Multiple sequence alignment - TraesCS4A01G399900

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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 TraesCS4A01G399900 chr4A 100.000 5514 0 0 1 5514 674434416 674439929 0.000000e+00 10183.0
1 TraesCS4A01G399900 chr4A 92.980 1282 78 9 1989 3266 673782259 673780986 0.000000e+00 1858.0
2 TraesCS4A01G399900 chr4A 90.306 1176 97 10 424 1587 673783779 673782609 0.000000e+00 1524.0
3 TraesCS4A01G399900 chr4A 93.239 917 58 3 4043 4955 673781001 673780085 0.000000e+00 1347.0
4 TraesCS4A01G399900 chr4A 97.892 427 9 0 1 427 537245722 537245296 0.000000e+00 739.0
5 TraesCS4A01G399900 chr4A 97.658 427 10 0 1 427 542524979 542525405 0.000000e+00 734.0
6 TraesCS4A01G399900 chr4A 89.696 427 44 0 1 427 32410428 32410854 3.760000e-151 545.0
7 TraesCS4A01G399900 chr4A 89.696 427 44 0 1 427 640911855 640911429 3.760000e-151 545.0
8 TraesCS4A01G399900 chr4A 89.696 427 44 0 1 427 677124592 677124166 3.760000e-151 545.0
9 TraesCS4A01G399900 chr7A 93.240 2352 112 25 939 3266 62484330 62486658 0.000000e+00 3419.0
10 TraesCS4A01G399900 chr7A 89.010 828 83 6 4054 4877 62486748 62487571 0.000000e+00 1018.0
11 TraesCS4A01G399900 chr7A 92.075 530 40 2 425 953 62482475 62483003 0.000000e+00 745.0
12 TraesCS4A01G399900 chr7A 92.037 427 34 0 1 427 11089912 11089486 7.900000e-168 601.0
13 TraesCS4A01G399900 chr7A 83.005 406 52 9 3265 3654 168797102 168797506 8.790000e-93 351.0
14 TraesCS4A01G399900 chr7D 92.148 1299 72 12 1989 3266 58160270 58161559 0.000000e+00 1807.0
15 TraesCS4A01G399900 chr7D 87.638 1181 123 13 424 1587 58158754 58159928 0.000000e+00 1351.0
16 TraesCS4A01G399900 chr7D 83.440 936 104 29 4038 4952 58161537 58162442 0.000000e+00 822.0
17 TraesCS4A01G399900 chr7D 96.429 196 7 0 4957 5152 467993830 467994025 1.920000e-84 324.0
18 TraesCS4A01G399900 chr7D 82.700 237 36 5 430 663 541963966 541964200 7.240000e-49 206.0
19 TraesCS4A01G399900 chr7D 89.524 105 11 0 20 124 504500143 504500247 3.470000e-27 134.0
20 TraesCS4A01G399900 chr1B 88.000 825 56 19 3254 4053 10251662 10252468 0.000000e+00 935.0
21 TraesCS4A01G399900 chr1B 90.164 427 42 0 1 427 363451630 363452056 1.740000e-154 556.0
22 TraesCS4A01G399900 chr1B 87.799 418 27 10 3265 3662 98396322 98396735 8.360000e-128 468.0
23 TraesCS4A01G399900 chr1B 87.589 419 27 11 3265 3662 98416440 98416854 3.890000e-126 462.0
24 TraesCS4A01G399900 chr1B 87.589 419 27 11 3265 3662 98444120 98444534 3.890000e-126 462.0
25 TraesCS4A01G399900 chr1B 85.387 349 34 9 3703 4049 98396656 98396323 4.090000e-91 346.0
26 TraesCS4A01G399900 chr1B 85.387 349 34 9 3703 4049 98416774 98416441 4.090000e-91 346.0
27 TraesCS4A01G399900 chr1B 85.387 349 34 9 3703 4049 98444454 98444121 4.090000e-91 346.0
28 TraesCS4A01G399900 chr1B 89.868 227 21 2 3827 4051 98396728 98396954 1.940000e-74 291.0
29 TraesCS4A01G399900 chr1B 89.868 227 21 2 3827 4051 98416847 98417073 1.940000e-74 291.0
30 TraesCS4A01G399900 chr1B 89.823 226 22 1 3827 4051 98444527 98444752 6.990000e-74 289.0
31 TraesCS4A01G399900 chr6B 88.221 815 50 17 3250 4050 678718231 678719013 0.000000e+00 931.0
32 TraesCS4A01G399900 chr6B 94.848 427 22 0 1 427 529900476 529900902 0.000000e+00 667.0
33 TraesCS4A01G399900 chr6B 96.035 227 9 0 4957 5183 225541329 225541103 2.430000e-98 370.0
34 TraesCS4A01G399900 chr6B 82.857 140 19 5 431 568 469786911 469787047 2.700000e-23 121.0
35 TraesCS4A01G399900 chr2B 93.011 558 34 2 4957 5514 247371403 247370851 0.000000e+00 809.0
36 TraesCS4A01G399900 chr2B 97.190 427 12 0 1 427 429458505 429458079 0.000000e+00 723.0
37 TraesCS4A01G399900 chr2B 80.925 173 29 3 424 595 278440279 278440448 3.470000e-27 134.0
38 TraesCS4A01G399900 chr3D 91.552 580 26 8 4957 5514 268942688 268943266 0.000000e+00 778.0
39 TraesCS4A01G399900 chr3D 90.164 427 41 1 1 427 459220529 459220104 6.240000e-154 555.0
40 TraesCS4A01G399900 chr3D 90.196 306 29 1 1 306 465020752 465021056 1.110000e-106 398.0
41 TraesCS4A01G399900 chr3D 92.337 261 20 0 1 261 31098456 31098196 6.750000e-99 372.0
42 TraesCS4A01G399900 chr3D 89.286 168 18 0 260 427 31096452 31096285 1.560000e-50 211.0
43 TraesCS4A01G399900 chr3D 80.368 163 25 5 489 646 74348502 74348662 3.490000e-22 117.0
44 TraesCS4A01G399900 chr3D 81.707 82 11 3 538 619 543971684 543971761 1.280000e-06 65.8
45 TraesCS4A01G399900 chr7B 91.034 580 30 7 4957 5514 458784229 458784808 0.000000e+00 763.0
46 TraesCS4A01G399900 chr7B 96.447 197 7 0 4956 5152 711744652 711744456 5.330000e-85 326.0
47 TraesCS4A01G399900 chr7B 79.795 292 49 9 3266 3557 750317646 750317927 2.600000e-48 204.0
48 TraesCS4A01G399900 chr5B 91.413 559 43 2 4956 5514 461825119 461825672 0.000000e+00 761.0
49 TraesCS4A01G399900 chr5B 90.862 580 31 7 4957 5514 130923659 130924238 0.000000e+00 758.0
50 TraesCS4A01G399900 chr5B 90.862 580 30 8 4957 5514 157390787 157391365 0.000000e+00 756.0
51 TraesCS4A01G399900 chr5B 90.179 224 12 4 4957 5180 461826647 461826860 3.250000e-72 283.0
52 TraesCS4A01G399900 chr4B 90.582 584 31 9 4953 5514 250728421 250727840 0.000000e+00 752.0
53 TraesCS4A01G399900 chr4B 89.461 427 45 0 1 427 120503942 120504368 1.750000e-149 540.0
54 TraesCS4A01G399900 chr4B 88.290 427 50 0 1 427 624404501 624404075 3.810000e-141 512.0
55 TraesCS4A01G399900 chr4B 84.028 432 39 16 3252 3661 4542528 4542105 6.700000e-104 388.0
56 TraesCS4A01G399900 chr4B 90.135 223 20 2 3829 4049 4542110 4541888 6.990000e-74 289.0
57 TraesCS4A01G399900 chr4B 92.021 188 13 2 3258 3444 4541881 4542067 4.240000e-66 263.0
58 TraesCS4A01G399900 chr4B 82.993 147 22 3 424 568 619362144 619362289 4.480000e-26 130.0
59 TraesCS4A01G399900 chr3B 90.603 564 47 1 4957 5514 391792227 391792790 0.000000e+00 743.0
60 TraesCS4A01G399900 chr3B 90.240 584 29 11 4957 5514 54779677 54779096 0.000000e+00 737.0
61 TraesCS4A01G399900 chr3B 94.144 222 11 1 4959 5180 574702532 574702751 2.460000e-88 337.0
62 TraesCS4A01G399900 chr3B 92.982 228 13 3 4957 5183 581649790 581650015 4.120000e-86 329.0
63 TraesCS4A01G399900 chr3B 82.322 379 47 14 3267 3630 172760816 172761189 1.490000e-80 311.0
64 TraesCS4A01G399900 chr3B 86.806 144 15 4 477 619 488531383 488531243 2.060000e-34 158.0
65 TraesCS4A01G399900 chr5A 97.658 427 10 0 1 427 123388337 123388763 0.000000e+00 734.0
66 TraesCS4A01G399900 chr5A 83.511 376 40 11 3675 4043 562029530 562029170 1.140000e-86 331.0
67 TraesCS4A01G399900 chr2A 89.930 427 43 0 1 427 519349104 519348678 8.070000e-153 551.0
68 TraesCS4A01G399900 chr1D 90.238 420 39 2 8 427 334454861 334454444 1.040000e-151 547.0
69 TraesCS4A01G399900 chr1D 89.676 339 33 2 8 345 373998588 373998251 1.100000e-116 431.0
70 TraesCS4A01G399900 chr1D 96.447 197 7 0 4956 5152 36841374 36841178 5.330000e-85 326.0
71 TraesCS4A01G399900 chr1D 95.745 47 2 0 381 427 373998255 373998209 5.920000e-10 76.8
72 TraesCS4A01G399900 chr6A 89.720 428 42 2 1 427 49743201 49743627 3.760000e-151 545.0
73 TraesCS4A01G399900 chr1A 92.973 370 26 0 1 370 516079232 516079601 1.750000e-149 540.0
74 TraesCS4A01G399900 chr1A 83.246 382 44 12 3677 4051 505768864 505768496 3.180000e-87 333.0
75 TraesCS4A01G399900 chr1A 80.660 212 31 9 440 646 552982462 552982256 7.400000e-34 156.0
76 TraesCS4A01G399900 chr5D 88.941 425 44 1 1 425 435968761 435969182 6.330000e-144 521.0
77 TraesCS4A01G399900 chr5D 83.641 379 40 13 3679 4049 350984058 350983694 2.460000e-88 337.0
78 TraesCS4A01G399900 chr5D 82.169 415 47 15 3266 3654 350984647 350984234 1.140000e-86 331.0
79 TraesCS4A01G399900 chrUn 84.680 359 37 9 3696 4049 470511206 470510861 5.290000e-90 342.0
80 TraesCS4A01G399900 chr3A 83.905 379 40 12 3677 4049 681124029 681124392 5.290000e-90 342.0
81 TraesCS4A01G399900 chr3A 82.415 381 42 15 3677 4048 24426867 24427231 5.360000e-80 309.0
82 TraesCS4A01G399900 chr3A 83.505 194 28 3 425 616 497647893 497647702 1.580000e-40 178.0
83 TraesCS4A01G399900 chr3A 80.000 120 20 4 538 655 716781274 716781157 9.840000e-13 86.1
84 TraesCS4A01G399900 chr6D 75.532 376 50 23 3682 4049 436375174 436374833 4.450000e-31 147.0
85 TraesCS4A01G399900 chr2D 82.877 146 21 4 466 607 250627719 250627574 1.610000e-25 128.0
86 TraesCS4A01G399900 chr2D 80.469 128 20 5 487 613 413788564 413788441 5.880000e-15 93.5
87 TraesCS4A01G399900 chr4D 90.164 61 6 0 3459 3519 280416054 280415994 4.580000e-11 80.5
88 TraesCS4A01G399900 chr4D 85.714 63 8 1 3589 3650 506195153 506195215 1.280000e-06 65.8
89 TraesCS4A01G399900 chr4D 96.970 33 1 0 538 570 500462746 500462714 7.720000e-04 56.5


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 TraesCS4A01G399900 chr4A 674434416 674439929 5513 False 10183.000000 10183 100.000000 1 5514 1 chr4A.!!$F3 5513
1 TraesCS4A01G399900 chr4A 673780085 673783779 3694 True 1576.333333 1858 92.175000 424 4955 3 chr4A.!!$R4 4531
2 TraesCS4A01G399900 chr7A 62482475 62487571 5096 False 1727.333333 3419 91.441667 425 4877 3 chr7A.!!$F2 4452
3 TraesCS4A01G399900 chr7D 58158754 58162442 3688 False 1326.666667 1807 87.742000 424 4952 3 chr7D.!!$F4 4528
4 TraesCS4A01G399900 chr1B 10251662 10252468 806 False 935.000000 935 88.000000 3254 4053 1 chr1B.!!$F1 799
5 TraesCS4A01G399900 chr1B 98396322 98396954 632 False 379.500000 468 88.833500 3265 4051 2 chr1B.!!$F3 786
6 TraesCS4A01G399900 chr1B 98416440 98417073 633 False 376.500000 462 88.728500 3265 4051 2 chr1B.!!$F4 786
7 TraesCS4A01G399900 chr1B 98444120 98444752 632 False 375.500000 462 88.706000 3265 4051 2 chr1B.!!$F5 786
8 TraesCS4A01G399900 chr6B 678718231 678719013 782 False 931.000000 931 88.221000 3250 4050 1 chr6B.!!$F3 800
9 TraesCS4A01G399900 chr2B 247370851 247371403 552 True 809.000000 809 93.011000 4957 5514 1 chr2B.!!$R1 557
10 TraesCS4A01G399900 chr3D 268942688 268943266 578 False 778.000000 778 91.552000 4957 5514 1 chr3D.!!$F2 557
11 TraesCS4A01G399900 chr3D 31096285 31098456 2171 True 291.500000 372 90.811500 1 427 2 chr3D.!!$R2 426
12 TraesCS4A01G399900 chr7B 458784229 458784808 579 False 763.000000 763 91.034000 4957 5514 1 chr7B.!!$F1 557
13 TraesCS4A01G399900 chr5B 130923659 130924238 579 False 758.000000 758 90.862000 4957 5514 1 chr5B.!!$F1 557
14 TraesCS4A01G399900 chr5B 157390787 157391365 578 False 756.000000 756 90.862000 4957 5514 1 chr5B.!!$F2 557
15 TraesCS4A01G399900 chr5B 461825119 461826860 1741 False 522.000000 761 90.796000 4956 5514 2 chr5B.!!$F3 558
16 TraesCS4A01G399900 chr4B 250727840 250728421 581 True 752.000000 752 90.582000 4953 5514 1 chr4B.!!$R1 561
17 TraesCS4A01G399900 chr4B 4541888 4542528 640 True 338.500000 388 87.081500 3252 4049 2 chr4B.!!$R3 797
18 TraesCS4A01G399900 chr3B 391792227 391792790 563 False 743.000000 743 90.603000 4957 5514 1 chr3B.!!$F2 557
19 TraesCS4A01G399900 chr3B 54779096 54779677 581 True 737.000000 737 90.240000 4957 5514 1 chr3B.!!$R1 557
20 TraesCS4A01G399900 chr5D 350983694 350984647 953 True 334.000000 337 82.905000 3266 4049 2 chr5D.!!$R1 783

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
275 276 0.181350 AGCTGGGATTTCATCGGACC 59.819 55.000 0.00 0.00 0.00 4.46 F
409 410 0.244721 GTGGCCATTCTCCAAACAGC 59.755 55.000 9.72 0.00 35.01 4.40 F
1703 3209 0.110486 AGGGTCGGAATGTGCACTTT 59.890 50.000 19.41 18.17 0.00 2.66 F
3206 4827 0.097674 GTAGCGCCACATTGCTCTTG 59.902 55.000 2.29 0.00 42.48 3.02 F
3512 5151 2.047274 ATGTGCAAGGTCCGACCG 60.047 61.111 12.04 0.00 44.90 4.79 F
4438 6280 1.488393 AGGAGGAGAAAGCTATGTGCC 59.512 52.381 0.00 0.00 44.23 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 3185 0.521735 GCACATTCCGACCCTGAAAC 59.478 55.000 0.00 0.00 0.00 2.78 R
1739 3270 1.000274 GCAAGAGCATTTTTGGTCGGT 60.000 47.619 0.08 0.00 40.82 4.69 R
3631 5297 0.165944 GTCACACCTTGCGCATGTAC 59.834 55.000 12.75 8.45 0.00 2.90 R
4402 6244 0.250901 TCCTTGCCAAGAACAGCCTC 60.251 55.000 5.89 0.00 0.00 4.70 R
4471 6313 0.321122 CCCTGGAGTGTCTCTGCAAC 60.321 60.000 0.00 0.00 43.54 4.17 R
5446 7662 1.691195 TTGCGACCACTTCCAGGTGA 61.691 55.000 0.00 0.00 40.09 4.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.300971 CCACTGAGCCACCAACATCG 61.301 60.000 0.00 0.00 0.00 3.84
77 78 2.568090 GGATTGCAACACAGCCGG 59.432 61.111 0.00 0.00 0.00 6.13
78 79 2.568090 GATTGCAACACAGCCGGG 59.432 61.111 0.00 0.00 0.00 5.73
83 84 2.908073 GCAACACAGCCGGGACAAG 61.908 63.158 2.18 0.00 0.00 3.16
105 106 2.046507 AGCTTTCCCAGAGCAGCG 60.047 61.111 0.00 0.00 42.56 5.18
108 109 1.294780 CTTTCCCAGAGCAGCGTCT 59.705 57.895 0.00 0.00 0.00 4.18
161 162 4.598894 CTCCGCCTGCGCTGCTAT 62.599 66.667 17.97 0.00 38.24 2.97
169 170 0.598680 CTGCGCTGCTATAGTGGACC 60.599 60.000 9.73 0.00 37.39 4.46
174 175 0.315568 CTGCTATAGTGGACCGGAGC 59.684 60.000 9.46 4.12 0.00 4.70
183 184 1.065928 GGACCGGAGCAGTACATCG 59.934 63.158 9.46 0.00 0.00 3.84
193 194 1.810412 GCAGTACATCGGATGGGGTTC 60.810 57.143 21.19 7.30 33.60 3.62
217 218 0.859232 CTCAACGTGAGTGGAAACGG 59.141 55.000 0.00 0.00 45.00 4.44
261 262 2.612115 ACCTTGGAGGGGAGCTGG 60.612 66.667 0.00 0.00 40.58 4.85
263 264 2.285668 CTTGGAGGGGAGCTGGGA 60.286 66.667 0.00 0.00 0.00 4.37
265 266 1.230281 TTGGAGGGGAGCTGGGATT 60.230 57.895 0.00 0.00 0.00 3.01
266 267 0.850883 TTGGAGGGGAGCTGGGATTT 60.851 55.000 0.00 0.00 0.00 2.17
267 268 1.281925 TGGAGGGGAGCTGGGATTTC 61.282 60.000 0.00 0.00 0.00 2.17
268 269 1.281925 GGAGGGGAGCTGGGATTTCA 61.282 60.000 0.00 0.00 0.00 2.69
269 270 0.849417 GAGGGGAGCTGGGATTTCAT 59.151 55.000 0.00 0.00 0.00 2.57
270 271 0.849417 AGGGGAGCTGGGATTTCATC 59.151 55.000 0.00 0.00 0.00 2.92
271 272 0.536006 GGGGAGCTGGGATTTCATCG 60.536 60.000 0.00 0.00 0.00 3.84
273 274 0.469917 GGAGCTGGGATTTCATCGGA 59.530 55.000 0.00 0.00 0.00 4.55
274 275 1.587547 GAGCTGGGATTTCATCGGAC 58.412 55.000 0.00 0.00 0.00 4.79
275 276 0.181350 AGCTGGGATTTCATCGGACC 59.819 55.000 0.00 0.00 0.00 4.46
276 277 0.819666 GCTGGGATTTCATCGGACCC 60.820 60.000 0.00 0.00 40.79 4.46
277 278 0.839946 CTGGGATTTCATCGGACCCT 59.160 55.000 0.00 0.00 40.98 4.34
278 279 0.837272 TGGGATTTCATCGGACCCTC 59.163 55.000 0.00 0.00 40.98 4.30
279 280 0.837272 GGGATTTCATCGGACCCTCA 59.163 55.000 0.00 0.00 37.75 3.86
280 281 1.475213 GGGATTTCATCGGACCCTCAC 60.475 57.143 0.00 0.00 37.75 3.51
281 282 1.209504 GGATTTCATCGGACCCTCACA 59.790 52.381 0.00 0.00 0.00 3.58
282 283 2.355716 GGATTTCATCGGACCCTCACAA 60.356 50.000 0.00 0.00 0.00 3.33
283 284 2.472695 TTTCATCGGACCCTCACAAG 57.527 50.000 0.00 0.00 0.00 3.16
286 287 1.550524 TCATCGGACCCTCACAAGAAG 59.449 52.381 0.00 0.00 0.00 2.85
287 288 0.250513 ATCGGACCCTCACAAGAAGC 59.749 55.000 0.00 0.00 0.00 3.86
288 289 0.832135 TCGGACCCTCACAAGAAGCT 60.832 55.000 0.00 0.00 0.00 3.74
290 291 1.134965 CGGACCCTCACAAGAAGCTAG 60.135 57.143 0.00 0.00 0.00 3.42
291 292 2.180276 GGACCCTCACAAGAAGCTAGA 58.820 52.381 0.00 0.00 0.00 2.43
292 293 2.167487 GGACCCTCACAAGAAGCTAGAG 59.833 54.545 0.00 0.00 0.00 2.43
303 304 2.327244 GCTAGAGCTGCGCAATGC 59.673 61.111 13.05 13.21 46.70 3.56
304 305 2.178890 GCTAGAGCTGCGCAATGCT 61.179 57.895 22.53 22.53 46.63 3.79
308 309 3.599584 AGCTGCGCAATGCTCATT 58.400 50.000 17.56 0.00 46.63 2.57
317 318 1.904144 CAATGCTCATTGTCAAGGCG 58.096 50.000 13.01 0.00 42.32 5.52
318 319 1.469703 CAATGCTCATTGTCAAGGCGA 59.530 47.619 13.01 0.00 42.32 5.54
319 320 1.376543 ATGCTCATTGTCAAGGCGAG 58.623 50.000 0.00 0.00 0.00 5.03
320 321 0.321346 TGCTCATTGTCAAGGCGAGA 59.679 50.000 11.65 0.00 0.00 4.04
321 322 0.723981 GCTCATTGTCAAGGCGAGAC 59.276 55.000 11.65 5.57 36.55 3.36
322 323 1.363744 CTCATTGTCAAGGCGAGACC 58.636 55.000 9.34 0.00 35.15 3.85
323 324 0.389817 TCATTGTCAAGGCGAGACCG 60.390 55.000 9.34 0.00 46.52 4.79
324 325 0.670546 CATTGTCAAGGCGAGACCGT 60.671 55.000 9.34 0.00 46.52 4.83
326 327 2.432628 GTCAAGGCGAGACCGTGG 60.433 66.667 1.56 0.00 46.89 4.94
327 328 4.373116 TCAAGGCGAGACCGTGGC 62.373 66.667 0.00 0.00 46.89 5.01
343 344 4.884257 GCGGCATGGCAAGGCATG 62.884 66.667 26.53 26.53 33.81 4.06
353 354 2.869636 CAAGGCATGCAAGAGAGCT 58.130 52.632 21.36 1.85 34.99 4.09
354 355 0.452184 CAAGGCATGCAAGAGAGCTG 59.548 55.000 21.36 0.37 34.99 4.24
355 356 0.327259 AAGGCATGCAAGAGAGCTGA 59.673 50.000 21.36 0.00 34.99 4.26
356 357 0.327259 AGGCATGCAAGAGAGCTGAA 59.673 50.000 21.36 0.00 34.99 3.02
357 358 1.064611 AGGCATGCAAGAGAGCTGAAT 60.065 47.619 21.36 0.00 34.99 2.57
358 359 1.065701 GGCATGCAAGAGAGCTGAATG 59.934 52.381 21.36 0.00 34.99 2.67
359 360 1.065701 GCATGCAAGAGAGCTGAATGG 59.934 52.381 14.21 0.00 34.99 3.16
360 361 2.640184 CATGCAAGAGAGCTGAATGGA 58.360 47.619 0.00 0.00 34.99 3.41
361 362 2.105006 TGCAAGAGAGCTGAATGGAC 57.895 50.000 0.00 0.00 34.99 4.02
362 363 1.005340 GCAAGAGAGCTGAATGGACG 58.995 55.000 0.00 0.00 0.00 4.79
363 364 1.005340 CAAGAGAGCTGAATGGACGC 58.995 55.000 0.00 0.00 0.00 5.19
364 365 0.901124 AAGAGAGCTGAATGGACGCT 59.099 50.000 0.00 0.00 36.57 5.07
365 366 1.769026 AGAGAGCTGAATGGACGCTA 58.231 50.000 0.00 0.00 33.47 4.26
366 367 2.103373 AGAGAGCTGAATGGACGCTAA 58.897 47.619 0.00 0.00 33.47 3.09
367 368 2.100584 AGAGAGCTGAATGGACGCTAAG 59.899 50.000 0.00 0.00 33.47 2.18
368 369 0.933796 GAGCTGAATGGACGCTAAGC 59.066 55.000 0.00 0.00 33.47 3.09
369 370 0.250234 AGCTGAATGGACGCTAAGCA 59.750 50.000 0.00 0.00 33.08 3.91
370 371 1.134280 AGCTGAATGGACGCTAAGCAT 60.134 47.619 0.00 0.00 33.08 3.79
371 372 1.672881 GCTGAATGGACGCTAAGCATT 59.327 47.619 0.00 0.00 0.00 3.56
372 373 2.540361 GCTGAATGGACGCTAAGCATTG 60.540 50.000 0.00 0.00 0.00 2.82
373 374 2.679837 CTGAATGGACGCTAAGCATTGT 59.320 45.455 0.00 0.00 0.00 2.71
374 375 2.419673 TGAATGGACGCTAAGCATTGTG 59.580 45.455 0.00 0.00 0.00 3.33
375 376 2.401583 ATGGACGCTAAGCATTGTGA 57.598 45.000 0.00 0.00 0.00 3.58
376 377 1.438651 TGGACGCTAAGCATTGTGAC 58.561 50.000 0.00 0.00 0.00 3.67
377 378 1.270571 TGGACGCTAAGCATTGTGACA 60.271 47.619 0.00 0.00 0.00 3.58
378 379 1.128692 GGACGCTAAGCATTGTGACAC 59.871 52.381 0.00 0.00 0.00 3.67
379 380 1.128692 GACGCTAAGCATTGTGACACC 59.871 52.381 2.45 0.00 0.00 4.16
380 381 0.447801 CGCTAAGCATTGTGACACCC 59.552 55.000 2.45 0.00 0.00 4.61
381 382 1.533625 GCTAAGCATTGTGACACCCA 58.466 50.000 2.45 0.00 0.00 4.51
382 383 1.200020 GCTAAGCATTGTGACACCCAC 59.800 52.381 2.45 0.00 45.88 4.61
403 404 3.089838 CCCAGTGGCCATTCTCCA 58.910 61.111 9.72 0.00 0.00 3.86
404 405 1.383799 CCCAGTGGCCATTCTCCAA 59.616 57.895 9.72 0.00 35.01 3.53
405 406 0.251742 CCCAGTGGCCATTCTCCAAA 60.252 55.000 9.72 0.00 35.01 3.28
406 407 0.890683 CCAGTGGCCATTCTCCAAAC 59.109 55.000 9.72 0.00 35.01 2.93
407 408 1.619654 CAGTGGCCATTCTCCAAACA 58.380 50.000 9.72 0.00 35.01 2.83
408 409 1.542915 CAGTGGCCATTCTCCAAACAG 59.457 52.381 9.72 0.00 35.01 3.16
409 410 0.244721 GTGGCCATTCTCCAAACAGC 59.755 55.000 9.72 0.00 35.01 4.40
410 411 1.243342 TGGCCATTCTCCAAACAGCG 61.243 55.000 0.00 0.00 0.00 5.18
411 412 1.508088 GCCATTCTCCAAACAGCGG 59.492 57.895 0.00 0.00 0.00 5.52
412 413 1.937546 GCCATTCTCCAAACAGCGGG 61.938 60.000 0.00 0.00 0.00 6.13
413 414 0.322456 CCATTCTCCAAACAGCGGGA 60.322 55.000 0.00 0.00 0.00 5.14
700 704 5.583061 ACGAGTTCAACTTTCAACACATGTA 59.417 36.000 0.00 0.00 0.00 2.29
735 739 2.165998 CCTCCTTTTCCTCCAAAGCTG 58.834 52.381 0.00 0.00 33.08 4.24
850 946 5.048504 TGCTTAGCTGATTTTCTTTCCACAG 60.049 40.000 5.60 0.00 0.00 3.66
852 948 6.149474 GCTTAGCTGATTTTCTTTCCACAGTA 59.851 38.462 0.00 0.00 0.00 2.74
908 1004 2.950309 AGCCAATCATTCATGAGCAGAC 59.050 45.455 0.00 0.00 40.64 3.51
1008 2452 2.093973 AGAGAAGTAGACCATGTTGCGG 60.094 50.000 0.00 0.00 0.00 5.69
1143 2593 1.837051 AGAGGTGGAGTTCACGCCA 60.837 57.895 0.00 0.00 46.96 5.69
1350 2800 2.330216 CTCTTCCGGGGAATGGTCTAT 58.670 52.381 0.00 0.00 33.28 1.98
1372 2822 1.644786 CCATCCCGAAAAGGTGACGC 61.645 60.000 0.00 0.00 38.74 5.19
1376 2826 0.794473 CCCGAAAAGGTGACGCTTAC 59.206 55.000 0.00 0.00 38.74 2.34
1378 2828 2.073816 CCGAAAAGGTGACGCTTACAT 58.926 47.619 0.00 0.00 34.51 2.29
1383 2833 4.685169 AAAGGTGACGCTTACATCATTG 57.315 40.909 0.00 0.00 0.00 2.82
1384 2834 2.009774 AGGTGACGCTTACATCATTGC 58.990 47.619 0.00 0.00 0.00 3.56
1402 2852 7.509141 TCATTGCTAACATTCTTGTTCTTCA 57.491 32.000 0.00 0.00 42.43 3.02
1406 2860 6.959361 TGCTAACATTCTTGTTCTTCACTTC 58.041 36.000 0.00 0.00 42.43 3.01
1530 2984 0.255890 AACCTGCCGCCACATTATCT 59.744 50.000 0.00 0.00 0.00 1.98
1543 2997 6.400409 CGCCACATTATCTCAATACATCTTCG 60.400 42.308 0.00 0.00 0.00 3.79
1614 3119 7.605410 TTAACAAAGAATTATCGACTGGGAC 57.395 36.000 0.00 0.00 0.00 4.46
1679 3185 3.986970 GTTTTGAAACCAGGGCCAG 57.013 52.632 6.18 0.00 32.82 4.85
1691 3197 2.359975 GGCCAGTTTCAGGGTCGG 60.360 66.667 0.00 0.00 0.00 4.79
1703 3209 0.110486 AGGGTCGGAATGTGCACTTT 59.890 50.000 19.41 18.17 0.00 2.66
1731 3262 7.566760 ACACAATTCAACATAGACTTTCACA 57.433 32.000 0.00 0.00 0.00 3.58
1732 3263 7.995289 ACACAATTCAACATAGACTTTCACAA 58.005 30.769 0.00 0.00 0.00 3.33
1733 3264 8.632679 ACACAATTCAACATAGACTTTCACAAT 58.367 29.630 0.00 0.00 0.00 2.71
1741 3272 9.559958 CAACATAGACTTTCACAATATTTGACC 57.440 33.333 0.00 0.00 0.00 4.02
1742 3273 7.974675 ACATAGACTTTCACAATATTTGACCG 58.025 34.615 0.00 0.00 0.00 4.79
1743 3274 7.822334 ACATAGACTTTCACAATATTTGACCGA 59.178 33.333 0.00 0.00 0.00 4.69
1744 3275 6.481954 AGACTTTCACAATATTTGACCGAC 57.518 37.500 0.00 0.00 0.00 4.79
1745 3276 5.411669 AGACTTTCACAATATTTGACCGACC 59.588 40.000 0.00 0.00 0.00 4.79
1777 3308 6.256757 GCTCTTGCAATAGTTGAACCTACTAG 59.743 42.308 12.83 0.00 39.41 2.57
1802 3333 7.855904 AGTTAGCTATTTTTGTTGAAGTTGACG 59.144 33.333 0.00 0.00 0.00 4.35
1913 3444 4.023365 GGTGATGCTATCTCCAAATGCTTC 60.023 45.833 10.48 0.00 41.42 3.86
2019 3609 7.445402 GTCATACATAGTTATTCACTGCCCATT 59.555 37.037 0.00 0.00 35.97 3.16
2023 3613 3.356290 AGTTATTCACTGCCCATTGTCC 58.644 45.455 0.00 0.00 32.83 4.02
2070 3660 0.820482 ATATTTGTTACCGGCCGCCC 60.820 55.000 22.85 7.15 0.00 6.13
2077 3667 1.751349 TTACCGGCCGCCCTTAGATC 61.751 60.000 22.85 0.00 0.00 2.75
2080 3670 2.504519 GGCCGCCCTTAGATCGTT 59.495 61.111 0.00 0.00 0.00 3.85
2128 3718 5.334569 GCCTGTACTCGAGATAGAGAATGAC 60.335 48.000 21.68 1.82 40.57 3.06
2136 3726 4.215965 GAGATAGAGAATGACGCGAGAAC 58.784 47.826 15.93 1.38 0.00 3.01
2137 3727 3.628032 AGATAGAGAATGACGCGAGAACA 59.372 43.478 15.93 7.85 0.00 3.18
2138 3728 1.983972 AGAGAATGACGCGAGAACAC 58.016 50.000 15.93 0.00 0.00 3.32
2200 3790 3.654201 CAGGCGTGCAAGCAAGTA 58.346 55.556 25.75 0.00 39.27 2.24
2204 3794 1.234615 GGCGTGCAAGCAAGTAAGGA 61.235 55.000 25.75 0.00 39.27 3.36
2462 4052 2.432510 GACATGGAGAAGTACCTGGAGG 59.567 54.545 0.00 0.00 42.17 4.30
2528 4118 8.718102 TCAAGGTAGTAAGCTTCATTCATAAC 57.282 34.615 0.00 0.00 41.45 1.89
2543 4137 5.950544 TTCATAACTATAGCACCACCAGT 57.049 39.130 0.00 0.00 0.00 4.00
2556 4150 4.083271 GCACCACCAGTAAATTTCTCAGTC 60.083 45.833 0.00 0.00 0.00 3.51
2576 4171 6.036735 TCAGTCGTTTGTGACCTTCTTTTAAG 59.963 38.462 0.00 0.00 39.77 1.85
2856 4451 6.931840 CCTCTCTCTAATACCTAAAACCATGC 59.068 42.308 0.00 0.00 0.00 4.06
2860 4455 5.120399 TCTAATACCTAAAACCATGCACCG 58.880 41.667 0.00 0.00 0.00 4.94
2961 4581 6.908870 TCAGATCTGTGGTGAAAAATATCG 57.091 37.500 21.92 0.00 0.00 2.92
2979 4600 2.016318 TCGCCATTTATGACCTTGCAG 58.984 47.619 0.00 0.00 0.00 4.41
3092 4713 4.954826 TCATATCAATTGCACATTGGACCA 59.045 37.500 16.44 0.00 0.00 4.02
3200 4821 0.240678 TTTGCTGTAGCGCCACATTG 59.759 50.000 9.60 0.00 45.83 2.82
3202 4823 2.401766 GCTGTAGCGCCACATTGCT 61.402 57.895 9.60 0.00 45.04 3.91
3203 4824 1.717937 CTGTAGCGCCACATTGCTC 59.282 57.895 9.60 0.00 42.48 4.26
3204 4825 0.742281 CTGTAGCGCCACATTGCTCT 60.742 55.000 9.60 0.00 42.48 4.09
3205 4826 0.321564 TGTAGCGCCACATTGCTCTT 60.322 50.000 4.01 0.00 42.48 2.85
3206 4827 0.097674 GTAGCGCCACATTGCTCTTG 59.902 55.000 2.29 0.00 42.48 3.02
3242 4863 2.179427 GCCATGGCTTAAAAAGTCCCT 58.821 47.619 29.98 0.00 38.26 4.20
3252 4873 7.052248 GGCTTAAAAAGTCCCTATAGCTGTTA 58.948 38.462 0.00 0.00 0.00 2.41
3309 4934 5.358725 TCCCTCAAGTTTCCAAAAAGTACAC 59.641 40.000 0.00 0.00 0.00 2.90
3364 4989 3.028130 GGTCCCTCAAGTTTCAAAACCA 58.972 45.455 2.08 0.00 39.71 3.67
3375 5000 6.844097 AGTTTCAAAACCAGGTAAGTTTGA 57.156 33.333 12.25 12.25 39.71 2.69
3401 5026 6.014012 CCTAAACCAGATTTTGACCCCTTTA 58.986 40.000 0.00 0.00 0.00 1.85
3406 5031 3.824443 CAGATTTTGACCCCTTTAACCGT 59.176 43.478 0.00 0.00 0.00 4.83
3512 5151 2.047274 ATGTGCAAGGTCCGACCG 60.047 61.111 12.04 0.00 44.90 4.79
3981 5822 5.487488 AGACTTGAGGGACCAAATGTATACA 59.513 40.000 8.27 8.27 0.00 2.29
4186 6028 5.601729 ACTCCAGATGAAGATGCAAGAGATA 59.398 40.000 0.00 0.00 0.00 1.98
4402 6244 2.665052 GACGTTACAGGACTTTAAGCGG 59.335 50.000 0.00 0.00 0.00 5.52
4438 6280 1.488393 AGGAGGAGAAAGCTATGTGCC 59.512 52.381 0.00 0.00 44.23 5.01
4443 6285 2.086869 GAGAAAGCTATGTGCCAAGCA 58.913 47.619 0.00 0.00 44.23 3.91
4465 6307 7.749666 AGCATAGTTTTGATATGGACAGGTAT 58.250 34.615 0.00 0.00 32.35 2.73
4468 6310 9.784531 CATAGTTTTGATATGGACAGGTATCTT 57.215 33.333 0.00 0.00 0.00 2.40
4471 6313 9.838339 AGTTTTGATATGGACAGGTATCTTAAG 57.162 33.333 0.00 0.00 0.00 1.85
4479 6321 5.112686 GGACAGGTATCTTAAGTTGCAGAG 58.887 45.833 1.63 0.00 0.00 3.35
4486 6328 4.258702 TCTTAAGTTGCAGAGACACTCC 57.741 45.455 1.63 0.00 0.00 3.85
4491 6333 1.483595 TTGCAGAGACACTCCAGGGG 61.484 60.000 0.00 0.00 0.00 4.79
4523 6371 7.405292 TGAAGGTGATTATTGATCTCAAGGTT 58.595 34.615 0.00 0.00 39.47 3.50
4536 6384 6.543465 TGATCTCAAGGTTGTAAGCATTATGG 59.457 38.462 0.00 0.00 30.46 2.74
4540 6388 5.777732 TCAAGGTTGTAAGCATTATGGGTTT 59.222 36.000 0.00 0.00 30.46 3.27
4544 6392 7.836842 AGGTTGTAAGCATTATGGGTTTTAAG 58.163 34.615 0.00 0.00 30.46 1.85
4549 6397 8.519526 TGTAAGCATTATGGGTTTTAAGTTCTG 58.480 33.333 0.00 0.00 30.46 3.02
4551 6399 7.158099 AGCATTATGGGTTTTAAGTTCTGAC 57.842 36.000 0.00 0.00 0.00 3.51
4597 6446 1.765314 ACCTCATGCTGATAGTGTCCC 59.235 52.381 0.00 0.00 0.00 4.46
4603 6452 3.619900 TGCTGATAGTGTCCCCTCTAT 57.380 47.619 0.00 0.00 31.69 1.98
4629 6478 0.686789 GAATGGCTGCCTTTGGGTTT 59.313 50.000 22.75 0.00 34.45 3.27
4832 6688 6.477253 TGTAAATGTACAAACCCAGCATCTA 58.523 36.000 0.00 0.00 37.29 1.98
4834 6690 7.613801 TGTAAATGTACAAACCCAGCATCTAAT 59.386 33.333 0.00 0.00 37.29 1.73
4846 6704 4.639310 CCAGCATCTAATTTCAAGTCTGCT 59.361 41.667 0.00 0.00 35.74 4.24
5032 6900 4.360405 GGCCGGGCAAGAGGGAAA 62.360 66.667 25.33 0.00 0.00 3.13
5176 7113 4.652421 TCATTAGGCCCATTACGTACTCTT 59.348 41.667 0.00 0.00 0.00 2.85
5187 7124 6.127925 CCATTACGTACTCTTACACTACACCA 60.128 42.308 0.00 0.00 0.00 4.17
5190 7127 4.763793 ACGTACTCTTACACTACACCACAT 59.236 41.667 0.00 0.00 0.00 3.21
5192 7129 4.803098 ACTCTTACACTACACCACATCC 57.197 45.455 0.00 0.00 0.00 3.51
5208 7145 0.322816 ATCCGGACATGCAGCTTGTT 60.323 50.000 6.12 0.00 0.00 2.83
5212 7149 1.818642 GGACATGCAGCTTGTTCTCT 58.181 50.000 14.75 0.00 0.00 3.10
5215 7152 3.368843 GGACATGCAGCTTGTTCTCTAGA 60.369 47.826 14.75 0.00 0.00 2.43
5225 7162 4.367450 CTTGTTCTCTAGATGCAGCCTAC 58.633 47.826 0.00 0.00 0.00 3.18
5278 7215 9.192642 ACACAAACCTAACACCTAAAAATAAGT 57.807 29.630 0.00 0.00 0.00 2.24
5336 7273 4.501071 TGAAATGGACTAGGACGCTTTAC 58.499 43.478 0.00 0.00 0.00 2.01
5422 7360 0.549902 ATCCCATGGACACCACCTGA 60.550 55.000 15.22 0.00 35.80 3.86
5446 7662 5.503927 ACAAAAGGAGTGCATGAGTATGAT 58.496 37.500 0.00 0.00 36.36 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 3.426117 AATCCGCTCCTACGCCACG 62.426 63.158 0.00 0.00 0.00 4.94
73 74 1.893919 AAGCTCTCTCTTGTCCCGGC 61.894 60.000 0.00 0.00 0.00 6.13
77 78 1.625818 TGGGAAAGCTCTCTCTTGTCC 59.374 52.381 0.00 0.00 0.00 4.02
78 79 2.564947 TCTGGGAAAGCTCTCTCTTGTC 59.435 50.000 0.00 0.00 0.00 3.18
83 84 0.901124 TGCTCTGGGAAAGCTCTCTC 59.099 55.000 0.00 0.00 40.50 3.20
105 106 1.357991 GCTTTCTGGAGCGAGCAGAC 61.358 60.000 0.00 0.00 35.29 3.51
147 148 2.028190 ACTATAGCAGCGCAGGCG 59.972 61.111 11.47 9.68 46.35 5.52
153 154 1.007271 CCGGTCCACTATAGCAGCG 60.007 63.158 0.00 5.69 0.00 5.18
161 162 0.038599 TGTACTGCTCCGGTCCACTA 59.961 55.000 0.00 0.00 0.00 2.74
169 170 0.319040 CCATCCGATGTACTGCTCCG 60.319 60.000 7.60 0.00 0.00 4.63
174 175 1.202651 GGAACCCCATCCGATGTACTG 60.203 57.143 7.60 0.00 0.00 2.74
202 203 2.280592 GGCCGTTTCCACTCACGT 60.281 61.111 0.00 0.00 34.47 4.49
203 204 3.411351 CGGCCGTTTCCACTCACG 61.411 66.667 19.50 0.00 36.12 4.35
217 218 4.864334 CAGGTCCTGGGCATCGGC 62.864 72.222 11.46 0.00 40.13 5.54
261 262 1.209504 TGTGAGGGTCCGATGAAATCC 59.790 52.381 0.00 0.00 41.39 3.01
263 264 2.571653 TCTTGTGAGGGTCCGATGAAAT 59.428 45.455 0.00 0.00 0.00 2.17
265 266 1.639722 TCTTGTGAGGGTCCGATGAA 58.360 50.000 0.00 0.00 0.00 2.57
266 267 1.550524 CTTCTTGTGAGGGTCCGATGA 59.449 52.381 0.00 0.00 0.00 2.92
267 268 2.009042 GCTTCTTGTGAGGGTCCGATG 61.009 57.143 0.00 0.00 0.00 3.84
268 269 0.250513 GCTTCTTGTGAGGGTCCGAT 59.749 55.000 0.00 0.00 0.00 4.18
269 270 0.832135 AGCTTCTTGTGAGGGTCCGA 60.832 55.000 0.00 0.00 0.00 4.55
270 271 0.895530 TAGCTTCTTGTGAGGGTCCG 59.104 55.000 0.00 0.00 32.34 4.79
271 272 2.167487 CTCTAGCTTCTTGTGAGGGTCC 59.833 54.545 0.00 0.00 32.34 4.46
273 274 1.552792 GCTCTAGCTTCTTGTGAGGGT 59.447 52.381 0.00 0.00 38.21 4.34
274 275 2.307934 GCTCTAGCTTCTTGTGAGGG 57.692 55.000 0.00 0.00 38.21 4.30
300 301 1.065926 TCTCGCCTTGACAATGAGCAT 60.066 47.619 7.14 0.00 0.00 3.79
301 302 0.321346 TCTCGCCTTGACAATGAGCA 59.679 50.000 7.14 0.00 0.00 4.26
302 303 0.723981 GTCTCGCCTTGACAATGAGC 59.276 55.000 7.14 2.38 34.80 4.26
303 304 1.363744 GGTCTCGCCTTGACAATGAG 58.636 55.000 6.09 6.09 36.26 2.90
304 305 0.389817 CGGTCTCGCCTTGACAATGA 60.390 55.000 0.00 0.00 36.26 2.57
305 306 0.670546 ACGGTCTCGCCTTGACAATG 60.671 55.000 0.00 0.00 40.63 2.82
307 308 1.300620 CACGGTCTCGCCTTGACAA 60.301 57.895 0.00 0.00 38.67 3.18
308 309 2.338620 CACGGTCTCGCCTTGACA 59.661 61.111 0.00 0.00 38.67 3.58
309 310 2.432628 CCACGGTCTCGCCTTGAC 60.433 66.667 0.00 0.00 38.67 3.18
310 311 4.373116 GCCACGGTCTCGCCTTGA 62.373 66.667 0.00 0.00 38.67 3.02
326 327 4.884257 CATGCCTTGCCATGCCGC 62.884 66.667 0.00 0.00 36.52 6.53
335 336 0.452184 CAGCTCTCTTGCATGCCTTG 59.548 55.000 16.68 5.26 34.99 3.61
336 337 0.327259 TCAGCTCTCTTGCATGCCTT 59.673 50.000 16.68 0.00 34.99 4.35
337 338 0.327259 TTCAGCTCTCTTGCATGCCT 59.673 50.000 16.68 0.00 34.99 4.75
338 339 1.065701 CATTCAGCTCTCTTGCATGCC 59.934 52.381 16.68 0.00 34.99 4.40
339 340 1.065701 CCATTCAGCTCTCTTGCATGC 59.934 52.381 11.82 11.82 34.99 4.06
340 341 2.355132 GTCCATTCAGCTCTCTTGCATG 59.645 50.000 0.00 0.00 34.99 4.06
341 342 2.641305 GTCCATTCAGCTCTCTTGCAT 58.359 47.619 0.00 0.00 34.99 3.96
342 343 1.673923 CGTCCATTCAGCTCTCTTGCA 60.674 52.381 0.00 0.00 34.99 4.08
343 344 1.005340 CGTCCATTCAGCTCTCTTGC 58.995 55.000 0.00 0.00 0.00 4.01
344 345 1.005340 GCGTCCATTCAGCTCTCTTG 58.995 55.000 0.00 0.00 0.00 3.02
345 346 0.901124 AGCGTCCATTCAGCTCTCTT 59.099 50.000 0.00 0.00 36.33 2.85
346 347 1.769026 TAGCGTCCATTCAGCTCTCT 58.231 50.000 0.00 0.00 41.88 3.10
347 348 2.468831 CTTAGCGTCCATTCAGCTCTC 58.531 52.381 0.00 0.00 41.88 3.20
348 349 1.472376 GCTTAGCGTCCATTCAGCTCT 60.472 52.381 0.00 0.00 41.88 4.09
349 350 0.933796 GCTTAGCGTCCATTCAGCTC 59.066 55.000 0.00 0.00 41.88 4.09
350 351 0.250234 TGCTTAGCGTCCATTCAGCT 59.750 50.000 0.00 0.00 44.24 4.24
351 352 1.303309 ATGCTTAGCGTCCATTCAGC 58.697 50.000 0.00 0.00 0.00 4.26
352 353 2.679837 ACAATGCTTAGCGTCCATTCAG 59.320 45.455 0.00 0.00 0.00 3.02
353 354 2.419673 CACAATGCTTAGCGTCCATTCA 59.580 45.455 0.00 0.00 0.00 2.57
354 355 2.677836 TCACAATGCTTAGCGTCCATTC 59.322 45.455 0.00 0.00 0.00 2.67
355 356 2.420022 GTCACAATGCTTAGCGTCCATT 59.580 45.455 0.00 0.00 0.00 3.16
356 357 2.009774 GTCACAATGCTTAGCGTCCAT 58.990 47.619 0.00 0.00 0.00 3.41
357 358 1.270571 TGTCACAATGCTTAGCGTCCA 60.271 47.619 0.00 0.00 0.00 4.02
358 359 1.128692 GTGTCACAATGCTTAGCGTCC 59.871 52.381 0.00 0.00 0.00 4.79
359 360 1.128692 GGTGTCACAATGCTTAGCGTC 59.871 52.381 5.12 0.00 0.00 5.19
360 361 1.156736 GGTGTCACAATGCTTAGCGT 58.843 50.000 5.12 0.00 0.00 5.07
361 362 0.447801 GGGTGTCACAATGCTTAGCG 59.552 55.000 5.12 0.00 0.00 4.26
362 363 1.200020 GTGGGTGTCACAATGCTTAGC 59.800 52.381 5.12 0.00 45.39 3.09
363 364 1.464608 CGTGGGTGTCACAATGCTTAG 59.535 52.381 5.12 0.00 46.36 2.18
364 365 1.518325 CGTGGGTGTCACAATGCTTA 58.482 50.000 5.12 0.00 46.36 3.09
365 366 1.795170 GCGTGGGTGTCACAATGCTT 61.795 55.000 5.12 0.00 46.36 3.91
366 367 2.260869 GCGTGGGTGTCACAATGCT 61.261 57.895 5.12 0.00 46.36 3.79
367 368 2.255252 GCGTGGGTGTCACAATGC 59.745 61.111 5.12 5.88 46.36 3.56
368 369 2.555782 CGCGTGGGTGTCACAATG 59.444 61.111 5.12 0.00 46.36 2.82
369 370 3.353836 GCGCGTGGGTGTCACAAT 61.354 61.111 8.43 0.00 46.36 2.71
386 387 0.251742 TTTGGAGAATGGCCACTGGG 60.252 55.000 8.16 0.00 34.56 4.45
387 388 0.890683 GTTTGGAGAATGGCCACTGG 59.109 55.000 8.16 0.00 34.56 4.00
388 389 1.542915 CTGTTTGGAGAATGGCCACTG 59.457 52.381 8.16 0.00 34.56 3.66
389 390 1.915141 CTGTTTGGAGAATGGCCACT 58.085 50.000 8.16 0.00 34.56 4.00
390 391 0.244721 GCTGTTTGGAGAATGGCCAC 59.755 55.000 8.16 0.00 34.56 5.01
391 392 1.243342 CGCTGTTTGGAGAATGGCCA 61.243 55.000 8.56 8.56 0.00 5.36
392 393 1.508088 CGCTGTTTGGAGAATGGCC 59.492 57.895 0.00 0.00 0.00 5.36
393 394 1.508088 CCGCTGTTTGGAGAATGGC 59.492 57.895 0.00 0.00 0.00 4.40
394 395 0.322456 TCCCGCTGTTTGGAGAATGG 60.322 55.000 0.00 0.00 0.00 3.16
395 396 3.248043 TCCCGCTGTTTGGAGAATG 57.752 52.632 0.00 0.00 0.00 2.67
400 401 2.281484 GTGCTCCCGCTGTTTGGA 60.281 61.111 0.00 0.00 36.97 3.53
401 402 3.365265 GGTGCTCCCGCTGTTTGG 61.365 66.667 0.00 0.00 36.97 3.28
402 403 2.281761 AGGTGCTCCCGCTGTTTG 60.282 61.111 0.00 0.00 38.74 2.93
403 404 2.032681 GAGGTGCTCCCGCTGTTT 59.967 61.111 0.00 0.00 38.74 2.83
404 405 2.738213 CTTGAGGTGCTCCCGCTGTT 62.738 60.000 0.00 0.00 38.74 3.16
405 406 3.241530 TTGAGGTGCTCCCGCTGT 61.242 61.111 0.00 0.00 38.74 4.40
406 407 2.435586 CTTGAGGTGCTCCCGCTG 60.436 66.667 0.00 0.00 38.74 5.18
407 408 3.710722 CCTTGAGGTGCTCCCGCT 61.711 66.667 0.00 0.00 38.74 5.52
408 409 4.785453 CCCTTGAGGTGCTCCCGC 62.785 72.222 0.00 0.00 38.74 6.13
409 410 3.003173 TCCCTTGAGGTGCTCCCG 61.003 66.667 0.00 0.00 38.74 5.14
410 411 1.492993 AAGTCCCTTGAGGTGCTCCC 61.493 60.000 0.00 0.00 36.75 4.30
411 412 0.322008 CAAGTCCCTTGAGGTGCTCC 60.322 60.000 0.00 0.00 43.42 4.70
412 413 0.687354 TCAAGTCCCTTGAGGTGCTC 59.313 55.000 2.65 0.00 44.27 4.26
413 414 2.854253 TCAAGTCCCTTGAGGTGCT 58.146 52.632 2.65 0.00 44.27 4.40
419 420 5.576563 TTTTCCATAGTCAAGTCCCTTGA 57.423 39.130 2.65 2.65 46.50 3.02
420 421 5.065218 CGATTTTCCATAGTCAAGTCCCTTG 59.935 44.000 0.00 0.00 42.25 3.61
421 422 5.045869 TCGATTTTCCATAGTCAAGTCCCTT 60.046 40.000 0.00 0.00 0.00 3.95
422 423 4.469945 TCGATTTTCCATAGTCAAGTCCCT 59.530 41.667 0.00 0.00 0.00 4.20
466 467 7.283625 ACTAAACTTGCCATGATAACAAACA 57.716 32.000 0.00 0.00 0.00 2.83
467 468 8.487176 CAAACTAAACTTGCCATGATAACAAAC 58.513 33.333 0.00 0.00 0.00 2.93
468 469 8.200792 ACAAACTAAACTTGCCATGATAACAAA 58.799 29.630 0.00 0.00 0.00 2.83
471 472 9.341899 CTTACAAACTAAACTTGCCATGATAAC 57.658 33.333 0.00 0.00 0.00 1.89
472 473 8.026607 GCTTACAAACTAAACTTGCCATGATAA 58.973 33.333 0.00 0.00 0.00 1.75
533 536 0.179062 TTGGCAAGCACGGCAATTTT 60.179 45.000 9.84 0.00 45.48 1.82
595 598 4.582441 TGATCATGACAAATCGAACGTG 57.418 40.909 0.00 0.00 0.00 4.49
700 704 4.851639 AAGGAGGTCATTCTACAGCAAT 57.148 40.909 0.00 0.00 0.00 3.56
850 946 0.179045 ACTCCGCAAGCATGGGATAC 60.179 55.000 7.65 0.00 41.79 2.24
852 948 1.033746 CAACTCCGCAAGCATGGGAT 61.034 55.000 7.65 0.00 41.79 3.85
908 1004 3.686016 ACTAATAGGGTGTTGTTGCAGG 58.314 45.455 0.00 0.00 0.00 4.85
1056 2503 3.192922 GTACATGCCGCCGTGACC 61.193 66.667 0.00 0.00 0.00 4.02
1058 2505 2.125713 CAGTACATGCCGCCGTGA 60.126 61.111 0.00 0.00 0.00 4.35
1130 2577 4.680237 CCGCTGGCGTGAACTCCA 62.680 66.667 13.84 0.00 37.81 3.86
1350 2800 1.278127 GTCACCTTTTCGGGATGGAGA 59.722 52.381 0.00 0.00 36.97 3.71
1456 2910 9.066892 TGAAAAGTGTAGCAAATATGAACTTCT 57.933 29.630 0.00 0.00 0.00 2.85
1457 2911 9.846248 ATGAAAAGTGTAGCAAATATGAACTTC 57.154 29.630 0.00 0.00 0.00 3.01
1476 2930 6.930722 AGTTAGGGCATGACAAAAATGAAAAG 59.069 34.615 0.00 0.00 0.00 2.27
1543 2997 7.518731 GTCAATGAGTCTAGTTTGACATCTC 57.481 40.000 16.73 0.00 44.56 2.75
1606 3111 1.374758 CTCACTTGCCGTCCCAGTC 60.375 63.158 0.00 0.00 0.00 3.51
1614 3119 2.068837 TACCGTTTACTCACTTGCCG 57.931 50.000 0.00 0.00 0.00 5.69
1679 3185 0.521735 GCACATTCCGACCCTGAAAC 59.478 55.000 0.00 0.00 0.00 2.78
1691 3197 5.971895 ATTGTGTTGAAAAGTGCACATTC 57.028 34.783 21.04 21.49 40.82 2.67
1703 3209 8.681806 TGAAAGTCTATGTTGAATTGTGTTGAA 58.318 29.630 0.00 0.00 0.00 2.69
1731 3262 6.036577 AGCATTTTTGGTCGGTCAAATATT 57.963 33.333 5.26 0.00 36.63 1.28
1732 3263 5.418840 AGAGCATTTTTGGTCGGTCAAATAT 59.581 36.000 5.26 4.12 40.82 1.28
1733 3264 4.764823 AGAGCATTTTTGGTCGGTCAAATA 59.235 37.500 5.26 2.29 40.82 1.40
1734 3265 3.573967 AGAGCATTTTTGGTCGGTCAAAT 59.426 39.130 5.26 0.00 40.82 2.32
1735 3266 2.955660 AGAGCATTTTTGGTCGGTCAAA 59.044 40.909 0.08 1.07 40.82 2.69
1736 3267 2.582052 AGAGCATTTTTGGTCGGTCAA 58.418 42.857 0.08 0.00 40.82 3.18
1737 3268 2.270352 AGAGCATTTTTGGTCGGTCA 57.730 45.000 0.08 0.00 40.82 4.02
1738 3269 2.922335 GCAAGAGCATTTTTGGTCGGTC 60.922 50.000 0.08 0.00 40.82 4.79
1739 3270 1.000274 GCAAGAGCATTTTTGGTCGGT 60.000 47.619 0.08 0.00 40.82 4.69
1740 3271 1.701704 GCAAGAGCATTTTTGGTCGG 58.298 50.000 0.08 0.00 40.82 4.79
1777 3308 7.853929 TCGTCAACTTCAACAAAAATAGCTAAC 59.146 33.333 0.00 0.00 0.00 2.34
1793 3324 3.985925 ACGGTTTACTGATCGTCAACTTC 59.014 43.478 11.66 1.07 31.83 3.01
1794 3325 3.986277 ACGGTTTACTGATCGTCAACTT 58.014 40.909 11.66 1.95 31.83 2.66
1795 3326 3.655276 ACGGTTTACTGATCGTCAACT 57.345 42.857 11.66 0.00 31.83 3.16
1802 3333 2.541556 GAGGCTGACGGTTTACTGATC 58.458 52.381 0.00 0.00 0.00 2.92
1853 3384 9.473007 CTCCATCATCTATCTACCTTTAGATCA 57.527 37.037 0.00 0.00 43.03 2.92
1913 3444 4.589908 ACCAACAGGTATGAAAGGCTAAG 58.410 43.478 0.00 0.00 32.67 2.18
2019 3609 5.935206 TCAGCTGAAAATTGTATAACGGACA 59.065 36.000 15.67 0.00 0.00 4.02
2023 3613 6.598525 TGTGTCAGCTGAAAATTGTATAACG 58.401 36.000 20.19 0.00 0.00 3.18
2070 3660 5.578005 TCTAACCAGGTCAACGATCTAAG 57.422 43.478 0.00 0.00 0.00 2.18
2077 3667 1.068474 CGCTTCTAACCAGGTCAACG 58.932 55.000 0.00 0.00 0.00 4.10
2080 3670 1.295423 GGCGCTTCTAACCAGGTCA 59.705 57.895 7.64 0.00 0.00 4.02
2110 3700 2.222213 CGCGTCATTCTCTATCTCGAGT 59.778 50.000 13.13 2.46 32.83 4.18
2128 3718 1.858458 TCAAACTCTTGTGTTCTCGCG 59.142 47.619 0.00 0.00 33.94 5.87
2136 3726 5.292765 TCTTCAGTAGCTCAAACTCTTGTG 58.707 41.667 0.00 0.00 33.94 3.33
2137 3727 5.537300 TCTTCAGTAGCTCAAACTCTTGT 57.463 39.130 0.00 0.00 33.94 3.16
2138 3728 6.851222 TTTCTTCAGTAGCTCAAACTCTTG 57.149 37.500 0.00 0.00 0.00 3.02
2204 3794 1.836802 GAAGCCAGACCAGAGGATTCT 59.163 52.381 0.00 0.00 44.64 2.40
2462 4052 0.392193 CACCTCATGTGCCTCTCCAC 60.392 60.000 0.00 0.00 38.34 4.02
2528 4118 7.047891 TGAGAAATTTACTGGTGGTGCTATAG 58.952 38.462 0.00 0.00 0.00 1.31
2543 4137 6.053005 AGGTCACAAACGACTGAGAAATTTA 58.947 36.000 0.00 0.00 36.12 1.40
2556 4150 5.065474 TGGTCTTAAAAGAAGGTCACAAACG 59.935 40.000 0.00 0.00 36.68 3.60
2618 4213 2.099263 TCGCTCGATTTCTCCGAAGATT 59.901 45.455 0.00 0.00 35.48 2.40
2809 4404 6.002082 AGGTGTAAATGGAGAACCTAACAAC 58.998 40.000 0.00 0.00 39.48 3.32
2856 4451 5.424121 AGAGAATTTGAAGTGTTTCGGTG 57.576 39.130 0.00 0.00 36.04 4.94
2860 4455 7.745620 TCCCTTAGAGAATTTGAAGTGTTTC 57.254 36.000 0.00 0.00 0.00 2.78
2935 4530 4.771590 TTTTTCACCACAGATCTGATGC 57.228 40.909 29.27 0.00 0.00 3.91
2961 4581 4.157656 TGTTACTGCAAGGTCATAAATGGC 59.842 41.667 0.00 0.00 39.30 4.40
2963 4583 9.669353 GAATATGTTACTGCAAGGTCATAAATG 57.331 33.333 0.00 0.00 39.30 2.32
2965 4585 8.800370 TGAATATGTTACTGCAAGGTCATAAA 57.200 30.769 0.00 0.00 39.30 1.40
3092 4713 3.568007 TGAAAAAGCAGGCACGATACTTT 59.432 39.130 0.00 0.00 32.15 2.66
3149 4770 1.259609 ACTCCAATGTGGCAATGTGG 58.740 50.000 5.45 5.45 37.47 4.17
3202 4823 4.041567 TGGCATAAAAGTCACTCCTCAAGA 59.958 41.667 0.00 0.00 0.00 3.02
3203 4824 4.326826 TGGCATAAAAGTCACTCCTCAAG 58.673 43.478 0.00 0.00 0.00 3.02
3204 4825 4.365514 TGGCATAAAAGTCACTCCTCAA 57.634 40.909 0.00 0.00 0.00 3.02
3205 4826 4.264253 CATGGCATAAAAGTCACTCCTCA 58.736 43.478 0.00 0.00 0.00 3.86
3206 4827 3.629398 CCATGGCATAAAAGTCACTCCTC 59.371 47.826 0.00 0.00 0.00 3.71
3364 4989 6.697641 TCTGGTTTAGGATCAAACTTACCT 57.302 37.500 8.17 0.00 38.27 3.08
3375 5000 4.294970 AGGGGTCAAAATCTGGTTTAGGAT 59.705 41.667 0.00 0.00 0.00 3.24
3427 5052 7.962964 AAAATCGAGTTTACTGTTCATCTGA 57.037 32.000 9.43 0.00 0.00 3.27
3479 5118 4.525996 TGCACATGTAAGCATATTGGACT 58.474 39.130 6.75 0.00 35.51 3.85
3512 5151 6.020678 CGAGTGTCAAAAGACCACAAAAATTC 60.021 38.462 0.00 0.00 0.00 2.17
3631 5297 0.165944 GTCACACCTTGCGCATGTAC 59.834 55.000 12.75 8.45 0.00 2.90
3853 5694 7.298122 ACAGTAAACTGACATTAAATTGCGAG 58.702 34.615 16.74 0.00 46.59 5.03
3869 5710 5.746990 ACCTGCTAGATGAACAGTAAACT 57.253 39.130 0.00 0.00 0.00 2.66
3885 5726 2.430367 GACCGGGTCAAACCTGCT 59.570 61.111 22.10 0.00 43.40 4.24
4013 5855 5.358725 TGTTTTTAGTCCCTCAAGTTTCCAC 59.641 40.000 0.00 0.00 0.00 4.02
4066 5908 4.093850 GCAATCTGCAAATGGAACAATTCC 59.906 41.667 0.34 0.34 46.06 3.01
4402 6244 0.250901 TCCTTGCCAAGAACAGCCTC 60.251 55.000 5.89 0.00 0.00 4.70
4438 6280 6.319658 ACCTGTCCATATCAAAACTATGCTTG 59.680 38.462 0.00 0.00 0.00 4.01
4465 6307 3.641436 TGGAGTGTCTCTGCAACTTAAGA 59.359 43.478 10.09 0.00 41.37 2.10
4468 6310 2.300152 CCTGGAGTGTCTCTGCAACTTA 59.700 50.000 0.00 0.00 43.54 2.24
4471 6313 0.321122 CCCTGGAGTGTCTCTGCAAC 60.321 60.000 0.00 0.00 43.54 4.17
4479 6321 1.990614 GGAGGACCCCTGGAGTGTC 60.991 68.421 0.00 0.00 31.76 3.67
4491 6333 6.183361 AGATCAATAATCACCTTCAGGAGGAC 60.183 42.308 0.00 0.00 41.53 3.85
4523 6371 8.519526 CAGAACTTAAAACCCATAATGCTTACA 58.480 33.333 0.00 0.00 0.00 2.41
4560 6408 6.763135 GCATGAGGTAATAACTGAGACATTCA 59.237 38.462 0.00 0.00 0.00 2.57
4762 6615 6.648879 TCCTTGGGTTTAGTTTTTCATGAG 57.351 37.500 0.00 0.00 0.00 2.90
4826 6682 5.808042 TCAGCAGACTTGAAATTAGATGC 57.192 39.130 0.00 0.00 32.73 3.91
4832 6688 3.076621 TCGCATCAGCAGACTTGAAATT 58.923 40.909 0.00 0.00 42.27 1.82
4834 6690 2.071540 CTCGCATCAGCAGACTTGAAA 58.928 47.619 0.00 0.00 42.27 2.69
4872 6732 0.879090 CTTACAAGAACCCCGGCAAC 59.121 55.000 0.00 0.00 0.00 4.17
5176 7113 1.820519 GTCCGGATGTGGTGTAGTGTA 59.179 52.381 7.81 0.00 0.00 2.90
5187 7124 1.028330 CAAGCTGCATGTCCGGATGT 61.028 55.000 7.81 0.00 0.00 3.06
5190 7127 0.955428 GAACAAGCTGCATGTCCGGA 60.955 55.000 11.22 0.00 0.00 5.14
5192 7129 0.445436 GAGAACAAGCTGCATGTCCG 59.555 55.000 11.22 0.00 0.00 4.79
5208 7145 1.217942 TGGGTAGGCTGCATCTAGAGA 59.782 52.381 4.64 0.00 0.00 3.10
5212 7149 1.879575 AGTTGGGTAGGCTGCATCTA 58.120 50.000 4.64 0.00 0.00 1.98
5215 7152 4.461198 GTTATAAGTTGGGTAGGCTGCAT 58.539 43.478 4.64 0.00 0.00 3.96
5225 7162 4.809426 GTCGAGTCATGGTTATAAGTTGGG 59.191 45.833 0.00 0.00 0.00 4.12
5278 7215 7.681939 ATAAAACAAGCCGAGATGTAAAAGA 57.318 32.000 0.00 0.00 0.00 2.52
5336 7273 3.964688 ACTTTTGGTTAAGGGGTCCAAAG 59.035 43.478 7.15 5.46 33.05 2.77
5422 7360 5.316167 TCATACTCATGCACTCCTTTTGTT 58.684 37.500 0.00 0.00 31.73 2.83
5446 7662 1.691195 TTGCGACCACTTCCAGGTGA 61.691 55.000 0.00 0.00 40.09 4.02


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

AutoCloner maintained by Alex Coulton.