Multiple sequence alignment - TraesCS2B01G587700

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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 TraesCS2B01G587700 chr2B 100.000 4192 0 0 1 4192 774873977 774878168 0.000000e+00 7742.0
1 TraesCS2B01G587700 chr2B 91.039 491 14 8 2278 2745 793806239 793805756 1.640000e-178 636.0
2 TraesCS2B01G587700 chr2B 89.370 508 19 8 2795 3286 793805590 793805102 1.290000e-169 606.0
3 TraesCS2B01G587700 chr2B 95.330 364 16 1 1 364 646684189 646684551 1.010000e-160 577.0
4 TraesCS2B01G587700 chr2B 96.181 288 9 2 363 648 583409714 583410001 1.760000e-128 470.0
5 TraesCS2B01G587700 chr2B 86.029 408 30 12 3462 3858 793805103 793804712 3.020000e-111 412.0
6 TraesCS2B01G587700 chr2B 91.923 260 19 2 638 895 646684542 646684801 3.080000e-96 363.0
7 TraesCS2B01G587700 chr2B 100.000 32 0 0 2112 2143 793806475 793806444 4.530000e-05 60.2
8 TraesCS2B01G587700 chr2D 95.588 1904 60 14 899 2798 631406132 631408015 0.000000e+00 3029.0
9 TraesCS2B01G587700 chr2D 96.157 1327 46 1 2795 4116 631408045 631409371 0.000000e+00 2163.0
10 TraesCS2B01G587700 chr2D 97.368 76 2 0 4117 4192 631409425 631409500 3.400000e-26 130.0
11 TraesCS2B01G587700 chr3A 88.478 1189 51 25 1651 2798 663182254 663181111 0.000000e+00 1358.0
12 TraesCS2B01G587700 chr3A 87.975 973 38 33 2795 3716 663181081 663180137 0.000000e+00 1075.0
13 TraesCS2B01G587700 chr3A 81.110 757 68 33 895 1627 663183069 663182364 1.720000e-148 536.0
14 TraesCS2B01G587700 chr3A 96.970 33 0 1 1620 1652 663182315 663182284 2.000000e-03 54.7
15 TraesCS2B01G587700 chr7B 95.890 365 14 1 1 364 644219764 644220128 1.300000e-164 590.0
16 TraesCS2B01G587700 chr7B 96.820 283 8 1 363 644 31801365 31801083 4.910000e-129 472.0
17 TraesCS2B01G587700 chr7B 88.187 364 43 0 1 364 93340726 93341089 6.440000e-118 435.0
18 TraesCS2B01G587700 chr7B 87.547 265 19 7 638 901 644220119 644220370 1.140000e-75 294.0
19 TraesCS2B01G587700 chr6B 95.028 362 18 0 3 364 638485007 638485368 1.690000e-158 569.0
20 TraesCS2B01G587700 chr6B 95.563 293 12 1 361 652 65064967 65064675 6.350000e-128 468.0
21 TraesCS2B01G587700 chr6B 93.846 260 13 3 638 895 638485359 638485617 5.080000e-104 388.0
22 TraesCS2B01G587700 chr4B 93.407 364 24 0 1 364 670270304 670270667 1.330000e-149 540.0
23 TraesCS2B01G587700 chr4B 93.846 260 12 4 638 895 670270658 670270915 5.080000e-104 388.0
24 TraesCS2B01G587700 chr1B 91.484 364 31 0 1 364 427751562 427751199 6.260000e-138 501.0
25 TraesCS2B01G587700 chr1B 96.516 287 9 1 363 648 625144487 625144201 1.360000e-129 473.0
26 TraesCS2B01G587700 chr1B 96.820 283 8 1 363 644 495803964 495804246 4.910000e-129 472.0
27 TraesCS2B01G587700 chr1B 88.931 262 24 5 638 895 427751208 427750948 6.760000e-83 318.0
28 TraesCS2B01G587700 chr1B 92.222 90 5 1 2560 2647 477403826 477403915 4.400000e-25 126.0
29 TraesCS2B01G587700 chr4A 90.934 364 33 0 1 364 632783218 632783581 1.350000e-134 490.0
30 TraesCS2B01G587700 chr4A 96.516 287 9 1 363 648 721419427 721419141 1.360000e-129 473.0
31 TraesCS2B01G587700 chr4A 91.892 259 19 2 638 895 632783572 632783829 1.110000e-95 361.0
32 TraesCS2B01G587700 chr4A 94.118 85 4 1 2560 2643 618462258 618462174 1.220000e-25 128.0
33 TraesCS2B01G587700 chr3B 95.946 296 11 1 353 647 17350581 17350286 2.930000e-131 479.0
34 TraesCS2B01G587700 chr3B 93.791 306 16 3 363 666 821215076 821214772 1.370000e-124 457.0
35 TraesCS2B01G587700 chr5D 95.033 302 11 3 363 661 450608769 450609069 4.910000e-129 472.0
36 TraesCS2B01G587700 chr6D 88.462 364 42 0 1 364 29176838 29177201 1.380000e-119 440.0
37 TraesCS2B01G587700 chr1A 88.187 364 43 0 1 364 29015914 29015551 6.440000e-118 435.0
38 TraesCS2B01G587700 chr1A 93.182 88 5 1 2560 2646 498666622 498666535 1.220000e-25 128.0
39 TraesCS2B01G587700 chr3D 89.683 126 8 4 2988 3110 604778810 604778933 5.610000e-34 156.0
40 TraesCS2B01G587700 chr5B 78.295 258 39 14 649 895 425723525 425723776 2.610000e-32 150.0
41 TraesCS2B01G587700 chr5B 77.432 257 40 14 649 895 437609862 437610110 2.030000e-28 137.0
42 TraesCS2B01G587700 chr2A 78.261 253 42 11 650 895 630783917 630784163 2.610000e-32 150.0
43 TraesCS2B01G587700 chr7A 95.349 86 3 1 2559 2643 33885809 33885894 7.310000e-28 135.0
44 TraesCS2B01G587700 chr7D 91.304 92 6 2 2555 2645 83656301 83656211 1.580000e-24 124.0
45 TraesCS2B01G587700 chr1D 92.045 88 6 1 2560 2646 403516130 403516043 5.690000e-24 122.0
46 TraesCS2B01G587700 chr4D 90.217 92 6 3 2560 2650 415913129 415913218 2.650000e-22 117.0
47 TraesCS2B01G587700 chrUn 97.500 40 1 0 2798 2837 124808640 124808679 7.520000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G587700 chr2B 774873977 774878168 4191 False 7742.000 7742 100.00000 1 4192 1 chr2B.!!$F2 4191
1 TraesCS2B01G587700 chr2B 646684189 646684801 612 False 470.000 577 93.62650 1 895 2 chr2B.!!$F3 894
2 TraesCS2B01G587700 chr2B 793804712 793806475 1763 True 428.550 636 91.60950 2112 3858 4 chr2B.!!$R1 1746
3 TraesCS2B01G587700 chr2D 631406132 631409500 3368 False 1774.000 3029 96.37100 899 4192 3 chr2D.!!$F1 3293
4 TraesCS2B01G587700 chr3A 663180137 663183069 2932 True 755.925 1358 88.63325 895 3716 4 chr3A.!!$R1 2821
5 TraesCS2B01G587700 chr7B 644219764 644220370 606 False 442.000 590 91.71850 1 901 2 chr7B.!!$F2 900
6 TraesCS2B01G587700 chr6B 638485007 638485617 610 False 478.500 569 94.43700 3 895 2 chr6B.!!$F1 892
7 TraesCS2B01G587700 chr4B 670270304 670270915 611 False 464.000 540 93.62650 1 895 2 chr4B.!!$F1 894
8 TraesCS2B01G587700 chr1B 427750948 427751562 614 True 409.500 501 90.20750 1 895 2 chr1B.!!$R2 894
9 TraesCS2B01G587700 chr4A 632783218 632783829 611 False 425.500 490 91.41300 1 895 2 chr4A.!!$F1 894

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
373 375 0.038744 ACCATCTCAGGCCCTGTTTG 59.961 55.000 11.27 6.96 32.61 2.93 F
375 377 0.038744 CATCTCAGGCCCTGTTTGGT 59.961 55.000 11.27 0.00 32.61 3.67 F
1539 1581 0.106569 TCATGGAATGCCTTCGCCAT 60.107 50.000 0.00 0.00 46.21 4.40 F
2023 2182 1.338674 CGGCAAGGTGACCAGATACAA 60.339 52.381 3.63 0.00 0.00 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 2162 0.249120 TGTATCTGGTCACCTTGCCG 59.751 55.000 0.0 0.0 0.00 5.69 R
2084 2243 1.831736 GGCAGTAAGGAGAAGTAGCCA 59.168 52.381 0.0 0.0 40.50 4.75 R
2776 3191 0.532862 CGAAGGCACTGACAAGGTGT 60.533 55.000 0.0 0.0 40.86 4.16 R
3488 3990 0.834687 TGGTACACCCTGGACTGGAC 60.835 60.000 0.0 0.0 30.12 4.02 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 213 3.106986 GCGCAGGGCCTCCTCAATA 62.107 63.158 0.95 0.00 42.67 1.90
287 288 4.347813 GTTCTTCGATCCTCTCTTCTTCG 58.652 47.826 0.00 0.00 0.00 3.79
292 293 2.685897 CGATCCTCTCTTCTTCGTCCTT 59.314 50.000 0.00 0.00 0.00 3.36
299 300 5.982516 CCTCTCTTCTTCGTCCTTATCAATG 59.017 44.000 0.00 0.00 0.00 2.82
357 359 1.342496 GATCCATCATCTGCTCGACCA 59.658 52.381 0.00 0.00 0.00 4.02
358 360 1.417288 TCCATCATCTGCTCGACCAT 58.583 50.000 0.00 0.00 0.00 3.55
359 361 1.342496 TCCATCATCTGCTCGACCATC 59.658 52.381 0.00 0.00 0.00 3.51
360 362 1.343789 CCATCATCTGCTCGACCATCT 59.656 52.381 0.00 0.00 0.00 2.90
361 363 2.609984 CCATCATCTGCTCGACCATCTC 60.610 54.545 0.00 0.00 0.00 2.75
362 364 1.767759 TCATCTGCTCGACCATCTCA 58.232 50.000 0.00 0.00 0.00 3.27
363 365 1.680207 TCATCTGCTCGACCATCTCAG 59.320 52.381 0.00 0.00 0.00 3.35
364 366 1.039068 ATCTGCTCGACCATCTCAGG 58.961 55.000 0.00 0.00 0.00 3.86
365 367 1.227205 CTGCTCGACCATCTCAGGC 60.227 63.158 0.00 0.00 0.00 4.85
366 368 2.107953 GCTCGACCATCTCAGGCC 59.892 66.667 0.00 0.00 0.00 5.19
367 369 2.818132 CTCGACCATCTCAGGCCC 59.182 66.667 0.00 0.00 0.00 5.80
368 370 1.760086 CTCGACCATCTCAGGCCCT 60.760 63.158 0.00 0.00 0.00 5.19
369 371 2.025767 CTCGACCATCTCAGGCCCTG 62.026 65.000 3.69 3.69 0.00 4.45
370 372 2.362369 CGACCATCTCAGGCCCTGT 61.362 63.158 11.27 0.00 32.61 4.00
371 373 1.903877 CGACCATCTCAGGCCCTGTT 61.904 60.000 11.27 0.00 32.61 3.16
372 374 0.329596 GACCATCTCAGGCCCTGTTT 59.670 55.000 11.27 0.00 32.61 2.83
373 375 0.038744 ACCATCTCAGGCCCTGTTTG 59.961 55.000 11.27 6.96 32.61 2.93
374 376 0.682209 CCATCTCAGGCCCTGTTTGG 60.682 60.000 11.27 12.11 32.61 3.28
375 377 0.038744 CATCTCAGGCCCTGTTTGGT 59.961 55.000 11.27 0.00 32.61 3.67
376 378 0.779997 ATCTCAGGCCCTGTTTGGTT 59.220 50.000 11.27 0.00 32.61 3.67
377 379 0.110486 TCTCAGGCCCTGTTTGGTTC 59.890 55.000 11.27 0.00 32.61 3.62
378 380 0.178992 CTCAGGCCCTGTTTGGTTCA 60.179 55.000 11.27 0.00 32.61 3.18
379 381 0.482446 TCAGGCCCTGTTTGGTTCAT 59.518 50.000 11.27 0.00 32.61 2.57
380 382 1.707989 TCAGGCCCTGTTTGGTTCATA 59.292 47.619 11.27 0.00 32.61 2.15
381 383 2.109128 TCAGGCCCTGTTTGGTTCATAA 59.891 45.455 11.27 0.00 32.61 1.90
382 384 2.493278 CAGGCCCTGTTTGGTTCATAAG 59.507 50.000 1.39 0.00 0.00 1.73
383 385 2.110011 AGGCCCTGTTTGGTTCATAAGT 59.890 45.455 0.00 0.00 0.00 2.24
384 386 2.492088 GGCCCTGTTTGGTTCATAAGTC 59.508 50.000 0.00 0.00 0.00 3.01
385 387 3.421844 GCCCTGTTTGGTTCATAAGTCT 58.578 45.455 0.00 0.00 0.00 3.24
386 388 3.826729 GCCCTGTTTGGTTCATAAGTCTT 59.173 43.478 0.00 0.00 0.00 3.01
387 389 5.007682 GCCCTGTTTGGTTCATAAGTCTTA 58.992 41.667 0.00 0.00 0.00 2.10
388 390 5.123979 GCCCTGTTTGGTTCATAAGTCTTAG 59.876 44.000 0.00 0.00 0.00 2.18
389 391 5.648092 CCCTGTTTGGTTCATAAGTCTTAGG 59.352 44.000 0.00 0.00 0.00 2.69
390 392 6.472887 CCTGTTTGGTTCATAAGTCTTAGGA 58.527 40.000 2.85 2.85 0.00 2.94
391 393 6.371825 CCTGTTTGGTTCATAAGTCTTAGGAC 59.628 42.308 6.47 0.00 42.41 3.85
419 421 6.956102 TTTAGTCCCAACTTATAAGTCCCA 57.044 37.500 18.28 1.06 38.57 4.37
420 422 6.956102 TTAGTCCCAACTTATAAGTCCCAA 57.044 37.500 18.28 3.05 38.57 4.12
421 423 5.437191 AGTCCCAACTTATAAGTCCCAAG 57.563 43.478 18.28 6.66 38.57 3.61
422 424 4.850386 AGTCCCAACTTATAAGTCCCAAGT 59.150 41.667 18.28 5.74 38.57 3.16
423 425 5.045797 AGTCCCAACTTATAAGTCCCAAGTC 60.046 44.000 18.28 6.78 38.57 3.01
424 426 4.226620 TCCCAACTTATAAGTCCCAAGTCC 59.773 45.833 18.28 0.00 38.57 3.85
425 427 4.524053 CCAACTTATAAGTCCCAAGTCCC 58.476 47.826 18.28 0.00 38.57 4.46
426 428 4.227527 CCAACTTATAAGTCCCAAGTCCCT 59.772 45.833 18.28 0.00 38.57 4.20
427 429 5.427481 CCAACTTATAAGTCCCAAGTCCCTA 59.573 44.000 18.28 0.00 38.57 3.53
428 430 6.069847 CCAACTTATAAGTCCCAAGTCCCTAA 60.070 42.308 18.28 0.00 38.57 2.69
429 431 7.399634 CAACTTATAAGTCCCAAGTCCCTAAA 58.600 38.462 18.28 0.00 38.57 1.85
430 432 7.578458 ACTTATAAGTCCCAAGTCCCTAAAA 57.422 36.000 12.50 0.00 32.86 1.52
431 433 7.992295 ACTTATAAGTCCCAAGTCCCTAAAAA 58.008 34.615 12.50 0.00 32.86 1.94
432 434 8.107729 ACTTATAAGTCCCAAGTCCCTAAAAAG 58.892 37.037 12.50 0.00 32.86 2.27
433 435 4.808767 AAGTCCCAAGTCCCTAAAAAGT 57.191 40.909 0.00 0.00 0.00 2.66
434 436 4.368565 AGTCCCAAGTCCCTAAAAAGTC 57.631 45.455 0.00 0.00 0.00 3.01
435 437 3.074094 AGTCCCAAGTCCCTAAAAAGTCC 59.926 47.826 0.00 0.00 0.00 3.85
436 438 3.074094 GTCCCAAGTCCCTAAAAAGTCCT 59.926 47.826 0.00 0.00 0.00 3.85
437 439 3.725267 TCCCAAGTCCCTAAAAAGTCCTT 59.275 43.478 0.00 0.00 0.00 3.36
438 440 4.915194 TCCCAAGTCCCTAAAAAGTCCTTA 59.085 41.667 0.00 0.00 0.00 2.69
439 441 5.008331 CCCAAGTCCCTAAAAAGTCCTTAC 58.992 45.833 0.00 0.00 0.00 2.34
440 442 5.008331 CCAAGTCCCTAAAAAGTCCTTACC 58.992 45.833 0.00 0.00 0.00 2.85
441 443 5.222068 CCAAGTCCCTAAAAAGTCCTTACCT 60.222 44.000 0.00 0.00 0.00 3.08
442 444 5.500546 AGTCCCTAAAAAGTCCTTACCTG 57.499 43.478 0.00 0.00 0.00 4.00
443 445 4.912133 AGTCCCTAAAAAGTCCTTACCTGT 59.088 41.667 0.00 0.00 0.00 4.00
444 446 5.371769 AGTCCCTAAAAAGTCCTTACCTGTT 59.628 40.000 0.00 0.00 0.00 3.16
445 447 6.066690 GTCCCTAAAAAGTCCTTACCTGTTT 58.933 40.000 0.00 0.00 0.00 2.83
446 448 6.016527 GTCCCTAAAAAGTCCTTACCTGTTTG 60.017 42.308 0.00 0.00 0.00 2.93
447 449 5.243060 CCCTAAAAAGTCCTTACCTGTTTGG 59.757 44.000 0.00 0.00 42.93 3.28
457 459 3.036431 CCTGTTTGGTTCCTGGGAC 57.964 57.895 0.00 0.00 0.00 4.46
458 460 0.478507 CCTGTTTGGTTCCTGGGACT 59.521 55.000 4.84 0.00 0.00 3.85
459 461 1.133482 CCTGTTTGGTTCCTGGGACTT 60.133 52.381 4.84 0.00 0.00 3.01
460 462 2.107552 CCTGTTTGGTTCCTGGGACTTA 59.892 50.000 4.84 0.00 0.00 2.24
461 463 3.245264 CCTGTTTGGTTCCTGGGACTTAT 60.245 47.826 4.84 0.00 0.00 1.73
462 464 4.018779 CCTGTTTGGTTCCTGGGACTTATA 60.019 45.833 4.84 0.00 0.00 0.98
463 465 5.515886 CCTGTTTGGTTCCTGGGACTTATAA 60.516 44.000 4.84 0.00 0.00 0.98
464 466 5.566469 TGTTTGGTTCCTGGGACTTATAAG 58.434 41.667 11.05 11.05 0.00 1.73
465 467 5.073965 TGTTTGGTTCCTGGGACTTATAAGT 59.926 40.000 18.05 18.05 43.16 2.24
488 490 9.448587 AAGTCCCTATAAGACCATATTACAACT 57.551 33.333 0.09 0.00 34.67 3.16
498 500 9.448587 AAGACCATATTACAACTATAAGTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
507 509 7.852550 ACAACTATAAGTCCCTATAAGTCCC 57.147 40.000 0.00 0.00 0.00 4.46
508 510 7.602868 ACAACTATAAGTCCCTATAAGTCCCT 58.397 38.462 0.00 0.00 0.00 4.20
509 511 7.729431 ACAACTATAAGTCCCTATAAGTCCCTC 59.271 40.741 0.00 0.00 0.00 4.30
510 512 6.803017 ACTATAAGTCCCTATAAGTCCCTCC 58.197 44.000 0.00 0.00 0.00 4.30
511 513 5.970692 ATAAGTCCCTATAAGTCCCTCCT 57.029 43.478 0.00 0.00 0.00 3.69
512 514 4.645968 AAGTCCCTATAAGTCCCTCCTT 57.354 45.455 0.00 0.00 0.00 3.36
513 515 4.201894 AGTCCCTATAAGTCCCTCCTTC 57.798 50.000 0.00 0.00 0.00 3.46
514 516 3.536434 AGTCCCTATAAGTCCCTCCTTCA 59.464 47.826 0.00 0.00 0.00 3.02
515 517 3.898741 GTCCCTATAAGTCCCTCCTTCAG 59.101 52.174 0.00 0.00 0.00 3.02
516 518 3.797845 TCCCTATAAGTCCCTCCTTCAGA 59.202 47.826 0.00 0.00 0.00 3.27
517 519 4.140900 TCCCTATAAGTCCCTCCTTCAGAG 60.141 50.000 0.00 0.00 42.83 3.35
518 520 4.388118 CCCTATAAGTCCCTCCTTCAGAGT 60.388 50.000 0.00 0.00 41.47 3.24
519 521 4.830600 CCTATAAGTCCCTCCTTCAGAGTC 59.169 50.000 0.00 0.00 41.47 3.36
520 522 4.618378 ATAAGTCCCTCCTTCAGAGTCT 57.382 45.455 0.00 0.00 41.47 3.24
521 523 3.268034 AAGTCCCTCCTTCAGAGTCTT 57.732 47.619 0.00 0.00 41.47 3.01
522 524 4.405756 AAGTCCCTCCTTCAGAGTCTTA 57.594 45.455 0.00 0.00 41.47 2.10
523 525 4.618378 AGTCCCTCCTTCAGAGTCTTAT 57.382 45.455 0.00 0.00 41.47 1.73
524 526 4.954089 AGTCCCTCCTTCAGAGTCTTATT 58.046 43.478 0.00 0.00 41.47 1.40
525 527 5.346270 AGTCCCTCCTTCAGAGTCTTATTT 58.654 41.667 0.00 0.00 41.47 1.40
526 528 5.423931 AGTCCCTCCTTCAGAGTCTTATTTC 59.576 44.000 0.00 0.00 41.47 2.17
527 529 5.187967 GTCCCTCCTTCAGAGTCTTATTTCA 59.812 44.000 0.00 0.00 41.47 2.69
528 530 5.966935 TCCCTCCTTCAGAGTCTTATTTCAT 59.033 40.000 0.00 0.00 41.47 2.57
529 531 7.070074 GTCCCTCCTTCAGAGTCTTATTTCATA 59.930 40.741 0.00 0.00 41.47 2.15
530 532 7.623677 TCCCTCCTTCAGAGTCTTATTTCATAA 59.376 37.037 0.00 0.00 41.47 1.90
531 533 7.930865 CCCTCCTTCAGAGTCTTATTTCATAAG 59.069 40.741 0.00 0.00 41.47 1.73
532 534 8.482128 CCTCCTTCAGAGTCTTATTTCATAAGT 58.518 37.037 0.00 0.00 41.47 2.24
533 535 9.528018 CTCCTTCAGAGTCTTATTTCATAAGTC 57.472 37.037 0.00 0.00 37.60 3.01
534 536 8.478877 TCCTTCAGAGTCTTATTTCATAAGTCC 58.521 37.037 0.00 0.00 42.21 3.85
535 537 7.713073 CCTTCAGAGTCTTATTTCATAAGTCCC 59.287 40.741 0.00 0.00 42.21 4.46
536 538 7.733773 TCAGAGTCTTATTTCATAAGTCCCA 57.266 36.000 0.00 0.00 42.21 4.37
537 539 8.146053 TCAGAGTCTTATTTCATAAGTCCCAA 57.854 34.615 0.00 0.00 42.21 4.12
538 540 8.602424 TCAGAGTCTTATTTCATAAGTCCCAAA 58.398 33.333 0.00 0.00 42.21 3.28
539 541 9.401058 CAGAGTCTTATTTCATAAGTCCCAAAT 57.599 33.333 0.00 0.00 42.21 2.32
540 542 9.401058 AGAGTCTTATTTCATAAGTCCCAAATG 57.599 33.333 3.93 0.00 42.21 2.32
541 543 8.000780 AGTCTTATTTCATAAGTCCCAAATGC 57.999 34.615 3.93 0.00 42.21 3.56
542 544 7.068716 AGTCTTATTTCATAAGTCCCAAATGCC 59.931 37.037 3.93 0.00 42.21 4.40
543 545 6.323739 TCTTATTTCATAAGTCCCAAATGCCC 59.676 38.462 3.93 0.00 42.21 5.36
544 546 3.464720 TTCATAAGTCCCAAATGCCCA 57.535 42.857 0.00 0.00 0.00 5.36
545 547 3.686227 TCATAAGTCCCAAATGCCCAT 57.314 42.857 0.00 0.00 0.00 4.00
546 548 3.992999 TCATAAGTCCCAAATGCCCATT 58.007 40.909 0.00 0.00 0.00 3.16
547 549 4.360889 TCATAAGTCCCAAATGCCCATTT 58.639 39.130 0.57 0.57 41.33 2.32
548 550 5.523588 TCATAAGTCCCAAATGCCCATTTA 58.476 37.500 5.97 0.00 38.84 1.40
549 551 5.960811 TCATAAGTCCCAAATGCCCATTTAA 59.039 36.000 5.97 0.00 38.84 1.52
550 552 4.824479 AAGTCCCAAATGCCCATTTAAG 57.176 40.909 5.97 1.94 38.84 1.85
551 553 3.790126 AGTCCCAAATGCCCATTTAAGT 58.210 40.909 5.97 0.00 38.84 2.24
552 554 3.769300 AGTCCCAAATGCCCATTTAAGTC 59.231 43.478 5.97 0.45 38.84 3.01
553 555 3.103742 TCCCAAATGCCCATTTAAGTCC 58.896 45.455 5.97 0.00 38.84 3.85
554 556 2.170397 CCCAAATGCCCATTTAAGTCCC 59.830 50.000 5.97 0.00 38.84 4.46
555 557 3.106827 CCAAATGCCCATTTAAGTCCCT 58.893 45.455 5.97 0.00 38.84 4.20
556 558 4.285863 CCAAATGCCCATTTAAGTCCCTA 58.714 43.478 5.97 0.00 38.84 3.53
557 559 4.901250 CCAAATGCCCATTTAAGTCCCTAT 59.099 41.667 5.97 0.00 38.84 2.57
558 560 6.074648 CCAAATGCCCATTTAAGTCCCTATA 58.925 40.000 5.97 0.00 38.84 1.31
559 561 6.553100 CCAAATGCCCATTTAAGTCCCTATAA 59.447 38.462 5.97 0.00 38.84 0.98
560 562 7.255942 CCAAATGCCCATTTAAGTCCCTATAAG 60.256 40.741 5.97 0.00 38.84 1.73
561 563 5.987019 TGCCCATTTAAGTCCCTATAAGT 57.013 39.130 0.00 0.00 0.00 2.24
562 564 5.937111 TGCCCATTTAAGTCCCTATAAGTC 58.063 41.667 0.00 0.00 0.00 3.01
563 565 5.163131 TGCCCATTTAAGTCCCTATAAGTCC 60.163 44.000 0.00 0.00 0.00 3.85
564 566 5.748139 GCCCATTTAAGTCCCTATAAGTCCC 60.748 48.000 0.00 0.00 0.00 4.46
565 567 5.611408 CCCATTTAAGTCCCTATAAGTCCCT 59.389 44.000 0.00 0.00 0.00 4.20
566 568 6.239915 CCCATTTAAGTCCCTATAAGTCCCTC 60.240 46.154 0.00 0.00 0.00 4.30
567 569 6.239915 CCATTTAAGTCCCTATAAGTCCCTCC 60.240 46.154 0.00 0.00 0.00 4.30
568 570 5.763239 TTAAGTCCCTATAAGTCCCTCCT 57.237 43.478 0.00 0.00 0.00 3.69
569 571 3.621682 AGTCCCTATAAGTCCCTCCTG 57.378 52.381 0.00 0.00 0.00 3.86
570 572 2.866454 AGTCCCTATAAGTCCCTCCTGT 59.134 50.000 0.00 0.00 0.00 4.00
571 573 3.275228 AGTCCCTATAAGTCCCTCCTGTT 59.725 47.826 0.00 0.00 0.00 3.16
572 574 4.038633 GTCCCTATAAGTCCCTCCTGTTT 58.961 47.826 0.00 0.00 0.00 2.83
573 575 4.037927 TCCCTATAAGTCCCTCCTGTTTG 58.962 47.826 0.00 0.00 0.00 2.93
574 576 3.136626 CCCTATAAGTCCCTCCTGTTTGG 59.863 52.174 0.00 0.00 37.10 3.28
575 577 3.780850 CCTATAAGTCCCTCCTGTTTGGT 59.219 47.826 0.00 0.00 37.07 3.67
576 578 4.227527 CCTATAAGTCCCTCCTGTTTGGTT 59.772 45.833 0.00 0.00 37.07 3.67
577 579 4.741928 ATAAGTCCCTCCTGTTTGGTTT 57.258 40.909 0.00 0.00 37.07 3.27
578 580 5.853572 ATAAGTCCCTCCTGTTTGGTTTA 57.146 39.130 0.00 0.00 37.07 2.01
579 581 3.790089 AGTCCCTCCTGTTTGGTTTAG 57.210 47.619 0.00 0.00 37.07 1.85
580 582 3.323775 AGTCCCTCCTGTTTGGTTTAGA 58.676 45.455 0.00 0.00 37.07 2.10
581 583 3.916989 AGTCCCTCCTGTTTGGTTTAGAT 59.083 43.478 0.00 0.00 37.07 1.98
582 584 4.010349 GTCCCTCCTGTTTGGTTTAGATG 58.990 47.826 0.00 0.00 37.07 2.90
583 585 3.010138 TCCCTCCTGTTTGGTTTAGATGG 59.990 47.826 0.00 0.00 37.07 3.51
584 586 3.356290 CCTCCTGTTTGGTTTAGATGGG 58.644 50.000 0.00 0.00 37.07 4.00
585 587 3.010138 CCTCCTGTTTGGTTTAGATGGGA 59.990 47.826 0.00 0.00 37.07 4.37
586 588 4.010349 CTCCTGTTTGGTTTAGATGGGAC 58.990 47.826 0.00 0.00 37.07 4.46
587 589 3.655777 TCCTGTTTGGTTTAGATGGGACT 59.344 43.478 0.00 0.00 37.07 3.85
588 590 4.105697 TCCTGTTTGGTTTAGATGGGACTT 59.894 41.667 0.00 0.00 37.07 3.01
589 591 5.311121 TCCTGTTTGGTTTAGATGGGACTTA 59.689 40.000 0.00 0.00 37.07 2.24
590 592 6.011981 TCCTGTTTGGTTTAGATGGGACTTAT 60.012 38.462 0.00 0.00 37.07 1.73
591 593 7.183112 TCCTGTTTGGTTTAGATGGGACTTATA 59.817 37.037 0.00 0.00 37.07 0.98
592 594 7.499232 CCTGTTTGGTTTAGATGGGACTTATAG 59.501 40.741 0.00 0.00 0.00 1.31
593 595 8.153221 TGTTTGGTTTAGATGGGACTTATAGA 57.847 34.615 0.00 0.00 0.00 1.98
594 596 8.265055 TGTTTGGTTTAGATGGGACTTATAGAG 58.735 37.037 0.00 0.00 0.00 2.43
595 597 8.483758 GTTTGGTTTAGATGGGACTTATAGAGA 58.516 37.037 0.00 0.00 0.00 3.10
596 598 7.598759 TGGTTTAGATGGGACTTATAGAGAC 57.401 40.000 0.00 0.00 0.00 3.36
597 599 7.363031 TGGTTTAGATGGGACTTATAGAGACT 58.637 38.462 0.00 0.00 0.00 3.24
598 600 7.844779 TGGTTTAGATGGGACTTATAGAGACTT 59.155 37.037 0.00 0.00 0.00 3.01
599 601 8.706521 GGTTTAGATGGGACTTATAGAGACTTT 58.293 37.037 0.00 0.00 0.00 2.66
624 626 9.511272 TTTTTAAGTCCCTAAGTCAATAAGTCC 57.489 33.333 0.00 0.00 0.00 3.85
625 627 5.695424 AAGTCCCTAAGTCAATAAGTCCC 57.305 43.478 0.00 0.00 0.00 4.46
626 628 4.961585 AGTCCCTAAGTCAATAAGTCCCT 58.038 43.478 0.00 0.00 0.00 4.20
627 629 4.717280 AGTCCCTAAGTCAATAAGTCCCTG 59.283 45.833 0.00 0.00 0.00 4.45
628 630 4.037927 TCCCTAAGTCAATAAGTCCCTGG 58.962 47.826 0.00 0.00 0.00 4.45
629 631 4.037927 CCCTAAGTCAATAAGTCCCTGGA 58.962 47.826 0.00 0.00 0.00 3.86
630 632 4.473559 CCCTAAGTCAATAAGTCCCTGGAA 59.526 45.833 0.00 0.00 0.00 3.53
631 633 5.045140 CCCTAAGTCAATAAGTCCCTGGAAA 60.045 44.000 0.00 0.00 0.00 3.13
632 634 5.880887 CCTAAGTCAATAAGTCCCTGGAAAC 59.119 44.000 0.00 0.00 0.00 2.78
633 635 4.993705 AGTCAATAAGTCCCTGGAAACA 57.006 40.909 0.00 0.00 39.59 2.83
634 636 5.319043 AGTCAATAAGTCCCTGGAAACAA 57.681 39.130 0.00 0.00 42.06 2.83
635 637 5.701224 AGTCAATAAGTCCCTGGAAACAAA 58.299 37.500 0.00 0.00 42.06 2.83
636 638 5.535030 AGTCAATAAGTCCCTGGAAACAAAC 59.465 40.000 0.00 0.00 42.06 2.93
637 639 5.300792 GTCAATAAGTCCCTGGAAACAAACA 59.699 40.000 0.00 0.00 42.06 2.83
638 640 5.300792 TCAATAAGTCCCTGGAAACAAACAC 59.699 40.000 0.00 0.00 42.06 3.32
639 641 2.067365 AGTCCCTGGAAACAAACACC 57.933 50.000 0.00 0.00 42.06 4.16
640 642 1.037493 GTCCCTGGAAACAAACACCC 58.963 55.000 0.00 0.00 42.06 4.61
827 833 2.327200 TCGGAGAGCAGATAAGTCGA 57.673 50.000 0.00 0.00 0.00 4.20
855 862 2.426305 AAACCCTAGCCTTGCGCCTT 62.426 55.000 4.18 0.00 38.78 4.35
895 902 2.654877 TCGCCACTCGAAACCCTC 59.345 61.111 0.00 0.00 45.36 4.30
1050 1062 2.675056 CCTCGTCGTCGTCGGAAGT 61.675 63.158 11.74 0.00 38.33 3.01
1105 1129 2.567049 CGGAAGCGGAGACTCGTT 59.433 61.111 0.00 0.00 0.00 3.85
1115 1139 1.004080 AGACTCGTTCCCTCGTCGA 60.004 57.895 0.00 0.00 0.00 4.20
1190 1214 1.306141 TGATTGCGAGGAGGGAGGT 60.306 57.895 0.00 0.00 0.00 3.85
1211 1241 3.394836 GCTCTCGGAGTGGGCCTT 61.395 66.667 4.53 0.00 42.35 4.35
1223 1253 3.706373 GGCCTTGTCGGAGCCAGA 61.706 66.667 0.00 0.00 46.34 3.86
1224 1254 2.125350 GCCTTGTCGGAGCCAGAG 60.125 66.667 0.00 0.00 33.16 3.35
1225 1255 2.125350 CCTTGTCGGAGCCAGAGC 60.125 66.667 0.00 0.00 40.32 4.09
1226 1256 2.125350 CTTGTCGGAGCCAGAGCC 60.125 66.667 0.00 0.00 41.25 4.70
1227 1257 2.922503 TTGTCGGAGCCAGAGCCA 60.923 61.111 0.00 0.00 41.25 4.75
1228 1258 2.849120 CTTGTCGGAGCCAGAGCCAG 62.849 65.000 0.00 0.00 41.25 4.85
1229 1259 3.071206 GTCGGAGCCAGAGCCAGA 61.071 66.667 0.00 0.00 41.25 3.86
1404 1443 1.890552 TCTCCCTACTCCTCGTACCT 58.109 55.000 0.00 0.00 0.00 3.08
1405 1444 3.051940 TCTCCCTACTCCTCGTACCTA 57.948 52.381 0.00 0.00 0.00 3.08
1419 1458 7.743749 TCCTCGTACCTATAACTAACTCATCT 58.256 38.462 0.00 0.00 0.00 2.90
1539 1581 0.106569 TCATGGAATGCCTTCGCCAT 60.107 50.000 0.00 0.00 46.21 4.40
1569 1611 8.378172 ACTTAAATCATCCGGTATGTATTGTG 57.622 34.615 0.00 4.87 36.89 3.33
1579 1624 5.766670 CCGGTATGTATTGTGTCTACTCCTA 59.233 44.000 0.00 0.00 0.00 2.94
1591 1636 2.623889 TCTACTCCTATCGCTTTGCTCC 59.376 50.000 0.00 0.00 0.00 4.70
1700 1834 4.382040 CCCGTCCCTATATGCAGTCATTAG 60.382 50.000 0.00 0.00 34.22 1.73
1712 1846 5.724328 TGCAGTCATTAGTAACTCTTCCAG 58.276 41.667 0.00 0.00 0.00 3.86
1733 1872 2.134789 ATCTCAAGCGGCCTTCAAAT 57.865 45.000 0.00 0.00 0.00 2.32
1764 1908 3.443099 TTGATCGCTCCTACTGTCATG 57.557 47.619 0.00 0.00 0.00 3.07
1975 2134 1.418334 TTCCATGGTTGGTTGGTTGG 58.582 50.000 12.58 0.00 44.06 3.77
1987 2146 1.416030 GTTGGTTGGCCAGGAAAATGT 59.584 47.619 5.11 0.00 46.91 2.71
2003 2162 1.619807 ATGTGTACGTACCTGCCCCC 61.620 60.000 22.43 3.17 0.00 5.40
2023 2182 1.338674 CGGCAAGGTGACCAGATACAA 60.339 52.381 3.63 0.00 0.00 2.41
2726 3016 6.603599 GGCTCCTAGTTTTTATTCCATGTTCT 59.396 38.462 0.00 0.00 0.00 3.01
2785 3200 1.342174 TCCACGGAACTACACCTTGTC 59.658 52.381 0.00 0.00 0.00 3.18
2831 3283 6.402222 TCCTTGCTTGTGTTTGTTTTACATT 58.598 32.000 0.00 0.00 0.00 2.71
2842 3294 4.944962 TGTTTTACATTCAGATGAGCCG 57.055 40.909 0.00 0.00 36.73 5.52
2894 3349 1.057851 TCTTGGGTGGGGAACTCGTT 61.058 55.000 0.00 0.00 28.32 3.85
2915 3374 2.017049 GTGATGGCAGTTGTATGTCCC 58.983 52.381 0.00 0.00 0.00 4.46
3354 3841 3.603532 TGTGAAACAGATGATGGCTCTC 58.396 45.455 0.00 0.00 45.67 3.20
3411 3906 1.226746 AGCAACGCTGTGGTTAACTC 58.773 50.000 5.42 0.28 37.57 3.01
3441 3936 4.910195 TGGCAACTCAACTTCATCATACT 58.090 39.130 0.00 0.00 37.61 2.12
3448 3943 6.872920 ACTCAACTTCATCATACTCCTCTTC 58.127 40.000 0.00 0.00 0.00 2.87
3488 3990 8.484641 TCATGTCTTACTTATTCTCTTTGCAG 57.515 34.615 0.00 0.00 0.00 4.41
3620 4138 9.903682 CTTGATAGTTCAACTGTTTGATGAAAT 57.096 29.630 0.00 0.00 41.50 2.17
3947 4467 6.308371 TCGTGGTTCACTTCTTTTTATTCC 57.692 37.500 0.00 0.00 31.34 3.01
3983 4503 4.129380 TGTACTGAATGCCATGCTACATC 58.871 43.478 0.00 0.00 0.00 3.06
3991 4511 1.027357 CCATGCTACATCCCTTGTGC 58.973 55.000 0.00 0.00 39.48 4.57
3999 4519 2.894257 ATCCCTTGTGCGAGCACCA 61.894 57.895 23.31 13.13 45.63 4.17
4063 4583 5.905913 AGCATGTACCTTAAGTATTCCCTCT 59.094 40.000 0.97 0.00 32.28 3.69
4084 4604 7.174426 CCCTCTGTTCCTTTTTATAAGTCGTTT 59.826 37.037 0.00 0.00 0.00 3.60
4105 4625 9.058174 TCGTTTTAGACAGATGATTTTAAACCA 57.942 29.630 0.00 0.00 0.00 3.67
4182 4755 1.680207 GATCCAGAAGCAAGGCATTCC 59.320 52.381 0.00 0.00 0.00 3.01
4184 4757 1.660560 CCAGAAGCAAGGCATTCCGG 61.661 60.000 0.00 0.00 37.47 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
212 213 1.967319 AGGCGTTTCATGTCAACACT 58.033 45.000 10.02 5.59 0.00 3.55
287 288 4.631813 ACGAAGCTTGTCATTGATAAGGAC 59.368 41.667 20.50 8.40 42.21 3.85
292 293 6.128282 GGAGAAAACGAAGCTTGTCATTGATA 60.128 38.462 2.10 0.00 0.00 2.15
299 300 3.810386 AGAAGGAGAAAACGAAGCTTGTC 59.190 43.478 2.10 0.00 0.00 3.18
357 359 0.779997 AACCAAACAGGGCCTGAGAT 59.220 50.000 38.99 21.26 43.89 2.75
358 360 0.110486 GAACCAAACAGGGCCTGAGA 59.890 55.000 38.99 0.00 43.89 3.27
359 361 0.178992 TGAACCAAACAGGGCCTGAG 60.179 55.000 38.99 25.46 43.89 3.35
360 362 0.482446 ATGAACCAAACAGGGCCTGA 59.518 50.000 38.99 15.25 43.89 3.86
361 363 2.214376 TATGAACCAAACAGGGCCTG 57.786 50.000 31.62 31.62 43.89 4.85
362 364 2.110011 ACTTATGAACCAAACAGGGCCT 59.890 45.455 0.00 0.00 43.89 5.19
363 365 2.492088 GACTTATGAACCAAACAGGGCC 59.508 50.000 0.00 0.00 43.89 5.80
364 366 3.421844 AGACTTATGAACCAAACAGGGC 58.578 45.455 0.00 0.00 43.89 5.19
365 367 5.648092 CCTAAGACTTATGAACCAAACAGGG 59.352 44.000 0.00 0.00 43.89 4.45
366 368 6.371825 GTCCTAAGACTTATGAACCAAACAGG 59.628 42.308 2.20 0.00 40.95 4.00
367 369 7.365840 GTCCTAAGACTTATGAACCAAACAG 57.634 40.000 2.20 0.00 40.10 3.16
394 396 7.757611 TGGGACTTATAAGTTGGGACTAAAAA 58.242 34.615 18.96 0.00 39.88 1.94
395 397 7.332433 TGGGACTTATAAGTTGGGACTAAAA 57.668 36.000 18.96 0.00 39.88 1.52
396 398 6.956102 TGGGACTTATAAGTTGGGACTAAA 57.044 37.500 18.96 0.00 39.88 1.85
397 399 6.502863 ACTTGGGACTTATAAGTTGGGACTAA 59.497 38.462 18.96 10.32 39.88 2.24
398 400 6.027482 ACTTGGGACTTATAAGTTGGGACTA 58.973 40.000 18.96 3.96 39.88 2.59
399 401 4.850386 ACTTGGGACTTATAAGTTGGGACT 59.150 41.667 18.96 0.00 39.88 3.85
400 402 5.175388 ACTTGGGACTTATAAGTTGGGAC 57.825 43.478 18.96 6.19 39.88 4.46
401 403 4.226620 GGACTTGGGACTTATAAGTTGGGA 59.773 45.833 18.96 6.15 39.88 4.37
402 404 4.524053 GGACTTGGGACTTATAAGTTGGG 58.476 47.826 18.96 10.37 39.88 4.12
403 405 4.227527 AGGGACTTGGGACTTATAAGTTGG 59.772 45.833 18.96 10.07 34.84 3.77
404 406 5.437191 AGGGACTTGGGACTTATAAGTTG 57.563 43.478 18.96 9.81 34.84 3.16
405 407 7.578458 TTTAGGGACTTGGGACTTATAAGTT 57.422 36.000 18.96 2.29 38.78 2.66
406 408 7.578458 TTTTAGGGACTTGGGACTTATAAGT 57.422 36.000 18.05 18.05 40.66 2.24
407 409 8.107729 ACTTTTTAGGGACTTGGGACTTATAAG 58.892 37.037 11.05 11.05 41.75 1.73
408 410 7.992295 ACTTTTTAGGGACTTGGGACTTATAA 58.008 34.615 0.00 0.00 41.75 0.98
409 411 7.311486 GGACTTTTTAGGGACTTGGGACTTATA 60.311 40.741 0.00 0.00 41.75 0.98
410 412 6.464530 ACTTTTTAGGGACTTGGGACTTAT 57.535 37.500 0.00 0.00 41.75 1.73
411 413 5.221986 GGACTTTTTAGGGACTTGGGACTTA 60.222 44.000 0.00 0.00 41.75 2.24
412 414 4.447325 GGACTTTTTAGGGACTTGGGACTT 60.447 45.833 0.00 0.00 41.75 3.01
413 415 3.074094 GGACTTTTTAGGGACTTGGGACT 59.926 47.826 0.00 0.00 41.75 3.85
414 416 3.074094 AGGACTTTTTAGGGACTTGGGAC 59.926 47.826 0.00 0.00 41.75 4.46
415 417 3.332968 AGGACTTTTTAGGGACTTGGGA 58.667 45.455 0.00 0.00 41.75 4.37
416 418 3.808834 AGGACTTTTTAGGGACTTGGG 57.191 47.619 0.00 0.00 41.75 4.12
417 419 5.008331 GGTAAGGACTTTTTAGGGACTTGG 58.992 45.833 0.00 0.00 41.75 3.61
418 420 5.705905 CAGGTAAGGACTTTTTAGGGACTTG 59.294 44.000 0.00 0.00 41.75 3.16
419 421 5.371769 ACAGGTAAGGACTTTTTAGGGACTT 59.628 40.000 0.00 0.00 41.75 3.01
420 422 4.912133 ACAGGTAAGGACTTTTTAGGGACT 59.088 41.667 0.00 0.00 46.37 3.85
421 423 5.238624 ACAGGTAAGGACTTTTTAGGGAC 57.761 43.478 0.00 0.00 0.00 4.46
422 424 5.917545 AACAGGTAAGGACTTTTTAGGGA 57.082 39.130 0.00 0.00 0.00 4.20
423 425 5.243060 CCAAACAGGTAAGGACTTTTTAGGG 59.757 44.000 0.00 0.00 0.00 3.53
424 426 6.327279 CCAAACAGGTAAGGACTTTTTAGG 57.673 41.667 0.00 0.00 0.00 2.69
439 441 0.478507 AGTCCCAGGAACCAAACAGG 59.521 55.000 0.00 0.00 45.67 4.00
440 442 2.364972 AAGTCCCAGGAACCAAACAG 57.635 50.000 0.00 0.00 0.00 3.16
441 443 5.073965 ACTTATAAGTCCCAGGAACCAAACA 59.926 40.000 12.50 0.00 32.86 2.83
442 444 5.567430 ACTTATAAGTCCCAGGAACCAAAC 58.433 41.667 12.50 0.00 32.86 2.93
443 445 5.853572 ACTTATAAGTCCCAGGAACCAAA 57.146 39.130 12.50 0.00 32.86 3.28
462 464 9.448587 AGTTGTAATATGGTCTTATAGGGACTT 57.551 33.333 7.52 0.00 41.75 3.01
472 474 9.448587 AGGGACTTATAGTTGTAATATGGTCTT 57.551 33.333 0.00 0.00 27.25 3.01
481 483 9.372189 GGGACTTATAGGGACTTATAGTTGTAA 57.628 37.037 0.00 0.00 41.75 2.41
482 484 8.740512 AGGGACTTATAGGGACTTATAGTTGTA 58.259 37.037 0.00 0.00 34.75 2.41
483 485 7.602868 AGGGACTTATAGGGACTTATAGTTGT 58.397 38.462 0.00 0.00 34.75 3.32
484 486 7.178805 GGAGGGACTTATAGGGACTTATAGTTG 59.821 44.444 0.00 0.00 41.55 3.16
485 487 7.076566 AGGAGGGACTTATAGGGACTTATAGTT 59.923 40.741 0.00 0.00 41.55 2.24
486 488 6.571180 AGGAGGGACTTATAGGGACTTATAGT 59.429 42.308 0.00 0.00 41.55 2.12
487 489 7.046891 AGGAGGGACTTATAGGGACTTATAG 57.953 44.000 0.00 0.00 41.55 1.31
488 490 7.075915 TGAAGGAGGGACTTATAGGGACTTATA 59.924 40.741 0.00 0.00 41.55 0.98
489 491 5.970692 AGGAGGGACTTATAGGGACTTAT 57.029 43.478 0.00 0.00 41.55 1.73
490 492 5.197189 TGAAGGAGGGACTTATAGGGACTTA 59.803 44.000 0.00 0.00 41.55 2.24
491 493 4.015541 TGAAGGAGGGACTTATAGGGACTT 60.016 45.833 0.00 0.00 41.55 3.01
492 494 3.536434 TGAAGGAGGGACTTATAGGGACT 59.464 47.826 0.00 0.00 41.55 3.85
493 495 3.898741 CTGAAGGAGGGACTTATAGGGAC 59.101 52.174 0.00 0.00 41.55 4.46
494 496 3.797845 TCTGAAGGAGGGACTTATAGGGA 59.202 47.826 0.00 0.00 41.55 4.20
495 497 4.156477 CTCTGAAGGAGGGACTTATAGGG 58.844 52.174 0.00 0.00 41.55 3.53
496 498 4.810345 ACTCTGAAGGAGGGACTTATAGG 58.190 47.826 0.00 0.00 45.83 2.57
497 499 5.701224 AGACTCTGAAGGAGGGACTTATAG 58.299 45.833 0.00 0.00 45.83 1.31
498 500 5.735733 AGACTCTGAAGGAGGGACTTATA 57.264 43.478 0.00 0.00 45.83 0.98
499 501 4.618378 AGACTCTGAAGGAGGGACTTAT 57.382 45.455 0.00 0.00 45.83 1.73
500 502 4.405756 AAGACTCTGAAGGAGGGACTTA 57.594 45.455 0.00 0.00 45.83 2.24
501 503 3.268034 AAGACTCTGAAGGAGGGACTT 57.732 47.619 0.00 0.00 45.83 3.01
502 504 4.618378 ATAAGACTCTGAAGGAGGGACT 57.382 45.455 0.00 0.00 45.83 3.85
503 505 5.187967 TGAAATAAGACTCTGAAGGAGGGAC 59.812 44.000 0.00 0.00 45.83 4.46
504 506 5.342017 TGAAATAAGACTCTGAAGGAGGGA 58.658 41.667 0.00 0.00 45.83 4.20
505 507 5.683876 TGAAATAAGACTCTGAAGGAGGG 57.316 43.478 0.00 0.00 45.83 4.30
520 522 5.960811 TGGGCATTTGGGACTTATGAAATAA 59.039 36.000 0.00 0.00 36.20 1.40
521 523 5.523588 TGGGCATTTGGGACTTATGAAATA 58.476 37.500 0.00 0.00 0.00 1.40
522 524 4.360889 TGGGCATTTGGGACTTATGAAAT 58.639 39.130 0.00 0.00 0.00 2.17
523 525 3.784178 TGGGCATTTGGGACTTATGAAA 58.216 40.909 0.00 0.00 0.00 2.69
524 526 3.464720 TGGGCATTTGGGACTTATGAA 57.535 42.857 0.00 0.00 0.00 2.57
525 527 3.686227 ATGGGCATTTGGGACTTATGA 57.314 42.857 0.00 0.00 0.00 2.15
526 528 4.758773 AAATGGGCATTTGGGACTTATG 57.241 40.909 0.00 0.00 39.36 1.90
527 529 5.963865 ACTTAAATGGGCATTTGGGACTTAT 59.036 36.000 0.00 0.00 40.83 1.73
528 530 5.337788 ACTTAAATGGGCATTTGGGACTTA 58.662 37.500 0.00 0.00 40.83 2.24
529 531 4.167319 ACTTAAATGGGCATTTGGGACTT 58.833 39.130 0.00 0.00 40.83 3.01
530 532 3.769300 GACTTAAATGGGCATTTGGGACT 59.231 43.478 0.00 0.00 40.83 3.85
531 533 3.118775 GGACTTAAATGGGCATTTGGGAC 60.119 47.826 0.00 0.00 40.83 4.46
532 534 3.103742 GGACTTAAATGGGCATTTGGGA 58.896 45.455 0.00 0.00 40.83 4.37
533 535 2.170397 GGGACTTAAATGGGCATTTGGG 59.830 50.000 0.00 0.00 40.83 4.12
534 536 3.106827 AGGGACTTAAATGGGCATTTGG 58.893 45.455 0.00 0.00 40.83 3.28
535 537 7.287696 ACTTATAGGGACTTAAATGGGCATTTG 59.712 37.037 0.00 0.00 39.68 2.32
536 538 7.362234 ACTTATAGGGACTTAAATGGGCATTT 58.638 34.615 0.00 0.00 41.22 2.32
537 539 6.922540 ACTTATAGGGACTTAAATGGGCATT 58.077 36.000 0.00 0.00 41.75 3.56
538 540 6.467339 GGACTTATAGGGACTTAAATGGGCAT 60.467 42.308 0.00 0.00 41.75 4.40
539 541 5.163131 GGACTTATAGGGACTTAAATGGGCA 60.163 44.000 0.00 0.00 41.75 5.36
540 542 5.314529 GGACTTATAGGGACTTAAATGGGC 58.685 45.833 0.00 0.00 41.75 5.36
541 543 5.611408 AGGGACTTATAGGGACTTAAATGGG 59.389 44.000 0.00 0.00 34.75 4.00
542 544 6.239915 GGAGGGACTTATAGGGACTTAAATGG 60.240 46.154 0.00 0.00 41.55 3.16
543 545 6.559157 AGGAGGGACTTATAGGGACTTAAATG 59.441 42.308 0.00 0.00 41.55 2.32
544 546 6.559157 CAGGAGGGACTTATAGGGACTTAAAT 59.441 42.308 0.00 0.00 41.55 1.40
545 547 5.903589 CAGGAGGGACTTATAGGGACTTAAA 59.096 44.000 0.00 0.00 41.55 1.52
546 548 5.042827 ACAGGAGGGACTTATAGGGACTTAA 60.043 44.000 0.00 0.00 41.55 1.85
547 549 4.485021 ACAGGAGGGACTTATAGGGACTTA 59.515 45.833 0.00 0.00 41.55 2.24
548 550 3.275228 ACAGGAGGGACTTATAGGGACTT 59.725 47.826 0.00 0.00 41.55 3.01
549 551 2.866454 ACAGGAGGGACTTATAGGGACT 59.134 50.000 0.00 0.00 41.55 3.85
550 552 3.331718 ACAGGAGGGACTTATAGGGAC 57.668 52.381 0.00 0.00 41.55 4.46
551 553 4.037927 CAAACAGGAGGGACTTATAGGGA 58.962 47.826 0.00 0.00 41.55 4.20
552 554 3.136626 CCAAACAGGAGGGACTTATAGGG 59.863 52.174 0.00 0.00 41.55 3.53
553 555 3.780850 ACCAAACAGGAGGGACTTATAGG 59.219 47.826 0.00 0.00 41.55 2.57
554 556 5.437191 AACCAAACAGGAGGGACTTATAG 57.563 43.478 0.00 0.00 41.55 1.31
555 557 5.853572 AAACCAAACAGGAGGGACTTATA 57.146 39.130 0.00 0.00 41.55 0.98
556 558 4.741928 AAACCAAACAGGAGGGACTTAT 57.258 40.909 0.00 0.00 41.55 1.73
557 559 4.909088 TCTAAACCAAACAGGAGGGACTTA 59.091 41.667 0.00 0.00 41.55 2.24
558 560 3.720002 TCTAAACCAAACAGGAGGGACTT 59.280 43.478 0.00 0.00 41.55 3.01
560 562 3.782656 TCTAAACCAAACAGGAGGGAC 57.217 47.619 0.00 0.00 41.22 4.46
561 563 3.010138 CCATCTAAACCAAACAGGAGGGA 59.990 47.826 0.00 0.00 41.22 4.20
562 564 3.356290 CCATCTAAACCAAACAGGAGGG 58.644 50.000 0.00 0.00 41.22 4.30
563 565 3.010138 TCCCATCTAAACCAAACAGGAGG 59.990 47.826 0.00 0.00 41.22 4.30
564 566 4.010349 GTCCCATCTAAACCAAACAGGAG 58.990 47.826 0.00 0.00 41.22 3.69
565 567 3.655777 AGTCCCATCTAAACCAAACAGGA 59.344 43.478 0.00 0.00 41.22 3.86
566 568 4.034285 AGTCCCATCTAAACCAAACAGG 57.966 45.455 0.00 0.00 45.67 4.00
567 569 8.265055 TCTATAAGTCCCATCTAAACCAAACAG 58.735 37.037 0.00 0.00 0.00 3.16
568 570 8.153221 TCTATAAGTCCCATCTAAACCAAACA 57.847 34.615 0.00 0.00 0.00 2.83
569 571 8.483758 TCTCTATAAGTCCCATCTAAACCAAAC 58.516 37.037 0.00 0.00 0.00 2.93
570 572 8.483758 GTCTCTATAAGTCCCATCTAAACCAAA 58.516 37.037 0.00 0.00 0.00 3.28
571 573 7.844779 AGTCTCTATAAGTCCCATCTAAACCAA 59.155 37.037 0.00 0.00 0.00 3.67
572 574 7.363031 AGTCTCTATAAGTCCCATCTAAACCA 58.637 38.462 0.00 0.00 0.00 3.67
573 575 7.842887 AGTCTCTATAAGTCCCATCTAAACC 57.157 40.000 0.00 0.00 0.00 3.27
598 600 9.511272 GGACTTATTGACTTAGGGACTTAAAAA 57.489 33.333 0.00 0.00 41.75 1.94
599 601 8.105197 GGGACTTATTGACTTAGGGACTTAAAA 58.895 37.037 0.00 0.00 41.75 1.52
600 602 7.460082 AGGGACTTATTGACTTAGGGACTTAAA 59.540 37.037 0.00 0.00 34.75 1.52
601 603 6.964086 AGGGACTTATTGACTTAGGGACTTAA 59.036 38.462 0.00 0.00 34.75 1.85
602 604 6.383147 CAGGGACTTATTGACTTAGGGACTTA 59.617 42.308 0.00 0.00 36.39 2.24
603 605 5.189934 CAGGGACTTATTGACTTAGGGACTT 59.810 44.000 0.00 0.00 36.39 3.01
604 606 4.717280 CAGGGACTTATTGACTTAGGGACT 59.283 45.833 0.00 0.00 39.39 3.85
605 607 4.141688 CCAGGGACTTATTGACTTAGGGAC 60.142 50.000 0.00 0.00 34.60 4.46
606 608 4.037927 CCAGGGACTTATTGACTTAGGGA 58.962 47.826 0.00 0.00 34.60 4.20
607 609 4.037927 TCCAGGGACTTATTGACTTAGGG 58.962 47.826 0.00 0.00 34.60 3.53
608 610 5.693769 TTCCAGGGACTTATTGACTTAGG 57.306 43.478 0.00 0.00 34.60 2.69
609 611 6.472887 TGTTTCCAGGGACTTATTGACTTAG 58.527 40.000 0.00 0.00 34.60 2.18
610 612 6.442541 TGTTTCCAGGGACTTATTGACTTA 57.557 37.500 0.00 0.00 34.60 2.24
611 613 5.319043 TGTTTCCAGGGACTTATTGACTT 57.681 39.130 0.00 0.00 34.60 3.01
612 614 4.993705 TGTTTCCAGGGACTTATTGACT 57.006 40.909 0.00 0.00 34.60 3.41
613 615 5.300792 TGTTTGTTTCCAGGGACTTATTGAC 59.699 40.000 0.00 0.00 34.60 3.18
614 616 5.300792 GTGTTTGTTTCCAGGGACTTATTGA 59.699 40.000 0.00 0.00 34.60 2.57
615 617 5.508994 GGTGTTTGTTTCCAGGGACTTATTG 60.509 44.000 0.00 0.00 34.60 1.90
616 618 4.587262 GGTGTTTGTTTCCAGGGACTTATT 59.413 41.667 0.00 0.00 34.60 1.40
617 619 4.149598 GGTGTTTGTTTCCAGGGACTTAT 58.850 43.478 0.00 0.00 34.60 1.73
618 620 3.558033 GGTGTTTGTTTCCAGGGACTTA 58.442 45.455 0.00 0.00 34.60 2.24
619 621 2.384828 GGTGTTTGTTTCCAGGGACTT 58.615 47.619 0.00 0.00 34.60 3.01
620 622 1.411074 GGGTGTTTGTTTCCAGGGACT 60.411 52.381 0.00 0.00 43.88 3.85
621 623 1.037493 GGGTGTTTGTTTCCAGGGAC 58.963 55.000 0.00 0.00 0.00 4.46
622 624 0.930726 AGGGTGTTTGTTTCCAGGGA 59.069 50.000 0.00 0.00 0.00 4.20
623 625 1.133482 AGAGGGTGTTTGTTTCCAGGG 60.133 52.381 0.00 0.00 0.00 4.45
624 626 2.230660 GAGAGGGTGTTTGTTTCCAGG 58.769 52.381 0.00 0.00 0.00 4.45
625 627 2.880890 CTGAGAGGGTGTTTGTTTCCAG 59.119 50.000 0.00 0.00 0.00 3.86
626 628 2.241176 ACTGAGAGGGTGTTTGTTTCCA 59.759 45.455 0.00 0.00 0.00 3.53
627 629 2.879026 GACTGAGAGGGTGTTTGTTTCC 59.121 50.000 0.00 0.00 0.00 3.13
628 630 3.809905 AGACTGAGAGGGTGTTTGTTTC 58.190 45.455 0.00 0.00 0.00 2.78
629 631 3.433740 GGAGACTGAGAGGGTGTTTGTTT 60.434 47.826 0.00 0.00 0.00 2.83
630 632 2.104963 GGAGACTGAGAGGGTGTTTGTT 59.895 50.000 0.00 0.00 0.00 2.83
631 633 1.694696 GGAGACTGAGAGGGTGTTTGT 59.305 52.381 0.00 0.00 0.00 2.83
632 634 1.002544 GGGAGACTGAGAGGGTGTTTG 59.997 57.143 0.00 0.00 0.00 2.93
633 635 1.132689 AGGGAGACTGAGAGGGTGTTT 60.133 52.381 0.00 0.00 0.00 2.83
634 636 0.489567 AGGGAGACTGAGAGGGTGTT 59.510 55.000 0.00 0.00 0.00 3.32
635 637 0.040499 GAGGGAGACTGAGAGGGTGT 59.960 60.000 0.00 0.00 0.00 4.16
636 638 0.040351 TGAGGGAGACTGAGAGGGTG 59.960 60.000 0.00 0.00 0.00 4.61
637 639 1.014804 ATGAGGGAGACTGAGAGGGT 58.985 55.000 0.00 0.00 0.00 4.34
638 640 1.217689 AGATGAGGGAGACTGAGAGGG 59.782 57.143 0.00 0.00 0.00 4.30
639 641 2.754012 AGATGAGGGAGACTGAGAGG 57.246 55.000 0.00 0.00 0.00 3.69
640 642 3.384467 GGAAAGATGAGGGAGACTGAGAG 59.616 52.174 0.00 0.00 0.00 3.20
824 830 2.159282 GCTAGGGTTTGAAGATCGTCGA 60.159 50.000 0.00 0.00 0.00 4.20
827 833 2.188817 AGGCTAGGGTTTGAAGATCGT 58.811 47.619 0.00 0.00 0.00 3.73
895 902 9.455847 ACGGAGTAATAATAAAGTAAAGTAGCG 57.544 33.333 0.00 0.00 41.94 4.26
919 927 4.147322 GCGATTCGGCCACACACG 62.147 66.667 2.24 2.56 0.00 4.49
943 951 1.078528 GGGGGCTAGGGTTTGCTTT 59.921 57.895 0.00 0.00 0.00 3.51
1067 1079 2.978010 CCGCGGCAGAAACCTTGT 60.978 61.111 14.67 0.00 0.00 3.16
1094 1118 1.979831 GACGAGGGAACGAGTCTCCG 61.980 65.000 0.00 0.00 38.18 4.63
1105 1129 2.646175 CCTTGGCTTCGACGAGGGA 61.646 63.158 9.18 0.00 38.57 4.20
1115 1139 2.037847 GCCCCATCACCTTGGCTT 59.962 61.111 0.00 0.00 40.77 4.35
1190 1214 2.650116 GCCCACTCCGAGAGCAAGA 61.650 63.158 1.33 0.00 32.04 3.02
1211 1241 3.385384 CTGGCTCTGGCTCCGACA 61.385 66.667 0.00 0.00 38.73 4.35
1275 1308 1.653151 GTAGGCAACGGGACAAGATC 58.347 55.000 0.00 0.00 46.39 2.75
1382 1421 2.106166 GGTACGAGGAGTAGGGAGATCA 59.894 54.545 0.00 0.00 35.72 2.92
1456 1495 4.576463 CGGCATCATCATCATCATCATCAT 59.424 41.667 0.00 0.00 0.00 2.45
1457 1496 3.938963 CGGCATCATCATCATCATCATCA 59.061 43.478 0.00 0.00 0.00 3.07
1458 1497 4.189231 TCGGCATCATCATCATCATCATC 58.811 43.478 0.00 0.00 0.00 2.92
1569 1611 3.551250 GGAGCAAAGCGATAGGAGTAGAC 60.551 52.174 0.00 0.00 0.00 2.59
1579 1624 0.524862 CTGCAAAGGAGCAAAGCGAT 59.475 50.000 0.00 0.00 45.13 4.58
1712 1846 1.453155 TTGAAGGCCGCTTGAGATTC 58.547 50.000 0.00 0.00 0.00 2.52
1733 1872 8.397906 CAGTAGGAGCGATCAAAATTGAAATTA 58.602 33.333 1.84 0.00 41.13 1.40
1764 1908 8.903723 CATCTTCTCGAGATAACCGTTTTATAC 58.096 37.037 17.44 0.00 43.32 1.47
1975 2134 2.417586 GGTACGTACACATTTTCCTGGC 59.582 50.000 26.02 1.31 0.00 4.85
1987 2146 3.069946 CGGGGGCAGGTACGTACA 61.070 66.667 26.02 0.00 0.00 2.90
2003 2162 0.249120 TGTATCTGGTCACCTTGCCG 59.751 55.000 0.00 0.00 0.00 5.69
2023 2182 3.480470 CAAGAACCATTGTGAGGACTGT 58.520 45.455 0.00 0.00 0.00 3.55
2084 2243 1.831736 GGCAGTAAGGAGAAGTAGCCA 59.168 52.381 0.00 0.00 40.50 4.75
2759 3174 5.431179 AGGTGTAGTTCCGTGGATATTTT 57.569 39.130 0.00 0.00 0.00 1.82
2761 3176 4.224370 ACAAGGTGTAGTTCCGTGGATATT 59.776 41.667 0.00 0.00 38.42 1.28
2766 3181 1.069513 TGACAAGGTGTAGTTCCGTGG 59.930 52.381 0.00 0.00 38.42 4.94
2770 3185 2.143925 GCACTGACAAGGTGTAGTTCC 58.856 52.381 0.00 0.00 37.07 3.62
2771 3186 2.143925 GGCACTGACAAGGTGTAGTTC 58.856 52.381 0.00 0.00 37.07 3.01
2772 3187 1.768870 AGGCACTGACAAGGTGTAGTT 59.231 47.619 0.00 0.00 37.18 2.24
2773 3188 1.424638 AGGCACTGACAAGGTGTAGT 58.575 50.000 0.00 0.00 37.18 2.73
2774 3189 2.417719 GAAGGCACTGACAAGGTGTAG 58.582 52.381 0.00 0.00 40.86 2.74
2775 3190 1.270094 CGAAGGCACTGACAAGGTGTA 60.270 52.381 0.00 0.00 40.86 2.90
2776 3191 0.532862 CGAAGGCACTGACAAGGTGT 60.533 55.000 0.00 0.00 40.86 4.16
2777 3192 1.845809 GCGAAGGCACTGACAAGGTG 61.846 60.000 0.00 0.00 40.86 4.00
2785 3200 3.559238 ATAAACAAAGCGAAGGCACTG 57.441 42.857 0.00 0.00 40.86 3.66
2831 3283 1.847328 TCAGTAACCGGCTCATCTGA 58.153 50.000 0.00 6.34 0.00 3.27
2842 3294 4.386711 ACAAACTGTAGGCTTCAGTAACC 58.613 43.478 24.38 0.00 44.03 2.85
2894 3349 2.617788 GGGACATACAACTGCCATCACA 60.618 50.000 0.00 0.00 0.00 3.58
2977 3440 5.507817 CCACTAAGTCAACAAACATGCACAT 60.508 40.000 0.00 0.00 0.00 3.21
3041 3507 1.601903 TCAACAAGACGGTTGCATGTC 59.398 47.619 6.22 6.22 45.98 3.06
3441 3936 6.299922 TGAGCTATAAGAAGATCGAAGAGGA 58.700 40.000 0.00 0.00 43.63 3.71
3448 3943 8.511321 AGTAAGACATGAGCTATAAGAAGATCG 58.489 37.037 0.00 0.00 34.59 3.69
3488 3990 0.834687 TGGTACACCCTGGACTGGAC 60.835 60.000 0.00 0.00 30.12 4.02
3620 4138 7.974501 GCAGAATAGCAACTACAAGTAGACTAA 59.025 37.037 13.79 0.00 36.97 2.24
3688 4208 6.073058 TGTTTTATCTCTCTGTGCATCAACAC 60.073 38.462 0.00 0.00 41.10 3.32
3797 4317 9.553064 GAACATAGGAAAACTGATACAGATCAT 57.447 33.333 5.76 2.23 41.33 2.45
3999 4519 3.678289 TGTTGTGTAAGATGAGCAGCAT 58.322 40.909 0.00 0.00 40.77 3.79
4056 4576 6.877322 CGACTTATAAAAAGGAACAGAGGGAA 59.123 38.462 0.00 0.00 0.00 3.97
4099 4619 1.271102 GCGTGCTCCCAAAATGGTTTA 59.729 47.619 0.00 0.00 35.17 2.01
4100 4620 0.033366 GCGTGCTCCCAAAATGGTTT 59.967 50.000 0.00 0.00 35.17 3.27
4105 4625 0.037590 TACCAGCGTGCTCCCAAAAT 59.962 50.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.