Multiple sequence alignment - TraesCS4D01G097400

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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 TraesCS4D01G097400 chr4D 100.000 3570 0 0 1 3570 74161169 74157600 0.000000e+00 6593.0
1 TraesCS4D01G097400 chr4B 96.851 2350 61 8 428 2769 106493469 106491125 0.000000e+00 3917.0
2 TraesCS4D01G097400 chr4B 95.402 435 17 2 3139 3570 106489504 106489070 0.000000e+00 689.0
3 TraesCS4D01G097400 chr4B 90.691 376 17 4 2770 3129 106491053 106490680 5.360000e-133 484.0
4 TraesCS4D01G097400 chr4B 93.151 73 5 0 4 76 106493843 106493771 1.360000e-19 108.0
5 TraesCS4D01G097400 chr4B 100.000 30 0 0 115 144 106493752 106493723 4.980000e-04 56.5
6 TraesCS4D01G097400 chr4A 94.396 2302 78 18 466 2747 513803878 513806148 0.000000e+00 3489.0
7 TraesCS4D01G097400 chr4A 100.000 33 0 0 443 475 513803437 513803469 1.070000e-05 62.1
8 TraesCS4D01G097400 chr5A 87.500 640 78 2 1932 2570 230454341 230454979 0.000000e+00 737.0
9 TraesCS4D01G097400 chr5A 83.670 643 80 15 1044 1681 230453273 230453895 1.850000e-162 582.0
10 TraesCS4D01G097400 chr5A 81.790 637 116 0 1932 2568 225243112 225243748 5.250000e-148 534.0
11 TraesCS4D01G097400 chr5D 87.344 640 79 2 1932 2570 192538786 192539424 0.000000e+00 732.0
12 TraesCS4D01G097400 chr5D 83.956 642 80 17 1044 1681 192537826 192538448 8.530000e-166 593.0
13 TraesCS4D01G097400 chr5D 80.223 627 120 3 1944 2568 201851163 201850539 5.400000e-128 468.0
14 TraesCS4D01G097400 chr5D 92.715 151 11 0 275 425 354839364 354839214 6.000000e-53 219.0
15 TraesCS4D01G097400 chr5B 87.363 641 77 4 1932 2570 197193188 197192550 0.000000e+00 732.0
16 TraesCS4D01G097400 chr5B 80.691 637 114 4 1932 2568 212635546 212634919 1.490000e-133 486.0
17 TraesCS4D01G097400 chr5B 91.772 158 13 0 275 432 143713612 143713455 1.670000e-53 220.0
18 TraesCS4D01G097400 chr5B 91.946 149 12 0 278 426 618269859 618270007 3.610000e-50 209.0
19 TraesCS4D01G097400 chr2B 81.487 632 100 11 1932 2547 523234151 523234781 1.480000e-138 503.0
20 TraesCS4D01G097400 chr2B 91.026 156 14 0 274 429 627873720 627873565 1.000000e-50 211.0
21 TraesCS4D01G097400 chr2B 85.246 122 16 2 1563 1683 523233618 523233738 1.350000e-24 124.0
22 TraesCS4D01G097400 chr2D 81.230 634 98 12 1932 2547 445060739 445061369 3.200000e-135 492.0
23 TraesCS4D01G097400 chr2D 87.097 124 13 2 2 123 601244405 601244283 1.730000e-28 137.0
24 TraesCS4D01G097400 chr2D 85.593 118 15 2 1563 1679 445060211 445060327 4.840000e-24 122.0
25 TraesCS4D01G097400 chr2D 88.158 76 9 0 1606 1681 594577612 594577537 1.360000e-14 91.6
26 TraesCS4D01G097400 chr3A 81.387 548 85 7 1127 1673 651962412 651962943 7.080000e-117 431.0
27 TraesCS4D01G097400 chr3A 81.307 551 86 7 1124 1673 651996513 651997047 7.080000e-117 431.0
28 TraesCS4D01G097400 chr3B 81.022 548 87 7 1127 1673 680732611 680732080 1.530000e-113 420.0
29 TraesCS4D01G097400 chr3B 80.839 548 88 7 1127 1673 680477780 680477249 7.130000e-112 414.0
30 TraesCS4D01G097400 chr3B 89.286 56 6 0 2770 2825 507009039 507009094 1.780000e-08 71.3
31 TraesCS4D01G097400 chr3D 80.839 548 88 11 1127 1673 516671486 516672017 7.130000e-112 414.0
32 TraesCS4D01G097400 chr1D 84.887 311 44 2 1519 1829 360467780 360468087 9.620000e-81 311.0
33 TraesCS4D01G097400 chr1B 84.244 311 46 2 1519 1829 482697511 482697818 2.080000e-77 300.0
34 TraesCS4D01G097400 chr1B 91.613 155 13 0 275 429 683992175 683992021 7.760000e-52 215.0
35 TraesCS4D01G097400 chr1A 83.601 311 48 1 1519 1829 460281531 460281838 4.510000e-74 289.0
36 TraesCS4D01G097400 chr2A 92.715 151 11 0 275 425 729555245 729555095 6.000000e-53 219.0
37 TraesCS4D01G097400 chr2A 91.667 156 13 0 274 429 7915769 7915614 2.160000e-52 217.0
38 TraesCS4D01G097400 chr2A 85.593 118 15 2 1563 1679 587405286 587405402 4.840000e-24 122.0
39 TraesCS4D01G097400 chr7B 91.558 154 13 0 276 429 746714535 746714382 2.790000e-51 213.0
40 TraesCS4D01G097400 chr6A 91.026 156 13 1 275 429 515289073 515288918 3.610000e-50 209.0
41 TraesCS4D01G097400 chr7D 74.914 291 57 11 1553 1835 474006415 474006133 6.260000e-23 119.0


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 TraesCS4D01G097400 chr4D 74157600 74161169 3569 True 6593.00 6593 100.0000 1 3570 1 chr4D.!!$R1 3569
1 TraesCS4D01G097400 chr4B 106489070 106493843 4773 True 1050.90 3917 95.2190 4 3570 5 chr4B.!!$R1 3566
2 TraesCS4D01G097400 chr4A 513803437 513806148 2711 False 1775.55 3489 97.1980 443 2747 2 chr4A.!!$F1 2304
3 TraesCS4D01G097400 chr5A 230453273 230454979 1706 False 659.50 737 85.5850 1044 2570 2 chr5A.!!$F2 1526
4 TraesCS4D01G097400 chr5A 225243112 225243748 636 False 534.00 534 81.7900 1932 2568 1 chr5A.!!$F1 636
5 TraesCS4D01G097400 chr5D 192537826 192539424 1598 False 662.50 732 85.6500 1044 2570 2 chr5D.!!$F1 1526
6 TraesCS4D01G097400 chr5D 201850539 201851163 624 True 468.00 468 80.2230 1944 2568 1 chr5D.!!$R1 624
7 TraesCS4D01G097400 chr5B 197192550 197193188 638 True 732.00 732 87.3630 1932 2570 1 chr5B.!!$R2 638
8 TraesCS4D01G097400 chr5B 212634919 212635546 627 True 486.00 486 80.6910 1932 2568 1 chr5B.!!$R3 636
9 TraesCS4D01G097400 chr2B 523233618 523234781 1163 False 313.50 503 83.3665 1563 2547 2 chr2B.!!$F1 984
10 TraesCS4D01G097400 chr2D 445060211 445061369 1158 False 307.00 492 83.4115 1563 2547 2 chr2D.!!$F1 984
11 TraesCS4D01G097400 chr3A 651962412 651962943 531 False 431.00 431 81.3870 1127 1673 1 chr3A.!!$F1 546
12 TraesCS4D01G097400 chr3A 651996513 651997047 534 False 431.00 431 81.3070 1124 1673 1 chr3A.!!$F2 549
13 TraesCS4D01G097400 chr3B 680732080 680732611 531 True 420.00 420 81.0220 1127 1673 1 chr3B.!!$R2 546
14 TraesCS4D01G097400 chr3B 680477249 680477780 531 True 414.00 414 80.8390 1127 1673 1 chr3B.!!$R1 546
15 TraesCS4D01G097400 chr3D 516671486 516672017 531 False 414.00 414 80.8390 1127 1673 1 chr3D.!!$F1 546

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
82 83 0.039180 TCACCCTTCACGCCTAGAGA 59.961 55.0 0.0 0.0 0.00 3.10 F
84 85 0.039911 ACCCTTCACGCCTAGAGAGT 59.960 55.0 0.0 0.0 0.00 3.24 F
353 498 0.041663 ATAAACGCACACACGCACAC 60.042 50.0 0.0 0.0 36.19 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2852 0.818040 GCCTTCACCGTGTCCTGTTT 60.818 55.000 0.00 0.00 0.00 2.83 R
2077 3001 4.699522 AAGCCGAACCCCGTGAGC 62.700 66.667 0.00 0.00 36.31 4.26 R
2751 3690 1.003972 AGTAACAACGACGACGACGAA 60.004 47.619 25.15 3.56 42.66 3.85 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
42 43 1.950484 GCACAACCCCGATCACATCTT 60.950 52.381 0.00 0.00 0.00 2.40
58 59 1.003839 CTTAGGCTGGGTCAACGCA 60.004 57.895 0.00 0.00 37.27 5.24
64 65 1.569479 GCTGGGTCAACGCACTCTTC 61.569 60.000 0.00 0.00 34.94 2.87
68 69 1.228657 GGTCAACGCACTCTTCACCC 61.229 60.000 0.00 0.00 0.00 4.61
76 77 0.951040 CACTCTTCACCCTTCACGCC 60.951 60.000 0.00 0.00 0.00 5.68
78 79 0.895530 CTCTTCACCCTTCACGCCTA 59.104 55.000 0.00 0.00 0.00 3.93
79 80 0.895530 TCTTCACCCTTCACGCCTAG 59.104 55.000 0.00 0.00 0.00 3.02
80 81 0.895530 CTTCACCCTTCACGCCTAGA 59.104 55.000 0.00 0.00 0.00 2.43
81 82 0.895530 TTCACCCTTCACGCCTAGAG 59.104 55.000 0.00 0.00 0.00 2.43
82 83 0.039180 TCACCCTTCACGCCTAGAGA 59.961 55.000 0.00 0.00 0.00 3.10
83 84 0.457851 CACCCTTCACGCCTAGAGAG 59.542 60.000 0.00 0.00 0.00 3.20
84 85 0.039911 ACCCTTCACGCCTAGAGAGT 59.960 55.000 0.00 0.00 0.00 3.24
85 86 0.741915 CCCTTCACGCCTAGAGAGTC 59.258 60.000 0.00 0.00 0.00 3.36
86 87 0.741915 CCTTCACGCCTAGAGAGTCC 59.258 60.000 0.00 0.00 0.00 3.85
87 88 0.378962 CTTCACGCCTAGAGAGTCCG 59.621 60.000 0.00 0.00 0.00 4.79
88 89 1.654954 TTCACGCCTAGAGAGTCCGC 61.655 60.000 0.00 0.00 0.00 5.54
89 90 2.045242 ACGCCTAGAGAGTCCGCA 60.045 61.111 0.00 0.00 0.00 5.69
90 91 1.677966 ACGCCTAGAGAGTCCGCAA 60.678 57.895 0.00 0.00 0.00 4.85
91 92 1.248785 ACGCCTAGAGAGTCCGCAAA 61.249 55.000 0.00 0.00 0.00 3.68
92 93 0.103208 CGCCTAGAGAGTCCGCAAAT 59.897 55.000 0.00 0.00 0.00 2.32
93 94 1.576356 GCCTAGAGAGTCCGCAAATG 58.424 55.000 0.00 0.00 0.00 2.32
94 95 1.137086 GCCTAGAGAGTCCGCAAATGA 59.863 52.381 0.00 0.00 0.00 2.57
95 96 2.801342 GCCTAGAGAGTCCGCAAATGAG 60.801 54.545 0.00 0.00 0.00 2.90
96 97 2.468831 CTAGAGAGTCCGCAAATGAGC 58.531 52.381 0.00 0.00 0.00 4.26
97 98 0.610174 AGAGAGTCCGCAAATGAGCA 59.390 50.000 0.00 0.00 0.00 4.26
98 99 1.005340 GAGAGTCCGCAAATGAGCAG 58.995 55.000 0.00 0.00 0.00 4.24
99 100 1.023513 AGAGTCCGCAAATGAGCAGC 61.024 55.000 0.00 0.00 0.00 5.25
104 105 1.136147 CGCAAATGAGCAGCAGGAC 59.864 57.895 0.00 0.00 0.00 3.85
109 110 1.580845 AATGAGCAGCAGGACGCAAC 61.581 55.000 0.00 0.00 46.13 4.17
113 114 3.114616 CAGCAGGACGCAACCGAG 61.115 66.667 0.00 0.00 46.13 4.63
158 302 5.630121 AGACATTACTTGACAACCATCCAA 58.370 37.500 0.00 0.00 0.00 3.53
172 316 3.074538 ACCATCCAAAGCTCTAAACCACT 59.925 43.478 0.00 0.00 0.00 4.00
186 330 4.335400 AAACCACTGCCACTAAAATTGG 57.665 40.909 0.00 0.00 37.17 3.16
213 357 7.711339 TGGGTTAATCTTATTTTGTGCGTTTTT 59.289 29.630 0.00 0.00 0.00 1.94
234 378 6.727824 TTTTTGGAATGAAAGAAACGCAAA 57.272 29.167 0.00 0.00 0.00 3.68
261 406 2.511373 CATGTTGGCCGCTAGCGA 60.511 61.111 37.39 17.58 45.17 4.93
303 448 6.968131 TTGAACATCAGTACAGACATAAGC 57.032 37.500 0.00 0.00 0.00 3.09
304 449 5.102313 TGAACATCAGTACAGACATAAGCG 58.898 41.667 0.00 0.00 0.00 4.68
305 450 3.448686 ACATCAGTACAGACATAAGCGC 58.551 45.455 0.00 0.00 0.00 5.92
306 451 3.131223 ACATCAGTACAGACATAAGCGCT 59.869 43.478 2.64 2.64 0.00 5.92
307 452 3.422417 TCAGTACAGACATAAGCGCTC 57.578 47.619 12.06 0.00 0.00 5.03
308 453 2.752903 TCAGTACAGACATAAGCGCTCA 59.247 45.455 12.06 0.00 0.00 4.26
309 454 3.111838 CAGTACAGACATAAGCGCTCAG 58.888 50.000 12.06 6.23 0.00 3.35
310 455 3.017442 AGTACAGACATAAGCGCTCAGA 58.983 45.455 12.06 0.00 0.00 3.27
311 456 2.285827 ACAGACATAAGCGCTCAGAC 57.714 50.000 12.06 4.11 0.00 3.51
312 457 1.546029 ACAGACATAAGCGCTCAGACA 59.454 47.619 12.06 0.00 0.00 3.41
313 458 2.167281 ACAGACATAAGCGCTCAGACAT 59.833 45.455 12.06 0.00 0.00 3.06
314 459 3.381590 ACAGACATAAGCGCTCAGACATA 59.618 43.478 12.06 0.00 0.00 2.29
315 460 3.733224 CAGACATAAGCGCTCAGACATAC 59.267 47.826 12.06 0.00 0.00 2.39
316 461 2.721603 GACATAAGCGCTCAGACATACG 59.278 50.000 12.06 0.00 0.00 3.06
320 465 2.579518 CGCTCAGACATACGCGCA 60.580 61.111 5.73 0.00 39.11 6.09
321 466 1.946156 CGCTCAGACATACGCGCAT 60.946 57.895 5.73 0.00 39.11 4.73
322 467 0.660300 CGCTCAGACATACGCGCATA 60.660 55.000 5.73 0.00 39.11 3.14
323 468 0.778815 GCTCAGACATACGCGCATAC 59.221 55.000 5.73 0.00 0.00 2.39
324 469 1.864029 GCTCAGACATACGCGCATACA 60.864 52.381 5.73 0.00 0.00 2.29
325 470 1.781429 CTCAGACATACGCGCATACAC 59.219 52.381 5.73 0.00 0.00 2.90
326 471 1.404035 TCAGACATACGCGCATACACT 59.596 47.619 5.73 0.00 0.00 3.55
327 472 1.781429 CAGACATACGCGCATACACTC 59.219 52.381 5.73 0.00 0.00 3.51
328 473 1.404035 AGACATACGCGCATACACTCA 59.596 47.619 5.73 0.00 0.00 3.41
329 474 1.517276 GACATACGCGCATACACTCAC 59.483 52.381 5.73 0.00 0.00 3.51
330 475 0.852777 CATACGCGCATACACTCACC 59.147 55.000 5.73 0.00 0.00 4.02
331 476 0.249322 ATACGCGCATACACTCACCC 60.249 55.000 5.73 0.00 0.00 4.61
332 477 2.287457 TACGCGCATACACTCACCCC 62.287 60.000 5.73 0.00 0.00 4.95
333 478 2.584608 GCGCATACACTCACCCCT 59.415 61.111 0.30 0.00 0.00 4.79
334 479 1.820581 GCGCATACACTCACCCCTA 59.179 57.895 0.30 0.00 0.00 3.53
335 480 0.393077 GCGCATACACTCACCCCTAT 59.607 55.000 0.30 0.00 0.00 2.57
336 481 1.616865 GCGCATACACTCACCCCTATA 59.383 52.381 0.30 0.00 0.00 1.31
337 482 2.036733 GCGCATACACTCACCCCTATAA 59.963 50.000 0.30 0.00 0.00 0.98
338 483 3.493699 GCGCATACACTCACCCCTATAAA 60.494 47.826 0.30 0.00 0.00 1.40
339 484 4.056050 CGCATACACTCACCCCTATAAAC 58.944 47.826 0.00 0.00 0.00 2.01
340 485 4.056050 GCATACACTCACCCCTATAAACG 58.944 47.826 0.00 0.00 0.00 3.60
341 486 2.685850 ACACTCACCCCTATAAACGC 57.314 50.000 0.00 0.00 0.00 4.84
342 487 1.903860 ACACTCACCCCTATAAACGCA 59.096 47.619 0.00 0.00 0.00 5.24
343 488 2.277084 CACTCACCCCTATAAACGCAC 58.723 52.381 0.00 0.00 0.00 5.34
344 489 1.903860 ACTCACCCCTATAAACGCACA 59.096 47.619 0.00 0.00 0.00 4.57
345 490 2.277084 CTCACCCCTATAAACGCACAC 58.723 52.381 0.00 0.00 0.00 3.82
346 491 1.624312 TCACCCCTATAAACGCACACA 59.376 47.619 0.00 0.00 0.00 3.72
347 492 1.735571 CACCCCTATAAACGCACACAC 59.264 52.381 0.00 0.00 0.00 3.82
348 493 1.003851 CCCCTATAAACGCACACACG 58.996 55.000 0.00 0.00 39.50 4.49
349 494 0.372334 CCCTATAAACGCACACACGC 59.628 55.000 0.00 0.00 36.19 5.34
350 495 1.072391 CCTATAAACGCACACACGCA 58.928 50.000 0.00 0.00 36.19 5.24
351 496 1.201877 CCTATAAACGCACACACGCAC 60.202 52.381 0.00 0.00 36.19 5.34
352 497 1.457683 CTATAAACGCACACACGCACA 59.542 47.619 0.00 0.00 36.19 4.57
353 498 0.041663 ATAAACGCACACACGCACAC 60.042 50.000 0.00 0.00 36.19 3.82
354 499 2.037913 TAAACGCACACACGCACACC 62.038 55.000 0.00 0.00 36.19 4.16
357 502 3.952675 GCACACACGCACACCCTG 61.953 66.667 0.00 0.00 0.00 4.45
358 503 3.952675 CACACACGCACACCCTGC 61.953 66.667 0.00 0.00 43.21 4.85
359 504 4.175337 ACACACGCACACCCTGCT 62.175 61.111 0.00 0.00 44.64 4.24
360 505 2.901840 CACACGCACACCCTGCTT 60.902 61.111 0.00 0.00 44.64 3.91
361 506 2.591715 ACACGCACACCCTGCTTC 60.592 61.111 0.00 0.00 44.64 3.86
362 507 2.281070 CACGCACACCCTGCTTCT 60.281 61.111 0.00 0.00 44.64 2.85
363 508 1.005037 CACGCACACCCTGCTTCTA 60.005 57.895 0.00 0.00 44.64 2.10
364 509 0.391661 CACGCACACCCTGCTTCTAT 60.392 55.000 0.00 0.00 44.64 1.98
365 510 0.391661 ACGCACACCCTGCTTCTATG 60.392 55.000 0.00 0.00 44.64 2.23
366 511 0.108186 CGCACACCCTGCTTCTATGA 60.108 55.000 0.00 0.00 44.64 2.15
367 512 1.661341 GCACACCCTGCTTCTATGAG 58.339 55.000 0.00 0.00 43.33 2.90
368 513 1.661341 CACACCCTGCTTCTATGAGC 58.339 55.000 0.00 0.00 43.00 4.26
375 520 3.280920 GCTTCTATGAGCACCTCCG 57.719 57.895 0.00 0.00 42.25 4.63
376 521 0.747255 GCTTCTATGAGCACCTCCGA 59.253 55.000 0.00 0.00 42.25 4.55
377 522 1.137086 GCTTCTATGAGCACCTCCGAA 59.863 52.381 0.00 0.00 42.25 4.30
378 523 2.418746 GCTTCTATGAGCACCTCCGAAA 60.419 50.000 0.00 0.00 42.25 3.46
379 524 3.452474 CTTCTATGAGCACCTCCGAAAG 58.548 50.000 0.00 0.00 0.00 2.62
380 525 2.735151 TCTATGAGCACCTCCGAAAGA 58.265 47.619 0.00 0.00 0.00 2.52
381 526 2.427453 TCTATGAGCACCTCCGAAAGAC 59.573 50.000 0.00 0.00 0.00 3.01
382 527 1.270907 ATGAGCACCTCCGAAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
383 528 1.919240 TGAGCACCTCCGAAAGACTA 58.081 50.000 0.00 0.00 0.00 2.59
384 529 2.244695 TGAGCACCTCCGAAAGACTAA 58.755 47.619 0.00 0.00 0.00 2.24
385 530 2.231478 TGAGCACCTCCGAAAGACTAAG 59.769 50.000 0.00 0.00 0.00 2.18
386 531 2.492484 GAGCACCTCCGAAAGACTAAGA 59.508 50.000 0.00 0.00 0.00 2.10
387 532 2.231721 AGCACCTCCGAAAGACTAAGAC 59.768 50.000 0.00 0.00 0.00 3.01
388 533 2.864968 CACCTCCGAAAGACTAAGACG 58.135 52.381 0.00 0.00 0.00 4.18
389 534 2.486982 CACCTCCGAAAGACTAAGACGA 59.513 50.000 0.00 0.00 0.00 4.20
390 535 2.487372 ACCTCCGAAAGACTAAGACGAC 59.513 50.000 0.00 0.00 0.00 4.34
391 536 2.486982 CCTCCGAAAGACTAAGACGACA 59.513 50.000 0.00 0.00 0.00 4.35
392 537 3.128938 CCTCCGAAAGACTAAGACGACAT 59.871 47.826 0.00 0.00 0.00 3.06
393 538 4.092771 TCCGAAAGACTAAGACGACATG 57.907 45.455 0.00 0.00 0.00 3.21
394 539 3.504906 TCCGAAAGACTAAGACGACATGT 59.495 43.478 0.00 0.00 0.00 3.21
410 555 6.534059 ACGACATGTCATCTTGAAATTTACG 58.466 36.000 24.93 8.56 0.00 3.18
411 556 6.367695 ACGACATGTCATCTTGAAATTTACGA 59.632 34.615 24.93 0.00 0.00 3.43
412 557 7.095397 ACGACATGTCATCTTGAAATTTACGAA 60.095 33.333 24.93 0.00 0.00 3.85
413 558 7.423598 CGACATGTCATCTTGAAATTTACGAAG 59.576 37.037 24.93 0.00 0.00 3.79
415 560 8.230486 ACATGTCATCTTGAAATTTACGAAGTC 58.770 33.333 0.00 0.00 43.93 3.01
416 561 7.722795 TGTCATCTTGAAATTTACGAAGTCA 57.277 32.000 0.00 0.00 43.93 3.41
417 562 7.572759 TGTCATCTTGAAATTTACGAAGTCAC 58.427 34.615 0.00 0.00 43.93 3.67
418 563 7.015877 GTCATCTTGAAATTTACGAAGTCACC 58.984 38.462 0.00 0.00 43.93 4.02
419 564 5.585500 TCTTGAAATTTACGAAGTCACCG 57.415 39.130 0.00 0.00 43.93 4.94
420 565 5.051816 TCTTGAAATTTACGAAGTCACCGT 58.948 37.500 0.00 0.00 43.93 4.83
421 566 6.215121 TCTTGAAATTTACGAAGTCACCGTA 58.785 36.000 0.00 0.00 43.93 4.02
422 567 6.364165 TCTTGAAATTTACGAAGTCACCGTAG 59.636 38.462 0.00 0.00 43.93 3.51
434 579 3.759544 CCGTAGGCATCTAGCGGA 58.240 61.111 0.00 0.00 46.14 5.54
435 580 1.581954 CCGTAGGCATCTAGCGGAG 59.418 63.158 0.00 0.00 46.14 4.63
511 1078 3.652581 GGGACTCCCAACTTCCTTG 57.347 57.895 9.53 0.00 44.65 3.61
577 1144 7.062605 CACATCAGCACTAACAAAAATCCAATC 59.937 37.037 0.00 0.00 0.00 2.67
591 1158 9.359653 CAAAAATCCAATCAATCCTCCTACTAT 57.640 33.333 0.00 0.00 0.00 2.12
601 1168 4.101645 TCCTCCTACTATACAGTGCTCC 57.898 50.000 0.00 0.00 36.14 4.70
631 1198 2.125912 CACGCGAAGACCAGGAGG 60.126 66.667 15.93 0.00 42.21 4.30
861 1430 4.148825 CGCCTCTCCCTTGTCCCG 62.149 72.222 0.00 0.00 0.00 5.14
869 1438 4.452733 CCTTGTCCCGTCGCCTCC 62.453 72.222 0.00 0.00 0.00 4.30
922 1497 0.750182 ACCACCAACAAGAACCACCG 60.750 55.000 0.00 0.00 0.00 4.94
959 1534 2.062519 GCCGCTAGCTAGCTAATCAAC 58.937 52.381 36.02 17.40 46.85 3.18
1410 1986 1.736645 CCAGTACGCCAACCTCGTG 60.737 63.158 0.00 0.00 40.69 4.35
1704 2525 2.933287 AACGGTGGCATCCAGGGA 60.933 61.111 0.00 0.00 32.34 4.20
1893 2814 3.199677 TGTTCTTTTGACGTGGTACTGG 58.800 45.455 0.00 0.00 0.00 4.00
1928 2852 3.053455 CGCGTGCCCTTTTCAAAATTTA 58.947 40.909 0.00 0.00 0.00 1.40
2751 3690 5.248380 AGTACTCTTTCCCTGCATTTTCT 57.752 39.130 0.00 0.00 0.00 2.52
2753 3692 5.707764 AGTACTCTTTCCCTGCATTTTCTTC 59.292 40.000 0.00 0.00 0.00 2.87
2756 3695 3.502211 TCTTTCCCTGCATTTTCTTCGTC 59.498 43.478 0.00 0.00 0.00 4.20
2759 3698 1.128692 CCCTGCATTTTCTTCGTCGTC 59.871 52.381 0.00 0.00 0.00 4.20
2762 3701 1.454276 TGCATTTTCTTCGTCGTCGTC 59.546 47.619 1.33 0.00 38.33 4.20
2776 3786 4.655778 CGTCGTCGTCGTTGTTACTAAAAC 60.656 45.833 3.67 0.00 38.33 2.43
2844 3854 8.552034 CGAGGGAATATTTAACATCAAGAAGAC 58.448 37.037 0.00 0.00 0.00 3.01
2964 3990 2.093625 GCATAGTCATTTGCGTGTTCGA 59.906 45.455 0.00 0.00 39.71 3.71
2976 4002 2.224784 GCGTGTTCGAACCATTAAACCT 59.775 45.455 24.78 0.00 39.71 3.50
2979 4005 5.614760 CGTGTTCGAACCATTAAACCTAAG 58.385 41.667 24.78 1.51 39.71 2.18
3033 4059 3.247648 ACGGTTTTGAAGACAATCAGACG 59.752 43.478 0.00 0.00 35.85 4.18
3039 4065 4.271696 TGAAGACAATCAGACGGTTGAT 57.728 40.909 0.00 0.00 39.42 2.57
3040 4066 5.400066 TGAAGACAATCAGACGGTTGATA 57.600 39.130 4.61 0.00 36.81 2.15
3041 4067 5.789521 TGAAGACAATCAGACGGTTGATAA 58.210 37.500 4.61 0.00 36.81 1.75
3042 4068 6.227522 TGAAGACAATCAGACGGTTGATAAA 58.772 36.000 4.61 0.00 36.81 1.40
3043 4069 6.708502 TGAAGACAATCAGACGGTTGATAAAA 59.291 34.615 4.61 0.00 36.81 1.52
3044 4070 7.390440 TGAAGACAATCAGACGGTTGATAAAAT 59.610 33.333 4.61 0.00 36.81 1.82
3045 4071 8.786826 AAGACAATCAGACGGTTGATAAAATA 57.213 30.769 4.61 0.00 36.81 1.40
3047 4073 8.258007 AGACAATCAGACGGTTGATAAAATAGA 58.742 33.333 4.61 0.00 36.81 1.98
3081 4107 8.547173 ACCATAAATAAATCAGGGAAATTGCAA 58.453 29.630 0.00 0.00 0.00 4.08
3217 5411 3.846405 TAGGGCTAGGGCATCCGGG 62.846 68.421 0.00 0.00 40.87 5.73
3234 5428 3.781407 TCCGGGGTTAATAGGATGTTTCA 59.219 43.478 0.00 0.00 0.00 2.69
3293 5487 0.456142 TGCTTCGGTCATCGTTCTCG 60.456 55.000 0.00 0.00 40.32 4.04
3294 5488 1.743855 GCTTCGGTCATCGTTCTCGC 61.744 60.000 0.00 0.00 40.32 5.03
3336 5530 6.982160 TGTACGATATACCCAACCTTGTAT 57.018 37.500 0.00 0.00 0.00 2.29
3382 5576 5.827797 TGAAAAGATACACAAGCCTTTCTGT 59.172 36.000 0.00 0.00 0.00 3.41
3398 5592 6.806739 GCCTTTCTGTATACATGAAACAAACC 59.193 38.462 18.52 8.22 0.00 3.27
3406 5600 8.952278 TGTATACATGAAACAAACCTTGATACC 58.048 33.333 0.08 0.00 0.00 2.73
3446 5640 4.197750 GTGTGAGTCGGAATAGTCTCCTA 58.802 47.826 0.00 0.00 32.82 2.94
3518 5712 0.317938 GCAACAGTCTCACTCGACGT 60.318 55.000 0.00 0.00 38.90 4.34
3539 5733 7.216973 ACGTAGGAACCATACTCTTGATATC 57.783 40.000 0.00 0.00 0.00 1.63
3542 5737 8.361139 CGTAGGAACCATACTCTTGATATCTTT 58.639 37.037 3.98 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.461135 TTAGGTATCCGGCGTTGGTC 59.539 55.000 6.01 0.00 0.00 4.02
1 2 0.903942 TTTAGGTATCCGGCGTTGGT 59.096 50.000 6.01 0.00 0.00 3.67
2 3 1.937899 CTTTTAGGTATCCGGCGTTGG 59.062 52.381 6.01 0.00 0.00 3.77
12 13 2.306512 TCGGGGTTGTGCTTTTAGGTAT 59.693 45.455 0.00 0.00 0.00 2.73
42 43 2.167398 GAGTGCGTTGACCCAGCCTA 62.167 60.000 0.00 0.00 0.00 3.93
58 59 1.122019 AGGCGTGAAGGGTGAAGAGT 61.122 55.000 0.00 0.00 0.00 3.24
64 65 0.457851 CTCTCTAGGCGTGAAGGGTG 59.542 60.000 0.00 0.00 0.00 4.61
68 69 0.378962 CGGACTCTCTAGGCGTGAAG 59.621 60.000 0.00 0.00 0.00 3.02
76 77 2.159184 TGCTCATTTGCGGACTCTCTAG 60.159 50.000 0.00 0.00 35.36 2.43
78 79 0.610174 TGCTCATTTGCGGACTCTCT 59.390 50.000 0.00 0.00 35.36 3.10
79 80 1.005340 CTGCTCATTTGCGGACTCTC 58.995 55.000 0.00 0.00 41.56 3.20
80 81 1.023513 GCTGCTCATTTGCGGACTCT 61.024 55.000 0.00 0.00 41.56 3.24
81 82 1.300971 TGCTGCTCATTTGCGGACTC 61.301 55.000 0.00 0.00 41.56 3.36
82 83 1.302752 TGCTGCTCATTTGCGGACT 60.303 52.632 0.00 0.00 41.56 3.85
83 84 1.136147 CTGCTGCTCATTTGCGGAC 59.864 57.895 0.00 0.00 41.56 4.79
84 85 2.042259 CCTGCTGCTCATTTGCGGA 61.042 57.895 0.00 0.00 41.56 5.54
85 86 2.042259 TCCTGCTGCTCATTTGCGG 61.042 57.895 0.00 0.00 41.91 5.69
86 87 1.136147 GTCCTGCTGCTCATTTGCG 59.864 57.895 0.00 0.00 35.36 4.85
87 88 1.136147 CGTCCTGCTGCTCATTTGC 59.864 57.895 0.00 0.00 0.00 3.68
88 89 1.136147 GCGTCCTGCTGCTCATTTG 59.864 57.895 0.00 0.00 41.73 2.32
89 90 0.890542 TTGCGTCCTGCTGCTCATTT 60.891 50.000 0.00 0.00 46.63 2.32
90 91 1.302752 TTGCGTCCTGCTGCTCATT 60.303 52.632 0.00 0.00 46.63 2.57
91 92 2.037136 GTTGCGTCCTGCTGCTCAT 61.037 57.895 0.00 0.00 46.63 2.90
92 93 2.666190 GTTGCGTCCTGCTGCTCA 60.666 61.111 0.00 0.00 46.63 4.26
93 94 3.426568 GGTTGCGTCCTGCTGCTC 61.427 66.667 0.00 0.00 46.63 4.26
96 97 2.842394 ATCTCGGTTGCGTCCTGCTG 62.842 60.000 0.00 0.00 46.63 4.41
97 98 2.172483 AATCTCGGTTGCGTCCTGCT 62.172 55.000 0.00 0.00 46.63 4.24
98 99 1.741770 AATCTCGGTTGCGTCCTGC 60.742 57.895 0.00 0.00 46.70 4.85
99 100 0.389817 TCAATCTCGGTTGCGTCCTG 60.390 55.000 0.00 0.00 0.00 3.86
104 105 0.787787 TTTCGTCAATCTCGGTTGCG 59.212 50.000 2.01 2.01 33.26 4.85
109 110 2.806244 ACCAACTTTTCGTCAATCTCGG 59.194 45.455 0.00 0.00 0.00 4.63
112 113 8.718734 GTCTAATAACCAACTTTTCGTCAATCT 58.281 33.333 0.00 0.00 0.00 2.40
113 114 8.500773 TGTCTAATAACCAACTTTTCGTCAATC 58.499 33.333 0.00 0.00 0.00 2.67
158 302 1.421646 AGTGGCAGTGGTTTAGAGCTT 59.578 47.619 0.00 0.00 0.00 3.74
186 330 5.705902 ACGCACAAAATAAGATTAACCCAC 58.294 37.500 0.00 0.00 0.00 4.61
213 357 4.808364 CCTTTGCGTTTCTTTCATTCCAAA 59.192 37.500 0.00 0.00 0.00 3.28
215 359 3.383185 ACCTTTGCGTTTCTTTCATTCCA 59.617 39.130 0.00 0.00 0.00 3.53
216 360 3.977427 ACCTTTGCGTTTCTTTCATTCC 58.023 40.909 0.00 0.00 0.00 3.01
220 364 3.854809 CGAAAACCTTTGCGTTTCTTTCA 59.145 39.130 0.00 0.00 34.89 2.69
229 373 2.399396 ACATGTCGAAAACCTTTGCG 57.601 45.000 0.00 0.00 40.56 4.85
234 378 0.958822 GGCCAACATGTCGAAAACCT 59.041 50.000 0.00 0.00 0.00 3.50
277 422 8.289618 GCTTATGTCTGTACTGATGTTCAAAAA 58.710 33.333 5.69 0.00 0.00 1.94
278 423 7.360017 CGCTTATGTCTGTACTGATGTTCAAAA 60.360 37.037 5.69 0.00 0.00 2.44
279 424 6.090763 CGCTTATGTCTGTACTGATGTTCAAA 59.909 38.462 5.69 0.00 0.00 2.69
280 425 5.576774 CGCTTATGTCTGTACTGATGTTCAA 59.423 40.000 5.69 0.00 0.00 2.69
281 426 5.102313 CGCTTATGTCTGTACTGATGTTCA 58.898 41.667 5.69 0.00 0.00 3.18
282 427 4.026475 GCGCTTATGTCTGTACTGATGTTC 60.026 45.833 0.00 0.00 0.00 3.18
283 428 3.865745 GCGCTTATGTCTGTACTGATGTT 59.134 43.478 0.00 0.00 0.00 2.71
284 429 3.131223 AGCGCTTATGTCTGTACTGATGT 59.869 43.478 2.64 1.12 0.00 3.06
285 430 3.711086 AGCGCTTATGTCTGTACTGATG 58.289 45.455 2.64 0.00 0.00 3.07
286 431 3.381590 TGAGCGCTTATGTCTGTACTGAT 59.618 43.478 13.26 0.00 0.00 2.90
287 432 2.752903 TGAGCGCTTATGTCTGTACTGA 59.247 45.455 13.26 0.00 0.00 3.41
288 433 3.111838 CTGAGCGCTTATGTCTGTACTG 58.888 50.000 13.26 0.00 0.00 2.74
289 434 3.017442 TCTGAGCGCTTATGTCTGTACT 58.983 45.455 13.26 0.00 0.00 2.73
290 435 3.109619 GTCTGAGCGCTTATGTCTGTAC 58.890 50.000 13.26 0.00 0.00 2.90
291 436 2.752903 TGTCTGAGCGCTTATGTCTGTA 59.247 45.455 13.26 0.00 0.00 2.74
292 437 1.546029 TGTCTGAGCGCTTATGTCTGT 59.454 47.619 13.26 0.00 0.00 3.41
293 438 2.284263 TGTCTGAGCGCTTATGTCTG 57.716 50.000 13.26 2.38 0.00 3.51
294 439 3.549019 CGTATGTCTGAGCGCTTATGTCT 60.549 47.826 13.26 0.00 0.00 3.41
295 440 2.721603 CGTATGTCTGAGCGCTTATGTC 59.278 50.000 13.26 0.00 0.00 3.06
296 441 2.732366 CGTATGTCTGAGCGCTTATGT 58.268 47.619 13.26 0.00 0.00 2.29
297 442 1.453524 GCGTATGTCTGAGCGCTTATG 59.546 52.381 13.26 5.30 45.48 1.90
298 443 1.772182 GCGTATGTCTGAGCGCTTAT 58.228 50.000 13.26 4.36 45.48 1.73
299 444 0.591488 CGCGTATGTCTGAGCGCTTA 60.591 55.000 13.26 6.52 46.56 3.09
300 445 1.874019 CGCGTATGTCTGAGCGCTT 60.874 57.895 13.26 0.00 46.56 4.68
301 446 2.278206 CGCGTATGTCTGAGCGCT 60.278 61.111 11.27 11.27 46.56 5.92
304 449 0.778815 GTATGCGCGTATGTCTGAGC 59.221 55.000 20.45 0.00 0.00 4.26
305 450 1.781429 GTGTATGCGCGTATGTCTGAG 59.219 52.381 20.45 0.00 0.00 3.35
306 451 1.404035 AGTGTATGCGCGTATGTCTGA 59.596 47.619 20.45 0.00 0.00 3.27
307 452 1.781429 GAGTGTATGCGCGTATGTCTG 59.219 52.381 20.45 0.00 0.00 3.51
308 453 1.404035 TGAGTGTATGCGCGTATGTCT 59.596 47.619 20.45 13.96 0.00 3.41
309 454 1.517276 GTGAGTGTATGCGCGTATGTC 59.483 52.381 20.45 12.76 0.00 3.06
310 455 1.556564 GTGAGTGTATGCGCGTATGT 58.443 50.000 20.45 0.00 0.00 2.29
311 456 0.852777 GGTGAGTGTATGCGCGTATG 59.147 55.000 20.45 0.00 0.00 2.39
312 457 0.249322 GGGTGAGTGTATGCGCGTAT 60.249 55.000 15.52 15.52 0.00 3.06
313 458 1.140161 GGGTGAGTGTATGCGCGTA 59.860 57.895 8.43 4.92 0.00 4.42
314 459 2.125673 GGGTGAGTGTATGCGCGT 60.126 61.111 8.43 7.55 0.00 6.01
315 460 2.011741 TAGGGGTGAGTGTATGCGCG 62.012 60.000 0.00 0.00 0.00 6.86
316 461 0.393077 ATAGGGGTGAGTGTATGCGC 59.607 55.000 0.00 0.00 0.00 6.09
317 462 4.056050 GTTTATAGGGGTGAGTGTATGCG 58.944 47.826 0.00 0.00 0.00 4.73
318 463 4.056050 CGTTTATAGGGGTGAGTGTATGC 58.944 47.826 0.00 0.00 0.00 3.14
319 464 4.056050 GCGTTTATAGGGGTGAGTGTATG 58.944 47.826 0.00 0.00 0.00 2.39
320 465 3.707611 TGCGTTTATAGGGGTGAGTGTAT 59.292 43.478 0.00 0.00 0.00 2.29
321 466 3.098377 TGCGTTTATAGGGGTGAGTGTA 58.902 45.455 0.00 0.00 0.00 2.90
322 467 1.903860 TGCGTTTATAGGGGTGAGTGT 59.096 47.619 0.00 0.00 0.00 3.55
323 468 2.277084 GTGCGTTTATAGGGGTGAGTG 58.723 52.381 0.00 0.00 0.00 3.51
324 469 1.903860 TGTGCGTTTATAGGGGTGAGT 59.096 47.619 0.00 0.00 0.00 3.41
325 470 2.277084 GTGTGCGTTTATAGGGGTGAG 58.723 52.381 0.00 0.00 0.00 3.51
326 471 1.624312 TGTGTGCGTTTATAGGGGTGA 59.376 47.619 0.00 0.00 0.00 4.02
327 472 1.735571 GTGTGTGCGTTTATAGGGGTG 59.264 52.381 0.00 0.00 0.00 4.61
328 473 1.673626 CGTGTGTGCGTTTATAGGGGT 60.674 52.381 0.00 0.00 0.00 4.95
329 474 1.003851 CGTGTGTGCGTTTATAGGGG 58.996 55.000 0.00 0.00 0.00 4.79
330 475 0.372334 GCGTGTGTGCGTTTATAGGG 59.628 55.000 0.00 0.00 0.00 3.53
331 476 1.072391 TGCGTGTGTGCGTTTATAGG 58.928 50.000 0.00 0.00 37.81 2.57
332 477 1.457683 TGTGCGTGTGTGCGTTTATAG 59.542 47.619 0.00 0.00 37.81 1.31
333 478 1.192757 GTGTGCGTGTGTGCGTTTATA 59.807 47.619 0.00 0.00 37.81 0.98
334 479 0.041663 GTGTGCGTGTGTGCGTTTAT 60.042 50.000 0.00 0.00 37.81 1.40
335 480 1.348938 GTGTGCGTGTGTGCGTTTA 59.651 52.632 0.00 0.00 37.81 2.01
336 481 2.099446 GTGTGCGTGTGTGCGTTT 59.901 55.556 0.00 0.00 37.81 3.60
337 482 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
340 485 3.952675 CAGGGTGTGCGTGTGTGC 61.953 66.667 0.00 0.00 0.00 4.57
341 486 3.952675 GCAGGGTGTGCGTGTGTG 61.953 66.667 0.00 0.00 43.99 3.82
349 494 1.065926 TGCTCATAGAAGCAGGGTGTG 60.066 52.381 0.00 0.00 47.00 3.82
350 495 1.279496 TGCTCATAGAAGCAGGGTGT 58.721 50.000 0.00 0.00 47.00 4.16
357 502 0.747255 TCGGAGGTGCTCATAGAAGC 59.253 55.000 0.00 0.00 42.82 3.86
358 503 3.131223 TCTTTCGGAGGTGCTCATAGAAG 59.869 47.826 0.00 0.00 31.08 2.85
359 504 3.096852 TCTTTCGGAGGTGCTCATAGAA 58.903 45.455 0.00 0.00 31.08 2.10
360 505 2.427453 GTCTTTCGGAGGTGCTCATAGA 59.573 50.000 0.00 0.00 31.08 1.98
361 506 2.428890 AGTCTTTCGGAGGTGCTCATAG 59.571 50.000 0.00 0.00 31.08 2.23
362 507 2.457598 AGTCTTTCGGAGGTGCTCATA 58.542 47.619 0.00 0.00 31.08 2.15
363 508 1.270907 AGTCTTTCGGAGGTGCTCAT 58.729 50.000 0.00 0.00 31.08 2.90
364 509 1.919240 TAGTCTTTCGGAGGTGCTCA 58.081 50.000 0.00 0.00 31.08 4.26
365 510 2.492484 TCTTAGTCTTTCGGAGGTGCTC 59.508 50.000 0.00 0.00 0.00 4.26
366 511 2.231721 GTCTTAGTCTTTCGGAGGTGCT 59.768 50.000 0.00 0.00 0.00 4.40
367 512 2.608268 GTCTTAGTCTTTCGGAGGTGC 58.392 52.381 0.00 0.00 0.00 5.01
368 513 2.486982 TCGTCTTAGTCTTTCGGAGGTG 59.513 50.000 0.00 0.00 0.00 4.00
369 514 2.487372 GTCGTCTTAGTCTTTCGGAGGT 59.513 50.000 0.00 0.00 0.00 3.85
370 515 2.486982 TGTCGTCTTAGTCTTTCGGAGG 59.513 50.000 0.00 0.00 0.00 4.30
371 516 3.826236 TGTCGTCTTAGTCTTTCGGAG 57.174 47.619 0.00 0.00 0.00 4.63
372 517 3.504906 ACATGTCGTCTTAGTCTTTCGGA 59.495 43.478 0.00 0.00 0.00 4.55
373 518 3.834610 ACATGTCGTCTTAGTCTTTCGG 58.165 45.455 0.00 0.00 0.00 4.30
374 519 4.473199 TGACATGTCGTCTTAGTCTTTCG 58.527 43.478 20.54 0.00 45.60 3.46
375 520 6.561945 GATGACATGTCGTCTTAGTCTTTC 57.438 41.667 31.95 9.84 45.60 2.62
385 530 6.678663 CGTAAATTTCAAGATGACATGTCGTC 59.321 38.462 32.11 32.11 45.61 4.20
386 531 6.367695 TCGTAAATTTCAAGATGACATGTCGT 59.632 34.615 20.50 20.50 0.00 4.34
387 532 6.761117 TCGTAAATTTCAAGATGACATGTCG 58.239 36.000 20.54 6.37 0.00 4.35
388 533 8.230486 ACTTCGTAAATTTCAAGATGACATGTC 58.770 33.333 19.27 19.27 0.00 3.06
389 534 8.099364 ACTTCGTAAATTTCAAGATGACATGT 57.901 30.769 0.00 0.00 0.00 3.21
390 535 8.229811 TGACTTCGTAAATTTCAAGATGACATG 58.770 33.333 0.00 0.00 0.00 3.21
391 536 8.230486 GTGACTTCGTAAATTTCAAGATGACAT 58.770 33.333 0.00 0.00 0.00 3.06
392 537 7.307751 GGTGACTTCGTAAATTTCAAGATGACA 60.308 37.037 0.00 0.26 0.00 3.58
393 538 7.015877 GGTGACTTCGTAAATTTCAAGATGAC 58.984 38.462 0.00 0.00 0.00 3.06
394 539 6.128661 CGGTGACTTCGTAAATTTCAAGATGA 60.129 38.462 0.00 0.00 0.00 2.92
395 540 6.015504 CGGTGACTTCGTAAATTTCAAGATG 58.984 40.000 0.00 0.00 0.00 2.90
396 541 5.699458 ACGGTGACTTCGTAAATTTCAAGAT 59.301 36.000 0.00 0.00 39.22 2.40
397 542 5.051816 ACGGTGACTTCGTAAATTTCAAGA 58.948 37.500 0.00 0.00 39.22 3.02
398 543 5.338614 ACGGTGACTTCGTAAATTTCAAG 57.661 39.130 0.00 0.00 39.22 3.02
399 544 5.406175 CCTACGGTGACTTCGTAAATTTCAA 59.594 40.000 0.00 0.00 41.62 2.69
400 545 4.925054 CCTACGGTGACTTCGTAAATTTCA 59.075 41.667 0.00 0.00 41.62 2.69
401 546 4.201656 GCCTACGGTGACTTCGTAAATTTC 60.202 45.833 0.00 0.00 41.62 2.17
402 547 3.681417 GCCTACGGTGACTTCGTAAATTT 59.319 43.478 0.00 0.00 41.62 1.82
403 548 3.256558 GCCTACGGTGACTTCGTAAATT 58.743 45.455 0.00 0.00 41.62 1.82
404 549 2.231964 TGCCTACGGTGACTTCGTAAAT 59.768 45.455 0.00 0.00 41.62 1.40
405 550 1.612950 TGCCTACGGTGACTTCGTAAA 59.387 47.619 0.00 0.00 41.62 2.01
406 551 1.246649 TGCCTACGGTGACTTCGTAA 58.753 50.000 0.00 0.00 41.62 3.18
407 552 1.402968 GATGCCTACGGTGACTTCGTA 59.597 52.381 0.00 0.00 41.38 3.43
408 553 0.172803 GATGCCTACGGTGACTTCGT 59.827 55.000 0.00 0.00 43.64 3.85
409 554 0.456221 AGATGCCTACGGTGACTTCG 59.544 55.000 0.00 0.00 0.00 3.79
410 555 2.544069 GCTAGATGCCTACGGTGACTTC 60.544 54.545 0.00 0.00 35.15 3.01
411 556 1.409427 GCTAGATGCCTACGGTGACTT 59.591 52.381 0.00 0.00 35.15 3.01
412 557 1.033574 GCTAGATGCCTACGGTGACT 58.966 55.000 0.00 0.00 35.15 3.41
413 558 0.317938 CGCTAGATGCCTACGGTGAC 60.318 60.000 0.00 0.00 38.78 3.67
414 559 1.452953 CCGCTAGATGCCTACGGTGA 61.453 60.000 0.00 0.00 36.12 4.02
415 560 1.007271 CCGCTAGATGCCTACGGTG 60.007 63.158 0.00 0.00 36.12 4.94
416 561 1.152819 TCCGCTAGATGCCTACGGT 60.153 57.895 0.00 0.00 38.96 4.83
417 562 1.581954 CTCCGCTAGATGCCTACGG 59.418 63.158 0.00 0.00 39.10 4.02
418 563 1.081108 GCTCCGCTAGATGCCTACG 60.081 63.158 0.00 0.00 38.78 3.51
419 564 1.290639 GGCTCCGCTAGATGCCTAC 59.709 63.158 0.00 0.00 41.92 3.18
420 565 3.778955 GGCTCCGCTAGATGCCTA 58.221 61.111 0.00 0.00 41.92 3.93
422 567 1.596477 CAAGGCTCCGCTAGATGCC 60.596 63.158 0.00 0.50 45.21 4.40
423 568 1.596477 CCAAGGCTCCGCTAGATGC 60.596 63.158 0.00 0.00 38.57 3.91
424 569 1.596477 GCCAAGGCTCCGCTAGATG 60.596 63.158 3.29 0.00 38.26 2.90
425 570 2.825264 GCCAAGGCTCCGCTAGAT 59.175 61.111 3.29 0.00 38.26 1.98
435 580 1.750780 GCCCTCAAGTAGCCAAGGC 60.751 63.158 2.02 2.02 42.33 4.35
436 581 0.329596 AAGCCCTCAAGTAGCCAAGG 59.670 55.000 0.00 0.00 0.00 3.61
437 582 1.271597 ACAAGCCCTCAAGTAGCCAAG 60.272 52.381 0.00 0.00 0.00 3.61
438 583 0.771127 ACAAGCCCTCAAGTAGCCAA 59.229 50.000 0.00 0.00 0.00 4.52
439 584 0.036732 CACAAGCCCTCAAGTAGCCA 59.963 55.000 0.00 0.00 0.00 4.75
440 585 0.036875 ACACAAGCCCTCAAGTAGCC 59.963 55.000 0.00 0.00 0.00 3.93
441 586 2.289444 TGTACACAAGCCCTCAAGTAGC 60.289 50.000 0.00 0.00 0.00 3.58
506 1073 6.569610 GCTTTTGTTTCGTCCATTATCAAGGA 60.570 38.462 0.00 0.00 0.00 3.36
510 1077 5.957842 AGCTTTTGTTTCGTCCATTATCA 57.042 34.783 0.00 0.00 0.00 2.15
511 1078 8.021396 AGTTTAGCTTTTGTTTCGTCCATTATC 58.979 33.333 0.00 0.00 0.00 1.75
577 1144 5.047660 GGAGCACTGTATAGTAGGAGGATTG 60.048 48.000 0.00 0.00 34.74 2.67
591 1158 0.179043 TTTGCGTTGGGAGCACTGTA 60.179 50.000 0.00 0.00 45.10 2.74
592 1159 1.447317 CTTTGCGTTGGGAGCACTGT 61.447 55.000 0.00 0.00 45.10 3.55
593 1160 1.165907 TCTTTGCGTTGGGAGCACTG 61.166 55.000 0.00 0.00 45.10 3.66
601 1168 2.427410 GCGTGCTCTTTGCGTTGG 60.427 61.111 0.00 0.00 46.63 3.77
631 1198 3.745803 GCAACTGGCAGCAGCTCC 61.746 66.667 15.89 0.00 43.97 4.70
745 1314 0.655733 CGTCGAGCTTTTTGGTGTGT 59.344 50.000 0.00 0.00 0.00 3.72
861 1430 4.143543 GGAGGTATATATAGGGAGGCGAC 58.856 52.174 0.00 0.00 0.00 5.19
869 1438 5.461317 GGGATGGGAGGGAGGTATATATAGG 60.461 52.000 0.00 0.00 0.00 2.57
950 1525 2.119029 GCCGGTGGGGTTGATTAGC 61.119 63.158 1.90 0.00 38.44 3.09
951 1526 1.817941 CGCCGGTGGGGTTGATTAG 60.818 63.158 7.26 0.00 38.44 1.73
1082 1658 2.125912 CAAGCCAGTCGGACTCGG 60.126 66.667 7.89 13.82 36.95 4.63
1083 1659 1.444553 GTCAAGCCAGTCGGACTCG 60.445 63.158 7.89 2.56 37.82 4.18
1893 2814 2.572647 CGCGTCGTCGTCAGTACC 60.573 66.667 0.00 0.00 39.49 3.34
1928 2852 0.818040 GCCTTCACCGTGTCCTGTTT 60.818 55.000 0.00 0.00 0.00 2.83
2077 3001 4.699522 AAGCCGAACCCCGTGAGC 62.700 66.667 0.00 0.00 36.31 4.26
2751 3690 1.003972 AGTAACAACGACGACGACGAA 60.004 47.619 25.15 3.56 42.66 3.85
2753 3692 2.211449 TAGTAACAACGACGACGACG 57.789 50.000 17.60 17.60 42.66 5.12
2756 3695 4.674440 TGTTTTAGTAACAACGACGACG 57.326 40.909 5.58 5.58 45.75 5.12
2759 3698 8.693504 TCTAGATTTGTTTTAGTAACAACGACG 58.306 33.333 2.80 0.00 39.57 5.12
2776 3786 9.045223 TCGGACAAATGAATGTATCTAGATTTG 57.955 33.333 11.25 9.74 36.10 2.32
2817 3827 8.482943 TCTTCTTGATGTTAAATATTCCCTCGA 58.517 33.333 0.00 0.00 0.00 4.04
2844 3854 1.873591 GGGACGCATATTACTTGGCAG 59.126 52.381 0.00 0.00 0.00 4.85
2909 3935 7.524698 GCCTTGTGAATAACAATCCCTGTTTTA 60.525 37.037 0.00 0.00 46.49 1.52
2940 3966 4.260172 CGAACACGCAAATGACTATGCATA 60.260 41.667 6.20 6.20 42.68 3.14
2964 3990 8.739972 CAATGTCTTAGCTTAGGTTTAATGGTT 58.260 33.333 0.00 0.00 0.00 3.67
2976 4002 6.999950 TGTTCAGGTACAATGTCTTAGCTTA 58.000 36.000 0.00 0.00 0.00 3.09
2979 4005 6.554334 TTTGTTCAGGTACAATGTCTTAGC 57.446 37.500 0.00 0.00 37.81 3.09
3068 4094 4.057406 TGTCTTTGTTGCAATTTCCCTG 57.943 40.909 0.59 0.00 0.00 4.45
3070 4096 5.537188 TGTATGTCTTTGTTGCAATTTCCC 58.463 37.500 0.59 0.00 0.00 3.97
3081 4107 6.659242 CCTCCACCTTAAATGTATGTCTTTGT 59.341 38.462 0.00 0.00 0.00 2.83
3142 5336 7.165485 TGCACAAGGAGTATTATAGTTGTGTT 58.835 34.615 12.98 0.00 44.22 3.32
3144 5338 7.239166 CTGCACAAGGAGTATTATAGTTGTG 57.761 40.000 8.33 8.33 44.84 3.33
3217 5411 6.650120 TGTCTCCTGAAACATCCTATTAACC 58.350 40.000 0.00 0.00 0.00 2.85
3218 5412 9.482627 CTATGTCTCCTGAAACATCCTATTAAC 57.517 37.037 0.00 0.00 37.33 2.01
3232 5426 3.300388 CAACCTAGCCTATGTCTCCTGA 58.700 50.000 0.00 0.00 0.00 3.86
3234 5428 2.043227 GCAACCTAGCCTATGTCTCCT 58.957 52.381 0.00 0.00 0.00 3.69
3371 5565 7.759489 TTGTTTCATGTATACAGAAAGGCTT 57.241 32.000 20.98 0.00 32.48 4.35
3382 5576 7.825270 ACGGTATCAAGGTTTGTTTCATGTATA 59.175 33.333 0.00 0.00 0.00 1.47
3398 5592 2.146342 GGATGGCATGACGGTATCAAG 58.854 52.381 3.81 0.00 41.93 3.02
3446 5640 0.324614 TGGGCGTGATTCATGTGTCT 59.675 50.000 7.67 0.00 0.00 3.41
3453 5647 2.296792 CAATACCATGGGCGTGATTCA 58.703 47.619 18.09 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.