Multiple sequence alignment - TraesCS3B01G255000

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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 TraesCS3B01G255000 chr3B 100.000 7758 0 0 1 7758 411428845 411421088 0.000000e+00 14327.0
1 TraesCS3B01G255000 chr3B 94.570 221 8 2 7210 7430 411421420 411421204 9.640000e-89 339.0
2 TraesCS3B01G255000 chr3B 94.570 221 8 2 7426 7642 411421636 411421416 9.640000e-89 339.0
3 TraesCS3B01G255000 chr3B 100.000 36 0 0 7622 7657 411421190 411421155 5.020000e-07 67.6
4 TraesCS3B01G255000 chr3B 100.000 36 0 0 7656 7691 411421224 411421189 5.020000e-07 67.6
5 TraesCS3B01G255000 chr3D 96.257 5958 135 29 2 5889 309910780 309916719 0.000000e+00 9686.0
6 TraesCS3B01G255000 chr3D 93.722 1561 55 25 5899 7430 309917016 309918562 0.000000e+00 2300.0
7 TraesCS3B01G255000 chr3D 90.868 219 17 1 7442 7657 309918359 309918577 2.740000e-74 291.0
8 TraesCS3B01G255000 chr3D 96.907 97 3 0 7656 7752 309918542 309918638 6.230000e-36 163.0
9 TraesCS3B01G255000 chr3A 92.934 3071 108 38 3 3019 422918297 422915282 0.000000e+00 4368.0
10 TraesCS3B01G255000 chr3A 98.463 1561 23 1 3116 4676 422915281 422913722 0.000000e+00 2748.0
11 TraesCS3B01G255000 chr3A 92.140 1883 99 25 5565 7411 422910928 422909059 0.000000e+00 2612.0
12 TraesCS3B01G255000 chr3A 95.276 868 25 8 4705 5569 422911941 422911087 0.000000e+00 1362.0
13 TraesCS3B01G255000 chr3A 97.826 46 1 0 4664 4709 422912004 422911959 6.450000e-11 80.5
14 TraesCS3B01G255000 chr5B 86.842 1596 166 22 3130 4709 12573011 12574578 0.000000e+00 1744.0
15 TraesCS3B01G255000 chr5B 83.469 1355 166 26 1681 2990 12571629 12572970 0.000000e+00 1208.0
16 TraesCS3B01G255000 chr5B 85.737 638 80 10 6134 6763 12576795 12577429 0.000000e+00 664.0
17 TraesCS3B01G255000 chr5B 82.619 420 53 14 5354 5767 12575818 12576223 3.440000e-93 353.0
18 TraesCS3B01G255000 chr5B 81.972 355 43 13 4957 5308 12575170 12575506 1.650000e-71 281.0
19 TraesCS3B01G255000 chr5D 87.693 1487 151 14 3163 4638 12226554 12225089 0.000000e+00 1703.0
20 TraesCS3B01G255000 chr5D 83.582 871 97 21 5922 6769 12223355 12222508 0.000000e+00 774.0
21 TraesCS3B01G255000 chr5D 83.602 683 89 16 2321 2990 12227276 12226604 3.080000e-173 619.0
22 TraesCS3B01G255000 chr5D 83.961 611 78 13 6176 6769 12174941 12174334 1.130000e-157 568.0
23 TraesCS3B01G255000 chr5D 87.205 508 52 9 1681 2177 12227827 12227322 4.060000e-157 566.0
24 TraesCS3B01G255000 chr5D 79.493 829 106 38 4957 5767 12224778 12223996 1.480000e-146 531.0
25 TraesCS3B01G255000 chr5D 78.038 469 64 24 5318 5767 12215583 12215135 7.720000e-65 259.0
26 TraesCS3B01G255000 chr5D 89.683 126 9 3 2993 3116 558970558 558970435 2.900000e-34 158.0
27 TraesCS3B01G255000 chr5D 83.824 136 21 1 4960 5094 12165909 12165774 2.270000e-25 128.0
28 TraesCS3B01G255000 chr5A 86.144 1595 179 23 3130 4709 9614488 9612921 0.000000e+00 1683.0
29 TraesCS3B01G255000 chr5A 83.829 841 104 21 2206 3024 9615324 9614494 0.000000e+00 771.0
30 TraesCS3B01G255000 chr5A 82.604 891 110 20 5902 6769 9611522 9610654 0.000000e+00 745.0
31 TraesCS3B01G255000 chr5A 80.120 830 109 36 4957 5767 9612702 9611910 1.130000e-157 568.0
32 TraesCS3B01G255000 chr5A 86.417 508 56 9 1681 2177 9615891 9615386 1.900000e-150 544.0
33 TraesCS3B01G255000 chr5A 79.858 422 57 18 5354 5767 9608411 9608010 4.580000e-72 283.0
34 TraesCS3B01G255000 chr5A 88.362 232 24 2 6203 6431 9607827 9607596 7.670000e-70 276.0
35 TraesCS3B01G255000 chr5A 79.474 190 29 4 5576 5765 9502177 9501998 8.170000e-25 126.0
36 TraesCS3B01G255000 chr6B 96.117 103 4 0 3017 3119 424084089 424084191 1.340000e-37 169.0
37 TraesCS3B01G255000 chr6B 96.117 103 4 0 3017 3119 424306787 424306889 1.340000e-37 169.0
38 TraesCS3B01G255000 chr1B 90.625 128 10 2 2994 3120 359902023 359902149 1.340000e-37 169.0
39 TraesCS3B01G255000 chr7B 93.636 110 6 1 3014 3123 747370734 747370626 6.230000e-36 163.0
40 TraesCS3B01G255000 chr7B 89.130 46 5 0 7012 7057 649116789 649116834 3.020000e-04 58.4
41 TraesCS3B01G255000 chr1A 96.000 100 4 0 3014 3113 474641671 474641770 6.230000e-36 163.0
42 TraesCS3B01G255000 chr7D 94.340 106 4 2 3013 3116 426783467 426783572 2.240000e-35 161.0
43 TraesCS3B01G255000 chr1D 95.050 101 5 0 3019 3119 483907679 483907579 8.060000e-35 159.0


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 TraesCS3B01G255000 chr3B 411421088 411428845 7757 True 14327.000000 14327 100.000000 1 7758 1 chr3B.!!$R1 7757
1 TraesCS3B01G255000 chr3D 309910780 309918638 7858 False 3110.000000 9686 94.438500 2 7752 4 chr3D.!!$F1 7750
2 TraesCS3B01G255000 chr3A 422909059 422918297 9238 True 2234.100000 4368 95.327800 3 7411 5 chr3A.!!$R1 7408
3 TraesCS3B01G255000 chr5B 12571629 12577429 5800 False 850.000000 1744 84.127800 1681 6763 5 chr5B.!!$F1 5082
4 TraesCS3B01G255000 chr5D 12222508 12227827 5319 True 838.600000 1703 84.315000 1681 6769 5 chr5D.!!$R5 5088
5 TraesCS3B01G255000 chr5D 12174334 12174941 607 True 568.000000 568 83.961000 6176 6769 1 chr5D.!!$R2 593
6 TraesCS3B01G255000 chr5A 9607596 9615891 8295 True 695.714286 1683 83.904857 1681 6769 7 chr5A.!!$R2 5088

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
843 885 0.535335 TTATCCAGTGAGCCACGACC 59.465 55.000 0.00 0.00 39.64 4.79 F
1122 1180 0.034186 TTTCGCTGGATCAGGCCATT 60.034 50.000 5.01 0.00 37.30 3.16 F
1209 1282 0.397816 TTGGGTTGGGTTGAGTTGGG 60.398 55.000 0.00 0.00 0.00 4.12 F
1232 1305 0.814457 TGCTTTTGTCTTGGCGTTGT 59.186 45.000 0.00 0.00 0.00 3.32 F
1676 1772 0.905357 TAGAGCCCTTCTTGGACAGC 59.095 55.000 0.00 0.00 37.36 4.40 F
3278 3467 1.003580 TCAGGTGACCTTCTTGATGCC 59.996 52.381 0.00 0.00 0.00 4.40 F
4562 4761 0.676466 TTGGGCGGTATGACTTGCTG 60.676 55.000 0.00 0.00 0.00 4.41 F
5095 7504 3.146066 GCTGGTTATCTTGTGTGTTCCA 58.854 45.455 0.00 0.00 0.00 3.53 F
6646 10078 1.077429 GCTGGAGTGGACCATTCCC 60.077 63.158 28.15 15.88 42.01 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1843 1947 0.530744 ACGGACTTGATAGCGCAAGA 59.469 50.000 11.47 0.00 46.31 3.02 R
2092 2199 2.290641 AGATTCACAAAGACAACACGCC 59.709 45.455 0.00 0.00 0.00 5.68 R
3155 3332 0.958091 AAAAACGCAGGCAGCATACA 59.042 45.000 1.96 0.00 46.13 2.29 R
3278 3467 3.499737 GGGCTGCGATTCACACCG 61.500 66.667 0.00 0.00 0.00 4.94 R
3388 3577 0.613777 ACTTCCAACTGGACCCGATC 59.386 55.000 0.00 0.00 45.39 3.69 R
4710 6663 2.496899 AAGGAATGTGACATTCGCCT 57.503 45.000 26.47 19.15 0.00 5.52 R
5380 8056 0.663153 GTCAGTTGTGGACTTGTGGC 59.337 55.000 0.00 0.00 36.10 5.01 R
6649 10081 0.957395 AAACACCAGAGGCAGCATCG 60.957 55.000 0.42 0.00 0.00 3.84 R
7580 12888 0.103937 GTCCGATCTTCAGCTCTGGG 59.896 60.000 0.00 0.00 0.00 4.45 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
31 32 6.319658 ACTTCTCTCAAACTTGCAAGAATTCA 59.680 34.615 32.50 12.62 32.18 2.57
32 33 6.309712 TCTCTCAAACTTGCAAGAATTCAG 57.690 37.500 32.50 20.70 0.00 3.02
37 45 5.295787 TCAAACTTGCAAGAATTCAGTACGT 59.704 36.000 32.50 3.46 0.00 3.57
51 59 1.735198 TACGTTTGAAGAGGCGCCG 60.735 57.895 23.20 8.19 0.00 6.46
202 211 3.420893 TGCCTTGAATGGTGGTTCTAAG 58.579 45.455 0.00 0.00 0.00 2.18
297 306 5.300286 GGACCCAATTCATGAGACCATAAAG 59.700 44.000 0.00 0.00 0.00 1.85
370 379 9.035607 CATTTAGTAAAGCATTCTATCGTCTGT 57.964 33.333 1.21 0.00 0.00 3.41
386 395 0.734889 CTGTCAAACGATGGGATGGC 59.265 55.000 0.00 0.00 0.00 4.40
413 422 4.171878 TGAGTCAGATCTACCTACCAGG 57.828 50.000 0.00 0.00 42.49 4.45
468 477 2.125673 GCATGCTGCAAGGGCTTG 60.126 61.111 11.37 0.00 44.26 4.01
471 480 1.681327 ATGCTGCAAGGGCTTGAGG 60.681 57.895 6.36 0.00 42.93 3.86
472 481 3.756727 GCTGCAAGGGCTTGAGGC 61.757 66.667 0.00 0.00 42.93 4.70
613 634 3.256960 GTTGAGGCCTCCCCCACA 61.257 66.667 29.95 8.00 0.00 4.17
614 635 3.256960 TTGAGGCCTCCCCCACAC 61.257 66.667 29.95 3.30 0.00 3.82
735 756 4.416738 GCCCCTGTCTCCACTGCC 62.417 72.222 0.00 0.00 0.00 4.85
742 763 1.305718 GTCTCCACTGCCTCCTCCT 60.306 63.158 0.00 0.00 0.00 3.69
743 764 1.000993 TCTCCACTGCCTCCTCCTC 59.999 63.158 0.00 0.00 0.00 3.71
744 765 1.305633 CTCCACTGCCTCCTCCTCA 60.306 63.158 0.00 0.00 0.00 3.86
843 885 0.535335 TTATCCAGTGAGCCACGACC 59.465 55.000 0.00 0.00 39.64 4.79
846 888 2.734723 CAGTGAGCCACGACCACG 60.735 66.667 0.00 0.00 45.75 4.94
1021 1075 2.738521 TGAGTTCGCTTGCTCGGC 60.739 61.111 0.00 0.00 34.67 5.54
1122 1180 0.034186 TTTCGCTGGATCAGGCCATT 60.034 50.000 5.01 0.00 37.30 3.16
1200 1273 4.280019 GCTCCGGTTGGGTTGGGT 62.280 66.667 0.00 0.00 37.00 4.51
1201 1274 2.518933 CTCCGGTTGGGTTGGGTT 59.481 61.111 0.00 0.00 37.00 4.11
1202 1275 1.901464 CTCCGGTTGGGTTGGGTTG 60.901 63.158 0.00 0.00 37.00 3.77
1203 1276 2.196229 CCGGTTGGGTTGGGTTGA 59.804 61.111 0.00 0.00 0.00 3.18
1204 1277 1.901464 CCGGTTGGGTTGGGTTGAG 60.901 63.158 0.00 0.00 0.00 3.02
1205 1278 1.152839 CGGTTGGGTTGGGTTGAGT 60.153 57.895 0.00 0.00 0.00 3.41
1206 1279 0.753848 CGGTTGGGTTGGGTTGAGTT 60.754 55.000 0.00 0.00 0.00 3.01
1207 1280 0.750249 GGTTGGGTTGGGTTGAGTTG 59.250 55.000 0.00 0.00 0.00 3.16
1208 1281 0.750249 GTTGGGTTGGGTTGAGTTGG 59.250 55.000 0.00 0.00 0.00 3.77
1209 1282 0.397816 TTGGGTTGGGTTGAGTTGGG 60.398 55.000 0.00 0.00 0.00 4.12
1215 1288 1.040339 TGGGTTGAGTTGGGTTGTGC 61.040 55.000 0.00 0.00 0.00 4.57
1232 1305 0.814457 TGCTTTTGTCTTGGCGTTGT 59.186 45.000 0.00 0.00 0.00 3.32
1297 1370 2.125753 GTGAGAGAGTGGCCGCAG 60.126 66.667 20.59 0.00 0.00 5.18
1390 1464 3.282745 GAGAGACGCGGCCTTGACA 62.283 63.158 9.25 0.00 0.00 3.58
1441 1515 1.680338 AAGGATTCAATAGGGTGCGC 58.320 50.000 0.00 0.00 0.00 6.09
1466 1540 2.932614 CGACCTGGTGATTTAGAAGCAG 59.067 50.000 2.82 0.00 40.72 4.24
1556 1643 2.673368 GTGACAATGTCGAGGAATCCAC 59.327 50.000 9.00 0.00 34.95 4.02
1676 1772 0.905357 TAGAGCCCTTCTTGGACAGC 59.095 55.000 0.00 0.00 37.36 4.40
1703 1799 3.130340 ACCATTTCCCGTTGCATCATTAC 59.870 43.478 0.00 0.00 0.00 1.89
1789 1888 5.413309 TCTTCTCTGGAGATTTTGGACTC 57.587 43.478 0.88 0.00 37.29 3.36
1843 1947 2.781757 TCCTGATGGAGGCATCATCTTT 59.218 45.455 16.92 0.00 42.47 2.52
1883 1987 3.067601 GTGGTTTTGGTTCGTTCAGGATT 59.932 43.478 0.00 0.00 0.00 3.01
2080 2184 1.395068 CGCGCGTTTATTGTTGCTGG 61.395 55.000 24.19 0.00 0.00 4.85
2092 2199 1.106285 GTTGCTGGGCCTAATGGAAG 58.894 55.000 4.53 0.00 34.57 3.46
2293 2439 3.281727 TGCCTGGTTACATCATCCTTC 57.718 47.619 0.00 0.00 0.00 3.46
2401 2565 5.734220 GCCACCATTAACTGCTGATATTGTG 60.734 44.000 0.00 0.76 0.00 3.33
3002 3179 6.043411 GTCTGGCTACAATCTTATTTCTCGT 58.957 40.000 0.00 0.00 0.00 4.18
3003 3180 7.068348 AGTCTGGCTACAATCTTATTTCTCGTA 59.932 37.037 0.00 0.00 0.00 3.43
3120 3297 2.674420 TGGGACGGAGGGAGTAATAAG 58.326 52.381 0.00 0.00 0.00 1.73
3124 3301 2.429610 GACGGAGGGAGTAATAAGTGCA 59.570 50.000 0.00 0.00 0.00 4.57
3155 3332 9.646522 AGTATAATTTTGCATGTTCTATTCCCT 57.353 29.630 0.00 0.00 0.00 4.20
3278 3467 1.003580 TCAGGTGACCTTCTTGATGCC 59.996 52.381 0.00 0.00 0.00 4.40
3388 3577 6.659242 ACCCTTGTTAAGTTTGTAGATGATGG 59.341 38.462 0.00 0.00 0.00 3.51
3841 4030 9.122613 GCATTAGAAGTTCTCAAGAAAACAATC 57.877 33.333 9.12 0.00 35.58 2.67
4044 4233 3.788333 TCCGTACACATAAGCCACTAC 57.212 47.619 0.00 0.00 0.00 2.73
4562 4761 0.676466 TTGGGCGGTATGACTTGCTG 60.676 55.000 0.00 0.00 0.00 4.41
5095 7504 3.146066 GCTGGTTATCTTGTGTGTTCCA 58.854 45.455 0.00 0.00 0.00 3.53
5132 7541 5.878406 ATTCGTCAATCCTAGGATGTCTT 57.122 39.130 25.20 7.31 34.70 3.01
5176 7586 9.553064 GTGGTTCTTTGATCTATTGAGATATGT 57.447 33.333 0.00 0.00 42.80 2.29
5505 8195 2.576191 AGAGTTAGGTGGGCAATTGCTA 59.424 45.455 28.42 15.94 41.70 3.49
5536 8226 4.133078 GAGCTAGCAAGGCAAATACTCAT 58.867 43.478 18.83 0.00 0.00 2.90
5537 8227 4.530875 AGCTAGCAAGGCAAATACTCATT 58.469 39.130 18.83 0.00 0.00 2.57
5538 8228 4.578105 AGCTAGCAAGGCAAATACTCATTC 59.422 41.667 18.83 0.00 0.00 2.67
5539 8229 4.261363 GCTAGCAAGGCAAATACTCATTCC 60.261 45.833 10.63 0.00 0.00 3.01
5540 8230 3.973425 AGCAAGGCAAATACTCATTCCT 58.027 40.909 0.00 0.00 0.00 3.36
5541 8231 3.950395 AGCAAGGCAAATACTCATTCCTC 59.050 43.478 0.00 0.00 0.00 3.71
5542 8232 3.696051 GCAAGGCAAATACTCATTCCTCA 59.304 43.478 0.00 0.00 0.00 3.86
5920 9323 8.486210 AGAGATGTGTTAGAATGCTGGTTATTA 58.514 33.333 0.00 0.00 0.00 0.98
5927 9330 8.318412 TGTTAGAATGCTGGTTATTACTCTTCA 58.682 33.333 0.00 0.00 0.00 3.02
6011 9414 1.077663 ACTTGTTTCAGCCCCATCCAT 59.922 47.619 0.00 0.00 0.00 3.41
6099 9503 3.830755 AGTTGGCTTTCATTGATGCTTCT 59.169 39.130 10.56 5.78 0.00 2.85
6174 9592 4.039730 AGACCCACTCAGCATATGTATCAC 59.960 45.833 4.29 0.00 0.00 3.06
6529 9961 1.502231 TCGCACTTGTTGAGAAGCTC 58.498 50.000 0.00 0.00 29.94 4.09
6646 10078 1.077429 GCTGGAGTGGACCATTCCC 60.077 63.158 28.15 15.88 42.01 3.97
6649 10081 1.221021 GGAGTGGACCATTCCCGAC 59.779 63.158 22.61 0.38 42.01 4.79
6800 10232 4.359105 AGGTATACCTGCCAGAGTTTACA 58.641 43.478 24.01 0.00 46.55 2.41
6986 10423 6.129717 GCTTTTTATTGATGCGTAATGTAGCG 60.130 38.462 0.00 0.00 35.87 4.26
7045 10482 3.313803 TGCACACAATCAACAATACACGT 59.686 39.130 0.00 0.00 0.00 4.49
7087 10530 1.007238 TGTCTAGGTGAAGAGAGGGGG 59.993 57.143 0.00 0.00 0.00 5.40
7114 11239 7.733402 AACCAAAGCGATAAAAACAGTAGTA 57.267 32.000 0.00 0.00 0.00 1.82
7154 11291 1.471119 TCACCTCCTACCGTGTCATC 58.529 55.000 0.00 0.00 0.00 2.92
7160 11297 1.972075 TCCTACCGTGTCATCCAACAA 59.028 47.619 0.00 0.00 0.00 2.83
7163 11300 3.566322 CCTACCGTGTCATCCAACAAAAA 59.434 43.478 0.00 0.00 0.00 1.94
7190 11995 6.624352 TTCTGAAAGTGACATCTCCAAAAG 57.376 37.500 0.00 0.00 33.76 2.27
7244 12049 2.484264 CCAACCGTCAAAGAGTTGATCC 59.516 50.000 3.79 0.00 45.38 3.36
7247 12052 2.368875 ACCGTCAAAGAGTTGATCCTGT 59.631 45.455 0.00 0.00 45.38 4.00
7259 12064 1.203505 TGATCCTGTGGTTTCCCCCTA 60.204 52.381 0.00 0.00 0.00 3.53
7295 12100 2.477754 GCAAACTTCAAGCAATGCCTTC 59.522 45.455 0.00 0.00 0.00 3.46
7300 12105 3.575256 ACTTCAAGCAATGCCTTCATGAA 59.425 39.130 8.12 8.12 32.23 2.57
7336 12644 7.277098 ACAAAGAACGTCACCATATACATGTAC 59.723 37.037 7.96 0.00 0.00 2.90
7383 12691 0.537188 TCAACCCGGAGCTGAAGATC 59.463 55.000 0.73 0.00 0.00 2.75
7384 12692 0.250234 CAACCCGGAGCTGAAGATCA 59.750 55.000 0.73 0.00 30.87 2.92
7398 12706 5.904362 TGAAGATCAGACATTCGAGAAGA 57.096 39.130 0.00 0.00 0.00 2.87
7399 12707 6.272822 TGAAGATCAGACATTCGAGAAGAA 57.727 37.500 0.00 0.00 43.93 2.52
7400 12708 6.096036 TGAAGATCAGACATTCGAGAAGAAC 58.904 40.000 0.00 0.00 42.39 3.01
7401 12709 5.004922 AGATCAGACATTCGAGAAGAACC 57.995 43.478 0.00 0.00 42.39 3.62
7402 12710 4.464244 AGATCAGACATTCGAGAAGAACCA 59.536 41.667 0.00 0.00 42.39 3.67
7403 12711 3.914312 TCAGACATTCGAGAAGAACCAC 58.086 45.455 0.00 0.00 42.39 4.16
7404 12712 2.996621 CAGACATTCGAGAAGAACCACC 59.003 50.000 0.00 0.00 42.39 4.61
7405 12713 2.900546 AGACATTCGAGAAGAACCACCT 59.099 45.455 0.00 0.00 42.39 4.00
7406 12714 4.082190 CAGACATTCGAGAAGAACCACCTA 60.082 45.833 0.00 0.00 42.39 3.08
7407 12715 4.527038 AGACATTCGAGAAGAACCACCTAA 59.473 41.667 0.00 0.00 42.39 2.69
7408 12716 5.187967 AGACATTCGAGAAGAACCACCTAAT 59.812 40.000 0.00 0.00 42.39 1.73
7410 12718 5.046591 ACATTCGAGAAGAACCACCTAATGA 60.047 40.000 0.00 0.00 42.39 2.57
7411 12719 5.477607 TTCGAGAAGAACCACCTAATGAA 57.522 39.130 0.00 0.00 33.14 2.57
7412 12720 5.477607 TCGAGAAGAACCACCTAATGAAA 57.522 39.130 0.00 0.00 0.00 2.69
7413 12721 5.479306 TCGAGAAGAACCACCTAATGAAAG 58.521 41.667 0.00 0.00 0.00 2.62
7414 12722 5.011738 TCGAGAAGAACCACCTAATGAAAGT 59.988 40.000 0.00 0.00 0.00 2.66
7415 12723 5.348997 CGAGAAGAACCACCTAATGAAAGTC 59.651 44.000 0.00 0.00 0.00 3.01
7416 12724 6.187727 AGAAGAACCACCTAATGAAAGTCA 57.812 37.500 0.00 0.00 0.00 3.41
7417 12725 6.784031 AGAAGAACCACCTAATGAAAGTCAT 58.216 36.000 0.00 0.00 39.09 3.06
7418 12726 6.881602 AGAAGAACCACCTAATGAAAGTCATC 59.118 38.462 0.00 0.00 35.76 2.92
7422 12730 6.831664 ACCACCTAATGAAAGTCATCCTAT 57.168 37.500 0.00 0.00 35.76 2.57
7423 12731 6.595682 ACCACCTAATGAAAGTCATCCTATG 58.404 40.000 0.00 0.00 35.76 2.23
7441 12749 3.806591 GACGTCTTGTCGGATCCAA 57.193 52.632 13.41 0.00 37.96 3.53
7442 12750 1.347320 GACGTCTTGTCGGATCCAAC 58.653 55.000 13.41 3.67 37.96 3.77
7443 12751 0.037605 ACGTCTTGTCGGATCCAACC 60.038 55.000 13.41 0.00 34.94 3.77
7451 12759 3.525619 CGGATCCAACCGTCAAAGA 57.474 52.632 13.41 0.00 46.70 2.52
7452 12760 1.359848 CGGATCCAACCGTCAAAGAG 58.640 55.000 13.41 0.00 46.70 2.85
7453 12761 1.337823 CGGATCCAACCGTCAAAGAGT 60.338 52.381 13.41 0.00 46.70 3.24
7454 12762 2.779506 GGATCCAACCGTCAAAGAGTT 58.220 47.619 6.95 0.00 0.00 3.01
7456 12764 2.992124 TCCAACCGTCAAAGAGTTGA 57.008 45.000 3.79 0.00 42.76 3.18
7460 12768 3.403038 CAACCGTCAAAGAGTTGATCCT 58.597 45.455 0.00 0.00 45.38 3.24
7461 12769 3.045601 ACCGTCAAAGAGTTGATCCTG 57.954 47.619 0.00 0.00 45.38 3.86
7462 12770 2.289694 ACCGTCAAAGAGTTGATCCTGG 60.290 50.000 0.00 0.00 45.38 4.45
7463 12771 2.350522 CGTCAAAGAGTTGATCCTGGG 58.649 52.381 0.00 0.00 45.38 4.45
7464 12772 2.716217 GTCAAAGAGTTGATCCTGGGG 58.284 52.381 0.00 0.00 45.38 4.96
7468 12776 3.441500 AAGAGTTGATCCTGGGGTTTC 57.558 47.619 0.00 0.00 0.00 2.78
7469 12777 1.636003 AGAGTTGATCCTGGGGTTTCC 59.364 52.381 0.00 0.00 0.00 3.13
7499 12807 4.695217 AACAAGTTCGAGCAAACTTCAA 57.305 36.364 1.01 0.00 45.36 2.69
7500 12808 4.278678 ACAAGTTCGAGCAAACTTCAAG 57.721 40.909 1.01 0.00 45.36 3.02
7501 12809 3.038710 CAAGTTCGAGCAAACTTCAAGC 58.961 45.455 1.01 0.00 45.36 4.01
7502 12810 2.288666 AGTTCGAGCAAACTTCAAGCA 58.711 42.857 1.01 0.00 36.02 3.91
7503 12811 2.682856 AGTTCGAGCAAACTTCAAGCAA 59.317 40.909 1.01 0.00 36.02 3.91
7504 12812 3.316308 AGTTCGAGCAAACTTCAAGCAAT 59.684 39.130 1.01 0.00 36.02 3.56
7505 12813 3.272439 TCGAGCAAACTTCAAGCAATG 57.728 42.857 0.00 0.00 0.00 2.82
7507 12815 2.064014 GAGCAAACTTCAAGCAATGCC 58.936 47.619 0.00 0.00 34.44 4.40
7508 12816 1.690352 AGCAAACTTCAAGCAATGCCT 59.310 42.857 0.00 0.00 34.44 4.75
7509 12817 2.103601 AGCAAACTTCAAGCAATGCCTT 59.896 40.909 0.00 0.00 34.44 4.35
7510 12818 2.477754 GCAAACTTCAAGCAATGCCTTC 59.522 45.455 0.00 0.00 0.00 3.46
7511 12819 3.719924 CAAACTTCAAGCAATGCCTTCA 58.280 40.909 0.00 0.00 0.00 3.02
7512 12820 4.312443 CAAACTTCAAGCAATGCCTTCAT 58.688 39.130 0.00 0.00 33.53 2.57
7513 12821 3.587797 ACTTCAAGCAATGCCTTCATG 57.412 42.857 0.00 0.00 32.23 3.07
7514 12822 3.159472 ACTTCAAGCAATGCCTTCATGA 58.841 40.909 0.00 0.00 32.23 3.07
7517 12825 1.136305 CAAGCAATGCCTTCATGAGGG 59.864 52.381 19.29 19.29 46.40 4.30
7518 12826 0.333993 AGCAATGCCTTCATGAGGGT 59.666 50.000 23.56 3.44 46.40 4.34
7519 12827 1.565759 AGCAATGCCTTCATGAGGGTA 59.434 47.619 23.56 20.35 46.40 3.69
7520 12828 2.025037 AGCAATGCCTTCATGAGGGTAA 60.025 45.455 23.56 13.66 46.40 2.85
7521 12829 2.961062 GCAATGCCTTCATGAGGGTAAT 59.039 45.455 23.56 15.19 46.40 1.89
7524 12832 3.281727 TGCCTTCATGAGGGTAATGAC 57.718 47.619 23.56 7.71 46.40 3.06
7525 12833 2.575735 TGCCTTCATGAGGGTAATGACA 59.424 45.455 23.56 10.15 46.40 3.58
7526 12834 3.010027 TGCCTTCATGAGGGTAATGACAA 59.990 43.478 23.56 0.00 46.40 3.18
7527 12835 3.629398 GCCTTCATGAGGGTAATGACAAG 59.371 47.826 23.56 0.94 46.40 3.16
7528 12836 4.626287 GCCTTCATGAGGGTAATGACAAGA 60.626 45.833 23.56 0.00 46.40 3.02
7529 12837 5.500234 CCTTCATGAGGGTAATGACAAGAA 58.500 41.667 15.62 0.00 42.26 2.52
7530 12838 5.355350 CCTTCATGAGGGTAATGACAAGAAC 59.645 44.000 15.62 0.00 42.26 3.01
7531 12839 4.503910 TCATGAGGGTAATGACAAGAACG 58.496 43.478 0.00 0.00 0.00 3.95
7532 12840 4.020573 TCATGAGGGTAATGACAAGAACGT 60.021 41.667 0.00 0.00 0.00 3.99
7533 12841 3.921677 TGAGGGTAATGACAAGAACGTC 58.078 45.455 0.00 0.00 36.40 4.34
7545 12853 5.810074 TGACAAGAACGTCACCATATACATG 59.190 40.000 0.00 0.00 40.94 3.21
7546 12854 5.730550 ACAAGAACGTCACCATATACATGT 58.269 37.500 2.69 2.69 0.00 3.21
7547 12855 6.869695 ACAAGAACGTCACCATATACATGTA 58.130 36.000 8.27 8.27 0.00 2.29
7549 12857 6.459670 AGAACGTCACCATATACATGTACA 57.540 37.500 7.96 0.00 0.00 2.90
7550 12858 6.869695 AGAACGTCACCATATACATGTACAA 58.130 36.000 7.96 0.00 0.00 2.41
7552 12860 5.968254 ACGTCACCATATACATGTACAACA 58.032 37.500 7.96 0.00 0.00 3.33
7553 12861 6.399743 ACGTCACCATATACATGTACAACAA 58.600 36.000 7.96 0.00 0.00 2.83
7554 12862 6.874664 ACGTCACCATATACATGTACAACAAA 59.125 34.615 7.96 0.00 0.00 2.83
7555 12863 7.551262 ACGTCACCATATACATGTACAACAAAT 59.449 33.333 7.96 0.00 0.00 2.32
7556 12864 8.394877 CGTCACCATATACATGTACAACAAATT 58.605 33.333 7.96 0.00 0.00 1.82
7567 12875 8.349983 ACATGTACAACAAATTAGAGTCAAACC 58.650 33.333 0.00 0.00 0.00 3.27
7568 12876 8.567948 CATGTACAACAAATTAGAGTCAAACCT 58.432 33.333 0.00 0.00 0.00 3.50
7569 12877 9.787435 ATGTACAACAAATTAGAGTCAAACCTA 57.213 29.630 0.00 0.00 0.00 3.08
7570 12878 9.787435 TGTACAACAAATTAGAGTCAAACCTAT 57.213 29.630 0.00 0.00 0.00 2.57
7581 12889 9.886132 TTAGAGTCAAACCTATAATTCTCAACC 57.114 33.333 0.00 0.00 0.00 3.77
7582 12890 7.339482 AGAGTCAAACCTATAATTCTCAACCC 58.661 38.462 0.00 0.00 0.00 4.11
7583 12891 7.027874 AGTCAAACCTATAATTCTCAACCCA 57.972 36.000 0.00 0.00 0.00 4.51
7584 12892 7.112779 AGTCAAACCTATAATTCTCAACCCAG 58.887 38.462 0.00 0.00 0.00 4.45
7585 12893 7.037586 AGTCAAACCTATAATTCTCAACCCAGA 60.038 37.037 0.00 0.00 0.00 3.86
7586 12894 7.281100 GTCAAACCTATAATTCTCAACCCAGAG 59.719 40.741 0.00 0.00 36.97 3.35
7587 12895 5.297569 ACCTATAATTCTCAACCCAGAGC 57.702 43.478 0.00 0.00 35.59 4.09
7588 12896 4.971924 ACCTATAATTCTCAACCCAGAGCT 59.028 41.667 0.00 0.00 35.59 4.09
7589 12897 5.163258 ACCTATAATTCTCAACCCAGAGCTG 60.163 44.000 0.00 0.00 35.59 4.24
7590 12898 5.070981 CCTATAATTCTCAACCCAGAGCTGA 59.929 44.000 0.00 0.00 35.59 4.26
7591 12899 3.795688 AATTCTCAACCCAGAGCTGAA 57.204 42.857 0.00 0.00 35.59 3.02
7592 12900 2.847327 TTCTCAACCCAGAGCTGAAG 57.153 50.000 0.00 0.00 35.59 3.02
7593 12901 2.015456 TCTCAACCCAGAGCTGAAGA 57.985 50.000 0.00 0.00 35.59 2.87
7594 12902 2.544721 TCTCAACCCAGAGCTGAAGAT 58.455 47.619 0.00 0.00 35.59 2.40
7598 12906 0.324738 ACCCAGAGCTGAAGATCGGA 60.325 55.000 0.00 0.00 35.26 4.55
7647 12955 3.832527 TCATCCTATGACGTCTCATCCA 58.167 45.455 17.92 0.00 38.21 3.41
7649 12957 3.298686 TCCTATGACGTCTCATCCACT 57.701 47.619 17.92 0.00 38.21 4.00
7650 12958 3.632333 TCCTATGACGTCTCATCCACTT 58.368 45.455 17.92 0.00 38.21 3.16
7651 12959 3.381590 TCCTATGACGTCTCATCCACTTG 59.618 47.826 17.92 0.00 38.21 3.16
7652 12960 2.015736 ATGACGTCTCATCCACTTGC 57.984 50.000 17.92 0.00 30.64 4.01
7653 12961 0.388520 TGACGTCTCATCCACTTGCG 60.389 55.000 17.92 0.00 0.00 4.85
7654 12962 0.109272 GACGTCTCATCCACTTGCGA 60.109 55.000 8.70 0.00 0.00 5.10
7655 12963 0.109086 ACGTCTCATCCACTTGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
7656 12964 0.171231 CGTCTCATCCACTTGCGAGA 59.829 55.000 8.31 0.00 32.21 4.04
7657 12965 1.402852 CGTCTCATCCACTTGCGAGAA 60.403 52.381 8.31 0.00 36.33 2.87
7658 12966 2.688507 GTCTCATCCACTTGCGAGAAA 58.311 47.619 8.31 0.00 36.33 2.52
7660 12968 2.300152 TCTCATCCACTTGCGAGAAAGT 59.700 45.455 8.31 0.00 41.08 2.66
7661 12969 2.670414 CTCATCCACTTGCGAGAAAGTC 59.330 50.000 8.31 0.00 38.34 3.01
7664 12972 2.688507 TCCACTTGCGAGAAAGTCATC 58.311 47.619 8.31 0.00 38.34 2.92
7665 12973 1.734465 CCACTTGCGAGAAAGTCATCC 59.266 52.381 8.31 0.00 38.34 3.51
7666 12974 2.613977 CCACTTGCGAGAAAGTCATCCT 60.614 50.000 8.31 0.00 38.34 3.24
7669 12977 4.269603 CACTTGCGAGAAAGTCATCCTATG 59.730 45.833 8.31 0.00 38.34 2.23
7670 12978 4.160439 ACTTGCGAGAAAGTCATCCTATGA 59.840 41.667 8.31 0.00 35.44 2.15
7726 13034 3.617735 TGCACGGTCCTAACGGCA 61.618 61.111 0.00 0.00 35.99 5.69
7754 13062 3.282157 ATGCCGGCATGATCACGC 61.282 61.111 40.10 4.90 35.03 5.34
7756 13064 3.945434 GCCGGCATGATCACGCTG 61.945 66.667 24.80 15.61 0.00 5.18
7757 13065 2.202919 CCGGCATGATCACGCTGA 60.203 61.111 23.59 0.00 36.59 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.670485 TGCAAGTTTGAGAGAAGTAACTGA 58.330 37.500 0.00 0.00 31.64 3.41
31 32 0.669625 GGCGCCTCTTCAAACGTACT 60.670 55.000 22.15 0.00 0.00 2.73
32 33 1.785951 GGCGCCTCTTCAAACGTAC 59.214 57.895 22.15 0.00 0.00 3.67
37 45 2.736995 CGTCGGCGCCTCTTCAAA 60.737 61.111 26.68 0.00 0.00 2.69
51 59 3.633235 CACATGTATGAGCTACCTCGTC 58.367 50.000 0.00 0.00 41.13 4.20
103 111 7.704271 AGCATGAATTACATCAACAGATTCTG 58.296 34.615 12.17 12.17 37.07 3.02
137 146 0.952497 CATCAGACTGCACAACGGCT 60.952 55.000 0.00 0.00 34.04 5.52
202 211 1.132453 GTACAGCTGGGCCGATTTTTC 59.868 52.381 19.93 0.00 0.00 2.29
297 306 2.389962 TAATGGGTGTCTTGTACGGC 57.610 50.000 0.00 0.00 0.00 5.68
370 379 4.655921 GGCCATCCCATCGTTTGA 57.344 55.556 0.00 0.00 0.00 2.69
386 395 5.654650 GGTAGGTAGATCTGACTCATATGGG 59.345 48.000 5.18 0.00 0.00 4.00
413 422 1.071605 GTTGTCATCGTCTGGCAGAC 58.928 55.000 32.72 32.72 41.38 3.51
456 465 3.437795 CGCCTCAAGCCCTTGCAG 61.438 66.667 3.18 2.78 40.24 4.41
471 480 2.876368 AAGCTGGTAGATGGCCACGC 62.876 60.000 8.16 2.66 33.46 5.34
472 481 0.811616 GAAGCTGGTAGATGGCCACG 60.812 60.000 8.16 0.00 31.85 4.94
596 617 3.256960 TGTGGGGGAGGCCTCAAC 61.257 66.667 33.29 24.21 0.00 3.18
613 634 5.778750 GGTATACTGGTACTATGGTGATGGT 59.221 44.000 2.25 0.00 0.00 3.55
614 635 5.187186 GGGTATACTGGTACTATGGTGATGG 59.813 48.000 2.25 0.00 0.00 3.51
660 681 4.388499 GCCACGGCTCGGAAAGGA 62.388 66.667 0.00 0.00 38.26 3.36
735 756 2.560542 CGGGAATGAGTATGAGGAGGAG 59.439 54.545 0.00 0.00 0.00 3.69
742 763 1.412710 GACAGGCGGGAATGAGTATGA 59.587 52.381 0.00 0.00 0.00 2.15
743 764 1.414181 AGACAGGCGGGAATGAGTATG 59.586 52.381 0.00 0.00 0.00 2.39
744 765 1.689273 GAGACAGGCGGGAATGAGTAT 59.311 52.381 0.00 0.00 0.00 2.12
843 885 3.245668 AAGAGCAGGGTGCCTCGTG 62.246 63.158 0.00 0.00 46.52 4.35
846 888 2.045536 CCAAGAGCAGGGTGCCTC 60.046 66.667 0.00 0.00 46.52 4.70
954 1002 3.673599 GGAACCTCAGTTGCTGCC 58.326 61.111 0.00 0.00 40.87 4.85
1021 1075 1.694525 GAAGGAAGGGGGAGGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
1122 1180 3.119316 CCCTGGCACAATTACGCAATTTA 60.119 43.478 0.00 0.00 38.70 1.40
1200 1273 2.564947 ACAAAAGCACAACCCAACTCAA 59.435 40.909 0.00 0.00 0.00 3.02
1201 1274 2.165437 GACAAAAGCACAACCCAACTCA 59.835 45.455 0.00 0.00 0.00 3.41
1202 1275 2.427095 AGACAAAAGCACAACCCAACTC 59.573 45.455 0.00 0.00 0.00 3.01
1203 1276 2.456577 AGACAAAAGCACAACCCAACT 58.543 42.857 0.00 0.00 0.00 3.16
1204 1277 2.929398 CAAGACAAAAGCACAACCCAAC 59.071 45.455 0.00 0.00 0.00 3.77
1205 1278 2.093764 CCAAGACAAAAGCACAACCCAA 60.094 45.455 0.00 0.00 0.00 4.12
1206 1279 1.480137 CCAAGACAAAAGCACAACCCA 59.520 47.619 0.00 0.00 0.00 4.51
1207 1280 1.806247 GCCAAGACAAAAGCACAACCC 60.806 52.381 0.00 0.00 0.00 4.11
1208 1281 1.570813 GCCAAGACAAAAGCACAACC 58.429 50.000 0.00 0.00 0.00 3.77
1209 1282 1.199624 CGCCAAGACAAAAGCACAAC 58.800 50.000 0.00 0.00 0.00 3.32
1215 1288 3.502211 AGGATACAACGCCAAGACAAAAG 59.498 43.478 0.00 0.00 41.41 2.27
1232 1305 2.286045 TGGGGCACTGGCAGGATA 60.286 61.111 20.34 0.00 43.71 2.59
1297 1370 4.389576 CAGCAAAGCGACACGGGC 62.390 66.667 0.00 0.00 0.00 6.13
1390 1464 3.722295 CAACCAACGCGACCGCAT 61.722 61.111 15.93 0.00 42.06 4.73
1441 1515 1.475280 TCTAAATCACCAGGTCGACCG 59.525 52.381 28.26 21.63 42.08 4.79
1491 1566 4.466370 GGCACACATATAGTAGGGCAGATA 59.534 45.833 0.00 0.00 31.82 1.98
1531 1612 2.444624 CCTCGACATTGTCACGGCG 61.445 63.158 16.61 4.80 32.09 6.46
1556 1643 7.092079 TGAAGAAATTTATGTTGCCTGACATG 58.908 34.615 7.48 0.00 40.33 3.21
1676 1772 1.883275 TGCAACGGGAAATGGTGTAAG 59.117 47.619 0.00 0.00 0.00 2.34
1703 1799 6.287107 ACAAAATAGCCGAACATTCTATCG 57.713 37.500 0.00 0.00 38.74 2.92
1843 1947 0.530744 ACGGACTTGATAGCGCAAGA 59.469 50.000 11.47 0.00 46.31 3.02
1883 1987 7.719633 ACAAGAAGTAAAAGAAGACATAGCCAA 59.280 33.333 0.00 0.00 0.00 4.52
2092 2199 2.290641 AGATTCACAAAGACAACACGCC 59.709 45.455 0.00 0.00 0.00 5.68
2132 2239 4.096984 AGCACCTTTATATTCACAAGCTGC 59.903 41.667 0.00 0.00 31.77 5.25
2401 2565 9.956720 AGTTCAATAATCTAAATAATGTGCAGC 57.043 29.630 0.00 0.00 0.00 5.25
3002 3179 7.342284 GGAGGGAGTATTATATAGCTGCAGTTA 59.658 40.741 16.64 14.76 0.00 2.24
3003 3180 6.155393 GGAGGGAGTATTATATAGCTGCAGTT 59.845 42.308 16.64 12.62 0.00 3.16
3087 3264 4.335594 CCTCCGTCCCAAAATAAATGTCTC 59.664 45.833 0.00 0.00 0.00 3.36
3120 3297 5.309323 TGCAAAATTATACTCTGGTGCAC 57.691 39.130 8.80 8.80 35.93 4.57
3124 3301 7.944729 AGAACATGCAAAATTATACTCTGGT 57.055 32.000 0.00 0.00 0.00 4.00
3155 3332 0.958091 AAAAACGCAGGCAGCATACA 59.042 45.000 1.96 0.00 46.13 2.29
3278 3467 3.499737 GGGCTGCGATTCACACCG 61.500 66.667 0.00 0.00 0.00 4.94
3388 3577 0.613777 ACTTCCAACTGGACCCGATC 59.386 55.000 0.00 0.00 45.39 3.69
3682 3871 8.996024 GGTTTATGCACAACCTAATATGTTTT 57.004 30.769 18.60 0.00 40.66 2.43
3841 4030 3.935027 AAACGCGGAAACAAATTTTGG 57.065 38.095 12.47 0.00 34.12 3.28
4562 4761 4.397417 AGCCTGCTTATGATCACTGAAAAC 59.603 41.667 0.00 0.00 0.00 2.43
4571 4770 3.075866 GCAACAAGCCTGCTTATGATC 57.924 47.619 16.53 0.00 36.84 2.92
4709 6662 3.627395 AAGGAATGTGACATTCGCCTA 57.373 42.857 26.47 0.00 0.00 3.93
4710 6663 2.496899 AAGGAATGTGACATTCGCCT 57.503 45.000 26.47 19.15 0.00 5.52
4711 6664 3.270877 AGTAAGGAATGTGACATTCGCC 58.729 45.455 26.47 17.42 0.00 5.54
5095 7504 8.095169 GGATTGACGAATTGTAATATACCTCCT 58.905 37.037 0.00 0.00 0.00 3.69
5132 7541 4.460263 ACCACATGCACTTCTAACTTGAA 58.540 39.130 0.00 0.00 0.00 2.69
5176 7586 5.014202 AGCATGAGCATGGCATTATCATAA 58.986 37.500 18.79 0.00 45.49 1.90
5380 8056 0.663153 GTCAGTTGTGGACTTGTGGC 59.337 55.000 0.00 0.00 36.10 5.01
5505 8195 3.103742 GCCTTGCTAGCTCTATATCCCT 58.896 50.000 17.23 0.00 0.00 4.20
5554 8244 3.439857 AAAGAATTAGGAGTGCTGGCA 57.560 42.857 0.00 0.00 0.00 4.92
5830 8946 6.943718 CCCATAAAACCCAGTAACTCTGTAAA 59.056 38.462 0.00 0.00 42.19 2.01
5920 9323 3.801293 GCCTTGCAAGCAAATTGAAGAGT 60.801 43.478 21.43 0.00 41.83 3.24
6529 9961 3.623060 CAGGAATCCAGTCGTTACCATTG 59.377 47.826 0.61 0.00 0.00 2.82
6646 10078 2.584418 CCAGAGGCAGCATCGTCG 60.584 66.667 0.42 0.00 0.00 5.12
6649 10081 0.957395 AAACACCAGAGGCAGCATCG 60.957 55.000 0.42 0.00 0.00 3.84
6763 10195 6.751888 CAGGTATACCTTTAAAAGCATTGTGC 59.248 38.462 22.36 0.00 46.09 4.57
6776 10208 4.929146 AAACTCTGGCAGGTATACCTTT 57.071 40.909 22.36 9.20 46.09 3.11
6800 10232 9.490379 GTAGAATAACGGATTACATTCCAAGAT 57.510 33.333 0.00 0.00 35.34 2.40
7012 10449 7.334858 TGTTGATTGTGTGCATCCTAGTTATA 58.665 34.615 0.00 0.00 0.00 0.98
7045 10482 9.890629 AGACATAGCTTTGTGATTCTTTGTATA 57.109 29.630 14.90 0.00 0.00 1.47
7087 10530 6.822073 ACTGTTTTTATCGCTTTGGTTTTC 57.178 33.333 0.00 0.00 0.00 2.29
7114 11239 5.412594 GTGATGGTCACTGTTGTACAATCAT 59.587 40.000 12.26 0.00 43.73 2.45
7138 11275 1.134788 GTTGGATGACACGGTAGGAGG 60.135 57.143 0.00 0.00 0.00 4.30
7163 11300 7.587037 TTGGAGATGTCACTTTCAGAATTTT 57.413 32.000 0.00 0.00 0.00 1.82
7164 11301 7.587037 TTTGGAGATGTCACTTTCAGAATTT 57.413 32.000 0.00 0.00 0.00 1.82
7166 11303 6.208204 CCTTTTGGAGATGTCACTTTCAGAAT 59.792 38.462 0.00 0.00 44.07 2.40
7190 11995 1.133025 CGATGCTTGTTGTCATTCCCC 59.867 52.381 0.00 0.00 0.00 4.81
7295 12100 6.079763 CGTTCTTTGTGTCATTACCTTCATG 58.920 40.000 0.00 0.00 0.00 3.07
7300 12105 4.510340 GTGACGTTCTTTGTGTCATTACCT 59.490 41.667 0.00 0.00 43.75 3.08
7351 12659 5.681639 CTCCGGGTTGAGAATTATAGGTTT 58.318 41.667 0.00 0.00 34.11 3.27
7383 12691 2.996621 GGTGGTTCTTCTCGAATGTCTG 59.003 50.000 0.00 0.00 33.45 3.51
7384 12692 2.900546 AGGTGGTTCTTCTCGAATGTCT 59.099 45.455 0.00 0.00 33.45 3.41
7388 12696 5.677319 TCATTAGGTGGTTCTTCTCGAAT 57.323 39.130 0.00 0.00 33.45 3.34
7390 12698 5.011738 ACTTTCATTAGGTGGTTCTTCTCGA 59.988 40.000 0.00 0.00 0.00 4.04
7391 12699 5.238583 ACTTTCATTAGGTGGTTCTTCTCG 58.761 41.667 0.00 0.00 0.00 4.04
7393 12701 6.187727 TGACTTTCATTAGGTGGTTCTTCT 57.812 37.500 0.00 0.00 0.00 2.85
7395 12703 5.946377 GGATGACTTTCATTAGGTGGTTCTT 59.054 40.000 0.00 0.00 37.20 2.52
7396 12704 5.251700 AGGATGACTTTCATTAGGTGGTTCT 59.748 40.000 0.00 0.00 37.20 3.01
7398 12706 5.520748 AGGATGACTTTCATTAGGTGGTT 57.479 39.130 0.00 0.00 37.20 3.67
7399 12707 6.386927 TCATAGGATGACTTTCATTAGGTGGT 59.613 38.462 0.00 0.00 37.20 4.16
7400 12708 6.830912 TCATAGGATGACTTTCATTAGGTGG 58.169 40.000 0.00 0.00 37.20 4.61
7414 12722 2.357952 CCGACAAGACGTCATAGGATGA 59.642 50.000 19.50 0.00 45.70 2.92
7415 12723 2.357952 TCCGACAAGACGTCATAGGATG 59.642 50.000 19.50 8.84 45.70 3.51
7416 12724 2.651455 TCCGACAAGACGTCATAGGAT 58.349 47.619 19.50 0.00 45.70 3.24
7417 12725 2.118313 TCCGACAAGACGTCATAGGA 57.882 50.000 19.50 14.29 45.70 2.94
7418 12726 2.287668 GGATCCGACAAGACGTCATAGG 60.288 54.545 19.50 12.21 45.70 2.57
7422 12730 0.963225 TTGGATCCGACAAGACGTCA 59.037 50.000 19.50 0.00 45.70 4.35
7423 12731 1.347320 GTTGGATCCGACAAGACGTC 58.653 55.000 25.05 7.70 41.62 4.34
7425 12733 2.750815 GGTTGGATCCGACAAGACG 58.249 57.895 29.59 0.00 32.12 4.18
7434 12742 2.474410 ACTCTTTGACGGTTGGATCC 57.526 50.000 4.20 4.20 0.00 3.36
7435 12743 3.399330 TCAACTCTTTGACGGTTGGATC 58.601 45.455 0.00 0.00 40.20 3.36
7437 12745 2.992124 TCAACTCTTTGACGGTTGGA 57.008 45.000 0.00 0.00 40.20 3.53
7438 12746 2.484264 GGATCAACTCTTTGACGGTTGG 59.516 50.000 0.00 0.00 44.66 3.77
7439 12747 3.187227 CAGGATCAACTCTTTGACGGTTG 59.813 47.826 0.00 0.00 44.66 3.77
7441 12749 2.289694 CCAGGATCAACTCTTTGACGGT 60.290 50.000 0.00 0.00 44.66 4.83
7442 12750 2.350522 CCAGGATCAACTCTTTGACGG 58.649 52.381 0.00 0.00 44.66 4.79
7443 12751 2.350522 CCCAGGATCAACTCTTTGACG 58.649 52.381 0.00 0.00 44.66 4.35
7444 12752 2.040412 ACCCCAGGATCAACTCTTTGAC 59.960 50.000 0.00 0.00 44.66 3.18
7445 12753 2.348472 ACCCCAGGATCAACTCTTTGA 58.652 47.619 0.00 0.00 45.93 2.69
7446 12754 2.887151 ACCCCAGGATCAACTCTTTG 57.113 50.000 0.00 0.00 0.00 2.77
7447 12755 3.500471 GGAAACCCCAGGATCAACTCTTT 60.500 47.826 0.00 0.00 34.14 2.52
7448 12756 2.041755 GGAAACCCCAGGATCAACTCTT 59.958 50.000 0.00 0.00 34.14 2.85
7450 12758 2.130272 GGAAACCCCAGGATCAACTC 57.870 55.000 0.00 0.00 34.14 3.01
7475 12783 5.465935 TGAAGTTTGCTCGAACTTGTTTTT 58.534 33.333 17.34 0.00 46.73 1.94
7477 12785 4.695217 TGAAGTTTGCTCGAACTTGTTT 57.305 36.364 17.34 0.00 46.73 2.83
7478 12786 4.662145 CTTGAAGTTTGCTCGAACTTGTT 58.338 39.130 17.34 0.00 46.73 2.83
7479 12787 3.487544 GCTTGAAGTTTGCTCGAACTTGT 60.488 43.478 17.34 0.00 46.73 3.16
7480 12788 3.038710 GCTTGAAGTTTGCTCGAACTTG 58.961 45.455 17.34 6.97 46.73 3.16
7482 12790 2.288666 TGCTTGAAGTTTGCTCGAACT 58.711 42.857 0.00 0.00 41.44 3.01
7484 12792 3.631144 CATTGCTTGAAGTTTGCTCGAA 58.369 40.909 0.00 0.00 0.00 3.71
7486 12794 1.717645 GCATTGCTTGAAGTTTGCTCG 59.282 47.619 0.16 0.00 0.00 5.03
7487 12795 2.064014 GGCATTGCTTGAAGTTTGCTC 58.936 47.619 8.82 3.86 0.00 4.26
7490 12798 3.719924 TGAAGGCATTGCTTGAAGTTTG 58.280 40.909 8.82 0.00 0.00 2.93
7492 12800 3.575256 TCATGAAGGCATTGCTTGAAGTT 59.425 39.130 8.82 0.00 30.68 2.66
7493 12801 3.159472 TCATGAAGGCATTGCTTGAAGT 58.841 40.909 8.82 0.00 30.68 3.01
7495 12803 2.494471 CCTCATGAAGGCATTGCTTGAA 59.506 45.455 8.82 0.00 38.67 2.69
7496 12804 2.097036 CCTCATGAAGGCATTGCTTGA 58.903 47.619 8.82 4.10 38.67 3.02
7497 12805 1.136305 CCCTCATGAAGGCATTGCTTG 59.864 52.381 8.82 0.00 44.71 4.01
7499 12807 0.333993 ACCCTCATGAAGGCATTGCT 59.666 50.000 10.46 0.00 44.71 3.91
7500 12808 2.057137 TACCCTCATGAAGGCATTGC 57.943 50.000 10.46 0.00 44.71 3.56
7501 12809 4.037208 GTCATTACCCTCATGAAGGCATTG 59.963 45.833 10.46 4.87 44.71 2.82
7502 12810 4.210331 GTCATTACCCTCATGAAGGCATT 58.790 43.478 10.46 0.00 44.71 3.56
7503 12811 3.202818 TGTCATTACCCTCATGAAGGCAT 59.797 43.478 10.46 0.19 44.71 4.40
7504 12812 2.575735 TGTCATTACCCTCATGAAGGCA 59.424 45.455 10.46 0.00 44.71 4.75
7505 12813 3.281727 TGTCATTACCCTCATGAAGGC 57.718 47.619 10.46 0.00 44.71 4.35
7507 12815 5.063944 CGTTCTTGTCATTACCCTCATGAAG 59.936 44.000 0.00 0.00 32.37 3.02
7508 12816 4.935205 CGTTCTTGTCATTACCCTCATGAA 59.065 41.667 0.00 0.00 32.37 2.57
7509 12817 4.020573 ACGTTCTTGTCATTACCCTCATGA 60.021 41.667 0.00 0.00 0.00 3.07
7510 12818 4.253685 ACGTTCTTGTCATTACCCTCATG 58.746 43.478 0.00 0.00 0.00 3.07
7511 12819 4.020573 TGACGTTCTTGTCATTACCCTCAT 60.021 41.667 0.00 0.00 43.62 2.90
7512 12820 3.322541 TGACGTTCTTGTCATTACCCTCA 59.677 43.478 0.00 0.00 43.62 3.86
7513 12821 3.921677 TGACGTTCTTGTCATTACCCTC 58.078 45.455 0.00 0.00 43.62 4.30
7520 12828 7.847878 ACATGTATATGGTGACGTTCTTGTCAT 60.848 37.037 0.00 0.00 42.61 3.06
7521 12829 5.394224 TGTATATGGTGACGTTCTTGTCA 57.606 39.130 0.00 0.00 46.15 3.58
7524 12832 6.754675 TGTACATGTATATGGTGACGTTCTTG 59.245 38.462 9.18 0.00 38.66 3.02
7525 12833 6.869695 TGTACATGTATATGGTGACGTTCTT 58.130 36.000 9.18 0.00 38.66 2.52
7526 12834 6.459670 TGTACATGTATATGGTGACGTTCT 57.540 37.500 9.18 0.00 38.66 3.01
7527 12835 6.532302 TGTTGTACATGTATATGGTGACGTTC 59.468 38.462 9.18 0.00 38.66 3.95
7528 12836 6.399743 TGTTGTACATGTATATGGTGACGTT 58.600 36.000 9.18 0.00 38.66 3.99
7529 12837 5.968254 TGTTGTACATGTATATGGTGACGT 58.032 37.500 9.18 0.00 38.66 4.34
7530 12838 6.895607 TTGTTGTACATGTATATGGTGACG 57.104 37.500 9.18 0.00 38.66 4.35
7541 12849 8.349983 GGTTTGACTCTAATTTGTTGTACATGT 58.650 33.333 2.69 2.69 0.00 3.21
7542 12850 8.567948 AGGTTTGACTCTAATTTGTTGTACATG 58.432 33.333 0.00 0.00 0.00 3.21
7555 12863 9.886132 GGTTGAGAATTATAGGTTTGACTCTAA 57.114 33.333 0.00 0.00 0.00 2.10
7556 12864 8.483758 GGGTTGAGAATTATAGGTTTGACTCTA 58.516 37.037 0.00 0.00 0.00 2.43
7557 12865 7.037586 TGGGTTGAGAATTATAGGTTTGACTCT 60.038 37.037 0.00 0.00 0.00 3.24
7559 12867 7.027874 TGGGTTGAGAATTATAGGTTTGACT 57.972 36.000 0.00 0.00 0.00 3.41
7560 12868 7.110155 TCTGGGTTGAGAATTATAGGTTTGAC 58.890 38.462 0.00 0.00 0.00 3.18
7561 12869 7.265599 TCTGGGTTGAGAATTATAGGTTTGA 57.734 36.000 0.00 0.00 0.00 2.69
7562 12870 6.038714 GCTCTGGGTTGAGAATTATAGGTTTG 59.961 42.308 0.00 0.00 36.23 2.93
7563 12871 6.069381 AGCTCTGGGTTGAGAATTATAGGTTT 60.069 38.462 0.00 0.00 36.23 3.27
7564 12872 5.430089 AGCTCTGGGTTGAGAATTATAGGTT 59.570 40.000 0.00 0.00 36.23 3.50
7565 12873 4.971924 AGCTCTGGGTTGAGAATTATAGGT 59.028 41.667 0.00 0.00 36.23 3.08
7566 12874 5.070981 TCAGCTCTGGGTTGAGAATTATAGG 59.929 44.000 0.00 0.00 36.23 2.57
7567 12875 6.166984 TCAGCTCTGGGTTGAGAATTATAG 57.833 41.667 0.00 0.00 36.23 1.31
7568 12876 6.384015 TCTTCAGCTCTGGGTTGAGAATTATA 59.616 38.462 0.00 0.00 36.57 0.98
7569 12877 5.190528 TCTTCAGCTCTGGGTTGAGAATTAT 59.809 40.000 0.00 0.00 36.57 1.28
7570 12878 4.532126 TCTTCAGCTCTGGGTTGAGAATTA 59.468 41.667 0.00 0.00 36.57 1.40
7571 12879 3.328931 TCTTCAGCTCTGGGTTGAGAATT 59.671 43.478 0.00 0.00 36.57 2.17
7572 12880 2.909006 TCTTCAGCTCTGGGTTGAGAAT 59.091 45.455 0.00 0.00 36.57 2.40
7573 12881 2.329267 TCTTCAGCTCTGGGTTGAGAA 58.671 47.619 0.00 0.00 36.57 2.87
7574 12882 2.015456 TCTTCAGCTCTGGGTTGAGA 57.985 50.000 0.00 0.00 36.57 3.27
7576 12884 1.205655 CGATCTTCAGCTCTGGGTTGA 59.794 52.381 0.00 0.00 33.41 3.18
7577 12885 1.649664 CGATCTTCAGCTCTGGGTTG 58.350 55.000 0.00 0.00 0.00 3.77
7578 12886 0.539051 CCGATCTTCAGCTCTGGGTT 59.461 55.000 0.00 0.00 0.00 4.11
7579 12887 0.324738 TCCGATCTTCAGCTCTGGGT 60.325 55.000 0.00 0.00 0.00 4.51
7580 12888 0.103937 GTCCGATCTTCAGCTCTGGG 59.896 60.000 0.00 0.00 0.00 4.45
7581 12889 0.820226 TGTCCGATCTTCAGCTCTGG 59.180 55.000 0.00 0.00 0.00 3.86
7582 12890 2.886862 ATGTCCGATCTTCAGCTCTG 57.113 50.000 0.00 0.00 0.00 3.35
7583 12891 2.223688 CGAATGTCCGATCTTCAGCTCT 60.224 50.000 0.00 0.00 0.00 4.09
7584 12892 2.123342 CGAATGTCCGATCTTCAGCTC 58.877 52.381 0.00 0.00 0.00 4.09
7585 12893 1.751351 TCGAATGTCCGATCTTCAGCT 59.249 47.619 0.00 0.00 33.14 4.24
7586 12894 2.123342 CTCGAATGTCCGATCTTCAGC 58.877 52.381 0.00 0.00 37.96 4.26
7587 12895 3.699779 TCTCGAATGTCCGATCTTCAG 57.300 47.619 0.00 0.00 37.96 3.02
7588 12896 3.735208 GCTTCTCGAATGTCCGATCTTCA 60.735 47.826 0.00 0.00 37.96 3.02
7589 12897 2.792116 GCTTCTCGAATGTCCGATCTTC 59.208 50.000 0.00 0.00 37.96 2.87
7590 12898 2.166459 TGCTTCTCGAATGTCCGATCTT 59.834 45.455 0.00 0.00 37.96 2.40
7591 12899 1.751351 TGCTTCTCGAATGTCCGATCT 59.249 47.619 0.00 0.00 37.96 2.75
7592 12900 1.855360 GTGCTTCTCGAATGTCCGATC 59.145 52.381 0.00 0.00 37.96 3.69
7593 12901 1.471676 GGTGCTTCTCGAATGTCCGAT 60.472 52.381 0.00 0.00 37.96 4.18
7594 12902 0.108804 GGTGCTTCTCGAATGTCCGA 60.109 55.000 0.00 0.00 37.03 4.55
7598 12906 0.687354 AGGTGGTGCTTCTCGAATGT 59.313 50.000 0.00 0.00 0.00 2.71
7640 12948 2.670414 GACTTTCTCGCAAGTGGATGAG 59.330 50.000 0.00 0.00 37.11 2.90
7641 12949 2.037121 TGACTTTCTCGCAAGTGGATGA 59.963 45.455 0.00 0.00 37.11 2.92
7644 12952 2.612972 GGATGACTTTCTCGCAAGTGGA 60.613 50.000 0.00 0.00 37.11 4.02
7645 12953 1.734465 GGATGACTTTCTCGCAAGTGG 59.266 52.381 0.00 0.00 37.11 4.00
7646 12954 2.693069 AGGATGACTTTCTCGCAAGTG 58.307 47.619 0.00 0.00 37.11 3.16
7647 12955 4.160439 TCATAGGATGACTTTCTCGCAAGT 59.840 41.667 0.00 0.00 39.84 3.16
7649 12957 4.736126 TCATAGGATGACTTTCTCGCAA 57.264 40.909 0.00 0.00 33.59 4.85
7660 12968 3.570125 GTGGATGAGACGTCATAGGATGA 59.430 47.826 19.50 0.00 43.92 2.92
7661 12969 3.571828 AGTGGATGAGACGTCATAGGATG 59.428 47.826 19.50 0.00 43.92 3.51
7664 12972 3.711086 CAAGTGGATGAGACGTCATAGG 58.289 50.000 19.50 0.00 43.92 2.57
7665 12973 3.119291 GCAAGTGGATGAGACGTCATAG 58.881 50.000 19.50 0.00 43.92 2.23
7666 12974 2.479560 CGCAAGTGGATGAGACGTCATA 60.480 50.000 19.50 6.26 43.92 2.15
7669 12977 0.109272 TCGCAAGTGGATGAGACGTC 60.109 55.000 7.70 7.70 39.48 4.34
7670 12978 0.109086 CTCGCAAGTGGATGAGACGT 60.109 55.000 0.00 0.00 39.48 4.34
7671 12979 0.171231 TCTCGCAAGTGGATGAGACG 59.829 55.000 0.00 0.00 32.80 4.18
7672 12980 2.159184 TGATCTCGCAAGTGGATGAGAC 60.159 50.000 0.00 0.00 40.03 3.36


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

AutoCloner maintained by Alex Coulton.