Multiple sequence alignment - TraesCS6A01G163900

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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 TraesCS6A01G163900 chr6A 100.000 4508 0 0 1 4508 160473005 160477512 0.000000e+00 8325.0
1 TraesCS6A01G163900 chr6A 87.252 353 20 9 1 328 160447051 160447403 3.290000e-101 379.0
2 TraesCS6A01G163900 chr6D 93.941 2971 92 31 834 3772 122517389 122520303 0.000000e+00 4409.0
3 TraesCS6A01G163900 chr6D 91.368 475 20 7 329 801 122516937 122517392 8.230000e-177 630.0
4 TraesCS6A01G163900 chr6D 96.825 252 8 0 4256 4507 396997938 396998189 5.390000e-114 422.0
5 TraesCS6A01G163900 chr6D 96.443 253 9 0 4256 4508 429002985 429003237 6.970000e-113 418.0
6 TraesCS6A01G163900 chr6D 89.860 286 24 4 1 281 15583295 15583580 3.310000e-96 363.0
7 TraesCS6A01G163900 chr6D 84.034 357 23 8 1 328 386161173 386160822 3.390000e-81 313.0
8 TraesCS6A01G163900 chr6B 95.089 2586 87 11 1199 3772 216354759 216357316 0.000000e+00 4036.0
9 TraesCS6A01G163900 chr6B 92.690 342 18 2 862 1203 216352689 216353023 1.890000e-133 486.0
10 TraesCS6A01G163900 chr6B 84.034 357 26 7 1 328 18005095 18004741 9.410000e-82 315.0
11 TraesCS6A01G163900 chr6B 83.520 358 26 9 1 328 17731930 17732284 2.040000e-78 303.0
12 TraesCS6A01G163900 chr6B 91.469 211 12 2 603 813 216352489 216352693 7.380000e-73 285.0
13 TraesCS6A01G163900 chr6B 82.913 357 20 12 1 328 17734148 17734492 2.650000e-72 283.0
14 TraesCS6A01G163900 chr6B 83.276 293 27 14 336 612 216350137 216350423 2.690000e-62 250.0
15 TraesCS6A01G163900 chr6B 97.727 88 2 0 1 88 680158011 680158098 7.810000e-33 152.0
16 TraesCS6A01G163900 chr7B 77.814 2452 396 82 1095 3490 617557873 617555514 0.000000e+00 1378.0
17 TraesCS6A01G163900 chr7B 77.966 2124 343 71 1094 3180 616823184 616821149 0.000000e+00 1214.0
18 TraesCS6A01G163900 chr7B 80.696 1207 190 26 1095 2284 616749837 616748657 0.000000e+00 898.0
19 TraesCS6A01G163900 chr7B 82.277 1010 123 34 2502 3495 617487293 617488262 0.000000e+00 822.0
20 TraesCS6A01G163900 chr7B 77.216 1286 233 35 1094 2350 617485903 617487157 0.000000e+00 697.0
21 TraesCS6A01G163900 chr7B 77.490 1195 224 22 1094 2270 616836316 616837483 0.000000e+00 675.0
22 TraesCS6A01G163900 chr7B 84.844 673 74 17 2520 3175 617579198 617579859 0.000000e+00 652.0
23 TraesCS6A01G163900 chr7B 83.406 687 88 12 2501 3171 616837699 616838375 8.290000e-172 614.0
24 TraesCS6A01G163900 chr7B 82.941 680 87 10 2515 3175 616748456 616747787 1.810000e-163 586.0
25 TraesCS6A01G163900 chr7B 83.529 510 59 12 3770 4257 27133188 27132682 1.910000e-123 453.0
26 TraesCS6A01G163900 chr7B 83.333 510 60 13 3770 4257 27099927 27099421 8.900000e-122 448.0
27 TraesCS6A01G163900 chr7B 83.237 519 51 16 3772 4257 112000595 112000080 1.150000e-120 444.0
28 TraesCS6A01G163900 chr7B 82.908 509 58 16 3772 4263 591215756 591216252 8.960000e-117 431.0
29 TraesCS6A01G163900 chr7B 85.778 225 32 0 3256 3480 616838430 616838654 5.830000e-59 239.0
30 TraesCS6A01G163900 chr7B 82.833 233 40 0 3263 3495 617579920 617580152 4.570000e-50 209.0
31 TraesCS6A01G163900 chr7A 76.644 2449 421 78 1095 3495 652356987 652359332 0.000000e+00 1214.0
32 TraesCS6A01G163900 chr7A 77.382 2131 349 64 1094 3175 652195269 652197315 0.000000e+00 1142.0
33 TraesCS6A01G163900 chr7A 80.060 993 137 39 2519 3495 652339459 652340406 0.000000e+00 680.0
34 TraesCS6A01G163900 chr7A 76.515 1205 232 29 1095 2278 652338059 652339233 1.070000e-170 610.0
35 TraesCS6A01G163900 chr7A 87.698 504 41 11 3772 4257 68349439 68349939 6.540000e-158 568.0
36 TraesCS6A01G163900 chr7A 77.560 918 169 23 1423 2337 652163852 652164735 1.860000e-143 520.0
37 TraesCS6A01G163900 chr7A 85.634 355 21 6 1 327 595810022 595809670 3.340000e-91 346.0
38 TraesCS6A01G163900 chr7A 85.593 354 23 3 1 328 736115992 736116343 3.340000e-91 346.0
39 TraesCS6A01G163900 chr7A 84.255 235 31 3 1095 1323 652162162 652162396 1.630000e-54 224.0
40 TraesCS6A01G163900 chr7A 84.783 138 21 0 1188 1325 652232094 652232231 6.080000e-29 139.0
41 TraesCS6A01G163900 chr7A 81.308 107 15 4 2726 2829 200064889 200064785 1.040000e-11 82.4
42 TraesCS6A01G163900 chr7A 80.374 107 17 3 2726 2830 200032607 200032503 1.340000e-10 78.7
43 TraesCS6A01G163900 chr7D 82.803 1006 119 31 2500 3490 566015437 566016403 0.000000e+00 850.0
44 TraesCS6A01G163900 chr7D 82.290 1022 122 44 2504 3506 565645108 565646089 0.000000e+00 830.0
45 TraesCS6A01G163900 chr7D 79.671 1215 183 33 1095 2274 566014044 566015229 0.000000e+00 817.0
46 TraesCS6A01G163900 chr7D 81.809 995 124 35 2519 3495 566038929 566039884 0.000000e+00 782.0
47 TraesCS6A01G163900 chr7D 77.397 1283 236 30 1094 2350 565643716 565644970 0.000000e+00 713.0
48 TraesCS6A01G163900 chr7D 77.713 1207 216 32 1094 2278 566037534 566038709 0.000000e+00 689.0
49 TraesCS6A01G163900 chr7D 83.954 698 85 14 2495 3175 565618837 565619524 1.060000e-180 643.0
50 TraesCS6A01G163900 chr7D 96.838 253 8 0 4256 4508 509691367 509691115 1.500000e-114 424.0
51 TraesCS6A01G163900 chr7D 87.320 347 28 10 3919 4257 458962139 458961801 2.540000e-102 383.0
52 TraesCS6A01G163900 chr7D 86.280 328 45 0 2853 3180 565613909 565613582 1.540000e-94 357.0
53 TraesCS6A01G163900 chr7D 85.634 355 24 3 1 328 189435803 189435449 9.280000e-92 348.0
54 TraesCS6A01G163900 chr7D 79.292 367 71 3 1445 1807 565615042 565614677 7.490000e-63 252.0
55 TraesCS6A01G163900 chr7D 83.186 226 36 2 3256 3480 565619575 565619799 5.910000e-49 206.0
56 TraesCS6A01G163900 chr5D 88.554 498 34 7 3770 4257 59920364 59920848 2.340000e-162 582.0
57 TraesCS6A01G163900 chr5D 96.838 253 8 0 4256 4508 520370690 520370438 1.500000e-114 424.0
58 TraesCS6A01G163900 chr5D 80.220 91 15 3 2720 2807 322001581 322001671 1.050000e-06 65.8
59 TraesCS6A01G163900 chr5D 100.000 30 0 0 1463 1492 438364783 438364754 6.300000e-04 56.5
60 TraesCS6A01G163900 chr5D 90.698 43 3 1 1463 1505 438390107 438390066 6.300000e-04 56.5
61 TraesCS6A01G163900 chr3A 85.057 522 46 13 3766 4257 408860728 408861247 1.870000e-138 503.0
62 TraesCS6A01G163900 chr3A 84.146 492 64 13 3772 4255 664143065 664142580 8.830000e-127 464.0
63 TraesCS6A01G163900 chr2A 85.089 503 53 11 3769 4257 613359105 613359599 1.130000e-135 494.0
64 TraesCS6A01G163900 chr2A 91.429 245 14 7 88 328 759091250 759091491 3.360000e-86 329.0
65 TraesCS6A01G163900 chr4B 84.449 508 57 13 3768 4257 601198861 601199364 8.770000e-132 481.0
66 TraesCS6A01G163900 chr4B 76.858 592 99 33 2591 3168 455756383 455756950 2.640000e-77 300.0
67 TraesCS6A01G163900 chr2D 96.838 253 8 0 4256 4508 641228632 641228884 1.500000e-114 424.0
68 TraesCS6A01G163900 chr2D 96.825 252 8 0 4256 4507 5665733 5665482 5.390000e-114 422.0
69 TraesCS6A01G163900 chr2D 96.443 253 8 1 4256 4508 628952774 628952523 2.510000e-112 416.0
70 TraesCS6A01G163900 chr2D 85.154 357 26 5 1 330 537451616 537451972 1.550000e-89 340.0
71 TraesCS6A01G163900 chr3D 96.443 253 9 0 4256 4508 594974121 594973869 6.970000e-113 418.0
72 TraesCS6A01G163900 chr3D 85.876 354 22 4 1 327 606920919 606920567 7.170000e-93 351.0
73 TraesCS6A01G163900 chr3D 85.634 355 24 3 1 328 606923331 606922977 9.280000e-92 348.0
74 TraesCS6A01G163900 chr3D 97.727 88 2 0 1 88 358635462 358635375 7.810000e-33 152.0
75 TraesCS6A01G163900 chr3D 100.000 31 0 0 1463 1493 429909974 429910004 1.750000e-04 58.4
76 TraesCS6A01G163900 chr3D 94.595 37 2 0 2783 2819 433415094 433415130 1.750000e-04 58.4
77 TraesCS6A01G163900 chr1D 96.443 253 9 0 4256 4508 283079315 283079567 6.970000e-113 418.0
78 TraesCS6A01G163900 chr1D 85.806 310 18 2 1 284 465123669 465123360 5.670000e-79 305.0
79 TraesCS6A01G163900 chr1D 94.444 36 2 0 1459 1494 420860252 420860217 6.300000e-04 56.5
80 TraesCS6A01G163900 chr1B 92.116 241 18 1 88 327 678561334 678561574 5.590000e-89 339.0
81 TraesCS6A01G163900 chr1B 94.444 36 2 0 1459 1494 569566020 569565985 6.300000e-04 56.5
82 TraesCS6A01G163900 chr5B 91.322 242 17 4 88 327 659634780 659635019 1.210000e-85 327.0
83 TraesCS6A01G163900 chr5B 80.220 91 15 3 2720 2807 373220151 373220061 1.050000e-06 65.8
84 TraesCS6A01G163900 chr1A 78.244 524 97 14 2638 3154 453074253 453074766 2.020000e-83 320.0
85 TraesCS6A01G163900 chr4D 77.798 545 88 29 2637 3168 370674657 370675181 5.670000e-79 305.0
86 TraesCS6A01G163900 chr3B 94.595 37 2 0 2783 2819 566162057 566162093 1.750000e-04 58.4


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 TraesCS6A01G163900 chr6A 160473005 160477512 4507 False 8325.000000 8325 100.000000 1 4508 1 chr6A.!!$F2 4507
1 TraesCS6A01G163900 chr6D 122516937 122520303 3366 False 2519.500000 4409 92.654500 329 3772 2 chr6D.!!$F4 3443
2 TraesCS6A01G163900 chr6B 216350137 216357316 7179 False 1264.250000 4036 90.631000 336 3772 4 chr6B.!!$F3 3436
3 TraesCS6A01G163900 chr6B 17731930 17734492 2562 False 293.000000 303 83.216500 1 328 2 chr6B.!!$F2 327
4 TraesCS6A01G163900 chr7B 617555514 617557873 2359 True 1378.000000 1378 77.814000 1095 3490 1 chr7B.!!$R5 2395
5 TraesCS6A01G163900 chr7B 616821149 616823184 2035 True 1214.000000 1214 77.966000 1094 3180 1 chr7B.!!$R4 2086
6 TraesCS6A01G163900 chr7B 617485903 617488262 2359 False 759.500000 822 79.746500 1094 3495 2 chr7B.!!$F3 2401
7 TraesCS6A01G163900 chr7B 616747787 616749837 2050 True 742.000000 898 81.818500 1095 3175 2 chr7B.!!$R6 2080
8 TraesCS6A01G163900 chr7B 616836316 616838654 2338 False 509.333333 675 82.224667 1094 3480 3 chr7B.!!$F2 2386
9 TraesCS6A01G163900 chr7B 27132682 27133188 506 True 453.000000 453 83.529000 3770 4257 1 chr7B.!!$R2 487
10 TraesCS6A01G163900 chr7B 27099421 27099927 506 True 448.000000 448 83.333000 3770 4257 1 chr7B.!!$R1 487
11 TraesCS6A01G163900 chr7B 112000080 112000595 515 True 444.000000 444 83.237000 3772 4257 1 chr7B.!!$R3 485
12 TraesCS6A01G163900 chr7B 617579198 617580152 954 False 430.500000 652 83.838500 2520 3495 2 chr7B.!!$F4 975
13 TraesCS6A01G163900 chr7A 652356987 652359332 2345 False 1214.000000 1214 76.644000 1095 3495 1 chr7A.!!$F4 2400
14 TraesCS6A01G163900 chr7A 652195269 652197315 2046 False 1142.000000 1142 77.382000 1094 3175 1 chr7A.!!$F2 2081
15 TraesCS6A01G163900 chr7A 652338059 652340406 2347 False 645.000000 680 78.287500 1095 3495 2 chr7A.!!$F7 2400
16 TraesCS6A01G163900 chr7A 68349439 68349939 500 False 568.000000 568 87.698000 3772 4257 1 chr7A.!!$F1 485
17 TraesCS6A01G163900 chr7A 652162162 652164735 2573 False 372.000000 520 80.907500 1095 2337 2 chr7A.!!$F6 1242
18 TraesCS6A01G163900 chr7D 566014044 566016403 2359 False 833.500000 850 81.237000 1095 3490 2 chr7D.!!$F3 2395
19 TraesCS6A01G163900 chr7D 565643716 565646089 2373 False 771.500000 830 79.843500 1094 3506 2 chr7D.!!$F2 2412
20 TraesCS6A01G163900 chr7D 566037534 566039884 2350 False 735.500000 782 79.761000 1094 3495 2 chr7D.!!$F4 2401
21 TraesCS6A01G163900 chr7D 565618837 565619799 962 False 424.500000 643 83.570000 2495 3480 2 chr7D.!!$F1 985
22 TraesCS6A01G163900 chr7D 565613582 565615042 1460 True 304.500000 357 82.786000 1445 3180 2 chr7D.!!$R4 1735
23 TraesCS6A01G163900 chr3A 408860728 408861247 519 False 503.000000 503 85.057000 3766 4257 1 chr3A.!!$F1 491
24 TraesCS6A01G163900 chr4B 601198861 601199364 503 False 481.000000 481 84.449000 3768 4257 1 chr4B.!!$F2 489
25 TraesCS6A01G163900 chr4B 455756383 455756950 567 False 300.000000 300 76.858000 2591 3168 1 chr4B.!!$F1 577
26 TraesCS6A01G163900 chr3D 606920567 606923331 2764 True 349.500000 351 85.755000 1 328 2 chr3D.!!$R3 327
27 TraesCS6A01G163900 chr1A 453074253 453074766 513 False 320.000000 320 78.244000 2638 3154 1 chr1A.!!$F1 516
28 TraesCS6A01G163900 chr4D 370674657 370675181 524 False 305.000000 305 77.798000 2637 3168 1 chr4D.!!$F1 531

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
966 3092 0.031716 CCATCCACCTCTCCTCCTGA 60.032 60.0 0.0 0.0 0.00 3.86 F
1602 6863 0.385974 GCATGTTCAGCAACACCGTC 60.386 55.0 0.0 0.0 45.47 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 7440 0.886490 ACTCTGTTTTGCTCAGGGCG 60.886 55.0 0.0 0.00 45.43 6.13 R
3567 10141 0.108615 ACGATCTAGCTTTGCTGCGT 60.109 50.0 0.0 4.47 40.10 5.24 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
49 50 4.121317 CGTTTGGACTTGGTGTTGTAGTA 58.879 43.478 0.00 0.00 0.00 1.82
129 155 3.003378 CCATGACGACTAGATAGCGACAA 59.997 47.826 0.00 0.00 34.15 3.18
259 286 4.383649 CCGAAACTCGTTAACAAATCTCGA 59.616 41.667 14.43 1.16 38.40 4.04
266 293 6.590292 ACTCGTTAACAAATCTCGATGTCATT 59.410 34.615 6.39 0.00 0.00 2.57
274 302 9.599866 AACAAATCTCGATGTCATTATTGTCTA 57.400 29.630 0.00 0.00 0.00 2.59
281 309 9.201127 CTCGATGTCATTATTGTCTATGATTGT 57.799 33.333 0.00 0.00 33.69 2.71
293 321 5.175859 GTCTATGATTGTTTGTTCCTCGGA 58.824 41.667 0.00 0.00 0.00 4.55
294 322 5.817816 GTCTATGATTGTTTGTTCCTCGGAT 59.182 40.000 0.00 0.00 0.00 4.18
295 323 6.018669 GTCTATGATTGTTTGTTCCTCGGATC 60.019 42.308 0.00 0.00 0.00 3.36
299 327 3.694043 TGTTTGTTCCTCGGATCATCA 57.306 42.857 0.00 0.00 0.00 3.07
302 330 2.293677 TGTTCCTCGGATCATCAACG 57.706 50.000 0.00 0.00 0.00 4.10
304 332 1.134788 GTTCCTCGGATCATCAACGGT 60.135 52.381 0.00 0.00 0.00 4.83
305 333 2.061509 TCCTCGGATCATCAACGGTA 57.938 50.000 0.00 0.00 0.00 4.02
307 335 2.296190 TCCTCGGATCATCAACGGTATG 59.704 50.000 0.00 0.00 0.00 2.39
309 338 1.686587 TCGGATCATCAACGGTATGCT 59.313 47.619 0.00 0.00 0.00 3.79
317 346 3.804786 TCAACGGTATGCTTCGGATTA 57.195 42.857 0.00 0.00 0.00 1.75
319 348 4.699637 TCAACGGTATGCTTCGGATTAAT 58.300 39.130 0.00 0.00 0.00 1.40
320 349 5.120399 TCAACGGTATGCTTCGGATTAATT 58.880 37.500 0.00 0.00 0.00 1.40
321 350 5.235616 TCAACGGTATGCTTCGGATTAATTC 59.764 40.000 0.00 0.00 0.00 2.17
322 351 4.957296 ACGGTATGCTTCGGATTAATTCT 58.043 39.130 0.00 0.00 0.00 2.40
323 352 6.092955 ACGGTATGCTTCGGATTAATTCTA 57.907 37.500 0.00 0.00 0.00 2.10
324 353 6.518493 ACGGTATGCTTCGGATTAATTCTAA 58.482 36.000 0.00 0.00 0.00 2.10
325 354 6.423001 ACGGTATGCTTCGGATTAATTCTAAC 59.577 38.462 0.00 0.00 0.00 2.34
326 355 6.422701 CGGTATGCTTCGGATTAATTCTAACA 59.577 38.462 0.00 0.00 0.00 2.41
327 356 7.042321 CGGTATGCTTCGGATTAATTCTAACAA 60.042 37.037 0.00 0.00 0.00 2.83
344 373 6.498538 TCTAACAAATACCACCCATTCCATT 58.501 36.000 0.00 0.00 0.00 3.16
351 380 3.998279 ACCACCCATTCCATTCATGATT 58.002 40.909 0.00 0.00 0.00 2.57
352 381 4.364470 ACCACCCATTCCATTCATGATTT 58.636 39.130 0.00 0.00 0.00 2.17
353 382 4.162698 ACCACCCATTCCATTCATGATTTG 59.837 41.667 0.00 0.00 0.00 2.32
354 383 4.406326 CCACCCATTCCATTCATGATTTGA 59.594 41.667 0.00 0.00 0.00 2.69
405 434 4.623002 GGAGATCTATCCTTTTCACGTCC 58.377 47.826 0.00 0.00 36.35 4.79
446 489 2.539338 TTTGAACGCACGGCCACTC 61.539 57.895 2.24 0.00 0.00 3.51
462 505 2.325761 CACTCGAGACGGTAACCAAAG 58.674 52.381 21.68 0.00 0.00 2.77
463 506 1.336609 ACTCGAGACGGTAACCAAAGC 60.337 52.381 21.68 0.00 0.00 3.51
464 507 0.037975 TCGAGACGGTAACCAAAGCC 60.038 55.000 0.00 0.00 0.00 4.35
465 508 0.320073 CGAGACGGTAACCAAAGCCA 60.320 55.000 0.00 0.00 0.00 4.75
466 509 1.439679 GAGACGGTAACCAAAGCCAG 58.560 55.000 0.00 0.00 0.00 4.85
479 522 0.890683 AAGCCAGCCAAATTTCTCCG 59.109 50.000 0.00 0.00 0.00 4.63
488 531 2.480037 CCAAATTTCTCCGGCTTTTTGC 59.520 45.455 0.00 0.00 41.94 3.68
601 648 3.190849 CGAGCATCCGTGGTGCAG 61.191 66.667 11.02 2.19 44.87 4.41
701 2823 2.983592 CCGGCTCAACACCAACCC 60.984 66.667 0.00 0.00 0.00 4.11
711 2833 1.833934 CACCAACCCTGCAGCCTTT 60.834 57.895 8.66 0.00 0.00 3.11
755 2877 2.746279 ACATTTGTGGGAGGTGACAA 57.254 45.000 0.00 0.00 0.00 3.18
756 2878 2.586425 ACATTTGTGGGAGGTGACAAG 58.414 47.619 0.00 0.00 33.73 3.16
757 2879 2.174639 ACATTTGTGGGAGGTGACAAGA 59.825 45.455 0.00 0.00 33.73 3.02
758 2880 2.341846 TTTGTGGGAGGTGACAAGAC 57.658 50.000 0.00 0.00 33.73 3.01
759 2881 1.208706 TTGTGGGAGGTGACAAGACA 58.791 50.000 0.00 0.00 0.00 3.41
782 2904 4.084888 CCGTTTTGGTCGCTCGCC 62.085 66.667 0.00 0.00 0.00 5.54
808 2930 9.167311 CAGGGAAAATAGTGGCTATATATTCAC 57.833 37.037 0.00 7.24 0.00 3.18
809 2931 8.041323 AGGGAAAATAGTGGCTATATATTCACG 58.959 37.037 0.00 0.00 35.50 4.35
810 2932 7.280205 GGGAAAATAGTGGCTATATATTCACGG 59.720 40.741 0.00 0.00 35.50 4.94
811 2933 8.038944 GGAAAATAGTGGCTATATATTCACGGA 58.961 37.037 0.00 4.17 35.50 4.69
812 2934 9.601217 GAAAATAGTGGCTATATATTCACGGAT 57.399 33.333 0.00 5.66 35.50 4.18
815 2937 9.642343 AATAGTGGCTATATATTCACGGATAGA 57.358 33.333 0.00 0.00 35.50 1.98
816 2938 7.336161 AGTGGCTATATATTCACGGATAGAC 57.664 40.000 0.00 0.00 35.50 2.59
817 2939 6.890268 AGTGGCTATATATTCACGGATAGACA 59.110 38.462 0.00 0.00 37.53 3.41
818 2940 7.096884 TGGCTATATATTCACGGATAGACAC 57.903 40.000 0.00 0.00 35.45 3.67
819 2941 6.661805 TGGCTATATATTCACGGATAGACACA 59.338 38.462 0.00 0.00 35.45 3.72
820 2942 7.148069 TGGCTATATATTCACGGATAGACACAG 60.148 40.741 0.00 0.00 35.45 3.66
821 2943 7.067129 GGCTATATATTCACGGATAGACACAGA 59.933 40.741 0.00 0.00 31.31 3.41
822 2944 7.911205 GCTATATATTCACGGATAGACACAGAC 59.089 40.741 0.00 0.00 0.00 3.51
823 2945 9.168451 CTATATATTCACGGATAGACACAGACT 57.832 37.037 0.00 0.00 0.00 3.24
824 2946 4.640789 ATTCACGGATAGACACAGACTC 57.359 45.455 0.00 0.00 0.00 3.36
825 2947 2.366533 TCACGGATAGACACAGACTCC 58.633 52.381 0.00 0.00 0.00 3.85
826 2948 2.092323 CACGGATAGACACAGACTCCA 58.908 52.381 0.00 0.00 0.00 3.86
827 2949 2.690497 CACGGATAGACACAGACTCCAT 59.310 50.000 0.00 0.00 0.00 3.41
828 2950 2.690497 ACGGATAGACACAGACTCCATG 59.310 50.000 0.00 0.00 0.00 3.66
829 2951 2.952310 CGGATAGACACAGACTCCATGA 59.048 50.000 0.00 0.00 0.00 3.07
830 2952 3.381590 CGGATAGACACAGACTCCATGAA 59.618 47.826 0.00 0.00 0.00 2.57
831 2953 4.498850 CGGATAGACACAGACTCCATGAAG 60.499 50.000 0.00 0.00 0.00 3.02
832 2954 4.646945 GGATAGACACAGACTCCATGAAGA 59.353 45.833 0.00 0.00 0.00 2.87
833 2955 3.951775 AGACACAGACTCCATGAAGAC 57.048 47.619 0.00 0.00 0.00 3.01
834 2956 3.505386 AGACACAGACTCCATGAAGACT 58.495 45.455 0.00 0.00 0.00 3.24
835 2957 4.667573 AGACACAGACTCCATGAAGACTA 58.332 43.478 0.00 0.00 0.00 2.59
836 2958 5.268387 AGACACAGACTCCATGAAGACTAT 58.732 41.667 0.00 0.00 0.00 2.12
921 3047 2.005537 GCAAACGCGACAGCAACTG 61.006 57.895 15.93 0.00 45.49 3.16
922 3048 2.005537 CAAACGCGACAGCAACTGC 61.006 57.895 15.93 0.00 45.49 4.40
923 3049 3.181169 AAACGCGACAGCAACTGCC 62.181 57.895 15.93 0.00 45.49 4.85
924 3050 4.609018 ACGCGACAGCAACTGCCT 62.609 61.111 15.93 0.00 45.49 4.75
925 3051 4.081030 CGCGACAGCAACTGCCTG 62.081 66.667 0.00 0.00 45.49 4.85
965 3091 1.694133 GCCATCCACCTCTCCTCCTG 61.694 65.000 0.00 0.00 0.00 3.86
966 3092 0.031716 CCATCCACCTCTCCTCCTGA 60.032 60.000 0.00 0.00 0.00 3.86
967 3093 1.414245 CCATCCACCTCTCCTCCTGAT 60.414 57.143 0.00 0.00 0.00 2.90
968 3094 1.969923 CATCCACCTCTCCTCCTGATC 59.030 57.143 0.00 0.00 0.00 2.92
1362 5249 0.952010 TGTGGTCGTCGTCGAGATCA 60.952 55.000 4.68 0.00 46.96 2.92
1552 6813 2.683933 AGTACCAGGGGCTCACGG 60.684 66.667 0.00 0.00 0.00 4.94
1602 6863 0.385974 GCATGTTCAGCAACACCGTC 60.386 55.000 0.00 0.00 45.47 4.79
2073 7362 3.186047 GATGGCAACGGGTCGTCG 61.186 66.667 0.00 0.00 39.99 5.12
2379 7689 0.250770 ACAAGAAGAACGAAGGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
2638 7951 2.525629 TGAAGAGCGGGGACACCA 60.526 61.111 0.00 0.00 40.22 4.17
3524 10096 3.371097 GATGCGAGGCGAGGGTTCA 62.371 63.158 0.00 0.00 0.00 3.18
3567 10141 6.669125 AAAATCATCAAACCACATCAGGAA 57.331 33.333 0.00 0.00 0.00 3.36
3572 10146 1.069022 CAAACCACATCAGGAACGCAG 60.069 52.381 0.00 0.00 0.00 5.18
3574 10148 1.672030 CCACATCAGGAACGCAGCA 60.672 57.895 0.00 0.00 0.00 4.41
3601 10175 3.384668 AGATCGTTGCTGAATGATACCG 58.615 45.455 0.00 0.00 37.85 4.02
3615 10206 2.301870 TGATACCGCCTCAGTTCAGTTT 59.698 45.455 0.00 0.00 0.00 2.66
3617 10208 0.180406 ACCGCCTCAGTTCAGTTTGT 59.820 50.000 0.00 0.00 0.00 2.83
3618 10209 1.414919 ACCGCCTCAGTTCAGTTTGTA 59.585 47.619 0.00 0.00 0.00 2.41
3620 10211 2.288825 CCGCCTCAGTTCAGTTTGTAGA 60.289 50.000 0.00 0.00 0.00 2.59
3622 10213 4.381612 CCGCCTCAGTTCAGTTTGTAGATA 60.382 45.833 0.00 0.00 0.00 1.98
3623 10214 4.800993 CGCCTCAGTTCAGTTTGTAGATAG 59.199 45.833 0.00 0.00 0.00 2.08
3624 10215 5.112686 GCCTCAGTTCAGTTTGTAGATAGG 58.887 45.833 0.00 0.00 0.00 2.57
3625 10216 5.337652 GCCTCAGTTCAGTTTGTAGATAGGT 60.338 44.000 0.00 0.00 0.00 3.08
3627 10218 7.259161 CCTCAGTTCAGTTTGTAGATAGGTAC 58.741 42.308 0.00 0.00 0.00 3.34
3628 10219 7.093902 CCTCAGTTCAGTTTGTAGATAGGTACA 60.094 40.741 0.00 0.00 0.00 2.90
3630 10221 7.450634 TCAGTTCAGTTTGTAGATAGGTACAGT 59.549 37.037 0.00 0.00 34.41 3.55
3631 10222 8.737175 CAGTTCAGTTTGTAGATAGGTACAGTA 58.263 37.037 0.00 0.00 34.41 2.74
3632 10223 8.738106 AGTTCAGTTTGTAGATAGGTACAGTAC 58.262 37.037 1.59 1.59 34.41 2.73
3633 10224 8.738106 GTTCAGTTTGTAGATAGGTACAGTACT 58.262 37.037 10.62 0.00 34.41 2.73
3641 10232 9.503399 TGTAGATAGGTACAGTACTATGTGATG 57.497 37.037 10.62 0.00 34.56 3.07
3738 11235 7.727578 TGGAGTAGACTGAATACAAATGGTA 57.272 36.000 0.00 0.00 36.16 3.25
3871 11632 3.842923 CGAGATGCCCCAGTCGCT 61.843 66.667 0.00 0.00 0.00 4.93
3927 11689 4.496183 TCACAAACACGACGCAAATTAAAC 59.504 37.500 0.00 0.00 0.00 2.01
3937 11699 4.922719 ACGCAAATTAAACCAAACTTCGA 58.077 34.783 0.00 0.00 0.00 3.71
4040 11831 1.546476 CTTGCAGTTCTACGAGGAGGT 59.454 52.381 0.00 0.00 0.00 3.85
4087 11893 4.394078 TCGTCGTTGTCGCCTCCG 62.394 66.667 0.00 0.00 36.96 4.63
4259 12066 4.479993 GCTGCCGGACCATCTGCT 62.480 66.667 5.05 0.00 0.00 4.24
4260 12067 2.202987 CTGCCGGACCATCTGCTC 60.203 66.667 5.05 0.00 0.00 4.26
4261 12068 4.147449 TGCCGGACCATCTGCTCG 62.147 66.667 5.05 0.00 0.00 5.03
4262 12069 4.899239 GCCGGACCATCTGCTCGG 62.899 72.222 5.05 0.00 43.13 4.63
4263 12070 4.899239 CCGGACCATCTGCTCGGC 62.899 72.222 0.00 0.00 34.17 5.54
4265 12072 4.148825 GGACCATCTGCTCGGCGT 62.149 66.667 6.85 0.00 0.00 5.68
4266 12073 2.887568 GACCATCTGCTCGGCGTG 60.888 66.667 6.85 5.49 0.00 5.34
4267 12074 3.356639 GACCATCTGCTCGGCGTGA 62.357 63.158 13.77 5.22 0.00 4.35
4268 12075 2.887568 CCATCTGCTCGGCGTGAC 60.888 66.667 13.77 4.89 0.00 3.67
4269 12076 3.250323 CATCTGCTCGGCGTGACG 61.250 66.667 13.77 0.00 0.00 4.35
4270 12077 4.498520 ATCTGCTCGGCGTGACGG 62.499 66.667 13.77 9.18 0.00 4.79
4281 12088 2.260434 GTGACGGCTGCGGAAGTA 59.740 61.111 14.45 0.00 0.00 2.24
4282 12089 2.092882 GTGACGGCTGCGGAAGTAC 61.093 63.158 14.45 3.72 0.00 2.73
4283 12090 2.879462 GACGGCTGCGGAAGTACG 60.879 66.667 14.45 2.40 35.43 3.67
4284 12091 4.430765 ACGGCTGCGGAAGTACGG 62.431 66.667 14.45 0.00 34.18 4.02
4286 12093 4.452733 GGCTGCGGAAGTACGGCT 62.453 66.667 0.00 0.00 43.66 5.52
4287 12094 2.886124 GCTGCGGAAGTACGGCTC 60.886 66.667 0.00 0.00 43.66 4.70
4288 12095 2.202756 CTGCGGAAGTACGGCTCC 60.203 66.667 0.00 2.52 43.66 4.70
4289 12096 3.718210 CTGCGGAAGTACGGCTCCC 62.718 68.421 6.22 1.66 43.66 4.30
4290 12097 3.766691 GCGGAAGTACGGCTCCCA 61.767 66.667 6.22 0.00 40.81 4.37
4291 12098 2.494918 CGGAAGTACGGCTCCCAG 59.505 66.667 6.22 0.00 0.00 4.45
4292 12099 2.050350 CGGAAGTACGGCTCCCAGA 61.050 63.158 6.22 0.00 0.00 3.86
4293 12100 1.817209 GGAAGTACGGCTCCCAGAG 59.183 63.158 1.38 0.00 0.00 3.35
4355 12162 4.971125 GCAGGGAGGCGCGGATAC 62.971 72.222 8.83 0.00 0.00 2.24
4367 12174 2.502080 GGATACGCGCGATCTCCG 60.502 66.667 39.36 5.77 42.21 4.63
4428 12235 4.838152 GCCGGCGCTGATTCTCCA 62.838 66.667 20.25 0.00 0.00 3.86
4429 12236 2.109799 CCGGCGCTGATTCTCCAT 59.890 61.111 20.25 0.00 0.00 3.41
4430 12237 2.249535 CCGGCGCTGATTCTCCATG 61.250 63.158 20.25 0.00 0.00 3.66
4431 12238 2.890109 CGGCGCTGATTCTCCATGC 61.890 63.158 11.90 0.00 0.00 4.06
4432 12239 2.550101 GGCGCTGATTCTCCATGCC 61.550 63.158 7.64 0.00 32.74 4.40
4433 12240 2.550101 GCGCTGATTCTCCATGCCC 61.550 63.158 0.00 0.00 0.00 5.36
4434 12241 1.895707 CGCTGATTCTCCATGCCCC 60.896 63.158 0.00 0.00 0.00 5.80
4435 12242 1.895707 GCTGATTCTCCATGCCCCG 60.896 63.158 0.00 0.00 0.00 5.73
4436 12243 1.228063 CTGATTCTCCATGCCCCGG 60.228 63.158 0.00 0.00 0.00 5.73
4437 12244 2.113986 GATTCTCCATGCCCCGGG 59.886 66.667 15.80 15.80 0.00 5.73
4476 12283 3.136123 CGGGTACTCGGCCTCGAA 61.136 66.667 7.42 0.00 45.47 3.71
4477 12284 2.806237 GGGTACTCGGCCTCGAAG 59.194 66.667 0.00 0.00 45.47 3.79
4478 12285 1.751927 GGGTACTCGGCCTCGAAGA 60.752 63.158 0.00 0.00 45.47 2.87
4489 12296 2.044848 TCGAAGAGGAGCCGAGCT 60.045 61.111 0.00 0.00 43.88 4.09
4490 12297 1.679305 TCGAAGAGGAGCCGAGCTT 60.679 57.895 0.00 0.00 39.88 3.74
4491 12298 1.226831 CGAAGAGGAGCCGAGCTTC 60.227 63.158 0.00 0.00 39.88 3.86
4492 12299 1.226831 GAAGAGGAGCCGAGCTTCG 60.227 63.158 0.00 0.00 39.54 3.79
4493 12300 1.939769 GAAGAGGAGCCGAGCTTCGT 61.940 60.000 0.00 0.00 39.54 3.85
4494 12301 1.939769 AAGAGGAGCCGAGCTTCGTC 61.940 60.000 0.00 0.00 39.54 4.20
4495 12302 3.418744 GAGGAGCCGAGCTTCGTCC 62.419 68.421 0.00 0.00 39.54 4.79
4496 12303 3.453679 GGAGCCGAGCTTCGTCCT 61.454 66.667 0.00 0.00 39.88 3.85
4497 12304 2.103340 GAGCCGAGCTTCGTCCTC 59.897 66.667 0.00 0.00 39.88 3.71
4501 12308 2.868196 CGAGCTTCGTCCTCGTGA 59.132 61.111 11.82 0.00 45.17 4.35
4502 12309 1.209383 CGAGCTTCGTCCTCGTGAA 59.791 57.895 11.82 0.00 45.17 3.18
4503 12310 0.794981 CGAGCTTCGTCCTCGTGAAG 60.795 60.000 11.82 0.00 45.17 3.02
4505 12312 1.179814 AGCTTCGTCCTCGTGAAGGT 61.180 55.000 1.20 1.20 46.32 3.50
4506 12313 1.009389 GCTTCGTCCTCGTGAAGGTG 61.009 60.000 4.36 0.00 46.32 4.00
4507 12314 0.388649 CTTCGTCCTCGTGAAGGTGG 60.389 60.000 0.00 0.00 46.32 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 4.583489 CGACACTACAAGTATCCTACCCAT 59.417 45.833 0.00 0.00 0.00 4.00
241 268 5.466819 TGACATCGAGATTTGTTAACGAGT 58.533 37.500 0.26 0.00 36.49 4.18
266 293 7.279981 CCGAGGAACAAACAATCATAGACAATA 59.720 37.037 0.00 0.00 0.00 1.90
274 302 4.588899 TGATCCGAGGAACAAACAATCAT 58.411 39.130 0.00 0.00 0.00 2.45
281 309 3.000041 CGTTGATGATCCGAGGAACAAA 59.000 45.455 6.19 0.00 30.98 2.83
293 321 2.102420 TCCGAAGCATACCGTTGATGAT 59.898 45.455 0.00 0.00 0.00 2.45
294 322 1.478916 TCCGAAGCATACCGTTGATGA 59.521 47.619 0.00 0.00 0.00 2.92
295 323 1.934589 TCCGAAGCATACCGTTGATG 58.065 50.000 0.00 0.00 0.00 3.07
299 327 5.365619 AGAATTAATCCGAAGCATACCGTT 58.634 37.500 0.00 0.00 0.00 4.44
302 330 7.724305 TGTTAGAATTAATCCGAAGCATACC 57.276 36.000 0.00 0.00 0.00 2.73
307 335 8.617809 TGGTATTTGTTAGAATTAATCCGAAGC 58.382 33.333 0.00 0.00 0.00 3.86
309 338 8.895737 GGTGGTATTTGTTAGAATTAATCCGAA 58.104 33.333 0.00 0.00 0.00 4.30
317 346 6.957020 TGGAATGGGTGGTATTTGTTAGAATT 59.043 34.615 0.00 0.00 0.00 2.17
319 348 5.893500 TGGAATGGGTGGTATTTGTTAGAA 58.106 37.500 0.00 0.00 0.00 2.10
320 349 5.522315 TGGAATGGGTGGTATTTGTTAGA 57.478 39.130 0.00 0.00 0.00 2.10
321 350 6.379703 TGAATGGAATGGGTGGTATTTGTTAG 59.620 38.462 0.00 0.00 0.00 2.34
322 351 6.256819 TGAATGGAATGGGTGGTATTTGTTA 58.743 36.000 0.00 0.00 0.00 2.41
323 352 5.090139 TGAATGGAATGGGTGGTATTTGTT 58.910 37.500 0.00 0.00 0.00 2.83
324 353 4.682563 TGAATGGAATGGGTGGTATTTGT 58.317 39.130 0.00 0.00 0.00 2.83
325 354 5.363292 TCATGAATGGAATGGGTGGTATTTG 59.637 40.000 0.00 0.00 0.00 2.32
326 355 5.527385 TCATGAATGGAATGGGTGGTATTT 58.473 37.500 0.00 0.00 0.00 1.40
327 356 5.141455 TCATGAATGGAATGGGTGGTATT 57.859 39.130 0.00 0.00 0.00 1.89
344 373 4.037565 GCAGAGCCATCAATCAAATCATGA 59.962 41.667 0.00 0.00 43.67 3.07
351 380 3.575256 ACAAAAGCAGAGCCATCAATCAA 59.425 39.130 0.00 0.00 0.00 2.57
352 381 3.159472 ACAAAAGCAGAGCCATCAATCA 58.841 40.909 0.00 0.00 0.00 2.57
353 382 3.863142 ACAAAAGCAGAGCCATCAATC 57.137 42.857 0.00 0.00 0.00 2.67
354 383 4.612264 AAACAAAAGCAGAGCCATCAAT 57.388 36.364 0.00 0.00 0.00 2.57
446 489 0.320073 TGGCTTTGGTTACCGTCTCG 60.320 55.000 0.00 0.00 0.00 4.04
451 494 1.175983 TTGGCTGGCTTTGGTTACCG 61.176 55.000 2.00 0.00 0.00 4.02
462 505 1.512694 CCGGAGAAATTTGGCTGGC 59.487 57.895 0.00 0.00 0.00 4.85
463 506 1.512694 GCCGGAGAAATTTGGCTGG 59.487 57.895 5.05 9.43 44.16 4.85
488 531 6.952935 AAAGAAAGTGTAGCAGATTCGTAG 57.047 37.500 0.00 0.00 0.00 3.51
581 628 4.457496 CACCACGGATGCTCGCCT 62.457 66.667 0.00 0.00 0.00 5.52
669 2791 2.325082 CCGGTCCGTGGCTTTTCTG 61.325 63.158 11.06 0.00 0.00 3.02
711 2833 7.610580 AAAATGTCAATGGGAAGAGGTAAAA 57.389 32.000 0.00 0.00 0.00 1.52
755 2877 1.336755 GACCAAAACGGCACATTGTCT 59.663 47.619 0.00 0.00 39.03 3.41
756 2878 1.766069 GACCAAAACGGCACATTGTC 58.234 50.000 0.00 0.00 39.03 3.18
757 2879 0.030101 CGACCAAAACGGCACATTGT 59.970 50.000 0.00 0.00 39.03 2.71
758 2880 1.274798 GCGACCAAAACGGCACATTG 61.275 55.000 0.00 0.00 39.03 2.82
759 2881 1.007849 GCGACCAAAACGGCACATT 60.008 52.632 0.00 0.00 39.03 2.71
782 2904 9.167311 GTGAATATATAGCCACTATTTTCCCTG 57.833 37.037 9.01 0.00 0.00 4.45
801 2923 5.241949 GGAGTCTGTGTCTATCCGTGAATAT 59.758 44.000 0.00 0.00 0.00 1.28
803 2925 3.381908 GGAGTCTGTGTCTATCCGTGAAT 59.618 47.826 0.00 0.00 0.00 2.57
805 2927 2.290705 TGGAGTCTGTGTCTATCCGTGA 60.291 50.000 0.00 0.00 32.47 4.35
808 2930 2.952310 TCATGGAGTCTGTGTCTATCCG 59.048 50.000 0.00 0.00 32.47 4.18
809 2931 4.646945 TCTTCATGGAGTCTGTGTCTATCC 59.353 45.833 0.00 0.00 0.00 2.59
810 2932 5.359576 AGTCTTCATGGAGTCTGTGTCTATC 59.640 44.000 0.00 0.00 0.00 2.08
811 2933 5.268387 AGTCTTCATGGAGTCTGTGTCTAT 58.732 41.667 0.00 0.00 0.00 1.98
812 2934 4.667573 AGTCTTCATGGAGTCTGTGTCTA 58.332 43.478 0.00 0.00 0.00 2.59
813 2935 3.505386 AGTCTTCATGGAGTCTGTGTCT 58.495 45.455 0.00 0.00 0.00 3.41
814 2936 3.951775 AGTCTTCATGGAGTCTGTGTC 57.048 47.619 0.00 0.00 0.00 3.67
815 2937 6.665680 ACTTATAGTCTTCATGGAGTCTGTGT 59.334 38.462 10.68 0.00 0.00 3.72
816 2938 7.106439 ACTTATAGTCTTCATGGAGTCTGTG 57.894 40.000 10.68 0.00 0.00 3.66
817 2939 6.892456 TGACTTATAGTCTTCATGGAGTCTGT 59.108 38.462 10.68 6.86 45.27 3.41
818 2940 7.340122 TGACTTATAGTCTTCATGGAGTCTG 57.660 40.000 10.68 0.00 45.27 3.51
819 2941 7.232534 GGATGACTTATAGTCTTCATGGAGTCT 59.767 40.741 18.55 6.03 45.74 3.24
820 2942 7.014711 TGGATGACTTATAGTCTTCATGGAGTC 59.985 40.741 18.55 0.00 45.74 3.36
821 2943 6.841229 TGGATGACTTATAGTCTTCATGGAGT 59.159 38.462 18.55 0.00 45.74 3.85
822 2944 7.232330 TCTGGATGACTTATAGTCTTCATGGAG 59.768 40.741 18.55 0.00 45.74 3.86
823 2945 7.014711 GTCTGGATGACTTATAGTCTTCATGGA 59.985 40.741 18.55 12.35 45.74 3.41
824 2946 7.151308 GTCTGGATGACTTATAGTCTTCATGG 58.849 42.308 18.55 10.93 45.74 3.66
825 2947 6.860539 CGTCTGGATGACTTATAGTCTTCATG 59.139 42.308 18.55 12.62 45.74 3.07
826 2948 6.773200 TCGTCTGGATGACTTATAGTCTTCAT 59.227 38.462 18.55 3.17 45.74 2.57
827 2949 6.038382 GTCGTCTGGATGACTTATAGTCTTCA 59.962 42.308 18.55 9.53 45.74 3.02
828 2950 6.432107 GTCGTCTGGATGACTTATAGTCTTC 58.568 44.000 13.75 11.99 45.27 2.87
829 2951 5.007823 CGTCGTCTGGATGACTTATAGTCTT 59.992 44.000 17.36 2.12 45.27 3.01
830 2952 4.512198 CGTCGTCTGGATGACTTATAGTCT 59.488 45.833 17.36 0.00 45.27 3.24
831 2953 4.510711 TCGTCGTCTGGATGACTTATAGTC 59.489 45.833 17.36 0.00 45.26 2.59
832 2954 4.449131 TCGTCGTCTGGATGACTTATAGT 58.551 43.478 17.36 0.00 43.36 2.12
833 2955 4.083749 CCTCGTCGTCTGGATGACTTATAG 60.084 50.000 17.36 10.70 43.36 1.31
834 2956 3.813724 CCTCGTCGTCTGGATGACTTATA 59.186 47.826 17.36 3.86 43.36 0.98
835 2957 2.619177 CCTCGTCGTCTGGATGACTTAT 59.381 50.000 17.36 0.00 43.36 1.73
836 2958 2.014857 CCTCGTCGTCTGGATGACTTA 58.985 52.381 17.36 7.62 43.36 2.24
891 3013 3.491934 CGTTTGCACGCAGCTATAC 57.508 52.632 2.02 0.00 45.94 1.47
954 3080 1.164411 CGATCGATCAGGAGGAGAGG 58.836 60.000 24.40 0.96 0.00 3.69
965 3091 5.694006 AGGTGAATTGAATTCTCGATCGATC 59.306 40.000 19.78 15.68 39.96 3.69
966 3092 5.464722 CAGGTGAATTGAATTCTCGATCGAT 59.535 40.000 19.78 2.92 39.96 3.59
967 3093 4.805719 CAGGTGAATTGAATTCTCGATCGA 59.194 41.667 18.32 18.32 39.96 3.59
968 3094 4.805719 TCAGGTGAATTGAATTCTCGATCG 59.194 41.667 17.76 9.36 39.96 3.69
1362 5249 2.920912 TCCTCCGCCGACAGGTTT 60.921 61.111 2.50 0.00 40.50 3.27
1827 7100 1.089920 GCACCCAGATGTACTGCTTG 58.910 55.000 0.00 0.00 44.52 4.01
2056 7345 3.186047 CGACGACCCGTTGCCATC 61.186 66.667 0.00 0.00 41.37 3.51
2149 7438 3.599792 CTGTTTTGCTCAGGGCGCG 62.600 63.158 0.00 0.00 45.43 6.86
2150 7439 2.192608 CTCTGTTTTGCTCAGGGCGC 62.193 60.000 0.00 0.00 45.43 6.53
2151 7440 0.886490 ACTCTGTTTTGCTCAGGGCG 60.886 55.000 0.00 0.00 45.43 6.13
2156 7448 1.220529 CTCGCACTCTGTTTTGCTCA 58.779 50.000 0.00 0.00 36.54 4.26
2379 7689 1.016130 CGACAAGCTGCAGTGGTAGG 61.016 60.000 16.64 2.18 0.00 3.18
3517 10089 4.016706 CGGCCGGAGTTGAACCCT 62.017 66.667 20.10 0.00 0.00 4.34
3553 10125 1.238439 CTGCGTTCCTGATGTGGTTT 58.762 50.000 0.00 0.00 0.00 3.27
3554 10126 1.237285 GCTGCGTTCCTGATGTGGTT 61.237 55.000 0.00 0.00 0.00 3.67
3555 10127 1.672356 GCTGCGTTCCTGATGTGGT 60.672 57.895 0.00 0.00 0.00 4.16
3567 10141 0.108615 ACGATCTAGCTTTGCTGCGT 60.109 50.000 0.00 4.47 40.10 5.24
3572 10146 2.002586 TCAGCAACGATCTAGCTTTGC 58.997 47.619 9.97 9.97 41.64 3.68
3574 10148 4.507710 TCATTCAGCAACGATCTAGCTTT 58.492 39.130 0.00 0.00 36.26 3.51
3601 10175 5.112686 CCTATCTACAAACTGAACTGAGGC 58.887 45.833 0.00 0.00 0.00 4.70
3615 10206 9.503399 CATCACATAGTACTGTACCTATCTACA 57.497 37.037 14.05 0.00 0.00 2.74
3617 10208 9.503399 CACATCACATAGTACTGTACCTATCTA 57.497 37.037 14.05 0.80 0.00 1.98
3618 10209 8.218488 TCACATCACATAGTACTGTACCTATCT 58.782 37.037 14.05 0.00 0.00 1.98
3620 10211 8.941995 ATCACATCACATAGTACTGTACCTAT 57.058 34.615 14.05 8.68 0.00 2.57
3622 10213 7.013750 CAGATCACATCACATAGTACTGTACCT 59.986 40.741 14.05 5.01 0.00 3.08
3623 10214 7.013369 TCAGATCACATCACATAGTACTGTACC 59.987 40.741 14.05 0.00 0.00 3.34
3624 10215 7.931275 TCAGATCACATCACATAGTACTGTAC 58.069 38.462 9.93 9.93 0.00 2.90
3625 10216 7.993183 TCTCAGATCACATCACATAGTACTGTA 59.007 37.037 5.39 0.00 0.00 2.74
3627 10218 7.228308 TCTCTCAGATCACATCACATAGTACTG 59.772 40.741 5.39 0.00 0.00 2.74
3628 10219 7.228507 GTCTCTCAGATCACATCACATAGTACT 59.771 40.741 0.00 0.00 0.00 2.73
3630 10221 7.286313 AGTCTCTCAGATCACATCACATAGTA 58.714 38.462 0.00 0.00 0.00 1.82
3631 10222 6.128486 AGTCTCTCAGATCACATCACATAGT 58.872 40.000 0.00 0.00 0.00 2.12
3632 10223 6.638096 AGTCTCTCAGATCACATCACATAG 57.362 41.667 0.00 0.00 0.00 2.23
3633 10224 7.512992 TCTAGTCTCTCAGATCACATCACATA 58.487 38.462 0.00 0.00 0.00 2.29
3641 10232 4.881273 TGCTCTTCTAGTCTCTCAGATCAC 59.119 45.833 0.00 0.00 0.00 3.06
3728 11225 9.817809 GAGAGATATTGACTTGTACCATTTGTA 57.182 33.333 0.00 0.00 0.00 2.41
3738 11235 9.307121 CTATTTGAACGAGAGATATTGACTTGT 57.693 33.333 0.00 0.00 0.00 3.16
3754 11251 9.123709 GAGATGCTCTAAGTATCTATTTGAACG 57.876 37.037 7.42 0.00 45.64 3.95
3755 11252 9.418045 GGAGATGCTCTAAGTATCTATTTGAAC 57.582 37.037 7.42 0.00 45.64 3.18
3756 11253 9.147732 TGGAGATGCTCTAAGTATCTATTTGAA 57.852 33.333 7.42 0.00 45.64 2.69
3815 11574 4.659172 CAGGTGCGCCCCCAAAGA 62.659 66.667 14.07 0.00 34.57 2.52
3856 11615 4.479993 GCAGCGACTGGGGCATCT 62.480 66.667 8.57 0.00 31.21 2.90
3927 11689 3.493129 TGAATGAACTCGTCGAAGTTTGG 59.507 43.478 4.09 0.00 39.55 3.28
3973 11736 3.094484 AGGAGCAGACTAGTAGCAGTT 57.906 47.619 18.71 2.05 0.00 3.16
3975 11738 2.481104 GCAAGGAGCAGACTAGTAGCAG 60.481 54.545 18.71 7.02 44.79 4.24
3976 11739 1.478510 GCAAGGAGCAGACTAGTAGCA 59.521 52.381 18.71 0.00 44.79 3.49
4040 11831 3.323729 CGACTATACGCGGTTCTACAA 57.676 47.619 12.47 0.00 0.00 2.41
4263 12070 3.620300 TACTTCCGCAGCCGTCACG 62.620 63.158 0.00 0.00 0.00 4.35
4264 12071 2.092882 GTACTTCCGCAGCCGTCAC 61.093 63.158 0.00 0.00 0.00 3.67
4265 12072 2.260434 GTACTTCCGCAGCCGTCA 59.740 61.111 0.00 0.00 0.00 4.35
4266 12073 2.879462 CGTACTTCCGCAGCCGTC 60.879 66.667 0.00 0.00 0.00 4.79
4267 12074 4.430765 CCGTACTTCCGCAGCCGT 62.431 66.667 0.00 0.00 0.00 5.68
4269 12076 4.452733 AGCCGTACTTCCGCAGCC 62.453 66.667 0.00 0.00 0.00 4.85
4270 12077 2.886124 GAGCCGTACTTCCGCAGC 60.886 66.667 0.00 0.00 0.00 5.25
4271 12078 2.202756 GGAGCCGTACTTCCGCAG 60.203 66.667 0.00 0.00 0.00 5.18
4272 12079 3.766691 GGGAGCCGTACTTCCGCA 61.767 66.667 0.00 0.00 32.95 5.69
4275 12082 1.817209 CTCTGGGAGCCGTACTTCC 59.183 63.158 0.00 0.00 45.76 3.46
4295 12102 3.834799 CTACGTCCCCGACAGCCC 61.835 72.222 0.00 0.00 37.88 5.19
4296 12103 4.509737 GCTACGTCCCCGACAGCC 62.510 72.222 0.00 0.00 38.69 4.85
4297 12104 4.849329 CGCTACGTCCCCGACAGC 62.849 72.222 0.00 0.00 40.09 4.40
4298 12105 4.849329 GCGCTACGTCCCCGACAG 62.849 72.222 0.00 0.00 37.88 3.51
4338 12145 4.971125 GTATCCGCGCCTCCCTGC 62.971 72.222 0.00 0.00 0.00 4.85
4339 12146 4.647615 CGTATCCGCGCCTCCCTG 62.648 72.222 0.00 0.00 0.00 4.45
4349 12156 2.502080 GGAGATCGCGCGTATCCG 60.502 66.667 30.98 2.04 37.07 4.18
4350 12157 2.502080 CGGAGATCGCGCGTATCC 60.502 66.667 30.98 29.33 0.00 2.59
4411 12218 4.838152 TGGAGAATCAGCGCCGGC 62.838 66.667 19.07 19.07 36.25 6.13
4412 12219 2.109799 ATGGAGAATCAGCGCCGG 59.890 61.111 2.29 0.00 36.25 6.13
4413 12220 2.890109 GCATGGAGAATCAGCGCCG 61.890 63.158 2.29 0.00 36.25 6.46
4414 12221 2.550101 GGCATGGAGAATCAGCGCC 61.550 63.158 2.29 0.00 36.25 6.53
4415 12222 2.550101 GGGCATGGAGAATCAGCGC 61.550 63.158 0.00 0.00 36.25 5.92
4416 12223 1.895707 GGGGCATGGAGAATCAGCG 60.896 63.158 0.00 0.00 36.25 5.18
4417 12224 1.895707 CGGGGCATGGAGAATCAGC 60.896 63.158 0.00 0.00 36.25 4.26
4418 12225 1.228063 CCGGGGCATGGAGAATCAG 60.228 63.158 0.00 0.00 36.25 2.90
4419 12226 2.756042 CCCGGGGCATGGAGAATCA 61.756 63.158 14.71 0.00 36.25 2.57
4420 12227 2.113986 CCCGGGGCATGGAGAATC 59.886 66.667 14.71 0.00 0.00 2.52
4459 12266 3.122250 CTTCGAGGCCGAGTACCCG 62.122 68.421 0.00 0.00 46.39 5.28
4460 12267 1.726533 CTCTTCGAGGCCGAGTACCC 61.727 65.000 0.00 0.00 46.39 3.69
4461 12268 1.726533 CCTCTTCGAGGCCGAGTACC 61.727 65.000 0.00 0.00 46.39 3.34
4462 12269 1.728672 CCTCTTCGAGGCCGAGTAC 59.271 63.158 0.00 0.00 46.39 2.73
4463 12270 4.237445 CCTCTTCGAGGCCGAGTA 57.763 61.111 0.00 0.00 46.39 2.59
4472 12279 1.658686 GAAGCTCGGCTCCTCTTCGA 61.659 60.000 0.00 0.00 38.25 3.71
4473 12280 1.226831 GAAGCTCGGCTCCTCTTCG 60.227 63.158 0.00 0.00 38.25 3.79
4474 12281 1.226831 CGAAGCTCGGCTCCTCTTC 60.227 63.158 0.00 0.00 38.25 2.87
4475 12282 1.939769 GACGAAGCTCGGCTCCTCTT 61.940 60.000 9.75 0.00 46.20 2.85
4476 12283 2.361865 ACGAAGCTCGGCTCCTCT 60.362 61.111 9.75 0.00 45.59 3.69
4477 12284 2.103340 GACGAAGCTCGGCTCCTC 59.897 66.667 9.75 0.00 46.20 3.71
4483 12290 2.196382 TTCACGAGGACGAAGCTCGG 62.196 60.000 0.00 0.00 45.59 4.63
4484 12291 0.794981 CTTCACGAGGACGAAGCTCG 60.795 60.000 0.00 0.00 46.93 5.03
4485 12292 3.022981 CTTCACGAGGACGAAGCTC 57.977 57.895 0.00 0.00 42.66 4.09


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

AutoCloner maintained by Alex Coulton.