Multiple sequence alignment - TraesCS3A01G228200

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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 TraesCS3A01G228200 chr3A 100.000 4165 0 0 1 4165 427104858 427100694 0.000000e+00 7692.0
1 TraesCS3A01G228200 chr3A 93.458 642 31 6 3530 4165 712731163 712730527 0.000000e+00 942.0
2 TraesCS3A01G228200 chr3A 96.522 115 4 0 424 538 630924428 630924314 1.530000e-44 191.0
3 TraesCS3A01G228200 chr3B 94.483 2846 105 25 535 3369 413957840 413960644 0.000000e+00 4338.0
4 TraesCS3A01G228200 chr3B 93.146 642 36 4 3528 4165 773137380 773136743 0.000000e+00 935.0
5 TraesCS3A01G228200 chr3B 88.235 340 26 6 106 432 413957504 413957842 1.090000e-105 394.0
6 TraesCS3A01G228200 chr3B 95.763 118 5 0 422 539 447231797 447231680 1.530000e-44 191.0
7 TraesCS3A01G228200 chr3D 94.712 1891 58 17 1573 3457 307837291 307835437 0.000000e+00 2900.0
8 TraesCS3A01G228200 chr3D 93.289 909 38 7 535 1443 307838332 307837447 0.000000e+00 1319.0
9 TraesCS3A01G228200 chr3D 88.787 437 37 4 8 432 307838766 307838330 3.690000e-145 525.0
10 TraesCS3A01G228200 chr3D 84.848 99 12 3 219 317 56231138 56231233 3.430000e-16 97.1
11 TraesCS3A01G228200 chr6B 93.721 637 30 7 3530 4162 526739811 526740441 0.000000e+00 946.0
12 TraesCS3A01G228200 chr6B 93.045 647 33 8 3519 4159 704376433 704377073 0.000000e+00 935.0
13 TraesCS3A01G228200 chr6B 92.604 649 40 6 3518 4162 691347033 691347677 0.000000e+00 926.0
14 TraesCS3A01G228200 chr6B 84.146 82 12 1 219 300 646544 646624 1.240000e-10 78.7
15 TraesCS3A01G228200 chrUn 93.323 644 31 9 3524 4162 459863962 459864598 0.000000e+00 941.0
16 TraesCS3A01G228200 chrUn 82.927 82 13 1 220 301 43173169 43173089 5.780000e-09 73.1
17 TraesCS3A01G228200 chrUn 82.927 82 13 1 220 301 178596235 178596155 5.780000e-09 73.1
18 TraesCS3A01G228200 chr4B 93.292 641 35 6 3530 4165 95716751 95716114 0.000000e+00 939.0
19 TraesCS3A01G228200 chr5B 93.045 647 33 7 3524 4165 106171721 106171082 0.000000e+00 935.0
20 TraesCS3A01G228200 chr5B 96.552 116 4 0 421 536 558558760 558558875 4.250000e-45 193.0
21 TraesCS3A01G228200 chr7B 92.672 655 37 8 3519 4165 716137737 716137086 0.000000e+00 933.0
22 TraesCS3A01G228200 chr1D 78.540 904 153 23 2295 3166 106371989 106371095 1.310000e-154 556.0
23 TraesCS3A01G228200 chr1D 73.810 588 123 20 1600 2171 106373968 106373396 1.960000e-48 204.0
24 TraesCS3A01G228200 chr1B 83.295 437 66 5 2735 3166 160487146 160487580 3.020000e-106 396.0
25 TraesCS3A01G228200 chr1B 79.849 397 66 10 2276 2664 160486657 160487047 1.140000e-70 278.0
26 TraesCS3A01G228200 chr1B 91.791 134 9 2 404 535 533752007 533752140 7.110000e-43 185.0
27 TraesCS3A01G228200 chr7D 98.214 112 2 0 424 535 227507232 227507121 3.280000e-46 196.0
28 TraesCS3A01G228200 chr7D 97.345 113 3 0 427 539 280404931 280404819 4.250000e-45 193.0
29 TraesCS3A01G228200 chr6D 96.552 116 4 0 422 537 3196375 3196490 4.250000e-45 193.0
30 TraesCS3A01G228200 chr2D 96.522 115 4 0 424 538 627971624 627971510 1.530000e-44 191.0
31 TraesCS3A01G228200 chr7A 94.262 122 6 1 414 535 192671842 192671962 7.110000e-43 185.0
32 TraesCS3A01G228200 chr7A 83.333 96 14 2 214 307 695729755 695729850 2.060000e-13 87.9
33 TraesCS3A01G228200 chr4A 86.364 88 8 3 218 301 739157981 739158068 4.430000e-15 93.5
34 TraesCS3A01G228200 chr4A 81.308 107 14 4 1 107 531366696 531366796 9.600000e-12 82.4
35 TraesCS3A01G228200 chr4D 83.333 84 13 1 218 301 410407863 410407945 4.460000e-10 76.8


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 TraesCS3A01G228200 chr3A 427100694 427104858 4164 True 7692.000000 7692 100.000000 1 4165 1 chr3A.!!$R1 4164
1 TraesCS3A01G228200 chr3A 712730527 712731163 636 True 942.000000 942 93.458000 3530 4165 1 chr3A.!!$R3 635
2 TraesCS3A01G228200 chr3B 413957504 413960644 3140 False 2366.000000 4338 91.359000 106 3369 2 chr3B.!!$F1 3263
3 TraesCS3A01G228200 chr3B 773136743 773137380 637 True 935.000000 935 93.146000 3528 4165 1 chr3B.!!$R2 637
4 TraesCS3A01G228200 chr3D 307835437 307838766 3329 True 1581.333333 2900 92.262667 8 3457 3 chr3D.!!$R1 3449
5 TraesCS3A01G228200 chr6B 526739811 526740441 630 False 946.000000 946 93.721000 3530 4162 1 chr6B.!!$F2 632
6 TraesCS3A01G228200 chr6B 704376433 704377073 640 False 935.000000 935 93.045000 3519 4159 1 chr6B.!!$F4 640
7 TraesCS3A01G228200 chr6B 691347033 691347677 644 False 926.000000 926 92.604000 3518 4162 1 chr6B.!!$F3 644
8 TraesCS3A01G228200 chrUn 459863962 459864598 636 False 941.000000 941 93.323000 3524 4162 1 chrUn.!!$F1 638
9 TraesCS3A01G228200 chr4B 95716114 95716751 637 True 939.000000 939 93.292000 3530 4165 1 chr4B.!!$R1 635
10 TraesCS3A01G228200 chr5B 106171082 106171721 639 True 935.000000 935 93.045000 3524 4165 1 chr5B.!!$R1 641
11 TraesCS3A01G228200 chr7B 716137086 716137737 651 True 933.000000 933 92.672000 3519 4165 1 chr7B.!!$R1 646
12 TraesCS3A01G228200 chr1D 106371095 106373968 2873 True 380.000000 556 76.175000 1600 3166 2 chr1D.!!$R1 1566
13 TraesCS3A01G228200 chr1B 160486657 160487580 923 False 337.000000 396 81.572000 2276 3166 2 chr1B.!!$F2 890

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
444 459 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.0 13.34 13.34 0.0 4.55 F
1556 1633 0.037017 TTTTCTCCAATTCCCGCGGA 59.963 50.0 30.73 8.21 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2259 0.250295 TGGTACAGGAAGTGTGCAGC 60.250 55.0 0.00 0.0 43.26 5.25 R
3461 4889 0.461870 GCCTGACGCATGTGTCCATA 60.462 55.0 31.02 15.6 38.11 2.74 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
40 41 3.181437 GGGACTAGACAAAAAGGGTCCAA 60.181 47.826 11.25 0.00 43.30 3.53
42 43 3.819337 GACTAGACAAAAAGGGTCCAACC 59.181 47.826 0.00 0.00 35.89 3.77
75 76 4.595538 GCCACGACACCACCACGA 62.596 66.667 0.00 0.00 0.00 4.35
90 92 3.272334 CGATGCCTAACAGCCGGC 61.272 66.667 21.89 21.89 46.46 6.13
118 120 1.377202 CACACCACGCTAGCCCATT 60.377 57.895 9.66 0.00 0.00 3.16
122 124 2.438254 CACGCTAGCCCATTGCCA 60.438 61.111 9.66 0.00 42.71 4.92
123 125 2.438434 ACGCTAGCCCATTGCCAC 60.438 61.111 9.66 0.00 42.71 5.01
136 138 2.045926 GCCACAGAACCGAGCCAT 60.046 61.111 0.00 0.00 0.00 4.40
206 208 2.031163 ACCACAGAAGCGCCTCAC 59.969 61.111 9.03 0.00 0.00 3.51
230 242 4.632153 CGGCTTATTGCTATGTAGAGGTT 58.368 43.478 0.00 0.00 42.39 3.50
234 246 2.710096 TTGCTATGTAGAGGTTGGGC 57.290 50.000 0.00 0.00 0.00 5.36
279 291 5.947228 TTTCTCGATGCTTCATTTTGAGT 57.053 34.783 0.08 0.00 0.00 3.41
314 326 6.718454 CCATCCTTTGTCAATAATGATAGCCT 59.282 38.462 4.68 0.00 38.01 4.58
316 328 7.807977 TCCTTTGTCAATAATGATAGCCTTC 57.192 36.000 0.00 0.00 38.01 3.46
409 423 7.173735 TCACCTAAAATCCGTTTTCTAGAAACC 59.826 37.037 17.51 10.02 38.44 3.27
428 443 2.038557 ACCGAGCTGTATCCAAACAACT 59.961 45.455 0.00 0.00 0.00 3.16
429 444 3.259876 ACCGAGCTGTATCCAAACAACTA 59.740 43.478 0.00 0.00 0.00 2.24
430 445 3.617263 CCGAGCTGTATCCAAACAACTAC 59.383 47.826 0.00 0.00 0.00 2.73
431 446 4.495422 CGAGCTGTATCCAAACAACTACT 58.505 43.478 0.00 0.00 0.00 2.57
432 447 4.563184 CGAGCTGTATCCAAACAACTACTC 59.437 45.833 0.00 0.00 0.00 2.59
433 448 4.833390 AGCTGTATCCAAACAACTACTCC 58.167 43.478 0.00 0.00 0.00 3.85
434 449 3.939592 GCTGTATCCAAACAACTACTCCC 59.060 47.826 0.00 0.00 0.00 4.30
435 450 4.323562 GCTGTATCCAAACAACTACTCCCT 60.324 45.833 0.00 0.00 0.00 4.20
436 451 5.416271 TGTATCCAAACAACTACTCCCTC 57.584 43.478 0.00 0.00 0.00 4.30
437 452 4.224370 TGTATCCAAACAACTACTCCCTCC 59.776 45.833 0.00 0.00 0.00 4.30
438 453 1.621814 TCCAAACAACTACTCCCTCCG 59.378 52.381 0.00 0.00 0.00 4.63
439 454 1.346722 CCAAACAACTACTCCCTCCGT 59.653 52.381 0.00 0.00 0.00 4.69
440 455 2.224450 CCAAACAACTACTCCCTCCGTT 60.224 50.000 0.00 0.00 0.00 4.44
441 456 3.064931 CAAACAACTACTCCCTCCGTTC 58.935 50.000 0.00 0.00 0.00 3.95
442 457 0.886563 ACAACTACTCCCTCCGTTCG 59.113 55.000 0.00 0.00 0.00 3.95
443 458 0.172803 CAACTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
444 459 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
445 460 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
446 461 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
447 462 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
448 463 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
449 464 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
450 465 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
451 466 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
452 467 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
453 468 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
454 469 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
455 470 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
456 471 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
457 472 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
458 473 2.471749 CGTTCGGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 0.00 5.34
459 474 2.442212 TCGGAATTACTTGTCGCACA 57.558 45.000 0.00 0.00 0.00 4.57
460 475 2.756829 TCGGAATTACTTGTCGCACAA 58.243 42.857 2.49 2.49 36.54 3.33
461 476 3.132160 TCGGAATTACTTGTCGCACAAA 58.868 40.909 3.84 0.00 37.69 2.83
462 477 3.749088 TCGGAATTACTTGTCGCACAAAT 59.251 39.130 3.84 0.00 37.69 2.32
463 478 3.845775 CGGAATTACTTGTCGCACAAATG 59.154 43.478 3.84 0.00 37.69 2.32
464 479 4.165779 GGAATTACTTGTCGCACAAATGG 58.834 43.478 3.84 0.00 37.69 3.16
465 480 4.083003 GGAATTACTTGTCGCACAAATGGA 60.083 41.667 3.84 0.00 37.69 3.41
466 481 5.393027 GGAATTACTTGTCGCACAAATGGAT 60.393 40.000 3.84 0.00 37.69 3.41
467 482 2.995466 ACTTGTCGCACAAATGGATG 57.005 45.000 3.84 0.00 37.69 3.51
468 483 2.229792 ACTTGTCGCACAAATGGATGT 58.770 42.857 3.84 0.00 37.69 3.06
469 484 3.407698 ACTTGTCGCACAAATGGATGTA 58.592 40.909 3.84 0.00 37.69 2.29
470 485 4.009675 ACTTGTCGCACAAATGGATGTAT 58.990 39.130 3.84 0.00 37.69 2.29
471 486 4.094887 ACTTGTCGCACAAATGGATGTATC 59.905 41.667 3.84 0.00 37.69 2.24
472 487 3.872696 TGTCGCACAAATGGATGTATCT 58.127 40.909 0.00 0.00 30.84 1.98
473 488 5.017294 TGTCGCACAAATGGATGTATCTA 57.983 39.130 0.00 0.00 30.84 1.98
474 489 5.049828 TGTCGCACAAATGGATGTATCTAG 58.950 41.667 0.00 0.00 30.84 2.43
475 490 5.163457 TGTCGCACAAATGGATGTATCTAGA 60.163 40.000 0.00 0.00 30.84 2.43
476 491 5.175856 GTCGCACAAATGGATGTATCTAGAC 59.824 44.000 0.00 0.00 30.84 2.59
477 492 4.148871 CGCACAAATGGATGTATCTAGACG 59.851 45.833 0.00 0.00 30.84 4.18
478 493 5.050490 GCACAAATGGATGTATCTAGACGT 58.950 41.667 0.00 0.00 30.84 4.34
479 494 6.213677 GCACAAATGGATGTATCTAGACGTA 58.786 40.000 0.00 0.00 30.84 3.57
480 495 6.868864 GCACAAATGGATGTATCTAGACGTAT 59.131 38.462 0.00 0.00 30.84 3.06
481 496 7.385205 GCACAAATGGATGTATCTAGACGTATT 59.615 37.037 0.00 0.00 30.84 1.89
482 497 9.261180 CACAAATGGATGTATCTAGACGTATTT 57.739 33.333 0.00 0.00 30.84 1.40
483 498 9.832445 ACAAATGGATGTATCTAGACGTATTTT 57.168 29.630 0.00 0.00 0.00 1.82
507 522 9.893634 TTTAGTTCTAAATACATCCATTTCCGA 57.106 29.630 1.47 0.00 30.84 4.55
508 523 9.542462 TTAGTTCTAAATACATCCATTTCCGAG 57.458 33.333 0.00 0.00 30.84 4.63
509 524 7.792032 AGTTCTAAATACATCCATTTCCGAGA 58.208 34.615 0.00 0.00 30.84 4.04
510 525 7.711339 AGTTCTAAATACATCCATTTCCGAGAC 59.289 37.037 0.00 0.00 30.84 3.36
511 526 7.119709 TCTAAATACATCCATTTCCGAGACA 57.880 36.000 0.00 0.00 30.84 3.41
512 527 7.561251 TCTAAATACATCCATTTCCGAGACAA 58.439 34.615 0.00 0.00 30.84 3.18
513 528 6.683974 AAATACATCCATTTCCGAGACAAG 57.316 37.500 0.00 0.00 0.00 3.16
514 529 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
515 530 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
516 531 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
517 532 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
518 533 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
519 534 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
520 535 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
521 536 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
522 537 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
523 538 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
524 539 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
525 540 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
526 541 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
527 542 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
528 543 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
529 544 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
530 545 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
531 546 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
532 547 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
533 548 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
626 641 4.514577 CATCCTTCGGCTCCGCGT 62.515 66.667 4.92 0.00 39.59 6.01
653 668 3.932710 TCTCGATTCCACGAAAATGAAGG 59.067 43.478 0.00 0.00 41.67 3.46
676 691 6.891908 AGGCAACATCCTGATTTATTAACAGT 59.108 34.615 0.00 0.00 41.41 3.55
677 692 7.397192 AGGCAACATCCTGATTTATTAACAGTT 59.603 33.333 0.00 0.00 41.41 3.16
678 693 8.682710 GGCAACATCCTGATTTATTAACAGTTA 58.317 33.333 0.00 0.00 0.00 2.24
739 754 5.723678 GCCGATGAAAACAACAACAAACAAG 60.724 40.000 0.00 0.00 0.00 3.16
774 789 0.751643 GCTTGTCCTTGGTGTGTGGT 60.752 55.000 0.00 0.00 0.00 4.16
800 815 2.486203 CGTTTTCCACAATTCCCATCGA 59.514 45.455 0.00 0.00 0.00 3.59
824 839 1.305482 CGCGAAAATGTTGTGACGAC 58.695 50.000 0.00 0.00 0.00 4.34
869 884 1.913778 AACATGTGATGCCAAGCAGA 58.086 45.000 0.00 0.00 43.65 4.26
894 909 0.532862 GCACCCACCCTCGTATCATG 60.533 60.000 0.00 0.00 0.00 3.07
926 941 6.432936 CACTTGCTGTGCCTATATAACATTG 58.567 40.000 0.00 0.00 40.06 2.82
927 942 5.532406 ACTTGCTGTGCCTATATAACATTGG 59.468 40.000 0.00 0.00 0.00 3.16
928 943 4.397420 TGCTGTGCCTATATAACATTGGG 58.603 43.478 0.00 0.00 0.00 4.12
929 944 4.103943 TGCTGTGCCTATATAACATTGGGA 59.896 41.667 0.00 0.00 0.00 4.37
966 981 1.202582 CTGCTCTAGTTGTACCGCACT 59.797 52.381 0.00 0.00 0.00 4.40
967 982 2.422479 CTGCTCTAGTTGTACCGCACTA 59.578 50.000 0.00 0.00 0.00 2.74
968 983 2.163010 TGCTCTAGTTGTACCGCACTAC 59.837 50.000 0.00 0.00 33.61 2.73
982 997 3.500680 CCGCACTACCACACAGTTTTATT 59.499 43.478 0.00 0.00 0.00 1.40
983 998 4.691685 CCGCACTACCACACAGTTTTATTA 59.308 41.667 0.00 0.00 0.00 0.98
984 999 5.353123 CCGCACTACCACACAGTTTTATTAT 59.647 40.000 0.00 0.00 0.00 1.28
1014 1031 4.181578 AGAAATTAATGGAGGTCGACGTG 58.818 43.478 16.63 0.00 0.00 4.49
1025 1042 1.080772 TCGACGTGGCAGCAACTAG 60.081 57.895 0.00 0.00 0.00 2.57
1284 1301 1.288419 CGCTGTGCCACGACATTGTA 61.288 55.000 0.00 0.00 0.00 2.41
1555 1632 0.885196 TTTTTCTCCAATTCCCGCGG 59.115 50.000 21.04 21.04 0.00 6.46
1556 1633 0.037017 TTTTCTCCAATTCCCGCGGA 59.963 50.000 30.73 8.21 0.00 5.54
1693 1773 6.454223 AAGCTAGTGAGAGAGATCCTATCT 57.546 41.667 0.00 0.00 43.70 1.98
1702 1782 5.385198 AGAGAGATCCTATCTGACAAGTCC 58.615 45.833 0.00 0.00 40.38 3.85
1798 1878 3.067985 TGGGCGATGCACAGAAGA 58.932 55.556 0.00 0.00 36.87 2.87
1804 1884 3.198068 GGCGATGCACAGAAGAATCTTA 58.802 45.455 0.00 0.00 32.03 2.10
1859 1939 9.353431 AGGTAGTACTATTCTTTCTTACTAGGC 57.647 37.037 5.75 0.00 0.00 3.93
1890 1970 1.301637 CGATCAGGGTGTGTGTGCA 60.302 57.895 0.00 0.00 0.00 4.57
1977 2061 5.509498 TGATAAGCAGCTGGGAAAGTAAAT 58.491 37.500 17.12 0.00 0.00 1.40
2293 3669 2.608016 GGCCTTTTTCAGCTTCTTTCCG 60.608 50.000 0.00 0.00 0.00 4.30
2396 3772 0.673644 AATGGAGAACGACGGGCTTG 60.674 55.000 0.00 0.00 0.00 4.01
2398 3774 3.119096 GAGAACGACGGGCTTGGC 61.119 66.667 0.00 0.00 0.00 4.52
2443 3822 0.318441 TGCAGTCGAACAAGGAGAGG 59.682 55.000 0.00 0.00 0.00 3.69
2723 4125 2.554142 TGCTGACTATGATTTGGCTCG 58.446 47.619 0.00 0.00 0.00 5.03
2724 4126 1.869767 GCTGACTATGATTTGGCTCGG 59.130 52.381 0.00 0.00 0.00 4.63
2786 4196 4.011517 CTGTACCCACCGGCGGTT 62.012 66.667 32.12 18.66 31.02 4.44
2828 4238 2.435069 CAGAGAGATGCAGATTGGAGGT 59.565 50.000 0.00 0.00 0.00 3.85
3182 4595 3.056607 TCTGATCGTCATCTTGTCTTGCA 60.057 43.478 0.00 0.00 0.00 4.08
3207 4635 4.883026 CGACCTGTCGTGGGTAAG 57.117 61.111 11.37 0.00 46.99 2.34
3208 4636 1.962144 CGACCTGTCGTGGGTAAGT 59.038 57.895 11.37 0.00 46.99 2.24
3209 4637 0.316204 CGACCTGTCGTGGGTAAGTT 59.684 55.000 11.37 0.00 46.99 2.66
3210 4638 1.541147 CGACCTGTCGTGGGTAAGTTA 59.459 52.381 11.37 0.00 46.99 2.24
3211 4639 2.669391 CGACCTGTCGTGGGTAAGTTAC 60.669 54.545 11.37 4.32 46.99 2.50
3212 4640 5.756916 CGACCTGTCGTGGGTAAGTTACC 62.757 56.522 21.95 21.95 46.99 2.85
3234 4662 2.778850 TGTGGGGTAACTTGGTAAGTGT 59.221 45.455 0.00 0.00 41.91 3.55
3243 4671 7.816513 GGGTAACTTGGTAAGTGTAAGAAGTAG 59.183 40.741 0.00 0.00 41.91 2.57
3262 4690 9.646427 AGAAGTAGATTGAATCAAGTGAACTAC 57.354 33.333 8.03 9.45 0.00 2.73
3263 4691 9.646427 GAAGTAGATTGAATCAAGTGAACTACT 57.354 33.333 8.03 15.93 42.89 2.57
3272 4700 8.731605 TGAATCAAGTGAACTACTACTAGACTG 58.268 37.037 0.00 0.00 39.18 3.51
3280 4708 9.130312 GTGAACTACTACTAGACTGTTTCATTG 57.870 37.037 0.00 0.00 0.00 2.82
3281 4709 8.857098 TGAACTACTACTAGACTGTTTCATTGT 58.143 33.333 0.00 0.00 0.00 2.71
3338 4766 1.134877 TGTTGTTCACACCGGTTACGA 60.135 47.619 2.97 0.00 44.60 3.43
3354 4782 4.209911 GGTTACGAGGAACACAACTGTTAC 59.790 45.833 0.24 0.00 40.93 2.50
3378 4806 7.056844 CCAAAGTTGGTTTATACAGGGAAAA 57.943 36.000 1.63 0.00 43.43 2.29
3391 4819 2.526304 GGGAAAAGGTGCCTGAAAAC 57.474 50.000 0.00 0.00 34.08 2.43
3395 4823 3.621268 GGAAAAGGTGCCTGAAAACAAAC 59.379 43.478 0.00 0.00 0.00 2.93
3396 4824 3.971245 AAAGGTGCCTGAAAACAAACA 57.029 38.095 0.00 0.00 0.00 2.83
3399 4827 3.595173 AGGTGCCTGAAAACAAACAAAC 58.405 40.909 0.00 0.00 0.00 2.93
3401 4829 3.748568 GGTGCCTGAAAACAAACAAACAA 59.251 39.130 0.00 0.00 0.00 2.83
3402 4830 4.214332 GGTGCCTGAAAACAAACAAACAAA 59.786 37.500 0.00 0.00 0.00 2.83
3403 4831 5.143660 GTGCCTGAAAACAAACAAACAAAC 58.856 37.500 0.00 0.00 0.00 2.93
3404 4832 4.816385 TGCCTGAAAACAAACAAACAAACA 59.184 33.333 0.00 0.00 0.00 2.83
3405 4833 5.296780 TGCCTGAAAACAAACAAACAAACAA 59.703 32.000 0.00 0.00 0.00 2.83
3406 4834 6.183360 TGCCTGAAAACAAACAAACAAACAAA 60.183 30.769 0.00 0.00 0.00 2.83
3407 4835 6.693113 GCCTGAAAACAAACAAACAAACAAAA 59.307 30.769 0.00 0.00 0.00 2.44
3408 4836 7.220875 GCCTGAAAACAAACAAACAAACAAAAA 59.779 29.630 0.00 0.00 0.00 1.94
3440 4868 2.676232 CTCTTCAGAGGAGGCACCA 58.324 57.895 3.18 0.00 42.04 4.17
3450 4878 3.054802 AGAGGAGGCACCAATACAGAAAG 60.055 47.826 3.18 0.00 42.04 2.62
3457 4885 1.628846 ACCAATACAGAAAGGAGGCGT 59.371 47.619 0.00 0.00 0.00 5.68
3458 4886 2.280628 CCAATACAGAAAGGAGGCGTC 58.719 52.381 0.00 0.00 0.00 5.19
3459 4887 2.280628 CAATACAGAAAGGAGGCGTCC 58.719 52.381 17.88 17.88 44.33 4.79
3460 4888 1.568504 ATACAGAAAGGAGGCGTCCA 58.431 50.000 26.40 5.04 46.80 4.02
3461 4889 1.568504 TACAGAAAGGAGGCGTCCAT 58.431 50.000 26.40 13.02 46.80 3.41
3462 4890 1.568504 ACAGAAAGGAGGCGTCCATA 58.431 50.000 26.40 0.00 46.80 2.74
3463 4891 2.119495 ACAGAAAGGAGGCGTCCATAT 58.881 47.619 26.40 12.24 46.80 1.78
3464 4892 2.158900 ACAGAAAGGAGGCGTCCATATG 60.159 50.000 26.40 21.86 46.80 1.78
3465 4893 1.417890 AGAAAGGAGGCGTCCATATGG 59.582 52.381 26.40 16.25 46.80 2.74
3466 4894 1.416401 GAAAGGAGGCGTCCATATGGA 59.584 52.381 26.40 20.98 46.80 3.41
3476 4904 2.238942 TCCATATGGACACATGCGTC 57.761 50.000 20.98 5.25 39.78 5.19
3477 4905 1.484240 TCCATATGGACACATGCGTCA 59.516 47.619 20.98 2.83 39.78 4.35
3478 4906 1.869132 CCATATGGACACATGCGTCAG 59.131 52.381 17.49 0.54 37.97 3.51
3479 4907 1.869132 CATATGGACACATGCGTCAGG 59.131 52.381 15.39 0.00 37.97 3.86
3480 4908 0.461870 TATGGACACATGCGTCAGGC 60.462 55.000 15.39 0.00 43.96 4.85
3508 4936 4.697756 ACACATGTGTCCGCCCGG 62.698 66.667 25.76 0.00 40.24 5.73
3520 4948 3.715015 GCCCGGGGCCAAATTTAA 58.285 55.556 28.23 0.00 44.06 1.52
3521 4949 2.217106 GCCCGGGGCCAAATTTAAT 58.783 52.632 28.23 0.00 44.06 1.40
3522 4950 0.179059 GCCCGGGGCCAAATTTAATG 60.179 55.000 28.23 0.00 44.06 1.90
3523 4951 1.199615 CCCGGGGCCAAATTTAATGT 58.800 50.000 14.71 0.00 0.00 2.71
3524 4952 1.557371 CCCGGGGCCAAATTTAATGTT 59.443 47.619 14.71 0.00 0.00 2.71
3525 4953 2.026729 CCCGGGGCCAAATTTAATGTTT 60.027 45.455 14.71 0.00 0.00 2.83
3526 4954 3.560239 CCCGGGGCCAAATTTAATGTTTT 60.560 43.478 14.71 0.00 0.00 2.43
3576 5007 1.679305 AGATCGTCCACACGCCTCT 60.679 57.895 0.00 0.00 46.28 3.69
3601 5032 4.944317 TCACCATTCATTTTGCCACGTATA 59.056 37.500 0.00 0.00 0.00 1.47
3744 5175 4.357918 ACTAGACCCCATGTTGATATGC 57.642 45.455 0.00 0.00 0.00 3.14
3902 5338 9.695526 CAATTCCAGTACTTTGATCATGAAAAA 57.304 29.630 0.00 3.11 0.00 1.94
4108 5548 1.818060 TGTGCAATAGACATGGCAACC 59.182 47.619 0.00 0.00 42.87 3.77
4114 5554 5.421693 TGCAATAGACATGGCAACCTTTAAT 59.578 36.000 0.00 0.00 38.19 1.40
4118 5558 7.716799 ATAGACATGGCAACCTTTAATCAAA 57.283 32.000 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.018515 CTAGTCCCCGTCAGAGAAGAC 58.981 57.143 0.00 0.00 35.19 3.01
101 103 1.377202 CAATGGGCTAGCGTGGTGT 60.377 57.895 9.00 0.00 0.00 4.16
118 120 2.803155 GATGGCTCGGTTCTGTGGCA 62.803 60.000 11.18 11.18 41.24 4.92
230 242 2.112928 ACAATGAGCACACGCCCA 59.887 55.556 0.00 0.00 39.83 5.36
234 246 3.811722 ACATAACACAATGAGCACACG 57.188 42.857 0.00 0.00 0.00 4.49
292 304 6.772716 GGAAGGCTATCATTATTGACAAAGGA 59.227 38.462 0.00 0.00 33.85 3.36
366 380 8.491045 TTTAGGTGAAATTTGAGGAAAAGGAT 57.509 30.769 0.00 0.00 0.00 3.24
428 443 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
429 444 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
430 445 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
431 446 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
432 447 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
433 448 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
434 449 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
435 450 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
436 451 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
437 452 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
438 453 2.477375 TGTGCGACAAGTAATTCCGAAC 59.523 45.455 0.00 0.00 0.00 3.95
439 454 2.756829 TGTGCGACAAGTAATTCCGAA 58.243 42.857 0.00 0.00 0.00 4.30
440 455 2.442212 TGTGCGACAAGTAATTCCGA 57.558 45.000 0.00 0.00 0.00 4.55
441 456 3.529634 TTTGTGCGACAAGTAATTCCG 57.470 42.857 0.00 0.00 39.53 4.30
442 457 4.083003 TCCATTTGTGCGACAAGTAATTCC 60.083 41.667 0.00 0.00 39.53 3.01
443 458 5.041951 TCCATTTGTGCGACAAGTAATTC 57.958 39.130 0.00 0.00 39.53 2.17
444 459 5.048083 ACATCCATTTGTGCGACAAGTAATT 60.048 36.000 0.00 0.00 39.53 1.40
445 460 4.458989 ACATCCATTTGTGCGACAAGTAAT 59.541 37.500 0.00 0.00 39.53 1.89
446 461 3.818210 ACATCCATTTGTGCGACAAGTAA 59.182 39.130 0.00 0.00 39.53 2.24
447 462 3.407698 ACATCCATTTGTGCGACAAGTA 58.592 40.909 0.00 0.00 39.53 2.24
448 463 2.229792 ACATCCATTTGTGCGACAAGT 58.770 42.857 0.00 0.00 39.53 3.16
449 464 2.995466 ACATCCATTTGTGCGACAAG 57.005 45.000 0.00 0.00 39.53 3.16
450 465 4.260985 AGATACATCCATTTGTGCGACAA 58.739 39.130 0.00 0.00 36.11 3.18
451 466 3.872696 AGATACATCCATTTGTGCGACA 58.127 40.909 0.00 0.00 0.00 4.35
452 467 5.175856 GTCTAGATACATCCATTTGTGCGAC 59.824 44.000 0.00 0.00 0.00 5.19
453 468 5.289595 GTCTAGATACATCCATTTGTGCGA 58.710 41.667 0.00 0.00 0.00 5.10
454 469 4.148871 CGTCTAGATACATCCATTTGTGCG 59.851 45.833 0.00 0.00 0.00 5.34
455 470 5.050490 ACGTCTAGATACATCCATTTGTGC 58.950 41.667 0.00 0.00 0.00 4.57
456 471 8.818141 AATACGTCTAGATACATCCATTTGTG 57.182 34.615 0.00 0.00 0.00 3.33
457 472 9.832445 AAAATACGTCTAGATACATCCATTTGT 57.168 29.630 0.00 0.00 0.00 2.83
481 496 9.893634 TCGGAAATGGATGTATTTAGAACTAAA 57.106 29.630 9.03 9.03 39.12 1.85
482 497 9.542462 CTCGGAAATGGATGTATTTAGAACTAA 57.458 33.333 0.00 0.00 30.78 2.24
483 498 8.920174 TCTCGGAAATGGATGTATTTAGAACTA 58.080 33.333 0.00 0.00 30.78 2.24
484 499 7.711339 GTCTCGGAAATGGATGTATTTAGAACT 59.289 37.037 0.00 0.00 30.78 3.01
485 500 7.494625 TGTCTCGGAAATGGATGTATTTAGAAC 59.505 37.037 0.00 0.00 30.78 3.01
486 501 7.561251 TGTCTCGGAAATGGATGTATTTAGAA 58.439 34.615 0.00 0.00 30.78 2.10
487 502 7.119709 TGTCTCGGAAATGGATGTATTTAGA 57.880 36.000 0.00 0.00 30.78 2.10
488 503 7.495934 ACTTGTCTCGGAAATGGATGTATTTAG 59.504 37.037 0.00 0.00 30.78 1.85
489 504 7.335627 ACTTGTCTCGGAAATGGATGTATTTA 58.664 34.615 0.00 0.00 30.78 1.40
490 505 6.180472 ACTTGTCTCGGAAATGGATGTATTT 58.820 36.000 0.00 0.00 33.19 1.40
491 506 5.745227 ACTTGTCTCGGAAATGGATGTATT 58.255 37.500 0.00 0.00 0.00 1.89
492 507 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
493 508 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
494 509 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
495 510 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
496 511 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
497 512 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
498 513 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
499 514 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
500 515 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
501 516 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
502 517 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
503 518 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
504 519 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
505 520 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
506 521 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
507 522 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
508 523 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
509 524 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
510 525 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
511 526 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
512 527 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
513 528 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
514 529 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
515 530 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
516 531 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
517 532 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
518 533 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
519 534 1.403323 GTAAGTACTCCCTCCGTTCGG 59.597 57.143 4.74 4.74 0.00 4.30
520 535 1.063174 CGTAAGTACTCCCTCCGTTCG 59.937 57.143 0.00 0.00 0.00 3.95
521 536 2.840296 CGTAAGTACTCCCTCCGTTC 57.160 55.000 0.00 0.00 0.00 3.95
533 548 8.164240 TGTATGACCTACGCAGATACGTAAGTA 61.164 40.741 0.00 0.00 46.90 2.24
626 641 2.448926 TTCGTGGAATCGAGAGCAAA 57.551 45.000 0.00 0.00 40.86 3.68
739 754 4.483711 GCAAAAGGCTGGATTCGC 57.516 55.556 0.00 0.00 40.25 4.70
774 789 4.399219 TGGGAATTGTGGAAAACGATGTA 58.601 39.130 0.00 0.00 0.00 2.29
800 815 3.665848 CGTCACAACATTTTCGCGGTTAT 60.666 43.478 6.13 0.00 0.00 1.89
869 884 3.325753 GAGGGTGGGTGCTCTGCT 61.326 66.667 0.00 0.00 0.00 4.24
894 909 1.846648 CACAGCAAGTGTCGTCGAC 59.153 57.895 18.51 18.51 43.40 4.20
926 941 2.124695 GCGGTGGAAGATGGTCCC 60.125 66.667 0.00 0.00 36.80 4.46
927 942 1.745489 GTGCGGTGGAAGATGGTCC 60.745 63.158 0.00 0.00 38.27 4.46
928 943 1.745489 GGTGCGGTGGAAGATGGTC 60.745 63.158 0.00 0.00 0.00 4.02
929 944 2.224159 AGGTGCGGTGGAAGATGGT 61.224 57.895 0.00 0.00 0.00 3.55
966 981 7.753309 ACTGCAATAATAAAACTGTGTGGTA 57.247 32.000 0.00 0.00 0.00 3.25
967 982 6.648879 ACTGCAATAATAAAACTGTGTGGT 57.351 33.333 0.00 0.00 0.00 4.16
968 983 8.511321 TCTTACTGCAATAATAAAACTGTGTGG 58.489 33.333 0.00 0.00 0.00 4.17
982 997 9.120538 GACCTCCATTAATTTCTTACTGCAATA 57.879 33.333 0.00 0.00 0.00 1.90
983 998 7.201732 CGACCTCCATTAATTTCTTACTGCAAT 60.202 37.037 0.00 0.00 0.00 3.56
984 999 6.093495 CGACCTCCATTAATTTCTTACTGCAA 59.907 38.462 0.00 0.00 0.00 4.08
997 1014 0.108520 GCCACGTCGACCTCCATTAA 60.109 55.000 10.58 0.00 0.00 1.40
1014 1031 0.179124 CTCCGAGTCTAGTTGCTGCC 60.179 60.000 0.00 0.00 0.00 4.85
1025 1042 0.748729 ATCACCTCCGACTCCGAGTC 60.749 60.000 17.31 17.31 41.71 3.36
1268 1285 0.604243 GGGTACAATGTCGTGGCACA 60.604 55.000 19.09 1.83 0.00 4.57
1306 1323 2.096909 CGTGTTCCTTGACGATGTTGAC 60.097 50.000 0.00 0.00 37.81 3.18
1391 1408 4.634184 TTCATGTCGGGAAAACGAAAAA 57.366 36.364 0.00 0.00 45.38 1.94
1541 1617 0.885196 TTTTTCCGCGGGAATTGGAG 59.115 50.000 27.83 0.00 41.71 3.86
1542 1618 3.037941 TTTTTCCGCGGGAATTGGA 57.962 47.368 27.83 4.35 41.71 3.53
1579 1656 3.626028 AAACTGATTGCCGTCAGAAAC 57.374 42.857 18.90 0.00 46.77 2.78
1693 1773 0.953471 CGAAATGGCCGGACTTGTCA 60.953 55.000 9.82 0.00 0.00 3.58
1702 1782 2.666022 GGTGAATTTTTCGAAATGGCCG 59.334 45.455 12.12 0.00 0.00 6.13
1795 1875 3.762288 GGAAAGCGGGGTTTAAGATTCTT 59.238 43.478 4.03 4.03 0.00 2.52
1798 1878 3.163616 TGGAAAGCGGGGTTTAAGATT 57.836 42.857 0.00 0.00 0.00 2.40
1804 1884 0.676782 CGAGATGGAAAGCGGGGTTT 60.677 55.000 0.00 0.00 0.00 3.27
1859 1939 1.889829 CCTGATCGGGTTAGGAGCTAG 59.110 57.143 12.93 0.00 35.64 3.42
1890 1970 3.479269 GCTTCAGTTAGCGCGCGT 61.479 61.111 32.35 20.00 0.00 6.01
1977 2061 2.115427 TGATCCATCAGAACCGGCTAA 58.885 47.619 0.00 0.00 32.11 3.09
2169 2259 0.250295 TGGTACAGGAAGTGTGCAGC 60.250 55.000 0.00 0.00 43.26 5.25
2170 2260 2.254546 TTGGTACAGGAAGTGTGCAG 57.745 50.000 0.00 0.00 43.26 4.41
2171 2261 2.949177 ATTGGTACAGGAAGTGTGCA 57.051 45.000 0.00 0.00 43.26 4.57
2273 3637 2.293399 TCGGAAAGAAGCTGAAAAAGGC 59.707 45.455 0.00 0.00 0.00 4.35
2293 3669 6.377327 TTCATCCTCTTGTTGTTTTCAGTC 57.623 37.500 0.00 0.00 0.00 3.51
2377 3753 0.673644 CAAGCCCGTCGTTCTCCATT 60.674 55.000 0.00 0.00 0.00 3.16
2398 3774 3.777925 CCAAGCAAGTCGTCGCCG 61.778 66.667 0.00 0.00 0.00 6.46
2402 3781 0.674895 ATCAGGCCAAGCAAGTCGTC 60.675 55.000 5.01 0.00 0.00 4.20
2443 3822 0.976073 TCCTCATCCTTGACGTCCCC 60.976 60.000 14.12 0.00 0.00 4.81
2786 4196 0.892755 ATGTCTTCCGGTTCAGCGTA 59.107 50.000 0.00 0.00 0.00 4.42
3047 4460 1.376543 AACGCTGAAGGATCATGCTG 58.623 50.000 0.00 0.00 34.37 4.41
3210 4638 4.213398 ACTTACCAAGTTACCCCACAGGT 61.213 47.826 0.00 0.00 41.31 4.00
3211 4639 2.374170 ACTTACCAAGTTACCCCACAGG 59.626 50.000 0.00 0.00 39.04 4.00
3212 4640 3.181448 ACACTTACCAAGTTACCCCACAG 60.181 47.826 0.00 0.00 40.46 3.66
3213 4641 2.778850 ACACTTACCAAGTTACCCCACA 59.221 45.455 0.00 0.00 40.46 4.17
3214 4642 3.497103 ACACTTACCAAGTTACCCCAC 57.503 47.619 0.00 0.00 40.46 4.61
3215 4643 4.906664 TCTTACACTTACCAAGTTACCCCA 59.093 41.667 0.00 0.00 40.46 4.96
3216 4644 5.488262 TCTTACACTTACCAAGTTACCCC 57.512 43.478 0.00 0.00 40.46 4.95
3217 4645 6.528321 ACTTCTTACACTTACCAAGTTACCC 58.472 40.000 0.00 0.00 40.46 3.69
3218 4646 8.579863 TCTACTTCTTACACTTACCAAGTTACC 58.420 37.037 0.00 0.00 40.46 2.85
3259 4687 9.953697 GGATACAATGAAACAGTCTAGTAGTAG 57.046 37.037 0.00 0.00 0.00 2.57
3260 4688 9.696572 AGGATACAATGAAACAGTCTAGTAGTA 57.303 33.333 0.00 0.00 41.41 1.82
3261 4689 8.596781 AGGATACAATGAAACAGTCTAGTAGT 57.403 34.615 0.00 0.00 41.41 2.73
3272 4700 7.462571 ACCCAGTTTTAGGATACAATGAAAC 57.537 36.000 0.00 0.00 41.41 2.78
3280 4708 9.623000 ATGTACAAATACCCAGTTTTAGGATAC 57.377 33.333 0.00 0.00 0.00 2.24
3281 4709 9.621629 CATGTACAAATACCCAGTTTTAGGATA 57.378 33.333 0.00 0.00 0.00 2.59
3378 4806 3.007398 TGTTTGTTTGTTTTCAGGCACCT 59.993 39.130 0.00 0.00 0.00 4.00
3424 4852 2.237143 TGTATTGGTGCCTCCTCTGAAG 59.763 50.000 0.00 0.00 37.07 3.02
3432 4860 3.274288 CTCCTTTCTGTATTGGTGCCTC 58.726 50.000 0.00 0.00 0.00 4.70
3440 4868 1.906574 TGGACGCCTCCTTTCTGTATT 59.093 47.619 3.30 0.00 37.48 1.89
3457 4885 1.484240 TGACGCATGTGTCCATATGGA 59.516 47.619 31.02 20.98 43.08 3.41
3458 4886 1.869132 CTGACGCATGTGTCCATATGG 59.131 52.381 31.02 16.25 38.11 2.74
3459 4887 1.869132 CCTGACGCATGTGTCCATATG 59.131 52.381 31.02 17.47 38.11 1.78
3460 4888 1.811558 GCCTGACGCATGTGTCCATAT 60.812 52.381 31.02 0.46 38.11 1.78
3461 4889 0.461870 GCCTGACGCATGTGTCCATA 60.462 55.000 31.02 15.60 38.11 2.74
3462 4890 1.746615 GCCTGACGCATGTGTCCAT 60.747 57.895 31.02 1.64 38.11 3.41
3463 4891 2.358615 GCCTGACGCATGTGTCCA 60.359 61.111 31.02 19.78 38.11 4.02
3464 4892 3.490759 CGCCTGACGCATGTGTCC 61.491 66.667 31.02 17.74 38.11 4.02
3504 4932 1.199615 ACATTAAATTTGGCCCCGGG 58.800 50.000 15.80 15.80 0.00 5.73
3505 4933 3.342377 AAACATTAAATTTGGCCCCGG 57.658 42.857 0.00 0.00 0.00 5.73
3506 4934 3.438434 CCAAAACATTAAATTTGGCCCCG 59.562 43.478 14.22 0.00 46.35 5.73
3525 4953 5.509927 CGTGTGGACGTTGGTTTTTCCAA 62.510 47.826 0.00 0.00 44.12 3.53
3526 4954 1.473278 GTGTGGACGTTGGTTTTTCCA 59.527 47.619 0.00 0.00 45.60 3.53
3540 4968 1.218875 CTGCAAACGCTACGTGTGGA 61.219 55.000 11.87 8.25 44.27 4.02
3576 5007 3.761218 ACGTGGCAAAATGAATGGTGATA 59.239 39.130 0.00 0.00 0.00 2.15
4035 5475 9.248291 GTTGTCATGACATGTTTCAACTATTTT 57.752 29.630 28.32 0.00 41.52 1.82
4051 5491 8.935844 TGATATTTACACTGAAGTTGTCATGAC 58.064 33.333 19.27 19.27 35.07 3.06


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

AutoCloner maintained by Alex Coulton.