Multiple sequence alignment - TraesCS5B01G036400

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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 TraesCS5B01G036400 chr5B 100.000 2453 0 0 1 2453 40556506 40558958 0.000000e+00 4530
1 TraesCS5B01G036400 chr5B 84.058 1035 160 5 358 1390 40458465 40459496 0.000000e+00 992
2 TraesCS5B01G036400 chr5B 80.071 1119 191 17 358 1454 40775556 40776664 0.000000e+00 802
3 TraesCS5B01G036400 chr5B 80.037 1092 201 8 366 1444 57498694 57497607 0.000000e+00 793
4 TraesCS5B01G036400 chr5B 85.833 720 64 13 1767 2453 543224735 543225449 0.000000e+00 730
5 TraesCS5B01G036400 chr5B 93.220 118 4 2 1 118 693064098 693063985 1.170000e-38 171
6 TraesCS5B01G036400 chr5D 90.133 1581 141 12 180 1753 43091911 43093483 0.000000e+00 2041
7 TraesCS5B01G036400 chr5D 83.602 1116 169 8 342 1454 42809107 42808003 0.000000e+00 1035
8 TraesCS5B01G036400 chr5D 81.900 1105 183 8 366 1454 43135051 43136154 0.000000e+00 917
9 TraesCS5B01G036400 chr5D 80.857 1097 183 20 366 1444 54919559 54918472 0.000000e+00 837
10 TraesCS5B01G036400 chr5A 83.363 1106 156 16 365 1453 32992592 32993686 0.000000e+00 998
11 TraesCS5B01G036400 chr5A 82.176 1094 174 13 366 1444 43270320 43269233 0.000000e+00 920
12 TraesCS5B01G036400 chr5A 81.627 1094 180 8 366 1444 42735776 42734689 0.000000e+00 887
13 TraesCS5B01G036400 chr5A 80.675 1097 192 9 359 1454 32998988 33000065 0.000000e+00 833
14 TraesCS5B01G036400 chr5A 88.288 111 12 1 1 111 480917415 480917524 5.500000e-27 132
15 TraesCS5B01G036400 chr5A 88.288 111 12 1 1 111 481019222 481019331 5.500000e-27 132
16 TraesCS5B01G036400 chr5A 85.470 117 16 1 1 117 129788908 129788793 1.190000e-23 121
17 TraesCS5B01G036400 chr5A 85.965 114 15 1 1 114 152466269 152466381 1.190000e-23 121
18 TraesCS5B01G036400 chr6B 87.660 705 71 9 1760 2453 512825823 512825124 0.000000e+00 806
19 TraesCS5B01G036400 chr6B 85.655 725 65 13 1762 2453 76861760 76862478 0.000000e+00 726
20 TraesCS5B01G036400 chr6B 84.743 721 63 17 1766 2453 479295677 479294971 0.000000e+00 678
21 TraesCS5B01G036400 chr6B 91.371 394 30 1 2060 2453 641221521 641221132 9.980000e-149 536
22 TraesCS5B01G036400 chr4B 85.714 721 65 9 1766 2453 646377730 646378445 0.000000e+00 726
23 TraesCS5B01G036400 chr4B 91.117 394 30 2 2060 2453 672202159 672202547 1.670000e-146 529
24 TraesCS5B01G036400 chr2B 85.535 719 65 14 1768 2453 144599581 144598869 0.000000e+00 715
25 TraesCS5B01G036400 chr2B 84.225 729 73 16 1758 2453 86679091 86678372 0.000000e+00 671
26 TraesCS5B01G036400 chr2B 83.911 721 74 14 1762 2449 65865028 65864317 0.000000e+00 651
27 TraesCS5B01G036400 chr2B 82.370 692 60 12 1766 2424 419294454 419295116 1.660000e-151 545
28 TraesCS5B01G036400 chr3D 85.429 700 75 17 1769 2453 409033340 409032653 0.000000e+00 702
29 TraesCS5B01G036400 chr3B 84.765 722 68 15 1766 2453 534528611 534527898 0.000000e+00 686
30 TraesCS5B01G036400 chr6D 91.117 394 29 3 2060 2453 137121776 137122163 1.670000e-146 529
31 TraesCS5B01G036400 chr4D 91.117 394 28 4 2060 2453 32770829 32771215 6.010000e-146 527
32 TraesCS5B01G036400 chrUn 98.198 111 2 0 1 111 49991605 49991715 6.920000e-46 195
33 TraesCS5B01G036400 chr1D 92.793 111 7 1 1 111 328861342 328861451 2.520000e-35 159
34 TraesCS5B01G036400 chr2A 85.965 114 15 1 1 114 182680411 182680299 1.190000e-23 121
35 TraesCS5B01G036400 chr1A 86.486 111 14 1 1 111 56225832 56225941 1.190000e-23 121


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 TraesCS5B01G036400 chr5B 40556506 40558958 2452 False 4530 4530 100.000 1 2453 1 chr5B.!!$F2 2452
1 TraesCS5B01G036400 chr5B 40458465 40459496 1031 False 992 992 84.058 358 1390 1 chr5B.!!$F1 1032
2 TraesCS5B01G036400 chr5B 40775556 40776664 1108 False 802 802 80.071 358 1454 1 chr5B.!!$F3 1096
3 TraesCS5B01G036400 chr5B 57497607 57498694 1087 True 793 793 80.037 366 1444 1 chr5B.!!$R1 1078
4 TraesCS5B01G036400 chr5B 543224735 543225449 714 False 730 730 85.833 1767 2453 1 chr5B.!!$F4 686
5 TraesCS5B01G036400 chr5D 43091911 43093483 1572 False 2041 2041 90.133 180 1753 1 chr5D.!!$F1 1573
6 TraesCS5B01G036400 chr5D 42808003 42809107 1104 True 1035 1035 83.602 342 1454 1 chr5D.!!$R1 1112
7 TraesCS5B01G036400 chr5D 43135051 43136154 1103 False 917 917 81.900 366 1454 1 chr5D.!!$F2 1088
8 TraesCS5B01G036400 chr5D 54918472 54919559 1087 True 837 837 80.857 366 1444 1 chr5D.!!$R2 1078
9 TraesCS5B01G036400 chr5A 32992592 32993686 1094 False 998 998 83.363 365 1453 1 chr5A.!!$F1 1088
10 TraesCS5B01G036400 chr5A 43269233 43270320 1087 True 920 920 82.176 366 1444 1 chr5A.!!$R2 1078
11 TraesCS5B01G036400 chr5A 42734689 42735776 1087 True 887 887 81.627 366 1444 1 chr5A.!!$R1 1078
12 TraesCS5B01G036400 chr5A 32998988 33000065 1077 False 833 833 80.675 359 1454 1 chr5A.!!$F2 1095
13 TraesCS5B01G036400 chr6B 512825124 512825823 699 True 806 806 87.660 1760 2453 1 chr6B.!!$R2 693
14 TraesCS5B01G036400 chr6B 76861760 76862478 718 False 726 726 85.655 1762 2453 1 chr6B.!!$F1 691
15 TraesCS5B01G036400 chr6B 479294971 479295677 706 True 678 678 84.743 1766 2453 1 chr6B.!!$R1 687
16 TraesCS5B01G036400 chr4B 646377730 646378445 715 False 726 726 85.714 1766 2453 1 chr4B.!!$F1 687
17 TraesCS5B01G036400 chr2B 144598869 144599581 712 True 715 715 85.535 1768 2453 1 chr2B.!!$R3 685
18 TraesCS5B01G036400 chr2B 86678372 86679091 719 True 671 671 84.225 1758 2453 1 chr2B.!!$R2 695
19 TraesCS5B01G036400 chr2B 65864317 65865028 711 True 651 651 83.911 1762 2449 1 chr2B.!!$R1 687
20 TraesCS5B01G036400 chr2B 419294454 419295116 662 False 545 545 82.370 1766 2424 1 chr2B.!!$F1 658
21 TraesCS5B01G036400 chr3D 409032653 409033340 687 True 702 702 85.429 1769 2453 1 chr3D.!!$R1 684
22 TraesCS5B01G036400 chr3B 534527898 534528611 713 True 686 686 84.765 1766 2453 1 chr3B.!!$R1 687

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
52 53 0.035152 GGCATGTGTGATGAGGTGGA 60.035 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 1955 0.036388 GGACGAACTCTCCAATGCCA 60.036 55.0 0.0 0.0 0.0 4.92 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 7.874940 CATGTGAAGAAAAATAAGAGGTGACA 58.125 34.615 0.00 0.00 0.00 3.58
26 27 8.517878 CATGTGAAGAAAAATAAGAGGTGACAT 58.482 33.333 0.00 0.00 0.00 3.06
27 28 7.874940 TGTGAAGAAAAATAAGAGGTGACATG 58.125 34.615 0.00 0.00 0.00 3.21
28 29 7.502226 TGTGAAGAAAAATAAGAGGTGACATGT 59.498 33.333 0.00 0.00 0.00 3.21
29 30 7.805071 GTGAAGAAAAATAAGAGGTGACATGTG 59.195 37.037 1.15 0.00 0.00 3.21
30 31 7.502226 TGAAGAAAAATAAGAGGTGACATGTGT 59.498 33.333 1.15 0.00 0.00 3.72
31 32 7.206981 AGAAAAATAAGAGGTGACATGTGTG 57.793 36.000 1.15 0.00 0.00 3.82
32 33 5.964958 AAAATAAGAGGTGACATGTGTGG 57.035 39.130 1.15 0.00 0.00 4.17
33 34 3.634397 ATAAGAGGTGACATGTGTGGG 57.366 47.619 1.15 0.00 0.00 4.61
34 35 0.401738 AAGAGGTGACATGTGTGGGG 59.598 55.000 1.15 0.00 0.00 4.96
35 36 1.675641 GAGGTGACATGTGTGGGGC 60.676 63.158 1.15 0.00 0.00 5.80
36 37 2.115052 GGTGACATGTGTGGGGCA 59.885 61.111 1.15 0.00 0.00 5.36
37 38 1.304381 GGTGACATGTGTGGGGCAT 60.304 57.895 1.15 0.00 0.00 4.40
38 39 1.597797 GGTGACATGTGTGGGGCATG 61.598 60.000 1.15 4.02 46.51 4.06
41 42 4.100479 CATGTGTGGGGCATGTGT 57.900 55.556 0.00 0.00 38.96 3.72
42 43 1.587568 CATGTGTGGGGCATGTGTG 59.412 57.895 0.00 0.00 38.96 3.82
43 44 0.894642 CATGTGTGGGGCATGTGTGA 60.895 55.000 0.00 0.00 38.96 3.58
44 45 0.040058 ATGTGTGGGGCATGTGTGAT 59.960 50.000 0.00 0.00 0.00 3.06
45 46 0.894642 TGTGTGGGGCATGTGTGATG 60.895 55.000 0.00 0.00 0.00 3.07
46 47 0.608856 GTGTGGGGCATGTGTGATGA 60.609 55.000 0.00 0.00 0.00 2.92
47 48 0.322726 TGTGGGGCATGTGTGATGAG 60.323 55.000 0.00 0.00 0.00 2.90
48 49 1.033746 GTGGGGCATGTGTGATGAGG 61.034 60.000 0.00 0.00 0.00 3.86
49 50 1.304282 GGGGCATGTGTGATGAGGT 59.696 57.895 0.00 0.00 0.00 3.85
50 51 1.033746 GGGGCATGTGTGATGAGGTG 61.034 60.000 0.00 0.00 0.00 4.00
51 52 1.033746 GGGCATGTGTGATGAGGTGG 61.034 60.000 0.00 0.00 0.00 4.61
52 53 0.035152 GGCATGTGTGATGAGGTGGA 60.035 55.000 0.00 0.00 0.00 4.02
53 54 1.409241 GGCATGTGTGATGAGGTGGAT 60.409 52.381 0.00 0.00 0.00 3.41
54 55 2.158769 GGCATGTGTGATGAGGTGGATA 60.159 50.000 0.00 0.00 0.00 2.59
55 56 3.136763 GCATGTGTGATGAGGTGGATAG 58.863 50.000 0.00 0.00 0.00 2.08
56 57 3.736720 CATGTGTGATGAGGTGGATAGG 58.263 50.000 0.00 0.00 0.00 2.57
57 58 2.118679 TGTGTGATGAGGTGGATAGGG 58.881 52.381 0.00 0.00 0.00 3.53
58 59 2.119495 GTGTGATGAGGTGGATAGGGT 58.881 52.381 0.00 0.00 0.00 4.34
59 60 2.118679 TGTGATGAGGTGGATAGGGTG 58.881 52.381 0.00 0.00 0.00 4.61
60 61 1.131638 TGATGAGGTGGATAGGGTGC 58.868 55.000 0.00 0.00 0.00 5.01
61 62 1.131638 GATGAGGTGGATAGGGTGCA 58.868 55.000 0.00 0.00 0.00 4.57
62 63 1.701847 GATGAGGTGGATAGGGTGCAT 59.298 52.381 0.00 0.00 0.00 3.96
63 64 0.839277 TGAGGTGGATAGGGTGCATG 59.161 55.000 0.00 0.00 0.00 4.06
64 65 0.839946 GAGGTGGATAGGGTGCATGT 59.160 55.000 0.00 0.00 0.00 3.21
65 66 0.839946 AGGTGGATAGGGTGCATGTC 59.160 55.000 0.00 0.00 0.00 3.06
66 67 0.546122 GGTGGATAGGGTGCATGTCA 59.454 55.000 0.00 0.00 0.00 3.58
67 68 1.064758 GGTGGATAGGGTGCATGTCAA 60.065 52.381 0.00 0.00 0.00 3.18
68 69 2.292267 GTGGATAGGGTGCATGTCAAG 58.708 52.381 0.00 0.00 0.00 3.02
69 70 2.092968 GTGGATAGGGTGCATGTCAAGA 60.093 50.000 0.00 0.00 0.00 3.02
70 71 2.779430 TGGATAGGGTGCATGTCAAGAT 59.221 45.455 0.00 0.00 0.00 2.40
71 72 3.973305 TGGATAGGGTGCATGTCAAGATA 59.027 43.478 0.00 0.00 0.00 1.98
72 73 4.411869 TGGATAGGGTGCATGTCAAGATAA 59.588 41.667 0.00 0.00 0.00 1.75
73 74 5.073554 TGGATAGGGTGCATGTCAAGATAAT 59.926 40.000 0.00 0.00 0.00 1.28
74 75 6.006449 GGATAGGGTGCATGTCAAGATAATT 58.994 40.000 0.00 0.00 0.00 1.40
75 76 6.072286 GGATAGGGTGCATGTCAAGATAATTG 60.072 42.308 0.00 0.00 0.00 2.32
76 77 4.858850 AGGGTGCATGTCAAGATAATTGA 58.141 39.130 0.00 0.00 0.00 2.57
77 78 4.885907 AGGGTGCATGTCAAGATAATTGAG 59.114 41.667 0.00 0.00 0.00 3.02
78 79 4.883585 GGGTGCATGTCAAGATAATTGAGA 59.116 41.667 0.00 0.00 0.00 3.27
79 80 5.533903 GGGTGCATGTCAAGATAATTGAGAT 59.466 40.000 0.00 0.00 33.39 2.75
80 81 6.712095 GGGTGCATGTCAAGATAATTGAGATA 59.288 38.462 0.00 0.00 32.15 1.98
81 82 7.094890 GGGTGCATGTCAAGATAATTGAGATAG 60.095 40.741 0.00 0.00 32.15 2.08
82 83 7.443575 GGTGCATGTCAAGATAATTGAGATAGT 59.556 37.037 0.00 0.00 32.15 2.12
83 84 8.281194 GTGCATGTCAAGATAATTGAGATAGTG 58.719 37.037 0.00 0.00 32.15 2.74
84 85 7.443272 TGCATGTCAAGATAATTGAGATAGTGG 59.557 37.037 0.00 0.00 32.15 4.00
85 86 7.094890 GCATGTCAAGATAATTGAGATAGTGGG 60.095 40.741 0.00 0.00 32.15 4.61
86 87 6.830912 TGTCAAGATAATTGAGATAGTGGGG 58.169 40.000 0.00 0.00 0.00 4.96
87 88 6.615316 TGTCAAGATAATTGAGATAGTGGGGA 59.385 38.462 0.00 0.00 0.00 4.81
88 89 7.293299 TGTCAAGATAATTGAGATAGTGGGGAT 59.707 37.037 0.00 0.00 0.00 3.85
89 90 7.605691 GTCAAGATAATTGAGATAGTGGGGATG 59.394 40.741 0.00 0.00 0.00 3.51
90 91 7.513781 TCAAGATAATTGAGATAGTGGGGATGA 59.486 37.037 0.00 0.00 0.00 2.92
91 92 7.878621 AGATAATTGAGATAGTGGGGATGAA 57.121 36.000 0.00 0.00 0.00 2.57
92 93 7.684529 AGATAATTGAGATAGTGGGGATGAAC 58.315 38.462 0.00 0.00 0.00 3.18
93 94 5.983333 AATTGAGATAGTGGGGATGAACT 57.017 39.130 0.00 0.00 0.00 3.01
94 95 5.983333 ATTGAGATAGTGGGGATGAACTT 57.017 39.130 0.00 0.00 0.00 2.66
95 96 5.359194 TTGAGATAGTGGGGATGAACTTC 57.641 43.478 0.00 0.00 0.00 3.01
96 97 4.624913 TGAGATAGTGGGGATGAACTTCT 58.375 43.478 0.00 0.00 0.00 2.85
97 98 5.032846 TGAGATAGTGGGGATGAACTTCTT 58.967 41.667 0.00 0.00 0.00 2.52
98 99 5.488919 TGAGATAGTGGGGATGAACTTCTTT 59.511 40.000 0.00 0.00 0.00 2.52
99 100 6.672218 TGAGATAGTGGGGATGAACTTCTTTA 59.328 38.462 0.00 0.00 0.00 1.85
100 101 7.130681 AGATAGTGGGGATGAACTTCTTTAG 57.869 40.000 0.00 0.00 0.00 1.85
101 102 6.674419 AGATAGTGGGGATGAACTTCTTTAGT 59.326 38.462 0.00 0.00 39.32 2.24
102 103 7.844779 AGATAGTGGGGATGAACTTCTTTAGTA 59.155 37.037 0.00 0.00 35.54 1.82
103 104 6.893020 AGTGGGGATGAACTTCTTTAGTAT 57.107 37.500 0.00 0.00 35.54 2.12
104 105 7.989947 AGTGGGGATGAACTTCTTTAGTATA 57.010 36.000 0.00 0.00 35.54 1.47
105 106 8.568617 AGTGGGGATGAACTTCTTTAGTATAT 57.431 34.615 0.00 0.00 35.54 0.86
106 107 9.670442 AGTGGGGATGAACTTCTTTAGTATATA 57.330 33.333 0.00 0.00 35.54 0.86
107 108 9.930693 GTGGGGATGAACTTCTTTAGTATATAG 57.069 37.037 0.00 0.00 35.54 1.31
108 109 9.101325 TGGGGATGAACTTCTTTAGTATATAGG 57.899 37.037 0.00 0.00 35.54 2.57
109 110 9.322769 GGGGATGAACTTCTTTAGTATATAGGA 57.677 37.037 0.00 0.00 35.54 2.94
132 133 8.198109 AGGATATGTATACGATGCTTTGTATCC 58.802 37.037 14.18 10.94 34.76 2.59
133 134 7.979537 GGATATGTATACGATGCTTTGTATCCA 59.020 37.037 14.18 10.68 35.87 3.41
134 135 8.932945 ATATGTATACGATGCTTTGTATCCAG 57.067 34.615 14.18 0.00 34.76 3.86
135 136 6.399639 TGTATACGATGCTTTGTATCCAGA 57.600 37.500 14.18 0.00 34.76 3.86
136 137 6.447162 TGTATACGATGCTTTGTATCCAGAG 58.553 40.000 14.18 0.00 34.76 3.35
137 138 3.895232 ACGATGCTTTGTATCCAGAGT 57.105 42.857 0.00 0.00 0.00 3.24
138 139 4.207891 ACGATGCTTTGTATCCAGAGTT 57.792 40.909 0.00 0.00 0.00 3.01
139 140 4.184629 ACGATGCTTTGTATCCAGAGTTC 58.815 43.478 0.00 0.00 0.00 3.01
140 141 3.243877 CGATGCTTTGTATCCAGAGTTCG 59.756 47.826 0.00 0.00 30.52 3.95
141 142 3.678056 TGCTTTGTATCCAGAGTTCGT 57.322 42.857 0.00 0.00 0.00 3.85
142 143 3.325870 TGCTTTGTATCCAGAGTTCGTG 58.674 45.455 0.00 0.00 0.00 4.35
143 144 3.006430 TGCTTTGTATCCAGAGTTCGTGA 59.994 43.478 0.00 0.00 0.00 4.35
144 145 3.994392 GCTTTGTATCCAGAGTTCGTGAA 59.006 43.478 0.00 0.00 0.00 3.18
145 146 4.451096 GCTTTGTATCCAGAGTTCGTGAAA 59.549 41.667 0.00 0.00 0.00 2.69
146 147 5.389935 GCTTTGTATCCAGAGTTCGTGAAAG 60.390 44.000 0.00 0.00 0.00 2.62
147 148 4.188247 TGTATCCAGAGTTCGTGAAAGG 57.812 45.455 0.00 0.00 0.00 3.11
148 149 3.830178 TGTATCCAGAGTTCGTGAAAGGA 59.170 43.478 0.00 0.00 0.00 3.36
149 150 4.466370 TGTATCCAGAGTTCGTGAAAGGAT 59.534 41.667 0.00 0.00 38.00 3.24
150 151 3.594603 TCCAGAGTTCGTGAAAGGATC 57.405 47.619 0.00 0.00 0.00 3.36
151 152 2.094700 TCCAGAGTTCGTGAAAGGATCG 60.095 50.000 0.00 0.00 0.00 3.69
152 153 2.094700 CCAGAGTTCGTGAAAGGATCGA 60.095 50.000 0.00 0.00 0.00 3.59
153 154 3.429547 CCAGAGTTCGTGAAAGGATCGAT 60.430 47.826 0.00 0.00 33.72 3.59
154 155 3.794028 CAGAGTTCGTGAAAGGATCGATC 59.206 47.826 17.36 17.36 33.72 3.69
155 156 3.444034 AGAGTTCGTGAAAGGATCGATCA 59.556 43.478 25.93 4.54 33.72 2.92
156 157 4.098654 AGAGTTCGTGAAAGGATCGATCAT 59.901 41.667 25.93 17.57 33.72 2.45
157 158 4.363999 AGTTCGTGAAAGGATCGATCATC 58.636 43.478 25.93 19.50 33.72 2.92
158 159 4.098654 AGTTCGTGAAAGGATCGATCATCT 59.901 41.667 25.93 12.56 33.72 2.90
159 160 4.655762 TCGTGAAAGGATCGATCATCTT 57.344 40.909 25.93 17.47 0.00 2.40
160 161 4.363138 TCGTGAAAGGATCGATCATCTTG 58.637 43.478 25.93 15.55 0.00 3.02
161 162 4.115516 CGTGAAAGGATCGATCATCTTGT 58.884 43.478 25.93 11.59 0.00 3.16
162 163 4.026228 CGTGAAAGGATCGATCATCTTGTG 60.026 45.833 25.93 7.36 0.00 3.33
163 164 5.111989 GTGAAAGGATCGATCATCTTGTGA 58.888 41.667 25.93 6.88 42.06 3.58
172 173 2.022195 ATCATCTTGTGATGGCTGTGC 58.978 47.619 6.24 0.00 45.76 4.57
173 174 1.170442 CATCTTGTGATGGCTGTGCA 58.830 50.000 0.00 0.00 44.63 4.57
174 175 1.542472 CATCTTGTGATGGCTGTGCAA 59.458 47.619 0.00 0.00 44.63 4.08
175 176 1.241165 TCTTGTGATGGCTGTGCAAG 58.759 50.000 0.00 0.00 38.20 4.01
176 177 0.242825 CTTGTGATGGCTGTGCAAGG 59.757 55.000 0.00 0.00 34.58 3.61
177 178 1.180456 TTGTGATGGCTGTGCAAGGG 61.180 55.000 0.00 0.00 0.00 3.95
178 179 2.677524 TGATGGCTGTGCAAGGGC 60.678 61.111 6.76 6.76 41.68 5.19
214 215 1.798223 TGAAGAACTGCGGTTTCATCG 59.202 47.619 13.23 0.00 35.58 3.84
247 248 3.490759 GTCGCCGTCGTCCTCGTA 61.491 66.667 0.00 0.00 38.33 3.43
248 249 2.741985 TCGCCGTCGTCCTCGTAA 60.742 61.111 0.00 0.00 38.33 3.18
249 250 2.108514 TCGCCGTCGTCCTCGTAAT 61.109 57.895 0.00 0.00 38.33 1.89
277 278 2.344203 CCGGAAGACCTCAGCGAGT 61.344 63.158 0.00 0.00 0.00 4.18
282 283 1.173444 AAGACCTCAGCGAGTCACGT 61.173 55.000 0.00 0.00 44.60 4.49
290 291 1.173444 AGCGAGTCACGTCCAGAAGT 61.173 55.000 0.00 0.00 44.60 3.01
291 292 0.729816 GCGAGTCACGTCCAGAAGTC 60.730 60.000 0.00 0.00 44.60 3.01
298 299 1.442184 CGTCCAGAAGTCACGTCCG 60.442 63.158 0.00 0.00 0.00 4.79
310 311 0.528901 CACGTCCGAGTCCAACACAA 60.529 55.000 0.00 0.00 0.00 3.33
361 362 4.074259 CACAATCCAAGTCCAGTCAATGA 58.926 43.478 0.00 0.00 0.00 2.57
381 382 1.009389 CAGAGCGTCCGAAAGTCACC 61.009 60.000 0.00 0.00 0.00 4.02
462 463 3.864789 AGAACCAAGGAGCTTCTCAAA 57.135 42.857 0.00 0.00 31.08 2.69
500 501 2.100916 CGTCTATCCCTTTCATGGTCGT 59.899 50.000 0.00 0.00 0.00 4.34
557 588 0.396435 TACAAGGCACCTGGTCACAG 59.604 55.000 0.00 0.00 44.51 3.66
681 715 8.169977 ACATCAAAACTGTGACAGAACATATT 57.830 30.769 20.97 0.00 35.18 1.28
686 720 7.581213 AAACTGTGACAGAACATATTTTCCA 57.419 32.000 20.97 0.00 35.18 3.53
705 739 3.565063 TCCAAAGCAAAGGTTACGGTTAC 59.435 43.478 0.00 0.00 0.00 2.50
755 789 2.037901 TCTGGAGAGATCAGCACATCC 58.962 52.381 0.00 0.00 32.63 3.51
766 800 0.254178 AGCACATCCAAGAGGCGATT 59.746 50.000 0.00 0.00 33.74 3.34
790 824 1.827344 TCAGAATCAGGTGCGATGTCT 59.173 47.619 0.00 0.00 0.00 3.41
821 855 0.763652 ATGATCCGCAGCCAAGAGAT 59.236 50.000 0.00 0.00 0.00 2.75
831 865 1.476891 AGCCAAGAGATGCATGCAAAG 59.523 47.619 26.68 10.55 0.00 2.77
909 943 0.654683 GCAATGATGGAGCAGACGTC 59.345 55.000 7.70 7.70 0.00 4.34
911 945 1.931841 CAATGATGGAGCAGACGTCAG 59.068 52.381 19.50 11.47 37.30 3.51
920 954 1.950098 GCAGACGTCAGCTTTCGAGC 61.950 60.000 23.94 6.90 0.00 5.03
921 955 0.664466 CAGACGTCAGCTTTCGAGCA 60.664 55.000 19.50 0.00 37.25 4.26
926 960 0.601311 GTCAGCTTTCGAGCAGGTGT 60.601 55.000 19.57 0.00 40.12 4.16
933 967 0.888619 TTCGAGCAGGTGTCGAGATT 59.111 50.000 0.00 0.00 46.50 2.40
985 1019 2.204461 TCACCGGTCTTCAAGGCGA 61.204 57.895 2.59 0.00 0.00 5.54
1021 1055 0.618981 GAGGGGGAAAGTCGGTGATT 59.381 55.000 0.00 0.00 0.00 2.57
1023 1057 0.393944 GGGGGAAAGTCGGTGATTCC 60.394 60.000 0.00 0.00 41.53 3.01
1082 1116 5.178096 TCCTTGCTCCATTTCATCTACAA 57.822 39.130 0.00 0.00 0.00 2.41
1189 1235 0.453793 CGACATCGAGAGGCTGAAGT 59.546 55.000 0.00 0.00 43.02 3.01
1191 1237 2.672478 CGACATCGAGAGGCTGAAGTTT 60.672 50.000 0.00 0.00 43.02 2.66
1255 1301 3.181480 GGTTGCAACTAGTTTGGCTTTGA 60.181 43.478 27.64 0.00 35.51 2.69
1256 1302 4.501400 GGTTGCAACTAGTTTGGCTTTGAT 60.501 41.667 27.64 0.00 35.51 2.57
1263 1309 2.440409 AGTTTGGCTTTGATCGAGCAT 58.560 42.857 18.93 0.00 41.89 3.79
1322 1369 1.303309 CTTGCATCTCCGTCCAATCC 58.697 55.000 0.00 0.00 0.00 3.01
1340 1387 1.519455 CGGAGAGGGTGATCGCAAC 60.519 63.158 8.82 0.13 0.00 4.17
1344 1391 0.534412 AGAGGGTGATCGCAACTGAG 59.466 55.000 8.82 0.00 0.00 3.35
1456 1503 8.051535 GGGATATTATCAGGTCAATGTGATCAT 58.948 37.037 0.00 0.00 35.08 2.45
1491 1541 3.447586 TGGTATCTCTTTTGTAGCTCGCT 59.552 43.478 0.00 0.00 0.00 4.93
1492 1542 4.081642 TGGTATCTCTTTTGTAGCTCGCTT 60.082 41.667 0.00 0.00 0.00 4.68
1494 1544 2.069273 TCTCTTTTGTAGCTCGCTTGC 58.931 47.619 0.00 0.00 0.00 4.01
1502 1552 0.389817 TAGCTCGCTTGCGAATGTGT 60.390 50.000 18.28 4.71 38.13 3.72
1538 1588 9.686683 AAAGGTATCTATTTGTGCAAGTAGAAT 57.313 29.630 17.03 10.58 41.07 2.40
1543 1593 6.953101 TCTATTTGTGCAAGTAGAATGGGTA 58.047 36.000 12.64 0.00 36.91 3.69
1546 1596 5.895636 TTGTGCAAGTAGAATGGGTATTG 57.104 39.130 0.00 0.00 0.00 1.90
1556 1606 3.011708 AGAATGGGTATTGTTGGCTCCTT 59.988 43.478 0.00 0.00 0.00 3.36
1557 1607 2.507407 TGGGTATTGTTGGCTCCTTC 57.493 50.000 0.00 0.00 0.00 3.46
1564 1614 2.205022 TGTTGGCTCCTTCATTCTGG 57.795 50.000 0.00 0.00 0.00 3.86
1572 1622 3.192212 GCTCCTTCATTCTGGGTTTTCTG 59.808 47.826 0.00 0.00 0.00 3.02
1576 1626 5.945784 TCCTTCATTCTGGGTTTTCTGTATG 59.054 40.000 0.00 0.00 0.00 2.39
1586 1636 4.705023 GGGTTTTCTGTATGCCTTGTGTAT 59.295 41.667 0.00 0.00 0.00 2.29
1587 1637 5.883673 GGGTTTTCTGTATGCCTTGTGTATA 59.116 40.000 0.00 0.00 0.00 1.47
1592 1642 8.887036 TTTCTGTATGCCTTGTGTATATACAG 57.113 34.615 15.93 13.64 46.25 2.74
1597 1647 7.926018 TGTATGCCTTGTGTATATACAGTTCAG 59.074 37.037 15.93 9.10 36.78 3.02
1598 1648 6.538945 TGCCTTGTGTATATACAGTTCAGA 57.461 37.500 15.93 0.00 36.78 3.27
1601 1651 6.986817 GCCTTGTGTATATACAGTTCAGATGT 59.013 38.462 15.93 0.00 36.78 3.06
1609 1659 5.929697 ATACAGTTCAGATGTTGTGTGTG 57.070 39.130 0.00 0.00 32.02 3.82
1610 1660 3.872696 ACAGTTCAGATGTTGTGTGTGA 58.127 40.909 0.00 0.00 0.00 3.58
1611 1661 3.873361 ACAGTTCAGATGTTGTGTGTGAG 59.127 43.478 0.00 0.00 0.00 3.51
1614 1664 4.067896 GTTCAGATGTTGTGTGTGAGGAT 58.932 43.478 0.00 0.00 0.00 3.24
1617 1667 3.683340 CAGATGTTGTGTGTGAGGATGAG 59.317 47.826 0.00 0.00 0.00 2.90
1620 1670 2.700371 TGTTGTGTGTGAGGATGAGTCT 59.300 45.455 0.00 0.00 0.00 3.24
1655 1708 5.235850 TCTATCTTTGTTGTGGGCTTGTA 57.764 39.130 0.00 0.00 0.00 2.41
1667 1720 2.307392 TGGGCTTGTAGTTGCAATCCTA 59.693 45.455 0.59 0.00 35.60 2.94
1670 1723 4.757149 GGGCTTGTAGTTGCAATCCTATAG 59.243 45.833 0.59 4.03 35.60 1.31
1678 1731 7.764443 TGTAGTTGCAATCCTATAGTTGTTCTC 59.236 37.037 0.59 0.00 0.00 2.87
1695 1748 8.265764 AGTTGTTCTCTCCTACTTAAAACTTGT 58.734 33.333 0.00 0.00 0.00 3.16
1699 1752 9.194271 GTTCTCTCCTACTTAAAACTTGTGTAG 57.806 37.037 0.00 0.00 0.00 2.74
1714 1767 3.804036 TGTGTAGTTGTAAGTTGCTGCT 58.196 40.909 0.00 0.00 0.00 4.24
1715 1768 4.951254 TGTGTAGTTGTAAGTTGCTGCTA 58.049 39.130 0.00 0.00 0.00 3.49
1725 1778 2.406559 AGTTGCTGCTAGATGATCCCT 58.593 47.619 0.00 0.00 0.00 4.20
1738 1791 7.602265 GCTAGATGATCCCTATTTCTTCTGTTC 59.398 40.741 0.00 0.00 31.25 3.18
1740 1793 8.789767 AGATGATCCCTATTTCTTCTGTTCTA 57.210 34.615 0.00 0.00 0.00 2.10
1743 1796 8.609617 TGATCCCTATTTCTTCTGTTCTAGAA 57.390 34.615 0.00 0.00 43.01 2.10
1757 1810 9.793259 TTCTGTTCTAGAAGTGGAAAATGTATT 57.207 29.630 5.12 0.00 40.43 1.89
1758 1811 9.793259 TCTGTTCTAGAAGTGGAAAATGTATTT 57.207 29.630 5.12 0.00 30.84 1.40
1843 1896 1.544691 ACCGTCTAGTCGAGTTTGCAT 59.455 47.619 11.05 0.00 0.00 3.96
1847 1900 4.265556 CCGTCTAGTCGAGTTTGCATAAAG 59.734 45.833 11.05 0.00 0.00 1.85
1865 1918 2.211250 AGCTTGACACATTGAGGCAT 57.789 45.000 0.00 0.00 0.00 4.40
1900 1955 2.995547 GGACGGGCCTGGTGTATT 59.004 61.111 18.00 0.00 0.00 1.89
1948 2008 1.070105 AGCACGCGGTTTTGGTAGA 59.930 52.632 12.47 0.00 0.00 2.59
1955 2015 2.352388 GCGGTTTTGGTAGATGTGCTA 58.648 47.619 0.00 0.00 0.00 3.49
1992 2052 0.747644 CTGTCCACACAGCCAACACA 60.748 55.000 0.00 0.00 43.77 3.72
2038 2111 0.250124 ATTTCGCCCACACGACTTGA 60.250 50.000 0.00 0.00 42.78 3.02
2077 2171 3.559655 GCGTACATGGCAACTATGATTCA 59.440 43.478 0.00 0.00 37.61 2.57
2107 2201 0.719465 GTAACTGCAGTTGCGCGTAT 59.281 50.000 36.50 14.83 45.83 3.06
2118 2212 2.972144 GCGCGTATGTGGCAACCAA 61.972 57.895 8.43 0.00 34.18 3.67
2123 2217 3.434637 GCGTATGTGGCAACCAAATAAG 58.565 45.455 5.63 5.63 35.69 1.73
2124 2218 3.127895 GCGTATGTGGCAACCAAATAAGA 59.872 43.478 12.29 0.00 35.69 2.10
2220 2314 4.069304 TGGCAACTACTGTTTGACCATAC 58.931 43.478 0.00 0.00 33.52 2.39
2333 2427 8.506437 CAAAACAGATAGAGTTGTCATGCTTTA 58.494 33.333 0.00 0.00 0.00 1.85
2390 2484 2.276732 CATCCCGGATGGCAACTAAT 57.723 50.000 18.55 0.00 36.51 1.73
2391 2485 2.586425 CATCCCGGATGGCAACTAATT 58.414 47.619 18.55 0.00 36.51 1.40
2392 2486 3.750371 CATCCCGGATGGCAACTAATTA 58.250 45.455 18.55 0.00 36.51 1.40
2393 2487 3.935818 TCCCGGATGGCAACTAATTAA 57.064 42.857 0.73 0.00 37.61 1.40
2397 2491 4.582656 CCCGGATGGCAACTAATTAAATCA 59.417 41.667 0.73 0.00 37.61 2.57
2425 2519 0.665298 CGGGAGTACCTAACGTAGCC 59.335 60.000 0.00 0.00 36.97 3.93
2441 2535 2.032528 CCGTGCCAGGATGTGTGT 59.967 61.111 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.874940 TGTCACCTCTTATTTTTCTTCACATG 58.125 34.615 0.00 0.00 0.00 3.21
1 2 8.517878 CATGTCACCTCTTATTTTTCTTCACAT 58.482 33.333 0.00 0.00 0.00 3.21
3 4 7.805071 CACATGTCACCTCTTATTTTTCTTCAC 59.195 37.037 0.00 0.00 0.00 3.18
7 8 6.207417 CCACACATGTCACCTCTTATTTTTCT 59.793 38.462 0.00 0.00 0.00 2.52
8 9 6.381801 CCACACATGTCACCTCTTATTTTTC 58.618 40.000 0.00 0.00 0.00 2.29
9 10 5.243730 CCCACACATGTCACCTCTTATTTTT 59.756 40.000 0.00 0.00 0.00 1.94
10 11 4.766891 CCCACACATGTCACCTCTTATTTT 59.233 41.667 0.00 0.00 0.00 1.82
11 12 4.335416 CCCACACATGTCACCTCTTATTT 58.665 43.478 0.00 0.00 0.00 1.40
12 13 3.308402 CCCCACACATGTCACCTCTTATT 60.308 47.826 0.00 0.00 0.00 1.40
13 14 2.239654 CCCCACACATGTCACCTCTTAT 59.760 50.000 0.00 0.00 0.00 1.73
14 15 1.628340 CCCCACACATGTCACCTCTTA 59.372 52.381 0.00 0.00 0.00 2.10
15 16 0.401738 CCCCACACATGTCACCTCTT 59.598 55.000 0.00 0.00 0.00 2.85
16 17 2.069776 CCCCACACATGTCACCTCT 58.930 57.895 0.00 0.00 0.00 3.69
17 18 1.675641 GCCCCACACATGTCACCTC 60.676 63.158 0.00 0.00 0.00 3.85
18 19 1.792757 ATGCCCCACACATGTCACCT 61.793 55.000 0.00 0.00 0.00 4.00
19 20 1.304381 ATGCCCCACACATGTCACC 60.304 57.895 0.00 0.00 0.00 4.02
20 21 1.885157 CATGCCCCACACATGTCAC 59.115 57.895 0.00 0.00 40.04 3.67
21 22 4.419502 CATGCCCCACACATGTCA 57.580 55.556 0.00 0.00 40.04 3.58
25 26 0.040058 ATCACACATGCCCCACACAT 59.960 50.000 0.00 0.00 0.00 3.21
26 27 0.894642 CATCACACATGCCCCACACA 60.895 55.000 0.00 0.00 0.00 3.72
27 28 0.608856 TCATCACACATGCCCCACAC 60.609 55.000 0.00 0.00 0.00 3.82
28 29 0.322726 CTCATCACACATGCCCCACA 60.323 55.000 0.00 0.00 0.00 4.17
29 30 1.033746 CCTCATCACACATGCCCCAC 61.034 60.000 0.00 0.00 0.00 4.61
30 31 1.303948 CCTCATCACACATGCCCCA 59.696 57.895 0.00 0.00 0.00 4.96
31 32 1.033746 CACCTCATCACACATGCCCC 61.034 60.000 0.00 0.00 0.00 5.80
32 33 1.033746 CCACCTCATCACACATGCCC 61.034 60.000 0.00 0.00 0.00 5.36
33 34 0.035152 TCCACCTCATCACACATGCC 60.035 55.000 0.00 0.00 0.00 4.40
34 35 2.048444 ATCCACCTCATCACACATGC 57.952 50.000 0.00 0.00 0.00 4.06
35 36 3.495629 CCCTATCCACCTCATCACACATG 60.496 52.174 0.00 0.00 0.00 3.21
36 37 2.707791 CCCTATCCACCTCATCACACAT 59.292 50.000 0.00 0.00 0.00 3.21
37 38 2.118679 CCCTATCCACCTCATCACACA 58.881 52.381 0.00 0.00 0.00 3.72
38 39 2.119495 ACCCTATCCACCTCATCACAC 58.881 52.381 0.00 0.00 0.00 3.82
39 40 2.118679 CACCCTATCCACCTCATCACA 58.881 52.381 0.00 0.00 0.00 3.58
40 41 1.202698 GCACCCTATCCACCTCATCAC 60.203 57.143 0.00 0.00 0.00 3.06
41 42 1.131638 GCACCCTATCCACCTCATCA 58.868 55.000 0.00 0.00 0.00 3.07
42 43 1.131638 TGCACCCTATCCACCTCATC 58.868 55.000 0.00 0.00 0.00 2.92
43 44 1.422781 CATGCACCCTATCCACCTCAT 59.577 52.381 0.00 0.00 0.00 2.90
44 45 0.839277 CATGCACCCTATCCACCTCA 59.161 55.000 0.00 0.00 0.00 3.86
45 46 0.839946 ACATGCACCCTATCCACCTC 59.160 55.000 0.00 0.00 0.00 3.85
46 47 0.839946 GACATGCACCCTATCCACCT 59.160 55.000 0.00 0.00 0.00 4.00
47 48 0.546122 TGACATGCACCCTATCCACC 59.454 55.000 0.00 0.00 0.00 4.61
48 49 2.092968 TCTTGACATGCACCCTATCCAC 60.093 50.000 0.00 0.00 0.00 4.02
49 50 2.195727 TCTTGACATGCACCCTATCCA 58.804 47.619 0.00 0.00 0.00 3.41
50 51 3.498774 ATCTTGACATGCACCCTATCC 57.501 47.619 0.00 0.00 0.00 2.59
51 52 6.712095 TCAATTATCTTGACATGCACCCTATC 59.288 38.462 0.00 0.00 0.00 2.08
52 53 6.604171 TCAATTATCTTGACATGCACCCTAT 58.396 36.000 0.00 0.00 0.00 2.57
53 54 6.000246 TCAATTATCTTGACATGCACCCTA 58.000 37.500 0.00 0.00 0.00 3.53
54 55 4.858850 TCAATTATCTTGACATGCACCCT 58.141 39.130 0.00 0.00 0.00 4.34
55 56 4.883585 TCTCAATTATCTTGACATGCACCC 59.116 41.667 0.00 0.00 0.00 4.61
56 57 6.630444 ATCTCAATTATCTTGACATGCACC 57.370 37.500 0.00 0.00 0.00 5.01
57 58 8.281194 CACTATCTCAATTATCTTGACATGCAC 58.719 37.037 0.00 0.00 0.00 4.57
58 59 7.443272 CCACTATCTCAATTATCTTGACATGCA 59.557 37.037 0.00 0.00 0.00 3.96
59 60 7.094890 CCCACTATCTCAATTATCTTGACATGC 60.095 40.741 0.00 0.00 0.00 4.06
60 61 7.389884 CCCCACTATCTCAATTATCTTGACATG 59.610 40.741 0.00 0.00 0.00 3.21
61 62 7.293299 TCCCCACTATCTCAATTATCTTGACAT 59.707 37.037 0.00 0.00 0.00 3.06
62 63 6.615316 TCCCCACTATCTCAATTATCTTGACA 59.385 38.462 0.00 0.00 0.00 3.58
63 64 7.067496 TCCCCACTATCTCAATTATCTTGAC 57.933 40.000 0.00 0.00 0.00 3.18
64 65 7.513781 TCATCCCCACTATCTCAATTATCTTGA 59.486 37.037 0.00 0.00 0.00 3.02
65 66 7.683578 TCATCCCCACTATCTCAATTATCTTG 58.316 38.462 0.00 0.00 0.00 3.02
66 67 7.878621 TCATCCCCACTATCTCAATTATCTT 57.121 36.000 0.00 0.00 0.00 2.40
67 68 7.515514 AGTTCATCCCCACTATCTCAATTATCT 59.484 37.037 0.00 0.00 0.00 1.98
68 69 7.684529 AGTTCATCCCCACTATCTCAATTATC 58.315 38.462 0.00 0.00 0.00 1.75
69 70 7.639062 AGTTCATCCCCACTATCTCAATTAT 57.361 36.000 0.00 0.00 0.00 1.28
70 71 7.348274 AGAAGTTCATCCCCACTATCTCAATTA 59.652 37.037 5.50 0.00 0.00 1.40
71 72 5.983333 AGTTCATCCCCACTATCTCAATT 57.017 39.130 0.00 0.00 0.00 2.32
72 73 5.669447 AGAAGTTCATCCCCACTATCTCAAT 59.331 40.000 5.50 0.00 0.00 2.57
73 74 5.032846 AGAAGTTCATCCCCACTATCTCAA 58.967 41.667 5.50 0.00 0.00 3.02
74 75 4.624913 AGAAGTTCATCCCCACTATCTCA 58.375 43.478 5.50 0.00 0.00 3.27
75 76 5.622346 AAGAAGTTCATCCCCACTATCTC 57.378 43.478 5.50 0.00 0.00 2.75
76 77 6.674419 ACTAAAGAAGTTCATCCCCACTATCT 59.326 38.462 5.50 0.00 33.35 1.98
77 78 6.890293 ACTAAAGAAGTTCATCCCCACTATC 58.110 40.000 5.50 0.00 33.35 2.08
78 79 6.893020 ACTAAAGAAGTTCATCCCCACTAT 57.107 37.500 5.50 0.00 33.35 2.12
79 80 7.989947 ATACTAAAGAAGTTCATCCCCACTA 57.010 36.000 5.50 0.00 39.80 2.74
80 81 6.893020 ATACTAAAGAAGTTCATCCCCACT 57.107 37.500 5.50 0.00 39.80 4.00
81 82 9.930693 CTATATACTAAAGAAGTTCATCCCCAC 57.069 37.037 5.50 0.00 39.80 4.61
82 83 9.101325 CCTATATACTAAAGAAGTTCATCCCCA 57.899 37.037 5.50 0.00 39.80 4.96
83 84 9.322769 TCCTATATACTAAAGAAGTTCATCCCC 57.677 37.037 5.50 0.00 39.80 4.81
106 107 8.198109 GGATACAAAGCATCGTATACATATCCT 58.802 37.037 3.32 0.00 34.18 3.24
107 108 8.354011 GGATACAAAGCATCGTATACATATCC 57.646 38.462 3.32 0.00 30.51 2.59
127 128 4.451629 TCCTTTCACGAACTCTGGATAC 57.548 45.455 0.00 0.00 0.00 2.24
128 129 4.202020 CGATCCTTTCACGAACTCTGGATA 60.202 45.833 0.00 0.00 33.56 2.59
129 130 3.429547 CGATCCTTTCACGAACTCTGGAT 60.430 47.826 0.00 0.00 35.78 3.41
130 131 2.094700 CGATCCTTTCACGAACTCTGGA 60.095 50.000 0.00 0.00 0.00 3.86
131 132 2.094700 TCGATCCTTTCACGAACTCTGG 60.095 50.000 0.00 0.00 33.20 3.86
132 133 3.217599 TCGATCCTTTCACGAACTCTG 57.782 47.619 0.00 0.00 33.20 3.35
133 134 3.444034 TGATCGATCCTTTCACGAACTCT 59.556 43.478 22.31 0.00 39.38 3.24
134 135 3.770666 TGATCGATCCTTTCACGAACTC 58.229 45.455 22.31 0.00 39.38 3.01
135 136 3.868757 TGATCGATCCTTTCACGAACT 57.131 42.857 22.31 0.00 39.38 3.01
136 137 4.363999 AGATGATCGATCCTTTCACGAAC 58.636 43.478 22.31 0.46 39.38 3.95
137 138 4.655762 AGATGATCGATCCTTTCACGAA 57.344 40.909 22.31 0.75 39.38 3.85
138 139 4.142160 ACAAGATGATCGATCCTTTCACGA 60.142 41.667 22.31 1.51 40.18 4.35
139 140 4.026228 CACAAGATGATCGATCCTTTCACG 60.026 45.833 22.31 12.83 0.00 4.35
140 141 5.111989 TCACAAGATGATCGATCCTTTCAC 58.888 41.667 22.31 7.53 29.99 3.18
141 142 5.343307 TCACAAGATGATCGATCCTTTCA 57.657 39.130 22.31 5.48 29.99 2.69
155 156 1.816835 CTTGCACAGCCATCACAAGAT 59.183 47.619 0.00 0.00 40.06 2.40
156 157 1.241165 CTTGCACAGCCATCACAAGA 58.759 50.000 0.00 0.00 40.06 3.02
157 158 0.242825 CCTTGCACAGCCATCACAAG 59.757 55.000 0.00 0.00 37.94 3.16
158 159 1.180456 CCCTTGCACAGCCATCACAA 61.180 55.000 0.00 0.00 0.00 3.33
159 160 1.604308 CCCTTGCACAGCCATCACA 60.604 57.895 0.00 0.00 0.00 3.58
160 161 2.998279 GCCCTTGCACAGCCATCAC 61.998 63.158 0.00 0.00 37.47 3.06
161 162 2.677524 GCCCTTGCACAGCCATCA 60.678 61.111 0.00 0.00 37.47 3.07
162 163 3.455469 GGCCCTTGCACAGCCATC 61.455 66.667 14.42 0.00 46.34 3.51
166 167 2.034066 TACTGGCCCTTGCACAGC 59.966 61.111 0.00 0.00 38.55 4.40
167 168 1.377725 CCTACTGGCCCTTGCACAG 60.378 63.158 0.00 0.02 39.92 3.66
168 169 2.756400 CCTACTGGCCCTTGCACA 59.244 61.111 0.00 0.00 40.13 4.57
190 191 4.002906 TGAAACCGCAGTTCTTCATAGT 57.997 40.909 0.00 0.00 34.19 2.12
192 193 3.616821 CGATGAAACCGCAGTTCTTCATA 59.383 43.478 0.94 0.00 34.86 2.15
197 198 1.298859 GCCGATGAAACCGCAGTTCT 61.299 55.000 0.00 0.00 34.19 3.01
198 199 1.134694 GCCGATGAAACCGCAGTTC 59.865 57.895 0.00 0.00 34.19 3.01
199 200 2.332654 GGCCGATGAAACCGCAGTT 61.333 57.895 0.00 0.00 38.03 3.16
200 201 2.746277 GGCCGATGAAACCGCAGT 60.746 61.111 0.00 0.00 0.00 4.40
214 215 1.448717 GACGAAGCTTCTCCAGGCC 60.449 63.158 23.50 0.00 0.00 5.19
242 243 3.925238 GCGGCGGCACATTACGAG 61.925 66.667 9.78 0.00 39.62 4.18
261 262 0.109039 GTGACTCGCTGAGGTCTTCC 60.109 60.000 9.75 0.00 33.35 3.46
271 272 1.173444 ACTTCTGGACGTGACTCGCT 61.173 55.000 0.00 0.00 44.19 4.93
277 278 0.309922 GACGTGACTTCTGGACGTGA 59.690 55.000 0.00 0.00 45.84 4.35
282 283 0.536687 ACTCGGACGTGACTTCTGGA 60.537 55.000 0.00 0.00 0.00 3.86
290 291 1.361271 GTGTTGGACTCGGACGTGA 59.639 57.895 0.00 0.00 0.00 4.35
291 292 0.528901 TTGTGTTGGACTCGGACGTG 60.529 55.000 0.00 0.00 0.00 4.49
298 299 1.534729 GGATGGGTTGTGTTGGACTC 58.465 55.000 0.00 0.00 0.00 3.36
310 311 0.037605 GACGTGACTTTCGGATGGGT 60.038 55.000 0.00 0.00 0.00 4.51
361 362 0.318784 GTGACTTTCGGACGCTCTGT 60.319 55.000 0.00 0.00 0.00 3.41
381 382 1.303236 TTGGGCCACAATGGTCGAG 60.303 57.895 5.23 0.00 44.85 4.04
462 463 6.761714 GGATAGACGTGGTAAACTCATCAATT 59.238 38.462 0.00 0.00 0.00 2.32
500 501 2.688446 CTCACAGCCCAGTTACGATCTA 59.312 50.000 0.00 0.00 0.00 1.98
560 591 6.769822 AGCCGAATCAAGAATCAGAAATACAT 59.230 34.615 0.00 0.00 0.00 2.29
681 715 3.025262 ACCGTAACCTTTGCTTTGGAAA 58.975 40.909 0.00 0.00 0.00 3.13
686 720 2.549329 CCGTAACCGTAACCTTTGCTTT 59.451 45.455 0.00 0.00 0.00 3.51
750 784 2.496899 AACAATCGCCTCTTGGATGT 57.503 45.000 0.00 0.00 34.57 3.06
755 789 4.154737 TGATTCTGAAACAATCGCCTCTTG 59.845 41.667 0.00 0.00 33.57 3.02
766 800 2.542020 TCGCACCTGATTCTGAAACA 57.458 45.000 0.34 0.34 0.00 2.83
790 824 0.459899 CGGATCATCTTCACCACGGA 59.540 55.000 0.00 0.00 0.00 4.69
821 855 0.385029 AACGAACTGCTTTGCATGCA 59.615 45.000 18.46 18.46 38.13 3.96
831 865 0.586802 GAGGAACCACAACGAACTGC 59.413 55.000 0.00 0.00 0.00 4.40
865 899 1.150536 GGAGGCCACCAAGTTGTCA 59.849 57.895 15.24 0.00 0.00 3.58
870 904 0.555769 TTTTCAGGAGGCCACCAAGT 59.444 50.000 22.29 0.00 0.00 3.16
920 954 2.160417 GCCAAGAAAATCTCGACACCTG 59.840 50.000 0.00 0.00 0.00 4.00
921 955 2.039084 AGCCAAGAAAATCTCGACACCT 59.961 45.455 0.00 0.00 0.00 4.00
926 960 4.162320 ACCTATGAGCCAAGAAAATCTCGA 59.838 41.667 0.00 0.00 0.00 4.04
933 967 1.906574 ACGGACCTATGAGCCAAGAAA 59.093 47.619 0.00 0.00 0.00 2.52
966 1000 2.027625 CGCCTTGAAGACCGGTGAC 61.028 63.158 14.63 0.00 0.00 3.67
985 1019 1.303561 TCATGGCGCCAAAGAGCTT 60.304 52.632 36.33 12.84 39.06 3.74
1007 1041 1.933853 CGATGGAATCACCGACTTTCC 59.066 52.381 0.00 0.00 45.97 3.13
1013 1047 3.867857 TCAATTTCGATGGAATCACCGA 58.132 40.909 0.00 0.00 45.97 4.69
1021 1055 8.316946 AGCTTCTATATCATCAATTTCGATGGA 58.683 33.333 6.06 0.00 42.58 3.41
1023 1057 9.148104 TCAGCTTCTATATCATCAATTTCGATG 57.852 33.333 0.36 0.36 43.50 3.84
1189 1235 6.000840 TGCACAGTTTGTCCTCACATATAAA 58.999 36.000 0.00 0.00 30.55 1.40
1191 1237 5.159273 TGCACAGTTTGTCCTCACATATA 57.841 39.130 0.00 0.00 30.55 0.86
1255 1301 0.108662 TCGCAACTGTGATGCTCGAT 60.109 50.000 3.28 0.00 41.64 3.59
1256 1302 0.108662 ATCGCAACTGTGATGCTCGA 60.109 50.000 4.98 0.00 43.00 4.04
1263 1309 1.375908 GAGCCCATCGCAACTGTGA 60.376 57.895 0.00 0.00 41.38 3.58
1322 1369 1.519455 GTTGCGATCACCCTCTCCG 60.519 63.158 0.00 0.00 0.00 4.63
1328 1375 1.450312 CCCTCAGTTGCGATCACCC 60.450 63.158 0.00 0.00 0.00 4.61
1340 1387 6.349363 GCTTTTTAGATGTTGGTAACCCTCAG 60.349 42.308 0.00 0.00 0.00 3.35
1344 1391 5.243060 ACTGCTTTTTAGATGTTGGTAACCC 59.757 40.000 0.00 0.00 0.00 4.11
1407 1454 0.250209 CTGCTGTCAGCTCAACAGGT 60.250 55.000 24.76 0.00 43.50 4.00
1491 1541 4.362932 TTTTGTTCTGACACATTCGCAA 57.637 36.364 0.00 0.00 34.98 4.85
1492 1542 4.362932 TTTTTGTTCTGACACATTCGCA 57.637 36.364 0.00 0.00 34.98 5.10
1516 1566 7.499232 ACCCATTCTACTTGCACAAATAGATAC 59.501 37.037 2.72 0.00 0.00 2.24
1538 1588 1.707989 TGAAGGAGCCAACAATACCCA 59.292 47.619 0.00 0.00 0.00 4.51
1543 1593 3.094572 CCAGAATGAAGGAGCCAACAAT 58.905 45.455 0.00 0.00 39.69 2.71
1546 1596 1.272147 ACCCAGAATGAAGGAGCCAAC 60.272 52.381 0.00 0.00 39.69 3.77
1556 1606 4.016444 GGCATACAGAAAACCCAGAATGA 58.984 43.478 0.00 0.00 39.69 2.57
1557 1607 4.019174 AGGCATACAGAAAACCCAGAATG 58.981 43.478 0.00 0.00 0.00 2.67
1564 1614 5.897377 ATACACAAGGCATACAGAAAACC 57.103 39.130 0.00 0.00 0.00 3.27
1572 1622 8.141909 TCTGAACTGTATATACACAAGGCATAC 58.858 37.037 11.62 0.00 31.93 2.39
1576 1626 6.986817 ACATCTGAACTGTATATACACAAGGC 59.013 38.462 11.62 1.44 31.93 4.35
1586 1636 6.754193 TCACACACAACATCTGAACTGTATA 58.246 36.000 0.00 0.00 0.00 1.47
1587 1637 5.610398 TCACACACAACATCTGAACTGTAT 58.390 37.500 0.00 0.00 0.00 2.29
1592 1642 3.466836 TCCTCACACACAACATCTGAAC 58.533 45.455 0.00 0.00 0.00 3.18
1597 1647 3.668447 ACTCATCCTCACACACAACATC 58.332 45.455 0.00 0.00 0.00 3.06
1598 1648 3.326006 AGACTCATCCTCACACACAACAT 59.674 43.478 0.00 0.00 0.00 2.71
1601 1651 4.422073 AAAGACTCATCCTCACACACAA 57.578 40.909 0.00 0.00 0.00 3.33
1655 1708 6.951971 AGAGAACAACTATAGGATTGCAACT 58.048 36.000 0.00 0.00 0.00 3.16
1670 1723 8.336080 CACAAGTTTTAAGTAGGAGAGAACAAC 58.664 37.037 0.00 0.00 0.00 3.32
1678 1731 8.658499 ACAACTACACAAGTTTTAAGTAGGAG 57.342 34.615 0.00 0.00 46.61 3.69
1692 1745 4.196193 AGCAGCAACTTACAACTACACAA 58.804 39.130 0.00 0.00 0.00 3.33
1695 1748 5.462530 TCTAGCAGCAACTTACAACTACA 57.537 39.130 0.00 0.00 0.00 2.74
1699 1752 5.007136 GGATCATCTAGCAGCAACTTACAAC 59.993 44.000 0.00 0.00 0.00 3.32
1709 1762 5.419239 AGAAATAGGGATCATCTAGCAGC 57.581 43.478 0.00 0.00 0.00 5.25
1714 1767 8.789767 AGAACAGAAGAAATAGGGATCATCTA 57.210 34.615 0.00 0.00 0.00 1.98
1715 1768 7.688918 AGAACAGAAGAAATAGGGATCATCT 57.311 36.000 0.00 0.00 0.00 2.90
1758 1811 3.187022 GGCGTTAGTCTTTCCGCTAAAAA 59.813 43.478 0.00 0.00 45.11 1.94
1759 1812 2.738314 GGCGTTAGTCTTTCCGCTAAAA 59.262 45.455 0.00 0.00 45.11 1.52
1760 1813 2.340337 GGCGTTAGTCTTTCCGCTAAA 58.660 47.619 0.00 0.00 45.11 1.85
1761 1814 1.404583 GGGCGTTAGTCTTTCCGCTAA 60.405 52.381 0.00 0.00 45.11 3.09
1762 1815 0.174162 GGGCGTTAGTCTTTCCGCTA 59.826 55.000 0.00 0.00 45.11 4.26
1763 1816 1.079336 GGGCGTTAGTCTTTCCGCT 60.079 57.895 0.00 0.00 45.11 5.52
1764 1817 1.375013 TGGGCGTTAGTCTTTCCGC 60.375 57.895 0.00 0.00 45.05 5.54
1843 1896 3.485394 TGCCTCAATGTGTCAAGCTTTA 58.515 40.909 0.00 0.00 0.00 1.85
1847 1900 4.644103 ATTATGCCTCAATGTGTCAAGC 57.356 40.909 0.00 0.00 0.00 4.01
1891 1946 2.947652 CTCTCCAATGCCAATACACCAG 59.052 50.000 0.00 0.00 0.00 4.00
1898 1953 2.359900 GACGAACTCTCCAATGCCAAT 58.640 47.619 0.00 0.00 0.00 3.16
1900 1955 0.036388 GGACGAACTCTCCAATGCCA 60.036 55.000 0.00 0.00 0.00 4.92
1933 1993 1.153353 CACATCTACCAAAACCGCGT 58.847 50.000 4.92 0.00 0.00 6.01
1934 1994 0.179200 GCACATCTACCAAAACCGCG 60.179 55.000 0.00 0.00 0.00 6.46
1935 1995 1.165270 AGCACATCTACCAAAACCGC 58.835 50.000 0.00 0.00 0.00 5.68
1936 1996 3.938963 ACATAGCACATCTACCAAAACCG 59.061 43.478 0.00 0.00 0.00 4.44
1937 1997 4.096382 CCACATAGCACATCTACCAAAACC 59.904 45.833 0.00 0.00 0.00 3.27
1939 1999 4.269183 CCCACATAGCACATCTACCAAAA 58.731 43.478 0.00 0.00 0.00 2.44
1948 2008 0.253044 AGTTCGCCCACATAGCACAT 59.747 50.000 0.00 0.00 0.00 3.21
1955 2015 3.686016 ACAGAAATTAGTTCGCCCACAT 58.314 40.909 0.00 0.00 41.52 3.21
2038 2111 1.804151 ACGCGTACTGCATTTGACATT 59.196 42.857 11.67 0.00 46.97 2.71
2077 2171 1.806542 CTGCAGTTACCGTCTTGCAAT 59.193 47.619 5.25 0.00 0.00 3.56
2107 2201 3.701542 TGTGTTCTTATTTGGTTGCCACA 59.298 39.130 0.00 0.00 30.78 4.17
2118 2212 7.886629 ATCATAGTTGCCATGTGTTCTTATT 57.113 32.000 0.00 0.00 0.00 1.40
2123 2217 6.127758 TGGTTAATCATAGTTGCCATGTGTTC 60.128 38.462 0.00 0.00 0.00 3.18
2124 2218 5.714333 TGGTTAATCATAGTTGCCATGTGTT 59.286 36.000 0.00 0.00 0.00 3.32
2151 2245 4.497291 TGGTCCAACCATAGTTACCATC 57.503 45.455 0.00 0.00 44.79 3.51
2220 2314 3.743911 TGTGTGATTAACTACTTGCCACG 59.256 43.478 0.00 0.00 0.00 4.94
2333 2427 2.831526 GGGGATGGCAAATGTAGTTGTT 59.168 45.455 0.00 0.00 0.00 2.83
2390 2484 1.418264 TCCCGCGGGATGATGATTTAA 59.582 47.619 42.66 16.84 39.76 1.52
2391 2485 1.001974 CTCCCGCGGGATGATGATTTA 59.998 52.381 45.15 20.73 44.24 1.40
2392 2486 0.250467 CTCCCGCGGGATGATGATTT 60.250 55.000 45.15 0.00 44.24 2.17
2393 2487 1.372683 CTCCCGCGGGATGATGATT 59.627 57.895 45.15 0.00 44.24 2.57
2397 2491 2.207924 GGTACTCCCGCGGGATGAT 61.208 63.158 45.15 33.33 44.24 2.45
2425 2519 2.969806 GCACACACATCCTGGCACG 61.970 63.158 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.