Multiple sequence alignment - TraesCS3A01G213600

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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 TraesCS3A01G213600 chr3A 100.000 8259 0 0 1 8259 385532735 385524477 0.000000e+00 15252.0
1 TraesCS3A01G213600 chr3A 86.765 204 23 3 6982 7183 681462987 681462786 3.000000e-54 224.0
2 TraesCS3A01G213600 chr3A 93.204 103 7 0 562 664 737319339 737319237 1.440000e-32 152.0
3 TraesCS3A01G213600 chr3A 80.488 205 32 7 6983 7183 9378351 9378551 5.160000e-32 150.0
4 TraesCS3A01G213600 chr3D 95.622 3449 96 28 4848 8259 292370445 292373875 0.000000e+00 5481.0
5 TraesCS3A01G213600 chr3D 97.928 3041 47 9 1770 4801 292367407 292370440 0.000000e+00 5252.0
6 TraesCS3A01G213600 chr3D 96.118 979 28 7 761 1737 292366438 292367408 0.000000e+00 1589.0
7 TraesCS3A01G213600 chr3D 82.591 247 30 7 4551 4786 302947118 302947362 1.090000e-48 206.0
8 TraesCS3A01G213600 chr3D 100.000 31 0 0 6955 6985 447575038 447575008 3.220000e-04 58.4
9 TraesCS3A01G213600 chr3B 96.749 2861 70 8 1950 4801 386382488 386379642 0.000000e+00 4747.0
10 TraesCS3A01G213600 chr3B 96.448 2703 78 11 5452 8144 386378699 386376005 0.000000e+00 4444.0
11 TraesCS3A01G213600 chr3B 94.906 962 23 4 796 1737 386383731 386382776 0.000000e+00 1482.0
12 TraesCS3A01G213600 chr3B 96.791 561 17 1 4848 5407 386379637 386379077 0.000000e+00 935.0
13 TraesCS3A01G213600 chr3B 92.935 368 24 1 119 484 104420999 104420632 1.220000e-147 534.0
14 TraesCS3A01G213600 chr3B 84.211 361 43 8 367 714 747703442 747703801 1.030000e-88 339.0
15 TraesCS3A01G213600 chr3B 95.082 183 8 1 1770 1951 386382777 386382595 3.770000e-73 287.0
16 TraesCS3A01G213600 chr3B 82.927 246 30 6 4551 4786 418440312 418440069 2.340000e-50 211.0
17 TraesCS3A01G213600 chr3B 95.082 122 6 0 1 122 453510319 453510440 8.460000e-45 193.0
18 TraesCS3A01G213600 chr3B 82.990 194 31 2 6990 7183 236510412 236510603 3.060000e-39 174.0
19 TraesCS3A01G213600 chr3B 100.000 30 0 0 6956 6985 135670746 135670775 1.000000e-03 56.5
20 TraesCS3A01G213600 chr7D 89.447 597 52 6 119 707 105517699 105518292 0.000000e+00 743.0
21 TraesCS3A01G213600 chr2B 92.120 368 27 1 119 484 557103441 557103808 1.230000e-142 518.0
22 TraesCS3A01G213600 chr2B 80.488 205 31 7 6986 7183 697730807 697730605 1.860000e-31 148.0
23 TraesCS3A01G213600 chr2B 100.000 30 0 0 6954 6983 763960373 763960402 1.000000e-03 56.5
24 TraesCS3A01G213600 chr4A 93.361 241 16 0 2489 2729 109786856 109787096 2.830000e-94 357.0
25 TraesCS3A01G213600 chr4A 89.655 116 11 1 1 115 667688424 667688539 6.680000e-31 147.0
26 TraesCS3A01G213600 chr4A 85.593 118 10 5 7071 7187 42777437 42777326 5.240000e-22 117.0
27 TraesCS3A01G213600 chr6D 93.506 231 15 0 2489 2719 459190559 459190329 2.210000e-90 344.0
28 TraesCS3A01G213600 chr7B 87.213 305 34 4 362 661 60366457 60366153 7.940000e-90 342.0
29 TraesCS3A01G213600 chr5B 90.400 250 18 1 2485 2734 56071090 56071333 2.880000e-84 324.0
30 TraesCS3A01G213600 chr5B 89.720 107 10 1 7077 7183 190119477 190119372 1.450000e-27 135.0
31 TraesCS3A01G213600 chr6A 89.243 251 27 0 2486 2736 168022358 168022608 1.730000e-81 315.0
32 TraesCS3A01G213600 chr6A 82.283 254 36 8 2485 2735 438581177 438580930 2.340000e-50 211.0
33 TraesCS3A01G213600 chr7A 89.388 245 26 0 2489 2733 127913957 127913713 8.050000e-80 309.0
34 TraesCS3A01G213600 chr4B 80.161 373 48 15 362 709 59873841 59874212 1.060000e-63 255.0
35 TraesCS3A01G213600 chr6B 84.064 251 35 5 2484 2732 698828639 698828886 3.850000e-58 237.0
36 TraesCS3A01G213600 chr1D 82.353 204 30 5 6981 7183 474085153 474085351 1.100000e-38 172.0
37 TraesCS3A01G213600 chr4D 83.200 125 13 3 7065 7187 421340199 421340317 3.150000e-19 108.0
38 TraesCS3A01G213600 chr2D 100.000 30 0 0 6956 6985 22472138 22472109 1.000000e-03 56.5
39 TraesCS3A01G213600 chr2D 100.000 30 0 0 6956 6985 622228229 622228258 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G213600 chr3A 385524477 385532735 8258 True 15252.000000 15252 100.0000 1 8259 1 chr3A.!!$R1 8258
1 TraesCS3A01G213600 chr3D 292366438 292373875 7437 False 4107.333333 5481 96.5560 761 8259 3 chr3D.!!$F2 7498
2 TraesCS3A01G213600 chr3B 386376005 386383731 7726 True 2379.000000 4747 95.9952 796 8144 5 chr3B.!!$R3 7348
3 TraesCS3A01G213600 chr7D 105517699 105518292 593 False 743.000000 743 89.4470 119 707 1 chr7D.!!$F1 588

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
130 131 0.179108 ACGGCGCCTAAGCTTTCTAG 60.179 55.000 26.68 6.43 36.60 2.43 F
720 729 0.248289 TCTAGTTGTACAAGGCCGCC 59.752 55.000 8.98 0.00 0.00 6.13 F
748 757 0.385098 TACGATATTGCGACGGCTCG 60.385 55.000 0.00 0.00 43.28 5.03 F
932 941 0.822164 TCCCTTCGATTCGAACTCCC 59.178 55.000 17.08 0.00 41.05 4.30 F
2755 2898 0.464036 TGTCCGGGACATATGCTGAC 59.536 55.000 25.53 3.53 37.67 3.51 F
4638 4786 0.320771 CCTCCATACATAGGCGCCAC 60.321 60.000 31.54 1.27 0.00 5.01 F
4639 4787 0.681733 CTCCATACATAGGCGCCACT 59.318 55.000 31.54 12.06 0.00 4.00 F
5095 5244 1.002134 ATGTCCACCTTGCCTTCCG 60.002 57.895 0.00 0.00 0.00 4.30 F
5387 5536 2.050985 GTGTGCAAAGCGGTCTGC 60.051 61.111 5.84 5.84 46.98 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1377 0.934901 CGCGTGGTCATCATACTCCG 60.935 60.000 0.00 0.0 0.00 4.63 R
2132 2270 0.828022 TATGTGCCTAACCCTGTCGG 59.172 55.000 0.00 0.0 37.81 4.79 R
2378 2516 1.021202 GCAAAAACCCAGCCAAAACC 58.979 50.000 0.00 0.0 0.00 3.27 R
2840 2983 1.550072 TCATGCACGTTCATCTCCTCA 59.450 47.619 0.00 0.0 0.00 3.86 R
4656 4804 1.321474 TTCTTGCAGAAGCTGTTGGG 58.679 50.000 0.00 0.0 42.74 4.12 R
5811 6293 2.162608 CCACGCCATTTCGTTATTTCCA 59.837 45.455 0.00 0.0 41.21 3.53 R
5975 6457 5.177881 TGCATTCAAATGATTCAGTGCAAAC 59.822 36.000 6.91 0.0 38.27 2.93 R
6524 7008 5.791336 AGTAATATCGGCTCATTCTGACA 57.209 39.130 0.00 0.0 0.00 3.58 R
7365 7882 0.110104 GGGCCTGCATAAGATGAGCT 59.890 55.000 0.84 0.0 0.00 4.09 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
35 36 3.467374 TTTTTGTGGAGGCCAAACATC 57.533 42.857 5.01 0.00 34.18 3.06
36 37 2.380064 TTTGTGGAGGCCAAACATCT 57.620 45.000 5.01 0.00 34.18 2.90
37 38 1.909700 TTGTGGAGGCCAAACATCTC 58.090 50.000 5.01 0.00 34.18 2.75
38 39 0.770499 TGTGGAGGCCAAACATCTCA 59.230 50.000 5.01 0.00 34.18 3.27
39 40 1.144708 TGTGGAGGCCAAACATCTCAA 59.855 47.619 5.01 0.00 34.18 3.02
40 41 2.238521 GTGGAGGCCAAACATCTCAAA 58.761 47.619 5.01 0.00 34.18 2.69
41 42 2.229784 GTGGAGGCCAAACATCTCAAAG 59.770 50.000 5.01 0.00 34.18 2.77
42 43 2.158475 TGGAGGCCAAACATCTCAAAGT 60.158 45.455 5.01 0.00 0.00 2.66
43 44 3.073798 TGGAGGCCAAACATCTCAAAGTA 59.926 43.478 5.01 0.00 0.00 2.24
44 45 4.079253 GGAGGCCAAACATCTCAAAGTAA 58.921 43.478 5.01 0.00 0.00 2.24
45 46 4.522789 GGAGGCCAAACATCTCAAAGTAAA 59.477 41.667 5.01 0.00 0.00 2.01
46 47 5.185828 GGAGGCCAAACATCTCAAAGTAAAT 59.814 40.000 5.01 0.00 0.00 1.40
47 48 6.295292 GGAGGCCAAACATCTCAAAGTAAATT 60.295 38.462 5.01 0.00 0.00 1.82
48 49 7.093945 GGAGGCCAAACATCTCAAAGTAAATTA 60.094 37.037 5.01 0.00 0.00 1.40
49 50 8.189119 AGGCCAAACATCTCAAAGTAAATTAA 57.811 30.769 5.01 0.00 0.00 1.40
50 51 8.646900 AGGCCAAACATCTCAAAGTAAATTAAA 58.353 29.630 5.01 0.00 0.00 1.52
51 52 8.708742 GGCCAAACATCTCAAAGTAAATTAAAC 58.291 33.333 0.00 0.00 0.00 2.01
52 53 8.708742 GCCAAACATCTCAAAGTAAATTAAACC 58.291 33.333 0.00 0.00 0.00 3.27
53 54 8.911662 CCAAACATCTCAAAGTAAATTAAACCG 58.088 33.333 0.00 0.00 0.00 4.44
54 55 9.458374 CAAACATCTCAAAGTAAATTAAACCGT 57.542 29.630 0.00 0.00 0.00 4.83
55 56 9.458374 AAACATCTCAAAGTAAATTAAACCGTG 57.542 29.630 0.00 0.00 0.00 4.94
56 57 7.590279 ACATCTCAAAGTAAATTAAACCGTGG 58.410 34.615 0.00 0.00 0.00 4.94
57 58 7.229907 ACATCTCAAAGTAAATTAAACCGTGGT 59.770 33.333 0.00 0.00 0.00 4.16
58 59 8.723311 CATCTCAAAGTAAATTAAACCGTGGTA 58.277 33.333 0.00 0.00 0.00 3.25
59 60 8.851541 TCTCAAAGTAAATTAAACCGTGGTAT 57.148 30.769 0.00 0.00 0.00 2.73
60 61 9.287373 TCTCAAAGTAAATTAAACCGTGGTATT 57.713 29.630 0.00 0.00 0.00 1.89
61 62 9.902196 CTCAAAGTAAATTAAACCGTGGTATTT 57.098 29.630 0.00 0.00 0.00 1.40
62 63 9.680315 TCAAAGTAAATTAAACCGTGGTATTTG 57.320 29.630 8.02 0.00 0.00 2.32
63 64 8.917655 CAAAGTAAATTAAACCGTGGTATTTGG 58.082 33.333 8.02 0.00 0.00 3.28
64 65 7.999450 AGTAAATTAAACCGTGGTATTTGGA 57.001 32.000 8.02 0.00 0.00 3.53
65 66 8.406730 AGTAAATTAAACCGTGGTATTTGGAA 57.593 30.769 8.02 0.00 0.00 3.53
66 67 8.858094 AGTAAATTAAACCGTGGTATTTGGAAA 58.142 29.630 8.02 0.00 0.00 3.13
67 68 9.473640 GTAAATTAAACCGTGGTATTTGGAAAA 57.526 29.630 8.02 0.00 0.00 2.29
68 69 8.959705 AAATTAAACCGTGGTATTTGGAAAAA 57.040 26.923 0.00 0.00 0.00 1.94
69 70 7.949903 ATTAAACCGTGGTATTTGGAAAAAC 57.050 32.000 0.00 0.00 0.00 2.43
70 71 5.601583 AAACCGTGGTATTTGGAAAAACT 57.398 34.783 0.00 0.00 0.00 2.66
71 72 4.577834 ACCGTGGTATTTGGAAAAACTG 57.422 40.909 0.00 0.00 0.00 3.16
72 73 3.243602 ACCGTGGTATTTGGAAAAACTGC 60.244 43.478 0.00 0.00 0.00 4.40
73 74 2.977169 CGTGGTATTTGGAAAAACTGCG 59.023 45.455 0.00 0.00 0.00 5.18
74 75 3.313690 GTGGTATTTGGAAAAACTGCGG 58.686 45.455 0.00 0.00 0.00 5.69
75 76 2.959707 TGGTATTTGGAAAAACTGCGGT 59.040 40.909 0.00 0.00 0.00 5.68
76 77 4.023021 GTGGTATTTGGAAAAACTGCGGTA 60.023 41.667 0.00 0.00 0.00 4.02
77 78 4.767928 TGGTATTTGGAAAAACTGCGGTAT 59.232 37.500 0.00 0.00 0.00 2.73
78 79 5.244178 TGGTATTTGGAAAAACTGCGGTATT 59.756 36.000 0.00 0.00 0.00 1.89
79 80 6.160684 GGTATTTGGAAAAACTGCGGTATTT 58.839 36.000 0.00 0.00 0.00 1.40
80 81 6.647481 GGTATTTGGAAAAACTGCGGTATTTT 59.353 34.615 14.44 14.44 0.00 1.82
81 82 7.171848 GGTATTTGGAAAAACTGCGGTATTTTT 59.828 33.333 7.63 7.63 39.97 1.94
113 114 8.230486 ACTTAGAAAATGCAGAGTTATCAAACG 58.770 33.333 0.00 0.00 40.73 3.60
114 115 5.942872 AGAAAATGCAGAGTTATCAAACGG 58.057 37.500 0.00 0.00 40.73 4.44
115 116 3.764885 AATGCAGAGTTATCAAACGGC 57.235 42.857 0.00 0.00 40.73 5.68
116 117 1.075542 TGCAGAGTTATCAAACGGCG 58.924 50.000 4.80 4.80 40.73 6.46
117 118 0.247695 GCAGAGTTATCAAACGGCGC 60.248 55.000 6.90 0.00 40.73 6.53
130 131 0.179108 ACGGCGCCTAAGCTTTCTAG 60.179 55.000 26.68 6.43 36.60 2.43
137 138 3.118884 CGCCTAAGCTTTCTAGGGTTGTA 60.119 47.826 14.31 0.00 36.60 2.41
138 139 4.443034 CGCCTAAGCTTTCTAGGGTTGTAT 60.443 45.833 14.31 0.00 36.60 2.29
141 142 7.225011 GCCTAAGCTTTCTAGGGTTGTATTAT 58.775 38.462 14.31 0.00 35.50 1.28
173 174 5.019498 CGCTTGAAACCATTTCGTGTATAC 58.981 41.667 0.00 0.00 42.55 1.47
318 321 8.093659 TGTGTCTATTCATTCGATTTTTGACA 57.906 30.769 0.00 0.00 0.00 3.58
321 324 9.393249 TGTCTATTCATTCGATTTTTGACAAAC 57.607 29.630 0.00 0.00 0.00 2.93
328 331 9.179552 TCATTCGATTTTTGACAAACTATGTTG 57.820 29.630 0.00 0.00 44.12 3.33
351 354 6.133356 TGACCTTAAGTTGGACCATCTTTTT 58.867 36.000 20.32 2.38 0.00 1.94
359 362 5.012354 AGTTGGACCATCTTTTTCATGCATT 59.988 36.000 0.00 0.00 0.00 3.56
360 363 4.823157 TGGACCATCTTTTTCATGCATTG 58.177 39.130 0.00 0.00 0.00 2.82
418 421 7.167535 TGATCGGAATGATATCATTTAGCCAA 58.832 34.615 27.45 13.48 45.72 4.52
424 427 9.768662 GGAATGATATCATTTAGCCAAACAAAT 57.231 29.630 27.45 4.65 45.72 2.32
468 471 7.469043 GCAAGTTGCCTTATGTATGATTCATGA 60.469 37.037 17.36 0.00 37.42 3.07
500 503 4.406326 TGATACTCCCATAGTTTTGCCGTA 59.594 41.667 0.00 0.00 39.80 4.02
501 504 3.926058 ACTCCCATAGTTTTGCCGTAT 57.074 42.857 0.00 0.00 33.35 3.06
515 518 7.604927 AGTTTTGCCGTATTAATCAGACAACTA 59.395 33.333 0.00 0.00 0.00 2.24
520 523 6.418226 GCCGTATTAATCAGACAACTAGAGTG 59.582 42.308 0.00 0.00 0.00 3.51
521 524 7.481642 CCGTATTAATCAGACAACTAGAGTGT 58.518 38.462 0.00 0.00 0.00 3.55
523 526 7.968956 CGTATTAATCAGACAACTAGAGTGTGT 59.031 37.037 13.67 6.26 32.63 3.72
538 541 9.284968 ACTAGAGTGTGTTAAAATTATTGTGCT 57.715 29.630 0.00 0.00 0.00 4.40
600 603 2.010582 TTGTCTGTTGTTTGGCGGGC 62.011 55.000 0.00 0.00 0.00 6.13
603 606 1.591327 CTGTTGTTTGGCGGGCAAC 60.591 57.895 17.22 12.28 41.81 4.17
631 634 2.254051 CCGCGCCATCAAAACGTT 59.746 55.556 0.00 0.00 0.00 3.99
641 644 5.163794 CGCCATCAAAACGTTAATTCCTACT 60.164 40.000 0.00 0.00 0.00 2.57
652 655 9.662947 AACGTTAATTCCTACTAACTTAGCATT 57.337 29.630 0.00 0.00 0.00 3.56
663 666 3.560636 ACTTAGCATTACGGGCTTGAT 57.439 42.857 0.00 0.00 42.62 2.57
664 667 3.886123 ACTTAGCATTACGGGCTTGATT 58.114 40.909 0.00 0.00 42.62 2.57
669 677 2.165437 GCATTACGGGCTTGATTTTGGA 59.835 45.455 0.00 0.00 0.00 3.53
671 679 4.680440 GCATTACGGGCTTGATTTTGGAAT 60.680 41.667 0.00 0.00 0.00 3.01
676 684 1.548986 GCTTGATTTTGGAATCGGCG 58.451 50.000 0.00 0.00 43.75 6.46
707 716 0.674534 GGCACGATCCCGATCTAGTT 59.325 55.000 3.35 0.00 39.50 2.24
708 717 1.603172 GGCACGATCCCGATCTAGTTG 60.603 57.143 3.35 0.00 39.50 3.16
709 718 1.067212 GCACGATCCCGATCTAGTTGT 59.933 52.381 3.35 0.00 39.50 3.32
710 719 2.292569 GCACGATCCCGATCTAGTTGTA 59.707 50.000 3.35 0.00 39.50 2.41
711 720 3.852572 GCACGATCCCGATCTAGTTGTAC 60.853 52.174 3.35 0.00 39.50 2.90
712 721 3.314357 CACGATCCCGATCTAGTTGTACA 59.686 47.826 0.00 0.00 39.50 2.90
713 722 3.949754 ACGATCCCGATCTAGTTGTACAA 59.050 43.478 3.59 3.59 39.50 2.41
714 723 4.036498 ACGATCCCGATCTAGTTGTACAAG 59.964 45.833 8.98 0.00 39.50 3.16
715 724 4.556898 CGATCCCGATCTAGTTGTACAAGG 60.557 50.000 8.98 4.68 38.22 3.61
716 725 2.429610 TCCCGATCTAGTTGTACAAGGC 59.570 50.000 8.98 0.00 0.00 4.35
717 726 2.483188 CCCGATCTAGTTGTACAAGGCC 60.483 54.545 8.98 0.00 0.00 5.19
718 727 2.460918 CGATCTAGTTGTACAAGGCCG 58.539 52.381 8.98 3.75 0.00 6.13
719 728 2.202566 GATCTAGTTGTACAAGGCCGC 58.797 52.381 8.98 0.00 0.00 6.53
720 729 0.248289 TCTAGTTGTACAAGGCCGCC 59.752 55.000 8.98 0.00 0.00 6.13
721 730 1.079681 TAGTTGTACAAGGCCGCCG 60.080 57.895 8.98 0.00 0.00 6.46
722 731 2.510064 TAGTTGTACAAGGCCGCCGG 62.510 60.000 8.98 0.00 0.00 6.13
723 732 3.943691 TTGTACAAGGCCGCCGGT 61.944 61.111 4.45 13.33 0.00 5.28
724 733 3.887335 TTGTACAAGGCCGCCGGTC 62.887 63.158 0.00 0.00 0.00 4.79
744 753 0.782384 GCCTTACGATATTGCGACGG 59.218 55.000 0.00 0.00 34.83 4.79
745 754 0.782384 CCTTACGATATTGCGACGGC 59.218 55.000 0.00 0.00 40.52 5.68
746 755 1.602165 CCTTACGATATTGCGACGGCT 60.602 52.381 0.00 0.00 40.82 5.52
747 756 1.714460 CTTACGATATTGCGACGGCTC 59.286 52.381 0.00 0.00 40.82 4.70
748 757 0.385098 TACGATATTGCGACGGCTCG 60.385 55.000 0.00 0.00 43.28 5.03
749 758 2.365068 CGATATTGCGACGGCTCGG 61.365 63.158 0.00 0.00 40.53 4.63
750 759 2.658707 GATATTGCGACGGCTCGGC 61.659 63.158 0.00 0.00 40.53 5.54
751 760 3.439513 ATATTGCGACGGCTCGGCA 62.440 57.895 0.00 0.00 40.53 5.69
773 782 2.607668 GATGCATCGACCGACCGACA 62.608 60.000 11.68 0.00 41.70 4.35
932 941 0.822164 TCCCTTCGATTCGAACTCCC 59.178 55.000 17.08 0.00 41.05 4.30
1173 1183 3.518998 CTCCCGGAGATGCGTCGT 61.519 66.667 9.01 0.00 0.00 4.34
1373 1389 1.239347 CTCGAGGCGGAGTATGATGA 58.761 55.000 3.91 0.00 0.00 2.92
1694 1724 1.523938 GCAGGGCTGGGTTCGTATC 60.524 63.158 0.00 0.00 0.00 2.24
1737 1767 1.089920 GCACTTCCATCAGCGTGAAT 58.910 50.000 0.00 0.00 0.00 2.57
1738 1768 2.093500 AGCACTTCCATCAGCGTGAATA 60.093 45.455 0.00 0.00 0.00 1.75
1739 1769 2.874701 GCACTTCCATCAGCGTGAATAT 59.125 45.455 0.00 0.00 0.00 1.28
1740 1770 3.313526 GCACTTCCATCAGCGTGAATATT 59.686 43.478 0.00 0.00 0.00 1.28
1741 1771 4.553547 GCACTTCCATCAGCGTGAATATTC 60.554 45.833 8.60 8.60 0.00 1.75
1742 1772 4.024556 CACTTCCATCAGCGTGAATATTCC 60.025 45.833 12.90 3.77 0.00 3.01
1743 1773 3.836365 TCCATCAGCGTGAATATTCCA 57.164 42.857 12.90 0.00 0.00 3.53
1744 1774 3.466836 TCCATCAGCGTGAATATTCCAC 58.533 45.455 12.90 9.76 0.00 4.02
1765 1795 9.672086 TTCCACGAAATTAGACTTAATGTTTTG 57.328 29.630 0.00 0.00 30.00 2.44
1766 1796 7.806014 TCCACGAAATTAGACTTAATGTTTTGC 59.194 33.333 0.00 0.00 30.00 3.68
1767 1797 7.593273 CCACGAAATTAGACTTAATGTTTTGCA 59.407 33.333 0.00 0.00 30.00 4.08
1768 1798 8.963130 CACGAAATTAGACTTAATGTTTTGCAA 58.037 29.630 0.00 0.00 30.00 4.08
1769 1799 9.522804 ACGAAATTAGACTTAATGTTTTGCAAA 57.477 25.926 8.05 8.05 30.00 3.68
1794 1824 6.007703 ACAGGAAGCTCCAGTATCTATAGAC 58.992 44.000 4.10 0.00 39.61 2.59
1943 1973 7.664318 AGTGTTATTTAGTCCCAACCTTTACTG 59.336 37.037 0.00 0.00 0.00 2.74
2132 2270 4.201822 GCTGTCAGATTCGTTATGTTTCCC 60.202 45.833 3.32 0.00 0.00 3.97
2378 2516 3.243805 TGAACTTGTTGGCCATTGTCATG 60.244 43.478 6.09 8.88 0.00 3.07
2447 2590 1.470098 GTCTTGTTAGCATGCCACTGG 59.530 52.381 15.66 8.70 0.00 4.00
2554 2697 2.124507 TTGACCAGCTGTAGGGTGCC 62.125 60.000 13.81 0.00 41.62 5.01
2755 2898 0.464036 TGTCCGGGACATATGCTGAC 59.536 55.000 25.53 3.53 37.67 3.51
3080 3224 5.551760 AAGATAGCGACAACCAAAATCAG 57.448 39.130 0.00 0.00 0.00 2.90
3212 3356 8.665685 CAGTAAGTAACAAATATCTTGGGACAC 58.334 37.037 0.00 0.00 39.29 3.67
3315 3461 2.711922 AAGATCTCGCGAACCGGCT 61.712 57.895 11.33 0.20 37.59 5.52
3423 3569 1.732259 AGCTTAAATTCTGCGTCACCG 59.268 47.619 0.00 0.00 37.07 4.94
4029 4175 1.128188 AAGAAACTGGACGGGGCTCT 61.128 55.000 0.00 0.00 0.00 4.09
4141 4287 5.221441 GGTTTGCTTTCTTAACCATCCAACT 60.221 40.000 0.00 0.00 40.77 3.16
4270 4418 3.511934 GGTTCATCGCAGGTCCTATCTAT 59.488 47.826 0.00 0.00 0.00 1.98
4428 4576 1.615424 ACCTATGCCGGTGGGAGTT 60.615 57.895 1.90 0.00 35.52 3.01
4455 4603 2.893489 GGTTGCTCAATGGGAAGTTCTT 59.107 45.455 2.25 0.00 0.00 2.52
4547 4695 4.026744 AGCTCACAGCCACTTATCTTCTA 58.973 43.478 0.00 0.00 43.77 2.10
4565 4713 6.344500 TCTTCTATCTCTGCTCAATTTGGTC 58.656 40.000 0.00 0.00 0.00 4.02
4636 4784 0.905357 ATCCTCCATACATAGGCGCC 59.095 55.000 21.89 21.89 32.55 6.53
4637 4785 0.471022 TCCTCCATACATAGGCGCCA 60.471 55.000 31.54 15.56 32.55 5.69
4638 4786 0.320771 CCTCCATACATAGGCGCCAC 60.321 60.000 31.54 1.27 0.00 5.01
4639 4787 0.681733 CTCCATACATAGGCGCCACT 59.318 55.000 31.54 12.06 0.00 4.00
4641 4789 1.893137 TCCATACATAGGCGCCACTAG 59.107 52.381 31.54 17.63 0.00 2.57
4642 4790 1.618837 CCATACATAGGCGCCACTAGT 59.381 52.381 31.54 22.43 0.00 2.57
4643 4791 2.823747 CCATACATAGGCGCCACTAGTA 59.176 50.000 31.54 23.81 0.00 1.82
4644 4792 3.447586 CCATACATAGGCGCCACTAGTAT 59.552 47.826 31.54 24.86 0.00 2.12
4647 4795 2.558795 ACATAGGCGCCACTAGTATGAG 59.441 50.000 29.23 12.08 0.00 2.90
4656 4804 5.050972 GCGCCACTAGTATGAGAAACAATAC 60.051 44.000 0.00 0.00 0.00 1.89
4801 4949 4.941873 GCCACTAGTATTGCTGTTTAGGTT 59.058 41.667 0.00 0.00 0.00 3.50
4802 4950 5.064834 GCCACTAGTATTGCTGTTTAGGTTC 59.935 44.000 0.00 0.00 0.00 3.62
4803 4951 6.407202 CCACTAGTATTGCTGTTTAGGTTCT 58.593 40.000 0.00 0.00 0.00 3.01
4804 4952 6.879458 CCACTAGTATTGCTGTTTAGGTTCTT 59.121 38.462 0.00 0.00 0.00 2.52
4805 4953 7.148407 CCACTAGTATTGCTGTTTAGGTTCTTG 60.148 40.741 0.00 0.00 0.00 3.02
4806 4954 7.387948 CACTAGTATTGCTGTTTAGGTTCTTGT 59.612 37.037 0.00 0.00 0.00 3.16
4807 4955 6.803154 AGTATTGCTGTTTAGGTTCTTGTC 57.197 37.500 0.00 0.00 0.00 3.18
4808 4956 6.296026 AGTATTGCTGTTTAGGTTCTTGTCA 58.704 36.000 0.00 0.00 0.00 3.58
4809 4957 6.770785 AGTATTGCTGTTTAGGTTCTTGTCAA 59.229 34.615 0.00 0.00 0.00 3.18
4810 4958 5.499139 TTGCTGTTTAGGTTCTTGTCAAG 57.501 39.130 6.21 6.21 0.00 3.02
4811 4959 4.776349 TGCTGTTTAGGTTCTTGTCAAGA 58.224 39.130 11.36 11.36 35.26 3.02
4812 4960 5.376625 TGCTGTTTAGGTTCTTGTCAAGAT 58.623 37.500 15.95 4.40 37.38 2.40
4813 4961 5.827797 TGCTGTTTAGGTTCTTGTCAAGATT 59.172 36.000 15.95 7.82 37.38 2.40
4814 4962 6.017109 TGCTGTTTAGGTTCTTGTCAAGATTC 60.017 38.462 15.95 11.73 37.38 2.52
4815 4963 6.205658 GCTGTTTAGGTTCTTGTCAAGATTCT 59.794 38.462 15.95 16.64 37.38 2.40
4816 4964 7.572168 GCTGTTTAGGTTCTTGTCAAGATTCTC 60.572 40.741 15.95 7.38 37.38 2.87
4817 4965 7.509546 TGTTTAGGTTCTTGTCAAGATTCTCT 58.490 34.615 15.95 12.47 37.38 3.10
4818 4966 7.442364 TGTTTAGGTTCTTGTCAAGATTCTCTG 59.558 37.037 15.95 0.00 37.38 3.35
4819 4967 4.904241 AGGTTCTTGTCAAGATTCTCTGG 58.096 43.478 15.95 0.00 37.38 3.86
4820 4968 4.349342 AGGTTCTTGTCAAGATTCTCTGGT 59.651 41.667 15.95 0.00 37.38 4.00
4821 4969 5.066593 GGTTCTTGTCAAGATTCTCTGGTT 58.933 41.667 15.95 0.00 37.38 3.67
4822 4970 5.180304 GGTTCTTGTCAAGATTCTCTGGTTC 59.820 44.000 15.95 0.00 37.38 3.62
4823 4971 5.815233 TCTTGTCAAGATTCTCTGGTTCT 57.185 39.130 11.36 0.00 31.20 3.01
4824 4972 5.788450 TCTTGTCAAGATTCTCTGGTTCTC 58.212 41.667 11.36 0.00 31.20 2.87
4825 4973 5.305386 TCTTGTCAAGATTCTCTGGTTCTCA 59.695 40.000 11.36 0.00 31.20 3.27
4826 4974 5.144692 TGTCAAGATTCTCTGGTTCTCAG 57.855 43.478 0.00 0.00 44.68 3.35
4827 4975 3.932089 GTCAAGATTCTCTGGTTCTCAGC 59.068 47.826 0.00 0.00 43.06 4.26
4828 4976 3.580022 TCAAGATTCTCTGGTTCTCAGCA 59.420 43.478 0.00 0.00 43.06 4.41
4829 4977 4.040829 TCAAGATTCTCTGGTTCTCAGCAA 59.959 41.667 0.00 0.00 43.06 3.91
4830 4978 4.205065 AGATTCTCTGGTTCTCAGCAAG 57.795 45.455 0.00 0.00 43.06 4.01
4831 4979 3.837146 AGATTCTCTGGTTCTCAGCAAGA 59.163 43.478 0.00 0.00 43.06 3.02
4832 4980 4.470664 AGATTCTCTGGTTCTCAGCAAGAT 59.529 41.667 0.00 0.00 43.06 2.40
4833 4981 3.883830 TCTCTGGTTCTCAGCAAGATC 57.116 47.619 0.00 0.00 43.06 2.75
4834 4982 3.168292 TCTCTGGTTCTCAGCAAGATCA 58.832 45.455 0.00 0.00 43.06 2.92
4835 4983 3.773667 TCTCTGGTTCTCAGCAAGATCAT 59.226 43.478 0.00 0.00 43.06 2.45
4836 4984 4.121317 CTCTGGTTCTCAGCAAGATCATC 58.879 47.826 0.00 0.00 43.06 2.92
4837 4985 3.118482 TCTGGTTCTCAGCAAGATCATCC 60.118 47.826 0.00 0.00 43.06 3.51
4838 4986 2.842496 TGGTTCTCAGCAAGATCATCCT 59.158 45.455 0.00 0.00 32.82 3.24
4839 4987 3.118482 TGGTTCTCAGCAAGATCATCCTC 60.118 47.826 0.00 0.00 32.82 3.71
4840 4988 3.465871 GTTCTCAGCAAGATCATCCTCC 58.534 50.000 0.00 0.00 32.82 4.30
4841 4989 2.755686 TCTCAGCAAGATCATCCTCCA 58.244 47.619 0.00 0.00 0.00 3.86
4842 4990 3.315596 TCTCAGCAAGATCATCCTCCAT 58.684 45.455 0.00 0.00 0.00 3.41
4843 4991 4.486839 TCTCAGCAAGATCATCCTCCATA 58.513 43.478 0.00 0.00 0.00 2.74
4844 4992 4.282957 TCTCAGCAAGATCATCCTCCATAC 59.717 45.833 0.00 0.00 0.00 2.39
4845 4993 3.969312 TCAGCAAGATCATCCTCCATACA 59.031 43.478 0.00 0.00 0.00 2.29
4846 4994 4.596212 TCAGCAAGATCATCCTCCATACAT 59.404 41.667 0.00 0.00 0.00 2.29
5095 5244 1.002134 ATGTCCACCTTGCCTTCCG 60.002 57.895 0.00 0.00 0.00 4.30
5163 5312 3.700577 CGGGTTACGTACACATCGT 57.299 52.632 0.00 0.00 43.86 3.73
5387 5536 2.050985 GTGTGCAAAGCGGTCTGC 60.051 61.111 5.84 5.84 46.98 4.26
5489 5971 9.917129 GAAAAGATATACTAGCTTTCTAGGTCC 57.083 37.037 0.00 0.00 42.93 4.46
5627 6109 2.233271 CCAGCTGACACACCTCAAATT 58.767 47.619 17.39 0.00 0.00 1.82
5628 6110 2.624838 CCAGCTGACACACCTCAAATTT 59.375 45.455 17.39 0.00 0.00 1.82
5629 6111 3.820467 CCAGCTGACACACCTCAAATTTA 59.180 43.478 17.39 0.00 0.00 1.40
5642 6124 8.170730 ACACCTCAAATTTATTTTAGGACCTCT 58.829 33.333 17.91 0.00 41.48 3.69
5850 6332 6.481976 TGGCGTGGTATATTTCATTAGTCTTG 59.518 38.462 0.00 0.00 0.00 3.02
5975 6457 5.603170 AAATGGATCAAGCCCAAACATAG 57.397 39.130 0.00 0.00 37.22 2.23
6008 6490 9.181805 CTGAATCATTTGAATGCATGTATCTTC 57.818 33.333 0.00 0.00 36.36 2.87
6335 6819 7.891183 TTTGCTCTCTATCTTACAACACTTC 57.109 36.000 0.00 0.00 0.00 3.01
6524 7008 3.228188 TCACCTTTTGAATCAGCCACT 57.772 42.857 0.00 0.00 0.00 4.00
6632 7116 6.476378 CCCCTGTTCCAACCTGATAATATAG 58.524 44.000 0.00 0.00 0.00 1.31
6691 7175 4.540502 AGGTTCCTTCTAAGCATAAAGGGT 59.459 41.667 7.17 0.00 40.03 4.34
7365 7882 5.088680 TCTGCATACTCATTGTGACATGA 57.911 39.130 0.00 0.00 0.00 3.07
7559 8076 2.095461 GATGTTCCCCCTTTTCTCTGC 58.905 52.381 0.00 0.00 0.00 4.26
7570 8087 4.217334 CCCTTTTCTCTGCTTTTCTCCTTC 59.783 45.833 0.00 0.00 0.00 3.46
7594 8111 0.036732 TTCTATCCCCCGCATGCATC 59.963 55.000 19.57 0.00 0.00 3.91
7624 8141 5.653769 CCAATCATGTAAATCCTGACTTGGT 59.346 40.000 0.00 0.00 32.33 3.67
7626 8143 5.241403 TCATGTAAATCCTGACTTGGTGT 57.759 39.130 0.00 0.00 0.00 4.16
7708 8225 3.136626 GCTGTAGTTATCTGATGGGGGTT 59.863 47.826 0.00 0.00 0.00 4.11
7862 8379 2.948979 TGTTGCTTGGTCGAAATGTCTT 59.051 40.909 0.00 0.00 0.00 3.01
7886 8403 1.142667 TGTTGGTGGCATCTGAAGACA 59.857 47.619 0.00 0.00 0.00 3.41
8000 8518 4.637091 TCGAGTTTATGTCGGTATGAGTCA 59.363 41.667 0.00 0.00 38.02 3.41
8103 8623 2.290896 TGTGGGAATGTGGGTGAGATTC 60.291 50.000 0.00 0.00 34.27 2.52
8192 8712 2.210116 CTAAGTTGACGGCAGTGTTGT 58.790 47.619 0.00 0.00 0.00 3.32
8219 8740 3.063997 GTCACAACCAAGTCACTCAACTG 59.936 47.826 0.00 0.00 0.00 3.16
8220 8741 2.017049 ACAACCAAGTCACTCAACTGC 58.983 47.619 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.037549 AGATGTTTGGCCTCCACAAAAA 58.962 40.909 3.32 0.00 39.29 1.94
16 17 2.627699 GAGATGTTTGGCCTCCACAAAA 59.372 45.455 3.32 0.00 39.29 2.44
17 18 2.238521 GAGATGTTTGGCCTCCACAAA 58.761 47.619 3.32 0.00 35.62 2.83
18 19 1.144708 TGAGATGTTTGGCCTCCACAA 59.855 47.619 3.32 0.00 30.78 3.33
19 20 0.770499 TGAGATGTTTGGCCTCCACA 59.230 50.000 3.32 4.30 30.78 4.17
20 21 1.909700 TTGAGATGTTTGGCCTCCAC 58.090 50.000 3.32 0.00 30.78 4.02
21 22 2.158475 ACTTTGAGATGTTTGGCCTCCA 60.158 45.455 3.32 0.00 0.00 3.86
22 23 2.519013 ACTTTGAGATGTTTGGCCTCC 58.481 47.619 3.32 0.00 0.00 4.30
23 24 5.705609 TTTACTTTGAGATGTTTGGCCTC 57.294 39.130 3.32 0.00 0.00 4.70
24 25 6.670695 AATTTACTTTGAGATGTTTGGCCT 57.329 33.333 3.32 0.00 0.00 5.19
25 26 8.708742 GTTTAATTTACTTTGAGATGTTTGGCC 58.291 33.333 0.00 0.00 0.00 5.36
26 27 8.708742 GGTTTAATTTACTTTGAGATGTTTGGC 58.291 33.333 0.00 0.00 0.00 4.52
27 28 8.911662 CGGTTTAATTTACTTTGAGATGTTTGG 58.088 33.333 0.00 0.00 0.00 3.28
28 29 9.458374 ACGGTTTAATTTACTTTGAGATGTTTG 57.542 29.630 0.00 0.00 0.00 2.93
29 30 9.458374 CACGGTTTAATTTACTTTGAGATGTTT 57.542 29.630 0.00 0.00 0.00 2.83
30 31 8.079809 CCACGGTTTAATTTACTTTGAGATGTT 58.920 33.333 0.00 0.00 0.00 2.71
31 32 7.229907 ACCACGGTTTAATTTACTTTGAGATGT 59.770 33.333 0.00 0.00 0.00 3.06
32 33 7.590279 ACCACGGTTTAATTTACTTTGAGATG 58.410 34.615 0.00 0.00 0.00 2.90
33 34 7.754851 ACCACGGTTTAATTTACTTTGAGAT 57.245 32.000 0.00 0.00 0.00 2.75
34 35 8.851541 ATACCACGGTTTAATTTACTTTGAGA 57.148 30.769 0.00 0.00 0.00 3.27
35 36 9.902196 AAATACCACGGTTTAATTTACTTTGAG 57.098 29.630 0.00 0.00 0.00 3.02
36 37 9.680315 CAAATACCACGGTTTAATTTACTTTGA 57.320 29.630 0.00 0.00 0.00 2.69
37 38 8.917655 CCAAATACCACGGTTTAATTTACTTTG 58.082 33.333 0.00 0.00 0.00 2.77
38 39 8.858094 TCCAAATACCACGGTTTAATTTACTTT 58.142 29.630 0.00 0.00 0.00 2.66
39 40 8.406730 TCCAAATACCACGGTTTAATTTACTT 57.593 30.769 0.00 0.00 0.00 2.24
40 41 7.999450 TCCAAATACCACGGTTTAATTTACT 57.001 32.000 0.00 0.00 0.00 2.24
41 42 9.473640 TTTTCCAAATACCACGGTTTAATTTAC 57.526 29.630 0.00 0.00 0.00 2.01
43 44 8.828644 GTTTTTCCAAATACCACGGTTTAATTT 58.171 29.630 0.00 0.00 0.00 1.82
44 45 8.205512 AGTTTTTCCAAATACCACGGTTTAATT 58.794 29.630 0.00 0.00 0.00 1.40
45 46 7.654116 CAGTTTTTCCAAATACCACGGTTTAAT 59.346 33.333 0.00 0.00 0.00 1.40
46 47 6.979238 CAGTTTTTCCAAATACCACGGTTTAA 59.021 34.615 0.00 0.00 0.00 1.52
47 48 6.505272 CAGTTTTTCCAAATACCACGGTTTA 58.495 36.000 0.00 0.00 0.00 2.01
48 49 5.353111 CAGTTTTTCCAAATACCACGGTTT 58.647 37.500 0.00 0.00 0.00 3.27
49 50 4.738243 GCAGTTTTTCCAAATACCACGGTT 60.738 41.667 0.00 0.00 0.00 4.44
50 51 3.243602 GCAGTTTTTCCAAATACCACGGT 60.244 43.478 0.00 0.00 0.00 4.83
51 52 3.313690 GCAGTTTTTCCAAATACCACGG 58.686 45.455 0.00 0.00 0.00 4.94
52 53 2.977169 CGCAGTTTTTCCAAATACCACG 59.023 45.455 0.00 0.00 0.00 4.94
53 54 3.243602 ACCGCAGTTTTTCCAAATACCAC 60.244 43.478 0.00 0.00 0.00 4.16
54 55 2.959707 ACCGCAGTTTTTCCAAATACCA 59.040 40.909 0.00 0.00 0.00 3.25
55 56 3.653539 ACCGCAGTTTTTCCAAATACC 57.346 42.857 0.00 0.00 0.00 2.73
56 57 7.646446 AAAATACCGCAGTTTTTCCAAATAC 57.354 32.000 0.00 0.00 0.00 1.89
87 88 8.230486 CGTTTGATAACTCTGCATTTTCTAAGT 58.770 33.333 0.00 0.00 31.89 2.24
88 89 7.693951 CCGTTTGATAACTCTGCATTTTCTAAG 59.306 37.037 0.00 0.00 31.89 2.18
89 90 7.526608 CCGTTTGATAACTCTGCATTTTCTAA 58.473 34.615 0.00 0.00 31.89 2.10
90 91 6.403200 GCCGTTTGATAACTCTGCATTTTCTA 60.403 38.462 0.00 0.00 31.89 2.10
91 92 5.619981 GCCGTTTGATAACTCTGCATTTTCT 60.620 40.000 0.00 0.00 31.89 2.52
92 93 4.558860 GCCGTTTGATAACTCTGCATTTTC 59.441 41.667 0.00 0.00 31.89 2.29
93 94 4.485163 GCCGTTTGATAACTCTGCATTTT 58.515 39.130 0.00 0.00 31.89 1.82
94 95 3.426159 CGCCGTTTGATAACTCTGCATTT 60.426 43.478 0.00 0.00 31.89 2.32
95 96 2.095853 CGCCGTTTGATAACTCTGCATT 59.904 45.455 0.00 0.00 31.89 3.56
96 97 1.665679 CGCCGTTTGATAACTCTGCAT 59.334 47.619 0.00 0.00 31.89 3.96
97 98 1.075542 CGCCGTTTGATAACTCTGCA 58.924 50.000 0.00 0.00 31.89 4.41
98 99 0.247695 GCGCCGTTTGATAACTCTGC 60.248 55.000 0.00 0.00 31.89 4.26
99 100 0.373716 GGCGCCGTTTGATAACTCTG 59.626 55.000 12.58 0.00 31.89 3.35
100 101 0.249398 AGGCGCCGTTTGATAACTCT 59.751 50.000 23.20 0.00 31.89 3.24
101 102 1.930567 TAGGCGCCGTTTGATAACTC 58.069 50.000 23.20 0.00 31.89 3.01
102 103 2.277084 CTTAGGCGCCGTTTGATAACT 58.723 47.619 23.20 0.95 31.89 2.24
103 104 1.267882 GCTTAGGCGCCGTTTGATAAC 60.268 52.381 23.20 4.52 0.00 1.89
104 105 1.011333 GCTTAGGCGCCGTTTGATAA 58.989 50.000 23.20 12.06 0.00 1.75
105 106 0.177141 AGCTTAGGCGCCGTTTGATA 59.823 50.000 23.20 3.27 44.37 2.15
106 107 0.676782 AAGCTTAGGCGCCGTTTGAT 60.677 50.000 23.20 8.83 44.37 2.57
107 108 0.887387 AAAGCTTAGGCGCCGTTTGA 60.887 50.000 23.20 5.41 44.37 2.69
108 109 0.454452 GAAAGCTTAGGCGCCGTTTG 60.454 55.000 23.20 13.85 44.37 2.93
109 110 0.605589 AGAAAGCTTAGGCGCCGTTT 60.606 50.000 23.20 16.23 44.37 3.60
110 111 0.248289 TAGAAAGCTTAGGCGCCGTT 59.752 50.000 23.20 7.21 44.37 4.44
111 112 0.179108 CTAGAAAGCTTAGGCGCCGT 60.179 55.000 23.20 12.38 44.37 5.68
112 113 0.876342 CCTAGAAAGCTTAGGCGCCG 60.876 60.000 23.20 8.34 44.37 6.46
113 114 0.533085 CCCTAGAAAGCTTAGGCGCC 60.533 60.000 21.89 21.89 44.37 6.53
114 115 0.178301 ACCCTAGAAAGCTTAGGCGC 59.822 55.000 8.09 0.00 44.37 6.53
115 116 2.280628 CAACCCTAGAAAGCTTAGGCG 58.719 52.381 8.09 4.91 44.37 5.52
116 117 3.351794 ACAACCCTAGAAAGCTTAGGC 57.648 47.619 8.09 0.00 39.06 3.93
117 118 8.652290 AGATAATACAACCCTAGAAAGCTTAGG 58.348 37.037 0.00 2.59 0.00 2.69
130 131 4.755123 AGCGCAATGTAGATAATACAACCC 59.245 41.667 11.47 0.00 0.00 4.11
137 138 5.356751 TGGTTTCAAGCGCAATGTAGATAAT 59.643 36.000 11.47 0.00 0.00 1.28
138 139 4.697828 TGGTTTCAAGCGCAATGTAGATAA 59.302 37.500 11.47 0.00 0.00 1.75
141 142 2.499197 TGGTTTCAAGCGCAATGTAGA 58.501 42.857 11.47 0.00 0.00 2.59
173 174 8.657074 TCGATATTACAACTGAATAAACCCAG 57.343 34.615 0.00 0.00 36.53 4.45
231 234 3.951680 TGTGGTATACATGCTTCTCTCGA 59.048 43.478 5.01 0.00 33.42 4.04
233 236 5.011090 TGTGTGGTATACATGCTTCTCTC 57.989 43.478 5.01 0.00 42.24 3.20
245 248 4.764308 TGCTGCAAAAGAATGTGTGGTATA 59.236 37.500 0.00 0.00 0.00 1.47
246 249 3.573538 TGCTGCAAAAGAATGTGTGGTAT 59.426 39.130 0.00 0.00 0.00 2.73
295 298 9.393249 GTTTGTCAAAAATCGAATGAATAGACA 57.607 29.630 0.00 0.00 0.00 3.41
307 310 7.138736 AGGTCAACATAGTTTGTCAAAAATCG 58.861 34.615 0.00 0.00 37.68 3.34
318 321 6.489022 GGTCCAACTTAAGGTCAACATAGTTT 59.511 38.462 7.53 0.00 0.00 2.66
321 324 5.556915 TGGTCCAACTTAAGGTCAACATAG 58.443 41.667 7.53 0.00 0.00 2.23
328 331 6.264518 TGAAAAAGATGGTCCAACTTAAGGTC 59.735 38.462 14.28 9.84 0.00 3.85
351 354 6.993786 TTAAACGAAGGATACAATGCATGA 57.006 33.333 0.00 0.00 41.41 3.07
397 400 6.969366 TGTTTGGCTAAATGATATCATTCCG 58.031 36.000 27.04 21.17 45.06 4.30
418 421 6.491403 GCCACATAATCCCTCTATGATTTGTT 59.509 38.462 0.00 0.00 34.43 2.83
424 427 4.660303 ACTTGCCACATAATCCCTCTATGA 59.340 41.667 0.00 0.00 32.20 2.15
484 487 6.485313 TCTGATTAATACGGCAAAACTATGGG 59.515 38.462 0.00 0.00 0.00 4.00
486 489 7.915508 TGTCTGATTAATACGGCAAAACTATG 58.084 34.615 0.00 0.00 0.00 2.23
495 498 6.418226 CACTCTAGTTGTCTGATTAATACGGC 59.582 42.308 0.00 0.00 0.00 5.68
515 518 9.893305 GTAAGCACAATAATTTTAACACACTCT 57.107 29.630 0.00 0.00 0.00 3.24
523 526 8.392612 GCGGAGTAGTAAGCACAATAATTTTAA 58.607 33.333 0.00 0.00 0.00 1.52
532 535 4.081862 ACAATAGCGGAGTAGTAAGCACAA 60.082 41.667 0.00 0.00 0.00 3.33
584 587 1.754621 TTGCCCGCCAAACAACAGA 60.755 52.632 0.00 0.00 0.00 3.41
585 588 1.591327 GTTGCCCGCCAAACAACAG 60.591 57.895 0.00 0.00 42.50 3.16
631 634 8.362639 CCCGTAATGCTAAGTTAGTAGGAATTA 58.637 37.037 11.51 0.62 0.00 1.40
641 644 4.475051 TCAAGCCCGTAATGCTAAGTTA 57.525 40.909 0.00 0.00 38.34 2.24
652 655 2.680841 CGATTCCAAAATCAAGCCCGTA 59.319 45.455 0.00 0.00 41.22 4.02
663 666 2.034999 AGGGCGCCGATTCCAAAA 59.965 55.556 22.54 0.00 0.00 2.44
664 667 2.437716 GAGGGCGCCGATTCCAAA 60.438 61.111 22.54 0.00 0.00 3.28
683 691 4.812476 TCGGGATCGTGCCTTGCG 62.812 66.667 0.00 0.00 37.69 4.85
691 700 3.548770 TGTACAACTAGATCGGGATCGT 58.451 45.455 0.00 0.00 42.48 3.73
698 707 2.460918 CGGCCTTGTACAACTAGATCG 58.539 52.381 3.59 0.00 0.00 3.69
707 716 4.382320 GACCGGCGGCCTTGTACA 62.382 66.667 28.71 0.00 0.00 2.90
725 734 0.782384 CCGTCGCAATATCGTAAGGC 59.218 55.000 0.00 0.00 38.47 4.35
726 735 0.782384 GCCGTCGCAATATCGTAAGG 59.218 55.000 0.00 0.00 33.89 2.69
727 736 1.714460 GAGCCGTCGCAATATCGTAAG 59.286 52.381 0.00 0.00 37.52 2.34
728 737 1.762419 GAGCCGTCGCAATATCGTAA 58.238 50.000 0.00 0.00 37.52 3.18
729 738 0.385098 CGAGCCGTCGCAATATCGTA 60.385 55.000 0.00 0.00 39.88 3.43
730 739 1.657487 CGAGCCGTCGCAATATCGT 60.657 57.895 0.00 0.00 39.88 3.73
731 740 2.365068 CCGAGCCGTCGCAATATCG 61.365 63.158 0.00 0.00 45.41 2.92
732 741 2.658707 GCCGAGCCGTCGCAATATC 61.659 63.158 0.00 0.00 45.41 1.63
733 742 2.661866 GCCGAGCCGTCGCAATAT 60.662 61.111 0.00 0.00 45.41 1.28
734 743 4.136511 TGCCGAGCCGTCGCAATA 62.137 61.111 0.00 0.00 45.41 1.90
754 763 1.944676 GTCGGTCGGTCGATGCATC 60.945 63.158 17.10 17.10 41.40 3.91
755 764 2.104331 GTCGGTCGGTCGATGCAT 59.896 61.111 0.00 0.00 41.40 3.96
756 765 3.336715 CTGTCGGTCGGTCGATGCA 62.337 63.158 0.00 0.00 41.40 3.96
757 766 2.579787 CTGTCGGTCGGTCGATGC 60.580 66.667 4.54 0.00 41.40 3.91
758 767 1.226323 GTCTGTCGGTCGGTCGATG 60.226 63.158 4.54 0.00 41.40 3.84
759 768 2.404995 GGTCTGTCGGTCGGTCGAT 61.405 63.158 4.54 0.00 41.40 3.59
764 773 4.456253 CGTCGGTCTGTCGGTCGG 62.456 72.222 0.00 0.00 0.00 4.79
768 777 3.669036 CTCTGCGTCGGTCTGTCGG 62.669 68.421 0.00 0.00 0.00 4.79
773 782 2.492090 GATGCTCTGCGTCGGTCT 59.508 61.111 0.00 0.00 34.82 3.85
932 941 1.079256 TGTGGGGAGAGGTCAGAGG 59.921 63.158 0.00 0.00 0.00 3.69
1361 1377 0.934901 CGCGTGGTCATCATACTCCG 60.935 60.000 0.00 0.00 0.00 4.63
1457 1473 1.535444 TCTTCCCCGTCAGCCTCAA 60.535 57.895 0.00 0.00 0.00 3.02
1600 1616 2.833943 TCCAGAAACTATGAGCTGCAGA 59.166 45.455 20.43 0.00 0.00 4.26
1719 1749 4.024556 GGAATATTCACGCTGATGGAAGTG 60.025 45.833 17.07 0.00 36.06 3.16
1739 1769 9.672086 CAAAACATTAAGTCTAATTTCGTGGAA 57.328 29.630 0.00 0.00 0.00 3.53
1740 1770 7.806014 GCAAAACATTAAGTCTAATTTCGTGGA 59.194 33.333 0.00 0.00 0.00 4.02
1741 1771 7.593273 TGCAAAACATTAAGTCTAATTTCGTGG 59.407 33.333 0.00 0.00 0.00 4.94
1742 1772 8.500837 TGCAAAACATTAAGTCTAATTTCGTG 57.499 30.769 0.00 0.00 0.00 4.35
1743 1773 9.522804 TTTGCAAAACATTAAGTCTAATTTCGT 57.477 25.926 10.02 0.00 0.00 3.85
1760 1790 2.866156 GGAGCTTCCTGTTTTGCAAAAC 59.134 45.455 36.78 36.78 46.40 2.43
1761 1791 2.499289 TGGAGCTTCCTGTTTTGCAAAA 59.501 40.909 20.46 20.46 37.46 2.44
1762 1792 2.101249 CTGGAGCTTCCTGTTTTGCAAA 59.899 45.455 8.05 8.05 37.46 3.68
1763 1793 1.682854 CTGGAGCTTCCTGTTTTGCAA 59.317 47.619 0.00 0.00 37.46 4.08
1764 1794 1.321474 CTGGAGCTTCCTGTTTTGCA 58.679 50.000 0.00 0.00 37.46 4.08
1765 1795 1.322442 ACTGGAGCTTCCTGTTTTGC 58.678 50.000 8.31 0.00 44.87 3.68
1766 1796 4.583871 AGATACTGGAGCTTCCTGTTTTG 58.416 43.478 15.97 0.30 44.87 2.44
1767 1797 4.917906 AGATACTGGAGCTTCCTGTTTT 57.082 40.909 15.97 7.89 44.87 2.43
1768 1798 7.014808 GTCTATAGATACTGGAGCTTCCTGTTT 59.985 40.741 15.97 10.63 44.87 2.83
1769 1799 6.492087 GTCTATAGATACTGGAGCTTCCTGTT 59.508 42.308 15.97 7.72 44.87 3.16
1771 1801 5.417580 GGTCTATAGATACTGGAGCTTCCTG 59.582 48.000 5.57 0.00 40.80 3.86
1794 1824 9.491675 GATGCAGATGATAATCTATATCCTTGG 57.508 37.037 0.00 0.00 0.00 3.61
1847 1877 9.885934 AAAACCAAATTAAAACACAAACACTTC 57.114 25.926 0.00 0.00 0.00 3.01
1943 1973 6.540189 ACACTGCCATCATTGAACTAGTAATC 59.460 38.462 0.00 0.00 0.00 1.75
1980 2118 3.319122 ACAACCTCTTGAGGCACAATTTC 59.681 43.478 15.93 0.00 37.88 2.17
2132 2270 0.828022 TATGTGCCTAACCCTGTCGG 59.172 55.000 0.00 0.00 37.81 4.79
2378 2516 1.021202 GCAAAAACCCAGCCAAAACC 58.979 50.000 0.00 0.00 0.00 3.27
2447 2590 6.925165 CAGCCAACATTATCCAATATTCCAAC 59.075 38.462 0.00 0.00 0.00 3.77
2755 2898 8.531530 GCATTCGCCTAGTTTATAACAAAAATG 58.468 33.333 0.00 0.00 0.00 2.32
2840 2983 1.550072 TCATGCACGTTCATCTCCTCA 59.450 47.619 0.00 0.00 0.00 3.86
2921 3064 7.572523 TGCAGAGAATTAACCTCAATATTGG 57.427 36.000 15.36 2.97 33.25 3.16
3080 3224 0.591659 GCCGGTTCTGGTTTTCACTC 59.408 55.000 1.90 0.00 0.00 3.51
3259 3403 5.647658 AGTGATGACAAGAAAAGTGTGTGAA 59.352 36.000 0.00 0.00 0.00 3.18
3260 3404 5.185454 AGTGATGACAAGAAAAGTGTGTGA 58.815 37.500 0.00 0.00 0.00 3.58
3315 3461 3.129502 GCCGCTGCAGAATGAGCA 61.130 61.111 20.43 0.00 39.69 4.26
3384 3530 8.801715 TTAAGCTTGAATTGACAACATTCTTC 57.198 30.769 9.86 0.00 0.00 2.87
3423 3569 1.683385 GCACCAGAGGGATAAAATGGC 59.317 52.381 0.00 0.00 38.05 4.40
3856 4002 3.009363 TGCTGAGTTGGGATTCTCATTGA 59.991 43.478 0.00 0.00 39.48 2.57
4029 4175 1.638070 TGGGCTCCACCATACATGAAA 59.362 47.619 0.00 0.00 42.05 2.69
4166 4312 5.073965 AGGACCTTGGGTACATTTTACTCAA 59.926 40.000 1.53 0.00 39.47 3.02
4270 4418 3.039011 GGGTAAGTCAGGCCTAGAATCA 58.961 50.000 3.98 0.00 0.00 2.57
4547 4695 2.012673 GCGACCAAATTGAGCAGAGAT 58.987 47.619 0.00 0.00 0.00 2.75
4636 4784 7.822334 TGTTGGGTATTGTTTCTCATACTAGTG 59.178 37.037 5.39 0.00 0.00 2.74
4637 4785 7.913789 TGTTGGGTATTGTTTCTCATACTAGT 58.086 34.615 0.00 0.00 0.00 2.57
4638 4786 7.011482 GCTGTTGGGTATTGTTTCTCATACTAG 59.989 40.741 0.00 0.00 0.00 2.57
4639 4787 6.821665 GCTGTTGGGTATTGTTTCTCATACTA 59.178 38.462 0.00 0.00 0.00 1.82
4641 4789 5.648092 AGCTGTTGGGTATTGTTTCTCATAC 59.352 40.000 0.00 0.00 0.00 2.39
4642 4790 5.815581 AGCTGTTGGGTATTGTTTCTCATA 58.184 37.500 0.00 0.00 0.00 2.15
4643 4791 4.666512 AGCTGTTGGGTATTGTTTCTCAT 58.333 39.130 0.00 0.00 0.00 2.90
4644 4792 4.098914 AGCTGTTGGGTATTGTTTCTCA 57.901 40.909 0.00 0.00 0.00 3.27
4647 4795 4.798574 CAGAAGCTGTTGGGTATTGTTTC 58.201 43.478 0.00 0.00 0.00 2.78
4656 4804 1.321474 TTCTTGCAGAAGCTGTTGGG 58.679 50.000 0.00 0.00 42.74 4.12
4806 4954 9.157154 ATCTTGCTGAGAACCAGAGAATCTTGA 62.157 40.741 0.00 0.00 45.78 3.02
4807 4955 7.075520 ATCTTGCTGAGAACCAGAGAATCTTG 61.076 42.308 0.00 0.00 45.78 3.02
4808 4956 5.045724 ATCTTGCTGAGAACCAGAGAATCTT 60.046 40.000 0.00 0.00 45.78 2.40
4809 4957 4.470664 ATCTTGCTGAGAACCAGAGAATCT 59.529 41.667 0.00 0.00 45.78 2.40
4810 4958 4.199432 TCTTGCTGAGAACCAGAGAATC 57.801 45.455 0.00 0.00 45.78 2.52
4811 4959 4.224594 TGATCTTGCTGAGAACCAGAGAAT 59.775 41.667 0.00 0.00 45.78 2.40
4812 4960 3.580022 TGATCTTGCTGAGAACCAGAGAA 59.420 43.478 0.00 0.00 45.78 2.87
4813 4961 3.168292 TGATCTTGCTGAGAACCAGAGA 58.832 45.455 0.00 0.00 45.78 3.10
4814 4962 3.606595 TGATCTTGCTGAGAACCAGAG 57.393 47.619 0.00 0.00 45.78 3.35
4815 4963 3.118482 GGATGATCTTGCTGAGAACCAGA 60.118 47.826 0.00 0.00 45.78 3.86
4816 4964 3.118334 AGGATGATCTTGCTGAGAACCAG 60.118 47.826 1.61 0.00 45.67 4.00
4817 4965 2.842496 AGGATGATCTTGCTGAGAACCA 59.158 45.455 1.61 0.00 38.06 3.67
4818 4966 3.465871 GAGGATGATCTTGCTGAGAACC 58.534 50.000 7.38 0.00 38.06 3.62
4819 4967 3.118482 TGGAGGATGATCTTGCTGAGAAC 60.118 47.826 7.38 0.00 38.06 3.01
4820 4968 3.109928 TGGAGGATGATCTTGCTGAGAA 58.890 45.455 7.38 0.00 38.06 2.87
4821 4969 2.755686 TGGAGGATGATCTTGCTGAGA 58.244 47.619 7.38 0.00 39.13 3.27
4822 4970 3.773418 ATGGAGGATGATCTTGCTGAG 57.227 47.619 7.38 0.00 0.00 3.35
4823 4971 3.969312 TGTATGGAGGATGATCTTGCTGA 59.031 43.478 7.38 0.00 0.00 4.26
4824 4972 4.347360 TGTATGGAGGATGATCTTGCTG 57.653 45.455 7.38 0.00 0.00 4.41
4825 4973 4.907809 CATGTATGGAGGATGATCTTGCT 58.092 43.478 2.05 2.05 0.00 3.91
4840 4988 5.957798 ACAATCTTGACAAAGCCATGTATG 58.042 37.500 0.00 0.00 32.57 2.39
4841 4989 5.948162 AGACAATCTTGACAAAGCCATGTAT 59.052 36.000 0.00 0.00 32.57 2.29
4842 4990 5.316167 AGACAATCTTGACAAAGCCATGTA 58.684 37.500 0.00 0.00 32.57 2.29
4843 4991 4.147321 AGACAATCTTGACAAAGCCATGT 58.853 39.130 0.00 0.00 35.90 3.21
4844 4992 4.670992 CGAGACAATCTTGACAAAGCCATG 60.671 45.833 0.00 0.00 33.06 3.66
4845 4993 3.438087 CGAGACAATCTTGACAAAGCCAT 59.562 43.478 0.00 0.00 33.06 4.40
4846 4994 2.807967 CGAGACAATCTTGACAAAGCCA 59.192 45.455 0.00 0.00 33.06 4.75
5030 5178 2.383527 GGTGAGTCGCTTGCGGAAG 61.384 63.158 12.94 12.94 0.00 3.46
5031 5179 2.357034 GGTGAGTCGCTTGCGGAA 60.357 61.111 15.10 0.00 0.00 4.30
5156 5305 2.471607 GCACACGAGCACGATGTG 59.528 61.111 23.66 23.66 45.00 3.21
5157 5306 2.738521 GGCACACGAGCACGATGT 60.739 61.111 11.40 8.16 42.66 3.06
5368 5517 2.203015 AGACCGCTTTGCACACGT 60.203 55.556 0.00 0.00 0.00 4.49
5373 5522 2.979676 CTGGCAGACCGCTTTGCA 60.980 61.111 9.42 0.00 42.02 4.08
5387 5536 5.586643 GGTTATTTAGCTGGAAGTTCTCTGG 59.413 44.000 2.25 0.00 35.30 3.86
5489 5971 9.076596 GCCATGTAAGCTCTATTTTGTAAAAAG 57.923 33.333 0.00 0.00 0.00 2.27
5811 6293 2.162608 CCACGCCATTTCGTTATTTCCA 59.837 45.455 0.00 0.00 41.21 3.53
5850 6332 6.648725 AACAGACAGAACGATAAACATAGC 57.351 37.500 0.00 0.00 0.00 2.97
5881 6363 7.768582 ACAAACATCATTTCATAGACGGTGATA 59.231 33.333 0.00 0.00 0.00 2.15
5975 6457 5.177881 TGCATTCAAATGATTCAGTGCAAAC 59.822 36.000 6.91 0.00 38.27 2.93
6008 6490 7.116090 CAGATGTAGTCAAAAGTGAGAGACAAG 59.884 40.741 0.00 0.00 33.27 3.16
6277 6761 6.706270 ACAAATATTATAACAGGTGGCTCTCG 59.294 38.462 0.00 0.00 0.00 4.04
6524 7008 5.791336 AGTAATATCGGCTCATTCTGACA 57.209 39.130 0.00 0.00 0.00 3.58
6537 7021 6.255670 TGCACAGCTAACAAGAAGTAATATCG 59.744 38.462 0.00 0.00 0.00 2.92
6632 7116 9.956720 AAGCAACAGATAAATAGTGAAATATGC 57.043 29.630 0.00 0.00 0.00 3.14
6945 7434 8.446489 TCAATTATTTTGAAACGTGCATAGTG 57.554 30.769 0.00 0.00 0.00 2.74
7365 7882 0.110104 GGGCCTGCATAAGATGAGCT 59.890 55.000 0.84 0.00 0.00 4.09
7528 8045 0.902531 GGGAACATCTCGGAGGAACA 59.097 55.000 4.96 0.00 0.00 3.18
7559 8076 5.432645 GGATAGAAGGGTGAAGGAGAAAAG 58.567 45.833 0.00 0.00 0.00 2.27
7570 8087 1.418908 ATGCGGGGGATAGAAGGGTG 61.419 60.000 0.00 0.00 0.00 4.61
7594 8111 6.206243 GTCAGGATTTACATGATTGGGAGATG 59.794 42.308 0.00 0.00 41.30 2.90
7624 8141 6.215841 TCATAGTTAACCCAGGTATCCAAACA 59.784 38.462 0.88 0.00 0.00 2.83
7626 8143 6.894735 TCATAGTTAACCCAGGTATCCAAA 57.105 37.500 0.88 0.00 0.00 3.28
7708 8225 1.302271 CCTGCTCTGCTGTGAAGCA 60.302 57.895 0.00 0.00 43.22 3.91
7833 8350 2.614983 TCGACCAAGCAACACCTAAAAC 59.385 45.455 0.00 0.00 0.00 2.43
7862 8379 4.458989 GTCTTCAGATGCCACCAACAAATA 59.541 41.667 0.00 0.00 0.00 1.40
7886 8403 2.613977 CCTCTCTTCAACAACCGCTCAT 60.614 50.000 0.00 0.00 0.00 2.90
8000 8518 8.645902 TGGAGGATAGATAGATAGGTACATCT 57.354 38.462 0.00 0.00 38.76 2.90
8103 8623 3.058016 ACTCATCAGGCACAAAATTGACG 60.058 43.478 0.00 0.00 0.00 4.35
8192 8712 2.766263 AGTGACTTGGTTGTGACTGAGA 59.234 45.455 0.00 0.00 33.39 3.27
8219 8740 2.284417 CCAACTAAACGATTAGGCGAGC 59.716 50.000 15.81 0.00 42.39 5.03
8220 8741 3.550678 GTCCAACTAAACGATTAGGCGAG 59.449 47.826 15.81 3.34 42.39 5.03


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

AutoCloner maintained by Alex Coulton.