Multiple sequence alignment - TraesCS6B01G201500

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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 TraesCS6B01G201500 chr6B 100.000 3482 0 0 1 3482 245590135 245593616 0.000000e+00 6431.0
1 TraesCS6B01G201500 chr6B 76.740 546 48 44 1 485 347552915 347552388 7.520000e-57 231.0
2 TraesCS6B01G201500 chr6A 93.395 2362 83 25 646 2966 186528312 186530641 0.000000e+00 3430.0
3 TraesCS6B01G201500 chr6A 86.154 195 20 4 313 502 49137037 49137229 1.640000e-48 204.0
4 TraesCS6B01G201500 chr6A 75.641 312 65 6 1654 1965 411628251 411627951 1.010000e-30 145.0
5 TraesCS6B01G201500 chr6A 87.500 64 7 1 597 660 186528231 186528293 4.820000e-09 73.1
6 TraesCS6B01G201500 chr6D 93.202 2236 72 29 527 2725 141589619 141591811 0.000000e+00 3214.0
7 TraesCS6B01G201500 chr6D 82.301 339 27 14 1 308 28267005 28266669 2.670000e-66 263.0
8 TraesCS6B01G201500 chr6D 84.151 265 23 13 228 485 28266670 28266418 4.490000e-59 239.0
9 TraesCS6B01G201500 chr6D 81.868 182 16 9 160 329 468259925 468260101 1.690000e-28 137.0
10 TraesCS6B01G201500 chr3D 87.579 1425 156 8 981 2389 546613747 546612328 0.000000e+00 1631.0
11 TraesCS6B01G201500 chr3D 79.032 372 39 18 1 340 548820687 548821051 5.850000e-53 219.0
12 TraesCS6B01G201500 chr3B 87.368 1425 159 8 981 2389 723613291 723611872 0.000000e+00 1615.0
13 TraesCS6B01G201500 chr3B 91.992 512 21 10 2985 3480 741701513 741701006 0.000000e+00 701.0
14 TraesCS6B01G201500 chr3B 92.121 495 27 8 2997 3480 781840705 781841198 0.000000e+00 688.0
15 TraesCS6B01G201500 chr3B 77.306 542 61 27 2 485 363258471 363257934 2.670000e-66 263.0
16 TraesCS6B01G201500 chr3B 76.007 546 58 33 1 482 715070541 715071077 7.570000e-52 215.0
17 TraesCS6B01G201500 chr3B 85.641 195 21 4 313 502 807805977 807806169 7.620000e-47 198.0
18 TraesCS6B01G201500 chr5B 92.525 495 27 9 2995 3480 159923663 159924156 0.000000e+00 701.0
19 TraesCS6B01G201500 chr5B 91.633 502 24 7 2994 3480 668536901 668536403 0.000000e+00 678.0
20 TraesCS6B01G201500 chr5B 91.417 501 27 11 2995 3480 41397775 41398274 0.000000e+00 673.0
21 TraesCS6B01G201500 chr5B 79.882 507 44 33 1 469 685634149 685634635 5.610000e-83 318.0
22 TraesCS6B01G201500 chr5B 86.154 195 20 4 313 502 480747770 480747578 1.640000e-48 204.0
23 TraesCS6B01G201500 chr5B 83.700 227 20 11 93 304 710419065 710419289 7.620000e-47 198.0
24 TraesCS6B01G201500 chr5B 83.951 81 13 0 2787 2867 1948867 1948947 1.040000e-10 78.7
25 TraesCS6B01G201500 chr1B 92.184 499 28 9 2992 3480 44016898 44017395 0.000000e+00 695.0
26 TraesCS6B01G201500 chr1B 91.749 509 28 12 2982 3480 398155690 398156194 0.000000e+00 695.0
27 TraesCS6B01G201500 chr1B 79.354 557 55 24 1 499 256199878 256200432 1.550000e-88 337.0
28 TraesCS6B01G201500 chr1B 89.732 224 19 3 282 502 666837581 666837359 2.050000e-72 283.0
29 TraesCS6B01G201500 chr1B 80.186 323 33 12 1 293 666845707 666845386 2.720000e-51 213.0
30 TraesCS6B01G201500 chr1B 76.839 367 53 21 160 502 141724509 141724867 9.930000e-41 178.0
31 TraesCS6B01G201500 chr7B 92.016 501 24 13 2995 3480 499638436 499637937 0.000000e+00 689.0
32 TraesCS6B01G201500 chr7B 81.287 171 17 7 1 156 658472735 658472905 1.310000e-24 124.0
33 TraesCS6B01G201500 chr7B 87.778 90 7 3 1 88 721809431 721809344 6.150000e-18 102.0
34 TraesCS6B01G201500 chrUn 92.089 493 32 5 2994 3480 447950806 447951297 0.000000e+00 688.0
35 TraesCS6B01G201500 chr7D 84.198 405 57 6 1973 2374 8005002 8005402 1.520000e-103 387.0
36 TraesCS6B01G201500 chr7D 78.327 526 58 27 1 484 22541943 22541432 4.400000e-74 289.0
37 TraesCS6B01G201500 chr7D 89.401 217 23 0 1459 1675 390933671 390933887 1.230000e-69 274.0
38 TraesCS6B01G201500 chr7D 78.182 385 39 24 1 348 568646039 568645663 1.640000e-48 204.0
39 TraesCS6B01G201500 chr7D 86.517 89 10 2 2787 2874 99458738 99458651 2.860000e-16 97.1
40 TraesCS6B01G201500 chr2D 83.288 371 37 13 1 348 597892942 597892574 5.610000e-83 318.0
41 TraesCS6B01G201500 chr2D 82.078 385 29 22 1 348 641947006 641946625 3.400000e-75 292.0
42 TraesCS6B01G201500 chr1D 76.814 565 56 31 1 500 363858547 363859101 7.460000e-62 248.0
43 TraesCS6B01G201500 chr4A 77.386 482 47 23 1 424 665711157 665711634 2.700000e-56 230.0
44 TraesCS6B01G201500 chr4A 76.423 492 44 38 1 426 668440093 668440578 2.120000e-47 200.0
45 TraesCS6B01G201500 chr4A 77.108 166 27 10 2011 2170 456475072 456475232 6.190000e-13 86.1
46 TraesCS6B01G201500 chr4A 76.506 166 28 10 2011 2170 586728194 586728354 2.880000e-11 80.5
47 TraesCS6B01G201500 chr2B 80.294 340 30 13 1 308 134705249 134704915 4.520000e-54 222.0
48 TraesCS6B01G201500 chr2A 79.063 363 39 19 1 333 715901595 715901950 7.570000e-52 215.0
49 TraesCS6B01G201500 chr2A 79.468 263 19 16 1 230 27354168 27353908 1.670000e-33 154.0
50 TraesCS6B01G201500 chr2A 76.490 302 58 5 1649 1950 499676652 499676940 6.020000e-33 152.0
51 TraesCS6B01G201500 chr2A 76.842 285 54 4 1654 1938 150708104 150708376 2.160000e-32 150.0
52 TraesCS6B01G201500 chr2A 75.000 336 71 5 1630 1965 132784865 132784543 3.620000e-30 143.0
53 TraesCS6B01G201500 chr7A 85.641 195 21 5 313 502 670031266 670031458 7.620000e-47 198.0
54 TraesCS6B01G201500 chr7A 74.747 297 62 6 1654 1950 415359065 415359348 1.700000e-23 121.0
55 TraesCS6B01G201500 chr7A 86.364 88 12 0 1 88 459514573 459514660 2.860000e-16 97.1
56 TraesCS6B01G201500 chr7A 75.843 178 39 4 2006 2181 643993316 643993491 1.720000e-13 87.9
57 TraesCS6B01G201500 chr5D 87.662 154 17 2 5 156 244637141 244636988 9.930000e-41 178.0
58 TraesCS6B01G201500 chr5D 83.951 81 13 0 2787 2867 391879 391799 1.040000e-10 78.7
59 TraesCS6B01G201500 chr3A 76.052 309 62 4 1654 1962 409684272 409684568 2.160000e-32 150.0
60 TraesCS6B01G201500 chr3A 77.037 270 26 13 1 239 16260271 16260535 4.720000e-24 122.0
61 TraesCS6B01G201500 chr1A 74.679 312 58 12 1654 1965 204546015 204545725 6.110000e-23 119.0
62 TraesCS6B01G201500 chr4D 77.500 160 25 10 2017 2170 14830598 14830444 6.190000e-13 86.1
63 TraesCS6B01G201500 chr5A 78.000 150 17 7 1 135 458476634 458476782 2.880000e-11 80.5
64 TraesCS6B01G201500 chr5A 83.951 81 13 0 2787 2867 225607 225687 1.040000e-10 78.7


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 TraesCS6B01G201500 chr6B 245590135 245593616 3481 False 6431.00 6431 100.0000 1 3482 1 chr6B.!!$F1 3481
1 TraesCS6B01G201500 chr6B 347552388 347552915 527 True 231.00 231 76.7400 1 485 1 chr6B.!!$R1 484
2 TraesCS6B01G201500 chr6A 186528231 186530641 2410 False 1751.55 3430 90.4475 597 2966 2 chr6A.!!$F2 2369
3 TraesCS6B01G201500 chr6D 141589619 141591811 2192 False 3214.00 3214 93.2020 527 2725 1 chr6D.!!$F1 2198
4 TraesCS6B01G201500 chr6D 28266418 28267005 587 True 251.00 263 83.2260 1 485 2 chr6D.!!$R1 484
5 TraesCS6B01G201500 chr3D 546612328 546613747 1419 True 1631.00 1631 87.5790 981 2389 1 chr3D.!!$R1 1408
6 TraesCS6B01G201500 chr3B 723611872 723613291 1419 True 1615.00 1615 87.3680 981 2389 1 chr3B.!!$R2 1408
7 TraesCS6B01G201500 chr3B 741701006 741701513 507 True 701.00 701 91.9920 2985 3480 1 chr3B.!!$R3 495
8 TraesCS6B01G201500 chr3B 363257934 363258471 537 True 263.00 263 77.3060 2 485 1 chr3B.!!$R1 483
9 TraesCS6B01G201500 chr3B 715070541 715071077 536 False 215.00 215 76.0070 1 482 1 chr3B.!!$F1 481
10 TraesCS6B01G201500 chr1B 398155690 398156194 504 False 695.00 695 91.7490 2982 3480 1 chr1B.!!$F4 498
11 TraesCS6B01G201500 chr1B 256199878 256200432 554 False 337.00 337 79.3540 1 499 1 chr1B.!!$F3 498
12 TraesCS6B01G201500 chr7D 22541432 22541943 511 True 289.00 289 78.3270 1 484 1 chr7D.!!$R1 483
13 TraesCS6B01G201500 chr1D 363858547 363859101 554 False 248.00 248 76.8140 1 500 1 chr1D.!!$F1 499

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
491 612 0.029300 CCGCGCCAAACCTTATGATG 59.971 55.0 0.00 0.00 0.00 3.07 F
779 952 0.042448 GACGGCACAAAACTGTCGAC 60.042 55.0 9.11 9.11 41.96 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1864 1.216977 CGACGCCTTGTGGATGGTA 59.783 57.895 0.0 0.0 34.57 3.25 R
2634 2862 0.107654 ATGGACTTCAGTTAGGCGGC 60.108 55.000 0.0 0.0 0.00 6.53 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
55 56 2.888464 CTACTGGGCGGAGAGGACGA 62.888 65.000 0.00 0.00 0.00 4.20
64 65 3.282745 GAGAGGACGACAAGGCGCA 62.283 63.158 10.83 0.00 33.86 6.09
129 145 0.843309 TTGAAGCAGGTGGGAAGTCA 59.157 50.000 0.00 0.00 0.00 3.41
145 161 4.322080 AAGTCAATCTTCACGACAGACA 57.678 40.909 0.00 0.00 33.51 3.41
213 247 1.816835 TGATGCGACTCGGAGTAGTTT 59.183 47.619 17.66 7.30 0.00 2.66
222 256 3.195825 ACTCGGAGTAGTTTTAGCTGCAT 59.804 43.478 9.33 0.00 0.00 3.96
241 276 4.738252 TGCATCGTAGTTTATCTAGTTGCG 59.262 41.667 0.00 0.00 32.20 4.85
242 277 4.738740 GCATCGTAGTTTATCTAGTTGCGT 59.261 41.667 0.00 0.00 0.00 5.24
244 279 4.913376 TCGTAGTTTATCTAGTTGCGTCC 58.087 43.478 0.00 0.00 0.00 4.79
251 286 7.384477 AGTTTATCTAGTTGCGTCCTAGTTTT 58.616 34.615 0.00 0.00 34.72 2.43
252 287 8.526147 AGTTTATCTAGTTGCGTCCTAGTTTTA 58.474 33.333 0.00 0.00 34.72 1.52
257 292 8.248117 TCTAGTTGCGTCCTAGTTTTAATTTC 57.752 34.615 0.00 0.00 34.72 2.17
271 318 7.721402 AGTTTTAATTTCATGTAGTTGCACCA 58.279 30.769 0.00 0.00 0.00 4.17
279 326 5.178061 TCATGTAGTTGCACCATAGTTCTG 58.822 41.667 0.00 0.00 0.00 3.02
387 508 1.333308 TCAAATATGAACATGCGCGGG 59.667 47.619 8.83 0.00 30.99 6.13
388 509 0.030638 AAATATGAACATGCGCGGGC 59.969 50.000 18.81 18.81 40.52 6.13
389 510 0.819259 AATATGAACATGCGCGGGCT 60.819 50.000 25.62 4.62 40.82 5.19
390 511 1.509644 ATATGAACATGCGCGGGCTG 61.510 55.000 25.62 21.06 40.82 4.85
411 532 2.873851 GCGCGCGCTGCATTTTAA 60.874 55.556 44.38 0.00 46.97 1.52
412 533 2.979036 CGCGCGCTGCATTTTAAC 59.021 55.556 30.48 0.00 46.97 2.01
413 534 1.511887 CGCGCGCTGCATTTTAACT 60.512 52.632 30.48 0.00 46.97 2.24
414 535 1.455908 CGCGCGCTGCATTTTAACTC 61.456 55.000 30.48 0.00 46.97 3.01
415 536 1.455908 GCGCGCTGCATTTTAACTCG 61.456 55.000 26.67 0.00 45.45 4.18
416 537 1.455908 CGCGCTGCATTTTAACTCGC 61.456 55.000 5.56 0.00 38.00 5.03
417 538 1.133946 GCGCTGCATTTTAACTCGCC 61.134 55.000 0.00 0.00 35.71 5.54
418 539 0.857311 CGCTGCATTTTAACTCGCCG 60.857 55.000 0.00 0.00 0.00 6.46
419 540 1.133946 GCTGCATTTTAACTCGCCGC 61.134 55.000 0.00 0.00 0.00 6.53
420 541 0.447801 CTGCATTTTAACTCGCCGCT 59.552 50.000 0.00 0.00 0.00 5.52
421 542 0.167908 TGCATTTTAACTCGCCGCTG 59.832 50.000 0.00 0.00 0.00 5.18
422 543 0.523335 GCATTTTAACTCGCCGCTGG 60.523 55.000 0.00 0.00 0.00 4.85
423 544 1.083489 CATTTTAACTCGCCGCTGGA 58.917 50.000 0.00 0.00 0.00 3.86
424 545 1.062587 CATTTTAACTCGCCGCTGGAG 59.937 52.381 0.00 0.00 37.54 3.86
425 546 1.296056 TTTTAACTCGCCGCTGGAGC 61.296 55.000 0.00 0.00 34.87 4.70
426 547 2.167398 TTTAACTCGCCGCTGGAGCT 62.167 55.000 0.00 0.00 39.32 4.09
427 548 2.835701 TTAACTCGCCGCTGGAGCTG 62.836 60.000 0.00 0.00 39.32 4.24
436 557 4.081030 CTGGAGCTGCGCGTGTTG 62.081 66.667 8.43 0.00 0.00 3.33
437 558 4.908687 TGGAGCTGCGCGTGTTGT 62.909 61.111 8.43 0.00 0.00 3.32
438 559 2.736995 GGAGCTGCGCGTGTTGTA 60.737 61.111 8.43 0.00 0.00 2.41
439 560 2.100631 GGAGCTGCGCGTGTTGTAT 61.101 57.895 8.43 0.00 0.00 2.29
440 561 1.635663 GGAGCTGCGCGTGTTGTATT 61.636 55.000 8.43 0.00 0.00 1.89
441 562 0.165944 GAGCTGCGCGTGTTGTATTT 59.834 50.000 8.43 0.00 0.00 1.40
442 563 0.591170 AGCTGCGCGTGTTGTATTTT 59.409 45.000 8.43 0.00 0.00 1.82
443 564 1.801771 AGCTGCGCGTGTTGTATTTTA 59.198 42.857 8.43 0.00 0.00 1.52
444 565 2.159707 AGCTGCGCGTGTTGTATTTTAG 60.160 45.455 8.43 0.00 0.00 1.85
445 566 2.166007 CTGCGCGTGTTGTATTTTAGC 58.834 47.619 8.43 0.00 0.00 3.09
447 568 1.168588 CGCGTGTTGTATTTTAGCGC 58.831 50.000 0.00 0.00 39.68 5.92
448 569 1.168588 GCGTGTTGTATTTTAGCGCG 58.831 50.000 0.00 0.00 34.34 6.86
449 570 1.793113 CGTGTTGTATTTTAGCGCGG 58.207 50.000 8.83 0.00 0.00 6.46
450 571 1.530856 GTGTTGTATTTTAGCGCGGC 58.469 50.000 8.83 0.00 0.00 6.53
451 572 1.129811 GTGTTGTATTTTAGCGCGGCT 59.870 47.619 8.83 8.38 43.41 5.52
452 573 1.129624 TGTTGTATTTTAGCGCGGCTG 59.870 47.619 8.83 0.00 40.10 4.85
453 574 0.098025 TTGTATTTTAGCGCGGCTGC 59.902 50.000 8.83 7.70 40.10 5.25
455 576 0.316196 GTATTTTAGCGCGGCTGCTG 60.316 55.000 22.96 10.42 46.70 4.41
456 577 1.436195 TATTTTAGCGCGGCTGCTGG 61.436 55.000 22.96 1.40 46.70 4.85
457 578 3.770371 TATTTTAGCGCGGCTGCTGGA 62.770 52.381 22.96 12.50 46.70 3.86
458 579 4.819761 TTAGCGCGGCTGCTGGAG 62.820 66.667 22.96 0.14 46.70 3.86
463 584 3.426568 GCGGCTGCTGGAGTCAAC 61.427 66.667 11.21 0.00 38.39 3.18
464 585 3.114616 CGGCTGCTGGAGTCAACG 61.115 66.667 0.83 0.00 0.00 4.10
465 586 2.031163 GGCTGCTGGAGTCAACGT 59.969 61.111 0.00 0.00 0.00 3.99
466 587 1.598130 GGCTGCTGGAGTCAACGTT 60.598 57.895 0.00 0.00 0.00 3.99
467 588 1.571460 GCTGCTGGAGTCAACGTTG 59.429 57.895 22.35 22.35 0.00 4.10
468 589 1.160329 GCTGCTGGAGTCAACGTTGT 61.160 55.000 26.47 9.72 0.00 3.32
469 590 0.583438 CTGCTGGAGTCAACGTTGTG 59.417 55.000 26.47 4.36 0.00 3.33
470 591 1.279840 GCTGGAGTCAACGTTGTGC 59.720 57.895 26.47 19.75 0.00 4.57
472 593 2.248431 GGAGTCAACGTTGTGCGC 59.752 61.111 26.47 20.35 46.11 6.09
473 594 2.248431 GAGTCAACGTTGTGCGCC 59.752 61.111 26.47 14.02 46.11 6.53
474 595 3.558282 GAGTCAACGTTGTGCGCCG 62.558 63.158 26.47 2.99 46.11 6.46
487 608 3.505184 CGCCGCGCCAAACCTTAT 61.505 61.111 0.00 0.00 0.00 1.73
488 609 2.102161 GCCGCGCCAAACCTTATG 59.898 61.111 0.00 0.00 0.00 1.90
489 610 2.403378 GCCGCGCCAAACCTTATGA 61.403 57.895 0.00 0.00 0.00 2.15
490 611 1.724582 GCCGCGCCAAACCTTATGAT 61.725 55.000 0.00 0.00 0.00 2.45
491 612 0.029300 CCGCGCCAAACCTTATGATG 59.971 55.000 0.00 0.00 0.00 3.07
492 613 1.013596 CGCGCCAAACCTTATGATGA 58.986 50.000 0.00 0.00 0.00 2.92
493 614 1.003545 CGCGCCAAACCTTATGATGAG 60.004 52.381 0.00 0.00 0.00 2.90
494 615 1.268743 GCGCCAAACCTTATGATGAGC 60.269 52.381 0.00 0.00 0.00 4.26
495 616 1.003545 CGCCAAACCTTATGATGAGCG 60.004 52.381 0.00 0.00 34.70 5.03
496 617 1.268743 GCCAAACCTTATGATGAGCGC 60.269 52.381 0.00 0.00 0.00 5.92
497 618 1.003545 CCAAACCTTATGATGAGCGCG 60.004 52.381 0.00 0.00 0.00 6.86
498 619 0.657840 AAACCTTATGATGAGCGCGC 59.342 50.000 26.66 26.66 0.00 6.86
499 620 1.160329 AACCTTATGATGAGCGCGCC 61.160 55.000 30.33 19.97 0.00 6.53
500 621 2.661566 CCTTATGATGAGCGCGCCG 61.662 63.158 30.33 4.78 0.00 6.46
521 642 4.445545 GTTGCGCGGCTTTCGGAG 62.446 66.667 8.83 0.00 39.69 4.63
522 643 4.673298 TTGCGCGGCTTTCGGAGA 62.673 61.111 8.83 0.00 39.69 3.71
523 644 3.950794 TTGCGCGGCTTTCGGAGAT 62.951 57.895 8.83 0.00 39.69 2.75
524 645 3.929948 GCGCGGCTTTCGGAGATG 61.930 66.667 8.83 0.00 39.69 2.90
525 646 3.929948 CGCGGCTTTCGGAGATGC 61.930 66.667 0.00 0.00 39.69 3.91
535 656 2.437085 TCGGAGATGCTCTAACCTCA 57.563 50.000 0.00 0.00 0.00 3.86
539 660 3.295973 GGAGATGCTCTAACCTCACTCT 58.704 50.000 0.00 0.00 0.00 3.24
540 661 4.465886 GGAGATGCTCTAACCTCACTCTA 58.534 47.826 0.00 0.00 0.00 2.43
541 662 4.518970 GGAGATGCTCTAACCTCACTCTAG 59.481 50.000 0.00 0.00 0.00 2.43
542 663 3.888930 AGATGCTCTAACCTCACTCTAGC 59.111 47.826 0.00 0.00 0.00 3.42
543 664 3.374042 TGCTCTAACCTCACTCTAGCT 57.626 47.619 0.00 0.00 0.00 3.32
544 665 3.283751 TGCTCTAACCTCACTCTAGCTC 58.716 50.000 0.00 0.00 0.00 4.09
545 666 3.053991 TGCTCTAACCTCACTCTAGCTCT 60.054 47.826 0.00 0.00 0.00 4.09
546 667 3.315191 GCTCTAACCTCACTCTAGCTCTG 59.685 52.174 0.00 0.00 0.00 3.35
547 668 4.776349 CTCTAACCTCACTCTAGCTCTGA 58.224 47.826 0.00 0.00 0.00 3.27
551 676 3.352648 ACCTCACTCTAGCTCTGACTTC 58.647 50.000 0.00 0.00 0.00 3.01
553 678 3.627577 CCTCACTCTAGCTCTGACTTCTC 59.372 52.174 0.00 0.00 0.00 2.87
567 692 7.066284 GCTCTGACTTCTCAAGCCATATTTTAA 59.934 37.037 0.00 0.00 30.44 1.52
568 693 9.118300 CTCTGACTTCTCAAGCCATATTTTAAT 57.882 33.333 0.00 0.00 0.00 1.40
569 694 8.896744 TCTGACTTCTCAAGCCATATTTTAATG 58.103 33.333 0.00 0.00 0.00 1.90
571 696 9.023962 TGACTTCTCAAGCCATATTTTAATGTT 57.976 29.630 0.00 0.00 0.00 2.71
607 732 4.908966 CATAGATTGCATCACGCGATAA 57.091 40.909 15.93 0.00 45.36 1.75
608 733 4.632023 CATAGATTGCATCACGCGATAAC 58.368 43.478 15.93 0.00 45.36 1.89
617 750 6.817396 TGCATCACGCGATAACTATTTTATC 58.183 36.000 15.93 0.00 46.97 1.75
619 752 6.090898 GCATCACGCGATAACTATTTTATCCT 59.909 38.462 15.93 0.00 0.00 3.24
624 757 6.641314 ACGCGATAACTATTTTATCCTGTCAG 59.359 38.462 15.93 0.00 0.00 3.51
630 763 5.352284 ACTATTTTATCCTGTCAGACGCAG 58.648 41.667 0.00 0.00 0.00 5.18
660 826 5.662208 TGTCTCCCCGGAGTGTTATTTTATA 59.338 40.000 0.73 0.00 42.49 0.98
730 900 1.090052 GCATACGTTGGGAGAGCCAC 61.090 60.000 0.00 0.00 35.15 5.01
731 901 0.249120 CATACGTTGGGAGAGCCACA 59.751 55.000 0.00 0.00 35.15 4.17
776 949 1.278637 CGGACGGCACAAAACTGTC 59.721 57.895 0.00 0.00 41.76 3.51
778 951 1.155424 GGACGGCACAAAACTGTCGA 61.155 55.000 0.00 0.00 41.96 4.20
779 952 0.042448 GACGGCACAAAACTGTCGAC 60.042 55.000 9.11 9.11 41.96 4.20
780 953 1.083657 CGGCACAAAACTGTCGACG 60.084 57.895 11.62 8.41 41.96 5.12
783 956 0.042448 GCACAAAACTGTCGACGACC 60.042 55.000 24.33 7.89 0.00 4.79
839 1028 3.998672 ACGTCACCGCCGAACCAT 61.999 61.111 0.00 0.00 37.70 3.55
840 1029 2.740826 CGTCACCGCCGAACCATT 60.741 61.111 0.00 0.00 0.00 3.16
841 1030 2.322081 CGTCACCGCCGAACCATTT 61.322 57.895 0.00 0.00 0.00 2.32
896 1091 2.064581 GGCCCACGTATCAGTCCCT 61.065 63.158 0.00 0.00 0.00 4.20
897 1092 1.442148 GCCCACGTATCAGTCCCTC 59.558 63.158 0.00 0.00 0.00 4.30
899 1094 1.400530 CCCACGTATCAGTCCCTCCC 61.401 65.000 0.00 0.00 0.00 4.30
901 1096 0.747255 CACGTATCAGTCCCTCCCAG 59.253 60.000 0.00 0.00 0.00 4.45
902 1097 0.335361 ACGTATCAGTCCCTCCCAGT 59.665 55.000 0.00 0.00 0.00 4.00
903 1098 1.033574 CGTATCAGTCCCTCCCAGTC 58.966 60.000 0.00 0.00 0.00 3.51
904 1099 1.685180 CGTATCAGTCCCTCCCAGTCA 60.685 57.143 0.00 0.00 0.00 3.41
905 1100 2.683768 GTATCAGTCCCTCCCAGTCAT 58.316 52.381 0.00 0.00 0.00 3.06
907 1102 0.684479 TCAGTCCCTCCCAGTCATCG 60.684 60.000 0.00 0.00 0.00 3.84
910 1105 2.187946 CCCTCCCAGTCATCGCAC 59.812 66.667 0.00 0.00 0.00 5.34
911 1106 2.187946 CCTCCCAGTCATCGCACC 59.812 66.667 0.00 0.00 0.00 5.01
912 1107 2.187946 CTCCCAGTCATCGCACCC 59.812 66.667 0.00 0.00 0.00 4.61
913 1108 2.606213 TCCCAGTCATCGCACCCA 60.606 61.111 0.00 0.00 0.00 4.51
914 1109 1.976132 CTCCCAGTCATCGCACCCAT 61.976 60.000 0.00 0.00 0.00 4.00
920 1116 1.153309 TCATCGCACCCATCTGCAG 60.153 57.895 7.63 7.63 36.94 4.41
922 1118 3.333899 ATCGCACCCATCTGCAGCA 62.334 57.895 9.47 0.00 36.94 4.41
973 1172 2.425668 ACATTTATTTTCTTCCCCCGCG 59.574 45.455 0.00 0.00 0.00 6.46
994 1193 1.456196 GGAGATCGATCACAGCCGGA 61.456 60.000 26.47 0.00 0.00 5.14
1647 1864 1.736032 GCGATACTGAAGCAGTTCCGT 60.736 52.381 5.31 0.00 42.59 4.69
1689 1906 3.056035 GGGTGTTCGTCAACTCCTTCTAT 60.056 47.826 7.70 0.00 43.22 1.98
2190 2416 1.005394 CACGGACGCCAAGTACCTT 60.005 57.895 0.00 0.00 0.00 3.50
2426 2652 2.875786 GCGCACGAGCAGATAAGGC 61.876 63.158 0.30 0.00 42.27 4.35
2488 2714 7.093322 TCTCTACGTGGAAACTAAGGATTAC 57.907 40.000 2.37 0.00 0.00 1.89
2561 2787 1.344942 GACACGCACAAGGCTACTCG 61.345 60.000 0.00 0.00 41.67 4.18
2584 2810 0.663153 GAAGCAACTTTGTCGCAGGT 59.337 50.000 0.00 0.00 0.00 4.00
2632 2860 1.547820 AGCATCGATCGGTATGAGCAT 59.452 47.619 16.41 0.00 30.45 3.79
2633 2861 1.923204 GCATCGATCGGTATGAGCATC 59.077 52.381 16.41 0.00 30.45 3.91
2634 2862 2.180397 CATCGATCGGTATGAGCATCG 58.820 52.381 16.41 0.00 38.61 3.84
2635 2863 0.109735 TCGATCGGTATGAGCATCGC 60.110 55.000 16.41 0.00 38.40 4.58
2636 2864 1.073216 CGATCGGTATGAGCATCGCC 61.073 60.000 7.38 0.00 38.61 5.54
2637 2865 1.073216 GATCGGTATGAGCATCGCCG 61.073 60.000 15.61 15.61 38.61 6.46
2638 2866 3.406361 CGGTATGAGCATCGCCGC 61.406 66.667 11.49 0.00 38.61 6.53
2639 2867 3.044305 GGTATGAGCATCGCCGCC 61.044 66.667 0.00 0.00 38.61 6.13
2640 2868 2.029666 GTATGAGCATCGCCGCCT 59.970 61.111 0.00 0.00 38.61 5.52
2641 2869 1.289066 GTATGAGCATCGCCGCCTA 59.711 57.895 0.00 0.00 38.61 3.93
2657 2885 2.541556 GCCTAACTGAAGTCCATCGTC 58.458 52.381 0.00 0.00 0.00 4.20
2711 2939 0.737715 AAGTCTGAAGATGCCGCGAC 60.738 55.000 8.23 0.00 0.00 5.19
2719 2947 3.362851 GATGCCGCGACAACCGAAC 62.363 63.158 8.23 0.00 41.76 3.95
2725 2953 1.073177 CGCGACAACCGAACCTAATT 58.927 50.000 0.00 0.00 41.76 1.40
2729 2957 4.085415 CGCGACAACCGAACCTAATTATAC 60.085 45.833 0.00 0.00 41.76 1.47
2770 3002 6.417191 ACGACGTAGCATGATATTTTGTTT 57.583 33.333 0.00 0.00 0.00 2.83
2794 3026 9.965824 TTTTCTTTGATCCTCTTGTTATGTTTC 57.034 29.630 0.00 0.00 0.00 2.78
2818 3050 3.020274 GTCAGTCATACAGAGAGCCAGA 58.980 50.000 0.00 0.00 0.00 3.86
2834 3066 3.057969 CCAGACAGGCTACATGTTTCA 57.942 47.619 2.30 0.00 0.00 2.69
2838 3070 5.647658 CCAGACAGGCTACATGTTTCAATTA 59.352 40.000 2.30 0.00 0.00 1.40
2925 3163 0.995024 ACCCTCCTCCTGTGAAATGG 59.005 55.000 0.00 0.00 0.00 3.16
2966 3204 1.186200 TGCTTCCAGCGAGAGTGTAT 58.814 50.000 0.00 0.00 46.26 2.29
2967 3205 1.550524 TGCTTCCAGCGAGAGTGTATT 59.449 47.619 0.00 0.00 46.26 1.89
2968 3206 2.197577 GCTTCCAGCGAGAGTGTATTC 58.802 52.381 0.00 0.00 0.00 1.75
2969 3207 2.417379 GCTTCCAGCGAGAGTGTATTCA 60.417 50.000 0.00 0.00 0.00 2.57
2970 3208 3.443037 CTTCCAGCGAGAGTGTATTCAG 58.557 50.000 0.00 0.00 0.00 3.02
2971 3209 1.751351 TCCAGCGAGAGTGTATTCAGG 59.249 52.381 0.00 0.00 0.00 3.86
2972 3210 1.202463 CCAGCGAGAGTGTATTCAGGG 60.202 57.143 0.00 0.00 0.00 4.45
2973 3211 1.751351 CAGCGAGAGTGTATTCAGGGA 59.249 52.381 0.00 0.00 0.00 4.20
2974 3212 1.751924 AGCGAGAGTGTATTCAGGGAC 59.248 52.381 0.00 0.00 0.00 4.46
2975 3213 1.202428 GCGAGAGTGTATTCAGGGACC 60.202 57.143 0.00 0.00 0.00 4.46
2976 3214 2.100197 CGAGAGTGTATTCAGGGACCA 58.900 52.381 0.00 0.00 0.00 4.02
2977 3215 2.159226 CGAGAGTGTATTCAGGGACCAC 60.159 54.545 0.00 0.00 0.00 4.16
2978 3216 2.832129 GAGAGTGTATTCAGGGACCACA 59.168 50.000 0.00 0.00 0.00 4.17
2979 3217 3.452627 GAGAGTGTATTCAGGGACCACAT 59.547 47.826 0.00 0.00 0.00 3.21
2980 3218 3.452627 AGAGTGTATTCAGGGACCACATC 59.547 47.826 0.00 0.00 0.00 3.06
2981 3219 3.181329 AGTGTATTCAGGGACCACATCA 58.819 45.455 0.00 0.00 0.00 3.07
2982 3220 3.198635 AGTGTATTCAGGGACCACATCAG 59.801 47.826 0.00 0.00 0.00 2.90
2983 3221 3.197766 GTGTATTCAGGGACCACATCAGA 59.802 47.826 0.00 0.00 0.00 3.27
2984 3222 3.843619 TGTATTCAGGGACCACATCAGAA 59.156 43.478 0.00 0.00 0.00 3.02
2985 3223 2.859165 TTCAGGGACCACATCAGAAC 57.141 50.000 0.00 0.00 0.00 3.01
2986 3224 2.030027 TCAGGGACCACATCAGAACT 57.970 50.000 0.00 0.00 0.00 3.01
2987 3225 3.184382 TCAGGGACCACATCAGAACTA 57.816 47.619 0.00 0.00 0.00 2.24
2988 3226 2.832129 TCAGGGACCACATCAGAACTAC 59.168 50.000 0.00 0.00 0.00 2.73
2998 3236 5.995282 CCACATCAGAACTACCACAAACTAA 59.005 40.000 0.00 0.00 0.00 2.24
3009 3247 2.359531 CCACAAACTAAAAGAACGCCCA 59.640 45.455 0.00 0.00 0.00 5.36
3010 3248 3.181485 CCACAAACTAAAAGAACGCCCAA 60.181 43.478 0.00 0.00 0.00 4.12
3033 3272 3.512033 GTTGCAACGGGCCATATTAAA 57.488 42.857 14.90 0.00 43.89 1.52
3094 3333 4.356405 TCATCAAATCCTCACACACACT 57.644 40.909 0.00 0.00 0.00 3.55
3116 3358 2.040359 CCCCCTCCCTCTTCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
3174 3431 5.220854 CCGCCAATAAGACTTACTCAATTGG 60.221 44.000 17.20 17.20 45.20 3.16
3176 3433 6.757897 CCAATAAGACTTACTCAATTGGCA 57.242 37.500 11.83 0.00 41.11 4.92
3187 3444 9.019656 ACTTACTCAATTGGCAAATAATGTGTA 57.980 29.630 3.01 9.62 0.00 2.90
3221 3478 6.818644 GTGAGCTTGACTGAACTAATGGATAA 59.181 38.462 0.00 0.00 0.00 1.75
3307 3564 2.511659 AGTCGTTAGCTACAGTGACCA 58.488 47.619 0.00 0.00 0.00 4.02
3382 3639 8.782144 TGATAAAAATCAAAGCCCAATTCAAAC 58.218 29.630 0.00 0.00 0.00 2.93
3471 3728 6.506500 AATTCCACTGATCTTTGACATGTC 57.493 37.500 19.27 19.27 0.00 3.06
3480 3737 2.086869 CTTTGACATGTCGAGCCCAAT 58.913 47.619 20.54 0.00 0.00 3.16
3481 3738 3.055458 TCTTTGACATGTCGAGCCCAATA 60.055 43.478 20.54 1.55 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.047059 GTTGGCGACGTCCTCCGA 62.047 66.667 10.58 8.60 40.70 4.55
77 78 1.227176 GATAGTCAACGCCGGTCCC 60.227 63.158 1.90 0.00 0.00 4.46
129 145 3.364889 TCGTTGTCTGTCGTGAAGATT 57.635 42.857 0.00 0.00 0.00 2.40
139 155 2.288961 AGTCAACGTTCGTTGTCTGT 57.711 45.000 28.46 14.47 44.00 3.41
145 161 3.426695 CCGAGGTATAGTCAACGTTCGTT 60.427 47.826 0.00 4.72 0.00 3.85
156 172 1.341679 TGGTGCTGTCCGAGGTATAGT 60.342 52.381 0.00 0.00 0.00 2.12
182 212 3.661944 GAGTCGCATCATCATCCTCATT 58.338 45.455 0.00 0.00 0.00 2.57
213 247 7.273320 ACTAGATAAACTACGATGCAGCTAA 57.727 36.000 0.00 0.00 0.00 3.09
222 256 4.637534 AGGACGCAACTAGATAAACTACGA 59.362 41.667 0.00 0.00 0.00 3.43
241 276 9.556030 GCAACTACATGAAATTAAAACTAGGAC 57.444 33.333 0.00 0.00 0.00 3.85
242 277 9.290988 TGCAACTACATGAAATTAAAACTAGGA 57.709 29.630 0.00 0.00 0.00 2.94
244 279 9.341899 GGTGCAACTACATGAAATTAAAACTAG 57.658 33.333 0.00 0.00 36.74 2.57
251 286 8.574251 AACTATGGTGCAACTACATGAAATTA 57.426 30.769 2.04 0.00 36.74 1.40
252 287 7.394359 AGAACTATGGTGCAACTACATGAAATT 59.606 33.333 2.04 0.00 36.74 1.82
257 292 4.937620 ACAGAACTATGGTGCAACTACATG 59.062 41.667 2.04 0.00 36.74 3.21
365 486 3.188254 CCCGCGCATGTTCATATTTGATA 59.812 43.478 8.75 0.00 0.00 2.15
394 515 2.873851 TTAAAATGCAGCGCGCGC 60.874 55.556 45.10 45.10 46.97 6.86
395 516 1.455908 GAGTTAAAATGCAGCGCGCG 61.456 55.000 28.44 28.44 46.97 6.86
396 517 1.455908 CGAGTTAAAATGCAGCGCGC 61.456 55.000 26.66 26.66 42.89 6.86
397 518 1.455908 GCGAGTTAAAATGCAGCGCG 61.456 55.000 0.00 0.00 33.56 6.86
398 519 1.133946 GGCGAGTTAAAATGCAGCGC 61.134 55.000 0.00 0.00 41.95 5.92
399 520 0.857311 CGGCGAGTTAAAATGCAGCG 60.857 55.000 0.00 0.00 0.00 5.18
400 521 1.133946 GCGGCGAGTTAAAATGCAGC 61.134 55.000 12.98 4.10 40.95 5.25
401 522 0.447801 AGCGGCGAGTTAAAATGCAG 59.552 50.000 12.98 0.00 0.00 4.41
402 523 0.167908 CAGCGGCGAGTTAAAATGCA 59.832 50.000 12.98 0.00 0.00 3.96
403 524 0.523335 CCAGCGGCGAGTTAAAATGC 60.523 55.000 12.98 0.00 0.00 3.56
404 525 1.062587 CTCCAGCGGCGAGTTAAAATG 59.937 52.381 12.98 0.00 0.00 2.32
405 526 1.369625 CTCCAGCGGCGAGTTAAAAT 58.630 50.000 12.98 0.00 0.00 1.82
406 527 1.296056 GCTCCAGCGGCGAGTTAAAA 61.296 55.000 12.98 0.00 0.00 1.52
407 528 1.740296 GCTCCAGCGGCGAGTTAAA 60.740 57.895 12.98 0.00 0.00 1.52
408 529 2.125673 GCTCCAGCGGCGAGTTAA 60.126 61.111 12.98 0.00 0.00 2.01
425 546 2.166007 GCTAAAATACAACACGCGCAG 58.834 47.619 5.73 0.55 0.00 5.18
426 547 1.462705 CGCTAAAATACAACACGCGCA 60.463 47.619 5.73 0.00 32.60 6.09
427 548 1.168588 CGCTAAAATACAACACGCGC 58.831 50.000 5.73 0.00 32.60 6.86
428 549 1.168588 GCGCTAAAATACAACACGCG 58.831 50.000 3.53 3.53 41.74 6.01
429 550 1.168588 CGCGCTAAAATACAACACGC 58.831 50.000 5.56 0.00 41.32 5.34
430 551 1.793113 CCGCGCTAAAATACAACACG 58.207 50.000 5.56 0.00 0.00 4.49
431 552 1.129811 AGCCGCGCTAAAATACAACAC 59.870 47.619 5.56 0.00 36.99 3.32
432 553 1.129624 CAGCCGCGCTAAAATACAACA 59.870 47.619 5.56 0.00 36.40 3.33
433 554 1.810197 CAGCCGCGCTAAAATACAAC 58.190 50.000 5.56 0.00 36.40 3.32
434 555 0.098025 GCAGCCGCGCTAAAATACAA 59.902 50.000 5.56 0.00 36.40 2.41
435 556 0.742990 AGCAGCCGCGCTAAAATACA 60.743 50.000 5.56 0.00 45.49 2.29
436 557 0.316196 CAGCAGCCGCGCTAAAATAC 60.316 55.000 5.56 0.00 45.49 1.89
437 558 1.436195 CCAGCAGCCGCGCTAAAATA 61.436 55.000 5.56 0.00 45.49 1.40
438 559 2.764314 CCAGCAGCCGCGCTAAAAT 61.764 57.895 5.56 0.00 45.49 1.82
439 560 3.430862 CCAGCAGCCGCGCTAAAA 61.431 61.111 5.56 0.00 45.49 1.52
440 561 4.386951 TCCAGCAGCCGCGCTAAA 62.387 61.111 5.56 0.00 45.49 1.85
441 562 4.819761 CTCCAGCAGCCGCGCTAA 62.820 66.667 5.56 1.87 45.49 3.09
446 567 3.426568 GTTGACTCCAGCAGCCGC 61.427 66.667 0.00 0.00 38.99 6.53
447 568 3.114616 CGTTGACTCCAGCAGCCG 61.115 66.667 0.00 0.00 0.00 5.52
448 569 1.598130 AACGTTGACTCCAGCAGCC 60.598 57.895 0.00 0.00 0.00 4.85
449 570 1.160329 ACAACGTTGACTCCAGCAGC 61.160 55.000 33.66 0.00 0.00 5.25
450 571 0.583438 CACAACGTTGACTCCAGCAG 59.417 55.000 33.66 4.29 0.00 4.24
451 572 1.436195 GCACAACGTTGACTCCAGCA 61.436 55.000 33.66 0.00 0.00 4.41
452 573 1.279840 GCACAACGTTGACTCCAGC 59.720 57.895 33.66 20.76 0.00 4.85
453 574 1.564622 CGCACAACGTTGACTCCAG 59.435 57.895 33.66 15.88 36.87 3.86
454 575 2.530497 GCGCACAACGTTGACTCCA 61.530 57.895 33.66 0.00 46.11 3.86
455 576 2.248431 GCGCACAACGTTGACTCC 59.752 61.111 33.66 16.44 46.11 3.85
456 577 2.248431 GGCGCACAACGTTGACTC 59.752 61.111 33.66 18.94 46.11 3.36
457 578 3.636043 CGGCGCACAACGTTGACT 61.636 61.111 33.66 10.62 46.11 3.41
470 591 3.505184 ATAAGGTTTGGCGCGGCG 61.505 61.111 28.22 19.62 0.00 6.46
471 592 1.724582 ATCATAAGGTTTGGCGCGGC 61.725 55.000 27.61 27.61 0.00 6.53
472 593 0.029300 CATCATAAGGTTTGGCGCGG 59.971 55.000 8.83 0.00 0.00 6.46
473 594 1.003545 CTCATCATAAGGTTTGGCGCG 60.004 52.381 0.00 0.00 0.00 6.86
474 595 1.268743 GCTCATCATAAGGTTTGGCGC 60.269 52.381 0.00 0.00 0.00 6.53
475 596 1.003545 CGCTCATCATAAGGTTTGGCG 60.004 52.381 0.00 0.00 0.00 5.69
476 597 1.268743 GCGCTCATCATAAGGTTTGGC 60.269 52.381 0.00 0.00 0.00 4.52
477 598 1.003545 CGCGCTCATCATAAGGTTTGG 60.004 52.381 5.56 0.00 0.00 3.28
478 599 1.595489 GCGCGCTCATCATAAGGTTTG 60.595 52.381 26.67 0.00 0.00 2.93
479 600 0.657840 GCGCGCTCATCATAAGGTTT 59.342 50.000 26.67 0.00 0.00 3.27
480 601 1.160329 GGCGCGCTCATCATAAGGTT 61.160 55.000 32.29 0.00 0.00 3.50
481 602 1.595382 GGCGCGCTCATCATAAGGT 60.595 57.895 32.29 0.00 0.00 3.50
482 603 2.661566 CGGCGCGCTCATCATAAGG 61.662 63.158 32.29 1.93 0.00 2.69
483 604 2.849007 CGGCGCGCTCATCATAAG 59.151 61.111 32.29 7.30 0.00 1.73
504 625 4.445545 CTCCGAAAGCCGCGCAAC 62.446 66.667 8.75 0.00 36.84 4.17
505 626 3.950794 ATCTCCGAAAGCCGCGCAA 62.951 57.895 8.75 0.00 36.84 4.85
506 627 4.451150 ATCTCCGAAAGCCGCGCA 62.451 61.111 8.75 0.00 36.84 6.09
507 628 3.929948 CATCTCCGAAAGCCGCGC 61.930 66.667 0.00 0.00 36.84 6.86
508 629 3.929948 GCATCTCCGAAAGCCGCG 61.930 66.667 0.00 0.00 36.84 6.46
509 630 2.512515 AGCATCTCCGAAAGCCGC 60.513 61.111 0.00 0.00 36.84 6.53
510 631 3.711348 GAGCATCTCCGAAAGCCG 58.289 61.111 0.00 0.00 38.18 5.52
521 642 3.888930 AGCTAGAGTGAGGTTAGAGCATC 59.111 47.826 0.00 0.00 0.00 3.91
522 643 3.888930 GAGCTAGAGTGAGGTTAGAGCAT 59.111 47.826 0.00 0.00 0.00 3.79
523 644 3.053991 AGAGCTAGAGTGAGGTTAGAGCA 60.054 47.826 0.00 0.00 0.00 4.26
524 645 3.315191 CAGAGCTAGAGTGAGGTTAGAGC 59.685 52.174 0.00 0.00 0.00 4.09
525 646 4.574828 GTCAGAGCTAGAGTGAGGTTAGAG 59.425 50.000 0.00 0.00 0.00 2.43
535 656 3.443681 GCTTGAGAAGTCAGAGCTAGAGT 59.556 47.826 0.00 0.00 35.57 3.24
539 660 2.529632 TGGCTTGAGAAGTCAGAGCTA 58.470 47.619 0.00 0.00 38.40 3.32
540 661 1.346062 TGGCTTGAGAAGTCAGAGCT 58.654 50.000 0.00 0.00 38.40 4.09
541 662 3.923354 TGGCTTGAGAAGTCAGAGC 57.077 52.632 0.00 0.00 38.40 4.09
568 693 8.779303 CAATCTATGCCCGTAAATGTAATAACA 58.221 33.333 0.00 0.00 40.69 2.41
601 726 7.148950 CGTCTGACAGGATAAAATAGTTATCGC 60.149 40.741 8.73 0.00 33.38 4.58
603 728 7.652105 TGCGTCTGACAGGATAAAATAGTTATC 59.348 37.037 8.73 0.00 0.00 1.75
605 730 6.869695 TGCGTCTGACAGGATAAAATAGTTA 58.130 36.000 8.73 0.00 0.00 2.24
606 731 5.730550 TGCGTCTGACAGGATAAAATAGTT 58.269 37.500 8.73 0.00 0.00 2.24
607 732 5.339008 TGCGTCTGACAGGATAAAATAGT 57.661 39.130 8.73 0.00 0.00 2.12
608 733 4.210120 GCTGCGTCTGACAGGATAAAATAG 59.790 45.833 8.73 0.00 35.62 1.73
617 750 2.505777 CTCGCTGCGTCTGACAGG 60.506 66.667 22.48 0.00 35.62 4.00
660 826 4.460263 TGTACAGCAAGAATTTGACCTGT 58.540 39.130 0.00 0.00 39.43 4.00
711 877 1.220749 TGGCTCTCCCAACGTATGC 59.779 57.895 0.00 0.00 41.82 3.14
736 906 1.322538 CGAAGGAGGGGCCAAATTGG 61.323 60.000 7.84 7.84 41.55 3.16
740 910 4.360405 GGCGAAGGAGGGGCCAAA 62.360 66.667 4.39 0.00 46.13 3.28
759 932 1.155424 TCGACAGTTTTGTGCCGTCC 61.155 55.000 0.00 0.00 37.76 4.79
776 949 1.227147 ACACACACTTGGGTCGTCG 60.227 57.895 0.00 0.00 31.85 5.12
778 951 0.461339 GACACACACACTTGGGTCGT 60.461 55.000 0.00 0.00 37.20 4.34
779 952 2.307363 GACACACACACTTGGGTCG 58.693 57.895 0.00 0.00 37.20 4.79
896 1091 1.971505 GATGGGTGCGATGACTGGGA 61.972 60.000 0.00 0.00 0.00 4.37
897 1092 1.524621 GATGGGTGCGATGACTGGG 60.525 63.158 0.00 0.00 0.00 4.45
899 1094 1.434622 GCAGATGGGTGCGATGACTG 61.435 60.000 0.00 0.00 32.74 3.51
901 1096 3.414272 GCAGATGGGTGCGATGAC 58.586 61.111 0.00 0.00 32.74 3.06
907 1102 3.823330 GCTGCTGCAGATGGGTGC 61.823 66.667 32.30 12.79 44.27 5.01
910 1105 2.829003 CTGGCTGCTGCAGATGGG 60.829 66.667 32.30 14.48 41.91 4.00
911 1106 3.518998 GCTGGCTGCTGCAGATGG 61.519 66.667 32.30 19.77 41.91 3.51
920 1116 1.593750 CCGATACTGAGCTGGCTGC 60.594 63.158 8.47 8.47 43.29 5.25
922 1118 2.801631 GCCCGATACTGAGCTGGCT 61.802 63.158 0.00 0.00 38.25 4.75
933 1129 3.096852 TGTCTTCTCTTCTTGCCCGATA 58.903 45.455 0.00 0.00 0.00 2.92
973 1172 1.369321 GGCTGTGATCGATCTCCCC 59.631 63.158 25.02 18.97 0.00 4.81
1238 1440 1.269166 CAAGAACTCGAACCGGATCG 58.731 55.000 26.47 26.47 44.04 3.69
1278 1480 1.062685 CATCAGGTCGTCGAGGTCG 59.937 63.158 4.85 0.00 41.45 4.79
1647 1864 1.216977 CGACGCCTTGTGGATGGTA 59.783 57.895 0.00 0.00 34.57 3.25
1995 2212 3.188324 ACGGAGTCCAGGTACCCT 58.812 61.111 8.74 0.00 29.74 4.34
2190 2416 1.630369 CCCATCTTGAACTCCTCCACA 59.370 52.381 0.00 0.00 0.00 4.17
2296 2522 2.276116 ACGCTCTGGCCTTCTCGAA 61.276 57.895 3.32 0.00 34.44 3.71
2488 2714 2.005451 CTTCACTGAAGATGGCCGAAG 58.995 52.381 12.82 0.00 41.71 3.79
2554 2780 0.109226 AGTTGCTTCGGTCGAGTAGC 60.109 55.000 9.35 9.35 0.00 3.58
2561 2787 0.384353 GCGACAAAGTTGCTTCGGTC 60.384 55.000 2.19 0.00 39.63 4.79
2632 2860 1.214589 GACTTCAGTTAGGCGGCGA 59.785 57.895 12.98 0.00 0.00 5.54
2633 2861 1.810030 GGACTTCAGTTAGGCGGCG 60.810 63.158 0.51 0.51 0.00 6.46
2634 2862 0.107654 ATGGACTTCAGTTAGGCGGC 60.108 55.000 0.00 0.00 0.00 6.53
2635 2863 1.802880 CGATGGACTTCAGTTAGGCGG 60.803 57.143 0.00 0.00 0.00 6.13
2636 2864 1.135083 ACGATGGACTTCAGTTAGGCG 60.135 52.381 0.00 0.00 0.00 5.52
2637 2865 2.541556 GACGATGGACTTCAGTTAGGC 58.458 52.381 0.00 0.00 0.00 3.93
2638 2866 2.422479 TCGACGATGGACTTCAGTTAGG 59.578 50.000 0.00 0.00 0.00 2.69
2639 2867 3.427243 GTCGACGATGGACTTCAGTTAG 58.573 50.000 0.00 0.00 0.00 2.34
2640 2868 2.159612 CGTCGACGATGGACTTCAGTTA 60.160 50.000 33.35 0.00 43.02 2.24
2641 2869 1.401148 CGTCGACGATGGACTTCAGTT 60.401 52.381 33.35 0.00 43.02 3.16
2711 2939 8.937634 AGTACAAGTATAATTAGGTTCGGTTG 57.062 34.615 0.00 0.00 0.00 3.77
2729 2957 6.597614 ACGTCGTTAAGAAGACTAGTACAAG 58.402 40.000 0.00 0.00 35.38 3.16
2743 2975 7.618442 ACAAAATATCATGCTACGTCGTTAAG 58.382 34.615 1.78 0.00 0.00 1.85
2744 2976 7.528481 ACAAAATATCATGCTACGTCGTTAA 57.472 32.000 1.78 0.00 0.00 2.01
2745 2977 7.528481 AACAAAATATCATGCTACGTCGTTA 57.472 32.000 1.78 0.00 0.00 3.18
2746 2978 6.417191 AACAAAATATCATGCTACGTCGTT 57.583 33.333 1.78 0.00 0.00 3.85
2747 2979 6.417191 AAACAAAATATCATGCTACGTCGT 57.583 33.333 2.21 2.21 0.00 4.34
2748 2980 7.180079 AGAAAACAAAATATCATGCTACGTCG 58.820 34.615 0.00 0.00 0.00 5.12
2749 2981 8.895932 AAGAAAACAAAATATCATGCTACGTC 57.104 30.769 0.00 0.00 0.00 4.34
2750 2982 9.128107 CAAAGAAAACAAAATATCATGCTACGT 57.872 29.630 0.00 0.00 0.00 3.57
2770 3002 8.924511 AGAAACATAACAAGAGGATCAAAGAA 57.075 30.769 0.00 0.00 37.82 2.52
2794 3026 3.194329 TGGCTCTCTGTATGACTGACAAG 59.806 47.826 0.00 0.00 0.00 3.16
2818 3050 6.490040 ACACTTAATTGAAACATGTAGCCTGT 59.510 34.615 0.00 0.00 0.00 4.00
2889 3125 1.073177 GGTTGCTAGCGCTTTAACGA 58.927 50.000 18.68 0.00 36.97 3.85
2901 3137 0.116342 TCACAGGAGGAGGGTTGCTA 59.884 55.000 0.00 0.00 0.00 3.49
2950 3188 2.166459 CCTGAATACACTCTCGCTGGAA 59.834 50.000 0.00 0.00 0.00 3.53
2951 3189 1.751351 CCTGAATACACTCTCGCTGGA 59.249 52.381 0.00 0.00 0.00 3.86
2960 3198 3.181329 TGATGTGGTCCCTGAATACACT 58.819 45.455 0.00 0.00 33.44 3.55
2966 3204 2.338809 AGTTCTGATGTGGTCCCTGAA 58.661 47.619 0.00 0.00 0.00 3.02
2967 3205 2.030027 AGTTCTGATGTGGTCCCTGA 57.970 50.000 0.00 0.00 0.00 3.86
2968 3206 2.093447 GGTAGTTCTGATGTGGTCCCTG 60.093 54.545 0.00 0.00 0.00 4.45
2969 3207 2.188817 GGTAGTTCTGATGTGGTCCCT 58.811 52.381 0.00 0.00 0.00 4.20
2970 3208 1.906574 TGGTAGTTCTGATGTGGTCCC 59.093 52.381 0.00 0.00 0.00 4.46
2971 3209 2.301870 TGTGGTAGTTCTGATGTGGTCC 59.698 50.000 0.00 0.00 0.00 4.46
2972 3210 3.678056 TGTGGTAGTTCTGATGTGGTC 57.322 47.619 0.00 0.00 0.00 4.02
2973 3211 4.134563 GTTTGTGGTAGTTCTGATGTGGT 58.865 43.478 0.00 0.00 0.00 4.16
2974 3212 4.389374 AGTTTGTGGTAGTTCTGATGTGG 58.611 43.478 0.00 0.00 0.00 4.17
2975 3213 7.490962 TTTAGTTTGTGGTAGTTCTGATGTG 57.509 36.000 0.00 0.00 0.00 3.21
2976 3214 7.990886 TCTTTTAGTTTGTGGTAGTTCTGATGT 59.009 33.333 0.00 0.00 0.00 3.06
2977 3215 8.378172 TCTTTTAGTTTGTGGTAGTTCTGATG 57.622 34.615 0.00 0.00 0.00 3.07
2978 3216 8.837389 GTTCTTTTAGTTTGTGGTAGTTCTGAT 58.163 33.333 0.00 0.00 0.00 2.90
2979 3217 7.010738 CGTTCTTTTAGTTTGTGGTAGTTCTGA 59.989 37.037 0.00 0.00 0.00 3.27
2980 3218 7.123830 CGTTCTTTTAGTTTGTGGTAGTTCTG 58.876 38.462 0.00 0.00 0.00 3.02
2981 3219 6.238293 GCGTTCTTTTAGTTTGTGGTAGTTCT 60.238 38.462 0.00 0.00 0.00 3.01
2982 3220 5.905733 GCGTTCTTTTAGTTTGTGGTAGTTC 59.094 40.000 0.00 0.00 0.00 3.01
2983 3221 5.220912 GGCGTTCTTTTAGTTTGTGGTAGTT 60.221 40.000 0.00 0.00 0.00 2.24
2984 3222 4.274214 GGCGTTCTTTTAGTTTGTGGTAGT 59.726 41.667 0.00 0.00 0.00 2.73
2985 3223 4.319984 GGGCGTTCTTTTAGTTTGTGGTAG 60.320 45.833 0.00 0.00 0.00 3.18
2986 3224 3.565063 GGGCGTTCTTTTAGTTTGTGGTA 59.435 43.478 0.00 0.00 0.00 3.25
2987 3225 2.359848 GGGCGTTCTTTTAGTTTGTGGT 59.640 45.455 0.00 0.00 0.00 4.16
2988 3226 2.359531 TGGGCGTTCTTTTAGTTTGTGG 59.640 45.455 0.00 0.00 0.00 4.17
3094 3333 1.595058 GGAAGAGGGAGGGGGAGAGA 61.595 65.000 0.00 0.00 0.00 3.10
3116 3358 3.570125 TGTGTGTGTGTTAGAGAGAGAGG 59.430 47.826 0.00 0.00 0.00 3.69
3174 3431 6.072728 TCACCACAAGTCTACACATTATTTGC 60.073 38.462 0.00 0.00 0.00 3.68
3175 3432 7.433708 TCACCACAAGTCTACACATTATTTG 57.566 36.000 0.00 0.00 0.00 2.32
3176 3433 6.149474 GCTCACCACAAGTCTACACATTATTT 59.851 38.462 0.00 0.00 0.00 1.40
3187 3444 1.765314 AGTCAAGCTCACCACAAGTCT 59.235 47.619 0.00 0.00 0.00 3.24
3267 3524 7.159372 ACGACTTGAGGTGTTACATAATCTTT 58.841 34.615 0.00 0.00 0.00 2.52
3307 3564 1.145738 GACATGGCATCATTAGGGGGT 59.854 52.381 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.