Multiple sequence alignment - TraesCS3D01G380200

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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 TraesCS3D01G380200 chr3D 100.000 3678 0 0 1 3678 496743427 496739750 0.000000e+00 6793.0
1 TraesCS3D01G380200 chr3D 89.831 295 26 4 391 682 544444256 544443963 3.470000e-100 375.0
2 TraesCS3D01G380200 chr3D 89.456 294 22 9 391 678 536441804 536441514 2.700000e-96 363.0
3 TraesCS3D01G380200 chr3D 89.078 293 24 8 391 678 536440561 536440272 1.260000e-94 357.0
4 TraesCS3D01G380200 chr3D 85.460 337 39 9 3283 3614 19839843 19839512 3.520000e-90 342.0
5 TraesCS3D01G380200 chr3A 89.155 1918 115 35 1 1864 638064038 638065916 0.000000e+00 2303.0
6 TraesCS3D01G380200 chr3A 88.926 1210 84 23 2059 3222 638066158 638067363 0.000000e+00 1447.0
7 TraesCS3D01G380200 chr3A 84.681 235 31 4 1633 1864 506244368 506244136 2.860000e-56 230.0
8 TraesCS3D01G380200 chr3A 84.332 217 21 7 2390 2603 127276120 127275914 2.240000e-47 200.0
9 TraesCS3D01G380200 chr3B 94.421 1452 50 14 1867 3306 655855649 655854217 0.000000e+00 2204.0
10 TraesCS3D01G380200 chr3B 88.966 1432 88 22 257 1645 655857321 655855917 0.000000e+00 1705.0
11 TraesCS3D01G380200 chr3B 89.831 295 25 5 391 681 720265210 720264917 1.250000e-99 374.0
12 TraesCS3D01G380200 chr3B 84.322 236 32 4 1633 1865 47248497 47248264 3.700000e-55 226.0
13 TraesCS3D01G380200 chr3B 89.431 123 11 2 1 123 655857567 655857447 1.770000e-33 154.0
14 TraesCS3D01G380200 chr3B 92.308 78 1 3 3601 3678 655854128 655854056 5.020000e-19 106.0
15 TraesCS3D01G380200 chr1B 86.341 410 37 10 1868 2269 12934929 12935327 2.620000e-116 429.0
16 TraesCS3D01G380200 chr1B 87.417 302 33 4 3303 3603 457463550 457463847 3.520000e-90 342.0
17 TraesCS3D01G380200 chr7A 86.131 411 38 10 1867 2269 610202511 610202112 3.390000e-115 425.0
18 TraesCS3D01G380200 chr7B 86.098 410 38 10 1868 2269 426965654 426965256 1.220000e-114 424.0
19 TraesCS3D01G380200 chr7B 84.322 236 32 4 1633 1865 426965952 426965719 3.700000e-55 226.0
20 TraesCS3D01G380200 chr7B 93.023 86 5 1 2519 2603 713206397 713206482 1.390000e-24 124.0
21 TraesCS3D01G380200 chr6A 86.098 410 38 10 1868 2269 577738689 577739087 1.220000e-114 424.0
22 TraesCS3D01G380200 chr5B 86.098 410 38 10 1868 2269 326923291 326923689 1.220000e-114 424.0
23 TraesCS3D01G380200 chr5B 88.673 309 29 5 3302 3606 87982291 87981985 4.490000e-99 372.0
24 TraesCS3D01G380200 chr5A 86.098 410 38 11 1868 2269 119184367 119183969 1.220000e-114 424.0
25 TraesCS3D01G380200 chr5A 87.651 332 39 2 3284 3613 436260753 436260422 5.760000e-103 385.0
26 TraesCS3D01G380200 chr5A 84.016 244 34 4 1624 1864 119185707 119185466 2.860000e-56 230.0
27 TraesCS3D01G380200 chr2A 86.098 410 38 10 1868 2269 277172091 277171693 1.220000e-114 424.0
28 TraesCS3D01G380200 chr2A 85.460 337 43 5 3281 3611 663656591 663656255 2.720000e-91 346.0
29 TraesCS3D01G380200 chr2A 83.871 217 22 7 2390 2603 509994341 509994547 1.040000e-45 195.0
30 TraesCS3D01G380200 chr1A 88.923 325 34 2 3284 3607 368368674 368368351 2.060000e-107 399.0
31 TraesCS3D01G380200 chr1A 84.255 235 32 4 1633 1864 579993819 579993587 1.330000e-54 224.0
32 TraesCS3D01G380200 chr6B 89.251 307 30 3 3302 3606 446720928 446720623 7.450000e-102 381.0
33 TraesCS3D01G380200 chr6B 83.954 349 45 8 3284 3626 147682299 147682642 1.270000e-84 324.0
34 TraesCS3D01G380200 chr6B 84.322 236 32 4 1633 1865 600611960 600611727 3.700000e-55 226.0
35 TraesCS3D01G380200 chr7D 87.156 327 39 2 3286 3609 102965040 102964714 5.800000e-98 368.0
36 TraesCS3D01G380200 chr7D 85.714 217 23 6 2390 2603 406870511 406870722 4.780000e-54 222.0
37 TraesCS3D01G380200 chrUn 89.456 294 22 9 391 678 404926739 404927029 2.700000e-96 363.0
38 TraesCS3D01G380200 chrUn 89.456 294 22 9 391 678 466164471 466164181 2.700000e-96 363.0
39 TraesCS3D01G380200 chrUn 89.116 294 23 9 391 678 359852775 359852485 1.260000e-94 357.0
40 TraesCS3D01G380200 chrUn 83.607 244 35 4 1624 1864 459710633 459710874 1.330000e-54 224.0
41 TraesCS3D01G380200 chr2B 84.681 235 31 4 1633 1864 762200625 762200393 2.860000e-56 230.0
42 TraesCS3D01G380200 chr5D 85.714 217 23 6 2390 2603 433474469 433474680 4.780000e-54 222.0
43 TraesCS3D01G380200 chr4B 85.253 217 19 7 2390 2603 445023254 445023460 1.030000e-50 211.0
44 TraesCS3D01G380200 chr4B 92.188 64 5 0 2519 2582 654067139 654067202 1.410000e-14 91.6


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 TraesCS3D01G380200 chr3D 496739750 496743427 3677 True 6793.00 6793 100.0000 1 3678 1 chr3D.!!$R2 3677
1 TraesCS3D01G380200 chr3D 536440272 536441804 1532 True 360.00 363 89.2670 391 678 2 chr3D.!!$R4 287
2 TraesCS3D01G380200 chr3A 638064038 638067363 3325 False 1875.00 2303 89.0405 1 3222 2 chr3A.!!$F1 3221
3 TraesCS3D01G380200 chr3B 655854056 655857567 3511 True 1042.25 2204 91.2815 1 3678 4 chr3B.!!$R3 3677
4 TraesCS3D01G380200 chr7B 426965256 426965952 696 True 325.00 424 85.2100 1633 2269 2 chr7B.!!$R1 636
5 TraesCS3D01G380200 chr5A 119183969 119185707 1738 True 327.00 424 85.0570 1624 2269 2 chr5A.!!$R2 645

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
682 732 0.173255 CGCACCCCACCAAATCAATC 59.827 55.0 0.0 0.0 0.0 2.67 F
1610 2332 0.034337 TGCCGACGAAAGCCTAGTTT 59.966 50.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 3591 2.039084 AGGGCAAACAAACACCAAAACA 59.961 40.909 0.0 0.00 0.0 2.83 R
2865 4739 1.812571 AGATGAAACATGCCGGTTCAC 59.187 47.619 1.9 0.34 0.0 3.18 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
45 46 0.307760 CCGCACCACTTCAACTGTTC 59.692 55.000 0.00 0.00 0.00 3.18
47 48 2.479837 CGCACCACTTCAACTGTTCTA 58.520 47.619 0.00 0.00 0.00 2.10
52 53 6.273071 GCACCACTTCAACTGTTCTATTTTT 58.727 36.000 0.00 0.00 0.00 1.94
53 54 6.417930 GCACCACTTCAACTGTTCTATTTTTC 59.582 38.462 0.00 0.00 0.00 2.29
54 55 7.682021 GCACCACTTCAACTGTTCTATTTTTCT 60.682 37.037 0.00 0.00 0.00 2.52
55 56 7.645340 CACCACTTCAACTGTTCTATTTTTCTG 59.355 37.037 0.00 0.00 0.00 3.02
56 57 6.638468 CCACTTCAACTGTTCTATTTTTCTGC 59.362 38.462 0.00 0.00 0.00 4.26
97 98 4.656100 TTGAGGGACAGGAAATCATCAA 57.344 40.909 0.00 0.00 0.00 2.57
182 221 7.698506 AAAAGCCTATAAAGTTACTCCAACC 57.301 36.000 0.00 0.00 37.93 3.77
183 222 6.638021 AAGCCTATAAAGTTACTCCAACCT 57.362 37.500 0.00 0.00 37.93 3.50
184 223 5.990668 AGCCTATAAAGTTACTCCAACCTG 58.009 41.667 0.00 0.00 37.93 4.00
185 224 5.724854 AGCCTATAAAGTTACTCCAACCTGA 59.275 40.000 0.00 0.00 37.93 3.86
186 225 5.816258 GCCTATAAAGTTACTCCAACCTGAC 59.184 44.000 0.00 0.00 37.93 3.51
187 226 6.351966 GCCTATAAAGTTACTCCAACCTGACT 60.352 42.308 0.00 0.00 37.93 3.41
274 313 5.065474 CGAAACTCTAGACTAGAAGAGGTGG 59.935 48.000 13.18 2.89 38.85 4.61
278 317 1.142097 GACTAGAAGAGGTGGCCGC 59.858 63.158 8.12 8.12 0.00 6.53
280 319 1.192146 ACTAGAAGAGGTGGCCGCAA 61.192 55.000 19.98 0.00 0.00 4.85
281 320 0.741221 CTAGAAGAGGTGGCCGCAAC 60.741 60.000 19.98 11.18 0.00 4.17
282 321 1.192146 TAGAAGAGGTGGCCGCAACT 61.192 55.000 19.98 13.42 0.00 3.16
314 353 0.906282 AAAGGCCCAATTCAGCAGGG 60.906 55.000 0.00 0.00 45.68 4.45
379 427 2.835431 ACCATCCTCGCCTCTCGG 60.835 66.667 0.00 0.00 39.05 4.63
558 606 1.845791 TCTGATATGTGGGCCATGTGT 59.154 47.619 10.70 0.00 34.86 3.72
559 607 2.241941 TCTGATATGTGGGCCATGTGTT 59.758 45.455 10.70 0.00 34.86 3.32
677 727 4.612279 TGGCGCACCCCACCAAAT 62.612 61.111 10.83 0.00 33.59 2.32
678 728 3.758931 GGCGCACCCCACCAAATC 61.759 66.667 10.83 0.00 0.00 2.17
679 729 2.988684 GCGCACCCCACCAAATCA 60.989 61.111 0.30 0.00 0.00 2.57
681 731 1.887344 GCGCACCCCACCAAATCAAT 61.887 55.000 0.30 0.00 0.00 2.57
682 732 0.173255 CGCACCCCACCAAATCAATC 59.827 55.000 0.00 0.00 0.00 2.67
683 733 0.536724 GCACCCCACCAAATCAATCC 59.463 55.000 0.00 0.00 0.00 3.01
684 734 1.935799 CACCCCACCAAATCAATCCA 58.064 50.000 0.00 0.00 0.00 3.41
686 736 2.839425 CACCCCACCAAATCAATCCAAT 59.161 45.455 0.00 0.00 0.00 3.16
687 737 3.263937 CACCCCACCAAATCAATCCAATT 59.736 43.478 0.00 0.00 0.00 2.32
694 1056 7.712205 CCCACCAAATCAATCCAATTTATCTTC 59.288 37.037 0.00 0.00 0.00 2.87
696 1058 9.880157 CACCAAATCAATCCAATTTATCTTCTT 57.120 29.630 0.00 0.00 0.00 2.52
716 1078 9.921637 TCTTCTTTGAAAATTACACACAAACTT 57.078 25.926 0.00 0.00 0.00 2.66
729 1091 7.259290 ACACACAAACTTTTATCTAGTGGTG 57.741 36.000 0.00 0.00 37.56 4.17
744 1106 6.536731 CTAGTGGTGATTAAGCAGCATTAG 57.463 41.667 28.81 28.81 46.45 1.73
773 1157 4.799564 TGGGATTGAAGTTTGGCATTAC 57.200 40.909 0.00 0.00 0.00 1.89
824 1208 3.860641 CACAAATACCTGGGCCAAATTC 58.139 45.455 8.04 0.00 0.00 2.17
835 1219 3.118592 TGGGCCAAATTCGTTCAAAAACT 60.119 39.130 2.13 0.00 32.95 2.66
879 1263 6.995511 CCAAGATTTGGCATCAAAAATCAT 57.004 33.333 10.52 0.00 45.17 2.45
888 1274 4.992951 GGCATCAAAAATCATATTCTGGCC 59.007 41.667 0.00 0.00 0.00 5.36
896 1282 6.718593 AAATCATATTCTGGCCCCATAGTA 57.281 37.500 0.00 0.00 0.00 1.82
1269 1980 0.678048 GCCTCGAGGACAATGGCTTT 60.678 55.000 35.69 0.00 40.36 3.51
1307 2024 4.083862 GTGAGCCCCCTCCGTCAC 62.084 72.222 0.00 0.00 37.29 3.67
1341 2058 3.056749 CACCGGACTCTAGCTTTTAGTGT 60.057 47.826 9.46 0.00 0.00 3.55
1357 2074 1.004320 TGTGCGGTGCGATTTAGGT 60.004 52.632 0.00 0.00 0.00 3.08
1358 2075 1.017177 TGTGCGGTGCGATTTAGGTC 61.017 55.000 0.00 0.00 0.00 3.85
1423 2140 4.846168 TTGGTGGTAGTGGTATATGCAA 57.154 40.909 0.00 0.00 0.00 4.08
1517 2236 3.753272 TGCATCTAAGGTCAACTCAAAGC 59.247 43.478 0.00 0.00 0.00 3.51
1573 2295 5.229423 TGCAGTTGGTGATTTTTCAATAGC 58.771 37.500 0.00 0.00 0.00 2.97
1610 2332 0.034337 TGCCGACGAAAGCCTAGTTT 59.966 50.000 0.00 0.00 0.00 2.66
1611 2333 0.720027 GCCGACGAAAGCCTAGTTTC 59.280 55.000 0.00 0.00 33.74 2.78
1732 2454 3.504906 TCTCTTGCAGCAGAAATTCAAGG 59.495 43.478 0.00 0.00 35.94 3.61
1751 2475 5.414454 TCAAGGGAACTGTTATGCATAACAC 59.586 40.000 36.85 28.81 45.41 3.32
1834 3591 8.511321 TCAGATAAATAAACTGAACGTTGCATT 58.489 29.630 5.00 0.00 37.66 3.56
1835 3592 8.577939 CAGATAAATAAACTGAACGTTGCATTG 58.422 33.333 5.00 0.00 35.61 2.82
1865 3622 2.978156 TGTTTGCCCTCCTGAGAATT 57.022 45.000 0.00 0.00 0.00 2.17
1879 3717 7.094890 CCTCCTGAGAATTATGAACATACATGC 60.095 40.741 0.00 0.00 0.00 4.06
1880 3718 7.512130 TCCTGAGAATTATGAACATACATGCT 58.488 34.615 0.00 0.00 0.00 3.79
1881 3719 7.443272 TCCTGAGAATTATGAACATACATGCTG 59.557 37.037 0.00 0.00 0.00 4.41
1882 3720 7.228108 CCTGAGAATTATGAACATACATGCTGT 59.772 37.037 0.00 0.00 0.00 4.40
1883 3721 9.264719 CTGAGAATTATGAACATACATGCTGTA 57.735 33.333 2.24 0.00 37.24 2.74
1884 3722 9.783081 TGAGAATTATGAACATACATGCTGTAT 57.217 29.630 2.24 3.78 43.81 2.29
1925 3770 2.902705 TGTGTACTTGTGACCTCACC 57.097 50.000 2.98 0.00 45.88 4.02
1991 3836 3.125316 CACACGCTCCAGGTAAATTTCTC 59.875 47.826 0.00 0.00 0.00 2.87
1996 3845 3.619038 GCTCCAGGTAAATTTCTCGACAG 59.381 47.826 0.00 0.00 0.00 3.51
2193 4042 0.322906 CCCTTCTTTGCCTGGGAGTC 60.323 60.000 0.00 0.00 42.11 3.36
2229 4085 2.081462 GGATCTTGGTTTGGGTGTACG 58.919 52.381 0.00 0.00 0.00 3.67
2249 4105 3.756963 ACGCTGATCTTGTGTACTCAGTA 59.243 43.478 8.75 0.00 37.90 2.74
2294 4150 3.071892 TGATCATGGACTATGCATGCTGA 59.928 43.478 20.33 11.73 44.48 4.26
2365 4223 4.061596 GCCTAGCTATCACTCAATGTTCC 58.938 47.826 0.00 0.00 0.00 3.62
2466 4325 6.257411 CAGATTCTGGTGATAAACTGCTGTAG 59.743 42.308 5.73 0.00 0.00 2.74
2865 4739 5.303165 TGCTCTGAATGGTATGCTTATGAG 58.697 41.667 0.00 0.00 0.00 2.90
2872 4746 3.792401 TGGTATGCTTATGAGTGAACCG 58.208 45.455 0.00 0.00 0.00 4.44
2930 4805 6.765915 ATTTTCAGGGAAGCTTGATTCTAC 57.234 37.500 2.10 0.00 0.00 2.59
3015 4890 5.451908 GGGATACATTATGCATGTTGTTCG 58.548 41.667 17.97 0.45 44.40 3.95
3143 5036 3.714798 AGGACTGGTGACTTGTTTCCTTA 59.285 43.478 0.00 0.00 0.00 2.69
3207 5105 1.517832 GCCATGCCGTCTGACTAGT 59.482 57.895 6.21 0.00 0.00 2.57
3209 5107 0.817654 CCATGCCGTCTGACTAGTGA 59.182 55.000 0.00 0.00 0.00 3.41
3291 5189 5.128827 CAGGTTGCTAAGAATGTACTCCCTA 59.871 44.000 0.00 0.00 0.00 3.53
3292 5190 5.724854 AGGTTGCTAAGAATGTACTCCCTAA 59.275 40.000 0.00 0.00 0.00 2.69
3295 5193 6.869206 TGCTAAGAATGTACTCCCTAAGTT 57.131 37.500 0.00 0.00 39.55 2.66
3297 5195 6.127140 TGCTAAGAATGTACTCCCTAAGTTCC 60.127 42.308 0.00 0.00 39.55 3.62
3298 5196 6.098552 GCTAAGAATGTACTCCCTAAGTTCCT 59.901 42.308 0.00 0.00 39.55 3.36
3306 5204 8.530804 TGTACTCCCTAAGTTCCTAAATACTC 57.469 38.462 0.00 0.00 39.55 2.59
3307 5205 7.562821 TGTACTCCCTAAGTTCCTAAATACTCC 59.437 40.741 0.00 0.00 39.55 3.85
3308 5206 5.904169 ACTCCCTAAGTTCCTAAATACTCCC 59.096 44.000 0.00 0.00 33.03 4.30
3309 5207 6.114151 TCCCTAAGTTCCTAAATACTCCCT 57.886 41.667 0.00 0.00 0.00 4.20
3311 5209 5.307456 CCCTAAGTTCCTAAATACTCCCTCC 59.693 48.000 0.00 0.00 0.00 4.30
3312 5210 5.010820 CCTAAGTTCCTAAATACTCCCTCCG 59.989 48.000 0.00 0.00 0.00 4.63
3313 5211 3.991683 AGTTCCTAAATACTCCCTCCGT 58.008 45.455 0.00 0.00 0.00 4.69
3314 5212 4.359996 AGTTCCTAAATACTCCCTCCGTT 58.640 43.478 0.00 0.00 0.00 4.44
3315 5213 4.405036 AGTTCCTAAATACTCCCTCCGTTC 59.595 45.833 0.00 0.00 0.00 3.95
3316 5214 3.303049 TCCTAAATACTCCCTCCGTTCC 58.697 50.000 0.00 0.00 0.00 3.62
3317 5215 2.367894 CCTAAATACTCCCTCCGTTCCC 59.632 54.545 0.00 0.00 0.00 3.97
3318 5216 1.961133 AAATACTCCCTCCGTTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
3320 5218 1.961133 ATACTCCCTCCGTTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3321 5219 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
3322 5220 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3323 5221 2.488836 ACTCCCTCCGTTCCCAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3324 5222 2.850568 ACTCCCTCCGTTCCCAAATATT 59.149 45.455 0.00 0.00 0.00 1.28
3325 5223 3.268595 ACTCCCTCCGTTCCCAAATATTT 59.731 43.478 0.00 0.00 0.00 1.40
3326 5224 3.626930 TCCCTCCGTTCCCAAATATTTG 58.373 45.455 19.40 19.40 37.90 2.32
3327 5225 3.010808 TCCCTCCGTTCCCAAATATTTGT 59.989 43.478 23.24 0.00 36.45 2.83
3328 5226 3.380320 CCCTCCGTTCCCAAATATTTGTC 59.620 47.826 23.24 11.68 36.45 3.18
3329 5227 4.270008 CCTCCGTTCCCAAATATTTGTCT 58.730 43.478 23.24 0.00 36.45 3.41
3330 5228 4.705023 CCTCCGTTCCCAAATATTTGTCTT 59.295 41.667 23.24 0.00 36.45 3.01
3331 5229 5.185056 CCTCCGTTCCCAAATATTTGTCTTT 59.815 40.000 23.24 0.00 36.45 2.52
3332 5230 6.262193 TCCGTTCCCAAATATTTGTCTTTC 57.738 37.500 23.24 10.84 36.45 2.62
3333 5231 6.007703 TCCGTTCCCAAATATTTGTCTTTCT 58.992 36.000 23.24 0.00 36.45 2.52
3334 5232 7.169591 TCCGTTCCCAAATATTTGTCTTTCTA 58.830 34.615 23.24 5.03 36.45 2.10
3335 5233 7.335924 TCCGTTCCCAAATATTTGTCTTTCTAG 59.664 37.037 23.24 8.23 36.45 2.43
3336 5234 7.335924 CCGTTCCCAAATATTTGTCTTTCTAGA 59.664 37.037 23.24 7.17 36.45 2.43
3353 5251 9.567776 TCTTTCTAGACATTTCAAATGGTTACA 57.432 29.630 14.70 0.00 0.00 2.41
3355 5253 9.959749 TTTCTAGACATTTCAAATGGTTACAAC 57.040 29.630 14.70 0.00 0.00 3.32
3356 5254 8.684386 TCTAGACATTTCAAATGGTTACAACA 57.316 30.769 14.70 0.00 0.00 3.33
3357 5255 9.295825 TCTAGACATTTCAAATGGTTACAACAT 57.704 29.630 14.70 0.00 0.00 2.71
3360 5258 8.020819 AGACATTTCAAATGGTTACAACATACG 58.979 33.333 14.70 0.00 0.00 3.06
3361 5259 7.087639 ACATTTCAAATGGTTACAACATACGG 58.912 34.615 14.70 0.00 0.00 4.02
3373 5271 8.758715 GGTTACAACATACGGATGTATTTAGAC 58.241 37.037 15.10 8.31 45.93 2.59
3374 5272 9.304731 GTTACAACATACGGATGTATTTAGACA 57.695 33.333 15.10 0.00 45.93 3.41
3407 5305 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
3408 5306 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
3410 5308 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
3411 5309 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
3412 5310 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
3413 5311 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
3414 5312 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
3416 5314 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
3419 5317 6.818644 ACTCATTTTGCTTCGTATGTAGTCAT 59.181 34.615 0.00 0.00 38.00 3.06
3420 5318 7.334421 ACTCATTTTGCTTCGTATGTAGTCATT 59.666 33.333 0.00 0.00 35.70 2.57
3421 5319 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
3422 5320 9.157104 TCATTTTGCTTCGTATGTAGTCATTTA 57.843 29.630 0.00 0.00 35.70 1.40
3423 5321 9.935682 CATTTTGCTTCGTATGTAGTCATTTAT 57.064 29.630 0.00 0.00 35.70 1.40
3425 5323 9.767684 TTTTGCTTCGTATGTAGTCATTTATTG 57.232 29.630 0.00 0.00 35.70 1.90
3426 5324 8.710835 TTGCTTCGTATGTAGTCATTTATTGA 57.289 30.769 0.00 0.00 35.70 2.57
3427 5325 8.710835 TGCTTCGTATGTAGTCATTTATTGAA 57.289 30.769 0.00 0.00 35.70 2.69
3428 5326 9.157104 TGCTTCGTATGTAGTCATTTATTGAAA 57.843 29.630 0.00 0.00 35.70 2.69
3457 5355 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
3458 5356 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
3459 5357 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
3460 5358 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
3461 5359 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3462 5360 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3463 5361 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3464 5362 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
3465 5363 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
3466 5364 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
3467 5365 8.591072 CAAATATTTAGGAACGGAGGGAGTATA 58.409 37.037 0.00 0.00 0.00 1.47
3468 5366 8.731591 AATATTTAGGAACGGAGGGAGTATAA 57.268 34.615 0.00 0.00 0.00 0.98
3469 5367 6.667558 ATTTAGGAACGGAGGGAGTATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3470 5368 3.684408 AGGAACGGAGGGAGTATAAGT 57.316 47.619 0.00 0.00 0.00 2.24
3471 5369 3.564264 AGGAACGGAGGGAGTATAAGTC 58.436 50.000 0.00 0.00 0.00 3.01
3472 5370 3.204831 AGGAACGGAGGGAGTATAAGTCT 59.795 47.826 0.00 0.00 0.00 3.24
3473 5371 3.959449 GGAACGGAGGGAGTATAAGTCTT 59.041 47.826 0.00 0.00 0.00 3.01
3474 5372 4.405036 GGAACGGAGGGAGTATAAGTCTTT 59.595 45.833 0.00 0.00 0.00 2.52
3475 5373 5.340439 AACGGAGGGAGTATAAGTCTTTG 57.660 43.478 0.00 0.00 0.00 2.77
3476 5374 4.351127 ACGGAGGGAGTATAAGTCTTTGT 58.649 43.478 0.00 0.00 0.00 2.83
3477 5375 5.513233 ACGGAGGGAGTATAAGTCTTTGTA 58.487 41.667 0.00 0.00 0.00 2.41
3478 5376 5.593502 ACGGAGGGAGTATAAGTCTTTGTAG 59.406 44.000 0.00 0.00 0.00 2.74
3479 5377 5.826737 CGGAGGGAGTATAAGTCTTTGTAGA 59.173 44.000 0.00 0.00 0.00 2.59
3480 5378 6.016943 CGGAGGGAGTATAAGTCTTTGTAGAG 60.017 46.154 0.00 0.00 0.00 2.43
3481 5379 6.265876 GGAGGGAGTATAAGTCTTTGTAGAGG 59.734 46.154 0.00 0.00 0.00 3.69
3482 5380 6.743788 AGGGAGTATAAGTCTTTGTAGAGGT 58.256 40.000 0.00 0.00 0.00 3.85
3483 5381 7.190501 AGGGAGTATAAGTCTTTGTAGAGGTT 58.809 38.462 0.00 0.00 0.00 3.50
3484 5382 7.679025 AGGGAGTATAAGTCTTTGTAGAGGTTT 59.321 37.037 0.00 0.00 0.00 3.27
3485 5383 7.980662 GGGAGTATAAGTCTTTGTAGAGGTTTC 59.019 40.741 0.00 0.00 0.00 2.78
3486 5384 8.529476 GGAGTATAAGTCTTTGTAGAGGTTTCA 58.471 37.037 0.00 0.00 0.00 2.69
3487 5385 9.356433 GAGTATAAGTCTTTGTAGAGGTTTCAC 57.644 37.037 0.00 0.00 0.00 3.18
3488 5386 9.091220 AGTATAAGTCTTTGTAGAGGTTTCACT 57.909 33.333 0.00 0.00 0.00 3.41
3491 5389 9.877178 ATAAGTCTTTGTAGAGGTTTCACTATG 57.123 33.333 0.00 0.00 0.00 2.23
3492 5390 6.702329 AGTCTTTGTAGAGGTTTCACTATGG 58.298 40.000 0.00 0.00 0.00 2.74
3493 5391 6.497259 AGTCTTTGTAGAGGTTTCACTATGGA 59.503 38.462 0.00 0.00 0.00 3.41
3494 5392 6.590677 GTCTTTGTAGAGGTTTCACTATGGAC 59.409 42.308 0.00 0.00 0.00 4.02
3495 5393 6.497259 TCTTTGTAGAGGTTTCACTATGGACT 59.503 38.462 0.00 0.00 0.00 3.85
3496 5394 7.672660 TCTTTGTAGAGGTTTCACTATGGACTA 59.327 37.037 0.00 0.00 0.00 2.59
3497 5395 6.770746 TGTAGAGGTTTCACTATGGACTAC 57.229 41.667 0.00 0.00 0.00 2.73
3498 5396 6.250711 TGTAGAGGTTTCACTATGGACTACA 58.749 40.000 0.00 0.00 36.46 2.74
3499 5397 6.895756 TGTAGAGGTTTCACTATGGACTACAT 59.104 38.462 0.00 0.00 43.68 2.29
3500 5398 8.057011 TGTAGAGGTTTCACTATGGACTACATA 58.943 37.037 0.00 0.00 41.03 2.29
3501 5399 9.080097 GTAGAGGTTTCACTATGGACTACATAT 57.920 37.037 0.00 0.00 41.07 1.78
3502 5400 7.957002 AGAGGTTTCACTATGGACTACATATG 58.043 38.462 0.00 0.00 41.07 1.78
3503 5401 7.785028 AGAGGTTTCACTATGGACTACATATGA 59.215 37.037 10.38 0.00 41.07 2.15
3504 5402 8.319057 AGGTTTCACTATGGACTACATATGAA 57.681 34.615 10.38 0.00 41.07 2.57
3505 5403 8.424918 AGGTTTCACTATGGACTACATATGAAG 58.575 37.037 10.38 0.00 41.07 3.02
3506 5404 7.171678 GGTTTCACTATGGACTACATATGAAGC 59.828 40.741 10.38 1.05 41.07 3.86
3507 5405 6.976934 TCACTATGGACTACATATGAAGCA 57.023 37.500 10.38 0.00 41.07 3.91
3508 5406 7.360113 TCACTATGGACTACATATGAAGCAA 57.640 36.000 10.38 0.00 41.07 3.91
3509 5407 7.791029 TCACTATGGACTACATATGAAGCAAA 58.209 34.615 10.38 0.00 41.07 3.68
3510 5408 8.264347 TCACTATGGACTACATATGAAGCAAAA 58.736 33.333 10.38 0.00 41.07 2.44
3511 5409 9.060347 CACTATGGACTACATATGAAGCAAAAT 57.940 33.333 10.38 0.00 41.07 1.82
3512 5410 9.060347 ACTATGGACTACATATGAAGCAAAATG 57.940 33.333 10.38 0.00 41.07 2.32
3513 5411 9.276590 CTATGGACTACATATGAAGCAAAATGA 57.723 33.333 10.38 0.00 41.07 2.57
3514 5412 7.558161 TGGACTACATATGAAGCAAAATGAG 57.442 36.000 10.38 0.00 0.00 2.90
3515 5413 7.112122 TGGACTACATATGAAGCAAAATGAGT 58.888 34.615 10.38 0.00 0.00 3.41
3516 5414 7.066163 TGGACTACATATGAAGCAAAATGAGTG 59.934 37.037 10.38 0.00 0.00 3.51
3517 5415 7.280876 GGACTACATATGAAGCAAAATGAGTGA 59.719 37.037 10.38 0.00 0.00 3.41
3518 5416 8.565896 ACTACATATGAAGCAAAATGAGTGAA 57.434 30.769 10.38 0.00 0.00 3.18
3519 5417 9.182214 ACTACATATGAAGCAAAATGAGTGAAT 57.818 29.630 10.38 0.00 0.00 2.57
3520 5418 9.661187 CTACATATGAAGCAAAATGAGTGAATC 57.339 33.333 10.38 0.00 0.00 2.52
3521 5419 8.058667 ACATATGAAGCAAAATGAGTGAATCA 57.941 30.769 10.38 0.00 43.70 2.57
3522 5420 7.972277 ACATATGAAGCAAAATGAGTGAATCAC 59.028 33.333 10.38 5.02 41.91 3.06
3523 5421 5.771153 TGAAGCAAAATGAGTGAATCACA 57.229 34.783 16.38 0.00 41.91 3.58
3538 5436 7.081526 GTGAATCACACTCTAAAATGCATCT 57.918 36.000 8.74 0.00 45.13 2.90
3539 5437 8.201554 GTGAATCACACTCTAAAATGCATCTA 57.798 34.615 8.74 0.00 45.13 1.98
3540 5438 8.834465 GTGAATCACACTCTAAAATGCATCTAT 58.166 33.333 8.74 0.00 45.13 1.98
3557 5455 5.664457 CATCTATATGCATCCGTATGTGGT 58.336 41.667 0.19 0.00 35.38 4.16
3558 5456 5.324784 TCTATATGCATCCGTATGTGGTC 57.675 43.478 0.19 0.00 35.38 4.02
3559 5457 5.016831 TCTATATGCATCCGTATGTGGTCT 58.983 41.667 0.19 0.00 35.38 3.85
3560 5458 6.184789 TCTATATGCATCCGTATGTGGTCTA 58.815 40.000 0.19 0.00 35.38 2.59
3561 5459 5.939764 ATATGCATCCGTATGTGGTCTAT 57.060 39.130 0.19 0.00 35.38 1.98
3562 5460 7.996644 TCTATATGCATCCGTATGTGGTCTATA 59.003 37.037 0.19 0.00 35.38 1.31
3563 5461 4.783764 TGCATCCGTATGTGGTCTATAG 57.216 45.455 0.00 0.00 35.38 1.31
3564 5462 4.149598 TGCATCCGTATGTGGTCTATAGT 58.850 43.478 0.00 0.00 35.38 2.12
3565 5463 4.022329 TGCATCCGTATGTGGTCTATAGTG 60.022 45.833 0.00 0.00 35.38 2.74
3566 5464 4.618460 GCATCCGTATGTGGTCTATAGTGG 60.618 50.000 0.00 0.00 35.38 4.00
3567 5465 4.442401 TCCGTATGTGGTCTATAGTGGA 57.558 45.455 0.00 0.00 0.00 4.02
3568 5466 4.795469 TCCGTATGTGGTCTATAGTGGAA 58.205 43.478 0.00 0.00 0.00 3.53
3569 5467 5.391256 TCCGTATGTGGTCTATAGTGGAAT 58.609 41.667 0.00 0.00 0.00 3.01
3570 5468 5.475909 TCCGTATGTGGTCTATAGTGGAATC 59.524 44.000 0.00 0.00 0.00 2.52
3571 5469 5.477291 CCGTATGTGGTCTATAGTGGAATCT 59.523 44.000 0.00 0.00 0.00 2.40
3572 5470 6.349445 CCGTATGTGGTCTATAGTGGAATCTC 60.349 46.154 0.00 0.00 0.00 2.75
3573 5471 6.431543 CGTATGTGGTCTATAGTGGAATCTCT 59.568 42.308 0.00 0.00 0.00 3.10
3574 5472 7.606839 CGTATGTGGTCTATAGTGGAATCTCTA 59.393 40.741 0.00 0.00 0.00 2.43
3575 5473 7.768807 ATGTGGTCTATAGTGGAATCTCTAC 57.231 40.000 0.00 0.00 0.00 2.59
3576 5474 6.669631 TGTGGTCTATAGTGGAATCTCTACA 58.330 40.000 0.00 0.00 29.47 2.74
3577 5475 7.123383 TGTGGTCTATAGTGGAATCTCTACAA 58.877 38.462 0.00 0.00 29.47 2.41
3578 5476 7.618117 TGTGGTCTATAGTGGAATCTCTACAAA 59.382 37.037 0.00 0.00 29.47 2.83
3579 5477 8.138712 GTGGTCTATAGTGGAATCTCTACAAAG 58.861 40.741 0.00 0.00 29.47 2.77
3580 5478 8.059461 TGGTCTATAGTGGAATCTCTACAAAGA 58.941 37.037 0.00 0.00 29.47 2.52
3581 5479 8.354426 GGTCTATAGTGGAATCTCTACAAAGAC 58.646 40.741 0.00 9.23 32.70 3.01
3582 5480 9.127277 GTCTATAGTGGAATCTCTACAAAGACT 57.873 37.037 0.00 0.00 31.92 3.24
3583 5481 9.702253 TCTATAGTGGAATCTCTACAAAGACTT 57.298 33.333 0.00 0.00 29.47 3.01
3619 5517 9.988815 AACAGATGGAGTAGTTATTATAAGCTG 57.011 33.333 0.00 0.00 0.00 4.24
3658 5556 7.066284 GTCATAGAACTGTAGAATTTGGCATGT 59.934 37.037 0.00 0.00 0.00 3.21
3659 5557 8.264347 TCATAGAACTGTAGAATTTGGCATGTA 58.736 33.333 0.00 0.00 0.00 2.29
3660 5558 6.743575 AGAACTGTAGAATTTGGCATGTAC 57.256 37.500 0.00 0.00 0.00 2.90
3661 5559 6.476378 AGAACTGTAGAATTTGGCATGTACT 58.524 36.000 0.00 0.00 0.00 2.73
3662 5560 6.372659 AGAACTGTAGAATTTGGCATGTACTG 59.627 38.462 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.909357 GTGATGATTTCCTCGCAGAAAAATAG 59.091 38.462 4.17 0.00 39.11 1.73
47 48 5.416952 AGTGATGATTTCCTCGCAGAAAAAT 59.583 36.000 4.17 2.39 39.11 1.82
52 53 3.616956 AAGTGATGATTTCCTCGCAGA 57.383 42.857 0.42 0.00 0.00 4.26
53 54 4.691860 AAAAGTGATGATTTCCTCGCAG 57.308 40.909 0.42 0.00 0.00 5.18
177 216 2.669569 CGGTGGCAGTCAGGTTGG 60.670 66.667 0.00 0.00 0.00 3.77
178 217 2.669569 CCGGTGGCAGTCAGGTTG 60.670 66.667 0.00 0.00 0.00 3.77
179 218 3.953775 CCCGGTGGCAGTCAGGTT 61.954 66.667 0.00 0.00 0.00 3.50
274 313 2.033194 GGACACCAGTAGTTGCGGC 61.033 63.158 0.00 0.00 0.00 6.53
314 353 0.108019 CCTCCGGGTTAGGCCAATAC 59.892 60.000 5.01 0.00 39.65 1.89
379 427 1.868251 CGAGTCGCGTAGAACCAGC 60.868 63.158 5.77 0.00 34.64 4.85
471 519 2.280628 GCCGAGAAAGGTATGAGTTGG 58.719 52.381 0.00 0.00 0.00 3.77
703 1065 8.832521 CACCACTAGATAAAAGTTTGTGTGTAA 58.167 33.333 0.00 0.00 0.00 2.41
704 1066 8.205512 TCACCACTAGATAAAAGTTTGTGTGTA 58.794 33.333 0.00 0.00 32.70 2.90
706 1068 7.490962 TCACCACTAGATAAAAGTTTGTGTG 57.509 36.000 0.00 0.00 32.70 3.82
707 1069 8.691661 AATCACCACTAGATAAAAGTTTGTGT 57.308 30.769 0.00 0.00 32.70 3.72
710 1072 9.774742 GCTTAATCACCACTAGATAAAAGTTTG 57.225 33.333 0.00 0.00 0.00 2.93
712 1074 9.167311 CTGCTTAATCACCACTAGATAAAAGTT 57.833 33.333 0.00 0.00 0.00 2.66
713 1075 7.281100 GCTGCTTAATCACCACTAGATAAAAGT 59.719 37.037 0.00 0.00 0.00 2.66
715 1077 7.109501 TGCTGCTTAATCACCACTAGATAAAA 58.890 34.615 0.00 0.00 0.00 1.52
716 1078 6.649155 TGCTGCTTAATCACCACTAGATAAA 58.351 36.000 0.00 0.00 0.00 1.40
717 1079 6.233905 TGCTGCTTAATCACCACTAGATAA 57.766 37.500 0.00 0.00 0.00 1.75
718 1080 5.869649 TGCTGCTTAATCACCACTAGATA 57.130 39.130 0.00 0.00 0.00 1.98
719 1081 4.760530 TGCTGCTTAATCACCACTAGAT 57.239 40.909 0.00 0.00 0.00 1.98
720 1082 4.760530 ATGCTGCTTAATCACCACTAGA 57.239 40.909 0.00 0.00 0.00 2.43
721 1083 5.468072 CCTAATGCTGCTTAATCACCACTAG 59.532 44.000 0.00 0.00 0.00 2.57
727 1089 7.912056 TGATATCCTAATGCTGCTTAATCAC 57.088 36.000 0.00 0.00 0.00 3.06
729 1091 7.013083 CCCATGATATCCTAATGCTGCTTAATC 59.987 40.741 0.00 0.00 0.00 1.75
744 1106 5.279156 GCCAAACTTCAATCCCATGATATCC 60.279 44.000 0.00 0.00 0.00 2.59
866 1250 4.992951 GGGCCAGAATATGATTTTTGATGC 59.007 41.667 4.39 0.00 0.00 3.91
875 1259 5.426833 GTCTACTATGGGGCCAGAATATGAT 59.573 44.000 4.39 0.00 0.00 2.45
876 1260 4.777896 GTCTACTATGGGGCCAGAATATGA 59.222 45.833 4.39 0.00 0.00 2.15
877 1261 4.532126 TGTCTACTATGGGGCCAGAATATG 59.468 45.833 4.39 0.00 0.00 1.78
878 1262 4.763355 TGTCTACTATGGGGCCAGAATAT 58.237 43.478 4.39 0.00 0.00 1.28
879 1263 4.207698 TGTCTACTATGGGGCCAGAATA 57.792 45.455 4.39 0.00 0.00 1.75
880 1264 3.060479 TGTCTACTATGGGGCCAGAAT 57.940 47.619 4.39 0.00 0.00 2.40
888 1274 4.700213 CCACCAAGTTTTGTCTACTATGGG 59.300 45.833 0.00 0.00 32.68 4.00
896 1282 2.838637 TTCCCCACCAAGTTTTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
1269 1980 1.212688 CATGGGATGTACTTGAGGGCA 59.787 52.381 0.00 0.00 0.00 5.36
1341 2058 0.459585 GAGACCTAAATCGCACCGCA 60.460 55.000 0.00 0.00 0.00 5.69
1357 2074 4.544152 AGGAATCCCCAAATTAACCAGAGA 59.456 41.667 0.00 0.00 37.41 3.10
1358 2075 4.646492 CAGGAATCCCCAAATTAACCAGAG 59.354 45.833 0.00 0.00 37.41 3.35
1517 2236 7.903431 GGAAAATAACTACAGATGTAAGCAACG 59.097 37.037 0.00 0.00 0.00 4.10
1573 2295 3.796178 CGGCATCCAAATTGATTTTACCG 59.204 43.478 0.00 0.00 0.00 4.02
1610 2332 2.295070 TGTTTCTGATGGACTTCGTCGA 59.705 45.455 0.00 0.00 34.17 4.20
1611 2333 2.408704 GTGTTTCTGATGGACTTCGTCG 59.591 50.000 0.00 0.00 34.17 5.12
1630 2352 6.969366 TCAGTAAACCAATTGATCACAAGTG 58.031 36.000 7.12 0.00 46.98 3.16
1829 3586 4.614535 GCAAACAAACACCAAAACAATGCA 60.615 37.500 0.00 0.00 0.00 3.96
1834 3591 2.039084 AGGGCAAACAAACACCAAAACA 59.961 40.909 0.00 0.00 0.00 2.83
1835 3592 2.675844 GAGGGCAAACAAACACCAAAAC 59.324 45.455 0.00 0.00 0.00 2.43
2193 4042 6.153340 ACCAAGATCCAACTGAACCAATTATG 59.847 38.462 0.00 0.00 0.00 1.90
2229 4085 5.521735 CCAATACTGAGTACACAAGATCAGC 59.478 44.000 7.30 0.00 42.33 4.26
2249 4105 9.911788 ATCAAAGAACTGATTATACACTCCAAT 57.088 29.630 0.00 0.00 31.84 3.16
2365 4223 7.606858 ACAGAGATGAGTTGTATCAACAATG 57.393 36.000 13.74 5.34 46.84 2.82
2434 4293 3.623906 ATCACCAGAATCTGTCACCAG 57.376 47.619 9.63 0.00 40.25 4.00
2449 4308 5.459107 CGTACATCTACAGCAGTTTATCACC 59.541 44.000 0.00 0.00 0.00 4.02
2466 4325 5.668558 ACTTGAGAAAAACCACGTACATC 57.331 39.130 0.00 0.00 0.00 3.06
2514 4373 6.939132 AGATCTGAAAATAAGCACATCCAG 57.061 37.500 0.00 0.00 0.00 3.86
2520 4380 7.437862 CCTCTCTGTAGATCTGAAAATAAGCAC 59.562 40.741 5.18 0.00 0.00 4.40
2865 4739 1.812571 AGATGAAACATGCCGGTTCAC 59.187 47.619 1.90 0.34 0.00 3.18
2872 4746 8.992835 AAGAAATTTAGAAGATGAAACATGCC 57.007 30.769 0.00 0.00 0.00 4.40
2963 4838 2.546778 GCAACCTGCTAGCACGTATAA 58.453 47.619 14.93 0.00 40.96 0.98
3015 4890 7.817641 AGTTATTTAGCAACTAAAGGAGCAAC 58.182 34.615 6.04 5.23 38.97 4.17
3291 5189 4.359996 ACGGAGGGAGTATTTAGGAACTT 58.640 43.478 0.00 0.00 41.75 2.66
3292 5190 3.991683 ACGGAGGGAGTATTTAGGAACT 58.008 45.455 0.00 0.00 46.37 3.01
3295 5193 3.303049 GGAACGGAGGGAGTATTTAGGA 58.697 50.000 0.00 0.00 0.00 2.94
3297 5195 3.036091 TGGGAACGGAGGGAGTATTTAG 58.964 50.000 0.00 0.00 0.00 1.85
3298 5196 3.119009 TGGGAACGGAGGGAGTATTTA 57.881 47.619 0.00 0.00 0.00 1.40
3306 5204 3.361786 ACAAATATTTGGGAACGGAGGG 58.638 45.455 27.43 3.22 42.34 4.30
3307 5205 4.270008 AGACAAATATTTGGGAACGGAGG 58.730 43.478 27.43 3.68 42.34 4.30
3308 5206 5.897377 AAGACAAATATTTGGGAACGGAG 57.103 39.130 27.43 4.34 42.34 4.63
3309 5207 6.007703 AGAAAGACAAATATTTGGGAACGGA 58.992 36.000 27.43 0.00 42.34 4.69
3311 5209 8.263940 TCTAGAAAGACAAATATTTGGGAACG 57.736 34.615 27.43 11.14 42.34 3.95
3327 5225 9.567776 TGTAACCATTTGAAATGTCTAGAAAGA 57.432 29.630 15.93 0.00 0.00 2.52
3329 5227 9.959749 GTTGTAACCATTTGAAATGTCTAGAAA 57.040 29.630 15.93 0.00 0.00 2.52
3330 5228 9.126151 TGTTGTAACCATTTGAAATGTCTAGAA 57.874 29.630 15.93 8.86 0.00 2.10
3331 5229 8.684386 TGTTGTAACCATTTGAAATGTCTAGA 57.316 30.769 15.93 3.81 0.00 2.43
3334 5232 8.020819 CGTATGTTGTAACCATTTGAAATGTCT 58.979 33.333 15.93 5.83 0.00 3.41
3335 5233 7.272515 CCGTATGTTGTAACCATTTGAAATGTC 59.727 37.037 15.93 5.28 0.00 3.06
3336 5234 7.040340 TCCGTATGTTGTAACCATTTGAAATGT 60.040 33.333 15.93 2.12 0.00 2.71
3337 5235 7.309177 TCCGTATGTTGTAACCATTTGAAATG 58.691 34.615 10.84 10.84 0.00 2.32
3338 5236 7.455641 TCCGTATGTTGTAACCATTTGAAAT 57.544 32.000 0.00 0.00 0.00 2.17
3339 5237 6.879276 TCCGTATGTTGTAACCATTTGAAA 57.121 33.333 0.00 0.00 0.00 2.69
3340 5238 6.431543 ACATCCGTATGTTGTAACCATTTGAA 59.568 34.615 0.00 0.00 44.07 2.69
3341 5239 5.941058 ACATCCGTATGTTGTAACCATTTGA 59.059 36.000 0.00 0.00 44.07 2.69
3342 5240 6.189677 ACATCCGTATGTTGTAACCATTTG 57.810 37.500 0.00 0.00 44.07 2.32
3343 5241 8.514330 AATACATCCGTATGTTGTAACCATTT 57.486 30.769 0.00 0.00 44.07 2.32
3344 5242 8.514330 AAATACATCCGTATGTTGTAACCATT 57.486 30.769 0.00 0.00 44.07 3.16
3345 5243 9.268268 CTAAATACATCCGTATGTTGTAACCAT 57.732 33.333 0.00 0.00 44.07 3.55
3346 5244 8.476447 TCTAAATACATCCGTATGTTGTAACCA 58.524 33.333 0.00 0.00 44.07 3.67
3347 5245 8.758715 GTCTAAATACATCCGTATGTTGTAACC 58.241 37.037 0.00 0.00 44.07 2.85
3348 5246 9.304731 TGTCTAAATACATCCGTATGTTGTAAC 57.695 33.333 0.00 0.00 44.07 2.50
3384 5282 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
3385 5283 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
3386 5284 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
3387 5285 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
3389 5287 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
3390 5288 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
3391 5289 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
3392 5290 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
3393 5291 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
3394 5292 6.163476 TGACTACATACGAAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
3396 5294 7.609760 AATGACTACATACGAAGCAAAATGA 57.390 32.000 0.00 0.00 35.50 2.57
3397 5295 9.935682 ATAAATGACTACATACGAAGCAAAATG 57.064 29.630 0.00 0.00 35.50 2.32
3401 5299 8.710835 TCAATAAATGACTACATACGAAGCAA 57.289 30.769 0.00 0.00 35.50 3.91
3431 5329 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
3432 5330 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
3433 5331 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
3434 5332 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
3435 5333 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
3436 5334 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3437 5335 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3438 5336 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3439 5337 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3440 5338 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3441 5339 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3442 5340 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3443 5341 8.731591 TTATACTCCCTCCGTTCCTAAATATT 57.268 34.615 0.00 0.00 0.00 1.28
3444 5342 7.954620 ACTTATACTCCCTCCGTTCCTAAATAT 59.045 37.037 0.00 0.00 0.00 1.28
3445 5343 7.300658 ACTTATACTCCCTCCGTTCCTAAATA 58.699 38.462 0.00 0.00 0.00 1.40
3446 5344 6.141790 ACTTATACTCCCTCCGTTCCTAAAT 58.858 40.000 0.00 0.00 0.00 1.40
3447 5345 5.522641 ACTTATACTCCCTCCGTTCCTAAA 58.477 41.667 0.00 0.00 0.00 1.85
3448 5346 5.103771 AGACTTATACTCCCTCCGTTCCTAA 60.104 44.000 0.00 0.00 0.00 2.69
3449 5347 4.414846 AGACTTATACTCCCTCCGTTCCTA 59.585 45.833 0.00 0.00 0.00 2.94
3450 5348 3.204831 AGACTTATACTCCCTCCGTTCCT 59.795 47.826 0.00 0.00 0.00 3.36
3451 5349 3.564264 AGACTTATACTCCCTCCGTTCC 58.436 50.000 0.00 0.00 0.00 3.62
3452 5350 5.105432 ACAAAGACTTATACTCCCTCCGTTC 60.105 44.000 0.00 0.00 0.00 3.95
3453 5351 4.776308 ACAAAGACTTATACTCCCTCCGTT 59.224 41.667 0.00 0.00 0.00 4.44
3454 5352 4.351127 ACAAAGACTTATACTCCCTCCGT 58.649 43.478 0.00 0.00 0.00 4.69
3455 5353 5.826737 TCTACAAAGACTTATACTCCCTCCG 59.173 44.000 0.00 0.00 0.00 4.63
3456 5354 6.265876 CCTCTACAAAGACTTATACTCCCTCC 59.734 46.154 0.00 0.00 0.00 4.30
3457 5355 6.834969 ACCTCTACAAAGACTTATACTCCCTC 59.165 42.308 0.00 0.00 0.00 4.30
3458 5356 6.743788 ACCTCTACAAAGACTTATACTCCCT 58.256 40.000 0.00 0.00 0.00 4.20
3459 5357 7.421087 AACCTCTACAAAGACTTATACTCCC 57.579 40.000 0.00 0.00 0.00 4.30
3460 5358 8.529476 TGAAACCTCTACAAAGACTTATACTCC 58.471 37.037 0.00 0.00 0.00 3.85
3461 5359 9.356433 GTGAAACCTCTACAAAGACTTATACTC 57.644 37.037 0.00 0.00 0.00 2.59
3462 5360 9.091220 AGTGAAACCTCTACAAAGACTTATACT 57.909 33.333 0.00 0.00 37.80 2.12
3465 5363 9.877178 CATAGTGAAACCTCTACAAAGACTTAT 57.123 33.333 0.00 0.00 37.80 1.73
3466 5364 8.311836 CCATAGTGAAACCTCTACAAAGACTTA 58.688 37.037 0.00 0.00 37.80 2.24
3467 5365 7.016268 TCCATAGTGAAACCTCTACAAAGACTT 59.984 37.037 0.00 0.00 37.80 3.01
3468 5366 6.497259 TCCATAGTGAAACCTCTACAAAGACT 59.503 38.462 0.00 0.00 37.80 3.24
3469 5367 6.590677 GTCCATAGTGAAACCTCTACAAAGAC 59.409 42.308 0.00 0.00 37.80 3.01
3470 5368 6.497259 AGTCCATAGTGAAACCTCTACAAAGA 59.503 38.462 0.00 0.00 37.80 2.52
3471 5369 6.702329 AGTCCATAGTGAAACCTCTACAAAG 58.298 40.000 0.00 0.00 37.80 2.77
3472 5370 6.681729 AGTCCATAGTGAAACCTCTACAAA 57.318 37.500 0.00 0.00 37.80 2.83
3473 5371 6.722590 TGTAGTCCATAGTGAAACCTCTACAA 59.277 38.462 0.00 0.00 37.80 2.41
3474 5372 6.250711 TGTAGTCCATAGTGAAACCTCTACA 58.749 40.000 0.00 0.00 37.80 2.74
3475 5373 6.770746 TGTAGTCCATAGTGAAACCTCTAC 57.229 41.667 0.00 0.00 37.80 2.59
3476 5374 9.078990 CATATGTAGTCCATAGTGAAACCTCTA 57.921 37.037 0.00 0.00 39.36 2.43
3477 5375 7.785028 TCATATGTAGTCCATAGTGAAACCTCT 59.215 37.037 1.90 0.00 39.36 3.69
3478 5376 7.952671 TCATATGTAGTCCATAGTGAAACCTC 58.047 38.462 1.90 0.00 39.36 3.85
3479 5377 7.914427 TCATATGTAGTCCATAGTGAAACCT 57.086 36.000 1.90 0.00 39.36 3.50
3480 5378 7.171678 GCTTCATATGTAGTCCATAGTGAAACC 59.828 40.741 10.61 0.00 39.36 3.27
3481 5379 7.710907 TGCTTCATATGTAGTCCATAGTGAAAC 59.289 37.037 10.61 0.00 39.36 2.78
3482 5380 7.791029 TGCTTCATATGTAGTCCATAGTGAAA 58.209 34.615 10.61 0.00 39.36 2.69
3483 5381 7.360113 TGCTTCATATGTAGTCCATAGTGAA 57.640 36.000 10.61 0.00 39.36 3.18
3484 5382 6.976934 TGCTTCATATGTAGTCCATAGTGA 57.023 37.500 10.61 0.00 39.36 3.41
3485 5383 8.437360 TTTTGCTTCATATGTAGTCCATAGTG 57.563 34.615 10.61 0.00 39.36 2.74
3486 5384 9.060347 CATTTTGCTTCATATGTAGTCCATAGT 57.940 33.333 10.61 0.00 39.36 2.12
3487 5385 9.276590 TCATTTTGCTTCATATGTAGTCCATAG 57.723 33.333 10.61 0.00 39.36 2.23
3488 5386 9.276590 CTCATTTTGCTTCATATGTAGTCCATA 57.723 33.333 10.61 0.00 40.27 2.74
3489 5387 7.776969 ACTCATTTTGCTTCATATGTAGTCCAT 59.223 33.333 10.61 0.00 37.58 3.41
3490 5388 7.066163 CACTCATTTTGCTTCATATGTAGTCCA 59.934 37.037 10.61 0.00 0.00 4.02
3491 5389 7.280876 TCACTCATTTTGCTTCATATGTAGTCC 59.719 37.037 10.61 0.00 0.00 3.85
3492 5390 8.201554 TCACTCATTTTGCTTCATATGTAGTC 57.798 34.615 10.61 4.54 0.00 2.59
3493 5391 8.565896 TTCACTCATTTTGCTTCATATGTAGT 57.434 30.769 10.61 0.00 0.00 2.73
3494 5392 9.661187 GATTCACTCATTTTGCTTCATATGTAG 57.339 33.333 5.04 5.04 0.00 2.74
3495 5393 9.176460 TGATTCACTCATTTTGCTTCATATGTA 57.824 29.630 1.90 0.00 0.00 2.29
3496 5394 7.972277 GTGATTCACTCATTTTGCTTCATATGT 59.028 33.333 9.59 0.00 35.97 2.29
3497 5395 7.971722 TGTGATTCACTCATTTTGCTTCATATG 59.028 33.333 17.26 0.00 35.97 1.78
3498 5396 7.972277 GTGTGATTCACTCATTTTGCTTCATAT 59.028 33.333 17.26 0.00 43.13 1.78
3499 5397 7.307694 GTGTGATTCACTCATTTTGCTTCATA 58.692 34.615 17.26 0.00 43.13 2.15
3500 5398 6.154445 GTGTGATTCACTCATTTTGCTTCAT 58.846 36.000 17.26 0.00 43.13 2.57
3501 5399 5.522456 GTGTGATTCACTCATTTTGCTTCA 58.478 37.500 17.26 0.00 43.13 3.02
3514 5412 7.081526 AGATGCATTTTAGAGTGTGATTCAC 57.918 36.000 9.93 9.93 46.46 3.18
3515 5413 8.969260 ATAGATGCATTTTAGAGTGTGATTCA 57.031 30.769 0.00 0.00 0.00 2.57
3534 5432 5.664457 ACCACATACGGATGCATATAGATG 58.336 41.667 7.78 4.42 36.43 2.90
3535 5433 5.658634 AGACCACATACGGATGCATATAGAT 59.341 40.000 7.78 0.00 36.43 1.98
3536 5434 5.016831 AGACCACATACGGATGCATATAGA 58.983 41.667 7.78 0.00 36.43 1.98
3537 5435 5.330455 AGACCACATACGGATGCATATAG 57.670 43.478 7.78 0.00 36.43 1.31
3538 5436 7.778382 ACTATAGACCACATACGGATGCATATA 59.222 37.037 7.78 3.14 36.43 0.86
3539 5437 5.939764 ATAGACCACATACGGATGCATAT 57.060 39.130 7.78 0.00 36.43 1.78
3540 5438 5.949952 ACTATAGACCACATACGGATGCATA 59.050 40.000 7.78 0.00 36.43 3.14
3541 5439 4.772624 ACTATAGACCACATACGGATGCAT 59.227 41.667 7.78 0.00 36.43 3.96
3542 5440 4.022329 CACTATAGACCACATACGGATGCA 60.022 45.833 7.78 0.00 36.43 3.96
3543 5441 4.486090 CACTATAGACCACATACGGATGC 58.514 47.826 7.78 0.00 36.43 3.91
3544 5442 4.765339 TCCACTATAGACCACATACGGATG 59.235 45.833 5.94 5.94 39.16 3.51
3545 5443 4.994282 TCCACTATAGACCACATACGGAT 58.006 43.478 6.78 0.00 0.00 4.18
3546 5444 4.442401 TCCACTATAGACCACATACGGA 57.558 45.455 6.78 0.00 0.00 4.69
3547 5445 5.477291 AGATTCCACTATAGACCACATACGG 59.523 44.000 6.78 0.00 0.00 4.02
3548 5446 6.431543 AGAGATTCCACTATAGACCACATACG 59.568 42.308 6.78 0.00 0.00 3.06
3549 5447 7.768807 AGAGATTCCACTATAGACCACATAC 57.231 40.000 6.78 0.00 0.00 2.39
3550 5448 8.445588 TGTAGAGATTCCACTATAGACCACATA 58.554 37.037 6.78 0.00 0.00 2.29
3551 5449 7.298374 TGTAGAGATTCCACTATAGACCACAT 58.702 38.462 6.78 0.00 0.00 3.21
3552 5450 6.669631 TGTAGAGATTCCACTATAGACCACA 58.330 40.000 6.78 0.00 0.00 4.17
3553 5451 7.584122 TTGTAGAGATTCCACTATAGACCAC 57.416 40.000 6.78 0.00 0.00 4.16
3554 5452 8.059461 TCTTTGTAGAGATTCCACTATAGACCA 58.941 37.037 6.78 0.00 0.00 4.02
3555 5453 8.354426 GTCTTTGTAGAGATTCCACTATAGACC 58.646 40.741 6.78 0.00 0.00 3.85
3556 5454 9.127277 AGTCTTTGTAGAGATTCCACTATAGAC 57.873 37.037 6.78 0.00 31.99 2.59
3557 5455 9.702253 AAGTCTTTGTAGAGATTCCACTATAGA 57.298 33.333 6.78 0.00 0.00 1.98
3578 5476 9.440761 ACTCCATCTGTTCCTAAATATAAGTCT 57.559 33.333 0.00 0.00 0.00 3.24
3591 5489 9.425577 GCTTATAATAACTACTCCATCTGTTCC 57.574 37.037 0.00 0.00 0.00 3.62
3593 5491 9.988815 CAGCTTATAATAACTACTCCATCTGTT 57.011 33.333 0.00 0.00 0.00 3.16
3599 5497 8.889717 GCAAAACAGCTTATAATAACTACTCCA 58.110 33.333 0.00 0.00 0.00 3.86
3619 5517 5.565259 CAGTTCTATGACAATGACGCAAAAC 59.435 40.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.