Multiple sequence alignment - TraesCS2D01G134500

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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 TraesCS2D01G134500 chr2D 100.000 3849 0 0 1 3849 79097081 79093233 0.000000e+00 7108.0
1 TraesCS2D01G134500 chr2D 100.000 77 0 0 2064 2140 137146829 137146753 4.010000e-30 143.0
2 TraesCS2D01G134500 chr2D 100.000 75 0 0 2066 2140 467988850 467988776 5.190000e-29 139.0
3 TraesCS2D01G134500 chr2D 98.113 53 0 1 2173 2225 79094970 79095021 1.470000e-14 91.6
4 TraesCS2D01G134500 chr2D 98.000 50 0 1 2173 2222 137146781 137146829 6.850000e-13 86.1
5 TraesCS2D01G134500 chr2D 97.826 46 1 0 2173 2218 13710858 13710903 3.190000e-11 80.5
6 TraesCS2D01G134500 chr2A 95.905 1636 48 7 2217 3849 79354406 79352787 0.000000e+00 2632.0
7 TraesCS2D01G134500 chr2A 92.701 548 29 5 1517 2059 79354944 79354403 0.000000e+00 780.0
8 TraesCS2D01G134500 chr2A 84.699 830 45 34 710 1512 79355762 79354988 0.000000e+00 754.0
9 TraesCS2D01G134500 chr2A 95.538 381 15 2 1 380 79356251 79355872 3.290000e-170 608.0
10 TraesCS2D01G134500 chr2A 84.354 294 39 7 153 443 40362725 40363014 8.140000e-72 281.0
11 TraesCS2D01G134500 chr2A 84.175 297 39 7 151 442 59123408 59123701 8.140000e-72 281.0
12 TraesCS2D01G134500 chr2B 89.911 1011 62 18 511 1510 123064679 123063698 0.000000e+00 1266.0
13 TraesCS2D01G134500 chr2B 90.389 822 39 14 3053 3849 123062179 123061373 0.000000e+00 1044.0
14 TraesCS2D01G134500 chr2B 89.406 623 41 10 2438 3060 123062819 123062222 0.000000e+00 761.0
15 TraesCS2D01G134500 chr2B 94.805 308 16 0 1752 2059 123063310 123063003 7.480000e-132 481.0
16 TraesCS2D01G134500 chr2B 95.041 242 9 2 1515 1753 123063655 123063414 1.010000e-100 377.0
17 TraesCS2D01G134500 chr2B 97.861 187 4 0 2217 2403 123063006 123062820 1.330000e-84 324.0
18 TraesCS2D01G134500 chr2B 85.050 301 37 8 146 442 541164151 541163855 2.250000e-77 300.0
19 TraesCS2D01G134500 chr1A 89.438 445 32 7 10 442 223989238 223988797 7.270000e-152 547.0
20 TraesCS2D01G134500 chr1A 85.135 296 38 6 151 443 74747594 74747302 8.080000e-77 298.0
21 TraesCS2D01G134500 chr1A 93.478 46 1 1 412 457 372636275 372636318 2.480000e-07 67.6
22 TraesCS2D01G134500 chr1A 100.000 33 0 0 411 443 256681098 256681130 1.150000e-05 62.1
23 TraesCS2D01G134500 chr4A 90.058 342 24 7 79 418 395091870 395091537 5.910000e-118 435.0
24 TraesCS2D01G134500 chr6B 85.085 295 36 8 151 442 693692719 693692430 1.050000e-75 294.0
25 TraesCS2D01G134500 chr5B 89.730 185 15 4 260 442 50288456 50288274 2.310000e-57 233.0
26 TraesCS2D01G134500 chr5B 87.209 172 20 2 273 442 393839340 393839169 1.090000e-45 195.0
27 TraesCS2D01G134500 chr5B 86.628 172 21 2 273 442 670802594 670802423 5.080000e-44 189.0
28 TraesCS2D01G134500 chr5B 96.875 32 1 0 1050 1081 433548424 433548455 2.000000e-03 54.7
29 TraesCS2D01G134500 chr6A 89.189 185 15 5 260 442 50194345 50194164 3.870000e-55 226.0
30 TraesCS2D01G134500 chr6A 87.952 83 9 1 359 440 485781230 485781148 3.170000e-16 97.1
31 TraesCS2D01G134500 chr7D 88.172 186 20 2 260 443 127254763 127254578 1.800000e-53 220.0
32 TraesCS2D01G134500 chr7D 100.000 76 0 0 2065 2140 194604397 194604322 1.440000e-29 141.0
33 TraesCS2D01G134500 chr7D 93.478 46 0 3 2137 2182 194604116 194604158 8.930000e-07 65.8
34 TraesCS2D01G134500 chr1B 86.705 173 20 3 273 443 316608615 316608786 5.080000e-44 189.0
35 TraesCS2D01G134500 chr4D 98.734 79 1 0 2062 2140 277701851 277701773 1.440000e-29 141.0
36 TraesCS2D01G134500 chr4D 100.000 75 0 0 2066 2140 357121246 357121172 5.190000e-29 139.0
37 TraesCS2D01G134500 chr4D 91.935 62 3 2 2173 2233 277701801 277701861 6.850000e-13 86.1
38 TraesCS2D01G134500 chr4D 97.674 43 1 0 401 443 506421126 506421084 1.480000e-09 75.0
39 TraesCS2D01G134500 chr4D 100.000 37 0 0 2137 2173 4080674 4080710 6.900000e-08 69.4
40 TraesCS2D01G134500 chr4D 94.737 38 2 0 405 442 372832558 372832521 4.150000e-05 60.2
41 TraesCS2D01G134500 chr3D 100.000 76 0 0 2065 2140 21421169 21421094 1.440000e-29 141.0
42 TraesCS2D01G134500 chr3D 96.226 53 0 2 2171 2222 511532661 511532610 6.850000e-13 86.1
43 TraesCS2D01G134500 chr3D 97.368 38 1 0 405 442 593648469 593648432 8.930000e-07 65.8
44 TraesCS2D01G134500 chr3D 100.000 34 0 0 412 445 459880984 459880951 3.210000e-06 63.9
45 TraesCS2D01G134500 chr1D 100.000 76 0 0 2065 2140 19642637 19642712 1.440000e-29 141.0
46 TraesCS2D01G134500 chr1D 100.000 46 0 0 2173 2218 58504947 58504992 6.850000e-13 86.1
47 TraesCS2D01G134500 chr1D 100.000 31 0 0 412 442 156287427 156287457 1.490000e-04 58.4
48 TraesCS2D01G134500 chr1D 100.000 30 0 0 412 441 51555891 51555920 5.370000e-04 56.5
49 TraesCS2D01G134500 chr5D 95.455 88 2 2 2054 2140 108004776 108004862 5.190000e-29 139.0
50 TraesCS2D01G134500 chr5D 90.909 66 3 3 2173 2238 108004834 108004772 6.850000e-13 86.1
51 TraesCS2D01G134500 chr5D 97.826 46 0 1 2173 2218 64016664 64016708 1.150000e-10 78.7
52 TraesCS2D01G134500 chr5D 97.619 42 1 0 403 444 336766035 336765994 5.330000e-09 73.1
53 TraesCS2D01G134500 chr5D 100.000 32 0 0 412 443 549425104 549425073 4.150000e-05 60.2
54 TraesCS2D01G134500 chr6D 96.341 82 1 2 2059 2140 432810073 432810152 2.410000e-27 134.0
55 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 11693852 11693888 6.900000e-08 69.4
56 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 15629654 15629618 6.900000e-08 69.4
57 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 38874320 38874356 6.900000e-08 69.4
58 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 48531043 48531007 6.900000e-08 69.4
59 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 109695144 109695108 6.900000e-08 69.4
60 TraesCS2D01G134500 chr6D 97.500 40 1 0 403 442 322534507 322534546 6.900000e-08 69.4
61 TraesCS2D01G134500 chr6D 100.000 37 0 0 2137 2173 467280864 467280900 6.900000e-08 69.4
62 TraesCS2D01G134500 chrUn 100.000 44 0 0 2173 2216 79074552 79074595 8.860000e-12 82.4
63 TraesCS2D01G134500 chrUn 100.000 37 0 0 2137 2173 79074222 79074258 6.900000e-08 69.4
64 TraesCS2D01G134500 chrUn 100.000 33 0 0 410 442 301083545 301083513 1.150000e-05 62.1
65 TraesCS2D01G134500 chrUn 100.000 29 0 0 416 444 265419480 265419452 2.000000e-03 54.7
66 TraesCS2D01G134500 chr4B 97.674 43 1 0 401 443 662756405 662756447 1.480000e-09 75.0
67 TraesCS2D01G134500 chr4B 97.674 43 1 0 401 443 663810592 663810550 1.480000e-09 75.0


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 TraesCS2D01G134500 chr2D 79093233 79097081 3848 True 7108.000000 7108 100.000000 1 3849 1 chr2D.!!$R1 3848
1 TraesCS2D01G134500 chr2A 79352787 79356251 3464 True 1193.500000 2632 92.210750 1 3849 4 chr2A.!!$R1 3848
2 TraesCS2D01G134500 chr2B 123061373 123064679 3306 True 708.833333 1266 92.902167 511 3849 6 chr2B.!!$R2 3338

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
882 887 0.105658 TATCTCCTCCTCCAACCCCG 60.106 60.0 0.0 0.0 0.0 5.73 F
2157 2343 0.321298 TCCCTTTTGCTCCTACGTGC 60.321 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2208 2394 0.109226 GTTAGACAGAGACGCGGCTT 60.109 55.0 19.64 0.0 0.00 4.35 R
3206 3447 1.151668 ACATCTTGCACGAAGACTGC 58.848 50.0 2.15 0.0 43.71 4.40 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
66 67 8.974408 TGAACTTCGATACGTTTCATAATATGG 58.026 33.333 6.81 0.00 0.00 2.74
77 78 7.229907 ACGTTTCATAATATGGTTGGGTATTCC 59.770 37.037 0.00 0.00 0.00 3.01
128 130 6.219417 TCCACAATTATGCACCCTAATTTG 57.781 37.500 0.00 0.00 28.67 2.32
242 244 7.530426 AATAGCTTTCCATGGATAATGAACC 57.470 36.000 17.06 0.00 38.72 3.62
273 275 6.127647 TGGTGGCTTTATTAATCTTCAAGCAG 60.128 38.462 16.99 0.00 41.42 4.24
306 308 7.660112 TGTTAGTGATCTTGAATGCATGTTTT 58.340 30.769 0.00 0.00 0.00 2.43
343 345 1.302431 TGCGTGATTGGGAGTGGTG 60.302 57.895 0.00 0.00 0.00 4.17
374 376 9.076781 TCAGAAAATAAAATTGATGTCTCACCA 57.923 29.630 0.00 0.00 0.00 4.17
393 395 4.789012 CCAGTTGGTTTGCTCATTGTAT 57.211 40.909 0.00 0.00 0.00 2.29
394 396 5.138125 CCAGTTGGTTTGCTCATTGTATT 57.862 39.130 0.00 0.00 0.00 1.89
395 397 6.266168 CCAGTTGGTTTGCTCATTGTATTA 57.734 37.500 0.00 0.00 0.00 0.98
397 399 7.322664 CCAGTTGGTTTGCTCATTGTATTATT 58.677 34.615 0.00 0.00 0.00 1.40
398 400 7.818930 CCAGTTGGTTTGCTCATTGTATTATTT 59.181 33.333 0.00 0.00 0.00 1.40
401 403 8.434661 GTTGGTTTGCTCATTGTATTATTTGTG 58.565 33.333 0.00 0.00 0.00 3.33
402 404 7.665690 TGGTTTGCTCATTGTATTATTTGTGT 58.334 30.769 0.00 0.00 0.00 3.72
403 405 8.797438 TGGTTTGCTCATTGTATTATTTGTGTA 58.203 29.630 0.00 0.00 0.00 2.90
404 406 9.801873 GGTTTGCTCATTGTATTATTTGTGTAT 57.198 29.630 0.00 0.00 0.00 2.29
418 420 5.585500 TTTGTGTATTAGTCAAGACGTGC 57.415 39.130 0.00 0.00 36.20 5.34
419 421 4.245845 TGTGTATTAGTCAAGACGTGCA 57.754 40.909 0.00 0.00 36.20 4.57
421 423 5.234752 TGTGTATTAGTCAAGACGTGCATT 58.765 37.500 0.00 0.00 36.20 3.56
422 424 5.120053 TGTGTATTAGTCAAGACGTGCATTG 59.880 40.000 0.00 0.00 36.20 2.82
423 425 3.747099 ATTAGTCAAGACGTGCATTGC 57.253 42.857 0.46 0.46 36.20 3.56
441 443 1.429463 GCACGTGCAAGCTTACTAGT 58.571 50.000 34.52 0.00 41.59 2.57
442 444 2.602878 GCACGTGCAAGCTTACTAGTA 58.397 47.619 34.52 0.00 41.59 1.82
443 445 2.344741 GCACGTGCAAGCTTACTAGTAC 59.655 50.000 34.52 0.00 41.59 2.73
444 446 2.592897 CACGTGCAAGCTTACTAGTACG 59.407 50.000 18.78 18.78 33.92 3.67
445 447 1.582502 CGTGCAAGCTTACTAGTACGC 59.417 52.381 20.63 20.63 0.00 4.42
446 448 1.925185 GTGCAAGCTTACTAGTACGCC 59.075 52.381 23.51 11.96 31.53 5.68
447 449 1.822990 TGCAAGCTTACTAGTACGCCT 59.177 47.619 23.51 11.55 31.53 5.52
448 450 3.018856 TGCAAGCTTACTAGTACGCCTA 58.981 45.455 23.51 8.51 31.53 3.93
449 451 3.444742 TGCAAGCTTACTAGTACGCCTAA 59.555 43.478 23.51 8.22 31.53 2.69
450 452 4.098960 TGCAAGCTTACTAGTACGCCTAAT 59.901 41.667 23.51 6.43 31.53 1.73
451 453 5.300034 TGCAAGCTTACTAGTACGCCTAATA 59.700 40.000 23.51 7.92 31.53 0.98
452 454 6.183360 TGCAAGCTTACTAGTACGCCTAATAA 60.183 38.462 23.51 6.42 31.53 1.40
453 455 6.698766 GCAAGCTTACTAGTACGCCTAATAAA 59.301 38.462 23.51 0.00 31.53 1.40
454 456 7.096147 GCAAGCTTACTAGTACGCCTAATAAAG 60.096 40.741 23.51 8.64 31.53 1.85
455 457 6.445475 AGCTTACTAGTACGCCTAATAAAGC 58.555 40.000 23.51 16.73 36.21 3.51
456 458 6.040166 AGCTTACTAGTACGCCTAATAAAGCA 59.960 38.462 23.51 0.00 37.27 3.91
457 459 6.698766 GCTTACTAGTACGCCTAATAAAGCAA 59.301 38.462 18.19 0.00 36.11 3.91
460 462 9.603921 TTACTAGTACGCCTAATAAAGCAAATT 57.396 29.630 0.91 0.00 0.00 1.82
461 463 8.139521 ACTAGTACGCCTAATAAAGCAAATTC 57.860 34.615 0.00 0.00 0.00 2.17
462 464 6.995511 AGTACGCCTAATAAAGCAAATTCA 57.004 33.333 0.00 0.00 0.00 2.57
463 465 7.385778 AGTACGCCTAATAAAGCAAATTCAA 57.614 32.000 0.00 0.00 0.00 2.69
465 467 6.267496 ACGCCTAATAAAGCAAATTCAACT 57.733 33.333 0.00 0.00 0.00 3.16
468 470 7.094549 ACGCCTAATAAAGCAAATTCAACTGTA 60.095 33.333 0.00 0.00 0.00 2.74
469 471 7.915397 CGCCTAATAAAGCAAATTCAACTGTAT 59.085 33.333 0.00 0.00 0.00 2.29
470 472 9.586435 GCCTAATAAAGCAAATTCAACTGTATT 57.414 29.630 0.00 0.00 30.70 1.89
475 477 7.481275 AAAGCAAATTCAACTGTATTTGGTG 57.519 32.000 20.15 2.56 45.75 4.17
476 478 4.990426 AGCAAATTCAACTGTATTTGGTGC 59.010 37.500 19.27 9.57 45.21 5.01
477 479 4.990426 GCAAATTCAACTGTATTTGGTGCT 59.010 37.500 17.94 0.00 40.70 4.40
478 480 6.015519 AGCAAATTCAACTGTATTTGGTGCTA 60.016 34.615 19.27 0.00 45.21 3.49
479 481 6.813152 GCAAATTCAACTGTATTTGGTGCTAT 59.187 34.615 17.94 0.00 40.70 2.97
480 482 7.973388 GCAAATTCAACTGTATTTGGTGCTATA 59.027 33.333 17.94 0.00 40.70 1.31
481 483 9.507280 CAAATTCAACTGTATTTGGTGCTATAG 57.493 33.333 11.78 0.00 38.39 1.31
482 484 7.807977 ATTCAACTGTATTTGGTGCTATAGG 57.192 36.000 1.04 0.00 0.00 2.57
483 485 5.123227 TCAACTGTATTTGGTGCTATAGGC 58.877 41.667 1.04 0.00 42.22 3.93
485 487 3.134081 ACTGTATTTGGTGCTATAGGCGT 59.866 43.478 1.04 0.00 45.43 5.68
486 488 3.724374 TGTATTTGGTGCTATAGGCGTC 58.276 45.455 1.04 0.00 45.43 5.19
487 489 3.133183 TGTATTTGGTGCTATAGGCGTCA 59.867 43.478 1.04 0.00 45.43 4.35
488 490 2.772077 TTTGGTGCTATAGGCGTCAA 57.228 45.000 1.04 1.14 45.43 3.18
489 491 2.772077 TTGGTGCTATAGGCGTCAAA 57.228 45.000 1.04 0.00 45.43 2.69
490 492 3.275617 TTGGTGCTATAGGCGTCAAAT 57.724 42.857 1.04 0.00 45.43 2.32
491 493 4.409718 TTGGTGCTATAGGCGTCAAATA 57.590 40.909 1.04 0.00 45.43 1.40
492 494 4.617253 TGGTGCTATAGGCGTCAAATAT 57.383 40.909 1.04 0.00 45.43 1.28
493 495 4.314961 TGGTGCTATAGGCGTCAAATATG 58.685 43.478 1.04 0.00 45.43 1.78
494 496 4.202315 TGGTGCTATAGGCGTCAAATATGT 60.202 41.667 1.04 0.00 45.43 2.29
495 497 4.755123 GGTGCTATAGGCGTCAAATATGTT 59.245 41.667 1.04 0.00 45.43 2.71
496 498 5.238650 GGTGCTATAGGCGTCAAATATGTTT 59.761 40.000 1.04 0.00 45.43 2.83
497 499 6.136071 GTGCTATAGGCGTCAAATATGTTTG 58.864 40.000 8.53 8.53 43.76 2.93
498 500 5.820423 TGCTATAGGCGTCAAATATGTTTGT 59.180 36.000 13.78 0.00 43.33 2.83
499 501 6.018262 TGCTATAGGCGTCAAATATGTTTGTC 60.018 38.462 13.78 8.19 43.33 3.18
500 502 6.018262 GCTATAGGCGTCAAATATGTTTGTCA 60.018 38.462 13.78 0.00 44.03 3.58
501 503 6.942532 ATAGGCGTCAAATATGTTTGTCAT 57.057 33.333 13.78 6.08 44.03 3.06
502 504 4.985413 AGGCGTCAAATATGTTTGTCATG 58.015 39.130 13.78 3.73 44.03 3.07
503 505 3.547468 GGCGTCAAATATGTTTGTCATGC 59.453 43.478 13.78 11.96 44.03 4.06
504 506 4.414852 GCGTCAAATATGTTTGTCATGCT 58.585 39.130 13.78 0.00 44.03 3.79
505 507 4.858692 GCGTCAAATATGTTTGTCATGCTT 59.141 37.500 13.78 0.00 44.03 3.91
506 508 5.345741 GCGTCAAATATGTTTGTCATGCTTT 59.654 36.000 13.78 0.00 44.03 3.51
507 509 6.526325 GCGTCAAATATGTTTGTCATGCTTTA 59.474 34.615 13.78 0.00 44.03 1.85
508 510 7.220683 GCGTCAAATATGTTTGTCATGCTTTAT 59.779 33.333 13.78 0.00 44.03 1.40
509 511 9.075519 CGTCAAATATGTTTGTCATGCTTTATT 57.924 29.630 13.78 0.00 44.03 1.40
538 540 9.651913 TTTTTCTTCAAATGCTACACTCTTTTT 57.348 25.926 0.00 0.00 0.00 1.94
634 639 6.579666 ATGCTACATTCTTTTTCTCAAGCA 57.420 33.333 0.00 0.00 41.22 3.91
646 651 3.924918 TCTCAAGCACTCACACTAGTC 57.075 47.619 0.00 0.00 0.00 2.59
650 655 3.062763 CAAGCACTCACACTAGTCCAAG 58.937 50.000 0.00 0.00 0.00 3.61
653 658 1.269723 CACTCACACTAGTCCAAGCGA 59.730 52.381 0.00 0.00 0.00 4.93
654 659 1.269998 ACTCACACTAGTCCAAGCGAC 59.730 52.381 0.00 0.00 42.32 5.19
658 663 3.067106 CACACTAGTCCAAGCGACAAAT 58.933 45.455 0.00 0.00 44.66 2.32
659 664 3.067106 ACACTAGTCCAAGCGACAAATG 58.933 45.455 0.00 0.00 44.66 2.32
830 835 2.126965 CGACACGGTCTGACGGTC 60.127 66.667 16.84 14.57 38.39 4.79
831 836 2.900167 CGACACGGTCTGACGGTCA 61.900 63.158 16.84 10.88 38.39 4.02
832 837 1.371389 GACACGGTCTGACGGTCAC 60.371 63.158 16.84 10.67 38.39 3.67
833 838 2.067091 GACACGGTCTGACGGTCACA 62.067 60.000 16.84 0.00 38.39 3.58
882 887 0.105658 TATCTCCTCCTCCAACCCCG 60.106 60.000 0.00 0.00 0.00 5.73
963 969 4.315122 CGACTCGGATCTCGGCGG 62.315 72.222 7.21 0.00 39.77 6.13
983 989 2.040544 GGGTTGCAGTGGTCATCCG 61.041 63.158 0.00 0.00 36.30 4.18
1077 1083 4.308458 TGCGCGCACTGGTAACCT 62.308 61.111 33.09 0.00 0.00 3.50
1088 1094 1.350019 CTGGTAACCTTCCTTTCCGGT 59.650 52.381 0.00 0.00 0.00 5.28
1176 1209 3.623960 TCCGTCCGGCAATATTTTTACTG 59.376 43.478 0.00 0.00 34.68 2.74
1234 1270 2.115348 GCGATGGCAATTCATCAGTG 57.885 50.000 7.63 0.00 42.58 3.66
1241 1277 4.507710 TGGCAATTCATCAGTGAGTAGTC 58.492 43.478 0.00 0.00 35.39 2.59
1245 1281 2.921634 TCATCAGTGAGTAGTCGCAC 57.078 50.000 13.45 0.00 43.01 5.34
1251 1287 2.257371 GAGTAGTCGCACCGCACA 59.743 61.111 0.00 0.00 0.00 4.57
1263 1299 1.393539 CACCGCACACACTGCTTATAC 59.606 52.381 0.00 0.00 44.64 1.47
1277 1313 5.363868 ACTGCTTATACAGATAGTGCTTGGA 59.636 40.000 0.00 0.00 40.25 3.53
1278 1314 6.042552 ACTGCTTATACAGATAGTGCTTGGAT 59.957 38.462 0.00 0.00 40.25 3.41
1445 1481 1.064463 TCCCAAGGAAGCACATGGATC 60.064 52.381 0.00 0.00 34.82 3.36
1513 1549 5.564550 ACCCTATCCAGAATGTATTCATGC 58.435 41.667 7.30 0.00 39.23 4.06
1547 1622 0.607217 CCTGTGATGCTGCTCAACCA 60.607 55.000 0.00 0.00 0.00 3.67
1646 1721 3.075884 GGTAACCAAATAACCTGCGTGA 58.924 45.455 0.00 0.00 0.00 4.35
1693 1772 3.686241 TCATGTCAGTGTCTTATGCTTGC 59.314 43.478 0.00 0.00 0.00 4.01
1769 1953 9.167311 ACAGATAAACATCTTACTGGATTTGTC 57.833 33.333 0.00 0.00 0.00 3.18
1775 1959 9.574516 AAACATCTTACTGGATTTGTCTACTTT 57.425 29.630 0.00 0.00 0.00 2.66
1791 1975 7.134815 TGTCTACTTTCGGTATTACTAATCGC 58.865 38.462 0.00 0.00 0.00 4.58
1931 2115 1.919918 GCGTGCCAATATTGCAAGTTC 59.080 47.619 10.11 0.41 41.06 3.01
2041 2227 7.142680 TCTTTTCCTAAAAACATTAAGCCACG 58.857 34.615 0.00 0.00 31.23 4.94
2055 2241 4.826274 AAGCCACGCATATATAGTCCAT 57.174 40.909 0.00 0.00 0.00 3.41
2056 2242 4.392921 AGCCACGCATATATAGTCCATC 57.607 45.455 0.00 0.00 0.00 3.51
2057 2243 4.026744 AGCCACGCATATATAGTCCATCT 58.973 43.478 0.00 0.00 0.00 2.90
2058 2244 4.098654 AGCCACGCATATATAGTCCATCTC 59.901 45.833 0.00 0.00 0.00 2.75
2059 2245 4.737946 GCCACGCATATATAGTCCATCTCC 60.738 50.000 0.00 0.00 0.00 3.71
2060 2246 4.402474 CCACGCATATATAGTCCATCTCCA 59.598 45.833 0.00 0.00 0.00 3.86
2061 2247 5.451103 CCACGCATATATAGTCCATCTCCAG 60.451 48.000 0.00 0.00 0.00 3.86
2062 2248 5.358160 CACGCATATATAGTCCATCTCCAGA 59.642 44.000 0.00 0.00 0.00 3.86
2063 2249 5.358442 ACGCATATATAGTCCATCTCCAGAC 59.642 44.000 0.00 0.00 0.00 3.51
2064 2250 5.358160 CGCATATATAGTCCATCTCCAGACA 59.642 44.000 0.00 0.00 35.38 3.41
2065 2251 6.459435 CGCATATATAGTCCATCTCCAGACAG 60.459 46.154 0.00 0.00 35.38 3.51
2066 2252 6.183360 GCATATATAGTCCATCTCCAGACAGG 60.183 46.154 0.00 0.00 35.38 4.00
2067 2253 3.981516 ATAGTCCATCTCCAGACAGGA 57.018 47.619 0.00 0.00 46.75 3.86
2068 2254 1.859302 AGTCCATCTCCAGACAGGAC 58.141 55.000 16.89 16.89 45.50 3.85
2069 2255 0.457851 GTCCATCTCCAGACAGGACG 59.542 60.000 12.07 0.00 43.07 4.79
2070 2256 1.142748 CCATCTCCAGACAGGACGC 59.857 63.158 0.00 0.00 43.07 5.19
2071 2257 1.226802 CATCTCCAGACAGGACGCG 60.227 63.158 3.53 3.53 43.07 6.01
2072 2258 2.418910 ATCTCCAGACAGGACGCGG 61.419 63.158 12.47 0.00 43.07 6.46
2073 2259 4.803426 CTCCAGACAGGACGCGGC 62.803 72.222 12.47 7.53 43.07 6.53
2075 2261 4.379243 CCAGACAGGACGCGGCTT 62.379 66.667 13.91 0.00 41.22 4.35
2076 2262 2.357517 CAGACAGGACGCGGCTTT 60.358 61.111 13.91 0.00 0.00 3.51
2077 2263 1.961277 CAGACAGGACGCGGCTTTT 60.961 57.895 13.91 0.00 0.00 2.27
2078 2264 1.227853 AGACAGGACGCGGCTTTTT 60.228 52.632 13.91 0.00 0.00 1.94
2097 2283 2.260844 TTGCTCCTAGGTGCATATGC 57.739 50.000 32.88 21.09 42.86 3.14
2108 2294 3.851620 GCATATGCACCCATTGTCG 57.148 52.632 22.84 0.00 41.59 4.35
2109 2295 1.308047 GCATATGCACCCATTGTCGA 58.692 50.000 22.84 0.00 41.59 4.20
2110 2296 1.675483 GCATATGCACCCATTGTCGAA 59.325 47.619 22.84 0.00 41.59 3.71
2111 2297 2.098934 GCATATGCACCCATTGTCGAAA 59.901 45.455 22.84 0.00 41.59 3.46
2112 2298 3.428725 GCATATGCACCCATTGTCGAAAA 60.429 43.478 22.84 0.00 41.59 2.29
2113 2299 2.723124 ATGCACCCATTGTCGAAAAC 57.277 45.000 0.00 0.00 0.00 2.43
2114 2300 1.393603 TGCACCCATTGTCGAAAACA 58.606 45.000 0.00 0.00 35.59 2.83
2115 2301 1.066303 TGCACCCATTGTCGAAAACAC 59.934 47.619 0.00 0.00 37.70 3.32
2116 2302 1.066303 GCACCCATTGTCGAAAACACA 59.934 47.619 0.00 0.00 37.70 3.72
2117 2303 2.726633 CACCCATTGTCGAAAACACAC 58.273 47.619 0.00 0.00 37.70 3.82
2118 2304 2.098280 CACCCATTGTCGAAAACACACA 59.902 45.455 0.00 0.00 37.70 3.72
2119 2305 2.955660 ACCCATTGTCGAAAACACACAT 59.044 40.909 0.00 0.00 37.70 3.21
2120 2306 3.383185 ACCCATTGTCGAAAACACACATT 59.617 39.130 0.00 0.00 37.70 2.71
2121 2307 4.142049 ACCCATTGTCGAAAACACACATTT 60.142 37.500 0.00 0.00 37.70 2.32
2122 2308 4.808364 CCCATTGTCGAAAACACACATTTT 59.192 37.500 0.00 0.00 37.70 1.82
2123 2309 5.276773 CCCATTGTCGAAAACACACATTTTG 60.277 40.000 0.00 0.00 37.70 2.44
2124 2310 5.518128 CCATTGTCGAAAACACACATTTTGA 59.482 36.000 0.00 0.00 37.70 2.69
2125 2311 6.035435 CCATTGTCGAAAACACACATTTTGAA 59.965 34.615 0.00 0.00 37.70 2.69
2126 2312 7.412346 CCATTGTCGAAAACACACATTTTGAAA 60.412 33.333 0.00 0.00 37.70 2.69
2127 2313 7.408132 TTGTCGAAAACACACATTTTGAAAA 57.592 28.000 0.00 0.00 37.70 2.29
2128 2314 7.043454 TGTCGAAAACACACATTTTGAAAAG 57.957 32.000 0.00 0.00 33.22 2.27
2129 2315 6.642950 TGTCGAAAACACACATTTTGAAAAGT 59.357 30.769 0.00 0.00 33.22 2.66
2130 2316 7.169982 TGTCGAAAACACACATTTTGAAAAGTT 59.830 29.630 0.00 0.00 33.22 2.66
2131 2317 7.474025 GTCGAAAACACACATTTTGAAAAGTTG 59.526 33.333 0.00 0.00 33.22 3.16
2132 2318 7.382488 TCGAAAACACACATTTTGAAAAGTTGA 59.618 29.630 7.93 0.00 31.90 3.18
2133 2319 8.006590 CGAAAACACACATTTTGAAAAGTTGAA 58.993 29.630 7.93 0.00 31.90 2.69
2134 2320 9.657121 GAAAACACACATTTTGAAAAGTTGAAA 57.343 25.926 7.93 0.00 31.90 2.69
2140 2326 9.838975 ACACATTTTGAAAAGTTGAAAAATTCC 57.161 25.926 7.93 0.00 30.03 3.01
2141 2327 9.288124 CACATTTTGAAAAGTTGAAAAATTCCC 57.712 29.630 0.00 0.00 30.03 3.97
2142 2328 9.241919 ACATTTTGAAAAGTTGAAAAATTCCCT 57.758 25.926 0.00 0.00 30.03 4.20
2146 2332 9.905171 TTTGAAAAGTTGAAAAATTCCCTTTTG 57.095 25.926 15.97 0.00 38.66 2.44
2147 2333 7.534282 TGAAAAGTTGAAAAATTCCCTTTTGC 58.466 30.769 15.97 11.01 38.66 3.68
2148 2334 7.392953 TGAAAAGTTGAAAAATTCCCTTTTGCT 59.607 29.630 15.97 1.41 38.66 3.91
2149 2335 6.925610 AAGTTGAAAAATTCCCTTTTGCTC 57.074 33.333 0.00 0.00 37.14 4.26
2150 2336 5.368145 AGTTGAAAAATTCCCTTTTGCTCC 58.632 37.500 0.00 0.00 37.14 4.70
2151 2337 5.130975 AGTTGAAAAATTCCCTTTTGCTCCT 59.869 36.000 0.00 0.00 37.14 3.69
2152 2338 6.326323 AGTTGAAAAATTCCCTTTTGCTCCTA 59.674 34.615 0.00 0.00 37.14 2.94
2153 2339 6.096673 TGAAAAATTCCCTTTTGCTCCTAC 57.903 37.500 0.00 0.00 37.14 3.18
2154 2340 4.783764 AAAATTCCCTTTTGCTCCTACG 57.216 40.909 0.00 0.00 35.71 3.51
2155 2341 3.434940 AATTCCCTTTTGCTCCTACGT 57.565 42.857 0.00 0.00 0.00 3.57
2156 2342 2.178912 TTCCCTTTTGCTCCTACGTG 57.821 50.000 0.00 0.00 0.00 4.49
2157 2343 0.321298 TCCCTTTTGCTCCTACGTGC 60.321 55.000 0.00 0.00 0.00 5.34
2158 2344 0.605319 CCCTTTTGCTCCTACGTGCA 60.605 55.000 0.00 0.00 36.73 4.57
2159 2345 1.453155 CCTTTTGCTCCTACGTGCAT 58.547 50.000 0.00 0.00 38.24 3.96
2160 2346 2.627945 CCTTTTGCTCCTACGTGCATA 58.372 47.619 0.00 0.00 38.24 3.14
2161 2347 3.206150 CCTTTTGCTCCTACGTGCATAT 58.794 45.455 0.00 0.00 38.24 1.78
2162 2348 3.002656 CCTTTTGCTCCTACGTGCATATG 59.997 47.826 0.00 0.00 38.24 1.78
2163 2349 1.581934 TTGCTCCTACGTGCATATGC 58.418 50.000 21.09 21.09 38.24 3.14
2176 2362 2.462889 GCATATGCACCCATTGTTTCG 58.537 47.619 22.84 0.00 41.59 3.46
2177 2363 2.098934 GCATATGCACCCATTGTTTCGA 59.901 45.455 22.84 0.00 41.59 3.71
2178 2364 3.694734 CATATGCACCCATTGTTTCGAC 58.305 45.455 0.00 0.00 32.85 4.20
2179 2365 1.614996 ATGCACCCATTGTTTCGACA 58.385 45.000 0.00 0.00 0.00 4.35
2180 2366 1.393603 TGCACCCATTGTTTCGACAA 58.606 45.000 0.00 0.00 0.00 3.18
2181 2367 1.959985 TGCACCCATTGTTTCGACAAT 59.040 42.857 0.00 0.00 40.59 2.71
2187 2373 2.723124 ATTGTTTCGACAATGGGTGC 57.277 45.000 4.14 0.00 38.72 5.01
2188 2374 1.393603 TTGTTTCGACAATGGGTGCA 58.606 45.000 0.00 0.00 0.00 4.57
2189 2375 1.614996 TGTTTCGACAATGGGTGCAT 58.385 45.000 0.00 0.00 0.00 3.96
2190 2376 2.784347 TGTTTCGACAATGGGTGCATA 58.216 42.857 0.00 0.00 0.00 3.14
2191 2377 3.351740 TGTTTCGACAATGGGTGCATAT 58.648 40.909 0.00 0.00 0.00 1.78
2192 2378 3.128415 TGTTTCGACAATGGGTGCATATG 59.872 43.478 0.00 0.00 0.00 1.78
2193 2379 1.308047 TCGACAATGGGTGCATATGC 58.692 50.000 21.09 21.09 42.50 3.14
2205 2391 2.260844 GCATATGCACCTAGGAGCAA 57.739 50.000 33.23 22.94 44.05 3.91
2206 2392 2.575532 GCATATGCACCTAGGAGCAAA 58.424 47.619 33.23 15.09 44.05 3.68
2207 2393 2.951642 GCATATGCACCTAGGAGCAAAA 59.048 45.455 33.23 24.84 44.05 2.44
2208 2394 3.381272 GCATATGCACCTAGGAGCAAAAA 59.619 43.478 33.23 22.64 44.05 1.94
2714 2900 3.566351 CTGGAAAAAGAAGAGGGTGGTT 58.434 45.455 0.00 0.00 0.00 3.67
2734 2920 0.882927 GTCACAAGCAAGTACGCCCA 60.883 55.000 0.00 0.00 0.00 5.36
2746 2932 1.881324 GTACGCCCAGCTTTTGGTTTA 59.119 47.619 0.00 0.00 46.25 2.01
2749 2935 2.367241 ACGCCCAGCTTTTGGTTTAAAT 59.633 40.909 0.00 0.00 46.25 1.40
2762 2948 5.590530 TGGTTTAAATCACAAGCAACTGT 57.409 34.783 0.00 0.00 0.00 3.55
2933 3120 6.647334 TGCACAAGTTCTTCCATAATCAAA 57.353 33.333 0.00 0.00 0.00 2.69
2982 3169 6.545666 TGTTCAGAACACAAACCATGTAGAAT 59.454 34.615 12.24 0.00 41.46 2.40
2983 3170 7.717436 TGTTCAGAACACAAACCATGTAGAATA 59.283 33.333 12.24 0.00 41.46 1.75
2984 3171 7.667043 TCAGAACACAAACCATGTAGAATAC 57.333 36.000 0.00 0.00 41.46 1.89
2985 3172 7.450074 TCAGAACACAAACCATGTAGAATACT 58.550 34.615 0.00 0.00 43.54 2.12
2986 3173 7.602644 TCAGAACACAAACCATGTAGAATACTC 59.397 37.037 0.00 0.00 43.54 2.59
2987 3174 6.879458 AGAACACAAACCATGTAGAATACTCC 59.121 38.462 0.00 0.00 43.54 3.85
2988 3175 6.374417 ACACAAACCATGTAGAATACTCCT 57.626 37.500 0.00 0.00 43.54 3.69
2989 3176 7.490657 ACACAAACCATGTAGAATACTCCTA 57.509 36.000 0.00 0.00 43.54 2.94
2990 3177 8.090788 ACACAAACCATGTAGAATACTCCTAT 57.909 34.615 0.00 0.00 43.54 2.57
2991 3178 7.987458 ACACAAACCATGTAGAATACTCCTATG 59.013 37.037 0.00 0.00 43.54 2.23
2992 3179 7.987458 CACAAACCATGTAGAATACTCCTATGT 59.013 37.037 0.00 0.00 43.54 2.29
2993 3180 8.204836 ACAAACCATGTAGAATACTCCTATGTC 58.795 37.037 0.00 0.00 43.54 3.06
2994 3181 6.919775 ACCATGTAGAATACTCCTATGTCC 57.080 41.667 0.00 0.00 43.54 4.02
3013 3200 6.566079 TGTCCTATCAGAAATCACCTGATT 57.434 37.500 10.39 0.00 46.03 2.57
3016 3203 7.147426 TGTCCTATCAGAAATCACCTGATTGAT 60.147 37.037 10.39 4.26 46.03 2.57
3155 3392 8.836268 TGTTGTTAATGATAGACCTTTTACGT 57.164 30.769 0.00 0.00 0.00 3.57
3206 3447 3.982701 TCATTTCAACAAATTGCGCTCTG 59.017 39.130 9.73 2.86 35.63 3.35
3207 3448 1.769733 TTCAACAAATTGCGCTCTGC 58.230 45.000 9.73 0.00 46.70 4.26
3236 3477 5.747565 TCGTGCAAGATGTTTAAAGTTGAG 58.252 37.500 0.00 0.00 0.00 3.02
3360 3605 4.476846 TCATGAAGGGGAAAATAGGCTACA 59.523 41.667 0.00 0.00 0.00 2.74
3391 3652 2.762535 TACTAGAACAGGCAGCAACC 57.237 50.000 0.00 0.00 0.00 3.77
3439 3700 2.896685 TGTAAGTTGATTTTGGCAGGGG 59.103 45.455 0.00 0.00 0.00 4.79
3457 3718 0.179097 GGCCCTTGCACAAACGAAAA 60.179 50.000 0.00 0.00 40.13 2.29
3597 3858 6.455647 CCATAGCTCGAACCTGTATCAAATA 58.544 40.000 0.00 0.00 0.00 1.40
3598 3859 6.929049 CCATAGCTCGAACCTGTATCAAATAA 59.071 38.462 0.00 0.00 0.00 1.40
3757 4020 4.933400 AGATTTGATGGTGCTTGCAATTTC 59.067 37.500 0.00 0.00 0.00 2.17
3783 4046 5.181811 TGACACTGCAAGAAATTCCATACAG 59.818 40.000 0.00 0.00 37.43 2.74
3809 4072 7.566760 AATGACATACTGAAACAGTGAAACA 57.433 32.000 13.62 9.34 45.01 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.370584 TGAGAGGTATCATCCATTCCATGTT 59.629 40.000 0.00 0.00 0.00 2.71
8 9 4.909695 TGAGAGGTATCATCCATTCCATGT 59.090 41.667 0.00 0.00 0.00 3.21
17 18 7.556844 TCAAACTTAAGTGAGAGGTATCATCC 58.443 38.462 9.34 0.00 0.00 3.51
128 130 7.524065 ACAAGTTATAAAGGCAATACGAACAC 58.476 34.615 0.00 0.00 0.00 3.32
242 244 6.861065 AGATTAATAAAGCCACCATACACG 57.139 37.500 0.00 0.00 0.00 4.49
273 275 9.869844 GCATTCAAGATCACTAACATGTAATAC 57.130 33.333 0.00 0.00 0.00 1.89
343 345 9.852091 AGACATCAATTTTATTTTCTGAGAAGC 57.148 29.630 0.00 0.00 0.00 3.86
374 376 8.367156 ACAAATAATACAATGAGCAAACCAACT 58.633 29.630 0.00 0.00 0.00 3.16
392 394 8.388103 GCACGTCTTGACTAATACACAAATAAT 58.612 33.333 0.00 0.00 0.00 1.28
393 395 7.385478 TGCACGTCTTGACTAATACACAAATAA 59.615 33.333 0.00 0.00 0.00 1.40
394 396 6.869388 TGCACGTCTTGACTAATACACAAATA 59.131 34.615 0.00 0.00 0.00 1.40
395 397 5.699001 TGCACGTCTTGACTAATACACAAAT 59.301 36.000 0.00 0.00 0.00 2.32
397 399 4.623002 TGCACGTCTTGACTAATACACAA 58.377 39.130 0.00 0.00 0.00 3.33
398 400 4.245845 TGCACGTCTTGACTAATACACA 57.754 40.909 0.00 0.00 0.00 3.72
401 403 4.092821 TGCAATGCACGTCTTGACTAATAC 59.907 41.667 2.72 0.00 31.71 1.89
402 404 4.249661 TGCAATGCACGTCTTGACTAATA 58.750 39.130 2.72 0.00 31.71 0.98
403 405 3.073678 TGCAATGCACGTCTTGACTAAT 58.926 40.909 2.72 0.00 31.71 1.73
404 406 2.488952 TGCAATGCACGTCTTGACTAA 58.511 42.857 2.72 0.00 31.71 2.24
406 408 3.005205 TGCAATGCACGTCTTGACT 57.995 47.368 2.72 0.00 31.71 3.41
422 424 1.429463 ACTAGTAAGCTTGCACGTGC 58.571 50.000 33.11 33.11 42.50 5.34
423 425 2.592897 CGTACTAGTAAGCTTGCACGTG 59.407 50.000 17.21 12.28 34.28 4.49
425 427 1.582502 GCGTACTAGTAAGCTTGCACG 59.417 52.381 27.16 17.06 39.20 5.34
426 428 1.925185 GGCGTACTAGTAAGCTTGCAC 59.075 52.381 30.94 16.22 39.82 4.57
428 430 2.580966 AGGCGTACTAGTAAGCTTGC 57.419 50.000 30.94 19.27 39.82 4.01
432 434 6.211515 TGCTTTATTAGGCGTACTAGTAAGC 58.788 40.000 26.70 26.70 39.27 3.09
433 435 8.638685 TTTGCTTTATTAGGCGTACTAGTAAG 57.361 34.615 11.06 11.06 35.90 2.34
434 436 9.603921 AATTTGCTTTATTAGGCGTACTAGTAA 57.396 29.630 3.61 0.00 33.57 2.24
437 439 8.138365 TGAATTTGCTTTATTAGGCGTACTAG 57.862 34.615 0.00 0.00 32.16 2.57
438 440 8.392612 GTTGAATTTGCTTTATTAGGCGTACTA 58.607 33.333 0.00 0.00 0.00 1.82
439 441 6.995511 TGAATTTGCTTTATTAGGCGTACT 57.004 33.333 0.00 0.00 0.00 2.73
441 443 7.094549 ACAGTTGAATTTGCTTTATTAGGCGTA 60.095 33.333 0.00 0.00 0.00 4.42
442 444 6.092748 CAGTTGAATTTGCTTTATTAGGCGT 58.907 36.000 0.00 0.00 0.00 5.68
443 445 6.092748 ACAGTTGAATTTGCTTTATTAGGCG 58.907 36.000 0.00 0.00 0.00 5.52
444 446 9.586435 AATACAGTTGAATTTGCTTTATTAGGC 57.414 29.630 0.00 0.00 0.00 3.93
448 450 9.777297 ACCAAATACAGTTGAATTTGCTTTATT 57.223 25.926 2.74 0.00 40.27 1.40
449 451 9.206870 CACCAAATACAGTTGAATTTGCTTTAT 57.793 29.630 2.74 0.00 40.27 1.40
450 452 7.170658 GCACCAAATACAGTTGAATTTGCTTTA 59.829 33.333 2.74 0.00 40.27 1.85
451 453 6.018016 GCACCAAATACAGTTGAATTTGCTTT 60.018 34.615 2.74 0.00 40.27 3.51
452 454 5.466393 GCACCAAATACAGTTGAATTTGCTT 59.534 36.000 2.74 0.00 40.27 3.91
453 455 4.990426 GCACCAAATACAGTTGAATTTGCT 59.010 37.500 2.74 0.00 40.27 3.91
454 456 4.990426 AGCACCAAATACAGTTGAATTTGC 59.010 37.500 2.74 0.00 40.27 3.68
455 457 9.507280 CTATAGCACCAAATACAGTTGAATTTG 57.493 33.333 1.58 1.58 40.94 2.32
456 458 8.686334 CCTATAGCACCAAATACAGTTGAATTT 58.314 33.333 0.00 0.00 0.00 1.82
457 459 7.201821 GCCTATAGCACCAAATACAGTTGAATT 60.202 37.037 0.00 0.00 42.97 2.17
460 462 5.123227 GCCTATAGCACCAAATACAGTTGA 58.877 41.667 0.00 0.00 42.97 3.18
461 463 4.024893 CGCCTATAGCACCAAATACAGTTG 60.025 45.833 0.00 0.00 44.04 3.16
462 464 4.127171 CGCCTATAGCACCAAATACAGTT 58.873 43.478 0.00 0.00 44.04 3.16
463 465 3.134081 ACGCCTATAGCACCAAATACAGT 59.866 43.478 0.00 0.00 44.04 3.55
465 467 3.133183 TGACGCCTATAGCACCAAATACA 59.867 43.478 0.00 0.00 44.04 2.29
468 470 3.275617 TTGACGCCTATAGCACCAAAT 57.724 42.857 0.00 0.00 44.04 2.32
469 471 2.772077 TTGACGCCTATAGCACCAAA 57.228 45.000 0.00 0.00 44.04 3.28
470 472 2.772077 TTTGACGCCTATAGCACCAA 57.228 45.000 0.00 0.00 44.04 3.67
471 473 4.202315 ACATATTTGACGCCTATAGCACCA 60.202 41.667 0.00 0.00 44.04 4.17
472 474 4.315803 ACATATTTGACGCCTATAGCACC 58.684 43.478 0.00 0.00 44.04 5.01
473 475 5.924475 AACATATTTGACGCCTATAGCAC 57.076 39.130 0.00 0.00 44.04 4.40
538 540 3.185880 ACTAGTGCCTCCTCACCTAAA 57.814 47.619 0.00 0.00 37.68 1.85
541 543 2.031495 AAACTAGTGCCTCCTCACCT 57.969 50.000 0.00 0.00 37.68 4.00
542 544 2.861147 AAAACTAGTGCCTCCTCACC 57.139 50.000 0.00 0.00 37.68 4.02
616 620 5.357878 TGTGAGTGCTTGAGAAAAAGAATGT 59.642 36.000 0.00 0.00 0.00 2.71
634 639 1.269998 GTCGCTTGGACTAGTGTGAGT 59.730 52.381 0.00 0.00 42.62 3.41
646 651 4.328440 TGAACAAAAACATTTGTCGCTTGG 59.672 37.500 7.34 0.00 43.66 3.61
650 655 7.270151 ACAAATTTGAACAAAAACATTTGTCGC 59.730 29.630 24.64 4.46 43.66 5.19
659 664 9.193602 CGTGTGATAACAAATTTGAACAAAAAC 57.806 29.630 24.64 12.88 33.56 2.43
672 677 3.861113 GCTCGTATCCGTGTGATAACAAA 59.139 43.478 0.00 0.00 37.69 2.83
682 687 1.153901 AACCGTGCTCGTATCCGTG 60.154 57.895 7.47 0.00 35.01 4.94
684 689 1.876714 CCAACCGTGCTCGTATCCG 60.877 63.158 7.47 0.00 35.01 4.18
789 794 4.506255 GGGGCTGTGGGGAATCGG 62.506 72.222 0.00 0.00 0.00 4.18
823 828 1.758906 TGAGGTGGTGTGACCGTCA 60.759 57.895 0.00 0.00 42.58 4.35
824 829 1.300697 GTGAGGTGGTGTGACCGTC 60.301 63.158 0.00 0.00 42.58 4.79
825 830 2.803817 GGTGAGGTGGTGTGACCGT 61.804 63.158 0.00 0.00 42.58 4.83
826 831 2.030562 GGTGAGGTGGTGTGACCG 59.969 66.667 0.00 0.00 42.58 4.79
827 832 1.371558 GAGGTGAGGTGGTGTGACC 59.628 63.158 0.00 0.00 39.22 4.02
828 833 0.249911 GTGAGGTGAGGTGGTGTGAC 60.250 60.000 0.00 0.00 0.00 3.67
829 834 1.407656 GGTGAGGTGAGGTGGTGTGA 61.408 60.000 0.00 0.00 0.00 3.58
830 835 1.071471 GGTGAGGTGAGGTGGTGTG 59.929 63.158 0.00 0.00 0.00 3.82
831 836 1.383943 TGGTGAGGTGAGGTGGTGT 60.384 57.895 0.00 0.00 0.00 4.16
832 837 1.071471 GTGGTGAGGTGAGGTGGTG 59.929 63.158 0.00 0.00 0.00 4.17
833 838 2.507854 CGTGGTGAGGTGAGGTGGT 61.508 63.158 0.00 0.00 0.00 4.16
882 887 2.202864 GGAGGCGAGAAGAGCAGC 60.203 66.667 0.00 0.00 36.08 5.25
963 969 1.678970 GATGACCACTGCAACCCCC 60.679 63.158 0.00 0.00 0.00 5.40
974 980 1.313091 CGAGTCCTGACGGATGACCA 61.313 60.000 0.00 0.00 42.43 4.02
978 984 1.517257 GTGCGAGTCCTGACGGATG 60.517 63.158 0.00 0.00 42.43 3.51
983 989 3.649277 ATGGCGTGCGAGTCCTGAC 62.649 63.158 0.00 0.00 0.00 3.51
1077 1083 1.677552 GCCAGAGACCGGAAAGGAA 59.322 57.895 9.46 0.00 45.00 3.36
1176 1209 4.109050 GCTACTGACTGATGAACTACTGC 58.891 47.826 0.00 0.00 0.00 4.40
1234 1270 2.087009 GTGTGCGGTGCGACTACTC 61.087 63.158 0.00 0.00 0.00 2.59
1251 1287 5.860941 AGCACTATCTGTATAAGCAGTGT 57.139 39.130 0.00 0.00 39.26 3.55
1277 1313 3.623703 TCCACAAGCATAAGACATGCAT 58.376 40.909 11.46 0.00 46.77 3.96
1278 1314 3.070476 TCCACAAGCATAAGACATGCA 57.930 42.857 11.46 0.00 46.77 3.96
1354 1390 0.179181 CAGAATGCAGCGCGATGTTT 60.179 50.000 26.61 19.21 0.00 2.83
1445 1481 5.001874 AGCATGGTTATCATCATAGTGCTG 58.998 41.667 0.00 0.00 32.92 4.41
1493 1529 7.660617 AGAACAGCATGAATACATTCTGGATAG 59.339 37.037 12.52 0.00 46.49 2.08
1512 1548 0.654683 CAGGCTATGCGAAGAACAGC 59.345 55.000 0.00 0.00 0.00 4.40
1513 1549 1.662629 CACAGGCTATGCGAAGAACAG 59.337 52.381 0.00 0.00 0.00 3.16
1646 1721 5.300034 TGATCAAATCACAGTCTTTTGCTGT 59.700 36.000 0.00 0.00 46.86 4.40
1693 1772 8.187480 TGGTTATATGAATGAATGTTTTCCACG 58.813 33.333 0.00 0.00 0.00 4.94
1750 1934 9.220767 GAAAGTAGACAAATCCAGTAAGATGTT 57.779 33.333 0.00 0.00 0.00 2.71
1769 1953 7.433131 TGTTGCGATTAGTAATACCGAAAGTAG 59.567 37.037 7.87 0.00 33.42 2.57
1775 1959 4.362279 GGTGTTGCGATTAGTAATACCGA 58.638 43.478 7.87 0.00 43.88 4.69
1791 1975 6.851222 ATAAGAATCTGATTAGCGGTGTTG 57.149 37.500 2.28 0.00 0.00 3.33
1931 2115 1.805945 GTCAGCTGCGGGTAGTTCG 60.806 63.158 9.47 0.00 0.00 3.95
2001 2185 6.149129 AGGAAAAGAATGTTGTCCAGTTTC 57.851 37.500 1.98 0.00 0.00 2.78
2041 2227 6.183360 CCTGTCTGGAGATGGACTATATATGC 60.183 46.154 0.00 0.00 38.35 3.14
2058 2244 3.883744 AAAGCCGCGTCCTGTCTGG 62.884 63.158 4.92 0.00 37.10 3.86
2059 2245 1.507141 AAAAAGCCGCGTCCTGTCTG 61.507 55.000 4.92 0.00 0.00 3.51
2060 2246 1.227853 AAAAAGCCGCGTCCTGTCT 60.228 52.632 4.92 0.00 0.00 3.41
2061 2247 3.340789 AAAAAGCCGCGTCCTGTC 58.659 55.556 4.92 0.00 0.00 3.51
2075 2261 3.381272 GCATATGCACCTAGGAGCAAAAA 59.619 43.478 33.23 22.64 44.05 1.94
2076 2262 2.951642 GCATATGCACCTAGGAGCAAAA 59.048 45.455 33.23 24.84 44.05 2.44
2077 2263 2.575532 GCATATGCACCTAGGAGCAAA 58.424 47.619 33.23 15.09 44.05 3.68
2078 2264 2.260844 GCATATGCACCTAGGAGCAA 57.739 50.000 33.23 22.94 44.05 3.91
2090 2276 1.308047 TCGACAATGGGTGCATATGC 58.692 50.000 21.09 21.09 42.50 3.14
2091 2277 4.104776 GTTTTCGACAATGGGTGCATATG 58.895 43.478 0.00 0.00 0.00 1.78
2092 2278 3.761218 TGTTTTCGACAATGGGTGCATAT 59.239 39.130 0.00 0.00 34.69 1.78
2093 2279 3.057876 GTGTTTTCGACAATGGGTGCATA 60.058 43.478 0.00 0.00 40.65 3.14
2094 2280 1.959985 TGTTTTCGACAATGGGTGCAT 59.040 42.857 0.00 0.00 34.69 3.96
2095 2281 1.066303 GTGTTTTCGACAATGGGTGCA 59.934 47.619 0.00 0.00 40.65 4.57
2096 2282 1.066303 TGTGTTTTCGACAATGGGTGC 59.934 47.619 0.00 0.00 40.65 5.01
2097 2283 2.098280 TGTGTGTTTTCGACAATGGGTG 59.902 45.455 0.00 0.00 40.65 4.61
2098 2284 2.370349 TGTGTGTTTTCGACAATGGGT 58.630 42.857 0.00 0.00 40.65 4.51
2099 2285 3.641437 ATGTGTGTTTTCGACAATGGG 57.359 42.857 0.00 0.00 40.65 4.00
2100 2286 5.518128 TCAAAATGTGTGTTTTCGACAATGG 59.482 36.000 0.00 0.00 40.65 3.16
2101 2287 6.566310 TCAAAATGTGTGTTTTCGACAATG 57.434 33.333 0.00 0.00 40.65 2.82
2102 2288 7.588143 TTTCAAAATGTGTGTTTTCGACAAT 57.412 28.000 0.00 0.00 40.65 2.71
2103 2289 7.169982 ACTTTTCAAAATGTGTGTTTTCGACAA 59.830 29.630 0.00 0.00 40.65 3.18
2104 2290 6.642950 ACTTTTCAAAATGTGTGTTTTCGACA 59.357 30.769 0.00 0.00 35.42 4.35
2105 2291 7.044589 ACTTTTCAAAATGTGTGTTTTCGAC 57.955 32.000 0.00 0.00 0.00 4.20
2106 2292 7.382488 TCAACTTTTCAAAATGTGTGTTTTCGA 59.618 29.630 0.00 0.00 0.00 3.71
2107 2293 7.505646 TCAACTTTTCAAAATGTGTGTTTTCG 58.494 30.769 0.00 0.00 0.00 3.46
2108 2294 9.657121 TTTCAACTTTTCAAAATGTGTGTTTTC 57.343 25.926 0.00 0.00 0.00 2.29
2114 2300 9.838975 GGAATTTTTCAACTTTTCAAAATGTGT 57.161 25.926 0.00 0.00 30.89 3.72
2115 2301 9.288124 GGGAATTTTTCAACTTTTCAAAATGTG 57.712 29.630 0.00 0.00 30.89 3.21
2116 2302 9.241919 AGGGAATTTTTCAACTTTTCAAAATGT 57.758 25.926 0.00 0.00 30.89 2.71
2120 2306 9.905171 CAAAAGGGAATTTTTCAACTTTTCAAA 57.095 25.926 13.95 0.00 41.83 2.69
2121 2307 8.026026 GCAAAAGGGAATTTTTCAACTTTTCAA 58.974 29.630 13.95 0.00 41.83 2.69
2122 2308 7.392953 AGCAAAAGGGAATTTTTCAACTTTTCA 59.607 29.630 13.95 0.00 41.83 2.69
2123 2309 7.761409 AGCAAAAGGGAATTTTTCAACTTTTC 58.239 30.769 13.95 10.95 41.83 2.29
2124 2310 7.148086 GGAGCAAAAGGGAATTTTTCAACTTTT 60.148 33.333 12.29 12.29 43.14 2.27
2125 2311 6.318648 GGAGCAAAAGGGAATTTTTCAACTTT 59.681 34.615 0.00 0.00 39.11 2.66
2126 2312 5.822519 GGAGCAAAAGGGAATTTTTCAACTT 59.177 36.000 0.00 0.00 39.11 2.66
2127 2313 5.130975 AGGAGCAAAAGGGAATTTTTCAACT 59.869 36.000 0.00 0.00 39.11 3.16
2128 2314 5.368145 AGGAGCAAAAGGGAATTTTTCAAC 58.632 37.500 0.00 0.00 39.11 3.18
2129 2315 5.628797 AGGAGCAAAAGGGAATTTTTCAA 57.371 34.783 0.00 0.00 39.11 2.69
2130 2316 5.278758 CGTAGGAGCAAAAGGGAATTTTTCA 60.279 40.000 0.00 0.00 39.11 2.69
2131 2317 5.161358 CGTAGGAGCAAAAGGGAATTTTTC 58.839 41.667 0.00 0.00 39.11 2.29
2132 2318 4.587262 ACGTAGGAGCAAAAGGGAATTTTT 59.413 37.500 0.00 0.00 39.11 1.94
2133 2319 4.022329 CACGTAGGAGCAAAAGGGAATTTT 60.022 41.667 0.00 0.00 41.91 1.82
2134 2320 3.506067 CACGTAGGAGCAAAAGGGAATTT 59.494 43.478 0.00 0.00 0.00 1.82
2135 2321 3.081804 CACGTAGGAGCAAAAGGGAATT 58.918 45.455 0.00 0.00 0.00 2.17
2136 2322 2.711542 CACGTAGGAGCAAAAGGGAAT 58.288 47.619 0.00 0.00 0.00 3.01
2137 2323 1.880646 GCACGTAGGAGCAAAAGGGAA 60.881 52.381 0.00 0.00 32.99 3.97
2138 2324 0.321298 GCACGTAGGAGCAAAAGGGA 60.321 55.000 0.00 0.00 32.99 4.20
2139 2325 0.605319 TGCACGTAGGAGCAAAAGGG 60.605 55.000 5.02 0.00 39.51 3.95
2140 2326 1.453155 ATGCACGTAGGAGCAAAAGG 58.547 50.000 11.45 0.00 44.85 3.11
2141 2327 3.546815 GCATATGCACGTAGGAGCAAAAG 60.547 47.826 22.84 5.72 44.85 2.27
2142 2328 2.354510 GCATATGCACGTAGGAGCAAAA 59.645 45.455 22.84 4.03 44.85 2.44
2143 2329 1.939934 GCATATGCACGTAGGAGCAAA 59.060 47.619 22.84 0.00 44.85 3.68
2144 2330 1.581934 GCATATGCACGTAGGAGCAA 58.418 50.000 22.84 2.63 44.85 3.91
2145 2331 3.289128 GCATATGCACGTAGGAGCA 57.711 52.632 22.84 9.91 45.65 4.26
2156 2342 2.098934 TCGAAACAATGGGTGCATATGC 59.901 45.455 21.09 21.09 42.50 3.14
2157 2343 3.128415 TGTCGAAACAATGGGTGCATATG 59.872 43.478 0.00 0.00 30.70 1.78
2158 2344 3.351740 TGTCGAAACAATGGGTGCATAT 58.648 40.909 0.00 0.00 30.70 1.78
2159 2345 2.784347 TGTCGAAACAATGGGTGCATA 58.216 42.857 0.00 0.00 30.70 3.14
2160 2346 1.614996 TGTCGAAACAATGGGTGCAT 58.385 45.000 0.00 0.00 30.70 3.96
2161 2347 1.393603 TTGTCGAAACAATGGGTGCA 58.606 45.000 0.00 0.00 40.45 4.57
2169 2355 7.838523 GCATATGCACCCATTGTCGAAACAA 62.839 44.000 22.84 0.00 44.23 2.83
2170 2356 1.614996 ATGCACCCATTGTCGAAACA 58.385 45.000 0.00 0.00 0.00 2.83
2171 2357 3.694734 CATATGCACCCATTGTCGAAAC 58.305 45.455 0.00 0.00 32.85 2.78
2172 2358 2.098934 GCATATGCACCCATTGTCGAAA 59.901 45.455 22.84 0.00 41.59 3.46
2173 2359 1.675483 GCATATGCACCCATTGTCGAA 59.325 47.619 22.84 0.00 41.59 3.71
2174 2360 1.308047 GCATATGCACCCATTGTCGA 58.692 50.000 22.84 0.00 41.59 4.20
2175 2361 3.851620 GCATATGCACCCATTGTCG 57.148 52.632 22.84 0.00 41.59 4.35
2186 2372 2.260844 TTGCTCCTAGGTGCATATGC 57.739 50.000 32.88 21.09 42.86 3.14
2205 2391 0.249911 AGACAGAGACGCGGCTTTTT 60.250 50.000 19.64 2.02 0.00 1.94
2206 2392 0.601558 TAGACAGAGACGCGGCTTTT 59.398 50.000 19.64 4.62 0.00 2.27
2207 2393 0.601558 TTAGACAGAGACGCGGCTTT 59.398 50.000 19.64 7.97 0.00 3.51
2208 2394 0.109226 GTTAGACAGAGACGCGGCTT 60.109 55.000 19.64 0.00 0.00 4.35
2209 2395 0.961358 AGTTAGACAGAGACGCGGCT 60.961 55.000 18.34 18.34 0.00 5.52
2210 2396 0.731417 TAGTTAGACAGAGACGCGGC 59.269 55.000 12.47 7.86 0.00 6.53
2211 2397 4.451435 TCATATAGTTAGACAGAGACGCGG 59.549 45.833 12.47 0.00 0.00 6.46
2212 2398 5.177881 ACTCATATAGTTAGACAGAGACGCG 59.822 44.000 3.53 3.53 33.35 6.01
2213 2399 6.548441 ACTCATATAGTTAGACAGAGACGC 57.452 41.667 0.00 0.00 33.35 5.19
2432 2618 7.175641 AGCAGCATTGTTCTAACTGAAACTTAT 59.824 33.333 0.00 0.00 36.30 1.73
2628 2814 5.335897 GGCTCAAATTGAATTAGCTGTGACA 60.336 40.000 11.25 0.00 33.67 3.58
2714 2900 0.882927 GGGCGTACTTGCTTGTGACA 60.883 55.000 0.00 0.00 34.52 3.58
2746 2932 3.953612 TGAGGAACAGTTGCTTGTGATTT 59.046 39.130 8.95 0.00 0.00 2.17
2749 2935 2.288666 GTGAGGAACAGTTGCTTGTGA 58.711 47.619 8.95 0.00 0.00 3.58
2762 2948 3.192422 CCGGTTATTGCAATTGTGAGGAA 59.808 43.478 18.75 0.40 0.00 3.36
2982 3169 7.451877 GGTGATTTCTGATAGGACATAGGAGTA 59.548 40.741 0.00 0.00 0.00 2.59
2983 3170 6.268847 GGTGATTTCTGATAGGACATAGGAGT 59.731 42.308 0.00 0.00 0.00 3.85
2984 3171 6.496565 AGGTGATTTCTGATAGGACATAGGAG 59.503 42.308 0.00 0.00 0.00 3.69
2985 3172 6.268617 CAGGTGATTTCTGATAGGACATAGGA 59.731 42.308 0.00 0.00 34.36 2.94
2986 3173 6.268617 TCAGGTGATTTCTGATAGGACATAGG 59.731 42.308 0.00 0.00 36.46 2.57
2987 3174 7.295322 TCAGGTGATTTCTGATAGGACATAG 57.705 40.000 0.00 0.00 36.46 2.23
2988 3175 7.862274 ATCAGGTGATTTCTGATAGGACATA 57.138 36.000 4.95 0.00 46.52 2.29
2989 3176 6.760440 ATCAGGTGATTTCTGATAGGACAT 57.240 37.500 4.95 0.00 46.52 3.06
3013 3200 5.159273 TGTGAGGCACAGTACATTTATCA 57.841 39.130 0.00 0.00 39.62 2.15
3016 3203 5.312895 ACATTGTGAGGCACAGTACATTTA 58.687 37.500 0.00 0.00 45.39 1.40
3206 3447 1.151668 ACATCTTGCACGAAGACTGC 58.848 50.000 2.15 0.00 43.71 4.40
3207 3448 3.885484 AAACATCTTGCACGAAGACTG 57.115 42.857 2.15 0.00 43.71 3.51
3215 3456 5.173854 GTGCTCAACTTTAAACATCTTGCAC 59.826 40.000 0.00 0.00 38.90 4.57
3360 3605 5.567823 GCCTGTTCTAGTAAGCAGAAAGTCT 60.568 44.000 0.00 0.00 33.95 3.24
3391 3652 5.473066 AGAGGAATTTTGGGATTGTTGTG 57.527 39.130 0.00 0.00 0.00 3.33
3439 3700 1.646189 TTTTTCGTTTGTGCAAGGGC 58.354 45.000 0.00 0.00 41.68 5.19
3457 3718 7.070821 TCGGTTAGATAGGAAATAGAGCCTTTT 59.929 37.037 0.00 0.00 35.73 2.27
3475 3736 6.348213 GCTTTAAAGAAGCAACATCGGTTAGA 60.348 38.462 19.48 0.00 42.56 2.10
3603 3864 3.213206 TGCTGACACTGTTCCTTGATT 57.787 42.857 0.00 0.00 0.00 2.57
3665 3926 7.891498 TCAGTTCTTAGCATACTGGTATGTA 57.109 36.000 18.24 9.43 43.57 2.29
3757 4020 4.508461 TGGAATTTCTTGCAGTGTCATG 57.492 40.909 0.00 0.00 0.00 3.07
3783 4046 8.128582 TGTTTCACTGTTTCAGTATGTCATTTC 58.871 33.333 2.03 0.00 43.43 2.17
3809 4072 6.248433 ACATCCTTGATTTAGTGTTCATGGT 58.752 36.000 0.00 0.00 38.01 3.55


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

AutoCloner maintained by Alex Coulton.