Multiple sequence alignment - TraesCS2D01G117100

Loading Multiple Alignment...

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 TraesCS2D01G117100 chr2D 100.000 5264 0 0 1 5264 66755736 66760999 0.000000e+00 9721.0
1 TraesCS2D01G117100 chr2A 93.042 3277 126 44 271 3494 68256925 68253698 0.000000e+00 4695.0
2 TraesCS2D01G117100 chr2A 93.017 1790 88 19 3491 5264 68252262 68250494 0.000000e+00 2579.0
3 TraesCS2D01G117100 chr2B 94.844 2056 76 17 2566 4608 104819466 104817428 0.000000e+00 3182.0
4 TraesCS2D01G117100 chr2B 92.891 1491 58 15 1101 2567 104821056 104819590 0.000000e+00 2122.0
5 TraesCS2D01G117100 chr2B 98.073 882 17 0 2656 3537 104826263 104825382 0.000000e+00 1535.0
6 TraesCS2D01G117100 chr2B 95.748 588 23 2 4576 5162 104817427 104816841 0.000000e+00 946.0
7 TraesCS2D01G117100 chr2B 81.781 988 103 48 158 1105 104822069 104821119 0.000000e+00 756.0
8 TraesCS2D01G117100 chr6D 81.159 138 19 6 145 276 408903156 408903020 2.590000e-18 104.0
9 TraesCS2D01G117100 chr3B 94.737 38 1 1 231 267 414486351 414486388 2.050000e-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 TraesCS2D01G117100 chr2D 66755736 66760999 5263 False 9721.0 9721 100.0000 1 5264 1 chr2D.!!$F1 5263
1 TraesCS2D01G117100 chr2A 68250494 68256925 6431 True 3637.0 4695 93.0295 271 5264 2 chr2A.!!$R1 4993
2 TraesCS2D01G117100 chr2B 104816841 104826263 9422 True 1708.2 3182 92.6674 158 5162 5 chr2B.!!$R1 5004

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
78 79 0.096976 GCACGCGCATAAACTCACAT 59.903 50.0 5.73 0.00 38.36 3.21 F
881 4957 0.310854 CGCCGCCCATTTATTCTTCC 59.689 55.0 0.00 0.00 0.00 3.46 F
1327 5481 0.377203 GCTCCCTGTAAATTTCGCCG 59.623 55.0 0.00 0.00 0.00 6.46 F
1644 5802 0.957888 GCTTGACTTGCTCTGGGGAC 60.958 60.0 0.00 0.00 0.00 4.46 F
3226 7531 0.613012 AAGGAAAGGCAGATGCACCC 60.613 55.0 7.19 2.01 44.36 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 5745 0.869880 GTTGTTTGCTGCCACGGTTC 60.870 55.000 0.00 0.0 0.00 3.62 R
2052 6223 1.127582 GCAGCTTCTAGCACAAGTTCG 59.872 52.381 1.09 0.0 45.56 3.95 R
2141 6313 4.679654 GGACAAACATTTACGCCAAGAAAG 59.320 41.667 0.00 0.0 0.00 2.62 R
3496 9240 2.031682 GGAATATGATGCAAGACCGCAC 60.032 50.000 0.00 0.0 46.56 5.34 R
4962 10754 0.037697 AATAACAGCGTCACTCGGCA 60.038 50.000 0.00 0.0 40.26 5.69 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
48 49 8.906636 TTTTTAACACAGTAATACAAACGCAA 57.093 26.923 0.00 0.00 0.00 4.85
76 77 1.495509 TGCACGCGCATAAACTCAC 59.504 52.632 5.73 0.00 45.36 3.51
78 79 0.096976 GCACGCGCATAAACTCACAT 59.903 50.000 5.73 0.00 38.36 3.21
79 80 1.326245 GCACGCGCATAAACTCACATA 59.674 47.619 5.73 0.00 38.36 2.29
80 81 2.845764 GCACGCGCATAAACTCACATAC 60.846 50.000 5.73 0.00 38.36 2.39
81 82 2.603110 CACGCGCATAAACTCACATACT 59.397 45.455 5.73 0.00 0.00 2.12
82 83 3.794564 CACGCGCATAAACTCACATACTA 59.205 43.478 5.73 0.00 0.00 1.82
84 85 5.047847 ACGCGCATAAACTCACATACTATT 58.952 37.500 5.73 0.00 0.00 1.73
85 86 5.522460 ACGCGCATAAACTCACATACTATTT 59.478 36.000 5.73 0.00 0.00 1.40
86 87 6.036735 ACGCGCATAAACTCACATACTATTTT 59.963 34.615 5.73 0.00 0.00 1.82
87 88 6.905076 CGCGCATAAACTCACATACTATTTTT 59.095 34.615 8.75 0.00 0.00 1.94
88 89 7.097449 CGCGCATAAACTCACATACTATTTTTG 60.097 37.037 8.75 0.00 0.00 2.44
89 90 7.908082 GCGCATAAACTCACATACTATTTTTGA 59.092 33.333 0.30 0.00 0.00 2.69
90 91 9.210426 CGCATAAACTCACATACTATTTTTGAC 57.790 33.333 0.00 0.00 0.00 3.18
91 92 9.210426 GCATAAACTCACATACTATTTTTGACG 57.790 33.333 0.00 0.00 0.00 4.35
94 95 6.627690 ACTCACATACTATTTTTGACGACG 57.372 37.500 0.00 0.00 0.00 5.12
95 96 5.575606 ACTCACATACTATTTTTGACGACGG 59.424 40.000 0.00 0.00 0.00 4.79
96 97 4.327898 TCACATACTATTTTTGACGACGGC 59.672 41.667 0.00 0.00 0.00 5.68
97 98 4.092237 CACATACTATTTTTGACGACGGCA 59.908 41.667 0.00 0.00 0.00 5.69
99 100 5.353123 ACATACTATTTTTGACGACGGCATT 59.647 36.000 3.10 0.00 0.00 3.56
100 101 4.759516 ACTATTTTTGACGACGGCATTT 57.240 36.364 3.10 0.00 0.00 2.32
101 102 4.719040 ACTATTTTTGACGACGGCATTTC 58.281 39.130 3.10 0.00 0.00 2.17
102 103 2.025544 TTTTTGACGACGGCATTTCG 57.974 45.000 3.10 0.00 42.36 3.46
104 105 0.600518 TTTGACGACGGCATTTCGGA 60.601 50.000 3.10 0.00 40.92 4.55
105 106 1.286354 TTGACGACGGCATTTCGGAC 61.286 55.000 3.10 1.22 40.92 4.79
106 107 2.433664 ACGACGGCATTTCGGACC 60.434 61.111 0.00 0.00 40.92 4.46
107 108 2.125673 CGACGGCATTTCGGACCT 60.126 61.111 0.00 0.00 32.66 3.85
110 111 0.672401 GACGGCATTTCGGACCTTGA 60.672 55.000 0.00 0.00 0.00 3.02
112 113 1.803289 GGCATTTCGGACCTTGAGC 59.197 57.895 0.00 0.00 0.00 4.26
113 114 0.678048 GGCATTTCGGACCTTGAGCT 60.678 55.000 0.00 0.00 0.00 4.09
114 115 0.729690 GCATTTCGGACCTTGAGCTC 59.270 55.000 6.82 6.82 0.00 4.09
115 116 1.373570 CATTTCGGACCTTGAGCTCC 58.626 55.000 12.15 0.00 0.00 4.70
116 117 1.065854 CATTTCGGACCTTGAGCTCCT 60.066 52.381 12.15 0.00 0.00 3.69
119 120 0.624254 TCGGACCTTGAGCTCCTCTA 59.376 55.000 12.15 0.00 0.00 2.43
120 121 1.215673 TCGGACCTTGAGCTCCTCTAT 59.784 52.381 12.15 0.00 0.00 1.98
121 122 2.442126 TCGGACCTTGAGCTCCTCTATA 59.558 50.000 12.15 0.00 0.00 1.31
122 123 2.554893 CGGACCTTGAGCTCCTCTATAC 59.445 54.545 12.15 0.00 0.00 1.47
123 124 3.749310 CGGACCTTGAGCTCCTCTATACT 60.749 52.174 12.15 0.00 0.00 2.12
125 126 4.447180 GGACCTTGAGCTCCTCTATACTCT 60.447 50.000 12.15 0.00 0.00 3.24
126 127 5.221966 GGACCTTGAGCTCCTCTATACTCTA 60.222 48.000 12.15 0.00 0.00 2.43
127 128 6.463053 ACCTTGAGCTCCTCTATACTCTAT 57.537 41.667 12.15 0.00 0.00 1.98
128 129 6.481643 ACCTTGAGCTCCTCTATACTCTATC 58.518 44.000 12.15 0.00 0.00 2.08
130 131 7.459763 ACCTTGAGCTCCTCTATACTCTATCTA 59.540 40.741 12.15 0.00 0.00 1.98
131 132 8.494433 CCTTGAGCTCCTCTATACTCTATCTAT 58.506 40.741 12.15 0.00 0.00 1.98
205 4244 5.004345 CGAACCAAAATGAGTGAACAAACAC 59.996 40.000 0.00 0.00 40.60 3.32
207 4246 5.410067 ACCAAAATGAGTGAACAAACACAG 58.590 37.500 0.00 0.00 42.45 3.66
208 4247 5.047377 ACCAAAATGAGTGAACAAACACAGT 60.047 36.000 0.00 0.00 42.45 3.55
209 4248 6.151985 ACCAAAATGAGTGAACAAACACAGTA 59.848 34.615 0.00 0.00 42.45 2.74
210 4249 6.692681 CCAAAATGAGTGAACAAACACAGTAG 59.307 38.462 0.00 0.00 42.45 2.57
212 4251 7.624360 AAATGAGTGAACAAACACAGTAGAA 57.376 32.000 0.00 0.00 42.45 2.10
218 4257 6.374333 AGTGAACAAACACAGTAGAACATGTT 59.626 34.615 11.78 11.78 42.45 2.71
219 4258 7.551262 AGTGAACAAACACAGTAGAACATGTTA 59.449 33.333 11.95 0.00 42.45 2.41
220 4259 8.342634 GTGAACAAACACAGTAGAACATGTTAT 58.657 33.333 11.95 11.45 40.11 1.89
221 4260 8.341903 TGAACAAACACAGTAGAACATGTTATG 58.658 33.333 15.84 12.26 34.24 1.90
222 4261 6.668323 ACAAACACAGTAGAACATGTTATGC 58.332 36.000 15.84 14.22 34.24 3.14
223 4262 5.530519 AACACAGTAGAACATGTTATGCG 57.469 39.130 15.84 12.35 33.59 4.73
224 4263 3.370978 ACACAGTAGAACATGTTATGCGC 59.629 43.478 15.84 0.00 0.00 6.09
225 4264 3.370672 CACAGTAGAACATGTTATGCGCA 59.629 43.478 14.96 14.96 0.00 6.09
226 4265 4.034394 CACAGTAGAACATGTTATGCGCAT 59.966 41.667 28.23 28.23 0.00 4.73
227 4266 4.271049 ACAGTAGAACATGTTATGCGCATC 59.729 41.667 29.11 14.56 0.00 3.91
228 4267 4.509230 CAGTAGAACATGTTATGCGCATCT 59.491 41.667 29.11 18.30 0.00 2.90
229 4268 5.691754 CAGTAGAACATGTTATGCGCATCTA 59.308 40.000 29.11 17.19 0.00 1.98
230 4269 6.200854 CAGTAGAACATGTTATGCGCATCTAA 59.799 38.462 29.11 14.39 0.00 2.10
231 4270 6.931281 AGTAGAACATGTTATGCGCATCTAAT 59.069 34.615 29.11 16.27 0.00 1.73
234 4273 8.153479 AGAACATGTTATGCGCATCTAATTTA 57.847 30.769 29.11 4.00 0.00 1.40
235 4274 8.285394 AGAACATGTTATGCGCATCTAATTTAG 58.715 33.333 29.11 12.63 0.00 1.85
355 4408 1.002366 GCACAAGTGTCCTAGATGCG 58.998 55.000 1.79 0.00 0.00 4.73
356 4409 1.673033 GCACAAGTGTCCTAGATGCGT 60.673 52.381 1.79 0.00 0.00 5.24
373 4426 1.669502 GCGTGCAGAATTTCATGGCAA 60.670 47.619 10.62 0.00 36.08 4.52
400 4453 6.542821 TGATATTGGGAAGCTCCGAAAATAT 58.457 36.000 4.32 8.72 37.78 1.28
402 4455 8.160765 TGATATTGGGAAGCTCCGAAAATATAA 58.839 33.333 4.32 2.49 37.78 0.98
404 4457 6.693315 TTGGGAAGCTCCGAAAATATAAAG 57.307 37.500 0.00 0.00 37.43 1.85
408 4461 6.238402 GGGAAGCTCCGAAAATATAAAGACAC 60.238 42.308 0.00 0.00 37.43 3.67
409 4462 5.968387 AGCTCCGAAAATATAAAGACACG 57.032 39.130 0.00 0.00 0.00 4.49
410 4463 5.657474 AGCTCCGAAAATATAAAGACACGA 58.343 37.500 0.00 0.00 0.00 4.35
412 4465 6.761714 AGCTCCGAAAATATAAAGACACGATT 59.238 34.615 0.00 0.00 0.00 3.34
413 4466 7.280205 AGCTCCGAAAATATAAAGACACGATTT 59.720 33.333 0.00 0.00 0.00 2.17
414 4467 8.545420 GCTCCGAAAATATAAAGACACGATTTA 58.455 33.333 0.00 0.00 0.00 1.40
445 4498 2.997485 AGCTTCGAAAACAGGCATTC 57.003 45.000 8.76 0.00 0.00 2.67
473 4526 7.120789 AGCAATCCTTTTAATTTTCAAAGCG 57.879 32.000 0.00 0.00 0.00 4.68
540 4593 7.328493 CGAGCATATTCGATGTCCAAATAGTAA 59.672 37.037 0.00 0.00 43.03 2.24
542 4595 9.507329 AGCATATTCGATGTCCAAATAGTAATT 57.493 29.630 0.00 0.00 0.00 1.40
543 4596 9.760660 GCATATTCGATGTCCAAATAGTAATTC 57.239 33.333 0.00 0.00 0.00 2.17
712 4787 4.338879 CAACTCCAATCCAATCTCACCTT 58.661 43.478 0.00 0.00 0.00 3.50
713 4788 4.227864 ACTCCAATCCAATCTCACCTTC 57.772 45.455 0.00 0.00 0.00 3.46
714 4789 3.848975 ACTCCAATCCAATCTCACCTTCT 59.151 43.478 0.00 0.00 0.00 2.85
767 4843 1.747745 GCCGCCGAGGTACCAAATT 60.748 57.895 15.94 0.00 43.70 1.82
768 4844 1.712018 GCCGCCGAGGTACCAAATTC 61.712 60.000 15.94 1.30 43.70 2.17
769 4845 1.426041 CCGCCGAGGTACCAAATTCG 61.426 60.000 15.94 14.20 34.51 3.34
770 4846 0.738412 CGCCGAGGTACCAAATTCGT 60.738 55.000 15.94 0.00 0.00 3.85
771 4847 1.004595 GCCGAGGTACCAAATTCGTC 58.995 55.000 15.94 0.01 0.00 4.20
772 4848 1.405121 GCCGAGGTACCAAATTCGTCT 60.405 52.381 15.94 0.00 0.00 4.18
777 4853 3.442076 AGGTACCAAATTCGTCTCCTCT 58.558 45.455 15.94 0.00 0.00 3.69
781 4857 2.498078 ACCAAATTCGTCTCCTCTCCTC 59.502 50.000 0.00 0.00 0.00 3.71
786 4862 2.588464 TCGTCTCCTCTCCTCAACTT 57.412 50.000 0.00 0.00 0.00 2.66
787 4863 2.877866 TCGTCTCCTCTCCTCAACTTT 58.122 47.619 0.00 0.00 0.00 2.66
841 4917 1.803289 GCCAAATCCAAGCTCGGTC 59.197 57.895 0.00 0.00 0.00 4.79
876 4952 1.077357 TGGACGCCGCCCATTTATT 60.077 52.632 0.00 0.00 0.00 1.40
881 4957 0.310854 CGCCGCCCATTTATTCTTCC 59.689 55.000 0.00 0.00 0.00 3.46
944 5020 1.959848 GCTCCCACAGCTGTTTTCC 59.040 57.895 18.94 0.85 45.83 3.13
956 5032 2.550180 GCTGTTTTCCACTCTCTTGTCC 59.450 50.000 0.00 0.00 0.00 4.02
975 5051 3.096852 TCCGTGTGATGGTAGTCTCATT 58.903 45.455 0.00 0.00 0.00 2.57
1184 5335 1.560923 CGATCGGGCTGTTTACTGAG 58.439 55.000 7.38 0.00 0.00 3.35
1207 5358 4.224991 TCATTCTGACTGCCATGATTGA 57.775 40.909 0.00 0.00 0.00 2.57
1210 5361 2.362736 TCTGACTGCCATGATTGAAGC 58.637 47.619 0.00 0.00 0.00 3.86
1327 5481 0.377203 GCTCCCTGTAAATTTCGCCG 59.623 55.000 0.00 0.00 0.00 6.46
1348 5502 3.338249 GAGTTCTGATTGCCTGTTAGCA 58.662 45.455 0.00 0.00 42.17 3.49
1476 5633 3.832490 ACAGAAAAGGAAATTAGGTGGCC 59.168 43.478 0.00 0.00 0.00 5.36
1489 5646 1.227853 GTGGCCGACAGTTGGAACT 60.228 57.895 11.58 0.00 40.60 3.01
1515 5672 4.057432 CTGGTGCCTTGTTAACAAAATGG 58.943 43.478 20.89 18.67 35.15 3.16
1532 5689 6.014327 ACAAAATGGAGTTCTGGTTGCATATT 60.014 34.615 0.00 0.00 0.00 1.28
1542 5699 3.439154 TGGTTGCATATTGGTTGGTCAT 58.561 40.909 0.00 0.00 0.00 3.06
1546 5703 4.508551 TGCATATTGGTTGGTCATCTCT 57.491 40.909 0.00 0.00 0.00 3.10
1587 5744 8.777865 TGAATTAAGAAGAACGAGTTGATGAT 57.222 30.769 0.00 0.00 0.00 2.45
1588 5745 8.659491 TGAATTAAGAAGAACGAGTTGATGATG 58.341 33.333 0.00 0.00 0.00 3.07
1589 5746 8.777865 AATTAAGAAGAACGAGTTGATGATGA 57.222 30.769 0.00 0.00 0.00 2.92
1598 5756 1.164411 GTTGATGATGAACCGTGGCA 58.836 50.000 0.00 0.00 0.00 4.92
1644 5802 0.957888 GCTTGACTTGCTCTGGGGAC 60.958 60.000 0.00 0.00 0.00 4.46
1662 5820 3.257127 GGGACTCTACTAGCATCATCCAC 59.743 52.174 5.57 0.00 0.00 4.02
1778 5936 4.733850 TGACAGATCTAGTGCGTTTACAG 58.266 43.478 0.00 0.00 0.00 2.74
1841 5999 3.688185 CCACCTGATTTCTGTCTGTCATG 59.312 47.826 0.00 0.00 0.00 3.07
1852 6010 6.305693 TCTGTCTGTCATGTACTCATATCG 57.694 41.667 0.00 0.00 32.47 2.92
2043 6214 7.879677 TCCCTCAGATATTATATGCACAAACTG 59.120 37.037 0.00 0.00 0.00 3.16
2052 6223 8.638685 ATTATATGCACAAACTGAATCAAAGC 57.361 30.769 0.00 0.00 0.00 3.51
2065 6236 4.083855 TGAATCAAAGCGAACTTGTGCTAG 60.084 41.667 0.00 0.00 41.46 3.42
2126 6297 7.099120 GGGTCATTTATTCTGTTTGCTTTCAT 58.901 34.615 0.00 0.00 0.00 2.57
2141 6313 8.787884 GTTTGCTTTCATTTTGTTCAATTTGTC 58.212 29.630 0.00 0.00 0.00 3.18
2214 6386 3.844577 ATTGATCTTCTGCACTTGTGC 57.155 42.857 17.73 17.73 0.00 4.57
2218 6390 2.330440 TCTTCTGCACTTGTGCTCAA 57.670 45.000 23.53 15.43 35.49 3.02
2241 6413 8.953313 TCAAGATGGCATCATTTAATATGCTAG 58.047 33.333 27.93 1.55 46.16 3.42
2284 6459 2.922387 CGCAGAGTTCTCTGTCAATCAG 59.078 50.000 24.56 9.20 44.85 2.90
2332 6507 2.565391 TCTTGCTAAGACCATCGTGGAA 59.435 45.455 10.46 0.00 41.78 3.53
2352 6527 5.054477 GGAATATGCTTCGGCTGTAAGTTA 58.946 41.667 0.00 0.00 42.37 2.24
2418 6594 8.308931 TCTAAATGGAGCTTTAGTTCGTCTTTA 58.691 33.333 3.46 0.00 38.98 1.85
2422 6598 7.400599 TGGAGCTTTAGTTCGTCTTTATCTA 57.599 36.000 0.00 0.00 0.00 1.98
2599 6900 8.708742 GGTGCTTATTTGTTTTCCTGAAATTAC 58.291 33.333 0.00 0.00 0.00 1.89
2986 7288 6.606395 GGGACTCAAGAGAACAGGTACTAATA 59.394 42.308 3.73 0.00 36.02 0.98
3226 7531 0.613012 AAGGAAAGGCAGATGCACCC 60.613 55.000 7.19 2.01 44.36 4.61
3496 9240 9.907229 ACTCTTAATTCCTTCCAGGTTATAAAG 57.093 33.333 0.00 0.00 36.53 1.85
3507 9251 3.007635 AGGTTATAAAGTGCGGTCTTGC 58.992 45.455 0.00 0.00 0.00 4.01
3537 9281 6.614694 TTCCTAACACCAGCACTCTAATAA 57.385 37.500 0.00 0.00 0.00 1.40
3685 9429 4.202050 GCCTCCTACTTTGCCAAATATGTG 60.202 45.833 0.00 0.00 0.00 3.21
3721 9465 4.547532 GACTGGTACACGGACATGATATC 58.452 47.826 0.00 0.00 0.00 1.63
3807 9551 1.741145 GGTATACCTTGGGCACAAACG 59.259 52.381 15.09 0.00 35.89 3.60
3813 9557 3.692690 ACCTTGGGCACAAACGTATAAT 58.307 40.909 1.48 0.00 35.89 1.28
3816 9560 5.124297 ACCTTGGGCACAAACGTATAATTAC 59.876 40.000 1.48 0.00 35.89 1.89
3832 9576 9.135843 CGTATAATTACGCTTTCTTGGATATCA 57.864 33.333 4.83 0.00 44.11 2.15
3835 9579 7.865706 AATTACGCTTTCTTGGATATCAACT 57.134 32.000 4.83 0.00 0.00 3.16
3836 9580 6.903883 TTACGCTTTCTTGGATATCAACTC 57.096 37.500 4.83 0.00 0.00 3.01
3837 9581 4.832248 ACGCTTTCTTGGATATCAACTCA 58.168 39.130 4.83 0.00 0.00 3.41
3838 9582 4.872691 ACGCTTTCTTGGATATCAACTCAG 59.127 41.667 4.83 0.00 0.00 3.35
3839 9583 4.872691 CGCTTTCTTGGATATCAACTCAGT 59.127 41.667 4.83 0.00 0.00 3.41
3840 9584 5.006165 CGCTTTCTTGGATATCAACTCAGTC 59.994 44.000 4.83 0.00 0.00 3.51
3841 9585 5.295540 GCTTTCTTGGATATCAACTCAGTCC 59.704 44.000 4.83 0.00 0.00 3.85
3842 9586 5.359194 TTCTTGGATATCAACTCAGTCCC 57.641 43.478 4.83 0.00 0.00 4.46
3843 9587 4.624913 TCTTGGATATCAACTCAGTCCCT 58.375 43.478 4.83 0.00 0.00 4.20
3844 9588 4.406972 TCTTGGATATCAACTCAGTCCCTG 59.593 45.833 4.83 0.00 0.00 4.45
3845 9589 3.041211 TGGATATCAACTCAGTCCCTGG 58.959 50.000 4.83 0.00 31.51 4.45
3846 9590 2.370189 GGATATCAACTCAGTCCCTGGG 59.630 54.545 6.33 6.33 38.07 4.45
3850 9594 0.322008 CAACTCAGTCCCTGGGCTTC 60.322 60.000 8.22 0.90 34.91 3.86
3854 9598 0.252881 TCAGTCCCTGGGCTTCATCT 60.253 55.000 8.22 0.00 31.51 2.90
3860 9604 0.747283 CCTGGGCTTCATCTCTGTGC 60.747 60.000 0.00 0.00 0.00 4.57
3869 9613 4.996122 GCTTCATCTCTGTGCTATGCTTAT 59.004 41.667 0.00 0.00 0.00 1.73
3873 9617 3.982475 TCTCTGTGCTATGCTTATTCCG 58.018 45.455 0.00 0.00 0.00 4.30
3874 9618 2.478134 CTCTGTGCTATGCTTATTCCGC 59.522 50.000 0.00 0.00 0.00 5.54
3875 9619 1.532868 CTGTGCTATGCTTATTCCGCC 59.467 52.381 0.00 0.00 0.00 6.13
3877 9621 0.472044 TGCTATGCTTATTCCGCCCA 59.528 50.000 0.00 0.00 0.00 5.36
3878 9622 1.133945 TGCTATGCTTATTCCGCCCAA 60.134 47.619 0.00 0.00 0.00 4.12
3881 9625 3.005791 GCTATGCTTATTCCGCCCAAATT 59.994 43.478 0.00 0.00 0.00 1.82
3883 9627 3.518634 TGCTTATTCCGCCCAAATTTC 57.481 42.857 0.00 0.00 0.00 2.17
3897 9643 5.072741 CCCAAATTTCAGGTATGGATCGAT 58.927 41.667 0.00 0.00 32.82 3.59
3900 9646 6.432162 CCAAATTTCAGGTATGGATCGATGAT 59.568 38.462 0.54 0.00 32.82 2.45
3906 9652 5.047731 TCAGGTATGGATCGATGATTCTGAC 60.048 44.000 0.54 0.00 0.00 3.51
3908 9654 4.082733 GGTATGGATCGATGATTCTGACGA 60.083 45.833 0.54 0.00 39.01 4.20
3918 9664 2.869801 TGATTCTGACGACAACACAACC 59.130 45.455 0.00 0.00 0.00 3.77
3927 9673 2.286833 CGACAACACAACCGAACAGATT 59.713 45.455 0.00 0.00 0.00 2.40
3968 9714 1.686052 CCCAAACTGCTGCAGGTTTTA 59.314 47.619 29.04 0.00 38.32 1.52
3969 9715 2.545742 CCCAAACTGCTGCAGGTTTTAC 60.546 50.000 29.04 0.00 38.32 2.01
3990 9739 0.036022 GCTCAGACCTTCCTTGCAGT 59.964 55.000 0.00 0.00 0.00 4.40
3995 9744 3.152341 CAGACCTTCCTTGCAGTTCAAT 58.848 45.455 0.00 0.00 33.57 2.57
4014 9766 4.532126 TCAATTGCCTGTCTCTTCTCCTAA 59.468 41.667 0.00 0.00 0.00 2.69
4031 9784 6.659824 TCTCCTAATTCTAACATTTCCCCAC 58.340 40.000 0.00 0.00 0.00 4.61
4032 9785 6.447084 TCTCCTAATTCTAACATTTCCCCACT 59.553 38.462 0.00 0.00 0.00 4.00
4037 9790 5.512942 TTCTAACATTTCCCCACTGATCA 57.487 39.130 0.00 0.00 0.00 2.92
4060 9813 5.609533 TTTTACTAGGTGCCTCTCCATAC 57.390 43.478 0.00 0.00 0.00 2.39
4065 9818 1.007721 AGGTGCCTCTCCATACTGAGT 59.992 52.381 0.00 0.00 33.93 3.41
4066 9819 1.834263 GGTGCCTCTCCATACTGAGTT 59.166 52.381 0.00 0.00 33.93 3.01
4101 9854 3.054361 ACCATTTCACATACCTGGGAGTC 60.054 47.826 0.00 0.00 35.83 3.36
4104 9857 2.454336 TCACATACCTGGGAGTCGAT 57.546 50.000 0.00 0.00 29.24 3.59
4152 9905 3.057736 GCAGAATCATCACAGCACAAAGT 60.058 43.478 0.00 0.00 0.00 2.66
4162 9915 3.148823 GCACAAAGTGTTGAGCGAC 57.851 52.632 0.00 0.00 40.69 5.19
4167 9920 1.455786 CAAAGTGTTGAGCGACTACGG 59.544 52.381 0.00 0.00 36.83 4.02
4178 9931 0.041135 CGACTACGGAAGGATCTCGC 60.041 60.000 0.00 0.00 35.72 5.03
4234 9987 3.046390 GTCTCCATTGTCGAGAATAGCG 58.954 50.000 7.56 0.00 38.09 4.26
4270 10023 5.551233 GGAGCAGTTCCATATAGCATACAA 58.449 41.667 0.00 0.00 46.01 2.41
4275 10028 6.128172 GCAGTTCCATATAGCATACAACATCC 60.128 42.308 0.00 0.00 0.00 3.51
4288 10041 7.176515 AGCATACAACATCCTGTTAACATCAAA 59.823 33.333 9.13 0.00 38.77 2.69
4289 10042 7.812191 GCATACAACATCCTGTTAACATCAAAA 59.188 33.333 9.13 0.00 38.77 2.44
4307 10060 7.397192 ACATCAAAATTTATAGCAGAAGGTGGT 59.603 33.333 0.00 0.00 40.92 4.16
4329 10082 5.242615 GGTGCCTTTTCTTTCTCTTGAAGAT 59.757 40.000 0.00 0.00 32.82 2.40
4358 10112 5.221621 GGTTCAGTTGGGGAATTTCATTCAA 60.222 40.000 0.00 0.00 41.03 2.69
4585 10374 5.468072 GCCATGAAATGTCTACTAGATGTGG 59.532 44.000 0.00 0.00 44.81 4.17
4614 10403 7.694093 AGAATTCTAAACTGAAATCTGACCCT 58.306 34.615 6.06 0.00 35.57 4.34
4616 10405 6.688073 TTCTAAACTGAAATCTGACCCTCT 57.312 37.500 0.00 0.00 0.00 3.69
4700 10489 4.423625 ACCTTTCACAGCAGTTAGAACT 57.576 40.909 0.00 0.00 40.60 3.01
4833 10623 5.566469 TCTTACAAGGTATGGACAAAAGGG 58.434 41.667 0.00 0.00 0.00 3.95
4848 10638 8.174085 TGGACAAAAGGGAAAATCCTCTAATAA 58.826 33.333 0.00 0.00 36.57 1.40
4931 10723 7.776618 AAACCAAAGAAAACCTTATCCTAGG 57.223 36.000 0.82 0.82 41.31 3.02
4964 10756 6.058183 ACAAAGTGGGTGATCTTCTATATGC 58.942 40.000 0.00 0.00 0.00 3.14
5009 10801 2.315443 AGGCATCCTGGGAGAAAGG 58.685 57.895 0.00 0.00 36.02 3.11
5229 11022 1.795872 GGCAAAATTAACGGCAACACC 59.204 47.619 0.00 0.00 0.00 4.16
5240 11033 4.007940 CAACACCGCCCGTTCGTG 62.008 66.667 0.00 0.00 0.00 4.35
5241 11034 4.224274 AACACCGCCCGTTCGTGA 62.224 61.111 0.00 0.00 0.00 4.35
5242 11035 3.736732 AACACCGCCCGTTCGTGAA 62.737 57.895 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 8.182881 ACTTGCGTTTGTATTACTGTGTTAAAA 58.817 29.630 0.00 0.00 0.00 1.52
25 26 7.640630 CACTTGCGTTTGTATTACTGTGTTAAA 59.359 33.333 0.00 0.00 0.00 1.52
26 27 7.127042 CACTTGCGTTTGTATTACTGTGTTAA 58.873 34.615 0.00 0.00 0.00 2.01
27 28 6.651308 CACTTGCGTTTGTATTACTGTGTTA 58.349 36.000 0.00 0.00 0.00 2.41
28 29 5.507077 CACTTGCGTTTGTATTACTGTGTT 58.493 37.500 0.00 0.00 0.00 3.32
29 30 4.553938 GCACTTGCGTTTGTATTACTGTGT 60.554 41.667 0.00 0.00 0.00 3.72
30 31 3.906008 GCACTTGCGTTTGTATTACTGTG 59.094 43.478 0.00 0.00 0.00 3.66
59 60 0.096976 ATGTGAGTTTATGCGCGTGC 59.903 50.000 15.48 15.48 43.20 5.34
60 61 2.603110 AGTATGTGAGTTTATGCGCGTG 59.397 45.455 13.61 0.00 0.00 5.34
61 62 2.888594 AGTATGTGAGTTTATGCGCGT 58.111 42.857 8.43 7.55 0.00 6.01
62 63 5.576337 AATAGTATGTGAGTTTATGCGCG 57.424 39.130 0.00 0.00 0.00 6.86
63 64 7.908082 TCAAAAATAGTATGTGAGTTTATGCGC 59.092 33.333 0.00 0.00 0.00 6.09
65 66 9.210426 CGTCAAAAATAGTATGTGAGTTTATGC 57.790 33.333 0.00 0.00 0.00 3.14
69 70 7.359765 CCGTCGTCAAAAATAGTATGTGAGTTT 60.360 37.037 0.00 0.00 0.00 2.66
70 71 6.090358 CCGTCGTCAAAAATAGTATGTGAGTT 59.910 38.462 0.00 0.00 0.00 3.01
71 72 5.575606 CCGTCGTCAAAAATAGTATGTGAGT 59.424 40.000 0.00 0.00 0.00 3.41
72 73 5.500290 GCCGTCGTCAAAAATAGTATGTGAG 60.500 44.000 0.00 0.00 0.00 3.51
73 74 4.327898 GCCGTCGTCAAAAATAGTATGTGA 59.672 41.667 0.00 0.00 0.00 3.58
74 75 4.092237 TGCCGTCGTCAAAAATAGTATGTG 59.908 41.667 0.00 0.00 0.00 3.21
76 77 4.850859 TGCCGTCGTCAAAAATAGTATG 57.149 40.909 0.00 0.00 0.00 2.39
78 79 5.444877 CGAAATGCCGTCGTCAAAAATAGTA 60.445 40.000 0.00 0.00 33.80 1.82
79 80 4.668177 CGAAATGCCGTCGTCAAAAATAGT 60.668 41.667 0.00 0.00 33.80 2.12
80 81 3.778718 CGAAATGCCGTCGTCAAAAATAG 59.221 43.478 0.00 0.00 33.80 1.73
81 82 3.425094 CCGAAATGCCGTCGTCAAAAATA 60.425 43.478 0.00 0.00 36.77 1.40
82 83 2.580589 CGAAATGCCGTCGTCAAAAAT 58.419 42.857 0.00 0.00 33.80 1.82
84 85 0.236187 CCGAAATGCCGTCGTCAAAA 59.764 50.000 0.00 0.00 36.77 2.44
85 86 0.600518 TCCGAAATGCCGTCGTCAAA 60.601 50.000 0.00 0.00 36.77 2.69
86 87 1.005984 TCCGAAATGCCGTCGTCAA 60.006 52.632 0.00 0.00 36.77 3.18
87 88 1.735198 GTCCGAAATGCCGTCGTCA 60.735 57.895 0.00 0.00 36.77 4.35
88 89 2.450345 GGTCCGAAATGCCGTCGTC 61.450 63.158 0.00 0.00 36.77 4.20
89 90 2.433664 GGTCCGAAATGCCGTCGT 60.434 61.111 0.00 0.00 36.77 4.34
90 91 1.740296 AAGGTCCGAAATGCCGTCG 60.740 57.895 0.00 0.00 38.24 5.12
91 92 0.672401 TCAAGGTCCGAAATGCCGTC 60.672 55.000 0.00 0.00 0.00 4.79
92 93 0.673644 CTCAAGGTCCGAAATGCCGT 60.674 55.000 0.00 0.00 0.00 5.68
93 94 1.982073 GCTCAAGGTCCGAAATGCCG 61.982 60.000 0.00 0.00 0.00 5.69
94 95 0.678048 AGCTCAAGGTCCGAAATGCC 60.678 55.000 0.00 0.00 0.00 4.40
95 96 0.729690 GAGCTCAAGGTCCGAAATGC 59.270 55.000 9.40 0.00 36.62 3.56
104 105 4.806952 AGAGTATAGAGGAGCTCAAGGT 57.193 45.455 17.19 0.00 32.06 3.50
105 106 6.721318 AGATAGAGTATAGAGGAGCTCAAGG 58.279 44.000 17.19 0.00 32.06 3.61
106 107 9.905713 AATAGATAGAGTATAGAGGAGCTCAAG 57.094 37.037 17.19 0.00 32.06 3.02
180 4218 4.974368 TTGTTCACTCATTTTGGTTCGT 57.026 36.364 0.00 0.00 0.00 3.85
181 4219 5.004345 GTGTTTGTTCACTCATTTTGGTTCG 59.996 40.000 0.00 0.00 35.68 3.95
182 4220 5.866633 TGTGTTTGTTCACTCATTTTGGTTC 59.133 36.000 0.00 0.00 38.90 3.62
183 4221 5.788450 TGTGTTTGTTCACTCATTTTGGTT 58.212 33.333 0.00 0.00 38.90 3.67
196 4235 7.323656 GCATAACATGTTCTACTGTGTTTGTTC 59.676 37.037 15.85 0.00 36.34 3.18
205 4244 4.509230 AGATGCGCATAACATGTTCTACTG 59.491 41.667 25.40 9.78 0.00 2.74
207 4246 6.525121 TTAGATGCGCATAACATGTTCTAC 57.475 37.500 25.40 6.00 0.00 2.59
208 4247 7.728847 AATTAGATGCGCATAACATGTTCTA 57.271 32.000 25.40 15.62 0.00 2.10
209 4248 6.624352 AATTAGATGCGCATAACATGTTCT 57.376 33.333 25.40 16.72 0.00 3.01
210 4249 8.282592 TCTAAATTAGATGCGCATAACATGTTC 58.717 33.333 25.40 9.27 0.00 3.18
212 4251 7.728847 TCTAAATTAGATGCGCATAACATGT 57.271 32.000 25.40 12.45 0.00 3.21
220 4259 9.900710 TTTAACTTTTTCTAAATTAGATGCGCA 57.099 25.926 14.96 14.96 34.22 6.09
322 4375 2.226437 ACTTGTGCATTTTCGGTGCTAG 59.774 45.455 0.00 0.00 42.92 3.42
355 4408 3.581024 TCTTGCCATGAAATTCTGCAC 57.419 42.857 0.00 0.00 0.00 4.57
356 4409 3.764972 TCATCTTGCCATGAAATTCTGCA 59.235 39.130 0.00 0.00 29.41 4.41
373 4426 3.242867 TCGGAGCTTCCCAATATCATCT 58.757 45.455 0.00 0.00 31.13 2.90
400 4453 6.680810 TCTTCGGAGTTAAATCGTGTCTTTA 58.319 36.000 0.00 0.00 0.00 1.85
402 4455 5.130292 TCTTCGGAGTTAAATCGTGTCTT 57.870 39.130 0.00 0.00 0.00 3.01
404 4457 5.668132 GCTTTCTTCGGAGTTAAATCGTGTC 60.668 44.000 0.00 0.00 0.00 3.67
408 4461 5.532025 AAGCTTTCTTCGGAGTTAAATCG 57.468 39.130 0.00 0.00 0.00 3.34
437 4490 2.941480 AGGATTGCTTAGGAATGCCTG 58.059 47.619 13.56 0.00 46.45 4.85
490 4543 2.159430 TGCTCGTGTGGAATTTCATTCG 59.841 45.455 7.04 7.04 40.17 3.34
564 4624 8.816894 CAGCTCATCTACTCCCCTATAAATAAA 58.183 37.037 0.00 0.00 0.00 1.40
685 4760 2.027385 GATTGGATTGGAGTTGGAGGC 58.973 52.381 0.00 0.00 0.00 4.70
692 4767 3.848975 AGAAGGTGAGATTGGATTGGAGT 59.151 43.478 0.00 0.00 0.00 3.85
712 4787 2.448961 TGGAAATGGGTGGGAAGAAAGA 59.551 45.455 0.00 0.00 0.00 2.52
713 4788 2.827921 CTGGAAATGGGTGGGAAGAAAG 59.172 50.000 0.00 0.00 0.00 2.62
714 4789 2.888212 CTGGAAATGGGTGGGAAGAAA 58.112 47.619 0.00 0.00 0.00 2.52
767 4843 2.588464 AAGTTGAGGAGAGGAGACGA 57.412 50.000 0.00 0.00 0.00 4.20
768 4844 2.823154 AGAAAGTTGAGGAGAGGAGACG 59.177 50.000 0.00 0.00 0.00 4.18
769 4845 3.194755 GGAGAAAGTTGAGGAGAGGAGAC 59.805 52.174 0.00 0.00 0.00 3.36
770 4846 3.076785 AGGAGAAAGTTGAGGAGAGGAGA 59.923 47.826 0.00 0.00 0.00 3.71
771 4847 3.440127 AGGAGAAAGTTGAGGAGAGGAG 58.560 50.000 0.00 0.00 0.00 3.69
772 4848 3.551635 AGGAGAAAGTTGAGGAGAGGA 57.448 47.619 0.00 0.00 0.00 3.71
777 4853 2.907042 GGGAGAAGGAGAAAGTTGAGGA 59.093 50.000 0.00 0.00 0.00 3.71
781 4857 2.498644 GGGGGAGAAGGAGAAAGTTG 57.501 55.000 0.00 0.00 0.00 3.16
841 4917 2.484264 GTCCAGGACCAAATTGACGAAG 59.516 50.000 8.65 0.00 0.00 3.79
876 4952 0.321653 GCGGAGGCAGAAAAGGAAGA 60.322 55.000 0.00 0.00 39.62 2.87
944 5020 2.332104 CATCACACGGACAAGAGAGTG 58.668 52.381 0.00 0.00 40.17 3.51
956 5032 4.110036 TGAATGAGACTACCATCACACG 57.890 45.455 0.00 0.00 0.00 4.49
975 5051 2.507452 CAGGGCGCATCTCCATGA 59.493 61.111 10.83 0.00 37.57 3.07
1207 5358 6.072618 GCACTGATATTCATCTATGCTTGCTT 60.073 38.462 0.00 0.00 38.58 3.91
1210 5361 6.796705 TGCACTGATATTCATCTATGCTTG 57.203 37.500 11.99 0.00 40.51 4.01
1327 5481 3.338249 TGCTAACAGGCAATCAGAACTC 58.662 45.455 0.00 0.00 39.43 3.01
1348 5502 1.076777 AGTTGTTGGCCAGTGTGCT 60.077 52.632 5.11 0.00 0.00 4.40
1476 5633 2.224209 ACCAGGTAAGTTCCAACTGTCG 60.224 50.000 0.00 0.00 39.66 4.35
1489 5646 3.579534 TGTTAACAAGGCACCAGGTAA 57.420 42.857 5.64 0.00 0.00 2.85
1515 5672 4.380867 CCAACCAATATGCAACCAGAACTC 60.381 45.833 0.00 0.00 0.00 3.01
1532 5689 9.231297 CTTTTATTTTCTAGAGATGACCAACCA 57.769 33.333 0.00 0.00 0.00 3.67
1587 5744 1.315981 TTGTTTGCTGCCACGGTTCA 61.316 50.000 0.00 0.00 0.00 3.18
1588 5745 0.869880 GTTGTTTGCTGCCACGGTTC 60.870 55.000 0.00 0.00 0.00 3.62
1589 5746 1.140804 GTTGTTTGCTGCCACGGTT 59.859 52.632 0.00 0.00 0.00 4.44
1598 5756 4.681744 CAACAGTACAATGGTTGTTTGCT 58.318 39.130 0.20 0.00 42.22 3.91
1644 5802 4.731720 CATCGTGGATGATGCTAGTAGAG 58.268 47.826 0.00 0.00 42.09 2.43
1662 5820 1.696063 AAGATCAATTGGGGGCATCG 58.304 50.000 5.42 0.00 0.00 3.84
1778 5936 5.855045 AGTACTAGGTTAAGTGCCATATGC 58.145 41.667 0.00 0.00 41.77 3.14
1797 5955 4.907809 GGGGGCTTATCAAATAGGAGTAC 58.092 47.826 0.00 0.00 0.00 2.73
1822 5980 5.728471 AGTACATGACAGACAGAAATCAGG 58.272 41.667 0.00 0.00 0.00 3.86
1841 5999 9.586150 CTGAAAATATTGCAACGATATGAGTAC 57.414 33.333 0.00 0.00 0.00 2.73
1852 6010 8.863049 CAAGTGGATAACTGAAAATATTGCAAC 58.137 33.333 0.00 0.00 39.81 4.17
2043 6214 3.273919 AGCACAAGTTCGCTTTGATTC 57.726 42.857 0.00 0.00 33.81 2.52
2052 6223 1.127582 GCAGCTTCTAGCACAAGTTCG 59.872 52.381 1.09 0.00 45.56 3.95
2065 6236 2.871022 CTGTCATATCTGTGGCAGCTTC 59.129 50.000 0.00 0.00 43.93 3.86
2126 6297 6.183360 CGCCAAGAAAGACAAATTGAACAAAA 60.183 34.615 0.00 0.00 0.00 2.44
2141 6313 4.679654 GGACAAACATTTACGCCAAGAAAG 59.320 41.667 0.00 0.00 0.00 2.62
2187 6359 5.876612 AGTGCAGAAGATCAATTTCAGAC 57.123 39.130 0.00 0.00 0.00 3.51
2332 6507 6.113411 AGTTTAACTTACAGCCGAAGCATAT 58.887 36.000 0.00 0.00 43.56 1.78
2538 6714 5.047566 TGAATGGAAGAGAACAGTTGGAA 57.952 39.130 0.00 0.00 0.00 3.53
2986 7288 7.260603 GGAATACTAGAAGCACATGCAATTTT 58.739 34.615 6.64 0.00 45.16 1.82
3439 7744 9.761504 ACATTGAATGTATTTGTGAAACATTGA 57.238 25.926 9.41 0.00 45.06 2.57
3496 9240 2.031682 GGAATATGATGCAAGACCGCAC 60.032 50.000 0.00 0.00 46.56 5.34
3507 9251 5.371526 AGTGCTGGTGTTAGGAATATGATG 58.628 41.667 0.00 0.00 0.00 3.07
3512 9256 6.808321 ATTAGAGTGCTGGTGTTAGGAATA 57.192 37.500 0.00 0.00 0.00 1.75
3537 9281 7.557719 ACAGCTTACATAATAACAAGCCTCAAT 59.442 33.333 1.77 0.00 43.48 2.57
3685 9429 1.336755 ACCAGTCGAATTGTGTTTGGC 59.663 47.619 0.00 0.00 0.00 4.52
3813 9557 6.403049 TGAGTTGATATCCAAGAAAGCGTAA 58.597 36.000 0.00 0.00 35.03 3.18
3816 9560 4.872691 ACTGAGTTGATATCCAAGAAAGCG 59.127 41.667 0.00 0.00 35.03 4.68
3837 9581 0.043940 AGAGATGAAGCCCAGGGACT 59.956 55.000 10.89 2.59 43.88 3.85
3838 9582 0.179936 CAGAGATGAAGCCCAGGGAC 59.820 60.000 10.89 0.00 0.00 4.46
3839 9583 0.252881 ACAGAGATGAAGCCCAGGGA 60.253 55.000 10.89 0.00 0.00 4.20
3840 9584 0.107312 CACAGAGATGAAGCCCAGGG 60.107 60.000 0.00 0.00 0.00 4.45
3841 9585 0.747283 GCACAGAGATGAAGCCCAGG 60.747 60.000 0.00 0.00 0.00 4.45
3842 9586 0.252479 AGCACAGAGATGAAGCCCAG 59.748 55.000 0.00 0.00 0.00 4.45
3843 9587 1.571955 TAGCACAGAGATGAAGCCCA 58.428 50.000 0.00 0.00 0.00 5.36
3844 9588 2.492012 CATAGCACAGAGATGAAGCCC 58.508 52.381 0.00 0.00 0.00 5.19
3845 9589 1.872313 GCATAGCACAGAGATGAAGCC 59.128 52.381 0.00 0.00 0.00 4.35
3846 9590 2.836262 AGCATAGCACAGAGATGAAGC 58.164 47.619 0.00 0.00 0.00 3.86
3850 9594 4.388165 CGGAATAAGCATAGCACAGAGATG 59.612 45.833 0.00 0.00 0.00 2.90
3854 9598 2.483876 GCGGAATAAGCATAGCACAGA 58.516 47.619 0.00 0.00 34.19 3.41
3860 9604 4.853924 AATTTGGGCGGAATAAGCATAG 57.146 40.909 0.00 0.00 36.08 2.23
3869 9613 2.588464 TACCTGAAATTTGGGCGGAA 57.412 45.000 0.00 0.00 0.00 4.30
3873 9617 3.004734 CGATCCATACCTGAAATTTGGGC 59.995 47.826 0.00 0.00 0.00 5.36
3874 9618 4.460263 TCGATCCATACCTGAAATTTGGG 58.540 43.478 0.00 0.00 0.00 4.12
3875 9619 5.764686 TCATCGATCCATACCTGAAATTTGG 59.235 40.000 0.00 0.00 0.00 3.28
3877 9621 7.941238 AGAATCATCGATCCATACCTGAAATTT 59.059 33.333 0.00 0.00 0.00 1.82
3878 9622 7.389884 CAGAATCATCGATCCATACCTGAAATT 59.610 37.037 0.00 0.00 0.00 1.82
3881 9625 5.539955 TCAGAATCATCGATCCATACCTGAA 59.460 40.000 0.00 0.00 0.00 3.02
3883 9627 5.167121 GTCAGAATCATCGATCCATACCTG 58.833 45.833 0.00 3.00 0.00 4.00
3897 9643 2.869801 GGTTGTGTTGTCGTCAGAATCA 59.130 45.455 0.00 0.00 0.00 2.57
3900 9646 1.135053 TCGGTTGTGTTGTCGTCAGAA 60.135 47.619 0.00 0.00 0.00 3.02
3906 9652 1.282817 TCTGTTCGGTTGTGTTGTCG 58.717 50.000 0.00 0.00 0.00 4.35
3908 9654 3.442273 ACAAATCTGTTCGGTTGTGTTGT 59.558 39.130 0.00 0.00 33.09 3.32
3918 9664 2.730090 GCTGGCATCACAAATCTGTTCG 60.730 50.000 0.00 0.00 31.64 3.95
3968 9714 0.036022 GCAAGGAAGGTCTGAGCTGT 59.964 55.000 10.52 0.90 0.00 4.40
3969 9715 0.035881 TGCAAGGAAGGTCTGAGCTG 59.964 55.000 10.52 0.00 0.00 4.24
3973 9722 1.768275 TGAACTGCAAGGAAGGTCTGA 59.232 47.619 0.00 0.00 39.30 3.27
3990 9739 3.328931 AGGAGAAGAGACAGGCAATTGAA 59.671 43.478 10.34 0.00 0.00 2.69
3995 9744 4.780021 AGAATTAGGAGAAGAGACAGGCAA 59.220 41.667 0.00 0.00 0.00 4.52
4014 9766 6.078456 TGATCAGTGGGGAAATGTTAGAAT 57.922 37.500 0.00 0.00 0.00 2.40
4031 9784 5.923204 AGAGGCACCTAGTAAAATGATCAG 58.077 41.667 0.09 0.00 0.00 2.90
4032 9785 5.163301 GGAGAGGCACCTAGTAAAATGATCA 60.163 44.000 0.00 0.00 0.00 2.92
4037 9790 5.905913 AGTATGGAGAGGCACCTAGTAAAAT 59.094 40.000 0.00 0.00 0.00 1.82
4060 9813 2.746362 GGTCCTGAATGCTCAAACTCAG 59.254 50.000 0.00 0.00 35.99 3.35
4065 9818 4.022068 GTGAAATGGTCCTGAATGCTCAAA 60.022 41.667 0.00 0.00 0.00 2.69
4066 9819 3.507233 GTGAAATGGTCCTGAATGCTCAA 59.493 43.478 0.00 0.00 0.00 3.02
4101 9854 5.397142 TCCAGTCATCTGATTCCATATCG 57.603 43.478 0.00 0.00 43.76 2.92
4104 9857 3.969312 TGCTCCAGTCATCTGATTCCATA 59.031 43.478 0.00 0.00 43.76 2.74
4152 9905 0.242825 CCTTCCGTAGTCGCTCAACA 59.757 55.000 0.00 0.00 35.54 3.33
4162 9915 0.312416 CTGGCGAGATCCTTCCGTAG 59.688 60.000 0.00 0.00 0.00 3.51
4167 9920 0.391661 TGTTGCTGGCGAGATCCTTC 60.392 55.000 0.00 0.00 0.00 3.46
4178 9931 4.421058 CTTTGTCATGATGATGTTGCTGG 58.579 43.478 0.00 0.00 0.00 4.85
4234 9987 0.669932 CTGCTCCAGTCTGTCTGCAC 60.670 60.000 0.00 0.00 42.38 4.57
4284 10037 6.350110 GCACCACCTTCTGCTATAAATTTTGA 60.350 38.462 0.00 0.00 0.00 2.69
4288 10041 3.954258 GGCACCACCTTCTGCTATAAATT 59.046 43.478 0.00 0.00 33.63 1.82
4289 10042 3.555966 GGCACCACCTTCTGCTATAAAT 58.444 45.455 0.00 0.00 33.63 1.40
4291 10044 2.710096 GGCACCACCTTCTGCTATAA 57.290 50.000 0.00 0.00 33.63 0.98
4303 10056 3.632145 TCAAGAGAAAGAAAAGGCACCAC 59.368 43.478 0.00 0.00 0.00 4.16
4307 10060 5.242393 CCATCTTCAAGAGAAAGAAAAGGCA 59.758 40.000 0.00 0.00 38.06 4.75
4358 10112 7.118496 TGAAAGAACAATGTACAACCCAATT 57.882 32.000 0.00 0.00 0.00 2.32
4585 10374 9.928236 GTCAGATTTCAGTTTAGAATTCTATGC 57.072 33.333 15.82 11.35 36.57 3.14
4616 10405 6.742109 CAGAATTTGCCTCTTTTTCTCAAGA 58.258 36.000 0.00 0.00 0.00 3.02
4678 10467 4.781934 AGTTCTAACTGCTGTGAAAGGTT 58.218 39.130 0.00 0.00 37.98 3.50
4738 10528 7.572539 GCATGGTTGTACAGACTAAAGTAAACC 60.573 40.741 0.00 0.00 34.99 3.27
4848 10638 6.722129 AGAGTTGTCTTGTAAGTAGATCCTGT 59.278 38.462 0.00 0.00 0.00 4.00
4855 10646 8.348983 TCGAAAAAGAGTTGTCTTGTAAGTAG 57.651 34.615 0.00 0.00 42.59 2.57
4931 10723 5.527582 AGATCACCCACTTTGTATTTATCGC 59.472 40.000 0.00 0.00 0.00 4.58
4962 10754 0.037697 AATAACAGCGTCACTCGGCA 60.038 50.000 0.00 0.00 40.26 5.69
4964 10756 1.990799 TCAATAACAGCGTCACTCGG 58.009 50.000 0.00 0.00 40.26 4.63
5009 10801 0.312102 GCTGTTCAACTGCTGGGAAC 59.688 55.000 11.92 17.58 39.55 3.62
5162 10955 1.066502 GGGGTGAGTGCTTCTCTTCTC 60.067 57.143 9.94 0.00 43.13 2.87
5163 10956 0.980423 GGGGTGAGTGCTTCTCTTCT 59.020 55.000 9.94 0.00 43.13 2.85
5164 10957 0.980423 AGGGGTGAGTGCTTCTCTTC 59.020 55.000 9.94 4.74 43.13 2.87
5165 10958 0.980423 GAGGGGTGAGTGCTTCTCTT 59.020 55.000 9.94 0.00 43.13 2.85
5240 11033 4.248058 CAGGTTTGAATTTGATGGCCTTC 58.752 43.478 11.69 11.69 0.00 3.46
5241 11034 3.557686 GCAGGTTTGAATTTGATGGCCTT 60.558 43.478 3.32 0.00 0.00 4.35
5242 11035 2.027837 GCAGGTTTGAATTTGATGGCCT 60.028 45.455 3.32 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.