Multiple sequence alignment - TraesCS5B01G294200

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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 TraesCS5B01G294200 chr5B 100.000 2621 0 0 1 2621 478513716 478516336 0.000000e+00 4841.0
1 TraesCS5B01G294200 chr5B 95.890 73 3 0 1 73 478502532 478502604 4.580000e-23 119.0
2 TraesCS5B01G294200 chr5B 97.015 67 2 0 1 67 360936514 360936448 2.130000e-21 113.0
3 TraesCS5B01G294200 chr5B 91.045 67 3 3 1874 1939 458618848 458618912 1.290000e-13 87.9
4 TraesCS5B01G294200 chr5A 88.679 1590 109 34 66 1625 503622036 503623584 0.000000e+00 1873.0
5 TraesCS5B01G294200 chr5A 85.009 527 53 6 2092 2617 503623927 503624428 1.800000e-141 512.0
6 TraesCS5B01G294200 chr5A 92.222 180 13 1 1630 1809 503623679 503623857 1.200000e-63 254.0
7 TraesCS5B01G294200 chr5A 82.075 212 16 11 66 275 503544755 503544946 7.510000e-36 161.0
8 TraesCS5B01G294200 chr5A 87.407 135 17 0 1072 1206 503233496 503233630 3.490000e-34 156.0
9 TraesCS5B01G294200 chr5D 89.085 1530 95 30 411 1892 398547283 398548788 0.000000e+00 1834.0
10 TraesCS5B01G294200 chr5D 87.106 667 71 12 1960 2621 398548774 398549430 0.000000e+00 741.0
11 TraesCS5B01G294200 chr5D 82.206 281 27 16 130 405 398546567 398546829 1.220000e-53 220.0
12 TraesCS5B01G294200 chr5D 84.507 142 22 0 1072 1213 398124882 398125023 9.780000e-30 141.0
13 TraesCS5B01G294200 chr3D 79.130 230 40 8 2306 2531 390081195 390081420 4.520000e-33 152.0
14 TraesCS5B01G294200 chr3D 91.176 68 4 2 1873 1939 134495860 134495926 9.990000e-15 91.6
15 TraesCS5B01G294200 chr3D 90.769 65 6 0 1875 1939 87522447 87522511 1.290000e-13 87.9
16 TraesCS5B01G294200 chr2A 96.970 66 2 0 1 66 768200762 768200697 7.670000e-21 111.0
17 TraesCS5B01G294200 chr4D 95.522 67 3 0 1 67 35449141 35449207 9.920000e-20 108.0
18 TraesCS5B01G294200 chr2B 95.522 67 3 0 1 67 678966427 678966361 9.920000e-20 108.0
19 TraesCS5B01G294200 chr2B 96.429 56 2 0 1884 1939 519018491 519018546 2.780000e-15 93.5
20 TraesCS5B01G294200 chr1B 94.366 71 3 1 1 70 1847421 1847491 9.920000e-20 108.0
21 TraesCS5B01G294200 chr1B 95.522 67 3 0 1 67 657167732 657167798 9.920000e-20 108.0
22 TraesCS5B01G294200 chr1B 94.286 70 3 1 2 71 25739188 25739256 3.570000e-19 106.0
23 TraesCS5B01G294200 chr4B 94.203 69 4 0 1 69 568662212 568662144 3.570000e-19 106.0
24 TraesCS5B01G294200 chr7B 91.429 70 2 4 1889 1957 408954802 408954736 2.780000e-15 93.5
25 TraesCS5B01G294200 chr3B 96.429 56 2 0 1884 1939 332607879 332607824 2.780000e-15 93.5
26 TraesCS5B01G294200 chr3B 93.443 61 4 0 1879 1939 454613831 454613891 9.990000e-15 91.6
27 TraesCS5B01G294200 chr3A 90.141 71 5 2 1871 1939 644809275 644809205 9.990000e-15 91.6
28 TraesCS5B01G294200 chr1D 93.443 61 3 1 1880 1939 336626994 336626934 3.590000e-14 89.8


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 TraesCS5B01G294200 chr5B 478513716 478516336 2620 False 4841.000000 4841 100.000000 1 2621 1 chr5B.!!$F3 2620
1 TraesCS5B01G294200 chr5A 503622036 503624428 2392 False 879.666667 1873 88.636667 66 2617 3 chr5A.!!$F3 2551
2 TraesCS5B01G294200 chr5D 398546567 398549430 2863 False 931.666667 1834 86.132333 130 2621 3 chr5D.!!$F2 2491

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
919 1407 0.179097 GCTCGAGGACAAGACCCATC 60.179 60.0 15.58 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2697 0.600782 GGCACATGCTTGGTTGGTTG 60.601 55.0 3.48 0.0 41.7 3.77 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
17 18 4.695560 GACTTGAACTCGGGTGGG 57.304 61.111 0.00 0.00 0.00 4.61
18 19 1.671379 GACTTGAACTCGGGTGGGC 60.671 63.158 0.00 0.00 0.00 5.36
19 20 2.113243 GACTTGAACTCGGGTGGGCT 62.113 60.000 0.00 0.00 0.00 5.19
20 21 1.672356 CTTGAACTCGGGTGGGCTG 60.672 63.158 0.00 0.00 0.00 4.85
21 22 3.190738 TTGAACTCGGGTGGGCTGG 62.191 63.158 0.00 0.00 0.00 4.85
30 31 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
31 32 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
32 33 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
33 34 2.598394 GGCTGGCAGCAACCTCAA 60.598 61.111 37.49 0.00 44.75 3.02
34 35 1.980772 GGCTGGCAGCAACCTCAAT 60.981 57.895 37.49 0.00 44.75 2.57
35 36 1.538687 GGCTGGCAGCAACCTCAATT 61.539 55.000 37.49 0.00 44.75 2.32
36 37 0.389426 GCTGGCAGCAACCTCAATTG 60.389 55.000 33.33 0.00 41.89 2.32
43 44 1.593265 CAACCTCAATTGCCCAGCC 59.407 57.895 0.00 0.00 0.00 4.85
44 45 1.155859 AACCTCAATTGCCCAGCCA 59.844 52.632 0.00 0.00 0.00 4.75
45 46 0.471591 AACCTCAATTGCCCAGCCAA 60.472 50.000 0.00 0.00 0.00 4.52
46 47 1.187567 ACCTCAATTGCCCAGCCAAC 61.188 55.000 0.00 0.00 0.00 3.77
47 48 1.213537 CTCAATTGCCCAGCCAACG 59.786 57.895 0.00 0.00 0.00 4.10
48 49 2.216750 CTCAATTGCCCAGCCAACGG 62.217 60.000 0.00 0.00 0.00 4.44
50 51 3.826265 AATTGCCCAGCCAACGGGT 62.826 57.895 0.00 0.00 46.40 5.28
51 52 4.966787 TTGCCCAGCCAACGGGTC 62.967 66.667 0.00 0.00 46.40 4.46
55 56 4.003788 CCAGCCAACGGGTCGACT 62.004 66.667 16.46 0.00 36.17 4.18
56 57 2.432628 CAGCCAACGGGTCGACTC 60.433 66.667 16.46 11.18 36.17 3.36
57 58 3.692406 AGCCAACGGGTCGACTCC 61.692 66.667 16.46 13.73 36.17 3.85
58 59 4.754667 GCCAACGGGTCGACTCCC 62.755 72.222 16.46 8.39 43.78 4.30
59 60 4.078516 CCAACGGGTCGACTCCCC 62.079 72.222 16.46 7.58 44.32 4.81
64 65 4.755507 GGGTCGACTCCCCGTCCT 62.756 72.222 16.46 0.00 41.54 3.85
87 88 5.788450 TCACAAACCTGAAAAGAAAAAGCA 58.212 33.333 0.00 0.00 0.00 3.91
110 111 1.808411 GGTATGTGTGGACTGTGGTG 58.192 55.000 0.00 0.00 0.00 4.17
113 114 1.679139 ATGTGTGGACTGTGGTGTTG 58.321 50.000 0.00 0.00 0.00 3.33
114 115 0.615850 TGTGTGGACTGTGGTGTTGA 59.384 50.000 0.00 0.00 0.00 3.18
115 116 1.299541 GTGTGGACTGTGGTGTTGAG 58.700 55.000 0.00 0.00 0.00 3.02
123 124 2.027192 ACTGTGGTGTTGAGTCTGTTGT 60.027 45.455 0.00 0.00 0.00 3.32
124 125 2.609459 CTGTGGTGTTGAGTCTGTTGTC 59.391 50.000 0.00 0.00 0.00 3.18
125 126 2.236146 TGTGGTGTTGAGTCTGTTGTCT 59.764 45.455 0.00 0.00 0.00 3.41
126 127 2.609459 GTGGTGTTGAGTCTGTTGTCTG 59.391 50.000 0.00 0.00 0.00 3.51
127 128 2.499693 TGGTGTTGAGTCTGTTGTCTGA 59.500 45.455 0.00 0.00 0.00 3.27
128 129 2.866762 GGTGTTGAGTCTGTTGTCTGAC 59.133 50.000 0.00 0.00 40.99 3.51
169 170 0.532573 AGCACATACTGTCCGTCCAG 59.467 55.000 0.00 0.00 38.45 3.86
192 193 4.477975 CTCCGCTCGGTCGTCACC 62.478 72.222 8.28 0.00 39.69 4.02
246 247 1.141657 CATTGGTCGATGGTGGAGGAT 59.858 52.381 0.00 0.00 0.00 3.24
269 271 4.075910 CGCACGCACGCAGTTGAT 62.076 61.111 0.00 0.00 41.61 2.57
270 272 2.202222 GCACGCACGCAGTTGATC 60.202 61.111 0.00 0.00 41.61 2.92
288 301 2.113860 TCCAAGGATAGCACTGCAAC 57.886 50.000 3.30 0.00 0.00 4.17
296 309 7.412853 CAAGGATAGCACTGCAACTTAATTAG 58.587 38.462 3.30 0.00 0.00 1.73
300 313 3.372206 AGCACTGCAACTTAATTAGCTCG 59.628 43.478 3.30 0.00 0.00 5.03
301 314 3.370978 GCACTGCAACTTAATTAGCTCGA 59.629 43.478 0.00 0.00 0.00 4.04
302 315 4.493220 GCACTGCAACTTAATTAGCTCGAG 60.493 45.833 8.45 8.45 0.00 4.04
303 316 4.627467 CACTGCAACTTAATTAGCTCGAGT 59.373 41.667 15.13 3.51 0.00 4.18
304 317 5.805486 CACTGCAACTTAATTAGCTCGAGTA 59.195 40.000 15.13 2.48 0.00 2.59
305 318 5.805994 ACTGCAACTTAATTAGCTCGAGTAC 59.194 40.000 15.13 0.00 0.00 2.73
306 319 4.796830 TGCAACTTAATTAGCTCGAGTACG 59.203 41.667 15.13 0.00 41.26 3.67
307 320 4.797349 GCAACTTAATTAGCTCGAGTACGT 59.203 41.667 15.13 0.00 40.69 3.57
308 321 5.275788 GCAACTTAATTAGCTCGAGTACGTG 60.276 44.000 15.13 0.31 40.69 4.49
309 322 4.918037 ACTTAATTAGCTCGAGTACGTGG 58.082 43.478 15.13 1.09 40.69 4.94
310 323 4.637534 ACTTAATTAGCTCGAGTACGTGGA 59.362 41.667 15.13 0.00 40.69 4.02
311 324 5.298777 ACTTAATTAGCTCGAGTACGTGGAT 59.701 40.000 15.13 0.00 40.69 3.41
312 325 4.650754 AATTAGCTCGAGTACGTGGATT 57.349 40.909 15.13 2.91 40.69 3.01
313 326 4.650754 ATTAGCTCGAGTACGTGGATTT 57.349 40.909 15.13 0.00 40.69 2.17
314 327 2.563471 AGCTCGAGTACGTGGATTTC 57.437 50.000 15.13 0.00 40.69 2.17
315 328 1.134560 AGCTCGAGTACGTGGATTTCC 59.865 52.381 15.13 0.00 40.69 3.13
358 372 1.376037 GTGACCCTGGCTTTCTCGG 60.376 63.158 0.00 0.00 0.00 4.63
364 378 2.359107 TGGCTTTCTCGGCTGCAG 60.359 61.111 10.11 10.11 0.00 4.41
394 410 1.849976 GATATGCTGCCTTCGCCAGC 61.850 60.000 6.44 6.44 38.70 4.85
459 925 3.773630 CGTTACGCGCACACAGGG 61.774 66.667 5.73 0.00 0.00 4.45
462 928 1.739929 TTACGCGCACACAGGGATG 60.740 57.895 5.73 0.00 0.00 3.51
469 935 1.679977 CACACAGGGATGGCAAGGG 60.680 63.158 0.00 0.00 0.00 3.95
506 972 3.302344 CCCCCGGTTTGGTTGCTG 61.302 66.667 0.00 0.00 35.15 4.41
522 996 0.731417 GCTGCTGCTTCATACCACTG 59.269 55.000 8.53 0.00 36.03 3.66
607 1092 0.332632 TCCCAAAGAGCCAATCAGGG 59.667 55.000 0.00 0.00 37.84 4.45
635 1122 4.465632 TGCGCTCTTTAGACCTAATTGA 57.534 40.909 9.73 0.00 0.00 2.57
666 1153 6.152638 ACTTTCCCCATATTTTTCCTCTCA 57.847 37.500 0.00 0.00 0.00 3.27
676 1163 3.520290 TTTTCCTCTCACGCGTATCAT 57.480 42.857 13.44 0.00 0.00 2.45
690 1177 2.679837 CGTATCATGTTGCTGGCTTTCT 59.320 45.455 0.00 0.00 0.00 2.52
691 1178 3.242543 CGTATCATGTTGCTGGCTTTCTC 60.243 47.826 0.00 0.00 0.00 2.87
692 1179 1.159285 TCATGTTGCTGGCTTTCTCG 58.841 50.000 0.00 0.00 0.00 4.04
693 1180 0.455633 CATGTTGCTGGCTTTCTCGC 60.456 55.000 0.00 0.00 0.00 5.03
713 1201 2.628178 GCCTTTTTACCTTGCTTCCACT 59.372 45.455 0.00 0.00 0.00 4.00
740 1228 0.179161 CTCTCGTAGTGCCAACTCCG 60.179 60.000 0.00 0.00 37.12 4.63
741 1229 1.805945 CTCGTAGTGCCAACTCCGC 60.806 63.158 0.00 0.00 35.85 5.54
742 1230 2.048597 CGTAGTGCCAACTCCGCA 60.049 61.111 0.00 0.00 37.88 5.69
743 1231 1.447838 CGTAGTGCCAACTCCGCAT 60.448 57.895 0.00 0.00 38.76 4.73
807 1295 3.756933 TGGACTACGTACCAAAAGCTT 57.243 42.857 2.56 0.00 32.93 3.74
809 1297 3.069872 TGGACTACGTACCAAAAGCTTGA 59.930 43.478 0.00 0.00 34.14 3.02
811 1299 4.329256 GGACTACGTACCAAAAGCTTGATC 59.671 45.833 0.00 0.00 34.14 2.92
812 1300 4.890088 ACTACGTACCAAAAGCTTGATCA 58.110 39.130 0.00 0.00 34.14 2.92
813 1301 5.488341 ACTACGTACCAAAAGCTTGATCAT 58.512 37.500 0.00 0.00 34.14 2.45
815 1303 7.101054 ACTACGTACCAAAAGCTTGATCATTA 58.899 34.615 0.00 0.00 34.14 1.90
816 1304 6.178239 ACGTACCAAAAGCTTGATCATTAC 57.822 37.500 0.00 0.00 34.14 1.89
817 1305 5.703592 ACGTACCAAAAGCTTGATCATTACA 59.296 36.000 0.00 0.00 34.14 2.41
819 1307 6.688385 CGTACCAAAAGCTTGATCATTACATG 59.312 38.462 0.00 0.00 34.14 3.21
919 1407 0.179097 GCTCGAGGACAAGACCCATC 60.179 60.000 15.58 0.00 0.00 3.51
937 1425 1.923356 TCAATCCAAACCCTGAAGCC 58.077 50.000 0.00 0.00 0.00 4.35
938 1426 1.428912 TCAATCCAAACCCTGAAGCCT 59.571 47.619 0.00 0.00 0.00 4.58
939 1427 2.647299 TCAATCCAAACCCTGAAGCCTA 59.353 45.455 0.00 0.00 0.00 3.93
940 1428 3.269381 TCAATCCAAACCCTGAAGCCTAT 59.731 43.478 0.00 0.00 0.00 2.57
941 1429 4.026052 CAATCCAAACCCTGAAGCCTATT 58.974 43.478 0.00 0.00 0.00 1.73
959 1447 2.908688 TTCTCTTGTGCAGCACTGTA 57.091 45.000 25.83 10.68 35.11 2.74
986 1478 1.000731 CTAGCTATCAGCAGGGCACTC 59.999 57.143 0.00 0.00 45.56 3.51
1032 1524 2.816958 CGCAGCAGCTCATCGGTT 60.817 61.111 0.00 0.00 39.10 4.44
1045 1537 3.487372 TCATCGGTTATCATCCTCGACT 58.513 45.455 0.00 0.00 32.60 4.18
1212 1704 2.821366 CTCATGGTGGCAGCCGAC 60.821 66.667 14.97 6.21 0.00 4.79
1215 1707 3.321648 ATGGTGGCAGCCGACTCA 61.322 61.111 14.97 2.55 0.00 3.41
1216 1708 2.894257 ATGGTGGCAGCCGACTCAA 61.894 57.895 14.97 0.00 0.00 3.02
1338 1830 2.758089 GCTGGCGCTGTTCCATCAG 61.758 63.158 7.64 4.34 38.35 2.90
1355 1847 3.195698 GGAAGATGGCGACGGTGC 61.196 66.667 0.00 0.00 0.00 5.01
1467 1959 2.327343 GCTGCTGGATGTGTGCGAA 61.327 57.895 0.00 0.00 0.00 4.70
1484 1976 3.133691 GCGAAGATGAGCATGATACCAA 58.866 45.455 0.00 0.00 0.00 3.67
1625 2117 6.043411 GGATGAACGGGAGCATATAGTTATC 58.957 44.000 0.00 0.00 0.00 1.75
1627 2119 6.025749 TGAACGGGAGCATATAGTTATCTG 57.974 41.667 0.00 0.00 0.00 2.90
1628 2120 4.457834 ACGGGAGCATATAGTTATCTGC 57.542 45.455 2.32 2.32 36.42 4.26
1671 2257 2.031595 CCGAGTGACAGTAGATCGATGG 60.032 54.545 0.54 0.00 35.47 3.51
1734 2320 3.096092 GGGGTGAAAAATGACATGGCTA 58.904 45.455 0.00 0.00 0.00 3.93
1777 2363 2.249535 CCCCGCTTCTGCATCGATG 61.250 63.158 21.27 21.27 39.64 3.84
1789 2375 2.573009 TGCATCGATGGGATATGGTGAT 59.427 45.455 26.00 0.00 32.85 3.06
1794 2380 2.440409 GATGGGATATGGTGATGGTGC 58.560 52.381 0.00 0.00 0.00 5.01
1881 2492 6.016276 TCTGAAAAATTGGCAACTACTTCCTC 60.016 38.462 0.00 0.00 37.61 3.71
1882 2493 5.833131 TGAAAAATTGGCAACTACTTCCTCT 59.167 36.000 0.00 0.00 37.61 3.69
1883 2494 5.712152 AAAATTGGCAACTACTTCCTCTG 57.288 39.130 0.00 0.00 37.61 3.35
1884 2495 4.373156 AATTGGCAACTACTTCCTCTGT 57.627 40.909 0.00 0.00 37.61 3.41
1885 2496 5.499004 AATTGGCAACTACTTCCTCTGTA 57.501 39.130 0.00 0.00 37.61 2.74
1886 2497 5.700402 ATTGGCAACTACTTCCTCTGTAT 57.300 39.130 0.00 0.00 37.61 2.29
1887 2498 4.737855 TGGCAACTACTTCCTCTGTATC 57.262 45.455 0.00 0.00 37.61 2.24
1888 2499 4.353777 TGGCAACTACTTCCTCTGTATCT 58.646 43.478 0.00 0.00 37.61 1.98
1889 2500 5.516044 TGGCAACTACTTCCTCTGTATCTA 58.484 41.667 0.00 0.00 37.61 1.98
1890 2501 5.360144 TGGCAACTACTTCCTCTGTATCTAC 59.640 44.000 0.00 0.00 37.61 2.59
1891 2502 5.595133 GGCAACTACTTCCTCTGTATCTACT 59.405 44.000 0.00 0.00 0.00 2.57
1892 2503 6.238814 GGCAACTACTTCCTCTGTATCTACTC 60.239 46.154 0.00 0.00 0.00 2.59
1893 2504 6.544564 GCAACTACTTCCTCTGTATCTACTCT 59.455 42.308 0.00 0.00 0.00 3.24
1894 2505 7.255001 GCAACTACTTCCTCTGTATCTACTCTC 60.255 44.444 0.00 0.00 0.00 3.20
1895 2506 7.685849 ACTACTTCCTCTGTATCTACTCTCT 57.314 40.000 0.00 0.00 0.00 3.10
1896 2507 7.732996 ACTACTTCCTCTGTATCTACTCTCTC 58.267 42.308 0.00 0.00 0.00 3.20
1897 2508 5.937111 ACTTCCTCTGTATCTACTCTCTCC 58.063 45.833 0.00 0.00 0.00 3.71
1898 2509 4.610605 TCCTCTGTATCTACTCTCTCCG 57.389 50.000 0.00 0.00 0.00 4.63
1899 2510 3.968649 TCCTCTGTATCTACTCTCTCCGT 59.031 47.826 0.00 0.00 0.00 4.69
1900 2511 4.039488 TCCTCTGTATCTACTCTCTCCGTC 59.961 50.000 0.00 0.00 0.00 4.79
1901 2512 4.312443 CTCTGTATCTACTCTCTCCGTCC 58.688 52.174 0.00 0.00 0.00 4.79
1902 2513 3.061322 CTGTATCTACTCTCTCCGTCCG 58.939 54.545 0.00 0.00 0.00 4.79
1903 2514 2.697229 TGTATCTACTCTCTCCGTCCGA 59.303 50.000 0.00 0.00 0.00 4.55
1904 2515 3.133542 TGTATCTACTCTCTCCGTCCGAA 59.866 47.826 0.00 0.00 0.00 4.30
1905 2516 2.775911 TCTACTCTCTCCGTCCGAAA 57.224 50.000 0.00 0.00 0.00 3.46
1906 2517 3.063510 TCTACTCTCTCCGTCCGAAAA 57.936 47.619 0.00 0.00 0.00 2.29
1907 2518 3.618351 TCTACTCTCTCCGTCCGAAAAT 58.382 45.455 0.00 0.00 0.00 1.82
1908 2519 4.774124 TCTACTCTCTCCGTCCGAAAATA 58.226 43.478 0.00 0.00 0.00 1.40
1909 2520 3.779271 ACTCTCTCCGTCCGAAAATAC 57.221 47.619 0.00 0.00 0.00 1.89
1910 2521 3.354467 ACTCTCTCCGTCCGAAAATACT 58.646 45.455 0.00 0.00 0.00 2.12
1911 2522 3.762823 ACTCTCTCCGTCCGAAAATACTT 59.237 43.478 0.00 0.00 0.00 2.24
1912 2523 4.106029 TCTCTCCGTCCGAAAATACTTG 57.894 45.455 0.00 0.00 0.00 3.16
1913 2524 3.508793 TCTCTCCGTCCGAAAATACTTGT 59.491 43.478 0.00 0.00 0.00 3.16
1914 2525 3.841643 TCTCCGTCCGAAAATACTTGTC 58.158 45.455 0.00 0.00 0.00 3.18
1915 2526 3.256383 TCTCCGTCCGAAAATACTTGTCA 59.744 43.478 0.00 0.00 0.00 3.58
1916 2527 4.081862 TCTCCGTCCGAAAATACTTGTCAT 60.082 41.667 0.00 0.00 0.00 3.06
1917 2528 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
1918 2529 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
1919 2530 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
1920 2531 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
1921 2532 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
1922 2533 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
1923 2534 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
1924 2535 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
1925 2536 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
1926 2537 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
1933 2544 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
1934 2545 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
1935 2546 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
1936 2547 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
1937 2548 7.147689 TGTCATCAAAATGGATAAAAGGGGATG 60.148 37.037 0.00 0.00 33.42 3.51
1938 2549 6.902416 TCATCAAAATGGATAAAAGGGGATGT 59.098 34.615 0.00 0.00 33.42 3.06
1939 2550 6.543430 TCAAAATGGATAAAAGGGGATGTG 57.457 37.500 0.00 0.00 0.00 3.21
1940 2551 6.259893 TCAAAATGGATAAAAGGGGATGTGA 58.740 36.000 0.00 0.00 0.00 3.58
1941 2552 6.380846 TCAAAATGGATAAAAGGGGATGTGAG 59.619 38.462 0.00 0.00 0.00 3.51
1942 2553 5.472301 AATGGATAAAAGGGGATGTGAGT 57.528 39.130 0.00 0.00 0.00 3.41
1943 2554 6.590656 AATGGATAAAAGGGGATGTGAGTA 57.409 37.500 0.00 0.00 0.00 2.59
1944 2555 5.367945 TGGATAAAAGGGGATGTGAGTAC 57.632 43.478 0.00 0.00 0.00 2.73
1945 2556 5.036916 TGGATAAAAGGGGATGTGAGTACT 58.963 41.667 0.00 0.00 0.00 2.73
1946 2557 5.491078 TGGATAAAAGGGGATGTGAGTACTT 59.509 40.000 0.00 0.00 0.00 2.24
1947 2558 6.011981 TGGATAAAAGGGGATGTGAGTACTTT 60.012 38.462 0.00 0.00 0.00 2.66
1948 2559 6.890268 GGATAAAAGGGGATGTGAGTACTTTT 59.110 38.462 0.00 0.00 40.17 2.27
1949 2560 7.396339 GGATAAAAGGGGATGTGAGTACTTTTT 59.604 37.037 0.00 0.00 38.58 1.94
1977 2588 8.751242 AGAAAAGGTCCTCTGTATCTACTAAAC 58.249 37.037 0.00 0.00 0.00 2.01
2019 2630 9.007901 CAGTTCAAATATGAAGGAAGAAGAAGT 57.992 33.333 0.00 0.00 45.88 3.01
2033 2645 7.559897 AGGAAGAAGAAGTTTGATAACCAACAA 59.440 33.333 0.00 0.00 34.71 2.83
2052 2664 6.695713 CCAACAAGTAAAGTAGCCTGTTTTTC 59.304 38.462 0.00 0.00 0.00 2.29
2062 2675 7.530426 AGTAGCCTGTTTTTCTTTGATCAAT 57.470 32.000 9.40 0.00 0.00 2.57
2079 2692 5.190132 TGATCAATCATTGGGAAGCCAAATT 59.810 36.000 0.00 0.00 33.20 1.82
2081 2694 5.878627 TCAATCATTGGGAAGCCAAATTTT 58.121 33.333 0.00 0.00 33.20 1.82
2117 2730 6.736110 AGCATGTGCCCTATATCAATTTTT 57.264 33.333 0.57 0.00 43.38 1.94
2153 2766 7.722949 ATCTGTTGTGGTGAAATTTATCCAT 57.277 32.000 14.26 0.00 32.45 3.41
2233 2846 3.805207 ACTTGGAGTACAACACCTTCAC 58.195 45.455 0.00 0.00 34.76 3.18
2263 2876 9.347240 CATACCTGGAGATTCAGATTAATTTGT 57.653 33.333 0.00 0.00 36.93 2.83
2264 2877 9.927081 ATACCTGGAGATTCAGATTAATTTGTT 57.073 29.630 0.00 0.00 36.93 2.83
2265 2878 8.286191 ACCTGGAGATTCAGATTAATTTGTTC 57.714 34.615 0.00 5.15 36.93 3.18
2279 2892 9.836739 GATTAATTTGTTCGTTAATCTCTCTCG 57.163 33.333 9.44 0.00 41.08 4.04
2312 2925 8.967664 ATTTCGGCCCGCTTTATATATAAATA 57.032 30.769 16.41 0.00 32.36 1.40
2314 2927 8.789825 TTCGGCCCGCTTTATATATAAATAAA 57.210 30.769 16.41 0.00 32.36 1.40
2315 2928 8.428186 TCGGCCCGCTTTATATATAAATAAAG 57.572 34.615 16.41 9.21 45.84 1.85
2349 2962 1.745087 CACACAACCAAGTCAAGTGCT 59.255 47.619 0.00 0.00 33.69 4.40
2350 2963 1.745087 ACACAACCAAGTCAAGTGCTG 59.255 47.619 0.00 0.00 33.69 4.41
2367 2980 8.190122 TCAAGTGCTGCATCGAATATAAAATTT 58.810 29.630 5.27 0.00 0.00 1.82
2372 2985 8.190122 TGCTGCATCGAATATAAAATTTTCTGT 58.810 29.630 6.72 0.00 0.00 3.41
2404 3017 2.167487 ACACAAACACGCCCAAGAAAAT 59.833 40.909 0.00 0.00 0.00 1.82
2526 3140 0.321653 GGTCAAGCCGGTCACAATCT 60.322 55.000 1.90 0.00 0.00 2.40
2535 3149 3.126831 CCGGTCACAATCTTGCTATCTC 58.873 50.000 0.00 0.00 0.00 2.75
2579 3193 6.925165 TCCATGAAAGCAAGAAATTTGAAGAC 59.075 34.615 0.00 0.00 0.00 3.01
2592 3206 1.985116 GAAGACAGTCGGAGGCCCT 60.985 63.158 0.00 0.00 0.00 5.19
2617 3231 4.337555 CCTGAAAAAGATCCGCTCAATCAT 59.662 41.667 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.671379 GCCCACCCGAGTTCAAGTC 60.671 63.158 0.00 0.00 0.00 3.01
1 2 2.147387 AGCCCACCCGAGTTCAAGT 61.147 57.895 0.00 0.00 0.00 3.16
2 3 1.672356 CAGCCCACCCGAGTTCAAG 60.672 63.158 0.00 0.00 0.00 3.02
3 4 2.429930 CAGCCCACCCGAGTTCAA 59.570 61.111 0.00 0.00 0.00 2.69
4 5 3.636231 CCAGCCCACCCGAGTTCA 61.636 66.667 0.00 0.00 0.00 3.18
13 14 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
14 15 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
15 16 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
16 17 1.538687 AATTGAGGTTGCTGCCAGCC 61.539 55.000 15.29 0.00 41.51 4.85
17 18 0.389426 CAATTGAGGTTGCTGCCAGC 60.389 55.000 10.45 10.45 42.82 4.85
18 19 3.806591 CAATTGAGGTTGCTGCCAG 57.193 52.632 0.00 0.00 0.00 4.85
25 26 1.186917 TGGCTGGGCAATTGAGGTTG 61.187 55.000 10.34 0.00 0.00 3.77
26 27 0.471591 TTGGCTGGGCAATTGAGGTT 60.472 50.000 10.34 0.00 0.00 3.50
27 28 1.155859 TTGGCTGGGCAATTGAGGT 59.844 52.632 10.34 0.00 0.00 3.85
28 29 1.593265 GTTGGCTGGGCAATTGAGG 59.407 57.895 10.34 0.00 0.00 3.86
29 30 1.213537 CGTTGGCTGGGCAATTGAG 59.786 57.895 10.34 0.00 0.00 3.02
30 31 2.274645 CCGTTGGCTGGGCAATTGA 61.275 57.895 10.34 0.00 0.00 2.57
31 32 2.262292 CCGTTGGCTGGGCAATTG 59.738 61.111 12.43 0.00 0.00 2.32
32 33 2.996734 CCCGTTGGCTGGGCAATT 60.997 61.111 12.43 0.00 40.47 2.32
38 39 3.934391 GAGTCGACCCGTTGGCTGG 62.934 68.421 13.01 0.00 33.59 4.85
39 40 2.432628 GAGTCGACCCGTTGGCTG 60.433 66.667 13.01 0.00 33.59 4.85
40 41 3.692406 GGAGTCGACCCGTTGGCT 61.692 66.667 13.01 0.00 33.59 4.75
41 42 4.754667 GGGAGTCGACCCGTTGGC 62.755 72.222 13.01 0.00 40.49 4.52
53 54 1.752833 GTTTGTGAGGACGGGGAGT 59.247 57.895 0.00 0.00 0.00 3.85
54 55 1.003718 GGTTTGTGAGGACGGGGAG 60.004 63.158 0.00 0.00 0.00 4.30
55 56 1.460689 AGGTTTGTGAGGACGGGGA 60.461 57.895 0.00 0.00 0.00 4.81
56 57 1.302511 CAGGTTTGTGAGGACGGGG 60.303 63.158 0.00 0.00 0.00 5.73
57 58 0.107831 TTCAGGTTTGTGAGGACGGG 59.892 55.000 0.00 0.00 0.00 5.28
58 59 1.961793 TTTCAGGTTTGTGAGGACGG 58.038 50.000 0.00 0.00 0.00 4.79
59 60 3.202906 TCTTTTCAGGTTTGTGAGGACG 58.797 45.455 0.00 0.00 0.00 4.79
60 61 5.576447 TTTCTTTTCAGGTTTGTGAGGAC 57.424 39.130 0.00 0.00 0.00 3.85
61 62 6.597832 TTTTTCTTTTCAGGTTTGTGAGGA 57.402 33.333 0.00 0.00 0.00 3.71
62 63 5.291858 GCTTTTTCTTTTCAGGTTTGTGAGG 59.708 40.000 0.00 0.00 0.00 3.86
63 64 5.868801 TGCTTTTTCTTTTCAGGTTTGTGAG 59.131 36.000 0.00 0.00 0.00 3.51
64 65 5.637387 GTGCTTTTTCTTTTCAGGTTTGTGA 59.363 36.000 0.00 0.00 0.00 3.58
98 99 1.139058 AGACTCAACACCACAGTCCAC 59.861 52.381 0.00 0.00 37.82 4.02
101 102 2.604046 ACAGACTCAACACCACAGTC 57.396 50.000 0.00 0.00 37.42 3.51
102 103 2.027192 ACAACAGACTCAACACCACAGT 60.027 45.455 0.00 0.00 0.00 3.55
103 104 2.609459 GACAACAGACTCAACACCACAG 59.391 50.000 0.00 0.00 0.00 3.66
110 111 3.786635 ACAGTCAGACAACAGACTCAAC 58.213 45.455 2.66 0.00 40.09 3.18
113 114 2.288518 GGGACAGTCAGACAACAGACTC 60.289 54.545 2.66 0.00 40.09 3.36
114 115 1.689273 GGGACAGTCAGACAACAGACT 59.311 52.381 2.66 0.00 42.18 3.24
115 116 1.412710 TGGGACAGTCAGACAACAGAC 59.587 52.381 2.66 0.00 33.64 3.51
202 203 1.666872 GTGCACGTACGGGAGCTTT 60.667 57.895 24.33 0.00 0.00 3.51
260 262 1.869767 GCTATCCTTGGATCAACTGCG 59.130 52.381 5.30 0.00 0.00 5.18
261 263 2.615912 GTGCTATCCTTGGATCAACTGC 59.384 50.000 5.30 5.32 0.00 4.40
262 264 3.875727 CAGTGCTATCCTTGGATCAACTG 59.124 47.826 17.23 17.23 0.00 3.16
263 265 3.683847 GCAGTGCTATCCTTGGATCAACT 60.684 47.826 8.18 5.84 0.00 3.16
264 266 2.615912 GCAGTGCTATCCTTGGATCAAC 59.384 50.000 8.18 3.77 0.00 3.18
266 268 1.839354 TGCAGTGCTATCCTTGGATCA 59.161 47.619 17.60 0.00 0.00 2.92
267 269 2.615912 GTTGCAGTGCTATCCTTGGATC 59.384 50.000 17.60 0.00 0.00 3.36
269 271 1.630369 AGTTGCAGTGCTATCCTTGGA 59.370 47.619 17.60 0.00 0.00 3.53
270 272 2.119801 AGTTGCAGTGCTATCCTTGG 57.880 50.000 17.60 0.00 0.00 3.61
288 301 5.165911 TCCACGTACTCGAGCTAATTAAG 57.834 43.478 13.61 1.86 40.62 1.85
296 309 1.134560 AGGAAATCCACGTACTCGAGC 59.865 52.381 13.61 0.00 40.62 5.03
300 313 3.870633 ACTCAGGAAATCCACGTACTC 57.129 47.619 1.67 0.00 38.89 2.59
301 314 3.128242 CGTACTCAGGAAATCCACGTACT 59.872 47.826 16.64 0.00 38.89 2.73
302 315 3.119708 ACGTACTCAGGAAATCCACGTAC 60.120 47.826 11.71 12.01 40.37 3.67
303 316 3.084039 ACGTACTCAGGAAATCCACGTA 58.916 45.455 11.71 3.23 40.37 3.57
304 317 1.891150 ACGTACTCAGGAAATCCACGT 59.109 47.619 8.56 8.56 38.34 4.49
305 318 2.649331 ACGTACTCAGGAAATCCACG 57.351 50.000 1.67 5.10 38.89 4.94
306 319 4.624452 GTGTAACGTACTCAGGAAATCCAC 59.376 45.833 1.67 0.00 38.89 4.02
307 320 4.281435 TGTGTAACGTACTCAGGAAATCCA 59.719 41.667 1.67 0.00 42.39 3.41
308 321 4.813027 TGTGTAACGTACTCAGGAAATCC 58.187 43.478 0.00 0.00 42.39 3.01
309 322 6.423001 AGTTTGTGTAACGTACTCAGGAAATC 59.577 38.462 0.00 0.00 42.39 2.17
310 323 6.285990 AGTTTGTGTAACGTACTCAGGAAAT 58.714 36.000 0.00 0.00 42.39 2.17
311 324 5.663456 AGTTTGTGTAACGTACTCAGGAAA 58.337 37.500 0.00 0.00 42.39 3.13
312 325 5.266733 AGTTTGTGTAACGTACTCAGGAA 57.733 39.130 0.00 0.00 42.39 3.36
313 326 4.924305 AGTTTGTGTAACGTACTCAGGA 57.076 40.909 0.00 0.00 42.39 3.86
314 327 5.521010 TCAAAGTTTGTGTAACGTACTCAGG 59.479 40.000 15.08 0.00 42.39 3.86
315 328 6.578020 TCAAAGTTTGTGTAACGTACTCAG 57.422 37.500 15.08 0.00 42.39 3.35
342 355 2.436824 GCCGAGAAAGCCAGGGTC 60.437 66.667 0.00 0.00 0.00 4.46
358 372 4.712425 CTGGCCGCAAACTGCAGC 62.712 66.667 15.27 0.00 45.49 5.25
364 378 0.029834 CAGCATATCTGGCCGCAAAC 59.970 55.000 0.00 0.00 39.15 2.93
372 386 2.242113 GCGAAGGCAGCATATCTGG 58.758 57.895 0.00 0.00 43.06 3.86
394 410 2.535984 CGCTCTACGGCACTTTATTCAG 59.464 50.000 0.00 0.00 38.44 3.02
434 900 1.225827 TGCGCGTAACGTACTCGAG 60.226 57.895 11.84 11.84 46.11 4.04
459 925 0.544120 TTTGGGGTTCCCTTGCCATC 60.544 55.000 7.87 0.00 45.70 3.51
462 928 1.913262 CCTTTGGGGTTCCCTTGCC 60.913 63.158 7.87 0.00 45.70 4.52
469 935 2.364324 GGTGACTTTTCCTTTGGGGTTC 59.636 50.000 0.00 0.00 36.25 3.62
486 952 2.196229 CAACCAAACCGGGGGTGA 59.804 61.111 14.47 0.00 46.34 4.02
506 972 0.449388 GTGCAGTGGTATGAAGCAGC 59.551 55.000 0.00 0.00 35.66 5.25
522 996 2.493278 ACTAATCAAACATGGCTGGTGC 59.507 45.455 0.00 0.00 38.76 5.01
569 1047 2.493278 GGATCCAACCAAGTTCACCATG 59.507 50.000 6.95 0.00 0.00 3.66
572 1050 1.203001 TGGGATCCAACCAAGTTCACC 60.203 52.381 15.23 0.00 34.44 4.02
607 1092 1.091771 TCTAAAGAGCGCATGCAGGC 61.092 55.000 19.57 14.55 46.23 4.85
608 1093 0.654683 GTCTAAAGAGCGCATGCAGG 59.345 55.000 19.57 3.00 46.23 4.85
609 1094 0.654683 GGTCTAAAGAGCGCATGCAG 59.345 55.000 19.57 11.69 46.23 4.41
610 1095 0.250234 AGGTCTAAAGAGCGCATGCA 59.750 50.000 19.57 0.00 46.33 3.96
661 1148 1.256376 GCAACATGATACGCGTGAGAG 59.744 52.381 24.59 10.42 36.97 3.20
662 1149 1.135112 AGCAACATGATACGCGTGAGA 60.135 47.619 24.59 1.10 36.97 3.27
666 1153 1.705337 GCCAGCAACATGATACGCGT 61.705 55.000 19.17 19.17 0.00 6.01
676 1163 3.343972 GCGAGAAAGCCAGCAACA 58.656 55.556 0.00 0.00 0.00 3.33
690 1177 1.883926 GGAAGCAAGGTAAAAAGGCGA 59.116 47.619 0.00 0.00 0.00 5.54
691 1178 1.611491 TGGAAGCAAGGTAAAAAGGCG 59.389 47.619 0.00 0.00 0.00 5.52
692 1179 2.628178 AGTGGAAGCAAGGTAAAAAGGC 59.372 45.455 0.00 0.00 0.00 4.35
693 1180 3.552890 GCAGTGGAAGCAAGGTAAAAAGG 60.553 47.826 0.00 0.00 0.00 3.11
695 1182 2.364002 GGCAGTGGAAGCAAGGTAAAAA 59.636 45.455 0.00 0.00 0.00 1.94
740 1228 1.008361 AAACAATTCGGCGTGCATGC 61.008 50.000 22.99 22.99 0.00 4.06
741 1229 1.386412 GAAAACAATTCGGCGTGCATG 59.614 47.619 6.85 0.09 0.00 4.06
742 1230 1.269448 AGAAAACAATTCGGCGTGCAT 59.731 42.857 6.85 0.00 0.00 3.96
743 1231 0.665835 AGAAAACAATTCGGCGTGCA 59.334 45.000 6.85 0.00 0.00 4.57
904 1392 2.239654 TGGATTGATGGGTCTTGTCCTC 59.760 50.000 0.00 0.00 0.00 3.71
919 1407 1.928868 AGGCTTCAGGGTTTGGATTG 58.071 50.000 0.00 0.00 0.00 2.67
937 1425 3.332919 ACAGTGCTGCACAAGAGAATAG 58.667 45.455 31.90 13.16 36.74 1.73
938 1426 3.407424 ACAGTGCTGCACAAGAGAATA 57.593 42.857 31.90 0.00 36.74 1.75
939 1427 2.267174 ACAGTGCTGCACAAGAGAAT 57.733 45.000 31.90 9.02 36.74 2.40
940 1428 2.483876 GTACAGTGCTGCACAAGAGAA 58.516 47.619 31.90 13.37 36.74 2.87
941 1429 1.270305 GGTACAGTGCTGCACAAGAGA 60.270 52.381 31.90 15.33 36.74 3.10
959 1447 3.164268 CCTGCTGATAGCTAGAGATGGT 58.836 50.000 0.00 0.00 42.97 3.55
986 1478 0.180642 AGGCATGAGCAGATCACTGG 59.819 55.000 0.00 0.00 41.91 4.00
1016 1508 0.864455 GATAACCGATGAGCTGCTGC 59.136 55.000 7.01 7.62 40.05 5.25
1026 1518 3.058155 CGAAGTCGAGGATGATAACCGAT 60.058 47.826 0.00 0.00 43.02 4.18
1032 1524 1.263484 GACGCGAAGTCGAGGATGATA 59.737 52.381 15.93 0.00 43.37 2.15
1045 1537 2.270923 CATCTTCATCTTGGACGCGAA 58.729 47.619 15.93 0.00 0.00 4.70
1117 1609 2.048127 GACGAGGAGCTTTGCCGT 60.048 61.111 0.00 4.50 36.08 5.68
1122 1614 2.574399 GCGAGGACGAGGAGCTTT 59.426 61.111 0.00 0.00 42.66 3.51
1124 1616 4.434354 AGGCGAGGACGAGGAGCT 62.434 66.667 0.00 0.00 42.66 4.09
1152 1644 4.530857 CCGACCGTGGCCATCCTC 62.531 72.222 9.72 2.22 0.00 3.71
1206 1698 1.545706 GGTCCTTCCTTGAGTCGGCT 61.546 60.000 0.00 0.00 0.00 5.52
1207 1699 1.079057 GGTCCTTCCTTGAGTCGGC 60.079 63.158 0.00 0.00 0.00 5.54
1338 1830 3.195698 GCACCGTCGCCATCTTCC 61.196 66.667 0.00 0.00 0.00 3.46
1355 1847 3.314331 ACCAGTCAGGGCAGTCGG 61.314 66.667 0.00 0.00 43.89 4.79
1455 1947 0.654683 GCTCATCTTCGCACACATCC 59.345 55.000 0.00 0.00 0.00 3.51
1467 1959 3.801638 GCTCGTTGGTATCATGCTCATCT 60.802 47.826 0.00 0.00 0.00 2.90
1484 1976 4.129737 CCATGACCGACGGCTCGT 62.130 66.667 15.39 9.43 45.10 4.18
1625 2117 2.609002 GTGCAAAAGGAAAACAAGGCAG 59.391 45.455 0.00 0.00 0.00 4.85
1627 2119 2.609002 CAGTGCAAAAGGAAAACAAGGC 59.391 45.455 0.00 0.00 0.00 4.35
1628 2120 3.865164 GTCAGTGCAAAAGGAAAACAAGG 59.135 43.478 0.00 0.00 0.00 3.61
1671 2257 4.849111 GATTTCAATCGGTCTCACTCAC 57.151 45.455 0.00 0.00 0.00 3.51
1701 2287 8.208903 GTCATTTTTCACCCCTATAGCTACTAA 58.791 37.037 0.00 0.00 0.00 2.24
1758 2344 3.466791 ATCGATGCAGAAGCGGGGG 62.467 63.158 0.00 0.00 46.23 5.40
1777 2363 1.133823 TGTGCACCATCACCATATCCC 60.134 52.381 15.69 0.00 36.17 3.85
1815 2426 6.934645 CCCTAATCTTTCACAGTAAACAGTGA 59.065 38.462 4.43 4.43 39.99 3.41
1881 2492 3.061322 CGGACGGAGAGAGTAGATACAG 58.939 54.545 0.00 0.00 0.00 2.74
1882 2493 2.697229 TCGGACGGAGAGAGTAGATACA 59.303 50.000 0.00 0.00 0.00 2.29
1883 2494 3.383620 TCGGACGGAGAGAGTAGATAC 57.616 52.381 0.00 0.00 0.00 2.24
1884 2495 4.412796 TTTCGGACGGAGAGAGTAGATA 57.587 45.455 0.00 0.00 0.00 1.98
1885 2496 3.278668 TTTCGGACGGAGAGAGTAGAT 57.721 47.619 0.00 0.00 0.00 1.98
1886 2497 2.775911 TTTCGGACGGAGAGAGTAGA 57.224 50.000 0.00 0.00 0.00 2.59
1887 2498 4.575645 AGTATTTTCGGACGGAGAGAGTAG 59.424 45.833 0.00 0.00 0.00 2.57
1888 2499 4.521146 AGTATTTTCGGACGGAGAGAGTA 58.479 43.478 0.00 0.00 0.00 2.59
1889 2500 3.354467 AGTATTTTCGGACGGAGAGAGT 58.646 45.455 0.00 0.00 0.00 3.24
1890 2501 4.106197 CAAGTATTTTCGGACGGAGAGAG 58.894 47.826 0.00 0.00 0.00 3.20
1891 2502 3.508793 ACAAGTATTTTCGGACGGAGAGA 59.491 43.478 0.00 0.00 0.00 3.10
1892 2503 3.846360 ACAAGTATTTTCGGACGGAGAG 58.154 45.455 0.00 0.00 0.00 3.20
1893 2504 3.256383 TGACAAGTATTTTCGGACGGAGA 59.744 43.478 0.00 0.00 0.00 3.71
1894 2505 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
1895 2506 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
1896 2507 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
1897 2508 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
1898 2509 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
1899 2510 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
1900 2511 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
1901 2512 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
1907 2518 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
1908 2519 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
1909 2520 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
1910 2521 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
1911 2522 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
1912 2523 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
1913 2524 6.902416 ACATCCCCTTTTATCCATTTTGATGA 59.098 34.615 0.00 0.00 32.39 2.92
1914 2525 6.987992 CACATCCCCTTTTATCCATTTTGATG 59.012 38.462 0.00 0.00 33.80 3.07
1915 2526 6.902416 TCACATCCCCTTTTATCCATTTTGAT 59.098 34.615 0.00 0.00 0.00 2.57
1916 2527 6.259893 TCACATCCCCTTTTATCCATTTTGA 58.740 36.000 0.00 0.00 0.00 2.69
1917 2528 6.155049 ACTCACATCCCCTTTTATCCATTTTG 59.845 38.462 0.00 0.00 0.00 2.44
1918 2529 6.263754 ACTCACATCCCCTTTTATCCATTTT 58.736 36.000 0.00 0.00 0.00 1.82
1919 2530 5.842339 ACTCACATCCCCTTTTATCCATTT 58.158 37.500 0.00 0.00 0.00 2.32
1920 2531 5.472301 ACTCACATCCCCTTTTATCCATT 57.528 39.130 0.00 0.00 0.00 3.16
1921 2532 5.672194 AGTACTCACATCCCCTTTTATCCAT 59.328 40.000 0.00 0.00 0.00 3.41
1922 2533 5.036916 AGTACTCACATCCCCTTTTATCCA 58.963 41.667 0.00 0.00 0.00 3.41
1923 2534 5.632034 AGTACTCACATCCCCTTTTATCC 57.368 43.478 0.00 0.00 0.00 2.59
1924 2535 7.939784 AAAAGTACTCACATCCCCTTTTATC 57.060 36.000 0.00 0.00 32.17 1.75
1946 2557 9.939802 GTAGATACAGAGGACCTTTTCTAAAAA 57.060 33.333 0.00 0.00 0.00 1.94
1947 2558 9.322769 AGTAGATACAGAGGACCTTTTCTAAAA 57.677 33.333 0.00 0.00 0.00 1.52
1948 2559 8.896722 AGTAGATACAGAGGACCTTTTCTAAA 57.103 34.615 0.00 0.00 0.00 1.85
1949 2560 9.986157 TTAGTAGATACAGAGGACCTTTTCTAA 57.014 33.333 0.00 0.00 0.00 2.10
1950 2561 9.986157 TTTAGTAGATACAGAGGACCTTTTCTA 57.014 33.333 0.00 0.00 0.00 2.10
1951 2562 8.751242 GTTTAGTAGATACAGAGGACCTTTTCT 58.249 37.037 0.00 0.00 0.00 2.52
1952 2563 8.751242 AGTTTAGTAGATACAGAGGACCTTTTC 58.249 37.037 0.00 0.00 0.00 2.29
1953 2564 8.667592 AGTTTAGTAGATACAGAGGACCTTTT 57.332 34.615 0.00 0.00 0.00 2.27
1954 2565 9.939424 ATAGTTTAGTAGATACAGAGGACCTTT 57.061 33.333 0.00 0.00 0.00 3.11
2019 2630 7.722285 AGGCTACTTTACTTGTTGGTTATCAAA 59.278 33.333 0.00 0.00 37.08 2.69
2033 2645 7.875327 TCAAAGAAAAACAGGCTACTTTACT 57.125 32.000 0.00 0.00 0.00 2.24
2052 2664 4.160814 TGGCTTCCCAATGATTGATCAAAG 59.839 41.667 13.09 2.97 38.46 2.77
2079 2692 0.835941 ATGCTTGGTTGGTTGCCAAA 59.164 45.000 1.79 0.00 45.73 3.28
2081 2694 1.047596 ACATGCTTGGTTGGTTGCCA 61.048 50.000 4.44 0.00 0.00 4.92
2084 2697 0.600782 GGCACATGCTTGGTTGGTTG 60.601 55.000 3.48 0.00 41.70 3.77
2117 2730 6.770303 TCACCACAACAGATAAACATCTTCAA 59.230 34.615 0.00 0.00 0.00 2.69
2129 2742 7.616935 AGATGGATAAATTTCACCACAACAGAT 59.383 33.333 15.36 2.29 35.19 2.90
2172 2785 5.066505 ACATTTGCCATAGCTAAAGTGCTAC 59.933 40.000 0.00 0.00 46.60 3.58
2175 2788 4.376340 ACATTTGCCATAGCTAAAGTGC 57.624 40.909 0.00 0.00 35.03 4.40
2202 2815 6.423001 GTGTTGTACTCCAAGTAGTAAACAGG 59.577 42.308 0.00 0.00 35.76 4.00
2263 2876 5.182570 TCCTGTTTCGAGAGAGATTAACGAA 59.817 40.000 1.20 0.00 43.69 3.85
2264 2877 4.698780 TCCTGTTTCGAGAGAGATTAACGA 59.301 41.667 1.20 0.00 43.69 3.85
2265 2878 4.982999 TCCTGTTTCGAGAGAGATTAACG 58.017 43.478 1.20 0.00 43.69 3.18
2279 2892 1.800681 CGGGCCGAAATCCTGTTTC 59.199 57.895 24.41 0.00 0.00 2.78
2312 2925 6.369799 GTTGTGTGAATTTGTTTGTTGCTTT 58.630 32.000 0.00 0.00 0.00 3.51
2314 2927 4.391523 GGTTGTGTGAATTTGTTTGTTGCT 59.608 37.500 0.00 0.00 0.00 3.91
2315 2928 4.153117 TGGTTGTGTGAATTTGTTTGTTGC 59.847 37.500 0.00 0.00 0.00 4.17
2320 2933 5.788450 TGACTTGGTTGTGTGAATTTGTTT 58.212 33.333 0.00 0.00 0.00 2.83
2349 2962 9.299963 CCAACAGAAAATTTTATATTCGATGCA 57.700 29.630 2.75 0.00 0.00 3.96
2350 2963 8.755018 CCCAACAGAAAATTTTATATTCGATGC 58.245 33.333 2.75 0.00 0.00 3.91
2372 2985 2.163815 CGTGTTTGTGTTGTTACCCCAA 59.836 45.455 0.00 0.00 0.00 4.12
2431 3045 2.479566 TGATCTTCTGGCCACTTGAC 57.520 50.000 0.00 0.00 0.00 3.18
2481 3095 2.546321 GACGTGTTGACTGCTGCG 59.454 61.111 0.00 0.00 0.00 5.18
2526 3140 0.752009 ACCCGCTCTCGAGATAGCAA 60.752 55.000 22.11 0.00 38.70 3.91
2558 3172 6.866480 ACTGTCTTCAAATTTCTTGCTTTCA 58.134 32.000 0.00 0.00 0.00 2.69
2567 3181 3.120165 GCCTCCGACTGTCTTCAAATTTC 60.120 47.826 6.21 0.00 0.00 2.17
2568 3182 2.814336 GCCTCCGACTGTCTTCAAATTT 59.186 45.455 6.21 0.00 0.00 1.82
2592 3206 1.628340 TGAGCGGATCTTTTTCAGGGA 59.372 47.619 0.00 0.00 0.00 4.20
2595 3209 4.952262 TGATTGAGCGGATCTTTTTCAG 57.048 40.909 0.00 0.00 0.00 3.02
2596 3210 4.943093 TGATGATTGAGCGGATCTTTTTCA 59.057 37.500 0.00 0.00 0.00 2.69
2597 3211 5.490139 TGATGATTGAGCGGATCTTTTTC 57.510 39.130 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.