Multiple sequence alignment - TraesCS3B01G305200

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 TraesCS3B01G305200 chr3B 100.000 6394 0 0 1 6394 490589566 490595959 0.000000e+00 11808.0
1 TraesCS3B01G305200 chr3D 93.156 2776 116 35 2726 5473 376159439 376162168 0.000000e+00 4006.0
2 TraesCS3B01G305200 chr3D 94.181 1117 35 7 1623 2725 376158300 376159400 0.000000e+00 1676.0
3 TraesCS3B01G305200 chr3D 96.324 789 22 5 881 1669 376157535 376158316 0.000000e+00 1290.0
4 TraesCS3B01G305200 chr3D 94.899 745 20 3 5655 6394 376162198 376162929 0.000000e+00 1149.0
5 TraesCS3B01G305200 chr3D 87.688 333 24 5 1 333 376156812 376157127 7.830000e-99 372.0
6 TraesCS3B01G305200 chr3D 86.628 172 23 0 490 661 376157365 376157536 2.350000e-44 191.0
7 TraesCS3B01G305200 chr3D 95.349 86 2 2 659 743 107089333 107089249 1.120000e-27 135.0
8 TraesCS3B01G305200 chr3D 98.592 71 1 0 812 882 471435771 471435701 6.730000e-25 126.0
9 TraesCS3B01G305200 chr3D 100.000 39 0 0 4343 4381 376161088 376161126 8.890000e-09 73.1
10 TraesCS3B01G305200 chr3A 93.481 2025 91 23 4343 6353 500972639 500974636 0.000000e+00 2970.0
11 TraesCS3B01G305200 chr3A 95.218 1861 63 11 881 2725 500969146 500970996 0.000000e+00 2920.0
12 TraesCS3B01G305200 chr3A 93.348 917 34 14 2726 3640 500971035 500971926 0.000000e+00 1330.0
13 TraesCS3B01G305200 chr3A 94.690 791 24 7 3668 4446 500971923 500972707 0.000000e+00 1212.0
14 TraesCS3B01G305200 chr3A 84.314 612 82 10 40 648 500968542 500969142 2.570000e-163 586.0
15 TraesCS3B01G305200 chr5D 91.916 569 17 9 3900 4446 22743866 22744427 0.000000e+00 769.0
16 TraesCS3B01G305200 chr5D 95.349 86 2 2 659 743 503284544 503284460 1.120000e-27 135.0
17 TraesCS3B01G305200 chr5D 94.186 86 3 2 659 743 6183698 6183782 5.200000e-26 130.0
18 TraesCS3B01G305200 chr5D 98.592 71 1 0 812 882 6183762 6183832 6.730000e-25 126.0
19 TraesCS3B01G305200 chr5D 100.000 39 0 0 4343 4381 22744356 22744394 8.890000e-09 73.1
20 TraesCS3B01G305200 chr5B 92.205 449 25 3 2189 2628 528735284 528735731 1.510000e-175 627.0
21 TraesCS3B01G305200 chr2B 92.205 449 24 4 2189 2628 132611328 132611774 5.440000e-175 625.0
22 TraesCS3B01G305200 chr2B 95.294 85 3 1 659 743 657477564 657477481 4.020000e-27 134.0
23 TraesCS3B01G305200 chr4B 91.314 449 29 5 2189 2628 112879306 112879753 7.090000e-169 604.0
24 TraesCS3B01G305200 chr7B 93.208 265 17 1 2365 2628 708149797 708150061 7.770000e-104 388.0
25 TraesCS3B01G305200 chr6B 79.566 553 89 16 1 530 205358717 205358166 2.180000e-99 374.0
26 TraesCS3B01G305200 chr6B 77.844 167 32 4 262 423 17391450 17391616 1.470000e-16 99.0
27 TraesCS3B01G305200 chr6D 79.348 552 93 15 1 535 105812965 105812418 1.010000e-97 368.0
28 TraesCS3B01G305200 chr6D 94.186 86 3 2 659 743 45514326 45514410 5.200000e-26 130.0
29 TraesCS3B01G305200 chr6D 97.183 71 2 0 812 882 45514390 45514460 3.130000e-23 121.0
30 TraesCS3B01G305200 chr2A 95.175 228 11 0 2365 2592 27204687 27204460 1.690000e-95 361.0
31 TraesCS3B01G305200 chr2A 98.592 71 1 0 812 882 335833467 335833537 6.730000e-25 126.0
32 TraesCS3B01G305200 chr2A 85.047 107 11 5 258 361 70321929 70322033 3.150000e-18 104.0
33 TraesCS3B01G305200 chr1A 94.298 228 13 0 2365 2592 45538186 45538413 3.670000e-92 350.0
34 TraesCS3B01G305200 chr1A 83.704 135 15 7 258 387 523397870 523398002 3.130000e-23 121.0
35 TraesCS3B01G305200 chr1A 100.000 28 0 0 5595 5622 8124879 8124906 1.200000e-02 52.8
36 TraesCS3B01G305200 chr5A 92.982 228 16 0 2365 2592 546047839 546047612 3.690000e-87 333.0
37 TraesCS3B01G305200 chr1B 79.388 490 75 18 1 474 459816448 459815969 8.000000e-84 322.0
38 TraesCS3B01G305200 chr7D 78.750 400 65 16 53 434 8007002 8007399 3.830000e-62 250.0
39 TraesCS3B01G305200 chr7D 79.310 203 36 4 263 459 105844568 105844366 3.110000e-28 137.0
40 TraesCS3B01G305200 chr7D 98.592 71 1 0 812 882 79175747 79175817 6.730000e-25 126.0
41 TraesCS3B01G305200 chr2D 80.569 211 35 5 263 467 507436410 507436200 2.390000e-34 158.0
42 TraesCS3B01G305200 chr1D 79.245 212 36 7 263 467 58965 59175 2.400000e-29 141.0
43 TraesCS3B01G305200 chr1D 95.349 86 2 2 659 743 51880826 51880910 1.120000e-27 135.0
44 TraesCS3B01G305200 chr1D 98.592 71 1 0 812 882 51880890 51880960 6.730000e-25 126.0
45 TraesCS3B01G305200 chr6A 95.349 86 2 2 659 743 53799708 53799792 1.120000e-27 135.0
46 TraesCS3B01G305200 chr4D 95.349 86 2 2 659 743 35178394 35178478 1.120000e-27 135.0
47 TraesCS3B01G305200 chr4D 98.592 71 1 0 812 882 35178458 35178528 6.730000e-25 126.0
48 TraesCS3B01G305200 chr4D 73.519 287 54 14 129 397 439870460 439870742 8.830000e-14 89.8
49 TraesCS3B01G305200 chrUn 94.186 86 3 2 659 743 442414188 442414272 5.200000e-26 130.0
50 TraesCS3B01G305200 chrUn 97.183 71 2 0 812 882 442414252 442414322 3.130000e-23 121.0
51 TraesCS3B01G305200 chr4A 98.592 71 1 0 812 882 310733412 310733482 6.730000e-25 126.0
52 TraesCS3B01G305200 chr4A 80.120 166 23 5 261 416 728700477 728700312 1.460000e-21 115.0
53 TraesCS3B01G305200 chr7A 82.609 138 20 2 258 391 634775773 634775636 1.130000e-22 119.0


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 TraesCS3B01G305200 chr3B 490589566 490595959 6393 False 11808.000000 11808 100.0000 1 6394 1 chr3B.!!$F1 6393
1 TraesCS3B01G305200 chr3D 376156812 376162929 6117 False 1251.014286 4006 93.2680 1 6394 7 chr3D.!!$F1 6393
2 TraesCS3B01G305200 chr3A 500968542 500974636 6094 False 1803.600000 2970 92.2102 40 6353 5 chr3A.!!$F1 6313
3 TraesCS3B01G305200 chr5D 22743866 22744427 561 False 421.050000 769 95.9580 3900 4446 2 chr5D.!!$F2 546
4 TraesCS3B01G305200 chr6B 205358166 205358717 551 True 374.000000 374 79.5660 1 530 1 chr6B.!!$R1 529
5 TraesCS3B01G305200 chr6D 105812418 105812965 547 True 368.000000 368 79.3480 1 535 1 chr6D.!!$R1 534

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
474 517 0.179018 GATCCGGATTTGGGGGTGAG 60.179 60.000 20.22 0.0 0.00 3.51 F
1368 1490 0.030773 CGAGATCGCTTGAATCGGGA 59.969 55.000 0.00 0.0 33.61 5.14 F
1787 1939 2.559381 ATCTTGGGAGCTAGGTCTGT 57.441 50.000 20.67 0.0 0.00 3.41 F
2314 2479 0.250640 AGCTTGGACACTGCAAGAGG 60.251 55.000 7.60 0.0 46.92 3.69 F
3244 3450 1.843851 ACTTTGGAATATCGAGGGGCA 59.156 47.619 0.00 0.0 0.00 5.36 F
4025 4238 0.321919 GAATGGCTGTGCTGGACTCA 60.322 55.000 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1759 1911 0.464554 GCTCCCAAGATACCAGCACC 60.465 60.000 0.00 0.0 0.00 5.01 R
2256 2413 1.026718 AGATGCCAGCAGCCGTTTAC 61.027 55.000 3.92 0.0 42.71 2.01 R
3609 3822 2.093288 TGCATTCGCTCCTTCAATCTCT 60.093 45.455 0.00 0.0 39.64 3.10 R
3611 3824 2.408271 TGCATTCGCTCCTTCAATCT 57.592 45.000 0.00 0.0 39.64 2.40 R
4888 5163 0.036010 CTCATCCGAAGCCACCTGTT 60.036 55.000 0.00 0.0 0.00 3.16 R
5876 6167 0.106217 GGAGAGGAGAGGGACTGAGG 60.106 65.000 0.00 0.0 41.55 3.86 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
50 52 5.493735 GTGCAAACTCTAAATAGATGCGAC 58.506 41.667 8.97 6.03 36.39 5.19
152 158 5.406767 GCATTTGCAAAGTTGAATGAACA 57.593 34.783 18.19 0.00 41.59 3.18
257 293 4.530094 AATGTCCATGTTATAACGCACG 57.470 40.909 10.92 0.00 0.00 5.34
258 294 2.272678 TGTCCATGTTATAACGCACGG 58.727 47.619 10.92 8.25 0.00 4.94
318 354 0.250234 CTCCAGCGAGAAATGTCCCA 59.750 55.000 0.00 0.00 38.52 4.37
321 357 1.402968 CCAGCGAGAAATGTCCCATTG 59.597 52.381 0.00 0.00 0.00 2.82
333 369 1.606313 CCCATTGTGGCGGGAAACT 60.606 57.895 0.00 0.00 46.34 2.66
373 413 3.222603 ACAGGAAAAAGAAGGATGCGTT 58.777 40.909 0.00 0.00 0.00 4.84
387 430 2.852180 GCGTTGTGGGGTGGGTTTC 61.852 63.158 0.00 0.00 0.00 2.78
417 460 3.684305 CCTGCGTGTTGAAGATAACATGA 59.316 43.478 13.32 0.94 45.82 3.07
418 461 4.333649 CCTGCGTGTTGAAGATAACATGAT 59.666 41.667 13.32 0.00 45.82 2.45
425 468 5.300034 TGTTGAAGATAACATGATGGATGGC 59.700 40.000 0.00 0.00 35.75 4.40
436 479 2.519302 GGATGGCCCGGACAATGG 60.519 66.667 0.73 0.00 0.00 3.16
456 499 3.459227 TGGCATTTCTCCTCCACATATGA 59.541 43.478 10.38 0.00 0.00 2.15
474 517 0.179018 GATCCGGATTTGGGGGTGAG 60.179 60.000 20.22 0.00 0.00 3.51
483 600 3.961414 GGGGGTGAGCGGGTTGAA 61.961 66.667 0.00 0.00 0.00 2.69
488 605 0.390472 GGTGAGCGGGTTGAAGAGAG 60.390 60.000 0.00 0.00 0.00 3.20
531 648 2.032634 GGCGCTCGTTTGATGTCCA 61.033 57.895 7.64 0.00 0.00 4.02
543 660 1.887854 TGATGTCCAAACGTACGAGGA 59.112 47.619 24.41 21.36 0.00 3.71
557 674 8.816640 AACGTACGAGGAAGAAATAAACTTTA 57.183 30.769 24.41 0.00 0.00 1.85
560 677 8.919661 CGTACGAGGAAGAAATAAACTTTAACT 58.080 33.333 10.44 0.00 0.00 2.24
563 680 9.946165 ACGAGGAAGAAATAAACTTTAACTTTG 57.054 29.630 0.00 0.00 0.00 2.77
650 767 6.493116 GCAGCGTTCTACTAGTAATCTTACA 58.507 40.000 3.76 0.00 36.12 2.41
661 778 8.319057 ACTAGTAATCTTACATTGTGGGATGA 57.681 34.615 0.00 0.00 36.12 2.92
662 779 8.768397 ACTAGTAATCTTACATTGTGGGATGAA 58.232 33.333 0.00 0.00 36.12 2.57
663 780 9.784531 CTAGTAATCTTACATTGTGGGATGAAT 57.215 33.333 0.00 0.00 36.12 2.57
665 782 9.784531 AGTAATCTTACATTGTGGGATGAATAG 57.215 33.333 0.00 0.00 36.12 1.73
666 783 9.778741 GTAATCTTACATTGTGGGATGAATAGA 57.221 33.333 0.00 0.00 33.88 1.98
668 785 9.699410 AATCTTACATTGTGGGATGAATAGAAA 57.301 29.630 0.00 0.00 0.00 2.52
669 786 9.699410 ATCTTACATTGTGGGATGAATAGAAAA 57.301 29.630 0.00 0.00 0.00 2.29
670 787 9.527157 TCTTACATTGTGGGATGAATAGAAAAA 57.473 29.630 0.00 0.00 0.00 1.94
674 791 8.416329 ACATTGTGGGATGAATAGAAAAATAGC 58.584 33.333 0.00 0.00 0.00 2.97
675 792 7.953005 TTGTGGGATGAATAGAAAAATAGCA 57.047 32.000 0.00 0.00 0.00 3.49
676 793 8.537728 TTGTGGGATGAATAGAAAAATAGCAT 57.462 30.769 0.00 0.00 0.00 3.79
677 794 7.944061 TGTGGGATGAATAGAAAAATAGCATG 58.056 34.615 0.00 0.00 0.00 4.06
678 795 7.560991 TGTGGGATGAATAGAAAAATAGCATGT 59.439 33.333 0.00 0.00 0.00 3.21
679 796 8.078596 GTGGGATGAATAGAAAAATAGCATGTC 58.921 37.037 0.00 0.00 0.00 3.06
680 797 7.041167 TGGGATGAATAGAAAAATAGCATGTCG 60.041 37.037 0.00 0.00 0.00 4.35
681 798 7.041098 GGGATGAATAGAAAAATAGCATGTCGT 60.041 37.037 0.00 0.00 0.00 4.34
682 799 8.988934 GGATGAATAGAAAAATAGCATGTCGTA 58.011 33.333 0.00 0.00 0.00 3.43
723 840 9.717942 TTTTTGAATGGAATCCAAAATTACGAT 57.282 25.926 5.89 0.00 36.95 3.73
724 841 9.717942 TTTTGAATGGAATCCAAAATTACGATT 57.282 25.926 5.89 0.00 36.95 3.34
725 842 9.717942 TTTGAATGGAATCCAAAATTACGATTT 57.282 25.926 5.89 0.00 36.95 2.17
726 843 9.717942 TTGAATGGAATCCAAAATTACGATTTT 57.282 25.926 5.89 0.00 44.24 1.82
727 844 9.364989 TGAATGGAATCCAAAATTACGATTTTC 57.635 29.630 5.89 1.46 42.14 2.29
728 845 9.586435 GAATGGAATCCAAAATTACGATTTTCT 57.414 29.630 5.89 0.00 42.14 2.52
729 846 8.931385 ATGGAATCCAAAATTACGATTTTCTG 57.069 30.769 5.89 0.00 42.14 3.02
730 847 7.319646 TGGAATCCAAAATTACGATTTTCTGG 58.680 34.615 0.00 0.00 42.14 3.86
731 848 6.756542 GGAATCCAAAATTACGATTTTCTGGG 59.243 38.462 0.00 0.00 42.14 4.45
732 849 6.850752 ATCCAAAATTACGATTTTCTGGGT 57.149 33.333 0.00 0.00 42.14 4.51
733 850 6.262193 TCCAAAATTACGATTTTCTGGGTC 57.738 37.500 0.00 0.00 42.14 4.46
734 851 6.007703 TCCAAAATTACGATTTTCTGGGTCT 58.992 36.000 0.00 0.00 42.14 3.85
735 852 7.169591 TCCAAAATTACGATTTTCTGGGTCTA 58.830 34.615 0.00 0.00 42.14 2.59
736 853 7.666388 TCCAAAATTACGATTTTCTGGGTCTAA 59.334 33.333 0.00 0.00 42.14 2.10
737 854 8.466798 CCAAAATTACGATTTTCTGGGTCTAAT 58.533 33.333 0.00 0.00 42.14 1.73
738 855 9.289303 CAAAATTACGATTTTCTGGGTCTAATG 57.711 33.333 0.00 0.00 42.14 1.90
739 856 8.801882 AAATTACGATTTTCTGGGTCTAATGA 57.198 30.769 0.00 0.00 31.48 2.57
740 857 8.801882 AATTACGATTTTCTGGGTCTAATGAA 57.198 30.769 0.00 0.00 0.00 2.57
741 858 8.980481 ATTACGATTTTCTGGGTCTAATGAAT 57.020 30.769 0.00 0.00 0.00 2.57
744 861 8.980481 ACGATTTTCTGGGTCTAATGAATATT 57.020 30.769 0.00 0.00 0.00 1.28
745 862 9.408648 ACGATTTTCTGGGTCTAATGAATATTT 57.591 29.630 0.00 0.00 0.00 1.40
772 889 8.810990 TTGATAATCATATATGCCTGCAATCA 57.189 30.769 7.92 7.96 0.00 2.57
773 890 8.217131 TGATAATCATATATGCCTGCAATCAC 57.783 34.615 7.92 0.00 0.00 3.06
774 891 8.050930 TGATAATCATATATGCCTGCAATCACT 58.949 33.333 7.92 0.00 0.00 3.41
775 892 8.818622 ATAATCATATATGCCTGCAATCACTT 57.181 30.769 7.92 0.00 0.00 3.16
776 893 9.910267 ATAATCATATATGCCTGCAATCACTTA 57.090 29.630 7.92 0.00 0.00 2.24
777 894 8.640063 AATCATATATGCCTGCAATCACTTAA 57.360 30.769 7.92 0.00 0.00 1.85
778 895 8.640063 ATCATATATGCCTGCAATCACTTAAA 57.360 30.769 7.92 0.00 0.00 1.52
779 896 8.640063 TCATATATGCCTGCAATCACTTAAAT 57.360 30.769 7.92 0.00 0.00 1.40
780 897 8.733458 TCATATATGCCTGCAATCACTTAAATC 58.267 33.333 7.92 0.00 0.00 2.17
781 898 8.737175 CATATATGCCTGCAATCACTTAAATCT 58.263 33.333 0.00 0.00 0.00 2.40
782 899 5.927281 ATGCCTGCAATCACTTAAATCTT 57.073 34.783 0.00 0.00 0.00 2.40
783 900 5.726980 TGCCTGCAATCACTTAAATCTTT 57.273 34.783 0.00 0.00 0.00 2.52
784 901 6.100404 TGCCTGCAATCACTTAAATCTTTT 57.900 33.333 0.00 0.00 0.00 2.27
785 902 6.523840 TGCCTGCAATCACTTAAATCTTTTT 58.476 32.000 0.00 0.00 0.00 1.94
828 945 9.919416 TGAATGAATATTTTCTGGGTCTAATGA 57.081 29.630 0.00 0.00 32.78 2.57
837 954 9.713684 ATTTTCTGGGTCTAATGAATAAATGGA 57.286 29.630 0.00 0.00 0.00 3.41
838 955 9.713684 TTTTCTGGGTCTAATGAATAAATGGAT 57.286 29.630 0.00 0.00 0.00 3.41
841 958 9.392506 TCTGGGTCTAATGAATAAATGGATAGA 57.607 33.333 0.00 0.00 0.00 1.98
842 959 9.664332 CTGGGTCTAATGAATAAATGGATAGAG 57.336 37.037 0.00 0.00 0.00 2.43
843 960 8.103305 TGGGTCTAATGAATAAATGGATAGAGC 58.897 37.037 0.00 0.00 36.31 4.09
844 961 7.554476 GGGTCTAATGAATAAATGGATAGAGCC 59.446 40.741 11.08 11.08 44.42 4.70
845 962 8.325046 GGTCTAATGAATAAATGGATAGAGCCT 58.675 37.037 0.00 0.00 32.90 4.58
846 963 9.160496 GTCTAATGAATAAATGGATAGAGCCTG 57.840 37.037 0.00 0.00 0.00 4.85
847 964 8.324306 TCTAATGAATAAATGGATAGAGCCTGG 58.676 37.037 0.00 0.00 0.00 4.45
848 965 4.655963 TGAATAAATGGATAGAGCCTGGC 58.344 43.478 11.65 11.65 0.00 4.85
849 966 4.352001 TGAATAAATGGATAGAGCCTGGCT 59.648 41.667 23.64 23.64 43.88 4.75
859 976 2.391226 AGCCTGGCTCCAATTCTGA 58.609 52.632 17.22 0.00 30.62 3.27
860 977 0.924823 AGCCTGGCTCCAATTCTGAT 59.075 50.000 17.22 0.00 30.62 2.90
861 978 2.130193 AGCCTGGCTCCAATTCTGATA 58.870 47.619 17.22 0.00 30.62 2.15
862 979 2.511218 AGCCTGGCTCCAATTCTGATAA 59.489 45.455 17.22 0.00 30.62 1.75
863 980 3.053395 AGCCTGGCTCCAATTCTGATAAA 60.053 43.478 17.22 0.00 30.62 1.40
864 981 3.701040 GCCTGGCTCCAATTCTGATAAAA 59.299 43.478 12.43 0.00 0.00 1.52
865 982 4.343239 GCCTGGCTCCAATTCTGATAAAAT 59.657 41.667 12.43 0.00 0.00 1.82
866 983 5.536161 GCCTGGCTCCAATTCTGATAAAATA 59.464 40.000 12.43 0.00 0.00 1.40
867 984 6.040842 GCCTGGCTCCAATTCTGATAAAATAA 59.959 38.462 12.43 0.00 0.00 1.40
868 985 7.417797 GCCTGGCTCCAATTCTGATAAAATAAA 60.418 37.037 12.43 0.00 0.00 1.40
869 986 8.477256 CCTGGCTCCAATTCTGATAAAATAAAA 58.523 33.333 0.00 0.00 0.00 1.52
870 987 9.874205 CTGGCTCCAATTCTGATAAAATAAAAA 57.126 29.630 0.00 0.00 0.00 1.94
871 988 9.874205 TGGCTCCAATTCTGATAAAATAAAAAG 57.126 29.630 0.00 0.00 0.00 2.27
872 989 8.820933 GGCTCCAATTCTGATAAAATAAAAAGC 58.179 33.333 0.00 0.00 0.00 3.51
873 990 9.369904 GCTCCAATTCTGATAAAATAAAAAGCA 57.630 29.630 0.00 0.00 0.00 3.91
876 993 9.956797 CCAATTCTGATAAAATAAAAAGCAACG 57.043 29.630 0.00 0.00 0.00 4.10
879 996 8.447787 TTCTGATAAAATAAAAAGCAACGAGC 57.552 30.769 0.00 0.00 46.19 5.03
922 1039 2.309898 GTGAACGCACGCAGTATTTT 57.690 45.000 0.00 0.00 41.61 1.82
924 1041 1.195900 TGAACGCACGCAGTATTTTCC 59.804 47.619 0.00 0.00 41.61 3.13
943 1060 1.224069 CTGTGGACAGGTCACAAGCG 61.224 60.000 1.41 0.00 43.45 4.68
1204 1326 4.941713 AGTATGCCCCAACCTGAAATTTA 58.058 39.130 0.00 0.00 0.00 1.40
1248 1370 9.987272 CCTTCTATTTTTCTTTCCAGATTGTTT 57.013 29.630 0.00 0.00 0.00 2.83
1283 1405 0.393808 GCTTCTTGGCCCGGTCAATA 60.394 55.000 4.55 0.00 0.00 1.90
1356 1478 1.351430 TTTGTTGAGCGCCGAGATCG 61.351 55.000 2.29 0.00 38.28 3.69
1368 1490 0.030773 CGAGATCGCTTGAATCGGGA 59.969 55.000 0.00 0.00 33.61 5.14
1390 1512 3.941188 CTGTCCCACGCCACCAGT 61.941 66.667 0.00 0.00 0.00 4.00
1512 1634 4.644498 CATTTTTGCAGGAAATGGAGGTT 58.356 39.130 21.07 0.00 39.59 3.50
1759 1911 2.997899 GGAGGATCGCATGGTTCTG 58.002 57.895 0.00 0.00 34.37 3.02
1783 1935 2.683768 CTGGTATCTTGGGAGCTAGGT 58.316 52.381 0.00 0.00 0.00 3.08
1787 1939 2.559381 ATCTTGGGAGCTAGGTCTGT 57.441 50.000 20.67 0.00 0.00 3.41
1832 1984 2.868583 CGGCACACAAATCTAGAGATGG 59.131 50.000 11.12 0.00 34.49 3.51
2155 2307 6.524734 TCTGTTGCTTACTTCTCAATCTTGA 58.475 36.000 0.00 0.00 35.57 3.02
2159 2311 6.732531 TGCTTACTTCTCAATCTTGATGTG 57.267 37.500 0.00 0.00 36.46 3.21
2213 2370 3.558418 TGTTGTTTTCTTCTACCAGTCGC 59.442 43.478 0.00 0.00 0.00 5.19
2234 2391 3.755378 GCTTCTTGGCTTCTTCTGATGAA 59.245 43.478 5.93 5.93 0.00 2.57
2256 2413 8.032952 TGAATTCACTACTGATGCAAGTTTAG 57.967 34.615 3.38 0.00 0.00 1.85
2270 2435 2.423577 AGTTTAGTAAACGGCTGCTGG 58.576 47.619 17.85 1.43 45.88 4.85
2314 2479 0.250640 AGCTTGGACACTGCAAGAGG 60.251 55.000 7.60 0.00 46.92 3.69
2460 2628 8.102676 TGTGATCATCTTCTTATGAAAAGTGGA 58.897 33.333 0.00 0.00 39.25 4.02
2464 2632 7.765307 TCATCTTCTTATGAAAAGTGGAATGC 58.235 34.615 0.00 0.00 32.97 3.56
2497 2665 9.856488 TTAGTTATGAGTTATGACTGAACTGAC 57.144 33.333 14.58 0.86 37.27 3.51
2518 2686 5.104569 TGACATGTTGATGCCCATAACTCTA 60.105 40.000 0.00 0.00 32.14 2.43
2669 2837 4.703575 ACATCATATATGCCTGCAATCACC 59.296 41.667 7.92 0.00 0.00 4.02
2688 2856 4.105057 TCACCTAATACCTGTTGTTGGGTT 59.895 41.667 0.00 0.00 34.92 4.11
2689 2857 5.310068 TCACCTAATACCTGTTGTTGGGTTA 59.690 40.000 0.00 0.00 34.92 2.85
2690 2858 5.413523 CACCTAATACCTGTTGTTGGGTTAC 59.586 44.000 0.00 0.00 34.92 2.50
2786 2992 8.511465 CTTGTATTTCAAGTTCCAACTTCATG 57.489 34.615 1.52 0.00 45.65 3.07
2844 3050 6.091437 GCATTCTGTTGATTCTTTTCCTCAG 58.909 40.000 0.00 0.00 0.00 3.35
2857 3063 5.190528 TCTTTTCCTCAGTTATCTGCATCCT 59.809 40.000 0.00 0.00 41.10 3.24
3070 3276 7.690256 ACAAAATGTAGGACTCCTTGATAAGT 58.310 34.615 1.94 0.00 34.61 2.24
3071 3277 8.164070 ACAAAATGTAGGACTCCTTGATAAGTT 58.836 33.333 1.94 0.00 34.61 2.66
3072 3278 8.669243 CAAAATGTAGGACTCCTTGATAAGTTC 58.331 37.037 1.94 0.00 34.61 3.01
3073 3279 7.741554 AATGTAGGACTCCTTGATAAGTTCT 57.258 36.000 1.94 0.00 35.49 3.01
3074 3280 7.741554 ATGTAGGACTCCTTGATAAGTTCTT 57.258 36.000 1.94 0.00 33.35 2.52
3077 3283 8.437575 TGTAGGACTCCTTGATAAGTTCTTTTT 58.562 33.333 1.94 0.00 33.35 1.94
3143 3349 7.918033 TCGTTTCTCAGATGATTATCTCTCAAC 59.082 37.037 0.00 0.00 41.71 3.18
3244 3450 1.843851 ACTTTGGAATATCGAGGGGCA 59.156 47.619 0.00 0.00 0.00 5.36
3342 3548 9.507280 CATACTTCTTGCATTTTATTGGTAGTG 57.493 33.333 0.00 0.00 0.00 2.74
3407 3613 9.537192 ACAATACATTTGATTAATCAATGCCTG 57.463 29.630 27.11 22.22 45.30 4.85
3463 3670 3.843619 CCATAAATTTTCCTTGGGGTGGT 59.156 43.478 0.00 0.00 0.00 4.16
3488 3695 6.831868 TGTACTAAAGCAAAACCCTTCTTTCT 59.168 34.615 0.00 0.00 31.92 2.52
3527 3737 3.008375 GGCCACATCAGCATAAGAGGATA 59.992 47.826 0.00 0.00 0.00 2.59
3528 3738 3.999663 GCCACATCAGCATAAGAGGATAC 59.000 47.826 0.00 0.00 0.00 2.24
3630 3843 2.093288 AGAGATTGAAGGAGCGAATGCA 60.093 45.455 0.00 0.00 46.23 3.96
3670 3883 2.659016 CTCTGAGCAGTGCCGGAA 59.341 61.111 12.58 0.00 0.00 4.30
3760 3973 6.576662 TCAGCTAACTATTCTTATCGAGGG 57.423 41.667 0.00 0.00 0.00 4.30
3941 4154 5.656859 TGTGCCTCTATTACTGTCTATGTGT 59.343 40.000 0.00 0.00 0.00 3.72
4025 4238 0.321919 GAATGGCTGTGCTGGACTCA 60.322 55.000 0.00 0.00 0.00 3.41
4050 4263 3.978718 AAGAAGCACTTGAAAGCTGTC 57.021 42.857 0.00 0.00 41.70 3.51
4140 4361 5.277442 GGTGCAATGTTGTTTTGATGGAAAG 60.277 40.000 0.00 0.00 0.00 2.62
4141 4362 5.294060 GTGCAATGTTGTTTTGATGGAAAGT 59.706 36.000 0.00 0.00 0.00 2.66
4227 4449 4.185467 TGCATGTGTTGTTTGTTTCTGT 57.815 36.364 0.00 0.00 0.00 3.41
4284 4506 9.681062 AGTGCTAATTCCTAAAACAGCTTTATA 57.319 29.630 0.00 0.00 0.00 0.98
4336 4558 3.323775 TCACCCTTCCAACCTCTACTTT 58.676 45.455 0.00 0.00 0.00 2.66
4384 4617 5.603750 TGGCTATCCTCATACTCCCAATAT 58.396 41.667 0.00 0.00 0.00 1.28
4388 4621 7.044798 GCTATCCTCATACTCCCAATATGTTC 58.955 42.308 0.00 0.00 32.75 3.18
4418 4651 3.177228 GGCTATCCTCATACTCCCACAT 58.823 50.000 0.00 0.00 0.00 3.21
4541 4813 2.226200 CGCTTGATGACAACAACCATCA 59.774 45.455 0.00 0.00 45.03 3.07
4601 4874 5.578727 CACTATCTGTTGCTGAGGTTCTTAC 59.421 44.000 0.00 0.00 0.00 2.34
4653 4926 2.689983 GCATTATCTGTGGGGTTTGGAG 59.310 50.000 0.00 0.00 0.00 3.86
4655 4928 2.352561 TATCTGTGGGGTTTGGAGGA 57.647 50.000 0.00 0.00 0.00 3.71
4799 5073 6.072175 GCACACAAATTCCATAAAGAGGTACA 60.072 38.462 0.00 0.00 0.00 2.90
4804 5078 6.699575 AATTCCATAAAGAGGTACACATGC 57.300 37.500 0.00 0.00 0.00 4.06
4806 5080 5.372343 TCCATAAAGAGGTACACATGCAT 57.628 39.130 0.00 0.00 0.00 3.96
4808 5082 5.822519 TCCATAAAGAGGTACACATGCATTC 59.177 40.000 0.00 0.00 0.00 2.67
4813 5087 5.620738 AGAGGTACACATGCATTCTGTAT 57.379 39.130 14.35 3.27 0.00 2.29
5027 5303 1.648467 GCCATTTCGACACTCCTGGC 61.648 60.000 0.00 0.00 42.00 4.85
5033 5309 4.148825 GACACTCCTGGCGCCGAT 62.149 66.667 23.90 1.33 0.00 4.18
5047 5323 0.515564 GCCGATGTGCGTAAACAACT 59.484 50.000 0.00 0.00 38.67 3.16
5053 5330 4.838642 CGATGTGCGTAAACAACTTTGTAG 59.161 41.667 0.00 0.00 36.30 2.74
5181 5466 3.550820 ACAGGGCATCGCAAATATTGTA 58.449 40.909 0.00 0.00 0.00 2.41
5229 5515 3.177228 GGGGAGATGTGTGATATAGCCT 58.823 50.000 0.00 0.00 0.00 4.58
5242 5528 5.349817 GTGATATAGCCTGATTTCCATGTCG 59.650 44.000 0.00 0.00 0.00 4.35
5266 5552 1.112950 GGCCCTGTCCTGTAGTAGTC 58.887 60.000 0.00 0.00 0.00 2.59
5327 5614 1.195115 TCGGTTCTGGGATCCTGAAG 58.805 55.000 12.58 7.47 41.01 3.02
5473 5761 8.782533 AAATTGTTCAGAATTTCGTGTTACTC 57.217 30.769 0.00 0.00 31.21 2.59
5497 5785 1.265236 CCTGCCAAGGGTAAATTGCA 58.735 50.000 0.00 0.00 40.27 4.08
5545 5833 7.498070 GAAGTTATCAATGCTTCGGAAAAAG 57.502 36.000 0.00 0.00 30.94 2.27
5551 5839 1.289066 GCTTCGGAAAAAGCCCACC 59.711 57.895 0.00 0.00 44.75 4.61
5573 5861 5.221682 ACCAGAAAACATGCATTTTGATGGA 60.222 36.000 24.90 0.00 37.27 3.41
5593 5881 4.161333 GGATGTTTGATGACTTTTGCTCG 58.839 43.478 0.00 0.00 0.00 5.03
5597 5885 6.552859 TGTTTGATGACTTTTGCTCGATTA 57.447 33.333 0.00 0.00 0.00 1.75
5600 5888 5.739752 TGATGACTTTTGCTCGATTATGG 57.260 39.130 0.00 0.00 0.00 2.74
5604 5892 3.686016 ACTTTTGCTCGATTATGGTGGT 58.314 40.909 0.00 0.00 0.00 4.16
5607 5895 3.627395 TTGCTCGATTATGGTGGTCTT 57.373 42.857 0.00 0.00 0.00 3.01
5619 5907 5.806654 ATGGTGGTCTTTTGCAATTTACT 57.193 34.783 0.00 0.00 0.00 2.24
5648 5936 2.181975 CCAAGCACATCCCCATTCTTT 58.818 47.619 0.00 0.00 0.00 2.52
5705 5993 4.463891 AGGCAATGGAGGTGAAAATTACTG 59.536 41.667 0.00 0.00 0.00 2.74
5739 6029 6.937436 ACTCGGAAATGTATATTTTCCCAC 57.063 37.500 17.78 0.00 36.66 4.61
5878 6169 2.431023 CGATTCCGGATCACTCCCT 58.569 57.895 4.15 0.00 38.45 4.20
5879 6170 0.315568 CGATTCCGGATCACTCCCTC 59.684 60.000 4.15 0.00 38.45 4.30
5880 6171 1.414158 GATTCCGGATCACTCCCTCA 58.586 55.000 4.15 0.00 38.45 3.86
5881 6172 1.342819 GATTCCGGATCACTCCCTCAG 59.657 57.143 4.15 0.00 38.45 3.35
5882 6173 0.041238 TTCCGGATCACTCCCTCAGT 59.959 55.000 4.15 0.00 38.45 3.41
5883 6174 0.395862 TCCGGATCACTCCCTCAGTC 60.396 60.000 0.00 0.00 38.45 3.51
5884 6175 1.395826 CCGGATCACTCCCTCAGTCC 61.396 65.000 0.00 0.00 38.45 3.85
5885 6176 1.395826 CGGATCACTCCCTCAGTCCC 61.396 65.000 0.00 0.00 38.45 4.46
5886 6177 0.031616 GGATCACTCCCTCAGTCCCT 60.032 60.000 0.00 0.00 35.28 4.20
5887 6178 1.408969 GATCACTCCCTCAGTCCCTC 58.591 60.000 0.00 0.00 30.26 4.30
5888 6179 1.014804 ATCACTCCCTCAGTCCCTCT 58.985 55.000 0.00 0.00 30.26 3.69
6305 6606 2.895372 CACGCCGGTAAGCCCATC 60.895 66.667 1.90 0.00 0.00 3.51
6311 6612 3.489513 GGTAAGCCCATCCCCGCT 61.490 66.667 0.00 0.00 36.74 5.52
6353 6658 2.882876 GCGTCTTAGTCCCGCTCA 59.117 61.111 0.00 0.00 43.81 4.26
6380 6685 5.559694 ATTTGTTTCATTTGTTTCGAGCG 57.440 34.783 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.519408 TTAGAGTTTGCACGCCTTCC 58.481 50.000 0.00 0.00 0.00 3.46
229 248 8.731605 TGCGTTATAACATGGACATTTTCTTTA 58.268 29.630 15.67 0.00 0.00 1.85
257 293 3.050275 GCGCACCTCACCTTCACC 61.050 66.667 0.30 0.00 0.00 4.02
258 294 3.414700 CGCGCACCTCACCTTCAC 61.415 66.667 8.75 0.00 0.00 3.18
318 354 1.244019 GCTCAGTTTCCCGCCACAAT 61.244 55.000 0.00 0.00 0.00 2.71
321 357 2.281484 TGCTCAGTTTCCCGCCAC 60.281 61.111 0.00 0.00 0.00 5.01
333 369 4.741239 GGACCCCCTCCCTGCTCA 62.741 72.222 0.00 0.00 31.83 4.26
373 413 0.396417 CAACAGAAACCCACCCCACA 60.396 55.000 0.00 0.00 0.00 4.17
387 430 2.906897 AACACGCAGGCCCAACAG 60.907 61.111 0.00 0.00 0.00 3.16
417 460 1.152694 CATTGTCCGGGCCATCCAT 60.153 57.895 2.12 0.00 34.36 3.41
418 461 2.275089 CATTGTCCGGGCCATCCA 59.725 61.111 2.12 0.00 34.36 3.41
425 468 0.740737 GAGAAATGCCATTGTCCGGG 59.259 55.000 0.00 0.00 0.00 5.73
436 479 4.699257 GGATCATATGTGGAGGAGAAATGC 59.301 45.833 1.90 0.00 0.00 3.56
456 499 1.922821 CTCACCCCCAAATCCGGAT 59.077 57.895 12.38 12.38 0.00 4.18
474 517 2.699954 TCAATTCTCTCTTCAACCCGC 58.300 47.619 0.00 0.00 0.00 6.13
483 600 5.267587 CCTCCCCAAAATTCAATTCTCTCT 58.732 41.667 0.00 0.00 0.00 3.10
488 605 4.711846 AGTAGCCTCCCCAAAATTCAATTC 59.288 41.667 0.00 0.00 0.00 2.17
531 648 7.719778 AAGTTTATTTCTTCCTCGTACGTTT 57.280 32.000 16.05 0.00 0.00 3.60
605 722 4.506288 TGCGTTTCCATGTCTTATATGACG 59.494 41.667 12.61 0.00 39.64 4.35
614 731 1.301716 ACGCTGCGTTTCCATGTCT 60.302 52.632 23.57 0.00 36.35 3.41
650 767 8.537728 TGCTATTTTTCTATTCATCCCACAAT 57.462 30.769 0.00 0.00 0.00 2.71
697 814 9.717942 ATCGTAATTTTGGATTCCATTCAAAAA 57.282 25.926 6.15 4.15 41.63 1.94
698 815 9.717942 AATCGTAATTTTGGATTCCATTCAAAA 57.282 25.926 6.15 4.53 42.22 2.44
699 816 9.717942 AAATCGTAATTTTGGATTCCATTCAAA 57.282 25.926 6.15 4.89 30.79 2.69
700 817 9.717942 AAAATCGTAATTTTGGATTCCATTCAA 57.282 25.926 6.15 0.75 42.21 2.69
701 818 9.364989 GAAAATCGTAATTTTGGATTCCATTCA 57.635 29.630 6.15 0.00 43.48 2.57
702 819 9.586435 AGAAAATCGTAATTTTGGATTCCATTC 57.414 29.630 6.15 2.97 43.48 2.67
703 820 9.369904 CAGAAAATCGTAATTTTGGATTCCATT 57.630 29.630 6.15 0.59 43.48 3.16
704 821 7.981225 CCAGAAAATCGTAATTTTGGATTCCAT 59.019 33.333 6.15 0.00 43.48 3.41
705 822 7.319646 CCAGAAAATCGTAATTTTGGATTCCA 58.680 34.615 0.00 0.00 43.48 3.53
706 823 6.756542 CCCAGAAAATCGTAATTTTGGATTCC 59.243 38.462 0.00 0.00 43.48 3.01
707 824 7.320399 ACCCAGAAAATCGTAATTTTGGATTC 58.680 34.615 1.13 0.00 43.48 2.52
708 825 7.178451 AGACCCAGAAAATCGTAATTTTGGATT 59.822 33.333 1.13 0.00 43.48 3.01
709 826 6.663523 AGACCCAGAAAATCGTAATTTTGGAT 59.336 34.615 1.13 0.00 43.48 3.41
710 827 6.007703 AGACCCAGAAAATCGTAATTTTGGA 58.992 36.000 1.13 0.00 43.48 3.53
711 828 6.267496 AGACCCAGAAAATCGTAATTTTGG 57.733 37.500 1.13 0.79 43.48 3.28
712 829 9.289303 CATTAGACCCAGAAAATCGTAATTTTG 57.711 33.333 1.13 0.00 43.48 2.44
713 830 9.238368 TCATTAGACCCAGAAAATCGTAATTTT 57.762 29.630 0.00 0.00 45.55 1.82
714 831 8.801882 TCATTAGACCCAGAAAATCGTAATTT 57.198 30.769 0.00 0.00 36.64 1.82
715 832 8.801882 TTCATTAGACCCAGAAAATCGTAATT 57.198 30.769 0.00 0.00 0.00 1.40
716 833 8.980481 ATTCATTAGACCCAGAAAATCGTAAT 57.020 30.769 0.00 0.00 0.00 1.89
719 836 8.980481 AATATTCATTAGACCCAGAAAATCGT 57.020 30.769 0.00 0.00 0.00 3.73
746 863 9.245481 TGATTGCAGGCATATATGATTATCAAA 57.755 29.630 17.10 2.22 0.00 2.69
747 864 8.680001 GTGATTGCAGGCATATATGATTATCAA 58.320 33.333 17.10 12.07 0.00 2.57
748 865 8.050930 AGTGATTGCAGGCATATATGATTATCA 58.949 33.333 17.10 11.49 0.00 2.15
749 866 8.447924 AGTGATTGCAGGCATATATGATTATC 57.552 34.615 17.10 9.43 0.00 1.75
750 867 8.818622 AAGTGATTGCAGGCATATATGATTAT 57.181 30.769 17.10 0.72 0.00 1.28
751 868 9.737844 TTAAGTGATTGCAGGCATATATGATTA 57.262 29.630 17.10 0.00 0.00 1.75
752 869 8.640063 TTAAGTGATTGCAGGCATATATGATT 57.360 30.769 17.10 0.32 0.00 2.57
753 870 8.640063 TTTAAGTGATTGCAGGCATATATGAT 57.360 30.769 17.10 0.97 0.00 2.45
754 871 8.640063 ATTTAAGTGATTGCAGGCATATATGA 57.360 30.769 17.10 0.00 0.00 2.15
755 872 8.737175 AGATTTAAGTGATTGCAGGCATATATG 58.263 33.333 8.45 8.45 0.00 1.78
756 873 8.874744 AGATTTAAGTGATTGCAGGCATATAT 57.125 30.769 0.00 0.00 0.00 0.86
757 874 8.696043 AAGATTTAAGTGATTGCAGGCATATA 57.304 30.769 0.00 0.00 0.00 0.86
758 875 7.592885 AAGATTTAAGTGATTGCAGGCATAT 57.407 32.000 0.00 0.00 0.00 1.78
759 876 7.408756 AAAGATTTAAGTGATTGCAGGCATA 57.591 32.000 0.00 0.00 0.00 3.14
760 877 5.927281 AAGATTTAAGTGATTGCAGGCAT 57.073 34.783 0.00 0.00 0.00 4.40
761 878 5.726980 AAAGATTTAAGTGATTGCAGGCA 57.273 34.783 0.00 0.00 0.00 4.75
802 919 9.919416 TCATTAGACCCAGAAAATATTCATTCA 57.081 29.630 3.37 0.00 38.06 2.57
811 928 9.713684 TCCATTTATTCATTAGACCCAGAAAAT 57.286 29.630 0.00 0.00 0.00 1.82
812 929 9.713684 ATCCATTTATTCATTAGACCCAGAAAA 57.286 29.630 0.00 0.00 0.00 2.29
815 932 9.392506 TCTATCCATTTATTCATTAGACCCAGA 57.607 33.333 0.00 0.00 0.00 3.86
816 933 9.664332 CTCTATCCATTTATTCATTAGACCCAG 57.336 37.037 0.00 0.00 0.00 4.45
817 934 8.103305 GCTCTATCCATTTATTCATTAGACCCA 58.897 37.037 0.00 0.00 0.00 4.51
818 935 7.554476 GGCTCTATCCATTTATTCATTAGACCC 59.446 40.741 0.00 0.00 0.00 4.46
819 936 8.325046 AGGCTCTATCCATTTATTCATTAGACC 58.675 37.037 0.00 0.00 0.00 3.85
820 937 9.160496 CAGGCTCTATCCATTTATTCATTAGAC 57.840 37.037 0.00 0.00 0.00 2.59
821 938 8.324306 CCAGGCTCTATCCATTTATTCATTAGA 58.676 37.037 0.00 0.00 0.00 2.10
822 939 7.066766 GCCAGGCTCTATCCATTTATTCATTAG 59.933 40.741 3.29 0.00 0.00 1.73
823 940 6.886459 GCCAGGCTCTATCCATTTATTCATTA 59.114 38.462 3.29 0.00 0.00 1.90
824 941 5.713861 GCCAGGCTCTATCCATTTATTCATT 59.286 40.000 3.29 0.00 0.00 2.57
825 942 5.014966 AGCCAGGCTCTATCCATTTATTCAT 59.985 40.000 8.70 0.00 30.62 2.57
826 943 4.352001 AGCCAGGCTCTATCCATTTATTCA 59.648 41.667 8.70 0.00 30.62 2.57
827 944 4.916183 AGCCAGGCTCTATCCATTTATTC 58.084 43.478 8.70 0.00 30.62 1.75
841 958 0.924823 ATCAGAATTGGAGCCAGGCT 59.075 50.000 16.12 16.12 43.88 4.58
842 959 2.645838 TATCAGAATTGGAGCCAGGC 57.354 50.000 1.84 1.84 0.00 4.85
843 960 7.587037 TTATTTTATCAGAATTGGAGCCAGG 57.413 36.000 0.00 0.00 0.00 4.45
844 961 9.874205 TTTTTATTTTATCAGAATTGGAGCCAG 57.126 29.630 0.00 0.00 0.00 4.85
845 962 9.874205 CTTTTTATTTTATCAGAATTGGAGCCA 57.126 29.630 0.00 0.00 0.00 4.75
846 963 8.820933 GCTTTTTATTTTATCAGAATTGGAGCC 58.179 33.333 0.00 0.00 0.00 4.70
847 964 9.369904 TGCTTTTTATTTTATCAGAATTGGAGC 57.630 29.630 0.00 0.00 0.00 4.70
850 967 9.956797 CGTTGCTTTTTATTTTATCAGAATTGG 57.043 29.630 0.00 0.00 0.00 3.16
853 970 9.076596 GCTCGTTGCTTTTTATTTTATCAGAAT 57.923 29.630 0.00 0.00 38.95 2.40
854 971 8.447787 GCTCGTTGCTTTTTATTTTATCAGAA 57.552 30.769 0.00 0.00 38.95 3.02
871 988 1.605058 TACCTCCTCCAGCTCGTTGC 61.605 60.000 0.00 0.00 43.29 4.17
872 989 0.457851 CTACCTCCTCCAGCTCGTTG 59.542 60.000 0.00 0.00 0.00 4.10
873 990 0.331954 TCTACCTCCTCCAGCTCGTT 59.668 55.000 0.00 0.00 0.00 3.85
874 991 0.553819 ATCTACCTCCTCCAGCTCGT 59.446 55.000 0.00 0.00 0.00 4.18
875 992 1.243902 GATCTACCTCCTCCAGCTCG 58.756 60.000 0.00 0.00 0.00 5.03
876 993 1.243902 CGATCTACCTCCTCCAGCTC 58.756 60.000 0.00 0.00 0.00 4.09
877 994 0.178975 CCGATCTACCTCCTCCAGCT 60.179 60.000 0.00 0.00 0.00 4.24
878 995 0.468400 ACCGATCTACCTCCTCCAGC 60.468 60.000 0.00 0.00 0.00 4.85
879 996 1.133761 TGACCGATCTACCTCCTCCAG 60.134 57.143 0.00 0.00 0.00 3.86
880 997 0.924090 TGACCGATCTACCTCCTCCA 59.076 55.000 0.00 0.00 0.00 3.86
881 998 2.068834 TTGACCGATCTACCTCCTCC 57.931 55.000 0.00 0.00 0.00 4.30
924 1041 1.224069 CGCTTGTGACCTGTCCACAG 61.224 60.000 0.00 0.00 44.22 3.66
1148 1265 2.545810 AGGAGAAACAAGGGAGAGAGG 58.454 52.381 0.00 0.00 0.00 3.69
1204 1326 2.660661 AGGAAAAAGGGAAGGGAGGAT 58.339 47.619 0.00 0.00 0.00 3.24
1283 1405 2.747446 CGTTGAATGACCGGGAAGAAAT 59.253 45.455 6.32 0.00 0.00 2.17
1356 1478 3.181496 GGACAGAAATTCCCGATTCAAGC 60.181 47.826 0.00 0.00 0.00 4.01
1368 1490 0.893727 GGTGGCGTGGGACAGAAATT 60.894 55.000 0.00 0.00 41.80 1.82
1390 1512 4.634004 TGACACGAAGAAGCTCAAGAAAAA 59.366 37.500 0.00 0.00 0.00 1.94
1445 1567 8.595533 GCAACTTCTCTTTTACAAAGAAAAAGG 58.404 33.333 17.21 8.18 41.92 3.11
1447 1569 9.482627 TTGCAACTTCTCTTTTACAAAGAAAAA 57.517 25.926 0.00 0.00 0.00 1.94
1512 1634 1.349357 TCGGATGACACCAAATCCACA 59.651 47.619 2.85 0.00 42.21 4.17
1759 1911 0.464554 GCTCCCAAGATACCAGCACC 60.465 60.000 0.00 0.00 0.00 5.01
1783 1935 0.625316 CATGAATCCCACCCCACAGA 59.375 55.000 0.00 0.00 0.00 3.41
1787 1939 0.552367 ACTCCATGAATCCCACCCCA 60.552 55.000 0.00 0.00 0.00 4.96
1832 1984 0.790814 CTCGGCCGTTTCACTTCTTC 59.209 55.000 27.15 0.00 0.00 2.87
2213 2370 6.150641 TGAATTCATCAGAAGAAGCCAAGAAG 59.849 38.462 3.38 0.00 37.14 2.85
2234 2391 9.502091 TTTACTAAACTTGCATCAGTAGTGAAT 57.498 29.630 3.93 0.00 35.88 2.57
2256 2413 1.026718 AGATGCCAGCAGCCGTTTAC 61.027 55.000 3.92 0.00 42.71 2.01
2270 2435 2.030946 GTCGTATCAACCTGCAAGATGC 59.969 50.000 0.00 0.00 45.29 3.91
2331 2496 2.444421 CCCTCTCTTGCAGCAATTCTT 58.556 47.619 8.67 0.00 0.00 2.52
2343 2508 3.454082 CAGAACTAGATTGGCCCTCTCTT 59.546 47.826 8.14 2.44 0.00 2.85
2497 2665 5.824624 ACTTAGAGTTATGGGCATCAACATG 59.175 40.000 0.00 0.00 0.00 3.21
2518 2686 3.025262 TGGTTTCCGGCAAACTTAACTT 58.975 40.909 21.12 0.00 43.63 2.66
2669 2837 7.618137 AGTAGTAACCCAACAACAGGTATTAG 58.382 38.462 0.00 0.00 34.45 1.73
2688 2856 9.186837 CTGAGTATTCTCCCAAGTTAAGTAGTA 57.813 37.037 0.00 0.00 39.75 1.82
2689 2857 7.674772 ACTGAGTATTCTCCCAAGTTAAGTAGT 59.325 37.037 0.00 0.00 39.75 2.73
2690 2858 8.068892 ACTGAGTATTCTCCCAAGTTAAGTAG 57.931 38.462 0.00 0.00 39.75 2.57
2844 3050 5.753721 AGGAAGGATAGGATGCAGATAAC 57.246 43.478 0.00 0.00 0.00 1.89
3085 3291 5.362717 TCAGTCCTTAGTCAAGTGAAGTTCA 59.637 40.000 0.08 0.08 0.00 3.18
3088 3294 4.649674 TGTCAGTCCTTAGTCAAGTGAAGT 59.350 41.667 0.00 0.00 0.00 3.01
3101 3307 2.550830 ACGAGCAAATGTCAGTCCTT 57.449 45.000 0.00 0.00 0.00 3.36
3143 3349 2.888834 CCAAAACACCCTTTGGTCAG 57.111 50.000 6.90 0.00 46.94 3.51
3404 3610 8.472007 TGTTGTTATTATTATTTAGGGGCAGG 57.528 34.615 0.00 0.00 0.00 4.85
3463 3670 6.831868 AGAAAGAAGGGTTTTGCTTTAGTACA 59.168 34.615 0.00 0.00 31.30 2.90
3609 3822 2.093288 TGCATTCGCTCCTTCAATCTCT 60.093 45.455 0.00 0.00 39.64 3.10
3611 3824 2.408271 TGCATTCGCTCCTTCAATCT 57.592 45.000 0.00 0.00 39.64 2.40
3630 3843 4.765856 GCCTTTATGATTGCATCCTGAGAT 59.234 41.667 0.00 0.00 35.94 2.75
3670 3883 7.801104 ACCAACCAAAGAATAAACTTCCAATT 58.199 30.769 0.00 0.00 0.00 2.32
3776 3989 7.581011 CAATTGGCTAATTGTTTAGTTGGTC 57.419 36.000 23.26 0.00 45.14 4.02
4050 4263 4.895889 TGAATCTGTAGGATAGGTGTCTGG 59.104 45.833 0.00 0.00 33.71 3.86
4140 4361 2.557920 ATATAGCCTGGCTGCAGAAC 57.442 50.000 30.83 10.09 40.10 3.01
4141 4362 4.916041 ATTATATAGCCTGGCTGCAGAA 57.084 40.909 30.83 20.15 40.10 3.02
4326 4548 7.672122 CCTATTGGGTACTAAAAGTAGAGGT 57.328 40.000 0.00 0.00 30.12 3.85
4384 4617 4.962362 TGAGGATAGCCATCTAAGTGAACA 59.038 41.667 0.00 0.00 36.29 3.18
4388 4621 6.127479 GGAGTATGAGGATAGCCATCTAAGTG 60.127 46.154 0.00 0.00 36.29 3.16
4418 4651 7.826744 TGCATGAACCAACAAGTAGTATGAATA 59.173 33.333 0.00 0.00 0.00 1.75
4541 4813 1.617850 CACTGTCAGAAGCTCCTCTGT 59.382 52.381 13.78 0.00 42.93 3.41
4626 4899 2.241941 ACCCCACAGATAATGCACATCA 59.758 45.455 11.60 0.00 0.00 3.07
4653 4926 3.431068 GGAGAGGCAAGTAAGTTAGCTCC 60.431 52.174 0.00 0.00 33.45 4.70
4655 4928 2.502130 GGGAGAGGCAAGTAAGTTAGCT 59.498 50.000 0.00 0.00 0.00 3.32
4707 4981 0.905337 ATATAGGGCAGGGCTCGTCC 60.905 60.000 0.00 0.00 32.17 4.79
4770 5044 5.771469 TCTTTATGGAATTTGTGTGCACAG 58.229 37.500 22.40 2.97 42.94 3.66
4773 5047 4.832266 ACCTCTTTATGGAATTTGTGTGCA 59.168 37.500 0.00 0.00 0.00 4.57
4799 5073 5.472478 CAGCTCCAATATACAGAATGCATGT 59.528 40.000 0.00 0.00 42.53 3.21
4804 5078 5.859521 GAGCAGCTCCAATATACAGAATG 57.140 43.478 11.84 0.00 46.00 2.67
4888 5163 0.036010 CTCATCCGAAGCCACCTGTT 60.036 55.000 0.00 0.00 0.00 3.16
4938 5213 3.747976 GCGGCGCCCTGTCAAAAT 61.748 61.111 23.58 0.00 0.00 1.82
4957 5232 0.401738 ACAGGTGCTGCAGTTGGTAT 59.598 50.000 16.64 0.00 34.37 2.73
5032 5308 5.065474 ACACTACAAAGTTGTTTACGCACAT 59.935 36.000 1.35 0.00 42.35 3.21
5033 5309 4.392445 ACACTACAAAGTTGTTTACGCACA 59.608 37.500 1.35 0.00 42.35 4.57
5041 5317 4.428615 AACGCAACACTACAAAGTTGTT 57.571 36.364 1.35 0.00 45.16 2.83
5124 5408 7.661437 GCAACAGAAGAGATAGATAGAGAGAGA 59.339 40.741 0.00 0.00 0.00 3.10
5125 5409 7.094634 GGCAACAGAAGAGATAGATAGAGAGAG 60.095 44.444 0.00 0.00 0.00 3.20
5126 5410 6.714810 GGCAACAGAAGAGATAGATAGAGAGA 59.285 42.308 0.00 0.00 0.00 3.10
5127 5411 6.716628 AGGCAACAGAAGAGATAGATAGAGAG 59.283 42.308 0.00 0.00 41.41 3.20
5128 5412 6.489700 CAGGCAACAGAAGAGATAGATAGAGA 59.510 42.308 0.00 0.00 41.41 3.10
5181 5466 6.267070 CACAAAAATTGCAGCAAAAAGGAAT 58.733 32.000 12.97 0.00 0.00 3.01
5229 5515 1.819928 CCCACACGACATGGAAATCA 58.180 50.000 0.00 0.00 39.87 2.57
5242 5528 2.185310 CTACAGGACAGGGCCCACAC 62.185 65.000 27.56 14.10 0.00 3.82
5266 5552 5.394553 GCAGAATAAACCTTTCATCCCCTTG 60.395 44.000 0.00 0.00 0.00 3.61
5358 5645 0.813210 GGATGCTTTCAGCTCGAGGG 60.813 60.000 15.58 0.00 42.97 4.30
5473 5761 0.539438 TTTACCCTTGGCAGGTGCAG 60.539 55.000 8.58 0.00 44.36 4.41
5503 5791 2.465860 TCGACCCGATTGTGATGTTT 57.534 45.000 0.00 0.00 0.00 2.83
5504 5792 2.289444 ACTTCGACCCGATTGTGATGTT 60.289 45.455 0.00 0.00 35.23 2.71
5505 5793 1.275291 ACTTCGACCCGATTGTGATGT 59.725 47.619 0.00 0.00 35.23 3.06
5515 5803 2.550978 AGCATTGATAACTTCGACCCG 58.449 47.619 0.00 0.00 0.00 5.28
5538 5826 2.169561 TGTTTTCTGGTGGGCTTTTTCC 59.830 45.455 0.00 0.00 0.00 3.13
5545 5833 0.609662 ATGCATGTTTTCTGGTGGGC 59.390 50.000 0.00 0.00 0.00 5.36
5551 5839 6.370442 ACATCCATCAAAATGCATGTTTTCTG 59.630 34.615 0.00 0.00 40.65 3.02
5573 5861 5.633830 ATCGAGCAAAAGTCATCAAACAT 57.366 34.783 0.00 0.00 0.00 2.71
5593 5881 8.034804 AGTAAATTGCAAAAGACCACCATAATC 58.965 33.333 1.71 0.00 0.00 1.75
5597 5885 5.304101 TGAGTAAATTGCAAAAGACCACCAT 59.696 36.000 1.71 0.00 0.00 3.55
5600 5888 4.982295 GGTGAGTAAATTGCAAAAGACCAC 59.018 41.667 1.71 10.92 0.00 4.16
5604 5892 5.735922 GCACAGGTGAGTAAATTGCAAAAGA 60.736 40.000 1.71 0.00 0.00 2.52
5607 5895 3.243704 GGCACAGGTGAGTAAATTGCAAA 60.244 43.478 1.71 0.00 0.00 3.68
5705 5993 2.024176 TTTCCGAGTTGCATAGGAGC 57.976 50.000 0.00 0.00 33.89 4.70
5739 6029 1.915614 CTAGTTGCCACTTGCCAGCG 61.916 60.000 0.00 0.00 40.16 5.18
5876 6167 0.106217 GGAGAGGAGAGGGACTGAGG 60.106 65.000 0.00 0.00 41.55 3.86
5877 6168 0.926293 AGGAGAGGAGAGGGACTGAG 59.074 60.000 0.00 0.00 41.55 3.35
5878 6169 0.923358 GAGGAGAGGAGAGGGACTGA 59.077 60.000 0.00 0.00 41.55 3.41
5879 6170 0.926293 AGAGGAGAGGAGAGGGACTG 59.074 60.000 0.00 0.00 41.55 3.51
5881 6172 0.185175 GGAGAGGAGAGGAGAGGGAC 59.815 65.000 0.00 0.00 0.00 4.46
5882 6173 0.253868 TGGAGAGGAGAGGAGAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
5883 6174 0.106217 GTGGAGAGGAGAGGAGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
5884 6175 0.926293 AGTGGAGAGGAGAGGAGAGG 59.074 60.000 0.00 0.00 0.00 3.69
5885 6176 1.133792 GGAGTGGAGAGGAGAGGAGAG 60.134 61.905 0.00 0.00 0.00 3.20
5886 6177 0.923358 GGAGTGGAGAGGAGAGGAGA 59.077 60.000 0.00 0.00 0.00 3.71
5887 6178 0.106217 GGGAGTGGAGAGGAGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
5888 6179 0.851332 TGGGAGTGGAGAGGAGAGGA 60.851 60.000 0.00 0.00 0.00 3.71
6057 6358 6.017523 GCTTCTTCTTGGGCAGTATTATCTTC 60.018 42.308 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.