Multiple sequence alignment - TraesCS2B01G239100

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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 TraesCS2B01G239100 chr2B 100.000 2999 0 0 1 2999 242540268 242543266 0.000000e+00 5539.0
1 TraesCS2B01G239100 chr2B 78.965 1507 265 42 997 2484 72971309 72969836 0.000000e+00 979.0
2 TraesCS2B01G239100 chr2B 96.712 517 13 1 2483 2999 241574513 241575025 0.000000e+00 857.0
3 TraesCS2B01G239100 chr2B 96.325 517 15 1 2483 2999 102480431 102480943 0.000000e+00 846.0
4 TraesCS2B01G239100 chr2B 90.799 413 18 2 1 393 153595246 153595658 4.400000e-148 534.0
5 TraesCS2B01G239100 chr2B 86.996 223 11 3 378 583 153606781 153607002 5.000000e-58 235.0
6 TraesCS2B01G239100 chr3A 90.129 1317 112 13 611 1919 158591412 158590106 0.000000e+00 1696.0
7 TraesCS2B01G239100 chr3A 79.164 1507 268 37 994 2484 728246346 728247822 0.000000e+00 1002.0
8 TraesCS2B01G239100 chr3A 88.596 570 43 10 1915 2484 158540695 158540148 0.000000e+00 673.0
9 TraesCS2B01G239100 chr3A 84.571 525 51 10 1 508 146765132 146764621 7.470000e-136 494.0
10 TraesCS2B01G239100 chr6A 79.297 1507 266 37 994 2484 485769708 485771184 0.000000e+00 1013.0
11 TraesCS2B01G239100 chr6A 77.572 486 62 24 1 454 68557371 68556901 1.780000e-62 250.0
12 TraesCS2B01G239100 chr1B 96.724 519 15 1 2483 2999 393918227 393918745 0.000000e+00 863.0
13 TraesCS2B01G239100 chr1B 96.525 518 16 2 2483 2999 37131282 37130766 0.000000e+00 856.0
14 TraesCS2B01G239100 chr1B 83.301 521 58 15 1 504 265288035 265288543 1.270000e-123 453.0
15 TraesCS2B01G239100 chr1B 82.275 378 44 13 151 510 221923131 221923503 3.760000e-79 305.0
16 TraesCS2B01G239100 chr7B 96.712 517 17 0 2483 2999 275674072 275673556 0.000000e+00 861.0
17 TraesCS2B01G239100 chr7B 96.712 517 14 2 2483 2999 546659195 546658682 0.000000e+00 857.0
18 TraesCS2B01G239100 chr3B 96.325 517 17 1 2483 2999 320022138 320022652 0.000000e+00 848.0
19 TraesCS2B01G239100 chr3B 96.161 521 15 5 2481 2999 598723564 598724081 0.000000e+00 846.0
20 TraesCS2B01G239100 chr3B 80.401 847 144 19 994 1835 31196689 31197518 2.540000e-175 625.0
21 TraesCS2B01G239100 chr3B 91.935 62 4 1 449 510 58199994 58199934 5.330000e-13 86.1
22 TraesCS2B01G239100 chr3B 100.000 32 0 0 449 480 58142930 58142899 3.230000e-05 60.2
23 TraesCS2B01G239100 chr5B 96.325 517 14 2 2483 2999 665383207 665382696 0.000000e+00 845.0
24 TraesCS2B01G239100 chr3D 79.834 843 149 17 997 1835 379587564 379586739 1.990000e-166 595.0
25 TraesCS2B01G239100 chr3D 92.157 153 12 0 1 153 35063679 35063527 1.810000e-52 217.0
26 TraesCS2B01G239100 chr2D 86.373 477 47 5 1 461 609556789 609556315 3.450000e-139 505.0
27 TraesCS2B01G239100 chr7D 84.277 477 51 9 1 461 200452570 200452102 7.630000e-121 444.0
28 TraesCS2B01G239100 chr4A 82.510 526 58 11 1 510 628946524 628947031 5.940000e-117 431.0
29 TraesCS2B01G239100 chr7A 91.216 148 13 0 1 148 539708247 539708100 5.070000e-48 202.0
30 TraesCS2B01G239100 chr6B 96.970 33 0 1 391 422 231687288 231687320 2.000000e-03 54.7
31 TraesCS2B01G239100 chr6B 96.970 33 0 1 391 422 231692256 231692288 2.000000e-03 54.7


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G239100 chr2B 242540268 242543266 2998 False 5539 5539 100.000 1 2999 1 chr2B.!!$F5 2998
1 TraesCS2B01G239100 chr2B 72969836 72971309 1473 True 979 979 78.965 997 2484 1 chr2B.!!$R1 1487
2 TraesCS2B01G239100 chr2B 241574513 241575025 512 False 857 857 96.712 2483 2999 1 chr2B.!!$F4 516
3 TraesCS2B01G239100 chr2B 102480431 102480943 512 False 846 846 96.325 2483 2999 1 chr2B.!!$F1 516
4 TraesCS2B01G239100 chr3A 158590106 158591412 1306 True 1696 1696 90.129 611 1919 1 chr3A.!!$R3 1308
5 TraesCS2B01G239100 chr3A 728246346 728247822 1476 False 1002 1002 79.164 994 2484 1 chr3A.!!$F1 1490
6 TraesCS2B01G239100 chr3A 158540148 158540695 547 True 673 673 88.596 1915 2484 1 chr3A.!!$R2 569
7 TraesCS2B01G239100 chr3A 146764621 146765132 511 True 494 494 84.571 1 508 1 chr3A.!!$R1 507
8 TraesCS2B01G239100 chr6A 485769708 485771184 1476 False 1013 1013 79.297 994 2484 1 chr6A.!!$F1 1490
9 TraesCS2B01G239100 chr1B 393918227 393918745 518 False 863 863 96.724 2483 2999 1 chr1B.!!$F3 516
10 TraesCS2B01G239100 chr1B 37130766 37131282 516 True 856 856 96.525 2483 2999 1 chr1B.!!$R1 516
11 TraesCS2B01G239100 chr1B 265288035 265288543 508 False 453 453 83.301 1 504 1 chr1B.!!$F2 503
12 TraesCS2B01G239100 chr7B 275673556 275674072 516 True 861 861 96.712 2483 2999 1 chr7B.!!$R1 516
13 TraesCS2B01G239100 chr7B 546658682 546659195 513 True 857 857 96.712 2483 2999 1 chr7B.!!$R2 516
14 TraesCS2B01G239100 chr3B 320022138 320022652 514 False 848 848 96.325 2483 2999 1 chr3B.!!$F2 516
15 TraesCS2B01G239100 chr3B 598723564 598724081 517 False 846 846 96.161 2481 2999 1 chr3B.!!$F3 518
16 TraesCS2B01G239100 chr3B 31196689 31197518 829 False 625 625 80.401 994 1835 1 chr3B.!!$F1 841
17 TraesCS2B01G239100 chr5B 665382696 665383207 511 True 845 845 96.325 2483 2999 1 chr5B.!!$R1 516
18 TraesCS2B01G239100 chr3D 379586739 379587564 825 True 595 595 79.834 997 1835 1 chr3D.!!$R2 838
19 TraesCS2B01G239100 chr4A 628946524 628947031 507 False 431 431 82.510 1 510 1 chr4A.!!$F1 509

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
521 539 0.034574 TCCAGCCCGCAACACATTAT 60.035 50.0 0.0 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2096 1.205655 TCTTCTCCCTTCACATGAGCG 59.794 52.381 0.0 0.0 0.0 5.03 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
27 28 1.686052 GTTGGTTGCATTGTTCCTCCA 59.314 47.619 0.00 0.00 0.00 3.86
69 70 3.795623 ATTCAAGGACATCAAGCATGC 57.204 42.857 10.51 10.51 35.65 4.06
73 74 2.154567 AGGACATCAAGCATGCCATT 57.845 45.000 15.66 0.00 35.65 3.16
127 128 7.639113 TGAGAACAATTAAAGACTTTGTGGT 57.361 32.000 10.80 4.72 34.04 4.16
133 134 8.181904 ACAATTAAAGACTTTGTGGTCATGAT 57.818 30.769 10.80 0.00 38.57 2.45
183 198 5.062934 CACTCGTATAAACCGAAATCAGCAA 59.937 40.000 0.00 0.00 33.34 3.91
189 204 2.040544 CCGAAATCAGCAACGCCCT 61.041 57.895 0.00 0.00 0.00 5.19
206 221 7.521529 CAACGCCCTGAGATAATTTATGTATG 58.478 38.462 0.00 0.00 0.00 2.39
253 268 4.927782 TGCCGCAGTGTGTGACCC 62.928 66.667 2.46 0.00 0.00 4.46
261 276 1.066858 CAGTGTGTGACCCGAGCTATT 60.067 52.381 0.00 0.00 0.00 1.73
271 286 6.127281 TGTGACCCGAGCTATTTAGTCAATAA 60.127 38.462 6.22 0.00 36.13 1.40
272 287 6.759827 GTGACCCGAGCTATTTAGTCAATAAA 59.240 38.462 6.22 0.00 36.13 1.40
277 292 9.490379 CCCGAGCTATTTAGTCAATAAAAGTAT 57.510 33.333 0.00 0.00 36.94 2.12
311 326 4.151157 GCAAACAGATGCAAATCCAACTTC 59.849 41.667 0.00 0.00 45.70 3.01
332 347 9.586435 AACTTCAAAGAAAATGTAGAACCAAAG 57.414 29.630 0.00 0.00 0.00 2.77
334 349 7.106439 TCAAAGAAAATGTAGAACCAAAGCA 57.894 32.000 0.00 0.00 0.00 3.91
335 350 7.202526 TCAAAGAAAATGTAGAACCAAAGCAG 58.797 34.615 0.00 0.00 0.00 4.24
359 374 0.930310 CGTGTGCATGTAGATTCGGG 59.070 55.000 0.00 0.00 0.00 5.14
360 375 1.470805 CGTGTGCATGTAGATTCGGGA 60.471 52.381 0.00 0.00 0.00 5.14
362 377 2.609459 GTGTGCATGTAGATTCGGGAAG 59.391 50.000 0.00 0.00 0.00 3.46
380 397 4.309099 GGAAGAAAGAAAATGCATGCACA 58.691 39.130 25.37 0.00 0.00 4.57
389 406 4.789075 GCATGCACAGCCAAGCGG 62.789 66.667 14.21 0.00 0.00 5.52
424 441 0.251653 AGCGTGTCCCTCCTAGTCAA 60.252 55.000 0.00 0.00 0.00 3.18
430 447 4.401519 CGTGTCCCTCCTAGTCAATTCTTA 59.598 45.833 0.00 0.00 0.00 2.10
491 509 4.948004 TCTAGCTAATCTTCAGTCGGTGAA 59.052 41.667 0.00 1.84 43.26 3.18
516 534 3.660111 GTGTCCAGCCCGCAACAC 61.660 66.667 4.86 4.86 35.69 3.32
517 535 4.182433 TGTCCAGCCCGCAACACA 62.182 61.111 0.00 0.00 0.00 3.72
518 536 2.672996 GTCCAGCCCGCAACACAT 60.673 61.111 0.00 0.00 0.00 3.21
519 537 2.115052 TCCAGCCCGCAACACATT 59.885 55.556 0.00 0.00 0.00 2.71
520 538 0.958382 GTCCAGCCCGCAACACATTA 60.958 55.000 0.00 0.00 0.00 1.90
521 539 0.034574 TCCAGCCCGCAACACATTAT 60.035 50.000 0.00 0.00 0.00 1.28
522 540 0.381801 CCAGCCCGCAACACATTATC 59.618 55.000 0.00 0.00 0.00 1.75
523 541 0.381801 CAGCCCGCAACACATTATCC 59.618 55.000 0.00 0.00 0.00 2.59
524 542 0.034574 AGCCCGCAACACATTATCCA 60.035 50.000 0.00 0.00 0.00 3.41
525 543 0.381801 GCCCGCAACACATTATCCAG 59.618 55.000 0.00 0.00 0.00 3.86
526 544 0.381801 CCCGCAACACATTATCCAGC 59.618 55.000 0.00 0.00 0.00 4.85
527 545 1.382522 CCGCAACACATTATCCAGCT 58.617 50.000 0.00 0.00 0.00 4.24
528 546 1.064505 CCGCAACACATTATCCAGCTG 59.935 52.381 6.78 6.78 0.00 4.24
529 547 1.739466 CGCAACACATTATCCAGCTGT 59.261 47.619 13.81 0.00 0.00 4.40
530 548 2.476686 CGCAACACATTATCCAGCTGTG 60.477 50.000 13.81 6.33 44.51 3.66
531 549 2.159338 GCAACACATTATCCAGCTGTGG 60.159 50.000 13.81 0.00 43.53 4.17
532 550 1.755179 ACACATTATCCAGCTGTGGC 58.245 50.000 13.81 0.00 44.60 5.01
559 577 5.489011 AAAACAAAAGACAACGAAACGTG 57.511 34.783 0.00 0.00 39.99 4.49
560 578 3.817148 ACAAAAGACAACGAAACGTGT 57.183 38.095 0.00 0.00 39.99 4.49
561 579 4.149910 ACAAAAGACAACGAAACGTGTT 57.850 36.364 0.00 0.00 39.99 3.32
567 585 2.512289 CAACGAAACGTGTTGTCACA 57.488 45.000 0.00 0.00 44.02 3.58
568 586 3.046285 CAACGAAACGTGTTGTCACAT 57.954 42.857 0.00 0.00 44.02 3.21
569 587 3.026349 CAACGAAACGTGTTGTCACATC 58.974 45.455 0.00 0.00 44.02 3.06
570 588 1.595794 ACGAAACGTGTTGTCACATCC 59.404 47.619 0.00 0.00 44.02 3.51
571 589 1.396690 CGAAACGTGTTGTCACATCCG 60.397 52.381 0.00 0.00 44.02 4.18
572 590 0.941542 AAACGTGTTGTCACATCCGG 59.058 50.000 0.00 0.00 44.02 5.14
573 591 0.105224 AACGTGTTGTCACATCCGGA 59.895 50.000 6.61 6.61 44.02 5.14
574 592 0.319555 ACGTGTTGTCACATCCGGAG 60.320 55.000 11.34 4.72 44.02 4.63
575 593 0.038618 CGTGTTGTCACATCCGGAGA 60.039 55.000 11.34 0.00 44.02 3.71
576 594 1.404181 CGTGTTGTCACATCCGGAGAT 60.404 52.381 11.34 0.00 44.02 2.75
577 595 2.271800 GTGTTGTCACATCCGGAGATC 58.728 52.381 11.34 0.00 43.37 2.75
578 596 1.207089 TGTTGTCACATCCGGAGATCC 59.793 52.381 11.34 0.00 0.00 3.36
579 597 0.830648 TTGTCACATCCGGAGATCCC 59.169 55.000 11.34 0.00 0.00 3.85
580 598 0.325203 TGTCACATCCGGAGATCCCA 60.325 55.000 11.34 0.57 34.14 4.37
581 599 0.105039 GTCACATCCGGAGATCCCAC 59.895 60.000 11.34 0.00 34.14 4.61
582 600 0.325203 TCACATCCGGAGATCCCACA 60.325 55.000 11.34 0.00 34.14 4.17
583 601 0.541392 CACATCCGGAGATCCCACAA 59.459 55.000 11.34 0.00 34.14 3.33
584 602 1.065491 CACATCCGGAGATCCCACAAA 60.065 52.381 11.34 0.00 34.14 2.83
585 603 1.210478 ACATCCGGAGATCCCACAAAG 59.790 52.381 11.34 0.00 34.14 2.77
586 604 0.181350 ATCCGGAGATCCCACAAAGC 59.819 55.000 11.34 0.00 34.14 3.51
587 605 1.198094 TCCGGAGATCCCACAAAGCA 61.198 55.000 0.00 0.00 34.14 3.91
588 606 0.322456 CCGGAGATCCCACAAAGCAA 60.322 55.000 0.00 0.00 34.14 3.91
589 607 1.533625 CGGAGATCCCACAAAGCAAA 58.466 50.000 0.00 0.00 34.14 3.68
590 608 1.885887 CGGAGATCCCACAAAGCAAAA 59.114 47.619 0.00 0.00 34.14 2.44
591 609 2.493278 CGGAGATCCCACAAAGCAAAAT 59.507 45.455 0.00 0.00 34.14 1.82
592 610 3.428045 CGGAGATCCCACAAAGCAAAATC 60.428 47.826 0.00 0.00 34.14 2.17
593 611 3.118992 GGAGATCCCACAAAGCAAAATCC 60.119 47.826 0.00 0.00 34.14 3.01
594 612 3.509442 AGATCCCACAAAGCAAAATCCA 58.491 40.909 0.00 0.00 0.00 3.41
595 613 3.903090 AGATCCCACAAAGCAAAATCCAA 59.097 39.130 0.00 0.00 0.00 3.53
596 614 4.347583 AGATCCCACAAAGCAAAATCCAAA 59.652 37.500 0.00 0.00 0.00 3.28
597 615 3.802866 TCCCACAAAGCAAAATCCAAAC 58.197 40.909 0.00 0.00 0.00 2.93
598 616 3.454082 TCCCACAAAGCAAAATCCAAACT 59.546 39.130 0.00 0.00 0.00 2.66
599 617 4.080638 TCCCACAAAGCAAAATCCAAACTT 60.081 37.500 0.00 0.00 0.00 2.66
600 618 5.129485 TCCCACAAAGCAAAATCCAAACTTA 59.871 36.000 0.00 0.00 0.00 2.24
601 619 5.236263 CCCACAAAGCAAAATCCAAACTTAC 59.764 40.000 0.00 0.00 0.00 2.34
602 620 6.048509 CCACAAAGCAAAATCCAAACTTACT 58.951 36.000 0.00 0.00 0.00 2.24
603 621 6.200854 CCACAAAGCAAAATCCAAACTTACTC 59.799 38.462 0.00 0.00 0.00 2.59
604 622 6.980397 CACAAAGCAAAATCCAAACTTACTCT 59.020 34.615 0.00 0.00 0.00 3.24
605 623 7.168135 CACAAAGCAAAATCCAAACTTACTCTC 59.832 37.037 0.00 0.00 0.00 3.20
606 624 5.613358 AGCAAAATCCAAACTTACTCTCG 57.387 39.130 0.00 0.00 0.00 4.04
607 625 5.305585 AGCAAAATCCAAACTTACTCTCGA 58.694 37.500 0.00 0.00 0.00 4.04
608 626 5.409826 AGCAAAATCCAAACTTACTCTCGAG 59.590 40.000 5.93 5.93 0.00 4.04
609 627 5.408604 GCAAAATCCAAACTTACTCTCGAGA 59.591 40.000 15.70 15.70 0.00 4.04
614 632 4.217983 TCCAAACTTACTCTCGAGAAGTCC 59.782 45.833 17.36 0.00 32.02 3.85
664 682 2.556287 CGTGTTCTTGGCGCTTCC 59.444 61.111 7.64 0.00 0.00 3.46
708 727 4.554036 GCCGCCAGGGTCTGATCC 62.554 72.222 0.00 0.00 38.44 3.36
711 730 1.528824 CGCCAGGGTCTGATCCAAT 59.471 57.895 10.10 0.00 32.44 3.16
716 735 2.648059 CAGGGTCTGATCCAATTCCAC 58.352 52.381 10.10 0.00 32.44 4.02
731 750 5.414454 CCAATTCCACAAAATCTCGAACCTA 59.586 40.000 0.00 0.00 0.00 3.08
732 751 6.072175 CCAATTCCACAAAATCTCGAACCTAA 60.072 38.462 0.00 0.00 0.00 2.69
734 753 7.703058 ATTCCACAAAATCTCGAACCTAAAT 57.297 32.000 0.00 0.00 0.00 1.40
739 758 7.549488 CCACAAAATCTCGAACCTAAATCTAGT 59.451 37.037 0.00 0.00 0.00 2.57
741 760 9.152595 ACAAAATCTCGAACCTAAATCTAGTTC 57.847 33.333 0.00 0.00 0.00 3.01
742 761 8.604890 CAAAATCTCGAACCTAAATCTAGTTCC 58.395 37.037 0.00 0.00 0.00 3.62
747 766 5.296283 TCGAACCTAAATCTAGTTCCTCTCG 59.704 44.000 0.00 0.00 0.00 4.04
757 776 1.766496 AGTTCCTCTCGTTTTCCACCA 59.234 47.619 0.00 0.00 0.00 4.17
776 795 5.312079 CACCAAAAAGAGAAGAGATCCAGT 58.688 41.667 0.00 0.00 0.00 4.00
784 803 7.790782 AAGAGAAGAGATCCAGTCTAGTTTT 57.209 36.000 0.00 0.00 37.29 2.43
786 805 6.379988 AGAGAAGAGATCCAGTCTAGTTTTCC 59.620 42.308 0.00 0.00 37.29 3.13
787 806 6.019748 AGAAGAGATCCAGTCTAGTTTTCCA 58.980 40.000 0.00 0.00 37.29 3.53
788 807 5.669164 AGAGATCCAGTCTAGTTTTCCAC 57.331 43.478 0.00 0.00 37.29 4.02
789 808 5.087323 AGAGATCCAGTCTAGTTTTCCACA 58.913 41.667 0.00 0.00 37.29 4.17
790 809 5.186797 AGAGATCCAGTCTAGTTTTCCACAG 59.813 44.000 0.00 0.00 37.29 3.66
791 810 3.402628 TCCAGTCTAGTTTTCCACAGC 57.597 47.619 0.00 0.00 0.00 4.40
792 811 2.972713 TCCAGTCTAGTTTTCCACAGCT 59.027 45.455 0.00 0.00 0.00 4.24
793 812 3.006967 TCCAGTCTAGTTTTCCACAGCTC 59.993 47.826 0.00 0.00 0.00 4.09
794 813 3.244215 CCAGTCTAGTTTTCCACAGCTCA 60.244 47.826 0.00 0.00 0.00 4.26
797 816 4.345257 AGTCTAGTTTTCCACAGCTCAGAA 59.655 41.667 0.00 0.00 0.00 3.02
824 843 3.971702 AGGCAGTCTTGGGGGCAC 61.972 66.667 0.00 0.00 0.00 5.01
852 871 1.133009 ACCAGATCGGAGGAGGCTTAT 60.133 52.381 10.05 0.00 38.63 1.73
853 872 1.974236 CCAGATCGGAGGAGGCTTATT 59.026 52.381 0.00 0.00 36.56 1.40
864 883 0.755686 AGGCTTATTCGAGGAGGCAG 59.244 55.000 16.60 0.00 38.33 4.85
877 896 2.607750 GGCAGAGGTGGAGGGACA 60.608 66.667 0.00 0.00 0.00 4.02
898 917 2.607892 GCGTCAGTGCAAGGTGTCC 61.608 63.158 0.00 0.00 34.15 4.02
899 918 2.310233 CGTCAGTGCAAGGTGTCCG 61.310 63.158 0.00 0.00 0.00 4.79
942 961 1.152247 AGGTGTGTGAGGAGGCAGA 60.152 57.895 0.00 0.00 0.00 4.26
943 962 0.764369 AGGTGTGTGAGGAGGCAGAA 60.764 55.000 0.00 0.00 0.00 3.02
966 985 0.912006 AGTTCTGAAGGAGGAGGGGC 60.912 60.000 0.00 0.00 0.00 5.80
968 987 4.168291 CTGAAGGAGGAGGGGCGC 62.168 72.222 0.00 0.00 0.00 6.53
975 994 4.335647 AGGAGGGGCGCTGTGTTG 62.336 66.667 9.52 0.00 0.00 3.33
1015 1034 5.675323 GCGGTTACAATGGGAAGTGAAATAC 60.675 44.000 0.00 0.00 0.00 1.89
1028 1047 6.349363 GGAAGTGAAATACTACAAGCTTTGGG 60.349 42.308 0.00 0.00 39.18 4.12
1118 1140 3.594134 AGAAGAGCGGAAATCACTTGAG 58.406 45.455 0.00 0.00 0.00 3.02
1203 1226 1.840635 GGGAGGACATTAGCAGGAGTT 59.159 52.381 0.00 0.00 0.00 3.01
1217 1240 0.696501 GGAGTTTGGTGCCCCTTCTA 59.303 55.000 0.00 0.00 0.00 2.10
1281 1307 3.830744 TGTTTTCGTGAAGAGAAGGGA 57.169 42.857 0.00 0.00 0.00 4.20
1299 1325 4.998051 AGGGAAAAATGAAGGCAGTAGAA 58.002 39.130 0.00 0.00 0.00 2.10
1350 1376 2.733227 GCTGGTGATGGAAGATTTTGCG 60.733 50.000 0.00 0.00 0.00 4.85
1417 1443 7.528205 CGATATGGGTAAGGGTGTATGGTATTT 60.528 40.741 0.00 0.00 0.00 1.40
1489 1515 3.493350 CGGTGAAGTCTTGGATATGGAGG 60.493 52.174 0.00 0.00 0.00 4.30
1552 1578 7.987458 GGATCAAAGTAAGAATGGACATCACTA 59.013 37.037 0.00 0.00 0.00 2.74
1567 1593 6.040955 GGACATCACTATACCACTGATGAGAA 59.959 42.308 12.61 0.00 42.65 2.87
1583 1609 5.306419 TGATGAGAAGGATCACTATTGAGGG 59.694 44.000 0.00 0.00 34.35 4.30
1618 1644 2.769095 GAGCAGTACCAGAAGAAGGGAT 59.231 50.000 0.00 0.00 0.00 3.85
1619 1645 3.185455 AGCAGTACCAGAAGAAGGGATT 58.815 45.455 0.00 0.00 0.00 3.01
1633 1659 3.166636 AGGGATTAATGGGAGAAGGGT 57.833 47.619 0.00 0.00 0.00 4.34
1646 1672 5.163034 TGGGAGAAGGGTGTAATGAAGAAAA 60.163 40.000 0.00 0.00 0.00 2.29
1648 1674 6.238648 GGAGAAGGGTGTAATGAAGAAAAGA 58.761 40.000 0.00 0.00 0.00 2.52
1659 1685 8.163408 TGTAATGAAGAAAAGAATGAGGAGGAA 58.837 33.333 0.00 0.00 0.00 3.36
1766 1792 3.560902 TTGCACAACGAAAACAGAACA 57.439 38.095 0.00 0.00 0.00 3.18
1773 1799 4.398044 ACAACGAAAACAGAACATGAAGGT 59.602 37.500 0.00 0.00 0.00 3.50
1774 1800 5.587043 ACAACGAAAACAGAACATGAAGGTA 59.413 36.000 0.00 0.00 0.00 3.08
1844 1870 2.759535 CCAGTGATGAGAAGAGCAGAGA 59.240 50.000 0.00 0.00 0.00 3.10
1854 1880 5.075858 AGAAGAGCAGAGAATCAAGTGAG 57.924 43.478 0.00 0.00 37.82 3.51
1880 1906 8.528044 AAAGGTGATTTCTGTAAAGGTAACAA 57.472 30.769 0.00 0.00 41.41 2.83
1913 1939 2.301738 GCAGTAGGCAGGGAAGGGT 61.302 63.158 0.00 0.00 43.97 4.34
2069 2096 5.805486 GGTTTTTGAGGAAGAACAACAGAAC 59.195 40.000 0.00 0.00 0.00 3.01
2088 2115 1.066573 ACGCTCATGTGAAGGGAGAAG 60.067 52.381 0.00 0.00 0.00 2.85
2095 2122 2.846193 TGTGAAGGGAGAAGAAAACGG 58.154 47.619 0.00 0.00 0.00 4.44
2115 2142 2.439507 GGGAAGGATAAGCACATGGAGA 59.560 50.000 0.00 0.00 0.00 3.71
2156 2183 3.028130 GGGACCAACAAAGAAACCAGAA 58.972 45.455 0.00 0.00 0.00 3.02
2164 2191 2.618709 CAAAGAAACCAGAAAGAGCGGT 59.381 45.455 0.00 0.00 33.32 5.68
2182 2209 1.970114 TCTCGACCTGGGACGACAC 60.970 63.158 9.77 0.00 37.38 3.67
2183 2210 3.324099 CTCGACCTGGGACGACACG 62.324 68.421 9.77 0.00 37.38 4.49
2199 2226 3.682858 CGACACGGAACCTGAATATGTTT 59.317 43.478 0.00 0.00 0.00 2.83
2209 2236 8.314021 GGAACCTGAATATGTTTTCCTGAATTT 58.686 33.333 0.00 0.00 31.54 1.82
2250 2277 0.165511 CACTTTCAAGCGCAGAGAGC 59.834 55.000 11.47 0.00 40.87 4.09
2277 2304 6.035005 GCAAGAAGGAGTGAAAACTCAAAAAC 59.965 38.462 8.06 0.00 38.44 2.43
2385 2412 3.438434 GGAGAAGAAAACAGATGGAGTGC 59.562 47.826 0.00 0.00 0.00 4.40
2401 2428 3.767131 GGAGTGCTAGGAGAAGAAGTCTT 59.233 47.826 0.00 0.00 36.41 3.01
2464 2491 2.098293 CCGGCGGGAGAAAATGAAG 58.902 57.895 20.56 0.00 34.06 3.02
2540 2567 4.522114 TGTTGTGACTCAAGGATCAAACA 58.478 39.130 0.00 0.00 36.66 2.83
2576 2603 4.909355 TCTAGAGGGGGAGAGAGAAATT 57.091 45.455 0.00 0.00 0.00 1.82
2670 2699 9.261035 TCATTTTAGAGAGAGTATCACCTTCTT 57.739 33.333 0.00 0.00 37.82 2.52
2673 2702 9.756571 TTTTAGAGAGAGTATCACCTTCTTAGT 57.243 33.333 0.00 0.00 37.82 2.24
2714 2743 4.963318 GAGAGAGAGAGAGAGATCTCCA 57.037 50.000 19.30 0.00 45.77 3.86
2719 2749 3.130450 AGAGAGAGAGATCTCCAAGGGA 58.870 50.000 19.30 0.00 45.77 4.20
2803 2833 1.003580 GCCACATGTCTTCTTGAGGGA 59.996 52.381 0.00 0.00 32.87 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.591527 TGAAGGTGGTATGGAGGAACAAT 59.408 43.478 0.00 0.00 0.00 2.71
27 28 4.591321 ATGGTCATGTTGAAGGTGGTAT 57.409 40.909 0.00 0.00 0.00 2.73
69 70 3.281727 TCCGGATCAGGAAGAAAATGG 57.718 47.619 12.63 0.00 37.36 3.16
158 173 4.565564 GCTGATTTCGGTTTATACGAGTGT 59.434 41.667 0.00 0.00 41.81 3.55
183 198 6.769512 ACATACATAAATTATCTCAGGGCGT 58.230 36.000 0.00 0.00 0.00 5.68
206 221 2.934553 GCCTGGACGTCCAATAAAGTAC 59.065 50.000 35.36 15.14 46.97 2.73
218 233 1.737838 CAACATGTATGCCTGGACGT 58.262 50.000 0.00 0.00 0.00 4.34
242 257 1.267121 AATAGCTCGGGTCACACACT 58.733 50.000 0.00 0.00 0.00 3.55
288 303 3.656559 AGTTGGATTTGCATCTGTTTGC 58.343 40.909 0.00 0.00 43.07 3.68
311 326 6.074142 GCTGCTTTGGTTCTACATTTTCTTTG 60.074 38.462 0.00 0.00 0.00 2.77
332 347 0.447406 TACATGCACACGATTGCTGC 59.553 50.000 12.93 0.00 43.41 5.25
334 349 2.385013 TCTACATGCACACGATTGCT 57.615 45.000 12.93 0.00 43.41 3.91
335 350 3.611517 GAATCTACATGCACACGATTGC 58.388 45.455 6.12 6.12 43.31 3.56
359 374 4.143179 GCTGTGCATGCATTTTCTTTCTTC 60.143 41.667 25.64 6.62 0.00 2.87
360 375 3.744426 GCTGTGCATGCATTTTCTTTCTT 59.256 39.130 25.64 0.00 0.00 2.52
362 377 2.414138 GGCTGTGCATGCATTTTCTTTC 59.586 45.455 25.64 8.75 0.00 2.62
380 397 1.978617 CCCATCAAACCGCTTGGCT 60.979 57.895 0.00 0.00 35.56 4.75
389 406 2.161609 CACGCTCCTTTACCCATCAAAC 59.838 50.000 0.00 0.00 0.00 2.93
480 497 1.596934 GGGAGCATTCACCGACTGA 59.403 57.895 0.00 0.00 0.00 3.41
481 498 4.208632 GGGAGCATTCACCGACTG 57.791 61.111 0.00 0.00 0.00 3.51
491 509 4.101448 GGCTGGACACGGGAGCAT 62.101 66.667 0.00 0.00 34.20 3.79
510 528 2.159338 CCACAGCTGGATAATGTGTTGC 60.159 50.000 19.93 0.00 42.17 4.17
511 529 2.159338 GCCACAGCTGGATAATGTGTTG 60.159 50.000 19.93 2.54 42.17 3.33
512 530 2.094675 GCCACAGCTGGATAATGTGTT 58.905 47.619 19.93 0.00 42.17 3.32
513 531 1.755179 GCCACAGCTGGATAATGTGT 58.245 50.000 19.93 0.00 42.17 3.72
536 554 5.459434 ACACGTTTCGTTGTCTTTTGTTTTT 59.541 32.000 0.00 0.00 38.32 1.94
537 555 4.977347 ACACGTTTCGTTGTCTTTTGTTTT 59.023 33.333 0.00 0.00 38.32 2.43
538 556 4.538917 ACACGTTTCGTTGTCTTTTGTTT 58.461 34.783 0.00 0.00 38.32 2.83
539 557 4.149910 ACACGTTTCGTTGTCTTTTGTT 57.850 36.364 0.00 0.00 38.32 2.83
540 558 3.817148 ACACGTTTCGTTGTCTTTTGT 57.183 38.095 0.00 0.00 38.32 2.83
541 559 4.462987 CAACACGTTTCGTTGTCTTTTG 57.537 40.909 8.63 0.00 38.32 2.44
557 575 2.271800 GATCTCCGGATGTGACAACAC 58.728 52.381 3.57 0.00 46.09 3.32
558 576 1.207089 GGATCTCCGGATGTGACAACA 59.793 52.381 3.57 0.00 41.58 3.33
559 577 1.473434 GGGATCTCCGGATGTGACAAC 60.473 57.143 3.57 0.00 36.71 3.32
560 578 0.830648 GGGATCTCCGGATGTGACAA 59.169 55.000 3.57 0.00 36.71 3.18
561 579 0.325203 TGGGATCTCCGGATGTGACA 60.325 55.000 3.57 0.00 38.76 3.58
562 580 0.105039 GTGGGATCTCCGGATGTGAC 59.895 60.000 3.57 0.00 38.76 3.67
563 581 0.325203 TGTGGGATCTCCGGATGTGA 60.325 55.000 3.57 0.00 38.76 3.58
564 582 0.541392 TTGTGGGATCTCCGGATGTG 59.459 55.000 3.57 0.00 38.76 3.21
565 583 1.210478 CTTTGTGGGATCTCCGGATGT 59.790 52.381 3.57 0.00 38.76 3.06
566 584 1.959042 CTTTGTGGGATCTCCGGATG 58.041 55.000 3.57 0.00 38.76 3.51
567 585 0.181350 GCTTTGTGGGATCTCCGGAT 59.819 55.000 3.57 0.00 38.76 4.18
568 586 1.198094 TGCTTTGTGGGATCTCCGGA 61.198 55.000 2.93 2.93 38.76 5.14
569 587 0.322456 TTGCTTTGTGGGATCTCCGG 60.322 55.000 0.00 0.00 38.76 5.14
570 588 1.533625 TTTGCTTTGTGGGATCTCCG 58.466 50.000 0.00 0.00 38.76 4.63
571 589 3.118992 GGATTTTGCTTTGTGGGATCTCC 60.119 47.826 0.00 0.00 0.00 3.71
572 590 3.511146 TGGATTTTGCTTTGTGGGATCTC 59.489 43.478 0.00 0.00 0.00 2.75
573 591 3.509442 TGGATTTTGCTTTGTGGGATCT 58.491 40.909 0.00 0.00 0.00 2.75
574 592 3.959535 TGGATTTTGCTTTGTGGGATC 57.040 42.857 0.00 0.00 0.00 3.36
575 593 4.102996 AGTTTGGATTTTGCTTTGTGGGAT 59.897 37.500 0.00 0.00 0.00 3.85
576 594 3.454082 AGTTTGGATTTTGCTTTGTGGGA 59.546 39.130 0.00 0.00 0.00 4.37
577 595 3.807553 AGTTTGGATTTTGCTTTGTGGG 58.192 40.909 0.00 0.00 0.00 4.61
578 596 6.048509 AGTAAGTTTGGATTTTGCTTTGTGG 58.951 36.000 0.00 0.00 0.00 4.17
579 597 6.980397 AGAGTAAGTTTGGATTTTGCTTTGTG 59.020 34.615 0.00 0.00 0.00 3.33
580 598 7.112452 AGAGTAAGTTTGGATTTTGCTTTGT 57.888 32.000 0.00 0.00 0.00 2.83
581 599 6.360681 CGAGAGTAAGTTTGGATTTTGCTTTG 59.639 38.462 0.00 0.00 0.00 2.77
582 600 6.262273 TCGAGAGTAAGTTTGGATTTTGCTTT 59.738 34.615 0.00 0.00 0.00 3.51
583 601 5.763204 TCGAGAGTAAGTTTGGATTTTGCTT 59.237 36.000 0.00 0.00 0.00 3.91
584 602 5.305585 TCGAGAGTAAGTTTGGATTTTGCT 58.694 37.500 0.00 0.00 0.00 3.91
585 603 5.408604 TCTCGAGAGTAAGTTTGGATTTTGC 59.591 40.000 12.08 0.00 0.00 3.68
586 604 7.171678 ACTTCTCGAGAGTAAGTTTGGATTTTG 59.828 37.037 15.94 0.00 30.33 2.44
587 605 7.217906 ACTTCTCGAGAGTAAGTTTGGATTTT 58.782 34.615 15.94 0.00 30.33 1.82
588 606 6.760291 ACTTCTCGAGAGTAAGTTTGGATTT 58.240 36.000 15.94 0.00 30.33 2.17
589 607 6.347859 ACTTCTCGAGAGTAAGTTTGGATT 57.652 37.500 15.94 0.00 30.33 3.01
590 608 5.105675 GGACTTCTCGAGAGTAAGTTTGGAT 60.106 44.000 15.94 0.00 32.77 3.41
591 609 4.217983 GGACTTCTCGAGAGTAAGTTTGGA 59.782 45.833 15.94 0.00 32.77 3.53
592 610 4.487019 GGACTTCTCGAGAGTAAGTTTGG 58.513 47.826 15.94 1.93 32.77 3.28
593 611 4.159857 CGGACTTCTCGAGAGTAAGTTTG 58.840 47.826 15.94 9.02 32.77 2.93
594 612 3.819902 ACGGACTTCTCGAGAGTAAGTTT 59.180 43.478 15.94 2.98 32.77 2.66
595 613 3.410508 ACGGACTTCTCGAGAGTAAGTT 58.589 45.455 15.94 0.00 32.77 2.66
596 614 3.002102 GACGGACTTCTCGAGAGTAAGT 58.998 50.000 16.28 16.28 34.16 2.24
597 615 2.352342 GGACGGACTTCTCGAGAGTAAG 59.648 54.545 15.94 12.86 0.00 2.34
598 616 2.027377 AGGACGGACTTCTCGAGAGTAA 60.027 50.000 15.94 0.00 0.00 2.24
599 617 1.554160 AGGACGGACTTCTCGAGAGTA 59.446 52.381 15.94 0.34 0.00 2.59
600 618 0.325602 AGGACGGACTTCTCGAGAGT 59.674 55.000 15.94 15.23 0.00 3.24
601 619 1.011333 GAGGACGGACTTCTCGAGAG 58.989 60.000 15.94 12.15 0.00 3.20
602 620 0.614294 AGAGGACGGACTTCTCGAGA 59.386 55.000 12.08 12.08 28.56 4.04
603 621 1.011333 GAGAGGACGGACTTCTCGAG 58.989 60.000 5.93 5.93 40.79 4.04
604 622 3.156157 GAGAGGACGGACTTCTCGA 57.844 57.895 4.14 0.00 40.79 4.04
606 624 0.448593 CACGAGAGGACGGACTTCTC 59.551 60.000 9.01 9.01 44.74 2.87
607 625 0.036448 TCACGAGAGGACGGACTTCT 59.964 55.000 0.00 0.00 37.65 2.85
608 626 0.168568 GTCACGAGAGGACGGACTTC 59.831 60.000 0.00 0.00 37.61 3.01
609 627 2.255430 GTCACGAGAGGACGGACTT 58.745 57.895 0.00 0.00 37.61 3.01
664 682 1.756375 GCCGACGCTGAACTGCTATG 61.756 60.000 0.00 0.00 0.00 2.23
693 712 0.107017 AATTGGATCAGACCCTGGCG 60.107 55.000 0.00 0.00 31.51 5.69
698 717 2.806945 TGTGGAATTGGATCAGACCC 57.193 50.000 0.00 0.00 0.00 4.46
708 727 5.376854 AGGTTCGAGATTTTGTGGAATTG 57.623 39.130 0.00 0.00 0.00 2.32
711 730 6.940298 AGATTTAGGTTCGAGATTTTGTGGAA 59.060 34.615 0.00 0.00 0.00 3.53
716 735 8.604890 GGAACTAGATTTAGGTTCGAGATTTTG 58.395 37.037 0.00 0.00 0.00 2.44
731 750 5.932883 GTGGAAAACGAGAGGAACTAGATTT 59.067 40.000 0.00 0.00 41.55 2.17
732 751 5.480205 GTGGAAAACGAGAGGAACTAGATT 58.520 41.667 0.00 0.00 41.55 2.40
734 753 3.257624 GGTGGAAAACGAGAGGAACTAGA 59.742 47.826 0.00 0.00 41.55 2.43
739 758 3.284793 TTTGGTGGAAAACGAGAGGAA 57.715 42.857 0.00 0.00 0.00 3.36
741 760 3.630312 TCTTTTTGGTGGAAAACGAGAGG 59.370 43.478 0.00 0.00 33.09 3.69
742 761 4.574828 TCTCTTTTTGGTGGAAAACGAGAG 59.425 41.667 10.40 6.97 46.31 3.20
747 766 6.451064 TCTCTTCTCTTTTTGGTGGAAAAC 57.549 37.500 0.00 0.00 33.09 2.43
757 776 7.790782 ACTAGACTGGATCTCTTCTCTTTTT 57.209 36.000 0.00 0.00 39.04 1.94
765 784 5.544176 TGTGGAAAACTAGACTGGATCTCTT 59.456 40.000 0.00 0.00 39.04 2.85
776 795 4.955811 TTCTGAGCTGTGGAAAACTAGA 57.044 40.909 0.00 0.00 0.00 2.43
784 803 2.232452 GCTACTCTTTCTGAGCTGTGGA 59.768 50.000 0.00 0.00 46.41 4.02
786 805 2.028658 TGGCTACTCTTTCTGAGCTGTG 60.029 50.000 0.00 0.00 46.41 3.66
787 806 2.233431 CTGGCTACTCTTTCTGAGCTGT 59.767 50.000 0.00 0.00 46.41 4.40
788 807 2.418471 CCTGGCTACTCTTTCTGAGCTG 60.418 54.545 0.00 0.00 46.41 4.24
789 808 1.830477 CCTGGCTACTCTTTCTGAGCT 59.170 52.381 0.00 0.00 46.41 4.09
790 809 1.742071 GCCTGGCTACTCTTTCTGAGC 60.742 57.143 12.43 0.00 46.41 4.26
792 811 1.552337 CTGCCTGGCTACTCTTTCTGA 59.448 52.381 21.03 0.00 0.00 3.27
793 812 1.277557 ACTGCCTGGCTACTCTTTCTG 59.722 52.381 21.03 0.19 0.00 3.02
794 813 1.552792 GACTGCCTGGCTACTCTTTCT 59.447 52.381 21.03 0.00 0.00 2.52
797 816 1.277557 CAAGACTGCCTGGCTACTCTT 59.722 52.381 21.03 17.84 30.64 2.85
835 854 1.889829 CGAATAAGCCTCCTCCGATCT 59.110 52.381 0.00 0.00 0.00 2.75
852 871 1.984570 CCACCTCTGCCTCCTCGAA 60.985 63.158 0.00 0.00 0.00 3.71
853 872 2.363018 CCACCTCTGCCTCCTCGA 60.363 66.667 0.00 0.00 0.00 4.04
877 896 4.235762 ACCTTGCACTGACGCGGT 62.236 61.111 12.47 0.00 33.35 5.68
885 904 3.953775 CCCCGGACACCTTGCACT 61.954 66.667 0.73 0.00 0.00 4.40
911 930 2.819608 CACACACCTGATTTACCTTGGG 59.180 50.000 0.00 0.00 0.00 4.12
913 932 3.753272 CCTCACACACCTGATTTACCTTG 59.247 47.826 0.00 0.00 0.00 3.61
942 961 3.329225 CCCTCCTCCTTCAGAACTTCTTT 59.671 47.826 0.00 0.00 0.00 2.52
943 962 2.909662 CCCTCCTCCTTCAGAACTTCTT 59.090 50.000 0.00 0.00 0.00 2.52
957 976 4.021925 AACACAGCGCCCCTCCTC 62.022 66.667 2.29 0.00 0.00 3.71
966 985 3.953775 AGGGACCCCAACACAGCG 61.954 66.667 7.00 0.00 38.92 5.18
968 987 2.282462 GCAGGGACCCCAACACAG 60.282 66.667 7.00 0.00 38.92 3.66
989 1008 0.402504 ACTTCCCATTGTAACCGCCA 59.597 50.000 0.00 0.00 0.00 5.69
991 1010 1.816074 TCACTTCCCATTGTAACCGC 58.184 50.000 0.00 0.00 0.00 5.68
992 1011 5.646360 AGTATTTCACTTCCCATTGTAACCG 59.354 40.000 0.00 0.00 31.59 4.44
995 1014 9.226606 CTTGTAGTATTTCACTTCCCATTGTAA 57.773 33.333 0.00 0.00 38.80 2.41
1015 1034 2.154462 CACTCCACCCAAAGCTTGTAG 58.846 52.381 0.00 0.00 0.00 2.74
1028 1047 6.266786 TCCTTTTAATTTTCCTTCCACTCCAC 59.733 38.462 0.00 0.00 0.00 4.02
1118 1140 0.250901 TGCTTGGAGCTTTCCCACTC 60.251 55.000 1.29 0.00 42.97 3.51
1217 1240 2.512896 AGATCCTTGCACTCCAATCCAT 59.487 45.455 0.00 0.00 31.91 3.41
1262 1288 5.494632 TTTTCCCTTCTCTTCACGAAAAC 57.505 39.130 0.00 0.00 0.00 2.43
1266 1292 4.968259 TCATTTTTCCCTTCTCTTCACGA 58.032 39.130 0.00 0.00 0.00 4.35
1281 1307 7.154656 GTCCATTTTCTACTGCCTTCATTTTT 58.845 34.615 0.00 0.00 0.00 1.94
1299 1325 8.986929 TTTTATTGAAAAACCATGGTCCATTT 57.013 26.923 20.07 18.83 31.51 2.32
1350 1376 9.023962 TGATATTCATCTATGGTTTTATTGGGC 57.976 33.333 0.00 0.00 31.93 5.36
1392 1418 6.886178 ATACCATACACCCTTACCCATATC 57.114 41.667 0.00 0.00 0.00 1.63
1417 1443 3.011708 TCTCTATCCATCATCCCCATCGA 59.988 47.826 0.00 0.00 0.00 3.59
1489 1515 6.037391 CCAAATGCAAAACCATTATCATCCAC 59.963 38.462 0.00 0.00 34.50 4.02
1552 1578 5.215069 AGTGATCCTTCTCATCAGTGGTAT 58.785 41.667 0.00 0.00 33.44 2.73
1567 1593 3.051803 TCCTCACCCTCAATAGTGATCCT 60.052 47.826 0.00 0.00 41.90 3.24
1583 1609 1.830477 ACTGCTCATCTTCCTCCTCAC 59.170 52.381 0.00 0.00 0.00 3.51
1618 1644 6.216662 TCTTCATTACACCCTTCTCCCATTAA 59.783 38.462 0.00 0.00 0.00 1.40
1619 1645 5.729229 TCTTCATTACACCCTTCTCCCATTA 59.271 40.000 0.00 0.00 0.00 1.90
1633 1659 7.689299 TCCTCCTCATTCTTTTCTTCATTACA 58.311 34.615 0.00 0.00 0.00 2.41
1646 1672 3.113191 TCTGCTCTTCCTCCTCATTCT 57.887 47.619 0.00 0.00 0.00 2.40
1648 1674 3.448934 TCTTCTGCTCTTCCTCCTCATT 58.551 45.455 0.00 0.00 0.00 2.57
1659 1685 4.156455 TGAAACCACTTTCTTCTGCTCT 57.844 40.909 0.00 0.00 37.30 4.09
1745 1771 4.103365 TGTTCTGTTTTCGTTGTGCAAT 57.897 36.364 0.00 0.00 0.00 3.56
1762 1788 4.175787 ACTGTCGACTACCTTCATGTTC 57.824 45.455 17.92 0.00 0.00 3.18
1766 1792 4.279145 ACCATACTGTCGACTACCTTCAT 58.721 43.478 17.92 0.00 0.00 2.57
1773 1799 2.956333 CCATGGACCATACTGTCGACTA 59.044 50.000 17.92 1.63 36.07 2.59
1774 1800 1.757118 CCATGGACCATACTGTCGACT 59.243 52.381 17.92 0.00 36.07 4.18
1808 1834 5.366768 TCATCACTGGAACTCCCTTTATAGG 59.633 44.000 0.00 0.00 41.60 2.57
1854 1880 8.161699 TGTTACCTTTACAGAAATCACCTTTC 57.838 34.615 0.00 0.00 43.07 2.62
1869 1895 3.140623 GCTTCCCACGTTGTTACCTTTA 58.859 45.455 0.00 0.00 0.00 1.85
1873 1899 1.265905 CTTGCTTCCCACGTTGTTACC 59.734 52.381 0.00 0.00 0.00 2.85
1880 1906 3.850098 CTGCCCTTGCTTCCCACGT 62.850 63.158 0.00 0.00 38.71 4.49
2069 2096 1.205655 TCTTCTCCCTTCACATGAGCG 59.794 52.381 0.00 0.00 0.00 5.03
2088 2115 3.078837 TGTGCTTATCCTTCCCGTTTTC 58.921 45.455 0.00 0.00 0.00 2.29
2095 2122 3.845781 TCTCCATGTGCTTATCCTTCC 57.154 47.619 0.00 0.00 0.00 3.46
2115 2142 4.486529 TCCCTCTAGGTTCTCCTCCTTATT 59.513 45.833 0.00 0.00 43.94 1.40
2164 2191 1.970114 GTGTCGTCCCAGGTCGAGA 60.970 63.158 6.27 2.72 36.50 4.04
2173 2200 2.048503 CAGGTTCCGTGTCGTCCC 60.049 66.667 0.00 0.00 0.00 4.46
2176 2203 2.232941 ACATATTCAGGTTCCGTGTCGT 59.767 45.455 0.00 0.00 0.00 4.34
2177 2204 2.888594 ACATATTCAGGTTCCGTGTCG 58.111 47.619 0.00 0.00 0.00 4.35
2182 2209 4.941263 TCAGGAAAACATATTCAGGTTCCG 59.059 41.667 0.00 0.00 39.60 4.30
2183 2210 6.834168 TTCAGGAAAACATATTCAGGTTCC 57.166 37.500 0.00 0.00 35.74 3.62
2250 2277 2.222027 AGTTTTCACTCCTTCTTGCCG 58.778 47.619 0.00 0.00 0.00 5.69
2366 2393 4.633565 CCTAGCACTCCATCTGTTTTCTTC 59.366 45.833 0.00 0.00 0.00 2.87
2367 2394 4.287067 TCCTAGCACTCCATCTGTTTTCTT 59.713 41.667 0.00 0.00 0.00 2.52
2401 2428 8.690203 TTCCTTGTCTGAATCATCTTTGTTAA 57.310 30.769 0.00 0.00 0.00 2.01
2464 2491 1.440145 GGCAGTTCCAGGCGATAAGC 61.440 60.000 0.00 0.00 39.07 3.09
2540 2567 5.178797 CCCTCTAGAATTTGTCGTGAATGT 58.821 41.667 0.00 0.00 0.00 2.71
2576 2603 5.588648 CCAAGAAGGGCTCGATAAAAATGTA 59.411 40.000 0.00 0.00 0.00 2.29
2670 2699 3.117322 CCTGAAGGATCTCTCTCCCACTA 60.117 52.174 0.00 0.00 35.79 2.74
2673 2702 1.062581 CCCTGAAGGATCTCTCTCCCA 60.063 57.143 0.00 0.00 38.24 4.37
2974 3004 5.512942 TTGATTAGACATGTCCCCAAGAA 57.487 39.130 22.21 7.63 0.00 2.52


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

AutoCloner maintained by Alex Coulton.