Multiple sequence alignment - TraesCS3D01G532700

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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 TraesCS3D01G532700 chr3D 100.000 2727 0 0 1 2727 608513155 608510429 0.000000e+00 5036.0
1 TraesCS3D01G532700 chr3A 81.127 2289 148 132 146 2345 741626085 741623992 0.000000e+00 1572.0
2 TraesCS3D01G532700 chr3A 88.235 391 19 14 2344 2720 741623940 741623563 2.490000e-120 442.0
3 TraesCS3D01G532700 chr3A 86.905 84 5 5 59 136 741626203 741626120 3.740000e-14 89.8
4 TraesCS3D01G532700 chr3B 79.723 1879 135 114 389 2162 818927411 818925674 0.000000e+00 1133.0
5 TraesCS3D01G532700 chr3B 85.791 556 32 24 2200 2726 818925423 818924886 1.850000e-151 545.0
6 TraesCS3D01G532700 chr3B 78.402 338 28 17 73 394 818932883 818932575 7.760000e-41 178.0
7 TraesCS3D01G532700 chr5D 100.000 30 0 0 1089 1118 99418743 99418714 3.790000e-04 56.5
8 TraesCS3D01G532700 chr5A 100.000 30 0 0 1089 1118 103569118 103569147 3.790000e-04 56.5


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 TraesCS3D01G532700 chr3D 608510429 608513155 2726 True 5036.000000 5036 100.000000 1 2727 1 chr3D.!!$R1 2726
1 TraesCS3D01G532700 chr3A 741623563 741626203 2640 True 701.266667 1572 85.422333 59 2720 3 chr3A.!!$R1 2661
2 TraesCS3D01G532700 chr3B 818924886 818927411 2525 True 839.000000 1133 82.757000 389 2726 2 chr3B.!!$R2 2337

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
301 333 0.099436 GTACTGCGTGTAGTACCGGG 59.901 60.0 14.9 0.0 44.55 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2400 0.031043 GCTGCATCACTTGTGTTGCA 59.969 50.0 27.13 27.13 42.41 4.08 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
25 26 3.521995 CAGTACTCACTGCCAGTGG 57.478 57.895 23.85 16.53 45.94 4.00
26 27 0.681733 CAGTACTCACTGCCAGTGGT 59.318 55.000 23.85 20.80 45.94 4.16
27 28 1.893137 CAGTACTCACTGCCAGTGGTA 59.107 52.381 23.85 19.87 45.94 3.25
28 29 2.094494 CAGTACTCACTGCCAGTGGTAG 60.094 54.545 24.21 24.21 45.94 3.18
30 31 1.424638 ACTCACTGCCAGTGGTAGTT 58.575 50.000 28.27 13.25 46.02 2.24
31 32 1.070758 ACTCACTGCCAGTGGTAGTTG 59.929 52.381 28.27 23.98 46.02 3.16
32 33 1.070758 CTCACTGCCAGTGGTAGTTGT 59.929 52.381 28.27 7.49 46.02 3.32
33 34 2.299013 CTCACTGCCAGTGGTAGTTGTA 59.701 50.000 28.27 16.22 46.02 2.41
34 35 2.299013 TCACTGCCAGTGGTAGTTGTAG 59.701 50.000 28.27 17.70 46.02 2.74
35 36 2.037251 CACTGCCAGTGGTAGTTGTAGT 59.963 50.000 28.27 5.97 46.02 2.73
36 37 2.704065 ACTGCCAGTGGTAGTTGTAGTT 59.296 45.455 25.61 2.79 46.02 2.24
37 38 3.899360 ACTGCCAGTGGTAGTTGTAGTTA 59.101 43.478 25.61 0.00 46.02 2.24
38 39 4.243270 CTGCCAGTGGTAGTTGTAGTTAC 58.757 47.826 18.49 0.00 30.75 2.50
39 40 3.007182 TGCCAGTGGTAGTTGTAGTTACC 59.993 47.826 11.74 0.00 39.81 2.85
40 41 3.007182 GCCAGTGGTAGTTGTAGTTACCA 59.993 47.826 11.74 0.00 45.25 3.25
45 46 5.204409 TGGTAGTTGTAGTTACCAGTGTG 57.796 43.478 0.00 0.00 43.23 3.82
46 47 4.039488 TGGTAGTTGTAGTTACCAGTGTGG 59.961 45.833 0.00 0.00 43.23 4.17
47 48 3.121738 AGTTGTAGTTACCAGTGTGGC 57.878 47.619 0.00 0.00 42.67 5.01
48 49 2.436542 AGTTGTAGTTACCAGTGTGGCA 59.563 45.455 0.00 0.00 42.67 4.92
49 50 3.118186 AGTTGTAGTTACCAGTGTGGCAA 60.118 43.478 0.00 0.00 42.67 4.52
50 51 3.562343 TGTAGTTACCAGTGTGGCAAA 57.438 42.857 0.00 0.00 42.67 3.68
51 52 4.093472 TGTAGTTACCAGTGTGGCAAAT 57.907 40.909 0.00 0.00 42.67 2.32
52 53 5.230323 TGTAGTTACCAGTGTGGCAAATA 57.770 39.130 0.00 0.00 42.67 1.40
53 54 4.998672 TGTAGTTACCAGTGTGGCAAATAC 59.001 41.667 8.83 8.83 41.94 1.89
54 55 4.367039 AGTTACCAGTGTGGCAAATACT 57.633 40.909 0.00 0.00 42.67 2.12
55 56 4.725490 AGTTACCAGTGTGGCAAATACTT 58.275 39.130 0.00 0.00 42.67 2.24
56 57 5.137551 AGTTACCAGTGTGGCAAATACTTT 58.862 37.500 0.00 0.00 42.67 2.66
57 58 5.009610 AGTTACCAGTGTGGCAAATACTTTG 59.990 40.000 0.00 0.00 42.67 2.77
83 86 9.317936 GCAGGAGAAAAATATATTTCAAAAGGG 57.682 33.333 11.08 2.06 40.89 3.95
127 134 2.339556 TGCAACGGCTAACATGGGC 61.340 57.895 0.00 0.00 41.91 5.36
137 149 2.754552 GCTAACATGGGCTGATTTGACA 59.245 45.455 0.00 0.00 0.00 3.58
144 156 0.955428 GGCTGATTTGACAGTGGCGA 60.955 55.000 0.00 0.00 39.73 5.54
188 220 2.016961 GCGATCATGTGGCGTGATT 58.983 52.632 5.46 0.00 39.81 2.57
198 230 2.000447 GTGGCGTGATTCAGAGGTTAC 59.000 52.381 0.00 0.00 0.00 2.50
217 249 1.067693 CGCACAGTGATCGCAGTAAA 58.932 50.000 9.33 0.00 0.00 2.01
220 252 2.285256 GCACAGTGATCGCAGTAAATCG 60.285 50.000 9.33 0.00 0.00 3.34
222 254 2.165641 ACAGTGATCGCAGTAAATCGGA 59.834 45.455 9.33 0.00 0.00 4.55
223 255 2.791560 CAGTGATCGCAGTAAATCGGAG 59.208 50.000 9.33 0.00 0.00 4.63
226 258 0.753262 ATCGCAGTAAATCGGAGGCT 59.247 50.000 0.00 0.00 0.00 4.58
227 259 0.179111 TCGCAGTAAATCGGAGGCTG 60.179 55.000 0.00 0.00 0.00 4.85
228 260 1.154205 CGCAGTAAATCGGAGGCTGG 61.154 60.000 0.00 0.00 0.00 4.85
229 261 1.440145 GCAGTAAATCGGAGGCTGGC 61.440 60.000 0.00 0.00 0.00 4.85
230 262 0.179000 CAGTAAATCGGAGGCTGGCT 59.821 55.000 2.24 2.24 0.00 4.75
231 263 0.179000 AGTAAATCGGAGGCTGGCTG 59.821 55.000 9.06 0.00 0.00 4.85
232 264 0.815615 GTAAATCGGAGGCTGGCTGG 60.816 60.000 9.06 0.00 0.00 4.85
233 265 2.608970 TAAATCGGAGGCTGGCTGGC 62.609 60.000 9.06 10.02 42.15 4.85
248 280 4.509737 GGCCGTGAGCGAGGGTAC 62.510 72.222 0.00 0.00 45.17 3.34
249 281 3.450115 GCCGTGAGCGAGGGTACT 61.450 66.667 0.00 0.00 41.33 2.73
250 282 2.117156 GCCGTGAGCGAGGGTACTA 61.117 63.158 0.00 0.00 41.33 1.82
251 283 1.726265 CCGTGAGCGAGGGTACTAC 59.274 63.158 0.00 0.00 41.33 2.73
252 284 0.747283 CCGTGAGCGAGGGTACTACT 60.747 60.000 0.00 0.00 41.33 2.57
253 285 1.473965 CCGTGAGCGAGGGTACTACTA 60.474 57.143 0.00 0.00 41.33 1.82
254 286 1.596727 CGTGAGCGAGGGTACTACTAC 59.403 57.143 0.00 0.00 41.33 2.73
255 287 2.636830 GTGAGCGAGGGTACTACTACA 58.363 52.381 0.00 0.00 0.00 2.74
256 288 2.354199 GTGAGCGAGGGTACTACTACAC 59.646 54.545 0.00 0.00 0.00 2.90
257 289 1.946081 GAGCGAGGGTACTACTACACC 59.054 57.143 0.00 0.00 0.00 4.16
258 290 1.283029 AGCGAGGGTACTACTACACCA 59.717 52.381 0.00 0.00 36.48 4.17
259 291 1.403323 GCGAGGGTACTACTACACCAC 59.597 57.143 0.00 0.00 36.48 4.16
260 292 2.943199 GCGAGGGTACTACTACACCACT 60.943 54.545 0.00 0.00 36.48 4.00
261 293 3.350833 CGAGGGTACTACTACACCACTT 58.649 50.000 0.00 0.00 36.48 3.16
262 294 3.128242 CGAGGGTACTACTACACCACTTG 59.872 52.174 0.00 0.00 36.48 3.16
263 295 4.085009 GAGGGTACTACTACACCACTTGT 58.915 47.826 0.00 0.00 42.84 3.16
264 296 5.256474 GAGGGTACTACTACACCACTTGTA 58.744 45.833 0.00 0.00 39.91 2.41
267 299 5.478332 GGGTACTACTACACCACTTGTAACT 59.522 44.000 0.00 0.00 40.33 2.24
270 302 8.576442 GGTACTACTACACCACTTGTAACTTTA 58.424 37.037 0.00 0.00 40.33 1.85
301 333 0.099436 GTACTGCGTGTAGTACCGGG 59.901 60.000 14.90 0.00 44.55 5.73
302 334 1.031571 TACTGCGTGTAGTACCGGGG 61.032 60.000 6.32 0.00 32.19 5.73
303 335 3.711541 CTGCGTGTAGTACCGGGGC 62.712 68.421 6.32 0.00 0.00 5.80
315 350 3.454573 CGGGGCTGGTACGCTACA 61.455 66.667 0.00 0.00 0.00 2.74
316 351 2.186125 GGGGCTGGTACGCTACAC 59.814 66.667 0.00 0.00 0.00 2.90
317 352 2.356780 GGGGCTGGTACGCTACACT 61.357 63.158 0.00 0.00 0.00 3.55
318 353 1.039233 GGGGCTGGTACGCTACACTA 61.039 60.000 0.00 0.00 0.00 2.74
319 354 1.038280 GGGCTGGTACGCTACACTAT 58.962 55.000 0.00 0.00 0.00 2.12
320 355 2.233271 GGGCTGGTACGCTACACTATA 58.767 52.381 0.00 0.00 0.00 1.31
321 356 2.030451 GGGCTGGTACGCTACACTATAC 60.030 54.545 0.00 0.00 0.00 1.47
322 357 2.883386 GGCTGGTACGCTACACTATACT 59.117 50.000 0.00 0.00 0.00 2.12
323 358 3.058363 GGCTGGTACGCTACACTATACTC 60.058 52.174 0.00 0.00 0.00 2.59
329 364 3.212685 ACGCTACACTATACTCCTCCAC 58.787 50.000 0.00 0.00 0.00 4.02
333 368 2.389715 ACACTATACTCCTCCACCAGC 58.610 52.381 0.00 0.00 0.00 4.85
357 392 3.568743 GTGCGTGGTTGTGCGTGA 61.569 61.111 0.00 0.00 0.00 4.35
359 394 2.399356 TGCGTGGTTGTGCGTGAAA 61.399 52.632 0.00 0.00 0.00 2.69
360 395 1.937362 GCGTGGTTGTGCGTGAAAC 60.937 57.895 0.00 0.00 0.00 2.78
375 410 3.638484 GTGAAACGAAGTGAAATTGGGG 58.362 45.455 0.00 0.00 45.00 4.96
376 411 3.316868 GTGAAACGAAGTGAAATTGGGGA 59.683 43.478 0.00 0.00 45.00 4.81
377 412 3.568007 TGAAACGAAGTGAAATTGGGGAG 59.432 43.478 0.00 0.00 45.00 4.30
379 414 0.811281 CGAAGTGAAATTGGGGAGGC 59.189 55.000 0.00 0.00 0.00 4.70
381 416 0.404040 AAGTGAAATTGGGGAGGCGA 59.596 50.000 0.00 0.00 0.00 5.54
382 417 0.322546 AGTGAAATTGGGGAGGCGAC 60.323 55.000 0.00 0.00 0.00 5.19
430 465 2.182030 GCGTAGGCTTCTGCGTCT 59.818 61.111 0.00 0.00 45.99 4.18
460 498 1.089481 CATCTGCGGCGGCTTTTCTA 61.089 55.000 17.76 0.00 40.82 2.10
506 547 4.090588 GGATCCGACGGGCCACAA 62.091 66.667 15.25 0.00 0.00 3.33
578 622 5.833082 CATACGGAATGTACTCTGCTACTT 58.167 41.667 0.00 0.00 35.44 2.24
583 627 4.160626 GGAATGTACTCTGCTACTTGGAGT 59.839 45.833 0.00 0.00 42.13 3.85
585 629 2.826128 TGTACTCTGCTACTTGGAGTGG 59.174 50.000 0.00 0.00 40.08 4.00
590 634 1.004918 GCTACTTGGAGTGGTGCGT 60.005 57.895 0.00 0.00 0.00 5.24
591 635 1.014564 GCTACTTGGAGTGGTGCGTC 61.015 60.000 0.00 0.00 0.00 5.19
646 694 3.146066 GAGTGAGTGAGTGAGAGTGAGT 58.854 50.000 0.00 0.00 0.00 3.41
647 695 2.884012 AGTGAGTGAGTGAGAGTGAGTG 59.116 50.000 0.00 0.00 0.00 3.51
648 696 2.881513 GTGAGTGAGTGAGAGTGAGTGA 59.118 50.000 0.00 0.00 0.00 3.41
650 698 1.885887 AGTGAGTGAGAGTGAGTGAGC 59.114 52.381 0.00 0.00 0.00 4.26
652 700 1.160989 GAGTGAGAGTGAGTGAGCGA 58.839 55.000 0.00 0.00 0.00 4.93
653 701 1.130373 GAGTGAGAGTGAGTGAGCGAG 59.870 57.143 0.00 0.00 0.00 5.03
654 702 0.878416 GTGAGAGTGAGTGAGCGAGT 59.122 55.000 0.00 0.00 0.00 4.18
655 703 0.877743 TGAGAGTGAGTGAGCGAGTG 59.122 55.000 0.00 0.00 0.00 3.51
656 704 1.160989 GAGAGTGAGTGAGCGAGTGA 58.839 55.000 0.00 0.00 0.00 3.41
657 705 1.130373 GAGAGTGAGTGAGCGAGTGAG 59.870 57.143 0.00 0.00 0.00 3.51
658 706 0.878416 GAGTGAGTGAGCGAGTGAGT 59.122 55.000 0.00 0.00 0.00 3.41
659 707 0.595588 AGTGAGTGAGCGAGTGAGTG 59.404 55.000 0.00 0.00 0.00 3.51
660 708 0.387878 GTGAGTGAGCGAGTGAGTGG 60.388 60.000 0.00 0.00 0.00 4.00
661 709 0.823769 TGAGTGAGCGAGTGAGTGGT 60.824 55.000 0.00 0.00 0.00 4.16
662 710 0.387878 GAGTGAGCGAGTGAGTGGTG 60.388 60.000 0.00 0.00 0.00 4.17
663 711 2.024319 GTGAGCGAGTGAGTGGTGC 61.024 63.158 0.00 0.00 0.00 5.01
664 712 2.807045 GAGCGAGTGAGTGGTGCG 60.807 66.667 0.00 0.00 0.00 5.34
665 713 4.363990 AGCGAGTGAGTGGTGCGG 62.364 66.667 0.00 0.00 0.00 5.69
666 714 4.664677 GCGAGTGAGTGGTGCGGT 62.665 66.667 0.00 0.00 0.00 5.68
667 715 2.734723 CGAGTGAGTGGTGCGGTG 60.735 66.667 0.00 0.00 0.00 4.94
668 716 2.357517 GAGTGAGTGGTGCGGTGG 60.358 66.667 0.00 0.00 0.00 4.61
669 717 3.161450 AGTGAGTGGTGCGGTGGT 61.161 61.111 0.00 0.00 0.00 4.16
670 718 1.812686 GAGTGAGTGGTGCGGTGGTA 61.813 60.000 0.00 0.00 0.00 3.25
671 719 1.666872 GTGAGTGGTGCGGTGGTAC 60.667 63.158 0.00 0.00 0.00 3.34
672 720 2.431942 GAGTGGTGCGGTGGTACG 60.432 66.667 0.00 0.00 0.00 3.67
673 721 3.216944 GAGTGGTGCGGTGGTACGT 62.217 63.158 0.00 0.00 35.98 3.57
674 722 1.865788 GAGTGGTGCGGTGGTACGTA 61.866 60.000 0.00 0.00 35.98 3.57
675 723 1.444895 GTGGTGCGGTGGTACGTAG 60.445 63.158 0.00 0.00 35.98 3.51
676 724 2.507769 GGTGCGGTGGTACGTAGC 60.508 66.667 17.67 17.67 39.48 3.58
730 783 2.047560 GTCGAAGGGTTGGGGTCG 60.048 66.667 0.00 0.00 34.85 4.79
731 784 3.315949 TCGAAGGGTTGGGGTCGG 61.316 66.667 0.00 0.00 34.32 4.79
763 816 2.288579 GGGGTCGGGTTTCATTTGTTTC 60.289 50.000 0.00 0.00 0.00 2.78
764 817 2.606065 GGGTCGGGTTTCATTTGTTTCG 60.606 50.000 0.00 0.00 0.00 3.46
765 818 2.606065 GGTCGGGTTTCATTTGTTTCGG 60.606 50.000 0.00 0.00 0.00 4.30
766 819 2.291190 GTCGGGTTTCATTTGTTTCGGA 59.709 45.455 0.00 0.00 0.00 4.55
767 820 2.550606 TCGGGTTTCATTTGTTTCGGAG 59.449 45.455 0.00 0.00 0.00 4.63
768 821 2.672714 GGGTTTCATTTGTTTCGGAGC 58.327 47.619 0.00 0.00 0.00 4.70
808 866 3.296851 GCTGAGCTGAGCTGAGGA 58.703 61.111 21.96 0.00 40.13 3.71
921 987 3.624300 CGCTCGCTCGCTCCATTG 61.624 66.667 0.00 0.00 0.00 2.82
933 999 3.386078 TCGCTCCATTGCTTCTTCTATCT 59.614 43.478 0.00 0.00 0.00 1.98
934 1000 4.584743 TCGCTCCATTGCTTCTTCTATCTA 59.415 41.667 0.00 0.00 0.00 1.98
935 1001 5.244851 TCGCTCCATTGCTTCTTCTATCTAT 59.755 40.000 0.00 0.00 0.00 1.98
936 1002 5.576384 CGCTCCATTGCTTCTTCTATCTATC 59.424 44.000 0.00 0.00 0.00 2.08
937 1003 5.874261 GCTCCATTGCTTCTTCTATCTATCC 59.126 44.000 0.00 0.00 0.00 2.59
938 1004 6.365970 TCCATTGCTTCTTCTATCTATCCC 57.634 41.667 0.00 0.00 0.00 3.85
939 1005 6.087456 TCCATTGCTTCTTCTATCTATCCCT 58.913 40.000 0.00 0.00 0.00 4.20
940 1006 6.560304 TCCATTGCTTCTTCTATCTATCCCTT 59.440 38.462 0.00 0.00 0.00 3.95
941 1007 6.654161 CCATTGCTTCTTCTATCTATCCCTTG 59.346 42.308 0.00 0.00 0.00 3.61
942 1008 5.220710 TGCTTCTTCTATCTATCCCTTGC 57.779 43.478 0.00 0.00 0.00 4.01
943 1009 4.904251 TGCTTCTTCTATCTATCCCTTGCT 59.096 41.667 0.00 0.00 0.00 3.91
944 1010 5.011533 TGCTTCTTCTATCTATCCCTTGCTC 59.988 44.000 0.00 0.00 0.00 4.26
945 1011 5.245977 GCTTCTTCTATCTATCCCTTGCTCT 59.754 44.000 0.00 0.00 0.00 4.09
1011 1085 0.476415 ATCCCCATCCATCCACCGAT 60.476 55.000 0.00 0.00 0.00 4.18
1026 1100 0.532862 CCGATCCGCCTGCATTTACT 60.533 55.000 0.00 0.00 0.00 2.24
1027 1101 0.861837 CGATCCGCCTGCATTTACTC 59.138 55.000 0.00 0.00 0.00 2.59
1029 1103 0.179018 ATCCGCCTGCATTTACTCCC 60.179 55.000 0.00 0.00 0.00 4.30
1033 1109 0.107654 GCCTGCATTTACTCCCGTCT 60.108 55.000 0.00 0.00 0.00 4.18
1060 1136 4.447989 GCGGCAGAGCTGAGCTGA 62.448 66.667 13.71 0.00 39.88 4.26
1061 1137 2.500165 CGGCAGAGCTGAGCTGAT 59.500 61.111 13.71 0.00 39.88 2.90
1062 1138 1.592131 CGGCAGAGCTGAGCTGATC 60.592 63.158 13.71 0.00 39.88 2.92
1064 1140 1.039068 GGCAGAGCTGAGCTGATCTA 58.961 55.000 13.71 0.00 39.88 1.98
1066 1142 1.000060 GCAGAGCTGAGCTGATCTAGG 60.000 57.143 13.71 0.00 39.88 3.02
1067 1143 2.309613 CAGAGCTGAGCTGATCTAGGT 58.690 52.381 13.71 0.00 39.88 3.08
1068 1144 2.694628 CAGAGCTGAGCTGATCTAGGTT 59.305 50.000 13.71 0.00 39.88 3.50
1069 1145 2.694628 AGAGCTGAGCTGATCTAGGTTG 59.305 50.000 13.71 0.00 39.88 3.77
1070 1146 1.761784 AGCTGAGCTGATCTAGGTTGG 59.238 52.381 5.97 0.00 37.57 3.77
1071 1147 1.202627 GCTGAGCTGATCTAGGTTGGG 60.203 57.143 0.00 0.00 37.23 4.12
1072 1148 1.415659 CTGAGCTGATCTAGGTTGGGG 59.584 57.143 0.00 0.00 37.23 4.96
1073 1149 0.761802 GAGCTGATCTAGGTTGGGGG 59.238 60.000 0.00 0.00 37.23 5.40
1074 1150 1.149401 GCTGATCTAGGTTGGGGGC 59.851 63.158 0.00 0.00 0.00 5.80
1075 1151 1.447643 CTGATCTAGGTTGGGGGCG 59.552 63.158 0.00 0.00 0.00 6.13
1076 1152 2.044806 CTGATCTAGGTTGGGGGCGG 62.045 65.000 0.00 0.00 0.00 6.13
1077 1153 2.772622 ATCTAGGTTGGGGGCGGG 60.773 66.667 0.00 0.00 0.00 6.13
1419 1507 2.655685 GCTGGCGCGACTACTAGC 60.656 66.667 15.80 10.49 0.00 3.42
1420 1508 3.111939 CTGGCGCGACTACTAGCT 58.888 61.111 15.80 0.00 0.00 3.32
1423 1511 2.052060 GCGCGACTACTAGCTCCG 60.052 66.667 12.10 0.00 0.00 4.63
1429 1517 3.296054 CTACTAGCTCCGGCCGGG 61.296 72.222 42.36 32.16 39.73 5.73
1430 1518 3.786884 CTACTAGCTCCGGCCGGGA 62.787 68.421 42.36 27.36 44.68 5.14
1458 1560 3.674753 CCACATTCTTTCAATCGTTTGCC 59.325 43.478 1.18 0.00 32.61 4.52
1468 1570 1.446907 ATCGTTTGCCTCTGCTCTTG 58.553 50.000 0.00 0.00 38.71 3.02
1471 1573 0.039708 GTTTGCCTCTGCTCTTGCAC 60.040 55.000 0.00 0.00 45.31 4.57
1472 1574 0.179009 TTTGCCTCTGCTCTTGCACT 60.179 50.000 0.00 0.00 45.31 4.40
1473 1575 0.887836 TTGCCTCTGCTCTTGCACTG 60.888 55.000 0.00 0.00 45.31 3.66
1545 1652 1.288439 CGAGCTCTCCATCCATCCG 59.712 63.158 12.85 0.00 0.00 4.18
1574 1681 5.051153 GCCTATATAATCTTAGCCGCTTCC 58.949 45.833 0.00 0.00 0.00 3.46
1588 1695 2.999355 CCGCTTCCTCTTCTTCTTCTTG 59.001 50.000 0.00 0.00 0.00 3.02
1589 1696 2.414825 CGCTTCCTCTTCTTCTTCTTGC 59.585 50.000 0.00 0.00 0.00 4.01
1591 1698 4.619394 CGCTTCCTCTTCTTCTTCTTGCTA 60.619 45.833 0.00 0.00 0.00 3.49
1592 1699 4.629634 GCTTCCTCTTCTTCTTCTTGCTAC 59.370 45.833 0.00 0.00 0.00 3.58
1602 1740 7.986085 TCTTCTTCTTGCTACTGCTTAATTT 57.014 32.000 0.00 0.00 40.48 1.82
1603 1741 8.396272 TCTTCTTCTTGCTACTGCTTAATTTT 57.604 30.769 0.00 0.00 40.48 1.82
1604 1742 8.292448 TCTTCTTCTTGCTACTGCTTAATTTTG 58.708 33.333 0.00 0.00 40.48 2.44
1605 1743 6.381801 TCTTCTTGCTACTGCTTAATTTTGC 58.618 36.000 0.00 0.00 40.48 3.68
1607 1745 5.702865 TCTTGCTACTGCTTAATTTTGCTG 58.297 37.500 7.38 7.38 40.48 4.41
1625 1764 2.547855 GCTGTTGATGTTTTTCCCCACC 60.548 50.000 0.00 0.00 0.00 4.61
1637 1776 2.675075 CCCACCGCGATTTGGGTT 60.675 61.111 24.55 0.00 46.74 4.11
1662 1801 5.895362 TGTACAGTACATCAGCCATGAGCA 61.895 45.833 9.51 0.00 39.29 4.26
1670 1809 2.282391 GCCATGAGCACCACCACA 60.282 61.111 0.00 0.00 42.97 4.17
1673 1812 1.246056 CCATGAGCACCACCACAAGG 61.246 60.000 0.00 0.00 42.21 3.61
1706 1853 0.382515 CTAGCTAGCAGTCCCGTCAC 59.617 60.000 18.83 0.00 0.00 3.67
1707 1854 0.323087 TAGCTAGCAGTCCCGTCACA 60.323 55.000 18.83 0.00 0.00 3.58
1708 1855 1.185618 AGCTAGCAGTCCCGTCACAA 61.186 55.000 18.83 0.00 0.00 3.33
1709 1856 0.108138 GCTAGCAGTCCCGTCACAAT 60.108 55.000 10.63 0.00 0.00 2.71
1764 1911 3.767902 AGCTCTGCTCTCTTCTTTGTT 57.232 42.857 0.00 0.00 30.62 2.83
1765 1912 4.084011 AGCTCTGCTCTCTTCTTTGTTT 57.916 40.909 0.00 0.00 30.62 2.83
1768 1915 5.874261 AGCTCTGCTCTCTTCTTTGTTTATC 59.126 40.000 0.00 0.00 30.62 1.75
1771 1918 6.402222 TCTGCTCTCTTCTTTGTTTATCTCC 58.598 40.000 0.00 0.00 0.00 3.71
1772 1919 6.212388 TCTGCTCTCTTCTTTGTTTATCTCCT 59.788 38.462 0.00 0.00 0.00 3.69
1773 1920 6.402222 TGCTCTCTTCTTTGTTTATCTCCTC 58.598 40.000 0.00 0.00 0.00 3.71
1776 1923 7.176589 TCTCTTCTTTGTTTATCTCCTCCTC 57.823 40.000 0.00 0.00 0.00 3.71
1777 1924 6.155393 TCTCTTCTTTGTTTATCTCCTCCTCC 59.845 42.308 0.00 0.00 0.00 4.30
1794 1942 5.829391 CCTCCTCCTTTTCCTAGTACTACTC 59.171 48.000 0.00 0.00 0.00 2.59
1795 1943 6.398655 TCCTCCTTTTCCTAGTACTACTCA 57.601 41.667 0.00 0.00 0.00 3.41
1796 1944 6.982899 TCCTCCTTTTCCTAGTACTACTCAT 58.017 40.000 0.00 0.00 0.00 2.90
1797 1945 8.110743 TCCTCCTTTTCCTAGTACTACTCATA 57.889 38.462 0.00 0.00 0.00 2.15
1833 1981 5.166398 GTGCAGCTAGCTTCATTTCAATTT 58.834 37.500 20.04 0.00 45.94 1.82
1834 1982 5.061808 GTGCAGCTAGCTTCATTTCAATTTG 59.938 40.000 20.04 3.97 45.94 2.32
1836 1984 6.040878 GCAGCTAGCTTCATTTCAATTTGAT 58.959 36.000 16.46 0.00 41.15 2.57
1837 1985 6.019801 GCAGCTAGCTTCATTTCAATTTGATG 60.020 38.462 16.46 0.00 41.15 3.07
1845 2017 9.537848 GCTTCATTTCAATTTGATGTTTGATTC 57.462 29.630 0.00 0.00 32.27 2.52
1865 2037 0.609406 TGAGTGAGTGAGGGAGGTCG 60.609 60.000 0.00 0.00 0.00 4.79
1866 2038 0.609681 GAGTGAGTGAGGGAGGTCGT 60.610 60.000 0.00 0.00 0.00 4.34
1870 2042 1.228490 AGTGAGGGAGGTCGTTCGT 60.228 57.895 0.00 0.00 0.00 3.85
1909 2084 5.335127 CAAGATCAATCCATGTCGTTTTCC 58.665 41.667 0.00 0.00 0.00 3.13
1919 2094 5.181245 TCCATGTCGTTTTCCTTCATCTTTC 59.819 40.000 0.00 0.00 0.00 2.62
1946 2124 4.634004 TGATTAATTGCTGGTCCTTGTACG 59.366 41.667 0.00 0.00 0.00 3.67
1947 2125 2.561478 AATTGCTGGTCCTTGTACGT 57.439 45.000 0.00 0.00 0.00 3.57
1989 2171 1.211709 GGTTCAAATCCGGTTGGCG 59.788 57.895 0.00 0.00 34.14 5.69
1990 2172 1.211709 GTTCAAATCCGGTTGGCGG 59.788 57.895 0.00 0.00 34.14 6.13
1991 2173 1.073373 TTCAAATCCGGTTGGCGGA 59.927 52.632 0.00 0.00 40.06 5.54
2028 2226 2.107750 CGGATGAGGCTCACGCAT 59.892 61.111 21.37 3.15 42.62 4.73
2051 2252 0.043566 CGCACGCAGAGATTGAATCG 60.044 55.000 0.00 0.00 0.00 3.34
2056 2257 3.181973 CACGCAGAGATTGAATCGATCAG 59.818 47.826 12.62 3.81 39.77 2.90
2057 2258 2.730404 CGCAGAGATTGAATCGATCAGG 59.270 50.000 12.62 3.16 39.77 3.86
2058 2259 2.479656 GCAGAGATTGAATCGATCAGGC 59.520 50.000 12.62 8.74 39.77 4.85
2059 2260 3.803021 GCAGAGATTGAATCGATCAGGCT 60.803 47.826 12.62 4.43 39.77 4.58
2060 2261 3.989167 CAGAGATTGAATCGATCAGGCTC 59.011 47.826 12.62 8.98 39.77 4.70
2061 2262 3.640498 AGAGATTGAATCGATCAGGCTCA 59.360 43.478 12.62 10.32 40.07 4.26
2066 2267 1.686052 GAATCGATCAGGCTCAGGAGT 59.314 52.381 0.00 0.00 0.00 3.85
2068 2269 2.437085 TCGATCAGGCTCAGGAGTTA 57.563 50.000 0.00 0.00 0.00 2.24
2078 2279 0.252103 TCAGGAGTTAAGGGGCTCGT 60.252 55.000 0.00 0.00 32.83 4.18
2137 2346 1.493950 CCGGTCAATCGATCTGCTGC 61.494 60.000 0.00 0.00 0.00 5.25
2149 2358 3.665190 GATCTGCTGCTGATGATGATGA 58.335 45.455 24.01 0.00 0.00 2.92
2186 2396 2.174854 AGTACAATTAGGTGGGGGATGC 59.825 50.000 0.00 0.00 0.00 3.91
2187 2397 1.006813 ACAATTAGGTGGGGGATGCA 58.993 50.000 0.00 0.00 0.00 3.96
2189 2399 2.225496 ACAATTAGGTGGGGGATGCAAA 60.225 45.455 0.00 0.00 0.00 3.68
2190 2400 3.040477 CAATTAGGTGGGGGATGCAAAT 58.960 45.455 0.00 0.00 0.00 2.32
2205 2619 3.781341 GCAAATGCAACACAAGTGATG 57.219 42.857 7.28 6.65 41.59 3.07
2288 2718 4.218578 CTCGCTCATGCTCGCCCT 62.219 66.667 0.00 0.00 36.97 5.19
2289 2719 4.212913 TCGCTCATGCTCGCCCTC 62.213 66.667 0.00 0.00 36.97 4.30
2291 2721 4.925861 GCTCATGCTCGCCCTCCC 62.926 72.222 0.00 0.00 36.03 4.30
2292 2722 3.160047 CTCATGCTCGCCCTCCCT 61.160 66.667 0.00 0.00 0.00 4.20
2325 2755 4.460382 AGCCAATCAGTAGACCAAATGTTG 59.540 41.667 0.00 0.00 0.00 3.33
2338 2768 4.824289 CCAAATGTTGGCTTGCTTAATCT 58.176 39.130 0.00 0.00 45.17 2.40
2339 2769 4.866486 CCAAATGTTGGCTTGCTTAATCTC 59.134 41.667 0.00 0.00 45.17 2.75
2340 2770 4.361451 AATGTTGGCTTGCTTAATCTCG 57.639 40.909 0.00 0.00 0.00 4.04
2341 2771 1.468520 TGTTGGCTTGCTTAATCTCGC 59.531 47.619 0.00 0.00 0.00 5.03
2342 2772 1.468520 GTTGGCTTGCTTAATCTCGCA 59.531 47.619 0.00 0.00 0.00 5.10
2410 2898 3.103742 AGGGCTCACTCTAGAAGAAAGG 58.896 50.000 0.00 0.00 0.00 3.11
2440 2928 3.641648 AGATTCAACGCATTGTGTTTGG 58.358 40.909 12.74 3.76 33.78 3.28
2447 2939 2.228822 ACGCATTGTGTTTGGATCCTTC 59.771 45.455 14.23 3.98 0.00 3.46
2475 2967 8.827832 TTTTACTGGTATACTCTAGCAGGTTA 57.172 34.615 13.98 0.00 44.64 2.85
2613 3108 3.768757 GCCAAGGGCCATGCAAATATATA 59.231 43.478 6.18 0.00 44.06 0.86
2615 3110 5.682990 GCCAAGGGCCATGCAAATATATATG 60.683 44.000 6.18 0.00 44.06 1.78
2617 3112 6.606796 CCAAGGGCCATGCAAATATATATGTA 59.393 38.462 6.18 0.00 0.00 2.29
2618 3113 7.288389 CCAAGGGCCATGCAAATATATATGTAT 59.712 37.037 6.18 0.00 0.00 2.29
2619 3114 7.828508 AGGGCCATGCAAATATATATGTATG 57.171 36.000 6.18 7.20 38.77 2.39
2620 3115 6.266103 AGGGCCATGCAAATATATATGTATGC 59.734 38.462 6.18 16.03 38.04 3.14
2621 3116 6.040729 GGGCCATGCAAATATATATGTATGCA 59.959 38.462 22.81 22.81 46.43 3.96
2635 3134 2.166664 TGTATGCATATATACGCGCCCA 59.833 45.455 10.16 0.00 36.54 5.36
2726 3231 6.649041 AGTTCCAACTACCTAGTAGGAGTA 57.351 41.667 23.50 4.83 40.13 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.037251 ACTACAACTACCACTGGCAGTG 59.963 50.000 35.08 35.08 45.53 3.66
15 16 2.326428 ACTACAACTACCACTGGCAGT 58.674 47.619 15.88 15.88 0.00 4.40
16 17 3.402628 AACTACAACTACCACTGGCAG 57.597 47.619 14.16 14.16 0.00 4.85
17 18 3.007182 GGTAACTACAACTACCACTGGCA 59.993 47.826 0.00 0.00 37.98 4.92
18 19 3.007182 TGGTAACTACAACTACCACTGGC 59.993 47.826 0.00 0.00 42.09 4.85
19 20 4.282703 ACTGGTAACTACAACTACCACTGG 59.717 45.833 0.00 0.00 42.09 4.00
20 21 5.221382 ACACTGGTAACTACAACTACCACTG 60.221 44.000 0.00 2.53 42.09 3.66
21 22 4.897670 ACACTGGTAACTACAACTACCACT 59.102 41.667 0.00 0.00 42.09 4.00
22 23 4.986659 CACACTGGTAACTACAACTACCAC 59.013 45.833 0.00 0.00 42.09 4.16
23 24 4.039488 CCACACTGGTAACTACAACTACCA 59.961 45.833 1.30 1.30 44.21 3.25
24 25 4.563061 CCACACTGGTAACTACAACTACC 58.437 47.826 0.00 0.00 38.47 3.18
25 26 3.992427 GCCACACTGGTAACTACAACTAC 59.008 47.826 0.00 0.00 40.46 2.73
26 27 3.642377 TGCCACACTGGTAACTACAACTA 59.358 43.478 0.00 0.00 40.46 2.24
27 28 2.436542 TGCCACACTGGTAACTACAACT 59.563 45.455 0.00 0.00 40.46 3.16
28 29 2.841215 TGCCACACTGGTAACTACAAC 58.159 47.619 0.00 0.00 40.46 3.32
29 30 3.562343 TTGCCACACTGGTAACTACAA 57.438 42.857 0.00 0.00 37.20 2.41
30 31 3.562343 TTTGCCACACTGGTAACTACA 57.438 42.857 0.00 0.00 41.82 2.74
31 32 5.243207 AGTATTTGCCACACTGGTAACTAC 58.757 41.667 9.97 9.97 41.82 2.73
32 33 5.492855 AGTATTTGCCACACTGGTAACTA 57.507 39.130 0.00 0.00 41.82 2.24
33 34 4.367039 AGTATTTGCCACACTGGTAACT 57.633 40.909 0.00 0.00 41.82 2.24
34 35 5.447624 AAAGTATTTGCCACACTGGTAAC 57.552 39.130 0.00 0.00 41.82 2.50
56 57 9.874205 CCTTTTGAAATATATTTTTCTCCTGCA 57.126 29.630 11.92 0.75 36.71 4.41
57 58 9.317936 CCCTTTTGAAATATATTTTTCTCCTGC 57.682 33.333 11.92 0.00 36.71 4.85
68 69 5.826208 GGTCGGTGACCCTTTTGAAATATAT 59.174 40.000 4.60 0.00 46.19 0.86
70 71 4.014406 GGTCGGTGACCCTTTTGAAATAT 58.986 43.478 4.60 0.00 46.19 1.28
71 72 3.414269 GGTCGGTGACCCTTTTGAAATA 58.586 45.455 4.60 0.00 46.19 1.40
73 74 1.682740 GGTCGGTGACCCTTTTGAAA 58.317 50.000 4.60 0.00 46.19 2.69
127 134 0.445436 GCTCGCCACTGTCAAATCAG 59.555 55.000 0.00 0.00 40.80 2.90
188 220 1.324383 TCACTGTGCGTAACCTCTGA 58.676 50.000 2.12 0.00 0.00 3.27
198 230 1.067693 TTTACTGCGATCACTGTGCG 58.932 50.000 2.12 3.13 0.00 5.34
231 263 4.509737 GTACCCTCGCTCACGGCC 62.510 72.222 0.00 0.00 40.63 6.13
232 264 2.117156 TAGTACCCTCGCTCACGGC 61.117 63.158 0.00 0.00 40.63 5.68
233 265 0.747283 AGTAGTACCCTCGCTCACGG 60.747 60.000 0.00 0.00 40.63 4.94
235 267 2.354199 GTGTAGTAGTACCCTCGCTCAC 59.646 54.545 5.26 0.00 0.00 3.51
236 268 2.636830 GTGTAGTAGTACCCTCGCTCA 58.363 52.381 5.26 0.00 0.00 4.26
237 269 1.946081 GGTGTAGTAGTACCCTCGCTC 59.054 57.143 5.26 0.00 0.00 5.03
238 270 1.283029 TGGTGTAGTAGTACCCTCGCT 59.717 52.381 5.26 0.00 36.10 4.93
239 271 1.403323 GTGGTGTAGTAGTACCCTCGC 59.597 57.143 5.26 0.00 36.10 5.03
240 272 2.996631 AGTGGTGTAGTAGTACCCTCG 58.003 52.381 5.26 0.00 36.10 4.63
241 273 4.085009 ACAAGTGGTGTAGTAGTACCCTC 58.915 47.826 5.26 7.09 39.29 4.30
242 274 4.123729 ACAAGTGGTGTAGTAGTACCCT 57.876 45.455 5.26 0.00 39.29 4.34
243 275 5.478332 AGTTACAAGTGGTGTAGTAGTACCC 59.522 44.000 5.26 6.75 43.61 3.69
244 276 6.581171 AGTTACAAGTGGTGTAGTAGTACC 57.419 41.667 5.26 0.00 43.61 3.34
245 277 9.965824 TTAAAGTTACAAGTGGTGTAGTAGTAC 57.034 33.333 0.37 0.37 43.61 2.73
264 296 9.738832 ACGCAGTACAAACATAAAATTAAAGTT 57.261 25.926 0.00 0.00 41.94 2.66
270 302 7.867752 ACTACACGCAGTACAAACATAAAATT 58.132 30.769 0.00 0.00 41.61 1.82
272 304 6.847956 ACTACACGCAGTACAAACATAAAA 57.152 33.333 0.00 0.00 41.61 1.52
273 305 7.337150 GTACTACACGCAGTACAAACATAAA 57.663 36.000 14.39 0.00 46.72 1.40
297 329 4.217159 GTAGCGTACCAGCCCCGG 62.217 72.222 0.00 0.00 38.01 5.73
298 330 3.454573 TGTAGCGTACCAGCCCCG 61.455 66.667 0.00 0.00 38.01 5.73
299 331 1.039233 TAGTGTAGCGTACCAGCCCC 61.039 60.000 0.00 0.00 38.01 5.80
301 333 2.883386 AGTATAGTGTAGCGTACCAGCC 59.117 50.000 0.00 0.00 38.01 4.85
302 334 3.058363 GGAGTATAGTGTAGCGTACCAGC 60.058 52.174 0.00 0.00 37.41 4.85
303 335 4.387598 AGGAGTATAGTGTAGCGTACCAG 58.612 47.826 0.00 0.00 0.00 4.00
315 350 2.672098 CAGCTGGTGGAGGAGTATAGT 58.328 52.381 5.57 0.00 0.00 2.12
316 351 1.342819 GCAGCTGGTGGAGGAGTATAG 59.657 57.143 17.12 0.00 0.00 1.31
317 352 1.062886 AGCAGCTGGTGGAGGAGTATA 60.063 52.381 19.45 0.00 0.00 1.47
318 353 0.326048 AGCAGCTGGTGGAGGAGTAT 60.326 55.000 19.45 0.00 0.00 2.12
319 354 1.079256 AGCAGCTGGTGGAGGAGTA 59.921 57.895 19.45 0.00 0.00 2.59
320 355 2.203907 AGCAGCTGGTGGAGGAGT 60.204 61.111 19.45 0.00 0.00 3.85
321 356 2.268280 CAGCAGCTGGTGGAGGAG 59.732 66.667 33.27 10.92 39.67 3.69
322 357 4.025858 GCAGCAGCTGGTGGAGGA 62.026 66.667 38.56 0.00 43.24 3.71
333 368 4.671549 CAACCACGCACGCAGCAG 62.672 66.667 0.00 0.00 46.13 4.24
357 392 2.890945 CCTCCCCAATTTCACTTCGTTT 59.109 45.455 0.00 0.00 0.00 3.60
359 394 1.886655 GCCTCCCCAATTTCACTTCGT 60.887 52.381 0.00 0.00 0.00 3.85
360 395 0.811281 GCCTCCCCAATTTCACTTCG 59.189 55.000 0.00 0.00 0.00 3.79
366 401 0.322546 ACTGTCGCCTCCCCAATTTC 60.323 55.000 0.00 0.00 0.00 2.17
367 402 0.609131 CACTGTCGCCTCCCCAATTT 60.609 55.000 0.00 0.00 0.00 1.82
368 403 1.002134 CACTGTCGCCTCCCCAATT 60.002 57.895 0.00 0.00 0.00 2.32
369 404 0.907704 TACACTGTCGCCTCCCCAAT 60.908 55.000 0.00 0.00 0.00 3.16
370 405 1.534476 TACACTGTCGCCTCCCCAA 60.534 57.895 0.00 0.00 0.00 4.12
371 406 1.982395 CTACACTGTCGCCTCCCCA 60.982 63.158 0.00 0.00 0.00 4.96
373 408 0.682209 TACCTACACTGTCGCCTCCC 60.682 60.000 0.00 0.00 0.00 4.30
375 410 0.455005 GGTACCTACACTGTCGCCTC 59.545 60.000 4.06 0.00 0.00 4.70
376 411 0.251474 TGGTACCTACACTGTCGCCT 60.251 55.000 14.36 0.00 0.00 5.52
377 412 0.604578 TTGGTACCTACACTGTCGCC 59.395 55.000 14.36 0.00 0.00 5.54
379 414 2.555325 TCTGTTGGTACCTACACTGTCG 59.445 50.000 23.00 14.06 0.00 4.35
381 416 5.562298 AATTCTGTTGGTACCTACACTGT 57.438 39.130 23.00 10.18 0.00 3.55
382 417 6.877611 AAAATTCTGTTGGTACCTACACTG 57.122 37.500 23.00 15.35 0.00 3.66
481 522 4.873129 CGTCGGATCCACCTGCCG 62.873 72.222 13.41 0.00 46.08 5.69
506 547 0.478072 TGGTGGTGCAAGTGGAATCT 59.522 50.000 0.00 0.00 0.00 2.40
517 558 2.573083 CCAATGGTGGTGGTGGTGC 61.573 63.158 0.00 0.00 40.42 5.01
518 559 3.776158 CCAATGGTGGTGGTGGTG 58.224 61.111 0.00 0.00 40.42 4.17
557 601 4.097437 CCAAGTAGCAGAGTACATTCCGTA 59.903 45.833 0.00 0.00 0.00 4.02
575 619 1.069765 CAGACGCACCACTCCAAGT 59.930 57.895 0.00 0.00 0.00 3.16
578 622 4.662961 CGCAGACGCACCACTCCA 62.663 66.667 0.00 0.00 38.40 3.86
583 627 1.163420 ATGAAAACGCAGACGCACCA 61.163 50.000 0.00 0.00 45.53 4.17
585 629 0.725784 CCATGAAAACGCAGACGCAC 60.726 55.000 0.00 0.00 45.53 5.34
590 634 0.320858 TACCGCCATGAAAACGCAGA 60.321 50.000 0.00 0.00 0.00 4.26
591 635 0.096976 CTACCGCCATGAAAACGCAG 59.903 55.000 0.00 0.00 0.00 5.18
632 680 0.877743 CGCTCACTCACTCTCACTCA 59.122 55.000 0.00 0.00 0.00 3.41
633 681 1.130373 CTCGCTCACTCACTCTCACTC 59.870 57.143 0.00 0.00 0.00 3.51
634 682 1.164411 CTCGCTCACTCACTCTCACT 58.836 55.000 0.00 0.00 0.00 3.41
635 683 0.878416 ACTCGCTCACTCACTCTCAC 59.122 55.000 0.00 0.00 0.00 3.51
646 694 2.340078 GCACCACTCACTCGCTCA 59.660 61.111 0.00 0.00 0.00 4.26
647 695 2.807045 CGCACCACTCACTCGCTC 60.807 66.667 0.00 0.00 0.00 5.03
648 696 4.363990 CCGCACCACTCACTCGCT 62.364 66.667 0.00 0.00 0.00 4.93
650 698 2.734723 CACCGCACCACTCACTCG 60.735 66.667 0.00 0.00 0.00 4.18
652 700 1.835267 TACCACCGCACCACTCACT 60.835 57.895 0.00 0.00 0.00 3.41
653 701 1.666872 GTACCACCGCACCACTCAC 60.667 63.158 0.00 0.00 0.00 3.51
654 702 2.738480 GTACCACCGCACCACTCA 59.262 61.111 0.00 0.00 0.00 3.41
655 703 1.865788 TACGTACCACCGCACCACTC 61.866 60.000 0.00 0.00 0.00 3.51
656 704 1.870055 CTACGTACCACCGCACCACT 61.870 60.000 0.00 0.00 0.00 4.00
657 705 1.444895 CTACGTACCACCGCACCAC 60.445 63.158 0.00 0.00 0.00 4.16
658 706 2.964174 CTACGTACCACCGCACCA 59.036 61.111 0.00 0.00 0.00 4.17
659 707 1.656818 TAGCTACGTACCACCGCACC 61.657 60.000 6.54 0.00 0.00 5.01
660 708 0.248377 CTAGCTACGTACCACCGCAC 60.248 60.000 6.54 0.00 0.00 5.34
661 709 1.996786 GCTAGCTACGTACCACCGCA 61.997 60.000 7.70 0.00 0.00 5.69
662 710 1.298938 GCTAGCTACGTACCACCGC 60.299 63.158 7.70 0.00 0.00 5.68
663 711 0.029035 CAGCTAGCTACGTACCACCG 59.971 60.000 18.86 0.00 0.00 4.94
664 712 0.384669 CCAGCTAGCTACGTACCACC 59.615 60.000 18.86 0.00 0.00 4.61
665 713 1.101331 ACCAGCTAGCTACGTACCAC 58.899 55.000 18.86 0.00 0.00 4.16
666 714 1.100510 CACCAGCTAGCTACGTACCA 58.899 55.000 18.86 0.00 0.00 3.25
667 715 0.248949 GCACCAGCTAGCTACGTACC 60.249 60.000 18.86 7.43 37.91 3.34
668 716 0.248949 GGCACCAGCTAGCTACGTAC 60.249 60.000 18.86 11.04 41.70 3.67
669 717 0.395311 AGGCACCAGCTAGCTACGTA 60.395 55.000 18.86 0.00 41.70 3.57
670 718 1.682684 AGGCACCAGCTAGCTACGT 60.683 57.895 18.86 13.78 41.70 3.57
671 719 1.227089 CAGGCACCAGCTAGCTACG 60.227 63.158 18.86 13.08 41.70 3.51
672 720 1.144936 CCAGGCACCAGCTAGCTAC 59.855 63.158 18.86 7.29 41.70 3.58
673 721 0.909610 AACCAGGCACCAGCTAGCTA 60.910 55.000 18.86 0.00 41.70 3.32
674 722 2.227036 AACCAGGCACCAGCTAGCT 61.227 57.895 12.68 12.68 41.70 3.32
675 723 2.042831 CAACCAGGCACCAGCTAGC 61.043 63.158 6.62 6.62 41.70 3.42
676 724 1.377725 CCAACCAGGCACCAGCTAG 60.378 63.158 0.00 0.00 41.70 3.42
737 790 4.399395 GAAACCCGACCCCGACCC 62.399 72.222 0.00 0.00 38.22 4.46
738 791 2.473891 AATGAAACCCGACCCCGACC 62.474 60.000 0.00 0.00 38.22 4.79
739 792 0.607217 AAATGAAACCCGACCCCGAC 60.607 55.000 0.00 0.00 38.22 4.79
740 793 0.606944 CAAATGAAACCCGACCCCGA 60.607 55.000 0.00 0.00 38.22 5.14
741 794 0.891904 ACAAATGAAACCCGACCCCG 60.892 55.000 0.00 0.00 0.00 5.73
802 860 0.396974 CCTGTCTCCTCCCTCCTCAG 60.397 65.000 0.00 0.00 0.00 3.35
803 861 1.700368 CCTGTCTCCTCCCTCCTCA 59.300 63.158 0.00 0.00 0.00 3.86
805 863 3.114390 CCCTGTCTCCTCCCTCCT 58.886 66.667 0.00 0.00 0.00 3.69
806 864 2.766229 GCCCTGTCTCCTCCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
807 865 3.151022 CGCCCTGTCTCCTCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
808 866 4.787280 CCGCCCTGTCTCCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
921 987 5.245977 AGAGCAAGGGATAGATAGAAGAAGC 59.754 44.000 0.00 0.00 0.00 3.86
933 999 1.045350 AGCGAGCAGAGCAAGGGATA 61.045 55.000 0.00 0.00 37.01 2.59
934 1000 2.188994 GCGAGCAGAGCAAGGGAT 59.811 61.111 0.00 0.00 34.19 3.85
935 1001 2.999648 AGCGAGCAGAGCAAGGGA 61.000 61.111 0.00 0.00 37.01 4.20
936 1002 2.511145 GAGCGAGCAGAGCAAGGG 60.511 66.667 0.00 0.00 37.01 3.95
937 1003 1.810441 CAGAGCGAGCAGAGCAAGG 60.810 63.158 0.00 0.00 37.01 3.61
938 1004 2.454464 GCAGAGCGAGCAGAGCAAG 61.454 63.158 0.00 0.00 37.01 4.01
939 1005 2.433838 GCAGAGCGAGCAGAGCAA 60.434 61.111 0.00 0.00 37.01 3.91
940 1006 3.353770 GAGCAGAGCGAGCAGAGCA 62.354 63.158 0.00 0.00 37.01 4.26
941 1007 2.583045 GAGCAGAGCGAGCAGAGC 60.583 66.667 0.00 0.00 0.00 4.09
942 1008 0.179105 AATGAGCAGAGCGAGCAGAG 60.179 55.000 0.00 0.00 0.00 3.35
943 1009 0.179116 GAATGAGCAGAGCGAGCAGA 60.179 55.000 0.00 0.00 0.00 4.26
944 1010 1.152989 GGAATGAGCAGAGCGAGCAG 61.153 60.000 0.00 0.00 0.00 4.24
945 1011 1.153489 GGAATGAGCAGAGCGAGCA 60.153 57.895 0.00 0.00 0.00 4.26
1011 1085 1.223487 GGGAGTAAATGCAGGCGGA 59.777 57.895 0.00 0.00 0.00 5.54
1050 1126 1.761784 CCAACCTAGATCAGCTCAGCT 59.238 52.381 0.00 0.00 40.77 4.24
1056 1132 1.149401 GCCCCCAACCTAGATCAGC 59.851 63.158 0.00 0.00 0.00 4.26
1060 1136 2.772622 CCCGCCCCCAACCTAGAT 60.773 66.667 0.00 0.00 0.00 1.98
1077 1153 4.176752 GTCGTCCCCCTCCATGCC 62.177 72.222 0.00 0.00 0.00 4.40
1429 1517 1.538047 TGAAAGAATGTGGGCAGCTC 58.462 50.000 0.00 0.00 0.00 4.09
1430 1518 1.999648 TTGAAAGAATGTGGGCAGCT 58.000 45.000 0.00 0.00 0.00 4.24
1431 1519 2.733227 CGATTGAAAGAATGTGGGCAGC 60.733 50.000 0.00 0.00 0.00 5.25
1433 1521 2.513753 ACGATTGAAAGAATGTGGGCA 58.486 42.857 0.00 0.00 0.00 5.36
1434 1522 3.575965 AACGATTGAAAGAATGTGGGC 57.424 42.857 0.00 0.00 0.00 5.36
1545 1652 6.500041 CGGCTAAGATTATATAGGCTGAGAC 58.500 44.000 0.00 0.00 41.21 3.36
1574 1681 4.819769 AGCAGTAGCAAGAAGAAGAAGAG 58.180 43.478 0.00 0.00 45.49 2.85
1588 1695 5.460646 TCAACAGCAAAATTAAGCAGTAGC 58.539 37.500 5.04 0.00 42.56 3.58
1589 1696 7.086376 ACATCAACAGCAAAATTAAGCAGTAG 58.914 34.615 5.04 0.00 29.97 2.57
1591 1698 5.846203 ACATCAACAGCAAAATTAAGCAGT 58.154 33.333 5.04 0.40 31.48 4.40
1592 1699 6.774354 AACATCAACAGCAAAATTAAGCAG 57.226 33.333 5.04 0.00 0.00 4.24
1602 1740 2.768527 TGGGGAAAAACATCAACAGCAA 59.231 40.909 0.00 0.00 0.00 3.91
1603 1741 2.102252 GTGGGGAAAAACATCAACAGCA 59.898 45.455 0.00 0.00 0.00 4.41
1604 1742 2.547855 GGTGGGGAAAAACATCAACAGC 60.548 50.000 0.00 0.00 0.00 4.40
1605 1743 2.288152 CGGTGGGGAAAAACATCAACAG 60.288 50.000 0.00 0.00 0.00 3.16
1607 1745 1.604438 GCGGTGGGGAAAAACATCAAC 60.604 52.381 0.00 0.00 0.00 3.18
1625 1764 2.933906 ACTGTACATAACCCAAATCGCG 59.066 45.455 0.00 0.00 0.00 5.87
1637 1776 5.509670 GCTCATGGCTGATGTACTGTACATA 60.510 44.000 28.09 15.82 42.56 2.29
1662 1801 0.553819 TTACCTTGCCTTGTGGTGGT 59.446 50.000 0.00 0.00 37.35 4.16
1670 1809 3.970640 AGCTAGCTAGATTACCTTGCCTT 59.029 43.478 25.15 0.00 43.24 4.35
1673 1812 4.490743 GCTAGCTAGCTAGATTACCTTGC 58.509 47.826 42.59 26.70 46.56 4.01
1706 1853 5.278169 GCTAGTAATGGTGGCTGATTGATTG 60.278 44.000 0.00 0.00 0.00 2.67
1707 1854 4.823989 GCTAGTAATGGTGGCTGATTGATT 59.176 41.667 0.00 0.00 0.00 2.57
1708 1855 4.103785 AGCTAGTAATGGTGGCTGATTGAT 59.896 41.667 0.00 0.00 31.68 2.57
1709 1856 3.455910 AGCTAGTAATGGTGGCTGATTGA 59.544 43.478 0.00 0.00 31.68 2.57
1749 1896 6.365970 AGGAGATAAACAAAGAAGAGAGCA 57.634 37.500 0.00 0.00 0.00 4.26
1750 1897 5.815222 GGAGGAGATAAACAAAGAAGAGAGC 59.185 44.000 0.00 0.00 0.00 4.09
1751 1898 7.181569 AGGAGGAGATAAACAAAGAAGAGAG 57.818 40.000 0.00 0.00 0.00 3.20
1752 1899 6.155393 GGAGGAGGAGATAAACAAAGAAGAGA 59.845 42.308 0.00 0.00 0.00 3.10
1753 1900 6.156083 AGGAGGAGGAGATAAACAAAGAAGAG 59.844 42.308 0.00 0.00 0.00 2.85
1754 1901 6.026186 AGGAGGAGGAGATAAACAAAGAAGA 58.974 40.000 0.00 0.00 0.00 2.87
1755 1902 6.306643 AGGAGGAGGAGATAAACAAAGAAG 57.693 41.667 0.00 0.00 0.00 2.85
1756 1903 6.704056 AAGGAGGAGGAGATAAACAAAGAA 57.296 37.500 0.00 0.00 0.00 2.52
1757 1904 6.704056 AAAGGAGGAGGAGATAAACAAAGA 57.296 37.500 0.00 0.00 0.00 2.52
1758 1905 6.375736 GGAAAAGGAGGAGGAGATAAACAAAG 59.624 42.308 0.00 0.00 0.00 2.77
1759 1906 6.045577 AGGAAAAGGAGGAGGAGATAAACAAA 59.954 38.462 0.00 0.00 0.00 2.83
1760 1907 5.551977 AGGAAAAGGAGGAGGAGATAAACAA 59.448 40.000 0.00 0.00 0.00 2.83
1761 1908 5.101529 AGGAAAAGGAGGAGGAGATAAACA 58.898 41.667 0.00 0.00 0.00 2.83
1762 1909 5.702065 AGGAAAAGGAGGAGGAGATAAAC 57.298 43.478 0.00 0.00 0.00 2.01
1763 1910 6.513033 ACTAGGAAAAGGAGGAGGAGATAAA 58.487 40.000 0.00 0.00 0.00 1.40
1764 1911 6.106407 ACTAGGAAAAGGAGGAGGAGATAA 57.894 41.667 0.00 0.00 0.00 1.75
1765 1912 5.752864 ACTAGGAAAAGGAGGAGGAGATA 57.247 43.478 0.00 0.00 0.00 1.98
1768 1915 4.874199 AGTACTAGGAAAAGGAGGAGGAG 58.126 47.826 0.00 0.00 0.00 3.69
1771 1918 6.424883 TGAGTAGTACTAGGAAAAGGAGGAG 58.575 44.000 1.87 0.00 0.00 3.69
1772 1919 6.398655 TGAGTAGTACTAGGAAAAGGAGGA 57.601 41.667 1.87 0.00 0.00 3.71
1773 1920 8.763984 TTATGAGTAGTACTAGGAAAAGGAGG 57.236 38.462 1.87 0.00 0.00 4.30
1776 1923 9.411189 AGTCTTATGAGTAGTACTAGGAAAAGG 57.589 37.037 1.87 0.00 0.00 3.11
1794 1942 7.430502 GCTAGCTGCACAAATTTAAGTCTTATG 59.569 37.037 7.70 0.00 42.31 1.90
1795 1943 7.337942 AGCTAGCTGCACAAATTTAAGTCTTAT 59.662 33.333 18.57 0.00 45.94 1.73
1796 1944 6.655003 AGCTAGCTGCACAAATTTAAGTCTTA 59.345 34.615 18.57 0.00 45.94 2.10
1797 1945 5.474876 AGCTAGCTGCACAAATTTAAGTCTT 59.525 36.000 18.57 0.00 45.94 3.01
1833 1981 5.857268 TCACTCACTCAGAATCAAACATCA 58.143 37.500 0.00 0.00 0.00 3.07
1834 1982 5.350914 CCTCACTCACTCAGAATCAAACATC 59.649 44.000 0.00 0.00 0.00 3.06
1836 1984 4.503817 CCCTCACTCACTCAGAATCAAACA 60.504 45.833 0.00 0.00 0.00 2.83
1837 1985 3.999663 CCCTCACTCACTCAGAATCAAAC 59.000 47.826 0.00 0.00 0.00 2.93
1845 2017 1.181786 GACCTCCCTCACTCACTCAG 58.818 60.000 0.00 0.00 0.00 3.35
1866 2038 4.362932 TGCATGTTTGTTCTTCAACGAA 57.637 36.364 0.00 0.00 35.61 3.85
1870 2042 6.146601 TGATCTTGCATGTTTGTTCTTCAA 57.853 33.333 0.00 0.00 0.00 2.69
1909 2084 7.219535 CAGCAATTAATCAACGGAAAGATGAAG 59.780 37.037 0.00 0.00 35.25 3.02
1919 2094 3.016736 AGGACCAGCAATTAATCAACGG 58.983 45.455 0.00 0.00 0.00 4.44
1946 2124 7.061326 CCGCAAACAACAAATTATTGGTACTAC 59.939 37.037 7.16 0.00 41.01 2.73
1947 2125 7.085116 CCGCAAACAACAAATTATTGGTACTA 58.915 34.615 7.16 0.00 41.01 1.82
1989 2171 2.680370 AATTGACCGCCCTCCCTCC 61.680 63.158 0.00 0.00 0.00 4.30
1990 2172 1.452108 CAATTGACCGCCCTCCCTC 60.452 63.158 0.00 0.00 0.00 4.30
1991 2173 1.923395 TCAATTGACCGCCCTCCCT 60.923 57.895 3.38 0.00 0.00 4.20
2028 2226 2.357396 AATCTCTGCGTGCGTGCA 60.357 55.556 2.51 2.51 43.95 4.57
2051 2252 2.103941 CCCTTAACTCCTGAGCCTGATC 59.896 54.545 0.00 0.00 0.00 2.92
2056 2257 1.224870 GCCCCTTAACTCCTGAGCC 59.775 63.158 0.00 0.00 0.00 4.70
2057 2258 0.179234 GAGCCCCTTAACTCCTGAGC 59.821 60.000 0.00 0.00 0.00 4.26
2058 2259 0.461961 CGAGCCCCTTAACTCCTGAG 59.538 60.000 0.00 0.00 0.00 3.35
2059 2260 0.252103 ACGAGCCCCTTAACTCCTGA 60.252 55.000 0.00 0.00 0.00 3.86
2060 2261 0.175989 GACGAGCCCCTTAACTCCTG 59.824 60.000 0.00 0.00 0.00 3.86
2061 2262 1.321074 CGACGAGCCCCTTAACTCCT 61.321 60.000 0.00 0.00 0.00 3.69
2078 2279 2.828095 CAATGATTGGCCGGCCGA 60.828 61.111 37.50 37.50 39.42 5.54
2083 2292 3.009723 AGACTAACACAATGATTGGCCG 58.990 45.455 10.27 0.33 34.12 6.13
2091 2300 4.091509 GCGTCCACTAAGACTAACACAATG 59.908 45.833 0.00 0.00 34.46 2.82
2124 2333 2.904697 TCATCAGCAGCAGATCGATT 57.095 45.000 0.00 0.00 0.00 3.34
2125 2334 2.299297 TCATCATCAGCAGCAGATCGAT 59.701 45.455 0.00 0.00 0.00 3.59
2137 2346 6.261826 CCCATCATCATCATCATCATCATCAG 59.738 42.308 0.00 0.00 0.00 2.90
2149 2358 3.601520 TGTACTCCCCCATCATCATCAT 58.398 45.455 0.00 0.00 0.00 2.45
2186 2396 3.124560 TGCATCACTTGTGTTGCATTTG 58.875 40.909 26.01 6.80 39.98 2.32
2187 2397 3.386486 CTGCATCACTTGTGTTGCATTT 58.614 40.909 28.30 0.00 43.51 2.32
2189 2399 1.336517 GCTGCATCACTTGTGTTGCAT 60.337 47.619 28.30 4.00 43.51 3.96
2190 2400 0.031043 GCTGCATCACTTGTGTTGCA 59.969 50.000 27.13 27.13 42.41 4.08
2204 2618 2.168106 ACCAACAAATTGACAAGCTGCA 59.832 40.909 1.02 0.00 38.15 4.41
2205 2619 2.540931 CACCAACAAATTGACAAGCTGC 59.459 45.455 0.00 0.00 38.15 5.25
2206 2620 3.125316 CCACCAACAAATTGACAAGCTG 58.875 45.455 0.00 0.00 38.15 4.24
2288 2718 3.523157 TGATTGGCTTGACTGAATAGGGA 59.477 43.478 0.00 0.00 0.00 4.20
2289 2719 3.881688 CTGATTGGCTTGACTGAATAGGG 59.118 47.826 0.00 0.00 0.00 3.53
2290 2720 4.521146 ACTGATTGGCTTGACTGAATAGG 58.479 43.478 0.00 0.00 0.00 2.57
2291 2721 6.478344 GTCTACTGATTGGCTTGACTGAATAG 59.522 42.308 0.00 0.00 0.00 1.73
2292 2722 6.341316 GTCTACTGATTGGCTTGACTGAATA 58.659 40.000 0.00 0.00 0.00 1.75
2325 2755 0.028637 GCTGCGAGATTAAGCAAGCC 59.971 55.000 7.73 0.00 43.31 4.35
2330 2760 1.812214 CGACGGCTGCGAGATTAAGC 61.812 60.000 3.66 0.00 36.17 3.09
2331 2761 1.812214 GCGACGGCTGCGAGATTAAG 61.812 60.000 12.56 0.00 35.83 1.85
2333 2763 2.278596 GCGACGGCTGCGAGATTA 60.279 61.111 12.56 0.00 35.83 1.75
2410 2898 6.087291 CACAATGCGTTGAATCTTCTTTCTTC 59.913 38.462 25.13 0.00 38.71 2.87
2453 2945 9.512588 GTAATAACCTGCTAGAGTATACCAGTA 57.487 37.037 0.00 0.00 0.00 2.74
2454 2946 8.226112 AGTAATAACCTGCTAGAGTATACCAGT 58.774 37.037 0.00 0.00 0.00 4.00
2455 2947 8.638629 AGTAATAACCTGCTAGAGTATACCAG 57.361 38.462 0.00 0.00 0.00 4.00
2456 2948 9.512588 GTAGTAATAACCTGCTAGAGTATACCA 57.487 37.037 0.00 0.00 0.00 3.25
2459 2951 9.228949 GCAGTAGTAATAACCTGCTAGAGTATA 57.771 37.037 5.76 0.00 45.25 1.47
2460 2952 8.113173 GCAGTAGTAATAACCTGCTAGAGTAT 57.887 38.462 5.76 0.00 45.25 2.12
2475 2967 8.537016 TGAAAGTACTTACCATGCAGTAGTAAT 58.463 33.333 8.92 0.38 30.35 1.89
2613 3108 3.181470 TGGGCGCGTATATATGCATACAT 60.181 43.478 23.34 5.51 38.09 2.29
2615 3110 2.794910 CTGGGCGCGTATATATGCATAC 59.205 50.000 23.34 13.35 38.09 2.39
2617 3112 1.939974 CTGGGCGCGTATATATGCAT 58.060 50.000 23.34 3.79 38.09 3.96
2618 3113 0.739462 GCTGGGCGCGTATATATGCA 60.739 55.000 23.34 6.21 38.09 3.96
2619 3114 2.006772 GCTGGGCGCGTATATATGC 58.993 57.895 15.74 15.74 34.93 3.14
2635 3134 2.361357 AGAGGCAGTCCGTACGCT 60.361 61.111 10.49 0.00 37.47 5.07


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

AutoCloner maintained by Alex Coulton.