Multiple sequence alignment - TraesCS2A01G110700

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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 TraesCS2A01G110700 chr2A 100.000 2214 0 0 754 2967 62296357 62298570 0.000000e+00 4089.0
1 TraesCS2A01G110700 chr2A 100.000 420 0 0 1 420 62295604 62296023 0.000000e+00 776.0
2 TraesCS2A01G110700 chr2A 87.786 131 12 4 1217 1346 601333356 601333229 1.840000e-32 150.0
3 TraesCS2A01G110700 chr2B 88.222 2284 119 67 754 2967 97187369 97189572 0.000000e+00 2590.0
4 TraesCS2A01G110700 chr2B 89.627 241 16 6 187 420 97186694 97186932 6.220000e-77 298.0
5 TraesCS2A01G110700 chr2B 89.623 106 9 2 1217 1322 515118557 515118454 1.860000e-27 134.0
6 TraesCS2A01G110700 chr2D 90.954 1404 75 25 789 2177 61977160 61978526 0.000000e+00 1842.0
7 TraesCS2A01G110700 chr2D 93.703 794 31 7 2190 2967 61978510 61979300 0.000000e+00 1171.0
8 TraesCS2A01G110700 chr2D 95.408 196 9 0 225 420 61976840 61977035 2.220000e-81 313.0
9 TraesCS2A01G110700 chr4A 89.824 737 51 8 1460 2177 651342986 651342255 0.000000e+00 924.0
10 TraesCS2A01G110700 chr4A 79.573 328 45 17 880 1194 651343394 651343076 6.440000e-52 215.0
11 TraesCS2A01G110700 chr7D 79.630 756 96 29 1431 2154 537679902 537680631 9.560000e-135 490.0
12 TraesCS2A01G110700 chr7A 86.040 351 23 11 1649 1979 43043830 43043486 1.310000e-93 353.0
13 TraesCS2A01G110700 chr7A 80.510 431 44 18 1744 2156 619038892 619039300 8.040000e-76 294.0
14 TraesCS2A01G110700 chr7A 86.792 106 12 2 1217 1322 303630255 303630152 1.870000e-22 117.0
15 TraesCS2A01G110700 chr7A 88.158 76 9 0 1548 1623 43043906 43043831 1.130000e-14 91.6
16 TraesCS2A01G110700 chr7B 79.245 530 62 24 1484 1979 580182454 580182969 2.850000e-85 326.0
17 TraesCS2A01G110700 chr4B 87.023 131 15 2 1216 1346 134121285 134121157 2.380000e-31 147.0
18 TraesCS2A01G110700 chr4B 86.916 107 10 4 1220 1325 22850687 22850790 1.870000e-22 117.0
19 TraesCS2A01G110700 chr6D 85.496 131 16 3 1217 1346 229422030 229421902 1.860000e-27 134.0
20 TraesCS2A01G110700 chr6B 86.792 106 12 2 1217 1322 390847983 390848086 1.870000e-22 117.0


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 TraesCS2A01G110700 chr2A 62295604 62298570 2966 False 2432.500000 4089 100.0000 1 2967 2 chr2A.!!$F1 2966
1 TraesCS2A01G110700 chr2B 97186694 97189572 2878 False 1444.000000 2590 88.9245 187 2967 2 chr2B.!!$F1 2780
2 TraesCS2A01G110700 chr2D 61976840 61979300 2460 False 1108.666667 1842 93.3550 225 2967 3 chr2D.!!$F1 2742
3 TraesCS2A01G110700 chr4A 651342255 651343394 1139 True 569.500000 924 84.6985 880 2177 2 chr4A.!!$R1 1297
4 TraesCS2A01G110700 chr7D 537679902 537680631 729 False 490.000000 490 79.6300 1431 2154 1 chr7D.!!$F1 723
5 TraesCS2A01G110700 chr7B 580182454 580182969 515 False 326.000000 326 79.2450 1484 1979 1 chr7B.!!$F1 495

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
941 1061 0.036022 GGGTTGCTGTGCTCTCTCTT 59.964 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2446 1.304381 CCCCACCCACACAGGATTG 60.304 63.158 0.0 0.0 41.22 2.67 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
29 30 8.634335 TTGTTCAAGATTTCACAGGAATATCA 57.366 30.769 0.00 0.00 31.93 2.15
30 31 8.044060 TGTTCAAGATTTCACAGGAATATCAC 57.956 34.615 0.00 0.00 31.93 3.06
31 32 7.121168 TGTTCAAGATTTCACAGGAATATCACC 59.879 37.037 0.00 0.00 31.93 4.02
32 33 6.962182 TCAAGATTTCACAGGAATATCACCT 58.038 36.000 0.00 0.00 38.40 4.00
45 46 8.692710 CAGGAATATCACCTGTTAAGTACTACA 58.307 37.037 16.25 0.00 46.71 2.74
46 47 9.435570 AGGAATATCACCTGTTAAGTACTACAT 57.564 33.333 0.00 0.00 36.30 2.29
49 50 9.832445 AATATCACCTGTTAAGTACTACATTGG 57.168 33.333 0.00 0.00 0.00 3.16
50 51 6.045072 TCACCTGTTAAGTACTACATTGGG 57.955 41.667 0.00 0.00 0.00 4.12
51 52 5.781306 TCACCTGTTAAGTACTACATTGGGA 59.219 40.000 0.00 0.00 0.00 4.37
52 53 5.873164 CACCTGTTAAGTACTACATTGGGAC 59.127 44.000 0.00 0.00 0.00 4.46
53 54 5.046087 ACCTGTTAAGTACTACATTGGGACC 60.046 44.000 0.00 0.00 0.00 4.46
54 55 5.189145 CCTGTTAAGTACTACATTGGGACCT 59.811 44.000 0.00 0.00 0.00 3.85
55 56 6.381994 CCTGTTAAGTACTACATTGGGACCTA 59.618 42.308 0.00 0.00 0.00 3.08
56 57 7.174107 TGTTAAGTACTACATTGGGACCTAC 57.826 40.000 0.00 0.00 0.00 3.18
57 58 6.725369 TGTTAAGTACTACATTGGGACCTACA 59.275 38.462 0.00 0.00 0.00 2.74
58 59 7.235193 TGTTAAGTACTACATTGGGACCTACAA 59.765 37.037 0.00 0.00 0.00 2.41
59 60 6.886178 AAGTACTACATTGGGACCTACAAT 57.114 37.500 0.00 0.00 39.00 2.71
60 61 7.983166 AAGTACTACATTGGGACCTACAATA 57.017 36.000 0.00 0.00 36.47 1.90
61 62 7.983166 AGTACTACATTGGGACCTACAATAA 57.017 36.000 0.00 0.00 36.47 1.40
62 63 8.562949 AGTACTACATTGGGACCTACAATAAT 57.437 34.615 0.00 0.00 36.47 1.28
63 64 8.648693 AGTACTACATTGGGACCTACAATAATC 58.351 37.037 0.00 0.00 36.47 1.75
64 65 6.522054 ACTACATTGGGACCTACAATAATCG 58.478 40.000 0.00 0.00 36.47 3.34
65 66 5.367945 ACATTGGGACCTACAATAATCGT 57.632 39.130 0.00 0.00 36.47 3.73
66 67 6.488769 ACATTGGGACCTACAATAATCGTA 57.511 37.500 0.00 0.00 36.47 3.43
67 68 6.285990 ACATTGGGACCTACAATAATCGTAC 58.714 40.000 0.00 0.00 36.47 3.67
68 69 4.572985 TGGGACCTACAATAATCGTACG 57.427 45.455 9.53 9.53 0.00 3.67
69 70 3.953612 TGGGACCTACAATAATCGTACGT 59.046 43.478 16.05 0.00 0.00 3.57
70 71 5.129634 TGGGACCTACAATAATCGTACGTA 58.870 41.667 16.05 1.13 0.00 3.57
71 72 5.769662 TGGGACCTACAATAATCGTACGTAT 59.230 40.000 16.05 7.93 0.00 3.06
72 73 6.939730 TGGGACCTACAATAATCGTACGTATA 59.060 38.462 16.05 9.95 0.00 1.47
73 74 7.446931 TGGGACCTACAATAATCGTACGTATAA 59.553 37.037 16.05 0.00 0.00 0.98
74 75 8.462016 GGGACCTACAATAATCGTACGTATAAT 58.538 37.037 16.05 0.00 0.00 1.28
75 76 9.282247 GGACCTACAATAATCGTACGTATAATG 57.718 37.037 16.05 14.13 0.00 1.90
76 77 8.679288 ACCTACAATAATCGTACGTATAATGC 57.321 34.615 16.05 0.00 0.00 3.56
77 78 7.756722 ACCTACAATAATCGTACGTATAATGCC 59.243 37.037 16.05 0.00 0.00 4.40
78 79 7.972277 CCTACAATAATCGTACGTATAATGCCT 59.028 37.037 16.05 1.90 0.00 4.75
79 80 7.576750 ACAATAATCGTACGTATAATGCCTG 57.423 36.000 16.05 3.77 0.00 4.85
80 81 6.588756 ACAATAATCGTACGTATAATGCCTGG 59.411 38.462 16.05 0.00 0.00 4.45
81 82 4.859304 AATCGTACGTATAATGCCTGGA 57.141 40.909 16.05 0.00 0.00 3.86
82 83 4.859304 ATCGTACGTATAATGCCTGGAA 57.141 40.909 16.05 0.00 0.00 3.53
83 84 4.859304 TCGTACGTATAATGCCTGGAAT 57.141 40.909 16.05 0.00 0.00 3.01
84 85 4.552355 TCGTACGTATAATGCCTGGAATG 58.448 43.478 16.05 0.00 0.00 2.67
85 86 4.038282 TCGTACGTATAATGCCTGGAATGT 59.962 41.667 16.05 0.00 0.00 2.71
86 87 4.748102 CGTACGTATAATGCCTGGAATGTT 59.252 41.667 7.22 0.00 0.00 2.71
87 88 5.333035 CGTACGTATAATGCCTGGAATGTTG 60.333 44.000 7.22 0.00 0.00 3.33
88 89 4.776349 ACGTATAATGCCTGGAATGTTGA 58.224 39.130 0.00 0.00 0.00 3.18
89 90 4.816385 ACGTATAATGCCTGGAATGTTGAG 59.184 41.667 0.00 0.00 0.00 3.02
90 91 5.056480 CGTATAATGCCTGGAATGTTGAGA 58.944 41.667 0.00 0.00 0.00 3.27
91 92 5.050091 CGTATAATGCCTGGAATGTTGAGAC 60.050 44.000 0.00 0.00 0.00 3.36
92 93 3.446442 AATGCCTGGAATGTTGAGACT 57.554 42.857 0.00 0.00 0.00 3.24
93 94 4.574674 AATGCCTGGAATGTTGAGACTA 57.425 40.909 0.00 0.00 0.00 2.59
94 95 4.574674 ATGCCTGGAATGTTGAGACTAA 57.425 40.909 0.00 0.00 0.00 2.24
95 96 4.574674 TGCCTGGAATGTTGAGACTAAT 57.425 40.909 0.00 0.00 0.00 1.73
96 97 4.517285 TGCCTGGAATGTTGAGACTAATC 58.483 43.478 0.00 0.00 0.00 1.75
97 98 3.557595 GCCTGGAATGTTGAGACTAATCG 59.442 47.826 0.00 0.00 0.00 3.34
98 99 4.759782 CCTGGAATGTTGAGACTAATCGT 58.240 43.478 0.00 0.00 0.00 3.73
99 100 4.568359 CCTGGAATGTTGAGACTAATCGTG 59.432 45.833 0.00 0.00 0.00 4.35
100 101 5.400066 TGGAATGTTGAGACTAATCGTGA 57.600 39.130 0.00 0.00 0.00 4.35
101 102 5.977635 TGGAATGTTGAGACTAATCGTGAT 58.022 37.500 0.00 0.00 0.00 3.06
102 103 6.406370 TGGAATGTTGAGACTAATCGTGATT 58.594 36.000 0.22 0.22 34.93 2.57
103 104 6.878923 TGGAATGTTGAGACTAATCGTGATTT 59.121 34.615 0.00 0.00 32.50 2.17
104 105 7.148423 TGGAATGTTGAGACTAATCGTGATTTG 60.148 37.037 0.00 1.61 32.50 2.32
105 106 6.668541 ATGTTGAGACTAATCGTGATTTGG 57.331 37.500 0.00 0.00 32.50 3.28
106 107 5.547465 TGTTGAGACTAATCGTGATTTGGT 58.453 37.500 0.00 1.19 32.50 3.67
107 108 5.995282 TGTTGAGACTAATCGTGATTTGGTT 59.005 36.000 0.00 0.00 32.50 3.67
108 109 6.485313 TGTTGAGACTAATCGTGATTTGGTTT 59.515 34.615 0.00 0.00 32.50 3.27
109 110 6.480524 TGAGACTAATCGTGATTTGGTTTG 57.519 37.500 0.00 0.00 32.50 2.93
110 111 6.227522 TGAGACTAATCGTGATTTGGTTTGA 58.772 36.000 0.00 0.00 32.50 2.69
111 112 6.147164 TGAGACTAATCGTGATTTGGTTTGAC 59.853 38.462 0.00 0.00 32.50 3.18
112 113 5.995282 AGACTAATCGTGATTTGGTTTGACA 59.005 36.000 0.00 0.00 32.50 3.58
113 114 6.147821 AGACTAATCGTGATTTGGTTTGACAG 59.852 38.462 0.00 0.00 32.50 3.51
114 115 5.995282 ACTAATCGTGATTTGGTTTGACAGA 59.005 36.000 0.00 0.00 32.50 3.41
115 116 5.362556 AATCGTGATTTGGTTTGACAGAG 57.637 39.130 0.00 0.00 0.00 3.35
116 117 3.804036 TCGTGATTTGGTTTGACAGAGT 58.196 40.909 0.00 0.00 0.00 3.24
117 118 4.196193 TCGTGATTTGGTTTGACAGAGTT 58.804 39.130 0.00 0.00 0.00 3.01
118 119 4.272504 TCGTGATTTGGTTTGACAGAGTTC 59.727 41.667 0.00 0.00 0.00 3.01
119 120 4.273480 CGTGATTTGGTTTGACAGAGTTCT 59.727 41.667 0.00 0.00 0.00 3.01
130 131 2.077413 CAGAGTTCTGTGACCTGAGC 57.923 55.000 0.91 0.00 39.09 4.26
131 132 1.342496 CAGAGTTCTGTGACCTGAGCA 59.658 52.381 0.91 0.00 39.09 4.26
132 133 1.342819 AGAGTTCTGTGACCTGAGCAC 59.657 52.381 0.00 0.00 36.81 4.40
133 134 1.069204 GAGTTCTGTGACCTGAGCACA 59.931 52.381 0.00 0.00 43.41 4.57
134 135 1.202580 AGTTCTGTGACCTGAGCACAC 60.203 52.381 0.00 0.00 41.00 3.82
135 136 0.829990 TTCTGTGACCTGAGCACACA 59.170 50.000 8.93 8.93 41.00 3.72
136 137 1.051008 TCTGTGACCTGAGCACACAT 58.949 50.000 9.52 0.00 42.30 3.21
137 138 1.417517 TCTGTGACCTGAGCACACATT 59.582 47.619 9.52 0.00 42.30 2.71
138 139 2.158769 TCTGTGACCTGAGCACACATTT 60.159 45.455 9.52 0.00 42.30 2.32
139 140 1.948834 TGTGACCTGAGCACACATTTG 59.051 47.619 6.00 0.00 41.00 2.32
140 141 1.267806 GTGACCTGAGCACACATTTGG 59.732 52.381 0.00 0.00 36.31 3.28
141 142 1.142667 TGACCTGAGCACACATTTGGA 59.857 47.619 0.00 0.00 0.00 3.53
142 143 2.229792 GACCTGAGCACACATTTGGAA 58.770 47.619 0.00 0.00 0.00 3.53
143 144 2.622942 GACCTGAGCACACATTTGGAAA 59.377 45.455 0.00 0.00 0.00 3.13
144 145 3.030291 ACCTGAGCACACATTTGGAAAA 58.970 40.909 0.00 0.00 0.00 2.29
145 146 3.068590 ACCTGAGCACACATTTGGAAAAG 59.931 43.478 0.00 0.00 0.00 2.27
146 147 3.553508 CCTGAGCACACATTTGGAAAAGG 60.554 47.826 0.00 0.00 0.00 3.11
147 148 3.295093 TGAGCACACATTTGGAAAAGGA 58.705 40.909 0.00 0.00 0.00 3.36
148 149 3.703556 TGAGCACACATTTGGAAAAGGAA 59.296 39.130 0.00 0.00 0.00 3.36
149 150 4.161189 TGAGCACACATTTGGAAAAGGAAA 59.839 37.500 0.00 0.00 0.00 3.13
150 151 4.696455 AGCACACATTTGGAAAAGGAAAG 58.304 39.130 0.00 0.00 0.00 2.62
151 152 3.809279 GCACACATTTGGAAAAGGAAAGG 59.191 43.478 0.00 0.00 0.00 3.11
152 153 4.379652 CACACATTTGGAAAAGGAAAGGG 58.620 43.478 0.00 0.00 0.00 3.95
153 154 4.100808 CACACATTTGGAAAAGGAAAGGGA 59.899 41.667 0.00 0.00 0.00 4.20
154 155 4.719273 ACACATTTGGAAAAGGAAAGGGAA 59.281 37.500 0.00 0.00 0.00 3.97
155 156 5.163311 ACACATTTGGAAAAGGAAAGGGAAG 60.163 40.000 0.00 0.00 0.00 3.46
156 157 5.070313 CACATTTGGAAAAGGAAAGGGAAGA 59.930 40.000 0.00 0.00 0.00 2.87
157 158 5.665360 ACATTTGGAAAAGGAAAGGGAAGAA 59.335 36.000 0.00 0.00 0.00 2.52
158 159 5.607939 TTTGGAAAAGGAAAGGGAAGAAC 57.392 39.130 0.00 0.00 0.00 3.01
159 160 3.219281 TGGAAAAGGAAAGGGAAGAACG 58.781 45.455 0.00 0.00 0.00 3.95
160 161 3.117813 TGGAAAAGGAAAGGGAAGAACGA 60.118 43.478 0.00 0.00 0.00 3.85
161 162 3.887110 GGAAAAGGAAAGGGAAGAACGAA 59.113 43.478 0.00 0.00 0.00 3.85
162 163 4.340097 GGAAAAGGAAAGGGAAGAACGAAA 59.660 41.667 0.00 0.00 0.00 3.46
163 164 5.163488 GGAAAAGGAAAGGGAAGAACGAAAA 60.163 40.000 0.00 0.00 0.00 2.29
164 165 5.925506 AAAGGAAAGGGAAGAACGAAAAA 57.074 34.783 0.00 0.00 0.00 1.94
165 166 4.913335 AGGAAAGGGAAGAACGAAAAAC 57.087 40.909 0.00 0.00 0.00 2.43
166 167 4.274978 AGGAAAGGGAAGAACGAAAAACA 58.725 39.130 0.00 0.00 0.00 2.83
167 168 4.707934 AGGAAAGGGAAGAACGAAAAACAA 59.292 37.500 0.00 0.00 0.00 2.83
168 169 4.802039 GGAAAGGGAAGAACGAAAAACAAC 59.198 41.667 0.00 0.00 0.00 3.32
169 170 5.393787 GGAAAGGGAAGAACGAAAAACAACT 60.394 40.000 0.00 0.00 0.00 3.16
170 171 5.654603 AAGGGAAGAACGAAAAACAACTT 57.345 34.783 0.00 0.00 0.00 2.66
171 172 5.654603 AGGGAAGAACGAAAAACAACTTT 57.345 34.783 0.00 0.00 0.00 2.66
172 173 6.032956 AGGGAAGAACGAAAAACAACTTTT 57.967 33.333 0.00 0.00 40.03 2.27
173 174 6.460781 AGGGAAGAACGAAAAACAACTTTTT 58.539 32.000 0.00 0.00 41.42 1.94
218 219 6.627395 TTATTTTCACACCAAAGACGACAT 57.373 33.333 0.00 0.00 0.00 3.06
220 221 4.974368 TTTCACACCAAAGACGACATTT 57.026 36.364 0.00 0.00 0.00 2.32
221 222 4.974368 TTCACACCAAAGACGACATTTT 57.026 36.364 0.00 0.00 0.00 1.82
222 223 4.974368 TCACACCAAAGACGACATTTTT 57.026 36.364 0.00 0.00 0.00 1.94
375 382 1.882623 CTGTTTTTCCTCTCCTGCCAC 59.117 52.381 0.00 0.00 0.00 5.01
786 899 1.077716 GGGCGTGGGTGCTTATTCT 60.078 57.895 0.00 0.00 34.52 2.40
795 908 2.633488 GGTGCTTATTCTCGGCTTCTT 58.367 47.619 0.00 0.00 0.00 2.52
853 969 0.319555 GGGGCCGCTTTTTCTTTGTC 60.320 55.000 13.57 0.00 0.00 3.18
864 980 5.745769 GCTTTTTCTTTGTCTGTTTGGAGAG 59.254 40.000 0.00 0.00 0.00 3.20
912 1032 2.029838 ATCTGAGAACCACAATCGGC 57.970 50.000 0.00 0.00 0.00 5.54
941 1061 0.036022 GGGTTGCTGTGCTCTCTCTT 59.964 55.000 0.00 0.00 0.00 2.85
942 1062 1.276421 GGGTTGCTGTGCTCTCTCTTA 59.724 52.381 0.00 0.00 0.00 2.10
943 1063 2.615869 GGTTGCTGTGCTCTCTCTTAG 58.384 52.381 0.00 0.00 0.00 2.18
944 1064 2.028567 GGTTGCTGTGCTCTCTCTTAGT 60.029 50.000 0.00 0.00 0.00 2.24
949 1069 4.952957 TGCTGTGCTCTCTCTTAGTCTTAT 59.047 41.667 0.00 0.00 0.00 1.73
1017 1151 1.673168 AAATGGCCGAGCATCTCTTC 58.327 50.000 0.00 0.00 0.00 2.87
1115 1249 8.458843 GTTATGCATGGTGAATTTACAGTTACT 58.541 33.333 10.16 0.00 0.00 2.24
1116 1250 9.674068 TTATGCATGGTGAATTTACAGTTACTA 57.326 29.630 10.16 0.00 0.00 1.82
1226 1370 8.850156 ACCTAGCAACATAATTTATCATGGTTC 58.150 33.333 0.00 0.00 0.00 3.62
1287 1432 2.481104 CCTTGCGCTTTTCTGACCAAAA 60.481 45.455 9.73 0.00 0.00 2.44
1352 1497 2.943033 GCGCTAGGCCTTTTGAGATTTA 59.057 45.455 12.58 0.00 34.80 1.40
1356 1504 5.651530 GCTAGGCCTTTTGAGATTTAAACC 58.348 41.667 12.58 0.00 0.00 3.27
1362 1510 6.463755 GGCCTTTTGAGATTTAAACCTTGGAA 60.464 38.462 0.00 0.00 0.00 3.53
1363 1511 7.161404 GCCTTTTGAGATTTAAACCTTGGAAT 58.839 34.615 0.00 0.00 0.00 3.01
1364 1512 7.661437 GCCTTTTGAGATTTAAACCTTGGAATT 59.339 33.333 0.00 0.00 0.00 2.17
1365 1513 9.559732 CCTTTTGAGATTTAAACCTTGGAATTT 57.440 29.630 0.00 0.00 0.00 1.82
1385 1533 6.877611 ATTTATTTATGCCTACCCAGTTCG 57.122 37.500 0.00 0.00 0.00 3.95
1406 1560 2.813754 GCAGTGCTCTACAATGTTTGGA 59.186 45.455 8.18 0.00 46.06 3.53
1443 1597 5.073311 ACACTTAACATCATAGCGACACT 57.927 39.130 0.00 0.00 0.00 3.55
1479 1635 3.539604 AGCTGCAGATGATTACTGAACC 58.460 45.455 20.43 0.00 37.54 3.62
1569 1725 7.099120 AGATGTACATGCAATTAGATATCGCA 58.901 34.615 14.43 4.95 36.95 5.10
1644 1801 0.108138 CACTGAATCTGGACGGGACC 60.108 60.000 0.00 0.00 0.00 4.46
1692 1849 7.778470 GGTAACATGACCTGATTCTTCTTAG 57.222 40.000 0.00 0.00 36.47 2.18
1696 1854 7.251321 ACATGACCTGATTCTTCTTAGAAGT 57.749 36.000 19.87 3.46 43.33 3.01
1719 1877 8.712285 AGTTTGATCATGAAATAATTTGGCAG 57.288 30.769 0.00 0.00 0.00 4.85
1727 1885 6.283544 TGAAATAATTTGGCAGCTGAATGA 57.716 33.333 20.43 1.59 0.00 2.57
1733 1911 2.430248 TGGCAGCTGAATGATGTGAT 57.570 45.000 20.43 0.00 34.02 3.06
1777 1990 4.556233 TGTCTTACATGGACTTGTCTTCG 58.444 43.478 0.00 0.00 35.04 3.79
1806 2019 2.230660 GCATGTTTAGGGGCTGATACC 58.769 52.381 0.00 0.00 0.00 2.73
2088 2317 6.432162 TCATATAGCTGATGAAGAATTTGCCC 59.568 38.462 9.94 0.00 30.35 5.36
2166 2395 2.706190 GCCCTTCAGCTCCTTAATCCTA 59.294 50.000 0.00 0.00 0.00 2.94
2177 2406 8.589338 CAGCTCCTTAATCCTAGCTTCTTAATA 58.411 37.037 0.00 0.00 42.52 0.98
2178 2407 9.332713 AGCTCCTTAATCCTAGCTTCTTAATAT 57.667 33.333 0.00 0.00 42.52 1.28
2179 2408 9.377312 GCTCCTTAATCCTAGCTTCTTAATATG 57.623 37.037 0.00 0.00 32.18 1.78
2217 2446 6.148480 CCTAGCTTCTTAATGCATGTCCATAC 59.852 42.308 0.00 0.00 0.00 2.39
2278 2507 2.801063 TGCGCGTATTACTGAGTAACC 58.199 47.619 7.28 0.76 30.49 2.85
2336 2566 5.702670 TGAGATTGCTTCCTTTGAGTGTTAG 59.297 40.000 0.00 0.00 0.00 2.34
2399 2629 0.608130 GGGTGGGGCAGTTCAAATTC 59.392 55.000 0.00 0.00 0.00 2.17
2408 2638 4.462483 GGGCAGTTCAAATTCCTTGATGTA 59.538 41.667 0.00 0.00 43.64 2.29
2410 2640 6.351286 GGGCAGTTCAAATTCCTTGATGTAAT 60.351 38.462 0.00 0.00 43.64 1.89
2473 2711 6.777782 TGGTTTTGGGATTGCTTAATTTGAT 58.222 32.000 0.00 0.00 0.00 2.57
2526 2764 0.392193 CCAAGATGAAGCTCGGCTGT 60.392 55.000 0.00 0.00 39.62 4.40
2534 2772 0.178990 AAGCTCGGCTGTTTTCCCTT 60.179 50.000 0.00 0.00 39.62 3.95
2581 2823 0.974010 CATGGGCATTGGGCTGTTCT 60.974 55.000 0.00 0.00 44.01 3.01
2590 2832 0.770499 TGGGCTGTTCTCATGTGGAA 59.230 50.000 0.00 0.00 0.00 3.53
2687 2929 8.564574 TGGTTTTACATATTTGATATTCCTCGC 58.435 33.333 0.00 0.00 0.00 5.03
2755 3001 9.649167 AAAGGAGCTCATTTTTCTTATGAAATG 57.351 29.630 20.07 2.38 41.24 2.32
2792 3054 4.033587 TGACGGTCTTTTCTCGTTTTTGAG 59.966 41.667 9.88 0.00 37.25 3.02
2796 3058 4.439563 GGTCTTTTCTCGTTTTTGAGCCAA 60.440 41.667 0.00 0.00 35.90 4.52
2914 3176 3.744426 CGAACCTACACCTTTTACACCTG 59.256 47.826 0.00 0.00 0.00 4.00
2915 3177 4.711399 GAACCTACACCTTTTACACCTGT 58.289 43.478 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.246670 TGATATTCCTGTGAAATCTTGAACAAT 57.753 29.630 0.00 0.00 33.32 2.71
4 5 8.514594 GTGATATTCCTGTGAAATCTTGAACAA 58.485 33.333 0.00 0.00 33.32 2.83
5 6 7.121168 GGTGATATTCCTGTGAAATCTTGAACA 59.879 37.037 0.00 0.00 33.32 3.18
6 7 7.337942 AGGTGATATTCCTGTGAAATCTTGAAC 59.662 37.037 0.48 0.00 33.32 3.18
7 8 7.337689 CAGGTGATATTCCTGTGAAATCTTGAA 59.662 37.037 15.48 0.00 45.09 2.69
8 9 6.825213 CAGGTGATATTCCTGTGAAATCTTGA 59.175 38.462 15.48 0.00 45.09 3.02
9 10 7.024340 CAGGTGATATTCCTGTGAAATCTTG 57.976 40.000 15.48 0.00 45.09 3.02
20 21 8.834004 TGTAGTACTTAACAGGTGATATTCCT 57.166 34.615 0.00 0.00 35.45 3.36
23 24 9.832445 CCAATGTAGTACTTAACAGGTGATATT 57.168 33.333 0.00 0.00 0.00 1.28
24 25 8.429641 CCCAATGTAGTACTTAACAGGTGATAT 58.570 37.037 0.00 0.00 0.00 1.63
25 26 7.620491 TCCCAATGTAGTACTTAACAGGTGATA 59.380 37.037 0.00 0.00 0.00 2.15
26 27 6.442564 TCCCAATGTAGTACTTAACAGGTGAT 59.557 38.462 0.00 0.00 0.00 3.06
27 28 5.781306 TCCCAATGTAGTACTTAACAGGTGA 59.219 40.000 0.00 0.00 0.00 4.02
28 29 5.873164 GTCCCAATGTAGTACTTAACAGGTG 59.127 44.000 0.00 3.28 0.00 4.00
29 30 5.046087 GGTCCCAATGTAGTACTTAACAGGT 60.046 44.000 0.00 0.00 0.00 4.00
30 31 5.189145 AGGTCCCAATGTAGTACTTAACAGG 59.811 44.000 0.00 0.00 0.00 4.00
31 32 6.295719 AGGTCCCAATGTAGTACTTAACAG 57.704 41.667 0.00 0.00 0.00 3.16
32 33 6.725369 TGTAGGTCCCAATGTAGTACTTAACA 59.275 38.462 0.00 0.00 0.00 2.41
33 34 7.174107 TGTAGGTCCCAATGTAGTACTTAAC 57.826 40.000 0.00 0.00 0.00 2.01
34 35 7.795534 TTGTAGGTCCCAATGTAGTACTTAA 57.204 36.000 0.00 0.00 0.00 1.85
35 36 7.983166 ATTGTAGGTCCCAATGTAGTACTTA 57.017 36.000 0.00 0.00 31.52 2.24
36 37 6.886178 ATTGTAGGTCCCAATGTAGTACTT 57.114 37.500 0.00 0.00 31.52 2.24
37 38 7.983166 TTATTGTAGGTCCCAATGTAGTACT 57.017 36.000 0.00 0.00 34.51 2.73
38 39 7.597743 CGATTATTGTAGGTCCCAATGTAGTAC 59.402 40.741 4.16 0.00 34.51 2.73
39 40 7.288389 ACGATTATTGTAGGTCCCAATGTAGTA 59.712 37.037 4.16 0.00 34.51 1.82
40 41 6.099269 ACGATTATTGTAGGTCCCAATGTAGT 59.901 38.462 4.16 0.00 34.51 2.73
41 42 6.522054 ACGATTATTGTAGGTCCCAATGTAG 58.478 40.000 4.16 0.00 34.51 2.74
42 43 6.488769 ACGATTATTGTAGGTCCCAATGTA 57.511 37.500 4.16 0.00 34.51 2.29
43 44 5.367945 ACGATTATTGTAGGTCCCAATGT 57.632 39.130 4.16 0.00 34.51 2.71
44 45 5.404366 CGTACGATTATTGTAGGTCCCAATG 59.596 44.000 10.44 0.00 34.51 2.82
45 46 5.069516 ACGTACGATTATTGTAGGTCCCAAT 59.930 40.000 24.41 0.00 36.49 3.16
46 47 4.402155 ACGTACGATTATTGTAGGTCCCAA 59.598 41.667 24.41 0.00 36.49 4.12
47 48 3.953612 ACGTACGATTATTGTAGGTCCCA 59.046 43.478 24.41 0.00 36.49 4.37
48 49 4.574599 ACGTACGATTATTGTAGGTCCC 57.425 45.455 24.41 0.00 36.49 4.46
49 50 9.282247 CATTATACGTACGATTATTGTAGGTCC 57.718 37.037 24.41 0.00 40.31 4.46
50 51 8.792538 GCATTATACGTACGATTATTGTAGGTC 58.207 37.037 24.41 3.53 40.31 3.85
51 52 7.756722 GGCATTATACGTACGATTATTGTAGGT 59.243 37.037 24.41 18.24 41.93 3.08
52 53 7.972277 AGGCATTATACGTACGATTATTGTAGG 59.028 37.037 24.41 9.90 34.69 3.18
53 54 8.795341 CAGGCATTATACGTACGATTATTGTAG 58.205 37.037 24.41 4.28 0.00 2.74
54 55 7.756272 CCAGGCATTATACGTACGATTATTGTA 59.244 37.037 24.41 1.68 0.00 2.41
55 56 6.588756 CCAGGCATTATACGTACGATTATTGT 59.411 38.462 24.41 0.00 0.00 2.71
56 57 6.809689 TCCAGGCATTATACGTACGATTATTG 59.190 38.462 24.41 17.59 0.00 1.90
57 58 6.927416 TCCAGGCATTATACGTACGATTATT 58.073 36.000 24.41 0.61 0.00 1.40
58 59 6.519679 TCCAGGCATTATACGTACGATTAT 57.480 37.500 24.41 12.70 0.00 1.28
59 60 5.963176 TCCAGGCATTATACGTACGATTA 57.037 39.130 24.41 9.95 0.00 1.75
60 61 4.859304 TCCAGGCATTATACGTACGATT 57.141 40.909 24.41 11.02 0.00 3.34
61 62 4.859304 TTCCAGGCATTATACGTACGAT 57.141 40.909 24.41 13.27 0.00 3.73
62 63 4.038282 ACATTCCAGGCATTATACGTACGA 59.962 41.667 24.41 6.04 0.00 3.43
63 64 4.304110 ACATTCCAGGCATTATACGTACG 58.696 43.478 15.01 15.01 0.00 3.67
64 65 5.756347 TCAACATTCCAGGCATTATACGTAC 59.244 40.000 0.00 0.00 0.00 3.67
65 66 5.919755 TCAACATTCCAGGCATTATACGTA 58.080 37.500 0.00 0.00 0.00 3.57
66 67 4.776349 TCAACATTCCAGGCATTATACGT 58.224 39.130 0.00 0.00 0.00 3.57
67 68 5.050091 GTCTCAACATTCCAGGCATTATACG 60.050 44.000 0.00 0.00 0.00 3.06
68 69 6.058183 AGTCTCAACATTCCAGGCATTATAC 58.942 40.000 0.00 0.00 0.00 1.47
69 70 6.252599 AGTCTCAACATTCCAGGCATTATA 57.747 37.500 0.00 0.00 0.00 0.98
70 71 5.121380 AGTCTCAACATTCCAGGCATTAT 57.879 39.130 0.00 0.00 0.00 1.28
71 72 4.574674 AGTCTCAACATTCCAGGCATTA 57.425 40.909 0.00 0.00 0.00 1.90
72 73 3.446442 AGTCTCAACATTCCAGGCATT 57.554 42.857 0.00 0.00 0.00 3.56
73 74 4.574674 TTAGTCTCAACATTCCAGGCAT 57.425 40.909 0.00 0.00 0.00 4.40
74 75 4.517285 GATTAGTCTCAACATTCCAGGCA 58.483 43.478 0.00 0.00 0.00 4.75
75 76 3.557595 CGATTAGTCTCAACATTCCAGGC 59.442 47.826 0.00 0.00 0.00 4.85
76 77 4.568359 CACGATTAGTCTCAACATTCCAGG 59.432 45.833 0.00 0.00 0.00 4.45
77 78 5.410924 TCACGATTAGTCTCAACATTCCAG 58.589 41.667 0.00 0.00 0.00 3.86
78 79 5.400066 TCACGATTAGTCTCAACATTCCA 57.600 39.130 0.00 0.00 0.00 3.53
79 80 6.910536 AATCACGATTAGTCTCAACATTCC 57.089 37.500 0.00 0.00 0.00 3.01
80 81 7.148407 ACCAAATCACGATTAGTCTCAACATTC 60.148 37.037 0.00 0.00 0.00 2.67
81 82 6.655003 ACCAAATCACGATTAGTCTCAACATT 59.345 34.615 0.00 0.00 0.00 2.71
82 83 6.173339 ACCAAATCACGATTAGTCTCAACAT 58.827 36.000 0.00 0.00 0.00 2.71
83 84 5.547465 ACCAAATCACGATTAGTCTCAACA 58.453 37.500 0.00 0.00 0.00 3.33
84 85 6.481954 AACCAAATCACGATTAGTCTCAAC 57.518 37.500 0.00 0.00 0.00 3.18
85 86 6.708502 TCAAACCAAATCACGATTAGTCTCAA 59.291 34.615 0.00 0.00 0.00 3.02
86 87 6.147164 GTCAAACCAAATCACGATTAGTCTCA 59.853 38.462 0.00 0.00 0.00 3.27
87 88 6.147164 TGTCAAACCAAATCACGATTAGTCTC 59.853 38.462 0.00 0.00 0.00 3.36
88 89 5.995282 TGTCAAACCAAATCACGATTAGTCT 59.005 36.000 0.00 0.00 0.00 3.24
89 90 6.147164 TCTGTCAAACCAAATCACGATTAGTC 59.853 38.462 0.00 0.00 0.00 2.59
90 91 5.995282 TCTGTCAAACCAAATCACGATTAGT 59.005 36.000 0.00 0.00 0.00 2.24
91 92 6.147821 ACTCTGTCAAACCAAATCACGATTAG 59.852 38.462 0.00 0.00 0.00 1.73
92 93 5.995282 ACTCTGTCAAACCAAATCACGATTA 59.005 36.000 0.00 0.00 0.00 1.75
93 94 4.821805 ACTCTGTCAAACCAAATCACGATT 59.178 37.500 0.00 0.00 0.00 3.34
94 95 4.389374 ACTCTGTCAAACCAAATCACGAT 58.611 39.130 0.00 0.00 0.00 3.73
95 96 3.804036 ACTCTGTCAAACCAAATCACGA 58.196 40.909 0.00 0.00 0.00 4.35
96 97 4.273480 AGAACTCTGTCAAACCAAATCACG 59.727 41.667 0.00 0.00 0.00 4.35
97 98 5.514279 CAGAACTCTGTCAAACCAAATCAC 58.486 41.667 0.00 0.00 39.09 3.06
98 99 5.756195 CAGAACTCTGTCAAACCAAATCA 57.244 39.130 0.00 0.00 39.09 2.57
112 113 1.342819 GTGCTCAGGTCACAGAACTCT 59.657 52.381 0.00 0.00 34.73 3.24
113 114 1.069204 TGTGCTCAGGTCACAGAACTC 59.931 52.381 0.00 0.00 39.29 3.01
114 115 1.123077 TGTGCTCAGGTCACAGAACT 58.877 50.000 0.00 0.00 39.29 3.01
115 116 1.221414 GTGTGCTCAGGTCACAGAAC 58.779 55.000 0.00 0.00 44.11 3.01
116 117 0.829990 TGTGTGCTCAGGTCACAGAA 59.170 50.000 0.00 0.00 44.11 3.02
117 118 1.051008 ATGTGTGCTCAGGTCACAGA 58.949 50.000 0.00 0.00 44.11 3.41
118 119 1.888215 AATGTGTGCTCAGGTCACAG 58.112 50.000 0.00 0.00 44.11 3.66
119 120 1.948834 CAAATGTGTGCTCAGGTCACA 59.051 47.619 0.00 0.00 44.29 3.58
120 121 1.267806 CCAAATGTGTGCTCAGGTCAC 59.732 52.381 0.00 0.00 35.14 3.67
121 122 1.142667 TCCAAATGTGTGCTCAGGTCA 59.857 47.619 0.00 0.00 0.00 4.02
122 123 1.896220 TCCAAATGTGTGCTCAGGTC 58.104 50.000 0.00 0.00 0.00 3.85
123 124 2.363306 TTCCAAATGTGTGCTCAGGT 57.637 45.000 0.00 0.00 0.00 4.00
124 125 3.553508 CCTTTTCCAAATGTGTGCTCAGG 60.554 47.826 0.00 0.00 0.00 3.86
125 126 3.318839 TCCTTTTCCAAATGTGTGCTCAG 59.681 43.478 0.00 0.00 0.00 3.35
126 127 3.295093 TCCTTTTCCAAATGTGTGCTCA 58.705 40.909 0.00 0.00 0.00 4.26
127 128 4.320608 TTCCTTTTCCAAATGTGTGCTC 57.679 40.909 0.00 0.00 0.00 4.26
128 129 4.443315 CCTTTCCTTTTCCAAATGTGTGCT 60.443 41.667 0.00 0.00 0.00 4.40
129 130 3.809279 CCTTTCCTTTTCCAAATGTGTGC 59.191 43.478 0.00 0.00 0.00 4.57
130 131 4.100808 TCCCTTTCCTTTTCCAAATGTGTG 59.899 41.667 0.00 0.00 0.00 3.82
131 132 4.294347 TCCCTTTCCTTTTCCAAATGTGT 58.706 39.130 0.00 0.00 0.00 3.72
132 133 4.953940 TCCCTTTCCTTTTCCAAATGTG 57.046 40.909 0.00 0.00 0.00 3.21
133 134 5.215845 TCTTCCCTTTCCTTTTCCAAATGT 58.784 37.500 0.00 0.00 0.00 2.71
134 135 5.806654 TCTTCCCTTTCCTTTTCCAAATG 57.193 39.130 0.00 0.00 0.00 2.32
135 136 5.221441 CGTTCTTCCCTTTCCTTTTCCAAAT 60.221 40.000 0.00 0.00 0.00 2.32
136 137 4.098807 CGTTCTTCCCTTTCCTTTTCCAAA 59.901 41.667 0.00 0.00 0.00 3.28
137 138 3.634910 CGTTCTTCCCTTTCCTTTTCCAA 59.365 43.478 0.00 0.00 0.00 3.53
138 139 3.117813 TCGTTCTTCCCTTTCCTTTTCCA 60.118 43.478 0.00 0.00 0.00 3.53
139 140 3.483421 TCGTTCTTCCCTTTCCTTTTCC 58.517 45.455 0.00 0.00 0.00 3.13
140 141 5.509716 TTTCGTTCTTCCCTTTCCTTTTC 57.490 39.130 0.00 0.00 0.00 2.29
141 142 5.925506 TTTTCGTTCTTCCCTTTCCTTTT 57.074 34.783 0.00 0.00 0.00 2.27
142 143 5.186215 TGTTTTTCGTTCTTCCCTTTCCTTT 59.814 36.000 0.00 0.00 0.00 3.11
143 144 4.707934 TGTTTTTCGTTCTTCCCTTTCCTT 59.292 37.500 0.00 0.00 0.00 3.36
144 145 4.274978 TGTTTTTCGTTCTTCCCTTTCCT 58.725 39.130 0.00 0.00 0.00 3.36
145 146 4.642445 TGTTTTTCGTTCTTCCCTTTCC 57.358 40.909 0.00 0.00 0.00 3.13
146 147 5.647589 AGTTGTTTTTCGTTCTTCCCTTTC 58.352 37.500 0.00 0.00 0.00 2.62
147 148 5.654603 AGTTGTTTTTCGTTCTTCCCTTT 57.345 34.783 0.00 0.00 0.00 3.11
148 149 5.654603 AAGTTGTTTTTCGTTCTTCCCTT 57.345 34.783 0.00 0.00 0.00 3.95
149 150 5.654603 AAAGTTGTTTTTCGTTCTTCCCT 57.345 34.783 0.00 0.00 0.00 4.20
150 151 6.715344 AAAAAGTTGTTTTTCGTTCTTCCC 57.285 33.333 0.00 0.00 41.15 3.97
196 197 6.627395 AATGTCGTCTTTGGTGTGAAAATA 57.373 33.333 0.00 0.00 0.00 1.40
197 198 5.514274 AATGTCGTCTTTGGTGTGAAAAT 57.486 34.783 0.00 0.00 0.00 1.82
220 221 3.249080 CGTCGCCCTGTCTTTCTTAAAAA 59.751 43.478 0.00 0.00 0.00 1.94
221 222 2.803956 CGTCGCCCTGTCTTTCTTAAAA 59.196 45.455 0.00 0.00 0.00 1.52
222 223 2.224113 ACGTCGCCCTGTCTTTCTTAAA 60.224 45.455 0.00 0.00 0.00 1.52
223 224 1.342174 ACGTCGCCCTGTCTTTCTTAA 59.658 47.619 0.00 0.00 0.00 1.85
227 228 2.668280 GCACGTCGCCCTGTCTTTC 61.668 63.158 0.00 0.00 32.94 2.62
375 382 4.227134 CGGAGGCGATGTGGGGAG 62.227 72.222 0.00 0.00 0.00 4.30
769 879 1.429148 CGAGAATAAGCACCCACGCC 61.429 60.000 0.00 0.00 0.00 5.68
775 888 2.317530 AGAAGCCGAGAATAAGCACC 57.682 50.000 0.00 0.00 0.00 5.01
818 931 2.230660 GCCCCCGAATCCTAAATCAAG 58.769 52.381 0.00 0.00 0.00 3.02
853 969 3.121030 CCCGCGCTCTCCAAACAG 61.121 66.667 5.56 0.00 0.00 3.16
864 980 0.743345 AAGTGAATCCTAACCCGCGC 60.743 55.000 0.00 0.00 0.00 6.86
912 1032 0.254178 ACAGCAACCCTAGCATCCTG 59.746 55.000 0.00 0.00 0.00 3.86
1115 1249 0.174845 AAGCACCGCGCAGTAGAATA 59.825 50.000 8.75 0.00 46.13 1.75
1116 1250 0.673644 AAAGCACCGCGCAGTAGAAT 60.674 50.000 8.75 0.00 46.13 2.40
1140 1274 1.504647 ATGAGCAGCATGATTCGGCG 61.505 55.000 0.00 0.00 39.69 6.46
1200 1344 8.766994 AACCATGATAAATTATGTTGCTAGGT 57.233 30.769 0.00 0.00 0.00 3.08
1201 1345 8.849168 TGAACCATGATAAATTATGTTGCTAGG 58.151 33.333 0.00 0.00 0.00 3.02
1298 1443 2.480224 ATCTGCACATAATTGCGCAC 57.520 45.000 11.12 0.00 46.20 5.34
1328 1473 1.553248 TCTCAAAAGGCCTAGCGCTTA 59.447 47.619 18.68 0.00 37.74 3.09
1352 1497 8.482943 GGTAGGCATAAATAAATTCCAAGGTTT 58.517 33.333 0.00 0.00 0.00 3.27
1356 1504 7.287696 ACTGGGTAGGCATAAATAAATTCCAAG 59.712 37.037 0.00 0.00 0.00 3.61
1362 1510 5.240844 GCGAACTGGGTAGGCATAAATAAAT 59.759 40.000 0.00 0.00 0.00 1.40
1363 1511 4.577283 GCGAACTGGGTAGGCATAAATAAA 59.423 41.667 0.00 0.00 0.00 1.40
1364 1512 4.131596 GCGAACTGGGTAGGCATAAATAA 58.868 43.478 0.00 0.00 0.00 1.40
1365 1513 3.134985 TGCGAACTGGGTAGGCATAAATA 59.865 43.478 0.00 0.00 0.00 1.40
1385 1533 2.813754 TCCAAACATTGTAGAGCACTGC 59.186 45.455 0.00 0.00 31.77 4.40
1443 1597 1.225855 CAGCTACGAGGTTGCACAAA 58.774 50.000 5.12 0.00 36.81 2.83
1479 1635 5.086058 CGATGTGGAAAGGTAAATGTTTCG 58.914 41.667 0.00 0.00 34.11 3.46
1569 1725 1.280710 TGCATTGGGTAGACATCGGTT 59.719 47.619 0.00 0.00 0.00 4.44
1692 1849 9.153721 TGCCAAATTATTTCATGATCAAACTTC 57.846 29.630 0.00 0.00 0.00 3.01
1696 1854 7.279090 CAGCTGCCAAATTATTTCATGATCAAA 59.721 33.333 0.00 0.00 0.00 2.69
1719 1877 4.220533 GGCAACTATCACATCATTCAGC 57.779 45.455 0.00 0.00 0.00 4.26
1777 1990 1.369625 CCTAAACATGCGTCCTCCAC 58.630 55.000 0.00 0.00 0.00 4.02
1806 2019 6.405176 GGAAAGAAATAACATGAGCTTCCTGG 60.405 42.308 0.00 0.00 0.00 4.45
2046 2274 9.732130 AGCTATATGAAGGTAAGAAATCAATCC 57.268 33.333 0.00 0.00 0.00 3.01
2088 2317 4.877823 TGAGCTTCAGCAACATGGTTATAG 59.122 41.667 0.75 0.00 45.16 1.31
2186 2415 8.071177 ACATGCATTAAGAAGCTAGGATTTTT 57.929 30.769 0.00 0.00 0.00 1.94
2187 2416 7.201857 GGACATGCATTAAGAAGCTAGGATTTT 60.202 37.037 0.00 0.00 0.00 1.82
2188 2417 6.264067 GGACATGCATTAAGAAGCTAGGATTT 59.736 38.462 0.00 0.00 0.00 2.17
2189 2418 5.767168 GGACATGCATTAAGAAGCTAGGATT 59.233 40.000 0.00 0.00 0.00 3.01
2190 2419 5.163163 TGGACATGCATTAAGAAGCTAGGAT 60.163 40.000 0.00 0.00 0.00 3.24
2191 2420 4.164030 TGGACATGCATTAAGAAGCTAGGA 59.836 41.667 0.00 0.00 0.00 2.94
2192 2421 4.454678 TGGACATGCATTAAGAAGCTAGG 58.545 43.478 0.00 0.00 0.00 3.02
2193 2422 6.707608 TGTATGGACATGCATTAAGAAGCTAG 59.292 38.462 0.00 0.00 0.00 3.42
2194 2423 6.591001 TGTATGGACATGCATTAAGAAGCTA 58.409 36.000 0.00 0.00 0.00 3.32
2195 2424 5.439721 TGTATGGACATGCATTAAGAAGCT 58.560 37.500 0.00 0.00 0.00 3.74
2196 2425 5.756195 TGTATGGACATGCATTAAGAAGC 57.244 39.130 0.00 0.00 0.00 3.86
2197 2426 7.230108 AGGATTGTATGGACATGCATTAAGAAG 59.770 37.037 0.00 0.00 34.86 2.85
2198 2427 7.013559 CAGGATTGTATGGACATGCATTAAGAA 59.986 37.037 0.00 0.00 34.86 2.52
2199 2428 6.487668 CAGGATTGTATGGACATGCATTAAGA 59.512 38.462 0.00 0.00 34.86 2.10
2200 2429 6.263842 ACAGGATTGTATGGACATGCATTAAG 59.736 38.462 0.00 0.00 35.25 1.85
2201 2430 6.039605 CACAGGATTGTATGGACATGCATTAA 59.960 38.462 0.00 0.00 35.25 1.40
2202 2431 5.532032 CACAGGATTGTATGGACATGCATTA 59.468 40.000 0.00 0.00 35.25 1.90
2203 2432 4.340097 CACAGGATTGTATGGACATGCATT 59.660 41.667 0.00 1.21 35.25 3.56
2204 2433 3.887110 CACAGGATTGTATGGACATGCAT 59.113 43.478 3.97 0.00 35.25 3.96
2205 2434 3.281158 CACAGGATTGTATGGACATGCA 58.719 45.455 0.00 0.00 35.25 3.96
2217 2446 1.304381 CCCCACCCACACAGGATTG 60.304 63.158 0.00 0.00 41.22 2.67
2278 2507 8.267894 CCCCTTATATTGGAGTATATTCACCAG 58.732 40.741 0.00 0.00 33.85 4.00
2336 2566 6.817184 ACCATGTATACATCAGGTTACTCAC 58.183 40.000 17.94 0.00 31.02 3.51
2399 2629 9.832445 ATACACTAGGTTACAATTACATCAAGG 57.168 33.333 0.00 0.00 0.00 3.61
2410 2640 8.863086 GGACCATGTATATACACTAGGTTACAA 58.137 37.037 25.41 2.06 38.49 2.41
2419 2657 8.816894 CCTTATCTTGGACCATGTATATACACT 58.183 37.037 17.69 3.69 39.30 3.55
2473 2711 3.861840 GCATCAGGCTACTCAGTAACAA 58.138 45.455 0.00 0.00 40.25 2.83
2526 2764 9.757227 CATTTGTACTAACATTTCAAGGGAAAA 57.243 29.630 0.00 0.00 45.52 2.29
2581 2823 3.229293 TGCACCAAAGATTTCCACATGA 58.771 40.909 0.00 0.00 0.00 3.07
2590 2832 5.564550 AGACTATGAGTTGCACCAAAGATT 58.435 37.500 0.00 0.00 0.00 2.40
2754 3000 3.101437 ACCGTCAACACACCTATATCCA 58.899 45.455 0.00 0.00 0.00 3.41
2755 3001 3.383825 AGACCGTCAACACACCTATATCC 59.616 47.826 0.40 0.00 0.00 2.59
2796 3058 5.829924 ACAACTAGCCAAGCATGCTTATATT 59.170 36.000 31.48 18.96 40.23 1.28
2914 3176 8.723942 ATCACTTGGTTGAGTTTGAGATATAC 57.276 34.615 0.00 0.00 0.00 1.47
2915 3177 9.739276 AAATCACTTGGTTGAGTTTGAGATATA 57.261 29.630 0.00 0.00 29.70 0.86


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

AutoCloner maintained by Alex Coulton.