Multiple sequence alignment - TraesCS3B01G133900

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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 TraesCS3B01G133900 chr3B 100.000 3324 0 0 1 3324 116113713 116110390 0.000000e+00 6139.0
1 TraesCS3B01G133900 chr3D 90.924 3118 180 47 232 3322 70247462 70244421 0.000000e+00 4095.0
2 TraesCS3B01G133900 chr3D 85.783 415 47 12 425 834 70274495 70274088 2.370000e-116 429.0
3 TraesCS3B01G133900 chr3D 85.909 220 31 0 198 417 70274755 70274536 5.540000e-58 235.0
4 TraesCS3B01G133900 chr3A 93.750 1056 41 15 1436 2477 81696283 81695239 0.000000e+00 1561.0
5 TraesCS3B01G133900 chr3A 93.293 835 43 9 557 1390 81697107 81696285 0.000000e+00 1219.0
6 TraesCS3B01G133900 chr3A 93.523 633 37 3 2693 3322 81695240 81694609 0.000000e+00 939.0
7 TraesCS3B01G133900 chr3A 83.333 282 35 2 203 483 81699324 81699054 1.980000e-62 250.0
8 TraesCS3B01G133900 chr1B 77.318 701 133 24 1498 2187 677914597 677913912 1.120000e-104 390.0
9 TraesCS3B01G133900 chr1A 83.573 347 54 3 1498 1842 584374515 584374170 4.140000e-84 322.0
10 TraesCS3B01G133900 chr1A 84.932 146 18 4 480 622 394425665 394425809 9.610000e-31 145.0
11 TraesCS3B01G133900 chr1A 84.247 146 19 4 480 622 394514027 394514171 4.470000e-29 139.0
12 TraesCS3B01G133900 chr1D 88.384 198 21 2 2 198 295385791 295385987 1.540000e-58 237.0
13 TraesCS3B01G133900 chr5A 85.616 146 17 4 480 622 542010482 542010338 2.070000e-32 150.0
14 TraesCS3B01G133900 chr5A 85.616 146 17 4 480 622 561110958 561111102 2.070000e-32 150.0
15 TraesCS3B01G133900 chr2A 78.981 157 26 7 477 629 197793839 197793686 2.110000e-17 100.0
16 TraesCS3B01G133900 chr2B 78.912 147 22 7 475 619 239198598 239198459 1.270000e-14 91.6


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 TraesCS3B01G133900 chr3B 116110390 116113713 3323 True 6139.00 6139 100.00000 1 3324 1 chr3B.!!$R1 3323
1 TraesCS3B01G133900 chr3D 70244421 70247462 3041 True 4095.00 4095 90.92400 232 3322 1 chr3D.!!$R1 3090
2 TraesCS3B01G133900 chr3D 70274088 70274755 667 True 332.00 429 85.84600 198 834 2 chr3D.!!$R2 636
3 TraesCS3B01G133900 chr3A 81694609 81699324 4715 True 992.25 1561 90.97475 203 3322 4 chr3A.!!$R1 3119
4 TraesCS3B01G133900 chr1B 677913912 677914597 685 True 390.00 390 77.31800 1498 2187 1 chr1B.!!$R1 689

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
64 65 0.094901 CGATCGACTCGGGCTATACG 59.905 60.0 10.26 0.0 43.82 3.06 F
189 190 0.180171 CATACCCGACCTGATTGCCA 59.820 55.0 0.00 0.0 0.00 4.92 F
1350 3277 0.468226 TCCTCTGCGACAAGTTTGGT 59.532 50.0 0.00 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 3408 0.095245 AAGCACAAACGCATCGATCG 59.905 50.000 9.36 9.36 0.0 3.69 R
1672 3604 4.335647 AAGTCCAGCGGGCACAGG 62.336 66.667 0.00 0.00 0.0 4.00 R
2542 4502 0.171903 GCATGCAGGTGAAAATCGCT 59.828 50.000 14.21 0.00 0.0 4.93 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
21 22 3.482722 TCGGTACATCTCGTTGAGAAC 57.517 47.619 0.00 0.00 42.27 3.01
33 34 3.148026 GTTGAGAACGCCTACTCTACC 57.852 52.381 0.00 0.00 34.61 3.18
34 35 1.760192 TGAGAACGCCTACTCTACCC 58.240 55.000 0.00 0.00 34.65 3.69
35 36 0.662085 GAGAACGCCTACTCTACCCG 59.338 60.000 0.00 0.00 0.00 5.28
36 37 0.254178 AGAACGCCTACTCTACCCGA 59.746 55.000 0.00 0.00 0.00 5.14
37 38 1.133853 AGAACGCCTACTCTACCCGAT 60.134 52.381 0.00 0.00 0.00 4.18
38 39 1.001597 GAACGCCTACTCTACCCGATG 60.002 57.143 0.00 0.00 0.00 3.84
39 40 0.822532 ACGCCTACTCTACCCGATGG 60.823 60.000 0.00 0.00 37.80 3.51
49 50 4.626081 CCCGATGGGTGCCCGATC 62.626 72.222 2.44 6.27 38.25 3.69
50 51 4.969196 CCGATGGGTGCCCGATCG 62.969 72.222 22.65 22.65 41.81 3.69
51 52 3.911698 CGATGGGTGCCCGATCGA 61.912 66.667 24.20 0.00 43.22 3.59
52 53 2.280186 GATGGGTGCCCGATCGAC 60.280 66.667 18.66 9.01 39.42 4.20
53 54 2.764128 ATGGGTGCCCGATCGACT 60.764 61.111 18.66 0.00 39.42 4.18
54 55 2.701163 GATGGGTGCCCGATCGACTC 62.701 65.000 18.66 7.59 39.42 3.36
63 64 3.971858 CGATCGACTCGGGCTATAC 57.028 57.895 10.26 0.00 43.82 1.47
64 65 0.094901 CGATCGACTCGGGCTATACG 59.905 60.000 10.26 0.00 43.82 3.06
65 66 1.436600 GATCGACTCGGGCTATACGA 58.563 55.000 0.00 0.00 38.79 3.43
66 67 1.128321 GATCGACTCGGGCTATACGAC 59.872 57.143 0.00 0.00 36.25 4.34
67 68 1.203563 CGACTCGGGCTATACGACG 59.796 63.158 0.00 0.00 36.25 5.12
68 69 1.573436 GACTCGGGCTATACGACGG 59.427 63.158 0.00 0.00 36.25 4.79
69 70 1.849976 GACTCGGGCTATACGACGGG 61.850 65.000 0.00 0.00 36.25 5.28
70 71 1.895707 CTCGGGCTATACGACGGGT 60.896 63.158 0.00 0.00 36.25 5.28
71 72 1.450531 CTCGGGCTATACGACGGGTT 61.451 60.000 0.00 0.00 36.25 4.11
72 73 1.008079 CGGGCTATACGACGGGTTC 60.008 63.158 0.00 0.00 0.00 3.62
81 82 2.511600 GACGGGTTCGAGCATGGG 60.512 66.667 0.53 0.00 40.11 4.00
82 83 4.778143 ACGGGTTCGAGCATGGGC 62.778 66.667 0.53 0.00 40.11 5.36
83 84 4.776322 CGGGTTCGAGCATGGGCA 62.776 66.667 0.53 0.00 44.61 5.36
84 85 2.124151 GGGTTCGAGCATGGGCAT 60.124 61.111 0.53 0.00 44.61 4.40
85 86 2.484062 GGGTTCGAGCATGGGCATG 61.484 63.158 0.53 0.00 44.61 4.06
86 87 1.451927 GGTTCGAGCATGGGCATGA 60.452 57.895 0.53 0.00 44.61 3.07
87 88 1.442526 GGTTCGAGCATGGGCATGAG 61.443 60.000 0.53 0.00 44.61 2.90
88 89 0.745845 GTTCGAGCATGGGCATGAGT 60.746 55.000 0.00 0.00 44.61 3.41
89 90 0.462581 TTCGAGCATGGGCATGAGTC 60.463 55.000 0.00 0.00 44.61 3.36
90 91 1.153309 CGAGCATGGGCATGAGTCA 60.153 57.895 0.00 0.00 44.61 3.41
91 92 0.745486 CGAGCATGGGCATGAGTCAA 60.745 55.000 0.00 0.00 44.61 3.18
92 93 1.022735 GAGCATGGGCATGAGTCAAG 58.977 55.000 0.00 0.00 44.61 3.02
93 94 0.622136 AGCATGGGCATGAGTCAAGA 59.378 50.000 0.00 0.00 44.61 3.02
94 95 0.737219 GCATGGGCATGAGTCAAGAC 59.263 55.000 0.00 0.00 41.20 3.01
95 96 1.386533 CATGGGCATGAGTCAAGACC 58.613 55.000 13.60 13.60 41.20 3.85
96 97 0.257039 ATGGGCATGAGTCAAGACCC 59.743 55.000 17.57 17.54 37.88 4.46
97 98 1.450312 GGGCATGAGTCAAGACCCG 60.450 63.158 9.23 0.00 0.00 5.28
98 99 1.296715 GGCATGAGTCAAGACCCGT 59.703 57.895 0.00 0.00 0.00 5.28
99 100 1.021390 GGCATGAGTCAAGACCCGTG 61.021 60.000 0.00 0.16 0.00 4.94
100 101 1.021390 GCATGAGTCAAGACCCGTGG 61.021 60.000 0.00 0.00 0.00 4.94
101 102 0.391661 CATGAGTCAAGACCCGTGGG 60.392 60.000 2.58 2.58 42.03 4.61
111 112 3.766691 CCCGTGGGTAGGGTCGTG 61.767 72.222 0.00 0.00 43.89 4.35
112 113 3.766691 CCGTGGGTAGGGTCGTGG 61.767 72.222 0.00 0.00 0.00 4.94
113 114 3.766691 CGTGGGTAGGGTCGTGGG 61.767 72.222 0.00 0.00 0.00 4.61
114 115 4.091939 GTGGGTAGGGTCGTGGGC 62.092 72.222 0.00 0.00 0.00 5.36
123 124 2.435234 GTCGTGGGCGCCAACATA 60.435 61.111 32.67 17.96 34.18 2.29
124 125 2.435234 TCGTGGGCGCCAACATAC 60.435 61.111 32.67 18.54 34.18 2.39
125 126 3.505184 CGTGGGCGCCAACATACC 61.505 66.667 32.67 12.25 34.18 2.73
126 127 3.138128 GTGGGCGCCAACATACCC 61.138 66.667 29.55 8.71 43.14 3.69
127 128 4.787286 TGGGCGCCAACATACCCG 62.787 66.667 30.85 0.00 46.02 5.28
128 129 4.476752 GGGCGCCAACATACCCGA 62.477 66.667 30.85 0.00 31.32 5.14
129 130 2.203153 GGCGCCAACATACCCGAT 60.203 61.111 24.80 0.00 0.00 4.18
130 131 1.070105 GGCGCCAACATACCCGATA 59.930 57.895 24.80 0.00 0.00 2.92
131 132 0.533308 GGCGCCAACATACCCGATAA 60.533 55.000 24.80 0.00 0.00 1.75
132 133 0.865769 GCGCCAACATACCCGATAAG 59.134 55.000 0.00 0.00 0.00 1.73
133 134 1.539496 GCGCCAACATACCCGATAAGA 60.539 52.381 0.00 0.00 0.00 2.10
134 135 2.870435 GCGCCAACATACCCGATAAGAT 60.870 50.000 0.00 0.00 0.00 2.40
135 136 3.399330 CGCCAACATACCCGATAAGATT 58.601 45.455 0.00 0.00 0.00 2.40
136 137 3.813166 CGCCAACATACCCGATAAGATTT 59.187 43.478 0.00 0.00 0.00 2.17
137 138 4.274950 CGCCAACATACCCGATAAGATTTT 59.725 41.667 0.00 0.00 0.00 1.82
138 139 5.560183 CGCCAACATACCCGATAAGATTTTC 60.560 44.000 0.00 0.00 0.00 2.29
139 140 5.560183 GCCAACATACCCGATAAGATTTTCG 60.560 44.000 0.00 0.00 35.19 3.46
145 146 2.645628 CGATAAGATTTTCGGCCGTG 57.354 50.000 27.15 0.00 0.00 4.94
146 147 1.260561 CGATAAGATTTTCGGCCGTGG 59.739 52.381 27.15 0.00 0.00 4.94
147 148 1.602377 GATAAGATTTTCGGCCGTGGG 59.398 52.381 27.15 0.00 0.00 4.61
148 149 0.325602 TAAGATTTTCGGCCGTGGGT 59.674 50.000 27.15 10.41 0.00 4.51
149 150 0.958876 AAGATTTTCGGCCGTGGGTC 60.959 55.000 27.15 18.56 0.00 4.46
150 151 1.376812 GATTTTCGGCCGTGGGTCT 60.377 57.895 27.15 6.21 0.00 3.85
151 152 1.644786 GATTTTCGGCCGTGGGTCTG 61.645 60.000 27.15 0.00 0.00 3.51
152 153 3.835790 TTTTCGGCCGTGGGTCTGG 62.836 63.158 27.15 0.00 0.00 3.86
154 155 4.682334 TCGGCCGTGGGTCTGGTA 62.682 66.667 27.15 0.00 0.00 3.25
155 156 4.143333 CGGCCGTGGGTCTGGTAG 62.143 72.222 19.50 0.00 0.00 3.18
156 157 2.682494 GGCCGTGGGTCTGGTAGA 60.682 66.667 0.00 0.00 0.00 2.59
157 158 2.722201 GGCCGTGGGTCTGGTAGAG 61.722 68.421 0.00 0.00 0.00 2.43
158 159 2.722201 GCCGTGGGTCTGGTAGAGG 61.722 68.421 0.00 0.00 0.00 3.69
159 160 1.305046 CCGTGGGTCTGGTAGAGGT 60.305 63.158 0.00 0.00 0.00 3.85
160 161 0.903454 CCGTGGGTCTGGTAGAGGTT 60.903 60.000 0.00 0.00 0.00 3.50
161 162 0.246635 CGTGGGTCTGGTAGAGGTTG 59.753 60.000 0.00 0.00 0.00 3.77
162 163 1.640917 GTGGGTCTGGTAGAGGTTGA 58.359 55.000 0.00 0.00 0.00 3.18
163 164 1.275573 GTGGGTCTGGTAGAGGTTGAC 59.724 57.143 0.00 0.00 0.00 3.18
164 165 0.903236 GGGTCTGGTAGAGGTTGACC 59.097 60.000 0.00 0.00 44.51 4.02
165 166 0.903236 GGTCTGGTAGAGGTTGACCC 59.097 60.000 0.00 0.00 40.74 4.46
166 167 0.903236 GTCTGGTAGAGGTTGACCCC 59.097 60.000 0.00 0.00 34.58 4.95
167 168 0.613853 TCTGGTAGAGGTTGACCCCG 60.614 60.000 0.00 0.00 34.58 5.73
168 169 0.613853 CTGGTAGAGGTTGACCCCGA 60.614 60.000 0.00 0.00 34.58 5.14
169 170 0.901580 TGGTAGAGGTTGACCCCGAC 60.902 60.000 0.00 0.00 34.58 4.79
170 171 1.611474 GGTAGAGGTTGACCCCGACC 61.611 65.000 0.00 0.00 45.52 4.79
174 175 4.948257 GGTTGACCCCGACCATAC 57.052 61.111 0.00 0.00 44.71 2.39
175 176 1.222661 GGTTGACCCCGACCATACC 59.777 63.158 0.00 0.00 44.71 2.73
176 177 1.222661 GTTGACCCCGACCATACCC 59.777 63.158 0.00 0.00 0.00 3.69
177 178 2.360767 TTGACCCCGACCATACCCG 61.361 63.158 0.00 0.00 0.00 5.28
178 179 2.442643 GACCCCGACCATACCCGA 60.443 66.667 0.00 0.00 0.00 5.14
179 180 2.761213 ACCCCGACCATACCCGAC 60.761 66.667 0.00 0.00 0.00 4.79
180 181 3.543641 CCCCGACCATACCCGACC 61.544 72.222 0.00 0.00 0.00 4.79
181 182 2.443390 CCCGACCATACCCGACCT 60.443 66.667 0.00 0.00 0.00 3.85
182 183 2.792947 CCCGACCATACCCGACCTG 61.793 68.421 0.00 0.00 0.00 4.00
183 184 1.755395 CCGACCATACCCGACCTGA 60.755 63.158 0.00 0.00 0.00 3.86
184 185 1.113517 CCGACCATACCCGACCTGAT 61.114 60.000 0.00 0.00 0.00 2.90
185 186 0.750850 CGACCATACCCGACCTGATT 59.249 55.000 0.00 0.00 0.00 2.57
186 187 1.538204 CGACCATACCCGACCTGATTG 60.538 57.143 0.00 0.00 0.00 2.67
187 188 0.180406 ACCATACCCGACCTGATTGC 59.820 55.000 0.00 0.00 0.00 3.56
188 189 0.535102 CCATACCCGACCTGATTGCC 60.535 60.000 0.00 0.00 0.00 4.52
189 190 0.180171 CATACCCGACCTGATTGCCA 59.820 55.000 0.00 0.00 0.00 4.92
190 191 0.469917 ATACCCGACCTGATTGCCAG 59.530 55.000 0.00 0.00 42.55 4.85
225 226 3.954904 CAGTACCTAGGCACACATAGAGT 59.045 47.826 14.76 0.00 0.00 3.24
228 229 3.714144 ACCTAGGCACACATAGAGTTCT 58.286 45.455 9.30 0.00 0.00 3.01
230 231 3.701542 CCTAGGCACACATAGAGTTCTGA 59.298 47.826 0.00 0.00 0.00 3.27
284 285 0.543174 AGGAAGCTCACGGAGGAGTT 60.543 55.000 0.00 0.00 37.24 3.01
294 295 2.299297 CACGGAGGAGTTAAGTCACCTT 59.701 50.000 12.31 5.93 32.53 3.50
341 342 0.613292 AGTCATGAGCCCACTCGACT 60.613 55.000 0.00 0.00 46.69 4.18
374 375 4.377762 CCATGGTGATGTCTATGGGATT 57.622 45.455 2.57 0.00 40.97 3.01
375 376 4.733165 CCATGGTGATGTCTATGGGATTT 58.267 43.478 2.57 0.00 40.97 2.17
378 379 5.715439 TGGTGATGTCTATGGGATTTTCT 57.285 39.130 0.00 0.00 0.00 2.52
381 382 4.883585 GTGATGTCTATGGGATTTTCTGCA 59.116 41.667 0.00 0.00 0.00 4.41
385 386 4.883585 TGTCTATGGGATTTTCTGCATCAC 59.116 41.667 0.00 0.00 0.00 3.06
399 400 9.639563 TTTTCTGCATCACCAATATCCTATTAA 57.360 29.630 0.00 0.00 0.00 1.40
406 407 9.923143 CATCACCAATATCCTATTAAACGACTA 57.077 33.333 0.00 0.00 0.00 2.59
464 500 9.520515 AGAAGACTTATAATTTTTGGCTGAAGA 57.479 29.630 0.00 0.00 0.00 2.87
649 2575 6.903534 TCAGAGGAGGGAGTAGAAAATAACAT 59.096 38.462 0.00 0.00 0.00 2.71
653 2579 9.713713 GAGGAGGGAGTAGAAAATAACATAATC 57.286 37.037 0.00 0.00 0.00 1.75
712 2638 3.807622 CCTAACATCGTGAACACAACTGT 59.192 43.478 5.80 2.80 0.00 3.55
729 2655 2.034812 ACTGTGACCGAAAGACAGTCTC 59.965 50.000 2.72 0.00 45.69 3.36
802 2728 3.193263 CCCTCAGATGACAAGAATCGTG 58.807 50.000 0.00 0.00 0.00 4.35
911 2838 0.814010 GCCTCCGACGTTGGCATATT 60.814 55.000 17.75 0.00 45.46 1.28
912 2839 1.663695 CCTCCGACGTTGGCATATTT 58.336 50.000 17.75 0.00 0.00 1.40
969 2896 6.166984 TCTCAATCTCCATGTGATAGTTCC 57.833 41.667 0.00 0.00 0.00 3.62
976 2903 0.736636 ATGTGATAGTTCCGCGACGA 59.263 50.000 8.23 0.00 0.00 4.20
1040 2967 1.666553 GGATGACGTCGTGGTGCAA 60.667 57.895 16.54 0.00 0.00 4.08
1350 3277 0.468226 TCCTCTGCGACAAGTTTGGT 59.532 50.000 0.00 0.00 0.00 3.67
1403 3330 5.238583 CGGTAGTGATTAATCCCAGAATCC 58.761 45.833 12.90 5.74 32.13 3.01
1404 3331 5.238583 GGTAGTGATTAATCCCAGAATCCG 58.761 45.833 12.90 0.00 32.13 4.18
1418 3350 4.024387 CCAGAATCCGTTCACGAAAGAAAA 60.024 41.667 0.00 0.00 43.02 2.29
1419 3351 4.904154 CAGAATCCGTTCACGAAAGAAAAC 59.096 41.667 0.00 0.00 43.02 2.43
1424 3356 3.215244 CGTTCACGAAAGAAAACATCGG 58.785 45.455 0.00 0.00 43.02 4.18
1446 3378 1.133216 CGAGAAGCCATCGAGAAGTGA 59.867 52.381 0.00 0.00 42.76 3.41
1447 3379 2.794282 CGAGAAGCCATCGAGAAGTGAG 60.794 54.545 0.00 0.00 42.76 3.51
1448 3380 1.134848 AGAAGCCATCGAGAAGTGAGC 60.135 52.381 0.00 0.00 0.00 4.26
1449 3381 0.610174 AAGCCATCGAGAAGTGAGCA 59.390 50.000 0.00 0.00 0.00 4.26
1450 3382 0.610174 AGCCATCGAGAAGTGAGCAA 59.390 50.000 0.00 0.00 0.00 3.91
1452 3384 1.674221 GCCATCGAGAAGTGAGCAAGT 60.674 52.381 0.00 0.00 0.00 3.16
1453 3385 1.998315 CCATCGAGAAGTGAGCAAGTG 59.002 52.381 0.00 0.00 0.00 3.16
1454 3386 2.611473 CCATCGAGAAGTGAGCAAGTGT 60.611 50.000 0.00 0.00 0.00 3.55
1455 3387 3.367395 CCATCGAGAAGTGAGCAAGTGTA 60.367 47.826 0.00 0.00 0.00 2.90
1456 3388 4.428209 CATCGAGAAGTGAGCAAGTGTAT 58.572 43.478 0.00 0.00 0.00 2.29
1457 3389 4.098055 TCGAGAAGTGAGCAAGTGTATC 57.902 45.455 0.00 0.00 0.00 2.24
1458 3390 3.759086 TCGAGAAGTGAGCAAGTGTATCT 59.241 43.478 0.00 0.00 0.00 1.98
1459 3391 4.101942 CGAGAAGTGAGCAAGTGTATCTC 58.898 47.826 0.00 0.00 0.00 2.75
1460 3392 4.379918 CGAGAAGTGAGCAAGTGTATCTCA 60.380 45.833 0.00 0.00 33.40 3.27
1461 3393 5.659463 GAGAAGTGAGCAAGTGTATCTCAT 58.341 41.667 0.00 0.00 38.85 2.90
1462 3394 5.659463 AGAAGTGAGCAAGTGTATCTCATC 58.341 41.667 0.00 0.00 38.85 2.92
1485 3417 3.826466 TCATCTGATGTACGATCGATGC 58.174 45.455 24.34 11.42 33.45 3.91
1672 3604 2.125793 GACGGGTACAACGAGGCC 60.126 66.667 14.89 0.00 34.93 5.19
2089 4030 1.617322 TCTCCGATACCGCTGCTATT 58.383 50.000 0.00 0.00 0.00 1.73
2284 4225 2.668120 GCCCCAGCTCTGCTCTTCT 61.668 63.158 0.00 0.00 36.40 2.85
2326 4267 1.439543 AGCCCTTTCTCCTGTGACTT 58.560 50.000 0.00 0.00 0.00 3.01
2327 4268 1.349357 AGCCCTTTCTCCTGTGACTTC 59.651 52.381 0.00 0.00 0.00 3.01
2328 4269 1.349357 GCCCTTTCTCCTGTGACTTCT 59.651 52.381 0.00 0.00 0.00 2.85
2329 4270 2.224646 GCCCTTTCTCCTGTGACTTCTT 60.225 50.000 0.00 0.00 0.00 2.52
2360 4302 4.935808 GGAGTTGTTCCGAGTCATGTAATT 59.064 41.667 0.00 0.00 35.91 1.40
2361 4303 5.163854 GGAGTTGTTCCGAGTCATGTAATTG 60.164 44.000 0.00 0.00 35.91 2.32
2362 4304 4.695455 AGTTGTTCCGAGTCATGTAATTGG 59.305 41.667 0.00 0.00 0.00 3.16
2363 4305 3.006940 TGTTCCGAGTCATGTAATTGGC 58.993 45.455 0.00 0.00 0.00 4.52
2389 4334 2.093890 TGCCTTACCAATGATGCTGTG 58.906 47.619 0.00 0.00 0.00 3.66
2397 4342 2.165167 CAATGATGCTGTGGTCCTGTT 58.835 47.619 0.00 0.00 0.00 3.16
2485 4435 6.371548 TCACTGATTAAAATCACGGGAGAAAG 59.628 38.462 0.00 0.00 40.32 2.62
2486 4436 5.648092 ACTGATTAAAATCACGGGAGAAAGG 59.352 40.000 0.00 0.00 40.32 3.11
2491 4441 7.533289 TTAAAATCACGGGAGAAAGGAAATT 57.467 32.000 0.00 0.00 0.00 1.82
2528 4478 4.664188 TGCCGCGAAATTTTATCCTAAAC 58.336 39.130 8.23 0.00 0.00 2.01
2529 4479 4.039703 GCCGCGAAATTTTATCCTAAACC 58.960 43.478 8.23 0.00 0.00 3.27
2533 4483 4.603985 CGAAATTTTATCCTAAACCGGCC 58.396 43.478 0.00 0.00 0.00 6.13
2534 4484 4.337274 CGAAATTTTATCCTAAACCGGCCT 59.663 41.667 0.00 0.00 0.00 5.19
2542 4502 0.830648 CTAAACCGGCCTGATCTCCA 59.169 55.000 0.00 0.00 0.00 3.86
2555 4515 2.237143 TGATCTCCAGCGATTTTCACCT 59.763 45.455 0.00 0.00 0.00 4.00
2558 4518 0.250684 TCCAGCGATTTTCACCTGCA 60.251 50.000 0.00 0.00 0.00 4.41
2567 4527 3.747854 TTTTCACCTGCATGCAAATCA 57.252 38.095 22.88 3.29 0.00 2.57
2568 4528 3.965379 TTTCACCTGCATGCAAATCAT 57.035 38.095 22.88 2.36 35.31 2.45
2576 4536 2.502213 CATGCAAATCATGGTGCGAT 57.498 45.000 10.87 5.02 46.81 4.58
2577 4537 2.816689 CATGCAAATCATGGTGCGATT 58.183 42.857 10.87 0.00 46.81 3.34
2578 4538 2.565210 TGCAAATCATGGTGCGATTC 57.435 45.000 10.87 0.00 43.93 2.52
2580 4540 2.159352 TGCAAATCATGGTGCGATTCAG 60.159 45.455 10.87 0.00 43.93 3.02
2581 4541 2.456989 CAAATCATGGTGCGATTCAGC 58.543 47.619 0.00 0.00 43.23 4.26
2582 4542 0.659427 AATCATGGTGCGATTCAGCG 59.341 50.000 0.00 0.00 45.75 5.18
2583 4543 1.162181 ATCATGGTGCGATTCAGCGG 61.162 55.000 0.00 0.00 45.75 5.52
2584 4544 3.204827 ATGGTGCGATTCAGCGGC 61.205 61.111 0.00 0.00 45.75 6.53
2585 4545 3.974835 ATGGTGCGATTCAGCGGCA 62.975 57.895 1.45 0.00 45.75 5.69
2586 4546 3.430862 GGTGCGATTCAGCGGCAA 61.431 61.111 1.45 0.00 38.58 4.52
2587 4547 2.764314 GGTGCGATTCAGCGGCAAT 61.764 57.895 1.45 0.00 38.58 3.56
2588 4548 1.137404 GTGCGATTCAGCGGCAATT 59.863 52.632 1.45 0.00 38.58 2.32
2589 4549 1.135699 GTGCGATTCAGCGGCAATTG 61.136 55.000 1.45 0.00 38.58 2.32
2590 4550 2.226225 GCGATTCAGCGGCAATTGC 61.226 57.895 22.47 22.47 41.14 3.56
2598 4558 3.873449 CGGCAATTGCGGCAAAAT 58.127 50.000 23.48 9.01 43.26 1.82
2600 4560 1.709182 GGCAATTGCGGCAAAATCG 59.291 52.632 23.48 9.29 43.26 3.34
2623 4583 4.911610 GCCCACGATTTAAAATCATGATCG 59.088 41.667 9.06 9.78 43.65 3.69
2626 4586 7.192913 CCCACGATTTAAAATCATGATCGAAA 58.807 34.615 16.97 13.43 41.37 3.46
2641 4601 8.792633 TCATGATCGAAATTTTAAGTCCAAACT 58.207 29.630 0.00 0.00 37.32 2.66
2642 4602 8.853345 CATGATCGAAATTTTAAGTCCAAACTG 58.147 33.333 0.00 0.00 35.36 3.16
2648 4608 7.043656 CGAAATTTTAAGTCCAAACTGAACCAC 60.044 37.037 0.00 0.00 35.36 4.16
2652 4612 3.297134 AGTCCAAACTGAACCACATGT 57.703 42.857 0.00 0.00 33.32 3.21
2656 4616 4.097892 GTCCAAACTGAACCACATGTTTCT 59.902 41.667 10.75 0.00 37.29 2.52
2659 4619 5.530915 CCAAACTGAACCACATGTTTCTAGA 59.469 40.000 10.75 0.00 37.29 2.43
2684 4644 2.665165 ACATTTCAGTTGCTCAACCCA 58.335 42.857 8.95 0.00 42.06 4.51
2685 4645 2.362077 ACATTTCAGTTGCTCAACCCAC 59.638 45.455 8.95 0.00 42.06 4.61
2691 4651 0.240945 GTTGCTCAACCCACCGAATG 59.759 55.000 1.45 0.00 35.36 2.67
2740 4700 1.069906 GCTGAACGCATCGAACAGTTT 60.070 47.619 0.00 0.00 38.92 2.66
2750 4710 4.154195 GCATCGAACAGTTTAGGTGTGAAT 59.846 41.667 0.00 0.00 0.00 2.57
2844 4805 0.321122 CTGTGAGGCTGACAAGGGAC 60.321 60.000 8.44 0.00 0.00 4.46
2868 4829 1.342074 CGATCCCAGGGCTGATCTTA 58.658 55.000 0.00 0.00 36.15 2.10
2889 4850 2.672996 GCAAGGGCGCCTTTCTCA 60.673 61.111 28.56 0.00 41.69 3.27
2901 4862 3.616379 CGCCTTTCTCAGAGATCAGAAAC 59.384 47.826 0.00 0.00 34.39 2.78
2982 4943 4.052608 CTGCAACATTGTGAAGAAATGCA 58.947 39.130 9.11 9.11 38.36 3.96
3012 4973 7.936847 AGGAATTGCATAATCATTAGTAACGGA 59.063 33.333 0.00 0.00 0.00 4.69
3083 5044 0.512518 GCAAAGAAAATGCCGCAACC 59.487 50.000 0.00 0.00 37.85 3.77
3093 5054 1.081242 GCCGCAACCATGACACAAG 60.081 57.895 0.00 0.00 0.00 3.16
3103 5064 2.603110 CCATGACACAAGTACGGAATCG 59.397 50.000 0.00 0.00 43.02 3.34
3131 5094 6.059484 CACTACTTTTCACCAGGTAAGGAAA 58.941 40.000 5.70 3.07 0.00 3.13
3144 5107 3.442273 GGTAAGGAAATCATGCGGTGAAA 59.558 43.478 0.00 0.00 40.97 2.69
3146 5109 3.575965 AGGAAATCATGCGGTGAAAAC 57.424 42.857 0.00 0.00 40.97 2.43
3147 5110 2.890311 AGGAAATCATGCGGTGAAAACA 59.110 40.909 0.00 0.00 40.97 2.83
3165 5128 6.531240 TGAAAACAAGCAATTCAACAGACTTC 59.469 34.615 0.00 0.00 30.60 3.01
3232 5195 2.094417 GCATCAAACCTACTTCGACAGC 59.906 50.000 0.00 0.00 0.00 4.40
3248 5211 4.243383 GCACCGAAATGCACCAAC 57.757 55.556 0.00 0.00 45.39 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.482722 GTTCTCAACGAGATGTACCGA 57.517 47.619 0.00 0.00 38.56 4.69
13 14 2.159268 GGGTAGAGTAGGCGTTCTCAAC 60.159 54.545 14.34 4.49 33.63 3.18
14 15 2.097825 GGGTAGAGTAGGCGTTCTCAA 58.902 52.381 14.34 0.00 33.63 3.02
15 16 1.760192 GGGTAGAGTAGGCGTTCTCA 58.240 55.000 14.34 0.00 33.63 3.27
16 17 0.662085 CGGGTAGAGTAGGCGTTCTC 59.338 60.000 5.02 5.02 0.00 2.87
17 18 0.254178 TCGGGTAGAGTAGGCGTTCT 59.746 55.000 0.00 0.00 0.00 3.01
18 19 1.001597 CATCGGGTAGAGTAGGCGTTC 60.002 57.143 0.00 0.00 0.00 3.95
19 20 1.030457 CATCGGGTAGAGTAGGCGTT 58.970 55.000 0.00 0.00 0.00 4.84
20 21 0.822532 CCATCGGGTAGAGTAGGCGT 60.823 60.000 0.00 0.00 0.00 5.68
21 22 1.524863 CCCATCGGGTAGAGTAGGCG 61.525 65.000 0.00 0.00 38.25 5.52
22 23 2.352817 CCCATCGGGTAGAGTAGGC 58.647 63.158 0.00 0.00 38.25 3.93
46 47 1.128321 GTCGTATAGCCCGAGTCGATC 59.872 57.143 15.64 4.95 34.56 3.69
47 48 1.155042 GTCGTATAGCCCGAGTCGAT 58.845 55.000 15.64 1.50 34.56 3.59
48 49 1.217585 CGTCGTATAGCCCGAGTCGA 61.218 60.000 15.64 0.00 34.56 4.20
49 50 1.203563 CGTCGTATAGCCCGAGTCG 59.796 63.158 5.29 5.29 34.56 4.18
50 51 1.573436 CCGTCGTATAGCCCGAGTC 59.427 63.158 0.00 0.00 34.56 3.36
51 52 1.895707 CCCGTCGTATAGCCCGAGT 60.896 63.158 0.00 0.00 34.56 4.18
52 53 1.450531 AACCCGTCGTATAGCCCGAG 61.451 60.000 0.00 0.00 34.56 4.63
53 54 1.447317 GAACCCGTCGTATAGCCCGA 61.447 60.000 0.00 0.00 0.00 5.14
54 55 1.008079 GAACCCGTCGTATAGCCCG 60.008 63.158 0.00 0.00 0.00 6.13
55 56 1.008079 CGAACCCGTCGTATAGCCC 60.008 63.158 0.00 0.00 45.09 5.19
56 57 4.622364 CGAACCCGTCGTATAGCC 57.378 61.111 0.00 0.00 45.09 3.93
64 65 2.511600 CCCATGCTCGAACCCGTC 60.512 66.667 0.00 0.00 37.05 4.79
65 66 4.778143 GCCCATGCTCGAACCCGT 62.778 66.667 0.00 0.00 37.05 5.28
66 67 4.776322 TGCCCATGCTCGAACCCG 62.776 66.667 0.00 0.00 38.71 5.28
67 68 2.124151 ATGCCCATGCTCGAACCC 60.124 61.111 0.00 0.00 38.71 4.11
68 69 1.442526 CTCATGCCCATGCTCGAACC 61.443 60.000 3.41 0.00 38.65 3.62
69 70 0.745845 ACTCATGCCCATGCTCGAAC 60.746 55.000 3.41 0.00 38.65 3.95
70 71 0.462581 GACTCATGCCCATGCTCGAA 60.463 55.000 3.41 0.00 38.65 3.71
71 72 1.144716 GACTCATGCCCATGCTCGA 59.855 57.895 3.41 0.00 38.65 4.04
72 73 0.745486 TTGACTCATGCCCATGCTCG 60.745 55.000 3.41 0.00 38.65 5.03
73 74 1.022735 CTTGACTCATGCCCATGCTC 58.977 55.000 3.41 2.08 38.65 4.26
74 75 0.622136 TCTTGACTCATGCCCATGCT 59.378 50.000 3.41 0.00 38.65 3.79
75 76 0.737219 GTCTTGACTCATGCCCATGC 59.263 55.000 3.41 0.00 38.65 4.06
76 77 1.386533 GGTCTTGACTCATGCCCATG 58.613 55.000 1.86 1.86 40.09 3.66
77 78 0.257039 GGGTCTTGACTCATGCCCAT 59.743 55.000 14.45 0.00 36.25 4.00
78 79 1.685224 GGGTCTTGACTCATGCCCA 59.315 57.895 14.45 0.00 36.25 5.36
79 80 1.450312 CGGGTCTTGACTCATGCCC 60.450 63.158 1.38 11.42 0.00 5.36
80 81 1.021390 CACGGGTCTTGACTCATGCC 61.021 60.000 1.38 0.00 0.00 4.40
81 82 1.021390 CCACGGGTCTTGACTCATGC 61.021 60.000 1.38 0.00 0.00 4.06
82 83 0.391661 CCCACGGGTCTTGACTCATG 60.392 60.000 1.38 0.00 0.00 3.07
83 84 1.983224 CCCACGGGTCTTGACTCAT 59.017 57.895 1.38 0.00 0.00 2.90
84 85 3.466881 CCCACGGGTCTTGACTCA 58.533 61.111 1.38 0.00 0.00 3.41
95 96 3.766691 CCACGACCCTACCCACGG 61.767 72.222 0.00 0.00 0.00 4.94
96 97 3.766691 CCCACGACCCTACCCACG 61.767 72.222 0.00 0.00 0.00 4.94
97 98 4.091939 GCCCACGACCCTACCCAC 62.092 72.222 0.00 0.00 0.00 4.61
107 108 2.435234 GTATGTTGGCGCCCACGA 60.435 61.111 26.77 12.67 43.93 4.35
108 109 3.505184 GGTATGTTGGCGCCCACG 61.505 66.667 26.77 0.00 44.07 4.94
109 110 3.138128 GGGTATGTTGGCGCCCAC 61.138 66.667 26.77 24.81 40.76 4.61
110 111 4.787286 CGGGTATGTTGGCGCCCA 62.787 66.667 26.77 16.76 41.11 5.36
111 112 2.386064 TATCGGGTATGTTGGCGCCC 62.386 60.000 26.77 10.34 37.79 6.13
112 113 0.533308 TTATCGGGTATGTTGGCGCC 60.533 55.000 22.73 22.73 0.00 6.53
113 114 0.865769 CTTATCGGGTATGTTGGCGC 59.134 55.000 0.00 0.00 0.00 6.53
114 115 2.519377 TCTTATCGGGTATGTTGGCG 57.481 50.000 0.00 0.00 0.00 5.69
115 116 5.560183 CGAAAATCTTATCGGGTATGTTGGC 60.560 44.000 0.00 0.00 35.49 4.52
116 117 5.985781 CGAAAATCTTATCGGGTATGTTGG 58.014 41.667 0.00 0.00 35.49 3.77
126 127 1.260561 CCACGGCCGAAAATCTTATCG 59.739 52.381 35.90 0.00 38.74 2.92
127 128 1.602377 CCCACGGCCGAAAATCTTATC 59.398 52.381 35.90 0.00 0.00 1.75
128 129 1.064979 ACCCACGGCCGAAAATCTTAT 60.065 47.619 35.90 1.64 0.00 1.73
129 130 0.325602 ACCCACGGCCGAAAATCTTA 59.674 50.000 35.90 0.00 0.00 2.10
130 131 0.958876 GACCCACGGCCGAAAATCTT 60.959 55.000 35.90 3.57 0.00 2.40
131 132 1.376812 GACCCACGGCCGAAAATCT 60.377 57.895 35.90 4.54 0.00 2.40
132 133 1.376812 AGACCCACGGCCGAAAATC 60.377 57.895 35.90 22.51 0.00 2.17
133 134 1.674322 CAGACCCACGGCCGAAAAT 60.674 57.895 35.90 14.78 0.00 1.82
134 135 2.281208 CAGACCCACGGCCGAAAA 60.281 61.111 35.90 0.00 0.00 2.29
135 136 4.323477 CCAGACCCACGGCCGAAA 62.323 66.667 35.90 0.00 0.00 3.46
137 138 4.682334 TACCAGACCCACGGCCGA 62.682 66.667 35.90 0.68 0.00 5.54
138 139 4.143333 CTACCAGACCCACGGCCG 62.143 72.222 26.86 26.86 0.00 6.13
139 140 2.682494 TCTACCAGACCCACGGCC 60.682 66.667 0.00 0.00 0.00 6.13
140 141 2.722201 CCTCTACCAGACCCACGGC 61.722 68.421 0.00 0.00 0.00 5.68
141 142 0.903454 AACCTCTACCAGACCCACGG 60.903 60.000 0.00 0.00 0.00 4.94
142 143 0.246635 CAACCTCTACCAGACCCACG 59.753 60.000 0.00 0.00 0.00 4.94
143 144 1.275573 GTCAACCTCTACCAGACCCAC 59.724 57.143 0.00 0.00 0.00 4.61
144 145 1.640917 GTCAACCTCTACCAGACCCA 58.359 55.000 0.00 0.00 0.00 4.51
145 146 0.903236 GGTCAACCTCTACCAGACCC 59.097 60.000 0.00 0.00 42.21 4.46
146 147 0.903236 GGGTCAACCTCTACCAGACC 59.097 60.000 0.00 0.00 46.16 3.85
147 148 0.903236 GGGGTCAACCTCTACCAGAC 59.097 60.000 0.00 0.00 40.03 3.51
148 149 0.613853 CGGGGTCAACCTCTACCAGA 60.614 60.000 0.00 0.00 40.03 3.86
149 150 0.613853 TCGGGGTCAACCTCTACCAG 60.614 60.000 0.00 0.00 40.03 4.00
150 151 0.901580 GTCGGGGTCAACCTCTACCA 60.902 60.000 0.00 0.00 40.03 3.25
151 152 1.611474 GGTCGGGGTCAACCTCTACC 61.611 65.000 6.98 6.98 43.93 3.18
152 153 0.901580 TGGTCGGGGTCAACCTCTAC 60.902 60.000 0.00 0.00 40.03 2.59
153 154 0.042131 ATGGTCGGGGTCAACCTCTA 59.958 55.000 0.00 0.00 40.03 2.43
154 155 0.042131 TATGGTCGGGGTCAACCTCT 59.958 55.000 0.00 0.00 40.03 3.69
155 156 0.177373 GTATGGTCGGGGTCAACCTC 59.823 60.000 0.00 0.00 40.03 3.85
156 157 1.269703 GGTATGGTCGGGGTCAACCT 61.270 60.000 0.00 0.00 40.03 3.50
157 158 1.222661 GGTATGGTCGGGGTCAACC 59.777 63.158 0.00 0.00 39.11 3.77
158 159 1.222661 GGGTATGGTCGGGGTCAAC 59.777 63.158 0.00 0.00 0.00 3.18
159 160 2.360767 CGGGTATGGTCGGGGTCAA 61.361 63.158 0.00 0.00 0.00 3.18
160 161 2.760799 CGGGTATGGTCGGGGTCA 60.761 66.667 0.00 0.00 0.00 4.02
161 162 2.442643 TCGGGTATGGTCGGGGTC 60.443 66.667 0.00 0.00 0.00 4.46
162 163 2.761213 GTCGGGTATGGTCGGGGT 60.761 66.667 0.00 0.00 0.00 4.95
163 164 3.543641 GGTCGGGTATGGTCGGGG 61.544 72.222 0.00 0.00 0.00 5.73
164 165 2.443390 AGGTCGGGTATGGTCGGG 60.443 66.667 0.00 0.00 0.00 5.14
165 166 1.113517 ATCAGGTCGGGTATGGTCGG 61.114 60.000 0.00 0.00 0.00 4.79
166 167 0.750850 AATCAGGTCGGGTATGGTCG 59.249 55.000 0.00 0.00 0.00 4.79
167 168 1.810412 GCAATCAGGTCGGGTATGGTC 60.810 57.143 0.00 0.00 0.00 4.02
168 169 0.180406 GCAATCAGGTCGGGTATGGT 59.820 55.000 0.00 0.00 0.00 3.55
169 170 0.535102 GGCAATCAGGTCGGGTATGG 60.535 60.000 0.00 0.00 0.00 2.74
170 171 0.180171 TGGCAATCAGGTCGGGTATG 59.820 55.000 0.00 0.00 0.00 2.39
171 172 0.469917 CTGGCAATCAGGTCGGGTAT 59.530 55.000 0.00 0.00 39.76 2.73
172 173 1.904771 CTGGCAATCAGGTCGGGTA 59.095 57.895 0.00 0.00 39.76 3.69
173 174 2.671070 CTGGCAATCAGGTCGGGT 59.329 61.111 0.00 0.00 39.76 5.28
180 181 2.189594 TGAGTCAACCTGGCAATCAG 57.810 50.000 0.00 0.00 43.00 2.90
181 182 2.040145 TGATGAGTCAACCTGGCAATCA 59.960 45.455 0.00 0.00 29.00 2.57
182 183 2.421424 GTGATGAGTCAACCTGGCAATC 59.579 50.000 0.00 0.00 35.80 2.67
183 184 2.224843 TGTGATGAGTCAACCTGGCAAT 60.225 45.455 0.00 0.00 35.80 3.56
184 185 1.142667 TGTGATGAGTCAACCTGGCAA 59.857 47.619 0.00 0.00 35.80 4.52
185 186 0.764271 TGTGATGAGTCAACCTGGCA 59.236 50.000 0.00 0.00 35.80 4.92
186 187 1.271054 ACTGTGATGAGTCAACCTGGC 60.271 52.381 0.00 0.00 35.80 4.85
187 188 2.847327 ACTGTGATGAGTCAACCTGG 57.153 50.000 0.00 0.00 35.80 4.45
188 189 3.259374 AGGTACTGTGATGAGTCAACCTG 59.741 47.826 9.19 3.00 39.34 4.00
189 190 3.511477 AGGTACTGTGATGAGTCAACCT 58.489 45.455 4.84 4.84 37.15 3.50
190 191 3.963428 AGGTACTGTGATGAGTCAACC 57.037 47.619 0.00 0.00 37.18 3.77
191 192 4.678309 GCCTAGGTACTGTGATGAGTCAAC 60.678 50.000 11.31 0.00 41.52 3.18
192 193 3.447586 GCCTAGGTACTGTGATGAGTCAA 59.552 47.826 11.31 0.00 41.52 3.18
193 194 3.024547 GCCTAGGTACTGTGATGAGTCA 58.975 50.000 11.31 0.00 41.52 3.41
194 195 3.024547 TGCCTAGGTACTGTGATGAGTC 58.975 50.000 11.31 0.00 41.52 3.36
195 196 2.761208 GTGCCTAGGTACTGTGATGAGT 59.239 50.000 21.62 0.00 41.52 3.41
196 197 2.760650 TGTGCCTAGGTACTGTGATGAG 59.239 50.000 27.54 0.00 41.52 2.90
259 260 0.175760 TCCGTGAGCTTCCTATGCAC 59.824 55.000 0.00 0.00 0.00 4.57
294 295 2.642129 CACGCGCCATTCAAACCA 59.358 55.556 5.73 0.00 0.00 3.67
341 342 2.350895 CCATGGGCTCACCGACAA 59.649 61.111 2.85 0.00 44.64 3.18
374 375 9.639563 TTTAATAGGATATTGGTGATGCAGAAA 57.360 29.630 0.00 0.00 0.00 2.52
375 376 9.066892 GTTTAATAGGATATTGGTGATGCAGAA 57.933 33.333 0.00 0.00 0.00 3.02
378 379 7.172532 GTCGTTTAATAGGATATTGGTGATGCA 59.827 37.037 0.00 0.00 0.00 3.96
411 412 9.567776 TTCAAAGATGGAGTGAATACAAGTTAA 57.432 29.630 0.00 0.00 0.00 2.01
421 422 6.595682 AGTCTTCTTTCAAAGATGGAGTGAA 58.404 36.000 11.99 0.00 37.59 3.18
451 487 4.440880 CACCATTTGTCTTCAGCCAAAAA 58.559 39.130 0.00 0.00 34.52 1.94
464 500 5.971763 TCTTACAAACTTTGCACCATTTGT 58.028 33.333 19.55 19.55 44.96 2.83
604 2530 5.079689 TGAGATCAAACCGTGCATAGTTA 57.920 39.130 4.91 0.00 0.00 2.24
653 2579 7.141100 ACGAATACATAAGAAAGTTGTTGGG 57.859 36.000 0.00 0.00 0.00 4.12
729 2655 2.095567 CACCAAGCCAATCTTCTTGTCG 60.096 50.000 0.00 0.00 38.33 4.35
802 2728 0.664166 CGTGTGGTTGGCATGAAAGC 60.664 55.000 0.00 0.00 0.00 3.51
976 2903 0.459237 CGGATGAAAGCTGAGCTCGT 60.459 55.000 7.72 0.00 38.25 4.18
1020 2947 1.245376 TGCACCACGACGTCATCCTA 61.245 55.000 17.16 0.00 0.00 2.94
1027 2954 3.269347 GTGCTTGCACCACGACGT 61.269 61.111 14.17 0.00 0.00 4.34
1304 3231 0.803768 CATCAGCTCGACGTCCTTGG 60.804 60.000 10.58 0.00 0.00 3.61
1350 3277 3.006728 ATGGAGTCGCCGGGGAAA 61.007 61.111 24.36 9.73 40.66 3.13
1396 3323 4.725556 TTTCTTTCGTGAACGGATTCTG 57.274 40.909 2.59 0.00 40.29 3.02
1403 3330 3.215244 CCGATGTTTTCTTTCGTGAACG 58.785 45.455 0.00 0.00 41.45 3.95
1404 3331 2.971261 GCCGATGTTTTCTTTCGTGAAC 59.029 45.455 0.00 0.00 0.00 3.18
1424 3356 0.873743 CTTCTCGATGGCTTCTCGGC 60.874 60.000 0.00 0.00 36.78 5.54
1434 3366 2.681706 ACACTTGCTCACTTCTCGATG 58.318 47.619 0.00 0.00 0.00 3.84
1446 3378 6.041751 TCAGATGATGATGAGATACACTTGCT 59.958 38.462 0.00 0.00 31.12 3.91
1447 3379 6.221659 TCAGATGATGATGAGATACACTTGC 58.778 40.000 0.00 0.00 31.12 4.01
1476 3408 0.095245 AAGCACAAACGCATCGATCG 59.905 50.000 9.36 9.36 0.00 3.69
1672 3604 4.335647 AAGTCCAGCGGGCACAGG 62.336 66.667 0.00 0.00 0.00 4.00
2089 4030 4.758251 CTGTCCGTCATGGCGCCA 62.758 66.667 34.80 34.80 37.80 5.69
2343 4285 3.270877 AGCCAATTACATGACTCGGAAC 58.729 45.455 0.00 0.00 0.00 3.62
2362 4304 1.810151 TCATTGGTAAGGCAAACGAGC 59.190 47.619 0.00 0.00 0.00 5.03
2363 4305 3.731867 GCATCATTGGTAAGGCAAACGAG 60.732 47.826 0.00 0.00 0.00 4.18
2389 4334 1.227943 TGCAGTGCAGAACAGGACC 60.228 57.895 15.37 0.00 33.32 4.46
2397 4342 1.162181 GCTCACAAGTGCAGTGCAGA 61.162 55.000 20.42 10.98 40.08 4.26
2509 4459 4.276460 CCGGTTTAGGATAAAATTTCGCG 58.724 43.478 0.00 0.00 0.00 5.87
2521 4471 1.120530 GAGATCAGGCCGGTTTAGGA 58.879 55.000 1.90 0.00 0.00 2.94
2528 4478 4.598894 CGCTGGAGATCAGGCCGG 62.599 72.222 0.00 0.00 43.54 6.13
2529 4479 2.374830 AATCGCTGGAGATCAGGCCG 62.375 60.000 0.00 0.00 43.54 6.13
2533 4483 2.611292 GGTGAAAATCGCTGGAGATCAG 59.389 50.000 0.00 0.00 46.03 2.90
2534 4484 2.237143 AGGTGAAAATCGCTGGAGATCA 59.763 45.455 0.00 0.00 0.00 2.92
2542 4502 0.171903 GCATGCAGGTGAAAATCGCT 59.828 50.000 14.21 0.00 0.00 4.93
2558 4518 2.427812 TGAATCGCACCATGATTTGCAT 59.572 40.909 12.54 4.74 38.76 3.96
2567 4527 3.204827 GCCGCTGAATCGCACCAT 61.205 61.111 0.00 0.00 0.00 3.55
2568 4528 4.695993 TGCCGCTGAATCGCACCA 62.696 61.111 0.00 0.00 0.00 4.17
2569 4529 2.270297 AATTGCCGCTGAATCGCACC 62.270 55.000 0.00 0.00 0.00 5.01
2571 4531 1.137194 CAATTGCCGCTGAATCGCA 59.863 52.632 0.00 0.00 0.00 5.10
2576 4536 4.418401 GCCGCAATTGCCGCTGAA 62.418 61.111 28.95 0.00 41.04 3.02
2578 4538 4.721111 TTGCCGCAATTGCCGCTG 62.721 61.111 33.21 17.76 43.81 5.18
2580 4540 2.295394 GATTTTGCCGCAATTGCCGC 62.295 55.000 29.35 29.35 43.75 6.53
2581 4541 1.709182 GATTTTGCCGCAATTGCCG 59.291 52.632 24.24 18.71 37.91 5.69
2582 4542 1.709182 CGATTTTGCCGCAATTGCC 59.291 52.632 24.24 12.00 37.91 4.52
2600 4560 4.911610 CGATCATGATTTTAAATCGTGGGC 59.088 41.667 28.71 21.79 36.12 5.36
2602 4562 8.786937 ATTTCGATCATGATTTTAAATCGTGG 57.213 30.769 28.71 18.24 39.98 4.94
2623 4583 7.762159 TGTGGTTCAGTTTGGACTTAAAATTTC 59.238 33.333 0.00 0.00 32.54 2.17
2626 4586 6.783708 TGTGGTTCAGTTTGGACTTAAAAT 57.216 33.333 0.00 0.00 32.54 1.82
2629 4589 5.197451 ACATGTGGTTCAGTTTGGACTTAA 58.803 37.500 0.00 0.00 32.54 1.85
2630 4590 4.787551 ACATGTGGTTCAGTTTGGACTTA 58.212 39.130 0.00 0.00 32.54 2.24
2631 4591 3.631250 ACATGTGGTTCAGTTTGGACTT 58.369 40.909 0.00 0.00 32.54 3.01
2632 4592 3.297134 ACATGTGGTTCAGTTTGGACT 57.703 42.857 0.00 0.00 36.25 3.85
2633 4593 4.097892 AGAAACATGTGGTTCAGTTTGGAC 59.902 41.667 12.83 0.00 43.92 4.02
2634 4594 4.277476 AGAAACATGTGGTTCAGTTTGGA 58.723 39.130 12.83 0.00 43.92 3.53
2636 4596 6.618287 TCTAGAAACATGTGGTTCAGTTTG 57.382 37.500 12.83 0.00 43.92 2.93
2652 4612 7.771183 AGCAACTGAAATGTTGTTTCTAGAAA 58.229 30.769 13.99 13.99 46.33 2.52
2656 4616 6.691754 TGAGCAACTGAAATGTTGTTTCTA 57.308 33.333 8.78 0.00 46.33 2.10
2659 4619 4.869861 GGTTGAGCAACTGAAATGTTGTTT 59.130 37.500 12.54 0.00 46.33 2.83
2684 4644 3.417069 TCTGGAAACATGTCATTCGGT 57.583 42.857 0.00 0.00 41.51 4.69
2685 4645 4.764679 TTTCTGGAAACATGTCATTCGG 57.235 40.909 0.00 0.00 41.51 4.30
2740 4700 5.630121 AGTCCACATGAAAATTCACACCTA 58.370 37.500 0.00 0.00 40.49 3.08
2750 4710 2.037902 TGCCGAGTAGTCCACATGAAAA 59.962 45.455 0.00 0.00 0.00 2.29
2790 4751 1.486310 CTAGGCACATTACAGGAGGCA 59.514 52.381 0.00 0.00 0.00 4.75
2844 4805 1.153289 CAGCCCTGGGATCGTGAAG 60.153 63.158 19.27 0.00 0.00 3.02
2868 4829 2.036256 AAAGGCGCCCTTGCTGAT 59.964 55.556 26.15 0.00 43.92 2.90
2889 4850 4.340617 AGGAGAAGTCGTTTCTGATCTCT 58.659 43.478 9.15 0.00 46.12 3.10
2901 4862 2.734079 GAGCTTTGTGAAGGAGAAGTCG 59.266 50.000 0.00 0.00 33.34 4.18
3012 4973 2.027100 GGTCAGGGTTAGCAAGCTTAGT 60.027 50.000 0.00 0.00 0.00 2.24
3083 5044 2.603110 CCGATTCCGTACTTGTGTCATG 59.397 50.000 0.00 0.00 0.00 3.07
3093 5054 4.564940 AAGTAGTGATCCGATTCCGTAC 57.435 45.455 0.00 0.00 0.00 3.67
3103 5064 4.287766 ACCTGGTGAAAAGTAGTGATCC 57.712 45.455 0.00 0.00 0.00 3.36
3131 5094 1.612950 TGCTTGTTTTCACCGCATGAT 59.387 42.857 0.00 0.00 37.11 2.45
3144 5107 5.357878 TCAGAAGTCTGTTGAATTGCTTGTT 59.642 36.000 8.14 0.00 44.12 2.83
3146 5109 5.428496 TCAGAAGTCTGTTGAATTGCTTG 57.572 39.130 8.14 0.00 44.12 4.01
3147 5110 6.645790 ATTCAGAAGTCTGTTGAATTGCTT 57.354 33.333 8.14 0.00 44.12 3.91
3165 5128 9.025041 AGGAGGGTTTATTTCAAGTTTATTCAG 57.975 33.333 0.00 0.00 0.00 3.02
3232 5195 1.336440 TGAAGTTGGTGCATTTCGGTG 59.664 47.619 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.