Multiple sequence alignment - TraesCS4B01G124000

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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 TraesCS4B01G124000 chr4B 100.000 4703 0 0 1 4703 148919366 148924068 0.000000e+00 8685.0
1 TraesCS4B01G124000 chr4B 94.643 168 5 3 412 575 66471515 66471348 1.680000e-64 257.0
2 TraesCS4B01G124000 chr4D 95.923 3998 111 17 640 4614 105134723 105138691 0.000000e+00 6433.0
3 TraesCS4B01G124000 chr4D 94.048 168 6 3 401 567 13359908 13360072 7.810000e-63 252.0
4 TraesCS4B01G124000 chr4D 83.516 182 18 5 174 346 105134309 105134487 4.870000e-35 159.0
5 TraesCS4B01G124000 chr4A 95.251 3622 120 23 1009 4614 470689936 470686351 0.000000e+00 5688.0
6 TraesCS4B01G124000 chr4A 92.806 417 25 2 2 413 470691176 470690760 2.420000e-167 599.0
7 TraesCS4B01G124000 chr4A 93.286 283 11 6 632 908 470690590 470690310 1.220000e-110 411.0
8 TraesCS4B01G124000 chr4A 97.727 44 1 0 4660 4703 725933043 725933000 5.050000e-10 76.8
9 TraesCS4B01G124000 chr4A 95.455 44 2 0 4660 4703 609578530 609578487 2.350000e-08 71.3
10 TraesCS4B01G124000 chr5A 86.018 894 105 11 1717 2606 319753905 319753028 0.000000e+00 941.0
11 TraesCS4B01G124000 chr5A 84.123 422 67 0 3260 3681 319752481 319752060 4.380000e-110 409.0
12 TraesCS4B01G124000 chr5A 92.025 163 13 0 1454 1616 319754132 319753970 3.660000e-56 230.0
13 TraesCS4B01G124000 chr5A 95.455 44 2 0 4660 4703 454393246 454393289 2.350000e-08 71.3
14 TraesCS4B01G124000 chr5D 85.857 898 107 10 1713 2606 234821863 234822744 0.000000e+00 937.0
15 TraesCS4B01G124000 chr5D 83.886 422 68 0 3260 3681 234823309 234823730 2.040000e-108 403.0
16 TraesCS4B01G124000 chr5D 96.250 160 5 1 412 570 181626276 181626117 1.300000e-65 261.0
17 TraesCS4B01G124000 chr5D 91.124 169 15 0 1448 1616 234821634 234821802 3.660000e-56 230.0
18 TraesCS4B01G124000 chr5B 86.067 890 92 12 1716 2601 270013463 270012602 0.000000e+00 928.0
19 TraesCS4B01G124000 chr5B 85.106 423 63 0 3259 3681 270011722 270011300 2.600000e-117 433.0
20 TraesCS4B01G124000 chr5B 92.025 163 13 0 1454 1616 270013683 270013521 3.660000e-56 230.0
21 TraesCS4B01G124000 chr5B 95.455 44 2 0 4660 4703 514005687 514005730 2.350000e-08 71.3
22 TraesCS4B01G124000 chr3B 96.835 158 4 1 411 567 342882177 342882334 3.610000e-66 263.0
23 TraesCS4B01G124000 chr3B 83.784 74 8 4 4631 4703 25419343 25419413 3.040000e-07 67.6
24 TraesCS4B01G124000 chr1D 96.226 159 5 1 410 567 36612131 36612289 4.670000e-65 259.0
25 TraesCS4B01G124000 chr2D 94.083 169 9 1 400 567 316334124 316333956 6.040000e-64 255.0
26 TraesCS4B01G124000 chr6D 95.062 162 7 1 407 567 142867207 142867046 2.170000e-63 254.0
27 TraesCS4B01G124000 chr7D 92.614 176 9 2 407 578 202716849 202716674 2.810000e-62 250.0
28 TraesCS4B01G124000 chr3D 94.969 159 7 1 410 567 426536114 426535956 1.010000e-61 248.0
29 TraesCS4B01G124000 chr6A 97.727 44 1 0 4660 4703 465234624 465234667 5.050000e-10 76.8
30 TraesCS4B01G124000 chr2B 97.727 44 1 0 4660 4703 25576965 25577008 5.050000e-10 76.8
31 TraesCS4B01G124000 chr7A 95.455 44 2 0 4660 4703 519565531 519565488 2.350000e-08 71.3
32 TraesCS4B01G124000 chr3A 95.455 44 2 0 4660 4703 514047394 514047437 2.350000e-08 71.3


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 TraesCS4B01G124000 chr4B 148919366 148924068 4702 False 8685.000000 8685 100.000000 1 4703 1 chr4B.!!$F1 4702
1 TraesCS4B01G124000 chr4D 105134309 105138691 4382 False 3296.000000 6433 89.719500 174 4614 2 chr4D.!!$F2 4440
2 TraesCS4B01G124000 chr4A 470686351 470691176 4825 True 2232.666667 5688 93.781000 2 4614 3 chr4A.!!$R3 4612
3 TraesCS4B01G124000 chr5A 319752060 319754132 2072 True 526.666667 941 87.388667 1454 3681 3 chr5A.!!$R1 2227
4 TraesCS4B01G124000 chr5D 234821634 234823730 2096 False 523.333333 937 86.955667 1448 3681 3 chr5D.!!$F1 2233
5 TraesCS4B01G124000 chr5B 270011300 270013683 2383 True 530.333333 928 87.732667 1454 3681 3 chr5B.!!$R1 2227

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
672 913 0.469144 TTTTGTGCCAGGAACCCTCC 60.469 55.000 0.00 0.00 42.81 4.30 F
1083 1605 0.106167 ATTCCCATGCTCATGCTGCT 60.106 50.000 0.00 0.00 40.48 4.24 F
1629 2151 1.227823 CGACCTTGTCCAGCACCAA 60.228 57.895 0.00 0.00 0.00 3.67 F
2418 2970 1.227853 AAAGCGGCTGTCGGACTTT 60.228 52.632 1.81 2.53 39.69 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 2991 0.822164 CCACCGGGTAGAACTCGAAT 59.178 55.000 6.32 0.00 46.98 3.34 R
3080 4092 0.529555 GGACGAGCAGATCAGCCTTC 60.530 60.000 6.46 0.91 34.23 3.46 R
3155 4186 0.322277 GGGATGGCGATGATGCATCT 60.322 55.000 26.32 12.70 38.59 2.90 R
3881 4927 1.202915 TGAGCATGAAGTGGGCAGAAA 60.203 47.619 0.00 0.00 0.00 2.52 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
158 159 3.305744 GGATTAGAGCGGAGAAGACATCC 60.306 52.174 0.00 0.00 0.00 3.51
163 164 1.144936 CGGAGAAGACATCCCAGCC 59.855 63.158 0.00 0.00 32.86 4.85
170 171 3.137360 AGAAGACATCCCAGCCCTTTATC 59.863 47.826 0.00 0.00 0.00 1.75
172 173 2.708325 AGACATCCCAGCCCTTTATCTC 59.292 50.000 0.00 0.00 0.00 2.75
194 195 8.940397 TCTCTTTCCCTGTTTTTCATCTAATT 57.060 30.769 0.00 0.00 0.00 1.40
195 196 9.367160 TCTCTTTCCCTGTTTTTCATCTAATTT 57.633 29.630 0.00 0.00 0.00 1.82
246 247 8.726870 AATTATACAAAGTGCCTACGTAACAT 57.273 30.769 0.00 0.00 0.00 2.71
247 248 7.760131 TTATACAAAGTGCCTACGTAACATC 57.240 36.000 0.00 0.00 0.00 3.06
418 549 5.287674 GGTTATCTTGTAACCTACTCCCC 57.712 47.826 9.20 0.00 42.68 4.81
419 550 4.102210 GGTTATCTTGTAACCTACTCCCCC 59.898 50.000 9.20 0.00 42.68 5.40
420 551 1.856629 TCTTGTAACCTACTCCCCCG 58.143 55.000 0.00 0.00 0.00 5.73
421 552 1.077663 TCTTGTAACCTACTCCCCCGT 59.922 52.381 0.00 0.00 0.00 5.28
422 553 1.904537 CTTGTAACCTACTCCCCCGTT 59.095 52.381 0.00 0.00 0.00 4.44
423 554 1.560505 TGTAACCTACTCCCCCGTTC 58.439 55.000 0.00 0.00 0.00 3.95
424 555 0.826715 GTAACCTACTCCCCCGTTCC 59.173 60.000 0.00 0.00 0.00 3.62
425 556 0.712380 TAACCTACTCCCCCGTTCCT 59.288 55.000 0.00 0.00 0.00 3.36
426 557 0.712380 AACCTACTCCCCCGTTCCTA 59.288 55.000 0.00 0.00 0.00 2.94
427 558 0.712380 ACCTACTCCCCCGTTCCTAA 59.288 55.000 0.00 0.00 0.00 2.69
428 559 1.079323 ACCTACTCCCCCGTTCCTAAA 59.921 52.381 0.00 0.00 0.00 1.85
429 560 2.293385 ACCTACTCCCCCGTTCCTAAAT 60.293 50.000 0.00 0.00 0.00 1.40
430 561 3.051880 ACCTACTCCCCCGTTCCTAAATA 60.052 47.826 0.00 0.00 0.00 1.40
431 562 4.165760 CCTACTCCCCCGTTCCTAAATAT 58.834 47.826 0.00 0.00 0.00 1.28
432 563 4.596212 CCTACTCCCCCGTTCCTAAATATT 59.404 45.833 0.00 0.00 0.00 1.28
433 564 5.072736 CCTACTCCCCCGTTCCTAAATATTT 59.927 44.000 5.89 5.89 0.00 1.40
434 565 4.788679 ACTCCCCCGTTCCTAAATATTTG 58.211 43.478 11.05 1.40 0.00 2.32
435 566 4.228895 ACTCCCCCGTTCCTAAATATTTGT 59.771 41.667 11.05 0.00 0.00 2.83
436 567 4.784177 TCCCCCGTTCCTAAATATTTGTC 58.216 43.478 11.05 0.00 0.00 3.18
437 568 4.475747 TCCCCCGTTCCTAAATATTTGTCT 59.524 41.667 11.05 0.00 0.00 3.41
438 569 5.044698 TCCCCCGTTCCTAAATATTTGTCTT 60.045 40.000 11.05 0.00 0.00 3.01
439 570 5.655090 CCCCCGTTCCTAAATATTTGTCTTT 59.345 40.000 11.05 0.00 0.00 2.52
440 571 6.183360 CCCCCGTTCCTAAATATTTGTCTTTC 60.183 42.308 11.05 0.00 0.00 2.62
441 572 6.602009 CCCCGTTCCTAAATATTTGTCTTTCT 59.398 38.462 11.05 0.00 0.00 2.52
442 573 7.415206 CCCCGTTCCTAAATATTTGTCTTTCTG 60.415 40.741 11.05 0.00 0.00 3.02
443 574 7.415206 CCCGTTCCTAAATATTTGTCTTTCTGG 60.415 40.741 11.05 3.70 0.00 3.86
444 575 7.335924 CCGTTCCTAAATATTTGTCTTTCTGGA 59.664 37.037 11.05 3.34 0.00 3.86
445 576 8.391106 CGTTCCTAAATATTTGTCTTTCTGGAG 58.609 37.037 11.05 0.00 0.00 3.86
446 577 9.449719 GTTCCTAAATATTTGTCTTTCTGGAGA 57.550 33.333 11.05 0.00 0.00 3.71
454 585 7.587037 ATTTGTCTTTCTGGAGATTTCAACA 57.413 32.000 0.00 0.00 0.00 3.33
455 586 7.403312 TTTGTCTTTCTGGAGATTTCAACAA 57.597 32.000 0.00 0.00 0.00 2.83
456 587 6.624352 TGTCTTTCTGGAGATTTCAACAAG 57.376 37.500 0.00 0.00 0.00 3.16
457 588 6.122277 TGTCTTTCTGGAGATTTCAACAAGT 58.878 36.000 0.00 0.00 0.00 3.16
458 589 6.038603 TGTCTTTCTGGAGATTTCAACAAGTG 59.961 38.462 0.00 0.00 0.00 3.16
459 590 6.260936 GTCTTTCTGGAGATTTCAACAAGTGA 59.739 38.462 0.00 0.00 0.00 3.41
460 591 6.260936 TCTTTCTGGAGATTTCAACAAGTGAC 59.739 38.462 0.00 0.00 35.39 3.67
461 592 5.296151 TCTGGAGATTTCAACAAGTGACT 57.704 39.130 0.00 0.00 35.39 3.41
462 593 6.419484 TCTGGAGATTTCAACAAGTGACTA 57.581 37.500 0.00 0.00 35.39 2.59
463 594 6.223852 TCTGGAGATTTCAACAAGTGACTAC 58.776 40.000 0.00 0.00 35.39 2.73
464 595 5.924356 TGGAGATTTCAACAAGTGACTACA 58.076 37.500 0.00 0.00 35.39 2.74
465 596 6.533730 TGGAGATTTCAACAAGTGACTACAT 58.466 36.000 0.00 0.00 35.39 2.29
466 597 7.676004 TGGAGATTTCAACAAGTGACTACATA 58.324 34.615 0.00 0.00 35.39 2.29
467 598 7.602644 TGGAGATTTCAACAAGTGACTACATAC 59.397 37.037 0.00 0.00 35.39 2.39
468 599 7.201444 GGAGATTTCAACAAGTGACTACATACG 60.201 40.741 0.00 0.00 35.39 3.06
469 600 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
470 601 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
471 602 5.456548 TCAACAAGTGACTACATACGGAA 57.543 39.130 0.00 0.00 0.00 4.30
472 603 5.224888 TCAACAAGTGACTACATACGGAAC 58.775 41.667 0.00 0.00 0.00 3.62
473 604 4.859304 ACAAGTGACTACATACGGAACA 57.141 40.909 0.00 0.00 0.00 3.18
474 605 5.204409 ACAAGTGACTACATACGGAACAA 57.796 39.130 0.00 0.00 0.00 2.83
475 606 5.603596 ACAAGTGACTACATACGGAACAAA 58.396 37.500 0.00 0.00 0.00 2.83
476 607 6.050432 ACAAGTGACTACATACGGAACAAAA 58.950 36.000 0.00 0.00 0.00 2.44
477 608 6.708949 ACAAGTGACTACATACGGAACAAAAT 59.291 34.615 0.00 0.00 0.00 1.82
478 609 6.721571 AGTGACTACATACGGAACAAAATG 57.278 37.500 0.00 0.00 0.00 2.32
479 610 6.460781 AGTGACTACATACGGAACAAAATGA 58.539 36.000 0.00 0.00 0.00 2.57
480 611 6.590292 AGTGACTACATACGGAACAAAATGAG 59.410 38.462 0.00 0.00 0.00 2.90
481 612 6.367969 GTGACTACATACGGAACAAAATGAGT 59.632 38.462 0.00 0.00 0.00 3.41
482 613 6.367695 TGACTACATACGGAACAAAATGAGTG 59.632 38.462 0.00 0.00 0.00 3.51
483 614 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
484 615 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
485 616 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
486 617 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
487 618 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
488 619 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
489 620 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
490 621 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
491 622 6.655003 ACGGAACAAAATGAGTGAATCTACAT 59.345 34.615 0.00 0.00 0.00 2.29
492 623 6.963242 CGGAACAAAATGAGTGAATCTACATG 59.037 38.462 0.00 0.00 0.00 3.21
493 624 6.749118 GGAACAAAATGAGTGAATCTACATGC 59.251 38.462 0.00 0.00 0.00 4.06
494 625 7.362401 GGAACAAAATGAGTGAATCTACATGCT 60.362 37.037 0.00 0.00 0.00 3.79
495 626 8.565896 AACAAAATGAGTGAATCTACATGCTA 57.434 30.769 0.00 0.00 0.00 3.49
496 627 8.565896 ACAAAATGAGTGAATCTACATGCTAA 57.434 30.769 0.00 0.00 0.00 3.09
497 628 9.013229 ACAAAATGAGTGAATCTACATGCTAAA 57.987 29.630 0.00 0.00 0.00 1.85
498 629 9.844790 CAAAATGAGTGAATCTACATGCTAAAA 57.155 29.630 0.00 0.00 0.00 1.52
503 634 9.836864 TGAGTGAATCTACATGCTAAAATATGT 57.163 29.630 0.00 0.00 40.39 2.29
524 655 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
526 657 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
527 658 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
528 659 8.954350 GTCTATATACATCCGTATGTGGTAGTT 58.046 37.037 3.56 0.00 45.99 2.24
529 660 9.170734 TCTATATACATCCGTATGTGGTAGTTC 57.829 37.037 3.56 0.00 45.99 3.01
530 661 7.770366 ATATACATCCGTATGTGGTAGTTCA 57.230 36.000 3.56 0.00 45.99 3.18
531 662 6.665992 ATACATCCGTATGTGGTAGTTCAT 57.334 37.500 3.56 0.00 45.99 2.57
532 663 5.353394 ACATCCGTATGTGGTAGTTCATT 57.647 39.130 0.00 0.00 44.79 2.57
533 664 5.741011 ACATCCGTATGTGGTAGTTCATTT 58.259 37.500 0.00 0.00 44.79 2.32
534 665 5.584649 ACATCCGTATGTGGTAGTTCATTTG 59.415 40.000 0.00 0.00 44.79 2.32
535 666 5.408880 TCCGTATGTGGTAGTTCATTTGA 57.591 39.130 0.00 0.00 0.00 2.69
536 667 5.795972 TCCGTATGTGGTAGTTCATTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
537 668 6.231951 TCCGTATGTGGTAGTTCATTTGAAA 58.768 36.000 0.00 0.00 35.58 2.69
538 669 6.882140 TCCGTATGTGGTAGTTCATTTGAAAT 59.118 34.615 0.00 0.00 35.58 2.17
539 670 7.065324 TCCGTATGTGGTAGTTCATTTGAAATC 59.935 37.037 0.00 0.00 35.58 2.17
540 671 7.065803 CCGTATGTGGTAGTTCATTTGAAATCT 59.934 37.037 0.00 0.00 35.58 2.40
541 672 8.116753 CGTATGTGGTAGTTCATTTGAAATCTC 58.883 37.037 0.00 0.00 35.58 2.75
542 673 9.167311 GTATGTGGTAGTTCATTTGAAATCTCT 57.833 33.333 0.00 0.00 35.58 3.10
544 675 9.739276 ATGTGGTAGTTCATTTGAAATCTCTAA 57.261 29.630 0.00 0.00 35.58 2.10
545 676 9.567776 TGTGGTAGTTCATTTGAAATCTCTAAA 57.432 29.630 0.00 0.00 35.58 1.85
583 714 3.715628 ACGGTAGTATTTTACGGCGAT 57.284 42.857 16.62 0.00 0.00 4.58
609 740 4.141287 TCCACACTTGTACATTTTCCCTG 58.859 43.478 0.00 0.00 0.00 4.45
612 743 2.825532 CACTTGTACATTTTCCCTGGGG 59.174 50.000 14.00 2.42 0.00 4.96
615 746 3.163616 TGTACATTTTCCCTGGGGTTC 57.836 47.619 14.00 0.85 36.47 3.62
624 755 1.203212 TCCCTGGGGTTCTCGTTCTTA 60.203 52.381 14.00 0.00 36.47 2.10
672 913 0.469144 TTTTGTGCCAGGAACCCTCC 60.469 55.000 0.00 0.00 42.81 4.30
727 968 1.678627 CAGAGGAGTACATCAGACCGG 59.321 57.143 0.00 0.00 0.00 5.28
761 1006 5.078949 TGAGACACACATGGATGGATTTTT 58.921 37.500 0.00 0.00 0.00 1.94
762 1007 6.244654 TGAGACACACATGGATGGATTTTTA 58.755 36.000 0.00 0.00 0.00 1.52
763 1008 6.375174 TGAGACACACATGGATGGATTTTTAG 59.625 38.462 0.00 0.00 0.00 1.85
768 1013 7.451255 ACACACATGGATGGATTTTTAGAAAGA 59.549 33.333 0.00 0.00 0.00 2.52
769 1014 8.306038 CACACATGGATGGATTTTTAGAAAGAA 58.694 33.333 0.00 0.00 0.00 2.52
908 1157 1.885163 CTTTACTCCTCCGCCACCGT 61.885 60.000 0.00 0.00 0.00 4.83
1046 1568 2.517402 CTCGTCCTCCTCCTCCGG 60.517 72.222 0.00 0.00 0.00 5.14
1083 1605 0.106167 ATTCCCATGCTCATGCTGCT 60.106 50.000 0.00 0.00 40.48 4.24
1110 1632 2.754664 CTTCCCACTCCGCCTTGCTT 62.755 60.000 0.00 0.00 0.00 3.91
1452 1974 5.467735 GGAGGTTAACGTCAACAATAACAGT 59.532 40.000 25.07 0.00 31.46 3.55
1628 2150 2.425592 CGACCTTGTCCAGCACCA 59.574 61.111 0.00 0.00 0.00 4.17
1629 2151 1.227823 CGACCTTGTCCAGCACCAA 60.228 57.895 0.00 0.00 0.00 3.67
1649 2171 2.366570 GCCACCTCCTCCTCCTCT 59.633 66.667 0.00 0.00 0.00 3.69
1938 2490 1.669115 GCTGACGCTCCTTCTGCAA 60.669 57.895 0.00 0.00 37.74 4.08
2418 2970 1.227853 AAAGCGGCTGTCGGACTTT 60.228 52.632 1.81 2.53 39.69 2.66
2424 2976 1.675641 GCTGTCGGACTTTGCCCAT 60.676 57.895 9.88 0.00 0.00 4.00
2439 2991 4.488136 CATACGCTGGGCCTGCCA 62.488 66.667 27.01 16.74 37.98 4.92
2606 3158 4.820894 ACCTCATCCAAAGGTACTGTAC 57.179 45.455 9.46 9.46 45.40 2.90
2607 3159 4.426704 ACCTCATCCAAAGGTACTGTACT 58.573 43.478 16.79 1.60 45.40 2.73
2609 3161 5.421374 ACCTCATCCAAAGGTACTGTACTAC 59.579 44.000 16.79 2.38 45.40 2.73
2610 3162 5.450137 CCTCATCCAAAGGTACTGTACTACG 60.450 48.000 16.79 4.55 40.86 3.51
2612 3164 5.356190 TCATCCAAAGGTACTGTACTACGAG 59.644 44.000 16.79 5.05 40.86 4.18
2656 3267 7.063074 GCTTCCATTGTGAAATGAATCTTCAAG 59.937 37.037 0.00 0.00 41.13 3.02
2667 3278 7.941795 AATGAATCTTCAAGCTTTTCACTTG 57.058 32.000 11.66 0.00 44.76 3.16
2705 3316 2.146920 TGGCATCAGGCATCAATCAA 57.853 45.000 0.00 0.00 46.46 2.57
2760 3371 7.247728 GCCATTGATTGATTTAACGACTAACA 58.752 34.615 0.00 0.00 0.00 2.41
3080 4092 3.002791 TCAATTGACAAGGCTAAGCTCG 58.997 45.455 3.38 0.00 0.00 5.03
3092 4104 2.741612 CTAAGCTCGAAGGCTGATCTG 58.258 52.381 0.00 0.00 42.24 2.90
3146 4177 7.598869 GGAACTAAGAAATCAACCAAAATGTCC 59.401 37.037 0.00 0.00 0.00 4.02
3147 4178 7.839680 ACTAAGAAATCAACCAAAATGTCCT 57.160 32.000 0.00 0.00 0.00 3.85
3148 4179 8.250143 ACTAAGAAATCAACCAAAATGTCCTT 57.750 30.769 0.00 0.00 0.00 3.36
3149 4180 8.704668 ACTAAGAAATCAACCAAAATGTCCTTT 58.295 29.630 0.00 0.00 0.00 3.11
3150 4181 7.790823 AAGAAATCAACCAAAATGTCCTTTG 57.209 32.000 0.00 0.00 36.28 2.77
3151 4182 7.123355 AGAAATCAACCAAAATGTCCTTTGA 57.877 32.000 0.00 0.00 38.35 2.69
3152 4183 6.986231 AGAAATCAACCAAAATGTCCTTTGAC 59.014 34.615 0.00 0.00 38.35 3.18
3153 4184 6.484364 AATCAACCAAAATGTCCTTTGACT 57.516 33.333 0.00 0.00 42.28 3.41
3154 4185 5.930837 TCAACCAAAATGTCCTTTGACTT 57.069 34.783 0.00 0.00 42.28 3.01
3155 4186 7.595819 ATCAACCAAAATGTCCTTTGACTTA 57.404 32.000 0.00 0.00 42.28 2.24
3156 4187 7.038154 TCAACCAAAATGTCCTTTGACTTAG 57.962 36.000 0.00 0.00 42.28 2.18
3157 4188 6.831353 TCAACCAAAATGTCCTTTGACTTAGA 59.169 34.615 0.00 0.00 42.28 2.10
3158 4189 7.505585 TCAACCAAAATGTCCTTTGACTTAGAT 59.494 33.333 0.00 0.00 42.28 1.98
3159 4190 7.219484 ACCAAAATGTCCTTTGACTTAGATG 57.781 36.000 0.00 0.00 42.28 2.90
3160 4191 6.095377 CCAAAATGTCCTTTGACTTAGATGC 58.905 40.000 0.00 0.00 42.28 3.91
3161 4192 6.294675 CCAAAATGTCCTTTGACTTAGATGCA 60.295 38.462 0.00 0.00 42.28 3.96
3162 4193 7.318141 CAAAATGTCCTTTGACTTAGATGCAT 58.682 34.615 0.00 0.00 42.28 3.96
3163 4194 6.690194 AATGTCCTTTGACTTAGATGCATC 57.310 37.500 19.37 19.37 42.28 3.91
3171 4202 3.244318 TGACTTAGATGCATCATCGCCAT 60.244 43.478 27.81 8.45 44.67 4.40
3174 4205 0.322277 AGATGCATCATCGCCATCCC 60.322 55.000 27.81 0.00 44.67 3.85
3682 4724 3.515286 CATCTGCTTGGCGCCCAG 61.515 66.667 26.77 24.62 38.05 4.45
3795 4837 5.233263 GCTCAGTTCGATCAATTCTAAGACC 59.767 44.000 0.00 0.00 0.00 3.85
3914 4960 5.183904 ACTTCATGCTCAACTTTACCATTCC 59.816 40.000 0.00 0.00 0.00 3.01
3924 4970 4.542697 ACTTTACCATTCCGGCCAATTAT 58.457 39.130 2.24 0.00 39.03 1.28
3925 4971 5.697067 ACTTTACCATTCCGGCCAATTATA 58.303 37.500 2.24 0.00 39.03 0.98
3975 5021 4.776435 TCCTTGTTGATATCAGATGCCA 57.224 40.909 5.39 0.00 0.00 4.92
4116 5170 5.511234 GCATATTGAAGCCATTCACTCTT 57.489 39.130 0.00 0.00 45.07 2.85
4133 5195 8.450578 TTCACTCTTTGTTCATGTTTGATAGT 57.549 30.769 0.00 0.00 0.00 2.12
4289 5354 7.555306 GGATGTATCCTCTCCTTTTAACAAC 57.445 40.000 3.63 0.00 43.73 3.32
4290 5355 7.110155 GGATGTATCCTCTCCTTTTAACAACA 58.890 38.462 3.63 0.00 43.73 3.33
4378 5445 5.604650 TGGATCCAAGTTTGGGTATTTGTTT 59.395 36.000 13.46 0.00 43.10 2.83
4443 5510 3.953612 ACAATTCTTGTGTGCTTCTTGGA 59.046 39.130 0.00 0.00 43.48 3.53
4485 5552 1.968540 GCCTGGCTGTTGGACACTC 60.969 63.158 12.43 0.00 0.00 3.51
4495 5562 6.374333 TGGCTGTTGGACACTCTTAATTTATC 59.626 38.462 0.00 0.00 0.00 1.75
4496 5563 6.374333 GGCTGTTGGACACTCTTAATTTATCA 59.626 38.462 0.00 0.00 0.00 2.15
4505 5572 8.206325 ACACTCTTAATTTATCAGCACATCAG 57.794 34.615 0.00 0.00 0.00 2.90
4522 5589 6.632909 CACATCAGTTTCTCAGATCTTCTCT 58.367 40.000 0.00 0.00 33.14 3.10
4561 5630 9.635520 CCATGAATCCTTTAATATGATTTCTGC 57.364 33.333 0.00 0.00 0.00 4.26
4579 5648 6.916360 TTCTGCCTCTTTTGGTATCAATTT 57.084 33.333 0.00 0.00 32.28 1.82
4581 5650 6.248433 TCTGCCTCTTTTGGTATCAATTTCT 58.752 36.000 0.00 0.00 32.28 2.52
4583 5652 5.774690 TGCCTCTTTTGGTATCAATTTCTGT 59.225 36.000 0.00 0.00 32.28 3.41
4591 5660 9.959749 TTTTGGTATCAATTTCTGTGTAAGTTC 57.040 29.630 0.00 0.00 32.28 3.01
4610 5679 4.881850 AGTTCTTGGACGTTCACTTTGATT 59.118 37.500 0.00 0.00 0.00 2.57
4665 5734 2.933495 GGTTAAAACCCCAGCGATTC 57.067 50.000 0.02 0.00 43.43 2.52
4666 5735 2.164338 GGTTAAAACCCCAGCGATTCA 58.836 47.619 0.02 0.00 43.43 2.57
4667 5736 2.758423 GGTTAAAACCCCAGCGATTCAT 59.242 45.455 0.02 0.00 43.43 2.57
4668 5737 3.949113 GGTTAAAACCCCAGCGATTCATA 59.051 43.478 0.02 0.00 43.43 2.15
4669 5738 4.201980 GGTTAAAACCCCAGCGATTCATAC 60.202 45.833 0.02 0.00 43.43 2.39
4670 5739 2.799126 AAACCCCAGCGATTCATACA 57.201 45.000 0.00 0.00 0.00 2.29
4671 5740 2.799126 AACCCCAGCGATTCATACAA 57.201 45.000 0.00 0.00 0.00 2.41
4672 5741 2.038387 ACCCCAGCGATTCATACAAC 57.962 50.000 0.00 0.00 0.00 3.32
4673 5742 1.308998 CCCCAGCGATTCATACAACC 58.691 55.000 0.00 0.00 0.00 3.77
4674 5743 1.408127 CCCCAGCGATTCATACAACCA 60.408 52.381 0.00 0.00 0.00 3.67
4675 5744 2.575532 CCCAGCGATTCATACAACCAT 58.424 47.619 0.00 0.00 0.00 3.55
4676 5745 2.951642 CCCAGCGATTCATACAACCATT 59.048 45.455 0.00 0.00 0.00 3.16
4677 5746 3.381272 CCCAGCGATTCATACAACCATTT 59.619 43.478 0.00 0.00 0.00 2.32
4678 5747 4.142182 CCCAGCGATTCATACAACCATTTT 60.142 41.667 0.00 0.00 0.00 1.82
4679 5748 5.410067 CCAGCGATTCATACAACCATTTTT 58.590 37.500 0.00 0.00 0.00 1.94
4680 5749 6.405286 CCCAGCGATTCATACAACCATTTTTA 60.405 38.462 0.00 0.00 0.00 1.52
4681 5750 7.202526 CCAGCGATTCATACAACCATTTTTAT 58.797 34.615 0.00 0.00 0.00 1.40
4682 5751 7.706179 CCAGCGATTCATACAACCATTTTTATT 59.294 33.333 0.00 0.00 0.00 1.40
4683 5752 9.729023 CAGCGATTCATACAACCATTTTTATTA 57.271 29.630 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 8.704668 TCTATGAGGTTTCACATAATGCTAAGA 58.295 33.333 0.00 0.00 35.83 2.10
145 146 1.144936 GGCTGGGATGTCTTCTCCG 59.855 63.158 0.00 0.00 33.29 4.63
158 159 2.511637 AGGGAAAGAGATAAAGGGCTGG 59.488 50.000 0.00 0.00 0.00 4.85
163 164 7.524717 TGAAAAACAGGGAAAGAGATAAAGG 57.475 36.000 0.00 0.00 0.00 3.11
170 171 9.987272 AAAATTAGATGAAAAACAGGGAAAGAG 57.013 29.630 0.00 0.00 0.00 2.85
225 226 5.974108 AGATGTTACGTAGGCACTTTGTAT 58.026 37.500 0.00 0.00 41.75 2.29
411 542 5.429435 ACAAATATTTAGGAACGGGGGAGTA 59.571 40.000 0.00 0.00 0.00 2.59
412 543 4.228895 ACAAATATTTAGGAACGGGGGAGT 59.771 41.667 0.00 0.00 0.00 3.85
413 544 4.788679 ACAAATATTTAGGAACGGGGGAG 58.211 43.478 0.00 0.00 0.00 4.30
414 545 4.475747 AGACAAATATTTAGGAACGGGGGA 59.524 41.667 0.00 0.00 0.00 4.81
415 546 4.788679 AGACAAATATTTAGGAACGGGGG 58.211 43.478 0.00 0.00 0.00 5.40
416 547 6.602009 AGAAAGACAAATATTTAGGAACGGGG 59.398 38.462 0.00 0.00 0.00 5.73
417 548 7.415206 CCAGAAAGACAAATATTTAGGAACGGG 60.415 40.741 0.00 0.00 0.00 5.28
418 549 7.335924 TCCAGAAAGACAAATATTTAGGAACGG 59.664 37.037 0.00 0.00 0.00 4.44
419 550 8.263940 TCCAGAAAGACAAATATTTAGGAACG 57.736 34.615 0.00 0.00 0.00 3.95
420 551 9.449719 TCTCCAGAAAGACAAATATTTAGGAAC 57.550 33.333 0.00 0.00 28.49 3.62
428 559 9.300681 TGTTGAAATCTCCAGAAAGACAAATAT 57.699 29.630 0.00 0.00 0.00 1.28
429 560 8.690203 TGTTGAAATCTCCAGAAAGACAAATA 57.310 30.769 0.00 0.00 0.00 1.40
430 561 7.587037 TGTTGAAATCTCCAGAAAGACAAAT 57.413 32.000 0.00 0.00 0.00 2.32
431 562 7.122650 ACTTGTTGAAATCTCCAGAAAGACAAA 59.877 33.333 0.00 0.00 0.00 2.83
432 563 6.603201 ACTTGTTGAAATCTCCAGAAAGACAA 59.397 34.615 0.00 0.00 0.00 3.18
433 564 6.038603 CACTTGTTGAAATCTCCAGAAAGACA 59.961 38.462 0.00 0.00 0.00 3.41
434 565 6.260936 TCACTTGTTGAAATCTCCAGAAAGAC 59.739 38.462 0.00 0.00 0.00 3.01
435 566 6.260936 GTCACTTGTTGAAATCTCCAGAAAGA 59.739 38.462 0.00 0.00 35.39 2.52
436 567 6.261826 AGTCACTTGTTGAAATCTCCAGAAAG 59.738 38.462 0.00 0.00 35.39 2.62
437 568 6.122277 AGTCACTTGTTGAAATCTCCAGAAA 58.878 36.000 0.00 0.00 35.39 2.52
438 569 5.684704 AGTCACTTGTTGAAATCTCCAGAA 58.315 37.500 0.00 0.00 35.39 3.02
439 570 5.296151 AGTCACTTGTTGAAATCTCCAGA 57.704 39.130 0.00 0.00 35.39 3.86
440 571 5.991606 TGTAGTCACTTGTTGAAATCTCCAG 59.008 40.000 0.00 0.00 35.39 3.86
441 572 5.924356 TGTAGTCACTTGTTGAAATCTCCA 58.076 37.500 0.00 0.00 35.39 3.86
442 573 7.201444 CGTATGTAGTCACTTGTTGAAATCTCC 60.201 40.741 0.00 0.00 35.39 3.71
443 574 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
444 575 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
445 576 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
446 577 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
447 578 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
448 579 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
449 580 5.221283 TGTTCCGTATGTAGTCACTTGTTGA 60.221 40.000 0.00 0.00 0.00 3.18
450 581 4.986034 TGTTCCGTATGTAGTCACTTGTTG 59.014 41.667 0.00 0.00 0.00 3.33
451 582 5.204409 TGTTCCGTATGTAGTCACTTGTT 57.796 39.130 0.00 0.00 0.00 2.83
452 583 4.859304 TGTTCCGTATGTAGTCACTTGT 57.141 40.909 0.00 0.00 0.00 3.16
453 584 6.533819 TTTTGTTCCGTATGTAGTCACTTG 57.466 37.500 0.00 0.00 0.00 3.16
454 585 6.932400 TCATTTTGTTCCGTATGTAGTCACTT 59.068 34.615 0.00 0.00 0.00 3.16
455 586 6.460781 TCATTTTGTTCCGTATGTAGTCACT 58.539 36.000 0.00 0.00 0.00 3.41
456 587 6.367969 ACTCATTTTGTTCCGTATGTAGTCAC 59.632 38.462 0.00 0.00 0.00 3.67
457 588 6.367695 CACTCATTTTGTTCCGTATGTAGTCA 59.632 38.462 0.00 0.00 0.00 3.41
458 589 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
459 590 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
460 591 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
461 592 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
462 593 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
463 594 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
464 595 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
465 596 7.156000 TGTAGATTCACTCATTTTGTTCCGTA 58.844 34.615 0.00 0.00 0.00 4.02
466 597 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
467 598 6.480524 TGTAGATTCACTCATTTTGTTCCG 57.519 37.500 0.00 0.00 0.00 4.30
468 599 6.749118 GCATGTAGATTCACTCATTTTGTTCC 59.251 38.462 0.00 0.00 0.00 3.62
469 600 7.533426 AGCATGTAGATTCACTCATTTTGTTC 58.467 34.615 0.00 0.00 0.00 3.18
470 601 7.458409 AGCATGTAGATTCACTCATTTTGTT 57.542 32.000 0.00 0.00 0.00 2.83
471 602 8.565896 TTAGCATGTAGATTCACTCATTTTGT 57.434 30.769 0.00 0.00 0.00 2.83
472 603 9.844790 TTTTAGCATGTAGATTCACTCATTTTG 57.155 29.630 0.00 0.00 0.00 2.44
477 608 9.836864 ACATATTTTAGCATGTAGATTCACTCA 57.163 29.630 0.00 0.00 33.66 3.41
498 629 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
500 631 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
501 632 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
502 633 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
503 634 9.170734 GAACTACCACATACGGATGTATATAGA 57.829 37.037 22.62 5.04 44.82 1.98
504 635 8.953313 TGAACTACCACATACGGATGTATATAG 58.047 37.037 14.23 16.35 44.82 1.31
505 636 8.866970 TGAACTACCACATACGGATGTATATA 57.133 34.615 14.23 5.36 44.82 0.86
506 637 7.770366 TGAACTACCACATACGGATGTATAT 57.230 36.000 14.23 4.37 44.82 0.86
507 638 7.770366 ATGAACTACCACATACGGATGTATA 57.230 36.000 14.23 8.27 44.82 1.47
508 639 6.665992 ATGAACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
509 640 6.474140 AATGAACTACCACATACGGATGTA 57.526 37.500 14.23 0.00 44.82 2.29
511 642 5.815222 TCAAATGAACTACCACATACGGATG 59.185 40.000 5.94 5.94 39.16 3.51
512 643 5.984725 TCAAATGAACTACCACATACGGAT 58.015 37.500 0.00 0.00 0.00 4.18
513 644 5.408880 TCAAATGAACTACCACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
514 645 6.489127 TTTCAAATGAACTACCACATACGG 57.511 37.500 0.00 0.00 33.13 4.02
515 646 7.974675 AGATTTCAAATGAACTACCACATACG 58.025 34.615 0.00 0.00 33.13 3.06
516 647 9.167311 AGAGATTTCAAATGAACTACCACATAC 57.833 33.333 0.00 0.00 33.13 2.39
518 649 9.739276 TTAGAGATTTCAAATGAACTACCACAT 57.261 29.630 0.00 0.00 33.13 3.21
519 650 9.567776 TTTAGAGATTTCAAATGAACTACCACA 57.432 29.630 0.00 0.00 33.13 4.17
544 675 9.511272 ACTACCGTTCCTAAATATTTGTCTTTT 57.489 29.630 11.05 0.00 0.00 2.27
553 684 9.696917 CCGTAAAATACTACCGTTCCTAAATAT 57.303 33.333 0.00 0.00 0.00 1.28
554 685 7.651704 GCCGTAAAATACTACCGTTCCTAAATA 59.348 37.037 0.00 0.00 0.00 1.40
555 686 6.479990 GCCGTAAAATACTACCGTTCCTAAAT 59.520 38.462 0.00 0.00 0.00 1.40
556 687 5.810074 GCCGTAAAATACTACCGTTCCTAAA 59.190 40.000 0.00 0.00 0.00 1.85
557 688 5.348164 GCCGTAAAATACTACCGTTCCTAA 58.652 41.667 0.00 0.00 0.00 2.69
558 689 4.497340 CGCCGTAAAATACTACCGTTCCTA 60.497 45.833 0.00 0.00 0.00 2.94
559 690 3.734902 CGCCGTAAAATACTACCGTTCCT 60.735 47.826 0.00 0.00 0.00 3.36
560 691 2.535574 CGCCGTAAAATACTACCGTTCC 59.464 50.000 0.00 0.00 0.00 3.62
561 692 3.434637 TCGCCGTAAAATACTACCGTTC 58.565 45.455 0.00 0.00 0.00 3.95
562 693 3.502191 TCGCCGTAAAATACTACCGTT 57.498 42.857 0.00 0.00 0.00 4.44
563 694 3.715628 ATCGCCGTAAAATACTACCGT 57.284 42.857 0.00 0.00 0.00 4.83
564 695 3.798337 ACAATCGCCGTAAAATACTACCG 59.202 43.478 0.00 0.00 0.00 4.02
565 696 5.277011 GGAACAATCGCCGTAAAATACTACC 60.277 44.000 0.00 0.00 0.00 3.18
566 697 5.291614 TGGAACAATCGCCGTAAAATACTAC 59.708 40.000 0.00 0.00 31.92 2.73
567 698 5.291614 GTGGAACAATCGCCGTAAAATACTA 59.708 40.000 0.00 0.00 44.16 1.82
568 699 4.093850 GTGGAACAATCGCCGTAAAATACT 59.906 41.667 0.00 0.00 44.16 2.12
569 700 4.336932 GTGGAACAATCGCCGTAAAATAC 58.663 43.478 0.00 0.00 44.16 1.89
609 740 6.168389 TCTAAATTGTAAGAACGAGAACCCC 58.832 40.000 0.00 0.00 0.00 4.95
612 743 9.408069 TCTCTTCTAAATTGTAAGAACGAGAAC 57.592 33.333 15.57 0.00 35.49 3.01
615 746 9.627395 TCTTCTCTTCTAAATTGTAAGAACGAG 57.373 33.333 0.00 12.55 33.28 4.18
624 755 6.118852 GCCCATCTCTTCTCTTCTAAATTGT 58.881 40.000 0.00 0.00 0.00 2.71
672 913 1.447838 CCATCGACAGTGAACCCGG 60.448 63.158 0.00 0.00 0.00 5.73
683 924 4.135306 TCCTAGTAGTGATGTCCATCGAC 58.865 47.826 3.04 3.17 40.63 4.20
727 968 8.450578 TCCATGTGTGTCTCATATTTATTTCC 57.549 34.615 0.00 0.00 0.00 3.13
769 1014 3.228188 TGGGCTCTGTGTCATCTTTTT 57.772 42.857 0.00 0.00 0.00 1.94
908 1157 1.002533 GGGGGTGGTGGAGTAGCTA 59.997 63.158 0.00 0.00 0.00 3.32
1046 1568 0.919710 ATAAGAGGAGTGGTTGGGGC 59.080 55.000 0.00 0.00 0.00 5.80
1083 1605 1.300963 GGAGTGGGAAGCTGATGCA 59.699 57.895 0.00 0.00 42.74 3.96
1086 1608 2.586792 GCGGAGTGGGAAGCTGAT 59.413 61.111 0.00 0.00 0.00 2.90
1089 1611 2.930562 AAGGCGGAGTGGGAAGCT 60.931 61.111 0.00 0.00 0.00 3.74
1131 1653 1.215679 AGAGGAAGAGGTCGGAGGGA 61.216 60.000 0.00 0.00 0.00 4.20
1391 1913 4.470170 CGACGACGTCCATCGCCA 62.470 66.667 21.63 0.00 46.22 5.69
1628 2150 3.003763 GAGGAGGAGGTGGCGGTT 61.004 66.667 0.00 0.00 0.00 4.44
1649 2171 3.928779 GCGAGGGCGGATGATGGA 61.929 66.667 0.00 0.00 38.16 3.41
2077 2629 3.859414 GCCGAGGCAGGAGCTGAT 61.859 66.667 9.58 0.00 41.70 2.90
2400 2952 1.227853 AAAGTCCGACAGCCGCTTT 60.228 52.632 0.40 0.00 36.84 3.51
2439 2991 0.822164 CCACCGGGTAGAACTCGAAT 59.178 55.000 6.32 0.00 46.98 3.34
2606 3158 6.183360 GCAACATAGCAGCATATTACTCGTAG 60.183 42.308 0.00 0.00 0.00 3.51
2607 3159 5.633601 GCAACATAGCAGCATATTACTCGTA 59.366 40.000 0.00 0.00 0.00 3.43
2609 3161 4.687948 AGCAACATAGCAGCATATTACTCG 59.312 41.667 0.00 0.00 36.85 4.18
2610 3162 6.348050 GGAAGCAACATAGCAGCATATTACTC 60.348 42.308 0.00 0.00 36.85 2.59
2612 3164 5.239306 TGGAAGCAACATAGCAGCATATTAC 59.761 40.000 0.00 0.00 36.85 1.89
2656 3267 5.679734 TTGACATCTCTCAAGTGAAAAGC 57.320 39.130 0.00 0.00 0.00 3.51
2705 3316 7.966339 TGGACTAGTACCATACTAACATTGT 57.034 36.000 1.66 0.00 40.49 2.71
2760 3371 5.305585 TCTAAACGACATCTTTTCCTGCTT 58.694 37.500 0.00 0.00 0.00 3.91
3080 4092 0.529555 GGACGAGCAGATCAGCCTTC 60.530 60.000 6.46 0.91 34.23 3.46
3092 4104 1.815840 GCTTAGCCTTGGGACGAGC 60.816 63.158 0.00 0.00 0.00 5.03
3146 4177 4.319333 GGCGATGATGCATCTAAGTCAAAG 60.319 45.833 26.32 7.23 38.59 2.77
3147 4178 3.561310 GGCGATGATGCATCTAAGTCAAA 59.439 43.478 26.32 4.91 38.59 2.69
3148 4179 3.133691 GGCGATGATGCATCTAAGTCAA 58.866 45.455 26.32 5.68 38.59 3.18
3149 4180 2.102925 TGGCGATGATGCATCTAAGTCA 59.897 45.455 26.32 20.18 38.59 3.41
3150 4181 2.759191 TGGCGATGATGCATCTAAGTC 58.241 47.619 26.32 18.07 38.59 3.01
3151 4182 2.916702 TGGCGATGATGCATCTAAGT 57.083 45.000 26.32 10.67 38.59 2.24
3152 4183 2.676839 GGATGGCGATGATGCATCTAAG 59.323 50.000 26.32 17.35 38.59 2.18
3153 4184 2.616256 GGGATGGCGATGATGCATCTAA 60.616 50.000 26.32 8.74 38.59 2.10
3154 4185 1.065926 GGGATGGCGATGATGCATCTA 60.066 52.381 26.32 13.82 38.59 1.98
3155 4186 0.322277 GGGATGGCGATGATGCATCT 60.322 55.000 26.32 12.70 38.59 2.90
3156 4187 0.607217 TGGGATGGCGATGATGCATC 60.607 55.000 20.14 20.14 37.50 3.91
3157 4188 0.892358 GTGGGATGGCGATGATGCAT 60.892 55.000 0.00 0.00 36.28 3.96
3158 4189 1.526686 GTGGGATGGCGATGATGCA 60.527 57.895 0.00 0.00 36.28 3.96
3159 4190 1.228063 AGTGGGATGGCGATGATGC 60.228 57.895 0.00 0.00 0.00 3.91
3160 4191 0.395686 AGAGTGGGATGGCGATGATG 59.604 55.000 0.00 0.00 0.00 3.07
3161 4192 0.395686 CAGAGTGGGATGGCGATGAT 59.604 55.000 0.00 0.00 0.00 2.45
3162 4193 0.977627 ACAGAGTGGGATGGCGATGA 60.978 55.000 0.00 0.00 0.00 2.92
3163 4194 0.752658 TACAGAGTGGGATGGCGATG 59.247 55.000 0.00 0.00 0.00 3.84
3174 4205 5.408604 GGAACACAACCACTAATACAGAGTG 59.591 44.000 0.00 0.00 43.32 3.51
3427 4469 3.849951 GCGGATCTCCCTCGCCAA 61.850 66.667 2.32 0.00 43.17 4.52
3471 4513 3.605749 CTTGATGTCCCCGGTGCGT 62.606 63.158 0.00 0.00 0.00 5.24
3708 4750 9.751542 GTAAAATCTAGTGATGCTTTAGCTCTA 57.248 33.333 3.10 1.24 42.66 2.43
3795 4837 5.458041 TCAGAATGCTTTCCTTTTTCCTG 57.542 39.130 8.62 0.00 34.76 3.86
3881 4927 1.202915 TGAGCATGAAGTGGGCAGAAA 60.203 47.619 0.00 0.00 0.00 2.52
3887 4933 3.191371 GGTAAAGTTGAGCATGAAGTGGG 59.809 47.826 0.00 0.00 0.00 4.61
3914 4960 9.191995 GATGAAAAAGGTAAATATAATTGGCCG 57.808 33.333 0.00 0.00 0.00 6.13
3924 4970 9.974980 GGAAACACAAGATGAAAAAGGTAAATA 57.025 29.630 0.00 0.00 0.00 1.40
3925 4971 8.704668 AGGAAACACAAGATGAAAAAGGTAAAT 58.295 29.630 0.00 0.00 0.00 1.40
4050 5096 4.439305 TTCACTAGAAAATGCACATGCC 57.561 40.909 0.00 0.00 41.18 4.40
4051 5097 5.643664 TGATTCACTAGAAAATGCACATGC 58.356 37.500 0.00 0.00 37.29 4.06
4116 5170 9.462174 GAATCAACAACTATCAAACATGAACAA 57.538 29.630 0.00 0.00 0.00 2.83
4149 5211 7.335627 TCAACAGAACTTCTACCAAGAAAAGA 58.664 34.615 0.00 0.00 41.19 2.52
4288 5353 4.152647 GGAGGGAAAAGTGAAAAGGATGT 58.847 43.478 0.00 0.00 0.00 3.06
4289 5354 4.151883 TGGAGGGAAAAGTGAAAAGGATG 58.848 43.478 0.00 0.00 0.00 3.51
4290 5355 4.469469 TGGAGGGAAAAGTGAAAAGGAT 57.531 40.909 0.00 0.00 0.00 3.24
4378 5445 1.685803 GCATGATGGGGATGGTGAACA 60.686 52.381 0.00 0.00 0.00 3.18
4478 5545 6.985188 TGTGCTGATAAATTAAGAGTGTCC 57.015 37.500 0.00 0.00 0.00 4.02
4485 5552 9.713740 GAGAAACTGATGTGCTGATAAATTAAG 57.286 33.333 0.00 0.00 0.00 1.85
4495 5562 4.505808 AGATCTGAGAAACTGATGTGCTG 58.494 43.478 0.00 0.00 37.32 4.41
4496 5563 4.822685 AGATCTGAGAAACTGATGTGCT 57.177 40.909 0.00 0.00 37.32 4.40
4505 5572 5.659440 ACAGGAGAGAAGATCTGAGAAAC 57.341 43.478 0.00 0.00 38.84 2.78
4522 5589 6.575244 AGGATTCATGGTATTACAACAGGA 57.425 37.500 0.00 0.00 0.00 3.86
4556 5623 6.721208 AGAAATTGATACCAAAAGAGGCAGAA 59.279 34.615 0.00 0.00 35.67 3.02
4561 5630 7.219484 ACACAGAAATTGATACCAAAAGAGG 57.781 36.000 0.00 0.00 35.67 3.69
4579 5648 4.142116 TGAACGTCCAAGAACTTACACAGA 60.142 41.667 0.00 0.00 0.00 3.41
4581 5650 3.866910 GTGAACGTCCAAGAACTTACACA 59.133 43.478 0.00 0.00 0.00 3.72
4583 5652 4.395959 AGTGAACGTCCAAGAACTTACA 57.604 40.909 0.00 0.00 0.00 2.41
4647 5716 4.396790 TGTATGAATCGCTGGGGTTTTAAC 59.603 41.667 0.00 0.00 0.00 2.01
4648 5717 4.590918 TGTATGAATCGCTGGGGTTTTAA 58.409 39.130 0.00 0.00 0.00 1.52
4649 5718 4.223556 TGTATGAATCGCTGGGGTTTTA 57.776 40.909 0.00 0.00 0.00 1.52
4650 5719 3.080300 TGTATGAATCGCTGGGGTTTT 57.920 42.857 0.00 0.00 0.00 2.43
4651 5720 2.752903 GTTGTATGAATCGCTGGGGTTT 59.247 45.455 0.00 0.00 0.00 3.27
4652 5721 2.365582 GTTGTATGAATCGCTGGGGTT 58.634 47.619 0.00 0.00 0.00 4.11
4653 5722 1.408266 GGTTGTATGAATCGCTGGGGT 60.408 52.381 0.00 0.00 0.00 4.95
4654 5723 1.308998 GGTTGTATGAATCGCTGGGG 58.691 55.000 0.00 0.00 0.00 4.96
4655 5724 2.036958 TGGTTGTATGAATCGCTGGG 57.963 50.000 0.00 0.00 0.00 4.45
4656 5725 4.637483 AAATGGTTGTATGAATCGCTGG 57.363 40.909 0.00 0.00 0.00 4.85
4657 5726 8.633075 AATAAAAATGGTTGTATGAATCGCTG 57.367 30.769 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.