Multiple sequence alignment - TraesCS1D01G349600

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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 TraesCS1D01G349600 chr1D 100.000 5045 0 0 998 6042 435760149 435755105 0.000000e+00 9317.0
1 TraesCS1D01G349600 chr1D 100.000 605 0 0 1 605 435761146 435760542 0.000000e+00 1118.0
2 TraesCS1D01G349600 chr1D 92.021 188 14 1 1 188 31344042 31343856 4.640000e-66 263.0
3 TraesCS1D01G349600 chr1B 91.579 4109 137 71 1600 5603 589073949 589069945 0.000000e+00 5478.0
4 TraesCS1D01G349600 chr1B 92.055 579 19 10 998 1569 589074498 589073940 0.000000e+00 789.0
5 TraesCS1D01G349600 chr1B 93.955 397 11 5 210 596 589074930 589074537 6.750000e-164 588.0
6 TraesCS1D01G349600 chr1B 93.651 189 10 2 1 189 502644780 502644594 1.280000e-71 281.0
7 TraesCS1D01G349600 chr1B 79.118 340 48 16 1428 1750 684796694 684797027 4.740000e-51 213.0
8 TraesCS1D01G349600 chr4D 89.784 2682 113 43 1008 3616 138697404 138699997 0.000000e+00 3286.0
9 TraesCS1D01G349600 chr4D 86.642 1325 97 32 3681 4951 138699996 138701294 0.000000e+00 1393.0
10 TraesCS1D01G349600 chr4D 92.872 491 22 5 4944 5428 138703558 138704041 0.000000e+00 701.0
11 TraesCS1D01G349600 chr4D 93.610 313 20 0 278 590 138696781 138697093 9.170000e-128 468.0
12 TraesCS1D01G349600 chr4D 83.055 419 30 11 5643 6042 138704652 138705048 5.800000e-90 342.0
13 TraesCS1D01G349600 chr4A 89.600 1000 51 15 2038 3016 415866093 415865126 0.000000e+00 1221.0
14 TraesCS1D01G349600 chr4A 88.789 776 28 25 1096 1844 415866924 415866181 0.000000e+00 896.0
15 TraesCS1D01G349600 chr4A 93.090 521 27 1 3105 3616 415862481 415861961 0.000000e+00 754.0
16 TraesCS1D01G349600 chr4A 86.969 706 44 18 4201 4872 415859044 415858353 0.000000e+00 750.0
17 TraesCS1D01G349600 chr4A 93.913 345 12 4 5085 5429 415857675 415857340 4.180000e-141 512.0
18 TraesCS1D01G349600 chr4A 92.604 338 16 7 4857 5190 415858050 415857718 1.520000e-130 477.0
19 TraesCS1D01G349600 chr4A 92.357 314 23 1 278 590 415881529 415881216 4.300000e-121 446.0
20 TraesCS1D01G349600 chr4A 90.303 330 24 6 3742 4071 415861904 415861583 5.600000e-115 425.0
21 TraesCS1D01G349600 chr4A 92.083 240 18 1 5727 5966 415856566 415856328 2.700000e-88 337.0
22 TraesCS1D01G349600 chr4A 94.340 106 2 3 5085 5190 415857747 415857646 6.270000e-35 159.0
23 TraesCS1D01G349600 chr4A 85.714 126 15 1 4084 4209 415861535 415861413 4.910000e-26 130.0
24 TraesCS1D01G349600 chr4B 83.528 1196 90 47 1008 2141 227241931 227243081 0.000000e+00 1018.0
25 TraesCS1D01G349600 chr4B 86.648 719 64 19 2645 3355 227248311 227249005 0.000000e+00 767.0
26 TraesCS1D01G349600 chr4B 85.251 678 63 13 4354 5010 227283870 227284531 0.000000e+00 664.0
27 TraesCS1D01G349600 chr4B 91.295 448 34 2 2145 2588 227244359 227244805 1.860000e-169 606.0
28 TraesCS1D01G349600 chr4B 84.694 392 39 11 3742 4125 227270562 227270940 7.400000e-99 372.0
29 TraesCS1D01G349600 chr4B 91.353 266 22 1 3351 3616 227270174 227270438 4.450000e-96 363.0
30 TraesCS1D01G349600 chr4B 86.957 322 40 1 278 599 227241553 227241872 1.600000e-95 361.0
31 TraesCS1D01G349600 chr4B 89.344 244 25 1 5725 5967 227300921 227301164 7.610000e-79 305.0
32 TraesCS1D01G349600 chr4B 92.308 182 14 0 1 182 655092906 655092725 6.010000e-65 259.0
33 TraesCS1D01G349600 chr5D 94.022 184 9 1 1 184 450524771 450524952 1.660000e-70 278.0
34 TraesCS1D01G349600 chr5D 88.947 190 13 5 5458 5642 5112350 5112164 1.690000e-55 228.0
35 TraesCS1D01G349600 chr5D 92.025 163 12 1 5457 5619 476690149 476690310 1.690000e-55 228.0
36 TraesCS1D01G349600 chr2D 93.989 183 10 1 1 183 605402174 605402355 5.970000e-70 276.0
37 TraesCS1D01G349600 chr2D 91.566 166 14 0 5458 5623 218046988 218046823 4.710000e-56 230.0
38 TraesCS1D01G349600 chr2D 91.358 162 14 0 5458 5619 299891715 299891554 7.880000e-54 222.0
39 TraesCS1D01G349600 chr2D 86.387 191 25 1 5429 5619 387193884 387193695 2.210000e-49 207.0
40 TraesCS1D01G349600 chr2D 82.186 247 33 10 5772 6015 430625506 430625744 1.030000e-47 202.0
41 TraesCS1D01G349600 chr6B 92.228 193 11 4 1 192 204167863 204167674 2.780000e-68 270.0
42 TraesCS1D01G349600 chr6D 92.935 184 11 1 1 184 471619030 471618849 3.590000e-67 267.0
43 TraesCS1D01G349600 chr7D 92.857 182 13 0 1 182 543095826 543095645 1.290000e-66 265.0
44 TraesCS1D01G349600 chr7D 89.444 180 18 1 5455 5634 183790426 183790248 6.090000e-55 226.0
45 TraesCS1D01G349600 chr7A 92.350 183 14 0 1 183 275204 275022 1.670000e-65 261.0
46 TraesCS1D01G349600 chr7A 80.237 253 39 9 5777 6027 391906749 391906506 4.810000e-41 180.0
47 TraesCS1D01G349600 chr5A 92.121 165 13 0 5457 5621 320214243 320214407 3.640000e-57 233.0
48 TraesCS1D01G349600 chr5A 82.171 258 33 11 5772 6024 445133912 445134161 6.140000e-50 209.0
49 TraesCS1D01G349600 chr5A 95.652 46 1 1 3043 3087 40100264 40100309 8.400000e-09 73.1
50 TraesCS1D01G349600 chr2A 91.124 169 15 0 5455 5623 324614922 324615090 4.710000e-56 230.0
51 TraesCS1D01G349600 chr5B 90.230 174 15 2 5457 5629 607838389 607838561 6.090000e-55 226.0
52 TraesCS1D01G349600 chr5B 95.652 46 1 1 3043 3087 53659775 53659820 8.400000e-09 73.1
53 TraesCS1D01G349600 chr2B 83.740 246 30 8 5772 6015 508959386 508959623 2.190000e-54 224.0
54 TraesCS1D01G349600 chr2B 91.525 59 4 1 3030 3087 763631610 763631552 5.020000e-11 80.5
55 TraesCS1D01G349600 chr7B 83.796 216 32 2 5776 5990 156706585 156706798 1.030000e-47 202.0
56 TraesCS1D01G349600 chr7B 81.743 241 33 9 5777 6015 297400480 297400711 2.220000e-44 191.0
57 TraesCS1D01G349600 chr3B 95.745 47 2 0 3041 3087 680423291 680423337 6.490000e-10 76.8
58 TraesCS1D01G349600 chr3D 93.750 48 2 1 3040 3087 467284181 467284227 3.020000e-08 71.3
59 TraesCS1D01G349600 chr1A 92.000 50 4 0 3038 3087 379498259 379498308 3.020000e-08 71.3


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 TraesCS1D01G349600 chr1D 435755105 435761146 6041 True 5217.5 9317 100.000000 1 6042 2 chr1D.!!$R2 6041
1 TraesCS1D01G349600 chr1B 589069945 589074930 4985 True 2285.0 5478 92.529667 210 5603 3 chr1B.!!$R2 5393
2 TraesCS1D01G349600 chr4D 138696781 138705048 8267 False 1238.0 3286 89.192600 278 6042 5 chr4D.!!$F1 5764
3 TraesCS1D01G349600 chr4A 415856328 415866924 10596 True 566.1 1221 90.740500 1096 5966 10 chr4A.!!$R2 4870
4 TraesCS1D01G349600 chr4B 227241553 227249005 7452 False 688.0 1018 87.107000 278 3355 4 chr4B.!!$F3 3077
5 TraesCS1D01G349600 chr4B 227283870 227284531 661 False 664.0 664 85.251000 4354 5010 1 chr4B.!!$F1 656
6 TraesCS1D01G349600 chr4B 227270174 227270940 766 False 367.5 372 88.023500 3351 4125 2 chr4B.!!$F4 774

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
110 111 0.169230 CGGCGAGGATAGGAATCGAG 59.831 60.0 0.00 0.0 38.72 4.04 F
122 123 0.398664 GAATCGAGAAGGGGAGGGGA 60.399 60.0 0.00 0.0 0.00 4.81 F
1513 1573 0.178533 GCAGCAGCAGATTCTCCTCT 59.821 55.0 0.00 0.0 41.58 3.69 F
2032 2123 1.251527 TGGAGAACCTGAGCTCGGAC 61.252 60.0 24.60 17.4 37.04 4.79 F
2653 7509 0.798776 GTTCCATGACGTGAAGCCAG 59.201 55.0 0.00 0.0 0.00 4.85 F
4460 14481 0.036199 CCCATTCCGTCGGTAAACCA 60.036 55.0 11.88 0.0 35.14 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1131 0.104304 AGCTATACGCCGGAAAGTGG 59.896 55.0 5.05 0.0 40.39 4.00 R
2002 2093 1.028868 GGTTCTCCAGTGGCAGCATC 61.029 60.0 3.51 0.0 0.00 3.91 R
2653 7509 0.532573 TCAAGTGCAGATCGGAGGAC 59.467 55.0 0.00 0.0 0.00 3.85 R
3926 11500 0.954938 TGATGTGCACCACCATCACG 60.955 55.0 15.69 0.0 31.97 4.35 R
4529 14550 0.173708 CTGACGACCTAGCCTTGGAC 59.826 60.0 0.00 0.0 0.00 4.02 R
5638 19010 0.321671 GCCTGGTCAACTAGACTGCA 59.678 55.0 0.00 0.0 46.72 4.41 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
52 53 4.899239 CTCGCCGCCACCCTCATC 62.899 72.222 0.00 0.00 0.00 2.92
56 57 4.873129 CCGCCACCCTCATCGACG 62.873 72.222 0.00 0.00 0.00 5.12
57 58 4.873129 CGCCACCCTCATCGACGG 62.873 72.222 0.00 0.00 0.00 4.79
59 60 4.530857 CCACCCTCATCGACGGCC 62.531 72.222 0.00 0.00 0.00 6.13
60 61 4.873129 CACCCTCATCGACGGCCG 62.873 72.222 26.86 26.86 40.25 6.13
102 103 4.685026 CGACGGCGGCGAGGATAG 62.685 72.222 38.93 16.82 0.00 2.08
103 104 4.344474 GACGGCGGCGAGGATAGG 62.344 72.222 38.93 6.53 0.00 2.57
104 105 4.889112 ACGGCGGCGAGGATAGGA 62.889 66.667 38.93 0.00 0.00 2.94
105 106 3.602677 CGGCGGCGAGGATAGGAA 61.603 66.667 29.19 0.00 0.00 3.36
106 107 2.932234 CGGCGGCGAGGATAGGAAT 61.932 63.158 29.19 0.00 0.00 3.01
107 108 1.079750 GGCGGCGAGGATAGGAATC 60.080 63.158 12.98 0.00 0.00 2.52
108 109 1.444553 GCGGCGAGGATAGGAATCG 60.445 63.158 12.98 0.00 39.40 3.34
109 110 1.863662 GCGGCGAGGATAGGAATCGA 61.864 60.000 12.98 0.00 38.72 3.59
110 111 0.169230 CGGCGAGGATAGGAATCGAG 59.831 60.000 0.00 0.00 38.72 4.04
111 112 1.535833 GGCGAGGATAGGAATCGAGA 58.464 55.000 0.00 0.00 38.72 4.04
112 113 1.887198 GGCGAGGATAGGAATCGAGAA 59.113 52.381 0.00 0.00 38.72 2.87
113 114 2.094957 GGCGAGGATAGGAATCGAGAAG 60.095 54.545 0.00 0.00 38.72 2.85
114 115 2.094957 GCGAGGATAGGAATCGAGAAGG 60.095 54.545 0.00 0.00 38.72 3.46
115 116 2.490115 CGAGGATAGGAATCGAGAAGGG 59.510 54.545 0.00 0.00 38.72 3.95
116 117 2.829120 GAGGATAGGAATCGAGAAGGGG 59.171 54.545 0.00 0.00 32.44 4.79
117 118 2.451273 AGGATAGGAATCGAGAAGGGGA 59.549 50.000 0.00 0.00 32.44 4.81
118 119 2.829120 GGATAGGAATCGAGAAGGGGAG 59.171 54.545 0.00 0.00 32.44 4.30
119 120 2.383442 TAGGAATCGAGAAGGGGAGG 57.617 55.000 0.00 0.00 0.00 4.30
120 121 0.399233 AGGAATCGAGAAGGGGAGGG 60.399 60.000 0.00 0.00 0.00 4.30
121 122 1.411651 GGAATCGAGAAGGGGAGGGG 61.412 65.000 0.00 0.00 0.00 4.79
122 123 0.398664 GAATCGAGAAGGGGAGGGGA 60.399 60.000 0.00 0.00 0.00 4.81
123 124 0.691413 AATCGAGAAGGGGAGGGGAC 60.691 60.000 0.00 0.00 0.00 4.46
124 125 2.930777 ATCGAGAAGGGGAGGGGACG 62.931 65.000 0.00 0.00 0.00 4.79
125 126 2.764547 GAGAAGGGGAGGGGACGG 60.765 72.222 0.00 0.00 0.00 4.79
126 127 3.281787 AGAAGGGGAGGGGACGGA 61.282 66.667 0.00 0.00 0.00 4.69
127 128 3.082055 GAAGGGGAGGGGACGGAC 61.082 72.222 0.00 0.00 0.00 4.79
137 138 2.362889 GGACGGACGGGGAGGTTA 60.363 66.667 0.00 0.00 0.00 2.85
138 139 2.421399 GGACGGACGGGGAGGTTAG 61.421 68.421 0.00 0.00 0.00 2.34
139 140 1.680314 GACGGACGGGGAGGTTAGT 60.680 63.158 0.00 0.00 0.00 2.24
140 141 1.661498 GACGGACGGGGAGGTTAGTC 61.661 65.000 0.00 0.00 0.00 2.59
141 142 2.768492 CGGACGGGGAGGTTAGTCG 61.768 68.421 0.00 0.00 34.68 4.18
142 143 2.493501 GACGGGGAGGTTAGTCGC 59.506 66.667 0.00 0.00 0.00 5.19
143 144 3.073101 ACGGGGAGGTTAGTCGCC 61.073 66.667 0.00 0.00 44.34 5.54
144 145 3.846430 CGGGGAGGTTAGTCGCCC 61.846 72.222 0.00 0.00 44.84 6.13
146 147 3.477346 GGGAGGTTAGTCGCCCCC 61.477 72.222 0.00 0.00 34.39 5.40
147 148 3.846430 GGAGGTTAGTCGCCCCCG 61.846 72.222 0.00 0.00 0.00 5.73
148 149 2.757099 GAGGTTAGTCGCCCCCGA 60.757 66.667 0.00 0.00 42.01 5.14
149 150 2.758737 AGGTTAGTCGCCCCCGAG 60.759 66.667 0.00 0.00 45.38 4.63
151 152 2.493501 GTTAGTCGCCCCCGAGTC 59.506 66.667 0.00 0.00 43.27 3.36
152 153 3.136123 TTAGTCGCCCCCGAGTCG 61.136 66.667 5.29 5.29 43.27 4.18
203 204 3.226884 CGGGGAACGTCAATCAACT 57.773 52.632 0.00 0.00 37.93 3.16
204 205 1.076332 CGGGGAACGTCAATCAACTC 58.924 55.000 0.00 0.00 37.93 3.01
205 206 1.337823 CGGGGAACGTCAATCAACTCT 60.338 52.381 0.00 0.00 37.93 3.24
206 207 2.076863 GGGGAACGTCAATCAACTCTG 58.923 52.381 0.00 0.00 0.00 3.35
207 208 2.289444 GGGGAACGTCAATCAACTCTGA 60.289 50.000 0.00 0.00 35.56 3.27
208 209 2.996621 GGGAACGTCAATCAACTCTGAG 59.003 50.000 2.45 2.45 34.23 3.35
255 256 3.256631 GCCCAGATTTTCTGTGTCATTGT 59.743 43.478 4.00 0.00 42.80 2.71
310 311 0.811281 CGACCCAAAGGCAAGAATCC 59.189 55.000 0.00 0.00 36.11 3.01
331 332 2.029110 CACCAGCAAACCCATTAACTGG 60.029 50.000 5.34 5.34 44.49 4.00
396 397 4.455877 ACAGAGCTACCAACACTTAAATGC 59.544 41.667 0.00 0.00 0.00 3.56
450 460 2.509336 CACCACAGACGATCCGGC 60.509 66.667 0.00 0.00 33.59 6.13
590 600 1.649664 CTGGACTAGACATGCAGCAC 58.350 55.000 0.00 0.00 0.00 4.40
591 601 0.975887 TGGACTAGACATGCAGCACA 59.024 50.000 0.00 0.00 0.00 4.57
592 602 1.066645 TGGACTAGACATGCAGCACAG 60.067 52.381 0.00 0.00 0.00 3.66
593 603 1.005340 GACTAGACATGCAGCACAGC 58.995 55.000 0.00 0.00 0.00 4.40
600 610 3.284449 TGCAGCACAGCAGCAGTG 61.284 61.111 13.45 13.45 45.45 3.66
1116 1131 0.946221 CTCTCCAGTGTGGTGCGAAC 60.946 60.000 0.00 0.00 39.03 3.95
1202 1217 1.135721 GCATTCTTGTGGCTTGGGATC 59.864 52.381 0.00 0.00 0.00 3.36
1210 1226 0.399949 TGGCTTGGGATCGGTAGGAT 60.400 55.000 0.00 0.00 38.35 3.24
1211 1227 0.765510 GGCTTGGGATCGGTAGGATT 59.234 55.000 0.00 0.00 34.82 3.01
1212 1228 1.270893 GGCTTGGGATCGGTAGGATTC 60.271 57.143 0.00 0.00 34.82 2.52
1325 1342 4.277921 GCCATCAAGATCCAAGAAAGATCC 59.722 45.833 0.00 0.00 40.92 3.36
1392 1430 3.543680 AGCTTGGCTCGCTCTTTATTA 57.456 42.857 0.00 0.00 30.62 0.98
1393 1431 3.873910 AGCTTGGCTCGCTCTTTATTAA 58.126 40.909 0.00 0.00 30.62 1.40
1394 1432 4.455606 AGCTTGGCTCGCTCTTTATTAAT 58.544 39.130 0.00 0.00 30.62 1.40
1395 1433 4.884164 AGCTTGGCTCGCTCTTTATTAATT 59.116 37.500 0.00 0.00 30.62 1.40
1470 1530 1.339151 CCCTGTTTCCCGAGGAGAAAG 60.339 57.143 6.18 0.00 34.04 2.62
1513 1573 0.178533 GCAGCAGCAGATTCTCCTCT 59.821 55.000 0.00 0.00 41.58 3.69
1525 1585 7.072708 AGCAGATTCTCCTCTAAGGTACTAGTA 59.927 40.741 0.00 0.00 38.49 1.82
1584 1644 5.300792 TCTTTTTGTCCATGTGGTAACTTCC 59.699 40.000 0.00 0.00 36.34 3.46
1869 1949 6.070538 ACAAAGATAGTGCTGATACTCTGGTT 60.071 38.462 0.00 0.00 32.19 3.67
1870 1950 5.782893 AGATAGTGCTGATACTCTGGTTC 57.217 43.478 0.00 0.00 32.19 3.62
1871 1951 4.586841 AGATAGTGCTGATACTCTGGTTCC 59.413 45.833 0.00 0.00 32.19 3.62
1872 1952 2.826488 AGTGCTGATACTCTGGTTCCT 58.174 47.619 0.00 0.00 0.00 3.36
1873 1953 3.177228 AGTGCTGATACTCTGGTTCCTT 58.823 45.455 0.00 0.00 0.00 3.36
1874 1954 3.584848 AGTGCTGATACTCTGGTTCCTTT 59.415 43.478 0.00 0.00 0.00 3.11
1875 1955 3.935828 GTGCTGATACTCTGGTTCCTTTC 59.064 47.826 0.00 0.00 0.00 2.62
1876 1956 3.055094 TGCTGATACTCTGGTTCCTTTCC 60.055 47.826 0.00 0.00 0.00 3.13
1877 1957 3.682999 GCTGATACTCTGGTTCCTTTCCC 60.683 52.174 0.00 0.00 0.00 3.97
1878 1958 3.519510 CTGATACTCTGGTTCCTTTCCCA 59.480 47.826 0.00 0.00 0.00 4.37
1933 2024 3.177228 TCTGAGGAAGGAAGGAAGGAAG 58.823 50.000 0.00 0.00 0.00 3.46
1934 2025 2.238395 CTGAGGAAGGAAGGAAGGAAGG 59.762 54.545 0.00 0.00 0.00 3.46
1935 2026 2.158004 TGAGGAAGGAAGGAAGGAAGGA 60.158 50.000 0.00 0.00 0.00 3.36
1936 2027 2.913617 GAGGAAGGAAGGAAGGAAGGAA 59.086 50.000 0.00 0.00 0.00 3.36
1937 2028 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
1938 2029 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
1939 2030 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
1940 2031 2.556766 AGGAAGGAAGGAAGGAAGGAG 58.443 52.381 0.00 0.00 0.00 3.69
2032 2123 1.251527 TGGAGAACCTGAGCTCGGAC 61.252 60.000 24.60 17.40 37.04 4.79
2185 3558 4.216472 GGTGGTGTTTCAGAAGAGATTTCC 59.784 45.833 0.00 0.00 0.00 3.13
2254 3627 3.451141 CTGGACAAGCTCATAGACCTC 57.549 52.381 0.00 0.00 0.00 3.85
2347 3725 4.810191 TTCCTTGAGACTCTAAGAAGCC 57.190 45.455 3.68 0.00 0.00 4.35
2354 3732 5.411781 TGAGACTCTAAGAAGCCGAATTTC 58.588 41.667 3.68 0.00 0.00 2.17
2563 3947 4.134563 TCTTGCTTCACTACCTTTTCACC 58.865 43.478 0.00 0.00 0.00 4.02
2588 3972 7.306051 CCGCGTATCTATCTTTTTCAAGTGTAG 60.306 40.741 4.92 0.00 0.00 2.74
2591 3975 8.808529 CGTATCTATCTTTTTCAAGTGTAGGTG 58.191 37.037 0.00 0.00 0.00 4.00
2592 3976 9.654663 GTATCTATCTTTTTCAAGTGTAGGTGT 57.345 33.333 0.00 0.00 0.00 4.16
2593 3977 7.962964 TCTATCTTTTTCAAGTGTAGGTGTG 57.037 36.000 0.00 0.00 0.00 3.82
2594 3978 7.506114 TCTATCTTTTTCAAGTGTAGGTGTGT 58.494 34.615 0.00 0.00 0.00 3.72
2595 3979 8.644216 TCTATCTTTTTCAAGTGTAGGTGTGTA 58.356 33.333 0.00 0.00 0.00 2.90
2596 3980 9.268268 CTATCTTTTTCAAGTGTAGGTGTGTAA 57.732 33.333 0.00 0.00 0.00 2.41
2597 3981 7.311364 TCTTTTTCAAGTGTAGGTGTGTAAC 57.689 36.000 0.00 0.00 37.35 2.50
2598 3982 7.107542 TCTTTTTCAAGTGTAGGTGTGTAACT 58.892 34.615 0.00 0.00 38.04 2.24
2599 3983 8.259411 TCTTTTTCAAGTGTAGGTGTGTAACTA 58.741 33.333 0.00 0.00 38.04 2.24
2600 3984 8.428186 TTTTTCAAGTGTAGGTGTGTAACTAG 57.572 34.615 0.00 0.00 38.04 2.57
2601 3985 6.720112 TTCAAGTGTAGGTGTGTAACTAGT 57.280 37.500 0.00 0.00 38.04 2.57
2602 3986 6.323203 TCAAGTGTAGGTGTGTAACTAGTC 57.677 41.667 0.00 0.00 38.04 2.59
2603 3987 5.829391 TCAAGTGTAGGTGTGTAACTAGTCA 59.171 40.000 0.00 0.00 38.04 3.41
2604 3988 5.961396 AGTGTAGGTGTGTAACTAGTCAG 57.039 43.478 0.00 0.00 38.04 3.51
2605 3989 4.217983 AGTGTAGGTGTGTAACTAGTCAGC 59.782 45.833 0.00 0.00 38.04 4.26
2653 7509 0.798776 GTTCCATGACGTGAAGCCAG 59.201 55.000 0.00 0.00 0.00 4.85
2746 7602 1.904287 TACAATGGTCAGTTGGTGCC 58.096 50.000 0.00 0.00 0.00 5.01
3016 7882 6.010219 ACAGAAGGCAATACAACTTGGTAAT 58.990 36.000 0.00 0.00 0.00 1.89
3017 7883 6.493458 ACAGAAGGCAATACAACTTGGTAATT 59.507 34.615 0.00 0.00 0.00 1.40
3018 7884 7.668052 ACAGAAGGCAATACAACTTGGTAATTA 59.332 33.333 0.00 0.00 0.00 1.40
3019 7885 8.519526 CAGAAGGCAATACAACTTGGTAATTAA 58.480 33.333 0.00 0.00 0.00 1.40
3046 10505 5.127031 ACCCATCAATGCACCTGTAAATTAC 59.873 40.000 0.00 0.00 0.00 1.89
3337 10810 3.185391 GTCTACACAGAGTTTCAGCTTGC 59.815 47.826 0.00 0.00 0.00 4.01
3360 10833 5.681982 GCGCAGTATGTAGTAGTAACTTGAG 59.318 44.000 0.30 0.00 39.31 3.02
3403 10876 3.191581 TCTTAGCTCTGTCTGTGTGTAGC 59.808 47.826 0.00 0.00 0.00 3.58
3481 10954 1.296715 GCTCGTGGATCTTGGTGGT 59.703 57.895 0.00 0.00 0.00 4.16
3556 11029 3.381908 AGGCTATAAACCTGTCTCTGTCG 59.618 47.826 0.00 0.00 35.72 4.35
3709 11182 7.989741 CAGTTCCTTCATATCTTGACAGGTTAT 59.010 37.037 0.00 0.00 35.66 1.89
3710 11183 9.213777 AGTTCCTTCATATCTTGACAGGTTATA 57.786 33.333 0.00 0.00 35.66 0.98
3738 11211 3.338249 TGATGCTTCAAGTTACCTCAGC 58.662 45.455 0.00 0.00 0.00 4.26
3809 11370 3.196685 AGCTTACCCAGATTCTCAGTGAC 59.803 47.826 0.00 0.00 0.00 3.67
3874 11448 8.396272 AGCATCAAATGTGGAAACCTATATAC 57.604 34.615 0.00 0.00 0.00 1.47
3917 11491 1.812571 CTGCTAAAAACAGGCGATGGT 59.187 47.619 0.00 0.00 0.00 3.55
3926 11500 1.880027 ACAGGCGATGGTTCAAAAGTC 59.120 47.619 0.00 0.00 0.00 3.01
4020 11594 2.028294 AGAGCCATGCTGATAGAATCCG 60.028 50.000 0.00 0.00 39.88 4.18
4025 11599 0.394192 TGCTGATAGAATCCGGCAGG 59.606 55.000 0.00 0.00 34.05 4.85
4263 14263 1.119684 GGAGGAGAGGAAGAAGCTCC 58.880 60.000 0.00 0.00 46.75 4.70
4275 14275 2.864770 GAAGCTCCCTCCCTCCGTCT 62.865 65.000 0.00 0.00 0.00 4.18
4276 14276 3.151022 GCTCCCTCCCTCCGTCTG 61.151 72.222 0.00 0.00 0.00 3.51
4277 14277 2.360980 CTCCCTCCCTCCGTCTGT 59.639 66.667 0.00 0.00 0.00 3.41
4278 14278 1.755008 CTCCCTCCCTCCGTCTGTC 60.755 68.421 0.00 0.00 0.00 3.51
4279 14279 2.037367 CCCTCCCTCCGTCTGTCA 59.963 66.667 0.00 0.00 0.00 3.58
4280 14280 2.055042 CCCTCCCTCCGTCTGTCAG 61.055 68.421 0.00 0.00 0.00 3.51
4287 14290 1.987704 CTCCGTCTGTCAGCCTCTCG 61.988 65.000 0.00 0.00 0.00 4.04
4327 14330 1.509923 GAAGCATTCTGGTGGCAGC 59.490 57.895 10.30 10.30 43.23 5.25
4328 14331 1.941999 GAAGCATTCTGGTGGCAGCC 61.942 60.000 14.97 3.66 43.23 4.85
4329 14332 3.818787 GCATTCTGGTGGCAGCCG 61.819 66.667 14.97 8.13 0.00 5.52
4333 14336 2.809861 ATTCTGGTGGCAGCCGACAG 62.810 60.000 23.04 23.04 33.25 3.51
4460 14481 0.036199 CCCATTCCGTCGGTAAACCA 60.036 55.000 11.88 0.00 35.14 3.67
4486 14507 1.125021 GACAAGATCAGTGAACGCGTG 59.875 52.381 14.98 0.00 0.00 5.34
4529 14550 4.717629 TCGTTCAGCCACTCCGCG 62.718 66.667 0.00 0.00 0.00 6.46
4549 14570 1.153549 CCAAGGCTAGGTCGTCAGC 60.154 63.158 0.00 0.00 37.05 4.26
4565 14586 3.654020 GCGGCATTCTCATCCGGC 61.654 66.667 0.00 0.00 43.11 6.13
4688 14715 3.365265 GTTTCCAGGCCGGTGCAG 61.365 66.667 1.90 0.00 40.13 4.41
4737 14764 4.384647 GGAGAAGGATGTCATGCTTAACCT 60.385 45.833 18.44 12.00 41.25 3.50
4738 14765 4.521146 AGAAGGATGTCATGCTTAACCTG 58.479 43.478 18.44 0.00 41.25 4.00
4739 14766 4.225942 AGAAGGATGTCATGCTTAACCTGA 59.774 41.667 18.44 0.00 41.25 3.86
4740 14767 4.785346 AGGATGTCATGCTTAACCTGAT 57.215 40.909 0.13 0.00 0.00 2.90
4805 14832 4.629200 TGATTTTGACTTGTTGTTTGGTGC 59.371 37.500 0.00 0.00 0.00 5.01
4814 14858 4.199432 TGTTGTTTGGTGCTCAAATGTT 57.801 36.364 8.55 0.00 45.79 2.71
4852 14900 5.465935 AGTTTGGTTGTGTTAACTTGTGTG 58.534 37.500 7.22 0.00 0.00 3.82
4853 14901 5.010213 AGTTTGGTTGTGTTAACTTGTGTGT 59.990 36.000 7.22 0.00 0.00 3.72
4854 14902 6.207025 AGTTTGGTTGTGTTAACTTGTGTGTA 59.793 34.615 7.22 0.00 0.00 2.90
4855 14903 5.804692 TGGTTGTGTTAACTTGTGTGTAG 57.195 39.130 7.22 0.00 0.00 2.74
4900 15270 4.267690 GCTCTTTTTGGTTTCAAACGGAAG 59.732 41.667 0.00 0.00 41.97 3.46
4947 17588 6.161526 AGGGGTATGGTAAATGGAGTTGTAAT 59.838 38.462 0.00 0.00 0.00 1.89
4979 17620 7.894708 TGGATTTGACTAATGCTTTTGATTGA 58.105 30.769 3.17 0.00 35.74 2.57
5084 17732 6.154203 TGATTGTTTCAGGTTTGTTGCATA 57.846 33.333 0.00 0.00 0.00 3.14
5240 18034 2.762535 TAGCTGCACCTCAGTTTACC 57.237 50.000 1.02 0.00 44.66 2.85
5249 18043 0.108329 CTCAGTTTACCGGACCGCAT 60.108 55.000 9.46 0.61 0.00 4.73
5280 18074 5.047731 TGGATGTCACTACTCTTTCACTGAG 60.048 44.000 0.00 0.00 37.55 3.35
5420 18788 4.269183 TCCAACACAAGGCAAGTATATGG 58.731 43.478 0.00 0.00 0.00 2.74
5448 18816 3.443037 GTGTAGTACTGCAGCATCTCAG 58.557 50.000 14.45 0.00 36.45 3.35
5451 18819 3.455990 AGTACTGCAGCATCTCAGATG 57.544 47.619 15.27 10.64 34.57 2.90
5457 18829 6.111669 ACTGCAGCATCTCAGATGTATTAT 57.888 37.500 15.27 0.00 34.57 1.28
5458 18830 7.237209 ACTGCAGCATCTCAGATGTATTATA 57.763 36.000 15.27 0.00 34.57 0.98
5459 18831 7.095910 ACTGCAGCATCTCAGATGTATTATAC 58.904 38.462 15.27 0.00 34.57 1.47
5460 18832 7.039152 ACTGCAGCATCTCAGATGTATTATACT 60.039 37.037 15.27 0.00 34.57 2.12
5461 18833 7.318893 TGCAGCATCTCAGATGTATTATACTC 58.681 38.462 16.28 0.00 0.00 2.59
5462 18834 6.756074 GCAGCATCTCAGATGTATTATACTCC 59.244 42.308 16.28 0.00 0.00 3.85
5463 18835 7.264221 CAGCATCTCAGATGTATTATACTCCC 58.736 42.308 16.28 0.00 0.00 4.30
5464 18836 7.123997 CAGCATCTCAGATGTATTATACTCCCT 59.876 40.741 16.28 0.00 0.00 4.20
5465 18837 7.341769 AGCATCTCAGATGTATTATACTCCCTC 59.658 40.741 16.28 0.00 0.00 4.30
5466 18838 7.417342 GCATCTCAGATGTATTATACTCCCTCC 60.417 44.444 16.28 0.00 0.00 4.30
5467 18839 6.181190 TCTCAGATGTATTATACTCCCTCCG 58.819 44.000 3.92 0.00 0.00 4.63
5468 18840 5.888901 TCAGATGTATTATACTCCCTCCGT 58.111 41.667 3.92 0.00 0.00 4.69
5469 18841 6.312529 TCAGATGTATTATACTCCCTCCGTT 58.687 40.000 3.92 0.00 0.00 4.44
5470 18842 6.433404 TCAGATGTATTATACTCCCTCCGTTC 59.567 42.308 3.92 0.00 0.00 3.95
5471 18843 5.715753 AGATGTATTATACTCCCTCCGTTCC 59.284 44.000 3.92 0.00 0.00 3.62
5480 18852 9.827198 TTATACTCCCTCCGTTCCTAAATATAA 57.173 33.333 0.00 0.00 0.00 0.98
5485 18857 6.492772 TCCCTCCGTTCCTAAATATAAGTCTC 59.507 42.308 0.00 0.00 0.00 3.36
5514 18886 7.484975 AGAGATTCCAAAAGAGACTACATACG 58.515 38.462 0.00 0.00 0.00 3.06
5515 18887 7.339721 AGAGATTCCAAAAGAGACTACATACGA 59.660 37.037 0.00 0.00 0.00 3.43
5529 18901 4.685169 ACATACGAAGCAAAATGAGTGG 57.315 40.909 0.00 0.00 0.00 4.00
5641 19013 9.355916 AGTATATAGTCTTGTCATAAGAGTGCA 57.644 33.333 1.81 0.00 32.59 4.57
5670 19042 2.750350 CAGGCCTCTGGTCCGTTT 59.250 61.111 0.00 0.00 37.36 3.60
5671 19043 1.980052 CAGGCCTCTGGTCCGTTTA 59.020 57.895 0.00 0.00 37.36 2.01
5729 19173 8.687292 AAAGTTTTACGTAATCCTTTTCTCCT 57.313 30.769 19.23 4.94 0.00 3.69
5760 19204 9.846248 AAACACTTAAAATATCTACGTACGTCT 57.154 29.630 26.53 13.34 0.00 4.18
5762 19206 9.922305 ACACTTAAAATATCTACGTACGTCTAC 57.078 33.333 26.53 0.00 0.00 2.59
5763 19207 9.920826 CACTTAAAATATCTACGTACGTCTACA 57.079 33.333 26.53 9.63 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.899239 GATGAGGGTGGCGGCGAG 62.899 72.222 12.98 0.00 0.00 5.03
39 40 4.873129 CGTCGATGAGGGTGGCGG 62.873 72.222 0.00 0.00 0.00 6.13
40 41 4.873129 CCGTCGATGAGGGTGGCG 62.873 72.222 6.11 0.00 33.46 5.69
42 43 4.530857 GGCCGTCGATGAGGGTGG 62.531 72.222 6.11 0.00 39.49 4.61
43 44 4.873129 CGGCCGTCGATGAGGGTG 62.873 72.222 19.50 0.00 39.49 4.61
85 86 4.685026 CTATCCTCGCCGCCGTCG 62.685 72.222 0.00 0.00 35.54 5.12
86 87 4.344474 CCTATCCTCGCCGCCGTC 62.344 72.222 0.00 0.00 35.54 4.79
87 88 4.889112 TCCTATCCTCGCCGCCGT 62.889 66.667 0.00 0.00 35.54 5.68
88 89 2.820767 GATTCCTATCCTCGCCGCCG 62.821 65.000 0.00 0.00 0.00 6.46
89 90 1.079750 GATTCCTATCCTCGCCGCC 60.080 63.158 0.00 0.00 0.00 6.13
90 91 1.444553 CGATTCCTATCCTCGCCGC 60.445 63.158 0.00 0.00 0.00 6.53
91 92 0.169230 CTCGATTCCTATCCTCGCCG 59.831 60.000 0.00 0.00 32.62 6.46
92 93 1.535833 TCTCGATTCCTATCCTCGCC 58.464 55.000 0.00 0.00 32.62 5.54
93 94 2.094957 CCTTCTCGATTCCTATCCTCGC 60.095 54.545 0.00 0.00 32.62 5.03
94 95 2.490115 CCCTTCTCGATTCCTATCCTCG 59.510 54.545 0.00 0.00 0.00 4.63
95 96 2.829120 CCCCTTCTCGATTCCTATCCTC 59.171 54.545 0.00 0.00 0.00 3.71
96 97 2.451273 TCCCCTTCTCGATTCCTATCCT 59.549 50.000 0.00 0.00 0.00 3.24
97 98 2.829120 CTCCCCTTCTCGATTCCTATCC 59.171 54.545 0.00 0.00 0.00 2.59
98 99 2.829120 CCTCCCCTTCTCGATTCCTATC 59.171 54.545 0.00 0.00 0.00 2.08
99 100 2.493687 CCCTCCCCTTCTCGATTCCTAT 60.494 54.545 0.00 0.00 0.00 2.57
100 101 1.133136 CCCTCCCCTTCTCGATTCCTA 60.133 57.143 0.00 0.00 0.00 2.94
101 102 0.399233 CCCTCCCCTTCTCGATTCCT 60.399 60.000 0.00 0.00 0.00 3.36
102 103 1.411651 CCCCTCCCCTTCTCGATTCC 61.412 65.000 0.00 0.00 0.00 3.01
103 104 0.398664 TCCCCTCCCCTTCTCGATTC 60.399 60.000 0.00 0.00 0.00 2.52
104 105 0.691413 GTCCCCTCCCCTTCTCGATT 60.691 60.000 0.00 0.00 0.00 3.34
105 106 1.075151 GTCCCCTCCCCTTCTCGAT 60.075 63.158 0.00 0.00 0.00 3.59
106 107 2.363361 GTCCCCTCCCCTTCTCGA 59.637 66.667 0.00 0.00 0.00 4.04
107 108 3.148279 CGTCCCCTCCCCTTCTCG 61.148 72.222 0.00 0.00 0.00 4.04
108 109 2.764547 CCGTCCCCTCCCCTTCTC 60.765 72.222 0.00 0.00 0.00 2.87
109 110 3.281787 TCCGTCCCCTCCCCTTCT 61.282 66.667 0.00 0.00 0.00 2.85
110 111 3.082055 GTCCGTCCCCTCCCCTTC 61.082 72.222 0.00 0.00 0.00 3.46
119 120 3.963124 TAACCTCCCCGTCCGTCCC 62.963 68.421 0.00 0.00 0.00 4.46
120 121 2.362889 TAACCTCCCCGTCCGTCC 60.363 66.667 0.00 0.00 0.00 4.79
121 122 1.661498 GACTAACCTCCCCGTCCGTC 61.661 65.000 0.00 0.00 0.00 4.79
122 123 1.680314 GACTAACCTCCCCGTCCGT 60.680 63.158 0.00 0.00 0.00 4.69
123 124 2.768492 CGACTAACCTCCCCGTCCG 61.768 68.421 0.00 0.00 0.00 4.79
124 125 3.073742 GCGACTAACCTCCCCGTCC 62.074 68.421 0.00 0.00 0.00 4.79
125 126 2.493501 GCGACTAACCTCCCCGTC 59.506 66.667 0.00 0.00 0.00 4.79
126 127 3.073101 GGCGACTAACCTCCCCGT 61.073 66.667 0.00 0.00 0.00 5.28
127 128 3.846430 GGGCGACTAACCTCCCCG 61.846 72.222 0.00 0.00 32.60 5.73
129 130 3.477346 GGGGGCGACTAACCTCCC 61.477 72.222 0.00 0.00 42.70 4.30
130 131 3.846430 CGGGGGCGACTAACCTCC 61.846 72.222 0.00 0.00 45.35 4.30
131 132 2.757099 TCGGGGGCGACTAACCTC 60.757 66.667 0.00 0.00 0.00 3.85
132 133 2.758737 CTCGGGGGCGACTAACCT 60.759 66.667 0.00 0.00 0.00 3.50
133 134 3.073101 ACTCGGGGGCGACTAACC 61.073 66.667 0.00 0.00 0.00 2.85
134 135 2.493501 GACTCGGGGGCGACTAAC 59.506 66.667 0.00 0.00 0.00 2.34
170 171 4.446413 CCGTTCCCCGTTCCCTCG 62.446 72.222 0.00 0.00 33.66 4.63
171 172 4.091939 CCCGTTCCCCGTTCCCTC 62.092 72.222 0.00 0.00 33.66 4.30
174 175 3.639361 TTCCCCGTTCCCCGTTCC 61.639 66.667 0.00 0.00 33.66 3.62
175 176 2.359107 GTTCCCCGTTCCCCGTTC 60.359 66.667 0.00 0.00 33.66 3.95
176 177 4.318949 CGTTCCCCGTTCCCCGTT 62.319 66.667 0.00 0.00 33.66 4.44
185 186 1.076332 GAGTTGATTGACGTTCCCCG 58.924 55.000 0.00 0.00 44.03 5.73
186 187 2.076863 CAGAGTTGATTGACGTTCCCC 58.923 52.381 0.00 0.00 0.00 4.81
187 188 2.996621 CTCAGAGTTGATTGACGTTCCC 59.003 50.000 0.00 0.00 31.68 3.97
188 189 3.654414 ACTCAGAGTTGATTGACGTTCC 58.346 45.455 0.00 0.00 31.68 3.62
189 190 5.462405 ACTACTCAGAGTTGATTGACGTTC 58.538 41.667 17.70 0.00 31.68 3.95
190 191 5.455056 ACTACTCAGAGTTGATTGACGTT 57.545 39.130 17.70 0.00 31.68 3.99
191 192 5.455056 AACTACTCAGAGTTGATTGACGT 57.545 39.130 17.70 0.00 38.25 4.34
192 193 7.085116 AGTAAACTACTCAGAGTTGATTGACG 58.915 38.462 17.70 0.00 39.62 4.35
193 194 8.819643 AAGTAAACTACTCAGAGTTGATTGAC 57.180 34.615 17.70 11.12 39.62 3.18
200 201 9.930693 CCAAGATAAAGTAAACTACTCAGAGTT 57.069 33.333 8.80 0.00 41.50 3.01
201 202 8.035984 GCCAAGATAAAGTAAACTACTCAGAGT 58.964 37.037 8.50 8.50 38.26 3.24
202 203 8.035394 TGCCAAGATAAAGTAAACTACTCAGAG 58.965 37.037 0.00 0.00 38.26 3.35
203 204 7.903145 TGCCAAGATAAAGTAAACTACTCAGA 58.097 34.615 0.00 0.00 38.26 3.27
204 205 7.201565 GCTGCCAAGATAAAGTAAACTACTCAG 60.202 40.741 0.00 0.00 38.26 3.35
205 206 6.594159 GCTGCCAAGATAAAGTAAACTACTCA 59.406 38.462 0.00 0.00 38.26 3.41
206 207 6.037281 GGCTGCCAAGATAAAGTAAACTACTC 59.963 42.308 15.17 0.00 38.26 2.59
207 208 5.880887 GGCTGCCAAGATAAAGTAAACTACT 59.119 40.000 15.17 0.00 41.73 2.57
208 209 5.066117 GGGCTGCCAAGATAAAGTAAACTAC 59.934 44.000 22.05 0.00 0.00 2.73
276 277 4.700365 TCGATAGGATGGCGCGCG 62.700 66.667 28.44 28.44 0.00 6.86
310 311 2.029110 CCAGTTAATGGGTTTGCTGGTG 60.029 50.000 0.00 0.00 46.36 4.17
331 332 7.518731 TTCTGTTAAATTTTGTTGCTGACAC 57.481 32.000 0.00 0.00 38.18 3.67
396 397 1.102809 TTGCTGTGTTGTCTGCTGGG 61.103 55.000 0.00 0.00 34.27 4.45
1017 1027 4.292186 TCAGAGGAAGAAACCCATCAAG 57.708 45.455 0.00 0.00 0.00 3.02
1099 1114 1.961277 GGTTCGCACCACACTGGAG 60.961 63.158 0.00 0.00 43.61 3.86
1116 1131 0.104304 AGCTATACGCCGGAAAGTGG 59.896 55.000 5.05 0.00 40.39 4.00
1202 1217 5.346181 AAGAAGGAAGAAGAATCCTACCG 57.654 43.478 0.00 0.00 46.65 4.02
1210 1226 3.496870 GGCTGTGGAAGAAGGAAGAAGAA 60.497 47.826 0.00 0.00 0.00 2.52
1211 1227 2.039084 GGCTGTGGAAGAAGGAAGAAGA 59.961 50.000 0.00 0.00 0.00 2.87
1212 1228 2.224621 TGGCTGTGGAAGAAGGAAGAAG 60.225 50.000 0.00 0.00 0.00 2.85
1325 1342 3.004106 CAGCTCAAGACTTTTTGGTCCTG 59.996 47.826 0.00 0.00 36.95 3.86
1393 1431 9.386122 ACAGTAAGGACAGATAATATGAGGAAT 57.614 33.333 0.00 0.00 0.00 3.01
1394 1432 8.642432 CACAGTAAGGACAGATAATATGAGGAA 58.358 37.037 0.00 0.00 0.00 3.36
1395 1433 7.233553 CCACAGTAAGGACAGATAATATGAGGA 59.766 40.741 0.00 0.00 0.00 3.71
1418 1477 2.715046 TGATCTTTGATCTGGTGCCAC 58.285 47.619 8.71 0.00 0.00 5.01
1470 1530 1.988982 GCCTCCTGTCCCTGATTCCC 61.989 65.000 0.00 0.00 0.00 3.97
1525 1585 7.293073 AGATCACCAATCCAGCATAATTTACT 58.707 34.615 0.00 0.00 34.67 2.24
1584 1644 8.162878 ACAAGATAGAAGAATATGTTGGCATG 57.837 34.615 8.05 0.00 39.50 4.06
1728 1800 5.468072 GGCAGGAAGACATCAATATGTGTAG 59.532 44.000 0.00 0.00 46.49 2.74
1869 1949 3.580458 CTGAGAGAAGAACTGGGAAAGGA 59.420 47.826 0.00 0.00 0.00 3.36
1870 1950 3.326297 ACTGAGAGAAGAACTGGGAAAGG 59.674 47.826 0.00 0.00 0.00 3.11
1871 1951 4.615588 ACTGAGAGAAGAACTGGGAAAG 57.384 45.455 0.00 0.00 0.00 2.62
1872 1952 5.780282 TCATACTGAGAGAAGAACTGGGAAA 59.220 40.000 0.00 0.00 0.00 3.13
1873 1953 5.333581 TCATACTGAGAGAAGAACTGGGAA 58.666 41.667 0.00 0.00 0.00 3.97
1874 1954 4.935578 TCATACTGAGAGAAGAACTGGGA 58.064 43.478 0.00 0.00 0.00 4.37
1875 1955 5.659463 CTTCATACTGAGAGAAGAACTGGG 58.341 45.833 7.82 0.00 40.85 4.45
1876 1956 5.108517 GCTTCATACTGAGAGAAGAACTGG 58.891 45.833 14.60 0.00 40.85 4.00
1877 1957 5.718146 TGCTTCATACTGAGAGAAGAACTG 58.282 41.667 14.60 0.00 40.85 3.16
1878 1958 5.714333 TCTGCTTCATACTGAGAGAAGAACT 59.286 40.000 14.60 0.00 40.85 3.01
1879 1959 5.960113 TCTGCTTCATACTGAGAGAAGAAC 58.040 41.667 14.60 3.16 40.85 3.01
1933 2024 2.837591 AGAGCTTCTTCTTCCTCCTTCC 59.162 50.000 0.00 0.00 0.00 3.46
1934 2025 4.020662 TCAAGAGCTTCTTCTTCCTCCTTC 60.021 45.833 0.00 0.00 33.78 3.46
1935 2026 3.906846 TCAAGAGCTTCTTCTTCCTCCTT 59.093 43.478 0.00 0.00 33.78 3.36
1936 2027 3.515562 TCAAGAGCTTCTTCTTCCTCCT 58.484 45.455 0.00 0.00 33.78 3.69
1937 2028 3.971245 TCAAGAGCTTCTTCTTCCTCC 57.029 47.619 0.00 0.00 33.78 4.30
1938 2029 6.172630 AGAAATCAAGAGCTTCTTCTTCCTC 58.827 40.000 0.00 0.00 33.78 3.71
1939 2030 6.125589 AGAAATCAAGAGCTTCTTCTTCCT 57.874 37.500 0.00 0.00 33.78 3.36
1940 2031 6.816134 AAGAAATCAAGAGCTTCTTCTTCC 57.184 37.500 0.00 0.00 35.03 3.46
2002 2093 1.028868 GGTTCTCCAGTGGCAGCATC 61.029 60.000 3.51 0.00 0.00 3.91
2071 2162 3.603532 TCAACCATGCAGAGTTGAGATC 58.396 45.455 23.38 0.00 45.53 2.75
2102 2193 7.121759 ACATGAATGAACTGAATAAACAGGAGG 59.878 37.037 0.00 0.00 41.59 4.30
2185 3558 1.008652 CTGCCTCGATCTCAGAGCG 60.009 63.158 5.81 5.81 43.08 5.03
2354 3732 5.278169 CCCTGATGCTTCCTGAATTTTATCG 60.278 44.000 0.00 0.00 0.00 2.92
2563 3947 6.332504 ACACTTGAAAAAGATAGATACGCG 57.667 37.500 3.53 3.53 0.00 6.01
2588 3972 1.403780 CCGGCTGACTAGTTACACACC 60.404 57.143 0.00 0.00 0.00 4.16
2591 3975 2.688958 AGATCCGGCTGACTAGTTACAC 59.311 50.000 0.00 0.00 0.00 2.90
2592 3976 3.014304 AGATCCGGCTGACTAGTTACA 57.986 47.619 0.00 0.00 0.00 2.41
2593 3977 3.130693 ACAAGATCCGGCTGACTAGTTAC 59.869 47.826 0.00 0.00 0.00 2.50
2594 3978 3.362706 ACAAGATCCGGCTGACTAGTTA 58.637 45.455 0.00 0.00 0.00 2.24
2595 3979 2.180276 ACAAGATCCGGCTGACTAGTT 58.820 47.619 0.00 0.00 0.00 2.24
2596 3980 1.853963 ACAAGATCCGGCTGACTAGT 58.146 50.000 0.00 0.00 0.00 2.57
2597 3981 2.166459 TCAACAAGATCCGGCTGACTAG 59.834 50.000 0.00 0.00 0.00 2.57
2598 3982 2.176045 TCAACAAGATCCGGCTGACTA 58.824 47.619 0.00 0.00 0.00 2.59
2599 3983 0.976641 TCAACAAGATCCGGCTGACT 59.023 50.000 0.00 0.00 0.00 3.41
2600 3984 1.667724 CATCAACAAGATCCGGCTGAC 59.332 52.381 0.00 0.00 33.72 3.51
2601 3985 1.554617 TCATCAACAAGATCCGGCTGA 59.445 47.619 0.00 0.00 33.72 4.26
2602 3986 2.028420 TCATCAACAAGATCCGGCTG 57.972 50.000 0.00 0.00 33.72 4.85
2603 3987 2.569059 CATCATCAACAAGATCCGGCT 58.431 47.619 0.00 0.00 33.72 5.52
2604 3988 1.002033 GCATCATCAACAAGATCCGGC 60.002 52.381 0.00 0.00 33.72 6.13
2605 3989 2.289820 CTGCATCATCAACAAGATCCGG 59.710 50.000 0.00 0.00 33.72 5.14
2653 7509 0.532573 TCAAGTGCAGATCGGAGGAC 59.467 55.000 0.00 0.00 0.00 3.85
2771 7631 4.080129 ACAGGTGAGATGGAATTACAGCAT 60.080 41.667 8.95 0.00 34.44 3.79
2772 7632 3.264193 ACAGGTGAGATGGAATTACAGCA 59.736 43.478 8.95 0.00 34.44 4.41
2773 7633 3.873952 GACAGGTGAGATGGAATTACAGC 59.126 47.826 0.00 0.00 33.04 4.40
3016 7882 3.763360 CAGGTGCATTGATGGGTCTTTAA 59.237 43.478 0.00 0.00 0.00 1.52
3017 7883 3.245229 ACAGGTGCATTGATGGGTCTTTA 60.245 43.478 8.02 0.00 0.00 1.85
3018 7884 2.173519 CAGGTGCATTGATGGGTCTTT 58.826 47.619 0.00 0.00 0.00 2.52
3019 7885 1.076024 ACAGGTGCATTGATGGGTCTT 59.924 47.619 8.02 0.00 0.00 3.01
3088 10547 9.770097 TTGAGAATTGAAGGCAGAATATACTAG 57.230 33.333 0.00 0.00 0.00 2.57
3098 10557 5.443185 TTCACTTTGAGAATTGAAGGCAG 57.557 39.130 0.00 0.00 31.79 4.85
3099 10558 4.261741 GCTTCACTTTGAGAATTGAAGGCA 60.262 41.667 16.06 0.00 45.44 4.75
3337 10810 5.681982 GCTCAAGTTACTACTACATACTGCG 59.318 44.000 0.00 0.00 33.17 5.18
3360 10833 6.759497 AGACAAGATAAAATTGGGTACTGC 57.241 37.500 0.00 0.00 31.76 4.40
3403 10876 6.409704 TCTCCTTATGGTGATTCTTGTCAAG 58.590 40.000 6.21 6.21 31.62 3.02
3556 11029 1.863267 CGATGACATCTCCAAGAGCC 58.137 55.000 13.45 0.00 0.00 4.70
3663 11136 4.407945 ACTGCTAGTCCGTTTACCCATATT 59.592 41.667 0.00 0.00 0.00 1.28
3664 11137 3.965347 ACTGCTAGTCCGTTTACCCATAT 59.035 43.478 0.00 0.00 0.00 1.78
3665 11138 3.368248 ACTGCTAGTCCGTTTACCCATA 58.632 45.455 0.00 0.00 0.00 2.74
3897 11471 1.812571 ACCATCGCCTGTTTTTAGCAG 59.187 47.619 0.00 0.00 0.00 4.24
3917 11491 2.616376 CACCACCATCACGACTTTTGAA 59.384 45.455 0.00 0.00 0.00 2.69
3926 11500 0.954938 TGATGTGCACCACCATCACG 60.955 55.000 15.69 0.00 31.97 4.35
3974 11548 1.701704 CAAAGCCCAGCGAACAAATC 58.298 50.000 0.00 0.00 0.00 2.17
3998 11572 3.598299 GGATTCTATCAGCATGGCTCTC 58.402 50.000 0.00 0.00 36.40 3.20
4020 11594 1.077858 CCTCTGAAAGCTCCCTGCC 60.078 63.158 0.00 0.00 44.23 4.85
4025 11599 4.810191 TCTTCTTACCTCTGAAAGCTCC 57.190 45.455 0.00 0.00 0.00 4.70
4121 11741 6.206634 TCAACATTTTCAGGTCCTACATCAAC 59.793 38.462 0.00 0.00 0.00 3.18
4195 11815 1.627297 ATTCAGAACCCCGAGCTCCC 61.627 60.000 8.47 0.00 0.00 4.30
4263 14263 2.716017 GCTGACAGACGGAGGGAGG 61.716 68.421 6.65 0.00 0.00 4.30
4287 14290 4.493747 CGACCCCTTCTCGTCGCC 62.494 72.222 0.00 0.00 44.54 5.54
4327 14330 4.463879 CCTGCAGAGGGCTGTCGG 62.464 72.222 17.39 0.00 44.17 4.79
4334 14337 3.965539 CTCGGTTGCCTGCAGAGGG 62.966 68.421 17.39 0.00 40.19 4.30
4335 14338 2.435586 CTCGGTTGCCTGCAGAGG 60.436 66.667 17.39 0.19 43.19 3.69
4336 14339 1.447489 CTCTCGGTTGCCTGCAGAG 60.447 63.158 17.39 6.56 0.00 3.35
4338 14341 2.435586 CCTCTCGGTTGCCTGCAG 60.436 66.667 6.78 6.78 0.00 4.41
4339 14342 4.020617 CCCTCTCGGTTGCCTGCA 62.021 66.667 0.00 0.00 0.00 4.41
4421 14442 4.389576 GCTGCGCCGTGTCTTTGG 62.390 66.667 4.18 0.00 0.00 3.28
4436 14457 4.473520 CCGACGGAATGGGCTGCT 62.474 66.667 8.64 0.00 0.00 4.24
4440 14461 1.371337 GGTTTACCGACGGAATGGGC 61.371 60.000 23.38 5.21 0.00 5.36
4486 14507 1.227674 CCACCGGGCTTAGATGAGC 60.228 63.158 6.32 0.00 41.96 4.26
4529 14550 0.173708 CTGACGACCTAGCCTTGGAC 59.826 60.000 0.00 0.00 0.00 4.02
4549 14570 3.341043 CGCCGGATGAGAATGCCG 61.341 66.667 5.05 0.00 44.42 5.69
4665 14692 1.365999 CCGGCCTGGAAACAAAACC 59.634 57.895 7.77 0.00 42.06 3.27
4688 14715 2.663423 GATGCAGGGGAGCTCTCAGC 62.663 65.000 17.22 18.85 42.84 4.26
4689 14716 1.335882 TGATGCAGGGGAGCTCTCAG 61.336 60.000 17.22 8.50 34.99 3.35
4690 14717 1.306397 TGATGCAGGGGAGCTCTCA 60.306 57.895 17.22 5.67 34.99 3.27
4737 14764 4.633126 GCAGTATTTCTGTGAGCTCAATCA 59.367 41.667 20.19 12.50 45.23 2.57
4738 14765 4.874966 AGCAGTATTTCTGTGAGCTCAATC 59.125 41.667 20.19 7.78 45.23 2.67
4739 14766 4.634883 CAGCAGTATTTCTGTGAGCTCAAT 59.365 41.667 20.19 10.60 45.23 2.57
4740 14767 3.999001 CAGCAGTATTTCTGTGAGCTCAA 59.001 43.478 20.19 2.01 45.23 3.02
4762 14789 4.129380 TCAGTGGTATGCAATCTGTATGC 58.871 43.478 0.00 0.00 44.08 3.14
4805 14832 8.292448 ACTATCAAACAGCTGTAAACATTTGAG 58.708 33.333 25.31 18.27 35.74 3.02
4814 14858 6.320164 ACAACCAAACTATCAAACAGCTGTAA 59.680 34.615 22.01 9.44 0.00 2.41
4852 14900 0.691413 AAGGGCCCTCCAGTAGCTAC 60.691 60.000 28.84 16.43 38.24 3.58
4853 14901 0.398664 GAAGGGCCCTCCAGTAGCTA 60.399 60.000 28.84 0.00 38.24 3.32
4854 14902 1.690985 GAAGGGCCCTCCAGTAGCT 60.691 63.158 28.84 6.36 38.24 3.32
4855 14903 2.747443 GGAAGGGCCCTCCAGTAGC 61.747 68.421 28.84 8.50 38.24 3.58
4947 17588 9.995003 AAAAGCATTAGTCAAATCCAATTACAA 57.005 25.926 0.00 0.00 0.00 2.41
5007 17655 8.580720 CAGTATATTAAGTGATGCTGTACTCCT 58.419 37.037 0.00 0.00 32.84 3.69
5009 17657 9.751542 AACAGTATATTAAGTGATGCTGTACTC 57.248 33.333 14.58 0.00 44.90 2.59
5240 18034 0.390603 TCCAACACTTATGCGGTCCG 60.391 55.000 6.99 6.99 0.00 4.79
5249 18043 6.665992 AAGAGTAGTGACATCCAACACTTA 57.334 37.500 0.00 0.00 43.52 2.24
5280 18074 6.538742 TCAATTAGCAACTAAGGTATGCAGAC 59.461 38.462 1.94 1.94 42.45 3.51
5420 18788 2.931320 GCTGCAGTACTACACCCAGTTC 60.931 54.545 16.64 0.00 32.39 3.01
5448 18816 5.715753 AGGAACGGAGGGAGTATAATACATC 59.284 44.000 0.00 0.00 0.00 3.06
5451 18819 7.530426 TTTAGGAACGGAGGGAGTATAATAC 57.470 40.000 0.00 0.00 0.00 1.89
5457 18829 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
5458 18830 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
5459 18831 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
5460 18832 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
5461 18833 6.494146 AGAGACTTATATTTAGGAACGGAGGG 59.506 42.308 0.00 0.00 0.00 4.30
5462 18834 7.449086 AGAGAGACTTATATTTAGGAACGGAGG 59.551 40.741 0.00 0.00 0.00 4.30
5463 18835 8.398878 AGAGAGACTTATATTTAGGAACGGAG 57.601 38.462 0.00 0.00 0.00 4.63
5464 18836 9.504708 CTAGAGAGACTTATATTTAGGAACGGA 57.495 37.037 0.00 0.00 0.00 4.69
5465 18837 9.504708 TCTAGAGAGACTTATATTTAGGAACGG 57.495 37.037 0.00 0.00 0.00 4.44
5485 18857 8.287439 TGTAGTCTCTTTTGGAATCTCTAGAG 57.713 38.462 13.98 13.98 0.00 2.43
5494 18866 5.867716 GCTTCGTATGTAGTCTCTTTTGGAA 59.132 40.000 0.00 0.00 0.00 3.53
5496 18868 5.168569 TGCTTCGTATGTAGTCTCTTTTGG 58.831 41.667 0.00 0.00 0.00 3.28
5503 18875 6.311445 CACTCATTTTGCTTCGTATGTAGTCT 59.689 38.462 0.00 0.00 0.00 3.24
5514 18886 5.645497 AGTGTAGATCCACTCATTTTGCTTC 59.355 40.000 0.00 0.00 41.84 3.86
5515 18887 5.564550 AGTGTAGATCCACTCATTTTGCTT 58.435 37.500 0.00 0.00 41.84 3.91
5603 18975 9.440761 ACAAGACTATATACTTCCTTCATTCCT 57.559 33.333 0.00 0.00 0.00 3.36
5604 18976 9.699703 GACAAGACTATATACTTCCTTCATTCC 57.300 37.037 0.00 0.00 0.00 3.01
5615 18987 9.355916 TGCACTCTTATGACAAGACTATATACT 57.644 33.333 0.00 0.00 0.00 2.12
5616 18988 9.619316 CTGCACTCTTATGACAAGACTATATAC 57.381 37.037 0.00 0.00 0.00 1.47
5617 18989 9.355916 ACTGCACTCTTATGACAAGACTATATA 57.644 33.333 0.00 0.00 0.00 0.86
5618 18990 8.243961 ACTGCACTCTTATGACAAGACTATAT 57.756 34.615 0.00 0.00 0.00 0.86
5619 18991 7.558081 AGACTGCACTCTTATGACAAGACTATA 59.442 37.037 0.00 0.00 0.00 1.31
5620 18992 6.379703 AGACTGCACTCTTATGACAAGACTAT 59.620 38.462 0.00 0.00 0.00 2.12
5632 19004 4.149598 TGGTCAACTAGACTGCACTCTTA 58.850 43.478 0.00 0.00 46.72 2.10
5633 19005 2.965831 TGGTCAACTAGACTGCACTCTT 59.034 45.455 0.00 0.00 46.72 2.85
5634 19006 2.560542 CTGGTCAACTAGACTGCACTCT 59.439 50.000 0.00 1.37 46.72 3.24
5635 19007 2.353208 CCTGGTCAACTAGACTGCACTC 60.353 54.545 0.00 0.00 46.72 3.51
5636 19008 1.620819 CCTGGTCAACTAGACTGCACT 59.379 52.381 0.00 0.00 46.72 4.40
5637 19009 1.941668 GCCTGGTCAACTAGACTGCAC 60.942 57.143 0.00 0.00 46.72 4.57
5638 19010 0.321671 GCCTGGTCAACTAGACTGCA 59.678 55.000 0.00 0.00 46.72 4.41
5639 19011 0.391793 GGCCTGGTCAACTAGACTGC 60.392 60.000 0.00 0.00 46.72 4.40
5640 19012 1.205893 GAGGCCTGGTCAACTAGACTG 59.794 57.143 12.00 0.00 46.72 3.51
5641 19013 1.077993 AGAGGCCTGGTCAACTAGACT 59.922 52.381 12.00 0.00 46.72 3.24
5681 19053 5.874897 TGTAAGTTTGTGTAGGTGTAGGT 57.125 39.130 0.00 0.00 0.00 3.08
5756 19200 9.262472 GTATTTTGAAACTAGCAATTGTAGACG 57.738 33.333 16.84 2.77 0.00 4.18
5766 19210 9.120538 AGAACTTCAAGTATTTTGAAACTAGCA 57.879 29.630 0.00 0.00 37.89 3.49
5906 19350 9.773328 CAACACCTACAATGTCATATTAGTTTG 57.227 33.333 0.00 0.00 0.00 2.93
5968 19413 9.978044 ACTAGTAGATTTTTCGTAAGTCAAACT 57.022 29.630 3.59 0.00 39.48 2.66


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

AutoCloner maintained by Alex Coulton.