Multiple sequence alignment - TraesCS7D01G233700

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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 TraesCS7D01G233700 chr7D 100.000 3881 0 0 4155 8035 195618602 195622482 0.000000e+00 7167.0
1 TraesCS7D01G233700 chr7D 100.000 3772 0 0 1 3772 195614448 195618219 0.000000e+00 6966.0
2 TraesCS7D01G233700 chr7D 98.341 2351 38 1 1422 3772 224467431 224465082 0.000000e+00 4124.0
3 TraesCS7D01G233700 chr7D 98.052 2361 38 3 1419 3772 525724594 525726953 0.000000e+00 4098.0
4 TraesCS7D01G233700 chr7D 99.465 561 3 0 4155 4715 525727643 525728203 0.000000e+00 1020.0
5 TraesCS7D01G233700 chr7D 100.000 32 0 0 9 40 127491295 127491264 8.710000e-05 60.2
6 TraesCS7D01G233700 chr7D 100.000 32 0 0 9 40 402802926 402802895 8.710000e-05 60.2
7 TraesCS7D01G233700 chr7A 93.810 3360 117 21 4715 8030 205455186 205458498 0.000000e+00 4968.0
8 TraesCS7D01G233700 chr7A 92.484 479 22 5 942 1419 205454725 205455190 0.000000e+00 673.0
9 TraesCS7D01G233700 chr7B 94.919 2972 112 16 5093 8035 159506280 159509241 0.000000e+00 4615.0
10 TraesCS7D01G233700 chr7B 88.222 1367 105 29 38 1376 159504579 159505917 0.000000e+00 1581.0
11 TraesCS7D01G233700 chr7B 95.833 216 7 1 4717 4932 159505945 159506158 1.660000e-91 348.0
12 TraesCS7D01G233700 chr7B 97.143 35 1 0 5061 5095 159506201 159506235 8.710000e-05 60.2
13 TraesCS7D01G233700 chr7B 100.000 29 0 0 4896 4924 742481562 742481534 4.000000e-03 54.7
14 TraesCS7D01G233700 chr3D 98.088 2354 41 2 1422 3772 329692671 329690319 0.000000e+00 4095.0
15 TraesCS7D01G233700 chr3D 98.006 2357 39 3 1422 3772 70697410 70695056 0.000000e+00 4085.0
16 TraesCS7D01G233700 chr3D 97.839 2360 44 2 1419 3772 481544401 481546759 0.000000e+00 4069.0
17 TraesCS7D01G233700 chr2D 97.879 2357 44 1 1422 3772 110999008 110996652 0.000000e+00 4071.0
18 TraesCS7D01G233700 chr2D 97.841 2362 42 4 1416 3772 593910406 593912763 0.000000e+00 4071.0
19 TraesCS7D01G233700 chr2D 97.873 2351 50 0 1422 3772 625830228 625827878 0.000000e+00 4065.0
20 TraesCS7D01G233700 chr1D 97.876 2354 45 3 1422 3772 194925003 194922652 0.000000e+00 4065.0
21 TraesCS7D01G233700 chr1D 99.468 564 3 0 4155 4718 194921989 194921426 0.000000e+00 1026.0
22 TraesCS7D01G233700 chr1D 99.113 564 5 0 4155 4718 414140766 414140203 0.000000e+00 1014.0
23 TraesCS7D01G233700 chr6D 99.113 564 5 0 4155 4718 115025960 115025397 0.000000e+00 1014.0
24 TraesCS7D01G233700 chr6D 80.044 907 151 15 33 918 7870201 7869304 0.000000e+00 645.0
25 TraesCS7D01G233700 chr6D 81.423 253 40 3 595 840 105570176 105569924 4.920000e-47 200.0
26 TraesCS7D01G233700 chr6D 100.000 32 0 0 9 40 286010546 286010515 8.710000e-05 60.2
27 TraesCS7D01G233700 chr6D 100.000 29 0 0 4896 4924 276910911 276910883 4.000000e-03 54.7
28 TraesCS7D01G233700 chr5D 99.113 564 5 0 4155 4718 88162933 88162370 0.000000e+00 1014.0
29 TraesCS7D01G233700 chr4D 99.287 561 4 0 4155 4715 138287609 138288169 0.000000e+00 1014.0
30 TraesCS7D01G233700 chr4D 99.287 561 4 0 4155 4715 274554366 274554926 0.000000e+00 1014.0
31 TraesCS7D01G233700 chr4D 99.287 561 4 0 4155 4715 333056127 333056687 0.000000e+00 1014.0
32 TraesCS7D01G233700 chr4D 99.113 564 5 0 4155 4718 449195287 449194724 0.000000e+00 1014.0
33 TraesCS7D01G233700 chr2A 82.048 830 119 10 40 847 121597831 121597010 0.000000e+00 680.0
34 TraesCS7D01G233700 chr2A 100.000 32 0 0 9 40 225826882 225826851 8.710000e-05 60.2
35 TraesCS7D01G233700 chr6A 81.851 832 106 13 48 847 268961516 268962334 0.000000e+00 658.0
36 TraesCS7D01G233700 chr5B 81.772 790 117 15 136 918 405719591 405718822 3.160000e-178 636.0
37 TraesCS7D01G233700 chr5B 97.143 35 1 0 6 40 460059240 460059274 8.710000e-05 60.2
38 TraesCS7D01G233700 chr5B 90.476 42 3 1 4896 4936 408983269 408983228 4.000000e-03 54.7
39 TraesCS7D01G233700 chr2B 80.633 821 127 14 41 841 654745841 654746649 2.480000e-169 606.0
40 TraesCS7D01G233700 chr2B 87.861 173 19 2 38 209 690925615 690925444 1.370000e-47 202.0
41 TraesCS7D01G233700 chr2B 100.000 29 0 0 4896 4924 571714499 571714527 4.000000e-03 54.7
42 TraesCS7D01G233700 chr4B 79.234 496 73 18 40 515 19982931 19983416 1.300000e-82 318.0
43 TraesCS7D01G233700 chr4A 83.740 123 18 2 249 369 674916859 674916981 1.830000e-21 115.0
44 TraesCS7D01G233700 chr6B 100.000 32 0 0 9 40 613534807 613534776 8.710000e-05 60.2
45 TraesCS7D01G233700 chr6B 100.000 29 0 0 4896 4924 460089059 460089031 4.000000e-03 54.7
46 TraesCS7D01G233700 chr1B 97.143 35 1 0 6 40 330902018 330902052 8.710000e-05 60.2


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 TraesCS7D01G233700 chr7D 195614448 195622482 8034 False 7066.50 7167 100.00000 1 8035 2 chr7D.!!$F1 8034
1 TraesCS7D01G233700 chr7D 224465082 224467431 2349 True 4124.00 4124 98.34100 1422 3772 1 chr7D.!!$R2 2350
2 TraesCS7D01G233700 chr7D 525724594 525728203 3609 False 2559.00 4098 98.75850 1419 4715 2 chr7D.!!$F2 3296
3 TraesCS7D01G233700 chr7A 205454725 205458498 3773 False 2820.50 4968 93.14700 942 8030 2 chr7A.!!$F1 7088
4 TraesCS7D01G233700 chr7B 159504579 159509241 4662 False 1651.05 4615 94.02925 38 8035 4 chr7B.!!$F1 7997
5 TraesCS7D01G233700 chr3D 329690319 329692671 2352 True 4095.00 4095 98.08800 1422 3772 1 chr3D.!!$R2 2350
6 TraesCS7D01G233700 chr3D 70695056 70697410 2354 True 4085.00 4085 98.00600 1422 3772 1 chr3D.!!$R1 2350
7 TraesCS7D01G233700 chr3D 481544401 481546759 2358 False 4069.00 4069 97.83900 1419 3772 1 chr3D.!!$F1 2353
8 TraesCS7D01G233700 chr2D 110996652 110999008 2356 True 4071.00 4071 97.87900 1422 3772 1 chr2D.!!$R1 2350
9 TraesCS7D01G233700 chr2D 593910406 593912763 2357 False 4071.00 4071 97.84100 1416 3772 1 chr2D.!!$F1 2356
10 TraesCS7D01G233700 chr2D 625827878 625830228 2350 True 4065.00 4065 97.87300 1422 3772 1 chr2D.!!$R2 2350
11 TraesCS7D01G233700 chr1D 194921426 194925003 3577 True 2545.50 4065 98.67200 1422 4718 2 chr1D.!!$R2 3296
12 TraesCS7D01G233700 chr1D 414140203 414140766 563 True 1014.00 1014 99.11300 4155 4718 1 chr1D.!!$R1 563
13 TraesCS7D01G233700 chr6D 115025397 115025960 563 True 1014.00 1014 99.11300 4155 4718 1 chr6D.!!$R3 563
14 TraesCS7D01G233700 chr6D 7869304 7870201 897 True 645.00 645 80.04400 33 918 1 chr6D.!!$R1 885
15 TraesCS7D01G233700 chr5D 88162370 88162933 563 True 1014.00 1014 99.11300 4155 4718 1 chr5D.!!$R1 563
16 TraesCS7D01G233700 chr4D 138287609 138288169 560 False 1014.00 1014 99.28700 4155 4715 1 chr4D.!!$F1 560
17 TraesCS7D01G233700 chr4D 274554366 274554926 560 False 1014.00 1014 99.28700 4155 4715 1 chr4D.!!$F2 560
18 TraesCS7D01G233700 chr4D 333056127 333056687 560 False 1014.00 1014 99.28700 4155 4715 1 chr4D.!!$F3 560
19 TraesCS7D01G233700 chr4D 449194724 449195287 563 True 1014.00 1014 99.11300 4155 4718 1 chr4D.!!$R1 563
20 TraesCS7D01G233700 chr2A 121597010 121597831 821 True 680.00 680 82.04800 40 847 1 chr2A.!!$R1 807
21 TraesCS7D01G233700 chr6A 268961516 268962334 818 False 658.00 658 81.85100 48 847 1 chr6A.!!$F1 799
22 TraesCS7D01G233700 chr5B 405718822 405719591 769 True 636.00 636 81.77200 136 918 1 chr5B.!!$R1 782
23 TraesCS7D01G233700 chr2B 654745841 654746649 808 False 606.00 606 80.63300 41 841 1 chr2B.!!$F2 800

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
782 805 0.175760 GCTTGTCCGCATCCACTAGA 59.824 55.000 0.00 0.0 0.00 2.43 F
844 868 0.754957 TGTTGTTGTCCCAGCCCTTG 60.755 55.000 0.00 0.0 0.00 3.61 F
2016 2063 0.617413 CAACATCTGGCACTCCCTCT 59.383 55.000 0.00 0.0 0.00 3.69 F
2874 2922 0.412244 TGCCTACTACACTCCCCAGT 59.588 55.000 0.00 0.0 0.00 4.00 F
4337 4979 1.279558 TGCGTACTAGGGCCAAATCAA 59.720 47.619 6.18 0.0 0.00 2.57 F
5013 5800 0.254462 GCTAGAGCAAGGAGCCCTTT 59.746 55.000 3.93 0.0 41.69 3.11 F
5270 6131 2.083774 TCAACGACCTTTCATGCCATC 58.916 47.619 0.00 0.0 0.00 3.51 F
5724 6589 3.577805 ACTGTGCACCCTAAACTCTTT 57.422 42.857 15.69 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1888 1935 1.081556 CAACCATTGCGGATCGTCGA 61.082 55.000 0.0 0.0 38.63 4.20 R
2027 2074 1.495584 GAGCGTCGGTGTTGCTTTGA 61.496 55.000 0.0 0.0 39.49 2.69 R
4337 4979 3.701664 GGTCTTGGGGTTGATGAAATCT 58.298 45.455 0.0 0.0 45.81 2.40 R
4725 5509 0.532115 ATTCTGACCCAAAATGGCGC 59.468 50.000 0.0 0.0 35.79 6.53 R
5247 6108 1.197721 GGCATGAAAGGTCGTTGACTG 59.802 52.381 0.0 0.0 32.47 3.51 R
6357 7224 1.779092 AGAGTGCAGCCATAATCCCAT 59.221 47.619 0.0 0.0 0.00 4.00 R
6403 7270 1.991264 GTCTTCTTCCGCCGTAAAGAC 59.009 52.381 0.0 0.0 39.11 3.01 R
7979 8876 2.605823 CGAGCTTCCTACCATCGATCAC 60.606 54.545 0.0 0.0 35.47 3.06 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
36 37 7.170393 ACGAGGCTATAAGTAATCATGCATA 57.830 36.000 0.00 0.00 0.00 3.14
117 118 0.482446 TTGGGCAGGTGGAGAATGTT 59.518 50.000 0.00 0.00 0.00 2.71
146 147 0.995024 AGATTGTGGGCAGCCTTACT 59.005 50.000 12.43 0.05 0.00 2.24
168 169 0.806102 CGGTGTTGCTGGACTATCCG 60.806 60.000 0.00 0.00 40.17 4.18
211 212 2.273179 CCGTCGGGTGAGTTCTCCA 61.273 63.158 2.34 0.00 0.00 3.86
236 237 2.106511 ACTCGGCATACCAGGCATTATT 59.893 45.455 0.00 0.00 34.57 1.40
237 238 2.744202 CTCGGCATACCAGGCATTATTC 59.256 50.000 0.00 0.00 34.57 1.75
239 240 2.553028 CGGCATACCAGGCATTATTCCT 60.553 50.000 0.00 0.00 34.57 3.36
240 241 3.307410 CGGCATACCAGGCATTATTCCTA 60.307 47.826 0.00 0.00 34.57 2.94
289 307 7.547019 CCTTTGCCCTTAAAGATCAAGATTTTC 59.453 37.037 0.00 0.00 39.46 2.29
358 376 4.935495 CGGCATGGTCCGGGGATG 62.935 72.222 0.00 2.56 45.38 3.51
361 379 3.492353 CATGGTCCGGGGATGGCT 61.492 66.667 0.00 0.00 0.00 4.75
362 380 2.696125 ATGGTCCGGGGATGGCTT 60.696 61.111 0.00 0.00 0.00 4.35
363 381 3.060614 ATGGTCCGGGGATGGCTTG 62.061 63.158 0.00 0.00 0.00 4.01
364 382 3.728373 GGTCCGGGGATGGCTTGT 61.728 66.667 0.00 0.00 0.00 3.16
365 383 2.438434 GTCCGGGGATGGCTTGTG 60.438 66.667 0.00 0.00 0.00 3.33
366 384 4.424711 TCCGGGGATGGCTTGTGC 62.425 66.667 0.00 0.00 38.76 4.57
377 396 2.508361 GCTTGTGCCCCTTATGCAT 58.492 52.632 3.79 3.79 41.46 3.96
382 401 1.757731 TGCCCCTTATGCATGGTGC 60.758 57.895 10.16 6.51 45.29 5.01
392 411 1.297689 GCATGGTGCCTGAGACTGA 59.702 57.895 0.00 0.00 37.42 3.41
410 429 6.252995 AGACTGAGACCCATATCCTATTCTC 58.747 44.000 0.00 0.00 0.00 2.87
411 430 5.970289 ACTGAGACCCATATCCTATTCTCA 58.030 41.667 0.00 0.00 37.69 3.27
412 431 6.569737 ACTGAGACCCATATCCTATTCTCAT 58.430 40.000 0.00 0.00 38.94 2.90
413 432 6.440010 ACTGAGACCCATATCCTATTCTCATG 59.560 42.308 0.00 0.00 38.94 3.07
414 433 6.326161 TGAGACCCATATCCTATTCTCATGT 58.674 40.000 0.00 0.00 35.65 3.21
415 434 7.478721 TGAGACCCATATCCTATTCTCATGTA 58.521 38.462 0.00 0.00 35.65 2.29
416 435 7.397476 TGAGACCCATATCCTATTCTCATGTAC 59.603 40.741 0.00 0.00 35.65 2.90
417 436 6.378564 AGACCCATATCCTATTCTCATGTACG 59.621 42.308 0.00 0.00 0.00 3.67
418 437 5.105310 ACCCATATCCTATTCTCATGTACGC 60.105 44.000 0.00 0.00 0.00 4.42
434 453 2.954868 GCATGTACGACGGCTCGG 60.955 66.667 0.00 0.00 44.80 4.63
454 473 2.430546 GTCCTATGGACGCTCATCTG 57.569 55.000 0.67 0.00 43.14 2.90
462 481 1.674221 GGACGCTCATCTGTGAAGCTT 60.674 52.381 0.00 0.00 33.05 3.74
465 484 3.257393 ACGCTCATCTGTGAAGCTTTAG 58.743 45.455 0.00 0.00 33.05 1.85
471 490 0.681243 CTGTGAAGCTTTAGGGCCCC 60.681 60.000 21.43 1.47 0.00 5.80
491 510 2.121506 TGGGAGGCCCTGAACCTT 60.122 61.111 0.00 0.00 45.70 3.50
495 514 3.249189 AGGCCCTGAACCTTGCGA 61.249 61.111 0.00 0.00 31.87 5.10
506 525 0.472471 ACCTTGCGAAGTTCCTCCAA 59.528 50.000 0.00 0.00 0.00 3.53
508 527 2.162681 CCTTGCGAAGTTCCTCCAAAT 58.837 47.619 0.00 0.00 0.00 2.32
511 530 2.426522 TGCGAAGTTCCTCCAAATCAG 58.573 47.619 0.00 0.00 0.00 2.90
524 543 2.091665 CCAAATCAGGGCTATCCAACCT 60.092 50.000 0.00 0.00 38.24 3.50
529 548 2.203209 GGCTATCCAACCTGGGCG 60.203 66.667 0.00 0.00 38.32 6.13
551 571 2.599645 ATCGCCGCTCATTCTGGCTT 62.600 55.000 0.60 0.00 46.67 4.35
561 581 3.872696 TCATTCTGGCTTATCTTTGCGA 58.127 40.909 0.00 0.00 0.00 5.10
568 588 2.033662 GGCTTATCTTTGCGACGATGTC 60.034 50.000 0.00 0.00 0.00 3.06
586 606 2.135933 GTCGTGGACTCTTTGGACAAG 58.864 52.381 0.00 0.00 0.00 3.16
587 607 2.036387 TCGTGGACTCTTTGGACAAGA 58.964 47.619 0.00 0.00 0.00 3.02
606 626 7.000575 ACAAGACGTAATAAAATGGTGATCG 57.999 36.000 0.00 0.00 0.00 3.69
610 630 4.208460 ACGTAATAAAATGGTGATCGAGCG 59.792 41.667 0.00 0.00 0.00 5.03
628 648 1.971695 GGGTGTTTCCGAGGCAAGG 60.972 63.158 0.00 0.00 37.00 3.61
633 653 0.611714 GTTTCCGAGGCAAGGGTCTA 59.388 55.000 0.00 0.00 0.00 2.59
637 660 0.175989 CCGAGGCAAGGGTCTAACTC 59.824 60.000 0.00 0.00 0.00 3.01
648 671 6.241645 CAAGGGTCTAACTCCTTCAAATTCT 58.758 40.000 0.00 0.00 41.06 2.40
653 676 6.715264 GGTCTAACTCCTTCAAATTCTTTCCA 59.285 38.462 0.00 0.00 0.00 3.53
661 684 6.268387 TCCTTCAAATTCTTTCCATTTCTGCT 59.732 34.615 0.00 0.00 0.00 4.24
666 689 1.888512 TCTTTCCATTTCTGCTGCACC 59.111 47.619 0.00 0.00 0.00 5.01
729 752 1.469703 TCATGTTTGATGCGCTTCTGG 59.530 47.619 22.11 7.27 0.00 3.86
735 758 0.460811 TGATGCGCTTCTGGCTACAG 60.461 55.000 22.11 0.00 46.30 2.74
736 759 1.770085 GATGCGCTTCTGGCTACAGC 61.770 60.000 15.51 0.00 44.54 4.40
760 783 1.146637 CGACTATCGTCCTCGTAGGG 58.853 60.000 1.76 0.00 36.82 3.53
762 785 0.536915 ACTATCGTCCTCGTAGGGCC 60.537 60.000 0.00 0.00 36.37 5.80
770 793 3.718210 CTCGTAGGGCCGCTTGTCC 62.718 68.421 0.00 0.00 0.00 4.02
782 805 0.175760 GCTTGTCCGCATCCACTAGA 59.824 55.000 0.00 0.00 0.00 2.43
823 847 5.716228 TCTCTTGTGTTTATTGGGCATGATT 59.284 36.000 0.00 0.00 0.00 2.57
833 857 2.037901 TGGGCATGATTGTGTTGTTGT 58.962 42.857 0.00 0.00 0.00 3.32
837 861 2.035704 GCATGATTGTGTTGTTGTCCCA 59.964 45.455 0.00 0.00 0.00 4.37
839 863 1.680735 TGATTGTGTTGTTGTCCCAGC 59.319 47.619 0.00 0.00 0.00 4.85
842 866 1.152756 GTGTTGTTGTCCCAGCCCT 60.153 57.895 0.00 0.00 0.00 5.19
844 868 0.754957 TGTTGTTGTCCCAGCCCTTG 60.755 55.000 0.00 0.00 0.00 3.61
845 869 0.755327 GTTGTTGTCCCAGCCCTTGT 60.755 55.000 0.00 0.00 0.00 3.16
848 872 1.119684 GTTGTCCCAGCCCTTGTTTT 58.880 50.000 0.00 0.00 0.00 2.43
901 928 8.869897 TCATTGCTTTAGTTATAAAGTGAGACG 58.130 33.333 8.96 0.00 46.48 4.18
921 948 4.755411 ACGAAAGTCTGTTTCAAGAGTCA 58.245 39.130 0.00 0.00 44.19 3.41
922 949 5.360591 ACGAAAGTCTGTTTCAAGAGTCAT 58.639 37.500 0.00 0.00 44.19 3.06
923 950 5.235186 ACGAAAGTCTGTTTCAAGAGTCATG 59.765 40.000 0.00 0.00 44.19 3.07
924 951 5.429957 AAAGTCTGTTTCAAGAGTCATGC 57.570 39.130 0.00 0.00 0.00 4.06
925 952 4.077300 AGTCTGTTTCAAGAGTCATGCA 57.923 40.909 0.00 0.00 0.00 3.96
926 953 4.649692 AGTCTGTTTCAAGAGTCATGCAT 58.350 39.130 0.00 0.00 0.00 3.96
927 954 5.068636 AGTCTGTTTCAAGAGTCATGCATT 58.931 37.500 0.00 0.00 0.00 3.56
928 955 5.533903 AGTCTGTTTCAAGAGTCATGCATTT 59.466 36.000 0.00 0.00 0.00 2.32
929 956 5.855395 GTCTGTTTCAAGAGTCATGCATTTC 59.145 40.000 0.00 0.00 0.00 2.17
930 957 4.786507 TGTTTCAAGAGTCATGCATTTCG 58.213 39.130 0.00 0.00 0.00 3.46
931 958 4.275689 TGTTTCAAGAGTCATGCATTTCGT 59.724 37.500 0.00 0.00 0.00 3.85
932 959 4.408993 TTCAAGAGTCATGCATTTCGTG 57.591 40.909 0.00 4.44 0.00 4.35
933 960 3.663025 TCAAGAGTCATGCATTTCGTGA 58.337 40.909 13.50 13.50 38.33 4.35
934 961 3.681417 TCAAGAGTCATGCATTTCGTGAG 59.319 43.478 13.50 0.00 41.10 3.51
935 962 2.005451 AGAGTCATGCATTTCGTGAGC 58.995 47.619 0.00 0.00 41.10 4.26
936 963 2.005451 GAGTCATGCATTTCGTGAGCT 58.995 47.619 0.00 0.00 41.10 4.09
937 964 2.005451 AGTCATGCATTTCGTGAGCTC 58.995 47.619 6.82 6.82 41.10 4.09
940 967 3.000724 GTCATGCATTTCGTGAGCTCTAC 59.999 47.826 16.19 10.43 41.10 2.59
1037 1064 2.023673 CCACTTCACTGCACTTTTCCA 58.976 47.619 0.00 0.00 0.00 3.53
1106 1133 6.205784 TGTTCTTGCCTTGTTCTATTTTTCG 58.794 36.000 0.00 0.00 0.00 3.46
1327 1354 4.803426 CGTCGAGGTCAGCAGCCC 62.803 72.222 0.00 0.00 0.00 5.19
1346 1373 2.419297 CCCTCGTGCTCTTCTTTGCTAT 60.419 50.000 0.00 0.00 0.00 2.97
1381 1408 6.301169 TCCTTCCTCTGTTTTTATCTCTCC 57.699 41.667 0.00 0.00 0.00 3.71
1414 1442 7.936496 AGTTGGTAGGTCTAACTTCTAGTAC 57.064 40.000 0.00 0.00 43.60 2.73
1415 1443 7.697946 AGTTGGTAGGTCTAACTTCTAGTACT 58.302 38.462 0.00 0.00 43.60 2.73
1416 1444 8.830741 AGTTGGTAGGTCTAACTTCTAGTACTA 58.169 37.037 1.89 1.89 43.60 1.82
1417 1445 9.454859 GTTGGTAGGTCTAACTTCTAGTACTAA 57.545 37.037 3.76 0.00 35.18 2.24
1418 1446 9.678260 TTGGTAGGTCTAACTTCTAGTACTAAG 57.322 37.037 3.76 4.00 0.00 2.18
1419 1447 8.830741 TGGTAGGTCTAACTTCTAGTACTAAGT 58.169 37.037 3.76 4.66 37.54 2.24
1477 1506 7.184022 AGTCCAAGTCAGTTTTATACCCCTATT 59.816 37.037 0.00 0.00 0.00 1.73
1479 1508 7.183112 TCCAAGTCAGTTTTATACCCCTATTCA 59.817 37.037 0.00 0.00 0.00 2.57
1706 1753 5.431765 CTCACCATAGCTCCACAAAACTAT 58.568 41.667 0.00 0.00 0.00 2.12
1710 1757 5.665812 ACCATAGCTCCACAAAACTATCCTA 59.334 40.000 0.00 0.00 0.00 2.94
1814 1861 2.354303 CGCCCACAACTACTACCATTGA 60.354 50.000 0.00 0.00 0.00 2.57
1888 1935 2.750350 CAACTGTCTTCCCCGCCT 59.250 61.111 0.00 0.00 0.00 5.52
1942 1989 2.099263 CGATCGTCCAGTGGTTCTACAT 59.901 50.000 9.54 0.00 0.00 2.29
1970 2017 3.767131 TCACCACCGAGATCTTCAACATA 59.233 43.478 0.00 0.00 0.00 2.29
2016 2063 0.617413 CAACATCTGGCACTCCCTCT 59.383 55.000 0.00 0.00 0.00 3.69
2027 2074 1.622811 CACTCCCTCTGTCAGCTCTTT 59.377 52.381 0.00 0.00 0.00 2.52
2282 2329 3.366679 CCTTCGCTGAAGTACGTTCCTTA 60.367 47.826 14.33 0.00 37.92 2.69
2641 2689 1.828660 CCTAGTCCGCTCCGTCCAT 60.829 63.158 0.00 0.00 0.00 3.41
2672 2720 2.903357 CCGGCATACTCAGGTGCT 59.097 61.111 4.54 0.00 41.04 4.40
2874 2922 0.412244 TGCCTACTACACTCCCCAGT 59.588 55.000 0.00 0.00 0.00 4.00
3112 3446 4.352001 CCCTTCCATTATCCTTGGAGATGA 59.648 45.833 13.83 0.00 43.87 2.92
3259 3593 2.736144 TGCGACAATCTAGTTTCGGT 57.264 45.000 0.00 0.00 32.04 4.69
4337 4979 1.279558 TGCGTACTAGGGCCAAATCAA 59.720 47.619 6.18 0.00 0.00 2.57
4725 5509 2.301346 GCCCATTCACTAAGGATGGTG 58.699 52.381 1.98 0.00 39.24 4.17
4726 5510 2.301346 CCCATTCACTAAGGATGGTGC 58.699 52.381 1.98 0.00 37.89 5.01
4741 5525 1.080569 GTGCGCCATTTTGGGTCAG 60.081 57.895 4.18 0.00 38.19 3.51
4887 5672 6.933521 GTGGCATATCTATGAACAAGACAGAT 59.066 38.462 1.37 0.00 35.75 2.90
4936 5721 8.528044 AGCCCGGTTAAAATAGATAAATTCAA 57.472 30.769 0.00 0.00 0.00 2.69
4956 5741 7.587037 TTCAACAAGACAGAAATCAAGGAAT 57.413 32.000 0.00 0.00 0.00 3.01
5013 5800 0.254462 GCTAGAGCAAGGAGCCCTTT 59.746 55.000 3.93 0.00 41.69 3.11
5030 5817 4.437930 GCCCTTTCATTCTGTTCGATTCAG 60.438 45.833 10.60 10.60 0.00 3.02
5059 5846 9.941664 GATCAAATAAACAGTCATGTAAGATGG 57.058 33.333 0.00 0.00 39.29 3.51
5063 5850 5.886960 AAACAGTCATGTAAGATGGCTTC 57.113 39.130 0.00 0.00 39.29 3.86
5109 5970 9.455847 GATTTGCTTGGATTATGTACAGAATTC 57.544 33.333 16.39 14.97 0.00 2.17
5145 6006 7.800155 ATCTGCTAGGCTTTTTAAGATTCTC 57.200 36.000 0.00 0.00 0.00 2.87
5180 6041 2.368221 CCAATTTGCTGGGGACAAAAGA 59.632 45.455 0.00 0.00 40.19 2.52
5181 6042 3.392882 CAATTTGCTGGGGACAAAAGAC 58.607 45.455 0.00 0.00 40.19 3.01
5186 6047 4.046286 TGCTGGGGACAAAAGACATATT 57.954 40.909 0.00 0.00 42.06 1.28
5205 6066 7.349711 ACATATTTTGTAACACAGTCGTTGTC 58.650 34.615 0.00 0.00 35.53 3.18
5208 6069 4.652421 TTGTAACACAGTCGTTGTCCTA 57.348 40.909 0.00 0.00 38.16 2.94
5211 6072 6.330004 TGTAACACAGTCGTTGTCCTATTA 57.670 37.500 0.00 0.00 38.16 0.98
5270 6131 2.083774 TCAACGACCTTTCATGCCATC 58.916 47.619 0.00 0.00 0.00 3.51
5593 6458 8.786937 ATCATCAATATCAAATTGTTACGTGC 57.213 30.769 0.00 0.00 0.00 5.34
5671 6536 9.770097 TTTCTTTGTTATTGATGGTTATGCAAA 57.230 25.926 0.00 0.00 0.00 3.68
5672 6537 9.770097 TTCTTTGTTATTGATGGTTATGCAAAA 57.230 25.926 0.00 0.00 0.00 2.44
5673 6538 9.202273 TCTTTGTTATTGATGGTTATGCAAAAC 57.798 29.630 0.00 0.00 0.00 2.43
5674 6539 9.206870 CTTTGTTATTGATGGTTATGCAAAACT 57.793 29.630 0.00 0.00 0.00 2.66
5675 6540 8.531622 TTGTTATTGATGGTTATGCAAAACTG 57.468 30.769 0.00 0.00 0.00 3.16
5676 6541 7.665690 TGTTATTGATGGTTATGCAAAACTGT 58.334 30.769 0.00 0.00 0.00 3.55
5724 6589 3.577805 ACTGTGCACCCTAAACTCTTT 57.422 42.857 15.69 0.00 0.00 2.52
6295 7162 8.716674 ATCAAGATGCCCTTAATATGATTGTT 57.283 30.769 0.00 0.00 32.86 2.83
6299 7166 5.772825 TGCCCTTAATATGATTGTTCAGC 57.227 39.130 0.00 0.00 34.73 4.26
6357 7224 8.417884 AGAACGGAATTTAAATCAAACAAGGAA 58.582 29.630 0.10 0.00 0.00 3.36
6403 7270 6.961359 TGTGTGTATTTTCGACAATAGGAG 57.039 37.500 4.27 0.00 0.00 3.69
6409 7276 9.362539 GTGTATTTTCGACAATAGGAGTCTTTA 57.637 33.333 4.27 0.00 33.89 1.85
6696 7565 1.480954 TGCTCTCTCGGGTATGTTTCC 59.519 52.381 0.00 0.00 0.00 3.13
6707 7576 2.527100 GTATGTTTCCGAGTCGTCAGG 58.473 52.381 12.31 0.00 0.00 3.86
6716 7585 4.803426 GTCGTCAGGGCCGCTGAG 62.803 72.222 20.38 15.11 0.00 3.35
6721 7590 2.125512 CAGGGCCGCTGAGTGTAC 60.126 66.667 14.21 0.00 0.00 2.90
7220 8092 2.559998 AAGTGTCACACGCCAAAAAG 57.440 45.000 1.22 0.00 39.64 2.27
7260 8132 8.561738 TTTTTACTTTGTTCTGTCTTCTGTCT 57.438 30.769 0.00 0.00 0.00 3.41
7317 8193 1.808945 AGATGAAACTTGAGCTTGCCG 59.191 47.619 0.00 0.00 0.00 5.69
7357 8233 6.614906 TCCAAGGAATATTGTTGCCCATATTT 59.385 34.615 0.00 0.00 0.00 1.40
7549 8425 8.995027 TATATAATTATATTGGCCAGCCTTGG 57.005 34.615 20.37 0.00 37.50 3.61
7568 8444 9.866655 AGCCTTGGTCAATATATCTCATTTTTA 57.133 29.630 0.00 0.00 0.00 1.52
7723 8612 6.550854 TCATCCTATAAAATGCCCTTCCTTTG 59.449 38.462 0.00 0.00 0.00 2.77
7745 8634 6.926630 TGTAACCTTCCAAATTAGCCAAAT 57.073 33.333 0.00 0.00 0.00 2.32
7746 8635 7.309770 TGTAACCTTCCAAATTAGCCAAATT 57.690 32.000 0.00 0.00 39.56 1.82
7897 8794 9.515226 TTTTCTTCATAACCTATGTAAAGTGCT 57.485 29.630 0.00 0.00 37.45 4.40
7979 8876 6.208007 TCAGATTAGCCTTATGATGCCAAATG 59.792 38.462 0.00 0.00 0.00 2.32
8030 8927 5.799827 TTTCTTCCGATTTGTGGGAATTT 57.200 34.783 0.00 0.00 41.26 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 8.936864 GCATGATTACTTATAGCCTCGTATTTT 58.063 33.333 0.00 0.00 0.00 1.82
8 9 8.094548 TGCATGATTACTTATAGCCTCGTATTT 58.905 33.333 0.00 0.00 0.00 1.40
9 10 7.611770 TGCATGATTACTTATAGCCTCGTATT 58.388 34.615 0.00 0.00 0.00 1.89
10 11 7.170393 TGCATGATTACTTATAGCCTCGTAT 57.830 36.000 0.00 0.00 0.00 3.06
11 12 6.584185 TGCATGATTACTTATAGCCTCGTA 57.416 37.500 0.00 0.00 0.00 3.43
12 13 5.468540 TGCATGATTACTTATAGCCTCGT 57.531 39.130 0.00 0.00 0.00 4.18
13 14 7.922811 TGATATGCATGATTACTTATAGCCTCG 59.077 37.037 10.16 0.00 0.00 4.63
14 15 9.039870 GTGATATGCATGATTACTTATAGCCTC 57.960 37.037 10.16 0.00 0.00 4.70
15 16 8.766476 AGTGATATGCATGATTACTTATAGCCT 58.234 33.333 10.16 0.00 0.00 4.58
16 17 8.954950 AGTGATATGCATGATTACTTATAGCC 57.045 34.615 10.16 0.00 0.00 3.93
21 22 9.836864 ACAAGAAGTGATATGCATGATTACTTA 57.163 29.630 10.16 0.00 34.35 2.24
22 23 8.743085 ACAAGAAGTGATATGCATGATTACTT 57.257 30.769 10.16 15.41 36.23 2.24
23 24 8.209584 AGACAAGAAGTGATATGCATGATTACT 58.790 33.333 10.16 8.33 0.00 2.24
24 25 8.375608 AGACAAGAAGTGATATGCATGATTAC 57.624 34.615 10.16 6.26 0.00 1.89
25 26 7.658982 GGAGACAAGAAGTGATATGCATGATTA 59.341 37.037 10.16 0.00 0.00 1.75
26 27 6.485984 GGAGACAAGAAGTGATATGCATGATT 59.514 38.462 10.16 0.00 0.00 2.57
27 28 5.996513 GGAGACAAGAAGTGATATGCATGAT 59.003 40.000 10.16 0.00 0.00 2.45
28 29 5.104817 TGGAGACAAGAAGTGATATGCATGA 60.105 40.000 10.16 0.00 37.44 3.07
29 30 5.007430 GTGGAGACAAGAAGTGATATGCATG 59.993 44.000 10.16 0.00 46.06 4.06
30 31 5.121811 GTGGAGACAAGAAGTGATATGCAT 58.878 41.667 3.79 3.79 46.06 3.96
31 32 4.507710 GTGGAGACAAGAAGTGATATGCA 58.492 43.478 0.00 0.00 46.06 3.96
36 37 1.338200 GCCGTGGAGACAAGAAGTGAT 60.338 52.381 0.00 0.00 46.06 3.06
117 118 1.555075 GCCCACAATCTAGTCCACTCA 59.445 52.381 0.00 0.00 0.00 3.41
146 147 1.836999 ATAGTCCAGCAACACCGGCA 61.837 55.000 0.00 0.00 0.00 5.69
149 150 0.806102 CGGATAGTCCAGCAACACCG 60.806 60.000 0.00 0.00 35.91 4.94
168 169 2.106332 CGCCAGGATACGGTGTCC 59.894 66.667 15.39 15.39 46.39 4.02
211 212 0.179045 GCCTGGTATGCCGAGTTGAT 60.179 55.000 0.00 0.00 37.67 2.57
236 237 1.342474 CCACAAGGGAGAGAGCTAGGA 60.342 57.143 0.00 0.00 40.01 2.94
237 238 1.118838 CCACAAGGGAGAGAGCTAGG 58.881 60.000 0.00 0.00 40.01 3.02
289 307 4.846137 CGATTTCTAAGAAGTTGCCAAACG 59.154 41.667 0.00 0.00 41.45 3.60
360 378 0.748450 CCATGCATAAGGGGCACAAG 59.252 55.000 0.00 0.00 45.23 3.16
361 379 0.040942 ACCATGCATAAGGGGCACAA 59.959 50.000 0.00 0.00 45.23 3.33
362 380 0.683828 CACCATGCATAAGGGGCACA 60.684 55.000 0.00 0.00 45.23 4.57
363 381 2.118132 CACCATGCATAAGGGGCAC 58.882 57.895 0.00 0.00 45.23 5.01
364 382 4.682553 CACCATGCATAAGGGGCA 57.317 55.556 0.00 0.00 46.66 5.36
377 396 1.188219 GGTCTCAGTCTCAGGCACCA 61.188 60.000 0.00 0.00 0.00 4.17
382 401 2.896685 GGATATGGGTCTCAGTCTCAGG 59.103 54.545 0.00 0.00 0.00 3.86
392 411 6.378564 CGTACATGAGAATAGGATATGGGTCT 59.621 42.308 0.00 0.00 0.00 3.85
413 432 1.198608 GAGCCGTCGTACATGCGTAC 61.199 60.000 0.00 0.00 43.91 3.67
414 433 1.063006 GAGCCGTCGTACATGCGTA 59.937 57.895 0.00 0.00 0.00 4.42
415 434 2.202570 GAGCCGTCGTACATGCGT 60.203 61.111 0.00 0.00 0.00 5.24
416 435 3.312504 CGAGCCGTCGTACATGCG 61.313 66.667 0.00 0.00 41.57 4.73
417 436 2.954868 CCGAGCCGTCGTACATGC 60.955 66.667 0.00 0.00 45.30 4.06
418 437 2.278596 CCCGAGCCGTCGTACATG 60.279 66.667 0.00 0.00 45.30 3.21
426 445 2.838225 CCATAGGACCCGAGCCGT 60.838 66.667 0.00 0.00 0.00 5.68
445 464 2.606725 CCTAAAGCTTCACAGATGAGCG 59.393 50.000 0.00 0.00 35.83 5.03
447 466 2.941720 GCCCTAAAGCTTCACAGATGAG 59.058 50.000 0.00 0.00 35.83 2.90
453 472 1.382629 GGGGCCCTAAAGCTTCACA 59.617 57.895 24.38 0.00 0.00 3.58
454 473 0.965866 GTGGGGCCCTAAAGCTTCAC 60.966 60.000 25.93 14.81 0.00 3.18
486 505 0.472471 TGGAGGAACTTCGCAAGGTT 59.528 50.000 1.84 0.00 41.55 3.50
491 510 2.426522 CTGATTTGGAGGAACTTCGCA 58.573 47.619 0.00 0.00 41.55 5.10
495 514 1.713078 AGCCCTGATTTGGAGGAACTT 59.287 47.619 0.00 0.00 41.55 2.66
511 530 2.195956 GCCCAGGTTGGATAGCCC 59.804 66.667 0.00 0.00 40.96 5.19
529 548 1.493950 CCAGAATGAGCGGCGATGTC 61.494 60.000 12.98 3.97 39.69 3.06
541 560 3.544834 CGTCGCAAAGATAAGCCAGAATG 60.545 47.826 0.00 0.00 0.00 2.67
568 588 2.135933 GTCTTGTCCAAAGAGTCCACG 58.864 52.381 0.00 0.00 0.00 4.94
586 606 5.609696 CGCTCGATCACCATTTTATTACGTC 60.610 44.000 0.00 0.00 0.00 4.34
587 607 4.208460 CGCTCGATCACCATTTTATTACGT 59.792 41.667 0.00 0.00 0.00 3.57
610 630 1.971695 CCTTGCCTCGGAAACACCC 60.972 63.158 0.00 0.00 34.64 4.61
628 648 6.715264 TGGAAAGAATTTGAAGGAGTTAGACC 59.285 38.462 0.00 0.00 39.27 3.85
633 653 8.146412 CAGAAATGGAAAGAATTTGAAGGAGTT 58.854 33.333 0.00 0.00 39.27 3.01
637 660 6.367969 CAGCAGAAATGGAAAGAATTTGAAGG 59.632 38.462 0.00 0.00 39.27 3.46
648 671 0.597568 CGGTGCAGCAGAAATGGAAA 59.402 50.000 17.33 0.00 0.00 3.13
653 676 2.282391 TGCCGGTGCAGCAGAAAT 60.282 55.556 17.33 0.00 44.23 2.17
666 689 2.109126 GCCTAGAAAGCAGGTGCCG 61.109 63.158 0.00 0.00 43.38 5.69
673 696 0.670546 GTCACGCTGCCTAGAAAGCA 60.671 55.000 14.56 5.00 39.47 3.91
689 712 1.083489 GACCAAAATGATCGCGGTCA 58.917 50.000 26.40 26.40 44.55 4.02
695 718 5.941733 TCAAACATGAGACCAAAATGATCG 58.058 37.500 0.00 0.00 0.00 3.69
729 752 0.992757 GATAGTCGACGCGCTGTAGC 60.993 60.000 5.73 0.00 37.78 3.58
762 785 1.148157 CTAGTGGATGCGGACAAGCG 61.148 60.000 0.00 0.00 40.67 4.68
803 827 5.221601 ACACAATCATGCCCAATAAACACAA 60.222 36.000 0.00 0.00 0.00 3.33
805 829 4.819769 ACACAATCATGCCCAATAAACAC 58.180 39.130 0.00 0.00 0.00 3.32
814 838 2.610232 GGACAACAACACAATCATGCCC 60.610 50.000 0.00 0.00 0.00 5.36
823 847 1.454847 GGGCTGGGACAACAACACA 60.455 57.895 0.00 0.00 38.70 3.72
875 899 8.869897 CGTCTCACTTTATAACTAAAGCAATGA 58.130 33.333 5.29 2.41 45.15 2.57
877 901 8.997621 TCGTCTCACTTTATAACTAAAGCAAT 57.002 30.769 5.29 0.00 45.15 3.56
899 926 4.755411 TGACTCTTGAAACAGACTTTCGT 58.245 39.130 0.00 0.00 0.00 3.85
900 927 5.674008 CATGACTCTTGAAACAGACTTTCG 58.326 41.667 0.00 0.00 0.00 3.46
901 928 5.008019 TGCATGACTCTTGAAACAGACTTTC 59.992 40.000 0.00 0.00 0.00 2.62
906 933 5.334337 CGAAATGCATGACTCTTGAAACAGA 60.334 40.000 0.00 0.00 0.00 3.41
909 936 4.614284 CACGAAATGCATGACTCTTGAAAC 59.386 41.667 0.00 0.00 0.00 2.78
911 938 4.064388 TCACGAAATGCATGACTCTTGAA 58.936 39.130 0.00 0.00 0.00 2.69
912 939 3.663025 TCACGAAATGCATGACTCTTGA 58.337 40.909 0.00 4.48 0.00 3.02
913 940 3.727079 GCTCACGAAATGCATGACTCTTG 60.727 47.826 0.00 2.03 0.00 3.02
914 941 2.417933 GCTCACGAAATGCATGACTCTT 59.582 45.455 0.00 0.00 0.00 2.85
916 943 2.005451 AGCTCACGAAATGCATGACTC 58.995 47.619 0.00 0.00 0.00 3.36
917 944 2.005451 GAGCTCACGAAATGCATGACT 58.995 47.619 9.40 0.00 0.00 3.41
918 945 2.005451 AGAGCTCACGAAATGCATGAC 58.995 47.619 17.77 0.00 0.00 3.06
920 947 3.193263 AGTAGAGCTCACGAAATGCATG 58.807 45.455 17.77 0.00 0.00 4.06
921 948 3.533606 AGTAGAGCTCACGAAATGCAT 57.466 42.857 17.77 0.00 0.00 3.96
922 949 4.363138 CATAGTAGAGCTCACGAAATGCA 58.637 43.478 17.77 0.00 0.00 3.96
923 950 3.183373 GCATAGTAGAGCTCACGAAATGC 59.817 47.826 17.77 20.82 0.00 3.56
924 951 3.738282 GGCATAGTAGAGCTCACGAAATG 59.262 47.826 17.77 16.52 0.00 2.32
925 952 3.551046 CGGCATAGTAGAGCTCACGAAAT 60.551 47.826 17.77 6.32 0.00 2.17
926 953 2.223502 CGGCATAGTAGAGCTCACGAAA 60.224 50.000 17.77 4.40 0.00 3.46
927 954 1.333931 CGGCATAGTAGAGCTCACGAA 59.666 52.381 17.77 6.66 0.00 3.85
928 955 0.945099 CGGCATAGTAGAGCTCACGA 59.055 55.000 17.77 8.85 0.00 4.35
929 956 0.661780 GCGGCATAGTAGAGCTCACG 60.662 60.000 17.77 7.92 0.00 4.35
930 957 0.319125 GGCGGCATAGTAGAGCTCAC 60.319 60.000 17.77 11.98 0.00 3.51
931 958 0.468214 AGGCGGCATAGTAGAGCTCA 60.468 55.000 17.77 0.00 0.00 4.26
932 959 0.676736 AAGGCGGCATAGTAGAGCTC 59.323 55.000 13.08 5.27 0.00 4.09
933 960 0.676736 GAAGGCGGCATAGTAGAGCT 59.323 55.000 13.08 0.00 0.00 4.09
934 961 0.319986 GGAAGGCGGCATAGTAGAGC 60.320 60.000 13.08 0.00 0.00 4.09
935 962 1.333177 AGGAAGGCGGCATAGTAGAG 58.667 55.000 13.08 0.00 0.00 2.43
936 963 1.687123 GAAGGAAGGCGGCATAGTAGA 59.313 52.381 13.08 0.00 0.00 2.59
937 964 1.270358 GGAAGGAAGGCGGCATAGTAG 60.270 57.143 13.08 0.00 0.00 2.57
940 967 1.595382 CGGAAGGAAGGCGGCATAG 60.595 63.158 13.08 0.00 0.00 2.23
976 1003 2.876581 ACAGGGGAAAAGGTGTGATTC 58.123 47.619 0.00 0.00 0.00 2.52
1043 1070 9.793259 AGAATGTAGTGGTTTTCTGAGAAAATA 57.207 29.630 21.69 12.29 0.00 1.40
1044 1071 8.571336 CAGAATGTAGTGGTTTTCTGAGAAAAT 58.429 33.333 21.69 9.69 44.97 1.82
1049 1076 4.154918 GGCAGAATGTAGTGGTTTTCTGAG 59.845 45.833 13.96 0.00 44.97 3.35
1106 1133 2.176273 CGCCATGTACAGCAGAGCC 61.176 63.158 0.33 0.00 0.00 4.70
1305 1332 2.583593 GCTGACCTCGACGATGGC 60.584 66.667 0.00 0.00 0.00 4.40
1327 1354 4.180057 AGAATAGCAAAGAAGAGCACGAG 58.820 43.478 0.00 0.00 0.00 4.18
1346 1373 5.533112 ACAGAGGAAGGATCTGGATAAGAA 58.467 41.667 7.77 0.00 46.89 2.52
1381 1408 9.503399 AAGTTAGACCTACCAACTTCATAAAAG 57.497 33.333 0.00 0.00 37.87 2.27
1413 1441 9.844257 ACCGTAATGACTACTCTAATACTTAGT 57.156 33.333 0.00 0.00 34.81 2.24
1420 1448 8.930760 GTCGTATACCGTAATGACTACTCTAAT 58.069 37.037 0.00 0.00 37.94 1.73
1436 1464 4.574013 ACTTGGACTAGAAGTCGTATACCG 59.426 45.833 0.00 0.00 45.96 4.02
1706 1753 1.760875 GGCGAGGATGGGTGTAGGA 60.761 63.158 0.00 0.00 0.00 2.94
1814 1861 3.383185 GGTGGAGATCGAAGAGATGTCTT 59.617 47.826 4.50 4.50 45.79 3.01
1888 1935 1.081556 CAACCATTGCGGATCGTCGA 61.082 55.000 0.00 0.00 38.63 4.20
1942 1989 2.016393 GATCTCGGTGGTGATGCGGA 62.016 60.000 0.00 0.00 0.00 5.54
1970 2017 4.831307 GCGCCGTCGTGATCGAGT 62.831 66.667 0.00 0.00 46.96 4.18
2016 2063 3.016031 TGTTGCTTTGAAAGAGCTGACA 58.984 40.909 9.48 2.35 40.75 3.58
2027 2074 1.495584 GAGCGTCGGTGTTGCTTTGA 61.496 55.000 0.00 0.00 39.49 2.69
2282 2329 2.424705 TTTCCGCCGCGAGTTGTAGT 62.425 55.000 15.93 0.00 0.00 2.73
2626 2674 3.148279 GGATGGACGGAGCGGACT 61.148 66.667 0.00 0.00 0.00 3.85
4337 4979 3.701664 GGTCTTGGGGTTGATGAAATCT 58.298 45.455 0.00 0.00 45.81 2.40
4725 5509 0.532115 ATTCTGACCCAAAATGGCGC 59.468 50.000 0.00 0.00 35.79 6.53
4726 5510 1.818060 TCATTCTGACCCAAAATGGCG 59.182 47.619 0.00 0.00 35.79 5.69
4741 5525 8.654230 TCTTATCACTGTTTCTGCTATCATTC 57.346 34.615 0.00 0.00 0.00 2.67
4887 5672 7.256691 GCTAATCCCCTTTCCATTACTCTCATA 60.257 40.741 0.00 0.00 0.00 2.15
4936 5721 6.486657 TCGAAATTCCTTGATTTCTGTCTTGT 59.513 34.615 8.25 0.00 41.61 3.16
4944 5729 6.677913 TGAAACCTCGAAATTCCTTGATTTC 58.322 36.000 0.00 0.00 40.80 2.17
5030 5817 8.869897 TCTTACATGACTGTTTATTTGATCGAC 58.130 33.333 0.00 0.00 36.79 4.20
5059 5846 8.324163 TCACCTAATCTTTACTTTCTTGAAGC 57.676 34.615 0.00 0.00 39.04 3.86
5063 5850 9.346725 GCAAATCACCTAATCTTTACTTTCTTG 57.653 33.333 0.00 0.00 0.00 3.02
5109 5970 7.507733 AAGCCTAGCAGATTTGATAAAGATG 57.492 36.000 0.00 0.00 0.00 2.90
5145 6006 1.341080 AATTGGGGCTTGAACACTGG 58.659 50.000 0.00 0.00 0.00 4.00
5180 6041 7.254227 ACAACGACTGTGTTACAAAATATGT 57.746 32.000 0.00 0.00 40.68 2.29
5181 6042 6.795114 GGACAACGACTGTGTTACAAAATATG 59.205 38.462 0.00 0.00 38.84 1.78
5186 6047 3.864243 AGGACAACGACTGTGTTACAAA 58.136 40.909 0.00 0.00 38.84 2.83
5247 6108 1.197721 GGCATGAAAGGTCGTTGACTG 59.802 52.381 0.00 0.00 32.47 3.51
5255 6116 2.424956 GTCTTGGATGGCATGAAAGGTC 59.575 50.000 3.81 2.58 0.00 3.85
5270 6131 7.624360 TGCCAACATTATAGTTTAGTCTTGG 57.376 36.000 0.00 0.00 0.00 3.61
5589 6454 2.784596 CCATAAGGTGTGCGCACG 59.215 61.111 33.22 17.95 46.13 5.34
5593 6458 1.665679 CAGTAAGCCATAAGGTGTGCG 59.334 52.381 0.00 0.00 37.19 5.34
5645 6510 9.770097 TTTGCATAACCATCAATAACAAAGAAA 57.230 25.926 0.00 0.00 0.00 2.52
5671 6536 6.909550 TTTACAGGCCATCATTTAACAGTT 57.090 33.333 5.01 0.00 0.00 3.16
5672 6537 7.322664 CAATTTACAGGCCATCATTTAACAGT 58.677 34.615 5.01 0.00 0.00 3.55
5673 6538 6.256321 GCAATTTACAGGCCATCATTTAACAG 59.744 38.462 5.01 0.00 0.00 3.16
5674 6539 6.105333 GCAATTTACAGGCCATCATTTAACA 58.895 36.000 5.01 0.00 0.00 2.41
5675 6540 6.105333 TGCAATTTACAGGCCATCATTTAAC 58.895 36.000 5.01 0.00 0.00 2.01
5676 6541 6.291648 TGCAATTTACAGGCCATCATTTAA 57.708 33.333 5.01 0.00 0.00 1.52
5867 6733 4.700213 CACAACTAATTCCCGTCCATCTTT 59.300 41.667 0.00 0.00 0.00 2.52
5868 6734 4.261801 CACAACTAATTCCCGTCCATCTT 58.738 43.478 0.00 0.00 0.00 2.40
6136 7003 6.386927 TGGAAGAGACATATGTGTAGGGAATT 59.613 38.462 14.43 0.00 39.09 2.17
6357 7224 1.779092 AGAGTGCAGCCATAATCCCAT 59.221 47.619 0.00 0.00 0.00 4.00
6403 7270 1.991264 GTCTTCTTCCGCCGTAAAGAC 59.009 52.381 0.00 0.00 39.11 3.01
6409 7276 2.049433 CACGTCTTCTTCCGCCGT 60.049 61.111 0.00 0.00 0.00 5.68
6579 7446 4.524714 TGAATCTTCTTCAGGAGTTCGTCT 59.475 41.667 0.00 0.00 0.00 4.18
6631 7499 6.844696 ATAGACGGCAACTACAACATTATG 57.155 37.500 0.00 0.00 0.00 1.90
7178 8050 9.941325 ACTTATTCATCATTTAACAAAATGGCA 57.059 25.926 10.12 0.00 39.84 4.92
7317 8193 3.199946 TCCTTGGATGTAGGATCAACCAC 59.800 47.826 0.00 0.00 39.37 4.16
7357 8233 5.659525 AGATTTGATGAATTCCAGGCATTGA 59.340 36.000 2.27 0.00 0.00 2.57
7568 8444 6.942005 CCAAAAAGGGCAGGAAAGAAATAATT 59.058 34.615 0.00 0.00 0.00 1.40
7570 8446 5.863965 CCAAAAAGGGCAGGAAAGAAATAA 58.136 37.500 0.00 0.00 0.00 1.40
7571 8447 5.482163 CCAAAAAGGGCAGGAAAGAAATA 57.518 39.130 0.00 0.00 0.00 1.40
7572 8448 4.356405 CCAAAAAGGGCAGGAAAGAAAT 57.644 40.909 0.00 0.00 0.00 2.17
7604 8485 8.774546 TTGACAGGGCCATAAATATGATTTAA 57.225 30.769 6.18 0.00 35.75 1.52
7609 8490 7.564660 AGAATTTTGACAGGGCCATAAATATGA 59.435 33.333 6.18 0.00 35.75 2.15
7689 8578 6.248433 GCATTTTATAGGATGATCTTGGGGA 58.752 40.000 0.00 0.00 0.00 4.81
7723 8612 8.308207 TGTAATTTGGCTAATTTGGAAGGTTAC 58.692 33.333 11.93 2.53 37.60 2.50
7979 8876 2.605823 CGAGCTTCCTACCATCGATCAC 60.606 54.545 0.00 0.00 35.47 3.06


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

AutoCloner maintained by Alex Coulton.