Multiple sequence alignment - TraesCS5D01G333600

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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 TraesCS5D01G333600 chr5D 100.000 3173 0 0 1 3173 423536303 423533131 0.000000e+00 5860.0
1 TraesCS5D01G333600 chr5D 76.378 1469 248 62 950 2350 497820271 497821708 0.000000e+00 699.0
2 TraesCS5D01G333600 chr5B 95.084 1912 59 10 670 2552 511373232 511371327 0.000000e+00 2977.0
3 TraesCS5D01G333600 chr5B 94.507 619 28 5 2557 3173 511371187 511370573 0.000000e+00 950.0
4 TraesCS5D01G333600 chr5B 86.414 449 39 10 2557 3000 511365932 511365501 3.700000e-129 472.0
5 TraesCS5D01G333600 chr5B 90.278 72 6 1 6 76 511395220 511395149 3.370000e-15 93.5
6 TraesCS5D01G333600 chr5A 93.849 1967 71 27 631 2556 537125351 537123394 0.000000e+00 2916.0
7 TraesCS5D01G333600 chr5A 95.082 549 24 3 2557 3103 537123190 537122643 0.000000e+00 861.0
8 TraesCS5D01G333600 chr5A 77.588 937 166 27 899 1809 621847370 621848288 7.800000e-146 527.0
9 TraesCS5D01G333600 chr5A 87.781 401 40 7 2557 2949 537120446 537120047 8.020000e-126 460.0
10 TraesCS5D01G333600 chr5A 84.889 450 51 9 202 648 537125797 537125362 3.760000e-119 438.0
11 TraesCS5D01G333600 chrUn 79.810 1471 239 42 916 2350 87219736 87221184 0.000000e+00 1018.0
12 TraesCS5D01G333600 chrUn 74.860 1432 281 57 899 2288 330579768 330578374 7.630000e-161 577.0
13 TraesCS5D01G333600 chr7D 79.496 1468 247 38 916 2350 602291765 602293211 0.000000e+00 994.0
14 TraesCS5D01G333600 chr7D 77.735 1545 238 61 870 2350 602286623 602288125 0.000000e+00 850.0
15 TraesCS5D01G333600 chr7D 75.624 1202 225 48 1003 2185 560713153 560712001 4.660000e-148 534.0
16 TraesCS5D01G333600 chr7D 75.574 1175 223 46 1003 2160 560677027 560675900 3.630000e-144 521.0
17 TraesCS5D01G333600 chr7D 76.009 867 179 22 970 1822 566519905 566520756 3.780000e-114 422.0
18 TraesCS5D01G333600 chr6B 79.471 1398 226 40 975 2346 718230999 718232361 0.000000e+00 935.0
19 TraesCS5D01G333600 chr6B 79.018 1039 184 13 985 2006 718294211 718295232 0.000000e+00 680.0
20 TraesCS5D01G333600 chr6B 75.703 1387 261 48 1004 2350 716425734 716427084 2.690000e-175 625.0
21 TraesCS5D01G333600 chr6B 77.008 909 181 20 1290 2178 717930334 717929434 2.200000e-136 496.0
22 TraesCS5D01G333600 chr7A 78.778 1277 205 33 1069 2307 694044500 694045748 0.000000e+00 797.0
23 TraesCS5D01G333600 chr7A 80.535 411 67 10 1431 1833 652701848 652702253 1.430000e-78 303.0
24 TraesCS5D01G333600 chr7B 76.495 1204 211 44 1003 2185 608478065 608476913 9.800000e-165 590.0
25 TraesCS5D01G333600 chr7B 74.930 1432 282 55 899 2288 726363338 726361942 4.560000e-163 584.0
26 TraesCS5D01G333600 chr6D 77.705 915 164 31 1290 2178 472811176 472810276 1.010000e-144 523.0
27 TraesCS5D01G333600 chr6D 77.570 107 23 1 1106 1212 473059164 473059269 2.640000e-06 63.9


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 TraesCS5D01G333600 chr5D 423533131 423536303 3172 True 5860.00 5860 100.00000 1 3173 1 chr5D.!!$R1 3172
1 TraesCS5D01G333600 chr5D 497820271 497821708 1437 False 699.00 699 76.37800 950 2350 1 chr5D.!!$F1 1400
2 TraesCS5D01G333600 chr5B 511370573 511373232 2659 True 1963.50 2977 94.79550 670 3173 2 chr5B.!!$R3 2503
3 TraesCS5D01G333600 chr5A 537120047 537125797 5750 True 1168.75 2916 90.40025 202 3103 4 chr5A.!!$R1 2901
4 TraesCS5D01G333600 chr5A 621847370 621848288 918 False 527.00 527 77.58800 899 1809 1 chr5A.!!$F1 910
5 TraesCS5D01G333600 chrUn 87219736 87221184 1448 False 1018.00 1018 79.81000 916 2350 1 chrUn.!!$F1 1434
6 TraesCS5D01G333600 chrUn 330578374 330579768 1394 True 577.00 577 74.86000 899 2288 1 chrUn.!!$R1 1389
7 TraesCS5D01G333600 chr7D 602286623 602293211 6588 False 922.00 994 78.61550 870 2350 2 chr7D.!!$F2 1480
8 TraesCS5D01G333600 chr7D 560712001 560713153 1152 True 534.00 534 75.62400 1003 2185 1 chr7D.!!$R2 1182
9 TraesCS5D01G333600 chr7D 560675900 560677027 1127 True 521.00 521 75.57400 1003 2160 1 chr7D.!!$R1 1157
10 TraesCS5D01G333600 chr7D 566519905 566520756 851 False 422.00 422 76.00900 970 1822 1 chr7D.!!$F1 852
11 TraesCS5D01G333600 chr6B 718230999 718232361 1362 False 935.00 935 79.47100 975 2346 1 chr6B.!!$F2 1371
12 TraesCS5D01G333600 chr6B 718294211 718295232 1021 False 680.00 680 79.01800 985 2006 1 chr6B.!!$F3 1021
13 TraesCS5D01G333600 chr6B 716425734 716427084 1350 False 625.00 625 75.70300 1004 2350 1 chr6B.!!$F1 1346
14 TraesCS5D01G333600 chr6B 717929434 717930334 900 True 496.00 496 77.00800 1290 2178 1 chr6B.!!$R1 888
15 TraesCS5D01G333600 chr7A 694044500 694045748 1248 False 797.00 797 78.77800 1069 2307 1 chr7A.!!$F2 1238
16 TraesCS5D01G333600 chr7B 608476913 608478065 1152 True 590.00 590 76.49500 1003 2185 1 chr7B.!!$R1 1182
17 TraesCS5D01G333600 chr7B 726361942 726363338 1396 True 584.00 584 74.93000 899 2288 1 chr7B.!!$R2 1389
18 TraesCS5D01G333600 chr6D 472810276 472811176 900 True 523.00 523 77.70500 1290 2178 1 chr6D.!!$R1 888

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
107 108 0.108615 GGCTGTGTGCGTAGTCTCAT 60.109 55.0 0.0 0.0 44.05 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 7537 6.614496 AGAGGATCCATATATGCATAAGAGCA 59.386 38.462 15.82 0.0 42.99 4.26 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
26 27 2.665777 CGACTACGGTTGGCAGATG 58.334 57.895 0.00 0.00 35.72 2.90
27 28 0.172578 CGACTACGGTTGGCAGATGA 59.827 55.000 0.00 0.00 35.72 2.92
28 29 1.202417 CGACTACGGTTGGCAGATGAT 60.202 52.381 0.00 0.00 35.72 2.45
29 30 2.738643 CGACTACGGTTGGCAGATGATT 60.739 50.000 0.00 0.00 35.72 2.57
30 31 3.490249 CGACTACGGTTGGCAGATGATTA 60.490 47.826 0.00 0.00 35.72 1.75
31 32 3.793559 ACTACGGTTGGCAGATGATTAC 58.206 45.455 0.00 0.00 0.00 1.89
32 33 2.779755 ACGGTTGGCAGATGATTACA 57.220 45.000 0.00 0.00 0.00 2.41
33 34 3.281727 ACGGTTGGCAGATGATTACAT 57.718 42.857 0.00 0.00 39.67 2.29
34 35 2.945008 ACGGTTGGCAGATGATTACATG 59.055 45.455 0.00 0.00 36.82 3.21
35 36 3.205338 CGGTTGGCAGATGATTACATGA 58.795 45.455 0.00 0.00 36.82 3.07
36 37 3.627123 CGGTTGGCAGATGATTACATGAA 59.373 43.478 0.00 0.00 36.82 2.57
37 38 4.260907 CGGTTGGCAGATGATTACATGAAG 60.261 45.833 0.00 0.00 36.82 3.02
38 39 4.498682 GGTTGGCAGATGATTACATGAAGC 60.499 45.833 0.00 0.00 36.82 3.86
39 40 4.160642 TGGCAGATGATTACATGAAGCT 57.839 40.909 0.00 0.00 36.82 3.74
40 41 4.132336 TGGCAGATGATTACATGAAGCTC 58.868 43.478 0.00 0.00 36.82 4.09
41 42 3.501445 GGCAGATGATTACATGAAGCTCC 59.499 47.826 0.00 0.00 36.82 4.70
42 43 3.186001 GCAGATGATTACATGAAGCTCCG 59.814 47.826 0.00 0.00 36.82 4.63
43 44 3.744942 CAGATGATTACATGAAGCTCCGG 59.255 47.826 0.00 0.00 36.82 5.14
44 45 3.389329 AGATGATTACATGAAGCTCCGGT 59.611 43.478 0.00 0.00 36.82 5.28
45 46 3.627395 TGATTACATGAAGCTCCGGTT 57.373 42.857 0.00 0.00 0.00 4.44
46 47 3.270027 TGATTACATGAAGCTCCGGTTG 58.730 45.455 0.00 0.00 0.00 3.77
47 48 2.107950 TTACATGAAGCTCCGGTTGG 57.892 50.000 0.00 0.00 0.00 3.77
48 49 0.392461 TACATGAAGCTCCGGTTGGC 60.392 55.000 0.00 4.94 34.14 4.52
49 50 1.377725 CATGAAGCTCCGGTTGGCT 60.378 57.895 0.00 7.46 40.85 4.75
51 52 0.962356 ATGAAGCTCCGGTTGGCTTG 60.962 55.000 26.69 3.82 46.91 4.01
52 53 1.302511 GAAGCTCCGGTTGGCTTGA 60.303 57.895 26.69 0.00 46.91 3.02
53 54 0.678048 GAAGCTCCGGTTGGCTTGAT 60.678 55.000 26.69 11.25 46.91 2.57
54 55 0.251341 AAGCTCCGGTTGGCTTGATT 60.251 50.000 23.16 6.97 45.49 2.57
55 56 0.251341 AGCTCCGGTTGGCTTGATTT 60.251 50.000 0.00 0.00 34.96 2.17
56 57 0.603065 GCTCCGGTTGGCTTGATTTT 59.397 50.000 0.00 0.00 34.14 1.82
57 58 1.402852 GCTCCGGTTGGCTTGATTTTC 60.403 52.381 0.00 0.00 34.14 2.29
58 59 2.162681 CTCCGGTTGGCTTGATTTTCT 58.837 47.619 0.00 0.00 34.14 2.52
59 60 2.159382 TCCGGTTGGCTTGATTTTCTC 58.841 47.619 0.00 0.00 34.14 2.87
60 61 1.202348 CCGGTTGGCTTGATTTTCTCC 59.798 52.381 0.00 0.00 0.00 3.71
61 62 1.202348 CGGTTGGCTTGATTTTCTCCC 59.798 52.381 0.00 0.00 0.00 4.30
62 63 2.529632 GGTTGGCTTGATTTTCTCCCT 58.470 47.619 0.00 0.00 0.00 4.20
63 64 2.899900 GGTTGGCTTGATTTTCTCCCTT 59.100 45.455 0.00 0.00 0.00 3.95
64 65 3.324846 GGTTGGCTTGATTTTCTCCCTTT 59.675 43.478 0.00 0.00 0.00 3.11
65 66 4.202357 GGTTGGCTTGATTTTCTCCCTTTT 60.202 41.667 0.00 0.00 0.00 2.27
66 67 5.368145 GTTGGCTTGATTTTCTCCCTTTTT 58.632 37.500 0.00 0.00 0.00 1.94
67 68 5.213891 TGGCTTGATTTTCTCCCTTTTTC 57.786 39.130 0.00 0.00 0.00 2.29
68 69 4.901250 TGGCTTGATTTTCTCCCTTTTTCT 59.099 37.500 0.00 0.00 0.00 2.52
69 70 5.011023 TGGCTTGATTTTCTCCCTTTTTCTC 59.989 40.000 0.00 0.00 0.00 2.87
70 71 5.244851 GGCTTGATTTTCTCCCTTTTTCTCT 59.755 40.000 0.00 0.00 0.00 3.10
71 72 6.239430 GGCTTGATTTTCTCCCTTTTTCTCTT 60.239 38.462 0.00 0.00 0.00 2.85
72 73 6.865726 GCTTGATTTTCTCCCTTTTTCTCTTC 59.134 38.462 0.00 0.00 0.00 2.87
73 74 7.255766 GCTTGATTTTCTCCCTTTTTCTCTTCT 60.256 37.037 0.00 0.00 0.00 2.85
74 75 8.539117 TTGATTTTCTCCCTTTTTCTCTTCTT 57.461 30.769 0.00 0.00 0.00 2.52
75 76 7.945134 TGATTTTCTCCCTTTTTCTCTTCTTG 58.055 34.615 0.00 0.00 0.00 3.02
76 77 7.561356 TGATTTTCTCCCTTTTTCTCTTCTTGT 59.439 33.333 0.00 0.00 0.00 3.16
77 78 6.699575 TTTCTCCCTTTTTCTCTTCTTGTG 57.300 37.500 0.00 0.00 0.00 3.33
78 79 4.718961 TCTCCCTTTTTCTCTTCTTGTGG 58.281 43.478 0.00 0.00 0.00 4.17
79 80 3.823304 CTCCCTTTTTCTCTTCTTGTGGG 59.177 47.826 0.00 0.00 0.00 4.61
80 81 2.297315 CCCTTTTTCTCTTCTTGTGGGC 59.703 50.000 0.00 0.00 0.00 5.36
81 82 2.958355 CCTTTTTCTCTTCTTGTGGGCA 59.042 45.455 0.00 0.00 0.00 5.36
82 83 3.575687 CCTTTTTCTCTTCTTGTGGGCAT 59.424 43.478 0.00 0.00 0.00 4.40
83 84 4.321527 CCTTTTTCTCTTCTTGTGGGCATC 60.322 45.833 0.00 0.00 0.00 3.91
84 85 2.099141 TTCTCTTCTTGTGGGCATCG 57.901 50.000 0.00 0.00 0.00 3.84
85 86 0.250234 TCTCTTCTTGTGGGCATCGG 59.750 55.000 0.00 0.00 0.00 4.18
86 87 1.372087 CTCTTCTTGTGGGCATCGGC 61.372 60.000 0.00 0.00 40.13 5.54
87 88 1.377725 CTTCTTGTGGGCATCGGCT 60.378 57.895 0.00 0.00 40.87 5.52
88 89 1.651240 CTTCTTGTGGGCATCGGCTG 61.651 60.000 0.00 0.00 40.87 4.85
89 90 3.136123 CTTGTGGGCATCGGCTGG 61.136 66.667 0.00 0.00 40.87 4.85
96 97 3.807538 GCATCGGCTGGCTGTGTG 61.808 66.667 0.00 3.83 36.96 3.82
97 98 3.807538 CATCGGCTGGCTGTGTGC 61.808 66.667 0.00 0.00 41.94 4.57
101 102 3.121030 GGCTGGCTGTGTGCGTAG 61.121 66.667 0.00 0.00 44.05 3.51
102 103 2.357517 GCTGGCTGTGTGCGTAGT 60.358 61.111 0.00 0.00 44.05 2.73
103 104 2.383527 GCTGGCTGTGTGCGTAGTC 61.384 63.158 0.00 0.00 44.05 2.59
104 105 1.290324 CTGGCTGTGTGCGTAGTCT 59.710 57.895 0.00 0.00 44.05 3.24
105 106 0.734253 CTGGCTGTGTGCGTAGTCTC 60.734 60.000 0.00 0.00 44.05 3.36
106 107 1.289066 GGCTGTGTGCGTAGTCTCA 59.711 57.895 0.00 0.00 44.05 3.27
107 108 0.108615 GGCTGTGTGCGTAGTCTCAT 60.109 55.000 0.00 0.00 44.05 2.90
108 109 1.134367 GGCTGTGTGCGTAGTCTCATA 59.866 52.381 0.00 0.00 44.05 2.15
109 110 2.455032 GCTGTGTGCGTAGTCTCATAG 58.545 52.381 0.00 0.00 0.00 2.23
110 111 2.796383 GCTGTGTGCGTAGTCTCATAGG 60.796 54.545 0.00 0.00 0.00 2.57
111 112 2.423892 CTGTGTGCGTAGTCTCATAGGT 59.576 50.000 0.00 0.00 0.00 3.08
112 113 2.163613 TGTGTGCGTAGTCTCATAGGTG 59.836 50.000 0.00 0.00 0.00 4.00
113 114 2.422479 GTGTGCGTAGTCTCATAGGTGA 59.578 50.000 0.00 0.00 0.00 4.02
114 115 3.086282 TGTGCGTAGTCTCATAGGTGAA 58.914 45.455 0.00 0.00 33.05 3.18
115 116 3.128764 TGTGCGTAGTCTCATAGGTGAAG 59.871 47.826 0.00 0.00 33.05 3.02
116 117 3.377485 GTGCGTAGTCTCATAGGTGAAGA 59.623 47.826 0.00 0.00 33.05 2.87
117 118 4.014406 TGCGTAGTCTCATAGGTGAAGAA 58.986 43.478 0.00 0.00 33.05 2.52
118 119 4.645136 TGCGTAGTCTCATAGGTGAAGAAT 59.355 41.667 0.00 0.00 33.05 2.40
119 120 4.979197 GCGTAGTCTCATAGGTGAAGAATG 59.021 45.833 0.00 0.00 33.05 2.67
120 121 5.524284 CGTAGTCTCATAGGTGAAGAATGG 58.476 45.833 0.00 0.00 33.05 3.16
121 122 4.414337 AGTCTCATAGGTGAAGAATGGC 57.586 45.455 0.00 0.00 33.05 4.40
122 123 3.126831 GTCTCATAGGTGAAGAATGGCG 58.873 50.000 0.00 0.00 33.05 5.69
123 124 2.103094 TCTCATAGGTGAAGAATGGCGG 59.897 50.000 0.00 0.00 33.05 6.13
124 125 1.837439 TCATAGGTGAAGAATGGCGGT 59.163 47.619 0.00 0.00 0.00 5.68
125 126 1.942657 CATAGGTGAAGAATGGCGGTG 59.057 52.381 0.00 0.00 0.00 4.94
126 127 1.271856 TAGGTGAAGAATGGCGGTGA 58.728 50.000 0.00 0.00 0.00 4.02
127 128 0.321653 AGGTGAAGAATGGCGGTGAC 60.322 55.000 0.00 0.00 0.00 3.67
140 141 1.790387 GGTGACGATCAGTTGCTGC 59.210 57.895 0.00 0.00 0.00 5.25
141 142 0.671781 GGTGACGATCAGTTGCTGCT 60.672 55.000 0.00 0.00 0.00 4.24
142 143 0.718343 GTGACGATCAGTTGCTGCTC 59.282 55.000 0.00 0.00 0.00 4.26
144 145 3.392431 CGATCAGTTGCTGCTCGG 58.608 61.111 12.69 0.00 43.45 4.63
145 146 2.169789 CGATCAGTTGCTGCTCGGG 61.170 63.158 12.69 0.00 43.45 5.14
146 147 1.078848 GATCAGTTGCTGCTCGGGT 60.079 57.895 0.00 0.00 0.00 5.28
147 148 1.364626 GATCAGTTGCTGCTCGGGTG 61.365 60.000 0.00 0.00 0.00 4.61
148 149 3.730761 CAGTTGCTGCTCGGGTGC 61.731 66.667 0.00 0.00 0.00 5.01
149 150 4.254709 AGTTGCTGCTCGGGTGCA 62.255 61.111 0.00 1.09 41.05 4.57
150 151 3.058160 GTTGCTGCTCGGGTGCAT 61.058 61.111 5.99 0.00 42.48 3.96
151 152 1.745115 GTTGCTGCTCGGGTGCATA 60.745 57.895 5.99 0.00 42.48 3.14
152 153 1.745115 TTGCTGCTCGGGTGCATAC 60.745 57.895 5.99 0.00 42.48 2.39
153 154 2.125147 GCTGCTCGGGTGCATACA 60.125 61.111 0.00 0.00 42.48 2.29
154 155 1.524621 GCTGCTCGGGTGCATACAT 60.525 57.895 0.00 0.00 42.48 2.29
155 156 1.779025 GCTGCTCGGGTGCATACATG 61.779 60.000 0.00 0.00 42.48 3.21
156 157 1.153188 TGCTCGGGTGCATACATGG 60.153 57.895 0.00 0.00 38.12 3.66
157 158 1.146041 GCTCGGGTGCATACATGGA 59.854 57.895 0.00 0.00 0.00 3.41
158 159 0.250467 GCTCGGGTGCATACATGGAT 60.250 55.000 0.00 0.00 0.00 3.41
159 160 1.800805 CTCGGGTGCATACATGGATC 58.199 55.000 0.00 0.00 0.00 3.36
160 161 1.345741 CTCGGGTGCATACATGGATCT 59.654 52.381 0.00 0.00 29.23 2.75
161 162 1.768275 TCGGGTGCATACATGGATCTT 59.232 47.619 0.00 0.00 29.23 2.40
162 163 1.875514 CGGGTGCATACATGGATCTTG 59.124 52.381 0.00 0.00 29.23 3.02
163 164 2.746142 CGGGTGCATACATGGATCTTGT 60.746 50.000 0.00 6.98 29.23 3.16
164 165 3.494223 CGGGTGCATACATGGATCTTGTA 60.494 47.826 10.22 10.22 34.29 2.41
165 166 3.815401 GGGTGCATACATGGATCTTGTAC 59.185 47.826 10.07 0.00 32.70 2.90
166 167 3.494626 GGTGCATACATGGATCTTGTACG 59.505 47.826 10.07 5.12 32.70 3.67
167 168 4.368315 GTGCATACATGGATCTTGTACGA 58.632 43.478 10.07 0.00 32.70 3.43
168 169 4.445718 GTGCATACATGGATCTTGTACGAG 59.554 45.833 3.44 3.44 32.70 4.18
169 170 3.990469 GCATACATGGATCTTGTACGAGG 59.010 47.826 10.33 0.00 32.70 4.63
170 171 4.262036 GCATACATGGATCTTGTACGAGGA 60.262 45.833 10.33 0.00 32.70 3.71
171 172 5.567623 GCATACATGGATCTTGTACGAGGAT 60.568 44.000 10.33 2.77 32.70 3.24
172 173 4.592485 ACATGGATCTTGTACGAGGATC 57.408 45.455 10.33 11.08 36.20 3.36
173 174 4.219115 ACATGGATCTTGTACGAGGATCT 58.781 43.478 10.33 0.00 36.88 2.75
174 175 4.038522 ACATGGATCTTGTACGAGGATCTG 59.961 45.833 10.33 9.26 36.88 2.90
175 176 2.959030 TGGATCTTGTACGAGGATCTGG 59.041 50.000 10.33 0.00 36.88 3.86
176 177 2.297597 GGATCTTGTACGAGGATCTGGG 59.702 54.545 10.33 0.00 36.88 4.45
177 178 2.820728 TCTTGTACGAGGATCTGGGA 57.179 50.000 10.33 0.00 0.00 4.37
178 179 3.095912 TCTTGTACGAGGATCTGGGAA 57.904 47.619 10.33 0.00 0.00 3.97
179 180 3.643237 TCTTGTACGAGGATCTGGGAAT 58.357 45.455 10.33 0.00 0.00 3.01
180 181 4.800023 TCTTGTACGAGGATCTGGGAATA 58.200 43.478 10.33 0.00 0.00 1.75
181 182 4.583489 TCTTGTACGAGGATCTGGGAATAC 59.417 45.833 10.33 0.00 0.00 1.89
182 183 3.905968 TGTACGAGGATCTGGGAATACA 58.094 45.455 0.00 0.00 0.00 2.29
183 184 3.889538 TGTACGAGGATCTGGGAATACAG 59.110 47.826 0.00 0.00 39.84 2.74
184 185 2.320781 ACGAGGATCTGGGAATACAGG 58.679 52.381 0.00 0.00 38.98 4.00
185 186 2.091278 ACGAGGATCTGGGAATACAGGA 60.091 50.000 0.00 0.00 38.98 3.86
186 187 2.297597 CGAGGATCTGGGAATACAGGAC 59.702 54.545 0.00 0.00 38.98 3.85
187 188 2.635427 GAGGATCTGGGAATACAGGACC 59.365 54.545 0.00 0.00 38.98 4.46
188 189 2.251338 AGGATCTGGGAATACAGGACCT 59.749 50.000 0.00 0.00 38.52 3.85
189 190 2.370189 GGATCTGGGAATACAGGACCTG 59.630 54.545 20.45 20.45 38.98 4.00
190 191 2.940514 TCTGGGAATACAGGACCTGA 57.059 50.000 28.56 11.96 38.98 3.86
191 192 2.752030 TCTGGGAATACAGGACCTGAG 58.248 52.381 28.56 12.71 38.98 3.35
192 193 2.314852 TCTGGGAATACAGGACCTGAGA 59.685 50.000 28.56 14.85 38.98 3.27
193 194 3.051803 TCTGGGAATACAGGACCTGAGAT 60.052 47.826 28.56 16.80 38.98 2.75
194 195 3.041211 TGGGAATACAGGACCTGAGATG 58.959 50.000 28.56 1.88 35.18 2.90
195 196 3.041946 GGGAATACAGGACCTGAGATGT 58.958 50.000 28.56 8.55 35.18 3.06
196 197 3.456277 GGGAATACAGGACCTGAGATGTT 59.544 47.826 28.56 10.23 35.18 2.71
197 198 4.080299 GGGAATACAGGACCTGAGATGTTT 60.080 45.833 28.56 10.94 35.18 2.83
198 199 5.501156 GGAATACAGGACCTGAGATGTTTT 58.499 41.667 28.56 7.31 35.18 2.43
199 200 5.946377 GGAATACAGGACCTGAGATGTTTTT 59.054 40.000 28.56 5.76 35.18 1.94
200 201 6.094186 GGAATACAGGACCTGAGATGTTTTTC 59.906 42.308 28.56 13.74 35.18 2.29
209 210 5.651139 ACCTGAGATGTTTTTCCTCATCATG 59.349 40.000 7.68 0.00 41.74 3.07
215 216 7.348815 AGATGTTTTTCCTCATCATGGATACA 58.651 34.615 7.68 0.00 43.63 2.29
240 241 7.108841 TGCTACGAATAGACCAAGAAATACT 57.891 36.000 0.00 0.00 0.00 2.12
241 242 8.229253 TGCTACGAATAGACCAAGAAATACTA 57.771 34.615 0.00 0.00 0.00 1.82
242 243 8.133627 TGCTACGAATAGACCAAGAAATACTAC 58.866 37.037 0.00 0.00 0.00 2.73
243 244 8.133627 GCTACGAATAGACCAAGAAATACTACA 58.866 37.037 0.00 0.00 0.00 2.74
284 285 8.012809 TGTTTGTTATTTATTCGTGCTAGTGTG 58.987 33.333 0.00 0.00 0.00 3.82
285 286 6.102006 TGTTATTTATTCGTGCTAGTGTGC 57.898 37.500 0.00 0.00 0.00 4.57
286 287 5.639931 TGTTATTTATTCGTGCTAGTGTGCA 59.360 36.000 0.00 0.00 41.05 4.57
289 290 5.712217 TTTATTCGTGCTAGTGTGCATAC 57.288 39.130 5.29 5.29 45.23 2.39
302 303 0.108662 TGCATACTCAGTCGTGGCAG 60.109 55.000 0.00 0.00 0.00 4.85
368 369 3.065371 CGCGAAATAATCCAGCCTTTCTT 59.935 43.478 0.00 0.00 0.00 2.52
374 375 6.475596 AATAATCCAGCCTTTCTTGGAATG 57.524 37.500 0.00 0.00 33.78 2.67
390 391 3.646162 TGGAATGTGGATATCGGTAGCTT 59.354 43.478 0.00 0.00 0.00 3.74
394 395 4.233123 TGTGGATATCGGTAGCTTTACG 57.767 45.455 0.00 0.00 0.00 3.18
405 406 4.147653 CGGTAGCTTTACGATATTGTTCGG 59.852 45.833 0.00 0.00 43.33 4.30
406 407 4.446719 GGTAGCTTTACGATATTGTTCGGG 59.553 45.833 0.00 0.00 43.33 5.14
420 421 1.265905 GTTCGGGAAGTCGCAACATTT 59.734 47.619 0.00 0.00 0.00 2.32
423 424 1.662876 CGGGAAGTCGCAACATTTGTG 60.663 52.381 0.00 0.00 42.36 3.33
424 425 1.606668 GGGAAGTCGCAACATTTGTGA 59.393 47.619 0.00 0.00 46.95 3.58
431 432 2.685388 TCGCAACATTTGTGAGGTCAAA 59.315 40.909 0.00 0.00 44.54 2.69
434 435 4.507388 CGCAACATTTGTGAGGTCAAAAAT 59.493 37.500 2.72 2.72 42.77 1.82
436 437 5.050159 GCAACATTTGTGAGGTCAAAAATCC 60.050 40.000 5.30 0.00 40.72 3.01
471 472 3.873910 ACACAGTCCCATTACAGCATAC 58.126 45.455 0.00 0.00 0.00 2.39
478 479 3.951037 TCCCATTACAGCATACGCAAAAT 59.049 39.130 0.00 0.00 42.27 1.82
479 480 4.400884 TCCCATTACAGCATACGCAAAATT 59.599 37.500 0.00 0.00 42.27 1.82
481 482 6.095580 TCCCATTACAGCATACGCAAAATTTA 59.904 34.615 0.00 0.00 42.27 1.40
482 483 6.417635 CCCATTACAGCATACGCAAAATTTAG 59.582 38.462 0.00 0.00 42.27 1.85
483 484 6.074888 CCATTACAGCATACGCAAAATTTAGC 60.075 38.462 0.00 0.00 42.27 3.09
484 485 3.769536 ACAGCATACGCAAAATTTAGCC 58.230 40.909 0.00 0.00 42.27 3.93
485 486 3.192422 ACAGCATACGCAAAATTTAGCCA 59.808 39.130 0.00 0.00 42.27 4.75
486 487 4.142182 ACAGCATACGCAAAATTTAGCCAT 60.142 37.500 0.00 0.00 42.27 4.40
487 488 4.805192 CAGCATACGCAAAATTTAGCCATT 59.195 37.500 0.00 0.00 42.27 3.16
488 489 5.976534 CAGCATACGCAAAATTTAGCCATTA 59.023 36.000 0.00 0.00 42.27 1.90
489 490 6.142798 CAGCATACGCAAAATTTAGCCATTAG 59.857 38.462 0.00 0.00 42.27 1.73
492 493 7.112984 GCATACGCAAAATTTAGCCATTAGTAC 59.887 37.037 0.00 0.00 38.36 2.73
509 510 2.158871 AGTACGTGTTCCCTGCAAAAGA 60.159 45.455 0.00 0.00 0.00 2.52
523 524 5.344743 TGCAAAAGATGTTGGTTTTGGTA 57.655 34.783 9.03 0.00 41.80 3.25
527 528 6.700978 CAAAAGATGTTGGTTTTGGTAAACG 58.299 36.000 0.00 0.00 43.68 3.60
540 541 1.541670 GGTAAACGCAGAGGTGGACAA 60.542 52.381 0.00 0.00 0.00 3.18
547 548 2.350772 CGCAGAGGTGGACAATTTTGAC 60.351 50.000 0.00 0.00 0.00 3.18
555 556 5.598005 AGGTGGACAATTTTGACTGAATTCA 59.402 36.000 8.12 8.12 0.00 2.57
557 558 6.272318 GTGGACAATTTTGACTGAATTCACA 58.728 36.000 3.38 0.00 0.00 3.58
562 563 8.807667 ACAATTTTGACTGAATTCACAGAATC 57.192 30.769 3.38 0.00 40.63 2.52
573 574 6.543465 TGAATTCACAGAATCACAGACAAAGT 59.457 34.615 3.38 0.00 0.00 2.66
579 580 4.686091 CAGAATCACAGACAAAGTTAGCGA 59.314 41.667 0.00 0.00 0.00 4.93
583 584 6.560253 ATCACAGACAAAGTTAGCGATTTT 57.440 33.333 0.00 0.00 0.00 1.82
584 585 5.985781 TCACAGACAAAGTTAGCGATTTTC 58.014 37.500 0.00 0.00 0.00 2.29
704 734 1.754803 TCGATTTATCAGGCCGTGAGT 59.245 47.619 10.13 3.11 39.07 3.41
706 736 2.481276 CGATTTATCAGGCCGTGAGTGA 60.481 50.000 10.13 2.85 39.07 3.41
708 738 3.627395 TTTATCAGGCCGTGAGTGATT 57.373 42.857 9.49 0.00 39.07 2.57
709 739 2.602257 TATCAGGCCGTGAGTGATTG 57.398 50.000 9.49 0.00 39.07 2.67
718 761 2.298300 CGTGAGTGATTGTTTTGCGTC 58.702 47.619 0.00 0.00 0.00 5.19
867 910 1.668151 AAACTCTGCTTCCGGCGAC 60.668 57.895 9.30 0.00 45.43 5.19
868 911 2.100879 AAACTCTGCTTCCGGCGACT 62.101 55.000 9.30 0.00 45.43 4.18
869 912 2.507992 CTCTGCTTCCGGCGACTG 60.508 66.667 9.30 0.00 45.43 3.51
871 914 4.069232 CTGCTTCCGGCGACTGGA 62.069 66.667 9.30 3.61 45.43 3.86
872 915 3.997064 CTGCTTCCGGCGACTGGAG 62.997 68.421 9.30 4.19 45.43 3.86
935 6097 1.811266 CAGCTCATCGACCCCAACG 60.811 63.158 0.00 0.00 0.00 4.10
957 6121 0.951558 GGAACTTGGCGTGTCAATGT 59.048 50.000 0.00 0.00 0.00 2.71
2215 7537 3.853207 TGTTCCTTAGACCTGTAGTGGT 58.147 45.455 0.00 0.00 44.10 4.16
2268 7598 1.546834 GTCATAGTCCGTGCGTCTTC 58.453 55.000 0.00 0.00 0.00 2.87
2458 7801 7.772292 GCAACATATGGTGGATAGTGATATCAT 59.228 37.037 22.01 1.07 32.22 2.45
2473 7816 6.323482 AGTGATATCATGTCTAACACTCTGCT 59.677 38.462 9.02 0.00 29.32 4.24
2489 7832 5.639082 CACTCTGCTTGTTTGTTTTCCTTTT 59.361 36.000 0.00 0.00 0.00 2.27
2547 7890 3.071457 TCATCGGCACCAATCATCTACAT 59.929 43.478 0.00 0.00 0.00 2.29
2556 7899 2.552743 CAATCATCTACATGCAGCTGGG 59.447 50.000 17.12 0.00 0.00 4.45
2557 7900 1.206878 TCATCTACATGCAGCTGGGT 58.793 50.000 17.12 0.00 0.00 4.51
2558 7901 1.561076 TCATCTACATGCAGCTGGGTT 59.439 47.619 17.12 0.00 0.00 4.11
2593 8141 8.849168 TCTGTTTGCTGATAAAGAAAATTGAGA 58.151 29.630 0.00 0.00 35.77 3.27
2624 8172 9.803315 GAACTGAACTTTCTTGTTAGGAAAAAT 57.197 29.630 0.00 0.00 33.17 1.82
2841 8390 2.303022 CAACATGGTCAGGTACTCAGGT 59.697 50.000 0.00 0.00 34.60 4.00
2872 8421 4.147449 CTGATCCGGTCGGCAGCA 62.147 66.667 0.00 2.58 34.68 4.41
2883 8432 2.479560 GGTCGGCAGCAATTGGATTTAC 60.480 50.000 7.72 0.00 0.00 2.01
2885 8434 1.533756 CGGCAGCAATTGGATTTACCG 60.534 52.381 7.72 0.00 42.61 4.02
2953 8502 3.935203 CCTGCATGTTCCATCGGTATATC 59.065 47.826 0.00 0.00 0.00 1.63
3034 8583 9.090692 GCAAAAGCATCATCATGTATAAAAAGT 57.909 29.630 0.00 0.00 31.86 2.66
3051 8600 3.375782 AAGTTGCAAATTGAGGTGAGC 57.624 42.857 11.95 0.00 0.00 4.26
3107 8809 6.154877 ACATGGTTTGATTAAAGGATGCATCA 59.845 34.615 27.25 7.59 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.172578 TCATCTGCCAACCGTAGTCG 59.827 55.000 0.00 0.00 0.00 4.18
9 10 2.604046 ATCATCTGCCAACCGTAGTC 57.396 50.000 0.00 0.00 0.00 2.59
10 11 3.196901 TGTAATCATCTGCCAACCGTAGT 59.803 43.478 0.00 0.00 0.00 2.73
11 12 3.792401 TGTAATCATCTGCCAACCGTAG 58.208 45.455 0.00 0.00 0.00 3.51
12 13 3.897141 TGTAATCATCTGCCAACCGTA 57.103 42.857 0.00 0.00 0.00 4.02
13 14 2.779755 TGTAATCATCTGCCAACCGT 57.220 45.000 0.00 0.00 0.00 4.83
14 15 3.205338 TCATGTAATCATCTGCCAACCG 58.795 45.455 0.00 0.00 31.15 4.44
15 16 4.498682 GCTTCATGTAATCATCTGCCAACC 60.499 45.833 0.00 0.00 31.15 3.77
16 17 4.337555 AGCTTCATGTAATCATCTGCCAAC 59.662 41.667 0.00 0.00 31.15 3.77
17 18 4.529897 AGCTTCATGTAATCATCTGCCAA 58.470 39.130 0.00 0.00 31.15 4.52
18 19 4.132336 GAGCTTCATGTAATCATCTGCCA 58.868 43.478 0.00 0.00 31.15 4.92
19 20 3.501445 GGAGCTTCATGTAATCATCTGCC 59.499 47.826 0.00 0.00 31.15 4.85
20 21 3.186001 CGGAGCTTCATGTAATCATCTGC 59.814 47.826 0.00 0.00 31.15 4.26
21 22 3.744942 CCGGAGCTTCATGTAATCATCTG 59.255 47.826 0.00 0.00 31.15 2.90
22 23 3.389329 ACCGGAGCTTCATGTAATCATCT 59.611 43.478 9.46 0.00 31.15 2.90
23 24 3.733337 ACCGGAGCTTCATGTAATCATC 58.267 45.455 9.46 0.00 31.15 2.92
24 25 3.845781 ACCGGAGCTTCATGTAATCAT 57.154 42.857 9.46 0.00 34.21 2.45
25 26 3.270027 CAACCGGAGCTTCATGTAATCA 58.730 45.455 9.46 0.00 0.00 2.57
26 27 2.614057 CCAACCGGAGCTTCATGTAATC 59.386 50.000 9.46 0.00 0.00 1.75
27 28 2.643551 CCAACCGGAGCTTCATGTAAT 58.356 47.619 9.46 0.00 0.00 1.89
28 29 1.948611 GCCAACCGGAGCTTCATGTAA 60.949 52.381 9.46 0.00 0.00 2.41
29 30 0.392461 GCCAACCGGAGCTTCATGTA 60.392 55.000 9.46 0.00 0.00 2.29
30 31 1.675641 GCCAACCGGAGCTTCATGT 60.676 57.895 9.46 0.00 0.00 3.21
31 32 0.962356 AAGCCAACCGGAGCTTCATG 60.962 55.000 20.33 0.00 46.11 3.07
32 33 0.962356 CAAGCCAACCGGAGCTTCAT 60.962 55.000 22.30 5.69 46.11 2.57
33 34 1.600636 CAAGCCAACCGGAGCTTCA 60.601 57.895 22.30 0.00 46.11 3.02
34 35 0.678048 ATCAAGCCAACCGGAGCTTC 60.678 55.000 22.30 3.38 46.11 3.86
36 37 0.251341 AAATCAAGCCAACCGGAGCT 60.251 50.000 9.46 10.91 42.40 4.09
37 38 0.603065 AAAATCAAGCCAACCGGAGC 59.397 50.000 9.46 8.31 0.00 4.70
38 39 2.162408 GAGAAAATCAAGCCAACCGGAG 59.838 50.000 9.46 0.00 0.00 4.63
39 40 2.159382 GAGAAAATCAAGCCAACCGGA 58.841 47.619 9.46 0.00 0.00 5.14
40 41 1.202348 GGAGAAAATCAAGCCAACCGG 59.798 52.381 0.00 0.00 0.00 5.28
41 42 1.202348 GGGAGAAAATCAAGCCAACCG 59.798 52.381 0.00 0.00 0.00 4.44
42 43 2.529632 AGGGAGAAAATCAAGCCAACC 58.470 47.619 0.00 0.00 0.00 3.77
43 44 4.607293 AAAGGGAGAAAATCAAGCCAAC 57.393 40.909 0.00 0.00 0.00 3.77
44 45 5.366477 AGAAAAAGGGAGAAAATCAAGCCAA 59.634 36.000 0.00 0.00 0.00 4.52
45 46 4.901250 AGAAAAAGGGAGAAAATCAAGCCA 59.099 37.500 0.00 0.00 0.00 4.75
46 47 5.244851 AGAGAAAAAGGGAGAAAATCAAGCC 59.755 40.000 0.00 0.00 0.00 4.35
47 48 6.338214 AGAGAAAAAGGGAGAAAATCAAGC 57.662 37.500 0.00 0.00 0.00 4.01
48 49 8.175925 AGAAGAGAAAAAGGGAGAAAATCAAG 57.824 34.615 0.00 0.00 0.00 3.02
49 50 8.416329 CAAGAAGAGAAAAAGGGAGAAAATCAA 58.584 33.333 0.00 0.00 0.00 2.57
50 51 7.561356 ACAAGAAGAGAAAAAGGGAGAAAATCA 59.439 33.333 0.00 0.00 0.00 2.57
51 52 7.864882 CACAAGAAGAGAAAAAGGGAGAAAATC 59.135 37.037 0.00 0.00 0.00 2.17
52 53 7.201947 CCACAAGAAGAGAAAAAGGGAGAAAAT 60.202 37.037 0.00 0.00 0.00 1.82
53 54 6.096846 CCACAAGAAGAGAAAAAGGGAGAAAA 59.903 38.462 0.00 0.00 0.00 2.29
54 55 5.594317 CCACAAGAAGAGAAAAAGGGAGAAA 59.406 40.000 0.00 0.00 0.00 2.52
55 56 5.133221 CCACAAGAAGAGAAAAAGGGAGAA 58.867 41.667 0.00 0.00 0.00 2.87
56 57 4.446311 CCCACAAGAAGAGAAAAAGGGAGA 60.446 45.833 0.00 0.00 35.81 3.71
57 58 3.823304 CCCACAAGAAGAGAAAAAGGGAG 59.177 47.826 0.00 0.00 35.81 4.30
58 59 3.832527 CCCACAAGAAGAGAAAAAGGGA 58.167 45.455 0.00 0.00 35.81 4.20
59 60 2.297315 GCCCACAAGAAGAGAAAAAGGG 59.703 50.000 0.00 0.00 36.85 3.95
60 61 2.958355 TGCCCACAAGAAGAGAAAAAGG 59.042 45.455 0.00 0.00 0.00 3.11
61 62 4.614535 CGATGCCCACAAGAAGAGAAAAAG 60.615 45.833 0.00 0.00 0.00 2.27
62 63 3.253188 CGATGCCCACAAGAAGAGAAAAA 59.747 43.478 0.00 0.00 0.00 1.94
63 64 2.813754 CGATGCCCACAAGAAGAGAAAA 59.186 45.455 0.00 0.00 0.00 2.29
64 65 2.426522 CGATGCCCACAAGAAGAGAAA 58.573 47.619 0.00 0.00 0.00 2.52
65 66 1.339055 CCGATGCCCACAAGAAGAGAA 60.339 52.381 0.00 0.00 0.00 2.87
66 67 0.250234 CCGATGCCCACAAGAAGAGA 59.750 55.000 0.00 0.00 0.00 3.10
67 68 1.372087 GCCGATGCCCACAAGAAGAG 61.372 60.000 0.00 0.00 0.00 2.85
68 69 1.377202 GCCGATGCCCACAAGAAGA 60.377 57.895 0.00 0.00 0.00 2.87
69 70 1.377725 AGCCGATGCCCACAAGAAG 60.378 57.895 0.00 0.00 38.69 2.85
70 71 1.675310 CAGCCGATGCCCACAAGAA 60.675 57.895 0.00 0.00 38.69 2.52
71 72 2.046023 CAGCCGATGCCCACAAGA 60.046 61.111 0.00 0.00 38.69 3.02
72 73 3.136123 CCAGCCGATGCCCACAAG 61.136 66.667 0.00 0.00 38.69 3.16
79 80 3.807538 CACACAGCCAGCCGATGC 61.808 66.667 0.00 0.00 37.95 3.91
80 81 3.807538 GCACACAGCCAGCCGATG 61.808 66.667 0.00 0.00 37.23 3.84
84 85 3.121030 CTACGCACACAGCCAGCC 61.121 66.667 0.00 0.00 41.38 4.85
85 86 2.357517 ACTACGCACACAGCCAGC 60.358 61.111 0.00 0.00 41.38 4.85
86 87 0.734253 GAGACTACGCACACAGCCAG 60.734 60.000 0.00 0.00 41.38 4.85
87 88 1.289066 GAGACTACGCACACAGCCA 59.711 57.895 0.00 0.00 41.38 4.75
88 89 0.108615 ATGAGACTACGCACACAGCC 60.109 55.000 0.00 0.00 41.38 4.85
89 90 2.455032 CTATGAGACTACGCACACAGC 58.545 52.381 0.00 0.00 40.87 4.40
90 91 2.423892 ACCTATGAGACTACGCACACAG 59.576 50.000 0.00 0.00 0.00 3.66
91 92 2.163613 CACCTATGAGACTACGCACACA 59.836 50.000 0.00 0.00 0.00 3.72
92 93 2.422479 TCACCTATGAGACTACGCACAC 59.578 50.000 0.00 0.00 0.00 3.82
93 94 2.718563 TCACCTATGAGACTACGCACA 58.281 47.619 0.00 0.00 0.00 4.57
94 95 3.377485 TCTTCACCTATGAGACTACGCAC 59.623 47.826 0.00 0.00 35.83 5.34
95 96 3.617284 TCTTCACCTATGAGACTACGCA 58.383 45.455 0.00 0.00 35.83 5.24
96 97 4.634184 TTCTTCACCTATGAGACTACGC 57.366 45.455 0.00 0.00 35.83 4.42
97 98 5.524284 CCATTCTTCACCTATGAGACTACG 58.476 45.833 0.00 0.00 35.83 3.51
98 99 5.293560 GCCATTCTTCACCTATGAGACTAC 58.706 45.833 0.00 0.00 35.83 2.73
99 100 4.038042 CGCCATTCTTCACCTATGAGACTA 59.962 45.833 0.00 0.00 35.83 2.59
100 101 3.181471 CGCCATTCTTCACCTATGAGACT 60.181 47.826 0.00 0.00 35.83 3.24
101 102 3.126831 CGCCATTCTTCACCTATGAGAC 58.873 50.000 0.00 0.00 35.83 3.36
102 103 2.103094 CCGCCATTCTTCACCTATGAGA 59.897 50.000 0.00 0.00 35.83 3.27
103 104 2.158900 ACCGCCATTCTTCACCTATGAG 60.159 50.000 0.00 0.00 35.83 2.90
104 105 1.837439 ACCGCCATTCTTCACCTATGA 59.163 47.619 0.00 0.00 0.00 2.15
105 106 1.942657 CACCGCCATTCTTCACCTATG 59.057 52.381 0.00 0.00 0.00 2.23
106 107 1.837439 TCACCGCCATTCTTCACCTAT 59.163 47.619 0.00 0.00 0.00 2.57
107 108 1.066430 GTCACCGCCATTCTTCACCTA 60.066 52.381 0.00 0.00 0.00 3.08
108 109 0.321653 GTCACCGCCATTCTTCACCT 60.322 55.000 0.00 0.00 0.00 4.00
109 110 1.635663 CGTCACCGCCATTCTTCACC 61.636 60.000 0.00 0.00 0.00 4.02
110 111 0.669318 TCGTCACCGCCATTCTTCAC 60.669 55.000 0.00 0.00 0.00 3.18
111 112 0.249120 ATCGTCACCGCCATTCTTCA 59.751 50.000 0.00 0.00 0.00 3.02
112 113 0.931005 GATCGTCACCGCCATTCTTC 59.069 55.000 0.00 0.00 0.00 2.87
113 114 0.249120 TGATCGTCACCGCCATTCTT 59.751 50.000 0.00 0.00 0.00 2.52
114 115 0.179100 CTGATCGTCACCGCCATTCT 60.179 55.000 0.00 0.00 0.00 2.40
115 116 0.460284 ACTGATCGTCACCGCCATTC 60.460 55.000 0.00 0.00 0.00 2.67
116 117 0.036388 AACTGATCGTCACCGCCATT 60.036 50.000 0.00 0.00 0.00 3.16
117 118 0.740868 CAACTGATCGTCACCGCCAT 60.741 55.000 0.00 0.00 0.00 4.40
118 119 1.374125 CAACTGATCGTCACCGCCA 60.374 57.895 0.00 0.00 0.00 5.69
119 120 2.740714 GCAACTGATCGTCACCGCC 61.741 63.158 0.00 0.00 0.00 6.13
120 121 1.738099 AGCAACTGATCGTCACCGC 60.738 57.895 0.00 0.00 0.00 5.68
121 122 1.959899 GCAGCAACTGATCGTCACCG 61.960 60.000 0.00 0.00 32.44 4.94
122 123 0.671781 AGCAGCAACTGATCGTCACC 60.672 55.000 0.00 0.00 32.44 4.02
123 124 0.718343 GAGCAGCAACTGATCGTCAC 59.282 55.000 0.00 0.00 37.16 3.67
124 125 3.128259 GAGCAGCAACTGATCGTCA 57.872 52.632 0.00 0.00 37.16 4.35
128 129 1.078848 ACCCGAGCAGCAACTGATC 60.079 57.895 2.82 2.82 42.60 2.92
129 130 1.376424 CACCCGAGCAGCAACTGAT 60.376 57.895 0.00 0.00 32.44 2.90
130 131 2.031012 CACCCGAGCAGCAACTGA 59.969 61.111 0.00 0.00 32.44 3.41
131 132 3.730761 GCACCCGAGCAGCAACTG 61.731 66.667 0.00 0.00 34.12 3.16
132 133 4.254709 TGCACCCGAGCAGCAACT 62.255 61.111 0.00 0.00 40.11 3.16
139 140 0.250467 ATCCATGTATGCACCCGAGC 60.250 55.000 0.00 0.00 0.00 5.03
140 141 1.345741 AGATCCATGTATGCACCCGAG 59.654 52.381 0.00 0.00 0.00 4.63
141 142 1.423584 AGATCCATGTATGCACCCGA 58.576 50.000 0.00 0.00 0.00 5.14
142 143 1.875514 CAAGATCCATGTATGCACCCG 59.124 52.381 0.00 0.00 0.00 5.28
143 144 2.936202 ACAAGATCCATGTATGCACCC 58.064 47.619 0.00 0.00 0.00 4.61
144 145 3.494626 CGTACAAGATCCATGTATGCACC 59.505 47.826 12.84 1.69 35.84 5.01
145 146 4.368315 TCGTACAAGATCCATGTATGCAC 58.632 43.478 17.59 6.68 39.19 4.57
146 147 4.501400 CCTCGTACAAGATCCATGTATGCA 60.501 45.833 17.59 0.00 39.19 3.96
147 148 3.990469 CCTCGTACAAGATCCATGTATGC 59.010 47.826 17.59 5.65 39.19 3.14
148 149 5.453567 TCCTCGTACAAGATCCATGTATG 57.546 43.478 16.79 16.79 40.19 2.39
149 150 6.013379 AGATCCTCGTACAAGATCCATGTAT 58.987 40.000 11.01 0.00 37.69 2.29
150 151 5.241728 CAGATCCTCGTACAAGATCCATGTA 59.758 44.000 11.27 5.16 37.69 2.29
151 152 4.038522 CAGATCCTCGTACAAGATCCATGT 59.961 45.833 11.27 6.93 37.69 3.21
152 153 4.554292 CAGATCCTCGTACAAGATCCATG 58.446 47.826 11.27 0.00 37.69 3.66
153 154 3.576118 CCAGATCCTCGTACAAGATCCAT 59.424 47.826 11.27 0.00 37.69 3.41
154 155 2.959030 CCAGATCCTCGTACAAGATCCA 59.041 50.000 11.27 0.00 37.69 3.41
155 156 2.297597 CCCAGATCCTCGTACAAGATCC 59.702 54.545 11.27 0.00 37.69 3.36
156 157 3.223435 TCCCAGATCCTCGTACAAGATC 58.777 50.000 8.14 8.14 37.31 2.75
157 158 3.314307 TCCCAGATCCTCGTACAAGAT 57.686 47.619 0.00 0.00 0.00 2.40
158 159 2.820728 TCCCAGATCCTCGTACAAGA 57.179 50.000 0.00 0.00 0.00 3.02
159 160 4.341235 TGTATTCCCAGATCCTCGTACAAG 59.659 45.833 0.00 0.00 0.00 3.16
160 161 4.283337 TGTATTCCCAGATCCTCGTACAA 58.717 43.478 0.00 0.00 0.00 2.41
161 162 3.889538 CTGTATTCCCAGATCCTCGTACA 59.110 47.826 0.00 0.00 34.23 2.90
162 163 3.256136 CCTGTATTCCCAGATCCTCGTAC 59.744 52.174 0.00 0.00 34.23 3.67
163 164 3.139584 TCCTGTATTCCCAGATCCTCGTA 59.860 47.826 0.00 0.00 34.23 3.43
164 165 2.091278 TCCTGTATTCCCAGATCCTCGT 60.091 50.000 0.00 0.00 34.23 4.18
165 166 2.297597 GTCCTGTATTCCCAGATCCTCG 59.702 54.545 0.00 0.00 34.23 4.63
166 167 2.635427 GGTCCTGTATTCCCAGATCCTC 59.365 54.545 0.00 0.00 34.23 3.71
167 168 2.251338 AGGTCCTGTATTCCCAGATCCT 59.749 50.000 0.00 0.00 34.23 3.24
168 169 2.370189 CAGGTCCTGTATTCCCAGATCC 59.630 54.545 11.09 0.00 34.23 3.36
169 170 3.309296 TCAGGTCCTGTATTCCCAGATC 58.691 50.000 18.65 0.00 34.23 2.75
170 171 3.051803 TCTCAGGTCCTGTATTCCCAGAT 60.052 47.826 18.65 0.00 34.23 2.90
171 172 2.314852 TCTCAGGTCCTGTATTCCCAGA 59.685 50.000 18.65 9.20 34.23 3.86
172 173 2.752030 TCTCAGGTCCTGTATTCCCAG 58.248 52.381 18.65 6.94 32.61 4.45
173 174 2.940514 TCTCAGGTCCTGTATTCCCA 57.059 50.000 18.65 0.00 32.61 4.37
174 175 3.041946 ACATCTCAGGTCCTGTATTCCC 58.958 50.000 18.65 0.00 32.61 3.97
175 176 4.762289 AACATCTCAGGTCCTGTATTCC 57.238 45.455 18.65 0.00 32.61 3.01
176 177 6.094186 GGAAAAACATCTCAGGTCCTGTATTC 59.906 42.308 18.65 11.27 32.61 1.75
177 178 5.946377 GGAAAAACATCTCAGGTCCTGTATT 59.054 40.000 18.65 4.70 32.61 1.89
178 179 5.251700 AGGAAAAACATCTCAGGTCCTGTAT 59.748 40.000 18.65 10.67 32.79 2.29
179 180 4.597507 AGGAAAAACATCTCAGGTCCTGTA 59.402 41.667 18.65 8.79 32.79 2.74
180 181 3.395941 AGGAAAAACATCTCAGGTCCTGT 59.604 43.478 18.65 0.00 32.79 4.00
181 182 4.006319 GAGGAAAAACATCTCAGGTCCTG 58.994 47.826 13.21 13.21 34.17 3.86
182 183 3.652869 TGAGGAAAAACATCTCAGGTCCT 59.347 43.478 0.00 0.00 36.73 3.85
183 184 4.021102 TGAGGAAAAACATCTCAGGTCC 57.979 45.455 0.00 0.00 33.21 4.46
184 185 5.248640 TGATGAGGAAAAACATCTCAGGTC 58.751 41.667 0.00 0.00 42.05 3.85
185 186 5.246981 TGATGAGGAAAAACATCTCAGGT 57.753 39.130 0.00 0.00 42.05 4.00
186 187 5.067413 CCATGATGAGGAAAAACATCTCAGG 59.933 44.000 0.00 0.00 42.05 3.86
187 188 5.884232 TCCATGATGAGGAAAAACATCTCAG 59.116 40.000 0.00 0.00 42.05 3.35
188 189 5.818887 TCCATGATGAGGAAAAACATCTCA 58.181 37.500 0.00 0.00 42.05 3.27
189 190 6.956202 ATCCATGATGAGGAAAAACATCTC 57.044 37.500 0.00 0.00 42.05 2.75
190 191 7.348815 TGTATCCATGATGAGGAAAAACATCT 58.651 34.615 0.00 0.00 42.05 2.90
191 192 7.572523 TGTATCCATGATGAGGAAAAACATC 57.427 36.000 0.00 0.00 41.94 3.06
209 210 5.386958 TGGTCTATTCGTAGCATGTATCC 57.613 43.478 0.00 0.00 0.00 2.59
215 216 7.727181 AGTATTTCTTGGTCTATTCGTAGCAT 58.273 34.615 0.00 0.00 0.00 3.79
216 217 7.108841 AGTATTTCTTGGTCTATTCGTAGCA 57.891 36.000 0.00 0.00 0.00 3.49
222 223 9.915629 ATCGATGTAGTATTTCTTGGTCTATTC 57.084 33.333 0.00 0.00 0.00 1.75
255 256 8.941977 ACTAGCACGAATAAATAACAAACATGA 58.058 29.630 0.00 0.00 0.00 3.07
261 262 6.147985 TGCACACTAGCACGAATAAATAACAA 59.852 34.615 0.00 0.00 40.11 2.83
284 285 1.424493 GCTGCCACGACTGAGTATGC 61.424 60.000 0.00 0.00 0.00 3.14
285 286 0.807667 GGCTGCCACGACTGAGTATG 60.808 60.000 15.17 0.00 0.00 2.39
286 287 1.517832 GGCTGCCACGACTGAGTAT 59.482 57.895 15.17 0.00 0.00 2.12
302 303 1.448985 TTCTATTTCACTGCACCGGC 58.551 50.000 0.00 0.00 41.68 6.13
306 307 3.536158 TGCGTTTCTATTTCACTGCAC 57.464 42.857 0.00 0.00 0.00 4.57
345 346 2.325583 AAGGCTGGATTATTTCGCGA 57.674 45.000 3.71 3.71 0.00 5.87
346 347 2.614057 AGAAAGGCTGGATTATTTCGCG 59.386 45.455 0.00 0.00 36.88 5.87
347 348 4.354587 CAAGAAAGGCTGGATTATTTCGC 58.645 43.478 0.00 0.00 36.88 4.70
348 349 4.640201 TCCAAGAAAGGCTGGATTATTTCG 59.360 41.667 0.00 0.00 36.88 3.46
349 350 6.530019 TTCCAAGAAAGGCTGGATTATTTC 57.470 37.500 0.00 0.00 32.95 2.17
352 353 5.361857 CACATTCCAAGAAAGGCTGGATTAT 59.638 40.000 0.00 0.00 0.00 1.28
353 354 4.706476 CACATTCCAAGAAAGGCTGGATTA 59.294 41.667 0.00 0.00 0.00 1.75
368 369 3.239449 AGCTACCGATATCCACATTCCA 58.761 45.455 0.00 0.00 0.00 3.53
374 375 4.494350 TCGTAAAGCTACCGATATCCAC 57.506 45.455 0.00 0.00 0.00 4.02
390 391 4.353737 CGACTTCCCGAACAATATCGTAA 58.646 43.478 0.00 0.00 41.16 3.18
394 395 2.546778 TGCGACTTCCCGAACAATATC 58.453 47.619 0.00 0.00 0.00 1.63
399 400 0.250124 ATGTTGCGACTTCCCGAACA 60.250 50.000 5.50 0.00 35.66 3.18
405 406 2.350772 CCTCACAAATGTTGCGACTTCC 60.351 50.000 5.50 0.00 0.00 3.46
406 407 2.290641 ACCTCACAAATGTTGCGACTTC 59.709 45.455 5.50 0.00 0.00 3.01
420 421 2.238521 GGCAGGATTTTTGACCTCACA 58.761 47.619 0.00 0.00 33.91 3.58
423 424 1.821216 TCGGCAGGATTTTTGACCTC 58.179 50.000 0.00 0.00 33.91 3.85
424 425 2.162681 CTTCGGCAGGATTTTTGACCT 58.837 47.619 0.00 0.00 36.92 3.85
431 432 3.057526 GTGTTAAAGCTTCGGCAGGATTT 60.058 43.478 0.00 0.00 44.74 2.17
434 435 1.202710 TGTGTTAAAGCTTCGGCAGGA 60.203 47.619 0.00 0.00 44.74 3.86
436 437 1.873591 ACTGTGTTAAAGCTTCGGCAG 59.126 47.619 0.00 7.12 44.74 4.85
471 472 5.451023 CACGTACTAATGGCTAAATTTTGCG 59.549 40.000 16.55 6.70 0.00 4.85
478 479 4.223477 AGGGAACACGTACTAATGGCTAAA 59.777 41.667 0.00 0.00 0.00 1.85
479 480 3.770933 AGGGAACACGTACTAATGGCTAA 59.229 43.478 0.00 0.00 0.00 3.09
481 482 2.093658 CAGGGAACACGTACTAATGGCT 60.094 50.000 0.00 0.00 0.00 4.75
482 483 2.277084 CAGGGAACACGTACTAATGGC 58.723 52.381 0.00 0.00 0.00 4.40
483 484 2.277084 GCAGGGAACACGTACTAATGG 58.723 52.381 0.00 0.00 0.00 3.16
484 485 2.967362 TGCAGGGAACACGTACTAATG 58.033 47.619 0.00 0.00 0.00 1.90
485 486 3.688694 TTGCAGGGAACACGTACTAAT 57.311 42.857 0.00 0.00 0.00 1.73
486 487 3.472283 TTTGCAGGGAACACGTACTAA 57.528 42.857 0.00 0.00 0.00 2.24
487 488 3.069872 TCTTTTGCAGGGAACACGTACTA 59.930 43.478 0.00 0.00 0.00 1.82
488 489 2.158871 TCTTTTGCAGGGAACACGTACT 60.159 45.455 0.00 0.00 0.00 2.73
489 490 2.215196 TCTTTTGCAGGGAACACGTAC 58.785 47.619 0.00 0.00 0.00 3.67
492 493 1.608590 ACATCTTTTGCAGGGAACACG 59.391 47.619 0.00 0.00 0.00 4.49
509 510 3.381908 TCTGCGTTTACCAAAACCAACAT 59.618 39.130 0.00 0.00 41.68 2.71
523 524 1.981256 AATTGTCCACCTCTGCGTTT 58.019 45.000 0.00 0.00 0.00 3.60
527 528 2.887152 AGTCAAAATTGTCCACCTCTGC 59.113 45.455 0.00 0.00 0.00 4.26
540 541 7.944061 TGTGATTCTGTGAATTCAGTCAAAAT 58.056 30.769 8.80 2.87 36.85 1.82
547 548 6.549912 TTGTCTGTGATTCTGTGAATTCAG 57.450 37.500 8.80 0.00 36.85 3.02
555 556 4.449068 CGCTAACTTTGTCTGTGATTCTGT 59.551 41.667 0.00 0.00 0.00 3.41
557 558 4.883083 TCGCTAACTTTGTCTGTGATTCT 58.117 39.130 0.00 0.00 0.00 2.40
562 563 5.990408 AGAAAATCGCTAACTTTGTCTGTG 58.010 37.500 0.00 0.00 0.00 3.66
637 667 9.125026 AGAGTATATTCCAGCCAAAACAATTAG 57.875 33.333 0.00 0.00 0.00 1.73
638 668 9.474313 AAGAGTATATTCCAGCCAAAACAATTA 57.526 29.630 0.00 0.00 0.00 1.40
649 679 4.694509 CAGGATGCAAGAGTATATTCCAGC 59.305 45.833 0.00 3.47 0.00 4.85
674 704 4.611581 GCCTGATAAATCGAGCCGAATTTC 60.612 45.833 1.44 2.59 39.99 2.17
681 711 0.249911 ACGGCCTGATAAATCGAGCC 60.250 55.000 0.00 11.26 41.54 4.70
704 734 1.082431 CGCCGACGCAAAACAATCA 60.082 52.632 0.00 0.00 34.03 2.57
706 736 0.932585 CAACGCCGACGCAAAACAAT 60.933 50.000 0.00 0.00 45.53 2.71
708 738 1.426816 TACAACGCCGACGCAAAACA 61.427 50.000 0.00 0.00 45.53 2.83
709 739 0.110554 ATACAACGCCGACGCAAAAC 60.111 50.000 0.00 0.00 45.53 2.43
718 761 1.136565 CAAAGCCCATACAACGCCG 59.863 57.895 0.00 0.00 0.00 6.46
759 802 4.704540 TCGTCACAATGATTGGGCTTTTAT 59.295 37.500 10.27 0.00 32.92 1.40
896 964 2.074967 CAGAGGGGCAAACCTGGTA 58.925 57.895 0.00 0.00 42.10 3.25
935 6097 1.444119 TTGACACGCCAAGTTCCAGC 61.444 55.000 0.00 0.00 0.00 4.85
957 6121 7.759886 CACCGAAAATCTATCTAACTCAGTCAA 59.240 37.037 0.00 0.00 0.00 3.18
967 6136 4.261489 GCGAGTCCACCGAAAATCTATCTA 60.261 45.833 0.00 0.00 0.00 1.98
2215 7537 6.614496 AGAGGATCCATATATGCATAAGAGCA 59.386 38.462 15.82 0.00 42.99 4.26
2268 7598 7.115378 GGCAAATTACATGACTGAGACAAAAAG 59.885 37.037 0.00 0.00 0.00 2.27
2420 7762 5.921976 CACCATATGTTGCAATGCGATAAAT 59.078 36.000 0.59 0.00 0.00 1.40
2423 7765 3.252944 CCACCATATGTTGCAATGCGATA 59.747 43.478 0.59 0.00 0.00 2.92
2458 7801 4.513442 ACAAACAAGCAGAGTGTTAGACA 58.487 39.130 0.00 0.00 38.24 3.41
2489 7832 8.379902 GCGTTTGAAATTCTCTCAAAAGAAAAA 58.620 29.630 16.33 0.00 42.73 1.94
2547 7890 3.054139 AGAATTCAGATAACCCAGCTGCA 60.054 43.478 8.66 0.00 40.63 4.41
2558 7901 9.671279 TCTTTATCAGCAAACAGAATTCAGATA 57.329 29.630 8.44 0.30 0.00 1.98
2593 8141 8.429641 TCCTAACAAGAAAGTTCAGTTCATACT 58.570 33.333 5.51 0.00 32.52 2.12
2841 8390 1.757118 GGATCAGAATGGAGGTCGACA 59.243 52.381 18.91 0.00 36.16 4.35
2872 8421 4.219725 CCACAAAGACCGGTAAATCCAATT 59.780 41.667 7.34 0.00 35.57 2.32
2883 8432 4.839668 TTAATCAAACCACAAAGACCGG 57.160 40.909 0.00 0.00 0.00 5.28
2885 8434 8.573035 TGAACTATTAATCAAACCACAAAGACC 58.427 33.333 0.00 0.00 0.00 3.85
2953 8502 6.780457 ATGACATTGGAAAGTGATTAAGGG 57.220 37.500 0.00 0.00 0.00 3.95
3034 8583 1.000060 GCAGCTCACCTCAATTTGCAA 60.000 47.619 0.00 0.00 0.00 4.08
3133 8835 2.094762 AGCATAGAAACACGGTGGTC 57.905 50.000 13.48 9.31 0.00 4.02


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

AutoCloner maintained by Alex Coulton.