Multiple sequence alignment - TraesCS5A01G220600

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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 TraesCS5A01G220600 chr5A 100.000 2779 0 0 1001 3779 437040883 437038105 0.000000e+00 5132
1 TraesCS5A01G220600 chr5A 100.000 662 0 0 1 662 437041883 437041222 0.000000e+00 1223
2 TraesCS5A01G220600 chr5B 89.116 1470 100 30 1966 3422 393844414 393842992 0.000000e+00 1773
3 TraesCS5A01G220600 chr5B 90.536 634 41 10 1001 1630 393845379 393844761 0.000000e+00 821
4 TraesCS5A01G220600 chr5B 91.176 340 24 4 3441 3779 393839169 393838835 1.240000e-124 457
5 TraesCS5A01G220600 chr5B 93.981 216 12 1 1652 1867 393844690 393844476 3.640000e-85 326
6 TraesCS5A01G220600 chr5B 79.796 490 33 17 214 661 393845943 393845478 2.850000e-76 296
7 TraesCS5A01G220600 chr5D 89.384 1413 86 24 2382 3779 335876329 335874966 0.000000e+00 1720
8 TraesCS5A01G220600 chr5D 96.712 517 17 0 1001 1517 335877564 335877048 0.000000e+00 861
9 TraesCS5A01G220600 chr5D 81.445 609 36 24 105 661 335878242 335877659 9.700000e-116 427
10 TraesCS5A01G220600 chr5D 89.231 260 17 4 2096 2355 335876577 335876329 7.880000e-82 315
11 TraesCS5A01G220600 chr5D 89.041 219 21 2 1652 1867 335876939 335876721 6.220000e-68 268
12 TraesCS5A01G220600 chr3A 93.694 111 7 0 1 111 657458237 657458127 2.330000e-37 167
13 TraesCS5A01G220600 chr2D 94.444 108 5 1 1 108 642827207 642827313 8.400000e-37 165
14 TraesCS5A01G220600 chr2D 92.793 111 8 0 1 111 451013030 451012920 1.090000e-35 161
15 TraesCS5A01G220600 chr7A 93.578 109 7 0 1 109 182722256 182722148 3.020000e-36 163
16 TraesCS5A01G220600 chr4D 93.519 108 7 0 1 108 11504248 11504355 1.090000e-35 161
17 TraesCS5A01G220600 chr4D 93.519 108 7 0 1 108 30506559 30506666 1.090000e-35 161
18 TraesCS5A01G220600 chr4D 93.519 108 7 0 1 108 76612076 76612183 1.090000e-35 161
19 TraesCS5A01G220600 chr3D 93.519 108 7 0 1 108 71518778 71518885 1.090000e-35 161
20 TraesCS5A01G220600 chr1D 93.519 108 7 0 1 108 377374205 377374312 1.090000e-35 161


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 TraesCS5A01G220600 chr5A 437038105 437041883 3778 True 3177.5 5132 100.0000 1 3779 2 chr5A.!!$R1 3778
1 TraesCS5A01G220600 chr5B 393838835 393845943 7108 True 734.6 1773 88.9210 214 3779 5 chr5B.!!$R1 3565
2 TraesCS5A01G220600 chr5D 335874966 335878242 3276 True 718.2 1720 89.1626 105 3779 5 chr5D.!!$R1 3674

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
440 491 0.591741 CGAGTCGCGGTCAATAGTCC 60.592 60.0 6.13 0.0 36.03 3.85 F
2213 2348 0.028902 GTTGCAACGTGGAACCAGAC 59.971 55.0 14.90 0.0 41.94 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2422 2562 0.03601 AAATGGTCAGTCAGCCTCCG 60.036 55.0 0.00 0.00 0.0 4.63 R
3121 3275 0.09473 CACGAGCGAATTTCCGGAAC 59.905 55.0 18.64 4.83 0.0 3.62 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
22 23 3.877508 ACTGATATAACTTTTGCTCCCGC 59.122 43.478 0.00 0.00 0.00 6.13
23 24 3.211045 TGATATAACTTTTGCTCCCGCC 58.789 45.455 0.00 0.00 34.43 6.13
24 25 1.658994 TATAACTTTTGCTCCCGCCG 58.341 50.000 0.00 0.00 34.43 6.46
25 26 1.654023 ATAACTTTTGCTCCCGCCGC 61.654 55.000 0.00 0.00 34.43 6.53
26 27 4.887932 TATAACTTTTGCTCCCGCCGCA 62.888 50.000 0.00 0.00 35.22 5.69
27 28 3.669344 CTTTTGCTCCCGCCGCAA 61.669 61.111 0.00 0.00 44.83 4.85
28 29 2.988684 TTTTGCTCCCGCCGCAAT 60.989 55.556 5.33 0.00 45.67 3.56
29 30 2.872337 CTTTTGCTCCCGCCGCAATC 62.872 60.000 5.33 0.00 45.67 2.67
47 48 7.734538 CGCAATCGGTTTTGATAGTTAAATT 57.265 32.000 0.00 0.00 0.00 1.82
48 49 8.168681 CGCAATCGGTTTTGATAGTTAAATTT 57.831 30.769 0.00 0.00 0.00 1.82
49 50 9.279904 CGCAATCGGTTTTGATAGTTAAATTTA 57.720 29.630 0.00 0.00 0.00 1.40
52 53 9.777575 AATCGGTTTTGATAGTTAAATTTACGG 57.222 29.630 0.00 0.00 0.00 4.02
53 54 8.321650 TCGGTTTTGATAGTTAAATTTACGGT 57.678 30.769 0.00 0.00 0.00 4.83
54 55 8.442384 TCGGTTTTGATAGTTAAATTTACGGTC 58.558 33.333 0.00 0.00 0.00 4.79
55 56 8.229137 CGGTTTTGATAGTTAAATTTACGGTCA 58.771 33.333 0.00 0.00 0.00 4.02
56 57 9.896263 GGTTTTGATAGTTAAATTTACGGTCAA 57.104 29.630 0.00 4.35 0.00 3.18
68 69 7.667984 AATTTACGGTCAAAGTTAAAACACG 57.332 32.000 0.00 0.00 0.00 4.49
69 70 6.414408 TTTACGGTCAAAGTTAAAACACGA 57.586 33.333 0.00 0.00 0.00 4.35
70 71 4.525411 ACGGTCAAAGTTAAAACACGAG 57.475 40.909 0.00 0.00 0.00 4.18
71 72 3.310501 ACGGTCAAAGTTAAAACACGAGG 59.689 43.478 0.00 0.00 0.00 4.63
72 73 3.556775 CGGTCAAAGTTAAAACACGAGGA 59.443 43.478 0.00 0.00 0.00 3.71
73 74 4.212636 CGGTCAAAGTTAAAACACGAGGAT 59.787 41.667 0.00 0.00 0.00 3.24
74 75 5.406175 CGGTCAAAGTTAAAACACGAGGATA 59.594 40.000 0.00 0.00 0.00 2.59
75 76 6.400727 CGGTCAAAGTTAAAACACGAGGATAG 60.401 42.308 0.00 0.00 0.00 2.08
76 77 6.647895 GGTCAAAGTTAAAACACGAGGATAGA 59.352 38.462 0.00 0.00 0.00 1.98
77 78 7.148623 GGTCAAAGTTAAAACACGAGGATAGAG 60.149 40.741 0.00 0.00 0.00 2.43
78 79 6.872020 TCAAAGTTAAAACACGAGGATAGAGG 59.128 38.462 0.00 0.00 0.00 3.69
79 80 6.600882 AAGTTAAAACACGAGGATAGAGGA 57.399 37.500 0.00 0.00 0.00 3.71
80 81 6.600882 AGTTAAAACACGAGGATAGAGGAA 57.399 37.500 0.00 0.00 0.00 3.36
81 82 6.631962 AGTTAAAACACGAGGATAGAGGAAG 58.368 40.000 0.00 0.00 0.00 3.46
82 83 3.528597 AAACACGAGGATAGAGGAAGC 57.471 47.619 0.00 0.00 0.00 3.86
83 84 2.145397 ACACGAGGATAGAGGAAGCA 57.855 50.000 0.00 0.00 0.00 3.91
84 85 1.751924 ACACGAGGATAGAGGAAGCAC 59.248 52.381 0.00 0.00 0.00 4.40
85 86 1.751351 CACGAGGATAGAGGAAGCACA 59.249 52.381 0.00 0.00 0.00 4.57
86 87 2.166459 CACGAGGATAGAGGAAGCACAA 59.834 50.000 0.00 0.00 0.00 3.33
87 88 2.166664 ACGAGGATAGAGGAAGCACAAC 59.833 50.000 0.00 0.00 0.00 3.32
88 89 2.166459 CGAGGATAGAGGAAGCACAACA 59.834 50.000 0.00 0.00 0.00 3.33
89 90 3.181471 CGAGGATAGAGGAAGCACAACAT 60.181 47.826 0.00 0.00 0.00 2.71
90 91 4.681781 CGAGGATAGAGGAAGCACAACATT 60.682 45.833 0.00 0.00 0.00 2.71
91 92 5.451937 CGAGGATAGAGGAAGCACAACATTA 60.452 44.000 0.00 0.00 0.00 1.90
92 93 6.506538 AGGATAGAGGAAGCACAACATTAT 57.493 37.500 0.00 0.00 0.00 1.28
93 94 6.294473 AGGATAGAGGAAGCACAACATTATG 58.706 40.000 0.00 0.00 0.00 1.90
94 95 5.471456 GGATAGAGGAAGCACAACATTATGG 59.529 44.000 0.00 0.00 0.00 2.74
95 96 4.574674 AGAGGAAGCACAACATTATGGA 57.425 40.909 0.00 0.00 0.00 3.41
96 97 4.922206 AGAGGAAGCACAACATTATGGAA 58.078 39.130 0.00 0.00 0.00 3.53
97 98 5.513233 AGAGGAAGCACAACATTATGGAAT 58.487 37.500 0.00 0.00 0.00 3.01
98 99 5.954150 AGAGGAAGCACAACATTATGGAATT 59.046 36.000 0.00 0.00 0.00 2.17
99 100 5.969423 AGGAAGCACAACATTATGGAATTG 58.031 37.500 0.00 0.00 0.00 2.32
100 101 5.716228 AGGAAGCACAACATTATGGAATTGA 59.284 36.000 0.00 0.00 0.00 2.57
101 102 6.038356 GGAAGCACAACATTATGGAATTGAG 58.962 40.000 0.00 0.00 0.00 3.02
102 103 5.587388 AGCACAACATTATGGAATTGAGG 57.413 39.130 0.00 0.00 0.00 3.86
103 104 4.403432 AGCACAACATTATGGAATTGAGGG 59.597 41.667 0.00 0.00 0.00 4.30
112 113 7.293299 ACATTATGGAATTGAGGGAGTAGATCA 59.707 37.037 0.00 0.00 0.00 2.92
114 115 3.711704 TGGAATTGAGGGAGTAGATCACC 59.288 47.826 0.00 0.00 27.93 4.02
115 116 3.970640 GGAATTGAGGGAGTAGATCACCT 59.029 47.826 0.00 0.00 32.92 4.00
116 117 4.202305 GGAATTGAGGGAGTAGATCACCTG 60.202 50.000 0.00 0.00 31.06 4.00
123 124 3.371965 GGAGTAGATCACCTGGGTGTAA 58.628 50.000 17.87 1.98 45.55 2.41
126 127 5.104485 GGAGTAGATCACCTGGGTGTAAAAT 60.104 44.000 17.87 5.66 45.55 1.82
127 128 5.745227 AGTAGATCACCTGGGTGTAAAATG 58.255 41.667 17.87 0.00 45.55 2.32
130 131 3.866703 TCACCTGGGTGTAAAATGTGA 57.133 42.857 17.87 0.00 45.55 3.58
149 151 9.673454 AAATGTGAAAACGAGAAAAATACTACC 57.327 29.630 0.00 0.00 0.00 3.18
177 179 4.046998 CTGACGTGCGTGCGACAC 62.047 66.667 0.67 2.76 33.64 3.67
233 246 2.818296 CTTTTCTTCAGCGCGTCGGC 62.818 60.000 8.43 0.00 0.00 5.54
255 268 4.077188 GGCTCGCACACACTTCGC 62.077 66.667 0.00 0.00 0.00 4.70
261 274 2.546321 CACACACTTCGCTGTCGC 59.454 61.111 0.00 0.00 35.26 5.19
342 376 2.158726 ACAGTAGCGTCCCCTTTTTGAA 60.159 45.455 0.00 0.00 0.00 2.69
359 393 4.577834 TTGAATTTTGAACCCTTCGTCC 57.422 40.909 0.00 0.00 0.00 4.79
439 490 1.201098 GCGAGTCGCGGTCAATAGTC 61.201 60.000 23.39 0.00 44.55 2.59
440 491 0.591741 CGAGTCGCGGTCAATAGTCC 60.592 60.000 6.13 0.00 36.03 3.85
458 509 3.499737 CCGTGCCCAGCAACGATC 61.500 66.667 11.33 0.00 41.47 3.69
459 510 3.499737 CGTGCCCAGCAACGATCC 61.500 66.667 0.00 0.00 41.47 3.36
460 511 2.359850 GTGCCCAGCAACGATCCA 60.360 61.111 0.00 0.00 41.47 3.41
461 512 1.750399 GTGCCCAGCAACGATCCAT 60.750 57.895 0.00 0.00 41.47 3.41
462 513 1.451927 TGCCCAGCAACGATCCATC 60.452 57.895 0.00 0.00 34.76 3.51
463 514 2.189499 GCCCAGCAACGATCCATCC 61.189 63.158 0.00 0.00 0.00 3.51
472 523 0.610174 ACGATCCATCCATCCATCCG 59.390 55.000 0.00 0.00 0.00 4.18
533 591 3.602205 AAAGCCCAAGAACTTTCCTCT 57.398 42.857 0.00 0.00 30.35 3.69
573 641 4.326766 CCCAAACCACGCGCACAG 62.327 66.667 5.73 0.00 0.00 3.66
592 661 3.214328 CAGCCCCATCTACAAATACCAC 58.786 50.000 0.00 0.00 0.00 4.16
593 662 2.158813 AGCCCCATCTACAAATACCACG 60.159 50.000 0.00 0.00 0.00 4.94
594 663 2.218603 CCCCATCTACAAATACCACGC 58.781 52.381 0.00 0.00 0.00 5.34
595 664 2.218603 CCCATCTACAAATACCACGCC 58.781 52.381 0.00 0.00 0.00 5.68
625 694 2.242965 ACCATCCCACATCATCACACAT 59.757 45.455 0.00 0.00 0.00 3.21
626 695 2.882761 CCATCCCACATCATCACACATC 59.117 50.000 0.00 0.00 0.00 3.06
627 696 3.434596 CCATCCCACATCATCACACATCT 60.435 47.826 0.00 0.00 0.00 2.90
628 697 3.548745 TCCCACATCATCACACATCTC 57.451 47.619 0.00 0.00 0.00 2.75
631 700 3.813724 CCCACATCATCACACATCTCATC 59.186 47.826 0.00 0.00 0.00 2.92
633 702 4.448210 CACATCATCACACATCTCATCCA 58.552 43.478 0.00 0.00 0.00 3.41
642 711 1.205655 ACATCTCATCCACAGACCACG 59.794 52.381 0.00 0.00 0.00 4.94
1041 1110 1.326951 TGATCGGGATCCTGAACGCA 61.327 55.000 27.03 20.64 37.02 5.24
1174 1243 0.248825 CTTCCTCATGCTCGTCTCCG 60.249 60.000 0.00 0.00 0.00 4.63
1301 1370 2.339100 TTCGTCGTCACGCACAAGGA 62.339 55.000 0.00 0.00 46.28 3.36
1440 1509 1.896660 GGACGCCAAGGTCTGCAAA 60.897 57.895 0.00 0.00 37.12 3.68
1461 1530 2.124693 GCTCGAGGACAGGAGGGAG 61.125 68.421 15.58 0.00 0.00 4.30
1518 1588 5.203528 CCCATCCAGGTAATTCATTTCACT 58.796 41.667 0.00 0.00 34.66 3.41
1537 1607 0.535335 TGCCGATTCGCCTTCTTACT 59.465 50.000 0.00 0.00 0.00 2.24
1539 1609 2.007608 GCCGATTCGCCTTCTTACTTT 58.992 47.619 0.00 0.00 0.00 2.66
1540 1610 2.418976 GCCGATTCGCCTTCTTACTTTT 59.581 45.455 0.00 0.00 0.00 2.27
1541 1611 3.119955 GCCGATTCGCCTTCTTACTTTTT 60.120 43.478 0.00 0.00 0.00 1.94
1542 1612 4.093850 GCCGATTCGCCTTCTTACTTTTTA 59.906 41.667 0.00 0.00 0.00 1.52
1543 1613 5.220796 GCCGATTCGCCTTCTTACTTTTTAT 60.221 40.000 0.00 0.00 0.00 1.40
1546 1616 8.557029 CCGATTCGCCTTCTTACTTTTTATTAT 58.443 33.333 0.00 0.00 0.00 1.28
1600 1670 4.200092 GCCTGAAGATAACAAACCTAGGG 58.800 47.826 14.81 0.00 0.00 3.53
1624 1695 9.231297 GGGAAAATATATTTGATGATCCGAGAA 57.769 33.333 11.42 0.00 0.00 2.87
1632 1703 4.760530 TGATGATCCGAGAAGAATTGGT 57.239 40.909 0.00 0.00 0.00 3.67
1633 1704 4.697514 TGATGATCCGAGAAGAATTGGTC 58.302 43.478 0.00 0.00 0.00 4.02
1634 1705 4.162131 TGATGATCCGAGAAGAATTGGTCA 59.838 41.667 0.00 0.00 0.00 4.02
1636 1707 4.507710 TGATCCGAGAAGAATTGGTCAAG 58.492 43.478 0.00 0.00 0.00 3.02
1637 1708 4.020218 TGATCCGAGAAGAATTGGTCAAGT 60.020 41.667 0.00 0.00 0.00 3.16
1639 1710 4.817517 TCCGAGAAGAATTGGTCAAGTAC 58.182 43.478 0.00 0.00 0.00 2.73
1640 1711 4.527038 TCCGAGAAGAATTGGTCAAGTACT 59.473 41.667 0.00 0.00 0.00 2.73
1642 1713 6.209986 TCCGAGAAGAATTGGTCAAGTACTTA 59.790 38.462 8.04 0.00 0.00 2.24
1643 1714 6.310711 CCGAGAAGAATTGGTCAAGTACTTAC 59.689 42.308 8.04 7.16 0.00 2.34
1645 1716 7.384115 CGAGAAGAATTGGTCAAGTACTTACAA 59.616 37.037 8.04 13.70 0.00 2.41
1705 1832 1.140816 GTGCTCGCCGAGATATTTCC 58.859 55.000 20.05 0.00 0.00 3.13
1743 1873 2.324541 AGATAGTAGCTCCTGCCCAAG 58.675 52.381 0.00 0.00 40.80 3.61
1757 1887 1.782044 CCCAAGGTCAACAAATTGCG 58.218 50.000 0.00 0.00 35.63 4.85
1775 1905 5.508200 TTGCGGTTTGAGAAATTGTAGTT 57.492 34.783 0.00 0.00 0.00 2.24
1778 1908 3.906008 CGGTTTGAGAAATTGTAGTTGCG 59.094 43.478 0.00 0.00 0.00 4.85
1794 1924 1.645034 TGCGCAACTTGATCTAGAGC 58.355 50.000 8.16 12.39 0.00 4.09
1806 1936 4.845387 TGATCTAGAGCGATGTTTACGTC 58.155 43.478 3.11 0.00 0.00 4.34
1867 1997 6.294731 GGTCAATCAAATTACTCCACTTGCTT 60.295 38.462 0.00 0.00 0.00 3.91
1868 1998 7.147976 GTCAATCAAATTACTCCACTTGCTTT 58.852 34.615 0.00 0.00 0.00 3.51
1869 1999 7.653311 GTCAATCAAATTACTCCACTTGCTTTT 59.347 33.333 0.00 0.00 0.00 2.27
1870 2000 7.652909 TCAATCAAATTACTCCACTTGCTTTTG 59.347 33.333 0.00 0.00 0.00 2.44
1871 2001 6.463995 TCAAATTACTCCACTTGCTTTTGT 57.536 33.333 0.00 0.00 0.00 2.83
1872 2002 6.872920 TCAAATTACTCCACTTGCTTTTGTT 58.127 32.000 0.00 0.00 0.00 2.83
1873 2003 6.756074 TCAAATTACTCCACTTGCTTTTGTTG 59.244 34.615 0.00 0.00 0.00 3.33
1874 2004 6.463995 AATTACTCCACTTGCTTTTGTTGA 57.536 33.333 0.00 0.00 0.00 3.18
1875 2005 6.655078 ATTACTCCACTTGCTTTTGTTGAT 57.345 33.333 0.00 0.00 0.00 2.57
1876 2006 6.463995 TTACTCCACTTGCTTTTGTTGATT 57.536 33.333 0.00 0.00 0.00 2.57
1877 2007 4.685924 ACTCCACTTGCTTTTGTTGATTG 58.314 39.130 0.00 0.00 0.00 2.67
1878 2008 4.160252 ACTCCACTTGCTTTTGTTGATTGT 59.840 37.500 0.00 0.00 0.00 2.71
1879 2009 5.359576 ACTCCACTTGCTTTTGTTGATTGTA 59.640 36.000 0.00 0.00 0.00 2.41
1880 2010 6.040842 ACTCCACTTGCTTTTGTTGATTGTAT 59.959 34.615 0.00 0.00 0.00 2.29
1881 2011 6.815089 TCCACTTGCTTTTGTTGATTGTATT 58.185 32.000 0.00 0.00 0.00 1.89
1882 2012 7.271511 TCCACTTGCTTTTGTTGATTGTATTT 58.728 30.769 0.00 0.00 0.00 1.40
1883 2013 7.768120 TCCACTTGCTTTTGTTGATTGTATTTT 59.232 29.630 0.00 0.00 0.00 1.82
1884 2014 7.851963 CCACTTGCTTTTGTTGATTGTATTTTG 59.148 33.333 0.00 0.00 0.00 2.44
1885 2015 8.602328 CACTTGCTTTTGTTGATTGTATTTTGA 58.398 29.630 0.00 0.00 0.00 2.69
1886 2016 8.819974 ACTTGCTTTTGTTGATTGTATTTTGAG 58.180 29.630 0.00 0.00 0.00 3.02
1887 2017 8.939201 TTGCTTTTGTTGATTGTATTTTGAGA 57.061 26.923 0.00 0.00 0.00 3.27
1888 2018 9.545105 TTGCTTTTGTTGATTGTATTTTGAGAT 57.455 25.926 0.00 0.00 0.00 2.75
1892 2022 8.894409 TTTGTTGATTGTATTTTGAGATAGCG 57.106 30.769 0.00 0.00 0.00 4.26
1893 2023 7.841915 TGTTGATTGTATTTTGAGATAGCGA 57.158 32.000 0.00 0.00 0.00 4.93
1894 2024 8.262715 TGTTGATTGTATTTTGAGATAGCGAA 57.737 30.769 0.00 0.00 0.00 4.70
1895 2025 8.175069 TGTTGATTGTATTTTGAGATAGCGAAC 58.825 33.333 0.00 0.00 0.00 3.95
1896 2026 7.246674 TGATTGTATTTTGAGATAGCGAACC 57.753 36.000 0.00 0.00 0.00 3.62
1897 2027 5.712217 TTGTATTTTGAGATAGCGAACCG 57.288 39.130 0.00 0.00 0.00 4.44
1911 2041 1.641577 GAACCGCTCTGCTTATTCGT 58.358 50.000 0.00 0.00 0.00 3.85
1914 2044 1.270968 CGCTCTGCTTATTCGTGCG 59.729 57.895 0.00 0.00 34.97 5.34
1924 2054 4.334203 TGCTTATTCGTGCGGACAATAATT 59.666 37.500 17.81 0.00 0.00 1.40
1930 2060 5.954434 TCGTGCGGACAATAATTAACTAC 57.046 39.130 8.11 0.00 0.00 2.73
1931 2061 4.805192 TCGTGCGGACAATAATTAACTACC 59.195 41.667 8.11 0.00 0.00 3.18
1932 2062 4.567558 CGTGCGGACAATAATTAACTACCA 59.432 41.667 8.11 0.00 0.00 3.25
1941 2071 6.888088 ACAATAATTAACTACCAGTCCCAACC 59.112 38.462 0.00 0.00 0.00 3.77
1945 2075 2.112279 ACTACCAGTCCCAACCTCAA 57.888 50.000 0.00 0.00 0.00 3.02
1947 2077 2.572104 ACTACCAGTCCCAACCTCAATC 59.428 50.000 0.00 0.00 0.00 2.67
1948 2078 1.444933 ACCAGTCCCAACCTCAATCA 58.555 50.000 0.00 0.00 0.00 2.57
1949 2079 1.780309 ACCAGTCCCAACCTCAATCAA 59.220 47.619 0.00 0.00 0.00 2.57
1951 2081 3.181418 ACCAGTCCCAACCTCAATCAAAT 60.181 43.478 0.00 0.00 0.00 2.32
1952 2082 4.044065 ACCAGTCCCAACCTCAATCAAATA 59.956 41.667 0.00 0.00 0.00 1.40
1953 2083 5.016173 CCAGTCCCAACCTCAATCAAATAA 58.984 41.667 0.00 0.00 0.00 1.40
1956 2086 6.884295 CAGTCCCAACCTCAATCAAATAACTA 59.116 38.462 0.00 0.00 0.00 2.24
1957 2087 6.884836 AGTCCCAACCTCAATCAAATAACTAC 59.115 38.462 0.00 0.00 0.00 2.73
1958 2088 6.657541 GTCCCAACCTCAATCAAATAACTACA 59.342 38.462 0.00 0.00 0.00 2.74
1959 2089 6.657541 TCCCAACCTCAATCAAATAACTACAC 59.342 38.462 0.00 0.00 0.00 2.90
1960 2090 6.432783 CCCAACCTCAATCAAATAACTACACA 59.567 38.462 0.00 0.00 0.00 3.72
1964 2094 8.099364 ACCTCAATCAAATAACTACACACAAG 57.901 34.615 0.00 0.00 0.00 3.16
1975 2109 1.391577 ACACACAAGAGTTGCATGCA 58.608 45.000 18.46 18.46 0.00 3.96
1990 2124 6.813152 AGTTGCATGCATGGTTAAAAAGATAC 59.187 34.615 27.34 11.15 0.00 2.24
1991 2125 6.528537 TGCATGCATGGTTAAAAAGATACT 57.471 33.333 27.34 0.00 0.00 2.12
1992 2126 7.637631 TGCATGCATGGTTAAAAAGATACTA 57.362 32.000 27.34 0.00 0.00 1.82
1993 2127 7.479980 TGCATGCATGGTTAAAAAGATACTAC 58.520 34.615 27.34 5.53 0.00 2.73
1994 2128 7.339212 TGCATGCATGGTTAAAAAGATACTACT 59.661 33.333 27.34 0.00 0.00 2.57
1995 2129 8.836413 GCATGCATGGTTAAAAAGATACTACTA 58.164 33.333 27.34 0.00 0.00 1.82
2014 2148 8.789825 ACTACTAGTAAGAAATCGTCAAGAGA 57.210 34.615 3.76 0.00 0.00 3.10
2033 2167 6.541111 AGAGAAGACCAACGTTTTGAATAC 57.459 37.500 0.00 0.00 34.24 1.89
2034 2168 6.289064 AGAGAAGACCAACGTTTTGAATACT 58.711 36.000 0.00 0.00 34.24 2.12
2044 2178 7.060633 CCAACGTTTTGAATACTAGCAATGTTC 59.939 37.037 0.00 0.00 34.24 3.18
2071 2205 2.808206 CCTCCCGATTTCCGAGGGG 61.808 68.421 0.00 0.00 45.13 4.79
2085 2219 2.359975 GGGGTGACTTTGAGCCGG 60.360 66.667 0.00 0.00 0.00 6.13
2145 2279 3.708563 TTTTTCTTCGACCCAAAGCAG 57.291 42.857 0.00 0.00 0.00 4.24
2165 2299 2.045131 CCTCAGGGCTGCTGCTTTC 61.045 63.158 15.64 5.87 39.59 2.62
2210 2345 3.102985 CGTTGCAACGTGGAACCA 58.897 55.556 37.16 0.00 44.39 3.67
2211 2346 1.010125 CGTTGCAACGTGGAACCAG 60.010 57.895 37.16 11.84 44.39 4.00
2212 2347 1.433053 CGTTGCAACGTGGAACCAGA 61.433 55.000 37.16 0.00 44.39 3.86
2213 2348 0.028902 GTTGCAACGTGGAACCAGAC 59.971 55.000 14.90 0.00 41.94 3.51
2214 2349 1.098712 TTGCAACGTGGAACCAGACC 61.099 55.000 0.00 0.00 0.00 3.85
2215 2350 1.525077 GCAACGTGGAACCAGACCA 60.525 57.895 0.00 0.00 34.84 4.02
2216 2351 1.507141 GCAACGTGGAACCAGACCAG 61.507 60.000 0.00 0.00 38.14 4.00
2228 2363 1.417890 CCAGACCAGAGACCACAAGTT 59.582 52.381 0.00 0.00 0.00 2.66
2287 2422 9.529325 GCCATTTTACCAAACTTTCCTATTATC 57.471 33.333 0.00 0.00 0.00 1.75
2296 2431 4.950050 ACTTTCCTATTATCAGGTCGCAG 58.050 43.478 0.00 0.00 36.99 5.18
2360 2495 6.910536 ATAAAAATAACAGCGAGGACTGAG 57.089 37.500 0.00 0.00 40.25 3.35
2361 2496 2.301577 AATAACAGCGAGGACTGAGC 57.698 50.000 0.00 0.00 40.25 4.26
2362 2497 0.461961 ATAACAGCGAGGACTGAGCC 59.538 55.000 0.00 0.00 40.25 4.70
2364 2499 1.548357 AACAGCGAGGACTGAGCCAT 61.548 55.000 0.00 0.00 40.25 4.40
2365 2500 1.220206 CAGCGAGGACTGAGCCATT 59.780 57.895 0.00 0.00 40.25 3.16
2366 2501 1.088340 CAGCGAGGACTGAGCCATTG 61.088 60.000 0.00 0.00 40.25 2.82
2367 2502 1.219124 GCGAGGACTGAGCCATTGA 59.781 57.895 0.00 0.00 0.00 2.57
2368 2503 0.391661 GCGAGGACTGAGCCATTGAA 60.392 55.000 0.00 0.00 0.00 2.69
2369 2504 1.363744 CGAGGACTGAGCCATTGAAC 58.636 55.000 0.00 0.00 0.00 3.18
2422 2562 9.910511 TCTTTAATCGACTATTTTATTTGCGAC 57.089 29.630 0.00 0.00 0.00 5.19
2452 2592 4.455533 TGACTGACCATTTCATCTTTTCCG 59.544 41.667 0.00 0.00 32.17 4.30
2456 2596 1.742831 CCATTTCATCTTTTCCGGCGA 59.257 47.619 9.30 0.00 0.00 5.54
2784 2928 2.355244 GCCTACGCCTGATCGCTC 60.355 66.667 0.00 0.00 0.00 5.03
2789 2933 4.880537 CGCCTGATCGCTCGGCTT 62.881 66.667 16.16 0.00 38.28 4.35
2793 2937 1.880340 CTGATCGCTCGGCTTGGTC 60.880 63.158 0.00 0.00 0.00 4.02
2795 2939 2.125512 ATCGCTCGGCTTGGTCAC 60.126 61.111 0.00 0.00 0.00 3.67
2804 2948 1.398390 CGGCTTGGTCACTTATTGCTC 59.602 52.381 0.00 0.00 0.00 4.26
2809 2953 2.905075 TGGTCACTTATTGCTCGGATG 58.095 47.619 0.00 0.00 0.00 3.51
2811 2955 2.158957 GGTCACTTATTGCTCGGATGGA 60.159 50.000 0.00 0.00 0.00 3.41
2812 2956 3.495100 GGTCACTTATTGCTCGGATGGAT 60.495 47.826 0.00 0.00 0.00 3.41
2813 2957 3.496130 GTCACTTATTGCTCGGATGGATG 59.504 47.826 0.00 0.00 0.00 3.51
2814 2958 2.225019 CACTTATTGCTCGGATGGATGC 59.775 50.000 0.00 0.00 0.00 3.91
2820 2964 3.443588 TCGGATGGATGCGATCGT 58.556 55.556 17.81 0.00 45.57 3.73
2821 2965 1.285950 TCGGATGGATGCGATCGTC 59.714 57.895 17.81 7.09 45.57 4.20
2863 3012 2.156917 TCGTCGTGCTTCTCTTAGGAA 58.843 47.619 0.00 0.00 0.00 3.36
2894 3043 3.059352 AGCTTTGTACAGGCGAGATTT 57.941 42.857 14.31 0.00 0.00 2.17
2895 3044 4.202245 AGCTTTGTACAGGCGAGATTTA 57.798 40.909 14.31 0.00 0.00 1.40
2896 3045 4.770795 AGCTTTGTACAGGCGAGATTTAT 58.229 39.130 14.31 0.00 0.00 1.40
2897 3046 5.186198 AGCTTTGTACAGGCGAGATTTATT 58.814 37.500 14.31 0.00 0.00 1.40
2916 3065 9.270640 GATTTATTATTCTGTGCTCTGATCACT 57.729 33.333 12.30 0.00 35.58 3.41
2959 3110 1.611673 GGTCATGAGGAGGGTTGTGTG 60.612 57.143 0.00 0.00 0.00 3.82
3096 3250 4.828939 TGATCTGCACCTTTGATTGTTTCT 59.171 37.500 0.00 0.00 0.00 2.52
3248 3406 6.969366 TCAAGTGTTTTAGATGGTTGATGTG 58.031 36.000 0.00 0.00 0.00 3.21
3265 3425 3.696281 TGTGTTGCTCATTCAGTGTTG 57.304 42.857 0.00 0.00 0.00 3.33
3345 3505 5.578336 GCTGTATTTTTCCAAGATGGCTTTC 59.422 40.000 0.00 0.00 37.47 2.62
3362 3522 4.465512 CAAGCGCGATGGGCACAC 62.466 66.667 12.10 0.00 44.06 3.82
3377 3537 0.235665 CACACGCATGCTTTCGAACT 59.764 50.000 17.13 0.00 0.00 3.01
3402 3562 4.081142 TCTGTGTCACCTTCACTTTCTTGA 60.081 41.667 0.00 0.00 36.83 3.02
3409 3570 5.065914 CACCTTCACTTTCTTGATTCTCCA 58.934 41.667 0.00 0.00 0.00 3.86
3416 3577 2.084610 TCTTGATTCTCCAGCGTGTG 57.915 50.000 0.00 0.00 0.00 3.82
3418 3579 2.037121 TCTTGATTCTCCAGCGTGTGAA 59.963 45.455 0.00 0.00 0.00 3.18
3423 3584 0.240145 TCTCCAGCGTGTGAACTACG 59.760 55.000 0.00 0.00 43.93 3.51
3425 3586 1.198408 CTCCAGCGTGTGAACTACGTA 59.802 52.381 0.00 0.00 43.09 3.57
3426 3587 1.069022 TCCAGCGTGTGAACTACGTAC 60.069 52.381 0.00 0.00 43.09 3.67
3427 3588 1.335233 CCAGCGTGTGAACTACGTACA 60.335 52.381 0.00 0.00 43.09 2.90
3428 3589 2.592194 CAGCGTGTGAACTACGTACAT 58.408 47.619 0.00 0.00 43.09 2.29
3429 3590 2.592897 CAGCGTGTGAACTACGTACATC 59.407 50.000 0.00 0.00 43.09 3.06
3430 3591 2.227149 AGCGTGTGAACTACGTACATCA 59.773 45.455 0.00 0.00 43.09 3.07
3431 3592 2.981805 GCGTGTGAACTACGTACATCAA 59.018 45.455 7.03 0.00 43.09 2.57
3432 3593 3.181546 GCGTGTGAACTACGTACATCAAC 60.182 47.826 7.03 7.27 43.09 3.18
3459 7431 8.561738 TGTTCATTATCAGTAAAGGAGAAACC 57.438 34.615 0.00 0.00 39.35 3.27
3498 7470 1.470051 ATTACCGTCCCCATTTGCAC 58.530 50.000 0.00 0.00 0.00 4.57
3547 7520 4.624336 TGCTCTCAATCTTCTCGACTAC 57.376 45.455 0.00 0.00 0.00 2.73
3565 7538 0.706433 ACTTGTGCCATCCTTCCCAT 59.294 50.000 0.00 0.00 0.00 4.00
3586 7559 6.456501 CCATCGAAGTATTACTAGAAAGGGG 58.543 44.000 0.00 0.00 0.00 4.79
3604 7577 2.549778 GGGGAGCTATGAAGACAGATGC 60.550 54.545 0.00 0.00 0.00 3.91
3621 7594 1.026182 TGCGCTGGATCATGGTTCAC 61.026 55.000 9.73 0.00 0.00 3.18
3628 7601 3.033909 TGGATCATGGTTCACGAGAGAT 58.966 45.455 0.00 0.00 0.00 2.75
3654 7627 3.580319 AGCCCACCACAACCTCCC 61.580 66.667 0.00 0.00 0.00 4.30
3672 7645 4.408276 CTCCCAAGATATCCTCCTCGTTA 58.592 47.826 0.00 0.00 0.00 3.18
3712 7686 2.492088 TCGTTATAGCTAGGCATCGCAT 59.508 45.455 0.00 0.00 0.00 4.73
3759 7733 2.987821 GACTCTTTCGTGTTGGACTAGC 59.012 50.000 0.00 0.00 0.00 3.42
3760 7734 2.628657 ACTCTTTCGTGTTGGACTAGCT 59.371 45.455 0.00 0.00 0.00 3.32
3761 7735 3.825014 ACTCTTTCGTGTTGGACTAGCTA 59.175 43.478 0.00 0.00 0.00 3.32
3762 7736 4.082679 ACTCTTTCGTGTTGGACTAGCTAG 60.083 45.833 19.44 19.44 0.00 3.42
3763 7737 3.825014 TCTTTCGTGTTGGACTAGCTAGT 59.175 43.478 26.35 26.35 39.71 2.57
3764 7738 3.570926 TTCGTGTTGGACTAGCTAGTG 57.429 47.619 30.70 14.23 36.50 2.74
3773 7747 2.112190 GACTAGCTAGTGGCCCTTCTT 58.888 52.381 30.70 1.70 43.05 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 7.734538 AATTTAACTATCAAAACCGATTGCG 57.265 32.000 0.00 0.00 37.24 4.85
26 27 9.777575 CCGTAAATTTAACTATCAAAACCGATT 57.222 29.630 0.00 0.00 0.00 3.34
27 28 8.949177 ACCGTAAATTTAACTATCAAAACCGAT 58.051 29.630 0.00 0.00 0.00 4.18
28 29 8.321650 ACCGTAAATTTAACTATCAAAACCGA 57.678 30.769 0.00 0.00 0.00 4.69
29 30 8.229137 TGACCGTAAATTTAACTATCAAAACCG 58.771 33.333 0.00 0.00 0.00 4.44
30 31 9.896263 TTGACCGTAAATTTAACTATCAAAACC 57.104 29.630 0.00 0.00 0.00 3.27
42 43 9.219497 CGTGTTTTAACTTTGACCGTAAATTTA 57.781 29.630 0.00 0.00 0.00 1.40
43 44 7.967303 TCGTGTTTTAACTTTGACCGTAAATTT 59.033 29.630 0.00 0.00 0.00 1.82
44 45 7.470900 TCGTGTTTTAACTTTGACCGTAAATT 58.529 30.769 0.00 0.00 0.00 1.82
45 46 7.014092 TCGTGTTTTAACTTTGACCGTAAAT 57.986 32.000 0.00 0.00 0.00 1.40
46 47 6.414408 TCGTGTTTTAACTTTGACCGTAAA 57.586 33.333 0.00 0.00 0.00 2.01
47 48 5.006552 CCTCGTGTTTTAACTTTGACCGTAA 59.993 40.000 0.00 0.00 0.00 3.18
48 49 4.507388 CCTCGTGTTTTAACTTTGACCGTA 59.493 41.667 0.00 0.00 0.00 4.02
49 50 3.310501 CCTCGTGTTTTAACTTTGACCGT 59.689 43.478 0.00 0.00 0.00 4.83
50 51 3.556775 TCCTCGTGTTTTAACTTTGACCG 59.443 43.478 0.00 0.00 0.00 4.79
51 52 5.684550 ATCCTCGTGTTTTAACTTTGACC 57.315 39.130 0.00 0.00 0.00 4.02
52 53 7.148623 CCTCTATCCTCGTGTTTTAACTTTGAC 60.149 40.741 0.00 0.00 0.00 3.18
53 54 6.872020 CCTCTATCCTCGTGTTTTAACTTTGA 59.128 38.462 0.00 0.00 0.00 2.69
54 55 6.872020 TCCTCTATCCTCGTGTTTTAACTTTG 59.128 38.462 0.00 0.00 0.00 2.77
55 56 7.001099 TCCTCTATCCTCGTGTTTTAACTTT 57.999 36.000 0.00 0.00 0.00 2.66
56 57 6.600882 TCCTCTATCCTCGTGTTTTAACTT 57.399 37.500 0.00 0.00 0.00 2.66
57 58 6.600882 TTCCTCTATCCTCGTGTTTTAACT 57.399 37.500 0.00 0.00 0.00 2.24
58 59 5.291371 GCTTCCTCTATCCTCGTGTTTTAAC 59.709 44.000 0.00 0.00 0.00 2.01
59 60 5.046878 TGCTTCCTCTATCCTCGTGTTTTAA 60.047 40.000 0.00 0.00 0.00 1.52
60 61 4.464951 TGCTTCCTCTATCCTCGTGTTTTA 59.535 41.667 0.00 0.00 0.00 1.52
61 62 3.260884 TGCTTCCTCTATCCTCGTGTTTT 59.739 43.478 0.00 0.00 0.00 2.43
62 63 2.832129 TGCTTCCTCTATCCTCGTGTTT 59.168 45.455 0.00 0.00 0.00 2.83
63 64 2.166664 GTGCTTCCTCTATCCTCGTGTT 59.833 50.000 0.00 0.00 0.00 3.32
64 65 1.751924 GTGCTTCCTCTATCCTCGTGT 59.248 52.381 0.00 0.00 0.00 4.49
65 66 1.751351 TGTGCTTCCTCTATCCTCGTG 59.249 52.381 0.00 0.00 0.00 4.35
66 67 2.145397 TGTGCTTCCTCTATCCTCGT 57.855 50.000 0.00 0.00 0.00 4.18
67 68 2.166459 TGTTGTGCTTCCTCTATCCTCG 59.834 50.000 0.00 0.00 0.00 4.63
68 69 3.895232 TGTTGTGCTTCCTCTATCCTC 57.105 47.619 0.00 0.00 0.00 3.71
69 70 4.851639 AATGTTGTGCTTCCTCTATCCT 57.148 40.909 0.00 0.00 0.00 3.24
70 71 5.471456 CCATAATGTTGTGCTTCCTCTATCC 59.529 44.000 0.00 0.00 0.00 2.59
71 72 6.291377 TCCATAATGTTGTGCTTCCTCTATC 58.709 40.000 0.00 0.00 0.00 2.08
72 73 6.252599 TCCATAATGTTGTGCTTCCTCTAT 57.747 37.500 0.00 0.00 0.00 1.98
73 74 5.692115 TCCATAATGTTGTGCTTCCTCTA 57.308 39.130 0.00 0.00 0.00 2.43
74 75 4.574674 TCCATAATGTTGTGCTTCCTCT 57.425 40.909 0.00 0.00 0.00 3.69
75 76 5.841957 ATTCCATAATGTTGTGCTTCCTC 57.158 39.130 0.00 0.00 0.00 3.71
76 77 5.716228 TCAATTCCATAATGTTGTGCTTCCT 59.284 36.000 0.00 0.00 0.00 3.36
77 78 5.964758 TCAATTCCATAATGTTGTGCTTCC 58.035 37.500 0.00 0.00 0.00 3.46
78 79 6.038356 CCTCAATTCCATAATGTTGTGCTTC 58.962 40.000 0.00 0.00 0.00 3.86
79 80 5.105228 CCCTCAATTCCATAATGTTGTGCTT 60.105 40.000 0.00 0.00 0.00 3.91
80 81 4.403432 CCCTCAATTCCATAATGTTGTGCT 59.597 41.667 0.00 0.00 0.00 4.40
81 82 4.402155 TCCCTCAATTCCATAATGTTGTGC 59.598 41.667 0.00 0.00 0.00 4.57
82 83 5.653769 ACTCCCTCAATTCCATAATGTTGTG 59.346 40.000 0.00 0.00 0.00 3.33
83 84 5.831103 ACTCCCTCAATTCCATAATGTTGT 58.169 37.500 0.00 0.00 0.00 3.32
84 85 7.282585 TCTACTCCCTCAATTCCATAATGTTG 58.717 38.462 0.00 0.00 0.00 3.33
85 86 7.451731 TCTACTCCCTCAATTCCATAATGTT 57.548 36.000 0.00 0.00 0.00 2.71
86 87 7.293299 TGATCTACTCCCTCAATTCCATAATGT 59.707 37.037 0.00 0.00 0.00 2.71
87 88 7.605691 GTGATCTACTCCCTCAATTCCATAATG 59.394 40.741 0.00 0.00 0.00 1.90
88 89 7.256835 GGTGATCTACTCCCTCAATTCCATAAT 60.257 40.741 0.00 0.00 0.00 1.28
89 90 6.043243 GGTGATCTACTCCCTCAATTCCATAA 59.957 42.308 0.00 0.00 0.00 1.90
90 91 5.544176 GGTGATCTACTCCCTCAATTCCATA 59.456 44.000 0.00 0.00 0.00 2.74
91 92 4.349342 GGTGATCTACTCCCTCAATTCCAT 59.651 45.833 0.00 0.00 0.00 3.41
92 93 3.711704 GGTGATCTACTCCCTCAATTCCA 59.288 47.826 0.00 0.00 0.00 3.53
93 94 3.970640 AGGTGATCTACTCCCTCAATTCC 59.029 47.826 0.00 0.00 33.10 3.01
94 95 4.202305 CCAGGTGATCTACTCCCTCAATTC 60.202 50.000 0.00 0.00 33.10 2.17
95 96 3.713764 CCAGGTGATCTACTCCCTCAATT 59.286 47.826 0.00 0.00 33.10 2.32
96 97 3.312890 CCAGGTGATCTACTCCCTCAAT 58.687 50.000 0.00 0.00 33.10 2.57
97 98 2.626950 CCCAGGTGATCTACTCCCTCAA 60.627 54.545 0.00 0.00 33.10 3.02
98 99 1.062886 CCCAGGTGATCTACTCCCTCA 60.063 57.143 0.00 0.00 33.10 3.86
99 100 1.062810 ACCCAGGTGATCTACTCCCTC 60.063 57.143 0.00 0.00 33.10 4.30
100 101 1.019650 ACCCAGGTGATCTACTCCCT 58.980 55.000 0.00 0.00 33.10 4.20
101 102 3.637065 ACCCAGGTGATCTACTCCC 57.363 57.895 0.00 0.00 33.10 4.30
112 113 4.202070 CGTTTTCACATTTTACACCCAGGT 60.202 41.667 0.00 0.00 0.00 4.00
114 115 5.008217 TCTCGTTTTCACATTTTACACCCAG 59.992 40.000 0.00 0.00 0.00 4.45
115 116 4.882427 TCTCGTTTTCACATTTTACACCCA 59.118 37.500 0.00 0.00 0.00 4.51
116 117 5.427036 TCTCGTTTTCACATTTTACACCC 57.573 39.130 0.00 0.00 0.00 4.61
123 124 9.673454 GGTAGTATTTTTCTCGTTTTCACATTT 57.327 29.630 0.00 0.00 0.00 2.32
126 127 7.929785 AGAGGTAGTATTTTTCTCGTTTTCACA 59.070 33.333 0.00 0.00 0.00 3.58
127 128 8.307921 AGAGGTAGTATTTTTCTCGTTTTCAC 57.692 34.615 0.00 0.00 0.00 3.18
130 131 8.095937 CCAAGAGGTAGTATTTTTCTCGTTTT 57.904 34.615 0.00 0.00 0.00 2.43
148 150 2.046892 CGTCAGCCCACCAAGAGG 60.047 66.667 0.00 0.00 42.21 3.69
149 151 1.669115 CACGTCAGCCCACCAAGAG 60.669 63.158 0.00 0.00 0.00 2.85
176 178 3.903282 ACCACGTACACGCACGGT 61.903 61.111 0.85 3.64 46.12 4.83
177 179 3.399770 CACCACGTACACGCACGG 61.400 66.667 0.85 3.01 46.12 4.94
179 181 4.054455 CGCACCACGTACACGCAC 62.054 66.667 0.85 0.00 44.43 5.34
198 211 3.995506 AAGTATGGCACGCCCCTGC 62.996 63.158 5.42 0.00 36.33 4.85
199 212 0.965363 AAAAGTATGGCACGCCCCTG 60.965 55.000 5.42 0.00 34.56 4.45
205 218 2.474526 CGCTGAAGAAAAGTATGGCACG 60.475 50.000 0.00 0.00 0.00 5.34
243 256 2.546321 CGACAGCGAAGTGTGTGC 59.454 61.111 0.00 0.00 40.82 4.57
255 268 0.179161 CCGAGACTTGGTAGCGACAG 60.179 60.000 0.00 0.00 0.00 3.51
261 274 0.324460 AGGACCCCGAGACTTGGTAG 60.324 60.000 8.01 1.54 30.97 3.18
342 376 3.146847 GTCTGGACGAAGGGTTCAAAAT 58.853 45.455 0.00 0.00 32.40 1.82
359 393 2.262915 GGCTCGTGTCAGGGTCTG 59.737 66.667 0.00 0.00 0.00 3.51
421 472 0.591741 GGACTATTGACCGCGACTCG 60.592 60.000 8.23 0.00 38.08 4.18
454 505 0.610174 ACGGATGGATGGATGGATCG 59.390 55.000 0.00 0.00 0.00 3.69
456 507 0.987294 GGACGGATGGATGGATGGAT 59.013 55.000 0.00 0.00 0.00 3.41
457 508 0.399806 TGGACGGATGGATGGATGGA 60.400 55.000 0.00 0.00 0.00 3.41
458 509 0.694771 ATGGACGGATGGATGGATGG 59.305 55.000 0.00 0.00 0.00 3.51
459 510 1.348696 TGATGGACGGATGGATGGATG 59.651 52.381 0.00 0.00 0.00 3.51
460 511 1.627329 CTGATGGACGGATGGATGGAT 59.373 52.381 0.00 0.00 0.00 3.41
461 512 1.051008 CTGATGGACGGATGGATGGA 58.949 55.000 0.00 0.00 0.00 3.41
462 513 0.604780 GCTGATGGACGGATGGATGG 60.605 60.000 0.00 0.00 0.00 3.51
463 514 0.107268 TGCTGATGGACGGATGGATG 59.893 55.000 0.00 0.00 0.00 3.51
472 523 2.359850 TGGCGGTTGCTGATGGAC 60.360 61.111 0.00 0.00 42.25 4.02
556 624 4.326766 CTGTGCGCGTGGTTTGGG 62.327 66.667 8.43 0.00 0.00 4.12
573 641 2.218603 CGTGGTATTTGTAGATGGGGC 58.781 52.381 0.00 0.00 0.00 5.80
578 647 1.808891 GCGGGCGTGGTATTTGTAGAT 60.809 52.381 0.00 0.00 0.00 1.98
601 670 0.106569 TGATGATGTGGGATGGTGGC 60.107 55.000 0.00 0.00 0.00 5.01
625 694 1.591703 GCGTGGTCTGTGGATGAGA 59.408 57.895 0.00 0.00 0.00 3.27
626 695 1.448540 GGCGTGGTCTGTGGATGAG 60.449 63.158 0.00 0.00 0.00 2.90
627 696 2.662596 GGCGTGGTCTGTGGATGA 59.337 61.111 0.00 0.00 0.00 2.92
628 697 2.815211 CGGCGTGGTCTGTGGATG 60.815 66.667 0.00 0.00 0.00 3.51
1440 1509 1.826054 CCTCCTGTCCTCGAGCGAT 60.826 63.158 6.99 0.00 0.00 4.58
1461 1530 0.608640 ACATGAACTGGTCGAGGGTC 59.391 55.000 0.00 0.00 0.00 4.46
1464 1533 0.898320 AGGACATGAACTGGTCGAGG 59.102 55.000 0.00 0.00 34.87 4.63
1465 1534 1.134965 GGAGGACATGAACTGGTCGAG 60.135 57.143 0.00 0.00 34.87 4.04
1565 1635 8.533657 TGTTATCTTCAGGCATCAAATGAAATT 58.466 29.630 0.00 0.00 38.98 1.82
1575 1645 5.529060 CCTAGGTTTGTTATCTTCAGGCATC 59.471 44.000 0.00 0.00 0.00 3.91
1663 1790 2.210116 ACGCAGACACGTGAAAAAGAT 58.790 42.857 25.01 0.00 46.28 2.40
1705 1832 3.241067 TCTTATCCTTTTCCGTGGTCG 57.759 47.619 0.00 0.00 0.00 4.79
1743 1873 2.794350 CTCAAACCGCAATTTGTTGACC 59.206 45.455 8.95 0.00 39.97 4.02
1757 1887 3.668656 GCGCAACTACAATTTCTCAAACC 59.331 43.478 0.30 0.00 0.00 3.27
1775 1905 1.645034 GCTCTAGATCAAGTTGCGCA 58.355 50.000 5.66 5.66 0.00 6.09
1778 1908 3.452474 ACATCGCTCTAGATCAAGTTGC 58.548 45.455 0.00 0.00 0.00 4.17
1792 1922 1.470098 ACCGTAGACGTAAACATCGCT 59.530 47.619 0.85 0.00 37.74 4.93
1794 1924 3.058520 CACAACCGTAGACGTAAACATCG 59.941 47.826 0.85 0.00 37.74 3.84
1806 1936 0.389948 GACCTCTGGCACAACCGTAG 60.390 60.000 0.00 0.00 43.94 3.51
1867 1997 8.726068 TCGCTATCTCAAAATACAATCAACAAA 58.274 29.630 0.00 0.00 0.00 2.83
1868 1998 8.262715 TCGCTATCTCAAAATACAATCAACAA 57.737 30.769 0.00 0.00 0.00 2.83
1869 1999 7.841915 TCGCTATCTCAAAATACAATCAACA 57.158 32.000 0.00 0.00 0.00 3.33
1870 2000 7.640240 GGTTCGCTATCTCAAAATACAATCAAC 59.360 37.037 0.00 0.00 0.00 3.18
1871 2001 7.465379 CGGTTCGCTATCTCAAAATACAATCAA 60.465 37.037 0.00 0.00 0.00 2.57
1872 2002 6.019075 CGGTTCGCTATCTCAAAATACAATCA 60.019 38.462 0.00 0.00 0.00 2.57
1873 2003 6.355638 CGGTTCGCTATCTCAAAATACAATC 58.644 40.000 0.00 0.00 0.00 2.67
1874 2004 6.287107 CGGTTCGCTATCTCAAAATACAAT 57.713 37.500 0.00 0.00 0.00 2.71
1875 2005 5.712217 CGGTTCGCTATCTCAAAATACAA 57.288 39.130 0.00 0.00 0.00 2.41
1891 2021 0.572590 CGAATAAGCAGAGCGGTTCG 59.427 55.000 10.24 10.24 36.52 3.95
1892 2022 1.324736 CACGAATAAGCAGAGCGGTTC 59.675 52.381 0.00 0.00 36.52 3.62
1893 2023 1.359848 CACGAATAAGCAGAGCGGTT 58.640 50.000 0.00 0.00 39.17 4.44
1894 2024 1.084370 GCACGAATAAGCAGAGCGGT 61.084 55.000 0.00 0.00 0.00 5.68
1895 2025 1.638467 GCACGAATAAGCAGAGCGG 59.362 57.895 0.00 0.00 0.00 5.52
1896 2026 1.270968 CGCACGAATAAGCAGAGCG 59.729 57.895 0.00 0.00 38.41 5.03
1897 2027 0.806102 TCCGCACGAATAAGCAGAGC 60.806 55.000 0.00 0.00 0.00 4.09
1898 2028 0.924090 GTCCGCACGAATAAGCAGAG 59.076 55.000 0.00 0.00 0.00 3.35
1899 2029 0.245266 TGTCCGCACGAATAAGCAGA 59.755 50.000 0.00 0.00 0.00 4.26
1900 2030 1.075542 TTGTCCGCACGAATAAGCAG 58.924 50.000 0.00 0.00 0.00 4.24
1901 2031 1.732941 ATTGTCCGCACGAATAAGCA 58.267 45.000 0.00 0.00 0.00 3.91
1902 2032 3.936902 TTATTGTCCGCACGAATAAGC 57.063 42.857 0.00 0.00 0.00 3.09
1903 2033 7.627340 AGTTAATTATTGTCCGCACGAATAAG 58.373 34.615 0.00 0.00 0.00 1.73
1904 2034 7.542534 AGTTAATTATTGTCCGCACGAATAA 57.457 32.000 0.00 0.00 0.00 1.40
1905 2035 7.169645 GGTAGTTAATTATTGTCCGCACGAATA 59.830 37.037 0.00 0.00 0.00 1.75
1909 2039 4.567558 TGGTAGTTAATTATTGTCCGCACG 59.432 41.667 0.00 0.00 0.00 5.34
1911 2041 5.736813 ACTGGTAGTTAATTATTGTCCGCA 58.263 37.500 0.00 0.00 0.00 5.69
1914 2044 6.655930 TGGGACTGGTAGTTAATTATTGTCC 58.344 40.000 13.51 13.51 40.25 4.02
1924 2054 3.263369 TGAGGTTGGGACTGGTAGTTA 57.737 47.619 0.00 0.00 0.00 2.24
1930 2060 2.584835 TTGATTGAGGTTGGGACTGG 57.415 50.000 0.00 0.00 0.00 4.00
1931 2061 5.711976 AGTTATTTGATTGAGGTTGGGACTG 59.288 40.000 0.00 0.00 0.00 3.51
1932 2062 5.892348 AGTTATTTGATTGAGGTTGGGACT 58.108 37.500 0.00 0.00 0.00 3.85
1941 2071 8.993121 ACTCTTGTGTGTAGTTATTTGATTGAG 58.007 33.333 0.00 0.00 0.00 3.02
1945 2075 7.228507 TGCAACTCTTGTGTGTAGTTATTTGAT 59.771 33.333 0.00 0.00 32.35 2.57
1947 2077 6.724263 TGCAACTCTTGTGTGTAGTTATTTG 58.276 36.000 0.00 0.00 32.35 2.32
1948 2078 6.935741 TGCAACTCTTGTGTGTAGTTATTT 57.064 33.333 0.00 0.00 32.35 1.40
1949 2079 6.568462 GCATGCAACTCTTGTGTGTAGTTATT 60.568 38.462 14.21 0.00 32.35 1.40
1951 2081 4.213270 GCATGCAACTCTTGTGTGTAGTTA 59.787 41.667 14.21 0.00 32.35 2.24
1952 2082 3.003689 GCATGCAACTCTTGTGTGTAGTT 59.996 43.478 14.21 0.00 33.82 2.24
1953 2083 2.549754 GCATGCAACTCTTGTGTGTAGT 59.450 45.455 14.21 0.00 0.00 2.73
1956 2086 1.391577 TGCATGCAACTCTTGTGTGT 58.608 45.000 20.30 0.00 0.00 3.72
1957 2087 2.324860 CATGCATGCAACTCTTGTGTG 58.675 47.619 26.68 11.19 0.00 3.82
1958 2088 1.271379 CCATGCATGCAACTCTTGTGT 59.729 47.619 26.68 0.80 0.00 3.72
1959 2089 1.271379 ACCATGCATGCAACTCTTGTG 59.729 47.619 26.68 16.06 0.00 3.33
1960 2090 1.624336 ACCATGCATGCAACTCTTGT 58.376 45.000 26.68 12.30 0.00 3.16
1964 2094 5.229423 TCTTTTTAACCATGCATGCAACTC 58.771 37.500 26.68 0.00 0.00 3.01
1990 2124 9.710979 CTTCTCTTGACGATTTCTTACTAGTAG 57.289 37.037 2.23 0.00 0.00 2.57
1991 2125 9.445878 TCTTCTCTTGACGATTTCTTACTAGTA 57.554 33.333 0.00 0.00 0.00 1.82
1992 2126 8.238631 GTCTTCTCTTGACGATTTCTTACTAGT 58.761 37.037 0.00 0.00 0.00 2.57
1993 2127 7.698970 GGTCTTCTCTTGACGATTTCTTACTAG 59.301 40.741 0.00 0.00 35.45 2.57
1994 2128 7.176165 TGGTCTTCTCTTGACGATTTCTTACTA 59.824 37.037 0.00 0.00 35.45 1.82
1995 2129 6.015350 TGGTCTTCTCTTGACGATTTCTTACT 60.015 38.462 0.00 0.00 35.45 2.24
1996 2130 6.157211 TGGTCTTCTCTTGACGATTTCTTAC 58.843 40.000 0.00 0.00 35.45 2.34
1997 2131 6.340962 TGGTCTTCTCTTGACGATTTCTTA 57.659 37.500 0.00 0.00 35.45 2.10
2006 2140 4.331717 TCAAAACGTTGGTCTTCTCTTGAC 59.668 41.667 0.00 0.00 35.29 3.18
2012 2146 6.147328 GCTAGTATTCAAAACGTTGGTCTTCT 59.853 38.462 0.00 0.00 35.29 2.85
2014 2148 5.761234 TGCTAGTATTCAAAACGTTGGTCTT 59.239 36.000 0.00 0.00 35.29 3.01
2033 2167 4.799678 AGGATCGTATCGAACATTGCTAG 58.200 43.478 0.00 0.00 39.99 3.42
2034 2168 4.321008 GGAGGATCGTATCGAACATTGCTA 60.321 45.833 0.00 0.00 39.99 3.49
2044 2178 2.415625 GGAAATCGGGAGGATCGTATCG 60.416 54.545 4.21 4.21 33.02 2.92
2071 2205 3.423154 CCGCCGGCTCAAAGTCAC 61.423 66.667 26.68 0.00 0.00 3.67
2085 2219 2.514013 CCGTTGACAGTATCGCCGC 61.514 63.158 0.00 0.00 0.00 6.53
2154 2288 4.752146 AGAATTTAATGGAAAGCAGCAGC 58.248 39.130 0.00 0.00 42.56 5.25
2165 2299 7.865385 TCAGAACGTTTGGAAAGAATTTAATGG 59.135 33.333 0.46 0.00 39.27 3.16
2210 2345 2.158755 CCAAACTTGTGGTCTCTGGTCT 60.159 50.000 0.00 0.00 33.63 3.85
2211 2346 2.222027 CCAAACTTGTGGTCTCTGGTC 58.778 52.381 0.00 0.00 33.63 4.02
2212 2347 1.750682 GCCAAACTTGTGGTCTCTGGT 60.751 52.381 0.00 0.00 41.12 4.00
2213 2348 0.954452 GCCAAACTTGTGGTCTCTGG 59.046 55.000 0.00 0.00 41.12 3.86
2214 2349 1.605710 CTGCCAAACTTGTGGTCTCTG 59.394 52.381 0.00 0.00 41.12 3.35
2215 2350 1.212935 ACTGCCAAACTTGTGGTCTCT 59.787 47.619 0.00 0.00 41.12 3.10
2216 2351 1.334869 CACTGCCAAACTTGTGGTCTC 59.665 52.381 0.00 0.00 41.12 3.36
2228 2363 0.036732 GATGGAGGTGTCACTGCCAA 59.963 55.000 17.28 5.73 31.53 4.52
2287 2422 1.071471 AGTTGGGTTCTGCGACCTG 59.929 57.895 4.07 0.00 39.71 4.00
2296 2431 1.070786 TCACGGAGCAGTTGGGTTC 59.929 57.895 0.00 0.00 0.00 3.62
2299 2434 2.358737 GGTCACGGAGCAGTTGGG 60.359 66.667 0.00 0.00 0.00 4.12
2300 2435 0.817634 TTTGGTCACGGAGCAGTTGG 60.818 55.000 6.03 0.00 41.12 3.77
2336 2471 6.183360 GCTCAGTCCTCGCTGTTATTTTTATT 60.183 38.462 0.00 0.00 37.70 1.40
2347 2482 1.088340 CAATGGCTCAGTCCTCGCTG 61.088 60.000 0.00 0.00 37.81 5.18
2349 2484 0.391661 TTCAATGGCTCAGTCCTCGC 60.392 55.000 0.00 0.00 0.00 5.03
2379 2514 9.334693 CGATTAAAGAATTTCTTTTCTGACCAG 57.665 33.333 25.04 9.04 43.62 4.00
2396 2531 9.910511 GTCGCAAATAAAATAGTCGATTAAAGA 57.089 29.630 0.00 0.00 0.00 2.52
2397 2532 8.869688 CGTCGCAAATAAAATAGTCGATTAAAG 58.130 33.333 0.00 0.00 0.00 1.85
2412 2547 0.248012 TCAGCCTCCGTCGCAAATAA 59.752 50.000 0.00 0.00 0.00 1.40
2422 2562 0.036010 AAATGGTCAGTCAGCCTCCG 60.036 55.000 0.00 0.00 0.00 4.63
2769 2909 2.050895 CCGAGCGATCAGGCGTAG 60.051 66.667 0.00 0.00 38.18 3.51
2784 2928 1.398390 GAGCAATAAGTGACCAAGCCG 59.602 52.381 0.00 0.00 0.00 5.52
2789 2933 2.419990 CCATCCGAGCAATAAGTGACCA 60.420 50.000 0.00 0.00 0.00 4.02
2793 2937 2.225019 GCATCCATCCGAGCAATAAGTG 59.775 50.000 0.00 0.00 0.00 3.16
2795 2939 1.462283 CGCATCCATCCGAGCAATAAG 59.538 52.381 0.00 0.00 0.00 1.73
2804 2948 0.730834 GAGACGATCGCATCCATCCG 60.731 60.000 16.60 0.00 0.00 4.18
2818 2962 1.136057 TGAGAATGACACGACGAGACG 60.136 52.381 0.00 0.00 39.31 4.18
2819 2963 2.613730 TGAGAATGACACGACGAGAC 57.386 50.000 0.00 0.00 0.00 3.36
2820 2964 3.190535 TGAATGAGAATGACACGACGAGA 59.809 43.478 0.00 0.00 0.00 4.04
2821 2965 3.501950 TGAATGAGAATGACACGACGAG 58.498 45.455 0.00 0.00 0.00 4.18
2863 3012 3.107601 TGTACAAAGCTAGATCAGGCCT 58.892 45.455 0.00 0.00 0.00 5.19
2894 3043 8.918116 AGTAAGTGATCAGAGCACAGAATAATA 58.082 33.333 20.72 0.24 38.70 0.98
2895 3044 7.790027 AGTAAGTGATCAGAGCACAGAATAAT 58.210 34.615 20.72 5.10 38.70 1.28
2896 3045 7.175347 AGTAAGTGATCAGAGCACAGAATAA 57.825 36.000 20.72 0.00 38.70 1.40
2897 3046 6.782082 AGTAAGTGATCAGAGCACAGAATA 57.218 37.500 20.72 5.71 38.70 1.75
2916 3065 6.493458 ACCACGGAGTAAAACCTAACTAGTAA 59.507 38.462 0.00 0.00 41.61 2.24
3068 3222 4.730949 ATCAAAGGTGCAGATCAATTGG 57.269 40.909 5.42 0.00 0.00 3.16
3121 3275 0.094730 CACGAGCGAATTTCCGGAAC 59.905 55.000 18.64 4.83 0.00 3.62
3179 3337 2.769095 CCCCCTGGTGACTTTTCAAAAA 59.231 45.455 0.00 0.00 31.90 1.94
3180 3338 2.393646 CCCCCTGGTGACTTTTCAAAA 58.606 47.619 0.00 0.00 31.90 2.44
3181 3339 2.032151 GCCCCCTGGTGACTTTTCAAA 61.032 52.381 0.00 0.00 31.90 2.69
3236 3394 4.082625 TGAATGAGCAACACATCAACCATC 60.083 41.667 0.00 0.00 0.00 3.51
3248 3406 3.065233 TGTCACAACACTGAATGAGCAAC 59.935 43.478 0.00 0.00 0.00 4.17
3362 3522 0.792640 AGACAGTTCGAAAGCATGCG 59.207 50.000 13.01 0.00 0.00 4.73
3377 3537 3.197766 AGAAAGTGAAGGTGACACAGACA 59.802 43.478 8.08 1.05 40.25 3.41
3402 3562 2.671351 CGTAGTTCACACGCTGGAGAAT 60.671 50.000 0.00 0.00 31.94 2.40
3409 3570 2.227149 TGATGTACGTAGTTCACACGCT 59.773 45.455 0.00 0.00 41.38 5.07
3416 3577 6.758593 TGAACAAGTTGATGTACGTAGTTC 57.241 37.500 10.54 3.67 45.11 3.01
3426 3587 9.778993 CCTTTACTGATAATGAACAAGTTGATG 57.221 33.333 10.54 0.00 0.00 3.07
3427 3588 9.739276 TCCTTTACTGATAATGAACAAGTTGAT 57.261 29.630 10.54 0.00 0.00 2.57
3428 3589 9.219603 CTCCTTTACTGATAATGAACAAGTTGA 57.780 33.333 10.54 0.00 0.00 3.18
3429 3590 9.219603 TCTCCTTTACTGATAATGAACAAGTTG 57.780 33.333 0.00 0.00 0.00 3.16
3430 3591 9.793259 TTCTCCTTTACTGATAATGAACAAGTT 57.207 29.630 0.00 0.00 0.00 2.66
3431 3592 9.793259 TTTCTCCTTTACTGATAATGAACAAGT 57.207 29.630 0.00 0.00 0.00 3.16
3459 7431 2.163818 TAGGTGAACAACTTCAGGCG 57.836 50.000 0.00 0.00 37.06 5.52
3498 7470 1.224069 CGTCTGTCTGCCACCTTGTG 61.224 60.000 0.00 0.00 0.00 3.33
3565 7538 5.301298 GCTCCCCTTTCTAGTAATACTTCGA 59.699 44.000 0.00 0.00 0.00 3.71
3586 7559 1.791785 GCGCATCTGTCTTCATAGCTC 59.208 52.381 0.30 0.00 0.00 4.09
3604 7577 0.460109 TCGTGAACCATGATCCAGCG 60.460 55.000 0.00 0.00 0.00 5.18
3621 7594 0.809241 GGCTGGACTTGCATCTCTCG 60.809 60.000 0.00 0.00 0.00 4.04
3628 7601 3.497115 TGGTGGGCTGGACTTGCA 61.497 61.111 0.00 0.00 0.00 4.08
3654 7627 5.776173 AGTGTAACGAGGAGGATATCTTG 57.224 43.478 2.05 0.00 45.86 3.02
3712 7686 2.162338 AAACGACATCGGGAAGGCGA 62.162 55.000 6.13 0.00 44.95 5.54


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

AutoCloner maintained by Alex Coulton.