Multiple sequence alignment - TraesCS1D01G433000

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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 TraesCS1D01G433000 chr1D 100.000 3163 0 0 1 3163 482438513 482441675 0.000000e+00 5842
1 TraesCS1D01G433000 chr1D 97.199 821 22 1 2343 3163 19620342 19619523 0.000000e+00 1387
2 TraesCS1D01G433000 chr1D 97.000 400 12 0 2032 2431 19620608 19620209 0.000000e+00 673
3 TraesCS1D01G433000 chr1D 80.617 583 100 11 1455 2031 482489225 482489800 3.750000e-119 438
4 TraesCS1D01G433000 chr7D 97.171 1131 31 1 2033 3163 109999489 110000618 0.000000e+00 1910
5 TraesCS1D01G433000 chr5D 96.825 1134 33 2 2030 3163 21200705 21199575 0.000000e+00 1892
6 TraesCS1D01G433000 chr6D 96.293 1133 36 3 2031 3163 365458913 365460039 0.000000e+00 1855
7 TraesCS1D01G433000 chr6D 98.217 561 10 0 2603 3163 298926653 298927213 0.000000e+00 981
8 TraesCS1D01G433000 chrUn 95.981 821 31 2 2343 3163 70528335 70527517 0.000000e+00 1332
9 TraesCS1D01G433000 chr3B 98.224 563 8 1 2603 3163 171059296 171058734 0.000000e+00 983
10 TraesCS1D01G433000 chr3B 95.761 401 17 0 2031 2431 43352297 43352697 0.000000e+00 647
11 TraesCS1D01G433000 chr3B 91.705 217 17 1 2388 2604 1273899 1273684 1.840000e-77 300
12 TraesCS1D01G433000 chr4D 98.217 561 10 0 2603 3163 449186938 449186378 0.000000e+00 981
13 TraesCS1D01G433000 chr2D 98.039 561 11 0 2603 3163 73091061 73090501 0.000000e+00 976
14 TraesCS1D01G433000 chr2D 96.491 513 17 1 2340 2852 640895626 640896137 0.000000e+00 846
15 TraesCS1D01G433000 chr1A 92.006 663 30 10 753 1397 579418204 579418861 0.000000e+00 909
16 TraesCS1D01G433000 chr1A 92.540 496 28 4 1544 2032 579421519 579422012 0.000000e+00 702
17 TraesCS1D01G433000 chr1A 85.491 641 81 6 1372 2000 579677448 579678088 0.000000e+00 658
18 TraesCS1D01G433000 chr1A 85.529 539 51 9 156 687 579417501 579418019 3.590000e-149 538
19 TraesCS1D01G433000 chr1A 96.639 119 3 1 1430 1548 579418859 579418976 2.490000e-46 196
20 TraesCS1D01G433000 chr7B 92.919 579 37 4 2027 2604 510630664 510631239 0.000000e+00 839
21 TraesCS1D01G433000 chr7B 93.243 444 26 3 2033 2476 154416276 154416715 0.000000e+00 651
22 TraesCS1D01G433000 chr7B 92.568 444 29 3 2033 2476 154440524 154440963 4.450000e-178 634
23 TraesCS1D01G433000 chr7B 92.534 442 28 4 2033 2474 154464657 154465093 2.070000e-176 628
24 TraesCS1D01G433000 chr1B 82.835 769 102 16 1286 2032 670927087 670926327 0.000000e+00 662
25 TraesCS1D01G433000 chr1B 87.048 525 17 9 1104 1589 670962007 670961495 2.150000e-151 545
26 TraesCS1D01G433000 chr1B 94.510 255 13 1 2350 2604 531690193 531689940 2.960000e-105 392


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 TraesCS1D01G433000 chr1D 482438513 482441675 3162 False 5842.00 5842 100.0000 1 3163 1 chr1D.!!$F1 3162
1 TraesCS1D01G433000 chr1D 19619523 19620608 1085 True 1030.00 1387 97.0995 2032 3163 2 chr1D.!!$R1 1131
2 TraesCS1D01G433000 chr1D 482489225 482489800 575 False 438.00 438 80.6170 1455 2031 1 chr1D.!!$F2 576
3 TraesCS1D01G433000 chr7D 109999489 110000618 1129 False 1910.00 1910 97.1710 2033 3163 1 chr7D.!!$F1 1130
4 TraesCS1D01G433000 chr5D 21199575 21200705 1130 True 1892.00 1892 96.8250 2030 3163 1 chr5D.!!$R1 1133
5 TraesCS1D01G433000 chr6D 365458913 365460039 1126 False 1855.00 1855 96.2930 2031 3163 1 chr6D.!!$F2 1132
6 TraesCS1D01G433000 chr6D 298926653 298927213 560 False 981.00 981 98.2170 2603 3163 1 chr6D.!!$F1 560
7 TraesCS1D01G433000 chrUn 70527517 70528335 818 True 1332.00 1332 95.9810 2343 3163 1 chrUn.!!$R1 820
8 TraesCS1D01G433000 chr3B 171058734 171059296 562 True 983.00 983 98.2240 2603 3163 1 chr3B.!!$R2 560
9 TraesCS1D01G433000 chr4D 449186378 449186938 560 True 981.00 981 98.2170 2603 3163 1 chr4D.!!$R1 560
10 TraesCS1D01G433000 chr2D 73090501 73091061 560 True 976.00 976 98.0390 2603 3163 1 chr2D.!!$R1 560
11 TraesCS1D01G433000 chr2D 640895626 640896137 511 False 846.00 846 96.4910 2340 2852 1 chr2D.!!$F1 512
12 TraesCS1D01G433000 chr1A 579677448 579678088 640 False 658.00 658 85.4910 1372 2000 1 chr1A.!!$F1 628
13 TraesCS1D01G433000 chr1A 579417501 579422012 4511 False 586.25 909 91.6785 156 2032 4 chr1A.!!$F2 1876
14 TraesCS1D01G433000 chr7B 510630664 510631239 575 False 839.00 839 92.9190 2027 2604 1 chr7B.!!$F4 577
15 TraesCS1D01G433000 chr1B 670926327 670927087 760 True 662.00 662 82.8350 1286 2032 1 chr1B.!!$R2 746
16 TraesCS1D01G433000 chr1B 670961495 670962007 512 True 545.00 545 87.0480 1104 1589 1 chr1B.!!$R3 485

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
25 26 0.034283 GAGAGAGGGGGTACTGTCGT 60.034 60.0 0.0 0.0 36.03 4.34 F
53 54 0.104409 GGGGGAGGTAGTGGGATGAT 60.104 60.0 0.0 0.0 0.00 2.45 F
69 70 0.104777 TGATGAGGGGATCTGGGGAG 60.105 60.0 0.0 0.0 0.00 4.30 F
522 527 0.107410 AATTCGCCCGCCACTAATGA 60.107 50.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 4741 1.004560 TGGCAGGCGTCAAGAAGAG 60.005 57.895 0.00 0.0 0.0 2.85 R
1952 4745 2.031012 CTGTGGCAGGCGTCAAGA 59.969 61.111 0.00 0.0 0.0 3.02 R
2012 4805 8.902540 TGACTCTTTCTAATTTCTAAGCAACA 57.097 30.769 0.00 0.0 0.0 3.33 R
2479 5318 0.389391 GAGATCGCGAGGGAATTGGA 59.611 55.000 16.66 0.0 0.0 3.53 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 2.788589 GGGGAAGAGAGAGGGGGT 59.211 66.667 0.00 0.00 0.00 4.95
18 19 2.025236 GGGGAAGAGAGAGGGGGTA 58.975 63.158 0.00 0.00 0.00 3.69
19 20 0.398806 GGGGAAGAGAGAGGGGGTAC 60.399 65.000 0.00 0.00 0.00 3.34
20 21 0.637743 GGGAAGAGAGAGGGGGTACT 59.362 60.000 0.00 0.00 0.00 2.73
21 22 1.689892 GGGAAGAGAGAGGGGGTACTG 60.690 61.905 0.00 0.00 0.00 2.74
22 23 1.007359 GGAAGAGAGAGGGGGTACTGT 59.993 57.143 0.00 0.00 0.00 3.55
23 24 2.380941 GAAGAGAGAGGGGGTACTGTC 58.619 57.143 0.00 0.00 0.00 3.51
24 25 0.256464 AGAGAGAGGGGGTACTGTCG 59.744 60.000 0.00 0.00 36.03 4.35
25 26 0.034283 GAGAGAGGGGGTACTGTCGT 60.034 60.000 0.00 0.00 36.03 4.34
26 27 0.323542 AGAGAGGGGGTACTGTCGTG 60.324 60.000 0.00 0.00 36.03 4.35
27 28 1.305046 AGAGGGGGTACTGTCGTGG 60.305 63.158 0.00 0.00 0.00 4.94
28 29 1.608627 GAGGGGGTACTGTCGTGGT 60.609 63.158 0.00 0.00 0.00 4.16
29 30 0.323725 GAGGGGGTACTGTCGTGGTA 60.324 60.000 0.00 0.00 0.00 3.25
30 31 0.324091 AGGGGGTACTGTCGTGGTAG 60.324 60.000 0.00 0.00 0.00 3.18
31 32 0.323725 GGGGGTACTGTCGTGGTAGA 60.324 60.000 0.00 0.00 0.00 2.59
32 33 1.687368 GGGGGTACTGTCGTGGTAGAT 60.687 57.143 0.00 0.00 0.00 1.98
33 34 1.680207 GGGGTACTGTCGTGGTAGATC 59.320 57.143 0.00 0.00 0.00 2.75
34 35 1.332997 GGGTACTGTCGTGGTAGATCG 59.667 57.143 0.00 0.00 0.00 3.69
35 36 1.332997 GGTACTGTCGTGGTAGATCGG 59.667 57.143 0.00 0.00 0.00 4.18
36 37 1.332997 GTACTGTCGTGGTAGATCGGG 59.667 57.143 0.00 0.00 0.00 5.14
37 38 1.035932 ACTGTCGTGGTAGATCGGGG 61.036 60.000 0.00 0.00 0.00 5.73
38 39 1.735376 CTGTCGTGGTAGATCGGGGG 61.735 65.000 0.00 0.00 0.00 5.40
39 40 1.454479 GTCGTGGTAGATCGGGGGA 60.454 63.158 0.00 0.00 0.00 4.81
40 41 1.152819 TCGTGGTAGATCGGGGGAG 60.153 63.158 0.00 0.00 0.00 4.30
41 42 2.201022 CGTGGTAGATCGGGGGAGG 61.201 68.421 0.00 0.00 0.00 4.30
42 43 1.075450 GTGGTAGATCGGGGGAGGT 60.075 63.158 0.00 0.00 0.00 3.85
43 44 0.186873 GTGGTAGATCGGGGGAGGTA 59.813 60.000 0.00 0.00 0.00 3.08
44 45 0.481567 TGGTAGATCGGGGGAGGTAG 59.518 60.000 0.00 0.00 0.00 3.18
45 46 0.482006 GGTAGATCGGGGGAGGTAGT 59.518 60.000 0.00 0.00 0.00 2.73
46 47 1.618487 GTAGATCGGGGGAGGTAGTG 58.382 60.000 0.00 0.00 0.00 2.74
47 48 0.481567 TAGATCGGGGGAGGTAGTGG 59.518 60.000 0.00 0.00 0.00 4.00
48 49 1.837499 GATCGGGGGAGGTAGTGGG 60.837 68.421 0.00 0.00 0.00 4.61
49 50 2.308118 GATCGGGGGAGGTAGTGGGA 62.308 65.000 0.00 0.00 0.00 4.37
50 51 1.675936 ATCGGGGGAGGTAGTGGGAT 61.676 60.000 0.00 0.00 0.00 3.85
51 52 2.140792 CGGGGGAGGTAGTGGGATG 61.141 68.421 0.00 0.00 0.00 3.51
52 53 1.316969 GGGGGAGGTAGTGGGATGA 59.683 63.158 0.00 0.00 0.00 2.92
53 54 0.104409 GGGGGAGGTAGTGGGATGAT 60.104 60.000 0.00 0.00 0.00 2.45
54 55 1.059913 GGGGAGGTAGTGGGATGATG 58.940 60.000 0.00 0.00 0.00 3.07
55 56 1.414538 GGGGAGGTAGTGGGATGATGA 60.415 57.143 0.00 0.00 0.00 2.92
56 57 1.974236 GGGAGGTAGTGGGATGATGAG 59.026 57.143 0.00 0.00 0.00 2.90
57 58 1.974236 GGAGGTAGTGGGATGATGAGG 59.026 57.143 0.00 0.00 0.00 3.86
58 59 1.974236 GAGGTAGTGGGATGATGAGGG 59.026 57.143 0.00 0.00 0.00 4.30
59 60 1.059913 GGTAGTGGGATGATGAGGGG 58.940 60.000 0.00 0.00 0.00 4.79
60 61 1.414538 GGTAGTGGGATGATGAGGGGA 60.415 57.143 0.00 0.00 0.00 4.81
61 62 2.625639 GTAGTGGGATGATGAGGGGAT 58.374 52.381 0.00 0.00 0.00 3.85
62 63 1.739750 AGTGGGATGATGAGGGGATC 58.260 55.000 0.00 0.00 0.00 3.36
63 64 1.225168 AGTGGGATGATGAGGGGATCT 59.775 52.381 0.00 0.00 0.00 2.75
64 65 1.350351 GTGGGATGATGAGGGGATCTG 59.650 57.143 0.00 0.00 0.00 2.90
65 66 0.990374 GGGATGATGAGGGGATCTGG 59.010 60.000 0.00 0.00 0.00 3.86
66 67 0.990374 GGATGATGAGGGGATCTGGG 59.010 60.000 0.00 0.00 0.00 4.45
67 68 0.990374 GATGATGAGGGGATCTGGGG 59.010 60.000 0.00 0.00 0.00 4.96
68 69 0.574818 ATGATGAGGGGATCTGGGGA 59.425 55.000 0.00 0.00 0.00 4.81
69 70 0.104777 TGATGAGGGGATCTGGGGAG 60.105 60.000 0.00 0.00 0.00 4.30
70 71 0.839853 GATGAGGGGATCTGGGGAGG 60.840 65.000 0.00 0.00 0.00 4.30
71 72 2.122189 GAGGGGATCTGGGGAGGG 60.122 72.222 0.00 0.00 0.00 4.30
72 73 2.628465 AGGGGATCTGGGGAGGGA 60.628 66.667 0.00 0.00 0.00 4.20
73 74 2.122189 GGGGATCTGGGGAGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
74 75 2.727071 GGGGATCTGGGGAGGGAGA 61.727 68.421 0.00 0.00 0.00 3.71
75 76 1.556561 GGGATCTGGGGAGGGAGAT 59.443 63.158 0.00 0.00 0.00 2.75
76 77 0.839853 GGGATCTGGGGAGGGAGATG 60.840 65.000 0.00 0.00 0.00 2.90
77 78 0.839853 GGATCTGGGGAGGGAGATGG 60.840 65.000 0.00 0.00 0.00 3.51
78 79 0.839853 GATCTGGGGAGGGAGATGGG 60.840 65.000 0.00 0.00 0.00 4.00
79 80 2.352553 ATCTGGGGAGGGAGATGGGG 62.353 65.000 0.00 0.00 0.00 4.96
80 81 4.122670 TGGGGAGGGAGATGGGGG 62.123 72.222 0.00 0.00 0.00 5.40
104 105 4.075793 CTGGAGGGGACGAGGGGA 62.076 72.222 0.00 0.00 0.00 4.81
105 106 3.364964 TGGAGGGGACGAGGGGAT 61.365 66.667 0.00 0.00 0.00 3.85
106 107 2.524640 GGAGGGGACGAGGGGATC 60.525 72.222 0.00 0.00 0.00 3.36
107 108 2.609920 GAGGGGACGAGGGGATCT 59.390 66.667 0.00 0.00 0.00 2.75
108 109 1.834822 GAGGGGACGAGGGGATCTG 60.835 68.421 0.00 0.00 0.00 2.90
109 110 2.844839 GGGGACGAGGGGATCTGG 60.845 72.222 0.00 0.00 0.00 3.86
110 111 2.844839 GGGACGAGGGGATCTGGG 60.845 72.222 0.00 0.00 0.00 4.45
111 112 2.844839 GGACGAGGGGATCTGGGG 60.845 72.222 0.00 0.00 0.00 4.96
112 113 2.844839 GACGAGGGGATCTGGGGG 60.845 72.222 0.00 0.00 0.00 5.40
113 114 3.364964 ACGAGGGGATCTGGGGGA 61.365 66.667 0.00 0.00 0.00 4.81
114 115 2.525381 CGAGGGGATCTGGGGGAG 60.525 72.222 0.00 0.00 0.00 4.30
115 116 2.122189 GAGGGGATCTGGGGGAGG 60.122 72.222 0.00 0.00 0.00 4.30
116 117 3.795924 AGGGGATCTGGGGGAGGG 61.796 72.222 0.00 0.00 0.00 4.30
117 118 3.791076 GGGGATCTGGGGGAGGGA 61.791 72.222 0.00 0.00 0.00 4.20
118 119 2.122189 GGGATCTGGGGGAGGGAG 60.122 72.222 0.00 0.00 0.00 4.30
119 120 2.727071 GGGATCTGGGGGAGGGAGA 61.727 68.421 0.00 0.00 0.00 3.71
120 121 1.152139 GGATCTGGGGGAGGGAGAG 60.152 68.421 0.00 0.00 0.00 3.20
121 122 1.152139 GATCTGGGGGAGGGAGAGG 60.152 68.421 0.00 0.00 0.00 3.69
122 123 3.418623 ATCTGGGGGAGGGAGAGGC 62.419 68.421 0.00 0.00 0.00 4.70
123 124 4.421554 CTGGGGGAGGGAGAGGCA 62.422 72.222 0.00 0.00 0.00 4.75
124 125 4.741239 TGGGGGAGGGAGAGGCAC 62.741 72.222 0.00 0.00 0.00 5.01
128 129 4.779733 GGAGGGAGAGGCACGGGA 62.780 72.222 0.00 0.00 0.00 5.14
129 130 3.151022 GAGGGAGAGGCACGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
130 131 4.787280 AGGGAGAGGCACGGGAGG 62.787 72.222 0.00 0.00 0.00 4.30
134 135 4.658786 AGAGGCACGGGAGGGGTT 62.659 66.667 0.00 0.00 0.00 4.11
135 136 2.686106 GAGGCACGGGAGGGGTTA 60.686 66.667 0.00 0.00 0.00 2.85
136 137 2.687566 AGGCACGGGAGGGGTTAG 60.688 66.667 0.00 0.00 0.00 2.34
137 138 3.793888 GGCACGGGAGGGGTTAGG 61.794 72.222 0.00 0.00 0.00 2.69
138 139 2.686106 GCACGGGAGGGGTTAGGA 60.686 66.667 0.00 0.00 0.00 2.94
139 140 2.070650 GCACGGGAGGGGTTAGGAT 61.071 63.158 0.00 0.00 0.00 3.24
140 141 1.632965 GCACGGGAGGGGTTAGGATT 61.633 60.000 0.00 0.00 0.00 3.01
141 142 1.797320 CACGGGAGGGGTTAGGATTA 58.203 55.000 0.00 0.00 0.00 1.75
142 143 1.692519 CACGGGAGGGGTTAGGATTAG 59.307 57.143 0.00 0.00 0.00 1.73
143 144 1.577242 ACGGGAGGGGTTAGGATTAGA 59.423 52.381 0.00 0.00 0.00 2.10
144 145 2.181642 ACGGGAGGGGTTAGGATTAGAT 59.818 50.000 0.00 0.00 0.00 1.98
145 146 2.567615 CGGGAGGGGTTAGGATTAGATG 59.432 54.545 0.00 0.00 0.00 2.90
146 147 3.599348 GGGAGGGGTTAGGATTAGATGT 58.401 50.000 0.00 0.00 0.00 3.06
147 148 4.755106 CGGGAGGGGTTAGGATTAGATGTA 60.755 50.000 0.00 0.00 0.00 2.29
148 149 4.531339 GGGAGGGGTTAGGATTAGATGTAC 59.469 50.000 0.00 0.00 0.00 2.90
149 150 4.220163 GGAGGGGTTAGGATTAGATGTACG 59.780 50.000 0.00 0.00 0.00 3.67
150 151 4.158015 AGGGGTTAGGATTAGATGTACGG 58.842 47.826 0.00 0.00 0.00 4.02
151 152 3.899980 GGGGTTAGGATTAGATGTACGGT 59.100 47.826 0.00 0.00 0.00 4.83
152 153 4.346127 GGGGTTAGGATTAGATGTACGGTT 59.654 45.833 0.00 0.00 0.00 4.44
153 154 5.163269 GGGGTTAGGATTAGATGTACGGTTT 60.163 44.000 0.00 0.00 0.00 3.27
154 155 6.041979 GGGGTTAGGATTAGATGTACGGTTTA 59.958 42.308 0.00 0.00 0.00 2.01
164 165 2.463752 TGTACGGTTTAGATGGGCTCT 58.536 47.619 0.00 0.00 38.06 4.09
165 166 2.167693 TGTACGGTTTAGATGGGCTCTG 59.832 50.000 0.00 0.00 35.28 3.35
245 246 3.363575 CCCGTTACTGTCATTTGTGTTCG 60.364 47.826 0.00 0.00 0.00 3.95
289 290 2.948979 CCGCCAGTGCTATTTTTCCATA 59.051 45.455 0.00 0.00 34.43 2.74
290 291 3.380004 CCGCCAGTGCTATTTTTCCATAA 59.620 43.478 0.00 0.00 34.43 1.90
359 360 3.596214 CGCCATTGGTAACTCAAGTACT 58.404 45.455 4.26 0.00 37.61 2.73
360 361 4.382254 CCGCCATTGGTAACTCAAGTACTA 60.382 45.833 4.26 0.00 37.61 1.82
361 362 4.804139 CGCCATTGGTAACTCAAGTACTAG 59.196 45.833 4.26 0.00 37.61 2.57
363 364 6.405065 CGCCATTGGTAACTCAAGTACTAGTA 60.405 42.308 4.26 0.00 37.61 1.82
366 367 7.363530 CCATTGGTAACTCAAGTACTAGTAGCA 60.364 40.741 1.87 0.36 37.61 3.49
372 373 4.339814 ACTCAAGTACTAGTAGCAGGCATC 59.660 45.833 1.87 0.00 0.00 3.91
382 383 1.443194 GCAGGCATCAGTTTGTGCG 60.443 57.895 0.00 0.00 42.15 5.34
384 385 1.898094 AGGCATCAGTTTGTGCGCA 60.898 52.632 5.66 5.66 42.15 6.09
386 387 1.730547 GCATCAGTTTGTGCGCACC 60.731 57.895 35.72 21.46 0.00 5.01
396 397 2.110006 TGCGCACCACTGCTAACA 59.890 55.556 5.66 0.00 41.77 2.41
427 432 2.587080 CCACTCTGGCCGTTACCTA 58.413 57.895 0.00 0.00 0.00 3.08
428 433 0.899720 CCACTCTGGCCGTTACCTAA 59.100 55.000 0.00 0.00 0.00 2.69
437 442 2.191375 GTTACCTAAGGCGGGCCC 59.809 66.667 13.57 13.57 36.58 5.80
446 451 4.354162 GGCGGGCCCAAACTGGTA 62.354 66.667 24.92 0.00 35.17 3.25
450 455 2.847650 GGGCCCAAACTGGTACCCA 61.848 63.158 19.95 0.00 46.16 4.51
469 474 4.352893 ACCCACCACTGGTAAGAAAATAGT 59.647 41.667 0.00 0.00 35.46 2.12
488 493 2.501223 TAGTGGCGAGCGAGGTTTGG 62.501 60.000 0.00 0.00 0.00 3.28
505 510 4.058797 GCGCCCGCCACTTATAAT 57.941 55.556 0.00 0.00 34.56 1.28
522 527 0.107410 AATTCGCCCGCCACTAATGA 60.107 50.000 0.00 0.00 0.00 2.57
540 545 4.917906 ATGAGGGTTCATCTATAAGCCC 57.082 45.455 0.00 0.00 43.95 5.19
544 549 5.163195 TGAGGGTTCATCTATAAGCCCTTTC 60.163 44.000 0.00 0.00 45.63 2.62
546 551 4.104897 GGGTTCATCTATAAGCCCTTTCCT 59.895 45.833 0.00 0.00 38.32 3.36
547 552 5.399152 GGGTTCATCTATAAGCCCTTTCCTT 60.399 44.000 0.00 0.00 38.32 3.36
548 553 5.532779 GGTTCATCTATAAGCCCTTTCCTTG 59.467 44.000 0.00 0.00 0.00 3.61
559 564 3.682999 GCCCTTTCCTTGTAGTGATCCTC 60.683 52.174 0.00 0.00 0.00 3.71
563 568 5.477607 TTTCCTTGTAGTGATCCTCGAAA 57.522 39.130 0.00 0.00 0.00 3.46
566 571 3.557595 CCTTGTAGTGATCCTCGAAATGC 59.442 47.826 0.00 0.00 0.00 3.56
610 615 5.656480 TCCTAAAGTTGCACCTTCAAAAAC 58.344 37.500 0.00 0.00 0.00 2.43
617 622 2.499289 TGCACCTTCAAAAACCACACAT 59.501 40.909 0.00 0.00 0.00 3.21
632 637 9.444600 AAAACCACACATTATCTATTAGAACGT 57.555 29.630 0.00 0.00 0.00 3.99
634 639 8.644318 ACCACACATTATCTATTAGAACGTTC 57.356 34.615 20.71 20.71 0.00 3.95
677 683 0.320421 ACGTCTGGACATGGAAACGG 60.320 55.000 0.00 0.00 34.63 4.44
679 685 0.605319 GTCTGGACATGGAAACGGCA 60.605 55.000 0.00 0.00 0.00 5.69
680 686 0.327924 TCTGGACATGGAAACGGCAT 59.672 50.000 0.00 0.00 0.00 4.40
681 687 0.452987 CTGGACATGGAAACGGCATG 59.547 55.000 0.00 0.00 0.00 4.06
682 688 0.251121 TGGACATGGAAACGGCATGT 60.251 50.000 0.00 0.00 41.62 3.21
683 689 1.003696 TGGACATGGAAACGGCATGTA 59.996 47.619 0.00 0.00 39.36 2.29
684 690 2.088423 GGACATGGAAACGGCATGTAA 58.912 47.619 0.00 0.00 39.36 2.41
685 691 2.159435 GGACATGGAAACGGCATGTAAC 60.159 50.000 0.00 0.00 39.36 2.50
686 692 2.747446 GACATGGAAACGGCATGTAACT 59.253 45.455 0.00 0.00 39.36 2.24
687 693 3.153919 ACATGGAAACGGCATGTAACTT 58.846 40.909 0.00 0.00 37.73 2.66
688 694 3.190535 ACATGGAAACGGCATGTAACTTC 59.809 43.478 0.00 0.00 37.73 3.01
689 695 2.852449 TGGAAACGGCATGTAACTTCA 58.148 42.857 0.00 0.00 0.00 3.02
690 696 2.550606 TGGAAACGGCATGTAACTTCAC 59.449 45.455 0.00 0.00 0.00 3.18
691 697 2.095415 GGAAACGGCATGTAACTTCACC 60.095 50.000 0.00 0.00 0.00 4.02
692 698 2.264005 AACGGCATGTAACTTCACCA 57.736 45.000 0.00 0.00 0.00 4.17
693 699 2.264005 ACGGCATGTAACTTCACCAA 57.736 45.000 0.00 0.00 0.00 3.67
694 700 1.877443 ACGGCATGTAACTTCACCAAC 59.123 47.619 0.00 0.00 0.00 3.77
695 701 2.151202 CGGCATGTAACTTCACCAACT 58.849 47.619 0.00 0.00 0.00 3.16
696 702 3.244284 ACGGCATGTAACTTCACCAACTA 60.244 43.478 0.00 0.00 0.00 2.24
697 703 3.370978 CGGCATGTAACTTCACCAACTAG 59.629 47.826 0.00 0.00 0.00 2.57
698 704 4.324267 GGCATGTAACTTCACCAACTAGT 58.676 43.478 0.00 0.00 0.00 2.57
699 705 4.760204 GGCATGTAACTTCACCAACTAGTT 59.240 41.667 1.12 1.12 36.23 2.24
700 706 5.240844 GGCATGTAACTTCACCAACTAGTTT 59.759 40.000 5.07 0.00 34.26 2.66
701 707 6.142817 GCATGTAACTTCACCAACTAGTTTG 58.857 40.000 5.07 5.14 34.26 2.93
702 708 6.238648 GCATGTAACTTCACCAACTAGTTTGT 60.239 38.462 5.07 5.88 34.26 2.83
703 709 7.041644 GCATGTAACTTCACCAACTAGTTTGTA 60.042 37.037 11.68 0.00 34.26 2.41
704 710 8.999431 CATGTAACTTCACCAACTAGTTTGTAT 58.001 33.333 11.68 0.00 34.26 2.29
705 711 8.967664 TGTAACTTCACCAACTAGTTTGTATT 57.032 30.769 11.68 7.30 34.26 1.89
706 712 8.832521 TGTAACTTCACCAACTAGTTTGTATTG 58.167 33.333 11.68 7.52 34.26 1.90
707 713 6.313744 ACTTCACCAACTAGTTTGTATTGC 57.686 37.500 11.68 0.00 32.71 3.56
708 714 5.825679 ACTTCACCAACTAGTTTGTATTGCA 59.174 36.000 11.68 0.00 32.71 4.08
709 715 6.320164 ACTTCACCAACTAGTTTGTATTGCAA 59.680 34.615 11.68 0.00 32.71 4.08
710 716 6.892658 TCACCAACTAGTTTGTATTGCAAT 57.107 33.333 17.56 17.56 36.89 3.56
711 717 7.987750 TCACCAACTAGTTTGTATTGCAATA 57.012 32.000 15.21 15.21 36.89 1.90
712 718 7.812648 TCACCAACTAGTTTGTATTGCAATAC 58.187 34.615 33.26 33.26 41.24 1.89
713 719 7.445707 TCACCAACTAGTTTGTATTGCAATACA 59.554 33.333 36.85 36.85 46.88 2.29
806 971 8.934023 TTTTTGAGTTTCCAATCTAGTATGGT 57.066 30.769 13.75 0.00 37.94 3.55
852 1017 4.865776 TGGTTATCGAAAGTTTGGCAAAG 58.134 39.130 13.94 1.05 0.00 2.77
856 1021 6.256975 GGTTATCGAAAGTTTGGCAAAGTTTT 59.743 34.615 34.09 25.87 42.44 2.43
872 1037 8.817100 GGCAAAGTTTTATGATAAACCTAATGC 58.183 33.333 17.22 17.22 38.49 3.56
877 1042 9.030452 AGTTTTATGATAAACCTAATGCCACAA 57.970 29.630 0.00 0.00 38.49 3.33
889 1054 8.546597 ACCTAATGCCACAATTTTTATTCAAC 57.453 30.769 0.00 0.00 0.00 3.18
927 1092 4.469657 ACCTTAACAGCCAAAATGAGTGA 58.530 39.130 0.00 0.00 0.00 3.41
932 1097 7.442062 CCTTAACAGCCAAAATGAGTGAAAATT 59.558 33.333 0.00 0.00 0.00 1.82
1044 1210 7.367285 ACATTTGTACATAACGTTGATTTGCT 58.633 30.769 11.99 0.00 0.00 3.91
1218 1387 3.947132 CTGCTCTGCACTGACGGGG 62.947 68.421 0.00 0.00 33.79 5.73
1397 1617 1.349627 GCGTGCATTCATGGAGTCG 59.650 57.895 0.00 0.00 0.00 4.18
1398 1618 2.009108 CGTGCATTCATGGAGTCGG 58.991 57.895 0.00 0.00 0.00 4.79
1399 1619 0.460109 CGTGCATTCATGGAGTCGGA 60.460 55.000 0.00 0.00 0.00 4.55
1400 1620 1.807755 CGTGCATTCATGGAGTCGGAT 60.808 52.381 0.00 0.00 0.00 4.18
1401 1621 1.869767 GTGCATTCATGGAGTCGGATC 59.130 52.381 0.00 0.00 0.00 3.36
1402 1622 1.143305 GCATTCATGGAGTCGGATCG 58.857 55.000 0.00 0.00 0.00 3.69
1403 1623 1.539065 GCATTCATGGAGTCGGATCGT 60.539 52.381 0.00 0.00 0.00 3.73
1404 1624 2.398498 CATTCATGGAGTCGGATCGTC 58.602 52.381 0.00 0.00 0.00 4.20
1405 1625 0.744874 TTCATGGAGTCGGATCGTCC 59.255 55.000 0.00 0.00 0.00 4.79
1426 1646 3.314553 CGTGTTTAGACATCAAGGACGT 58.685 45.455 0.00 0.00 38.23 4.34
1497 1734 1.753078 CCCGACGACATCCTCCTCA 60.753 63.158 0.00 0.00 0.00 3.86
1589 4372 1.153086 GTGCATGCTCCCCGATCTT 60.153 57.895 20.33 0.00 0.00 2.40
1599 4382 0.530650 CCCCGATCTTGACATGGACG 60.531 60.000 0.00 0.00 0.00 4.79
1657 4447 1.475280 CTTGGATTGTGTCATGGCCAG 59.525 52.381 13.05 3.43 0.00 4.85
1675 4465 3.677190 CCAGGTACACCAATTCCGTAAA 58.323 45.455 0.38 0.00 38.89 2.01
1694 4484 1.529244 GTGGTTTCTGCTGCCCACT 60.529 57.895 15.08 0.00 43.21 4.00
1968 4761 1.597854 CTTCTTGACGCCTGCCACA 60.598 57.895 0.00 0.00 0.00 4.17
2019 4812 2.282745 GCAGGGCCTCTGTTGCTT 60.283 61.111 18.80 0.00 45.08 3.91
2064 4857 3.244805 ACAGTGCATCCAGATGATATGGG 60.245 47.826 11.81 0.00 41.20 4.00
2204 4998 5.576447 TTTTCCTCCCAAATATTTCGAGC 57.424 39.130 13.16 0.00 0.00 5.03
2240 5034 4.672409 GAATTTCAGGGCTATTTTCGGTG 58.328 43.478 0.00 0.00 0.00 4.94
2259 5053 2.094734 GTGCGATTTTTATCCCGTTCGT 59.905 45.455 0.00 0.00 0.00 3.85
2321 5115 2.851071 GCAGGATCTAGCCGCTCGT 61.851 63.158 0.00 0.00 0.00 4.18
2412 5251 1.141881 CAGGATCTAGCCGCACGTT 59.858 57.895 0.00 0.00 0.00 3.99
2479 5318 1.306568 GCCCCTCTCTTCCTCCACT 60.307 63.158 0.00 0.00 0.00 4.00
2514 5353 2.045561 TCTCGCACCACCTTTTCAAA 57.954 45.000 0.00 0.00 0.00 2.69
2766 5605 4.856801 CCATTCGTCCAGCCCCGG 62.857 72.222 0.00 0.00 0.00 5.73
3095 5936 1.462670 CCTCGCAAAAAGCAGAGAGAC 59.537 52.381 9.37 0.00 46.13 3.36
3114 5955 5.950549 AGAGACAGGAATGAGCATTTGATTT 59.049 36.000 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.398806 GTACCCCCTCTCTCTTCCCC 60.399 65.000 0.00 0.00 0.00 4.81
1 2 0.637743 AGTACCCCCTCTCTCTTCCC 59.362 60.000 0.00 0.00 0.00 3.97
3 4 2.380941 GACAGTACCCCCTCTCTCTTC 58.619 57.143 0.00 0.00 0.00 2.87
5 6 0.256464 CGACAGTACCCCCTCTCTCT 59.744 60.000 0.00 0.00 0.00 3.10
6 7 0.034283 ACGACAGTACCCCCTCTCTC 60.034 60.000 0.00 0.00 0.00 3.20
7 8 0.323542 CACGACAGTACCCCCTCTCT 60.324 60.000 0.00 0.00 0.00 3.10
8 9 1.321074 CCACGACAGTACCCCCTCTC 61.321 65.000 0.00 0.00 0.00 3.20
9 10 1.305046 CCACGACAGTACCCCCTCT 60.305 63.158 0.00 0.00 0.00 3.69
10 11 0.323725 TACCACGACAGTACCCCCTC 60.324 60.000 0.00 0.00 0.00 4.30
11 12 0.324091 CTACCACGACAGTACCCCCT 60.324 60.000 0.00 0.00 0.00 4.79
12 13 0.323725 TCTACCACGACAGTACCCCC 60.324 60.000 0.00 0.00 0.00 5.40
13 14 1.680207 GATCTACCACGACAGTACCCC 59.320 57.143 0.00 0.00 0.00 4.95
14 15 1.332997 CGATCTACCACGACAGTACCC 59.667 57.143 0.00 0.00 0.00 3.69
15 16 1.332997 CCGATCTACCACGACAGTACC 59.667 57.143 0.00 0.00 0.00 3.34
16 17 1.332997 CCCGATCTACCACGACAGTAC 59.667 57.143 0.00 0.00 0.00 2.73
17 18 1.671979 CCCGATCTACCACGACAGTA 58.328 55.000 0.00 0.00 0.00 2.74
18 19 1.035932 CCCCGATCTACCACGACAGT 61.036 60.000 0.00 0.00 0.00 3.55
19 20 1.734137 CCCCGATCTACCACGACAG 59.266 63.158 0.00 0.00 0.00 3.51
20 21 1.755395 CCCCCGATCTACCACGACA 60.755 63.158 0.00 0.00 0.00 4.35
21 22 1.453762 CTCCCCCGATCTACCACGAC 61.454 65.000 0.00 0.00 0.00 4.34
22 23 1.152819 CTCCCCCGATCTACCACGA 60.153 63.158 0.00 0.00 0.00 4.35
23 24 2.201022 CCTCCCCCGATCTACCACG 61.201 68.421 0.00 0.00 0.00 4.94
24 25 0.186873 TACCTCCCCCGATCTACCAC 59.813 60.000 0.00 0.00 0.00 4.16
25 26 0.481567 CTACCTCCCCCGATCTACCA 59.518 60.000 0.00 0.00 0.00 3.25
26 27 0.482006 ACTACCTCCCCCGATCTACC 59.518 60.000 0.00 0.00 0.00 3.18
27 28 1.618487 CACTACCTCCCCCGATCTAC 58.382 60.000 0.00 0.00 0.00 2.59
28 29 0.481567 CCACTACCTCCCCCGATCTA 59.518 60.000 0.00 0.00 0.00 1.98
29 30 1.233369 CCACTACCTCCCCCGATCT 59.767 63.158 0.00 0.00 0.00 2.75
30 31 1.837499 CCCACTACCTCCCCCGATC 60.837 68.421 0.00 0.00 0.00 3.69
31 32 1.675936 ATCCCACTACCTCCCCCGAT 61.676 60.000 0.00 0.00 0.00 4.18
32 33 2.330209 ATCCCACTACCTCCCCCGA 61.330 63.158 0.00 0.00 0.00 5.14
33 34 2.140792 CATCCCACTACCTCCCCCG 61.141 68.421 0.00 0.00 0.00 5.73
34 35 0.104409 ATCATCCCACTACCTCCCCC 60.104 60.000 0.00 0.00 0.00 5.40
35 36 1.059913 CATCATCCCACTACCTCCCC 58.940 60.000 0.00 0.00 0.00 4.81
36 37 1.974236 CTCATCATCCCACTACCTCCC 59.026 57.143 0.00 0.00 0.00 4.30
37 38 1.974236 CCTCATCATCCCACTACCTCC 59.026 57.143 0.00 0.00 0.00 4.30
38 39 1.974236 CCCTCATCATCCCACTACCTC 59.026 57.143 0.00 0.00 0.00 3.85
39 40 1.415126 CCCCTCATCATCCCACTACCT 60.415 57.143 0.00 0.00 0.00 3.08
40 41 1.059913 CCCCTCATCATCCCACTACC 58.940 60.000 0.00 0.00 0.00 3.18
41 42 2.103153 TCCCCTCATCATCCCACTAC 57.897 55.000 0.00 0.00 0.00 2.73
42 43 2.456340 AGATCCCCTCATCATCCCACTA 59.544 50.000 0.00 0.00 0.00 2.74
43 44 1.225168 AGATCCCCTCATCATCCCACT 59.775 52.381 0.00 0.00 0.00 4.00
44 45 1.350351 CAGATCCCCTCATCATCCCAC 59.650 57.143 0.00 0.00 0.00 4.61
45 46 1.738474 CAGATCCCCTCATCATCCCA 58.262 55.000 0.00 0.00 0.00 4.37
46 47 0.990374 CCAGATCCCCTCATCATCCC 59.010 60.000 0.00 0.00 0.00 3.85
47 48 0.990374 CCCAGATCCCCTCATCATCC 59.010 60.000 0.00 0.00 0.00 3.51
48 49 0.990374 CCCCAGATCCCCTCATCATC 59.010 60.000 0.00 0.00 0.00 2.92
49 50 0.574818 TCCCCAGATCCCCTCATCAT 59.425 55.000 0.00 0.00 0.00 2.45
50 51 0.104777 CTCCCCAGATCCCCTCATCA 60.105 60.000 0.00 0.00 0.00 3.07
51 52 0.839853 CCTCCCCAGATCCCCTCATC 60.840 65.000 0.00 0.00 0.00 2.92
52 53 1.241327 CCTCCCCAGATCCCCTCAT 59.759 63.158 0.00 0.00 0.00 2.90
53 54 2.705410 CCTCCCCAGATCCCCTCA 59.295 66.667 0.00 0.00 0.00 3.86
54 55 2.122189 CCCTCCCCAGATCCCCTC 60.122 72.222 0.00 0.00 0.00 4.30
55 56 2.628465 TCCCTCCCCAGATCCCCT 60.628 66.667 0.00 0.00 0.00 4.79
56 57 2.054834 ATCTCCCTCCCCAGATCCCC 62.055 65.000 0.00 0.00 0.00 4.81
57 58 0.839853 CATCTCCCTCCCCAGATCCC 60.840 65.000 0.00 0.00 0.00 3.85
58 59 0.839853 CCATCTCCCTCCCCAGATCC 60.840 65.000 0.00 0.00 0.00 3.36
59 60 0.839853 CCCATCTCCCTCCCCAGATC 60.840 65.000 0.00 0.00 0.00 2.75
60 61 1.241327 CCCATCTCCCTCCCCAGAT 59.759 63.158 0.00 0.00 0.00 2.90
61 62 2.705410 CCCATCTCCCTCCCCAGA 59.295 66.667 0.00 0.00 0.00 3.86
62 63 2.449322 CCCCATCTCCCTCCCCAG 60.449 72.222 0.00 0.00 0.00 4.45
63 64 4.122670 CCCCCATCTCCCTCCCCA 62.123 72.222 0.00 0.00 0.00 4.96
87 88 3.396822 ATCCCCTCGTCCCCTCCAG 62.397 68.421 0.00 0.00 0.00 3.86
88 89 3.364964 ATCCCCTCGTCCCCTCCA 61.365 66.667 0.00 0.00 0.00 3.86
89 90 2.524640 GATCCCCTCGTCCCCTCC 60.525 72.222 0.00 0.00 0.00 4.30
90 91 1.834822 CAGATCCCCTCGTCCCCTC 60.835 68.421 0.00 0.00 0.00 4.30
91 92 2.283809 CAGATCCCCTCGTCCCCT 59.716 66.667 0.00 0.00 0.00 4.79
92 93 2.844839 CCAGATCCCCTCGTCCCC 60.845 72.222 0.00 0.00 0.00 4.81
93 94 2.844839 CCCAGATCCCCTCGTCCC 60.845 72.222 0.00 0.00 0.00 4.46
94 95 2.844839 CCCCAGATCCCCTCGTCC 60.845 72.222 0.00 0.00 0.00 4.79
95 96 2.844839 CCCCCAGATCCCCTCGTC 60.845 72.222 0.00 0.00 0.00 4.20
96 97 3.364964 TCCCCCAGATCCCCTCGT 61.365 66.667 0.00 0.00 0.00 4.18
97 98 2.525381 CTCCCCCAGATCCCCTCG 60.525 72.222 0.00 0.00 0.00 4.63
98 99 2.122189 CCTCCCCCAGATCCCCTC 60.122 72.222 0.00 0.00 0.00 4.30
99 100 3.795924 CCCTCCCCCAGATCCCCT 61.796 72.222 0.00 0.00 0.00 4.79
100 101 3.791076 TCCCTCCCCCAGATCCCC 61.791 72.222 0.00 0.00 0.00 4.81
101 102 2.122189 CTCCCTCCCCCAGATCCC 60.122 72.222 0.00 0.00 0.00 3.85
102 103 1.152139 CTCTCCCTCCCCCAGATCC 60.152 68.421 0.00 0.00 0.00 3.36
103 104 1.152139 CCTCTCCCTCCCCCAGATC 60.152 68.421 0.00 0.00 0.00 2.75
104 105 3.041365 CCTCTCCCTCCCCCAGAT 58.959 66.667 0.00 0.00 0.00 2.90
105 106 4.095400 GCCTCTCCCTCCCCCAGA 62.095 72.222 0.00 0.00 0.00 3.86
106 107 4.421554 TGCCTCTCCCTCCCCCAG 62.422 72.222 0.00 0.00 0.00 4.45
107 108 4.741239 GTGCCTCTCCCTCCCCCA 62.741 72.222 0.00 0.00 0.00 4.96
111 112 4.779733 TCCCGTGCCTCTCCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
112 113 3.151022 CTCCCGTGCCTCTCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
113 114 4.787280 CCTCCCGTGCCTCTCCCT 62.787 72.222 0.00 0.00 0.00 4.20
117 118 3.248248 TAACCCCTCCCGTGCCTCT 62.248 63.158 0.00 0.00 0.00 3.69
118 119 2.686106 TAACCCCTCCCGTGCCTC 60.686 66.667 0.00 0.00 0.00 4.70
119 120 2.687566 CTAACCCCTCCCGTGCCT 60.688 66.667 0.00 0.00 0.00 4.75
120 121 3.793888 CCTAACCCCTCCCGTGCC 61.794 72.222 0.00 0.00 0.00 5.01
121 122 1.632965 AATCCTAACCCCTCCCGTGC 61.633 60.000 0.00 0.00 0.00 5.34
122 123 1.692519 CTAATCCTAACCCCTCCCGTG 59.307 57.143 0.00 0.00 0.00 4.94
123 124 1.577242 TCTAATCCTAACCCCTCCCGT 59.423 52.381 0.00 0.00 0.00 5.28
124 125 2.393630 TCTAATCCTAACCCCTCCCG 57.606 55.000 0.00 0.00 0.00 5.14
125 126 3.599348 ACATCTAATCCTAACCCCTCCC 58.401 50.000 0.00 0.00 0.00 4.30
126 127 4.220163 CGTACATCTAATCCTAACCCCTCC 59.780 50.000 0.00 0.00 0.00 4.30
127 128 4.220163 CCGTACATCTAATCCTAACCCCTC 59.780 50.000 0.00 0.00 0.00 4.30
128 129 4.158015 CCGTACATCTAATCCTAACCCCT 58.842 47.826 0.00 0.00 0.00 4.79
129 130 3.899980 ACCGTACATCTAATCCTAACCCC 59.100 47.826 0.00 0.00 0.00 4.95
130 131 5.541953 AACCGTACATCTAATCCTAACCC 57.458 43.478 0.00 0.00 0.00 4.11
131 132 7.945134 TCTAAACCGTACATCTAATCCTAACC 58.055 38.462 0.00 0.00 0.00 2.85
132 133 9.408069 CATCTAAACCGTACATCTAATCCTAAC 57.592 37.037 0.00 0.00 0.00 2.34
133 134 8.582437 CCATCTAAACCGTACATCTAATCCTAA 58.418 37.037 0.00 0.00 0.00 2.69
134 135 7.177921 CCCATCTAAACCGTACATCTAATCCTA 59.822 40.741 0.00 0.00 0.00 2.94
135 136 6.014499 CCCATCTAAACCGTACATCTAATCCT 60.014 42.308 0.00 0.00 0.00 3.24
136 137 6.164176 CCCATCTAAACCGTACATCTAATCC 58.836 44.000 0.00 0.00 0.00 3.01
137 138 5.638234 GCCCATCTAAACCGTACATCTAATC 59.362 44.000 0.00 0.00 0.00 1.75
138 139 5.307196 AGCCCATCTAAACCGTACATCTAAT 59.693 40.000 0.00 0.00 0.00 1.73
139 140 4.652421 AGCCCATCTAAACCGTACATCTAA 59.348 41.667 0.00 0.00 0.00 2.10
140 141 4.220724 AGCCCATCTAAACCGTACATCTA 58.779 43.478 0.00 0.00 0.00 1.98
141 142 3.039011 AGCCCATCTAAACCGTACATCT 58.961 45.455 0.00 0.00 0.00 2.90
142 143 3.069729 AGAGCCCATCTAAACCGTACATC 59.930 47.826 0.00 0.00 36.10 3.06
143 144 3.039011 AGAGCCCATCTAAACCGTACAT 58.961 45.455 0.00 0.00 36.10 2.29
144 145 2.167693 CAGAGCCCATCTAAACCGTACA 59.832 50.000 0.00 0.00 36.10 2.90
145 146 2.167900 ACAGAGCCCATCTAAACCGTAC 59.832 50.000 0.00 0.00 36.10 3.67
146 147 2.167693 CACAGAGCCCATCTAAACCGTA 59.832 50.000 0.00 0.00 36.10 4.02
147 148 1.066143 CACAGAGCCCATCTAAACCGT 60.066 52.381 0.00 0.00 36.10 4.83
148 149 1.656652 CACAGAGCCCATCTAAACCG 58.343 55.000 0.00 0.00 36.10 4.44
149 150 1.408822 CCCACAGAGCCCATCTAAACC 60.409 57.143 0.00 0.00 36.10 3.27
150 151 2.019156 GCCCACAGAGCCCATCTAAAC 61.019 57.143 0.00 0.00 36.10 2.01
151 152 0.255890 GCCCACAGAGCCCATCTAAA 59.744 55.000 0.00 0.00 36.10 1.85
152 153 0.621571 AGCCCACAGAGCCCATCTAA 60.622 55.000 0.00 0.00 36.10 2.10
153 154 0.621571 AAGCCCACAGAGCCCATCTA 60.622 55.000 0.00 0.00 36.10 1.98
154 155 1.504275 AAAGCCCACAGAGCCCATCT 61.504 55.000 0.00 0.00 39.56 2.90
187 188 3.435186 GCTGCGTTCAAGAGGGGC 61.435 66.667 0.00 0.00 0.00 5.80
217 218 0.108138 ATGACAGTAACGGGCTCTGC 60.108 55.000 0.00 0.00 33.12 4.26
220 221 2.159627 CACAAATGACAGTAACGGGCTC 59.840 50.000 0.00 0.00 0.00 4.70
228 229 4.055360 CCACTCGAACACAAATGACAGTA 58.945 43.478 0.00 0.00 0.00 2.74
270 271 7.848223 AAATTTATGGAAAAATAGCACTGGC 57.152 32.000 0.00 0.00 41.61 4.85
334 335 2.437716 AGTTACCAATGGCGGGCG 60.438 61.111 0.00 0.00 0.00 6.13
335 336 0.963355 TTGAGTTACCAATGGCGGGC 60.963 55.000 0.00 0.00 0.00 6.13
340 341 6.979238 GCTACTAGTACTTGAGTTACCAATGG 59.021 42.308 11.43 0.00 0.00 3.16
343 344 6.152323 CCTGCTACTAGTACTTGAGTTACCAA 59.848 42.308 11.43 0.00 0.00 3.67
359 360 3.599343 CACAAACTGATGCCTGCTACTA 58.401 45.455 0.00 0.00 0.00 1.82
360 361 2.430465 CACAAACTGATGCCTGCTACT 58.570 47.619 0.00 0.00 0.00 2.57
361 362 1.135575 GCACAAACTGATGCCTGCTAC 60.136 52.381 0.00 0.00 35.73 3.58
363 364 1.859427 CGCACAAACTGATGCCTGCT 61.859 55.000 0.00 0.00 38.69 4.24
366 367 1.898094 TGCGCACAAACTGATGCCT 60.898 52.632 5.66 0.00 38.69 4.75
372 373 1.298563 CAGTGGTGCGCACAAACTG 60.299 57.895 38.54 38.54 39.48 3.16
384 385 4.085357 TGAGACAAATGTTAGCAGTGGT 57.915 40.909 0.00 0.00 28.26 4.16
386 387 4.673580 GCCATGAGACAAATGTTAGCAGTG 60.674 45.833 0.00 0.00 0.00 3.66
396 397 2.619849 CCAGAGTGGCCATGAGACAAAT 60.620 50.000 9.72 0.00 0.00 2.32
418 419 2.202974 GCCCGCCTTAGGTAACGG 60.203 66.667 8.53 8.53 45.21 4.44
425 430 2.046285 CAGTTTGGGCCCGCCTTAG 61.046 63.158 19.37 0.81 36.10 2.18
427 432 4.994756 CCAGTTTGGGCCCGCCTT 62.995 66.667 19.37 0.00 32.67 4.35
450 455 6.708285 CCACTACTATTTTCTTACCAGTGGT 58.292 40.000 20.91 20.91 44.33 4.16
469 474 1.080093 CAAACCTCGCTCGCCACTA 60.080 57.895 0.00 0.00 0.00 2.74
488 493 0.237498 GAATTATAAGTGGCGGGCGC 59.763 55.000 7.06 7.06 41.06 6.53
489 494 0.511221 CGAATTATAAGTGGCGGGCG 59.489 55.000 0.00 0.00 0.00 6.13
490 495 0.237498 GCGAATTATAAGTGGCGGGC 59.763 55.000 4.18 0.00 0.00 6.13
491 496 0.872388 GGCGAATTATAAGTGGCGGG 59.128 55.000 12.68 0.00 0.00 6.13
492 497 0.872388 GGGCGAATTATAAGTGGCGG 59.128 55.000 12.68 0.00 0.00 6.13
493 498 0.511221 CGGGCGAATTATAAGTGGCG 59.489 55.000 12.68 2.30 0.00 5.69
494 499 0.237498 GCGGGCGAATTATAAGTGGC 59.763 55.000 10.93 10.93 0.00 5.01
495 500 0.872388 GGCGGGCGAATTATAAGTGG 59.128 55.000 0.00 0.00 0.00 4.00
496 501 1.263217 GTGGCGGGCGAATTATAAGTG 59.737 52.381 0.00 0.00 0.00 3.16
497 502 1.140252 AGTGGCGGGCGAATTATAAGT 59.860 47.619 0.00 0.00 0.00 2.24
498 503 1.878953 AGTGGCGGGCGAATTATAAG 58.121 50.000 0.00 0.00 0.00 1.73
499 504 3.472283 TTAGTGGCGGGCGAATTATAA 57.528 42.857 0.00 0.00 0.00 0.98
500 505 3.007074 TCATTAGTGGCGGGCGAATTATA 59.993 43.478 0.00 0.00 0.00 0.98
501 506 2.151202 CATTAGTGGCGGGCGAATTAT 58.849 47.619 0.00 0.00 0.00 1.28
502 507 1.139256 TCATTAGTGGCGGGCGAATTA 59.861 47.619 0.00 0.00 0.00 1.40
503 508 0.107410 TCATTAGTGGCGGGCGAATT 60.107 50.000 0.00 0.00 0.00 2.17
504 509 0.532862 CTCATTAGTGGCGGGCGAAT 60.533 55.000 0.00 0.00 0.00 3.34
505 510 1.153449 CTCATTAGTGGCGGGCGAA 60.153 57.895 0.00 0.00 0.00 4.70
540 545 4.720649 TCGAGGATCACTACAAGGAAAG 57.279 45.455 0.00 0.00 33.17 2.62
544 549 3.557595 GCATTTCGAGGATCACTACAAGG 59.442 47.826 0.00 0.00 33.17 3.61
546 551 4.160439 AGAGCATTTCGAGGATCACTACAA 59.840 41.667 0.00 0.00 33.17 2.41
547 552 3.701542 AGAGCATTTCGAGGATCACTACA 59.298 43.478 0.00 0.00 33.17 2.74
548 553 4.314740 AGAGCATTTCGAGGATCACTAC 57.685 45.455 0.00 0.00 33.17 2.73
559 564 9.994432 AAAGAAAACATAATCTAGAGCATTTCG 57.006 29.630 0.00 0.00 31.45 3.46
610 615 8.873215 AGAACGTTCTAATAGATAATGTGTGG 57.127 34.615 28.80 0.00 35.34 4.17
617 622 8.557864 CGAGAAGGAGAACGTTCTAATAGATAA 58.442 37.037 29.79 0.00 46.61 1.75
630 635 0.241213 TGTGAGCGAGAAGGAGAACG 59.759 55.000 0.00 0.00 0.00 3.95
631 636 2.440539 TTGTGAGCGAGAAGGAGAAC 57.559 50.000 0.00 0.00 0.00 3.01
632 637 3.469008 TTTTGTGAGCGAGAAGGAGAA 57.531 42.857 0.00 0.00 0.00 2.87
634 639 2.481952 CCTTTTTGTGAGCGAGAAGGAG 59.518 50.000 0.00 0.00 40.85 3.69
642 648 0.655733 ACGTCACCTTTTTGTGAGCG 59.344 50.000 11.63 11.63 45.40 5.03
677 683 5.941948 AACTAGTTGGTGAAGTTACATGC 57.058 39.130 7.48 0.00 31.84 4.06
679 685 9.569122 AATACAAACTAGTTGGTGAAGTTACAT 57.431 29.630 23.49 5.56 41.97 2.29
680 686 8.832521 CAATACAAACTAGTTGGTGAAGTTACA 58.167 33.333 23.49 3.40 41.97 2.41
681 687 7.801783 GCAATACAAACTAGTTGGTGAAGTTAC 59.198 37.037 23.49 6.43 41.97 2.50
682 688 7.499563 TGCAATACAAACTAGTTGGTGAAGTTA 59.500 33.333 23.49 4.82 41.97 2.24
683 689 6.320164 TGCAATACAAACTAGTTGGTGAAGTT 59.680 34.615 23.49 11.15 41.97 2.66
684 690 5.825679 TGCAATACAAACTAGTTGGTGAAGT 59.174 36.000 23.49 11.22 41.97 3.01
685 691 6.312399 TGCAATACAAACTAGTTGGTGAAG 57.688 37.500 23.49 13.95 41.97 3.02
686 692 6.701145 TTGCAATACAAACTAGTTGGTGAA 57.299 33.333 23.49 6.96 41.97 3.18
687 693 6.892658 ATTGCAATACAAACTAGTTGGTGA 57.107 33.333 23.49 9.65 42.86 4.02
688 694 7.589395 TGTATTGCAATACAAACTAGTTGGTG 58.411 34.615 37.82 14.64 45.91 4.17
689 695 7.753309 TGTATTGCAATACAAACTAGTTGGT 57.247 32.000 37.82 19.44 45.91 3.67
740 746 9.414295 TCGACTCGAAAAGTAATTTTCAGAATA 57.586 29.630 23.59 5.93 40.07 1.75
852 1017 9.816354 ATTGTGGCATTAGGTTTATCATAAAAC 57.184 29.630 0.00 0.00 38.39 2.43
870 1035 5.923204 ACTGGTTGAATAAAAATTGTGGCA 58.077 33.333 0.00 0.00 0.00 4.92
872 1037 7.432869 TCAGACTGGTTGAATAAAAATTGTGG 58.567 34.615 1.81 0.00 0.00 4.17
889 1054 9.209175 GCTGTTAAGGTATTATTATCAGACTGG 57.791 37.037 1.81 0.00 34.21 4.00
910 1075 8.729805 TTTAATTTTCACTCATTTTGGCTGTT 57.270 26.923 0.00 0.00 0.00 3.16
975 1140 2.358737 AGGAAAAGCGCAGGACCG 60.359 61.111 11.47 0.00 0.00 4.79
1044 1210 5.508200 AAAAAGTTCATCCTGTGCGTAAA 57.492 34.783 0.00 0.00 0.00 2.01
1073 1239 3.213206 TCGCTATGCATCCCATCTTTT 57.787 42.857 0.19 0.00 35.34 2.27
1079 1245 2.158769 ACTTCAATCGCTATGCATCCCA 60.159 45.455 0.19 0.00 0.00 4.37
1122 1288 8.725148 CAAAACTAGTACTGAGCATTCTTTCAT 58.275 33.333 5.39 0.00 0.00 2.57
1123 1289 7.931407 TCAAAACTAGTACTGAGCATTCTTTCA 59.069 33.333 5.39 0.00 0.00 2.69
1282 1472 4.194640 CGTTTCAGATCCCAACTCATCAT 58.805 43.478 0.00 0.00 0.00 2.45
1283 1473 3.007940 ACGTTTCAGATCCCAACTCATCA 59.992 43.478 0.00 0.00 0.00 3.07
1397 1617 2.642139 TGTCTAAACACGGACGATCC 57.358 50.000 0.00 0.00 0.00 3.36
1398 1618 3.766151 TGATGTCTAAACACGGACGATC 58.234 45.455 0.00 0.00 38.48 3.69
1399 1619 3.861276 TGATGTCTAAACACGGACGAT 57.139 42.857 0.00 0.00 38.48 3.73
1400 1620 3.571571 CTTGATGTCTAAACACGGACGA 58.428 45.455 0.00 0.00 38.48 4.20
1401 1621 2.666508 CCTTGATGTCTAAACACGGACG 59.333 50.000 0.00 0.00 38.48 4.79
1402 1622 3.678548 GTCCTTGATGTCTAAACACGGAC 59.321 47.826 0.00 0.00 38.48 4.79
1403 1623 3.613193 CGTCCTTGATGTCTAAACACGGA 60.613 47.826 0.00 0.00 38.48 4.69
1404 1624 2.666508 CGTCCTTGATGTCTAAACACGG 59.333 50.000 0.00 0.00 38.48 4.94
1405 1625 3.314553 ACGTCCTTGATGTCTAAACACG 58.685 45.455 0.00 0.00 38.48 4.49
1406 1626 4.084013 CCAACGTCCTTGATGTCTAAACAC 60.084 45.833 0.00 0.00 38.48 3.32
1407 1627 4.062293 CCAACGTCCTTGATGTCTAAACA 58.938 43.478 0.00 0.00 40.38 2.83
1426 1646 3.369756 GCAATTCACTCGATTACGACCAA 59.630 43.478 0.00 0.00 43.81 3.67
1589 4372 2.048597 GTGGCGACGTCCATGTCA 60.049 61.111 10.58 0.38 38.84 3.58
1599 4382 2.510691 CGGTACCATGGTGGCGAC 60.511 66.667 28.17 16.93 42.67 5.19
1657 4447 3.437741 CCACTTTACGGAATTGGTGTACC 59.562 47.826 1.02 0.00 34.32 3.34
1675 4465 2.926250 TGGGCAGCAGAAACCACT 59.074 55.556 0.00 0.00 0.00 4.00
1694 4484 2.362503 AGGCTCGTCCGGTGATGA 60.363 61.111 0.00 0.00 40.77 2.92
1716 4506 2.760634 TCTGCAAGGTAGAATGCGAA 57.239 45.000 0.00 0.00 45.47 4.70
1721 4511 4.162509 GGGTCTACTTCTGCAAGGTAGAAT 59.837 45.833 18.38 1.07 33.99 2.40
1948 4741 1.004560 TGGCAGGCGTCAAGAAGAG 60.005 57.895 0.00 0.00 0.00 2.85
1952 4745 2.031012 CTGTGGCAGGCGTCAAGA 59.969 61.111 0.00 0.00 0.00 3.02
2012 4805 8.902540 TGACTCTTTCTAATTTCTAAGCAACA 57.097 30.769 0.00 0.00 0.00 3.33
2185 4979 2.169769 ACGCTCGAAATATTTGGGAGGA 59.830 45.455 19.71 5.63 0.00 3.71
2204 4998 4.440103 CCTGAAATTCGTACCGAGAATACG 59.560 45.833 0.00 0.00 45.35 3.06
2240 5034 3.394313 AACGAACGGGATAAAAATCGC 57.606 42.857 0.00 0.00 33.88 4.58
2259 5053 2.282407 GCGGCGAAGAATAAACCCTAA 58.718 47.619 12.98 0.00 0.00 2.69
2341 5135 2.336809 CTAGATCCTGCCGGCGAC 59.663 66.667 23.90 10.83 0.00 5.19
2468 5307 1.916181 GGGAATTGGAGTGGAGGAAGA 59.084 52.381 0.00 0.00 0.00 2.87
2479 5318 0.389391 GAGATCGCGAGGGAATTGGA 59.611 55.000 16.66 0.00 0.00 3.53
2514 5353 2.237392 GTGGGCCTTCTCTAGTGTTCAT 59.763 50.000 4.53 0.00 0.00 2.57
2554 5393 4.443266 GCCGACTCTTCGCTGGCT 62.443 66.667 0.00 0.00 44.43 4.75
2766 5605 1.560923 ACGTTCGTAGATCATGCAGC 58.439 50.000 0.00 0.00 35.04 5.25
3095 5936 6.167685 TGGAAAAATCAAATGCTCATTCCTG 58.832 36.000 0.00 0.00 36.80 3.86
3114 5955 7.765360 GGAAGAATGAAATGCAACATATGGAAA 59.235 33.333 7.80 0.00 30.96 3.13


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

AutoCloner maintained by Alex Coulton.