Multiple sequence alignment - TraesCS2D01G498000

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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 TraesCS2D01G498000 chr2D 100.000 2966 0 0 1 2966 593525098 593522133 0.000000e+00 5478.0
1 TraesCS2D01G498000 chr2D 84.983 293 38 4 2515 2807 600426212 600426498 2.890000e-75 292.0
2 TraesCS2D01G498000 chr2D 78.235 170 27 9 1242 1406 87762438 87762602 1.880000e-17 100.0
3 TraesCS2D01G498000 chr2D 75.714 210 29 19 1345 1549 87806539 87806731 5.270000e-13 86.1
4 TraesCS2D01G498000 chr2D 84.706 85 12 1 158 242 596994525 596994608 1.890000e-12 84.2
5 TraesCS2D01G498000 chr2D 83.333 72 6 3 2101 2169 76887818 76887750 8.880000e-06 62.1
6 TraesCS2D01G498000 chr2A 90.393 1707 105 26 326 2016 728419334 728417671 0.000000e+00 2189.0
7 TraesCS2D01G498000 chr2A 86.471 170 20 3 158 327 731256787 731256953 1.820000e-42 183.0
8 TraesCS2D01G498000 chr2A 88.966 145 11 4 191 334 731205337 731205477 1.090000e-39 174.0
9 TraesCS2D01G498000 chr2A 84.699 183 19 8 154 333 731254392 731254568 1.090000e-39 174.0
10 TraesCS2D01G498000 chr2A 84.444 180 25 3 162 341 731259674 731259850 1.090000e-39 174.0
11 TraesCS2D01G498000 chr2A 76.667 210 27 19 1345 1549 88281225 88281417 2.430000e-16 97.1
12 TraesCS2D01G498000 chr2A 76.786 168 33 6 1242 1406 88118016 88118180 4.070000e-14 89.8
13 TraesCS2D01G498000 chr2B 90.966 1439 87 20 681 2102 719984419 719983007 0.000000e+00 1897.0
14 TraesCS2D01G498000 chr2B 94.840 717 33 4 2095 2810 331026721 331026008 0.000000e+00 1116.0
15 TraesCS2D01G498000 chr2B 87.719 171 18 3 158 328 726119033 726119200 2.330000e-46 196.0
16 TraesCS2D01G498000 chr2B 85.311 177 22 4 158 334 726081228 726081400 2.350000e-41 180.0
17 TraesCS2D01G498000 chr6D 99.080 870 8 0 2095 2964 87371060 87370191 0.000000e+00 1563.0
18 TraesCS2D01G498000 chr6D 100.000 412 0 0 2096 2507 441655074 441654663 0.000000e+00 761.0
19 TraesCS2D01G498000 chr6D 84.983 293 38 4 2515 2807 446723846 446724132 2.890000e-75 292.0
20 TraesCS2D01G498000 chr6D 94.444 72 4 0 2096 2167 441652908 441652979 8.690000e-21 111.0
21 TraesCS2D01G498000 chr6D 92.857 70 5 0 2098 2167 87368978 87369047 5.230000e-18 102.0
22 TraesCS2D01G498000 chr5D 82.129 996 130 24 1005 1961 495308565 495309551 0.000000e+00 809.0
23 TraesCS2D01G498000 chr5D 79.520 542 76 21 1459 1968 504102506 504101968 1.310000e-93 353.0
24 TraesCS2D01G498000 chr5D 84.983 293 38 4 2515 2807 398486024 398486310 2.890000e-75 292.0
25 TraesCS2D01G498000 chr5D 74.841 314 66 11 1243 1548 75354247 75353939 2.400000e-26 130.0
26 TraesCS2D01G498000 chr5D 74.013 304 58 15 1243 1543 355796323 355796038 1.450000e-18 104.0
27 TraesCS2D01G498000 chr5B 82.100 1000 129 21 1005 1961 611952887 611953879 0.000000e+00 809.0
28 TraesCS2D01G498000 chr5B 91.348 497 34 6 1251 1738 251917775 251918271 0.000000e+00 671.0
29 TraesCS2D01G498000 chr5B 92.123 292 22 1 2516 2807 655262703 655262993 7.650000e-111 411.0
30 TraesCS2D01G498000 chr5B 87.660 235 20 3 2249 2479 655262476 655262705 6.300000e-67 265.0
31 TraesCS2D01G498000 chr5B 85.606 132 9 10 2095 2223 655262076 655262200 2.400000e-26 130.0
32 TraesCS2D01G498000 chr5A 82.513 955 128 19 1042 1960 619454367 619455318 0.000000e+00 802.0
33 TraesCS2D01G498000 chr5A 80.672 952 136 20 1039 1967 631859134 631858208 0.000000e+00 695.0
34 TraesCS2D01G498000 chr5A 76.266 316 58 15 1243 1548 70482810 70482502 5.120000e-33 152.0
35 TraesCS2D01G498000 chr5A 83.333 84 14 0 1350 1433 457515107 457515190 8.810000e-11 78.7
36 TraesCS2D01G498000 chr7D 95.131 267 12 1 2516 2782 38515728 38515993 1.270000e-113 420.0
37 TraesCS2D01G498000 chr7D 96.610 59 2 0 2421 2479 38515672 38515730 6.770000e-17 99.0
38 TraesCS2D01G498000 chr7D 81.609 87 7 5 2086 2169 474273515 474273435 2.470000e-06 63.9
39 TraesCS2D01G498000 chr4B 84.238 387 26 17 2096 2478 667848514 667848869 7.870000e-91 344.0
40 TraesCS2D01G498000 chr7B 86.121 281 31 5 2530 2810 66975613 66975341 2.240000e-76 296.0
41 TraesCS2D01G498000 chr7B 100.000 34 0 0 1341 1374 394949376 394949343 2.470000e-06 63.9
42 TraesCS2D01G498000 chr1B 84.642 293 39 4 2515 2807 560245511 560245797 1.350000e-73 287.0
43 TraesCS2D01G498000 chr7A 96.203 158 6 0 2807 2964 717402733 717402890 2.930000e-65 259.0
44 TraesCS2D01G498000 chr7A 90.667 75 7 0 2405 2479 38370869 38370943 1.880000e-17 100.0
45 TraesCS2D01G498000 chr1A 94.969 159 8 0 2806 2964 486412399 486412557 1.770000e-62 250.0
46 TraesCS2D01G498000 chr6A 94.340 159 9 0 2806 2964 106457781 106457939 8.210000e-61 244.0
47 TraesCS2D01G498000 chr6A 94.340 159 9 0 2806 2964 613977721 613977879 8.210000e-61 244.0
48 TraesCS2D01G498000 chr6A 93.711 159 10 0 2806 2964 3752130 3751972 3.820000e-59 239.0
49 TraesCS2D01G498000 chr3A 94.340 159 9 0 2806 2964 661836402 661836244 8.210000e-61 244.0
50 TraesCS2D01G498000 chr3B 94.304 158 9 0 2806 2963 777021510 777021667 2.950000e-60 243.0
51 TraesCS2D01G498000 chr3B 80.399 301 24 14 2118 2417 828793445 828793179 2.330000e-46 196.0
52 TraesCS2D01G498000 chr6B 93.711 159 10 0 2806 2964 674563463 674563621 3.820000e-59 239.0


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 TraesCS2D01G498000 chr2D 593522133 593525098 2965 True 5478.000000 5478 100.000 1 2966 1 chr2D.!!$R2 2965
1 TraesCS2D01G498000 chr2A 728417671 728419334 1663 True 2189.000000 2189 90.393 326 2016 1 chr2A.!!$R1 1690
2 TraesCS2D01G498000 chr2B 719983007 719984419 1412 True 1897.000000 1897 90.966 681 2102 1 chr2B.!!$R2 1421
3 TraesCS2D01G498000 chr2B 331026008 331026721 713 True 1116.000000 1116 94.840 2095 2810 1 chr2B.!!$R1 715
4 TraesCS2D01G498000 chr6D 87370191 87371060 869 True 1563.000000 1563 99.080 2095 2964 1 chr6D.!!$R1 869
5 TraesCS2D01G498000 chr5D 495308565 495309551 986 False 809.000000 809 82.129 1005 1961 1 chr5D.!!$F2 956
6 TraesCS2D01G498000 chr5D 504101968 504102506 538 True 353.000000 353 79.520 1459 1968 1 chr5D.!!$R3 509
7 TraesCS2D01G498000 chr5B 611952887 611953879 992 False 809.000000 809 82.100 1005 1961 1 chr5B.!!$F2 956
8 TraesCS2D01G498000 chr5B 655262076 655262993 917 False 268.666667 411 88.463 2095 2807 3 chr5B.!!$F3 712
9 TraesCS2D01G498000 chr5A 619454367 619455318 951 False 802.000000 802 82.513 1042 1960 1 chr5A.!!$F2 918
10 TraesCS2D01G498000 chr5A 631858208 631859134 926 True 695.000000 695 80.672 1039 1967 1 chr5A.!!$R2 928

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
267 268 0.032267 GCTCGTCACCCCAGCTATAC 59.968 60.0 0.0 0.0 0.0 1.47 F
269 270 0.260816 TCGTCACCCCAGCTATACCT 59.739 55.0 0.0 0.0 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 1992 0.035630 GCTGATGACCTTGTCCTGCT 60.036 55.000 0.0 0.0 0.0 4.24 R
1985 2049 1.884926 CTTCCTCTTCCGGCGATGC 60.885 63.158 9.3 0.0 0.0 3.91 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
31 32 2.941210 AAAAATGAAGAGCGCCCGA 58.059 47.368 2.29 0.00 0.00 5.14
32 33 1.463674 AAAAATGAAGAGCGCCCGAT 58.536 45.000 2.29 0.00 0.00 4.18
33 34 0.734889 AAAATGAAGAGCGCCCGATG 59.265 50.000 2.29 0.00 0.00 3.84
34 35 0.107703 AAATGAAGAGCGCCCGATGA 60.108 50.000 2.29 0.00 0.00 2.92
35 36 0.107456 AATGAAGAGCGCCCGATGAT 59.893 50.000 2.29 0.00 0.00 2.45
36 37 0.602106 ATGAAGAGCGCCCGATGATG 60.602 55.000 2.29 0.00 0.00 3.07
37 38 1.958205 GAAGAGCGCCCGATGATGG 60.958 63.158 2.29 0.00 0.00 3.51
38 39 2.369257 GAAGAGCGCCCGATGATGGA 62.369 60.000 2.29 0.00 0.00 3.41
39 40 2.650813 AAGAGCGCCCGATGATGGAC 62.651 60.000 2.29 0.00 0.00 4.02
40 41 4.241555 AGCGCCCGATGATGGACC 62.242 66.667 2.29 0.00 0.00 4.46
42 43 3.911698 CGCCCGATGATGGACCGA 61.912 66.667 0.00 0.00 0.00 4.69
43 44 2.280186 GCCCGATGATGGACCGAC 60.280 66.667 0.00 0.00 0.00 4.79
44 45 3.088941 GCCCGATGATGGACCGACA 62.089 63.158 0.00 0.00 0.00 4.35
45 46 1.520192 CCCGATGATGGACCGACAA 59.480 57.895 0.00 0.00 0.00 3.18
46 47 0.530650 CCCGATGATGGACCGACAAG 60.531 60.000 0.00 0.00 0.00 3.16
48 49 0.459899 CGATGATGGACCGACAAGGA 59.540 55.000 0.00 0.00 45.00 3.36
49 50 1.134818 CGATGATGGACCGACAAGGAA 60.135 52.381 0.00 0.00 45.00 3.36
50 51 2.676750 CGATGATGGACCGACAAGGAAA 60.677 50.000 0.00 0.00 45.00 3.13
51 52 2.178912 TGATGGACCGACAAGGAAAC 57.821 50.000 0.00 0.00 45.00 2.78
52 53 1.076332 GATGGACCGACAAGGAAACG 58.924 55.000 0.00 0.00 45.00 3.60
53 54 0.953960 ATGGACCGACAAGGAAACGC 60.954 55.000 0.00 0.00 45.00 4.84
54 55 2.664436 GGACCGACAAGGAAACGCG 61.664 63.158 3.53 3.53 45.00 6.01
55 56 1.662446 GACCGACAAGGAAACGCGA 60.662 57.895 15.93 0.00 45.00 5.87
56 57 1.615107 GACCGACAAGGAAACGCGAG 61.615 60.000 15.93 0.00 45.00 5.03
57 58 1.663702 CCGACAAGGAAACGCGAGT 60.664 57.895 15.93 0.00 46.85 4.18
58 59 1.886861 CCGACAAGGAAACGCGAGTG 61.887 60.000 15.93 3.44 44.53 3.51
67 68 3.307906 ACGCGAGTGGGCTTGGTA 61.308 61.111 15.93 0.00 46.97 3.25
68 69 2.813908 CGCGAGTGGGCTTGGTAC 60.814 66.667 0.00 0.00 0.00 3.34
69 70 2.345991 GCGAGTGGGCTTGGTACA 59.654 61.111 0.00 0.00 0.00 2.90
70 71 1.078426 GCGAGTGGGCTTGGTACAT 60.078 57.895 0.00 0.00 39.30 2.29
71 72 1.369091 GCGAGTGGGCTTGGTACATG 61.369 60.000 0.00 0.00 39.30 3.21
72 73 0.744414 CGAGTGGGCTTGGTACATGG 60.744 60.000 0.00 0.00 39.30 3.66
73 74 0.394352 GAGTGGGCTTGGTACATGGG 60.394 60.000 0.00 0.00 39.30 4.00
74 75 2.052104 GTGGGCTTGGTACATGGGC 61.052 63.158 0.00 0.00 39.30 5.36
75 76 2.442087 GGGCTTGGTACATGGGCC 60.442 66.667 0.00 0.00 45.52 5.80
76 77 2.828549 GGCTTGGTACATGGGCCG 60.829 66.667 0.00 0.00 38.52 6.13
77 78 2.270850 GCTTGGTACATGGGCCGA 59.729 61.111 0.00 0.00 39.30 5.54
78 79 1.152963 GCTTGGTACATGGGCCGAT 60.153 57.895 0.00 0.00 39.30 4.18
79 80 1.447317 GCTTGGTACATGGGCCGATG 61.447 60.000 24.68 24.68 39.30 3.84
80 81 0.180171 CTTGGTACATGGGCCGATGA 59.820 55.000 31.80 14.13 39.30 2.92
81 82 0.843309 TTGGTACATGGGCCGATGAT 59.157 50.000 31.80 18.58 39.30 2.45
82 83 0.843309 TGGTACATGGGCCGATGATT 59.157 50.000 31.80 14.64 0.00 2.57
83 84 2.050918 TGGTACATGGGCCGATGATTA 58.949 47.619 31.80 13.62 0.00 1.75
84 85 2.439880 TGGTACATGGGCCGATGATTAA 59.560 45.455 31.80 13.09 0.00 1.40
85 86 3.074412 GGTACATGGGCCGATGATTAAG 58.926 50.000 31.80 6.84 0.00 1.85
86 87 1.609208 ACATGGGCCGATGATTAAGC 58.391 50.000 31.80 0.00 0.00 3.09
87 88 0.883833 CATGGGCCGATGATTAAGCC 59.116 55.000 22.34 0.00 44.99 4.35
88 89 0.606401 ATGGGCCGATGATTAAGCCG 60.606 55.000 0.00 0.00 46.75 5.52
89 90 2.617274 GGGCCGATGATTAAGCCGC 61.617 63.158 0.00 0.00 46.75 6.53
90 91 2.551270 GCCGATGATTAAGCCGCG 59.449 61.111 0.00 0.00 0.00 6.46
91 92 2.551270 CCGATGATTAAGCCGCGC 59.449 61.111 0.00 0.00 0.00 6.86
92 93 1.956170 CCGATGATTAAGCCGCGCT 60.956 57.895 5.56 0.00 42.56 5.92
93 94 1.202568 CGATGATTAAGCCGCGCTG 59.797 57.895 5.56 0.00 39.62 5.18
94 95 1.082496 GATGATTAAGCCGCGCTGC 60.082 57.895 16.70 16.70 39.62 5.25
105 106 3.338676 GCGCTGCGTATACTGGGC 61.339 66.667 24.04 7.36 39.52 5.36
106 107 2.661866 CGCTGCGTATACTGGGCC 60.662 66.667 14.93 0.00 0.00 5.80
107 108 2.504032 GCTGCGTATACTGGGCCA 59.496 61.111 5.85 5.85 0.00 5.36
108 109 1.595382 GCTGCGTATACTGGGCCAG 60.595 63.158 31.62 31.62 37.52 4.85
109 110 2.028125 GCTGCGTATACTGGGCCAGA 62.028 60.000 38.99 22.54 35.18 3.86
110 111 0.464036 CTGCGTATACTGGGCCAGAA 59.536 55.000 38.99 20.65 35.18 3.02
111 112 0.464036 TGCGTATACTGGGCCAGAAG 59.536 55.000 38.99 23.09 35.18 2.85
112 113 0.750850 GCGTATACTGGGCCAGAAGA 59.249 55.000 38.99 23.03 35.18 2.87
113 114 1.344763 GCGTATACTGGGCCAGAAGAT 59.655 52.381 38.99 27.29 35.18 2.40
114 115 2.868044 GCGTATACTGGGCCAGAAGATG 60.868 54.545 38.99 25.50 35.18 2.90
115 116 2.772287 GTATACTGGGCCAGAAGATGC 58.228 52.381 38.99 25.08 35.18 3.91
116 117 1.516110 ATACTGGGCCAGAAGATGCT 58.484 50.000 38.99 17.74 35.18 3.79
117 118 1.289160 TACTGGGCCAGAAGATGCTT 58.711 50.000 38.99 16.97 35.18 3.91
118 119 1.289160 ACTGGGCCAGAAGATGCTTA 58.711 50.000 38.99 0.00 35.18 3.09
119 120 1.635487 ACTGGGCCAGAAGATGCTTAA 59.365 47.619 38.99 0.00 35.18 1.85
120 121 2.243221 ACTGGGCCAGAAGATGCTTAAT 59.757 45.455 38.99 9.92 35.18 1.40
121 122 3.294214 CTGGGCCAGAAGATGCTTAATT 58.706 45.455 29.96 0.00 32.44 1.40
122 123 4.079787 ACTGGGCCAGAAGATGCTTAATTA 60.080 41.667 38.99 0.00 35.18 1.40
123 124 4.464008 TGGGCCAGAAGATGCTTAATTAG 58.536 43.478 0.00 0.00 0.00 1.73
124 125 3.823304 GGGCCAGAAGATGCTTAATTAGG 59.177 47.826 4.39 0.00 0.00 2.69
125 126 3.254411 GGCCAGAAGATGCTTAATTAGGC 59.746 47.826 12.39 12.39 37.69 3.93
126 127 4.140536 GCCAGAAGATGCTTAATTAGGCT 58.859 43.478 19.03 6.25 35.63 4.58
127 128 4.215185 GCCAGAAGATGCTTAATTAGGCTC 59.785 45.833 19.03 13.68 35.63 4.70
128 129 5.371526 CCAGAAGATGCTTAATTAGGCTCA 58.628 41.667 19.03 1.89 0.00 4.26
129 130 5.824624 CCAGAAGATGCTTAATTAGGCTCAA 59.175 40.000 19.03 1.19 0.00 3.02
130 131 6.489361 CCAGAAGATGCTTAATTAGGCTCAAT 59.511 38.462 19.03 5.95 0.00 2.57
131 132 7.663081 CCAGAAGATGCTTAATTAGGCTCAATA 59.337 37.037 19.03 0.49 0.00 1.90
132 133 9.228949 CAGAAGATGCTTAATTAGGCTCAATAT 57.771 33.333 19.03 5.27 0.00 1.28
133 134 9.804977 AGAAGATGCTTAATTAGGCTCAATATT 57.195 29.630 19.03 8.98 0.00 1.28
145 146 3.814945 GCTCAATATTAAGCCATCGTGC 58.185 45.455 0.00 0.00 32.22 5.34
146 147 3.665323 GCTCAATATTAAGCCATCGTGCG 60.665 47.826 0.00 0.00 36.02 5.34
147 148 2.805671 TCAATATTAAGCCATCGTGCGG 59.194 45.455 0.00 0.00 36.02 5.69
148 149 1.808411 ATATTAAGCCATCGTGCGGG 58.192 50.000 0.00 0.00 36.02 6.13
149 150 0.250124 TATTAAGCCATCGTGCGGGG 60.250 55.000 0.00 0.00 36.02 5.73
150 151 2.958578 ATTAAGCCATCGTGCGGGGG 62.959 60.000 5.64 2.72 36.02 5.40
154 155 3.467226 CCATCGTGCGGGGGTACT 61.467 66.667 0.00 0.00 0.00 2.73
155 156 2.202878 CATCGTGCGGGGGTACTG 60.203 66.667 0.00 0.00 0.00 2.74
156 157 2.363276 ATCGTGCGGGGGTACTGA 60.363 61.111 0.00 0.00 0.00 3.41
157 158 2.718073 ATCGTGCGGGGGTACTGAC 61.718 63.158 0.00 0.00 0.00 3.51
158 159 4.446413 CGTGCGGGGGTACTGACC 62.446 72.222 0.00 0.00 46.13 4.02
168 169 2.109425 GGTACTGACCACATTGTCCC 57.891 55.000 0.00 0.00 46.12 4.46
169 170 1.349688 GGTACTGACCACATTGTCCCA 59.650 52.381 0.00 0.00 46.12 4.37
170 171 2.423577 GTACTGACCACATTGTCCCAC 58.576 52.381 0.00 0.00 34.25 4.61
171 172 0.110486 ACTGACCACATTGTCCCACC 59.890 55.000 0.00 0.00 34.25 4.61
172 173 0.401738 CTGACCACATTGTCCCACCT 59.598 55.000 0.00 0.00 34.25 4.00
173 174 0.400213 TGACCACATTGTCCCACCTC 59.600 55.000 0.00 0.00 34.25 3.85
174 175 0.673644 GACCACATTGTCCCACCTCG 60.674 60.000 0.00 0.00 0.00 4.63
175 176 1.125093 ACCACATTGTCCCACCTCGA 61.125 55.000 0.00 0.00 0.00 4.04
176 177 0.391661 CCACATTGTCCCACCTCGAG 60.392 60.000 5.13 5.13 0.00 4.04
177 178 0.608130 CACATTGTCCCACCTCGAGA 59.392 55.000 15.71 0.00 0.00 4.04
178 179 1.208052 CACATTGTCCCACCTCGAGAT 59.792 52.381 15.71 0.00 0.00 2.75
179 180 1.482593 ACATTGTCCCACCTCGAGATC 59.517 52.381 15.71 0.00 0.00 2.75
180 181 1.123928 ATTGTCCCACCTCGAGATCC 58.876 55.000 15.71 0.00 0.00 3.36
181 182 0.976073 TTGTCCCACCTCGAGATCCC 60.976 60.000 15.71 0.00 0.00 3.85
182 183 1.381327 GTCCCACCTCGAGATCCCA 60.381 63.158 15.71 0.00 0.00 4.37
183 184 1.075970 TCCCACCTCGAGATCCCAG 60.076 63.158 15.71 0.00 0.00 4.45
184 185 2.801631 CCCACCTCGAGATCCCAGC 61.802 68.421 15.71 0.00 0.00 4.85
185 186 1.760086 CCACCTCGAGATCCCAGCT 60.760 63.158 15.71 0.00 0.00 4.24
186 187 1.739049 CACCTCGAGATCCCAGCTC 59.261 63.158 15.71 0.00 0.00 4.09
187 188 1.039785 CACCTCGAGATCCCAGCTCA 61.040 60.000 15.71 0.00 32.67 4.26
188 189 0.754957 ACCTCGAGATCCCAGCTCAG 60.755 60.000 15.71 0.00 32.67 3.35
189 190 1.462731 CCTCGAGATCCCAGCTCAGG 61.463 65.000 15.71 0.00 32.67 3.86
197 198 2.046892 CCAGCTCAGGGAACACCG 60.047 66.667 0.00 0.00 46.96 4.94
198 199 2.743928 CAGCTCAGGGAACACCGC 60.744 66.667 0.00 0.00 46.96 5.68
199 200 2.925170 AGCTCAGGGAACACCGCT 60.925 61.111 0.00 0.00 46.96 5.52
200 201 2.032681 GCTCAGGGAACACCGCTT 59.967 61.111 0.00 0.00 46.96 4.68
201 202 1.600916 GCTCAGGGAACACCGCTTT 60.601 57.895 0.00 0.00 46.96 3.51
202 203 0.321298 GCTCAGGGAACACCGCTTTA 60.321 55.000 0.00 0.00 46.96 1.85
203 204 1.880646 GCTCAGGGAACACCGCTTTAA 60.881 52.381 0.00 0.00 46.96 1.52
204 205 2.500229 CTCAGGGAACACCGCTTTAAA 58.500 47.619 0.00 0.00 46.96 1.52
205 206 2.223745 TCAGGGAACACCGCTTTAAAC 58.776 47.619 0.00 0.00 46.96 2.01
206 207 1.950909 CAGGGAACACCGCTTTAAACA 59.049 47.619 0.00 0.00 46.96 2.83
207 208 2.359531 CAGGGAACACCGCTTTAAACAA 59.640 45.455 0.00 0.00 46.96 2.83
208 209 2.621526 AGGGAACACCGCTTTAAACAAG 59.378 45.455 0.00 0.00 46.96 3.16
209 210 2.287970 GGGAACACCGCTTTAAACAAGG 60.288 50.000 0.00 0.00 0.00 3.61
210 211 2.390938 GAACACCGCTTTAAACAAGGC 58.609 47.619 0.00 0.00 0.00 4.35
211 212 1.687563 ACACCGCTTTAAACAAGGCT 58.312 45.000 0.00 0.00 0.00 4.58
212 213 1.607148 ACACCGCTTTAAACAAGGCTC 59.393 47.619 0.00 0.00 0.00 4.70
213 214 1.068541 CACCGCTTTAAACAAGGCTCC 60.069 52.381 0.00 0.00 0.00 4.70
214 215 0.168128 CCGCTTTAAACAAGGCTCCG 59.832 55.000 0.00 0.00 0.00 4.63
215 216 0.872388 CGCTTTAAACAAGGCTCCGT 59.128 50.000 0.00 0.00 0.00 4.69
216 217 1.265905 CGCTTTAAACAAGGCTCCGTT 59.734 47.619 0.00 0.00 0.00 4.44
217 218 2.287368 CGCTTTAAACAAGGCTCCGTTT 60.287 45.455 16.33 16.33 38.76 3.60
218 219 3.049912 GCTTTAAACAAGGCTCCGTTTG 58.950 45.455 19.63 3.78 36.10 2.93
219 220 3.243267 GCTTTAAACAAGGCTCCGTTTGA 60.243 43.478 19.63 12.07 36.10 2.69
220 221 4.537015 CTTTAAACAAGGCTCCGTTTGAG 58.463 43.478 19.63 14.58 44.47 3.02
221 222 2.341846 AAACAAGGCTCCGTTTGAGA 57.658 45.000 12.62 0.00 44.42 3.27
222 223 2.568623 AACAAGGCTCCGTTTGAGAT 57.431 45.000 0.00 0.00 44.42 2.75
223 224 1.813513 ACAAGGCTCCGTTTGAGATG 58.186 50.000 0.00 0.00 44.42 2.90
224 225 0.449388 CAAGGCTCCGTTTGAGATGC 59.551 55.000 0.00 0.00 44.42 3.91
225 226 0.326264 AAGGCTCCGTTTGAGATGCT 59.674 50.000 0.00 0.00 44.42 3.79
226 227 0.107945 AGGCTCCGTTTGAGATGCTC 60.108 55.000 0.00 0.00 44.42 4.26
227 228 0.107945 GGCTCCGTTTGAGATGCTCT 60.108 55.000 0.00 0.00 44.42 4.09
228 229 1.285578 GCTCCGTTTGAGATGCTCTC 58.714 55.000 6.31 6.31 44.42 3.20
229 230 1.554392 CTCCGTTTGAGATGCTCTCG 58.446 55.000 8.15 0.00 46.25 4.04
230 231 0.458543 TCCGTTTGAGATGCTCTCGC 60.459 55.000 8.15 0.00 46.25 5.03
231 232 1.424493 CCGTTTGAGATGCTCTCGCC 61.424 60.000 8.15 0.31 46.25 5.54
232 233 1.746727 CGTTTGAGATGCTCTCGCCG 61.747 60.000 8.15 6.62 46.25 6.46
233 234 0.458543 GTTTGAGATGCTCTCGCCGA 60.459 55.000 8.15 0.00 46.25 5.54
234 235 0.179127 TTTGAGATGCTCTCGCCGAG 60.179 55.000 8.05 8.05 46.25 4.63
241 242 4.504916 CTCTCGCCGAGCCCAGTG 62.505 72.222 9.77 0.00 31.99 3.66
264 265 3.075005 GGCTCGTCACCCCAGCTA 61.075 66.667 0.00 0.00 33.38 3.32
265 266 2.435693 GGCTCGTCACCCCAGCTAT 61.436 63.158 0.00 0.00 33.38 2.97
266 267 1.113517 GGCTCGTCACCCCAGCTATA 61.114 60.000 0.00 0.00 33.38 1.31
267 268 0.032267 GCTCGTCACCCCAGCTATAC 59.968 60.000 0.00 0.00 0.00 1.47
268 269 0.674534 CTCGTCACCCCAGCTATACC 59.325 60.000 0.00 0.00 0.00 2.73
269 270 0.260816 TCGTCACCCCAGCTATACCT 59.739 55.000 0.00 0.00 0.00 3.08
270 271 1.496001 TCGTCACCCCAGCTATACCTA 59.504 52.381 0.00 0.00 0.00 3.08
271 272 2.091720 TCGTCACCCCAGCTATACCTAA 60.092 50.000 0.00 0.00 0.00 2.69
272 273 2.296471 CGTCACCCCAGCTATACCTAAG 59.704 54.545 0.00 0.00 0.00 2.18
273 274 2.633481 GTCACCCCAGCTATACCTAAGG 59.367 54.545 0.00 0.00 0.00 2.69
274 275 1.978580 CACCCCAGCTATACCTAAGGG 59.021 57.143 0.00 0.00 39.09 3.95
276 277 1.657804 CCCAGCTATACCTAAGGGGG 58.342 60.000 0.00 0.00 40.03 5.40
292 293 4.284550 GGGGCAGCAGTTGGTGGA 62.285 66.667 12.65 0.00 43.24 4.02
293 294 2.985847 GGGCAGCAGTTGGTGGAC 60.986 66.667 12.65 0.00 43.24 4.02
294 295 2.985847 GGCAGCAGTTGGTGGACC 60.986 66.667 12.65 3.34 43.24 4.46
295 296 3.357079 GCAGCAGTTGGTGGACCG 61.357 66.667 12.65 0.00 43.24 4.79
296 297 3.357079 CAGCAGTTGGTGGACCGC 61.357 66.667 3.47 0.00 39.67 5.68
297 298 3.872603 AGCAGTTGGTGGACCGCA 61.873 61.111 7.48 0.00 39.43 5.69
298 299 2.672996 GCAGTTGGTGGACCGCAT 60.673 61.111 7.48 0.00 39.43 4.73
299 300 2.981560 GCAGTTGGTGGACCGCATG 61.982 63.158 7.48 1.20 39.43 4.06
300 301 2.672996 AGTTGGTGGACCGCATGC 60.673 61.111 7.91 7.91 39.43 4.06
301 302 3.747976 GTTGGTGGACCGCATGCC 61.748 66.667 13.15 0.00 39.43 4.40
302 303 3.965258 TTGGTGGACCGCATGCCT 61.965 61.111 13.15 0.00 39.43 4.75
303 304 3.505790 TTGGTGGACCGCATGCCTT 62.506 57.895 13.15 0.00 39.43 4.35
304 305 3.134127 GGTGGACCGCATGCCTTC 61.134 66.667 13.15 8.41 0.00 3.46
305 306 3.499737 GTGGACCGCATGCCTTCG 61.500 66.667 13.15 0.00 0.00 3.79
373 374 8.760980 AAATCCGAATTTCATATTTAGACCCA 57.239 30.769 0.00 0.00 28.70 4.51
374 375 7.745620 ATCCGAATTTCATATTTAGACCCAC 57.254 36.000 0.00 0.00 0.00 4.61
375 376 6.654959 TCCGAATTTCATATTTAGACCCACA 58.345 36.000 0.00 0.00 0.00 4.17
376 377 7.287061 TCCGAATTTCATATTTAGACCCACAT 58.713 34.615 0.00 0.00 0.00 3.21
391 392 6.341316 AGACCCACATATATATTGTCGCATC 58.659 40.000 0.00 0.00 0.00 3.91
443 444 5.844301 AACCAATTTGTCGAATTTCATGC 57.156 34.783 0.00 0.00 35.79 4.06
469 470 5.182950 TCGTTACAAGCATCAATTTGTCCAT 59.817 36.000 0.00 0.00 38.41 3.41
471 472 6.365789 CGTTACAAGCATCAATTTGTCCATTT 59.634 34.615 0.00 0.00 38.41 2.32
472 473 7.512297 GTTACAAGCATCAATTTGTCCATTTG 58.488 34.615 0.00 0.50 38.41 2.32
473 474 5.856156 ACAAGCATCAATTTGTCCATTTGA 58.144 33.333 0.00 0.00 32.32 2.69
474 475 6.289834 ACAAGCATCAATTTGTCCATTTGAA 58.710 32.000 0.00 0.00 32.32 2.69
504 505 7.490962 ACAAGAAACGAGATATTGTTGTCAA 57.509 32.000 0.00 0.00 38.25 3.18
550 553 1.600023 TTTAGGTTCAGGGCGTTGTG 58.400 50.000 0.00 0.00 0.00 3.33
556 559 2.672651 CAGGGCGTTGTGATGGCA 60.673 61.111 0.00 0.00 39.01 4.92
568 571 0.994247 TGATGGCATCCACCACTCTT 59.006 50.000 23.92 0.00 44.17 2.85
596 599 4.609947 TGTTTTTGATGACTGTGTGCATC 58.390 39.130 0.00 0.00 40.92 3.91
599 602 5.518848 TTTTGATGACTGTGTGCATCTTT 57.481 34.783 0.00 0.00 41.08 2.52
600 603 5.518848 TTTGATGACTGTGTGCATCTTTT 57.481 34.783 0.00 0.00 41.08 2.27
601 604 4.492791 TGATGACTGTGTGCATCTTTTG 57.507 40.909 0.00 0.00 41.08 2.44
602 605 4.136051 TGATGACTGTGTGCATCTTTTGA 58.864 39.130 0.00 0.00 41.08 2.69
603 606 4.763279 TGATGACTGTGTGCATCTTTTGAT 59.237 37.500 0.00 0.00 41.08 2.57
616 619 3.766545 TCTTTTGATGAAGAGGTTGGGG 58.233 45.455 0.00 0.00 32.19 4.96
617 620 3.140144 TCTTTTGATGAAGAGGTTGGGGT 59.860 43.478 0.00 0.00 32.19 4.95
618 621 3.611025 TTTGATGAAGAGGTTGGGGTT 57.389 42.857 0.00 0.00 0.00 4.11
619 622 3.611025 TTGATGAAGAGGTTGGGGTTT 57.389 42.857 0.00 0.00 0.00 3.27
620 623 3.154827 TGATGAAGAGGTTGGGGTTTC 57.845 47.619 0.00 0.00 0.00 2.78
621 624 2.445145 TGATGAAGAGGTTGGGGTTTCA 59.555 45.455 0.00 0.00 32.90 2.69
622 625 3.117322 TGATGAAGAGGTTGGGGTTTCAA 60.117 43.478 0.00 0.00 32.21 2.69
623 626 2.661718 TGAAGAGGTTGGGGTTTCAAC 58.338 47.619 0.00 0.00 44.42 3.18
671 674 4.210331 AGCTCACCAGTCAAACAAGAAAT 58.790 39.130 0.00 0.00 0.00 2.17
673 676 5.471456 AGCTCACCAGTCAAACAAGAAATAG 59.529 40.000 0.00 0.00 0.00 1.73
679 682 7.965107 CACCAGTCAAACAAGAAATAGCTAATC 59.035 37.037 0.00 0.00 0.00 1.75
833 836 7.440523 AGTAATTGAAGTTTGGCAGTAGAAG 57.559 36.000 0.00 0.00 0.00 2.85
841 844 3.695830 TTGGCAGTAGAAGTTACCTGG 57.304 47.619 0.00 0.00 0.00 4.45
852 856 2.643551 AGTTACCTGGCATTTCCATCG 58.356 47.619 0.00 0.00 45.50 3.84
857 861 1.731433 CTGGCATTTCCATCGGCTGG 61.731 60.000 0.00 0.00 45.50 4.85
868 875 2.595386 CATCGGCTGGCAAACTTAAAC 58.405 47.619 1.08 0.00 0.00 2.01
898 905 1.009389 GTGACTTCTCGGCGAGTTGG 61.009 60.000 33.31 24.84 0.00 3.77
908 915 1.863267 GGCGAGTTGGATGAGATCAG 58.137 55.000 0.00 0.00 0.00 2.90
946 953 2.069273 GTAGCCAGCTACCGCAATATG 58.931 52.381 17.26 0.00 42.11 1.78
955 962 3.058016 GCTACCGCAATATGTACTACCGA 60.058 47.826 0.00 0.00 35.78 4.69
2030 2097 1.883084 GTGTAGCTTCATCCCCGCG 60.883 63.158 0.00 0.00 0.00 6.46
2041 2108 4.993029 TCATCCCCGCGAAATAAAAATT 57.007 36.364 8.23 0.00 0.00 1.82
2067 2134 7.647907 AAAACTGTAACTTCACCGTATACTG 57.352 36.000 0.56 0.00 0.00 2.74
2070 2137 4.487948 TGTAACTTCACCGTATACTGTGC 58.512 43.478 19.35 7.71 32.20 4.57
2072 2139 3.671008 ACTTCACCGTATACTGTGCAA 57.329 42.857 19.35 13.92 32.20 4.08
2073 2140 3.997762 ACTTCACCGTATACTGTGCAAA 58.002 40.909 19.35 10.64 32.20 3.68
2074 2141 4.575885 ACTTCACCGTATACTGTGCAAAT 58.424 39.130 19.35 5.52 32.20 2.32
2093 2160 6.120812 GCAAATAATAACTGTAGCTTCGTCG 58.879 40.000 0.00 0.00 0.00 5.12
2715 3033 0.605589 AGTCTTGAGGAAGAGGCGTG 59.394 55.000 0.00 0.00 38.95 5.34
2810 3128 9.528018 CAGATAAGTCTTTAAGTTCCAGAGATC 57.472 37.037 0.00 0.00 30.42 2.75
2889 3207 4.778415 CGCGTGTCCTCCTCGTGG 62.778 72.222 0.00 0.00 0.00 4.94
2964 3282 3.664025 CTTCGCCATGACCCGCTCA 62.664 63.158 0.00 0.00 0.00 4.26
2965 3283 2.930385 CTTCGCCATGACCCGCTCAT 62.930 60.000 0.00 0.00 40.59 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.133025 CATCGGGCGCTCTTCATTTTT 59.867 47.619 5.36 0.00 0.00 1.94
14 15 0.734889 CATCGGGCGCTCTTCATTTT 59.265 50.000 5.36 0.00 0.00 1.82
15 16 0.107703 TCATCGGGCGCTCTTCATTT 60.108 50.000 5.36 0.00 0.00 2.32
16 17 0.107456 ATCATCGGGCGCTCTTCATT 59.893 50.000 5.36 0.00 0.00 2.57
17 18 0.602106 CATCATCGGGCGCTCTTCAT 60.602 55.000 5.36 0.00 0.00 2.57
18 19 1.227350 CATCATCGGGCGCTCTTCA 60.227 57.895 5.36 0.00 0.00 3.02
19 20 1.958205 CCATCATCGGGCGCTCTTC 60.958 63.158 5.36 0.00 0.00 2.87
20 21 2.109799 CCATCATCGGGCGCTCTT 59.890 61.111 5.36 0.00 0.00 2.85
21 22 2.839632 TCCATCATCGGGCGCTCT 60.840 61.111 5.36 0.00 0.00 4.09
22 23 2.663188 GTCCATCATCGGGCGCTC 60.663 66.667 7.64 0.06 0.00 5.03
23 24 4.241555 GGTCCATCATCGGGCGCT 62.242 66.667 7.64 0.00 0.00 5.92
25 26 3.911698 TCGGTCCATCATCGGGCG 61.912 66.667 0.00 0.00 0.00 6.13
26 27 2.280186 GTCGGTCCATCATCGGGC 60.280 66.667 0.00 0.00 0.00 6.13
27 28 0.530650 CTTGTCGGTCCATCATCGGG 60.531 60.000 0.00 0.00 0.00 5.14
28 29 0.530650 CCTTGTCGGTCCATCATCGG 60.531 60.000 0.00 0.00 0.00 4.18
29 30 0.459899 TCCTTGTCGGTCCATCATCG 59.540 55.000 0.00 0.00 0.00 3.84
30 31 2.678336 GTTTCCTTGTCGGTCCATCATC 59.322 50.000 0.00 0.00 0.00 2.92
31 32 2.711542 GTTTCCTTGTCGGTCCATCAT 58.288 47.619 0.00 0.00 0.00 2.45
32 33 1.606994 CGTTTCCTTGTCGGTCCATCA 60.607 52.381 0.00 0.00 0.00 3.07
33 34 1.076332 CGTTTCCTTGTCGGTCCATC 58.924 55.000 0.00 0.00 0.00 3.51
34 35 0.953960 GCGTTTCCTTGTCGGTCCAT 60.954 55.000 0.00 0.00 0.00 3.41
35 36 1.595929 GCGTTTCCTTGTCGGTCCA 60.596 57.895 0.00 0.00 0.00 4.02
36 37 2.664436 CGCGTTTCCTTGTCGGTCC 61.664 63.158 0.00 0.00 0.00 4.46
37 38 1.615107 CTCGCGTTTCCTTGTCGGTC 61.615 60.000 5.77 0.00 0.00 4.79
38 39 1.663702 CTCGCGTTTCCTTGTCGGT 60.664 57.895 5.77 0.00 0.00 4.69
39 40 1.663702 ACTCGCGTTTCCTTGTCGG 60.664 57.895 5.77 0.00 0.00 4.79
40 41 1.487231 CACTCGCGTTTCCTTGTCG 59.513 57.895 5.77 0.00 0.00 4.35
41 42 1.566018 CCCACTCGCGTTTCCTTGTC 61.566 60.000 5.77 0.00 0.00 3.18
42 43 1.597027 CCCACTCGCGTTTCCTTGT 60.597 57.895 5.77 0.00 0.00 3.16
43 44 2.966309 GCCCACTCGCGTTTCCTTG 61.966 63.158 5.77 0.00 0.00 3.61
44 45 2.668550 GCCCACTCGCGTTTCCTT 60.669 61.111 5.77 0.00 0.00 3.36
45 46 3.178540 AAGCCCACTCGCGTTTCCT 62.179 57.895 5.77 0.00 0.00 3.36
46 47 2.668550 AAGCCCACTCGCGTTTCC 60.669 61.111 5.77 0.00 0.00 3.13
47 48 2.556287 CAAGCCCACTCGCGTTTC 59.444 61.111 5.77 0.00 0.00 2.78
48 49 2.386064 TACCAAGCCCACTCGCGTTT 62.386 55.000 5.77 0.00 0.00 3.60
49 50 2.874664 TACCAAGCCCACTCGCGTT 61.875 57.895 5.77 0.00 0.00 4.84
50 51 3.307906 TACCAAGCCCACTCGCGT 61.308 61.111 5.77 0.00 0.00 6.01
51 52 2.813908 GTACCAAGCCCACTCGCG 60.814 66.667 0.00 0.00 0.00 5.87
52 53 1.078426 ATGTACCAAGCCCACTCGC 60.078 57.895 0.00 0.00 0.00 5.03
53 54 0.744414 CCATGTACCAAGCCCACTCG 60.744 60.000 0.00 0.00 0.00 4.18
54 55 0.394352 CCCATGTACCAAGCCCACTC 60.394 60.000 0.00 0.00 0.00 3.51
55 56 1.691219 CCCATGTACCAAGCCCACT 59.309 57.895 0.00 0.00 0.00 4.00
56 57 2.052104 GCCCATGTACCAAGCCCAC 61.052 63.158 0.00 0.00 0.00 4.61
57 58 2.358619 GCCCATGTACCAAGCCCA 59.641 61.111 0.00 0.00 0.00 5.36
58 59 2.442087 GGCCCATGTACCAAGCCC 60.442 66.667 0.00 0.00 37.66 5.19
59 60 2.624674 ATCGGCCCATGTACCAAGCC 62.625 60.000 0.00 3.82 40.33 4.35
60 61 1.152963 ATCGGCCCATGTACCAAGC 60.153 57.895 0.00 0.00 0.00 4.01
61 62 0.180171 TCATCGGCCCATGTACCAAG 59.820 55.000 10.37 0.00 0.00 3.61
62 63 0.843309 ATCATCGGCCCATGTACCAA 59.157 50.000 10.37 0.00 0.00 3.67
63 64 0.843309 AATCATCGGCCCATGTACCA 59.157 50.000 10.37 0.00 0.00 3.25
64 65 2.851263 TAATCATCGGCCCATGTACC 57.149 50.000 10.37 0.00 0.00 3.34
65 66 2.484264 GCTTAATCATCGGCCCATGTAC 59.516 50.000 10.37 0.00 0.00 2.90
66 67 2.552155 GGCTTAATCATCGGCCCATGTA 60.552 50.000 10.37 0.00 38.77 2.29
67 68 1.609208 GCTTAATCATCGGCCCATGT 58.391 50.000 10.37 0.00 0.00 3.21
68 69 0.883833 GGCTTAATCATCGGCCCATG 59.116 55.000 3.56 3.56 38.77 3.66
69 70 0.606401 CGGCTTAATCATCGGCCCAT 60.606 55.000 0.00 0.00 41.35 4.00
70 71 1.227823 CGGCTTAATCATCGGCCCA 60.228 57.895 0.00 0.00 41.35 5.36
71 72 2.617274 GCGGCTTAATCATCGGCCC 61.617 63.158 0.00 0.00 41.35 5.80
72 73 2.946762 GCGGCTTAATCATCGGCC 59.053 61.111 0.00 0.00 41.02 6.13
73 74 2.551270 CGCGGCTTAATCATCGGC 59.449 61.111 0.00 0.00 0.00 5.54
74 75 1.956170 AGCGCGGCTTAATCATCGG 60.956 57.895 8.83 0.00 33.89 4.18
75 76 1.202568 CAGCGCGGCTTAATCATCG 59.797 57.895 8.83 0.00 36.40 3.84
76 77 1.082496 GCAGCGCGGCTTAATCATC 60.082 57.895 25.57 0.00 36.40 2.92
77 78 3.025619 GCAGCGCGGCTTAATCAT 58.974 55.556 25.57 0.00 36.40 2.45
88 89 3.338676 GCCCAGTATACGCAGCGC 61.339 66.667 16.61 0.00 0.00 5.92
89 90 2.661866 GGCCCAGTATACGCAGCG 60.662 66.667 14.82 14.82 0.00 5.18
90 91 1.595382 CTGGCCCAGTATACGCAGC 60.595 63.158 1.39 1.57 0.00 5.25
91 92 0.464036 TTCTGGCCCAGTATACGCAG 59.536 55.000 11.27 0.00 32.61 5.18
92 93 0.464036 CTTCTGGCCCAGTATACGCA 59.536 55.000 11.27 0.00 32.61 5.24
93 94 0.750850 TCTTCTGGCCCAGTATACGC 59.249 55.000 11.27 0.00 32.61 4.42
94 95 2.868044 GCATCTTCTGGCCCAGTATACG 60.868 54.545 11.27 0.00 32.61 3.06
95 96 2.370189 AGCATCTTCTGGCCCAGTATAC 59.630 50.000 11.27 0.00 32.61 1.47
96 97 2.694397 AGCATCTTCTGGCCCAGTATA 58.306 47.619 11.27 0.00 32.61 1.47
97 98 1.516110 AGCATCTTCTGGCCCAGTAT 58.484 50.000 11.27 0.40 32.61 2.12
98 99 1.289160 AAGCATCTTCTGGCCCAGTA 58.711 50.000 11.27 0.00 32.61 2.74
99 100 1.289160 TAAGCATCTTCTGGCCCAGT 58.711 50.000 11.27 0.00 32.61 4.00
100 101 2.425143 TTAAGCATCTTCTGGCCCAG 57.575 50.000 3.69 3.69 0.00 4.45
101 102 3.386932 AATTAAGCATCTTCTGGCCCA 57.613 42.857 0.00 0.00 0.00 5.36
102 103 3.823304 CCTAATTAAGCATCTTCTGGCCC 59.177 47.826 0.00 0.00 0.00 5.80
103 104 3.254411 GCCTAATTAAGCATCTTCTGGCC 59.746 47.826 0.00 0.00 0.00 5.36
104 105 4.140536 AGCCTAATTAAGCATCTTCTGGC 58.859 43.478 8.72 3.28 37.15 4.85
105 106 5.371526 TGAGCCTAATTAAGCATCTTCTGG 58.628 41.667 8.72 0.00 0.00 3.86
106 107 6.932356 TTGAGCCTAATTAAGCATCTTCTG 57.068 37.500 8.72 0.00 0.00 3.02
107 108 9.804977 AATATTGAGCCTAATTAAGCATCTTCT 57.195 29.630 8.72 0.00 0.00 2.85
124 125 3.665323 CGCACGATGGCTTAATATTGAGC 60.665 47.826 20.88 20.88 38.89 4.26
125 126 3.120546 CCGCACGATGGCTTAATATTGAG 60.121 47.826 2.91 2.91 0.00 3.02
126 127 2.805671 CCGCACGATGGCTTAATATTGA 59.194 45.455 0.00 0.00 0.00 2.57
127 128 2.095768 CCCGCACGATGGCTTAATATTG 60.096 50.000 0.00 0.00 0.00 1.90
128 129 2.151202 CCCGCACGATGGCTTAATATT 58.849 47.619 0.00 0.00 0.00 1.28
129 130 1.610624 CCCCGCACGATGGCTTAATAT 60.611 52.381 0.00 0.00 0.00 1.28
130 131 0.250124 CCCCGCACGATGGCTTAATA 60.250 55.000 0.00 0.00 0.00 0.98
131 132 1.525995 CCCCGCACGATGGCTTAAT 60.526 57.895 0.00 0.00 0.00 1.40
132 133 2.124901 CCCCGCACGATGGCTTAA 60.125 61.111 0.00 0.00 0.00 1.85
133 134 4.169696 CCCCCGCACGATGGCTTA 62.170 66.667 0.00 0.00 0.00 3.09
137 138 3.467226 AGTACCCCCGCACGATGG 61.467 66.667 0.00 0.00 0.00 3.51
138 139 2.202878 CAGTACCCCCGCACGATG 60.203 66.667 0.00 0.00 0.00 3.84
139 140 2.363276 TCAGTACCCCCGCACGAT 60.363 61.111 0.00 0.00 0.00 3.73
140 141 3.376078 GTCAGTACCCCCGCACGA 61.376 66.667 0.00 0.00 0.00 4.35
141 142 4.446413 GGTCAGTACCCCCGCACG 62.446 72.222 0.00 0.00 40.21 5.34
142 143 3.315949 TGGTCAGTACCCCCGCAC 61.316 66.667 0.00 0.00 46.16 5.34
143 144 3.315949 GTGGTCAGTACCCCCGCA 61.316 66.667 0.00 0.00 46.16 5.69
144 145 2.193087 AATGTGGTCAGTACCCCCGC 62.193 60.000 0.00 0.00 46.16 6.13
145 146 0.392461 CAATGTGGTCAGTACCCCCG 60.392 60.000 0.00 0.00 46.16 5.73
146 147 0.696501 ACAATGTGGTCAGTACCCCC 59.303 55.000 0.00 0.00 46.16 5.40
147 148 1.339727 GGACAATGTGGTCAGTACCCC 60.340 57.143 0.00 0.00 46.16 4.95
148 149 1.339727 GGGACAATGTGGTCAGTACCC 60.340 57.143 0.00 0.00 46.16 3.69
149 150 1.349688 TGGGACAATGTGGTCAGTACC 59.650 52.381 0.00 0.00 40.74 3.34
150 151 2.423577 GTGGGACAATGTGGTCAGTAC 58.576 52.381 0.00 0.00 44.16 2.73
151 152 1.349688 GGTGGGACAATGTGGTCAGTA 59.650 52.381 0.00 0.00 44.16 2.74
152 153 0.110486 GGTGGGACAATGTGGTCAGT 59.890 55.000 0.00 0.00 44.16 3.41
153 154 0.401738 AGGTGGGACAATGTGGTCAG 59.598 55.000 0.00 0.00 44.16 3.51
154 155 0.400213 GAGGTGGGACAATGTGGTCA 59.600 55.000 0.00 0.00 44.16 4.02
155 156 0.673644 CGAGGTGGGACAATGTGGTC 60.674 60.000 0.00 0.00 44.16 4.02
156 157 1.125093 TCGAGGTGGGACAATGTGGT 61.125 55.000 0.00 0.00 44.16 4.16
157 158 0.391661 CTCGAGGTGGGACAATGTGG 60.392 60.000 3.91 0.00 44.16 4.17
158 159 0.608130 TCTCGAGGTGGGACAATGTG 59.392 55.000 13.56 0.00 44.16 3.21
159 160 1.482593 GATCTCGAGGTGGGACAATGT 59.517 52.381 13.56 0.00 44.16 2.71
160 161 1.202580 GGATCTCGAGGTGGGACAATG 60.203 57.143 13.56 0.00 44.16 2.82
161 162 1.123928 GGATCTCGAGGTGGGACAAT 58.876 55.000 13.56 0.00 44.16 2.71
162 163 0.976073 GGGATCTCGAGGTGGGACAA 60.976 60.000 13.56 0.00 44.16 3.18
163 164 1.381327 GGGATCTCGAGGTGGGACA 60.381 63.158 13.56 0.00 0.00 4.02
164 165 1.381327 TGGGATCTCGAGGTGGGAC 60.381 63.158 13.56 0.00 0.00 4.46
165 166 1.075970 CTGGGATCTCGAGGTGGGA 60.076 63.158 13.56 0.00 0.00 4.37
166 167 2.801631 GCTGGGATCTCGAGGTGGG 61.802 68.421 13.56 0.00 0.00 4.61
167 168 1.743321 GAGCTGGGATCTCGAGGTGG 61.743 65.000 13.56 0.00 32.13 4.61
168 169 1.039785 TGAGCTGGGATCTCGAGGTG 61.040 60.000 13.56 0.00 32.13 4.00
169 170 0.754957 CTGAGCTGGGATCTCGAGGT 60.755 60.000 13.56 4.76 34.65 3.85
170 171 1.462731 CCTGAGCTGGGATCTCGAGG 61.463 65.000 13.56 0.00 33.41 4.63
171 172 2.040330 CCTGAGCTGGGATCTCGAG 58.960 63.158 5.93 5.93 33.41 4.04
172 173 4.266962 CCTGAGCTGGGATCTCGA 57.733 61.111 0.00 0.00 33.41 4.04
180 181 2.046892 CGGTGTTCCCTGAGCTGG 60.047 66.667 0.00 0.00 0.00 4.85
181 182 2.738213 AAGCGGTGTTCCCTGAGCTG 62.738 60.000 0.00 0.00 34.94 4.24
182 183 2.056906 AAAGCGGTGTTCCCTGAGCT 62.057 55.000 0.00 0.00 36.40 4.09
183 184 0.321298 TAAAGCGGTGTTCCCTGAGC 60.321 55.000 0.00 0.00 0.00 4.26
184 185 2.178912 TTAAAGCGGTGTTCCCTGAG 57.821 50.000 0.00 0.00 0.00 3.35
185 186 2.223745 GTTTAAAGCGGTGTTCCCTGA 58.776 47.619 0.00 0.00 0.00 3.86
186 187 1.950909 TGTTTAAAGCGGTGTTCCCTG 59.049 47.619 0.00 0.00 0.00 4.45
187 188 2.351706 TGTTTAAAGCGGTGTTCCCT 57.648 45.000 0.00 0.00 0.00 4.20
188 189 2.287970 CCTTGTTTAAAGCGGTGTTCCC 60.288 50.000 0.00 0.00 0.00 3.97
189 190 2.860971 GCCTTGTTTAAAGCGGTGTTCC 60.861 50.000 0.00 0.00 0.00 3.62
190 191 2.034179 AGCCTTGTTTAAAGCGGTGTTC 59.966 45.455 0.00 0.00 0.00 3.18
191 192 2.028876 AGCCTTGTTTAAAGCGGTGTT 58.971 42.857 0.00 0.00 0.00 3.32
192 193 1.607148 GAGCCTTGTTTAAAGCGGTGT 59.393 47.619 0.00 0.00 0.00 4.16
193 194 1.068541 GGAGCCTTGTTTAAAGCGGTG 60.069 52.381 0.00 0.00 0.00 4.94
194 195 1.244816 GGAGCCTTGTTTAAAGCGGT 58.755 50.000 0.00 0.00 0.00 5.68
195 196 0.168128 CGGAGCCTTGTTTAAAGCGG 59.832 55.000 0.00 0.00 0.00 5.52
196 197 0.872388 ACGGAGCCTTGTTTAAAGCG 59.128 50.000 0.00 0.00 0.00 4.68
197 198 3.049912 CAAACGGAGCCTTGTTTAAAGC 58.950 45.455 0.00 0.00 36.22 3.51
198 199 4.274950 TCTCAAACGGAGCCTTGTTTAAAG 59.725 41.667 0.00 1.00 43.70 1.85
199 200 4.200874 TCTCAAACGGAGCCTTGTTTAAA 58.799 39.130 0.00 0.00 43.70 1.52
200 201 3.811083 TCTCAAACGGAGCCTTGTTTAA 58.189 40.909 0.00 0.00 43.70 1.52
201 202 3.478857 TCTCAAACGGAGCCTTGTTTA 57.521 42.857 0.00 0.00 43.70 2.01
202 203 2.341846 TCTCAAACGGAGCCTTGTTT 57.658 45.000 0.00 0.00 43.70 2.83
203 204 2.154462 CATCTCAAACGGAGCCTTGTT 58.846 47.619 0.00 0.00 43.70 2.83
204 205 1.813513 CATCTCAAACGGAGCCTTGT 58.186 50.000 0.00 0.00 43.70 3.16
205 206 0.449388 GCATCTCAAACGGAGCCTTG 59.551 55.000 0.00 0.00 43.70 3.61
206 207 0.326264 AGCATCTCAAACGGAGCCTT 59.674 50.000 0.00 0.00 43.70 4.35
207 208 0.107945 GAGCATCTCAAACGGAGCCT 60.108 55.000 0.00 0.00 43.70 4.58
208 209 2.388347 GAGCATCTCAAACGGAGCC 58.612 57.895 0.00 0.00 43.70 4.70
249 250 0.674534 GGTATAGCTGGGGTGACGAG 59.325 60.000 0.00 0.00 0.00 4.18
250 251 0.260816 AGGTATAGCTGGGGTGACGA 59.739 55.000 3.03 0.00 0.00 4.20
251 252 1.991121 TAGGTATAGCTGGGGTGACG 58.009 55.000 14.72 0.00 0.00 4.35
252 253 2.633481 CCTTAGGTATAGCTGGGGTGAC 59.367 54.545 14.72 0.00 0.00 3.67
253 254 2.427297 CCCTTAGGTATAGCTGGGGTGA 60.427 54.545 24.66 2.18 0.00 4.02
254 255 1.978580 CCCTTAGGTATAGCTGGGGTG 59.021 57.143 24.66 13.38 0.00 4.61
255 256 1.132495 CCCCTTAGGTATAGCTGGGGT 60.132 57.143 27.45 2.70 46.84 4.95
256 257 1.657804 CCCCTTAGGTATAGCTGGGG 58.342 60.000 24.67 24.67 46.89 4.96
257 258 1.657804 CCCCCTTAGGTATAGCTGGG 58.342 60.000 16.89 16.89 34.68 4.45
275 276 4.284550 TCCACCAACTGCTGCCCC 62.285 66.667 0.00 0.00 0.00 5.80
276 277 2.985847 GTCCACCAACTGCTGCCC 60.986 66.667 0.00 0.00 0.00 5.36
277 278 2.985847 GGTCCACCAACTGCTGCC 60.986 66.667 0.00 0.00 35.64 4.85
278 279 3.357079 CGGTCCACCAACTGCTGC 61.357 66.667 0.00 0.00 35.14 5.25
279 280 3.357079 GCGGTCCACCAACTGCTG 61.357 66.667 0.70 0.00 46.04 4.41
282 283 2.981560 GCATGCGGTCCACCAACTG 61.982 63.158 0.00 0.00 35.14 3.16
283 284 2.672996 GCATGCGGTCCACCAACT 60.673 61.111 0.00 0.00 35.14 3.16
284 285 3.747976 GGCATGCGGTCCACCAAC 61.748 66.667 12.44 0.00 35.14 3.77
285 286 3.505790 AAGGCATGCGGTCCACCAA 62.506 57.895 12.44 0.00 35.14 3.67
286 287 3.918253 GAAGGCATGCGGTCCACCA 62.918 63.158 12.44 0.00 35.14 4.17
287 288 3.134127 GAAGGCATGCGGTCCACC 61.134 66.667 12.44 0.00 0.00 4.61
288 289 3.499737 CGAAGGCATGCGGTCCAC 61.500 66.667 12.44 0.00 0.00 4.02
289 290 4.776322 CCGAAGGCATGCGGTCCA 62.776 66.667 10.37 0.00 46.14 4.02
307 308 3.542629 AAAAGCAGTTGAGCCGCGC 62.543 57.895 0.00 0.00 34.23 6.86
308 309 1.008538 AAAAAGCAGTTGAGCCGCG 60.009 52.632 0.00 0.00 34.23 6.46
362 363 9.811995 GCGACAATATATATGTGGGTCTAAATA 57.188 33.333 0.00 0.00 0.00 1.40
364 365 7.672240 TGCGACAATATATATGTGGGTCTAAA 58.328 34.615 0.00 0.00 0.00 1.85
373 374 6.701340 ACTGGTGATGCGACAATATATATGT 58.299 36.000 0.00 0.00 0.00 2.29
374 375 7.601073 AACTGGTGATGCGACAATATATATG 57.399 36.000 0.00 0.00 0.00 1.78
375 376 7.877612 TGAAACTGGTGATGCGACAATATATAT 59.122 33.333 0.00 0.00 0.00 0.86
376 377 7.213678 TGAAACTGGTGATGCGACAATATATA 58.786 34.615 0.00 0.00 0.00 0.86
417 418 7.275341 GCATGAAATTCGACAAATTGGTTATGA 59.725 33.333 0.00 0.00 37.64 2.15
421 422 4.385447 CGCATGAAATTCGACAAATTGGTT 59.615 37.500 0.00 0.00 37.64 3.67
432 433 3.362281 TGTAACGACGCATGAAATTCG 57.638 42.857 0.00 0.22 37.50 3.34
443 444 4.463209 ACAAATTGATGCTTGTAACGACG 58.537 39.130 0.00 0.00 34.04 5.12
469 470 4.884744 TCTCGTTTCTTGTTCCCATTCAAA 59.115 37.500 0.00 0.00 0.00 2.69
471 472 4.079980 TCTCGTTTCTTGTTCCCATTCA 57.920 40.909 0.00 0.00 0.00 2.57
472 473 6.927294 ATATCTCGTTTCTTGTTCCCATTC 57.073 37.500 0.00 0.00 0.00 2.67
473 474 6.659242 ACAATATCTCGTTTCTTGTTCCCATT 59.341 34.615 0.00 0.00 0.00 3.16
474 475 6.180472 ACAATATCTCGTTTCTTGTTCCCAT 58.820 36.000 0.00 0.00 0.00 4.00
483 484 8.023128 CCAAATTGACAACAATATCTCGTTTCT 58.977 33.333 0.00 0.00 44.67 2.52
529 530 2.359531 CACAACGCCCTGAACCTAAAAA 59.640 45.455 0.00 0.00 0.00 1.94
530 531 1.950909 CACAACGCCCTGAACCTAAAA 59.049 47.619 0.00 0.00 0.00 1.52
531 532 1.141254 TCACAACGCCCTGAACCTAAA 59.859 47.619 0.00 0.00 0.00 1.85
534 537 0.606401 CATCACAACGCCCTGAACCT 60.606 55.000 0.00 0.00 0.00 3.50
540 543 1.750399 GATGCCATCACAACGCCCT 60.750 57.895 0.00 0.00 0.00 5.19
550 553 1.065199 TCAAGAGTGGTGGATGCCATC 60.065 52.381 0.00 0.00 41.08 3.51
556 559 5.505181 AAACATACTCAAGAGTGGTGGAT 57.495 39.130 12.77 0.00 42.52 3.41
568 571 6.513230 GCACACAGTCATCAAAAACATACTCA 60.513 38.462 0.00 0.00 0.00 3.41
596 599 3.500343 ACCCCAACCTCTTCATCAAAAG 58.500 45.455 0.00 0.00 0.00 2.27
599 602 3.117322 TGAAACCCCAACCTCTTCATCAA 60.117 43.478 0.00 0.00 0.00 2.57
600 603 2.445145 TGAAACCCCAACCTCTTCATCA 59.555 45.455 0.00 0.00 0.00 3.07
601 604 3.154827 TGAAACCCCAACCTCTTCATC 57.845 47.619 0.00 0.00 0.00 2.92
602 605 3.230976 GTTGAAACCCCAACCTCTTCAT 58.769 45.455 0.00 0.00 40.24 2.57
603 606 2.661718 GTTGAAACCCCAACCTCTTCA 58.338 47.619 0.00 0.00 40.24 3.02
642 645 1.131638 TGACTGGTGAGCTCAACCTT 58.868 50.000 28.50 15.46 31.06 3.50
644 647 1.604278 GTTTGACTGGTGAGCTCAACC 59.396 52.381 28.50 24.46 31.06 3.77
701 704 6.884832 TCTACTGTCAAAACCTTCTTCAAGA 58.115 36.000 0.00 0.00 0.00 3.02
852 856 5.385509 TTCATAGTTTAAGTTTGCCAGCC 57.614 39.130 0.00 0.00 0.00 4.85
857 861 7.378728 GTCACTGGTTTCATAGTTTAAGTTTGC 59.621 37.037 0.00 0.00 0.00 3.68
868 875 4.177026 CCGAGAAGTCACTGGTTTCATAG 58.823 47.826 0.00 0.00 0.00 2.23
898 905 4.518590 TGCAGCTACTACTCTGATCTCATC 59.481 45.833 0.00 0.00 32.26 2.92
908 915 2.663826 ACTTGCTGCAGCTACTACTC 57.336 50.000 36.61 8.49 42.66 2.59
946 953 2.364324 TGATGGATGGCTTCGGTAGTAC 59.636 50.000 0.00 0.00 0.00 2.73
955 962 3.657398 TGATCAAGTGATGGATGGCTT 57.343 42.857 0.00 0.00 34.37 4.35
1018 1029 3.702048 CGTGGTCACCGGGGACAT 61.702 66.667 36.51 0.00 39.59 3.06
1040 1051 1.005340 GTACAGGATCTCGTCGTCGT 58.995 55.000 1.33 0.00 38.33 4.34
1434 1454 4.697756 CCGGCGCTGTGGGAGAAA 62.698 66.667 16.49 0.00 0.00 2.52
1856 1920 4.783621 GCGCCTGCCACATCTCCA 62.784 66.667 0.00 0.00 33.98 3.86
1928 1992 0.035630 GCTGATGACCTTGTCCTGCT 60.036 55.000 0.00 0.00 0.00 4.24
1985 2049 1.884926 CTTCCTCTTCCGGCGATGC 60.885 63.158 9.30 0.00 0.00 3.91
2041 2108 9.195411 CAGTATACGGTGAAGTTACAGTTTTTA 57.805 33.333 0.00 0.00 31.55 1.52
2065 2132 6.901887 CGAAGCTACAGTTATTATTTGCACAG 59.098 38.462 0.00 0.00 0.00 3.66
2067 2134 6.772078 ACGAAGCTACAGTTATTATTTGCAC 58.228 36.000 0.00 0.00 0.00 4.57
2070 2137 6.120812 GCGACGAAGCTACAGTTATTATTTG 58.879 40.000 0.00 0.00 0.00 2.32
2072 2139 4.440103 CGCGACGAAGCTACAGTTATTATT 59.560 41.667 0.00 0.00 34.40 1.40
2073 2140 3.973135 CGCGACGAAGCTACAGTTATTAT 59.027 43.478 0.00 0.00 34.40 1.28
2074 2141 3.357021 CGCGACGAAGCTACAGTTATTA 58.643 45.455 0.00 0.00 34.40 0.98
2093 2160 3.181523 GGTCGTACAAGATTTTCTTCCGC 60.182 47.826 0.00 0.00 33.78 5.54
2889 3207 1.524008 AAAACTACTGGGCAAGGCGC 61.524 55.000 0.00 0.00 41.94 6.53


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

AutoCloner maintained by Alex Coulton.