Multiple sequence alignment - TraesCS1B01G068000

Loading Multiple Alignment...

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 TraesCS1B01G068000 chr1B 100.000 5569 0 0 1 5569 52897267 52902835 0.000000e+00 10285.0
1 TraesCS1B01G068000 chr1B 84.597 422 65 0 3510 3931 52900692 52901113 2.400000e-113 420.0
2 TraesCS1B01G068000 chr1B 84.597 422 65 0 3426 3847 52900776 52901197 2.400000e-113 420.0
3 TraesCS1B01G068000 chr1B 80.473 169 20 7 130 296 52781321 52781478 3.520000e-22 117.0
4 TraesCS1B01G068000 chr1B 79.310 174 26 7 1642 1815 504140694 504140857 4.560000e-21 113.0
5 TraesCS1B01G068000 chr1A 91.883 4497 238 50 1119 5565 32890789 32895208 0.000000e+00 6165.0
6 TraesCS1B01G068000 chr1A 80.142 846 83 35 163 960 32889555 32890363 2.270000e-153 553.0
7 TraesCS1B01G068000 chr1A 86.256 422 58 0 3510 3931 32893096 32893517 5.080000e-125 459.0
8 TraesCS1B01G068000 chr1A 83.529 340 56 0 3436 3775 32893274 32893613 9.000000e-83 318.0
9 TraesCS1B01G068000 chr1A 96.296 54 2 0 981 1034 32890600 32890653 7.680000e-14 89.8
10 TraesCS1B01G068000 chr1D 91.074 4683 229 89 983 5565 34617511 34622104 0.000000e+00 6157.0
11 TraesCS1B01G068000 chr1D 86.823 554 20 19 441 949 34616629 34617174 2.250000e-158 569.0
12 TraesCS1B01G068000 chr1D 78.853 889 143 24 1537 2402 474503663 474502797 4.870000e-155 558.0
13 TraesCS1B01G068000 chr1D 85.986 421 59 0 3427 3847 34620078 34620498 8.510000e-123 451.0
14 TraesCS1B01G068000 chr1D 84.834 422 64 0 3510 3931 34619993 34620414 5.160000e-115 425.0
15 TraesCS1B01G068000 chr1D 80.919 283 14 9 142 398 34616350 34616618 2.650000e-43 187.0
16 TraesCS1B01G068000 chr2D 79.685 699 106 20 1724 2402 626409958 626409276 6.530000e-129 472.0
17 TraesCS1B01G068000 chr2A 79.775 356 50 13 1917 2259 756118772 756118426 7.210000e-59 239.0
18 TraesCS1B01G068000 chr2A 79.321 324 50 9 2087 2402 756068711 756068397 1.570000e-50 211.0
19 TraesCS1B01G068000 chr2A 79.012 324 51 9 2087 2402 756042614 756042300 7.310000e-49 206.0
20 TraesCS1B01G068000 chrUn 79.257 323 50 9 2087 2401 180874491 180874178 5.650000e-50 209.0
21 TraesCS1B01G068000 chrUn 78.704 324 52 9 2087 2402 180905231 180904917 3.400000e-47 200.0
22 TraesCS1B01G068000 chr7B 80.473 169 19 5 1645 1813 689900968 689900814 3.520000e-22 117.0
23 TraesCS1B01G068000 chr7B 79.882 169 20 5 1645 1813 689899400 689899246 1.640000e-20 111.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1B01G068000 chr1B 52897267 52902835 5568 False 3708.333333 10285 89.731333 1 5569 3 chr1B.!!$F3 5568
1 TraesCS1B01G068000 chr1A 32889555 32895208 5653 False 1516.960000 6165 87.621200 163 5565 5 chr1A.!!$F1 5402
2 TraesCS1B01G068000 chr1D 34616350 34622104 5754 False 1557.800000 6157 85.927200 142 5565 5 chr1D.!!$F1 5423
3 TraesCS1B01G068000 chr1D 474502797 474503663 866 True 558.000000 558 78.853000 1537 2402 1 chr1D.!!$R1 865
4 TraesCS1B01G068000 chr2D 626409276 626409958 682 True 472.000000 472 79.685000 1724 2402 1 chr2D.!!$R1 678

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
126 127 0.031449 GGGATGTGCTAGAGACGCTC 59.969 60.000 0.00 0.0 0.00 5.03 F
1235 1698 0.039256 CGGAACCGACAGTTTCCGTA 60.039 55.000 14.44 0.0 40.88 4.02 F
1409 1878 0.168128 CGTTCGGGGTCTTGCATTTC 59.832 55.000 0.00 0.0 0.00 2.17 F
2574 3119 0.723981 CGAGGAGCTTAAAGCACAGC 59.276 55.000 0.00 0.0 45.56 4.40 F
2639 3184 2.095461 GAGGAATGGAAGAACAAGGCC 58.905 52.381 0.00 0.0 0.00 5.19 F
3563 4108 0.461870 TAATGCGCACGGAATCAGCT 60.462 50.000 14.90 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1854 0.168128 GAAATGCAAGACCCCGAACG 59.832 55.000 0.00 0.00 0.00 3.95 R
2574 3119 0.172803 GCCTTCTTTGCATCAGCCAG 59.827 55.000 0.00 0.00 41.13 4.85 R
2864 3409 0.183492 TCTGCAGCCCAAACAACTCT 59.817 50.000 9.47 0.00 0.00 3.24 R
3512 4057 0.108089 GACCCTCTTTCTCCGCCTTC 60.108 60.000 0.00 0.00 0.00 3.46 R
3629 4174 1.349627 CGCTGATTCCGTGTGCATC 59.650 57.895 0.00 0.00 0.00 3.91 R
5482 6071 0.396139 GGGAATGAATGCTGCTCCCA 60.396 55.000 15.33 4.58 44.53 4.37 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
29 30 4.748144 GGGTGCAGGGCTTGGAGG 62.748 72.222 0.00 0.00 0.00 4.30
39 40 4.821589 CTTGGAGGCGGCGAGGTC 62.822 72.222 12.98 2.60 0.00 3.85
43 44 3.818787 GAGGCGGCGAGGTCGTAA 61.819 66.667 12.98 0.00 42.22 3.18
44 45 3.346631 GAGGCGGCGAGGTCGTAAA 62.347 63.158 12.98 0.00 42.22 2.01
45 46 3.184003 GGCGGCGAGGTCGTAAAC 61.184 66.667 12.98 0.00 42.22 2.01
54 55 3.302968 GGTCGTAAACCTCGTCTCG 57.697 57.895 0.00 0.00 45.45 4.04
55 56 0.519077 GGTCGTAAACCTCGTCTCGT 59.481 55.000 0.00 0.00 45.45 4.18
56 57 1.732259 GGTCGTAAACCTCGTCTCGTA 59.268 52.381 0.00 0.00 45.45 3.43
57 58 2.159627 GGTCGTAAACCTCGTCTCGTAA 59.840 50.000 0.00 0.00 45.45 3.18
58 59 3.364964 GGTCGTAAACCTCGTCTCGTAAA 60.365 47.826 0.00 0.00 45.45 2.01
59 60 4.406943 GTCGTAAACCTCGTCTCGTAAAT 58.593 43.478 0.00 0.00 0.00 1.40
60 61 4.853743 GTCGTAAACCTCGTCTCGTAAATT 59.146 41.667 0.00 0.00 0.00 1.82
61 62 5.343325 GTCGTAAACCTCGTCTCGTAAATTT 59.657 40.000 0.00 0.00 0.00 1.82
62 63 5.920273 TCGTAAACCTCGTCTCGTAAATTTT 59.080 36.000 0.00 0.00 0.00 1.82
63 64 6.005289 CGTAAACCTCGTCTCGTAAATTTTG 58.995 40.000 0.00 0.00 0.00 2.44
64 65 5.996669 AAACCTCGTCTCGTAAATTTTGT 57.003 34.783 0.00 0.00 0.00 2.83
65 66 5.996669 AACCTCGTCTCGTAAATTTTGTT 57.003 34.783 0.00 0.00 0.00 2.83
66 67 5.996669 ACCTCGTCTCGTAAATTTTGTTT 57.003 34.783 0.00 0.00 0.00 2.83
67 68 7.481275 AACCTCGTCTCGTAAATTTTGTTTA 57.519 32.000 0.00 0.00 0.00 2.01
68 69 6.881017 ACCTCGTCTCGTAAATTTTGTTTAC 58.119 36.000 0.00 1.60 0.00 2.01
89 90 3.564235 GGAAGCCCGTAAACGAATTTT 57.436 42.857 3.65 0.00 43.02 1.82
90 91 3.239254 GGAAGCCCGTAAACGAATTTTG 58.761 45.455 3.65 0.00 43.02 2.44
91 92 2.341318 AGCCCGTAAACGAATTTTGC 57.659 45.000 3.65 0.00 43.02 3.68
92 93 1.609555 AGCCCGTAAACGAATTTTGCA 59.390 42.857 3.65 0.00 43.02 4.08
93 94 1.982913 GCCCGTAAACGAATTTTGCAG 59.017 47.619 3.65 0.00 43.02 4.41
94 95 1.982913 CCCGTAAACGAATTTTGCAGC 59.017 47.619 3.65 0.00 43.02 5.25
95 96 1.982913 CCGTAAACGAATTTTGCAGCC 59.017 47.619 3.65 0.00 43.02 4.85
96 97 1.982913 CGTAAACGAATTTTGCAGCCC 59.017 47.619 0.00 0.00 43.02 5.19
97 98 1.982913 GTAAACGAATTTTGCAGCCCG 59.017 47.619 0.00 0.00 30.54 6.13
98 99 0.319469 AAACGAATTTTGCAGCCCGG 60.319 50.000 0.00 0.00 0.00 5.73
99 100 1.460273 AACGAATTTTGCAGCCCGGT 61.460 50.000 0.00 0.00 0.00 5.28
100 101 1.154035 CGAATTTTGCAGCCCGGTC 60.154 57.895 0.00 0.00 0.00 4.79
101 102 1.154035 GAATTTTGCAGCCCGGTCG 60.154 57.895 0.00 0.00 0.00 4.79
102 103 2.542211 GAATTTTGCAGCCCGGTCGG 62.542 60.000 0.00 1.86 0.00 4.79
117 118 4.529219 CGGCTGCGGGATGTGCTA 62.529 66.667 0.00 0.00 0.00 3.49
118 119 2.590007 GGCTGCGGGATGTGCTAG 60.590 66.667 0.00 0.00 0.00 3.42
119 120 2.501128 GCTGCGGGATGTGCTAGA 59.499 61.111 0.00 0.00 0.00 2.43
120 121 1.593750 GCTGCGGGATGTGCTAGAG 60.594 63.158 0.00 0.00 0.00 2.43
121 122 2.021068 GCTGCGGGATGTGCTAGAGA 62.021 60.000 0.00 0.00 0.00 3.10
122 123 0.249238 CTGCGGGATGTGCTAGAGAC 60.249 60.000 0.00 0.00 0.00 3.36
123 124 1.299468 GCGGGATGTGCTAGAGACG 60.299 63.158 0.00 0.00 0.00 4.18
124 125 1.299468 CGGGATGTGCTAGAGACGC 60.299 63.158 0.00 0.00 0.00 5.19
125 126 1.729470 CGGGATGTGCTAGAGACGCT 61.729 60.000 0.00 0.00 0.00 5.07
126 127 0.031449 GGGATGTGCTAGAGACGCTC 59.969 60.000 0.00 0.00 0.00 5.03
127 128 1.028905 GGATGTGCTAGAGACGCTCT 58.971 55.000 12.81 12.81 43.83 4.09
128 129 1.268999 GGATGTGCTAGAGACGCTCTG 60.269 57.143 16.48 9.47 41.37 3.35
129 130 1.673400 GATGTGCTAGAGACGCTCTGA 59.327 52.381 16.48 1.88 41.37 3.27
130 131 1.756430 TGTGCTAGAGACGCTCTGAT 58.244 50.000 16.48 0.00 41.37 2.90
131 132 1.673400 TGTGCTAGAGACGCTCTGATC 59.327 52.381 16.48 8.07 41.37 2.92
132 133 1.673400 GTGCTAGAGACGCTCTGATCA 59.327 52.381 16.48 0.00 41.37 2.92
133 134 2.098280 GTGCTAGAGACGCTCTGATCAA 59.902 50.000 16.48 0.00 41.37 2.57
134 135 2.357323 TGCTAGAGACGCTCTGATCAAG 59.643 50.000 16.48 8.64 41.37 3.02
135 136 2.858260 GCTAGAGACGCTCTGATCAAGC 60.858 54.545 16.48 15.67 41.37 4.01
143 144 1.407258 GCTCTGATCAAGCGGTAGAGT 59.593 52.381 11.75 0.00 37.71 3.24
155 156 2.365408 GGTAGAGTCCACCGAACAAG 57.635 55.000 0.00 0.00 0.00 3.16
157 158 1.272769 GTAGAGTCCACCGAACAAGCT 59.727 52.381 0.00 0.00 0.00 3.74
158 159 1.629043 AGAGTCCACCGAACAAGCTA 58.371 50.000 0.00 0.00 0.00 3.32
193 195 0.971386 GTTCAAGGTAGGTGGACGGA 59.029 55.000 0.00 0.00 0.00 4.69
209 212 1.333636 CGGACTCCCTCTCCATGCTT 61.334 60.000 0.00 0.00 0.00 3.91
241 249 2.022129 GTCAAGTCGGCGTCACCTG 61.022 63.158 6.85 0.00 35.61 4.00
242 250 2.738521 CAAGTCGGCGTCACCTGG 60.739 66.667 6.85 0.00 35.61 4.45
243 251 4.681978 AAGTCGGCGTCACCTGGC 62.682 66.667 6.85 0.00 35.61 4.85
362 390 2.173669 GGCGTCATGGTCACGATGG 61.174 63.158 9.39 0.00 39.75 3.51
366 394 1.359848 GTCATGGTCACGATGGTCAC 58.640 55.000 0.00 0.00 0.00 3.67
416 444 8.879342 CATACATGGAAGGAAAAGTAGTAGAG 57.121 38.462 0.00 0.00 0.00 2.43
418 446 9.710818 ATACATGGAAGGAAAAGTAGTAGAGTA 57.289 33.333 0.00 0.00 0.00 2.59
419 447 8.068892 ACATGGAAGGAAAAGTAGTAGAGTAG 57.931 38.462 0.00 0.00 0.00 2.57
420 448 6.527057 TGGAAGGAAAAGTAGTAGAGTAGC 57.473 41.667 0.00 0.00 0.00 3.58
421 449 5.421374 TGGAAGGAAAAGTAGTAGAGTAGCC 59.579 44.000 0.00 0.00 0.00 3.93
422 450 5.450274 GGAAGGAAAAGTAGTAGAGTAGCCG 60.450 48.000 0.00 0.00 0.00 5.52
533 578 3.445518 ATGGCGTGGCATCGATCGT 62.446 57.895 15.94 0.00 0.00 3.73
585 634 0.395311 ATCGGTAGGTGAGGCGAGAA 60.395 55.000 0.00 0.00 0.00 2.87
586 635 0.609957 TCGGTAGGTGAGGCGAGAAA 60.610 55.000 0.00 0.00 0.00 2.52
587 636 0.179134 CGGTAGGTGAGGCGAGAAAG 60.179 60.000 0.00 0.00 0.00 2.62
621 680 2.336478 CCAGCGTCTCTGTCCGTCT 61.336 63.158 0.00 0.00 41.25 4.18
629 688 3.680786 CTGTCCGTCTCCGTGCCA 61.681 66.667 0.00 0.00 0.00 4.92
638 706 3.240606 CTCCGTGCCAAGCGTGTTG 62.241 63.158 0.00 0.00 0.00 3.33
713 793 3.005791 GGCCAACAATAATAGCATCACCC 59.994 47.826 0.00 0.00 0.00 4.61
781 863 0.178935 TCCTTCTTTGCCTTTGGGGG 60.179 55.000 0.00 0.00 35.12 5.40
826 908 1.363807 GCCTTTGCAGCCTTTTCGT 59.636 52.632 0.00 0.00 37.47 3.85
949 1045 1.675007 CTTCTTCTTCCCCTTCCCCT 58.325 55.000 0.00 0.00 0.00 4.79
954 1050 1.230314 CTTCCCCTTCCCCTTCCCT 60.230 63.158 0.00 0.00 0.00 4.20
960 1056 1.606531 CTTCCCCTTCCCTGCTCTG 59.393 63.158 0.00 0.00 0.00 3.35
961 1057 2.549169 CTTCCCCTTCCCTGCTCTGC 62.549 65.000 0.00 0.00 0.00 4.26
962 1058 4.120755 CCCCTTCCCTGCTCTGCC 62.121 72.222 0.00 0.00 0.00 4.85
963 1059 4.479993 CCCTTCCCTGCTCTGCCG 62.480 72.222 0.00 0.00 0.00 5.69
965 1061 4.093291 CTTCCCTGCTCTGCCGCT 62.093 66.667 0.00 0.00 0.00 5.52
966 1062 3.618780 CTTCCCTGCTCTGCCGCTT 62.619 63.158 0.00 0.00 0.00 4.68
967 1063 3.612247 TTCCCTGCTCTGCCGCTTC 62.612 63.158 0.00 0.00 0.00 3.86
1040 1439 2.297129 GGTGCCTCCTCCTCTGCTT 61.297 63.158 0.00 0.00 0.00 3.91
1043 1442 0.546267 TGCCTCCTCCTCTGCTTCTT 60.546 55.000 0.00 0.00 0.00 2.52
1044 1443 0.617935 GCCTCCTCCTCTGCTTCTTT 59.382 55.000 0.00 0.00 0.00 2.52
1045 1444 1.004161 GCCTCCTCCTCTGCTTCTTTT 59.996 52.381 0.00 0.00 0.00 2.27
1047 1446 2.571202 CCTCCTCCTCTGCTTCTTTTCT 59.429 50.000 0.00 0.00 0.00 2.52
1049 1448 2.569404 TCCTCCTCTGCTTCTTTTCTCC 59.431 50.000 0.00 0.00 0.00 3.71
1051 1450 2.304180 CTCCTCTGCTTCTTTTCTCCCA 59.696 50.000 0.00 0.00 0.00 4.37
1056 1455 5.011431 CCTCTGCTTCTTTTCTCCCATTTTT 59.989 40.000 0.00 0.00 0.00 1.94
1057 1456 5.846203 TCTGCTTCTTTTCTCCCATTTTTG 58.154 37.500 0.00 0.00 0.00 2.44
1058 1457 5.363580 TCTGCTTCTTTTCTCCCATTTTTGT 59.636 36.000 0.00 0.00 0.00 2.83
1059 1458 5.358922 TGCTTCTTTTCTCCCATTTTTGTG 58.641 37.500 0.00 0.00 0.00 3.33
1090 1521 0.549950 TTCGGTTGGGTTGGTTGGTA 59.450 50.000 0.00 0.00 0.00 3.25
1113 1549 1.709578 TCCTCTTCTCCATCCATCCG 58.290 55.000 0.00 0.00 0.00 4.18
1149 1599 1.447838 GATCTCGCCGCCACTTCAA 60.448 57.895 0.00 0.00 0.00 2.69
1154 1607 4.660938 GCCGCCACTTCAACCCCT 62.661 66.667 0.00 0.00 0.00 4.79
1163 1618 0.321653 CTTCAACCCCTCTCCGTTGG 60.322 60.000 0.00 0.00 39.84 3.77
1166 1621 0.179001 CAACCCCTCTCCGTTGGTTT 60.179 55.000 0.00 0.00 39.01 3.27
1177 1632 1.008194 GTTGGTTTCCGCCGTTTCC 60.008 57.895 0.00 0.00 0.00 3.13
1178 1633 1.152922 TTGGTTTCCGCCGTTTCCT 60.153 52.632 0.00 0.00 0.00 3.36
1235 1698 0.039256 CGGAACCGACAGTTTCCGTA 60.039 55.000 14.44 0.00 40.88 4.02
1277 1741 1.002366 CGGAACTGCTTCTTGATCCG 58.998 55.000 0.00 0.00 43.08 4.18
1298 1762 0.461339 TTAATTCCGCCTCTCCGTGC 60.461 55.000 0.00 0.00 0.00 5.34
1309 1773 3.865929 CTCCGTGCCACAGCTTCGT 62.866 63.158 0.00 0.00 40.80 3.85
1358 1822 1.667236 CAACATATGCGCCTGGAGAA 58.333 50.000 4.18 0.00 0.00 2.87
1361 1825 1.069765 ATATGCGCCTGGAGAACCG 59.930 57.895 4.18 0.00 39.42 4.44
1362 1826 2.996168 ATATGCGCCTGGAGAACCGC 62.996 60.000 4.18 5.09 45.99 5.68
1368 1832 3.423154 CTGGAGAACCGCGGTTGC 61.423 66.667 45.58 33.81 38.60 4.17
1371 1835 2.677979 GGAGAACCGCGGTTGCTTC 61.678 63.158 45.58 34.20 38.60 3.86
1375 1839 2.171489 GAACCGCGGTTGCTTCTGTC 62.171 60.000 45.58 26.00 38.60 3.51
1380 1844 1.664649 CGGTTGCTTCTGTCTGCGA 60.665 57.895 0.00 0.00 0.00 5.10
1409 1878 0.168128 CGTTCGGGGTCTTGCATTTC 59.832 55.000 0.00 0.00 0.00 2.17
1432 1912 2.358039 TCCGTAGTGGAGTGGTTGG 58.642 57.895 0.00 0.00 43.74 3.77
1441 1921 1.623811 TGGAGTGGTTGGAGCTCTAAC 59.376 52.381 29.21 29.21 36.72 2.34
1442 1922 1.903183 GGAGTGGTTGGAGCTCTAACT 59.097 52.381 33.36 20.00 37.47 2.24
1448 1928 2.237392 GGTTGGAGCTCTAACTGATGGT 59.763 50.000 33.36 0.00 37.47 3.55
1747 2261 4.598319 TCCCCGAGATCCGCCGAT 62.598 66.667 0.00 0.00 36.84 4.18
2159 2697 4.615815 GAGCAGGCGGGCATCGAT 62.616 66.667 3.78 0.00 42.43 3.59
2180 2718 1.585006 GTCGCAGAAGAGGGACGAA 59.415 57.895 0.00 0.00 40.81 3.85
2279 2823 2.496817 GAGAGGTTCAGGCGCGAT 59.503 61.111 12.10 0.00 0.00 4.58
2357 2902 3.701604 GATCGCCGAGGTCAACGCT 62.702 63.158 0.00 0.00 0.00 5.07
2423 2968 3.126879 CTTGATTCCAGCGCGGCA 61.127 61.111 8.83 3.45 33.14 5.69
2574 3119 0.723981 CGAGGAGCTTAAAGCACAGC 59.276 55.000 0.00 0.00 45.56 4.40
2639 3184 2.095461 GAGGAATGGAAGAACAAGGCC 58.905 52.381 0.00 0.00 0.00 5.19
2663 3208 5.105797 CGGATCACTTGAAATGGAATTGGAA 60.106 40.000 0.00 0.00 36.10 3.53
2705 3250 2.293399 GGCCAAAAGCGATACCCTTATG 59.707 50.000 0.00 0.00 45.17 1.90
2780 3325 2.892852 TGAAATGGAAGTGCTGAAAGGG 59.107 45.455 0.00 0.00 0.00 3.95
2828 3373 3.134442 TGGCAAGGCTTTCAACAGAAATT 59.866 39.130 0.00 0.00 31.37 1.82
2864 3409 2.659016 CTGGACGCCTCTCAGCAA 59.341 61.111 0.00 0.00 0.00 3.91
3132 3677 6.149142 AGCACATGAGAGATTTCTGAAGAAAC 59.851 38.462 7.62 3.22 45.55 2.78
3152 3697 2.874701 ACAAGATGATTATGAGCACGCC 59.125 45.455 0.00 0.00 0.00 5.68
3158 3703 2.310327 ATTATGAGCACGCCCTCGCA 62.310 55.000 0.00 0.00 39.84 5.10
3236 3781 3.713248 TGATTGAGGAGGCACACTATGAT 59.287 43.478 0.00 0.00 0.00 2.45
3269 3814 9.504708 TGTTTAAGGAATACAGTCGGAAAATTA 57.495 29.630 0.00 0.00 0.00 1.40
3302 3847 6.382570 AGGTGAGCAAGTATAGAGAAGAATGT 59.617 38.462 0.00 0.00 0.00 2.71
3344 3889 5.888691 TTGTCAGTTTAAACAAGCAGTCA 57.111 34.783 20.06 6.68 31.97 3.41
3431 3976 2.538939 GCACGAACTCCAAACTGTCAAC 60.539 50.000 0.00 0.00 0.00 3.18
3512 4057 2.044555 CAGGGCTGTGCAGGATGTG 61.045 63.158 1.11 0.00 39.31 3.21
3518 4063 1.642037 CTGTGCAGGATGTGAAGGCG 61.642 60.000 0.00 0.00 39.31 5.52
3533 4078 0.973496 AGGCGGAGAAAGAGGGTCTC 60.973 60.000 0.00 0.00 40.75 3.36
3563 4108 0.461870 TAATGCGCACGGAATCAGCT 60.462 50.000 14.90 0.00 0.00 4.24
3564 4109 1.709147 AATGCGCACGGAATCAGCTC 61.709 55.000 14.90 0.00 0.00 4.09
3577 4122 2.578128 AGCTCTCGCTGAAGCCAG 59.422 61.111 0.00 0.00 46.86 4.85
3593 4138 1.909700 CCAGCAAGGCTTTACAGGAA 58.090 50.000 0.00 0.00 36.40 3.36
3629 4174 2.553086 GAGGATCTTCAAGAGCAGCTG 58.447 52.381 10.11 10.11 30.96 4.24
3783 4328 3.967987 GGTAAAGGCTGAGAAGGAGGATA 59.032 47.826 0.00 0.00 0.00 2.59
3953 4498 1.217882 CGTCCGAGAGTTTGCAACTT 58.782 50.000 0.00 0.00 43.03 2.66
4198 4743 3.237268 AGACACAGAAGGAGAGAGTGT 57.763 47.619 0.00 0.00 45.21 3.55
4199 4744 3.571590 AGACACAGAAGGAGAGAGTGTT 58.428 45.455 0.00 0.00 42.86 3.32
4272 4817 5.885465 ACATGAACCAAGAGGAAGAGAAAT 58.115 37.500 0.00 0.00 38.69 2.17
4343 4888 1.935933 ACGAGAGCGACAAAGTTGTT 58.064 45.000 0.00 0.00 42.43 2.83
4427 4972 1.112315 AGGAGGATAGCAGCACCGAG 61.112 60.000 0.00 0.00 0.00 4.63
4490 5041 2.867472 GCAATGTCCCCGACAACG 59.133 61.111 0.00 0.00 45.96 4.10
4538 5089 0.600057 CCCTGCTGAAGAAGTTTGGC 59.400 55.000 0.00 0.00 0.00 4.52
4613 5164 7.766219 AACACATGTACTATTATCGGTGTTC 57.234 36.000 0.00 0.00 42.58 3.18
4648 5201 9.844257 TCTGATCTTTCTTTTTCTTCTTCTTCT 57.156 29.630 0.00 0.00 0.00 2.85
4692 5245 5.472137 AGTGTGCTTAATTTCCACGTGTAAT 59.528 36.000 15.65 10.75 32.32 1.89
4766 5325 6.697455 GTGGGTGTTTTCATTTTTCTCTCTTC 59.303 38.462 0.00 0.00 0.00 2.87
4770 5329 9.371136 GGTGTTTTCATTTTTCTCTCTTCTTTT 57.629 29.630 0.00 0.00 0.00 2.27
4774 5333 9.599866 TTTTCATTTTTCTCTCTTCTTTTTCCC 57.400 29.630 0.00 0.00 0.00 3.97
4775 5334 7.290110 TCATTTTTCTCTCTTCTTTTTCCCC 57.710 36.000 0.00 0.00 0.00 4.81
4776 5335 6.267699 TCATTTTTCTCTCTTCTTTTTCCCCC 59.732 38.462 0.00 0.00 0.00 5.40
4864 5423 2.095263 CGTTTGCTTGTAACCAGATGGG 60.095 50.000 3.48 0.00 44.81 4.00
4865 5424 3.153919 GTTTGCTTGTAACCAGATGGGA 58.846 45.455 3.48 0.00 41.15 4.37
4866 5425 2.787473 TGCTTGTAACCAGATGGGAG 57.213 50.000 3.48 0.00 41.15 4.30
4867 5426 2.265367 TGCTTGTAACCAGATGGGAGA 58.735 47.619 3.48 0.00 41.15 3.71
4868 5427 2.237143 TGCTTGTAACCAGATGGGAGAG 59.763 50.000 3.48 0.00 41.15 3.20
4904 5471 1.966845 ACTGTGTAGCCCCTTATGGT 58.033 50.000 0.00 0.00 0.00 3.55
4921 5488 4.767578 ATGGTAAGCTGATGTCACTCAT 57.232 40.909 0.00 0.00 39.77 2.90
5127 5710 0.322277 AGAGGGCAGCACTCATGTTG 60.322 55.000 26.87 0.00 39.88 3.33
5165 5748 4.615588 TCCCATCCATGGTTTGTTTTTC 57.384 40.909 12.58 0.00 46.65 2.29
5202 5785 8.945195 ATGGATTGATCTGATTTGGCTTTATA 57.055 30.769 0.00 0.00 0.00 0.98
5375 5964 5.439721 AGCTGTGATTTCATAATGGTGCTA 58.560 37.500 0.00 0.00 0.00 3.49
5381 5970 6.005823 TGATTTCATAATGGTGCTAGATGGG 58.994 40.000 0.00 0.00 0.00 4.00
5382 5971 4.371624 TTCATAATGGTGCTAGATGGGG 57.628 45.455 0.00 0.00 0.00 4.96
5383 5972 2.644299 TCATAATGGTGCTAGATGGGGG 59.356 50.000 0.00 0.00 0.00 5.40
5384 5973 0.771127 TAATGGTGCTAGATGGGGGC 59.229 55.000 0.00 0.00 0.00 5.80
5385 5974 0.995675 AATGGTGCTAGATGGGGGCT 60.996 55.000 0.00 0.00 0.00 5.19
5386 5975 1.713005 ATGGTGCTAGATGGGGGCTG 61.713 60.000 0.00 0.00 0.00 4.85
5387 5976 2.512896 GTGCTAGATGGGGGCTGG 59.487 66.667 0.00 0.00 0.00 4.85
5388 5977 3.492353 TGCTAGATGGGGGCTGGC 61.492 66.667 0.00 0.00 39.91 4.85
5389 5978 3.174265 GCTAGATGGGGGCTGGCT 61.174 66.667 0.00 0.00 36.97 4.75
5462 6051 0.106066 TAATTGCATCCTGGCTGGGG 60.106 55.000 10.79 4.74 36.20 4.96
5480 6069 5.417580 GCTGGGGTGTAAAGTATCAAATGAA 59.582 40.000 0.00 0.00 0.00 2.57
5482 6071 7.363793 GCTGGGGTGTAAAGTATCAAATGAAAT 60.364 37.037 0.00 0.00 0.00 2.17
5484 6073 7.093552 TGGGGTGTAAAGTATCAAATGAAATGG 60.094 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.748144 CCTCCAAGCCCTGCACCC 62.748 72.222 0.00 0.00 0.00 4.61
22 23 4.821589 GACCTCGCCGCCTCCAAG 62.822 72.222 0.00 0.00 0.00 3.61
26 27 3.346631 TTTACGACCTCGCCGCCTC 62.347 63.158 0.00 0.00 44.43 4.70
27 28 3.376078 TTTACGACCTCGCCGCCT 61.376 61.111 0.00 0.00 44.43 5.52
28 29 3.184003 GTTTACGACCTCGCCGCC 61.184 66.667 0.00 0.00 44.43 6.13
29 30 3.184003 GGTTTACGACCTCGCCGC 61.184 66.667 0.00 0.00 45.55 6.53
37 38 3.455619 TTACGAGACGAGGTTTACGAC 57.544 47.619 0.00 0.00 34.70 4.34
38 39 4.685169 ATTTACGAGACGAGGTTTACGA 57.315 40.909 0.00 0.00 34.70 3.43
39 40 5.752098 AAATTTACGAGACGAGGTTTACG 57.248 39.130 0.00 0.00 0.00 3.18
40 41 6.881017 ACAAAATTTACGAGACGAGGTTTAC 58.119 36.000 0.00 0.00 0.00 2.01
41 42 7.481275 AACAAAATTTACGAGACGAGGTTTA 57.519 32.000 0.00 0.00 0.00 2.01
42 43 5.996669 ACAAAATTTACGAGACGAGGTTT 57.003 34.783 0.00 0.00 0.00 3.27
43 44 5.996669 AACAAAATTTACGAGACGAGGTT 57.003 34.783 0.00 0.00 0.00 3.50
44 45 5.996669 AAACAAAATTTACGAGACGAGGT 57.003 34.783 0.00 0.00 0.00 3.85
69 70 3.239254 CAAAATTCGTTTACGGGCTTCC 58.761 45.455 2.09 0.00 40.29 3.46
70 71 2.659757 GCAAAATTCGTTTACGGGCTTC 59.340 45.455 2.09 0.00 40.29 3.86
71 72 2.034812 TGCAAAATTCGTTTACGGGCTT 59.965 40.909 2.09 0.00 40.29 4.35
72 73 1.609555 TGCAAAATTCGTTTACGGGCT 59.390 42.857 2.09 0.00 40.29 5.19
73 74 1.982913 CTGCAAAATTCGTTTACGGGC 59.017 47.619 2.09 0.00 40.29 6.13
74 75 1.982913 GCTGCAAAATTCGTTTACGGG 59.017 47.619 2.09 0.00 40.29 5.28
75 76 1.982913 GGCTGCAAAATTCGTTTACGG 59.017 47.619 0.50 0.00 40.29 4.02
76 77 1.982913 GGGCTGCAAAATTCGTTTACG 59.017 47.619 0.50 0.00 41.45 3.18
77 78 1.982913 CGGGCTGCAAAATTCGTTTAC 59.017 47.619 0.50 0.00 0.00 2.01
78 79 1.068194 CCGGGCTGCAAAATTCGTTTA 60.068 47.619 0.50 0.00 0.00 2.01
79 80 0.319469 CCGGGCTGCAAAATTCGTTT 60.319 50.000 0.50 0.00 0.00 3.60
80 81 1.288752 CCGGGCTGCAAAATTCGTT 59.711 52.632 0.50 0.00 0.00 3.85
81 82 1.862602 GACCGGGCTGCAAAATTCGT 61.863 55.000 6.32 0.00 0.00 3.85
82 83 1.154035 GACCGGGCTGCAAAATTCG 60.154 57.895 6.32 0.00 0.00 3.34
83 84 1.154035 CGACCGGGCTGCAAAATTC 60.154 57.895 5.33 0.00 0.00 2.17
84 85 2.635443 CCGACCGGGCTGCAAAATT 61.635 57.895 5.33 0.00 0.00 1.82
85 86 3.061848 CCGACCGGGCTGCAAAAT 61.062 61.111 5.33 0.00 0.00 1.82
100 101 4.529219 TAGCACATCCCGCAGCCG 62.529 66.667 0.00 0.00 0.00 5.52
101 102 2.590007 CTAGCACATCCCGCAGCC 60.590 66.667 0.00 0.00 0.00 4.85
102 103 1.593750 CTCTAGCACATCCCGCAGC 60.594 63.158 0.00 0.00 0.00 5.25
103 104 0.249238 GTCTCTAGCACATCCCGCAG 60.249 60.000 0.00 0.00 0.00 5.18
104 105 1.816537 GTCTCTAGCACATCCCGCA 59.183 57.895 0.00 0.00 0.00 5.69
105 106 1.299468 CGTCTCTAGCACATCCCGC 60.299 63.158 0.00 0.00 0.00 6.13
106 107 1.299468 GCGTCTCTAGCACATCCCG 60.299 63.158 0.00 0.00 34.19 5.14
107 108 0.031449 GAGCGTCTCTAGCACATCCC 59.969 60.000 0.00 0.00 37.01 3.85
108 109 1.028905 AGAGCGTCTCTAGCACATCC 58.971 55.000 7.48 0.00 39.28 3.51
109 110 1.673400 TCAGAGCGTCTCTAGCACATC 59.327 52.381 8.70 0.00 38.99 3.06
110 111 1.756430 TCAGAGCGTCTCTAGCACAT 58.244 50.000 8.70 0.00 38.99 3.21
111 112 1.673400 GATCAGAGCGTCTCTAGCACA 59.327 52.381 8.70 0.00 38.99 4.57
112 113 1.673400 TGATCAGAGCGTCTCTAGCAC 59.327 52.381 8.70 3.59 38.99 4.40
113 114 2.044123 TGATCAGAGCGTCTCTAGCA 57.956 50.000 8.70 5.60 38.99 3.49
114 115 2.858260 GCTTGATCAGAGCGTCTCTAGC 60.858 54.545 12.15 9.79 38.99 3.42
115 116 2.998772 GCTTGATCAGAGCGTCTCTAG 58.001 52.381 12.15 4.73 38.99 2.43
123 124 1.407258 ACTCTACCGCTTGATCAGAGC 59.593 52.381 15.67 15.67 36.95 4.09
124 125 2.034053 GGACTCTACCGCTTGATCAGAG 59.966 54.545 0.00 0.00 38.92 3.35
125 126 2.025155 GGACTCTACCGCTTGATCAGA 58.975 52.381 0.00 0.00 0.00 3.27
126 127 1.751351 TGGACTCTACCGCTTGATCAG 59.249 52.381 0.00 0.00 0.00 2.90
127 128 1.476891 GTGGACTCTACCGCTTGATCA 59.523 52.381 0.00 0.00 37.45 2.92
128 129 1.202428 GGTGGACTCTACCGCTTGATC 60.202 57.143 0.00 0.00 39.98 2.92
129 130 0.824759 GGTGGACTCTACCGCTTGAT 59.175 55.000 0.00 0.00 39.98 2.57
130 131 2.273908 GGTGGACTCTACCGCTTGA 58.726 57.895 0.00 0.00 39.98 3.02
131 132 4.913126 GGTGGACTCTACCGCTTG 57.087 61.111 0.00 0.00 39.98 4.01
136 137 1.672145 GCTTGTTCGGTGGACTCTACC 60.672 57.143 1.35 1.35 34.81 3.18
137 138 1.272769 AGCTTGTTCGGTGGACTCTAC 59.727 52.381 0.00 0.00 0.00 2.59
138 139 1.629043 AGCTTGTTCGGTGGACTCTA 58.371 50.000 0.00 0.00 0.00 2.43
139 140 1.629043 TAGCTTGTTCGGTGGACTCT 58.371 50.000 0.00 0.00 0.00 3.24
140 141 2.674796 ATAGCTTGTTCGGTGGACTC 57.325 50.000 0.00 0.00 0.00 3.36
143 144 1.138266 GGCTATAGCTTGTTCGGTGGA 59.862 52.381 23.53 0.00 41.70 4.02
193 195 1.203441 TGCAAGCATGGAGAGGGAGT 61.203 55.000 0.00 0.00 0.00 3.85
241 249 1.889573 CTTTAGCTAGCTGCCCGCC 60.890 63.158 27.68 0.00 44.23 6.13
242 250 2.538448 GCTTTAGCTAGCTGCCCGC 61.538 63.158 27.68 18.69 44.23 6.13
243 251 2.240500 CGCTTTAGCTAGCTGCCCG 61.241 63.158 27.68 18.63 44.23 6.13
244 252 0.878086 CTCGCTTTAGCTAGCTGCCC 60.878 60.000 27.68 11.35 44.23 5.36
245 253 0.103208 TCTCGCTTTAGCTAGCTGCC 59.897 55.000 27.68 11.01 44.23 4.85
246 254 1.066303 TCTCTCGCTTTAGCTAGCTGC 59.934 52.381 27.68 20.21 39.03 5.25
247 255 3.564511 GATCTCTCGCTTTAGCTAGCTG 58.435 50.000 27.68 11.86 39.03 4.24
248 256 2.556622 GGATCTCTCGCTTTAGCTAGCT 59.443 50.000 23.12 23.12 39.03 3.32
249 257 2.294791 TGGATCTCTCGCTTTAGCTAGC 59.705 50.000 6.62 6.62 39.32 3.42
250 258 3.305064 GGTGGATCTCTCGCTTTAGCTAG 60.305 52.174 0.00 0.00 39.32 3.42
251 259 2.623889 GGTGGATCTCTCGCTTTAGCTA 59.376 50.000 0.00 0.00 39.32 3.32
267 275 2.288025 GCTACCCCTTCACGGTGGA 61.288 63.158 8.50 0.00 33.89 4.02
362 390 3.660111 GTGTGCGCTTGGGGTGAC 61.660 66.667 9.73 0.00 0.00 3.67
412 440 0.970937 AAGTGCAGGCGGCTACTCTA 60.971 55.000 12.74 0.00 45.15 2.43
415 443 0.391263 GTAAAGTGCAGGCGGCTACT 60.391 55.000 12.74 10.28 45.15 2.57
416 444 1.366854 GGTAAAGTGCAGGCGGCTAC 61.367 60.000 12.74 6.74 45.15 3.58
418 446 2.359975 GGTAAAGTGCAGGCGGCT 60.360 61.111 5.25 5.25 45.15 5.52
419 447 3.440415 GGGTAAAGTGCAGGCGGC 61.440 66.667 0.00 0.00 45.13 6.53
420 448 1.745489 GAGGGTAAAGTGCAGGCGG 60.745 63.158 0.00 0.00 0.00 6.13
421 449 0.535335 TAGAGGGTAAAGTGCAGGCG 59.465 55.000 0.00 0.00 0.00 5.52
422 450 1.407025 GGTAGAGGGTAAAGTGCAGGC 60.407 57.143 0.00 0.00 0.00 4.85
466 498 0.464916 TGTAGCGTATCGGCAGGAGA 60.465 55.000 0.00 0.00 34.64 3.71
520 565 0.924090 GACTTGACGATCGATGCCAC 59.076 55.000 24.34 5.28 0.00 5.01
528 573 1.766143 GCGCCATGGACTTGACGATC 61.766 60.000 18.40 0.00 0.00 3.69
533 578 4.015406 ACCGCGCCATGGACTTGA 62.015 61.111 18.40 0.00 0.00 3.02
565 614 0.395311 TCTCGCCTCACCTACCGATT 60.395 55.000 0.00 0.00 0.00 3.34
621 680 3.276091 CAACACGCTTGGCACGGA 61.276 61.111 2.51 0.00 34.00 4.69
629 688 0.944386 CTAACACTGCCAACACGCTT 59.056 50.000 0.00 0.00 0.00 4.68
638 706 2.614734 GGGAGGTTACACTAACACTGCC 60.615 54.545 0.00 0.00 40.39 4.85
713 793 9.926751 CACTACATCTGCAAAGAAATATTACTG 57.073 33.333 0.00 0.00 0.00 2.74
801 883 2.564721 GGCTGCAAAGGCGAAAGGT 61.565 57.895 0.50 0.00 45.35 3.50
940 1036 2.615288 AGCAGGGAAGGGGAAGGG 60.615 66.667 0.00 0.00 0.00 3.95
949 1045 3.612247 GAAGCGGCAGAGCAGGGAA 62.612 63.158 1.45 0.00 40.15 3.97
1037 1436 4.751600 CCACAAAAATGGGAGAAAAGAAGC 59.248 41.667 0.00 0.00 35.95 3.86
1040 1439 5.948742 AACCACAAAAATGGGAGAAAAGA 57.051 34.783 0.00 0.00 44.81 2.52
1043 1442 6.112058 CAGAAAACCACAAAAATGGGAGAAA 58.888 36.000 0.00 0.00 44.81 2.52
1044 1443 5.188751 ACAGAAAACCACAAAAATGGGAGAA 59.811 36.000 0.00 0.00 44.81 2.87
1045 1444 4.714308 ACAGAAAACCACAAAAATGGGAGA 59.286 37.500 0.00 0.00 44.81 3.71
1047 1446 5.428184 AACAGAAAACCACAAAAATGGGA 57.572 34.783 0.00 0.00 44.81 4.37
1049 1448 6.740453 CGAAAAACAGAAAACCACAAAAATGG 59.260 34.615 0.00 0.00 46.10 3.16
1051 1450 6.428465 ACCGAAAAACAGAAAACCACAAAAAT 59.572 30.769 0.00 0.00 0.00 1.82
1056 1455 4.238514 CAACCGAAAAACAGAAAACCACA 58.761 39.130 0.00 0.00 0.00 4.17
1057 1456 3.615056 CCAACCGAAAAACAGAAAACCAC 59.385 43.478 0.00 0.00 0.00 4.16
1058 1457 3.368531 CCCAACCGAAAAACAGAAAACCA 60.369 43.478 0.00 0.00 0.00 3.67
1059 1458 3.191669 CCCAACCGAAAAACAGAAAACC 58.808 45.455 0.00 0.00 0.00 3.27
1090 1521 4.424842 GGATGGATGGAGAAGAGGATAGT 58.575 47.826 0.00 0.00 0.00 2.12
1149 1599 1.759236 GAAACCAACGGAGAGGGGT 59.241 57.895 0.00 0.00 33.80 4.95
1154 1607 2.031465 GGCGGAAACCAACGGAGA 59.969 61.111 0.00 0.00 0.00 3.71
1163 1618 2.951458 CCAGGAAACGGCGGAAAC 59.049 61.111 13.24 0.00 0.00 2.78
1208 1671 2.126189 GTCGGTTCCGAACTCCCG 60.126 66.667 15.59 6.76 40.26 5.14
1252 1716 2.300152 TCAAGAAGCAGTTCCGAGTGAT 59.700 45.455 0.00 0.00 32.48 3.06
1277 1741 0.179081 ACGGAGAGGCGGAATTAAGC 60.179 55.000 0.00 0.00 0.00 3.09
1321 1785 1.964373 GCCGTCGGCCAGAGAAAAA 60.964 57.895 26.23 0.00 44.06 1.94
1339 1803 1.331756 GTTCTCCAGGCGCATATGTTG 59.668 52.381 10.83 0.00 0.00 3.33
1340 1804 1.668419 GTTCTCCAGGCGCATATGTT 58.332 50.000 10.83 0.00 0.00 2.71
1341 1805 0.179045 GGTTCTCCAGGCGCATATGT 60.179 55.000 10.83 0.00 0.00 2.29
1342 1806 1.224069 CGGTTCTCCAGGCGCATATG 61.224 60.000 10.83 4.41 0.00 1.78
1343 1807 1.069765 CGGTTCTCCAGGCGCATAT 59.930 57.895 10.83 0.00 0.00 1.78
1344 1808 2.499205 CGGTTCTCCAGGCGCATA 59.501 61.111 10.83 0.00 0.00 3.14
1351 1815 3.423154 GCAACCGCGGTTCTCCAG 61.423 66.667 39.38 27.83 36.00 3.86
1352 1816 3.469863 AAGCAACCGCGGTTCTCCA 62.470 57.895 39.38 0.00 45.49 3.86
1353 1817 2.668550 AAGCAACCGCGGTTCTCC 60.669 61.111 39.38 28.09 45.49 3.71
1354 1818 2.861006 GAAGCAACCGCGGTTCTC 59.139 61.111 39.38 30.90 45.49 2.87
1358 1822 2.665185 GACAGAAGCAACCGCGGT 60.665 61.111 28.70 28.70 45.49 5.68
1361 1825 2.558313 GCAGACAGAAGCAACCGC 59.442 61.111 0.00 0.00 38.99 5.68
1362 1826 1.016130 ATCGCAGACAGAAGCAACCG 61.016 55.000 0.00 0.00 42.51 4.44
1368 1832 3.095685 CGAACAAATCGCAGACAGAAG 57.904 47.619 0.00 0.00 45.89 2.85
1380 1844 2.329614 CCCCGAACGGCGAACAAAT 61.330 57.895 16.62 0.00 44.57 2.32
1389 1853 1.241315 AAATGCAAGACCCCGAACGG 61.241 55.000 6.25 6.25 0.00 4.44
1390 1854 0.168128 GAAATGCAAGACCCCGAACG 59.832 55.000 0.00 0.00 0.00 3.95
1391 1855 0.168128 CGAAATGCAAGACCCCGAAC 59.832 55.000 0.00 0.00 0.00 3.95
1409 1878 0.806102 CCACTCCACTACGGATTGCG 60.806 60.000 0.00 0.00 45.19 4.85
1415 1884 0.246635 CTCCAACCACTCCACTACGG 59.753 60.000 0.00 0.00 0.00 4.02
1420 1889 1.267121 TAGAGCTCCAACCACTCCAC 58.733 55.000 10.93 0.00 0.00 4.02
1426 1905 2.237143 CCATCAGTTAGAGCTCCAACCA 59.763 50.000 19.59 8.75 0.00 3.67
1432 1912 2.234908 ACACCACCATCAGTTAGAGCTC 59.765 50.000 5.27 5.27 0.00 4.09
1441 1921 1.162698 CAAGAGCACACCACCATCAG 58.837 55.000 0.00 0.00 0.00 2.90
1442 1922 0.473755 ACAAGAGCACACCACCATCA 59.526 50.000 0.00 0.00 0.00 3.07
1448 1928 3.552132 TCTGTAAACAAGAGCACACCA 57.448 42.857 0.00 0.00 0.00 4.17
2159 2697 1.587043 CGTCCCTCTTCTGCGACTCA 61.587 60.000 0.00 0.00 0.00 3.41
2180 2718 1.305718 GACCTCCCTCTGCCACTCT 60.306 63.158 0.00 0.00 0.00 3.24
2423 2968 4.100498 TCACGGTTTTTACTCTCCTCAACT 59.900 41.667 0.00 0.00 0.00 3.16
2574 3119 0.172803 GCCTTCTTTGCATCAGCCAG 59.827 55.000 0.00 0.00 41.13 4.85
2639 3184 4.398988 TCCAATTCCATTTCAAGTGATCCG 59.601 41.667 0.00 0.00 0.00 4.18
2705 3250 2.742589 GTCCAATTCTTCTTCCGTGGAC 59.257 50.000 4.99 4.99 45.85 4.02
2780 3325 5.531634 TCAATTTCCAATGCTGTTGTCTTC 58.468 37.500 2.54 0.00 0.00 2.87
2828 3373 0.459585 GGTGCTCGCTGGATTCGTTA 60.460 55.000 0.00 0.00 0.00 3.18
2864 3409 0.183492 TCTGCAGCCCAAACAACTCT 59.817 50.000 9.47 0.00 0.00 3.24
2933 3478 4.647611 TCTCATTGTTTAAAGCCTCCGAA 58.352 39.130 0.00 0.00 0.00 4.30
2972 3517 1.207089 TCCTCGGTCAGGCTTACAATG 59.793 52.381 0.68 0.00 43.08 2.82
3132 3677 2.225019 GGGCGTGCTCATAATCATCTTG 59.775 50.000 0.00 0.00 0.00 3.02
3158 3703 3.118482 ACATCTTGAGATCGCCAATCTGT 60.118 43.478 1.14 7.79 45.06 3.41
3236 3781 7.762615 CCGACTGTATTCCTTAAACAAGTGATA 59.237 37.037 0.00 0.00 0.00 2.15
3269 3814 0.835543 ACTTGCTCACCTCAGCCTCT 60.836 55.000 0.00 0.00 38.80 3.69
3344 3889 1.280421 AGAGCGGCAATTTCTTCCTCT 59.720 47.619 1.45 0.00 0.00 3.69
3401 3946 1.086634 GGAGTTCGTGCTCTGCATCC 61.087 60.000 8.39 0.00 41.91 3.51
3431 3976 6.317642 TCTCTTGAAGTATCTCTTTCTCCTCG 59.682 42.308 0.00 0.00 36.40 4.63
3512 4057 0.108089 GACCCTCTTTCTCCGCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
3585 4130 5.818678 TTCTCAGCCTTTACTTCCTGTAA 57.181 39.130 0.00 0.00 39.17 2.41
3587 4132 4.348168 TCTTTCTCAGCCTTTACTTCCTGT 59.652 41.667 0.00 0.00 0.00 4.00
3593 4138 5.029474 AGATCCTCTTTCTCAGCCTTTACT 58.971 41.667 0.00 0.00 0.00 2.24
3629 4174 1.349627 CGCTGATTCCGTGTGCATC 59.650 57.895 0.00 0.00 0.00 3.91
3689 4234 3.133721 GCTGCTCTTGAAGATCCTCCTTA 59.866 47.826 0.00 0.00 0.00 2.69
4323 4868 2.787601 ACAACTTTGTCGCTCTCGTA 57.212 45.000 0.00 0.00 36.50 3.43
4343 4888 2.359602 GCCTGCAGCTGCTTCTCA 60.360 61.111 36.61 17.40 42.66 3.27
4427 4972 2.725815 GCTGTTCCGTTTGCGTGC 60.726 61.111 0.00 0.00 36.15 5.34
4490 5041 3.064820 TCTTCTTCTGCGGTTTTGTTGTC 59.935 43.478 0.00 0.00 0.00 3.18
4538 5089 6.183360 TGCTGTTCTTCTTTTTCAGTAGGTTG 60.183 38.462 0.00 0.00 0.00 3.77
4606 5157 8.425577 AAAGATCAGAGTAATAATGAACACCG 57.574 34.615 0.00 0.00 0.00 4.94
4647 5200 3.996150 ACCTTGCTGTCATCAAACAAG 57.004 42.857 0.00 0.00 37.46 3.16
4648 5201 4.275689 CACTACCTTGCTGTCATCAAACAA 59.724 41.667 0.00 0.00 0.00 2.83
4649 5202 3.814842 CACTACCTTGCTGTCATCAAACA 59.185 43.478 0.00 0.00 0.00 2.83
4698 5251 1.527034 AGTACAGGCGTCGACAGTAA 58.473 50.000 17.16 0.00 0.00 2.24
4773 5332 2.055579 GGAGGTCCAACTTATAGGGGG 58.944 57.143 0.00 0.00 35.64 5.40
4774 5333 2.706190 CAGGAGGTCCAACTTATAGGGG 59.294 54.545 0.00 0.00 38.89 4.79
4775 5334 3.385115 ACAGGAGGTCCAACTTATAGGG 58.615 50.000 0.00 0.00 38.89 3.53
4776 5335 4.717280 AGAACAGGAGGTCCAACTTATAGG 59.283 45.833 0.00 0.00 38.89 2.57
4784 5343 1.478654 GGCAAAGAACAGGAGGTCCAA 60.479 52.381 0.00 0.00 38.89 3.53
4864 5423 3.933861 TTTTAATCAGGAGGGGCTCTC 57.066 47.619 5.60 5.60 41.71 3.20
4865 5424 3.593780 AGTTTTTAATCAGGAGGGGCTCT 59.406 43.478 0.00 0.00 0.00 4.09
4866 5425 3.696548 CAGTTTTTAATCAGGAGGGGCTC 59.303 47.826 0.00 0.00 0.00 4.70
4867 5426 3.076032 ACAGTTTTTAATCAGGAGGGGCT 59.924 43.478 0.00 0.00 0.00 5.19
4868 5427 3.193479 CACAGTTTTTAATCAGGAGGGGC 59.807 47.826 0.00 0.00 0.00 5.80
4904 5471 6.426025 GCATGATAATGAGTGACATCAGCTTA 59.574 38.462 0.00 0.00 38.38 3.09
5024 5600 6.765036 ACAGACATGATTAGAATAGCCAACAG 59.235 38.462 0.00 0.00 0.00 3.16
5061 5637 1.065102 CAGCAGGCATGTGAATGCTAC 59.935 52.381 13.25 1.41 46.84 3.58
5065 5641 4.806571 GCAGCAGGCATGTGAATG 57.193 55.556 0.00 0.00 43.97 2.67
5165 5748 2.710377 TCAATCCATCTCAACCGTTGG 58.290 47.619 11.35 2.83 0.00 3.77
5212 5795 9.150028 ACCACACCCAAAAAGTAAGTAAATAAT 57.850 29.630 0.00 0.00 0.00 1.28
5223 5808 1.828595 GTCCAACCACACCCAAAAAGT 59.171 47.619 0.00 0.00 0.00 2.66
5329 5918 4.978438 TTTTAGCCAGTTGTACCACCTA 57.022 40.909 0.00 0.00 0.00 3.08
5363 5952 2.881403 GCCCCCATCTAGCACCATTATG 60.881 54.545 0.00 0.00 0.00 1.90
5366 5955 0.995675 AGCCCCCATCTAGCACCATT 60.996 55.000 0.00 0.00 0.00 3.16
5371 5960 3.492353 GCCAGCCCCCATCTAGCA 61.492 66.667 0.00 0.00 0.00 3.49
5396 5985 1.000060 CATGTGACAAAACCCAGCCAG 60.000 52.381 0.00 0.00 0.00 4.85
5400 5989 1.269726 GGTGCATGTGACAAAACCCAG 60.270 52.381 0.00 0.00 0.00 4.45
5462 6051 7.702348 GCTCCCATTTCATTTGATACTTTACAC 59.298 37.037 0.00 0.00 0.00 2.90
5480 6069 2.037144 GGAATGAATGCTGCTCCCATT 58.963 47.619 0.00 7.35 35.73 3.16
5482 6071 0.396139 GGGAATGAATGCTGCTCCCA 60.396 55.000 15.33 4.58 44.53 4.37
5484 6073 1.030457 CTGGGAATGAATGCTGCTCC 58.970 55.000 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.