Multiple sequence alignment - TraesCS3B01G566600

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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 TraesCS3B01G566600 chr3B 100.000 7218 0 0 1 7218 798468374 798461157 0.000000e+00 13330
1 TraesCS3B01G566600 chr3B 99.307 722 4 1 1 721 785286556 785287277 0.000000e+00 1304
2 TraesCS3B01G566600 chr3D 94.595 3441 116 23 2450 5850 595024161 595020751 0.000000e+00 5260
3 TraesCS3B01G566600 chr3D 87.596 1306 92 33 5962 7218 595020490 595019206 0.000000e+00 1450
4 TraesCS3B01G566600 chr3D 86.766 869 68 18 1615 2449 595024975 595024120 0.000000e+00 924
5 TraesCS3B01G566600 chr3D 86.406 434 26 15 725 1138 595026434 595026014 1.850000e-120 444
6 TraesCS3B01G566600 chr3D 86.498 237 20 8 1142 1366 595025895 595025659 4.320000e-62 250
7 TraesCS3B01G566600 chr3A 94.685 3029 109 20 2977 5968 726024519 726021506 0.000000e+00 4654
8 TraesCS3B01G566600 chr3A 98.632 731 9 1 1 730 668571202 668571932 0.000000e+00 1293
9 TraesCS3B01G566600 chr3A 88.583 981 70 19 5962 6913 726021390 726020423 0.000000e+00 1153
10 TraesCS3B01G566600 chr3A 92.011 751 40 10 1711 2449 726025931 726025189 0.000000e+00 1037
11 TraesCS3B01G566600 chr3A 96.442 534 12 4 2450 2978 726025232 726024701 0.000000e+00 874
12 TraesCS3B01G566600 chr3A 88.481 599 36 16 859 1427 726026847 726026252 0.000000e+00 693
13 TraesCS3B01G566600 chr3A 80.062 321 45 15 6911 7218 726020300 726019986 3.390000e-53 220
14 TraesCS3B01G566600 chr2B 99.308 723 4 1 1 722 224844392 224845114 0.000000e+00 1306
15 TraesCS3B01G566600 chr2A 99.170 723 5 1 1 722 177952899 177953621 0.000000e+00 1301
16 TraesCS3B01G566600 chr7A 99.169 722 5 1 1 721 43553448 43554169 0.000000e+00 1299
17 TraesCS3B01G566600 chr5B 99.169 722 5 1 1 721 32474643 32473922 0.000000e+00 1299
18 TraesCS3B01G566600 chr5B 80.610 459 63 15 3143 3584 277236248 277236697 1.500000e-86 331
19 TraesCS3B01G566600 chr5B 85.317 252 28 8 5392 5640 56189757 56189512 1.200000e-62 252
20 TraesCS3B01G566600 chr1B 98.769 731 8 1 1 730 467198470 467199200 0.000000e+00 1299
21 TraesCS3B01G566600 chr7B 98.767 730 8 1 1 729 148297576 148296847 0.000000e+00 1297
22 TraesCS3B01G566600 chr7B 80.200 500 70 15 3111 3584 583166591 583166095 1.490000e-91 348
23 TraesCS3B01G566600 chr6A 99.033 724 6 1 1 723 560643651 560642928 0.000000e+00 1297


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 TraesCS3B01G566600 chr3B 798461157 798468374 7217 True 13330.0 13330 100.0000 1 7218 1 chr3B.!!$R1 7217
1 TraesCS3B01G566600 chr3B 785286556 785287277 721 False 1304.0 1304 99.3070 1 721 1 chr3B.!!$F1 720
2 TraesCS3B01G566600 chr3D 595019206 595026434 7228 True 1665.6 5260 88.3722 725 7218 5 chr3D.!!$R1 6493
3 TraesCS3B01G566600 chr3A 726019986 726026847 6861 True 1438.5 4654 90.0440 859 7218 6 chr3A.!!$R1 6359
4 TraesCS3B01G566600 chr3A 668571202 668571932 730 False 1293.0 1293 98.6320 1 730 1 chr3A.!!$F1 729
5 TraesCS3B01G566600 chr2B 224844392 224845114 722 False 1306.0 1306 99.3080 1 722 1 chr2B.!!$F1 721
6 TraesCS3B01G566600 chr2A 177952899 177953621 722 False 1301.0 1301 99.1700 1 722 1 chr2A.!!$F1 721
7 TraesCS3B01G566600 chr7A 43553448 43554169 721 False 1299.0 1299 99.1690 1 721 1 chr7A.!!$F1 720
8 TraesCS3B01G566600 chr5B 32473922 32474643 721 True 1299.0 1299 99.1690 1 721 1 chr5B.!!$R1 720
9 TraesCS3B01G566600 chr1B 467198470 467199200 730 False 1299.0 1299 98.7690 1 730 1 chr1B.!!$F1 729
10 TraesCS3B01G566600 chr7B 148296847 148297576 729 True 1297.0 1297 98.7670 1 729 1 chr7B.!!$R1 728
11 TraesCS3B01G566600 chr6A 560642928 560643651 723 True 1297.0 1297 99.0330 1 723 1 chr6A.!!$R1 722

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
774 776 0.179056 CTGTCTCAAACACGGTGGGT 60.179 55.000 13.48 0.0 33.24 4.51 F
784 786 0.383949 CACGGTGGGTGTTTTTGAGG 59.616 55.000 0.00 0.0 41.89 3.86 F
1446 1882 0.503961 GTTGAACAATGTGCAAGCGC 59.496 50.000 7.11 0.0 30.95 5.92 F
1895 2502 0.423956 TCTCCTTGGGGATGGGGTTA 59.576 55.000 0.00 0.0 41.36 2.85 F
1906 2513 1.494721 GATGGGGTTATGGGCTGAGAA 59.505 52.381 0.00 0.0 0.00 2.87 F
3335 4164 1.927174 CCGATCACAGTCCGAAACATC 59.073 52.381 0.00 0.0 0.00 3.06 F
4313 5145 0.912487 TGGGTCCAGGGTCCACATAC 60.912 60.000 4.04 0.0 0.00 2.39 F
5237 6089 0.179127 TCATAGCACGACAGCAGAGC 60.179 55.000 0.00 0.0 36.85 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 2486 0.188342 CCATAACCCCATCCCCAAGG 59.812 60.000 0.00 0.00 0.00 3.61 R
1884 2491 1.153756 CAGCCCATAACCCCATCCC 59.846 63.158 0.00 0.00 0.00 3.85 R
3335 4164 5.694816 TCTGCAACAAACAAATATACGGTG 58.305 37.500 0.00 0.00 0.00 4.94 R
3844 4676 3.554934 TGTCCTGAAATGGGCATATCAC 58.445 45.455 0.00 0.00 36.71 3.06 R
3878 4710 6.836242 AGATTAGGATCCAGAAAATCAGGTC 58.164 40.000 15.82 0.72 32.44 3.85 R
4397 5235 0.549950 CTGATGCAGTCCTTGGGGAT 59.450 55.000 0.00 0.00 44.33 3.85 R
6106 7130 0.710567 CTTGCTGTCGCTTGTACTCG 59.289 55.000 0.00 0.00 36.97 4.18 R
6854 7919 0.035152 TTACTGATGGTGCCTGCCTG 60.035 55.000 0.00 0.00 0.00 4.85 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
723 725 2.936498 CACGGTCCCTTTTGCTAGTATG 59.064 50.000 0.00 0.00 0.00 2.39
774 776 0.179056 CTGTCTCAAACACGGTGGGT 60.179 55.000 13.48 0.00 33.24 4.51
784 786 0.383949 CACGGTGGGTGTTTTTGAGG 59.616 55.000 0.00 0.00 41.89 3.86
794 796 4.022849 GGGTGTTTTTGAGGATCTTCACAG 60.023 45.833 7.09 0.00 34.92 3.66
812 814 4.530553 TCACAGAGTGGTTATGTGGTATGT 59.469 41.667 4.86 0.00 43.54 2.29
821 823 4.394920 GGTTATGTGGTATGTGGTGACTTG 59.605 45.833 0.00 0.00 0.00 3.16
829 837 6.017934 GTGGTATGTGGTGACTTGCTATAATG 60.018 42.308 0.00 0.00 0.00 1.90
883 899 6.043706 AGGATGAATTTACTAGACTCCCATGG 59.956 42.308 4.14 4.14 0.00 3.66
907 923 3.575805 TGAGGGTCCTTTTTGCAAGATT 58.424 40.909 0.00 0.00 0.00 2.40
971 987 2.202905 GCAGAGCAGAGCGCAGAT 60.203 61.111 11.47 0.00 46.13 2.90
1155 1292 2.284995 ACAGGAGGAGGGCTGGAC 60.285 66.667 0.00 0.00 0.00 4.02
1304 1441 1.977544 AGGTCTGCTCCGTTACGCT 60.978 57.895 0.00 0.00 0.00 5.07
1305 1442 1.516603 GGTCTGCTCCGTTACGCTC 60.517 63.158 0.00 0.00 0.00 5.03
1306 1443 1.516603 GTCTGCTCCGTTACGCTCC 60.517 63.158 0.00 0.00 0.00 4.70
1307 1444 1.677966 TCTGCTCCGTTACGCTCCT 60.678 57.895 0.00 0.00 0.00 3.69
1317 1464 2.476519 CGTTACGCTCCTCTTCTCAGTC 60.477 54.545 0.00 0.00 0.00 3.51
1327 1474 6.390048 TCCTCTTCTCAGTCTAGGTTTCTA 57.610 41.667 0.00 0.00 0.00 2.10
1332 1479 6.655848 TCTTCTCAGTCTAGGTTTCTACAGTC 59.344 42.308 0.00 0.00 0.00 3.51
1345 1492 2.647529 TACAGTCGTGTAGTGGCATG 57.352 50.000 0.00 0.00 38.19 4.06
1370 1565 4.381292 CCTTTTGGTTGGCAAATTTGCAAA 60.381 37.500 36.60 31.48 44.42 3.68
1392 1587 3.273434 TGAGCTCATGTGCTAAATGGAC 58.727 45.455 21.47 8.56 44.17 4.02
1397 1592 3.879295 CTCATGTGCTAAATGGACGGATT 59.121 43.478 0.00 0.00 40.08 3.01
1411 1606 1.821332 GGATTCGAGCAAGCCAGGG 60.821 63.158 0.00 0.00 40.68 4.45
1422 1617 2.360165 GCAAGCCAGGGATAATGTTCAG 59.640 50.000 0.00 0.00 0.00 3.02
1443 1879 1.411977 TGGGGTTGAACAATGTGCAAG 59.588 47.619 7.11 0.00 30.95 4.01
1444 1880 1.501169 GGGTTGAACAATGTGCAAGC 58.499 50.000 24.01 24.01 45.65 4.01
1445 1881 1.130955 GGTTGAACAATGTGCAAGCG 58.869 50.000 19.02 0.00 39.32 4.68
1446 1882 0.503961 GTTGAACAATGTGCAAGCGC 59.496 50.000 7.11 0.00 30.95 5.92
1488 1924 2.357396 TGTAGGCTGCAGCACACG 60.357 61.111 37.63 1.95 44.36 4.49
1494 1930 3.357079 CTGCAGCACACGGGTTCC 61.357 66.667 0.00 0.00 0.00 3.62
1518 1954 5.751028 CGTTACAAATTTTGATGTTGGTGGT 59.249 36.000 15.81 0.00 0.00 4.16
1519 1955 6.918569 CGTTACAAATTTTGATGTTGGTGGTA 59.081 34.615 15.81 0.00 0.00 3.25
1520 1956 7.596995 CGTTACAAATTTTGATGTTGGTGGTAT 59.403 33.333 15.81 0.00 0.00 2.73
1521 1957 8.921670 GTTACAAATTTTGATGTTGGTGGTATC 58.078 33.333 15.81 0.00 0.00 2.24
1522 1958 7.301868 ACAAATTTTGATGTTGGTGGTATCT 57.698 32.000 15.81 0.00 0.00 1.98
1523 1959 7.153985 ACAAATTTTGATGTTGGTGGTATCTG 58.846 34.615 15.81 0.00 0.00 2.90
1524 1960 7.015098 ACAAATTTTGATGTTGGTGGTATCTGA 59.985 33.333 15.81 0.00 0.00 3.27
1525 1961 7.722949 AATTTTGATGTTGGTGGTATCTGAT 57.277 32.000 0.00 0.00 0.00 2.90
1526 1962 6.757897 TTTTGATGTTGGTGGTATCTGATC 57.242 37.500 0.00 0.00 0.00 2.92
1533 1969 1.202818 GGTGGTATCTGATCCAAGGGC 60.203 57.143 9.44 0.63 35.38 5.19
1534 1970 1.771255 GTGGTATCTGATCCAAGGGCT 59.229 52.381 9.44 0.00 35.38 5.19
1535 1971 2.972713 GTGGTATCTGATCCAAGGGCTA 59.027 50.000 9.44 0.00 35.38 3.93
1536 1972 3.007398 GTGGTATCTGATCCAAGGGCTAG 59.993 52.174 9.44 0.00 35.38 3.42
1537 1973 3.116746 TGGTATCTGATCCAAGGGCTAGA 60.117 47.826 0.00 0.00 0.00 2.43
1551 1987 6.550108 CCAAGGGCTAGACTAGATAACTACAA 59.450 42.308 13.91 0.00 0.00 2.41
1558 1994 9.724839 GCTAGACTAGATAACTACAAAAGACAG 57.275 37.037 13.91 0.00 0.00 3.51
1582 2018 5.523369 AGCTGTTTGAATTTGCAGTAGAAC 58.477 37.500 0.00 0.00 0.00 3.01
1591 2027 2.060326 TGCAGTAGAACGGAACTTCG 57.940 50.000 0.00 0.00 0.00 3.79
1598 2034 4.643784 AGTAGAACGGAACTTCGATATGGT 59.356 41.667 0.00 0.00 0.00 3.55
1599 2035 4.467198 AGAACGGAACTTCGATATGGTT 57.533 40.909 0.00 0.00 0.00 3.67
1613 2049 6.092092 TCGATATGGTTGTTGCAAATTTCTG 58.908 36.000 0.00 0.00 0.00 3.02
1619 2215 4.152223 GGTTGTTGCAAATTTCTGTATGCC 59.848 41.667 0.00 0.00 38.00 4.40
1637 2233 4.844349 TGCCATAAAGAGCTAAGGAAGT 57.156 40.909 0.00 0.00 0.00 3.01
1668 2264 2.805099 CAAGGAGCTGTCTGTCAGTTTC 59.195 50.000 0.00 0.00 45.23 2.78
1680 2276 1.136336 GTCAGTTTCGCGACATTCCAC 60.136 52.381 9.15 0.00 32.24 4.02
1746 2353 5.630415 TTATACAGCCTTGTAATCCAGCT 57.370 39.130 0.00 0.00 42.72 4.24
1749 2356 2.440409 CAGCCTTGTAATCCAGCTGTT 58.560 47.619 13.81 3.71 44.59 3.16
1797 2404 1.492176 CATGAGGTAGATGCCCTTGGT 59.508 52.381 0.00 0.00 30.60 3.67
1860 2467 5.641709 TCTGCTCTTGTTTATACAGACGAG 58.358 41.667 0.00 5.56 35.28 4.18
1865 2472 6.020281 GCTCTTGTTTATACAGACGAGTCATG 60.020 42.308 5.99 4.04 35.28 3.07
1895 2502 0.423956 TCTCCTTGGGGATGGGGTTA 59.576 55.000 0.00 0.00 41.36 2.85
1906 2513 1.494721 GATGGGGTTATGGGCTGAGAA 59.505 52.381 0.00 0.00 0.00 2.87
1932 2539 3.591196 TGCAATGCTACCAAATCAACC 57.409 42.857 6.82 0.00 0.00 3.77
2183 2797 7.328737 ACAATGTAAGTCGTTAGTGCTAAAGAG 59.671 37.037 7.62 0.00 35.00 2.85
2218 2836 6.566079 TTGGTGGTCTCTCATCTAAATCAT 57.434 37.500 0.00 0.00 0.00 2.45
2336 2961 4.058817 GTGTTACTCCTGACCAAAGACTG 58.941 47.826 0.00 0.00 0.00 3.51
2338 2963 4.897076 TGTTACTCCTGACCAAAGACTGTA 59.103 41.667 0.00 0.00 0.00 2.74
2339 2964 5.010719 TGTTACTCCTGACCAAAGACTGTAG 59.989 44.000 0.00 0.00 0.00 2.74
2340 2965 2.900546 ACTCCTGACCAAAGACTGTAGG 59.099 50.000 0.00 0.00 0.00 3.18
2414 3054 3.766051 AGGTGAATGCAGATTTTTCTCCC 59.234 43.478 12.30 6.40 34.90 4.30
2423 3063 6.957631 TGCAGATTTTTCTCCCTATCAACTA 58.042 36.000 0.00 0.00 0.00 2.24
2448 3088 5.823861 AAAAACCCAATGTGAAGGCTATT 57.176 34.783 0.00 0.00 0.00 1.73
2449 3089 5.823861 AAAACCCAATGTGAAGGCTATTT 57.176 34.783 0.00 0.00 0.00 1.40
2450 3090 5.823861 AAACCCAATGTGAAGGCTATTTT 57.176 34.783 0.00 0.00 0.00 1.82
2451 3091 5.823861 AACCCAATGTGAAGGCTATTTTT 57.176 34.783 0.00 0.00 0.00 1.94
2939 3584 8.268850 AGGTGTGTAGAACATGTGAAATATTC 57.731 34.615 0.00 0.00 41.97 1.75
3080 3908 2.049228 ACGCGAACTACAAAAGAGACG 58.951 47.619 15.93 0.00 0.00 4.18
3216 4044 6.593770 ACATTTTTGGTCTTTGACTTTGTTCC 59.406 34.615 0.00 0.00 32.47 3.62
3335 4164 1.927174 CCGATCACAGTCCGAAACATC 59.073 52.381 0.00 0.00 0.00 3.06
3571 4403 9.229784 GATATTTTCTGCATCATTGTGTTACTG 57.770 33.333 0.00 0.00 0.00 2.74
3844 4676 2.606308 GCTCAGGTGTGTTCATTGCTTG 60.606 50.000 0.00 0.00 0.00 4.01
3878 4710 7.436118 CCATTTCAGGACATATGGTTAATTGG 58.564 38.462 7.80 6.42 34.23 3.16
4257 5089 3.530535 GTTTGCCACTCAATTTGTTGGT 58.469 40.909 16.26 4.85 34.12 3.67
4305 5137 2.770904 AACACGTGGGTCCAGGGT 60.771 61.111 21.57 6.39 36.28 4.34
4312 5144 1.476631 TGGGTCCAGGGTCCACATA 59.523 57.895 4.04 0.00 0.00 2.29
4313 5145 0.912487 TGGGTCCAGGGTCCACATAC 60.912 60.000 4.04 0.00 0.00 2.39
4370 5208 5.222631 CAAGGAATGTAGTGGCAAGTTTTC 58.777 41.667 0.00 0.00 0.00 2.29
4400 5238 9.950496 ACCATAGAGTAACAATCATGATTATCC 57.050 33.333 20.32 9.06 0.00 2.59
4477 5315 4.123506 TGTCACAAAACTATGCTCGAACA 58.876 39.130 0.00 0.00 0.00 3.18
4484 5322 7.589587 CACAAAACTATGCTCGAACAATGTTAA 59.410 33.333 0.00 0.00 0.00 2.01
4617 5464 6.898041 TGCTGTGATGTTTTATGTTGTCTAC 58.102 36.000 0.00 0.00 0.00 2.59
4811 5660 7.875554 GGGAGAGAGATTGGTTTAATAGATGAC 59.124 40.741 0.00 0.00 0.00 3.06
4889 5738 6.573434 ACGATTGAAGCATACAAGAGTATCA 58.427 36.000 0.00 0.00 38.88 2.15
4921 5770 7.117812 GCTTTATATACTTCCGAAGCTGCATTA 59.882 37.037 8.11 0.00 37.21 1.90
5033 5885 2.432444 TCAAGTATTCCGTTTGCAGGG 58.568 47.619 0.00 0.00 0.00 4.45
5048 5900 0.680618 CAGGGGTTGAATTTGCTGCA 59.319 50.000 0.00 0.00 0.00 4.41
5057 5909 4.503741 TGAATTTGCTGCAGAAGTTACC 57.496 40.909 20.43 0.00 0.00 2.85
5102 5954 1.651138 GAGTCATCGACACTTGAAGCG 59.349 52.381 0.53 0.00 34.60 4.68
5150 6002 1.166531 AACTTCTGGACAAGCACGGC 61.167 55.000 0.00 0.00 0.00 5.68
5237 6089 0.179127 TCATAGCACGACAGCAGAGC 60.179 55.000 0.00 0.00 36.85 4.09
5285 6137 6.462552 TGGTCATGTCATTTTGTTCTGAAA 57.537 33.333 0.00 0.00 0.00 2.69
5314 6166 3.181445 TGCAAGGGAGCTTCTTTCAAGTA 60.181 43.478 0.00 0.00 34.99 2.24
5357 6209 2.479566 TTAAGAAGCCTGGCAGTGAG 57.520 50.000 22.65 0.00 0.00 3.51
5358 6210 1.644509 TAAGAAGCCTGGCAGTGAGA 58.355 50.000 22.65 0.00 0.00 3.27
5459 6321 2.305343 AGCTGATTCTGTGCCTTTCTCT 59.695 45.455 0.00 0.00 0.00 3.10
5475 6337 9.077885 TGCCTTTCTCTGTTGTAATAAAGAATT 57.922 29.630 0.00 0.00 0.00 2.17
5476 6338 9.346725 GCCTTTCTCTGTTGTAATAAAGAATTG 57.653 33.333 0.00 0.00 0.00 2.32
5487 6349 8.271312 TGTAATAAAGAATTGTCGGGGTTTAG 57.729 34.615 0.00 0.00 0.00 1.85
5600 6467 2.132686 ACCTGCCGACCCCTAATAATT 58.867 47.619 0.00 0.00 0.00 1.40
5786 6653 8.950208 AGAATATGTTCAAGAGCCTTACTTAC 57.050 34.615 4.92 0.00 36.79 2.34
5787 6654 8.540388 AGAATATGTTCAAGAGCCTTACTTACA 58.460 33.333 4.92 0.00 36.79 2.41
5788 6655 8.494016 AATATGTTCAAGAGCCTTACTTACAC 57.506 34.615 0.00 0.00 0.00 2.90
5889 6792 7.013178 TGCACTTCAGTCTTTTGTGATAAATCA 59.987 33.333 0.00 0.00 0.00 2.57
5921 6824 5.365619 GGAATCTTAAGATGCCGTCCTTTA 58.634 41.667 24.17 0.00 40.28 1.85
5923 6826 7.159372 GGAATCTTAAGATGCCGTCCTTTATA 58.841 38.462 24.17 0.00 40.28 0.98
5950 6853 5.047519 CCAACATTTCCTCAAGATTTCAGCT 60.048 40.000 0.00 0.00 0.00 4.24
5952 6855 4.394300 ACATTTCCTCAAGATTTCAGCTCG 59.606 41.667 0.00 0.00 0.00 5.03
5968 6992 3.126514 CAGCTCGACAAATTTGATCTGCT 59.873 43.478 24.64 21.35 0.00 4.24
6288 7318 5.584649 CCCTATCAATAGAAGTTGCGTTTCA 59.415 40.000 0.00 0.00 32.05 2.69
6289 7319 6.260936 CCCTATCAATAGAAGTTGCGTTTCAT 59.739 38.462 0.00 0.00 32.05 2.57
6295 7325 1.815817 AAGTTGCGTTTCATGGGGCC 61.816 55.000 0.00 0.00 0.00 5.80
6318 7357 1.452399 GACGAAATAGAATCTCGCGGC 59.548 52.381 6.13 0.00 36.03 6.53
6321 7360 1.452399 GAAATAGAATCTCGCGGCGAC 59.548 52.381 22.69 11.89 0.00 5.19
6391 7431 4.152647 TGCTATACCTGGACATCTACCTG 58.847 47.826 0.00 0.00 0.00 4.00
6465 7506 0.737219 GCATGTGGATGACTGAAGCC 59.263 55.000 0.00 0.00 0.00 4.35
6472 7513 4.019411 TGTGGATGACTGAAGCCTATTTGA 60.019 41.667 0.00 0.00 0.00 2.69
6473 7514 4.574013 GTGGATGACTGAAGCCTATTTGAG 59.426 45.833 0.00 0.00 0.00 3.02
6507 7548 0.473501 GAGGAGGCCATGGAGGATCT 60.474 60.000 18.40 5.31 41.22 2.75
6524 7573 2.047655 TGTTGCGCTTAGGGGTCG 60.048 61.111 9.73 0.00 0.00 4.79
6536 7585 1.683365 GGGGTCGGTAGTAGGCACA 60.683 63.158 0.00 0.00 0.00 4.57
6539 7588 1.405121 GGGTCGGTAGTAGGCACAAAG 60.405 57.143 0.00 0.00 0.00 2.77
6544 7594 3.577848 TCGGTAGTAGGCACAAAGGTAAA 59.422 43.478 0.00 0.00 0.00 2.01
6550 7600 7.176165 GGTAGTAGGCACAAAGGTAAAGAAAAT 59.824 37.037 0.00 0.00 0.00 1.82
6580 7630 1.291184 TGAACCGATGCTCGCTGTTG 61.291 55.000 0.72 0.00 38.82 3.33
6640 7690 3.640029 CCTGGAATAATGCAATGAAGCCT 59.360 43.478 0.00 0.00 0.00 4.58
6677 7727 4.228210 TCAAGGGAGCTGTCATTAGGATTT 59.772 41.667 0.00 0.00 0.00 2.17
6686 7736 8.723942 AGCTGTCATTAGGATTTACAGTTAAG 57.276 34.615 0.00 0.00 39.74 1.85
6687 7737 7.770897 AGCTGTCATTAGGATTTACAGTTAAGG 59.229 37.037 0.00 0.00 39.74 2.69
6688 7738 7.012421 GCTGTCATTAGGATTTACAGTTAAGGG 59.988 40.741 0.00 0.00 39.74 3.95
6689 7739 7.343357 TGTCATTAGGATTTACAGTTAAGGGG 58.657 38.462 0.00 0.00 0.00 4.79
6753 7810 9.502091 AACTATTAACTCTCAAACACATTGCTA 57.498 29.630 0.00 0.00 38.98 3.49
6781 7838 9.877178 AATGAAGATCGATTAGTAAGTTGAAGT 57.123 29.630 0.00 0.00 0.00 3.01
6782 7839 9.877178 ATGAAGATCGATTAGTAAGTTGAAGTT 57.123 29.630 0.00 0.00 0.00 2.66
6783 7840 9.706691 TGAAGATCGATTAGTAAGTTGAAGTTT 57.293 29.630 0.00 0.00 0.00 2.66
6787 7844 9.907576 GATCGATTAGTAAGTTGAAGTTTCATG 57.092 33.333 0.00 0.00 37.00 3.07
6788 7845 8.827177 TCGATTAGTAAGTTGAAGTTTCATGT 57.173 30.769 0.00 0.00 37.00 3.21
6789 7846 9.917129 TCGATTAGTAAGTTGAAGTTTCATGTA 57.083 29.630 0.00 0.00 37.00 2.29
6828 7892 2.230664 TGGGAGCACCACTGAAACT 58.769 52.632 1.58 0.00 46.80 2.66
6830 7894 1.239347 GGGAGCACCACTGAAACTTC 58.761 55.000 1.58 0.00 39.85 3.01
6833 7897 2.485479 GGAGCACCACTGAAACTTCTGA 60.485 50.000 0.00 0.00 35.97 3.27
6849 7914 1.359474 TCTGAAGCTCCCCTCTACTGT 59.641 52.381 0.00 0.00 0.00 3.55
6851 7916 1.077169 TGAAGCTCCCCTCTACTGTGA 59.923 52.381 0.00 0.00 0.00 3.58
6852 7917 1.754226 GAAGCTCCCCTCTACTGTGAG 59.246 57.143 0.00 0.00 0.00 3.51
6853 7918 0.707616 AGCTCCCCTCTACTGTGAGT 59.292 55.000 0.00 0.00 32.50 3.41
6854 7919 1.107945 GCTCCCCTCTACTGTGAGTC 58.892 60.000 0.00 0.00 32.50 3.36
6878 7948 2.668279 GCAGGCACCATCAGTAAAAACG 60.668 50.000 0.00 0.00 0.00 3.60
6895 7965 3.313274 AACGTCTGCAAAACACTAACG 57.687 42.857 0.00 0.00 32.60 3.18
6896 7966 2.273557 ACGTCTGCAAAACACTAACGT 58.726 42.857 0.00 0.00 34.04 3.99
6897 7967 2.674357 ACGTCTGCAAAACACTAACGTT 59.326 40.909 5.88 5.88 34.79 3.99
6917 8112 6.501781 ACGTTTTCTATCTAATCTACCACCG 58.498 40.000 0.00 0.00 0.00 4.94
6921 8116 9.242477 GTTTTCTATCTAATCTACCACCGTAAC 57.758 37.037 0.00 0.00 0.00 2.50
6930 8126 1.514873 CCACCGTAACCGTCGTAGC 60.515 63.158 0.00 0.00 0.00 3.58
6936 8132 2.169179 CGTAACCGTCGTAGCAACTAC 58.831 52.381 0.00 0.00 33.99 2.73
6969 8165 5.709164 CCCCAGAATGAACCAATGATCTATC 59.291 44.000 0.00 0.00 39.69 2.08
6977 8173 6.582636 TGAACCAATGATCTATCTACACACC 58.417 40.000 0.00 0.00 0.00 4.16
6982 8181 7.500227 ACCAATGATCTATCTACACACCAAATG 59.500 37.037 0.00 0.00 0.00 2.32
6983 8182 7.358066 CAATGATCTATCTACACACCAAATGC 58.642 38.462 0.00 0.00 0.00 3.56
7026 8228 3.366052 ACCACCTCAGTCACAAAAACT 57.634 42.857 0.00 0.00 0.00 2.66
7027 8229 3.016736 ACCACCTCAGTCACAAAAACTG 58.983 45.455 0.00 0.00 44.43 3.16
7031 8233 4.396166 CACCTCAGTCACAAAAACTGTCTT 59.604 41.667 3.45 0.00 43.68 3.01
7033 8235 4.878397 CCTCAGTCACAAAAACTGTCTTCT 59.122 41.667 3.45 0.00 43.68 2.85
7036 8238 6.173339 TCAGTCACAAAAACTGTCTTCTCTT 58.827 36.000 3.45 0.00 43.68 2.85
7037 8239 6.313905 TCAGTCACAAAAACTGTCTTCTCTTC 59.686 38.462 3.45 0.00 43.68 2.87
7038 8240 6.314896 CAGTCACAAAAACTGTCTTCTCTTCT 59.685 38.462 0.00 0.00 39.42 2.85
7039 8241 6.314896 AGTCACAAAAACTGTCTTCTCTTCTG 59.685 38.462 0.00 0.00 35.47 3.02
7041 8243 4.943705 ACAAAAACTGTCTTCTCTTCTGCA 59.056 37.500 0.00 0.00 29.87 4.41
7042 8244 5.415701 ACAAAAACTGTCTTCTCTTCTGCAA 59.584 36.000 0.00 0.00 29.87 4.08
7043 8245 6.071952 ACAAAAACTGTCTTCTCTTCTGCAAA 60.072 34.615 0.00 0.00 29.87 3.68
7044 8246 5.747951 AAACTGTCTTCTCTTCTGCAAAG 57.252 39.130 0.00 0.00 0.00 2.77
7045 8247 4.679373 ACTGTCTTCTCTTCTGCAAAGA 57.321 40.909 9.84 9.84 0.00 2.52
7046 8248 4.376146 ACTGTCTTCTCTTCTGCAAAGAC 58.624 43.478 16.35 16.35 44.96 3.01
7049 8251 5.280328 GTCTTCTCTTCTGCAAAGACATG 57.720 43.478 17.70 0.00 44.41 3.21
7050 8252 3.750130 TCTTCTCTTCTGCAAAGACATGC 59.250 43.478 7.09 0.00 46.58 4.06
7051 8253 2.430465 TCTCTTCTGCAAAGACATGCC 58.570 47.619 7.09 0.00 45.83 4.40
7058 8260 1.140161 CAAAGACATGCCCATGCCG 59.860 57.895 8.11 0.00 42.39 5.69
7161 8384 1.072505 GTTCCCGTGGAAGAAGCCA 59.927 57.895 5.71 0.00 42.88 4.75
7162 8385 0.955919 GTTCCCGTGGAAGAAGCCAG 60.956 60.000 5.71 0.00 42.88 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 1.488705 ATTGACGGACCCTGCCTGAA 61.489 55.000 0.00 0.00 0.00 3.02
396 397 8.970020 TGAACTGGCAAACATTCTATAATCAAT 58.030 29.630 0.00 0.00 0.00 2.57
397 398 8.347004 TGAACTGGCAAACATTCTATAATCAA 57.653 30.769 0.00 0.00 0.00 2.57
707 709 6.065374 TGTTTGTTCATACTAGCAAAAGGGA 58.935 36.000 0.00 0.00 33.43 4.20
723 725 4.728534 TGCAGCCGTATTTATGTTTGTTC 58.271 39.130 0.00 0.00 0.00 3.18
736 738 1.506718 CTCGTCTCTTGCAGCCGTA 59.493 57.895 0.00 0.00 0.00 4.02
739 741 2.099431 CAGCTCGTCTCTTGCAGCC 61.099 63.158 0.00 0.00 31.81 4.85
767 769 1.539827 GATCCTCAAAAACACCCACCG 59.460 52.381 0.00 0.00 0.00 4.94
774 776 5.528690 CACTCTGTGAAGATCCTCAAAAACA 59.471 40.000 0.00 0.00 35.23 2.83
775 777 5.049129 CCACTCTGTGAAGATCCTCAAAAAC 60.049 44.000 0.00 0.00 35.23 2.43
776 778 5.065914 CCACTCTGTGAAGATCCTCAAAAA 58.934 41.667 0.00 0.00 35.23 1.94
784 786 4.872691 CCACATAACCACTCTGTGAAGATC 59.127 45.833 3.61 0.00 42.20 2.75
794 796 3.938963 CACCACATACCACATAACCACTC 59.061 47.826 0.00 0.00 0.00 3.51
812 814 6.538945 TCAGTACATTATAGCAAGTCACCA 57.461 37.500 0.00 0.00 0.00 4.17
840 848 4.939052 TCCTCCGGCATTTTGTTTTTAA 57.061 36.364 0.00 0.00 0.00 1.52
841 849 4.524714 TCATCCTCCGGCATTTTGTTTTTA 59.475 37.500 0.00 0.00 0.00 1.52
847 863 3.806625 AATTCATCCTCCGGCATTTTG 57.193 42.857 0.00 0.00 0.00 2.44
848 864 4.956075 AGTAAATTCATCCTCCGGCATTTT 59.044 37.500 0.00 0.00 0.00 1.82
883 899 3.132111 TCTTGCAAAAAGGACCCTCAAAC 59.868 43.478 0.00 0.00 0.00 2.93
907 923 1.490490 CGGATGGAGATTGAAAGGGGA 59.510 52.381 0.00 0.00 0.00 4.81
971 987 2.643808 GGTGAGGGGGAGGGACCTA 61.644 68.421 0.00 0.00 37.18 3.08
1044 1066 2.446802 GCGGAGGGGAGGAAGGAT 60.447 66.667 0.00 0.00 0.00 3.24
1138 1160 2.284995 GTCCAGCCCTCCTCCTGT 60.285 66.667 0.00 0.00 0.00 4.00
1239 1376 3.674050 GAGGAGGAGGGTACGGGCA 62.674 68.421 0.00 0.00 0.00 5.36
1245 1382 0.854039 TGAGGGTGAGGAGGAGGGTA 60.854 60.000 0.00 0.00 0.00 3.69
1295 1432 0.809385 TGAGAAGAGGAGCGTAACGG 59.191 55.000 0.00 0.00 0.00 4.44
1298 1435 3.074675 AGACTGAGAAGAGGAGCGTAA 57.925 47.619 0.00 0.00 0.00 3.18
1300 1437 2.639065 CTAGACTGAGAAGAGGAGCGT 58.361 52.381 0.00 0.00 0.00 5.07
1301 1438 1.946768 CCTAGACTGAGAAGAGGAGCG 59.053 57.143 0.00 0.00 0.00 5.03
1304 1441 5.263872 AGAAACCTAGACTGAGAAGAGGA 57.736 43.478 5.54 0.00 0.00 3.71
1305 1442 5.946972 TGTAGAAACCTAGACTGAGAAGAGG 59.053 44.000 0.00 0.00 0.00 3.69
1306 1443 6.657541 ACTGTAGAAACCTAGACTGAGAAGAG 59.342 42.308 0.00 0.00 0.00 2.85
1307 1444 6.544650 ACTGTAGAAACCTAGACTGAGAAGA 58.455 40.000 0.00 0.00 0.00 2.87
1327 1474 0.679505 ACATGCCACTACACGACTGT 59.320 50.000 0.00 0.00 0.00 3.55
1332 1479 1.808411 AAAGGACATGCCACTACACG 58.192 50.000 8.58 0.00 40.02 4.49
1345 1492 4.550577 CAAATTTGCCAACCAAAAGGAC 57.449 40.909 5.01 0.00 45.80 3.85
1370 1565 3.881688 GTCCATTTAGCACATGAGCTCAT 59.118 43.478 23.75 23.75 45.26 2.90
1375 1570 2.905075 TCCGTCCATTTAGCACATGAG 58.095 47.619 0.00 0.00 0.00 2.90
1392 1587 2.176273 CCTGGCTTGCTCGAATCCG 61.176 63.158 0.00 0.00 37.07 4.18
1397 1592 1.131638 ATTATCCCTGGCTTGCTCGA 58.868 50.000 0.00 0.00 0.00 4.04
1422 1617 0.749649 TGCACATTGTTCAACCCCAC 59.250 50.000 0.00 0.00 0.00 4.61
1443 1879 9.825972 ATACACTAATATATGAAAATGTTGCGC 57.174 29.630 0.00 0.00 0.00 6.09
1454 1890 8.687242 GCAGCCTACAGATACACTAATATATGA 58.313 37.037 0.00 0.00 30.04 2.15
1455 1891 8.470002 TGCAGCCTACAGATACACTAATATATG 58.530 37.037 0.00 0.00 31.41 1.78
1460 1896 4.502259 GCTGCAGCCTACAGATACACTAAT 60.502 45.833 28.76 0.00 37.32 1.73
1488 1924 5.534407 ACATCAAAATTTGTAACGGAACCC 58.466 37.500 5.56 0.00 0.00 4.11
1494 1930 5.751028 ACCACCAACATCAAAATTTGTAACG 59.249 36.000 5.56 0.00 0.00 3.18
1518 1954 4.477536 AGTCTAGCCCTTGGATCAGATA 57.522 45.455 0.00 0.00 0.00 1.98
1519 1955 3.342926 AGTCTAGCCCTTGGATCAGAT 57.657 47.619 0.00 0.00 0.00 2.90
1520 1956 2.856760 AGTCTAGCCCTTGGATCAGA 57.143 50.000 0.00 0.00 0.00 3.27
1521 1957 3.838565 TCTAGTCTAGCCCTTGGATCAG 58.161 50.000 1.60 0.00 0.00 2.90
1522 1958 3.973472 TCTAGTCTAGCCCTTGGATCA 57.027 47.619 1.60 0.00 0.00 2.92
1523 1959 6.014012 AGTTATCTAGTCTAGCCCTTGGATC 58.986 44.000 1.60 0.00 0.00 3.36
1524 1960 5.971493 AGTTATCTAGTCTAGCCCTTGGAT 58.029 41.667 1.60 0.00 0.00 3.41
1525 1961 5.405063 AGTTATCTAGTCTAGCCCTTGGA 57.595 43.478 1.60 0.00 0.00 3.53
1526 1962 6.069331 TGTAGTTATCTAGTCTAGCCCTTGG 58.931 44.000 1.60 0.00 0.00 3.61
1535 1971 8.463607 GCTCTGTCTTTTGTAGTTATCTAGTCT 58.536 37.037 0.00 0.00 0.00 3.24
1536 1972 8.463607 AGCTCTGTCTTTTGTAGTTATCTAGTC 58.536 37.037 0.00 0.00 0.00 2.59
1537 1973 8.247562 CAGCTCTGTCTTTTGTAGTTATCTAGT 58.752 37.037 0.00 0.00 0.00 2.57
1551 1987 5.045872 GCAAATTCAAACAGCTCTGTCTTT 58.954 37.500 2.68 0.00 44.13 2.52
1558 1994 5.362556 TCTACTGCAAATTCAAACAGCTC 57.637 39.130 0.00 0.00 33.35 4.09
1582 2018 3.485216 GCAACAACCATATCGAAGTTCCG 60.485 47.826 0.00 0.00 0.00 4.30
1591 2027 8.810427 CATACAGAAATTTGCAACAACCATATC 58.190 33.333 0.00 0.00 0.00 1.63
1598 2034 4.953667 TGGCATACAGAAATTTGCAACAA 58.046 34.783 0.00 0.00 36.82 2.83
1599 2035 4.597404 TGGCATACAGAAATTTGCAACA 57.403 36.364 0.00 0.00 36.82 3.33
1613 2049 6.292150 ACTTCCTTAGCTCTTTATGGCATAC 58.708 40.000 6.72 0.00 0.00 2.39
1680 2276 2.411806 GCAGAAATGCATTTTTGGTGCG 60.412 45.455 32.06 15.42 45.37 5.34
1723 2321 6.000219 CAGCTGGATTACAAGGCTGTATAAT 59.000 40.000 5.57 0.00 43.44 1.28
1743 2350 4.643387 GCGGGACCACCAACAGCT 62.643 66.667 0.00 0.00 40.22 4.24
1746 2353 1.826054 CTTTGCGGGACCACCAACA 60.826 57.895 0.00 0.00 40.22 3.33
1749 2356 2.112297 GACTTTGCGGGACCACCA 59.888 61.111 0.00 0.00 40.22 4.17
1755 2362 1.134220 ACAAGTTGAGACTTTGCGGGA 60.134 47.619 10.54 0.00 43.48 5.14
1758 2365 1.939934 TGGACAAGTTGAGACTTTGCG 59.060 47.619 10.54 0.00 43.48 4.85
1797 2404 5.508567 TCTGCAATCTTTCCAATATCACCA 58.491 37.500 0.00 0.00 0.00 4.17
1879 2486 0.188342 CCATAACCCCATCCCCAAGG 59.812 60.000 0.00 0.00 0.00 3.61
1884 2491 1.153756 CAGCCCATAACCCCATCCC 59.846 63.158 0.00 0.00 0.00 3.85
1895 2502 2.318908 TGCAAGTTTTTCTCAGCCCAT 58.681 42.857 0.00 0.00 0.00 4.00
1906 2513 5.609423 TGATTTGGTAGCATTGCAAGTTTT 58.391 33.333 11.91 0.00 0.00 2.43
1932 2539 8.969267 GTAATGAGTACATACCAAAAGATCTCG 58.031 37.037 0.00 0.00 35.50 4.04
2129 2737 7.897575 ACAAATTTTTGACTAAGTGTGCAAA 57.102 28.000 9.88 0.00 40.55 3.68
2183 2797 2.228822 AGACCACCAAAATGAACATCGC 59.771 45.455 0.00 0.00 0.00 4.58
2225 2843 8.938883 TCTTTCAGAGCCACCTAAGAATATATT 58.061 33.333 0.00 0.00 0.00 1.28
3335 4164 5.694816 TCTGCAACAAACAAATATACGGTG 58.305 37.500 0.00 0.00 0.00 4.94
3844 4676 3.554934 TGTCCTGAAATGGGCATATCAC 58.445 45.455 0.00 0.00 36.71 3.06
3878 4710 6.836242 AGATTAGGATCCAGAAAATCAGGTC 58.164 40.000 15.82 0.72 32.44 3.85
3974 4806 2.439507 ACTGCTTTCCCTCTCAAGAACA 59.560 45.455 0.00 0.00 0.00 3.18
4134 4966 8.737168 TTGCTTTGTCTTAATATACATGAGCT 57.263 30.769 0.00 0.00 36.70 4.09
4257 5089 8.479689 AGACATCAATTTGCAAATCCATGAATA 58.520 29.630 31.21 13.78 0.00 1.75
4305 5137 7.219322 CACTTCATATCTCATTGGTATGTGGA 58.781 38.462 0.00 0.00 33.34 4.02
4312 5144 4.508551 TGCCACTTCATATCTCATTGGT 57.491 40.909 0.00 0.00 0.00 3.67
4313 5145 5.840243 TTTGCCACTTCATATCTCATTGG 57.160 39.130 0.00 0.00 0.00 3.16
4370 5208 8.899427 ATCATGATTGTTACTCTATGGTCAAG 57.101 34.615 1.18 0.00 0.00 3.02
4397 5235 0.549950 CTGATGCAGTCCTTGGGGAT 59.450 55.000 0.00 0.00 44.33 3.85
4400 5238 2.089980 CTTTCTGATGCAGTCCTTGGG 58.910 52.381 0.00 0.00 32.61 4.12
4449 5287 5.199024 AGCATAGTTTTGTGACATTTGCA 57.801 34.783 3.05 0.00 0.00 4.08
4450 5288 4.321745 CGAGCATAGTTTTGTGACATTTGC 59.678 41.667 0.00 0.00 0.00 3.68
4458 5296 5.451908 ACATTGTTCGAGCATAGTTTTGTG 58.548 37.500 1.75 0.00 0.00 3.33
4477 5315 7.857569 TGAGTTTCTCGAAAATCGTTAACATT 58.142 30.769 13.12 2.32 45.24 2.71
4484 5322 3.390135 TGCTGAGTTTCTCGAAAATCGT 58.610 40.909 13.12 0.00 45.24 3.73
4567 5414 4.632153 TGTCAGTAAAGTTCTTCTGGCTC 58.368 43.478 7.16 0.14 34.23 4.70
4617 5464 9.565090 TCATTGATTCCTTCTAATGGACAATAG 57.435 33.333 0.00 0.00 32.24 1.73
4666 5515 3.058639 AGTCAAACTGCGATTCAAAGAGC 60.059 43.478 0.00 0.00 0.00 4.09
4678 5527 8.130307 ACAACAAAAATTATCAGTCAAACTGC 57.870 30.769 2.18 0.00 45.54 4.40
4889 5738 7.015389 AGCTTCGGAAGTATATAAAGCTTACCT 59.985 37.037 18.32 0.00 45.14 3.08
4908 5757 1.382522 ATGTGGTAATGCAGCTTCGG 58.617 50.000 0.00 0.00 0.00 4.30
4921 5770 6.597672 TCTGAACTTCGCATAAAATATGTGGT 59.402 34.615 10.14 0.71 0.00 4.16
4974 5826 5.880332 ACCATGCTTGTAAATACACGAAGAT 59.120 36.000 1.66 0.00 35.64 2.40
5033 5885 3.375782 ACTTCTGCAGCAAATTCAACC 57.624 42.857 9.47 0.00 0.00 3.77
5048 5900 4.251268 GGTTTGATACTGCGGTAACTTCT 58.749 43.478 9.98 0.00 0.00 2.85
5057 5909 2.151202 ACAGGTTGGTTTGATACTGCG 58.849 47.619 0.00 0.00 0.00 5.18
5102 5954 6.149474 ACTGTACATGTGGCTTTTTCAGTATC 59.851 38.462 9.11 0.00 32.95 2.24
5150 6002 7.991084 TGGAGATAAATGCTCATTTCCATAG 57.009 36.000 10.73 0.00 40.99 2.23
5256 6108 5.329035 ACAAAATGACATGACCATAAGCC 57.671 39.130 0.00 0.00 0.00 4.35
5285 6137 6.835488 TGAAAGAAGCTCCCTTGCATATTTAT 59.165 34.615 5.61 0.00 34.99 1.40
5357 6209 4.152402 ACGACAGATACTTGCACAACAATC 59.848 41.667 0.00 0.00 37.72 2.67
5358 6210 4.065088 ACGACAGATACTTGCACAACAAT 58.935 39.130 0.00 0.00 37.72 2.71
5450 6312 9.346725 CAATTCTTTATTACAACAGAGAAAGGC 57.653 33.333 0.00 0.00 0.00 4.35
5459 6321 6.005198 ACCCCGACAATTCTTTATTACAACA 58.995 36.000 0.00 0.00 0.00 3.33
5600 6467 9.231297 CTGGTTTATAATCTGAAGAGGAAAACA 57.769 33.333 0.00 0.00 0.00 2.83
5850 6722 1.262950 GAAGTGCACGCAACATGTGTA 59.737 47.619 12.01 0.00 39.36 2.90
5861 6762 2.351418 TCACAAAAGACTGAAGTGCACG 59.649 45.455 12.01 0.00 0.00 5.34
5889 6792 4.646492 GCATCTTAAGATTCCCACACCATT 59.354 41.667 15.49 0.00 31.21 3.16
5914 6817 5.201243 AGGAAATGTTGGGCTATAAAGGAC 58.799 41.667 0.00 0.00 0.00 3.85
5921 6824 4.591321 TCTTGAGGAAATGTTGGGCTAT 57.409 40.909 0.00 0.00 0.00 2.97
5923 6826 2.978156 TCTTGAGGAAATGTTGGGCT 57.022 45.000 0.00 0.00 0.00 5.19
5950 6853 3.125146 CGGAAGCAGATCAAATTTGTCGA 59.875 43.478 17.47 0.00 0.00 4.20
5952 6855 4.685169 TCGGAAGCAGATCAAATTTGTC 57.315 40.909 17.47 13.64 0.00 3.18
5968 6992 7.430441 TCATCGAAATATGAGTTGTATCGGAA 58.570 34.615 0.00 0.00 32.18 4.30
6106 7130 0.710567 CTTGCTGTCGCTTGTACTCG 59.289 55.000 0.00 0.00 36.97 4.18
6128 7152 2.202756 GGCGACGGACCTCATCAC 60.203 66.667 0.00 0.00 0.00 3.06
6263 7293 3.467803 ACGCAACTTCTATTGATAGGGC 58.532 45.455 0.00 0.00 0.00 5.19
6288 7318 2.989055 CTATTTCGTCGCGGCCCCAT 62.989 60.000 4.51 0.00 0.00 4.00
6289 7319 3.726595 CTATTTCGTCGCGGCCCCA 62.727 63.158 4.51 0.00 0.00 4.96
6295 7325 1.120903 GCGAGATTCTATTTCGTCGCG 59.879 52.381 0.00 0.00 42.75 5.87
6297 7327 1.709203 CCGCGAGATTCTATTTCGTCG 59.291 52.381 8.23 0.00 36.74 5.12
6318 7357 4.111016 TGCGTCCCAGCTACGTCG 62.111 66.667 9.12 2.49 42.26 5.12
6330 7370 1.891060 CTGAACAACTCCGCTGCGTC 61.891 60.000 21.59 10.27 0.00 5.19
6341 7381 3.325293 TCTCAGCATCTCCTGAACAAC 57.675 47.619 0.00 0.00 41.02 3.32
6368 7408 4.219507 CAGGTAGATGTCCAGGTATAGCAG 59.780 50.000 4.48 0.00 0.00 4.24
6391 7431 0.672401 TCCGTCAGGCCATCGAAAAC 60.672 55.000 5.01 0.00 37.47 2.43
6465 7506 4.637534 CACTGGACCCAACATCTCAAATAG 59.362 45.833 0.00 0.00 0.00 1.73
6472 7513 0.987294 CCTCACTGGACCCAACATCT 59.013 55.000 0.00 0.00 38.35 2.90
6473 7514 0.984230 TCCTCACTGGACCCAACATC 59.016 55.000 0.00 0.00 40.56 3.06
6494 7535 1.442526 CGCAACAGATCCTCCATGGC 61.443 60.000 6.96 0.00 35.26 4.40
6507 7548 2.047655 CGACCCCTAAGCGCAACA 60.048 61.111 11.47 0.00 0.00 3.33
6524 7573 5.156608 TCTTTACCTTTGTGCCTACTACC 57.843 43.478 0.00 0.00 0.00 3.18
6536 7585 4.609783 CGTCGTCGCATTTTCTTTACCTTT 60.610 41.667 0.00 0.00 0.00 3.11
6539 7588 2.409378 TCGTCGTCGCATTTTCTTTACC 59.591 45.455 0.00 0.00 36.96 2.85
6544 7594 1.990799 TCATCGTCGTCGCATTTTCT 58.009 45.000 0.00 0.00 36.96 2.52
6550 7600 2.261172 ATCGGTTCATCGTCGTCGCA 62.261 55.000 0.00 0.00 36.96 5.10
6601 7651 2.420022 CCAGGATCTCAAAAACGCGAAT 59.580 45.455 15.93 0.00 0.00 3.34
6603 7653 1.001520 TCCAGGATCTCAAAAACGCGA 59.998 47.619 15.93 0.00 0.00 5.87
6604 7654 1.438651 TCCAGGATCTCAAAAACGCG 58.561 50.000 3.53 3.53 0.00 6.01
6605 7655 5.560966 TTATTCCAGGATCTCAAAAACGC 57.439 39.130 0.00 0.00 0.00 4.84
6606 7656 5.973565 GCATTATTCCAGGATCTCAAAAACG 59.026 40.000 0.00 0.00 0.00 3.60
6613 7663 6.569994 GCTTCATTGCATTATTCCAGGATCTC 60.570 42.308 0.00 0.00 0.00 2.75
6640 7690 3.223435 TCCCTTGAAACATAAACGGCAA 58.777 40.909 0.00 0.00 0.00 4.52
6677 7727 4.289238 TCGCATTTTCCCCTTAACTGTA 57.711 40.909 0.00 0.00 0.00 2.74
6686 7736 0.377203 CGCTACTTCGCATTTTCCCC 59.623 55.000 0.00 0.00 0.00 4.81
6687 7737 3.897819 CGCTACTTCGCATTTTCCC 57.102 52.632 0.00 0.00 0.00 3.97
6790 7847 8.850156 GCTCCCATTTATTCTGTACATTGTTAT 58.150 33.333 0.00 0.00 0.00 1.89
6795 7852 5.594317 GGTGCTCCCATTTATTCTGTACATT 59.406 40.000 0.00 0.00 0.00 2.71
6811 7875 1.202818 AGAAGTTTCAGTGGTGCTCCC 60.203 52.381 1.59 0.00 0.00 4.30
6828 7892 2.225394 ACAGTAGAGGGGAGCTTCAGAA 60.225 50.000 0.00 0.00 0.00 3.02
6830 7894 1.480137 CACAGTAGAGGGGAGCTTCAG 59.520 57.143 0.00 0.00 0.00 3.02
6833 7897 1.077993 ACTCACAGTAGAGGGGAGCTT 59.922 52.381 0.00 0.00 39.97 3.74
6849 7914 2.189191 GATGGTGCCTGCCTGACTCA 62.189 60.000 0.00 0.00 0.00 3.41
6851 7916 2.194388 CTGATGGTGCCTGCCTGACT 62.194 60.000 0.00 0.00 0.00 3.41
6852 7917 1.748122 CTGATGGTGCCTGCCTGAC 60.748 63.158 0.00 0.00 0.00 3.51
6853 7918 0.909133 TACTGATGGTGCCTGCCTGA 60.909 55.000 0.00 0.00 0.00 3.86
6854 7919 0.035152 TTACTGATGGTGCCTGCCTG 60.035 55.000 0.00 0.00 0.00 4.85
6857 7927 2.668279 CGTTTTTACTGATGGTGCCTGC 60.668 50.000 0.00 0.00 0.00 4.85
6895 7965 9.242477 GTTACGGTGGTAGATTAGATAGAAAAC 57.758 37.037 0.00 0.00 0.00 2.43
6896 7966 8.416329 GGTTACGGTGGTAGATTAGATAGAAAA 58.584 37.037 0.00 0.00 0.00 2.29
6897 7967 7.255242 CGGTTACGGTGGTAGATTAGATAGAAA 60.255 40.741 0.00 0.00 36.18 2.52
6930 8126 0.325602 TGGGGTTTAGGCCGTAGTTG 59.674 55.000 0.00 0.00 0.00 3.16
6936 8132 0.254747 TCATTCTGGGGTTTAGGCCG 59.745 55.000 0.00 0.00 0.00 6.13
6969 8165 0.527565 GCTGGGCATTTGGTGTGTAG 59.472 55.000 0.00 0.00 0.00 2.74
6977 8173 1.322538 GGGGTAGTGCTGGGCATTTG 61.323 60.000 0.00 0.00 41.91 2.32
6998 8197 3.448660 TGTGACTGAGGTGGTAGATGATG 59.551 47.826 0.00 0.00 0.00 3.07
6999 8198 3.713003 TGTGACTGAGGTGGTAGATGAT 58.287 45.455 0.00 0.00 0.00 2.45
7002 8204 4.974645 TTTTGTGACTGAGGTGGTAGAT 57.025 40.909 0.00 0.00 0.00 1.98
7027 8229 4.378253 GCATGTCTTTGCAGAAGAGAAGAC 60.378 45.833 16.35 16.35 45.04 3.01
7031 8233 2.430465 GGCATGTCTTTGCAGAAGAGA 58.570 47.619 10.39 10.01 44.59 3.10
7033 8235 1.202915 TGGGCATGTCTTTGCAGAAGA 60.203 47.619 0.00 7.09 44.59 2.87
7036 8238 1.179152 CATGGGCATGTCTTTGCAGA 58.821 50.000 0.00 0.00 44.59 4.26
7037 8239 0.459585 GCATGGGCATGTCTTTGCAG 60.460 55.000 16.60 0.00 44.59 4.41
7038 8240 1.592743 GCATGGGCATGTCTTTGCA 59.407 52.632 16.60 0.00 44.59 4.08
7039 8241 1.153509 GGCATGGGCATGTCTTTGC 60.154 57.895 14.15 14.15 43.71 3.68
7041 8243 1.304381 ACGGCATGGGCATGTCTTT 60.304 52.632 0.00 0.00 41.05 2.52
7042 8244 1.750399 GACGGCATGGGCATGTCTT 60.750 57.895 0.00 0.00 41.05 3.01
7043 8245 2.124570 GACGGCATGGGCATGTCT 60.125 61.111 0.00 0.00 41.05 3.41
7044 8246 2.438254 TGACGGCATGGGCATGTC 60.438 61.111 0.00 0.00 43.33 3.06
7045 8247 2.438975 CTGACGGCATGGGCATGT 60.439 61.111 0.00 0.00 43.71 3.21
7046 8248 3.896133 GCTGACGGCATGGGCATG 61.896 66.667 0.00 0.00 43.71 4.06
7050 8252 3.136123 CTTGGCTGACGGCATGGG 61.136 66.667 8.86 0.00 45.87 4.00
7146 8369 2.747855 GCTGGCTTCTTCCACGGG 60.748 66.667 0.00 0.00 31.74 5.28
7149 8372 0.107945 AGATCGCTGGCTTCTTCCAC 60.108 55.000 0.00 0.00 31.74 4.02


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

AutoCloner maintained by Alex Coulton.