Multiple sequence alignment - TraesCS1A01G341900

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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 TraesCS1A01G341900 chr1A 100.000 3688 0 0 1 3688 531284015 531280328 0.000000e+00 6811.0
1 TraesCS1A01G341900 chr1A 100.000 46 0 0 1696 1741 531282275 531282230 6.560000e-13 86.1
2 TraesCS1A01G341900 chr1A 100.000 46 0 0 1741 1786 531282320 531282275 6.560000e-13 86.1
3 TraesCS1A01G341900 chr1D 90.319 971 29 20 1746 2702 432808602 432807683 0.000000e+00 1212.0
4 TraesCS1A01G341900 chr1D 84.456 1113 84 48 416 1492 432809830 432808771 0.000000e+00 1014.0
5 TraesCS1A01G341900 chr1D 82.492 594 49 26 3106 3681 432807288 432806732 1.550000e-128 470.0
6 TraesCS1A01G341900 chr1D 91.477 176 11 3 1542 1717 432808773 432808602 4.760000e-59 239.0
7 TraesCS1A01G341900 chr1D 90.909 132 2 3 24 155 432810225 432810104 6.330000e-38 169.0
8 TraesCS1A01G341900 chr1D 92.157 51 0 1 220 266 432810022 432809972 6.610000e-08 69.4
9 TraesCS1A01G341900 chr1B 88.444 874 55 19 861 1717 584326309 584325465 0.000000e+00 1013.0
10 TraesCS1A01G341900 chr1B 95.455 440 14 2 2081 2514 584325185 584324746 0.000000e+00 697.0
11 TraesCS1A01G341900 chr1B 85.597 486 33 17 2546 3003 584324746 584324270 3.330000e-130 475.0
12 TraesCS1A01G341900 chr1B 92.657 286 14 3 1753 2038 584325458 584325180 4.430000e-109 405.0
13 TraesCS1A01G341900 chr1B 82.881 479 34 21 222 666 584326957 584326493 1.610000e-103 387.0
14 TraesCS1A01G341900 chr1B 87.838 148 11 7 3518 3662 584320594 584320451 2.280000e-37 167.0
15 TraesCS1A01G341900 chr1B 89.062 128 2 6 24 146 584327164 584327044 8.250000e-32 148.0
16 TraesCS1A01G341900 chr1B 82.812 128 7 8 3134 3246 584323772 584323645 2.340000e-17 100.0
17 TraesCS1A01G341900 chr1B 100.000 34 0 0 3078 3111 584323859 584323826 3.070000e-06 63.9
18 TraesCS1A01G341900 chr3B 82.703 185 25 5 1789 1971 498326275 498326096 1.370000e-34 158.0
19 TraesCS1A01G341900 chr3B 86.364 132 16 2 1788 1918 104971043 104971173 3.840000e-30 143.0
20 TraesCS1A01G341900 chr3D 87.597 129 16 0 1789 1917 382630515 382630387 2.290000e-32 150.0
21 TraesCS1A01G341900 chr3A 86.364 132 16 2 1788 1918 73513082 73513212 3.840000e-30 143.0


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 TraesCS1A01G341900 chr1A 531280328 531284015 3687 True 2327.733333 6811 100.000000 1 3688 3 chr1A.!!$R1 3687
1 TraesCS1A01G341900 chr1D 432806732 432810225 3493 True 528.900000 1212 88.635000 24 3681 6 chr1D.!!$R1 3657
2 TraesCS1A01G341900 chr1B 584320451 584327164 6713 True 383.988889 1013 89.416222 24 3662 9 chr1B.!!$R1 3638


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
443 524 0.247736 TTCGCTCCTTCTCTGCTTCC 59.752 55.0 0.0 0.0 0.00 3.46 F
2037 2228 0.165944 GAACCGCATTTCGTCTGGTG 59.834 55.0 0.0 0.0 36.19 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 2270 0.110823 CGCTCCTACGCAACAACAAC 60.111 55.0 0.0 0.0 0.0 3.32 R
3076 3652 0.036010 CTTCGTCCCAGCTTCCATGT 60.036 55.0 0.0 0.0 0.0 3.21 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
20 21 2.183679 CCCTATCCCATCCACTCTAGC 58.816 57.143 0.00 0.00 0.00 3.42
21 22 1.821753 CCTATCCCATCCACTCTAGCG 59.178 57.143 0.00 0.00 0.00 4.26
22 23 1.821753 CTATCCCATCCACTCTAGCGG 59.178 57.143 0.00 0.00 0.00 5.52
211 221 1.804372 GCAGGCGAGGTGAGATACAAG 60.804 57.143 0.00 0.00 0.00 3.16
213 223 1.478510 AGGCGAGGTGAGATACAAGTG 59.521 52.381 0.00 0.00 0.00 3.16
214 224 1.476891 GGCGAGGTGAGATACAAGTGA 59.523 52.381 0.00 0.00 0.00 3.41
270 322 3.283684 TTTTGCTCGTGCCCGTGG 61.284 61.111 7.05 0.00 38.71 4.94
283 335 4.514577 CGTGGGACGCTGGCCTAG 62.515 72.222 3.32 0.34 33.65 3.02
292 344 3.595819 CTGGCCTAGCTTGTTGCC 58.404 61.111 3.32 8.17 44.23 4.52
330 382 3.006430 TCGTAGACAAGCCTTGTTCATCA 59.994 43.478 12.09 0.00 45.52 3.07
331 383 3.123621 CGTAGACAAGCCTTGTTCATCAC 59.876 47.826 12.09 5.01 45.52 3.06
332 384 3.213206 AGACAAGCCTTGTTCATCACA 57.787 42.857 12.09 0.00 45.52 3.58
334 386 3.504906 AGACAAGCCTTGTTCATCACATG 59.495 43.478 12.09 0.00 45.52 3.21
336 388 1.180029 AGCCTTGTTCATCACATGCC 58.820 50.000 0.00 0.00 35.19 4.40
341 422 0.883153 TGTTCATCACATGCCACAGC 59.117 50.000 0.00 0.00 40.48 4.40
385 466 2.657237 CGTGCGTTCCCTTCTCCT 59.343 61.111 0.00 0.00 0.00 3.69
389 470 1.262640 TGCGTTCCCTTCTCCTACCC 61.263 60.000 0.00 0.00 0.00 3.69
390 471 1.262640 GCGTTCCCTTCTCCTACCCA 61.263 60.000 0.00 0.00 0.00 4.51
393 474 0.797579 TTCCCTTCTCCTACCCACCT 59.202 55.000 0.00 0.00 0.00 4.00
394 475 0.797579 TCCCTTCTCCTACCCACCTT 59.202 55.000 0.00 0.00 0.00 3.50
395 476 1.205055 CCCTTCTCCTACCCACCTTC 58.795 60.000 0.00 0.00 0.00 3.46
396 477 1.205055 CCTTCTCCTACCCACCTTCC 58.795 60.000 0.00 0.00 0.00 3.46
397 478 1.205055 CTTCTCCTACCCACCTTCCC 58.795 60.000 0.00 0.00 0.00 3.97
398 479 0.253020 TTCTCCTACCCACCTTCCCC 60.253 60.000 0.00 0.00 0.00 4.81
399 480 2.039951 TCCTACCCACCTTCCCCG 59.960 66.667 0.00 0.00 0.00 5.73
400 481 3.793888 CCTACCCACCTTCCCCGC 61.794 72.222 0.00 0.00 0.00 6.13
401 482 3.793888 CTACCCACCTTCCCCGCC 61.794 72.222 0.00 0.00 0.00 6.13
440 521 1.204467 CTTCTTCGCTCCTTCTCTGCT 59.796 52.381 0.00 0.00 0.00 4.24
441 522 1.261480 TCTTCGCTCCTTCTCTGCTT 58.739 50.000 0.00 0.00 0.00 3.91
443 524 0.247736 TTCGCTCCTTCTCTGCTTCC 59.752 55.000 0.00 0.00 0.00 3.46
444 525 0.613292 TCGCTCCTTCTCTGCTTCCT 60.613 55.000 0.00 0.00 0.00 3.36
445 526 0.459934 CGCTCCTTCTCTGCTTCCTG 60.460 60.000 0.00 0.00 0.00 3.86
446 527 0.612744 GCTCCTTCTCTGCTTCCTGT 59.387 55.000 0.00 0.00 0.00 4.00
447 528 1.003003 GCTCCTTCTCTGCTTCCTGTT 59.997 52.381 0.00 0.00 0.00 3.16
474 560 2.975799 TTCGTTCGTTGGGGCTGC 60.976 61.111 0.00 0.00 0.00 5.25
515 603 2.391389 GCCTGAAAAGCTCGTCCGG 61.391 63.158 0.00 0.00 0.00 5.14
556 644 2.033194 GCTTCACGTAGGTGGCCAC 61.033 63.158 28.57 28.57 44.50 5.01
592 680 1.002366 CGCTTCCTTTCACTGATCCG 58.998 55.000 0.00 0.00 0.00 4.18
602 690 0.463204 CACTGATCCGACTGCCATCT 59.537 55.000 0.00 0.00 0.00 2.90
616 707 2.209809 ATCTCCCACCCACCCACA 59.790 61.111 0.00 0.00 0.00 4.17
666 773 1.968540 GCCGCTGGCTCTTTTCTGT 60.969 57.895 11.61 0.00 46.69 3.41
673 780 0.606673 GGCTCTTTTCTGTTCGGCCT 60.607 55.000 0.00 0.00 35.73 5.19
675 782 1.443802 CTCTTTTCTGTTCGGCCTCC 58.556 55.000 0.00 0.00 0.00 4.30
687 829 4.214327 GCCTCCTCTTCCTCGCCG 62.214 72.222 0.00 0.00 0.00 6.46
709 851 1.393883 GCGCCTCTCTAAAAGGTTTCG 59.606 52.381 0.00 0.00 36.21 3.46
722 864 3.503800 AGGTTTCGCCTCTTTTACCTT 57.496 42.857 0.00 0.00 46.96 3.50
735 877 4.279169 TCTTTTACCTTCCGACGAGAAAGA 59.721 41.667 0.00 0.00 31.61 2.52
758 900 4.767409 AGACAGAAACTTATCTTTTGGGGC 59.233 41.667 0.00 0.00 0.00 5.80
764 908 1.400494 CTTATCTTTTGGGGCGGTTCG 59.600 52.381 0.00 0.00 0.00 3.95
767 911 2.907917 TTTTGGGGCGGTTCGGTG 60.908 61.111 0.00 0.00 0.00 4.94
797 941 3.744660 TGCTTTCTTCCTCAACCTTCTC 58.255 45.455 0.00 0.00 0.00 2.87
815 959 2.171870 TCTCCCCGTTTCAGTTTCAACT 59.828 45.455 0.00 0.00 40.60 3.16
855 999 0.856641 TCTTGTTTACGCACGCTGTC 59.143 50.000 0.00 0.00 0.00 3.51
863 1014 1.661509 CGCACGCTGTCTCAACTCA 60.662 57.895 0.00 0.00 0.00 3.41
887 1038 4.760047 GGTCGACGCCATGGCTGT 62.760 66.667 33.07 29.63 39.32 4.40
896 1047 1.676678 GCCATGGCTGTCGTCTCCTA 61.677 60.000 29.98 0.00 38.26 2.94
918 1069 1.121967 GTTCTTGCAGTTCGTCGTACG 59.878 52.381 9.53 9.53 44.19 3.67
931 1082 5.879948 TCGTCGTACGATTTTGTGTTTTA 57.120 34.783 22.57 0.00 46.73 1.52
934 1085 7.343691 TCGTCGTACGATTTTGTGTTTTATTT 58.656 30.769 22.57 0.00 46.73 1.40
935 1086 7.318439 TCGTCGTACGATTTTGTGTTTTATTTG 59.682 33.333 22.57 0.00 46.73 2.32
936 1087 7.208429 GTCGTACGATTTTGTGTTTTATTTGC 58.792 34.615 22.57 0.00 0.00 3.68
937 1088 6.360148 TCGTACGATTTTGTGTTTTATTTGCC 59.640 34.615 15.28 0.00 0.00 4.52
938 1089 5.568747 ACGATTTTGTGTTTTATTTGCCG 57.431 34.783 0.00 0.00 0.00 5.69
939 1090 5.282510 ACGATTTTGTGTTTTATTTGCCGA 58.717 33.333 0.00 0.00 0.00 5.54
940 1091 5.749109 ACGATTTTGTGTTTTATTTGCCGAA 59.251 32.000 0.00 0.00 0.00 4.30
941 1092 6.422400 ACGATTTTGTGTTTTATTTGCCGAAT 59.578 30.769 0.00 0.00 0.00 3.34
942 1093 6.947680 CGATTTTGTGTTTTATTTGCCGAATC 59.052 34.615 0.00 0.00 0.00 2.52
943 1094 7.148820 CGATTTTGTGTTTTATTTGCCGAATCT 60.149 33.333 0.00 0.00 0.00 2.40
944 1095 7.778470 TTTTGTGTTTTATTTGCCGAATCTT 57.222 28.000 0.00 0.00 0.00 2.40
945 1096 6.761731 TTGTGTTTTATTTGCCGAATCTTG 57.238 33.333 0.00 0.00 0.00 3.02
946 1097 6.078202 TGTGTTTTATTTGCCGAATCTTGA 57.922 33.333 0.00 0.00 0.00 3.02
947 1098 6.148948 TGTGTTTTATTTGCCGAATCTTGAG 58.851 36.000 0.00 0.00 0.00 3.02
948 1099 6.149633 GTGTTTTATTTGCCGAATCTTGAGT 58.850 36.000 0.00 0.00 0.00 3.41
978 1129 1.443872 CGTTCTTCGCGCAGGTAGT 60.444 57.895 8.75 0.00 0.00 2.73
1030 1181 1.377725 ATGCGGTGGCTCAAGAAGG 60.378 57.895 0.00 0.00 40.82 3.46
1107 1258 2.265182 GCCGATCGAGAGGAGGAGG 61.265 68.421 18.66 0.00 0.00 4.30
1341 1504 6.038603 TCCTTTTCTCTCACACAAACATCAAG 59.961 38.462 0.00 0.00 0.00 3.02
1352 1515 6.036300 CACACAAACATCAAGCTGAATTTTGT 59.964 34.615 15.17 15.17 41.80 2.83
1372 1539 3.332761 TGATGAACACACGTTTGAAGC 57.667 42.857 9.03 0.00 34.75 3.86
1385 1557 3.920412 CGTTTGAAGCTAGGCCAATTTTC 59.080 43.478 5.01 4.26 0.00 2.29
1400 1572 4.331717 CCAATTTTCAGGCATTTCATCTGC 59.668 41.667 0.00 0.00 38.93 4.26
1413 1585 6.459710 GCATTTCATCTGCATCATCTCTTGAA 60.460 38.462 0.00 0.00 38.03 2.69
1432 1604 9.370126 CTCTTGAAAGATTAACAGTTGTAAACG 57.630 33.333 0.00 0.00 42.71 3.60
1444 1616 0.730265 TGTAAACGGCGATGGAATGC 59.270 50.000 16.62 0.00 0.00 3.56
1525 1697 0.464036 TTGACTTCACTGTGCGTCCT 59.536 50.000 19.88 0.00 0.00 3.85
1530 1702 1.436195 TTCACTGTGCGTCCTGTTGC 61.436 55.000 2.12 0.00 0.00 4.17
1531 1703 2.179547 CACTGTGCGTCCTGTTGCA 61.180 57.895 0.00 0.00 39.13 4.08
1532 1704 1.227943 ACTGTGCGTCCTGTTGCAT 60.228 52.632 0.00 0.00 43.96 3.96
1533 1705 1.230635 ACTGTGCGTCCTGTTGCATC 61.231 55.000 0.00 0.00 43.96 3.91
1608 1780 0.726827 CTGCTGCCGCTTCGAATTTA 59.273 50.000 0.00 0.00 36.97 1.40
1662 1834 1.004918 ACAAGCCTAGTCGGTGCAC 60.005 57.895 8.80 8.80 34.25 4.57
1677 1849 1.078201 TGCACTCGTCATCATCGCAC 61.078 55.000 0.00 0.00 0.00 5.34
1711 1883 8.784043 ACCTATCAAACACTAAAGAAATGTGTC 58.216 33.333 0.00 0.00 43.11 3.67
1736 1922 7.806014 TCAAAGATTTGAAATTTGTACTACCGC 59.194 33.333 5.55 0.00 43.62 5.68
1737 1923 5.864986 AGATTTGAAATTTGTACTACCGCG 58.135 37.500 0.00 0.00 0.00 6.46
1738 1924 5.640357 AGATTTGAAATTTGTACTACCGCGA 59.360 36.000 8.23 0.00 0.00 5.87
1739 1925 4.650545 TTGAAATTTGTACTACCGCGAC 57.349 40.909 8.23 0.00 0.00 5.19
1740 1926 2.995258 TGAAATTTGTACTACCGCGACC 59.005 45.455 8.23 0.00 0.00 4.79
1741 1927 2.747396 AATTTGTACTACCGCGACCA 57.253 45.000 8.23 0.00 0.00 4.02
1742 1928 2.000429 ATTTGTACTACCGCGACCAC 58.000 50.000 8.23 0.00 0.00 4.16
1743 1929 0.961019 TTTGTACTACCGCGACCACT 59.039 50.000 8.23 0.00 0.00 4.00
1744 1930 1.819928 TTGTACTACCGCGACCACTA 58.180 50.000 8.23 0.00 0.00 2.74
1745 1931 1.819928 TGTACTACCGCGACCACTAA 58.180 50.000 8.23 0.00 0.00 2.24
1746 1932 2.158559 TGTACTACCGCGACCACTAAA 58.841 47.619 8.23 0.00 0.00 1.85
1747 1933 2.162208 TGTACTACCGCGACCACTAAAG 59.838 50.000 8.23 0.00 0.00 1.85
1748 1934 1.538047 ACTACCGCGACCACTAAAGA 58.462 50.000 8.23 0.00 0.00 2.52
1749 1935 1.888512 ACTACCGCGACCACTAAAGAA 59.111 47.619 8.23 0.00 0.00 2.52
1750 1936 2.297033 ACTACCGCGACCACTAAAGAAA 59.703 45.455 8.23 0.00 0.00 2.52
1751 1937 2.467566 ACCGCGACCACTAAAGAAAT 57.532 45.000 8.23 0.00 0.00 2.17
1752 1938 2.073816 ACCGCGACCACTAAAGAAATG 58.926 47.619 8.23 0.00 0.00 2.32
1753 1939 2.073816 CCGCGACCACTAAAGAAATGT 58.926 47.619 8.23 0.00 0.00 2.71
1754 1940 2.159707 CCGCGACCACTAAAGAAATGTG 60.160 50.000 8.23 0.00 0.00 3.21
1755 1941 2.478894 CGCGACCACTAAAGAAATGTGT 59.521 45.455 0.00 0.00 0.00 3.72
1756 1942 3.423123 CGCGACCACTAAAGAAATGTGTC 60.423 47.826 0.00 0.00 0.00 3.67
1757 1943 3.496884 GCGACCACTAAAGAAATGTGTCA 59.503 43.478 0.00 0.00 0.00 3.58
1758 1944 4.024387 GCGACCACTAAAGAAATGTGTCAA 60.024 41.667 0.00 0.00 0.00 3.18
1759 1945 5.504994 GCGACCACTAAAGAAATGTGTCAAA 60.505 40.000 0.00 0.00 0.00 2.69
1760 1946 6.136071 CGACCACTAAAGAAATGTGTCAAAG 58.864 40.000 0.00 0.00 0.00 2.77
1761 1947 6.018262 CGACCACTAAAGAAATGTGTCAAAGA 60.018 38.462 0.00 0.00 0.00 2.52
1762 1948 7.307989 CGACCACTAAAGAAATGTGTCAAAGAT 60.308 37.037 0.00 0.00 0.00 2.40
1763 1949 8.237811 ACCACTAAAGAAATGTGTCAAAGATT 57.762 30.769 0.00 0.00 0.00 2.40
1764 1950 8.695456 ACCACTAAAGAAATGTGTCAAAGATTT 58.305 29.630 0.00 0.00 34.59 2.17
1765 1951 8.971321 CCACTAAAGAAATGTGTCAAAGATTTG 58.029 33.333 0.00 0.00 32.17 2.32
1766 1952 9.734620 CACTAAAGAAATGTGTCAAAGATTTGA 57.265 29.630 3.91 3.91 44.31 2.69
1941 2127 1.846712 GCAGGCCCTCAAGAACCTCT 61.847 60.000 0.00 0.00 0.00 3.69
1942 2128 0.251634 CAGGCCCTCAAGAACCTCTC 59.748 60.000 0.00 0.00 0.00 3.20
1943 2129 0.912006 AGGCCCTCAAGAACCTCTCC 60.912 60.000 0.00 0.00 0.00 3.71
1980 2171 0.526524 CGAGCAGGTCCGTCAGAATC 60.527 60.000 0.00 0.00 0.00 2.52
1986 2177 0.178301 GGTCCGTCAGAATCCCTTCC 59.822 60.000 0.00 0.00 31.27 3.46
1992 2183 4.176752 AGAATCCCTTCCCGCCGC 62.177 66.667 0.00 0.00 31.27 6.53
2012 2203 2.285486 GCGCATCGTGATTCTTCTTCTG 60.285 50.000 0.30 0.00 0.00 3.02
2013 2204 2.283617 CGCATCGTGATTCTTCTTCTGG 59.716 50.000 0.00 0.00 0.00 3.86
2035 2226 1.062587 GATGAACCGCATTTCGTCTGG 59.937 52.381 8.59 0.00 38.16 3.86
2036 2227 0.250124 TGAACCGCATTTCGTCTGGT 60.250 50.000 0.00 0.00 36.19 4.00
2037 2228 0.165944 GAACCGCATTTCGTCTGGTG 59.834 55.000 0.00 0.00 36.19 4.17
2038 2229 0.250124 AACCGCATTTCGTCTGGTGA 60.250 50.000 0.00 0.00 36.19 4.02
2039 2230 0.250124 ACCGCATTTCGTCTGGTGAA 60.250 50.000 0.00 0.00 36.19 3.18
2069 2260 3.988379 AGCTGAAAATTTGACGCTTGA 57.012 38.095 0.00 0.00 0.00 3.02
2071 2262 4.232221 AGCTGAAAATTTGACGCTTGATG 58.768 39.130 0.00 0.00 0.00 3.07
2072 2263 4.022935 AGCTGAAAATTTGACGCTTGATGA 60.023 37.500 0.00 0.00 0.00 2.92
2074 2265 5.346822 GCTGAAAATTTGACGCTTGATGATT 59.653 36.000 0.00 0.00 0.00 2.57
2075 2266 6.669032 GCTGAAAATTTGACGCTTGATGATTG 60.669 38.462 0.00 0.00 0.00 2.67
2076 2267 6.215121 TGAAAATTTGACGCTTGATGATTGT 58.785 32.000 0.00 0.00 0.00 2.71
2077 2268 6.700960 TGAAAATTTGACGCTTGATGATTGTT 59.299 30.769 0.00 0.00 0.00 2.83
2078 2269 7.224362 TGAAAATTTGACGCTTGATGATTGTTT 59.776 29.630 0.00 0.00 0.00 2.83
2079 2270 6.456447 AATTTGACGCTTGATGATTGTTTG 57.544 33.333 0.00 0.00 0.00 2.93
2102 2293 0.249953 TTGTTGCGTAGGAGCGGAAA 60.250 50.000 0.00 0.00 43.21 3.13
2114 2305 2.663852 CGGAAAACGTCGGTGCCT 60.664 61.111 0.00 0.00 37.93 4.75
2119 2310 2.879813 AAAACGTCGGTGCCTGTGGT 62.880 55.000 0.00 0.00 0.00 4.16
2523 2726 4.639171 GCAACAACAACCCCGCCG 62.639 66.667 0.00 0.00 0.00 6.46
2524 2727 4.639171 CAACAACAACCCCGCCGC 62.639 66.667 0.00 0.00 0.00 6.53
2694 2903 0.879400 CCAGCTCTGGTGATGATCGC 60.879 60.000 7.75 0.00 45.53 4.58
2712 2921 2.027024 CCGGCGCGCTACTAATCA 59.973 61.111 32.29 0.00 0.00 2.57
2718 2927 1.067582 GCGCTACTAATCAGGGCGT 59.932 57.895 0.00 0.00 44.35 5.68
2723 2932 2.866762 GCTACTAATCAGGGCGTGAAAG 59.133 50.000 14.47 15.80 39.19 2.62
2724 2933 1.739067 ACTAATCAGGGCGTGAAAGC 58.261 50.000 14.47 0.00 39.19 3.51
2735 2944 2.440501 GCGTGAAAGCCATTAACATCG 58.559 47.619 0.00 0.00 0.00 3.84
2738 2947 3.670203 GTGAAAGCCATTAACATCGTCG 58.330 45.455 0.00 0.00 0.00 5.12
2790 3002 7.975616 TCATTCAGGATTAACAAAATGCTTAGC 59.024 33.333 0.00 0.00 0.00 3.09
2798 3013 8.970691 ATTAACAAAATGCTTAGCAGTAGTTG 57.029 30.769 24.69 20.19 43.65 3.16
2813 3028 1.808411 AGTTGTAGTTGATGGCACGG 58.192 50.000 0.00 0.00 0.00 4.94
2829 3044 0.175531 ACGGCACATCATCATCGTCA 59.824 50.000 0.00 0.00 0.00 4.35
2834 3049 2.222678 GCACATCATCATCGTCATGGTC 59.777 50.000 0.00 0.00 0.00 4.02
2835 3050 3.460103 CACATCATCATCGTCATGGTCA 58.540 45.455 0.00 0.00 0.00 4.02
2838 3053 3.391506 TCATCATCGTCATGGTCATCC 57.608 47.619 0.00 0.00 0.00 3.51
2839 3054 2.064014 CATCATCGTCATGGTCATCCG 58.936 52.381 0.00 0.00 36.30 4.18
2840 3055 1.398692 TCATCGTCATGGTCATCCGA 58.601 50.000 0.00 5.20 36.30 4.55
2841 3056 1.963515 TCATCGTCATGGTCATCCGAT 59.036 47.619 8.39 8.39 38.68 4.18
2843 3058 1.111277 TCGTCATGGTCATCCGATGT 58.889 50.000 8.24 0.00 36.30 3.06
2859 3095 2.286184 CGATGTTAACCGCCATTGTAGC 60.286 50.000 2.48 0.00 0.00 3.58
2921 3161 0.521735 AAAATCCGTTCTGCTTCCGC 59.478 50.000 0.00 0.00 0.00 5.54
2924 3164 2.890847 ATCCGTTCTGCTTCCGCGAG 62.891 60.000 8.23 0.00 39.65 5.03
2930 3170 1.880340 CTGCTTCCGCGAGACCATC 60.880 63.158 8.23 0.00 39.65 3.51
2971 3211 0.890683 CAAAGCTCATGAACCCCACC 59.109 55.000 0.00 0.00 0.00 4.61
2972 3212 0.482446 AAAGCTCATGAACCCCACCA 59.518 50.000 0.00 0.00 0.00 4.17
2973 3213 0.251341 AAGCTCATGAACCCCACCAC 60.251 55.000 0.00 0.00 0.00 4.16
2977 3217 1.000896 CATGAACCCCACCACCCTC 60.001 63.158 0.00 0.00 0.00 4.30
2978 3218 2.602676 ATGAACCCCACCACCCTCG 61.603 63.158 0.00 0.00 0.00 4.63
2979 3219 3.246880 GAACCCCACCACCCTCGT 61.247 66.667 0.00 0.00 0.00 4.18
2980 3220 3.546714 GAACCCCACCACCCTCGTG 62.547 68.421 0.00 0.00 39.91 4.35
2983 3223 4.394712 CCCACCACCCTCGTGCTC 62.395 72.222 0.00 0.00 38.79 4.26
2999 3239 1.516892 CTCTGCTCTGCTCTGTCCC 59.483 63.158 0.00 0.00 0.00 4.46
3019 3259 4.827087 CGCTGCCAGCCTCGATGT 62.827 66.667 11.83 0.00 38.18 3.06
3022 3262 0.948141 GCTGCCAGCCTCGATGTATC 60.948 60.000 5.06 0.00 34.48 2.24
3024 3264 0.829990 TGCCAGCCTCGATGTATCAA 59.170 50.000 0.00 0.00 0.00 2.57
3043 3306 4.368543 GGTGACACCGACGTCCCC 62.369 72.222 9.33 0.00 34.88 4.81
3068 3635 4.354662 CTCTAGAAAACAGAGGGGGTAGT 58.645 47.826 0.00 0.00 36.65 2.73
3069 3636 4.094476 TCTAGAAAACAGAGGGGGTAGTG 58.906 47.826 0.00 0.00 0.00 2.74
3070 3637 1.351350 AGAAAACAGAGGGGGTAGTGC 59.649 52.381 0.00 0.00 0.00 4.40
3071 3638 1.073284 GAAAACAGAGGGGGTAGTGCA 59.927 52.381 0.00 0.00 0.00 4.57
3076 3652 0.413832 AGAGGGGGTAGTGCAGAAGA 59.586 55.000 0.00 0.00 0.00 2.87
3130 3745 4.809070 GCAGTGAAGCCAGAGGTT 57.191 55.556 0.00 0.00 36.10 3.50
3131 3746 3.027419 GCAGTGAAGCCAGAGGTTT 57.973 52.632 0.00 0.00 32.71 3.27
3132 3747 0.877743 GCAGTGAAGCCAGAGGTTTC 59.122 55.000 5.78 5.78 42.10 2.78
3168 3789 0.388520 TACGCACTGCACTGCACTAG 60.389 55.000 16.94 4.68 36.94 2.57
3255 3892 2.353958 CAGATGGCCTGGCTGTGT 59.646 61.111 19.68 3.09 39.23 3.72
3347 6307 4.593864 GACGATCCAGCGCCTCCC 62.594 72.222 2.29 0.00 33.86 4.30
3370 6330 1.036707 CGTCCCCAGAATCTCTCTCC 58.963 60.000 0.00 0.00 29.07 3.71
3374 6334 1.361993 CCAGAATCTCTCTCCGCGG 59.638 63.158 22.12 22.12 29.07 6.46
3376 6336 2.028337 GAATCTCTCTCCGCGGGC 59.972 66.667 27.83 0.00 0.00 6.13
3388 6348 3.799755 GCGGGCGTCAATGTGACC 61.800 66.667 2.91 0.00 44.20 4.02
3389 6349 3.487202 CGGGCGTCAATGTGACCG 61.487 66.667 7.98 7.98 44.20 4.79
3391 6351 2.388232 GGGCGTCAATGTGACCGAC 61.388 63.158 2.91 1.05 44.20 4.79
3393 6353 3.459027 CGTCAATGTGACCGACGG 58.541 61.111 13.61 13.61 46.59 4.79
3394 6354 2.092291 CGTCAATGTGACCGACGGG 61.092 63.158 20.00 0.00 46.59 5.28
3395 6355 1.290955 GTCAATGTGACCGACGGGA 59.709 57.895 20.00 0.55 41.37 5.14
3396 6356 0.320073 GTCAATGTGACCGACGGGAA 60.320 55.000 20.00 2.28 41.37 3.97
3397 6357 0.037697 TCAATGTGACCGACGGGAAG 60.038 55.000 20.00 0.73 36.97 3.46
3398 6358 1.019278 CAATGTGACCGACGGGAAGG 61.019 60.000 20.00 0.00 36.97 3.46
3399 6359 1.189524 AATGTGACCGACGGGAAGGA 61.190 55.000 20.00 0.00 36.97 3.36
3400 6360 1.885163 ATGTGACCGACGGGAAGGAC 61.885 60.000 20.00 7.38 36.97 3.85
3473 6433 3.769965 TACGTGCGTACAATGGCG 58.230 55.556 4.09 0.00 0.00 5.69
3480 6440 2.276430 GTACAATGGCGCGCGTTC 60.276 61.111 32.35 23.28 0.00 3.95
3543 6969 1.535636 GATCACGTCGCTGCAGATCG 61.536 60.000 20.43 19.34 0.00 3.69
3567 7002 3.561213 CTGCGTGCATCTCGGCAG 61.561 66.667 10.67 10.67 45.96 4.85
3568 7003 3.995219 CTGCGTGCATCTCGGCAGA 62.995 63.158 16.57 0.00 45.96 4.26
3569 7004 3.260483 GCGTGCATCTCGGCAGAG 61.260 66.667 7.64 7.64 45.96 3.35
3570 7005 2.182791 CGTGCATCTCGGCAGAGT 59.817 61.111 13.75 0.00 45.96 3.24
3571 7006 2.163390 CGTGCATCTCGGCAGAGTG 61.163 63.158 13.75 11.82 45.96 3.51
3572 7007 1.079543 GTGCATCTCGGCAGAGTGT 60.080 57.895 13.75 1.49 45.96 3.55
3573 7008 1.079612 TGCATCTCGGCAGAGTGTG 60.080 57.895 13.75 13.95 44.65 3.82
3613 7048 0.850856 GGATTACGCGCGAGGTAAAG 59.149 55.000 39.36 4.66 33.92 1.85
3676 7112 3.677963 AGCTTTACCTGCTGCCAAT 57.322 47.368 0.00 0.00 39.56 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.183679 GCTAGAGTGGATGGGATAGGG 58.816 57.143 0.00 0.00 0.00 3.53
1 2 1.821753 CGCTAGAGTGGATGGGATAGG 59.178 57.143 0.00 0.00 0.00 2.57
12 13 2.512515 GGGCTTGCCGCTAGAGTG 60.513 66.667 5.98 0.00 39.13 3.51
13 14 3.787001 GGGGCTTGCCGCTAGAGT 61.787 66.667 19.46 0.00 39.13 3.24
14 15 4.899239 CGGGGCTTGCCGCTAGAG 62.899 72.222 22.95 6.97 39.13 2.43
169 179 2.022129 AAAACTCTCGTCGCCGCTG 61.022 57.895 0.00 0.00 0.00 5.18
193 203 1.478510 CACTTGTATCTCACCTCGCCT 59.521 52.381 0.00 0.00 0.00 5.52
211 221 1.384222 GGCGGTGGGGAAATCATCAC 61.384 60.000 0.00 0.00 0.00 3.06
213 223 2.186826 CGGCGGTGGGGAAATCATC 61.187 63.158 0.00 0.00 0.00 2.92
214 224 2.124320 CGGCGGTGGGGAAATCAT 60.124 61.111 0.00 0.00 0.00 2.45
280 332 1.154150 GCGCAAGGCAACAAGCTAG 60.154 57.895 0.30 0.00 44.79 3.42
321 373 1.270274 GCTGTGGCATGTGATGAACAA 59.730 47.619 0.00 0.00 43.61 2.83
322 374 0.883153 GCTGTGGCATGTGATGAACA 59.117 50.000 0.00 0.00 44.79 3.18
324 376 0.966875 GGGCTGTGGCATGTGATGAA 60.967 55.000 0.00 0.00 40.87 2.57
325 377 1.378911 GGGCTGTGGCATGTGATGA 60.379 57.895 0.00 0.00 40.87 2.92
326 378 1.679641 TGGGCTGTGGCATGTGATG 60.680 57.895 0.00 0.00 40.87 3.07
330 382 2.282674 CTGTGGGCTGTGGCATGT 60.283 61.111 0.00 0.00 40.87 3.21
331 383 3.066190 CCTGTGGGCTGTGGCATG 61.066 66.667 0.00 0.00 40.87 4.06
371 452 1.262640 TGGGTAGGAGAAGGGAACGC 61.263 60.000 0.00 0.00 0.00 4.84
414 495 2.094234 AGAAGGAGCGAAGAAGAGAAGC 60.094 50.000 0.00 0.00 0.00 3.86
447 528 3.426426 CCCAACGAACGAACAGTGAAAAA 60.426 43.478 0.00 0.00 0.00 1.94
452 533 1.938861 CCCCAACGAACGAACAGTG 59.061 57.895 0.14 0.00 0.00 3.66
455 536 1.890041 CAGCCCCAACGAACGAACA 60.890 57.895 0.14 0.00 0.00 3.18
570 658 2.275318 GATCAGTGAAAGGAAGCGAGG 58.725 52.381 0.00 0.00 0.00 4.63
592 680 2.300967 TGGGTGGGAGATGGCAGTC 61.301 63.158 0.00 0.00 0.00 3.51
602 690 2.002018 GAGTTTGTGGGTGGGTGGGA 62.002 60.000 0.00 0.00 0.00 4.37
666 773 2.052690 CGAGGAAGAGGAGGCCGAA 61.053 63.158 0.00 0.00 0.00 4.30
687 829 1.019805 AACCTTTTAGAGAGGCGCGC 61.020 55.000 25.94 25.94 37.84 6.86
709 851 1.067354 TCGTCGGAAGGTAAAAGAGGC 60.067 52.381 0.00 0.00 0.00 4.70
722 864 2.180432 TCTGTCTCTTTCTCGTCGGA 57.820 50.000 0.00 0.00 0.00 4.55
735 877 4.767409 GCCCCAAAAGATAAGTTTCTGTCT 59.233 41.667 0.00 0.00 0.00 3.41
758 900 1.685302 CAAAAGCATTCACCGAACCG 58.315 50.000 0.00 0.00 0.00 4.44
764 908 3.742882 GGAAGAAAGCAAAAGCATTCACC 59.257 43.478 7.95 6.95 0.00 4.02
767 911 4.874970 TGAGGAAGAAAGCAAAAGCATTC 58.125 39.130 0.00 0.00 0.00 2.67
797 941 2.798145 GCAAGTTGAAACTGAAACGGGG 60.798 50.000 7.16 0.00 39.66 5.73
835 979 1.259507 GACAGCGTGCGTAAACAAGAA 59.740 47.619 0.00 0.00 0.00 2.52
855 999 2.743718 ACCTGCGGGTGAGTTGAG 59.256 61.111 18.90 0.00 45.43 3.02
880 1031 1.781786 ACATAGGAGACGACAGCCAT 58.218 50.000 0.00 0.00 0.00 4.40
887 1038 2.826128 ACTGCAAGAACATAGGAGACGA 59.174 45.455 0.00 0.00 37.43 4.20
889 1040 3.614616 CGAACTGCAAGAACATAGGAGAC 59.385 47.826 0.00 0.00 37.43 3.36
896 1047 1.865865 ACGACGAACTGCAAGAACAT 58.134 45.000 0.00 0.00 37.43 2.71
918 1069 8.017587 AGATTCGGCAAATAAAACACAAAATC 57.982 30.769 0.00 0.00 0.00 2.17
919 1070 7.961325 AGATTCGGCAAATAAAACACAAAAT 57.039 28.000 0.00 0.00 0.00 1.82
928 1079 6.817765 AGAACTCAAGATTCGGCAAATAAA 57.182 33.333 0.00 0.00 0.00 1.40
931 1082 4.761739 TCAAGAACTCAAGATTCGGCAAAT 59.238 37.500 0.00 0.00 0.00 2.32
934 1085 3.067106 GTCAAGAACTCAAGATTCGGCA 58.933 45.455 0.00 0.00 0.00 5.69
935 1086 2.092838 CGTCAAGAACTCAAGATTCGGC 59.907 50.000 0.00 0.00 0.00 5.54
936 1087 2.092838 GCGTCAAGAACTCAAGATTCGG 59.907 50.000 0.00 0.00 0.00 4.30
937 1088 2.222376 CGCGTCAAGAACTCAAGATTCG 60.222 50.000 0.00 0.00 0.00 3.34
938 1089 2.731976 ACGCGTCAAGAACTCAAGATTC 59.268 45.455 5.58 0.00 0.00 2.52
939 1090 2.731976 GACGCGTCAAGAACTCAAGATT 59.268 45.455 33.09 0.00 0.00 2.40
940 1091 2.329379 GACGCGTCAAGAACTCAAGAT 58.671 47.619 33.09 0.00 0.00 2.40
941 1092 1.767289 GACGCGTCAAGAACTCAAGA 58.233 50.000 33.09 0.00 0.00 3.02
942 1093 0.431233 CGACGCGTCAAGAACTCAAG 59.569 55.000 35.71 13.90 0.00 3.02
943 1094 0.248743 ACGACGCGTCAAGAACTCAA 60.249 50.000 35.71 0.00 33.69 3.02
944 1095 0.248743 AACGACGCGTCAAGAACTCA 60.249 50.000 35.71 0.00 39.99 3.41
945 1096 0.430110 GAACGACGCGTCAAGAACTC 59.570 55.000 35.71 18.71 39.99 3.01
946 1097 0.030369 AGAACGACGCGTCAAGAACT 59.970 50.000 35.71 23.08 39.99 3.01
947 1098 0.850856 AAGAACGACGCGTCAAGAAC 59.149 50.000 35.71 21.45 39.99 3.01
948 1099 1.126079 GAAGAACGACGCGTCAAGAA 58.874 50.000 35.71 0.00 39.99 2.52
978 1129 0.514255 CGCGACGACCGATCCTATTA 59.486 55.000 0.00 0.00 41.76 0.98
1236 1393 2.125106 ATCAAGACGGCGGCTTCC 60.125 61.111 27.85 0.85 0.00 3.46
1237 1394 2.174319 GGATCAAGACGGCGGCTTC 61.174 63.158 27.85 15.37 0.00 3.86
1238 1395 2.125106 GGATCAAGACGGCGGCTT 60.125 61.111 24.79 24.79 0.00 4.35
1239 1396 3.376935 CTGGATCAAGACGGCGGCT 62.377 63.158 10.88 10.88 0.00 5.52
1307 1466 6.884295 TGTGTGAGAGAAAAGGAAAAGAGAAA 59.116 34.615 0.00 0.00 0.00 2.52
1352 1515 2.942376 AGCTTCAAACGTGTGTTCATCA 59.058 40.909 5.45 0.00 37.31 3.07
1385 1557 3.570125 AGATGATGCAGATGAAATGCCTG 59.430 43.478 0.00 0.00 43.18 4.85
1397 1569 7.982224 TGTTAATCTTTCAAGAGATGATGCAG 58.018 34.615 0.00 0.00 38.66 4.41
1400 1572 9.770503 CAACTGTTAATCTTTCAAGAGATGATG 57.229 33.333 0.00 0.00 38.66 3.07
1413 1585 4.751098 TCGCCGTTTACAACTGTTAATCTT 59.249 37.500 0.00 0.00 0.00 2.40
1432 1604 2.703416 TCATCTATGCATTCCATCGCC 58.297 47.619 3.54 0.00 35.34 5.54
1434 1606 6.036844 CACCTATTCATCTATGCATTCCATCG 59.963 42.308 3.54 0.00 35.34 3.84
1435 1607 7.108194 TCACCTATTCATCTATGCATTCCATC 58.892 38.462 3.54 0.00 35.34 3.51
1499 1671 2.551459 GCACAGTGAAGTCAAATCTGCT 59.449 45.455 4.15 0.00 0.00 4.24
1530 1702 1.033746 AAGGCAGCAACCATCGGATG 61.034 55.000 11.07 11.07 0.00 3.51
1531 1703 0.749454 GAAGGCAGCAACCATCGGAT 60.749 55.000 0.00 0.00 0.00 4.18
1532 1704 1.377202 GAAGGCAGCAACCATCGGA 60.377 57.895 0.00 0.00 0.00 4.55
1533 1705 1.372087 GAGAAGGCAGCAACCATCGG 61.372 60.000 0.00 0.00 32.62 4.18
1608 1780 7.178274 TGCAGAACTGTGGGAATAAACATAAAT 59.822 33.333 3.77 0.00 0.00 1.40
1622 1794 1.591594 ACGACGTGCAGAACTGTGG 60.592 57.895 0.00 0.00 0.00 4.17
1662 1834 6.347881 GTTTAATAAGTGCGATGATGACGAG 58.652 40.000 0.00 0.00 0.00 4.18
1711 1883 7.201232 CGCGGTAGTACAAATTTCAAATCTTTG 60.201 37.037 0.00 0.00 39.48 2.77
1731 1917 3.255725 CATTTCTTTAGTGGTCGCGGTA 58.744 45.455 6.13 0.00 0.00 4.02
1732 1918 2.073816 CATTTCTTTAGTGGTCGCGGT 58.926 47.619 6.13 0.00 0.00 5.68
1733 1919 2.073816 ACATTTCTTTAGTGGTCGCGG 58.926 47.619 6.13 0.00 0.00 6.46
1734 1920 2.478894 ACACATTTCTTTAGTGGTCGCG 59.521 45.455 0.00 0.00 37.58 5.87
1735 1921 3.496884 TGACACATTTCTTTAGTGGTCGC 59.503 43.478 0.00 0.00 37.58 5.19
1736 1922 5.666969 TTGACACATTTCTTTAGTGGTCG 57.333 39.130 0.00 0.00 37.58 4.79
1737 1923 7.259290 TCTTTGACACATTTCTTTAGTGGTC 57.741 36.000 0.00 0.00 37.58 4.02
1738 1924 7.823745 ATCTTTGACACATTTCTTTAGTGGT 57.176 32.000 0.00 0.00 37.58 4.16
1739 1925 8.971321 CAAATCTTTGACACATTTCTTTAGTGG 58.029 33.333 0.00 0.00 40.55 4.00
1740 1926 9.734620 TCAAATCTTTGACACATTTCTTTAGTG 57.265 29.630 1.28 0.00 41.88 2.74
1753 1939 9.959749 GGTAGTACAAATTTCAAATCTTTGACA 57.040 29.630 4.89 0.00 45.99 3.58
1754 1940 9.113876 CGGTAGTACAAATTTCAAATCTTTGAC 57.886 33.333 4.89 0.00 45.99 3.18
1755 1941 7.806014 GCGGTAGTACAAATTTCAAATCTTTGA 59.194 33.333 2.06 1.28 44.78 2.69
1756 1942 7.201232 CGCGGTAGTACAAATTTCAAATCTTTG 60.201 37.037 0.00 0.00 39.48 2.77
1757 1943 6.799925 CGCGGTAGTACAAATTTCAAATCTTT 59.200 34.615 0.00 0.00 0.00 2.52
1758 1944 6.148150 TCGCGGTAGTACAAATTTCAAATCTT 59.852 34.615 6.13 0.00 0.00 2.40
1759 1945 5.640357 TCGCGGTAGTACAAATTTCAAATCT 59.360 36.000 6.13 0.00 0.00 2.40
1760 1946 5.731263 GTCGCGGTAGTACAAATTTCAAATC 59.269 40.000 6.13 0.00 0.00 2.17
1761 1947 5.391203 GGTCGCGGTAGTACAAATTTCAAAT 60.391 40.000 6.13 0.00 0.00 2.32
1762 1948 4.083908 GGTCGCGGTAGTACAAATTTCAAA 60.084 41.667 6.13 0.00 0.00 2.69
1763 1949 3.432933 GGTCGCGGTAGTACAAATTTCAA 59.567 43.478 6.13 0.00 0.00 2.69
1764 1950 2.995258 GGTCGCGGTAGTACAAATTTCA 59.005 45.455 6.13 0.00 0.00 2.69
1765 1951 2.028404 CGGTCGCGGTAGTACAAATTTC 59.972 50.000 6.13 0.00 0.00 2.17
1766 1952 1.994779 CGGTCGCGGTAGTACAAATTT 59.005 47.619 6.13 0.00 0.00 1.82
1767 1953 1.632422 CGGTCGCGGTAGTACAAATT 58.368 50.000 6.13 0.00 0.00 1.82
1768 1954 0.179129 CCGGTCGCGGTAGTACAAAT 60.179 55.000 6.13 0.00 0.00 2.32
1769 1955 1.212490 CCGGTCGCGGTAGTACAAA 59.788 57.895 6.13 0.00 0.00 2.83
1770 1956 2.876955 CCGGTCGCGGTAGTACAA 59.123 61.111 6.13 0.00 0.00 2.41
1771 1957 3.814268 GCCGGTCGCGGTAGTACA 61.814 66.667 6.13 0.00 0.00 2.90
1772 1958 3.746409 CTGCCGGTCGCGGTAGTAC 62.746 68.421 6.13 0.00 42.08 2.73
1773 1959 3.511595 CTGCCGGTCGCGGTAGTA 61.512 66.667 6.13 0.00 42.08 1.82
1992 2183 2.283617 CCAGAAGAAGAATCACGATGCG 59.716 50.000 0.00 0.00 0.00 4.73
1999 2190 5.248640 GGTTCATCACCAGAAGAAGAATCA 58.751 41.667 0.00 0.00 46.42 2.57
2012 2203 0.802494 ACGAAATGCGGTTCATCACC 59.198 50.000 0.00 0.00 46.49 4.02
2013 2204 1.732259 AGACGAAATGCGGTTCATCAC 59.268 47.619 0.00 0.00 46.49 3.06
2035 2226 9.377383 CAAATTTTCAGCTTCATTTTCATTCAC 57.623 29.630 0.00 0.00 0.00 3.18
2036 2227 9.327628 TCAAATTTTCAGCTTCATTTTCATTCA 57.672 25.926 0.00 0.00 0.00 2.57
2037 2228 9.590088 GTCAAATTTTCAGCTTCATTTTCATTC 57.410 29.630 0.00 0.00 0.00 2.67
2038 2229 8.277713 CGTCAAATTTTCAGCTTCATTTTCATT 58.722 29.630 0.00 0.00 0.00 2.57
2039 2230 7.569957 GCGTCAAATTTTCAGCTTCATTTTCAT 60.570 33.333 0.00 0.00 0.00 2.57
2069 2260 4.180057 ACGCAACAACAACAAACAATCAT 58.820 34.783 0.00 0.00 0.00 2.45
2071 2262 4.206200 CCTACGCAACAACAACAAACAATC 59.794 41.667 0.00 0.00 0.00 2.67
2072 2263 4.109050 CCTACGCAACAACAACAAACAAT 58.891 39.130 0.00 0.00 0.00 2.71
2074 2265 2.747989 TCCTACGCAACAACAACAAACA 59.252 40.909 0.00 0.00 0.00 2.83
2075 2266 3.359654 CTCCTACGCAACAACAACAAAC 58.640 45.455 0.00 0.00 0.00 2.93
2076 2267 2.223386 GCTCCTACGCAACAACAACAAA 60.223 45.455 0.00 0.00 0.00 2.83
2077 2268 1.332375 GCTCCTACGCAACAACAACAA 59.668 47.619 0.00 0.00 0.00 2.83
2078 2269 0.941542 GCTCCTACGCAACAACAACA 59.058 50.000 0.00 0.00 0.00 3.33
2079 2270 0.110823 CGCTCCTACGCAACAACAAC 60.111 55.000 0.00 0.00 0.00 3.32
2102 2293 3.857038 ACCACAGGCACCGACGTT 61.857 61.111 0.00 0.00 0.00 3.99
2694 2903 2.733593 GATTAGTAGCGCGCCGGG 60.734 66.667 30.33 0.00 0.00 5.73
2705 2914 1.679032 GGCTTTCACGCCCTGATTAGT 60.679 52.381 0.00 0.00 44.41 2.24
2718 2927 3.331150 ACGACGATGTTAATGGCTTTCA 58.669 40.909 0.00 0.00 0.00 2.69
2723 2932 1.517276 CGAGACGACGATGTTAATGGC 59.483 52.381 0.00 0.00 35.09 4.40
2724 2933 2.117137 CCGAGACGACGATGTTAATGG 58.883 52.381 0.00 0.00 35.09 3.16
2725 2934 2.793933 ACCGAGACGACGATGTTAATG 58.206 47.619 0.00 0.00 35.09 1.90
2726 2935 4.825546 ATACCGAGACGACGATGTTAAT 57.174 40.909 0.00 0.00 35.09 1.40
2727 2936 5.929697 ATATACCGAGACGACGATGTTAA 57.070 39.130 0.00 0.00 35.09 2.01
2728 2937 6.159293 ACTATATACCGAGACGACGATGTTA 58.841 40.000 0.00 0.00 35.09 2.41
2729 2938 4.993584 ACTATATACCGAGACGACGATGTT 59.006 41.667 0.00 0.00 35.09 2.71
2730 2939 4.564041 ACTATATACCGAGACGACGATGT 58.436 43.478 0.00 0.00 35.09 3.06
2731 2940 5.527511 AACTATATACCGAGACGACGATG 57.472 43.478 0.00 0.00 35.09 3.84
2733 2942 5.773575 ACTAACTATATACCGAGACGACGA 58.226 41.667 0.00 0.00 35.09 4.20
2735 2944 7.316640 TCCTACTAACTATATACCGAGACGAC 58.683 42.308 0.00 0.00 0.00 4.34
2789 3001 3.125316 GTGCCATCAACTACAACTACTGC 59.875 47.826 0.00 0.00 0.00 4.40
2790 3002 3.367932 CGTGCCATCAACTACAACTACTG 59.632 47.826 0.00 0.00 0.00 2.74
2798 3013 0.953471 TGTGCCGTGCCATCAACTAC 60.953 55.000 0.00 0.00 0.00 2.73
2813 3028 2.216046 ACCATGACGATGATGATGTGC 58.784 47.619 0.00 0.00 0.00 4.57
2829 3044 2.833794 CGGTTAACATCGGATGACCAT 58.166 47.619 23.98 9.61 35.59 3.55
2834 3049 1.593196 ATGGCGGTTAACATCGGATG 58.407 50.000 16.20 16.20 0.00 3.51
2835 3050 1.946768 CAATGGCGGTTAACATCGGAT 59.053 47.619 8.10 0.00 0.00 4.18
2838 3053 2.286184 GCTACAATGGCGGTTAACATCG 60.286 50.000 8.10 3.90 0.00 3.84
2839 3054 2.680841 TGCTACAATGGCGGTTAACATC 59.319 45.455 8.10 0.00 0.00 3.06
2840 3055 2.682856 CTGCTACAATGGCGGTTAACAT 59.317 45.455 8.10 0.00 0.00 2.71
2841 3056 2.080693 CTGCTACAATGGCGGTTAACA 58.919 47.619 8.10 0.00 0.00 2.41
2843 3058 1.091537 GCTGCTACAATGGCGGTTAA 58.908 50.000 0.00 0.00 38.25 2.01
2877 3113 1.478837 CCATTCTCTCTGGCATGCCAT 60.479 52.381 38.47 20.23 46.15 4.40
2878 3114 0.106868 CCATTCTCTCTGGCATGCCA 60.107 55.000 36.26 36.26 45.02 4.92
2921 3161 0.618458 TTTTCCCCCAGATGGTCTCG 59.382 55.000 0.00 0.00 0.00 4.04
2924 3164 0.326927 TCGTTTTCCCCCAGATGGTC 59.673 55.000 0.00 0.00 0.00 4.02
2930 3170 2.361230 GGCCTCGTTTTCCCCCAG 60.361 66.667 0.00 0.00 0.00 4.45
2972 3212 2.283532 AGAGCAGAGCACGAGGGT 60.284 61.111 0.00 0.00 0.00 4.34
2973 3213 2.183811 CAGAGCAGAGCACGAGGG 59.816 66.667 0.00 0.00 0.00 4.30
2977 3217 1.806351 CAGAGCAGAGCAGAGCACG 60.806 63.158 0.00 0.00 0.00 5.34
2978 3218 0.737019 GACAGAGCAGAGCAGAGCAC 60.737 60.000 0.00 0.00 0.00 4.40
2979 3219 1.590665 GACAGAGCAGAGCAGAGCA 59.409 57.895 0.00 0.00 0.00 4.26
2980 3220 1.153588 GGACAGAGCAGAGCAGAGC 60.154 63.158 0.00 0.00 0.00 4.09
2983 3223 2.183811 CGGGACAGAGCAGAGCAG 59.816 66.667 0.00 0.00 0.00 4.24
3005 3245 0.829990 TTGATACATCGAGGCTGGCA 59.170 50.000 3.38 0.00 0.00 4.92
3006 3246 1.802960 CATTGATACATCGAGGCTGGC 59.197 52.381 0.00 0.00 0.00 4.85
3007 3247 2.224378 ACCATTGATACATCGAGGCTGG 60.224 50.000 0.00 0.00 0.00 4.85
3008 3248 2.804527 CACCATTGATACATCGAGGCTG 59.195 50.000 0.00 0.00 0.00 4.85
3010 3250 2.802816 GTCACCATTGATACATCGAGGC 59.197 50.000 0.00 0.00 33.11 4.70
3011 3251 3.804325 GTGTCACCATTGATACATCGAGG 59.196 47.826 0.00 0.00 42.08 4.63
3013 3253 3.736740 CGGTGTCACCATTGATACATCGA 60.737 47.826 21.91 0.00 43.79 3.59
3014 3254 2.539688 CGGTGTCACCATTGATACATCG 59.460 50.000 21.91 0.00 43.79 3.84
3015 3255 3.555956 GTCGGTGTCACCATTGATACATC 59.444 47.826 21.91 0.00 43.79 3.06
3016 3256 3.531538 GTCGGTGTCACCATTGATACAT 58.468 45.455 21.91 0.00 43.79 2.29
3017 3257 2.672760 CGTCGGTGTCACCATTGATACA 60.673 50.000 21.91 0.00 43.79 2.29
3018 3258 1.924524 CGTCGGTGTCACCATTGATAC 59.075 52.381 21.91 8.30 41.84 2.24
3019 3259 1.546923 ACGTCGGTGTCACCATTGATA 59.453 47.619 21.91 0.00 38.47 2.15
3022 3262 1.289109 GGACGTCGGTGTCACCATTG 61.289 60.000 21.91 12.07 38.47 2.82
3024 3264 2.654877 GGACGTCGGTGTCACCAT 59.345 61.111 21.91 3.87 38.47 3.55
3051 3618 1.073284 TGCACTACCCCCTCTGTTTTC 59.927 52.381 0.00 0.00 0.00 2.29
3068 3635 1.612462 CCAGCTTCCATGTCTTCTGCA 60.612 52.381 0.00 0.00 0.00 4.41
3069 3636 1.093159 CCAGCTTCCATGTCTTCTGC 58.907 55.000 0.00 0.00 0.00 4.26
3070 3637 1.280133 TCCCAGCTTCCATGTCTTCTG 59.720 52.381 0.00 0.00 0.00 3.02
3071 3638 1.280421 GTCCCAGCTTCCATGTCTTCT 59.720 52.381 0.00 0.00 0.00 2.85
3076 3652 0.036010 CTTCGTCCCAGCTTCCATGT 60.036 55.000 0.00 0.00 0.00 3.21
3125 3740 3.445805 TCCAAACAACCACAAGAAACCTC 59.554 43.478 0.00 0.00 0.00 3.85
3130 3745 3.623960 CGTACTCCAAACAACCACAAGAA 59.376 43.478 0.00 0.00 0.00 2.52
3131 3746 3.199677 CGTACTCCAAACAACCACAAGA 58.800 45.455 0.00 0.00 0.00 3.02
3132 3747 2.286772 GCGTACTCCAAACAACCACAAG 60.287 50.000 0.00 0.00 0.00 3.16
3168 3789 3.159984 CGGTGCGCTTCAGTTCTC 58.840 61.111 9.73 0.00 0.00 2.87
3219 3856 3.197766 TCTGGTACTACTGCCATTTCCAG 59.802 47.826 0.00 0.00 41.47 3.86
3255 3892 1.073763 CACCACCTCAACATCAAGGGA 59.926 52.381 0.00 0.00 36.95 4.20
3343 6303 0.912486 ATTCTGGGGACGAAAGGGAG 59.088 55.000 0.00 0.00 0.00 4.30
3347 6307 2.763448 AGAGAGATTCTGGGGACGAAAG 59.237 50.000 0.00 0.00 33.93 2.62
3356 6316 1.361993 CCGCGGAGAGAGATTCTGG 59.638 63.158 24.07 0.00 35.87 3.86
3370 6330 4.147322 GTCACATTGACGCCCGCG 62.147 66.667 7.69 7.69 37.67 6.46
3379 6339 1.019278 CCTTCCCGTCGGTCACATTG 61.019 60.000 11.06 0.00 0.00 2.82
3388 6348 0.524816 CGTATGTGTCCTTCCCGTCG 60.525 60.000 0.00 0.00 0.00 5.12
3389 6349 0.179119 CCGTATGTGTCCTTCCCGTC 60.179 60.000 0.00 0.00 0.00 4.79
3391 6351 0.459585 CACCGTATGTGTCCTTCCCG 60.460 60.000 0.00 0.00 40.26 5.14
3392 6352 3.453559 CACCGTATGTGTCCTTCCC 57.546 57.895 0.00 0.00 40.26 3.97
3424 6384 1.153369 GCAAGCTACGATGCTGGGA 60.153 57.895 7.57 0.00 43.24 4.37
3505 6465 6.514048 CGTGATCAGTGATCTACAGATTGCTA 60.514 42.308 28.73 6.06 39.56 3.49
3509 6469 5.504830 CGACGTGATCAGTGATCTACAGATT 60.505 44.000 28.73 12.46 39.56 2.40
3512 6472 3.612539 CGACGTGATCAGTGATCTACAG 58.387 50.000 28.73 21.05 39.56 2.74
3522 6948 0.527169 ATCTGCAGCGACGTGATCAG 60.527 55.000 9.47 0.00 0.00 2.90
3563 6998 0.321122 CTGAACCTCCACACTCTGCC 60.321 60.000 0.00 0.00 0.00 4.85
3564 6999 0.681733 TCTGAACCTCCACACTCTGC 59.318 55.000 0.00 0.00 0.00 4.26
3565 7000 3.692257 AATCTGAACCTCCACACTCTG 57.308 47.619 0.00 0.00 0.00 3.35
3566 7001 4.160329 TGTAATCTGAACCTCCACACTCT 58.840 43.478 0.00 0.00 0.00 3.24
3567 7002 4.499183 CTGTAATCTGAACCTCCACACTC 58.501 47.826 0.00 0.00 0.00 3.51
3568 7003 3.307059 GCTGTAATCTGAACCTCCACACT 60.307 47.826 0.00 0.00 0.00 3.55
3569 7004 3.003480 GCTGTAATCTGAACCTCCACAC 58.997 50.000 0.00 0.00 0.00 3.82
3570 7005 2.353704 CGCTGTAATCTGAACCTCCACA 60.354 50.000 0.00 0.00 0.00 4.17
3571 7006 2.271800 CGCTGTAATCTGAACCTCCAC 58.728 52.381 0.00 0.00 0.00 4.02
3572 7007 1.405526 GCGCTGTAATCTGAACCTCCA 60.406 52.381 0.00 0.00 0.00 3.86
3573 7008 1.291132 GCGCTGTAATCTGAACCTCC 58.709 55.000 0.00 0.00 0.00 4.30



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

AutoCloner maintained by Alex Coulton.