Multiple sequence alignment - TraesCS1A01G121600

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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 TraesCS1A01G121600 chr1A 100.000 2285 0 0 1 2285 135506797 135509081 0.000000e+00 4220.0
1 TraesCS1A01G121600 chr1A 100.000 34 0 0 1070 1103 135507834 135507867 1.900000e-06 63.9
2 TraesCS1A01G121600 chr1A 100.000 34 0 0 1038 1071 135507866 135507899 1.900000e-06 63.9
3 TraesCS1A01G121600 chr1D 87.433 1114 75 24 471 1549 123100645 123101728 0.000000e+00 1221.0
4 TraesCS1A01G121600 chr1D 91.326 611 23 10 1697 2285 123101733 123102335 0.000000e+00 808.0
5 TraesCS1A01G121600 chr1D 92.208 385 29 1 82 465 123085739 123086123 5.550000e-151 544.0
6 TraesCS1A01G121600 chr1B 86.064 1184 105 24 81 1227 187689475 187690635 0.000000e+00 1218.0
7 TraesCS1A01G121600 chr1B 94.737 190 2 1 2104 2285 187700086 187700275 2.870000e-74 289.0
8 TraesCS1A01G121600 chr1B 86.296 270 23 3 1831 2090 187691085 187691350 4.810000e-72 281.0
9 TraesCS1A01G121600 chr1B 89.130 184 16 3 1340 1522 187690769 187690949 2.280000e-55 226.0
10 TraesCS1A01G121600 chr5A 83.660 153 17 4 1912 2062 569715027 569715173 1.100000e-28 137.0
11 TraesCS1A01G121600 chr5A 95.082 61 3 0 1603 1663 59700882 59700822 1.870000e-16 97.1
12 TraesCS1A01G121600 chr5A 97.297 37 0 1 1665 1700 663212439 663212403 6.820000e-06 62.1
13 TraesCS1A01G121600 chr4D 82.781 151 23 2 1912 2062 163791066 163791213 5.120000e-27 132.0
14 TraesCS1A01G121600 chr4D 93.443 61 4 0 1603 1663 50156124 50156064 8.690000e-15 91.6
15 TraesCS1A01G121600 chr4D 82.432 74 13 0 1912 1985 448109958 448110031 5.270000e-07 65.8
16 TraesCS1A01G121600 chr3B 80.392 153 25 2 1912 2063 428257280 428257428 6.670000e-21 111.0
17 TraesCS1A01G121600 chr5D 94.286 70 3 1 1603 1671 69096386 69096317 3.100000e-19 106.0
18 TraesCS1A01G121600 chr2D 96.721 61 1 1 1603 1663 267985 267926 1.440000e-17 100.0
19 TraesCS1A01G121600 chr2D 93.651 63 4 0 1601 1663 263419154 263419092 6.720000e-16 95.3
20 TraesCS1A01G121600 chr2D 95.122 41 2 0 1907 1947 637390509 637390469 5.270000e-07 65.8
21 TraesCS1A01G121600 chr6B 95.082 61 3 0 1603 1663 675195027 675195087 1.870000e-16 97.1
22 TraesCS1A01G121600 chr2A 95.000 60 2 1 1603 1662 268714 268772 2.420000e-15 93.5
23 TraesCS1A01G121600 chr6D 93.443 61 4 0 1603 1663 25002246 25002306 8.690000e-15 91.6
24 TraesCS1A01G121600 chr2B 93.548 62 3 1 1602 1663 11036247 11036187 8.690000e-15 91.6
25 TraesCS1A01G121600 chrUn 86.207 58 8 0 1950 2007 369725096 369725039 1.900000e-06 63.9
26 TraesCS1A01G121600 chr7D 86.207 58 8 0 1950 2007 270291152 270291209 1.900000e-06 63.9
27 TraesCS1A01G121600 chr6A 100.000 33 0 0 1666 1698 609231753 609231785 6.820000e-06 62.1
28 TraesCS1A01G121600 chr4B 91.304 46 2 2 1897 1942 116221565 116221608 6.820000e-06 62.1
29 TraesCS1A01G121600 chr7A 92.500 40 2 1 1909 1947 296464234 296464195 3.170000e-04 56.5
30 TraesCS1A01G121600 chr4A 100.000 29 0 0 1671 1699 618527503 618527475 1.000000e-03 54.7


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 TraesCS1A01G121600 chr1A 135506797 135509081 2284 False 1449.266667 4220 100.000000 1 2285 3 chr1A.!!$F1 2284
1 TraesCS1A01G121600 chr1D 123100645 123102335 1690 False 1014.500000 1221 89.379500 471 2285 2 chr1D.!!$F2 1814
2 TraesCS1A01G121600 chr1B 187689475 187691350 1875 False 575.000000 1218 87.163333 81 2090 3 chr1B.!!$F2 2009

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
339 341 0.108186 ATGCTCTCCATTCGCGTTCA 60.108 50.0 5.77 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1679 1844 0.042731 CTACTCCCTCCCTCCCACAA 59.957 60.0 0.0 0.0 0.0 3.33 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
24 25 7.773489 TTGTTTCCATAAGATTCAACCATGA 57.227 32.000 0.00 0.00 0.00 3.07
25 26 7.959658 TGTTTCCATAAGATTCAACCATGAT 57.040 32.000 0.00 0.00 34.96 2.45
26 27 9.473007 TTGTTTCCATAAGATTCAACCATGATA 57.527 29.630 0.00 0.00 34.96 2.15
27 28 8.902806 TGTTTCCATAAGATTCAACCATGATAC 58.097 33.333 0.00 0.00 34.96 2.24
28 29 7.728847 TTCCATAAGATTCAACCATGATACG 57.271 36.000 0.00 0.00 34.96 3.06
29 30 7.061566 TCCATAAGATTCAACCATGATACGA 57.938 36.000 0.00 0.00 34.96 3.43
30 31 7.679783 TCCATAAGATTCAACCATGATACGAT 58.320 34.615 0.00 0.00 34.96 3.73
31 32 7.819415 TCCATAAGATTCAACCATGATACGATC 59.181 37.037 0.00 0.00 34.96 3.69
32 33 7.603784 CCATAAGATTCAACCATGATACGATCA 59.396 37.037 0.00 0.00 44.55 2.92
33 34 8.654215 CATAAGATTCAACCATGATACGATCAG 58.346 37.037 0.00 0.00 43.53 2.90
34 35 6.166984 AGATTCAACCATGATACGATCAGT 57.833 37.500 0.00 0.00 43.53 3.41
35 36 6.586344 AGATTCAACCATGATACGATCAGTT 58.414 36.000 0.00 0.00 43.53 3.16
36 37 6.703607 AGATTCAACCATGATACGATCAGTTC 59.296 38.462 0.00 0.00 43.53 3.01
37 38 4.693283 TCAACCATGATACGATCAGTTCC 58.307 43.478 0.00 0.00 43.53 3.62
38 39 4.161377 TCAACCATGATACGATCAGTTCCA 59.839 41.667 0.00 0.00 43.53 3.53
39 40 4.327982 ACCATGATACGATCAGTTCCAG 57.672 45.455 0.00 0.00 43.53 3.86
40 41 3.706594 ACCATGATACGATCAGTTCCAGT 59.293 43.478 0.00 0.00 43.53 4.00
41 42 4.202161 ACCATGATACGATCAGTTCCAGTC 60.202 45.833 0.00 0.00 43.53 3.51
42 43 3.692791 TGATACGATCAGTTCCAGTCG 57.307 47.619 0.00 0.00 39.78 4.18
45 46 2.915738 ACGATCAGTTCCAGTCGTAC 57.084 50.000 0.00 0.00 44.49 3.67
46 47 1.471684 ACGATCAGTTCCAGTCGTACC 59.528 52.381 0.00 0.00 44.49 3.34
47 48 1.531264 CGATCAGTTCCAGTCGTACCG 60.531 57.143 0.00 0.00 0.00 4.02
48 49 1.741706 GATCAGTTCCAGTCGTACCGA 59.258 52.381 0.00 0.00 0.00 4.69
49 50 1.830279 TCAGTTCCAGTCGTACCGAT 58.170 50.000 0.00 0.00 38.42 4.18
50 51 1.471287 TCAGTTCCAGTCGTACCGATG 59.529 52.381 0.00 0.00 38.42 3.84
51 52 1.471287 CAGTTCCAGTCGTACCGATGA 59.529 52.381 0.00 0.00 38.42 2.92
52 53 1.471684 AGTTCCAGTCGTACCGATGAC 59.528 52.381 0.00 0.00 41.28 3.06
53 54 1.200716 GTTCCAGTCGTACCGATGACA 59.799 52.381 2.17 0.00 43.11 3.58
54 55 1.536940 TCCAGTCGTACCGATGACAA 58.463 50.000 2.17 0.00 43.11 3.18
55 56 1.471287 TCCAGTCGTACCGATGACAAG 59.529 52.381 2.17 0.00 43.11 3.16
56 57 1.469251 CCAGTCGTACCGATGACAAGG 60.469 57.143 2.17 0.00 43.11 3.61
57 58 1.471287 CAGTCGTACCGATGACAAGGA 59.529 52.381 7.26 0.00 43.11 3.36
58 59 2.099263 CAGTCGTACCGATGACAAGGAT 59.901 50.000 7.26 0.00 43.11 3.24
59 60 2.099263 AGTCGTACCGATGACAAGGATG 59.901 50.000 7.26 0.00 43.11 3.51
60 61 2.098607 GTCGTACCGATGACAAGGATGA 59.901 50.000 7.26 0.36 40.75 2.92
61 62 2.098607 TCGTACCGATGACAAGGATGAC 59.901 50.000 7.26 2.46 0.00 3.06
62 63 2.159296 CGTACCGATGACAAGGATGACA 60.159 50.000 7.26 0.00 35.75 3.58
63 64 3.490933 CGTACCGATGACAAGGATGACAT 60.491 47.826 7.26 0.00 43.13 3.06
64 65 4.261447 CGTACCGATGACAAGGATGACATA 60.261 45.833 7.26 0.00 41.06 2.29
65 66 4.060038 ACCGATGACAAGGATGACATAC 57.940 45.455 7.26 0.00 41.06 2.39
66 67 3.450817 ACCGATGACAAGGATGACATACA 59.549 43.478 0.00 0.00 41.06 2.29
67 68 4.081142 ACCGATGACAAGGATGACATACAA 60.081 41.667 0.00 0.00 41.06 2.41
68 69 4.509230 CCGATGACAAGGATGACATACAAG 59.491 45.833 0.00 0.00 41.06 3.16
69 70 4.025396 CGATGACAAGGATGACATACAAGC 60.025 45.833 0.00 0.00 41.06 4.01
70 71 4.558226 TGACAAGGATGACATACAAGCT 57.442 40.909 0.00 0.00 0.00 3.74
71 72 4.256110 TGACAAGGATGACATACAAGCTG 58.744 43.478 0.00 0.00 0.00 4.24
72 73 3.012518 ACAAGGATGACATACAAGCTGC 58.987 45.455 0.00 0.00 0.00 5.25
73 74 2.338577 AGGATGACATACAAGCTGCC 57.661 50.000 0.00 0.00 0.00 4.85
74 75 1.842562 AGGATGACATACAAGCTGCCT 59.157 47.619 0.00 0.00 0.00 4.75
75 76 2.158842 AGGATGACATACAAGCTGCCTC 60.159 50.000 0.00 0.00 0.00 4.70
76 77 2.216898 GATGACATACAAGCTGCCTCC 58.783 52.381 0.00 0.00 0.00 4.30
77 78 0.983467 TGACATACAAGCTGCCTCCA 59.017 50.000 0.00 0.00 0.00 3.86
78 79 1.350684 TGACATACAAGCTGCCTCCAA 59.649 47.619 0.00 0.00 0.00 3.53
79 80 2.025981 TGACATACAAGCTGCCTCCAAT 60.026 45.455 0.00 0.00 0.00 3.16
84 85 1.377725 AAGCTGCCTCCAATGTCCG 60.378 57.895 0.00 0.00 0.00 4.79
149 150 2.106332 GGACCTCCGCCACGTATG 59.894 66.667 0.00 0.00 0.00 2.39
209 210 4.452733 CCGCTCCAACCGTCCCTC 62.453 72.222 0.00 0.00 0.00 4.30
234 235 0.322816 AGAGGCGCCACATTCATGTT 60.323 50.000 31.54 2.38 39.39 2.71
241 242 1.203052 GCCACATTCATGTTGGTCCAG 59.797 52.381 0.00 0.00 39.39 3.86
244 245 3.415212 CACATTCATGTTGGTCCAGAGT 58.585 45.455 0.00 0.00 39.39 3.24
245 246 4.565444 CCACATTCATGTTGGTCCAGAGTA 60.565 45.833 0.00 0.00 39.39 2.59
249 250 2.492088 TCATGTTGGTCCAGAGTAGACG 59.508 50.000 0.00 0.00 34.97 4.18
252 253 1.884579 GTTGGTCCAGAGTAGACGTGA 59.115 52.381 0.00 0.00 34.97 4.35
254 255 1.073444 TGGTCCAGAGTAGACGTGACT 59.927 52.381 0.00 0.00 34.97 3.41
260 261 2.160615 CAGAGTAGACGTGACTGGTCTG 59.839 54.545 4.48 4.42 44.14 3.51
262 263 0.596577 GTAGACGTGACTGGTCTGCA 59.403 55.000 0.00 0.00 44.14 4.41
263 264 0.881796 TAGACGTGACTGGTCTGCAG 59.118 55.000 7.63 7.63 44.14 4.41
264 265 1.109920 AGACGTGACTGGTCTGCAGT 61.110 55.000 14.67 0.00 42.87 4.40
275 276 1.683011 GGTCTGCAGTATGTTGGGCAT 60.683 52.381 14.67 0.00 39.31 4.40
282 283 0.381801 GTATGTTGGGCATTGAGGCG 59.618 55.000 0.00 0.00 45.36 5.52
305 306 3.357079 GCCAAGAGCACCACCACG 61.357 66.667 0.00 0.00 42.97 4.94
318 319 3.190849 CCACGCCACATCTGCTCG 61.191 66.667 0.00 0.00 0.00 5.03
320 321 4.377708 ACGCCACATCTGCTCGCA 62.378 61.111 0.00 0.00 0.00 5.10
321 322 2.893895 CGCCACATCTGCTCGCAT 60.894 61.111 0.00 0.00 0.00 4.73
331 332 0.814410 CTGCTCGCATGCTCTCCATT 60.814 55.000 17.13 0.00 29.71 3.16
332 333 0.812811 TGCTCGCATGCTCTCCATTC 60.813 55.000 17.13 0.00 29.71 2.67
333 334 1.829349 GCTCGCATGCTCTCCATTCG 61.829 60.000 17.13 0.00 41.08 3.34
334 335 1.829349 CTCGCATGCTCTCCATTCGC 61.829 60.000 17.13 0.00 39.83 4.70
335 336 2.630317 GCATGCTCTCCATTCGCG 59.370 61.111 11.37 0.00 29.71 5.87
339 341 0.108186 ATGCTCTCCATTCGCGTTCA 60.108 50.000 5.77 0.00 0.00 3.18
344 346 1.999735 TCTCCATTCGCGTTCAATGTC 59.000 47.619 15.31 0.00 30.40 3.06
349 351 1.623081 TTCGCGTTCAATGTCGGCTC 61.623 55.000 5.77 0.00 0.00 4.70
357 359 1.827344 TCAATGTCGGCTCAGAGTGAT 59.173 47.619 0.00 0.00 0.00 3.06
361 363 2.584418 CGGCTCAGAGTGATGCGG 60.584 66.667 0.00 0.00 0.00 5.69
362 364 2.894387 GGCTCAGAGTGATGCGGC 60.894 66.667 0.00 0.00 0.00 6.53
380 382 4.065281 CGGACTGGGTGACGGGAC 62.065 72.222 0.00 0.00 0.00 4.46
397 399 1.406539 GGACGGCTTCCTACGACATTA 59.593 52.381 2.18 0.00 41.95 1.90
401 403 2.159282 CGGCTTCCTACGACATTACAGT 60.159 50.000 0.00 0.00 0.00 3.55
413 415 1.535028 CATTACAGTCGGTTGCTTGCA 59.465 47.619 0.00 0.00 0.00 4.08
425 427 2.554032 GTTGCTTGCATGTTCACCTACT 59.446 45.455 1.14 0.00 0.00 2.57
427 429 1.394917 GCTTGCATGTTCACCTACTCG 59.605 52.381 1.14 0.00 0.00 4.18
450 452 4.596180 GAACATGCGCGATGGCCG 62.596 66.667 12.10 0.00 36.23 6.13
497 499 1.053424 AAACCGGCACTTCACCTAGA 58.947 50.000 0.00 0.00 0.00 2.43
502 504 0.253044 GGCACTTCACCTAGATGGCA 59.747 55.000 0.00 0.00 40.22 4.92
625 632 2.530177 ACGAGATGTGCAAGTGTATCG 58.470 47.619 0.00 0.00 35.21 2.92
645 652 4.656117 TCGGCGCAGAAGCACGAA 62.656 61.111 8.08 0.00 43.63 3.85
841 848 3.829044 CACATCGGGGCCGTCGTA 61.829 66.667 15.18 4.84 40.74 3.43
850 857 2.098831 GGCCGTCGTAGCAAAGGAC 61.099 63.158 0.00 2.75 39.19 3.85
913 921 5.010922 AGAGCTACAGGATGAGAAGCAATAG 59.989 44.000 0.00 0.00 40.48 1.73
922 930 5.530171 GGATGAGAAGCAATAGAATCTGCAA 59.470 40.000 0.00 0.00 41.17 4.08
974 982 3.766691 TCAAGGGCGAGCGGGTAC 61.767 66.667 0.00 0.00 0.00 3.34
978 986 4.157120 GGGCGAGCGGGTACACAT 62.157 66.667 0.00 0.00 0.00 3.21
980 988 2.125673 GCGAGCGGGTACACATGT 60.126 61.111 0.00 0.00 0.00 3.21
1013 1040 2.681848 CAACCTTCATGGATGAGCAGTC 59.318 50.000 0.00 0.00 40.62 3.51
1019 1063 3.867549 TGGATGAGCAGTCCATGTG 57.132 52.632 1.10 0.00 40.72 3.21
1069 1113 2.821366 GGCTGCACGTCATGGAGG 60.821 66.667 0.50 0.00 46.53 4.30
1070 1114 3.503363 GCTGCACGTCATGGAGGC 61.503 66.667 0.00 0.00 46.53 4.70
1071 1115 2.267006 CTGCACGTCATGGAGGCT 59.733 61.111 0.00 0.00 42.88 4.58
1072 1116 2.046988 TGCACGTCATGGAGGCTG 60.047 61.111 0.00 0.00 0.00 4.85
1073 1117 2.046892 GCACGTCATGGAGGCTGT 60.047 61.111 0.00 0.00 0.00 4.40
1074 1118 2.393768 GCACGTCATGGAGGCTGTG 61.394 63.158 0.00 0.00 32.25 3.66
1075 1119 1.293179 CACGTCATGGAGGCTGTGA 59.707 57.895 0.00 0.00 31.22 3.58
1076 1120 0.738762 CACGTCATGGAGGCTGTGAG 60.739 60.000 0.00 0.00 31.22 3.51
1077 1121 1.188219 ACGTCATGGAGGCTGTGAGT 61.188 55.000 0.00 0.00 0.00 3.41
1078 1122 0.738762 CGTCATGGAGGCTGTGAGTG 60.739 60.000 0.00 0.00 0.00 3.51
1079 1123 0.392193 GTCATGGAGGCTGTGAGTGG 60.392 60.000 0.00 0.00 0.00 4.00
1080 1124 0.837691 TCATGGAGGCTGTGAGTGGT 60.838 55.000 0.00 0.00 0.00 4.16
1081 1125 0.675837 CATGGAGGCTGTGAGTGGTG 60.676 60.000 0.00 0.00 0.00 4.17
1082 1126 1.845627 ATGGAGGCTGTGAGTGGTGG 61.846 60.000 0.00 0.00 0.00 4.61
1083 1127 2.359230 GAGGCTGTGAGTGGTGGC 60.359 66.667 0.00 0.00 0.00 5.01
1084 1128 4.320456 AGGCTGTGAGTGGTGGCG 62.320 66.667 0.00 0.00 0.00 5.69
1087 1131 4.320456 CTGTGAGTGGTGGCGGCT 62.320 66.667 11.43 0.00 0.00 5.52
1088 1132 4.624364 TGTGAGTGGTGGCGGCTG 62.624 66.667 11.43 0.00 0.00 4.85
1113 1157 3.023949 ATGGAGGCAGAGCGTGACC 62.024 63.158 0.00 0.00 32.48 4.02
1187 1240 1.792949 GTCGACAACTCTGCATCGTTT 59.207 47.619 11.55 0.00 36.03 3.60
1216 1269 0.743345 GCAACTACCACTAAGCCGGG 60.743 60.000 2.18 0.00 0.00 5.73
1229 1282 3.524606 CCGGGCCGTCACGTCTAT 61.525 66.667 26.32 0.00 0.00 1.98
1247 1300 1.970114 TCGTGGACCTCACCTCGAC 60.970 63.158 0.00 0.00 46.14 4.20
1287 1340 5.171476 CACGACACTGATGAAAAGTAGGAT 58.829 41.667 0.00 0.00 0.00 3.24
1324 1377 6.042638 CCATCCATGGTCAGGTAATAGTAG 57.957 45.833 12.58 0.00 43.05 2.57
1330 1383 3.949754 TGGTCAGGTAATAGTAGGACGTG 59.050 47.826 0.00 2.12 0.00 4.49
1337 1390 4.022503 GGTAATAGTAGGACGTGGGACATC 60.023 50.000 0.00 0.00 44.52 3.06
1338 1391 2.812836 TAGTAGGACGTGGGACATCA 57.187 50.000 0.00 0.00 44.52 3.07
1489 1654 1.003262 CGCAAATGTTTGGAGGCACG 61.003 55.000 7.51 0.00 38.57 5.34
1500 1665 2.740714 GAGGCACGACGTTGGATGC 61.741 63.158 7.90 8.74 37.35 3.91
1515 1680 2.375174 TGGATGCCCAACTACCATATCC 59.625 50.000 0.00 0.00 40.09 2.59
1516 1681 2.375174 GGATGCCCAACTACCATATCCA 59.625 50.000 0.00 0.00 34.27 3.41
1521 1686 3.810743 GCCCAACTACCATATCCATGTCC 60.811 52.174 0.00 0.00 0.00 4.02
1522 1687 3.557054 CCCAACTACCATATCCATGTCCG 60.557 52.174 0.00 0.00 0.00 4.79
1523 1688 3.071023 CCAACTACCATATCCATGTCCGT 59.929 47.826 0.00 0.00 0.00 4.69
1525 1690 3.572642 ACTACCATATCCATGTCCGTGA 58.427 45.455 0.00 0.00 0.00 4.35
1529 1694 2.872245 CCATATCCATGTCCGTGAACAC 59.128 50.000 0.00 0.00 30.55 3.32
1549 1714 2.482235 CGCAGACGTTTGAAATACACG 58.518 47.619 10.75 0.00 33.53 4.49
1550 1715 2.097104 CGCAGACGTTTGAAATACACGT 60.097 45.455 10.75 0.00 39.86 4.49
1551 1716 3.215244 GCAGACGTTTGAAATACACGTG 58.785 45.455 15.48 15.48 37.15 4.49
1552 1717 3.794536 CAGACGTTTGAAATACACGTGG 58.205 45.455 21.57 1.66 37.15 4.94
1553 1718 3.491639 CAGACGTTTGAAATACACGTGGA 59.508 43.478 21.57 13.01 37.15 4.02
1554 1719 4.025563 CAGACGTTTGAAATACACGTGGAA 60.026 41.667 21.57 8.00 37.15 3.53
1555 1720 4.210537 AGACGTTTGAAATACACGTGGAAG 59.789 41.667 21.57 0.00 37.15 3.46
1556 1721 3.872771 ACGTTTGAAATACACGTGGAAGT 59.127 39.130 21.57 2.93 35.63 3.01
1557 1722 4.208355 CGTTTGAAATACACGTGGAAGTG 58.792 43.478 21.57 0.00 46.83 3.16
1558 1723 4.533222 GTTTGAAATACACGTGGAAGTGG 58.467 43.478 21.57 0.00 45.80 4.00
1559 1724 2.147958 TGAAATACACGTGGAAGTGGC 58.852 47.619 21.57 1.57 45.80 5.01
1580 1745 0.108804 AACATCGGTCGAGACGCAAT 60.109 50.000 4.68 0.00 0.00 3.56
1582 1747 0.525455 CATCGGTCGAGACGCAATCA 60.525 55.000 4.68 0.00 0.00 2.57
1603 1768 8.367911 CAATCATTATACTCTAGTTGGGCACTA 58.632 37.037 0.00 0.00 36.88 2.74
1604 1769 7.286215 TCATTATACTCTAGTTGGGCACTAC 57.714 40.000 0.00 0.00 36.88 2.73
1605 1770 7.067421 TCATTATACTCTAGTTGGGCACTACT 58.933 38.462 8.43 8.43 36.88 2.57
1606 1771 7.563924 TCATTATACTCTAGTTGGGCACTACTT 59.436 37.037 8.72 0.00 36.88 2.24
1607 1772 5.855740 ATACTCTAGTTGGGCACTACTTC 57.144 43.478 8.72 0.00 36.88 3.01
1608 1773 2.832733 ACTCTAGTTGGGCACTACTTCC 59.167 50.000 8.72 0.00 36.88 3.46
1609 1774 3.100671 CTCTAGTTGGGCACTACTTCCT 58.899 50.000 8.72 0.00 36.88 3.36
1610 1775 3.097614 TCTAGTTGGGCACTACTTCCTC 58.902 50.000 8.72 0.00 36.88 3.71
1611 1776 0.984995 AGTTGGGCACTACTTCCTCC 59.015 55.000 0.00 0.00 31.97 4.30
1612 1777 0.690762 GTTGGGCACTACTTCCTCCA 59.309 55.000 0.00 0.00 0.00 3.86
1613 1778 1.282157 GTTGGGCACTACTTCCTCCAT 59.718 52.381 0.00 0.00 0.00 3.41
1614 1779 1.204146 TGGGCACTACTTCCTCCATC 58.796 55.000 0.00 0.00 0.00 3.51
1615 1780 0.470341 GGGCACTACTTCCTCCATCC 59.530 60.000 0.00 0.00 0.00 3.51
1616 1781 1.501582 GGCACTACTTCCTCCATCCT 58.498 55.000 0.00 0.00 0.00 3.24
1617 1782 2.679082 GGCACTACTTCCTCCATCCTA 58.321 52.381 0.00 0.00 0.00 2.94
1618 1783 3.243724 GGCACTACTTCCTCCATCCTAT 58.756 50.000 0.00 0.00 0.00 2.57
1619 1784 4.417437 GGCACTACTTCCTCCATCCTATA 58.583 47.826 0.00 0.00 0.00 1.31
1620 1785 4.838986 GGCACTACTTCCTCCATCCTATAA 59.161 45.833 0.00 0.00 0.00 0.98
1621 1786 5.485708 GGCACTACTTCCTCCATCCTATAAT 59.514 44.000 0.00 0.00 0.00 1.28
1622 1787 6.668283 GGCACTACTTCCTCCATCCTATAATA 59.332 42.308 0.00 0.00 0.00 0.98
1623 1788 7.345914 GGCACTACTTCCTCCATCCTATAATAT 59.654 40.741 0.00 0.00 0.00 1.28
1624 1789 9.422681 GCACTACTTCCTCCATCCTATAATATA 57.577 37.037 0.00 0.00 0.00 0.86
1648 1813 9.793252 ATAAGATGTTTTTGCAAGCTAACATAG 57.207 29.630 24.36 0.00 40.29 2.23
1662 1827 5.975138 CTAACATAGCTTGCAAAAACGTC 57.025 39.130 0.00 0.00 0.00 4.34
1663 1828 2.916111 ACATAGCTTGCAAAAACGTCG 58.084 42.857 0.00 0.00 0.00 5.12
1664 1829 1.643810 CATAGCTTGCAAAAACGTCGC 59.356 47.619 0.00 0.00 0.00 5.19
1665 1830 0.658368 TAGCTTGCAAAAACGTCGCA 59.342 45.000 0.00 0.00 0.00 5.10
1666 1831 0.179150 AGCTTGCAAAAACGTCGCAA 60.179 45.000 0.00 12.25 43.02 4.85
1667 1832 0.642800 GCTTGCAAAAACGTCGCAAA 59.357 45.000 13.37 2.07 44.43 3.68
1668 1833 1.059835 GCTTGCAAAAACGTCGCAAAA 59.940 42.857 13.37 0.00 44.43 2.44
1669 1834 2.473049 GCTTGCAAAAACGTCGCAAAAA 60.473 40.909 13.37 0.00 44.43 1.94
1670 1835 2.771210 TGCAAAAACGTCGCAAAAAC 57.229 40.000 0.00 0.00 31.46 2.43
1671 1836 1.057847 TGCAAAAACGTCGCAAAAACG 59.942 42.857 0.00 0.00 45.37 3.60
1681 1846 5.810653 CGTCGCAAAAACGTCTTATATTG 57.189 39.130 0.00 0.00 35.47 1.90
1682 1847 5.310489 CGTCGCAAAAACGTCTTATATTGT 58.690 37.500 0.00 0.00 35.47 2.71
1683 1848 5.222286 CGTCGCAAAAACGTCTTATATTGTG 59.778 40.000 0.00 0.00 35.47 3.33
1684 1849 5.506832 GTCGCAAAAACGTCTTATATTGTGG 59.493 40.000 0.00 0.00 0.00 4.17
1685 1850 4.791163 CGCAAAAACGTCTTATATTGTGGG 59.209 41.667 0.00 0.00 0.00 4.61
1686 1851 5.391097 CGCAAAAACGTCTTATATTGTGGGA 60.391 40.000 0.00 0.00 0.00 4.37
1687 1852 6.027749 GCAAAAACGTCTTATATTGTGGGAG 58.972 40.000 0.00 0.00 0.00 4.30
1688 1853 6.551736 CAAAAACGTCTTATATTGTGGGAGG 58.448 40.000 0.00 0.00 0.00 4.30
1689 1854 4.417426 AACGTCTTATATTGTGGGAGGG 57.583 45.455 0.00 0.00 0.00 4.30
1690 1855 3.649843 ACGTCTTATATTGTGGGAGGGA 58.350 45.455 0.00 0.00 0.00 4.20
1691 1856 3.641906 ACGTCTTATATTGTGGGAGGGAG 59.358 47.826 0.00 0.00 0.00 4.30
1692 1857 3.006967 CGTCTTATATTGTGGGAGGGAGG 59.993 52.174 0.00 0.00 0.00 4.30
1693 1858 3.328050 GTCTTATATTGTGGGAGGGAGGG 59.672 52.174 0.00 0.00 0.00 4.30
1694 1859 3.211232 TCTTATATTGTGGGAGGGAGGGA 59.789 47.826 0.00 0.00 0.00 4.20
1695 1860 2.124560 ATATTGTGGGAGGGAGGGAG 57.875 55.000 0.00 0.00 0.00 4.30
1738 1903 1.977056 ATCGCAGTATCACCTACGGA 58.023 50.000 0.00 0.00 35.35 4.69
1784 1949 1.145571 TGGGCAAAGTCCTTGTAGGT 58.854 50.000 0.00 0.00 37.36 3.08
1811 1976 3.491639 GTCGTTGCATGTGTAGTGTTGTA 59.508 43.478 0.00 0.00 0.00 2.41
1812 1977 4.025563 GTCGTTGCATGTGTAGTGTTGTAA 60.026 41.667 0.00 0.00 0.00 2.41
1839 2004 3.503363 GTGATGTGCTGGCCGCTC 61.503 66.667 18.14 15.29 40.11 5.03
1900 2065 4.227197 CATGGTGTATTCTACTCCCTCCT 58.773 47.826 3.65 0.00 40.65 3.69
1929 2108 9.575783 CGCACTTTTAAATATAAGCCCTTTTAA 57.424 29.630 0.00 0.00 0.00 1.52
2114 2293 5.408880 TGTGTTGATCCTAACGTTGGATA 57.591 39.130 23.48 12.39 43.68 2.59
2199 2386 7.327214 TGGGCATTTAAAATATGGAAACTCAC 58.673 34.615 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.365060 ATCATGGTTGAATCTTATGGAAACAA 57.635 30.769 0.00 0.00 38.79 2.83
1 2 7.959658 ATCATGGTTGAATCTTATGGAAACA 57.040 32.000 0.00 0.00 39.41 2.83
2 3 8.070171 CGTATCATGGTTGAATCTTATGGAAAC 58.930 37.037 0.00 0.00 34.96 2.78
3 4 7.990314 TCGTATCATGGTTGAATCTTATGGAAA 59.010 33.333 0.00 0.00 34.96 3.13
4 5 7.505258 TCGTATCATGGTTGAATCTTATGGAA 58.495 34.615 0.00 0.00 34.96 3.53
5 6 7.061566 TCGTATCATGGTTGAATCTTATGGA 57.938 36.000 0.00 0.00 34.96 3.41
6 7 7.603784 TGATCGTATCATGGTTGAATCTTATGG 59.396 37.037 0.00 0.00 34.96 2.74
7 8 8.538409 TGATCGTATCATGGTTGAATCTTATG 57.462 34.615 0.00 0.00 34.96 1.90
8 9 8.370940 ACTGATCGTATCATGGTTGAATCTTAT 58.629 33.333 0.00 0.00 38.85 1.73
9 10 7.726216 ACTGATCGTATCATGGTTGAATCTTA 58.274 34.615 0.00 0.00 38.85 2.10
10 11 6.586344 ACTGATCGTATCATGGTTGAATCTT 58.414 36.000 0.00 0.00 38.85 2.40
11 12 6.166984 ACTGATCGTATCATGGTTGAATCT 57.833 37.500 0.00 0.00 38.85 2.40
12 13 6.073548 GGAACTGATCGTATCATGGTTGAATC 60.074 42.308 0.00 0.00 38.85 2.52
13 14 5.760253 GGAACTGATCGTATCATGGTTGAAT 59.240 40.000 0.00 0.00 38.85 2.57
14 15 5.116180 GGAACTGATCGTATCATGGTTGAA 58.884 41.667 0.00 0.00 38.85 2.69
15 16 4.161377 TGGAACTGATCGTATCATGGTTGA 59.839 41.667 0.00 0.00 38.85 3.18
16 17 4.441792 TGGAACTGATCGTATCATGGTTG 58.558 43.478 0.00 0.00 38.85 3.77
17 18 4.162320 ACTGGAACTGATCGTATCATGGTT 59.838 41.667 0.00 0.00 38.85 3.67
18 19 3.706594 ACTGGAACTGATCGTATCATGGT 59.293 43.478 0.00 0.00 38.85 3.55
19 20 4.302455 GACTGGAACTGATCGTATCATGG 58.698 47.826 0.00 0.00 38.85 3.66
20 21 3.977579 CGACTGGAACTGATCGTATCATG 59.022 47.826 0.00 0.00 38.85 3.07
21 22 3.632604 ACGACTGGAACTGATCGTATCAT 59.367 43.478 0.00 0.00 40.03 2.45
22 23 3.014623 ACGACTGGAACTGATCGTATCA 58.985 45.455 0.00 0.00 40.03 2.15
23 24 3.694535 ACGACTGGAACTGATCGTATC 57.305 47.619 0.00 0.00 40.03 2.24
24 25 3.314635 GGTACGACTGGAACTGATCGTAT 59.685 47.826 8.40 0.00 42.44 3.06
25 26 2.679837 GGTACGACTGGAACTGATCGTA 59.320 50.000 1.49 1.49 41.16 3.43
26 27 1.471684 GGTACGACTGGAACTGATCGT 59.528 52.381 3.46 3.46 42.42 3.73
27 28 2.190325 GGTACGACTGGAACTGATCG 57.810 55.000 0.00 0.00 37.08 3.69
42 43 3.520290 TGTCATCCTTGTCATCGGTAC 57.480 47.619 0.00 0.00 0.00 3.34
43 44 4.647399 TGTATGTCATCCTTGTCATCGGTA 59.353 41.667 0.00 0.00 34.23 4.02
44 45 3.450817 TGTATGTCATCCTTGTCATCGGT 59.549 43.478 0.00 0.00 34.23 4.69
45 46 4.058721 TGTATGTCATCCTTGTCATCGG 57.941 45.455 0.00 0.00 34.23 4.18
46 47 4.025396 GCTTGTATGTCATCCTTGTCATCG 60.025 45.833 0.00 0.00 34.23 3.84
47 48 5.007430 CAGCTTGTATGTCATCCTTGTCATC 59.993 44.000 0.00 0.00 34.23 2.92
48 49 4.880120 CAGCTTGTATGTCATCCTTGTCAT 59.120 41.667 0.00 0.00 36.00 3.06
49 50 4.256110 CAGCTTGTATGTCATCCTTGTCA 58.744 43.478 0.00 0.00 0.00 3.58
50 51 3.064545 GCAGCTTGTATGTCATCCTTGTC 59.935 47.826 0.00 0.00 0.00 3.18
51 52 3.012518 GCAGCTTGTATGTCATCCTTGT 58.987 45.455 0.00 0.00 0.00 3.16
52 53 2.357009 GGCAGCTTGTATGTCATCCTTG 59.643 50.000 0.00 0.00 0.00 3.61
53 54 2.240667 AGGCAGCTTGTATGTCATCCTT 59.759 45.455 0.00 0.00 0.00 3.36
54 55 1.842562 AGGCAGCTTGTATGTCATCCT 59.157 47.619 0.00 0.00 0.00 3.24
55 56 2.216898 GAGGCAGCTTGTATGTCATCC 58.783 52.381 0.00 0.00 0.00 3.51
56 57 2.216898 GGAGGCAGCTTGTATGTCATC 58.783 52.381 0.00 0.00 0.00 2.92
57 58 1.561076 TGGAGGCAGCTTGTATGTCAT 59.439 47.619 0.00 0.00 0.00 3.06
58 59 0.983467 TGGAGGCAGCTTGTATGTCA 59.017 50.000 0.00 0.00 0.00 3.58
59 60 2.113860 TTGGAGGCAGCTTGTATGTC 57.886 50.000 0.00 0.00 0.00 3.06
60 61 2.291153 ACATTGGAGGCAGCTTGTATGT 60.291 45.455 0.00 0.00 0.00 2.29
61 62 2.357009 GACATTGGAGGCAGCTTGTATG 59.643 50.000 0.00 0.00 0.00 2.39
62 63 2.648059 GACATTGGAGGCAGCTTGTAT 58.352 47.619 0.00 0.00 0.00 2.29
63 64 1.340017 GGACATTGGAGGCAGCTTGTA 60.340 52.381 0.00 0.00 0.00 2.41
64 65 0.610232 GGACATTGGAGGCAGCTTGT 60.610 55.000 0.00 0.00 0.00 3.16
65 66 1.651240 CGGACATTGGAGGCAGCTTG 61.651 60.000 0.00 0.00 0.00 4.01
66 67 1.377725 CGGACATTGGAGGCAGCTT 60.378 57.895 0.00 0.00 0.00 3.74
67 68 1.841302 TTCGGACATTGGAGGCAGCT 61.841 55.000 0.00 0.00 0.00 4.24
68 69 0.749454 ATTCGGACATTGGAGGCAGC 60.749 55.000 0.00 0.00 0.00 5.25
69 70 1.672881 GAATTCGGACATTGGAGGCAG 59.327 52.381 0.00 0.00 0.00 4.85
70 71 1.681780 GGAATTCGGACATTGGAGGCA 60.682 52.381 0.00 0.00 0.00 4.75
71 72 1.025041 GGAATTCGGACATTGGAGGC 58.975 55.000 0.00 0.00 0.00 4.70
72 73 1.680338 GGGAATTCGGACATTGGAGG 58.320 55.000 0.00 0.00 0.00 4.30
73 74 1.299541 CGGGAATTCGGACATTGGAG 58.700 55.000 0.00 0.00 0.00 3.86
74 75 0.746563 GCGGGAATTCGGACATTGGA 60.747 55.000 0.00 0.00 0.00 3.53
75 76 1.029408 TGCGGGAATTCGGACATTGG 61.029 55.000 0.00 0.00 0.00 3.16
76 77 0.808125 TTGCGGGAATTCGGACATTG 59.192 50.000 0.00 0.00 0.00 2.82
77 78 1.201414 GTTTGCGGGAATTCGGACATT 59.799 47.619 0.00 0.00 0.00 2.71
78 79 0.808755 GTTTGCGGGAATTCGGACAT 59.191 50.000 0.00 0.00 0.00 3.06
79 80 0.250553 AGTTTGCGGGAATTCGGACA 60.251 50.000 0.00 0.00 0.00 4.02
84 85 0.388520 GTGCCAGTTTGCGGGAATTC 60.389 55.000 0.00 0.00 31.21 2.17
118 119 3.723348 GTCCGGACGCCAGCAAAC 61.723 66.667 20.85 0.00 0.00 2.93
151 152 1.595929 TGGGACCGCGTTTCTTGAC 60.596 57.895 4.92 0.00 0.00 3.18
157 158 3.717924 TTTGGGTGGGACCGCGTTT 62.718 57.895 4.92 0.00 39.83 3.60
178 179 1.394618 GAGCGGTCATACTGGAGAGT 58.605 55.000 10.30 0.00 36.07 3.24
188 189 2.264794 GACGGTTGGAGCGGTCAT 59.735 61.111 17.59 0.00 44.33 3.06
234 235 1.073444 AGTCACGTCTACTCTGGACCA 59.927 52.381 0.00 0.00 0.00 4.02
241 242 1.135632 GCAGACCAGTCACGTCTACTC 60.136 57.143 0.00 0.00 38.54 2.59
244 245 0.881796 CTGCAGACCAGTCACGTCTA 59.118 55.000 8.42 0.00 38.54 2.59
245 246 1.662608 CTGCAGACCAGTCACGTCT 59.337 57.895 8.42 0.00 41.29 4.18
254 255 0.322456 GCCCAACATACTGCAGACCA 60.322 55.000 23.35 5.22 0.00 4.02
260 261 1.406539 CCTCAATGCCCAACATACTGC 59.593 52.381 0.00 0.00 38.34 4.40
262 263 1.767759 GCCTCAATGCCCAACATACT 58.232 50.000 0.00 0.00 38.34 2.12
263 264 0.381801 CGCCTCAATGCCCAACATAC 59.618 55.000 0.00 0.00 38.34 2.39
264 265 1.383456 GCGCCTCAATGCCCAACATA 61.383 55.000 0.00 0.00 38.34 2.29
282 283 3.426568 GGTGCTCTTGGCTGTCGC 61.427 66.667 0.00 0.00 42.39 5.19
300 301 2.046892 GAGCAGATGTGGCGTGGT 60.047 61.111 0.00 0.00 36.08 4.16
305 306 2.713770 CATGCGAGCAGATGTGGC 59.286 61.111 3.58 0.00 0.00 5.01
318 319 1.709147 AACGCGAATGGAGAGCATGC 61.709 55.000 15.93 10.51 0.00 4.06
320 321 0.108186 TGAACGCGAATGGAGAGCAT 60.108 50.000 15.93 0.00 0.00 3.79
321 322 0.320334 TTGAACGCGAATGGAGAGCA 60.320 50.000 15.93 0.00 0.00 4.26
331 332 2.048597 AGCCGACATTGAACGCGA 60.049 55.556 15.93 0.00 0.00 5.87
332 333 2.283780 CTGAGCCGACATTGAACGCG 62.284 60.000 3.53 3.53 0.00 6.01
333 334 1.014044 TCTGAGCCGACATTGAACGC 61.014 55.000 0.00 0.00 0.00 4.84
334 335 0.994995 CTCTGAGCCGACATTGAACG 59.005 55.000 0.00 0.00 0.00 3.95
335 336 1.728971 CACTCTGAGCCGACATTGAAC 59.271 52.381 4.19 0.00 0.00 3.18
339 341 1.741732 GCATCACTCTGAGCCGACATT 60.742 52.381 4.19 0.00 0.00 2.71
344 346 2.584418 CCGCATCACTCTGAGCCG 60.584 66.667 4.19 0.00 0.00 5.52
349 351 4.147449 TCCGGCCGCATCACTCTG 62.147 66.667 22.85 2.11 0.00 3.35
380 382 2.159282 ACTGTAATGTCGTAGGAAGCCG 60.159 50.000 0.00 0.00 0.00 5.52
397 399 0.819259 ACATGCAAGCAACCGACTGT 60.819 50.000 0.00 0.00 0.00 3.55
401 403 0.310543 GTGAACATGCAAGCAACCGA 59.689 50.000 0.00 0.00 0.00 4.69
403 405 0.675633 AGGTGAACATGCAAGCAACC 59.324 50.000 0.00 1.56 0.00 3.77
413 415 2.236146 TCAATGCCGAGTAGGTGAACAT 59.764 45.455 0.00 0.00 43.70 2.71
425 427 2.484662 GCGCATGTTCAATGCCGA 59.515 55.556 0.30 0.00 41.71 5.54
427 429 1.064621 ATCGCGCATGTTCAATGCC 59.935 52.632 8.75 0.00 41.71 4.40
497 499 4.957954 CCATGCTTATATATTGGGTGCCAT 59.042 41.667 0.00 0.00 31.53 4.40
502 504 4.261801 GCGACCATGCTTATATATTGGGT 58.738 43.478 5.57 0.00 0.00 4.51
607 614 1.256376 CGCGATACACTTGCACATCTC 59.744 52.381 0.00 0.00 33.39 2.75
697 704 3.838120 CGAACTCAATGACAGTCTAGCA 58.162 45.455 1.31 0.00 0.00 3.49
767 774 1.931172 CGTGGACTCAAACTCGTTGTT 59.069 47.619 0.00 0.00 41.29 2.83
841 848 2.348998 CCGCTCCTGTCCTTTGCT 59.651 61.111 0.00 0.00 0.00 3.91
884 892 4.902443 TCTCATCCTGTAGCTCTAAACG 57.098 45.455 0.00 0.00 0.00 3.60
913 921 0.642800 GCTCGACGAGTTGCAGATTC 59.357 55.000 24.80 2.37 31.39 2.52
922 930 2.256764 CAGTGCTGCTCGACGAGT 59.743 61.111 24.80 2.08 31.39 4.18
972 980 6.895756 AGGTTGGATTCTCTACTACATGTGTA 59.104 38.462 9.11 8.14 0.00 2.90
974 982 6.227298 AGGTTGGATTCTCTACTACATGTG 57.773 41.667 9.11 0.93 0.00 3.21
978 986 6.127054 CCATGAAGGTTGGATTCTCTACTACA 60.127 42.308 0.00 0.00 36.26 2.74
980 988 6.202331 TCCATGAAGGTTGGATTCTCTACTA 58.798 40.000 0.00 0.00 38.35 1.82
1013 1040 3.566853 CGCAGGCGCTACACATGG 61.567 66.667 7.64 0.00 35.30 3.66
1064 1108 2.519622 CCACCACTCACAGCCTCCA 61.520 63.158 0.00 0.00 0.00 3.86
1065 1109 2.348998 CCACCACTCACAGCCTCC 59.651 66.667 0.00 0.00 0.00 4.30
1066 1110 2.359230 GCCACCACTCACAGCCTC 60.359 66.667 0.00 0.00 0.00 4.70
1067 1111 4.320456 CGCCACCACTCACAGCCT 62.320 66.667 0.00 0.00 0.00 4.58
1070 1114 4.320456 AGCCGCCACCACTCACAG 62.320 66.667 0.00 0.00 0.00 3.66
1071 1115 4.624364 CAGCCGCCACCACTCACA 62.624 66.667 0.00 0.00 0.00 3.58
1083 1127 3.190849 CTCCATGACGTGCAGCCG 61.191 66.667 0.00 0.00 0.00 5.52
1084 1128 2.821366 CCTCCATGACGTGCAGCC 60.821 66.667 0.00 0.00 0.00 4.85
1085 1129 3.503363 GCCTCCATGACGTGCAGC 61.503 66.667 0.00 0.00 0.00 5.25
1086 1130 2.046988 TGCCTCCATGACGTGCAG 60.047 61.111 0.00 0.00 0.00 4.41
1087 1131 2.046988 CTGCCTCCATGACGTGCA 60.047 61.111 0.00 0.00 0.00 4.57
1088 1132 1.812922 CTCTGCCTCCATGACGTGC 60.813 63.158 0.00 0.00 0.00 5.34
1089 1133 1.812922 GCTCTGCCTCCATGACGTG 60.813 63.158 0.00 0.00 0.00 4.49
1090 1134 2.581354 GCTCTGCCTCCATGACGT 59.419 61.111 0.00 0.00 0.00 4.34
1091 1135 2.584418 CGCTCTGCCTCCATGACG 60.584 66.667 0.00 0.00 0.00 4.35
1092 1136 1.812922 CACGCTCTGCCTCCATGAC 60.813 63.158 0.00 0.00 0.00 3.06
1187 1240 4.752879 GTAGTTGCGGCCTGGCGA 62.753 66.667 17.76 0.00 35.06 5.54
1229 1282 1.970114 GTCGAGGTGAGGTCCACGA 60.970 63.158 0.00 1.66 46.62 4.35
1265 1318 4.866508 TCCTACTTTTCATCAGTGTCGT 57.133 40.909 0.00 0.00 0.00 4.34
1267 1320 5.352569 CCACATCCTACTTTTCATCAGTGTC 59.647 44.000 0.00 0.00 0.00 3.67
1287 1340 1.418264 TGGATGGTTTCGTCTTCCACA 59.582 47.619 0.00 0.00 34.73 4.17
1313 1366 3.053395 TGTCCCACGTCCTACTATTACCT 60.053 47.826 0.00 0.00 0.00 3.08
1461 1565 5.107530 CCTCCAAACATTTGCGTGTATTTTG 60.108 40.000 0.00 0.00 36.86 2.44
1462 1566 4.987912 CCTCCAAACATTTGCGTGTATTTT 59.012 37.500 0.00 0.00 36.86 1.82
1500 1665 3.557054 CGGACATGGATATGGTAGTTGGG 60.557 52.174 0.00 0.00 38.66 4.12
1510 1675 2.821546 CGTGTTCACGGACATGGATAT 58.178 47.619 16.17 0.00 33.82 1.63
1515 1680 0.943835 TCTGCGTGTTCACGGACATG 60.944 55.000 23.27 11.56 39.10 3.21
1516 1681 0.944311 GTCTGCGTGTTCACGGACAT 60.944 55.000 23.27 0.00 0.00 3.06
1529 1694 2.097104 ACGTGTATTTCAAACGTCTGCG 60.097 45.455 0.00 0.00 46.86 5.18
1532 1697 3.719924 TCCACGTGTATTTCAAACGTCT 58.280 40.909 15.65 0.00 46.86 4.18
1535 1700 4.208355 CACTTCCACGTGTATTTCAAACG 58.792 43.478 15.65 0.00 42.82 3.60
1536 1701 4.533222 CCACTTCCACGTGTATTTCAAAC 58.467 43.478 15.65 0.00 33.07 2.93
1537 1702 3.003897 GCCACTTCCACGTGTATTTCAAA 59.996 43.478 15.65 0.00 33.07 2.69
1538 1703 2.550606 GCCACTTCCACGTGTATTTCAA 59.449 45.455 15.65 0.00 33.07 2.69
1539 1704 2.147958 GCCACTTCCACGTGTATTTCA 58.852 47.619 15.65 0.00 33.07 2.69
1540 1705 1.467342 GGCCACTTCCACGTGTATTTC 59.533 52.381 15.65 0.00 33.07 2.17
1541 1706 1.202830 TGGCCACTTCCACGTGTATTT 60.203 47.619 15.65 0.00 33.07 1.40
1542 1707 0.398696 TGGCCACTTCCACGTGTATT 59.601 50.000 15.65 0.00 33.07 1.89
1543 1708 0.398696 TTGGCCACTTCCACGTGTAT 59.601 50.000 15.65 0.00 35.50 2.29
1544 1709 0.533308 GTTGGCCACTTCCACGTGTA 60.533 55.000 15.65 0.00 35.50 2.90
1545 1710 1.822186 GTTGGCCACTTCCACGTGT 60.822 57.895 15.65 0.00 35.50 4.49
1546 1711 1.172180 ATGTTGGCCACTTCCACGTG 61.172 55.000 3.88 9.08 35.50 4.49
1547 1712 0.889186 GATGTTGGCCACTTCCACGT 60.889 55.000 3.88 0.66 35.50 4.49
1548 1713 1.875963 GATGTTGGCCACTTCCACG 59.124 57.895 3.88 0.00 35.50 4.94
1549 1714 1.586154 CCGATGTTGGCCACTTCCAC 61.586 60.000 3.88 0.00 35.50 4.02
1550 1715 1.303236 CCGATGTTGGCCACTTCCA 60.303 57.895 3.88 0.00 0.00 3.53
1551 1716 1.303317 ACCGATGTTGGCCACTTCC 60.303 57.895 3.88 0.00 0.00 3.46
1552 1717 1.635663 CGACCGATGTTGGCCACTTC 61.636 60.000 3.88 7.97 0.00 3.01
1553 1718 1.671054 CGACCGATGTTGGCCACTT 60.671 57.895 3.88 0.00 0.00 3.16
1554 1719 2.047274 CGACCGATGTTGGCCACT 60.047 61.111 3.88 0.00 0.00 4.00
1555 1720 2.047655 TCGACCGATGTTGGCCAC 60.048 61.111 3.88 0.75 0.00 5.01
1556 1721 2.264480 CTCGACCGATGTTGGCCA 59.736 61.111 0.00 0.00 0.00 5.36
1557 1722 1.810030 GTCTCGACCGATGTTGGCC 60.810 63.158 0.00 0.00 0.00 5.36
1558 1723 2.158959 CGTCTCGACCGATGTTGGC 61.159 63.158 0.00 0.00 0.00 4.52
1559 1724 2.158959 GCGTCTCGACCGATGTTGG 61.159 63.158 4.05 0.00 0.00 3.77
1580 1745 7.067421 AGTAGTGCCCAACTAGAGTATAATGA 58.933 38.462 0.00 0.00 42.15 2.57
1582 1747 7.015389 GGAAGTAGTGCCCAACTAGAGTATAAT 59.985 40.741 0.00 0.00 42.15 1.28
1622 1787 9.793252 CTATGTTAGCTTGCAAAAACATCTTAT 57.207 29.630 25.67 13.43 40.67 1.73
1640 1805 4.549599 CGACGTTTTTGCAAGCTATGTTAG 59.450 41.667 0.00 0.00 0.00 2.34
1641 1806 4.459606 CGACGTTTTTGCAAGCTATGTTA 58.540 39.130 0.00 0.00 0.00 2.41
1642 1807 3.296628 CGACGTTTTTGCAAGCTATGTT 58.703 40.909 0.00 0.00 0.00 2.71
1643 1808 2.916111 CGACGTTTTTGCAAGCTATGT 58.084 42.857 0.00 0.68 0.00 2.29
1644 1809 1.643810 GCGACGTTTTTGCAAGCTATG 59.356 47.619 0.00 0.00 34.24 2.23
1645 1810 1.265635 TGCGACGTTTTTGCAAGCTAT 59.734 42.857 0.00 0.00 42.12 2.97
1646 1811 0.658368 TGCGACGTTTTTGCAAGCTA 59.342 45.000 0.00 0.00 42.12 3.32
1647 1812 1.431440 TGCGACGTTTTTGCAAGCT 59.569 47.368 0.00 0.00 42.12 3.74
1648 1813 3.990141 TGCGACGTTTTTGCAAGC 58.010 50.000 0.00 0.00 42.12 4.01
1651 1816 1.057847 CGTTTTTGCGACGTTTTTGCA 59.942 42.857 0.00 0.00 43.50 4.08
1652 1817 1.697849 CGTTTTTGCGACGTTTTTGC 58.302 45.000 0.00 0.00 35.88 3.68
1659 1824 5.222286 CACAATATAAGACGTTTTTGCGACG 59.778 40.000 0.00 0.00 45.46 5.12
1660 1825 5.506832 CCACAATATAAGACGTTTTTGCGAC 59.493 40.000 0.00 0.00 35.59 5.19
1661 1826 5.391097 CCCACAATATAAGACGTTTTTGCGA 60.391 40.000 0.00 0.00 35.59 5.10
1662 1827 4.791163 CCCACAATATAAGACGTTTTTGCG 59.209 41.667 0.00 0.00 37.94 4.85
1663 1828 5.945155 TCCCACAATATAAGACGTTTTTGC 58.055 37.500 0.00 0.00 0.00 3.68
1664 1829 6.404293 CCCTCCCACAATATAAGACGTTTTTG 60.404 42.308 0.00 0.00 0.00 2.44
1665 1830 5.650703 CCCTCCCACAATATAAGACGTTTTT 59.349 40.000 0.00 0.00 0.00 1.94
1666 1831 5.045432 TCCCTCCCACAATATAAGACGTTTT 60.045 40.000 0.00 0.00 0.00 2.43
1667 1832 4.472108 TCCCTCCCACAATATAAGACGTTT 59.528 41.667 0.00 0.00 0.00 3.60
1668 1833 4.035112 TCCCTCCCACAATATAAGACGTT 58.965 43.478 0.00 0.00 0.00 3.99
1669 1834 3.641906 CTCCCTCCCACAATATAAGACGT 59.358 47.826 0.00 0.00 0.00 4.34
1670 1835 3.006967 CCTCCCTCCCACAATATAAGACG 59.993 52.174 0.00 0.00 0.00 4.18
1671 1836 3.328050 CCCTCCCTCCCACAATATAAGAC 59.672 52.174 0.00 0.00 0.00 3.01
1672 1837 3.211232 TCCCTCCCTCCCACAATATAAGA 59.789 47.826 0.00 0.00 0.00 2.10
1673 1838 3.584848 CTCCCTCCCTCCCACAATATAAG 59.415 52.174 0.00 0.00 0.00 1.73
1674 1839 3.050564 ACTCCCTCCCTCCCACAATATAA 60.051 47.826 0.00 0.00 0.00 0.98
1675 1840 2.527057 ACTCCCTCCCTCCCACAATATA 59.473 50.000 0.00 0.00 0.00 0.86
1676 1841 1.298382 ACTCCCTCCCTCCCACAATAT 59.702 52.381 0.00 0.00 0.00 1.28
1677 1842 0.722676 ACTCCCTCCCTCCCACAATA 59.277 55.000 0.00 0.00 0.00 1.90
1678 1843 0.722676 TACTCCCTCCCTCCCACAAT 59.277 55.000 0.00 0.00 0.00 2.71
1679 1844 0.042731 CTACTCCCTCCCTCCCACAA 59.957 60.000 0.00 0.00 0.00 3.33
1680 1845 1.153695 ACTACTCCCTCCCTCCCACA 61.154 60.000 0.00 0.00 0.00 4.17
1681 1846 0.042881 AACTACTCCCTCCCTCCCAC 59.957 60.000 0.00 0.00 0.00 4.61
1682 1847 0.338814 GAACTACTCCCTCCCTCCCA 59.661 60.000 0.00 0.00 0.00 4.37
1683 1848 0.398806 GGAACTACTCCCTCCCTCCC 60.399 65.000 0.00 0.00 38.44 4.30
1684 1849 3.227273 GGAACTACTCCCTCCCTCC 57.773 63.158 0.00 0.00 38.44 4.30
1692 1857 3.377798 CGAGACTAGTTGGGAACTACTCC 59.622 52.174 0.00 0.00 43.00 3.85
1693 1858 4.009002 ACGAGACTAGTTGGGAACTACTC 58.991 47.826 0.00 0.00 43.00 2.59
1695 1860 4.940654 ACTACGAGACTAGTTGGGAACTAC 59.059 45.833 0.00 0.00 42.81 2.73
1738 1903 3.926058 AAAATATCAGGTGCTACCGGT 57.074 42.857 13.98 13.98 44.90 5.28
1784 1949 2.939756 ACTACACATGCAACGACAACAA 59.060 40.909 0.00 0.00 0.00 2.83
1811 1976 1.956477 AGCACATCACTTTTCGGCTTT 59.044 42.857 0.00 0.00 0.00 3.51
1812 1977 1.267806 CAGCACATCACTTTTCGGCTT 59.732 47.619 0.00 0.00 0.00 4.35
1839 2004 1.407258 CCTGTAAGAGAGGAAGAGCCG 59.593 57.143 0.00 0.00 37.88 5.52
1900 2065 7.868906 AGGGCTTATATTTAAAAGTGCGTAA 57.131 32.000 0.00 0.00 0.00 3.18
2031 2210 7.935210 TCCTCCGTTTCTAAATGTAAGACTTTT 59.065 33.333 0.00 0.00 31.61 2.27
2032 2211 7.447594 TCCTCCGTTTCTAAATGTAAGACTTT 58.552 34.615 0.00 0.00 0.00 2.66
2033 2212 7.001099 TCCTCCGTTTCTAAATGTAAGACTT 57.999 36.000 0.00 0.00 0.00 3.01
2034 2213 6.600882 TCCTCCGTTTCTAAATGTAAGACT 57.399 37.500 0.00 0.00 0.00 3.24
2035 2214 6.872547 ACTTCCTCCGTTTCTAAATGTAAGAC 59.127 38.462 0.00 0.00 0.00 3.01
2036 2215 7.001099 ACTTCCTCCGTTTCTAAATGTAAGA 57.999 36.000 0.00 0.00 0.00 2.10
2041 2220 6.872020 TCTTGTACTTCCTCCGTTTCTAAATG 59.128 38.462 0.00 0.00 0.00 2.32
2123 2302 9.206690 AGAGTGATGTTTCTTCATTCTATAGGA 57.793 33.333 0.00 0.00 38.11 2.94
2199 2386 7.092137 TGAATGCTTCATCTGTGGATTAAAG 57.908 36.000 0.00 0.00 34.08 1.85


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

AutoCloner maintained by Alex Coulton.