0.00 0.00 1.40
1915 2311 5.023452 TCACTCTGCCAGAAATTAGGTCTA 58.977 41.667 0.00 0.00 0.00 2.59
1935 2331 5.437060 AGTCCTACATTCTCTCTCTCTCAC 58.563 45.833 0.00 0.00 0.00 3.51
1939 2335 7.817418 ACATTAGTCCTACATTCTCTCTCTC 57.183 40.000 0.00 0.00 0.00 3.20
2063 2469 3.364062 CTGTATCGTGCAGTGTAGCTAC 58.636 50.000 17.30 17.30 34.99 3.58
2064 2470 2.223502 GCTGTATCGTGCAGTGTAGCTA 60.224 50.000 0.00 0.00 36.42 3.32
2065 2471 1.469940 GCTGTATCGTGCAGTGTAGCT 60.470 52.381 0.00 0.00 36.42 3.32
2108 2518 7.387948 TCAAGTCAAAACTTAGCTATCAGTTCC 59.612 37.037 10.52 1.93 43.99 3.62
2152 2562 4.988540 TGATTGAACTCGTCACCTGTAAAG 59.011 41.667 0.00 0.00 35.39 1.85
2158 2568 2.417379 CGGATGATTGAACTCGTCACCT 60.417 50.000 0.00 0.00 35.39 4.00
2223 2639 4.201783 CGTCGGCCTAAAAAGTAATGGAAG 60.202 45.833 0.00 0.00 0.00 3.46
2322 2738 3.657015 ACTGGCATGAGATCTATGACG 57.343 47.619 13.25 10.12 36.32 4.35
2365 2781 6.612306 ACCGAGATAATTTCACTGAAAAAGC 58.388 36.000 8.28 3.39 35.11 3.51
2482 2999 1.954927 TATGCGTGTGTGGTTGTCAA 58.045 45.000 0.00 0.00 0.00 3.18
2563 3080 4.810790 CCCCTAAGTGCGTATATTCTCTG 58.189 47.826 0.00 0.00 0.00 3.35
2583 3100 9.863845 TTTATTTAATTAGCACTTACTTTGCCC 57.136 29.630 0.00 0.00 41.18 5.36
2637 3155 2.116869 AAAAGGGAACATTTGGGCCT 57.883 45.000 4.53 0.00 0.00 5.19
2667 3185 5.162925 TGGGGTCATCCTCCTTTTCTAAAAA 60.163 40.000 0.00 0.00 32.02 1.94
2668 3186 4.355588 TGGGGTCATCCTCCTTTTCTAAAA 59.644 41.667 0.00 0.00 32.02 1.52
2669 3187 3.920197 TGGGGTCATCCTCCTTTTCTAAA 59.080 43.478 0.00 0.00 32.02 1.85
2670 3188 3.537337 TGGGGTCATCCTCCTTTTCTAA 58.463 45.455 0.00 0.00 32.02 2.10
2671 3189 3.214694 TGGGGTCATCCTCCTTTTCTA 57.785 47.619 0.00 0.00 32.02 2.10
2672 3190 2.059756 TGGGGTCATCCTCCTTTTCT 57.940 50.000 0.00 0.00 32.02 2.52
2673 3191 2.899303 TTGGGGTCATCCTCCTTTTC 57.101 50.000 0.00 0.00 32.02 2.29
2674 3192 3.852858 ATTTGGGGTCATCCTCCTTTT 57.147 42.857 0.00 0.00 32.02 2.27
2675 3193 4.965283 TTATTTGGGGTCATCCTCCTTT 57.035 40.909 0.00 0.00 32.02 3.11
2676 3194 4.965283 TTTATTTGGGGTCATCCTCCTT 57.035 40.909 0.00 0.00 32.02 3.36
2677 3195 4.326132 CCTTTTATTTGGGGTCATCCTCCT 60.326 45.833 0.00 0.00 32.02 3.69
2678 3196 3.960755 CCTTTTATTTGGGGTCATCCTCC 59.039 47.826 0.00 0.00 32.02 4.30
2679 3197 3.960755 CCCTTTTATTTGGGGTCATCCTC 59.039 47.826 0.00 0.00 39.76 3.71
2680 3198 3.994317 CCCTTTTATTTGGGGTCATCCT 58.006 45.455 0.00 0.00 39.76 3.24
2704 3222 3.436704 TGTGATGAGGAACGCTTCATTTC 59.563 43.478 0.00 0.00 43.07 2.17
2713 3231 8.023128 AGAAAACATAAATTGTGATGAGGAACG 58.977 33.333 0.00 0.00 38.99 3.95
2716 3234 8.733458 CAGAGAAAACATAAATTGTGATGAGGA 58.267 33.333 0.00 0.00 38.99 3.71
2728 3246 9.791820 CATGCATGTAATCAGAGAAAACATAAA 57.208 29.630 18.91 0.00 0.00 1.40
2731 3249 7.400599 ACATGCATGTAATCAGAGAAAACAT 57.599 32.000 30.50 0.00 39.68 2.71
2797 3315 4.377021 TGTAGATGTGTGCTCGAAAGTTT 58.623 39.130 0.00 0.00 0.00 2.66
2803 3321 1.538075 TCGTTGTAGATGTGTGCTCGA 59.462 47.619 0.00 0.00 0.00 4.04
2827 3345 1.153745 GAAGCCGCTGTCGATGTCT 60.154 57.895 0.00 0.00 38.10 3.41
3103 3621 0.606401 CATTGTTCCCTGTGAGCGGT 60.606 55.000 0.00 0.00 0.00 5.68
3599 4131 2.369257 AATCGCTGACATCCGCCGAT 62.369 55.000 0.00 0.00 0.00 4.18
3807 4342 2.359900 CCTAAGAACAAGCGCCTTGAT 58.640 47.619 21.19 12.57 43.42 2.57
3821 4356 2.642254 CGTGGACGTGCCCCTAAGA 61.642 63.158 4.04 0.00 34.97 2.10
3930 4477 0.032952 TTTCCAGACCACCGAACGAG 59.967 55.000 0.00 0.00 0.00 4.18
4004 4551 9.199982 CTTCTTGATGCAATGTTTTGAGTTAAT 57.800 29.630 0.00 0.00 34.60 1.40
4019 4566 7.868906 TCATGATTTGTATCTTCTTGATGCA 57.131 32.000 0.00 0.00 44.12 3.96
4055 4602 2.174685 TCCTAACTATGCAGAGGCCA 57.825 50.000 13.85 0.00 40.13 5.36
4068 4615 1.533625 TTGCCTGTGTGCATCCTAAC 58.466 50.000 0.00 0.00 41.70 2.34
4072 4619 0.318955 GTGTTTGCCTGTGTGCATCC 60.319 55.000 0.00 0.00 41.70 3.51
4084 4631 7.985634 TTTCTTTCAGACTATTTGTGTTTGC 57.014 32.000 0.00 0.00 0.00 3.68
4129 4676 7.086230 ACGGTCTTATTTGACTCTACTAGTG 57.914 40.000 5.39 0.00 39.07 2.74


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

AutoCloner maintained by Alex Coulton.