Multiple sequence alignment - TraesCS3B01G281800

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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 TraesCS3B01G281800 chr3B 100.000 3656 0 0 1 3656 452492600 452488945 0.000000e+00 6752
1 TraesCS3B01G281800 chr3B 79.059 425 48 12 2565 2959 452489534 452489121 1.690000e-63 254
2 TraesCS3B01G281800 chr3B 79.059 425 48 12 3067 3480 452490036 452489642 1.690000e-63 254
3 TraesCS3B01G281800 chr4B 90.414 2608 140 40 434 3018 24901322 24903842 0.000000e+00 3330
4 TraesCS3B01G281800 chr4B 96.405 612 20 2 3045 3656 24903835 24904444 0.000000e+00 1007
5 TraesCS3B01G281800 chr4B 79.059 425 48 12 3067 3480 24903389 24903783 1.690000e-63 254
6 TraesCS3B01G281800 chr4B 85.593 118 14 3 1 117 24859855 24859970 1.780000e-23 121
7 TraesCS3B01G281800 chr4D 87.441 1903 148 32 1170 3010 14981572 14979699 0.000000e+00 2106
8 TraesCS3B01G281800 chr4D 93.095 420 21 3 3067 3480 14980168 14979751 3.120000e-170 608
9 TraesCS3B01G281800 chr4D 84.107 560 24 21 697 1228 14981970 14981448 7.100000e-132 481
10 TraesCS3B01G281800 chr4D 98.286 175 3 0 3482 3656 14979715 14979541 1.280000e-79 307
11 TraesCS3B01G281800 chr4A 83.666 2002 183 55 426 2366 586446320 586448238 0.000000e+00 1753
12 TraesCS3B01G281800 chr4A 89.599 923 73 14 2754 3656 586448590 586449509 0.000000e+00 1151
13 TraesCS3B01G281800 chr4A 88.615 325 28 8 114 433 586445621 586445941 1.590000e-103 387
14 TraesCS3B01G281800 chr4A 82.339 436 53 13 3067 3480 586448365 586448798 1.250000e-94 357
15 TraesCS3B01G281800 chr4A 86.893 206 24 1 2541 2743 586448341 586448546 1.020000e-55 228


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 TraesCS3B01G281800 chr3B 452488945 452492600 3655 True 2420.000000 6752 86.039333 1 3656 3 chr3B.!!$R1 3655
1 TraesCS3B01G281800 chr4B 24901322 24904444 3122 False 1530.333333 3330 88.626000 434 3656 3 chr4B.!!$F2 3222
2 TraesCS3B01G281800 chr4D 14979541 14981970 2429 True 875.500000 2106 90.732250 697 3656 4 chr4D.!!$R1 2959
3 TraesCS3B01G281800 chr4A 586445621 586449509 3888 False 775.200000 1753 86.222400 114 3656 5 chr4A.!!$F1 3542

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
30 31 0.039346 TGTTCATGTGCATGCAACCG 60.039 50.0 24.58 13.44 38.65 4.44 F
912 1360 0.114560 ACCGAGGAAGGAGAACCAGA 59.885 55.0 0.00 0.00 38.94 3.86 F
1797 2269 0.109532 TGACCGGCTCATTGGTTGAA 59.890 50.0 0.00 0.00 38.99 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 2089 0.271927 ATCCAGAGGCCTCCCCATTA 59.728 55.000 29.54 9.58 35.39 1.90 R
1911 2383 0.325933 CTCCCTGCAGTGGTGAATCA 59.674 55.000 13.81 0.00 0.00 2.57 R
2920 3443 1.604308 CCTCACCTGCAATGCCACA 60.604 57.895 1.53 0.00 0.00 4.17 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
25 26 2.921121 CACATCTTGTTCATGTGCATGC 59.079 45.455 11.82 11.82 43.48 4.06
26 27 2.559231 ACATCTTGTTCATGTGCATGCA 59.441 40.909 18.46 18.46 38.65 3.96
27 28 3.006003 ACATCTTGTTCATGTGCATGCAA 59.994 39.130 24.58 13.36 38.65 4.08
28 29 3.015934 TCTTGTTCATGTGCATGCAAC 57.984 42.857 24.58 17.13 38.65 4.17
29 30 2.063266 CTTGTTCATGTGCATGCAACC 58.937 47.619 24.58 12.00 38.65 3.77
30 31 0.039346 TGTTCATGTGCATGCAACCG 60.039 50.000 24.58 13.44 38.65 4.44
31 32 0.240678 GTTCATGTGCATGCAACCGA 59.759 50.000 24.58 15.67 38.65 4.69
32 33 0.240678 TTCATGTGCATGCAACCGAC 59.759 50.000 24.58 10.34 38.65 4.79
33 34 1.153978 CATGTGCATGCAACCGACC 60.154 57.895 24.58 9.53 31.39 4.79
34 35 1.603171 ATGTGCATGCAACCGACCA 60.603 52.632 24.58 15.53 0.00 4.02
35 36 0.966875 ATGTGCATGCAACCGACCAT 60.967 50.000 24.58 17.20 0.00 3.55
36 37 1.153978 GTGCATGCAACCGACCATG 60.154 57.895 24.58 0.00 41.27 3.66
40 41 3.276109 TGCAACCGACCATGCATG 58.724 55.556 20.19 20.19 46.87 4.06
62 63 6.174720 TGGTATAATGACCAACTCATCCTC 57.825 41.667 0.00 0.00 46.70 3.71
63 64 5.665360 TGGTATAATGACCAACTCATCCTCA 59.335 40.000 0.00 0.00 46.70 3.86
64 65 6.329986 TGGTATAATGACCAACTCATCCTCAT 59.670 38.462 0.00 0.00 46.70 2.90
65 66 6.876257 GGTATAATGACCAACTCATCCTCATC 59.124 42.308 0.00 0.00 38.82 2.92
66 67 2.967599 TGACCAACTCATCCTCATCG 57.032 50.000 0.00 0.00 0.00 3.84
67 68 1.134699 TGACCAACTCATCCTCATCGC 60.135 52.381 0.00 0.00 0.00 4.58
68 69 0.904649 ACCAACTCATCCTCATCGCA 59.095 50.000 0.00 0.00 0.00 5.10
69 70 1.278985 ACCAACTCATCCTCATCGCAA 59.721 47.619 0.00 0.00 0.00 4.85
70 71 2.290260 ACCAACTCATCCTCATCGCAAA 60.290 45.455 0.00 0.00 0.00 3.68
71 72 2.353889 CCAACTCATCCTCATCGCAAAG 59.646 50.000 0.00 0.00 0.00 2.77
72 73 3.005554 CAACTCATCCTCATCGCAAAGT 58.994 45.455 0.00 0.00 0.00 2.66
73 74 3.340814 ACTCATCCTCATCGCAAAGTT 57.659 42.857 0.00 0.00 0.00 2.66
74 75 3.005554 ACTCATCCTCATCGCAAAGTTG 58.994 45.455 0.00 0.00 0.00 3.16
75 76 2.353889 CTCATCCTCATCGCAAAGTTGG 59.646 50.000 0.00 0.00 0.00 3.77
76 77 1.098050 ATCCTCATCGCAAAGTTGGC 58.902 50.000 0.00 0.00 0.00 4.52
77 78 0.250684 TCCTCATCGCAAAGTTGGCA 60.251 50.000 2.51 0.00 0.00 4.92
78 79 0.813184 CCTCATCGCAAAGTTGGCAT 59.187 50.000 2.51 0.00 0.00 4.40
79 80 1.202222 CCTCATCGCAAAGTTGGCATC 60.202 52.381 2.51 0.00 0.00 3.91
80 81 0.810648 TCATCGCAAAGTTGGCATCC 59.189 50.000 2.51 0.00 0.00 3.51
81 82 0.527113 CATCGCAAAGTTGGCATCCA 59.473 50.000 2.51 0.00 0.00 3.41
82 83 0.527565 ATCGCAAAGTTGGCATCCAC 59.472 50.000 2.51 0.00 30.78 4.02
83 84 0.821301 TCGCAAAGTTGGCATCCACA 60.821 50.000 2.51 0.00 30.78 4.17
84 85 0.664166 CGCAAAGTTGGCATCCACAC 60.664 55.000 2.51 0.00 30.78 3.82
85 86 0.388659 GCAAAGTTGGCATCCACACA 59.611 50.000 0.00 0.00 30.78 3.72
86 87 1.001181 GCAAAGTTGGCATCCACACAT 59.999 47.619 0.00 0.00 30.78 3.21
87 88 2.927871 GCAAAGTTGGCATCCACACATC 60.928 50.000 0.00 0.00 30.78 3.06
88 89 2.559668 CAAAGTTGGCATCCACACATCT 59.440 45.455 0.00 0.00 30.78 2.90
89 90 2.592102 AGTTGGCATCCACACATCTT 57.408 45.000 0.00 0.00 30.78 2.40
90 91 2.880443 AGTTGGCATCCACACATCTTT 58.120 42.857 0.00 0.00 30.78 2.52
91 92 3.233507 AGTTGGCATCCACACATCTTTT 58.766 40.909 0.00 0.00 30.78 2.27
92 93 3.006110 AGTTGGCATCCACACATCTTTTG 59.994 43.478 0.00 0.00 30.78 2.44
93 94 2.596346 TGGCATCCACACATCTTTTGT 58.404 42.857 0.00 0.00 39.91 2.83
94 95 2.557924 TGGCATCCACACATCTTTTGTC 59.442 45.455 0.00 0.00 36.00 3.18
95 96 2.414559 GGCATCCACACATCTTTTGTCG 60.415 50.000 0.00 0.00 36.00 4.35
96 97 2.483877 GCATCCACACATCTTTTGTCGA 59.516 45.455 0.00 0.00 36.00 4.20
97 98 3.667960 GCATCCACACATCTTTTGTCGAC 60.668 47.826 9.11 9.11 36.00 4.20
98 99 3.469008 TCCACACATCTTTTGTCGACT 57.531 42.857 17.92 0.00 36.00 4.18
99 100 3.804036 TCCACACATCTTTTGTCGACTT 58.196 40.909 17.92 0.00 36.00 3.01
100 101 3.559655 TCCACACATCTTTTGTCGACTTG 59.440 43.478 17.92 7.27 36.00 3.16
101 102 3.303990 CCACACATCTTTTGTCGACTTGG 60.304 47.826 17.92 4.72 36.00 3.61
102 103 2.290641 ACACATCTTTTGTCGACTTGGC 59.709 45.455 17.92 0.00 36.00 4.52
103 104 2.549754 CACATCTTTTGTCGACTTGGCT 59.450 45.455 17.92 0.00 36.00 4.75
104 105 2.549754 ACATCTTTTGTCGACTTGGCTG 59.450 45.455 17.92 9.62 30.89 4.85
105 106 2.325583 TCTTTTGTCGACTTGGCTGT 57.674 45.000 17.92 0.00 0.00 4.40
106 107 3.462483 TCTTTTGTCGACTTGGCTGTA 57.538 42.857 17.92 0.00 0.00 2.74
107 108 3.390135 TCTTTTGTCGACTTGGCTGTAG 58.610 45.455 17.92 3.36 0.00 2.74
108 109 2.163818 TTTGTCGACTTGGCTGTAGG 57.836 50.000 17.92 0.00 0.00 3.18
109 110 1.334160 TTGTCGACTTGGCTGTAGGA 58.666 50.000 17.92 0.00 0.00 2.94
110 111 1.334160 TGTCGACTTGGCTGTAGGAA 58.666 50.000 17.92 0.00 0.00 3.36
111 112 1.272490 TGTCGACTTGGCTGTAGGAAG 59.728 52.381 17.92 0.00 0.00 3.46
112 113 0.895530 TCGACTTGGCTGTAGGAAGG 59.104 55.000 0.00 0.00 0.00 3.46
119 120 1.408453 GGCTGTAGGAAGGGCGGTAT 61.408 60.000 0.00 0.00 0.00 2.73
124 125 0.748450 TAGGAAGGGCGGTATCAACG 59.252 55.000 0.00 0.00 0.00 4.10
130 131 1.065709 AGGGCGGTATCAACGTTCAAT 60.066 47.619 0.00 0.00 0.00 2.57
148 149 1.931007 ATGAAGCAAGGGGAGAGGGC 61.931 60.000 0.00 0.00 0.00 5.19
149 150 3.689002 GAAGCAAGGGGAGAGGGCG 62.689 68.421 0.00 0.00 0.00 6.13
151 152 3.081409 GCAAGGGGAGAGGGCGTA 61.081 66.667 0.00 0.00 0.00 4.42
152 153 3.095347 GCAAGGGGAGAGGGCGTAG 62.095 68.421 0.00 0.00 0.00 3.51
153 154 1.686110 CAAGGGGAGAGGGCGTAGT 60.686 63.158 0.00 0.00 0.00 2.73
154 155 1.080538 AAGGGGAGAGGGCGTAGTT 59.919 57.895 0.00 0.00 0.00 2.24
155 156 1.265454 AAGGGGAGAGGGCGTAGTTG 61.265 60.000 0.00 0.00 0.00 3.16
156 157 2.187163 GGGAGAGGGCGTAGTTGC 59.813 66.667 0.00 0.00 0.00 4.17
157 158 2.202756 GGAGAGGGCGTAGTTGCG 60.203 66.667 0.00 0.00 35.06 4.85
158 159 2.572284 GAGAGGGCGTAGTTGCGT 59.428 61.111 0.00 0.00 35.06 5.24
175 177 1.066605 GCGTGCGGGAACTAGATAGAA 59.933 52.381 0.00 0.00 0.00 2.10
186 188 8.679100 CGGGAACTAGATAGAAGGATATAACAG 58.321 40.741 0.00 0.00 0.00 3.16
239 243 0.958091 CTCATGGCTAGACCGAGGAG 59.042 60.000 4.50 0.00 43.94 3.69
240 244 0.259065 TCATGGCTAGACCGAGGAGT 59.741 55.000 0.00 0.00 43.94 3.85
261 265 1.751927 GGCAGATCAAGGGCCACTG 60.752 63.158 6.18 2.18 46.92 3.66
264 268 1.001641 AGATCAAGGGCCACTGCAC 60.002 57.895 6.18 0.41 43.06 4.57
294 299 5.742446 GGAACGTGATATTGATTGCTTCTC 58.258 41.667 0.00 0.00 0.00 2.87
296 301 3.804325 ACGTGATATTGATTGCTTCTCGG 59.196 43.478 0.00 0.00 0.00 4.63
298 303 4.271049 CGTGATATTGATTGCTTCTCGGTT 59.729 41.667 0.00 0.00 0.00 4.44
317 322 0.179150 TGAAAACCATATTGCGGCGC 60.179 50.000 27.44 27.44 0.00 6.53
339 344 3.057386 CCAACTACAAACTGATGCATGCA 60.057 43.478 25.04 25.04 0.00 3.96
342 347 1.237533 ACAAACTGATGCATGCACGA 58.762 45.000 25.37 11.58 0.00 4.35
347 352 0.522626 CTGATGCATGCACGAACCAA 59.477 50.000 25.37 0.00 0.00 3.67
351 356 0.871722 TGCATGCACGAACCAACTAC 59.128 50.000 18.46 0.00 0.00 2.73
372 377 3.782443 GAGGGGATGCCCGTTCGT 61.782 66.667 17.80 0.00 46.66 3.85
413 418 6.474140 TTCCTATACGACTGCCATTTAGAA 57.526 37.500 0.00 0.00 0.00 2.10
414 419 6.474140 TCCTATACGACTGCCATTTAGAAA 57.526 37.500 0.00 0.00 0.00 2.52
451 842 2.102161 GCGCCTTTATTGCACGGG 59.898 61.111 0.00 0.00 0.00 5.28
505 896 4.080751 TGTGCCTGGTATCTTAGGGTTTAC 60.081 45.833 0.00 0.00 34.58 2.01
506 897 4.080751 GTGCCTGGTATCTTAGGGTTTACA 60.081 45.833 0.00 0.00 34.58 2.41
507 898 4.724798 TGCCTGGTATCTTAGGGTTTACAT 59.275 41.667 0.00 0.00 34.58 2.29
513 904 7.598248 TGGTATCTTAGGGTTTACATAGAGGA 58.402 38.462 0.00 0.00 0.00 3.71
533 924 4.785376 AGGAACTAGGATGAGGTGTGAAAT 59.215 41.667 0.00 0.00 36.02 2.17
556 947 0.674269 GAATAAACCGCCACCACCGA 60.674 55.000 0.00 0.00 0.00 4.69
564 955 0.179056 CGCCACCACCGATTTCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
582 973 2.606751 ATATACTCCCTCCGTCCCTG 57.393 55.000 0.00 0.00 0.00 4.45
615 1006 9.653516 AGTCTTTCTAGAGATTCTGATAATCCA 57.346 33.333 0.00 0.00 0.00 3.41
633 1024 3.450578 TCCATATCGTACGGAGCAAAAC 58.549 45.455 16.52 0.00 0.00 2.43
636 1027 2.068837 ATCGTACGGAGCAAAACGAA 57.931 45.000 16.52 0.00 46.18 3.85
644 1035 3.502211 ACGGAGCAAAACGAATGAATCTT 59.498 39.130 0.00 0.00 0.00 2.40
650 1041 4.853743 GCAAAACGAATGAATCTTCACTCC 59.146 41.667 0.00 0.00 40.49 3.85
655 1046 4.455877 ACGAATGAATCTTCACTCCAAACC 59.544 41.667 0.00 0.00 40.49 3.27
670 1061 6.641314 CACTCCAAACCACGTCTATATACATC 59.359 42.308 0.00 0.00 0.00 3.06
671 1062 6.550108 ACTCCAAACCACGTCTATATACATCT 59.450 38.462 0.00 0.00 0.00 2.90
672 1063 6.745116 TCCAAACCACGTCTATATACATCTG 58.255 40.000 0.00 0.00 0.00 2.90
731 1142 6.229936 TGAGTAGTAAATACCATGGTCCAC 57.770 41.667 23.76 14.60 34.67 4.02
732 1143 5.722441 TGAGTAGTAAATACCATGGTCCACA 59.278 40.000 23.76 3.54 34.67 4.17
782 1199 2.092753 TGTCCCATGCCTGAATCTTCTC 60.093 50.000 0.00 0.00 0.00 2.87
816 1233 1.971695 GTTTCTGAAGCCGGTGGGG 60.972 63.158 1.90 0.00 39.58 4.96
825 1242 4.410400 CCGGTGGGGCCAGAAGAC 62.410 72.222 4.39 0.00 36.97 3.01
861 1278 2.741122 TTCAACGCTACAAAACCACG 57.259 45.000 0.00 0.00 0.00 4.94
881 1318 1.332686 GCGGGTCACGGGAATATTTTC 59.667 52.381 0.00 0.00 44.51 2.29
897 1345 7.120726 GGAATATTTTCTTTCTTTCCTCACCGA 59.879 37.037 0.00 0.00 31.90 4.69
898 1346 5.948992 ATTTTCTTTCTTTCCTCACCGAG 57.051 39.130 0.00 0.00 0.00 4.63
912 1360 0.114560 ACCGAGGAAGGAGAACCAGA 59.885 55.000 0.00 0.00 38.94 3.86
917 1365 4.327680 CGAGGAAGGAGAACCAGAAAAAT 58.672 43.478 0.00 0.00 38.94 1.82
923 1371 9.822727 AGGAAGGAGAACCAGAAAAATAAAATA 57.177 29.630 0.00 0.00 38.94 1.40
1059 1513 3.493303 GACAGGCCCCTCATCCCC 61.493 72.222 0.00 0.00 0.00 4.81
1247 1701 1.706575 CCAAGGAGGAGGAGGAGGA 59.293 63.158 0.00 0.00 41.22 3.71
1248 1702 0.398381 CCAAGGAGGAGGAGGAGGAG 60.398 65.000 0.00 0.00 41.22 3.69
1249 1703 1.048160 CAAGGAGGAGGAGGAGGAGC 61.048 65.000 0.00 0.00 0.00 4.70
1250 1704 2.520741 GGAGGAGGAGGAGGAGCG 60.521 72.222 0.00 0.00 0.00 5.03
1251 1705 2.520741 GAGGAGGAGGAGGAGCGG 60.521 72.222 0.00 0.00 0.00 5.52
1252 1706 4.851214 AGGAGGAGGAGGAGCGGC 62.851 72.222 0.00 0.00 0.00 6.53
1271 1725 4.779733 GCGTCAGGGGGAGGAGGA 62.780 72.222 0.00 0.00 33.18 3.71
1272 1726 2.443016 CGTCAGGGGGAGGAGGAG 60.443 72.222 0.00 0.00 33.18 3.69
1273 1727 2.041405 GTCAGGGGGAGGAGGAGG 60.041 72.222 0.00 0.00 0.00 4.30
1441 1910 2.046314 AGGGTTCGGCCGTGAATG 60.046 61.111 27.15 0.00 38.44 2.67
1550 2022 3.090532 GATGGGGAAGGCCTCCGT 61.091 66.667 5.23 4.08 46.51 4.69
1558 2030 2.893682 GAAGGCCTCCGTGGGATTGG 62.894 65.000 5.23 0.00 36.00 3.16
1566 2038 2.282887 GTGGGATTGGTTGCCGGT 60.283 61.111 1.90 0.00 39.08 5.28
1567 2039 2.034999 TGGGATTGGTTGCCGGTC 59.965 61.111 1.90 0.00 39.08 4.79
1568 2040 2.754254 GGGATTGGTTGCCGGTCC 60.754 66.667 1.90 4.30 0.00 4.46
1569 2041 2.034999 GGATTGGTTGCCGGTCCA 59.965 61.111 1.90 7.21 32.30 4.02
1570 2042 2.046285 GGATTGGTTGCCGGTCCAG 61.046 63.158 1.90 0.00 35.05 3.86
1571 2043 2.035626 ATTGGTTGCCGGTCCAGG 59.964 61.111 1.90 0.00 35.05 4.45
1617 2089 1.846712 GCAAGCTGGAGGAGAAGGGT 61.847 60.000 0.00 0.00 0.00 4.34
1718 2190 1.226974 CATACCGAGGCACCGTCAG 60.227 63.158 0.00 0.00 0.00 3.51
1797 2269 0.109532 TGACCGGCTCATTGGTTGAA 59.890 50.000 0.00 0.00 38.99 2.69
1875 2347 1.751351 TCGAGTAATCAGAGCACTGGG 59.249 52.381 11.42 0.00 43.60 4.45
1911 2383 4.172512 CAGGGCGAGGCAGCTGAT 62.173 66.667 20.43 4.39 37.29 2.90
2208 2689 4.656100 TGGTCAAGGAATGATCAGGAAA 57.344 40.909 0.09 0.00 44.28 3.13
2242 2723 3.268103 TTTGGGGAGAAGGAGCCGC 62.268 63.158 0.00 0.00 37.60 6.53
2531 3015 1.813092 GCCATGTGATGCGAGGATCTT 60.813 52.381 6.19 0.00 0.00 2.40
2574 3058 1.960040 ATCACAGCCGAGCGAATGGA 61.960 55.000 0.00 0.00 0.00 3.41
2706 3193 1.331756 CATGCGCCAGTGGTAGATTTC 59.668 52.381 11.74 0.00 0.00 2.17
2778 3298 1.464219 GATTGCCAAATTGGTTTGCCG 59.536 47.619 14.17 0.00 42.66 5.69
2901 3424 4.553323 CAAGATCCTTGCTTTCCAAACAG 58.447 43.478 0.00 0.00 31.94 3.16
2944 3467 1.843368 CATTGCAGGTGAGGATGGTT 58.157 50.000 0.00 0.00 0.00 3.67
3010 3533 4.851558 GTGAAAATTTACCGACTGATGCAC 59.148 41.667 0.00 0.00 0.00 4.57
3012 3535 5.009110 TGAAAATTTACCGACTGATGCACAA 59.991 36.000 0.00 0.00 0.00 3.33
3020 3543 3.485633 CGACTGATGCACAATTCAACTG 58.514 45.455 0.00 0.00 0.00 3.16
3026 3549 5.283294 TGATGCACAATTCAACTGTGAAAG 58.717 37.500 2.41 0.00 46.66 2.62
3027 3550 4.979943 TGCACAATTCAACTGTGAAAGA 57.020 36.364 2.41 0.00 46.66 2.52
3028 3551 5.321959 TGCACAATTCAACTGTGAAAGAA 57.678 34.783 2.41 0.00 46.66 2.52
3029 3552 5.101628 TGCACAATTCAACTGTGAAAGAAC 58.898 37.500 2.41 0.00 46.66 3.01
3035 3558 2.612212 TCAACTGTGAAAGAACGAAGCC 59.388 45.455 0.00 0.00 0.00 4.35
3118 3647 4.269523 TGGGTGCCCACTGCTGTC 62.270 66.667 5.73 0.00 41.89 3.51
3121 3650 4.269523 GTGCCCACTGCTGTCCCA 62.270 66.667 0.00 0.00 42.00 4.37
3127 3656 4.008933 ACTGCTGTCCCAGTCCGC 62.009 66.667 0.00 0.00 42.10 5.54
3128 3657 4.007644 CTGCTGTCCCAGTCCGCA 62.008 66.667 0.00 0.00 33.43 5.69
3274 3814 2.445525 AGGTGTCCATGTAGGGTTTGTT 59.554 45.455 0.00 0.00 38.24 2.83
3336 3876 7.254932 GCTATTGCCAGATTGGTTTTAGAGTAG 60.255 40.741 0.00 0.00 40.46 2.57
3339 3879 6.403878 TGCCAGATTGGTTTTAGAGTAGTAC 58.596 40.000 0.00 0.00 40.46 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.937591 CACATGAACAAGATGTGTGGC 58.062 47.619 0.00 0.00 43.81 5.01
5 6 2.559231 TGCATGCACATGAACAAGATGT 59.441 40.909 18.46 0.00 41.20 3.06
6 7 3.224884 TGCATGCACATGAACAAGATG 57.775 42.857 18.46 0.00 41.20 2.90
7 8 3.581755 GTTGCATGCACATGAACAAGAT 58.418 40.909 22.58 0.00 41.20 2.40
8 9 2.288334 GGTTGCATGCACATGAACAAGA 60.288 45.455 22.58 0.00 41.20 3.02
9 10 2.063266 GGTTGCATGCACATGAACAAG 58.937 47.619 22.58 0.00 41.20 3.16
10 11 1.602416 CGGTTGCATGCACATGAACAA 60.602 47.619 22.58 0.00 41.20 2.83
11 12 0.039346 CGGTTGCATGCACATGAACA 60.039 50.000 22.58 0.00 41.20 3.18
12 13 0.240678 TCGGTTGCATGCACATGAAC 59.759 50.000 22.58 15.52 41.20 3.18
13 14 0.240678 GTCGGTTGCATGCACATGAA 59.759 50.000 22.58 1.43 41.20 2.57
14 15 1.585267 GGTCGGTTGCATGCACATGA 61.585 55.000 22.58 15.11 41.20 3.07
15 16 1.153978 GGTCGGTTGCATGCACATG 60.154 57.895 22.58 12.84 41.60 3.21
16 17 0.966875 ATGGTCGGTTGCATGCACAT 60.967 50.000 22.58 16.31 0.00 3.21
17 18 1.603171 ATGGTCGGTTGCATGCACA 60.603 52.632 22.58 14.57 0.00 4.57
18 19 1.153978 CATGGTCGGTTGCATGCAC 60.154 57.895 22.58 15.35 0.00 4.57
19 20 2.992273 GCATGGTCGGTTGCATGCA 61.992 57.895 18.46 18.46 46.71 3.96
20 21 2.202650 GCATGGTCGGTTGCATGC 60.203 61.111 11.82 11.82 42.60 4.06
21 22 3.276109 TGCATGGTCGGTTGCATG 58.724 55.556 0.00 0.00 43.54 4.06
24 25 2.491152 CCATGCATGGTCGGTTGC 59.509 61.111 33.68 0.00 43.05 4.17
39 40 5.665360 TGAGGATGAGTTGGTCATTATACCA 59.335 40.000 0.00 0.00 46.64 3.25
40 41 6.174720 TGAGGATGAGTTGGTCATTATACC 57.825 41.667 0.00 0.00 46.64 2.73
41 42 6.587990 CGATGAGGATGAGTTGGTCATTATAC 59.412 42.308 0.00 0.00 46.64 1.47
42 43 6.691508 CGATGAGGATGAGTTGGTCATTATA 58.308 40.000 0.00 0.00 46.64 0.98
43 44 5.545588 CGATGAGGATGAGTTGGTCATTAT 58.454 41.667 0.00 0.00 46.64 1.28
44 45 4.740634 GCGATGAGGATGAGTTGGTCATTA 60.741 45.833 0.00 0.00 46.64 1.90
45 46 3.801698 CGATGAGGATGAGTTGGTCATT 58.198 45.455 0.00 0.00 46.64 2.57
47 48 1.134699 GCGATGAGGATGAGTTGGTCA 60.135 52.381 0.00 0.00 40.38 4.02
48 49 1.134699 TGCGATGAGGATGAGTTGGTC 60.135 52.381 0.00 0.00 0.00 4.02
49 50 0.904649 TGCGATGAGGATGAGTTGGT 59.095 50.000 0.00 0.00 0.00 3.67
50 51 2.028420 TTGCGATGAGGATGAGTTGG 57.972 50.000 0.00 0.00 0.00 3.77
51 52 3.005554 ACTTTGCGATGAGGATGAGTTG 58.994 45.455 0.00 0.00 0.00 3.16
52 53 3.340814 ACTTTGCGATGAGGATGAGTT 57.659 42.857 0.00 0.00 0.00 3.01
53 54 3.005554 CAACTTTGCGATGAGGATGAGT 58.994 45.455 0.00 0.00 0.00 3.41
54 55 2.353889 CCAACTTTGCGATGAGGATGAG 59.646 50.000 0.00 0.00 0.00 2.90
55 56 2.358957 CCAACTTTGCGATGAGGATGA 58.641 47.619 0.00 0.00 0.00 2.92
56 57 1.202222 GCCAACTTTGCGATGAGGATG 60.202 52.381 0.00 0.00 0.00 3.51
57 58 1.098050 GCCAACTTTGCGATGAGGAT 58.902 50.000 0.00 0.00 0.00 3.24
58 59 0.250684 TGCCAACTTTGCGATGAGGA 60.251 50.000 0.00 0.00 0.00 3.71
59 60 0.813184 ATGCCAACTTTGCGATGAGG 59.187 50.000 0.00 0.00 0.00 3.86
60 61 1.202222 GGATGCCAACTTTGCGATGAG 60.202 52.381 0.00 0.00 0.00 2.90
61 62 0.810648 GGATGCCAACTTTGCGATGA 59.189 50.000 0.00 0.00 0.00 2.92
62 63 0.527113 TGGATGCCAACTTTGCGATG 59.473 50.000 0.00 0.00 0.00 3.84
63 64 0.527565 GTGGATGCCAACTTTGCGAT 59.472 50.000 0.00 0.00 34.18 4.58
64 65 0.821301 TGTGGATGCCAACTTTGCGA 60.821 50.000 0.00 0.00 34.18 5.10
65 66 0.664166 GTGTGGATGCCAACTTTGCG 60.664 55.000 0.00 0.00 34.18 4.85
66 67 0.388659 TGTGTGGATGCCAACTTTGC 59.611 50.000 0.00 0.00 34.18 3.68
67 68 2.559668 AGATGTGTGGATGCCAACTTTG 59.440 45.455 0.00 0.00 34.18 2.77
68 69 2.880443 AGATGTGTGGATGCCAACTTT 58.120 42.857 0.00 0.00 34.18 2.66
69 70 2.592102 AGATGTGTGGATGCCAACTT 57.408 45.000 0.00 0.00 34.18 2.66
70 71 2.592102 AAGATGTGTGGATGCCAACT 57.408 45.000 0.00 0.00 34.18 3.16
71 72 3.243839 ACAAAAGATGTGTGGATGCCAAC 60.244 43.478 0.00 0.00 41.93 3.77
72 73 2.964464 ACAAAAGATGTGTGGATGCCAA 59.036 40.909 0.00 0.00 41.93 4.52
73 74 2.557924 GACAAAAGATGTGTGGATGCCA 59.442 45.455 0.00 0.00 44.12 4.92
74 75 2.414559 CGACAAAAGATGTGTGGATGCC 60.415 50.000 0.00 0.00 44.12 4.40
75 76 2.483877 TCGACAAAAGATGTGTGGATGC 59.516 45.455 0.00 0.00 44.12 3.91
76 77 3.748048 AGTCGACAAAAGATGTGTGGATG 59.252 43.478 19.50 0.00 44.12 3.51
77 78 4.008074 AGTCGACAAAAGATGTGTGGAT 57.992 40.909 19.50 0.00 44.12 3.41
78 79 3.469008 AGTCGACAAAAGATGTGTGGA 57.531 42.857 19.50 0.00 44.12 4.02
79 80 3.303990 CCAAGTCGACAAAAGATGTGTGG 60.304 47.826 19.50 5.12 44.12 4.17
80 81 3.849645 GCCAAGTCGACAAAAGATGTGTG 60.850 47.826 19.50 0.00 44.12 3.82
81 82 2.290641 GCCAAGTCGACAAAAGATGTGT 59.709 45.455 19.50 0.00 44.12 3.72
82 83 2.549754 AGCCAAGTCGACAAAAGATGTG 59.450 45.455 19.50 2.40 44.12 3.21
84 85 2.549754 ACAGCCAAGTCGACAAAAGATG 59.450 45.455 19.50 14.03 0.00 2.90
85 86 2.851195 ACAGCCAAGTCGACAAAAGAT 58.149 42.857 19.50 0.00 0.00 2.40
86 87 2.325583 ACAGCCAAGTCGACAAAAGA 57.674 45.000 19.50 0.00 0.00 2.52
87 88 2.480419 CCTACAGCCAAGTCGACAAAAG 59.520 50.000 19.50 4.42 0.00 2.27
88 89 2.103432 TCCTACAGCCAAGTCGACAAAA 59.897 45.455 19.50 0.00 0.00 2.44
89 90 1.689813 TCCTACAGCCAAGTCGACAAA 59.310 47.619 19.50 0.00 0.00 2.83
90 91 1.334160 TCCTACAGCCAAGTCGACAA 58.666 50.000 19.50 0.00 0.00 3.18
91 92 1.272490 CTTCCTACAGCCAAGTCGACA 59.728 52.381 19.50 0.00 0.00 4.35
92 93 1.404315 CCTTCCTACAGCCAAGTCGAC 60.404 57.143 7.70 7.70 0.00 4.20
93 94 0.895530 CCTTCCTACAGCCAAGTCGA 59.104 55.000 0.00 0.00 0.00 4.20
94 95 0.108138 CCCTTCCTACAGCCAAGTCG 60.108 60.000 0.00 0.00 0.00 4.18
95 96 0.393132 GCCCTTCCTACAGCCAAGTC 60.393 60.000 0.00 0.00 0.00 3.01
96 97 1.685820 GCCCTTCCTACAGCCAAGT 59.314 57.895 0.00 0.00 0.00 3.16
97 98 1.450312 CGCCCTTCCTACAGCCAAG 60.450 63.158 0.00 0.00 0.00 3.61
98 99 2.668632 CGCCCTTCCTACAGCCAA 59.331 61.111 0.00 0.00 0.00 4.52
99 100 2.808761 TACCGCCCTTCCTACAGCCA 62.809 60.000 0.00 0.00 0.00 4.75
100 101 1.408453 ATACCGCCCTTCCTACAGCC 61.408 60.000 0.00 0.00 0.00 4.85
101 102 0.033642 GATACCGCCCTTCCTACAGC 59.966 60.000 0.00 0.00 0.00 4.40
102 103 1.410004 TGATACCGCCCTTCCTACAG 58.590 55.000 0.00 0.00 0.00 2.74
103 104 1.483415 GTTGATACCGCCCTTCCTACA 59.517 52.381 0.00 0.00 0.00 2.74
104 105 1.537562 CGTTGATACCGCCCTTCCTAC 60.538 57.143 0.00 0.00 0.00 3.18
105 106 0.748450 CGTTGATACCGCCCTTCCTA 59.252 55.000 0.00 0.00 0.00 2.94
106 107 1.262640 ACGTTGATACCGCCCTTCCT 61.263 55.000 0.00 0.00 0.00 3.36
107 108 0.392060 AACGTTGATACCGCCCTTCC 60.392 55.000 0.00 0.00 0.00 3.46
108 109 1.004595 GAACGTTGATACCGCCCTTC 58.995 55.000 5.00 0.00 0.00 3.46
109 110 0.322322 TGAACGTTGATACCGCCCTT 59.678 50.000 5.00 0.00 0.00 3.95
110 111 0.322322 TTGAACGTTGATACCGCCCT 59.678 50.000 5.00 0.00 0.00 5.19
111 112 1.063469 CATTGAACGTTGATACCGCCC 59.937 52.381 5.00 0.00 0.00 6.13
112 113 2.004017 TCATTGAACGTTGATACCGCC 58.996 47.619 5.00 0.00 0.00 6.13
119 120 2.293122 CCCTTGCTTCATTGAACGTTGA 59.707 45.455 5.00 0.00 0.00 3.18
124 125 2.751806 CTCTCCCCTTGCTTCATTGAAC 59.248 50.000 0.00 0.00 0.00 3.18
130 131 2.606587 GCCCTCTCCCCTTGCTTCA 61.607 63.158 0.00 0.00 0.00 3.02
148 149 2.735478 TTCCCGCACGCAACTACG 60.735 61.111 0.00 0.00 39.50 3.51
149 150 0.388907 TAGTTCCCGCACGCAACTAC 60.389 55.000 8.10 0.00 32.56 2.73
150 151 0.108992 CTAGTTCCCGCACGCAACTA 60.109 55.000 10.54 10.54 32.56 2.24
151 152 1.374252 CTAGTTCCCGCACGCAACT 60.374 57.895 9.61 9.61 34.68 3.16
152 153 0.739813 ATCTAGTTCCCGCACGCAAC 60.740 55.000 0.00 0.00 0.00 4.17
153 154 0.818938 TATCTAGTTCCCGCACGCAA 59.181 50.000 0.00 0.00 0.00 4.85
154 155 0.384309 CTATCTAGTTCCCGCACGCA 59.616 55.000 0.00 0.00 0.00 5.24
155 156 0.666913 TCTATCTAGTTCCCGCACGC 59.333 55.000 0.00 0.00 0.00 5.34
156 157 2.287668 CCTTCTATCTAGTTCCCGCACG 60.288 54.545 0.00 0.00 0.00 5.34
157 158 2.957006 TCCTTCTATCTAGTTCCCGCAC 59.043 50.000 0.00 0.00 0.00 5.34
158 159 3.308035 TCCTTCTATCTAGTTCCCGCA 57.692 47.619 0.00 0.00 0.00 5.69
175 177 2.959465 GCCCTTGGCTGTTATATCCT 57.041 50.000 0.00 0.00 46.69 3.24
220 224 0.958091 CTCCTCGGTCTAGCCATGAG 59.042 60.000 0.00 3.63 36.97 2.90
223 227 0.033011 ACACTCCTCGGTCTAGCCAT 60.033 55.000 4.43 0.00 36.97 4.40
239 243 2.048603 GGCCCTTGATCTGCCACAC 61.049 63.158 10.09 0.00 44.70 3.82
240 244 2.356278 GGCCCTTGATCTGCCACA 59.644 61.111 10.09 0.00 44.70 4.17
261 265 4.183146 CACGTTCCGTTTTCGTGC 57.817 55.556 4.16 0.00 45.66 5.34
264 268 4.571375 TCAATATCACGTTCCGTTTTCG 57.429 40.909 0.00 0.00 38.32 3.46
266 270 5.092781 GCAATCAATATCACGTTCCGTTTT 58.907 37.500 0.00 0.00 38.32 2.43
277 281 5.427378 TCAACCGAGAAGCAATCAATATCA 58.573 37.500 0.00 0.00 0.00 2.15
296 301 1.917303 CGCCGCAATATGGTTTTCAAC 59.083 47.619 0.00 0.00 0.00 3.18
298 303 0.179150 GCGCCGCAATATGGTTTTCA 60.179 50.000 3.15 0.00 0.00 2.69
314 319 1.729149 GCATCAGTTTGTAGTTGGCGC 60.729 52.381 0.00 0.00 0.00 6.53
315 320 1.535028 TGCATCAGTTTGTAGTTGGCG 59.465 47.619 0.00 0.00 0.00 5.69
317 322 3.057386 TGCATGCATCAGTTTGTAGTTGG 60.057 43.478 18.46 0.00 0.00 3.77
339 344 0.886563 CCTCTCCGTAGTTGGTTCGT 59.113 55.000 0.00 0.00 0.00 3.85
342 347 0.115745 TCCCCTCTCCGTAGTTGGTT 59.884 55.000 0.00 0.00 0.00 3.67
347 352 1.457831 GGCATCCCCTCTCCGTAGT 60.458 63.158 0.00 0.00 0.00 2.73
372 377 4.223953 AGGAAAACCGCTCCTAGATCATA 58.776 43.478 0.00 0.00 41.73 2.15
413 418 3.663025 CCGGTTTGATTGATGCCTTTTT 58.337 40.909 0.00 0.00 0.00 1.94
414 419 2.612721 GCCGGTTTGATTGATGCCTTTT 60.613 45.455 1.90 0.00 0.00 2.27
451 842 3.274067 AAAAATCGTGAGCCCGCC 58.726 55.556 0.00 0.00 0.00 6.13
479 870 2.439507 CCCTAAGATACCAGGCACACAT 59.560 50.000 0.00 0.00 0.00 3.21
480 871 1.837439 CCCTAAGATACCAGGCACACA 59.163 52.381 0.00 0.00 0.00 3.72
490 881 9.145442 AGTTCCTCTATGTAAACCCTAAGATAC 57.855 37.037 0.00 0.00 0.00 2.24
505 896 5.010516 CACACCTCATCCTAGTTCCTCTATG 59.989 48.000 0.00 0.00 0.00 2.23
506 897 5.103473 TCACACCTCATCCTAGTTCCTCTAT 60.103 44.000 0.00 0.00 0.00 1.98
507 898 4.229812 TCACACCTCATCCTAGTTCCTCTA 59.770 45.833 0.00 0.00 0.00 2.43
513 904 5.762179 TGATTTCACACCTCATCCTAGTT 57.238 39.130 0.00 0.00 0.00 2.24
516 907 5.955961 TCATGATTTCACACCTCATCCTA 57.044 39.130 0.00 0.00 0.00 2.94
533 924 2.088423 GTGGTGGCGGTTTATTCATGA 58.912 47.619 0.00 0.00 0.00 3.07
556 947 5.270794 GGACGGAGGGAGTATATAGGAAAT 58.729 45.833 0.00 0.00 0.00 2.17
564 955 1.526315 TCAGGGACGGAGGGAGTATA 58.474 55.000 0.00 0.00 0.00 1.47
606 997 4.703093 TGCTCCGTACGATATGGATTATCA 59.297 41.667 18.76 0.00 42.69 2.15
611 1002 4.056050 GTTTTGCTCCGTACGATATGGAT 58.944 43.478 18.76 0.00 42.69 3.41
612 1003 3.450578 GTTTTGCTCCGTACGATATGGA 58.549 45.455 18.76 3.75 41.46 3.41
613 1004 2.217847 CGTTTTGCTCCGTACGATATGG 59.782 50.000 18.76 0.00 36.16 2.74
614 1005 3.110358 TCGTTTTGCTCCGTACGATATG 58.890 45.455 18.76 0.00 38.02 1.78
615 1006 3.425577 TCGTTTTGCTCCGTACGATAT 57.574 42.857 18.76 0.00 38.02 1.63
618 1009 1.722464 CATTCGTTTTGCTCCGTACGA 59.278 47.619 18.76 1.79 40.80 3.43
619 1010 1.722464 TCATTCGTTTTGCTCCGTACG 59.278 47.619 8.69 8.69 35.46 3.67
620 1011 3.799137 TTCATTCGTTTTGCTCCGTAC 57.201 42.857 0.00 0.00 0.00 3.67
633 1024 4.455533 TGGTTTGGAGTGAAGATTCATTCG 59.544 41.667 10.73 0.00 42.71 3.34
636 1027 3.753272 CGTGGTTTGGAGTGAAGATTCAT 59.247 43.478 0.00 0.00 39.73 2.57
644 1035 5.653330 TGTATATAGACGTGGTTTGGAGTGA 59.347 40.000 0.00 0.00 0.00 3.41
650 1041 9.129209 CATACAGATGTATATAGACGTGGTTTG 57.871 37.037 5.21 0.00 39.06 2.93
782 1199 1.602377 GAAACTTCAGTCAACCCCACG 59.398 52.381 0.00 0.00 0.00 4.94
861 1278 1.332686 GAAAATATTCCCGTGACCCGC 59.667 52.381 0.00 0.00 34.38 6.13
897 1345 8.727100 ATTTTATTTTTCTGGTTCTCCTTCCT 57.273 30.769 0.00 0.00 34.23 3.36
923 1371 5.363005 ACGAGTTGGAGCTAGTACCAATATT 59.637 40.000 19.81 12.08 45.81 1.28
925 1373 4.275810 ACGAGTTGGAGCTAGTACCAATA 58.724 43.478 19.81 2.99 45.81 1.90
926 1374 3.097614 ACGAGTTGGAGCTAGTACCAAT 58.902 45.455 19.81 12.15 45.81 3.16
927 1375 2.522185 ACGAGTTGGAGCTAGTACCAA 58.478 47.619 15.27 15.27 42.78 3.67
928 1376 2.211250 ACGAGTTGGAGCTAGTACCA 57.789 50.000 6.05 6.05 0.00 3.25
929 1377 3.486542 CGTTACGAGTTGGAGCTAGTACC 60.487 52.174 0.00 0.00 0.00 3.34
932 1380 1.135460 GCGTTACGAGTTGGAGCTAGT 60.135 52.381 9.62 0.00 0.00 2.57
944 1392 0.037975 GGAAAGGACTGGCGTTACGA 60.038 55.000 9.62 0.00 0.00 3.43
976 1427 4.507916 TCCTCTCCTCTCCGGCGG 62.508 72.222 22.51 22.51 0.00 6.13
1254 1708 4.779733 TCCTCCTCCCCCTGACGC 62.780 72.222 0.00 0.00 0.00 5.19
1255 1709 2.443016 CTCCTCCTCCCCCTGACG 60.443 72.222 0.00 0.00 0.00 4.35
1256 1710 2.041405 CCTCCTCCTCCCCCTGAC 60.041 72.222 0.00 0.00 0.00 3.51
1257 1711 4.095400 GCCTCCTCCTCCCCCTGA 62.095 72.222 0.00 0.00 0.00 3.86
1314 1768 1.344496 CCCTTCATCTCCACCCTAGGT 60.344 57.143 8.29 0.00 35.62 3.08
1315 1769 1.428869 CCCTTCATCTCCACCCTAGG 58.571 60.000 0.06 0.06 0.00 3.02
1316 1770 0.761802 GCCCTTCATCTCCACCCTAG 59.238 60.000 0.00 0.00 0.00 3.02
1317 1771 0.343372 AGCCCTTCATCTCCACCCTA 59.657 55.000 0.00 0.00 0.00 3.53
1318 1772 0.985490 GAGCCCTTCATCTCCACCCT 60.985 60.000 0.00 0.00 0.00 4.34
1319 1773 1.529309 GAGCCCTTCATCTCCACCC 59.471 63.158 0.00 0.00 0.00 4.61
1320 1774 1.529309 GGAGCCCTTCATCTCCACC 59.471 63.158 3.60 0.00 46.24 4.61
1550 2022 2.034999 GACCGGCAACCAATCCCA 59.965 61.111 0.00 0.00 0.00 4.37
1554 2026 2.035626 CCTGGACCGGCAACCAAT 59.964 61.111 14.82 0.00 35.67 3.16
1604 2076 1.628043 CCCCATTACCCTTCTCCTCCA 60.628 57.143 0.00 0.00 0.00 3.86
1617 2089 0.271927 ATCCAGAGGCCTCCCCATTA 59.728 55.000 29.54 9.58 35.39 1.90
1688 2160 2.416027 CCTCGGTATGATGCAGTATCCG 60.416 54.545 11.88 11.88 34.77 4.18
1692 2164 1.068588 GTGCCTCGGTATGATGCAGTA 59.931 52.381 0.00 0.00 46.84 2.74
1698 2170 1.040893 TGACGGTGCCTCGGTATGAT 61.041 55.000 0.00 0.00 0.00 2.45
1711 2183 3.001406 GTACCTGGGCCTGACGGT 61.001 66.667 12.58 11.69 0.00 4.83
1712 2184 2.521958 CTTGTACCTGGGCCTGACGG 62.522 65.000 12.58 6.11 0.00 4.79
1718 2190 1.228429 TTGTGCTTGTACCTGGGCC 60.228 57.895 0.00 0.00 0.00 5.80
1797 2269 2.125269 GGTGATGCCGTTACCGCT 60.125 61.111 0.00 0.00 0.00 5.52
1831 2303 1.566231 AGCCTTCCCCTTGTTATCCAG 59.434 52.381 0.00 0.00 0.00 3.86
1832 2304 1.284785 CAGCCTTCCCCTTGTTATCCA 59.715 52.381 0.00 0.00 0.00 3.41
1836 2308 1.564348 GATCCAGCCTTCCCCTTGTTA 59.436 52.381 0.00 0.00 0.00 2.41
1911 2383 0.325933 CTCCCTGCAGTGGTGAATCA 59.674 55.000 13.81 0.00 0.00 2.57
2208 2689 3.160269 CCCAAAGTCCTCAAATTCTGCT 58.840 45.455 0.00 0.00 0.00 4.24
2242 2723 1.817099 GCGCCCTCATCTCAACCAG 60.817 63.158 0.00 0.00 0.00 4.00
2690 3177 1.737793 GTTGGAAATCTACCACTGGCG 59.262 52.381 0.00 0.00 37.13 5.69
2706 3193 4.321230 GGATTTAGCACCTTCACTTGTTGG 60.321 45.833 0.00 0.00 0.00 3.77
2778 3298 5.712152 CCAATCTGGTGATAATAAAGCCC 57.288 43.478 0.00 0.00 31.35 5.19
2920 3443 1.604308 CCTCACCTGCAATGCCACA 60.604 57.895 1.53 0.00 0.00 4.17
2976 3499 5.856455 CGGTAAATTTTCACAATGACCAGTC 59.144 40.000 0.00 0.00 0.00 3.51
3010 3533 5.172053 GCTTCGTTCTTTCACAGTTGAATTG 59.828 40.000 0.00 0.00 41.50 2.32
3012 3535 4.261197 GGCTTCGTTCTTTCACAGTTGAAT 60.261 41.667 0.00 0.00 41.50 2.57
3020 3543 3.548214 GGAAACAGGCTTCGTTCTTTCAC 60.548 47.826 0.00 0.00 0.00 3.18
3026 3549 1.878953 TGAGGAAACAGGCTTCGTTC 58.121 50.000 0.00 0.00 0.00 3.95
3027 3550 2.341846 TTGAGGAAACAGGCTTCGTT 57.658 45.000 0.00 0.00 0.00 3.85
3028 3551 2.568623 ATTGAGGAAACAGGCTTCGT 57.431 45.000 0.00 0.00 0.00 3.85
3029 3552 2.813754 TGAATTGAGGAAACAGGCTTCG 59.186 45.455 0.00 0.00 0.00 3.79
3035 3558 6.579666 TGAGGAATTGAATTGAGGAAACAG 57.420 37.500 0.00 0.00 0.00 3.16
3118 3647 3.934391 GACTTCGGTGCGGACTGGG 62.934 68.421 16.45 11.48 0.00 4.45
3237 3768 5.838521 TGGACACCTATGCACTTCATATCTA 59.161 40.000 0.00 0.00 37.07 1.98
3238 3769 4.655649 TGGACACCTATGCACTTCATATCT 59.344 41.667 0.00 0.00 37.07 1.98
3239 3770 4.960938 TGGACACCTATGCACTTCATATC 58.039 43.478 0.00 0.00 37.07 1.63
3348 3888 7.286087 TGATTTAATTGCAGCAGGAATCTACAT 59.714 33.333 16.44 0.00 34.42 2.29


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

AutoCloner maintained by Alex Coulton.