Multiple sequence alignment - TraesCS7D01G320700

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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 TraesCS7D01G320700 chr7D 100.000 3485 0 0 1 3485 410891089 410894573 0.000000e+00 6436.0
1 TraesCS7D01G320700 chr7D 95.323 1283 52 4 2206 3485 315167962 315166685 0.000000e+00 2030.0
2 TraesCS7D01G320700 chr7D 96.412 864 29 2 921 1782 37536777 37535914 0.000000e+00 1423.0
3 TraesCS7D01G320700 chr7D 92.132 699 26 8 250 922 37537518 37536823 0.000000e+00 959.0
4 TraesCS7D01G320700 chr7D 95.055 182 9 0 1 182 211653236 211653417 1.580000e-73 287.0
5 TraesCS7D01G320700 chr7D 94.505 182 10 0 1 182 270410820 270410639 7.360000e-72 281.0
6 TraesCS7D01G320700 chr7D 93.548 186 11 1 1 185 36345384 36345569 3.430000e-70 276.0
7 TraesCS7D01G320700 chr7D 82.031 256 41 4 3108 3362 91873067 91872816 2.720000e-51 213.0
8 TraesCS7D01G320700 chr7B 94.170 2573 115 14 921 3485 325470212 325472757 0.000000e+00 3888.0
9 TraesCS7D01G320700 chr7B 94.366 142 8 0 781 922 325470025 325470166 5.860000e-53 219.0
10 TraesCS7D01G320700 chr3D 95.881 2258 61 11 1244 3485 25283102 25285343 0.000000e+00 3626.0
11 TraesCS7D01G320700 chr3D 95.055 182 9 0 1 182 277258316 277258497 1.580000e-73 287.0
12 TraesCS7D01G320700 chr3D 84.279 229 31 4 3136 3362 128739765 128739990 5.860000e-53 219.0
13 TraesCS7D01G320700 chrUn 89.223 1661 114 34 810 2421 75190634 75188990 0.000000e+00 2015.0
14 TraesCS7D01G320700 chrUn 100.000 34 0 0 772 805 341211800 341211833 2.900000e-06 63.9
15 TraesCS7D01G320700 chr6D 92.162 791 56 3 1636 2421 468835352 468836141 0.000000e+00 1112.0
16 TraesCS7D01G320700 chr6D 91.718 326 19 4 1307 1625 468834848 468835172 2.470000e-121 446.0
17 TraesCS7D01G320700 chr6D 91.331 323 19 4 2427 2744 26606738 26607056 1.920000e-117 433.0
18 TraesCS7D01G320700 chr6D 95.429 175 8 0 2 176 237473705 237473879 2.650000e-71 279.0
19 TraesCS7D01G320700 chr6D 97.345 113 3 0 810 922 468834259 468834371 3.550000e-45 193.0
20 TraesCS7D01G320700 chr6B 84.394 1147 100 46 810 1904 714626749 714627868 0.000000e+00 1053.0
21 TraesCS7D01G320700 chr6B 91.262 515 38 4 1907 2421 714627954 714628461 0.000000e+00 695.0
22 TraesCS7D01G320700 chr6B 91.641 323 18 3 2427 2744 88283295 88282977 4.130000e-119 438.0
23 TraesCS7D01G320700 chr6B 91.077 325 18 4 2427 2744 88270209 88269889 2.490000e-116 429.0
24 TraesCS7D01G320700 chr6B 89.450 218 22 1 589 805 197739397 197739614 1.230000e-69 274.0
25 TraesCS7D01G320700 chr2B 88.791 455 32 5 486 922 754984190 754984643 1.100000e-149 540.0
26 TraesCS7D01G320700 chr2B 81.641 256 43 3 3108 3362 70768784 70769036 3.520000e-50 209.0
27 TraesCS7D01G320700 chr2A 92.000 325 19 4 2427 2750 560732537 560732219 1.910000e-122 449.0
28 TraesCS7D01G320700 chr5B 91.331 323 19 3 2427 2744 287784661 287784343 1.920000e-117 433.0
29 TraesCS7D01G320700 chr5B 82.422 256 41 3 3108 3362 621558513 621558765 1.630000e-53 220.0
30 TraesCS7D01G320700 chr5B 100.000 28 0 0 183 210 439682556 439682529 6.000000e-03 52.8
31 TraesCS7D01G320700 chr3B 91.331 323 19 3 2427 2744 60830768 60831086 1.920000e-117 433.0
32 TraesCS7D01G320700 chr1D 95.055 182 9 0 1 182 305057151 305057332 1.580000e-73 287.0
33 TraesCS7D01G320700 chr1D 94.505 182 10 0 1 182 320344737 320344556 7.360000e-72 281.0
34 TraesCS7D01G320700 chr1D 95.455 176 8 0 1 176 464775495 464775670 7.360000e-72 281.0
35 TraesCS7D01G320700 chr2D 94.505 182 10 0 1 182 331099496 331099315 7.360000e-72 281.0
36 TraesCS7D01G320700 chr2D 100.000 30 0 0 181 210 575270233 575270204 4.860000e-04 56.5
37 TraesCS7D01G320700 chr4D 84.279 229 31 4 3136 3362 451878370 451878145 5.860000e-53 219.0
38 TraesCS7D01G320700 chr1A 81.641 256 43 2 3108 3362 121455756 121456008 3.520000e-50 209.0
39 TraesCS7D01G320700 chr7A 89.231 65 3 2 294 355 471805621 471805684 1.040000e-10 78.7
40 TraesCS7D01G320700 chr4A 90.385 52 4 1 2791 2842 327608247 327608297 2.240000e-07 67.6
41 TraesCS7D01G320700 chr5D 100.000 31 0 0 180 210 114804771 114804801 1.350000e-04 58.4


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 TraesCS7D01G320700 chr7D 410891089 410894573 3484 False 6436.000000 6436 100.000000 1 3485 1 chr7D.!!$F3 3484
1 TraesCS7D01G320700 chr7D 315166685 315167962 1277 True 2030.000000 2030 95.323000 2206 3485 1 chr7D.!!$R3 1279
2 TraesCS7D01G320700 chr7D 37535914 37537518 1604 True 1191.000000 1423 94.272000 250 1782 2 chr7D.!!$R4 1532
3 TraesCS7D01G320700 chr7B 325470025 325472757 2732 False 2053.500000 3888 94.268000 781 3485 2 chr7B.!!$F1 2704
4 TraesCS7D01G320700 chr3D 25283102 25285343 2241 False 3626.000000 3626 95.881000 1244 3485 1 chr3D.!!$F1 2241
5 TraesCS7D01G320700 chrUn 75188990 75190634 1644 True 2015.000000 2015 89.223000 810 2421 1 chrUn.!!$R1 1611
6 TraesCS7D01G320700 chr6D 468834259 468836141 1882 False 583.666667 1112 93.741667 810 2421 3 chr6D.!!$F3 1611
7 TraesCS7D01G320700 chr6B 714626749 714628461 1712 False 874.000000 1053 87.828000 810 2421 2 chr6B.!!$F2 1611

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
82 83 0.036105 TGTCATGCCTAGCACACCTG 60.036 55.0 0.00 0.0 43.04 4.00 F
247 248 0.114560 TTTCGTCTCTCCTCCCACCT 59.885 55.0 0.00 0.0 0.00 4.00 F
609 636 0.171007 CCATGGACAACATTGACGCC 59.829 55.0 5.56 0.0 37.84 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1171 1274 1.004560 CGTCTTTGGCAGGAGCAGA 60.005 57.895 0.0 0.0 44.61 4.26 R
1809 2115 1.544314 GCCAGACTCCTTTTGACAGCT 60.544 52.381 0.0 0.0 0.00 4.24 R
2529 2933 0.253044 CCTGGACGATCATGGTTGGT 59.747 55.000 0.0 0.0 0.00 3.67 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
59 60 7.673641 TTGGTCTTTATATAACCCGGTAAGA 57.326 36.000 0.00 0.00 31.78 2.10
60 61 7.860649 TGGTCTTTATATAACCCGGTAAGAT 57.139 36.000 0.00 0.00 31.78 2.40
61 62 7.673180 TGGTCTTTATATAACCCGGTAAGATG 58.327 38.462 0.00 0.00 31.78 2.90
62 63 7.510001 TGGTCTTTATATAACCCGGTAAGATGA 59.490 37.037 0.00 0.00 31.78 2.92
63 64 8.537858 GGTCTTTATATAACCCGGTAAGATGAT 58.462 37.037 0.00 0.00 0.00 2.45
64 65 9.367444 GTCTTTATATAACCCGGTAAGATGATG 57.633 37.037 0.00 0.00 0.00 3.07
65 66 9.096823 TCTTTATATAACCCGGTAAGATGATGT 57.903 33.333 0.00 0.00 0.00 3.06
66 67 9.367444 CTTTATATAACCCGGTAAGATGATGTC 57.633 37.037 0.00 0.00 0.00 3.06
67 68 6.928348 ATATAACCCGGTAAGATGATGTCA 57.072 37.500 0.00 0.00 0.00 3.58
68 69 5.825593 ATAACCCGGTAAGATGATGTCAT 57.174 39.130 0.00 0.00 39.70 3.06
69 70 3.475566 ACCCGGTAAGATGATGTCATG 57.524 47.619 0.00 0.00 36.57 3.07
70 71 2.146342 CCCGGTAAGATGATGTCATGC 58.854 52.381 0.00 0.00 36.57 4.06
71 72 2.146342 CCGGTAAGATGATGTCATGCC 58.854 52.381 0.00 0.00 36.57 4.40
72 73 2.224378 CCGGTAAGATGATGTCATGCCT 60.224 50.000 0.00 0.00 36.57 4.75
73 74 3.006859 CCGGTAAGATGATGTCATGCCTA 59.993 47.826 0.00 0.00 36.57 3.93
74 75 4.240888 CGGTAAGATGATGTCATGCCTAG 58.759 47.826 0.00 0.00 36.57 3.02
75 76 3.999663 GGTAAGATGATGTCATGCCTAGC 59.000 47.826 0.00 0.00 36.57 3.42
76 77 3.851458 AAGATGATGTCATGCCTAGCA 57.149 42.857 0.00 0.00 44.86 3.49
77 78 3.123157 AGATGATGTCATGCCTAGCAC 57.877 47.619 0.00 0.00 43.04 4.40
78 79 2.436911 AGATGATGTCATGCCTAGCACA 59.563 45.455 0.00 0.00 43.04 4.57
79 80 2.028420 TGATGTCATGCCTAGCACAC 57.972 50.000 0.00 0.00 43.04 3.82
80 81 1.303309 GATGTCATGCCTAGCACACC 58.697 55.000 0.00 0.00 43.04 4.16
81 82 0.914644 ATGTCATGCCTAGCACACCT 59.085 50.000 0.00 0.00 43.04 4.00
82 83 0.036105 TGTCATGCCTAGCACACCTG 60.036 55.000 0.00 0.00 43.04 4.00
83 84 0.745845 GTCATGCCTAGCACACCTGG 60.746 60.000 0.00 0.00 43.04 4.45
84 85 2.117156 CATGCCTAGCACACCTGGC 61.117 63.158 0.00 0.00 43.04 4.85
85 86 3.350031 ATGCCTAGCACACCTGGCC 62.350 63.158 0.00 0.00 43.04 5.36
87 88 4.473520 CCTAGCACACCTGGCCGG 62.474 72.222 3.88 3.88 39.35 6.13
88 89 3.390521 CTAGCACACCTGGCCGGA 61.391 66.667 15.09 0.00 36.31 5.14
89 90 2.687200 TAGCACACCTGGCCGGAT 60.687 61.111 15.09 0.00 36.31 4.18
90 91 2.930385 CTAGCACACCTGGCCGGATG 62.930 65.000 15.09 9.47 36.31 3.51
91 92 4.408821 GCACACCTGGCCGGATGA 62.409 66.667 14.85 0.00 36.31 2.92
92 93 2.436646 CACACCTGGCCGGATGAC 60.437 66.667 14.85 0.00 36.31 3.06
93 94 3.717294 ACACCTGGCCGGATGACC 61.717 66.667 14.85 0.00 36.31 4.02
94 95 3.402681 CACCTGGCCGGATGACCT 61.403 66.667 15.09 0.00 36.31 3.85
95 96 2.063979 CACCTGGCCGGATGACCTA 61.064 63.158 15.09 0.00 36.31 3.08
96 97 1.074471 ACCTGGCCGGATGACCTAT 60.074 57.895 15.09 0.00 36.31 2.57
97 98 0.694444 ACCTGGCCGGATGACCTATT 60.694 55.000 15.09 0.00 36.31 1.73
98 99 0.250467 CCTGGCCGGATGACCTATTG 60.250 60.000 15.09 0.00 33.16 1.90
99 100 0.758734 CTGGCCGGATGACCTATTGA 59.241 55.000 5.28 0.00 0.00 2.57
100 101 1.349026 CTGGCCGGATGACCTATTGAT 59.651 52.381 5.28 0.00 0.00 2.57
101 102 2.567169 CTGGCCGGATGACCTATTGATA 59.433 50.000 5.28 0.00 0.00 2.15
102 103 2.301870 TGGCCGGATGACCTATTGATAC 59.698 50.000 5.05 0.00 0.00 2.24
103 104 2.301870 GGCCGGATGACCTATTGATACA 59.698 50.000 5.05 0.00 0.00 2.29
104 105 3.589988 GCCGGATGACCTATTGATACAG 58.410 50.000 5.05 0.00 0.00 2.74
105 106 3.006967 GCCGGATGACCTATTGATACAGT 59.993 47.826 5.05 0.00 0.00 3.55
106 107 4.219944 GCCGGATGACCTATTGATACAGTA 59.780 45.833 5.05 0.00 0.00 2.74
107 108 5.105310 GCCGGATGACCTATTGATACAGTAT 60.105 44.000 5.05 0.00 0.00 2.12
108 109 6.565234 CCGGATGACCTATTGATACAGTATC 58.435 44.000 13.06 13.06 35.74 2.24
109 110 6.378564 CCGGATGACCTATTGATACAGTATCT 59.621 42.308 19.39 5.09 36.17 1.98
110 111 7.093727 CCGGATGACCTATTGATACAGTATCTT 60.094 40.741 19.39 10.75 36.17 2.40
111 112 7.971168 CGGATGACCTATTGATACAGTATCTTC 59.029 40.741 19.39 8.32 36.17 2.87
112 113 9.030452 GGATGACCTATTGATACAGTATCTTCT 57.970 37.037 19.39 8.23 36.17 2.85
121 122 9.838339 ATTGATACAGTATCTTCTTTACCAAGG 57.162 33.333 19.39 0.00 36.17 3.61
122 123 8.375493 TGATACAGTATCTTCTTTACCAAGGT 57.625 34.615 19.39 0.00 36.17 3.50
123 124 8.822805 TGATACAGTATCTTCTTTACCAAGGTT 58.177 33.333 19.39 0.00 36.17 3.50
126 127 7.104290 ACAGTATCTTCTTTACCAAGGTTAGC 58.896 38.462 0.00 0.00 0.00 3.09
127 128 6.539103 CAGTATCTTCTTTACCAAGGTTAGCC 59.461 42.308 0.00 0.00 0.00 3.93
128 129 4.986054 TCTTCTTTACCAAGGTTAGCCA 57.014 40.909 0.00 0.00 37.19 4.75
129 130 5.514500 TCTTCTTTACCAAGGTTAGCCAT 57.486 39.130 0.00 0.00 37.19 4.40
130 131 5.887754 TCTTCTTTACCAAGGTTAGCCATT 58.112 37.500 0.00 0.00 37.19 3.16
131 132 5.944007 TCTTCTTTACCAAGGTTAGCCATTC 59.056 40.000 0.00 0.00 37.19 2.67
132 133 5.514500 TCTTTACCAAGGTTAGCCATTCT 57.486 39.130 0.00 0.00 37.19 2.40
133 134 5.887754 TCTTTACCAAGGTTAGCCATTCTT 58.112 37.500 0.00 0.00 37.19 2.52
134 135 6.311735 TCTTTACCAAGGTTAGCCATTCTTT 58.688 36.000 0.00 0.00 37.19 2.52
135 136 6.433093 TCTTTACCAAGGTTAGCCATTCTTTC 59.567 38.462 0.00 0.00 37.19 2.62
136 137 4.112634 ACCAAGGTTAGCCATTCTTTCA 57.887 40.909 0.00 0.00 37.19 2.69
137 138 4.677182 ACCAAGGTTAGCCATTCTTTCAT 58.323 39.130 0.00 0.00 37.19 2.57
138 139 4.463891 ACCAAGGTTAGCCATTCTTTCATG 59.536 41.667 0.00 0.00 37.19 3.07
139 140 4.706476 CCAAGGTTAGCCATTCTTTCATGA 59.294 41.667 0.00 0.00 37.19 3.07
140 141 5.163581 CCAAGGTTAGCCATTCTTTCATGAG 60.164 44.000 0.00 0.00 37.19 2.90
141 142 5.441718 AGGTTAGCCATTCTTTCATGAGA 57.558 39.130 0.00 0.00 37.19 3.27
142 143 5.819991 AGGTTAGCCATTCTTTCATGAGAA 58.180 37.500 0.00 0.00 39.76 2.87
143 144 6.248433 AGGTTAGCCATTCTTTCATGAGAAA 58.752 36.000 0.00 0.00 38.98 2.52
144 145 6.721208 AGGTTAGCCATTCTTTCATGAGAAAA 59.279 34.615 0.00 0.00 39.12 2.29
145 146 7.398332 AGGTTAGCCATTCTTTCATGAGAAAAT 59.602 33.333 0.00 0.00 39.12 1.82
146 147 8.037166 GGTTAGCCATTCTTTCATGAGAAAATT 58.963 33.333 0.00 0.00 38.98 1.82
147 148 8.866956 GTTAGCCATTCTTTCATGAGAAAATTG 58.133 33.333 0.00 0.00 42.78 2.32
148 149 7.001099 AGCCATTCTTTCATGAGAAAATTGT 57.999 32.000 0.00 0.00 42.78 2.71
149 150 7.447594 AGCCATTCTTTCATGAGAAAATTGTT 58.552 30.769 0.00 0.00 42.78 2.83
150 151 8.587608 AGCCATTCTTTCATGAGAAAATTGTTA 58.412 29.630 0.00 0.00 42.78 2.41
151 152 8.866956 GCCATTCTTTCATGAGAAAATTGTTAG 58.133 33.333 0.00 0.00 42.78 2.34
182 183 9.838339 ATTCTATAAATTGTTCCTGACGAATCT 57.162 29.630 0.00 0.00 31.67 2.40
183 184 8.873215 TCTATAAATTGTTCCTGACGAATCTC 57.127 34.615 0.00 0.00 31.67 2.75
184 185 8.696374 TCTATAAATTGTTCCTGACGAATCTCT 58.304 33.333 0.00 0.00 31.67 3.10
185 186 9.967346 CTATAAATTGTTCCTGACGAATCTCTA 57.033 33.333 0.00 0.00 31.67 2.43
186 187 6.969828 AAATTGTTCCTGACGAATCTCTAC 57.030 37.500 0.00 0.00 31.67 2.59
187 188 5.923733 ATTGTTCCTGACGAATCTCTACT 57.076 39.130 0.00 0.00 31.67 2.57
188 189 4.966965 TGTTCCTGACGAATCTCTACTC 57.033 45.455 0.00 0.00 31.67 2.59
189 190 3.695060 TGTTCCTGACGAATCTCTACTCC 59.305 47.826 0.00 0.00 31.67 3.85
190 191 3.935818 TCCTGACGAATCTCTACTCCT 57.064 47.619 0.00 0.00 0.00 3.69
191 192 5.124645 GTTCCTGACGAATCTCTACTCCTA 58.875 45.833 0.00 0.00 31.67 2.94
192 193 5.369409 TCCTGACGAATCTCTACTCCTAA 57.631 43.478 0.00 0.00 0.00 2.69
193 194 5.942961 TCCTGACGAATCTCTACTCCTAAT 58.057 41.667 0.00 0.00 0.00 1.73
194 195 5.765677 TCCTGACGAATCTCTACTCCTAATG 59.234 44.000 0.00 0.00 0.00 1.90
195 196 5.765677 CCTGACGAATCTCTACTCCTAATGA 59.234 44.000 0.00 0.00 0.00 2.57
196 197 6.263392 CCTGACGAATCTCTACTCCTAATGAA 59.737 42.308 0.00 0.00 0.00 2.57
197 198 7.028926 TGACGAATCTCTACTCCTAATGAAC 57.971 40.000 0.00 0.00 0.00 3.18
198 199 6.062434 ACGAATCTCTACTCCTAATGAACG 57.938 41.667 0.00 0.00 0.00 3.95
199 200 5.821470 ACGAATCTCTACTCCTAATGAACGA 59.179 40.000 0.00 0.00 0.00 3.85
200 201 6.137415 CGAATCTCTACTCCTAATGAACGAC 58.863 44.000 0.00 0.00 0.00 4.34
201 202 6.017770 CGAATCTCTACTCCTAATGAACGACT 60.018 42.308 0.00 0.00 0.00 4.18
202 203 7.467539 CGAATCTCTACTCCTAATGAACGACTT 60.468 40.741 0.00 0.00 0.00 3.01
203 204 6.438259 TCTCTACTCCTAATGAACGACTTG 57.562 41.667 0.00 0.00 0.00 3.16
204 205 6.178324 TCTCTACTCCTAATGAACGACTTGA 58.822 40.000 0.00 0.00 0.00 3.02
205 206 6.829298 TCTCTACTCCTAATGAACGACTTGAT 59.171 38.462 0.00 0.00 0.00 2.57
206 207 6.796426 TCTACTCCTAATGAACGACTTGATG 58.204 40.000 0.00 0.00 0.00 3.07
207 208 5.661056 ACTCCTAATGAACGACTTGATGA 57.339 39.130 0.00 0.00 0.00 2.92
208 209 6.037786 ACTCCTAATGAACGACTTGATGAA 57.962 37.500 0.00 0.00 0.00 2.57
209 210 6.644347 ACTCCTAATGAACGACTTGATGAAT 58.356 36.000 0.00 0.00 0.00 2.57
210 211 7.106239 ACTCCTAATGAACGACTTGATGAATT 58.894 34.615 0.00 0.00 0.00 2.17
211 212 7.607991 ACTCCTAATGAACGACTTGATGAATTT 59.392 33.333 0.00 0.00 0.00 1.82
212 213 9.098355 CTCCTAATGAACGACTTGATGAATTTA 57.902 33.333 0.00 0.00 0.00 1.40
213 214 9.613428 TCCTAATGAACGACTTGATGAATTTAT 57.387 29.630 0.00 0.00 0.00 1.40
218 219 8.653984 TGAACGACTTGATGAATTTATTTTCG 57.346 30.769 0.00 0.00 0.00 3.46
219 220 7.270365 TGAACGACTTGATGAATTTATTTTCGC 59.730 33.333 0.00 0.00 0.00 4.70
220 221 6.842163 ACGACTTGATGAATTTATTTTCGCT 58.158 32.000 0.00 0.00 0.00 4.93
221 222 6.742718 ACGACTTGATGAATTTATTTTCGCTG 59.257 34.615 0.00 0.00 0.00 5.18
222 223 6.195244 CGACTTGATGAATTTATTTTCGCTGG 59.805 38.462 0.00 0.00 0.00 4.85
223 224 6.332630 ACTTGATGAATTTATTTTCGCTGGG 58.667 36.000 0.00 0.00 0.00 4.45
224 225 5.913137 TGATGAATTTATTTTCGCTGGGT 57.087 34.783 0.00 0.00 0.00 4.51
225 226 6.279513 TGATGAATTTATTTTCGCTGGGTT 57.720 33.333 0.00 0.00 0.00 4.11
226 227 6.696411 TGATGAATTTATTTTCGCTGGGTTT 58.304 32.000 0.00 0.00 0.00 3.27
227 228 7.158021 TGATGAATTTATTTTCGCTGGGTTTT 58.842 30.769 0.00 0.00 0.00 2.43
228 229 7.659390 TGATGAATTTATTTTCGCTGGGTTTTT 59.341 29.630 0.00 0.00 0.00 1.94
245 246 2.833631 TTTTTCGTCTCTCCTCCCAC 57.166 50.000 0.00 0.00 0.00 4.61
246 247 0.974383 TTTTCGTCTCTCCTCCCACC 59.026 55.000 0.00 0.00 0.00 4.61
247 248 0.114560 TTTCGTCTCTCCTCCCACCT 59.885 55.000 0.00 0.00 0.00 4.00
248 249 0.323542 TTCGTCTCTCCTCCCACCTC 60.324 60.000 0.00 0.00 0.00 3.85
252 253 1.081092 CTCTCCTCCCACCTCCCAA 59.919 63.158 0.00 0.00 0.00 4.12
260 261 1.024579 CCCACCTCCCAATTTCGTCG 61.025 60.000 0.00 0.00 0.00 5.12
262 263 0.321298 CACCTCCCAATTTCGTCGGT 60.321 55.000 0.00 0.00 0.00 4.69
298 300 4.181010 CGCTCCACCCCATCCCAG 62.181 72.222 0.00 0.00 0.00 4.45
384 393 1.791103 CTCCGATCTCCCTCGCAGTC 61.791 65.000 0.00 0.00 37.33 3.51
392 401 2.262915 CCTCGCAGTCCACCAGAC 59.737 66.667 0.00 0.00 46.71 3.51
438 447 1.760086 CATCACCTCCTCGGCCTCT 60.760 63.158 0.00 0.00 35.61 3.69
601 628 1.004628 CACAGATCCCCATGGACAACA 59.995 52.381 15.22 0.00 45.58 3.33
609 636 0.171007 CCATGGACAACATTGACGCC 59.829 55.000 5.56 0.00 37.84 5.68
610 637 0.179192 CATGGACAACATTGACGCCG 60.179 55.000 0.00 0.00 37.84 6.46
611 638 1.922135 ATGGACAACATTGACGCCGC 61.922 55.000 0.00 0.00 35.97 6.53
732 759 3.129502 CCTGTCATGGCTGCCACG 61.130 66.667 25.99 17.53 35.80 4.94
733 760 3.129502 CTGTCATGGCTGCCACGG 61.130 66.667 25.99 19.19 35.80 4.94
766 793 1.395045 CGGCTCTCTGATGGCACCTA 61.395 60.000 0.00 0.00 0.00 3.08
776 803 0.912486 ATGGCACCTAAGGACTCCAC 59.088 55.000 0.00 0.00 0.00 4.02
805 832 3.868757 TGCTATACTGCTTCGTGAGTT 57.131 42.857 0.00 0.00 0.00 3.01
808 835 3.927142 GCTATACTGCTTCGTGAGTTGTT 59.073 43.478 0.00 0.00 0.00 2.83
850 877 2.239654 CCTTGGAGGAGTATTTGCCAGA 59.760 50.000 0.00 0.00 37.67 3.86
940 1019 5.814481 TCCATATCTTGTTCACACCATTCA 58.186 37.500 0.00 0.00 0.00 2.57
1084 1187 5.869753 AGATTAACATGTCTCTGTGTTGC 57.130 39.130 0.00 0.00 38.84 4.17
1225 1328 2.360165 CCATGCCAAAGTATCTGAAGGC 59.640 50.000 0.00 0.00 42.32 4.35
1328 1448 3.925379 TCAGAGAACAAATGCGCTTCTA 58.075 40.909 9.73 0.00 0.00 2.10
1772 2078 3.713858 TTGCCAGGCAATTGATATTCG 57.286 42.857 23.88 0.00 43.99 3.34
1809 2115 2.185387 GACAGTCCAAAGGCTACCCTA 58.815 52.381 0.00 0.00 41.90 3.53
2199 2591 5.622007 GCAAAAGTACATATGCAGGCTTTGA 60.622 40.000 16.12 0.00 38.63 2.69
2201 2596 5.762825 AAGTACATATGCAGGCTTTGATG 57.237 39.130 1.58 0.00 0.00 3.07
2251 2646 7.823745 AATGACTGAATTTTGGTCACTAAGT 57.176 32.000 9.94 0.00 41.75 2.24
2295 2690 1.604693 GCTGCGGCGTATTACTACCAT 60.605 52.381 9.37 0.00 0.00 3.55
2297 2692 1.409790 TGCGGCGTATTACTACCATGT 59.590 47.619 9.37 0.00 0.00 3.21
2304 2699 5.699458 GGCGTATTACTACCATGTGCTTATT 59.301 40.000 0.00 0.00 0.00 1.40
2314 2709 4.759693 ACCATGTGCTTATTCTTGACGAAA 59.240 37.500 0.00 0.00 34.79 3.46
2322 2717 5.560953 GCTTATTCTTGACGAAAGCAACACT 60.561 40.000 0.00 0.00 36.14 3.55
2423 2819 0.329261 TTCCACTCTGCATCCCCTTG 59.671 55.000 0.00 0.00 0.00 3.61
2530 2934 3.799755 GACCGCCGCATCACCAAC 61.800 66.667 0.00 0.00 0.00 3.77
2564 2969 4.702274 GGCTGTGGCATGGGGGTT 62.702 66.667 0.00 0.00 40.87 4.11
2575 2980 2.203480 GGGGGTTGTGCTTGCTGA 60.203 61.111 0.00 0.00 0.00 4.26
2651 3056 6.013984 AGGCTTCATCCATTCAATTTTGACTT 60.014 34.615 0.00 0.00 36.83 3.01
2740 3145 5.708948 TGCATTTTAGTGGTACAAGATTGC 58.291 37.500 0.00 0.00 44.16 3.56
2892 3300 2.132352 TGCATGCCCTGTTGCAACA 61.132 52.632 29.36 29.36 45.30 3.33
2897 3305 2.477176 GCCCTGTTGCAACACACGA 61.477 57.895 27.96 7.29 34.70 4.35
2899 3307 1.648720 CCTGTTGCAACACACGAGG 59.351 57.895 27.96 22.05 34.70 4.63
2912 3320 3.131755 ACACACGAGGTATTAACTAGCCC 59.868 47.826 0.00 0.00 0.00 5.19
2948 3356 1.415672 GGTGGTGGGAGGTGAGTCAA 61.416 60.000 0.00 0.00 0.00 3.18
3097 3508 5.423610 CCAATCTCTGATAAGATCCGGGTAT 59.576 44.000 0.00 0.00 34.90 2.73
3119 3530 2.362760 TAGCCGCCGGGTACAAGA 60.363 61.111 11.65 0.00 34.28 3.02
3319 3730 5.413213 CCGGTCATTGTTGGTATTCAAGTTA 59.587 40.000 0.00 0.00 35.80 2.24
3391 3802 4.575236 CAGATGAAGTTGCATGCTCATAGT 59.425 41.667 20.33 7.56 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 9.378504 TCTTACCGGGTTATATAAAGACCAATA 57.621 33.333 4.31 0.00 35.11 1.90
34 35 8.266363 TCTTACCGGGTTATATAAAGACCAAT 57.734 34.615 4.31 0.00 35.11 3.16
35 36 7.673641 TCTTACCGGGTTATATAAAGACCAA 57.326 36.000 4.31 0.00 35.11 3.67
36 37 7.510001 TCATCTTACCGGGTTATATAAAGACCA 59.490 37.037 4.31 0.00 35.11 4.02
37 38 7.899973 TCATCTTACCGGGTTATATAAAGACC 58.100 38.462 4.31 0.00 0.00 3.85
38 39 9.367444 CATCATCTTACCGGGTTATATAAAGAC 57.633 37.037 4.31 0.00 0.00 3.01
39 40 9.096823 ACATCATCTTACCGGGTTATATAAAGA 57.903 33.333 4.31 7.66 0.00 2.52
40 41 9.367444 GACATCATCTTACCGGGTTATATAAAG 57.633 37.037 4.31 1.46 0.00 1.85
41 42 8.872134 TGACATCATCTTACCGGGTTATATAAA 58.128 33.333 4.31 0.00 0.00 1.40
42 43 8.425237 TGACATCATCTTACCGGGTTATATAA 57.575 34.615 4.31 0.00 0.00 0.98
43 44 8.474831 CATGACATCATCTTACCGGGTTATATA 58.525 37.037 4.31 0.00 33.61 0.86
44 45 6.928348 TGACATCATCTTACCGGGTTATAT 57.072 37.500 4.31 0.00 0.00 0.86
45 46 6.697395 CATGACATCATCTTACCGGGTTATA 58.303 40.000 4.31 0.00 33.61 0.98
46 47 5.551233 CATGACATCATCTTACCGGGTTAT 58.449 41.667 4.31 0.00 33.61 1.89
47 48 4.742440 GCATGACATCATCTTACCGGGTTA 60.742 45.833 4.31 0.00 33.61 2.85
48 49 3.808728 CATGACATCATCTTACCGGGTT 58.191 45.455 4.31 0.00 33.61 4.11
49 50 2.485479 GCATGACATCATCTTACCGGGT 60.485 50.000 6.32 4.46 33.61 5.28
50 51 2.146342 GCATGACATCATCTTACCGGG 58.854 52.381 6.32 0.00 33.61 5.73
51 52 2.146342 GGCATGACATCATCTTACCGG 58.854 52.381 0.00 0.00 33.61 5.28
52 53 3.117491 AGGCATGACATCATCTTACCG 57.883 47.619 0.00 0.00 33.61 4.02
53 54 3.999663 GCTAGGCATGACATCATCTTACC 59.000 47.826 0.00 0.00 33.61 2.85
54 55 4.450419 GTGCTAGGCATGACATCATCTTAC 59.550 45.833 0.00 0.00 41.91 2.34
55 56 4.101430 TGTGCTAGGCATGACATCATCTTA 59.899 41.667 0.00 0.00 41.91 2.10
56 57 3.118149 TGTGCTAGGCATGACATCATCTT 60.118 43.478 0.00 0.00 41.91 2.40
57 58 2.436911 TGTGCTAGGCATGACATCATCT 59.563 45.455 0.00 0.00 41.91 2.90
58 59 2.547211 GTGTGCTAGGCATGACATCATC 59.453 50.000 0.00 0.00 41.91 2.92
59 60 2.569059 GTGTGCTAGGCATGACATCAT 58.431 47.619 0.00 0.00 41.91 2.45
60 61 1.407299 GGTGTGCTAGGCATGACATCA 60.407 52.381 0.00 0.00 41.91 3.07
61 62 1.134280 AGGTGTGCTAGGCATGACATC 60.134 52.381 0.00 0.00 41.91 3.06
62 63 0.914644 AGGTGTGCTAGGCATGACAT 59.085 50.000 0.00 0.00 41.91 3.06
63 64 0.036105 CAGGTGTGCTAGGCATGACA 60.036 55.000 0.00 0.00 41.91 3.58
64 65 0.745845 CCAGGTGTGCTAGGCATGAC 60.746 60.000 0.00 0.00 41.91 3.06
65 66 1.603842 CCAGGTGTGCTAGGCATGA 59.396 57.895 0.00 0.00 41.91 3.07
66 67 2.117156 GCCAGGTGTGCTAGGCATG 61.117 63.158 0.00 0.00 46.26 4.06
67 68 2.273449 GCCAGGTGTGCTAGGCAT 59.727 61.111 0.00 0.00 46.26 4.40
70 71 4.473520 CCGGCCAGGTGTGCTAGG 62.474 72.222 2.24 0.00 34.51 3.02
71 72 2.735772 ATCCGGCCAGGTGTGCTAG 61.736 63.158 2.24 0.00 41.99 3.42
72 73 2.687200 ATCCGGCCAGGTGTGCTA 60.687 61.111 2.24 0.00 41.99 3.49
73 74 4.415150 CATCCGGCCAGGTGTGCT 62.415 66.667 2.24 0.00 41.99 4.40
74 75 4.408821 TCATCCGGCCAGGTGTGC 62.409 66.667 2.24 0.00 41.99 4.57
75 76 2.436646 GTCATCCGGCCAGGTGTG 60.437 66.667 2.24 9.09 41.99 3.82
76 77 2.815684 TAGGTCATCCGGCCAGGTGT 62.816 60.000 2.24 0.00 41.99 4.16
77 78 1.410850 ATAGGTCATCCGGCCAGGTG 61.411 60.000 2.24 0.00 41.99 4.00
78 79 0.694444 AATAGGTCATCCGGCCAGGT 60.694 55.000 2.24 0.00 41.99 4.00
79 80 0.250467 CAATAGGTCATCCGGCCAGG 60.250 60.000 2.24 5.27 42.97 4.45
80 81 0.758734 TCAATAGGTCATCCGGCCAG 59.241 55.000 2.24 0.00 39.05 4.85
81 82 1.434188 ATCAATAGGTCATCCGGCCA 58.566 50.000 2.24 0.00 39.05 5.36
82 83 2.301870 TGTATCAATAGGTCATCCGGCC 59.698 50.000 0.00 0.00 39.05 6.13
83 84 3.006967 ACTGTATCAATAGGTCATCCGGC 59.993 47.826 0.00 0.00 39.05 6.13
84 85 4.873746 ACTGTATCAATAGGTCATCCGG 57.126 45.455 0.00 0.00 39.05 5.14
85 86 7.397892 AGATACTGTATCAATAGGTCATCCG 57.602 40.000 25.16 0.00 37.65 4.18
86 87 9.030452 AGAAGATACTGTATCAATAGGTCATCC 57.970 37.037 25.16 4.41 37.65 3.51
95 96 9.838339 CCTTGGTAAAGAAGATACTGTATCAAT 57.162 33.333 25.16 15.63 32.45 2.57
96 97 8.822805 ACCTTGGTAAAGAAGATACTGTATCAA 58.177 33.333 25.16 10.35 35.13 2.57
97 98 8.375493 ACCTTGGTAAAGAAGATACTGTATCA 57.625 34.615 25.16 5.13 35.13 2.15
100 101 8.255905 GCTAACCTTGGTAAAGAAGATACTGTA 58.744 37.037 6.34 0.00 35.19 2.74
101 102 7.104290 GCTAACCTTGGTAAAGAAGATACTGT 58.896 38.462 6.34 0.00 35.19 3.55
102 103 6.539103 GGCTAACCTTGGTAAAGAAGATACTG 59.461 42.308 6.34 0.00 35.19 2.74
103 104 6.214819 TGGCTAACCTTGGTAAAGAAGATACT 59.785 38.462 6.34 0.00 35.19 2.12
104 105 6.412214 TGGCTAACCTTGGTAAAGAAGATAC 58.588 40.000 6.34 0.00 35.19 2.24
105 106 6.630203 TGGCTAACCTTGGTAAAGAAGATA 57.370 37.500 6.34 0.00 35.19 1.98
106 107 5.514500 TGGCTAACCTTGGTAAAGAAGAT 57.486 39.130 6.34 0.00 35.19 2.40
107 108 4.986054 TGGCTAACCTTGGTAAAGAAGA 57.014 40.909 6.34 0.00 35.19 2.87
108 109 5.946377 AGAATGGCTAACCTTGGTAAAGAAG 59.054 40.000 6.34 0.00 35.19 2.85
109 110 5.887754 AGAATGGCTAACCTTGGTAAAGAA 58.112 37.500 6.34 0.00 35.19 2.52
110 111 5.514500 AGAATGGCTAACCTTGGTAAAGA 57.486 39.130 6.34 0.00 35.19 2.52
111 112 6.208599 TGAAAGAATGGCTAACCTTGGTAAAG 59.791 38.462 0.00 0.00 36.63 1.85
112 113 6.071984 TGAAAGAATGGCTAACCTTGGTAAA 58.928 36.000 0.00 0.00 36.63 2.01
113 114 5.636123 TGAAAGAATGGCTAACCTTGGTAA 58.364 37.500 0.00 0.00 36.63 2.85
114 115 5.249780 TGAAAGAATGGCTAACCTTGGTA 57.750 39.130 0.00 0.00 36.63 3.25
115 116 4.112634 TGAAAGAATGGCTAACCTTGGT 57.887 40.909 0.00 0.00 36.63 3.67
116 117 4.706476 TCATGAAAGAATGGCTAACCTTGG 59.294 41.667 0.00 0.00 36.63 3.61
117 118 5.649395 TCTCATGAAAGAATGGCTAACCTTG 59.351 40.000 0.00 0.00 36.63 3.61
118 119 5.819991 TCTCATGAAAGAATGGCTAACCTT 58.180 37.500 0.00 0.00 36.63 3.50
119 120 5.441718 TCTCATGAAAGAATGGCTAACCT 57.558 39.130 0.00 0.00 36.63 3.50
120 121 6.515272 TTTCTCATGAAAGAATGGCTAACC 57.485 37.500 0.00 0.00 37.27 2.85
121 122 8.866956 CAATTTTCTCATGAAAGAATGGCTAAC 58.133 33.333 0.00 0.00 42.34 2.34
122 123 8.587608 ACAATTTTCTCATGAAAGAATGGCTAA 58.412 29.630 0.00 0.00 42.34 3.09
123 124 8.125978 ACAATTTTCTCATGAAAGAATGGCTA 57.874 30.769 0.00 0.00 42.34 3.93
124 125 7.001099 ACAATTTTCTCATGAAAGAATGGCT 57.999 32.000 0.00 0.00 42.34 4.75
125 126 7.662604 AACAATTTTCTCATGAAAGAATGGC 57.337 32.000 0.00 0.00 42.34 4.40
156 157 9.838339 AGATTCGTCAGGAACAATTTATAGAAT 57.162 29.630 0.00 0.00 37.50 2.40
157 158 9.314321 GAGATTCGTCAGGAACAATTTATAGAA 57.686 33.333 0.00 0.00 37.50 2.10
158 159 8.696374 AGAGATTCGTCAGGAACAATTTATAGA 58.304 33.333 0.00 0.00 37.50 1.98
159 160 8.879342 AGAGATTCGTCAGGAACAATTTATAG 57.121 34.615 0.00 0.00 37.50 1.31
160 161 9.745880 GTAGAGATTCGTCAGGAACAATTTATA 57.254 33.333 0.00 0.00 37.50 0.98
161 162 8.478877 AGTAGAGATTCGTCAGGAACAATTTAT 58.521 33.333 0.00 0.00 37.50 1.40
162 163 7.837863 AGTAGAGATTCGTCAGGAACAATTTA 58.162 34.615 0.00 0.00 37.50 1.40
163 164 6.702329 AGTAGAGATTCGTCAGGAACAATTT 58.298 36.000 0.00 0.00 37.50 1.82
164 165 6.287589 AGTAGAGATTCGTCAGGAACAATT 57.712 37.500 0.00 0.00 37.50 2.32
165 166 5.163499 GGAGTAGAGATTCGTCAGGAACAAT 60.163 44.000 0.00 0.00 37.50 2.71
166 167 4.158025 GGAGTAGAGATTCGTCAGGAACAA 59.842 45.833 0.00 0.00 37.50 2.83
167 168 3.695060 GGAGTAGAGATTCGTCAGGAACA 59.305 47.826 0.00 0.00 37.50 3.18
168 169 3.949113 AGGAGTAGAGATTCGTCAGGAAC 59.051 47.826 0.00 0.00 37.50 3.62
169 170 4.237976 AGGAGTAGAGATTCGTCAGGAA 57.762 45.455 0.00 0.00 39.42 3.36
170 171 3.935818 AGGAGTAGAGATTCGTCAGGA 57.064 47.619 0.00 0.00 0.00 3.86
171 172 5.765677 TCATTAGGAGTAGAGATTCGTCAGG 59.234 44.000 0.00 0.00 0.00 3.86
172 173 6.869315 TCATTAGGAGTAGAGATTCGTCAG 57.131 41.667 0.00 0.00 0.00 3.51
173 174 6.238402 CGTTCATTAGGAGTAGAGATTCGTCA 60.238 42.308 0.00 0.00 0.00 4.35
174 175 6.018098 TCGTTCATTAGGAGTAGAGATTCGTC 60.018 42.308 0.00 0.00 0.00 4.20
175 176 5.821470 TCGTTCATTAGGAGTAGAGATTCGT 59.179 40.000 0.00 0.00 0.00 3.85
176 177 6.017770 AGTCGTTCATTAGGAGTAGAGATTCG 60.018 42.308 0.00 0.00 0.00 3.34
177 178 7.266922 AGTCGTTCATTAGGAGTAGAGATTC 57.733 40.000 0.00 0.00 0.00 2.52
178 179 7.339721 TCAAGTCGTTCATTAGGAGTAGAGATT 59.660 37.037 0.00 0.00 0.00 2.40
179 180 6.829298 TCAAGTCGTTCATTAGGAGTAGAGAT 59.171 38.462 0.00 0.00 0.00 2.75
180 181 6.178324 TCAAGTCGTTCATTAGGAGTAGAGA 58.822 40.000 0.00 0.00 0.00 3.10
181 182 6.438259 TCAAGTCGTTCATTAGGAGTAGAG 57.562 41.667 0.00 0.00 0.00 2.43
182 183 6.602009 TCATCAAGTCGTTCATTAGGAGTAGA 59.398 38.462 0.00 0.00 0.00 2.59
183 184 6.796426 TCATCAAGTCGTTCATTAGGAGTAG 58.204 40.000 0.00 0.00 0.00 2.57
184 185 6.769134 TCATCAAGTCGTTCATTAGGAGTA 57.231 37.500 0.00 0.00 0.00 2.59
185 186 5.661056 TCATCAAGTCGTTCATTAGGAGT 57.339 39.130 0.00 0.00 0.00 3.85
186 187 7.545362 AATTCATCAAGTCGTTCATTAGGAG 57.455 36.000 0.00 0.00 0.00 3.69
187 188 7.921786 AAATTCATCAAGTCGTTCATTAGGA 57.078 32.000 0.00 0.00 0.00 2.94
192 193 9.277565 CGAAAATAAATTCATCAAGTCGTTCAT 57.722 29.630 0.00 0.00 0.00 2.57
193 194 7.270365 GCGAAAATAAATTCATCAAGTCGTTCA 59.730 33.333 0.00 0.00 0.00 3.18
194 195 7.481798 AGCGAAAATAAATTCATCAAGTCGTTC 59.518 33.333 0.00 0.00 0.00 3.95
195 196 7.271223 CAGCGAAAATAAATTCATCAAGTCGTT 59.729 33.333 0.00 0.00 0.00 3.85
196 197 6.742718 CAGCGAAAATAAATTCATCAAGTCGT 59.257 34.615 0.00 0.00 0.00 4.34
197 198 6.195244 CCAGCGAAAATAAATTCATCAAGTCG 59.805 38.462 0.00 0.00 0.00 4.18
198 199 6.473455 CCCAGCGAAAATAAATTCATCAAGTC 59.527 38.462 0.00 0.00 0.00 3.01
199 200 6.071391 ACCCAGCGAAAATAAATTCATCAAGT 60.071 34.615 0.00 0.00 0.00 3.16
200 201 6.332630 ACCCAGCGAAAATAAATTCATCAAG 58.667 36.000 0.00 0.00 0.00 3.02
201 202 6.279513 ACCCAGCGAAAATAAATTCATCAA 57.720 33.333 0.00 0.00 0.00 2.57
202 203 5.913137 ACCCAGCGAAAATAAATTCATCA 57.087 34.783 0.00 0.00 0.00 3.07
203 204 7.595311 AAAACCCAGCGAAAATAAATTCATC 57.405 32.000 0.00 0.00 0.00 2.92
204 205 7.977789 AAAAACCCAGCGAAAATAAATTCAT 57.022 28.000 0.00 0.00 0.00 2.57
226 227 1.346722 GGTGGGAGGAGAGACGAAAAA 59.653 52.381 0.00 0.00 0.00 1.94
227 228 0.974383 GGTGGGAGGAGAGACGAAAA 59.026 55.000 0.00 0.00 0.00 2.29
228 229 0.114560 AGGTGGGAGGAGAGACGAAA 59.885 55.000 0.00 0.00 0.00 3.46
229 230 0.323542 GAGGTGGGAGGAGAGACGAA 60.324 60.000 0.00 0.00 0.00 3.85
230 231 1.303615 GAGGTGGGAGGAGAGACGA 59.696 63.158 0.00 0.00 0.00 4.20
231 232 1.755008 GGAGGTGGGAGGAGAGACG 60.755 68.421 0.00 0.00 0.00 4.18
232 233 1.382009 GGGAGGTGGGAGGAGAGAC 60.382 68.421 0.00 0.00 0.00 3.36
233 234 1.452226 TTGGGAGGTGGGAGGAGAGA 61.452 60.000 0.00 0.00 0.00 3.10
234 235 0.327000 ATTGGGAGGTGGGAGGAGAG 60.327 60.000 0.00 0.00 0.00 3.20
235 236 0.121197 AATTGGGAGGTGGGAGGAGA 59.879 55.000 0.00 0.00 0.00 3.71
236 237 1.002857 AAATTGGGAGGTGGGAGGAG 58.997 55.000 0.00 0.00 0.00 3.69
237 238 0.999712 GAAATTGGGAGGTGGGAGGA 59.000 55.000 0.00 0.00 0.00 3.71
238 239 0.394352 CGAAATTGGGAGGTGGGAGG 60.394 60.000 0.00 0.00 0.00 4.30
239 240 0.328258 ACGAAATTGGGAGGTGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
240 241 0.326927 GACGAAATTGGGAGGTGGGA 59.673 55.000 0.00 0.00 0.00 4.37
241 242 1.024579 CGACGAAATTGGGAGGTGGG 61.025 60.000 0.00 0.00 0.00 4.61
242 243 1.024579 CCGACGAAATTGGGAGGTGG 61.025 60.000 0.00 0.00 0.00 4.61
243 244 0.321298 ACCGACGAAATTGGGAGGTG 60.321 55.000 0.00 0.00 35.88 4.00
244 245 0.399075 AACCGACGAAATTGGGAGGT 59.601 50.000 0.00 0.00 35.88 3.85
245 246 1.530323 AAACCGACGAAATTGGGAGG 58.470 50.000 0.00 0.00 35.88 4.30
246 247 3.636282 AAAAACCGACGAAATTGGGAG 57.364 42.857 0.00 0.00 35.88 4.30
280 282 4.731853 TGGGATGGGGTGGAGCGA 62.732 66.667 0.00 0.00 0.00 4.93
282 284 3.813724 CCTGGGATGGGGTGGAGC 61.814 72.222 0.00 0.00 0.00 4.70
508 517 4.227134 CGACGCCCCTGGGATCTG 62.227 72.222 16.20 3.02 37.50 2.90
539 548 2.173669 CGATGGCGTGTGTGGATCC 61.174 63.158 4.20 4.20 0.00 3.36
574 583 4.530857 GGGGATCTGTGGCGTCCG 62.531 72.222 0.00 0.00 32.71 4.79
627 654 4.789075 CGTCTGGGGCGTACGTGG 62.789 72.222 17.90 3.24 32.16 4.94
749 776 1.202627 CCTTAGGTGCCATCAGAGAGC 60.203 57.143 0.00 0.00 0.00 4.09
766 793 2.815589 GCAAATCACCTGTGGAGTCCTT 60.816 50.000 11.33 0.00 0.00 3.36
776 803 4.025396 CGAAGCAGTATAGCAAATCACCTG 60.025 45.833 0.00 0.00 36.85 4.00
805 832 1.511850 CACAAGATCAGCGGACAACA 58.488 50.000 0.00 0.00 0.00 3.33
808 835 0.671472 CTGCACAAGATCAGCGGACA 60.671 55.000 0.00 0.00 36.79 4.02
850 877 2.852449 TCCTTTGCCATCCCTAGAATGT 59.148 45.455 0.00 0.00 0.00 2.71
970 1049 7.119699 TGCAAACTATATCTTGTCTTCCAACTG 59.880 37.037 0.00 0.00 0.00 3.16
1084 1187 4.767255 GGCAGTGCCGTCTCCTGG 62.767 72.222 20.55 0.00 39.62 4.45
1171 1274 1.004560 CGTCTTTGGCAGGAGCAGA 60.005 57.895 0.00 0.00 44.61 4.26
1225 1328 2.672961 TCAGTCGCAGTGGGAATTAG 57.327 50.000 12.00 0.00 0.00 1.73
1328 1448 3.368531 GCCGCCTTAAGGAATATCTCGAT 60.369 47.826 26.21 0.00 37.39 3.59
1369 1489 3.711190 TCCTAGGAAGAACATGCTGCATA 59.289 43.478 15.78 0.00 0.00 3.14
1510 1630 4.830600 GGAAAACCTTTCCTACACAATGGA 59.169 41.667 10.33 0.00 35.73 3.41
1680 1982 5.191426 ACATCTCAACTGCATGCTATCTTT 58.809 37.500 20.33 1.74 0.00 2.52
1768 2074 1.923356 ATTGCCAACCCAAGTCGAAT 58.077 45.000 0.00 0.00 0.00 3.34
1772 2078 1.686052 TGTCAATTGCCAACCCAAGTC 59.314 47.619 0.00 0.00 0.00 3.01
1809 2115 1.544314 GCCAGACTCCTTTTGACAGCT 60.544 52.381 0.00 0.00 0.00 4.24
2295 2690 3.812609 TGCTTTCGTCAAGAATAAGCACA 59.187 39.130 0.00 0.00 43.72 4.57
2297 2692 4.274705 TGTTGCTTTCGTCAAGAATAAGCA 59.725 37.500 0.00 0.00 45.65 3.91
2304 2699 2.866156 CTCAGTGTTGCTTTCGTCAAGA 59.134 45.455 1.85 0.00 33.80 3.02
2423 2819 2.126031 GCTCCCCGTCAACTCGAC 60.126 66.667 0.00 0.00 41.62 4.20
2527 2931 1.739466 CTGGACGATCATGGTTGGTTG 59.261 52.381 0.00 0.00 0.00 3.77
2528 2932 1.340017 CCTGGACGATCATGGTTGGTT 60.340 52.381 0.00 0.00 0.00 3.67
2529 2933 0.253044 CCTGGACGATCATGGTTGGT 59.747 55.000 0.00 0.00 0.00 3.67
2530 2934 1.097547 GCCTGGACGATCATGGTTGG 61.098 60.000 0.00 0.00 0.00 3.77
2563 2968 1.814394 GATCACCATCAGCAAGCACAA 59.186 47.619 0.00 0.00 0.00 3.33
2564 2969 1.456296 GATCACCATCAGCAAGCACA 58.544 50.000 0.00 0.00 0.00 4.57
2575 2980 2.709966 TCATGATGGAGGGATCACCAT 58.290 47.619 15.01 15.01 45.06 3.55
2651 3056 7.225931 CACTTACCAAAAGCTAGTTGTCTACAA 59.774 37.037 8.74 0.00 0.00 2.41
2740 3145 5.275927 CGTGACAGTCTATCAATTAGCAACG 60.276 44.000 1.31 0.00 0.00 4.10
2892 3300 2.360165 CGGGCTAGTTAATACCTCGTGT 59.640 50.000 0.00 0.00 0.00 4.49
2897 3305 1.339291 GCGTCGGGCTAGTTAATACCT 59.661 52.381 0.00 0.00 39.11 3.08
2948 3356 2.612604 GGTGCTTTTGTTCACCGTTTT 58.387 42.857 0.00 0.00 42.67 2.43
3097 3508 3.819652 TACCCGGCGGCTACCCTA 61.820 66.667 23.20 0.00 0.00 3.53
3319 3730 6.959639 ATAAAAACAGACAAGTCATGTGGT 57.040 33.333 2.72 0.00 44.12 4.16
3391 3802 8.593679 TCTTGACAAAGAACATAGACTGGAATA 58.406 33.333 0.00 0.00 39.52 1.75
3435 3846 1.040646 AGCGATGCTCGGATTCCTAA 58.959 50.000 0.30 0.00 40.84 2.69


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

AutoCloner maintained by Alex Coulton.