Multiple sequence alignment - TraesCS5A01G291600

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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 TraesCS5A01G291600 chr5A 100.000 7150 0 0 1 7150 502297207 502304356 0.000000e+00 13204
1 TraesCS5A01G291600 chr5A 100.000 260 0 0 7439 7698 502304645 502304904 1.500000e-131 481
2 TraesCS5A01G291600 chr5D 96.005 6182 137 34 681 6827 396689779 396695885 0.000000e+00 9947
3 TraesCS5A01G291600 chr5D 90.640 609 11 14 80 666 396689144 396689728 0.000000e+00 767
4 TraesCS5A01G291600 chr5D 96.653 239 7 1 7461 7698 396696273 396696511 5.600000e-106 396
5 TraesCS5A01G291600 chr5D 84.878 410 22 18 6749 7150 396695884 396696261 2.030000e-100 377
6 TraesCS5A01G291600 chr5B 94.885 1603 61 11 5359 6950 476636338 476637930 0.000000e+00 2486
7 TraesCS5A01G291600 chr5B 87.659 2042 145 38 680 2665 476631959 476633949 0.000000e+00 2276
8 TraesCS5A01G291600 chr5B 93.963 1259 59 11 4069 5321 476635092 476636339 0.000000e+00 1888
9 TraesCS5A01G291600 chr5B 92.436 1137 50 14 2822 3949 476633948 476635057 0.000000e+00 1591
10 TraesCS5A01G291600 chr5B 88.649 370 11 13 80 441 476631355 476631701 9.240000e-114 422
11 TraesCS5A01G291600 chr5B 95.817 263 8 3 7439 7698 476638309 476638571 9.240000e-114 422
12 TraesCS5A01G291600 chr5B 93.122 189 12 1 6962 7150 476638065 476638252 7.610000e-70 276
13 TraesCS5A01G291600 chr5B 86.818 220 11 11 462 666 476631690 476631906 6.010000e-56 230
14 TraesCS5A01G291600 chr5B 81.643 207 25 4 4222 4415 355055037 355054831 8.000000e-35 159
15 TraesCS5A01G291600 chr4D 93.939 165 8 2 2664 2826 479687421 479687257 1.660000e-61 248
16 TraesCS5A01G291600 chr6B 93.865 163 8 2 2663 2823 36133503 36133665 2.150000e-60 244
17 TraesCS5A01G291600 chr4B 93.333 165 9 2 2664 2826 606916924 606916760 7.720000e-60 243
18 TraesCS5A01G291600 chr4B 90.164 183 16 2 2663 2843 653312526 653312708 3.590000e-58 237
19 TraesCS5A01G291600 chr4B 90.217 184 11 7 2655 2835 406389287 406389466 4.640000e-57 233
20 TraesCS5A01G291600 chr4B 81.860 215 23 9 4207 4408 272458862 272459073 4.780000e-37 167
21 TraesCS5A01G291600 chr2D 92.771 166 9 3 2661 2824 296364046 296364210 3.590000e-58 237
22 TraesCS5A01G291600 chr6D 91.329 173 13 2 2658 2828 438321901 438321729 1.290000e-57 235
23 TraesCS5A01G291600 chr2A 92.638 163 10 2 2663 2823 184561153 184561315 4.640000e-57 233


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 TraesCS5A01G291600 chr5A 502297207 502304904 7697 False 6842.500 13204 100.000000 1 7698 2 chr5A.!!$F1 7697
1 TraesCS5A01G291600 chr5D 396689144 396696511 7367 False 2871.750 9947 92.044000 80 7698 4 chr5D.!!$F1 7618
2 TraesCS5A01G291600 chr5B 476631355 476638571 7216 False 1198.875 2486 91.668625 80 7698 8 chr5B.!!$F1 7618

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
49 50 0.179111 CCATCCTTCGCTCGTGCTAA 60.179 55.000 7.97 1.99 36.97 3.09 F
1167 1294 0.176910 CTCTCGCTTCTCCCTTTCCC 59.823 60.000 0.00 0.00 0.00 3.97 F
1169 1296 0.176910 CTCGCTTCTCCCTTTCCCTC 59.823 60.000 0.00 0.00 0.00 4.30 F
1510 1641 0.178958 ACGGTTCTGGGAGACTGTCT 60.179 55.000 10.66 10.66 0.00 3.41 F
2178 2323 0.179094 TCTGAACTTGTCGCCGTGTT 60.179 50.000 0.00 0.00 0.00 3.32 F
3680 3828 0.774276 TGGCCCATAAGACACAACCA 59.226 50.000 0.00 0.00 0.00 3.67 F
3681 3829 1.173913 GGCCCATAAGACACAACCAC 58.826 55.000 0.00 0.00 0.00 4.16 F
3682 3830 1.546773 GGCCCATAAGACACAACCACA 60.547 52.381 0.00 0.00 0.00 4.17 F
4611 4770 1.683385 TCGTACCCTGCTGAGATGATG 59.317 52.381 0.00 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1617 0.037232 GTCTCCCAGAACCGTTCCTG 60.037 60.000 7.68 5.84 0.00 3.86 R
2458 2605 0.322187 TTTGAAGAAGGGCGGCTACC 60.322 55.000 9.56 0.00 0.00 3.18 R
3105 3252 1.326213 TAGAGCTGGGAGTGCAGAGC 61.326 60.000 0.00 0.00 0.00 4.09 R
3232 3379 1.819903 GAGAGGGCGAGAAGTTGTACT 59.180 52.381 0.00 0.00 0.00 2.73 R
4089 4245 1.400500 GGCACCATGTTTTTCGTACGG 60.400 52.381 16.52 0.00 0.00 4.02 R
5508 5670 0.038892 GTTAAGAGCACCGACCACGA 60.039 55.000 0.00 0.00 42.66 4.35 R
5545 5707 3.291584 TGTGCACAAACCAAATCCAGTA 58.708 40.909 19.28 0.00 0.00 2.74 R
5980 6142 6.951971 ACTTGGTAGCTTATTGTCTCTCAAT 58.048 36.000 0.00 0.00 46.82 2.57 R
6707 6872 1.020861 TGCAGCGCTACACAGAATGG 61.021 55.000 10.99 0.00 43.62 3.16 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
19 20 2.951457 TGATTGAGTCGCCGTCATAA 57.049 45.000 0.00 0.00 0.00 1.90
20 21 3.239587 TGATTGAGTCGCCGTCATAAA 57.760 42.857 0.00 0.00 0.00 1.40
21 22 3.591023 TGATTGAGTCGCCGTCATAAAA 58.409 40.909 0.00 0.00 0.00 1.52
22 23 3.616821 TGATTGAGTCGCCGTCATAAAAG 59.383 43.478 0.00 0.00 0.00 2.27
23 24 2.004583 TGAGTCGCCGTCATAAAAGG 57.995 50.000 0.00 0.00 0.00 3.11
24 25 1.287425 GAGTCGCCGTCATAAAAGGG 58.713 55.000 0.00 0.00 0.00 3.95
25 26 0.743345 AGTCGCCGTCATAAAAGGGC 60.743 55.000 0.00 0.00 44.79 5.19
27 28 4.211986 GCCGTCATAAAAGGGCGA 57.788 55.556 0.00 0.00 40.08 5.54
28 29 2.014594 GCCGTCATAAAAGGGCGAG 58.985 57.895 0.00 0.00 40.08 5.03
29 30 0.461339 GCCGTCATAAAAGGGCGAGA 60.461 55.000 0.00 0.00 40.08 4.04
30 31 1.287425 CCGTCATAAAAGGGCGAGAC 58.713 55.000 0.00 0.00 0.00 3.36
31 32 1.287425 CGTCATAAAAGGGCGAGACC 58.713 55.000 0.00 0.00 37.93 3.85
32 33 1.404986 CGTCATAAAAGGGCGAGACCA 60.405 52.381 0.00 0.00 42.05 4.02
33 34 2.741878 CGTCATAAAAGGGCGAGACCAT 60.742 50.000 0.00 0.00 42.05 3.55
34 35 2.872858 GTCATAAAAGGGCGAGACCATC 59.127 50.000 0.00 0.00 42.05 3.51
35 36 2.158813 TCATAAAAGGGCGAGACCATCC 60.159 50.000 0.00 0.00 42.05 3.51
36 37 1.580059 TAAAAGGGCGAGACCATCCT 58.420 50.000 0.00 0.00 42.05 3.24
37 38 0.698818 AAAAGGGCGAGACCATCCTT 59.301 50.000 0.00 0.00 42.05 3.36
38 39 0.253327 AAAGGGCGAGACCATCCTTC 59.747 55.000 0.00 0.00 42.05 3.46
39 40 1.961180 AAGGGCGAGACCATCCTTCG 61.961 60.000 0.00 0.00 42.05 3.79
41 42 2.496817 GCGAGACCATCCTTCGCT 59.503 61.111 10.45 0.00 45.01 4.93
42 43 1.590259 GCGAGACCATCCTTCGCTC 60.590 63.158 10.45 0.00 45.01 5.03
43 44 1.298713 CGAGACCATCCTTCGCTCG 60.299 63.158 0.00 0.00 41.77 5.03
44 45 1.810532 GAGACCATCCTTCGCTCGT 59.189 57.895 0.00 0.00 0.00 4.18
45 46 0.526524 GAGACCATCCTTCGCTCGTG 60.527 60.000 0.00 0.00 0.00 4.35
46 47 2.125512 ACCATCCTTCGCTCGTGC 60.126 61.111 0.00 0.00 0.00 5.34
47 48 2.185350 CCATCCTTCGCTCGTGCT 59.815 61.111 7.97 0.00 36.97 4.40
48 49 1.320344 ACCATCCTTCGCTCGTGCTA 61.320 55.000 7.97 0.00 36.97 3.49
49 50 0.179111 CCATCCTTCGCTCGTGCTAA 60.179 55.000 7.97 1.99 36.97 3.09
50 51 1.539065 CCATCCTTCGCTCGTGCTAAT 60.539 52.381 7.97 0.00 36.97 1.73
51 52 2.288213 CCATCCTTCGCTCGTGCTAATA 60.288 50.000 7.97 0.00 36.97 0.98
52 53 3.381045 CATCCTTCGCTCGTGCTAATAA 58.619 45.455 7.97 0.00 36.97 1.40
53 54 3.728076 TCCTTCGCTCGTGCTAATAAT 57.272 42.857 7.97 0.00 36.97 1.28
54 55 4.841443 TCCTTCGCTCGTGCTAATAATA 57.159 40.909 7.97 0.00 36.97 0.98
55 56 5.190992 TCCTTCGCTCGTGCTAATAATAA 57.809 39.130 7.97 0.00 36.97 1.40
56 57 5.779922 TCCTTCGCTCGTGCTAATAATAAT 58.220 37.500 7.97 0.00 36.97 1.28
57 58 5.862323 TCCTTCGCTCGTGCTAATAATAATC 59.138 40.000 7.97 0.00 36.97 1.75
58 59 5.220043 CCTTCGCTCGTGCTAATAATAATCG 60.220 44.000 7.97 0.00 36.97 3.34
59 60 4.163552 TCGCTCGTGCTAATAATAATCGG 58.836 43.478 7.97 0.00 36.97 4.18
60 61 3.241678 CGCTCGTGCTAATAATAATCGGC 60.242 47.826 7.97 0.00 36.97 5.54
61 62 3.062234 GCTCGTGCTAATAATAATCGGCC 59.938 47.826 1.41 0.00 36.03 6.13
62 63 3.247442 TCGTGCTAATAATAATCGGCCG 58.753 45.455 22.12 22.12 0.00 6.13
63 64 2.222729 CGTGCTAATAATAATCGGCCGC 60.223 50.000 23.51 1.35 0.00 6.53
64 65 1.996898 TGCTAATAATAATCGGCCGCG 59.003 47.619 23.51 0.00 0.00 6.46
65 66 2.264813 GCTAATAATAATCGGCCGCGA 58.735 47.619 23.51 4.04 0.00 5.87
66 67 2.028883 GCTAATAATAATCGGCCGCGAC 59.971 50.000 23.51 0.00 0.00 5.19
67 68 2.157834 AATAATAATCGGCCGCGACA 57.842 45.000 23.51 2.57 0.00 4.35
68 69 2.157834 ATAATAATCGGCCGCGACAA 57.842 45.000 23.51 2.08 0.00 3.18
69 70 1.493772 TAATAATCGGCCGCGACAAG 58.506 50.000 23.51 0.00 0.00 3.16
70 71 1.772063 AATAATCGGCCGCGACAAGC 61.772 55.000 23.51 0.90 43.95 4.01
71 72 2.644555 ATAATCGGCCGCGACAAGCT 62.645 55.000 23.51 0.15 45.59 3.74
72 73 2.845752 TAATCGGCCGCGACAAGCTT 62.846 55.000 23.51 0.00 45.59 3.74
76 77 3.660111 GCCGCGACAAGCTTGGTT 61.660 61.111 29.18 10.46 45.59 3.67
77 78 2.252260 CCGCGACAAGCTTGGTTG 59.748 61.111 29.18 18.69 45.59 3.77
78 79 2.427410 CGCGACAAGCTTGGTTGC 60.427 61.111 29.18 25.29 45.59 4.17
133 134 8.492673 TGAGCATCACTTTAATACTAAACCAG 57.507 34.615 0.00 0.00 42.56 4.00
134 135 8.100791 TGAGCATCACTTTAATACTAAACCAGT 58.899 33.333 0.00 0.00 42.56 4.00
135 136 8.494016 AGCATCACTTTAATACTAAACCAGTC 57.506 34.615 0.00 0.00 38.80 3.51
227 240 0.591170 CCGCGGAATCTCTCTCTCTC 59.409 60.000 24.07 0.00 0.00 3.20
228 241 1.593196 CGCGGAATCTCTCTCTCTCT 58.407 55.000 0.00 0.00 0.00 3.10
229 242 1.531149 CGCGGAATCTCTCTCTCTCTC 59.469 57.143 0.00 0.00 0.00 3.20
230 243 2.806745 CGCGGAATCTCTCTCTCTCTCT 60.807 54.545 0.00 0.00 0.00 3.10
327 347 0.250640 CAGATCCCACCTGCATAGCC 60.251 60.000 0.00 0.00 0.00 3.93
346 366 0.459489 CTAGCAGTGTCTCTCAGCCC 59.541 60.000 0.00 0.00 0.00 5.19
351 371 3.385384 TGTCTCTCAGCCCGCCTG 61.385 66.667 0.00 0.00 43.17 4.85
360 388 4.729856 GCCCGCCTGCTTGCTTTG 62.730 66.667 0.00 0.00 0.00 2.77
398 426 2.516460 GGAGCGAGGACCGAGCTA 60.516 66.667 15.17 0.00 41.84 3.32
485 513 1.281287 AGCAGTACTAGTCCAGTCGGA 59.719 52.381 0.00 0.00 38.80 4.55
526 554 4.335647 CGGCAGCACCCAGACCTT 62.336 66.667 0.00 0.00 33.26 3.50
527 555 2.954684 CGGCAGCACCCAGACCTTA 61.955 63.158 0.00 0.00 33.26 2.69
528 556 1.377333 GGCAGCACCCAGACCTTAC 60.377 63.158 0.00 0.00 0.00 2.34
666 708 2.825205 CTTCAAAGCAACCCACAAAGG 58.175 47.619 0.00 0.00 37.03 3.11
723 804 1.315690 TCGCGGAGAAGAATACGGAT 58.684 50.000 6.13 0.00 0.00 4.18
735 816 5.579753 AGAATACGGATGGAGGACTAGTA 57.420 43.478 0.00 0.00 0.00 1.82
736 817 6.142259 AGAATACGGATGGAGGACTAGTAT 57.858 41.667 0.00 0.00 0.00 2.12
737 818 7.268212 AGAATACGGATGGAGGACTAGTATA 57.732 40.000 0.00 0.00 0.00 1.47
738 819 7.340256 AGAATACGGATGGAGGACTAGTATAG 58.660 42.308 0.00 0.00 46.50 1.31
915 1028 2.764547 AGCTAGGGTTCCGCTCCC 60.765 66.667 0.00 0.00 44.90 4.30
963 1076 1.749638 GGATCTGCTGCTGCTGCTT 60.750 57.895 27.67 15.16 40.48 3.91
965 1078 2.037913 GATCTGCTGCTGCTGCTTCG 62.038 60.000 27.67 17.50 40.48 3.79
1166 1293 1.134936 GTCTCTCGCTTCTCCCTTTCC 60.135 57.143 0.00 0.00 0.00 3.13
1167 1294 0.176910 CTCTCGCTTCTCCCTTTCCC 59.823 60.000 0.00 0.00 0.00 3.97
1169 1296 0.176910 CTCGCTTCTCCCTTTCCCTC 59.823 60.000 0.00 0.00 0.00 4.30
1413 1543 1.978617 CCCACCCAAGTGCCATGTC 60.979 63.158 0.00 0.00 43.09 3.06
1430 1560 2.091541 TGTCAATTGCCTCGGGATTTC 58.908 47.619 0.00 0.00 0.00 2.17
1431 1561 1.064060 GTCAATTGCCTCGGGATTTCG 59.936 52.381 0.00 0.00 0.00 3.46
1432 1562 0.248621 CAATTGCCTCGGGATTTCGC 60.249 55.000 0.00 0.00 0.00 4.70
1434 1564 0.815615 ATTGCCTCGGGATTTCGCTC 60.816 55.000 0.00 0.00 0.00 5.03
1486 1617 0.307146 GATCTGCGCTCCATTTCAGC 59.693 55.000 9.73 0.00 0.00 4.26
1487 1618 0.393402 ATCTGCGCTCCATTTCAGCA 60.393 50.000 9.73 0.00 36.61 4.41
1510 1641 0.178958 ACGGTTCTGGGAGACTGTCT 60.179 55.000 10.66 10.66 0.00 3.41
1535 1666 2.257034 GTTGATCGAACGGTAGTGACC 58.743 52.381 0.00 0.00 43.03 4.02
1568 1699 4.444449 GGTGTTGTTTTCTAGTCCAGTCCT 60.444 45.833 0.00 0.00 0.00 3.85
1569 1700 5.221581 GGTGTTGTTTTCTAGTCCAGTCCTA 60.222 44.000 0.00 0.00 0.00 2.94
1570 1701 5.927115 GTGTTGTTTTCTAGTCCAGTCCTAG 59.073 44.000 0.00 0.00 34.47 3.02
1578 1709 3.810721 AGTCCAGTCCTAGTAGTGTGT 57.189 47.619 0.00 0.00 0.00 3.72
1729 1860 3.181459 GGTGTGGTAATTTGGGCTTGTTT 60.181 43.478 0.00 0.00 0.00 2.83
1765 1897 1.141053 GCTTCATACGGAGGGGTGATT 59.859 52.381 0.00 0.00 0.00 2.57
1970 2104 4.709886 GCCCATGATTAAACTAGGGTTGTT 59.290 41.667 12.33 0.00 38.56 2.83
2024 2158 2.690497 TGGCTATGAGAAGAGACTTCCG 59.310 50.000 7.72 0.00 0.00 4.30
2172 2317 3.247648 TGCTAAAACTCTGAACTTGTCGC 59.752 43.478 0.00 0.00 0.00 5.19
2177 2322 0.597637 CTCTGAACTTGTCGCCGTGT 60.598 55.000 0.00 0.00 0.00 4.49
2178 2323 0.179094 TCTGAACTTGTCGCCGTGTT 60.179 50.000 0.00 0.00 0.00 3.32
2179 2324 1.067364 TCTGAACTTGTCGCCGTGTTA 59.933 47.619 0.00 0.00 0.00 2.41
2180 2325 1.862201 CTGAACTTGTCGCCGTGTTAA 59.138 47.619 0.00 0.00 0.00 2.01
2181 2326 1.862201 TGAACTTGTCGCCGTGTTAAG 59.138 47.619 0.00 0.00 0.00 1.85
2182 2327 2.129607 GAACTTGTCGCCGTGTTAAGA 58.870 47.619 0.00 0.00 0.00 2.10
2183 2328 1.494824 ACTTGTCGCCGTGTTAAGAC 58.505 50.000 0.00 0.00 0.00 3.01
2231 2376 8.641541 ACATATTTCCATCTTTGTTTCACACTT 58.358 29.630 0.00 0.00 0.00 3.16
2458 2605 8.656849 GCGAGTAATTAGGTTGGTATATGAATG 58.343 37.037 0.00 0.00 0.00 2.67
2792 2939 9.149225 GTATGCAGTCCATATTGAAATCTCTAG 57.851 37.037 0.00 0.00 38.60 2.43
3044 3191 6.531503 TCCCATGTGAACTTGTTTGTTTAA 57.468 33.333 0.00 0.00 0.00 1.52
3064 3211 7.174253 TGTTTAAGTTCAGTTACATGCTTAGGG 59.826 37.037 0.00 0.00 0.00 3.53
3105 3252 7.500559 AGCATTTAGGATTCTAAACTAGCCTTG 59.499 37.037 8.42 2.96 45.07 3.61
3226 3373 5.126384 ACCATCTTCTCTTGCTAGTCAGTAC 59.874 44.000 0.00 0.00 0.00 2.73
3227 3374 5.359576 CCATCTTCTCTTGCTAGTCAGTACT 59.640 44.000 0.00 0.00 39.91 2.73
3228 3375 6.459573 CCATCTTCTCTTGCTAGTCAGTACTC 60.460 46.154 0.00 0.00 37.15 2.59
3229 3376 5.561679 TCTTCTCTTGCTAGTCAGTACTCA 58.438 41.667 0.00 0.00 37.15 3.41
3230 3377 5.645929 TCTTCTCTTGCTAGTCAGTACTCAG 59.354 44.000 0.00 0.00 37.15 3.35
3231 3378 4.912586 TCTCTTGCTAGTCAGTACTCAGT 58.087 43.478 0.00 0.00 37.15 3.41
3232 3379 6.051179 TCTCTTGCTAGTCAGTACTCAGTA 57.949 41.667 0.00 0.00 37.15 2.74
3268 3415 3.057666 CCCTCTCTCTTTTGCAAGAAAGC 60.058 47.826 0.00 0.00 38.63 3.51
3464 3611 9.884465 GTTACTCATATTTATTAAAGCTGCAGG 57.116 33.333 17.12 0.00 0.00 4.85
3677 3825 3.517296 TCTTTGGCCCATAAGACACAA 57.483 42.857 0.00 0.00 0.00 3.33
3678 3826 3.153919 TCTTTGGCCCATAAGACACAAC 58.846 45.455 0.00 0.00 0.00 3.32
3679 3827 1.917872 TTGGCCCATAAGACACAACC 58.082 50.000 0.00 0.00 0.00 3.77
3680 3828 0.774276 TGGCCCATAAGACACAACCA 59.226 50.000 0.00 0.00 0.00 3.67
3681 3829 1.173913 GGCCCATAAGACACAACCAC 58.826 55.000 0.00 0.00 0.00 4.16
3682 3830 1.546773 GGCCCATAAGACACAACCACA 60.547 52.381 0.00 0.00 0.00 4.17
3683 3831 2.235016 GCCCATAAGACACAACCACAA 58.765 47.619 0.00 0.00 0.00 3.33
3684 3832 2.030274 GCCCATAAGACACAACCACAAC 60.030 50.000 0.00 0.00 0.00 3.32
3685 3833 3.218453 CCCATAAGACACAACCACAACA 58.782 45.455 0.00 0.00 0.00 3.33
3686 3834 3.634448 CCCATAAGACACAACCACAACAA 59.366 43.478 0.00 0.00 0.00 2.83
3687 3835 4.499019 CCCATAAGACACAACCACAACAAC 60.499 45.833 0.00 0.00 0.00 3.32
3688 3836 4.097135 CCATAAGACACAACCACAACAACA 59.903 41.667 0.00 0.00 0.00 3.33
3952 4108 5.674052 AGGATGACTGCATATCATACCTC 57.326 43.478 16.24 5.63 38.05 3.85
4174 4330 6.631016 TCTTCTTATGTTCTTATGACGCACT 58.369 36.000 0.00 0.00 0.00 4.40
4611 4770 1.683385 TCGTACCCTGCTGAGATGATG 59.317 52.381 0.00 0.00 0.00 3.07
5097 5257 8.347771 AGATGAAAATGATGACGATTACAATGG 58.652 33.333 0.00 0.00 0.00 3.16
5248 5408 8.819974 CAAACTGAAGAATTTGCTGTTATGTTT 58.180 29.630 0.00 0.00 0.00 2.83
5326 5487 5.659971 TCAAGTATCTTGGTAGTTACTCCCC 59.340 44.000 9.18 0.00 36.39 4.81
5372 5533 6.647212 TTTGACACGTATTTGCTATCTCTG 57.353 37.500 0.00 0.00 0.00 3.35
5377 5538 7.063426 TGACACGTATTTGCTATCTCTGAAAAG 59.937 37.037 0.00 0.00 0.00 2.27
5378 5539 6.183360 ACACGTATTTGCTATCTCTGAAAAGC 60.183 38.462 0.00 0.00 35.51 3.51
5379 5540 5.874810 ACGTATTTGCTATCTCTGAAAAGCA 59.125 36.000 4.65 4.65 42.91 3.91
5545 5707 7.468141 TCTTAACTCATGTCACTGTCTGTAT 57.532 36.000 0.00 0.00 0.00 2.29
5563 5725 5.414454 TCTGTATACTGGATTTGGTTTGTGC 59.586 40.000 9.59 0.00 0.00 4.57
5685 5847 5.710099 TCCGCCATCTGACTTTCTTATTTTT 59.290 36.000 0.00 0.00 0.00 1.94
5980 6142 3.003394 CCAAGCACACATATGGGAGAA 57.997 47.619 13.12 0.00 0.00 2.87
6256 6421 4.696877 CAGCCAACAATTCATGTGAGAGTA 59.303 41.667 0.00 0.00 42.99 2.59
6402 6567 2.525368 GTTGGTACCAAATTCTGCCCT 58.475 47.619 28.67 0.00 37.70 5.19
6491 6656 0.537143 TCCACAAACTGCATCGCCTT 60.537 50.000 0.00 0.00 0.00 4.35
6499 6664 0.096976 CTGCATCGCCTTTACCAACG 59.903 55.000 0.00 0.00 0.00 4.10
6520 6685 2.990479 CCTGGGCCTATATCCCGC 59.010 66.667 4.53 0.00 46.92 6.13
6601 6766 3.606972 AGATCATCAAGATAAGGGGGCT 58.393 45.455 0.00 0.00 37.00 5.19
6634 6799 3.260632 GCCTCTCTTCTCTTCCTTCAACT 59.739 47.826 0.00 0.00 0.00 3.16
6707 6872 4.946478 AGCAGAACATAGGGTGAGTATC 57.054 45.455 0.00 0.00 0.00 2.24
6759 6924 4.901197 TGAACTGTTACCTTGCAGGATA 57.099 40.909 8.91 0.00 37.67 2.59
6772 6937 8.011844 ACCTTGCAGGATAAAATTATTCTTCC 57.988 34.615 8.91 0.00 37.67 3.46
6865 7107 7.394144 AAATATAGTAATGAAGACTGCCCCT 57.606 36.000 0.00 0.00 0.00 4.79
6887 7130 2.482142 CGTGAAAGGGGACTAGAGATGC 60.482 54.545 0.00 0.00 42.68 3.91
6897 7140 1.561076 ACTAGAGATGCCATGGTGCAA 59.439 47.619 14.67 0.00 45.84 4.08
6902 7145 4.025360 AGAGATGCCATGGTGCAATTTAA 58.975 39.130 14.67 0.00 45.84 1.52
6956 7199 2.476241 GCTTTGTTGCCTTGTTATGCAC 59.524 45.455 0.00 0.00 37.18 4.57
6960 7203 5.459536 TTGTTGCCTTGTTATGCACATAA 57.540 34.783 0.00 0.00 37.18 1.90
6964 7330 6.207614 TGTTGCCTTGTTATGCACATAAACTA 59.792 34.615 4.70 0.00 37.18 2.24
6995 7361 4.314121 GGAACTAGATGCTGGATCATGAC 58.686 47.826 11.83 0.00 32.86 3.06
7015 7381 5.002516 TGACTCATGAATGTGCATGTACAA 58.997 37.500 20.75 4.95 44.59 2.41
7049 7415 4.081697 AGTTTTAGTGCCACAGTTGCTTTT 60.082 37.500 0.00 0.00 0.00 2.27
7102 7471 2.867975 AAAAGTGCAGCTTTGCATTGTC 59.132 40.909 12.87 0.00 45.91 3.18
7466 7835 2.394604 GCAGTGGCGGATTAACCTC 58.605 57.895 0.00 0.00 36.31 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.951457 TTATGACGGCGACTCAATCA 57.049 45.000 16.62 5.89 0.00 2.57
1 2 3.001330 CCTTTTATGACGGCGACTCAATC 59.999 47.826 16.62 0.00 0.00 2.67
2 3 2.936498 CCTTTTATGACGGCGACTCAAT 59.064 45.455 16.62 0.00 0.00 2.57
3 4 2.343101 CCTTTTATGACGGCGACTCAA 58.657 47.619 16.62 2.78 0.00 3.02
4 5 1.404986 CCCTTTTATGACGGCGACTCA 60.405 52.381 16.62 8.57 0.00 3.41
5 6 1.287425 CCCTTTTATGACGGCGACTC 58.713 55.000 16.62 1.19 0.00 3.36
6 7 0.743345 GCCCTTTTATGACGGCGACT 60.743 55.000 16.62 0.00 0.00 4.18
7 8 1.719709 GCCCTTTTATGACGGCGAC 59.280 57.895 16.62 8.59 0.00 5.19
8 9 4.211986 GCCCTTTTATGACGGCGA 57.788 55.556 16.62 0.00 0.00 5.54
10 11 0.461339 TCTCGCCCTTTTATGACGGC 60.461 55.000 0.00 0.00 38.07 5.68
11 12 1.287425 GTCTCGCCCTTTTATGACGG 58.713 55.000 0.00 0.00 0.00 4.79
12 13 1.287425 GGTCTCGCCCTTTTATGACG 58.713 55.000 0.00 0.00 0.00 4.35
13 14 2.396590 TGGTCTCGCCCTTTTATGAC 57.603 50.000 0.00 0.00 36.04 3.06
14 15 2.158813 GGATGGTCTCGCCCTTTTATGA 60.159 50.000 0.00 0.00 36.04 2.15
15 16 2.158755 AGGATGGTCTCGCCCTTTTATG 60.159 50.000 0.00 0.00 36.04 1.90
16 17 2.127708 AGGATGGTCTCGCCCTTTTAT 58.872 47.619 0.00 0.00 36.04 1.40
17 18 1.580059 AGGATGGTCTCGCCCTTTTA 58.420 50.000 0.00 0.00 36.04 1.52
18 19 0.698818 AAGGATGGTCTCGCCCTTTT 59.301 50.000 0.00 0.00 35.64 2.27
19 20 0.253327 GAAGGATGGTCTCGCCCTTT 59.747 55.000 0.00 0.00 38.97 3.11
20 21 1.908483 GAAGGATGGTCTCGCCCTT 59.092 57.895 0.00 0.00 41.34 3.95
21 22 2.427245 CGAAGGATGGTCTCGCCCT 61.427 63.158 0.00 0.00 36.04 5.19
22 23 2.107141 CGAAGGATGGTCTCGCCC 59.893 66.667 0.00 0.00 36.04 6.13
23 24 2.586357 GCGAAGGATGGTCTCGCC 60.586 66.667 4.41 0.00 43.03 5.54
25 26 1.298713 CGAGCGAAGGATGGTCTCG 60.299 63.158 0.00 0.00 40.22 4.04
26 27 0.526524 CACGAGCGAAGGATGGTCTC 60.527 60.000 0.00 0.00 0.00 3.36
27 28 1.513158 CACGAGCGAAGGATGGTCT 59.487 57.895 0.00 0.00 0.00 3.85
28 29 2.167861 GCACGAGCGAAGGATGGTC 61.168 63.158 0.00 0.00 0.00 4.02
29 30 2.125512 GCACGAGCGAAGGATGGT 60.126 61.111 0.00 0.00 0.00 3.55
39 40 3.062234 GGCCGATTATTATTAGCACGAGC 59.938 47.826 0.00 0.00 42.56 5.03
40 41 3.303495 CGGCCGATTATTATTAGCACGAG 59.697 47.826 24.07 0.00 0.00 4.18
41 42 3.247442 CGGCCGATTATTATTAGCACGA 58.753 45.455 24.07 0.00 0.00 4.35
42 43 2.222729 GCGGCCGATTATTATTAGCACG 60.223 50.000 33.48 0.00 0.00 5.34
43 44 2.222729 CGCGGCCGATTATTATTAGCAC 60.223 50.000 33.48 4.17 36.29 4.40
44 45 1.996898 CGCGGCCGATTATTATTAGCA 59.003 47.619 33.48 0.00 36.29 3.49
45 46 2.028883 GTCGCGGCCGATTATTATTAGC 59.971 50.000 33.48 4.82 46.38 3.09
46 47 3.247442 TGTCGCGGCCGATTATTATTAG 58.753 45.455 33.48 5.83 46.38 1.73
47 48 3.300852 TGTCGCGGCCGATTATTATTA 57.699 42.857 33.48 0.77 46.38 0.98
48 49 2.157834 TGTCGCGGCCGATTATTATT 57.842 45.000 33.48 0.00 46.38 1.40
49 50 2.066262 CTTGTCGCGGCCGATTATTAT 58.934 47.619 33.48 0.00 46.38 1.28
50 51 1.493772 CTTGTCGCGGCCGATTATTA 58.506 50.000 33.48 7.77 46.38 0.98
51 52 1.772063 GCTTGTCGCGGCCGATTATT 61.772 55.000 33.48 0.00 46.38 1.40
52 53 2.244651 GCTTGTCGCGGCCGATTAT 61.245 57.895 33.48 0.00 46.38 1.28
53 54 2.845752 AAGCTTGTCGCGGCCGATTA 62.846 55.000 33.48 10.33 46.38 1.75
54 55 4.760047 AGCTTGTCGCGGCCGATT 62.760 61.111 33.48 0.31 46.38 3.34
55 56 4.760047 AAGCTTGTCGCGGCCGAT 62.760 61.111 33.48 0.00 46.38 4.18
59 60 3.660111 AACCAAGCTTGTCGCGGC 61.660 61.111 24.35 2.29 45.59 6.53
60 61 2.252260 CAACCAAGCTTGTCGCGG 59.748 61.111 24.35 11.72 45.59 6.46
61 62 1.565156 TAGCAACCAAGCTTGTCGCG 61.565 55.000 24.35 11.84 43.70 5.87
62 63 0.591170 TTAGCAACCAAGCTTGTCGC 59.409 50.000 24.35 21.32 43.70 5.19
63 64 3.058293 TCAATTAGCAACCAAGCTTGTCG 60.058 43.478 24.35 12.91 43.70 4.35
64 65 4.479619 CTCAATTAGCAACCAAGCTTGTC 58.520 43.478 24.35 10.72 43.70 3.18
65 66 4.510038 CTCAATTAGCAACCAAGCTTGT 57.490 40.909 24.35 10.37 43.70 3.16
77 78 2.466654 CCGGATCGGTGCTCAATTAGC 61.467 57.143 0.00 0.00 44.67 3.09
78 79 1.502231 CCGGATCGGTGCTCAATTAG 58.498 55.000 0.00 0.00 42.73 1.73
99 100 2.906047 GTGATGCTCACGGGCTATC 58.094 57.895 1.40 0.00 37.67 2.08
227 240 1.251251 CCTTTTGGTCCAAGCCAGAG 58.749 55.000 4.09 0.18 40.01 3.35
228 241 0.827507 GCCTTTTGGTCCAAGCCAGA 60.828 55.000 4.09 0.00 42.99 3.86
229 242 1.667722 GCCTTTTGGTCCAAGCCAG 59.332 57.895 4.09 2.83 42.99 4.85
230 243 1.836604 GGCCTTTTGGTCCAAGCCA 60.837 57.895 22.51 0.00 42.99 4.75
271 285 0.586802 CGTCTCGTGTGAGTGAGTGA 59.413 55.000 0.00 0.00 43.09 3.41
272 286 0.999228 GCGTCTCGTGTGAGTGAGTG 60.999 60.000 0.00 0.00 43.09 3.51
273 287 1.283181 GCGTCTCGTGTGAGTGAGT 59.717 57.895 0.00 0.00 43.09 3.41
274 288 0.999228 GTGCGTCTCGTGTGAGTGAG 60.999 60.000 0.00 0.00 43.09 3.51
327 347 0.459489 GGGCTGAGAGACACTGCTAG 59.541 60.000 0.00 0.00 33.80 3.42
346 366 2.086251 TTTCCCAAAGCAAGCAGGCG 62.086 55.000 0.00 0.00 39.27 5.52
351 371 1.221466 GGCGTTTTCCCAAAGCAAGC 61.221 55.000 0.00 0.00 0.00 4.01
360 388 1.604438 GGTCAAACATGGCGTTTTCCC 60.604 52.381 0.00 0.00 45.79 3.97
395 423 3.059461 CGTACTAGCACTGTAGCTCTAGC 60.059 52.174 7.78 0.00 45.26 3.42
396 424 4.209703 GTCGTACTAGCACTGTAGCTCTAG 59.790 50.000 7.78 0.00 45.26 2.43
397 425 4.118410 GTCGTACTAGCACTGTAGCTCTA 58.882 47.826 7.78 0.00 45.26 2.43
398 426 2.937799 GTCGTACTAGCACTGTAGCTCT 59.062 50.000 7.78 0.00 45.26 4.09
409 437 0.802607 GCCTGCAGTGTCGTACTAGC 60.803 60.000 13.81 0.38 37.60 3.42
412 440 1.290324 CTGCCTGCAGTGTCGTACT 59.710 57.895 13.81 0.00 41.36 2.73
440 468 4.432712 CTTGCTTTGTTTACCTGTTGCTT 58.567 39.130 0.00 0.00 0.00 3.91
441 469 3.737972 GCTTGCTTTGTTTACCTGTTGCT 60.738 43.478 0.00 0.00 0.00 3.91
442 470 2.539688 GCTTGCTTTGTTTACCTGTTGC 59.460 45.455 0.00 0.00 0.00 4.17
485 513 2.551270 TCCTCTGCCTGTCTAATTGGT 58.449 47.619 0.00 0.00 0.00 3.67
723 804 6.116711 CTAGTGCTCTATACTAGTCCTCCA 57.883 45.833 0.00 0.00 41.58 3.86
735 816 2.251409 TACCGCGACTAGTGCTCTAT 57.749 50.000 8.23 0.00 0.00 1.98
736 817 2.028420 TTACCGCGACTAGTGCTCTA 57.972 50.000 8.23 0.00 0.00 2.43
737 818 1.171308 TTTACCGCGACTAGTGCTCT 58.829 50.000 8.23 0.00 0.00 4.09
738 819 1.986698 TTTTACCGCGACTAGTGCTC 58.013 50.000 8.23 0.00 0.00 4.26
764 856 7.972277 CGAGCGGCTCCTTTATTATTAGTATTA 59.028 37.037 23.36 0.00 0.00 0.98
994 1121 2.224885 GCGACGACTTCATCTCGCC 61.225 63.158 0.00 0.00 42.86 5.54
1208 1335 4.704833 CGCACAGTCCACCCCCAG 62.705 72.222 0.00 0.00 0.00 4.45
1230 1357 2.334653 CTGCCCTCGCGAGATCTC 59.665 66.667 36.59 20.80 40.84 2.75
1298 1425 0.785708 CGAACGCGCTAAACAGCTTG 60.786 55.000 5.73 0.00 0.00 4.01
1390 1520 4.218686 GCACTTGGGTGGGGGTGT 62.219 66.667 0.00 0.00 43.18 4.16
1391 1521 4.994756 GGCACTTGGGTGGGGGTG 62.995 72.222 0.00 0.00 43.18 4.61
1393 1523 3.996621 ATGGCACTTGGGTGGGGG 61.997 66.667 0.00 0.00 43.18 5.40
1394 1524 2.681064 CATGGCACTTGGGTGGGG 60.681 66.667 0.00 0.00 43.18 4.96
1395 1525 1.978617 GACATGGCACTTGGGTGGG 60.979 63.158 0.00 0.00 43.18 4.61
1396 1526 0.827089 TTGACATGGCACTTGGGTGG 60.827 55.000 0.00 0.00 43.18 4.61
1397 1527 1.259609 ATTGACATGGCACTTGGGTG 58.740 50.000 0.00 0.00 45.53 4.61
1398 1528 1.619827 CAATTGACATGGCACTTGGGT 59.380 47.619 20.97 0.00 0.00 4.51
1399 1529 1.673626 GCAATTGACATGGCACTTGGG 60.674 52.381 27.32 8.80 31.44 4.12
1400 1530 1.673626 GGCAATTGACATGGCACTTGG 60.674 52.381 27.32 13.16 42.45 3.61
1401 1531 1.274167 AGGCAATTGACATGGCACTTG 59.726 47.619 23.59 23.59 45.08 3.16
1402 1532 1.547372 GAGGCAATTGACATGGCACTT 59.453 47.619 15.18 0.00 45.08 3.16
1413 1543 0.248621 GCGAAATCCCGAGGCAATTG 60.249 55.000 0.00 0.00 0.00 2.32
1434 1564 2.044650 CATGGCACTCCACCAGGG 60.045 66.667 0.00 0.00 46.92 4.45
1454 1585 2.100631 CAGATCCGAACGGTGGCAC 61.101 63.158 9.70 9.70 36.47 5.01
1486 1617 0.037232 GTCTCCCAGAACCGTTCCTG 60.037 60.000 7.68 5.84 0.00 3.86
1487 1618 0.178929 AGTCTCCCAGAACCGTTCCT 60.179 55.000 7.68 0.00 0.00 3.36
1527 1658 2.488820 GGGCTCGTCGGTCACTAC 59.511 66.667 0.00 0.00 0.00 2.73
1535 1666 4.657824 ACAACACCGGGCTCGTCG 62.658 66.667 4.71 0.00 33.95 5.12
1568 1699 5.579119 CCAATTCACGCATTACACACTACTA 59.421 40.000 0.00 0.00 0.00 1.82
1569 1700 4.391830 CCAATTCACGCATTACACACTACT 59.608 41.667 0.00 0.00 0.00 2.57
1570 1701 4.153475 ACCAATTCACGCATTACACACTAC 59.847 41.667 0.00 0.00 0.00 2.73
1578 1709 4.762765 AGTAACCAACCAATTCACGCATTA 59.237 37.500 0.00 0.00 0.00 1.90
1729 1860 7.360861 CCGTATGAAGCACTAAAATTCAGTTGA 60.361 37.037 0.00 0.00 36.47 3.18
1765 1897 1.006805 CGCCAAAACCCAATCGCAA 60.007 52.632 0.00 0.00 0.00 4.85
2024 2158 2.793278 AAAACGACACTTGGGAATGC 57.207 45.000 0.00 0.00 0.00 3.56
2172 2317 3.368236 GCTGCTCTTAAGTCTTAACACGG 59.632 47.826 1.63 1.15 0.00 4.94
2177 2322 6.102897 ACAGAAGCTGCTCTTAAGTCTTAA 57.897 37.500 1.00 4.97 34.56 1.85
2178 2323 5.730296 ACAGAAGCTGCTCTTAAGTCTTA 57.270 39.130 1.00 0.00 34.56 2.10
2179 2324 4.615588 ACAGAAGCTGCTCTTAAGTCTT 57.384 40.909 1.00 0.00 34.56 3.01
2180 2325 5.323371 CTACAGAAGCTGCTCTTAAGTCT 57.677 43.478 1.00 0.00 34.56 3.24
2231 2376 9.609346 GCCATATCCTGTTAAAAGTAAAGTAGA 57.391 33.333 0.00 0.00 0.00 2.59
2416 2563 1.126846 CTCGCAGGAAACGATCAACAC 59.873 52.381 0.00 0.00 39.12 3.32
2458 2605 0.322187 TTTGAAGAAGGGCGGCTACC 60.322 55.000 9.56 0.00 0.00 3.18
2792 2939 7.153315 CCTCCGTTCCTAAATATAAGTCCTTC 58.847 42.308 0.00 0.00 0.00 3.46
3044 3191 4.286032 TGACCCTAAGCATGTAACTGAACT 59.714 41.667 0.00 0.00 0.00 3.01
3064 3211 9.664332 ATCCTAAATGCTATCATCATAACTGAC 57.336 33.333 0.00 0.00 33.22 3.51
3105 3252 1.326213 TAGAGCTGGGAGTGCAGAGC 61.326 60.000 0.00 0.00 0.00 4.09
3147 3294 8.923270 TCCACATTTTCCTTGAAGAACTTAATT 58.077 29.630 0.00 0.00 0.00 1.40
3226 3373 3.427773 GGGCGAGAAGTTGTACTACTGAG 60.428 52.174 10.78 4.50 0.00 3.35
3227 3374 2.490903 GGGCGAGAAGTTGTACTACTGA 59.509 50.000 10.78 0.00 0.00 3.41
3228 3375 2.492484 AGGGCGAGAAGTTGTACTACTG 59.508 50.000 10.78 0.00 0.00 2.74
3229 3376 2.754002 GAGGGCGAGAAGTTGTACTACT 59.246 50.000 3.98 3.98 0.00 2.57
3230 3377 2.754002 AGAGGGCGAGAAGTTGTACTAC 59.246 50.000 0.00 0.00 0.00 2.73
3231 3378 3.015327 GAGAGGGCGAGAAGTTGTACTA 58.985 50.000 0.00 0.00 0.00 1.82
3232 3379 1.819903 GAGAGGGCGAGAAGTTGTACT 59.180 52.381 0.00 0.00 0.00 2.73
3238 3385 1.931635 AAAGAGAGAGGGCGAGAAGT 58.068 50.000 0.00 0.00 0.00 3.01
3268 3415 9.599866 TCAATAACATTAAGGTGATAGTGAGTG 57.400 33.333 0.00 0.00 30.20 3.51
3441 3588 8.930846 ATCCTGCAGCTTTAATAAATATGAGT 57.069 30.769 8.66 0.00 0.00 3.41
3677 3825 3.735237 TGTTGTTGTTGTTGTTGTGGT 57.265 38.095 0.00 0.00 0.00 4.16
3678 3826 4.610231 GCTTTGTTGTTGTTGTTGTTGTGG 60.610 41.667 0.00 0.00 0.00 4.17
3679 3827 4.453339 GCTTTGTTGTTGTTGTTGTTGTG 58.547 39.130 0.00 0.00 0.00 3.33
3680 3828 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
3681 3829 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
3682 3830 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
3683 3831 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3684 3832 4.450419 TGAAAGGCTTTGTTGTTGTTGTTG 59.550 37.500 18.79 0.00 0.00 3.33
3685 3833 4.636249 TGAAAGGCTTTGTTGTTGTTGTT 58.364 34.783 18.79 0.00 0.00 2.83
3686 3834 4.244862 CTGAAAGGCTTTGTTGTTGTTGT 58.755 39.130 18.79 0.00 0.00 3.32
3687 3835 4.244862 ACTGAAAGGCTTTGTTGTTGTTG 58.755 39.130 18.79 0.00 39.30 3.33
3688 3836 4.494484 GACTGAAAGGCTTTGTTGTTGTT 58.506 39.130 18.79 0.00 40.68 2.83
3952 4108 2.715749 TGATATGCAGTCACCCCTTG 57.284 50.000 0.00 0.00 0.00 3.61
4089 4245 1.400500 GGCACCATGTTTTTCGTACGG 60.400 52.381 16.52 0.00 0.00 4.02
4169 4325 7.709613 ACCCTAAGTATTTTACATAAGAGTGCG 59.290 37.037 0.00 0.00 0.00 5.34
4372 4530 1.138069 CAAGGTTGTCCCACCAAAACC 59.862 52.381 0.00 0.00 42.00 3.27
4462 4620 4.280677 ACAGAGACATAGCTCTCTAATGGC 59.719 45.833 3.12 0.00 44.46 4.40
4611 4770 9.886132 TCTGAAAGGAGTATGGAGTAATTAAAC 57.114 33.333 0.00 0.00 0.00 2.01
4889 5049 8.725148 ACAATATGAGTTTCTGAAGAATGTGAC 58.275 33.333 0.00 0.00 33.54 3.67
5097 5257 3.132646 AGAGAGTTCTCCATCATGACTGC 59.867 47.826 0.00 0.00 43.88 4.40
5248 5408 6.183360 ACAGTTGTAAAAATGCCACATCAAGA 60.183 34.615 0.00 0.00 0.00 3.02
5326 5487 6.803154 AAAAGTCTTAGATTTTGAGACGGG 57.197 37.500 3.53 0.00 43.43 5.28
5503 5665 1.303074 AGCACCGACCACGACTCTA 60.303 57.895 0.00 0.00 42.66 2.43
5508 5670 0.038892 GTTAAGAGCACCGACCACGA 60.039 55.000 0.00 0.00 42.66 4.35
5545 5707 3.291584 TGTGCACAAACCAAATCCAGTA 58.708 40.909 19.28 0.00 0.00 2.74
5980 6142 6.951971 ACTTGGTAGCTTATTGTCTCTCAAT 58.048 36.000 0.00 0.00 46.82 2.57
6256 6421 1.995626 CGGGGAGGAACTGGGTGAT 60.996 63.158 0.00 0.00 41.55 3.06
6491 6656 4.708386 CCCAGGCGGCGTTGGTAA 62.708 66.667 23.98 0.00 32.40 2.85
6520 6685 6.056236 GCCCCTAGAAGGTATAGAAAAACTG 58.944 44.000 0.00 0.00 31.93 3.16
6595 6760 1.228094 GCTCATTCTAGCAGCCCCC 60.228 63.158 0.00 0.00 42.30 5.40
6601 6766 3.636300 GAGAAGAGAGGCTCATTCTAGCA 59.364 47.826 25.71 0.00 44.64 3.49
6634 6799 4.253685 GACGATCCTCCAAGAATGTTTGA 58.746 43.478 0.00 0.00 0.00 2.69
6707 6872 1.020861 TGCAGCGCTACACAGAATGG 61.021 55.000 10.99 0.00 43.62 3.16
6782 6947 9.661563 TTGTGTTTCTCTGTTTCTAGTTAAGAA 57.338 29.630 0.00 0.00 42.62 2.52
6865 7107 2.893215 TCTCTAGTCCCCTTTCACGA 57.107 50.000 0.00 0.00 0.00 4.35
6887 7130 3.995705 CCACAACTTAAATTGCACCATGG 59.004 43.478 11.19 11.19 32.47 3.66
6897 7140 9.255029 AGGCATATAAACTTCCACAACTTAAAT 57.745 29.630 0.00 0.00 0.00 1.40
6902 7145 6.067217 AGAGGCATATAAACTTCCACAACT 57.933 37.500 0.00 0.00 0.00 3.16
6945 7188 8.177663 CCTTCACTAGTTTATGTGCATAACAAG 58.822 37.037 4.31 5.41 43.61 3.16
6951 7194 4.526970 CCCCTTCACTAGTTTATGTGCAT 58.473 43.478 0.00 0.00 34.49 3.96
6952 7195 3.308117 CCCCCTTCACTAGTTTATGTGCA 60.308 47.826 0.00 0.00 34.49 4.57
6953 7196 3.054655 TCCCCCTTCACTAGTTTATGTGC 60.055 47.826 0.00 0.00 34.49 4.57
6956 7199 5.437191 AGTTCCCCCTTCACTAGTTTATG 57.563 43.478 0.00 0.00 0.00 1.90
6960 7203 4.415224 TCTAGTTCCCCCTTCACTAGTT 57.585 45.455 0.00 0.00 40.59 2.24
6964 7330 1.840635 GCATCTAGTTCCCCCTTCACT 59.159 52.381 0.00 0.00 0.00 3.41
6995 7361 6.183360 GCTTTTTGTACATGCACATTCATGAG 60.183 38.462 10.31 0.00 44.94 2.90
7015 7381 3.871006 GGCACTAAAACTTGCAAGCTTTT 59.129 39.130 27.54 27.39 0.00 2.27
7049 7415 9.822727 TGAAGGAGTATATCATATGGAACTACA 57.177 33.333 2.13 0.00 0.00 2.74
7102 7471 6.894339 AAAGTAGTTAAGAAACCACATGGG 57.106 37.500 2.32 0.00 44.81 4.00
7451 7820 1.653151 GAGTGAGGTTAATCCGCCAC 58.347 55.000 11.09 11.09 41.41 5.01
7454 7823 0.831307 AGGGAGTGAGGTTAATCCGC 59.169 55.000 0.00 0.00 41.99 5.54
7456 7825 6.502074 AAGAATAGGGAGTGAGGTTAATCC 57.498 41.667 0.00 0.00 34.18 3.01
7466 7835 3.691609 GCACAGGAAAAGAATAGGGAGTG 59.308 47.826 0.00 0.00 0.00 3.51
7541 7911 1.036707 AGTAGCCAAGCCTCTCGATC 58.963 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.