Multiple sequence alignment - TraesCS4B01G123400

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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 TraesCS4B01G123400 chr4B 100.000 2735 0 0 1 2735 147067890 147065156 0.000000e+00 5051.0
1 TraesCS4B01G123400 chr4B 91.753 97 7 1 1 97 667265468 667265563 1.710000e-27 134.0
2 TraesCS4B01G123400 chr4B 91.489 94 7 1 1 94 667287899 667287991 7.950000e-26 128.0
3 TraesCS4B01G123400 chr4D 93.873 1730 71 17 853 2579 102534577 102532880 0.000000e+00 2575.0
4 TraesCS4B01G123400 chr4D 95.862 145 4 2 645 788 102535095 102534952 1.640000e-57 233.0
5 TraesCS4B01G123400 chr4D 87.192 203 20 4 87 285 102535615 102535415 2.740000e-55 226.0
6 TraesCS4B01G123400 chr4A 94.642 1325 61 6 877 2200 472398447 472399762 0.000000e+00 2045.0
7 TraesCS4B01G123400 chr4A 85.117 383 29 9 2198 2577 472400052 472400409 1.550000e-97 366.0
8 TraesCS4B01G123400 chr4A 91.339 254 20 2 134 386 472397390 472397642 2.020000e-91 346.0
9 TraesCS4B01G123400 chr4A 96.124 129 4 1 645 773 472397646 472397773 2.760000e-50 209.0
10 TraesCS4B01G123400 chr4A 100.000 58 0 0 766 823 472398125 472398182 1.040000e-19 108.0
11 TraesCS4B01G123400 chr5D 78.814 590 74 31 1110 1675 233689153 233688591 1.560000e-92 350.0
12 TraesCS4B01G123400 chr5D 90.625 96 7 2 1 95 370635394 370635300 2.860000e-25 126.0
13 TraesCS4B01G123400 chr5B 77.797 590 86 26 1107 1675 271182035 271182600 3.400000e-84 322.0
14 TraesCS4B01G123400 chr5A 77.740 593 87 28 1107 1675 321052021 321052592 3.400000e-84 322.0
15 TraesCS4B01G123400 chr7B 85.496 262 36 2 388 648 484891335 484891075 3.470000e-69 272.0
16 TraesCS4B01G123400 chr7B 94.595 37 0 2 2130 2166 721054536 721054570 3.800000e-04 56.5
17 TraesCS4B01G123400 chr3D 85.830 247 34 1 400 645 134818560 134818806 7.510000e-66 261.0
18 TraesCS4B01G123400 chr3D 84.411 263 40 1 387 648 380482276 380482538 9.720000e-65 257.0
19 TraesCS4B01G123400 chr3D 89.691 97 8 2 1 97 68049808 68049902 3.700000e-24 122.0
20 TraesCS4B01G123400 chr7A 85.259 251 35 2 400 649 321124412 321124163 9.720000e-65 257.0
21 TraesCS4B01G123400 chr7A 84.706 255 37 2 396 649 103136386 103136133 1.260000e-63 254.0
22 TraesCS4B01G123400 chr7A 84.921 252 35 2 400 649 598923734 598923984 4.520000e-63 252.0
23 TraesCS4B01G123400 chr3B 84.291 261 39 2 389 648 562755936 562756195 1.260000e-63 254.0
24 TraesCS4B01G123400 chr3A 83.895 267 40 3 384 648 45151466 45151731 4.520000e-63 252.0
25 TraesCS4B01G123400 chr2D 83.895 267 39 4 384 648 368526795 368527059 4.520000e-63 252.0
26 TraesCS4B01G123400 chr2D 88.679 106 8 4 1 104 266899444 266899547 2.860000e-25 126.0
27 TraesCS4B01G123400 chr2D 97.222 36 1 0 2132 2167 574076764 574076729 8.180000e-06 62.1
28 TraesCS4B01G123400 chr1B 96.774 93 3 0 2643 2735 109707990 109708082 3.650000e-34 156.0
29 TraesCS4B01G123400 chr1B 82.759 87 15 0 1118 1204 538165236 538165150 8.120000e-11 78.7
30 TraesCS4B01G123400 chr7D 93.478 92 5 1 3 94 198028763 198028853 4.750000e-28 135.0
31 TraesCS4B01G123400 chr2B 91.579 95 7 1 1 95 239855164 239855071 2.210000e-26 130.0
32 TraesCS4B01G123400 chr2B 91.579 95 7 1 1 95 239856547 239856454 2.210000e-26 130.0
33 TraesCS4B01G123400 chr1A 90.323 93 9 0 2643 2735 20116871 20116779 3.700000e-24 122.0
34 TraesCS4B01G123400 chr1A 82.759 87 15 0 1118 1204 497192686 497192600 8.120000e-11 78.7
35 TraesCS4B01G123400 chr1D 88.119 101 10 2 1 101 386168259 386168161 4.780000e-23 119.0
36 TraesCS4B01G123400 chr1D 82.759 87 15 0 1118 1204 400956447 400956361 8.120000e-11 78.7


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 TraesCS4B01G123400 chr4B 147065156 147067890 2734 True 5051.000000 5051 100.0000 1 2735 1 chr4B.!!$R1 2734
1 TraesCS4B01G123400 chr4D 102532880 102535615 2735 True 1011.333333 2575 92.3090 87 2579 3 chr4D.!!$R1 2492
2 TraesCS4B01G123400 chr4A 472397390 472400409 3019 False 614.800000 2045 93.4444 134 2577 5 chr4A.!!$F1 2443
3 TraesCS4B01G123400 chr5D 233688591 233689153 562 True 350.000000 350 78.8140 1110 1675 1 chr5D.!!$R1 565
4 TraesCS4B01G123400 chr5B 271182035 271182600 565 False 322.000000 322 77.7970 1107 1675 1 chr5B.!!$F1 568
5 TraesCS4B01G123400 chr5A 321052021 321052592 571 False 322.000000 322 77.7400 1107 1675 1 chr5A.!!$F1 568

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
70 71 0.037303 ATTATGATGCAGAGGCCGGG 59.963 55.0 2.18 0.0 40.13 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 2663 0.635555 TTTCCCCATGCCATCCATCA 59.364 50.0 0.0 0.0 29.71 3.07 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
22 23 4.074627 TGATTTTGTGGTACTTCGTGGA 57.925 40.909 0.00 0.00 0.00 4.02
23 24 4.647611 TGATTTTGTGGTACTTCGTGGAT 58.352 39.130 0.00 0.00 0.00 3.41
24 25 5.067273 TGATTTTGTGGTACTTCGTGGATT 58.933 37.500 0.00 0.00 0.00 3.01
25 26 5.180492 TGATTTTGTGGTACTTCGTGGATTC 59.820 40.000 0.00 0.00 0.00 2.52
26 27 4.345859 TTTGTGGTACTTCGTGGATTCT 57.654 40.909 0.00 0.00 0.00 2.40
27 28 4.345859 TTGTGGTACTTCGTGGATTCTT 57.654 40.909 0.00 0.00 0.00 2.52
28 29 4.345859 TGTGGTACTTCGTGGATTCTTT 57.654 40.909 0.00 0.00 0.00 2.52
29 30 4.710324 TGTGGTACTTCGTGGATTCTTTT 58.290 39.130 0.00 0.00 0.00 2.27
30 31 5.856156 TGTGGTACTTCGTGGATTCTTTTA 58.144 37.500 0.00 0.00 0.00 1.52
31 32 6.289834 TGTGGTACTTCGTGGATTCTTTTAA 58.710 36.000 0.00 0.00 0.00 1.52
32 33 6.938030 TGTGGTACTTCGTGGATTCTTTTAAT 59.062 34.615 0.00 0.00 0.00 1.40
33 34 8.095792 TGTGGTACTTCGTGGATTCTTTTAATA 58.904 33.333 0.00 0.00 0.00 0.98
34 35 8.938906 GTGGTACTTCGTGGATTCTTTTAATAA 58.061 33.333 0.00 0.00 0.00 1.40
35 36 9.158233 TGGTACTTCGTGGATTCTTTTAATAAG 57.842 33.333 0.00 0.00 0.00 1.73
36 37 9.374838 GGTACTTCGTGGATTCTTTTAATAAGA 57.625 33.333 0.00 0.00 0.00 2.10
39 40 8.893727 ACTTCGTGGATTCTTTTAATAAGATGG 58.106 33.333 0.00 0.00 0.00 3.51
40 41 8.801882 TTCGTGGATTCTTTTAATAAGATGGT 57.198 30.769 0.00 0.00 0.00 3.55
41 42 8.801882 TCGTGGATTCTTTTAATAAGATGGTT 57.198 30.769 0.00 0.00 0.00 3.67
42 43 8.673711 TCGTGGATTCTTTTAATAAGATGGTTG 58.326 33.333 0.00 0.00 0.00 3.77
43 44 8.458843 CGTGGATTCTTTTAATAAGATGGTTGT 58.541 33.333 0.00 0.00 0.00 3.32
60 61 9.170734 AGATGGTTGTATGTATCATTATGATGC 57.829 33.333 17.09 15.91 37.70 3.91
67 68 4.582869 TGTATCATTATGATGCAGAGGCC 58.417 43.478 19.28 0.00 42.97 5.19
68 69 2.174363 TCATTATGATGCAGAGGCCG 57.826 50.000 0.00 0.00 40.13 6.13
69 70 1.162698 CATTATGATGCAGAGGCCGG 58.837 55.000 0.00 0.00 40.13 6.13
70 71 0.037303 ATTATGATGCAGAGGCCGGG 59.963 55.000 2.18 0.00 40.13 5.73
71 72 2.055689 TTATGATGCAGAGGCCGGGG 62.056 60.000 2.18 0.00 40.13 5.73
74 75 4.815973 ATGCAGAGGCCGGGGGTA 62.816 66.667 2.18 0.00 40.13 3.69
88 89 2.423446 GGGGTACGCCTCCATTTAAA 57.577 50.000 21.18 0.00 34.11 1.52
89 90 2.725637 GGGGTACGCCTCCATTTAAAA 58.274 47.619 21.18 0.00 34.11 1.52
90 91 3.090790 GGGGTACGCCTCCATTTAAAAA 58.909 45.455 21.18 0.00 34.11 1.94
128 129 7.715249 GTCATTATGTAGCTACAATTTCTCCCA 59.285 37.037 29.26 3.21 39.99 4.37
133 134 5.938125 TGTAGCTACAATTTCTCCCAGAAAC 59.062 40.000 24.15 0.00 45.83 2.78
212 216 3.553096 GCGAATCCTATGACCAAGATCGT 60.553 47.826 0.00 0.00 0.00 3.73
220 224 0.382515 GACCAAGATCGTCTCGGGAG 59.617 60.000 0.00 0.00 0.00 4.30
256 260 8.251721 GGGGTACTACATATGTAAGCAATAGAG 58.748 40.741 16.17 6.06 0.00 2.43
273 277 6.090088 GCAATAGAGATTCACTTATAGCACCG 59.910 42.308 0.00 0.00 0.00 4.94
295 492 4.682401 CGCTTTTTAATTTACCCTTTGCGT 59.318 37.500 0.00 0.00 34.89 5.24
304 501 0.981183 ACCCTTTGCGTATCACTGGA 59.019 50.000 0.00 0.00 0.00 3.86
341 539 4.157656 TGTCCTTTGCCGAAATAAATCCAG 59.842 41.667 0.00 0.00 0.00 3.86
394 623 8.172352 GACATTATGTCCTCTACAGTACATCT 57.828 38.462 13.92 0.00 42.70 2.90
395 624 8.540507 ACATTATGTCCTCTACAGTACATCTT 57.459 34.615 0.00 0.00 42.70 2.40
396 625 8.634444 ACATTATGTCCTCTACAGTACATCTTC 58.366 37.037 0.00 0.00 42.70 2.87
397 626 7.584122 TTATGTCCTCTACAGTACATCTTCC 57.416 40.000 0.00 0.00 42.70 3.46
398 627 4.930696 TGTCCTCTACAGTACATCTTCCA 58.069 43.478 0.00 0.00 33.01 3.53
399 628 5.519808 TGTCCTCTACAGTACATCTTCCAT 58.480 41.667 0.00 0.00 33.01 3.41
400 629 5.958380 TGTCCTCTACAGTACATCTTCCATT 59.042 40.000 0.00 0.00 33.01 3.16
401 630 6.440647 TGTCCTCTACAGTACATCTTCCATTT 59.559 38.462 0.00 0.00 33.01 2.32
402 631 7.038302 TGTCCTCTACAGTACATCTTCCATTTT 60.038 37.037 0.00 0.00 33.01 1.82
403 632 7.824779 GTCCTCTACAGTACATCTTCCATTTTT 59.175 37.037 0.00 0.00 0.00 1.94
404 633 9.042450 TCCTCTACAGTACATCTTCCATTTTTA 57.958 33.333 0.00 0.00 0.00 1.52
405 634 9.838339 CCTCTACAGTACATCTTCCATTTTTAT 57.162 33.333 0.00 0.00 0.00 1.40
413 642 9.931210 GTACATCTTCCATTTTTATTTACTCCG 57.069 33.333 0.00 0.00 0.00 4.63
414 643 7.480810 ACATCTTCCATTTTTATTTACTCCGC 58.519 34.615 0.00 0.00 0.00 5.54
415 644 7.122055 ACATCTTCCATTTTTATTTACTCCGCA 59.878 33.333 0.00 0.00 0.00 5.69
416 645 7.639113 TCTTCCATTTTTATTTACTCCGCAT 57.361 32.000 0.00 0.00 0.00 4.73
417 646 8.740123 TCTTCCATTTTTATTTACTCCGCATA 57.260 30.769 0.00 0.00 0.00 3.14
418 647 9.349713 TCTTCCATTTTTATTTACTCCGCATAT 57.650 29.630 0.00 0.00 0.00 1.78
419 648 9.965824 CTTCCATTTTTATTTACTCCGCATATT 57.034 29.630 0.00 0.00 0.00 1.28
428 657 7.875327 ATTTACTCCGCATATTAACTTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
429 658 6.913873 TTACTCCGCATATTAACTTTGGTC 57.086 37.500 0.00 0.00 0.00 4.02
430 659 4.839121 ACTCCGCATATTAACTTTGGTCA 58.161 39.130 0.00 0.00 0.00 4.02
431 660 5.250200 ACTCCGCATATTAACTTTGGTCAA 58.750 37.500 0.00 0.00 0.00 3.18
432 661 5.708230 ACTCCGCATATTAACTTTGGTCAAA 59.292 36.000 0.00 0.00 0.00 2.69
433 662 6.207810 ACTCCGCATATTAACTTTGGTCAAAA 59.792 34.615 0.00 0.00 0.00 2.44
434 663 7.093945 ACTCCGCATATTAACTTTGGTCAAAAT 60.094 33.333 0.00 0.00 0.00 1.82
435 664 7.607250 TCCGCATATTAACTTTGGTCAAAATT 58.393 30.769 0.00 0.00 0.00 1.82
436 665 8.740906 TCCGCATATTAACTTTGGTCAAAATTA 58.259 29.630 0.00 0.00 0.00 1.40
437 666 9.360093 CCGCATATTAACTTTGGTCAAAATTAA 57.640 29.630 10.93 10.93 36.72 1.40
446 675 9.508642 AACTTTGGTCAAAATTAAACTTCCAAA 57.491 25.926 0.00 0.00 40.04 3.28
447 676 9.508642 ACTTTGGTCAAAATTAAACTTCCAAAA 57.491 25.926 0.00 0.00 41.15 2.44
448 677 9.767684 CTTTGGTCAAAATTAAACTTCCAAAAC 57.232 29.630 0.00 0.00 41.15 2.43
449 678 9.508642 TTTGGTCAAAATTAAACTTCCAAAACT 57.491 25.926 0.00 0.00 39.60 2.66
450 679 9.508642 TTGGTCAAAATTAAACTTCCAAAACTT 57.491 25.926 0.00 0.00 32.01 2.66
451 680 9.508642 TGGTCAAAATTAAACTTCCAAAACTTT 57.491 25.926 0.00 0.00 0.00 2.66
452 681 9.767684 GGTCAAAATTAAACTTCCAAAACTTTG 57.232 29.630 0.00 0.00 37.90 2.77
526 755 8.743085 ACATCAGATTCACTATTAAATGTGCT 57.257 30.769 6.39 0.00 34.49 4.40
527 756 9.182214 ACATCAGATTCACTATTAAATGTGCTT 57.818 29.630 6.39 0.00 34.49 3.91
530 759 9.230122 TCAGATTCACTATTAAATGTGCTTTCA 57.770 29.630 6.39 0.00 34.49 2.69
531 760 9.282247 CAGATTCACTATTAAATGTGCTTTCAC 57.718 33.333 6.39 0.00 43.40 3.18
621 850 9.965824 AGTTTGATTTCAGTTAAACCTAATGTG 57.034 29.630 0.00 0.00 34.46 3.21
622 851 9.744468 GTTTGATTTCAGTTAAACCTAATGTGT 57.256 29.630 0.00 0.00 0.00 3.72
643 872 8.842358 TGTGTAGAGTAAATAAAAACAGAGGG 57.158 34.615 0.00 0.00 0.00 4.30
656 885 4.946478 AACAGAGGGAGTATATGCTGAC 57.054 45.455 0.00 0.00 0.00 3.51
674 903 2.548057 TGACTCGTGCAACTTTTCCATC 59.452 45.455 0.00 0.00 31.75 3.51
827 1416 4.498520 CGCGCCCTCATCAGTCGT 62.499 66.667 0.00 0.00 0.00 4.34
828 1417 2.583593 GCGCCCTCATCAGTCGTC 60.584 66.667 0.00 0.00 0.00 4.20
829 1418 2.885113 CGCCCTCATCAGTCGTCA 59.115 61.111 0.00 0.00 0.00 4.35
830 1419 1.517257 CGCCCTCATCAGTCGTCAC 60.517 63.158 0.00 0.00 0.00 3.67
831 1420 1.517257 GCCCTCATCAGTCGTCACG 60.517 63.158 0.00 0.00 0.00 4.35
832 1421 1.883732 CCCTCATCAGTCGTCACGT 59.116 57.895 0.00 0.00 0.00 4.49
833 1422 0.179161 CCCTCATCAGTCGTCACGTC 60.179 60.000 0.00 0.00 0.00 4.34
834 1423 0.521735 CCTCATCAGTCGTCACGTCA 59.478 55.000 0.00 0.00 0.00 4.35
835 1424 1.133216 CCTCATCAGTCGTCACGTCAT 59.867 52.381 0.00 0.00 0.00 3.06
836 1425 2.416027 CCTCATCAGTCGTCACGTCATT 60.416 50.000 0.00 0.00 0.00 2.57
837 1426 3.245797 CTCATCAGTCGTCACGTCATTT 58.754 45.455 0.00 0.00 0.00 2.32
838 1427 3.242518 TCATCAGTCGTCACGTCATTTC 58.757 45.455 0.00 0.00 0.00 2.17
839 1428 3.057526 TCATCAGTCGTCACGTCATTTCT 60.058 43.478 0.00 0.00 0.00 2.52
840 1429 2.929960 TCAGTCGTCACGTCATTTCTC 58.070 47.619 0.00 0.00 0.00 2.87
841 1430 2.292292 TCAGTCGTCACGTCATTTCTCA 59.708 45.455 0.00 0.00 0.00 3.27
842 1431 2.405357 CAGTCGTCACGTCATTTCTCAC 59.595 50.000 0.00 0.00 0.00 3.51
843 1432 1.719780 GTCGTCACGTCATTTCTCACC 59.280 52.381 0.00 0.00 0.00 4.02
844 1433 1.068474 CGTCACGTCATTTCTCACCC 58.932 55.000 0.00 0.00 0.00 4.61
845 1434 1.439679 GTCACGTCATTTCTCACCCC 58.560 55.000 0.00 0.00 0.00 4.95
846 1435 0.323629 TCACGTCATTTCTCACCCCC 59.676 55.000 0.00 0.00 0.00 5.40
847 1436 0.324943 CACGTCATTTCTCACCCCCT 59.675 55.000 0.00 0.00 0.00 4.79
848 1437 0.613777 ACGTCATTTCTCACCCCCTC 59.386 55.000 0.00 0.00 0.00 4.30
849 1438 0.613260 CGTCATTTCTCACCCCCTCA 59.387 55.000 0.00 0.00 0.00 3.86
850 1439 1.676014 CGTCATTTCTCACCCCCTCAC 60.676 57.143 0.00 0.00 0.00 3.51
851 1440 0.991920 TCATTTCTCACCCCCTCACC 59.008 55.000 0.00 0.00 0.00 4.02
862 1761 1.350019 CCCCCTCACCCGTATAAATCC 59.650 57.143 0.00 0.00 0.00 3.01
864 1763 2.335933 CCCTCACCCGTATAAATCCCT 58.664 52.381 0.00 0.00 0.00 4.20
870 1769 1.668047 CCCGTATAAATCCCTCGCGTC 60.668 57.143 5.77 0.00 0.00 5.19
940 1839 4.504916 CGTCTCCCGCAGCTCAGG 62.505 72.222 0.00 0.00 0.00 3.86
1374 2285 4.560856 CCGAAGCCGCTCCTCTCG 62.561 72.222 5.40 5.40 0.00 4.04
1737 2663 2.166664 GAGGAGCTGGTCGATGTAGTTT 59.833 50.000 0.00 0.00 0.00 2.66
1779 2705 0.482446 TTGAGGGCCCACTTGTCATT 59.518 50.000 27.56 0.00 0.00 2.57
1812 2738 2.258013 CCGCGCACAAGGGAAGAAA 61.258 57.895 8.75 0.00 0.00 2.52
1893 2820 5.143376 AGAAAAATGAATCTTGCACAGGG 57.857 39.130 0.00 0.00 0.00 4.45
1910 2837 4.878397 CACAGGGAATTAGGATCACAAGAC 59.122 45.833 0.00 0.00 0.00 3.01
1983 2910 1.482182 TCATGATCAGGAGGGTCAACG 59.518 52.381 5.84 0.00 0.00 4.10
1989 2916 1.286849 TCAGGAGGGTCAACGAGGATA 59.713 52.381 0.00 0.00 0.00 2.59
2038 2965 9.485206 AAGTTGATGATTTAGTTTGTACTACGT 57.515 29.630 0.00 0.00 36.61 3.57
2041 2968 9.911138 TTGATGATTTAGTTTGTACTACGTACA 57.089 29.630 2.93 2.93 45.63 2.90
2044 2971 9.865321 ATGATTTAGTTTGTACTACGTACATGT 57.135 29.630 2.69 2.69 46.36 3.21
2138 3066 9.094578 TCCAGAAATTCTTATATCTCTCCGATT 57.905 33.333 0.00 0.00 33.48 3.34
2204 3424 8.758633 TTTCTTCGAGAAGTTCAGGTATAAAG 57.241 34.615 12.01 0.00 35.37 1.85
2210 3430 6.147164 CGAGAAGTTCAGGTATAAAGTTTGCA 59.853 38.462 5.50 0.00 0.00 4.08
2294 3514 7.004086 AGTGAGGTCAAATTAATGAGAAACCA 58.996 34.615 0.00 0.00 0.00 3.67
2297 3517 7.669304 TGAGGTCAAATTAATGAGAAACCATGA 59.331 33.333 0.00 0.00 0.00 3.07
2298 3518 8.421249 AGGTCAAATTAATGAGAAACCATGAA 57.579 30.769 0.00 0.00 0.00 2.57
2299 3519 8.306761 AGGTCAAATTAATGAGAAACCATGAAC 58.693 33.333 0.00 0.00 0.00 3.18
2300 3520 7.545615 GGTCAAATTAATGAGAAACCATGAACC 59.454 37.037 0.00 0.00 0.00 3.62
2301 3521 8.087750 GTCAAATTAATGAGAAACCATGAACCA 58.912 33.333 0.00 0.00 0.00 3.67
2302 3522 8.646004 TCAAATTAATGAGAAACCATGAACCAA 58.354 29.630 0.00 0.00 0.00 3.67
2303 3523 8.928733 CAAATTAATGAGAAACCATGAACCAAG 58.071 33.333 0.00 0.00 0.00 3.61
2304 3524 6.588719 TTAATGAGAAACCATGAACCAAGG 57.411 37.500 0.00 0.00 0.00 3.61
2305 3525 2.238521 TGAGAAACCATGAACCAAGGC 58.761 47.619 0.00 0.00 0.00 4.35
2306 3526 2.158475 TGAGAAACCATGAACCAAGGCT 60.158 45.455 0.00 0.00 0.00 4.58
2307 3527 3.073798 TGAGAAACCATGAACCAAGGCTA 59.926 43.478 0.00 0.00 0.00 3.93
2308 3528 3.690460 AGAAACCATGAACCAAGGCTAG 58.310 45.455 0.00 0.00 0.00 3.42
2309 3529 2.514458 AACCATGAACCAAGGCTAGG 57.486 50.000 0.00 0.00 0.00 3.02
2310 3530 0.034089 ACCATGAACCAAGGCTAGGC 60.034 55.000 8.55 8.55 0.00 3.93
2311 3531 0.034186 CCATGAACCAAGGCTAGGCA 60.034 55.000 19.70 0.00 0.00 4.75
2312 3532 1.386533 CATGAACCAAGGCTAGGCAG 58.613 55.000 19.70 10.30 0.00 4.85
2313 3533 1.065199 CATGAACCAAGGCTAGGCAGA 60.065 52.381 19.70 0.00 0.00 4.26
2314 3534 1.289160 TGAACCAAGGCTAGGCAGAT 58.711 50.000 19.70 0.97 0.00 2.90
2315 3535 2.477245 TGAACCAAGGCTAGGCAGATA 58.523 47.619 19.70 0.00 0.00 1.98
2333 3553 7.714377 AGGCAGATATTGTGAAAGTCTAATCTG 59.286 37.037 0.00 0.00 41.16 2.90
2364 3584 4.122046 GCTGCAGAAAAAGAAATGTTGGT 58.878 39.130 20.43 0.00 0.00 3.67
2396 3616 4.463186 GGCTATGACCGACTCAAGGTATAT 59.537 45.833 0.00 0.00 43.01 0.86
2442 3663 9.925268 GACATACTTTTACGTTCTTTCTTCAAA 57.075 29.630 0.00 0.00 0.00 2.69
2453 3674 7.078228 CGTTCTTTCTTCAAATTTACTCCCAG 58.922 38.462 0.00 0.00 0.00 4.45
2486 3707 0.259647 TACCTACTAGGCTTGGCGGA 59.740 55.000 11.39 0.00 39.63 5.54
2579 3800 6.982852 TCTAATCATCCTGAGATTTACGTCC 58.017 40.000 0.00 0.00 37.02 4.79
2580 3801 5.878406 AATCATCCTGAGATTTACGTCCT 57.122 39.130 0.00 0.00 31.99 3.85
2581 3802 4.920640 TCATCCTGAGATTTACGTCCTC 57.079 45.455 0.00 0.00 0.00 3.71
2582 3803 4.537751 TCATCCTGAGATTTACGTCCTCT 58.462 43.478 0.00 0.00 0.00 3.69
2583 3804 5.691896 TCATCCTGAGATTTACGTCCTCTA 58.308 41.667 0.00 0.00 0.00 2.43
2584 3805 5.765677 TCATCCTGAGATTTACGTCCTCTAG 59.234 44.000 0.00 0.00 0.00 2.43
2585 3806 5.369409 TCCTGAGATTTACGTCCTCTAGA 57.631 43.478 0.00 0.00 0.00 2.43
2586 3807 5.124645 TCCTGAGATTTACGTCCTCTAGAC 58.875 45.833 0.00 0.00 42.54 2.59
2598 3819 5.517037 GTCCTCTAGACGTGAATTTTGTG 57.483 43.478 0.00 0.00 35.30 3.33
2599 3820 4.989168 GTCCTCTAGACGTGAATTTTGTGT 59.011 41.667 0.00 0.00 35.30 3.72
2600 3821 4.988540 TCCTCTAGACGTGAATTTTGTGTG 59.011 41.667 0.00 0.00 0.00 3.82
2601 3822 4.988540 CCTCTAGACGTGAATTTTGTGTGA 59.011 41.667 0.00 0.00 0.00 3.58
2602 3823 5.107453 CCTCTAGACGTGAATTTTGTGTGAC 60.107 44.000 0.00 0.00 0.00 3.67
2603 3824 5.353111 TCTAGACGTGAATTTTGTGTGACA 58.647 37.500 0.00 0.00 0.00 3.58
2604 3825 5.989168 TCTAGACGTGAATTTTGTGTGACAT 59.011 36.000 0.00 0.00 0.00 3.06
2605 3826 7.149307 TCTAGACGTGAATTTTGTGTGACATA 58.851 34.615 0.00 0.00 0.00 2.29
2606 3827 5.985781 AGACGTGAATTTTGTGTGACATAC 58.014 37.500 0.00 0.00 0.00 2.39
2607 3828 4.768145 ACGTGAATTTTGTGTGACATACG 58.232 39.130 0.00 0.00 0.00 3.06
2608 3829 4.148166 CGTGAATTTTGTGTGACATACGG 58.852 43.478 0.00 0.00 0.00 4.02
2609 3830 4.084276 CGTGAATTTTGTGTGACATACGGA 60.084 41.667 0.00 0.00 0.00 4.69
2610 3831 5.559225 CGTGAATTTTGTGTGACATACGGAA 60.559 40.000 0.00 0.00 0.00 4.30
2611 3832 5.623673 GTGAATTTTGTGTGACATACGGAAC 59.376 40.000 0.00 0.00 0.00 3.62
2612 3833 4.759516 ATTTTGTGTGACATACGGAACC 57.240 40.909 0.00 0.00 0.00 3.62
2613 3834 2.172851 TTGTGTGACATACGGAACCC 57.827 50.000 0.00 0.00 0.00 4.11
2623 3844 2.421739 CGGAACCCGGCTAGGATG 59.578 66.667 0.00 0.00 44.15 3.51
2624 3845 2.131709 CGGAACCCGGCTAGGATGA 61.132 63.158 0.00 0.00 44.15 2.92
2625 3846 1.682451 CGGAACCCGGCTAGGATGAA 61.682 60.000 0.00 0.00 44.15 2.57
2626 3847 0.544697 GGAACCCGGCTAGGATGAAA 59.455 55.000 0.00 0.00 45.00 2.69
2627 3848 1.475213 GGAACCCGGCTAGGATGAAAG 60.475 57.143 0.00 0.00 45.00 2.62
2628 3849 1.209747 GAACCCGGCTAGGATGAAAGT 59.790 52.381 0.00 0.00 45.00 2.66
2629 3850 0.541863 ACCCGGCTAGGATGAAAGTG 59.458 55.000 0.00 0.00 45.00 3.16
2630 3851 0.815615 CCCGGCTAGGATGAAAGTGC 60.816 60.000 0.00 0.00 45.00 4.40
2631 3852 0.179000 CCGGCTAGGATGAAAGTGCT 59.821 55.000 0.00 0.00 45.00 4.40
2632 3853 1.407437 CCGGCTAGGATGAAAGTGCTT 60.407 52.381 0.00 0.00 45.00 3.91
2633 3854 2.158957 CCGGCTAGGATGAAAGTGCTTA 60.159 50.000 0.00 0.00 45.00 3.09
2634 3855 3.126831 CGGCTAGGATGAAAGTGCTTAG 58.873 50.000 0.00 0.00 0.00 2.18
2635 3856 3.181475 CGGCTAGGATGAAAGTGCTTAGA 60.181 47.826 0.00 0.00 0.00 2.10
2636 3857 4.376146 GGCTAGGATGAAAGTGCTTAGAG 58.624 47.826 0.00 0.00 0.00 2.43
2637 3858 4.376146 GCTAGGATGAAAGTGCTTAGAGG 58.624 47.826 0.00 0.00 0.00 3.69
2638 3859 3.922171 AGGATGAAAGTGCTTAGAGGG 57.078 47.619 0.00 0.00 0.00 4.30
2639 3860 3.185455 AGGATGAAAGTGCTTAGAGGGT 58.815 45.455 0.00 0.00 0.00 4.34
2640 3861 3.054802 AGGATGAAAGTGCTTAGAGGGTG 60.055 47.826 0.00 0.00 0.00 4.61
2641 3862 3.055094 GGATGAAAGTGCTTAGAGGGTGA 60.055 47.826 0.00 0.00 0.00 4.02
2642 3863 3.402628 TGAAAGTGCTTAGAGGGTGAC 57.597 47.619 0.00 0.00 0.00 3.67
2655 3876 3.083997 GTGACCGGCCCTCTCCAT 61.084 66.667 0.00 0.00 0.00 3.41
2656 3877 2.285368 TGACCGGCCCTCTCCATT 60.285 61.111 0.00 0.00 0.00 3.16
2657 3878 2.190578 GACCGGCCCTCTCCATTG 59.809 66.667 0.00 0.00 0.00 2.82
2658 3879 2.285368 ACCGGCCCTCTCCATTGA 60.285 61.111 0.00 0.00 0.00 2.57
2659 3880 1.694169 ACCGGCCCTCTCCATTGAT 60.694 57.895 0.00 0.00 0.00 2.57
2660 3881 1.072159 CCGGCCCTCTCCATTGATC 59.928 63.158 0.00 0.00 0.00 2.92
2661 3882 1.301244 CGGCCCTCTCCATTGATCG 60.301 63.158 0.00 0.00 0.00 3.69
2662 3883 1.072159 GGCCCTCTCCATTGATCGG 59.928 63.158 0.00 0.00 0.00 4.18
2663 3884 1.599240 GCCCTCTCCATTGATCGGC 60.599 63.158 0.00 0.00 0.00 5.54
2664 3885 1.301244 CCCTCTCCATTGATCGGCG 60.301 63.158 0.00 0.00 0.00 6.46
2665 3886 1.958205 CCTCTCCATTGATCGGCGC 60.958 63.158 0.00 0.00 0.00 6.53
2666 3887 2.279451 TCTCCATTGATCGGCGCG 60.279 61.111 0.00 0.00 0.00 6.86
2667 3888 3.341043 CTCCATTGATCGGCGCGG 61.341 66.667 8.83 8.94 0.00 6.46
2668 3889 4.155733 TCCATTGATCGGCGCGGT 62.156 61.111 15.06 0.00 0.00 5.68
2669 3890 3.940640 CCATTGATCGGCGCGGTG 61.941 66.667 15.06 5.26 0.00 4.94
2670 3891 2.889988 CATTGATCGGCGCGGTGA 60.890 61.111 15.06 6.46 0.00 4.02
2671 3892 2.890474 ATTGATCGGCGCGGTGAC 60.890 61.111 15.06 8.09 0.00 3.67
2697 3918 2.363795 CGCCACCTCCACTCCCTA 60.364 66.667 0.00 0.00 0.00 3.53
2698 3919 2.722201 CGCCACCTCCACTCCCTAC 61.722 68.421 0.00 0.00 0.00 3.18
2699 3920 2.722201 GCCACCTCCACTCCCTACG 61.722 68.421 0.00 0.00 0.00 3.51
2700 3921 1.000019 CCACCTCCACTCCCTACGA 60.000 63.158 0.00 0.00 0.00 3.43
2701 3922 1.321074 CCACCTCCACTCCCTACGAC 61.321 65.000 0.00 0.00 0.00 4.34
2702 3923 1.000107 ACCTCCACTCCCTACGACC 60.000 63.158 0.00 0.00 0.00 4.79
2703 3924 1.000019 CCTCCACTCCCTACGACCA 60.000 63.158 0.00 0.00 0.00 4.02
2704 3925 1.321074 CCTCCACTCCCTACGACCAC 61.321 65.000 0.00 0.00 0.00 4.16
2705 3926 1.654954 CTCCACTCCCTACGACCACG 61.655 65.000 0.00 0.00 45.75 4.94
2706 3927 2.707849 CCACTCCCTACGACCACGG 61.708 68.421 0.00 0.00 44.46 4.94
2707 3928 3.066814 ACTCCCTACGACCACGGC 61.067 66.667 0.00 0.00 44.46 5.68
2708 3929 3.066190 CTCCCTACGACCACGGCA 61.066 66.667 0.00 0.00 44.46 5.69
2709 3930 3.352338 CTCCCTACGACCACGGCAC 62.352 68.421 0.00 0.00 44.46 5.01
2710 3931 3.687102 CCCTACGACCACGGCACA 61.687 66.667 0.00 0.00 44.46 4.57
2711 3932 2.126071 CCTACGACCACGGCACAG 60.126 66.667 0.00 0.00 44.46 3.66
2712 3933 2.809601 CTACGACCACGGCACAGC 60.810 66.667 0.00 0.00 44.46 4.40
2713 3934 3.567478 CTACGACCACGGCACAGCA 62.567 63.158 0.00 0.00 44.46 4.41
2714 3935 3.851845 TACGACCACGGCACAGCAC 62.852 63.158 0.00 0.00 44.46 4.40
2733 3954 4.416738 GCCGCCTGCTCTTTCCCT 62.417 66.667 0.00 0.00 36.87 4.20
2734 3955 2.124942 CCGCCTGCTCTTTCCCTC 60.125 66.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.074627 TCCACGAAGTACCACAAAATCA 57.925 40.909 0.00 0.00 41.61 2.57
2 3 5.411669 AGAATCCACGAAGTACCACAAAATC 59.588 40.000 0.00 0.00 41.61 2.17
5 6 4.345859 AGAATCCACGAAGTACCACAAA 57.654 40.909 0.00 0.00 41.61 2.83
7 8 4.345859 AAAGAATCCACGAAGTACCACA 57.654 40.909 0.00 0.00 41.61 4.17
8 9 6.790285 TTAAAAGAATCCACGAAGTACCAC 57.210 37.500 0.00 0.00 41.61 4.16
9 10 9.158233 CTTATTAAAAGAATCCACGAAGTACCA 57.842 33.333 0.00 0.00 41.61 3.25
10 11 9.374838 TCTTATTAAAAGAATCCACGAAGTACC 57.625 33.333 0.00 0.00 41.61 3.34
14 15 8.893727 ACCATCTTATTAAAAGAATCCACGAAG 58.106 33.333 0.00 0.00 0.00 3.79
15 16 8.801882 ACCATCTTATTAAAAGAATCCACGAA 57.198 30.769 0.00 0.00 0.00 3.85
16 17 8.673711 CAACCATCTTATTAAAAGAATCCACGA 58.326 33.333 0.00 0.00 0.00 4.35
17 18 8.458843 ACAACCATCTTATTAAAAGAATCCACG 58.541 33.333 4.82 0.00 0.00 4.94
34 35 9.170734 GCATCATAATGATACATACAACCATCT 57.829 33.333 0.00 0.00 34.28 2.90
35 36 8.949177 TGCATCATAATGATACATACAACCATC 58.051 33.333 0.00 0.00 34.28 3.51
36 37 8.866970 TGCATCATAATGATACATACAACCAT 57.133 30.769 0.00 0.00 34.28 3.55
37 38 8.156165 TCTGCATCATAATGATACATACAACCA 58.844 33.333 0.00 0.00 34.28 3.67
38 39 8.552083 TCTGCATCATAATGATACATACAACC 57.448 34.615 0.00 0.00 34.28 3.77
39 40 8.663025 CCTCTGCATCATAATGATACATACAAC 58.337 37.037 0.00 0.00 34.28 3.32
40 41 7.335171 GCCTCTGCATCATAATGATACATACAA 59.665 37.037 0.00 0.00 34.28 2.41
41 42 6.820152 GCCTCTGCATCATAATGATACATACA 59.180 38.462 0.00 0.00 34.28 2.29
42 43 6.259608 GGCCTCTGCATCATAATGATACATAC 59.740 42.308 0.00 0.00 34.28 2.39
43 44 6.351711 GGCCTCTGCATCATAATGATACATA 58.648 40.000 0.00 0.00 34.28 2.29
44 45 5.191426 GGCCTCTGCATCATAATGATACAT 58.809 41.667 0.00 0.00 34.28 2.29
45 46 4.582869 GGCCTCTGCATCATAATGATACA 58.417 43.478 0.00 0.00 34.28 2.29
46 47 3.620374 CGGCCTCTGCATCATAATGATAC 59.380 47.826 0.00 0.00 34.28 2.24
47 48 3.369787 CCGGCCTCTGCATCATAATGATA 60.370 47.826 0.00 0.00 34.28 2.15
48 49 2.617276 CCGGCCTCTGCATCATAATGAT 60.617 50.000 0.00 0.00 37.65 2.45
49 50 1.271001 CCGGCCTCTGCATCATAATGA 60.271 52.381 0.00 0.00 40.13 2.57
50 51 1.162698 CCGGCCTCTGCATCATAATG 58.837 55.000 0.00 0.00 40.13 1.90
51 52 0.037303 CCCGGCCTCTGCATCATAAT 59.963 55.000 0.00 0.00 40.13 1.28
52 53 1.451504 CCCGGCCTCTGCATCATAA 59.548 57.895 0.00 0.00 40.13 1.90
53 54 2.519622 CCCCGGCCTCTGCATCATA 61.520 63.158 0.00 0.00 40.13 2.15
54 55 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
57 58 4.815973 TACCCCCGGCCTCTGCAT 62.816 66.667 0.00 0.00 40.13 3.96
67 68 1.688269 TAAATGGAGGCGTACCCCCG 61.688 60.000 0.00 0.00 36.11 5.73
68 69 0.547553 TTAAATGGAGGCGTACCCCC 59.452 55.000 0.00 0.00 36.11 5.40
69 70 2.423446 TTTAAATGGAGGCGTACCCC 57.577 50.000 0.00 0.00 36.11 4.95
90 91 8.469309 AGCTACATAATGACATATGCCTTTTT 57.531 30.769 1.58 0.00 36.87 1.94
91 92 9.003658 GTAGCTACATAATGACATATGCCTTTT 57.996 33.333 19.15 0.00 36.87 2.27
102 103 7.715249 TGGGAGAAATTGTAGCTACATAATGAC 59.285 37.037 26.54 16.01 35.89 3.06
107 108 7.432148 TTCTGGGAGAAATTGTAGCTACATA 57.568 36.000 26.54 17.20 31.58 2.29
110 111 5.938125 TGTTTCTGGGAGAAATTGTAGCTAC 59.062 40.000 17.30 17.30 44.94 3.58
113 114 5.705609 TTGTTTCTGGGAGAAATTGTAGC 57.294 39.130 2.26 0.00 44.94 3.58
173 177 2.607187 TCGCCTCGAGATTCACTTTTC 58.393 47.619 15.71 0.00 0.00 2.29
204 208 0.382515 GTCCTCCCGAGACGATCTTG 59.617 60.000 0.00 0.00 0.00 3.02
230 234 8.130671 TCTATTGCTTACATATGTAGTACCCC 57.869 38.462 14.96 3.49 0.00 4.95
231 235 9.021807 TCTCTATTGCTTACATATGTAGTACCC 57.978 37.037 14.96 4.97 0.00 3.69
256 260 5.485662 AAAAGCGGTGCTATAAGTGAATC 57.514 39.130 0.00 0.00 38.25 2.52
273 277 7.542824 TGATACGCAAAGGGTAAATTAAAAAGC 59.457 33.333 0.00 0.00 34.79 3.51
295 492 6.938030 ACAAACCGAAGTTATTTCCAGTGATA 59.062 34.615 0.00 0.00 34.19 2.15
304 501 5.286438 GCAAAGGACAAACCGAAGTTATTT 58.714 37.500 0.00 0.00 44.74 1.40
341 539 1.869767 GATAGCTAGCCACATGTGCAC 59.130 52.381 20.81 10.75 0.00 4.57
387 616 9.931210 CGGAGTAAATAAAAATGGAAGATGTAC 57.069 33.333 0.00 0.00 0.00 2.90
388 617 8.617809 GCGGAGTAAATAAAAATGGAAGATGTA 58.382 33.333 0.00 0.00 0.00 2.29
389 618 7.122055 TGCGGAGTAAATAAAAATGGAAGATGT 59.878 33.333 0.00 0.00 0.00 3.06
390 619 7.479980 TGCGGAGTAAATAAAAATGGAAGATG 58.520 34.615 0.00 0.00 0.00 2.90
391 620 7.639113 TGCGGAGTAAATAAAAATGGAAGAT 57.361 32.000 0.00 0.00 0.00 2.40
392 621 7.639113 ATGCGGAGTAAATAAAAATGGAAGA 57.361 32.000 0.00 0.00 0.00 2.87
393 622 9.965824 AATATGCGGAGTAAATAAAAATGGAAG 57.034 29.630 0.00 0.00 0.00 3.46
402 631 9.398538 ACCAAAGTTAATATGCGGAGTAAATAA 57.601 29.630 0.00 0.00 0.00 1.40
403 632 8.967664 ACCAAAGTTAATATGCGGAGTAAATA 57.032 30.769 0.00 0.00 0.00 1.40
404 633 7.554835 TGACCAAAGTTAATATGCGGAGTAAAT 59.445 33.333 0.00 0.00 0.00 1.40
405 634 6.879993 TGACCAAAGTTAATATGCGGAGTAAA 59.120 34.615 0.00 0.00 0.00 2.01
406 635 6.408035 TGACCAAAGTTAATATGCGGAGTAA 58.592 36.000 0.00 0.00 0.00 2.24
407 636 5.979993 TGACCAAAGTTAATATGCGGAGTA 58.020 37.500 0.00 0.00 0.00 2.59
408 637 4.839121 TGACCAAAGTTAATATGCGGAGT 58.161 39.130 0.00 0.00 0.00 3.85
409 638 5.811399 TTGACCAAAGTTAATATGCGGAG 57.189 39.130 0.00 0.00 0.00 4.63
410 639 6.576662 TTTTGACCAAAGTTAATATGCGGA 57.423 33.333 0.00 0.00 0.00 5.54
411 640 7.826260 AATTTTGACCAAAGTTAATATGCGG 57.174 32.000 2.09 0.00 30.09 5.69
420 649 9.508642 TTTGGAAGTTTAATTTTGACCAAAGTT 57.491 25.926 0.00 8.03 39.91 2.66
421 650 9.508642 TTTTGGAAGTTTAATTTTGACCAAAGT 57.491 25.926 0.00 0.00 43.56 2.66
422 651 9.767684 GTTTTGGAAGTTTAATTTTGACCAAAG 57.232 29.630 0.00 0.00 43.56 2.77
423 652 9.508642 AGTTTTGGAAGTTTAATTTTGACCAAA 57.491 25.926 0.00 0.00 41.98 3.28
424 653 9.508642 AAGTTTTGGAAGTTTAATTTTGACCAA 57.491 25.926 0.00 0.00 34.94 3.67
425 654 9.508642 AAAGTTTTGGAAGTTTAATTTTGACCA 57.491 25.926 0.00 0.00 36.80 4.02
426 655 9.767684 CAAAGTTTTGGAAGTTTAATTTTGACC 57.232 29.630 0.00 0.00 36.50 4.02
500 729 9.182214 AGCACATTTAATAGTGAATCTGATGTT 57.818 29.630 10.88 0.00 37.97 2.71
501 730 8.743085 AGCACATTTAATAGTGAATCTGATGT 57.257 30.769 10.88 0.00 37.97 3.06
504 733 9.230122 TGAAAGCACATTTAATAGTGAATCTGA 57.770 29.630 10.88 0.00 37.97 3.27
505 734 9.282247 GTGAAAGCACATTTAATAGTGAATCTG 57.718 33.333 10.88 0.00 44.51 2.90
595 824 9.965824 CACATTAGGTTTAACTGAAATCAAACT 57.034 29.630 0.00 0.00 29.68 2.66
596 825 9.744468 ACACATTAGGTTTAACTGAAATCAAAC 57.256 29.630 0.00 0.00 29.68 2.93
617 846 9.449719 CCCTCTGTTTTTATTTACTCTACACAT 57.550 33.333 0.00 0.00 0.00 3.21
618 847 8.653191 TCCCTCTGTTTTTATTTACTCTACACA 58.347 33.333 0.00 0.00 0.00 3.72
619 848 9.152595 CTCCCTCTGTTTTTATTTACTCTACAC 57.847 37.037 0.00 0.00 0.00 2.90
620 849 8.877195 ACTCCCTCTGTTTTTATTTACTCTACA 58.123 33.333 0.00 0.00 0.00 2.74
628 857 9.125026 CAGCATATACTCCCTCTGTTTTTATTT 57.875 33.333 0.00 0.00 0.00 1.40
629 858 8.494433 TCAGCATATACTCCCTCTGTTTTTATT 58.506 33.333 0.00 0.00 0.00 1.40
630 859 7.934120 GTCAGCATATACTCCCTCTGTTTTTAT 59.066 37.037 0.00 0.00 0.00 1.40
631 860 7.125811 AGTCAGCATATACTCCCTCTGTTTTTA 59.874 37.037 0.00 0.00 0.00 1.52
632 861 6.069963 AGTCAGCATATACTCCCTCTGTTTTT 60.070 38.462 0.00 0.00 0.00 1.94
633 862 5.426833 AGTCAGCATATACTCCCTCTGTTTT 59.573 40.000 0.00 0.00 0.00 2.43
634 863 4.965532 AGTCAGCATATACTCCCTCTGTTT 59.034 41.667 0.00 0.00 0.00 2.83
635 864 4.551671 AGTCAGCATATACTCCCTCTGTT 58.448 43.478 0.00 0.00 0.00 3.16
636 865 4.148838 GAGTCAGCATATACTCCCTCTGT 58.851 47.826 0.00 0.00 36.86 3.41
637 866 3.190327 CGAGTCAGCATATACTCCCTCTG 59.810 52.174 0.00 0.00 39.16 3.35
638 867 3.181438 ACGAGTCAGCATATACTCCCTCT 60.181 47.826 0.00 0.00 39.16 3.69
639 868 3.057876 CACGAGTCAGCATATACTCCCTC 60.058 52.174 0.00 0.00 39.16 4.30
640 869 2.887783 CACGAGTCAGCATATACTCCCT 59.112 50.000 0.00 0.00 39.16 4.20
641 870 2.608261 GCACGAGTCAGCATATACTCCC 60.608 54.545 0.00 0.00 39.16 4.30
642 871 2.034685 TGCACGAGTCAGCATATACTCC 59.965 50.000 3.32 0.00 39.16 3.85
643 872 3.355626 TGCACGAGTCAGCATATACTC 57.644 47.619 3.32 0.00 39.00 2.59
656 885 2.095567 CCTGATGGAAAAGTTGCACGAG 60.096 50.000 0.00 0.00 32.41 4.18
674 903 1.144057 GATGCGTGGGGTCTACCTG 59.856 63.158 0.00 0.00 40.03 4.00
823 1412 1.719780 GGTGAGAAATGACGTGACGAC 59.280 52.381 13.70 6.16 0.00 4.34
824 1413 1.336517 GGGTGAGAAATGACGTGACGA 60.337 52.381 13.70 0.00 0.00 4.20
825 1414 1.068474 GGGTGAGAAATGACGTGACG 58.932 55.000 2.24 2.24 0.00 4.35
826 1415 1.439679 GGGGTGAGAAATGACGTGAC 58.560 55.000 0.00 0.00 0.00 3.67
827 1416 0.323629 GGGGGTGAGAAATGACGTGA 59.676 55.000 0.00 0.00 0.00 4.35
828 1417 0.324943 AGGGGGTGAGAAATGACGTG 59.675 55.000 0.00 0.00 0.00 4.49
829 1418 0.613777 GAGGGGGTGAGAAATGACGT 59.386 55.000 0.00 0.00 0.00 4.34
830 1419 0.613260 TGAGGGGGTGAGAAATGACG 59.387 55.000 0.00 0.00 0.00 4.35
831 1420 1.340114 GGTGAGGGGGTGAGAAATGAC 60.340 57.143 0.00 0.00 0.00 3.06
832 1421 0.991920 GGTGAGGGGGTGAGAAATGA 59.008 55.000 0.00 0.00 0.00 2.57
833 1422 0.034089 GGGTGAGGGGGTGAGAAATG 60.034 60.000 0.00 0.00 0.00 2.32
834 1423 1.562672 CGGGTGAGGGGGTGAGAAAT 61.563 60.000 0.00 0.00 0.00 2.17
835 1424 2.221299 CGGGTGAGGGGGTGAGAAA 61.221 63.158 0.00 0.00 0.00 2.52
836 1425 2.096707 TACGGGTGAGGGGGTGAGAA 62.097 60.000 0.00 0.00 0.00 2.87
837 1426 1.882189 ATACGGGTGAGGGGGTGAGA 61.882 60.000 0.00 0.00 0.00 3.27
838 1427 0.105862 TATACGGGTGAGGGGGTGAG 60.106 60.000 0.00 0.00 0.00 3.51
839 1428 0.339162 TTATACGGGTGAGGGGGTGA 59.661 55.000 0.00 0.00 0.00 4.02
840 1429 1.205966 TTTATACGGGTGAGGGGGTG 58.794 55.000 0.00 0.00 0.00 4.61
841 1430 2.052468 GATTTATACGGGTGAGGGGGT 58.948 52.381 0.00 0.00 0.00 4.95
842 1431 1.350019 GGATTTATACGGGTGAGGGGG 59.650 57.143 0.00 0.00 0.00 5.40
843 1432 1.350019 GGGATTTATACGGGTGAGGGG 59.650 57.143 0.00 0.00 0.00 4.79
844 1433 2.302157 GAGGGATTTATACGGGTGAGGG 59.698 54.545 0.00 0.00 0.00 4.30
845 1434 2.029290 CGAGGGATTTATACGGGTGAGG 60.029 54.545 0.00 0.00 0.00 3.86
846 1435 2.609737 GCGAGGGATTTATACGGGTGAG 60.610 54.545 0.00 0.00 0.00 3.51
847 1436 1.342174 GCGAGGGATTTATACGGGTGA 59.658 52.381 0.00 0.00 0.00 4.02
848 1437 1.792006 GCGAGGGATTTATACGGGTG 58.208 55.000 0.00 0.00 0.00 4.61
849 1438 0.316204 CGCGAGGGATTTATACGGGT 59.684 55.000 0.00 0.00 33.58 5.28
850 1439 0.316204 ACGCGAGGGATTTATACGGG 59.684 55.000 15.93 0.00 41.28 5.28
851 1440 1.268899 AGACGCGAGGGATTTATACGG 59.731 52.381 15.93 0.00 0.00 4.02
862 1761 3.917760 GATGGGGGAGACGCGAGG 61.918 72.222 15.93 0.00 45.87 4.63
864 1763 3.064491 TAGGATGGGGGAGACGCGA 62.064 63.158 15.93 0.00 45.87 5.87
870 1769 1.152008 GAGGGGTAGGATGGGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
1356 2267 3.141488 GAGAGGAGCGGCTTCGGA 61.141 66.667 2.97 0.00 0.00 4.55
1584 2510 2.847234 ACCAGCCGGAACACCTCA 60.847 61.111 5.05 0.00 35.59 3.86
1737 2663 0.635555 TTTCCCCATGCCATCCATCA 59.364 50.000 0.00 0.00 29.71 3.07
2035 2962 6.640499 CACAAATCCAATTCAAACATGTACGT 59.360 34.615 0.00 0.00 0.00 3.57
2036 2963 6.860539 TCACAAATCCAATTCAAACATGTACG 59.139 34.615 0.00 0.00 0.00 3.67
2037 2964 8.586570 TTCACAAATCCAATTCAAACATGTAC 57.413 30.769 0.00 0.00 0.00 2.90
2039 2966 9.206870 GTATTCACAAATCCAATTCAAACATGT 57.793 29.630 0.00 0.00 0.00 3.21
2040 2967 8.658609 GGTATTCACAAATCCAATTCAAACATG 58.341 33.333 0.00 0.00 0.00 3.21
2041 2968 8.596293 AGGTATTCACAAATCCAATTCAAACAT 58.404 29.630 0.00 0.00 0.00 2.71
2042 2969 7.961351 AGGTATTCACAAATCCAATTCAAACA 58.039 30.769 0.00 0.00 0.00 2.83
2113 3040 9.364989 GAATCGGAGAGATATAAGAATTTCTGG 57.635 37.037 0.00 0.00 43.63 3.86
2183 3111 7.095355 GCAAACTTTATACCTGAACTTCTCGAA 60.095 37.037 0.00 0.00 0.00 3.71
2204 3424 5.576774 GCAGGGTTCTTAATGTAATGCAAAC 59.423 40.000 0.00 0.00 0.00 2.93
2237 3457 9.827411 CACTTAAGTTTAAATTAGGAAGCACTC 57.173 33.333 5.07 0.00 0.00 3.51
2294 3514 1.289160 TCTGCCTAGCCTTGGTTCAT 58.711 50.000 0.00 0.00 0.00 2.57
2297 3517 3.203040 ACAATATCTGCCTAGCCTTGGTT 59.797 43.478 0.00 0.00 0.00 3.67
2298 3518 2.780010 ACAATATCTGCCTAGCCTTGGT 59.220 45.455 0.00 0.00 0.00 3.67
2299 3519 3.144506 CACAATATCTGCCTAGCCTTGG 58.855 50.000 0.00 0.00 0.00 3.61
2300 3520 4.077300 TCACAATATCTGCCTAGCCTTG 57.923 45.455 0.00 0.00 0.00 3.61
2301 3521 4.778213 TTCACAATATCTGCCTAGCCTT 57.222 40.909 0.00 0.00 0.00 4.35
2302 3522 4.164988 ACTTTCACAATATCTGCCTAGCCT 59.835 41.667 0.00 0.00 0.00 4.58
2303 3523 4.455606 ACTTTCACAATATCTGCCTAGCC 58.544 43.478 0.00 0.00 0.00 3.93
2304 3524 5.363939 AGACTTTCACAATATCTGCCTAGC 58.636 41.667 0.00 0.00 0.00 3.42
2305 3525 9.202273 GATTAGACTTTCACAATATCTGCCTAG 57.798 37.037 0.00 0.00 0.00 3.02
2306 3526 8.928448 AGATTAGACTTTCACAATATCTGCCTA 58.072 33.333 0.00 0.00 0.00 3.93
2307 3527 7.714377 CAGATTAGACTTTCACAATATCTGCCT 59.286 37.037 0.00 0.00 33.66 4.75
2308 3528 7.041508 CCAGATTAGACTTTCACAATATCTGCC 60.042 40.741 0.00 0.00 37.49 4.85
2309 3529 7.519649 GCCAGATTAGACTTTCACAATATCTGC 60.520 40.741 0.00 0.00 37.49 4.26
2310 3530 7.307042 CGCCAGATTAGACTTTCACAATATCTG 60.307 40.741 0.00 0.00 38.17 2.90
2311 3531 6.703607 CGCCAGATTAGACTTTCACAATATCT 59.296 38.462 0.00 0.00 0.00 1.98
2312 3532 6.073548 CCGCCAGATTAGACTTTCACAATATC 60.074 42.308 0.00 0.00 0.00 1.63
2313 3533 5.760253 CCGCCAGATTAGACTTTCACAATAT 59.240 40.000 0.00 0.00 0.00 1.28
2314 3534 5.116180 CCGCCAGATTAGACTTTCACAATA 58.884 41.667 0.00 0.00 0.00 1.90
2315 3535 3.941483 CCGCCAGATTAGACTTTCACAAT 59.059 43.478 0.00 0.00 0.00 2.71
2354 3574 1.336795 CCTTCGCCCAACCAACATTTC 60.337 52.381 0.00 0.00 0.00 2.17
2364 3584 1.223487 GGTCATAGCCTTCGCCCAA 59.777 57.895 0.00 0.00 34.57 4.12
2396 3616 9.534565 GTATGTCTTGAGAGCAGAAAATATGTA 57.465 33.333 0.00 0.00 0.00 2.29
2442 3663 6.208840 TCCCTTTGTAAACTGGGAGTAAAT 57.791 37.500 0.00 0.00 41.95 1.40
2453 3674 6.629068 GCCTAGTAGGTACTCCCTTTGTAAAC 60.629 46.154 17.69 0.00 42.73 2.01
2486 3707 4.429108 CTGAAACAAAACCGAACAATGGT 58.571 39.130 0.00 0.00 42.98 3.55
2494 3715 3.859411 ACTTTGCTGAAACAAAACCGA 57.141 38.095 0.00 0.00 38.96 4.69
2579 3800 5.462068 TGTCACACAAAATTCACGTCTAGAG 59.538 40.000 0.00 0.00 0.00 2.43
2580 3801 5.353111 TGTCACACAAAATTCACGTCTAGA 58.647 37.500 0.00 0.00 0.00 2.43
2581 3802 5.651172 TGTCACACAAAATTCACGTCTAG 57.349 39.130 0.00 0.00 0.00 2.43
2582 3803 6.129035 CGTATGTCACACAAAATTCACGTCTA 60.129 38.462 0.00 0.00 0.00 2.59
2583 3804 5.333035 CGTATGTCACACAAAATTCACGTCT 60.333 40.000 0.00 0.00 0.00 4.18
2584 3805 4.838642 CGTATGTCACACAAAATTCACGTC 59.161 41.667 0.00 0.00 0.00 4.34
2585 3806 4.319190 CCGTATGTCACACAAAATTCACGT 60.319 41.667 0.00 0.00 0.00 4.49
2586 3807 4.084276 TCCGTATGTCACACAAAATTCACG 60.084 41.667 0.00 0.00 0.00 4.35
2587 3808 5.351233 TCCGTATGTCACACAAAATTCAC 57.649 39.130 0.00 0.00 0.00 3.18
2588 3809 5.278071 GGTTCCGTATGTCACACAAAATTCA 60.278 40.000 0.00 0.00 0.00 2.57
2589 3810 5.151389 GGTTCCGTATGTCACACAAAATTC 58.849 41.667 0.00 0.00 0.00 2.17
2590 3811 4.022676 GGGTTCCGTATGTCACACAAAATT 60.023 41.667 0.00 0.00 0.00 1.82
2591 3812 3.504520 GGGTTCCGTATGTCACACAAAAT 59.495 43.478 0.00 0.00 0.00 1.82
2592 3813 2.879646 GGGTTCCGTATGTCACACAAAA 59.120 45.455 0.00 0.00 0.00 2.44
2593 3814 2.496111 GGGTTCCGTATGTCACACAAA 58.504 47.619 0.00 0.00 0.00 2.83
2594 3815 1.605968 CGGGTTCCGTATGTCACACAA 60.606 52.381 0.00 0.00 42.73 3.33
2595 3816 0.038067 CGGGTTCCGTATGTCACACA 60.038 55.000 0.00 0.00 42.73 3.72
2596 3817 0.738412 CCGGGTTCCGTATGTCACAC 60.738 60.000 5.60 0.00 46.80 3.82
2597 3818 1.592743 CCGGGTTCCGTATGTCACA 59.407 57.895 5.60 0.00 46.80 3.58
2598 3819 1.812507 GCCGGGTTCCGTATGTCAC 60.813 63.158 2.18 0.00 46.80 3.67
2599 3820 0.683828 TAGCCGGGTTCCGTATGTCA 60.684 55.000 13.43 0.00 46.80 3.58
2600 3821 0.031721 CTAGCCGGGTTCCGTATGTC 59.968 60.000 13.43 0.00 46.80 3.06
2601 3822 1.397390 CCTAGCCGGGTTCCGTATGT 61.397 60.000 13.43 0.00 46.80 2.29
2602 3823 1.111116 TCCTAGCCGGGTTCCGTATG 61.111 60.000 13.43 0.00 46.80 2.39
2603 3824 0.178941 ATCCTAGCCGGGTTCCGTAT 60.179 55.000 13.43 0.00 46.80 3.06
2604 3825 1.111116 CATCCTAGCCGGGTTCCGTA 61.111 60.000 13.43 0.00 46.80 4.02
2605 3826 2.042230 ATCCTAGCCGGGTTCCGT 60.042 61.111 13.43 0.00 46.80 4.69
2607 3828 0.544697 TTTCATCCTAGCCGGGTTCC 59.455 55.000 13.43 0.00 0.00 3.62
2608 3829 1.209747 ACTTTCATCCTAGCCGGGTTC 59.790 52.381 13.43 0.00 0.00 3.62
2609 3830 1.065418 CACTTTCATCCTAGCCGGGTT 60.065 52.381 13.43 0.00 0.00 4.11
2610 3831 0.541863 CACTTTCATCCTAGCCGGGT 59.458 55.000 12.58 12.58 0.00 5.28
2611 3832 0.815615 GCACTTTCATCCTAGCCGGG 60.816 60.000 2.18 0.00 0.00 5.73
2612 3833 0.179000 AGCACTTTCATCCTAGCCGG 59.821 55.000 0.00 0.00 0.00 6.13
2613 3834 2.029838 AAGCACTTTCATCCTAGCCG 57.970 50.000 0.00 0.00 0.00 5.52
2614 3835 4.376146 CTCTAAGCACTTTCATCCTAGCC 58.624 47.826 0.00 0.00 0.00 3.93
2615 3836 4.376146 CCTCTAAGCACTTTCATCCTAGC 58.624 47.826 0.00 0.00 0.00 3.42
2616 3837 4.407296 ACCCTCTAAGCACTTTCATCCTAG 59.593 45.833 0.00 0.00 0.00 3.02
2617 3838 4.162320 CACCCTCTAAGCACTTTCATCCTA 59.838 45.833 0.00 0.00 0.00 2.94
2618 3839 3.054802 CACCCTCTAAGCACTTTCATCCT 60.055 47.826 0.00 0.00 0.00 3.24
2619 3840 3.055094 TCACCCTCTAAGCACTTTCATCC 60.055 47.826 0.00 0.00 0.00 3.51
2620 3841 3.935828 GTCACCCTCTAAGCACTTTCATC 59.064 47.826 0.00 0.00 0.00 2.92
2621 3842 3.307762 GGTCACCCTCTAAGCACTTTCAT 60.308 47.826 0.00 0.00 0.00 2.57
2622 3843 2.038557 GGTCACCCTCTAAGCACTTTCA 59.961 50.000 0.00 0.00 0.00 2.69
2623 3844 2.701107 GGTCACCCTCTAAGCACTTTC 58.299 52.381 0.00 0.00 0.00 2.62
2624 3845 1.002087 CGGTCACCCTCTAAGCACTTT 59.998 52.381 0.00 0.00 0.00 2.66
2625 3846 0.608640 CGGTCACCCTCTAAGCACTT 59.391 55.000 0.00 0.00 0.00 3.16
2626 3847 1.258445 CCGGTCACCCTCTAAGCACT 61.258 60.000 0.00 0.00 0.00 4.40
2627 3848 1.218316 CCGGTCACCCTCTAAGCAC 59.782 63.158 0.00 0.00 0.00 4.40
2628 3849 2.656069 GCCGGTCACCCTCTAAGCA 61.656 63.158 1.90 0.00 0.00 3.91
2629 3850 2.187163 GCCGGTCACCCTCTAAGC 59.813 66.667 1.90 0.00 0.00 3.09
2630 3851 2.732619 GGGCCGGTCACCCTCTAAG 61.733 68.421 9.07 0.00 44.68 2.18
2631 3852 2.686106 GGGCCGGTCACCCTCTAA 60.686 66.667 9.07 0.00 44.68 2.10
2638 3859 2.670148 AATGGAGAGGGCCGGTCAC 61.670 63.158 9.07 0.36 0.00 3.67
2639 3860 2.285368 AATGGAGAGGGCCGGTCA 60.285 61.111 9.07 2.92 0.00 4.02
2640 3861 1.700042 ATCAATGGAGAGGGCCGGTC 61.700 60.000 1.90 0.00 0.00 4.79
2641 3862 1.694169 ATCAATGGAGAGGGCCGGT 60.694 57.895 1.90 0.00 0.00 5.28
2642 3863 1.072159 GATCAATGGAGAGGGCCGG 59.928 63.158 0.00 0.00 0.00 6.13
2643 3864 1.301244 CGATCAATGGAGAGGGCCG 60.301 63.158 0.00 0.00 0.00 6.13
2644 3865 1.072159 CCGATCAATGGAGAGGGCC 59.928 63.158 0.00 0.00 0.00 5.80
2645 3866 1.599240 GCCGATCAATGGAGAGGGC 60.599 63.158 0.00 0.00 35.02 5.19
2646 3867 1.301244 CGCCGATCAATGGAGAGGG 60.301 63.158 0.00 0.00 0.00 4.30
2647 3868 1.958205 GCGCCGATCAATGGAGAGG 60.958 63.158 0.00 0.00 0.00 3.69
2648 3869 2.305853 CGCGCCGATCAATGGAGAG 61.306 63.158 0.00 0.00 0.00 3.20
2649 3870 2.279451 CGCGCCGATCAATGGAGA 60.279 61.111 0.00 0.00 0.00 3.71
2650 3871 3.341043 CCGCGCCGATCAATGGAG 61.341 66.667 0.00 0.00 0.00 3.86
2651 3872 4.155733 ACCGCGCCGATCAATGGA 62.156 61.111 0.00 0.00 0.00 3.41
2652 3873 3.940640 CACCGCGCCGATCAATGG 61.941 66.667 0.00 0.00 0.00 3.16
2653 3874 2.889988 TCACCGCGCCGATCAATG 60.890 61.111 0.00 0.00 0.00 2.82
2654 3875 2.890474 GTCACCGCGCCGATCAAT 60.890 61.111 0.00 0.00 0.00 2.57
2679 3900 3.976490 TAGGGAGTGGAGGTGGCGG 62.976 68.421 0.00 0.00 0.00 6.13
2680 3901 2.363795 TAGGGAGTGGAGGTGGCG 60.364 66.667 0.00 0.00 0.00 5.69
2681 3902 2.722201 CGTAGGGAGTGGAGGTGGC 61.722 68.421 0.00 0.00 0.00 5.01
2682 3903 1.000019 TCGTAGGGAGTGGAGGTGG 60.000 63.158 0.00 0.00 0.00 4.61
2683 3904 1.321074 GGTCGTAGGGAGTGGAGGTG 61.321 65.000 0.00 0.00 0.00 4.00
2684 3905 1.000107 GGTCGTAGGGAGTGGAGGT 60.000 63.158 0.00 0.00 0.00 3.85
2685 3906 1.000019 TGGTCGTAGGGAGTGGAGG 60.000 63.158 0.00 0.00 0.00 4.30
2686 3907 1.654954 CGTGGTCGTAGGGAGTGGAG 61.655 65.000 0.00 0.00 0.00 3.86
2687 3908 1.676635 CGTGGTCGTAGGGAGTGGA 60.677 63.158 0.00 0.00 0.00 4.02
2688 3909 2.707849 CCGTGGTCGTAGGGAGTGG 61.708 68.421 0.00 0.00 35.01 4.00
2689 3910 2.882876 CCGTGGTCGTAGGGAGTG 59.117 66.667 0.00 0.00 35.01 3.51
2690 3911 3.066814 GCCGTGGTCGTAGGGAGT 61.067 66.667 0.00 0.00 35.01 3.85
2691 3912 3.066190 TGCCGTGGTCGTAGGGAG 61.066 66.667 0.00 0.00 35.01 4.30
2692 3913 3.376078 GTGCCGTGGTCGTAGGGA 61.376 66.667 0.00 0.00 35.01 4.20
2693 3914 3.642778 CTGTGCCGTGGTCGTAGGG 62.643 68.421 0.00 0.00 35.01 3.53
2694 3915 2.126071 CTGTGCCGTGGTCGTAGG 60.126 66.667 0.00 0.00 35.01 3.18
2695 3916 2.809601 GCTGTGCCGTGGTCGTAG 60.810 66.667 0.00 0.00 35.01 3.51
2696 3917 3.607661 TGCTGTGCCGTGGTCGTA 61.608 61.111 0.00 0.00 35.01 3.43
2716 3937 4.416738 AGGGAAAGAGCAGGCGGC 62.417 66.667 0.00 0.00 45.30 6.53
2717 3938 2.124942 GAGGGAAAGAGCAGGCGG 60.125 66.667 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.