Multiple sequence alignment - TraesCS3D01G468200

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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 TraesCS3D01G468200 chr3D 100.000 3032 0 0 1 3032 570569546 570572577 0.000000e+00 5600
1 TraesCS3D01G468200 chr3D 88.889 531 46 3 1023 1553 570772893 570773410 2.550000e-180 641
2 TraesCS3D01G468200 chr3D 82.810 669 80 22 1324 1967 520294959 520295617 1.580000e-157 566
3 TraesCS3D01G468200 chr3D 85.988 521 57 14 1618 2129 570773500 570774013 7.390000e-151 544
4 TraesCS3D01G468200 chr3D 82.196 674 67 20 369 1025 570772214 570772851 5.760000e-147 531
5 TraesCS3D01G468200 chr3D 95.833 240 9 1 2793 3032 64774146 64774384 1.320000e-103 387
6 TraesCS3D01G468200 chr3D 84.293 382 49 5 602 973 520294274 520294654 2.220000e-96 363
7 TraesCS3D01G468200 chr3D 92.361 144 11 0 1109 1252 520294786 520294929 3.960000e-49 206
8 TraesCS3D01G468200 chr3A 92.131 1131 57 15 1023 2140 703741590 703742701 0.000000e+00 1567
9 TraesCS3D01G468200 chr3A 94.184 705 30 5 322 1023 703740851 703741547 0.000000e+00 1064
10 TraesCS3D01G468200 chr3A 90.529 718 41 15 2142 2859 653955606 653954916 0.000000e+00 924
11 TraesCS3D01G468200 chr3A 85.736 645 58 16 386 1025 703784027 703784642 0.000000e+00 651
12 TraesCS3D01G468200 chr3A 89.077 531 45 3 1023 1553 703784684 703785201 0.000000e+00 647
13 TraesCS3D01G468200 chr3A 78.350 1030 170 32 1027 2035 703184509 703183512 4.290000e-173 617
14 TraesCS3D01G468200 chr3A 83.260 681 74 20 602 1252 655860404 655861074 9.360000e-165 590
15 TraesCS3D01G468200 chr3A 82.111 682 83 22 602 1252 655722048 655722721 5.720000e-152 547
16 TraesCS3D01G468200 chr3A 84.820 527 64 14 1612 2129 703785283 703785802 1.610000e-142 516
17 TraesCS3D01G468200 chr3A 83.252 412 44 13 322 731 703412120 703412508 3.720000e-94 355
18 TraesCS3D01G468200 chr3A 85.393 178 26 0 1858 2035 655723175 655723352 5.160000e-43 185
19 TraesCS3D01G468200 chr3A 85.393 178 26 0 1858 2035 655861544 655861721 5.160000e-43 185
20 TraesCS3D01G468200 chr6B 94.216 899 46 6 2135 3032 423013186 423014079 0.000000e+00 1367
21 TraesCS3D01G468200 chr6B 85.554 893 79 16 2141 3032 595033237 595032394 0.000000e+00 889
22 TraesCS3D01G468200 chr6D 92.833 893 32 10 2141 3032 419881387 419880526 0.000000e+00 1266
23 TraesCS3D01G468200 chr6D 92.256 594 42 4 2135 2728 97817546 97818135 0.000000e+00 839
24 TraesCS3D01G468200 chr6D 95.567 203 5 4 2833 3032 97821967 97822168 3.770000e-84 322
25 TraesCS3D01G468200 chr4A 90.749 908 53 13 2137 3032 578180080 578180968 0.000000e+00 1182
26 TraesCS3D01G468200 chr6A 90.476 903 55 13 2141 3032 494439745 494438863 0.000000e+00 1162
27 TraesCS3D01G468200 chr6A 89.602 904 61 13 2141 3032 184591588 184592470 0.000000e+00 1118
28 TraesCS3D01G468200 chr5A 90.330 910 54 19 2138 3032 33923790 33922900 0.000000e+00 1162
29 TraesCS3D01G468200 chr5A 89.956 906 57 16 2141 3032 524708238 524707353 0.000000e+00 1138
30 TraesCS3D01G468200 chr3B 85.555 1073 116 24 1023 2078 757866146 757867196 0.000000e+00 1086
31 TraesCS3D01G468200 chr3B 79.203 1029 159 34 1029 2035 757519108 757518113 0.000000e+00 664
32 TraesCS3D01G468200 chr3B 84.178 651 54 22 379 1029 757865507 757866108 1.210000e-163 586
33 TraesCS3D01G468200 chr3B 78.333 660 128 12 1373 2023 684912789 684912136 2.180000e-111 412
34 TraesCS3D01G468200 chr3B 85.882 340 43 5 1699 2035 685166344 685166681 1.030000e-94 357
35 TraesCS3D01G468200 chr3B 81.281 406 67 6 579 976 684942688 684942284 1.360000e-83 320
36 TraesCS3D01G468200 chr3B 79.890 363 59 9 631 989 757519565 757519213 1.400000e-63 254
37 TraesCS3D01G468200 chr4B 92.715 755 48 6 2139 2892 553920630 553921378 0.000000e+00 1083
38 TraesCS3D01G468200 chr4B 87.814 837 57 15 2141 2976 548199146 548199938 0.000000e+00 939
39 TraesCS3D01G468200 chr1A 88.121 926 60 20 2138 3032 10696214 10695308 0.000000e+00 1055
40 TraesCS3D01G468200 chr1A 95.911 269 11 0 2764 3032 97938849 97938581 1.290000e-118 436


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 TraesCS3D01G468200 chr3D 570569546 570572577 3031 False 5600.000000 5600 100.000000 1 3032 1 chr3D.!!$F2 3031
1 TraesCS3D01G468200 chr3D 570772214 570774013 1799 False 572.000000 641 85.691000 369 2129 3 chr3D.!!$F4 1760
2 TraesCS3D01G468200 chr3D 520294274 520295617 1343 False 378.333333 566 86.488000 602 1967 3 chr3D.!!$F3 1365
3 TraesCS3D01G468200 chr3A 703740851 703742701 1850 False 1315.500000 1567 93.157500 322 2140 2 chr3A.!!$F4 1818
4 TraesCS3D01G468200 chr3A 653954916 653955606 690 True 924.000000 924 90.529000 2142 2859 1 chr3A.!!$R1 717
5 TraesCS3D01G468200 chr3A 703183512 703184509 997 True 617.000000 617 78.350000 1027 2035 1 chr3A.!!$R2 1008
6 TraesCS3D01G468200 chr3A 703784027 703785802 1775 False 604.666667 651 86.544333 386 2129 3 chr3A.!!$F5 1743
7 TraesCS3D01G468200 chr3A 655860404 655861721 1317 False 387.500000 590 84.326500 602 2035 2 chr3A.!!$F3 1433
8 TraesCS3D01G468200 chr3A 655722048 655723352 1304 False 366.000000 547 83.752000 602 2035 2 chr3A.!!$F2 1433
9 TraesCS3D01G468200 chr6B 423013186 423014079 893 False 1367.000000 1367 94.216000 2135 3032 1 chr6B.!!$F1 897
10 TraesCS3D01G468200 chr6B 595032394 595033237 843 True 889.000000 889 85.554000 2141 3032 1 chr6B.!!$R1 891
11 TraesCS3D01G468200 chr6D 419880526 419881387 861 True 1266.000000 1266 92.833000 2141 3032 1 chr6D.!!$R1 891
12 TraesCS3D01G468200 chr6D 97817546 97822168 4622 False 580.500000 839 93.911500 2135 3032 2 chr6D.!!$F1 897
13 TraesCS3D01G468200 chr4A 578180080 578180968 888 False 1182.000000 1182 90.749000 2137 3032 1 chr4A.!!$F1 895
14 TraesCS3D01G468200 chr6A 494438863 494439745 882 True 1162.000000 1162 90.476000 2141 3032 1 chr6A.!!$R1 891
15 TraesCS3D01G468200 chr6A 184591588 184592470 882 False 1118.000000 1118 89.602000 2141 3032 1 chr6A.!!$F1 891
16 TraesCS3D01G468200 chr5A 33922900 33923790 890 True 1162.000000 1162 90.330000 2138 3032 1 chr5A.!!$R1 894
17 TraesCS3D01G468200 chr5A 524707353 524708238 885 True 1138.000000 1138 89.956000 2141 3032 1 chr5A.!!$R2 891
18 TraesCS3D01G468200 chr3B 757865507 757867196 1689 False 836.000000 1086 84.866500 379 2078 2 chr3B.!!$F2 1699
19 TraesCS3D01G468200 chr3B 757518113 757519565 1452 True 459.000000 664 79.546500 631 2035 2 chr3B.!!$R3 1404
20 TraesCS3D01G468200 chr3B 684912136 684912789 653 True 412.000000 412 78.333000 1373 2023 1 chr3B.!!$R1 650
21 TraesCS3D01G468200 chr4B 553920630 553921378 748 False 1083.000000 1083 92.715000 2139 2892 1 chr4B.!!$F2 753
22 TraesCS3D01G468200 chr4B 548199146 548199938 792 False 939.000000 939 87.814000 2141 2976 1 chr4B.!!$F1 835
23 TraesCS3D01G468200 chr1A 10695308 10696214 906 True 1055.000000 1055 88.121000 2138 3032 1 chr1A.!!$R1 894

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
37 38 0.035152 ATCCATGCCGTGAAGCTGAA 60.035 50.0 0.0 0.0 0.0 3.02 F
181 182 0.039074 CGTGAAGAAGACCGTGAGCT 60.039 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1474 0.743345 GGATGTAATATCCCGCGGGC 60.743 60.0 39.89 24.19 34.68 6.13 R
2163 2350 0.316204 CCGGTTCGTCTAGTTGGTGT 59.684 55.0 0.00 0.00 0.00 4.16 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
17 18 4.509756 CTGACTGGATCTGCGTGG 57.490 61.111 0.00 0.00 0.00 4.94
18 19 1.893062 CTGACTGGATCTGCGTGGA 59.107 57.895 0.00 0.00 0.00 4.02
19 20 0.463204 CTGACTGGATCTGCGTGGAT 59.537 55.000 0.00 0.00 0.00 3.41
20 21 0.461548 TGACTGGATCTGCGTGGATC 59.538 55.000 10.01 10.01 40.78 3.36
30 31 2.186644 CGTGGATCCATGCCGTGA 59.813 61.111 20.90 0.00 0.00 4.35
31 32 1.449423 CGTGGATCCATGCCGTGAA 60.449 57.895 20.90 0.00 0.00 3.18
32 33 1.431488 CGTGGATCCATGCCGTGAAG 61.431 60.000 20.90 0.00 0.00 3.02
33 34 1.451927 TGGATCCATGCCGTGAAGC 60.452 57.895 11.44 0.00 0.00 3.86
34 35 1.153086 GGATCCATGCCGTGAAGCT 60.153 57.895 6.95 0.00 0.00 3.74
35 36 1.442526 GGATCCATGCCGTGAAGCTG 61.443 60.000 6.95 0.00 0.00 4.24
36 37 0.462581 GATCCATGCCGTGAAGCTGA 60.463 55.000 0.00 0.00 0.00 4.26
37 38 0.035152 ATCCATGCCGTGAAGCTGAA 60.035 50.000 0.00 0.00 0.00 3.02
38 39 0.955428 TCCATGCCGTGAAGCTGAAC 60.955 55.000 0.00 0.00 0.00 3.18
39 40 1.133253 CATGCCGTGAAGCTGAACG 59.867 57.895 13.11 13.11 39.48 3.95
40 41 2.680913 ATGCCGTGAAGCTGAACGC 61.681 57.895 14.31 10.84 38.46 4.84
41 42 3.345808 GCCGTGAAGCTGAACGCA 61.346 61.111 14.31 0.00 42.61 5.24
42 43 2.856032 CCGTGAAGCTGAACGCAG 59.144 61.111 14.31 0.00 45.13 5.18
50 51 3.318875 CTGAACGCAGCACAACGA 58.681 55.556 0.00 0.00 34.95 3.85
51 52 1.862123 CTGAACGCAGCACAACGAT 59.138 52.632 0.00 0.00 34.95 3.73
52 53 0.179240 CTGAACGCAGCACAACGATC 60.179 55.000 0.00 0.00 34.95 3.69
53 54 1.132640 GAACGCAGCACAACGATCC 59.867 57.895 0.00 0.00 0.00 3.36
54 55 2.548587 GAACGCAGCACAACGATCCG 62.549 60.000 0.00 0.00 0.00 4.18
55 56 4.505217 CGCAGCACAACGATCCGC 62.505 66.667 0.00 0.00 0.00 5.54
73 74 2.047655 GTGGATCCACGCCGTGAA 60.048 61.111 28.52 0.00 37.19 3.18
74 75 2.100631 GTGGATCCACGCCGTGAAG 61.101 63.158 28.52 2.55 37.19 3.02
75 76 3.195698 GGATCCACGCCGTGAAGC 61.196 66.667 20.57 0.00 35.23 3.86
76 77 3.195698 GATCCACGCCGTGAAGCC 61.196 66.667 20.57 0.92 35.23 4.35
80 81 4.072088 CACGCCGTGAAGCCGAAC 62.072 66.667 12.85 0.00 35.23 3.95
81 82 4.595538 ACGCCGTGAAGCCGAACA 62.596 61.111 0.00 0.00 0.00 3.18
82 83 4.072088 CGCCGTGAAGCCGAACAC 62.072 66.667 0.00 0.00 0.00 3.32
83 84 2.970324 GCCGTGAAGCCGAACACA 60.970 61.111 0.00 0.00 36.91 3.72
84 85 2.954753 GCCGTGAAGCCGAACACAG 61.955 63.158 0.00 0.00 36.91 3.66
85 86 2.551270 CGTGAAGCCGAACACAGC 59.449 61.111 0.00 0.00 36.91 4.40
86 87 2.551270 GTGAAGCCGAACACAGCG 59.449 61.111 0.00 0.00 37.05 5.18
90 91 2.125512 AGCCGAACACAGCGGATC 60.126 61.111 6.18 0.00 45.48 3.36
91 92 2.942796 AGCCGAACACAGCGGATCA 61.943 57.895 6.18 0.00 45.48 2.92
92 93 2.449031 AGCCGAACACAGCGGATCAA 62.449 55.000 6.18 0.00 45.48 2.57
93 94 3.714598 AGCCGAACACAGCGGATCAAT 62.715 52.381 6.18 0.00 45.48 2.57
95 96 0.652592 CGAACACAGCGGATCAATCC 59.347 55.000 0.00 0.00 43.65 3.01
107 108 2.691409 ATCAATCCGTGTTGATCCGT 57.309 45.000 6.68 0.00 43.44 4.69
108 109 3.812156 ATCAATCCGTGTTGATCCGTA 57.188 42.857 6.68 0.00 43.44 4.02
109 110 2.883574 TCAATCCGTGTTGATCCGTAC 58.116 47.619 0.00 0.00 33.41 3.67
110 111 1.931172 CAATCCGTGTTGATCCGTACC 59.069 52.381 0.00 0.00 0.00 3.34
111 112 1.481871 ATCCGTGTTGATCCGTACCT 58.518 50.000 0.00 0.00 0.00 3.08
112 113 1.259609 TCCGTGTTGATCCGTACCTT 58.740 50.000 0.00 0.00 0.00 3.50
113 114 1.067425 TCCGTGTTGATCCGTACCTTG 60.067 52.381 0.00 0.00 0.00 3.61
114 115 1.067425 CCGTGTTGATCCGTACCTTGA 60.067 52.381 0.00 0.00 0.00 3.02
115 116 2.418197 CCGTGTTGATCCGTACCTTGAT 60.418 50.000 0.00 0.00 0.00 2.57
116 117 2.858344 CGTGTTGATCCGTACCTTGATC 59.142 50.000 7.43 7.43 38.27 2.92
117 118 2.858344 GTGTTGATCCGTACCTTGATCG 59.142 50.000 9.06 0.00 40.19 3.69
118 119 2.494471 TGTTGATCCGTACCTTGATCGT 59.506 45.455 9.06 0.00 40.19 3.73
119 120 2.858344 GTTGATCCGTACCTTGATCGTG 59.142 50.000 9.06 0.00 40.19 4.35
120 121 1.202371 TGATCCGTACCTTGATCGTGC 60.202 52.381 9.06 0.00 40.19 5.34
121 122 0.821517 ATCCGTACCTTGATCGTGCA 59.178 50.000 0.00 0.00 0.00 4.57
122 123 0.108992 TCCGTACCTTGATCGTGCAC 60.109 55.000 6.82 6.82 0.00 4.57
123 124 0.389296 CCGTACCTTGATCGTGCACA 60.389 55.000 18.64 4.45 0.00 4.57
124 125 0.713883 CGTACCTTGATCGTGCACAC 59.286 55.000 18.64 8.14 0.00 3.82
125 126 1.790755 GTACCTTGATCGTGCACACA 58.209 50.000 18.64 10.77 0.00 3.72
126 127 1.726791 GTACCTTGATCGTGCACACAG 59.273 52.381 18.64 0.04 0.00 3.66
127 128 0.392706 ACCTTGATCGTGCACACAGA 59.607 50.000 18.64 6.51 0.00 3.41
128 129 0.792640 CCTTGATCGTGCACACAGAC 59.207 55.000 18.64 3.76 0.00 3.51
129 130 1.501169 CTTGATCGTGCACACAGACA 58.499 50.000 18.64 6.39 0.00 3.41
130 131 1.866601 CTTGATCGTGCACACAGACAA 59.133 47.619 18.64 13.27 0.00 3.18
131 132 1.217001 TGATCGTGCACACAGACAAC 58.783 50.000 18.64 2.92 0.00 3.32
132 133 1.217001 GATCGTGCACACAGACAACA 58.783 50.000 18.64 0.00 0.00 3.33
133 134 1.597195 GATCGTGCACACAGACAACAA 59.403 47.619 18.64 0.00 0.00 2.83
134 135 1.443802 TCGTGCACACAGACAACAAA 58.556 45.000 18.64 0.00 0.00 2.83
135 136 2.013400 TCGTGCACACAGACAACAAAT 58.987 42.857 18.64 0.00 0.00 2.32
136 137 3.198872 TCGTGCACACAGACAACAAATA 58.801 40.909 18.64 0.00 0.00 1.40
137 138 3.623510 TCGTGCACACAGACAACAAATAA 59.376 39.130 18.64 0.00 0.00 1.40
138 139 4.095036 TCGTGCACACAGACAACAAATAAA 59.905 37.500 18.64 0.00 0.00 1.40
139 140 4.204168 CGTGCACACAGACAACAAATAAAC 59.796 41.667 18.64 0.00 0.00 2.01
140 141 5.098893 GTGCACACAGACAACAAATAAACA 58.901 37.500 13.17 0.00 0.00 2.83
141 142 5.748152 GTGCACACAGACAACAAATAAACAT 59.252 36.000 13.17 0.00 0.00 2.71
142 143 6.255453 GTGCACACAGACAACAAATAAACATT 59.745 34.615 13.17 0.00 0.00 2.71
143 144 6.255237 TGCACACAGACAACAAATAAACATTG 59.745 34.615 0.00 0.00 0.00 2.82
144 145 6.255453 GCACACAGACAACAAATAAACATTGT 59.745 34.615 0.00 0.00 42.56 2.71
145 146 7.611387 CACACAGACAACAAATAAACATTGTG 58.389 34.615 0.00 0.00 39.98 3.33
146 147 7.487509 CACACAGACAACAAATAAACATTGTGA 59.512 33.333 0.00 0.00 39.98 3.58
147 148 8.031864 ACACAGACAACAAATAAACATTGTGAA 58.968 29.630 0.00 0.00 39.98 3.18
148 149 8.867935 CACAGACAACAAATAAACATTGTGAAA 58.132 29.630 0.00 0.00 39.98 2.69
149 150 9.598517 ACAGACAACAAATAAACATTGTGAAAT 57.401 25.926 0.00 0.00 39.98 2.17
163 164 9.825972 AACATTGTGAAATCTAAGTGTAAATCG 57.174 29.630 0.00 0.00 0.00 3.34
164 165 8.999431 ACATTGTGAAATCTAAGTGTAAATCGT 58.001 29.630 0.00 0.00 0.00 3.73
165 166 9.265938 CATTGTGAAATCTAAGTGTAAATCGTG 57.734 33.333 0.00 0.00 0.00 4.35
166 167 8.596271 TTGTGAAATCTAAGTGTAAATCGTGA 57.404 30.769 0.00 0.00 0.00 4.35
167 168 8.596271 TGTGAAATCTAAGTGTAAATCGTGAA 57.404 30.769 0.00 0.00 0.00 3.18
168 169 8.708742 TGTGAAATCTAAGTGTAAATCGTGAAG 58.291 33.333 0.00 0.00 0.00 3.02
169 170 8.922676 GTGAAATCTAAGTGTAAATCGTGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
170 171 9.483916 TGAAATCTAAGTGTAAATCGTGAAGAA 57.516 29.630 0.00 0.00 0.00 2.52
171 172 9.959775 GAAATCTAAGTGTAAATCGTGAAGAAG 57.040 33.333 0.00 0.00 0.00 2.85
172 173 9.706691 AAATCTAAGTGTAAATCGTGAAGAAGA 57.293 29.630 0.00 0.00 0.00 2.87
173 174 8.690680 ATCTAAGTGTAAATCGTGAAGAAGAC 57.309 34.615 0.00 0.00 0.00 3.01
174 175 7.088905 TCTAAGTGTAAATCGTGAAGAAGACC 58.911 38.462 0.00 0.00 0.00 3.85
175 176 4.235360 AGTGTAAATCGTGAAGAAGACCG 58.765 43.478 0.00 0.00 0.00 4.79
176 177 3.985925 GTGTAAATCGTGAAGAAGACCGT 59.014 43.478 0.00 0.00 0.00 4.83
177 178 3.985279 TGTAAATCGTGAAGAAGACCGTG 59.015 43.478 0.00 0.00 0.00 4.94
178 179 3.380479 AAATCGTGAAGAAGACCGTGA 57.620 42.857 0.00 0.00 0.00 4.35
179 180 2.638556 ATCGTGAAGAAGACCGTGAG 57.361 50.000 0.00 0.00 0.00 3.51
180 181 0.039437 TCGTGAAGAAGACCGTGAGC 60.039 55.000 0.00 0.00 0.00 4.26
181 182 0.039074 CGTGAAGAAGACCGTGAGCT 60.039 55.000 0.00 0.00 0.00 4.09
182 183 1.199327 CGTGAAGAAGACCGTGAGCTA 59.801 52.381 0.00 0.00 0.00 3.32
183 184 2.597520 GTGAAGAAGACCGTGAGCTAC 58.402 52.381 0.00 0.00 0.00 3.58
184 185 2.030185 GTGAAGAAGACCGTGAGCTACA 60.030 50.000 0.00 0.00 0.00 2.74
185 186 2.826128 TGAAGAAGACCGTGAGCTACAT 59.174 45.455 0.00 0.00 0.00 2.29
186 187 2.949451 AGAAGACCGTGAGCTACATG 57.051 50.000 0.00 0.00 35.47 3.21
187 188 2.447443 AGAAGACCGTGAGCTACATGA 58.553 47.619 0.00 0.00 37.69 3.07
188 189 2.826128 AGAAGACCGTGAGCTACATGAA 59.174 45.455 0.00 0.00 37.69 2.57
189 190 3.258372 AGAAGACCGTGAGCTACATGAAA 59.742 43.478 0.00 0.00 37.69 2.69
190 191 2.960819 AGACCGTGAGCTACATGAAAC 58.039 47.619 0.00 0.00 37.69 2.78
191 192 2.299013 AGACCGTGAGCTACATGAAACA 59.701 45.455 0.00 0.00 37.69 2.83
192 193 3.055819 AGACCGTGAGCTACATGAAACAT 60.056 43.478 0.00 0.00 37.69 2.71
193 194 4.159693 AGACCGTGAGCTACATGAAACATA 59.840 41.667 0.00 0.00 37.69 2.29
194 195 4.827692 ACCGTGAGCTACATGAAACATAA 58.172 39.130 0.00 0.00 37.69 1.90
195 196 5.242434 ACCGTGAGCTACATGAAACATAAA 58.758 37.500 0.00 0.00 37.69 1.40
196 197 5.703592 ACCGTGAGCTACATGAAACATAAAA 59.296 36.000 0.00 0.00 37.69 1.52
197 198 6.374333 ACCGTGAGCTACATGAAACATAAAAT 59.626 34.615 0.00 0.00 37.69 1.82
198 199 7.094377 ACCGTGAGCTACATGAAACATAAAATT 60.094 33.333 0.00 0.00 37.69 1.82
199 200 8.394877 CCGTGAGCTACATGAAACATAAAATTA 58.605 33.333 0.00 0.00 37.69 1.40
200 201 9.425893 CGTGAGCTACATGAAACATAAAATTAG 57.574 33.333 0.00 0.00 37.69 1.73
220 221 7.816945 ATTAGAAAACAAAAAGGCATGATCG 57.183 32.000 0.00 0.00 0.00 3.69
221 222 5.452078 AGAAAACAAAAAGGCATGATCGA 57.548 34.783 0.00 0.00 0.00 3.59
222 223 5.464168 AGAAAACAAAAAGGCATGATCGAG 58.536 37.500 0.00 0.00 0.00 4.04
223 224 4.853924 AAACAAAAAGGCATGATCGAGT 57.146 36.364 0.00 0.00 0.00 4.18
224 225 3.837213 ACAAAAAGGCATGATCGAGTG 57.163 42.857 0.00 0.00 0.00 3.51
225 226 2.095059 ACAAAAAGGCATGATCGAGTGC 60.095 45.455 10.69 10.69 40.55 4.40
226 227 1.825090 AAAAGGCATGATCGAGTGCA 58.175 45.000 18.15 5.42 43.00 4.57
227 228 1.825090 AAAGGCATGATCGAGTGCAA 58.175 45.000 18.15 0.00 43.00 4.08
228 229 2.048444 AAGGCATGATCGAGTGCAAT 57.952 45.000 18.15 0.00 43.00 3.56
229 230 2.048444 AGGCATGATCGAGTGCAATT 57.952 45.000 18.15 4.66 43.00 2.32
230 231 2.372264 AGGCATGATCGAGTGCAATTT 58.628 42.857 18.15 2.74 43.00 1.82
231 232 2.357009 AGGCATGATCGAGTGCAATTTC 59.643 45.455 18.15 4.64 43.00 2.17
232 233 2.097954 GGCATGATCGAGTGCAATTTCA 59.902 45.455 18.15 3.47 43.00 2.69
233 234 3.427909 GGCATGATCGAGTGCAATTTCAA 60.428 43.478 18.15 0.00 43.00 2.69
234 235 4.168014 GCATGATCGAGTGCAATTTCAAA 58.832 39.130 13.39 0.00 40.94 2.69
235 236 4.622313 GCATGATCGAGTGCAATTTCAAAA 59.378 37.500 13.39 0.00 40.94 2.44
236 237 5.220154 GCATGATCGAGTGCAATTTCAAAAG 60.220 40.000 13.39 0.00 40.94 2.27
237 238 5.687770 TGATCGAGTGCAATTTCAAAAGA 57.312 34.783 0.00 0.00 0.00 2.52
238 239 6.070897 TGATCGAGTGCAATTTCAAAAGAA 57.929 33.333 0.00 0.00 0.00 2.52
239 240 6.502652 TGATCGAGTGCAATTTCAAAAGAAA 58.497 32.000 0.00 0.00 0.00 2.52
240 241 6.417635 TGATCGAGTGCAATTTCAAAAGAAAC 59.582 34.615 0.00 0.00 0.00 2.78
241 242 5.645624 TCGAGTGCAATTTCAAAAGAAACA 58.354 33.333 0.00 0.00 0.00 2.83
242 243 6.096036 TCGAGTGCAATTTCAAAAGAAACAA 58.904 32.000 0.00 0.00 0.00 2.83
243 244 6.034470 TCGAGTGCAATTTCAAAAGAAACAAC 59.966 34.615 0.00 0.00 0.00 3.32
244 245 6.421377 AGTGCAATTTCAAAAGAAACAACC 57.579 33.333 0.00 0.00 0.00 3.77
245 246 6.172630 AGTGCAATTTCAAAAGAAACAACCT 58.827 32.000 0.00 0.00 0.00 3.50
246 247 6.313658 AGTGCAATTTCAAAAGAAACAACCTC 59.686 34.615 0.00 0.00 0.00 3.85
247 248 6.313658 GTGCAATTTCAAAAGAAACAACCTCT 59.686 34.615 0.00 0.00 0.00 3.69
248 249 7.491048 GTGCAATTTCAAAAGAAACAACCTCTA 59.509 33.333 0.00 0.00 0.00 2.43
249 250 8.203485 TGCAATTTCAAAAGAAACAACCTCTAT 58.797 29.630 0.00 0.00 0.00 1.98
250 251 9.691362 GCAATTTCAAAAGAAACAACCTCTATA 57.309 29.630 0.00 0.00 0.00 1.31
275 276 8.918202 AATTAAATTGAGTGTGTACTGAGGAA 57.082 30.769 0.00 0.00 37.25 3.36
276 277 7.962964 TTAAATTGAGTGTGTACTGAGGAAG 57.037 36.000 0.00 0.00 37.25 3.46
277 278 5.808366 AATTGAGTGTGTACTGAGGAAGA 57.192 39.130 0.00 0.00 37.25 2.87
278 279 5.808366 ATTGAGTGTGTACTGAGGAAGAA 57.192 39.130 0.00 0.00 37.25 2.52
279 280 5.607939 TTGAGTGTGTACTGAGGAAGAAA 57.392 39.130 0.00 0.00 37.25 2.52
280 281 5.808366 TGAGTGTGTACTGAGGAAGAAAT 57.192 39.130 0.00 0.00 37.25 2.17
281 282 6.174720 TGAGTGTGTACTGAGGAAGAAATT 57.825 37.500 0.00 0.00 37.25 1.82
282 283 7.297936 TGAGTGTGTACTGAGGAAGAAATTA 57.702 36.000 0.00 0.00 37.25 1.40
283 284 7.378966 TGAGTGTGTACTGAGGAAGAAATTAG 58.621 38.462 0.00 0.00 37.25 1.73
284 285 6.702329 AGTGTGTACTGAGGAAGAAATTAGG 58.298 40.000 0.00 0.00 35.34 2.69
285 286 5.351740 GTGTGTACTGAGGAAGAAATTAGGC 59.648 44.000 0.00 0.00 0.00 3.93
286 287 4.567159 GTGTACTGAGGAAGAAATTAGGCG 59.433 45.833 0.00 0.00 0.00 5.52
287 288 4.464951 TGTACTGAGGAAGAAATTAGGCGA 59.535 41.667 0.00 0.00 0.00 5.54
288 289 3.863041 ACTGAGGAAGAAATTAGGCGAC 58.137 45.455 0.00 0.00 0.00 5.19
290 291 4.710375 ACTGAGGAAGAAATTAGGCGACTA 59.290 41.667 0.00 0.00 43.67 2.59
291 292 5.007385 TGAGGAAGAAATTAGGCGACTAC 57.993 43.478 0.00 0.00 44.30 2.73
292 293 4.710375 TGAGGAAGAAATTAGGCGACTACT 59.290 41.667 0.00 0.00 44.30 2.57
293 294 5.889853 TGAGGAAGAAATTAGGCGACTACTA 59.110 40.000 0.00 0.00 44.30 1.82
294 295 6.146601 AGGAAGAAATTAGGCGACTACTAC 57.853 41.667 0.00 0.00 44.30 2.73
295 296 5.892686 AGGAAGAAATTAGGCGACTACTACT 59.107 40.000 0.00 0.00 44.30 2.57
296 297 7.059156 AGGAAGAAATTAGGCGACTACTACTA 58.941 38.462 0.00 0.00 44.30 1.82
297 298 7.559170 AGGAAGAAATTAGGCGACTACTACTAA 59.441 37.037 0.00 0.00 44.30 2.24
298 299 7.861872 GGAAGAAATTAGGCGACTACTACTAAG 59.138 40.741 0.00 0.00 44.30 2.18
299 300 7.878547 AGAAATTAGGCGACTACTACTAAGT 57.121 36.000 0.00 0.00 44.30 2.24
300 301 8.291191 AGAAATTAGGCGACTACTACTAAGTT 57.709 34.615 0.00 0.00 44.30 2.66
301 302 8.747471 AGAAATTAGGCGACTACTACTAAGTTT 58.253 33.333 0.00 0.00 44.30 2.66
302 303 9.363763 GAAATTAGGCGACTACTACTAAGTTTT 57.636 33.333 0.00 0.00 44.30 2.43
305 306 5.889219 AGGCGACTACTACTAAGTTTTAGC 58.111 41.667 0.00 0.00 40.61 3.09
306 307 5.416952 AGGCGACTACTACTAAGTTTTAGCA 59.583 40.000 0.00 0.00 40.61 3.49
307 308 5.514559 GGCGACTACTACTAAGTTTTAGCAC 59.485 44.000 0.00 0.00 37.15 4.40
308 309 5.226772 GCGACTACTACTAAGTTTTAGCACG 59.773 44.000 0.00 0.00 37.15 5.34
309 310 5.226772 CGACTACTACTAAGTTTTAGCACGC 59.773 44.000 0.00 0.00 37.15 5.34
310 311 5.405797 ACTACTACTAAGTTTTAGCACGCC 58.594 41.667 0.00 0.00 37.15 5.68
311 312 4.532314 ACTACTAAGTTTTAGCACGCCT 57.468 40.909 0.00 0.00 29.00 5.52
312 313 4.891260 ACTACTAAGTTTTAGCACGCCTT 58.109 39.130 0.00 0.00 29.00 4.35
313 314 5.303165 ACTACTAAGTTTTAGCACGCCTTT 58.697 37.500 0.00 0.00 29.00 3.11
314 315 5.761726 ACTACTAAGTTTTAGCACGCCTTTT 59.238 36.000 0.00 0.00 29.00 2.27
315 316 5.509716 ACTAAGTTTTAGCACGCCTTTTT 57.490 34.783 0.00 0.00 0.00 1.94
316 317 5.516996 ACTAAGTTTTAGCACGCCTTTTTC 58.483 37.500 0.00 0.00 0.00 2.29
317 318 4.379339 AAGTTTTAGCACGCCTTTTTCA 57.621 36.364 0.00 0.00 0.00 2.69
318 319 3.702330 AGTTTTAGCACGCCTTTTTCAC 58.298 40.909 0.00 0.00 0.00 3.18
319 320 3.380320 AGTTTTAGCACGCCTTTTTCACT 59.620 39.130 0.00 0.00 0.00 3.41
320 321 4.577283 AGTTTTAGCACGCCTTTTTCACTA 59.423 37.500 0.00 0.00 0.00 2.74
323 324 3.559238 AGCACGCCTTTTTCACTAATG 57.441 42.857 0.00 0.00 0.00 1.90
328 329 5.469479 CACGCCTTTTTCACTAATGGATTT 58.531 37.500 0.00 0.00 0.00 2.17
330 331 7.087639 CACGCCTTTTTCACTAATGGATTTAA 58.912 34.615 0.00 0.00 0.00 1.52
334 335 9.435688 GCCTTTTTCACTAATGGATTTAATTGT 57.564 29.630 0.00 0.00 0.00 2.71
513 527 3.728221 CGCTCAAGATCGTGAAGTATCAG 59.272 47.826 12.50 0.72 35.88 2.90
534 548 5.064707 TCAGTTCACAGTTAACAAACTCTGC 59.935 40.000 8.61 0.00 0.00 4.26
556 578 6.566141 TGCGAGTAAGCAGTACAAATACATA 58.434 36.000 0.00 0.00 42.92 2.29
557 579 7.207383 TGCGAGTAAGCAGTACAAATACATAT 58.793 34.615 0.00 0.00 42.92 1.78
1069 1187 4.475135 GCTGCCCCCGGAAGAGTC 62.475 72.222 0.73 0.00 0.00 3.36
1070 1188 4.148825 CTGCCCCCGGAAGAGTCG 62.149 72.222 0.73 0.00 0.00 4.18
1072 1190 3.703127 GCCCCCGGAAGAGTCGTT 61.703 66.667 0.73 0.00 0.00 3.85
1073 1191 2.577593 CCCCCGGAAGAGTCGTTC 59.422 66.667 0.73 0.00 0.00 3.95
1074 1192 2.181021 CCCCGGAAGAGTCGTTCG 59.819 66.667 0.73 0.00 0.00 3.95
1075 1193 2.506438 CCCGGAAGAGTCGTTCGC 60.506 66.667 0.73 0.00 0.00 4.70
1128 1246 3.073735 CTGCTGAGGTCGCTCCCT 61.074 66.667 0.00 0.00 37.62 4.20
1533 1651 3.621520 GACCTGTTCGACGCGTTT 58.378 55.556 15.53 0.00 0.00 3.60
1553 1671 2.049433 CAAGGCCTTCGACGACGT 60.049 61.111 17.29 0.00 40.69 4.34
1577 1711 1.571919 ATCAGGTACGCATTCTTCGC 58.428 50.000 0.00 0.00 0.00 4.70
1581 1715 2.202824 TACGCATTCTTCGCCCGG 60.203 61.111 0.00 0.00 0.00 5.73
1603 1737 4.373116 CACGGCGCCACTACAGGT 62.373 66.667 28.98 11.53 0.00 4.00
1604 1738 4.065281 ACGGCGCCACTACAGGTC 62.065 66.667 28.98 0.00 0.00 3.85
1606 1740 2.412323 CGGCGCCACTACAGGTCTA 61.412 63.158 28.98 0.00 0.00 2.59
1634 1806 2.442643 ATGGCTGCCGGAAATGGG 60.443 61.111 14.98 0.00 0.00 4.00
1648 1824 3.607084 ATGGGGTGCAGGGGAAAGC 62.607 63.158 0.00 0.00 0.00 3.51
1908 2095 3.845259 GAGCCGGCGGTGGTGATA 61.845 66.667 28.82 0.00 0.00 2.15
1916 2103 2.585247 GGTGGTGATAGGCGCGAC 60.585 66.667 12.10 7.34 35.31 5.19
2163 2350 4.082463 CCTAAAATCTAAAAAGTGGCCGCA 60.082 41.667 20.59 0.00 0.00 5.69
2258 2446 3.411351 CGCCTGGTCGGTTTCGTG 61.411 66.667 0.00 0.00 37.69 4.35
2381 2569 1.448013 CGTTCTCGCCCTTTCTCCC 60.448 63.158 0.00 0.00 0.00 4.30
2422 2610 1.361993 CCATTCTCCGCTCCTCTCG 59.638 63.158 0.00 0.00 0.00 4.04
2484 2672 0.905357 CTCCAAATCTCCGGTGGACT 59.095 55.000 6.64 0.00 36.51 3.85
2525 2713 4.595538 TCGTCGGCGTTGCAGGTT 62.596 61.111 10.18 0.00 39.49 3.50
2585 2773 1.152989 CTAGGTCGTCTCGAGGTCGG 61.153 65.000 22.81 8.31 36.23 4.79
2632 2820 1.422402 TCCTAGGGTTTCTGCGGTTTT 59.578 47.619 9.46 0.00 0.00 2.43
2844 6728 1.127343 GACTGCCCTCTGCTATCCTT 58.873 55.000 0.00 0.00 42.00 3.36
2866 6826 3.726631 CTCTCTGTCTCGTCGCCGC 62.727 68.421 0.00 0.00 0.00 6.53
2958 6931 1.142778 TTGCTTCGTTTTTGTGCGGC 61.143 50.000 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.463204 ATCCACGCAGATCCAGTCAG 59.537 55.000 0.00 0.00 0.00 3.51
1 2 0.461548 GATCCACGCAGATCCAGTCA 59.538 55.000 4.32 0.00 37.31 3.41
2 3 3.280920 GATCCACGCAGATCCAGTC 57.719 57.895 4.32 0.00 37.31 3.51
7 8 1.233285 GGCATGGATCCACGCAGATC 61.233 60.000 31.90 12.72 41.69 2.75
8 9 1.228063 GGCATGGATCCACGCAGAT 60.228 57.895 31.90 6.28 36.81 2.90
9 10 2.190313 GGCATGGATCCACGCAGA 59.810 61.111 31.90 1.96 36.81 4.26
10 11 3.274586 CGGCATGGATCCACGCAG 61.275 66.667 31.90 25.34 36.81 5.18
11 12 4.094646 ACGGCATGGATCCACGCA 62.095 61.111 31.90 3.21 36.81 5.24
12 13 3.576356 CACGGCATGGATCCACGC 61.576 66.667 24.47 24.47 34.06 5.34
13 14 1.431488 CTTCACGGCATGGATCCACG 61.431 60.000 18.99 18.83 0.00 4.94
14 15 1.718757 GCTTCACGGCATGGATCCAC 61.719 60.000 18.99 5.01 0.00 4.02
15 16 1.451927 GCTTCACGGCATGGATCCA 60.452 57.895 18.88 18.88 0.00 3.41
16 17 1.153086 AGCTTCACGGCATGGATCC 60.153 57.895 4.20 4.20 34.17 3.36
17 18 0.462581 TCAGCTTCACGGCATGGATC 60.463 55.000 0.00 0.00 34.17 3.36
18 19 0.035152 TTCAGCTTCACGGCATGGAT 60.035 50.000 0.00 0.00 34.17 3.41
19 20 0.955428 GTTCAGCTTCACGGCATGGA 60.955 55.000 0.00 0.00 34.17 3.41
20 21 1.503542 GTTCAGCTTCACGGCATGG 59.496 57.895 0.00 0.00 34.17 3.66
21 22 1.133253 CGTTCAGCTTCACGGCATG 59.867 57.895 6.55 0.00 32.58 4.06
22 23 2.680913 GCGTTCAGCTTCACGGCAT 61.681 57.895 14.67 0.00 44.04 4.40
23 24 3.345808 GCGTTCAGCTTCACGGCA 61.346 61.111 14.67 0.00 44.04 5.69
33 34 0.179240 GATCGTTGTGCTGCGTTCAG 60.179 55.000 0.00 0.00 43.16 3.02
34 35 1.565156 GGATCGTTGTGCTGCGTTCA 61.565 55.000 0.00 0.00 0.00 3.18
35 36 1.132640 GGATCGTTGTGCTGCGTTC 59.867 57.895 0.00 0.00 0.00 3.95
36 37 2.667318 CGGATCGTTGTGCTGCGTT 61.667 57.895 0.00 0.00 0.00 4.84
37 38 3.112075 CGGATCGTTGTGCTGCGT 61.112 61.111 0.00 0.00 0.00 5.24
38 39 4.505217 GCGGATCGTTGTGCTGCG 62.505 66.667 0.00 0.00 0.00 5.18
39 40 4.505217 CGCGGATCGTTGTGCTGC 62.505 66.667 0.00 0.00 0.00 5.25
56 57 2.047655 TTCACGGCGTGGATCCAC 60.048 61.111 36.30 31.59 43.01 4.02
57 58 2.264480 CTTCACGGCGTGGATCCA 59.736 61.111 36.30 16.95 33.87 3.41
58 59 3.195698 GCTTCACGGCGTGGATCC 61.196 66.667 36.30 19.91 33.87 3.36
59 60 3.195698 GGCTTCACGGCGTGGATC 61.196 66.667 36.30 25.56 33.87 3.36
66 67 2.954753 CTGTGTTCGGCTTCACGGC 61.955 63.158 0.00 0.00 37.38 5.68
67 68 2.954753 GCTGTGTTCGGCTTCACGG 61.955 63.158 0.00 0.00 42.20 4.94
68 69 2.551270 GCTGTGTTCGGCTTCACG 59.449 61.111 0.00 0.00 42.20 4.35
69 70 2.551270 CGCTGTGTTCGGCTTCAC 59.449 61.111 0.00 0.00 43.19 3.18
70 71 2.449031 ATCCGCTGTGTTCGGCTTCA 62.449 55.000 0.00 0.00 46.05 3.02
71 72 1.696832 GATCCGCTGTGTTCGGCTTC 61.697 60.000 0.00 0.00 46.05 3.86
72 73 1.741770 GATCCGCTGTGTTCGGCTT 60.742 57.895 0.00 0.00 46.05 4.35
73 74 2.125512 GATCCGCTGTGTTCGGCT 60.126 61.111 0.00 0.00 46.05 5.52
74 75 1.369091 ATTGATCCGCTGTGTTCGGC 61.369 55.000 0.00 0.00 46.05 5.54
76 77 0.652592 GGATTGATCCGCTGTGTTCG 59.347 55.000 0.00 0.00 37.19 3.95
89 90 2.417651 GGTACGGATCAACACGGATTGA 60.418 50.000 6.13 6.13 42.62 2.57
90 91 1.931172 GGTACGGATCAACACGGATTG 59.069 52.381 0.00 0.00 0.00 2.67
91 92 1.829222 AGGTACGGATCAACACGGATT 59.171 47.619 0.00 0.00 0.00 3.01
92 93 1.481871 AGGTACGGATCAACACGGAT 58.518 50.000 0.00 0.00 0.00 4.18
93 94 1.067425 CAAGGTACGGATCAACACGGA 60.067 52.381 0.00 0.00 0.00 4.69
94 95 1.067425 TCAAGGTACGGATCAACACGG 60.067 52.381 0.00 0.00 0.00 4.94
95 96 2.357327 TCAAGGTACGGATCAACACG 57.643 50.000 0.00 0.00 0.00 4.49
96 97 2.858344 CGATCAAGGTACGGATCAACAC 59.142 50.000 16.26 0.00 41.67 3.32
97 98 2.494471 ACGATCAAGGTACGGATCAACA 59.506 45.455 16.26 0.00 41.67 3.33
98 99 2.858344 CACGATCAAGGTACGGATCAAC 59.142 50.000 16.26 0.00 41.67 3.18
99 100 2.737359 GCACGATCAAGGTACGGATCAA 60.737 50.000 16.26 0.00 41.67 2.57
100 101 1.202371 GCACGATCAAGGTACGGATCA 60.202 52.381 16.26 0.00 41.67 2.92
101 102 1.202371 TGCACGATCAAGGTACGGATC 60.202 52.381 9.52 9.52 39.46 3.36
102 103 0.821517 TGCACGATCAAGGTACGGAT 59.178 50.000 0.00 0.00 0.00 4.18
103 104 0.108992 GTGCACGATCAAGGTACGGA 60.109 55.000 0.00 0.00 0.00 4.69
104 105 0.389296 TGTGCACGATCAAGGTACGG 60.389 55.000 13.13 0.00 0.00 4.02
105 106 0.713883 GTGTGCACGATCAAGGTACG 59.286 55.000 13.13 0.00 0.00 3.67
106 107 1.726791 CTGTGTGCACGATCAAGGTAC 59.273 52.381 13.13 1.61 0.00 3.34
107 108 1.616374 TCTGTGTGCACGATCAAGGTA 59.384 47.619 13.13 0.00 0.00 3.08
108 109 0.392706 TCTGTGTGCACGATCAAGGT 59.607 50.000 13.13 0.00 0.00 3.50
109 110 0.792640 GTCTGTGTGCACGATCAAGG 59.207 55.000 13.13 1.52 0.00 3.61
110 111 1.501169 TGTCTGTGTGCACGATCAAG 58.499 50.000 13.13 5.12 0.00 3.02
111 112 1.597195 GTTGTCTGTGTGCACGATCAA 59.403 47.619 13.13 10.00 0.00 2.57
112 113 1.217001 GTTGTCTGTGTGCACGATCA 58.783 50.000 13.13 10.34 0.00 2.92
113 114 1.217001 TGTTGTCTGTGTGCACGATC 58.783 50.000 13.13 5.97 0.00 3.69
114 115 1.662517 TTGTTGTCTGTGTGCACGAT 58.337 45.000 13.13 0.00 0.00 3.73
115 116 1.443802 TTTGTTGTCTGTGTGCACGA 58.556 45.000 13.13 0.00 0.00 4.35
116 117 2.473530 ATTTGTTGTCTGTGTGCACG 57.526 45.000 13.13 0.00 0.00 5.34
117 118 5.098893 TGTTTATTTGTTGTCTGTGTGCAC 58.901 37.500 10.75 10.75 0.00 4.57
118 119 5.316327 TGTTTATTTGTTGTCTGTGTGCA 57.684 34.783 0.00 0.00 0.00 4.57
119 120 6.255453 ACAATGTTTATTTGTTGTCTGTGTGC 59.745 34.615 0.00 0.00 29.39 4.57
120 121 7.487509 TCACAATGTTTATTTGTTGTCTGTGTG 59.512 33.333 0.00 0.00 32.87 3.82
121 122 7.542890 TCACAATGTTTATTTGTTGTCTGTGT 58.457 30.769 0.00 0.00 32.87 3.72
122 123 7.984002 TCACAATGTTTATTTGTTGTCTGTG 57.016 32.000 0.00 0.00 32.87 3.66
123 124 8.994429 TTTCACAATGTTTATTTGTTGTCTGT 57.006 26.923 0.00 0.00 32.87 3.41
137 138 9.825972 CGATTTACACTTAGATTTCACAATGTT 57.174 29.630 0.00 0.00 0.00 2.71
138 139 8.999431 ACGATTTACACTTAGATTTCACAATGT 58.001 29.630 0.00 0.00 0.00 2.71
139 140 9.265938 CACGATTTACACTTAGATTTCACAATG 57.734 33.333 0.00 0.00 0.00 2.82
140 141 9.214957 TCACGATTTACACTTAGATTTCACAAT 57.785 29.630 0.00 0.00 0.00 2.71
141 142 8.596271 TCACGATTTACACTTAGATTTCACAA 57.404 30.769 0.00 0.00 0.00 3.33
142 143 8.596271 TTCACGATTTACACTTAGATTTCACA 57.404 30.769 0.00 0.00 0.00 3.58
143 144 8.922676 TCTTCACGATTTACACTTAGATTTCAC 58.077 33.333 0.00 0.00 0.00 3.18
144 145 9.483916 TTCTTCACGATTTACACTTAGATTTCA 57.516 29.630 0.00 0.00 0.00 2.69
145 146 9.959775 CTTCTTCACGATTTACACTTAGATTTC 57.040 33.333 0.00 0.00 0.00 2.17
146 147 9.706691 TCTTCTTCACGATTTACACTTAGATTT 57.293 29.630 0.00 0.00 0.00 2.17
147 148 9.141400 GTCTTCTTCACGATTTACACTTAGATT 57.859 33.333 0.00 0.00 0.00 2.40
148 149 7.760340 GGTCTTCTTCACGATTTACACTTAGAT 59.240 37.037 0.00 0.00 0.00 1.98
149 150 7.088905 GGTCTTCTTCACGATTTACACTTAGA 58.911 38.462 0.00 0.00 0.00 2.10
150 151 6.033619 CGGTCTTCTTCACGATTTACACTTAG 59.966 42.308 0.00 0.00 0.00 2.18
151 152 5.860182 CGGTCTTCTTCACGATTTACACTTA 59.140 40.000 0.00 0.00 0.00 2.24
152 153 4.684703 CGGTCTTCTTCACGATTTACACTT 59.315 41.667 0.00 0.00 0.00 3.16
153 154 4.235360 CGGTCTTCTTCACGATTTACACT 58.765 43.478 0.00 0.00 0.00 3.55
154 155 3.985925 ACGGTCTTCTTCACGATTTACAC 59.014 43.478 0.00 0.00 0.00 2.90
155 156 3.985279 CACGGTCTTCTTCACGATTTACA 59.015 43.478 0.00 0.00 0.00 2.41
156 157 4.232221 TCACGGTCTTCTTCACGATTTAC 58.768 43.478 0.00 0.00 0.00 2.01
157 158 4.482386 CTCACGGTCTTCTTCACGATTTA 58.518 43.478 0.00 0.00 0.00 1.40
158 159 3.318017 CTCACGGTCTTCTTCACGATTT 58.682 45.455 0.00 0.00 0.00 2.17
159 160 2.927014 GCTCACGGTCTTCTTCACGATT 60.927 50.000 0.00 0.00 0.00 3.34
160 161 1.402984 GCTCACGGTCTTCTTCACGAT 60.403 52.381 0.00 0.00 0.00 3.73
161 162 0.039437 GCTCACGGTCTTCTTCACGA 60.039 55.000 0.00 0.00 0.00 4.35
162 163 0.039074 AGCTCACGGTCTTCTTCACG 60.039 55.000 0.00 0.00 0.00 4.35
163 164 2.030185 TGTAGCTCACGGTCTTCTTCAC 60.030 50.000 0.00 0.00 0.00 3.18
164 165 2.235891 TGTAGCTCACGGTCTTCTTCA 58.764 47.619 0.00 0.00 0.00 3.02
165 166 3.119459 TCATGTAGCTCACGGTCTTCTTC 60.119 47.826 0.00 0.00 0.00 2.87
166 167 2.826128 TCATGTAGCTCACGGTCTTCTT 59.174 45.455 0.00 0.00 0.00 2.52
167 168 2.447443 TCATGTAGCTCACGGTCTTCT 58.553 47.619 0.00 0.00 0.00 2.85
168 169 2.941453 TCATGTAGCTCACGGTCTTC 57.059 50.000 0.00 0.00 0.00 2.87
169 170 3.244078 TGTTTCATGTAGCTCACGGTCTT 60.244 43.478 0.00 0.00 0.00 3.01
170 171 2.299013 TGTTTCATGTAGCTCACGGTCT 59.701 45.455 0.00 0.00 0.00 3.85
171 172 2.683968 TGTTTCATGTAGCTCACGGTC 58.316 47.619 0.00 0.00 0.00 4.79
172 173 2.831685 TGTTTCATGTAGCTCACGGT 57.168 45.000 0.00 0.00 0.00 4.83
173 174 5.794687 TTTATGTTTCATGTAGCTCACGG 57.205 39.130 0.00 0.00 0.00 4.94
174 175 9.425893 CTAATTTTATGTTTCATGTAGCTCACG 57.574 33.333 0.00 0.00 0.00 4.35
194 195 8.711457 CGATCATGCCTTTTTGTTTTCTAATTT 58.289 29.630 0.00 0.00 0.00 1.82
195 196 8.087750 TCGATCATGCCTTTTTGTTTTCTAATT 58.912 29.630 0.00 0.00 0.00 1.40
196 197 7.601856 TCGATCATGCCTTTTTGTTTTCTAAT 58.398 30.769 0.00 0.00 0.00 1.73
197 198 6.976088 TCGATCATGCCTTTTTGTTTTCTAA 58.024 32.000 0.00 0.00 0.00 2.10
198 199 6.206634 ACTCGATCATGCCTTTTTGTTTTCTA 59.793 34.615 0.00 0.00 0.00 2.10
199 200 5.010012 ACTCGATCATGCCTTTTTGTTTTCT 59.990 36.000 0.00 0.00 0.00 2.52
200 201 5.117592 CACTCGATCATGCCTTTTTGTTTTC 59.882 40.000 0.00 0.00 0.00 2.29
201 202 4.984161 CACTCGATCATGCCTTTTTGTTTT 59.016 37.500 0.00 0.00 0.00 2.43
202 203 4.549458 CACTCGATCATGCCTTTTTGTTT 58.451 39.130 0.00 0.00 0.00 2.83
203 204 3.612479 GCACTCGATCATGCCTTTTTGTT 60.612 43.478 5.39 0.00 35.73 2.83
204 205 2.095059 GCACTCGATCATGCCTTTTTGT 60.095 45.455 5.39 0.00 35.73 2.83
205 206 2.095110 TGCACTCGATCATGCCTTTTTG 60.095 45.455 12.36 0.00 41.33 2.44
206 207 2.161855 TGCACTCGATCATGCCTTTTT 58.838 42.857 12.36 0.00 41.33 1.94
207 208 1.825090 TGCACTCGATCATGCCTTTT 58.175 45.000 12.36 0.00 41.33 2.27
208 209 1.825090 TTGCACTCGATCATGCCTTT 58.175 45.000 12.36 0.00 41.33 3.11
209 210 2.048444 ATTGCACTCGATCATGCCTT 57.952 45.000 12.36 0.04 41.33 4.35
210 211 2.048444 AATTGCACTCGATCATGCCT 57.952 45.000 12.36 0.18 41.33 4.75
211 212 2.097954 TGAAATTGCACTCGATCATGCC 59.902 45.455 12.36 0.26 41.33 4.40
212 213 3.409851 TGAAATTGCACTCGATCATGC 57.590 42.857 8.98 8.98 42.40 4.06
213 214 6.088173 TCTTTTGAAATTGCACTCGATCATG 58.912 36.000 0.00 0.00 0.00 3.07
214 215 6.258230 TCTTTTGAAATTGCACTCGATCAT 57.742 33.333 0.00 0.00 0.00 2.45
215 216 5.687770 TCTTTTGAAATTGCACTCGATCA 57.312 34.783 0.00 0.00 0.00 2.92
216 217 6.991485 TTTCTTTTGAAATTGCACTCGATC 57.009 33.333 0.00 0.00 42.84 3.69
250 251 8.918202 TTCCTCAGTACACACTCAATTTAATT 57.082 30.769 0.00 0.00 30.46 1.40
251 252 8.375506 TCTTCCTCAGTACACACTCAATTTAAT 58.624 33.333 0.00 0.00 30.46 1.40
252 253 7.732025 TCTTCCTCAGTACACACTCAATTTAA 58.268 34.615 0.00 0.00 30.46 1.52
253 254 7.297936 TCTTCCTCAGTACACACTCAATTTA 57.702 36.000 0.00 0.00 30.46 1.40
254 255 6.174720 TCTTCCTCAGTACACACTCAATTT 57.825 37.500 0.00 0.00 30.46 1.82
255 256 5.808366 TCTTCCTCAGTACACACTCAATT 57.192 39.130 0.00 0.00 30.46 2.32
256 257 5.808366 TTCTTCCTCAGTACACACTCAAT 57.192 39.130 0.00 0.00 30.46 2.57
257 258 5.607939 TTTCTTCCTCAGTACACACTCAA 57.392 39.130 0.00 0.00 30.46 3.02
258 259 5.808366 ATTTCTTCCTCAGTACACACTCA 57.192 39.130 0.00 0.00 30.46 3.41
259 260 6.814146 CCTAATTTCTTCCTCAGTACACACTC 59.186 42.308 0.00 0.00 30.46 3.51
260 261 6.702329 CCTAATTTCTTCCTCAGTACACACT 58.298 40.000 0.00 0.00 34.42 3.55
261 262 5.351740 GCCTAATTTCTTCCTCAGTACACAC 59.648 44.000 0.00 0.00 0.00 3.82
262 263 5.488341 GCCTAATTTCTTCCTCAGTACACA 58.512 41.667 0.00 0.00 0.00 3.72
263 264 4.567159 CGCCTAATTTCTTCCTCAGTACAC 59.433 45.833 0.00 0.00 0.00 2.90
264 265 4.464951 TCGCCTAATTTCTTCCTCAGTACA 59.535 41.667 0.00 0.00 0.00 2.90
265 266 4.804665 GTCGCCTAATTTCTTCCTCAGTAC 59.195 45.833 0.00 0.00 0.00 2.73
266 267 4.710375 AGTCGCCTAATTTCTTCCTCAGTA 59.290 41.667 0.00 0.00 0.00 2.74
267 268 3.515901 AGTCGCCTAATTTCTTCCTCAGT 59.484 43.478 0.00 0.00 0.00 3.41
268 269 4.130286 AGTCGCCTAATTTCTTCCTCAG 57.870 45.455 0.00 0.00 0.00 3.35
269 270 4.710375 AGTAGTCGCCTAATTTCTTCCTCA 59.290 41.667 0.00 0.00 0.00 3.86
270 271 5.265350 AGTAGTCGCCTAATTTCTTCCTC 57.735 43.478 0.00 0.00 0.00 3.71
271 272 5.892686 AGTAGTAGTCGCCTAATTTCTTCCT 59.107 40.000 0.00 0.00 0.00 3.36
272 273 6.146601 AGTAGTAGTCGCCTAATTTCTTCC 57.853 41.667 0.00 0.00 0.00 3.46
273 274 8.404765 ACTTAGTAGTAGTCGCCTAATTTCTTC 58.595 37.037 0.00 0.00 31.21 2.87
274 275 8.291191 ACTTAGTAGTAGTCGCCTAATTTCTT 57.709 34.615 0.00 0.00 31.21 2.52
275 276 7.878547 ACTTAGTAGTAGTCGCCTAATTTCT 57.121 36.000 0.00 0.00 31.21 2.52
276 277 8.923609 AAACTTAGTAGTAGTCGCCTAATTTC 57.076 34.615 0.00 0.00 33.17 2.17
279 280 8.134261 GCTAAAACTTAGTAGTAGTCGCCTAAT 58.866 37.037 0.00 0.00 33.17 1.73
280 281 7.121168 TGCTAAAACTTAGTAGTAGTCGCCTAA 59.879 37.037 0.00 0.00 33.17 2.69
281 282 6.599244 TGCTAAAACTTAGTAGTAGTCGCCTA 59.401 38.462 0.00 0.00 33.17 3.93
282 283 5.416952 TGCTAAAACTTAGTAGTAGTCGCCT 59.583 40.000 0.00 0.00 33.17 5.52
283 284 5.514559 GTGCTAAAACTTAGTAGTAGTCGCC 59.485 44.000 0.00 0.00 33.17 5.54
284 285 5.226772 CGTGCTAAAACTTAGTAGTAGTCGC 59.773 44.000 0.00 0.00 33.17 5.19
285 286 5.226772 GCGTGCTAAAACTTAGTAGTAGTCG 59.773 44.000 12.37 12.37 33.17 4.18
286 287 5.514559 GGCGTGCTAAAACTTAGTAGTAGTC 59.485 44.000 0.00 0.00 33.17 2.59
287 288 5.184671 AGGCGTGCTAAAACTTAGTAGTAGT 59.815 40.000 0.00 0.00 33.17 2.73
288 289 5.648572 AGGCGTGCTAAAACTTAGTAGTAG 58.351 41.667 0.00 0.00 33.17 2.57
289 290 5.649782 AGGCGTGCTAAAACTTAGTAGTA 57.350 39.130 0.00 0.00 33.17 1.82
290 291 4.532314 AGGCGTGCTAAAACTTAGTAGT 57.468 40.909 0.00 0.00 35.68 2.73
291 292 5.857822 AAAGGCGTGCTAAAACTTAGTAG 57.142 39.130 0.00 0.00 0.00 2.57
292 293 6.260493 TGAAAAAGGCGTGCTAAAACTTAGTA 59.740 34.615 0.00 0.00 0.00 1.82
293 294 5.066764 TGAAAAAGGCGTGCTAAAACTTAGT 59.933 36.000 0.00 0.00 0.00 2.24
294 295 5.398416 GTGAAAAAGGCGTGCTAAAACTTAG 59.602 40.000 0.00 0.00 0.00 2.18
295 296 5.066764 AGTGAAAAAGGCGTGCTAAAACTTA 59.933 36.000 0.00 0.00 0.00 2.24
296 297 4.109766 GTGAAAAAGGCGTGCTAAAACTT 58.890 39.130 0.00 0.00 0.00 2.66
297 298 3.380320 AGTGAAAAAGGCGTGCTAAAACT 59.620 39.130 0.00 0.00 0.00 2.66
298 299 3.702330 AGTGAAAAAGGCGTGCTAAAAC 58.298 40.909 0.00 0.00 0.00 2.43
299 300 5.502153 TTAGTGAAAAAGGCGTGCTAAAA 57.498 34.783 0.00 0.00 0.00 1.52
300 301 5.457140 CATTAGTGAAAAAGGCGTGCTAAA 58.543 37.500 0.00 0.00 0.00 1.85
301 302 4.083003 CCATTAGTGAAAAAGGCGTGCTAA 60.083 41.667 0.00 0.00 0.00 3.09
302 303 3.438781 CCATTAGTGAAAAAGGCGTGCTA 59.561 43.478 0.00 0.00 0.00 3.49
303 304 2.228822 CCATTAGTGAAAAAGGCGTGCT 59.771 45.455 0.00 0.00 0.00 4.40
304 305 2.227865 TCCATTAGTGAAAAAGGCGTGC 59.772 45.455 0.00 0.00 0.00 5.34
305 306 4.701956 ATCCATTAGTGAAAAAGGCGTG 57.298 40.909 0.00 0.00 0.00 5.34
306 307 5.722021 AAATCCATTAGTGAAAAAGGCGT 57.278 34.783 0.00 0.00 0.00 5.68
307 308 8.594687 CAATTAAATCCATTAGTGAAAAAGGCG 58.405 33.333 0.00 0.00 0.00 5.52
308 309 9.435688 ACAATTAAATCCATTAGTGAAAAAGGC 57.564 29.630 0.00 0.00 0.00 4.35
361 362 9.396022 GGTCCAATTTCATCTCTTTAATCACTA 57.604 33.333 0.00 0.00 0.00 2.74
362 363 7.890127 TGGTCCAATTTCATCTCTTTAATCACT 59.110 33.333 0.00 0.00 0.00 3.41
363 364 8.055279 TGGTCCAATTTCATCTCTTTAATCAC 57.945 34.615 0.00 0.00 0.00 3.06
364 365 8.108999 TCTGGTCCAATTTCATCTCTTTAATCA 58.891 33.333 0.00 0.00 0.00 2.57
365 366 8.511604 TCTGGTCCAATTTCATCTCTTTAATC 57.488 34.615 0.00 0.00 0.00 1.75
367 368 8.108999 TGATCTGGTCCAATTTCATCTCTTTAA 58.891 33.333 0.00 0.00 0.00 1.52
371 372 5.682659 CTGATCTGGTCCAATTTCATCTCT 58.317 41.667 0.00 0.00 0.00 3.10
374 375 3.949754 TGCTGATCTGGTCCAATTTCATC 59.050 43.478 1.46 0.00 0.00 2.92
376 377 3.084039 GTGCTGATCTGGTCCAATTTCA 58.916 45.455 1.46 0.00 0.00 2.69
377 378 3.084039 TGTGCTGATCTGGTCCAATTTC 58.916 45.455 1.46 0.00 0.00 2.17
547 569 9.658475 GCTAGCTACTCGATCTATATGTATTTG 57.342 37.037 7.70 0.00 0.00 2.32
556 578 5.257262 TGAATGGCTAGCTACTCGATCTAT 58.743 41.667 15.72 0.00 0.00 1.98
557 579 4.652822 TGAATGGCTAGCTACTCGATCTA 58.347 43.478 15.72 0.00 0.00 1.98
1260 1378 2.742372 GGCGCCGACATGTTGACT 60.742 61.111 12.58 0.00 0.00 3.41
1356 1474 0.743345 GGATGTAATATCCCGCGGGC 60.743 60.000 39.89 24.19 34.68 6.13
1357 1475 3.453559 GGATGTAATATCCCGCGGG 57.546 57.895 39.13 39.13 32.09 6.13
1533 1651 3.621805 TCGTCGAAGGCCTTGGCA 61.622 61.111 26.25 9.13 0.00 4.92
1553 1671 4.982295 CGAAGAATGCGTACCTGATAATGA 59.018 41.667 0.00 0.00 27.27 2.57
1581 1715 2.357760 TAGTGGCGCCGTGGTTTC 60.358 61.111 23.90 5.83 0.00 2.78
1603 1737 2.679059 GCAGCCATCAGTGAGCTTTAGA 60.679 50.000 4.21 0.00 32.03 2.10
1604 1738 1.669779 GCAGCCATCAGTGAGCTTTAG 59.330 52.381 4.21 0.00 32.03 1.85
1606 1740 0.964358 GGCAGCCATCAGTGAGCTTT 60.964 55.000 6.55 0.00 32.03 3.51
1634 1806 3.056328 GACGCTTTCCCCTGCACC 61.056 66.667 0.00 0.00 0.00 5.01
1649 1825 2.202570 CCACGGTCGTCATCGGAC 60.203 66.667 0.00 0.00 40.77 4.79
1916 2103 1.302033 AGGTTGTTCTCCAGCTGCG 60.302 57.895 8.66 1.56 0.00 5.18
2163 2350 0.316204 CCGGTTCGTCTAGTTGGTGT 59.684 55.000 0.00 0.00 0.00 4.16
2302 2490 0.107214 CCGCTTACATGTGGGTCCAT 60.107 55.000 9.11 0.00 34.20 3.41
2381 2569 2.092699 GGAGGAACATGAGAGAAAGGGG 60.093 54.545 0.00 0.00 0.00 4.79
2503 2691 4.719369 GCAACGCCGACGAGGACT 62.719 66.667 0.00 0.00 45.00 3.85
2505 2693 4.717629 CTGCAACGCCGACGAGGA 62.718 66.667 0.00 0.00 45.00 3.71
2525 2713 0.909610 AAAGGAGAGATGCACCGGGA 60.910 55.000 6.32 0.00 31.80 5.14
2605 2793 2.025321 GCAGAAACCCTAGGAATCCCAA 60.025 50.000 11.48 0.00 33.88 4.12
2632 2820 1.522668 CGAGGAAGTTGATGCCACAA 58.477 50.000 0.00 0.00 0.00 3.33
2844 6728 0.741574 GCGACGAGACAGAGAGAGGA 60.742 60.000 0.00 0.00 0.00 3.71
2866 6826 1.513158 CTAGACACCACCTCGCCAG 59.487 63.158 0.00 0.00 0.00 4.85
2958 6931 1.134848 CAAAAACCACCACCACCACTG 60.135 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.