Multiple sequence alignment - TraesCS6D01G256700

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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 TraesCS6D01G256700 chr6D 100.000 4265 0 0 1 4265 362986278 362990542 0.000000e+00 7877.0
1 TraesCS6D01G256700 chr6A 89.260 3324 184 82 165 3451 503424737 503427924 0.000000e+00 4000.0
2 TraesCS6D01G256700 chr6A 91.240 605 33 12 3486 4087 503427929 503428516 0.000000e+00 806.0
3 TraesCS6D01G256700 chr6A 95.270 148 6 1 4110 4256 503428503 503428650 2.560000e-57 233.0
4 TraesCS6D01G256700 chr6A 89.130 138 11 2 8 145 503424617 503424750 7.330000e-38 169.0
5 TraesCS6D01G256700 chr6B 91.400 2128 109 43 1990 4087 544404220 544406303 0.000000e+00 2848.0
6 TraesCS6D01G256700 chr6B 89.649 1565 93 39 445 1993 544402405 544403916 0.000000e+00 1929.0
7 TraesCS6D01G256700 chr6B 92.547 161 6 3 4110 4265 544406290 544406449 4.290000e-55 226.0
8 TraesCS6D01G256700 chr7D 78.218 808 128 38 2354 3148 191492648 191491876 1.390000e-129 473.0
9 TraesCS6D01G256700 chr7D 91.266 229 18 2 1663 1890 191493347 191493120 1.150000e-80 311.0
10 TraesCS6D01G256700 chr7D 88.688 221 21 4 1663 1881 191557849 191557631 2.530000e-67 267.0
11 TraesCS6D01G256700 chr7D 79.018 224 40 7 2363 2584 191555908 191555690 3.440000e-31 147.0
12 TraesCS6D01G256700 chr7A 78.202 812 127 40 2354 3148 200032002 200031224 1.390000e-129 473.0
13 TraesCS6D01G256700 chr7A 91.739 230 16 3 1663 1890 200032714 200032486 2.480000e-82 316.0
14 TraesCS6D01G256700 chr7A 89.545 220 21 2 1663 1881 200064996 200064778 1.170000e-70 278.0
15 TraesCS6D01G256700 chr7A 78.571 224 41 7 2363 2584 200061783 200061565 1.600000e-29 141.0
16 TraesCS6D01G256700 chr7B 90.868 219 20 0 1663 1881 336647530 336647312 1.160000e-75 294.0
17 TraesCS6D01G256700 chr7B 88.235 221 24 2 1663 1882 336718601 336718382 3.270000e-66 263.0
18 TraesCS6D01G256700 chr7B 87.124 233 25 3 2354 2585 336646831 336646603 4.230000e-65 259.0
19 TraesCS6D01G256700 chr7B 77.679 224 43 7 2363 2584 336703415 336703197 3.460000e-26 130.0
20 TraesCS6D01G256700 chr5B 80.892 157 30 0 1721 1877 532933233 532933077 1.610000e-24 124.0
21 TraesCS6D01G256700 chr2A 76.608 171 40 0 2361 2531 203904286 203904116 1.260000e-15 95.3
22 TraesCS6D01G256700 chr4A 82.828 99 13 4 2690 2786 460239338 460239242 7.600000e-13 86.1
23 TraesCS6D01G256700 chr4D 81.818 99 14 4 2690 2786 116271046 116271142 3.540000e-11 80.5


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 TraesCS6D01G256700 chr6D 362986278 362990542 4264 False 7877.000000 7877 100.000000 1 4265 1 chr6D.!!$F1 4264
1 TraesCS6D01G256700 chr6A 503424617 503428650 4033 False 1302.000000 4000 91.225000 8 4256 4 chr6A.!!$F1 4248
2 TraesCS6D01G256700 chr6B 544402405 544406449 4044 False 1667.666667 2848 91.198667 445 4265 3 chr6B.!!$F1 3820
3 TraesCS6D01G256700 chr7D 191491876 191493347 1471 True 392.000000 473 84.742000 1663 3148 2 chr7D.!!$R1 1485
4 TraesCS6D01G256700 chr7D 191555690 191557849 2159 True 207.000000 267 83.853000 1663 2584 2 chr7D.!!$R2 921
5 TraesCS6D01G256700 chr7A 200031224 200032714 1490 True 394.500000 473 84.970500 1663 3148 2 chr7A.!!$R1 1485
6 TraesCS6D01G256700 chr7A 200061565 200064996 3431 True 209.500000 278 84.058000 1663 2584 2 chr7A.!!$R2 921
7 TraesCS6D01G256700 chr7B 336646603 336647530 927 True 276.500000 294 88.996000 1663 2585 2 chr7B.!!$R3 922

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
952 970 0.389391 CATACGATTCCCACGGCTCT 59.611 55.0 0.00 0.00 34.93 4.09 F
2445 5759 0.109086 ACTCGTGCCTCAAGATCGTG 60.109 55.0 1.76 1.76 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 5864 1.079681 GACGTGGCCGGTGTTGATA 60.080 57.895 1.9 0.0 38.78 2.15 R
3292 6625 0.108520 GAACTCCCCGCACGATTACA 60.109 55.000 0.0 0.0 0.00 2.41 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
46 47 4.760204 AGTAAAAGTGTGCATGGTTAGGTC 59.240 41.667 0.00 0.00 0.00 3.85
74 75 4.393062 AGCTGGATCATCTGTGTAAAAACG 59.607 41.667 0.00 0.00 0.00 3.60
88 89 6.485313 TGTGTAAAAACGATCTGTTGGAGATT 59.515 34.615 0.00 0.00 41.91 2.40
89 90 7.658167 TGTGTAAAAACGATCTGTTGGAGATTA 59.342 33.333 0.00 0.00 41.91 1.75
90 91 8.665685 GTGTAAAAACGATCTGTTGGAGATTAT 58.334 33.333 0.00 0.00 41.91 1.28
95 96 9.667107 AAAACGATCTGTTGGAGATTATTTAGA 57.333 29.630 0.00 0.00 41.91 2.10
97 98 8.239038 ACGATCTGTTGGAGATTATTTAGAGA 57.761 34.615 0.00 0.00 41.91 3.10
106 107 7.805163 TGGAGATTATTTAGAGAGCAATGGAA 58.195 34.615 0.00 0.00 0.00 3.53
114 115 3.759581 AGAGAGCAATGGAAAAGAGCAA 58.240 40.909 0.00 0.00 0.00 3.91
115 116 4.147321 AGAGAGCAATGGAAAAGAGCAAA 58.853 39.130 0.00 0.00 0.00 3.68
118 119 4.586001 AGAGCAATGGAAAAGAGCAAAAGA 59.414 37.500 0.00 0.00 0.00 2.52
123 124 6.294176 GCAATGGAAAAGAGCAAAAGACTCTA 60.294 38.462 0.00 0.00 43.71 2.43
124 125 7.303998 CAATGGAAAAGAGCAAAAGACTCTAG 58.696 38.462 0.00 0.00 43.71 2.43
125 126 5.308825 TGGAAAAGAGCAAAAGACTCTAGG 58.691 41.667 0.00 0.00 43.71 3.02
126 127 4.697828 GGAAAAGAGCAAAAGACTCTAGGG 59.302 45.833 0.00 0.00 43.71 3.53
161 162 4.806571 GCCTCGCGTAGAATGTGA 57.193 55.556 5.77 0.00 0.00 3.58
162 163 2.582959 GCCTCGCGTAGAATGTGAG 58.417 57.895 5.77 3.26 40.48 3.51
165 166 2.783828 CTCGCGTAGAATGTGAGGAT 57.216 50.000 5.77 0.00 37.92 3.24
166 167 2.389059 CTCGCGTAGAATGTGAGGATG 58.611 52.381 5.77 0.00 37.92 3.51
167 168 1.067060 TCGCGTAGAATGTGAGGATGG 59.933 52.381 5.77 0.00 0.00 3.51
168 169 1.221414 GCGTAGAATGTGAGGATGGC 58.779 55.000 0.00 0.00 0.00 4.40
169 170 1.491670 CGTAGAATGTGAGGATGGCG 58.508 55.000 0.00 0.00 0.00 5.69
170 171 1.067060 CGTAGAATGTGAGGATGGCGA 59.933 52.381 0.00 0.00 0.00 5.54
171 172 2.481276 CGTAGAATGTGAGGATGGCGAA 60.481 50.000 0.00 0.00 0.00 4.70
172 173 2.029838 AGAATGTGAGGATGGCGAAC 57.970 50.000 0.00 0.00 0.00 3.95
173 174 1.278985 AGAATGTGAGGATGGCGAACA 59.721 47.619 0.00 0.00 0.00 3.18
174 175 2.083774 GAATGTGAGGATGGCGAACAA 58.916 47.619 0.00 0.00 0.00 2.83
175 176 1.742761 ATGTGAGGATGGCGAACAAG 58.257 50.000 0.00 0.00 0.00 3.16
176 177 0.684535 TGTGAGGATGGCGAACAAGA 59.315 50.000 0.00 0.00 0.00 3.02
177 178 1.071542 TGTGAGGATGGCGAACAAGAA 59.928 47.619 0.00 0.00 0.00 2.52
178 179 2.151202 GTGAGGATGGCGAACAAGAAA 58.849 47.619 0.00 0.00 0.00 2.52
179 180 2.749621 GTGAGGATGGCGAACAAGAAAT 59.250 45.455 0.00 0.00 0.00 2.17
229 233 9.944376 AAGTAGTCAACATGTTGTATAATCAGT 57.056 29.630 31.99 18.77 41.16 3.41
249 253 5.470098 TCAGTAATGAAACAAACAGAGCTCC 59.530 40.000 10.93 0.00 0.00 4.70
288 292 6.651755 AAAATGAGCAAAAAGTGTGAACAG 57.348 33.333 0.00 0.00 0.00 3.16
291 295 3.130869 TGAGCAAAAAGTGTGAACAGCAT 59.869 39.130 0.00 0.00 0.00 3.79
320 326 5.648330 AACTGGTCTATAATCCCCTTTCC 57.352 43.478 0.00 0.00 0.00 3.13
325 331 6.399013 TGGTCTATAATCCCCTTTCCTGTAT 58.601 40.000 0.00 0.00 0.00 2.29
331 337 9.892130 CTATAATCCCCTTTCCTGTATATTCAC 57.108 37.037 0.00 0.00 0.00 3.18
387 393 2.521105 TCGACATCATCAGCATCAGG 57.479 50.000 0.00 0.00 0.00 3.86
392 398 4.197750 GACATCATCAGCATCAGGAAACT 58.802 43.478 0.00 0.00 46.44 2.66
399 405 5.164620 TCAGCATCAGGAAACTCAATGTA 57.835 39.130 0.00 0.00 40.21 2.29
420 426 1.156645 GCATCCGCAATCGAAGAGCT 61.157 55.000 0.00 0.00 38.01 4.09
423 429 1.448540 CCGCAATCGAAGAGCTGGT 60.449 57.895 0.00 0.00 43.63 4.00
426 432 1.442769 GCAATCGAAGAGCTGGTTCA 58.557 50.000 0.00 0.00 43.63 3.18
428 434 2.413371 GCAATCGAAGAGCTGGTTCAAC 60.413 50.000 0.00 0.00 43.63 3.18
429 435 2.807967 CAATCGAAGAGCTGGTTCAACA 59.192 45.455 0.00 0.00 43.63 3.33
430 436 2.839486 TCGAAGAGCTGGTTCAACAT 57.161 45.000 0.00 0.00 0.00 2.71
431 437 2.688507 TCGAAGAGCTGGTTCAACATC 58.311 47.619 0.00 0.00 0.00 3.06
439 445 3.693085 AGCTGGTTCAACATCATCATCAC 59.307 43.478 0.00 0.00 0.00 3.06
467 474 3.195002 CCACTGTATGCACCCGCG 61.195 66.667 0.00 0.00 42.97 6.46
523 530 0.752743 TGCACCAGCTCAGCAAAAGT 60.753 50.000 0.00 0.00 42.74 2.66
526 533 1.027357 ACCAGCTCAGCAAAAGTGTG 58.973 50.000 0.00 0.00 0.00 3.82
527 534 1.027357 CCAGCTCAGCAAAAGTGTGT 58.973 50.000 0.00 0.00 0.00 3.72
590 597 2.152016 GGAACAGAGAAAGGGGTTTCG 58.848 52.381 0.00 0.00 36.14 3.46
591 598 2.224450 GGAACAGAGAAAGGGGTTTCGA 60.224 50.000 0.00 0.00 36.14 3.71
596 605 3.189287 CAGAGAAAGGGGTTTCGAATGTG 59.811 47.826 0.00 0.00 36.14 3.21
598 607 3.146847 AGAAAGGGGTTTCGAATGTGAC 58.853 45.455 0.00 0.00 36.14 3.67
617 626 3.756727 GCTCTTGCAGGGCCAAGC 61.757 66.667 6.18 10.54 41.47 4.01
618 627 2.282674 CTCTTGCAGGGCCAAGCA 60.283 61.111 18.16 18.16 41.47 3.91
619 628 1.681327 CTCTTGCAGGGCCAAGCAT 60.681 57.895 21.81 0.00 41.47 3.79
620 629 1.228956 TCTTGCAGGGCCAAGCATT 60.229 52.632 21.81 0.00 41.47 3.56
634 643 1.188863 AGCATTGGATTTGGCAGACC 58.811 50.000 0.00 0.00 0.00 3.85
637 646 2.360165 GCATTGGATTTGGCAGACCTAG 59.640 50.000 7.85 0.00 36.63 3.02
649 658 2.613223 GCAGACCTAGAAGGACCAACAC 60.613 54.545 0.00 0.00 37.67 3.32
774 784 2.118403 TGGCCCCCTATTCTCCTAAG 57.882 55.000 0.00 0.00 0.00 2.18
852 865 3.100862 GAATCTCGCAAGCCACGGC 62.101 63.158 0.00 0.00 42.33 5.68
921 938 4.261801 GACCCAATAGCTAGCAAACAAGA 58.738 43.478 18.83 0.00 0.00 3.02
952 970 0.389391 CATACGATTCCCACGGCTCT 59.611 55.000 0.00 0.00 34.93 4.09
980 998 1.900486 GGAAGACCGGGAAGAAGAAGA 59.100 52.381 6.32 0.00 0.00 2.87
981 999 2.302157 GGAAGACCGGGAAGAAGAAGAA 59.698 50.000 6.32 0.00 0.00 2.52
982 1000 3.591023 GAAGACCGGGAAGAAGAAGAAG 58.409 50.000 6.32 0.00 0.00 2.85
983 1001 2.890814 AGACCGGGAAGAAGAAGAAGA 58.109 47.619 6.32 0.00 0.00 2.87
984 1002 3.240302 AGACCGGGAAGAAGAAGAAGAA 58.760 45.455 6.32 0.00 0.00 2.52
985 1003 3.259625 AGACCGGGAAGAAGAAGAAGAAG 59.740 47.826 6.32 0.00 0.00 2.85
986 1004 3.240302 ACCGGGAAGAAGAAGAAGAAGA 58.760 45.455 6.32 0.00 0.00 2.87
987 1005 3.646637 ACCGGGAAGAAGAAGAAGAAGAA 59.353 43.478 6.32 0.00 0.00 2.52
988 1006 4.249661 CCGGGAAGAAGAAGAAGAAGAAG 58.750 47.826 0.00 0.00 0.00 2.85
989 1007 4.021016 CCGGGAAGAAGAAGAAGAAGAAGA 60.021 45.833 0.00 0.00 0.00 2.87
990 1008 5.511545 CCGGGAAGAAGAAGAAGAAGAAGAA 60.512 44.000 0.00 0.00 0.00 2.52
991 1009 5.637387 CGGGAAGAAGAAGAAGAAGAAGAAG 59.363 44.000 0.00 0.00 0.00 2.85
992 1010 6.517529 CGGGAAGAAGAAGAAGAAGAAGAAGA 60.518 42.308 0.00 0.00 0.00 2.87
993 1011 7.220740 GGGAAGAAGAAGAAGAAGAAGAAGAA 58.779 38.462 0.00 0.00 0.00 2.52
994 1012 7.387673 GGGAAGAAGAAGAAGAAGAAGAAGAAG 59.612 40.741 0.00 0.00 0.00 2.85
995 1013 8.147704 GGAAGAAGAAGAAGAAGAAGAAGAAGA 58.852 37.037 0.00 0.00 0.00 2.87
996 1014 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
997 1015 8.887036 AGAAGAAGAAGAAGAAGAAGAAGAAC 57.113 34.615 0.00 0.00 0.00 3.01
998 1016 8.482128 AGAAGAAGAAGAAGAAGAAGAAGAACA 58.518 33.333 0.00 0.00 0.00 3.18
1080 1098 1.065928 GAGCGGTGATCCAGGTACG 59.934 63.158 0.00 0.00 0.00 3.67
1081 1099 1.664321 GAGCGGTGATCCAGGTACGT 61.664 60.000 0.00 0.00 0.00 3.57
1082 1100 0.394762 AGCGGTGATCCAGGTACGTA 60.395 55.000 0.00 0.00 0.00 3.57
1083 1101 0.248784 GCGGTGATCCAGGTACGTAC 60.249 60.000 17.56 17.56 0.00 3.67
1086 1104 2.288666 GGTGATCCAGGTACGTACGTA 58.711 52.381 23.60 23.60 0.00 3.57
1105 1123 3.745975 CGTACATCCAGTTCTTGCTTTGA 59.254 43.478 0.00 0.00 0.00 2.69
1107 1125 5.106555 CGTACATCCAGTTCTTGCTTTGATT 60.107 40.000 0.00 0.00 0.00 2.57
1108 1126 6.092122 CGTACATCCAGTTCTTGCTTTGATTA 59.908 38.462 0.00 0.00 0.00 1.75
1109 1127 7.201644 CGTACATCCAGTTCTTGCTTTGATTAT 60.202 37.037 0.00 0.00 0.00 1.28
1110 1128 7.472334 ACATCCAGTTCTTGCTTTGATTATT 57.528 32.000 0.00 0.00 0.00 1.40
1111 1129 7.899973 ACATCCAGTTCTTGCTTTGATTATTT 58.100 30.769 0.00 0.00 0.00 1.40
1112 1130 7.816031 ACATCCAGTTCTTGCTTTGATTATTTG 59.184 33.333 0.00 0.00 0.00 2.32
1113 1131 6.690530 TCCAGTTCTTGCTTTGATTATTTGG 58.309 36.000 0.00 0.00 0.00 3.28
1114 1132 5.870978 CCAGTTCTTGCTTTGATTATTTGGG 59.129 40.000 0.00 0.00 0.00 4.12
1116 1134 5.779771 AGTTCTTGCTTTGATTATTTGGGGA 59.220 36.000 0.00 0.00 0.00 4.81
1117 1135 5.920193 TCTTGCTTTGATTATTTGGGGAG 57.080 39.130 0.00 0.00 0.00 4.30
1118 1136 5.579047 TCTTGCTTTGATTATTTGGGGAGA 58.421 37.500 0.00 0.00 0.00 3.71
1121 1139 7.838696 TCTTGCTTTGATTATTTGGGGAGATAA 59.161 33.333 0.00 0.00 0.00 1.75
1122 1140 8.551682 TTGCTTTGATTATTTGGGGAGATAAT 57.448 30.769 0.00 0.00 32.61 1.28
1123 1141 9.653516 TTGCTTTGATTATTTGGGGAGATAATA 57.346 29.630 0.00 0.00 30.68 0.98
1124 1142 9.827198 TGCTTTGATTATTTGGGGAGATAATAT 57.173 29.630 0.00 0.00 30.68 1.28
1127 1145 8.593945 TTGATTATTTGGGGAGATAATATGGC 57.406 34.615 0.00 0.00 30.68 4.40
1128 1146 7.707648 TGATTATTTGGGGAGATAATATGGCA 58.292 34.615 0.00 0.00 30.68 4.92
1131 1149 4.371624 TTGGGGAGATAATATGGCAGTG 57.628 45.455 0.00 0.00 0.00 3.66
1132 1150 2.040278 TGGGGAGATAATATGGCAGTGC 59.960 50.000 6.55 6.55 0.00 4.40
1138 1156 5.279910 GGAGATAATATGGCAGTGCTCTTCT 60.280 44.000 16.11 7.84 0.00 2.85
1157 1175 0.690192 TGCCGAGGAAGGTGATTGAA 59.310 50.000 0.00 0.00 0.00 2.69
1158 1176 1.339055 TGCCGAGGAAGGTGATTGAAG 60.339 52.381 0.00 0.00 0.00 3.02
1160 1178 2.876079 GCCGAGGAAGGTGATTGAAGTT 60.876 50.000 0.00 0.00 0.00 2.66
1164 1182 4.320494 CGAGGAAGGTGATTGAAGTTTTGG 60.320 45.833 0.00 0.00 0.00 3.28
1165 1183 3.897505 AGGAAGGTGATTGAAGTTTTGGG 59.102 43.478 0.00 0.00 0.00 4.12
1167 1185 3.328535 AGGTGATTGAAGTTTTGGGGT 57.671 42.857 0.00 0.00 0.00 4.95
1168 1186 3.653164 AGGTGATTGAAGTTTTGGGGTT 58.347 40.909 0.00 0.00 0.00 4.11
1169 1187 3.387699 AGGTGATTGAAGTTTTGGGGTTG 59.612 43.478 0.00 0.00 0.00 3.77
1170 1188 3.133901 GGTGATTGAAGTTTTGGGGTTGT 59.866 43.478 0.00 0.00 0.00 3.32
1176 1194 0.534873 AGTTTTGGGGTTGTGTGTGC 59.465 50.000 0.00 0.00 0.00 4.57
1179 1197 0.613292 TTTGGGGTTGTGTGTGCTGT 60.613 50.000 0.00 0.00 0.00 4.40
1180 1198 0.613292 TTGGGGTTGTGTGTGCTGTT 60.613 50.000 0.00 0.00 0.00 3.16
1323 1349 3.370315 CCCTCTCTCTAGCTGTGCAATTT 60.370 47.826 0.00 0.00 0.00 1.82
1363 1392 6.506500 TGTTGGTAGTACTAGCACTAGAAC 57.493 41.667 29.49 24.03 42.44 3.01
1366 1395 6.058553 TGGTAGTACTAGCACTAGAACTGA 57.941 41.667 26.76 4.31 38.48 3.41
1392 1421 3.975035 GCTAAGCGAACTTTTTGGTTCTG 59.025 43.478 0.00 0.00 42.20 3.02
1559 1588 1.544691 CGTCTACAGGGTACAAGCACT 59.455 52.381 0.00 0.00 0.00 4.40
1560 1589 2.751259 CGTCTACAGGGTACAAGCACTA 59.249 50.000 0.00 0.00 0.00 2.74
1564 1593 2.051692 ACAGGGTACAAGCACTACCAA 58.948 47.619 0.00 0.00 36.14 3.67
1574 1603 4.469945 ACAAGCACTACCAAATCCTAGCTA 59.530 41.667 0.00 0.00 0.00 3.32
1575 1604 5.131142 ACAAGCACTACCAAATCCTAGCTAT 59.869 40.000 0.00 0.00 0.00 2.97
1576 1605 5.220710 AGCACTACCAAATCCTAGCTATG 57.779 43.478 0.00 0.00 0.00 2.23
1577 1606 4.656112 AGCACTACCAAATCCTAGCTATGT 59.344 41.667 0.00 0.00 0.00 2.29
1578 1607 5.131142 AGCACTACCAAATCCTAGCTATGTT 59.869 40.000 0.00 0.00 0.00 2.71
1579 1608 5.467063 GCACTACCAAATCCTAGCTATGTTC 59.533 44.000 0.00 0.00 0.00 3.18
1602 1631 2.009774 AGATGATACGTGCTGTTTGCC 58.990 47.619 0.00 0.00 42.00 4.52
1619 1648 2.158959 CCGGTGAGATCGCGTTGAC 61.159 63.158 5.77 0.00 0.00 3.18
1620 1649 2.497092 CGGTGAGATCGCGTTGACG 61.497 63.158 5.77 0.00 43.27 4.35
1621 1650 2.158959 GGTGAGATCGCGTTGACGG 61.159 63.158 5.77 0.00 40.23 4.79
1625 1654 0.456312 GAGATCGCGTTGACGGAACT 60.456 55.000 5.77 5.33 40.23 3.01
1641 1670 2.084546 GAACTAGCTTGGCCGTCATTT 58.915 47.619 0.00 0.00 0.00 2.32
1656 1685 3.670203 GTCATTTATGTCGCGAAACTGG 58.330 45.455 12.06 0.00 0.00 4.00
1943 2653 5.459107 CCTCGTGTCCAATTATTTACTCGAG 59.541 44.000 21.74 21.74 46.94 4.04
1980 4170 2.223782 CGCCAATGTCATTTGGTATGGG 60.224 50.000 12.67 4.44 46.54 4.00
2062 4599 3.419943 TGCACATGACTGAGCCAAATTA 58.580 40.909 0.00 0.00 38.09 1.40
2063 4600 3.441222 TGCACATGACTGAGCCAAATTAG 59.559 43.478 0.00 0.00 38.09 1.73
2107 4644 4.713553 TGCAGTCTCCATTGTTTACTGAA 58.286 39.130 11.52 1.50 39.93 3.02
2130 4667 7.669304 TGAATTTGAGTCAATTAGGTCCAATGA 59.331 33.333 6.36 0.00 0.00 2.57
2144 4681 2.564504 TCCAATGAGGCTATCAGATCGG 59.435 50.000 0.00 0.00 42.53 4.18
2170 4708 4.510167 AAGATAGGTCAATGGAACCCTG 57.490 45.455 0.00 0.00 0.00 4.45
2269 4807 6.325919 AGAACGGCTGTAATTTTCAAATCA 57.674 33.333 0.00 0.00 0.00 2.57
2343 5657 4.418013 TTTGTGCAATTCATCAGGTACG 57.582 40.909 0.00 0.00 0.00 3.67
2445 5759 0.109086 ACTCGTGCCTCAAGATCGTG 60.109 55.000 1.76 1.76 0.00 4.35
2604 5918 2.745100 CGCAGTGCAGCACTCCAT 60.745 61.111 25.89 1.51 43.43 3.41
2605 5919 1.448365 CGCAGTGCAGCACTCCATA 60.448 57.895 25.89 0.00 43.43 2.74
2607 5921 0.942962 GCAGTGCAGCACTCCATATC 59.057 55.000 25.89 6.85 43.43 1.63
2608 5922 1.590932 CAGTGCAGCACTCCATATCC 58.409 55.000 25.89 0.00 43.43 2.59
2609 5923 1.134310 CAGTGCAGCACTCCATATCCA 60.134 52.381 25.89 0.00 43.43 3.41
2610 5924 1.561076 AGTGCAGCACTCCATATCCAA 59.439 47.619 23.11 0.00 41.21 3.53
2611 5925 2.174210 AGTGCAGCACTCCATATCCAAT 59.826 45.455 23.11 0.00 41.21 3.16
2612 5926 3.392285 AGTGCAGCACTCCATATCCAATA 59.608 43.478 23.11 0.00 41.21 1.90
2638 5952 1.621317 TCTTCAGGCCGTGTGAATGTA 59.379 47.619 6.38 0.00 33.49 2.29
2639 5953 2.002586 CTTCAGGCCGTGTGAATGTAG 58.997 52.381 6.38 0.00 33.49 2.74
2673 5987 0.595095 GCTGACCTGAAGTTGCTTGG 59.405 55.000 0.00 0.00 0.00 3.61
2910 6228 4.873746 TTTCTCCTTCTCGTCTGAACAT 57.126 40.909 0.00 0.00 0.00 2.71
3265 6598 1.338484 CCATGATCCAGCCACGATAGG 60.338 57.143 0.00 0.00 43.77 2.57
3266 6599 1.620323 CATGATCCAGCCACGATAGGA 59.380 52.381 0.00 0.00 43.77 2.94
3267 6600 1.040646 TGATCCAGCCACGATAGGAC 58.959 55.000 0.00 0.00 43.77 3.85
3268 6601 0.318762 GATCCAGCCACGATAGGACC 59.681 60.000 0.00 0.00 43.77 4.46
3269 6602 0.105453 ATCCAGCCACGATAGGACCT 60.105 55.000 0.00 0.00 43.77 3.85
3287 6620 3.178046 ACCTCTCCTCCCTTCTTCTTTC 58.822 50.000 0.00 0.00 0.00 2.62
3288 6621 3.181400 ACCTCTCCTCCCTTCTTCTTTCT 60.181 47.826 0.00 0.00 0.00 2.52
3289 6622 3.197549 CCTCTCCTCCCTTCTTCTTTCTG 59.802 52.174 0.00 0.00 0.00 3.02
3290 6623 3.837731 CTCTCCTCCCTTCTTCTTTCTGT 59.162 47.826 0.00 0.00 0.00 3.41
3291 6624 5.011982 TCTCCTCCCTTCTTCTTTCTGTA 57.988 43.478 0.00 0.00 0.00 2.74
3292 6625 5.594777 TCTCCTCCCTTCTTCTTTCTGTAT 58.405 41.667 0.00 0.00 0.00 2.29
3293 6626 5.423610 TCTCCTCCCTTCTTCTTTCTGTATG 59.576 44.000 0.00 0.00 0.00 2.39
3294 6627 5.094387 TCCTCCCTTCTTCTTTCTGTATGT 58.906 41.667 0.00 0.00 0.00 2.29
3295 6628 6.261435 TCCTCCCTTCTTCTTTCTGTATGTA 58.739 40.000 0.00 0.00 0.00 2.29
3296 6629 6.729100 TCCTCCCTTCTTCTTTCTGTATGTAA 59.271 38.462 0.00 0.00 0.00 2.41
3297 6630 7.403231 TCCTCCCTTCTTCTTTCTGTATGTAAT 59.597 37.037 0.00 0.00 0.00 1.89
3299 6632 7.265673 TCCCTTCTTCTTTCTGTATGTAATCG 58.734 38.462 0.00 0.00 0.00 3.34
3300 6633 7.042335 CCCTTCTTCTTTCTGTATGTAATCGT 58.958 38.462 0.00 0.00 0.00 3.73
3301 6634 7.010552 CCCTTCTTCTTTCTGTATGTAATCGTG 59.989 40.741 0.00 0.00 0.00 4.35
3302 6635 6.887376 TCTTCTTTCTGTATGTAATCGTGC 57.113 37.500 0.00 0.00 0.00 5.34
3303 6636 5.515270 TCTTCTTTCTGTATGTAATCGTGCG 59.485 40.000 0.00 0.00 0.00 5.34
3317 6650 0.174845 CGTGCGGGGAGTTCTTGATA 59.825 55.000 0.00 0.00 0.00 2.15
3333 6666 5.359756 TCTTGATAAGATTCGTGGTGATGG 58.640 41.667 0.00 0.00 31.20 3.51
3335 6668 2.325583 TAAGATTCGTGGTGATGGGC 57.674 50.000 0.00 0.00 0.00 5.36
3351 6684 1.450134 GGCGAGATGTCCATGCACA 60.450 57.895 0.00 0.00 0.00 4.57
3357 6690 4.060205 CGAGATGTCCATGCACAATGATA 58.940 43.478 0.00 0.00 38.72 2.15
3362 6696 3.138839 TGTCCATGCACAATGATAGGGAT 59.861 43.478 0.00 0.00 38.72 3.85
3366 6700 4.506095 CCATGCACAATGATAGGGATGAGA 60.506 45.833 0.00 0.00 38.72 3.27
3376 6710 6.430962 TGATAGGGATGAGATTGGAAGAAG 57.569 41.667 0.00 0.00 0.00 2.85
3377 6711 6.146047 TGATAGGGATGAGATTGGAAGAAGA 58.854 40.000 0.00 0.00 0.00 2.87
3379 6713 5.109500 AGGGATGAGATTGGAAGAAGAAC 57.891 43.478 0.00 0.00 0.00 3.01
3382 6716 5.711976 GGGATGAGATTGGAAGAAGAACAAA 59.288 40.000 0.00 0.00 0.00 2.83
3383 6717 6.209391 GGGATGAGATTGGAAGAAGAACAAAA 59.791 38.462 0.00 0.00 0.00 2.44
3384 6718 7.311408 GGATGAGATTGGAAGAAGAACAAAAG 58.689 38.462 0.00 0.00 0.00 2.27
3385 6719 6.639632 TGAGATTGGAAGAAGAACAAAAGG 57.360 37.500 0.00 0.00 0.00 3.11
3386 6720 6.364701 TGAGATTGGAAGAAGAACAAAAGGA 58.635 36.000 0.00 0.00 0.00 3.36
3387 6721 7.006509 TGAGATTGGAAGAAGAACAAAAGGAT 58.993 34.615 0.00 0.00 0.00 3.24
3388 6722 7.040201 TGAGATTGGAAGAAGAACAAAAGGATG 60.040 37.037 0.00 0.00 0.00 3.51
3389 6723 6.779539 AGATTGGAAGAAGAACAAAAGGATGT 59.220 34.615 0.00 0.00 34.24 3.06
3391 6725 6.877611 TGGAAGAAGAACAAAAGGATGTAC 57.122 37.500 0.00 0.00 32.02 2.90
3392 6726 5.468746 TGGAAGAAGAACAAAAGGATGTACG 59.531 40.000 0.00 0.00 32.02 3.67
3394 6728 6.347483 GGAAGAAGAACAAAAGGATGTACGAC 60.347 42.308 0.00 0.00 32.02 4.34
3433 6768 0.549950 CATGGGGATTCTGTGAGCCT 59.450 55.000 0.00 0.00 0.00 4.58
3479 6814 4.139786 TCATTCTTTCAGCAAGAGCAACT 58.860 39.130 0.00 0.00 42.76 3.16
3503 6838 3.189287 GGCGCCCTGTAAATATCTCATTG 59.811 47.826 18.11 0.00 0.00 2.82
3616 6952 1.371337 CGTGACATGGACAGCATGGG 61.371 60.000 0.00 0.00 43.62 4.00
3638 6976 4.158394 GGGATGCTTTGAACTTGCTATGAA 59.842 41.667 0.00 0.00 0.00 2.57
3669 7007 4.278678 GAAATGATTCCACCGTGATGTC 57.721 45.455 0.00 0.00 0.00 3.06
3673 7011 0.391130 ATTCCACCGTGATGTCGTGG 60.391 55.000 0.00 0.00 35.25 4.94
3722 7061 2.556287 GTGCCGCTGAAAGGAACG 59.444 61.111 0.00 0.00 0.00 3.95
3832 7171 2.405025 GGTCAAAGAAATTTCGCAAGCG 59.595 45.455 12.42 8.36 41.35 4.68
3879 7218 3.010250 TCAGAGGCCACTAGACTTGTAGA 59.990 47.826 5.01 0.00 0.00 2.59
3880 7219 3.380004 CAGAGGCCACTAGACTTGTAGAG 59.620 52.174 5.01 0.00 0.00 2.43
3881 7220 3.010808 AGAGGCCACTAGACTTGTAGAGT 59.989 47.826 5.01 0.00 42.70 3.24
3890 7235 7.329499 CACTAGACTTGTAGAGTACTGGACTA 58.671 42.308 0.00 0.00 39.06 2.59
3895 7240 7.399765 AGACTTGTAGAGTACTGGACTAGTAGA 59.600 40.741 15.94 0.00 42.37 2.59
3899 7244 7.555087 TGTAGAGTACTGGACTAGTAGAAGAC 58.445 42.308 0.00 0.00 42.37 3.01
3900 7245 5.663456 AGAGTACTGGACTAGTAGAAGACG 58.337 45.833 0.00 0.00 42.37 4.18
3901 7246 5.187576 AGAGTACTGGACTAGTAGAAGACGT 59.812 44.000 0.00 0.00 42.37 4.34
3902 7247 5.177326 AGTACTGGACTAGTAGAAGACGTG 58.823 45.833 3.59 0.00 42.37 4.49
3903 7248 4.018484 ACTGGACTAGTAGAAGACGTGT 57.982 45.455 3.59 0.00 38.04 4.49
3906 7251 5.411053 ACTGGACTAGTAGAAGACGTGTTAC 59.589 44.000 3.59 0.00 38.04 2.50
4015 7370 2.307768 CTCCAACTAGCCGTCTATCCA 58.692 52.381 0.00 0.00 0.00 3.41
4018 7373 3.117776 TCCAACTAGCCGTCTATCCAGTA 60.118 47.826 0.00 0.00 0.00 2.74
4150 7505 0.240945 CAACTTTAACCAGGCGGCTG 59.759 55.000 30.63 30.63 34.57 4.85
4248 7607 3.987547 TGATGATGAGAAGCTTCGATCC 58.012 45.455 26.13 17.57 0.00 3.36
4260 7619 2.109799 CGATCCATCGCTTGGCCT 59.890 61.111 3.32 0.00 46.01 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.890311 TGTGAAACCAATCCATCCACAC 59.110 45.455 0.00 0.00 34.36 3.82
1 2 3.235750 TGTGAAACCAATCCATCCACA 57.764 42.857 0.00 0.00 34.36 4.17
3 4 5.191727 ACTATGTGAAACCAATCCATCCA 57.808 39.130 0.00 0.00 34.36 3.41
4 5 7.639113 TTTACTATGTGAAACCAATCCATCC 57.361 36.000 0.00 0.00 34.36 3.51
5 6 8.739972 ACTTTTACTATGTGAAACCAATCCATC 58.260 33.333 0.00 0.00 34.36 3.51
6 7 8.522830 CACTTTTACTATGTGAAACCAATCCAT 58.477 33.333 0.00 0.00 34.66 3.41
74 75 8.147058 TGCTCTCTAAATAATCTCCAACAGATC 58.853 37.037 0.00 0.00 41.47 2.75
88 89 7.112122 TGCTCTTTTCCATTGCTCTCTAAATA 58.888 34.615 0.00 0.00 0.00 1.40
89 90 5.948162 TGCTCTTTTCCATTGCTCTCTAAAT 59.052 36.000 0.00 0.00 0.00 1.40
90 91 5.316167 TGCTCTTTTCCATTGCTCTCTAAA 58.684 37.500 0.00 0.00 0.00 1.85
95 96 4.586001 TCTTTTGCTCTTTTCCATTGCTCT 59.414 37.500 0.00 0.00 0.00 4.09
97 98 4.343239 AGTCTTTTGCTCTTTTCCATTGCT 59.657 37.500 0.00 0.00 0.00 3.91
106 107 3.073062 TGCCCTAGAGTCTTTTGCTCTTT 59.927 43.478 0.00 0.00 42.63 2.52
114 115 2.158696 GCCATGATGCCCTAGAGTCTTT 60.159 50.000 0.00 0.00 0.00 2.52
115 116 1.419387 GCCATGATGCCCTAGAGTCTT 59.581 52.381 0.00 0.00 0.00 3.01
118 119 0.760567 TCGCCATGATGCCCTAGAGT 60.761 55.000 0.00 0.00 0.00 3.24
123 124 1.059098 TTCTATCGCCATGATGCCCT 58.941 50.000 0.00 0.00 37.99 5.19
124 125 1.160137 GTTCTATCGCCATGATGCCC 58.840 55.000 0.00 0.00 37.99 5.36
125 126 0.792640 CGTTCTATCGCCATGATGCC 59.207 55.000 0.00 0.00 37.99 4.40
145 146 0.738975 TCCTCACATTCTACGCGAGG 59.261 55.000 15.93 5.60 43.88 4.63
146 147 2.389059 CATCCTCACATTCTACGCGAG 58.611 52.381 15.93 6.12 0.00 5.03
147 148 1.067060 CCATCCTCACATTCTACGCGA 59.933 52.381 15.93 0.00 0.00 5.87
148 149 1.491670 CCATCCTCACATTCTACGCG 58.508 55.000 3.53 3.53 0.00 6.01
149 150 1.221414 GCCATCCTCACATTCTACGC 58.779 55.000 0.00 0.00 0.00 4.42
150 151 1.067060 TCGCCATCCTCACATTCTACG 59.933 52.381 0.00 0.00 0.00 3.51
151 152 2.866762 GTTCGCCATCCTCACATTCTAC 59.133 50.000 0.00 0.00 0.00 2.59
152 153 2.499693 TGTTCGCCATCCTCACATTCTA 59.500 45.455 0.00 0.00 0.00 2.10
153 154 1.278985 TGTTCGCCATCCTCACATTCT 59.721 47.619 0.00 0.00 0.00 2.40
154 155 1.737838 TGTTCGCCATCCTCACATTC 58.262 50.000 0.00 0.00 0.00 2.67
155 156 2.086869 CTTGTTCGCCATCCTCACATT 58.913 47.619 0.00 0.00 0.00 2.71
156 157 1.278985 TCTTGTTCGCCATCCTCACAT 59.721 47.619 0.00 0.00 0.00 3.21
157 158 0.684535 TCTTGTTCGCCATCCTCACA 59.315 50.000 0.00 0.00 0.00 3.58
158 159 1.808411 TTCTTGTTCGCCATCCTCAC 58.192 50.000 0.00 0.00 0.00 3.51
159 160 2.559698 TTTCTTGTTCGCCATCCTCA 57.440 45.000 0.00 0.00 0.00 3.86
160 161 4.440839 AAATTTCTTGTTCGCCATCCTC 57.559 40.909 0.00 0.00 0.00 3.71
161 162 4.871933 AAAATTTCTTGTTCGCCATCCT 57.128 36.364 0.00 0.00 0.00 3.24
162 163 4.749598 ACAAAAATTTCTTGTTCGCCATCC 59.250 37.500 10.86 0.00 33.16 3.51
163 164 5.905480 ACAAAAATTTCTTGTTCGCCATC 57.095 34.783 10.86 0.00 33.16 3.51
164 165 7.961325 ATAACAAAAATTTCTTGTTCGCCAT 57.039 28.000 22.94 14.39 43.98 4.40
165 166 7.778470 AATAACAAAAATTTCTTGTTCGCCA 57.222 28.000 22.94 13.34 43.98 5.69
225 229 5.470098 GGAGCTCTGTTTGTTTCATTACTGA 59.530 40.000 14.64 0.00 0.00 3.41
227 231 4.762251 GGGAGCTCTGTTTGTTTCATTACT 59.238 41.667 14.64 0.00 0.00 2.24
229 233 3.751175 CGGGAGCTCTGTTTGTTTCATTA 59.249 43.478 14.64 0.00 0.00 1.90
301 307 4.641868 ACAGGAAAGGGGATTATAGACCA 58.358 43.478 0.00 0.00 0.00 4.02
308 314 7.699709 TGTGAATATACAGGAAAGGGGATTA 57.300 36.000 0.00 0.00 0.00 1.75
310 316 6.160459 AGTTGTGAATATACAGGAAAGGGGAT 59.840 38.462 0.00 0.00 0.00 3.85
311 317 5.491078 AGTTGTGAATATACAGGAAAGGGGA 59.509 40.000 0.00 0.00 0.00 4.81
331 337 4.006989 TCCCGTTCCATTGTATTCAGTTG 58.993 43.478 0.00 0.00 0.00 3.16
342 348 2.355209 GCTCTTTCTCTCCCGTTCCATT 60.355 50.000 0.00 0.00 0.00 3.16
346 352 0.526662 TCGCTCTTTCTCTCCCGTTC 59.473 55.000 0.00 0.00 0.00 3.95
387 393 3.621794 GCGGATGCATACATTGAGTTTC 58.378 45.455 10.18 0.00 42.15 2.78
420 426 4.031636 TGGTGATGATGATGTTGAACCA 57.968 40.909 0.00 0.00 34.18 3.67
423 429 5.503002 ACTGATGGTGATGATGATGTTGAA 58.497 37.500 0.00 0.00 0.00 2.69
426 432 6.319658 GGTTTACTGATGGTGATGATGATGTT 59.680 38.462 0.00 0.00 0.00 2.71
428 434 5.824097 TGGTTTACTGATGGTGATGATGATG 59.176 40.000 0.00 0.00 0.00 3.07
429 435 5.824624 GTGGTTTACTGATGGTGATGATGAT 59.175 40.000 0.00 0.00 0.00 2.45
430 436 5.045651 AGTGGTTTACTGATGGTGATGATGA 60.046 40.000 0.00 0.00 38.49 2.92
431 437 5.188434 AGTGGTTTACTGATGGTGATGATG 58.812 41.667 0.00 0.00 38.49 3.07
467 474 2.005451 GCCATGCTATGTGATCCGATC 58.995 52.381 1.01 1.01 0.00 3.69
523 530 0.322906 TGGGCGGCAAATGATACACA 60.323 50.000 12.47 0.00 0.00 3.72
526 533 0.248458 CGTTGGGCGGCAAATGATAC 60.248 55.000 12.88 0.00 36.85 2.24
527 534 0.678366 ACGTTGGGCGGCAAATGATA 60.678 50.000 23.96 0.00 46.52 2.15
568 575 2.959465 AACCCCTTTCTCTGTTCCTG 57.041 50.000 0.00 0.00 0.00 3.86
571 578 3.121738 TCGAAACCCCTTTCTCTGTTC 57.878 47.619 0.00 0.00 34.62 3.18
574 581 3.189287 CACATTCGAAACCCCTTTCTCTG 59.811 47.826 0.00 0.00 34.62 3.35
578 585 2.882137 TGTCACATTCGAAACCCCTTTC 59.118 45.455 0.00 0.00 33.58 2.62
590 597 1.467734 CCTGCAAGAGCTGTCACATTC 59.532 52.381 0.00 0.00 42.74 2.67
591 598 1.531423 CCTGCAAGAGCTGTCACATT 58.469 50.000 0.00 0.00 42.74 2.71
596 605 2.749441 GGCCCTGCAAGAGCTGTC 60.749 66.667 0.00 0.00 42.74 3.51
598 607 2.282674 TTGGCCCTGCAAGAGCTG 60.283 61.111 0.00 0.00 42.74 4.24
617 626 3.889815 TCTAGGTCTGCCAAATCCAATG 58.110 45.455 0.00 0.00 37.19 2.82
618 627 4.530875 CTTCTAGGTCTGCCAAATCCAAT 58.469 43.478 0.00 0.00 37.19 3.16
619 628 3.308402 CCTTCTAGGTCTGCCAAATCCAA 60.308 47.826 0.00 0.00 37.19 3.53
620 629 2.239654 CCTTCTAGGTCTGCCAAATCCA 59.760 50.000 0.00 0.00 37.19 3.41
621 630 2.505819 TCCTTCTAGGTCTGCCAAATCC 59.494 50.000 0.00 0.00 36.53 3.01
626 635 0.116342 TGGTCCTTCTAGGTCTGCCA 59.884 55.000 0.00 0.00 36.53 4.92
632 641 2.005370 TCGTGTTGGTCCTTCTAGGT 57.995 50.000 0.00 0.00 36.53 3.08
634 643 3.724374 TGTTTCGTGTTGGTCCTTCTAG 58.276 45.455 0.00 0.00 0.00 2.43
637 646 3.550030 CCAATGTTTCGTGTTGGTCCTTC 60.550 47.826 0.00 0.00 38.03 3.46
649 658 0.243636 GGGTTCCTGCCAATGTTTCG 59.756 55.000 0.00 0.00 0.00 3.46
774 784 2.689983 AGGGCATATTTGTACAGCTTGC 59.310 45.455 11.49 11.49 0.00 4.01
921 938 2.773993 ATCGTATGGGGTGTTCGTTT 57.226 45.000 0.00 0.00 0.00 3.60
952 970 1.381327 CCCGGTCTTCCTCTGCCTA 60.381 63.158 0.00 0.00 0.00 3.93
980 998 6.261826 CACCATGTGTTCTTCTTCTTCTTCTT 59.738 38.462 0.00 0.00 0.00 2.52
981 999 5.762218 CACCATGTGTTCTTCTTCTTCTTCT 59.238 40.000 0.00 0.00 0.00 2.85
982 1000 5.049129 CCACCATGTGTTCTTCTTCTTCTTC 60.049 44.000 0.00 0.00 0.00 2.87
983 1001 4.823989 CCACCATGTGTTCTTCTTCTTCTT 59.176 41.667 0.00 0.00 0.00 2.52
984 1002 4.103153 TCCACCATGTGTTCTTCTTCTTCT 59.897 41.667 0.00 0.00 0.00 2.85
985 1003 4.389374 TCCACCATGTGTTCTTCTTCTTC 58.611 43.478 0.00 0.00 0.00 2.87
986 1004 4.437682 TCCACCATGTGTTCTTCTTCTT 57.562 40.909 0.00 0.00 0.00 2.52
987 1005 4.437682 TTCCACCATGTGTTCTTCTTCT 57.562 40.909 0.00 0.00 0.00 2.85
988 1006 4.142816 CGATTCCACCATGTGTTCTTCTTC 60.143 45.833 0.00 0.00 0.00 2.87
989 1007 3.753272 CGATTCCACCATGTGTTCTTCTT 59.247 43.478 0.00 0.00 0.00 2.52
990 1008 3.338249 CGATTCCACCATGTGTTCTTCT 58.662 45.455 0.00 0.00 0.00 2.85
991 1009 2.159517 GCGATTCCACCATGTGTTCTTC 60.160 50.000 0.00 0.00 0.00 2.87
992 1010 1.812571 GCGATTCCACCATGTGTTCTT 59.187 47.619 0.00 0.00 0.00 2.52
993 1011 1.453155 GCGATTCCACCATGTGTTCT 58.547 50.000 0.00 0.00 0.00 3.01
994 1012 0.451783 GGCGATTCCACCATGTGTTC 59.548 55.000 0.00 0.00 34.01 3.18
995 1013 1.305219 CGGCGATTCCACCATGTGTT 61.305 55.000 0.00 0.00 34.01 3.32
996 1014 1.745115 CGGCGATTCCACCATGTGT 60.745 57.895 0.00 0.00 34.01 3.72
997 1015 0.461163 TACGGCGATTCCACCATGTG 60.461 55.000 16.62 0.00 34.01 3.21
998 1016 0.461339 GTACGGCGATTCCACCATGT 60.461 55.000 16.62 0.00 34.01 3.21
1080 1098 3.846360 AGCAAGAACTGGATGTACGTAC 58.154 45.455 18.90 18.90 0.00 3.67
1081 1099 4.530710 AAGCAAGAACTGGATGTACGTA 57.469 40.909 0.00 0.00 0.00 3.57
1082 1100 3.402628 AAGCAAGAACTGGATGTACGT 57.597 42.857 0.00 0.00 0.00 3.57
1083 1101 3.745975 TCAAAGCAAGAACTGGATGTACG 59.254 43.478 0.00 0.00 0.00 3.67
1086 1104 7.472334 AATAATCAAAGCAAGAACTGGATGT 57.528 32.000 0.00 0.00 0.00 3.06
1105 1123 7.616935 CACTGCCATATTATCTCCCCAAATAAT 59.383 37.037 0.00 0.00 33.69 1.28
1107 1125 6.484288 CACTGCCATATTATCTCCCCAAATA 58.516 40.000 0.00 0.00 0.00 1.40
1108 1126 5.327732 CACTGCCATATTATCTCCCCAAAT 58.672 41.667 0.00 0.00 0.00 2.32
1109 1127 4.728772 CACTGCCATATTATCTCCCCAAA 58.271 43.478 0.00 0.00 0.00 3.28
1110 1128 3.498481 GCACTGCCATATTATCTCCCCAA 60.498 47.826 0.00 0.00 0.00 4.12
1111 1129 2.040278 GCACTGCCATATTATCTCCCCA 59.960 50.000 0.00 0.00 0.00 4.96
1112 1130 2.307098 AGCACTGCCATATTATCTCCCC 59.693 50.000 0.00 0.00 0.00 4.81
1113 1131 3.262915 AGAGCACTGCCATATTATCTCCC 59.737 47.826 0.00 0.00 0.00 4.30
1114 1132 4.550076 AGAGCACTGCCATATTATCTCC 57.450 45.455 0.00 0.00 0.00 3.71
1116 1134 5.549347 CAGAAGAGCACTGCCATATTATCT 58.451 41.667 0.00 0.00 0.00 1.98
1117 1135 5.859521 CAGAAGAGCACTGCCATATTATC 57.140 43.478 0.00 0.00 0.00 1.75
1127 1145 1.447489 CCTCGGCAGAAGAGCACTG 60.447 63.158 0.00 0.00 38.27 3.66
1128 1146 1.188219 TTCCTCGGCAGAAGAGCACT 61.188 55.000 0.00 0.00 34.56 4.40
1131 1149 1.153469 CCTTCCTCGGCAGAAGAGC 60.153 63.158 9.73 0.00 42.80 4.09
1132 1150 0.108424 CACCTTCCTCGGCAGAAGAG 60.108 60.000 9.73 0.00 42.80 2.85
1138 1156 0.690192 TTCAATCACCTTCCTCGGCA 59.310 50.000 0.00 0.00 0.00 5.69
1140 1158 2.770164 ACTTCAATCACCTTCCTCGG 57.230 50.000 0.00 0.00 0.00 4.63
1157 1175 0.534873 GCACACACAACCCCAAAACT 59.465 50.000 0.00 0.00 0.00 2.66
1158 1176 0.534873 AGCACACACAACCCCAAAAC 59.465 50.000 0.00 0.00 0.00 2.43
1160 1178 0.613292 ACAGCACACACAACCCCAAA 60.613 50.000 0.00 0.00 0.00 3.28
1164 1182 1.226945 GCAACAGCACACACAACCC 60.227 57.895 0.00 0.00 0.00 4.11
1165 1183 1.586042 CGCAACAGCACACACAACC 60.586 57.895 0.00 0.00 0.00 3.77
1167 1185 2.101965 GCGCAACAGCACACACAA 59.898 55.556 0.30 0.00 37.05 3.33
1168 1186 3.886694 GGCGCAACAGCACACACA 61.887 61.111 10.83 0.00 39.27 3.72
1169 1187 3.812166 CTGGCGCAACAGCACACAC 62.812 63.158 10.83 0.00 39.27 3.82
1170 1188 3.585020 CTGGCGCAACAGCACACA 61.585 61.111 10.83 0.00 39.27 3.72
1176 1194 2.693762 CCATGTCCTGGCGCAACAG 61.694 63.158 10.83 8.37 38.47 3.16
1323 1349 3.331150 CAACATCACGCCCAACTAGTAA 58.669 45.455 0.00 0.00 0.00 2.24
1363 1392 5.389935 CCAAAAAGTTCGCTTAGCTAGTCAG 60.390 44.000 1.76 0.00 36.20 3.51
1366 1395 4.386711 ACCAAAAAGTTCGCTTAGCTAGT 58.613 39.130 1.76 0.00 36.20 2.57
1392 1421 0.029300 TCTTCACAGCTGCAAAACGC 59.971 50.000 15.27 0.00 42.89 4.84
1536 1565 0.175073 CTTGTACCCTGTAGACGGGC 59.825 60.000 1.60 0.00 46.04 6.13
1559 1588 6.839134 TCTCAGAACATAGCTAGGATTTGGTA 59.161 38.462 13.23 0.00 0.00 3.25
1560 1589 5.663106 TCTCAGAACATAGCTAGGATTTGGT 59.337 40.000 13.23 0.00 0.00 3.67
1564 1593 7.795534 ATCATCTCAGAACATAGCTAGGATT 57.204 36.000 13.23 2.72 0.00 3.01
1574 1603 4.142071 ACAGCACGTATCATCTCAGAACAT 60.142 41.667 0.00 0.00 0.00 2.71
1575 1604 3.193479 ACAGCACGTATCATCTCAGAACA 59.807 43.478 0.00 0.00 0.00 3.18
1576 1605 3.775202 ACAGCACGTATCATCTCAGAAC 58.225 45.455 0.00 0.00 0.00 3.01
1577 1606 4.456280 AACAGCACGTATCATCTCAGAA 57.544 40.909 0.00 0.00 0.00 3.02
1578 1607 4.176271 CAAACAGCACGTATCATCTCAGA 58.824 43.478 0.00 0.00 0.00 3.27
1579 1608 3.242220 GCAAACAGCACGTATCATCTCAG 60.242 47.826 0.00 0.00 44.79 3.35
1602 1631 2.497092 CGTCAACGCGATCTCACCG 61.497 63.158 15.93 1.15 0.00 4.94
1619 1648 1.810030 GACGGCCAAGCTAGTTCCG 60.810 63.158 2.24 12.98 45.04 4.30
1620 1649 0.107654 ATGACGGCCAAGCTAGTTCC 60.108 55.000 2.24 0.00 0.00 3.62
1621 1650 1.739067 AATGACGGCCAAGCTAGTTC 58.261 50.000 2.24 0.00 0.00 3.01
1625 1654 3.202906 GACATAAATGACGGCCAAGCTA 58.797 45.455 2.24 0.00 0.00 3.32
1641 1670 3.799137 GAAAACCAGTTTCGCGACATA 57.201 42.857 9.15 0.00 36.52 2.29
1656 1685 1.896660 TCCAGCACGCCCTGAAAAC 60.897 57.895 4.63 0.00 34.77 2.43
1980 4170 5.598830 TCAATCTCCACACCTAATCTCTACC 59.401 44.000 0.00 0.00 0.00 3.18
2062 4599 1.258445 CCCGACCCAAGAGCTGTACT 61.258 60.000 0.00 0.00 0.00 2.73
2063 4600 1.218316 CCCGACCCAAGAGCTGTAC 59.782 63.158 0.00 0.00 0.00 2.90
2107 4644 6.604795 CCTCATTGGACCTAATTGACTCAAAT 59.395 38.462 0.00 0.00 38.35 2.32
2130 4667 1.123077 TTGCACCGATCTGATAGCCT 58.877 50.000 0.00 0.00 0.00 4.58
2144 4681 4.142381 GGTTCCATTGACCTATCTTTGCAC 60.142 45.833 0.00 0.00 34.27 4.57
2170 4708 4.508124 CACGAATTCCCATGCTACTTAGTC 59.492 45.833 0.00 0.00 0.00 2.59
2314 4854 6.347888 CCTGATGAATTGCACAAAATTCCAAC 60.348 38.462 6.42 0.46 43.13 3.77
2318 4858 6.033831 CGTACCTGATGAATTGCACAAAATTC 59.966 38.462 2.48 2.48 43.76 2.17
2343 5657 1.493311 CAAGTGCGCCGTCTTTCTC 59.507 57.895 4.18 0.00 0.00 2.87
2445 5759 2.360475 GCCTTGAGGTCCCTGTGC 60.360 66.667 0.00 0.00 37.57 4.57
2550 5864 1.079681 GACGTGGCCGGTGTTGATA 60.080 57.895 1.90 0.00 38.78 2.15
2596 5910 8.798859 AAGAACATATATTGGATATGGAGTGC 57.201 34.615 8.89 0.00 36.56 4.40
2600 5914 8.049117 GCCTGAAGAACATATATTGGATATGGA 58.951 37.037 8.89 0.00 36.56 3.41
2601 5915 7.284034 GGCCTGAAGAACATATATTGGATATGG 59.716 40.741 0.00 0.00 36.56 2.74
2602 5916 7.011763 CGGCCTGAAGAACATATATTGGATATG 59.988 40.741 0.00 3.54 37.84 1.78
2603 5917 7.050377 CGGCCTGAAGAACATATATTGGATAT 58.950 38.462 0.00 0.00 0.00 1.63
2604 5918 6.013725 ACGGCCTGAAGAACATATATTGGATA 60.014 38.462 0.00 0.00 0.00 2.59
2605 5919 5.221925 ACGGCCTGAAGAACATATATTGGAT 60.222 40.000 0.00 0.00 0.00 3.41
2607 5921 4.214119 CACGGCCTGAAGAACATATATTGG 59.786 45.833 0.00 0.00 0.00 3.16
2608 5922 4.816385 ACACGGCCTGAAGAACATATATTG 59.184 41.667 0.00 0.00 0.00 1.90
2609 5923 4.816385 CACACGGCCTGAAGAACATATATT 59.184 41.667 0.00 0.00 0.00 1.28
2610 5924 4.100963 TCACACGGCCTGAAGAACATATAT 59.899 41.667 0.00 0.00 0.00 0.86
2611 5925 3.449377 TCACACGGCCTGAAGAACATATA 59.551 43.478 0.00 0.00 0.00 0.86
2612 5926 2.236146 TCACACGGCCTGAAGAACATAT 59.764 45.455 0.00 0.00 0.00 1.78
2638 5952 3.307059 GGTCAGCACCTACAAAGATCACT 60.307 47.826 0.00 0.00 40.00 3.41
2639 5953 3.003480 GGTCAGCACCTACAAAGATCAC 58.997 50.000 0.00 0.00 40.00 3.06
2673 5987 2.687370 ACCCGCTGCATTTTCAATTTC 58.313 42.857 0.00 0.00 0.00 2.17
3265 6598 2.543037 AGAAGAAGGGAGGAGAGGTC 57.457 55.000 0.00 0.00 0.00 3.85
3266 6599 3.178046 GAAAGAAGAAGGGAGGAGAGGT 58.822 50.000 0.00 0.00 0.00 3.85
3267 6600 3.197549 CAGAAAGAAGAAGGGAGGAGAGG 59.802 52.174 0.00 0.00 0.00 3.69
3268 6601 3.837731 ACAGAAAGAAGAAGGGAGGAGAG 59.162 47.826 0.00 0.00 0.00 3.20
3269 6602 3.863086 ACAGAAAGAAGAAGGGAGGAGA 58.137 45.455 0.00 0.00 0.00 3.71
3287 6620 1.067974 TCCCCGCACGATTACATACAG 59.932 52.381 0.00 0.00 0.00 2.74
3288 6621 1.067974 CTCCCCGCACGATTACATACA 59.932 52.381 0.00 0.00 0.00 2.29
3289 6622 1.068127 ACTCCCCGCACGATTACATAC 59.932 52.381 0.00 0.00 0.00 2.39
3290 6623 1.405872 ACTCCCCGCACGATTACATA 58.594 50.000 0.00 0.00 0.00 2.29
3291 6624 0.539986 AACTCCCCGCACGATTACAT 59.460 50.000 0.00 0.00 0.00 2.29
3292 6625 0.108520 GAACTCCCCGCACGATTACA 60.109 55.000 0.00 0.00 0.00 2.41
3293 6626 0.175073 AGAACTCCCCGCACGATTAC 59.825 55.000 0.00 0.00 0.00 1.89
3294 6627 0.899720 AAGAACTCCCCGCACGATTA 59.100 50.000 0.00 0.00 0.00 1.75
3295 6628 0.673644 CAAGAACTCCCCGCACGATT 60.674 55.000 0.00 0.00 0.00 3.34
3296 6629 1.079127 CAAGAACTCCCCGCACGAT 60.079 57.895 0.00 0.00 0.00 3.73
3297 6630 1.541310 ATCAAGAACTCCCCGCACGA 61.541 55.000 0.00 0.00 0.00 4.35
3299 6632 2.093658 TCTTATCAAGAACTCCCCGCAC 60.094 50.000 0.00 0.00 33.83 5.34
3300 6633 2.184533 TCTTATCAAGAACTCCCCGCA 58.815 47.619 0.00 0.00 33.83 5.69
3301 6634 2.981859 TCTTATCAAGAACTCCCCGC 57.018 50.000 0.00 0.00 33.83 6.13
3302 6635 4.051922 CGAATCTTATCAAGAACTCCCCG 58.948 47.826 0.00 0.00 41.63 5.73
3303 6636 4.811557 CACGAATCTTATCAAGAACTCCCC 59.188 45.833 0.00 0.00 41.63 4.81
3317 6650 0.744414 CGCCCATCACCACGAATCTT 60.744 55.000 0.00 0.00 0.00 2.40
3333 6666 1.026182 TTGTGCATGGACATCTCGCC 61.026 55.000 21.42 0.00 0.00 5.54
3335 6668 2.282407 TCATTGTGCATGGACATCTCG 58.718 47.619 21.42 9.76 33.07 4.04
3347 6680 4.458295 CCAATCTCATCCCTATCATTGTGC 59.542 45.833 0.00 0.00 0.00 4.57
3351 6684 7.294245 TCTTCTTCCAATCTCATCCCTATCATT 59.706 37.037 0.00 0.00 0.00 2.57
3357 6690 4.537688 TGTTCTTCTTCCAATCTCATCCCT 59.462 41.667 0.00 0.00 0.00 4.20
3362 6696 6.364701 TCCTTTTGTTCTTCTTCCAATCTCA 58.635 36.000 0.00 0.00 0.00 3.27
3366 6700 6.983906 ACATCCTTTTGTTCTTCTTCCAAT 57.016 33.333 0.00 0.00 0.00 3.16
3376 6710 3.496884 TGCTGTCGTACATCCTTTTGTTC 59.503 43.478 0.00 0.00 0.00 3.18
3377 6711 3.472652 TGCTGTCGTACATCCTTTTGTT 58.527 40.909 0.00 0.00 0.00 2.83
3379 6713 3.242091 CGATGCTGTCGTACATCCTTTTG 60.242 47.826 4.26 0.00 45.19 2.44
3382 6716 2.209838 CGATGCTGTCGTACATCCTT 57.790 50.000 4.26 0.00 45.19 3.36
3383 6717 3.946950 CGATGCTGTCGTACATCCT 57.053 52.632 4.26 0.00 45.19 3.24
3392 6726 3.181506 GGATTTCTTTGGACGATGCTGTC 60.182 47.826 0.00 0.00 38.17 3.51
3394 6728 2.749076 TGGATTTCTTTGGACGATGCTG 59.251 45.455 0.00 0.00 0.00 4.41
3456 6791 4.215827 AGTTGCTCTTGCTGAAAGAATGAG 59.784 41.667 0.00 0.00 44.56 2.90
3457 6792 4.023450 CAGTTGCTCTTGCTGAAAGAATGA 60.023 41.667 0.00 0.00 44.38 2.57
3479 6814 1.071699 GAGATATTTACAGGGCGCCCA 59.928 52.381 45.13 26.77 38.92 5.36
3503 6838 1.202076 GCAAGATGCTACCGAAACAGC 60.202 52.381 0.00 0.00 40.96 4.40
3616 6952 4.970662 TCATAGCAAGTTCAAAGCATCC 57.029 40.909 0.00 0.00 0.00 3.51
3669 7007 6.907212 CCAAAAAGATCGATTTTATCTCCACG 59.093 38.462 0.00 0.00 32.48 4.94
3673 7011 9.937175 CCTTACCAAAAAGATCGATTTTATCTC 57.063 33.333 0.00 0.00 32.48 2.75
3747 7086 0.962855 GCCTCTCTGCTTTTCACCCC 60.963 60.000 0.00 0.00 0.00 4.95
3755 7094 2.578128 CTGCTCGCCTCTCTGCTT 59.422 61.111 0.00 0.00 0.00 3.91
3832 7171 4.166011 GGATGCGCGTGCTTGGAC 62.166 66.667 23.16 8.45 43.34 4.02
3847 7186 1.419012 GTGGCCTCTGATGATGATGGA 59.581 52.381 3.32 0.00 0.00 3.41
3879 7218 5.177326 CACGTCTTCTACTAGTCCAGTACT 58.823 45.833 0.00 0.00 42.62 2.73
3880 7219 4.934602 ACACGTCTTCTACTAGTCCAGTAC 59.065 45.833 0.00 0.00 38.80 2.73
3881 7220 5.157940 ACACGTCTTCTACTAGTCCAGTA 57.842 43.478 0.00 0.00 38.80 2.74
3890 7235 5.122082 GCAGAGTAGTAACACGTCTTCTACT 59.878 44.000 14.70 14.70 42.28 2.57
3895 7240 4.850347 AAGCAGAGTAGTAACACGTCTT 57.150 40.909 0.00 0.00 0.00 3.01
3899 7244 4.049186 ACACAAAGCAGAGTAGTAACACG 58.951 43.478 0.00 0.00 0.00 4.49
3900 7245 5.522460 TCAACACAAAGCAGAGTAGTAACAC 59.478 40.000 0.00 0.00 0.00 3.32
3901 7246 5.666462 TCAACACAAAGCAGAGTAGTAACA 58.334 37.500 0.00 0.00 0.00 2.41
3902 7247 5.333416 GCTCAACACAAAGCAGAGTAGTAAC 60.333 44.000 0.00 0.00 38.42 2.50
3903 7248 4.750098 GCTCAACACAAAGCAGAGTAGTAA 59.250 41.667 0.00 0.00 38.42 2.24
3906 7251 3.397482 AGCTCAACACAAAGCAGAGTAG 58.603 45.455 0.00 0.00 41.06 2.57
3993 7348 2.694109 GGATAGACGGCTAGTTGGAGTT 59.306 50.000 3.40 0.00 0.00 3.01
4015 7370 2.974935 TTTGTTCGCGTGCGGGTACT 62.975 55.000 14.89 0.00 40.25 2.73
4018 7373 3.203412 TTTTGTTCGCGTGCGGGT 61.203 55.556 14.89 0.00 40.25 5.28
4131 7486 0.240945 CAGCCGCCTGGTTAAAGTTG 59.759 55.000 0.00 0.00 37.67 3.16


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

AutoCloner maintained by Alex Coulton.