Multiple sequence alignment - TraesCS3A01G399000

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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 TraesCS3A01G399000 chr3A 100.000 5767 0 0 1 5767 646132432 646126666 0.000000e+00 10650
1 TraesCS3A01G399000 chr3A 94.286 105 5 1 5501 5605 606666471 606666574 5.980000e-35 159
2 TraesCS3A01G399000 chr3B 88.828 4538 309 102 4 4467 671022179 671017766 0.000000e+00 5389
3 TraesCS3A01G399000 chr3B 92.730 729 44 5 4800 5520 671017330 671016603 0.000000e+00 1044
4 TraesCS3A01G399000 chr3B 92.899 338 20 4 4467 4800 671017715 671017378 6.720000e-134 488
5 TraesCS3A01G399000 chr3B 90.361 166 16 0 5602 5767 671016605 671016440 9.730000e-53 219
6 TraesCS3A01G399000 chr3B 100.000 90 0 0 5517 5606 26656441 26656530 3.570000e-37 167
7 TraesCS3A01G399000 chr3D 87.922 2782 193 71 4 2713 508388000 508385290 0.000000e+00 3144
8 TraesCS3A01G399000 chr3D 93.664 2115 90 21 2711 4800 508385208 508383113 0.000000e+00 3123
9 TraesCS3A01G399000 chr3D 92.327 404 26 3 4800 5200 508383065 508382664 2.330000e-158 569
10 TraesCS3A01G399000 chr3D 89.241 316 9 11 5209 5520 508382594 508382300 7.060000e-99 372
11 TraesCS3A01G399000 chr3D 84.615 195 28 1 5310 5504 508382073 508381881 5.900000e-45 193
12 TraesCS3A01G399000 chr5B 98.925 93 0 1 5517 5608 546992568 546992660 1.290000e-36 165
13 TraesCS3A01G399000 chr5B 97.727 88 2 0 5516 5603 696964351 696964438 1.000000e-32 152
14 TraesCS3A01G399000 chr4A 98.913 92 1 0 5513 5604 637742387 637742296 1.290000e-36 165
15 TraesCS3A01G399000 chr2B 98.925 93 0 1 5515 5606 303097262 303097354 1.290000e-36 165
16 TraesCS3A01G399000 chr2B 92.727 110 6 2 5518 5626 719470761 719470869 2.150000e-34 158
17 TraesCS3A01G399000 chr5A 95.192 104 3 2 5518 5619 584680796 584680899 4.620000e-36 163
18 TraesCS3A01G399000 chr1B 94.286 105 5 1 5504 5607 248358706 248358602 5.980000e-35 159


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 TraesCS3A01G399000 chr3A 646126666 646132432 5766 True 10650.0 10650 100.0000 1 5767 1 chr3A.!!$R1 5766
1 TraesCS3A01G399000 chr3B 671016440 671022179 5739 True 1785.0 5389 91.2045 4 5767 4 chr3B.!!$R1 5763
2 TraesCS3A01G399000 chr3D 508381881 508388000 6119 True 1480.2 3144 89.5538 4 5520 5 chr3D.!!$R1 5516

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
206 209 1.409064 CAAGTAGTAGCATCCCTCGCA 59.591 52.381 0.00 0.0 0.00 5.10 F
1132 1211 0.381089 CGAAGGTAGTAGTGCTCCCG 59.619 60.000 0.00 0.0 0.00 5.14 F
1894 1993 0.179100 TCCTGCTTGCGCTAGCTTAG 60.179 55.000 36.44 27.7 45.42 2.18 F
1991 2090 0.841961 CCATCTCAGCCAAGATCCCA 59.158 55.000 0.00 0.0 33.68 4.37 F
2225 2324 1.205893 CCTAAGCAGACCCTGTCACTC 59.794 57.143 0.00 0.0 34.60 3.51 F
2682 2785 1.330655 GGGACATCTTGCCTCCTCGA 61.331 60.000 0.00 0.0 31.27 4.04 F
2850 3040 1.947456 GATCCAGATGCGGTTAAACCC 59.053 52.381 0.00 0.0 33.75 4.11 F
3425 3615 4.450757 GCAAGGTTTGTCTTGTTGTTTGTT 59.549 37.500 6.48 0.0 44.26 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 1848 0.386352 CTGCCGTGTGCTTGAACATG 60.386 55.000 0.0 0.0 42.00 3.21 R
2850 3040 0.802494 GTATGGGCACACAAACCTCG 59.198 55.000 0.0 0.0 0.00 4.63 R
3311 3501 2.575532 CCATGTGTCGGGCTGATTAAT 58.424 47.619 0.0 0.0 0.00 1.40 R
3425 3615 5.661056 AAAGTAGGATGAACGACTGATGA 57.339 39.130 0.0 0.0 0.00 2.92 R
4147 4338 6.502136 AGCAGTTATGTTTAGCTTCTTTCC 57.498 37.500 0.0 0.0 29.98 3.13 R
4490 4741 1.133792 CCCGGCCTTCAAGAATACCAT 60.134 52.381 0.0 0.0 0.00 3.55 R
4509 4761 2.417097 GCACAAGGCAACACACCC 59.583 61.111 0.0 0.0 43.97 4.61 R
5040 5359 1.414919 ACTCCTCGGCAACAACAGTTA 59.585 47.619 0.0 0.0 0.00 2.24 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
62 65 8.664798 TGTAATGGAATTTACAATCGACTTGAG 58.335 33.333 12.53 0.00 38.72 3.02
66 69 5.220416 GGAATTTACAATCGACTTGAGACCG 60.220 44.000 12.53 0.00 38.29 4.79
74 77 1.466024 CGACTTGAGACCGTGAGCTAC 60.466 57.143 0.00 0.00 0.00 3.58
86 89 4.524714 ACCGTGAGCTACTGCAGATATTAT 59.475 41.667 23.35 0.00 42.74 1.28
149 152 3.564053 AACTGTTTGAAACCCGTCCTA 57.436 42.857 5.50 0.00 0.00 2.94
150 153 3.121738 ACTGTTTGAAACCCGTCCTAG 57.878 47.619 5.50 0.00 0.00 3.02
151 154 2.436911 ACTGTTTGAAACCCGTCCTAGT 59.563 45.455 5.50 0.00 0.00 2.57
153 156 4.285260 ACTGTTTGAAACCCGTCCTAGTAT 59.715 41.667 5.50 0.00 0.00 2.12
167 170 5.646793 CGTCCTAGTATACAGCTGGCTTATA 59.353 44.000 19.93 8.47 0.00 0.98
183 186 5.609284 TGGCTTATACATACCCAACCTGTAT 59.391 40.000 0.00 0.00 39.00 2.29
185 188 6.239772 GGCTTATACATACCCAACCTGTATGA 60.240 42.308 15.20 2.53 45.38 2.15
186 189 6.649557 GCTTATACATACCCAACCTGTATGAC 59.350 42.308 15.20 0.00 45.38 3.06
187 190 7.678207 TTATACATACCCAACCTGTATGACA 57.322 36.000 15.20 5.17 45.38 3.58
189 192 4.843728 ACATACCCAACCTGTATGACAAG 58.156 43.478 15.20 0.00 45.38 3.16
190 193 4.288626 ACATACCCAACCTGTATGACAAGT 59.711 41.667 15.20 0.00 45.38 3.16
191 194 5.486063 ACATACCCAACCTGTATGACAAGTA 59.514 40.000 15.20 0.00 45.38 2.24
192 195 4.553330 ACCCAACCTGTATGACAAGTAG 57.447 45.455 0.00 0.00 0.00 2.57
196 199 5.109903 CCAACCTGTATGACAAGTAGTAGC 58.890 45.833 0.00 0.00 0.00 3.58
197 200 5.337250 CCAACCTGTATGACAAGTAGTAGCA 60.337 44.000 0.00 0.00 0.00 3.49
198 201 6.341316 CAACCTGTATGACAAGTAGTAGCAT 58.659 40.000 0.00 0.00 0.00 3.79
199 202 6.150396 ACCTGTATGACAAGTAGTAGCATC 57.850 41.667 0.00 0.00 0.00 3.91
200 203 5.069251 ACCTGTATGACAAGTAGTAGCATCC 59.931 44.000 0.00 0.00 0.00 3.51
201 204 5.509840 CCTGTATGACAAGTAGTAGCATCCC 60.510 48.000 0.00 0.00 0.00 3.85
204 207 2.688446 TGACAAGTAGTAGCATCCCTCG 59.312 50.000 0.00 0.00 0.00 4.63
206 209 1.409064 CAAGTAGTAGCATCCCTCGCA 59.591 52.381 0.00 0.00 0.00 5.10
207 210 1.776662 AGTAGTAGCATCCCTCGCAA 58.223 50.000 0.00 0.00 0.00 4.85
242 273 1.585521 CTTACGTAGCCGCCGTCAG 60.586 63.158 0.00 0.00 39.60 3.51
246 277 2.278661 GTAGCCGCCGTCAGTAGC 60.279 66.667 0.00 0.00 0.00 3.58
339 374 2.947542 CCTATCGGCTCGGACTCG 59.052 66.667 0.00 0.00 37.82 4.18
341 376 3.256716 CTATCGGCTCGGACTCGCC 62.257 68.421 0.00 0.00 42.86 5.54
342 377 3.769369 TATCGGCTCGGACTCGCCT 62.769 63.158 5.37 0.00 44.11 5.52
373 408 4.180946 CCTCTCGACGGAGCGGTG 62.181 72.222 0.00 0.00 39.78 4.94
374 409 4.838486 CTCTCGACGGAGCGGTGC 62.838 72.222 0.00 0.00 40.26 5.01
410 455 3.908508 TGGAATTCCACGACCCCA 58.091 55.556 23.63 0.00 42.01 4.96
412 457 1.743995 GGAATTCCACGACCCCACG 60.744 63.158 20.04 0.00 39.31 4.94
413 458 2.359478 AATTCCACGACCCCACGC 60.359 61.111 0.00 0.00 36.70 5.34
421 483 4.747529 GACCCCACGCGTACCACC 62.748 72.222 13.44 0.00 0.00 4.61
562 627 4.733542 GCCAGCACCGGGGCTTAA 62.734 66.667 33.42 0.00 46.74 1.85
563 628 2.438434 CCAGCACCGGGGCTTAAG 60.438 66.667 33.42 19.15 42.71 1.85
690 756 4.824166 CGTCCGGTGGCTACGACG 62.824 72.222 14.16 14.16 38.89 5.12
691 757 3.434319 GTCCGGTGGCTACGACGA 61.434 66.667 0.00 0.00 0.00 4.20
692 758 3.434319 TCCGGTGGCTACGACGAC 61.434 66.667 0.00 0.00 0.00 4.34
693 759 4.824166 CCGGTGGCTACGACGACG 62.824 72.222 5.58 5.58 45.75 5.12
694 760 3.792047 CGGTGGCTACGACGACGA 61.792 66.667 15.32 0.00 42.66 4.20
695 761 2.099831 GGTGGCTACGACGACGAG 59.900 66.667 15.32 8.18 42.66 4.18
699 765 2.105466 GGCTACGACGACGAGGACT 61.105 63.158 15.32 0.00 42.66 3.85
791 857 2.606108 GAATTCACGAAAATGCCACCC 58.394 47.619 0.00 0.00 0.00 4.61
812 878 3.144120 CTCCCCTCGCTGGATCACG 62.144 68.421 0.00 0.00 38.35 4.35
813 879 3.147595 CCCCTCGCTGGATCACGA 61.148 66.667 0.00 0.00 38.35 4.35
814 880 2.105128 CCCTCGCTGGATCACGAC 59.895 66.667 0.00 0.00 38.35 4.34
815 881 2.278206 CCTCGCTGGATCACGACG 60.278 66.667 0.00 0.00 38.35 5.12
816 882 2.951745 CTCGCTGGATCACGACGC 60.952 66.667 0.00 0.00 34.08 5.19
817 883 4.492160 TCGCTGGATCACGACGCC 62.492 66.667 0.00 0.00 32.45 5.68
819 885 4.148825 GCTGGATCACGACGCCCT 62.149 66.667 0.00 0.00 0.00 5.19
820 886 2.202797 CTGGATCACGACGCCCTG 60.203 66.667 0.00 0.00 0.00 4.45
821 887 3.723235 CTGGATCACGACGCCCTGG 62.723 68.421 0.00 0.00 0.00 4.45
822 888 3.771160 GGATCACGACGCCCTGGT 61.771 66.667 0.00 0.00 0.00 4.00
823 889 2.202756 GATCACGACGCCCTGGTC 60.203 66.667 0.00 0.00 0.00 4.02
824 890 2.994995 ATCACGACGCCCTGGTCA 60.995 61.111 0.00 0.00 36.73 4.02
825 891 2.890847 GATCACGACGCCCTGGTCAG 62.891 65.000 0.00 0.00 36.73 3.51
1050 1129 2.659016 CTCAAGCTCCTGCACCGA 59.341 61.111 0.00 0.00 42.74 4.69
1059 1138 4.803426 CTGCACCGACTCCTCGCC 62.803 72.222 0.00 0.00 38.70 5.54
1124 1203 2.879646 AGGAGCGATTCGAAGGTAGTAG 59.120 50.000 10.88 0.00 0.00 2.57
1132 1211 0.381089 CGAAGGTAGTAGTGCTCCCG 59.619 60.000 0.00 0.00 0.00 5.14
1133 1212 0.745468 GAAGGTAGTAGTGCTCCCGG 59.255 60.000 0.00 0.00 0.00 5.73
1154 1243 2.300437 GTTCCCAGCTCAGTAGACTTGT 59.700 50.000 0.00 0.00 0.00 3.16
1172 1261 6.038271 AGACTTGTTGCTTACTTACCAGTTTG 59.962 38.462 0.00 0.00 34.06 2.93
1214 1303 4.211374 CGTATTGTACCTGCTGCTATTTCC 59.789 45.833 0.00 0.00 0.00 3.13
1226 1315 1.941325 CTATTTCCGTGCTGGTCCTC 58.059 55.000 0.00 0.00 39.52 3.71
1228 1317 1.827399 ATTTCCGTGCTGGTCCTCGT 61.827 55.000 0.00 0.00 39.52 4.18
1233 1322 1.078759 CGTGCTGGTCCTCGTGAATC 61.079 60.000 0.00 0.00 0.00 2.52
1294 1385 1.204467 GATTGATGGGCGCCTGAAAAA 59.796 47.619 28.56 14.91 0.00 1.94
1301 1392 1.070821 GGCGCCTGAAAAATTTCTGC 58.929 50.000 22.15 8.57 38.02 4.26
1302 1393 1.605202 GGCGCCTGAAAAATTTCTGCA 60.605 47.619 22.15 0.00 38.02 4.41
1340 1432 3.763897 ACCAGTATTTTGTTCATGCCCTC 59.236 43.478 0.00 0.00 0.00 4.30
1348 1440 1.025041 GTTCATGCCCTCGGGAATTC 58.975 55.000 6.08 0.00 37.50 2.17
1372 1464 2.029020 GCTTCCCCTGTTCATGGTTTTC 60.029 50.000 0.00 0.00 0.00 2.29
1421 1513 2.569853 TGAAGGACCGAGCAAGGAATTA 59.430 45.455 4.39 0.00 34.73 1.40
1444 1536 1.072173 TGGTTGGAGGTGAGTGATGTG 59.928 52.381 0.00 0.00 0.00 3.21
1449 1541 1.066573 GGAGGTGAGTGATGTGGTGAG 60.067 57.143 0.00 0.00 0.00 3.51
1458 1550 1.168714 GATGTGGTGAGGTTTCCTGC 58.831 55.000 0.00 0.00 31.76 4.85
1463 1555 1.214175 TGGTGAGGTTTCCTGCTGAAA 59.786 47.619 0.00 0.00 40.64 2.69
1465 1557 2.229784 GGTGAGGTTTCCTGCTGAAATG 59.770 50.000 5.48 0.00 44.44 2.32
1467 1559 3.760684 GTGAGGTTTCCTGCTGAAATGAT 59.239 43.478 5.48 0.00 44.44 2.45
1475 1567 5.441718 TCCTGCTGAAATGATTAGTTCCT 57.558 39.130 0.00 0.00 30.15 3.36
1480 1572 6.240894 TGCTGAAATGATTAGTTCCTTCAGT 58.759 36.000 10.37 0.00 41.23 3.41
1481 1573 6.149973 TGCTGAAATGATTAGTTCCTTCAGTG 59.850 38.462 10.37 0.00 41.23 3.66
1482 1574 6.372659 GCTGAAATGATTAGTTCCTTCAGTGA 59.627 38.462 10.37 0.00 41.23 3.41
1488 1580 6.401394 TGATTAGTTCCTTCAGTGATGACAG 58.599 40.000 7.57 0.00 0.00 3.51
1494 1586 2.567169 CCTTCAGTGATGACAGTGGGTA 59.433 50.000 7.57 0.00 44.74 3.69
1510 1604 1.591768 GGTAGGAAGTGGGATTGGGA 58.408 55.000 0.00 0.00 0.00 4.37
1512 1606 2.356844 GGTAGGAAGTGGGATTGGGAAC 60.357 54.545 0.00 0.00 0.00 3.62
1513 1607 1.760405 AGGAAGTGGGATTGGGAACT 58.240 50.000 0.00 0.00 0.00 3.01
1514 1608 2.929301 AGGAAGTGGGATTGGGAACTA 58.071 47.619 0.00 0.00 0.00 2.24
1515 1609 2.846827 AGGAAGTGGGATTGGGAACTAG 59.153 50.000 0.00 0.00 0.00 2.57
1516 1610 2.644676 GAAGTGGGATTGGGAACTAGC 58.355 52.381 0.00 0.00 0.00 3.42
1517 1611 0.541863 AGTGGGATTGGGAACTAGCG 59.458 55.000 0.00 0.00 0.00 4.26
1518 1612 0.539986 GTGGGATTGGGAACTAGCGA 59.460 55.000 0.00 0.00 0.00 4.93
1519 1613 1.141053 GTGGGATTGGGAACTAGCGAT 59.859 52.381 0.00 0.00 0.00 4.58
1520 1614 1.140852 TGGGATTGGGAACTAGCGATG 59.859 52.381 0.00 0.00 0.00 3.84
1641 1739 4.009675 TGCCTTGTCCAATACATGAGTTC 58.990 43.478 0.00 0.00 38.10 3.01
1652 1750 9.529325 TCCAATACATGAGTTCGATTAAGTTAG 57.471 33.333 0.00 0.00 0.00 2.34
1657 1755 7.544622 ACATGAGTTCGATTAAGTTAGTGCTA 58.455 34.615 0.00 0.00 0.00 3.49
1658 1756 8.198109 ACATGAGTTCGATTAAGTTAGTGCTAT 58.802 33.333 0.00 0.00 0.00 2.97
1823 1922 4.679373 TGCTTTCTCATCCCTCATACTC 57.321 45.455 0.00 0.00 0.00 2.59
1824 1923 4.293494 TGCTTTCTCATCCCTCATACTCT 58.707 43.478 0.00 0.00 0.00 3.24
1825 1924 4.100653 TGCTTTCTCATCCCTCATACTCTG 59.899 45.833 0.00 0.00 0.00 3.35
1826 1925 4.100808 GCTTTCTCATCCCTCATACTCTGT 59.899 45.833 0.00 0.00 0.00 3.41
1855 1954 9.806203 TTGTTTAATTGATGATGATGATGGTTC 57.194 29.630 0.00 0.00 0.00 3.62
1869 1968 2.027625 GGTTCGGTCGCAGGTCAAG 61.028 63.158 0.00 0.00 0.00 3.02
1894 1993 0.179100 TCCTGCTTGCGCTAGCTTAG 60.179 55.000 36.44 27.70 45.42 2.18
1988 2087 2.048444 TTGCCATCTCAGCCAAGATC 57.952 50.000 0.00 0.00 33.68 2.75
1991 2090 0.841961 CCATCTCAGCCAAGATCCCA 59.158 55.000 0.00 0.00 33.68 4.37
2021 2120 1.301623 CAAGGGCCGGACATTGGTA 59.698 57.895 27.04 0.00 0.00 3.25
2093 2192 7.492994 GGCTATATTAAGCTAATGTCTGGCTAC 59.507 40.741 0.00 0.00 42.37 3.58
2197 2296 3.256631 ACAAAGATCCACCATTGCTGTTC 59.743 43.478 0.00 0.00 0.00 3.18
2225 2324 1.205893 CCTAAGCAGACCCTGTCACTC 59.794 57.143 0.00 0.00 34.60 3.51
2242 2341 5.008911 TGTCACTCTTTTGACCATGTGATTG 59.991 40.000 0.00 0.00 44.63 2.67
2244 2343 3.828451 ACTCTTTTGACCATGTGATTGGG 59.172 43.478 0.00 0.00 41.35 4.12
2249 2348 3.003394 TGACCATGTGATTGGGATGTC 57.997 47.619 0.00 0.00 41.35 3.06
2269 2368 7.280876 GGATGTCTGTATAGTTGATGAGCAAAA 59.719 37.037 0.00 0.00 38.44 2.44
2338 2441 3.007290 CCACCTAGATGCTATAGCTTGCA 59.993 47.826 24.61 6.56 43.67 4.08
2418 2521 6.071840 AGGTTTACTAGTCTACTGCTGAGTTG 60.072 42.308 0.00 0.00 33.21 3.16
2437 2540 5.564550 AGTTGTGCTGATAACCTTCTCATT 58.435 37.500 0.00 0.00 0.00 2.57
2553 2656 8.095452 ACCCTATCAAGAAAGATCTACAATGT 57.905 34.615 0.00 0.00 33.77 2.71
2559 2662 8.908786 TCAAGAAAGATCTACAATGTGAAACT 57.091 30.769 0.00 0.00 33.62 2.66
2682 2785 1.330655 GGGACATCTTGCCTCCTCGA 61.331 60.000 0.00 0.00 31.27 4.04
2703 2806 5.010112 TCGAAAAATTAAGGATGTTGGTGCA 59.990 36.000 0.00 0.00 0.00 4.57
2850 3040 1.947456 GATCCAGATGCGGTTAAACCC 59.053 52.381 0.00 0.00 33.75 4.11
3042 3232 7.121974 ACTCAAGACATCAAACATTAAGTCG 57.878 36.000 0.00 0.00 0.00 4.18
3043 3233 6.706270 ACTCAAGACATCAAACATTAAGTCGT 59.294 34.615 0.00 0.00 0.00 4.34
3117 3307 9.322776 GCATCATTCAGTTCTAATTTATTAGCG 57.677 33.333 4.90 0.00 39.60 4.26
3170 3360 5.118990 GCTCTACATATTTGGTCTTGCTGA 58.881 41.667 0.00 0.00 0.00 4.26
3172 3362 6.238320 GCTCTACATATTTGGTCTTGCTGAAG 60.238 42.308 0.00 0.00 0.00 3.02
3193 3383 5.856126 AGATGTTTTGCATTTGAAGCATG 57.144 34.783 3.30 0.00 42.33 4.06
3311 3501 9.949174 GATGACAAATATATGCATGTTGTGTTA 57.051 29.630 18.62 10.73 0.00 2.41
3425 3615 4.450757 GCAAGGTTTGTCTTGTTGTTTGTT 59.549 37.500 6.48 0.00 44.26 2.83
3578 3769 6.205658 GCAAATAGGAGAAGTGATATTGGACC 59.794 42.308 0.00 0.00 0.00 4.46
4096 4287 7.759489 TCTTCAATTAGCAATTGTTACTGGT 57.241 32.000 7.40 0.00 46.46 4.00
4147 4338 6.449698 ACAGCAAAAGAATAACTGTCATTGG 58.550 36.000 0.00 0.00 36.95 3.16
4376 4571 8.314751 CCCTAGAACTCTTTGAAGTCTTATTCA 58.685 37.037 0.00 0.00 37.41 2.57
4385 4580 7.607991 TCTTTGAAGTCTTATTCACTGATTCCC 59.392 37.037 0.00 0.00 38.87 3.97
4386 4581 6.627087 TGAAGTCTTATTCACTGATTCCCT 57.373 37.500 0.00 0.00 34.31 4.20
4427 4627 9.304335 TGACTGATGGAATATATCATTGCAAAT 57.696 29.630 1.71 0.00 34.33 2.32
4435 4635 7.816031 GGAATATATCATTGCAAATCCCAAGTG 59.184 37.037 1.71 0.00 0.00 3.16
4509 4761 2.348411 ATGGTATTCTTGAAGGCCGG 57.652 50.000 0.00 0.00 0.00 6.13
4587 4845 8.918116 ACTGTGACTGTGTAAGACATCATATAT 58.082 33.333 0.00 0.00 33.13 0.86
4686 4945 4.675190 AAGTTGTGAAGCATCTCATTCG 57.325 40.909 0.00 0.00 0.00 3.34
4771 5035 1.632409 TCAGGATGAGCTTTGAAGCCT 59.368 47.619 11.85 0.00 42.56 4.58
4780 5045 1.895131 GCTTTGAAGCCTCCCAAATCA 59.105 47.619 4.38 0.00 46.20 2.57
4794 5059 6.406624 CCTCCCAAATCATCAATTCTTCCAAG 60.407 42.308 0.00 0.00 0.00 3.61
4796 5061 5.422970 CCCAAATCATCAATTCTTCCAAGGA 59.577 40.000 0.00 0.00 0.00 3.36
4797 5062 6.406624 CCCAAATCATCAATTCTTCCAAGGAG 60.407 42.308 0.00 0.00 0.00 3.69
4798 5063 6.379133 CCAAATCATCAATTCTTCCAAGGAGA 59.621 38.462 0.00 0.00 0.00 3.71
4960 5275 1.890489 TGCGTGTAGTGTACATGGTCT 59.110 47.619 0.00 0.00 44.02 3.85
4962 5277 2.876091 CGTGTAGTGTACATGGTCTGG 58.124 52.381 0.00 0.00 41.00 3.86
5053 5372 6.346518 GCATAACACAAATAACTGTTGTTGCC 60.347 38.462 14.84 0.00 37.09 4.52
5118 5437 5.555966 TCCTGTAATCAGCATACACAAACA 58.444 37.500 0.00 0.00 40.09 2.83
5122 5441 5.411361 TGTAATCAGCATACACAAACACCTC 59.589 40.000 0.00 0.00 0.00 3.85
5127 5446 3.055094 AGCATACACAAACACCTCCTAGG 60.055 47.826 0.82 0.82 42.49 3.02
5131 5450 4.287766 ACACAAACACCTCCTAGGATTC 57.712 45.455 13.12 0.00 37.67 2.52
5135 5454 1.501582 ACACCTCCTAGGATTCAGCC 58.498 55.000 13.12 0.00 37.67 4.85
5145 5464 3.121929 AGGATTCAGCCTCTCAGGTAA 57.878 47.619 0.00 0.00 37.80 2.85
5152 5471 5.241403 TCAGCCTCTCAGGTAATGAAAAA 57.759 39.130 0.00 0.00 37.52 1.94
5153 5472 5.819991 TCAGCCTCTCAGGTAATGAAAAAT 58.180 37.500 0.00 0.00 37.52 1.82
5169 5488 6.040209 TGAAAAATAAAGCATGCATCCAGT 57.960 33.333 21.98 0.00 0.00 4.00
5346 5726 3.008375 ACAAGTCTGATGTATGCCTGTGT 59.992 43.478 0.00 0.00 0.00 3.72
5470 5854 9.250624 GTTTATAGCTTGAGTCTACACATTAGG 57.749 37.037 0.00 0.00 0.00 2.69
5518 5902 7.701924 CAGCACAAATTCAGTTGTTCTTTTCTA 59.298 33.333 0.00 0.00 39.73 2.10
5519 5903 7.702348 AGCACAAATTCAGTTGTTCTTTTCTAC 59.298 33.333 0.00 0.00 39.73 2.59
5520 5904 7.702348 GCACAAATTCAGTTGTTCTTTTCTACT 59.298 33.333 0.00 0.00 39.73 2.57
5521 5905 9.226345 CACAAATTCAGTTGTTCTTTTCTACTC 57.774 33.333 0.00 0.00 39.73 2.59
5522 5906 8.406297 ACAAATTCAGTTGTTCTTTTCTACTCC 58.594 33.333 0.00 0.00 38.60 3.85
5523 5907 7.511959 AATTCAGTTGTTCTTTTCTACTCCC 57.488 36.000 0.00 0.00 0.00 4.30
5524 5908 5.888982 TCAGTTGTTCTTTTCTACTCCCT 57.111 39.130 0.00 0.00 0.00 4.20
5525 5909 5.855045 TCAGTTGTTCTTTTCTACTCCCTC 58.145 41.667 0.00 0.00 0.00 4.30
5526 5910 4.998033 CAGTTGTTCTTTTCTACTCCCTCC 59.002 45.833 0.00 0.00 0.00 4.30
5527 5911 3.955650 TGTTCTTTTCTACTCCCTCCG 57.044 47.619 0.00 0.00 0.00 4.63
5528 5912 3.236896 TGTTCTTTTCTACTCCCTCCGT 58.763 45.455 0.00 0.00 0.00 4.69
5529 5913 3.644738 TGTTCTTTTCTACTCCCTCCGTT 59.355 43.478 0.00 0.00 0.00 4.44
5530 5914 4.244066 GTTCTTTTCTACTCCCTCCGTTC 58.756 47.826 0.00 0.00 0.00 3.95
5531 5915 2.830321 TCTTTTCTACTCCCTCCGTTCC 59.170 50.000 0.00 0.00 0.00 3.62
5532 5916 2.314071 TTTCTACTCCCTCCGTTCCA 57.686 50.000 0.00 0.00 0.00 3.53
5533 5917 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
5534 5918 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
5535 5919 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
5536 5920 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
5537 5921 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
5538 5922 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5539 5923 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5540 5924 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5541 5925 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5542 5926 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5543 5927 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5544 5928 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
5545 5929 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
5546 5930 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
5547 5931 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
5548 5932 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
5549 5933 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
5550 5934 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
5551 5935 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
5552 5936 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
5553 5937 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
5554 5938 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
5555 5939 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
5556 5940 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
5579 5963 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
5580 5964 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
5581 5965 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
5582 5966 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
5583 5967 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
5584 5968 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
5585 5969 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
5586 5970 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
5587 5971 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
5588 5972 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
5589 5973 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
5590 5974 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
5591 5975 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
5592 5976 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
5593 5977 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
5594 5978 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
5595 5979 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
5596 5980 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
5597 5981 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
5598 5982 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5599 5983 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5600 5984 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
5601 5985 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5620 6004 4.813697 GGAGTACATGCTTCTCATTCCTTC 59.186 45.833 12.25 0.00 31.79 3.46
5626 6010 2.751259 TGCTTCTCATTCCTTCACATGC 59.249 45.455 0.00 0.00 0.00 4.06
5633 6017 5.131642 TCTCATTCCTTCACATGCTATCCTT 59.868 40.000 0.00 0.00 0.00 3.36
5644 6028 8.213518 TCACATGCTATCCTTCATAAAAAGAC 57.786 34.615 0.00 0.00 0.00 3.01
5651 6035 7.558081 GCTATCCTTCATAAAAAGACTCCCTTT 59.442 37.037 0.00 0.00 46.47 3.11
5675 6066 4.933505 TTCAAAATGAACATGCACCTGA 57.066 36.364 0.00 0.00 30.26 3.86
5681 6072 2.929641 TGAACATGCACCTGAAAGTCA 58.070 42.857 0.00 0.00 0.00 3.41
5724 6115 2.964740 TCTGAGATGACCAAAGAAGCG 58.035 47.619 0.00 0.00 0.00 4.68
5735 6126 1.135689 CAAAGAAGCGCATACCACCAC 60.136 52.381 11.47 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 43 6.316390 GGTCTCAAGTCGATTGTAAATTCCAT 59.684 38.462 0.00 0.00 40.05 3.41
50 53 2.254459 CTCACGGTCTCAAGTCGATTG 58.746 52.381 0.00 0.00 40.52 2.67
54 57 0.803117 TAGCTCACGGTCTCAAGTCG 59.197 55.000 0.00 0.00 0.00 4.18
62 65 0.457851 ATCTGCAGTAGCTCACGGTC 59.542 55.000 14.67 0.00 42.74 4.79
123 126 6.717997 AGGACGGGTTTCAAACAGTTTATTAT 59.282 34.615 1.93 0.00 0.00 1.28
144 147 5.986501 ATAAGCCAGCTGTATACTAGGAC 57.013 43.478 13.81 0.00 0.00 3.85
149 152 6.154706 GGGTATGTATAAGCCAGCTGTATACT 59.845 42.308 23.16 15.52 33.64 2.12
150 153 6.070995 TGGGTATGTATAAGCCAGCTGTATAC 60.071 42.308 19.06 19.06 39.51 1.47
151 154 6.020389 TGGGTATGTATAAGCCAGCTGTATA 58.980 40.000 13.81 5.74 39.51 1.47
153 156 4.228010 TGGGTATGTATAAGCCAGCTGTA 58.772 43.478 13.81 0.00 39.51 2.74
167 170 4.288626 ACTTGTCATACAGGTTGGGTATGT 59.711 41.667 11.11 0.00 45.23 2.29
183 186 2.688446 CGAGGGATGCTACTACTTGTCA 59.312 50.000 0.00 0.00 0.00 3.58
184 187 2.544069 GCGAGGGATGCTACTACTTGTC 60.544 54.545 0.00 0.00 0.00 3.18
185 188 1.409427 GCGAGGGATGCTACTACTTGT 59.591 52.381 0.00 0.00 0.00 3.16
186 189 1.409064 TGCGAGGGATGCTACTACTTG 59.591 52.381 0.00 0.00 0.00 3.16
187 190 1.776662 TGCGAGGGATGCTACTACTT 58.223 50.000 0.00 0.00 0.00 2.24
189 192 2.596904 TTTGCGAGGGATGCTACTAC 57.403 50.000 0.00 0.00 0.00 2.73
190 193 3.620427 TTTTTGCGAGGGATGCTACTA 57.380 42.857 0.00 0.00 0.00 1.82
191 194 2.489938 TTTTTGCGAGGGATGCTACT 57.510 45.000 0.00 0.00 0.00 2.57
255 286 3.733224 GCTCAGTTAGTCATCTATGCGTG 59.267 47.826 0.00 0.00 0.00 5.34
256 287 3.634448 AGCTCAGTTAGTCATCTATGCGT 59.366 43.478 0.00 0.00 0.00 5.24
258 289 3.740321 GCAGCTCAGTTAGTCATCTATGC 59.260 47.826 0.00 0.00 0.00 3.14
264 295 0.460987 GCGGCAGCTCAGTTAGTCAT 60.461 55.000 0.00 0.00 41.01 3.06
265 296 1.079819 GCGGCAGCTCAGTTAGTCA 60.080 57.895 0.00 0.00 41.01 3.41
267 298 2.125912 CGCGGCAGCTCAGTTAGT 60.126 61.111 7.38 0.00 42.32 2.24
268 299 3.558411 GCGCGGCAGCTCAGTTAG 61.558 66.667 8.83 0.00 42.32 2.34
269 300 4.069232 AGCGCGGCAGCTCAGTTA 62.069 61.111 8.83 0.00 45.67 2.24
324 359 3.285215 GGCGAGTCCGAGCCGATA 61.285 66.667 0.00 0.00 44.22 2.92
357 392 4.838486 GCACCGCTCCGTCGAGAG 62.838 72.222 0.00 0.00 38.52 3.20
370 405 4.683334 GTGTCTTTGGCGCGCACC 62.683 66.667 34.42 17.47 0.00 5.01
407 452 3.927163 GACTGGTGGTACGCGTGGG 62.927 68.421 24.59 6.21 41.51 4.61
408 453 2.431942 GACTGGTGGTACGCGTGG 60.432 66.667 24.59 5.49 41.51 4.94
410 455 4.712425 GCGACTGGTGGTACGCGT 62.712 66.667 19.17 19.17 41.49 6.01
412 457 4.409218 TCGCGACTGGTGGTACGC 62.409 66.667 3.71 0.00 46.08 4.42
413 458 2.503375 GTCGCGACTGGTGGTACG 60.503 66.667 31.12 0.00 0.00 3.67
415 460 2.669229 TCGTCGCGACTGGTGGTA 60.669 61.111 33.94 10.74 0.00 3.25
455 517 4.838486 CGGAGAGGCTCGTCGTGC 62.838 72.222 19.22 10.73 0.00 5.34
456 518 4.180946 CCGGAGAGGCTCGTCGTG 62.181 72.222 23.23 14.75 0.00 4.35
536 601 2.401766 CGGTGCTGGCCAATGAGAC 61.402 63.158 7.01 0.00 0.00 3.36
537 602 2.046023 CGGTGCTGGCCAATGAGA 60.046 61.111 7.01 0.00 0.00 3.27
539 604 4.738998 CCCGGTGCTGGCCAATGA 62.739 66.667 7.01 0.00 0.00 2.57
547 612 3.134127 GCTTAAGCCCCGGTGCTG 61.134 66.667 13.72 0.46 41.80 4.41
548 613 4.778143 CGCTTAAGCCCCGGTGCT 62.778 66.667 21.53 5.25 45.43 4.40
561 626 0.109412 GCAGCAAATGAAGCTCGCTT 60.109 50.000 3.43 3.43 41.14 4.68
562 627 1.505353 GCAGCAAATGAAGCTCGCT 59.495 52.632 0.00 0.00 41.14 4.93
563 628 1.515736 GGCAGCAAATGAAGCTCGC 60.516 57.895 0.00 0.00 41.14 5.03
679 745 2.099831 CCTCGTCGTCGTAGCCAC 59.900 66.667 1.33 0.00 38.33 5.01
684 750 3.772636 CGAGTCCTCGTCGTCGTA 58.227 61.111 8.50 0.00 46.99 3.43
693 759 1.378124 CTTCTCCGTCCCGAGTCCTC 61.378 65.000 0.00 0.00 0.00 3.71
694 760 1.378778 CTTCTCCGTCCCGAGTCCT 60.379 63.158 0.00 0.00 0.00 3.85
695 761 2.416432 CCTTCTCCGTCCCGAGTCC 61.416 68.421 0.00 0.00 0.00 3.85
761 827 3.078560 GTGAATTCGCGACGACCC 58.921 61.111 9.15 0.00 34.89 4.46
799 865 2.951745 GCGTCGTGATCCAGCGAG 60.952 66.667 4.71 2.21 37.82 5.03
802 868 4.148825 AGGGCGTCGTGATCCAGC 62.149 66.667 0.00 0.00 0.00 4.85
804 870 3.770040 CCAGGGCGTCGTGATCCA 61.770 66.667 11.98 0.00 0.00 3.41
805 871 3.718210 GACCAGGGCGTCGTGATCC 62.718 68.421 11.98 0.00 0.00 3.36
812 878 4.767255 CCAGCTGACCAGGGCGTC 62.767 72.222 17.39 0.00 0.00 5.19
814 880 4.335647 AACCAGCTGACCAGGGCG 62.336 66.667 17.39 0.00 0.00 6.13
815 881 2.674380 CAACCAGCTGACCAGGGC 60.674 66.667 17.39 0.00 0.00 5.19
816 882 2.034687 CCAACCAGCTGACCAGGG 59.965 66.667 17.39 5.38 0.00 4.45
817 883 1.302832 GACCAACCAGCTGACCAGG 60.303 63.158 17.39 13.62 0.00 4.45
818 884 1.669115 CGACCAACCAGCTGACCAG 60.669 63.158 17.39 0.00 0.00 4.00
819 885 2.425592 CGACCAACCAGCTGACCA 59.574 61.111 17.39 0.00 0.00 4.02
820 886 2.358737 CCGACCAACCAGCTGACC 60.359 66.667 17.39 0.00 0.00 4.02
821 887 2.358737 CCCGACCAACCAGCTGAC 60.359 66.667 17.39 0.00 0.00 3.51
822 888 4.329545 GCCCGACCAACCAGCTGA 62.330 66.667 17.39 0.00 0.00 4.26
1032 1099 2.435586 CGGTGCAGGAGCTTGAGG 60.436 66.667 0.00 0.00 42.74 3.86
1033 1100 1.739562 GTCGGTGCAGGAGCTTGAG 60.740 63.158 0.00 0.00 42.74 3.02
1034 1101 2.159819 GAGTCGGTGCAGGAGCTTGA 62.160 60.000 0.00 0.00 42.74 3.02
1035 1102 1.739562 GAGTCGGTGCAGGAGCTTG 60.740 63.158 0.00 0.00 42.74 4.01
1036 1103 2.659610 GAGTCGGTGCAGGAGCTT 59.340 61.111 0.00 0.00 42.74 3.74
1037 1104 3.386237 GGAGTCGGTGCAGGAGCT 61.386 66.667 0.00 0.00 42.74 4.09
1050 1129 2.438795 GACGAGAGGGCGAGGAGT 60.439 66.667 0.00 0.00 34.83 3.85
1059 1138 3.137459 AGGAGCAGCGACGAGAGG 61.137 66.667 0.00 0.00 0.00 3.69
1133 1212 2.300437 ACAAGTCTACTGAGCTGGGAAC 59.700 50.000 0.00 0.00 0.00 3.62
1154 1243 4.394729 CTCCCAAACTGGTAAGTAAGCAA 58.605 43.478 0.00 0.00 34.77 3.91
1214 1303 1.078759 GATTCACGAGGACCAGCACG 61.079 60.000 0.00 0.00 0.00 5.34
1294 1385 1.454479 CAGGGGGCGATGCAGAAAT 60.454 57.895 0.00 0.00 0.00 2.17
1301 1392 1.526917 GTCAATCCAGGGGGCGATG 60.527 63.158 0.00 0.00 0.00 3.84
1302 1393 2.757124 GGTCAATCCAGGGGGCGAT 61.757 63.158 0.00 0.00 35.97 4.58
1348 1440 0.682209 CCATGAACAGGGGAAGCAGG 60.682 60.000 0.00 0.00 0.00 4.85
1372 1464 2.031157 GTCAACATCCTTTGTGAACCGG 60.031 50.000 0.00 0.00 38.99 5.28
1421 1513 1.507140 TCACTCACCTCCAACCACTT 58.493 50.000 0.00 0.00 0.00 3.16
1444 1536 1.981256 TTTCAGCAGGAAACCTCACC 58.019 50.000 0.00 0.00 40.51 4.02
1449 1541 8.713950 AGGAACTAATCATTTCAGCAGGAAACC 61.714 40.741 5.81 1.06 42.97 3.27
1458 1550 7.912056 TCACTGAAGGAACTAATCATTTCAG 57.088 36.000 14.83 14.83 46.30 3.02
1463 1555 6.950842 TGTCATCACTGAAGGAACTAATCAT 58.049 36.000 0.00 0.00 38.49 2.45
1465 1557 6.312426 CACTGTCATCACTGAAGGAACTAATC 59.688 42.308 0.00 0.00 38.49 1.75
1467 1559 5.511373 CCACTGTCATCACTGAAGGAACTAA 60.511 44.000 0.00 0.00 38.49 2.24
1475 1567 2.567169 CCTACCCACTGTCATCACTGAA 59.433 50.000 0.00 0.00 31.85 3.02
1480 1572 2.567169 CACTTCCTACCCACTGTCATCA 59.433 50.000 0.00 0.00 0.00 3.07
1481 1573 2.093447 CCACTTCCTACCCACTGTCATC 60.093 54.545 0.00 0.00 0.00 2.92
1482 1574 1.909302 CCACTTCCTACCCACTGTCAT 59.091 52.381 0.00 0.00 0.00 3.06
1488 1580 1.064685 CCAATCCCACTTCCTACCCAC 60.065 57.143 0.00 0.00 0.00 4.61
1494 1586 1.760405 AGTTCCCAATCCCACTTCCT 58.240 50.000 0.00 0.00 0.00 3.36
1510 1604 6.704493 TCAGTTCAACTTAAACATCGCTAGTT 59.296 34.615 0.00 0.00 0.00 2.24
1512 1606 6.706055 TCAGTTCAACTTAAACATCGCTAG 57.294 37.500 0.00 0.00 0.00 3.42
1513 1607 6.649141 ACATCAGTTCAACTTAAACATCGCTA 59.351 34.615 0.00 0.00 0.00 4.26
1514 1608 5.470098 ACATCAGTTCAACTTAAACATCGCT 59.530 36.000 0.00 0.00 0.00 4.93
1515 1609 5.689819 ACATCAGTTCAACTTAAACATCGC 58.310 37.500 0.00 0.00 0.00 4.58
1516 1610 7.011773 CAGACATCAGTTCAACTTAAACATCG 58.988 38.462 0.00 0.00 0.00 3.84
1517 1611 7.800380 CACAGACATCAGTTCAACTTAAACATC 59.200 37.037 0.00 0.00 0.00 3.06
1518 1612 7.283127 ACACAGACATCAGTTCAACTTAAACAT 59.717 33.333 0.00 0.00 0.00 2.71
1519 1613 6.597672 ACACAGACATCAGTTCAACTTAAACA 59.402 34.615 0.00 0.00 0.00 2.83
1520 1614 7.016361 ACACAGACATCAGTTCAACTTAAAC 57.984 36.000 0.00 0.00 0.00 2.01
1652 1750 7.928706 ACCATATGAGACACTAGAAAATAGCAC 59.071 37.037 3.65 0.00 0.00 4.40
1658 1756 9.599866 CATACAACCATATGAGACACTAGAAAA 57.400 33.333 3.65 0.00 34.94 2.29
1749 1848 0.386352 CTGCCGTGTGCTTGAACATG 60.386 55.000 0.00 0.00 42.00 3.21
1855 1954 0.788391 GTTTACTTGACCTGCGACCG 59.212 55.000 0.00 0.00 0.00 4.79
1894 1993 5.105146 ACAAGGATCAGACAGTATCCAGAAC 60.105 44.000 4.01 0.00 43.55 3.01
1973 2072 1.767088 TCTGGGATCTTGGCTGAGATG 59.233 52.381 8.36 0.00 36.54 2.90
1988 2087 2.876079 GCCCTTGTTACTGAACTCTGGG 60.876 54.545 0.00 0.00 40.15 4.45
1991 2090 1.002087 CGGCCCTTGTTACTGAACTCT 59.998 52.381 0.00 0.00 36.45 3.24
2021 2120 6.681729 TCAAACTTTATGGAGTACTGGACT 57.318 37.500 0.00 0.00 42.90 3.85
2093 2192 4.209288 CCGCTATATTTCTTCTGGTTGACG 59.791 45.833 0.00 0.00 0.00 4.35
2126 2225 7.985184 CAGAAGTAGGCAATAACATACCTGTAA 59.015 37.037 0.00 0.00 33.36 2.41
2225 2324 4.221262 ACATCCCAATCACATGGTCAAAAG 59.779 41.667 0.00 0.00 38.91 2.27
2242 2341 5.221521 TGCTCATCAACTATACAGACATCCC 60.222 44.000 0.00 0.00 0.00 3.85
2244 2343 7.776933 TTTGCTCATCAACTATACAGACATC 57.223 36.000 0.00 0.00 33.73 3.06
2249 2348 7.840342 AGACTTTTGCTCATCAACTATACAG 57.160 36.000 0.00 0.00 33.73 2.74
2301 2403 9.804758 GCATCTAGGTGGACTTATATACAATAC 57.195 37.037 4.87 0.00 0.00 1.89
2302 2404 9.769677 AGCATCTAGGTGGACTTATATACAATA 57.230 33.333 4.87 0.00 0.00 1.90
2303 2405 8.671987 AGCATCTAGGTGGACTTATATACAAT 57.328 34.615 4.87 0.00 0.00 2.71
2304 2406 9.769677 ATAGCATCTAGGTGGACTTATATACAA 57.230 33.333 4.87 0.00 0.00 2.41
2307 2409 9.575868 GCTATAGCATCTAGGTGGACTTATATA 57.424 37.037 20.01 0.00 41.59 0.86
2308 2410 8.285891 AGCTATAGCATCTAGGTGGACTTATAT 58.714 37.037 26.07 0.00 45.16 0.86
2338 2441 5.593909 TCGCCTTAATCATGAATGGACATTT 59.406 36.000 0.00 0.00 0.00 2.32
2387 2490 6.071840 AGCAGTAGACTAGTAAACCTGAACAG 60.072 42.308 12.84 0.00 0.00 3.16
2395 2498 6.583050 CACAACTCAGCAGTAGACTAGTAAAC 59.417 42.308 0.00 0.00 30.14 2.01
2418 2521 6.597280 AGAGAAAATGAGAAGGTTATCAGCAC 59.403 38.462 0.00 0.00 31.23 4.40
2437 2540 6.384224 CAAACATCAAGCTGCATAAGAGAAA 58.616 36.000 1.02 0.00 0.00 2.52
2553 2656 0.880278 GCGTCAGCCTGTCAGTTTCA 60.880 55.000 0.00 0.00 37.42 2.69
2559 2662 2.743060 ACATGCGTCAGCCTGTCA 59.257 55.556 0.00 0.00 46.74 3.58
2682 2785 7.872113 TTTTGCACCAACATCCTTAATTTTT 57.128 28.000 0.00 0.00 0.00 1.94
2741 2928 9.355215 CTCTCATTGTAACGTTTCTAGTTGTAT 57.645 33.333 5.91 0.00 33.42 2.29
2782 2969 4.022603 TCCTTAGGCTGCAAAAATGCATA 58.977 39.130 0.00 0.00 44.47 3.14
2850 3040 0.802494 GTATGGGCACACAAACCTCG 59.198 55.000 0.00 0.00 0.00 4.63
2909 3099 4.062677 TGAGCCGTTACAAAACTACAGT 57.937 40.909 0.00 0.00 33.15 3.55
2910 3100 4.929808 AGATGAGCCGTTACAAAACTACAG 59.070 41.667 0.00 0.00 33.15 2.74
2911 3101 4.890088 AGATGAGCCGTTACAAAACTACA 58.110 39.130 0.00 0.00 33.15 2.74
2912 3102 5.290400 GGTAGATGAGCCGTTACAAAACTAC 59.710 44.000 0.00 0.00 33.15 2.73
2913 3103 5.186409 AGGTAGATGAGCCGTTACAAAACTA 59.814 40.000 0.00 0.00 33.15 2.24
2914 3104 4.020485 AGGTAGATGAGCCGTTACAAAACT 60.020 41.667 0.00 0.00 33.15 2.66
3117 3307 4.583073 AGTGGTTAAATGGGTCAAGTTCAC 59.417 41.667 0.00 0.00 0.00 3.18
3170 3360 6.236017 CATGCTTCAAATGCAAAACATCTT 57.764 33.333 0.00 0.00 44.01 2.40
3193 3383 8.888579 ACAGTTTATGTGATGGTAACTATAGC 57.111 34.615 0.00 0.00 41.91 2.97
3281 3471 7.597369 ACAACATGCATATATTTGTCATCATGC 59.403 33.333 0.00 0.00 39.32 4.06
3311 3501 2.575532 CCATGTGTCGGGCTGATTAAT 58.424 47.619 0.00 0.00 0.00 1.40
3425 3615 5.661056 AAAGTAGGATGAACGACTGATGA 57.339 39.130 0.00 0.00 0.00 2.92
4147 4338 6.502136 AGCAGTTATGTTTAGCTTCTTTCC 57.498 37.500 0.00 0.00 29.98 3.13
4376 4571 3.910627 AGGTGTGTTAAGAGGGAATCAGT 59.089 43.478 0.00 0.00 0.00 3.41
4385 4580 6.536582 CCATCAGTCAATAGGTGTGTTAAGAG 59.463 42.308 0.00 0.00 0.00 2.85
4386 4581 6.212589 TCCATCAGTCAATAGGTGTGTTAAGA 59.787 38.462 0.00 0.00 0.00 2.10
4422 4622 1.888512 TCTCAAGCACTTGGGATTTGC 59.111 47.619 8.90 0.00 44.46 3.68
4427 4627 2.507484 CAATGTCTCAAGCACTTGGGA 58.493 47.619 8.90 8.90 46.89 4.37
4435 4635 7.496529 TTACCATATTAGCAATGTCTCAAGC 57.503 36.000 0.00 0.00 0.00 4.01
4490 4741 1.133792 CCCGGCCTTCAAGAATACCAT 60.134 52.381 0.00 0.00 0.00 3.55
4509 4761 2.417097 GCACAAGGCAACACACCC 59.583 61.111 0.00 0.00 43.97 4.61
4554 4806 2.779755 ACACAGTCACAGTTTCACCA 57.220 45.000 0.00 0.00 0.00 4.17
4555 4807 4.270325 GTCTTACACAGTCACAGTTTCACC 59.730 45.833 0.00 0.00 0.00 4.02
4587 4845 8.570488 GGATGTCAGTAATCATGCATTCATTTA 58.430 33.333 0.00 0.00 33.67 1.40
4686 4945 9.834628 TTCACGAGTTGGAATTATTAAATGAAC 57.165 29.630 0.00 0.00 0.00 3.18
4702 4961 6.292542 CCACATGCTATCTAATTCACGAGTTG 60.293 42.308 0.00 0.00 0.00 3.16
4720 4983 4.339247 ACCAGAATGTTATAAGCCACATGC 59.661 41.667 0.00 0.00 41.71 4.06
4771 5035 5.422970 CCTTGGAAGAATTGATGATTTGGGA 59.577 40.000 0.00 0.00 0.00 4.37
4794 5059 8.787852 AGACAAGAAACACTTCAATTATTCTCC 58.212 33.333 0.00 0.00 36.61 3.71
4796 5061 8.499162 CGAGACAAGAAACACTTCAATTATTCT 58.501 33.333 0.00 0.00 36.61 2.40
4797 5062 8.283291 ACGAGACAAGAAACACTTCAATTATTC 58.717 33.333 0.00 0.00 36.61 1.75
4798 5063 8.070171 CACGAGACAAGAAACACTTCAATTATT 58.930 33.333 0.00 0.00 36.61 1.40
4927 5242 2.404265 ACACGCACAACATCACATTG 57.596 45.000 0.00 0.00 0.00 2.82
4960 5275 6.607019 AGTTTACAAAAGGAAGTACATCCCA 58.393 36.000 13.46 0.00 40.59 4.37
4962 5277 7.660208 TCTGAGTTTACAAAAGGAAGTACATCC 59.340 37.037 9.17 9.17 39.96 3.51
5040 5359 1.414919 ACTCCTCGGCAACAACAGTTA 59.585 47.619 0.00 0.00 0.00 2.24
5053 5372 3.175152 CAAATCGAGTGAGAACTCCTCG 58.825 50.000 23.27 23.27 44.92 4.63
5118 5437 1.578215 AGAGGCTGAATCCTAGGAGGT 59.422 52.381 18.34 7.59 36.38 3.85
5122 5441 1.969923 CCTGAGAGGCTGAATCCTAGG 59.030 57.143 0.82 0.82 36.38 3.02
5127 5446 4.679373 TCATTACCTGAGAGGCTGAATC 57.321 45.455 0.00 0.00 39.63 2.52
5131 5450 7.630242 TTATTTTTCATTACCTGAGAGGCTG 57.370 36.000 0.00 0.00 39.63 4.85
5135 5454 9.512435 CATGCTTTATTTTTCATTACCTGAGAG 57.488 33.333 0.00 0.00 34.68 3.20
5145 5464 6.646267 ACTGGATGCATGCTTTATTTTTCAT 58.354 32.000 20.33 0.00 0.00 2.57
5152 5471 4.518211 GCTTCTACTGGATGCATGCTTTAT 59.482 41.667 20.33 3.62 42.46 1.40
5153 5472 3.879295 GCTTCTACTGGATGCATGCTTTA 59.121 43.478 20.33 9.11 42.46 1.85
5169 5488 9.758651 TGAAAGAAACGCTAATATATGCTTCTA 57.241 29.630 0.00 0.00 0.00 2.10
5365 5745 5.620206 TCCTTCTATTTGTCTTGAAGCACA 58.380 37.500 0.00 0.00 35.80 4.57
5368 5748 4.697352 TGCTCCTTCTATTTGTCTTGAAGC 59.303 41.667 0.00 0.00 35.80 3.86
5470 5854 7.041576 TGCTGTGCATATCAGATTGTTTCTATC 60.042 37.037 6.97 0.00 35.20 2.08
5518 5902 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
5519 5903 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
5520 5904 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
5521 5905 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
5522 5906 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
5523 5907 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
5524 5908 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
5525 5909 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
5526 5910 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
5527 5911 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
5528 5912 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
5529 5913 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
5530 5914 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
5553 5937 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
5554 5938 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
5555 5939 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
5556 5940 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
5558 5942 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
5559 5943 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
5560 5944 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
5561 5945 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
5562 5946 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
5563 5947 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
5564 5948 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
5565 5949 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
5566 5950 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
5567 5951 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
5568 5952 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
5569 5953 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
5570 5954 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
5571 5955 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
5572 5956 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
5573 5957 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
5574 5958 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
5575 5959 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
5576 5960 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
5577 5961 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
5578 5962 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
5579 5963 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
5580 5964 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
5581 5965 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
5582 5966 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
5583 5967 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
5584 5968 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
5585 5969 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
5586 5970 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
5587 5971 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
5588 5972 0.179081 GCATGTACTCCCTCCGTTCC 60.179 60.000 0.00 0.00 0.00 3.62
5589 5973 0.824759 AGCATGTACTCCCTCCGTTC 59.175 55.000 0.00 0.00 0.00 3.95
5590 5974 1.207329 GAAGCATGTACTCCCTCCGTT 59.793 52.381 0.00 0.00 0.00 4.44
5591 5975 0.824759 GAAGCATGTACTCCCTCCGT 59.175 55.000 0.00 0.00 0.00 4.69
5592 5976 1.067821 GAGAAGCATGTACTCCCTCCG 59.932 57.143 0.00 0.00 0.00 4.63
5593 5977 2.111384 TGAGAAGCATGTACTCCCTCC 58.889 52.381 11.27 0.00 0.00 4.30
5594 5978 4.376146 GAATGAGAAGCATGTACTCCCTC 58.624 47.826 11.27 0.00 37.28 4.30
5595 5979 3.135530 GGAATGAGAAGCATGTACTCCCT 59.864 47.826 11.27 0.00 37.28 4.20
5596 5980 3.135530 AGGAATGAGAAGCATGTACTCCC 59.864 47.826 11.27 7.21 37.28 4.30
5597 5981 4.414337 AGGAATGAGAAGCATGTACTCC 57.586 45.455 11.27 0.00 37.28 3.85
5598 5982 5.293079 GTGAAGGAATGAGAAGCATGTACTC 59.707 44.000 0.00 2.02 37.28 2.59
5599 5983 5.181748 GTGAAGGAATGAGAAGCATGTACT 58.818 41.667 0.00 0.00 37.28 2.73
5600 5984 4.937620 TGTGAAGGAATGAGAAGCATGTAC 59.062 41.667 0.00 0.00 37.28 2.90
5601 5985 5.164620 TGTGAAGGAATGAGAAGCATGTA 57.835 39.130 0.00 0.00 37.28 2.29
5620 6004 8.218338 AGTCTTTTTATGAAGGATAGCATGTG 57.782 34.615 0.00 0.00 0.00 3.21
5657 6041 5.163426 TGACTTTCAGGTGCATGTTCATTTT 60.163 36.000 0.00 0.00 0.00 1.82
5671 6062 6.017026 GGAGTTCTTTTACCTTGACTTTCAGG 60.017 42.308 0.00 0.00 0.00 3.86
5675 6066 6.014771 AGGGAGTTCTTTTACCTTGACTTT 57.985 37.500 0.00 0.00 0.00 2.66
5681 6072 5.382664 TGTGAAGGGAGTTCTTTTACCTT 57.617 39.130 0.00 0.00 43.79 3.50
5724 6115 3.951775 TTTGGAAATGTGGTGGTATGC 57.048 42.857 0.00 0.00 0.00 3.14
5735 6126 6.272318 TGCTGTACTTTCAGTTTTGGAAATG 58.728 36.000 0.00 0.00 37.70 2.32


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

AutoCloner maintained by Alex Coulton.