Multiple sequence alignment - TraesCS7B01G362000

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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 TraesCS7B01G362000 chr7B 100.000 2549 0 0 1 2549 623951733 623949185 0.000000e+00 4708.0
1 TraesCS7B01G362000 chr7B 87.027 185 23 1 1631 1815 639997600 639997783 9.240000e-50 207.0
2 TraesCS7B01G362000 chr7A 92.603 1798 87 6 335 2087 657024889 657023093 0.000000e+00 2542.0
3 TraesCS7B01G362000 chr7A 93.005 386 21 3 2164 2549 123426696 123426317 2.220000e-155 558.0
4 TraesCS7B01G362000 chr7A 94.118 153 4 2 2396 2548 657023058 657022911 7.090000e-56 228.0
5 TraesCS7B01G362000 chr7A 96.610 118 3 1 238 354 657025017 657024900 7.200000e-46 195.0
6 TraesCS7B01G362000 chr7D 94.161 1610 67 4 237 1842 568371707 568370121 0.000000e+00 2427.0
7 TraesCS7B01G362000 chr7D 88.812 724 21 8 1850 2549 568370001 568369314 0.000000e+00 833.0
8 TraesCS7B01G362000 chr6B 83.186 1356 174 30 238 1549 13819096 13817751 0.000000e+00 1192.0
9 TraesCS7B01G362000 chr6B 80.169 1180 205 20 381 1543 14340441 14341608 0.000000e+00 856.0
10 TraesCS7B01G362000 chr6B 79.342 1094 197 23 467 1543 39326217 39327298 0.000000e+00 741.0
11 TraesCS7B01G362000 chr6B 76.989 1169 244 21 396 1549 15751004 15749846 0.000000e+00 645.0
12 TraesCS7B01G362000 chr6B 78.161 1044 196 26 517 1543 39311207 39312235 9.950000e-179 636.0
13 TraesCS7B01G362000 chr6B 85.795 352 38 7 2142 2493 14360603 14360264 1.860000e-96 363.0
14 TraesCS7B01G362000 chr6B 84.524 168 26 0 1369 1536 178881752 178881585 1.570000e-37 167.0
15 TraesCS7B01G362000 chr6B 76.580 269 59 4 1572 1838 62708389 62708123 7.350000e-31 145.0
16 TraesCS7B01G362000 chr6B 83.553 152 25 0 1370 1521 670582037 670581886 2.640000e-30 143.0
17 TraesCS7B01G362000 chr6D 82.176 1195 187 19 369 1543 7901239 7902427 0.000000e+00 1003.0
18 TraesCS7B01G362000 chr6D 83.028 1037 149 14 517 1549 7404832 7403819 0.000000e+00 915.0
19 TraesCS7B01G362000 chr6D 79.141 978 126 41 1573 2493 7962818 7963774 2.810000e-169 604.0
20 TraesCS7B01G362000 chr6D 75.793 1198 267 13 374 1554 8552826 8551635 3.650000e-163 584.0
21 TraesCS7B01G362000 chr6D 82.081 692 100 15 364 1047 7728433 7729108 1.020000e-158 569.0
22 TraesCS7B01G362000 chr6A 82.188 1179 160 17 242 1392 7224885 7223729 0.000000e+00 968.0
23 TraesCS7B01G362000 chr6A 80.350 1201 180 32 369 1543 8174948 8176118 0.000000e+00 859.0
24 TraesCS7B01G362000 chr6A 75.258 873 126 54 1573 2368 8175902 8176761 1.460000e-87 333.0
25 TraesCS7B01G362000 chr6A 92.929 198 10 1 2164 2361 572389379 572389186 4.150000e-73 285.0
26 TraesCS7B01G362000 chr6A 95.000 60 3 0 2490 2549 572389191 572389132 7.510000e-16 95.3
27 TraesCS7B01G362000 chr1B 78.378 259 48 7 1573 1827 630650470 630650724 7.300000e-36 161.0
28 TraesCS7B01G362000 chrUn 76.895 277 63 1 1570 1845 101943332 101943056 3.400000e-34 156.0
29 TraesCS7B01G362000 chrUn 92.683 41 3 0 2290 2330 24973568 24973608 2.740000e-05 60.2
30 TraesCS7B01G362000 chr5D 83.333 150 25 0 1678 1827 524578571 524578720 3.420000e-29 139.0
31 TraesCS7B01G362000 chr5A 76.744 258 52 7 1574 1827 650825493 650825746 1.230000e-28 137.0


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 TraesCS7B01G362000 chr7B 623949185 623951733 2548 True 4708.000000 4708 100.000000 1 2549 1 chr7B.!!$R1 2548
1 TraesCS7B01G362000 chr7A 657022911 657025017 2106 True 988.333333 2542 94.443667 238 2548 3 chr7A.!!$R2 2310
2 TraesCS7B01G362000 chr7D 568369314 568371707 2393 True 1630.000000 2427 91.486500 237 2549 2 chr7D.!!$R1 2312
3 TraesCS7B01G362000 chr6B 13817751 13819096 1345 True 1192.000000 1192 83.186000 238 1549 1 chr6B.!!$R1 1311
4 TraesCS7B01G362000 chr6B 14340441 14341608 1167 False 856.000000 856 80.169000 381 1543 1 chr6B.!!$F1 1162
5 TraesCS7B01G362000 chr6B 39326217 39327298 1081 False 741.000000 741 79.342000 467 1543 1 chr6B.!!$F3 1076
6 TraesCS7B01G362000 chr6B 15749846 15751004 1158 True 645.000000 645 76.989000 396 1549 1 chr6B.!!$R3 1153
7 TraesCS7B01G362000 chr6B 39311207 39312235 1028 False 636.000000 636 78.161000 517 1543 1 chr6B.!!$F2 1026
8 TraesCS7B01G362000 chr6D 7901239 7902427 1188 False 1003.000000 1003 82.176000 369 1543 1 chr6D.!!$F2 1174
9 TraesCS7B01G362000 chr6D 7403819 7404832 1013 True 915.000000 915 83.028000 517 1549 1 chr6D.!!$R1 1032
10 TraesCS7B01G362000 chr6D 7962818 7963774 956 False 604.000000 604 79.141000 1573 2493 1 chr6D.!!$F3 920
11 TraesCS7B01G362000 chr6D 8551635 8552826 1191 True 584.000000 584 75.793000 374 1554 1 chr6D.!!$R2 1180
12 TraesCS7B01G362000 chr6D 7728433 7729108 675 False 569.000000 569 82.081000 364 1047 1 chr6D.!!$F1 683
13 TraesCS7B01G362000 chr6A 7223729 7224885 1156 True 968.000000 968 82.188000 242 1392 1 chr6A.!!$R1 1150
14 TraesCS7B01G362000 chr6A 8174948 8176761 1813 False 596.000000 859 77.804000 369 2368 2 chr6A.!!$F1 1999

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
215 216 0.034059 CTGCACTCCCTTCGAACTGT 59.966 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2380 0.319728 CTGGGATCATAGTCAGGCCG 59.68 60.0 0.0 0.0 0.0 6.13 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
23 24 6.647334 TCAGAACCAGCAAAATGTTATTGA 57.353 33.333 0.00 0.00 0.00 2.57
24 25 7.230849 TCAGAACCAGCAAAATGTTATTGAT 57.769 32.000 0.00 0.00 0.00 2.57
25 26 8.347004 TCAGAACCAGCAAAATGTTATTGATA 57.653 30.769 0.00 0.00 0.00 2.15
26 27 8.243426 TCAGAACCAGCAAAATGTTATTGATAC 58.757 33.333 0.00 0.00 0.00 2.24
27 28 8.028354 CAGAACCAGCAAAATGTTATTGATACA 58.972 33.333 0.00 0.00 0.00 2.29
28 29 8.752187 AGAACCAGCAAAATGTTATTGATACAT 58.248 29.630 0.00 0.00 37.82 2.29
29 30 9.369904 GAACCAGCAAAATGTTATTGATACATT 57.630 29.630 0.00 0.00 45.49 2.71
30 31 8.931385 ACCAGCAAAATGTTATTGATACATTC 57.069 30.769 0.00 0.00 43.44 2.67
31 32 7.701924 ACCAGCAAAATGTTATTGATACATTCG 59.298 33.333 0.00 0.00 43.44 3.34
32 33 7.167968 CCAGCAAAATGTTATTGATACATTCGG 59.832 37.037 0.00 0.00 43.44 4.30
33 34 7.701924 CAGCAAAATGTTATTGATACATTCGGT 59.298 33.333 0.00 0.00 43.44 4.69
34 35 7.915397 AGCAAAATGTTATTGATACATTCGGTC 59.085 33.333 0.00 0.00 43.44 4.79
35 36 7.097047 GCAAAATGTTATTGATACATTCGGTCG 60.097 37.037 0.00 0.00 43.44 4.79
36 37 7.780008 AAATGTTATTGATACATTCGGTCGA 57.220 32.000 0.00 0.00 43.44 4.20
37 38 6.764877 ATGTTATTGATACATTCGGTCGAC 57.235 37.500 7.13 7.13 32.48 4.20
38 39 5.898174 TGTTATTGATACATTCGGTCGACT 58.102 37.500 16.46 0.00 0.00 4.18
39 40 5.975344 TGTTATTGATACATTCGGTCGACTC 59.025 40.000 16.46 4.72 0.00 3.36
40 41 3.431922 TTGATACATTCGGTCGACTCC 57.568 47.619 16.46 0.00 0.00 3.85
48 49 4.131088 GGTCGACTCCGTGCCCTC 62.131 72.222 16.46 0.00 37.05 4.30
49 50 4.131088 GTCGACTCCGTGCCCTCC 62.131 72.222 8.70 0.00 37.05 4.30
50 51 4.671590 TCGACTCCGTGCCCTCCA 62.672 66.667 0.00 0.00 37.05 3.86
51 52 4.436998 CGACTCCGTGCCCTCCAC 62.437 72.222 0.00 0.00 41.15 4.02
52 53 3.311110 GACTCCGTGCCCTCCACA 61.311 66.667 0.00 0.00 44.91 4.17
53 54 2.847234 ACTCCGTGCCCTCCACAA 60.847 61.111 0.00 0.00 44.91 3.33
54 55 2.185310 GACTCCGTGCCCTCCACAAT 62.185 60.000 0.00 0.00 44.91 2.71
55 56 1.002134 CTCCGTGCCCTCCACAATT 60.002 57.895 0.00 0.00 44.91 2.32
56 57 1.002624 TCCGTGCCCTCCACAATTC 60.003 57.895 0.00 0.00 44.91 2.17
57 58 1.002134 CCGTGCCCTCCACAATTCT 60.002 57.895 0.00 0.00 44.91 2.40
58 59 0.251916 CCGTGCCCTCCACAATTCTA 59.748 55.000 0.00 0.00 44.91 2.10
59 60 1.339631 CCGTGCCCTCCACAATTCTAA 60.340 52.381 0.00 0.00 44.91 2.10
60 61 2.009774 CGTGCCCTCCACAATTCTAAG 58.990 52.381 0.00 0.00 44.91 2.18
61 62 1.745653 GTGCCCTCCACAATTCTAAGC 59.254 52.381 0.00 0.00 44.06 3.09
62 63 1.354031 TGCCCTCCACAATTCTAAGCA 59.646 47.619 0.00 0.00 0.00 3.91
63 64 1.745653 GCCCTCCACAATTCTAAGCAC 59.254 52.381 0.00 0.00 0.00 4.40
64 65 2.879756 GCCCTCCACAATTCTAAGCACA 60.880 50.000 0.00 0.00 0.00 4.57
65 66 3.420893 CCCTCCACAATTCTAAGCACAA 58.579 45.455 0.00 0.00 0.00 3.33
66 67 3.191371 CCCTCCACAATTCTAAGCACAAC 59.809 47.826 0.00 0.00 0.00 3.32
67 68 3.120199 CCTCCACAATTCTAAGCACAACG 60.120 47.826 0.00 0.00 0.00 4.10
68 69 3.472652 TCCACAATTCTAAGCACAACGT 58.527 40.909 0.00 0.00 0.00 3.99
69 70 3.880490 TCCACAATTCTAAGCACAACGTT 59.120 39.130 0.00 0.00 0.00 3.99
70 71 4.336993 TCCACAATTCTAAGCACAACGTTT 59.663 37.500 0.00 0.00 0.00 3.60
71 72 4.440758 CCACAATTCTAAGCACAACGTTTG 59.559 41.667 0.00 1.95 0.00 2.93
72 73 5.034152 CACAATTCTAAGCACAACGTTTGT 58.966 37.500 0.00 0.00 46.75 2.83
73 74 5.514914 CACAATTCTAAGCACAACGTTTGTT 59.485 36.000 0.00 0.00 43.23 2.83
74 75 6.689241 CACAATTCTAAGCACAACGTTTGTTA 59.311 34.615 0.00 2.77 43.23 2.41
75 76 6.689669 ACAATTCTAAGCACAACGTTTGTTAC 59.310 34.615 0.00 0.00 43.23 2.50
76 77 4.799419 TCTAAGCACAACGTTTGTTACC 57.201 40.909 0.00 0.00 43.23 2.85
77 78 4.444536 TCTAAGCACAACGTTTGTTACCT 58.555 39.130 0.00 0.00 43.23 3.08
78 79 3.685836 AAGCACAACGTTTGTTACCTC 57.314 42.857 0.00 0.00 43.23 3.85
79 80 1.595794 AGCACAACGTTTGTTACCTCG 59.404 47.619 0.00 0.00 43.23 4.63
80 81 1.328374 GCACAACGTTTGTTACCTCGT 59.672 47.619 0.00 0.00 43.23 4.18
81 82 2.598205 GCACAACGTTTGTTACCTCGTC 60.598 50.000 0.00 0.00 43.23 4.20
82 83 1.854126 ACAACGTTTGTTACCTCGTCG 59.146 47.619 0.00 0.00 42.22 5.12
83 84 0.854705 AACGTTTGTTACCTCGTCGC 59.145 50.000 0.00 0.00 36.28 5.19
84 85 0.940991 ACGTTTGTTACCTCGTCGCC 60.941 55.000 0.00 0.00 30.71 5.54
85 86 1.777199 GTTTGTTACCTCGTCGCCG 59.223 57.895 0.00 0.00 0.00 6.46
86 87 2.023223 TTTGTTACCTCGTCGCCGC 61.023 57.895 0.00 0.00 0.00 6.53
87 88 2.696409 TTTGTTACCTCGTCGCCGCA 62.696 55.000 0.00 0.00 0.00 5.69
88 89 2.431260 GTTACCTCGTCGCCGCAA 60.431 61.111 0.00 0.00 0.00 4.85
89 90 2.023223 GTTACCTCGTCGCCGCAAA 61.023 57.895 0.00 0.00 0.00 3.68
90 91 2.023223 TTACCTCGTCGCCGCAAAC 61.023 57.895 0.00 0.00 0.00 2.93
91 92 3.919973 TACCTCGTCGCCGCAAACC 62.920 63.158 0.00 0.00 0.00 3.27
93 94 3.041940 CTCGTCGCCGCAAACCTT 61.042 61.111 0.00 0.00 0.00 3.50
94 95 3.011760 CTCGTCGCCGCAAACCTTC 62.012 63.158 0.00 0.00 0.00 3.46
95 96 4.084888 CGTCGCCGCAAACCTTCC 62.085 66.667 0.00 0.00 0.00 3.46
96 97 2.975799 GTCGCCGCAAACCTTCCA 60.976 61.111 0.00 0.00 0.00 3.53
97 98 2.668212 TCGCCGCAAACCTTCCAG 60.668 61.111 0.00 0.00 0.00 3.86
98 99 2.978010 CGCCGCAAACCTTCCAGT 60.978 61.111 0.00 0.00 0.00 4.00
99 100 2.644992 GCCGCAAACCTTCCAGTG 59.355 61.111 0.00 0.00 0.00 3.66
100 101 1.896660 GCCGCAAACCTTCCAGTGA 60.897 57.895 0.00 0.00 0.00 3.41
101 102 1.949257 CCGCAAACCTTCCAGTGAC 59.051 57.895 0.00 0.00 0.00 3.67
102 103 1.569493 CGCAAACCTTCCAGTGACG 59.431 57.895 0.00 0.00 0.00 4.35
103 104 1.157870 CGCAAACCTTCCAGTGACGT 61.158 55.000 0.00 0.00 0.00 4.34
104 105 1.021968 GCAAACCTTCCAGTGACGTT 58.978 50.000 0.00 0.00 0.00 3.99
105 106 1.268539 GCAAACCTTCCAGTGACGTTG 60.269 52.381 0.00 0.00 0.00 4.10
106 107 1.333619 CAAACCTTCCAGTGACGTTGG 59.666 52.381 0.00 0.00 37.04 3.77
107 108 0.834612 AACCTTCCAGTGACGTTGGA 59.165 50.000 3.27 3.27 42.81 3.53
111 112 2.992124 TTCCAGTGACGTTGGAAGAA 57.008 45.000 14.75 2.21 46.84 2.52
112 113 2.992124 TCCAGTGACGTTGGAAGAAA 57.008 45.000 4.96 0.00 41.61 2.52
113 114 3.485463 TCCAGTGACGTTGGAAGAAAT 57.515 42.857 4.96 0.00 41.61 2.17
114 115 3.138304 TCCAGTGACGTTGGAAGAAATG 58.862 45.455 4.96 0.00 41.61 2.32
115 116 2.878406 CCAGTGACGTTGGAAGAAATGT 59.122 45.455 0.00 0.00 37.96 2.71
116 117 3.303990 CCAGTGACGTTGGAAGAAATGTG 60.304 47.826 0.00 0.00 37.96 3.21
117 118 2.290641 AGTGACGTTGGAAGAAATGTGC 59.709 45.455 0.00 0.00 29.40 4.57
118 119 1.262950 TGACGTTGGAAGAAATGTGCG 59.737 47.619 0.00 0.00 29.40 5.34
119 120 0.591170 ACGTTGGAAGAAATGTGCGG 59.409 50.000 0.00 0.00 0.00 5.69
120 121 0.109781 CGTTGGAAGAAATGTGCGGG 60.110 55.000 0.00 0.00 0.00 6.13
121 122 1.243902 GTTGGAAGAAATGTGCGGGA 58.756 50.000 0.00 0.00 0.00 5.14
122 123 1.611491 GTTGGAAGAAATGTGCGGGAA 59.389 47.619 0.00 0.00 0.00 3.97
123 124 1.988293 TGGAAGAAATGTGCGGGAAA 58.012 45.000 0.00 0.00 0.00 3.13
124 125 1.885887 TGGAAGAAATGTGCGGGAAAG 59.114 47.619 0.00 0.00 0.00 2.62
125 126 1.402852 GGAAGAAATGTGCGGGAAAGC 60.403 52.381 0.00 0.00 37.71 3.51
126 127 0.603065 AAGAAATGTGCGGGAAAGCC 59.397 50.000 0.00 0.00 36.02 4.35
127 128 0.539438 AGAAATGTGCGGGAAAGCCA 60.539 50.000 0.00 0.00 36.02 4.75
128 129 0.388520 GAAATGTGCGGGAAAGCCAC 60.389 55.000 0.00 0.00 36.02 5.01
129 130 1.815817 AAATGTGCGGGAAAGCCACC 61.816 55.000 0.00 0.00 36.02 4.61
130 131 2.713531 AATGTGCGGGAAAGCCACCT 62.714 55.000 0.00 0.00 36.02 4.00
131 132 3.056328 GTGCGGGAAAGCCACCTC 61.056 66.667 0.00 0.00 36.02 3.85
132 133 4.697756 TGCGGGAAAGCCACCTCG 62.698 66.667 0.00 0.00 36.02 4.63
133 134 4.388499 GCGGGAAAGCCACCTCGA 62.388 66.667 0.00 0.00 35.15 4.04
134 135 2.434359 CGGGAAAGCCACCTCGAC 60.434 66.667 0.00 0.00 35.15 4.20
135 136 2.046217 GGGAAAGCCACCTCGACC 60.046 66.667 0.00 0.00 35.15 4.79
136 137 2.046217 GGAAAGCCACCTCGACCC 60.046 66.667 0.00 0.00 0.00 4.46
137 138 2.434359 GAAAGCCACCTCGACCCG 60.434 66.667 0.00 0.00 0.00 5.28
138 139 3.952628 GAAAGCCACCTCGACCCGG 62.953 68.421 0.00 0.00 0.00 5.73
145 146 4.452733 CCTCGACCCGGTGCCTTC 62.453 72.222 0.00 0.00 0.00 3.46
146 147 3.691342 CTCGACCCGGTGCCTTCA 61.691 66.667 0.00 0.00 0.00 3.02
147 148 3.649277 CTCGACCCGGTGCCTTCAG 62.649 68.421 0.00 0.00 0.00 3.02
159 160 1.701704 GCCTTCAGCGGAAACATTTG 58.298 50.000 0.00 0.00 31.35 2.32
160 161 1.269448 GCCTTCAGCGGAAACATTTGA 59.731 47.619 0.00 0.00 31.35 2.69
161 162 2.288152 GCCTTCAGCGGAAACATTTGAA 60.288 45.455 0.00 0.00 31.35 2.69
162 163 3.798548 GCCTTCAGCGGAAACATTTGAAA 60.799 43.478 0.00 0.00 31.35 2.69
163 164 3.735746 CCTTCAGCGGAAACATTTGAAAC 59.264 43.478 0.00 0.00 31.35 2.78
164 165 4.358851 CTTCAGCGGAAACATTTGAAACA 58.641 39.130 0.00 0.00 31.35 2.83
165 166 4.377839 TCAGCGGAAACATTTGAAACAA 57.622 36.364 0.00 0.00 0.00 2.83
166 167 4.942852 TCAGCGGAAACATTTGAAACAAT 58.057 34.783 0.00 0.00 0.00 2.71
167 168 4.744137 TCAGCGGAAACATTTGAAACAATG 59.256 37.500 0.00 0.00 0.00 2.82
168 169 3.494251 AGCGGAAACATTTGAAACAATGC 59.506 39.130 0.00 0.00 0.00 3.56
169 170 3.494251 GCGGAAACATTTGAAACAATGCT 59.506 39.130 0.00 0.00 0.00 3.79
170 171 4.024977 GCGGAAACATTTGAAACAATGCTT 60.025 37.500 0.00 0.00 0.00 3.91
171 172 5.503846 GCGGAAACATTTGAAACAATGCTTT 60.504 36.000 0.00 0.00 0.00 3.51
172 173 6.485393 CGGAAACATTTGAAACAATGCTTTT 58.515 32.000 0.00 0.00 0.00 2.27
173 174 6.966066 CGGAAACATTTGAAACAATGCTTTTT 59.034 30.769 0.00 0.00 0.00 1.94
191 192 3.731652 TTTTAACCTCGTCCTCGTTCA 57.268 42.857 0.00 0.00 38.33 3.18
192 193 3.947910 TTTAACCTCGTCCTCGTTCAT 57.052 42.857 0.00 0.00 38.33 2.57
193 194 2.933495 TAACCTCGTCCTCGTTCATG 57.067 50.000 0.00 0.00 38.33 3.07
194 195 0.966920 AACCTCGTCCTCGTTCATGT 59.033 50.000 0.00 0.00 38.33 3.21
195 196 0.966920 ACCTCGTCCTCGTTCATGTT 59.033 50.000 0.00 0.00 38.33 2.71
196 197 1.067776 ACCTCGTCCTCGTTCATGTTC 60.068 52.381 0.00 0.00 38.33 3.18
197 198 1.202582 CCTCGTCCTCGTTCATGTTCT 59.797 52.381 0.00 0.00 38.33 3.01
198 199 2.254459 CTCGTCCTCGTTCATGTTCTG 58.746 52.381 0.00 0.00 38.33 3.02
199 200 0.716108 CGTCCTCGTTCATGTTCTGC 59.284 55.000 0.00 0.00 0.00 4.26
200 201 1.795768 GTCCTCGTTCATGTTCTGCA 58.204 50.000 0.00 0.00 0.00 4.41
201 202 1.461127 GTCCTCGTTCATGTTCTGCAC 59.539 52.381 0.00 0.00 0.00 4.57
202 203 1.344438 TCCTCGTTCATGTTCTGCACT 59.656 47.619 0.00 0.00 0.00 4.40
203 204 1.728971 CCTCGTTCATGTTCTGCACTC 59.271 52.381 0.00 0.00 0.00 3.51
204 205 1.728971 CTCGTTCATGTTCTGCACTCC 59.271 52.381 0.00 0.00 0.00 3.85
205 206 0.798776 CGTTCATGTTCTGCACTCCC 59.201 55.000 0.00 0.00 0.00 4.30
206 207 1.609061 CGTTCATGTTCTGCACTCCCT 60.609 52.381 0.00 0.00 0.00 4.20
207 208 2.508526 GTTCATGTTCTGCACTCCCTT 58.491 47.619 0.00 0.00 0.00 3.95
208 209 2.479566 TCATGTTCTGCACTCCCTTC 57.520 50.000 0.00 0.00 0.00 3.46
209 210 1.081892 CATGTTCTGCACTCCCTTCG 58.918 55.000 0.00 0.00 0.00 3.79
210 211 0.976641 ATGTTCTGCACTCCCTTCGA 59.023 50.000 0.00 0.00 0.00 3.71
211 212 0.756294 TGTTCTGCACTCCCTTCGAA 59.244 50.000 0.00 0.00 0.00 3.71
212 213 1.149148 GTTCTGCACTCCCTTCGAAC 58.851 55.000 0.00 0.00 0.00 3.95
213 214 1.048601 TTCTGCACTCCCTTCGAACT 58.951 50.000 0.00 0.00 0.00 3.01
214 215 0.318441 TCTGCACTCCCTTCGAACTG 59.682 55.000 0.00 0.00 0.00 3.16
215 216 0.034059 CTGCACTCCCTTCGAACTGT 59.966 55.000 0.00 0.00 0.00 3.55
216 217 1.272490 CTGCACTCCCTTCGAACTGTA 59.728 52.381 0.00 0.00 0.00 2.74
217 218 1.272490 TGCACTCCCTTCGAACTGTAG 59.728 52.381 0.00 0.00 0.00 2.74
218 219 1.544691 GCACTCCCTTCGAACTGTAGA 59.455 52.381 0.00 0.00 0.00 2.59
219 220 2.416162 GCACTCCCTTCGAACTGTAGAG 60.416 54.545 0.00 0.00 0.00 2.43
220 221 2.164624 CACTCCCTTCGAACTGTAGAGG 59.835 54.545 0.00 0.00 0.00 3.69
221 222 1.751924 CTCCCTTCGAACTGTAGAGGG 59.248 57.143 9.47 9.47 36.50 4.30
222 223 1.076677 TCCCTTCGAACTGTAGAGGGT 59.923 52.381 14.33 0.00 36.55 4.34
223 224 1.204941 CCCTTCGAACTGTAGAGGGTG 59.795 57.143 7.79 2.83 32.43 4.61
224 225 1.893801 CCTTCGAACTGTAGAGGGTGT 59.106 52.381 0.00 0.00 0.00 4.16
225 226 2.299297 CCTTCGAACTGTAGAGGGTGTT 59.701 50.000 0.00 0.00 0.00 3.32
226 227 3.508793 CCTTCGAACTGTAGAGGGTGTTA 59.491 47.826 0.00 0.00 0.00 2.41
227 228 4.159879 CCTTCGAACTGTAGAGGGTGTTAT 59.840 45.833 0.00 0.00 0.00 1.89
228 229 5.359009 CCTTCGAACTGTAGAGGGTGTTATA 59.641 44.000 0.00 0.00 0.00 0.98
229 230 6.127535 CCTTCGAACTGTAGAGGGTGTTATAA 60.128 42.308 0.00 0.00 0.00 0.98
230 231 6.839124 TCGAACTGTAGAGGGTGTTATAAA 57.161 37.500 0.00 0.00 0.00 1.40
231 232 7.230849 TCGAACTGTAGAGGGTGTTATAAAA 57.769 36.000 0.00 0.00 0.00 1.52
232 233 7.669427 TCGAACTGTAGAGGGTGTTATAAAAA 58.331 34.615 0.00 0.00 0.00 1.94
233 234 7.816031 TCGAACTGTAGAGGGTGTTATAAAAAG 59.184 37.037 0.00 0.00 0.00 2.27
234 235 7.412672 CGAACTGTAGAGGGTGTTATAAAAAGC 60.413 40.741 0.00 0.00 0.00 3.51
235 236 7.017319 ACTGTAGAGGGTGTTATAAAAAGCT 57.983 36.000 0.00 0.00 0.00 3.74
256 258 0.255890 TAGTGGATGAAAGCTGGGCC 59.744 55.000 0.00 0.00 0.00 5.80
794 880 4.838486 GCGACTCGTCCCGCTCAG 62.838 72.222 0.00 0.00 46.96 3.35
851 943 0.037326 GTGCACTACTACCTGCAGCA 60.037 55.000 10.32 0.00 43.97 4.41
863 955 4.096003 GCAGCACTTCGGCCCCTA 62.096 66.667 0.00 0.00 0.00 3.53
940 1032 0.250338 GAAGGTGGTCAAGCGGAACT 60.250 55.000 0.00 0.00 33.02 3.01
1137 1251 5.038033 GCGTTAGTTAGTGAGGAGAAGATG 58.962 45.833 0.00 0.00 0.00 2.90
1414 1528 6.708502 GCTAGATCATGACAGAGACTACTACA 59.291 42.308 0.00 0.00 0.00 2.74
1415 1529 6.935741 AGATCATGACAGAGACTACTACAC 57.064 41.667 0.00 0.00 0.00 2.90
1428 1542 7.670559 AGAGACTACTACACTATGGTCTTGTTT 59.329 37.037 0.00 0.00 34.73 2.83
1429 1543 7.603651 AGACTACTACACTATGGTCTTGTTTG 58.396 38.462 0.00 0.00 31.14 2.93
1445 1559 1.404035 GTTTGGCGAGAAGGTGTTTGT 59.596 47.619 0.00 0.00 0.00 2.83
1543 1657 6.473455 GGAAATGCCGACTAATTTCAGATTTG 59.527 38.462 9.58 0.00 42.18 2.32
1565 1679 0.821517 TGAGCTAATTTCGCGGAGGA 59.178 50.000 6.13 0.00 0.00 3.71
1606 1720 1.616374 GGCTCAGACCCTGCTACTATC 59.384 57.143 0.00 0.00 0.00 2.08
1611 1725 5.596845 CTCAGACCCTGCTACTATCTTTTC 58.403 45.833 0.00 0.00 0.00 2.29
1655 1769 0.671781 CTCAAAGGTGACCCGAGCTG 60.672 60.000 0.00 0.00 35.12 4.24
1697 1811 1.833630 TGAGAAGGCATTCGTGGAGAT 59.166 47.619 5.31 0.00 40.58 2.75
1730 1844 4.093952 CAAGGAAGCTGCACCGCG 62.094 66.667 0.00 0.00 34.40 6.46
1827 1942 7.339212 AGCATGCTATGAAAATTGGTAACTGTA 59.661 33.333 21.21 0.00 37.61 2.74
1839 1954 2.104144 GTAACTGTATACGGTGCGACG 58.896 52.381 18.03 0.00 35.26 5.12
2011 2270 2.743664 TGAACTTGTTCATCCTGATGCG 59.256 45.455 11.62 0.00 38.65 4.73
2024 2283 2.555325 CCTGATGCGCACATATTGGAAT 59.445 45.455 14.90 0.00 36.35 3.01
2028 2287 6.141560 TGATGCGCACATATTGGAATTAAA 57.858 33.333 14.90 0.00 36.35 1.52
2063 2322 2.101917 AGGCCATTCTGCAATGCATTAC 59.898 45.455 12.53 7.23 38.53 1.89
2116 2392 2.417516 CCGGACGGCCTGACTATG 59.582 66.667 5.33 0.00 0.00 2.23
2201 2502 1.620822 AAGATTTTGCTTGGCTCCGT 58.379 45.000 0.00 0.00 0.00 4.69
2202 2503 2.489938 AGATTTTGCTTGGCTCCGTA 57.510 45.000 0.00 0.00 0.00 4.02
2203 2504 2.790433 AGATTTTGCTTGGCTCCGTAA 58.210 42.857 0.00 0.00 0.00 3.18
2204 2505 2.749621 AGATTTTGCTTGGCTCCGTAAG 59.250 45.455 0.00 0.00 0.00 2.34
2205 2506 1.975660 TTTTGCTTGGCTCCGTAAGT 58.024 45.000 0.00 0.00 0.00 2.24
2206 2507 1.975660 TTTGCTTGGCTCCGTAAGTT 58.024 45.000 0.00 0.00 0.00 2.66
2207 2508 1.234821 TTGCTTGGCTCCGTAAGTTG 58.765 50.000 0.00 0.00 0.00 3.16
2208 2509 0.605319 TGCTTGGCTCCGTAAGTTGG 60.605 55.000 0.00 0.00 0.00 3.77
2209 2510 1.923227 GCTTGGCTCCGTAAGTTGGC 61.923 60.000 0.00 0.00 0.00 4.52
2210 2511 0.605319 CTTGGCTCCGTAAGTTGGCA 60.605 55.000 0.00 0.00 40.26 4.92
2211 2512 0.179015 TTGGCTCCGTAAGTTGGCAA 60.179 50.000 0.00 0.00 45.39 4.52
2212 2513 0.179015 TGGCTCCGTAAGTTGGCAAA 60.179 50.000 0.00 0.00 39.41 3.68
2213 2514 0.240145 GGCTCCGTAAGTTGGCAAAC 59.760 55.000 0.00 0.00 36.47 2.93
2268 2569 5.402630 TGGCCTCTGGTATAGTATGAATGA 58.597 41.667 3.32 0.00 0.00 2.57
2301 2602 4.829064 TTGGTCATTGCTAACACTTGAC 57.171 40.909 0.00 0.00 37.98 3.18
2477 2778 7.038659 CAGTTAATTTTGACCCAGTTTGTTGA 58.961 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.647334 TCAATAACATTTTGCTGGTTCTGA 57.353 33.333 0.00 0.00 0.00 3.27
1 2 8.028354 TGTATCAATAACATTTTGCTGGTTCTG 58.972 33.333 0.00 0.00 0.00 3.02
2 3 8.121305 TGTATCAATAACATTTTGCTGGTTCT 57.879 30.769 0.00 0.00 0.00 3.01
3 4 8.931385 ATGTATCAATAACATTTTGCTGGTTC 57.069 30.769 0.00 0.00 33.83 3.62
4 5 9.369904 GAATGTATCAATAACATTTTGCTGGTT 57.630 29.630 3.23 0.00 45.24 3.67
5 6 7.701924 CGAATGTATCAATAACATTTTGCTGGT 59.298 33.333 3.23 0.00 45.24 4.00
6 7 7.167968 CCGAATGTATCAATAACATTTTGCTGG 59.832 37.037 3.23 0.00 45.24 4.85
7 8 7.701924 ACCGAATGTATCAATAACATTTTGCTG 59.298 33.333 3.23 0.00 45.24 4.41
8 9 7.771183 ACCGAATGTATCAATAACATTTTGCT 58.229 30.769 3.23 0.00 45.24 3.91
9 10 7.097047 CGACCGAATGTATCAATAACATTTTGC 60.097 37.037 3.23 0.00 45.24 3.68
10 11 8.119845 TCGACCGAATGTATCAATAACATTTTG 58.880 33.333 3.23 1.47 45.24 2.44
11 12 8.120465 GTCGACCGAATGTATCAATAACATTTT 58.880 33.333 3.51 0.00 45.24 1.82
12 13 7.494625 AGTCGACCGAATGTATCAATAACATTT 59.505 33.333 13.01 0.00 45.24 2.32
14 15 6.513180 AGTCGACCGAATGTATCAATAACAT 58.487 36.000 13.01 0.00 39.22 2.71
15 16 5.898174 AGTCGACCGAATGTATCAATAACA 58.102 37.500 13.01 0.00 0.00 2.41
16 17 5.401674 GGAGTCGACCGAATGTATCAATAAC 59.598 44.000 13.01 0.00 0.00 1.89
17 18 5.526115 GGAGTCGACCGAATGTATCAATAA 58.474 41.667 13.01 0.00 0.00 1.40
18 19 5.117355 GGAGTCGACCGAATGTATCAATA 57.883 43.478 13.01 0.00 0.00 1.90
19 20 3.978687 GGAGTCGACCGAATGTATCAAT 58.021 45.455 13.01 0.00 0.00 2.57
20 21 3.431922 GGAGTCGACCGAATGTATCAA 57.568 47.619 13.01 0.00 0.00 2.57
31 32 4.131088 GAGGGCACGGAGTCGACC 62.131 72.222 13.01 3.55 41.61 4.79
32 33 4.131088 GGAGGGCACGGAGTCGAC 62.131 72.222 7.70 7.70 41.61 4.20
33 34 4.671590 TGGAGGGCACGGAGTCGA 62.672 66.667 0.00 0.00 41.61 4.20
34 35 4.436998 GTGGAGGGCACGGAGTCG 62.437 72.222 0.00 0.00 41.61 4.18
35 36 2.185310 ATTGTGGAGGGCACGGAGTC 62.185 60.000 0.00 0.00 41.61 3.36
37 38 1.002134 AATTGTGGAGGGCACGGAG 60.002 57.895 0.00 0.00 0.00 4.63
38 39 1.002624 GAATTGTGGAGGGCACGGA 60.003 57.895 0.00 0.00 0.00 4.69
39 40 0.251916 TAGAATTGTGGAGGGCACGG 59.748 55.000 0.00 0.00 0.00 4.94
40 41 2.009774 CTTAGAATTGTGGAGGGCACG 58.990 52.381 0.00 0.00 0.00 5.34
41 42 1.745653 GCTTAGAATTGTGGAGGGCAC 59.254 52.381 0.00 0.00 0.00 5.01
42 43 1.354031 TGCTTAGAATTGTGGAGGGCA 59.646 47.619 0.00 0.00 0.00 5.36
43 44 1.745653 GTGCTTAGAATTGTGGAGGGC 59.254 52.381 0.00 0.00 0.00 5.19
44 45 3.071874 TGTGCTTAGAATTGTGGAGGG 57.928 47.619 0.00 0.00 0.00 4.30
45 46 3.120199 CGTTGTGCTTAGAATTGTGGAGG 60.120 47.826 0.00 0.00 0.00 4.30
46 47 3.498397 ACGTTGTGCTTAGAATTGTGGAG 59.502 43.478 0.00 0.00 0.00 3.86
47 48 3.472652 ACGTTGTGCTTAGAATTGTGGA 58.527 40.909 0.00 0.00 0.00 4.02
48 49 3.896648 ACGTTGTGCTTAGAATTGTGG 57.103 42.857 0.00 0.00 0.00 4.17
49 50 5.034152 ACAAACGTTGTGCTTAGAATTGTG 58.966 37.500 0.00 0.00 43.48 3.33
50 51 5.243426 ACAAACGTTGTGCTTAGAATTGT 57.757 34.783 0.00 0.00 43.48 2.71
51 52 6.141685 GGTAACAAACGTTGTGCTTAGAATTG 59.858 38.462 0.00 0.00 44.59 2.32
52 53 6.038936 AGGTAACAAACGTTGTGCTTAGAATT 59.961 34.615 0.00 0.00 44.59 2.17
53 54 5.529800 AGGTAACAAACGTTGTGCTTAGAAT 59.470 36.000 0.00 0.00 44.59 2.40
54 55 4.877251 AGGTAACAAACGTTGTGCTTAGAA 59.123 37.500 0.00 0.00 44.59 2.10
55 56 4.444536 AGGTAACAAACGTTGTGCTTAGA 58.555 39.130 0.00 0.00 44.59 2.10
56 57 4.607557 CGAGGTAACAAACGTTGTGCTTAG 60.608 45.833 0.00 0.00 44.59 2.18
57 58 3.245754 CGAGGTAACAAACGTTGTGCTTA 59.754 43.478 0.00 2.49 44.59 3.09
58 59 2.031191 CGAGGTAACAAACGTTGTGCTT 59.969 45.455 0.00 3.32 44.59 3.91
59 60 1.595794 CGAGGTAACAAACGTTGTGCT 59.404 47.619 0.00 0.00 44.59 4.40
60 61 1.328374 ACGAGGTAACAAACGTTGTGC 59.672 47.619 0.00 0.00 44.59 4.57
61 62 2.346924 CGACGAGGTAACAAACGTTGTG 60.347 50.000 0.00 5.25 44.59 3.33
63 64 1.396316 GCGACGAGGTAACAAACGTTG 60.396 52.381 0.00 0.00 41.43 4.10
64 65 0.854705 GCGACGAGGTAACAAACGTT 59.145 50.000 0.00 0.00 41.43 3.99
65 66 0.940991 GGCGACGAGGTAACAAACGT 60.941 55.000 0.00 0.00 43.25 3.99
66 67 1.777199 GGCGACGAGGTAACAAACG 59.223 57.895 0.00 0.00 41.41 3.60
79 80 2.966309 CTGGAAGGTTTGCGGCGAC 61.966 63.158 12.98 2.02 0.00 5.19
80 81 2.668212 CTGGAAGGTTTGCGGCGA 60.668 61.111 12.98 0.00 0.00 5.54
81 82 2.978010 ACTGGAAGGTTTGCGGCG 60.978 61.111 0.51 0.51 39.30 6.46
82 83 1.896660 TCACTGGAAGGTTTGCGGC 60.897 57.895 0.00 0.00 39.30 6.53
83 84 1.841663 CGTCACTGGAAGGTTTGCGG 61.842 60.000 0.00 0.00 39.30 5.69
84 85 1.157870 ACGTCACTGGAAGGTTTGCG 61.158 55.000 0.00 0.00 39.30 4.85
85 86 1.021968 AACGTCACTGGAAGGTTTGC 58.978 50.000 0.00 0.00 39.30 3.68
86 87 1.333619 CCAACGTCACTGGAAGGTTTG 59.666 52.381 0.00 0.00 39.30 2.93
87 88 1.210967 TCCAACGTCACTGGAAGGTTT 59.789 47.619 4.96 0.00 40.08 3.27
88 89 0.834612 TCCAACGTCACTGGAAGGTT 59.165 50.000 4.96 0.00 40.08 3.50
89 90 0.834612 TTCCAACGTCACTGGAAGGT 59.165 50.000 14.75 0.00 45.88 3.50
90 91 3.698250 TTCCAACGTCACTGGAAGG 57.302 52.632 14.75 0.00 45.88 3.46
93 94 2.992124 TTTCTTCCAACGTCACTGGA 57.008 45.000 3.27 3.27 41.33 3.86
94 95 2.878406 ACATTTCTTCCAACGTCACTGG 59.122 45.455 0.00 0.00 35.05 4.00
95 96 3.849645 GCACATTTCTTCCAACGTCACTG 60.850 47.826 0.00 0.00 0.00 3.66
96 97 2.290641 GCACATTTCTTCCAACGTCACT 59.709 45.455 0.00 0.00 0.00 3.41
97 98 2.650608 GCACATTTCTTCCAACGTCAC 58.349 47.619 0.00 0.00 0.00 3.67
98 99 1.262950 CGCACATTTCTTCCAACGTCA 59.737 47.619 0.00 0.00 0.00 4.35
99 100 1.399727 CCGCACATTTCTTCCAACGTC 60.400 52.381 0.00 0.00 0.00 4.34
100 101 0.591170 CCGCACATTTCTTCCAACGT 59.409 50.000 0.00 0.00 0.00 3.99
101 102 0.109781 CCCGCACATTTCTTCCAACG 60.110 55.000 0.00 0.00 0.00 4.10
102 103 1.243902 TCCCGCACATTTCTTCCAAC 58.756 50.000 0.00 0.00 0.00 3.77
103 104 1.988293 TTCCCGCACATTTCTTCCAA 58.012 45.000 0.00 0.00 0.00 3.53
104 105 1.885887 CTTTCCCGCACATTTCTTCCA 59.114 47.619 0.00 0.00 0.00 3.53
105 106 1.402852 GCTTTCCCGCACATTTCTTCC 60.403 52.381 0.00 0.00 0.00 3.46
106 107 1.402852 GGCTTTCCCGCACATTTCTTC 60.403 52.381 0.00 0.00 0.00 2.87
107 108 0.603065 GGCTTTCCCGCACATTTCTT 59.397 50.000 0.00 0.00 0.00 2.52
108 109 0.539438 TGGCTTTCCCGCACATTTCT 60.539 50.000 0.00 0.00 35.87 2.52
109 110 0.388520 GTGGCTTTCCCGCACATTTC 60.389 55.000 0.00 0.00 43.83 2.17
110 111 1.665442 GTGGCTTTCCCGCACATTT 59.335 52.632 0.00 0.00 43.83 2.32
111 112 2.275380 GGTGGCTTTCCCGCACATT 61.275 57.895 0.00 0.00 46.29 2.71
112 113 2.676471 GGTGGCTTTCCCGCACAT 60.676 61.111 0.00 0.00 46.29 3.21
113 114 3.842925 GAGGTGGCTTTCCCGCACA 62.843 63.158 0.00 0.00 46.29 4.57
114 115 3.056328 GAGGTGGCTTTCCCGCAC 61.056 66.667 0.00 0.00 46.29 5.34
115 116 4.697756 CGAGGTGGCTTTCCCGCA 62.698 66.667 0.00 0.00 46.29 5.69
116 117 4.388499 TCGAGGTGGCTTTCCCGC 62.388 66.667 0.00 0.00 43.65 6.13
117 118 2.434359 GTCGAGGTGGCTTTCCCG 60.434 66.667 0.00 0.00 35.87 5.14
118 119 2.046217 GGTCGAGGTGGCTTTCCC 60.046 66.667 0.00 0.00 0.00 3.97
119 120 2.046217 GGGTCGAGGTGGCTTTCC 60.046 66.667 0.00 0.00 0.00 3.13
120 121 2.434359 CGGGTCGAGGTGGCTTTC 60.434 66.667 0.00 0.00 0.00 2.62
121 122 4.016706 CCGGGTCGAGGTGGCTTT 62.017 66.667 0.00 0.00 0.00 3.51
128 129 4.452733 GAAGGCACCGGGTCGAGG 62.453 72.222 6.32 0.00 0.00 4.63
129 130 3.649277 CTGAAGGCACCGGGTCGAG 62.649 68.421 6.32 0.00 0.00 4.04
130 131 3.691342 CTGAAGGCACCGGGTCGA 61.691 66.667 6.32 0.00 0.00 4.20
135 136 4.697756 TTCCGCTGAAGGCACCGG 62.698 66.667 0.00 0.00 43.13 5.28
136 137 2.668212 TTTCCGCTGAAGGCACCG 60.668 61.111 0.00 0.00 41.91 4.94
137 138 1.244019 ATGTTTCCGCTGAAGGCACC 61.244 55.000 0.00 0.00 41.91 5.01
138 139 0.598065 AATGTTTCCGCTGAAGGCAC 59.402 50.000 0.00 0.00 41.91 5.01
139 140 1.000385 CAAATGTTTCCGCTGAAGGCA 60.000 47.619 0.00 0.00 41.91 4.75
140 141 1.269448 TCAAATGTTTCCGCTGAAGGC 59.731 47.619 0.00 0.00 37.64 4.35
141 142 3.641437 TTCAAATGTTTCCGCTGAAGG 57.359 42.857 0.00 0.00 0.00 3.46
142 143 4.358851 TGTTTCAAATGTTTCCGCTGAAG 58.641 39.130 0.00 0.00 0.00 3.02
143 144 4.377839 TGTTTCAAATGTTTCCGCTGAA 57.622 36.364 0.00 0.00 0.00 3.02
144 145 4.377839 TTGTTTCAAATGTTTCCGCTGA 57.622 36.364 0.00 0.00 0.00 4.26
145 146 4.608890 GCATTGTTTCAAATGTTTCCGCTG 60.609 41.667 0.00 0.00 39.33 5.18
146 147 3.494251 GCATTGTTTCAAATGTTTCCGCT 59.506 39.130 0.00 0.00 39.33 5.52
147 148 3.494251 AGCATTGTTTCAAATGTTTCCGC 59.506 39.130 0.00 0.00 39.33 5.54
148 149 5.655893 AAGCATTGTTTCAAATGTTTCCG 57.344 34.783 0.00 0.00 36.58 4.30
170 171 4.057406 TGAACGAGGACGAGGTTAAAAA 57.943 40.909 0.00 0.00 42.66 1.94
171 172 3.731652 TGAACGAGGACGAGGTTAAAA 57.268 42.857 0.00 0.00 42.66 1.52
172 173 3.006110 ACATGAACGAGGACGAGGTTAAA 59.994 43.478 0.00 0.00 42.66 1.52
173 174 2.559668 ACATGAACGAGGACGAGGTTAA 59.440 45.455 0.00 0.00 42.66 2.01
174 175 2.165167 ACATGAACGAGGACGAGGTTA 58.835 47.619 0.00 0.00 42.66 2.85
175 176 0.966920 ACATGAACGAGGACGAGGTT 59.033 50.000 0.00 0.00 42.66 3.50
176 177 0.966920 AACATGAACGAGGACGAGGT 59.033 50.000 0.00 0.00 42.66 3.85
177 178 1.202582 AGAACATGAACGAGGACGAGG 59.797 52.381 0.00 0.00 42.66 4.63
178 179 2.254459 CAGAACATGAACGAGGACGAG 58.746 52.381 0.00 0.00 42.66 4.18
179 180 1.668919 GCAGAACATGAACGAGGACGA 60.669 52.381 0.00 0.00 42.66 4.20
180 181 0.716108 GCAGAACATGAACGAGGACG 59.284 55.000 0.00 0.00 45.75 4.79
181 182 1.461127 GTGCAGAACATGAACGAGGAC 59.539 52.381 0.00 0.00 0.00 3.85
182 183 1.344438 AGTGCAGAACATGAACGAGGA 59.656 47.619 0.00 0.00 43.06 3.71
183 184 1.728971 GAGTGCAGAACATGAACGAGG 59.271 52.381 0.00 0.00 43.06 4.63
184 185 1.728971 GGAGTGCAGAACATGAACGAG 59.271 52.381 0.00 0.00 43.06 4.18
185 186 1.608025 GGGAGTGCAGAACATGAACGA 60.608 52.381 0.00 0.00 43.06 3.85
186 187 0.798776 GGGAGTGCAGAACATGAACG 59.201 55.000 0.00 0.00 43.06 3.95
187 188 2.191128 AGGGAGTGCAGAACATGAAC 57.809 50.000 0.00 0.00 37.79 3.18
188 189 2.783135 GAAGGGAGTGCAGAACATGAA 58.217 47.619 0.00 0.00 0.00 2.57
189 190 1.338105 CGAAGGGAGTGCAGAACATGA 60.338 52.381 0.00 0.00 0.00 3.07
190 191 1.081892 CGAAGGGAGTGCAGAACATG 58.918 55.000 0.00 0.00 0.00 3.21
191 192 0.976641 TCGAAGGGAGTGCAGAACAT 59.023 50.000 0.00 0.00 0.00 2.71
192 193 0.756294 TTCGAAGGGAGTGCAGAACA 59.244 50.000 0.00 0.00 0.00 3.18
193 194 1.149148 GTTCGAAGGGAGTGCAGAAC 58.851 55.000 0.00 0.00 0.00 3.01
194 195 1.048601 AGTTCGAAGGGAGTGCAGAA 58.951 50.000 0.00 0.00 0.00 3.02
195 196 0.318441 CAGTTCGAAGGGAGTGCAGA 59.682 55.000 0.00 0.00 0.00 4.26
196 197 0.034059 ACAGTTCGAAGGGAGTGCAG 59.966 55.000 0.00 0.00 0.00 4.41
197 198 1.272490 CTACAGTTCGAAGGGAGTGCA 59.728 52.381 0.00 0.00 0.00 4.57
198 199 1.544691 TCTACAGTTCGAAGGGAGTGC 59.455 52.381 0.00 0.00 0.00 4.40
199 200 2.164624 CCTCTACAGTTCGAAGGGAGTG 59.835 54.545 0.00 1.08 0.00 3.51
200 201 2.448453 CCTCTACAGTTCGAAGGGAGT 58.552 52.381 0.00 0.00 0.00 3.85
201 202 1.751924 CCCTCTACAGTTCGAAGGGAG 59.248 57.143 10.10 6.46 37.29 4.30
202 203 1.076677 ACCCTCTACAGTTCGAAGGGA 59.923 52.381 20.48 2.50 38.42 4.20
203 204 1.204941 CACCCTCTACAGTTCGAAGGG 59.795 57.143 13.48 13.48 40.72 3.95
204 205 1.893801 ACACCCTCTACAGTTCGAAGG 59.106 52.381 0.00 0.00 0.00 3.46
205 206 3.662247 AACACCCTCTACAGTTCGAAG 57.338 47.619 0.00 0.00 0.00 3.79
206 207 6.839124 TTATAACACCCTCTACAGTTCGAA 57.161 37.500 0.00 0.00 0.00 3.71
207 208 6.839124 TTTATAACACCCTCTACAGTTCGA 57.161 37.500 0.00 0.00 0.00 3.71
208 209 7.412672 GCTTTTTATAACACCCTCTACAGTTCG 60.413 40.741 0.00 0.00 0.00 3.95
209 210 7.606839 AGCTTTTTATAACACCCTCTACAGTTC 59.393 37.037 0.00 0.00 0.00 3.01
210 211 7.390718 CAGCTTTTTATAACACCCTCTACAGTT 59.609 37.037 0.00 0.00 0.00 3.16
211 212 6.879458 CAGCTTTTTATAACACCCTCTACAGT 59.121 38.462 0.00 0.00 0.00 3.55
212 213 6.879458 ACAGCTTTTTATAACACCCTCTACAG 59.121 38.462 0.00 0.00 0.00 2.74
213 214 6.775708 ACAGCTTTTTATAACACCCTCTACA 58.224 36.000 0.00 0.00 0.00 2.74
214 215 8.039538 ACTACAGCTTTTTATAACACCCTCTAC 58.960 37.037 0.00 0.00 0.00 2.59
215 216 8.038944 CACTACAGCTTTTTATAACACCCTCTA 58.961 37.037 0.00 0.00 0.00 2.43
216 217 6.879458 CACTACAGCTTTTTATAACACCCTCT 59.121 38.462 0.00 0.00 0.00 3.69
217 218 6.093633 CCACTACAGCTTTTTATAACACCCTC 59.906 42.308 0.00 0.00 0.00 4.30
218 219 5.944007 CCACTACAGCTTTTTATAACACCCT 59.056 40.000 0.00 0.00 0.00 4.34
219 220 5.941647 TCCACTACAGCTTTTTATAACACCC 59.058 40.000 0.00 0.00 0.00 4.61
220 221 7.335924 TCATCCACTACAGCTTTTTATAACACC 59.664 37.037 0.00 0.00 0.00 4.16
221 222 8.263940 TCATCCACTACAGCTTTTTATAACAC 57.736 34.615 0.00 0.00 0.00 3.32
222 223 8.856153 TTCATCCACTACAGCTTTTTATAACA 57.144 30.769 0.00 0.00 0.00 2.41
223 224 9.774742 CTTTCATCCACTACAGCTTTTTATAAC 57.225 33.333 0.00 0.00 0.00 1.89
224 225 8.458843 GCTTTCATCCACTACAGCTTTTTATAA 58.541 33.333 0.00 0.00 0.00 0.98
225 226 7.829211 AGCTTTCATCCACTACAGCTTTTTATA 59.171 33.333 0.00 0.00 33.79 0.98
226 227 6.660949 AGCTTTCATCCACTACAGCTTTTTAT 59.339 34.615 0.00 0.00 33.79 1.40
227 228 6.003950 AGCTTTCATCCACTACAGCTTTTTA 58.996 36.000 0.00 0.00 33.79 1.52
228 229 4.829492 AGCTTTCATCCACTACAGCTTTTT 59.171 37.500 0.00 0.00 33.79 1.94
229 230 4.217118 CAGCTTTCATCCACTACAGCTTTT 59.783 41.667 0.00 0.00 35.39 2.27
230 231 3.755378 CAGCTTTCATCCACTACAGCTTT 59.245 43.478 0.00 0.00 35.39 3.51
231 232 3.341823 CAGCTTTCATCCACTACAGCTT 58.658 45.455 0.00 0.00 35.39 3.74
232 233 2.355513 CCAGCTTTCATCCACTACAGCT 60.356 50.000 0.00 0.00 38.13 4.24
233 234 2.012673 CCAGCTTTCATCCACTACAGC 58.987 52.381 0.00 0.00 0.00 4.40
234 235 2.636830 CCCAGCTTTCATCCACTACAG 58.363 52.381 0.00 0.00 0.00 2.74
235 236 1.340017 GCCCAGCTTTCATCCACTACA 60.340 52.381 0.00 0.00 0.00 2.74
256 258 1.294659 GCCCAACTCTTGTGAGCGAG 61.295 60.000 0.00 0.00 43.85 5.03
438 495 0.031716 TGAGAGGTGATGGGAGAGGG 60.032 60.000 0.00 0.00 0.00 4.30
794 880 2.980233 AGCGGAACTGCTTGGCAC 60.980 61.111 1.99 0.00 44.46 5.01
851 943 0.901580 TTTCTCGTAGGGGCCGAAGT 60.902 55.000 0.00 0.00 33.34 3.01
863 955 4.401519 TGAATACTCGGAGGAATTTCTCGT 59.598 41.667 10.23 3.14 34.74 4.18
940 1032 1.311859 CACTCCTGCAGCAACTTCAA 58.688 50.000 8.66 0.00 0.00 2.69
998 1090 1.746861 CGGTGAGCATCCTTGGCATAA 60.747 52.381 0.00 0.00 0.00 1.90
1027 1119 1.312371 ACCATCGCCCGGATTTGTTG 61.312 55.000 0.73 0.00 31.28 3.33
1158 1272 2.031870 GACCACCTTGTTGCCTTCTTT 58.968 47.619 0.00 0.00 0.00 2.52
1193 1307 0.599558 CCACTTGGACACAGCAATGG 59.400 55.000 0.00 0.00 37.39 3.16
1414 1528 2.301870 TCTCGCCAAACAAGACCATAGT 59.698 45.455 0.00 0.00 0.00 2.12
1415 1529 2.972625 TCTCGCCAAACAAGACCATAG 58.027 47.619 0.00 0.00 0.00 2.23
1428 1542 0.817634 CCACAAACACCTTCTCGCCA 60.818 55.000 0.00 0.00 0.00 5.69
1429 1543 0.534203 TCCACAAACACCTTCTCGCC 60.534 55.000 0.00 0.00 0.00 5.54
1445 1559 4.079844 TGTGAGGGCATATGAATTTCTCCA 60.080 41.667 6.97 3.55 0.00 3.86
1543 1657 2.731976 CCTCCGCGAAATTAGCTCATAC 59.268 50.000 8.23 0.00 0.00 2.39
1565 1679 1.909986 GGACCTCCAGGCTAAAGTTCT 59.090 52.381 0.00 0.00 39.32 3.01
1611 1725 6.143919 GCAATCCGTTTTCCTTAAGAAACTTG 59.856 38.462 3.36 9.20 44.20 3.16
1655 1769 5.350365 TCAGTGAACTTGGCGATTGTATAAC 59.650 40.000 0.00 0.00 0.00 1.89
1697 1811 2.989909 CCTTGTGAGGACATATGCACA 58.010 47.619 1.58 6.22 46.74 4.57
1730 1844 2.012673 CCACATAGTCTTCAGCAAGGC 58.987 52.381 0.00 0.00 34.05 4.35
1753 1867 1.293498 GCACTTCTCCTCGGCAAGA 59.707 57.895 0.00 0.00 0.00 3.02
1827 1942 0.458669 AGGAATTCGTCGCACCGTAT 59.541 50.000 0.00 0.00 0.00 3.06
1839 1954 7.121315 AGGCAAAGTACACAGAAATAGGAATTC 59.879 37.037 0.00 0.00 0.00 2.17
2028 2287 2.489938 TGGCCTATTCTCGCACTTTT 57.510 45.000 3.32 0.00 0.00 2.27
2041 2300 2.076207 ATGCATTGCAGAATGGCCTA 57.924 45.000 17.52 0.00 43.65 3.93
2063 2322 6.567050 ACAATGTAAGCCAGCATAGAAATTG 58.433 36.000 0.00 0.00 0.00 2.32
2104 2380 0.319728 CTGGGATCATAGTCAGGCCG 59.680 60.000 0.00 0.00 0.00 6.13
2116 2392 3.695830 TTACACCACAGAACTGGGATC 57.304 47.619 5.58 0.00 35.61 3.36
2172 2448 4.094590 CCAAGCAAAATCTTTGTGTTGCAA 59.905 37.500 9.62 0.00 46.92 4.08
2209 2510 4.318546 GCAAGAGCATTGAAGCAAAGTTTG 60.319 41.667 11.41 11.41 41.58 2.93
2210 2511 3.805971 GCAAGAGCATTGAAGCAAAGTTT 59.194 39.130 5.91 0.00 41.58 2.66
2211 2512 3.387397 GCAAGAGCATTGAAGCAAAGTT 58.613 40.909 5.91 0.00 41.58 2.66
2212 2513 2.288640 GGCAAGAGCATTGAAGCAAAGT 60.289 45.455 5.91 0.00 44.61 2.66
2213 2514 2.029290 AGGCAAGAGCATTGAAGCAAAG 60.029 45.455 5.91 0.00 44.61 2.77
2214 2515 1.965643 AGGCAAGAGCATTGAAGCAAA 59.034 42.857 5.91 0.00 44.61 3.68
2215 2516 1.624336 AGGCAAGAGCATTGAAGCAA 58.376 45.000 5.91 0.00 44.61 3.91
2216 2517 2.495155 TAGGCAAGAGCATTGAAGCA 57.505 45.000 5.91 0.00 44.61 3.91
2217 2518 3.012518 TCTTAGGCAAGAGCATTGAAGC 58.987 45.455 5.91 0.00 44.61 3.86
2218 2519 4.940046 TCTTCTTAGGCAAGAGCATTGAAG 59.060 41.667 5.91 9.54 41.75 3.02
2219 2520 4.910195 TCTTCTTAGGCAAGAGCATTGAA 58.090 39.130 5.91 0.00 41.75 2.69
2220 2521 4.558226 TCTTCTTAGGCAAGAGCATTGA 57.442 40.909 5.91 0.00 41.75 2.57
2221 2522 4.880120 TCATCTTCTTAGGCAAGAGCATTG 59.120 41.667 0.00 0.00 41.75 2.82
2222 2523 5.108187 TCATCTTCTTAGGCAAGAGCATT 57.892 39.130 0.00 0.00 41.75 3.56
2223 2524 4.767578 TCATCTTCTTAGGCAAGAGCAT 57.232 40.909 0.00 0.00 41.75 3.79
2268 2569 2.756760 CAATGACCAAACTAGCATGCCT 59.243 45.455 15.66 4.37 0.00 4.75
2331 2632 9.676861 ATTTTATGATGACATGGACATATCGAT 57.323 29.630 2.16 2.16 37.87 3.59
2332 2633 9.506018 AATTTTATGATGACATGGACATATCGA 57.494 29.630 0.00 0.00 37.87 3.59
2436 2737 1.207791 ACTGCCTCCTCGGATTGATT 58.792 50.000 0.00 0.00 33.16 2.57
2477 2778 6.879458 AGCTCACCGAAATTAGAACAAGTAAT 59.121 34.615 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.