Multiple sequence alignment - TraesCS7D01G496800

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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 TraesCS7D01G496800 chr7D 100.000 3203 0 0 1 3203 603649244 603652446 0.000000e+00 5915.0
1 TraesCS7D01G496800 chr7D 90.595 521 32 8 1 509 165113003 165113518 0.000000e+00 675.0
2 TraesCS7D01G496800 chr7D 74.532 1390 268 61 836 2198 603701151 603702481 7.870000e-146 527.0
3 TraesCS7D01G496800 chr7D 84.694 294 39 6 2253 2542 603605055 603605346 4.040000e-74 289.0
4 TraesCS7D01G496800 chr7D 76.744 215 35 4 2994 3194 189248429 189248642 4.370000e-19 106.0
5 TraesCS7D01G496800 chr7D 76.471 204 30 11 2994 3181 47223736 47223937 9.460000e-16 95.3
6 TraesCS7D01G496800 chr7D 80.000 125 11 12 3081 3194 575748667 575748788 2.650000e-11 80.5
7 TraesCS7D01G496800 chr7D 82.051 78 9 4 2585 2657 41801482 41801405 9.590000e-06 62.1
8 TraesCS7D01G496800 chr7B 93.612 2035 103 12 897 2922 685382996 685385012 0.000000e+00 3013.0
9 TraesCS7D01G496800 chr7B 84.392 551 35 27 12 512 537788766 537789315 7.980000e-136 494.0
10 TraesCS7D01G496800 chr7B 85.836 353 25 7 513 863 685382667 685382996 5.080000e-93 351.0
11 TraesCS7D01G496800 chr7B 99.138 116 1 0 3088 3203 685385003 685385118 3.240000e-50 209.0
12 TraesCS7D01G496800 chr7B 77.523 218 29 10 2995 3197 512763160 512762948 2.610000e-21 113.0
13 TraesCS7D01G496800 chr7B 88.235 85 10 0 3052 3136 639093183 639093267 5.650000e-18 102.0
14 TraesCS7D01G496800 chr7B 85.882 85 12 0 3052 3136 333961031 333961115 1.220000e-14 91.6
15 TraesCS7D01G496800 chr7B 80.833 120 8 7 3076 3181 332815397 332815279 2.650000e-11 80.5
16 TraesCS7D01G496800 chr7B 92.308 52 4 0 3152 3203 499649308 499649359 1.230000e-09 75.0
17 TraesCS7D01G496800 chr7A 93.750 592 33 2 1847 2434 696257111 696257702 0.000000e+00 885.0
18 TraesCS7D01G496800 chr7A 95.000 380 12 3 808 1185 696256736 696257110 9.900000e-165 590.0
19 TraesCS7D01G496800 chr7A 88.959 317 23 7 513 824 696256406 696256715 6.480000e-102 381.0
20 TraesCS7D01G496800 chr7A 88.235 170 19 1 3034 3203 696290414 696290582 5.420000e-48 202.0
21 TraesCS7D01G496800 chr7A 78.125 224 34 5 2994 3203 194793916 194793694 9.330000e-26 128.0
22 TraesCS7D01G496800 chr7A 91.860 86 7 0 853 938 696201384 696201299 1.560000e-23 121.0
23 TraesCS7D01G496800 chr7A 74.576 177 34 10 2400 2569 547526457 547526285 2.060000e-07 67.6
24 TraesCS7D01G496800 chr7A 84.127 63 5 4 2585 2642 427555994 427555932 4.460000e-04 56.5
25 TraesCS7D01G496800 chr2B 91.762 522 28 5 1 512 131288508 131287992 0.000000e+00 712.0
26 TraesCS7D01G496800 chr2B 77.703 148 28 4 2995 3139 68330011 68329866 5.690000e-13 86.1
27 TraesCS7D01G496800 chr2B 76.331 169 31 9 3018 3181 138959766 138959930 7.360000e-12 82.4
28 TraesCS7D01G496800 chr2A 91.231 536 25 10 1 517 598220931 598220399 0.000000e+00 710.0
29 TraesCS7D01G496800 chr2A 88.641 537 40 9 1 517 329113128 329112593 4.510000e-178 634.0
30 TraesCS7D01G496800 chr2A 89.873 79 6 1 2731 2809 674421922 674421998 2.030000e-17 100.0
31 TraesCS7D01G496800 chr2A 80.000 140 23 4 3003 3139 675390530 675390393 7.310000e-17 99.0
32 TraesCS7D01G496800 chr2A 76.042 192 29 6 3018 3194 175835622 175835433 2.050000e-12 84.2
33 TraesCS7D01G496800 chr3D 91.013 523 31 7 1 512 131348544 131349061 0.000000e+00 691.0
34 TraesCS7D01G496800 chr3D 90.631 523 34 10 1 512 521590743 521591261 0.000000e+00 680.0
35 TraesCS7D01G496800 chr3D 90.226 532 34 7 2 521 10516478 10515953 0.000000e+00 678.0
36 TraesCS7D01G496800 chr3D 82.166 157 23 4 2993 3146 502896925 502896771 2.590000e-26 130.0
37 TraesCS7D01G496800 chr3D 92.308 65 4 1 3076 3139 173618843 173618779 1.220000e-14 91.6
38 TraesCS7D01G496800 chr3D 78.070 114 11 9 3092 3191 356844722 356844835 3.450000e-05 60.2
39 TraesCS7D01G496800 chr3B 91.154 520 31 5 3 512 151575736 151575222 0.000000e+00 691.0
40 TraesCS7D01G496800 chr3B 77.093 227 30 16 2995 3203 603212659 603212437 9.390000e-21 111.0
41 TraesCS7D01G496800 chr5B 90.996 522 31 8 1 511 282847033 282846517 0.000000e+00 689.0
42 TraesCS7D01G496800 chr5B 91.013 523 30 6 1 513 492265155 492264640 0.000000e+00 689.0
43 TraesCS7D01G496800 chr5B 90.323 527 35 7 1 516 382631437 382630916 0.000000e+00 676.0
44 TraesCS7D01G496800 chr5B 97.674 43 1 0 2767 2809 656903736 656903778 1.230000e-09 75.0
45 TraesCS7D01G496800 chr5B 85.938 64 6 2 2582 2642 477641345 477641408 7.420000e-07 65.8
46 TraesCS7D01G496800 chr5B 92.308 39 3 0 2613 2651 534537431 534537393 4.460000e-04 56.5
47 TraesCS7D01G496800 chr4D 90.494 526 35 9 1 515 221285235 221284714 0.000000e+00 680.0
48 TraesCS7D01G496800 chr4D 78.286 175 27 9 2489 2656 10258576 10258746 5.650000e-18 102.0
49 TraesCS7D01G496800 chr4D 92.188 64 5 0 3076 3139 32419029 32418966 1.220000e-14 91.6
50 TraesCS7D01G496800 chr4D 87.500 80 9 1 3060 3139 55271419 55271341 1.220000e-14 91.6
51 TraesCS7D01G496800 chr4B 89.299 542 37 12 1 522 407060013 407060553 0.000000e+00 660.0
52 TraesCS7D01G496800 chr4B 79.500 200 25 9 3008 3194 388623322 388623518 9.330000e-26 128.0
53 TraesCS7D01G496800 chr4B 81.061 132 14 4 3060 3181 492759168 492759298 9.460000e-16 95.3
54 TraesCS7D01G496800 chr4B 100.000 35 0 0 2731 2765 12236132 12236098 7.420000e-07 65.8
55 TraesCS7D01G496800 chr2D 89.239 539 37 9 1 520 54130960 54130424 0.000000e+00 654.0
56 TraesCS7D01G496800 chr2D 80.000 140 23 4 3003 3139 531177196 531177059 7.310000e-17 99.0
57 TraesCS7D01G496800 chr2D 100.000 36 0 0 2731 2766 523618566 523618601 2.060000e-07 67.6
58 TraesCS7D01G496800 chr1D 88.766 543 41 9 1 524 486273579 486273038 0.000000e+00 647.0
59 TraesCS7D01G496800 chr1D 95.082 61 2 1 3080 3139 289965321 289965261 9.460000e-16 95.3
60 TraesCS7D01G496800 chr1D 75.097 257 35 22 2484 2717 463453070 463452820 3.400000e-15 93.5
61 TraesCS7D01G496800 chr1D 79.720 143 11 7 3055 3181 5863643 5863783 1.580000e-13 87.9
62 TraesCS7D01G496800 chr1D 95.122 41 1 1 1698 1738 443300968 443300929 2.670000e-06 63.9
63 TraesCS7D01G496800 chr3A 87.640 534 34 14 1 514 658498426 658498947 2.750000e-165 592.0
64 TraesCS7D01G496800 chr3A 76.596 235 31 16 2989 3203 21063347 21063117 1.210000e-19 108.0
65 TraesCS7D01G496800 chr5D 88.365 318 24 3 211 519 300102756 300102443 1.400000e-98 370.0
66 TraesCS7D01G496800 chr5D 90.164 61 6 0 3076 3136 540126199 540126259 2.650000e-11 80.5
67 TraesCS7D01G496800 chr5D 88.525 61 5 2 3080 3139 475580988 475581047 4.430000e-09 73.1
68 TraesCS7D01G496800 chr4A 79.452 219 28 12 2488 2689 558240153 558240371 4.310000e-29 139.0
69 TraesCS7D01G496800 chr4A 97.561 41 1 0 2731 2771 596582150 596582190 1.590000e-08 71.3
70 TraesCS7D01G496800 chr4A 100.000 31 0 0 2732 2762 734434082 734434052 1.240000e-04 58.4
71 TraesCS7D01G496800 chr6A 79.286 140 24 4 3003 3139 315391645 315391508 3.400000e-15 93.5
72 TraesCS7D01G496800 chr6A 74.429 219 34 12 2993 3194 162441419 162441206 1.230000e-09 75.0
73 TraesCS7D01G496800 chr6A 96.875 32 1 0 2785 2816 609594945 609594976 2.000000e-03 54.7
74 TraesCS7D01G496800 chr1A 78.947 133 12 6 3076 3194 99915849 99915719 3.430000e-10 76.8
75 TraesCS7D01G496800 chr1A 90.909 55 5 0 3080 3134 244495798 244495744 1.230000e-09 75.0
76 TraesCS7D01G496800 chr1A 97.561 41 0 1 1698 1738 539738169 539738208 5.730000e-08 69.4
77 TraesCS7D01G496800 chr1A 90.476 42 4 0 3153 3194 591305538 591305497 4.460000e-04 56.5
78 TraesCS7D01G496800 chr6D 88.333 60 5 2 3076 3134 38888646 38888588 1.590000e-08 71.3
79 TraesCS7D01G496800 chr6D 100.000 30 0 0 2613 2642 411016864 411016893 4.460000e-04 56.5
80 TraesCS7D01G496800 chrUn 90.196 51 2 3 3133 3181 240178207 240178256 2.670000e-06 63.9
81 TraesCS7D01G496800 chrUn 90.196 51 2 3 3133 3181 256275900 256275949 2.670000e-06 63.9
82 TraesCS7D01G496800 chrUn 90.909 44 4 0 2613 2656 95761491 95761448 3.450000e-05 60.2
83 TraesCS7D01G496800 chr1B 81.579 76 10 4 2613 2686 109267251 109267324 3.450000e-05 60.2
84 TraesCS7D01G496800 chr1B 100.000 30 0 0 2613 2642 656923944 656923915 4.460000e-04 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 TraesCS7D01G496800 chr7D 603649244 603652446 3202 False 5915.000000 5915 100.000000 1 3203 1 chr7D.!!$F6 3202
1 TraesCS7D01G496800 chr7D 165113003 165113518 515 False 675.000000 675 90.595000 1 509 1 chr7D.!!$F2 508
2 TraesCS7D01G496800 chr7D 603701151 603702481 1330 False 527.000000 527 74.532000 836 2198 1 chr7D.!!$F7 1362
3 TraesCS7D01G496800 chr7B 685382667 685385118 2451 False 1191.000000 3013 92.862000 513 3203 3 chr7B.!!$F5 2690
4 TraesCS7D01G496800 chr7B 537788766 537789315 549 False 494.000000 494 84.392000 12 512 1 chr7B.!!$F3 500
5 TraesCS7D01G496800 chr7A 696256406 696257702 1296 False 618.666667 885 92.569667 513 2434 3 chr7A.!!$F2 1921
6 TraesCS7D01G496800 chr2B 131287992 131288508 516 True 712.000000 712 91.762000 1 512 1 chr2B.!!$R2 511
7 TraesCS7D01G496800 chr2A 598220399 598220931 532 True 710.000000 710 91.231000 1 517 1 chr2A.!!$R3 516
8 TraesCS7D01G496800 chr2A 329112593 329113128 535 True 634.000000 634 88.641000 1 517 1 chr2A.!!$R2 516
9 TraesCS7D01G496800 chr3D 131348544 131349061 517 False 691.000000 691 91.013000 1 512 1 chr3D.!!$F1 511
10 TraesCS7D01G496800 chr3D 521590743 521591261 518 False 680.000000 680 90.631000 1 512 1 chr3D.!!$F3 511
11 TraesCS7D01G496800 chr3D 10515953 10516478 525 True 678.000000 678 90.226000 2 521 1 chr3D.!!$R1 519
12 TraesCS7D01G496800 chr3B 151575222 151575736 514 True 691.000000 691 91.154000 3 512 1 chr3B.!!$R1 509
13 TraesCS7D01G496800 chr5B 282846517 282847033 516 True 689.000000 689 90.996000 1 511 1 chr5B.!!$R1 510
14 TraesCS7D01G496800 chr5B 492264640 492265155 515 True 689.000000 689 91.013000 1 513 1 chr5B.!!$R3 512
15 TraesCS7D01G496800 chr5B 382630916 382631437 521 True 676.000000 676 90.323000 1 516 1 chr5B.!!$R2 515
16 TraesCS7D01G496800 chr4D 221284714 221285235 521 True 680.000000 680 90.494000 1 515 1 chr4D.!!$R3 514
17 TraesCS7D01G496800 chr4B 407060013 407060553 540 False 660.000000 660 89.299000 1 522 1 chr4B.!!$F2 521
18 TraesCS7D01G496800 chr2D 54130424 54130960 536 True 654.000000 654 89.239000 1 520 1 chr2D.!!$R1 519
19 TraesCS7D01G496800 chr1D 486273038 486273579 541 True 647.000000 647 88.766000 1 524 1 chr1D.!!$R4 523
20 TraesCS7D01G496800 chr3A 658498426 658498947 521 False 592.000000 592 87.640000 1 514 1 chr3A.!!$F1 513

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
698 780 0.179156 CGTCCGCGGTGTGTTATACT 60.179 55.0 27.15 0.0 0.00 2.12 F
700 782 0.457035 TCCGCGGTGTGTTATACTCC 59.543 55.0 27.15 0.0 39.13 3.85 F
1980 2139 0.106167 AGAGTGGCGGTAGATGGCTA 60.106 55.0 0.00 0.0 0.00 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 1830 0.606401 GCTTGAGTAGCCTGCAACCA 60.606 55.0 0.00 0.00 44.48 3.67 R
2087 2246 0.811616 GGCAGCGTAGAGGTTCATGG 60.812 60.0 0.00 0.00 0.00 3.66 R
2955 3126 0.039888 TTTTTCTGTAAAGGCGGCGC 60.040 50.0 26.17 26.17 0.00 6.53 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
298 341 7.978099 ATCCTATATTTTTGGCAAAGGTTCT 57.022 32.000 13.04 1.66 0.00 3.01
316 361 6.904626 AGGTTCTCAGCATATTCACCTTAAT 58.095 36.000 0.00 0.00 28.23 1.40
429 498 4.679197 GTCATGTTCTACAGCTCGATCATC 59.321 45.833 0.00 0.00 0.00 2.92
455 533 2.987149 TCACTCTCGCTCGAATTTTCAC 59.013 45.455 0.00 0.00 0.00 3.18
505 584 3.065015 GAGCTCGACTCGTTTGCG 58.935 61.111 0.00 0.00 35.18 4.85
622 701 2.273179 CCCCAACGTGTCTCGAGGA 61.273 63.158 13.56 0.00 42.86 3.71
697 779 0.456653 ACGTCCGCGGTGTGTTATAC 60.457 55.000 27.15 12.33 43.45 1.47
698 780 0.179156 CGTCCGCGGTGTGTTATACT 60.179 55.000 27.15 0.00 0.00 2.12
699 781 1.553308 GTCCGCGGTGTGTTATACTC 58.447 55.000 27.15 0.00 0.00 2.59
700 782 0.457035 TCCGCGGTGTGTTATACTCC 59.543 55.000 27.15 0.00 39.13 3.85
705 787 2.199291 GGTGTGTTATACTCCGTCGG 57.801 55.000 4.39 4.39 33.64 4.79
706 788 1.745087 GGTGTGTTATACTCCGTCGGA 59.255 52.381 14.54 14.54 33.64 4.55
760 871 4.805231 CCGGCCGTGTGCGTATCA 62.805 66.667 26.12 0.00 42.61 2.15
761 872 3.254654 CGGCCGTGTGCGTATCAG 61.255 66.667 19.50 0.00 42.61 2.90
762 873 3.564027 GGCCGTGTGCGTATCAGC 61.564 66.667 0.00 0.00 42.61 4.26
763 874 3.564027 GCCGTGTGCGTATCAGCC 61.564 66.667 0.00 0.00 36.15 4.85
764 875 3.254654 CCGTGTGCGTATCAGCCG 61.255 66.667 0.00 0.00 36.15 5.52
765 876 3.254654 CGTGTGCGTATCAGCCGG 61.255 66.667 0.00 0.00 36.02 6.13
766 877 3.564027 GTGTGCGTATCAGCCGGC 61.564 66.667 21.89 21.89 36.02 6.13
767 878 3.770040 TGTGCGTATCAGCCGGCT 61.770 61.111 27.08 27.08 36.02 5.52
768 879 3.264897 GTGCGTATCAGCCGGCTG 61.265 66.667 44.24 44.24 44.86 4.85
769 880 4.529219 TGCGTATCAGCCGGCTGG 62.529 66.667 46.58 34.10 43.75 4.85
803 914 2.102420 TCCGTCCATTAGATCGCAATGT 59.898 45.455 16.88 0.00 32.55 2.71
834 982 3.562557 TCGCCTGTTTCTACTTCCAAAAC 59.437 43.478 0.00 0.00 34.30 2.43
948 1097 1.978542 AGCTAGACACGTACGCAAAG 58.021 50.000 16.72 7.22 0.00 2.77
1104 1254 1.056700 ACCTCTTCCACTGTGCCAGT 61.057 55.000 1.29 2.38 46.51 4.00
1167 1317 2.997897 AGGCTGGAGTGGACGTCC 60.998 66.667 28.17 28.17 34.31 4.79
1305 1461 1.891060 GAGACCTCAGTTGCGCAACG 61.891 60.000 38.96 32.74 45.50 4.10
1382 1538 1.474077 GGCTCGCTCAAACCAAATCAT 59.526 47.619 0.00 0.00 0.00 2.45
1440 1596 1.142748 CGATGAGCTCCCACCACTC 59.857 63.158 12.15 0.00 0.00 3.51
1550 1706 3.308117 CCATGGGGCTACTCAACTTTGTA 60.308 47.826 2.85 0.00 0.00 2.41
1618 1774 2.521126 TCCTCCACACGTTCTCATACA 58.479 47.619 0.00 0.00 0.00 2.29
1663 1819 6.567050 CCTACAAATTTGGTTGATGAGGATG 58.433 40.000 21.74 0.00 32.70 3.51
1672 1828 4.935205 TGGTTGATGAGGATGTAAAGTTCG 59.065 41.667 0.00 0.00 0.00 3.95
1674 1830 5.817816 GGTTGATGAGGATGTAAAGTTCGAT 59.182 40.000 0.00 0.00 0.00 3.59
1681 1837 3.438781 GGATGTAAAGTTCGATGGTTGCA 59.561 43.478 0.00 0.00 0.00 4.08
1704 1860 2.350522 CTACTCAAGCATTCCAACGCT 58.649 47.619 0.00 0.00 41.20 5.07
1808 1967 2.042162 AGACTTGCCATGTTTCCCTGAT 59.958 45.455 0.00 0.00 0.00 2.90
1980 2139 0.106167 AGAGTGGCGGTAGATGGCTA 60.106 55.000 0.00 0.00 0.00 3.93
2013 2172 2.264005 TCGAGCTAAAAGCACCCAAA 57.736 45.000 1.22 0.00 45.56 3.28
2087 2246 2.347661 CGTTGCTCGTCAAAGACAACTC 60.348 50.000 0.00 0.00 38.72 3.01
2205 2364 1.095228 ATTGGCCGGTGTGCTAATCG 61.095 55.000 1.90 0.00 37.87 3.34
2209 2368 0.519961 GCCGGTGTGCTAATCGTTTT 59.480 50.000 1.90 0.00 0.00 2.43
2210 2369 1.465187 GCCGGTGTGCTAATCGTTTTC 60.465 52.381 1.90 0.00 0.00 2.29
2222 2383 4.806342 AATCGTTTTCAGTGTTTACGCT 57.194 36.364 8.18 0.00 37.13 5.07
2229 2390 7.543172 TCGTTTTCAGTGTTTACGCTATAGATT 59.457 33.333 3.21 0.00 34.49 2.40
2461 2624 8.564574 GGTGAACAGTAAAATCAGTGAAATACA 58.435 33.333 0.00 0.00 0.00 2.29
2531 2700 4.044426 GTGTGAGTTCTGTGCCAATTTTC 58.956 43.478 0.00 0.00 0.00 2.29
2541 2710 1.000618 TGCCAATTTTCAGCGCATTCA 59.999 42.857 11.47 0.00 0.00 2.57
2559 2728 5.006552 GCATTCAAACATCTGAGTAGCTCTC 59.993 44.000 0.00 0.00 43.03 3.20
2658 2829 2.794350 CCAAACACGCTGAAAATTGACC 59.206 45.455 0.00 0.00 0.00 4.02
2668 2839 4.619863 GCTGAAAATTGACCTGCACATCAT 60.620 41.667 0.00 0.00 0.00 2.45
2688 2859 5.875224 TCATGTACTCAAACATCTTTCCCA 58.125 37.500 0.00 0.00 38.01 4.37
2808 2979 8.101309 TCAATTATTTTGGATCAGAGGGAGTA 57.899 34.615 0.00 0.00 0.00 2.59
2816 2987 8.618240 TTTGGATCAGAGGGAGTAGTATTTTA 57.382 34.615 0.00 0.00 0.00 1.52
2820 2991 9.713713 GGATCAGAGGGAGTAGTATTTTATTTC 57.286 37.037 0.00 0.00 0.00 2.17
2821 2992 9.413048 GATCAGAGGGAGTAGTATTTTATTTCG 57.587 37.037 0.00 0.00 0.00 3.46
2864 3035 1.062488 AGATAAGCCCGGGAGCCATT 61.062 55.000 29.31 12.48 0.00 3.16
2913 3084 2.621055 CTCTGCACTCGAGCTAATAGGT 59.379 50.000 13.61 0.00 34.99 3.08
2914 3085 3.024547 TCTGCACTCGAGCTAATAGGTT 58.975 45.455 13.61 0.00 34.99 3.50
2915 3086 3.119291 CTGCACTCGAGCTAATAGGTTG 58.881 50.000 13.61 0.53 34.99 3.77
2916 3087 2.758423 TGCACTCGAGCTAATAGGTTGA 59.242 45.455 13.61 8.90 35.09 3.18
2917 3088 3.384789 TGCACTCGAGCTAATAGGTTGAT 59.615 43.478 13.61 0.00 35.74 2.57
2918 3089 4.141937 TGCACTCGAGCTAATAGGTTGATT 60.142 41.667 13.61 2.23 35.74 2.57
2919 3090 5.068591 TGCACTCGAGCTAATAGGTTGATTA 59.931 40.000 13.61 0.00 35.74 1.75
2920 3091 6.159988 GCACTCGAGCTAATAGGTTGATTAT 58.840 40.000 13.61 0.00 35.74 1.28
2921 3092 6.647067 GCACTCGAGCTAATAGGTTGATTATT 59.353 38.462 13.61 0.00 35.74 1.40
2922 3093 7.813148 GCACTCGAGCTAATAGGTTGATTATTA 59.187 37.037 13.61 0.00 35.74 0.98
2923 3094 9.347934 CACTCGAGCTAATAGGTTGATTATTAG 57.652 37.037 13.61 7.37 41.11 1.73
2924 3095 9.298250 ACTCGAGCTAATAGGTTGATTATTAGA 57.702 33.333 13.61 0.00 40.85 2.10
2935 3106 8.443953 AGGTTGATTATTAGAAGATCAAGTGC 57.556 34.615 0.00 0.00 39.63 4.40
2936 3107 7.225538 AGGTTGATTATTAGAAGATCAAGTGCG 59.774 37.037 0.00 0.00 39.63 5.34
2937 3108 7.348201 GTTGATTATTAGAAGATCAAGTGCGG 58.652 38.462 0.00 0.00 39.63 5.69
2938 3109 6.816136 TGATTATTAGAAGATCAAGTGCGGA 58.184 36.000 0.00 0.00 0.00 5.54
2939 3110 6.701841 TGATTATTAGAAGATCAAGTGCGGAC 59.298 38.462 0.00 0.00 0.00 4.79
2940 3111 4.744795 ATTAGAAGATCAAGTGCGGACT 57.255 40.909 2.68 2.68 0.00 3.85
2941 3112 2.376808 AGAAGATCAAGTGCGGACTG 57.623 50.000 11.44 5.23 30.61 3.51
2942 3113 1.620819 AGAAGATCAAGTGCGGACTGT 59.379 47.619 11.44 0.00 30.61 3.55
2943 3114 2.826128 AGAAGATCAAGTGCGGACTGTA 59.174 45.455 11.44 1.64 30.61 2.74
2944 3115 2.949451 AGATCAAGTGCGGACTGTAG 57.051 50.000 11.44 4.11 30.61 2.74
2945 3116 2.447443 AGATCAAGTGCGGACTGTAGA 58.553 47.619 11.44 9.94 30.61 2.59
2946 3117 2.425312 AGATCAAGTGCGGACTGTAGAG 59.575 50.000 11.44 0.00 30.61 2.43
2947 3118 1.905637 TCAAGTGCGGACTGTAGAGA 58.094 50.000 11.44 1.32 30.61 3.10
2948 3119 2.235891 TCAAGTGCGGACTGTAGAGAA 58.764 47.619 11.44 0.00 30.61 2.87
2949 3120 2.626266 TCAAGTGCGGACTGTAGAGAAA 59.374 45.455 11.44 0.00 30.61 2.52
2950 3121 3.069016 TCAAGTGCGGACTGTAGAGAAAA 59.931 43.478 11.44 0.00 30.61 2.29
2951 3122 3.027974 AGTGCGGACTGTAGAGAAAAC 57.972 47.619 9.49 0.00 0.00 2.43
2952 3123 2.364324 AGTGCGGACTGTAGAGAAAACA 59.636 45.455 9.49 0.00 0.00 2.83
2953 3124 3.006967 AGTGCGGACTGTAGAGAAAACAT 59.993 43.478 9.49 0.00 0.00 2.71
2954 3125 3.746492 GTGCGGACTGTAGAGAAAACATT 59.254 43.478 0.00 0.00 0.00 2.71
2955 3126 3.745975 TGCGGACTGTAGAGAAAACATTG 59.254 43.478 0.00 0.00 0.00 2.82
2956 3127 3.424962 GCGGACTGTAGAGAAAACATTGC 60.425 47.826 0.00 0.00 0.00 3.56
2957 3128 3.181530 CGGACTGTAGAGAAAACATTGCG 60.182 47.826 0.00 0.00 35.69 4.85
2958 3129 3.424962 GGACTGTAGAGAAAACATTGCGC 60.425 47.826 0.00 0.00 0.00 6.09
2959 3130 2.484264 ACTGTAGAGAAAACATTGCGCC 59.516 45.455 4.18 0.00 0.00 6.53
2960 3131 1.463056 TGTAGAGAAAACATTGCGCCG 59.537 47.619 4.18 0.00 0.00 6.46
2961 3132 0.446222 TAGAGAAAACATTGCGCCGC 59.554 50.000 4.18 0.00 0.00 6.53
2962 3133 1.801512 GAGAAAACATTGCGCCGCC 60.802 57.895 6.63 0.00 0.00 6.13
2963 3134 2.200170 GAGAAAACATTGCGCCGCCT 62.200 55.000 6.63 0.00 0.00 5.52
2964 3135 1.372872 GAAAACATTGCGCCGCCTT 60.373 52.632 6.63 0.00 0.00 4.35
2965 3136 0.943835 GAAAACATTGCGCCGCCTTT 60.944 50.000 6.63 0.00 0.00 3.11
2966 3137 0.315568 AAAACATTGCGCCGCCTTTA 59.684 45.000 6.63 0.00 0.00 1.85
2967 3138 0.388006 AAACATTGCGCCGCCTTTAC 60.388 50.000 6.63 0.00 0.00 2.01
2968 3139 1.519751 AACATTGCGCCGCCTTTACA 61.520 50.000 6.63 0.00 0.00 2.41
2969 3140 1.226379 CATTGCGCCGCCTTTACAG 60.226 57.895 6.63 0.00 0.00 2.74
2970 3141 1.376683 ATTGCGCCGCCTTTACAGA 60.377 52.632 6.63 0.00 0.00 3.41
2971 3142 0.958382 ATTGCGCCGCCTTTACAGAA 60.958 50.000 6.63 0.00 0.00 3.02
2972 3143 1.167155 TTGCGCCGCCTTTACAGAAA 61.167 50.000 6.63 0.00 0.00 2.52
2973 3144 1.167155 TGCGCCGCCTTTACAGAAAA 61.167 50.000 6.63 0.00 0.00 2.29
2974 3145 0.039888 GCGCCGCCTTTACAGAAAAA 60.040 50.000 0.00 0.00 0.00 1.94
2975 3146 1.963747 CGCCGCCTTTACAGAAAAAG 58.036 50.000 0.00 0.00 36.43 2.27
2976 3147 1.698165 GCCGCCTTTACAGAAAAAGC 58.302 50.000 0.00 0.00 35.53 3.51
2977 3148 1.000717 GCCGCCTTTACAGAAAAAGCA 60.001 47.619 0.00 0.00 35.53 3.91
2978 3149 2.661594 CCGCCTTTACAGAAAAAGCAC 58.338 47.619 0.00 0.00 35.53 4.40
2979 3150 2.607038 CCGCCTTTACAGAAAAAGCACC 60.607 50.000 0.00 0.00 35.53 5.01
2980 3151 2.661594 GCCTTTACAGAAAAAGCACCG 58.338 47.619 0.00 0.00 35.53 4.94
2981 3152 2.034179 GCCTTTACAGAAAAAGCACCGT 59.966 45.455 0.00 0.00 35.53 4.83
2982 3153 3.628017 CCTTTACAGAAAAAGCACCGTG 58.372 45.455 0.00 0.00 35.53 4.94
2983 3154 3.550030 CCTTTACAGAAAAAGCACCGTGG 60.550 47.826 0.00 0.00 35.53 4.94
2984 3155 2.623878 TACAGAAAAAGCACCGTGGA 57.376 45.000 0.00 0.00 0.00 4.02
2985 3156 1.757682 ACAGAAAAAGCACCGTGGAA 58.242 45.000 0.00 0.00 0.00 3.53
2986 3157 2.306847 ACAGAAAAAGCACCGTGGAAT 58.693 42.857 0.00 0.00 0.00 3.01
2987 3158 2.693074 ACAGAAAAAGCACCGTGGAATT 59.307 40.909 0.00 0.00 0.00 2.17
2988 3159 3.132111 ACAGAAAAAGCACCGTGGAATTT 59.868 39.130 0.00 0.00 0.00 1.82
2989 3160 4.339814 ACAGAAAAAGCACCGTGGAATTTA 59.660 37.500 0.00 0.00 0.00 1.40
2990 3161 4.917415 CAGAAAAAGCACCGTGGAATTTAG 59.083 41.667 0.00 0.00 0.00 1.85
2991 3162 4.825085 AGAAAAAGCACCGTGGAATTTAGA 59.175 37.500 0.00 0.00 0.00 2.10
2992 3163 5.300792 AGAAAAAGCACCGTGGAATTTAGAA 59.699 36.000 0.00 0.00 0.00 2.10
2993 3164 5.523438 AAAAGCACCGTGGAATTTAGAAA 57.477 34.783 0.00 0.00 0.00 2.52
2994 3165 5.722021 AAAGCACCGTGGAATTTAGAAAT 57.278 34.783 0.00 0.00 0.00 2.17
2995 3166 4.965119 AGCACCGTGGAATTTAGAAATC 57.035 40.909 0.00 0.00 0.00 2.17
2996 3167 4.589908 AGCACCGTGGAATTTAGAAATCT 58.410 39.130 0.00 0.00 0.00 2.40
2997 3168 4.636206 AGCACCGTGGAATTTAGAAATCTC 59.364 41.667 0.00 0.00 0.00 2.75
2998 3169 4.636206 GCACCGTGGAATTTAGAAATCTCT 59.364 41.667 0.00 0.00 35.52 3.10
2999 3170 5.447818 GCACCGTGGAATTTAGAAATCTCTG 60.448 44.000 0.00 0.00 32.70 3.35
3000 3171 4.636206 ACCGTGGAATTTAGAAATCTCTGC 59.364 41.667 0.00 0.00 32.70 4.26
3001 3172 4.035675 CCGTGGAATTTAGAAATCTCTGCC 59.964 45.833 0.00 0.00 32.70 4.85
3002 3173 4.635765 CGTGGAATTTAGAAATCTCTGCCA 59.364 41.667 0.00 0.00 32.70 4.92
3003 3174 5.447818 CGTGGAATTTAGAAATCTCTGCCAC 60.448 44.000 0.00 0.00 32.70 5.01
3004 3175 5.649831 GTGGAATTTAGAAATCTCTGCCACT 59.350 40.000 0.00 0.00 32.70 4.00
3005 3176 6.151817 GTGGAATTTAGAAATCTCTGCCACTT 59.848 38.462 0.00 0.00 32.70 3.16
3006 3177 7.336931 GTGGAATTTAGAAATCTCTGCCACTTA 59.663 37.037 0.00 0.00 32.70 2.24
3007 3178 7.888021 TGGAATTTAGAAATCTCTGCCACTTAA 59.112 33.333 0.00 0.00 32.70 1.85
3008 3179 8.739972 GGAATTTAGAAATCTCTGCCACTTAAA 58.260 33.333 0.00 0.00 32.70 1.52
3012 3183 8.918202 TTAGAAATCTCTGCCACTTAAAAAGA 57.082 30.769 0.00 0.00 32.70 2.52
3013 3184 7.823745 AGAAATCTCTGCCACTTAAAAAGAA 57.176 32.000 0.00 0.00 0.00 2.52
3014 3185 8.414629 AGAAATCTCTGCCACTTAAAAAGAAT 57.585 30.769 0.00 0.00 0.00 2.40
3015 3186 8.302438 AGAAATCTCTGCCACTTAAAAAGAATG 58.698 33.333 0.00 0.00 0.00 2.67
3016 3187 5.376854 TCTCTGCCACTTAAAAAGAATGC 57.623 39.130 0.00 0.00 0.00 3.56
3017 3188 4.826733 TCTCTGCCACTTAAAAAGAATGCA 59.173 37.500 0.00 0.00 0.00 3.96
3018 3189 5.301551 TCTCTGCCACTTAAAAAGAATGCAA 59.698 36.000 0.00 0.00 32.66 4.08
3019 3190 5.531634 TCTGCCACTTAAAAAGAATGCAAG 58.468 37.500 0.00 0.00 32.66 4.01
3020 3191 4.630111 TGCCACTTAAAAAGAATGCAAGG 58.370 39.130 0.00 0.00 31.06 3.61
3021 3192 4.100808 TGCCACTTAAAAAGAATGCAAGGT 59.899 37.500 0.00 0.00 31.06 3.50
3022 3193 5.056480 GCCACTTAAAAAGAATGCAAGGTT 58.944 37.500 0.00 0.00 0.00 3.50
3023 3194 5.527214 GCCACTTAAAAAGAATGCAAGGTTT 59.473 36.000 0.00 0.00 0.00 3.27
3024 3195 6.292865 GCCACTTAAAAAGAATGCAAGGTTTC 60.293 38.462 0.00 0.00 0.00 2.78
3025 3196 6.760770 CCACTTAAAAAGAATGCAAGGTTTCA 59.239 34.615 0.00 0.00 0.00 2.69
3026 3197 7.442062 CCACTTAAAAAGAATGCAAGGTTTCAT 59.558 33.333 0.00 0.00 0.00 2.57
3027 3198 8.277713 CACTTAAAAAGAATGCAAGGTTTCATG 58.722 33.333 0.00 0.00 0.00 3.07
3028 3199 7.986889 ACTTAAAAAGAATGCAAGGTTTCATGT 59.013 29.630 0.00 0.00 0.00 3.21
3029 3200 8.729805 TTAAAAAGAATGCAAGGTTTCATGTT 57.270 26.923 0.00 0.00 0.00 2.71
3030 3201 9.823647 TTAAAAAGAATGCAAGGTTTCATGTTA 57.176 25.926 0.00 0.00 0.00 2.41
3031 3202 8.907222 AAAAAGAATGCAAGGTTTCATGTTAT 57.093 26.923 0.00 0.00 0.00 1.89
3032 3203 9.995003 AAAAAGAATGCAAGGTTTCATGTTATA 57.005 25.926 0.00 0.00 0.00 0.98
3039 3210 8.770438 TGCAAGGTTTCATGTTATATTTTTCC 57.230 30.769 0.00 0.00 0.00 3.13
3040 3211 8.592809 TGCAAGGTTTCATGTTATATTTTTCCT 58.407 29.630 0.00 0.00 0.00 3.36
3041 3212 9.435688 GCAAGGTTTCATGTTATATTTTTCCTT 57.564 29.630 0.00 0.00 0.00 3.36
3044 3215 9.320295 AGGTTTCATGTTATATTTTTCCTTCCA 57.680 29.630 0.00 0.00 0.00 3.53
3045 3216 9.366216 GGTTTCATGTTATATTTTTCCTTCCAC 57.634 33.333 0.00 0.00 0.00 4.02
3055 3226 6.759497 ATTTTTCCTTCCACTATTTCTCCG 57.241 37.500 0.00 0.00 0.00 4.63
3056 3227 4.903045 TTTCCTTCCACTATTTCTCCGT 57.097 40.909 0.00 0.00 0.00 4.69
3057 3228 4.467198 TTCCTTCCACTATTTCTCCGTC 57.533 45.455 0.00 0.00 0.00 4.79
3058 3229 3.709587 TCCTTCCACTATTTCTCCGTCT 58.290 45.455 0.00 0.00 0.00 4.18
3059 3230 4.863548 TCCTTCCACTATTTCTCCGTCTA 58.136 43.478 0.00 0.00 0.00 2.59
3060 3231 5.266788 TCCTTCCACTATTTCTCCGTCTAA 58.733 41.667 0.00 0.00 0.00 2.10
3061 3232 5.126707 TCCTTCCACTATTTCTCCGTCTAAC 59.873 44.000 0.00 0.00 0.00 2.34
3062 3233 4.996788 TCCACTATTTCTCCGTCTAACC 57.003 45.455 0.00 0.00 0.00 2.85
3063 3234 4.607239 TCCACTATTTCTCCGTCTAACCT 58.393 43.478 0.00 0.00 0.00 3.50
3064 3235 5.021458 TCCACTATTTCTCCGTCTAACCTT 58.979 41.667 0.00 0.00 0.00 3.50
3065 3236 5.126707 TCCACTATTTCTCCGTCTAACCTTC 59.873 44.000 0.00 0.00 0.00 3.46
3066 3237 5.349809 CACTATTTCTCCGTCTAACCTTCC 58.650 45.833 0.00 0.00 0.00 3.46
3067 3238 3.908643 ATTTCTCCGTCTAACCTTCCC 57.091 47.619 0.00 0.00 0.00 3.97
3068 3239 1.565067 TTCTCCGTCTAACCTTCCCC 58.435 55.000 0.00 0.00 0.00 4.81
3069 3240 0.682209 TCTCCGTCTAACCTTCCCCG 60.682 60.000 0.00 0.00 0.00 5.73
3070 3241 0.969409 CTCCGTCTAACCTTCCCCGT 60.969 60.000 0.00 0.00 0.00 5.28
3071 3242 0.331278 TCCGTCTAACCTTCCCCGTA 59.669 55.000 0.00 0.00 0.00 4.02
3072 3243 0.743097 CCGTCTAACCTTCCCCGTAG 59.257 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.217200 AGCTACATAAAGTGTTCAAACTCAGA 58.783 34.615 0.00 0.00 42.29 3.27
238 277 2.740580 CGACCACGTGCCATAATTAGGT 60.741 50.000 10.91 0.00 34.56 3.08
352 399 6.018751 CGATCTCGAGCTAAATGAAATGGAAA 60.019 38.462 7.81 0.00 43.02 3.13
353 400 5.463392 CGATCTCGAGCTAAATGAAATGGAA 59.537 40.000 7.81 0.00 43.02 3.53
354 401 4.984785 CGATCTCGAGCTAAATGAAATGGA 59.015 41.667 7.81 0.00 43.02 3.41
429 498 0.109551 TTCGAGCGAGAGTGAAGCTG 60.110 55.000 0.00 0.00 41.84 4.24
455 533 3.341823 AGTTGGCTTAGCTCAACTCATG 58.658 45.455 24.69 0.00 42.04 3.07
622 701 1.210967 TGAGGTCCTTCAAAACCACGT 59.789 47.619 0.00 0.00 38.06 4.49
698 780 2.097466 GGTTACGAATTACTCCGACGGA 59.903 50.000 17.28 17.28 0.00 4.69
699 781 2.454055 GGTTACGAATTACTCCGACGG 58.546 52.381 7.84 7.84 0.00 4.79
700 782 2.104144 CGGTTACGAATTACTCCGACG 58.896 52.381 0.00 0.00 44.60 5.12
701 783 2.454055 CCGGTTACGAATTACTCCGAC 58.546 52.381 0.00 0.00 44.60 4.79
702 784 1.405105 CCCGGTTACGAATTACTCCGA 59.595 52.381 0.00 0.00 44.60 4.55
703 785 1.405105 TCCCGGTTACGAATTACTCCG 59.595 52.381 0.00 0.00 44.60 4.63
704 786 3.451526 CTTCCCGGTTACGAATTACTCC 58.548 50.000 0.00 0.00 44.60 3.85
705 787 3.118992 ACCTTCCCGGTTACGAATTACTC 60.119 47.826 0.00 0.00 46.37 2.59
706 788 2.833943 ACCTTCCCGGTTACGAATTACT 59.166 45.455 0.00 0.00 46.37 2.24
707 789 2.931969 CACCTTCCCGGTTACGAATTAC 59.068 50.000 0.00 0.00 46.37 1.89
708 790 2.566724 ACACCTTCCCGGTTACGAATTA 59.433 45.455 0.00 0.00 46.37 1.40
709 791 1.348696 ACACCTTCCCGGTTACGAATT 59.651 47.619 0.00 0.00 46.37 2.17
727 809 3.837578 GGGACGCCTCGAGATACA 58.162 61.111 15.71 0.00 0.00 2.29
762 873 2.187946 CAACTCCTAGCCAGCCGG 59.812 66.667 0.00 0.00 0.00 6.13
763 874 1.690219 ATCCAACTCCTAGCCAGCCG 61.690 60.000 0.00 0.00 0.00 5.52
764 875 0.107643 GATCCAACTCCTAGCCAGCC 59.892 60.000 0.00 0.00 0.00 4.85
765 876 0.107643 GGATCCAACTCCTAGCCAGC 59.892 60.000 6.95 0.00 32.18 4.85
766 877 0.390860 CGGATCCAACTCCTAGCCAG 59.609 60.000 13.41 0.00 32.77 4.85
767 878 0.325296 ACGGATCCAACTCCTAGCCA 60.325 55.000 13.41 0.00 32.77 4.75
768 879 0.389757 GACGGATCCAACTCCTAGCC 59.610 60.000 13.41 0.00 32.77 3.93
769 880 0.389757 GGACGGATCCAACTCCTAGC 59.610 60.000 13.41 0.00 45.47 3.42
803 914 1.555075 AGAAACAGGCGATAGGAGCAA 59.445 47.619 0.00 0.00 36.08 3.91
834 982 0.387239 TGTGTCACGAGCTCACGATG 60.387 55.000 15.40 6.25 35.20 3.84
923 1071 1.596727 CGTACGTGTCTAGCTAGGTCC 59.403 57.143 20.58 9.54 0.00 4.46
948 1097 4.391155 AGGGACACTCGTGATAGATAGAC 58.609 47.826 3.74 0.00 0.00 2.59
1104 1254 2.048597 CTCCACCGCTTGCACGTA 60.049 61.111 0.00 0.00 0.00 3.57
1167 1317 3.242608 TGAAAAAGCCAGAAACGAACGAG 60.243 43.478 0.14 0.00 0.00 4.18
1382 1538 2.842462 ACACAGCCAGGTGGACGA 60.842 61.111 0.00 0.00 43.08 4.20
1440 1596 2.196925 ATACCTCCAGCCGCTCTCG 61.197 63.158 0.00 0.00 0.00 4.04
1550 1706 6.015010 ACTGCTGTAGATGACTAGAACTTTGT 60.015 38.462 0.00 0.00 0.00 2.83
1608 1764 1.067821 CTCCCCTCGCTGTATGAGAAC 59.932 57.143 0.00 0.00 35.43 3.01
1618 1774 3.003763 GTTCCACCTCCCCTCGCT 61.004 66.667 0.00 0.00 0.00 4.93
1663 1819 2.414161 GCCTGCAACCATCGAACTTTAC 60.414 50.000 0.00 0.00 0.00 2.01
1672 1828 2.012673 CTTGAGTAGCCTGCAACCATC 58.987 52.381 0.00 0.00 0.00 3.51
1674 1830 0.606401 GCTTGAGTAGCCTGCAACCA 60.606 55.000 0.00 0.00 44.48 3.67
1704 1860 2.899838 GTGCCTTGGCACACGACA 60.900 61.111 32.37 0.81 39.29 4.35
1785 1944 1.425066 AGGGAAACATGGCAAGTCTCA 59.575 47.619 0.00 0.00 0.00 3.27
1808 1967 2.841266 TGGGTCGGGTTCATAATCTTCA 59.159 45.455 0.00 0.00 0.00 3.02
1980 2139 1.067084 CTCGATGACTCGGCTGCAT 59.933 57.895 0.50 0.00 45.10 3.96
2013 2172 3.737663 GCATCTCTTCTGCTCGAATCTGT 60.738 47.826 0.00 0.00 36.68 3.41
2079 2238 3.193691 CGTAGAGGTTCATGGAGTTGTCT 59.806 47.826 0.00 0.00 0.00 3.41
2087 2246 0.811616 GGCAGCGTAGAGGTTCATGG 60.812 60.000 0.00 0.00 0.00 3.66
2205 2364 8.653338 TGAATCTATAGCGTAAACACTGAAAAC 58.347 33.333 0.00 0.00 0.00 2.43
2209 2368 6.859017 TGTGAATCTATAGCGTAAACACTGA 58.141 36.000 0.00 0.00 0.00 3.41
2210 2369 7.435192 TCATGTGAATCTATAGCGTAAACACTG 59.565 37.037 0.00 0.00 0.00 3.66
2222 2383 9.942850 TTGAAGTCAAGTTCATGTGAATCTATA 57.057 29.630 1.30 0.00 36.34 1.31
2251 2412 9.872684 ATGAAATACAATTATGAGAGGATGGTT 57.127 29.630 0.00 0.00 0.00 3.67
2293 2454 7.875554 ACACCAAAACATAATGATTTACCCAAC 59.124 33.333 0.00 0.00 0.00 3.77
2434 2597 7.581213 ATTTCACTGATTTTACTGTTCACCA 57.419 32.000 0.00 0.00 0.00 4.17
2435 2598 8.564574 TGTATTTCACTGATTTTACTGTTCACC 58.435 33.333 0.00 0.00 0.00 4.02
2436 2599 9.944663 TTGTATTTCACTGATTTTACTGTTCAC 57.055 29.630 0.00 0.00 0.00 3.18
2486 2655 8.677300 ACACACTTAAATATCTTCGATGCAAAT 58.323 29.630 0.00 0.00 0.00 2.32
2505 2674 1.065491 TGGCACAGAACTCACACACTT 60.065 47.619 0.00 0.00 0.00 3.16
2531 2700 2.161012 ACTCAGATGTTTGAATGCGCTG 59.839 45.455 9.73 0.00 0.00 5.18
2600 2771 3.425162 TGGCAAAAACAAAACTGGGTT 57.575 38.095 0.00 0.00 0.00 4.11
2611 2782 3.815401 TCTGAGTAGCTCTTGGCAAAAAC 59.185 43.478 0.00 0.00 44.79 2.43
2658 2829 5.353400 AGATGTTTGAGTACATGATGTGCAG 59.647 40.000 15.78 0.00 38.80 4.41
2668 2839 7.411486 TTTTTGGGAAAGATGTTTGAGTACA 57.589 32.000 0.00 0.00 0.00 2.90
2725 2896 5.551760 AGAGGTTGCGTCAATTAAGATTG 57.448 39.130 0.00 0.00 43.24 2.67
2771 2942 8.537728 TCCAAAATAATTGATGCAACCTCTAT 57.462 30.769 0.00 0.00 0.00 1.98
2816 2987 5.331902 CGCCATAAACAGTGAAATCGAAAT 58.668 37.500 0.00 0.00 0.00 2.17
2820 2991 2.223249 CCCGCCATAAACAGTGAAATCG 60.223 50.000 0.00 0.00 0.00 3.34
2821 2992 3.013921 TCCCGCCATAAACAGTGAAATC 58.986 45.455 0.00 0.00 0.00 2.17
2844 3015 1.772819 ATGGCTCCCGGGCTTATCTG 61.773 60.000 18.49 0.33 41.48 2.90
2846 3017 0.178990 AAATGGCTCCCGGGCTTATC 60.179 55.000 18.49 3.79 41.48 1.75
2854 3025 4.496927 GCGGCAAAATGGCTCCCG 62.497 66.667 0.00 0.00 41.25 5.14
2864 3035 0.821517 TCGGATAAGAGAGCGGCAAA 59.178 50.000 1.45 0.00 0.00 3.68
2870 3041 7.328249 CAGAGTTGAATATTCGGATAAGAGAGC 59.672 40.741 10.80 0.00 0.00 4.09
2913 3084 7.224753 GTCCGCACTTGATCTTCTAATAATCAA 59.775 37.037 0.00 0.00 37.14 2.57
2914 3085 6.701841 GTCCGCACTTGATCTTCTAATAATCA 59.298 38.462 0.00 0.00 0.00 2.57
2915 3086 6.926272 AGTCCGCACTTGATCTTCTAATAATC 59.074 38.462 0.00 0.00 0.00 1.75
2916 3087 6.703607 CAGTCCGCACTTGATCTTCTAATAAT 59.296 38.462 0.00 0.00 0.00 1.28
2917 3088 6.042777 CAGTCCGCACTTGATCTTCTAATAA 58.957 40.000 0.00 0.00 0.00 1.40
2918 3089 5.127194 ACAGTCCGCACTTGATCTTCTAATA 59.873 40.000 0.00 0.00 0.00 0.98
2919 3090 4.081420 ACAGTCCGCACTTGATCTTCTAAT 60.081 41.667 0.00 0.00 0.00 1.73
2920 3091 3.258372 ACAGTCCGCACTTGATCTTCTAA 59.742 43.478 0.00 0.00 0.00 2.10
2921 3092 2.826128 ACAGTCCGCACTTGATCTTCTA 59.174 45.455 0.00 0.00 0.00 2.10
2922 3093 1.620819 ACAGTCCGCACTTGATCTTCT 59.379 47.619 0.00 0.00 0.00 2.85
2923 3094 2.086054 ACAGTCCGCACTTGATCTTC 57.914 50.000 0.00 0.00 0.00 2.87
2924 3095 2.826128 TCTACAGTCCGCACTTGATCTT 59.174 45.455 0.00 0.00 0.00 2.40
2925 3096 2.425312 CTCTACAGTCCGCACTTGATCT 59.575 50.000 0.00 0.00 0.00 2.75
2926 3097 2.423892 TCTCTACAGTCCGCACTTGATC 59.576 50.000 0.00 0.00 0.00 2.92
2927 3098 2.447443 TCTCTACAGTCCGCACTTGAT 58.553 47.619 0.00 0.00 0.00 2.57
2928 3099 1.905637 TCTCTACAGTCCGCACTTGA 58.094 50.000 0.00 0.00 0.00 3.02
2929 3100 2.724977 TTCTCTACAGTCCGCACTTG 57.275 50.000 0.00 0.00 0.00 3.16
2930 3101 3.181469 TGTTTTCTCTACAGTCCGCACTT 60.181 43.478 0.00 0.00 0.00 3.16
2931 3102 2.364324 TGTTTTCTCTACAGTCCGCACT 59.636 45.455 0.00 0.00 0.00 4.40
2932 3103 2.750948 TGTTTTCTCTACAGTCCGCAC 58.249 47.619 0.00 0.00 0.00 5.34
2933 3104 3.678056 ATGTTTTCTCTACAGTCCGCA 57.322 42.857 0.00 0.00 0.00 5.69
2934 3105 3.424962 GCAATGTTTTCTCTACAGTCCGC 60.425 47.826 0.00 0.00 0.00 5.54
2935 3106 3.181530 CGCAATGTTTTCTCTACAGTCCG 60.182 47.826 0.00 0.00 0.00 4.79
2936 3107 3.424962 GCGCAATGTTTTCTCTACAGTCC 60.425 47.826 0.30 0.00 0.00 3.85
2937 3108 3.424962 GGCGCAATGTTTTCTCTACAGTC 60.425 47.826 10.83 0.00 0.00 3.51
2938 3109 2.484264 GGCGCAATGTTTTCTCTACAGT 59.516 45.455 10.83 0.00 0.00 3.55
2939 3110 2.474526 CGGCGCAATGTTTTCTCTACAG 60.475 50.000 10.83 0.00 0.00 2.74
2940 3111 1.463056 CGGCGCAATGTTTTCTCTACA 59.537 47.619 10.83 0.00 0.00 2.74
2941 3112 1.790481 GCGGCGCAATGTTTTCTCTAC 60.790 52.381 29.21 0.00 0.00 2.59
2942 3113 0.446222 GCGGCGCAATGTTTTCTCTA 59.554 50.000 29.21 0.00 0.00 2.43
2943 3114 1.210155 GCGGCGCAATGTTTTCTCT 59.790 52.632 29.21 0.00 0.00 3.10
2944 3115 1.801512 GGCGGCGCAATGTTTTCTC 60.802 57.895 34.36 8.04 0.00 2.87
2945 3116 1.805428 AAGGCGGCGCAATGTTTTCT 61.805 50.000 34.36 15.73 0.00 2.52
2946 3117 0.943835 AAAGGCGGCGCAATGTTTTC 60.944 50.000 34.36 13.46 0.00 2.29
2947 3118 0.315568 TAAAGGCGGCGCAATGTTTT 59.684 45.000 34.36 23.65 0.00 2.43
2948 3119 0.388006 GTAAAGGCGGCGCAATGTTT 60.388 50.000 34.36 25.44 0.00 2.83
2949 3120 1.211709 GTAAAGGCGGCGCAATGTT 59.788 52.632 34.36 21.59 0.00 2.71
2950 3121 1.922135 CTGTAAAGGCGGCGCAATGT 61.922 55.000 34.36 18.84 0.00 2.71
2951 3122 1.226379 CTGTAAAGGCGGCGCAATG 60.226 57.895 34.36 11.65 0.00 2.82
2952 3123 0.958382 TTCTGTAAAGGCGGCGCAAT 60.958 50.000 34.36 19.04 0.00 3.56
2953 3124 1.167155 TTTCTGTAAAGGCGGCGCAA 61.167 50.000 34.36 13.76 0.00 4.85
2954 3125 1.167155 TTTTCTGTAAAGGCGGCGCA 61.167 50.000 34.36 10.38 0.00 6.09
2955 3126 0.039888 TTTTTCTGTAAAGGCGGCGC 60.040 50.000 26.17 26.17 0.00 6.53
2956 3127 1.963747 CTTTTTCTGTAAAGGCGGCG 58.036 50.000 0.51 0.51 32.67 6.46
2957 3128 1.698165 GCTTTTTCTGTAAAGGCGGC 58.302 50.000 0.00 0.00 38.77 6.53
2960 3131 2.034179 ACGGTGCTTTTTCTGTAAAGGC 59.966 45.455 6.87 6.87 45.99 4.35
2961 3132 3.550030 CCACGGTGCTTTTTCTGTAAAGG 60.550 47.826 1.68 0.00 36.00 3.11
2962 3133 3.314080 TCCACGGTGCTTTTTCTGTAAAG 59.686 43.478 1.68 0.00 38.00 1.85
2963 3134 3.280295 TCCACGGTGCTTTTTCTGTAAA 58.720 40.909 1.68 0.00 0.00 2.01
2964 3135 2.920524 TCCACGGTGCTTTTTCTGTAA 58.079 42.857 1.68 0.00 0.00 2.41
2965 3136 2.623878 TCCACGGTGCTTTTTCTGTA 57.376 45.000 1.68 0.00 0.00 2.74
2966 3137 1.757682 TTCCACGGTGCTTTTTCTGT 58.242 45.000 1.68 0.00 0.00 3.41
2967 3138 3.369546 AATTCCACGGTGCTTTTTCTG 57.630 42.857 1.68 0.00 0.00 3.02
2968 3139 4.825085 TCTAAATTCCACGGTGCTTTTTCT 59.175 37.500 1.68 0.00 0.00 2.52
2969 3140 5.116069 TCTAAATTCCACGGTGCTTTTTC 57.884 39.130 1.68 0.00 0.00 2.29
2970 3141 5.523438 TTCTAAATTCCACGGTGCTTTTT 57.477 34.783 1.68 4.43 0.00 1.94
2971 3142 5.523438 TTTCTAAATTCCACGGTGCTTTT 57.477 34.783 1.68 4.77 0.00 2.27
2972 3143 5.476945 AGATTTCTAAATTCCACGGTGCTTT 59.523 36.000 1.68 4.94 0.00 3.51
2973 3144 5.010282 AGATTTCTAAATTCCACGGTGCTT 58.990 37.500 1.68 0.00 0.00 3.91
2974 3145 4.589908 AGATTTCTAAATTCCACGGTGCT 58.410 39.130 1.68 0.00 0.00 4.40
2975 3146 4.636206 AGAGATTTCTAAATTCCACGGTGC 59.364 41.667 1.68 0.00 0.00 5.01
2976 3147 5.447818 GCAGAGATTTCTAAATTCCACGGTG 60.448 44.000 0.00 0.00 30.73 4.94
2977 3148 4.636206 GCAGAGATTTCTAAATTCCACGGT 59.364 41.667 0.00 0.00 30.73 4.83
2978 3149 4.035675 GGCAGAGATTTCTAAATTCCACGG 59.964 45.833 0.00 0.00 30.73 4.94
2979 3150 4.635765 TGGCAGAGATTTCTAAATTCCACG 59.364 41.667 0.00 0.00 30.73 4.94
2980 3151 5.649831 AGTGGCAGAGATTTCTAAATTCCAC 59.350 40.000 0.00 0.00 30.73 4.02
2981 3152 5.819991 AGTGGCAGAGATTTCTAAATTCCA 58.180 37.500 0.00 0.00 30.73 3.53
2982 3153 6.765915 AAGTGGCAGAGATTTCTAAATTCC 57.234 37.500 0.00 0.00 30.73 3.01
2986 3157 9.349713 TCTTTTTAAGTGGCAGAGATTTCTAAA 57.650 29.630 0.00 0.00 30.73 1.85
2987 3158 8.918202 TCTTTTTAAGTGGCAGAGATTTCTAA 57.082 30.769 0.00 0.00 30.73 2.10
2988 3159 8.918202 TTCTTTTTAAGTGGCAGAGATTTCTA 57.082 30.769 0.00 0.00 30.73 2.10
2989 3160 7.823745 TTCTTTTTAAGTGGCAGAGATTTCT 57.176 32.000 0.00 0.00 0.00 2.52
2990 3161 7.062722 GCATTCTTTTTAAGTGGCAGAGATTTC 59.937 37.037 0.00 0.00 0.00 2.17
2991 3162 6.870439 GCATTCTTTTTAAGTGGCAGAGATTT 59.130 34.615 0.00 0.00 0.00 2.17
2992 3163 6.015180 TGCATTCTTTTTAAGTGGCAGAGATT 60.015 34.615 0.00 0.00 0.00 2.40
2993 3164 5.477984 TGCATTCTTTTTAAGTGGCAGAGAT 59.522 36.000 0.00 0.00 0.00 2.75
2994 3165 4.826733 TGCATTCTTTTTAAGTGGCAGAGA 59.173 37.500 0.00 0.00 0.00 3.10
2995 3166 5.125100 TGCATTCTTTTTAAGTGGCAGAG 57.875 39.130 0.00 0.00 0.00 3.35
2996 3167 5.509501 CCTTGCATTCTTTTTAAGTGGCAGA 60.510 40.000 0.00 0.00 33.87 4.26
2997 3168 4.687483 CCTTGCATTCTTTTTAAGTGGCAG 59.313 41.667 0.00 0.00 33.87 4.85
2998 3169 4.100808 ACCTTGCATTCTTTTTAAGTGGCA 59.899 37.500 0.00 0.00 0.00 4.92
2999 3170 4.631131 ACCTTGCATTCTTTTTAAGTGGC 58.369 39.130 0.00 0.00 0.00 5.01
3000 3171 6.760770 TGAAACCTTGCATTCTTTTTAAGTGG 59.239 34.615 0.00 0.00 0.00 4.00
3001 3172 7.769272 TGAAACCTTGCATTCTTTTTAAGTG 57.231 32.000 0.00 0.00 0.00 3.16
3002 3173 7.986889 ACATGAAACCTTGCATTCTTTTTAAGT 59.013 29.630 0.00 0.00 0.00 2.24
3003 3174 8.369218 ACATGAAACCTTGCATTCTTTTTAAG 57.631 30.769 0.00 0.00 0.00 1.85
3004 3175 8.729805 AACATGAAACCTTGCATTCTTTTTAA 57.270 26.923 0.00 0.00 0.00 1.52
3005 3176 9.995003 ATAACATGAAACCTTGCATTCTTTTTA 57.005 25.926 0.00 0.00 0.00 1.52
3006 3177 8.907222 ATAACATGAAACCTTGCATTCTTTTT 57.093 26.923 0.00 0.00 0.00 1.94
3013 3184 9.382275 GGAAAAATATAACATGAAACCTTGCAT 57.618 29.630 0.00 0.00 0.00 3.96
3014 3185 8.592809 AGGAAAAATATAACATGAAACCTTGCA 58.407 29.630 0.00 0.00 0.00 4.08
3015 3186 9.435688 AAGGAAAAATATAACATGAAACCTTGC 57.564 29.630 0.00 0.00 32.72 4.01
3018 3189 9.320295 TGGAAGGAAAAATATAACATGAAACCT 57.680 29.630 0.00 0.00 0.00 3.50
3019 3190 9.366216 GTGGAAGGAAAAATATAACATGAAACC 57.634 33.333 0.00 0.00 0.00 3.27
3029 3200 9.555727 CGGAGAAATAGTGGAAGGAAAAATATA 57.444 33.333 0.00 0.00 0.00 0.86
3030 3201 8.053355 ACGGAGAAATAGTGGAAGGAAAAATAT 58.947 33.333 0.00 0.00 0.00 1.28
3031 3202 7.399634 ACGGAGAAATAGTGGAAGGAAAAATA 58.600 34.615 0.00 0.00 0.00 1.40
3032 3203 6.246163 ACGGAGAAATAGTGGAAGGAAAAAT 58.754 36.000 0.00 0.00 0.00 1.82
3033 3204 5.627135 ACGGAGAAATAGTGGAAGGAAAAA 58.373 37.500 0.00 0.00 0.00 1.94
3034 3205 5.012768 AGACGGAGAAATAGTGGAAGGAAAA 59.987 40.000 0.00 0.00 0.00 2.29
3035 3206 4.530946 AGACGGAGAAATAGTGGAAGGAAA 59.469 41.667 0.00 0.00 0.00 3.13
3036 3207 4.094476 AGACGGAGAAATAGTGGAAGGAA 58.906 43.478 0.00 0.00 0.00 3.36
3037 3208 3.709587 AGACGGAGAAATAGTGGAAGGA 58.290 45.455 0.00 0.00 0.00 3.36
3038 3209 5.349809 GTTAGACGGAGAAATAGTGGAAGG 58.650 45.833 0.00 0.00 0.00 3.46
3039 3210 5.127356 AGGTTAGACGGAGAAATAGTGGAAG 59.873 44.000 0.00 0.00 0.00 3.46
3040 3211 5.021458 AGGTTAGACGGAGAAATAGTGGAA 58.979 41.667 0.00 0.00 0.00 3.53
3041 3212 4.607239 AGGTTAGACGGAGAAATAGTGGA 58.393 43.478 0.00 0.00 0.00 4.02
3042 3213 5.340439 AAGGTTAGACGGAGAAATAGTGG 57.660 43.478 0.00 0.00 0.00 4.00
3043 3214 5.349809 GGAAGGTTAGACGGAGAAATAGTG 58.650 45.833 0.00 0.00 0.00 2.74
3044 3215 4.405036 GGGAAGGTTAGACGGAGAAATAGT 59.595 45.833 0.00 0.00 0.00 2.12
3045 3216 4.202233 GGGGAAGGTTAGACGGAGAAATAG 60.202 50.000 0.00 0.00 0.00 1.73
3046 3217 3.708121 GGGGAAGGTTAGACGGAGAAATA 59.292 47.826 0.00 0.00 0.00 1.40
3047 3218 2.504585 GGGGAAGGTTAGACGGAGAAAT 59.495 50.000 0.00 0.00 0.00 2.17
3048 3219 1.904537 GGGGAAGGTTAGACGGAGAAA 59.095 52.381 0.00 0.00 0.00 2.52
3049 3220 1.565067 GGGGAAGGTTAGACGGAGAA 58.435 55.000 0.00 0.00 0.00 2.87
3050 3221 0.682209 CGGGGAAGGTTAGACGGAGA 60.682 60.000 0.00 0.00 0.00 3.71
3051 3222 0.969409 ACGGGGAAGGTTAGACGGAG 60.969 60.000 0.00 0.00 0.00 4.63
3052 3223 0.331278 TACGGGGAAGGTTAGACGGA 59.669 55.000 0.00 0.00 0.00 4.69
3053 3224 0.743097 CTACGGGGAAGGTTAGACGG 59.257 60.000 0.00 0.00 0.00 4.79
3054 3225 0.743097 CCTACGGGGAAGGTTAGACG 59.257 60.000 0.00 0.00 37.23 4.18
3067 3238 1.835531 AGGTGATTGGTTACCCTACGG 59.164 52.381 0.00 0.00 37.70 4.02
3068 3239 3.622166 AAGGTGATTGGTTACCCTACG 57.378 47.619 0.00 0.00 37.70 3.51
3069 3240 7.949690 AAATTAAGGTGATTGGTTACCCTAC 57.050 36.000 0.00 0.00 37.70 3.18
3070 3241 8.838741 AGTAAATTAAGGTGATTGGTTACCCTA 58.161 33.333 0.00 0.00 37.70 3.53
3071 3242 7.705700 AGTAAATTAAGGTGATTGGTTACCCT 58.294 34.615 0.00 0.00 37.70 4.34
3072 3243 7.949690 AGTAAATTAAGGTGATTGGTTACCC 57.050 36.000 0.00 0.00 37.70 3.69
3076 3247 9.596308 AAGGTAAGTAAATTAAGGTGATTGGTT 57.404 29.630 0.00 0.00 0.00 3.67
3077 3248 9.239551 GAAGGTAAGTAAATTAAGGTGATTGGT 57.760 33.333 0.00 0.00 0.00 3.67
3078 3249 9.462606 AGAAGGTAAGTAAATTAAGGTGATTGG 57.537 33.333 0.00 0.00 0.00 3.16
3082 3253 9.948964 GGTTAGAAGGTAAGTAAATTAAGGTGA 57.051 33.333 0.00 0.00 0.00 4.02
3083 3254 9.170734 GGGTTAGAAGGTAAGTAAATTAAGGTG 57.829 37.037 0.00 0.00 0.00 4.00
3084 3255 8.893560 TGGGTTAGAAGGTAAGTAAATTAAGGT 58.106 33.333 0.00 0.00 0.00 3.50
3085 3256 9.743581 TTGGGTTAGAAGGTAAGTAAATTAAGG 57.256 33.333 0.00 0.00 0.00 2.69
3095 3266 5.866207 AGTGAAGTTGGGTTAGAAGGTAAG 58.134 41.667 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.