Multiple sequence alignment - TraesCS3D01G114600

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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 TraesCS3D01G114600 chr3D 100.000 7205 0 0 1 7205 68082891 68075687 0.000000e+00 13306.0
1 TraesCS3D01G114600 chr3D 85.539 408 48 8 6703 7104 549058931 549059333 4.020000e-112 416.0
2 TraesCS3D01G114600 chr3D 82.171 258 32 5 6855 7098 316166000 316166257 7.320000e-50 209.0
3 TraesCS3D01G114600 chr3D 91.358 81 5 2 2894 2973 68079919 68079998 7.640000e-20 110.0
4 TraesCS3D01G114600 chr3B 92.939 3484 141 37 2977 6420 113916618 113920036 0.000000e+00 4974.0
5 TraesCS3D01G114600 chr3B 89.668 1897 105 27 371 2214 113913657 113915515 0.000000e+00 2333.0
6 TraesCS3D01G114600 chr3B 93.050 705 20 5 2214 2916 113915552 113916229 0.000000e+00 1003.0
7 TraesCS3D01G114600 chr3B 91.185 658 35 10 6562 7205 113920330 113920978 0.000000e+00 872.0
8 TraesCS3D01G114600 chr3B 92.971 313 17 3 67 375 113913302 113913613 1.100000e-122 451.0
9 TraesCS3D01G114600 chr3B 100.000 34 0 0 736 769 643984733 643984766 6.030000e-06 63.9
10 TraesCS3D01G114600 chr3A 92.133 2898 117 40 3581 6420 80090964 80093808 0.000000e+00 3986.0
11 TraesCS3D01G114600 chr3A 95.669 1016 35 3 2214 3226 80089463 80090472 0.000000e+00 1624.0
12 TraesCS3D01G114600 chr3A 92.207 1065 52 9 1176 2214 80088367 80089426 0.000000e+00 1478.0
13 TraesCS3D01G114600 chr3A 93.231 650 35 7 6562 7205 80094044 80094690 0.000000e+00 948.0
14 TraesCS3D01G114600 chr3A 95.567 406 14 3 3223 3626 80090635 80091038 0.000000e+00 647.0
15 TraesCS3D01G114600 chr3A 94.624 372 18 2 5 375 80086796 80087166 6.270000e-160 575.0
16 TraesCS3D01G114600 chr3A 89.376 433 19 15 662 1077 80087607 80088029 2.980000e-143 520.0
17 TraesCS3D01G114600 chr3A 90.196 255 15 5 410 660 80087241 80087489 2.510000e-84 324.0
18 TraesCS3D01G114600 chr3A 92.537 134 7 2 6429 6561 80093882 80094013 9.540000e-44 189.0
19 TraesCS3D01G114600 chr3A 92.593 81 4 2 2894 2973 80090218 80090139 1.640000e-21 115.0
20 TraesCS3D01G114600 chr7D 87.252 353 34 9 6703 7045 69595089 69595440 6.780000e-105 392.0
21 TraesCS3D01G114600 chr7D 82.946 129 21 1 1633 1761 197183727 197183600 1.640000e-21 115.0
22 TraesCS3D01G114600 chr7D 89.796 49 5 0 1776 1824 501513319 501513367 6.030000e-06 63.9
23 TraesCS3D01G114600 chr6B 80.723 332 42 9 6729 7045 594448188 594447864 9.340000e-59 239.0
24 TraesCS3D01G114600 chr4A 84.513 226 20 3 6704 6918 29460079 29460300 7.320000e-50 209.0
25 TraesCS3D01G114600 chr2D 85.606 132 19 0 5838 5969 291862434 291862565 9.750000e-29 139.0
26 TraesCS3D01G114600 chr2D 88.750 80 4 4 2897 2971 181308287 181308366 7.700000e-15 93.5
27 TraesCS3D01G114600 chr2B 85.606 132 19 0 5838 5969 368312223 368312354 9.750000e-29 139.0
28 TraesCS3D01G114600 chr2B 86.905 84 7 2 2889 2970 357918832 357918913 2.770000e-14 91.6
29 TraesCS3D01G114600 chr2B 94.595 37 2 0 5457 5493 798117778 798117814 2.810000e-04 58.4
30 TraesCS3D01G114600 chr2A 85.606 132 19 0 5838 5969 367588030 367588161 9.750000e-29 139.0
31 TraesCS3D01G114600 chr5D 80.220 182 31 3 5327 5506 502028900 502028722 1.630000e-26 132.0
32 TraesCS3D01G114600 chr5B 80.220 182 31 3 5327 5506 625966889 625966711 1.630000e-26 132.0
33 TraesCS3D01G114600 chr5B 89.216 102 4 7 3440 3541 17982599 17982693 3.530000e-23 121.0
34 TraesCS3D01G114600 chr4B 89.524 105 8 3 3448 3549 544445377 544445273 5.870000e-26 130.0
35 TraesCS3D01G114600 chr4D 89.320 103 5 4 3448 3544 14609699 14609597 2.730000e-24 124.0
36 TraesCS3D01G114600 chr5A 89.691 97 6 4 3448 3541 375289117 375289212 3.530000e-23 121.0
37 TraesCS3D01G114600 chr7B 89.247 93 4 2 3448 3540 567598577 567598663 2.120000e-20 111.0
38 TraesCS3D01G114600 chr7B 88.172 93 8 1 3449 3541 695281322 695281411 2.750000e-19 108.0
39 TraesCS3D01G114600 chr6A 90.698 86 5 1 2891 2973 39440961 39440876 2.120000e-20 111.0
40 TraesCS3D01G114600 chr6A 91.358 81 4 1 2893 2970 39440875 39440955 2.750000e-19 108.0
41 TraesCS3D01G114600 chr1D 87.000 100 5 4 3445 3541 346867608 346867702 9.890000e-19 106.0
42 TraesCS3D01G114600 chrUn 85.577 104 8 5 3444 3547 46240435 46240339 1.280000e-17 102.0
43 TraesCS3D01G114600 chr7A 78.992 119 23 2 5388 5506 66456365 66456249 5.990000e-11 80.5
44 TraesCS3D01G114600 chr7A 85.333 75 6 3 2896 2970 492257265 492257334 1.000000e-08 73.1
45 TraesCS3D01G114600 chr6D 89.831 59 3 3 2913 2971 275674461 275674406 1.000000e-08 73.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G114600 chr3D 68075687 68082891 7204 True 13306.000000 13306 100.000000 1 7205 1 chr3D.!!$R1 7204
1 TraesCS3D01G114600 chr3B 113913302 113920978 7676 False 1926.600000 4974 91.962600 67 7205 5 chr3B.!!$F2 7138
2 TraesCS3D01G114600 chr3A 80086796 80094690 7894 False 1143.444444 3986 92.837778 5 7205 9 chr3A.!!$F1 7200

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
170 171 2.270352 TTCATGTCCGCCAAACTTCT 57.730 45.000 0.00 0.0 0.00 2.85 F
1429 1878 1.081442 GTAGCTTTTGTGGCGGTGC 60.081 57.895 0.00 0.0 34.52 5.01 F
1785 2234 0.685458 CCTGGGATTTCCTTGCTGGG 60.685 60.000 0.00 0.0 36.20 4.45 F
2253 2758 1.126113 CGCGTGTGATTAAGGTGTGTC 59.874 52.381 0.00 0.0 0.00 3.67 F
2342 2847 1.434696 GGGCGATGCAGACAAATGG 59.565 57.895 0.00 0.0 0.00 3.16 F
2522 3027 1.682854 CCGACATTGAAATGGGGATGG 59.317 52.381 7.87 0.0 40.70 3.51 F
3946 4997 1.869132 GAGTGCATGCATCGCTTATGA 59.131 47.619 25.64 0.0 37.86 2.15 F
4744 5823 0.246086 GCTCTGCTGTAGCTCTGTGT 59.754 55.000 5.38 0.0 42.66 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1769 2218 1.000866 AGCCCAGCAAGGAAATCCC 59.999 57.895 0.00 0.00 41.22 3.85 R
3153 3997 1.133407 CTGAGTTGACCTAGACTCGGC 59.867 57.143 5.47 0.00 44.03 5.54 R
3270 4283 2.295349 ACAGCTCAGCACAAAATGGAAG 59.705 45.455 0.00 0.00 0.00 3.46 R
3830 4881 1.027357 CAAGCCTTCACAGCACAACT 58.973 50.000 0.00 0.00 0.00 3.16 R
4100 5151 1.139853 GGGCTCCACTGATTCTGTAGG 59.860 57.143 0.00 1.88 0.00 3.18 R
4260 5311 9.171877 GACTCAAGACTTGAATAGATTCCAAAT 57.828 33.333 18.26 0.00 39.58 2.32 R
5085 6175 0.108585 GTGGCCAAGGTCAAGACTCA 59.891 55.000 7.24 0.00 0.00 3.41 R
6512 7823 0.038159 AGGACTTCTGCCGACTTTCG 60.038 55.000 0.00 0.00 40.07 3.46 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
40 41 9.193133 GAGAGAAAAGGTTTATTTTTACAAGCC 57.807 33.333 0.00 0.00 32.62 4.35
50 51 7.504926 TTATTTTTACAAGCCCCTCTCTAGA 57.495 36.000 0.00 0.00 0.00 2.43
59 60 2.392662 CCCCTCTCTAGACATCTTGCA 58.607 52.381 0.00 0.00 0.00 4.08
155 156 5.401550 CGTTGCTCAACCAACATATTTCAT 58.598 37.500 7.12 0.00 44.01 2.57
170 171 2.270352 TTCATGTCCGCCAAACTTCT 57.730 45.000 0.00 0.00 0.00 2.85
213 215 3.056393 AGCAATTGCAAGCTAAAGCATCA 60.056 39.130 30.89 0.00 43.49 3.07
255 257 3.069872 TGTTTGGTTGAGATGCAGCAAAT 59.930 39.130 4.07 0.00 41.17 2.32
317 322 8.546083 AAAATGTGGCCATAAGGTTATAATCA 57.454 30.769 9.72 0.00 37.19 2.57
323 328 5.817816 GGCCATAAGGTTATAATCATCTCCG 59.182 44.000 0.00 0.00 37.19 4.63
532 589 9.535878 GTAGATTAGGAGGTTGAACTTAGAATG 57.464 37.037 0.00 0.00 0.00 2.67
533 590 7.051000 AGATTAGGAGGTTGAACTTAGAATGC 58.949 38.462 0.00 0.00 0.00 3.56
559 616 5.540400 TCCTCCGTATTTGTATACAAGGG 57.460 43.478 17.36 16.22 38.81 3.95
562 619 5.298989 TCCGTATTTGTATACAAGGGCAT 57.701 39.130 17.36 11.16 37.12 4.40
563 620 5.302360 TCCGTATTTGTATACAAGGGCATC 58.698 41.667 17.36 6.76 37.12 3.91
701 878 5.622346 ACCTACTCCCTTCATTCTGAATC 57.378 43.478 0.00 0.00 35.59 2.52
790 968 5.766150 TCACACGAAAAATGAAATGACCT 57.234 34.783 0.00 0.00 0.00 3.85
812 990 7.238710 ACCTTTGTATAACAAAATGGAGGAGT 58.761 34.615 14.32 0.00 46.15 3.85
813 991 8.387813 ACCTTTGTATAACAAAATGGAGGAGTA 58.612 33.333 14.32 0.00 46.15 2.59
814 992 8.674607 CCTTTGTATAACAAAATGGAGGAGTAC 58.325 37.037 6.67 0.00 46.15 2.73
837 1015 9.382244 GTACTATGATTTTGTGCGATATTTTCC 57.618 33.333 0.00 0.00 0.00 3.13
841 1019 6.329496 TGATTTTGTGCGATATTTTCCCTTC 58.671 36.000 0.00 0.00 0.00 3.46
976 1154 2.374184 CTCGACTCTCCTGTCCAATCT 58.626 52.381 0.00 0.00 33.70 2.40
1009 1205 4.079253 CTCTTCTCTACATAGCCTCCCTC 58.921 52.174 0.00 0.00 0.00 4.30
1184 1619 2.513897 GCTCCCCCGATTCGGTTG 60.514 66.667 22.83 13.53 46.80 3.77
1185 1620 2.987125 CTCCCCCGATTCGGTTGT 59.013 61.111 22.83 0.00 46.80 3.32
1207 1645 4.901197 TTTTTGGGGAATTTCTTAGGCC 57.099 40.909 0.00 0.00 0.00 5.19
1233 1671 4.020928 AGCTCTCGATTCGACCTAGATAGA 60.021 45.833 4.29 0.00 0.00 1.98
1287 1736 4.643387 GGGGCACGAGCAGTTGGT 62.643 66.667 7.26 0.00 44.61 3.67
1360 1809 2.787680 CGAATTCCGTGTCCGTAGATTC 59.212 50.000 0.00 0.00 0.00 2.52
1383 1832 1.392168 TGTCCGATGTTCGCGAAAATC 59.608 47.619 32.93 32.93 38.82 2.17
1389 1838 1.153353 TGTTCGCGAAAATCTGGGTC 58.847 50.000 25.24 8.26 0.00 4.46
1429 1878 1.081442 GTAGCTTTTGTGGCGGTGC 60.081 57.895 0.00 0.00 34.52 5.01
1442 1891 2.669569 GGTGCGCTCACATGGTGT 60.670 61.111 9.73 0.00 44.87 4.16
1691 2140 4.641954 CTCATGCATTTACTCGTGTTGAC 58.358 43.478 0.00 0.00 0.00 3.18
1713 2162 2.844839 AGCCCTGACGATAGCCCC 60.845 66.667 0.00 0.00 42.67 5.80
1737 2186 3.067883 GGGACGGAGGTTAGTTGATCTAC 59.932 52.174 0.00 0.00 0.00 2.59
1757 2206 3.576648 ACGTGTAGTTGCTAGCTCTTTC 58.423 45.455 17.23 10.93 0.00 2.62
1764 2213 7.492669 GTGTAGTTGCTAGCTCTTTCAATGATA 59.507 37.037 17.23 0.00 0.00 2.15
1769 2218 6.228995 TGCTAGCTCTTTCAATGATATCCTG 58.771 40.000 17.23 0.00 0.00 3.86
1771 2220 4.983053 AGCTCTTTCAATGATATCCTGGG 58.017 43.478 0.00 0.00 0.00 4.45
1785 2234 0.685458 CCTGGGATTTCCTTGCTGGG 60.685 60.000 0.00 0.00 36.20 4.45
1821 2270 5.465935 TGGTTGTTCTTGAACTGTTGAAAC 58.534 37.500 13.65 8.63 0.00 2.78
1855 2304 2.344950 CTGCACTTGAGGTCTCATGTC 58.655 52.381 14.14 10.74 43.35 3.06
1890 2344 2.549329 TCATTTACATATGCTGCTGCCG 59.451 45.455 13.47 1.78 38.71 5.69
2015 2481 6.946340 TGTCACCTCACTGTCAAATACATAT 58.054 36.000 0.00 0.00 37.50 1.78
2021 2487 9.770097 ACCTCACTGTCAAATACATATTATCTG 57.230 33.333 0.00 0.00 37.50 2.90
2200 2668 7.598493 GCAATTATTAATGTTGGTGTCACTGTT 59.402 33.333 2.35 0.00 0.00 3.16
2253 2758 1.126113 CGCGTGTGATTAAGGTGTGTC 59.874 52.381 0.00 0.00 0.00 3.67
2337 2842 2.741985 CAACGGGCGATGCAGACA 60.742 61.111 0.00 0.00 0.00 3.41
2342 2847 1.434696 GGGCGATGCAGACAAATGG 59.565 57.895 0.00 0.00 0.00 3.16
2424 2929 5.984926 CACCAAAGATTAGCAATGTGTTTGT 59.015 36.000 0.00 0.00 37.65 2.83
2460 2965 6.014584 TGCATATCTCCTGTCGTAATATTGGT 60.015 38.462 0.00 0.00 0.00 3.67
2509 3014 1.846124 AGGGGTGTGGTCCGACATT 60.846 57.895 0.00 0.00 0.00 2.71
2522 3027 1.682854 CCGACATTGAAATGGGGATGG 59.317 52.381 7.87 0.00 40.70 3.51
2564 3069 3.842436 CCTCATGATGGATACCCTGATGA 59.158 47.826 0.00 0.00 0.00 2.92
2641 3146 7.343574 TGGAATAGTGTCTGCCTACTGTAATAA 59.656 37.037 0.00 0.00 0.00 1.40
2923 3430 3.558321 CCTCCGTCCCAAAATGTAAGACA 60.558 47.826 0.00 0.00 0.00 3.41
3089 3933 4.067192 GCTTAACGACTAGGGTCCAAAAA 58.933 43.478 0.00 0.00 39.15 1.94
3153 3997 9.831737 ACAGATCGAAAATACAAAATTTGAGAG 57.168 29.630 13.19 0.00 0.00 3.20
3155 3999 7.970614 AGATCGAAAATACAAAATTTGAGAGCC 59.029 33.333 13.19 0.00 0.00 4.70
3190 4037 3.111838 CTCAGTGCAGTAACTAGCATCG 58.888 50.000 0.00 0.00 43.44 3.84
3488 4501 9.469807 AGAAATATAAGAGCGTTTAGATCAGTG 57.530 33.333 0.00 0.00 37.82 3.66
3489 4502 8.594881 AAATATAAGAGCGTTTAGATCAGTGG 57.405 34.615 0.00 0.00 37.82 4.00
3491 4504 3.512033 AGAGCGTTTAGATCAGTGGTC 57.488 47.619 0.00 0.00 37.82 4.02
3492 4505 3.093057 AGAGCGTTTAGATCAGTGGTCT 58.907 45.455 11.46 11.46 37.82 3.85
3494 4507 4.705507 AGAGCGTTTAGATCAGTGGTCTAA 59.294 41.667 19.84 19.84 37.82 2.10
3495 4508 5.185249 AGAGCGTTTAGATCAGTGGTCTAAA 59.815 40.000 27.44 27.44 42.67 1.85
3499 4512 5.401531 TTTAGATCAGTGGTCTAAACGCT 57.598 39.130 27.44 0.00 41.04 5.07
3561 4574 9.507329 GAGGGAATACATAGATAAAATTGAGCA 57.493 33.333 0.00 0.00 0.00 4.26
3562 4575 9.866655 AGGGAATACATAGATAAAATTGAGCAA 57.133 29.630 0.00 0.00 0.00 3.91
3620 4633 9.907576 CACGTATTTCTAACTGAAAGATTGATC 57.092 33.333 0.00 0.00 46.39 2.92
3621 4634 9.877178 ACGTATTTCTAACTGAAAGATTGATCT 57.123 29.630 0.00 0.00 46.39 2.75
3625 4638 9.730705 ATTTCTAACTGAAAGATTGATCTGTCA 57.269 29.630 12.17 12.17 46.22 3.58
3626 4639 9.730705 TTTCTAACTGAAAGATTGATCTGTCAT 57.269 29.630 12.95 4.08 46.90 3.06
3627 4640 8.713737 TCTAACTGAAAGATTGATCTGTCATG 57.286 34.615 12.95 10.15 46.90 3.07
3628 4641 5.814764 ACTGAAAGATTGATCTGTCATGC 57.185 39.130 12.95 0.00 46.90 4.06
3629 4642 5.250982 ACTGAAAGATTGATCTGTCATGCA 58.749 37.500 12.95 0.00 46.90 3.96
3630 4643 5.886474 ACTGAAAGATTGATCTGTCATGCAT 59.114 36.000 12.95 0.00 46.90 3.96
3631 4644 6.377429 ACTGAAAGATTGATCTGTCATGCATT 59.623 34.615 12.95 0.00 46.90 3.56
3632 4645 7.093902 ACTGAAAGATTGATCTGTCATGCATTT 60.094 33.333 12.95 0.00 46.90 2.32
3633 4646 7.255569 TGAAAGATTGATCTGTCATGCATTTC 58.744 34.615 9.32 0.00 44.18 2.17
3634 4647 7.122204 TGAAAGATTGATCTGTCATGCATTTCT 59.878 33.333 9.32 0.00 44.18 2.52
3635 4648 8.515695 AAAGATTGATCTGTCATGCATTTCTA 57.484 30.769 0.00 0.00 37.19 2.10
3636 4649 8.515695 AAGATTGATCTGTCATGCATTTCTAA 57.484 30.769 0.00 0.00 37.19 2.10
3637 4650 7.928103 AGATTGATCTGTCATGCATTTCTAAC 58.072 34.615 0.00 0.00 35.42 2.34
3638 4651 7.774157 AGATTGATCTGTCATGCATTTCTAACT 59.226 33.333 0.00 0.00 35.42 2.24
3639 4652 6.673154 TGATCTGTCATGCATTTCTAACTG 57.327 37.500 0.00 0.00 0.00 3.16
3640 4653 6.408869 TGATCTGTCATGCATTTCTAACTGA 58.591 36.000 0.00 1.17 0.00 3.41
3641 4654 6.880529 TGATCTGTCATGCATTTCTAACTGAA 59.119 34.615 0.00 0.00 0.00 3.02
3643 4656 7.137490 TCTGTCATGCATTTCTAACTGAAAG 57.863 36.000 0.00 0.00 46.39 2.62
3644 4657 6.936335 TCTGTCATGCATTTCTAACTGAAAGA 59.064 34.615 0.00 0.00 46.39 2.52
3645 4658 7.609146 TCTGTCATGCATTTCTAACTGAAAGAT 59.391 33.333 0.00 0.00 46.39 2.40
3646 4659 7.532571 TGTCATGCATTTCTAACTGAAAGATG 58.467 34.615 0.00 0.00 46.39 2.90
3647 4660 7.391275 TGTCATGCATTTCTAACTGAAAGATGA 59.609 33.333 0.00 0.00 46.39 2.92
3648 4661 8.239314 GTCATGCATTTCTAACTGAAAGATGAA 58.761 33.333 0.00 0.00 46.39 2.57
3649 4662 8.795513 TCATGCATTTCTAACTGAAAGATGAAA 58.204 29.630 0.00 0.00 46.39 2.69
3650 4663 9.073368 CATGCATTTCTAACTGAAAGATGAAAG 57.927 33.333 0.00 0.00 46.39 2.62
3651 4664 8.394971 TGCATTTCTAACTGAAAGATGAAAGA 57.605 30.769 0.00 0.00 46.39 2.52
3652 4665 9.017509 TGCATTTCTAACTGAAAGATGAAAGAT 57.982 29.630 0.00 0.00 46.39 2.40
3653 4666 9.852091 GCATTTCTAACTGAAAGATGAAAGATT 57.148 29.630 0.00 0.00 46.39 2.40
3699 4749 9.988350 AGTGTATCTAATTTTTAAATCTGTGCG 57.012 29.630 0.00 0.00 0.00 5.34
3718 4769 7.604927 TCTGTGCGTACTTTTTATAAATGGAGT 59.395 33.333 4.97 6.67 0.00 3.85
3722 4773 9.826574 TGCGTACTTTTTATAAATGGAGTCTAT 57.173 29.630 10.76 0.00 0.00 1.98
3830 4881 7.041721 CCTGCTTTATAGATGTACACTTGTCA 58.958 38.462 0.00 0.00 0.00 3.58
3946 4997 1.869132 GAGTGCATGCATCGCTTATGA 59.131 47.619 25.64 0.00 37.86 2.15
3947 4998 2.483106 GAGTGCATGCATCGCTTATGAT 59.517 45.455 25.64 0.00 37.86 2.45
3948 4999 2.882761 AGTGCATGCATCGCTTATGATT 59.117 40.909 25.64 0.00 37.86 2.57
3987 5038 3.135994 TCGCTTTCTTTTTACTCCGCTT 58.864 40.909 0.00 0.00 0.00 4.68
4038 5089 6.272558 AGTCTTGTACCCTCCACTTCTATTTT 59.727 38.462 0.00 0.00 0.00 1.82
4183 5234 6.830873 ACAAGAAATAAGCAGCTCAGATTT 57.169 33.333 0.00 2.41 0.00 2.17
4383 5435 4.582656 TGGGGGATCAATTAAATTAGTGCG 59.417 41.667 0.00 0.00 0.00 5.34
4450 5502 4.808895 TGCCTGTATCTTGTAGTAAATGCG 59.191 41.667 0.00 0.00 0.00 4.73
4725 5804 1.386961 GTCGCTCGCTAAGTGATACG 58.613 55.000 3.01 0.00 45.87 3.06
4744 5823 0.246086 GCTCTGCTGTAGCTCTGTGT 59.754 55.000 5.38 0.00 42.66 3.72
4846 5925 6.314784 CGGTGATAGGAGAAAAACATTTCAC 58.685 40.000 4.34 0.00 33.53 3.18
4852 5931 5.130350 AGGAGAAAAACATTTCACGAGGAA 58.870 37.500 4.34 0.00 33.53 3.36
4899 5978 5.569355 TGGTTTCTCTCATCTGGCATTTTA 58.431 37.500 0.00 0.00 0.00 1.52
4909 5988 0.941542 TGGCATTTTATCGCGGCTAC 59.058 50.000 6.13 0.00 0.00 3.58
4911 5990 0.941542 GCATTTTATCGCGGCTACCA 59.058 50.000 6.13 0.00 0.00 3.25
4912 5991 1.332375 GCATTTTATCGCGGCTACCAA 59.668 47.619 6.13 0.00 0.00 3.67
4917 6005 3.671008 TTATCGCGGCTACCAACATAT 57.329 42.857 6.13 0.00 0.00 1.78
4966 6056 2.383442 TCCCTACAGACCTGCTATCC 57.617 55.000 0.00 0.00 0.00 2.59
4973 6063 2.503356 ACAGACCTGCTATCCTTCCTTG 59.497 50.000 0.00 0.00 0.00 3.61
5068 6158 4.163458 ACCACCTAAAATCTCGCCTAATCA 59.837 41.667 0.00 0.00 0.00 2.57
5082 6172 4.396166 CGCCTAATCACCTTGAAAGTCATT 59.604 41.667 0.00 0.00 0.00 2.57
5083 6173 5.447818 CGCCTAATCACCTTGAAAGTCATTC 60.448 44.000 0.00 0.00 38.60 2.67
5084 6174 5.649831 GCCTAATCACCTTGAAAGTCATTCT 59.350 40.000 0.00 0.00 38.92 2.40
5085 6175 6.151817 GCCTAATCACCTTGAAAGTCATTCTT 59.848 38.462 0.00 0.00 38.92 2.52
5086 6176 7.533426 CCTAATCACCTTGAAAGTCATTCTTG 58.467 38.462 0.00 0.00 38.92 3.02
5087 6177 7.391554 CCTAATCACCTTGAAAGTCATTCTTGA 59.608 37.037 0.00 0.00 38.92 3.02
5088 6178 6.814506 ATCACCTTGAAAGTCATTCTTGAG 57.185 37.500 0.00 0.00 38.92 3.02
5157 6247 8.725148 CCATACAATTCAGGACTATAATGCTTC 58.275 37.037 0.00 0.00 0.00 3.86
5170 6261 9.736023 GACTATAATGCTTCGATTCCAAATTTT 57.264 29.630 0.00 0.00 0.00 1.82
5207 6298 4.080863 TCAGTCTAAAAGGGAGATTGAGGC 60.081 45.833 0.00 0.00 35.47 4.70
5266 6357 4.359971 TGCACTGCACAATTATTGCTAG 57.640 40.909 4.68 3.87 40.86 3.42
5351 6443 7.119846 AGCTCGGTGATAATTTCCATAATTAGC 59.880 37.037 0.00 0.00 0.00 3.09
5380 6472 6.240549 ACTCCGTCCAAAGAATGATATCTT 57.759 37.500 3.98 0.00 41.34 2.40
5497 6589 2.737252 GTGATCCTCACGTCCAAAGAAC 59.263 50.000 0.00 0.00 37.67 3.01
5538 6632 6.072733 CGTGAAATAACCAAACGTACGAAAT 58.927 36.000 24.41 4.61 0.00 2.17
5540 6634 6.244883 GTGAAATAACCAAACGTACGAAATCG 59.755 38.462 24.41 7.38 46.33 3.34
5578 6672 1.679305 ATCACGACGGCAGACTCCT 60.679 57.895 0.00 0.00 0.00 3.69
5629 6724 4.142038 GGGTTTGATAGCCGTTGGATTAT 58.858 43.478 0.00 0.00 34.09 1.28
5652 6747 2.385803 GGATCAAGTCCCTCGGTTCTA 58.614 52.381 0.00 0.00 41.50 2.10
5737 6832 7.656707 AGCCTATGCAAGTTTTTAAAATGTG 57.343 32.000 0.55 2.09 41.13 3.21
5738 6833 7.441017 AGCCTATGCAAGTTTTTAAAATGTGA 58.559 30.769 0.55 0.00 41.13 3.58
5807 6917 1.040339 GGTGTTGGTTGTGCTTGGGA 61.040 55.000 0.00 0.00 0.00 4.37
5814 6924 1.270550 GGTTGTGCTTGGGATGAACTG 59.729 52.381 0.00 0.00 0.00 3.16
6160 7270 6.925211 TCTGGAACACAAACATTTTGTAACA 58.075 32.000 4.04 1.79 0.00 2.41
6193 7306 8.067784 GTGGGTTTGTAATGTTGTATCATATCG 58.932 37.037 0.00 0.00 0.00 2.92
6217 7330 0.811616 GATTCTGAACTCCGGCGCAT 60.812 55.000 10.83 0.00 0.00 4.73
6226 7339 0.032678 CTCCGGCGCATATCTTCACT 59.967 55.000 10.83 0.00 0.00 3.41
6293 7409 7.886629 ACAATGAAGTGGCTAAATATCATGT 57.113 32.000 0.00 0.00 0.00 3.21
6386 7505 4.409718 TTGATGCGGCTATAGTTGGTTA 57.590 40.909 0.00 0.00 0.00 2.85
6420 7539 7.926018 ACAAGGATGGACAAGAAATTTGTTTAC 59.074 33.333 0.00 0.00 31.96 2.01
6422 7541 8.934023 AGGATGGACAAGAAATTTGTTTACTA 57.066 30.769 0.00 0.00 31.96 1.82
6444 7755 8.978874 ACTATAATGATTCTTGTACAATGCCA 57.021 30.769 9.13 5.76 0.00 4.92
6457 7768 7.283625 TGTACAATGCCATTAACAAAGAGTT 57.716 32.000 0.00 0.00 44.27 3.01
6512 7823 1.795170 TTTGGAAGAGTTGCTGCCGC 61.795 55.000 0.00 0.00 46.61 6.53
6529 7840 1.782181 GCGAAAGTCGGCAGAAGTC 59.218 57.895 0.00 0.00 40.84 3.01
6532 7843 1.201647 CGAAAGTCGGCAGAAGTCCTA 59.798 52.381 0.00 0.00 36.00 2.94
6533 7844 2.352421 CGAAAGTCGGCAGAAGTCCTAA 60.352 50.000 0.00 0.00 36.00 2.69
6657 7999 7.023197 TGAAAATATGTGTCATGCATGAGAG 57.977 36.000 29.38 2.07 37.51 3.20
6726 8068 4.503910 GAAAATACCCTTTGGAACATGGC 58.496 43.478 0.00 0.00 39.30 4.40
6735 8077 4.340950 CCTTTGGAACATGGCGGTAATTAT 59.659 41.667 0.00 0.00 39.30 1.28
6804 8147 4.328712 CGTTCCAAAACTTTTTCCCAACAG 59.671 41.667 0.00 0.00 32.95 3.16
6903 8258 9.553064 CAGAGAATATAGCATGAAAAGTACCTT 57.447 33.333 0.00 0.00 0.00 3.50
6961 8319 7.916977 CACAAGAACATGAAAGTCATTTCTTCA 59.083 33.333 16.69 0.00 44.35 3.02
6962 8320 8.636213 ACAAGAACATGAAAGTCATTTCTTCAT 58.364 29.630 16.69 10.64 44.35 2.57
6988 8348 7.962373 TGAATTTTCTATACGAGTGCAACAATG 59.038 33.333 0.00 0.00 41.43 2.82
7007 8367 4.871993 ATGAATCTACTTTGCTCGCAAG 57.128 40.909 4.39 2.66 37.24 4.01
7130 8493 7.069578 GTCCTCCTTATCCTTAACACATAGACA 59.930 40.741 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.330944 TTTCTCTCAAGCAACGGTAGAA 57.669 40.909 0.00 0.00 0.00 2.10
2 3 3.433615 CCTTTTCTCTCAAGCAACGGTAG 59.566 47.826 0.00 0.00 0.00 3.18
3 4 3.181458 ACCTTTTCTCTCAAGCAACGGTA 60.181 43.478 0.00 0.00 0.00 4.02
40 41 4.141756 ACAATGCAAGATGTCTAGAGAGGG 60.142 45.833 0.00 0.00 0.00 4.30
50 51 8.213679 ACTAAGACCATATACAATGCAAGATGT 58.786 33.333 8.05 8.05 0.00 3.06
155 156 2.619646 GGTAAAAGAAGTTTGGCGGACA 59.380 45.455 0.00 0.00 0.00 4.02
170 171 4.295870 CTCGCGTGCATATAGAGGTAAAA 58.704 43.478 5.77 0.00 0.00 1.52
521 577 3.619038 CGGAGGAAGTGCATTCTAAGTTC 59.381 47.826 0.00 0.00 38.07 3.01
523 579 2.567615 ACGGAGGAAGTGCATTCTAAGT 59.432 45.455 0.00 0.00 38.07 2.24
532 589 5.353938 TGTATACAAATACGGAGGAAGTGC 58.646 41.667 2.20 0.00 40.84 4.40
533 590 6.479001 CCTTGTATACAAATACGGAGGAAGTG 59.521 42.308 18.55 2.85 42.01 3.16
605 663 6.785488 TCAGTGACATACAACTCACATTTC 57.215 37.500 0.00 0.00 39.49 2.17
669 846 7.931015 ATGAAGGGAGTAGGTTATATGTCAA 57.069 36.000 0.00 0.00 0.00 3.18
812 990 8.564574 GGGAAAATATCGCACAAAATCATAGTA 58.435 33.333 0.00 0.00 40.57 1.82
813 991 7.285401 AGGGAAAATATCGCACAAAATCATAGT 59.715 33.333 0.00 0.00 43.19 2.12
814 992 7.651808 AGGGAAAATATCGCACAAAATCATAG 58.348 34.615 0.00 0.00 43.19 2.23
837 1015 0.107993 TGCTGAGAAGGATGCGAAGG 60.108 55.000 0.00 0.00 0.00 3.46
841 1019 1.376543 ACAATGCTGAGAAGGATGCG 58.623 50.000 0.00 0.00 0.00 4.73
990 1168 2.158295 GGGAGGGAGGCTATGTAGAGAA 60.158 54.545 0.00 0.00 0.00 2.87
1083 1285 4.016706 GGTGGGGGTGGAGACGTG 62.017 72.222 0.00 0.00 0.00 4.49
1106 1308 2.202797 CGGTCACCTGAGATGCGG 60.203 66.667 0.00 0.00 0.00 5.69
1140 1342 2.653702 GATCGGGCGATCTGGGAG 59.346 66.667 0.00 0.00 45.42 4.30
1190 1625 2.242196 CTCTGGCCTAAGAAATTCCCCA 59.758 50.000 3.32 0.00 0.00 4.96
1191 1626 2.937519 CTCTGGCCTAAGAAATTCCCC 58.062 52.381 3.32 0.00 0.00 4.81
1196 1634 2.102252 CGAGAGCTCTGGCCTAAGAAAT 59.898 50.000 23.91 0.00 39.73 2.17
1207 1645 1.021202 AGGTCGAATCGAGAGCTCTG 58.979 55.000 23.91 13.64 42.02 3.35
1233 1671 4.552767 CGAATTTGACAAGAGAACAAGCGT 60.553 41.667 0.00 0.00 0.00 5.07
1287 1736 1.306997 AAATCCTCCCTCCTCCGCA 60.307 57.895 0.00 0.00 0.00 5.69
1360 1809 1.137459 TTCGCGAACATCGGACATCG 61.137 55.000 19.38 4.99 40.84 3.84
1383 1832 2.173669 CATAACGGCGCAGACCCAG 61.174 63.158 16.26 0.00 0.00 4.45
1389 1838 2.695055 CGACACATAACGGCGCAG 59.305 61.111 10.83 8.25 0.00 5.18
1411 1860 1.081442 GCACCGCCACAAAAGCTAC 60.081 57.895 0.00 0.00 0.00 3.58
1442 1891 4.606961 GAAATTCTCTGCGAAAACCACAA 58.393 39.130 0.00 0.00 34.79 3.33
1680 2129 1.160329 GGCTGCAAGTCAACACGAGT 61.160 55.000 0.50 0.00 39.41 4.18
1691 2140 1.156645 GCTATCGTCAGGGCTGCAAG 61.157 60.000 0.50 0.00 0.00 4.01
1713 2162 1.263356 TCAACTAACCTCCGTCCCAG 58.737 55.000 0.00 0.00 0.00 4.45
1737 2186 3.575630 TGAAAGAGCTAGCAACTACACG 58.424 45.455 18.83 0.00 0.00 4.49
1757 2206 5.047519 GCAAGGAAATCCCAGGATATCATTG 60.048 44.000 4.83 5.21 37.41 2.82
1764 2213 1.063417 CCAGCAAGGAAATCCCAGGAT 60.063 52.381 0.00 0.00 41.22 3.24
1769 2218 1.000866 AGCCCAGCAAGGAAATCCC 59.999 57.895 0.00 0.00 41.22 3.85
1771 2220 1.039785 GGGAGCCCAGCAAGGAAATC 61.040 60.000 0.00 0.00 41.22 2.17
1785 2234 1.119684 ACAACCAAAACCAAGGGAGC 58.880 50.000 0.00 0.00 0.00 4.70
1821 2270 3.802948 AGTGCAGGTAGAAACGATAGG 57.197 47.619 0.00 0.00 43.77 2.57
1890 2344 6.730960 TGGTATTAATCTTTCGTCACCAAC 57.269 37.500 0.00 0.00 32.10 3.77
1956 2422 4.460382 CCATATTTTGTTCTGCCAGACACT 59.540 41.667 0.00 0.00 0.00 3.55
2015 2481 3.004629 CACTGTGTTTGCTTGCCAGATAA 59.995 43.478 0.00 0.00 0.00 1.75
2021 2487 1.028905 TACCACTGTGTTTGCTTGCC 58.971 50.000 7.08 0.00 0.00 4.52
2200 2668 0.178992 CCACCCAACCTTTGCTCTCA 60.179 55.000 0.00 0.00 0.00 3.27
2337 2842 3.987745 TGTGCCATATACAACCCCATTT 58.012 40.909 0.00 0.00 0.00 2.32
2342 2847 4.692228 CCAAATTGTGCCATATACAACCC 58.308 43.478 0.00 0.00 40.47 4.11
2424 2929 5.072736 ACAGGAGATATGCAGATTGGAATCA 59.927 40.000 0.00 0.00 37.89 2.57
2460 2965 6.223120 CCACATCATTCCATATGTCGAACTA 58.777 40.000 1.24 0.00 34.12 2.24
2509 3014 2.161713 AACGGCCCATCCCCATTTCA 62.162 55.000 0.00 0.00 0.00 2.69
2564 3069 3.611530 GCAGTGGCAACGACAAAATACAT 60.612 43.478 0.00 0.00 40.72 2.29
2661 3166 6.942532 TTCCACTGCCTTACATGAATAATC 57.057 37.500 0.00 0.00 0.00 1.75
2834 3341 4.695396 TCAACTTCGTAACAAAGCCTACA 58.305 39.130 0.00 0.00 0.00 2.74
2979 3822 8.194769 GCCTTATCTAGCCATAACTCTTCTATC 58.805 40.741 0.00 0.00 0.00 2.08
2999 3842 8.752005 TTCAAATAGCTCAGTATTTGCCTTAT 57.248 30.769 12.81 0.00 44.73 1.73
3153 3997 1.133407 CTGAGTTGACCTAGACTCGGC 59.867 57.143 5.47 0.00 44.03 5.54
3155 3999 2.414824 GCACTGAGTTGACCTAGACTCG 60.415 54.545 5.20 3.49 44.03 4.18
3190 4037 3.713858 TGCCATACAAATAGTGCATGC 57.286 42.857 11.82 11.82 30.51 4.06
3269 4282 2.555325 CAGCTCAGCACAAAATGGAAGA 59.445 45.455 0.00 0.00 0.00 2.87
3270 4283 2.295349 ACAGCTCAGCACAAAATGGAAG 59.705 45.455 0.00 0.00 0.00 3.46
3486 4499 4.553323 TCACTAAAGAGCGTTTAGACCAC 58.447 43.478 21.60 0.00 36.23 4.16
3488 4501 5.652518 AGATCACTAAAGAGCGTTTAGACC 58.347 41.667 21.60 11.04 36.23 3.85
3489 4502 8.585436 GTTTAGATCACTAAAGAGCGTTTAGAC 58.415 37.037 21.60 12.60 45.42 2.59
3491 4504 7.601775 CGTTTAGATCACTAAAGAGCGTTTAG 58.398 38.462 15.99 15.99 45.42 1.85
3492 4505 6.034256 GCGTTTAGATCACTAAAGAGCGTTTA 59.966 38.462 0.00 0.00 45.42 2.01
3494 4507 4.326548 GCGTTTAGATCACTAAAGAGCGTT 59.673 41.667 0.00 0.00 45.42 4.84
3495 4508 3.858238 GCGTTTAGATCACTAAAGAGCGT 59.142 43.478 0.00 0.00 45.42 5.07
3496 4509 4.106197 AGCGTTTAGATCACTAAAGAGCG 58.894 43.478 16.38 11.92 46.12 5.03
3497 4510 5.344884 AGAGCGTTTAGATCACTAAAGAGC 58.655 41.667 15.46 15.46 45.42 4.09
3561 4574 9.459640 CAATCTTTCGATTAGAAATGCATGATT 57.540 29.630 0.00 0.00 46.60 2.57
3562 4575 8.843262 TCAATCTTTCGATTAGAAATGCATGAT 58.157 29.630 0.00 0.00 46.60 2.45
3620 4633 7.137490 TCTTTCAGTTAGAAATGCATGACAG 57.863 36.000 0.00 0.00 44.75 3.51
3621 4634 7.391275 TCATCTTTCAGTTAGAAATGCATGACA 59.609 33.333 0.00 0.00 44.75 3.58
3622 4635 7.755591 TCATCTTTCAGTTAGAAATGCATGAC 58.244 34.615 0.00 0.00 44.75 3.06
3623 4636 7.926674 TCATCTTTCAGTTAGAAATGCATGA 57.073 32.000 0.00 0.00 44.75 3.07
3624 4637 8.975410 TTTCATCTTTCAGTTAGAAATGCATG 57.025 30.769 0.00 0.00 44.75 4.06
3625 4638 9.017509 TCTTTCATCTTTCAGTTAGAAATGCAT 57.982 29.630 0.00 0.00 44.75 3.96
3626 4639 8.394971 TCTTTCATCTTTCAGTTAGAAATGCA 57.605 30.769 0.00 0.00 44.75 3.96
3627 4640 9.852091 AATCTTTCATCTTTCAGTTAGAAATGC 57.148 29.630 0.00 0.00 44.75 3.56
3634 4647 9.730705 ACAGATCAATCTTTCATCTTTCAGTTA 57.269 29.630 0.00 0.00 34.22 2.24
3635 4648 8.632906 ACAGATCAATCTTTCATCTTTCAGTT 57.367 30.769 0.00 0.00 34.22 3.16
3636 4649 7.881751 TGACAGATCAATCTTTCATCTTTCAGT 59.118 33.333 5.03 0.00 38.35 3.41
3637 4650 8.176365 GTGACAGATCAATCTTTCATCTTTCAG 58.824 37.037 11.01 0.00 43.20 3.02
3638 4651 7.662669 TGTGACAGATCAATCTTTCATCTTTCA 59.337 33.333 11.01 3.32 43.20 2.69
3639 4652 8.037382 TGTGACAGATCAATCTTTCATCTTTC 57.963 34.615 11.01 1.19 43.20 2.62
3640 4653 7.991084 TGTGACAGATCAATCTTTCATCTTT 57.009 32.000 11.01 0.00 43.20 2.52
3641 4654 9.107177 GTATGTGACAGATCAATCTTTCATCTT 57.893 33.333 11.01 7.02 43.20 2.40
3642 4655 8.484575 AGTATGTGACAGATCAATCTTTCATCT 58.515 33.333 11.01 5.75 43.20 2.90
3643 4656 8.659925 AGTATGTGACAGATCAATCTTTCATC 57.340 34.615 11.01 6.85 43.20 2.92
3644 4657 9.539825 GTAGTATGTGACAGATCAATCTTTCAT 57.460 33.333 11.01 6.65 43.20 2.57
3645 4658 7.981789 GGTAGTATGTGACAGATCAATCTTTCA 59.018 37.037 5.03 5.03 40.27 2.69
3646 4659 7.981789 TGGTAGTATGTGACAGATCAATCTTTC 59.018 37.037 0.00 0.19 36.31 2.62
3647 4660 7.851228 TGGTAGTATGTGACAGATCAATCTTT 58.149 34.615 0.00 0.00 36.31 2.52
3648 4661 7.423844 TGGTAGTATGTGACAGATCAATCTT 57.576 36.000 0.00 0.00 36.31 2.40
3649 4662 7.124901 ACTTGGTAGTATGTGACAGATCAATCT 59.875 37.037 0.00 0.00 32.04 2.40
3650 4663 7.223582 CACTTGGTAGTATGTGACAGATCAATC 59.776 40.741 0.00 0.00 32.39 2.67
3651 4664 7.044181 CACTTGGTAGTATGTGACAGATCAAT 58.956 38.462 0.00 0.00 32.39 2.57
3652 4665 6.014584 ACACTTGGTAGTATGTGACAGATCAA 60.015 38.462 0.00 0.00 32.39 2.57
3653 4666 5.480422 ACACTTGGTAGTATGTGACAGATCA 59.520 40.000 0.00 0.00 34.81 2.92
3654 4667 5.967088 ACACTTGGTAGTATGTGACAGATC 58.033 41.667 0.00 0.00 34.81 2.75
3655 4668 7.561722 AGATACACTTGGTAGTATGTGACAGAT 59.438 37.037 0.00 0.00 34.92 2.90
3656 4669 6.890268 AGATACACTTGGTAGTATGTGACAGA 59.110 38.462 0.00 0.00 34.92 3.41
3722 4773 8.245195 AGAGAACTAAGGGCAAACAAAATAAA 57.755 30.769 0.00 0.00 0.00 1.40
3830 4881 1.027357 CAAGCCTTCACAGCACAACT 58.973 50.000 0.00 0.00 0.00 3.16
3946 4997 5.471456 AGCGAGAGTTTCATCAGTTCAAAAT 59.529 36.000 0.00 0.00 0.00 1.82
3947 4998 4.816385 AGCGAGAGTTTCATCAGTTCAAAA 59.184 37.500 0.00 0.00 0.00 2.44
3948 4999 4.380531 AGCGAGAGTTTCATCAGTTCAAA 58.619 39.130 0.00 0.00 0.00 2.69
3987 5038 8.871629 TGTATCCTTGTTTTTGGCTTTCTATA 57.128 30.769 0.00 0.00 0.00 1.31
4023 5074 5.874810 TCACGATGAAAAATAGAAGTGGAGG 59.125 40.000 0.00 0.00 0.00 4.30
4038 5089 5.106317 GCCATAAGAAAAAGGTCACGATGAA 60.106 40.000 0.00 0.00 0.00 2.57
4100 5151 1.139853 GGGCTCCACTGATTCTGTAGG 59.860 57.143 0.00 1.88 0.00 3.18
4183 5234 9.530633 AAAACGTTGGTGCATAAAACTATAAAA 57.469 25.926 0.00 0.00 0.00 1.52
4260 5311 9.171877 GACTCAAGACTTGAATAGATTCCAAAT 57.828 33.333 18.26 0.00 39.58 2.32
4576 5631 3.031417 AAGCTAATGGGCGAGCGGT 62.031 57.895 0.00 0.00 43.72 5.68
4725 5804 0.246086 ACACAGAGCTACAGCAGAGC 59.754 55.000 3.70 0.00 45.16 4.09
4758 5837 0.975556 TCGCTAATCCCTGGCTGTGA 60.976 55.000 0.00 0.00 0.00 3.58
4846 5925 0.175760 TCGCAATTCCCTCTTCCTCG 59.824 55.000 0.00 0.00 0.00 4.63
4852 5931 1.517832 CGGAGTCGCAATTCCCTCT 59.482 57.895 0.00 0.00 0.00 3.69
4899 5978 2.823747 TCTATATGTTGGTAGCCGCGAT 59.176 45.455 8.23 0.00 0.00 4.58
4909 5988 7.394359 CCATTTGGGGAATACTCTATATGTTGG 59.606 40.741 0.00 0.00 0.00 3.77
4966 6056 5.519206 GCGATACCACTAGTTTACAAGGAAG 59.481 44.000 0.00 0.00 0.00 3.46
5068 6158 5.934781 AGACTCAAGAATGACTTTCAAGGT 58.065 37.500 4.12 0.00 36.61 3.50
5082 6172 1.072331 GGCCAAGGTCAAGACTCAAGA 59.928 52.381 0.00 0.00 0.00 3.02
5083 6173 1.202806 TGGCCAAGGTCAAGACTCAAG 60.203 52.381 0.61 0.00 0.00 3.02
5084 6174 0.843309 TGGCCAAGGTCAAGACTCAA 59.157 50.000 0.61 0.00 0.00 3.02
5085 6175 0.108585 GTGGCCAAGGTCAAGACTCA 59.891 55.000 7.24 0.00 0.00 3.41
5086 6176 0.108585 TGTGGCCAAGGTCAAGACTC 59.891 55.000 7.24 0.00 0.00 3.36
5087 6177 0.109342 CTGTGGCCAAGGTCAAGACT 59.891 55.000 7.24 0.00 0.00 3.24
5088 6178 0.890996 CCTGTGGCCAAGGTCAAGAC 60.891 60.000 7.24 0.00 0.00 3.01
5157 6247 4.321745 CGCTGACAGAAAAATTTGGAATCG 59.678 41.667 6.65 0.00 0.00 3.34
5170 6261 0.390340 GACTGATGGCGCTGACAGAA 60.390 55.000 25.19 3.30 34.88 3.02
5173 6264 0.894835 TTAGACTGATGGCGCTGACA 59.105 50.000 7.64 4.01 0.00 3.58
5207 6298 4.906437 GCTTTTTCAAGTCTAGTTTGAGCG 59.094 41.667 10.70 0.00 36.07 5.03
5262 6353 2.079925 GCATGGGCAATAGCTACTAGC 58.920 52.381 0.00 0.00 40.07 3.42
5359 6451 6.049149 GTGAAGATATCATTCTTTGGACGGA 58.951 40.000 5.32 0.00 40.97 4.69
5486 6578 7.982371 ATTATAGAGTAACGTTCTTTGGACG 57.018 36.000 2.82 0.00 0.00 4.79
5529 6623 2.475864 TGGTTTGGTTCGATTTCGTACG 59.524 45.455 9.53 9.53 39.93 3.67
5538 6632 0.383590 TACGTCGTGGTTTGGTTCGA 59.616 50.000 8.47 0.00 0.00 3.71
5540 6634 0.861185 GGTACGTCGTGGTTTGGTTC 59.139 55.000 8.47 0.00 0.00 3.62
5599 6693 2.487265 CGGCTATCAAACCCATAGGCTT 60.487 50.000 10.48 0.00 43.84 4.35
5646 6741 5.508320 GCAGGATAGCAGAAGTACTAGAACC 60.508 48.000 0.00 0.00 0.00 3.62
5652 6747 2.621055 CGAGCAGGATAGCAGAAGTACT 59.379 50.000 0.00 0.00 36.85 2.73
5735 6830 5.523916 ACAGCTTCCGTGTAATATCATTCAC 59.476 40.000 0.00 0.00 0.00 3.18
5736 6831 5.523552 CACAGCTTCCGTGTAATATCATTCA 59.476 40.000 0.00 0.00 0.00 2.57
5737 6832 5.523916 ACACAGCTTCCGTGTAATATCATTC 59.476 40.000 6.53 0.00 45.55 2.67
5738 6833 5.428253 ACACAGCTTCCGTGTAATATCATT 58.572 37.500 6.53 0.00 45.55 2.57
5751 6847 1.748493 TGGAAACACAACACAGCTTCC 59.252 47.619 0.00 0.00 33.40 3.46
5755 6851 3.115554 GTGATTGGAAACACAACACAGC 58.884 45.455 0.00 0.00 42.67 4.40
5807 6917 3.567164 CACAAAAGCTCAGGTCAGTTCAT 59.433 43.478 0.00 0.00 0.00 2.57
5814 6924 2.719376 TGGCACAAAAGCTCAGGTC 58.281 52.632 0.00 0.00 31.92 3.85
6160 7270 5.362430 ACAACATTACAAACCCACACAAGAT 59.638 36.000 0.00 0.00 0.00 2.40
6193 7306 2.540101 CGCCGGAGTTCAGAATCAATAC 59.460 50.000 5.05 0.00 0.00 1.89
6217 7330 9.201989 ACCATTCAACTATAGTGAGTGAAGATA 57.798 33.333 18.56 2.53 0.00 1.98
6226 7339 8.362464 ACTTCTACACCATTCAACTATAGTGA 57.638 34.615 6.06 3.68 0.00 3.41
6273 7389 5.192176 TGCACATGATATTTAGCCACTTCA 58.808 37.500 0.00 0.00 0.00 3.02
6366 7485 4.141801 ACTTAACCAACTATAGCCGCATCA 60.142 41.667 0.00 0.00 0.00 3.07
6386 7505 5.200483 TCTTGTCCATCCTTGTTTCAACTT 58.800 37.500 0.00 0.00 0.00 2.66
6424 7543 8.530311 TGTTAATGGCATTGTACAAGAATCATT 58.470 29.630 22.57 21.57 0.00 2.57
6425 7544 8.065473 TGTTAATGGCATTGTACAAGAATCAT 57.935 30.769 22.57 11.42 0.00 2.45
6426 7545 7.459795 TGTTAATGGCATTGTACAAGAATCA 57.540 32.000 22.57 9.74 0.00 2.57
6473 7784 1.555075 ACTCATCGCCAGTGGTGTTAT 59.445 47.619 21.92 6.85 34.40 1.89
6474 7785 0.973632 ACTCATCGCCAGTGGTGTTA 59.026 50.000 21.92 4.51 34.40 2.41
6512 7823 0.038159 AGGACTTCTGCCGACTTTCG 60.038 55.000 0.00 0.00 40.07 3.46
6560 7871 8.215050 TCAAAAAGGACATACCAAAGAGAACTA 58.785 33.333 0.00 0.00 42.04 2.24
6590 7932 5.417580 GGTGAAATGTTAGTGCAATAAGGGA 59.582 40.000 6.89 0.00 0.00 4.20
6657 7999 9.575783 GCACTATAGCCACTTCTATTCTTATAC 57.424 37.037 0.00 0.00 32.07 1.47
6702 8044 4.530161 CCATGTTCCAAAGGGTATTTTCCA 59.470 41.667 0.00 0.00 34.93 3.53
6764 8106 4.392445 TGGAACGTTTCGACTTTTTCTGAA 59.608 37.500 0.46 0.00 0.00 3.02
6767 8109 4.950434 TTGGAACGTTTCGACTTTTTCT 57.050 36.364 0.46 0.00 0.00 2.52
6768 8110 5.570206 AGTTTTGGAACGTTTCGACTTTTTC 59.430 36.000 0.46 0.00 40.75 2.29
6769 8111 5.463286 AGTTTTGGAACGTTTCGACTTTTT 58.537 33.333 0.46 0.00 40.75 1.94
6774 8116 5.220080 GGAAAAAGTTTTGGAACGTTTCGAC 60.220 40.000 0.46 0.60 43.45 4.20
6775 8117 4.858140 GGAAAAAGTTTTGGAACGTTTCGA 59.142 37.500 0.46 0.00 43.45 3.71
6776 8118 4.031991 GGGAAAAAGTTTTGGAACGTTTCG 59.968 41.667 0.46 0.00 43.45 3.46
6777 8119 4.930405 TGGGAAAAAGTTTTGGAACGTTTC 59.070 37.500 0.46 0.00 43.45 2.78
6778 8120 4.895961 TGGGAAAAAGTTTTGGAACGTTT 58.104 34.783 0.46 0.00 45.22 3.60
6804 8147 3.302740 CGACAGAAACAACAGCTCAAGTC 60.303 47.826 0.00 0.00 0.00 3.01
6845 8189 9.497030 TTGTCATTTTTGTCGGATAATATTTCG 57.503 29.630 0.00 0.00 0.00 3.46
6931 8289 4.522114 TGACTTTCATGTTCTTGTGGACA 58.478 39.130 0.00 0.00 0.00 4.02
6961 8319 7.609760 TGTTGCACTCGTATAGAAAATTCAT 57.390 32.000 0.00 0.00 0.00 2.57
6962 8320 7.428282 TTGTTGCACTCGTATAGAAAATTCA 57.572 32.000 0.00 0.00 0.00 2.57
6970 8328 6.834959 AGATTCATTGTTGCACTCGTATAG 57.165 37.500 0.00 0.00 0.00 1.31
6988 8348 3.308323 CCTCTTGCGAGCAAAGTAGATTC 59.692 47.826 11.83 0.00 35.90 2.52
7082 8445 3.790152 AGTTACGGACGGGAACTTATC 57.210 47.619 4.83 0.00 29.02 1.75


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

AutoCloner maintained by Alex Coulton.