Multiple sequence alignment - TraesCS5D01G148000

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 TraesCS5D01G148000 chr5D 100.000 4536 0 0 1 4536 234820214 234824749 0.000000e+00 8377.0
1 TraesCS5D01G148000 chr5A 91.609 3933 140 47 666 4536 319754889 319751085 0.000000e+00 5260.0
2 TraesCS5D01G148000 chr5A 86.111 180 20 5 489 663 648011728 648011549 5.990000e-44 189.0
3 TraesCS5D01G148000 chr5A 83.704 135 10 4 1 126 319762177 319762046 2.870000e-22 117.0
4 TraesCS5D01G148000 chr5B 93.540 1966 49 29 727 2685 270014342 270012448 0.000000e+00 2856.0
5 TraesCS5D01G148000 chr5B 90.951 1503 63 28 2698 4171 270012104 270010646 0.000000e+00 1954.0
6 TraesCS5D01G148000 chr5B 89.583 240 16 7 4035 4265 270008154 270007915 3.430000e-76 296.0
7 TraesCS5D01G148000 chr5B 87.143 210 12 4 269 464 270014639 270014431 1.640000e-54 224.0
8 TraesCS5D01G148000 chr5B 85.143 175 22 3 491 663 372169439 372169267 4.660000e-40 176.0
9 TraesCS5D01G148000 chr5B 83.770 191 21 7 483 663 543565822 543566012 6.030000e-39 172.0
10 TraesCS5D01G148000 chr5B 97.872 94 2 0 3955 4048 270010098 270010005 3.630000e-36 163.0
11 TraesCS5D01G148000 chr5B 84.177 158 22 3 116 272 270014831 270014676 2.830000e-32 150.0
12 TraesCS5D01G148000 chr4D 86.080 898 104 11 1647 2527 105135794 105136687 0.000000e+00 946.0
13 TraesCS5D01G148000 chr4D 84.360 422 66 0 3096 3517 105137324 105137745 9.080000e-112 414.0
14 TraesCS5D01G148000 chr4D 91.124 169 15 0 1421 1589 105135533 105135701 3.530000e-56 230.0
15 TraesCS5D01G148000 chr4D 95.455 44 1 1 229 272 503564462 503564420 8.140000e-08 69.4
16 TraesCS5D01G148000 chr4D 97.297 37 1 0 236 272 6982550 6982514 3.790000e-06 63.9
17 TraesCS5D01G148000 chr4D 97.297 37 1 0 236 272 7411046 7411010 3.790000e-06 63.9
18 TraesCS5D01G148000 chr4A 85.984 899 105 11 1647 2528 470689233 470688339 0.000000e+00 942.0
19 TraesCS5D01G148000 chr4A 84.123 422 67 0 3096 3517 470687713 470687292 4.220000e-110 409.0
20 TraesCS5D01G148000 chr4A 89.286 168 18 0 1422 1589 470689496 470689329 1.280000e-50 211.0
21 TraesCS5D01G148000 chr4A 79.699 133 23 4 4192 4322 740923653 740923783 4.830000e-15 93.5
22 TraesCS5D01G148000 chr4A 81.250 80 15 0 4143 4222 104146112 104146033 1.050000e-06 65.8
23 TraesCS5D01G148000 chr4B 85.857 898 107 10 1650 2531 148921078 148921971 0.000000e+00 937.0
24 TraesCS5D01G148000 chr4B 83.886 422 68 0 3096 3517 148922625 148923046 1.970000e-108 403.0
25 TraesCS5D01G148000 chr4B 91.124 169 15 0 1421 1589 148920813 148920981 3.530000e-56 230.0
26 TraesCS5D01G148000 chr4B 84.127 189 22 7 483 663 415901187 415901375 4.660000e-40 176.0
27 TraesCS5D01G148000 chr2D 85.714 182 21 5 487 663 110402078 110401897 2.150000e-43 187.0
28 TraesCS5D01G148000 chr2D 84.574 188 15 8 488 663 58894196 58894381 1.680000e-39 174.0
29 TraesCS5D01G148000 chr7D 85.484 186 17 9 483 658 44802278 44802093 7.750000e-43 185.0
30 TraesCS5D01G148000 chr7D 79.562 137 25 3 4175 4310 483101096 483101230 1.340000e-15 95.3
31 TraesCS5D01G148000 chr7A 85.870 184 15 3 489 662 701212115 701211933 7.750000e-43 185.0
32 TraesCS5D01G148000 chr3D 84.946 186 19 8 491 667 533955515 533955700 3.610000e-41 180.0
33 TraesCS5D01G148000 chr6D 80.992 121 22 1 4191 4311 388158756 388158875 1.340000e-15 95.3
34 TraesCS5D01G148000 chr2A 86.047 86 11 1 4244 4328 777895247 777895332 1.740000e-14 91.6
35 TraesCS5D01G148000 chr2A 97.297 37 1 0 236 272 611312296 611312260 3.790000e-06 63.9
36 TraesCS5D01G148000 chr3B 95.349 43 2 0 230 272 16048406 16048364 8.140000e-08 69.4
37 TraesCS5D01G148000 chr3B 93.182 44 3 0 229 272 107640586 107640629 1.050000e-06 65.8
38 TraesCS5D01G148000 chrUn 100.000 35 0 0 238 272 126990225 126990259 1.050000e-06 65.8
39 TraesCS5D01G148000 chr2B 93.023 43 2 1 231 272 760300038 760299996 1.360000e-05 62.1


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 TraesCS5D01G148000 chr5D 234820214 234824749 4535 False 8377.000000 8377 100.000000 1 4536 1 chr5D.!!$F1 4535
1 TraesCS5D01G148000 chr5A 319751085 319754889 3804 True 5260.000000 5260 91.609000 666 4536 1 chr5A.!!$R1 3870
2 TraesCS5D01G148000 chr5B 270007915 270014831 6916 True 940.500000 2856 90.544333 116 4265 6 chr5B.!!$R2 4149
3 TraesCS5D01G148000 chr4D 105135533 105137745 2212 False 530.000000 946 87.188000 1421 3517 3 chr4D.!!$F1 2096
4 TraesCS5D01G148000 chr4A 470687292 470689496 2204 True 520.666667 942 86.464333 1422 3517 3 chr4A.!!$R2 2095
5 TraesCS5D01G148000 chr4B 148920813 148923046 2233 False 523.333333 937 86.955667 1421 3517 3 chr4B.!!$F2 2096

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
718 777 0.033601 TCCTCCTCTCCTCTCACAGC 60.034 60.0 0.00 0.0 0.00 4.40 F
910 985 1.070471 CGGCGCCAAAGCACATAAAC 61.070 55.0 28.98 0.0 39.83 2.01 F
1620 1742 0.679960 AGCAGCATCAGCATCAGCAA 60.680 50.0 0.00 0.0 45.49 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1739 0.179097 CGTTAGGGAGGAGAGCTTGC 60.179 60.000 0.00 0.0 0.0 4.01 R
2664 2846 0.179234 TGTCACGGTGTCACATTGGT 59.821 50.000 8.17 0.0 0.0 3.67 R
3616 4376 1.466558 GCTAAGCAGACCAAGAAGCAC 59.533 52.381 0.00 0.0 0.0 4.40 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
61 62 4.343581 CGTATGGATGACGCTGGG 57.656 61.111 0.00 0.00 32.89 4.45
62 63 1.739667 CGTATGGATGACGCTGGGA 59.260 57.895 0.00 0.00 32.89 4.37
63 64 0.319040 CGTATGGATGACGCTGGGAG 60.319 60.000 0.00 0.00 32.89 4.30
64 65 0.753262 GTATGGATGACGCTGGGAGT 59.247 55.000 0.00 0.00 0.00 3.85
65 66 1.961394 GTATGGATGACGCTGGGAGTA 59.039 52.381 0.00 0.00 0.00 2.59
66 67 1.496060 ATGGATGACGCTGGGAGTAA 58.504 50.000 0.00 0.00 0.00 2.24
67 68 1.271856 TGGATGACGCTGGGAGTAAA 58.728 50.000 0.00 0.00 0.00 2.01
68 69 1.626321 TGGATGACGCTGGGAGTAAAA 59.374 47.619 0.00 0.00 0.00 1.52
69 70 2.280628 GGATGACGCTGGGAGTAAAAG 58.719 52.381 0.00 0.00 0.00 2.27
70 71 2.280628 GATGACGCTGGGAGTAAAAGG 58.719 52.381 0.00 0.00 0.00 3.11
71 72 1.053424 TGACGCTGGGAGTAAAAGGT 58.947 50.000 0.00 0.00 0.00 3.50
72 73 1.001633 TGACGCTGGGAGTAAAAGGTC 59.998 52.381 0.00 0.00 0.00 3.85
73 74 1.275573 GACGCTGGGAGTAAAAGGTCT 59.724 52.381 0.00 0.00 0.00 3.85
74 75 1.002087 ACGCTGGGAGTAAAAGGTCTG 59.998 52.381 0.00 0.00 0.00 3.51
75 76 1.454201 GCTGGGAGTAAAAGGTCTGC 58.546 55.000 0.00 0.00 0.00 4.26
76 77 1.003696 GCTGGGAGTAAAAGGTCTGCT 59.996 52.381 0.00 0.00 0.00 4.24
77 78 2.236395 GCTGGGAGTAAAAGGTCTGCTA 59.764 50.000 0.00 0.00 0.00 3.49
78 79 3.680196 GCTGGGAGTAAAAGGTCTGCTAG 60.680 52.174 0.00 0.00 34.79 3.42
79 80 2.236395 TGGGAGTAAAAGGTCTGCTAGC 59.764 50.000 8.10 8.10 0.00 3.42
80 81 2.502130 GGGAGTAAAAGGTCTGCTAGCT 59.498 50.000 17.23 0.00 37.60 3.32
81 82 3.526534 GGAGTAAAAGGTCTGCTAGCTG 58.473 50.000 17.23 16.05 35.65 4.24
82 83 3.526534 GAGTAAAAGGTCTGCTAGCTGG 58.473 50.000 20.06 11.19 35.65 4.85
83 84 2.010497 GTAAAAGGTCTGCTAGCTGGC 58.990 52.381 16.23 16.23 35.65 4.85
84 85 0.674895 AAAAGGTCTGCTAGCTGGCG 60.675 55.000 17.89 12.09 35.65 5.69
85 86 2.527951 AAAGGTCTGCTAGCTGGCGG 62.528 60.000 23.99 23.99 35.65 6.13
86 87 4.537433 GGTCTGCTAGCTGGCGGG 62.537 72.222 28.29 17.95 38.94 6.13
87 88 3.775654 GTCTGCTAGCTGGCGGGT 61.776 66.667 28.29 2.51 38.94 5.28
88 89 3.461773 TCTGCTAGCTGGCGGGTC 61.462 66.667 28.29 0.00 38.94 4.46
89 90 4.880537 CTGCTAGCTGGCGGGTCG 62.881 72.222 22.45 0.00 35.17 4.79
96 97 4.514577 CTGGCGGGTCGTGCTAGG 62.515 72.222 0.00 0.00 37.30 3.02
102 103 3.400054 GGTCGTGCTAGGGGGCTT 61.400 66.667 0.00 0.00 0.00 4.35
103 104 2.187163 GTCGTGCTAGGGGGCTTC 59.813 66.667 0.00 0.00 0.00 3.86
104 105 2.038975 TCGTGCTAGGGGGCTTCT 59.961 61.111 0.00 0.00 0.00 2.85
105 106 2.187946 CGTGCTAGGGGGCTTCTG 59.812 66.667 0.00 0.00 0.00 3.02
106 107 2.359169 CGTGCTAGGGGGCTTCTGA 61.359 63.158 0.00 0.00 0.00 3.27
107 108 1.524482 GTGCTAGGGGGCTTCTGAG 59.476 63.158 0.00 0.00 0.00 3.35
123 124 3.233259 GAGCGATCCTGCCCCTAGC 62.233 68.421 0.00 0.00 44.14 3.42
132 133 2.824489 GCCCCTAGCTGGCGTTTC 60.824 66.667 0.00 0.00 39.48 2.78
134 135 2.511600 CCCTAGCTGGCGTTTCCG 60.512 66.667 0.00 0.00 37.80 4.30
142 143 1.202031 GCTGGCGTTTCCGAGTTATTG 60.202 52.381 0.00 0.00 37.80 1.90
145 146 0.730840 GCGTTTCCGAGTTATTGGGG 59.269 55.000 0.00 0.00 35.63 4.96
146 147 1.375551 CGTTTCCGAGTTATTGGGGG 58.624 55.000 0.00 0.00 35.63 5.40
147 148 1.339342 CGTTTCCGAGTTATTGGGGGT 60.339 52.381 0.00 0.00 35.63 4.95
222 223 7.938563 TGAAAAATTCACCAAAAATACGAGG 57.061 32.000 0.00 0.00 34.08 4.63
226 227 5.897377 ATTCACCAAAAATACGAGGGAAG 57.103 39.130 0.00 0.00 0.00 3.46
227 228 3.078837 TCACCAAAAATACGAGGGAAGC 58.921 45.455 0.00 0.00 0.00 3.86
230 231 4.082245 CACCAAAAATACGAGGGAAGCAAT 60.082 41.667 0.00 0.00 0.00 3.56
234 235 5.830000 AAAATACGAGGGAAGCAATAACC 57.170 39.130 0.00 0.00 0.00 2.85
256 257 3.487574 CGGATTGCTAAATCTCAGTCGAC 59.512 47.826 7.70 7.70 41.74 4.20
258 259 4.505922 GGATTGCTAAATCTCAGTCGACTG 59.494 45.833 34.76 34.76 41.74 3.51
278 322 9.537192 TCGACTGAGACTTAACAAAGAAATAAA 57.463 29.630 0.00 0.00 0.00 1.40
347 401 2.104967 GCCCCACCCAACTAATAAACC 58.895 52.381 0.00 0.00 0.00 3.27
348 402 2.371306 CCCCACCCAACTAATAAACCG 58.629 52.381 0.00 0.00 0.00 4.44
352 406 3.692593 CCACCCAACTAATAAACCGGAAG 59.307 47.826 9.46 0.00 0.00 3.46
365 419 2.194326 GGAAGGGAGGATGCAGGC 59.806 66.667 0.00 0.00 0.00 4.85
388 442 3.259876 ACTGGTCGTACCACACATTGTAT 59.740 43.478 3.02 0.00 44.79 2.29
394 448 3.370103 CGTACCACACATTGTATTCCCCT 60.370 47.826 0.00 0.00 0.00 4.79
408 462 2.662535 TCCCCTGCATTGTCATATGG 57.337 50.000 2.13 0.00 0.00 2.74
450 504 1.822990 AGTGGATGAAAGCATTGCCAG 59.177 47.619 4.70 0.00 34.11 4.85
454 508 0.822164 ATGAAAGCATTGCCAGGAGC 59.178 50.000 4.70 0.00 44.14 4.70
464 518 3.800628 GCCAGGAGCAAATCACAAC 57.199 52.632 0.00 0.00 42.97 3.32
465 519 0.961019 GCCAGGAGCAAATCACAACA 59.039 50.000 0.00 0.00 42.97 3.33
467 521 2.863704 GCCAGGAGCAAATCACAACAAC 60.864 50.000 0.00 0.00 42.97 3.32
468 522 2.361757 CCAGGAGCAAATCACAACAACA 59.638 45.455 0.00 0.00 0.00 3.33
469 523 3.181477 CCAGGAGCAAATCACAACAACAA 60.181 43.478 0.00 0.00 0.00 2.83
475 529 6.168164 AGCAAATCACAACAACAAAAAGTG 57.832 33.333 0.00 0.00 0.00 3.16
476 530 5.931146 AGCAAATCACAACAACAAAAAGTGA 59.069 32.000 0.00 0.00 42.62 3.41
477 531 6.426328 AGCAAATCACAACAACAAAAAGTGAA 59.574 30.769 0.00 0.00 41.86 3.18
478 532 7.041508 AGCAAATCACAACAACAAAAAGTGAAA 60.042 29.630 0.00 0.00 41.86 2.69
479 533 7.268872 GCAAATCACAACAACAAAAAGTGAAAG 59.731 33.333 0.00 0.00 41.86 2.62
480 534 6.966435 ATCACAACAACAAAAAGTGAAAGG 57.034 33.333 0.00 0.00 41.86 3.11
481 535 6.090483 TCACAACAACAAAAAGTGAAAGGA 57.910 33.333 0.00 0.00 36.39 3.36
482 536 6.696411 TCACAACAACAAAAAGTGAAAGGAT 58.304 32.000 0.00 0.00 36.39 3.24
483 537 7.831753 TCACAACAACAAAAAGTGAAAGGATA 58.168 30.769 0.00 0.00 36.39 2.59
484 538 8.307483 TCACAACAACAAAAAGTGAAAGGATAA 58.693 29.630 0.00 0.00 36.39 1.75
485 539 8.930760 CACAACAACAAAAAGTGAAAGGATAAA 58.069 29.630 0.00 0.00 32.14 1.40
486 540 9.495572 ACAACAACAAAAAGTGAAAGGATAAAA 57.504 25.926 0.00 0.00 0.00 1.52
509 563 7.964545 AAAAACAGTTTGTCTAATTCACGTC 57.035 32.000 0.00 0.00 0.00 4.34
510 564 6.920569 AAACAGTTTGTCTAATTCACGTCT 57.079 33.333 0.00 0.00 0.00 4.18
511 565 8.428186 AAAACAGTTTGTCTAATTCACGTCTA 57.572 30.769 0.00 0.00 0.00 2.59
512 566 7.639162 AACAGTTTGTCTAATTCACGTCTAG 57.361 36.000 0.00 0.00 0.00 2.43
513 567 6.978338 ACAGTTTGTCTAATTCACGTCTAGA 58.022 36.000 0.00 0.00 0.00 2.43
514 568 7.603651 ACAGTTTGTCTAATTCACGTCTAGAT 58.396 34.615 0.00 0.00 0.00 1.98
515 569 7.542477 ACAGTTTGTCTAATTCACGTCTAGATG 59.458 37.037 10.54 10.54 0.00 2.90
516 570 7.542477 CAGTTTGTCTAATTCACGTCTAGATGT 59.458 37.037 11.99 11.99 0.00 3.06
517 571 8.088981 AGTTTGTCTAATTCACGTCTAGATGTT 58.911 33.333 15.12 3.67 0.00 2.71
518 572 8.709646 GTTTGTCTAATTCACGTCTAGATGTTT 58.290 33.333 15.12 9.87 0.00 2.83
519 573 8.827177 TTGTCTAATTCACGTCTAGATGTTTT 57.173 30.769 15.12 11.28 0.00 2.43
520 574 8.827177 TGTCTAATTCACGTCTAGATGTTTTT 57.173 30.769 15.12 10.96 0.00 1.94
521 575 9.917129 TGTCTAATTCACGTCTAGATGTTTTTA 57.083 29.630 15.12 11.44 0.00 1.52
525 579 8.842358 AATTCACGTCTAGATGTTTTTAAGGA 57.158 30.769 15.12 5.03 0.00 3.36
526 580 9.449719 AATTCACGTCTAGATGTTTTTAAGGAT 57.550 29.630 15.12 0.67 0.00 3.24
527 581 7.827819 TCACGTCTAGATGTTTTTAAGGATG 57.172 36.000 15.12 0.64 0.00 3.51
528 582 7.383687 TCACGTCTAGATGTTTTTAAGGATGT 58.616 34.615 15.12 0.00 0.00 3.06
529 583 7.544566 TCACGTCTAGATGTTTTTAAGGATGTC 59.455 37.037 15.12 0.00 0.00 3.06
530 584 7.330946 CACGTCTAGATGTTTTTAAGGATGTCA 59.669 37.037 15.12 0.00 0.00 3.58
531 585 7.331193 ACGTCTAGATGTTTTTAAGGATGTCAC 59.669 37.037 11.99 0.00 0.00 3.67
532 586 7.330946 CGTCTAGATGTTTTTAAGGATGTCACA 59.669 37.037 3.59 0.00 0.00 3.58
533 587 9.167311 GTCTAGATGTTTTTAAGGATGTCACAT 57.833 33.333 0.00 0.00 0.00 3.21
534 588 9.383519 TCTAGATGTTTTTAAGGATGTCACATC 57.616 33.333 9.53 9.53 39.46 3.06
535 589 9.388506 CTAGATGTTTTTAAGGATGTCACATCT 57.611 33.333 17.46 14.48 46.91 2.90
537 591 9.739276 AGATGTTTTTAAGGATGTCACATCTAA 57.261 29.630 17.46 6.57 44.74 2.10
540 594 9.349713 TGTTTTTAAGGATGTCACATCTAAACT 57.650 29.630 17.46 3.19 0.00 2.66
541 595 9.827411 GTTTTTAAGGATGTCACATCTAAACTC 57.173 33.333 17.46 7.31 0.00 3.01
542 596 8.561738 TTTTAAGGATGTCACATCTAAACTCC 57.438 34.615 17.46 0.18 0.00 3.85
543 597 4.762289 AGGATGTCACATCTAAACTCCC 57.238 45.455 17.46 0.00 0.00 4.30
544 598 4.104086 AGGATGTCACATCTAAACTCCCA 58.896 43.478 17.46 0.00 0.00 4.37
545 599 4.080863 AGGATGTCACATCTAAACTCCCAC 60.081 45.833 17.46 0.00 0.00 4.61
546 600 4.323485 GGATGTCACATCTAAACTCCCACA 60.323 45.833 17.46 0.00 0.00 4.17
547 601 4.698201 TGTCACATCTAAACTCCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
548 602 5.042463 TGTCACATCTAAACTCCCACAAA 57.958 39.130 0.00 0.00 0.00 2.83
549 603 5.630121 TGTCACATCTAAACTCCCACAAAT 58.370 37.500 0.00 0.00 0.00 2.32
550 604 6.774673 TGTCACATCTAAACTCCCACAAATA 58.225 36.000 0.00 0.00 0.00 1.40
551 605 7.402054 TGTCACATCTAAACTCCCACAAATAT 58.598 34.615 0.00 0.00 0.00 1.28
552 606 8.544622 TGTCACATCTAAACTCCCACAAATATA 58.455 33.333 0.00 0.00 0.00 0.86
553 607 9.561069 GTCACATCTAAACTCCCACAAATATAT 57.439 33.333 0.00 0.00 0.00 0.86
562 616 9.860650 AAACTCCCACAAATATATAATGTAGCA 57.139 29.630 4.31 0.00 0.00 3.49
563 617 9.860650 AACTCCCACAAATATATAATGTAGCAA 57.139 29.630 4.31 0.00 0.00 3.91
564 618 9.284968 ACTCCCACAAATATATAATGTAGCAAC 57.715 33.333 4.31 0.00 0.00 4.17
565 619 9.283768 CTCCCACAAATATATAATGTAGCAACA 57.716 33.333 4.31 0.00 40.69 3.33
566 620 9.634021 TCCCACAAATATATAATGTAGCAACAA 57.366 29.630 4.31 0.00 39.58 2.83
633 687 9.944376 ATCAGTTTAGATGTAACATAACTGTGT 57.056 29.630 14.98 7.02 41.76 3.72
634 688 9.419297 TCAGTTTAGATGTAACATAACTGTGTC 57.581 33.333 14.98 0.00 41.76 3.67
635 689 9.203421 CAGTTTAGATGTAACATAACTGTGTCA 57.797 33.333 0.00 0.00 38.28 3.58
636 690 9.944376 AGTTTAGATGTAACATAACTGTGTCAT 57.056 29.630 0.00 0.00 35.22 3.06
646 700 8.997621 AACATAACTGTGTCATATTTAGACGT 57.002 30.769 0.00 0.00 38.83 4.34
647 701 8.407457 ACATAACTGTGTCATATTTAGACGTG 57.593 34.615 0.00 0.00 38.83 4.49
648 702 8.033038 ACATAACTGTGTCATATTTAGACGTGT 58.967 33.333 0.00 0.00 38.83 4.49
649 703 6.946229 AACTGTGTCATATTTAGACGTGTC 57.054 37.500 0.00 0.00 38.83 3.67
650 704 6.268825 ACTGTGTCATATTTAGACGTGTCT 57.731 37.500 7.77 7.77 43.40 3.41
651 705 6.688578 ACTGTGTCATATTTAGACGTGTCTT 58.311 36.000 7.97 0.00 40.93 3.01
652 706 7.823665 ACTGTGTCATATTTAGACGTGTCTTA 58.176 34.615 7.97 0.00 40.93 2.10
653 707 7.968956 ACTGTGTCATATTTAGACGTGTCTTAG 59.031 37.037 7.97 0.00 40.93 2.18
654 708 8.047413 TGTGTCATATTTAGACGTGTCTTAGA 57.953 34.615 7.97 0.00 40.93 2.10
655 709 7.966753 TGTGTCATATTTAGACGTGTCTTAGAC 59.033 37.037 7.97 5.27 40.93 2.59
656 710 7.966753 GTGTCATATTTAGACGTGTCTTAGACA 59.033 37.037 11.42 11.42 40.93 3.41
657 711 8.182227 TGTCATATTTAGACGTGTCTTAGACAG 58.818 37.037 16.04 11.93 40.93 3.51
658 712 8.396390 GTCATATTTAGACGTGTCTTAGACAGA 58.604 37.037 16.04 2.08 43.57 3.41
659 713 8.953313 TCATATTTAGACGTGTCTTAGACAGAA 58.047 33.333 16.04 4.82 43.57 3.02
660 714 9.011407 CATATTTAGACGTGTCTTAGACAGAAC 57.989 37.037 16.04 9.47 43.57 3.01
661 715 3.919223 AGACGTGTCTTAGACAGAACC 57.081 47.619 16.04 3.01 43.57 3.62
662 716 3.488363 AGACGTGTCTTAGACAGAACCT 58.512 45.455 16.04 7.82 43.57 3.50
663 717 4.649692 AGACGTGTCTTAGACAGAACCTA 58.350 43.478 16.04 0.00 43.57 3.08
664 718 4.696402 AGACGTGTCTTAGACAGAACCTAG 59.304 45.833 16.04 4.34 43.57 3.02
686 740 4.876107 AGAAAGAAAGCGAAAACACAGAGA 59.124 37.500 0.00 0.00 0.00 3.10
709 768 1.283321 AGTGGCAAAATCCTCCTCTCC 59.717 52.381 0.00 0.00 0.00 3.71
718 777 0.033601 TCCTCCTCTCCTCTCACAGC 60.034 60.000 0.00 0.00 0.00 4.40
826 901 3.366679 CGTCGGCTTCTTCCACTTTACTA 60.367 47.826 0.00 0.00 0.00 1.82
827 902 3.925299 GTCGGCTTCTTCCACTTTACTAC 59.075 47.826 0.00 0.00 0.00 2.73
828 903 3.830755 TCGGCTTCTTCCACTTTACTACT 59.169 43.478 0.00 0.00 0.00 2.57
835 910 4.771054 TCTTCCACTTTACTACTCCACTCC 59.229 45.833 0.00 0.00 0.00 3.85
836 911 4.122337 TCCACTTTACTACTCCACTCCA 57.878 45.455 0.00 0.00 0.00 3.86
910 985 1.070471 CGGCGCCAAAGCACATAAAC 61.070 55.000 28.98 0.00 39.83 2.01
1042 1125 2.231540 CTTCCCCTCGTCCTCCTCCT 62.232 65.000 0.00 0.00 0.00 3.69
1043 1126 2.123640 CCCCTCGTCCTCCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1044 1127 2.123640 CCCTCGTCCTCCTCCTCC 60.124 72.222 0.00 0.00 0.00 4.30
1065 1148 2.528134 CCCCCGCTCCTCTTATTCA 58.472 57.895 0.00 0.00 0.00 2.57
1089 1172 4.467107 ACCGCCTCCTCCTCCTCC 62.467 72.222 0.00 0.00 0.00 4.30
1090 1173 4.150454 CCGCCTCCTCCTCCTCCT 62.150 72.222 0.00 0.00 0.00 3.69
1091 1174 2.520741 CGCCTCCTCCTCCTCCTC 60.521 72.222 0.00 0.00 0.00 3.71
1092 1175 2.123033 GCCTCCTCCTCCTCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1093 1176 2.710826 GCCTCCTCCTCCTCCTCCT 61.711 68.421 0.00 0.00 0.00 3.69
1094 1177 1.541672 CCTCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
1095 1178 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1096 1179 2.015726 TCCTCCTCCTCCTCCTCCC 61.016 68.421 0.00 0.00 0.00 4.30
1097 1180 2.328589 CCTCCTCCTCCTCCTCCCA 61.329 68.421 0.00 0.00 0.00 4.37
1145 1228 1.305381 ACTTCCTCCTCCACCTCCG 60.305 63.158 0.00 0.00 0.00 4.63
1368 1460 2.404995 GCAGCAGCAGGTGGATCAC 61.405 63.158 10.46 0.00 43.34 3.06
1614 1736 3.209812 CCGCAGCAGCATCAGCAT 61.210 61.111 0.82 0.00 45.49 3.79
1615 1737 2.328289 CGCAGCAGCATCAGCATC 59.672 61.111 0.82 0.00 45.49 3.91
1616 1738 2.469516 CGCAGCAGCATCAGCATCA 61.470 57.895 0.82 0.00 45.49 3.07
1617 1739 1.356979 GCAGCAGCATCAGCATCAG 59.643 57.895 0.00 0.00 45.49 2.90
1618 1740 1.356979 CAGCAGCATCAGCATCAGC 59.643 57.895 0.00 0.00 45.49 4.26
1619 1741 1.077716 AGCAGCATCAGCATCAGCA 60.078 52.632 0.00 0.00 45.49 4.41
1620 1742 0.679960 AGCAGCATCAGCATCAGCAA 60.680 50.000 0.00 0.00 45.49 3.91
2553 2723 2.424246 GAGCACTCCACTGTACTCTACC 59.576 54.545 0.00 0.00 30.01 3.18
2565 2741 6.208994 CACTGTACTCTACCTCTACCTTTGTT 59.791 42.308 0.00 0.00 0.00 2.83
2662 2844 1.106285 CAGCCTGCATTTCCTTACCC 58.894 55.000 0.00 0.00 0.00 3.69
2663 2845 0.033109 AGCCTGCATTTCCTTACCCC 60.033 55.000 0.00 0.00 0.00 4.95
2664 2846 0.324275 GCCTGCATTTCCTTACCCCA 60.324 55.000 0.00 0.00 0.00 4.96
2665 2847 1.474330 CCTGCATTTCCTTACCCCAC 58.526 55.000 0.00 0.00 0.00 4.61
2666 2848 1.474330 CTGCATTTCCTTACCCCACC 58.526 55.000 0.00 0.00 0.00 4.61
2690 2872 1.796459 GTGACACCGTGACATTGTACC 59.204 52.381 5.28 0.00 0.00 3.34
2712 3226 2.810274 ACAGTACACATCAAGCAAGCAG 59.190 45.455 0.00 0.00 0.00 4.24
2763 3281 6.358991 AGGTCAGGAGATGAAGTAGTAGTAC 58.641 44.000 0.00 0.00 40.43 2.73
2813 3339 5.511729 GCTAAAAGTTTGTCATTATGACCGC 59.488 40.000 20.91 11.57 46.40 5.68
2815 3341 2.006888 AGTTTGTCATTATGACCGCCG 58.993 47.619 20.91 0.00 46.40 6.46
2816 3342 1.063469 GTTTGTCATTATGACCGCCGG 59.937 52.381 20.91 0.00 46.40 6.13
2817 3343 1.092921 TTGTCATTATGACCGCCGGC 61.093 55.000 19.07 19.07 46.40 6.13
2818 3344 1.227556 GTCATTATGACCGCCGGCT 60.228 57.895 26.68 6.32 41.37 5.52
2819 3345 0.814010 GTCATTATGACCGCCGGCTT 60.814 55.000 26.68 11.62 41.37 4.35
2820 3346 0.813610 TCATTATGACCGCCGGCTTG 60.814 55.000 26.68 18.10 0.00 4.01
2821 3347 1.525995 ATTATGACCGCCGGCTTGG 60.526 57.895 26.68 21.88 42.50 3.61
2858 3390 5.299531 ACTCTAGAAAGGTTTCAACTTTGGC 59.700 40.000 5.30 0.00 38.21 4.52
2864 3396 1.611491 GGTTTCAACTTTGGCGATCCA 59.389 47.619 0.00 0.00 41.55 3.41
3000 3581 7.065563 CCACTCATGCTGATTCTATATTTAGCC 59.934 40.741 0.00 0.00 0.00 3.93
3021 3602 2.600420 CGACGGAAATCACTGTCATCTG 59.400 50.000 0.00 0.00 43.80 2.90
3025 3609 3.553511 CGGAAATCACTGTCATCTGCTAC 59.446 47.826 0.00 0.00 0.00 3.58
3076 3814 3.784763 ACTGATCCTGAGAATGGTGGATT 59.215 43.478 0.00 0.00 39.19 3.01
3078 3816 5.163258 ACTGATCCTGAGAATGGTGGATTAC 60.163 44.000 0.00 0.00 39.19 1.89
3603 4361 7.618019 AGAGTAGGAGTTATGATGCCAATTA 57.382 36.000 0.00 0.00 0.00 1.40
3604 4362 7.675062 AGAGTAGGAGTTATGATGCCAATTAG 58.325 38.462 0.00 0.00 0.00 1.73
3605 4363 6.234177 AGTAGGAGTTATGATGCCAATTAGC 58.766 40.000 0.00 0.00 0.00 3.09
3606 4364 5.316158 AGGAGTTATGATGCCAATTAGCT 57.684 39.130 0.00 0.00 0.00 3.32
3607 4365 6.439636 AGGAGTTATGATGCCAATTAGCTA 57.560 37.500 0.00 0.00 0.00 3.32
3616 4376 7.734924 TGATGCCAATTAGCTATAGTTCTTG 57.265 36.000 0.84 3.68 0.00 3.02
3629 4389 3.567478 AGTTCTTGTGCTTCTTGGTCT 57.433 42.857 0.00 0.00 0.00 3.85
3687 4447 8.345724 AGAAAACATTCTGATCACTAATTGCT 57.654 30.769 0.00 0.00 0.00 3.91
3688 4448 9.453572 AGAAAACATTCTGATCACTAATTGCTA 57.546 29.630 0.00 0.00 0.00 3.49
3689 4449 9.495754 GAAAACATTCTGATCACTAATTGCTAC 57.504 33.333 0.00 0.00 0.00 3.58
3690 4450 6.834959 ACATTCTGATCACTAATTGCTACG 57.165 37.500 0.00 0.00 0.00 3.51
3707 4467 3.119602 GCTACGTAGATCTTGTCACCACA 60.120 47.826 26.53 0.00 0.00 4.17
3759 4519 6.715347 ATCAGCTTATTTTCATGGTAACCC 57.285 37.500 0.00 0.00 0.00 4.11
4013 4778 0.837260 AGCCAATGGGGTTGTGCATT 60.837 50.000 0.00 0.00 44.14 3.56
4061 7454 0.319728 CTAGCTCACCATCCCCATCG 59.680 60.000 0.00 0.00 0.00 3.84
4112 7505 5.047021 TCCTTTTCTTCTCGTCTCATGTCAT 60.047 40.000 0.00 0.00 0.00 3.06
4117 7510 6.370433 TCTTCTCGTCTCATGTCATCTAAG 57.630 41.667 0.00 0.00 0.00 2.18
4156 7552 0.445436 CTCAAAGCATGCCACGTCTC 59.555 55.000 15.66 0.00 0.00 3.36
4266 7671 3.562635 CGAGGAACCAACTTCGGC 58.437 61.111 0.00 0.00 36.12 5.54
4269 7674 3.733960 GGAACCAACTTCGGCCGC 61.734 66.667 23.51 2.01 0.00 6.53
4352 7757 0.666274 TCGTCAGCATCGTCCACAAC 60.666 55.000 0.00 0.00 0.00 3.32
4353 7758 0.943835 CGTCAGCATCGTCCACAACA 60.944 55.000 0.00 0.00 0.00 3.33
4360 7765 3.055819 AGCATCGTCCACAACATACTCTT 60.056 43.478 0.00 0.00 0.00 2.85
4373 7778 5.193663 ACATACTCTTCACTCATCATCGG 57.806 43.478 0.00 0.00 0.00 4.18
4375 7780 1.137872 ACTCTTCACTCATCATCGGCC 59.862 52.381 0.00 0.00 0.00 6.13
4386 7791 3.474570 ATCGGCCTGCACCTCCTC 61.475 66.667 0.00 0.00 0.00 3.71
4429 7834 0.830648 CTGGCGATGGGGAAGTCTTA 59.169 55.000 0.00 0.00 0.00 2.10
4434 7839 0.474614 GATGGGGAAGTCTTAGGCCC 59.525 60.000 0.00 0.00 39.93 5.80
4439 7844 3.735037 GAAGTCTTAGGCCCCGGCG 62.735 68.421 0.00 0.00 43.06 6.46
4466 7871 0.339859 TAGGCTGGTCTGGATCAGGT 59.660 55.000 12.09 0.00 39.88 4.00
4469 7874 0.105778 GCTGGTCTGGATCAGGTAGC 59.894 60.000 12.09 0.71 39.88 3.58
4476 7881 2.178764 TCTGGATCAGGTAGCAGGAGAT 59.821 50.000 0.00 0.00 31.51 2.75
4477 7882 2.971330 CTGGATCAGGTAGCAGGAGATT 59.029 50.000 0.00 0.00 0.00 2.40
4520 7925 2.423898 GGGCCGTCTTGATCCTCGA 61.424 63.158 0.00 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.319040 CTCCCAGCGTCATCCATACG 60.319 60.000 0.00 0.00 43.12 3.06
45 46 0.753262 ACTCCCAGCGTCATCCATAC 59.247 55.000 0.00 0.00 0.00 2.39
46 47 2.375014 TACTCCCAGCGTCATCCATA 57.625 50.000 0.00 0.00 0.00 2.74
47 48 1.496060 TTACTCCCAGCGTCATCCAT 58.504 50.000 0.00 0.00 0.00 3.41
48 49 1.271856 TTTACTCCCAGCGTCATCCA 58.728 50.000 0.00 0.00 0.00 3.41
49 50 2.280628 CTTTTACTCCCAGCGTCATCC 58.719 52.381 0.00 0.00 0.00 3.51
50 51 2.280628 CCTTTTACTCCCAGCGTCATC 58.719 52.381 0.00 0.00 0.00 2.92
51 52 1.628846 ACCTTTTACTCCCAGCGTCAT 59.371 47.619 0.00 0.00 0.00 3.06
52 53 1.001633 GACCTTTTACTCCCAGCGTCA 59.998 52.381 0.00 0.00 0.00 4.35
53 54 1.275573 AGACCTTTTACTCCCAGCGTC 59.724 52.381 0.00 0.00 0.00 5.19
54 55 1.002087 CAGACCTTTTACTCCCAGCGT 59.998 52.381 0.00 0.00 0.00 5.07
55 56 1.726853 CAGACCTTTTACTCCCAGCG 58.273 55.000 0.00 0.00 0.00 5.18
56 57 1.003696 AGCAGACCTTTTACTCCCAGC 59.996 52.381 0.00 0.00 0.00 4.85
57 58 3.680196 GCTAGCAGACCTTTTACTCCCAG 60.680 52.174 10.63 0.00 0.00 4.45
58 59 2.236395 GCTAGCAGACCTTTTACTCCCA 59.764 50.000 10.63 0.00 0.00 4.37
59 60 2.502130 AGCTAGCAGACCTTTTACTCCC 59.498 50.000 18.83 0.00 0.00 4.30
60 61 3.526534 CAGCTAGCAGACCTTTTACTCC 58.473 50.000 18.83 0.00 0.00 3.85
61 62 3.526534 CCAGCTAGCAGACCTTTTACTC 58.473 50.000 18.83 0.00 0.00 2.59
62 63 2.355209 GCCAGCTAGCAGACCTTTTACT 60.355 50.000 18.83 0.00 0.00 2.24
63 64 2.010497 GCCAGCTAGCAGACCTTTTAC 58.990 52.381 18.83 0.00 0.00 2.01
64 65 1.405526 CGCCAGCTAGCAGACCTTTTA 60.406 52.381 18.83 0.00 0.00 1.52
65 66 0.674895 CGCCAGCTAGCAGACCTTTT 60.675 55.000 18.83 0.00 0.00 2.27
66 67 1.078848 CGCCAGCTAGCAGACCTTT 60.079 57.895 18.83 0.00 0.00 3.11
67 68 2.581354 CGCCAGCTAGCAGACCTT 59.419 61.111 18.83 0.00 0.00 3.50
68 69 3.465403 CCGCCAGCTAGCAGACCT 61.465 66.667 18.83 0.00 0.00 3.85
69 70 4.537433 CCCGCCAGCTAGCAGACC 62.537 72.222 18.83 2.67 0.00 3.85
70 71 3.724914 GACCCGCCAGCTAGCAGAC 62.725 68.421 18.83 0.00 0.00 3.51
71 72 3.461773 GACCCGCCAGCTAGCAGA 61.462 66.667 18.83 0.00 0.00 4.26
72 73 4.880537 CGACCCGCCAGCTAGCAG 62.881 72.222 18.83 9.15 0.00 4.24
79 80 4.514577 CCTAGCACGACCCGCCAG 62.515 72.222 0.00 0.00 0.00 4.85
85 86 3.387225 GAAGCCCCCTAGCACGACC 62.387 68.421 0.00 0.00 34.23 4.79
86 87 2.187163 GAAGCCCCCTAGCACGAC 59.813 66.667 0.00 0.00 34.23 4.34
87 88 2.038975 AGAAGCCCCCTAGCACGA 59.961 61.111 0.00 0.00 34.23 4.35
88 89 2.187946 CAGAAGCCCCCTAGCACG 59.812 66.667 0.00 0.00 34.23 5.34
89 90 1.524482 CTCAGAAGCCCCCTAGCAC 59.476 63.158 0.00 0.00 34.23 4.40
90 91 2.370445 GCTCAGAAGCCCCCTAGCA 61.370 63.158 0.00 0.00 43.10 3.49
91 92 2.508436 GCTCAGAAGCCCCCTAGC 59.492 66.667 0.00 0.00 43.10 3.42
92 93 1.118356 ATCGCTCAGAAGCCCCCTAG 61.118 60.000 0.00 0.00 46.34 3.02
93 94 1.075226 ATCGCTCAGAAGCCCCCTA 60.075 57.895 0.00 0.00 46.34 3.53
94 95 2.366167 ATCGCTCAGAAGCCCCCT 60.366 61.111 0.00 0.00 46.34 4.79
95 96 2.110006 GATCGCTCAGAAGCCCCC 59.890 66.667 0.00 0.00 46.34 5.40
96 97 2.110006 GGATCGCTCAGAAGCCCC 59.890 66.667 0.00 0.00 46.34 5.80
97 98 1.227497 CAGGATCGCTCAGAAGCCC 60.227 63.158 0.00 0.00 46.34 5.19
98 99 1.886777 GCAGGATCGCTCAGAAGCC 60.887 63.158 0.00 0.00 46.34 4.35
99 100 1.886777 GGCAGGATCGCTCAGAAGC 60.887 63.158 0.00 0.00 45.56 3.86
100 101 1.227497 GGGCAGGATCGCTCAGAAG 60.227 63.158 0.00 0.00 30.49 2.85
101 102 2.735772 GGGGCAGGATCGCTCAGAA 61.736 63.158 0.00 0.00 32.33 3.02
102 103 2.298335 TAGGGGCAGGATCGCTCAGA 62.298 60.000 0.00 0.00 32.33 3.27
103 104 1.814772 CTAGGGGCAGGATCGCTCAG 61.815 65.000 0.00 0.00 32.33 3.35
104 105 1.834378 CTAGGGGCAGGATCGCTCA 60.834 63.158 0.00 0.00 32.33 4.26
105 106 3.055580 CTAGGGGCAGGATCGCTC 58.944 66.667 0.00 0.00 0.00 5.03
106 107 3.237741 GCTAGGGGCAGGATCGCT 61.238 66.667 0.00 0.00 41.35 4.93
107 108 3.237741 AGCTAGGGGCAGGATCGC 61.238 66.667 0.00 0.00 44.79 4.58
108 109 2.739784 CAGCTAGGGGCAGGATCG 59.260 66.667 0.00 0.00 44.79 3.69
131 132 0.043637 AGGACCCCCAATAACTCGGA 59.956 55.000 0.00 0.00 33.88 4.55
132 133 1.797320 TAGGACCCCCAATAACTCGG 58.203 55.000 0.00 0.00 33.88 4.63
134 135 7.120716 TGTAAAAATAGGACCCCCAATAACTC 58.879 38.462 0.00 0.00 33.88 3.01
204 205 4.157840 GCTTCCCTCGTATTTTTGGTGAAT 59.842 41.667 0.00 0.00 0.00 2.57
207 208 2.817258 TGCTTCCCTCGTATTTTTGGTG 59.183 45.455 0.00 0.00 0.00 4.17
218 219 0.177141 TCCGGTTATTGCTTCCCTCG 59.823 55.000 0.00 0.00 0.00 4.63
227 228 6.260936 ACTGAGATTTAGCAATCCGGTTATTG 59.739 38.462 10.74 10.74 39.95 1.90
230 231 5.353394 ACTGAGATTTAGCAATCCGGTTA 57.647 39.130 0.00 0.00 39.95 2.85
234 235 3.487574 GTCGACTGAGATTTAGCAATCCG 59.512 47.826 8.70 0.00 39.95 4.18
296 340 9.967451 TCCCAGTCTTGACACAATATATAAAAA 57.033 29.630 3.49 0.00 0.00 1.94
305 349 4.383552 GCTAGATCCCAGTCTTGACACAAT 60.384 45.833 0.00 0.00 0.00 2.71
347 401 2.507944 CCTGCATCCTCCCTTCCG 59.492 66.667 0.00 0.00 0.00 4.30
348 402 2.194326 GCCTGCATCCTCCCTTCC 59.806 66.667 0.00 0.00 0.00 3.46
352 406 2.124403 CAGTGCCTGCATCCTCCC 60.124 66.667 0.00 0.00 0.00 4.30
369 423 3.619929 GGAATACAATGTGTGGTACGACC 59.380 47.826 5.50 0.00 39.22 4.79
388 442 2.244510 ACCATATGACAATGCAGGGGAA 59.755 45.455 3.65 0.00 0.00 3.97
394 448 2.759535 CCCAACACCATATGACAATGCA 59.240 45.455 3.65 0.00 0.00 3.96
408 462 5.590259 ACTGCTAATGATAATGTCCCAACAC 59.410 40.000 0.00 0.00 38.48 3.32
450 504 5.351189 ACTTTTTGTTGTTGTGATTTGCTCC 59.649 36.000 0.00 0.00 0.00 4.70
454 508 7.745594 CCTTTCACTTTTTGTTGTTGTGATTTG 59.254 33.333 0.00 0.00 37.47 2.32
485 539 7.758495 AGACGTGAATTAGACAAACTGTTTTT 58.242 30.769 2.41 0.00 0.00 1.94
486 540 7.316544 AGACGTGAATTAGACAAACTGTTTT 57.683 32.000 2.41 0.00 0.00 2.43
487 541 6.920569 AGACGTGAATTAGACAAACTGTTT 57.079 33.333 0.00 0.00 0.00 2.83
488 542 7.431249 TCTAGACGTGAATTAGACAAACTGTT 58.569 34.615 0.00 0.00 0.00 3.16
489 543 6.978338 TCTAGACGTGAATTAGACAAACTGT 58.022 36.000 0.00 0.00 0.00 3.55
490 544 7.542477 ACATCTAGACGTGAATTAGACAAACTG 59.458 37.037 0.00 0.00 0.00 3.16
491 545 7.603651 ACATCTAGACGTGAATTAGACAAACT 58.396 34.615 0.00 0.00 0.00 2.66
492 546 7.813852 ACATCTAGACGTGAATTAGACAAAC 57.186 36.000 0.00 0.00 0.00 2.93
493 547 8.827177 AAACATCTAGACGTGAATTAGACAAA 57.173 30.769 0.00 0.00 0.00 2.83
494 548 8.827177 AAAACATCTAGACGTGAATTAGACAA 57.173 30.769 0.00 0.00 0.00 3.18
495 549 8.827177 AAAAACATCTAGACGTGAATTAGACA 57.173 30.769 0.00 0.00 0.00 3.41
499 553 9.932207 TCCTTAAAAACATCTAGACGTGAATTA 57.068 29.630 0.00 0.00 0.00 1.40
500 554 8.842358 TCCTTAAAAACATCTAGACGTGAATT 57.158 30.769 0.00 0.00 0.00 2.17
501 555 8.883731 CATCCTTAAAAACATCTAGACGTGAAT 58.116 33.333 0.00 0.00 0.00 2.57
502 556 7.876068 ACATCCTTAAAAACATCTAGACGTGAA 59.124 33.333 0.00 0.00 0.00 3.18
503 557 7.383687 ACATCCTTAAAAACATCTAGACGTGA 58.616 34.615 0.00 0.00 0.00 4.35
504 558 7.330946 TGACATCCTTAAAAACATCTAGACGTG 59.669 37.037 0.00 0.00 0.00 4.49
505 559 7.331193 GTGACATCCTTAAAAACATCTAGACGT 59.669 37.037 0.00 0.00 0.00 4.34
506 560 7.330946 TGTGACATCCTTAAAAACATCTAGACG 59.669 37.037 0.00 0.00 0.00 4.18
507 561 8.547967 TGTGACATCCTTAAAAACATCTAGAC 57.452 34.615 0.00 0.00 0.00 2.59
508 562 9.383519 GATGTGACATCCTTAAAAACATCTAGA 57.616 33.333 14.48 0.00 39.39 2.43
509 563 9.388506 AGATGTGACATCCTTAAAAACATCTAG 57.611 33.333 21.05 0.00 46.59 2.43
514 568 9.349713 AGTTTAGATGTGACATCCTTAAAAACA 57.650 29.630 21.05 0.00 0.00 2.83
515 569 9.827411 GAGTTTAGATGTGACATCCTTAAAAAC 57.173 33.333 21.05 19.92 0.00 2.43
516 570 9.010029 GGAGTTTAGATGTGACATCCTTAAAAA 57.990 33.333 21.05 11.39 0.00 1.94
517 571 7.610305 GGGAGTTTAGATGTGACATCCTTAAAA 59.390 37.037 21.05 13.52 0.00 1.52
518 572 7.110155 GGGAGTTTAGATGTGACATCCTTAAA 58.890 38.462 21.05 16.39 0.00 1.52
519 573 6.214615 TGGGAGTTTAGATGTGACATCCTTAA 59.785 38.462 21.05 11.73 0.00 1.85
520 574 5.724370 TGGGAGTTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 0.00 2.69
521 575 4.536090 TGGGAGTTTAGATGTGACATCCTT 59.464 41.667 21.05 7.22 0.00 3.36
522 576 4.080863 GTGGGAGTTTAGATGTGACATCCT 60.081 45.833 21.05 11.37 0.00 3.24
523 577 4.192317 GTGGGAGTTTAGATGTGACATCC 58.808 47.826 21.05 6.28 0.00 3.51
524 578 4.832248 TGTGGGAGTTTAGATGTGACATC 58.168 43.478 17.46 17.46 0.00 3.06
525 579 4.908601 TGTGGGAGTTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
526 580 4.698201 TTGTGGGAGTTTAGATGTGACA 57.302 40.909 0.00 0.00 0.00 3.58
527 581 7.865706 ATATTTGTGGGAGTTTAGATGTGAC 57.134 36.000 0.00 0.00 0.00 3.67
536 590 9.860650 TGCTACATTATATATTTGTGGGAGTTT 57.139 29.630 9.93 0.00 0.00 2.66
537 591 9.860650 TTGCTACATTATATATTTGTGGGAGTT 57.139 29.630 9.93 0.00 0.00 3.01
538 592 9.284968 GTTGCTACATTATATATTTGTGGGAGT 57.715 33.333 9.93 0.00 0.00 3.85
539 593 9.283768 TGTTGCTACATTATATATTTGTGGGAG 57.716 33.333 0.00 3.34 0.00 4.30
540 594 9.634021 TTGTTGCTACATTATATATTTGTGGGA 57.366 29.630 0.81 6.61 33.44 4.37
607 661 9.944376 ACACAGTTATGTTACATCTAAACTGAT 57.056 29.630 30.25 20.61 44.03 2.90
608 662 9.419297 GACACAGTTATGTTACATCTAAACTGA 57.581 33.333 30.25 2.15 44.03 3.41
609 663 9.203421 TGACACAGTTATGTTACATCTAAACTG 57.797 33.333 25.55 25.55 45.76 3.16
610 664 9.944376 ATGACACAGTTATGTTACATCTAAACT 57.056 29.630 0.00 3.65 37.65 2.66
621 675 8.869897 CACGTCTAAATATGACACAGTTATGTT 58.130 33.333 0.00 0.00 37.65 2.71
622 676 8.033038 ACACGTCTAAATATGACACAGTTATGT 58.967 33.333 0.00 0.00 41.57 2.29
623 677 8.407457 ACACGTCTAAATATGACACAGTTATG 57.593 34.615 0.00 0.00 34.37 1.90
624 678 8.467598 AGACACGTCTAAATATGACACAGTTAT 58.532 33.333 0.00 0.00 38.35 1.89
625 679 7.823665 AGACACGTCTAAATATGACACAGTTA 58.176 34.615 0.00 0.00 38.35 2.24
626 680 6.688578 AGACACGTCTAAATATGACACAGTT 58.311 36.000 0.00 0.00 38.35 3.16
627 681 6.268825 AGACACGTCTAAATATGACACAGT 57.731 37.500 0.00 0.00 38.35 3.55
628 682 8.182227 TCTAAGACACGTCTAAATATGACACAG 58.818 37.037 0.00 0.00 39.39 3.66
629 683 7.966753 GTCTAAGACACGTCTAAATATGACACA 59.033 37.037 0.00 0.00 39.39 3.72
630 684 7.966753 TGTCTAAGACACGTCTAAATATGACAC 59.033 37.037 0.00 0.00 37.67 3.67
631 685 8.047413 TGTCTAAGACACGTCTAAATATGACA 57.953 34.615 0.00 6.48 37.67 3.58
632 686 8.396390 TCTGTCTAAGACACGTCTAAATATGAC 58.604 37.037 0.00 4.32 37.67 3.06
633 687 8.502105 TCTGTCTAAGACACGTCTAAATATGA 57.498 34.615 0.00 0.00 37.67 2.15
634 688 9.011407 GTTCTGTCTAAGACACGTCTAAATATG 57.989 37.037 0.00 0.00 37.67 1.78
635 689 8.189460 GGTTCTGTCTAAGACACGTCTAAATAT 58.811 37.037 0.00 0.00 37.67 1.28
636 690 7.392673 AGGTTCTGTCTAAGACACGTCTAAATA 59.607 37.037 0.00 0.00 37.67 1.40
637 691 6.208994 AGGTTCTGTCTAAGACACGTCTAAAT 59.791 38.462 0.00 0.00 37.67 1.40
638 692 5.533903 AGGTTCTGTCTAAGACACGTCTAAA 59.466 40.000 0.00 0.00 37.67 1.85
639 693 5.068636 AGGTTCTGTCTAAGACACGTCTAA 58.931 41.667 0.00 0.00 37.67 2.10
640 694 4.649692 AGGTTCTGTCTAAGACACGTCTA 58.350 43.478 0.00 0.00 37.67 2.59
641 695 3.488363 AGGTTCTGTCTAAGACACGTCT 58.512 45.455 0.00 0.00 37.67 4.18
642 696 3.919223 AGGTTCTGTCTAAGACACGTC 57.081 47.619 0.00 0.00 37.67 4.34
643 697 4.649692 TCTAGGTTCTGTCTAAGACACGT 58.350 43.478 0.00 0.00 37.67 4.49
644 698 5.624344 TTCTAGGTTCTGTCTAAGACACG 57.376 43.478 0.00 0.00 37.67 4.49
645 699 7.216973 TCTTTCTAGGTTCTGTCTAAGACAC 57.783 40.000 0.00 0.00 37.67 3.67
646 700 7.834881 TTCTTTCTAGGTTCTGTCTAAGACA 57.165 36.000 0.00 0.00 40.50 3.41
647 701 7.329962 GCTTTCTTTCTAGGTTCTGTCTAAGAC 59.670 40.741 0.00 0.00 33.46 3.01
648 702 7.379750 GCTTTCTTTCTAGGTTCTGTCTAAGA 58.620 38.462 0.00 0.00 0.00 2.10
649 703 6.309251 CGCTTTCTTTCTAGGTTCTGTCTAAG 59.691 42.308 0.00 0.00 0.00 2.18
650 704 6.015688 TCGCTTTCTTTCTAGGTTCTGTCTAA 60.016 38.462 0.00 0.00 0.00 2.10
651 705 5.475909 TCGCTTTCTTTCTAGGTTCTGTCTA 59.524 40.000 0.00 0.00 0.00 2.59
652 706 4.281182 TCGCTTTCTTTCTAGGTTCTGTCT 59.719 41.667 0.00 0.00 0.00 3.41
653 707 4.557205 TCGCTTTCTTTCTAGGTTCTGTC 58.443 43.478 0.00 0.00 0.00 3.51
654 708 4.602340 TCGCTTTCTTTCTAGGTTCTGT 57.398 40.909 0.00 0.00 0.00 3.41
655 709 5.924475 TTTCGCTTTCTTTCTAGGTTCTG 57.076 39.130 0.00 0.00 0.00 3.02
656 710 5.820947 TGTTTTCGCTTTCTTTCTAGGTTCT 59.179 36.000 0.00 0.00 0.00 3.01
657 711 5.907945 GTGTTTTCGCTTTCTTTCTAGGTTC 59.092 40.000 0.00 0.00 0.00 3.62
658 712 5.355910 TGTGTTTTCGCTTTCTTTCTAGGTT 59.644 36.000 0.00 0.00 0.00 3.50
659 713 4.879545 TGTGTTTTCGCTTTCTTTCTAGGT 59.120 37.500 0.00 0.00 0.00 3.08
660 714 5.236478 TCTGTGTTTTCGCTTTCTTTCTAGG 59.764 40.000 0.00 0.00 0.00 3.02
661 715 6.201044 TCTCTGTGTTTTCGCTTTCTTTCTAG 59.799 38.462 0.00 0.00 0.00 2.43
662 716 6.018994 GTCTCTGTGTTTTCGCTTTCTTTCTA 60.019 38.462 0.00 0.00 0.00 2.10
663 717 4.876107 TCTCTGTGTTTTCGCTTTCTTTCT 59.124 37.500 0.00 0.00 0.00 2.52
664 718 4.964555 GTCTCTGTGTTTTCGCTTTCTTTC 59.035 41.667 0.00 0.00 0.00 2.62
686 740 0.779997 AGGAGGATTTTGCCACTGGT 59.220 50.000 0.00 0.00 0.00 4.00
709 768 1.813178 TCGTACTTCCTGCTGTGAGAG 59.187 52.381 0.00 0.00 0.00 3.20
718 777 3.056821 TGGTTCATGACTCGTACTTCCTG 60.057 47.826 0.00 0.00 0.00 3.86
826 901 1.079438 GGGGAGAGTGGAGTGGAGT 59.921 63.158 0.00 0.00 0.00 3.85
827 902 1.079256 TGGGGAGAGTGGAGTGGAG 59.921 63.158 0.00 0.00 0.00 3.86
828 903 1.229209 GTGGGGAGAGTGGAGTGGA 60.229 63.158 0.00 0.00 0.00 4.02
835 910 3.721706 GCTGGGGTGGGGAGAGTG 61.722 72.222 0.00 0.00 0.00 3.51
901 976 5.239525 GGATTCTACTGGGATGTTTATGTGC 59.760 44.000 0.00 0.00 0.00 4.57
910 985 3.200825 AGGTTGTGGATTCTACTGGGATG 59.799 47.826 1.69 0.00 0.00 3.51
1065 1148 4.101448 GAGGAGGCGGTGGCATGT 62.101 66.667 0.00 0.00 42.47 3.21
1089 1172 2.930019 TGGCAGTGGTGGGAGGAG 60.930 66.667 0.00 0.00 0.00 3.69
1090 1173 3.249189 GTGGCAGTGGTGGGAGGA 61.249 66.667 0.00 0.00 0.00 3.71
1091 1174 4.351054 GGTGGCAGTGGTGGGAGG 62.351 72.222 0.00 0.00 0.00 4.30
1092 1175 3.252284 AGGTGGCAGTGGTGGGAG 61.252 66.667 0.00 0.00 0.00 4.30
1093 1176 3.569210 CAGGTGGCAGTGGTGGGA 61.569 66.667 0.00 0.00 0.00 4.37
1145 1228 0.827368 CTCTTGGTGGTCTAGGAGGC 59.173 60.000 0.00 0.00 0.00 4.70
1613 1735 0.326427 AGGGAGGAGAGCTTGCTGAT 60.326 55.000 0.00 0.00 0.00 2.90
1614 1736 0.336392 TAGGGAGGAGAGCTTGCTGA 59.664 55.000 0.00 0.00 0.00 4.26
1615 1737 1.134551 GTTAGGGAGGAGAGCTTGCTG 60.135 57.143 0.00 0.00 0.00 4.41
1616 1738 1.199615 GTTAGGGAGGAGAGCTTGCT 58.800 55.000 0.00 0.00 0.00 3.91
1617 1739 0.179097 CGTTAGGGAGGAGAGCTTGC 60.179 60.000 0.00 0.00 0.00 4.01
1618 1740 0.179097 GCGTTAGGGAGGAGAGCTTG 60.179 60.000 0.00 0.00 0.00 4.01
1619 1741 1.331399 GGCGTTAGGGAGGAGAGCTT 61.331 60.000 0.00 0.00 0.00 3.74
1620 1742 1.758906 GGCGTTAGGGAGGAGAGCT 60.759 63.158 0.00 0.00 0.00 4.09
2124 2288 0.398318 AGTGGGAGAACTTCACCAGC 59.602 55.000 7.47 0.29 32.84 4.85
2370 2534 1.301401 CACGGGGCAGAACTCGAAA 60.301 57.895 0.00 0.00 0.00 3.46
2553 2723 4.024556 CAGCACACAGAAACAAAGGTAGAG 60.025 45.833 0.00 0.00 0.00 2.43
2565 2741 1.270305 GGAGTAGCACAGCACACAGAA 60.270 52.381 0.00 0.00 0.00 3.02
2662 2844 0.533978 TCACGGTGTCACATTGGTGG 60.534 55.000 8.17 0.00 45.32 4.61
2663 2845 0.586319 GTCACGGTGTCACATTGGTG 59.414 55.000 8.17 7.24 46.66 4.17
2664 2846 0.179234 TGTCACGGTGTCACATTGGT 59.821 50.000 8.17 0.00 0.00 3.67
2665 2847 1.522668 ATGTCACGGTGTCACATTGG 58.477 50.000 10.13 0.00 0.00 3.16
2666 2848 2.919870 CAATGTCACGGTGTCACATTG 58.080 47.619 27.09 27.09 46.57 2.82
2690 2872 2.549329 TGCTTGCTTGATGTGTACTGTG 59.451 45.455 0.00 0.00 0.00 3.66
2712 3226 3.181528 CCAAATCAACGCATTGTCATTGC 60.182 43.478 9.24 9.24 37.11 3.56
2816 3342 4.527944 AGAGTAATCCTAAAAGGCCAAGC 58.472 43.478 5.01 0.00 34.61 4.01
2817 3343 7.125792 TCTAGAGTAATCCTAAAAGGCCAAG 57.874 40.000 5.01 0.00 34.61 3.61
2818 3344 7.504926 TTCTAGAGTAATCCTAAAAGGCCAA 57.495 36.000 5.01 0.00 34.61 4.52
2819 3345 7.365652 CCTTTCTAGAGTAATCCTAAAAGGCCA 60.366 40.741 5.01 0.00 36.26 5.36
2820 3346 6.993308 CCTTTCTAGAGTAATCCTAAAAGGCC 59.007 42.308 12.15 0.00 36.26 5.19
2821 3347 7.566569 ACCTTTCTAGAGTAATCCTAAAAGGC 58.433 38.462 19.51 0.00 43.30 4.35
2822 3348 9.961264 AAACCTTTCTAGAGTAATCCTAAAAGG 57.039 33.333 18.63 18.63 44.44 3.11
2864 3396 7.062957 TGGAAGAGAAATCTTTCCAACTTCTT 58.937 34.615 20.60 13.99 39.43 2.52
3000 3581 2.600420 CAGATGACAGTGATTTCCGTCG 59.400 50.000 0.00 0.00 0.00 5.12
3076 3814 7.611770 CCAACCTTGATATAAGATCATCGGTA 58.388 38.462 0.00 0.00 33.77 4.02
3078 3816 5.352569 GCCAACCTTGATATAAGATCATCGG 59.647 44.000 0.00 0.00 0.00 4.18
3079 3817 5.062683 CGCCAACCTTGATATAAGATCATCG 59.937 44.000 0.00 0.00 0.00 3.84
3081 3819 4.697352 GCGCCAACCTTGATATAAGATCAT 59.303 41.667 0.00 0.00 0.00 2.45
3082 3820 4.065088 GCGCCAACCTTGATATAAGATCA 58.935 43.478 0.00 0.00 0.00 2.92
3083 3821 3.437049 GGCGCCAACCTTGATATAAGATC 59.563 47.826 24.80 0.00 0.00 2.75
3084 3822 3.412386 GGCGCCAACCTTGATATAAGAT 58.588 45.455 24.80 0.00 0.00 2.40
3086 3824 1.880027 GGGCGCCAACCTTGATATAAG 59.120 52.381 30.85 0.00 0.00 1.73
3091 3829 1.978617 CTTGGGCGCCAACCTTGAT 60.979 57.895 30.85 0.00 38.75 2.57
3603 4361 5.181748 CCAAGAAGCACAAGAACTATAGCT 58.818 41.667 0.00 0.00 0.00 3.32
3604 4362 4.938226 ACCAAGAAGCACAAGAACTATAGC 59.062 41.667 0.00 0.00 0.00 2.97
3605 4363 6.312426 CAGACCAAGAAGCACAAGAACTATAG 59.688 42.308 0.00 0.00 0.00 1.31
3606 4364 6.166279 CAGACCAAGAAGCACAAGAACTATA 58.834 40.000 0.00 0.00 0.00 1.31
3607 4365 4.999950 CAGACCAAGAAGCACAAGAACTAT 59.000 41.667 0.00 0.00 0.00 2.12
3616 4376 1.466558 GCTAAGCAGACCAAGAAGCAC 59.533 52.381 0.00 0.00 0.00 4.40
3629 4389 2.892852 ACCAAATTTGAGCAGCTAAGCA 59.107 40.909 19.86 0.00 36.85 3.91
3687 4447 4.278919 TGTTGTGGTGACAAGATCTACGTA 59.721 41.667 0.00 0.00 42.87 3.57
3688 4448 3.069016 TGTTGTGGTGACAAGATCTACGT 59.931 43.478 0.00 0.00 42.87 3.57
3689 4449 3.649073 TGTTGTGGTGACAAGATCTACG 58.351 45.455 0.00 0.00 42.87 3.51
3690 4450 4.449068 CACTGTTGTGGTGACAAGATCTAC 59.551 45.833 0.00 0.00 42.87 2.59
3707 4467 6.096564 GCATTAGTACCTACTCTACCACTGTT 59.903 42.308 0.00 0.00 37.73 3.16
3759 4519 9.447040 CTAATAATGTTGATCACATGAAGCAAG 57.553 33.333 0.00 3.25 46.23 4.01
3782 4542 3.245087 TGAGCTGGCCAAAATGGTACTAA 60.245 43.478 7.01 0.00 40.46 2.24
4013 4778 1.344953 ACACTGGGTCCAAGCTGACA 61.345 55.000 6.54 0.00 36.97 3.58
4061 7454 5.010282 AGAATTACACACTGGGATTTGGTC 58.990 41.667 0.00 0.00 0.00 4.02
4100 7493 3.181482 ACCAGCTTAGATGACATGAGACG 60.181 47.826 0.00 0.00 0.00 4.18
4112 7505 7.343316 AGAAGCTCTTAGATTAACCAGCTTAGA 59.657 37.037 4.04 0.00 45.09 2.10
4117 7510 5.665459 TGAGAAGCTCTTAGATTAACCAGC 58.335 41.667 0.00 0.00 0.00 4.85
4156 7552 0.590481 CATCGCGTGGCATCAATGTG 60.590 55.000 5.77 0.00 0.00 3.21
4266 7671 3.707156 CTTCAATGCGTCGCAGCGG 62.707 63.158 25.78 16.37 43.65 5.52
4269 7674 1.225936 CTGCTTCAATGCGTCGCAG 60.226 57.895 25.78 13.00 43.65 5.18
4274 7679 1.302752 TCAGCCTGCTTCAATGCGT 60.303 52.632 0.00 0.00 35.36 5.24
4276 7681 1.509923 GGTCAGCCTGCTTCAATGC 59.490 57.895 0.00 0.00 0.00 3.56
4336 7741 2.233676 AGTATGTTGTGGACGATGCTGA 59.766 45.455 0.00 0.00 0.00 4.26
4338 7743 2.497675 AGAGTATGTTGTGGACGATGCT 59.502 45.455 0.00 0.00 0.00 3.79
4352 7757 3.986572 GCCGATGATGAGTGAAGAGTATG 59.013 47.826 0.00 0.00 0.00 2.39
4353 7758 3.006323 GGCCGATGATGAGTGAAGAGTAT 59.994 47.826 0.00 0.00 0.00 2.12
4360 7765 1.144716 GCAGGCCGATGATGAGTGA 59.855 57.895 0.00 0.00 0.00 3.41
4375 7780 4.154347 GGAGCGGAGGAGGTGCAG 62.154 72.222 0.00 0.00 0.00 4.41
4386 7791 1.110518 GTAGAGGAAGAGGGGAGCGG 61.111 65.000 0.00 0.00 0.00 5.52
4421 7826 2.189784 GCCGGGGCCTAAGACTTC 59.810 66.667 2.18 0.00 34.56 3.01
4439 7844 4.468689 GACCAGCCTACCGGTGCC 62.469 72.222 19.93 4.99 38.73 5.01
4442 7847 2.531483 ATCCAGACCAGCCTACCGGT 62.531 60.000 13.98 13.98 38.56 5.28
4444 7849 1.043116 TGATCCAGACCAGCCTACCG 61.043 60.000 0.00 0.00 0.00 4.02
4446 7851 0.755686 CCTGATCCAGACCAGCCTAC 59.244 60.000 0.00 0.00 32.44 3.18
4452 7857 1.489481 CTGCTACCTGATCCAGACCA 58.511 55.000 0.00 0.00 32.44 4.02
4466 7871 1.123077 ATCGCCACAATCTCCTGCTA 58.877 50.000 0.00 0.00 0.00 3.49
4469 7874 2.020131 GCATCGCCACAATCTCCTG 58.980 57.895 0.00 0.00 0.00 3.86
4501 7906 2.506472 GAGGATCAAGACGGCCCC 59.494 66.667 0.00 0.00 33.17 5.80


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

AutoCloner maintained by Alex Coulton.