Multiple sequence alignment - TraesCS3D01G095100

Loading Multiple Alignment...

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 TraesCS3D01G095100 chr3D 100.000 2675 0 0 1 2675 48363010 48365684 0.000000e+00 4940.0
1 TraesCS3D01G095100 chr3A 94.779 996 34 7 880 1869 60504901 60505884 0.000000e+00 1535.0
2 TraesCS3D01G095100 chr3A 94.730 759 29 5 1895 2646 60506727 60507481 0.000000e+00 1170.0
3 TraesCS3D01G095100 chr3A 86.331 417 33 15 851 1266 60454340 60454733 1.470000e-117 433.0
4 TraesCS3D01G095100 chr3A 85.714 308 29 6 175 481 60453759 60454052 7.190000e-81 311.0
5 TraesCS3D01G095100 chr3A 85.864 191 21 4 503 691 60454037 60454223 5.840000e-47 198.0
6 TraesCS3D01G095100 chr3B 93.672 964 39 11 880 1840 76431332 76430388 0.000000e+00 1423.0
7 TraesCS3D01G095100 chr3B 94.157 599 31 2 2079 2675 76432476 76433072 0.000000e+00 909.0
8 TraesCS3D01G095100 chr3B 92.288 389 21 4 1084 1472 668217399 668217020 6.510000e-151 544.0
9 TraesCS3D01G095100 chr6B 90.746 389 24 5 1084 1472 47946128 47945752 2.380000e-140 508.0
10 TraesCS3D01G095100 chr2B 88.235 102 7 1 71 172 544041600 544041696 1.680000e-22 117.0
11 TraesCS3D01G095100 chr2B 88.525 61 7 0 2615 2675 105540313 105540253 1.030000e-09 75.0
12 TraesCS3D01G095100 chr5D 79.058 191 15 9 1 172 456587777 456587961 1.010000e-19 108.0
13 TraesCS3D01G095100 chr5D 86.957 69 9 0 2607 2675 106520147 106520215 7.940000e-11 78.7
14 TraesCS3D01G095100 chr1D 89.535 86 4 2 71 156 288940458 288940538 1.310000e-18 104.0
15 TraesCS3D01G095100 chr1D 78.788 99 19 2 2577 2674 401667131 401667228 6.180000e-07 65.8
16 TraesCS3D01G095100 chr1D 100.000 30 0 0 712 741 208748405 208748434 3.720000e-04 56.5
17 TraesCS3D01G095100 chr2A 83.186 113 15 2 2 114 179350151 179350259 1.690000e-17 100.0
18 TraesCS3D01G095100 chr2A 88.525 61 7 0 2615 2675 68881032 68880972 1.030000e-09 75.0
19 TraesCS3D01G095100 chr6D 77.778 180 27 4 1 172 395505400 395505574 6.090000e-17 99.0
20 TraesCS3D01G095100 chr5A 92.593 54 4 0 2622 2675 109966934 109966881 7.940000e-11 78.7
21 TraesCS3D01G095100 chr2D 83.750 80 11 2 2597 2675 65690125 65690203 1.030000e-09 75.0
22 TraesCS3D01G095100 chr5B 85.915 71 5 2 79 149 423354033 423353968 1.330000e-08 71.3
23 TraesCS3D01G095100 chr1A 79.798 99 18 2 2577 2674 497504426 497504523 1.330000e-08 71.3
24 TraesCS3D01G095100 chr1A 89.583 48 5 0 71 118 99141891 99141938 8.000000e-06 62.1
25 TraesCS3D01G095100 chr4A 91.837 49 4 0 124 172 5430170 5430122 4.780000e-08 69.4
26 TraesCS3D01G095100 chr7B 100.000 28 0 0 118 145 620982907 620982934 5.000000e-03 52.8


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 TraesCS3D01G095100 chr3D 48363010 48365684 2674 False 4940.0 4940 100.000000 1 2675 1 chr3D.!!$F1 2674
1 TraesCS3D01G095100 chr3A 60504901 60507481 2580 False 1352.5 1535 94.754500 880 2646 2 chr3A.!!$F2 1766
2 TraesCS3D01G095100 chr3A 60453759 60454733 974 False 314.0 433 85.969667 175 1266 3 chr3A.!!$F1 1091
3 TraesCS3D01G095100 chr3B 76430388 76431332 944 True 1423.0 1423 93.672000 880 1840 1 chr3B.!!$R1 960
4 TraesCS3D01G095100 chr3B 76432476 76433072 596 False 909.0 909 94.157000 2079 2675 1 chr3B.!!$F1 596

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
348 349 0.095417 GAGCCGAATGTCACGAAAGC 59.905 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 1926 0.5312 GTACGTACTGCTCCAGCCTT 59.469 55.0 18.47 0.0 41.18 4.35 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
18 19 3.037485 GAGTGGCTAGTTGCTCGAC 57.963 57.895 0.00 0.00 42.39 4.20
19 20 0.798771 GAGTGGCTAGTTGCTCGACG 60.799 60.000 0.00 0.00 42.39 5.12
20 21 2.126071 TGGCTAGTTGCTCGACGC 60.126 61.111 0.00 0.58 42.39 5.19
21 22 2.886124 GGCTAGTTGCTCGACGCC 60.886 66.667 0.00 0.00 42.39 5.68
22 23 3.248171 GCTAGTTGCTCGACGCCG 61.248 66.667 4.73 0.00 38.95 6.46
23 24 2.579787 CTAGTTGCTCGACGCCGG 60.580 66.667 0.00 0.00 38.05 6.13
24 25 3.047718 CTAGTTGCTCGACGCCGGA 62.048 63.158 5.05 0.00 38.05 5.14
25 26 2.537792 CTAGTTGCTCGACGCCGGAA 62.538 60.000 5.05 0.00 38.05 4.30
26 27 1.940883 TAGTTGCTCGACGCCGGAAT 61.941 55.000 5.05 0.00 38.05 3.01
27 28 2.813474 TTGCTCGACGCCGGAATG 60.813 61.111 5.05 0.00 38.05 2.67
28 29 3.289704 TTGCTCGACGCCGGAATGA 62.290 57.895 5.05 0.00 38.05 2.57
29 30 2.279517 GCTCGACGCCGGAATGAT 60.280 61.111 5.05 0.00 36.24 2.45
30 31 2.589492 GCTCGACGCCGGAATGATG 61.589 63.158 5.05 0.00 36.24 3.07
31 32 1.951130 CTCGACGCCGGAATGATGG 60.951 63.158 5.05 0.00 36.24 3.51
32 33 2.967076 CGACGCCGGAATGATGGG 60.967 66.667 5.05 0.00 0.00 4.00
33 34 2.591715 GACGCCGGAATGATGGGG 60.592 66.667 5.05 0.00 43.36 4.96
34 35 3.087253 ACGCCGGAATGATGGGGA 61.087 61.111 5.05 0.00 40.41 4.81
35 36 2.281070 CGCCGGAATGATGGGGAG 60.281 66.667 5.05 0.00 40.41 4.30
36 37 2.595754 GCCGGAATGATGGGGAGC 60.596 66.667 5.05 0.00 0.00 4.70
37 38 2.918248 CCGGAATGATGGGGAGCA 59.082 61.111 0.00 0.00 0.00 4.26
38 39 1.228063 CCGGAATGATGGGGAGCAG 60.228 63.158 0.00 0.00 0.00 4.24
39 40 1.228063 CGGAATGATGGGGAGCAGG 60.228 63.158 0.00 0.00 0.00 4.85
40 41 1.152368 GGAATGATGGGGAGCAGGG 59.848 63.158 0.00 0.00 0.00 4.45
41 42 1.530183 GAATGATGGGGAGCAGGGC 60.530 63.158 0.00 0.00 0.00 5.19
42 43 3.426309 AATGATGGGGAGCAGGGCG 62.426 63.158 0.00 0.00 0.00 6.13
60 61 4.147322 GCACGGGCGTCATCGTTG 62.147 66.667 0.00 0.00 37.53 4.10
61 62 2.736995 CACGGGCGTCATCGTTGT 60.737 61.111 0.00 0.00 37.53 3.32
62 63 2.431942 ACGGGCGTCATCGTTGTC 60.432 61.111 0.00 0.00 36.04 3.18
63 64 3.541831 CGGGCGTCATCGTTGTCG 61.542 66.667 8.46 8.46 39.49 4.35
64 65 2.431942 GGGCGTCATCGTTGTCGT 60.432 61.111 13.18 0.00 36.86 4.34
65 66 2.442188 GGGCGTCATCGTTGTCGTC 61.442 63.158 13.18 11.10 38.10 4.20
66 67 2.681666 GCGTCATCGTTGTCGTCG 59.318 61.111 13.18 6.80 36.86 5.12
67 68 1.794785 GCGTCATCGTTGTCGTCGA 60.795 57.895 13.18 0.00 41.45 4.20
68 69 1.971336 CGTCATCGTTGTCGTCGAC 59.029 57.895 18.51 18.51 40.07 4.20
116 117 3.558411 GCCTCTCGTGCATGCGAC 61.558 66.667 14.09 11.32 36.80 5.19
117 118 2.887568 CCTCTCGTGCATGCGACC 60.888 66.667 14.09 2.31 36.80 4.79
118 119 3.250323 CTCTCGTGCATGCGACCG 61.250 66.667 14.09 14.92 36.80 4.79
157 158 3.127533 GACCGTGCCATGCAGGTC 61.128 66.667 16.35 16.35 43.53 3.85
159 160 4.758251 CCGTGCCATGCAGGTCGA 62.758 66.667 16.30 0.00 41.98 4.20
160 161 3.190849 CGTGCCATGCAGGTCGAG 61.191 66.667 0.00 0.00 40.08 4.04
161 162 2.821366 GTGCCATGCAGGTCGAGG 60.821 66.667 0.00 0.00 40.08 4.63
162 163 4.783621 TGCCATGCAGGTCGAGGC 62.784 66.667 0.00 2.80 45.41 4.70
163 164 4.783621 GCCATGCAGGTCGAGGCA 62.784 66.667 8.56 8.56 44.59 4.75
164 165 2.513204 CCATGCAGGTCGAGGCAG 60.513 66.667 11.37 4.94 44.24 4.85
165 166 2.580815 CATGCAGGTCGAGGCAGA 59.419 61.111 11.37 0.00 44.24 4.26
166 167 1.078918 CATGCAGGTCGAGGCAGAA 60.079 57.895 11.37 0.00 44.24 3.02
167 168 1.088340 CATGCAGGTCGAGGCAGAAG 61.088 60.000 11.37 2.18 44.24 2.85
168 169 2.817396 GCAGGTCGAGGCAGAAGC 60.817 66.667 0.00 0.00 41.10 3.86
184 185 0.890683 AAGCCGGCTCATCCAAAAAG 59.109 50.000 32.93 0.00 34.01 2.27
187 188 1.669795 GCCGGCTCATCCAAAAAGTTG 60.670 52.381 22.15 0.00 34.01 3.16
188 189 1.885887 CCGGCTCATCCAAAAAGTTGA 59.114 47.619 0.00 0.00 36.83 3.18
204 205 2.202676 GAGCTCAGACTTCGGCCG 60.203 66.667 22.12 22.12 0.00 6.13
254 255 3.426568 GCCAACGAGCTCTGGTGC 61.427 66.667 20.00 10.70 34.97 5.01
257 258 1.739562 CAACGAGCTCTGGTGCCTC 60.740 63.158 12.85 0.00 0.00 4.70
263 264 2.948720 GCTCTGGTGCCTCGAAGGT 61.949 63.158 3.38 0.00 37.80 3.50
267 268 4.452733 GGTGCCTCGAAGGTCCCG 62.453 72.222 3.38 0.00 37.80 5.14
272 273 3.068691 CTCGAAGGTCCCGAGCCA 61.069 66.667 4.83 0.00 45.37 4.75
302 303 1.226974 ATCCCGTCGCACAAGATCG 60.227 57.895 0.00 0.00 0.00 3.69
304 305 2.809174 CCGTCGCACAAGATCGCA 60.809 61.111 0.00 0.00 0.00 5.10
305 306 2.691522 CGTCGCACAAGATCGCAG 59.308 61.111 0.00 0.00 0.00 5.18
306 307 1.801512 CGTCGCACAAGATCGCAGA 60.802 57.895 0.00 0.00 45.75 4.26
307 308 1.704582 GTCGCACAAGATCGCAGAC 59.295 57.895 0.00 0.00 42.51 3.51
308 309 1.801512 TCGCACAAGATCGCAGACG 60.802 57.895 0.00 0.00 42.51 4.18
309 310 2.792290 CGCACAAGATCGCAGACGG 61.792 63.158 0.00 0.00 42.51 4.79
310 311 3.084579 CACAAGATCGCAGACGGC 58.915 61.111 0.00 0.00 42.51 5.68
311 312 1.737735 CACAAGATCGCAGACGGCA 60.738 57.895 0.00 0.00 42.51 5.69
312 313 1.086067 CACAAGATCGCAGACGGCAT 61.086 55.000 0.00 0.00 42.51 4.40
313 314 0.459899 ACAAGATCGCAGACGGCATA 59.540 50.000 0.00 0.00 42.51 3.14
348 349 0.095417 GAGCCGAATGTCACGAAAGC 59.905 55.000 0.00 0.00 0.00 3.51
349 350 0.320771 AGCCGAATGTCACGAAAGCT 60.321 50.000 0.00 0.00 0.00 3.74
350 351 0.095417 GCCGAATGTCACGAAAGCTC 59.905 55.000 0.00 0.00 0.00 4.09
367 368 2.202676 CGTGCTTCTCCTCGGCTC 60.203 66.667 0.00 0.00 0.00 4.70
381 382 3.643978 GCTCGGCGGTGATGATGC 61.644 66.667 7.21 0.00 0.00 3.91
383 384 1.596203 CTCGGCGGTGATGATGCAT 60.596 57.895 7.21 0.00 0.00 3.96
384 385 1.838568 CTCGGCGGTGATGATGCATG 61.839 60.000 2.46 0.00 0.00 4.06
385 386 2.900167 CGGCGGTGATGATGCATGG 61.900 63.158 2.46 0.00 0.00 3.66
386 387 1.526686 GGCGGTGATGATGCATGGA 60.527 57.895 2.46 0.00 0.00 3.41
387 388 1.512996 GGCGGTGATGATGCATGGAG 61.513 60.000 2.46 0.00 0.00 3.86
388 389 1.947013 CGGTGATGATGCATGGAGC 59.053 57.895 2.46 0.00 45.96 4.70
410 411 1.933181 GTGATTGATTCGGTCGATGCA 59.067 47.619 0.00 0.00 30.77 3.96
440 441 3.121019 CTAGACGAGCGAAGGGGG 58.879 66.667 0.00 0.00 0.00 5.40
478 479 4.562425 CGGTGTGGCAGTGGTGGT 62.562 66.667 0.00 0.00 0.00 4.16
479 480 2.906897 GGTGTGGCAGTGGTGGTG 60.907 66.667 0.00 0.00 0.00 4.17
480 481 2.906897 GTGTGGCAGTGGTGGTGG 60.907 66.667 0.00 0.00 0.00 4.61
481 482 3.415983 TGTGGCAGTGGTGGTGGT 61.416 61.111 0.00 0.00 0.00 4.16
482 483 2.906897 GTGGCAGTGGTGGTGGTG 60.907 66.667 0.00 0.00 0.00 4.17
483 484 3.093172 TGGCAGTGGTGGTGGTGA 61.093 61.111 0.00 0.00 0.00 4.02
484 485 2.436109 GGCAGTGGTGGTGGTGAT 59.564 61.111 0.00 0.00 0.00 3.06
485 486 1.973281 GGCAGTGGTGGTGGTGATG 60.973 63.158 0.00 0.00 0.00 3.07
486 487 1.973281 GCAGTGGTGGTGGTGATGG 60.973 63.158 0.00 0.00 0.00 3.51
487 488 1.760527 CAGTGGTGGTGGTGATGGA 59.239 57.895 0.00 0.00 0.00 3.41
488 489 0.110295 CAGTGGTGGTGGTGATGGAA 59.890 55.000 0.00 0.00 0.00 3.53
489 490 0.850100 AGTGGTGGTGGTGATGGAAA 59.150 50.000 0.00 0.00 0.00 3.13
490 491 1.428912 AGTGGTGGTGGTGATGGAAAT 59.571 47.619 0.00 0.00 0.00 2.17
491 492 1.818674 GTGGTGGTGGTGATGGAAATC 59.181 52.381 0.00 0.00 0.00 2.17
492 493 1.094785 GGTGGTGGTGATGGAAATCG 58.905 55.000 0.00 0.00 0.00 3.34
493 494 1.094785 GTGGTGGTGATGGAAATCGG 58.905 55.000 0.00 0.00 0.00 4.18
494 495 0.695924 TGGTGGTGATGGAAATCGGT 59.304 50.000 0.00 0.00 0.00 4.69
495 496 1.339631 TGGTGGTGATGGAAATCGGTC 60.340 52.381 0.00 0.00 0.00 4.79
496 497 1.006832 GTGGTGATGGAAATCGGTCG 58.993 55.000 0.00 0.00 0.00 4.79
497 498 0.899019 TGGTGATGGAAATCGGTCGA 59.101 50.000 0.00 0.00 0.00 4.20
498 499 1.287425 GGTGATGGAAATCGGTCGAC 58.713 55.000 7.13 7.13 0.00 4.20
499 500 1.404986 GGTGATGGAAATCGGTCGACA 60.405 52.381 18.91 0.00 0.00 4.35
500 501 2.550978 GTGATGGAAATCGGTCGACAT 58.449 47.619 18.91 0.00 0.00 3.06
501 502 2.285220 GTGATGGAAATCGGTCGACATG 59.715 50.000 18.91 9.36 0.00 3.21
502 503 1.867233 GATGGAAATCGGTCGACATGG 59.133 52.381 18.91 6.02 0.00 3.66
503 504 0.611200 TGGAAATCGGTCGACATGGT 59.389 50.000 18.91 1.95 0.00 3.55
504 505 1.006832 GGAAATCGGTCGACATGGTG 58.993 55.000 18.91 1.30 0.00 4.17
505 506 1.006832 GAAATCGGTCGACATGGTGG 58.993 55.000 18.91 0.00 0.00 4.61
506 507 1.024579 AAATCGGTCGACATGGTGGC 61.025 55.000 18.91 0.00 0.00 5.01
507 508 2.178876 AATCGGTCGACATGGTGGCA 62.179 55.000 18.91 0.00 0.00 4.92
508 509 2.852495 ATCGGTCGACATGGTGGCAC 62.852 60.000 18.91 9.70 0.00 5.01
509 510 2.347490 GGTCGACATGGTGGCACT 59.653 61.111 18.91 0.00 0.00 4.40
510 511 2.034879 GGTCGACATGGTGGCACTG 61.035 63.158 18.91 11.45 0.00 3.66
511 512 2.034879 GTCGACATGGTGGCACTGG 61.035 63.158 18.45 9.67 0.00 4.00
512 513 3.434319 CGACATGGTGGCACTGGC 61.434 66.667 18.45 10.22 40.13 4.85
532 533 3.697439 ATGGCGACCGAATGGGGTG 62.697 63.158 0.00 0.00 41.40 4.61
537 538 1.520787 GACCGAATGGGGTGTAGCG 60.521 63.158 0.00 0.00 41.40 4.26
541 542 1.600107 GAATGGGGTGTAGCGGTGA 59.400 57.895 0.00 0.00 0.00 4.02
564 565 3.825611 CCGGCGGCAAATGGAAGG 61.826 66.667 15.42 0.00 0.00 3.46
605 607 2.674084 GGGACGAGGCGTTTTTCGG 61.674 63.158 0.00 0.00 41.37 4.30
622 624 4.056125 GCCCAAAGTGCCCGAAGC 62.056 66.667 0.00 0.00 44.14 3.86
625 627 4.404654 CAAAGTGCCCGAAGCGGC 62.405 66.667 0.00 0.00 46.86 6.53
702 734 4.499357 GCTACCTCCGGTATGTAGAAACTG 60.499 50.000 22.91 5.54 37.56 3.16
703 735 3.438183 ACCTCCGGTATGTAGAAACTGT 58.562 45.455 0.00 0.00 32.11 3.55
707 739 3.579586 TCCGGTATGTAGAAACTGTTGGT 59.420 43.478 0.00 0.00 0.00 3.67
714 746 9.826574 GGTATGTAGAAACTGTTGGTCATATTA 57.173 33.333 0.00 0.00 0.00 0.98
753 785 9.793252 GTTTGAATTGCTTATGTTATGACTCAT 57.207 29.630 0.00 0.00 0.00 2.90
771 811 2.773661 TCATGTGGTCTGCTGGTCATAT 59.226 45.455 0.00 0.00 0.00 1.78
772 812 3.200605 TCATGTGGTCTGCTGGTCATATT 59.799 43.478 0.00 0.00 0.00 1.28
773 813 3.719268 TGTGGTCTGCTGGTCATATTT 57.281 42.857 0.00 0.00 0.00 1.40
774 814 3.609853 TGTGGTCTGCTGGTCATATTTC 58.390 45.455 0.00 0.00 0.00 2.17
775 815 3.008923 TGTGGTCTGCTGGTCATATTTCA 59.991 43.478 0.00 0.00 0.00 2.69
776 816 3.624861 GTGGTCTGCTGGTCATATTTCAG 59.375 47.826 0.00 0.00 0.00 3.02
777 817 3.264193 TGGTCTGCTGGTCATATTTCAGT 59.736 43.478 0.00 0.00 0.00 3.41
778 818 3.624861 GGTCTGCTGGTCATATTTCAGTG 59.375 47.826 0.00 0.00 0.00 3.66
779 819 3.624861 GTCTGCTGGTCATATTTCAGTGG 59.375 47.826 0.00 0.00 0.00 4.00
780 820 2.357009 CTGCTGGTCATATTTCAGTGGC 59.643 50.000 0.00 0.00 0.00 5.01
781 821 2.025981 TGCTGGTCATATTTCAGTGGCT 60.026 45.455 0.00 0.00 0.00 4.75
782 822 2.615912 GCTGGTCATATTTCAGTGGCTC 59.384 50.000 0.00 0.00 0.00 4.70
783 823 3.209410 CTGGTCATATTTCAGTGGCTCC 58.791 50.000 0.00 0.00 0.00 4.70
784 824 2.575735 TGGTCATATTTCAGTGGCTCCA 59.424 45.455 0.00 0.00 0.00 3.86
785 825 3.209410 GGTCATATTTCAGTGGCTCCAG 58.791 50.000 0.00 0.00 0.00 3.86
786 826 3.118261 GGTCATATTTCAGTGGCTCCAGA 60.118 47.826 0.00 0.00 0.00 3.86
787 827 4.517285 GTCATATTTCAGTGGCTCCAGAA 58.483 43.478 0.00 0.00 0.00 3.02
788 828 4.943705 GTCATATTTCAGTGGCTCCAGAAA 59.056 41.667 5.99 5.99 34.83 2.52
789 829 4.943705 TCATATTTCAGTGGCTCCAGAAAC 59.056 41.667 5.74 0.00 33.35 2.78
790 830 2.727123 TTTCAGTGGCTCCAGAAACA 57.273 45.000 0.00 0.00 0.00 2.83
791 831 2.957402 TTCAGTGGCTCCAGAAACAT 57.043 45.000 0.00 0.00 0.00 2.71
792 832 2.957402 TCAGTGGCTCCAGAAACATT 57.043 45.000 0.00 0.00 0.00 2.71
793 833 3.228188 TCAGTGGCTCCAGAAACATTT 57.772 42.857 0.00 0.00 0.00 2.32
794 834 3.149196 TCAGTGGCTCCAGAAACATTTC 58.851 45.455 0.00 0.00 37.45 2.17
795 835 2.229784 CAGTGGCTCCAGAAACATTTCC 59.770 50.000 0.68 0.00 37.92 3.13
796 836 2.158475 AGTGGCTCCAGAAACATTTCCA 60.158 45.455 0.68 0.00 37.92 3.53
797 837 2.627699 GTGGCTCCAGAAACATTTCCAA 59.372 45.455 0.68 0.00 37.92 3.53
798 838 3.069443 GTGGCTCCAGAAACATTTCCAAA 59.931 43.478 0.68 0.00 37.92 3.28
799 839 3.069443 TGGCTCCAGAAACATTTCCAAAC 59.931 43.478 0.68 0.00 37.92 2.93
800 840 3.069443 GGCTCCAGAAACATTTCCAAACA 59.931 43.478 0.68 0.00 37.92 2.83
801 841 4.442753 GGCTCCAGAAACATTTCCAAACAA 60.443 41.667 0.68 0.00 37.92 2.83
802 842 5.115480 GCTCCAGAAACATTTCCAAACAAA 58.885 37.500 0.68 0.00 37.92 2.83
803 843 5.759763 GCTCCAGAAACATTTCCAAACAAAT 59.240 36.000 0.68 0.00 37.92 2.32
804 844 6.260714 GCTCCAGAAACATTTCCAAACAAATT 59.739 34.615 0.68 0.00 37.92 1.82
805 845 7.440856 GCTCCAGAAACATTTCCAAACAAATTA 59.559 33.333 0.68 0.00 37.92 1.40
806 846 9.323985 CTCCAGAAACATTTCCAAACAAATTAA 57.676 29.630 0.68 0.00 37.92 1.40
807 847 9.844257 TCCAGAAACATTTCCAAACAAATTAAT 57.156 25.926 0.68 0.00 37.92 1.40
826 866 9.807921 AAATTAATACATGGAATTATCTCCGGT 57.192 29.630 0.00 0.00 38.44 5.28
827 867 8.792830 ATTAATACATGGAATTATCTCCGGTG 57.207 34.615 0.00 0.00 38.44 4.94
828 868 5.825593 ATACATGGAATTATCTCCGGTGT 57.174 39.130 0.00 0.00 39.16 4.16
829 869 4.073293 ACATGGAATTATCTCCGGTGTC 57.927 45.455 0.00 0.00 38.44 3.67
830 870 3.711704 ACATGGAATTATCTCCGGTGTCT 59.288 43.478 0.00 0.00 38.44 3.41
831 871 4.899457 ACATGGAATTATCTCCGGTGTCTA 59.101 41.667 0.00 0.00 38.44 2.59
832 872 5.011125 ACATGGAATTATCTCCGGTGTCTAG 59.989 44.000 0.00 0.00 38.44 2.43
833 873 4.543689 TGGAATTATCTCCGGTGTCTAGT 58.456 43.478 0.00 0.00 38.44 2.57
834 874 4.583489 TGGAATTATCTCCGGTGTCTAGTC 59.417 45.833 0.00 0.00 38.44 2.59
835 875 4.828387 GGAATTATCTCCGGTGTCTAGTCT 59.172 45.833 0.00 0.00 0.00 3.24
836 876 6.002704 GGAATTATCTCCGGTGTCTAGTCTA 58.997 44.000 0.00 0.00 0.00 2.59
837 877 6.149807 GGAATTATCTCCGGTGTCTAGTCTAG 59.850 46.154 0.00 0.00 0.00 2.43
838 878 2.328819 TCTCCGGTGTCTAGTCTAGC 57.671 55.000 0.00 0.00 0.00 3.42
839 879 1.838715 TCTCCGGTGTCTAGTCTAGCT 59.161 52.381 0.00 0.00 0.00 3.32
840 880 2.158928 TCTCCGGTGTCTAGTCTAGCTC 60.159 54.545 0.00 0.00 0.00 4.09
841 881 1.134159 TCCGGTGTCTAGTCTAGCTCC 60.134 57.143 0.00 7.06 0.00 4.70
842 882 1.134037 CCGGTGTCTAGTCTAGCTCCT 60.134 57.143 1.60 0.00 0.00 3.69
843 883 2.215196 CGGTGTCTAGTCTAGCTCCTC 58.785 57.143 1.60 0.00 0.00 3.71
844 884 2.420269 CGGTGTCTAGTCTAGCTCCTCA 60.420 54.545 1.60 0.00 0.00 3.86
845 885 3.622630 GGTGTCTAGTCTAGCTCCTCAA 58.377 50.000 1.60 0.00 0.00 3.02
846 886 3.630312 GGTGTCTAGTCTAGCTCCTCAAG 59.370 52.174 1.60 0.00 0.00 3.02
847 887 4.266714 GTGTCTAGTCTAGCTCCTCAAGT 58.733 47.826 1.60 0.00 0.00 3.16
848 888 5.430007 GTGTCTAGTCTAGCTCCTCAAGTA 58.570 45.833 1.60 0.00 0.00 2.24
849 889 5.881443 GTGTCTAGTCTAGCTCCTCAAGTAA 59.119 44.000 1.60 0.00 0.00 2.24
850 890 6.374894 GTGTCTAGTCTAGCTCCTCAAGTAAA 59.625 42.308 1.60 0.00 0.00 2.01
856 896 8.101654 AGTCTAGCTCCTCAAGTAAATATACG 57.898 38.462 0.00 0.00 37.11 3.06
862 902 6.366332 GCTCCTCAAGTAAATATACGATGTGG 59.634 42.308 0.00 0.00 37.97 4.17
867 907 8.528917 TCAAGTAAATATACGATGTGGTATGC 57.471 34.615 0.00 0.00 37.11 3.14
872 912 9.807386 GTAAATATACGATGTGGTATGCTTTTC 57.193 33.333 0.00 0.00 34.96 2.29
874 914 3.350219 ACGATGTGGTATGCTTTTCCT 57.650 42.857 0.00 0.00 0.00 3.36
877 917 4.522789 ACGATGTGGTATGCTTTTCCTTTT 59.477 37.500 0.00 0.00 0.00 2.27
878 918 4.858692 CGATGTGGTATGCTTTTCCTTTTG 59.141 41.667 0.00 0.00 0.00 2.44
925 969 4.499019 CCTCTCAAACCTTATCGCTCTCTC 60.499 50.000 0.00 0.00 0.00 3.20
981 1031 4.742201 ATGTGAGCCGCGAACGCT 62.742 61.111 8.23 8.16 39.32 5.07
1011 1061 3.667217 ATCCCAAATGCAGGCGCCT 62.667 57.895 27.08 27.08 37.32 5.52
1701 1755 1.133419 CCTCCTCCTCCTAGGTACCAC 60.133 61.905 15.94 0.00 37.91 4.16
1752 1806 8.423906 TTCTTCCAGTTCCTCTATCATATACC 57.576 38.462 0.00 0.00 0.00 2.73
1759 1813 8.549548 CAGTTCCTCTATCATATACCGTATACG 58.450 40.741 18.40 18.40 39.44 3.06
1845 1901 7.862741 TGTCTGAAATTTGTAGTACGTACTG 57.137 36.000 33.23 15.45 37.10 2.74
1856 1912 1.089920 TACGTACTGCTTCCTCCGTC 58.910 55.000 0.00 0.00 0.00 4.79
1869 1925 2.969950 TCCTCCGTCCCATAATGTAAGG 59.030 50.000 0.00 0.00 0.00 2.69
1870 1926 2.969950 CCTCCGTCCCATAATGTAAGGA 59.030 50.000 0.00 0.00 0.00 3.36
1872 1928 4.503296 CCTCCGTCCCATAATGTAAGGAAG 60.503 50.000 0.00 0.00 0.00 3.46
1873 1929 3.389983 TCCGTCCCATAATGTAAGGAAGG 59.610 47.826 3.77 3.77 46.02 3.46
1874 1930 3.139077 CGTCCCATAATGTAAGGAAGGC 58.861 50.000 0.00 0.00 0.00 4.35
1875 1931 3.181454 CGTCCCATAATGTAAGGAAGGCT 60.181 47.826 0.00 0.00 0.00 4.58
1877 1933 3.138283 TCCCATAATGTAAGGAAGGCTGG 59.862 47.826 0.00 0.00 0.00 4.85
1878 1934 3.138283 CCCATAATGTAAGGAAGGCTGGA 59.862 47.826 0.00 0.00 0.00 3.86
1879 1935 4.392940 CCATAATGTAAGGAAGGCTGGAG 58.607 47.826 0.00 0.00 0.00 3.86
1880 1936 2.426842 AATGTAAGGAAGGCTGGAGC 57.573 50.000 0.00 0.00 41.14 4.70
1881 1937 1.289160 ATGTAAGGAAGGCTGGAGCA 58.711 50.000 0.20 0.00 44.36 4.26
1882 1938 0.615331 TGTAAGGAAGGCTGGAGCAG 59.385 55.000 0.20 0.00 44.36 4.24
1884 1940 1.831736 GTAAGGAAGGCTGGAGCAGTA 59.168 52.381 0.20 0.00 44.36 2.74
1885 1941 0.615850 AAGGAAGGCTGGAGCAGTAC 59.384 55.000 0.20 0.00 44.36 2.73
1886 1942 1.153549 GGAAGGCTGGAGCAGTACG 60.154 63.158 0.20 0.00 44.36 3.67
1887 1943 1.592223 GAAGGCTGGAGCAGTACGT 59.408 57.895 0.20 0.00 44.36 3.57
1888 1944 0.815734 GAAGGCTGGAGCAGTACGTA 59.184 55.000 0.20 0.00 44.36 3.57
1889 1945 0.531200 AAGGCTGGAGCAGTACGTAC 59.469 55.000 18.10 18.10 44.36 3.67
1891 1947 1.064906 AGGCTGGAGCAGTACGTACTA 60.065 52.381 26.95 11.14 44.36 1.82
1892 1948 1.065251 GGCTGGAGCAGTACGTACTAC 59.935 57.143 26.95 21.69 44.36 2.73
1893 1949 2.015587 GCTGGAGCAGTACGTACTACT 58.984 52.381 25.12 25.12 41.59 2.57
1939 2812 4.871557 CGGGGATCGTATTTCTTTGTGTTA 59.128 41.667 0.00 0.00 0.00 2.41
1940 2813 5.006358 CGGGGATCGTATTTCTTTGTGTTAG 59.994 44.000 0.00 0.00 0.00 2.34
1941 2814 6.110707 GGGGATCGTATTTCTTTGTGTTAGA 58.889 40.000 0.00 0.00 0.00 2.10
1942 2815 6.596497 GGGGATCGTATTTCTTTGTGTTAGAA 59.404 38.462 0.00 0.00 0.00 2.10
1998 2871 9.643693 AGCATTTCTCATTTAATAACAAACAGG 57.356 29.630 0.00 0.00 0.00 4.00
2021 2894 7.607991 CAGGACTTTCTGATAAAAGGAAGCTAA 59.392 37.037 0.00 0.00 39.96 3.09
2023 2896 7.365840 ACTTTCTGATAAAAGGAAGCTAACG 57.634 36.000 0.00 0.00 39.96 3.18
2051 2924 1.347817 GCCAGCAGTTCGAACTCTCG 61.348 60.000 27.54 19.11 46.87 4.04
2081 2954 6.664428 AAGAGAAACTAACTCAGAGAGCTT 57.336 37.500 3.79 0.00 36.91 3.74
2106 2980 8.677148 TCTGTTTTATCCATTACCTAATGCTC 57.323 34.615 0.15 0.00 41.23 4.26
2113 2987 6.204852 TCCATTACCTAATGCTCAATCCAT 57.795 37.500 0.15 0.00 41.23 3.41
2187 3069 3.855689 ACATAGCACACAAATTCAGCC 57.144 42.857 0.00 0.00 0.00 4.85
2206 3088 1.568612 CCACGCATCACACTCACACC 61.569 60.000 0.00 0.00 0.00 4.16
2226 3108 3.576982 ACCTGATATGGTACGGTACATGG 59.423 47.826 19.14 11.47 38.79 3.66
2414 3296 2.824489 TCGATCTCGCTCACCGCT 60.824 61.111 0.00 0.00 39.60 5.52
2534 3416 4.954118 ACCGGGTCCAGCAGGTCA 62.954 66.667 6.32 0.00 35.89 4.02
2600 3482 4.580551 CGGACGATGTACCGCCCC 62.581 72.222 0.00 0.00 42.55 5.80
2657 3539 2.432628 AGCACGCCGAAGCTGTAC 60.433 61.111 7.90 0.00 40.13 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.951130 CCATCATTCCGGCGTCGAG 60.951 63.158 12.93 0.03 39.00 4.04
14 15 2.106131 CCATCATTCCGGCGTCGA 59.894 61.111 12.93 0.00 39.00 4.20
15 16 2.967076 CCCATCATTCCGGCGTCG 60.967 66.667 0.29 0.29 0.00 5.12
16 17 2.591715 CCCCATCATTCCGGCGTC 60.592 66.667 6.01 0.00 0.00 5.19
17 18 3.087253 TCCCCATCATTCCGGCGT 61.087 61.111 6.01 0.00 0.00 5.68
18 19 2.281070 CTCCCCATCATTCCGGCG 60.281 66.667 0.00 0.00 0.00 6.46
19 20 2.595754 GCTCCCCATCATTCCGGC 60.596 66.667 0.00 0.00 0.00 6.13
20 21 1.228063 CTGCTCCCCATCATTCCGG 60.228 63.158 0.00 0.00 0.00 5.14
21 22 1.228063 CCTGCTCCCCATCATTCCG 60.228 63.158 0.00 0.00 0.00 4.30
22 23 1.152368 CCCTGCTCCCCATCATTCC 59.848 63.158 0.00 0.00 0.00 3.01
23 24 1.530183 GCCCTGCTCCCCATCATTC 60.530 63.158 0.00 0.00 0.00 2.67
24 25 2.605299 GCCCTGCTCCCCATCATT 59.395 61.111 0.00 0.00 0.00 2.57
25 26 3.882326 CGCCCTGCTCCCCATCAT 61.882 66.667 0.00 0.00 0.00 2.45
43 44 4.147322 CAACGATGACGCCCGTGC 62.147 66.667 0.00 0.00 43.96 5.34
44 45 2.726691 GACAACGATGACGCCCGTG 61.727 63.158 0.00 0.00 43.96 4.94
45 46 2.431942 GACAACGATGACGCCCGT 60.432 61.111 0.00 0.00 43.96 5.28
46 47 3.541831 CGACAACGATGACGCCCG 61.542 66.667 4.56 0.00 43.96 6.13
47 48 2.431942 ACGACAACGATGACGCCC 60.432 61.111 16.29 0.00 46.27 6.13
48 49 2.774951 CGACGACAACGATGACGCC 61.775 63.158 16.29 5.68 46.27 5.68
49 50 1.794785 TCGACGACAACGATGACGC 60.795 57.895 16.29 9.05 46.27 5.19
51 52 1.393597 CCGTCGACGACAACGATGAC 61.394 60.000 37.65 0.00 45.70 3.06
52 53 1.154357 CCGTCGACGACAACGATGA 60.154 57.895 37.65 0.00 45.70 2.92
53 54 2.774951 GCCGTCGACGACAACGATG 61.775 63.158 37.65 19.51 43.51 3.84
54 55 2.503375 GCCGTCGACGACAACGAT 60.503 61.111 37.65 0.00 41.29 3.73
99 100 3.558411 GTCGCATGCACGAGAGGC 61.558 66.667 19.57 0.00 43.89 4.70
100 101 2.887568 GGTCGCATGCACGAGAGG 60.888 66.667 19.57 0.00 43.89 3.69
101 102 3.250323 CGGTCGCATGCACGAGAG 61.250 66.667 19.57 0.00 43.89 3.20
140 141 3.127533 GACCTGCATGGCACGGTC 61.128 66.667 17.61 17.61 43.53 4.79
142 143 4.758251 TCGACCTGCATGGCACGG 62.758 66.667 15.85 4.74 40.22 4.94
143 144 3.190849 CTCGACCTGCATGGCACG 61.191 66.667 0.00 5.98 40.22 5.34
144 145 2.821366 CCTCGACCTGCATGGCAC 60.821 66.667 0.00 0.00 40.22 5.01
145 146 4.783621 GCCTCGACCTGCATGGCA 62.784 66.667 4.83 0.00 42.79 4.92
146 147 4.783621 TGCCTCGACCTGCATGGC 62.784 66.667 2.80 2.80 43.49 4.40
147 148 2.513204 CTGCCTCGACCTGCATGG 60.513 66.667 0.00 0.00 42.93 3.66
148 149 1.078918 TTCTGCCTCGACCTGCATG 60.079 57.895 0.00 0.00 36.79 4.06
149 150 1.220206 CTTCTGCCTCGACCTGCAT 59.780 57.895 0.00 0.00 36.79 3.96
150 151 2.659016 CTTCTGCCTCGACCTGCA 59.341 61.111 0.00 0.00 35.86 4.41
151 152 2.817396 GCTTCTGCCTCGACCTGC 60.817 66.667 0.00 0.00 0.00 4.85
161 162 2.899339 GGATGAGCCGGCTTCTGC 60.899 66.667 33.34 21.88 38.76 4.26
162 163 0.677731 TTTGGATGAGCCGGCTTCTG 60.678 55.000 33.34 0.00 40.66 3.02
163 164 0.038166 TTTTGGATGAGCCGGCTTCT 59.962 50.000 33.34 21.26 40.66 2.85
164 165 0.887933 TTTTTGGATGAGCCGGCTTC 59.112 50.000 33.34 24.91 40.66 3.86
165 166 0.890683 CTTTTTGGATGAGCCGGCTT 59.109 50.000 33.34 17.05 40.66 4.35
166 167 0.251341 ACTTTTTGGATGAGCCGGCT 60.251 50.000 33.48 33.48 40.66 5.52
167 168 0.603065 AACTTTTTGGATGAGCCGGC 59.397 50.000 21.89 21.89 40.66 6.13
168 169 1.885887 TCAACTTTTTGGATGAGCCGG 59.114 47.619 0.00 0.00 40.66 6.13
169 170 3.207474 CTCAACTTTTTGGATGAGCCG 57.793 47.619 0.00 0.00 40.66 5.52
172 173 4.758674 TCTGAGCTCAACTTTTTGGATGAG 59.241 41.667 18.85 0.52 41.69 2.90
173 174 4.516698 GTCTGAGCTCAACTTTTTGGATGA 59.483 41.667 18.85 3.80 33.06 2.92
184 185 1.016653 GGCCGAAGTCTGAGCTCAAC 61.017 60.000 18.85 17.44 0.00 3.18
187 188 2.202676 CGGCCGAAGTCTGAGCTC 60.203 66.667 24.07 6.82 0.00 4.09
188 189 3.764466 CCGGCCGAAGTCTGAGCT 61.764 66.667 30.73 0.00 0.00 4.09
215 216 2.097202 GCGCTTATGACGTCATAGCTTG 60.097 50.000 32.78 25.85 39.69 4.01
220 221 0.937699 GGCGCGCTTATGACGTCATA 60.938 55.000 29.79 29.79 37.76 2.15
222 223 2.883730 GGCGCGCTTATGACGTCA 60.884 61.111 32.29 22.48 0.00 4.35
257 258 3.382832 ACTGGCTCGGGACCTTCG 61.383 66.667 0.00 0.00 0.00 3.79
263 264 4.783621 GCATGCACTGGCTCGGGA 62.784 66.667 14.21 0.00 41.91 5.14
348 349 2.202676 GCCGAGGAGAAGCACGAG 60.203 66.667 0.00 0.00 0.00 4.18
349 350 2.676822 AGCCGAGGAGAAGCACGA 60.677 61.111 0.00 0.00 0.00 4.35
350 351 2.202676 GAGCCGAGGAGAAGCACG 60.203 66.667 0.00 0.00 0.00 5.34
367 368 2.635338 CATGCATCATCACCGCCG 59.365 61.111 0.00 0.00 0.00 6.46
381 382 2.289820 CCGAATCAATCACTGCTCCATG 59.710 50.000 0.00 0.00 0.00 3.66
383 384 1.278985 ACCGAATCAATCACTGCTCCA 59.721 47.619 0.00 0.00 0.00 3.86
384 385 1.936547 GACCGAATCAATCACTGCTCC 59.063 52.381 0.00 0.00 0.00 4.70
385 386 1.590238 CGACCGAATCAATCACTGCTC 59.410 52.381 0.00 0.00 0.00 4.26
386 387 1.204704 TCGACCGAATCAATCACTGCT 59.795 47.619 0.00 0.00 0.00 4.24
387 388 1.640428 TCGACCGAATCAATCACTGC 58.360 50.000 0.00 0.00 0.00 4.40
388 389 2.033407 GCATCGACCGAATCAATCACTG 60.033 50.000 0.00 0.00 0.00 3.66
390 391 1.933181 TGCATCGACCGAATCAATCAC 59.067 47.619 0.00 0.00 0.00 3.06
391 392 2.204237 CTGCATCGACCGAATCAATCA 58.796 47.619 0.00 0.00 0.00 2.57
392 393 2.033407 CACTGCATCGACCGAATCAATC 60.033 50.000 0.00 0.00 0.00 2.67
393 394 1.935873 CACTGCATCGACCGAATCAAT 59.064 47.619 0.00 0.00 0.00 2.57
394 395 1.358877 CACTGCATCGACCGAATCAA 58.641 50.000 0.00 0.00 0.00 2.57
395 396 0.460109 CCACTGCATCGACCGAATCA 60.460 55.000 0.00 0.00 0.00 2.57
410 411 2.675423 TCTAGCCGACGCACCACT 60.675 61.111 0.00 0.00 37.52 4.00
476 477 1.379527 GACCGATTTCCATCACCACC 58.620 55.000 0.00 0.00 0.00 4.61
477 478 1.006832 CGACCGATTTCCATCACCAC 58.993 55.000 0.00 0.00 0.00 4.16
478 479 0.899019 TCGACCGATTTCCATCACCA 59.101 50.000 0.00 0.00 0.00 4.17
479 480 1.287425 GTCGACCGATTTCCATCACC 58.713 55.000 3.51 0.00 0.00 4.02
480 481 2.004583 TGTCGACCGATTTCCATCAC 57.995 50.000 14.12 0.00 0.00 3.06
481 482 2.549926 CATGTCGACCGATTTCCATCA 58.450 47.619 14.12 0.00 0.00 3.07
482 483 1.867233 CCATGTCGACCGATTTCCATC 59.133 52.381 14.12 0.00 0.00 3.51
483 484 1.209504 ACCATGTCGACCGATTTCCAT 59.790 47.619 14.12 0.00 0.00 3.41
484 485 0.611200 ACCATGTCGACCGATTTCCA 59.389 50.000 14.12 0.00 0.00 3.53
485 486 1.006832 CACCATGTCGACCGATTTCC 58.993 55.000 14.12 0.00 0.00 3.13
486 487 1.006832 CCACCATGTCGACCGATTTC 58.993 55.000 14.12 0.00 0.00 2.17
487 488 1.024579 GCCACCATGTCGACCGATTT 61.025 55.000 14.12 0.00 0.00 2.17
488 489 1.449601 GCCACCATGTCGACCGATT 60.450 57.895 14.12 0.00 0.00 3.34
489 490 2.186903 GCCACCATGTCGACCGAT 59.813 61.111 14.12 0.00 0.00 4.18
490 491 3.307108 TGCCACCATGTCGACCGA 61.307 61.111 14.12 0.00 0.00 4.69
491 492 3.118454 GTGCCACCATGTCGACCG 61.118 66.667 14.12 3.93 0.00 4.79
492 493 2.034879 CAGTGCCACCATGTCGACC 61.035 63.158 14.12 0.00 0.00 4.79
493 494 2.034879 CCAGTGCCACCATGTCGAC 61.035 63.158 9.11 9.11 0.00 4.20
494 495 2.347114 CCAGTGCCACCATGTCGA 59.653 61.111 0.00 0.00 0.00 4.20
495 496 3.434319 GCCAGTGCCACCATGTCG 61.434 66.667 0.00 0.00 0.00 4.35
496 497 3.434319 CGCCAGTGCCACCATGTC 61.434 66.667 0.00 0.00 0.00 3.06
497 498 3.272364 ATCGCCAGTGCCACCATGT 62.272 57.895 0.00 0.00 0.00 3.21
498 499 2.438975 ATCGCCAGTGCCACCATG 60.439 61.111 0.00 0.00 0.00 3.66
499 500 2.438975 CATCGCCAGTGCCACCAT 60.439 61.111 0.00 0.00 0.00 3.55
500 501 4.720902 CCATCGCCAGTGCCACCA 62.721 66.667 0.00 0.00 0.00 4.17
508 509 4.812476 TTCGGTCGCCATCGCCAG 62.812 66.667 0.00 0.00 33.51 4.85
509 510 4.155733 ATTCGGTCGCCATCGCCA 62.156 61.111 0.00 0.00 33.51 5.69
510 511 3.640000 CATTCGGTCGCCATCGCC 61.640 66.667 0.00 0.00 35.26 5.54
511 512 3.640000 CCATTCGGTCGCCATCGC 61.640 66.667 0.00 0.00 35.26 4.58
512 513 2.967076 CCCATTCGGTCGCCATCG 60.967 66.667 0.00 0.00 0.00 3.84
523 524 0.743345 GTCACCGCTACACCCCATTC 60.743 60.000 0.00 0.00 0.00 2.67
548 549 2.749839 TCCTTCCATTTGCCGCCG 60.750 61.111 0.00 0.00 0.00 6.46
575 576 4.530857 CGTCCCCGGATCCACTGC 62.531 72.222 13.41 0.00 0.00 4.40
576 577 2.758327 TCGTCCCCGGATCCACTG 60.758 66.667 13.41 0.00 33.95 3.66
578 579 3.537874 CCTCGTCCCCGGATCCAC 61.538 72.222 13.41 0.75 33.95 4.02
587 588 2.674084 CCGAAAAACGCCTCGTCCC 61.674 63.158 0.00 0.00 39.99 4.46
589 590 2.172659 GCCGAAAAACGCCTCGTC 59.827 61.111 0.00 0.00 39.99 4.20
590 591 3.351416 GGCCGAAAAACGCCTCGT 61.351 61.111 0.00 0.00 43.97 4.18
597 599 0.878523 GGCACTTTGGGCCGAAAAAC 60.879 55.000 14.30 6.35 42.39 2.43
605 607 4.056125 GCTTCGGGCACTTTGGGC 62.056 66.667 0.00 0.00 41.35 5.36
653 655 4.650734 TGCAGACTCCAACACATGATAAA 58.349 39.130 0.00 0.00 0.00 1.40
654 656 4.256110 CTGCAGACTCCAACACATGATAA 58.744 43.478 8.42 0.00 0.00 1.75
655 657 3.865446 CTGCAGACTCCAACACATGATA 58.135 45.455 8.42 0.00 0.00 2.15
741 773 3.261643 AGCAGACCACATGAGTCATAACA 59.738 43.478 18.44 0.00 36.68 2.41
742 774 3.620374 CAGCAGACCACATGAGTCATAAC 59.380 47.826 18.44 8.05 36.68 1.89
743 775 3.369787 CCAGCAGACCACATGAGTCATAA 60.370 47.826 18.44 0.00 36.68 1.90
744 776 2.169144 CCAGCAGACCACATGAGTCATA 59.831 50.000 18.44 0.00 36.68 2.15
747 779 0.322975 ACCAGCAGACCACATGAGTC 59.677 55.000 0.00 6.10 34.31 3.36
748 780 0.322975 GACCAGCAGACCACATGAGT 59.677 55.000 0.00 0.00 0.00 3.41
749 781 0.322648 TGACCAGCAGACCACATGAG 59.677 55.000 0.00 0.00 0.00 2.90
753 785 3.008923 TGAAATATGACCAGCAGACCACA 59.991 43.478 0.00 0.00 0.00 4.17
771 811 2.727123 TGTTTCTGGAGCCACTGAAA 57.273 45.000 6.30 6.30 36.41 2.69
772 812 2.957402 ATGTTTCTGGAGCCACTGAA 57.043 45.000 0.00 0.00 0.00 3.02
773 813 2.957402 AATGTTTCTGGAGCCACTGA 57.043 45.000 0.00 0.00 0.00 3.41
774 814 2.229784 GGAAATGTTTCTGGAGCCACTG 59.770 50.000 5.56 0.00 37.35 3.66
775 815 2.158475 TGGAAATGTTTCTGGAGCCACT 60.158 45.455 5.56 0.00 37.35 4.00
776 816 2.238521 TGGAAATGTTTCTGGAGCCAC 58.761 47.619 5.56 0.00 37.35 5.01
777 817 2.673775 TGGAAATGTTTCTGGAGCCA 57.326 45.000 5.56 0.00 37.35 4.75
778 818 3.069443 TGTTTGGAAATGTTTCTGGAGCC 59.931 43.478 5.56 0.00 37.35 4.70
779 819 4.320608 TGTTTGGAAATGTTTCTGGAGC 57.679 40.909 5.56 0.00 37.35 4.70
780 820 7.790823 AATTTGTTTGGAAATGTTTCTGGAG 57.209 32.000 5.56 0.00 37.35 3.86
781 821 9.844257 ATTAATTTGTTTGGAAATGTTTCTGGA 57.156 25.926 5.56 0.00 37.35 3.86
800 840 9.807921 ACCGGAGATAATTCCATGTATTAATTT 57.192 29.630 9.46 0.00 37.05 1.82
801 841 9.231297 CACCGGAGATAATTCCATGTATTAATT 57.769 33.333 9.46 0.00 37.05 1.40
802 842 8.383175 ACACCGGAGATAATTCCATGTATTAAT 58.617 33.333 9.46 0.00 37.05 1.40
803 843 7.741785 ACACCGGAGATAATTCCATGTATTAA 58.258 34.615 9.46 0.00 37.05 1.40
804 844 7.234782 AGACACCGGAGATAATTCCATGTATTA 59.765 37.037 9.46 0.00 37.05 0.98
805 845 6.043243 AGACACCGGAGATAATTCCATGTATT 59.957 38.462 9.46 0.00 37.05 1.89
806 846 5.544176 AGACACCGGAGATAATTCCATGTAT 59.456 40.000 9.46 0.00 37.05 2.29
807 847 4.899457 AGACACCGGAGATAATTCCATGTA 59.101 41.667 9.46 0.00 37.05 2.29
808 848 3.711704 AGACACCGGAGATAATTCCATGT 59.288 43.478 9.46 0.00 37.05 3.21
809 849 4.342862 AGACACCGGAGATAATTCCATG 57.657 45.455 9.46 0.00 37.05 3.66
810 850 5.148502 ACTAGACACCGGAGATAATTCCAT 58.851 41.667 9.46 0.00 37.05 3.41
811 851 4.543689 ACTAGACACCGGAGATAATTCCA 58.456 43.478 9.46 0.00 37.05 3.53
812 852 4.828387 AGACTAGACACCGGAGATAATTCC 59.172 45.833 9.46 0.00 0.00 3.01
813 853 6.348704 GCTAGACTAGACACCGGAGATAATTC 60.349 46.154 9.46 0.00 0.00 2.17
814 854 5.474189 GCTAGACTAGACACCGGAGATAATT 59.526 44.000 9.46 0.00 0.00 1.40
815 855 5.005094 GCTAGACTAGACACCGGAGATAAT 58.995 45.833 9.46 0.00 0.00 1.28
816 856 4.102838 AGCTAGACTAGACACCGGAGATAA 59.897 45.833 9.46 0.00 0.00 1.75
817 857 3.647113 AGCTAGACTAGACACCGGAGATA 59.353 47.826 9.46 0.00 0.00 1.98
818 858 2.440253 AGCTAGACTAGACACCGGAGAT 59.560 50.000 9.46 0.00 0.00 2.75
819 859 1.838715 AGCTAGACTAGACACCGGAGA 59.161 52.381 9.46 0.00 0.00 3.71
820 860 2.215196 GAGCTAGACTAGACACCGGAG 58.785 57.143 9.46 1.26 0.00 4.63
821 861 1.134159 GGAGCTAGACTAGACACCGGA 60.134 57.143 9.46 0.00 0.00 5.14
822 862 1.134037 AGGAGCTAGACTAGACACCGG 60.134 57.143 13.91 0.00 0.00 5.28
823 863 2.215196 GAGGAGCTAGACTAGACACCG 58.785 57.143 13.91 0.00 0.00 4.94
824 864 3.284793 TGAGGAGCTAGACTAGACACC 57.715 52.381 13.91 11.73 0.00 4.16
825 865 4.266714 ACTTGAGGAGCTAGACTAGACAC 58.733 47.826 13.91 3.71 0.00 3.67
826 866 4.577988 ACTTGAGGAGCTAGACTAGACA 57.422 45.455 13.91 2.44 0.00 3.41
827 867 7.576861 ATTTACTTGAGGAGCTAGACTAGAC 57.423 40.000 13.91 6.18 0.00 2.59
830 870 9.217278 CGTATATTTACTTGAGGAGCTAGACTA 57.783 37.037 0.00 0.00 0.00 2.59
831 871 7.937942 TCGTATATTTACTTGAGGAGCTAGACT 59.062 37.037 0.00 0.00 0.00 3.24
832 872 8.097078 TCGTATATTTACTTGAGGAGCTAGAC 57.903 38.462 0.00 0.00 0.00 2.59
833 873 8.731605 CATCGTATATTTACTTGAGGAGCTAGA 58.268 37.037 0.00 0.00 0.00 2.43
834 874 8.516234 ACATCGTATATTTACTTGAGGAGCTAG 58.484 37.037 0.00 0.00 0.00 3.42
835 875 8.297426 CACATCGTATATTTACTTGAGGAGCTA 58.703 37.037 0.00 0.00 0.00 3.32
836 876 7.148641 CACATCGTATATTTACTTGAGGAGCT 58.851 38.462 0.00 0.00 0.00 4.09
837 877 6.366332 CCACATCGTATATTTACTTGAGGAGC 59.634 42.308 4.75 0.00 29.41 4.70
838 878 7.434492 ACCACATCGTATATTTACTTGAGGAG 58.566 38.462 12.56 0.00 30.98 3.69
839 879 7.356089 ACCACATCGTATATTTACTTGAGGA 57.644 36.000 12.56 0.00 30.98 3.71
840 880 9.140286 CATACCACATCGTATATTTACTTGAGG 57.860 37.037 7.49 7.49 31.85 3.86
841 881 8.648097 GCATACCACATCGTATATTTACTTGAG 58.352 37.037 0.00 0.00 0.00 3.02
842 882 8.364894 AGCATACCACATCGTATATTTACTTGA 58.635 33.333 0.00 0.00 0.00 3.02
843 883 8.534333 AGCATACCACATCGTATATTTACTTG 57.466 34.615 0.00 0.00 0.00 3.16
844 884 9.555727 AAAGCATACCACATCGTATATTTACTT 57.444 29.630 0.00 0.00 0.00 2.24
845 885 9.555727 AAAAGCATACCACATCGTATATTTACT 57.444 29.630 0.00 0.00 0.00 2.24
846 886 9.807386 GAAAAGCATACCACATCGTATATTTAC 57.193 33.333 0.00 0.00 0.00 2.01
847 887 8.995220 GGAAAAGCATACCACATCGTATATTTA 58.005 33.333 0.00 0.00 0.00 1.40
848 888 7.719633 AGGAAAAGCATACCACATCGTATATTT 59.280 33.333 0.00 0.00 0.00 1.40
849 889 7.224297 AGGAAAAGCATACCACATCGTATATT 58.776 34.615 0.00 0.00 0.00 1.28
850 890 6.769512 AGGAAAAGCATACCACATCGTATAT 58.230 36.000 0.00 0.00 0.00 0.86
856 896 5.783111 ACAAAAGGAAAAGCATACCACATC 58.217 37.500 0.00 0.00 0.00 3.06
862 902 7.435192 GTGGCATATACAAAAGGAAAAGCATAC 59.565 37.037 0.00 0.00 0.00 2.39
867 907 6.686630 TGTGTGGCATATACAAAAGGAAAAG 58.313 36.000 0.00 0.00 0.00 2.27
872 912 7.771183 ACTAAATGTGTGGCATATACAAAAGG 58.229 34.615 6.34 2.28 36.67 3.11
874 914 7.414651 CGGACTAAATGTGTGGCATATACAAAA 60.415 37.037 6.34 0.00 36.67 2.44
877 917 5.053811 CGGACTAAATGTGTGGCATATACA 58.946 41.667 0.00 0.00 36.67 2.29
878 918 4.451096 CCGGACTAAATGTGTGGCATATAC 59.549 45.833 0.00 0.00 36.67 1.47
945 990 0.039256 TGCTCGCTACGTACCGTTTT 60.039 50.000 9.90 0.00 41.54 2.43
948 998 1.063649 CATGCTCGCTACGTACCGT 59.936 57.895 9.90 0.00 44.35 4.83
981 1031 0.483328 TTTGGGATTTGGGACGGGAA 59.517 50.000 0.00 0.00 0.00 3.97
1194 1244 4.753662 TAGCCGAGGTCCACCGCT 62.754 66.667 7.27 7.27 42.08 5.52
1407 1458 0.733150 CGATCTCGTACAGCACCAGA 59.267 55.000 0.00 0.00 34.11 3.86
1729 1783 6.434652 ACGGTATATGATAGAGGAACTGGAAG 59.565 42.308 0.00 0.00 41.55 3.46
1732 1786 7.883391 ATACGGTATATGATAGAGGAACTGG 57.117 40.000 0.00 0.00 41.55 4.00
1759 1813 5.987953 GGGTACAATTTAGTTCTCCGTATCC 59.012 44.000 0.00 0.00 0.00 2.59
1845 1901 1.141053 ACATTATGGGACGGAGGAAGC 59.859 52.381 0.00 0.00 0.00 3.86
1856 1912 3.138283 TCCAGCCTTCCTTACATTATGGG 59.862 47.826 0.00 0.00 0.00 4.00
1869 1925 0.815734 TACGTACTGCTCCAGCCTTC 59.184 55.000 0.00 0.00 41.18 3.46
1870 1926 0.531200 GTACGTACTGCTCCAGCCTT 59.469 55.000 18.47 0.00 41.18 4.35
1872 1928 1.065251 GTAGTACGTACTGCTCCAGCC 59.935 57.143 33.23 10.45 41.18 4.85
1873 1929 2.015587 AGTAGTACGTACTGCTCCAGC 58.984 52.381 32.58 16.27 44.28 4.85
1874 1930 3.181499 CCAAGTAGTACGTACTGCTCCAG 60.181 52.174 36.06 28.34 46.34 3.86
1875 1931 2.751259 CCAAGTAGTACGTACTGCTCCA 59.249 50.000 36.06 17.12 46.34 3.86
1877 1933 2.163010 TGCCAAGTAGTACGTACTGCTC 59.837 50.000 36.06 26.64 46.34 4.26
1879 1935 2.527100 CTGCCAAGTAGTACGTACTGC 58.473 52.381 33.23 31.37 41.50 4.40
1880 1936 2.751259 TCCTGCCAAGTAGTACGTACTG 59.249 50.000 33.23 19.47 41.50 2.74
1881 1937 3.015327 CTCCTGCCAAGTAGTACGTACT 58.985 50.000 29.62 29.62 44.51 2.73
1882 1938 3.012518 TCTCCTGCCAAGTAGTACGTAC 58.987 50.000 18.10 18.10 0.00 3.67
1884 1940 1.817447 GTCTCCTGCCAAGTAGTACGT 59.183 52.381 0.00 0.00 0.00 3.57
1885 1941 1.816835 TGTCTCCTGCCAAGTAGTACG 59.183 52.381 0.00 0.00 0.00 3.67
1886 1942 4.401519 TGTATGTCTCCTGCCAAGTAGTAC 59.598 45.833 0.00 0.00 0.00 2.73
1887 1943 4.401519 GTGTATGTCTCCTGCCAAGTAGTA 59.598 45.833 0.00 0.00 0.00 1.82
1888 1944 3.195825 GTGTATGTCTCCTGCCAAGTAGT 59.804 47.826 0.00 0.00 0.00 2.73
1889 1945 3.449018 AGTGTATGTCTCCTGCCAAGTAG 59.551 47.826 0.00 0.00 0.00 2.57
1891 1947 2.260822 AGTGTATGTCTCCTGCCAAGT 58.739 47.619 0.00 0.00 0.00 3.16
1892 1948 3.449018 AGTAGTGTATGTCTCCTGCCAAG 59.551 47.826 0.00 0.00 0.00 3.61
1893 1949 3.441101 AGTAGTGTATGTCTCCTGCCAA 58.559 45.455 0.00 0.00 0.00 4.52
1952 2825 7.816945 ATGCTTGTCAATAAGTGCAATAAAC 57.183 32.000 0.00 0.00 34.07 2.01
1988 2861 8.846211 CCTTTTATCAGAAAGTCCTGTTTGTTA 58.154 33.333 0.00 0.00 35.37 2.41
1998 2871 7.117956 ACGTTAGCTTCCTTTTATCAGAAAGTC 59.882 37.037 0.00 0.00 35.37 3.01
2007 2880 5.616204 GCGAACAACGTTAGCTTCCTTTTAT 60.616 40.000 0.00 0.00 44.60 1.40
2023 2896 3.181169 AACTGCTGGCGCGAACAAC 62.181 57.895 12.10 3.69 39.65 3.32
2051 2924 8.138712 TCTCTGAGTTAGTTTCTCTTTCACTTC 58.861 37.037 4.32 0.00 33.59 3.01
2081 2954 8.271458 TGAGCATTAGGTAATGGATAAAACAGA 58.729 33.333 10.92 0.00 42.46 3.41
2091 2965 6.942005 TGTATGGATTGAGCATTAGGTAATGG 59.058 38.462 10.92 0.00 42.46 3.16
2124 3000 7.816995 GCCTTATGTGTAAATTTTGGTTGATGA 59.183 33.333 0.00 0.00 0.00 2.92
2187 3069 1.568612 GGTGTGAGTGTGATGCGTGG 61.569 60.000 0.00 0.00 0.00 4.94
2206 3088 3.585862 GCCATGTACCGTACCATATCAG 58.414 50.000 6.23 0.00 0.00 2.90
2226 3108 1.965411 GCTAGCTAGCTGCCATGGC 60.965 63.158 33.71 30.54 45.62 4.40
2474 3356 4.840005 GGCGGGCTGGAGCAGTAC 62.840 72.222 0.20 0.00 44.36 2.73
2534 3416 2.584608 GACCTGTACGGCCTGCAT 59.415 61.111 0.00 0.00 35.61 3.96
2657 3539 2.561885 ACGGAGAAGAGCGACGTG 59.438 61.111 0.00 0.00 36.32 4.49


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

AutoCloner maintained by Alex Coulton.