Multiple sequence alignment - TraesCS6D01G324500

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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 TraesCS6D01G324500 chr6D 100.000 5645 0 0 1 5645 430950667 430945023 0.000000e+00 10425.0
1 TraesCS6D01G324500 chr6D 91.117 394 31 3 381 771 431056738 431056346 1.080000e-146 531.0
2 TraesCS6D01G324500 chr6D 90.110 91 6 1 4171 4258 430946386 430946296 1.290000e-21 115.0
3 TraesCS6D01G324500 chr6D 90.110 91 6 1 4282 4372 430946497 430946410 1.290000e-21 115.0
4 TraesCS6D01G324500 chr6A 92.825 2676 101 21 2639 5254 577782013 577779369 0.000000e+00 3794.0
5 TraesCS6D01G324500 chr6A 91.353 2128 138 24 1 2101 577784626 577782518 0.000000e+00 2868.0
6 TraesCS6D01G324500 chr6A 98.223 394 7 0 5252 5645 577779040 577778647 0.000000e+00 689.0
7 TraesCS6D01G324500 chr6A 84.936 312 35 6 2124 2432 577782536 577782234 7.110000e-79 305.0
8 TraesCS6D01G324500 chr6A 88.281 256 15 6 1223 1474 577835222 577834978 5.530000e-75 292.0
9 TraesCS6D01G324500 chr6A 87.692 130 11 3 4171 4296 577780371 577780243 4.560000e-31 147.0
10 TraesCS6D01G324500 chr6A 94.667 75 4 0 381 455 577835626 577835552 3.570000e-22 117.0
11 TraesCS6D01G324500 chr6A 92.000 75 6 0 4298 4372 577780469 577780395 7.730000e-19 106.0
12 TraesCS6D01G324500 chr6A 93.548 62 2 1 4016 4077 577780697 577780638 2.170000e-14 91.6
13 TraesCS6D01G324500 chr6A 100.000 42 0 0 414 455 577835505 577835464 1.690000e-10 78.7
14 TraesCS6D01G324500 chr6A 100.000 42 0 0 414 455 577835549 577835508 1.690000e-10 78.7
15 TraesCS6D01G324500 chr6A 97.143 35 1 0 414 448 577835461 577835427 6.110000e-05 60.2
16 TraesCS6D01G324500 chr6B 94.924 1379 67 2 2639 4015 650050901 650049524 0.000000e+00 2156.0
17 TraesCS6D01G324500 chr6B 92.035 904 51 13 925 1825 650054290 650053405 0.000000e+00 1251.0
18 TraesCS6D01G324500 chr6B 88.018 1085 92 18 4016 5080 650049585 650048519 0.000000e+00 1249.0
19 TraesCS6D01G324500 chr6B 86.576 812 53 11 4303 5080 650046025 650045236 0.000000e+00 845.0
20 TraesCS6D01G324500 chr6B 86.313 716 66 19 814 1511 9011865 9011164 0.000000e+00 750.0
21 TraesCS6D01G324500 chr6B 86.749 649 62 13 267 894 650055202 650054557 0.000000e+00 701.0
22 TraesCS6D01G324500 chr6B 85.528 691 74 13 1824 2511 650053311 650052644 0.000000e+00 699.0
23 TraesCS6D01G324500 chr6B 89.822 393 34 3 5258 5645 650048519 650048128 3.040000e-137 499.0
24 TraesCS6D01G324500 chr6B 88.071 394 40 4 5258 5645 650045238 650044846 1.430000e-125 460.0
25 TraesCS6D01G324500 chr6B 85.233 386 36 13 2128 2511 650051426 650051060 1.480000e-100 377.0
26 TraesCS6D01G324500 chr6B 87.857 280 24 9 1801 2078 650051970 650051699 2.540000e-83 320.0
27 TraesCS6D01G324500 chr6B 92.771 166 11 1 1451 1615 650052531 650052366 7.310000e-59 239.0
28 TraesCS6D01G324500 chr6B 94.690 113 6 0 2507 2619 650050997 650050885 5.810000e-40 176.0
29 TraesCS6D01G324500 chr6B 83.832 167 24 3 5470 5636 684436718 684436555 7.570000e-34 156.0
30 TraesCS6D01G324500 chr6B 89.655 116 9 1 4171 4283 650049311 650049196 1.640000e-30 145.0
31 TraesCS6D01G324500 chr6B 94.505 91 5 0 4282 4372 650049425 650049335 2.120000e-29 141.0
32 TraesCS6D01G324500 chr6B 94.595 74 4 0 2507 2580 650052603 650052530 1.290000e-21 115.0
33 TraesCS6D01G324500 chr4B 88.043 184 18 3 5076 5258 427278671 427278491 1.230000e-51 215.0
34 TraesCS6D01G324500 chr2D 87.766 188 17 4 5076 5260 623353380 623353196 1.230000e-51 215.0
35 TraesCS6D01G324500 chr2D 90.909 44 3 1 5596 5638 512680584 512680627 2.200000e-04 58.4
36 TraesCS6D01G324500 chr5D 86.528 193 24 1 5066 5258 488352516 488352326 1.590000e-50 211.0
37 TraesCS6D01G324500 chr5D 87.166 187 20 2 5075 5260 494223472 494223289 5.730000e-50 209.0
38 TraesCS6D01G324500 chr3A 87.500 184 19 4 5076 5258 701344668 701344488 5.730000e-50 209.0
39 TraesCS6D01G324500 chr7A 87.432 183 20 3 5077 5258 30261668 30261848 2.060000e-49 207.0
40 TraesCS6D01G324500 chr5A 87.097 186 18 5 5074 5258 569989548 569989728 7.410000e-49 206.0
41 TraesCS6D01G324500 chr1A 86.631 187 21 4 5075 5260 586291461 586291278 2.670000e-48 204.0
42 TraesCS6D01G324500 chr5B 86.316 190 21 2 5071 5260 537923599 537923415 9.590000e-48 202.0
43 TraesCS6D01G324500 chr7B 76.015 271 62 3 1 269 495187780 495187511 2.740000e-28 137.0
44 TraesCS6D01G324500 chr7B 91.837 49 4 0 274 322 732357531 732357483 1.010000e-07 69.4
45 TraesCS6D01G324500 chrUn 91.837 49 4 0 274 322 88404878 88404926 1.010000e-07 69.4
46 TraesCS6D01G324500 chrUn 91.837 49 4 0 274 322 88457078 88457126 1.010000e-07 69.4
47 TraesCS6D01G324500 chrUn 91.837 49 4 0 274 322 403152517 403152469 1.010000e-07 69.4


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 TraesCS6D01G324500 chr6D 430945023 430950667 5644 True 10425.000000 10425 100.0000 1 5645 1 chr6D.!!$R1 5644
1 TraesCS6D01G324500 chr6A 577778647 577784626 5979 True 1142.942857 3794 91.5110 1 5645 7 chr6A.!!$R1 5644
2 TraesCS6D01G324500 chr6B 9011164 9011865 701 True 750.000000 750 86.3130 814 1511 1 chr6B.!!$R1 697
3 TraesCS6D01G324500 chr6B 650044846 650055202 10356 True 624.866667 2156 90.0686 267 5645 15 chr6B.!!$R3 5378

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
38 39 0.038166 TTGTGGATGTGCCTCCTTCC 59.962 55.0 0.00 0.0 36.2 3.46 F
244 246 0.175073 ACTACATCCCGCTTCGTTCC 59.825 55.0 0.00 0.0 0.0 3.62 F
2096 3816 0.031616 AGGTCTAAGGAGAGGGGCTG 60.032 60.0 0.00 0.0 30.2 4.85 F
2411 4356 0.035458 AGCTCAAAGGGTTCTCGTGG 59.965 55.0 0.00 0.0 0.0 4.94 F
3149 5220 0.100146 GTAATCGAACGAGACGCCCT 59.900 55.0 2.94 0.0 0.0 5.19 F
3183 5254 0.454957 CAATCCGCTTGCTTTGGTCG 60.455 55.0 0.00 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1800 0.035458 CCTGCTCGAAGGGAACTGTT 59.965 55.000 0.00 0.00 42.68 3.16 R
2166 4109 0.173481 TCGAGCTACTGTGGCATGTC 59.827 55.000 18.51 6.38 0.00 3.06 R
3152 5223 1.078426 CGGATTGAAAGGGGAGCGT 60.078 57.895 0.00 0.00 0.00 5.07 R
3533 5604 1.330655 CGTAGGTGATCCTGTGGGCT 61.331 60.000 0.00 0.00 44.81 5.19 R
4430 6509 2.157738 CCTCCAAGCACAAAGAAGAGG 58.842 52.381 0.00 0.00 33.99 3.69 R
4745 6858 4.188247 TCCGGATGTCTAGAAACAACAG 57.812 45.455 0.00 0.00 31.81 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
29 30 2.165030 GCTTTCTGGGATTGTGGATGTG 59.835 50.000 0.00 0.00 0.00 3.21
38 39 0.038166 TTGTGGATGTGCCTCCTTCC 59.962 55.000 0.00 0.00 36.20 3.46
41 42 2.190578 GATGTGCCTCCTTCCCCG 59.809 66.667 0.00 0.00 0.00 5.73
81 82 3.438434 CCCTGTTAGCAAGAAGAAGAAGC 59.562 47.826 0.00 0.00 0.00 3.86
85 86 1.902938 AGCAAGAAGAAGAAGCCCAC 58.097 50.000 0.00 0.00 0.00 4.61
99 100 3.141767 AGCCCACTGTTAAGAAGTTCC 57.858 47.619 0.00 0.00 0.00 3.62
111 112 4.893829 AAGAAGTTCCCTACCAAGAGTC 57.106 45.455 0.00 0.00 0.00 3.36
134 135 1.566018 CCTCGTCGGGTTCAAAGCAC 61.566 60.000 0.00 0.00 0.00 4.40
136 137 0.599204 TCGTCGGGTTCAAAGCACTC 60.599 55.000 0.00 0.00 0.00 3.51
139 140 1.597027 CGGGTTCAAAGCACTCGGT 60.597 57.895 0.00 0.00 34.29 4.69
159 160 3.110358 GTGGCTGGTTTTTGTAAACGAC 58.890 45.455 0.00 0.00 43.68 4.34
167 168 3.529634 TTTTGTAAACGACTGGATGCG 57.470 42.857 0.00 0.00 0.00 4.73
168 169 2.157834 TTGTAAACGACTGGATGCGT 57.842 45.000 0.00 0.00 43.39 5.24
175 176 1.066430 ACGACTGGATGCGTATTTGGT 60.066 47.619 0.00 0.00 39.21 3.67
176 177 1.327460 CGACTGGATGCGTATTTGGTG 59.673 52.381 0.00 0.00 0.00 4.17
183 185 2.483288 CGTATTTGGTGTGGCGGC 59.517 61.111 0.00 0.00 0.00 6.53
184 186 2.483288 GTATTTGGTGTGGCGGCG 59.517 61.111 0.51 0.51 0.00 6.46
186 188 3.554696 TATTTGGTGTGGCGGCGGT 62.555 57.895 9.78 0.00 0.00 5.68
204 206 2.288992 TGGTGTCTCCACTGGGGT 59.711 61.111 0.00 0.00 41.93 4.95
211 213 4.308458 TCCACTGGGGTTGCGTCG 62.308 66.667 0.00 0.00 38.11 5.12
228 230 4.735132 GTCGCCGCTGGTGCACTA 62.735 66.667 17.98 10.29 39.64 2.74
238 240 1.078426 GGTGCACTACATCCCGCTT 60.078 57.895 17.98 0.00 0.00 4.68
244 246 0.175073 ACTACATCCCGCTTCGTTCC 59.825 55.000 0.00 0.00 0.00 3.62
308 310 6.609212 TGCCACCAATTCCTTAAAATATAGCA 59.391 34.615 0.00 0.00 0.00 3.49
353 368 5.833131 ACTTCTTGAAGCAATTCTTACCCAA 59.167 36.000 9.98 0.00 34.56 4.12
389 412 5.013079 TGGTAGCTTATGGGTGATATCTTGG 59.987 44.000 3.98 0.00 0.00 3.61
532 555 6.351626 GGAAAATCCCAAAATGAGCTCATCTT 60.352 38.462 28.83 19.52 35.10 2.40
537 560 5.649395 TCCCAAAATGAGCTCATCTTTACAG 59.351 40.000 28.83 18.80 35.10 2.74
579 602 1.768684 AACGGCACACCAGAGGTCAT 61.769 55.000 0.00 0.00 31.02 3.06
740 763 4.821260 TGTACACACAAAATGATGTCTGCT 59.179 37.500 0.00 0.00 0.00 4.24
804 827 2.622942 ACAAAACTGGTCATTCGCATGT 59.377 40.909 0.00 0.00 0.00 3.21
856 879 8.465273 AGATGGCCTAAATATAAAACACCTTC 57.535 34.615 3.32 0.00 0.00 3.46
882 905 2.041701 CCTCCAAAAATGCCTATGGGG 58.958 52.381 0.00 0.00 33.66 4.96
895 918 4.104383 CCTATGGGGCTATTGTCAATGT 57.896 45.455 8.39 0.00 0.00 2.71
898 921 0.663153 GGGGCTATTGTCAATGTCGC 59.337 55.000 8.39 7.81 0.00 5.19
902 925 1.308998 CTATTGTCAATGTCGCCCCC 58.691 55.000 8.39 0.00 0.00 5.40
1057 1316 3.264193 TCATAGTGGTGCACCTTCTCATT 59.736 43.478 34.75 14.75 34.49 2.57
1168 1428 1.805345 CTTCACTTGAGGAGCTGCAAG 59.195 52.381 8.35 12.81 45.27 4.01
1170 1430 1.155042 CACTTGAGGAGCTGCAAGAC 58.845 55.000 20.99 6.28 43.11 3.01
1187 1447 5.470098 TGCAAGACCTGTCTCTATTTGTTTC 59.530 40.000 0.00 0.00 39.39 2.78
1235 1495 7.202016 TGACAATACAAAGAACTTCATGACC 57.798 36.000 0.00 0.00 0.00 4.02
1247 1507 4.147321 ACTTCATGACCTGCTCAAAATGT 58.853 39.130 0.00 0.00 30.60 2.71
1250 1510 4.143543 TCATGACCTGCTCAAAATGTTGA 58.856 39.130 0.00 0.00 41.57 3.18
1253 1513 3.068024 TGACCTGCTCAAAATGTTGAACC 59.932 43.478 0.00 0.00 43.18 3.62
1254 1514 2.034558 ACCTGCTCAAAATGTTGAACCG 59.965 45.455 0.00 0.00 43.18 4.44
1255 1515 2.034558 CCTGCTCAAAATGTTGAACCGT 59.965 45.455 0.00 0.00 43.18 4.83
1256 1516 3.300009 CTGCTCAAAATGTTGAACCGTC 58.700 45.455 0.00 0.00 43.18 4.79
1257 1517 2.685388 TGCTCAAAATGTTGAACCGTCA 59.315 40.909 0.00 0.00 43.18 4.35
1407 1667 5.177511 CGAAAGTTCAGATTAGTGTGCTTCA 59.822 40.000 0.00 0.00 0.00 3.02
1408 1668 6.128445 CGAAAGTTCAGATTAGTGTGCTTCAT 60.128 38.462 0.00 0.00 0.00 2.57
1409 1669 6.734104 AAGTTCAGATTAGTGTGCTTCATC 57.266 37.500 0.00 0.00 0.00 2.92
1410 1670 4.867047 AGTTCAGATTAGTGTGCTTCATCG 59.133 41.667 0.00 0.00 0.00 3.84
1534 1797 9.569122 GGGACAATTTGTAGGCTAAAATAGATA 57.431 33.333 1.15 0.00 0.00 1.98
1618 1881 8.327271 AGATTCTTATATGGAATGCTGCTACAT 58.673 33.333 0.00 0.00 34.09 2.29
1784 2048 6.790285 TCGTATATACTAGAATGTGACGCA 57.210 37.500 11.05 0.00 0.00 5.24
1785 2049 7.373778 TCGTATATACTAGAATGTGACGCAT 57.626 36.000 11.05 0.00 40.03 4.73
1887 2247 4.094887 TCGCTCTTATCAACAATTTCAGCC 59.905 41.667 0.00 0.00 0.00 4.85
1902 2262 0.392193 CAGCCGTTGGAGCTCAAGAT 60.392 55.000 17.19 0.00 38.95 2.40
1926 2286 4.868195 GCAACCGCTTGATGAACC 57.132 55.556 0.00 0.00 34.30 3.62
1927 2287 2.257353 GCAACCGCTTGATGAACCT 58.743 52.632 0.00 0.00 34.30 3.50
1928 2288 0.169009 GCAACCGCTTGATGAACCTC 59.831 55.000 0.00 0.00 34.30 3.85
1996 2356 1.378646 TCGTCGATGCTCCCTCTGT 60.379 57.895 0.00 0.00 0.00 3.41
2020 2380 2.111384 CCGGATCCAAGAGAGGAAGAA 58.889 52.381 13.41 0.00 41.92 2.52
2022 2382 3.135530 CCGGATCCAAGAGAGGAAGAAAT 59.864 47.826 13.41 0.00 41.92 2.17
2055 3775 1.185618 ACAAGGCGAGCAGTAGGTCA 61.186 55.000 0.00 0.00 42.32 4.02
2082 3802 3.947612 TCGTCCCTGTAATCTAGGTCT 57.052 47.619 0.00 0.00 33.31 3.85
2084 3804 5.378230 TCGTCCCTGTAATCTAGGTCTAA 57.622 43.478 0.00 0.00 33.31 2.10
2086 3806 4.519730 CGTCCCTGTAATCTAGGTCTAAGG 59.480 50.000 0.00 0.00 33.31 2.69
2087 3807 5.689564 CGTCCCTGTAATCTAGGTCTAAGGA 60.690 48.000 0.45 0.00 33.31 3.36
2088 3808 5.771165 GTCCCTGTAATCTAGGTCTAAGGAG 59.229 48.000 0.45 0.00 33.31 3.69
2089 3809 5.675421 TCCCTGTAATCTAGGTCTAAGGAGA 59.325 44.000 0.45 0.00 33.31 3.71
2090 3810 6.007703 CCCTGTAATCTAGGTCTAAGGAGAG 58.992 48.000 0.45 0.00 33.31 3.20
2091 3811 6.007703 CCTGTAATCTAGGTCTAAGGAGAGG 58.992 48.000 0.00 0.00 30.20 3.69
2092 3812 5.954757 TGTAATCTAGGTCTAAGGAGAGGG 58.045 45.833 0.00 0.00 30.20 4.30
2093 3813 4.479156 AATCTAGGTCTAAGGAGAGGGG 57.521 50.000 0.00 0.00 30.20 4.79
2094 3814 1.499870 TCTAGGTCTAAGGAGAGGGGC 59.500 57.143 0.00 0.00 30.20 5.80
2095 3815 1.501604 CTAGGTCTAAGGAGAGGGGCT 59.498 57.143 0.00 0.00 30.20 5.19
2096 3816 0.031616 AGGTCTAAGGAGAGGGGCTG 60.032 60.000 0.00 0.00 30.20 4.85
2097 3817 1.051556 GGTCTAAGGAGAGGGGCTGG 61.052 65.000 0.00 0.00 30.20 4.85
2098 3818 1.051556 GTCTAAGGAGAGGGGCTGGG 61.052 65.000 0.00 0.00 30.20 4.45
2099 3819 1.768077 CTAAGGAGAGGGGCTGGGG 60.768 68.421 0.00 0.00 0.00 4.96
2100 3820 3.347562 TAAGGAGAGGGGCTGGGGG 62.348 68.421 0.00 0.00 0.00 5.40
2120 3840 4.553144 GGGGGTACACAGAGGACA 57.447 61.111 0.00 0.00 0.00 4.02
2121 3841 3.007581 GGGGGTACACAGAGGACAT 57.992 57.895 0.00 0.00 0.00 3.06
2122 3842 0.541863 GGGGGTACACAGAGGACATG 59.458 60.000 0.00 0.00 0.00 3.21
2123 3843 1.568504 GGGGTACACAGAGGACATGA 58.431 55.000 0.00 0.00 0.00 3.07
2124 3844 2.119495 GGGGTACACAGAGGACATGAT 58.881 52.381 0.00 0.00 0.00 2.45
2125 3845 2.158900 GGGGTACACAGAGGACATGATG 60.159 54.545 0.00 0.00 0.00 3.07
2126 3846 2.766263 GGGTACACAGAGGACATGATGA 59.234 50.000 0.00 0.00 0.00 2.92
2140 4083 0.776810 TGATGAAGAAGGGGTTGGCA 59.223 50.000 0.00 0.00 0.00 4.92
2166 4109 0.995024 ACACAGGATCAAAGAGGGGG 59.005 55.000 0.00 0.00 0.00 5.40
2168 4111 1.065126 CACAGGATCAAAGAGGGGGAC 60.065 57.143 0.00 0.00 0.00 4.46
2169 4112 1.289160 CAGGATCAAAGAGGGGGACA 58.711 55.000 0.00 0.00 0.00 4.02
2170 4113 1.849039 CAGGATCAAAGAGGGGGACAT 59.151 52.381 0.00 0.00 0.00 3.06
2177 4120 1.856539 AAGAGGGGGACATGCCACAG 61.857 60.000 10.09 0.00 44.24 3.66
2219 4162 2.289506 GGACCTACAACCGAGCTTTTCT 60.290 50.000 0.00 0.00 0.00 2.52
2220 4163 3.056322 GGACCTACAACCGAGCTTTTCTA 60.056 47.826 0.00 0.00 0.00 2.10
2229 4172 0.249398 GAGCTTTTCTAGGTGCCGGA 59.751 55.000 5.05 0.00 33.94 5.14
2239 4182 2.281484 GTGCCGGACAGCCTTTGA 60.281 61.111 5.05 0.00 0.00 2.69
2246 4189 1.879380 CGGACAGCCTTTGAATGACAA 59.121 47.619 0.00 0.00 36.65 3.18
2249 4192 3.507233 GGACAGCCTTTGAATGACAATCA 59.493 43.478 0.00 0.00 38.36 2.57
2293 4236 1.143838 CACGATGAAGGCCGGATGA 59.856 57.895 5.05 0.00 0.00 2.92
2294 4237 0.250038 CACGATGAAGGCCGGATGAT 60.250 55.000 5.05 0.00 0.00 2.45
2295 4238 0.469917 ACGATGAAGGCCGGATGATT 59.530 50.000 5.05 0.00 0.00 2.57
2296 4239 1.691976 ACGATGAAGGCCGGATGATTA 59.308 47.619 5.05 0.00 0.00 1.75
2297 4240 2.289072 ACGATGAAGGCCGGATGATTAG 60.289 50.000 5.05 0.00 0.00 1.73
2298 4241 2.029020 CGATGAAGGCCGGATGATTAGA 60.029 50.000 5.05 0.00 0.00 2.10
2299 4242 2.910688 TGAAGGCCGGATGATTAGAC 57.089 50.000 5.05 0.00 0.00 2.59
2300 4243 2.115427 TGAAGGCCGGATGATTAGACA 58.885 47.619 5.05 0.00 0.00 3.41
2326 4270 0.250295 AAAGGTGCTTGTCTGCGCTA 60.250 50.000 9.73 0.00 42.46 4.26
2342 4287 2.159693 GCGCTACCACTTAACTGCTTTC 60.160 50.000 0.00 0.00 0.00 2.62
2348 4293 4.137543 ACCACTTAACTGCTTTCCTCTTG 58.862 43.478 0.00 0.00 0.00 3.02
2350 4295 3.057946 CACTTAACTGCTTTCCTCTTGGC 60.058 47.826 0.00 0.00 0.00 4.52
2367 4312 5.305585 TCTTGGCTTATAAATTCGCCTAGG 58.694 41.667 18.22 3.67 42.82 3.02
2410 4355 1.270305 TGAGCTCAAAGGGTTCTCGTG 60.270 52.381 15.67 0.00 0.00 4.35
2411 4356 0.035458 AGCTCAAAGGGTTCTCGTGG 59.965 55.000 0.00 0.00 0.00 4.94
2421 4366 2.218603 GGTTCTCGTGGTGTGTGAAAT 58.781 47.619 0.00 0.00 0.00 2.17
2458 4403 1.959282 GATTGATGATGGTTGGGGAGC 59.041 52.381 0.00 0.00 0.00 4.70
2463 4408 3.329542 GATGGTTGGGGAGCGAGCA 62.330 63.158 0.00 0.00 0.00 4.26
2524 4588 4.395583 GCTGCTGCAACGACCTGC 62.396 66.667 11.11 0.00 42.95 4.85
2610 4681 4.082679 TGCGTCTTCTCCTTTACTTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
2611 4682 4.157105 GCGTCTTCTCCTTTACTTCTCTCT 59.843 45.833 0.00 0.00 0.00 3.10
2612 4683 5.675323 GCGTCTTCTCCTTTACTTCTCTCTC 60.675 48.000 0.00 0.00 0.00 3.20
2613 4684 5.163693 CGTCTTCTCCTTTACTTCTCTCTCC 60.164 48.000 0.00 0.00 0.00 3.71
2614 4685 4.944930 TCTTCTCCTTTACTTCTCTCTCCG 59.055 45.833 0.00 0.00 0.00 4.63
2615 4686 4.304048 TCTCCTTTACTTCTCTCTCCGT 57.696 45.455 0.00 0.00 0.00 4.69
2616 4687 4.664392 TCTCCTTTACTTCTCTCTCCGTT 58.336 43.478 0.00 0.00 0.00 4.44
2617 4688 5.078256 TCTCCTTTACTTCTCTCTCCGTTT 58.922 41.667 0.00 0.00 0.00 3.60
2618 4689 5.047943 TCTCCTTTACTTCTCTCTCCGTTTG 60.048 44.000 0.00 0.00 0.00 2.93
2619 4690 4.587684 TCCTTTACTTCTCTCTCCGTTTGT 59.412 41.667 0.00 0.00 0.00 2.83
2620 4691 4.924462 CCTTTACTTCTCTCTCCGTTTGTC 59.076 45.833 0.00 0.00 0.00 3.18
2621 4692 5.279056 CCTTTACTTCTCTCTCCGTTTGTCT 60.279 44.000 0.00 0.00 0.00 3.41
2622 4693 3.926821 ACTTCTCTCTCCGTTTGTCTC 57.073 47.619 0.00 0.00 0.00 3.36
2623 4694 3.223435 ACTTCTCTCTCCGTTTGTCTCA 58.777 45.455 0.00 0.00 0.00 3.27
2624 4695 3.637229 ACTTCTCTCTCCGTTTGTCTCAA 59.363 43.478 0.00 0.00 0.00 3.02
2625 4696 4.099573 ACTTCTCTCTCCGTTTGTCTCAAA 59.900 41.667 0.00 0.00 0.00 2.69
2626 4697 4.665833 TCTCTCTCCGTTTGTCTCAAAA 57.334 40.909 0.00 0.00 0.00 2.44
2627 4698 5.018539 TCTCTCTCCGTTTGTCTCAAAAA 57.981 39.130 0.00 0.00 0.00 1.94
2726 4797 1.478288 GCCTTCATTGCTATCCTGCCT 60.478 52.381 0.00 0.00 0.00 4.75
2732 4803 1.407656 TTGCTATCCTGCCTACCCCG 61.408 60.000 0.00 0.00 0.00 5.73
3149 5220 0.100146 GTAATCGAACGAGACGCCCT 59.900 55.000 2.94 0.00 0.00 5.19
3152 5223 0.813184 ATCGAACGAGACGCCCTAAA 59.187 50.000 2.94 0.00 0.00 1.85
3176 5247 0.967380 CCCCTTTCAATCCGCTTGCT 60.967 55.000 0.00 0.00 34.66 3.91
3183 5254 0.454957 CAATCCGCTTGCTTTGGTCG 60.455 55.000 0.00 0.00 0.00 4.79
3605 5676 1.213013 GTCGTCGGATCAGCAGTGT 59.787 57.895 0.00 0.00 0.00 3.55
3656 5727 4.681978 GCCGTGTTCCTCGTGGCT 62.682 66.667 0.00 0.00 42.44 4.75
3734 5805 2.525877 ACCGGGCCTGTGTACAGT 60.526 61.111 11.58 0.00 42.27 3.55
3869 5940 2.761213 ACCGTCCCCGTGTATCCC 60.761 66.667 0.00 0.00 0.00 3.85
4005 6076 8.881743 GTCTTCTCTAGTCTCGTTGAAGTATTA 58.118 37.037 0.00 0.00 34.37 0.98
4030 6101 2.565841 GCCTTAGCAATGTAGTCCTGG 58.434 52.381 0.00 0.00 39.53 4.45
4086 6157 9.596308 AAGTATTGGATTACCTTTGTTTACCTT 57.404 29.630 0.00 0.00 37.04 3.50
4119 6195 2.808543 GTGGTAAGTTGCTTCCAGTCTG 59.191 50.000 0.00 0.00 0.00 3.51
4420 6499 6.293027 GCTTGTTTGCAATGTTTATGCTTTCT 60.293 34.615 0.00 0.00 44.14 2.52
4421 6500 7.551035 TTGTTTGCAATGTTTATGCTTTCTT 57.449 28.000 0.00 0.00 44.14 2.52
4422 6501 6.946165 TGTTTGCAATGTTTATGCTTTCTTG 58.054 32.000 0.00 0.00 44.14 3.02
4423 6502 6.018098 TGTTTGCAATGTTTATGCTTTCTTGG 60.018 34.615 0.00 0.00 44.14 3.61
4424 6503 4.567971 TGCAATGTTTATGCTTTCTTGGG 58.432 39.130 0.00 0.00 44.14 4.12
4425 6504 4.040217 TGCAATGTTTATGCTTTCTTGGGT 59.960 37.500 0.00 0.00 44.14 4.51
4426 6505 4.996758 GCAATGTTTATGCTTTCTTGGGTT 59.003 37.500 0.00 0.00 40.64 4.11
4427 6506 6.162777 GCAATGTTTATGCTTTCTTGGGTTA 58.837 36.000 0.00 0.00 40.64 2.85
4428 6507 6.311200 GCAATGTTTATGCTTTCTTGGGTTAG 59.689 38.462 0.00 0.00 40.64 2.34
4429 6508 7.378181 CAATGTTTATGCTTTCTTGGGTTAGT 58.622 34.615 0.00 0.00 0.00 2.24
4430 6509 6.569179 TGTTTATGCTTTCTTGGGTTAGTC 57.431 37.500 0.00 0.00 0.00 2.59
4475 6561 1.407258 GGACTCGCTGCTTCTGTCTAT 59.593 52.381 0.00 0.00 0.00 1.98
4514 6622 1.911357 AGTGATGCAGATTGGAGGTCA 59.089 47.619 0.00 0.00 0.00 4.02
4522 6630 3.077359 CAGATTGGAGGTCAGTGTTTCC 58.923 50.000 0.00 0.00 0.00 3.13
4596 6704 6.591750 TTTTTGTAAGTTGTTGAAGGTCCA 57.408 33.333 0.00 0.00 0.00 4.02
4597 6705 5.570234 TTTGTAAGTTGTTGAAGGTCCAC 57.430 39.130 0.00 0.00 0.00 4.02
4598 6706 4.223556 TGTAAGTTGTTGAAGGTCCACA 57.776 40.909 0.00 0.00 0.00 4.17
4640 6748 2.025510 AGGCAAGCCAAAGAATCTAGCT 60.026 45.455 14.40 0.00 38.92 3.32
4646 6754 7.040132 GGCAAGCCAAAGAATCTAGCTAATAAT 60.040 37.037 6.14 0.00 35.81 1.28
4685 6798 9.269453 GTATACACAAAAGGAGAGTTACAACTT 57.731 33.333 0.00 0.00 39.88 2.66
4745 6858 6.073331 GCTCAAGAAGATATATGTGCTTCCAC 60.073 42.308 0.00 0.00 38.98 4.02
4764 6877 3.679980 CCACTGTTGTTTCTAGACATCCG 59.320 47.826 0.00 0.00 0.00 4.18
4792 6905 5.359716 CTCAAGCAGCAAGGATAATGATC 57.640 43.478 0.00 0.00 0.00 2.92
4797 6910 3.501445 GCAGCAAGGATAATGATCTCCAC 59.499 47.826 1.91 0.00 33.75 4.02
4837 6950 8.133754 TGAGTTTGCAATTCAAATCTTCAAAG 57.866 30.769 0.00 0.00 45.43 2.77
4895 7008 4.813161 GCAATAGATAAGCACTCTGAGCAA 59.187 41.667 4.19 0.00 0.00 3.91
4909 7022 3.444850 AGCAATTTGGGCTCAGTGT 57.555 47.368 0.00 0.00 36.81 3.55
4911 7024 2.875296 AGCAATTTGGGCTCAGTGTTA 58.125 42.857 0.00 0.00 36.81 2.41
5054 7190 3.002759 GGATTGTTCGAGGAAGCTAATGC 59.997 47.826 0.00 0.00 40.05 3.56
5152 7295 2.809446 TGTCATTGATCTTACGCGGAG 58.191 47.619 12.47 8.39 0.00 4.63
5156 7299 4.149046 GTCATTGATCTTACGCGGAGATTC 59.851 45.833 22.61 16.98 34.13 2.52
5170 7313 5.609696 CGCGGAGATTCGTGTATGTATTTTC 60.610 44.000 0.00 0.00 36.10 2.29
5171 7314 5.462398 GCGGAGATTCGTGTATGTATTTTCT 59.538 40.000 0.00 0.00 0.00 2.52
5172 7315 6.018994 GCGGAGATTCGTGTATGTATTTTCTT 60.019 38.462 0.00 0.00 0.00 2.52
5173 7316 7.465513 GCGGAGATTCGTGTATGTATTTTCTTT 60.466 37.037 0.00 0.00 0.00 2.52
5174 7317 8.388103 CGGAGATTCGTGTATGTATTTTCTTTT 58.612 33.333 0.00 0.00 0.00 2.27
5246 7389 6.918022 TGCAATAACTACGACACATCTAGATG 59.082 38.462 27.63 27.63 44.15 2.90
5346 7823 4.792068 TCTGGGGGCTAATAAAGTCATTG 58.208 43.478 0.00 0.00 0.00 2.82
5575 8054 5.597594 TGGCAATTAATCATTGTAGCATGGA 59.402 36.000 0.00 0.00 43.95 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.322456 TCCACAATCCCAGAAAGCGG 60.322 55.000 0.00 0.00 0.00 5.52
57 58 2.087646 CTTCTTCTTGCTAACAGGGCC 58.912 52.381 0.00 0.00 0.00 5.80
63 64 3.189495 GTGGGCTTCTTCTTCTTGCTAAC 59.811 47.826 0.00 0.00 0.00 2.34
81 82 3.790089 AGGGAACTTCTTAACAGTGGG 57.210 47.619 0.00 0.00 37.44 4.61
85 86 6.110411 TCTTGGTAGGGAACTTCTTAACAG 57.890 41.667 0.00 0.00 43.67 3.16
99 100 1.677637 GAGGCCCGACTCTTGGTAGG 61.678 65.000 0.00 0.00 39.89 3.18
134 135 1.600023 TACAAAAACCAGCCACCGAG 58.400 50.000 0.00 0.00 0.00 4.63
136 137 2.465855 GTTTACAAAAACCAGCCACCG 58.534 47.619 0.00 0.00 39.29 4.94
139 140 3.018149 AGTCGTTTACAAAAACCAGCCA 58.982 40.909 0.00 0.00 41.68 4.75
159 160 1.401552 CCACACCAAATACGCATCCAG 59.598 52.381 0.00 0.00 0.00 3.86
167 168 2.483288 CGCCGCCACACCAAATAC 59.517 61.111 0.00 0.00 0.00 1.89
168 169 2.748251 CCGCCGCCACACCAAATA 60.748 61.111 0.00 0.00 0.00 1.40
211 213 4.735132 TAGTGCACCAGCGGCGAC 62.735 66.667 14.63 1.23 46.23 5.19
218 220 1.815421 GCGGGATGTAGTGCACCAG 60.815 63.158 14.63 0.00 0.00 4.00
219 221 1.836999 AAGCGGGATGTAGTGCACCA 61.837 55.000 14.63 5.64 0.00 4.17
222 224 1.153647 CGAAGCGGGATGTAGTGCA 60.154 57.895 0.00 0.00 0.00 4.57
224 226 1.278238 GAACGAAGCGGGATGTAGTG 58.722 55.000 0.00 0.00 0.00 2.74
225 227 0.175073 GGAACGAAGCGGGATGTAGT 59.825 55.000 0.00 0.00 0.00 2.73
228 230 2.267961 GGGAACGAAGCGGGATGT 59.732 61.111 0.00 0.00 0.00 3.06
333 348 6.279882 TGTTTTGGGTAAGAATTGCTTCAAG 58.720 36.000 0.00 0.00 38.05 3.02
353 368 7.839200 ACCCATAAGCTACCATTATCTTTGTTT 59.161 33.333 0.00 0.00 0.00 2.83
389 412 1.913419 TGGATTCTAAGGGTGGTGGTC 59.087 52.381 0.00 0.00 0.00 4.02
562 585 1.448540 GATGACCTCTGGTGTGCCG 60.449 63.158 0.00 0.00 35.25 5.69
618 641 6.164176 ACTATCACTAAGAACTTGGTTTCCG 58.836 40.000 1.01 0.00 31.71 4.30
665 688 7.979786 TCTATCCCTTCTTTCTAAGTGATGT 57.020 36.000 0.00 0.00 0.00 3.06
724 747 3.693085 CAGCCTAGCAGACATCATTTTGT 59.307 43.478 0.00 0.00 0.00 2.83
740 763 0.185175 TAGATGGACCGAGCAGCCTA 59.815 55.000 0.00 0.00 0.00 3.93
856 879 1.348696 AGGCATTTTTGGAGGGCTTTG 59.651 47.619 0.00 0.00 31.46 2.77
882 905 0.663153 GGGGCGACATTGACAATAGC 59.337 55.000 0.00 7.07 0.00 2.97
883 906 1.308998 GGGGGCGACATTGACAATAG 58.691 55.000 0.00 0.00 0.00 1.73
902 925 7.178451 ACAATGAAAGTAATTACTTCTTGGGGG 59.822 37.037 28.98 20.16 45.17 5.40
935 1194 6.897259 ATATTGCTTGCAACAAGCTATTTG 57.103 33.333 26.00 0.05 45.94 2.32
1168 1428 3.994392 TGCGAAACAAATAGAGACAGGTC 59.006 43.478 0.00 0.00 0.00 3.85
1170 1430 4.393062 ACATGCGAAACAAATAGAGACAGG 59.607 41.667 0.00 0.00 0.00 4.00
1187 1447 3.325870 TGTTCACTTAGAGGAACATGCG 58.674 45.455 15.80 0.00 46.01 4.73
1235 1495 3.243035 TGACGGTTCAACATTTTGAGCAG 60.243 43.478 10.13 8.51 43.02 4.24
1247 1507 0.742505 AGTCTGACGTGACGGTTCAA 59.257 50.000 10.66 0.00 41.47 2.69
1250 1510 1.335689 GCTAAGTCTGACGTGACGGTT 60.336 52.381 10.66 0.00 41.47 4.44
1253 1513 1.607713 CTGCTAAGTCTGACGTGACG 58.392 55.000 2.24 2.24 41.47 4.35
1254 1514 1.269998 ACCTGCTAAGTCTGACGTGAC 59.730 52.381 6.50 0.00 37.23 3.67
1255 1515 1.617322 ACCTGCTAAGTCTGACGTGA 58.383 50.000 6.50 0.00 0.00 4.35
1256 1516 3.784701 ATACCTGCTAAGTCTGACGTG 57.215 47.619 6.50 0.54 0.00 4.49
1257 1517 4.778579 TCTATACCTGCTAAGTCTGACGT 58.221 43.478 1.52 1.36 0.00 4.34
1437 1697 3.472652 AGTTGTACAAAATGTCGCTCCA 58.527 40.909 10.51 0.00 0.00 3.86
1476 1739 3.429684 GGTTCGGTGGTTTGTGTTTTGAT 60.430 43.478 0.00 0.00 0.00 2.57
1481 1744 1.546961 TTGGTTCGGTGGTTTGTGTT 58.453 45.000 0.00 0.00 0.00 3.32
1482 1745 1.546961 TTTGGTTCGGTGGTTTGTGT 58.453 45.000 0.00 0.00 0.00 3.72
1534 1797 1.134220 TGCTCGAAGGGAACTGTTGTT 60.134 47.619 0.00 0.00 42.68 2.83
1537 1800 0.035458 CCTGCTCGAAGGGAACTGTT 59.965 55.000 0.00 0.00 42.68 3.16
1618 1881 3.492656 GCATACGATTCCTTGCTGTAGGA 60.493 47.826 0.00 0.00 42.56 2.94
1847 2206 4.870991 AGAGCGAGCCAACTAATCTAAAAC 59.129 41.667 0.00 0.00 0.00 2.43
1853 2212 4.621991 TGATAAGAGCGAGCCAACTAATC 58.378 43.478 0.00 0.00 0.00 1.75
1854 2213 4.672587 TGATAAGAGCGAGCCAACTAAT 57.327 40.909 0.00 0.00 0.00 1.73
1887 2247 1.857217 CATCGATCTTGAGCTCCAACG 59.143 52.381 12.15 10.00 0.00 4.10
1918 2278 2.230266 TCATTCACGACGAGGTTCATCA 59.770 45.455 0.00 0.00 0.00 3.07
1957 2317 1.822990 CCTAAGCAACTCAGGTACGGA 59.177 52.381 0.00 0.00 0.00 4.69
1958 2318 1.549170 ACCTAAGCAACTCAGGTACGG 59.451 52.381 0.00 0.00 40.93 4.02
1960 2320 2.230750 ACGACCTAAGCAACTCAGGTAC 59.769 50.000 0.00 0.00 42.78 3.34
1961 2321 2.490903 GACGACCTAAGCAACTCAGGTA 59.509 50.000 0.00 0.00 42.78 3.08
1996 2356 1.289830 TCCTCTCTTGGATCCGGGTTA 59.710 52.381 7.39 0.00 0.00 2.85
2020 2380 3.160269 CCTTGTCTCCTTGCTCCAAATT 58.840 45.455 0.00 0.00 0.00 1.82
2022 2382 1.819305 GCCTTGTCTCCTTGCTCCAAA 60.819 52.381 0.00 0.00 0.00 3.28
2055 3775 1.068741 GATTACAGGGACGAAGGCGAT 59.931 52.381 0.00 0.00 41.64 4.58
2082 3802 2.372688 CCCCAGCCCCTCTCCTTA 59.627 66.667 0.00 0.00 0.00 2.69
2103 3823 0.541863 CATGTCCTCTGTGTACCCCC 59.458 60.000 0.00 0.00 0.00 5.40
2104 3824 1.568504 TCATGTCCTCTGTGTACCCC 58.431 55.000 0.00 0.00 0.00 4.95
2105 3825 2.766263 TCATCATGTCCTCTGTGTACCC 59.234 50.000 0.00 0.00 0.00 3.69
2106 3826 4.160439 TCTTCATCATGTCCTCTGTGTACC 59.840 45.833 0.00 0.00 0.00 3.34
2107 3827 5.330455 TCTTCATCATGTCCTCTGTGTAC 57.670 43.478 0.00 0.00 0.00 2.90
2108 3828 5.105187 CCTTCTTCATCATGTCCTCTGTGTA 60.105 44.000 0.00 0.00 0.00 2.90
2109 3829 4.323333 CCTTCTTCATCATGTCCTCTGTGT 60.323 45.833 0.00 0.00 0.00 3.72
2110 3830 4.190001 CCTTCTTCATCATGTCCTCTGTG 58.810 47.826 0.00 0.00 0.00 3.66
2111 3831 3.199508 CCCTTCTTCATCATGTCCTCTGT 59.800 47.826 0.00 0.00 0.00 3.41
2112 3832 3.433314 CCCCTTCTTCATCATGTCCTCTG 60.433 52.174 0.00 0.00 0.00 3.35
2113 3833 2.776536 CCCCTTCTTCATCATGTCCTCT 59.223 50.000 0.00 0.00 0.00 3.69
2114 3834 2.507471 ACCCCTTCTTCATCATGTCCTC 59.493 50.000 0.00 0.00 0.00 3.71
2115 3835 2.566746 ACCCCTTCTTCATCATGTCCT 58.433 47.619 0.00 0.00 0.00 3.85
2116 3836 3.019564 CAACCCCTTCTTCATCATGTCC 58.980 50.000 0.00 0.00 0.00 4.02
2117 3837 3.019564 CCAACCCCTTCTTCATCATGTC 58.980 50.000 0.00 0.00 0.00 3.06
2118 3838 2.885554 GCCAACCCCTTCTTCATCATGT 60.886 50.000 0.00 0.00 0.00 3.21
2119 3839 1.753073 GCCAACCCCTTCTTCATCATG 59.247 52.381 0.00 0.00 0.00 3.07
2120 3840 1.358787 TGCCAACCCCTTCTTCATCAT 59.641 47.619 0.00 0.00 0.00 2.45
2121 3841 0.776810 TGCCAACCCCTTCTTCATCA 59.223 50.000 0.00 0.00 0.00 3.07
2122 3842 1.467920 CTGCCAACCCCTTCTTCATC 58.532 55.000 0.00 0.00 0.00 2.92
2123 3843 0.613012 GCTGCCAACCCCTTCTTCAT 60.613 55.000 0.00 0.00 0.00 2.57
2124 3844 1.228552 GCTGCCAACCCCTTCTTCA 60.229 57.895 0.00 0.00 0.00 3.02
2125 3845 1.228552 TGCTGCCAACCCCTTCTTC 60.229 57.895 0.00 0.00 0.00 2.87
2126 3846 1.228675 CTGCTGCCAACCCCTTCTT 60.229 57.895 0.00 0.00 0.00 2.52
2140 4083 2.568956 TCTTTGATCCTGTGTAGCTGCT 59.431 45.455 7.57 7.57 0.00 4.24
2166 4109 0.173481 TCGAGCTACTGTGGCATGTC 59.827 55.000 18.51 6.38 0.00 3.06
2168 4111 1.002366 GTTCGAGCTACTGTGGCATG 58.998 55.000 18.51 9.78 0.00 4.06
2169 4112 0.458543 CGTTCGAGCTACTGTGGCAT 60.459 55.000 18.51 3.51 0.00 4.40
2170 4113 1.080772 CGTTCGAGCTACTGTGGCA 60.081 57.895 18.51 0.00 0.00 4.92
2177 4120 0.802607 CTTGAGCCCGTTCGAGCTAC 60.803 60.000 0.69 0.00 40.11 3.58
2219 4162 2.221299 AAAGGCTGTCCGGCACCTA 61.221 57.895 15.01 0.00 41.46 3.08
2220 4163 3.570212 AAAGGCTGTCCGGCACCT 61.570 61.111 0.00 5.48 41.46 4.00
2225 4168 0.804989 GTCATTCAAAGGCTGTCCGG 59.195 55.000 0.00 0.00 37.47 5.14
2229 4172 3.058016 CGTGATTGTCATTCAAAGGCTGT 60.058 43.478 0.00 0.00 39.62 4.40
2239 4182 1.278985 TGCTCCTCCGTGATTGTCATT 59.721 47.619 0.00 0.00 0.00 2.57
2246 4189 0.397675 TGGATCTGCTCCTCCGTGAT 60.398 55.000 0.00 0.00 45.21 3.06
2249 4192 2.060980 GGTGGATCTGCTCCTCCGT 61.061 63.158 3.16 0.00 45.37 4.69
2286 4229 2.620251 TTGGCTGTCTAATCATCCGG 57.380 50.000 0.00 0.00 0.00 5.14
2310 4254 2.391389 GGTAGCGCAGACAAGCACC 61.391 63.158 11.47 0.00 35.48 5.01
2326 4270 4.137543 CAAGAGGAAAGCAGTTAAGTGGT 58.862 43.478 9.20 9.20 0.00 4.16
2350 4295 6.097915 TCAGTCCCTAGGCGAATTTATAAG 57.902 41.667 2.05 0.00 0.00 1.73
2382 4327 4.590850 ACCCTTTGAGCTCACAAAAATC 57.409 40.909 18.03 0.00 38.90 2.17
2388 4333 1.270305 CGAGAACCCTTTGAGCTCACA 60.270 52.381 18.03 9.56 0.00 3.58
2441 4386 1.224315 CGCTCCCCAACCATCATCA 59.776 57.895 0.00 0.00 0.00 3.07
2442 4387 0.533755 CTCGCTCCCCAACCATCATC 60.534 60.000 0.00 0.00 0.00 2.92
2443 4388 1.528824 CTCGCTCCCCAACCATCAT 59.471 57.895 0.00 0.00 0.00 2.45
2444 4389 2.989639 CTCGCTCCCCAACCATCA 59.010 61.111 0.00 0.00 0.00 3.07
2445 4390 2.514824 GCTCGCTCCCCAACCATC 60.515 66.667 0.00 0.00 0.00 3.51
2446 4391 2.215451 AATGCTCGCTCCCCAACCAT 62.215 55.000 0.00 0.00 0.00 3.55
2447 4392 2.424842 AAATGCTCGCTCCCCAACCA 62.425 55.000 0.00 0.00 0.00 3.67
2448 4393 1.250840 AAAATGCTCGCTCCCCAACC 61.251 55.000 0.00 0.00 0.00 3.77
2471 4416 0.178992 CAACTGGCAACTCCCCTCAA 60.179 55.000 0.00 0.00 37.61 3.02
2472 4417 1.455849 CAACTGGCAACTCCCCTCA 59.544 57.895 0.00 0.00 37.61 3.86
2473 4418 1.973812 GCAACTGGCAACTCCCCTC 60.974 63.158 0.00 0.00 43.97 4.30
2474 4419 2.116125 GCAACTGGCAACTCCCCT 59.884 61.111 0.00 0.00 43.97 4.79
2500 4445 2.866028 GTTGCAGCAGCTTCCTCG 59.134 61.111 1.76 0.00 42.74 4.63
2504 4449 1.963338 AGGTCGTTGCAGCAGCTTC 60.963 57.895 7.73 0.00 42.74 3.86
2505 4450 2.111878 AGGTCGTTGCAGCAGCTT 59.888 55.556 7.73 0.00 42.74 3.74
2524 4588 0.112412 AGGCCCAAGTGGTTAACAGG 59.888 55.000 8.10 1.07 36.04 4.00
2569 4640 4.320456 CGCTCACCAGCCCACACT 62.320 66.667 0.00 0.00 43.56 3.55
2726 4797 0.913924 GAACTGGGGATTTCGGGGTA 59.086 55.000 0.00 0.00 0.00 3.69
2732 4803 2.112815 CGGCGGAACTGGGGATTTC 61.113 63.158 0.00 0.00 0.00 2.17
3057 5128 1.827789 CTGCTCCTCCTCCTCCTCG 60.828 68.421 0.00 0.00 0.00 4.63
3149 5220 2.718563 GGATTGAAAGGGGAGCGTTTA 58.281 47.619 0.00 0.00 0.00 2.01
3152 5223 1.078426 CGGATTGAAAGGGGAGCGT 60.078 57.895 0.00 0.00 0.00 5.07
3183 5254 2.861935 CAATCAATCAAATCTTGGCCGC 59.138 45.455 0.00 0.00 0.00 6.53
3533 5604 1.330655 CGTAGGTGATCCTGTGGGCT 61.331 60.000 0.00 0.00 44.81 5.19
3596 5667 3.051210 CGGTCCTCACACTGCTGA 58.949 61.111 0.00 0.00 0.00 4.26
3818 5889 1.565156 GCGCCAACACATCGAACTCA 61.565 55.000 0.00 0.00 0.00 3.41
3869 5940 4.147449 TCCCCGTGCAGCATCTCG 62.147 66.667 0.00 0.00 0.00 4.04
3935 6006 3.274288 CTGATGCTTGTCTTAGGTTCCC 58.726 50.000 0.00 0.00 0.00 3.97
3936 6007 2.680339 GCTGATGCTTGTCTTAGGTTCC 59.320 50.000 0.00 0.00 36.03 3.62
3947 6018 3.064958 CAGGACTACATTGCTGATGCTTG 59.935 47.826 1.27 0.00 37.11 4.01
4086 6157 4.839121 CAACTTACCACCATACCTAAGCA 58.161 43.478 0.00 0.00 0.00 3.91
4119 6195 5.305585 TCAACTGAACCCTGAATACTTGAC 58.694 41.667 0.00 0.00 0.00 3.18
4371 6450 6.764085 GCATCATTCCAAATCATCCAAAATGA 59.236 34.615 0.00 0.00 36.44 2.57
4372 6451 6.765989 AGCATCATTCCAAATCATCCAAAATG 59.234 34.615 0.00 0.00 0.00 2.32
4373 6452 6.895782 AGCATCATTCCAAATCATCCAAAAT 58.104 32.000 0.00 0.00 0.00 1.82
4374 6453 6.302535 AGCATCATTCCAAATCATCCAAAA 57.697 33.333 0.00 0.00 0.00 2.44
4375 6454 5.943349 AGCATCATTCCAAATCATCCAAA 57.057 34.783 0.00 0.00 0.00 3.28
4376 6455 5.188163 ACAAGCATCATTCCAAATCATCCAA 59.812 36.000 0.00 0.00 0.00 3.53
4377 6456 4.712829 ACAAGCATCATTCCAAATCATCCA 59.287 37.500 0.00 0.00 0.00 3.41
4378 6457 5.272283 ACAAGCATCATTCCAAATCATCC 57.728 39.130 0.00 0.00 0.00 3.51
4379 6458 6.456449 GCAAACAAGCATCATTCCAAATCATC 60.456 38.462 0.00 0.00 0.00 2.92
4380 6459 5.353123 GCAAACAAGCATCATTCCAAATCAT 59.647 36.000 0.00 0.00 0.00 2.45
4381 6460 4.691685 GCAAACAAGCATCATTCCAAATCA 59.308 37.500 0.00 0.00 0.00 2.57
4382 6461 4.691685 TGCAAACAAGCATCATTCCAAATC 59.308 37.500 0.00 0.00 40.11 2.17
4420 6499 4.714632 CACAAAGAAGAGGACTAACCCAA 58.285 43.478 0.00 0.00 40.05 4.12
4421 6500 3.496160 GCACAAAGAAGAGGACTAACCCA 60.496 47.826 0.00 0.00 40.05 4.51
4422 6501 3.075148 GCACAAAGAAGAGGACTAACCC 58.925 50.000 0.00 0.00 40.05 4.11
4423 6502 4.009370 AGCACAAAGAAGAGGACTAACC 57.991 45.455 0.00 0.00 39.35 2.85
4424 6503 4.214332 CCAAGCACAAAGAAGAGGACTAAC 59.786 45.833 0.00 0.00 0.00 2.34
4425 6504 4.102524 TCCAAGCACAAAGAAGAGGACTAA 59.897 41.667 0.00 0.00 0.00 2.24
4426 6505 3.646162 TCCAAGCACAAAGAAGAGGACTA 59.354 43.478 0.00 0.00 0.00 2.59
4427 6506 2.439507 TCCAAGCACAAAGAAGAGGACT 59.560 45.455 0.00 0.00 0.00 3.85
4428 6507 2.810852 CTCCAAGCACAAAGAAGAGGAC 59.189 50.000 0.00 0.00 0.00 3.85
4429 6508 2.224621 CCTCCAAGCACAAAGAAGAGGA 60.225 50.000 0.00 0.00 41.61 3.71
4430 6509 2.157738 CCTCCAAGCACAAAGAAGAGG 58.842 52.381 0.00 0.00 33.99 3.69
4475 6561 4.406326 TCACTCAACTTAGTACACAACCCA 59.594 41.667 0.00 0.00 0.00 4.51
4514 6622 9.533253 CAACAAAATTAGATGAAAGGAAACACT 57.467 29.630 0.00 0.00 0.00 3.55
4522 6630 8.781067 TTCGTGTCAACAAAATTAGATGAAAG 57.219 30.769 0.00 0.00 0.00 2.62
4578 6686 4.396790 TGTTGTGGACCTTCAACAACTTAC 59.603 41.667 23.35 3.13 46.72 2.34
4596 6704 7.201821 GCCTTAAGCCATCTTGTATATTGTTGT 60.202 37.037 0.00 0.00 33.85 3.32
4597 6705 7.141363 GCCTTAAGCCATCTTGTATATTGTTG 58.859 38.462 0.00 0.00 33.85 3.33
4598 6706 6.833416 TGCCTTAAGCCATCTTGTATATTGTT 59.167 34.615 0.00 0.00 42.71 2.83
4745 6858 4.188247 TCCGGATGTCTAGAAACAACAG 57.812 45.455 0.00 0.00 31.81 3.16
4792 6905 6.176183 ACTCAATGTTCCTTTCTATGTGGAG 58.824 40.000 0.00 0.00 0.00 3.86
4797 6910 6.680810 TGCAAACTCAATGTTCCTTTCTATG 58.319 36.000 0.00 0.00 38.03 2.23
4837 6950 6.152831 ACATAAAATACCCTTTCTCAACAGCC 59.847 38.462 0.00 0.00 0.00 4.85
4906 7019 6.390721 TCTTGCTTCTGTCTATCAGTAACAC 58.609 40.000 0.00 0.00 43.97 3.32
4909 7022 8.314021 TCAATTCTTGCTTCTGTCTATCAGTAA 58.686 33.333 0.00 0.00 43.97 2.24
4911 7024 6.705302 TCAATTCTTGCTTCTGTCTATCAGT 58.295 36.000 0.00 0.00 43.97 3.41
5175 7318 8.704668 AGCATAGAAAGGAAAGGAAAAGAAAAA 58.295 29.630 0.00 0.00 0.00 1.94
5176 7319 8.250143 AGCATAGAAAGGAAAGGAAAAGAAAA 57.750 30.769 0.00 0.00 0.00 2.29
5177 7320 7.839680 AGCATAGAAAGGAAAGGAAAAGAAA 57.160 32.000 0.00 0.00 0.00 2.52
5178 7321 7.505585 TCAAGCATAGAAAGGAAAGGAAAAGAA 59.494 33.333 0.00 0.00 0.00 2.52
5179 7322 7.004086 TCAAGCATAGAAAGGAAAGGAAAAGA 58.996 34.615 0.00 0.00 0.00 2.52
5180 7323 7.219484 TCAAGCATAGAAAGGAAAGGAAAAG 57.781 36.000 0.00 0.00 0.00 2.27
5191 7334 6.492007 AGTGACACAATCAAGCATAGAAAG 57.508 37.500 8.59 0.00 39.72 2.62
5246 7389 4.808895 CCAAAAAGTTTTTGTCTAGGGCAC 59.191 41.667 29.84 0.00 0.00 5.01
5580 8059 5.992829 TGCAGCATGAAAAATCAACAGAAAT 59.007 32.000 0.00 0.00 39.69 2.17


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

AutoCloner maintained by Alex Coulton.