Multiple sequence alignment - TraesCS6D01G241700

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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 TraesCS6D01G241700 chr6D 100.000 3317 0 0 1 3317 344059937 344056621 0.000000e+00 6126.0
1 TraesCS6D01G241700 chr6D 90.538 539 33 8 1 521 454663210 454662672 0.000000e+00 697.0
2 TraesCS6D01G241700 chr6D 90.654 535 33 14 1 521 335061501 335062032 0.000000e+00 695.0
3 TraesCS6D01G241700 chr6D 88.787 544 31 13 1 521 12131307 12131843 1.000000e-179 640.0
4 TraesCS6D01G241700 chr6D 93.684 95 5 1 540 633 349035420 349035514 1.240000e-29 141.0
5 TraesCS6D01G241700 chr6D 95.455 44 2 0 59 102 312196226 312196183 1.650000e-08 71.3
6 TraesCS6D01G241700 chr6A 94.327 1604 66 8 750 2330 484410284 484408683 0.000000e+00 2435.0
7 TraesCS6D01G241700 chr6A 89.043 794 65 10 2527 3304 484400557 484399770 0.000000e+00 965.0
8 TraesCS6D01G241700 chr6A 91.429 105 5 3 536 636 121660121 121660017 1.240000e-29 141.0
9 TraesCS6D01G241700 chr6A 88.679 106 10 2 539 643 23355077 23355181 9.660000e-26 128.0
10 TraesCS6D01G241700 chr6B 90.462 1363 86 21 1666 3001 519323892 519322547 0.000000e+00 1757.0
11 TraesCS6D01G241700 chr6B 93.548 899 36 13 786 1671 519331158 519330269 0.000000e+00 1319.0
12 TraesCS6D01G241700 chr6B 91.909 309 25 0 2996 3304 519314486 519314178 1.830000e-117 433.0
13 TraesCS6D01G241700 chr6B 88.942 208 19 2 315 521 690342748 690342952 1.530000e-63 254.0
14 TraesCS6D01G241700 chr2D 82.561 1273 174 24 1022 2249 14373368 14374637 0.000000e+00 1077.0
15 TraesCS6D01G241700 chr2D 88.672 512 35 10 1 489 13199120 13199631 1.320000e-168 603.0
16 TraesCS6D01G241700 chr2D 89.474 114 9 3 535 645 468096948 468096835 1.240000e-29 141.0
17 TraesCS6D01G241700 chr2D 92.857 98 6 1 537 633 640827012 640827109 1.240000e-29 141.0
18 TraesCS6D01G241700 chr2A 81.532 888 120 23 1417 2264 16629997 16629114 0.000000e+00 691.0
19 TraesCS6D01G241700 chr2A 83.664 655 98 7 1025 1672 16617545 16616893 2.830000e-170 608.0
20 TraesCS6D01G241700 chr2A 82.805 599 85 12 1680 2264 16616851 16616257 1.360000e-143 520.0
21 TraesCS6D01G241700 chr2A 83.260 454 62 5 1876 2321 733657771 733658218 3.980000e-109 405.0
22 TraesCS6D01G241700 chr2A 83.488 430 66 3 1007 1432 733656376 733656804 2.400000e-106 396.0
23 TraesCS6D01G241700 chr2A 83.416 404 59 6 1027 1423 16630492 16630090 5.230000e-98 368.0
24 TraesCS6D01G241700 chr2A 94.309 123 7 0 349 471 716907780 716907658 4.370000e-44 189.0
25 TraesCS6D01G241700 chr4A 90.149 335 26 6 1 328 140298663 140298329 2.360000e-116 429.0
26 TraesCS6D01G241700 chr4A 92.486 173 10 1 349 521 140298258 140298089 9.190000e-61 244.0
27 TraesCS6D01G241700 chr7A 88.338 343 20 12 1 334 540002325 540001994 8.630000e-106 394.0
28 TraesCS6D01G241700 chr7A 90.431 209 19 1 314 521 540001967 540001759 1.170000e-69 274.0
29 TraesCS6D01G241700 chr3B 73.281 640 144 22 1024 1645 732110644 732111274 3.350000e-50 209.0
30 TraesCS6D01G241700 chr3B 100.000 35 0 0 477 511 50397391 50397425 7.680000e-07 65.8
31 TraesCS6D01G241700 chr7D 91.000 100 8 1 540 638 6082197 6082098 2.080000e-27 134.0
32 TraesCS6D01G241700 chr3D 90.196 102 8 2 540 639 290583915 290583814 7.470000e-27 132.0
33 TraesCS6D01G241700 chr3D 95.455 44 2 0 59 102 49539705 49539748 1.650000e-08 71.3
34 TraesCS6D01G241700 chr5D 90.099 101 9 1 540 639 269021944 269021844 2.690000e-26 130.0
35 TraesCS6D01G241700 chr5D 89.320 103 10 1 537 638 1790745 1790847 9.660000e-26 128.0
36 TraesCS6D01G241700 chr2B 86.869 99 13 0 1 99 524223768 524223670 9.730000e-21 111.0
37 TraesCS6D01G241700 chr1D 97.674 43 1 0 60 102 241241976 241242018 1.280000e-09 75.0
38 TraesCS6D01G241700 chr1D 95.652 46 2 0 60 105 487152411 487152366 1.280000e-09 75.0
39 TraesCS6D01G241700 chrUn 95.455 44 2 0 59 102 88913385 88913428 1.650000e-08 71.3
40 TraesCS6D01G241700 chr3A 82.500 80 13 1 25 103 23061026 23061105 5.940000e-08 69.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G241700 chr6D 344056621 344059937 3316 True 6126.0 6126 100.0000 1 3317 1 chr6D.!!$R2 3316
1 TraesCS6D01G241700 chr6D 454662672 454663210 538 True 697.0 697 90.5380 1 521 1 chr6D.!!$R3 520
2 TraesCS6D01G241700 chr6D 335061501 335062032 531 False 695.0 695 90.6540 1 521 1 chr6D.!!$F2 520
3 TraesCS6D01G241700 chr6D 12131307 12131843 536 False 640.0 640 88.7870 1 521 1 chr6D.!!$F1 520
4 TraesCS6D01G241700 chr6A 484408683 484410284 1601 True 2435.0 2435 94.3270 750 2330 1 chr6A.!!$R3 1580
5 TraesCS6D01G241700 chr6A 484399770 484400557 787 True 965.0 965 89.0430 2527 3304 1 chr6A.!!$R2 777
6 TraesCS6D01G241700 chr6B 519322547 519323892 1345 True 1757.0 1757 90.4620 1666 3001 1 chr6B.!!$R2 1335
7 TraesCS6D01G241700 chr6B 519330269 519331158 889 True 1319.0 1319 93.5480 786 1671 1 chr6B.!!$R3 885
8 TraesCS6D01G241700 chr2D 14373368 14374637 1269 False 1077.0 1077 82.5610 1022 2249 1 chr2D.!!$F2 1227
9 TraesCS6D01G241700 chr2D 13199120 13199631 511 False 603.0 603 88.6720 1 489 1 chr2D.!!$F1 488
10 TraesCS6D01G241700 chr2A 16616257 16617545 1288 True 564.0 608 83.2345 1025 2264 2 chr2A.!!$R2 1239
11 TraesCS6D01G241700 chr2A 16629114 16630492 1378 True 529.5 691 82.4740 1027 2264 2 chr2A.!!$R3 1237
12 TraesCS6D01G241700 chr2A 733656376 733658218 1842 False 400.5 405 83.3740 1007 2321 2 chr2A.!!$F1 1314
13 TraesCS6D01G241700 chr4A 140298089 140298663 574 True 336.5 429 91.3175 1 521 2 chr4A.!!$R1 520
14 TraesCS6D01G241700 chr7A 540001759 540002325 566 True 334.0 394 89.3845 1 521 2 chr7A.!!$R1 520
15 TraesCS6D01G241700 chr3B 732110644 732111274 630 False 209.0 209 73.2810 1024 1645 1 chr3B.!!$F2 621

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
931 997 0.035317 TGCATGCACCTTCGTCTTCT 59.965 50.0 18.46 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2808 3621 0.03254 GACCAAGCCCAACAAGCAAG 59.967 55.0 0.0 0.0 0.0 4.01 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
38 39 1.470098 AGCGCGAATCTTGAAGCAAAT 59.530 42.857 12.10 0.00 0.00 2.32
46 47 7.192232 GCGAATCTTGAAGCAAATAAAGATCT 58.808 34.615 0.00 0.00 38.18 2.75
90 91 6.375736 TGAGACTTCACTAAATCTCAGTCGAT 59.624 38.462 0.00 0.00 41.99 3.59
201 206 8.506168 AAAGAAAAATGGGAAAAGAAAAGACC 57.494 30.769 0.00 0.00 0.00 3.85
255 261 8.634475 AGGAAAATGAAGAAAAAGAAAAGACG 57.366 30.769 0.00 0.00 0.00 4.18
266 272 6.657836 AAAAGAAAAGACGAAGAACGAGAA 57.342 33.333 0.00 0.00 45.77 2.87
286 293 6.280855 AGAAAACAACAGCCTAAAAACACT 57.719 33.333 0.00 0.00 0.00 3.55
297 304 6.006449 AGCCTAAAAACACTCATTGAGATGT 58.994 36.000 20.33 15.98 34.77 3.06
303 310 5.745312 AACACTCATTGAGATGTGACCTA 57.255 39.130 20.33 0.00 34.77 3.08
308 315 7.667219 ACACTCATTGAGATGTGACCTAAAAAT 59.333 33.333 20.33 0.00 34.77 1.82
342 401 6.943981 TGAGAAAGACATCACGTAAAAACAG 58.056 36.000 0.00 0.00 0.00 3.16
345 405 8.154649 AGAAAGACATCACGTAAAAACAGAAT 57.845 30.769 0.00 0.00 0.00 2.40
363 424 1.541379 ATAGGCCCAAACAACGGAAC 58.459 50.000 0.00 0.00 0.00 3.62
371 432 2.357637 CCAAACAACGGAACACACAGAT 59.642 45.455 0.00 0.00 0.00 2.90
424 485 2.213499 CAGGCTGAAAACGAGACAACT 58.787 47.619 9.42 0.00 0.00 3.16
473 534 6.147821 GCAAGTAATAATCATACGGCTGACAT 59.852 38.462 0.00 0.00 0.00 3.06
492 553 1.512310 GTCGACTGAGACTTCGCGG 60.512 63.158 8.70 0.00 38.09 6.46
521 582 3.378742 AGTCGACTGAGATTTAGCGTCAT 59.621 43.478 19.30 0.00 0.00 3.06
522 583 4.575236 AGTCGACTGAGATTTAGCGTCATA 59.425 41.667 19.30 0.00 0.00 2.15
523 584 5.066117 AGTCGACTGAGATTTAGCGTCATAA 59.934 40.000 19.30 0.00 0.00 1.90
524 585 5.396947 GTCGACTGAGATTTAGCGTCATAAG 59.603 44.000 8.70 0.00 0.00 1.73
525 586 5.296035 TCGACTGAGATTTAGCGTCATAAGA 59.704 40.000 0.00 0.00 0.00 2.10
526 587 5.971792 CGACTGAGATTTAGCGTCATAAGAA 59.028 40.000 0.00 0.00 0.00 2.52
527 588 6.075310 CGACTGAGATTTAGCGTCATAAGAAC 60.075 42.308 0.00 0.00 0.00 3.01
528 589 6.631016 ACTGAGATTTAGCGTCATAAGAACA 58.369 36.000 0.00 0.00 0.00 3.18
529 590 7.268586 ACTGAGATTTAGCGTCATAAGAACAT 58.731 34.615 0.00 0.00 0.00 2.71
530 591 7.766278 ACTGAGATTTAGCGTCATAAGAACATT 59.234 33.333 0.00 0.00 0.00 2.71
531 592 8.492673 TGAGATTTAGCGTCATAAGAACATTT 57.507 30.769 0.00 0.00 0.00 2.32
532 593 9.594478 TGAGATTTAGCGTCATAAGAACATTTA 57.406 29.630 0.00 0.00 0.00 1.40
533 594 9.851043 GAGATTTAGCGTCATAAGAACATTTAC 57.149 33.333 0.00 0.00 0.00 2.01
534 595 9.378551 AGATTTAGCGTCATAAGAACATTTACA 57.621 29.630 0.00 0.00 0.00 2.41
539 600 8.718102 AGCGTCATAAGAACATTTACATTACT 57.282 30.769 0.00 0.00 0.00 2.24
540 601 9.811995 AGCGTCATAAGAACATTTACATTACTA 57.188 29.630 0.00 0.00 0.00 1.82
541 602 9.845305 GCGTCATAAGAACATTTACATTACTAC 57.155 33.333 0.00 0.00 0.00 2.73
548 609 7.793036 AGAACATTTACATTACTACTCCCTCC 58.207 38.462 0.00 0.00 0.00 4.30
549 610 6.158023 ACATTTACATTACTACTCCCTCCG 57.842 41.667 0.00 0.00 0.00 4.63
550 611 5.659971 ACATTTACATTACTACTCCCTCCGT 59.340 40.000 0.00 0.00 0.00 4.69
551 612 5.841957 TTTACATTACTACTCCCTCCGTC 57.158 43.478 0.00 0.00 0.00 4.79
552 613 3.666345 ACATTACTACTCCCTCCGTCT 57.334 47.619 0.00 0.00 0.00 4.18
553 614 3.553904 ACATTACTACTCCCTCCGTCTC 58.446 50.000 0.00 0.00 0.00 3.36
554 615 3.053842 ACATTACTACTCCCTCCGTCTCA 60.054 47.826 0.00 0.00 0.00 3.27
555 616 3.726557 TTACTACTCCCTCCGTCTCAA 57.273 47.619 0.00 0.00 0.00 3.02
556 617 2.599408 ACTACTCCCTCCGTCTCAAA 57.401 50.000 0.00 0.00 0.00 2.69
557 618 2.885616 ACTACTCCCTCCGTCTCAAAA 58.114 47.619 0.00 0.00 0.00 2.44
558 619 3.442076 ACTACTCCCTCCGTCTCAAAAT 58.558 45.455 0.00 0.00 0.00 1.82
559 620 4.607239 ACTACTCCCTCCGTCTCAAAATA 58.393 43.478 0.00 0.00 0.00 1.40
560 621 4.645588 ACTACTCCCTCCGTCTCAAAATAG 59.354 45.833 0.00 0.00 0.00 1.73
561 622 3.709587 ACTCCCTCCGTCTCAAAATAGA 58.290 45.455 0.00 0.00 0.00 1.98
562 623 4.290942 ACTCCCTCCGTCTCAAAATAGAT 58.709 43.478 0.00 0.00 0.00 1.98
563 624 4.100189 ACTCCCTCCGTCTCAAAATAGATG 59.900 45.833 0.00 0.00 33.12 2.90
564 625 4.286707 TCCCTCCGTCTCAAAATAGATGA 58.713 43.478 0.00 0.00 34.94 2.92
565 626 4.099573 TCCCTCCGTCTCAAAATAGATGAC 59.900 45.833 0.00 0.00 34.94 3.06
566 627 4.100189 CCCTCCGTCTCAAAATAGATGACT 59.900 45.833 0.00 0.00 34.94 3.41
567 628 5.285651 CCTCCGTCTCAAAATAGATGACTC 58.714 45.833 0.00 0.00 34.94 3.36
568 629 5.163509 CCTCCGTCTCAAAATAGATGACTCA 60.164 44.000 0.00 0.00 34.94 3.41
569 630 6.280855 TCCGTCTCAAAATAGATGACTCAA 57.719 37.500 0.00 0.00 34.94 3.02
570 631 6.100004 TCCGTCTCAAAATAGATGACTCAAC 58.900 40.000 0.00 0.00 34.94 3.18
571 632 6.071334 TCCGTCTCAAAATAGATGACTCAACT 60.071 38.462 0.00 0.00 34.94 3.16
572 633 6.591834 CCGTCTCAAAATAGATGACTCAACTT 59.408 38.462 0.00 0.00 34.94 2.66
573 634 7.118390 CCGTCTCAAAATAGATGACTCAACTTT 59.882 37.037 0.00 0.00 34.94 2.66
574 635 9.140286 CGTCTCAAAATAGATGACTCAACTTTA 57.860 33.333 0.00 0.00 34.94 1.85
626 687 7.665561 AATTGGGTCATTTATTTTGAAACGG 57.334 32.000 0.00 0.00 0.00 4.44
627 688 6.406692 TTGGGTCATTTATTTTGAAACGGA 57.593 33.333 0.00 0.00 0.00 4.69
628 689 6.019779 TGGGTCATTTATTTTGAAACGGAG 57.980 37.500 0.00 0.00 0.00 4.63
629 690 5.047660 TGGGTCATTTATTTTGAAACGGAGG 60.048 40.000 0.00 0.00 0.00 4.30
630 691 5.407502 GGTCATTTATTTTGAAACGGAGGG 58.592 41.667 0.00 0.00 0.00 4.30
631 692 5.184287 GGTCATTTATTTTGAAACGGAGGGA 59.816 40.000 0.00 0.00 0.00 4.20
632 693 6.322491 GTCATTTATTTTGAAACGGAGGGAG 58.678 40.000 0.00 0.00 0.00 4.30
633 694 6.150474 GTCATTTATTTTGAAACGGAGGGAGA 59.850 38.462 0.00 0.00 0.00 3.71
634 695 6.717540 TCATTTATTTTGAAACGGAGGGAGAA 59.282 34.615 0.00 0.00 0.00 2.87
635 696 5.952526 TTATTTTGAAACGGAGGGAGAAC 57.047 39.130 0.00 0.00 0.00 3.01
636 697 3.570912 TTTTGAAACGGAGGGAGAACT 57.429 42.857 0.00 0.00 0.00 3.01
637 698 3.570912 TTTGAAACGGAGGGAGAACTT 57.429 42.857 0.00 0.00 0.00 2.66
638 699 4.693042 TTTGAAACGGAGGGAGAACTTA 57.307 40.909 0.00 0.00 0.00 2.24
639 700 3.672767 TGAAACGGAGGGAGAACTTAC 57.327 47.619 0.00 0.00 0.00 2.34
640 701 2.967201 TGAAACGGAGGGAGAACTTACA 59.033 45.455 0.00 0.00 0.00 2.41
641 702 3.581332 TGAAACGGAGGGAGAACTTACAT 59.419 43.478 0.00 0.00 0.00 2.29
642 703 4.041198 TGAAACGGAGGGAGAACTTACATT 59.959 41.667 0.00 0.00 0.00 2.71
643 704 4.635699 AACGGAGGGAGAACTTACATTT 57.364 40.909 0.00 0.00 0.00 2.32
644 705 4.635699 ACGGAGGGAGAACTTACATTTT 57.364 40.909 0.00 0.00 0.00 1.82
645 706 4.981812 ACGGAGGGAGAACTTACATTTTT 58.018 39.130 0.00 0.00 0.00 1.94
646 707 6.117975 ACGGAGGGAGAACTTACATTTTTA 57.882 37.500 0.00 0.00 0.00 1.52
647 708 6.171213 ACGGAGGGAGAACTTACATTTTTAG 58.829 40.000 0.00 0.00 0.00 1.85
648 709 5.064834 CGGAGGGAGAACTTACATTTTTAGC 59.935 44.000 0.00 0.00 0.00 3.09
649 710 6.181190 GGAGGGAGAACTTACATTTTTAGCT 58.819 40.000 0.00 0.00 0.00 3.32
650 711 7.336396 GGAGGGAGAACTTACATTTTTAGCTA 58.664 38.462 0.00 0.00 0.00 3.32
651 712 7.827729 GGAGGGAGAACTTACATTTTTAGCTAA 59.172 37.037 0.86 0.86 0.00 3.09
652 713 9.227777 GAGGGAGAACTTACATTTTTAGCTAAA 57.772 33.333 14.96 14.96 0.00 1.85
653 714 9.011095 AGGGAGAACTTACATTTTTAGCTAAAC 57.989 33.333 18.45 3.51 0.00 2.01
654 715 8.242053 GGGAGAACTTACATTTTTAGCTAAACC 58.758 37.037 18.45 10.95 0.00 3.27
655 716 9.011095 GGAGAACTTACATTTTTAGCTAAACCT 57.989 33.333 18.45 6.18 0.00 3.50
656 717 9.827411 GAGAACTTACATTTTTAGCTAAACCTG 57.173 33.333 18.45 18.70 0.00 4.00
657 718 8.297426 AGAACTTACATTTTTAGCTAAACCTGC 58.703 33.333 18.45 5.58 0.00 4.85
658 719 7.519032 ACTTACATTTTTAGCTAAACCTGCA 57.481 32.000 18.45 7.13 0.00 4.41
659 720 8.122472 ACTTACATTTTTAGCTAAACCTGCAT 57.878 30.769 18.45 6.90 0.00 3.96
660 721 8.585018 ACTTACATTTTTAGCTAAACCTGCATT 58.415 29.630 18.45 6.31 0.00 3.56
662 723 9.849166 TTACATTTTTAGCTAAACCTGCATTAC 57.151 29.630 18.45 0.00 0.00 1.89
663 724 8.122472 ACATTTTTAGCTAAACCTGCATTACT 57.878 30.769 18.45 0.39 0.00 2.24
664 725 8.585018 ACATTTTTAGCTAAACCTGCATTACTT 58.415 29.630 18.45 0.00 0.00 2.24
665 726 8.863049 CATTTTTAGCTAAACCTGCATTACTTG 58.137 33.333 18.45 0.00 0.00 3.16
666 727 7.753309 TTTTAGCTAAACCTGCATTACTTGA 57.247 32.000 18.45 0.00 0.00 3.02
667 728 6.985188 TTAGCTAAACCTGCATTACTTGAG 57.015 37.500 2.97 0.00 0.00 3.02
668 729 5.165961 AGCTAAACCTGCATTACTTGAGA 57.834 39.130 0.00 0.00 0.00 3.27
669 730 5.749462 AGCTAAACCTGCATTACTTGAGAT 58.251 37.500 0.00 0.00 0.00 2.75
670 731 5.587844 AGCTAAACCTGCATTACTTGAGATG 59.412 40.000 0.00 0.00 0.00 2.90
671 732 5.220931 GCTAAACCTGCATTACTTGAGATGG 60.221 44.000 0.00 0.00 0.00 3.51
672 733 4.307032 AACCTGCATTACTTGAGATGGT 57.693 40.909 0.00 0.00 0.00 3.55
673 734 3.878778 ACCTGCATTACTTGAGATGGTC 58.121 45.455 0.00 0.00 0.00 4.02
674 735 3.264193 ACCTGCATTACTTGAGATGGTCA 59.736 43.478 0.00 0.00 0.00 4.02
675 736 3.624861 CCTGCATTACTTGAGATGGTCAC 59.375 47.826 0.00 0.00 33.71 3.67
676 737 4.256110 CTGCATTACTTGAGATGGTCACA 58.744 43.478 0.00 0.00 33.71 3.58
677 738 4.256110 TGCATTACTTGAGATGGTCACAG 58.744 43.478 0.00 0.00 33.71 3.66
678 739 4.020307 TGCATTACTTGAGATGGTCACAGA 60.020 41.667 0.00 0.00 33.71 3.41
679 740 5.121811 GCATTACTTGAGATGGTCACAGAT 58.878 41.667 0.00 0.00 33.71 2.90
680 741 5.007430 GCATTACTTGAGATGGTCACAGATG 59.993 44.000 0.00 0.00 33.71 2.90
681 742 3.623906 ACTTGAGATGGTCACAGATGG 57.376 47.619 0.00 0.00 33.71 3.51
682 743 2.286872 CTTGAGATGGTCACAGATGGC 58.713 52.381 0.00 0.00 33.71 4.40
683 744 1.278537 TGAGATGGTCACAGATGGCA 58.721 50.000 0.00 0.00 29.15 4.92
684 745 1.841919 TGAGATGGTCACAGATGGCAT 59.158 47.619 0.00 0.00 29.15 4.40
685 746 2.219458 GAGATGGTCACAGATGGCATG 58.781 52.381 3.81 0.00 29.15 4.06
686 747 1.562942 AGATGGTCACAGATGGCATGT 59.437 47.619 3.81 0.00 29.15 3.21
687 748 2.025605 AGATGGTCACAGATGGCATGTT 60.026 45.455 3.81 0.00 29.15 2.71
688 749 1.536940 TGGTCACAGATGGCATGTTG 58.463 50.000 3.81 5.84 29.15 3.33
689 750 0.171903 GGTCACAGATGGCATGTTGC 59.828 55.000 3.81 0.00 44.08 4.17
701 762 3.221964 GCATGTTGCCTTTTTCGATCT 57.778 42.857 0.00 0.00 37.42 2.75
702 763 4.355543 GCATGTTGCCTTTTTCGATCTA 57.644 40.909 0.00 0.00 37.42 1.98
703 764 4.346129 GCATGTTGCCTTTTTCGATCTAG 58.654 43.478 0.00 0.00 37.42 2.43
704 765 4.094887 GCATGTTGCCTTTTTCGATCTAGA 59.905 41.667 0.00 0.00 37.42 2.43
705 766 5.220931 GCATGTTGCCTTTTTCGATCTAGAT 60.221 40.000 4.47 4.47 37.42 1.98
706 767 6.017934 GCATGTTGCCTTTTTCGATCTAGATA 60.018 38.462 4.89 0.00 37.42 1.98
707 768 7.467267 GCATGTTGCCTTTTTCGATCTAGATAA 60.467 37.037 4.89 0.00 37.42 1.75
708 769 7.915293 TGTTGCCTTTTTCGATCTAGATAAA 57.085 32.000 4.89 0.69 0.00 1.40
709 770 7.974675 TGTTGCCTTTTTCGATCTAGATAAAG 58.025 34.615 14.80 14.80 38.23 1.85
710 771 7.822334 TGTTGCCTTTTTCGATCTAGATAAAGA 59.178 33.333 20.27 12.03 39.72 2.52
711 772 8.665685 GTTGCCTTTTTCGATCTAGATAAAGAA 58.334 33.333 20.27 15.98 39.72 2.52
712 773 8.964476 TGCCTTTTTCGATCTAGATAAAGAAT 57.036 30.769 20.27 0.00 39.72 2.40
733 794 9.525826 AAGAATAAAAATAGGATGGAGGCTATG 57.474 33.333 0.00 0.00 0.00 2.23
734 795 8.673251 AGAATAAAAATAGGATGGAGGCTATGT 58.327 33.333 0.00 0.00 0.00 2.29
735 796 9.959721 GAATAAAAATAGGATGGAGGCTATGTA 57.040 33.333 0.00 0.00 0.00 2.29
738 799 8.641498 AAAAATAGGATGGAGGCTATGTAATG 57.359 34.615 0.00 0.00 0.00 1.90
739 800 3.710209 AGGATGGAGGCTATGTAATGC 57.290 47.619 0.00 0.00 0.00 3.56
740 801 2.981784 AGGATGGAGGCTATGTAATGCA 59.018 45.455 0.00 0.00 0.00 3.96
741 802 3.395607 AGGATGGAGGCTATGTAATGCAA 59.604 43.478 0.00 0.00 0.00 4.08
742 803 3.503748 GGATGGAGGCTATGTAATGCAAC 59.496 47.826 0.00 0.00 0.00 4.17
743 804 3.931907 TGGAGGCTATGTAATGCAACT 57.068 42.857 0.00 0.00 0.00 3.16
744 805 5.513094 GGATGGAGGCTATGTAATGCAACTA 60.513 44.000 0.00 0.00 0.00 2.24
745 806 4.960938 TGGAGGCTATGTAATGCAACTAG 58.039 43.478 0.00 0.00 0.00 2.57
746 807 4.408921 TGGAGGCTATGTAATGCAACTAGT 59.591 41.667 0.00 0.00 0.00 2.57
747 808 4.991687 GGAGGCTATGTAATGCAACTAGTC 59.008 45.833 0.00 0.00 0.00 2.59
748 809 4.962155 AGGCTATGTAATGCAACTAGTCC 58.038 43.478 0.00 0.00 0.00 3.85
881 947 4.322574 CCATCCGCTATCAGAGATGTGATT 60.323 45.833 0.00 0.00 38.21 2.57
929 995 0.806868 CATGCATGCACCTTCGTCTT 59.193 50.000 25.37 0.00 0.00 3.01
930 996 1.089920 ATGCATGCACCTTCGTCTTC 58.910 50.000 25.37 0.00 0.00 2.87
931 997 0.035317 TGCATGCACCTTCGTCTTCT 59.965 50.000 18.46 0.00 0.00 2.85
932 998 0.723981 GCATGCACCTTCGTCTTCTC 59.276 55.000 14.21 0.00 0.00 2.87
934 1000 2.693069 CATGCACCTTCGTCTTCTCTT 58.307 47.619 0.00 0.00 0.00 2.85
936 1002 1.964223 TGCACCTTCGTCTTCTCTTCT 59.036 47.619 0.00 0.00 0.00 2.85
937 1003 2.288457 TGCACCTTCGTCTTCTCTTCTG 60.288 50.000 0.00 0.00 0.00 3.02
967 1033 8.630054 AGTATTTATTTATGCTTTGGCGGATA 57.370 30.769 0.00 0.00 42.25 2.59
969 1035 9.341899 GTATTTATTTATGCTTTGGCGGATAAG 57.658 33.333 0.00 0.00 42.25 1.73
970 1036 6.952773 TTATTTATGCTTTGGCGGATAAGT 57.047 33.333 0.00 0.00 42.25 2.24
1107 1205 3.644606 CTGGACCTGGTGCTGGCT 61.645 66.667 19.43 0.00 0.00 4.75
1270 1377 4.891727 ATCGTGACGGCCGCATCC 62.892 66.667 28.58 12.87 0.00 3.51
1314 1421 3.003113 GCTCTTCGTGGTAGCCCGT 62.003 63.158 0.00 0.00 0.00 5.28
1929 2710 2.562912 GCGGTGAAGGACGTCGTA 59.437 61.111 11.72 0.00 0.00 3.43
2024 2813 1.135344 GGCTGTGGACTACTTCGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
2305 3103 2.931325 GTTCAAACCGGCATCGTACATA 59.069 45.455 0.00 0.00 33.95 2.29
2330 3128 8.016301 ACGAGGCTGTGATCATATATTCATAT 57.984 34.615 0.00 0.00 0.00 1.78
2383 3181 4.798907 GTCTTCGTCGATTTCATTCTAGCA 59.201 41.667 0.00 0.00 0.00 3.49
2393 3191 6.566564 CGATTTCATTCTAGCATGCGGTAATT 60.567 38.462 13.01 0.00 0.00 1.40
2405 3203 7.996385 AGCATGCGGTAATTTTATTTTACTCT 58.004 30.769 13.01 0.00 31.62 3.24
2406 3204 8.129211 AGCATGCGGTAATTTTATTTTACTCTC 58.871 33.333 13.01 0.00 31.62 3.20
2431 3241 9.821662 TCTTCGATACATATTACTTGTCGTATG 57.178 33.333 0.00 0.00 0.00 2.39
2433 3243 8.944212 TCGATACATATTACTTGTCGTATGTG 57.056 34.615 15.18 0.00 38.04 3.21
2437 3247 9.856488 ATACATATTACTTGTCGTATGTGGATC 57.144 33.333 15.18 0.00 38.04 3.36
2439 3249 2.579207 ACTTGTCGTATGTGGATCGG 57.421 50.000 0.00 0.00 0.00 4.18
2442 3252 1.758936 TGTCGTATGTGGATCGGAGT 58.241 50.000 0.00 0.00 0.00 3.85
2447 3257 4.152045 GTCGTATGTGGATCGGAGTAGTAG 59.848 50.000 0.00 0.00 0.00 2.57
2454 3264 5.100943 GTGGATCGGAGTAGTAGTTTTGTC 58.899 45.833 0.00 0.00 0.00 3.18
2455 3265 5.014858 TGGATCGGAGTAGTAGTTTTGTCT 58.985 41.667 0.00 0.00 0.00 3.41
2478 3288 9.730420 GTCTGTTTTGTTTCATAAGTGTACAAT 57.270 29.630 0.00 0.00 33.98 2.71
2495 3308 6.816640 GTGTACAATATCAAGTGGTCAGCTTA 59.183 38.462 0.00 0.00 0.00 3.09
2500 3313 8.100791 ACAATATCAAGTGGTCAGCTTAGTAAA 58.899 33.333 0.00 0.00 0.00 2.01
2507 3320 5.001232 GTGGTCAGCTTAGTAAACCATCAA 58.999 41.667 7.31 0.00 41.71 2.57
2546 3359 8.421673 AAAGAAAGTGTACAAGACTACAAGTC 57.578 34.615 0.00 0.00 45.38 3.01
2700 3513 2.390225 AGATTGACCGCCTCCTAGAT 57.610 50.000 0.00 0.00 0.00 1.98
2714 3527 2.108168 CCTAGATTGTCGGAGGGAACA 58.892 52.381 0.00 0.00 0.00 3.18
2747 3560 1.068055 CAGATCTTGCAACAAGCCCAC 60.068 52.381 0.00 0.00 44.83 4.61
2797 3610 5.449177 CGGCCTTGATGTAATCTTTCTTTCC 60.449 44.000 0.00 0.00 45.81 3.13
2802 3615 9.987272 CCTTGATGTAATCTTTCTTTCCTTTTT 57.013 29.630 0.00 0.00 45.81 1.94
2808 3621 9.067986 TGTAATCTTTCTTTCCTTTTTCTCTCC 57.932 33.333 0.00 0.00 0.00 3.71
2819 3646 4.500375 CCTTTTTCTCTCCTTGCTTGTTGG 60.500 45.833 0.00 0.00 0.00 3.77
2832 3659 2.814097 GCTTGTTGGGCTTGGTCTTCTA 60.814 50.000 0.00 0.00 0.00 2.10
2864 3691 6.992766 AGTCTTGTTGCAAAAATCTTTTTCG 58.007 32.000 1.65 0.00 38.23 3.46
2875 3702 7.375808 GCAAAAATCTTTTTCGAACCATTTTCC 59.624 33.333 0.00 0.00 38.23 3.13
2929 3756 1.826327 CAACAAAGGTCGTGTTGCTG 58.174 50.000 4.52 0.00 46.63 4.41
2952 3779 3.857157 ACTTTTGCAACAGAGGTCCTA 57.143 42.857 19.17 0.00 0.00 2.94
2982 3810 2.388347 TTTTTGCAACAAAGCCCGC 58.612 47.368 0.00 0.00 0.00 6.13
3025 3853 1.584380 GCTGCAAGAGCTTGAGGTGG 61.584 60.000 14.04 0.62 45.21 4.61
3093 3921 0.957395 CAGCCGCTCATGTTTCAGGT 60.957 55.000 0.00 0.00 0.00 4.00
3096 3924 1.236616 CCGCTCATGTTTCAGGTGCA 61.237 55.000 8.61 0.00 34.97 4.57
3109 3937 2.528743 GGTGCATCGCCTGTCATCG 61.529 63.158 0.00 0.00 0.00 3.84
3111 3939 1.810853 TGCATCGCCTGTCATCGTG 60.811 57.895 0.00 0.00 0.00 4.35
3139 3967 1.280886 GCTCGCATCATAGGTGCTCG 61.281 60.000 0.42 0.00 40.37 5.03
3142 3970 1.963338 GCATCATAGGTGCTCGGGC 60.963 63.158 0.00 0.00 39.45 6.13
3181 4009 1.133790 GGACAGATCACAAGCAATGGC 59.866 52.381 0.00 0.00 41.61 4.40
3184 4012 1.033746 AGATCACAAGCAATGGCCCG 61.034 55.000 0.00 0.00 42.56 6.13
3205 4033 1.662446 AGCGTTACCGGTCGTTGTG 60.662 57.895 12.40 0.00 41.85 3.33
3238 4066 2.583593 GCTTCGGTGCTCTAGGCG 60.584 66.667 0.00 0.00 45.43 5.52
3259 4087 1.362717 CCGATCACCGCCGTTATCT 59.637 57.895 0.00 0.00 36.84 1.98
3260 4088 0.249322 CCGATCACCGCCGTTATCTT 60.249 55.000 0.00 0.00 36.84 2.40
3278 4106 0.179020 TTGAGTGGTGGCTGGACTTG 60.179 55.000 0.00 0.00 0.00 3.16
3294 4122 1.270678 ACTTGGGAAGTCCGCTAACAC 60.271 52.381 0.00 0.00 37.02 3.32
3304 4132 0.310543 CCGCTAACACTTGCAAGCAA 59.689 50.000 26.27 7.33 34.60 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.950555 TGCTTCAAGATTCGCGCTGT 60.951 50.000 5.56 0.00 0.00 4.40
38 39 1.538204 GCGCCATCCGTCAGATCTTTA 60.538 52.381 0.00 0.00 39.71 1.85
90 91 7.956420 TTTTAACAGACTCGCTAAATCTCAA 57.044 32.000 0.00 0.00 0.00 3.02
229 235 9.087424 CGTCTTTTCTTTTTCTTCATTTTCCTT 57.913 29.630 0.00 0.00 0.00 3.36
255 261 3.312697 AGGCTGTTGTTTTCTCGTTCTTC 59.687 43.478 0.00 0.00 0.00 2.87
266 272 5.652994 TGAGTGTTTTTAGGCTGTTGTTT 57.347 34.783 0.00 0.00 0.00 2.83
313 324 9.796120 TTTTTACGTGATGTCTTTCTCATTTTT 57.204 25.926 0.00 0.00 0.00 1.94
328 339 4.638865 GGGCCTATTCTGTTTTTACGTGAT 59.361 41.667 0.84 0.00 0.00 3.06
330 341 3.754323 TGGGCCTATTCTGTTTTTACGTG 59.246 43.478 4.53 0.00 0.00 4.49
331 342 4.023726 TGGGCCTATTCTGTTTTTACGT 57.976 40.909 4.53 0.00 0.00 3.57
332 343 5.158494 GTTTGGGCCTATTCTGTTTTTACG 58.842 41.667 4.53 0.00 0.00 3.18
334 345 6.517605 GTTGTTTGGGCCTATTCTGTTTTTA 58.482 36.000 4.53 0.00 0.00 1.52
335 346 5.364778 GTTGTTTGGGCCTATTCTGTTTTT 58.635 37.500 4.53 0.00 0.00 1.94
342 401 1.828979 TCCGTTGTTTGGGCCTATTC 58.171 50.000 4.53 0.00 0.00 1.75
345 405 0.183014 TGTTCCGTTGTTTGGGCCTA 59.817 50.000 4.53 0.00 0.00 3.93
363 424 3.679980 CCGGTTCTCTGTTTATCTGTGTG 59.320 47.826 0.00 0.00 0.00 3.82
371 432 0.323629 CCAGCCCGGTTCTCTGTTTA 59.676 55.000 0.00 0.00 0.00 2.01
424 485 6.367969 GCTTTAAGATTCGTGTTGGAGAGTTA 59.632 38.462 0.00 0.00 0.00 2.24
473 534 1.206831 CGCGAAGTCTCAGTCGACA 59.793 57.895 19.50 0.00 39.64 4.35
522 583 8.265764 GGAGGGAGTAGTAATGTAAATGTTCTT 58.734 37.037 0.00 0.00 0.00 2.52
523 584 7.417570 CGGAGGGAGTAGTAATGTAAATGTTCT 60.418 40.741 0.00 0.00 0.00 3.01
524 585 6.700520 CGGAGGGAGTAGTAATGTAAATGTTC 59.299 42.308 0.00 0.00 0.00 3.18
525 586 6.155737 ACGGAGGGAGTAGTAATGTAAATGTT 59.844 38.462 0.00 0.00 0.00 2.71
526 587 5.659971 ACGGAGGGAGTAGTAATGTAAATGT 59.340 40.000 0.00 0.00 0.00 2.71
527 588 6.040616 AGACGGAGGGAGTAGTAATGTAAATG 59.959 42.308 0.00 0.00 0.00 2.32
528 589 6.134754 AGACGGAGGGAGTAGTAATGTAAAT 58.865 40.000 0.00 0.00 0.00 1.40
529 590 5.513233 AGACGGAGGGAGTAGTAATGTAAA 58.487 41.667 0.00 0.00 0.00 2.01
530 591 5.121380 AGACGGAGGGAGTAGTAATGTAA 57.879 43.478 0.00 0.00 0.00 2.41
531 592 4.164796 TGAGACGGAGGGAGTAGTAATGTA 59.835 45.833 0.00 0.00 0.00 2.29
532 593 3.053842 TGAGACGGAGGGAGTAGTAATGT 60.054 47.826 0.00 0.00 0.00 2.71
533 594 3.552875 TGAGACGGAGGGAGTAGTAATG 58.447 50.000 0.00 0.00 0.00 1.90
534 595 3.947612 TGAGACGGAGGGAGTAGTAAT 57.052 47.619 0.00 0.00 0.00 1.89
535 596 3.726557 TTGAGACGGAGGGAGTAGTAA 57.273 47.619 0.00 0.00 0.00 2.24
536 597 3.726557 TTTGAGACGGAGGGAGTAGTA 57.273 47.619 0.00 0.00 0.00 1.82
537 598 2.599408 TTTGAGACGGAGGGAGTAGT 57.401 50.000 0.00 0.00 0.00 2.73
538 599 4.888239 TCTATTTTGAGACGGAGGGAGTAG 59.112 45.833 0.00 0.00 0.00 2.57
539 600 4.863548 TCTATTTTGAGACGGAGGGAGTA 58.136 43.478 0.00 0.00 0.00 2.59
540 601 3.709587 TCTATTTTGAGACGGAGGGAGT 58.290 45.455 0.00 0.00 0.00 3.85
541 602 4.342378 TCATCTATTTTGAGACGGAGGGAG 59.658 45.833 0.00 0.00 0.00 4.30
542 603 4.099573 GTCATCTATTTTGAGACGGAGGGA 59.900 45.833 0.00 0.00 0.00 4.20
543 604 4.100189 AGTCATCTATTTTGAGACGGAGGG 59.900 45.833 0.00 0.00 34.56 4.30
544 605 5.163509 TGAGTCATCTATTTTGAGACGGAGG 60.164 44.000 0.00 0.00 34.56 4.30
545 606 5.895928 TGAGTCATCTATTTTGAGACGGAG 58.104 41.667 0.00 0.00 34.56 4.63
546 607 5.914898 TGAGTCATCTATTTTGAGACGGA 57.085 39.130 0.00 0.00 34.56 4.69
547 608 6.102663 AGTTGAGTCATCTATTTTGAGACGG 58.897 40.000 1.70 0.00 34.56 4.79
548 609 7.588143 AAGTTGAGTCATCTATTTTGAGACG 57.412 36.000 4.14 0.00 34.56 4.18
600 661 8.563732 CCGTTTCAAAATAAATGACCCAATTTT 58.436 29.630 0.00 0.00 33.07 1.82
601 662 7.934120 TCCGTTTCAAAATAAATGACCCAATTT 59.066 29.630 0.00 0.00 34.24 1.82
602 663 7.445945 TCCGTTTCAAAATAAATGACCCAATT 58.554 30.769 0.00 0.00 0.00 2.32
603 664 6.998802 TCCGTTTCAAAATAAATGACCCAAT 58.001 32.000 0.00 0.00 0.00 3.16
604 665 6.406692 TCCGTTTCAAAATAAATGACCCAA 57.593 33.333 0.00 0.00 0.00 4.12
605 666 5.047660 CCTCCGTTTCAAAATAAATGACCCA 60.048 40.000 0.00 0.00 0.00 4.51
606 667 5.407502 CCTCCGTTTCAAAATAAATGACCC 58.592 41.667 0.00 0.00 0.00 4.46
607 668 5.184287 TCCCTCCGTTTCAAAATAAATGACC 59.816 40.000 0.00 0.00 0.00 4.02
608 669 6.150474 TCTCCCTCCGTTTCAAAATAAATGAC 59.850 38.462 0.00 0.00 0.00 3.06
609 670 6.242396 TCTCCCTCCGTTTCAAAATAAATGA 58.758 36.000 0.00 0.00 0.00 2.57
610 671 6.509418 TCTCCCTCCGTTTCAAAATAAATG 57.491 37.500 0.00 0.00 0.00 2.32
611 672 6.719829 AGTTCTCCCTCCGTTTCAAAATAAAT 59.280 34.615 0.00 0.00 0.00 1.40
612 673 6.066032 AGTTCTCCCTCCGTTTCAAAATAAA 58.934 36.000 0.00 0.00 0.00 1.40
613 674 5.627135 AGTTCTCCCTCCGTTTCAAAATAA 58.373 37.500 0.00 0.00 0.00 1.40
614 675 5.237236 AGTTCTCCCTCCGTTTCAAAATA 57.763 39.130 0.00 0.00 0.00 1.40
615 676 4.100279 AGTTCTCCCTCCGTTTCAAAAT 57.900 40.909 0.00 0.00 0.00 1.82
616 677 3.570912 AGTTCTCCCTCCGTTTCAAAA 57.429 42.857 0.00 0.00 0.00 2.44
617 678 3.570912 AAGTTCTCCCTCCGTTTCAAA 57.429 42.857 0.00 0.00 0.00 2.69
618 679 3.388676 TGTAAGTTCTCCCTCCGTTTCAA 59.611 43.478 0.00 0.00 0.00 2.69
619 680 2.967201 TGTAAGTTCTCCCTCCGTTTCA 59.033 45.455 0.00 0.00 0.00 2.69
620 681 3.672767 TGTAAGTTCTCCCTCCGTTTC 57.327 47.619 0.00 0.00 0.00 2.78
621 682 4.635699 AATGTAAGTTCTCCCTCCGTTT 57.364 40.909 0.00 0.00 0.00 3.60
622 683 4.635699 AAATGTAAGTTCTCCCTCCGTT 57.364 40.909 0.00 0.00 0.00 4.44
623 684 4.635699 AAAATGTAAGTTCTCCCTCCGT 57.364 40.909 0.00 0.00 0.00 4.69
624 685 5.064834 GCTAAAAATGTAAGTTCTCCCTCCG 59.935 44.000 0.00 0.00 0.00 4.63
625 686 6.181190 AGCTAAAAATGTAAGTTCTCCCTCC 58.819 40.000 0.00 0.00 0.00 4.30
626 687 8.788325 TTAGCTAAAAATGTAAGTTCTCCCTC 57.212 34.615 2.97 0.00 0.00 4.30
627 688 9.011095 GTTTAGCTAAAAATGTAAGTTCTCCCT 57.989 33.333 20.22 0.00 0.00 4.20
628 689 8.242053 GGTTTAGCTAAAAATGTAAGTTCTCCC 58.758 37.037 20.22 8.45 0.00 4.30
629 690 9.011095 AGGTTTAGCTAAAAATGTAAGTTCTCC 57.989 33.333 20.22 11.97 0.00 3.71
630 691 9.827411 CAGGTTTAGCTAAAAATGTAAGTTCTC 57.173 33.333 20.22 3.61 0.00 2.87
631 692 8.297426 GCAGGTTTAGCTAAAAATGTAAGTTCT 58.703 33.333 20.22 3.63 0.00 3.01
632 693 8.079809 TGCAGGTTTAGCTAAAAATGTAAGTTC 58.920 33.333 20.22 8.59 0.00 3.01
633 694 7.947282 TGCAGGTTTAGCTAAAAATGTAAGTT 58.053 30.769 20.22 0.00 0.00 2.66
634 695 7.519032 TGCAGGTTTAGCTAAAAATGTAAGT 57.481 32.000 20.22 0.00 0.00 2.24
635 696 8.986477 AATGCAGGTTTAGCTAAAAATGTAAG 57.014 30.769 20.22 7.80 0.00 2.34
636 697 9.849166 GTAATGCAGGTTTAGCTAAAAATGTAA 57.151 29.630 20.22 13.60 0.00 2.41
637 698 9.238368 AGTAATGCAGGTTTAGCTAAAAATGTA 57.762 29.630 20.22 19.18 0.00 2.29
638 699 8.122472 AGTAATGCAGGTTTAGCTAAAAATGT 57.878 30.769 20.22 8.93 0.00 2.71
639 700 8.863049 CAAGTAATGCAGGTTTAGCTAAAAATG 58.137 33.333 20.22 20.17 0.00 2.32
640 701 8.802267 TCAAGTAATGCAGGTTTAGCTAAAAAT 58.198 29.630 20.22 9.29 0.00 1.82
641 702 8.172352 TCAAGTAATGCAGGTTTAGCTAAAAA 57.828 30.769 20.22 0.00 0.00 1.94
642 703 7.663905 TCTCAAGTAATGCAGGTTTAGCTAAAA 59.336 33.333 20.22 5.27 0.00 1.52
643 704 7.165485 TCTCAAGTAATGCAGGTTTAGCTAAA 58.835 34.615 14.96 14.96 0.00 1.85
644 705 6.707290 TCTCAAGTAATGCAGGTTTAGCTAA 58.293 36.000 0.86 0.86 0.00 3.09
645 706 6.294361 TCTCAAGTAATGCAGGTTTAGCTA 57.706 37.500 0.00 0.00 0.00 3.32
646 707 5.165961 TCTCAAGTAATGCAGGTTTAGCT 57.834 39.130 0.00 0.00 0.00 3.32
647 708 5.220931 CCATCTCAAGTAATGCAGGTTTAGC 60.221 44.000 0.00 0.00 0.00 3.09
648 709 5.882557 ACCATCTCAAGTAATGCAGGTTTAG 59.117 40.000 0.00 0.00 0.00 1.85
649 710 5.815581 ACCATCTCAAGTAATGCAGGTTTA 58.184 37.500 0.00 0.00 0.00 2.01
650 711 4.666512 ACCATCTCAAGTAATGCAGGTTT 58.333 39.130 0.00 0.00 0.00 3.27
651 712 4.263462 TGACCATCTCAAGTAATGCAGGTT 60.263 41.667 0.00 0.00 0.00 3.50
652 713 3.264193 TGACCATCTCAAGTAATGCAGGT 59.736 43.478 0.00 0.00 0.00 4.00
653 714 3.624861 GTGACCATCTCAAGTAATGCAGG 59.375 47.826 0.00 0.00 0.00 4.85
654 715 4.256110 TGTGACCATCTCAAGTAATGCAG 58.744 43.478 0.00 0.00 0.00 4.41
655 716 4.020307 TCTGTGACCATCTCAAGTAATGCA 60.020 41.667 0.00 0.00 0.00 3.96
656 717 4.507710 TCTGTGACCATCTCAAGTAATGC 58.492 43.478 0.00 0.00 0.00 3.56
657 718 5.526479 CCATCTGTGACCATCTCAAGTAATG 59.474 44.000 0.00 0.00 0.00 1.90
658 719 5.678583 CCATCTGTGACCATCTCAAGTAAT 58.321 41.667 0.00 0.00 0.00 1.89
659 720 4.623886 GCCATCTGTGACCATCTCAAGTAA 60.624 45.833 0.00 0.00 0.00 2.24
660 721 3.118629 GCCATCTGTGACCATCTCAAGTA 60.119 47.826 0.00 0.00 0.00 2.24
661 722 2.355513 GCCATCTGTGACCATCTCAAGT 60.356 50.000 0.00 0.00 0.00 3.16
662 723 2.286872 GCCATCTGTGACCATCTCAAG 58.713 52.381 0.00 0.00 0.00 3.02
663 724 1.629861 TGCCATCTGTGACCATCTCAA 59.370 47.619 0.00 0.00 0.00 3.02
664 725 1.278537 TGCCATCTGTGACCATCTCA 58.721 50.000 0.00 0.00 0.00 3.27
665 726 2.219458 CATGCCATCTGTGACCATCTC 58.781 52.381 0.00 0.00 0.00 2.75
666 727 1.562942 ACATGCCATCTGTGACCATCT 59.437 47.619 0.00 0.00 0.00 2.90
667 728 2.048444 ACATGCCATCTGTGACCATC 57.952 50.000 0.00 0.00 0.00 3.51
668 729 2.097036 CAACATGCCATCTGTGACCAT 58.903 47.619 0.00 0.00 0.00 3.55
669 730 1.536940 CAACATGCCATCTGTGACCA 58.463 50.000 0.00 0.00 0.00 4.02
670 731 0.171903 GCAACATGCCATCTGTGACC 59.828 55.000 0.00 0.00 37.42 4.02
671 732 3.708195 GCAACATGCCATCTGTGAC 57.292 52.632 0.00 0.00 37.42 3.67
681 742 3.221964 AGATCGAAAAAGGCAACATGC 57.778 42.857 0.00 0.00 44.08 4.06
682 743 5.801350 TCTAGATCGAAAAAGGCAACATG 57.199 39.130 0.00 0.00 41.41 3.21
683 744 8.506168 TTTATCTAGATCGAAAAAGGCAACAT 57.494 30.769 8.95 0.00 41.41 2.71
684 745 7.822334 TCTTTATCTAGATCGAAAAAGGCAACA 59.178 33.333 18.95 4.07 41.41 3.33
685 746 8.197988 TCTTTATCTAGATCGAAAAAGGCAAC 57.802 34.615 18.95 0.00 0.00 4.17
686 747 8.786826 TTCTTTATCTAGATCGAAAAAGGCAA 57.213 30.769 18.95 9.32 0.00 4.52
687 748 8.964476 ATTCTTTATCTAGATCGAAAAAGGCA 57.036 30.769 18.95 10.89 0.00 4.75
707 768 9.525826 CATAGCCTCCATCCTATTTTTATTCTT 57.474 33.333 0.00 0.00 0.00 2.52
708 769 8.673251 ACATAGCCTCCATCCTATTTTTATTCT 58.327 33.333 0.00 0.00 0.00 2.40
709 770 8.870075 ACATAGCCTCCATCCTATTTTTATTC 57.130 34.615 0.00 0.00 0.00 1.75
712 773 9.739276 CATTACATAGCCTCCATCCTATTTTTA 57.261 33.333 0.00 0.00 0.00 1.52
713 774 7.177392 GCATTACATAGCCTCCATCCTATTTTT 59.823 37.037 0.00 0.00 0.00 1.94
714 775 6.660949 GCATTACATAGCCTCCATCCTATTTT 59.339 38.462 0.00 0.00 0.00 1.82
715 776 6.183347 GCATTACATAGCCTCCATCCTATTT 58.817 40.000 0.00 0.00 0.00 1.40
716 777 5.251468 TGCATTACATAGCCTCCATCCTATT 59.749 40.000 0.00 0.00 0.00 1.73
717 778 4.784838 TGCATTACATAGCCTCCATCCTAT 59.215 41.667 0.00 0.00 0.00 2.57
718 779 4.167319 TGCATTACATAGCCTCCATCCTA 58.833 43.478 0.00 0.00 0.00 2.94
719 780 2.981784 TGCATTACATAGCCTCCATCCT 59.018 45.455 0.00 0.00 0.00 3.24
720 781 3.423539 TGCATTACATAGCCTCCATCC 57.576 47.619 0.00 0.00 0.00 3.51
721 782 4.392940 AGTTGCATTACATAGCCTCCATC 58.607 43.478 0.00 0.00 0.00 3.51
722 783 4.443978 AGTTGCATTACATAGCCTCCAT 57.556 40.909 0.00 0.00 0.00 3.41
723 784 3.931907 AGTTGCATTACATAGCCTCCA 57.068 42.857 0.00 0.00 0.00 3.86
724 785 4.962155 ACTAGTTGCATTACATAGCCTCC 58.038 43.478 0.00 0.00 0.00 4.30
725 786 4.991687 GGACTAGTTGCATTACATAGCCTC 59.008 45.833 0.00 0.00 0.00 4.70
726 787 4.202367 GGGACTAGTTGCATTACATAGCCT 60.202 45.833 0.00 0.00 0.00 4.58
727 788 4.065789 GGGACTAGTTGCATTACATAGCC 58.934 47.826 0.00 0.00 0.00 3.93
728 789 4.065789 GGGGACTAGTTGCATTACATAGC 58.934 47.826 0.00 0.00 0.00 2.97
729 790 5.057149 GTGGGGACTAGTTGCATTACATAG 58.943 45.833 0.00 0.00 0.00 2.23
730 791 4.471747 TGTGGGGACTAGTTGCATTACATA 59.528 41.667 0.00 0.00 0.00 2.29
731 792 3.265737 TGTGGGGACTAGTTGCATTACAT 59.734 43.478 0.00 0.00 0.00 2.29
732 793 2.640332 TGTGGGGACTAGTTGCATTACA 59.360 45.455 0.00 0.00 0.00 2.41
733 794 3.343941 TGTGGGGACTAGTTGCATTAC 57.656 47.619 0.00 0.00 0.00 1.89
734 795 3.265737 ACATGTGGGGACTAGTTGCATTA 59.734 43.478 0.00 0.00 0.00 1.90
735 796 2.041620 ACATGTGGGGACTAGTTGCATT 59.958 45.455 0.00 0.00 0.00 3.56
736 797 1.635487 ACATGTGGGGACTAGTTGCAT 59.365 47.619 0.00 0.00 0.00 3.96
737 798 1.064003 ACATGTGGGGACTAGTTGCA 58.936 50.000 0.00 0.00 0.00 4.08
738 799 1.453155 CACATGTGGGGACTAGTTGC 58.547 55.000 18.51 0.00 0.00 4.17
739 800 2.113860 CCACATGTGGGGACTAGTTG 57.886 55.000 33.56 6.98 46.81 3.16
881 947 2.281484 GGCCGCCAGTTTGACAGA 60.281 61.111 3.91 0.00 0.00 3.41
936 1002 8.339714 GCCAAAGCATAAATAAATACTCGTACA 58.660 33.333 0.00 0.00 39.53 2.90
937 1003 7.529519 CGCCAAAGCATAAATAAATACTCGTAC 59.470 37.037 0.00 0.00 39.83 3.67
1107 1205 3.490851 GGGGTGTGGCCTCTGTTA 58.509 61.111 3.32 0.00 33.93 2.41
1270 1377 1.811266 CCCCGTTGCAGTCGATCTG 60.811 63.158 13.49 9.73 46.12 2.90
1314 1421 1.136774 CTCGACGGTGCGATCAGAA 59.863 57.895 0.00 0.00 39.85 3.02
1860 2570 1.817209 GAAGTAGCGACCAGGGAGG 59.183 63.158 0.00 0.00 45.67 4.30
1866 2576 1.373748 GTTGCCGAAGTAGCGACCA 60.374 57.895 0.00 0.00 38.48 4.02
1929 2710 3.532155 GAGGCCAGCGTCTCCGAT 61.532 66.667 5.01 0.00 35.63 4.18
1995 2784 2.203640 TCCACAGCCGACCTCAGT 60.204 61.111 0.00 0.00 0.00 3.41
2226 3024 2.498941 CGCCGCCTCCAAGGAGATA 61.499 63.158 17.57 0.00 44.53 1.98
2305 3103 5.728637 TGAATATATGATCACAGCCTCGT 57.271 39.130 0.00 0.00 0.00 4.18
2330 3128 5.809719 TGATTTAATCACGTGCAAGCATA 57.190 34.783 11.67 0.00 33.59 3.14
2363 3161 4.025730 GCATGCTAGAATGAAATCGACGAA 60.026 41.667 15.48 0.00 0.00 3.85
2366 3164 3.363378 CCGCATGCTAGAATGAAATCGAC 60.363 47.826 15.48 0.00 0.00 4.20
2405 3203 9.821662 CATACGACAAGTAATATGTATCGAAGA 57.178 33.333 0.00 0.00 39.24 2.87
2406 3204 9.608617 ACATACGACAAGTAATATGTATCGAAG 57.391 33.333 0.00 0.00 36.68 3.79
2413 3211 6.861572 CGATCCACATACGACAAGTAATATGT 59.138 38.462 0.00 4.02 38.49 2.29
2431 3241 5.069501 ACAAAACTACTACTCCGATCCAC 57.930 43.478 0.00 0.00 0.00 4.02
2433 3243 5.105837 ACAGACAAAACTACTACTCCGATCC 60.106 44.000 0.00 0.00 0.00 3.36
2437 3247 6.257193 ACAAAACAGACAAAACTACTACTCCG 59.743 38.462 0.00 0.00 0.00 4.63
2439 3249 9.486857 GAAACAAAACAGACAAAACTACTACTC 57.513 33.333 0.00 0.00 0.00 2.59
2447 3257 8.921670 ACACTTATGAAACAAAACAGACAAAAC 58.078 29.630 0.00 0.00 0.00 2.43
2478 3288 6.014070 TGGTTTACTAAGCTGACCACTTGATA 60.014 38.462 0.00 0.00 35.58 2.15
2480 3290 4.101898 TGGTTTACTAAGCTGACCACTTGA 59.898 41.667 0.00 0.00 35.58 3.02
2486 3299 5.001232 TGTTGATGGTTTACTAAGCTGACC 58.999 41.667 0.00 0.00 32.98 4.02
2517 3330 8.556213 TGTAGTCTTGTACACTTTCTTTTTGT 57.444 30.769 0.00 0.00 0.00 2.83
2524 3337 6.514063 AGGACTTGTAGTCTTGTACACTTTC 58.486 40.000 0.00 0.00 44.46 2.62
2525 3338 6.481434 AGGACTTGTAGTCTTGTACACTTT 57.519 37.500 0.00 0.00 44.46 2.66
2573 3386 8.645110 ACTAAGTACTACATCTCCTCTCTCTAC 58.355 40.741 0.00 0.00 0.00 2.59
2700 3513 0.178944 TCTCCTGTTCCCTCCGACAA 60.179 55.000 0.00 0.00 0.00 3.18
2714 3527 4.586421 TGCAAGATCTGACGATTATCTCCT 59.414 41.667 0.00 0.00 0.00 3.69
2797 3610 4.500375 CCCAACAAGCAAGGAGAGAAAAAG 60.500 45.833 0.00 0.00 0.00 2.27
2802 3615 0.250901 GCCCAACAAGCAAGGAGAGA 60.251 55.000 0.00 0.00 0.00 3.10
2807 3620 1.368579 CCAAGCCCAACAAGCAAGG 59.631 57.895 0.00 0.00 0.00 3.61
2808 3621 0.032540 GACCAAGCCCAACAAGCAAG 59.967 55.000 0.00 0.00 0.00 4.01
2819 3646 2.029290 TCTCGTTGTAGAAGACCAAGCC 60.029 50.000 0.00 0.00 0.00 4.35
2832 3659 2.309528 TGCAACAAGACTCTCGTTGT 57.690 45.000 10.82 0.00 41.60 3.32
2928 3755 3.130340 GGACCTCTGTTGCAAAAGTTTCA 59.870 43.478 16.28 0.74 0.00 2.69
2929 3756 3.381590 AGGACCTCTGTTGCAAAAGTTTC 59.618 43.478 16.28 10.55 0.00 2.78
2982 3810 2.819595 CACCATCCCTTCACGCCG 60.820 66.667 0.00 0.00 0.00 6.46
3043 3871 2.864471 AACACCCACCTCGTCCGTC 61.864 63.158 0.00 0.00 0.00 4.79
3056 3884 2.774799 GCCATCCGATGCCAACACC 61.775 63.158 2.53 0.00 0.00 4.16
3078 3906 0.806868 ATGCACCTGAAACATGAGCG 59.193 50.000 0.00 0.00 0.00 5.03
3079 3907 1.202110 CGATGCACCTGAAACATGAGC 60.202 52.381 0.00 0.00 0.00 4.26
3093 3921 1.810853 CACGATGACAGGCGATGCA 60.811 57.895 7.40 0.00 0.00 3.96
3096 3924 1.153568 CACCACGATGACAGGCGAT 60.154 57.895 7.40 0.00 0.00 4.58
3103 3931 3.118454 CGGCACCACCACGATGAC 61.118 66.667 0.00 0.00 39.03 3.06
3124 3952 1.963338 GCCCGAGCACCTATGATGC 60.963 63.158 0.00 0.00 43.74 3.91
3154 3982 0.034186 TTGTGATCTGTCCCATGGCC 60.034 55.000 6.09 0.00 0.00 5.36
3173 4001 4.845580 CGCTCTCGGGCCATTGCT 62.846 66.667 4.39 0.00 37.74 3.91
3244 4072 1.480954 ACTCAAGATAACGGCGGTGAT 59.519 47.619 8.19 0.00 0.00 3.06
3254 4082 2.027192 GTCCAGCCACCACTCAAGATAA 60.027 50.000 0.00 0.00 0.00 1.75
3259 4087 0.179020 CAAGTCCAGCCACCACTCAA 60.179 55.000 0.00 0.00 0.00 3.02
3260 4088 1.451504 CAAGTCCAGCCACCACTCA 59.548 57.895 0.00 0.00 0.00 3.41
3278 4106 1.439679 CAAGTGTTAGCGGACTTCCC 58.560 55.000 0.00 0.00 29.73 3.97


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

AutoCloner maintained by Alex Coulton.