Multiple sequence alignment - TraesCS7A01G542700

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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 TraesCS7A01G542700 chr7A 100.000 4364 0 0 1 4364 719473862 719469499 0.000000e+00 8059.0
1 TraesCS7A01G542700 chr7A 95.122 41 2 0 2981 3021 301679797 301679757 1.010000e-06 65.8
2 TraesCS7A01G542700 chr7A 95.122 41 2 0 2981 3021 301758596 301758556 1.010000e-06 65.8
3 TraesCS7A01G542700 chr7D 92.292 1453 59 20 1 1444 622544206 622545614 0.000000e+00 2013.0
4 TraesCS7A01G542700 chr7D 90.238 1219 87 19 3142 4351 622547211 622548406 0.000000e+00 1563.0
5 TraesCS7A01G542700 chr7D 83.926 647 59 23 2153 2760 622546314 622546954 1.050000e-160 577.0
6 TraesCS7A01G542700 chr7D 89.388 245 18 5 1606 1849 622545767 622546004 7.090000e-78 302.0
7 TraesCS7A01G542700 chr7D 94.068 118 7 0 2867 2984 622547021 622547138 3.470000e-41 180.0
8 TraesCS7A01G542700 chr7B 86.690 1698 136 41 1 1613 721066241 721064549 0.000000e+00 1801.0
9 TraesCS7A01G542700 chr7B 85.867 1125 113 21 3205 4310 721063225 721062128 0.000000e+00 1155.0
10 TraesCS7A01G542700 chr7B 90.065 765 54 12 2446 3204 721064039 721063291 0.000000e+00 972.0
11 TraesCS7A01G542700 chr7B 92.375 459 25 8 1625 2081 721064568 721064118 0.000000e+00 645.0
12 TraesCS7A01G542700 chr7B 87.097 248 23 3 187 432 721068435 721068195 5.560000e-69 272.0
13 TraesCS7A01G542700 chr7B 93.333 45 3 0 2977 3021 509206511 509206555 2.820000e-07 67.6
14 TraesCS7A01G542700 chr7B 95.122 41 0 2 1439 1477 522138238 522138198 3.640000e-06 63.9
15 TraesCS7A01G542700 chr3D 95.455 44 2 0 2978 3021 60275856 60275899 2.180000e-08 71.3
16 TraesCS7A01G542700 chr5B 91.667 48 4 0 2978 3025 584172624 584172671 2.820000e-07 67.6
17 TraesCS7A01G542700 chr5B 87.037 54 3 4 1428 1477 477078570 477078517 1.700000e-04 58.4
18 TraesCS7A01G542700 chr4D 95.349 43 0 2 1437 1477 252173694 252173736 2.820000e-07 67.6
19 TraesCS7A01G542700 chr4B 89.091 55 4 2 1429 1481 66469328 66469274 2.820000e-07 67.6
20 TraesCS7A01G542700 chr6D 97.436 39 0 1 1440 1477 58433751 58433789 1.010000e-06 65.8
21 TraesCS7A01G542700 chr5D 91.667 48 2 2 1431 1477 340758433 340758387 1.010000e-06 65.8
22 TraesCS7A01G542700 chr5D 82.500 80 5 7 2978 3050 308852280 308852357 1.310000e-05 62.1
23 TraesCS7A01G542700 chr5D 82.609 69 6 5 1414 1477 108535842 108535775 6.100000e-04 56.5
24 TraesCS7A01G542700 chr5A 95.122 41 2 0 2981 3021 70112650 70112610 1.010000e-06 65.8
25 TraesCS7A01G542700 chr5A 93.182 44 3 0 2978 3021 332952456 332952499 1.010000e-06 65.8
26 TraesCS7A01G542700 chr3B 97.436 39 0 1 1440 1477 247566303 247566265 1.010000e-06 65.8
27 TraesCS7A01G542700 chr1B 93.182 44 3 0 2978 3021 571964661 571964704 1.010000e-06 65.8
28 TraesCS7A01G542700 chr1B 93.023 43 1 2 1436 1477 352390062 352390103 1.310000e-05 62.1


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G542700 chr7A 719469499 719473862 4363 True 8059 8059 100.0000 1 4364 1 chr7A.!!$R3 4363
1 TraesCS7A01G542700 chr7D 622544206 622548406 4200 False 927 2013 89.9824 1 4351 5 chr7D.!!$F1 4350
2 TraesCS7A01G542700 chr7B 721062128 721068435 6307 True 969 1801 88.4188 1 4310 5 chr7B.!!$R2 4309

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
199 2418 0.109272 CATACGCCGGTCGCATCTAT 60.109 55.0 16.48 5.93 43.23 1.98 F
940 3184 0.535102 GCAGCACCACCACTAGTTGT 60.535 55.0 0.00 0.00 0.00 3.32 F
2387 4733 0.763652 CAGGATGGACATAGCAGGCT 59.236 55.0 0.00 0.00 0.00 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 4190 1.749634 AGAGTTGGATTAGGTCGACGG 59.250 52.381 9.92 0.0 0.00 4.79 R
2588 4946 0.179702 TGGATGGATGTCAGCAGCTC 59.820 55.000 0.00 0.0 32.50 4.09 R
4271 6744 0.178981 ACAAGGTGTGAAGCATGGCT 60.179 50.000 0.00 0.0 42.56 4.75 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
42 2237 1.135094 AGATCTCATGGCCATCCGTT 58.865 50.000 17.61 4.61 34.14 4.44
55 2250 0.541392 ATCCGTTGTGGCTCTGCATA 59.459 50.000 0.00 0.00 37.80 3.14
67 2262 6.127281 TGTGGCTCTGCATATGATTTCATTTT 60.127 34.615 6.97 0.00 37.76 1.82
85 2280 5.468409 TCATTTTCATTTCACACGTGCTCTA 59.532 36.000 17.22 0.00 0.00 2.43
121 2316 2.494059 CTTCCCATGTTTCAGACGTGT 58.506 47.619 0.00 0.00 42.57 4.49
126 2322 2.611751 CCATGTTTCAGACGTGTCAACA 59.388 45.455 8.85 8.85 42.57 3.33
133 2329 6.926826 TGTTTCAGACGTGTCAACATACTATT 59.073 34.615 0.00 0.00 0.00 1.73
147 2343 0.596600 ACTATTACCATCGCGCACGG 60.597 55.000 8.75 6.71 40.63 4.94
148 2344 0.596600 CTATTACCATCGCGCACGGT 60.597 55.000 15.69 15.69 40.63 4.83
158 2363 1.540607 CGCGCACGGTGTGATAGATC 61.541 60.000 24.71 5.38 35.23 2.75
161 2366 1.215655 GCACGGTGTGATAGATCGGC 61.216 60.000 10.24 0.00 35.23 5.54
199 2418 0.109272 CATACGCCGGTCGCATCTAT 60.109 55.000 16.48 5.93 43.23 1.98
818 3057 3.494336 GCTAGCACACCAGCAGCG 61.494 66.667 10.63 0.00 37.73 5.18
903 3147 3.790089 AGTTTAGCTTAACCCAGCACT 57.210 42.857 11.80 0.00 42.84 4.40
940 3184 0.535102 GCAGCACCACCACTAGTTGT 60.535 55.000 0.00 0.00 0.00 3.32
946 3190 3.003378 GCACCACCACTAGTTGTTTCTTC 59.997 47.826 0.00 0.00 0.00 2.87
948 3192 3.118519 ACCACCACTAGTTGTTTCTTCGT 60.119 43.478 0.00 0.00 0.00 3.85
949 3193 3.247648 CCACCACTAGTTGTTTCTTCGTG 59.752 47.826 0.00 0.00 0.00 4.35
950 3194 3.247648 CACCACTAGTTGTTTCTTCGTGG 59.752 47.826 0.00 0.00 40.39 4.94
951 3195 3.118519 ACCACTAGTTGTTTCTTCGTGGT 60.119 43.478 5.43 5.43 41.53 4.16
953 3197 3.869246 CACTAGTTGTTTCTTCGTGGTGT 59.131 43.478 0.00 0.00 0.00 4.16
954 3198 4.025979 CACTAGTTGTTTCTTCGTGGTGTC 60.026 45.833 0.00 0.00 0.00 3.67
955 3199 2.980568 AGTTGTTTCTTCGTGGTGTCA 58.019 42.857 0.00 0.00 0.00 3.58
956 3200 3.340034 AGTTGTTTCTTCGTGGTGTCAA 58.660 40.909 0.00 0.00 0.00 3.18
957 3201 3.945285 AGTTGTTTCTTCGTGGTGTCAAT 59.055 39.130 0.00 0.00 0.00 2.57
959 3203 4.285807 TGTTTCTTCGTGGTGTCAATTG 57.714 40.909 0.00 0.00 0.00 2.32
960 3204 3.042887 GTTTCTTCGTGGTGTCAATTGC 58.957 45.455 0.00 0.00 0.00 3.56
988 3237 3.422417 GATCGATCGAGGTGTCTTGAA 57.578 47.619 23.84 0.00 37.01 2.69
990 3239 3.422417 TCGATCGAGGTGTCTTGAATC 57.578 47.619 15.15 0.00 37.01 2.52
997 3246 1.026718 GGTGTCTTGAATCCCGGCTG 61.027 60.000 0.00 0.00 0.00 4.85
1171 3420 2.037367 CCGACCTCCACCTCCTCA 59.963 66.667 0.00 0.00 0.00 3.86
1209 3458 4.047059 TCCACGCCGGTCTCGTTC 62.047 66.667 1.90 0.00 38.19 3.95
1370 3622 2.670905 CACGAATACGCACATTCCTTCA 59.329 45.455 0.00 0.00 43.96 3.02
1383 3635 9.511144 CGCACATTCCTTCATATATACGTATAA 57.489 33.333 18.69 9.14 0.00 0.98
1416 3668 8.713036 AGAAGGAAGTCTATCATTAGCTCAAAT 58.287 33.333 0.00 0.00 0.00 2.32
1472 3724 8.138712 ACTCCTCTGTAAAGAAATATAAGAGCG 58.861 37.037 0.00 0.00 0.00 5.03
1475 3756 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1501 3782 8.999905 ACTCAAGGTAAACCAAGGTAAAATTA 57.000 30.769 1.26 0.00 38.89 1.40
1585 3866 4.217334 TGGCTAGAAATGTTTGAATTCGCA 59.783 37.500 0.04 0.45 0.00 5.10
1595 3876 3.574284 TTGAATTCGCATGGGAACTTG 57.426 42.857 25.55 0.00 38.46 3.16
1605 3886 1.961793 TGGGAACTTGTCAACTTCGG 58.038 50.000 0.62 0.00 0.00 4.30
1606 3887 1.487142 TGGGAACTTGTCAACTTCGGA 59.513 47.619 0.62 0.00 0.00 4.55
1607 3888 2.092861 TGGGAACTTGTCAACTTCGGAA 60.093 45.455 0.00 0.00 0.00 4.30
1610 3891 4.142337 GGGAACTTGTCAACTTCGGAAAAA 60.142 41.667 0.00 0.00 0.00 1.94
1611 3892 5.034797 GGAACTTGTCAACTTCGGAAAAAG 58.965 41.667 0.00 0.00 0.00 2.27
1619 3900 6.540914 TGTCAACTTCGGAAAAAGAACACTAT 59.459 34.615 0.00 0.00 0.00 2.12
1620 3901 6.851330 GTCAACTTCGGAAAAAGAACACTATG 59.149 38.462 0.00 0.00 0.00 2.23
1622 3903 7.711772 TCAACTTCGGAAAAAGAACACTATGTA 59.288 33.333 0.00 0.00 0.00 2.29
1639 3920 8.604035 ACACTATGTAAATCAGATTTTGTAGCG 58.396 33.333 13.71 9.79 33.82 4.26
1653 3934 7.602644 AGATTTTGTAGCGAAAGATAAGTGTCA 59.397 33.333 0.00 0.00 31.56 3.58
1827 4108 4.524053 TCTCTTCCGTGATTAGTGCTCTA 58.476 43.478 0.00 0.00 0.00 2.43
1935 4217 4.806247 CGACCTAATCCAACTCTAGCAAAG 59.194 45.833 0.00 0.00 0.00 2.77
1963 4245 9.520515 AACAACAGAAGGAACAATATACATCTT 57.479 29.630 0.00 0.00 0.00 2.40
1964 4246 9.167311 ACAACAGAAGGAACAATATACATCTTC 57.833 33.333 0.00 0.00 0.00 2.87
1965 4247 8.616076 CAACAGAAGGAACAATATACATCTTCC 58.384 37.037 0.00 0.00 32.15 3.46
1979 4261 3.646162 ACATCTTCCTGGACGGCATATAA 59.354 43.478 0.00 0.00 0.00 0.98
1984 4266 3.248024 TCCTGGACGGCATATAAATCCT 58.752 45.455 0.00 0.00 0.00 3.24
2023 4305 5.459536 TGTGATCAGCTGGATATAGACAC 57.540 43.478 15.13 12.20 36.00 3.67
2075 4369 9.922305 CAAGAGAAAAAGTAACTAAACTCAGTG 57.078 33.333 0.00 0.00 0.00 3.66
2099 4393 1.211703 TGGAGTTTGTGACCAGCTCAA 59.788 47.619 3.18 0.00 0.00 3.02
2118 4412 5.771469 CTCAAACCAAATCAGCAATACACA 58.229 37.500 0.00 0.00 0.00 3.72
2126 4420 7.123997 ACCAAATCAGCAATACACAAATATCCA 59.876 33.333 0.00 0.00 0.00 3.41
2127 4421 7.980662 CCAAATCAGCAATACACAAATATCCAA 59.019 33.333 0.00 0.00 0.00 3.53
2141 4435 9.912634 CACAAATATCCAAGTTGTTACAAGATT 57.087 29.630 0.00 0.00 33.27 2.40
2178 4512 9.810545 AGATAGTTATTTCTCTGTAAAGTGCTC 57.189 33.333 0.00 0.00 0.00 4.26
2191 4525 6.395629 TGTAAAGTGCTCATAGTAGTTGGAC 58.604 40.000 0.00 0.00 0.00 4.02
2193 4527 4.457834 AGTGCTCATAGTAGTTGGACAC 57.542 45.455 0.00 0.00 0.00 3.67
2196 4530 5.046304 AGTGCTCATAGTAGTTGGACACAAT 60.046 40.000 0.00 0.00 39.13 2.71
2197 4531 5.643777 GTGCTCATAGTAGTTGGACACAATT 59.356 40.000 0.00 0.00 39.13 2.32
2199 4533 6.371548 TGCTCATAGTAGTTGGACACAATTTC 59.628 38.462 0.00 0.00 39.13 2.17
2200 4534 6.595716 GCTCATAGTAGTTGGACACAATTTCT 59.404 38.462 0.00 0.00 39.13 2.52
2201 4535 7.201565 GCTCATAGTAGTTGGACACAATTTCTC 60.202 40.741 0.00 0.00 39.13 2.87
2202 4536 7.676004 TCATAGTAGTTGGACACAATTTCTCA 58.324 34.615 0.00 0.00 39.13 3.27
2203 4537 8.321353 TCATAGTAGTTGGACACAATTTCTCAT 58.679 33.333 0.00 0.00 39.13 2.90
2211 4545 9.696917 GTTGGACACAATTTCTCATTCTTTTAT 57.303 29.630 0.00 0.00 39.13 1.40
2226 4560 8.892723 TCATTCTTTTATACTTGTGCGAATCAT 58.107 29.630 0.00 0.00 0.00 2.45
2227 4561 9.162793 CATTCTTTTATACTTGTGCGAATCATC 57.837 33.333 0.00 0.00 0.00 2.92
2235 4569 3.044235 TGTGCGAATCATCAAGTCTGT 57.956 42.857 0.00 0.00 0.00 3.41
2237 4571 3.433274 TGTGCGAATCATCAAGTCTGTTC 59.567 43.478 0.00 0.00 0.00 3.18
2245 4579 3.692593 TCATCAAGTCTGTTCGGACGATA 59.307 43.478 6.19 0.00 40.76 2.92
2249 4583 1.749063 AGTCTGTTCGGACGATATGCA 59.251 47.619 6.19 0.00 40.76 3.96
2252 4586 2.927477 TCTGTTCGGACGATATGCAAAC 59.073 45.455 0.00 0.00 0.00 2.93
2260 4594 1.999735 ACGATATGCAAACGGTGACAG 59.000 47.619 13.26 0.00 0.00 3.51
2263 4597 3.124466 CGATATGCAAACGGTGACAGAAA 59.876 43.478 0.00 0.00 0.00 2.52
2306 4641 6.635030 AAAGAGAAATAGCAAAACCGAACT 57.365 33.333 0.00 0.00 0.00 3.01
2312 4648 5.767816 AATAGCAAAACCGAACTTGAAGT 57.232 34.783 0.00 0.00 0.00 3.01
2316 4652 6.870971 AGCAAAACCGAACTTGAAGTATTA 57.129 33.333 0.00 0.00 0.00 0.98
2325 4661 5.929992 CGAACTTGAAGTATTACTGGTTCCA 59.070 40.000 0.00 0.00 31.33 3.53
2326 4662 6.128634 CGAACTTGAAGTATTACTGGTTCCAC 60.129 42.308 0.00 3.58 31.33 4.02
2332 4668 7.215789 TGAAGTATTACTGGTTCCACGTTAAA 58.784 34.615 0.00 0.00 0.00 1.52
2357 4695 6.664428 AAAGTATTGCTGGTTATTTGGTGT 57.336 33.333 0.00 0.00 0.00 4.16
2364 4702 6.266168 TGCTGGTTATTTGGTGTTTATGAG 57.734 37.500 0.00 0.00 0.00 2.90
2365 4703 6.007076 TGCTGGTTATTTGGTGTTTATGAGA 58.993 36.000 0.00 0.00 0.00 3.27
2379 4717 5.128919 GTTTATGAGAAGCAGGATGGACAT 58.871 41.667 0.00 0.00 35.86 3.06
2387 4733 0.763652 CAGGATGGACATAGCAGGCT 59.236 55.000 0.00 0.00 0.00 4.58
2534 4883 4.968971 ACCCCTAACCAACTATATTCCG 57.031 45.455 0.00 0.00 0.00 4.30
2550 4908 2.545596 CCGCAGCACAGTTCAGCAA 61.546 57.895 0.00 0.00 0.00 3.91
2551 4909 1.082300 CGCAGCACAGTTCAGCAAG 60.082 57.895 0.00 0.00 0.00 4.01
2552 4910 1.501337 CGCAGCACAGTTCAGCAAGA 61.501 55.000 0.00 0.00 0.00 3.02
2588 4946 3.692791 TCGATAGACCGATGTCAGTTG 57.307 47.619 0.00 0.00 44.33 3.16
2683 5043 7.600752 ACAAGACTTTGCAGAAGATAACTACTC 59.399 37.037 13.35 1.64 37.85 2.59
2719 5079 3.533606 TGCTCTATGGCTTTCTCTCAC 57.466 47.619 0.00 0.00 0.00 3.51
2841 5223 8.566260 AGATTTGCAAGCTATTAGCAGAATTAG 58.434 33.333 17.59 1.16 45.56 1.73
2990 5372 7.343357 CACTTAACCAATTATTACTCCCTCCA 58.657 38.462 0.00 0.00 0.00 3.86
2995 5377 4.353788 CCAATTATTACTCCCTCCATCCCA 59.646 45.833 0.00 0.00 0.00 4.37
2996 5378 5.316987 CAATTATTACTCCCTCCATCCCAC 58.683 45.833 0.00 0.00 0.00 4.61
2997 5379 2.587060 ATTACTCCCTCCATCCCACA 57.413 50.000 0.00 0.00 0.00 4.17
2998 5380 2.352561 TTACTCCCTCCATCCCACAA 57.647 50.000 0.00 0.00 0.00 3.33
2999 5381 2.587060 TACTCCCTCCATCCCACAAT 57.413 50.000 0.00 0.00 0.00 2.71
3000 5382 0.921896 ACTCCCTCCATCCCACAATG 59.078 55.000 0.00 0.00 0.00 2.82
3001 5383 0.921896 CTCCCTCCATCCCACAATGT 59.078 55.000 0.00 0.00 0.00 2.71
3004 5386 2.509548 TCCCTCCATCCCACAATGTAAG 59.490 50.000 0.00 0.00 0.00 2.34
3005 5387 2.509548 CCCTCCATCCCACAATGTAAGA 59.490 50.000 0.00 0.00 0.00 2.10
3006 5388 3.545703 CCTCCATCCCACAATGTAAGAC 58.454 50.000 0.00 0.00 0.00 3.01
3007 5389 3.198068 CTCCATCCCACAATGTAAGACG 58.802 50.000 0.00 0.00 0.00 4.18
3010 5392 3.756434 CCATCCCACAATGTAAGACGTTT 59.244 43.478 0.00 0.00 0.00 3.60
3011 5393 4.217550 CCATCCCACAATGTAAGACGTTTT 59.782 41.667 0.00 0.00 0.00 2.43
3012 5394 5.390613 CATCCCACAATGTAAGACGTTTTC 58.609 41.667 0.00 0.00 0.00 2.29
3013 5395 4.452825 TCCCACAATGTAAGACGTTTTCA 58.547 39.130 0.00 0.00 0.00 2.69
3014 5396 4.273969 TCCCACAATGTAAGACGTTTTCAC 59.726 41.667 0.00 0.00 0.00 3.18
3015 5397 4.035792 CCCACAATGTAAGACGTTTTCACA 59.964 41.667 0.00 0.00 0.00 3.58
3016 5398 5.449314 CCCACAATGTAAGACGTTTTCACAA 60.449 40.000 0.00 0.00 0.00 3.33
3017 5399 5.681105 CCACAATGTAAGACGTTTTCACAAG 59.319 40.000 0.00 0.32 0.00 3.16
3018 5400 5.171337 CACAATGTAAGACGTTTTCACAAGC 59.829 40.000 0.00 0.00 0.00 4.01
3019 5401 5.065988 ACAATGTAAGACGTTTTCACAAGCT 59.934 36.000 0.00 0.00 0.00 3.74
3020 5402 6.259167 ACAATGTAAGACGTTTTCACAAGCTA 59.741 34.615 0.00 0.00 0.00 3.32
3021 5403 5.646467 TGTAAGACGTTTTCACAAGCTAC 57.354 39.130 0.00 0.00 0.00 3.58
3022 5404 5.110598 TGTAAGACGTTTTCACAAGCTACA 58.889 37.500 0.00 0.00 0.00 2.74
3023 5405 5.756347 TGTAAGACGTTTTCACAAGCTACAT 59.244 36.000 0.00 0.00 0.00 2.29
3024 5406 5.751243 AAGACGTTTTCACAAGCTACATT 57.249 34.783 0.00 0.00 0.00 2.71
3025 5407 5.095691 AGACGTTTTCACAAGCTACATTG 57.904 39.130 0.00 0.00 36.22 2.82
3026 5408 3.628017 ACGTTTTCACAAGCTACATTGC 58.372 40.909 0.00 0.00 33.28 3.56
3072 5454 4.458989 TCTGGACACTGCCAAATTGTAATC 59.541 41.667 0.00 0.00 37.52 1.75
3083 5467 8.121305 TGCCAAATTGTAATCTATGAAACTGT 57.879 30.769 0.00 0.00 0.00 3.55
3085 5469 9.722056 GCCAAATTGTAATCTATGAAACTGTAG 57.278 33.333 0.00 0.00 0.00 2.74
3100 5484 7.514721 TGAAACTGTAGAAAATTACCTCACCT 58.485 34.615 0.00 0.00 0.00 4.00
3113 5497 2.023673 CCTCACCTGTGCAACTCAAAA 58.976 47.619 0.00 0.00 38.04 2.44
3125 5509 4.516698 TGCAACTCAAAAGTGATCTTCTCC 59.483 41.667 0.00 0.00 35.36 3.71
3210 5659 8.627403 ACATATTACATCCAAATGCTTCTTCAG 58.373 33.333 0.00 0.00 36.26 3.02
3230 5679 8.704668 TCTTCAGTTAGCAACATATAATCTCCA 58.295 33.333 0.00 0.00 0.00 3.86
3261 5710 6.371548 TCTGTAATCTGACCACACTTAATTGC 59.628 38.462 0.00 0.00 0.00 3.56
3340 5789 0.967887 CACCAAGAGCTCTCTCCGGA 60.968 60.000 18.55 2.93 39.39 5.14
3348 5797 1.720694 GCTCTCTCCGGAGAACCTCG 61.721 65.000 32.94 21.45 46.50 4.63
3395 5844 3.123620 GCCCAAGACGCAGAGCAG 61.124 66.667 0.00 0.00 0.00 4.24
3399 5848 0.320247 CCAAGACGCAGAGCAGAAGT 60.320 55.000 0.00 0.00 0.00 3.01
3445 5894 9.581289 TTAGGAGAAAATTAATCAAACCTGTGA 57.419 29.630 0.00 0.00 0.00 3.58
3447 5896 8.923270 AGGAGAAAATTAATCAAACCTGTGAAA 58.077 29.630 0.00 0.00 0.00 2.69
3471 5926 4.635833 TTCGTCTACAGTGTGTGTGTAA 57.364 40.909 5.88 0.00 40.69 2.41
3524 5979 0.601046 GCTCTTGGGCCTTTTTGTGC 60.601 55.000 4.53 0.00 0.00 4.57
3639 6097 2.557924 TGCTTTGCTGGGATAAAGTGTG 59.442 45.455 0.00 0.00 36.52 3.82
3674 6132 2.765699 ACAGCAACCACCATTTCAAACT 59.234 40.909 0.00 0.00 0.00 2.66
3705 6163 2.903784 CCCGGATGGTTAGGACATGATA 59.096 50.000 0.73 0.00 0.00 2.15
3800 6258 1.435168 AGACCAGAGGAGTTCTCCCTT 59.565 52.381 14.40 1.65 43.44 3.95
3844 6313 6.909550 TTGCTCTTTTGGCCTCTTTATTTA 57.090 33.333 3.32 0.00 0.00 1.40
3845 6314 7.480760 TTGCTCTTTTGGCCTCTTTATTTAT 57.519 32.000 3.32 0.00 0.00 1.40
3848 6317 8.374743 TGCTCTTTTGGCCTCTTTATTTATTTT 58.625 29.630 3.32 0.00 0.00 1.82
3849 6318 9.869757 GCTCTTTTGGCCTCTTTATTTATTTTA 57.130 29.630 3.32 0.00 0.00 1.52
3915 6384 9.733556 TTTCATAGTATTGTTGGTATTGTCACT 57.266 29.630 0.00 0.00 0.00 3.41
4025 6497 2.825205 CAAGAAAAAGGTGGGTGCAAG 58.175 47.619 0.00 0.00 0.00 4.01
4057 6529 4.467082 TCCATTTTGGAATGTGATGGAAGG 59.533 41.667 1.13 0.00 45.00 3.46
4144 6616 5.823045 ACTTTAAATGATAGCGGAAGGAAGG 59.177 40.000 0.00 0.00 0.00 3.46
4147 6619 2.160721 TGATAGCGGAAGGAAGGACT 57.839 50.000 0.00 0.00 0.00 3.85
4204 6676 1.811965 CAATTCACACCGCCTCATTCA 59.188 47.619 0.00 0.00 0.00 2.57
4215 6687 4.156008 ACCGCCTCATTCAGTATTGTTTTC 59.844 41.667 0.00 0.00 0.00 2.29
4216 6688 4.334443 CGCCTCATTCAGTATTGTTTTCG 58.666 43.478 0.00 0.00 0.00 3.46
4218 6690 4.394920 GCCTCATTCAGTATTGTTTTCGGA 59.605 41.667 0.00 0.00 0.00 4.55
4220 6692 5.874810 CCTCATTCAGTATTGTTTTCGGAGA 59.125 40.000 0.00 0.00 0.00 3.71
4221 6693 6.540189 CCTCATTCAGTATTGTTTTCGGAGAT 59.460 38.462 0.00 0.00 35.04 2.75
4222 6694 7.254590 CCTCATTCAGTATTGTTTTCGGAGATC 60.255 40.741 0.00 0.00 35.04 2.75
4223 6695 7.102993 TCATTCAGTATTGTTTTCGGAGATCA 58.897 34.615 0.00 0.00 35.04 2.92
4224 6696 7.770433 TCATTCAGTATTGTTTTCGGAGATCAT 59.230 33.333 0.00 0.00 35.04 2.45
4228 6701 7.824289 TCAGTATTGTTTTCGGAGATCATCTTT 59.176 33.333 0.00 0.00 35.04 2.52
4235 6708 9.624697 TGTTTTCGGAGATCATCTTTAAATTTG 57.375 29.630 0.00 0.00 35.04 2.32
4266 6739 0.250124 TGGCACAGAACAACGGGTAG 60.250 55.000 0.00 0.00 0.00 3.18
4271 6744 3.199677 CACAGAACAACGGGTAGTTCAA 58.800 45.455 7.88 0.00 44.94 2.69
4295 6768 3.402110 CATGCTTCACACCTTGTACTGA 58.598 45.455 0.00 0.00 0.00 3.41
4351 6824 2.628178 TCAGAAATGGTGACGACTGAGT 59.372 45.455 0.00 0.00 32.04 3.41
4352 6825 3.824443 TCAGAAATGGTGACGACTGAGTA 59.176 43.478 0.00 0.00 32.04 2.59
4353 6826 4.462834 TCAGAAATGGTGACGACTGAGTAT 59.537 41.667 0.00 0.00 32.04 2.12
4354 6827 5.047306 TCAGAAATGGTGACGACTGAGTATT 60.047 40.000 0.00 0.00 32.04 1.89
4355 6828 6.152154 TCAGAAATGGTGACGACTGAGTATTA 59.848 38.462 0.00 0.00 32.04 0.98
4356 6829 6.473778 CAGAAATGGTGACGACTGAGTATTAG 59.526 42.308 0.00 0.00 0.00 1.73
4357 6830 4.920640 ATGGTGACGACTGAGTATTAGG 57.079 45.455 0.00 0.00 0.00 2.69
4358 6831 3.693807 TGGTGACGACTGAGTATTAGGT 58.306 45.455 0.00 0.00 0.00 3.08
4359 6832 4.084287 TGGTGACGACTGAGTATTAGGTT 58.916 43.478 0.00 0.00 0.00 3.50
4360 6833 4.525487 TGGTGACGACTGAGTATTAGGTTT 59.475 41.667 0.00 0.00 0.00 3.27
4361 6834 5.711506 TGGTGACGACTGAGTATTAGGTTTA 59.288 40.000 0.00 0.00 0.00 2.01
4362 6835 6.379133 TGGTGACGACTGAGTATTAGGTTTAT 59.621 38.462 0.00 0.00 0.00 1.40
4363 6836 6.916932 GGTGACGACTGAGTATTAGGTTTATC 59.083 42.308 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 2207 3.618351 CCATGAGATCTATGGGCAATCC 58.382 50.000 17.15 0.00 41.11 3.01
42 2237 3.888583 TGAAATCATATGCAGAGCCACA 58.111 40.909 0.00 0.00 0.00 4.17
55 2250 7.359431 GCACGTGTGAAATGAAAATGAAATCAT 60.359 33.333 18.38 0.00 37.88 2.45
67 2262 5.743026 TTTTTAGAGCACGTGTGAAATGA 57.257 34.783 18.38 0.00 0.00 2.57
121 2316 3.985279 GCGCGATGGTAATAGTATGTTGA 59.015 43.478 12.10 0.00 0.00 3.18
126 2322 2.592194 CGTGCGCGATGGTAATAGTAT 58.408 47.619 16.08 0.00 41.33 2.12
133 2329 4.058732 ACACCGTGCGCGATGGTA 62.059 61.111 23.45 0.00 42.70 3.25
147 2343 1.729472 CGATCGGCCGATCTATCACAC 60.729 57.143 46.91 29.68 46.36 3.82
148 2344 0.521735 CGATCGGCCGATCTATCACA 59.478 55.000 46.91 21.39 46.36 3.58
149 2345 0.798771 GCGATCGGCCGATCTATCAC 60.799 60.000 46.91 32.65 46.36 3.06
150 2346 1.506718 GCGATCGGCCGATCTATCA 59.493 57.895 46.91 22.83 46.36 2.15
199 2418 5.046304 CAGTTCTAGGTTTCATCTTGGAGGA 60.046 44.000 0.00 0.00 0.00 3.71
370 2590 2.279073 CTCAGCCGGGTCTCCCTA 59.721 66.667 1.27 0.00 42.67 3.53
441 2661 0.752054 TTTTGAAGGCAGGCAGTTGG 59.248 50.000 0.00 0.00 0.00 3.77
467 2687 6.126796 TGTGATGATAAGAAAGGGATGCTGTA 60.127 38.462 0.00 0.00 0.00 2.74
818 3057 6.460676 GCTTTTGCTCCCATATATATCATGCC 60.461 42.308 0.00 0.00 43.35 4.40
919 3163 0.474184 AACTAGTGGTGGTGCTGCTT 59.526 50.000 0.00 0.00 0.00 3.91
931 3175 3.869246 ACACCACGAAGAAACAACTAGTG 59.131 43.478 0.00 0.00 0.00 2.74
932 3176 4.117685 GACACCACGAAGAAACAACTAGT 58.882 43.478 0.00 0.00 0.00 2.57
933 3177 4.116961 TGACACCACGAAGAAACAACTAG 58.883 43.478 0.00 0.00 0.00 2.57
940 3184 2.948979 AGCAATTGACACCACGAAGAAA 59.051 40.909 10.34 0.00 0.00 2.52
946 3190 0.110056 GCTGAGCAATTGACACCACG 60.110 55.000 10.34 0.00 0.00 4.94
948 3192 1.527034 GAGCTGAGCAATTGACACCA 58.473 50.000 10.34 0.00 0.00 4.17
949 3193 0.445436 CGAGCTGAGCAATTGACACC 59.555 55.000 10.34 0.28 0.00 4.16
950 3194 1.432514 TCGAGCTGAGCAATTGACAC 58.567 50.000 10.34 0.09 0.00 3.67
951 3195 2.274437 GATCGAGCTGAGCAATTGACA 58.726 47.619 10.34 7.56 31.75 3.58
953 3197 1.134946 TCGATCGAGCTGAGCAATTGA 59.865 47.619 15.15 3.84 30.45 2.57
954 3198 1.564207 TCGATCGAGCTGAGCAATTG 58.436 50.000 15.15 0.00 30.45 2.32
955 3199 2.402305 GATCGATCGAGCTGAGCAATT 58.598 47.619 25.17 3.00 30.45 2.32
956 3200 2.063156 GATCGATCGAGCTGAGCAAT 57.937 50.000 25.17 3.81 30.45 3.56
957 3201 3.559015 GATCGATCGAGCTGAGCAA 57.441 52.632 25.17 0.00 30.45 3.91
997 3246 2.895372 CCGGTAGTTCGCCATGGC 60.895 66.667 27.67 27.67 37.85 4.40
1149 3398 4.988716 AGGTGGAGGTCGGCGTCA 62.989 66.667 12.28 0.00 0.00 4.35
1383 3635 7.951347 AATGATAGACTTCCTTCTGCAATTT 57.049 32.000 0.00 0.00 0.00 1.82
1446 3698 8.138712 CGCTCTTATATTTCTTTACAGAGGAGT 58.861 37.037 0.00 0.00 0.00 3.85
1447 3699 8.138712 ACGCTCTTATATTTCTTTACAGAGGAG 58.861 37.037 0.00 0.00 0.00 3.69
1448 3700 8.008513 ACGCTCTTATATTTCTTTACAGAGGA 57.991 34.615 0.00 0.00 0.00 3.71
1449 3701 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1457 3709 9.099454 CCTTGAGTAAACGCTCTTATATTTCTT 57.901 33.333 0.00 0.00 36.51 2.52
1459 3711 8.421673 ACCTTGAGTAAACGCTCTTATATTTC 57.578 34.615 0.00 0.00 36.51 2.17
1475 3756 8.999905 AATTTTACCTTGGTTTACCTTGAGTA 57.000 30.769 0.00 0.00 36.82 2.59
1501 3782 7.702772 GTGAATCTCTTCGTGTAACATAGTCAT 59.297 37.037 0.00 0.00 35.74 3.06
1542 3823 5.541484 AGCCAGTGAATCCTCATTTTCTTTT 59.459 36.000 0.00 0.00 33.05 2.27
1543 3824 5.082425 AGCCAGTGAATCCTCATTTTCTTT 58.918 37.500 0.00 0.00 33.05 2.52
1551 3832 4.225942 ACATTTCTAGCCAGTGAATCCTCA 59.774 41.667 0.00 0.00 0.00 3.86
1563 3844 4.732784 TGCGAATTCAAACATTTCTAGCC 58.267 39.130 6.22 0.00 0.00 3.93
1585 3866 2.105821 TCCGAAGTTGACAAGTTCCCAT 59.894 45.455 23.78 0.00 37.51 4.00
1595 3876 5.231265 AGTGTTCTTTTTCCGAAGTTGAC 57.769 39.130 0.00 0.00 0.00 3.18
1619 3900 8.317891 TCTTTCGCTACAAAATCTGATTTACA 57.682 30.769 15.45 4.09 0.00 2.41
1622 3903 9.994432 CTTATCTTTCGCTACAAAATCTGATTT 57.006 29.630 9.76 9.76 0.00 2.17
1632 3913 4.927425 GGTGACACTTATCTTTCGCTACAA 59.073 41.667 5.39 0.00 0.00 2.41
1633 3914 4.491676 GGTGACACTTATCTTTCGCTACA 58.508 43.478 5.39 0.00 0.00 2.74
1639 3920 4.451629 TCTCCGGTGACACTTATCTTTC 57.548 45.455 0.00 0.00 0.00 2.62
1653 3934 3.256136 CACTAGTTGAGAGTTTCTCCGGT 59.744 47.826 0.00 0.00 42.73 5.28
1805 4086 3.357203 AGAGCACTAATCACGGAAGAGA 58.643 45.455 0.00 0.00 34.56 3.10
1806 4087 3.791973 AGAGCACTAATCACGGAAGAG 57.208 47.619 0.00 0.00 0.00 2.85
1807 4088 4.270834 AGTAGAGCACTAATCACGGAAGA 58.729 43.478 0.00 0.00 34.98 2.87
1808 4089 4.640789 AGTAGAGCACTAATCACGGAAG 57.359 45.455 0.00 0.00 34.98 3.46
1812 4093 4.106197 GGTGAAGTAGAGCACTAATCACG 58.894 47.826 21.28 0.00 42.35 4.35
1827 4108 9.965902 AAATCAAGATTCTGTATTAGGTGAAGT 57.034 29.630 0.00 0.00 0.00 3.01
1908 4190 1.749634 AGAGTTGGATTAGGTCGACGG 59.250 52.381 9.92 0.00 0.00 4.79
1935 4217 7.681939 TGTATATTGTTCCTTCTGTTGTTCC 57.318 36.000 0.00 0.00 0.00 3.62
1963 4245 3.248024 AGGATTTATATGCCGTCCAGGA 58.752 45.455 0.00 0.00 45.00 3.86
1964 4246 3.703001 AGGATTTATATGCCGTCCAGG 57.297 47.619 0.00 0.00 44.97 4.45
1965 4247 4.320494 GCAAAGGATTTATATGCCGTCCAG 60.320 45.833 0.00 0.00 35.03 3.86
1979 4261 5.070847 ACAAACTTCCAAGATGCAAAGGATT 59.929 36.000 0.00 0.00 0.00 3.01
1984 4266 4.998671 TCACAAACTTCCAAGATGCAAA 57.001 36.364 0.00 0.00 0.00 3.68
2023 4305 9.581099 GTAACAACCTGGAAATTTATGTATTGG 57.419 33.333 0.00 0.00 0.00 3.16
2036 4318 6.661805 ACTTTTTCTCTTGTAACAACCTGGAA 59.338 34.615 0.00 0.00 0.00 3.53
2075 4369 2.887152 AGCTGGTCACAAACTCCAAATC 59.113 45.455 0.00 0.00 0.00 2.17
2081 4375 3.340337 GTTTGAGCTGGTCACAAACTC 57.660 47.619 16.60 0.00 46.10 3.01
2099 4393 7.981225 GGATATTTGTGTATTGCTGATTTGGTT 59.019 33.333 0.00 0.00 0.00 3.67
2101 4395 7.490840 TGGATATTTGTGTATTGCTGATTTGG 58.509 34.615 0.00 0.00 0.00 3.28
2160 4494 8.754080 ACTACTATGAGCACTTTACAGAGAAAT 58.246 33.333 0.00 0.00 0.00 2.17
2170 4504 5.221641 TGTGTCCAACTACTATGAGCACTTT 60.222 40.000 0.00 0.00 0.00 2.66
2178 4512 7.905604 TGAGAAATTGTGTCCAACTACTATG 57.094 36.000 0.00 0.00 32.26 2.23
2196 4530 8.317891 TCGCACAAGTATAAAAGAATGAGAAA 57.682 30.769 0.00 0.00 0.00 2.52
2197 4531 7.899178 TCGCACAAGTATAAAAGAATGAGAA 57.101 32.000 0.00 0.00 0.00 2.87
2199 4533 8.390354 TGATTCGCACAAGTATAAAAGAATGAG 58.610 33.333 0.00 0.00 0.00 2.90
2200 4534 8.262715 TGATTCGCACAAGTATAAAAGAATGA 57.737 30.769 0.00 0.00 0.00 2.57
2201 4535 9.162793 GATGATTCGCACAAGTATAAAAGAATG 57.837 33.333 0.00 0.00 0.00 2.67
2202 4536 8.892723 TGATGATTCGCACAAGTATAAAAGAAT 58.107 29.630 0.00 0.00 0.00 2.40
2203 4537 8.262715 TGATGATTCGCACAAGTATAAAAGAA 57.737 30.769 0.00 0.00 0.00 2.52
2211 4545 4.627035 CAGACTTGATGATTCGCACAAGTA 59.373 41.667 16.76 0.00 42.94 2.24
2215 4549 3.044235 ACAGACTTGATGATTCGCACA 57.956 42.857 0.00 0.00 0.00 4.57
2217 4551 2.667969 CGAACAGACTTGATGATTCGCA 59.332 45.455 0.00 0.00 33.42 5.10
2219 4553 3.304559 GTCCGAACAGACTTGATGATTCG 59.695 47.826 0.00 0.00 38.84 3.34
2226 4560 3.733988 GCATATCGTCCGAACAGACTTGA 60.734 47.826 0.00 0.00 34.46 3.02
2227 4561 2.535984 GCATATCGTCCGAACAGACTTG 59.464 50.000 0.00 0.00 34.46 3.16
2235 4569 1.282817 CCGTTTGCATATCGTCCGAA 58.717 50.000 0.00 0.00 0.00 4.30
2237 4571 0.300491 CACCGTTTGCATATCGTCCG 59.700 55.000 0.00 0.00 0.00 4.79
2245 4579 3.791973 TTTTTCTGTCACCGTTTGCAT 57.208 38.095 0.00 0.00 0.00 3.96
2263 4597 6.345298 TCTTTTGGCCGAGAAAAATCTTTTT 58.655 32.000 0.00 0.43 42.60 1.94
2268 4602 4.766404 TCTCTTTTGGCCGAGAAAAATC 57.234 40.909 5.68 0.00 33.62 2.17
2274 4609 3.270877 GCTATTTCTCTTTTGGCCGAGA 58.729 45.455 4.14 4.14 34.66 4.04
2280 4615 5.768317 TCGGTTTTGCTATTTCTCTTTTGG 58.232 37.500 0.00 0.00 0.00 3.28
2282 4617 7.039313 AGTTCGGTTTTGCTATTTCTCTTTT 57.961 32.000 0.00 0.00 0.00 2.27
2284 4619 6.262273 TCAAGTTCGGTTTTGCTATTTCTCTT 59.738 34.615 0.00 0.00 0.00 2.85
2285 4620 5.763204 TCAAGTTCGGTTTTGCTATTTCTCT 59.237 36.000 0.00 0.00 0.00 3.10
2306 4641 5.217978 ACGTGGAACCAGTAATACTTCAA 57.782 39.130 0.00 0.00 0.00 2.69
2332 4668 7.505258 ACACCAAATAACCAGCAATACTTTTT 58.495 30.769 0.00 0.00 0.00 1.94
2341 4679 6.007076 TCTCATAAACACCAAATAACCAGCA 58.993 36.000 0.00 0.00 0.00 4.41
2355 4693 4.019411 TGTCCATCCTGCTTCTCATAAACA 60.019 41.667 0.00 0.00 0.00 2.83
2357 4695 4.842531 TGTCCATCCTGCTTCTCATAAA 57.157 40.909 0.00 0.00 0.00 1.40
2364 4702 2.492012 CTGCTATGTCCATCCTGCTTC 58.508 52.381 0.00 0.00 0.00 3.86
2365 4703 1.142465 CCTGCTATGTCCATCCTGCTT 59.858 52.381 0.00 0.00 0.00 3.91
2399 4745 5.258051 GTGGGTTTGAAAGTCCACCATATA 58.742 41.667 15.40 0.00 42.66 0.86
2400 4746 4.086457 GTGGGTTTGAAAGTCCACCATAT 58.914 43.478 15.40 0.00 42.66 1.78
2401 4747 3.492337 GTGGGTTTGAAAGTCCACCATA 58.508 45.455 15.40 0.00 42.66 2.74
2402 4748 2.316108 GTGGGTTTGAAAGTCCACCAT 58.684 47.619 15.40 0.00 42.66 3.55
2437 4783 8.976986 AAGATGATGCTTTTCAACTAACAATC 57.023 30.769 0.00 0.00 29.62 2.67
2509 4858 6.261603 CGGAATATAGTTGGTTAGGGGTTTTC 59.738 42.308 0.00 0.00 0.00 2.29
2517 4866 4.211374 GTGCTGCGGAATATAGTTGGTTAG 59.789 45.833 0.00 0.00 0.00 2.34
2534 4883 0.664761 TTCTTGCTGAACTGTGCTGC 59.335 50.000 10.46 10.46 0.00 5.25
2550 4908 3.014623 TCGATGTCTACGGTGATGTTCT 58.985 45.455 0.00 0.00 0.00 3.01
2551 4909 3.416119 TCGATGTCTACGGTGATGTTC 57.584 47.619 0.00 0.00 0.00 3.18
2552 4910 4.820173 TCTATCGATGTCTACGGTGATGTT 59.180 41.667 8.54 0.00 0.00 2.71
2588 4946 0.179702 TGGATGGATGTCAGCAGCTC 59.820 55.000 0.00 0.00 32.50 4.09
2651 5009 2.899976 TCTGCAAAGTCTTGTCAACGA 58.100 42.857 0.00 0.00 34.79 3.85
2683 5043 7.149973 CCATAGAGCATTATTGGTTCATTTGG 58.850 38.462 0.00 0.00 32.62 3.28
2719 5079 3.620374 AGCACTTCAGATAAGAACATGCG 59.380 43.478 0.00 0.00 38.56 4.73
2802 5183 8.970859 AGCTTGCAAATCTTGTAGAATACTAT 57.029 30.769 0.00 0.00 43.54 2.12
2812 5193 5.649395 TCTGCTAATAGCTTGCAAATCTTGT 59.351 36.000 13.88 0.00 42.97 3.16
2828 5209 8.375608 CACTAATCAGTGCTAATTCTGCTAAT 57.624 34.615 5.21 0.00 45.44 1.73
2867 5249 0.666913 CTCCACATATGCCTGCAAGC 59.333 55.000 1.58 0.00 0.00 4.01
2990 5372 5.048991 GTGAAAACGTCTTACATTGTGGGAT 60.049 40.000 0.00 0.00 0.00 3.85
2995 5377 5.065988 AGCTTGTGAAAACGTCTTACATTGT 59.934 36.000 0.00 0.00 0.00 2.71
2996 5378 5.510671 AGCTTGTGAAAACGTCTTACATTG 58.489 37.500 0.00 0.00 0.00 2.82
2997 5379 5.751243 AGCTTGTGAAAACGTCTTACATT 57.249 34.783 0.00 0.00 0.00 2.71
2998 5380 5.756347 TGTAGCTTGTGAAAACGTCTTACAT 59.244 36.000 0.00 0.00 0.00 2.29
2999 5381 5.110598 TGTAGCTTGTGAAAACGTCTTACA 58.889 37.500 0.00 0.00 0.00 2.41
3000 5382 5.646467 TGTAGCTTGTGAAAACGTCTTAC 57.354 39.130 0.00 0.00 0.00 2.34
3001 5383 6.655062 CAATGTAGCTTGTGAAAACGTCTTA 58.345 36.000 0.00 0.00 0.00 2.10
3004 5386 3.664025 GCAATGTAGCTTGTGAAAACGTC 59.336 43.478 0.00 0.00 0.00 4.34
3005 5387 3.628017 GCAATGTAGCTTGTGAAAACGT 58.372 40.909 0.00 0.00 0.00 3.99
3006 5388 2.651703 CGCAATGTAGCTTGTGAAAACG 59.348 45.455 0.00 0.00 38.60 3.60
3007 5389 2.979813 CCGCAATGTAGCTTGTGAAAAC 59.020 45.455 0.00 0.00 38.60 2.43
3010 5392 1.164411 CCCGCAATGTAGCTTGTGAA 58.836 50.000 0.00 0.00 38.60 3.18
3011 5393 0.323302 TCCCGCAATGTAGCTTGTGA 59.677 50.000 0.00 0.00 38.60 3.58
3012 5394 0.447801 GTCCCGCAATGTAGCTTGTG 59.552 55.000 0.00 0.00 36.59 3.33
3013 5395 1.019278 CGTCCCGCAATGTAGCTTGT 61.019 55.000 0.00 0.00 0.00 3.16
3014 5396 1.705337 CCGTCCCGCAATGTAGCTTG 61.705 60.000 0.00 0.00 0.00 4.01
3015 5397 1.449601 CCGTCCCGCAATGTAGCTT 60.450 57.895 0.00 0.00 0.00 3.74
3016 5398 2.186903 CCGTCCCGCAATGTAGCT 59.813 61.111 0.00 0.00 0.00 3.32
3017 5399 1.883084 CTCCGTCCCGCAATGTAGC 60.883 63.158 0.00 0.00 0.00 3.58
3018 5400 1.227263 CCTCCGTCCCGCAATGTAG 60.227 63.158 0.00 0.00 0.00 2.74
3019 5401 2.727392 CCCTCCGTCCCGCAATGTA 61.727 63.158 0.00 0.00 0.00 2.29
3020 5402 4.096003 CCCTCCGTCCCGCAATGT 62.096 66.667 0.00 0.00 0.00 2.71
3021 5403 3.740128 CTCCCTCCGTCCCGCAATG 62.740 68.421 0.00 0.00 0.00 2.82
3022 5404 2.866523 TACTCCCTCCGTCCCGCAAT 62.867 60.000 0.00 0.00 0.00 3.56
3023 5405 3.588817 TACTCCCTCCGTCCCGCAA 62.589 63.158 0.00 0.00 0.00 4.85
3024 5406 4.051167 TACTCCCTCCGTCCCGCA 62.051 66.667 0.00 0.00 0.00 5.69
3025 5407 3.217743 CTACTCCCTCCGTCCCGC 61.218 72.222 0.00 0.00 0.00 6.13
3026 5408 0.107017 TAACTACTCCCTCCGTCCCG 60.107 60.000 0.00 0.00 0.00 5.14
3033 5415 6.070710 AGTGTCCAGAAATTAACTACTCCCTC 60.071 42.308 0.00 0.00 0.00 4.30
3037 5419 5.351740 GGCAGTGTCCAGAAATTAACTACTC 59.648 44.000 0.00 0.00 0.00 2.59
3083 5467 5.235850 TGCACAGGTGAGGTAATTTTCTA 57.764 39.130 3.10 0.00 0.00 2.10
3085 5469 4.278419 AGTTGCACAGGTGAGGTAATTTTC 59.722 41.667 3.10 0.00 0.00 2.29
3100 5484 4.883585 AGAAGATCACTTTTGAGTTGCACA 59.116 37.500 0.00 0.00 36.39 4.57
3113 5497 3.439154 TGAGAAGCAGGAGAAGATCACT 58.561 45.455 0.00 0.00 0.00 3.41
3125 5509 7.169645 GTCTCTAAGCAGATAAATGAGAAGCAG 59.830 40.741 0.00 0.00 32.05 4.24
3178 5562 5.176223 GCATTTGGATGTAATATGTTGCAGC 59.824 40.000 0.00 0.00 35.90 5.25
3230 5679 6.715280 AGTGTGGTCAGATTACAGAATCAAT 58.285 36.000 0.87 0.00 43.51 2.57
3261 5710 5.468072 CCGATCAGATTACAGAATCAAAGGG 59.532 44.000 0.00 0.00 43.51 3.95
3314 5763 3.635268 GAGCTCTTGGTGGGCAGGG 62.635 68.421 6.43 0.00 0.00 4.45
3340 5789 0.763223 AACTGGGTGGACGAGGTTCT 60.763 55.000 0.00 0.00 0.00 3.01
3348 5797 1.545651 CCCTTTCAGAACTGGGTGGAC 60.546 57.143 10.88 0.00 35.13 4.02
3395 5844 3.641437 TGTACTGCCAAAATGCACTTC 57.359 42.857 0.00 0.00 36.04 3.01
3399 5848 5.931146 CCTAAATTTGTACTGCCAAAATGCA 59.069 36.000 0.00 0.00 37.81 3.96
3445 5894 5.353123 ACACACACACTGTAGACGAAATTTT 59.647 36.000 0.00 0.00 0.00 1.82
3447 5896 4.439057 ACACACACACTGTAGACGAAATT 58.561 39.130 0.00 0.00 0.00 1.82
3471 5926 6.419484 TTGGATCGATCATGTACATAGGTT 57.581 37.500 25.93 0.00 0.00 3.50
3705 6163 3.464828 ACTCCATGGGTCAGGACTTATT 58.535 45.455 13.02 0.00 0.00 1.40
3800 6258 7.199766 AGCAATAAAATTCTTCAAACGTGACA 58.800 30.769 0.00 0.00 31.90 3.58
3915 6384 1.872952 CGAGTGAAATGCAGTTGTCCA 59.127 47.619 3.09 0.00 0.00 4.02
3929 6398 8.717821 CAACTAAAGAAAATGTTATCCGAGTGA 58.282 33.333 0.00 0.00 0.00 3.41
3952 6421 6.380095 TGTACCATTTAACAACTGTCCAAC 57.620 37.500 0.00 0.00 0.00 3.77
4049 6521 3.743899 GCCATTCAGAGAGTCCTTCCATC 60.744 52.174 0.00 0.00 0.00 3.51
4057 6529 5.212532 ACATGATAGCCATTCAGAGAGTC 57.787 43.478 0.00 0.00 31.94 3.36
4127 6599 2.683768 AGTCCTTCCTTCCGCTATCAT 58.316 47.619 0.00 0.00 0.00 2.45
4153 6625 7.018826 TGCTCTATTTGTTAATTGTTACGTGC 58.981 34.615 0.00 0.00 0.00 5.34
4190 6662 2.027192 ACAATACTGAATGAGGCGGTGT 60.027 45.455 0.00 0.00 0.00 4.16
4204 6676 9.667107 TTAAAGATGATCTCCGAAAACAATACT 57.333 29.630 0.00 0.00 0.00 2.12
4215 6687 9.708222 CAGTAACAAATTTAAAGATGATCTCCG 57.292 33.333 0.00 0.00 0.00 4.63
4228 6701 9.469807 CTGTGCCAATAAACAGTAACAAATTTA 57.530 29.630 0.00 0.00 39.17 1.40
4235 6708 6.067263 TGTTCTGTGCCAATAAACAGTAAC 57.933 37.500 3.01 6.85 43.49 2.50
4271 6744 0.178981 ACAAGGTGTGAAGCATGGCT 60.179 50.000 0.00 0.00 42.56 4.75
4310 6783 5.466728 TCTGATGCTCAACAAGAAAGTACAC 59.533 40.000 0.00 0.00 0.00 2.90
4312 6785 6.545504 TTCTGATGCTCAACAAGAAAGTAC 57.454 37.500 0.00 0.00 0.00 2.73
4328 6801 3.588955 TCAGTCGTCACCATTTCTGATG 58.411 45.455 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.