Multiple sequence alignment - TraesCS3D01G399300

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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 TraesCS3D01G399300 chr3D 100.000 3965 0 0 1 3965 514266881 514270845 0.000000e+00 7323.0
1 TraesCS3D01G399300 chr3A 85.761 1524 95 44 396 1857 649025113 649026576 0.000000e+00 1500.0
2 TraesCS3D01G399300 chr3A 91.332 946 54 11 2795 3740 649027532 649028449 0.000000e+00 1267.0
3 TraesCS3D01G399300 chr3A 92.571 848 52 8 1877 2714 649026670 649027516 0.000000e+00 1206.0
4 TraesCS3D01G399300 chr3A 96.543 376 9 3 1 373 649024587 649024961 1.570000e-173 619.0
5 TraesCS3D01G399300 chr3A 85.294 204 15 11 3772 3965 649028651 649028849 3.130000e-46 196.0
6 TraesCS3D01G399300 chr3B 86.438 1224 68 28 682 1857 676615283 676616456 0.000000e+00 1251.0
7 TraesCS3D01G399300 chr3B 92.166 868 63 4 1877 2739 676616523 676617390 0.000000e+00 1221.0
8 TraesCS3D01G399300 chr3B 89.227 854 58 15 2795 3640 676617389 676618216 0.000000e+00 1037.0
9 TraesCS3D01G399300 chr3B 90.122 739 27 17 1 698 676614537 676615270 0.000000e+00 918.0
10 TraesCS3D01G399300 chr3B 87.629 97 6 6 3873 3963 676624152 676624248 1.510000e-19 108.0
11 TraesCS3D01G399300 chr3B 85.455 55 6 2 3772 3825 711737988 711738041 5.540000e-04 56.5
12 TraesCS3D01G399300 chr2B 94.915 59 2 1 572 630 134045504 134045447 1.520000e-14 91.6
13 TraesCS3D01G399300 chr2B 96.000 50 2 0 572 621 765397978 765398027 9.130000e-12 82.4
14 TraesCS3D01G399300 chr2D 93.220 59 3 1 572 630 82181972 82181915 7.060000e-13 86.1
15 TraesCS3D01G399300 chr7B 97.872 47 1 0 572 618 255075448 255075402 9.130000e-12 82.4
16 TraesCS3D01G399300 chr7B 100.000 28 0 0 3772 3799 116072653 116072626 7.000000e-03 52.8
17 TraesCS3D01G399300 chr7A 97.872 47 1 0 572 618 632520596 632520642 9.130000e-12 82.4
18 TraesCS3D01G399300 chr4B 97.872 47 1 0 572 618 53590605 53590651 9.130000e-12 82.4
19 TraesCS3D01G399300 chr2A 91.525 59 3 2 572 630 82346278 82346222 3.280000e-11 80.5
20 TraesCS3D01G399300 chr1B 97.778 45 1 0 572 616 356207722 356207766 1.180000e-10 78.7
21 TraesCS3D01G399300 chr6B 85.455 55 6 2 3772 3825 720149085 720149138 5.540000e-04 56.5


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 TraesCS3D01G399300 chr3D 514266881 514270845 3964 False 7323.00 7323 100.00000 1 3965 1 chr3D.!!$F1 3964
1 TraesCS3D01G399300 chr3A 649024587 649028849 4262 False 957.60 1500 90.30020 1 3965 5 chr3A.!!$F1 3964
2 TraesCS3D01G399300 chr3B 676614537 676618216 3679 False 1106.75 1251 89.48825 1 3640 4 chr3B.!!$F3 3639

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
734 945 0.475906 AGTCTCAGCTGGGCAGTTTT 59.524 50.0 15.13 0.0 0.0 2.43 F
1202 1435 0.394216 TGGATTGACTTGGCGATGGG 60.394 55.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1545 1796 0.531090 GCACACACACTTCCACGGTA 60.531 55.0 0.0 0.0 0.00 4.02 R
3150 3497 1.156034 CCGTCACATGATGCTCGCAT 61.156 55.0 3.7 3.7 39.69 4.73 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
34 35 9.866798 AAAATTGAAATGGAGAAAATAGCTCTC 57.133 29.630 0.00 0.00 38.92 3.20
65 75 1.422531 CCTCCTCTAATGCCTGCTCT 58.577 55.000 0.00 0.00 0.00 4.09
357 370 9.713740 CTATAAGCAACATGTTTCTCATTCTTC 57.286 33.333 11.24 0.00 34.09 2.87
359 372 4.219288 AGCAACATGTTTCTCATTCTTCCC 59.781 41.667 8.77 0.00 34.09 3.97
394 407 2.280552 CCCGGCGGGCTAGCTTATA 61.281 63.158 34.87 0.00 35.35 0.98
537 684 4.820897 TGTTTGTCCTGCAGTATCTACAG 58.179 43.478 13.81 0.00 0.00 2.74
543 690 3.617540 CTGCAGTATCTACAGGACTCG 57.382 52.381 5.25 0.00 0.00 4.18
556 725 4.177026 ACAGGACTCGAATGATTTCTTCG 58.823 43.478 0.00 0.00 45.16 3.79
617 793 4.130118 CAAGAATTATGGAACGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
621 797 1.335132 TATGGAACGGAGGGAGCACC 61.335 60.000 0.00 0.00 40.67 5.01
685 862 5.136828 TCTTCAGGTCAATGGTGCTAAAAA 58.863 37.500 0.00 0.00 0.00 1.94
704 911 1.165907 AATGGCTCACACCACACACG 61.166 55.000 0.00 0.00 44.17 4.49
734 945 0.475906 AGTCTCAGCTGGGCAGTTTT 59.524 50.000 15.13 0.00 0.00 2.43
833 1046 4.201679 CGGCGCCTACACGGATCA 62.202 66.667 26.68 0.00 33.16 2.92
890 1103 1.285950 CGTTCAGCCGTCACTCTCA 59.714 57.895 0.00 0.00 0.00 3.27
893 1106 0.532573 TTCAGCCGTCACTCTCATCC 59.467 55.000 0.00 0.00 0.00 3.51
902 1116 2.844839 CTCTCATCCCCGTCCCCC 60.845 72.222 0.00 0.00 0.00 5.40
1005 1223 2.130426 GCGAGGGAGAGAGATGGCA 61.130 63.158 0.00 0.00 0.00 4.92
1159 1392 2.757314 GGTACGTACCTAGGCTTGTTCT 59.243 50.000 32.93 0.00 43.10 3.01
1178 1411 2.756283 CCGCCTCCTCTCTCCGTT 60.756 66.667 0.00 0.00 0.00 4.44
1191 1424 1.275291 TCTCCGTTGACCTGGATTGAC 59.725 52.381 0.00 0.00 32.83 3.18
1193 1426 1.697432 TCCGTTGACCTGGATTGACTT 59.303 47.619 0.00 0.00 0.00 3.01
1202 1435 0.394216 TGGATTGACTTGGCGATGGG 60.394 55.000 0.00 0.00 0.00 4.00
1210 1443 3.726144 TGGCGATGGGCATGGACA 61.726 61.111 0.00 0.00 44.78 4.02
1211 1444 3.211963 GGCGATGGGCATGGACAC 61.212 66.667 0.00 0.00 46.16 3.67
1212 1445 2.438254 GCGATGGGCATGGACACA 60.438 61.111 0.00 0.00 42.87 3.72
1213 1446 1.825191 GCGATGGGCATGGACACAT 60.825 57.895 0.00 0.00 42.87 3.21
1230 1463 2.268076 ATGTTTGCCTGCCACCGAC 61.268 57.895 0.00 0.00 0.00 4.79
1256 1491 1.883275 TGCCCGTGTTTAGTTTGGATG 59.117 47.619 0.00 0.00 0.00 3.51
1259 1494 3.243602 GCCCGTGTTTAGTTTGGATGTTT 60.244 43.478 0.00 0.00 0.00 2.83
1260 1495 4.295051 CCCGTGTTTAGTTTGGATGTTTG 58.705 43.478 0.00 0.00 0.00 2.93
1490 1741 6.306199 TGTATGGAATATTGGGTTCTGGATG 58.694 40.000 0.00 0.00 0.00 3.51
1504 1755 2.242965 TCTGGATGATTCCCATGCTGTT 59.757 45.455 0.00 0.00 43.16 3.16
1530 1781 6.713762 ATTCCTGTCAAAATCTGTGTTCAA 57.286 33.333 0.00 0.00 0.00 2.69
1539 1790 3.576078 ATCTGTGTTCAACCCACTTCA 57.424 42.857 0.00 0.00 33.92 3.02
1542 1793 4.641396 TCTGTGTTCAACCCACTTCATAG 58.359 43.478 0.00 0.00 33.92 2.23
1545 1796 5.630121 TGTGTTCAACCCACTTCATAGATT 58.370 37.500 0.00 0.00 33.92 2.40
1565 1818 2.542907 CCGTGGAAGTGTGTGTGCC 61.543 63.158 0.00 0.00 0.00 5.01
1585 1838 0.108585 ACCGTGCAATGCTATAGGGG 59.891 55.000 6.82 1.30 0.00 4.79
1622 1875 2.985282 TTCCCAGCCGCAGCAAAG 60.985 61.111 0.00 0.00 43.56 2.77
1623 1876 3.790416 TTCCCAGCCGCAGCAAAGT 62.790 57.895 0.00 0.00 43.56 2.66
1626 1879 2.050714 CAGCCGCAGCAAAGTGTG 60.051 61.111 0.00 0.00 43.56 3.82
1630 1883 4.853507 CGCAGCAAAGTGTGGATG 57.146 55.556 0.00 0.00 0.00 3.51
1631 1884 2.246841 CGCAGCAAAGTGTGGATGA 58.753 52.632 0.00 0.00 0.00 2.92
1632 1885 0.167470 CGCAGCAAAGTGTGGATGAG 59.833 55.000 0.00 0.00 0.00 2.90
1633 1886 1.242076 GCAGCAAAGTGTGGATGAGT 58.758 50.000 0.00 0.00 0.00 3.41
1634 1887 2.426522 GCAGCAAAGTGTGGATGAGTA 58.573 47.619 0.00 0.00 0.00 2.59
1635 1888 2.813754 GCAGCAAAGTGTGGATGAGTAA 59.186 45.455 0.00 0.00 0.00 2.24
1636 1889 3.441572 GCAGCAAAGTGTGGATGAGTAAT 59.558 43.478 0.00 0.00 0.00 1.89
1637 1890 4.082571 GCAGCAAAGTGTGGATGAGTAATT 60.083 41.667 0.00 0.00 0.00 1.40
1638 1891 5.123820 GCAGCAAAGTGTGGATGAGTAATTA 59.876 40.000 0.00 0.00 0.00 1.40
1639 1892 6.183360 GCAGCAAAGTGTGGATGAGTAATTAT 60.183 38.462 0.00 0.00 0.00 1.28
1640 1893 7.629222 GCAGCAAAGTGTGGATGAGTAATTATT 60.629 37.037 0.00 0.00 0.00 1.40
1641 1894 8.246180 CAGCAAAGTGTGGATGAGTAATTATTT 58.754 33.333 0.00 0.00 0.00 1.40
1642 1895 8.246180 AGCAAAGTGTGGATGAGTAATTATTTG 58.754 33.333 0.00 0.00 0.00 2.32
1643 1896 7.009540 GCAAAGTGTGGATGAGTAATTATTTGC 59.990 37.037 8.25 8.25 40.27 3.68
1644 1897 7.944729 AAGTGTGGATGAGTAATTATTTGCT 57.055 32.000 0.00 0.00 0.00 3.91
1645 1898 7.944729 AGTGTGGATGAGTAATTATTTGCTT 57.055 32.000 0.00 0.00 0.00 3.91
1646 1899 7.765307 AGTGTGGATGAGTAATTATTTGCTTG 58.235 34.615 0.00 0.00 0.00 4.01
1647 1900 6.974622 GTGTGGATGAGTAATTATTTGCTTGG 59.025 38.462 0.00 0.00 0.00 3.61
1648 1901 6.096705 TGTGGATGAGTAATTATTTGCTTGGG 59.903 38.462 0.00 0.00 0.00 4.12
1649 1902 6.321181 GTGGATGAGTAATTATTTGCTTGGGA 59.679 38.462 0.00 0.00 0.00 4.37
1650 1903 7.014615 GTGGATGAGTAATTATTTGCTTGGGAT 59.985 37.037 0.00 0.00 0.00 3.85
1651 1904 7.564660 TGGATGAGTAATTATTTGCTTGGGATT 59.435 33.333 0.00 0.00 0.00 3.01
1668 1921 4.192317 GGGATTGTGTGGATGACTAGTTC 58.808 47.826 0.00 0.00 0.00 3.01
1724 1980 4.557296 CGCAATACCTTTATGGAATGCCTG 60.557 45.833 0.00 0.00 38.20 4.85
1732 1988 7.227156 ACCTTTATGGAATGCCTGAATAGTAG 58.773 38.462 0.00 0.00 39.71 2.57
1734 1990 7.387265 TTTATGGAATGCCTGAATAGTAGGA 57.613 36.000 0.00 0.00 37.52 2.94
1736 1992 4.298626 TGGAATGCCTGAATAGTAGGAGT 58.701 43.478 0.00 0.00 37.52 3.85
1737 1993 5.464069 TGGAATGCCTGAATAGTAGGAGTA 58.536 41.667 0.00 0.00 37.52 2.59
1796 2053 4.460948 AGGCTTCCTGCAAATATTTGTG 57.539 40.909 25.15 18.52 45.15 3.33
1802 2059 5.212532 TCCTGCAAATATTTGTGCACTTT 57.787 34.783 25.15 6.80 45.52 2.66
1803 2060 4.989797 TCCTGCAAATATTTGTGCACTTTG 59.010 37.500 25.15 19.14 45.52 2.77
1826 2083 9.671279 TTTGAATGTCATTCTGAAGCTTATCTA 57.329 29.630 22.89 0.00 39.96 1.98
1835 2092 9.558396 CATTCTGAAGCTTATCTAAAGAGGAAT 57.442 33.333 0.00 0.00 0.00 3.01
1842 2099 7.115414 AGCTTATCTAAAGAGGAATTTGCAGT 58.885 34.615 0.00 0.00 0.00 4.40
1857 2114 9.173939 GGAATTTGCAGTTAATATTCGAGAATG 57.826 33.333 8.46 0.00 32.50 2.67
1858 2115 9.722056 GAATTTGCAGTTAATATTCGAGAATGT 57.278 29.630 8.46 0.00 32.50 2.71
1861 2118 7.015226 TGCAGTTAATATTCGAGAATGTTGG 57.985 36.000 15.08 6.14 34.63 3.77
1862 2119 6.597672 TGCAGTTAATATTCGAGAATGTTGGT 59.402 34.615 15.08 1.09 34.63 3.67
1864 2121 7.201609 GCAGTTAATATTCGAGAATGTTGGTGA 60.202 37.037 15.08 0.00 34.63 4.02
1865 2122 8.331022 CAGTTAATATTCGAGAATGTTGGTGAG 58.669 37.037 15.08 2.13 34.63 3.51
1866 2123 5.741388 AATATTCGAGAATGTTGGTGAGC 57.259 39.130 8.46 0.00 32.14 4.26
1867 2124 1.808411 TTCGAGAATGTTGGTGAGCC 58.192 50.000 0.00 0.00 0.00 4.70
1868 2125 0.684535 TCGAGAATGTTGGTGAGCCA 59.315 50.000 0.00 0.00 44.38 4.75
1901 2232 3.093057 AGCTCAGTAGACCACTCGAAAT 58.907 45.455 0.00 0.00 34.26 2.17
1915 2247 2.362397 CTCGAAATGGAGGCAGCTACTA 59.638 50.000 0.00 0.00 0.00 1.82
1983 2316 4.464244 ACTGGTGATCGAGATTTCTCTGAA 59.536 41.667 6.06 0.00 40.75 3.02
2064 2397 5.714047 TGAAGTCATCTGCGCTATATTAGG 58.286 41.667 9.73 0.00 0.00 2.69
2279 2616 6.043938 TGGGGAGAACGAATTATTTAGCCTAT 59.956 38.462 0.00 0.00 0.00 2.57
2300 2637 3.649073 TGACTCTGAACACCATAACACG 58.351 45.455 0.00 0.00 0.00 4.49
2324 2661 4.005650 CTGGTTCTGCATATGTTGACTGT 58.994 43.478 4.29 0.00 0.00 3.55
2437 2774 1.686325 TACAGCTGGGATTCGGAGCC 61.686 60.000 19.93 0.00 32.86 4.70
2485 2822 4.501743 GGTTTCGGCTATGGTTTTGGAAAA 60.502 41.667 0.00 0.00 0.00 2.29
2518 2855 3.441163 TGACGAGAACGGGAAATATTCG 58.559 45.455 0.00 0.00 44.46 3.34
2582 2919 5.378292 TGAGTAAGCAGTAACTCACTCTG 57.622 43.478 1.19 0.00 45.40 3.35
2606 2944 6.265196 TGAGCTTTGGACTATCACAAAAATGT 59.735 34.615 0.00 0.00 36.29 2.71
2618 2957 2.971330 ACAAAAATGTCTCCATTGGGCA 59.029 40.909 2.09 0.63 40.42 5.36
2619 2958 3.244181 ACAAAAATGTCTCCATTGGGCAC 60.244 43.478 2.09 0.54 40.42 5.01
2634 2973 2.183811 CACCTCCTGCTGCTCGAG 59.816 66.667 8.45 8.45 0.00 4.04
2636 2975 2.347322 ACCTCCTGCTGCTCGAGAC 61.347 63.158 18.75 8.32 0.00 3.36
2641 2980 1.137614 CTGCTGCTCGAGACGCTTA 59.862 57.895 18.75 1.61 0.00 3.09
2648 2987 1.269309 GCTCGAGACGCTTACATCCAT 60.269 52.381 18.75 0.00 0.00 3.41
2653 2992 3.251245 CGAGACGCTTACATCCATAGAGT 59.749 47.826 0.00 0.00 0.00 3.24
2666 3005 2.632377 CATAGAGTGGGCGTGTTTGAT 58.368 47.619 0.00 0.00 0.00 2.57
2672 3011 1.812571 GTGGGCGTGTTTGATCTTGAT 59.187 47.619 0.00 0.00 0.00 2.57
2683 3022 7.848051 CGTGTTTGATCTTGATTCTGCTTATAC 59.152 37.037 0.00 0.00 0.00 1.47
2713 3055 4.574674 AGATGTCAAAGGCTGGTTCATA 57.425 40.909 0.00 0.00 0.00 2.15
2714 3056 4.521146 AGATGTCAAAGGCTGGTTCATAG 58.479 43.478 0.00 0.00 0.00 2.23
2715 3057 3.788227 TGTCAAAGGCTGGTTCATAGT 57.212 42.857 0.00 0.00 0.00 2.12
2719 3061 3.751175 TCAAAGGCTGGTTCATAGTTTCG 59.249 43.478 0.00 0.00 0.00 3.46
2746 3088 6.959639 ACTTGATGTGAACTGTGGTAATTT 57.040 33.333 0.00 0.00 0.00 1.82
2747 3089 7.346751 ACTTGATGTGAACTGTGGTAATTTT 57.653 32.000 0.00 0.00 0.00 1.82
2748 3090 7.425606 ACTTGATGTGAACTGTGGTAATTTTC 58.574 34.615 0.00 0.00 0.00 2.29
2749 3091 5.996219 TGATGTGAACTGTGGTAATTTTCG 58.004 37.500 0.00 0.00 0.00 3.46
2750 3092 5.529430 TGATGTGAACTGTGGTAATTTTCGT 59.471 36.000 0.00 0.00 0.00 3.85
2751 3093 6.706716 TGATGTGAACTGTGGTAATTTTCGTA 59.293 34.615 0.00 0.00 0.00 3.43
2752 3094 6.533819 TGTGAACTGTGGTAATTTTCGTAG 57.466 37.500 0.00 0.00 0.00 3.51
2753 3095 5.467399 TGTGAACTGTGGTAATTTTCGTAGG 59.533 40.000 0.00 0.00 0.00 3.18
2754 3096 5.697633 GTGAACTGTGGTAATTTTCGTAGGA 59.302 40.000 0.00 0.00 0.00 2.94
2755 3097 5.929992 TGAACTGTGGTAATTTTCGTAGGAG 59.070 40.000 0.00 0.00 0.00 3.69
2756 3098 5.733620 ACTGTGGTAATTTTCGTAGGAGA 57.266 39.130 0.00 0.00 0.00 3.71
2757 3099 5.476614 ACTGTGGTAATTTTCGTAGGAGAC 58.523 41.667 0.00 0.00 0.00 3.36
2759 3101 6.435277 ACTGTGGTAATTTTCGTAGGAGACTA 59.565 38.462 0.00 0.00 43.67 2.59
2760 3102 7.123847 ACTGTGGTAATTTTCGTAGGAGACTAT 59.876 37.037 0.00 0.00 46.56 2.12
2761 3103 7.486647 TGTGGTAATTTTCGTAGGAGACTATC 58.513 38.462 0.00 0.00 46.56 2.08
2774 3116 3.654414 GAGACTATCCATGGTTAAGGCG 58.346 50.000 12.58 0.00 0.00 5.52
2775 3117 3.039011 AGACTATCCATGGTTAAGGCGT 58.961 45.455 12.58 1.95 0.00 5.68
2776 3118 3.454812 AGACTATCCATGGTTAAGGCGTT 59.545 43.478 12.58 0.00 0.00 4.84
2777 3119 4.652421 AGACTATCCATGGTTAAGGCGTTA 59.348 41.667 12.58 0.00 0.00 3.18
2778 3120 5.129815 AGACTATCCATGGTTAAGGCGTTAA 59.870 40.000 12.58 7.49 0.00 2.01
2779 3121 5.747342 ACTATCCATGGTTAAGGCGTTAAA 58.253 37.500 12.58 0.00 29.74 1.52
2780 3122 4.976224 ATCCATGGTTAAGGCGTTAAAC 57.024 40.909 17.88 17.88 36.50 2.01
2781 3123 4.023726 TCCATGGTTAAGGCGTTAAACT 57.976 40.909 23.26 9.80 36.85 2.66
2782 3124 3.754323 TCCATGGTTAAGGCGTTAAACTG 59.246 43.478 23.26 18.24 36.85 3.16
2783 3125 3.498082 CATGGTTAAGGCGTTAAACTGC 58.502 45.455 23.26 8.19 36.85 4.40
2784 3126 2.853705 TGGTTAAGGCGTTAAACTGCT 58.146 42.857 23.26 0.00 36.85 4.24
2785 3127 3.215975 TGGTTAAGGCGTTAAACTGCTT 58.784 40.909 23.26 0.52 36.85 3.91
2786 3128 4.387598 TGGTTAAGGCGTTAAACTGCTTA 58.612 39.130 23.26 4.54 36.85 3.09
2787 3129 5.005094 TGGTTAAGGCGTTAAACTGCTTAT 58.995 37.500 23.26 0.00 36.85 1.73
2788 3130 6.171921 TGGTTAAGGCGTTAAACTGCTTATA 58.828 36.000 23.26 3.27 36.85 0.98
2789 3131 6.314400 TGGTTAAGGCGTTAAACTGCTTATAG 59.686 38.462 23.26 0.00 36.85 1.31
2790 3132 6.314648 GGTTAAGGCGTTAAACTGCTTATAGT 59.685 38.462 17.53 0.00 33.60 2.12
2791 3133 7.148356 GGTTAAGGCGTTAAACTGCTTATAGTT 60.148 37.037 17.53 0.00 42.43 2.24
2792 3134 6.418585 AAGGCGTTAAACTGCTTATAGTTC 57.581 37.500 0.00 0.00 39.86 3.01
2793 3135 5.484715 AGGCGTTAAACTGCTTATAGTTCA 58.515 37.500 0.00 0.00 39.86 3.18
2794 3136 5.581085 AGGCGTTAAACTGCTTATAGTTCAG 59.419 40.000 0.00 0.00 39.86 3.02
2795 3137 5.350640 GGCGTTAAACTGCTTATAGTTCAGT 59.649 40.000 0.00 0.00 39.86 3.41
2796 3138 6.455246 GGCGTTAAACTGCTTATAGTTCAGTC 60.455 42.308 0.00 0.00 39.86 3.51
2797 3139 6.310711 GCGTTAAACTGCTTATAGTTCAGTCT 59.689 38.462 0.00 0.00 39.86 3.24
2798 3140 7.148623 GCGTTAAACTGCTTATAGTTCAGTCTT 60.149 37.037 0.00 0.00 39.86 3.01
2799 3141 8.373992 CGTTAAACTGCTTATAGTTCAGTCTTC 58.626 37.037 0.00 0.00 39.86 2.87
2831 3173 9.371136 TGTCTAAACTTCACATGTTATCTCATC 57.629 33.333 0.00 0.00 0.00 2.92
2992 3339 6.512578 CGAACATCACATGAACAAACAGGTTA 60.513 38.462 0.00 0.00 32.49 2.85
2993 3340 6.317789 ACATCACATGAACAAACAGGTTAG 57.682 37.500 0.00 0.00 32.49 2.34
2994 3341 5.827797 ACATCACATGAACAAACAGGTTAGT 59.172 36.000 0.00 0.00 32.49 2.24
2995 3342 6.995686 ACATCACATGAACAAACAGGTTAGTA 59.004 34.615 0.00 0.00 32.49 1.82
2996 3343 6.854496 TCACATGAACAAACAGGTTAGTAC 57.146 37.500 0.00 0.00 32.49 2.73
2997 3344 6.588204 TCACATGAACAAACAGGTTAGTACT 58.412 36.000 0.00 0.00 32.49 2.73
3014 3361 9.609950 GGTTAGTACTAGTATTTATCAGAAGCG 57.390 37.037 5.75 0.00 0.00 4.68
3038 3385 2.743928 GCCACGTGGAGCCTGAAG 60.744 66.667 38.30 8.59 37.39 3.02
3115 3462 1.269102 CGCCGTCAGTATTCTACCCTG 60.269 57.143 0.00 0.00 0.00 4.45
3150 3497 1.375908 GTCAAGGCATGTGCGAGGA 60.376 57.895 0.00 0.00 43.26 3.71
3168 3515 2.304428 ATGCGAGCATCATGTGACG 58.696 52.632 4.52 2.54 33.17 4.35
3170 3517 1.519234 GCGAGCATCATGTGACGGA 60.519 57.895 0.00 0.00 33.17 4.69
3307 3661 3.868077 CGCCTCGAATCAAATCTTTCTCT 59.132 43.478 0.00 0.00 0.00 3.10
3329 3683 5.242171 TCTGTCTCGTTAAACATGGTGTCTA 59.758 40.000 0.00 0.00 0.00 2.59
3375 3729 1.214062 GTCACCTCGCTGGAGTCAG 59.786 63.158 1.32 0.00 43.64 3.51
3386 3740 2.676839 GCTGGAGTCAGTGATGTTCATG 59.323 50.000 0.00 0.00 42.78 3.07
3396 3750 5.766670 TCAGTGATGTTCATGCTTCTTTCTT 59.233 36.000 0.00 0.00 0.00 2.52
3412 3766 6.662865 TCTTTCTTGGGCATCATTGTTAAA 57.337 33.333 0.00 0.00 0.00 1.52
3440 3794 1.070134 TGTGTTCCTCCACAGCAGTAC 59.930 52.381 0.00 0.00 40.30 2.73
3448 3802 3.699538 CCTCCACAGCAGTACTACATACA 59.300 47.826 0.00 0.00 36.09 2.29
3449 3803 4.440250 CCTCCACAGCAGTACTACATACAC 60.440 50.000 0.00 0.00 36.09 2.90
3450 3804 3.446161 TCCACAGCAGTACTACATACACC 59.554 47.826 0.00 0.00 36.09 4.16
3451 3805 3.194755 CCACAGCAGTACTACATACACCA 59.805 47.826 0.00 0.00 36.09 4.17
3452 3806 4.322424 CCACAGCAGTACTACATACACCAA 60.322 45.833 0.00 0.00 36.09 3.67
3482 3836 2.618053 CTTCCTACGTCAGGCGAAAAT 58.382 47.619 0.00 0.00 45.10 1.82
3487 3841 3.374058 CCTACGTCAGGCGAAAATGAAAT 59.626 43.478 0.00 0.00 44.77 2.17
3490 3844 2.414559 CGTCAGGCGAAAATGAAATGCT 60.415 45.455 0.00 0.00 44.77 3.79
3491 3845 3.578688 GTCAGGCGAAAATGAAATGCTT 58.421 40.909 0.00 0.00 0.00 3.91
3492 3846 3.365820 GTCAGGCGAAAATGAAATGCTTG 59.634 43.478 0.00 0.00 34.39 4.01
3493 3847 3.005684 TCAGGCGAAAATGAAATGCTTGT 59.994 39.130 0.00 0.00 34.66 3.16
3498 3852 7.436080 CAGGCGAAAATGAAATGCTTGTATTAT 59.564 33.333 0.00 0.00 0.00 1.28
3536 3890 2.887783 AGTATCAGCTGTCTCCCATACG 59.112 50.000 14.67 0.00 0.00 3.06
3614 3968 0.458543 ACACGCTAGGCTGTTGATCG 60.459 55.000 0.00 0.00 0.00 3.69
3640 3994 1.262950 TGAATCAACGGTCAGCGTTTG 59.737 47.619 12.92 8.45 0.00 2.93
3644 3998 3.181169 AACGGTCAGCGTTTGCAGC 62.181 57.895 9.27 0.00 46.23 5.25
3668 4022 2.364186 TCCAGCCGCATCTCCAGA 60.364 61.111 0.00 0.00 0.00 3.86
3701 4055 2.363018 TCTCCAGGACCAGAGCGG 60.363 66.667 6.67 0.00 42.50 5.52
3718 4072 2.964464 AGCGGACAAGATCATCAGAGAT 59.036 45.455 0.00 0.00 0.00 2.75
3720 4074 4.125703 GCGGACAAGATCATCAGAGATTT 58.874 43.478 0.00 0.00 0.00 2.17
3734 4088 9.076781 TCATCAGAGATTTTATCACCAAAAACA 57.923 29.630 0.00 0.00 31.54 2.83
3735 4089 9.132521 CATCAGAGATTTTATCACCAAAAACAC 57.867 33.333 0.00 0.00 31.54 3.32
3736 4090 8.463930 TCAGAGATTTTATCACCAAAAACACT 57.536 30.769 0.00 0.00 31.54 3.55
3737 4091 8.352201 TCAGAGATTTTATCACCAAAAACACTG 58.648 33.333 8.59 8.59 38.74 3.66
3738 4092 7.115378 CAGAGATTTTATCACCAAAAACACTGC 59.885 37.037 0.00 0.00 34.64 4.40
3739 4093 7.014615 AGAGATTTTATCACCAAAAACACTGCT 59.985 33.333 0.00 0.00 31.54 4.24
3740 4094 8.177119 AGATTTTATCACCAAAAACACTGCTA 57.823 30.769 0.00 0.00 31.54 3.49
3741 4095 8.082242 AGATTTTATCACCAAAAACACTGCTAC 58.918 33.333 0.00 0.00 31.54 3.58
3742 4096 3.896648 ATCACCAAAAACACTGCTACG 57.103 42.857 0.00 0.00 0.00 3.51
3743 4097 2.907634 TCACCAAAAACACTGCTACGA 58.092 42.857 0.00 0.00 0.00 3.43
3744 4098 2.869801 TCACCAAAAACACTGCTACGAG 59.130 45.455 0.00 0.00 0.00 4.18
3745 4099 2.612212 CACCAAAAACACTGCTACGAGT 59.388 45.455 0.00 0.00 0.00 4.18
3746 4100 3.805422 CACCAAAAACACTGCTACGAGTA 59.195 43.478 0.00 0.00 0.00 2.59
3747 4101 3.805971 ACCAAAAACACTGCTACGAGTAC 59.194 43.478 0.00 0.00 0.00 2.73
3748 4102 3.185797 CCAAAAACACTGCTACGAGTACC 59.814 47.826 0.00 0.00 0.00 3.34
3749 4103 4.056050 CAAAAACACTGCTACGAGTACCT 58.944 43.478 0.00 0.00 0.00 3.08
3765 4119 0.747255 ACCTCGCATCGCTCATACTT 59.253 50.000 0.00 0.00 0.00 2.24
3766 4120 1.954382 ACCTCGCATCGCTCATACTTA 59.046 47.619 0.00 0.00 0.00 2.24
3768 4122 2.320367 CTCGCATCGCTCATACTTACC 58.680 52.381 0.00 0.00 0.00 2.85
3769 4123 1.053048 CGCATCGCTCATACTTACCG 58.947 55.000 0.00 0.00 0.00 4.02
3770 4124 0.784778 GCATCGCTCATACTTACCGC 59.215 55.000 0.00 0.00 0.00 5.68
3781 4319 5.786311 TCATACTTACCGCAGTACAACTTT 58.214 37.500 0.00 0.00 31.92 2.66
3798 4337 5.107607 ACAACTTTGTACTAAATGAGCGACG 60.108 40.000 8.70 0.00 40.16 5.12
3805 4344 4.778842 ACTAAATGAGCGACGCTTATTG 57.221 40.909 32.31 24.48 42.56 1.90
3812 4351 2.006772 CGACGCTTATTGTGAGGCC 58.993 57.895 0.00 0.00 0.00 5.19
3822 4361 0.984230 TTGTGAGGCCAAGGGAGTAG 59.016 55.000 5.01 0.00 0.00 2.57
3823 4362 0.178903 TGTGAGGCCAAGGGAGTAGT 60.179 55.000 5.01 0.00 0.00 2.73
3824 4363 1.078159 TGTGAGGCCAAGGGAGTAGTA 59.922 52.381 5.01 0.00 0.00 1.82
3825 4364 1.481363 GTGAGGCCAAGGGAGTAGTAC 59.519 57.143 5.01 0.00 0.00 2.73
3827 4366 2.292918 TGAGGCCAAGGGAGTAGTACAT 60.293 50.000 5.01 0.00 0.00 2.29
3830 4369 2.420129 GGCCAAGGGAGTAGTACATGTG 60.420 54.545 9.11 0.00 0.00 3.21
3831 4370 2.500098 GCCAAGGGAGTAGTACATGTGA 59.500 50.000 9.11 0.00 0.00 3.58
3836 4375 6.331061 CAAGGGAGTAGTACATGTGAAGTAC 58.669 44.000 9.11 7.04 41.59 2.73
3838 4377 4.201990 GGGAGTAGTACATGTGAAGTACGG 60.202 50.000 9.11 0.00 44.92 4.02
3839 4378 4.397417 GGAGTAGTACATGTGAAGTACGGT 59.603 45.833 9.11 0.00 44.92 4.83
3840 4379 5.586243 GGAGTAGTACATGTGAAGTACGGTA 59.414 44.000 9.11 0.00 44.92 4.02
3841 4380 6.428385 AGTAGTACATGTGAAGTACGGTAC 57.572 41.667 9.11 10.29 44.92 3.34
3843 4382 4.081406 AGTACATGTGAAGTACGGTACCA 58.919 43.478 13.54 6.11 44.92 3.25
3844 4383 4.708421 AGTACATGTGAAGTACGGTACCAT 59.292 41.667 13.54 0.00 44.92 3.55
3845 4384 5.887598 AGTACATGTGAAGTACGGTACCATA 59.112 40.000 13.54 0.00 44.92 2.74
3846 4385 5.258456 ACATGTGAAGTACGGTACCATAG 57.742 43.478 13.54 0.00 0.00 2.23
3847 4386 4.708421 ACATGTGAAGTACGGTACCATAGT 59.292 41.667 13.54 0.01 0.00 2.12
3848 4387 5.887598 ACATGTGAAGTACGGTACCATAGTA 59.112 40.000 13.54 3.27 0.00 1.82
3850 4389 5.500234 TGTGAAGTACGGTACCATAGTAGT 58.500 41.667 13.54 6.35 0.00 2.73
3851 4390 6.649155 TGTGAAGTACGGTACCATAGTAGTA 58.351 40.000 13.54 1.71 0.00 1.82
3882 4421 5.544948 TGGTAAAGTCAGGCCTAGAAAACTA 59.455 40.000 3.98 0.00 0.00 2.24
3892 4431 3.181488 GCCTAGAAAACTACTCTCGTCCC 60.181 52.174 0.00 0.00 0.00 4.46
3940 4484 2.279069 ACCACACCAGAGGAGAGCG 61.279 63.158 0.00 0.00 0.00 5.03
3956 4500 0.254178 AGCGGAGAAAGGCATGTGAT 59.746 50.000 0.00 0.00 0.00 3.06
3957 4501 0.379669 GCGGAGAAAGGCATGTGATG 59.620 55.000 0.00 0.00 0.00 3.07
3958 4502 2.013563 GCGGAGAAAGGCATGTGATGA 61.014 52.381 0.00 0.00 0.00 2.92
3959 4503 1.938577 CGGAGAAAGGCATGTGATGAG 59.061 52.381 0.00 0.00 0.00 2.90
3960 4504 2.679059 CGGAGAAAGGCATGTGATGAGT 60.679 50.000 0.00 0.00 0.00 3.41
3961 4505 2.681848 GGAGAAAGGCATGTGATGAGTG 59.318 50.000 0.00 0.00 0.00 3.51
3962 4506 3.603532 GAGAAAGGCATGTGATGAGTGA 58.396 45.455 0.00 0.00 0.00 3.41
3963 4507 3.607741 AGAAAGGCATGTGATGAGTGAG 58.392 45.455 0.00 0.00 0.00 3.51
3964 4508 3.008813 AGAAAGGCATGTGATGAGTGAGT 59.991 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.250640 AGAGGAGGCAGTGCAAGTTG 60.251 55.000 18.61 0.00 0.00 3.16
65 75 4.753107 CCTCGTTAGTTTCCTGCAAGTTAA 59.247 41.667 0.00 0.00 0.00 2.01
378 391 0.317479 AACTATAAGCTAGCCCGCCG 59.683 55.000 12.13 0.00 0.00 6.46
386 399 5.414454 CACCTTTGCCAACAACTATAAGCTA 59.586 40.000 0.00 0.00 34.87 3.32
387 400 4.218417 CACCTTTGCCAACAACTATAAGCT 59.782 41.667 0.00 0.00 34.87 3.74
388 401 4.022329 ACACCTTTGCCAACAACTATAAGC 60.022 41.667 0.00 0.00 34.87 3.09
389 402 5.705609 ACACCTTTGCCAACAACTATAAG 57.294 39.130 0.00 0.00 34.87 1.73
390 403 6.016943 GTGTACACCTTTGCCAACAACTATAA 60.017 38.462 15.42 0.00 34.87 0.98
391 404 5.470777 GTGTACACCTTTGCCAACAACTATA 59.529 40.000 15.42 0.00 34.87 1.31
392 405 4.277423 GTGTACACCTTTGCCAACAACTAT 59.723 41.667 15.42 0.00 34.87 2.12
394 407 2.425668 GTGTACACCTTTGCCAACAACT 59.574 45.455 15.42 0.00 34.87 3.16
542 689 3.375299 AGCTTTCCCGAAGAAATCATTCG 59.625 43.478 1.29 1.29 43.50 3.34
543 690 4.156739 ACAGCTTTCCCGAAGAAATCATTC 59.843 41.667 1.73 0.00 43.50 2.67
556 725 4.965119 ATTTGAATCGTACAGCTTTCCC 57.035 40.909 0.00 0.00 0.00 3.97
685 862 1.165907 CGTGTGTGGTGTGAGCCATT 61.166 55.000 0.00 0.00 41.08 3.16
690 867 1.300931 CCTCCGTGTGTGGTGTGAG 60.301 63.158 0.00 0.00 0.00 3.51
734 945 5.308825 GACATCCACCTTTCTTTCTCTTCA 58.691 41.667 0.00 0.00 0.00 3.02
822 1035 0.248661 CAGCCTCGTGATCCGTGTAG 60.249 60.000 3.97 0.00 37.94 2.74
824 1037 1.323271 ATCAGCCTCGTGATCCGTGT 61.323 55.000 3.97 0.00 31.05 4.49
902 1116 4.354943 ACTGGGGTGGGGAGGAGG 62.355 72.222 0.00 0.00 0.00 4.30
1155 1388 2.185608 GAGAGGAGGCGGCAGAAC 59.814 66.667 13.08 0.00 0.00 3.01
1178 1411 0.321564 CGCCAAGTCAATCCAGGTCA 60.322 55.000 0.00 0.00 0.00 4.02
1191 1424 2.124193 TCCATGCCCATCGCCAAG 60.124 61.111 0.00 0.00 36.24 3.61
1193 1426 3.726144 TGTCCATGCCCATCGCCA 61.726 61.111 0.00 0.00 36.24 5.69
1208 1441 1.741525 GTGGCAGGCAAACATGTGT 59.258 52.632 0.00 0.00 0.00 3.72
1209 1442 1.005867 GGTGGCAGGCAAACATGTG 60.006 57.895 0.00 0.00 0.00 3.21
1210 1443 2.563798 CGGTGGCAGGCAAACATGT 61.564 57.895 0.00 0.00 0.00 3.21
1211 1444 2.259204 CGGTGGCAGGCAAACATG 59.741 61.111 0.00 0.00 0.00 3.21
1212 1445 2.115052 TCGGTGGCAGGCAAACAT 59.885 55.556 0.00 0.00 0.00 2.71
1213 1446 2.046009 TAGTCGGTGGCAGGCAAACA 62.046 55.000 0.00 0.00 0.00 2.83
1214 1447 1.298859 CTAGTCGGTGGCAGGCAAAC 61.299 60.000 0.00 0.00 0.00 2.93
1215 1448 1.003839 CTAGTCGGTGGCAGGCAAA 60.004 57.895 0.00 0.00 0.00 3.68
1230 1463 0.249398 ACTAAACACGGGCAGCCTAG 59.751 55.000 12.43 8.69 0.00 3.02
1236 1469 1.883275 CATCCAAACTAAACACGGGCA 59.117 47.619 0.00 0.00 0.00 5.36
1256 1491 3.030652 CCACTGACGGCACCAAAC 58.969 61.111 0.00 0.00 0.00 2.93
1490 1741 3.703052 AGGAATTCAACAGCATGGGAATC 59.297 43.478 7.93 0.00 41.34 2.52
1504 1755 6.320926 TGAACACAGATTTTGACAGGAATTCA 59.679 34.615 7.93 0.00 0.00 2.57
1530 1781 3.134081 CCACGGTAATCTATGAAGTGGGT 59.866 47.826 3.98 0.00 42.65 4.51
1539 1790 4.222145 ACACACACTTCCACGGTAATCTAT 59.778 41.667 0.00 0.00 0.00 1.98
1542 1793 2.478894 CACACACACTTCCACGGTAATC 59.521 50.000 0.00 0.00 0.00 1.75
1545 1796 0.531090 GCACACACACTTCCACGGTA 60.531 55.000 0.00 0.00 0.00 4.02
1565 1818 1.229428 CCCTATAGCATTGCACGGTG 58.771 55.000 11.91 3.15 0.00 4.94
1585 1838 4.503469 GGAAGGGGCTAGATTGCTAGTAAC 60.503 50.000 0.00 0.00 44.84 2.50
1617 1870 7.009540 GCAAATAATTACTCATCCACACTTTGC 59.990 37.037 8.25 8.25 37.49 3.68
1622 1875 6.974622 CCAAGCAAATAATTACTCATCCACAC 59.025 38.462 0.00 0.00 0.00 3.82
1623 1876 6.096705 CCCAAGCAAATAATTACTCATCCACA 59.903 38.462 0.00 0.00 0.00 4.17
1626 1879 6.959639 TCCCAAGCAAATAATTACTCATCC 57.040 37.500 0.00 0.00 0.00 3.51
1629 1882 7.178274 ACACAATCCCAAGCAAATAATTACTCA 59.822 33.333 0.00 0.00 0.00 3.41
1630 1883 7.489113 CACACAATCCCAAGCAAATAATTACTC 59.511 37.037 0.00 0.00 0.00 2.59
1631 1884 7.322664 CACACAATCCCAAGCAAATAATTACT 58.677 34.615 0.00 0.00 0.00 2.24
1632 1885 6.534793 CCACACAATCCCAAGCAAATAATTAC 59.465 38.462 0.00 0.00 0.00 1.89
1633 1886 6.438741 TCCACACAATCCCAAGCAAATAATTA 59.561 34.615 0.00 0.00 0.00 1.40
1634 1887 5.248020 TCCACACAATCCCAAGCAAATAATT 59.752 36.000 0.00 0.00 0.00 1.40
1635 1888 4.776837 TCCACACAATCCCAAGCAAATAAT 59.223 37.500 0.00 0.00 0.00 1.28
1636 1889 4.155709 TCCACACAATCCCAAGCAAATAA 58.844 39.130 0.00 0.00 0.00 1.40
1637 1890 3.772387 TCCACACAATCCCAAGCAAATA 58.228 40.909 0.00 0.00 0.00 1.40
1638 1891 2.607499 TCCACACAATCCCAAGCAAAT 58.393 42.857 0.00 0.00 0.00 2.32
1639 1892 2.079170 TCCACACAATCCCAAGCAAA 57.921 45.000 0.00 0.00 0.00 3.68
1640 1893 1.894466 CATCCACACAATCCCAAGCAA 59.106 47.619 0.00 0.00 0.00 3.91
1641 1894 1.075212 TCATCCACACAATCCCAAGCA 59.925 47.619 0.00 0.00 0.00 3.91
1642 1895 1.474077 GTCATCCACACAATCCCAAGC 59.526 52.381 0.00 0.00 0.00 4.01
1643 1896 3.077484 AGTCATCCACACAATCCCAAG 57.923 47.619 0.00 0.00 0.00 3.61
1644 1897 3.587061 ACTAGTCATCCACACAATCCCAA 59.413 43.478 0.00 0.00 0.00 4.12
1645 1898 3.181329 ACTAGTCATCCACACAATCCCA 58.819 45.455 0.00 0.00 0.00 4.37
1646 1899 3.914426 ACTAGTCATCCACACAATCCC 57.086 47.619 0.00 0.00 0.00 3.85
1647 1900 4.872691 CAGAACTAGTCATCCACACAATCC 59.127 45.833 0.00 0.00 0.00 3.01
1648 1901 4.331168 GCAGAACTAGTCATCCACACAATC 59.669 45.833 0.00 0.00 0.00 2.67
1649 1902 4.256920 GCAGAACTAGTCATCCACACAAT 58.743 43.478 0.00 0.00 0.00 2.71
1650 1903 3.070878 TGCAGAACTAGTCATCCACACAA 59.929 43.478 0.00 0.00 0.00 3.33
1651 1904 2.632512 TGCAGAACTAGTCATCCACACA 59.367 45.455 0.00 0.00 0.00 3.72
1705 1959 7.759607 ACTATTCAGGCATTCCATAAAGGTAT 58.240 34.615 0.00 0.00 39.02 2.73
1757 2014 1.737793 CCTTTTCGTTCGCAAGCCTAT 59.262 47.619 0.00 0.00 37.18 2.57
1826 2083 8.956426 TCGAATATTAACTGCAAATTCCTCTTT 58.044 29.630 0.00 0.00 0.00 2.52
1835 2092 7.967854 CCAACATTCTCGAATATTAACTGCAAA 59.032 33.333 0.00 0.00 0.00 3.68
1842 2099 6.260050 GGCTCACCAACATTCTCGAATATTAA 59.740 38.462 0.00 0.00 35.26 1.40
1846 2103 3.055458 TGGCTCACCAACATTCTCGAATA 60.055 43.478 0.00 0.00 45.37 1.75
1861 2118 2.869192 GCTCTGCTACTTATTGGCTCAC 59.131 50.000 0.00 0.00 0.00 3.51
1862 2119 2.768527 AGCTCTGCTACTTATTGGCTCA 59.231 45.455 0.00 0.00 36.99 4.26
1864 2121 2.768527 TGAGCTCTGCTACTTATTGGCT 59.231 45.455 16.19 0.00 39.88 4.75
1865 2122 3.129871 CTGAGCTCTGCTACTTATTGGC 58.870 50.000 16.19 0.00 39.88 4.52
1866 2123 4.399004 ACTGAGCTCTGCTACTTATTGG 57.601 45.455 19.49 0.00 39.88 3.16
1867 2124 6.205784 GTCTACTGAGCTCTGCTACTTATTG 58.794 44.000 19.49 1.21 39.88 1.90
1868 2125 5.300792 GGTCTACTGAGCTCTGCTACTTATT 59.699 44.000 19.49 1.39 39.88 1.40
1873 2130 2.098443 GTGGTCTACTGAGCTCTGCTAC 59.902 54.545 19.49 14.22 39.88 3.58
1874 2131 2.025793 AGTGGTCTACTGAGCTCTGCTA 60.026 50.000 19.49 10.54 41.21 3.49
1875 2132 1.181786 GTGGTCTACTGAGCTCTGCT 58.818 55.000 19.49 10.00 43.88 4.24
1901 2232 6.996180 AAGTTATATTAGTAGCTGCCTCCA 57.004 37.500 0.00 0.00 0.00 3.86
2001 2334 3.611766 AACAGCCGTATCTTACTGCTT 57.388 42.857 1.47 0.00 45.12 3.91
2014 2347 2.481568 CCATGTGCATATCTAACAGCCG 59.518 50.000 0.00 0.00 0.00 5.52
2258 2595 8.819643 AGTCATAGGCTAAATAATTCGTTCTC 57.180 34.615 0.00 0.00 0.00 2.87
2279 2616 3.319689 TCGTGTTATGGTGTTCAGAGTCA 59.680 43.478 0.00 0.00 0.00 3.41
2300 2637 4.093998 CAGTCAACATATGCAGAACCAGTC 59.906 45.833 1.58 0.00 0.00 3.51
2324 2661 8.538701 AGATAATTTGATGTTAAACAATGCCCA 58.461 29.630 0.00 0.00 0.00 5.36
2437 2774 1.586422 CTATTCCACATCCAGCACCG 58.414 55.000 0.00 0.00 0.00 4.94
2485 2822 3.804325 CGTTCTCGTCATATGCAATTCCT 59.196 43.478 0.00 0.00 0.00 3.36
2518 2855 6.596888 TGTTCTGAAATGATCTCCTGATGTTC 59.403 38.462 0.00 0.00 32.19 3.18
2582 2919 6.681777 ACATTTTTGTGATAGTCCAAAGCTC 58.318 36.000 0.00 0.00 32.61 4.09
2606 2944 1.229951 AGGAGGTGCCCAATGGAGA 60.230 57.895 0.00 0.00 37.37 3.71
2618 2957 2.036414 TCTCGAGCAGCAGGAGGT 59.964 61.111 7.81 0.00 0.00 3.85
2619 2958 2.493973 GTCTCGAGCAGCAGGAGG 59.506 66.667 7.81 0.00 0.00 4.30
2648 2987 1.899814 AGATCAAACACGCCCACTCTA 59.100 47.619 0.00 0.00 0.00 2.43
2653 2992 2.198827 ATCAAGATCAAACACGCCCA 57.801 45.000 0.00 0.00 0.00 5.36
2658 2997 7.848051 CGTATAAGCAGAATCAAGATCAAACAC 59.152 37.037 0.00 0.00 0.00 3.32
2661 3000 8.492673 AACGTATAAGCAGAATCAAGATCAAA 57.507 30.769 0.00 0.00 0.00 2.69
2683 3022 6.706270 ACCAGCCTTTGACATCTATAATAACG 59.294 38.462 0.00 0.00 0.00 3.18
2693 3034 4.265073 ACTATGAACCAGCCTTTGACATC 58.735 43.478 0.00 0.00 0.00 3.06
2701 3042 3.259876 TGTACGAAACTATGAACCAGCCT 59.740 43.478 0.00 0.00 0.00 4.58
2739 3081 7.047460 TGGATAGTCTCCTACGAAAATTACC 57.953 40.000 0.00 0.00 45.21 2.85
2740 3082 7.599245 CCATGGATAGTCTCCTACGAAAATTAC 59.401 40.741 5.56 0.00 45.21 1.89
2742 3084 6.099845 ACCATGGATAGTCTCCTACGAAAATT 59.900 38.462 21.47 0.00 45.21 1.82
2743 3085 5.602978 ACCATGGATAGTCTCCTACGAAAAT 59.397 40.000 21.47 0.00 45.21 1.82
2744 3086 4.960469 ACCATGGATAGTCTCCTACGAAAA 59.040 41.667 21.47 0.00 45.21 2.29
2745 3087 4.543689 ACCATGGATAGTCTCCTACGAAA 58.456 43.478 21.47 0.00 45.21 3.46
2746 3088 4.180377 ACCATGGATAGTCTCCTACGAA 57.820 45.455 21.47 0.00 45.21 3.85
2747 3089 3.878237 ACCATGGATAGTCTCCTACGA 57.122 47.619 21.47 0.00 45.21 3.43
2748 3090 5.047943 CCTTAACCATGGATAGTCTCCTACG 60.048 48.000 21.47 0.00 45.21 3.51
2749 3091 5.279556 GCCTTAACCATGGATAGTCTCCTAC 60.280 48.000 21.47 0.00 45.21 3.18
2750 3092 4.838986 GCCTTAACCATGGATAGTCTCCTA 59.161 45.833 21.47 0.00 45.21 2.94
2751 3093 3.648545 GCCTTAACCATGGATAGTCTCCT 59.351 47.826 21.47 0.00 45.21 3.69
2752 3094 3.555168 CGCCTTAACCATGGATAGTCTCC 60.555 52.174 21.47 0.00 45.19 3.71
2753 3095 3.069729 ACGCCTTAACCATGGATAGTCTC 59.930 47.826 21.47 0.68 0.00 3.36
2754 3096 3.039011 ACGCCTTAACCATGGATAGTCT 58.961 45.455 21.47 0.00 0.00 3.24
2755 3097 3.470645 ACGCCTTAACCATGGATAGTC 57.529 47.619 21.47 1.05 0.00 2.59
2756 3098 3.926058 AACGCCTTAACCATGGATAGT 57.074 42.857 21.47 2.03 0.00 2.12
2757 3099 5.820947 AGTTTAACGCCTTAACCATGGATAG 59.179 40.000 21.47 11.79 0.00 2.08
2758 3100 5.587043 CAGTTTAACGCCTTAACCATGGATA 59.413 40.000 21.47 8.52 0.00 2.59
2759 3101 4.398044 CAGTTTAACGCCTTAACCATGGAT 59.602 41.667 21.47 9.83 0.00 3.41
2760 3102 3.754323 CAGTTTAACGCCTTAACCATGGA 59.246 43.478 21.47 0.00 0.00 3.41
2761 3103 3.672241 GCAGTTTAACGCCTTAACCATGG 60.672 47.826 11.19 11.19 0.00 3.66
2762 3104 3.190535 AGCAGTTTAACGCCTTAACCATG 59.809 43.478 7.93 0.00 0.00 3.66
2763 3105 3.418047 AGCAGTTTAACGCCTTAACCAT 58.582 40.909 7.93 0.00 0.00 3.55
2764 3106 2.853705 AGCAGTTTAACGCCTTAACCA 58.146 42.857 7.93 0.00 0.00 3.67
2765 3107 3.909776 AAGCAGTTTAACGCCTTAACC 57.090 42.857 7.93 0.00 0.00 2.85
2766 3108 7.299787 ACTATAAGCAGTTTAACGCCTTAAC 57.700 36.000 11.98 0.00 0.00 2.01
2767 3109 7.603404 TGAACTATAAGCAGTTTAACGCCTTAA 59.397 33.333 11.98 4.76 38.86 1.85
2768 3110 7.098477 TGAACTATAAGCAGTTTAACGCCTTA 58.902 34.615 10.91 10.91 38.86 2.69
2769 3111 5.935789 TGAACTATAAGCAGTTTAACGCCTT 59.064 36.000 7.93 7.95 38.86 4.35
2770 3112 5.484715 TGAACTATAAGCAGTTTAACGCCT 58.515 37.500 7.93 0.00 38.86 5.52
2771 3113 5.350640 ACTGAACTATAAGCAGTTTAACGCC 59.649 40.000 7.93 0.00 39.69 5.68
2772 3114 6.310711 AGACTGAACTATAAGCAGTTTAACGC 59.689 38.462 0.00 4.33 42.47 4.84
2773 3115 7.813852 AGACTGAACTATAAGCAGTTTAACG 57.186 36.000 0.00 0.00 42.47 3.18
2774 3116 9.425577 AGAAGACTGAACTATAAGCAGTTTAAC 57.574 33.333 0.00 0.00 42.47 2.01
2775 3117 9.424319 CAGAAGACTGAACTATAAGCAGTTTAA 57.576 33.333 0.00 0.00 46.03 1.52
2776 3118 8.988064 CAGAAGACTGAACTATAAGCAGTTTA 57.012 34.615 0.00 0.00 46.03 2.01
2777 3119 7.897575 CAGAAGACTGAACTATAAGCAGTTT 57.102 36.000 0.00 0.00 46.03 2.66
2792 3134 6.925718 TGAAGTTTAGACATGTCAGAAGACTG 59.074 38.462 27.02 0.00 45.20 3.51
2793 3135 6.926272 GTGAAGTTTAGACATGTCAGAAGACT 59.074 38.462 27.02 17.80 45.20 3.24
2794 3136 6.701841 TGTGAAGTTTAGACATGTCAGAAGAC 59.298 38.462 27.02 16.07 45.19 3.01
2795 3137 6.816136 TGTGAAGTTTAGACATGTCAGAAGA 58.184 36.000 27.02 5.42 0.00 2.87
2796 3138 7.516481 CATGTGAAGTTTAGACATGTCAGAAG 58.484 38.462 27.02 4.10 41.30 2.85
2797 3139 7.425577 CATGTGAAGTTTAGACATGTCAGAA 57.574 36.000 27.02 17.27 41.30 3.02
2810 3152 8.641498 AAAGGATGAGATAACATGTGAAGTTT 57.359 30.769 0.00 0.00 0.00 2.66
2831 3173 8.730970 TTTTCGGAAAATATCGTGTTAAAAGG 57.269 30.769 11.68 0.00 0.00 3.11
2859 3201 3.049708 TCAAACTCCTGACTGCAGATG 57.950 47.619 23.35 9.45 45.17 2.90
2919 3261 1.798223 TCCTTTGTCGTCGCTTTGATG 59.202 47.619 0.00 0.00 34.73 3.07
2993 3340 9.941664 TGTTACGCTTCTGATAAATACTAGTAC 57.058 33.333 4.31 0.00 0.00 2.73
2994 3341 9.941664 GTGTTACGCTTCTGATAAATACTAGTA 57.058 33.333 4.77 4.77 0.00 1.82
2995 3342 7.642978 CGTGTTACGCTTCTGATAAATACTAGT 59.357 37.037 0.00 0.00 33.65 2.57
2996 3343 7.983253 CGTGTTACGCTTCTGATAAATACTAG 58.017 38.462 0.00 0.00 33.65 2.57
2997 3344 7.903452 CGTGTTACGCTTCTGATAAATACTA 57.097 36.000 0.00 0.00 33.65 1.82
3038 3385 1.739562 CAGACAAGCAGGAGGTCGC 60.740 63.158 0.00 0.00 36.68 5.19
3115 3462 4.142600 CCTTGACGAAATTGATCCTTCACC 60.143 45.833 0.00 0.00 0.00 4.02
3150 3497 1.156034 CCGTCACATGATGCTCGCAT 61.156 55.000 3.70 3.70 39.69 4.73
3281 3635 3.459232 AGATTTGATTCGAGGCGATGA 57.541 42.857 0.00 0.00 35.23 2.92
3307 3661 4.330944 AGACACCATGTTTAACGAGACA 57.669 40.909 0.00 0.00 0.00 3.41
3375 3729 5.159209 CCAAGAAAGAAGCATGAACATCAC 58.841 41.667 0.00 0.00 0.00 3.06
3378 3732 3.056322 GCCCAAGAAAGAAGCATGAACAT 60.056 43.478 0.00 0.00 0.00 2.71
3386 3740 3.056322 ACAATGATGCCCAAGAAAGAAGC 60.056 43.478 0.00 0.00 0.00 3.86
3396 3750 5.999205 ATCTTGTTTAACAATGATGCCCA 57.001 34.783 11.12 0.00 37.48 5.36
3422 3776 1.717032 AGTACTGCTGTGGAGGAACA 58.283 50.000 6.48 0.00 0.00 3.18
3440 3794 3.364565 GCGTTTGGTGTTGGTGTATGTAG 60.365 47.826 0.00 0.00 0.00 2.74
3448 3802 0.395173 AGGAAGCGTTTGGTGTTGGT 60.395 50.000 0.00 0.00 0.00 3.67
3449 3803 1.265905 GTAGGAAGCGTTTGGTGTTGG 59.734 52.381 0.00 0.00 0.00 3.77
3450 3804 1.070175 CGTAGGAAGCGTTTGGTGTTG 60.070 52.381 0.00 0.00 0.00 3.33
3451 3805 1.223187 CGTAGGAAGCGTTTGGTGTT 58.777 50.000 0.00 0.00 0.00 3.32
3452 3806 0.105408 ACGTAGGAAGCGTTTGGTGT 59.895 50.000 0.00 0.00 39.79 4.16
3506 3860 6.995091 GGGAGACAGCTGATACTGATAAAAAT 59.005 38.462 23.35 0.00 40.25 1.82
3515 3869 2.887783 CGTATGGGAGACAGCTGATACT 59.112 50.000 23.35 15.94 0.00 2.12
3518 3872 2.073252 TCGTATGGGAGACAGCTGAT 57.927 50.000 23.35 8.50 0.00 2.90
3536 3890 4.102367 ACTTCCCTATCTTGCTCTCCAATC 59.898 45.833 0.00 0.00 31.91 2.67
3614 3968 2.349886 GCTGACCGTTGATTCACTGATC 59.650 50.000 0.00 0.00 0.00 2.92
3668 4022 4.226168 CCTGGAGACCTGGACTAAGAAAAT 59.774 45.833 0.00 0.00 44.09 1.82
3701 4055 8.772705 GGTGATAAAATCTCTGATGATCTTGTC 58.227 37.037 0.00 0.00 0.00 3.18
3718 4072 6.038382 TCGTAGCAGTGTTTTTGGTGATAAAA 59.962 34.615 0.00 0.00 0.00 1.52
3720 4074 5.057819 TCGTAGCAGTGTTTTTGGTGATAA 58.942 37.500 0.00 0.00 0.00 1.75
3744 4098 1.267261 AGTATGAGCGATGCGAGGTAC 59.733 52.381 0.00 0.00 0.00 3.34
3745 4099 1.605753 AGTATGAGCGATGCGAGGTA 58.394 50.000 0.00 0.00 0.00 3.08
3746 4100 0.747255 AAGTATGAGCGATGCGAGGT 59.253 50.000 0.00 0.00 0.00 3.85
3747 4101 2.320367 GTAAGTATGAGCGATGCGAGG 58.680 52.381 0.00 0.00 0.00 4.63
3748 4102 2.320367 GGTAAGTATGAGCGATGCGAG 58.680 52.381 0.00 0.00 0.00 5.03
3749 4103 1.334689 CGGTAAGTATGAGCGATGCGA 60.335 52.381 0.00 0.00 45.08 5.10
3753 4107 1.681793 ACTGCGGTAAGTATGAGCGAT 59.318 47.619 0.00 0.00 45.08 4.58
3781 4319 2.933495 AGCGTCGCTCATTTAGTACA 57.067 45.000 15.47 0.00 30.62 2.90
3790 4328 1.629013 CTCACAATAAGCGTCGCTCA 58.371 50.000 21.98 6.30 38.25 4.26
3791 4329 0.924090 CCTCACAATAAGCGTCGCTC 59.076 55.000 21.98 0.00 38.25 5.03
3794 4333 0.739462 TGGCCTCACAATAAGCGTCG 60.739 55.000 3.32 0.00 0.00 5.12
3798 4337 1.106285 CCCTTGGCCTCACAATAAGC 58.894 55.000 3.32 0.00 0.00 3.09
3805 4344 1.481363 GTACTACTCCCTTGGCCTCAC 59.519 57.143 3.32 0.00 0.00 3.51
3812 4351 5.407407 ACTTCACATGTACTACTCCCTTG 57.593 43.478 0.00 0.00 0.00 3.61
3822 4361 4.439305 TGGTACCGTACTTCACATGTAC 57.561 45.455 7.57 0.00 35.66 2.90
3823 4362 5.887598 ACTATGGTACCGTACTTCACATGTA 59.112 40.000 9.93 0.00 0.00 2.29
3824 4363 4.708421 ACTATGGTACCGTACTTCACATGT 59.292 41.667 9.93 0.00 0.00 3.21
3825 4364 5.258456 ACTATGGTACCGTACTTCACATG 57.742 43.478 9.93 0.88 0.00 3.21
3827 4366 5.500234 ACTACTATGGTACCGTACTTCACA 58.500 41.667 9.93 0.00 0.00 3.58
3830 4369 7.604164 TGCTATACTACTATGGTACCGTACTTC 59.396 40.741 9.93 0.00 0.00 3.01
3831 4370 7.453393 TGCTATACTACTATGGTACCGTACTT 58.547 38.462 9.93 3.05 0.00 2.24
3836 4375 5.123502 CCACTGCTATACTACTATGGTACCG 59.876 48.000 7.57 0.00 0.00 4.02
3838 4377 8.627208 TTACCACTGCTATACTACTATGGTAC 57.373 38.462 0.00 0.00 40.30 3.34
3839 4378 9.293404 CTTTACCACTGCTATACTACTATGGTA 57.707 37.037 0.00 0.00 39.80 3.25
3840 4379 7.783596 ACTTTACCACTGCTATACTACTATGGT 59.216 37.037 0.00 0.00 41.89 3.55
3841 4380 8.179509 ACTTTACCACTGCTATACTACTATGG 57.820 38.462 0.00 0.00 0.00 2.74
3843 4382 8.991783 TGACTTTACCACTGCTATACTACTAT 57.008 34.615 0.00 0.00 0.00 2.12
3844 4383 7.501559 CCTGACTTTACCACTGCTATACTACTA 59.498 40.741 0.00 0.00 0.00 1.82
3845 4384 6.321690 CCTGACTTTACCACTGCTATACTACT 59.678 42.308 0.00 0.00 0.00 2.57
3846 4385 6.505272 CCTGACTTTACCACTGCTATACTAC 58.495 44.000 0.00 0.00 0.00 2.73
3847 4386 5.068723 GCCTGACTTTACCACTGCTATACTA 59.931 44.000 0.00 0.00 0.00 1.82
3848 4387 4.141914 GCCTGACTTTACCACTGCTATACT 60.142 45.833 0.00 0.00 0.00 2.12
3850 4389 3.134081 GGCCTGACTTTACCACTGCTATA 59.866 47.826 0.00 0.00 0.00 1.31
3851 4390 2.092914 GGCCTGACTTTACCACTGCTAT 60.093 50.000 0.00 0.00 0.00 2.97
3892 4431 1.128692 GTGCGGAAAGTTCGAATCAGG 59.871 52.381 0.00 0.00 0.00 3.86
3924 4463 1.943116 CTCCGCTCTCCTCTGGTGTG 61.943 65.000 0.00 0.00 0.00 3.82
3940 4484 2.681848 CACTCATCACATGCCTTTCTCC 59.318 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.