Multiple sequence alignment - TraesCS4D01G239200

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 TraesCS4D01G239200 chr4D 100.000 6502 0 0 1 6502 401365645 401372146 0.000000e+00 12008.0
1 TraesCS4D01G239200 chr4D 92.857 1834 82 25 875 2667 417807191 417809016 0.000000e+00 2615.0
2 TraesCS4D01G239200 chr4D 92.429 1651 69 26 3880 5496 417810070 417811698 0.000000e+00 2305.0
3 TraesCS4D01G239200 chr4D 94.427 933 36 5 2903 3834 417809157 417810074 0.000000e+00 1421.0
4 TraesCS4D01G239200 chr4D 84.038 733 104 5 5769 6499 471494265 471494986 0.000000e+00 693.0
5 TraesCS4D01G239200 chr4D 91.772 316 11 5 2289 2602 200996539 200996237 6.030000e-115 425.0
6 TraesCS4D01G239200 chr4D 91.304 184 11 3 5493 5676 417811790 417811968 5.040000e-61 246.0
7 TraesCS4D01G239200 chr4D 86.555 119 14 2 4863 4981 145529363 145529247 5.290000e-26 130.0
8 TraesCS4D01G239200 chr4D 78.974 195 35 4 4862 5056 145499225 145499037 1.900000e-25 128.0
9 TraesCS4D01G239200 chr4D 78.974 195 35 4 4862 5056 145519526 145519338 1.900000e-25 128.0
10 TraesCS4D01G239200 chr4D 80.368 163 26 4 4862 5024 145509331 145509175 1.150000e-22 119.0
11 TraesCS4D01G239200 chr4B 91.641 1974 119 28 875 2811 496421436 496423400 0.000000e+00 2689.0
12 TraesCS4D01G239200 chr4B 92.512 1429 64 17 4281 5676 496424443 496425861 0.000000e+00 2006.0
13 TraesCS4D01G239200 chr4B 88.482 764 49 16 2910 3648 496423433 496424182 0.000000e+00 887.0
14 TraesCS4D01G239200 chr4A 95.261 1456 51 9 875 2323 59230668 59232112 0.000000e+00 2290.0
15 TraesCS4D01G239200 chr4A 91.489 1457 91 20 4044 5486 59233855 59235292 0.000000e+00 1973.0
16 TraesCS4D01G239200 chr4A 88.443 1021 79 15 2907 3889 59232695 59233714 0.000000e+00 1195.0
17 TraesCS4D01G239200 chr4A 88.284 845 85 6 1 839 484959300 484960136 0.000000e+00 1000.0
18 TraesCS4D01G239200 chr4A 85.903 454 30 12 2326 2778 59232261 59232681 2.760000e-123 453.0
19 TraesCS4D01G239200 chr4A 90.323 186 13 3 5491 5676 59240941 59241121 8.430000e-59 239.0
20 TraesCS4D01G239200 chr4A 88.696 115 11 2 3947 4060 59233722 59233835 8.790000e-29 139.0
21 TraesCS4D01G239200 chr6D 95.261 844 15 1 1 844 469352840 469353658 0.000000e+00 1314.0
22 TraesCS4D01G239200 chr6D 93.199 647 38 2 5856 6502 447735169 447735809 0.000000e+00 946.0
23 TraesCS4D01G239200 chr6D 81.671 742 116 5 5769 6502 461326100 461325371 3.360000e-167 599.0
24 TraesCS4D01G239200 chr6D 84.407 590 92 0 5910 6499 428443243 428443832 1.220000e-161 580.0
25 TraesCS4D01G239200 chr6D 94.175 309 18 0 5834 6142 263043103 263043411 7.630000e-129 472.0
26 TraesCS4D01G239200 chr6D 90.536 317 15 5 2289 2603 117041932 117042235 7.850000e-109 405.0
27 TraesCS4D01G239200 chr6A 97.548 734 18 0 5769 6502 184711806 184712539 0.000000e+00 1256.0
28 TraesCS4D01G239200 chr6A 90.840 131 11 1 2600 2729 413093673 413093803 2.410000e-39 174.0
29 TraesCS4D01G239200 chr2A 97.411 734 19 0 5769 6502 768554376 768553643 0.000000e+00 1251.0
30 TraesCS4D01G239200 chr2A 88.235 850 86 7 1 844 141890738 141891579 0.000000e+00 1003.0
31 TraesCS4D01G239200 chr2A 95.556 45 2 0 5723 5767 27745731 27745775 9.040000e-09 73.1
32 TraesCS4D01G239200 chr2B 97.275 734 20 0 5769 6502 408290734 408290001 0.000000e+00 1245.0
33 TraesCS4D01G239200 chr2B 96.866 734 23 0 5769 6502 772543696 772544429 0.000000e+00 1229.0
34 TraesCS4D01G239200 chr2B 85.863 962 86 18 2910 3836 240186220 240185274 0.000000e+00 977.0
35 TraesCS4D01G239200 chr2B 91.904 457 36 1 4281 4736 240184727 240184271 7.110000e-179 638.0
36 TraesCS4D01G239200 chr2B 89.423 104 8 3 2697 2797 240186402 240186299 1.900000e-25 128.0
37 TraesCS4D01G239200 chr7D 97.003 734 22 0 5769 6502 106624747 106625480 0.000000e+00 1234.0
38 TraesCS4D01G239200 chr7D 92.574 808 41 8 1925 2729 157760285 157761076 0.000000e+00 1142.0
39 TraesCS4D01G239200 chr7D 90.544 846 75 4 1 844 505624032 505624874 0.000000e+00 1114.0
40 TraesCS4D01G239200 chr7D 92.254 723 47 2 5780 6502 627406239 627405526 0.000000e+00 1016.0
41 TraesCS4D01G239200 chr7D 95.588 136 3 3 2777 2911 270998670 270998537 1.420000e-51 215.0
42 TraesCS4D01G239200 chr7D 97.917 48 1 0 5722 5769 381848864 381848817 4.180000e-12 84.2
43 TraesCS4D01G239200 chr7D 97.778 45 1 0 5725 5769 508814122 508814078 1.940000e-10 78.7
44 TraesCS4D01G239200 chr5B 95.782 735 30 1 5769 6502 373222021 373222755 0.000000e+00 1184.0
45 TraesCS4D01G239200 chr5B 87.305 961 71 22 2910 3835 687363531 687362587 0.000000e+00 1051.0
46 TraesCS4D01G239200 chr5B 86.889 961 75 21 2910 3835 683038565 683039509 0.000000e+00 1029.0
47 TraesCS4D01G239200 chr5B 93.654 457 28 1 4281 4736 687362255 687361799 0.000000e+00 682.0
48 TraesCS4D01G239200 chr5B 82.900 731 115 2 5769 6499 429803905 429804625 0.000000e+00 649.0
49 TraesCS4D01G239200 chr5B 92.375 459 30 5 4281 4736 683039859 683040315 0.000000e+00 649.0
50 TraesCS4D01G239200 chr5B 95.620 137 5 1 2769 2905 67434372 67434237 1.100000e-52 219.0
51 TraesCS4D01G239200 chr5B 92.366 131 9 1 2600 2729 521744067 521743937 1.110000e-42 185.0
52 TraesCS4D01G239200 chr5B 91.603 131 10 1 2600 2729 24292937 24292807 5.180000e-41 180.0
53 TraesCS4D01G239200 chr6B 94.014 735 38 5 5769 6502 21463508 21462779 0.000000e+00 1109.0
54 TraesCS4D01G239200 chr6B 91.552 509 37 4 2910 3412 566644183 566643675 0.000000e+00 697.0
55 TraesCS4D01G239200 chr6B 88.947 380 34 4 1838 2217 279014173 279013802 4.590000e-126 462.0
56 TraesCS4D01G239200 chr7B 93.852 732 45 0 5771 6502 482023746 482024477 0.000000e+00 1103.0
57 TraesCS4D01G239200 chr7B 84.062 778 75 22 3092 3835 604515372 604516134 0.000000e+00 704.0
58 TraesCS4D01G239200 chr7B 91.904 457 36 1 4281 4736 604516483 604516939 7.110000e-179 638.0
59 TraesCS4D01G239200 chr7B 87.419 461 25 18 2289 2729 688016006 688016453 3.500000e-137 499.0
60 TraesCS4D01G239200 chr7B 84.615 416 48 8 1707 2121 612843297 612843697 3.650000e-107 399.0
61 TraesCS4D01G239200 chr7B 96.023 176 7 0 2910 3085 604509967 604510142 2.970000e-73 287.0
62 TraesCS4D01G239200 chr1B 93.793 725 41 2 5778 6502 305413474 305414194 0.000000e+00 1086.0
63 TraesCS4D01G239200 chr1B 88.283 734 51 12 5769 6502 547217922 547217224 0.000000e+00 846.0
64 TraesCS4D01G239200 chr1B 82.923 732 114 5 5769 6499 11631561 11632282 0.000000e+00 649.0
65 TraesCS4D01G239200 chr1B 92.216 167 10 1 6336 6502 47215205 47215042 3.920000e-57 233.0
66 TraesCS4D01G239200 chr5A 93.052 734 51 0 5769 6502 666311527 666312260 0.000000e+00 1074.0
67 TraesCS4D01G239200 chr5A 87.574 845 91 8 1 839 227564860 227565696 0.000000e+00 966.0
68 TraesCS4D01G239200 chr5A 90.840 131 11 1 2600 2729 511920498 511920368 2.410000e-39 174.0
69 TraesCS4D01G239200 chr5A 90.840 131 11 1 2600 2729 573420269 573420399 2.410000e-39 174.0
70 TraesCS4D01G239200 chrUn 87.574 845 91 8 1 839 83728180 83729016 0.000000e+00 966.0
71 TraesCS4D01G239200 chrUn 87.589 846 89 10 1 839 184049404 184050240 0.000000e+00 966.0
72 TraesCS4D01G239200 chrUn 87.500 848 92 8 1 842 392679261 392678422 0.000000e+00 966.0
73 TraesCS4D01G239200 chr7A 87.574 845 91 8 1 839 730057576 730058412 0.000000e+00 966.0
74 TraesCS4D01G239200 chr7A 95.652 138 4 2 2769 2905 732956106 732956242 3.050000e-53 220.0
75 TraesCS4D01G239200 chr7A 90.909 132 11 1 2600 2730 150151036 150150905 6.700000e-40 176.0
76 TraesCS4D01G239200 chr7A 95.745 47 2 0 5723 5769 301942862 301942816 6.990000e-10 76.8
77 TraesCS4D01G239200 chr7A 95.652 46 2 0 5724 5769 1319164 1319209 2.510000e-09 75.0
78 TraesCS4D01G239200 chr1D 88.011 734 78 2 5769 6502 62363195 62362472 0.000000e+00 859.0
79 TraesCS4D01G239200 chr1D 91.139 316 13 5 2290 2603 23948904 23949206 1.300000e-111 414.0
80 TraesCS4D01G239200 chr1D 96.269 134 5 0 2775 2908 299268418 299268551 3.050000e-53 220.0
81 TraesCS4D01G239200 chr1D 91.503 153 10 3 2757 2908 462901295 462901445 2.380000e-49 207.0
82 TraesCS4D01G239200 chr1D 91.447 152 12 1 2757 2908 462914120 462914270 2.380000e-49 207.0
83 TraesCS4D01G239200 chr1D 91.447 152 12 1 2757 2908 462921347 462921497 2.380000e-49 207.0
84 TraesCS4D01G239200 chr3D 84.196 734 107 1 5769 6502 508190620 508189896 0.000000e+00 704.0
85 TraesCS4D01G239200 chr3D 89.458 332 20 4 2289 2618 402475128 402474810 7.850000e-109 405.0
86 TraesCS4D01G239200 chr5D 83.447 731 111 4 5769 6499 376685606 376686326 0.000000e+00 671.0
87 TraesCS4D01G239200 chr5D 89.759 332 19 5 2289 2618 55335695 55335377 1.690000e-110 411.0
88 TraesCS4D01G239200 chr5D 97.872 47 1 0 5723 5769 475504825 475504779 1.500000e-11 82.4
89 TraesCS4D01G239200 chr1A 95.695 302 10 1 6201 6502 562938634 562938932 3.530000e-132 483.0
90 TraesCS4D01G239200 chr1A 96.269 134 5 0 2774 2907 455042838 455042971 3.050000e-53 220.0
91 TraesCS4D01G239200 chr2D 90.625 320 15 5 2289 2606 8647072 8646766 1.690000e-110 411.0
92 TraesCS4D01G239200 chr2D 94.286 140 6 2 2777 2915 286778363 286778225 5.110000e-51 213.0


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 TraesCS4D01G239200 chr4D 401365645 401372146 6501 False 12008.000000 12008 100.000000 1 6502 1 chr4D.!!$F1 6501
1 TraesCS4D01G239200 chr4D 417807191 417811968 4777 False 1646.750000 2615 92.754250 875 5676 4 chr4D.!!$F3 4801
2 TraesCS4D01G239200 chr4D 471494265 471494986 721 False 693.000000 693 84.038000 5769 6499 1 chr4D.!!$F2 730
3 TraesCS4D01G239200 chr4B 496421436 496425861 4425 False 1860.666667 2689 90.878333 875 5676 3 chr4B.!!$F1 4801
4 TraesCS4D01G239200 chr4A 59230668 59235292 4624 False 1210.000000 2290 89.958400 875 5486 5 chr4A.!!$F3 4611
5 TraesCS4D01G239200 chr4A 484959300 484960136 836 False 1000.000000 1000 88.284000 1 839 1 chr4A.!!$F2 838
6 TraesCS4D01G239200 chr6D 469352840 469353658 818 False 1314.000000 1314 95.261000 1 844 1 chr6D.!!$F5 843
7 TraesCS4D01G239200 chr6D 447735169 447735809 640 False 946.000000 946 93.199000 5856 6502 1 chr6D.!!$F4 646
8 TraesCS4D01G239200 chr6D 461325371 461326100 729 True 599.000000 599 81.671000 5769 6502 1 chr6D.!!$R1 733
9 TraesCS4D01G239200 chr6D 428443243 428443832 589 False 580.000000 580 84.407000 5910 6499 1 chr6D.!!$F3 589
10 TraesCS4D01G239200 chr6A 184711806 184712539 733 False 1256.000000 1256 97.548000 5769 6502 1 chr6A.!!$F1 733
11 TraesCS4D01G239200 chr2A 768553643 768554376 733 True 1251.000000 1251 97.411000 5769 6502 1 chr2A.!!$R1 733
12 TraesCS4D01G239200 chr2A 141890738 141891579 841 False 1003.000000 1003 88.235000 1 844 1 chr2A.!!$F2 843
13 TraesCS4D01G239200 chr2B 408290001 408290734 733 True 1245.000000 1245 97.275000 5769 6502 1 chr2B.!!$R1 733
14 TraesCS4D01G239200 chr2B 772543696 772544429 733 False 1229.000000 1229 96.866000 5769 6502 1 chr2B.!!$F1 733
15 TraesCS4D01G239200 chr2B 240184271 240186402 2131 True 581.000000 977 89.063333 2697 4736 3 chr2B.!!$R2 2039
16 TraesCS4D01G239200 chr7D 106624747 106625480 733 False 1234.000000 1234 97.003000 5769 6502 1 chr7D.!!$F1 733
17 TraesCS4D01G239200 chr7D 157760285 157761076 791 False 1142.000000 1142 92.574000 1925 2729 1 chr7D.!!$F2 804
18 TraesCS4D01G239200 chr7D 505624032 505624874 842 False 1114.000000 1114 90.544000 1 844 1 chr7D.!!$F3 843
19 TraesCS4D01G239200 chr7D 627405526 627406239 713 True 1016.000000 1016 92.254000 5780 6502 1 chr7D.!!$R4 722
20 TraesCS4D01G239200 chr5B 373222021 373222755 734 False 1184.000000 1184 95.782000 5769 6502 1 chr5B.!!$F1 733
21 TraesCS4D01G239200 chr5B 687361799 687363531 1732 True 866.500000 1051 90.479500 2910 4736 2 chr5B.!!$R4 1826
22 TraesCS4D01G239200 chr5B 683038565 683040315 1750 False 839.000000 1029 89.632000 2910 4736 2 chr5B.!!$F3 1826
23 TraesCS4D01G239200 chr5B 429803905 429804625 720 False 649.000000 649 82.900000 5769 6499 1 chr5B.!!$F2 730
24 TraesCS4D01G239200 chr6B 21462779 21463508 729 True 1109.000000 1109 94.014000 5769 6502 1 chr6B.!!$R1 733
25 TraesCS4D01G239200 chr6B 566643675 566644183 508 True 697.000000 697 91.552000 2910 3412 1 chr6B.!!$R3 502
26 TraesCS4D01G239200 chr7B 482023746 482024477 731 False 1103.000000 1103 93.852000 5771 6502 1 chr7B.!!$F1 731
27 TraesCS4D01G239200 chr7B 604515372 604516939 1567 False 671.000000 704 87.983000 3092 4736 2 chr7B.!!$F5 1644
28 TraesCS4D01G239200 chr1B 305413474 305414194 720 False 1086.000000 1086 93.793000 5778 6502 1 chr1B.!!$F2 724
29 TraesCS4D01G239200 chr1B 547217224 547217922 698 True 846.000000 846 88.283000 5769 6502 1 chr1B.!!$R2 733
30 TraesCS4D01G239200 chr1B 11631561 11632282 721 False 649.000000 649 82.923000 5769 6499 1 chr1B.!!$F1 730
31 TraesCS4D01G239200 chr5A 666311527 666312260 733 False 1074.000000 1074 93.052000 5769 6502 1 chr5A.!!$F3 733
32 TraesCS4D01G239200 chr5A 227564860 227565696 836 False 966.000000 966 87.574000 1 839 1 chr5A.!!$F1 838
33 TraesCS4D01G239200 chrUn 83728180 83729016 836 False 966.000000 966 87.574000 1 839 1 chrUn.!!$F1 838
34 TraesCS4D01G239200 chrUn 184049404 184050240 836 False 966.000000 966 87.589000 1 839 1 chrUn.!!$F2 838
35 TraesCS4D01G239200 chrUn 392678422 392679261 839 True 966.000000 966 87.500000 1 842 1 chrUn.!!$R1 841
36 TraesCS4D01G239200 chr7A 730057576 730058412 836 False 966.000000 966 87.574000 1 839 1 chr7A.!!$F2 838
37 TraesCS4D01G239200 chr1D 62362472 62363195 723 True 859.000000 859 88.011000 5769 6502 1 chr1D.!!$R1 733
38 TraesCS4D01G239200 chr3D 508189896 508190620 724 True 704.000000 704 84.196000 5769 6502 1 chr3D.!!$R2 733
39 TraesCS4D01G239200 chr5D 376685606 376686326 720 False 671.000000 671 83.447000 5769 6499 1 chr5D.!!$F1 730

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
449 450 1.089481 GCATCGCTGATGGAAACGGA 61.089 55.000 16.56 0.0 40.10 4.69 F
1794 1827 1.398390 GATCAGTGCGGTGTTTGATCC 59.602 52.381 2.69 0.0 39.83 3.36 F
2743 3003 0.524816 TTCTGAGAATACCGTCGCGC 60.525 55.000 0.00 0.0 0.00 6.86 F
3937 4269 0.801251 GCTTCAGGCAGTCATCACAC 59.199 55.000 0.00 0.0 41.35 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1835 1.001815 ACAAACATTCCAACGAAGCCG 60.002 47.619 0.0 0.0 42.5 5.52 R
2881 3142 1.553248 CTCCCTCCGTTCCACAATACA 59.447 52.381 0.0 0.0 0.0 2.29 R
3968 4300 0.622665 AGATGGAACTCTGGCAAGGG 59.377 55.000 0.0 0.0 0.0 3.95 R
5700 6563 0.231279 CGGTGTCCTGAAAACGAACG 59.769 55.000 0.0 0.0 0.0 3.95 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
449 450 1.089481 GCATCGCTGATGGAAACGGA 61.089 55.000 16.56 0.00 40.10 4.69
681 685 2.586079 CGGCGCGATCACAAGGAT 60.586 61.111 12.10 0.00 39.53 3.24
848 853 5.743636 AATGAAGGGGTACTACGTAAACA 57.256 39.130 0.00 0.00 0.00 2.83
849 854 5.743636 ATGAAGGGGTACTACGTAAACAA 57.256 39.130 0.00 0.00 0.00 2.83
850 855 4.881920 TGAAGGGGTACTACGTAAACAAC 58.118 43.478 0.00 0.00 0.00 3.32
851 856 4.588528 TGAAGGGGTACTACGTAAACAACT 59.411 41.667 0.00 0.00 0.00 3.16
852 857 5.772672 TGAAGGGGTACTACGTAAACAACTA 59.227 40.000 0.00 0.00 0.00 2.24
853 858 5.644977 AGGGGTACTACGTAAACAACTAC 57.355 43.478 0.00 0.00 0.00 2.73
854 859 5.076873 AGGGGTACTACGTAAACAACTACA 58.923 41.667 0.00 0.00 0.00 2.74
855 860 5.183904 AGGGGTACTACGTAAACAACTACAG 59.816 44.000 0.00 0.00 0.00 2.74
856 861 5.183140 GGGGTACTACGTAAACAACTACAGA 59.817 44.000 0.00 0.00 0.00 3.41
857 862 6.294508 GGGGTACTACGTAAACAACTACAGAA 60.295 42.308 0.00 0.00 0.00 3.02
858 863 6.803807 GGGTACTACGTAAACAACTACAGAAG 59.196 42.308 0.00 0.00 0.00 2.85
859 864 6.306596 GGTACTACGTAAACAACTACAGAAGC 59.693 42.308 0.00 0.00 0.00 3.86
860 865 6.081872 ACTACGTAAACAACTACAGAAGCT 57.918 37.500 0.00 0.00 0.00 3.74
861 866 7.206981 ACTACGTAAACAACTACAGAAGCTA 57.793 36.000 0.00 0.00 0.00 3.32
862 867 7.824672 ACTACGTAAACAACTACAGAAGCTAT 58.175 34.615 0.00 0.00 0.00 2.97
863 868 8.950210 ACTACGTAAACAACTACAGAAGCTATA 58.050 33.333 0.00 0.00 0.00 1.31
864 869 9.219497 CTACGTAAACAACTACAGAAGCTATAC 57.781 37.037 0.00 0.00 0.00 1.47
865 870 6.744537 ACGTAAACAACTACAGAAGCTATACG 59.255 38.462 0.00 0.00 37.74 3.06
866 871 6.195983 CGTAAACAACTACAGAAGCTATACGG 59.804 42.308 0.00 0.00 0.00 4.02
867 872 5.656213 AACAACTACAGAAGCTATACGGT 57.344 39.130 0.00 0.00 0.00 4.83
868 873 5.246145 ACAACTACAGAAGCTATACGGTC 57.754 43.478 0.00 0.00 0.00 4.79
869 874 4.948621 ACAACTACAGAAGCTATACGGTCT 59.051 41.667 0.00 0.00 0.00 3.85
870 875 6.118170 ACAACTACAGAAGCTATACGGTCTA 58.882 40.000 0.00 0.00 0.00 2.59
871 876 6.600822 ACAACTACAGAAGCTATACGGTCTAA 59.399 38.462 0.00 0.00 0.00 2.10
872 877 6.616774 ACTACAGAAGCTATACGGTCTAAC 57.383 41.667 0.00 0.00 0.00 2.34
873 878 6.118170 ACTACAGAAGCTATACGGTCTAACA 58.882 40.000 0.00 0.00 0.00 2.41
926 931 2.685017 TCATCCTCCTGCGGCACT 60.685 61.111 0.00 0.00 0.00 4.40
945 950 3.809013 CACCCCCATTCCCCTCCG 61.809 72.222 0.00 0.00 0.00 4.63
1385 1417 2.750637 GTCGAGGCCTCCGAGTCA 60.751 66.667 27.20 3.63 36.66 3.41
1401 1433 3.473647 CATCCTGCCTCCGCTCCA 61.474 66.667 0.00 0.00 35.36 3.86
1511 1543 2.124403 GACGCGGAGGAGGAGGTA 60.124 66.667 12.47 0.00 0.00 3.08
1601 1633 2.394912 GAGGACGACGACGACGAG 59.605 66.667 25.15 9.88 42.66 4.18
1750 1782 4.258543 CACGCAGTTCCCCTTAAAATCTA 58.741 43.478 0.00 0.00 41.61 1.98
1794 1827 1.398390 GATCAGTGCGGTGTTTGATCC 59.602 52.381 2.69 0.00 39.83 3.36
1802 1835 2.278026 GGTGTTTGATCCGATTTGGC 57.722 50.000 0.00 0.00 37.80 4.52
1936 1969 2.584608 AGGTGTACGCCTCCATGC 59.415 61.111 22.56 0.00 32.39 4.06
1938 1971 2.890474 GTGTACGCCTCCATGCCG 60.890 66.667 0.00 0.00 0.00 5.69
2007 2040 1.478105 TGGATCATCGAGGTCAGTGTG 59.522 52.381 0.00 0.00 0.00 3.82
2012 2045 2.492449 ATCGAGGTCAGTGTGCACCG 62.492 60.000 15.69 7.98 37.79 4.94
2457 2663 3.430790 GGCCATTAATTTTGAGGAGGTGC 60.431 47.826 0.00 0.00 0.00 5.01
2536 2744 4.671766 GCTGCAAAGTTATCCAGTAAACCG 60.672 45.833 0.00 0.00 0.00 4.44
2591 2812 5.641209 GTCTAGGAGGCACATTATAGCAATG 59.359 44.000 0.00 0.00 0.00 2.82
2661 2912 2.616842 GTCCGTATGTGCCCCTTTTATG 59.383 50.000 0.00 0.00 0.00 1.90
2667 2918 2.264455 TGTGCCCCTTTTATGCCATTT 58.736 42.857 0.00 0.00 0.00 2.32
2670 2921 2.909006 TGCCCCTTTTATGCCATTTCAA 59.091 40.909 0.00 0.00 0.00 2.69
2736 2996 6.930731 ACTTGAGAGAACTTCTGAGAATACC 58.069 40.000 0.00 0.00 35.87 2.73
2741 3001 2.563471 ACTTCTGAGAATACCGTCGC 57.437 50.000 0.00 0.00 0.00 5.19
2742 3002 1.202154 ACTTCTGAGAATACCGTCGCG 60.202 52.381 0.00 0.00 0.00 5.87
2743 3003 0.524816 TTCTGAGAATACCGTCGCGC 60.525 55.000 0.00 0.00 0.00 6.86
2745 3005 2.337749 CTGAGAATACCGTCGCGCCT 62.338 60.000 0.00 0.00 0.00 5.52
2746 3006 1.226888 GAGAATACCGTCGCGCCTT 60.227 57.895 0.00 0.00 0.00 4.35
2790 3051 0.896226 GCAACTACTCCCTCCGTTCT 59.104 55.000 0.00 0.00 0.00 3.01
2797 3058 6.462552 ACTACTCCCTCCGTTCTAAAATAC 57.537 41.667 0.00 0.00 0.00 1.89
2798 3059 6.193504 ACTACTCCCTCCGTTCTAAAATACT 58.806 40.000 0.00 0.00 0.00 2.12
2803 3064 5.482878 TCCCTCCGTTCTAAAATACTTGACT 59.517 40.000 0.00 0.00 0.00 3.41
2805 3066 6.313164 CCCTCCGTTCTAAAATACTTGACTTC 59.687 42.308 0.00 0.00 0.00 3.01
2806 3067 6.313164 CCTCCGTTCTAAAATACTTGACTTCC 59.687 42.308 0.00 0.00 0.00 3.46
2807 3068 6.761312 TCCGTTCTAAAATACTTGACTTCCA 58.239 36.000 0.00 0.00 0.00 3.53
2810 3071 8.512138 CCGTTCTAAAATACTTGACTTCCATTT 58.488 33.333 0.00 0.00 0.00 2.32
2811 3072 9.329913 CGTTCTAAAATACTTGACTTCCATTTG 57.670 33.333 0.00 0.00 0.00 2.32
2817 3078 9.883142 AAAATACTTGACTTCCATTTGTTCAAA 57.117 25.926 0.44 0.44 0.00 2.69
2818 3079 9.883142 AAATACTTGACTTCCATTTGTTCAAAA 57.117 25.926 2.11 0.00 0.00 2.44
2819 3080 9.883142 AATACTTGACTTCCATTTGTTCAAAAA 57.117 25.926 2.11 0.00 0.00 1.94
2821 3082 8.200364 ACTTGACTTCCATTTGTTCAAAAATG 57.800 30.769 2.11 3.25 43.94 2.32
2832 3093 9.874205 CATTTGTTCAAAAATGGATGTACCTAT 57.126 29.630 2.11 0.00 41.71 2.57
2879 3140 8.031277 ACATCTAGATTTTGACAAATGGAAAGC 58.969 33.333 1.33 0.00 32.35 3.51
2880 3141 7.523293 TCTAGATTTTGACAAATGGAAAGCA 57.477 32.000 0.50 0.00 32.35 3.91
2881 3142 8.125978 TCTAGATTTTGACAAATGGAAAGCAT 57.874 30.769 0.50 0.00 32.35 3.79
2882 3143 8.030692 TCTAGATTTTGACAAATGGAAAGCATG 58.969 33.333 0.50 0.00 32.35 4.06
2883 3144 6.527423 AGATTTTGACAAATGGAAAGCATGT 58.473 32.000 0.50 0.00 32.35 3.21
2887 3148 7.655236 TTTGACAAATGGAAAGCATGTATTG 57.345 32.000 0.00 0.00 0.00 1.90
3027 3299 1.184431 TTTGTAGCATGGGCATGTGG 58.816 50.000 0.00 0.00 44.61 4.17
3203 3476 3.181450 GGTATTGAGCTCCCTTGTGCTAT 60.181 47.826 12.15 0.00 41.19 2.97
3415 3717 1.689813 TCAGGTCCAAGTTTCAGCGTA 59.310 47.619 0.00 0.00 0.00 4.42
3444 3746 4.578105 CCTATTCTTTCCTCAGATGGTTGC 59.422 45.833 0.00 0.00 0.00 4.17
3504 3806 9.650539 CTATGATACATTGTCTCCTCTATTTGG 57.349 37.037 0.00 0.00 0.00 3.28
3684 4008 1.978454 AAGGCTTATCTCTGCATGCC 58.022 50.000 16.68 0.00 40.54 4.40
3694 4018 3.954200 TCTCTGCATGCCATTACTTCAA 58.046 40.909 16.68 0.00 0.00 2.69
3702 4026 6.485984 TGCATGCCATTACTTCAAAATTTGTT 59.514 30.769 16.68 0.00 0.00 2.83
3703 4027 7.013083 TGCATGCCATTACTTCAAAATTTGTTT 59.987 29.630 16.68 0.00 0.00 2.83
3802 4134 1.538512 CTCACCAACCACTTGAGCATG 59.461 52.381 0.00 0.00 30.90 4.06
3818 4150 4.162131 TGAGCATGGTAGTTAGCATCTTCA 59.838 41.667 0.00 5.79 41.99 3.02
3881 4213 5.781210 TGTGGTGAATTGAAGCATTGTAA 57.219 34.783 0.00 0.00 0.00 2.41
3883 4215 6.757237 TGTGGTGAATTGAAGCATTGTAAAT 58.243 32.000 0.00 0.00 0.00 1.40
3907 4239 6.759272 TGTGATGCTACCATAAGATCCTAAC 58.241 40.000 0.00 0.00 0.00 2.34
3918 4250 9.449719 ACCATAAGATCCTAACTTTAGTTTGTG 57.550 33.333 0.00 0.00 39.31 3.33
3930 4262 8.333898 AACTTTAGTTTGTGCTTCAGGCAGTC 62.334 42.308 0.00 0.00 43.09 3.51
3936 4268 3.238232 GCTTCAGGCAGTCATCACA 57.762 52.632 0.00 0.00 41.35 3.58
3937 4269 0.801251 GCTTCAGGCAGTCATCACAC 59.199 55.000 0.00 0.00 41.35 3.82
3968 4300 5.161358 GCCATTTTAACTTGGTTAGACAGC 58.839 41.667 5.09 0.00 35.34 4.40
3982 4515 0.957888 GACAGCCCTTGCCAGAGTTC 60.958 60.000 0.00 0.00 38.69 3.01
4070 4640 2.071540 TGCAAGAGAAATCAGAGCACG 58.928 47.619 0.00 0.00 0.00 5.34
4074 4644 4.152402 GCAAGAGAAATCAGAGCACGTTTA 59.848 41.667 0.00 0.00 0.00 2.01
4293 4991 7.939039 TGAATTAATTATCTCTGGGATCACCAC 59.061 37.037 0.00 0.00 46.80 4.16
4452 5150 1.619332 GTTCAGGAGGTCCTCGACTTT 59.381 52.381 12.91 0.00 46.65 2.66
4467 5165 2.220824 CGACTTTCAATGCTTCGTCACA 59.779 45.455 0.00 0.00 0.00 3.58
4558 5257 1.461127 CGAGAAGCCAACACTAACAGC 59.539 52.381 0.00 0.00 0.00 4.40
4563 5262 1.140852 AGCCAACACTAACAGCTCACA 59.859 47.619 0.00 0.00 0.00 3.58
4567 5266 4.499696 GCCAACACTAACAGCTCACATTTT 60.500 41.667 0.00 0.00 0.00 1.82
4575 5275 4.311816 ACAGCTCACATTTTGTTTCCTG 57.688 40.909 0.00 0.00 0.00 3.86
4783 5483 5.011090 TGGAGGTAAATGATCTGAACTCG 57.989 43.478 0.00 0.00 0.00 4.18
4818 5519 6.874288 AAGCTATGCATTTCTCTTATGTCC 57.126 37.500 3.54 0.00 0.00 4.02
4909 5660 1.227002 GAAGGACGACGATCTGCCC 60.227 63.158 0.00 0.00 0.00 5.36
4943 5697 0.178973 TCGATCCCTCCCTCGCATTA 60.179 55.000 0.00 0.00 34.94 1.90
4984 5747 2.432146 ACTGAACTGTGCTCTTGACAGA 59.568 45.455 8.03 0.00 43.04 3.41
5011 5775 6.480651 TGCAGAAACTTATGTCGTAACTGAAA 59.519 34.615 0.00 0.00 0.00 2.69
5024 5788 2.138596 ACTGAAATTTTGTGCTGCCG 57.861 45.000 0.00 0.00 0.00 5.69
5127 5891 3.181526 CTCCCAGGTTGAGCATTCC 57.818 57.895 0.00 0.00 0.00 3.01
5151 5915 4.010349 TCTAGTCTTCTGCTGATCGACAA 58.990 43.478 18.85 7.33 0.00 3.18
5152 5916 2.953020 AGTCTTCTGCTGATCGACAAC 58.047 47.619 18.85 4.05 0.00 3.32
5359 6123 2.742053 TCTTTTGCATCGTCAGTTAGCC 59.258 45.455 0.00 0.00 0.00 3.93
5489 6257 6.314784 GTCTTGTTTAATGGCAGTGTACATC 58.685 40.000 0.00 0.00 0.00 3.06
5524 6387 4.141459 TGGCCCGTTATGGTTGTCATTATA 60.141 41.667 0.00 0.00 37.30 0.98
5525 6388 5.007682 GGCCCGTTATGGTTGTCATTATAT 58.992 41.667 0.00 0.00 37.30 0.86
5526 6389 6.174760 GGCCCGTTATGGTTGTCATTATATA 58.825 40.000 0.00 0.00 37.30 0.86
5580 6443 2.638480 TTGGGATGAACGGGATGATC 57.362 50.000 0.00 0.00 0.00 2.92
5595 6458 0.182061 TGATCCCCTCAAGCAGATGC 59.818 55.000 0.00 0.00 42.49 3.91
5596 6459 4.770594 ATGATCCCCTCAAGCAGATGCG 62.771 54.545 0.00 0.00 40.10 4.73
5608 6471 2.398498 GCAGATGCGTAGTATGTCCTG 58.602 52.381 0.00 0.00 28.93 3.86
5625 6488 6.128138 TGTCCTGAGATCGATAAGGAGATA 57.872 41.667 19.29 9.86 39.48 1.98
5634 6497 6.435591 AGATCGATAAGGAGATATGCTTGTCA 59.564 38.462 16.28 6.19 0.00 3.58
5635 6498 5.773575 TCGATAAGGAGATATGCTTGTCAC 58.226 41.667 16.28 0.83 0.00 3.67
5676 6539 6.670695 AGAAAATGCCCAGTTTGACTAATT 57.329 33.333 0.00 0.00 0.00 1.40
5677 6540 7.775053 AGAAAATGCCCAGTTTGACTAATTA 57.225 32.000 0.00 0.00 0.00 1.40
5678 6541 8.366359 AGAAAATGCCCAGTTTGACTAATTAT 57.634 30.769 0.00 0.00 0.00 1.28
5679 6542 8.253113 AGAAAATGCCCAGTTTGACTAATTATG 58.747 33.333 0.00 0.00 0.00 1.90
5680 6543 4.981806 TGCCCAGTTTGACTAATTATGC 57.018 40.909 0.00 0.00 0.00 3.14
5681 6544 4.339748 TGCCCAGTTTGACTAATTATGCA 58.660 39.130 0.00 0.00 0.00 3.96
5682 6545 4.769488 TGCCCAGTTTGACTAATTATGCAA 59.231 37.500 0.00 0.00 0.00 4.08
5683 6546 5.244851 TGCCCAGTTTGACTAATTATGCAAA 59.755 36.000 0.00 8.13 0.00 3.68
5684 6547 6.162777 GCCCAGTTTGACTAATTATGCAAAA 58.837 36.000 11.97 0.00 32.71 2.44
5685 6548 6.311200 GCCCAGTTTGACTAATTATGCAAAAG 59.689 38.462 11.97 9.09 32.71 2.27
5686 6549 7.601856 CCCAGTTTGACTAATTATGCAAAAGA 58.398 34.615 11.97 0.00 32.71 2.52
5687 6550 7.756722 CCCAGTTTGACTAATTATGCAAAAGAG 59.243 37.037 11.97 7.22 32.71 2.85
5688 6551 8.514594 CCAGTTTGACTAATTATGCAAAAGAGA 58.485 33.333 11.97 0.00 32.71 3.10
5689 6552 9.552114 CAGTTTGACTAATTATGCAAAAGAGAG 57.448 33.333 11.97 0.00 32.71 3.20
5690 6553 9.507329 AGTTTGACTAATTATGCAAAAGAGAGA 57.493 29.630 11.97 0.00 32.71 3.10
5691 6554 9.766277 GTTTGACTAATTATGCAAAAGAGAGAG 57.234 33.333 11.97 0.00 32.71 3.20
5692 6555 9.507329 TTTGACTAATTATGCAAAAGAGAGAGT 57.493 29.630 9.26 0.00 0.00 3.24
5693 6556 8.709386 TGACTAATTATGCAAAAGAGAGAGTC 57.291 34.615 0.00 0.00 0.00 3.36
5694 6557 8.314021 TGACTAATTATGCAAAAGAGAGAGTCA 58.686 33.333 0.00 0.12 36.87 3.41
5695 6558 9.155975 GACTAATTATGCAAAAGAGAGAGTCAA 57.844 33.333 0.00 0.00 0.00 3.18
5696 6559 9.678260 ACTAATTATGCAAAAGAGAGAGTCAAT 57.322 29.630 0.00 0.00 0.00 2.57
5698 6561 6.992063 TTATGCAAAAGAGAGAGTCAATCC 57.008 37.500 0.00 0.00 0.00 3.01
5699 6562 4.630644 TGCAAAAGAGAGAGTCAATCCT 57.369 40.909 0.00 0.00 0.00 3.24
5700 6563 4.573900 TGCAAAAGAGAGAGTCAATCCTC 58.426 43.478 0.00 0.00 0.00 3.71
5701 6564 3.616379 GCAAAAGAGAGAGTCAATCCTCG 59.384 47.826 0.00 0.00 36.56 4.63
5702 6565 4.815269 CAAAAGAGAGAGTCAATCCTCGT 58.185 43.478 0.00 0.00 36.56 4.18
5703 6566 5.233988 CAAAAGAGAGAGTCAATCCTCGTT 58.766 41.667 0.00 0.00 36.56 3.85
5704 6567 4.712122 AAGAGAGAGTCAATCCTCGTTC 57.288 45.455 0.00 0.00 36.56 3.95
5705 6568 2.680841 AGAGAGAGTCAATCCTCGTTCG 59.319 50.000 0.00 0.00 36.56 3.95
5706 6569 2.420722 GAGAGAGTCAATCCTCGTTCGT 59.579 50.000 0.00 0.00 36.56 3.85
5707 6570 2.820787 AGAGAGTCAATCCTCGTTCGTT 59.179 45.455 0.00 0.00 36.56 3.85
5708 6571 3.256136 AGAGAGTCAATCCTCGTTCGTTT 59.744 43.478 0.00 0.00 36.56 3.60
5709 6572 3.988517 GAGAGTCAATCCTCGTTCGTTTT 59.011 43.478 0.00 0.00 36.56 2.43
5710 6573 3.988517 AGAGTCAATCCTCGTTCGTTTTC 59.011 43.478 0.00 0.00 36.56 2.29
5711 6574 3.724374 AGTCAATCCTCGTTCGTTTTCA 58.276 40.909 0.00 0.00 0.00 2.69
5712 6575 3.741344 AGTCAATCCTCGTTCGTTTTCAG 59.259 43.478 0.00 0.00 0.00 3.02
5713 6576 3.064207 TCAATCCTCGTTCGTTTTCAGG 58.936 45.455 0.00 0.00 0.00 3.86
5714 6577 3.064207 CAATCCTCGTTCGTTTTCAGGA 58.936 45.455 2.93 2.93 37.66 3.86
5715 6578 2.144482 TCCTCGTTCGTTTTCAGGAC 57.856 50.000 0.00 0.00 0.00 3.85
5716 6579 1.409790 TCCTCGTTCGTTTTCAGGACA 59.590 47.619 0.00 0.00 0.00 4.02
5717 6580 1.525619 CCTCGTTCGTTTTCAGGACAC 59.474 52.381 0.00 0.00 0.00 3.67
5718 6581 1.525619 CTCGTTCGTTTTCAGGACACC 59.474 52.381 0.00 0.00 0.00 4.16
5719 6582 0.231279 CGTTCGTTTTCAGGACACCG 59.769 55.000 0.00 0.00 0.00 4.94
5720 6583 1.574134 GTTCGTTTTCAGGACACCGA 58.426 50.000 0.00 0.00 0.00 4.69
5721 6584 1.525619 GTTCGTTTTCAGGACACCGAG 59.474 52.381 0.00 0.00 0.00 4.63
5722 6585 0.599204 TCGTTTTCAGGACACCGAGC 60.599 55.000 0.00 0.00 0.00 5.03
5723 6586 1.566018 CGTTTTCAGGACACCGAGCC 61.566 60.000 0.00 0.00 0.00 4.70
5724 6587 0.534203 GTTTTCAGGACACCGAGCCA 60.534 55.000 0.00 0.00 0.00 4.75
5725 6588 0.250295 TTTTCAGGACACCGAGCCAG 60.250 55.000 0.00 0.00 0.00 4.85
5726 6589 2.111999 TTTCAGGACACCGAGCCAGG 62.112 60.000 0.00 0.00 37.30 4.45
5727 6590 4.087892 CAGGACACCGAGCCAGGG 62.088 72.222 0.00 0.00 35.02 4.45
5751 6614 4.564110 CGGGGAAATCGGAGGCCC 62.564 72.222 0.00 0.00 39.93 5.80
5752 6615 3.097162 GGGGAAATCGGAGGCCCT 61.097 66.667 0.00 0.00 40.51 5.19
5753 6616 2.193248 GGGAAATCGGAGGCCCTG 59.807 66.667 0.00 0.00 37.59 4.45
5754 6617 2.193248 GGAAATCGGAGGCCCTGG 59.807 66.667 0.00 0.00 0.00 4.45
5755 6618 2.193248 GAAATCGGAGGCCCTGGG 59.807 66.667 8.86 8.86 0.00 4.45
5773 6636 5.490159 CCTGGGCAAATCAAAATTACACAT 58.510 37.500 0.00 0.00 0.00 3.21
5890 6753 0.253044 TGCTTGGCTCCATGGTAGAC 59.747 55.000 12.58 10.72 0.00 2.59
5972 6835 1.196808 CCGTTGTTTGGAGAATGGTCG 59.803 52.381 0.00 0.00 32.07 4.79
6241 7105 1.750780 TTGCAAGGTTGTGTGGCGA 60.751 52.632 0.00 0.00 0.00 5.54
6395 7266 4.287067 TGAGGAGTTGTATGGCTCTTTCTT 59.713 41.667 0.00 0.00 32.67 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
839 844 7.904977 CGTATAGCTTCTGTAGTTGTTTACGTA 59.095 37.037 0.00 0.00 0.00 3.57
844 849 6.034161 ACCGTATAGCTTCTGTAGTTGTTT 57.966 37.500 0.00 0.00 0.00 2.83
845 850 5.418209 AGACCGTATAGCTTCTGTAGTTGTT 59.582 40.000 0.00 0.00 0.00 2.83
846 851 4.948621 AGACCGTATAGCTTCTGTAGTTGT 59.051 41.667 0.00 0.00 0.00 3.32
847 852 5.502153 AGACCGTATAGCTTCTGTAGTTG 57.498 43.478 0.00 0.00 0.00 3.16
848 853 6.600822 TGTTAGACCGTATAGCTTCTGTAGTT 59.399 38.462 0.00 0.00 0.00 2.24
849 854 6.118170 TGTTAGACCGTATAGCTTCTGTAGT 58.882 40.000 0.00 0.00 0.00 2.73
850 855 6.615264 TGTTAGACCGTATAGCTTCTGTAG 57.385 41.667 0.00 0.00 0.00 2.74
851 856 7.395190 TTTGTTAGACCGTATAGCTTCTGTA 57.605 36.000 0.00 0.00 0.00 2.74
852 857 5.909621 TTGTTAGACCGTATAGCTTCTGT 57.090 39.130 0.00 0.00 0.00 3.41
853 858 7.772332 ATTTTGTTAGACCGTATAGCTTCTG 57.228 36.000 0.00 0.00 0.00 3.02
854 859 8.038944 TGAATTTTGTTAGACCGTATAGCTTCT 58.961 33.333 0.00 0.00 0.00 2.85
855 860 8.193250 TGAATTTTGTTAGACCGTATAGCTTC 57.807 34.615 0.00 0.00 0.00 3.86
856 861 8.556213 TTGAATTTTGTTAGACCGTATAGCTT 57.444 30.769 0.00 0.00 0.00 3.74
857 862 8.556213 TTTGAATTTTGTTAGACCGTATAGCT 57.444 30.769 0.00 0.00 0.00 3.32
858 863 9.221775 CATTTGAATTTTGTTAGACCGTATAGC 57.778 33.333 0.00 0.00 0.00 2.97
861 866 9.840427 CTTCATTTGAATTTTGTTAGACCGTAT 57.160 29.630 0.00 0.00 33.01 3.06
862 867 7.806014 GCTTCATTTGAATTTTGTTAGACCGTA 59.194 33.333 0.00 0.00 33.01 4.02
863 868 6.640907 GCTTCATTTGAATTTTGTTAGACCGT 59.359 34.615 0.00 0.00 33.01 4.83
864 869 6.183359 CGCTTCATTTGAATTTTGTTAGACCG 60.183 38.462 0.00 0.00 33.01 4.79
865 870 6.861055 TCGCTTCATTTGAATTTTGTTAGACC 59.139 34.615 0.00 0.00 33.01 3.85
866 871 7.851822 TCGCTTCATTTGAATTTTGTTAGAC 57.148 32.000 0.00 0.00 33.01 2.59
867 872 7.481483 CGATCGCTTCATTTGAATTTTGTTAGA 59.519 33.333 0.26 0.00 33.01 2.10
868 873 7.253420 CCGATCGCTTCATTTGAATTTTGTTAG 60.253 37.037 10.32 0.00 33.01 2.34
869 874 6.526325 CCGATCGCTTCATTTGAATTTTGTTA 59.474 34.615 10.32 0.00 33.01 2.41
870 875 5.345741 CCGATCGCTTCATTTGAATTTTGTT 59.654 36.000 10.32 0.00 33.01 2.83
871 876 4.858692 CCGATCGCTTCATTTGAATTTTGT 59.141 37.500 10.32 0.00 33.01 2.83
872 877 4.858692 ACCGATCGCTTCATTTGAATTTTG 59.141 37.500 10.32 0.00 33.01 2.44
873 878 5.059404 ACCGATCGCTTCATTTGAATTTT 57.941 34.783 10.32 0.00 33.01 1.82
926 931 3.346734 GAGGGGAATGGGGGTGCA 61.347 66.667 0.00 0.00 0.00 4.57
945 950 4.821589 CGACAGCGGGGAGGAAGC 62.822 72.222 0.00 0.00 0.00 3.86
1011 1016 2.821810 TGTGTGTGTGTGTGGCCG 60.822 61.111 0.00 0.00 0.00 6.13
1169 1198 2.885861 GATGTGGACGACTCCGCT 59.114 61.111 7.11 0.00 46.14 5.52
1385 1417 2.447379 ATGGAGCGGAGGCAGGAT 60.447 61.111 0.00 0.00 43.41 3.24
1401 1433 2.041819 GAGGTCGGGGTGGAGGAT 60.042 66.667 0.00 0.00 0.00 3.24
1451 1483 1.642037 CCGAAGAGTACTCCGTCGCA 61.642 60.000 28.55 0.00 36.74 5.10
1511 1543 3.325753 GGGCTGGGAGCACTGAGT 61.326 66.667 0.00 0.00 42.59 3.41
1750 1782 3.441572 CGCAGAGAGACCCAATTTCAAAT 59.558 43.478 0.00 0.00 0.00 2.32
1794 1827 1.511887 CAACGAAGCCGCCAAATCG 60.512 57.895 0.00 4.52 39.95 3.34
1802 1835 1.001815 ACAAACATTCCAACGAAGCCG 60.002 47.619 0.00 0.00 42.50 5.52
1938 1971 4.947147 TGACGGCCACAGTTGCCC 62.947 66.667 10.08 0.00 46.48 5.36
2007 2040 1.982073 GCAGAATACAGTGCCGGTGC 61.982 60.000 1.90 0.00 33.29 5.01
2012 2045 4.191544 TGTAGAATGCAGAATACAGTGCC 58.808 43.478 0.00 0.00 39.04 5.01
2021 2054 5.983118 CGTGGTATACATGTAGAATGCAGAA 59.017 40.000 11.91 0.00 31.11 3.02
2082 2115 5.142061 TGACTGTAAATCTGTAAGCCGAA 57.858 39.130 0.00 0.00 0.00 4.30
2352 2543 5.122519 TCACTCTGCTCAACAAACAATGTA 58.877 37.500 0.00 0.00 42.99 2.29
2413 2605 2.880890 AGACTCGCAATTCAAGTGCTTT 59.119 40.909 8.41 0.00 39.95 3.51
2457 2663 8.111836 CACTGAATGTCAAAATGTCAAAACAAG 58.888 33.333 0.00 0.00 39.30 3.16
2536 2744 6.340522 ACCATAAGCCAATCAAATAGCAAAC 58.659 36.000 0.00 0.00 0.00 2.93
2591 2812 4.514441 CACAGAAATGATGCTGGTATCCTC 59.486 45.833 0.00 0.00 36.47 3.71
2661 2912 7.222224 CAGAAGCTTAGATTTGATTGAAATGGC 59.778 37.037 0.00 0.00 34.18 4.40
2667 2918 7.553760 TGCATACAGAAGCTTAGATTTGATTGA 59.446 33.333 0.00 0.00 0.00 2.57
2670 2921 7.052873 AGTGCATACAGAAGCTTAGATTTGAT 58.947 34.615 0.00 0.00 0.00 2.57
2806 3067 9.874205 ATAGGTACATCCATTTTTGAACAAATG 57.126 29.630 0.00 0.04 41.86 2.32
2853 3114 8.031277 GCTTTCCATTTGTCAAAATCTAGATGT 58.969 33.333 5.86 0.00 33.59 3.06
2854 3115 8.030692 TGCTTTCCATTTGTCAAAATCTAGATG 58.969 33.333 5.86 0.00 33.59 2.90
2855 3116 8.125978 TGCTTTCCATTTGTCAAAATCTAGAT 57.874 30.769 1.31 0.00 33.59 1.98
2856 3117 7.523293 TGCTTTCCATTTGTCAAAATCTAGA 57.477 32.000 1.31 0.00 33.59 2.43
2857 3118 7.816031 ACATGCTTTCCATTTGTCAAAATCTAG 59.184 33.333 1.31 0.00 33.59 2.43
2858 3119 7.669427 ACATGCTTTCCATTTGTCAAAATCTA 58.331 30.769 1.31 0.00 33.59 1.98
2859 3120 6.527423 ACATGCTTTCCATTTGTCAAAATCT 58.473 32.000 1.31 0.00 33.59 2.40
2860 3121 6.790285 ACATGCTTTCCATTTGTCAAAATC 57.210 33.333 1.31 0.00 33.59 2.17
2861 3122 8.723311 CAATACATGCTTTCCATTTGTCAAAAT 58.277 29.630 1.31 0.00 36.39 1.82
2862 3123 7.714377 ACAATACATGCTTTCCATTTGTCAAAA 59.286 29.630 1.31 0.00 30.42 2.44
2863 3124 7.171167 CACAATACATGCTTTCCATTTGTCAAA 59.829 33.333 0.00 0.00 32.71 2.69
2864 3125 6.645827 CACAATACATGCTTTCCATTTGTCAA 59.354 34.615 0.00 0.00 32.71 3.18
2865 3126 6.157904 CACAATACATGCTTTCCATTTGTCA 58.842 36.000 0.00 0.00 32.71 3.58
2866 3127 5.577945 CCACAATACATGCTTTCCATTTGTC 59.422 40.000 0.00 0.00 32.71 3.18
2867 3128 5.245751 TCCACAATACATGCTTTCCATTTGT 59.754 36.000 0.00 0.00 34.39 2.83
2868 3129 5.722263 TCCACAATACATGCTTTCCATTTG 58.278 37.500 0.00 0.00 29.71 2.32
2869 3130 5.999205 TCCACAATACATGCTTTCCATTT 57.001 34.783 0.00 0.00 29.71 2.32
2870 3131 5.622007 CGTTCCACAATACATGCTTTCCATT 60.622 40.000 0.00 0.00 29.71 3.16
2871 3132 4.142403 CGTTCCACAATACATGCTTTCCAT 60.142 41.667 0.00 0.00 33.39 3.41
2872 3133 3.190327 CGTTCCACAATACATGCTTTCCA 59.810 43.478 0.00 0.00 0.00 3.53
2873 3134 3.427503 CCGTTCCACAATACATGCTTTCC 60.428 47.826 0.00 0.00 0.00 3.13
2874 3135 3.438781 TCCGTTCCACAATACATGCTTTC 59.561 43.478 0.00 0.00 0.00 2.62
2875 3136 3.417101 TCCGTTCCACAATACATGCTTT 58.583 40.909 0.00 0.00 0.00 3.51
2876 3137 3.009723 CTCCGTTCCACAATACATGCTT 58.990 45.455 0.00 0.00 0.00 3.91
2877 3138 2.632377 CTCCGTTCCACAATACATGCT 58.368 47.619 0.00 0.00 0.00 3.79
2878 3139 1.670811 CCTCCGTTCCACAATACATGC 59.329 52.381 0.00 0.00 0.00 4.06
2879 3140 2.093181 TCCCTCCGTTCCACAATACATG 60.093 50.000 0.00 0.00 0.00 3.21
2880 3141 2.170607 CTCCCTCCGTTCCACAATACAT 59.829 50.000 0.00 0.00 0.00 2.29
2881 3142 1.553248 CTCCCTCCGTTCCACAATACA 59.447 52.381 0.00 0.00 0.00 2.29
2882 3143 1.553704 ACTCCCTCCGTTCCACAATAC 59.446 52.381 0.00 0.00 0.00 1.89
2883 3144 1.946984 ACTCCCTCCGTTCCACAATA 58.053 50.000 0.00 0.00 0.00 1.90
2887 3148 1.777941 ATCTACTCCCTCCGTTCCAC 58.222 55.000 0.00 0.00 0.00 4.02
3415 3717 7.115414 CCATCTGAGGAAAGAATAGGAAACTT 58.885 38.462 0.00 0.00 43.67 2.66
3490 3792 4.081420 TGAACTCTGCCAAATAGAGGAGAC 60.081 45.833 6.92 0.00 44.65 3.36
3658 3982 6.238842 GCATGCAGAGATAAGCCTTTAATGAA 60.239 38.462 14.21 0.00 0.00 2.57
3802 4134 9.162764 TGTTCTAAATTGAAGATGCTAACTACC 57.837 33.333 0.00 0.00 0.00 3.18
3837 4169 9.243637 CCACAATGGATATAAAATTACAAACCG 57.756 33.333 0.00 0.00 40.96 4.44
3862 4194 6.867816 TCACATTTACAATGCTTCAATTCACC 59.132 34.615 0.00 0.00 0.00 4.02
3881 4213 6.445451 AGGATCTTATGGTAGCATCACATT 57.555 37.500 11.40 0.00 0.00 2.71
3883 4215 6.554982 AGTTAGGATCTTATGGTAGCATCACA 59.445 38.462 11.40 0.00 0.00 3.58
3918 4250 0.801251 GTGTGATGACTGCCTGAAGC 59.199 55.000 0.00 0.00 44.14 3.86
3930 4262 1.830279 ATGGCCACTGAAGTGTGATG 58.170 50.000 8.16 0.00 44.21 3.07
3932 4264 2.363306 AAATGGCCACTGAAGTGTGA 57.637 45.000 8.16 0.00 44.21 3.58
3935 4267 4.853924 AGTTAAAATGGCCACTGAAGTG 57.146 40.909 8.16 3.35 45.23 3.16
3936 4268 4.039124 CCAAGTTAAAATGGCCACTGAAGT 59.961 41.667 8.16 0.00 0.00 3.01
3937 4269 4.039124 ACCAAGTTAAAATGGCCACTGAAG 59.961 41.667 8.16 0.00 40.51 3.02
3945 4277 5.161358 GCTGTCTAACCAAGTTAAAATGGC 58.839 41.667 7.52 0.00 40.51 4.40
3953 4285 2.863809 CAAGGGCTGTCTAACCAAGTT 58.136 47.619 0.00 0.00 0.00 2.66
3968 4300 0.622665 AGATGGAACTCTGGCAAGGG 59.377 55.000 0.00 0.00 0.00 3.95
3982 4515 7.615757 AGGTTTACTTGGGAAAAGAATAGATGG 59.384 37.037 0.00 0.00 0.00 3.51
4070 4640 8.766151 TCAAAAACTTCAACAAAACCACTAAAC 58.234 29.630 0.00 0.00 0.00 2.01
4074 4644 5.408299 GCTCAAAAACTTCAACAAAACCACT 59.592 36.000 0.00 0.00 0.00 4.00
4293 4991 4.006319 GGAGACAAAGATGAGGGAACAAG 58.994 47.826 0.00 0.00 0.00 3.16
4452 5150 2.543848 GACTGTTGTGACGAAGCATTGA 59.456 45.455 0.00 0.00 0.00 2.57
4467 5165 4.536765 ACCAGAGAAAATTGTGGACTGTT 58.463 39.130 0.00 0.00 33.95 3.16
4558 5257 7.428020 TGAAGAATCAGGAAACAAAATGTGAG 58.572 34.615 0.00 0.00 0.00 3.51
4783 5483 1.878734 GCATAGCTTTGATGGAGGAGC 59.121 52.381 8.49 0.00 35.42 4.70
4909 5660 4.574828 AGGGATCGAACCATTAAACATTCG 59.425 41.667 14.28 10.46 44.04 3.34
4984 5747 5.405571 CAGTTACGACATAAGTTTCTGCACT 59.594 40.000 0.00 0.00 0.00 4.40
5011 5775 4.722855 GCCGCGGCAGCACAAAAT 62.723 61.111 43.55 0.00 45.49 1.82
5024 5788 0.651031 GAAGGAATGTTAGTCGCCGC 59.349 55.000 0.00 0.00 0.00 6.53
5127 5891 4.036144 TGTCGATCAGCAGAAGACTAGATG 59.964 45.833 15.38 0.00 36.81 2.90
5151 5915 2.357517 GGCTGTGCTACGCTGTGT 60.358 61.111 0.00 0.00 0.00 3.72
5152 5916 1.300971 AATGGCTGTGCTACGCTGTG 61.301 55.000 0.00 0.00 0.00 3.66
5359 6123 6.435904 TCCAACCTTATAATTGACCACAAAGG 59.564 38.462 1.17 0.00 45.67 3.11
5524 6387 6.441088 AGACCTTTGGTTCTCAAGAGTTAT 57.559 37.500 0.00 0.00 35.25 1.89
5525 6388 5.509163 CGAGACCTTTGGTTCTCAAGAGTTA 60.509 44.000 12.82 0.00 35.25 2.24
5526 6389 4.709250 GAGACCTTTGGTTCTCAAGAGTT 58.291 43.478 0.00 0.00 35.25 3.01
5540 6403 5.183904 CCAAAATCTGAAATCCGAGACCTTT 59.816 40.000 0.00 0.00 0.00 3.11
5580 6443 0.531532 CTACGCATCTGCTTGAGGGG 60.532 60.000 0.09 7.25 43.59 4.79
5595 6458 6.183360 CCTTATCGATCTCAGGACATACTACG 60.183 46.154 0.00 0.00 0.00 3.51
5596 6459 6.879993 TCCTTATCGATCTCAGGACATACTAC 59.120 42.308 14.20 0.00 29.97 2.73
5597 6460 7.017319 TCCTTATCGATCTCAGGACATACTA 57.983 40.000 14.20 0.00 29.97 1.82
5598 6461 5.882040 TCCTTATCGATCTCAGGACATACT 58.118 41.667 14.20 0.00 29.97 2.12
5606 6469 6.698008 AGCATATCTCCTTATCGATCTCAG 57.302 41.667 0.00 0.00 0.00 3.35
5608 6471 6.862209 ACAAGCATATCTCCTTATCGATCTC 58.138 40.000 0.00 0.00 0.00 2.75
5625 6488 1.002366 GCGATCTTCGTGACAAGCAT 58.998 50.000 0.00 0.00 42.81 3.79
5634 6497 0.242825 TTTGTCTCGGCGATCTTCGT 59.757 50.000 11.27 0.00 42.81 3.85
5635 6498 0.917259 CTTTGTCTCGGCGATCTTCG 59.083 55.000 11.27 0.00 43.89 3.79
5676 6539 6.305272 AGGATTGACTCTCTCTTTTGCATA 57.695 37.500 0.00 0.00 0.00 3.14
5677 6540 5.176741 AGGATTGACTCTCTCTTTTGCAT 57.823 39.130 0.00 0.00 0.00 3.96
5678 6541 4.573900 GAGGATTGACTCTCTCTTTTGCA 58.426 43.478 0.00 0.00 34.65 4.08
5679 6542 3.616379 CGAGGATTGACTCTCTCTTTTGC 59.384 47.826 0.00 0.00 35.33 3.68
5680 6543 4.815269 ACGAGGATTGACTCTCTCTTTTG 58.185 43.478 0.00 0.00 35.33 2.44
5681 6544 5.474825 GAACGAGGATTGACTCTCTCTTTT 58.525 41.667 0.00 0.00 35.33 2.27
5682 6545 4.380023 CGAACGAGGATTGACTCTCTCTTT 60.380 45.833 0.00 0.00 35.33 2.52
5683 6546 3.127895 CGAACGAGGATTGACTCTCTCTT 59.872 47.826 0.00 0.00 35.33 2.85
5684 6547 2.680841 CGAACGAGGATTGACTCTCTCT 59.319 50.000 0.00 0.00 35.33 3.10
5685 6548 2.420722 ACGAACGAGGATTGACTCTCTC 59.579 50.000 0.14 0.00 35.33 3.20
5686 6549 2.438411 ACGAACGAGGATTGACTCTCT 58.562 47.619 0.14 0.00 35.33 3.10
5687 6550 2.923605 ACGAACGAGGATTGACTCTC 57.076 50.000 0.14 0.00 35.33 3.20
5688 6551 3.662247 AAACGAACGAGGATTGACTCT 57.338 42.857 0.14 0.00 35.33 3.24
5689 6552 3.739300 TGAAAACGAACGAGGATTGACTC 59.261 43.478 0.14 0.00 0.00 3.36
5690 6553 3.724374 TGAAAACGAACGAGGATTGACT 58.276 40.909 0.14 0.00 0.00 3.41
5691 6554 3.120649 CCTGAAAACGAACGAGGATTGAC 60.121 47.826 0.14 0.00 0.00 3.18
5692 6555 3.064207 CCTGAAAACGAACGAGGATTGA 58.936 45.455 0.14 0.00 0.00 2.57
5693 6556 3.064207 TCCTGAAAACGAACGAGGATTG 58.936 45.455 0.14 0.00 0.00 2.67
5694 6557 3.064931 GTCCTGAAAACGAACGAGGATT 58.935 45.455 0.14 0.00 35.31 3.01
5695 6558 2.036733 TGTCCTGAAAACGAACGAGGAT 59.963 45.455 0.14 0.00 35.31 3.24
5696 6559 1.409790 TGTCCTGAAAACGAACGAGGA 59.590 47.619 0.14 0.00 0.00 3.71
5697 6560 1.525619 GTGTCCTGAAAACGAACGAGG 59.474 52.381 0.14 0.00 0.00 4.63
5698 6561 1.525619 GGTGTCCTGAAAACGAACGAG 59.474 52.381 0.14 0.00 0.00 4.18
5699 6562 1.574134 GGTGTCCTGAAAACGAACGA 58.426 50.000 0.14 0.00 0.00 3.85
5700 6563 0.231279 CGGTGTCCTGAAAACGAACG 59.769 55.000 0.00 0.00 0.00 3.95
5701 6564 1.525619 CTCGGTGTCCTGAAAACGAAC 59.474 52.381 0.00 0.00 0.00 3.95
5702 6565 1.860676 CTCGGTGTCCTGAAAACGAA 58.139 50.000 0.00 0.00 0.00 3.85
5703 6566 0.599204 GCTCGGTGTCCTGAAAACGA 60.599 55.000 0.00 0.00 0.00 3.85
5704 6567 1.566018 GGCTCGGTGTCCTGAAAACG 61.566 60.000 0.00 0.00 0.00 3.60
5705 6568 0.534203 TGGCTCGGTGTCCTGAAAAC 60.534 55.000 0.00 0.00 0.00 2.43
5706 6569 0.250295 CTGGCTCGGTGTCCTGAAAA 60.250 55.000 0.00 0.00 0.00 2.29
5707 6570 1.371183 CTGGCTCGGTGTCCTGAAA 59.629 57.895 0.00 0.00 0.00 2.69
5708 6571 2.583441 CCTGGCTCGGTGTCCTGAA 61.583 63.158 0.00 0.00 0.00 3.02
5709 6572 2.997315 CCTGGCTCGGTGTCCTGA 60.997 66.667 0.00 0.00 0.00 3.86
5710 6573 4.087892 CCCTGGCTCGGTGTCCTG 62.088 72.222 0.00 0.00 0.00 3.86
5730 6593 1.444672 CCTCCGATTTCCCCGGTAC 59.555 63.158 0.00 0.00 46.53 3.34
5731 6594 2.437396 GCCTCCGATTTCCCCGGTA 61.437 63.158 0.00 0.00 46.53 4.02
5732 6595 3.793888 GCCTCCGATTTCCCCGGT 61.794 66.667 0.00 0.00 46.53 5.28
5734 6597 4.564110 GGGCCTCCGATTTCCCCG 62.564 72.222 0.84 0.00 32.60 5.73
5735 6598 3.097162 AGGGCCTCCGATTTCCCC 61.097 66.667 0.00 0.00 39.59 4.81
5736 6599 2.193248 CAGGGCCTCCGATTTCCC 59.807 66.667 0.95 0.00 39.05 3.97
5737 6600 2.193248 CCAGGGCCTCCGATTTCC 59.807 66.667 0.95 0.00 38.33 3.13
5738 6601 2.193248 CCCAGGGCCTCCGATTTC 59.807 66.667 0.95 0.00 38.33 2.17
5739 6602 4.129148 GCCCAGGGCCTCCGATTT 62.129 66.667 21.62 0.00 44.06 2.17
5749 6612 4.252878 GTGTAATTTTGATTTGCCCAGGG 58.747 43.478 0.00 0.00 0.00 4.45
5750 6613 4.892433 TGTGTAATTTTGATTTGCCCAGG 58.108 39.130 0.00 0.00 0.00 4.45
5751 6614 5.933463 ACATGTGTAATTTTGATTTGCCCAG 59.067 36.000 0.00 0.00 0.00 4.45
5752 6615 5.699915 CACATGTGTAATTTTGATTTGCCCA 59.300 36.000 18.03 0.00 0.00 5.36
5753 6616 5.931146 TCACATGTGTAATTTTGATTTGCCC 59.069 36.000 24.63 0.00 0.00 5.36
5754 6617 6.091169 CCTCACATGTGTAATTTTGATTTGCC 59.909 38.462 24.63 0.00 0.00 4.52
5755 6618 6.091169 CCCTCACATGTGTAATTTTGATTTGC 59.909 38.462 24.63 0.00 0.00 3.68
5756 6619 7.153985 ACCCTCACATGTGTAATTTTGATTTG 58.846 34.615 24.63 0.00 0.00 2.32
5757 6620 7.301868 ACCCTCACATGTGTAATTTTGATTT 57.698 32.000 24.63 0.00 0.00 2.17
5758 6621 6.916360 ACCCTCACATGTGTAATTTTGATT 57.084 33.333 24.63 0.00 0.00 2.57
5759 6622 6.295236 CCAACCCTCACATGTGTAATTTTGAT 60.295 38.462 24.63 2.20 0.00 2.57
5760 6623 5.010516 CCAACCCTCACATGTGTAATTTTGA 59.989 40.000 24.63 2.63 0.00 2.69
5761 6624 5.229423 CCAACCCTCACATGTGTAATTTTG 58.771 41.667 24.63 19.47 0.00 2.44
5762 6625 4.262420 GCCAACCCTCACATGTGTAATTTT 60.262 41.667 24.63 10.43 0.00 1.82
5763 6626 3.258123 GCCAACCCTCACATGTGTAATTT 59.742 43.478 24.63 11.73 0.00 1.82
5764 6627 2.825532 GCCAACCCTCACATGTGTAATT 59.174 45.455 24.63 12.46 0.00 1.40
5765 6628 2.224992 TGCCAACCCTCACATGTGTAAT 60.225 45.455 24.63 7.22 0.00 1.89
5766 6629 1.143889 TGCCAACCCTCACATGTGTAA 59.856 47.619 24.63 6.40 0.00 2.41
5767 6630 0.767998 TGCCAACCCTCACATGTGTA 59.232 50.000 24.63 11.15 0.00 2.90
5773 6636 2.528818 CCTCCTGCCAACCCTCACA 61.529 63.158 0.00 0.00 0.00 3.58
5890 6753 3.002656 CCATAAGCAAGGCATCTACAACG 59.997 47.826 0.00 0.00 0.00 4.10
5972 6835 4.390584 GACGTTCACGCGCACGAC 62.391 66.667 26.67 19.01 43.93 4.34
6109 6973 0.250295 CGGTGAAGTGCCTTGGAAGA 60.250 55.000 0.00 0.00 0.00 2.87
6241 7105 1.627834 CTCCAGAAAGCTCTCAACCCT 59.372 52.381 0.00 0.00 0.00 4.34
6395 7266 0.544357 ATGGACTCCAACACGAGGGA 60.544 55.000 0.66 0.00 36.95 4.20


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

AutoCloner maintained by Alex Coulton.