Multiple sequence alignment - TraesCS6A01G065700

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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 TraesCS6A01G065700 chr6A 100.000 4177 0 0 1 4177 35178702 35182878 0.000000e+00 7714.0
1 TraesCS6A01G065700 chr6A 87.262 1837 163 35 1 1815 35142791 35144578 0.000000e+00 2030.0
2 TraesCS6A01G065700 chr6A 86.616 1569 124 39 1881 3422 35144578 35146087 0.000000e+00 1655.0
3 TraesCS6A01G065700 chr6A 82.485 491 56 16 2867 3352 158945746 158945281 1.810000e-108 403.0
4 TraesCS6A01G065700 chr6A 86.799 303 30 4 3514 3807 35146113 35146414 3.110000e-86 329.0
5 TraesCS6A01G065700 chr6B 87.590 2224 168 51 784 2969 64323914 64326067 0.000000e+00 2479.0
6 TraesCS6A01G065700 chr6B 93.258 534 28 3 3084 3611 64326085 64326616 0.000000e+00 780.0
7 TraesCS6A01G065700 chr6B 94.845 485 20 3 3697 4177 64326620 64327103 0.000000e+00 752.0
8 TraesCS6A01G065700 chr6B 81.174 494 63 16 2864 3352 212415277 212415745 1.830000e-98 370.0
9 TraesCS6A01G065700 chrUn 92.809 1627 84 11 744 2351 103111264 103112876 0.000000e+00 2326.0
10 TraesCS6A01G065700 chrUn 90.710 1141 62 17 698 1815 103127666 103128785 0.000000e+00 1480.0
11 TraesCS6A01G065700 chrUn 86.416 1384 100 47 1881 3248 103128785 103130096 0.000000e+00 1434.0
12 TraesCS6A01G065700 chrUn 85.338 1064 87 28 2363 3402 103112855 103113873 0.000000e+00 1037.0
13 TraesCS6A01G065700 chrUn 94.313 422 20 2 3244 3661 103130205 103130626 0.000000e+00 643.0
14 TraesCS6A01G065700 chrUn 92.711 439 23 6 3744 4177 103131979 103132413 3.550000e-175 625.0
15 TraesCS6A01G065700 chrUn 91.105 371 28 5 1 368 103116996 103117364 8.060000e-137 497.0
16 TraesCS6A01G065700 chrUn 81.862 419 40 15 2483 2876 103119812 103120219 1.870000e-83 320.0
17 TraesCS6A01G065700 chrUn 83.158 380 31 21 3053 3422 103120312 103120668 2.420000e-82 316.0
18 TraesCS6A01G065700 chr6D 81.466 491 60 17 2867 3352 120672954 120672490 1.420000e-99 374.0
19 TraesCS6A01G065700 chr7A 88.417 259 28 2 3921 4177 430756525 430756267 1.130000e-80 311.0
20 TraesCS6A01G065700 chr1B 96.000 50 2 0 2376 2425 647181734 647181783 9.620000e-12 82.4


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 TraesCS6A01G065700 chr6A 35178702 35182878 4176 False 7714.0 7714 100.000000 1 4177 1 chr6A.!!$F1 4176
1 TraesCS6A01G065700 chr6A 35142791 35146414 3623 False 1338.0 2030 86.892333 1 3807 3 chr6A.!!$F2 3806
2 TraesCS6A01G065700 chr6B 64323914 64327103 3189 False 1337.0 2479 91.897667 784 4177 3 chr6B.!!$F2 3393
3 TraesCS6A01G065700 chrUn 103127666 103132413 4747 False 1045.5 1480 91.037500 698 4177 4 chrUn.!!$F2 3479
4 TraesCS6A01G065700 chrUn 103111264 103120668 9404 False 899.2 2326 86.854400 1 3422 5 chrUn.!!$F1 3421

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
596 611 0.030908 GGTAGAAGATGACGCTCGGG 59.969 60.0 0.00 0.0 0.00 5.14 F
1716 1770 0.039180 TCTCGGTGGACCAGCTTCTA 59.961 55.0 20.92 3.8 35.14 2.10 F
1835 1970 0.033920 CACACTGGCAGCTACTGTGA 59.966 55.0 23.97 0.0 39.30 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 1951 0.033920 TCACAGTAGCTGCCAGTGTG 59.966 55.000 24.11 24.11 44.97 3.82 R
3005 3195 0.603569 AACTGTACGAGTGCTCCAGG 59.396 55.000 0.00 0.00 34.02 4.45 R
3573 3891 2.587473 GCAGAGCCTAGCCTTCGC 60.587 66.667 0.00 0.00 0.00 4.70 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
18 19 2.079049 GTCAAACACGATCCGAGCC 58.921 57.895 0.00 0.00 0.00 4.70
44 45 4.813296 AAAAGAACGTGATCAAGTGACC 57.187 40.909 15.21 7.81 0.00 4.02
48 49 1.338107 ACGTGATCAAGTGACCAGGA 58.662 50.000 13.75 0.00 28.64 3.86
55 56 5.127845 GTGATCAAGTGACCAGGAAGAGATA 59.872 44.000 0.00 0.00 0.00 1.98
56 57 5.901853 TGATCAAGTGACCAGGAAGAGATAT 59.098 40.000 0.00 0.00 0.00 1.63
59 60 3.226777 AGTGACCAGGAAGAGATATCCG 58.773 50.000 0.00 0.00 42.03 4.18
60 61 1.964223 TGACCAGGAAGAGATATCCGC 59.036 52.381 0.00 0.00 42.03 5.54
61 62 1.273886 GACCAGGAAGAGATATCCGCC 59.726 57.143 0.00 0.00 42.03 6.13
106 107 1.747774 GCATGGGTGCCAACAAACT 59.252 52.632 0.00 0.00 45.76 2.66
121 122 3.547746 ACAAACTTGTTCGGGCTCTTAA 58.452 40.909 0.00 0.00 38.47 1.85
124 125 1.697982 ACTTGTTCGGGCTCTTAAGGT 59.302 47.619 1.85 0.00 0.00 3.50
137 139 2.079925 CTTAAGGTGCTGAACAGGAGC 58.920 52.381 15.50 15.50 45.74 4.70
142 144 1.842920 TGCTGAACAGGAGCTCCCA 60.843 57.895 29.54 18.26 37.35 4.37
143 145 1.376553 GCTGAACAGGAGCTCCCAC 60.377 63.158 29.54 17.42 37.41 4.61
144 146 1.298014 CTGAACAGGAGCTCCCACC 59.702 63.158 29.54 15.98 37.41 4.61
151 153 1.070445 GGAGCTCCCACCATCATCG 59.930 63.158 23.19 0.00 34.14 3.84
160 162 1.452110 CACCATCATCGTCCTTGCAA 58.548 50.000 0.00 0.00 0.00 4.08
161 163 1.811965 CACCATCATCGTCCTTGCAAA 59.188 47.619 0.00 0.00 0.00 3.68
162 164 2.228582 CACCATCATCGTCCTTGCAAAA 59.771 45.455 0.00 0.00 0.00 2.44
163 165 2.890311 ACCATCATCGTCCTTGCAAAAA 59.110 40.909 0.00 0.00 0.00 1.94
165 167 3.861113 CCATCATCGTCCTTGCAAAAATG 59.139 43.478 0.00 0.61 0.00 2.32
168 170 4.545610 TCATCGTCCTTGCAAAAATGTTC 58.454 39.130 0.00 0.00 0.00 3.18
170 172 4.647424 TCGTCCTTGCAAAAATGTTCTT 57.353 36.364 0.00 0.00 0.00 2.52
188 198 5.984926 TGTTCTTTAAAATGCTTGGCTTCAG 59.015 36.000 0.00 0.00 0.00 3.02
189 199 6.183360 TGTTCTTTAAAATGCTTGGCTTCAGA 60.183 34.615 0.00 0.00 0.00 3.27
193 203 1.589716 AATGCTTGGCTTCAGACGGC 61.590 55.000 0.00 0.00 0.00 5.68
198 208 2.586357 GGCTTCAGACGGCGGATC 60.586 66.667 13.24 0.00 0.00 3.36
213 223 2.580470 GATCGCACGTGAGCATCCG 61.580 63.158 22.23 12.31 35.42 4.18
224 234 0.461548 GAGCATCCGTCTGTCATCCA 59.538 55.000 0.00 0.00 0.00 3.41
227 237 1.473965 GCATCCGTCTGTCATCCATGT 60.474 52.381 0.00 0.00 0.00 3.21
241 251 2.912771 TCCATGTGACGTGTGTCTTTT 58.087 42.857 3.87 0.00 45.70 2.27
256 266 0.535102 CTTTTGTCTCCCACGTGGCT 60.535 55.000 29.75 0.00 0.00 4.75
265 275 2.974148 CACGTGGCTGCTGCTTGA 60.974 61.111 15.64 0.00 39.59 3.02
267 277 1.020861 CACGTGGCTGCTGCTTGATA 61.021 55.000 15.64 0.00 39.59 2.15
271 281 0.460811 TGGCTGCTGCTTGATACTCG 60.461 55.000 15.64 0.00 39.59 4.18
275 285 2.123342 CTGCTGCTTGATACTCGCTAC 58.877 52.381 0.00 0.00 0.00 3.58
397 407 7.713764 ATTAAATTGCAACAAGACCTTTGTC 57.286 32.000 0.00 0.00 42.09 3.18
398 408 4.734398 AATTGCAACAAGACCTTTGTCA 57.266 36.364 0.00 0.00 44.33 3.58
405 419 5.351189 GCAACAAGACCTTTGTCACAAATTT 59.649 36.000 2.71 0.00 44.33 1.82
406 420 6.128309 GCAACAAGACCTTTGTCACAAATTTT 60.128 34.615 2.71 0.00 44.33 1.82
407 421 7.572910 GCAACAAGACCTTTGTCACAAATTTTT 60.573 33.333 2.71 0.00 44.33 1.94
481 495 6.018994 GCATATAAACTGTAACAAGACCTCGG 60.019 42.308 0.00 0.00 0.00 4.63
483 497 3.832615 AACTGTAACAAGACCTCGGTT 57.167 42.857 0.00 0.00 0.00 4.44
484 498 3.107642 ACTGTAACAAGACCTCGGTTG 57.892 47.619 0.00 0.00 0.00 3.77
485 499 1.798813 CTGTAACAAGACCTCGGTTGC 59.201 52.381 0.00 0.00 0.00 4.17
486 500 1.139256 TGTAACAAGACCTCGGTTGCA 59.861 47.619 0.00 0.00 35.32 4.08
515 529 6.764877 ATCCGTAACTTAATCTATGTTGCG 57.235 37.500 12.65 12.65 44.88 4.85
537 551 6.090129 GCGAAATTTTCTGCAACATAACCTA 58.910 36.000 15.95 0.00 32.28 3.08
559 573 8.903820 ACCTATATTACAGAAATTTCCTGCAAC 58.096 33.333 14.61 0.00 35.14 4.17
560 574 8.902806 CCTATATTACAGAAATTTCCTGCAACA 58.097 33.333 14.61 0.30 35.14 3.33
561 575 9.722056 CTATATTACAGAAATTTCCTGCAACAC 57.278 33.333 14.61 0.00 35.14 3.32
562 576 3.354089 ACAGAAATTTCCTGCAACACG 57.646 42.857 14.61 0.00 35.14 4.49
563 577 2.948979 ACAGAAATTTCCTGCAACACGA 59.051 40.909 14.61 0.00 35.14 4.35
564 578 3.243068 ACAGAAATTTCCTGCAACACGAC 60.243 43.478 14.61 0.00 35.14 4.34
565 579 2.948979 AGAAATTTCCTGCAACACGACA 59.051 40.909 14.61 0.00 0.00 4.35
566 580 3.569701 AGAAATTTCCTGCAACACGACAT 59.430 39.130 14.61 0.00 0.00 3.06
567 581 4.759693 AGAAATTTCCTGCAACACGACATA 59.240 37.500 14.61 0.00 0.00 2.29
568 582 5.415701 AGAAATTTCCTGCAACACGACATAT 59.584 36.000 14.61 0.00 0.00 1.78
569 583 4.621068 ATTTCCTGCAACACGACATATG 57.379 40.909 0.00 0.00 0.00 1.78
570 584 2.760634 TCCTGCAACACGACATATGT 57.239 45.000 8.43 8.43 0.00 2.29
571 585 2.616960 TCCTGCAACACGACATATGTC 58.383 47.619 23.47 23.47 41.47 3.06
587 602 5.698089 ACATATGTCGCAATGGTAGAAGATG 59.302 40.000 1.41 0.00 0.00 2.90
596 611 0.030908 GGTAGAAGATGACGCTCGGG 59.969 60.000 0.00 0.00 0.00 5.14
607 622 2.892425 GCTCGGGCACTCAATCCG 60.892 66.667 0.00 0.00 44.59 4.18
611 626 1.811266 CGGGCACTCAATCCGTCAG 60.811 63.158 0.00 0.00 39.04 3.51
625 641 2.167861 GTCAGATCCGACGGCTTGC 61.168 63.158 9.66 0.00 0.00 4.01
628 644 2.508439 GATCCGACGGCTTGCGAA 60.508 61.111 9.66 0.00 0.00 4.70
648 664 4.496895 CGAAGCGGCAGATCTTTTAAAATG 59.503 41.667 1.45 0.00 0.00 2.32
654 670 5.007626 CGGCAGATCTTTTAAAATGATCCGA 59.992 40.000 22.84 10.44 37.80 4.55
655 671 6.293626 CGGCAGATCTTTTAAAATGATCCGAT 60.294 38.462 22.84 13.55 37.80 4.18
659 675 5.168526 TCTTTTAAAATGATCCGATGGCG 57.831 39.130 0.09 0.00 37.24 5.69
664 680 0.179084 AATGATCCGATGGCGAACGT 60.179 50.000 0.00 0.00 40.82 3.99
665 681 0.875908 ATGATCCGATGGCGAACGTG 60.876 55.000 0.00 0.00 40.82 4.49
667 683 1.752501 GATCCGATGGCGAACGTGTG 61.753 60.000 0.00 0.00 40.82 3.82
670 686 3.047280 GATGGCGAACGTGTGGCA 61.047 61.111 16.96 16.96 45.22 4.92
671 687 2.593148 ATGGCGAACGTGTGGCAA 60.593 55.556 18.23 3.18 44.27 4.52
672 688 2.780149 GATGGCGAACGTGTGGCAAC 62.780 60.000 18.23 12.99 44.27 4.17
690 708 6.544650 TGGCAACACCCTTTTAGAAAGTATA 58.455 36.000 0.00 0.00 46.17 1.47
692 710 7.122055 TGGCAACACCCTTTTAGAAAGTATATG 59.878 37.037 0.00 0.00 46.17 1.78
696 714 9.582648 AACACCCTTTTAGAAAGTATATGTTGT 57.417 29.630 0.37 0.00 0.00 3.32
713 731 8.780846 ATATGTTGTAAATCTTCGGTGTGTAA 57.219 30.769 0.00 0.00 0.00 2.41
714 732 6.289745 TGTTGTAAATCTTCGGTGTGTAAC 57.710 37.500 0.00 0.00 37.35 2.50
725 743 0.311790 GTGTGTAACTCGGACCGACA 59.688 55.000 13.88 7.32 38.04 4.35
801 819 1.008206 CCCTCCCATCCCAAATCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
849 871 1.227527 CATACGCGCCATCCCTCAA 60.228 57.895 5.73 0.00 0.00 3.02
850 872 1.069765 ATACGCGCCATCCCTCAAG 59.930 57.895 5.73 0.00 0.00 3.02
870 892 7.909121 CCTCAAGATTCAAGATTCAAGATTTCG 59.091 37.037 0.00 0.00 0.00 3.46
1231 1267 3.372554 GAGAGGCGGTGCTGGTACC 62.373 68.421 4.43 4.43 37.37 3.34
1452 1494 2.748605 GAGTTCCGTATGGCTCATGAG 58.251 52.381 18.84 18.84 34.14 2.90
1641 1686 2.743928 GTTCCTCCTGCTGCACCG 60.744 66.667 0.00 0.00 0.00 4.94
1689 1737 2.355756 GCAAGACTTGAACAACTGCTCA 59.644 45.455 19.51 0.00 0.00 4.26
1701 1749 1.588403 CTGCTCAGATGGCGTCTCG 60.588 63.158 6.18 2.23 34.00 4.04
1716 1770 0.039180 TCTCGGTGGACCAGCTTCTA 59.961 55.000 20.92 3.80 35.14 2.10
1730 1784 5.366186 ACCAGCTTCTAGATGATCTCATGTT 59.634 40.000 9.72 0.00 32.38 2.71
1739 1793 1.764723 TGATCTCATGTTCGGCCTCAT 59.235 47.619 0.00 0.00 0.00 2.90
1755 1809 2.485124 CCTCATGCCTGATCAAGTCCTC 60.485 54.545 0.00 0.00 0.00 3.71
1810 1864 2.490903 GTCAATTGCAGCTTCTCCATGT 59.509 45.455 0.00 0.00 0.00 3.21
1815 1950 0.807496 GCAGCTTCTCCATGTCCAAC 59.193 55.000 0.00 0.00 0.00 3.77
1816 1951 1.457346 CAGCTTCTCCATGTCCAACC 58.543 55.000 0.00 0.00 0.00 3.77
1817 1952 1.067295 AGCTTCTCCATGTCCAACCA 58.933 50.000 0.00 0.00 0.00 3.67
1818 1953 1.168714 GCTTCTCCATGTCCAACCAC 58.831 55.000 0.00 0.00 0.00 4.16
1819 1954 1.545428 GCTTCTCCATGTCCAACCACA 60.545 52.381 0.00 0.00 0.00 4.17
1820 1955 2.154462 CTTCTCCATGTCCAACCACAC 58.846 52.381 0.00 0.00 0.00 3.82
1821 1956 1.434188 TCTCCATGTCCAACCACACT 58.566 50.000 0.00 0.00 0.00 3.55
1822 1957 1.072173 TCTCCATGTCCAACCACACTG 59.928 52.381 0.00 0.00 0.00 3.66
1823 1958 0.110295 TCCATGTCCAACCACACTGG 59.890 55.000 0.00 0.00 45.02 4.00
1824 1959 1.526575 CCATGTCCAACCACACTGGC 61.527 60.000 0.00 0.00 42.67 4.85
1825 1960 0.822944 CATGTCCAACCACACTGGCA 60.823 55.000 0.00 0.00 42.67 4.92
1826 1961 0.538057 ATGTCCAACCACACTGGCAG 60.538 55.000 14.16 14.16 42.67 4.85
1827 1962 2.203337 TCCAACCACACTGGCAGC 60.203 61.111 15.89 0.00 42.67 5.25
1828 1963 2.203394 CCAACCACACTGGCAGCT 60.203 61.111 15.89 0.00 42.67 4.24
1829 1964 1.073025 CCAACCACACTGGCAGCTA 59.927 57.895 15.89 0.00 42.67 3.32
1830 1965 1.237285 CCAACCACACTGGCAGCTAC 61.237 60.000 15.89 0.00 42.67 3.58
1831 1966 0.250467 CAACCACACTGGCAGCTACT 60.250 55.000 15.89 0.00 42.67 2.57
1832 1967 0.250467 AACCACACTGGCAGCTACTG 60.250 55.000 15.89 7.91 42.67 2.74
1833 1968 1.372683 CCACACTGGCAGCTACTGT 59.627 57.895 15.89 8.63 33.43 3.55
1834 1969 0.952497 CCACACTGGCAGCTACTGTG 60.952 60.000 22.28 22.28 41.66 3.66
1835 1970 0.033920 CACACTGGCAGCTACTGTGA 59.966 55.000 23.97 0.00 39.30 3.58
1836 1971 0.034059 ACACTGGCAGCTACTGTGAC 59.966 55.000 24.56 2.11 39.30 3.67
1837 1972 0.033920 CACTGGCAGCTACTGTGACA 59.966 55.000 15.89 0.53 39.30 3.58
1838 1973 0.319728 ACTGGCAGCTACTGTGACAG 59.680 55.000 15.89 11.70 36.61 3.51
1839 1974 0.390866 CTGGCAGCTACTGTGACAGG 60.391 60.000 17.92 0.71 35.51 4.00
1840 1975 1.078848 GGCAGCTACTGTGACAGGG 60.079 63.158 17.92 10.20 35.51 4.45
1841 1976 1.674057 GCAGCTACTGTGACAGGGT 59.326 57.895 17.92 2.51 35.51 4.34
1842 1977 0.390472 GCAGCTACTGTGACAGGGTC 60.390 60.000 17.92 4.93 35.51 4.46
1843 1978 0.247736 CAGCTACTGTGACAGGGTCC 59.752 60.000 17.92 2.34 35.51 4.46
1844 1979 0.115349 AGCTACTGTGACAGGGTCCT 59.885 55.000 17.92 4.66 35.51 3.85
1845 1980 0.533032 GCTACTGTGACAGGGTCCTC 59.467 60.000 17.92 0.00 35.51 3.71
1846 1981 1.187087 CTACTGTGACAGGGTCCTCC 58.813 60.000 17.92 0.00 35.51 4.30
1858 1993 4.113617 TCCTCCTGGACGAAGGTG 57.886 61.111 0.00 0.00 37.46 4.00
1859 1994 2.982130 CCTCCTGGACGAAGGTGG 59.018 66.667 0.00 9.23 42.88 4.61
1860 1995 1.913762 CCTCCTGGACGAAGGTGGT 60.914 63.158 13.16 0.00 43.29 4.16
1861 1996 1.293498 CTCCTGGACGAAGGTGGTG 59.707 63.158 0.00 0.00 38.58 4.17
1862 1997 1.152419 TCCTGGACGAAGGTGGTGA 60.152 57.895 0.00 0.00 38.58 4.02
1863 1998 1.004918 CCTGGACGAAGGTGGTGAC 60.005 63.158 0.00 0.00 32.17 3.67
1864 1999 1.472662 CCTGGACGAAGGTGGTGACT 61.473 60.000 0.00 0.00 32.17 3.41
1865 2000 0.393077 CTGGACGAAGGTGGTGACTT 59.607 55.000 0.00 0.00 0.00 3.01
1866 2001 0.105964 TGGACGAAGGTGGTGACTTG 59.894 55.000 0.00 0.00 0.00 3.16
1867 2002 0.106149 GGACGAAGGTGGTGACTTGT 59.894 55.000 0.00 0.00 0.00 3.16
1868 2003 1.474498 GGACGAAGGTGGTGACTTGTT 60.474 52.381 0.00 0.00 0.00 2.83
1869 2004 1.597663 GACGAAGGTGGTGACTTGTTG 59.402 52.381 0.00 0.00 0.00 3.33
1870 2005 1.208535 ACGAAGGTGGTGACTTGTTGA 59.791 47.619 0.00 0.00 0.00 3.18
1871 2006 2.158813 ACGAAGGTGGTGACTTGTTGAT 60.159 45.455 0.00 0.00 0.00 2.57
1872 2007 2.224079 CGAAGGTGGTGACTTGTTGATG 59.776 50.000 0.00 0.00 0.00 3.07
1873 2008 1.609208 AGGTGGTGACTTGTTGATGC 58.391 50.000 0.00 0.00 0.00 3.91
1874 2009 0.598065 GGTGGTGACTTGTTGATGCC 59.402 55.000 0.00 0.00 0.00 4.40
1875 2010 1.609208 GTGGTGACTTGTTGATGCCT 58.391 50.000 0.00 0.00 0.00 4.75
1876 2011 1.956477 GTGGTGACTTGTTGATGCCTT 59.044 47.619 0.00 0.00 0.00 4.35
1877 2012 3.146066 GTGGTGACTTGTTGATGCCTTA 58.854 45.455 0.00 0.00 0.00 2.69
1878 2013 3.758554 GTGGTGACTTGTTGATGCCTTAT 59.241 43.478 0.00 0.00 0.00 1.73
1879 2014 4.009675 TGGTGACTTGTTGATGCCTTATC 58.990 43.478 0.00 0.00 36.29 1.75
1880 2015 4.009675 GGTGACTTGTTGATGCCTTATCA 58.990 43.478 0.00 0.00 43.92 2.15
1929 2064 1.873591 GACTTGTTGATGCCTGTCGTT 59.126 47.619 0.00 0.00 0.00 3.85
1932 2067 0.107643 TGTTGATGCCTGTCGTTCCA 59.892 50.000 0.00 0.00 0.00 3.53
1995 2130 2.680805 CGGTTCCATGGTGAGCAACTAT 60.681 50.000 12.58 0.00 0.00 2.12
2007 2142 3.264193 TGAGCAACTATGACATGGTCCTT 59.736 43.478 4.76 0.00 40.03 3.36
2031 2166 0.250338 GTGGTTCAGTCACACCCCTC 60.250 60.000 0.00 0.00 35.39 4.30
2082 2217 1.134521 GTGCCCATCATCGAACCACTA 60.135 52.381 0.00 0.00 0.00 2.74
2225 2366 0.743688 AGCTGGTATGACTCTGCTCG 59.256 55.000 0.00 0.00 33.90 5.03
2600 2757 3.220507 GCATGTGCTTGCTTGTGATTA 57.779 42.857 0.00 0.00 39.57 1.75
2606 2764 2.030893 TGCTTGCTTGTGATTACTGTGC 60.031 45.455 0.00 0.00 0.00 4.57
2629 2787 5.036117 TGTAAGCTGTAATTGATCCCCTC 57.964 43.478 0.00 0.00 0.00 4.30
2640 2799 1.127343 GATCCCCTCTAGCTGCTGTT 58.873 55.000 13.43 0.00 0.00 3.16
2658 2817 4.074970 CTGTTTTTGATCCTACAGCTGGT 58.925 43.478 19.93 6.35 32.53 4.00
2679 2838 3.173953 TCATGCACTTGGGATCCTTTT 57.826 42.857 12.58 0.00 0.00 2.27
2685 2844 3.440522 GCACTTGGGATCCTTTTCTGTAC 59.559 47.826 12.58 0.00 0.00 2.90
2816 2997 7.561021 TTTACAGTTTCACATTGTTCTAGCA 57.439 32.000 0.00 0.00 0.00 3.49
2858 3039 8.100791 CCTAACATTTCATATCGGGATTCCTTA 58.899 37.037 2.01 0.00 0.00 2.69
2904 3092 5.601662 ACTATGGAATATTGGACAGTCACG 58.398 41.667 2.17 0.00 0.00 4.35
2930 3118 8.516234 GCAGATTATCTCGGTCTTAGAAATAGA 58.484 37.037 0.00 0.00 0.00 1.98
2998 3188 2.122783 TTTGTGGTAGGCCTATGTGC 57.877 50.000 17.38 2.23 35.27 4.57
2999 3189 1.285280 TTGTGGTAGGCCTATGTGCT 58.715 50.000 17.38 0.00 35.27 4.40
3000 3190 0.541392 TGTGGTAGGCCTATGTGCTG 59.459 55.000 17.38 0.00 35.27 4.41
3001 3191 0.179045 GTGGTAGGCCTATGTGCTGG 60.179 60.000 17.38 0.00 35.27 4.85
3002 3192 0.326143 TGGTAGGCCTATGTGCTGGA 60.326 55.000 17.38 0.00 35.27 3.86
3003 3193 0.394565 GGTAGGCCTATGTGCTGGAG 59.605 60.000 17.38 0.00 0.00 3.86
3004 3194 0.394565 GTAGGCCTATGTGCTGGAGG 59.605 60.000 17.38 0.00 0.00 4.30
3090 3287 6.402226 GCTTCCTTGTTCTGGTTCTAATAACG 60.402 42.308 0.00 0.00 0.00 3.18
3153 3350 3.447742 GCAAAGGTGCCTATTGTAATGC 58.552 45.455 11.71 0.00 45.68 3.56
3192 3389 2.300437 GTCTGACAGACAAGGTAGCCTT 59.700 50.000 27.15 0.00 45.88 4.35
3193 3390 2.972713 TCTGACAGACAAGGTAGCCTTT 59.027 45.455 0.00 0.00 41.69 3.11
3291 3601 7.336931 GTGACCATAGAACCAATGTATCTGTTT 59.663 37.037 0.00 0.00 0.00 2.83
3334 3644 7.933396 TGCAGTCATAATTCATGTAATTCAGG 58.067 34.615 6.44 0.00 38.71 3.86
3422 3734 7.290813 GGTAAGTGAATCTTCCCCTGATTAAT 58.709 38.462 0.00 0.00 37.56 1.40
3508 3823 5.204101 TGAAATGTATTTATCACGCATGCG 58.796 37.500 36.79 36.79 46.03 4.73
3539 3854 9.455847 CTTTTCTCCTTTATGTTGTTTCTCTTG 57.544 33.333 0.00 0.00 0.00 3.02
3544 3862 6.710744 TCCTTTATGTTGTTTCTCTTGTCCTC 59.289 38.462 0.00 0.00 0.00 3.71
3573 3891 8.391075 TGAAATGTACTTTCTTTTAGGGAGTG 57.609 34.615 14.65 0.00 43.14 3.51
3646 3964 5.065613 TGCAGAAGCCTATTGGGAATAAT 57.934 39.130 0.00 0.00 41.13 1.28
3654 3973 6.381250 AGCCTATTGGGAATAATGGCTTAAA 58.619 36.000 0.00 0.00 39.40 1.52
3655 3974 7.018769 AGCCTATTGGGAATAATGGCTTAAAT 58.981 34.615 0.00 0.00 39.40 1.40
3695 4321 4.594970 TGGTAACTGGGTTTGGATATGTG 58.405 43.478 0.00 0.00 37.61 3.21
3699 4333 4.584638 ACTGGGTTTGGATATGTGCTTA 57.415 40.909 0.00 0.00 0.00 3.09
3755 5671 3.146847 CAGTTTGGTAGAAAGTGGGACC 58.853 50.000 0.00 0.00 0.00 4.46
3757 5673 1.426751 TTGGTAGAAAGTGGGACCGT 58.573 50.000 0.00 0.00 34.49 4.83
3886 6124 9.533831 AAGATACATGGAATTTTTACTGGTCTT 57.466 29.630 0.00 0.00 0.00 3.01
3961 6464 0.598065 ATGCGGCCAAACTTTCACTC 59.402 50.000 2.24 0.00 0.00 3.51
3988 6651 2.877168 GGAAATCCAGCTGTCTGCATAG 59.123 50.000 13.81 0.00 45.94 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.029020 TCTTCCTGGTCACTTGATCACG 60.029 50.000 0.00 0.00 30.90 4.35
40 41 1.964223 GCGGATATCTCTTCCTGGTCA 59.036 52.381 2.05 0.00 0.00 4.02
44 45 2.896685 AGAAGGCGGATATCTCTTCCTG 59.103 50.000 20.01 0.00 37.05 3.86
48 49 2.370189 CCCAAGAAGGCGGATATCTCTT 59.630 50.000 2.05 4.69 35.39 2.85
91 92 2.983512 ACAAGTTTGTTGGCACCCA 58.016 47.368 0.00 0.00 38.47 4.51
100 101 2.052782 AAGAGCCCGAACAAGTTTGT 57.947 45.000 0.00 0.00 44.72 2.83
106 107 1.880646 GCACCTTAAGAGCCCGAACAA 60.881 52.381 3.36 0.00 0.00 2.83
112 113 1.271379 TGTTCAGCACCTTAAGAGCCC 60.271 52.381 3.36 0.00 0.00 5.19
115 116 3.594134 CTCCTGTTCAGCACCTTAAGAG 58.406 50.000 3.36 0.00 0.00 2.85
116 117 2.289694 GCTCCTGTTCAGCACCTTAAGA 60.290 50.000 3.36 0.00 36.82 2.10
121 122 1.676384 GAGCTCCTGTTCAGCACCT 59.324 57.895 0.87 0.00 39.56 4.00
124 125 1.842920 TGGGAGCTCCTGTTCAGCA 60.843 57.895 31.36 16.45 39.56 4.41
137 139 0.833287 AAGGACGATGATGGTGGGAG 59.167 55.000 0.00 0.00 0.00 4.30
142 144 2.198827 TTTGCAAGGACGATGATGGT 57.801 45.000 0.00 0.00 0.00 3.55
143 145 3.574284 TTTTTGCAAGGACGATGATGG 57.426 42.857 0.00 0.00 0.00 3.51
144 146 4.487948 ACATTTTTGCAAGGACGATGATG 58.512 39.130 0.00 0.00 0.00 3.07
151 153 9.437045 CATTTTAAAGAACATTTTTGCAAGGAC 57.563 29.630 0.00 0.00 0.00 3.85
160 162 7.806409 AGCCAAGCATTTTAAAGAACATTTT 57.194 28.000 0.00 0.00 0.00 1.82
161 163 7.498570 TGAAGCCAAGCATTTTAAAGAACATTT 59.501 29.630 0.00 0.00 0.00 2.32
162 164 6.991531 TGAAGCCAAGCATTTTAAAGAACATT 59.008 30.769 0.00 0.00 0.00 2.71
163 165 6.523840 TGAAGCCAAGCATTTTAAAGAACAT 58.476 32.000 0.00 0.00 0.00 2.71
165 167 6.144563 GTCTGAAGCCAAGCATTTTAAAGAAC 59.855 38.462 0.00 0.00 0.00 3.01
168 170 4.618489 CGTCTGAAGCCAAGCATTTTAAAG 59.382 41.667 0.00 0.00 0.00 1.85
170 172 3.057596 CCGTCTGAAGCCAAGCATTTTAA 60.058 43.478 0.00 0.00 0.00 1.52
193 203 2.580470 GATGCTCACGTGCGATCCG 61.580 63.158 11.67 0.00 35.36 4.18
202 212 0.179127 ATGACAGACGGATGCTCACG 60.179 55.000 0.00 0.00 0.00 4.35
204 214 0.461548 GGATGACAGACGGATGCTCA 59.538 55.000 0.00 0.00 0.00 4.26
224 234 3.531538 AGACAAAAGACACACGTCACAT 58.468 40.909 0.00 0.00 45.23 3.21
227 237 2.546778 GGAGACAAAAGACACACGTCA 58.453 47.619 0.00 0.00 45.23 4.35
232 242 1.208535 ACGTGGGAGACAAAAGACACA 59.791 47.619 0.00 0.00 0.00 3.72
241 251 4.314440 GCAGCCACGTGGGAGACA 62.314 66.667 34.58 0.00 40.01 3.41
256 266 1.476488 TGTAGCGAGTATCAAGCAGCA 59.524 47.619 0.00 0.00 33.17 4.41
286 296 2.878580 TGCAACAAAGACTTTGCTGTG 58.121 42.857 24.83 20.65 46.83 3.66
287 297 3.591196 TTGCAACAAAGACTTTGCTGT 57.409 38.095 24.83 11.71 46.83 4.40
311 321 4.146745 ACGGAGGTCTTGTTACAGTTTT 57.853 40.909 0.00 0.00 0.00 2.43
315 325 1.798813 GCAACGGAGGTCTTGTTACAG 59.201 52.381 0.00 0.00 0.00 2.74
317 327 1.873698 TGCAACGGAGGTCTTGTTAC 58.126 50.000 0.00 0.00 0.00 2.50
370 380 9.606631 ACAAAGGTCTTGTTGCAATTTAATTTA 57.393 25.926 0.59 0.00 0.00 1.40
371 381 8.504812 ACAAAGGTCTTGTTGCAATTTAATTT 57.495 26.923 0.59 0.00 0.00 1.82
374 384 6.533367 GTGACAAAGGTCTTGTTGCAATTTAA 59.467 34.615 0.59 0.00 44.61 1.52
376 386 4.869861 GTGACAAAGGTCTTGTTGCAATTT 59.130 37.500 0.59 0.00 44.61 1.82
405 419 4.493547 CAACAGAGGTCTTGTTGCAAAAA 58.506 39.130 0.00 0.00 36.86 1.94
406 420 4.108699 CAACAGAGGTCTTGTTGCAAAA 57.891 40.909 0.00 0.00 36.86 2.44
407 421 3.781079 CAACAGAGGTCTTGTTGCAAA 57.219 42.857 0.00 0.00 36.86 3.68
436 450 5.614324 TGCAATAGTGGTCTTGCTATAGT 57.386 39.130 8.52 0.00 46.16 2.12
437 451 9.875691 TTATATGCAATAGTGGTCTTGCTATAG 57.124 33.333 8.52 0.00 46.16 1.31
439 453 9.003658 GTTTATATGCAATAGTGGTCTTGCTAT 57.996 33.333 8.52 6.63 46.16 2.97
440 454 8.210946 AGTTTATATGCAATAGTGGTCTTGCTA 58.789 33.333 8.52 0.55 46.16 3.49
441 455 7.012704 CAGTTTATATGCAATAGTGGTCTTGCT 59.987 37.037 8.52 0.00 46.16 3.91
442 456 7.134815 CAGTTTATATGCAATAGTGGTCTTGC 58.865 38.462 0.00 0.51 46.19 4.01
443 457 8.213518 ACAGTTTATATGCAATAGTGGTCTTG 57.786 34.615 0.00 0.00 28.50 3.02
444 458 9.899661 TTACAGTTTATATGCAATAGTGGTCTT 57.100 29.630 0.00 0.00 28.50 3.01
445 459 9.326413 GTTACAGTTTATATGCAATAGTGGTCT 57.674 33.333 0.00 0.00 28.50 3.85
446 460 9.104965 TGTTACAGTTTATATGCAATAGTGGTC 57.895 33.333 0.00 0.00 28.50 4.02
447 461 9.456147 TTGTTACAGTTTATATGCAATAGTGGT 57.544 29.630 0.00 0.00 28.50 4.16
448 462 9.935682 CTTGTTACAGTTTATATGCAATAGTGG 57.064 33.333 0.00 0.00 28.50 4.00
452 466 9.899661 AGGTCTTGTTACAGTTTATATGCAATA 57.100 29.630 0.00 0.00 0.00 1.90
453 467 8.807948 AGGTCTTGTTACAGTTTATATGCAAT 57.192 30.769 0.00 0.00 0.00 3.56
454 468 7.064134 CGAGGTCTTGTTACAGTTTATATGCAA 59.936 37.037 0.00 0.00 0.00 4.08
455 469 6.533723 CGAGGTCTTGTTACAGTTTATATGCA 59.466 38.462 0.00 0.00 0.00 3.96
456 470 6.018994 CCGAGGTCTTGTTACAGTTTATATGC 60.019 42.308 0.00 0.00 0.00 3.14
457 471 7.039882 ACCGAGGTCTTGTTACAGTTTATATG 58.960 38.462 0.00 0.00 0.00 1.78
458 472 7.179076 ACCGAGGTCTTGTTACAGTTTATAT 57.821 36.000 0.00 0.00 0.00 0.86
459 473 6.594788 ACCGAGGTCTTGTTACAGTTTATA 57.405 37.500 0.00 0.00 0.00 0.98
460 474 5.479124 ACCGAGGTCTTGTTACAGTTTAT 57.521 39.130 0.00 0.00 0.00 1.40
461 475 4.942761 ACCGAGGTCTTGTTACAGTTTA 57.057 40.909 0.00 0.00 0.00 2.01
467 481 1.873698 TGCAACCGAGGTCTTGTTAC 58.126 50.000 0.00 0.00 0.00 2.50
495 509 9.485591 AAATTTCGCAACATAGATTAAGTTACG 57.514 29.630 0.00 0.00 34.33 3.18
503 517 6.389091 TGCAGAAAATTTCGCAACATAGATT 58.611 32.000 17.73 0.00 36.68 2.40
513 527 4.923281 AGGTTATGTTGCAGAAAATTTCGC 59.077 37.500 12.94 12.94 34.02 4.70
537 551 7.120579 TCGTGTTGCAGGAAATTTCTGTAATAT 59.879 33.333 17.42 0.00 38.63 1.28
542 556 2.948979 TCGTGTTGCAGGAAATTTCTGT 59.051 40.909 17.42 3.19 34.89 3.41
562 576 5.289595 TCTTCTACCATTGCGACATATGTC 58.710 41.667 23.47 23.47 41.47 3.06
563 577 5.276461 TCTTCTACCATTGCGACATATGT 57.724 39.130 8.43 8.43 0.00 2.29
564 578 5.928264 TCATCTTCTACCATTGCGACATATG 59.072 40.000 0.00 0.00 0.00 1.78
565 579 5.928839 GTCATCTTCTACCATTGCGACATAT 59.071 40.000 0.00 0.00 0.00 1.78
566 580 5.289595 GTCATCTTCTACCATTGCGACATA 58.710 41.667 0.00 0.00 0.00 2.29
567 581 4.122776 GTCATCTTCTACCATTGCGACAT 58.877 43.478 0.00 0.00 0.00 3.06
568 582 3.521560 GTCATCTTCTACCATTGCGACA 58.478 45.455 0.00 0.00 0.00 4.35
569 583 2.535984 CGTCATCTTCTACCATTGCGAC 59.464 50.000 0.00 0.00 0.00 5.19
570 584 2.809446 CGTCATCTTCTACCATTGCGA 58.191 47.619 0.00 0.00 0.00 5.10
571 585 1.258982 GCGTCATCTTCTACCATTGCG 59.741 52.381 0.00 0.00 0.00 4.85
578 593 0.595310 GCCCGAGCGTCATCTTCTAC 60.595 60.000 0.00 0.00 0.00 2.59
580 595 2.351244 TGCCCGAGCGTCATCTTCT 61.351 57.895 0.00 0.00 44.31 2.85
587 602 2.125512 ATTGAGTGCCCGAGCGTC 60.126 61.111 0.00 0.00 44.31 5.19
596 611 1.576356 GGATCTGACGGATTGAGTGC 58.424 55.000 0.00 0.00 34.33 4.40
607 622 2.167861 GCAAGCCGTCGGATCTGAC 61.168 63.158 22.64 22.64 35.49 3.51
611 626 2.508439 TTCGCAAGCCGTCGGATC 60.508 61.111 17.49 0.00 38.35 3.36
623 639 0.955428 AAAAGATCTGCCGCTTCGCA 60.955 50.000 0.00 0.00 37.19 5.10
625 641 3.740044 TTTAAAAGATCTGCCGCTTCG 57.260 42.857 0.00 0.00 0.00 3.79
628 644 5.221126 GGATCATTTTAAAAGATCTGCCGCT 60.221 40.000 24.09 0.99 38.51 5.52
632 648 6.860023 CCATCGGATCATTTTAAAAGATCTGC 59.140 38.462 25.50 16.29 42.27 4.26
634 650 6.293626 CGCCATCGGATCATTTTAAAAGATCT 60.294 38.462 24.09 12.68 38.51 2.75
648 664 1.518572 ACACGTTCGCCATCGGATC 60.519 57.895 0.00 0.00 36.13 3.36
654 670 2.593148 TTGCCACACGTTCGCCAT 60.593 55.556 0.00 0.00 0.00 4.40
655 671 3.578272 GTTGCCACACGTTCGCCA 61.578 61.111 0.00 0.00 0.00 5.69
664 680 2.738587 TCTAAAAGGGTGTTGCCACA 57.261 45.000 0.00 0.00 43.71 4.17
665 681 3.383505 ACTTTCTAAAAGGGTGTTGCCAC 59.616 43.478 4.60 0.00 41.06 5.01
667 683 5.977489 ATACTTTCTAAAAGGGTGTTGCC 57.023 39.130 4.60 0.00 0.00 4.52
670 686 9.582648 ACAACATATACTTTCTAAAAGGGTGTT 57.417 29.630 4.60 6.38 0.00 3.32
690 708 6.708949 AGTTACACACCGAAGATTTACAACAT 59.291 34.615 0.00 0.00 0.00 2.71
692 710 6.535274 AGTTACACACCGAAGATTTACAAC 57.465 37.500 0.00 0.00 0.00 3.32
696 714 4.218200 TCCGAGTTACACACCGAAGATTTA 59.782 41.667 0.00 0.00 0.00 1.40
705 723 0.387750 GTCGGTCCGAGTTACACACC 60.388 60.000 15.95 0.00 36.23 4.16
713 731 0.754472 TTCCTTTTGTCGGTCCGAGT 59.246 50.000 15.95 0.00 36.23 4.18
714 732 1.873698 TTTCCTTTTGTCGGTCCGAG 58.126 50.000 15.95 1.92 36.23 4.63
801 819 2.523168 CGGGTTTGGGTTTGGGCT 60.523 61.111 0.00 0.00 0.00 5.19
849 871 6.596888 TGCTCGAAATCTTGAATCTTGAATCT 59.403 34.615 0.00 0.00 0.00 2.40
850 872 6.686253 GTGCTCGAAATCTTGAATCTTGAATC 59.314 38.462 0.00 0.00 0.00 2.52
870 892 1.234615 TGCCGCCTTTTGTAGTGCTC 61.235 55.000 0.00 0.00 0.00 4.26
913 943 4.055227 GGCGGGTTTGGGATGGGA 62.055 66.667 0.00 0.00 0.00 4.37
1211 1247 3.897681 TACCAGCACCGCCTCTCCA 62.898 63.158 0.00 0.00 0.00 3.86
1452 1494 2.305009 CCTTTCTCATCATCCCCTTGC 58.695 52.381 0.00 0.00 0.00 4.01
1458 1503 2.478831 GTCTCGCCTTTCTCATCATCC 58.521 52.381 0.00 0.00 0.00 3.51
1670 1718 4.142609 TCTGAGCAGTTGTTCAAGTCTT 57.857 40.909 0.47 0.00 34.91 3.01
1689 1737 2.362503 TCCACCGAGACGCCATCT 60.363 61.111 0.00 0.00 41.91 2.90
1701 1749 2.111384 TCATCTAGAAGCTGGTCCACC 58.889 52.381 0.00 0.00 0.00 4.61
1716 1770 2.036992 GAGGCCGAACATGAGATCATCT 59.963 50.000 0.00 0.00 33.61 2.90
1739 1793 0.904865 ACCGAGGACTTGATCAGGCA 60.905 55.000 4.46 0.00 27.54 4.75
1755 1809 1.079819 AGGCATCACGAAGTCACCG 60.080 57.895 0.00 0.00 41.61 4.94
1810 1864 1.414866 TAGCTGCCAGTGTGGTTGGA 61.415 55.000 0.00 0.00 40.46 3.53
1815 1950 0.952497 CACAGTAGCTGCCAGTGTGG 60.952 60.000 22.89 8.87 41.58 4.17
1816 1951 0.033920 TCACAGTAGCTGCCAGTGTG 59.966 55.000 24.11 24.11 44.97 3.82
1817 1952 0.034059 GTCACAGTAGCTGCCAGTGT 59.966 55.000 19.38 2.61 34.37 3.55
1818 1953 0.033920 TGTCACAGTAGCTGCCAGTG 59.966 55.000 15.74 15.74 34.37 3.66
1819 1954 0.319728 CTGTCACAGTAGCTGCCAGT 59.680 55.000 0.00 0.00 34.37 4.00
1820 1955 0.390866 CCTGTCACAGTAGCTGCCAG 60.391 60.000 3.56 0.00 34.37 4.85
1821 1956 1.673477 CCTGTCACAGTAGCTGCCA 59.327 57.895 3.56 0.00 34.37 4.92
1822 1957 1.078848 CCCTGTCACAGTAGCTGCC 60.079 63.158 3.56 0.00 34.37 4.85
1823 1958 0.390472 GACCCTGTCACAGTAGCTGC 60.390 60.000 3.56 0.00 34.37 5.25
1824 1959 0.247736 GGACCCTGTCACAGTAGCTG 59.752 60.000 3.56 0.00 37.52 4.24
1825 1960 0.115349 AGGACCCTGTCACAGTAGCT 59.885 55.000 3.56 0.00 33.68 3.32
1826 1961 0.533032 GAGGACCCTGTCACAGTAGC 59.467 60.000 3.56 0.00 33.68 3.58
1827 1962 1.187087 GGAGGACCCTGTCACAGTAG 58.813 60.000 3.56 0.00 33.68 2.57
1828 1963 0.784495 AGGAGGACCCTGTCACAGTA 59.216 55.000 3.56 0.00 45.61 2.74
1829 1964 1.549297 AGGAGGACCCTGTCACAGT 59.451 57.895 3.56 0.00 45.61 3.55
1830 1965 4.549155 AGGAGGACCCTGTCACAG 57.451 61.111 0.00 0.00 45.61 3.66
1841 1976 1.609501 CCACCTTCGTCCAGGAGGA 60.610 63.158 7.83 7.83 45.33 3.71
1842 1977 2.982130 CCACCTTCGTCCAGGAGG 59.018 66.667 2.36 2.36 38.23 4.30
1843 1978 1.185618 TCACCACCTTCGTCCAGGAG 61.186 60.000 0.00 0.00 37.39 3.69
1844 1979 1.152419 TCACCACCTTCGTCCAGGA 60.152 57.895 5.26 0.00 37.39 3.86
1845 1980 1.004918 GTCACCACCTTCGTCCAGG 60.005 63.158 0.00 0.00 40.23 4.45
1846 1981 0.393077 AAGTCACCACCTTCGTCCAG 59.607 55.000 0.00 0.00 0.00 3.86
1847 1982 0.105964 CAAGTCACCACCTTCGTCCA 59.894 55.000 0.00 0.00 0.00 4.02
1848 1983 0.106149 ACAAGTCACCACCTTCGTCC 59.894 55.000 0.00 0.00 0.00 4.79
1849 1984 1.597663 CAACAAGTCACCACCTTCGTC 59.402 52.381 0.00 0.00 0.00 4.20
1850 1985 1.208535 TCAACAAGTCACCACCTTCGT 59.791 47.619 0.00 0.00 0.00 3.85
1851 1986 1.948104 TCAACAAGTCACCACCTTCG 58.052 50.000 0.00 0.00 0.00 3.79
1852 1987 2.030805 GCATCAACAAGTCACCACCTTC 60.031 50.000 0.00 0.00 0.00 3.46
1853 1988 1.956477 GCATCAACAAGTCACCACCTT 59.044 47.619 0.00 0.00 0.00 3.50
1854 1989 1.609208 GCATCAACAAGTCACCACCT 58.391 50.000 0.00 0.00 0.00 4.00
1855 1990 0.598065 GGCATCAACAAGTCACCACC 59.402 55.000 0.00 0.00 0.00 4.61
1856 1991 1.609208 AGGCATCAACAAGTCACCAC 58.391 50.000 0.00 0.00 0.00 4.16
1857 1992 2.363306 AAGGCATCAACAAGTCACCA 57.637 45.000 0.00 0.00 0.00 4.17
1858 1993 4.009675 TGATAAGGCATCAACAAGTCACC 58.990 43.478 0.00 0.00 40.80 4.02
1859 1994 5.814783 GATGATAAGGCATCAACAAGTCAC 58.185 41.667 0.00 0.00 46.66 3.67
1929 2064 5.627735 GCTGTAATTGACCTCTGATTCTGGA 60.628 44.000 0.00 0.00 0.00 3.86
1932 2067 5.690464 AGCTGTAATTGACCTCTGATTCT 57.310 39.130 0.00 0.00 0.00 2.40
1995 2130 1.004628 CCACCATGAAGGACCATGTCA 59.995 52.381 0.00 0.00 41.65 3.58
2000 2135 1.073763 CTGAACCACCATGAAGGACCA 59.926 52.381 9.97 6.42 41.22 4.02
2001 2136 1.073923 ACTGAACCACCATGAAGGACC 59.926 52.381 9.97 0.00 41.22 4.46
2007 2142 1.202758 GGTGTGACTGAACCACCATGA 60.203 52.381 0.00 0.00 46.33 3.07
2031 2166 9.472361 AAGTCAAATTGATCAGAATTGTCAAAG 57.528 29.630 0.00 0.00 35.70 2.77
2082 2217 0.536006 GGCTCTGCAAGTCAGTTGGT 60.536 55.000 0.00 0.00 43.32 3.67
2225 2366 3.119096 GAACCGCCGGTGAGCTTC 61.119 66.667 18.79 10.21 35.34 3.86
2326 2475 2.741159 ATCCTATCCATGGGGTAGCA 57.259 50.000 13.02 1.40 34.93 3.49
2600 2757 4.641396 TCAATTACAGCTTACAGCACAGT 58.359 39.130 0.00 0.00 45.56 3.55
2606 2764 5.041191 AGGGGATCAATTACAGCTTACAG 57.959 43.478 0.00 0.00 0.00 2.74
2621 2779 1.127343 AACAGCAGCTAGAGGGGATC 58.873 55.000 0.00 0.00 0.00 3.36
2629 2787 4.937620 TGTAGGATCAAAAACAGCAGCTAG 59.062 41.667 0.00 0.00 0.00 3.42
2640 2799 4.365514 TGAACCAGCTGTAGGATCAAAA 57.634 40.909 13.81 0.00 35.35 2.44
2658 2817 2.905415 AAGGATCCCAAGTGCATGAA 57.095 45.000 8.55 0.00 0.00 2.57
2679 2838 6.636454 ATTAAGATCCAAACCCTGTACAGA 57.364 37.500 24.68 2.61 0.00 3.41
2685 2844 6.038714 GCACTCTAATTAAGATCCAAACCCTG 59.961 42.308 0.00 0.00 32.41 4.45
2816 2997 8.747538 AAATGTTAGGTGTACTGAAAGAGTTT 57.252 30.769 0.00 0.00 37.43 2.66
2858 3039 7.967908 AGTCATAGGTTCGAGAATTATGGAAT 58.032 34.615 0.76 0.00 0.00 3.01
2904 3092 8.516234 TCTATTTCTAAGACCGAGATAATCTGC 58.484 37.037 0.00 0.00 0.00 4.26
2930 3118 3.306088 CGCATGAGTAATACGGAGGGAAT 60.306 47.826 0.00 0.00 0.00 3.01
2998 3188 3.007920 AGTGCTCCAGGCCTCCAG 61.008 66.667 0.00 1.91 40.92 3.86
2999 3189 3.005539 GAGTGCTCCAGGCCTCCA 61.006 66.667 0.00 0.00 40.92 3.86
3000 3190 4.154347 CGAGTGCTCCAGGCCTCC 62.154 72.222 0.00 0.00 40.92 4.30
3001 3191 2.052690 TACGAGTGCTCCAGGCCTC 61.053 63.158 0.00 0.00 40.92 4.70
3002 3192 2.037367 TACGAGTGCTCCAGGCCT 59.963 61.111 0.00 0.00 40.92 5.19
3003 3193 2.184579 GTACGAGTGCTCCAGGCC 59.815 66.667 0.00 0.00 40.92 5.19
3004 3194 1.153745 CTGTACGAGTGCTCCAGGC 60.154 63.158 0.00 0.00 42.22 4.85
3005 3195 0.603569 AACTGTACGAGTGCTCCAGG 59.396 55.000 0.00 0.00 34.02 4.45
3153 3350 4.152938 TCAGACTGACATGAATCTTTTGCG 59.847 41.667 0.00 0.00 0.00 4.85
3193 3390 9.188588 CTTGTACAGTTGTATACGAGAGAAAAA 57.811 33.333 0.00 0.00 35.57 1.94
3334 3644 3.264947 TCACATCTGCTGCATGAACTAC 58.735 45.455 10.01 0.00 0.00 2.73
3422 3734 8.705594 CCATCCTACTCAGAATACTTTTCCTTA 58.294 37.037 0.00 0.00 0.00 2.69
3508 3823 4.280929 ACAACATAAAGGAGAAAAGTGGGC 59.719 41.667 0.00 0.00 0.00 5.36
3573 3891 2.587473 GCAGAGCCTAGCCTTCGC 60.587 66.667 0.00 0.00 0.00 4.70
3646 3964 6.189859 AGAGATTGTTCCATCATTTAAGCCA 58.810 36.000 0.00 0.00 0.00 4.75
3654 3973 5.447778 ACCAGAAGAGATTGTTCCATCAT 57.552 39.130 0.00 0.00 0.00 2.45
3655 3974 4.916041 ACCAGAAGAGATTGTTCCATCA 57.084 40.909 0.00 0.00 0.00 3.07
3695 4321 7.506328 AAATCTAATTCACGGGGTAATAAGC 57.494 36.000 0.00 0.00 0.00 3.09
3886 6124 8.911918 TTCTTTTTGTGGAGTATTTAGTGCTA 57.088 30.769 0.00 0.00 0.00 3.49
3946 6185 3.065371 CCATATCGAGTGAAAGTTTGGCC 59.935 47.826 0.00 0.00 0.00 5.36
3961 6464 3.744942 CAGACAGCTGGATTTCCATATCG 59.255 47.826 19.93 0.00 46.46 2.92
3988 6651 9.324506 GGAGAAGCCAAAAGAAGAACTTCTGTC 62.325 44.444 16.25 1.83 42.79 3.51


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

AutoCloner maintained by Alex Coulton.