Multiple sequence alignment - TraesCS7A01G459700

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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 TraesCS7A01G459700 chr7A 100.000 4032 0 0 1 4032 655367791 655371822 0.000000e+00 7446
1 TraesCS7A01G459700 chr7D 93.588 1809 93 13 2238 4032 568011622 568013421 0.000000e+00 2676
2 TraesCS7A01G459700 chr7D 87.717 1555 136 23 1 1518 568009511 568011047 0.000000e+00 1762
3 TraesCS7A01G459700 chr7D 89.356 404 28 5 1534 1928 568011139 568011536 1.010000e-135 494
4 TraesCS7A01G459700 chr7B 91.488 1821 116 17 2237 4032 622624393 622626199 0.000000e+00 2468
5 TraesCS7A01G459700 chr7B 91.332 946 52 11 976 1910 622623343 622624269 0.000000e+00 1266
6 TraesCS7A01G459700 chr7B 85.141 1097 125 16 1 1062 622621909 622623002 0.000000e+00 1088


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 TraesCS7A01G459700 chr7A 655367791 655371822 4031 False 7446.000000 7446 100.000000 1 4032 1 chr7A.!!$F1 4031
1 TraesCS7A01G459700 chr7D 568009511 568013421 3910 False 1644.000000 2676 90.220333 1 4032 3 chr7D.!!$F1 4031
2 TraesCS7A01G459700 chr7B 622621909 622626199 4290 False 1607.333333 2468 89.320333 1 4032 3 chr7B.!!$F1 4031

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
261 263 0.888619 ACGCGTTGAGAAGAGGATCA 59.111 50.0 5.58 0.0 37.82 2.92 F
1922 2501 0.116342 TTCCCTCTGTCCCTGCTGTA 59.884 55.0 0.00 0.0 0.00 2.74 F
2221 2800 0.106268 TCATGTGTTGGTGCCCTGTT 60.106 50.0 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2640 0.248843 TTTTTGATGGATTGGCCCGC 59.751 50.000 0.00 0.0 34.97 6.13 R
2833 3415 1.035139 ACAGAAAGTTGCAGCAAGGG 58.965 50.000 8.49 0.0 0.00 3.95 R
3944 4548 1.513158 CTCTCGCTACCACCACCTG 59.487 63.158 0.00 0.0 0.00 4.00 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
183 184 1.193874 GCGGTACAAAAGAACACTCCG 59.806 52.381 0.00 0.00 39.71 4.63
214 215 2.183478 TCCAAAGAAGAGCGCAATCA 57.817 45.000 11.47 0.00 0.00 2.57
215 216 1.806542 TCCAAAGAAGAGCGCAATCAC 59.193 47.619 11.47 0.00 0.00 3.06
220 221 1.005037 AAGAGCGCAATCACCGTCA 60.005 52.632 11.47 0.00 0.00 4.35
228 230 1.867233 GCAATCACCGTCATATTCGCT 59.133 47.619 0.00 0.00 0.00 4.93
261 263 0.888619 ACGCGTTGAGAAGAGGATCA 59.111 50.000 5.58 0.00 37.82 2.92
274 276 2.202987 GATCAGGAGGCTGCCACG 60.203 66.667 22.65 5.89 0.00 4.94
333 336 2.420687 GGGGTGCATTAAGAGGAGACTG 60.421 54.545 0.00 0.00 44.43 3.51
396 399 3.933722 ATCTCCATGCCTCCGCCG 61.934 66.667 0.00 0.00 0.00 6.46
413 416 3.311322 CCGCCGAAGAGCACATTTTATTA 59.689 43.478 0.00 0.00 0.00 0.98
422 425 4.349663 GCACATTTTATTACTGGTGCGA 57.650 40.909 0.00 0.00 41.61 5.10
429 432 1.853963 ATTACTGGTGCGACTCCTCT 58.146 50.000 0.00 0.00 0.00 3.69
451 454 6.774673 TCTAATGACCACAGGTACAAAATCA 58.225 36.000 0.00 0.00 35.25 2.57
453 456 5.705609 ATGACCACAGGTACAAAATCAAC 57.294 39.130 0.00 0.00 35.25 3.18
476 479 4.388499 ACCATGGGTCGTCACGCC 62.388 66.667 18.09 0.00 34.50 5.68
502 505 1.191489 TGGAGATCAACCGTGGCAGA 61.191 55.000 0.00 0.00 0.00 4.26
527 530 2.053244 AGATGCAGATGGAACCCTAGG 58.947 52.381 0.06 0.06 0.00 3.02
601 604 1.477295 CGTCTTGGAACCCTAGAGGAC 59.523 57.143 10.19 0.00 41.30 3.85
603 606 3.108376 GTCTTGGAACCCTAGAGGACAT 58.892 50.000 0.00 0.00 36.20 3.06
605 608 1.879575 TGGAACCCTAGAGGACATGG 58.120 55.000 0.00 0.00 39.89 3.66
644 647 1.271856 TGGTGGAGCGATTCTTGGTA 58.728 50.000 0.00 0.00 0.00 3.25
648 651 3.069729 GGTGGAGCGATTCTTGGTATACT 59.930 47.826 2.25 0.00 0.00 2.12
652 655 4.038162 GGAGCGATTCTTGGTATACTGAGT 59.962 45.833 2.25 0.00 0.00 3.41
689 697 7.829706 AGGTGGAGTTTAGTTGGATAAAAGATC 59.170 37.037 0.00 0.00 0.00 2.75
702 713 6.889722 TGGATAAAAGATCGAAAAGAACCCAT 59.110 34.615 0.00 0.00 0.00 4.00
704 715 7.067008 GGATAAAAGATCGAAAAGAACCCATCA 59.933 37.037 0.00 0.00 0.00 3.07
708 719 3.712016 TCGAAAAGAACCCATCATGGA 57.288 42.857 4.75 0.00 40.96 3.41
739 752 6.912203 AAAAACAAGACAAAAATAACCCGG 57.088 33.333 0.00 0.00 0.00 5.73
740 753 3.653539 ACAAGACAAAAATAACCCGGC 57.346 42.857 0.00 0.00 0.00 6.13
744 757 2.078392 GACAAAAATAACCCGGCGAGA 58.922 47.619 9.30 0.00 0.00 4.04
760 773 2.094442 GCGAGAAGAAGCTACCAACTCT 60.094 50.000 0.00 0.00 0.00 3.24
768 781 6.420913 AGAAGCTACCAACTCTCACTTTAA 57.579 37.500 0.00 0.00 0.00 1.52
793 806 6.708949 AGAGTAAAAATTAGGTGCTTGTTCGA 59.291 34.615 0.00 0.00 0.00 3.71
794 807 7.390718 AGAGTAAAAATTAGGTGCTTGTTCGAT 59.609 33.333 0.00 0.00 0.00 3.59
807 820 3.179443 TGTTCGATAATCCACCAGCTC 57.821 47.619 0.00 0.00 0.00 4.09
808 821 2.766263 TGTTCGATAATCCACCAGCTCT 59.234 45.455 0.00 0.00 0.00 4.09
809 822 3.958147 TGTTCGATAATCCACCAGCTCTA 59.042 43.478 0.00 0.00 0.00 2.43
830 844 2.240493 AAAATACGAGGATCTGCGGG 57.760 50.000 11.33 0.00 0.00 6.13
836 850 3.543536 GAGGATCTGCGGGGCATCC 62.544 68.421 3.95 3.95 37.82 3.51
848 862 1.745489 GGCATCCGTTTCTCCGCTT 60.745 57.895 0.00 0.00 0.00 4.68
854 868 1.000385 TCCGTTTCTCCGCTTCGTTAA 60.000 47.619 0.00 0.00 0.00 2.01
856 870 3.119531 TCCGTTTCTCCGCTTCGTTAATA 60.120 43.478 0.00 0.00 0.00 0.98
864 878 4.751060 TCCGCTTCGTTAATATCAACTGT 58.249 39.130 0.00 0.00 0.00 3.55
872 886 5.066893 TCGTTAATATCAACTGTAGCTCCGT 59.933 40.000 0.00 0.00 0.00 4.69
873 887 5.173312 CGTTAATATCAACTGTAGCTCCGTG 59.827 44.000 0.00 0.00 0.00 4.94
875 889 5.847111 AATATCAACTGTAGCTCCGTGTA 57.153 39.130 0.00 0.00 0.00 2.90
877 891 1.198408 TCAACTGTAGCTCCGTGTACG 59.802 52.381 0.00 0.00 39.44 3.67
960 985 3.339141 CTGCAGTTAAGAGGTTCCTTCC 58.661 50.000 5.25 0.00 0.00 3.46
969 994 7.179872 AGTTAAGAGGTTCCTTCCGTAAGTTAT 59.820 37.037 0.00 0.00 0.00 1.89
970 995 6.370186 AAGAGGTTCCTTCCGTAAGTTATT 57.630 37.500 0.00 0.00 0.00 1.40
1182 1658 4.488136 CCAGCCGCCATGCCTACA 62.488 66.667 0.00 0.00 0.00 2.74
1330 1806 3.368501 CCTCCCCTCCCCTCCTCA 61.369 72.222 0.00 0.00 0.00 3.86
1339 1815 0.547712 TCCCCTCCTCACCTTCCTTG 60.548 60.000 0.00 0.00 0.00 3.61
1472 1948 7.911727 TGAATTAATTGTGCTGAATGAATCTCG 59.088 33.333 5.17 0.00 0.00 4.04
1551 2113 2.887568 CGCGAGTAAGCCTGCTGG 60.888 66.667 0.00 5.03 0.00 4.85
1594 2156 5.672321 GCAGAAACTGGAAATTTAGCTCTCG 60.672 44.000 0.00 0.00 31.21 4.04
1624 2186 4.367166 TCATGTTAACTCCCATCCCACTA 58.633 43.478 7.22 0.00 0.00 2.74
1625 2187 4.975147 TCATGTTAACTCCCATCCCACTAT 59.025 41.667 7.22 0.00 0.00 2.12
1632 2194 6.449830 AACTCCCATCCCACTATTTATACC 57.550 41.667 0.00 0.00 0.00 2.73
1641 2203 6.891388 TCCCACTATTTATACCGAACATGTT 58.109 36.000 11.78 11.78 0.00 2.71
1668 2230 4.866508 TCTTGGGTCTGTAGTGTACAAG 57.133 45.455 0.00 0.00 38.38 3.16
1687 2249 4.767409 ACAAGCCCTTCTTTTCCTATCAAC 59.233 41.667 0.00 0.00 31.27 3.18
1724 2295 1.780860 CTTTTTGCGTTTTCTCGGCTG 59.219 47.619 0.00 0.00 0.00 4.85
1741 2312 3.632145 CGGCTGCCAGGTAAGAAATTAAT 59.368 43.478 20.29 0.00 0.00 1.40
1742 2313 4.097892 CGGCTGCCAGGTAAGAAATTAATT 59.902 41.667 20.29 0.00 0.00 1.40
1776 2347 5.487433 TGTTCTCACTCAAAGTCTGAAACA 58.513 37.500 0.00 0.00 32.17 2.83
1779 2350 6.422776 TCTCACTCAAAGTCTGAAACAAAC 57.577 37.500 0.00 0.00 32.17 2.93
1781 2352 5.938322 TCACTCAAAGTCTGAAACAAACAC 58.062 37.500 0.00 0.00 32.17 3.32
1782 2353 5.705441 TCACTCAAAGTCTGAAACAAACACT 59.295 36.000 0.00 0.00 32.17 3.55
1783 2354 6.206634 TCACTCAAAGTCTGAAACAAACACTT 59.793 34.615 0.00 0.00 32.17 3.16
1792 2366 7.064728 AGTCTGAAACAAACACTTCTTCTACAC 59.935 37.037 0.00 0.00 0.00 2.90
1800 2374 4.360563 ACACTTCTTCTACACACTCAACG 58.639 43.478 0.00 0.00 0.00 4.10
1802 2376 3.181479 ACTTCTTCTACACACTCAACGCA 60.181 43.478 0.00 0.00 0.00 5.24
1823 2397 1.921982 ACAGCACACCCAAATATGCA 58.078 45.000 0.00 0.00 40.63 3.96
1848 2422 7.384660 CACATATGCTCCTAGTTTCTTCTCATC 59.615 40.741 1.58 0.00 0.00 2.92
1872 2446 0.798776 GCATGGAGTGGTCTTGTTCG 59.201 55.000 0.00 0.00 0.00 3.95
1910 2489 4.748701 TCACCACTTAACTAGTTCCCTCT 58.251 43.478 12.39 0.00 33.85 3.69
1911 2490 4.527038 TCACCACTTAACTAGTTCCCTCTG 59.473 45.833 12.39 2.44 33.85 3.35
1912 2491 4.283722 CACCACTTAACTAGTTCCCTCTGT 59.716 45.833 12.39 1.30 33.85 3.41
1914 2493 4.081586 CCACTTAACTAGTTCCCTCTGTCC 60.082 50.000 12.39 0.00 33.85 4.02
1915 2494 4.081586 CACTTAACTAGTTCCCTCTGTCCC 60.082 50.000 12.39 0.00 33.85 4.46
1916 2495 4.202803 ACTTAACTAGTTCCCTCTGTCCCT 60.203 45.833 12.39 0.00 31.29 4.20
1917 2496 2.239681 ACTAGTTCCCTCTGTCCCTG 57.760 55.000 0.00 0.00 0.00 4.45
1918 2497 0.827368 CTAGTTCCCTCTGTCCCTGC 59.173 60.000 0.00 0.00 0.00 4.85
1919 2498 0.413832 TAGTTCCCTCTGTCCCTGCT 59.586 55.000 0.00 0.00 0.00 4.24
1920 2499 1.197430 AGTTCCCTCTGTCCCTGCTG 61.197 60.000 0.00 0.00 0.00 4.41
1921 2500 1.152030 TTCCCTCTGTCCCTGCTGT 60.152 57.895 0.00 0.00 0.00 4.40
1922 2501 0.116342 TTCCCTCTGTCCCTGCTGTA 59.884 55.000 0.00 0.00 0.00 2.74
1923 2502 0.116342 TCCCTCTGTCCCTGCTGTAA 59.884 55.000 0.00 0.00 0.00 2.41
1924 2503 1.207791 CCCTCTGTCCCTGCTGTAAT 58.792 55.000 0.00 0.00 0.00 1.89
1925 2504 1.561542 CCCTCTGTCCCTGCTGTAATT 59.438 52.381 0.00 0.00 0.00 1.40
1926 2505 2.025887 CCCTCTGTCCCTGCTGTAATTT 60.026 50.000 0.00 0.00 0.00 1.82
1927 2506 3.562176 CCCTCTGTCCCTGCTGTAATTTT 60.562 47.826 0.00 0.00 0.00 1.82
1928 2507 4.082125 CCTCTGTCCCTGCTGTAATTTTT 58.918 43.478 0.00 0.00 0.00 1.94
1987 2566 1.002087 TGTGGTGTGTGTGTGTGTGTA 59.998 47.619 0.00 0.00 0.00 2.90
1988 2567 1.395608 GTGGTGTGTGTGTGTGTGTAC 59.604 52.381 0.00 0.00 0.00 2.90
1989 2568 1.011333 GGTGTGTGTGTGTGTGTACC 58.989 55.000 0.00 0.00 0.00 3.34
1990 2569 1.676314 GGTGTGTGTGTGTGTGTACCA 60.676 52.381 0.00 0.00 0.00 3.25
1991 2570 2.285083 GTGTGTGTGTGTGTGTACCAT 58.715 47.619 0.00 0.00 0.00 3.55
1992 2571 2.031560 GTGTGTGTGTGTGTGTACCATG 59.968 50.000 0.00 0.00 0.00 3.66
1993 2572 2.093447 TGTGTGTGTGTGTGTACCATGA 60.093 45.455 0.00 0.00 0.00 3.07
1999 2578 6.153680 TGTGTGTGTGTGTACCATGATATCTA 59.846 38.462 3.98 0.00 0.00 1.98
2001 2580 7.710907 GTGTGTGTGTGTACCATGATATCTATT 59.289 37.037 3.98 0.00 0.00 1.73
2002 2581 7.926018 TGTGTGTGTGTACCATGATATCTATTC 59.074 37.037 3.98 0.00 0.00 1.75
2003 2582 7.926018 GTGTGTGTGTACCATGATATCTATTCA 59.074 37.037 3.98 0.00 0.00 2.57
2004 2583 8.143835 TGTGTGTGTACCATGATATCTATTCAG 58.856 37.037 3.98 0.00 0.00 3.02
2005 2584 8.144478 GTGTGTGTACCATGATATCTATTCAGT 58.856 37.037 3.98 0.00 0.00 3.41
2006 2585 9.362151 TGTGTGTACCATGATATCTATTCAGTA 57.638 33.333 3.98 0.00 0.00 2.74
2008 2587 8.523658 TGTGTACCATGATATCTATTCAGTAGC 58.476 37.037 3.98 0.00 0.00 3.58
2010 2589 6.214191 ACCATGATATCTATTCAGTAGCGG 57.786 41.667 3.98 0.00 0.00 5.52
2011 2590 5.952347 ACCATGATATCTATTCAGTAGCGGA 59.048 40.000 3.98 0.00 0.00 5.54
2012 2591 6.096141 ACCATGATATCTATTCAGTAGCGGAG 59.904 42.308 3.98 0.00 0.00 4.63
2028 2607 3.687572 CGGAGCCAGAAAAATCAGATG 57.312 47.619 0.00 0.00 0.00 2.90
2029 2608 3.273434 CGGAGCCAGAAAAATCAGATGA 58.727 45.455 0.00 0.00 0.00 2.92
2030 2609 3.311871 CGGAGCCAGAAAAATCAGATGAG 59.688 47.826 0.00 0.00 0.00 2.90
2031 2610 3.631227 GGAGCCAGAAAAATCAGATGAGG 59.369 47.826 0.00 0.00 0.00 3.86
2033 2612 2.692041 GCCAGAAAAATCAGATGAGGGG 59.308 50.000 0.00 0.00 0.00 4.79
2034 2613 3.294214 CCAGAAAAATCAGATGAGGGGG 58.706 50.000 0.00 0.00 0.00 5.40
2051 2630 3.380479 GGGGGCTGAGTTTTGTTAAAC 57.620 47.619 0.00 0.00 43.19 2.01
2052 2631 2.036733 GGGGGCTGAGTTTTGTTAAACC 59.963 50.000 0.00 0.00 43.77 3.27
2053 2632 2.963101 GGGGCTGAGTTTTGTTAAACCT 59.037 45.455 0.00 0.00 43.77 3.50
2054 2633 3.386726 GGGGCTGAGTTTTGTTAAACCTT 59.613 43.478 0.00 0.00 43.77 3.50
2055 2634 4.368315 GGGCTGAGTTTTGTTAAACCTTG 58.632 43.478 0.00 0.00 43.77 3.61
2056 2635 4.142026 GGGCTGAGTTTTGTTAAACCTTGT 60.142 41.667 0.00 0.00 43.77 3.16
2057 2636 5.041287 GGCTGAGTTTTGTTAAACCTTGTC 58.959 41.667 0.00 0.00 43.77 3.18
2058 2637 4.733405 GCTGAGTTTTGTTAAACCTTGTCG 59.267 41.667 0.00 0.00 43.77 4.35
2059 2638 5.238006 TGAGTTTTGTTAAACCTTGTCGG 57.762 39.130 0.00 0.00 43.77 4.79
2060 2639 4.096682 TGAGTTTTGTTAAACCTTGTCGGG 59.903 41.667 0.00 0.00 43.77 5.14
2061 2640 3.382227 AGTTTTGTTAAACCTTGTCGGGG 59.618 43.478 0.00 0.00 43.77 5.73
2062 2641 1.320507 TTGTTAAACCTTGTCGGGGC 58.679 50.000 0.00 0.00 36.97 5.80
2063 2642 0.885596 TGTTAAACCTTGTCGGGGCG 60.886 55.000 0.00 0.00 36.97 6.13
2064 2643 1.302671 TTAAACCTTGTCGGGGCGG 60.303 57.895 0.00 0.00 36.97 6.13
2065 2644 2.751357 TTAAACCTTGTCGGGGCGGG 62.751 60.000 0.00 0.00 36.97 6.13
2076 2655 4.521292 GGGCGGGCCAATCCATCA 62.521 66.667 16.76 0.00 37.98 3.07
2077 2656 2.441901 GGCGGGCCAATCCATCAA 60.442 61.111 4.39 0.00 36.21 2.57
2078 2657 2.057408 GGCGGGCCAATCCATCAAA 61.057 57.895 4.39 0.00 36.21 2.69
2079 2658 1.612395 GGCGGGCCAATCCATCAAAA 61.612 55.000 4.39 0.00 36.21 2.44
2080 2659 0.248843 GCGGGCCAATCCATCAAAAA 59.751 50.000 4.39 0.00 36.21 1.94
2081 2660 1.740043 GCGGGCCAATCCATCAAAAAG 60.740 52.381 4.39 0.00 36.21 2.27
2082 2661 1.740043 CGGGCCAATCCATCAAAAAGC 60.740 52.381 4.39 0.00 36.21 3.51
2083 2662 1.278699 GGGCCAATCCATCAAAAAGCA 59.721 47.619 4.39 0.00 36.21 3.91
2084 2663 2.349590 GGCCAATCCATCAAAAAGCAC 58.650 47.619 0.00 0.00 34.01 4.40
2085 2664 2.349590 GCCAATCCATCAAAAAGCACC 58.650 47.619 0.00 0.00 0.00 5.01
2086 2665 2.289569 GCCAATCCATCAAAAAGCACCA 60.290 45.455 0.00 0.00 0.00 4.17
2087 2666 3.620472 GCCAATCCATCAAAAAGCACCAT 60.620 43.478 0.00 0.00 0.00 3.55
2088 2667 4.581868 CCAATCCATCAAAAAGCACCATT 58.418 39.130 0.00 0.00 0.00 3.16
2089 2668 5.005094 CCAATCCATCAAAAAGCACCATTT 58.995 37.500 0.00 0.00 0.00 2.32
2090 2669 5.474189 CCAATCCATCAAAAAGCACCATTTT 59.526 36.000 0.00 0.00 33.86 1.82
2091 2670 6.654161 CCAATCCATCAAAAAGCACCATTTTA 59.346 34.615 0.00 0.00 32.20 1.52
2092 2671 7.148373 CCAATCCATCAAAAAGCACCATTTTAG 60.148 37.037 0.00 0.00 32.20 1.85
2093 2672 5.237048 TCCATCAAAAAGCACCATTTTAGC 58.763 37.500 0.00 0.00 32.20 3.09
2094 2673 4.996122 CCATCAAAAAGCACCATTTTAGCA 59.004 37.500 0.00 0.00 32.20 3.49
2095 2674 5.121142 CCATCAAAAAGCACCATTTTAGCAG 59.879 40.000 0.00 0.00 32.20 4.24
2096 2675 5.528043 TCAAAAAGCACCATTTTAGCAGA 57.472 34.783 0.00 0.00 32.20 4.26
2097 2676 5.911752 TCAAAAAGCACCATTTTAGCAGAA 58.088 33.333 0.00 0.00 32.20 3.02
2098 2677 6.344500 TCAAAAAGCACCATTTTAGCAGAAA 58.656 32.000 0.00 0.00 32.20 2.52
2099 2678 6.820656 TCAAAAAGCACCATTTTAGCAGAAAA 59.179 30.769 0.00 0.00 32.20 2.29
2100 2679 7.335422 TCAAAAAGCACCATTTTAGCAGAAAAA 59.665 29.630 1.23 0.00 32.20 1.94
2127 2706 6.856135 AACCGTTTACTATTTATGCTAGGC 57.144 37.500 0.00 0.00 0.00 3.93
2128 2707 6.170846 ACCGTTTACTATTTATGCTAGGCT 57.829 37.500 0.00 0.00 0.00 4.58
2129 2708 6.589135 ACCGTTTACTATTTATGCTAGGCTT 58.411 36.000 0.00 0.00 0.00 4.35
2130 2709 7.729116 ACCGTTTACTATTTATGCTAGGCTTA 58.271 34.615 0.00 0.00 0.00 3.09
2131 2710 8.206189 ACCGTTTACTATTTATGCTAGGCTTAA 58.794 33.333 0.00 0.00 0.00 1.85
2132 2711 9.048446 CCGTTTACTATTTATGCTAGGCTTAAA 57.952 33.333 11.15 11.15 40.53 1.52
2142 2721 9.627123 TTTATGCTAGGCTTAAATTAGTGATGT 57.373 29.630 0.00 0.00 34.71 3.06
2143 2722 9.627123 TTATGCTAGGCTTAAATTAGTGATGTT 57.373 29.630 0.00 0.00 0.00 2.71
2145 2724 8.662781 TGCTAGGCTTAAATTAGTGATGTTAG 57.337 34.615 0.00 0.00 0.00 2.34
2146 2725 7.715249 TGCTAGGCTTAAATTAGTGATGTTAGG 59.285 37.037 0.00 0.00 0.00 2.69
2147 2726 7.173390 GCTAGGCTTAAATTAGTGATGTTAGGG 59.827 40.741 0.00 0.00 0.00 3.53
2148 2727 6.365520 AGGCTTAAATTAGTGATGTTAGGGG 58.634 40.000 0.00 0.00 0.00 4.79
2149 2728 5.535030 GGCTTAAATTAGTGATGTTAGGGGG 59.465 44.000 0.00 0.00 0.00 5.40
2172 2751 2.267324 GGCACCTCCTGTCTCTGC 59.733 66.667 0.00 0.00 0.00 4.26
2173 2752 2.267324 GCACCTCCTGTCTCTGCC 59.733 66.667 0.00 0.00 0.00 4.85
2174 2753 2.289532 GCACCTCCTGTCTCTGCCT 61.290 63.158 0.00 0.00 0.00 4.75
2175 2754 1.896694 CACCTCCTGTCTCTGCCTC 59.103 63.158 0.00 0.00 0.00 4.70
2176 2755 0.614415 CACCTCCTGTCTCTGCCTCT 60.614 60.000 0.00 0.00 0.00 3.69
2177 2756 0.614415 ACCTCCTGTCTCTGCCTCTG 60.614 60.000 0.00 0.00 0.00 3.35
2185 2764 4.343526 CCTGTCTCTGCCTCTGTATGTATT 59.656 45.833 0.00 0.00 0.00 1.89
2207 2786 1.562942 ACATGCATCCTCACCTCATGT 59.437 47.619 0.00 0.00 41.78 3.21
2208 2787 1.947456 CATGCATCCTCACCTCATGTG 59.053 52.381 0.00 0.00 46.88 3.21
2209 2788 0.986527 TGCATCCTCACCTCATGTGT 59.013 50.000 0.00 0.00 45.61 3.72
2210 2789 1.352017 TGCATCCTCACCTCATGTGTT 59.648 47.619 0.00 0.00 45.61 3.32
2211 2790 1.741706 GCATCCTCACCTCATGTGTTG 59.258 52.381 0.00 0.00 45.61 3.33
2212 2791 2.362736 CATCCTCACCTCATGTGTTGG 58.637 52.381 0.00 0.00 45.61 3.77
2213 2792 1.434188 TCCTCACCTCATGTGTTGGT 58.566 50.000 0.00 0.00 45.61 3.67
2216 2795 1.959085 CACCTCATGTGTTGGTGCC 59.041 57.895 13.56 0.00 43.61 5.01
2217 2796 1.228552 ACCTCATGTGTTGGTGCCC 60.229 57.895 0.00 0.00 32.16 5.36
2218 2797 1.075482 CCTCATGTGTTGGTGCCCT 59.925 57.895 0.00 0.00 0.00 5.19
2219 2798 1.246056 CCTCATGTGTTGGTGCCCTG 61.246 60.000 0.00 0.00 0.00 4.45
2220 2799 0.538057 CTCATGTGTTGGTGCCCTGT 60.538 55.000 0.00 0.00 0.00 4.00
2221 2800 0.106268 TCATGTGTTGGTGCCCTGTT 60.106 50.000 0.00 0.00 0.00 3.16
2222 2801 0.314935 CATGTGTTGGTGCCCTGTTC 59.685 55.000 0.00 0.00 0.00 3.18
2223 2802 0.106268 ATGTGTTGGTGCCCTGTTCA 60.106 50.000 0.00 0.00 0.00 3.18
2224 2803 0.323816 TGTGTTGGTGCCCTGTTCAA 60.324 50.000 0.00 0.00 0.00 2.69
2225 2804 0.820871 GTGTTGGTGCCCTGTTCAAA 59.179 50.000 0.00 0.00 0.00 2.69
2226 2805 1.205893 GTGTTGGTGCCCTGTTCAAAA 59.794 47.619 0.00 0.00 0.00 2.44
2227 2806 1.902508 TGTTGGTGCCCTGTTCAAAAA 59.097 42.857 0.00 0.00 0.00 1.94
2253 2832 7.112452 AGAAAGTGTTGGTGCTTATTTTTCT 57.888 32.000 0.00 0.00 0.00 2.52
2269 2848 4.519540 TTTTCTAAGGATGCCTTTGTGC 57.480 40.909 3.77 0.00 41.69 4.57
2273 2852 0.963962 AAGGATGCCTTTGTGCTGTG 59.036 50.000 0.00 0.00 41.69 3.66
2284 2863 1.374947 GTGCTGTGCCCTGTTCCTA 59.625 57.895 0.00 0.00 0.00 2.94
2292 2871 0.902531 GCCCTGTTCCTACTAGTGCA 59.097 55.000 5.39 0.00 0.00 4.57
2297 2876 4.565652 CCCTGTTCCTACTAGTGCAAATGT 60.566 45.833 5.39 0.00 0.00 2.71
2337 2916 8.746922 TTTTTCTCTTTCATGATGAAATTCCG 57.253 30.769 19.72 9.34 44.37 4.30
2386 2965 7.148255 CCTGCATATTACTACAGCTGTTCAAAA 60.148 37.037 27.06 14.53 0.00 2.44
2533 3112 1.762708 CACTGGAGTGTGGTTGGTTT 58.237 50.000 0.00 0.00 40.96 3.27
2576 3155 1.527034 GCCTTCTGTTCTGATGTGCA 58.473 50.000 0.00 0.00 0.00 4.57
2699 3280 3.187379 TGTACTGGTATGTACCCCACA 57.813 47.619 6.74 5.43 45.87 4.17
2700 3281 3.518639 TGTACTGGTATGTACCCCACAA 58.481 45.455 6.74 0.00 45.87 3.33
2701 3282 3.261390 TGTACTGGTATGTACCCCACAAC 59.739 47.826 6.74 0.14 45.87 3.32
2771 3352 5.967674 GTGCACAATGCTCAATATCACTAAC 59.032 40.000 13.17 0.00 45.31 2.34
2833 3415 0.392461 TCGCTTGCCCTGTTGTATCC 60.392 55.000 0.00 0.00 0.00 2.59
2874 3456 6.064060 TGTGGTTTCTCAAGTCAGATTGATT 58.936 36.000 0.00 0.00 38.47 2.57
3046 3628 9.959721 AAATACAAGTGAAGAAGAGCCTTATTA 57.040 29.630 0.00 0.00 0.00 0.98
3078 3660 8.330247 AGTCTACTCTGAAGTCTGAATAGGTAA 58.670 37.037 4.53 0.00 36.92 2.85
3168 3750 2.092968 TGGCTACATACTGAGCTTTGGG 60.093 50.000 0.00 0.00 38.79 4.12
3300 3883 3.515330 TTTCGCTACTACTACTTGGGC 57.485 47.619 0.00 0.00 0.00 5.36
3303 3886 2.022195 CGCTACTACTACTTGGGCTCA 58.978 52.381 0.00 0.00 0.00 4.26
3325 3908 9.971922 GCTCATGCCTATTAATATCTTGTTTTT 57.028 29.630 0.00 0.00 0.00 1.94
3591 4174 3.706373 GCCTCGGCTTCCCTGACA 61.706 66.667 0.00 0.00 38.26 3.58
3610 4193 3.951663 ACAAGTTTGTCCAGGTATAGGC 58.048 45.455 0.00 0.00 36.50 3.93
3640 4223 1.658114 TCGAAGTCGACACAGGTGG 59.342 57.895 19.50 0.00 44.22 4.61
3641 4224 1.105167 TCGAAGTCGACACAGGTGGT 61.105 55.000 19.50 0.00 44.22 4.16
3652 4235 3.498071 AGGTGGTGGTGGTGGTGG 61.498 66.667 0.00 0.00 0.00 4.61
3711 4294 1.421646 ACCCTGTCCAGTTCTTCTTGG 59.578 52.381 0.00 0.00 0.00 3.61
3749 4332 1.210155 GGTCAATGTTGCTGTCGGC 59.790 57.895 0.00 0.00 42.22 5.54
3803 4386 1.532921 CGTGAGCTCCTTCTCGATGAC 60.533 57.143 12.15 0.00 36.48 3.06
3813 4396 4.709982 TCGATGACGATGAAGCCG 57.290 55.556 0.00 0.00 43.81 5.52
3864 4468 2.270257 GCCATGCTGCTGGTTGTGA 61.270 57.895 16.03 0.00 38.63 3.58
3883 4487 2.290641 TGACTCTTGTTGGTGGTGTTGT 60.291 45.455 0.00 0.00 0.00 3.32
3954 4558 4.016706 GCGGTAGCAGGTGGTGGT 62.017 66.667 0.00 0.00 44.35 4.16
3993 4597 2.036414 AGAGCGAGGGTGAGCAGA 59.964 61.111 0.00 0.00 35.48 4.26
3994 4598 2.003658 GAGAGCGAGGGTGAGCAGAG 62.004 65.000 0.00 0.00 35.48 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.219322 CCATTTTTCACAGGGAAAGAAGATTT 58.781 34.615 0.00 0.00 45.70 2.17
165 166 2.479275 GCTCGGAGTGTTCTTTTGTACC 59.521 50.000 6.90 0.00 0.00 3.34
183 184 4.019174 TCTTCTTTGGATCCAAATGGCTC 58.981 43.478 34.40 0.00 43.78 4.70
214 215 3.448686 CTCTTCAAGCGAATATGACGGT 58.551 45.455 0.00 2.26 43.08 4.83
215 216 2.797156 CCTCTTCAAGCGAATATGACGG 59.203 50.000 0.00 0.00 0.00 4.79
220 221 1.871080 CGGCCTCTTCAAGCGAATAT 58.129 50.000 0.00 0.00 0.00 1.28
274 276 3.974293 TCCCCGGTTTCCTTGCCC 61.974 66.667 0.00 0.00 0.00 5.36
307 310 1.429148 CTCTTAATGCACCCCGCGAC 61.429 60.000 8.23 0.00 46.97 5.19
312 315 1.840635 AGTCTCCTCTTAATGCACCCC 59.159 52.381 0.00 0.00 0.00 4.95
333 336 2.761213 CAAGCCATGGCCTTCCCC 60.761 66.667 33.14 3.90 43.17 4.81
396 399 6.030228 GCACCAGTAATAAAATGTGCTCTTC 58.970 40.000 5.27 0.00 44.16 2.87
413 416 1.478510 CATTAGAGGAGTCGCACCAGT 59.521 52.381 0.00 0.00 0.00 4.00
422 425 3.191888 ACCTGTGGTCATTAGAGGAGT 57.808 47.619 0.00 0.00 0.00 3.85
429 432 6.207810 GGTTGATTTTGTACCTGTGGTCATTA 59.792 38.462 0.00 0.00 37.09 1.90
451 454 2.754375 GACCCATGGTGGTCGGTT 59.246 61.111 11.73 0.00 44.98 4.44
484 487 0.460987 CTCTGCCACGGTTGATCTCC 60.461 60.000 0.00 0.00 0.00 3.71
502 505 1.771255 GGTTCCATCTGCATCTACCCT 59.229 52.381 0.00 0.00 0.00 4.34
527 530 1.305046 TCTCTTCCTCCCGACCCAC 60.305 63.158 0.00 0.00 0.00 4.61
579 582 1.558233 CTCTAGGGTTCCAAGACGGT 58.442 55.000 0.00 0.00 35.57 4.83
601 604 0.179089 CCTTGTCTCTCTCGGCCATG 60.179 60.000 2.24 0.00 0.00 3.66
603 606 1.984570 CCCTTGTCTCTCTCGGCCA 60.985 63.158 2.24 0.00 0.00 5.36
605 608 0.968393 AGTCCCTTGTCTCTCTCGGC 60.968 60.000 0.00 0.00 0.00 5.54
659 667 3.858135 TCCAACTAAACTCCACCTCTCT 58.142 45.455 0.00 0.00 0.00 3.10
673 681 8.943002 GGTTCTTTTCGATCTTTTATCCAACTA 58.057 33.333 0.00 0.00 0.00 2.24
689 697 3.947196 TCATCCATGATGGGTTCTTTTCG 59.053 43.478 12.26 0.00 40.15 3.46
721 732 2.226912 TCGCCGGGTTATTTTTGTCTTG 59.773 45.455 2.18 0.00 0.00 3.02
735 748 1.227002 GTAGCTTCTTCTCGCCGGG 60.227 63.158 2.18 0.00 0.00 5.73
739 752 2.094442 AGAGTTGGTAGCTTCTTCTCGC 60.094 50.000 0.00 0.00 0.00 5.03
740 753 3.191581 TGAGAGTTGGTAGCTTCTTCTCG 59.808 47.826 0.00 0.00 0.00 4.04
744 757 4.965200 AAGTGAGAGTTGGTAGCTTCTT 57.035 40.909 0.00 0.00 0.00 2.52
760 773 9.569122 AGCACCTAATTTTTACTCTTAAAGTGA 57.431 29.630 0.00 0.00 39.11 3.41
768 781 6.708949 TCGAACAAGCACCTAATTTTTACTCT 59.291 34.615 0.00 0.00 0.00 3.24
774 787 7.122055 TGGATTATCGAACAAGCACCTAATTTT 59.878 33.333 0.00 0.00 0.00 1.82
776 789 6.038271 GTGGATTATCGAACAAGCACCTAATT 59.962 38.462 0.00 0.00 0.00 1.40
830 844 1.706287 GAAGCGGAGAAACGGATGCC 61.706 60.000 0.00 0.00 0.00 4.40
836 850 4.501559 TGATATTAACGAAGCGGAGAAACG 59.498 41.667 0.00 0.00 0.00 3.60
848 862 5.066893 ACGGAGCTACAGTTGATATTAACGA 59.933 40.000 0.00 0.00 35.73 3.85
854 868 4.261072 CGTACACGGAGCTACAGTTGATAT 60.261 45.833 0.00 0.00 35.37 1.63
856 870 2.159421 CGTACACGGAGCTACAGTTGAT 60.159 50.000 0.00 0.00 35.37 2.57
899 913 1.671742 GCTTGTTCGGAGTCCCTCA 59.328 57.895 2.80 0.00 31.08 3.86
977 1018 3.826729 GGCACATTAACAGAAGGAACCTT 59.173 43.478 5.74 5.74 39.23 3.50
1182 1658 4.265507 AGGGGACGGTGAGGGGTT 62.266 66.667 0.00 0.00 0.00 4.11
1472 1948 8.791355 AACAAACAAATAAACAATACGGAGAC 57.209 30.769 0.00 0.00 0.00 3.36
1529 2091 2.809601 AGGCTTACTCGCGCAACG 60.810 61.111 8.75 0.00 45.62 4.10
1530 2092 2.778679 CAGGCTTACTCGCGCAAC 59.221 61.111 8.75 0.00 0.00 4.17
1531 2093 3.118454 GCAGGCTTACTCGCGCAA 61.118 61.111 8.75 0.00 0.00 4.85
1532 2094 4.069232 AGCAGGCTTACTCGCGCA 62.069 61.111 8.75 0.00 0.00 6.09
1551 2113 5.280945 TCTGCTCAAACAACAAACAATAGC 58.719 37.500 0.00 0.00 0.00 2.97
1594 2156 3.568007 TGGGAGTTAACATGAACTTGCAC 59.432 43.478 8.61 0.00 39.79 4.57
1632 2194 5.181245 AGACCCAAGATGTAAAACATGTTCG 59.819 40.000 12.39 0.00 39.66 3.95
1641 2203 5.818678 ACACTACAGACCCAAGATGTAAA 57.181 39.130 0.00 0.00 0.00 2.01
1647 2209 3.006537 GCTTGTACACTACAGACCCAAGA 59.993 47.826 0.00 0.00 40.24 3.02
1648 2210 3.326747 GCTTGTACACTACAGACCCAAG 58.673 50.000 0.00 0.00 40.24 3.61
1649 2211 2.038033 GGCTTGTACACTACAGACCCAA 59.962 50.000 0.00 0.00 40.24 4.12
1668 2230 2.097629 GCGTTGATAGGAAAAGAAGGGC 59.902 50.000 0.00 0.00 0.00 5.19
1776 2347 5.291128 CGTTGAGTGTGTAGAAGAAGTGTTT 59.709 40.000 0.00 0.00 0.00 2.83
1779 2350 3.182572 GCGTTGAGTGTGTAGAAGAAGTG 59.817 47.826 0.00 0.00 0.00 3.16
1781 2352 3.381045 TGCGTTGAGTGTGTAGAAGAAG 58.619 45.455 0.00 0.00 0.00 2.85
1782 2353 3.446310 TGCGTTGAGTGTGTAGAAGAA 57.554 42.857 0.00 0.00 0.00 2.52
1783 2354 3.660501 ATGCGTTGAGTGTGTAGAAGA 57.339 42.857 0.00 0.00 0.00 2.87
1792 2366 1.136252 GTGTGCTGTATGCGTTGAGTG 60.136 52.381 0.00 0.00 46.63 3.51
1800 2374 3.796504 GCATATTTGGGTGTGCTGTATGC 60.797 47.826 0.00 0.00 43.25 3.14
1802 2376 3.381272 GTGCATATTTGGGTGTGCTGTAT 59.619 43.478 0.00 0.00 37.17 2.29
1823 2397 6.798427 TGAGAAGAAACTAGGAGCATATGT 57.202 37.500 4.29 0.00 0.00 2.29
1837 2411 2.743664 CCATGCGTGTGATGAGAAGAAA 59.256 45.455 4.96 0.00 0.00 2.52
1848 2422 0.603707 AAGACCACTCCATGCGTGTG 60.604 55.000 4.96 9.74 36.03 3.82
1899 2473 0.827368 GCAGGGACAGAGGGAACTAG 59.173 60.000 0.00 0.00 44.43 2.57
1931 2510 9.578576 TCAGAAAATTATAGCAGCCTGATAAAT 57.421 29.630 0.00 0.00 0.00 1.40
1932 2511 8.840321 GTCAGAAAATTATAGCAGCCTGATAAA 58.160 33.333 0.00 0.00 32.90 1.40
1933 2512 8.213679 AGTCAGAAAATTATAGCAGCCTGATAA 58.786 33.333 0.00 0.00 32.90 1.75
1934 2513 7.658982 CAGTCAGAAAATTATAGCAGCCTGATA 59.341 37.037 0.00 0.00 32.90 2.15
1935 2514 6.485984 CAGTCAGAAAATTATAGCAGCCTGAT 59.514 38.462 0.00 0.00 32.90 2.90
1936 2515 5.819379 CAGTCAGAAAATTATAGCAGCCTGA 59.181 40.000 0.00 0.00 0.00 3.86
1937 2516 5.587844 ACAGTCAGAAAATTATAGCAGCCTG 59.412 40.000 0.00 0.00 0.00 4.85
1938 2517 5.749462 ACAGTCAGAAAATTATAGCAGCCT 58.251 37.500 0.00 0.00 0.00 4.58
1939 2518 7.736447 ATACAGTCAGAAAATTATAGCAGCC 57.264 36.000 0.00 0.00 0.00 4.85
1987 2566 5.952347 TCCGCTACTGAATAGATATCATGGT 59.048 40.000 5.32 0.00 31.83 3.55
1988 2567 6.456795 TCCGCTACTGAATAGATATCATGG 57.543 41.667 5.32 0.00 31.83 3.66
1989 2568 5.976534 GCTCCGCTACTGAATAGATATCATG 59.023 44.000 5.32 0.00 31.83 3.07
1990 2569 5.068460 GGCTCCGCTACTGAATAGATATCAT 59.932 44.000 5.32 0.00 31.83 2.45
1991 2570 4.399618 GGCTCCGCTACTGAATAGATATCA 59.600 45.833 5.32 0.00 31.83 2.15
1992 2571 4.399618 TGGCTCCGCTACTGAATAGATATC 59.600 45.833 0.00 0.00 31.83 1.63
1993 2572 4.344978 TGGCTCCGCTACTGAATAGATAT 58.655 43.478 0.00 0.00 31.83 1.63
1999 2578 1.195115 TTCTGGCTCCGCTACTGAAT 58.805 50.000 0.00 0.00 0.00 2.57
2001 2580 0.973632 TTTTCTGGCTCCGCTACTGA 59.026 50.000 0.00 0.00 0.00 3.41
2002 2581 1.808411 TTTTTCTGGCTCCGCTACTG 58.192 50.000 0.00 0.00 0.00 2.74
2003 2582 2.027192 TGATTTTTCTGGCTCCGCTACT 60.027 45.455 0.00 0.00 0.00 2.57
2004 2583 2.352960 CTGATTTTTCTGGCTCCGCTAC 59.647 50.000 0.00 0.00 0.00 3.58
2005 2584 2.236146 TCTGATTTTTCTGGCTCCGCTA 59.764 45.455 0.00 0.00 0.00 4.26
2006 2585 1.003580 TCTGATTTTTCTGGCTCCGCT 59.996 47.619 0.00 0.00 0.00 5.52
2008 2587 3.273434 TCATCTGATTTTTCTGGCTCCG 58.727 45.455 0.00 0.00 0.00 4.63
2010 2589 3.631227 CCCTCATCTGATTTTTCTGGCTC 59.369 47.826 0.00 0.00 0.00 4.70
2011 2590 3.626729 CCCCTCATCTGATTTTTCTGGCT 60.627 47.826 0.00 0.00 0.00 4.75
2012 2591 2.692041 CCCCTCATCTGATTTTTCTGGC 59.308 50.000 0.00 0.00 0.00 4.85
2013 2592 3.294214 CCCCCTCATCTGATTTTTCTGG 58.706 50.000 0.00 0.00 0.00 3.86
2031 2610 2.036733 GGTTTAACAAAACTCAGCCCCC 59.963 50.000 0.00 0.00 33.37 5.40
2033 2612 4.142026 ACAAGGTTTAACAAAACTCAGCCC 60.142 41.667 0.00 0.00 37.47 5.19
2034 2613 5.006153 ACAAGGTTTAACAAAACTCAGCC 57.994 39.130 0.00 0.00 37.47 4.85
2035 2614 4.733405 CGACAAGGTTTAACAAAACTCAGC 59.267 41.667 0.00 0.00 37.47 4.26
2036 2615 5.270853 CCGACAAGGTTTAACAAAACTCAG 58.729 41.667 0.00 0.00 37.47 3.35
2037 2616 4.096682 CCCGACAAGGTTTAACAAAACTCA 59.903 41.667 0.00 0.00 37.47 3.41
2038 2617 4.498513 CCCCGACAAGGTTTAACAAAACTC 60.499 45.833 0.00 0.00 37.47 3.01
2039 2618 3.382227 CCCCGACAAGGTTTAACAAAACT 59.618 43.478 0.00 0.00 41.00 2.66
2040 2619 3.708890 CCCCGACAAGGTTTAACAAAAC 58.291 45.455 0.00 0.00 38.74 2.43
2041 2620 2.101082 GCCCCGACAAGGTTTAACAAAA 59.899 45.455 0.00 0.00 38.74 2.44
2042 2621 1.682323 GCCCCGACAAGGTTTAACAAA 59.318 47.619 0.00 0.00 38.74 2.83
2043 2622 1.320507 GCCCCGACAAGGTTTAACAA 58.679 50.000 0.00 0.00 38.74 2.83
2044 2623 0.885596 CGCCCCGACAAGGTTTAACA 60.886 55.000 0.00 0.00 38.74 2.41
2045 2624 1.579964 CCGCCCCGACAAGGTTTAAC 61.580 60.000 0.00 0.00 38.74 2.01
2046 2625 1.302671 CCGCCCCGACAAGGTTTAA 60.303 57.895 0.00 0.00 38.74 1.52
2047 2626 2.348243 CCGCCCCGACAAGGTTTA 59.652 61.111 0.00 0.00 38.74 2.01
2048 2627 4.653888 CCCGCCCCGACAAGGTTT 62.654 66.667 0.00 0.00 38.74 3.27
2059 2638 4.521292 TGATGGATTGGCCCGCCC 62.521 66.667 0.00 0.00 34.97 6.13
2060 2639 1.612395 TTTTGATGGATTGGCCCGCC 61.612 55.000 0.00 0.00 34.97 6.13
2061 2640 0.248843 TTTTTGATGGATTGGCCCGC 59.751 50.000 0.00 0.00 34.97 6.13
2062 2641 1.740043 GCTTTTTGATGGATTGGCCCG 60.740 52.381 0.00 0.00 34.97 6.13
2063 2642 1.278699 TGCTTTTTGATGGATTGGCCC 59.721 47.619 0.00 0.00 34.97 5.80
2064 2643 2.349590 GTGCTTTTTGATGGATTGGCC 58.650 47.619 0.00 0.00 37.10 5.36
2065 2644 2.289569 TGGTGCTTTTTGATGGATTGGC 60.290 45.455 0.00 0.00 0.00 4.52
2066 2645 3.681593 TGGTGCTTTTTGATGGATTGG 57.318 42.857 0.00 0.00 0.00 3.16
2067 2646 6.563222 AAAATGGTGCTTTTTGATGGATTG 57.437 33.333 0.00 0.00 0.00 2.67
2068 2647 6.372381 GCTAAAATGGTGCTTTTTGATGGATT 59.628 34.615 0.00 0.00 31.15 3.01
2069 2648 5.876460 GCTAAAATGGTGCTTTTTGATGGAT 59.124 36.000 0.00 0.00 31.15 3.41
2070 2649 5.221601 TGCTAAAATGGTGCTTTTTGATGGA 60.222 36.000 0.00 0.00 31.15 3.41
2071 2650 4.996122 TGCTAAAATGGTGCTTTTTGATGG 59.004 37.500 0.00 0.00 31.15 3.51
2072 2651 5.927689 TCTGCTAAAATGGTGCTTTTTGATG 59.072 36.000 0.00 0.00 31.15 3.07
2073 2652 6.100404 TCTGCTAAAATGGTGCTTTTTGAT 57.900 33.333 0.00 0.00 31.15 2.57
2074 2653 5.528043 TCTGCTAAAATGGTGCTTTTTGA 57.472 34.783 0.00 0.00 31.15 2.69
2075 2654 6.601741 TTTCTGCTAAAATGGTGCTTTTTG 57.398 33.333 0.00 0.00 31.15 2.44
2076 2655 7.622893 TTTTTCTGCTAAAATGGTGCTTTTT 57.377 28.000 0.00 0.00 31.15 1.94
2101 2680 8.996271 GCCTAGCATAAATAGTAAACGGTTATT 58.004 33.333 0.00 0.00 0.00 1.40
2102 2681 8.373220 AGCCTAGCATAAATAGTAAACGGTTAT 58.627 33.333 0.00 0.00 0.00 1.89
2103 2682 7.729116 AGCCTAGCATAAATAGTAAACGGTTA 58.271 34.615 0.00 0.00 0.00 2.85
2104 2683 6.589135 AGCCTAGCATAAATAGTAAACGGTT 58.411 36.000 0.00 0.00 0.00 4.44
2105 2684 6.170846 AGCCTAGCATAAATAGTAAACGGT 57.829 37.500 0.00 0.00 0.00 4.83
2106 2685 8.597662 TTAAGCCTAGCATAAATAGTAAACGG 57.402 34.615 0.00 0.00 0.00 4.44
2116 2695 9.627123 ACATCACTAATTTAAGCCTAGCATAAA 57.373 29.630 0.17 0.17 36.43 1.40
2117 2696 9.627123 AACATCACTAATTTAAGCCTAGCATAA 57.373 29.630 0.00 0.00 0.00 1.90
2119 2698 9.277783 CTAACATCACTAATTTAAGCCTAGCAT 57.722 33.333 0.00 0.00 0.00 3.79
2120 2699 7.715249 CCTAACATCACTAATTTAAGCCTAGCA 59.285 37.037 0.00 0.00 0.00 3.49
2121 2700 7.173390 CCCTAACATCACTAATTTAAGCCTAGC 59.827 40.741 0.00 0.00 0.00 3.42
2122 2701 7.661847 CCCCTAACATCACTAATTTAAGCCTAG 59.338 40.741 0.00 0.00 0.00 3.02
2123 2702 7.420913 CCCCCTAACATCACTAATTTAAGCCTA 60.421 40.741 0.00 0.00 0.00 3.93
2124 2703 6.365520 CCCCTAACATCACTAATTTAAGCCT 58.634 40.000 0.00 0.00 0.00 4.58
2125 2704 5.535030 CCCCCTAACATCACTAATTTAAGCC 59.465 44.000 0.00 0.00 0.00 4.35
2126 2705 6.635030 CCCCCTAACATCACTAATTTAAGC 57.365 41.667 0.00 0.00 0.00 3.09
2150 2729 4.035102 GACAGGAGGTGCCCCCAC 62.035 72.222 0.00 0.00 41.32 4.61
2151 2730 4.270153 AGACAGGAGGTGCCCCCA 62.270 66.667 0.00 0.00 37.37 4.96
2152 2731 3.403558 GAGACAGGAGGTGCCCCC 61.404 72.222 0.00 0.00 37.37 5.40
2153 2732 2.284995 AGAGACAGGAGGTGCCCC 60.285 66.667 0.00 0.00 37.37 5.80
2154 2733 2.985456 CAGAGACAGGAGGTGCCC 59.015 66.667 0.00 0.00 37.37 5.36
2155 2734 2.267324 GCAGAGACAGGAGGTGCC 59.733 66.667 0.00 0.00 0.00 5.01
2156 2735 2.237534 GAGGCAGAGACAGGAGGTGC 62.238 65.000 0.00 0.00 0.00 5.01
2157 2736 0.614415 AGAGGCAGAGACAGGAGGTG 60.614 60.000 0.00 0.00 0.00 4.00
2158 2737 0.614415 CAGAGGCAGAGACAGGAGGT 60.614 60.000 0.00 0.00 0.00 3.85
2159 2738 0.614415 ACAGAGGCAGAGACAGGAGG 60.614 60.000 0.00 0.00 0.00 4.30
2160 2739 2.136298 TACAGAGGCAGAGACAGGAG 57.864 55.000 0.00 0.00 0.00 3.69
2161 2740 2.291865 ACATACAGAGGCAGAGACAGGA 60.292 50.000 0.00 0.00 0.00 3.86
2162 2741 2.106566 ACATACAGAGGCAGAGACAGG 58.893 52.381 0.00 0.00 0.00 4.00
2163 2742 5.068329 TGAATACATACAGAGGCAGAGACAG 59.932 44.000 0.00 0.00 0.00 3.51
2164 2743 4.956075 TGAATACATACAGAGGCAGAGACA 59.044 41.667 0.00 0.00 0.00 3.41
2165 2744 5.163509 TGTGAATACATACAGAGGCAGAGAC 60.164 44.000 0.00 0.00 0.00 3.36
2166 2745 4.956075 TGTGAATACATACAGAGGCAGAGA 59.044 41.667 0.00 0.00 0.00 3.10
2167 2746 5.268118 TGTGAATACATACAGAGGCAGAG 57.732 43.478 0.00 0.00 0.00 3.35
2168 2747 5.604565 CATGTGAATACATACAGAGGCAGA 58.395 41.667 0.00 0.00 45.53 4.26
2169 2748 4.212847 GCATGTGAATACATACAGAGGCAG 59.787 45.833 0.00 0.00 45.53 4.85
2170 2749 4.129380 GCATGTGAATACATACAGAGGCA 58.871 43.478 0.00 0.00 45.53 4.75
2171 2750 4.129380 TGCATGTGAATACATACAGAGGC 58.871 43.478 0.00 0.00 45.53 4.70
2172 2751 5.410746 GGATGCATGTGAATACATACAGAGG 59.589 44.000 2.46 0.00 45.53 3.69
2173 2752 6.228995 AGGATGCATGTGAATACATACAGAG 58.771 40.000 2.46 0.00 45.53 3.35
2174 2753 6.178607 AGGATGCATGTGAATACATACAGA 57.821 37.500 2.46 0.00 45.53 3.41
2175 2754 5.993441 TGAGGATGCATGTGAATACATACAG 59.007 40.000 2.46 0.00 45.53 2.74
2176 2755 5.759763 GTGAGGATGCATGTGAATACATACA 59.240 40.000 2.46 0.00 45.53 2.29
2177 2756 5.180117 GGTGAGGATGCATGTGAATACATAC 59.820 44.000 2.46 0.00 45.53 2.39
2185 2764 1.278537 TGAGGTGAGGATGCATGTGA 58.721 50.000 2.46 0.00 0.00 3.58
2225 2804 8.560355 AAAATAAGCACCAACACTTTCTTTTT 57.440 26.923 0.00 0.00 0.00 1.94
2226 2805 8.560355 AAAAATAAGCACCAACACTTTCTTTT 57.440 26.923 0.00 0.00 0.00 2.27
2227 2806 8.040727 AGAAAAATAAGCACCAACACTTTCTTT 58.959 29.630 0.00 0.00 28.77 2.52
2228 2807 7.555965 AGAAAAATAAGCACCAACACTTTCTT 58.444 30.769 0.00 0.00 28.77 2.52
2229 2808 7.112452 AGAAAAATAAGCACCAACACTTTCT 57.888 32.000 0.00 0.00 0.00 2.52
2230 2809 8.865590 TTAGAAAAATAAGCACCAACACTTTC 57.134 30.769 0.00 0.00 0.00 2.62
2231 2810 7.926018 CCTTAGAAAAATAAGCACCAACACTTT 59.074 33.333 0.00 0.00 32.42 2.66
2232 2811 7.286775 TCCTTAGAAAAATAAGCACCAACACTT 59.713 33.333 0.00 0.00 32.42 3.16
2233 2812 6.775629 TCCTTAGAAAAATAAGCACCAACACT 59.224 34.615 0.00 0.00 32.42 3.55
2234 2813 6.977213 TCCTTAGAAAAATAAGCACCAACAC 58.023 36.000 0.00 0.00 32.42 3.32
2235 2814 7.601856 CATCCTTAGAAAAATAAGCACCAACA 58.398 34.615 0.00 0.00 32.42 3.33
2253 2832 2.161855 CACAGCACAAAGGCATCCTTA 58.838 47.619 0.00 0.00 43.92 2.69
2269 2848 2.093973 CACTAGTAGGAACAGGGCACAG 60.094 54.545 1.45 0.00 0.00 3.66
2273 2852 0.902531 TGCACTAGTAGGAACAGGGC 59.097 55.000 1.45 0.00 0.00 5.19
2284 2863 2.554032 GCCACAGAACATTTGCACTAGT 59.446 45.455 0.00 0.00 0.00 2.57
2292 2871 4.486125 AAAACAAGGCCACAGAACATTT 57.514 36.364 5.01 0.00 0.00 2.32
2386 2965 3.256704 TCCTTACTGACCCTCCATGTTT 58.743 45.455 0.00 0.00 0.00 2.83
2400 2979 0.107654 GCATCCACGGCTTCCTTACT 60.108 55.000 0.00 0.00 0.00 2.24
2576 3155 1.523758 GCGTGGAACTGAATCCTGTT 58.476 50.000 5.99 0.00 40.35 3.16
2582 3161 1.545582 CAATTGGGCGTGGAACTGAAT 59.454 47.619 0.00 0.00 31.75 2.57
2699 3280 2.802816 GCTGAGTCATGTCAAGAACGTT 59.197 45.455 0.00 0.00 0.00 3.99
2700 3281 2.036475 AGCTGAGTCATGTCAAGAACGT 59.964 45.455 0.00 0.00 0.00 3.99
2701 3282 2.411069 CAGCTGAGTCATGTCAAGAACG 59.589 50.000 8.42 0.00 0.00 3.95
2833 3415 1.035139 ACAGAAAGTTGCAGCAAGGG 58.965 50.000 8.49 0.00 0.00 3.95
2874 3456 1.212688 CCTGCCACCATCAGACCAATA 59.787 52.381 0.00 0.00 33.54 1.90
3007 3589 6.345298 TCACTTGTATTTCTCCATTATGCGA 58.655 36.000 0.00 0.00 0.00 5.10
3046 3628 4.704540 CAGACTTCAGAGTAGACTCACCAT 59.295 45.833 12.09 0.00 45.21 3.55
3078 3660 3.679389 CCACAGCAGGTATTTCTCTGTT 58.321 45.455 0.00 0.00 36.01 3.16
3092 3674 1.866483 ATCCATCCAAGGCCACAGCA 61.866 55.000 5.01 0.00 42.56 4.41
3160 3742 2.765699 TCTTGCTGAAAAACCCAAAGCT 59.234 40.909 0.00 0.00 34.92 3.74
3162 3744 4.947645 TCATCTTGCTGAAAAACCCAAAG 58.052 39.130 0.00 0.00 0.00 2.77
3168 3750 5.807011 ACAACAACTCATCTTGCTGAAAAAC 59.193 36.000 0.00 0.00 0.00 2.43
3334 3917 4.202388 ACTCTACTCTTTACCCCGCAAAAA 60.202 41.667 0.00 0.00 0.00 1.94
3335 3918 3.325716 ACTCTACTCTTTACCCCGCAAAA 59.674 43.478 0.00 0.00 0.00 2.44
3336 3919 2.901839 ACTCTACTCTTTACCCCGCAAA 59.098 45.455 0.00 0.00 0.00 3.68
3337 3920 2.532843 ACTCTACTCTTTACCCCGCAA 58.467 47.619 0.00 0.00 0.00 4.85
3338 3921 2.226962 ACTCTACTCTTTACCCCGCA 57.773 50.000 0.00 0.00 0.00 5.69
3339 3922 2.494870 TCAACTCTACTCTTTACCCCGC 59.505 50.000 0.00 0.00 0.00 6.13
3340 3923 5.105473 TCAATCAACTCTACTCTTTACCCCG 60.105 44.000 0.00 0.00 0.00 5.73
3342 3925 6.814146 CAGTCAATCAACTCTACTCTTTACCC 59.186 42.308 0.00 0.00 0.00 3.69
3344 3927 7.379750 ACCAGTCAATCAACTCTACTCTTTAC 58.620 38.462 0.00 0.00 0.00 2.01
3345 3928 7.540474 ACCAGTCAATCAACTCTACTCTTTA 57.460 36.000 0.00 0.00 0.00 1.85
3346 3929 6.426646 ACCAGTCAATCAACTCTACTCTTT 57.573 37.500 0.00 0.00 0.00 2.52
3347 3930 6.426646 AACCAGTCAATCAACTCTACTCTT 57.573 37.500 0.00 0.00 0.00 2.85
3394 3977 5.716228 TGTGCATTTTGGATCTACCTGATTT 59.284 36.000 0.00 0.00 39.86 2.17
3401 3984 8.190122 TGAATGTAATGTGCATTTTGGATCTAC 58.810 33.333 2.56 0.00 36.77 2.59
3591 4174 2.679930 GCGCCTATACCTGGACAAACTT 60.680 50.000 0.00 0.00 0.00 2.66
3632 4215 2.203337 CCACCACCACCACCTGTG 60.203 66.667 0.00 0.00 45.01 3.66
3633 4216 2.694616 ACCACCACCACCACCTGT 60.695 61.111 0.00 0.00 0.00 4.00
3634 4217 2.203337 CACCACCACCACCACCTG 60.203 66.667 0.00 0.00 0.00 4.00
3635 4218 3.498071 CCACCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
3711 4294 3.632145 ACCAAGACAACATGAAACTGGAC 59.368 43.478 0.00 0.00 0.00 4.02
3864 4468 2.507407 ACAACACCACCAACAAGAGT 57.493 45.000 0.00 0.00 0.00 3.24
3934 4538 3.009115 ACCACCTGCTACCGCCAT 61.009 61.111 0.00 0.00 34.43 4.40
3944 4548 1.513158 CTCTCGCTACCACCACCTG 59.487 63.158 0.00 0.00 0.00 4.00
3954 4558 2.202663 CGCAAGCTGCTCTCGCTA 60.203 61.111 1.00 0.00 42.25 4.26
3978 4582 3.768922 GCTCTGCTCACCCTCGCT 61.769 66.667 0.00 0.00 0.00 4.93


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

AutoCloner maintained by Alex Coulton.