Multiple sequence alignment - TraesCS6D01G231900

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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 TraesCS6D01G231900 chr6D 100.000 2760 0 0 1 2760 325598791 325601550 0.000000e+00 5097.0
1 TraesCS6D01G231900 chr6D 95.763 118 4 1 1962 2079 456557348 456557464 3.630000e-44 189.0
2 TraesCS6D01G231900 chr6D 92.373 118 8 1 1967 2083 249445795 249445912 1.700000e-37 167.0
3 TraesCS6D01G231900 chr6D 94.681 94 4 1 2666 2758 324753426 324753519 7.970000e-31 145.0
4 TraesCS6D01G231900 chr6A 95.947 1209 29 9 714 1917 464249315 464250508 0.000000e+00 1943.0
5 TraesCS6D01G231900 chr6A 96.537 462 15 1 2203 2664 464250690 464251150 0.000000e+00 763.0
6 TraesCS6D01G231900 chr6A 85.051 689 84 7 2 672 464248372 464249059 0.000000e+00 684.0
7 TraesCS6D01G231900 chr6A 94.595 37 1 1 1939 1975 464250514 464250549 3.840000e-04 56.5
8 TraesCS6D01G231900 chr6B 92.168 1264 57 20 714 1965 497434830 497433597 0.000000e+00 1748.0
9 TraesCS6D01G231900 chr6B 93.890 491 20 2 2184 2664 497433450 497432960 0.000000e+00 732.0
10 TraesCS6D01G231900 chr6B 77.454 377 72 11 303 670 278132032 278131660 2.150000e-51 213.0
11 TraesCS6D01G231900 chr6B 76.880 359 71 9 320 670 278136214 278135860 2.810000e-45 193.0
12 TraesCS6D01G231900 chr6B 76.705 352 58 21 337 670 494430046 494429701 1.020000e-39 174.0
13 TraesCS6D01G231900 chr6B 77.725 211 37 9 467 670 623293925 623293718 1.340000e-23 121.0
14 TraesCS6D01G231900 chr4A 80.695 259 37 8 415 664 420639785 420640039 3.630000e-44 189.0
15 TraesCS6D01G231900 chr3A 80.078 256 42 7 416 664 274945064 274945317 6.070000e-42 182.0
16 TraesCS6D01G231900 chr7B 95.536 112 4 1 1969 2079 420072685 420072796 7.850000e-41 178.0
17 TraesCS6D01G231900 chr2B 95.495 111 5 0 1969 2079 770902337 770902447 7.850000e-41 178.0
18 TraesCS6D01G231900 chr2B 96.262 107 4 0 1973 2079 734295904 734296010 2.820000e-40 176.0
19 TraesCS6D01G231900 chr4D 96.262 107 4 0 1973 2079 441486708 441486814 2.820000e-40 176.0
20 TraesCS6D01G231900 chr4D 94.737 95 3 2 2666 2758 421318584 421318490 2.210000e-31 147.0
21 TraesCS6D01G231900 chr4D 93.617 94 5 1 2666 2758 43577983 43578076 3.710000e-29 139.0
22 TraesCS6D01G231900 chr4D 91.667 96 5 3 2666 2758 320193722 320193627 2.230000e-26 130.0
23 TraesCS6D01G231900 chr5B 93.913 115 7 0 1973 2087 650990197 650990083 1.020000e-39 174.0
24 TraesCS6D01G231900 chr5D 94.595 111 5 1 1969 2079 399621840 399621949 1.310000e-38 171.0
25 TraesCS6D01G231900 chr5D 75.000 352 60 23 337 668 292263450 292263793 1.330000e-28 137.0
26 TraesCS6D01G231900 chr2D 93.805 113 7 0 1971 2083 207289017 207289129 1.310000e-38 171.0
27 TraesCS6D01G231900 chr2D 88.636 88 10 0 1401 1488 525698966 525698879 1.050000e-19 108.0
28 TraesCS6D01G231900 chr7D 93.684 95 5 1 2665 2758 452693681 452693775 1.030000e-29 141.0
29 TraesCS6D01G231900 chr7D 93.617 94 5 1 2666 2758 596326009 596325916 3.710000e-29 139.0
30 TraesCS6D01G231900 chr7D 92.632 95 5 2 2666 2758 436876406 436876312 4.790000e-28 135.0
31 TraesCS6D01G231900 chr7D 95.238 63 3 0 2688 2750 632610645 632610583 1.750000e-17 100.0
32 TraesCS6D01G231900 chr7D 100.000 36 0 0 2666 2701 505594265 505594230 1.770000e-07 67.6
33 TraesCS6D01G231900 chr5A 76.895 277 46 14 408 670 650514926 650514654 1.030000e-29 141.0
34 TraesCS6D01G231900 chr3D 93.023 86 5 1 2666 2750 615380389 615380304 1.040000e-24 124.0
35 TraesCS6D01G231900 chr1D 75.725 276 52 9 408 670 107530104 107529831 1.040000e-24 124.0
36 TraesCS6D01G231900 chr2A 86.905 84 11 0 1405 1488 670881453 670881536 8.140000e-16 95.3


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 TraesCS6D01G231900 chr6D 325598791 325601550 2759 False 5097.000 5097 100.0000 1 2760 1 chr6D.!!$F3 2759
1 TraesCS6D01G231900 chr6A 464248372 464251150 2778 False 861.625 1943 93.0325 2 2664 4 chr6A.!!$F1 2662
2 TraesCS6D01G231900 chr6B 497432960 497434830 1870 True 1240.000 1748 93.0290 714 2664 2 chr6B.!!$R4 1950
3 TraesCS6D01G231900 chr6B 278131660 278136214 4554 True 203.000 213 77.1670 303 670 2 chr6B.!!$R3 367

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
693 4604 0.512952 GCAAAGAGTACACAGTGCCG 59.487 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2056 6171 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.0 0.0 0.0 0.0 2.24 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
32 33 2.941210 TCAATTTGAGACCGGGTGC 58.059 52.632 3.30 0.00 0.00 5.01
41 42 2.769663 TGAGACCGGGTGCAATAGTTAT 59.230 45.455 3.30 0.00 0.00 1.89
78 79 4.630069 CGGTCCGATCACTAATGAAAAGTT 59.370 41.667 4.91 0.00 38.69 2.66
92 93 4.090090 TGAAAAGTTTCAACCAGGACCAA 58.910 39.130 4.00 0.00 43.62 3.67
104 105 3.202151 ACCAGGACCAAACACCCATATAG 59.798 47.826 0.00 0.00 0.00 1.31
112 113 2.957402 ACACCCATATAGCCCATGTG 57.043 50.000 0.00 0.00 0.00 3.21
116 117 2.782925 ACCCATATAGCCCATGTGTGAA 59.217 45.455 0.00 0.00 0.00 3.18
175 189 6.280855 TGAGAGATTCAACCGTTAAGATGA 57.719 37.500 0.00 0.00 31.34 2.92
176 190 6.100004 TGAGAGATTCAACCGTTAAGATGAC 58.900 40.000 0.00 0.00 31.34 3.06
184 198 7.372451 TCAACCGTTAAGATGACCTTAAATG 57.628 36.000 0.00 0.00 45.80 2.32
199 213 7.713073 TGACCTTAAATGGAAAAATGTTCAACC 59.287 33.333 0.00 0.00 0.00 3.77
224 238 3.463944 AGGTTGTTCAACTCGTCGAAAT 58.536 40.909 14.04 0.00 0.00 2.17
225 239 3.493503 AGGTTGTTCAACTCGTCGAAATC 59.506 43.478 14.04 0.00 0.00 2.17
287 303 1.000717 GGTGTGTGGATCCAAAAACGG 60.001 52.381 18.20 0.00 0.00 4.44
290 306 2.359531 TGTGTGGATCCAAAAACGGAAC 59.640 45.455 18.20 0.60 38.95 3.62
291 307 2.621526 GTGTGGATCCAAAAACGGAACT 59.378 45.455 18.20 0.00 38.95 3.01
293 309 2.882137 GTGGATCCAAAAACGGAACTGA 59.118 45.455 18.20 0.00 38.95 3.41
304 320 3.870633 ACGGAACTGATGTCTTAGACC 57.129 47.619 10.10 0.00 0.00 3.85
314 4195 7.907389 ACTGATGTCTTAGACCTAAATGTGAA 58.093 34.615 10.10 0.00 0.00 3.18
365 4246 4.326548 GGAATTCGTAGTCCTTTTCTCGTG 59.673 45.833 0.84 0.00 35.64 4.35
389 4270 5.104259 AGGAAGTCCAACCATCTCATAAC 57.896 43.478 0.00 0.00 38.89 1.89
423 4304 2.045561 TGACCGGTTGAACAACACAT 57.954 45.000 9.42 3.87 42.85 3.21
428 4309 4.138290 ACCGGTTGAACAACACATAATCA 58.862 39.130 17.43 0.00 42.85 2.57
432 4313 6.644592 CCGGTTGAACAACACATAATCAAAAT 59.355 34.615 17.43 0.00 42.85 1.82
479 4364 9.449719 TTTTTACATCTCTCCTATGTTCTTTCC 57.550 33.333 0.00 0.00 38.49 3.13
480 4365 7.979786 TTACATCTCTCCTATGTTCTTTCCT 57.020 36.000 0.00 0.00 38.49 3.36
493 4378 4.452455 TGTTCTTTCCTTCTCATTCTTCGC 59.548 41.667 0.00 0.00 0.00 4.70
498 4387 4.543590 TCCTTCTCATTCTTCGCTCTTT 57.456 40.909 0.00 0.00 0.00 2.52
501 4390 5.047306 TCCTTCTCATTCTTCGCTCTTTGTA 60.047 40.000 0.00 0.00 0.00 2.41
505 4394 5.582269 TCTCATTCTTCGCTCTTTGTATTGG 59.418 40.000 0.00 0.00 0.00 3.16
520 4409 3.197766 TGTATTGGAGAGCAACGATCCTT 59.802 43.478 0.00 0.00 34.04 3.36
528 4417 1.092345 GCAACGATCCTTGAGGCTCC 61.092 60.000 12.86 0.00 34.44 4.70
577 4466 3.814615 ATAGCCGCCGCATGTCCAG 62.815 63.158 0.00 0.00 37.52 3.86
625 4515 4.426112 GGGCCTGCAAAAGCGCTC 62.426 66.667 12.06 0.00 38.77 5.03
626 4516 3.368571 GGCCTGCAAAAGCGCTCT 61.369 61.111 12.06 0.00 0.00 4.09
663 4553 4.452733 CACTTCCGGCCGGGTCTC 62.453 72.222 42.36 0.00 37.00 3.36
672 4562 0.539986 GGCCGGGTCTCATTTGAGTA 59.460 55.000 2.18 0.00 42.60 2.59
673 4563 1.653151 GCCGGGTCTCATTTGAGTAC 58.347 55.000 2.18 4.96 42.60 2.73
676 4566 1.403647 CGGGTCTCATTTGAGTACGCA 60.404 52.381 18.08 0.00 42.60 5.24
691 4602 1.217882 ACGCAAAGAGTACACAGTGC 58.782 50.000 0.00 1.95 0.00 4.40
693 4604 0.512952 GCAAAGAGTACACAGTGCCG 59.487 55.000 0.00 0.00 0.00 5.69
703 4614 2.112198 ACAGTGCCGTGTTGGTGTG 61.112 57.895 0.00 0.00 41.21 3.82
705 4616 3.513438 GTGCCGTGTTGGTGTGCA 61.513 61.111 0.00 0.00 41.21 4.57
708 4619 1.153745 GCCGTGTTGGTGTGCAAAA 60.154 52.632 0.00 0.00 41.21 2.44
1005 5109 4.794439 CCGCTGCCACGATCACGA 62.794 66.667 0.00 0.00 42.66 4.35
1046 5150 3.459969 CCTCCTCCCAGTATTTAAAGCCT 59.540 47.826 0.00 0.00 0.00 4.58
1047 5151 4.079730 CCTCCTCCCAGTATTTAAAGCCTT 60.080 45.833 0.00 0.00 0.00 4.35
1048 5152 5.510430 CTCCTCCCAGTATTTAAAGCCTTT 58.490 41.667 0.00 0.00 0.00 3.11
1067 5171 1.502231 TCTTCTTCTTCGCTGCACAC 58.498 50.000 0.00 0.00 0.00 3.82
1103 5207 3.997064 CTGCCACTCCTTCCTCGCG 62.997 68.421 0.00 0.00 0.00 5.87
1360 5470 4.094887 CGGGGTACTGTCAAGATTTTGATG 59.905 45.833 1.53 1.84 44.62 3.07
1922 6036 0.248012 TGTTGTCGTGTGTGGTCAGT 59.752 50.000 0.00 0.00 0.00 3.41
1936 6051 4.574421 TGTGGTCAGTACTTTGAACATGTG 59.426 41.667 6.17 0.00 45.73 3.21
1968 6083 4.467795 AGTGTATGATCAGTGGCAGTAAGT 59.532 41.667 0.09 0.00 0.00 2.24
1972 6087 8.307483 GTGTATGATCAGTGGCAGTAAGTATAT 58.693 37.037 0.09 0.00 0.00 0.86
1973 6088 9.528489 TGTATGATCAGTGGCAGTAAGTATATA 57.472 33.333 0.09 0.00 0.00 0.86
1974 6089 9.790389 GTATGATCAGTGGCAGTAAGTATATAC 57.210 37.037 4.60 4.60 0.00 1.47
1975 6090 8.657387 ATGATCAGTGGCAGTAAGTATATACT 57.343 34.615 9.71 9.71 36.57 2.12
1976 6091 8.112016 TGATCAGTGGCAGTAAGTATATACTC 57.888 38.462 15.72 4.79 33.90 2.59
1977 6092 6.896021 TCAGTGGCAGTAAGTATATACTCC 57.104 41.667 15.72 12.23 33.90 3.85
1978 6093 5.773680 TCAGTGGCAGTAAGTATATACTCCC 59.226 44.000 15.72 9.29 34.77 4.30
1979 6094 5.775701 CAGTGGCAGTAAGTATATACTCCCT 59.224 44.000 15.72 11.26 35.18 4.20
1980 6095 6.011481 AGTGGCAGTAAGTATATACTCCCTC 58.989 44.000 15.72 11.27 35.18 4.30
1981 6096 5.185442 GTGGCAGTAAGTATATACTCCCTCC 59.815 48.000 15.72 15.15 35.18 4.30
1982 6097 4.398673 GGCAGTAAGTATATACTCCCTCCG 59.601 50.000 15.72 5.59 31.98 4.63
1983 6098 5.008980 GCAGTAAGTATATACTCCCTCCGT 58.991 45.833 15.72 1.38 33.90 4.69
1984 6099 5.476254 GCAGTAAGTATATACTCCCTCCGTT 59.524 44.000 15.72 0.67 33.90 4.44
1985 6100 6.349197 GCAGTAAGTATATACTCCCTCCGTTC 60.349 46.154 15.72 0.00 33.90 3.95
1986 6101 5.936956 AGTAAGTATATACTCCCTCCGTTCG 59.063 44.000 15.72 0.00 34.99 3.95
1987 6102 3.683802 AGTATATACTCCCTCCGTTCGG 58.316 50.000 9.71 4.74 0.00 4.30
1988 6103 2.965671 ATATACTCCCTCCGTTCGGA 57.034 50.000 13.34 13.34 0.00 4.55
1989 6104 2.965671 TATACTCCCTCCGTTCGGAT 57.034 50.000 14.34 2.21 33.34 4.18
1990 6105 2.083628 ATACTCCCTCCGTTCGGATT 57.916 50.000 14.34 0.62 33.34 3.01
1991 6106 1.856629 TACTCCCTCCGTTCGGATTT 58.143 50.000 14.34 0.93 33.34 2.17
1992 6107 1.856629 ACTCCCTCCGTTCGGATTTA 58.143 50.000 14.34 2.52 33.34 1.40
1993 6108 1.479730 ACTCCCTCCGTTCGGATTTAC 59.520 52.381 14.34 0.00 33.34 2.01
1994 6109 1.755380 CTCCCTCCGTTCGGATTTACT 59.245 52.381 14.34 0.00 33.34 2.24
1995 6110 2.167900 CTCCCTCCGTTCGGATTTACTT 59.832 50.000 14.34 0.00 33.34 2.24
1996 6111 2.093869 TCCCTCCGTTCGGATTTACTTG 60.094 50.000 14.34 1.37 33.34 3.16
1997 6112 2.354403 CCCTCCGTTCGGATTTACTTGT 60.354 50.000 14.34 0.00 33.34 3.16
1998 6113 2.928116 CCTCCGTTCGGATTTACTTGTC 59.072 50.000 14.34 0.00 33.34 3.18
1999 6114 3.581755 CTCCGTTCGGATTTACTTGTCA 58.418 45.455 14.34 0.00 33.34 3.58
2000 6115 4.181578 CTCCGTTCGGATTTACTTGTCAT 58.818 43.478 14.34 0.00 33.34 3.06
2001 6116 5.327616 TCCGTTCGGATTTACTTGTCATA 57.672 39.130 10.00 0.00 0.00 2.15
2002 6117 5.345702 TCCGTTCGGATTTACTTGTCATAG 58.654 41.667 10.00 0.00 0.00 2.23
2003 6118 5.125900 TCCGTTCGGATTTACTTGTCATAGA 59.874 40.000 10.00 0.00 0.00 1.98
2004 6119 5.808540 CCGTTCGGATTTACTTGTCATAGAA 59.191 40.000 5.19 0.00 0.00 2.10
2005 6120 6.311935 CCGTTCGGATTTACTTGTCATAGAAA 59.688 38.462 5.19 0.00 0.00 2.52
2006 6121 7.011109 CCGTTCGGATTTACTTGTCATAGAAAT 59.989 37.037 5.19 0.00 0.00 2.17
2007 6122 7.846107 CGTTCGGATTTACTTGTCATAGAAATG 59.154 37.037 0.00 0.00 0.00 2.32
2008 6123 7.786178 TCGGATTTACTTGTCATAGAAATGG 57.214 36.000 0.00 0.00 33.61 3.16
2009 6124 7.561251 TCGGATTTACTTGTCATAGAAATGGA 58.439 34.615 0.00 0.00 33.61 3.41
2010 6125 8.210946 TCGGATTTACTTGTCATAGAAATGGAT 58.789 33.333 0.00 0.00 33.61 3.41
2011 6126 9.489084 CGGATTTACTTGTCATAGAAATGGATA 57.511 33.333 0.00 0.00 33.61 2.59
2052 6167 7.664082 AATTCTAGATACATCCATTTCTGCG 57.336 36.000 0.00 0.00 0.00 5.18
2053 6168 6.405278 TTCTAGATACATCCATTTCTGCGA 57.595 37.500 0.00 0.00 0.00 5.10
2054 6169 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2055 6170 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2056 6171 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2057 6172 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2058 6173 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2059 6174 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2060 6175 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2061 6176 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2062 6177 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2063 6178 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
2064 6179 4.092821 TCCATTTCTGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 38.31 3.34
2065 6180 4.334443 CATTTCTGCGACAAGTAATTCGG 58.666 43.478 0.00 0.00 35.73 4.30
2066 6181 2.004583 TCTGCGACAAGTAATTCGGG 57.995 50.000 0.00 0.00 35.73 5.14
2067 6182 1.546923 TCTGCGACAAGTAATTCGGGA 59.453 47.619 0.00 0.00 35.73 5.14
2068 6183 1.659098 CTGCGACAAGTAATTCGGGAC 59.341 52.381 0.00 0.00 35.73 4.46
2110 6225 1.000385 CAAATGCAGACGCCCTTCAAA 60.000 47.619 0.00 0.00 37.32 2.69
2113 6228 2.192664 TGCAGACGCCCTTCAAATAA 57.807 45.000 0.00 0.00 37.32 1.40
2114 6229 2.083774 TGCAGACGCCCTTCAAATAAG 58.916 47.619 0.00 0.00 37.32 1.73
2115 6230 1.202188 GCAGACGCCCTTCAAATAAGC 60.202 52.381 0.00 0.00 0.00 3.09
2117 6232 2.096496 CAGACGCCCTTCAAATAAGCTG 59.904 50.000 0.00 0.00 0.00 4.24
2118 6233 2.027192 AGACGCCCTTCAAATAAGCTGA 60.027 45.455 0.00 0.00 0.00 4.26
2122 6237 3.290710 GCCCTTCAAATAAGCTGATGGA 58.709 45.455 6.44 0.00 39.40 3.41
2123 6238 3.893813 GCCCTTCAAATAAGCTGATGGAT 59.106 43.478 6.44 0.00 39.40 3.41
2124 6239 4.022503 GCCCTTCAAATAAGCTGATGGATC 60.023 45.833 6.44 0.00 39.40 3.36
2125 6240 4.214971 CCCTTCAAATAAGCTGATGGATCG 59.785 45.833 6.44 0.00 39.40 3.69
2126 6241 5.059161 CCTTCAAATAAGCTGATGGATCGA 58.941 41.667 0.00 0.00 39.40 3.59
2127 6242 5.704515 CCTTCAAATAAGCTGATGGATCGAT 59.295 40.000 0.00 0.00 39.40 3.59
2128 6243 6.206243 CCTTCAAATAAGCTGATGGATCGATT 59.794 38.462 0.00 0.00 39.40 3.34
2129 6244 6.791887 TCAAATAAGCTGATGGATCGATTC 57.208 37.500 0.00 0.00 0.00 2.52
2130 6245 6.528321 TCAAATAAGCTGATGGATCGATTCT 58.472 36.000 5.06 0.00 0.00 2.40
2131 6246 6.648310 TCAAATAAGCTGATGGATCGATTCTC 59.352 38.462 5.06 1.03 0.00 2.87
2132 6247 5.999205 ATAAGCTGATGGATCGATTCTCT 57.001 39.130 5.06 0.00 0.00 3.10
2133 6248 3.940209 AGCTGATGGATCGATTCTCTC 57.060 47.619 5.06 2.79 0.00 3.20
2134 6249 2.562298 AGCTGATGGATCGATTCTCTCC 59.438 50.000 5.06 0.00 0.00 3.71
2135 6250 2.353605 GCTGATGGATCGATTCTCTCCC 60.354 54.545 5.06 0.00 0.00 4.30
2136 6251 2.233431 CTGATGGATCGATTCTCTCCCC 59.767 54.545 5.06 0.00 0.00 4.81
2137 6252 2.158249 TGATGGATCGATTCTCTCCCCT 60.158 50.000 5.06 0.00 0.00 4.79
2138 6253 2.478872 TGGATCGATTCTCTCCCCTT 57.521 50.000 5.06 0.00 0.00 3.95
2139 6254 3.612795 TGGATCGATTCTCTCCCCTTA 57.387 47.619 5.06 0.00 0.00 2.69
2140 6255 4.133526 TGGATCGATTCTCTCCCCTTAT 57.866 45.455 5.06 0.00 0.00 1.73
2141 6256 5.270979 TGGATCGATTCTCTCCCCTTATA 57.729 43.478 5.06 0.00 0.00 0.98
2142 6257 5.843469 TGGATCGATTCTCTCCCCTTATAT 58.157 41.667 5.06 0.00 0.00 0.86
2143 6258 6.264528 TGGATCGATTCTCTCCCCTTATATT 58.735 40.000 5.06 0.00 0.00 1.28
2144 6259 6.730977 TGGATCGATTCTCTCCCCTTATATTT 59.269 38.462 5.06 0.00 0.00 1.40
2145 6260 7.044798 GGATCGATTCTCTCCCCTTATATTTG 58.955 42.308 0.00 0.00 0.00 2.32
2150 6265 3.006967 TCTCTCCCCTTATATTTGCTCGC 59.993 47.826 0.00 0.00 0.00 5.03
2151 6266 2.703536 TCTCCCCTTATATTTGCTCGCA 59.296 45.455 0.00 0.00 0.00 5.10
2162 6277 0.940991 TTGCTCGCATGATCGATCGG 60.941 55.000 20.03 15.38 37.87 4.18
2177 6292 0.250513 ATCGGTTCTCTTGGCCAGAC 59.749 55.000 5.11 1.06 0.00 3.51
2180 6295 1.611673 CGGTTCTCTTGGCCAGACATT 60.612 52.381 5.11 0.00 0.00 2.71
2186 6301 5.282055 TCTCTTGGCCAGACATTATGTAG 57.718 43.478 5.11 0.00 0.00 2.74
2188 6303 5.189736 TCTCTTGGCCAGACATTATGTAGTT 59.810 40.000 5.11 0.00 0.00 2.24
2189 6304 5.185454 TCTTGGCCAGACATTATGTAGTTG 58.815 41.667 5.11 0.00 0.00 3.16
2193 6308 5.182950 TGGCCAGACATTATGTAGTTGTTTG 59.817 40.000 0.00 0.00 0.00 2.93
2194 6309 5.183140 GGCCAGACATTATGTAGTTGTTTGT 59.817 40.000 0.00 0.00 0.00 2.83
2196 6311 6.801862 GCCAGACATTATGTAGTTGTTTGTTC 59.198 38.462 0.00 0.00 0.00 3.18
2197 6312 7.015289 CCAGACATTATGTAGTTGTTTGTTCG 58.985 38.462 0.00 0.00 0.00 3.95
2236 6407 8.918658 GTTTAGTTCGACATTCTATGTGTTACA 58.081 33.333 0.00 0.00 45.03 2.41
2243 6416 7.539710 TCGACATTCTATGTGTTACAGTGTTAC 59.460 37.037 0.00 2.63 45.03 2.50
2247 6420 9.817809 CATTCTATGTGTTACAGTGTTACCTAT 57.182 33.333 9.76 6.80 0.00 2.57
2253 6426 0.458669 ACAGTGTTACCTATCCCGCG 59.541 55.000 0.00 0.00 0.00 6.46
2313 6495 6.372381 CAGACATGAACCACATCATAGTTGAA 59.628 38.462 0.00 0.00 37.96 2.69
2689 6871 5.659440 TTTTTAGGAAAGACCATCATGGC 57.341 39.130 2.52 0.00 42.67 4.40
2690 6872 4.591321 TTTAGGAAAGACCATCATGGCT 57.409 40.909 2.52 0.00 42.67 4.75
2691 6873 5.708736 TTTAGGAAAGACCATCATGGCTA 57.291 39.130 2.52 0.00 42.67 3.93
2692 6874 3.853355 AGGAAAGACCATCATGGCTAG 57.147 47.619 2.52 0.00 42.67 3.42
2693 6875 2.158696 AGGAAAGACCATCATGGCTAGC 60.159 50.000 6.04 6.04 42.67 3.42
2694 6876 2.158696 GGAAAGACCATCATGGCTAGCT 60.159 50.000 15.72 0.00 42.67 3.32
2695 6877 3.549794 GAAAGACCATCATGGCTAGCTT 58.450 45.455 15.72 0.00 42.67 3.74
2696 6878 3.659183 AAGACCATCATGGCTAGCTTT 57.341 42.857 15.72 0.00 42.67 3.51
2697 6879 4.778213 AAGACCATCATGGCTAGCTTTA 57.222 40.909 15.72 1.83 42.67 1.85
2698 6880 4.989875 AGACCATCATGGCTAGCTTTAT 57.010 40.909 15.72 4.31 42.67 1.40
2699 6881 5.316158 AGACCATCATGGCTAGCTTTATT 57.684 39.130 15.72 0.00 42.67 1.40
2700 6882 6.439636 AGACCATCATGGCTAGCTTTATTA 57.560 37.500 15.72 0.00 42.67 0.98
2701 6883 6.841601 AGACCATCATGGCTAGCTTTATTAA 58.158 36.000 15.72 0.00 42.67 1.40
2702 6884 7.290061 AGACCATCATGGCTAGCTTTATTAAA 58.710 34.615 15.72 0.00 42.67 1.52
2703 6885 7.779798 AGACCATCATGGCTAGCTTTATTAAAA 59.220 33.333 15.72 0.00 42.67 1.52
2704 6886 8.305046 ACCATCATGGCTAGCTTTATTAAAAA 57.695 30.769 15.72 0.00 42.67 1.94
2705 6887 8.927411 ACCATCATGGCTAGCTTTATTAAAAAT 58.073 29.630 15.72 0.00 42.67 1.82
2706 6888 9.768662 CCATCATGGCTAGCTTTATTAAAAATT 57.231 29.630 15.72 0.00 0.00 1.82
2726 6908 9.634163 AAAAATTAAACAGGGATTACATCGTTC 57.366 29.630 0.00 0.00 0.00 3.95
2727 6909 7.931578 AATTAAACAGGGATTACATCGTTCA 57.068 32.000 0.00 0.00 0.00 3.18
2728 6910 6.730960 TTAAACAGGGATTACATCGTTCAC 57.269 37.500 0.00 0.00 0.00 3.18
2729 6911 3.973206 ACAGGGATTACATCGTTCACA 57.027 42.857 0.00 0.00 0.00 3.58
2730 6912 4.280436 ACAGGGATTACATCGTTCACAA 57.720 40.909 0.00 0.00 0.00 3.33
2731 6913 4.253685 ACAGGGATTACATCGTTCACAAG 58.746 43.478 0.00 0.00 0.00 3.16
2732 6914 3.623060 CAGGGATTACATCGTTCACAAGG 59.377 47.826 0.00 0.00 0.00 3.61
2733 6915 3.263425 AGGGATTACATCGTTCACAAGGT 59.737 43.478 0.00 0.00 0.00 3.50
2734 6916 4.007659 GGGATTACATCGTTCACAAGGTT 58.992 43.478 0.00 0.00 0.00 3.50
2735 6917 4.457949 GGGATTACATCGTTCACAAGGTTT 59.542 41.667 0.00 0.00 0.00 3.27
2736 6918 5.390613 GGATTACATCGTTCACAAGGTTTG 58.609 41.667 0.00 0.00 0.00 2.93
2737 6919 4.822036 TTACATCGTTCACAAGGTTTGG 57.178 40.909 0.00 0.00 34.12 3.28
2738 6920 2.925724 ACATCGTTCACAAGGTTTGGA 58.074 42.857 0.00 0.00 34.12 3.53
2739 6921 3.283751 ACATCGTTCACAAGGTTTGGAA 58.716 40.909 0.00 0.00 34.12 3.53
2740 6922 3.066203 ACATCGTTCACAAGGTTTGGAAC 59.934 43.478 10.48 10.48 37.42 3.62
2741 6923 2.993937 TCGTTCACAAGGTTTGGAACT 58.006 42.857 14.93 0.00 38.03 3.01
2742 6924 4.139859 TCGTTCACAAGGTTTGGAACTA 57.860 40.909 14.93 7.10 38.03 2.24
2743 6925 4.124238 TCGTTCACAAGGTTTGGAACTAG 58.876 43.478 14.93 0.00 38.03 2.57
2744 6926 3.250040 CGTTCACAAGGTTTGGAACTAGG 59.750 47.826 14.93 3.87 38.03 3.02
2745 6927 2.858745 TCACAAGGTTTGGAACTAGGC 58.141 47.619 0.00 0.00 34.12 3.93
2746 6928 2.173782 TCACAAGGTTTGGAACTAGGCA 59.826 45.455 0.00 0.00 34.12 4.75
2747 6929 2.554032 CACAAGGTTTGGAACTAGGCAG 59.446 50.000 0.00 0.00 34.12 4.85
2748 6930 1.541588 CAAGGTTTGGAACTAGGCAGC 59.458 52.381 0.00 0.00 0.00 5.25
2749 6931 0.038310 AGGTTTGGAACTAGGCAGCC 59.962 55.000 1.84 1.84 0.00 4.85
2750 6932 1.305930 GGTTTGGAACTAGGCAGCCG 61.306 60.000 5.55 0.00 0.00 5.52
2751 6933 0.321298 GTTTGGAACTAGGCAGCCGA 60.321 55.000 5.55 0.00 0.00 5.54
2752 6934 0.398696 TTTGGAACTAGGCAGCCGAA 59.601 50.000 5.55 0.00 0.00 4.30
2753 6935 0.036388 TTGGAACTAGGCAGCCGAAG 60.036 55.000 5.55 10.56 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 0.981183 ACTATTGCACCCGGTCTCAA 59.019 50.000 0.00 0.94 0.00 3.02
25 26 0.951558 GCCATAACTATTGCACCCGG 59.048 55.000 0.00 0.00 0.00 5.73
26 27 0.951558 GGCCATAACTATTGCACCCG 59.048 55.000 0.00 0.00 0.00 5.28
28 29 2.757868 TGTTGGCCATAACTATTGCACC 59.242 45.455 6.09 0.00 0.00 5.01
29 30 3.192422 TGTGTTGGCCATAACTATTGCAC 59.808 43.478 6.09 0.00 0.00 4.57
32 33 4.675146 GCACTGTGTTGGCCATAACTATTG 60.675 45.833 6.09 7.94 0.00 1.90
41 42 4.497984 ACCGCACTGTGTTGGCCA 62.498 61.111 17.43 0.00 0.00 5.36
78 79 1.686741 GGGTGTTTGGTCCTGGTTGAA 60.687 52.381 0.00 0.00 0.00 2.69
82 83 1.451449 TATGGGTGTTTGGTCCTGGT 58.549 50.000 0.00 0.00 0.00 4.00
92 93 2.513738 ACACATGGGCTATATGGGTGTT 59.486 45.455 0.00 0.00 40.48 3.32
112 113 5.065218 ACTGACAACTCTCAACATGTTTCAC 59.935 40.000 8.77 0.00 0.00 3.18
116 117 4.943705 ACAACTGACAACTCTCAACATGTT 59.056 37.500 4.92 4.92 0.00 2.71
155 169 5.420409 AGGTCATCTTAACGGTTGAATCTC 58.580 41.667 3.07 0.00 0.00 2.75
175 189 6.995686 GGGTTGAACATTTTTCCATTTAAGGT 59.004 34.615 0.00 0.00 0.00 3.50
176 190 6.995091 TGGGTTGAACATTTTTCCATTTAAGG 59.005 34.615 0.00 0.00 0.00 2.69
184 198 4.776349 ACCTTTGGGTTGAACATTTTTCC 58.224 39.130 0.00 0.00 44.73 3.13
199 213 2.286184 CGACGAGTTGAACAACCTTTGG 60.286 50.000 13.07 1.18 42.06 3.28
234 250 2.676748 AGATGGTCAAGCACCCAAAAA 58.323 42.857 0.00 0.00 46.18 1.94
260 276 0.814010 GGATCCACACACCGCATACC 60.814 60.000 6.95 0.00 0.00 2.73
267 283 1.000717 CCGTTTTTGGATCCACACACC 60.001 52.381 15.91 0.59 0.00 4.16
287 303 8.035394 TCACATTTAGGTCTAAGACATCAGTTC 58.965 37.037 0.00 0.00 33.68 3.01
290 306 8.954950 ATTCACATTTAGGTCTAAGACATCAG 57.045 34.615 0.00 0.00 33.68 2.90
291 307 9.383519 GAATTCACATTTAGGTCTAAGACATCA 57.616 33.333 0.00 0.00 33.68 3.07
293 309 7.495934 CCGAATTCACATTTAGGTCTAAGACAT 59.504 37.037 6.22 0.00 33.68 3.06
344 4225 4.879598 ACACGAGAAAAGGACTACGAATT 58.120 39.130 0.00 0.00 0.00 2.17
348 4229 3.438087 TCCTACACGAGAAAAGGACTACG 59.562 47.826 0.00 0.00 33.18 3.51
362 4243 2.233922 AGATGGTTGGACTTCCTACACG 59.766 50.000 11.29 0.00 42.34 4.49
365 4246 4.762289 ATGAGATGGTTGGACTTCCTAC 57.238 45.455 1.57 1.57 40.32 3.18
389 4270 5.277857 ACCGGTCATTACCTCTCATTTAG 57.722 43.478 0.00 0.00 44.35 1.85
402 4283 2.370349 TGTGTTGTTCAACCGGTCATT 58.630 42.857 8.04 0.00 0.00 2.57
406 4287 4.138290 TGATTATGTGTTGTTCAACCGGT 58.862 39.130 0.00 0.00 0.00 5.28
464 4349 7.563906 AGAATGAGAAGGAAAGAACATAGGAG 58.436 38.462 0.00 0.00 0.00 3.69
470 4355 4.452455 GCGAAGAATGAGAAGGAAAGAACA 59.548 41.667 0.00 0.00 0.00 3.18
479 4364 6.900568 ATACAAAGAGCGAAGAATGAGAAG 57.099 37.500 0.00 0.00 0.00 2.85
480 4365 6.092670 CCAATACAAAGAGCGAAGAATGAGAA 59.907 38.462 0.00 0.00 0.00 2.87
493 4378 4.245660 TCGTTGCTCTCCAATACAAAGAG 58.754 43.478 0.00 0.00 39.62 2.85
498 4387 2.766263 AGGATCGTTGCTCTCCAATACA 59.234 45.455 0.00 0.00 35.55 2.29
501 4390 2.237143 TCAAGGATCGTTGCTCTCCAAT 59.763 45.455 20.70 0.00 35.55 3.16
505 4394 1.933247 CCTCAAGGATCGTTGCTCTC 58.067 55.000 20.70 0.00 37.39 3.20
541 4430 3.541713 GGGCTGCTCTAGGTCGGG 61.542 72.222 0.00 0.00 0.00 5.14
651 4541 2.824041 CAAATGAGACCCGGCCGG 60.824 66.667 37.99 37.99 37.81 6.13
663 4553 5.176774 TGTGTACTCTTTGCGTACTCAAATG 59.823 40.000 11.21 9.80 37.98 2.32
672 4562 1.217882 GCACTGTGTACTCTTTGCGT 58.782 50.000 9.86 0.00 0.00 5.24
673 4563 0.512952 GGCACTGTGTACTCTTTGCG 59.487 55.000 9.86 0.00 0.00 4.85
676 4566 1.865865 CACGGCACTGTGTACTCTTT 58.134 50.000 9.86 0.00 35.12 2.52
691 4602 3.425578 TTTTTGCACACCAACACGG 57.574 47.368 0.00 0.00 42.50 4.94
708 4619 1.486726 GATCTGACCGGTCCCTCATTT 59.513 52.381 31.19 9.36 0.00 2.32
710 4621 0.032117 TGATCTGACCGGTCCCTCAT 60.032 55.000 31.19 16.95 0.00 2.90
712 4623 0.684805 ACTGATCTGACCGGTCCCTC 60.685 60.000 31.19 22.97 0.00 4.30
877 4981 1.736282 CATGTGGACGTGCGTGCTA 60.736 57.895 16.33 6.94 37.36 3.49
1005 5109 4.016444 GAGGCGATAGGAGAAGATGAGAT 58.984 47.826 0.00 0.00 0.00 2.75
1046 5150 2.287915 GTGTGCAGCGAAGAAGAAGAAA 59.712 45.455 0.00 0.00 0.00 2.52
1047 5151 1.867233 GTGTGCAGCGAAGAAGAAGAA 59.133 47.619 0.00 0.00 0.00 2.52
1048 5152 1.069204 AGTGTGCAGCGAAGAAGAAGA 59.931 47.619 0.00 0.00 0.00 2.87
1067 5171 2.831333 CAGGAAGGAATCGATGTGGAG 58.169 52.381 0.00 0.00 0.00 3.86
1110 5214 0.893727 TAGCAGTCTCGGTGCAGTCA 60.894 55.000 0.00 0.00 43.82 3.41
1111 5215 0.179150 CTAGCAGTCTCGGTGCAGTC 60.179 60.000 0.00 0.00 43.82 3.51
1112 5216 1.599606 CCTAGCAGTCTCGGTGCAGT 61.600 60.000 0.00 0.00 43.82 4.40
1174 5284 3.770040 CGATCGGGTGACAGGCCA 61.770 66.667 7.38 0.00 0.00 5.36
1181 5291 1.455773 ATCAGGAGCGATCGGGTGA 60.456 57.895 18.30 0.00 0.00 4.02
1192 5302 2.187946 GGTGCCGGACATCAGGAG 59.812 66.667 5.05 0.00 32.68 3.69
1360 5470 7.823745 ATTAACATGGGACTCATTAACATCC 57.176 36.000 0.00 0.00 32.92 3.51
1936 6051 5.106555 CCACTGATCATACACTTGTGGAAAC 60.107 44.000 18.53 0.00 44.21 2.78
1980 6095 5.345702 TCTATGACAAGTAAATCCGAACGG 58.654 41.667 6.94 6.94 0.00 4.44
1981 6096 6.880822 TTCTATGACAAGTAAATCCGAACG 57.119 37.500 0.00 0.00 0.00 3.95
1982 6097 8.122952 CCATTTCTATGACAAGTAAATCCGAAC 58.877 37.037 0.00 0.00 33.37 3.95
1983 6098 8.044309 TCCATTTCTATGACAAGTAAATCCGAA 58.956 33.333 0.00 0.00 33.37 4.30
1984 6099 7.561251 TCCATTTCTATGACAAGTAAATCCGA 58.439 34.615 0.00 0.00 33.37 4.55
1985 6100 7.786178 TCCATTTCTATGACAAGTAAATCCG 57.214 36.000 0.00 0.00 33.37 4.18
2026 6141 9.208022 CGCAGAAATGGATGTATCTAGAATTAA 57.792 33.333 0.00 0.00 0.00 1.40
2027 6142 8.585018 TCGCAGAAATGGATGTATCTAGAATTA 58.415 33.333 0.00 0.00 0.00 1.40
2028 6143 7.386299 GTCGCAGAAATGGATGTATCTAGAATT 59.614 37.037 0.00 0.00 39.69 2.17
2029 6144 6.870965 GTCGCAGAAATGGATGTATCTAGAAT 59.129 38.462 0.00 0.00 39.69 2.40
2030 6145 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
2031 6146 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
2032 6147 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
2033 6148 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2034 6149 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2035 6150 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2036 6151 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2037 6152 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2038 6153 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2039 6154 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2040 6155 5.220662 CGAATTACTTGTCGCAGAAATGGAT 60.221 40.000 0.00 0.00 39.69 3.41
2041 6156 4.092821 CGAATTACTTGTCGCAGAAATGGA 59.907 41.667 0.00 0.00 39.69 3.41
2042 6157 4.334443 CGAATTACTTGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
2043 6158 4.334443 CCGAATTACTTGTCGCAGAAATG 58.666 43.478 0.00 0.00 39.69 2.32
2044 6159 3.374058 CCCGAATTACTTGTCGCAGAAAT 59.626 43.478 0.00 0.00 39.69 2.17
2045 6160 2.739913 CCCGAATTACTTGTCGCAGAAA 59.260 45.455 0.00 0.00 39.69 2.52
2046 6161 2.028839 TCCCGAATTACTTGTCGCAGAA 60.029 45.455 0.00 0.00 39.69 3.02
2047 6162 1.546923 TCCCGAATTACTTGTCGCAGA 59.453 47.619 0.00 0.00 35.93 4.26
2048 6163 1.659098 GTCCCGAATTACTTGTCGCAG 59.341 52.381 0.00 0.00 35.93 5.18
2049 6164 1.717194 GTCCCGAATTACTTGTCGCA 58.283 50.000 0.00 0.00 35.93 5.10
2050 6165 0.643820 CGTCCCGAATTACTTGTCGC 59.356 55.000 0.00 0.00 35.93 5.19
2051 6166 1.135315 TCCGTCCCGAATTACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
2052 6167 2.537401 CTCCGTCCCGAATTACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
2053 6168 1.206371 CCTCCGTCCCGAATTACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
2054 6169 1.472728 CCCTCCGTCCCGAATTACTTG 60.473 57.143 0.00 0.00 0.00 3.16
2055 6170 0.828677 CCCTCCGTCCCGAATTACTT 59.171 55.000 0.00 0.00 0.00 2.24
2056 6171 0.032813 TCCCTCCGTCCCGAATTACT 60.033 55.000 0.00 0.00 0.00 2.24
2057 6172 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
2058 6173 0.032813 ACTCCCTCCGTCCCGAATTA 60.033 55.000 0.00 0.00 0.00 1.40
2059 6174 0.032813 TACTCCCTCCGTCCCGAATT 60.033 55.000 0.00 0.00 0.00 2.17
2060 6175 0.754587 GTACTCCCTCCGTCCCGAAT 60.755 60.000 0.00 0.00 0.00 3.34
2061 6176 1.379044 GTACTCCCTCCGTCCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
2062 6177 1.929860 ATGTACTCCCTCCGTCCCGA 61.930 60.000 0.00 0.00 0.00 5.14
2063 6178 1.455217 ATGTACTCCCTCCGTCCCG 60.455 63.158 0.00 0.00 0.00 5.14
2064 6179 0.686769 ACATGTACTCCCTCCGTCCC 60.687 60.000 0.00 0.00 0.00 4.46
2065 6180 0.460311 CACATGTACTCCCTCCGTCC 59.540 60.000 0.00 0.00 0.00 4.79
2066 6181 1.183549 ACACATGTACTCCCTCCGTC 58.816 55.000 0.00 0.00 0.00 4.79
2067 6182 1.549170 GAACACATGTACTCCCTCCGT 59.451 52.381 0.00 0.00 0.00 4.69
2068 6183 1.469251 CGAACACATGTACTCCCTCCG 60.469 57.143 0.00 0.00 0.00 4.63
2069 6184 1.549170 ACGAACACATGTACTCCCTCC 59.451 52.381 0.00 0.00 0.00 4.30
2070 6185 2.230508 TGACGAACACATGTACTCCCTC 59.769 50.000 0.00 0.00 0.00 4.30
2071 6186 2.244695 TGACGAACACATGTACTCCCT 58.755 47.619 0.00 0.00 0.00 4.20
2072 6187 2.736144 TGACGAACACATGTACTCCC 57.264 50.000 0.00 0.00 0.00 4.30
2073 6188 4.669197 GCATTTGACGAACACATGTACTCC 60.669 45.833 0.00 0.00 38.49 3.85
2074 6189 4.084066 TGCATTTGACGAACACATGTACTC 60.084 41.667 0.00 0.00 38.49 2.59
2075 6190 3.812609 TGCATTTGACGAACACATGTACT 59.187 39.130 0.00 0.00 38.49 2.73
2076 6191 4.084066 TCTGCATTTGACGAACACATGTAC 60.084 41.667 0.00 0.00 38.49 2.90
2110 6225 5.105392 GGAGAGAATCGATCCATCAGCTTAT 60.105 44.000 0.00 0.00 42.67 1.73
2113 6228 2.562298 GGAGAGAATCGATCCATCAGCT 59.438 50.000 0.00 0.00 42.67 4.24
2114 6229 2.353605 GGGAGAGAATCGATCCATCAGC 60.354 54.545 0.00 0.00 42.67 4.26
2115 6230 2.233431 GGGGAGAGAATCGATCCATCAG 59.767 54.545 0.00 0.00 42.67 2.90
2117 6232 2.534990 AGGGGAGAGAATCGATCCATC 58.465 52.381 0.00 0.00 42.67 3.51
2118 6233 2.711895 AGGGGAGAGAATCGATCCAT 57.288 50.000 0.00 0.00 42.67 3.41
2122 6237 6.214412 AGCAAATATAAGGGGAGAGAATCGAT 59.786 38.462 0.00 0.00 42.67 3.59
2123 6238 5.544176 AGCAAATATAAGGGGAGAGAATCGA 59.456 40.000 0.00 0.00 42.67 3.59
2124 6239 5.799213 AGCAAATATAAGGGGAGAGAATCG 58.201 41.667 0.00 0.00 42.67 3.34
2125 6240 5.872070 CGAGCAAATATAAGGGGAGAGAATC 59.128 44.000 0.00 0.00 0.00 2.52
2126 6241 5.799213 CGAGCAAATATAAGGGGAGAGAAT 58.201 41.667 0.00 0.00 0.00 2.40
2127 6242 4.503296 GCGAGCAAATATAAGGGGAGAGAA 60.503 45.833 0.00 0.00 0.00 2.87
2128 6243 3.006967 GCGAGCAAATATAAGGGGAGAGA 59.993 47.826 0.00 0.00 0.00 3.10
2129 6244 3.244215 TGCGAGCAAATATAAGGGGAGAG 60.244 47.826 0.00 0.00 0.00 3.20
2130 6245 2.703536 TGCGAGCAAATATAAGGGGAGA 59.296 45.455 0.00 0.00 0.00 3.71
2131 6246 3.126001 TGCGAGCAAATATAAGGGGAG 57.874 47.619 0.00 0.00 0.00 4.30
2132 6247 3.072330 TCATGCGAGCAAATATAAGGGGA 59.928 43.478 0.57 0.00 0.00 4.81
2133 6248 3.411446 TCATGCGAGCAAATATAAGGGG 58.589 45.455 0.57 0.00 0.00 4.79
2134 6249 4.201753 CGATCATGCGAGCAAATATAAGGG 60.202 45.833 0.57 0.00 0.00 3.95
2135 6250 4.627035 TCGATCATGCGAGCAAATATAAGG 59.373 41.667 0.57 0.00 35.01 2.69
2136 6251 5.768333 TCGATCATGCGAGCAAATATAAG 57.232 39.130 0.57 0.00 35.01 1.73
2137 6252 5.004726 CGATCGATCATGCGAGCAAATATAA 59.995 40.000 24.40 0.00 46.05 0.98
2138 6253 4.500477 CGATCGATCATGCGAGCAAATATA 59.500 41.667 24.40 0.00 46.05 0.86
2139 6254 3.305361 CGATCGATCATGCGAGCAAATAT 59.695 43.478 24.40 0.00 46.05 1.28
2140 6255 2.663119 CGATCGATCATGCGAGCAAATA 59.337 45.455 24.40 0.00 46.05 1.40
2141 6256 1.458445 CGATCGATCATGCGAGCAAAT 59.542 47.619 24.40 0.00 46.05 2.32
2142 6257 0.854705 CGATCGATCATGCGAGCAAA 59.145 50.000 24.40 0.00 46.05 3.68
2143 6258 0.940991 CCGATCGATCATGCGAGCAA 60.941 55.000 24.40 0.00 46.05 3.91
2144 6259 1.372128 CCGATCGATCATGCGAGCA 60.372 57.895 24.40 0.00 46.05 4.26
2145 6260 0.941463 AACCGATCGATCATGCGAGC 60.941 55.000 24.40 1.50 44.26 5.03
2150 6265 3.055591 CCAAGAGAACCGATCGATCATG 58.944 50.000 24.40 16.66 0.00 3.07
2151 6266 2.546795 GCCAAGAGAACCGATCGATCAT 60.547 50.000 24.40 9.65 0.00 2.45
2162 6277 4.265073 ACATAATGTCTGGCCAAGAGAAC 58.735 43.478 7.01 0.73 34.84 3.01
2177 6292 6.948228 CGAGTCGAACAAACAACTACATAATG 59.052 38.462 6.73 0.00 0.00 1.90
2180 6295 5.761003 TCGAGTCGAACAAACAACTACATA 58.239 37.500 13.98 0.00 31.06 2.29
2186 6301 5.220228 CCATAGATCGAGTCGAACAAACAAC 60.220 44.000 20.74 4.17 39.99 3.32
2188 6303 4.082408 ACCATAGATCGAGTCGAACAAACA 60.082 41.667 20.74 4.27 39.99 2.83
2189 6304 4.421948 ACCATAGATCGAGTCGAACAAAC 58.578 43.478 20.74 8.82 39.99 2.93
2193 6308 5.819059 ACTAAACCATAGATCGAGTCGAAC 58.181 41.667 20.74 17.32 39.99 3.95
2194 6309 6.446781 AACTAAACCATAGATCGAGTCGAA 57.553 37.500 20.74 3.19 39.99 3.71
2196 6311 4.904724 CGAACTAAACCATAGATCGAGTCG 59.095 45.833 6.09 6.09 40.67 4.18
2197 6312 5.908499 GTCGAACTAAACCATAGATCGAGTC 59.092 44.000 15.18 4.75 45.04 3.36
2236 6407 1.041447 AGCGCGGGATAGGTAACACT 61.041 55.000 8.83 0.00 41.41 3.55
2243 6416 3.445518 TTGAGCAGCGCGGGATAGG 62.446 63.158 8.83 0.00 0.00 2.57
2253 6426 3.376918 GCCCAAGGGTTGAGCAGC 61.377 66.667 7.05 0.00 34.19 5.25
2313 6495 2.636830 CGCATGAAGGGATTGAAGTCT 58.363 47.619 0.00 0.00 0.00 3.24
2667 6849 5.332743 AGCCATGATGGTCTTTCCTAAAAA 58.667 37.500 13.84 0.00 40.46 1.94
2668 6850 4.934356 AGCCATGATGGTCTTTCCTAAAA 58.066 39.130 13.84 0.00 40.46 1.52
2669 6851 4.591321 AGCCATGATGGTCTTTCCTAAA 57.409 40.909 13.84 0.00 40.46 1.85
2670 6852 4.444876 GCTAGCCATGATGGTCTTTCCTAA 60.445 45.833 13.84 0.00 40.46 2.69
2671 6853 3.071602 GCTAGCCATGATGGTCTTTCCTA 59.928 47.826 13.84 3.91 40.46 2.94
2672 6854 2.158696 GCTAGCCATGATGGTCTTTCCT 60.159 50.000 13.84 2.85 40.46 3.36
2673 6855 2.158696 AGCTAGCCATGATGGTCTTTCC 60.159 50.000 13.84 0.00 40.46 3.13
2674 6856 3.205784 AGCTAGCCATGATGGTCTTTC 57.794 47.619 13.84 6.25 40.46 2.62
2675 6857 3.659183 AAGCTAGCCATGATGGTCTTT 57.341 42.857 13.84 0.20 40.46 2.52
2676 6858 3.659183 AAAGCTAGCCATGATGGTCTT 57.341 42.857 13.84 8.62 40.46 3.01
2677 6859 4.989875 ATAAAGCTAGCCATGATGGTCT 57.010 40.909 13.84 12.73 40.46 3.85
2678 6860 7.510549 TTTAATAAAGCTAGCCATGATGGTC 57.489 36.000 13.84 5.58 40.46 4.02
2679 6861 7.896383 TTTTAATAAAGCTAGCCATGATGGT 57.104 32.000 13.84 2.65 40.46 3.55
2680 6862 9.768662 AATTTTTAATAAAGCTAGCCATGATGG 57.231 29.630 12.13 7.21 41.55 3.51
2700 6882 9.634163 GAACGATGTAATCCCTGTTTAATTTTT 57.366 29.630 0.00 0.00 41.39 1.94
2701 6883 8.798402 TGAACGATGTAATCCCTGTTTAATTTT 58.202 29.630 0.00 0.00 41.39 1.82
2702 6884 8.241367 GTGAACGATGTAATCCCTGTTTAATTT 58.759 33.333 0.00 0.00 41.39 1.82
2703 6885 7.392113 TGTGAACGATGTAATCCCTGTTTAATT 59.608 33.333 0.00 0.00 41.39 1.40
2704 6886 6.882140 TGTGAACGATGTAATCCCTGTTTAAT 59.118 34.615 0.00 0.00 41.39 1.40
2705 6887 6.231951 TGTGAACGATGTAATCCCTGTTTAA 58.768 36.000 0.00 0.00 41.39 1.52
2706 6888 5.795972 TGTGAACGATGTAATCCCTGTTTA 58.204 37.500 0.00 0.00 41.39 2.01
2707 6889 4.647611 TGTGAACGATGTAATCCCTGTTT 58.352 39.130 0.00 0.00 41.39 2.83
2708 6890 4.280436 TGTGAACGATGTAATCCCTGTT 57.720 40.909 0.00 0.00 41.39 3.16
2709 6891 3.973206 TGTGAACGATGTAATCCCTGT 57.027 42.857 0.00 0.00 41.39 4.00
2710 6892 3.623060 CCTTGTGAACGATGTAATCCCTG 59.377 47.826 0.00 0.00 41.39 4.45
2711 6893 3.263425 ACCTTGTGAACGATGTAATCCCT 59.737 43.478 0.00 0.00 41.39 4.20
2712 6894 3.606687 ACCTTGTGAACGATGTAATCCC 58.393 45.455 0.00 0.00 41.39 3.85
2713 6895 5.390613 CAAACCTTGTGAACGATGTAATCC 58.609 41.667 0.00 0.00 41.39 3.01
2714 6896 5.180492 TCCAAACCTTGTGAACGATGTAATC 59.820 40.000 0.00 0.00 40.89 1.75
2715 6897 5.067273 TCCAAACCTTGTGAACGATGTAAT 58.933 37.500 0.00 0.00 0.00 1.89
2716 6898 4.452825 TCCAAACCTTGTGAACGATGTAA 58.547 39.130 0.00 0.00 0.00 2.41
2717 6899 4.074627 TCCAAACCTTGTGAACGATGTA 57.925 40.909 0.00 0.00 0.00 2.29
2718 6900 2.925724 TCCAAACCTTGTGAACGATGT 58.074 42.857 0.00 0.00 0.00 3.06
2719 6901 3.315191 AGTTCCAAACCTTGTGAACGATG 59.685 43.478 0.00 0.00 41.51 3.84
2720 6902 3.551846 AGTTCCAAACCTTGTGAACGAT 58.448 40.909 0.00 0.00 41.51 3.73
2721 6903 2.993937 AGTTCCAAACCTTGTGAACGA 58.006 42.857 0.00 0.00 41.51 3.85
2722 6904 3.250040 CCTAGTTCCAAACCTTGTGAACG 59.750 47.826 11.59 0.00 41.51 3.95
2723 6905 3.004419 GCCTAGTTCCAAACCTTGTGAAC 59.996 47.826 10.34 10.34 39.25 3.18
2724 6906 3.219281 GCCTAGTTCCAAACCTTGTGAA 58.781 45.455 0.00 0.00 0.00 3.18
2725 6907 2.173782 TGCCTAGTTCCAAACCTTGTGA 59.826 45.455 0.00 0.00 0.00 3.58
2726 6908 2.554032 CTGCCTAGTTCCAAACCTTGTG 59.446 50.000 0.00 0.00 0.00 3.33
2727 6909 2.863809 CTGCCTAGTTCCAAACCTTGT 58.136 47.619 0.00 0.00 0.00 3.16
2728 6910 1.541588 GCTGCCTAGTTCCAAACCTTG 59.458 52.381 0.00 0.00 0.00 3.61
2729 6911 1.547901 GGCTGCCTAGTTCCAAACCTT 60.548 52.381 12.43 0.00 0.00 3.50
2730 6912 0.038310 GGCTGCCTAGTTCCAAACCT 59.962 55.000 12.43 0.00 0.00 3.50
2731 6913 1.305930 CGGCTGCCTAGTTCCAAACC 61.306 60.000 17.92 0.00 0.00 3.27
2732 6914 0.321298 TCGGCTGCCTAGTTCCAAAC 60.321 55.000 17.92 0.00 0.00 2.93
2733 6915 0.398696 TTCGGCTGCCTAGTTCCAAA 59.601 50.000 17.92 0.00 0.00 3.28
2734 6916 0.036388 CTTCGGCTGCCTAGTTCCAA 60.036 55.000 17.92 0.00 0.00 3.53
2735 6917 1.596934 CTTCGGCTGCCTAGTTCCA 59.403 57.895 17.92 0.00 0.00 3.53
2736 6918 1.153349 CCTTCGGCTGCCTAGTTCC 60.153 63.158 17.92 0.00 0.00 3.62
2737 6919 1.815840 GCCTTCGGCTGCCTAGTTC 60.816 63.158 17.92 4.63 46.69 3.01
2738 6920 2.269241 GCCTTCGGCTGCCTAGTT 59.731 61.111 17.92 0.00 46.69 2.24


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

AutoCloner maintained by Alex Coulton.