Multiple sequence alignment - TraesCS1D01G288800

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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 TraesCS1D01G288800 chr1D 100.000 2865 0 0 1 2865 387059052 387061916 0.000000e+00 5291.0
1 TraesCS1D01G288800 chr1D 83.827 878 122 12 1991 2864 386950544 386951405 0.000000e+00 817.0
2 TraesCS1D01G288800 chr1D 85.072 489 48 13 829 1306 386949558 386950032 2.580000e-130 475.0
3 TraesCS1D01G288800 chr1D 80.769 390 45 22 907 1288 387193564 387193931 7.820000e-71 278.0
4 TraesCS1D01G288800 chr1A 85.685 1481 111 53 163 1582 486895939 486897379 0.000000e+00 1467.0
5 TraesCS1D01G288800 chr1A 85.378 1231 148 18 1646 2864 486938394 486939604 0.000000e+00 1247.0
6 TraesCS1D01G288800 chr1A 81.447 1520 191 41 1369 2864 486751129 486752581 0.000000e+00 1160.0
7 TraesCS1D01G288800 chr1A 84.453 759 58 36 741 1464 486816555 486817288 0.000000e+00 693.0
8 TraesCS1D01G288800 chr1A 85.468 406 23 12 163 543 486815622 486816016 9.620000e-105 390.0
9 TraesCS1D01G288800 chr1A 81.764 499 48 14 828 1306 486750624 486751099 7.490000e-101 377.0
10 TraesCS1D01G288800 chr1A 78.923 427 45 21 863 1288 486953273 486953655 6.130000e-62 248.0
11 TraesCS1D01G288800 chr1A 91.150 113 8 2 207 319 486750278 486750388 4.940000e-33 152.0
12 TraesCS1D01G288800 chr1A 78.344 157 31 3 1810 1965 344436606 344436760 6.530000e-17 99.0
13 TraesCS1D01G288800 chr1B 85.983 956 71 36 706 1643 520390229 520391139 0.000000e+00 965.0
14 TraesCS1D01G288800 chr1B 82.861 811 117 13 2046 2853 520402171 520402962 0.000000e+00 708.0
15 TraesCS1D01G288800 chr1B 88.056 427 27 14 892 1306 520374087 520374501 4.290000e-133 484.0
16 TraesCS1D01G288800 chr1B 79.764 509 74 14 1750 2233 61963931 61963427 2.730000e-90 342.0
17 TraesCS1D01G288800 chr1B 87.500 304 14 13 172 457 520389904 520390201 2.130000e-86 329.0
18 TraesCS1D01G288800 chr1B 84.713 314 29 11 172 478 520395190 520394889 2.160000e-76 296.0
19 TraesCS1D01G288800 chr1B 81.360 397 45 15 907 1288 520468742 520469124 2.160000e-76 296.0
20 TraesCS1D01G288800 chr1B 78.402 338 62 5 2506 2835 520391424 520391758 2.890000e-50 209.0
21 TraesCS1D01G288800 chr1B 80.228 263 20 13 1392 1646 520374535 520374773 4.910000e-38 169.0
22 TraesCS1D01G288800 chr1B 80.460 261 18 12 1386 1645 520401339 520401567 4.910000e-38 169.0
23 TraesCS1D01G288800 chr7B 80.922 477 67 11 1756 2210 684153508 684153982 3.510000e-94 355.0
24 TraesCS1D01G288800 chr4A 76.647 501 89 16 1756 2236 555969833 555970325 4.740000e-63 252.0
25 TraesCS1D01G288800 chr4A 80.859 256 35 10 1763 2010 170732297 170732048 3.770000e-44 189.0
26 TraesCS1D01G288800 chrUn 82.320 181 27 4 1760 1939 1088846 1088670 4.940000e-33 152.0
27 TraesCS1D01G288800 chr5D 80.435 184 33 3 1761 1942 457334190 457334372 1.380000e-28 137.0
28 TraesCS1D01G288800 chr5B 80.838 167 21 5 1876 2036 678129739 678129900 1.390000e-23 121.0
29 TraesCS1D01G288800 chr5B 77.174 184 37 5 1761 1942 559184296 559184476 5.050000e-18 102.0
30 TraesCS1D01G288800 chr2B 100.000 28 0 0 2782 2809 436990855 436990882 5.000000e-03 52.8


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 TraesCS1D01G288800 chr1D 387059052 387061916 2864 False 5291.0 5291 100.000000 1 2865 1 chr1D.!!$F1 2864
1 TraesCS1D01G288800 chr1D 386949558 386951405 1847 False 646.0 817 84.449500 829 2864 2 chr1D.!!$F3 2035
2 TraesCS1D01G288800 chr1A 486895939 486897379 1440 False 1467.0 1467 85.685000 163 1582 1 chr1A.!!$F2 1419
3 TraesCS1D01G288800 chr1A 486938394 486939604 1210 False 1247.0 1247 85.378000 1646 2864 1 chr1A.!!$F3 1218
4 TraesCS1D01G288800 chr1A 486750278 486752581 2303 False 563.0 1160 84.787000 207 2864 3 chr1A.!!$F5 2657
5 TraesCS1D01G288800 chr1A 486815622 486817288 1666 False 541.5 693 84.960500 163 1464 2 chr1A.!!$F6 1301
6 TraesCS1D01G288800 chr1B 520389904 520391758 1854 False 501.0 965 83.961667 172 2835 3 chr1B.!!$F3 2663
7 TraesCS1D01G288800 chr1B 520401339 520402962 1623 False 438.5 708 81.660500 1386 2853 2 chr1B.!!$F4 1467
8 TraesCS1D01G288800 chr1B 61963427 61963931 504 True 342.0 342 79.764000 1750 2233 1 chr1B.!!$R1 483
9 TraesCS1D01G288800 chr1B 520374087 520374773 686 False 326.5 484 84.142000 892 1646 2 chr1B.!!$F2 754

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
802 1251 0.171455 ATCACTCCAGTCGTTCTCGC 59.829 55.0 0.0 0.0 36.96 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2635 3554 0.898326 GGACCGGCCCAAACTGATTT 60.898 55.0 0.0 0.0 0.0 2.17 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
25 26 3.384816 TGCTCTGGCATATTCGTGG 57.615 52.632 0.00 0.00 44.28 4.94
26 27 0.829990 TGCTCTGGCATATTCGTGGA 59.170 50.000 0.00 0.00 44.28 4.02
27 28 1.221414 GCTCTGGCATATTCGTGGAC 58.779 55.000 0.00 0.00 38.54 4.02
28 29 1.473257 GCTCTGGCATATTCGTGGACA 60.473 52.381 0.00 0.00 38.54 4.02
29 30 2.477825 CTCTGGCATATTCGTGGACAG 58.522 52.381 0.00 0.00 0.00 3.51
30 31 2.101415 CTCTGGCATATTCGTGGACAGA 59.899 50.000 0.00 0.00 33.08 3.41
31 32 2.101415 TCTGGCATATTCGTGGACAGAG 59.899 50.000 0.00 0.00 0.00 3.35
32 33 2.101415 CTGGCATATTCGTGGACAGAGA 59.899 50.000 0.00 0.00 0.00 3.10
33 34 2.700371 TGGCATATTCGTGGACAGAGAT 59.300 45.455 0.00 0.00 0.00 2.75
34 35 3.895041 TGGCATATTCGTGGACAGAGATA 59.105 43.478 0.00 0.00 0.00 1.98
35 36 4.528206 TGGCATATTCGTGGACAGAGATAT 59.472 41.667 0.00 0.00 0.00 1.63
36 37 4.867047 GGCATATTCGTGGACAGAGATATG 59.133 45.833 0.00 0.00 0.00 1.78
37 38 5.473931 GCATATTCGTGGACAGAGATATGT 58.526 41.667 0.00 0.00 35.68 2.29
38 39 5.347093 GCATATTCGTGGACAGAGATATGTG 59.653 44.000 0.00 0.00 32.25 3.21
39 40 3.801114 TTCGTGGACAGAGATATGTGG 57.199 47.619 0.00 0.00 32.25 4.17
40 41 3.012934 TCGTGGACAGAGATATGTGGA 57.987 47.619 0.00 0.00 32.25 4.02
41 42 2.688446 TCGTGGACAGAGATATGTGGAC 59.312 50.000 0.00 0.00 32.25 4.02
42 43 2.427095 CGTGGACAGAGATATGTGGACA 59.573 50.000 0.00 0.00 32.25 4.02
43 44 3.735208 CGTGGACAGAGATATGTGGACAC 60.735 52.174 4.45 4.45 32.25 3.67
44 45 2.427095 TGGACAGAGATATGTGGACACG 59.573 50.000 0.00 0.00 32.25 4.49
45 46 2.223829 GGACAGAGATATGTGGACACGG 60.224 54.545 0.00 0.00 32.25 4.94
46 47 2.688446 GACAGAGATATGTGGACACGGA 59.312 50.000 0.00 0.00 32.25 4.69
47 48 3.300388 ACAGAGATATGTGGACACGGAT 58.700 45.455 0.00 0.00 30.46 4.18
48 49 4.470602 ACAGAGATATGTGGACACGGATA 58.529 43.478 0.00 0.00 30.46 2.59
49 50 4.278669 ACAGAGATATGTGGACACGGATAC 59.721 45.833 0.00 0.00 30.46 2.24
65 66 2.295349 GGATACGAAAGACGGCTATCCA 59.705 50.000 11.50 0.00 43.46 3.41
66 67 3.243636 GGATACGAAAGACGGCTATCCAA 60.244 47.826 11.50 0.00 43.46 3.53
67 68 5.320228 GGATACGAAAGACGGCTATCCAAC 61.320 50.000 11.50 0.00 43.46 3.77
68 69 2.004583 CGAAAGACGGCTATCCAACA 57.995 50.000 0.00 0.00 38.46 3.33
69 70 2.343101 CGAAAGACGGCTATCCAACAA 58.657 47.619 0.00 0.00 38.46 2.83
70 71 2.936498 CGAAAGACGGCTATCCAACAAT 59.064 45.455 0.00 0.00 38.46 2.71
71 72 3.242413 CGAAAGACGGCTATCCAACAATG 60.242 47.826 0.00 0.00 38.46 2.82
72 73 3.350219 AAGACGGCTATCCAACAATGT 57.650 42.857 0.00 0.00 0.00 2.71
73 74 2.906354 AGACGGCTATCCAACAATGTC 58.094 47.619 0.00 0.00 0.00 3.06
74 75 1.940613 GACGGCTATCCAACAATGTCC 59.059 52.381 0.00 0.00 0.00 4.02
75 76 1.280710 ACGGCTATCCAACAATGTCCA 59.719 47.619 0.00 0.00 0.00 4.02
76 77 2.290641 ACGGCTATCCAACAATGTCCAA 60.291 45.455 0.00 0.00 0.00 3.53
77 78 2.951642 CGGCTATCCAACAATGTCCAAT 59.048 45.455 0.00 0.00 0.00 3.16
78 79 4.133820 CGGCTATCCAACAATGTCCAATA 58.866 43.478 0.00 0.00 0.00 1.90
79 80 4.578516 CGGCTATCCAACAATGTCCAATAA 59.421 41.667 0.00 0.00 0.00 1.40
80 81 5.241506 CGGCTATCCAACAATGTCCAATAAT 59.758 40.000 0.00 0.00 0.00 1.28
81 82 6.449698 GGCTATCCAACAATGTCCAATAATG 58.550 40.000 0.00 0.00 0.00 1.90
82 83 6.040842 GGCTATCCAACAATGTCCAATAATGT 59.959 38.462 0.00 0.00 0.00 2.71
83 84 7.417797 GGCTATCCAACAATGTCCAATAATGTT 60.418 37.037 0.00 0.00 34.74 2.71
84 85 7.649306 GCTATCCAACAATGTCCAATAATGTTC 59.351 37.037 0.00 0.00 32.25 3.18
85 86 5.948588 TCCAACAATGTCCAATAATGTTCG 58.051 37.500 0.00 0.00 32.25 3.95
86 87 5.475220 TCCAACAATGTCCAATAATGTTCGT 59.525 36.000 0.00 0.00 32.25 3.85
87 88 6.655425 TCCAACAATGTCCAATAATGTTCGTA 59.345 34.615 0.00 0.00 32.25 3.43
88 89 7.338196 TCCAACAATGTCCAATAATGTTCGTAT 59.662 33.333 0.00 0.00 32.25 3.06
89 90 8.616942 CCAACAATGTCCAATAATGTTCGTATA 58.383 33.333 0.00 0.00 32.25 1.47
90 91 9.433317 CAACAATGTCCAATAATGTTCGTATAC 57.567 33.333 0.00 0.00 32.25 1.47
91 92 8.149973 ACAATGTCCAATAATGTTCGTATACC 57.850 34.615 0.00 0.00 0.00 2.73
92 93 7.990886 ACAATGTCCAATAATGTTCGTATACCT 59.009 33.333 0.00 0.00 0.00 3.08
93 94 8.836413 CAATGTCCAATAATGTTCGTATACCTT 58.164 33.333 0.00 0.00 0.00 3.50
94 95 8.974060 ATGTCCAATAATGTTCGTATACCTTT 57.026 30.769 0.00 0.00 0.00 3.11
95 96 8.428186 TGTCCAATAATGTTCGTATACCTTTC 57.572 34.615 0.00 0.00 0.00 2.62
96 97 8.041919 TGTCCAATAATGTTCGTATACCTTTCA 58.958 33.333 0.00 0.00 0.00 2.69
97 98 8.885722 GTCCAATAATGTTCGTATACCTTTCAA 58.114 33.333 0.00 0.00 0.00 2.69
98 99 9.621629 TCCAATAATGTTCGTATACCTTTCAAT 57.378 29.630 0.00 0.00 0.00 2.57
99 100 9.878599 CCAATAATGTTCGTATACCTTTCAATC 57.121 33.333 0.00 0.00 0.00 2.67
102 103 6.583912 ATGTTCGTATACCTTTCAATCACG 57.416 37.500 0.00 0.00 0.00 4.35
103 104 5.712004 TGTTCGTATACCTTTCAATCACGA 58.288 37.500 0.00 0.00 35.38 4.35
104 105 6.334989 TGTTCGTATACCTTTCAATCACGAT 58.665 36.000 0.00 0.00 36.88 3.73
105 106 6.814644 TGTTCGTATACCTTTCAATCACGATT 59.185 34.615 0.00 0.00 36.88 3.34
106 107 7.332430 TGTTCGTATACCTTTCAATCACGATTT 59.668 33.333 0.00 0.00 36.88 2.17
107 108 7.229228 TCGTATACCTTTCAATCACGATTTG 57.771 36.000 0.00 0.00 32.57 2.32
108 109 7.036829 TCGTATACCTTTCAATCACGATTTGA 58.963 34.615 0.00 0.00 39.11 2.69
109 110 7.546316 TCGTATACCTTTCAATCACGATTTGAA 59.454 33.333 0.00 0.00 37.92 2.69
110 111 7.634817 CGTATACCTTTCAATCACGATTTGAAC 59.365 37.037 10.23 1.11 37.92 3.18
111 112 7.687941 ATACCTTTCAATCACGATTTGAACT 57.312 32.000 10.23 2.47 37.92 3.01
112 113 8.786826 ATACCTTTCAATCACGATTTGAACTA 57.213 30.769 10.23 3.97 37.92 2.24
113 114 7.504924 ACCTTTCAATCACGATTTGAACTAA 57.495 32.000 10.23 0.00 37.92 2.24
114 115 7.360361 ACCTTTCAATCACGATTTGAACTAAC 58.640 34.615 10.23 0.00 37.92 2.34
115 116 6.801862 CCTTTCAATCACGATTTGAACTAACC 59.198 38.462 10.23 0.00 37.92 2.85
116 117 5.524511 TCAATCACGATTTGAACTAACCG 57.475 39.130 0.00 0.00 37.92 4.44
117 118 5.231702 TCAATCACGATTTGAACTAACCGA 58.768 37.500 0.00 0.00 37.92 4.69
118 119 5.697178 TCAATCACGATTTGAACTAACCGAA 59.303 36.000 0.00 0.00 37.92 4.30
119 120 4.977741 TCACGATTTGAACTAACCGAAC 57.022 40.909 0.00 0.00 0.00 3.95
120 121 3.742369 TCACGATTTGAACTAACCGAACC 59.258 43.478 0.00 0.00 0.00 3.62
121 122 2.733026 ACGATTTGAACTAACCGAACCG 59.267 45.455 0.00 0.00 0.00 4.44
122 123 2.988493 CGATTTGAACTAACCGAACCGA 59.012 45.455 0.00 0.00 0.00 4.69
123 124 3.429543 CGATTTGAACTAACCGAACCGAA 59.570 43.478 0.00 0.00 0.00 4.30
124 125 4.092383 CGATTTGAACTAACCGAACCGAAT 59.908 41.667 0.00 0.00 0.00 3.34
125 126 5.390145 CGATTTGAACTAACCGAACCGAATT 60.390 40.000 0.00 0.00 0.00 2.17
126 127 4.996062 TTGAACTAACCGAACCGAATTC 57.004 40.909 0.00 0.00 0.00 2.17
127 128 3.992643 TGAACTAACCGAACCGAATTCA 58.007 40.909 6.22 0.00 37.12 2.57
128 129 4.571919 TGAACTAACCGAACCGAATTCAT 58.428 39.130 6.22 0.00 37.12 2.57
129 130 4.390603 TGAACTAACCGAACCGAATTCATG 59.609 41.667 6.22 0.00 37.12 3.07
130 131 2.676342 ACTAACCGAACCGAATTCATGC 59.324 45.455 6.22 0.00 37.12 4.06
131 132 1.529226 AACCGAACCGAATTCATGCA 58.471 45.000 6.22 0.00 37.12 3.96
132 133 1.529226 ACCGAACCGAATTCATGCAA 58.471 45.000 6.22 0.00 37.12 4.08
133 134 1.883275 ACCGAACCGAATTCATGCAAA 59.117 42.857 6.22 0.00 37.12 3.68
134 135 2.491693 ACCGAACCGAATTCATGCAAAT 59.508 40.909 6.22 0.00 37.12 2.32
135 136 3.692101 ACCGAACCGAATTCATGCAAATA 59.308 39.130 6.22 0.00 37.12 1.40
136 137 4.035017 CCGAACCGAATTCATGCAAATAC 58.965 43.478 6.22 0.00 37.12 1.89
137 138 4.201910 CCGAACCGAATTCATGCAAATACT 60.202 41.667 6.22 0.00 37.12 2.12
138 139 4.730042 CGAACCGAATTCATGCAAATACTG 59.270 41.667 6.22 0.00 37.12 2.74
139 140 4.500477 GAACCGAATTCATGCAAATACTGC 59.500 41.667 6.22 0.00 43.37 4.40
140 141 5.677091 GAACCGAATTCATGCAAATACTGCT 60.677 40.000 6.22 0.00 43.43 4.24
141 142 6.458206 GAACCGAATTCATGCAAATACTGCTA 60.458 38.462 6.22 0.00 43.43 3.49
142 143 8.198816 GAACCGAATTCATGCAAATACTGCTAG 61.199 40.741 6.22 0.00 43.43 3.42
153 154 6.305693 CAAATACTGCTAGCAAATACTCCC 57.694 41.667 19.86 0.00 0.00 4.30
154 155 5.630415 AATACTGCTAGCAAATACTCCCA 57.370 39.130 19.86 0.00 0.00 4.37
155 156 5.630415 ATACTGCTAGCAAATACTCCCAA 57.370 39.130 19.86 0.00 0.00 4.12
156 157 4.510167 ACTGCTAGCAAATACTCCCAAT 57.490 40.909 19.86 0.00 0.00 3.16
157 158 5.630415 ACTGCTAGCAAATACTCCCAATA 57.370 39.130 19.86 0.00 0.00 1.90
158 159 6.001449 ACTGCTAGCAAATACTCCCAATAA 57.999 37.500 19.86 0.00 0.00 1.40
159 160 5.823045 ACTGCTAGCAAATACTCCCAATAAC 59.177 40.000 19.86 0.00 0.00 1.89
160 161 5.750524 TGCTAGCAAATACTCCCAATAACA 58.249 37.500 16.84 0.00 0.00 2.41
161 162 6.184068 TGCTAGCAAATACTCCCAATAACAA 58.816 36.000 16.84 0.00 0.00 2.83
264 265 0.933509 GCACGTAGCGGATAAGGTCG 60.934 60.000 0.00 0.00 0.00 4.79
314 318 1.147376 TCACCCAAGTTGACACCCG 59.853 57.895 3.87 0.00 0.00 5.28
319 339 1.227823 CAAGTTGACACCCGAGGCA 60.228 57.895 0.00 0.00 0.00 4.75
320 340 1.071471 AAGTTGACACCCGAGGCAG 59.929 57.895 0.00 0.00 0.00 4.85
321 341 2.358737 GTTGACACCCGAGGCAGG 60.359 66.667 0.00 0.00 0.00 4.85
322 342 4.329545 TTGACACCCGAGGCAGGC 62.330 66.667 0.00 0.00 0.00 4.85
324 344 3.075005 GACACCCGAGGCAGGCTA 61.075 66.667 0.00 0.00 0.00 3.93
325 345 3.077556 ACACCCGAGGCAGGCTAG 61.078 66.667 0.00 0.00 0.00 3.42
326 346 4.537433 CACCCGAGGCAGGCTAGC 62.537 72.222 6.04 6.04 0.00 3.42
373 428 5.350633 TGCACTGAACCTTGAAAATTGAAG 58.649 37.500 0.00 0.00 0.00 3.02
507 571 4.112341 CGCCAGCCTTGCTCTTGC 62.112 66.667 0.00 0.00 36.40 4.01
510 574 2.633509 CCAGCCTTGCTCTTGCCAC 61.634 63.158 0.00 0.00 36.40 5.01
521 585 3.026694 GCTCTTGCCACCCTGAATTATT 58.973 45.455 0.00 0.00 0.00 1.40
522 586 4.207165 GCTCTTGCCACCCTGAATTATTA 58.793 43.478 0.00 0.00 0.00 0.98
523 587 4.829492 GCTCTTGCCACCCTGAATTATTAT 59.171 41.667 0.00 0.00 0.00 1.28
532 596 4.587684 ACCCTGAATTATTATCCGAGTCGT 59.412 41.667 12.31 0.00 0.00 4.34
536 600 5.220381 TGAATTATTATCCGAGTCGTCTGC 58.780 41.667 12.31 0.00 0.00 4.26
552 616 5.178809 GTCGTCTGCACAAACCTAATACTTT 59.821 40.000 0.00 0.00 0.00 2.66
561 625 7.692705 GCACAAACCTAATACTTTCTTCGATTC 59.307 37.037 0.00 0.00 0.00 2.52
596 660 9.025041 TGTCGATGATTTAGAGGATGTGTATAT 57.975 33.333 0.00 0.00 0.00 0.86
667 731 3.073678 TGGATGACACCGTGAATTTCTG 58.926 45.455 5.28 0.00 0.00 3.02
670 734 4.023193 GGATGACACCGTGAATTTCTGTTT 60.023 41.667 5.28 0.00 0.00 2.83
725 790 3.806521 CCGTCAGTGATCTTTGGATGATC 59.193 47.826 0.00 0.00 40.34 2.92
756 1198 1.075601 TGTCTTCAAAGATGCCCCCT 58.924 50.000 0.00 0.00 37.39 4.79
798 1247 3.849911 TGATGAATCACTCCAGTCGTTC 58.150 45.455 0.00 0.00 0.00 3.95
802 1251 0.171455 ATCACTCCAGTCGTTCTCGC 59.829 55.000 0.00 0.00 36.96 5.03
807 1256 1.944024 CTCCAGTCGTTCTCGCTCTAT 59.056 52.381 0.00 0.00 36.96 1.98
857 1306 2.345876 CGTGTTGGCACAGACATCATA 58.654 47.619 0.00 0.00 45.50 2.15
868 1317 3.393609 ACAGACATCATAGGCCACATCAT 59.606 43.478 5.01 0.00 0.00 2.45
871 1320 4.224594 AGACATCATAGGCCACATCATAGG 59.775 45.833 5.01 0.00 0.00 2.57
899 1348 7.543868 CGCAAGTGGTCAATTATTTTATTTCCA 59.456 33.333 0.00 0.00 0.00 3.53
974 1435 2.948979 TGGTTTGGCTCGCCTATAAATG 59.051 45.455 9.65 0.00 36.94 2.32
979 1440 4.079980 TGGCTCGCCTATAAATGCTTTA 57.920 40.909 9.65 0.00 36.94 1.85
993 1454 3.350219 TGCTTTACACCTTCCCATCTC 57.650 47.619 0.00 0.00 0.00 2.75
1007 1468 2.354503 CCCATCTCCTCTTCACACACAG 60.355 54.545 0.00 0.00 0.00 3.66
1023 1504 2.432146 ACACAGACTCACACTCACACAT 59.568 45.455 0.00 0.00 0.00 3.21
1064 1563 2.903135 AGAAGAGGAGGAAGGACAACAG 59.097 50.000 0.00 0.00 0.00 3.16
1065 1564 2.407340 AGAGGAGGAAGGACAACAGT 57.593 50.000 0.00 0.00 0.00 3.55
1066 1565 2.252714 AGAGGAGGAAGGACAACAGTC 58.747 52.381 0.00 0.00 0.00 3.51
1150 1667 1.078848 CACAAAGGAGAGGAGGCCG 60.079 63.158 0.00 0.00 0.00 6.13
1248 1771 2.892425 CGCGGACAAGAGGGCATC 60.892 66.667 0.00 0.00 0.00 3.91
1249 1772 2.586792 GCGGACAAGAGGGCATCT 59.413 61.111 0.00 0.00 41.27 2.90
1250 1773 1.817099 GCGGACAAGAGGGCATCTG 60.817 63.158 0.87 0.00 38.67 2.90
1291 1824 2.079925 GCCTACAACTGAAGCTCAAGG 58.920 52.381 0.00 0.00 0.00 3.61
1339 1876 0.673956 GGACGCCCCTTTCTTCAGAC 60.674 60.000 0.00 0.00 0.00 3.51
1340 1877 0.673956 GACGCCCCTTTCTTCAGACC 60.674 60.000 0.00 0.00 0.00 3.85
1342 1879 0.674895 CGCCCCTTTCTTCAGACCTG 60.675 60.000 0.00 0.00 0.00 4.00
1344 1881 1.611936 GCCCCTTTCTTCAGACCTGAC 60.612 57.143 0.00 0.00 39.66 3.51
1345 1882 1.981495 CCCCTTTCTTCAGACCTGACT 59.019 52.381 0.00 0.00 39.66 3.41
1347 1884 3.196685 CCCCTTTCTTCAGACCTGACTAG 59.803 52.174 0.00 0.00 39.66 2.57
1349 1886 4.284746 CCCTTTCTTCAGACCTGACTAGTT 59.715 45.833 0.00 0.00 39.66 2.24
1387 1946 5.940470 AGTCCTAGCTTCATACTGGTTTTTG 59.060 40.000 0.00 0.00 0.00 2.44
1441 2000 5.877012 AGTTCTGCGATTGTACAGATGAATT 59.123 36.000 0.00 0.00 42.26 2.17
1464 2023 5.483811 TGAGAGGTTATGTGCAATTTCGTA 58.516 37.500 0.00 0.00 0.00 3.43
1466 2025 6.257849 TGAGAGGTTATGTGCAATTTCGTATC 59.742 38.462 0.00 0.00 0.00 2.24
1467 2026 6.112734 AGAGGTTATGTGCAATTTCGTATCA 58.887 36.000 0.00 0.00 0.00 2.15
1468 2027 6.037172 AGAGGTTATGTGCAATTTCGTATCAC 59.963 38.462 0.00 0.00 0.00 3.06
1469 2028 5.880332 AGGTTATGTGCAATTTCGTATCACT 59.120 36.000 0.00 0.00 0.00 3.41
1470 2029 6.374333 AGGTTATGTGCAATTTCGTATCACTT 59.626 34.615 0.00 0.00 0.00 3.16
1471 2030 7.027161 GGTTATGTGCAATTTCGTATCACTTT 58.973 34.615 0.00 0.00 0.00 2.66
1472 2031 7.540745 GGTTATGTGCAATTTCGTATCACTTTT 59.459 33.333 0.00 0.00 0.00 2.27
1473 2032 8.911662 GTTATGTGCAATTTCGTATCACTTTTT 58.088 29.630 0.00 0.00 0.00 1.94
1562 2145 4.178540 GCTATAACTTGGTTGTGCGTAGA 58.821 43.478 0.00 0.00 0.00 2.59
1612 2232 0.034670 GGAAATCAGAGGCTGGCAGT 60.035 55.000 17.16 0.00 31.51 4.40
1613 2233 1.093159 GAAATCAGAGGCTGGCAGTG 58.907 55.000 17.16 6.43 31.51 3.66
1614 2234 0.403271 AAATCAGAGGCTGGCAGTGT 59.597 50.000 17.16 3.12 31.51 3.55
1615 2235 0.403271 AATCAGAGGCTGGCAGTGTT 59.597 50.000 17.16 1.58 31.51 3.32
1616 2236 1.279496 ATCAGAGGCTGGCAGTGTTA 58.721 50.000 17.16 0.00 31.51 2.41
1617 2237 0.610174 TCAGAGGCTGGCAGTGTTAG 59.390 55.000 17.16 4.30 31.51 2.34
1618 2238 0.610174 CAGAGGCTGGCAGTGTTAGA 59.390 55.000 17.16 0.00 0.00 2.10
1619 2239 1.002430 CAGAGGCTGGCAGTGTTAGAA 59.998 52.381 17.16 0.00 0.00 2.10
1620 2240 1.699634 AGAGGCTGGCAGTGTTAGAAA 59.300 47.619 17.16 0.00 0.00 2.52
1621 2241 2.106511 AGAGGCTGGCAGTGTTAGAAAA 59.893 45.455 17.16 0.00 0.00 2.29
1622 2242 3.084786 GAGGCTGGCAGTGTTAGAAAAT 58.915 45.455 17.16 0.00 0.00 1.82
1623 2243 4.019321 AGAGGCTGGCAGTGTTAGAAAATA 60.019 41.667 17.16 0.00 0.00 1.40
1624 2244 4.010349 AGGCTGGCAGTGTTAGAAAATAC 58.990 43.478 17.16 0.00 0.00 1.89
1625 2245 3.181510 GGCTGGCAGTGTTAGAAAATACG 60.182 47.826 17.16 0.00 32.39 3.06
1626 2246 3.181510 GCTGGCAGTGTTAGAAAATACGG 60.182 47.826 17.16 0.00 32.39 4.02
1627 2247 3.340034 TGGCAGTGTTAGAAAATACGGG 58.660 45.455 0.00 0.00 32.39 5.28
1628 2248 3.008157 TGGCAGTGTTAGAAAATACGGGA 59.992 43.478 0.00 0.00 32.39 5.14
1629 2249 4.004982 GGCAGTGTTAGAAAATACGGGAA 58.995 43.478 0.00 0.00 32.39 3.97
1630 2250 4.456566 GGCAGTGTTAGAAAATACGGGAAA 59.543 41.667 0.00 0.00 32.39 3.13
1631 2251 5.391629 GGCAGTGTTAGAAAATACGGGAAAG 60.392 44.000 0.00 0.00 32.39 2.62
1632 2252 5.410439 GCAGTGTTAGAAAATACGGGAAAGA 59.590 40.000 0.00 0.00 32.39 2.52
1633 2253 6.093633 GCAGTGTTAGAAAATACGGGAAAGAT 59.906 38.462 0.00 0.00 32.39 2.40
1634 2254 7.676572 GCAGTGTTAGAAAATACGGGAAAGATC 60.677 40.741 0.00 0.00 32.39 2.75
1635 2255 7.333423 CAGTGTTAGAAAATACGGGAAAGATCA 59.667 37.037 0.00 0.00 32.39 2.92
1636 2256 7.881232 AGTGTTAGAAAATACGGGAAAGATCAA 59.119 33.333 0.00 0.00 32.39 2.57
1637 2257 8.674607 GTGTTAGAAAATACGGGAAAGATCAAT 58.325 33.333 0.00 0.00 0.00 2.57
1638 2258 8.673711 TGTTAGAAAATACGGGAAAGATCAATG 58.326 33.333 0.00 0.00 0.00 2.82
1639 2259 6.136541 AGAAAATACGGGAAAGATCAATGC 57.863 37.500 0.00 0.00 0.00 3.56
1640 2260 5.652014 AGAAAATACGGGAAAGATCAATGCA 59.348 36.000 0.00 0.00 0.00 3.96
1641 2261 5.913137 AAATACGGGAAAGATCAATGCAA 57.087 34.783 0.00 0.00 0.00 4.08
1642 2262 5.913137 AATACGGGAAAGATCAATGCAAA 57.087 34.783 0.00 0.00 0.00 3.68
1643 2263 5.913137 ATACGGGAAAGATCAATGCAAAA 57.087 34.783 0.00 0.00 0.00 2.44
1644 2264 4.599047 ACGGGAAAGATCAATGCAAAAA 57.401 36.364 0.00 0.00 0.00 1.94
1725 2345 3.466836 TCTTAGAGGTGTTGTTGTGCAG 58.533 45.455 0.00 0.00 0.00 4.41
1729 2349 1.748493 GAGGTGTTGTTGTGCAGGAAA 59.252 47.619 0.00 0.00 0.00 3.13
1806 2428 4.767255 CTCAGGTCCTGGTGCCGC 62.767 72.222 19.11 0.00 31.51 6.53
1825 2449 3.000041 CGCCCTTTTATTTTGGCTTTCC 59.000 45.455 0.00 0.00 41.80 3.13
1911 2537 5.176774 TGTTTATTGTGACTAGCGTGTTGAG 59.823 40.000 0.00 0.00 0.00 3.02
1989 2629 5.068234 TGAAACTTAGTACCAGTGATCGG 57.932 43.478 0.00 0.00 0.00 4.18
2001 2641 8.262227 AGTACCAGTGATCGGTAAAAATCAATA 58.738 33.333 0.11 0.00 40.65 1.90
2064 2977 8.402798 TGTCTATGAAACTTGCCATTTTAGAA 57.597 30.769 0.00 0.00 0.00 2.10
2068 2981 5.531634 TGAAACTTGCCATTTTAGAAGCAG 58.468 37.500 0.00 0.00 36.44 4.24
2153 3068 2.073816 CGTGCGGGATTCAACTACTTT 58.926 47.619 0.00 0.00 0.00 2.66
2155 3070 3.680937 CGTGCGGGATTCAACTACTTTAA 59.319 43.478 0.00 0.00 0.00 1.52
2173 3088 4.427096 TTAAAAATCGCGAGGCAAATCA 57.573 36.364 16.66 0.00 0.00 2.57
2206 3123 1.201429 CCTTGGTAGGTGAGTGCCCT 61.201 60.000 0.00 0.00 36.74 5.19
2207 3124 0.693049 CTTGGTAGGTGAGTGCCCTT 59.307 55.000 0.00 0.00 33.35 3.95
2233 3150 1.244019 GCGTGCCCCTGTGAATTTCT 61.244 55.000 0.00 0.00 0.00 2.52
2235 3152 1.881925 CGTGCCCCTGTGAATTTCTGA 60.882 52.381 0.00 0.00 0.00 3.27
2283 3201 7.377766 TCTACTTATTGCATTTGACCTTGTC 57.622 36.000 0.00 0.00 0.00 3.18
2296 3214 3.449377 TGACCTTGTCGCCTTGTATCATA 59.551 43.478 0.00 0.00 34.95 2.15
2310 3228 6.261603 CCTTGTATCATAGTTGTGTGCATCAT 59.738 38.462 0.00 0.00 0.00 2.45
2311 3229 6.607735 TGTATCATAGTTGTGTGCATCATG 57.392 37.500 0.00 0.00 0.00 3.07
2361 3279 8.560374 ACCTCGTTTTCAAAGAAGAAGAAATAG 58.440 33.333 0.00 0.00 32.00 1.73
2364 3282 9.931210 TCGTTTTCAAAGAAGAAGAAATAGTTC 57.069 29.630 0.00 0.00 32.00 3.01
2374 3292 9.336171 AGAAGAAGAAATAGTTCATATGAAGCC 57.664 33.333 18.47 8.07 36.09 4.35
2376 3294 7.500992 AGAAGAAATAGTTCATATGAAGCCGA 58.499 34.615 18.47 5.00 36.09 5.54
2379 3297 6.708054 AGAAATAGTTCATATGAAGCCGAAGG 59.292 38.462 18.47 0.00 43.91 3.46
2451 3369 7.227049 ACCAAATATGTCTTGTAAACCCAAG 57.773 36.000 0.00 0.00 42.57 3.61
2477 3395 6.328934 TGGAGGAAATATGACATAACCTAGCA 59.671 38.462 14.77 0.00 0.00 3.49
2500 3418 3.757493 CCGACTCCTGAGTTTACTACAGT 59.243 47.826 0.63 0.00 42.66 3.55
2503 3421 5.048921 CGACTCCTGAGTTTACTACAGTGAA 60.049 44.000 0.00 0.00 42.66 3.18
2504 3422 6.086785 ACTCCTGAGTTTACTACAGTGAAC 57.913 41.667 8.54 8.54 42.61 3.18
2518 3436 4.973168 ACAGTGAACTCATACAACACCAT 58.027 39.130 0.00 0.00 32.76 3.55
2528 3446 7.725251 ACTCATACAACACCATCAAAAACATT 58.275 30.769 0.00 0.00 0.00 2.71
2587 3506 2.109128 TCACCAAACCCCTAGCAAATGA 59.891 45.455 0.00 0.00 0.00 2.57
2590 3509 2.524306 CAAACCCCTAGCAAATGACCA 58.476 47.619 0.00 0.00 0.00 4.02
2600 3519 1.786579 GCAAATGACCAAAACAGACGC 59.213 47.619 0.00 0.00 0.00 5.19
2602 3521 3.705604 CAAATGACCAAAACAGACGCTT 58.294 40.909 0.00 0.00 0.00 4.68
2635 3554 0.888736 CCATCCAACGCAACTCACCA 60.889 55.000 0.00 0.00 0.00 4.17
2640 3559 1.336440 CCAACGCAACTCACCAAATCA 59.664 47.619 0.00 0.00 0.00 2.57
2656 3575 4.323477 CAGTTTGGGCCGGTCCGA 62.323 66.667 22.68 17.86 34.94 4.55
2707 3626 2.568546 TATGGGAGCTTTGGAGGAGA 57.431 50.000 0.00 0.00 0.00 3.71
2709 3628 0.914644 TGGGAGCTTTGGAGGAGATG 59.085 55.000 0.00 0.00 0.00 2.90
2722 3648 1.302033 GAGATGGGGAATGCGCGAT 60.302 57.895 12.10 0.00 0.00 4.58
2761 3687 1.686355 GATCACACCACAAACCCACA 58.314 50.000 0.00 0.00 0.00 4.17
2813 3739 2.374184 TCATTGGATAAGGGGCAAACG 58.626 47.619 0.00 0.00 0.00 3.60
2816 3742 1.828979 TGGATAAGGGGCAAACGTTC 58.171 50.000 0.00 0.00 0.00 3.95
2854 3781 2.950172 CTTCGCCCGTTCGGTTGTG 61.950 63.158 10.36 3.04 0.00 3.33
2859 3786 3.266376 CCGTTCGGTTGTGTGCGT 61.266 61.111 2.82 0.00 0.00 5.24
2864 3791 1.262151 GTTCGGTTGTGTGCGTACATT 59.738 47.619 10.21 0.00 39.39 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.101415 TCTGTCCACGAATATGCCAGAG 59.899 50.000 0.00 0.00 0.00 3.35
10 11 2.101415 CTCTGTCCACGAATATGCCAGA 59.899 50.000 0.00 0.00 0.00 3.86
11 12 2.101415 TCTCTGTCCACGAATATGCCAG 59.899 50.000 0.00 0.00 0.00 4.85
12 13 2.107366 TCTCTGTCCACGAATATGCCA 58.893 47.619 0.00 0.00 0.00 4.92
13 14 2.890808 TCTCTGTCCACGAATATGCC 57.109 50.000 0.00 0.00 0.00 4.40
14 15 5.347093 CACATATCTCTGTCCACGAATATGC 59.653 44.000 0.00 0.00 0.00 3.14
15 16 5.866092 CCACATATCTCTGTCCACGAATATG 59.134 44.000 0.00 0.00 0.00 1.78
16 17 5.775195 TCCACATATCTCTGTCCACGAATAT 59.225 40.000 0.00 0.00 0.00 1.28
17 18 5.009710 GTCCACATATCTCTGTCCACGAATA 59.990 44.000 0.00 0.00 0.00 1.75
18 19 3.960755 TCCACATATCTCTGTCCACGAAT 59.039 43.478 0.00 0.00 0.00 3.34
19 20 3.130516 GTCCACATATCTCTGTCCACGAA 59.869 47.826 0.00 0.00 0.00 3.85
20 21 2.688446 GTCCACATATCTCTGTCCACGA 59.312 50.000 0.00 0.00 0.00 4.35
21 22 2.427095 TGTCCACATATCTCTGTCCACG 59.573 50.000 0.00 0.00 0.00 4.94
22 23 3.735208 CGTGTCCACATATCTCTGTCCAC 60.735 52.174 0.00 0.00 0.00 4.02
23 24 2.427095 CGTGTCCACATATCTCTGTCCA 59.573 50.000 0.00 0.00 0.00 4.02
24 25 2.223829 CCGTGTCCACATATCTCTGTCC 60.224 54.545 0.00 0.00 0.00 4.02
25 26 2.688446 TCCGTGTCCACATATCTCTGTC 59.312 50.000 0.00 0.00 0.00 3.51
26 27 2.735151 TCCGTGTCCACATATCTCTGT 58.265 47.619 0.00 0.00 0.00 3.41
27 28 4.613850 CGTATCCGTGTCCACATATCTCTG 60.614 50.000 0.00 0.00 0.00 3.35
28 29 3.502595 CGTATCCGTGTCCACATATCTCT 59.497 47.826 0.00 0.00 0.00 3.10
29 30 3.501062 TCGTATCCGTGTCCACATATCTC 59.499 47.826 0.00 0.00 35.01 2.75
30 31 3.483421 TCGTATCCGTGTCCACATATCT 58.517 45.455 0.00 0.00 35.01 1.98
31 32 3.909776 TCGTATCCGTGTCCACATATC 57.090 47.619 0.00 0.00 35.01 1.63
32 33 4.340097 TCTTTCGTATCCGTGTCCACATAT 59.660 41.667 0.00 0.00 35.01 1.78
33 34 3.695556 TCTTTCGTATCCGTGTCCACATA 59.304 43.478 0.00 0.00 35.01 2.29
34 35 2.494471 TCTTTCGTATCCGTGTCCACAT 59.506 45.455 0.00 0.00 35.01 3.21
35 36 1.887854 TCTTTCGTATCCGTGTCCACA 59.112 47.619 0.00 0.00 35.01 4.17
36 37 2.257034 GTCTTTCGTATCCGTGTCCAC 58.743 52.381 0.00 0.00 35.01 4.02
37 38 1.135603 CGTCTTTCGTATCCGTGTCCA 60.136 52.381 0.00 0.00 35.01 4.02
38 39 1.542544 CGTCTTTCGTATCCGTGTCC 58.457 55.000 0.00 0.00 35.01 4.02
39 40 1.542544 CCGTCTTTCGTATCCGTGTC 58.457 55.000 0.00 0.00 37.94 3.67
40 41 0.457337 GCCGTCTTTCGTATCCGTGT 60.457 55.000 0.00 0.00 37.94 4.49
41 42 0.179145 AGCCGTCTTTCGTATCCGTG 60.179 55.000 0.00 0.00 37.94 4.94
42 43 1.382522 TAGCCGTCTTTCGTATCCGT 58.617 50.000 0.00 0.00 37.94 4.69
43 44 2.582687 GATAGCCGTCTTTCGTATCCG 58.417 52.381 0.00 0.00 37.94 4.18
44 45 2.295349 TGGATAGCCGTCTTTCGTATCC 59.705 50.000 0.00 8.78 42.70 2.59
45 46 3.637998 TGGATAGCCGTCTTTCGTATC 57.362 47.619 0.00 0.00 37.94 2.24
46 47 3.131577 TGTTGGATAGCCGTCTTTCGTAT 59.868 43.478 0.00 0.00 37.94 3.06
47 48 2.492881 TGTTGGATAGCCGTCTTTCGTA 59.507 45.455 0.00 0.00 37.94 3.43
48 49 1.274167 TGTTGGATAGCCGTCTTTCGT 59.726 47.619 0.00 0.00 37.94 3.85
49 50 2.004583 TGTTGGATAGCCGTCTTTCG 57.995 50.000 0.00 0.00 36.79 3.46
50 51 3.689649 ACATTGTTGGATAGCCGTCTTTC 59.310 43.478 0.00 0.00 36.79 2.62
51 52 3.686016 ACATTGTTGGATAGCCGTCTTT 58.314 40.909 0.00 0.00 36.79 2.52
52 53 3.270877 GACATTGTTGGATAGCCGTCTT 58.729 45.455 0.00 0.00 36.79 3.01
53 54 2.420129 GGACATTGTTGGATAGCCGTCT 60.420 50.000 0.00 0.00 36.79 4.18
54 55 1.940613 GGACATTGTTGGATAGCCGTC 59.059 52.381 0.00 0.00 36.79 4.79
55 56 1.280710 TGGACATTGTTGGATAGCCGT 59.719 47.619 0.00 0.00 36.79 5.68
56 57 2.036958 TGGACATTGTTGGATAGCCG 57.963 50.000 0.00 0.00 36.79 5.52
57 58 6.040842 ACATTATTGGACATTGTTGGATAGCC 59.959 38.462 0.00 0.00 0.00 3.93
58 59 7.042797 ACATTATTGGACATTGTTGGATAGC 57.957 36.000 0.00 0.00 0.00 2.97
59 60 7.857389 CGAACATTATTGGACATTGTTGGATAG 59.143 37.037 0.00 0.00 31.09 2.08
60 61 7.338196 ACGAACATTATTGGACATTGTTGGATA 59.662 33.333 0.00 0.00 32.52 2.59
61 62 6.152661 ACGAACATTATTGGACATTGTTGGAT 59.847 34.615 0.00 0.00 32.52 3.41
62 63 5.475220 ACGAACATTATTGGACATTGTTGGA 59.525 36.000 0.00 0.00 32.52 3.53
63 64 5.708948 ACGAACATTATTGGACATTGTTGG 58.291 37.500 0.00 0.00 33.81 3.77
64 65 9.433317 GTATACGAACATTATTGGACATTGTTG 57.567 33.333 0.00 0.00 31.09 3.33
65 66 8.617809 GGTATACGAACATTATTGGACATTGTT 58.382 33.333 0.00 0.00 33.47 2.83
66 67 7.990886 AGGTATACGAACATTATTGGACATTGT 59.009 33.333 0.00 0.00 0.00 2.71
67 68 8.378172 AGGTATACGAACATTATTGGACATTG 57.622 34.615 0.00 0.00 0.00 2.82
68 69 8.974060 AAGGTATACGAACATTATTGGACATT 57.026 30.769 0.00 0.00 0.00 2.71
69 70 8.974060 AAAGGTATACGAACATTATTGGACAT 57.026 30.769 0.00 0.00 0.00 3.06
70 71 8.041919 TGAAAGGTATACGAACATTATTGGACA 58.958 33.333 0.00 0.00 0.00 4.02
71 72 8.428186 TGAAAGGTATACGAACATTATTGGAC 57.572 34.615 0.00 0.00 0.00 4.02
72 73 9.621629 ATTGAAAGGTATACGAACATTATTGGA 57.378 29.630 0.00 0.00 0.00 3.53
73 74 9.878599 GATTGAAAGGTATACGAACATTATTGG 57.121 33.333 0.00 0.00 0.00 3.16
76 77 8.761497 CGTGATTGAAAGGTATACGAACATTAT 58.239 33.333 0.00 0.00 32.36 1.28
77 78 7.975058 TCGTGATTGAAAGGTATACGAACATTA 59.025 33.333 0.00 0.00 36.33 1.90
78 79 6.814644 TCGTGATTGAAAGGTATACGAACATT 59.185 34.615 0.00 0.00 36.33 2.71
79 80 6.334989 TCGTGATTGAAAGGTATACGAACAT 58.665 36.000 0.00 0.00 36.33 2.71
80 81 5.712004 TCGTGATTGAAAGGTATACGAACA 58.288 37.500 0.00 0.00 36.33 3.18
81 82 6.823678 ATCGTGATTGAAAGGTATACGAAC 57.176 37.500 0.00 0.00 41.51 3.95
82 83 7.546316 TCAAATCGTGATTGAAAGGTATACGAA 59.454 33.333 0.00 0.00 41.51 3.85
83 84 7.036829 TCAAATCGTGATTGAAAGGTATACGA 58.963 34.615 0.00 0.00 42.23 3.43
84 85 7.229228 TCAAATCGTGATTGAAAGGTATACG 57.771 36.000 0.00 0.00 0.00 3.06
85 86 8.665685 AGTTCAAATCGTGATTGAAAGGTATAC 58.334 33.333 12.22 0.00 35.70 1.47
86 87 8.786826 AGTTCAAATCGTGATTGAAAGGTATA 57.213 30.769 12.22 0.00 35.70 1.47
87 88 7.687941 AGTTCAAATCGTGATTGAAAGGTAT 57.312 32.000 12.22 0.00 35.70 2.73
88 89 8.500773 GTTAGTTCAAATCGTGATTGAAAGGTA 58.499 33.333 12.22 5.22 35.70 3.08
89 90 7.360361 GTTAGTTCAAATCGTGATTGAAAGGT 58.640 34.615 12.22 5.88 35.70 3.50
90 91 6.801862 GGTTAGTTCAAATCGTGATTGAAAGG 59.198 38.462 12.22 0.00 35.70 3.11
91 92 6.519761 CGGTTAGTTCAAATCGTGATTGAAAG 59.480 38.462 12.22 0.00 35.70 2.62
92 93 6.203145 TCGGTTAGTTCAAATCGTGATTGAAA 59.797 34.615 12.22 0.00 35.70 2.69
93 94 5.697178 TCGGTTAGTTCAAATCGTGATTGAA 59.303 36.000 8.28 8.28 35.70 2.69
94 95 5.231702 TCGGTTAGTTCAAATCGTGATTGA 58.768 37.500 0.00 0.00 35.70 2.57
95 96 5.524511 TCGGTTAGTTCAAATCGTGATTG 57.475 39.130 0.00 0.00 35.70 2.67
96 97 5.106830 GGTTCGGTTAGTTCAAATCGTGATT 60.107 40.000 0.00 0.00 35.70 2.57
97 98 4.390909 GGTTCGGTTAGTTCAAATCGTGAT 59.609 41.667 0.00 0.00 35.70 3.06
98 99 3.742369 GGTTCGGTTAGTTCAAATCGTGA 59.258 43.478 0.00 0.00 0.00 4.35
99 100 3.422603 CGGTTCGGTTAGTTCAAATCGTG 60.423 47.826 0.00 0.00 0.00 4.35
100 101 2.733026 CGGTTCGGTTAGTTCAAATCGT 59.267 45.455 0.00 0.00 0.00 3.73
101 102 2.988493 TCGGTTCGGTTAGTTCAAATCG 59.012 45.455 0.00 0.00 0.00 3.34
102 103 4.996062 TTCGGTTCGGTTAGTTCAAATC 57.004 40.909 0.00 0.00 0.00 2.17
103 104 5.470777 TGAATTCGGTTCGGTTAGTTCAAAT 59.529 36.000 0.04 0.00 39.80 2.32
104 105 4.815308 TGAATTCGGTTCGGTTAGTTCAAA 59.185 37.500 0.04 0.00 39.80 2.69
105 106 4.378774 TGAATTCGGTTCGGTTAGTTCAA 58.621 39.130 0.04 0.00 39.80 2.69
106 107 3.992643 TGAATTCGGTTCGGTTAGTTCA 58.007 40.909 0.04 0.00 39.80 3.18
107 108 4.726876 GCATGAATTCGGTTCGGTTAGTTC 60.727 45.833 0.00 0.00 39.80 3.01
108 109 3.126343 GCATGAATTCGGTTCGGTTAGTT 59.874 43.478 0.00 0.00 39.80 2.24
109 110 2.676342 GCATGAATTCGGTTCGGTTAGT 59.324 45.455 0.00 0.00 39.80 2.24
110 111 2.675844 TGCATGAATTCGGTTCGGTTAG 59.324 45.455 0.00 0.00 39.80 2.34
111 112 2.701107 TGCATGAATTCGGTTCGGTTA 58.299 42.857 0.00 0.00 39.80 2.85
112 113 1.529226 TGCATGAATTCGGTTCGGTT 58.471 45.000 0.00 0.00 39.80 4.44
113 114 1.529226 TTGCATGAATTCGGTTCGGT 58.471 45.000 0.00 0.00 39.80 4.69
114 115 2.627863 TTTGCATGAATTCGGTTCGG 57.372 45.000 0.00 0.00 39.80 4.30
115 116 4.730042 CAGTATTTGCATGAATTCGGTTCG 59.270 41.667 0.00 0.00 39.80 3.95
130 131 5.822519 TGGGAGTATTTGCTAGCAGTATTTG 59.177 40.000 18.45 0.00 0.00 2.32
131 132 6.001449 TGGGAGTATTTGCTAGCAGTATTT 57.999 37.500 18.45 5.19 0.00 1.40
132 133 5.630415 TGGGAGTATTTGCTAGCAGTATT 57.370 39.130 18.45 11.60 0.00 1.89
133 134 5.630415 TTGGGAGTATTTGCTAGCAGTAT 57.370 39.130 18.45 16.91 0.00 2.12
134 135 5.630415 ATTGGGAGTATTTGCTAGCAGTA 57.370 39.130 18.45 12.20 0.00 2.74
135 136 4.510167 ATTGGGAGTATTTGCTAGCAGT 57.490 40.909 18.45 13.22 0.00 4.40
136 137 5.822519 TGTTATTGGGAGTATTTGCTAGCAG 59.177 40.000 18.45 0.00 0.00 4.24
137 138 5.750524 TGTTATTGGGAGTATTTGCTAGCA 58.249 37.500 14.93 14.93 0.00 3.49
138 139 6.693315 TTGTTATTGGGAGTATTTGCTAGC 57.307 37.500 8.10 8.10 0.00 3.42
141 142 9.420118 TCATTATTGTTATTGGGAGTATTTGCT 57.580 29.630 0.00 0.00 0.00 3.91
142 143 9.463443 GTCATTATTGTTATTGGGAGTATTTGC 57.537 33.333 0.00 0.00 0.00 3.68
149 150 9.965824 GGTTATTGTCATTATTGTTATTGGGAG 57.034 33.333 0.00 0.00 0.00 4.30
150 151 9.707957 AGGTTATTGTCATTATTGTTATTGGGA 57.292 29.630 0.00 0.00 0.00 4.37
151 152 9.965824 GAGGTTATTGTCATTATTGTTATTGGG 57.034 33.333 0.00 0.00 0.00 4.12
152 153 9.965824 GGAGGTTATTGTCATTATTGTTATTGG 57.034 33.333 0.00 0.00 0.00 3.16
153 154 9.965824 GGGAGGTTATTGTCATTATTGTTATTG 57.034 33.333 0.00 0.00 0.00 1.90
154 155 9.707957 TGGGAGGTTATTGTCATTATTGTTATT 57.292 29.630 0.00 0.00 0.00 1.40
155 156 9.707957 TTGGGAGGTTATTGTCATTATTGTTAT 57.292 29.630 0.00 0.00 0.00 1.89
156 157 9.707957 ATTGGGAGGTTATTGTCATTATTGTTA 57.292 29.630 0.00 0.00 0.00 2.41
157 158 8.608185 ATTGGGAGGTTATTGTCATTATTGTT 57.392 30.769 0.00 0.00 0.00 2.83
158 159 9.707957 TTATTGGGAGGTTATTGTCATTATTGT 57.292 29.630 0.00 0.00 0.00 2.71
159 160 9.965824 GTTATTGGGAGGTTATTGTCATTATTG 57.034 33.333 0.00 0.00 0.00 1.90
160 161 9.936329 AGTTATTGGGAGGTTATTGTCATTATT 57.064 29.630 0.00 0.00 0.00 1.40
264 265 1.521423 CGACCGAAATATCTTGACCGC 59.479 52.381 0.00 0.00 0.00 5.68
326 346 1.951130 CGTGGTGGCGCTATGCTAG 60.951 63.158 7.64 0.00 45.43 3.42
373 428 1.061711 CTGATTTGTACTGCAGCGAGC 59.938 52.381 15.27 1.89 45.96 5.03
457 521 2.739132 GGTGACCGTTTCCTCCGT 59.261 61.111 0.00 0.00 0.00 4.69
488 552 2.046507 AAGAGCAAGGCTGGCGAG 60.047 61.111 8.52 0.00 39.88 5.03
489 553 2.359107 CAAGAGCAAGGCTGGCGA 60.359 61.111 8.52 0.00 39.88 5.54
490 554 4.112341 GCAAGAGCAAGGCTGGCG 62.112 66.667 8.52 0.00 39.88 5.69
491 555 3.756727 GGCAAGAGCAAGGCTGGC 61.757 66.667 5.50 5.50 44.61 4.85
507 571 5.228945 ACTCGGATAATAATTCAGGGTGG 57.771 43.478 0.00 0.00 0.00 4.61
510 574 5.047943 AGACGACTCGGATAATAATTCAGGG 60.048 44.000 2.98 0.00 0.00 4.45
521 585 1.170442 TTGTGCAGACGACTCGGATA 58.830 50.000 2.98 0.00 0.00 2.59
522 586 0.317160 TTTGTGCAGACGACTCGGAT 59.683 50.000 2.98 0.00 0.00 4.18
523 587 0.596600 GTTTGTGCAGACGACTCGGA 60.597 55.000 2.98 0.00 0.00 4.55
532 596 6.147164 CGAAGAAAGTATTAGGTTTGTGCAGA 59.853 38.462 0.00 0.00 0.00 4.26
536 600 8.717821 TGAATCGAAGAAAGTATTAGGTTTGTG 58.282 33.333 0.00 0.00 43.58 3.33
552 616 9.691362 TCATCGACAATTAATATGAATCGAAGA 57.309 29.630 11.15 10.02 45.75 2.87
596 660 3.610040 ACGAGTGTGCATGGATTCTTA 57.390 42.857 0.00 0.00 0.00 2.10
598 662 2.479566 AACGAGTGTGCATGGATTCT 57.520 45.000 0.00 0.00 0.00 2.40
667 731 1.632422 CATTCTCGCCCATGCAAAAC 58.368 50.000 0.00 0.00 37.32 2.43
670 734 2.763273 CGCATTCTCGCCCATGCAA 61.763 57.895 11.50 0.00 45.23 4.08
756 1198 2.240918 AAGGGCAAGGGAGATGGCA 61.241 57.895 0.00 0.00 44.51 4.92
802 1251 1.202348 CCACACGAGTGCTCCATAGAG 60.202 57.143 7.54 0.00 44.53 2.43
807 1256 1.906333 TAGCCACACGAGTGCTCCA 60.906 57.895 7.54 0.00 44.53 3.86
842 1291 0.181114 GGCCTATGATGTCTGTGCCA 59.819 55.000 0.00 0.00 37.36 4.92
868 1317 0.037590 AATTGACCACTTGCGGCCTA 59.962 50.000 0.00 0.00 0.00 3.93
871 1320 2.939460 AATAATTGACCACTTGCGGC 57.061 45.000 0.00 0.00 0.00 6.53
899 1348 4.545610 CCGCACATGTTAATTTGTCTTGT 58.454 39.130 0.00 0.00 0.00 3.16
974 1435 2.239907 AGGAGATGGGAAGGTGTAAAGC 59.760 50.000 0.00 0.00 0.00 3.51
979 1440 2.192263 GAAGAGGAGATGGGAAGGTGT 58.808 52.381 0.00 0.00 0.00 4.16
993 1454 2.101415 TGTGAGTCTGTGTGTGAAGAGG 59.899 50.000 0.00 0.00 0.00 3.69
1007 1468 5.773575 TCTTCTTATGTGTGAGTGTGAGTC 58.226 41.667 0.00 0.00 0.00 3.36
1023 1504 7.957002 TCTTCTTGCTTTCTCTCTTCTTCTTA 58.043 34.615 0.00 0.00 0.00 2.10
1064 1563 3.733337 TGGCTCTTCTTTCTCTGTTGAC 58.267 45.455 0.00 0.00 0.00 3.18
1065 1564 4.321718 CATGGCTCTTCTTTCTCTGTTGA 58.678 43.478 0.00 0.00 0.00 3.18
1066 1565 3.439476 CCATGGCTCTTCTTTCTCTGTTG 59.561 47.826 0.00 0.00 0.00 3.33
1117 1634 1.227999 TTGTGCTGCCGTAGTTGCTC 61.228 55.000 0.00 0.00 0.00 4.26
1291 1824 1.227089 ATCTGACACTCGATGGCGC 60.227 57.895 0.00 0.00 40.51 6.53
1364 1913 5.705905 ACAAAAACCAGTATGAAGCTAGGAC 59.294 40.000 0.00 0.00 39.69 3.85
1365 1914 5.876357 ACAAAAACCAGTATGAAGCTAGGA 58.124 37.500 0.00 0.00 39.69 2.94
1366 1915 6.349363 GGAACAAAAACCAGTATGAAGCTAGG 60.349 42.308 0.00 0.00 39.69 3.02
1367 1916 6.349363 GGGAACAAAAACCAGTATGAAGCTAG 60.349 42.308 0.00 0.00 39.69 3.42
1387 1946 0.328592 GGGGGAGAAGACTTGGGAAC 59.671 60.000 0.00 0.00 0.00 3.62
1441 2000 4.323417 ACGAAATTGCACATAACCTCTCA 58.677 39.130 0.00 0.00 0.00 3.27
1483 2042 2.169978 AGTGATACGAAAGGGGTAAGCC 59.830 50.000 0.00 0.00 0.00 4.35
1484 2043 3.538634 AGTGATACGAAAGGGGTAAGC 57.461 47.619 0.00 0.00 0.00 3.09
1485 2044 5.121768 CACAAAGTGATACGAAAGGGGTAAG 59.878 44.000 0.00 0.00 35.23 2.34
1486 2045 4.998672 CACAAAGTGATACGAAAGGGGTAA 59.001 41.667 0.00 0.00 35.23 2.85
1487 2046 4.283978 TCACAAAGTGATACGAAAGGGGTA 59.716 41.667 0.00 0.00 37.67 3.69
1488 2047 3.071892 TCACAAAGTGATACGAAAGGGGT 59.928 43.478 0.00 0.00 37.67 4.95
1489 2048 3.670625 TCACAAAGTGATACGAAAGGGG 58.329 45.455 0.00 0.00 37.67 4.79
1529 2112 4.935808 ACCAAGTTATAGCGTTCAAGAAGG 59.064 41.667 0.00 0.00 0.00 3.46
1547 2130 2.294479 CGTTTCTACGCACAACCAAG 57.706 50.000 0.00 0.00 41.41 3.61
1562 2145 0.741915 ATTTGTTCACCCGTGCGTTT 59.258 45.000 0.00 0.00 0.00 3.60
1612 2232 8.673711 CATTGATCTTTCCCGTATTTTCTAACA 58.326 33.333 0.00 0.00 0.00 2.41
1613 2233 7.644157 GCATTGATCTTTCCCGTATTTTCTAAC 59.356 37.037 0.00 0.00 0.00 2.34
1614 2234 7.338196 TGCATTGATCTTTCCCGTATTTTCTAA 59.662 33.333 0.00 0.00 0.00 2.10
1615 2235 6.826231 TGCATTGATCTTTCCCGTATTTTCTA 59.174 34.615 0.00 0.00 0.00 2.10
1616 2236 5.652014 TGCATTGATCTTTCCCGTATTTTCT 59.348 36.000 0.00 0.00 0.00 2.52
1617 2237 5.890334 TGCATTGATCTTTCCCGTATTTTC 58.110 37.500 0.00 0.00 0.00 2.29
1618 2238 5.913137 TGCATTGATCTTTCCCGTATTTT 57.087 34.783 0.00 0.00 0.00 1.82
1619 2239 5.913137 TTGCATTGATCTTTCCCGTATTT 57.087 34.783 0.00 0.00 0.00 1.40
1620 2240 5.913137 TTTGCATTGATCTTTCCCGTATT 57.087 34.783 0.00 0.00 0.00 1.89
1621 2241 5.913137 TTTTGCATTGATCTTTCCCGTAT 57.087 34.783 0.00 0.00 0.00 3.06
1622 2242 5.713792 TTTTTGCATTGATCTTTCCCGTA 57.286 34.783 0.00 0.00 0.00 4.02
1623 2243 4.599047 TTTTTGCATTGATCTTTCCCGT 57.401 36.364 0.00 0.00 0.00 5.28
1641 2261 8.138712 TCATTGGCGTATTTTCTAACACTTTTT 58.861 29.630 0.00 0.00 0.00 1.94
1642 2262 7.653647 TCATTGGCGTATTTTCTAACACTTTT 58.346 30.769 0.00 0.00 0.00 2.27
1643 2263 7.209471 TCATTGGCGTATTTTCTAACACTTT 57.791 32.000 0.00 0.00 0.00 2.66
1644 2264 6.811253 TCATTGGCGTATTTTCTAACACTT 57.189 33.333 0.00 0.00 0.00 3.16
1686 2306 5.956563 TCTAAGAAGGGATTAACTTCCTCGT 59.043 40.000 0.00 0.00 44.13 4.18
1693 2313 6.272558 ACAACACCTCTAAGAAGGGATTAACT 59.727 38.462 0.00 0.00 41.04 2.24
1697 2317 5.163088 ACAACAACACCTCTAAGAAGGGATT 60.163 40.000 0.00 0.00 41.04 3.01
1725 2345 4.514066 ACACCAACGACTAAGTCAATTTCC 59.486 41.667 0.00 0.00 32.09 3.13
1729 2349 7.739498 AATTAACACCAACGACTAAGTCAAT 57.261 32.000 0.00 0.00 32.09 2.57
1786 2407 2.520536 GGCACCAGGACCTGAGTGT 61.521 63.158 28.84 16.64 36.11 3.55
1874 2498 8.500773 AGTCACAATAAACACGAATACGAAAAT 58.499 29.630 0.00 0.00 42.66 1.82
1880 2504 6.034256 ACGCTAGTCACAATAAACACGAATAC 59.966 38.462 0.00 0.00 0.00 1.89
1892 2516 3.660501 TCTCAACACGCTAGTCACAAT 57.339 42.857 0.00 0.00 0.00 2.71
2054 2966 7.875971 ACTTACAGTTTCTGCTTCTAAAATGG 58.124 34.615 0.00 0.00 35.57 3.16
2064 2977 7.225931 TCAACGATAAAACTTACAGTTTCTGCT 59.774 33.333 2.42 0.00 46.78 4.24
2068 2981 9.712359 AGTTTCAACGATAAAACTTACAGTTTC 57.288 29.630 2.42 0.00 46.78 2.78
2153 3068 4.411327 CTTGATTTGCCTCGCGATTTTTA 58.589 39.130 10.36 0.00 0.00 1.52
2155 3070 2.867429 CTTGATTTGCCTCGCGATTTT 58.133 42.857 10.36 0.00 0.00 1.82
2258 3176 7.201644 CGACAAGGTCAAATGCAATAAGTAGAT 60.202 37.037 0.00 0.00 32.09 1.98
2266 3184 1.067635 GGCGACAAGGTCAAATGCAAT 60.068 47.619 0.00 0.00 32.09 3.56
2270 3188 1.608590 ACAAGGCGACAAGGTCAAATG 59.391 47.619 0.00 0.00 32.09 2.32
2283 3201 3.242413 GCACACAACTATGATACAAGGCG 60.242 47.826 0.00 0.00 0.00 5.52
2296 3214 4.632538 CATCATCATGATGCACACAACT 57.367 40.909 27.68 4.85 46.37 3.16
2310 3228 2.278245 ACCCTGAACCCTTCATCATCA 58.722 47.619 0.00 0.00 39.30 3.07
2311 3229 3.372440 AACCCTGAACCCTTCATCATC 57.628 47.619 0.00 0.00 39.30 2.92
2361 3279 3.270877 ACACCTTCGGCTTCATATGAAC 58.729 45.455 14.23 10.90 0.00 3.18
2364 3282 5.056480 TGATAACACCTTCGGCTTCATATG 58.944 41.667 0.00 0.00 0.00 1.78
2374 3292 9.542462 TTATAGAGGAAAATGATAACACCTTCG 57.458 33.333 0.00 0.00 0.00 3.79
2451 3369 6.651225 GCTAGGTTATGTCATATTTCCTCCAC 59.349 42.308 12.18 0.00 0.00 4.02
2477 3395 3.757493 CTGTAGTAAACTCAGGAGTCGGT 59.243 47.826 1.86 0.00 41.58 4.69
2500 3418 6.951062 TTTTGATGGTGTTGTATGAGTTCA 57.049 33.333 0.00 0.00 0.00 3.18
2503 3421 6.707440 TGTTTTTGATGGTGTTGTATGAGT 57.293 33.333 0.00 0.00 0.00 3.41
2504 3422 9.859427 ATAATGTTTTTGATGGTGTTGTATGAG 57.141 29.630 0.00 0.00 0.00 2.90
2587 3506 1.164041 CCCGAAGCGTCTGTTTTGGT 61.164 55.000 0.00 0.00 37.98 3.67
2590 3509 3.340789 GCCCGAAGCGTCTGTTTT 58.659 55.556 0.00 0.00 0.00 2.43
2600 3519 3.905249 GGCTAAAGGTGCCCGAAG 58.095 61.111 0.00 0.00 44.32 3.79
2610 3529 1.812571 AGTTGCGTTGGATGGCTAAAG 59.187 47.619 0.00 0.00 0.00 1.85
2635 3554 0.898326 GGACCGGCCCAAACTGATTT 60.898 55.000 0.00 0.00 0.00 2.17
2640 3559 2.902457 ATTCGGACCGGCCCAAACT 61.902 57.895 15.25 0.00 0.00 2.66
2690 3609 0.914644 CATCTCCTCCAAAGCTCCCA 59.085 55.000 0.00 0.00 0.00 4.37
2707 3626 2.666190 CGATCGCGCATTCCCCAT 60.666 61.111 8.75 0.00 0.00 4.00
2761 3687 4.434195 AGAGAAGGGAGGAAGAGTGAAAT 58.566 43.478 0.00 0.00 0.00 2.17
2813 3739 5.413833 AGGCATTCAATCATATCCATCGAAC 59.586 40.000 0.00 0.00 0.00 3.95
2816 3742 5.446875 CGAAGGCATTCAATCATATCCATCG 60.447 44.000 12.16 0.00 34.94 3.84


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

AutoCloner maintained by Alex Coulton.