Multiple sequence alignment - TraesCS7D01G085700

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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 TraesCS7D01G085700 chr7D 100.000 4884 0 0 1 4884 52795517 52800400 0.000000e+00 9020
1 TraesCS7D01G085700 chr7D 90.754 3407 217 39 631 3972 53434767 53431394 0.000000e+00 4457
2 TraesCS7D01G085700 chr7D 86.164 1113 125 15 2564 3648 52830962 52832073 0.000000e+00 1175
3 TraesCS7D01G085700 chr7D 85.637 1114 129 11 2564 3648 52822724 52823835 0.000000e+00 1142
4 TraesCS7D01G085700 chr7D 83.127 1292 178 19 2539 3795 53508571 53507285 0.000000e+00 1142
5 TraesCS7D01G085700 chr7D 81.594 1418 200 37 977 2363 53498766 53497379 0.000000e+00 1116
6 TraesCS7D01G085700 chr7D 82.466 1249 197 18 1035 2279 52821427 52822657 0.000000e+00 1074
7 TraesCS7D01G085700 chr7D 80.230 1128 193 24 838 1954 52695087 52696195 0.000000e+00 821
8 TraesCS7D01G085700 chr7D 81.084 1052 162 28 925 1960 53485478 53484448 0.000000e+00 806
9 TraesCS7D01G085700 chr7D 82.189 932 156 8 1030 1960 52829683 52830605 0.000000e+00 793
10 TraesCS7D01G085700 chr7D 83.366 511 78 6 1030 1539 53416477 53415973 2.660000e-127 466
11 TraesCS7D01G085700 chr7A 90.117 3946 266 52 134 4014 55398855 55394969 0.000000e+00 5012
12 TraesCS7D01G085700 chr7A 83.584 1261 164 25 2573 3792 55383695 55382437 0.000000e+00 1142
13 TraesCS7D01G085700 chr7A 86.245 1076 118 15 2602 3648 55376091 55375017 0.000000e+00 1140
14 TraesCS7D01G085700 chr7A 81.719 1373 221 25 995 2358 55895508 55894157 0.000000e+00 1118
15 TraesCS7D01G085700 chr7A 81.138 1389 214 33 1005 2363 55883566 55882196 0.000000e+00 1070
16 TraesCS7D01G085700 chr7A 82.845 1195 175 11 2539 3705 55894129 55892937 0.000000e+00 1044
17 TraesCS7D01G085700 chr7A 77.465 1633 285 64 386 1975 55429071 55427479 0.000000e+00 900
18 TraesCS7D01G085700 chr4A 89.223 3925 276 78 134 3986 668097340 668093491 0.000000e+00 4769
19 TraesCS7D01G085700 chr4A 86.594 1104 119 15 2573 3648 667860177 667859075 0.000000e+00 1192
20 TraesCS7D01G085700 chr4A 85.701 1105 127 15 2573 3648 668084607 668083505 0.000000e+00 1136
21 TraesCS7D01G085700 chr4A 84.576 1167 149 15 2572 3709 668161472 668160308 0.000000e+00 1129
22 TraesCS7D01G085700 chr4A 79.401 1670 288 44 623 2282 668086303 668084680 0.000000e+00 1127
23 TraesCS7D01G085700 chr4A 78.972 1265 220 35 731 1975 668110595 668109357 0.000000e+00 821
24 TraesCS7D01G085700 chr4A 87.349 332 34 6 2032 2363 668147923 668147600 1.660000e-99 374
25 TraesCS7D01G085700 chr5D 97.861 561 10 2 4017 4577 324752744 324752186 0.000000e+00 968
26 TraesCS7D01G085700 chr5D 98.408 314 5 0 4571 4884 324752156 324751843 1.990000e-153 553
27 TraesCS7D01G085700 chr5D 98.901 273 3 0 4612 4884 558926231 558925959 5.680000e-134 488
28 TraesCS7D01G085700 chr3B 85.757 674 55 14 4052 4691 778788680 778788014 0.000000e+00 675
29 TraesCS7D01G085700 chr2D 99.636 275 1 0 667 941 214785439 214785165 2.030000e-138 503
30 TraesCS7D01G085700 chr2D 99.231 130 1 0 984 1113 214785166 214785037 8.170000e-58 235
31 TraesCS7D01G085700 chr2D 96.721 61 1 1 4815 4874 640052048 640051988 3.110000e-17 100
32 TraesCS7D01G085700 chr1D 99.636 275 1 0 667 941 38627939 38628213 2.030000e-138 503
33 TraesCS7D01G085700 chr1D 99.273 275 2 0 667 941 131765887 131765613 9.440000e-137 497
34 TraesCS7D01G085700 chr1D 99.200 250 2 0 667 916 104008302 104008053 7.450000e-123 451
35 TraesCS7D01G085700 chr1D 99.248 133 1 0 981 1113 38628209 38628341 1.760000e-59 241
36 TraesCS7D01G085700 chr1D 100.000 130 0 0 984 1113 131765614 131765485 1.760000e-59 241


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 TraesCS7D01G085700 chr7D 52795517 52800400 4883 False 9020.0 9020 100.0000 1 4884 1 chr7D.!!$F2 4883
1 TraesCS7D01G085700 chr7D 53431394 53434767 3373 True 4457.0 4457 90.7540 631 3972 1 chr7D.!!$R2 3341
2 TraesCS7D01G085700 chr7D 53507285 53508571 1286 True 1142.0 1142 83.1270 2539 3795 1 chr7D.!!$R5 1256
3 TraesCS7D01G085700 chr7D 53497379 53498766 1387 True 1116.0 1116 81.5940 977 2363 1 chr7D.!!$R4 1386
4 TraesCS7D01G085700 chr7D 52821427 52823835 2408 False 1108.0 1142 84.0515 1035 3648 2 chr7D.!!$F3 2613
5 TraesCS7D01G085700 chr7D 52829683 52832073 2390 False 984.0 1175 84.1765 1030 3648 2 chr7D.!!$F4 2618
6 TraesCS7D01G085700 chr7D 52695087 52696195 1108 False 821.0 821 80.2300 838 1954 1 chr7D.!!$F1 1116
7 TraesCS7D01G085700 chr7D 53484448 53485478 1030 True 806.0 806 81.0840 925 1960 1 chr7D.!!$R3 1035
8 TraesCS7D01G085700 chr7D 53415973 53416477 504 True 466.0 466 83.3660 1030 1539 1 chr7D.!!$R1 509
9 TraesCS7D01G085700 chr7A 55394969 55398855 3886 True 5012.0 5012 90.1170 134 4014 1 chr7A.!!$R3 3880
10 TraesCS7D01G085700 chr7A 55382437 55383695 1258 True 1142.0 1142 83.5840 2573 3792 1 chr7A.!!$R2 1219
11 TraesCS7D01G085700 chr7A 55375017 55376091 1074 True 1140.0 1140 86.2450 2602 3648 1 chr7A.!!$R1 1046
12 TraesCS7D01G085700 chr7A 55892937 55895508 2571 True 1081.0 1118 82.2820 995 3705 2 chr7A.!!$R6 2710
13 TraesCS7D01G085700 chr7A 55882196 55883566 1370 True 1070.0 1070 81.1380 1005 2363 1 chr7A.!!$R5 1358
14 TraesCS7D01G085700 chr7A 55427479 55429071 1592 True 900.0 900 77.4650 386 1975 1 chr7A.!!$R4 1589
15 TraesCS7D01G085700 chr4A 668093491 668097340 3849 True 4769.0 4769 89.2230 134 3986 1 chr4A.!!$R2 3852
16 TraesCS7D01G085700 chr4A 667859075 667860177 1102 True 1192.0 1192 86.5940 2573 3648 1 chr4A.!!$R1 1075
17 TraesCS7D01G085700 chr4A 668083505 668086303 2798 True 1131.5 1136 82.5510 623 3648 2 chr4A.!!$R6 3025
18 TraesCS7D01G085700 chr4A 668160308 668161472 1164 True 1129.0 1129 84.5760 2572 3709 1 chr4A.!!$R5 1137
19 TraesCS7D01G085700 chr4A 668109357 668110595 1238 True 821.0 821 78.9720 731 1975 1 chr4A.!!$R3 1244
20 TraesCS7D01G085700 chr5D 324751843 324752744 901 True 760.5 968 98.1345 4017 4884 2 chr5D.!!$R2 867
21 TraesCS7D01G085700 chr3B 778788014 778788680 666 True 675.0 675 85.7570 4052 4691 1 chr3B.!!$R1 639

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
277 287 0.037303 AGAATGTGGTGGTCCTGCAG 59.963 55.000 6.78 6.78 34.23 4.41 F
281 291 1.078848 GTGGTGGTCCTGCAGCTAG 60.079 63.158 8.66 0.00 34.23 3.42 F
1042 1095 1.678970 GCCCCTTGCCTACAGGTTG 60.679 63.158 0.00 0.00 37.57 3.77 F
1232 1285 1.267806 CCCTTCAGTGTCACATGCAAC 59.732 52.381 5.62 0.00 0.00 4.17 F
2101 2198 0.620556 ATGAGTGCGGACCTCCAAAT 59.379 50.000 2.38 0.00 35.14 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1147 1200 0.582005 GACGTTGCCACACTTGTCTC 59.418 55.000 0.00 0.00 0.00 3.36 R
1217 1270 0.936600 TCACGTTGCATGTGACACTG 59.063 50.000 15.94 4.12 39.05 3.66 R
1894 1950 2.338577 ACTTTGAGAGCAGTTGCAGT 57.661 45.000 6.90 0.00 45.16 4.40 R
3175 3342 1.275291 GGACTTGACATCTCCGTGGAA 59.725 52.381 0.00 0.00 0.00 3.53 R
3900 4085 0.035152 TGGCAAGCTCCACGATGATT 60.035 50.000 0.00 0.00 0.00 2.57 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
19 20 2.939460 GGGATTTTTGGGTGACGATG 57.061 50.000 0.00 0.00 0.00 3.84
20 21 1.476488 GGGATTTTTGGGTGACGATGG 59.524 52.381 0.00 0.00 0.00 3.51
21 22 2.442413 GGATTTTTGGGTGACGATGGA 58.558 47.619 0.00 0.00 0.00 3.41
22 23 2.163613 GGATTTTTGGGTGACGATGGAC 59.836 50.000 0.00 0.00 0.00 4.02
35 36 3.720949 CGATGGACGGTATGTAAGGAA 57.279 47.619 0.00 0.00 38.46 3.36
36 37 3.378339 CGATGGACGGTATGTAAGGAAC 58.622 50.000 0.00 0.00 38.46 3.62
37 38 3.725490 GATGGACGGTATGTAAGGAACC 58.275 50.000 0.00 0.00 0.00 3.62
38 39 2.538222 TGGACGGTATGTAAGGAACCA 58.462 47.619 0.00 0.00 32.55 3.67
39 40 2.234414 TGGACGGTATGTAAGGAACCAC 59.766 50.000 0.00 0.00 32.55 4.16
40 41 2.234414 GGACGGTATGTAAGGAACCACA 59.766 50.000 0.00 0.00 32.55 4.17
41 42 3.118519 GGACGGTATGTAAGGAACCACAT 60.119 47.826 0.00 0.00 38.01 3.21
42 43 4.510571 GACGGTATGTAAGGAACCACATT 58.489 43.478 2.92 0.00 36.22 2.71
43 44 4.510571 ACGGTATGTAAGGAACCACATTC 58.489 43.478 2.92 0.00 36.22 2.67
44 45 4.020039 ACGGTATGTAAGGAACCACATTCA 60.020 41.667 2.92 0.00 39.30 2.57
45 46 4.331717 CGGTATGTAAGGAACCACATTCAC 59.668 45.833 2.92 0.00 39.30 3.18
46 47 4.331717 GGTATGTAAGGAACCACATTCACG 59.668 45.833 2.92 0.00 39.30 4.35
47 48 3.755112 TGTAAGGAACCACATTCACGA 57.245 42.857 0.00 0.00 39.30 4.35
48 49 3.659786 TGTAAGGAACCACATTCACGAG 58.340 45.455 0.00 0.00 39.30 4.18
49 50 3.322541 TGTAAGGAACCACATTCACGAGA 59.677 43.478 0.00 0.00 39.30 4.04
50 51 3.703001 AAGGAACCACATTCACGAGAT 57.297 42.857 0.00 0.00 39.30 2.75
51 52 4.819105 AAGGAACCACATTCACGAGATA 57.181 40.909 0.00 0.00 39.30 1.98
52 53 4.392921 AGGAACCACATTCACGAGATAG 57.607 45.455 0.00 0.00 39.30 2.08
53 54 3.769844 AGGAACCACATTCACGAGATAGT 59.230 43.478 0.00 0.00 39.30 2.12
54 55 4.954202 AGGAACCACATTCACGAGATAGTA 59.046 41.667 0.00 0.00 39.30 1.82
55 56 5.598830 AGGAACCACATTCACGAGATAGTAT 59.401 40.000 0.00 0.00 39.30 2.12
56 57 5.921408 GGAACCACATTCACGAGATAGTATC 59.079 44.000 1.55 1.55 39.30 2.24
57 58 6.461092 GGAACCACATTCACGAGATAGTATCA 60.461 42.308 12.66 0.00 39.30 2.15
58 59 6.656632 ACCACATTCACGAGATAGTATCAT 57.343 37.500 12.66 0.00 0.00 2.45
59 60 6.682746 ACCACATTCACGAGATAGTATCATC 58.317 40.000 12.66 6.30 0.00 2.92
60 61 6.265422 ACCACATTCACGAGATAGTATCATCA 59.735 38.462 12.66 0.00 0.00 3.07
61 62 7.039434 ACCACATTCACGAGATAGTATCATCAT 60.039 37.037 12.66 0.00 0.00 2.45
62 63 7.275123 CCACATTCACGAGATAGTATCATCATG 59.725 40.741 12.66 6.22 0.00 3.07
63 64 8.025445 CACATTCACGAGATAGTATCATCATGA 58.975 37.037 12.66 0.00 0.00 3.07
64 65 8.579863 ACATTCACGAGATAGTATCATCATGAA 58.420 33.333 12.66 14.94 32.67 2.57
65 66 9.415544 CATTCACGAGATAGTATCATCATGAAA 57.584 33.333 17.19 0.00 32.27 2.69
66 67 9.636879 ATTCACGAGATAGTATCATCATGAAAG 57.363 33.333 17.19 0.00 32.27 2.62
67 68 8.396272 TCACGAGATAGTATCATCATGAAAGA 57.604 34.615 12.66 1.00 0.00 2.52
68 69 8.510505 TCACGAGATAGTATCATCATGAAAGAG 58.489 37.037 12.66 0.00 0.00 2.85
69 70 8.296000 CACGAGATAGTATCATCATGAAAGAGT 58.704 37.037 12.66 0.00 0.00 3.24
70 71 8.855110 ACGAGATAGTATCATCATGAAAGAGTT 58.145 33.333 12.66 0.00 0.00 3.01
87 88 9.695526 TGAAAGAGTTATGTCATTTTTCAATGG 57.304 29.630 0.00 0.00 40.41 3.16
88 89 8.538409 AAAGAGTTATGTCATTTTTCAATGGC 57.462 30.769 0.00 0.00 44.20 4.40
89 90 6.324819 AGAGTTATGTCATTTTTCAATGGCG 58.675 36.000 0.00 0.00 46.53 5.69
90 91 6.150976 AGAGTTATGTCATTTTTCAATGGCGA 59.849 34.615 0.00 0.00 46.53 5.54
91 92 6.686630 AGTTATGTCATTTTTCAATGGCGAA 58.313 32.000 0.00 0.00 46.53 4.70
92 93 7.322664 AGTTATGTCATTTTTCAATGGCGAAT 58.677 30.769 0.00 0.00 46.53 3.34
93 94 7.276218 AGTTATGTCATTTTTCAATGGCGAATG 59.724 33.333 0.00 0.00 46.53 2.67
94 95 4.880759 TGTCATTTTTCAATGGCGAATGT 58.119 34.783 0.00 0.00 46.53 2.71
95 96 4.685165 TGTCATTTTTCAATGGCGAATGTG 59.315 37.500 0.00 0.00 46.53 3.21
96 97 4.922692 GTCATTTTTCAATGGCGAATGTGA 59.077 37.500 0.00 0.00 40.41 3.58
97 98 5.061311 GTCATTTTTCAATGGCGAATGTGAG 59.939 40.000 0.00 0.00 40.41 3.51
98 99 4.844998 TTTTTCAATGGCGAATGTGAGA 57.155 36.364 0.00 0.00 0.00 3.27
99 100 5.389859 TTTTTCAATGGCGAATGTGAGAT 57.610 34.783 0.00 0.00 0.00 2.75
100 101 5.389859 TTTTCAATGGCGAATGTGAGATT 57.610 34.783 0.00 0.00 0.00 2.40
101 102 6.507958 TTTTCAATGGCGAATGTGAGATTA 57.492 33.333 0.00 0.00 0.00 1.75
102 103 5.739752 TTCAATGGCGAATGTGAGATTAG 57.260 39.130 0.00 0.00 0.00 1.73
103 104 5.022282 TCAATGGCGAATGTGAGATTAGA 57.978 39.130 0.00 0.00 0.00 2.10
104 105 5.614308 TCAATGGCGAATGTGAGATTAGAT 58.386 37.500 0.00 0.00 0.00 1.98
105 106 6.057533 TCAATGGCGAATGTGAGATTAGATT 58.942 36.000 0.00 0.00 0.00 2.40
106 107 5.936686 ATGGCGAATGTGAGATTAGATTG 57.063 39.130 0.00 0.00 0.00 2.67
107 108 3.561310 TGGCGAATGTGAGATTAGATTGC 59.439 43.478 0.00 0.00 0.00 3.56
108 109 3.812053 GGCGAATGTGAGATTAGATTGCT 59.188 43.478 0.00 0.00 0.00 3.91
109 110 4.991056 GGCGAATGTGAGATTAGATTGCTA 59.009 41.667 0.00 0.00 0.00 3.49
110 111 5.641209 GGCGAATGTGAGATTAGATTGCTAT 59.359 40.000 0.00 0.00 0.00 2.97
111 112 6.813649 GGCGAATGTGAGATTAGATTGCTATA 59.186 38.462 0.00 0.00 0.00 1.31
112 113 7.493971 GGCGAATGTGAGATTAGATTGCTATAT 59.506 37.037 0.00 0.00 0.00 0.86
113 114 8.877779 GCGAATGTGAGATTAGATTGCTATATT 58.122 33.333 0.00 0.00 0.00 1.28
127 128 9.053840 AGATTGCTATATTCAGTTCATCAGTTG 57.946 33.333 0.00 0.00 0.00 3.16
128 129 8.743085 ATTGCTATATTCAGTTCATCAGTTGT 57.257 30.769 0.00 0.00 0.00 3.32
129 130 7.543947 TGCTATATTCAGTTCATCAGTTGTG 57.456 36.000 0.00 0.00 0.00 3.33
130 131 6.037500 TGCTATATTCAGTTCATCAGTTGTGC 59.962 38.462 0.00 0.00 0.00 4.57
131 132 6.037500 GCTATATTCAGTTCATCAGTTGTGCA 59.962 38.462 0.00 0.00 0.00 4.57
132 133 3.969117 TTCAGTTCATCAGTTGTGCAC 57.031 42.857 10.75 10.75 0.00 4.57
136 137 3.065786 CAGTTCATCAGTTGTGCACAAGT 59.934 43.478 31.81 30.83 39.91 3.16
145 146 6.494842 TCAGTTGTGCACAAGTTTATTTCTC 58.505 36.000 32.36 17.15 37.41 2.87
146 147 6.094742 TCAGTTGTGCACAAGTTTATTTCTCA 59.905 34.615 32.36 9.39 37.41 3.27
174 179 7.587037 TTCTTTGTTTCAAGATGATGGAACT 57.413 32.000 0.67 0.00 39.19 3.01
175 180 7.587037 TCTTTGTTTCAAGATGATGGAACTT 57.413 32.000 0.67 0.00 39.19 2.66
179 184 9.528018 TTTGTTTCAAGATGATGGAACTTAAAC 57.472 29.630 0.67 0.00 39.19 2.01
188 194 9.082313 AGATGATGGAACTTAAACATGAAAAGT 57.918 29.630 0.00 2.97 35.01 2.66
200 206 0.179059 TGAAAAGTGCTGCTCGGACA 60.179 50.000 0.00 0.00 36.26 4.02
238 248 7.178274 TGCACCCAACATAAATCAGTAAAATCT 59.822 33.333 0.00 0.00 0.00 2.40
239 249 7.489113 GCACCCAACATAAATCAGTAAAATCTG 59.511 37.037 0.00 0.00 36.85 2.90
253 263 6.037720 CAGTAAAATCTGTGTGTGTTGTGGTA 59.962 38.462 0.00 0.00 0.00 3.25
260 270 1.210722 TGTGTGTTGTGGTAGGCAAGA 59.789 47.619 0.00 0.00 0.00 3.02
273 283 0.251341 GGCAAGAATGTGGTGGTCCT 60.251 55.000 0.00 0.00 34.23 3.85
274 284 0.883833 GCAAGAATGTGGTGGTCCTG 59.116 55.000 0.00 0.00 34.23 3.86
275 285 0.883833 CAAGAATGTGGTGGTCCTGC 59.116 55.000 0.00 0.00 34.23 4.85
276 286 0.478072 AAGAATGTGGTGGTCCTGCA 59.522 50.000 0.00 0.00 34.23 4.41
277 287 0.037303 AGAATGTGGTGGTCCTGCAG 59.963 55.000 6.78 6.78 34.23 4.41
279 289 2.072874 AATGTGGTGGTCCTGCAGCT 62.073 55.000 8.66 0.00 34.23 4.24
280 290 1.200760 ATGTGGTGGTCCTGCAGCTA 61.201 55.000 8.66 0.00 34.23 3.32
281 291 1.078848 GTGGTGGTCCTGCAGCTAG 60.079 63.158 8.66 0.00 34.23 3.42
282 292 2.293318 TGGTGGTCCTGCAGCTAGG 61.293 63.158 8.66 0.00 39.29 3.02
283 293 2.586792 GTGGTCCTGCAGCTAGGG 59.413 66.667 8.66 0.00 38.42 3.53
288 298 4.496336 CCTGCAGCTAGGGCCCAC 62.496 72.222 27.56 13.50 39.73 4.61
310 320 2.364632 CACCCGATGTGCCATTTTAGA 58.635 47.619 0.00 0.00 38.34 2.10
317 327 7.040686 ACCCGATGTGCCATTTTAGATTTATAC 60.041 37.037 0.00 0.00 0.00 1.47
333 343 8.621532 AGATTTATACACAAAGAGCAACAAGA 57.378 30.769 0.00 0.00 0.00 3.02
343 354 8.436200 CACAAAGAGCAACAAGATAGTTACTAC 58.564 37.037 0.00 0.00 0.00 2.73
439 455 9.471084 AAAGTTACATAGAAAAACCCAAAATCG 57.529 29.630 0.00 0.00 0.00 3.34
440 456 7.088272 AGTTACATAGAAAAACCCAAAATCGC 58.912 34.615 0.00 0.00 0.00 4.58
449 465 4.335400 AACCCAAAATCGCAAACTGAAT 57.665 36.364 0.00 0.00 0.00 2.57
464 488 6.183360 GCAAACTGAATCAAGCCATAATGTTG 60.183 38.462 0.00 0.00 0.00 3.33
474 498 7.222872 TCAAGCCATAATGTTGTTTTGGATTT 58.777 30.769 2.14 0.00 34.07 2.17
487 511 9.406828 GTTGTTTTGGATTTGAGGTAATACTTC 57.593 33.333 0.00 0.00 0.00 3.01
499 523 7.191210 TGAGGTAATACTTCCCCTACAGTTTA 58.809 38.462 0.00 0.00 0.00 2.01
508 536 7.793036 ACTTCCCCTACAGTTTATAGAATGAC 58.207 38.462 0.00 0.00 0.00 3.06
534 562 3.325135 AGAAAGAAACACGGAGTCTGGAT 59.675 43.478 3.50 0.00 41.61 3.41
536 564 3.045601 AGAAACACGGAGTCTGGATTG 57.954 47.619 3.50 0.00 41.61 2.67
538 566 3.576982 AGAAACACGGAGTCTGGATTGTA 59.423 43.478 3.50 0.00 41.61 2.41
540 568 3.526931 ACACGGAGTCTGGATTGTATG 57.473 47.619 3.50 0.00 41.61 2.39
545 573 3.726607 GGAGTCTGGATTGTATGCTGAG 58.273 50.000 0.00 0.00 29.93 3.35
548 576 5.163405 GGAGTCTGGATTGTATGCTGAGTAA 60.163 44.000 0.00 0.00 33.60 2.24
550 578 5.423610 AGTCTGGATTGTATGCTGAGTAACT 59.576 40.000 0.00 0.00 32.14 2.24
552 580 6.920758 GTCTGGATTGTATGCTGAGTAACTAG 59.079 42.308 0.00 0.00 29.93 2.57
553 581 6.607600 TCTGGATTGTATGCTGAGTAACTAGT 59.392 38.462 0.00 0.00 0.00 2.57
558 586 6.438259 TGTATGCTGAGTAACTAGTGACTC 57.562 41.667 27.63 27.63 42.08 3.36
560 588 3.090037 TGCTGAGTAACTAGTGACTCCC 58.910 50.000 30.00 22.58 41.22 4.30
626 654 9.790344 ATATGTCTTCCTTTCTGGATAGATTTG 57.210 33.333 0.00 0.00 45.68 2.32
627 655 7.257790 TGTCTTCCTTTCTGGATAGATTTGA 57.742 36.000 0.00 0.00 45.68 2.69
628 656 7.334090 TGTCTTCCTTTCTGGATAGATTTGAG 58.666 38.462 0.00 0.00 45.68 3.02
789 827 7.542534 AAACGTTTGTACTAGTGATCAAACA 57.457 32.000 29.60 16.70 45.29 2.83
792 830 6.420008 ACGTTTGTACTAGTGATCAAACACTC 59.580 38.462 29.60 16.83 46.36 3.51
794 832 7.358435 CGTTTGTACTAGTGATCAAACACTCAG 60.358 40.741 29.60 19.52 46.36 3.35
836 877 7.647827 TCCTTATGAATGGGGTTCTATGAAAA 58.352 34.615 0.00 0.00 37.72 2.29
860 901 8.442660 AATTTCCCTAAATGGTGTTTGGATTA 57.557 30.769 0.00 0.00 35.46 1.75
891 933 7.523293 TGGCTTTGACATATTCTGAAGAAAA 57.477 32.000 0.00 0.00 37.61 2.29
894 936 9.727627 GGCTTTGACATATTCTGAAGAAAATAG 57.272 33.333 0.00 0.00 37.61 1.73
956 1005 7.484035 TTTTTGTATTTTGTGGCGCTAAATT 57.516 28.000 21.77 9.43 35.03 1.82
957 1006 8.589335 TTTTTGTATTTTGTGGCGCTAAATTA 57.411 26.923 21.77 11.42 35.03 1.40
986 1035 4.441792 AGCGACAGTATAAACATGCATCA 58.558 39.130 0.00 0.00 0.00 3.07
1041 1094 1.725169 TTGCCCCTTGCCTACAGGTT 61.725 55.000 0.00 0.00 40.16 3.50
1042 1095 1.678970 GCCCCTTGCCTACAGGTTG 60.679 63.158 0.00 0.00 37.57 3.77
1092 1145 4.310769 GCTGACCCTGCAATATAGTACTG 58.689 47.826 5.39 0.00 0.00 2.74
1119 1172 2.359011 GGGCTGGGTACTTTGGGG 59.641 66.667 0.00 0.00 0.00 4.96
1217 1270 2.095461 GGATGCTTCCAAGAACCCTTC 58.905 52.381 13.60 0.00 42.12 3.46
1232 1285 1.267806 CCCTTCAGTGTCACATGCAAC 59.732 52.381 5.62 0.00 0.00 4.17
1754 1810 5.105752 AGCTCTACTGATTTCGCAAGTAAG 58.894 41.667 0.00 0.00 39.48 2.34
1894 1950 0.620990 TCTAATGGCCCCGGTTACCA 60.621 55.000 9.51 9.51 37.99 3.25
1911 1967 1.311859 CCACTGCAACTGCTCTCAAA 58.688 50.000 2.95 0.00 42.66 2.69
1960 2017 4.229582 AGGAGGGTGCAAAGGTATGAATAA 59.770 41.667 0.00 0.00 0.00 1.40
1961 2018 4.953579 GGAGGGTGCAAAGGTATGAATAAA 59.046 41.667 0.00 0.00 0.00 1.40
2091 2188 1.662629 GACAGACATCAATGAGTGCGG 59.337 52.381 0.00 0.00 0.00 5.69
2101 2198 0.620556 ATGAGTGCGGACCTCCAAAT 59.379 50.000 2.38 0.00 35.14 2.32
2393 2504 1.687123 ACGGTTTGTACAGAGCTCAGT 59.313 47.619 17.77 17.12 0.00 3.41
3004 3171 1.065418 GGCTTCTAGGGTGCTGCTTAA 60.065 52.381 0.00 0.00 0.00 1.85
3174 3341 4.164221 CCTCTGTCCACTAACCACCATATT 59.836 45.833 0.00 0.00 0.00 1.28
3175 3342 5.339200 CCTCTGTCCACTAACCACCATATTT 60.339 44.000 0.00 0.00 0.00 1.40
3399 3566 1.221293 GCTGCTGGAGCTGATCACT 59.779 57.895 14.33 0.00 45.21 3.41
3573 3740 4.424711 GGGCGGATGTGCTTGGGA 62.425 66.667 0.00 0.00 34.52 4.37
3733 3903 2.496291 CCGTGGTATCCCCCGTCTC 61.496 68.421 0.00 0.00 0.00 3.36
3765 3944 0.179000 GGGAGCTGTACATGTCTGGG 59.821 60.000 0.00 0.00 0.00 4.45
3808 3992 7.413000 CCAGATGATAGTTACGTTTGAACCTTG 60.413 40.741 0.00 0.00 0.00 3.61
3809 3993 6.594159 AGATGATAGTTACGTTTGAACCTTGG 59.406 38.462 0.00 0.00 0.00 3.61
3810 3994 4.998672 TGATAGTTACGTTTGAACCTTGGG 59.001 41.667 0.00 0.00 0.00 4.12
3819 4004 1.799933 TGAACCTTGGGCCAAAATGT 58.200 45.000 21.28 14.47 0.00 2.71
3821 4006 1.001974 GAACCTTGGGCCAAAATGTCC 59.998 52.381 21.28 1.96 0.00 4.02
3833 4018 6.459923 GGCCAAAATGTCCAACTAATTTACA 58.540 36.000 0.00 0.00 0.00 2.41
3883 4068 6.352516 AGCTAAGTAAATGTTCTCATGGGAG 58.647 40.000 0.00 0.00 42.80 4.30
3899 4084 0.455410 GGAGCTGTGTGTGTTTTGCA 59.545 50.000 0.00 0.00 0.00 4.08
3900 4085 1.135141 GGAGCTGTGTGTGTTTTGCAA 60.135 47.619 0.00 0.00 0.00 4.08
3901 4086 2.605030 GAGCTGTGTGTGTTTTGCAAA 58.395 42.857 8.05 8.05 0.00 3.68
3946 4132 1.003116 GCTATGCGGCATCTGAGTTTG 60.003 52.381 20.34 0.00 0.00 2.93
3982 4168 7.397892 TGTGAAGGAACACAAAATTCAGTTA 57.602 32.000 0.00 0.00 45.81 2.24
3990 4176 9.260002 GGAACACAAAATTCAGTTATCATGTTT 57.740 29.630 0.00 0.00 0.00 2.83
3993 4179 9.814899 ACACAAAATTCAGTTATCATGTTTTCA 57.185 25.926 0.00 0.00 0.00 2.69
4015 4201 3.503827 TCAGTATGAGAATTCGCACGT 57.496 42.857 14.40 2.30 42.56 4.49
4041 4227 1.151668 CCAACCGCTTCACTCTCTTG 58.848 55.000 0.00 0.00 0.00 3.02
4048 4234 2.345876 GCTTCACTCTCTTGCTTCTCC 58.654 52.381 0.00 0.00 0.00 3.71
4391 4597 1.078201 CTGTTACGCGCATCAGCAGA 61.078 55.000 5.73 0.00 42.27 4.26
4536 4742 3.214328 CCCTTGTGTTGGTAGGATATGC 58.786 50.000 0.00 0.00 0.00 3.14
4685 4926 3.023832 GGCCATGTGTTAAGCCATTAGT 58.976 45.455 0.00 0.00 45.07 2.24
4693 4934 9.325198 CATGTGTTAAGCCATTAGTATAGAACA 57.675 33.333 0.00 0.00 0.00 3.18
4772 5013 7.201384 GCTGCAACTATTGTGCTCTTATTTTTC 60.201 37.037 0.00 0.00 32.48 2.29
4782 5023 5.178809 GTGCTCTTATTTTTCTGTACACGGT 59.821 40.000 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.476488 CCATCGTCACCCAAAAATCCC 59.524 52.381 0.00 0.00 0.00 3.85
1 2 2.163613 GTCCATCGTCACCCAAAAATCC 59.836 50.000 0.00 0.00 0.00 3.01
6 7 1.004320 CCGTCCATCGTCACCCAAA 60.004 57.895 0.00 0.00 37.94 3.28
7 8 0.899253 TACCGTCCATCGTCACCCAA 60.899 55.000 0.00 0.00 37.94 4.12
8 9 0.685131 ATACCGTCCATCGTCACCCA 60.685 55.000 0.00 0.00 37.94 4.51
9 10 0.249322 CATACCGTCCATCGTCACCC 60.249 60.000 0.00 0.00 37.94 4.61
10 11 0.458669 ACATACCGTCCATCGTCACC 59.541 55.000 0.00 0.00 37.94 4.02
11 12 3.369385 CTTACATACCGTCCATCGTCAC 58.631 50.000 0.00 0.00 37.94 3.67
12 13 2.359848 CCTTACATACCGTCCATCGTCA 59.640 50.000 0.00 0.00 37.94 4.35
13 14 2.620115 TCCTTACATACCGTCCATCGTC 59.380 50.000 0.00 0.00 37.94 4.20
14 15 2.658285 TCCTTACATACCGTCCATCGT 58.342 47.619 0.00 0.00 37.94 3.73
15 16 3.378339 GTTCCTTACATACCGTCCATCG 58.622 50.000 0.00 0.00 39.52 3.84
16 17 3.133362 TGGTTCCTTACATACCGTCCATC 59.867 47.826 0.00 0.00 34.62 3.51
17 18 3.109151 TGGTTCCTTACATACCGTCCAT 58.891 45.455 0.00 0.00 34.62 3.41
18 19 2.234414 GTGGTTCCTTACATACCGTCCA 59.766 50.000 0.00 0.00 34.62 4.02
19 20 2.234414 TGTGGTTCCTTACATACCGTCC 59.766 50.000 0.00 0.00 34.62 4.79
20 21 3.598019 TGTGGTTCCTTACATACCGTC 57.402 47.619 0.00 0.00 34.62 4.79
21 22 4.020039 TGAATGTGGTTCCTTACATACCGT 60.020 41.667 0.00 0.00 36.56 4.83
22 23 4.331717 GTGAATGTGGTTCCTTACATACCG 59.668 45.833 0.00 0.00 36.56 4.02
23 24 4.331717 CGTGAATGTGGTTCCTTACATACC 59.668 45.833 0.00 0.00 36.56 2.73
24 25 5.172934 TCGTGAATGTGGTTCCTTACATAC 58.827 41.667 0.00 0.00 36.56 2.39
25 26 5.186215 TCTCGTGAATGTGGTTCCTTACATA 59.814 40.000 0.00 0.00 36.56 2.29
26 27 4.020573 TCTCGTGAATGTGGTTCCTTACAT 60.021 41.667 0.00 0.00 39.08 2.29
27 28 3.322541 TCTCGTGAATGTGGTTCCTTACA 59.677 43.478 0.00 0.00 35.91 2.41
28 29 3.921677 TCTCGTGAATGTGGTTCCTTAC 58.078 45.455 0.00 0.00 35.91 2.34
29 30 4.819105 ATCTCGTGAATGTGGTTCCTTA 57.181 40.909 0.00 0.00 35.91 2.69
30 31 3.703001 ATCTCGTGAATGTGGTTCCTT 57.297 42.857 0.00 0.00 35.91 3.36
31 32 3.769844 ACTATCTCGTGAATGTGGTTCCT 59.230 43.478 0.00 0.00 35.91 3.36
32 33 4.124851 ACTATCTCGTGAATGTGGTTCC 57.875 45.455 0.00 0.00 35.91 3.62
33 34 6.504398 TGATACTATCTCGTGAATGTGGTTC 58.496 40.000 0.00 0.00 37.35 3.62
34 35 6.465439 TGATACTATCTCGTGAATGTGGTT 57.535 37.500 0.00 0.00 0.00 3.67
35 36 6.265422 TGATGATACTATCTCGTGAATGTGGT 59.735 38.462 0.00 0.00 0.00 4.16
36 37 6.681777 TGATGATACTATCTCGTGAATGTGG 58.318 40.000 0.00 0.00 0.00 4.17
37 38 8.025445 TCATGATGATACTATCTCGTGAATGTG 58.975 37.037 12.98 0.00 33.57 3.21
38 39 8.115490 TCATGATGATACTATCTCGTGAATGT 57.885 34.615 12.98 0.00 33.57 2.71
39 40 8.976986 TTCATGATGATACTATCTCGTGAATG 57.023 34.615 18.04 7.79 37.43 2.67
40 41 9.636879 CTTTCATGATGATACTATCTCGTGAAT 57.363 33.333 20.16 1.49 39.40 2.57
41 42 8.850156 TCTTTCATGATGATACTATCTCGTGAA 58.150 33.333 18.04 18.04 38.78 3.18
42 43 8.396272 TCTTTCATGATGATACTATCTCGTGA 57.604 34.615 0.00 12.09 34.11 4.35
43 44 8.296000 ACTCTTTCATGATGATACTATCTCGTG 58.704 37.037 0.00 5.07 0.00 4.35
44 45 8.402798 ACTCTTTCATGATGATACTATCTCGT 57.597 34.615 0.00 0.00 0.00 4.18
61 62 9.695526 CCATTGAAAAATGACATAACTCTTTCA 57.304 29.630 0.05 0.00 31.98 2.69
62 63 8.650714 GCCATTGAAAAATGACATAACTCTTTC 58.349 33.333 0.05 0.00 31.98 2.62
63 64 7.329226 CGCCATTGAAAAATGACATAACTCTTT 59.671 33.333 0.05 0.00 31.98 2.52
64 65 6.808212 CGCCATTGAAAAATGACATAACTCTT 59.192 34.615 0.05 0.00 31.98 2.85
65 66 6.150976 TCGCCATTGAAAAATGACATAACTCT 59.849 34.615 0.05 0.00 31.98 3.24
66 67 6.321717 TCGCCATTGAAAAATGACATAACTC 58.678 36.000 0.05 0.00 31.98 3.01
67 68 6.266168 TCGCCATTGAAAAATGACATAACT 57.734 33.333 0.05 0.00 31.98 2.24
68 69 6.942886 TTCGCCATTGAAAAATGACATAAC 57.057 33.333 0.05 0.00 31.98 1.89
69 70 7.063191 CACATTCGCCATTGAAAAATGACATAA 59.937 33.333 0.05 0.00 32.86 1.90
70 71 6.530887 CACATTCGCCATTGAAAAATGACATA 59.469 34.615 0.05 0.00 32.86 2.29
71 72 5.349270 CACATTCGCCATTGAAAAATGACAT 59.651 36.000 0.05 0.00 32.86 3.06
72 73 4.685165 CACATTCGCCATTGAAAAATGACA 59.315 37.500 0.05 0.00 32.86 3.58
73 74 4.922692 TCACATTCGCCATTGAAAAATGAC 59.077 37.500 0.05 0.00 32.86 3.06
74 75 5.048154 TCTCACATTCGCCATTGAAAAATGA 60.048 36.000 0.05 0.00 32.86 2.57
75 76 5.162794 TCTCACATTCGCCATTGAAAAATG 58.837 37.500 0.00 0.00 34.34 2.32
76 77 5.389859 TCTCACATTCGCCATTGAAAAAT 57.610 34.783 0.00 0.00 0.00 1.82
77 78 4.844998 TCTCACATTCGCCATTGAAAAA 57.155 36.364 0.00 0.00 0.00 1.94
78 79 5.389859 AATCTCACATTCGCCATTGAAAA 57.610 34.783 0.00 0.00 0.00 2.29
79 80 5.879777 TCTAATCTCACATTCGCCATTGAAA 59.120 36.000 0.00 0.00 0.00 2.69
80 81 5.427378 TCTAATCTCACATTCGCCATTGAA 58.573 37.500 0.00 0.00 0.00 2.69
81 82 5.022282 TCTAATCTCACATTCGCCATTGA 57.978 39.130 0.00 0.00 0.00 2.57
82 83 5.936686 ATCTAATCTCACATTCGCCATTG 57.063 39.130 0.00 0.00 0.00 2.82
83 84 5.278169 GCAATCTAATCTCACATTCGCCATT 60.278 40.000 0.00 0.00 0.00 3.16
84 85 4.214971 GCAATCTAATCTCACATTCGCCAT 59.785 41.667 0.00 0.00 0.00 4.40
85 86 3.561310 GCAATCTAATCTCACATTCGCCA 59.439 43.478 0.00 0.00 0.00 5.69
86 87 3.812053 AGCAATCTAATCTCACATTCGCC 59.188 43.478 0.00 0.00 0.00 5.54
87 88 6.718454 ATAGCAATCTAATCTCACATTCGC 57.282 37.500 0.00 0.00 0.00 4.70
101 102 9.053840 CAACTGATGAACTGAATATAGCAATCT 57.946 33.333 0.00 0.00 0.00 2.40
102 103 8.834465 ACAACTGATGAACTGAATATAGCAATC 58.166 33.333 0.00 0.00 0.00 2.67
103 104 8.618677 CACAACTGATGAACTGAATATAGCAAT 58.381 33.333 0.00 0.00 0.00 3.56
104 105 7.414429 GCACAACTGATGAACTGAATATAGCAA 60.414 37.037 0.00 0.00 0.00 3.91
105 106 6.037500 GCACAACTGATGAACTGAATATAGCA 59.962 38.462 0.00 0.00 0.00 3.49
106 107 6.037500 TGCACAACTGATGAACTGAATATAGC 59.962 38.462 0.00 0.00 0.00 2.97
107 108 7.064966 TGTGCACAACTGATGAACTGAATATAG 59.935 37.037 19.28 0.00 0.00 1.31
108 109 6.878389 TGTGCACAACTGATGAACTGAATATA 59.122 34.615 19.28 0.00 0.00 0.86
109 110 5.706833 TGTGCACAACTGATGAACTGAATAT 59.293 36.000 19.28 0.00 0.00 1.28
110 111 5.062528 TGTGCACAACTGATGAACTGAATA 58.937 37.500 19.28 0.00 0.00 1.75
111 112 3.884693 TGTGCACAACTGATGAACTGAAT 59.115 39.130 19.28 0.00 0.00 2.57
112 113 3.277715 TGTGCACAACTGATGAACTGAA 58.722 40.909 19.28 0.00 0.00 3.02
113 114 2.916640 TGTGCACAACTGATGAACTGA 58.083 42.857 19.28 0.00 0.00 3.41
114 115 3.065786 ACTTGTGCACAACTGATGAACTG 59.934 43.478 27.96 16.02 0.00 3.16
115 116 3.282021 ACTTGTGCACAACTGATGAACT 58.718 40.909 27.96 0.15 0.00 3.01
116 117 3.698029 ACTTGTGCACAACTGATGAAC 57.302 42.857 27.96 0.00 0.00 3.18
117 118 4.717233 AAACTTGTGCACAACTGATGAA 57.283 36.364 27.96 5.77 0.00 2.57
118 119 6.389830 AATAAACTTGTGCACAACTGATGA 57.610 33.333 27.96 8.29 0.00 2.92
119 120 6.919662 AGAAATAAACTTGTGCACAACTGATG 59.080 34.615 27.96 19.51 0.00 3.07
120 121 7.042797 AGAAATAAACTTGTGCACAACTGAT 57.957 32.000 27.96 13.60 0.00 2.90
121 122 6.094742 TGAGAAATAAACTTGTGCACAACTGA 59.905 34.615 27.96 12.32 0.00 3.41
122 123 6.264832 TGAGAAATAAACTTGTGCACAACTG 58.735 36.000 27.96 20.94 0.00 3.16
123 124 6.449635 TGAGAAATAAACTTGTGCACAACT 57.550 33.333 27.96 19.70 0.00 3.16
124 125 7.518731 TTTGAGAAATAAACTTGTGCACAAC 57.481 32.000 27.96 15.36 0.00 3.32
125 126 8.715191 ATTTTGAGAAATAAACTTGTGCACAA 57.285 26.923 29.36 29.36 33.78 3.33
126 127 8.715191 AATTTTGAGAAATAAACTTGTGCACA 57.285 26.923 17.42 17.42 34.44 4.57
127 128 9.034544 AGAATTTTGAGAAATAAACTTGTGCAC 57.965 29.630 10.75 10.75 34.44 4.57
128 129 9.598517 AAGAATTTTGAGAAATAAACTTGTGCA 57.401 25.926 0.00 0.00 34.44 4.57
146 147 9.835389 TTCCATCATCTTGAAACAAAGAATTTT 57.165 25.926 0.00 0.00 39.54 1.82
155 156 8.231692 TGTTTAAGTTCCATCATCTTGAAACA 57.768 30.769 0.00 0.00 32.37 2.83
159 160 8.634335 TTCATGTTTAAGTTCCATCATCTTGA 57.366 30.769 0.00 0.00 0.00 3.02
163 164 9.132521 CACTTTTCATGTTTAAGTTCCATCATC 57.867 33.333 6.99 0.00 30.08 2.92
174 179 4.536065 CGAGCAGCACTTTTCATGTTTAA 58.464 39.130 0.00 0.00 0.00 1.52
175 180 3.058293 CCGAGCAGCACTTTTCATGTTTA 60.058 43.478 0.00 0.00 0.00 2.01
179 184 1.135859 GTCCGAGCAGCACTTTTCATG 60.136 52.381 0.00 0.00 0.00 3.07
188 194 2.760634 TTTCTATTGTCCGAGCAGCA 57.239 45.000 0.00 0.00 0.00 4.41
216 225 8.522830 ACACAGATTTTACTGATTTATGTTGGG 58.477 33.333 0.00 0.00 40.63 4.12
220 229 9.066892 ACACACACAGATTTTACTGATTTATGT 57.933 29.630 0.00 0.00 40.63 2.29
221 230 9.897744 AACACACACAGATTTTACTGATTTATG 57.102 29.630 0.00 0.00 40.63 1.90
229 239 4.947388 ACCACAACACACACAGATTTTACT 59.053 37.500 0.00 0.00 0.00 2.24
230 240 5.243426 ACCACAACACACACAGATTTTAC 57.757 39.130 0.00 0.00 0.00 2.01
238 248 0.253327 TGCCTACCACAACACACACA 59.747 50.000 0.00 0.00 0.00 3.72
239 249 1.333619 CTTGCCTACCACAACACACAC 59.666 52.381 0.00 0.00 0.00 3.82
253 263 0.251341 GGACCACCACATTCTTGCCT 60.251 55.000 0.00 0.00 35.97 4.75
260 270 1.604593 GCTGCAGGACCACCACATT 60.605 57.895 17.12 0.00 38.94 2.71
317 327 7.426929 AGTAACTATCTTGTTGCTCTTTGTG 57.573 36.000 0.00 0.00 38.20 3.33
419 435 5.461032 TGCGATTTTGGGTTTTTCTATGT 57.539 34.783 0.00 0.00 0.00 2.29
436 452 2.161855 TGGCTTGATTCAGTTTGCGAT 58.838 42.857 0.00 0.00 0.00 4.58
439 455 5.413499 ACATTATGGCTTGATTCAGTTTGC 58.587 37.500 0.00 0.00 0.00 3.68
440 456 6.869913 ACAACATTATGGCTTGATTCAGTTTG 59.130 34.615 0.00 0.00 0.00 2.93
449 465 5.798125 TCCAAAACAACATTATGGCTTGA 57.202 34.783 0.00 0.00 0.00 3.02
487 511 7.335627 TGTTGTCATTCTATAAACTGTAGGGG 58.664 38.462 0.00 0.00 0.00 4.79
499 523 7.307989 CCGTGTTTCTTTCTGTTGTCATTCTAT 60.308 37.037 0.00 0.00 0.00 1.98
508 536 3.871594 AGACTCCGTGTTTCTTTCTGTTG 59.128 43.478 0.00 0.00 0.00 3.33
523 551 2.101415 TCAGCATACAATCCAGACTCCG 59.899 50.000 0.00 0.00 0.00 4.63
534 562 6.127703 GGAGTCACTAGTTACTCAGCATACAA 60.128 42.308 29.35 0.00 43.21 2.41
536 564 5.221087 GGGAGTCACTAGTTACTCAGCATAC 60.221 48.000 29.35 15.94 43.21 2.39
538 566 3.702045 GGGAGTCACTAGTTACTCAGCAT 59.298 47.826 29.35 2.41 43.21 3.79
540 568 2.427812 GGGGAGTCACTAGTTACTCAGC 59.572 54.545 29.35 17.61 43.21 4.26
545 573 4.904895 AAAAGGGGGAGTCACTAGTTAC 57.095 45.455 0.00 0.00 0.00 2.50
548 576 2.375509 CCAAAAAGGGGGAGTCACTAGT 59.624 50.000 0.00 0.00 0.00 2.57
550 578 2.374170 GACCAAAAAGGGGGAGTCACTA 59.626 50.000 0.00 0.00 43.89 2.74
552 580 1.145119 AGACCAAAAAGGGGGAGTCAC 59.855 52.381 0.00 0.00 43.89 3.67
553 581 1.529744 AGACCAAAAAGGGGGAGTCA 58.470 50.000 0.00 0.00 43.89 3.41
558 586 1.005569 GGGAGTAGACCAAAAAGGGGG 59.994 57.143 0.00 0.00 43.89 5.40
560 588 1.708551 TGGGGAGTAGACCAAAAAGGG 59.291 52.381 0.00 0.00 43.89 3.95
616 644 9.113838 TGCAAGAGTTTAATCTCAAATCTATCC 57.886 33.333 14.47 0.00 36.97 2.59
619 647 8.896744 CCATGCAAGAGTTTAATCTCAAATCTA 58.103 33.333 14.47 0.00 36.97 1.98
620 648 7.395489 ACCATGCAAGAGTTTAATCTCAAATCT 59.605 33.333 14.47 0.00 36.97 2.40
621 649 7.487189 CACCATGCAAGAGTTTAATCTCAAATC 59.513 37.037 14.47 3.38 36.97 2.17
622 650 7.177216 TCACCATGCAAGAGTTTAATCTCAAAT 59.823 33.333 14.47 0.03 36.97 2.32
623 651 6.489700 TCACCATGCAAGAGTTTAATCTCAAA 59.510 34.615 14.47 0.00 36.97 2.69
625 653 5.559770 TCACCATGCAAGAGTTTAATCTCA 58.440 37.500 14.47 0.00 36.97 3.27
626 654 6.500684 TTCACCATGCAAGAGTTTAATCTC 57.499 37.500 5.54 5.54 34.96 2.75
627 655 6.716628 TCTTTCACCATGCAAGAGTTTAATCT 59.283 34.615 0.00 0.00 27.14 2.40
628 656 6.913170 TCTTTCACCATGCAAGAGTTTAATC 58.087 36.000 0.00 0.00 27.14 1.75
680 710 5.121811 AGCATCAATTCTGTATGTCACTCC 58.878 41.667 0.00 0.00 0.00 3.85
684 714 6.822667 ACAAAGCATCAATTCTGTATGTCA 57.177 33.333 0.00 0.00 0.00 3.58
695 725 8.499162 GCTCGTCTTATATAACAAAGCATCAAT 58.501 33.333 0.00 0.00 0.00 2.57
789 827 5.336849 GGAACACATCAGTAGTTAGCTGAGT 60.337 44.000 0.00 0.00 44.86 3.41
792 830 5.078411 AGGAACACATCAGTAGTTAGCTG 57.922 43.478 0.00 0.00 35.43 4.24
794 832 7.265673 TCATAAGGAACACATCAGTAGTTAGC 58.734 38.462 0.00 0.00 0.00 3.09
836 877 6.950860 AATCCAAACACCATTTAGGGAAAT 57.049 33.333 0.00 0.00 43.89 2.17
860 901 5.826737 CAGAATATGTCAAAGCCATTCCTCT 59.173 40.000 0.00 0.00 0.00 3.69
945 994 3.343617 GCTATGGGATAATTTAGCGCCA 58.656 45.455 2.29 5.56 0.00 5.69
949 998 5.238583 ACTGTCGCTATGGGATAATTTAGC 58.761 41.667 0.00 0.00 34.96 3.09
954 1003 7.903145 TGTTTATACTGTCGCTATGGGATAAT 58.097 34.615 0.00 0.00 0.00 1.28
955 1004 7.292713 TGTTTATACTGTCGCTATGGGATAA 57.707 36.000 0.00 0.00 0.00 1.75
956 1005 6.904463 TGTTTATACTGTCGCTATGGGATA 57.096 37.500 0.00 0.00 0.00 2.59
957 1006 5.801531 TGTTTATACTGTCGCTATGGGAT 57.198 39.130 0.00 0.00 0.00 3.85
1025 1078 1.000896 CCAACCTGTAGGCAAGGGG 60.001 63.158 0.00 0.00 39.32 4.79
1041 1094 3.367087 GCGACAAGTAGTAAGAGCTTCCA 60.367 47.826 0.00 0.00 0.00 3.53
1042 1095 3.119424 AGCGACAAGTAGTAAGAGCTTCC 60.119 47.826 0.00 0.00 0.00 3.46
1119 1172 3.896133 CCGTGCCATGCTGATGCC 61.896 66.667 0.00 0.00 38.71 4.40
1147 1200 0.582005 GACGTTGCCACACTTGTCTC 59.418 55.000 0.00 0.00 0.00 3.36
1217 1270 0.936600 TCACGTTGCATGTGACACTG 59.063 50.000 15.94 4.12 39.05 3.66
1232 1285 1.665916 CAGATATGCCCCGCTCACG 60.666 63.158 0.00 0.00 39.67 4.35
1754 1810 3.201290 CACAGGAACTCCATCTGCATAC 58.799 50.000 0.00 0.00 34.60 2.39
1894 1950 2.338577 ACTTTGAGAGCAGTTGCAGT 57.661 45.000 6.90 0.00 45.16 4.40
1960 2017 5.360714 ACATATCTGGAATTTTGGCGATGTT 59.639 36.000 0.00 0.00 0.00 2.71
1961 2018 4.889409 ACATATCTGGAATTTTGGCGATGT 59.111 37.500 0.00 0.00 0.00 3.06
2091 2188 3.425162 ACAAGGACTGATTTGGAGGTC 57.575 47.619 0.00 0.00 0.00 3.85
2101 2198 4.326826 CTTTGCAAGGATACAAGGACTGA 58.673 43.478 1.58 0.00 41.41 3.41
2343 2450 7.062749 AGTTGTCTAGTTGGACTTGTATGAA 57.937 36.000 0.00 0.00 37.16 2.57
2353 2460 4.940046 CCGTACTCTAGTTGTCTAGTTGGA 59.060 45.833 0.00 0.00 42.88 3.53
2393 2504 5.725551 ATCCCATTACCTATGACAAACCA 57.274 39.130 0.00 0.00 36.26 3.67
2555 2693 5.345741 GGCTAAAACACAATGCAGTATGTTG 59.654 40.000 12.02 3.37 39.31 3.33
2556 2694 5.010516 TGGCTAAAACACAATGCAGTATGTT 59.989 36.000 4.74 4.74 39.31 2.71
2561 2699 4.399004 TTTGGCTAAAACACAATGCAGT 57.601 36.364 0.00 0.00 0.00 4.40
3152 3319 5.359194 AATATGGTGGTTAGTGGACAGAG 57.641 43.478 0.00 0.00 0.00 3.35
3174 3341 2.289444 GGACTTGACATCTCCGTGGAAA 60.289 50.000 0.00 0.00 0.00 3.13
3175 3342 1.275291 GGACTTGACATCTCCGTGGAA 59.725 52.381 0.00 0.00 0.00 3.53
3399 3566 0.959553 GATAGATCGCCGTCTTCCCA 59.040 55.000 0.00 0.00 0.00 4.37
3453 3620 1.153568 CATCGCGAGCAGGAAGGAA 60.154 57.895 16.66 0.00 0.00 3.36
3573 3740 3.322466 CTGTCTTCGCCCCTGGGT 61.322 66.667 12.71 0.00 37.65 4.51
3765 3944 3.952931 TCTGGGCGTCTCTATACCTATC 58.047 50.000 0.00 0.00 0.00 2.08
3810 3994 7.151976 ACTGTAAATTAGTTGGACATTTTGGC 58.848 34.615 0.00 0.00 0.00 4.52
3833 4018 8.386264 TACTTGGTAGTTGGTACTTCTAGTACT 58.614 37.037 14.59 0.00 41.70 2.73
3850 4035 9.303537 GAGAACATTTACTTAGCTACTTGGTAG 57.696 37.037 0.00 0.82 38.97 3.18
3883 4068 2.928757 TGATTTGCAAAACACACACAGC 59.071 40.909 17.19 0.00 0.00 4.40
3899 4084 1.098050 GGCAAGCTCCACGATGATTT 58.902 50.000 0.00 0.00 0.00 2.17
3900 4085 0.035152 TGGCAAGCTCCACGATGATT 60.035 50.000 0.00 0.00 0.00 2.57
3901 4086 0.745845 GTGGCAAGCTCCACGATGAT 60.746 55.000 8.70 0.00 45.95 2.45
3923 4109 0.669932 CTCAGATGCCGCATAGCCTC 60.670 60.000 5.67 0.00 0.00 4.70
3946 4132 1.202604 TCCTTCACACCCGAAACTGAC 60.203 52.381 0.00 0.00 0.00 3.51
3990 4176 5.005682 CGTGCGAATTCTCATACTGAATGAA 59.994 40.000 0.73 0.00 44.05 2.57
3991 4177 4.504097 CGTGCGAATTCTCATACTGAATGA 59.496 41.667 0.73 0.00 42.48 2.57
3992 4178 4.268644 ACGTGCGAATTCTCATACTGAATG 59.731 41.667 0.73 0.00 34.74 2.67
3993 4179 4.433615 ACGTGCGAATTCTCATACTGAAT 58.566 39.130 0.73 0.00 35.88 2.57
4014 4200 2.876550 AGTGAAGCGGTTGGTTTCTAAC 59.123 45.455 3.70 0.00 36.86 2.34
4015 4201 3.135994 GAGTGAAGCGGTTGGTTTCTAA 58.864 45.455 3.70 0.00 36.86 2.10
4349 4554 4.329545 GAGCGACCCTTGGTGCCA 62.330 66.667 0.00 0.00 35.25 4.92
4391 4597 4.691216 GGCTATCTCACGAAGTTGTCTTTT 59.309 41.667 0.00 0.00 41.61 2.27
4536 4742 1.063027 CCAAGTAGCATGCATCACACG 59.937 52.381 21.98 9.14 0.00 4.49
4772 5013 3.232213 ACTGAATAGCACCGTGTACAG 57.768 47.619 0.00 0.00 0.00 2.74
4782 5023 5.588648 GCCTAATGTACCAAACTGAATAGCA 59.411 40.000 0.00 0.00 0.00 3.49
4849 5090 7.911727 TCAATGATGAAATAAGCTTCATGAACG 59.088 33.333 0.00 2.41 44.29 3.95


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

AutoCloner maintained by Alex Coulton.