Multiple sequence alignment - TraesCS3D01G134100

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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 TraesCS3D01G134100 chr3D 100.000 8426 0 0 859 9284 93264153 93255728 0.000000e+00 15560
1 TraesCS3D01G134100 chr3D 100.000 246 0 0 1 246 93265011 93264766 1.100000e-123 455
2 TraesCS3D01G134100 chr3D 91.781 146 8 4 7506 7649 93257363 93257506 5.690000e-47 200
3 TraesCS3D01G134100 chr3A 97.093 6674 129 27 859 7501 546610306 546616945 0.000000e+00 11189
4 TraesCS3D01G134100 chr3A 92.427 1677 77 18 7648 9284 546616946 546618612 0.000000e+00 2348
5 TraesCS3D01G134100 chr3A 92.105 228 7 6 18 245 546610018 546610234 2.520000e-80 311
6 TraesCS3D01G134100 chr3B 91.444 5540 317 76 2095 7519 142864135 142869632 0.000000e+00 7459
7 TraesCS3D01G134100 chr3B 93.401 1682 68 28 7636 9284 142869712 142871383 0.000000e+00 2451
8 TraesCS3D01G134100 chr3B 91.525 1239 77 14 859 2088 142862836 142864055 0.000000e+00 1681
9 TraesCS3D01G134100 chr3B 93.919 148 5 4 98 245 142862606 142862749 4.360000e-53 220
10 TraesCS3D01G134100 chrUn 87.809 1780 150 34 4523 6263 22881753 22880002 0.000000e+00 2023
11 TraesCS3D01G134100 chrUn 86.699 1030 97 22 4523 5525 22714605 22715621 0.000000e+00 1107
12 TraesCS3D01G134100 chrUn 89.130 368 38 2 6255 6621 22717135 22717501 3.060000e-124 457
13 TraesCS3D01G134100 chrUn 90.341 352 26 4 5648 5997 22715621 22715966 1.100000e-123 455
14 TraesCS3D01G134100 chrUn 87.371 388 38 6 6258 6642 22879567 22879188 1.430000e-117 435
15 TraesCS3D01G134100 chrUn 91.727 278 20 2 5988 6263 22716432 22716708 5.260000e-102 383
16 TraesCS3D01G134100 chr2B 89.231 1105 93 11 5171 6263 795619470 795618380 0.000000e+00 1358
17 TraesCS3D01G134100 chr2B 85.650 669 63 17 4528 5168 795621370 795620707 0.000000e+00 673
18 TraesCS3D01G134100 chr2B 88.646 229 25 1 6394 6621 795600590 795600362 2.550000e-70 278
19 TraesCS3D01G134100 chr2B 93.233 133 8 1 6258 6389 795617941 795617809 2.650000e-45 195
20 TraesCS3D01G134100 chr2A 92.279 531 36 5 4433 4960 761820930 761821458 0.000000e+00 749
21 TraesCS3D01G134100 chr2A 88.390 646 43 20 4433 5050 761963548 761964189 0.000000e+00 749
22 TraesCS3D01G134100 chr2A 88.217 645 46 6 4433 5050 761750984 761751625 0.000000e+00 743
23 TraesCS3D01G134100 chr2A 90.720 528 45 4 4435 4960 761724681 761725206 0.000000e+00 701
24 TraesCS3D01G134100 chr1D 75.447 615 82 43 4580 5149 366181141 366181731 1.560000e-57 235
25 TraesCS3D01G134100 chr1D 83.810 105 17 0 7274 7378 104569901 104569797 5.930000e-17 100
26 TraesCS3D01G134100 chr1B 74.919 614 86 45 4580 5149 231348956 231348367 1.570000e-52 219
27 TraesCS3D01G134100 chr1B 86.624 157 11 5 7498 7649 515917742 515917893 2.070000e-36 165
28 TraesCS3D01G134100 chr1B 83.810 105 17 0 7274 7378 161993925 161994029 5.930000e-17 100
29 TraesCS3D01G134100 chr7B 87.919 149 10 6 7504 7649 500790711 500790854 1.600000e-37 169
30 TraesCS3D01G134100 chr7B 87.671 146 16 2 7506 7650 526430874 526430730 1.600000e-37 169
31 TraesCS3D01G134100 chr7B 87.582 153 9 3 7506 7653 526430731 526430878 1.600000e-37 169
32 TraesCS3D01G134100 chr4A 84.848 165 16 6 7506 7661 288641653 288641489 3.470000e-34 158
33 TraesCS3D01G134100 chr1A 86.000 150 17 4 7506 7653 589444503 589444356 3.470000e-34 158
34 TraesCS3D01G134100 chr1A 83.810 105 17 0 7274 7378 107479183 107479287 5.930000e-17 100
35 TraesCS3D01G134100 chr5A 86.806 144 13 4 7506 7649 24557837 24557700 1.250000e-33 156
36 TraesCS3D01G134100 chr5A 85.185 162 13 7 7504 7660 438147592 438147747 1.250000e-33 156


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 TraesCS3D01G134100 chr3D 93255728 93265011 9283 True 8007.50 15560 100.000000 1 9284 2 chr3D.!!$R1 9283
1 TraesCS3D01G134100 chr3A 546610018 546618612 8594 False 4616.00 11189 93.875000 18 9284 3 chr3A.!!$F1 9266
2 TraesCS3D01G134100 chr3B 142862606 142871383 8777 False 2952.75 7459 92.572250 98 9284 4 chr3B.!!$F1 9186
3 TraesCS3D01G134100 chrUn 22879188 22881753 2565 True 1229.00 2023 87.590000 4523 6642 2 chrUn.!!$R1 2119
4 TraesCS3D01G134100 chrUn 22714605 22717501 2896 False 600.50 1107 89.474250 4523 6621 4 chrUn.!!$F1 2098
5 TraesCS3D01G134100 chr2B 795617809 795621370 3561 True 742.00 1358 89.371333 4528 6389 3 chr2B.!!$R2 1861
6 TraesCS3D01G134100 chr2A 761820930 761821458 528 False 749.00 749 92.279000 4433 4960 1 chr2A.!!$F3 527
7 TraesCS3D01G134100 chr2A 761963548 761964189 641 False 749.00 749 88.390000 4433 5050 1 chr2A.!!$F4 617
8 TraesCS3D01G134100 chr2A 761750984 761751625 641 False 743.00 743 88.217000 4433 5050 1 chr2A.!!$F2 617
9 TraesCS3D01G134100 chr2A 761724681 761725206 525 False 701.00 701 90.720000 4435 4960 1 chr2A.!!$F1 525
10 TraesCS3D01G134100 chr1D 366181141 366181731 590 False 235.00 235 75.447000 4580 5149 1 chr1D.!!$F1 569
11 TraesCS3D01G134100 chr1B 231348367 231348956 589 True 219.00 219 74.919000 4580 5149 1 chr1B.!!$R1 569

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
181 182 1.349357 GAACTCTGAACTGAAGCCCCT 59.651 52.381 0.00 0.00 0.00 4.79 F
1039 1041 2.122369 CCGCCCCTCTATTCCCCT 60.122 66.667 0.00 0.00 0.00 4.79 F
1266 1278 0.398318 AGAGTGAGAAGGGTTGCCAC 59.602 55.000 0.00 0.00 0.00 5.01 F
1431 1444 1.599419 GCGGCAAGTTAACCAAGTGTG 60.599 52.381 0.88 0.00 0.00 3.82 F
1434 1447 3.303526 CGGCAAGTTAACCAAGTGTGTAC 60.304 47.826 0.88 0.00 0.00 2.90 F
1438 1451 5.163693 GCAAGTTAACCAAGTGTGTACTGTT 60.164 40.000 0.88 0.00 37.19 3.16 F
3286 3401 0.106708 TTTCTGCTCCACTGTCGCTT 59.893 50.000 0.00 0.00 0.00 4.68 F
3302 3417 2.103094 TCGCTTGACTATGGCTATTGCT 59.897 45.455 0.00 0.00 39.59 3.91 F
4140 4275 3.526534 GAAGTTGACCTGGCAGATAGAC 58.473 50.000 17.94 9.30 0.00 2.59 F
5492 6941 4.010667 ACGGTGGCAGTAGAAATGTTTA 57.989 40.909 0.00 0.00 0.00 2.01 F
5906 7364 2.028130 GGCTAGTTCTAGCTGAGCTCA 58.972 52.381 24.67 17.19 42.45 4.26 F
6707 9092 0.603569 AGGCTGGTGTAGTCAAGACG 59.396 55.000 0.00 0.00 36.20 4.18 F
7828 10220 0.988832 ACGGCCAAACTTCCCATAGA 59.011 50.000 2.24 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1066 1076 0.250858 TCACACATCCCCAACAGCAG 60.251 55.000 0.0 0.0 0.00 4.24 R
2418 2526 4.793216 CACAAAACAGCGTAAGAATATGGC 59.207 41.667 0.0 0.0 43.02 4.40 R
3230 3345 1.474478 TCGCTCTAGTTCCTCAAGCAG 59.526 52.381 0.0 0.0 33.21 4.24 R
3238 3353 4.046938 TCACATTCATCGCTCTAGTTCC 57.953 45.455 0.0 0.0 0.00 3.62 R
3286 3401 7.059788 TCCATAAAAAGCAATAGCCATAGTCA 58.940 34.615 0.0 0.0 43.56 3.41 R
3302 3417 9.334947 CAATCTTATGCTCTCTCTCCATAAAAA 57.665 33.333 0.0 0.0 32.78 1.94 R
4827 4998 0.679960 ATGCGTGAAACCTTAGCCCC 60.680 55.000 0.0 0.0 0.00 5.80 R
5243 6692 4.290093 AGGGAGCAACATGACAGATACTA 58.710 43.478 0.0 0.0 0.00 1.82 R
5661 7117 1.597854 CTTGACTCGCTGGCAACCA 60.598 57.895 0.0 0.0 39.08 3.67 R
6416 8800 2.958355 AGTGAAATGTTGACCTGTTGGG 59.042 45.455 0.0 0.0 41.89 4.12 R
7868 10260 1.962807 CAGTTGCTGGGATCAAAACCA 59.037 47.619 0.0 0.0 35.05 3.67 R
7962 10354 0.459489 ACTCGAATGCCTCTCTCAGC 59.541 55.000 0.0 0.0 0.00 4.26 R
9177 11619 1.890894 CACCTACTCCCTGGACACG 59.109 63.158 0.0 0.0 0.00 4.49 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
24 25 3.332761 TTGCACAACAATTCAGTCGAC 57.667 42.857 7.70 7.70 31.73 4.20
25 26 2.560504 TGCACAACAATTCAGTCGACT 58.439 42.857 13.58 13.58 0.00 4.18
26 27 2.942376 TGCACAACAATTCAGTCGACTT 59.058 40.909 17.26 0.00 0.00 3.01
27 28 4.123506 TGCACAACAATTCAGTCGACTTA 58.876 39.130 17.26 5.05 0.00 2.24
28 29 4.754618 TGCACAACAATTCAGTCGACTTAT 59.245 37.500 17.26 9.74 0.00 1.73
29 30 5.929415 TGCACAACAATTCAGTCGACTTATA 59.071 36.000 17.26 4.30 0.00 0.98
181 182 1.349357 GAACTCTGAACTGAAGCCCCT 59.651 52.381 0.00 0.00 0.00 4.79
1039 1041 2.122369 CCGCCCCTCTATTCCCCT 60.122 66.667 0.00 0.00 0.00 4.79
1055 1057 2.669240 CTCACTCCCGAAACCCCC 59.331 66.667 0.00 0.00 0.00 5.40
1079 1089 1.551883 GAAATTGCTGCTGTTGGGGAT 59.448 47.619 0.00 0.00 0.00 3.85
1083 1093 1.604593 GCTGCTGTTGGGGATGTGT 60.605 57.895 0.00 0.00 0.00 3.72
1113 1123 7.174082 CGAGAAATTAGTCAAACCGAGATTTC 58.826 38.462 0.00 0.00 33.23 2.17
1114 1124 7.063544 CGAGAAATTAGTCAAACCGAGATTTCT 59.936 37.037 7.83 7.83 39.37 2.52
1115 1125 8.034058 AGAAATTAGTCAAACCGAGATTTCTG 57.966 34.615 7.41 0.00 37.45 3.02
1116 1126 7.661847 AGAAATTAGTCAAACCGAGATTTCTGT 59.338 33.333 7.41 0.00 37.45 3.41
1117 1127 6.727824 ATTAGTCAAACCGAGATTTCTGTG 57.272 37.500 0.00 0.00 0.00 3.66
1118 1128 4.073293 AGTCAAACCGAGATTTCTGTGT 57.927 40.909 0.00 0.00 0.00 3.72
1119 1129 5.209818 AGTCAAACCGAGATTTCTGTGTA 57.790 39.130 0.00 0.00 0.00 2.90
1120 1130 5.230942 AGTCAAACCGAGATTTCTGTGTAG 58.769 41.667 0.00 0.00 0.00 2.74
1121 1131 5.010719 AGTCAAACCGAGATTTCTGTGTAGA 59.989 40.000 0.00 0.00 0.00 2.59
1122 1132 5.118817 GTCAAACCGAGATTTCTGTGTAGAC 59.881 44.000 0.00 0.00 31.21 2.59
1123 1133 5.010719 TCAAACCGAGATTTCTGTGTAGACT 59.989 40.000 0.00 0.00 31.21 3.24
1124 1134 4.442375 ACCGAGATTTCTGTGTAGACTG 57.558 45.455 0.00 0.00 31.21 3.51
1230 1240 0.901124 GCCCCACATGTTATGGCAAA 59.099 50.000 19.98 0.00 41.76 3.68
1250 1260 7.067372 TGGCAAATTCATACTATGTTCCAAGAG 59.933 37.037 0.00 0.00 0.00 2.85
1254 1266 8.954950 AATTCATACTATGTTCCAAGAGTGAG 57.045 34.615 0.00 0.00 0.00 3.51
1255 1267 7.718334 TTCATACTATGTTCCAAGAGTGAGA 57.282 36.000 0.00 0.00 0.00 3.27
1258 1270 5.413309 ACTATGTTCCAAGAGTGAGAAGG 57.587 43.478 0.00 0.00 0.00 3.46
1259 1271 3.710209 ATGTTCCAAGAGTGAGAAGGG 57.290 47.619 0.00 0.00 0.00 3.95
1260 1272 2.408565 TGTTCCAAGAGTGAGAAGGGT 58.591 47.619 0.00 0.00 0.00 4.34
1261 1273 2.777692 TGTTCCAAGAGTGAGAAGGGTT 59.222 45.455 0.00 0.00 0.00 4.11
1262 1274 3.142174 GTTCCAAGAGTGAGAAGGGTTG 58.858 50.000 0.00 0.00 0.00 3.77
1263 1275 1.072331 TCCAAGAGTGAGAAGGGTTGC 59.928 52.381 0.00 0.00 0.00 4.17
1264 1276 1.528129 CAAGAGTGAGAAGGGTTGCC 58.472 55.000 0.00 0.00 0.00 4.52
1265 1277 1.140312 AAGAGTGAGAAGGGTTGCCA 58.860 50.000 0.00 0.00 0.00 4.92
1266 1278 0.398318 AGAGTGAGAAGGGTTGCCAC 59.602 55.000 0.00 0.00 0.00 5.01
1431 1444 1.599419 GCGGCAAGTTAACCAAGTGTG 60.599 52.381 0.88 0.00 0.00 3.82
1434 1447 3.303526 CGGCAAGTTAACCAAGTGTGTAC 60.304 47.826 0.88 0.00 0.00 2.90
1438 1451 5.163693 GCAAGTTAACCAAGTGTGTACTGTT 60.164 40.000 0.88 0.00 37.19 3.16
1967 1980 7.119116 TCACACAATGCTATTGTTCGTTCTTAT 59.881 33.333 10.56 0.00 0.00 1.73
2136 2223 8.470002 GTTGCTAATTTTTGGATAGGTTGATCT 58.530 33.333 0.00 0.00 0.00 2.75
2245 2337 9.567848 AAATATGGTTGTACACGAAAAATCATC 57.432 29.630 0.00 0.00 0.00 2.92
2395 2503 8.287439 TGGTTATTTACAATGTGTGGATAAGG 57.713 34.615 0.00 0.00 0.00 2.69
2397 2505 8.403236 GGTTATTTACAATGTGTGGATAAGGTC 58.597 37.037 0.00 0.00 0.00 3.85
2418 2526 8.904099 AGGTCCTTATATGTTTATTTTCGAGG 57.096 34.615 0.00 0.00 0.00 4.63
3230 3345 6.315642 GGTACTTTAAGGGTCTGCAGATTTAC 59.684 42.308 21.47 7.25 0.00 2.01
3286 3401 0.106708 TTTCTGCTCCACTGTCGCTT 59.893 50.000 0.00 0.00 0.00 4.68
3302 3417 2.103094 TCGCTTGACTATGGCTATTGCT 59.897 45.455 0.00 0.00 39.59 3.91
3549 3665 5.748630 TGAGCATTTATGTAACTAGCTGTCG 59.251 40.000 0.00 0.00 0.00 4.35
4140 4275 3.526534 GAAGTTGACCTGGCAGATAGAC 58.473 50.000 17.94 9.30 0.00 2.59
4233 4368 8.446489 TGATTATGTTAAATTTGTTCACTGCG 57.554 30.769 0.00 0.00 0.00 5.18
4370 4515 5.703130 GCTAACTGAATTCTCCACTTTGACT 59.297 40.000 7.05 0.00 0.00 3.41
4585 4731 9.733556 ACTGAATGTTACCTTTCACATAATACA 57.266 29.630 0.00 0.00 33.11 2.29
4784 4951 7.899648 AGTTGTATCCTATGCACTAGTACTT 57.100 36.000 0.00 0.00 0.00 2.24
4785 4956 7.942990 AGTTGTATCCTATGCACTAGTACTTC 58.057 38.462 0.00 0.00 0.00 3.01
4827 4998 4.497473 TGGCCGTAGAAGTTGATTTTTG 57.503 40.909 0.00 0.00 0.00 2.44
5120 5327 6.451393 AGCTTCCATACAATTCGTCTCTATC 58.549 40.000 0.00 0.00 0.00 2.08
5201 6650 6.359804 TCTTCATCGATGATCCCTTTGATTT 58.640 36.000 27.75 0.00 36.56 2.17
5202 6651 6.830324 TCTTCATCGATGATCCCTTTGATTTT 59.170 34.615 27.75 0.00 36.56 1.82
5203 6652 7.992608 TCTTCATCGATGATCCCTTTGATTTTA 59.007 33.333 27.75 7.62 36.56 1.52
5204 6653 8.696043 TTCATCGATGATCCCTTTGATTTTAT 57.304 30.769 27.75 0.00 36.56 1.40
5205 6654 8.102800 TCATCGATGATCCCTTTGATTTTATG 57.897 34.615 23.99 0.00 32.41 1.90
5206 6655 7.720957 TCATCGATGATCCCTTTGATTTTATGT 59.279 33.333 23.99 0.00 32.41 2.29
5207 6656 7.880160 TCGATGATCCCTTTGATTTTATGTT 57.120 32.000 0.00 0.00 32.41 2.71
5208 6657 8.292444 TCGATGATCCCTTTGATTTTATGTTT 57.708 30.769 0.00 0.00 32.41 2.83
5492 6941 4.010667 ACGGTGGCAGTAGAAATGTTTA 57.989 40.909 0.00 0.00 0.00 2.01
5661 7117 3.282021 GCACAGTGTTCATGGGATGTAT 58.718 45.455 1.61 0.00 0.00 2.29
5680 7136 2.328099 GGTTGCCAGCGAGTCAAGG 61.328 63.158 0.00 0.00 0.00 3.61
5867 7324 3.621953 GGTCACTTTGAGCTGAGCT 57.378 52.632 6.69 6.69 41.34 4.09
5906 7364 2.028130 GGCTAGTTCTAGCTGAGCTCA 58.972 52.381 24.67 17.19 42.45 4.26
6319 8702 3.509184 CCTCTCTGATGCAGGATTATCGA 59.491 47.826 0.00 0.00 31.51 3.59
6416 8800 3.938109 AGGTCCTTCCTCTTTTCGC 57.062 52.632 0.00 0.00 44.42 4.70
6707 9092 0.603569 AGGCTGGTGTAGTCAAGACG 59.396 55.000 0.00 0.00 36.20 4.18
6955 9347 7.379529 ACAAGCAATTTTATGAAGTTGACGAAG 59.620 33.333 9.28 0.00 35.24 3.79
7414 9806 7.655328 CCAATTGTGATGCTTACCTGTTTTTAA 59.345 33.333 4.43 0.00 0.00 1.52
7495 9887 4.659529 TGTATGTACCCATGTTTTCCCA 57.340 40.909 0.00 0.00 32.29 4.37
7514 9906 5.043762 TCCCACCAAAATTATACTCCCTCT 58.956 41.667 0.00 0.00 0.00 3.69
7519 9911 6.318900 CACCAAAATTATACTCCCTCTGTTCC 59.681 42.308 0.00 0.00 0.00 3.62
7520 9912 6.217693 ACCAAAATTATACTCCCTCTGTTCCT 59.782 38.462 0.00 0.00 0.00 3.36
7523 9915 9.681062 CAAAATTATACTCCCTCTGTTCCTAAA 57.319 33.333 0.00 0.00 0.00 1.85
7533 9925 8.855804 TCCCTCTGTTCCTAAATATAAGTCTT 57.144 34.615 0.00 0.00 0.00 3.01
7534 9926 9.280456 TCCCTCTGTTCCTAAATATAAGTCTTT 57.720 33.333 0.00 0.00 0.00 2.52
7535 9927 9.331282 CCCTCTGTTCCTAAATATAAGTCTTTG 57.669 37.037 0.00 0.00 0.00 2.77
7536 9928 9.892130 CCTCTGTTCCTAAATATAAGTCTTTGT 57.108 33.333 0.00 0.00 0.00 2.83
7552 9944 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
7563 9955 2.036387 TCCACTATGGACCACATACGG 58.964 52.381 0.00 0.00 42.67 4.02
7564 9956 2.036387 CCACTATGGACCACATACGGA 58.964 52.381 0.00 0.00 40.96 4.69
7565 9957 2.632996 CCACTATGGACCACATACGGAT 59.367 50.000 0.00 0.00 40.96 4.18
7566 9958 3.554960 CCACTATGGACCACATACGGATG 60.555 52.174 5.94 5.94 40.96 3.51
7567 9959 6.014967 CCACTATGGACCACATACGGATGT 62.015 50.000 7.68 7.68 43.21 3.06
7568 9960 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
7569 9961 5.047306 CACTATGGACCACATACGGATGTAT 60.047 44.000 14.23 4.48 44.82 2.29
7570 9962 6.152154 CACTATGGACCACATACGGATGTATA 59.848 42.308 14.23 6.48 44.82 1.47
7571 9963 4.859304 TGGACCACATACGGATGTATAC 57.141 45.455 14.23 6.20 44.82 1.47
7572 9964 4.216708 TGGACCACATACGGATGTATACA 58.783 43.478 14.23 9.02 44.82 2.29
7574 9966 5.128991 TGGACCACATACGGATGTATACAAA 59.871 40.000 14.23 0.00 44.82 2.83
7575 9967 6.050432 GGACCACATACGGATGTATACAAAA 58.950 40.000 14.23 0.00 44.82 2.44
7576 9968 6.708949 GGACCACATACGGATGTATACAAAAT 59.291 38.462 14.23 0.00 44.82 1.82
7577 9969 7.307751 GGACCACATACGGATGTATACAAAATG 60.308 40.741 14.23 11.07 44.82 2.32
7578 9970 7.276658 ACCACATACGGATGTATACAAAATGA 58.723 34.615 14.23 0.00 44.82 2.57
7579 9971 7.441157 ACCACATACGGATGTATACAAAATGAG 59.559 37.037 14.23 7.83 44.82 2.90
7581 9973 8.275632 CACATACGGATGTATACAAAATGAGTG 58.724 37.037 14.23 9.77 44.82 3.51
7582 9974 8.201464 ACATACGGATGTATACAAAATGAGTGA 58.799 33.333 12.79 0.00 44.77 3.41
7583 9975 9.208022 CATACGGATGTATACAAAATGAGTGAT 57.792 33.333 10.14 0.00 39.28 3.06
7596 9988 9.208022 ACAAAATGAGTGATATACATCCGTATG 57.792 33.333 0.00 0.00 38.79 2.39
7598 9990 8.763049 AAATGAGTGATATACATCCGTATGTG 57.237 34.615 3.56 0.00 45.99 3.21
7599 9991 6.267496 TGAGTGATATACATCCGTATGTGG 57.733 41.667 3.56 0.00 45.99 4.17
7600 9992 5.773176 TGAGTGATATACATCCGTATGTGGT 59.227 40.000 3.56 0.00 45.99 4.16
7601 9993 6.072119 TGAGTGATATACATCCGTATGTGGTC 60.072 42.308 3.56 0.36 45.99 4.02
7602 9994 5.185249 AGTGATATACATCCGTATGTGGTCC 59.815 44.000 3.56 0.00 45.99 4.46
7603 9995 5.047590 GTGATATACATCCGTATGTGGTCCA 60.048 44.000 3.56 0.00 45.99 4.02
7604 9996 5.719563 TGATATACATCCGTATGTGGTCCAT 59.280 40.000 3.56 0.00 45.99 3.41
7605 9997 6.893005 TGATATACATCCGTATGTGGTCCATA 59.107 38.462 3.56 0.00 45.99 2.74
7606 9998 5.661056 ATACATCCGTATGTGGTCCATAG 57.339 43.478 3.56 0.00 45.99 2.23
7607 9999 3.305720 ACATCCGTATGTGGTCCATAGT 58.694 45.455 0.00 0.00 44.79 2.12
7608 10000 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
7609 10001 2.036387 TCCGTATGTGGTCCATAGTGG 58.964 52.381 0.00 0.00 36.71 4.00
7610 10002 2.036387 CCGTATGTGGTCCATAGTGGA 58.964 52.381 0.00 0.00 45.98 4.02
7624 10016 7.113658 TCCATAGTGGAATCTCTACAAAGAC 57.886 40.000 0.00 0.00 45.00 3.01
7625 10017 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
7626 10018 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
7627 10019 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
7658 10050 3.263369 TGGAGGGAGTAGTTGGTTGTA 57.737 47.619 0.00 0.00 0.00 2.41
7828 10220 0.988832 ACGGCCAAACTTCCCATAGA 59.011 50.000 2.24 0.00 0.00 1.98
7868 10260 7.071824 TCCTTACAATTTCTTTGGTGGGAAATT 59.928 33.333 7.54 7.54 46.47 1.82
7881 10273 3.326297 GTGGGAAATTGGTTTTGATCCCA 59.674 43.478 7.24 7.24 43.15 4.37
7962 10354 6.866248 GGAGCTTATTTTCGGAGATAGAGAAG 59.134 42.308 0.00 0.00 35.04 2.85
8001 10393 1.337071 TCTATAGAAAGGCCGACGCTG 59.663 52.381 0.00 0.00 34.44 5.18
8149 10541 0.385390 GCAAACACTGGACCTTGGTG 59.615 55.000 0.00 9.95 37.05 4.17
8151 10543 0.033601 AAACACTGGACCTTGGTGCA 60.034 50.000 13.17 13.17 34.70 4.57
8297 10689 5.991328 ACGAAATAACCACATGCATCTAG 57.009 39.130 0.00 0.00 0.00 2.43
8302 10694 0.465705 ACCACATGCATCTAGACCGG 59.534 55.000 0.00 0.00 0.00 5.28
8303 10695 0.882042 CCACATGCATCTAGACCGGC 60.882 60.000 0.00 0.00 0.00 6.13
8306 10698 0.665670 CATGCATCTAGACCGGCGAG 60.666 60.000 9.30 0.06 0.00 5.03
8322 10714 3.032017 GCGAGATGCATACTATGGTGT 57.968 47.619 0.00 0.00 45.45 4.16
8324 10716 3.800261 GCGAGATGCATACTATGGTGTGT 60.800 47.826 0.00 0.00 45.45 3.72
8325 10717 3.983988 CGAGATGCATACTATGGTGTGTC 59.016 47.826 0.00 0.00 37.00 3.67
8344 10736 1.529010 CCTCTGGGCACTGCACAAA 60.529 57.895 7.53 0.00 43.23 2.83
8345 10737 0.896940 CCTCTGGGCACTGCACAAAT 60.897 55.000 7.53 0.00 43.23 2.32
8346 10738 0.524862 CTCTGGGCACTGCACAAATC 59.475 55.000 7.53 0.00 43.23 2.17
8347 10739 1.210931 CTGGGCACTGCACAAATCG 59.789 57.895 7.53 0.00 43.23 3.34
8350 10742 2.629656 GGCACTGCACAAATCGCCT 61.630 57.895 2.82 0.00 36.58 5.52
8365 10757 1.135527 TCGCCTAACACCCGAATGTAG 59.864 52.381 0.00 0.00 30.75 2.74
8426 10821 1.572085 GCGTGTGCATTGCTCTGTCT 61.572 55.000 10.49 0.00 42.15 3.41
8430 10830 3.665323 CGTGTGCATTGCTCTGTCTTTAC 60.665 47.826 10.49 0.00 0.00 2.01
8431 10831 3.499918 GTGTGCATTGCTCTGTCTTTACT 59.500 43.478 10.49 0.00 0.00 2.24
8432 10832 3.499537 TGTGCATTGCTCTGTCTTTACTG 59.500 43.478 10.49 0.00 0.00 2.74
8433 10833 3.499918 GTGCATTGCTCTGTCTTTACTGT 59.500 43.478 10.49 0.00 0.00 3.55
8435 10835 5.352569 GTGCATTGCTCTGTCTTTACTGTAT 59.647 40.000 10.49 0.00 0.00 2.29
8436 10836 5.352293 TGCATTGCTCTGTCTTTACTGTATG 59.648 40.000 10.49 0.00 0.00 2.39
8437 10837 5.582269 GCATTGCTCTGTCTTTACTGTATGA 59.418 40.000 0.16 0.00 0.00 2.15
8438 10838 6.238049 GCATTGCTCTGTCTTTACTGTATGAG 60.238 42.308 0.16 0.00 0.00 2.90
8439 10839 6.590234 TTGCTCTGTCTTTACTGTATGAGA 57.410 37.500 0.00 0.00 0.00 3.27
8440 10840 6.590234 TGCTCTGTCTTTACTGTATGAGAA 57.410 37.500 0.00 0.00 0.00 2.87
8449 10849 9.282247 GTCTTTACTGTATGAGAAATGCAAATG 57.718 33.333 0.00 0.00 0.00 2.32
8584 10988 6.207417 CCATGGATATGCCTTTCGTATTTCTT 59.793 38.462 5.56 0.00 37.63 2.52
8688 11094 4.323417 CACATGCTAACTTTGGTACTCCA 58.677 43.478 0.00 0.00 42.66 3.86
8695 11101 7.047891 TGCTAACTTTGGTACTCCATTATCAG 58.952 38.462 0.00 0.00 43.91 2.90
8813 11231 2.543012 CGTCTTATGCTTGATGAGGCAG 59.457 50.000 0.00 0.00 41.88 4.85
8814 11232 3.539604 GTCTTATGCTTGATGAGGCAGT 58.460 45.455 0.00 0.00 41.88 4.40
8899 11317 0.165944 GCGTCGTGTGAGAATTTGGG 59.834 55.000 0.00 0.00 0.00 4.12
9149 11591 2.511600 CCATGGCGGACCTCGTTC 60.512 66.667 0.00 0.00 41.72 3.95
9151 11593 2.683933 ATGGCGGACCTCGTTCCT 60.684 61.111 0.00 0.00 41.72 3.36
9152 11594 3.019003 ATGGCGGACCTCGTTCCTG 62.019 63.158 0.00 0.00 41.72 3.86
9156 11598 1.663739 CGGACCTCGTTCCTGTTGA 59.336 57.895 0.00 0.00 32.88 3.18
9165 11607 3.879295 CTCGTTCCTGTTGAATGCCATAT 59.121 43.478 0.00 0.00 39.42 1.78
9177 11619 7.228108 TGTTGAATGCCATATGAGATCTTCTTC 59.772 37.037 3.65 0.00 0.00 2.87
9223 11665 2.043852 TCGAGGAGACCCAGAGCC 60.044 66.667 0.00 0.00 33.88 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.238432 AGTCGACTGAATTGTTGTGCAATAA 59.762 36.000 19.30 0.00 46.29 1.40
2 3 4.754618 AGTCGACTGAATTGTTGTGCAATA 59.245 37.500 19.30 0.00 46.29 1.90
4 5 2.942376 AGTCGACTGAATTGTTGTGCAA 59.058 40.909 19.30 0.00 41.89 4.08
5 6 2.560504 AGTCGACTGAATTGTTGTGCA 58.439 42.857 19.30 0.00 0.00 4.57
6 7 3.609103 AAGTCGACTGAATTGTTGTGC 57.391 42.857 20.85 0.00 29.89 4.57
16 17 9.387257 TGTAGTGACTATTTATAAGTCGACTGA 57.613 33.333 20.85 13.02 45.19 3.41
17 18 9.999009 TTGTAGTGACTATTTATAAGTCGACTG 57.001 33.333 20.85 6.27 45.19 3.51
104 105 1.673920 TGTGCTTTTCGGTTTCTGTCC 59.326 47.619 0.00 0.00 0.00 4.02
181 182 3.583228 TCCCTTGTCTTGTCTTCAGGTA 58.417 45.455 0.00 0.00 0.00 3.08
1020 1021 2.217745 GGGGAATAGAGGGGCGGAG 61.218 68.421 0.00 0.00 0.00 4.63
1055 1057 1.401931 CCAACAGCAGCAATTTCGAGG 60.402 52.381 0.00 0.00 0.00 4.63
1056 1058 1.401931 CCCAACAGCAGCAATTTCGAG 60.402 52.381 0.00 0.00 0.00 4.04
1066 1076 0.250858 TCACACATCCCCAACAGCAG 60.251 55.000 0.00 0.00 0.00 4.24
1079 1089 4.951254 TGACTAATTTCTCGGTTCACACA 58.049 39.130 0.00 0.00 0.00 3.72
1083 1093 4.449743 CGGTTTGACTAATTTCTCGGTTCA 59.550 41.667 0.00 0.00 0.00 3.18
1113 1123 5.240623 TGTTTAATTTGGCCAGTCTACACAG 59.759 40.000 5.11 0.00 0.00 3.66
1114 1124 5.133941 TGTTTAATTTGGCCAGTCTACACA 58.866 37.500 5.11 5.32 0.00 3.72
1115 1125 5.699097 TGTTTAATTTGGCCAGTCTACAC 57.301 39.130 5.11 2.66 0.00 2.90
1116 1126 4.217550 GCTGTTTAATTTGGCCAGTCTACA 59.782 41.667 5.11 6.44 0.00 2.74
1117 1127 4.217550 TGCTGTTTAATTTGGCCAGTCTAC 59.782 41.667 5.11 1.66 0.00 2.59
1118 1128 4.402829 TGCTGTTTAATTTGGCCAGTCTA 58.597 39.130 5.11 0.00 0.00 2.59
1119 1129 3.230134 TGCTGTTTAATTTGGCCAGTCT 58.770 40.909 5.11 0.00 0.00 3.24
1120 1130 3.658757 TGCTGTTTAATTTGGCCAGTC 57.341 42.857 5.11 0.00 0.00 3.51
1121 1131 4.040217 TGAATGCTGTTTAATTTGGCCAGT 59.960 37.500 5.11 0.00 0.00 4.00
1122 1132 4.567971 TGAATGCTGTTTAATTTGGCCAG 58.432 39.130 5.11 0.00 0.00 4.85
1123 1133 4.613925 TGAATGCTGTTTAATTTGGCCA 57.386 36.364 0.00 0.00 0.00 5.36
1124 1134 4.142838 GCTTGAATGCTGTTTAATTTGGCC 60.143 41.667 0.00 0.00 0.00 5.36
1184 1194 2.171003 TCGTCCAATTGCTGAGAGAGA 58.829 47.619 0.00 0.00 0.00 3.10
1185 1195 2.662006 TCGTCCAATTGCTGAGAGAG 57.338 50.000 0.00 0.00 0.00 3.20
1230 1240 8.311395 TCTCACTCTTGGAACATAGTATGAAT 57.689 34.615 17.13 5.13 39.30 2.57
1250 1260 0.954452 CAAGTGGCAACCCTTCTCAC 59.046 55.000 0.00 0.00 0.00 3.51
1294 1306 7.673926 AGCCTAAAATCCCAAATACTCAAAAGA 59.326 33.333 0.00 0.00 0.00 2.52
1295 1307 7.840931 AGCCTAAAATCCCAAATACTCAAAAG 58.159 34.615 0.00 0.00 0.00 2.27
1376 1389 3.437052 GGATTCAGGGATAGGGCATTTGT 60.437 47.826 0.00 0.00 0.00 2.83
1431 1444 4.941263 TGGGTGATCTGCAAATAACAGTAC 59.059 41.667 0.00 0.00 36.50 2.73
1434 1447 4.264253 TCTGGGTGATCTGCAAATAACAG 58.736 43.478 0.00 0.00 36.44 3.16
1438 1451 4.574674 AGTTCTGGGTGATCTGCAAATA 57.425 40.909 0.00 0.00 0.00 1.40
1512 1525 1.668101 GAACTCTCTGATCCCCGCGT 61.668 60.000 4.92 0.00 0.00 6.01
1967 1980 9.587772 GTTTAGTTTGATAGCTTCTATCAGTGA 57.412 33.333 14.03 0.00 35.62 3.41
2136 2223 6.061022 TCTACAGATTGTTAAAGCCCATCA 57.939 37.500 0.00 0.00 0.00 3.07
2395 2503 7.227910 TGGCCTCGAAAATAAACATATAAGGAC 59.772 37.037 3.32 0.00 0.00 3.85
2397 2505 7.504924 TGGCCTCGAAAATAAACATATAAGG 57.495 36.000 3.32 0.00 0.00 2.69
2418 2526 4.793216 CACAAAACAGCGTAAGAATATGGC 59.207 41.667 0.00 0.00 43.02 4.40
2574 2683 7.870445 TGACAAATAGTTAAATGGAAAGGTTGC 59.130 33.333 0.00 0.00 0.00 4.17
2917 3030 9.793252 ATGTCATCAGTAAGCAAAAATATTGAC 57.207 29.630 0.00 0.00 0.00 3.18
3230 3345 1.474478 TCGCTCTAGTTCCTCAAGCAG 59.526 52.381 0.00 0.00 33.21 4.24
3238 3353 4.046938 TCACATTCATCGCTCTAGTTCC 57.953 45.455 0.00 0.00 0.00 3.62
3286 3401 7.059788 TCCATAAAAAGCAATAGCCATAGTCA 58.940 34.615 0.00 0.00 43.56 3.41
3302 3417 9.334947 CAATCTTATGCTCTCTCTCCATAAAAA 57.665 33.333 0.00 0.00 32.78 1.94
3549 3665 5.589050 ACAACCAGTAAGAAAACCAGACTTC 59.411 40.000 0.00 0.00 0.00 3.01
4001 4117 4.630069 TGGCGACTAAGCTAAATCAAGAAC 59.370 41.667 0.00 0.00 37.29 3.01
4140 4275 4.083324 AGTTGCATATGTTTTCACGGACAG 60.083 41.667 4.29 0.00 0.00 3.51
4146 4281 8.853345 CAATTAGTCAGTTGCATATGTTTTCAC 58.147 33.333 4.29 0.00 0.00 3.18
4370 4515 7.497595 TCAGTGAGTGCTTCTTTAAAAGACTA 58.502 34.615 0.00 0.00 37.23 2.59
4784 4951 1.326245 CGCGTTCAAGTGTTCAACAGA 59.674 47.619 0.00 0.00 0.00 3.41
4785 4956 1.326245 TCGCGTTCAAGTGTTCAACAG 59.674 47.619 5.77 0.00 0.00 3.16
4827 4998 0.679960 ATGCGTGAAACCTTAGCCCC 60.680 55.000 0.00 0.00 0.00 5.80
5120 5327 7.816031 AGTAAATCAAGTGGCATCAAAAGATTG 59.184 33.333 0.00 0.00 37.92 2.67
5243 6692 4.290093 AGGGAGCAACATGACAGATACTA 58.710 43.478 0.00 0.00 0.00 1.82
5516 6965 7.710907 CGATGAGAGTCCTATGTTCCAAAATAA 59.289 37.037 0.00 0.00 0.00 1.40
5533 6982 6.595326 TGCTAAATGAAAATCACGATGAGAGT 59.405 34.615 0.00 0.00 0.00 3.24
5661 7117 1.597854 CTTGACTCGCTGGCAACCA 60.598 57.895 0.00 0.00 39.08 3.67
5680 7136 2.887568 CATCGTGGCTGGCTCGAC 60.888 66.667 26.51 5.39 36.46 4.20
5742 7198 4.342378 TCGAGCTCAGCTAAACCTCATATT 59.658 41.667 15.40 0.00 39.88 1.28
5863 7320 6.152379 CCTCAATTAAGTTTGGTTCAAGCTC 58.848 40.000 0.00 0.00 34.01 4.09
5864 7321 5.509670 GCCTCAATTAAGTTTGGTTCAAGCT 60.510 40.000 0.00 0.00 36.52 3.74
5865 7322 4.686091 GCCTCAATTAAGTTTGGTTCAAGC 59.314 41.667 0.00 0.00 0.00 4.01
5866 7323 6.089249 AGCCTCAATTAAGTTTGGTTCAAG 57.911 37.500 0.00 0.00 0.00 3.02
5867 7324 6.775629 ACTAGCCTCAATTAAGTTTGGTTCAA 59.224 34.615 0.00 0.00 0.00 2.69
5926 7384 9.574516 ACATCCTAATAGCCTTATAAACAAAGG 57.425 33.333 0.00 0.00 45.36 3.11
6319 8702 4.706842 ATCACTGGTAACTCAACACCTT 57.293 40.909 0.00 0.00 35.73 3.50
6416 8800 2.958355 AGTGAAATGTTGACCTGTTGGG 59.042 45.455 0.00 0.00 41.89 4.12
6895 9287 3.441572 GCTCAGCACTGTGACCATAAAAT 59.558 43.478 12.86 0.00 0.00 1.82
7445 9837 9.396022 GGAATGTTTATTTAGAGAGGTTGATGA 57.604 33.333 0.00 0.00 0.00 2.92
7495 9887 6.217693 AGGAACAGAGGGAGTATAATTTTGGT 59.782 38.462 0.00 0.00 0.00 3.67
7526 9918 8.696374 CCATAGTGGAATCTCTACAAAGACTTA 58.304 37.037 0.00 0.00 40.96 2.24
7527 9919 7.400339 TCCATAGTGGAATCTCTACAAAGACTT 59.600 37.037 0.00 0.00 45.00 3.01
7528 9920 6.897966 TCCATAGTGGAATCTCTACAAAGACT 59.102 38.462 0.00 0.00 45.00 3.24
7544 9936 2.036387 TCCGTATGTGGTCCATAGTGG 58.964 52.381 0.00 0.00 36.71 4.00
7545 9937 3.069586 ACATCCGTATGTGGTCCATAGTG 59.930 47.826 0.00 0.00 44.79 2.74
7547 9939 5.661056 ATACATCCGTATGTGGTCCATAG 57.339 43.478 3.56 0.00 45.99 2.23
7548 9940 6.011481 TGTATACATCCGTATGTGGTCCATA 58.989 40.000 3.56 0.00 45.99 2.74
7549 9941 4.836175 TGTATACATCCGTATGTGGTCCAT 59.164 41.667 3.56 0.00 45.99 3.41
7550 9942 4.216708 TGTATACATCCGTATGTGGTCCA 58.783 43.478 3.56 0.00 45.99 4.02
7552 9944 7.439955 TCATTTTGTATACATCCGTATGTGGTC 59.560 37.037 6.36 0.00 45.99 4.02
7555 9947 8.275632 CACTCATTTTGTATACATCCGTATGTG 58.724 37.037 6.36 7.47 45.99 3.21
7557 9949 8.587952 TCACTCATTTTGTATACATCCGTATG 57.412 34.615 6.36 6.62 38.79 2.39
7570 9962 9.208022 CATACGGATGTATATCACTCATTTTGT 57.792 33.333 0.00 0.00 39.28 2.83
7571 9963 9.208022 ACATACGGATGTATATCACTCATTTTG 57.792 33.333 12.79 0.00 44.77 2.44
7572 9964 9.208022 CACATACGGATGTATATCACTCATTTT 57.792 33.333 14.23 0.00 44.82 1.82
7574 9966 7.039011 ACCACATACGGATGTATATCACTCATT 60.039 37.037 14.23 0.00 44.82 2.57
7575 9967 6.437477 ACCACATACGGATGTATATCACTCAT 59.563 38.462 14.23 0.00 44.82 2.90
7576 9968 5.773176 ACCACATACGGATGTATATCACTCA 59.227 40.000 14.23 0.00 44.82 3.41
7577 9969 6.268825 ACCACATACGGATGTATATCACTC 57.731 41.667 14.23 0.00 44.82 3.51
7578 9970 5.185249 GGACCACATACGGATGTATATCACT 59.815 44.000 14.23 0.00 44.82 3.41
7579 9971 5.047590 TGGACCACATACGGATGTATATCAC 60.048 44.000 14.23 2.85 44.82 3.06
7581 9973 5.654603 TGGACCACATACGGATGTATATC 57.345 43.478 14.23 10.89 44.82 1.63
7582 9974 6.895756 ACTATGGACCACATACGGATGTATAT 59.104 38.462 14.23 1.16 44.82 0.86
7583 9975 6.152154 CACTATGGACCACATACGGATGTATA 59.848 42.308 14.23 6.48 44.82 1.47
7585 9977 4.279922 CACTATGGACCACATACGGATGTA 59.720 45.833 14.23 0.00 44.82 2.29
7589 9981 2.036387 CCACTATGGACCACATACGGA 58.964 52.381 0.00 0.00 40.96 4.69
7590 9982 2.036387 TCCACTATGGACCACATACGG 58.964 52.381 0.00 0.00 42.67 4.02
7600 9992 6.897966 AGTCTTTGTAGAGATTCCACTATGGA 59.102 38.462 0.00 0.00 46.61 3.41
7601 9993 7.118496 AGTCTTTGTAGAGATTCCACTATGG 57.882 40.000 0.00 0.00 39.43 2.74
7617 10009 9.853177 CCTCCATTCCTAAATATAAGTCTTTGT 57.147 33.333 0.00 0.00 0.00 2.83
7618 10010 9.289782 CCCTCCATTCCTAAATATAAGTCTTTG 57.710 37.037 0.00 0.00 0.00 2.77
7619 10011 9.237706 TCCCTCCATTCCTAAATATAAGTCTTT 57.762 33.333 0.00 0.00 0.00 2.52
7620 10012 8.814448 TCCCTCCATTCCTAAATATAAGTCTT 57.186 34.615 0.00 0.00 0.00 3.01
7621 10013 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
7622 10014 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
7623 10015 9.327731 CTACTCCCTCCATTCCTAAATATAAGT 57.672 37.037 0.00 0.00 0.00 2.24
7624 10016 9.327731 ACTACTCCCTCCATTCCTAAATATAAG 57.672 37.037 0.00 0.00 0.00 1.73
7625 10017 9.684702 AACTACTCCCTCCATTCCTAAATATAA 57.315 33.333 0.00 0.00 0.00 0.98
7626 10018 9.101325 CAACTACTCCCTCCATTCCTAAATATA 57.899 37.037 0.00 0.00 0.00 0.86
7627 10019 7.017651 CCAACTACTCCCTCCATTCCTAAATAT 59.982 40.741 0.00 0.00 0.00 1.28
7628 10020 6.329197 CCAACTACTCCCTCCATTCCTAAATA 59.671 42.308 0.00 0.00 0.00 1.40
7629 10021 5.132816 CCAACTACTCCCTCCATTCCTAAAT 59.867 44.000 0.00 0.00 0.00 1.40
7630 10022 4.473559 CCAACTACTCCCTCCATTCCTAAA 59.526 45.833 0.00 0.00 0.00 1.85
7631 10023 4.037927 CCAACTACTCCCTCCATTCCTAA 58.962 47.826 0.00 0.00 0.00 2.69
7632 10024 3.013648 ACCAACTACTCCCTCCATTCCTA 59.986 47.826 0.00 0.00 0.00 2.94
7633 10025 2.225908 ACCAACTACTCCCTCCATTCCT 60.226 50.000 0.00 0.00 0.00 3.36
7634 10026 2.197465 ACCAACTACTCCCTCCATTCC 58.803 52.381 0.00 0.00 0.00 3.01
7638 10030 2.112279 ACAACCAACTACTCCCTCCA 57.888 50.000 0.00 0.00 0.00 3.86
7658 10050 5.304686 TCTGTTTATGTGGTTTCCTCTGT 57.695 39.130 0.00 0.00 0.00 3.41
7868 10260 1.962807 CAGTTGCTGGGATCAAAACCA 59.037 47.619 0.00 0.00 35.05 3.67
7909 10301 5.350504 TCTGGATCATCTCTCCTGAAAAC 57.649 43.478 0.00 0.00 37.68 2.43
7962 10354 0.459489 ACTCGAATGCCTCTCTCAGC 59.541 55.000 0.00 0.00 0.00 4.26
8149 10541 2.099431 CCAACTCTGCGAGCTCTGC 61.099 63.158 19.33 19.33 32.04 4.26
8151 10543 0.897863 ACTCCAACTCTGCGAGCTCT 60.898 55.000 12.85 0.00 32.04 4.09
8253 10645 3.726291 TCGCTCGATTTGGATATGTCA 57.274 42.857 0.00 0.00 0.00 3.58
8297 10689 0.596577 TAGTATGCATCTCGCCGGTC 59.403 55.000 0.19 0.00 41.33 4.79
8302 10694 2.733552 CACACCATAGTATGCATCTCGC 59.266 50.000 0.19 0.00 42.89 5.03
8303 10695 3.982475 ACACACCATAGTATGCATCTCG 58.018 45.455 0.19 0.00 0.00 4.04
8306 10698 3.071602 AGGGACACACCATAGTATGCATC 59.928 47.826 0.19 0.00 41.20 3.91
8344 10736 0.539986 ACATTCGGGTGTTAGGCGAT 59.460 50.000 0.00 0.00 0.00 4.58
8345 10737 1.135527 CTACATTCGGGTGTTAGGCGA 59.864 52.381 0.00 0.00 33.62 5.54
8346 10738 1.135527 TCTACATTCGGGTGTTAGGCG 59.864 52.381 0.00 0.00 33.62 5.52
8347 10739 2.973694 TCTACATTCGGGTGTTAGGC 57.026 50.000 0.00 0.00 33.62 3.93
8350 10742 6.071221 ACAACACTATCTACATTCGGGTGTTA 60.071 38.462 0.00 0.00 42.11 2.41
8365 10757 9.128107 CAATGGACACAATAAAACAACACTATC 57.872 33.333 0.00 0.00 0.00 2.08
8410 10805 3.499537 CAGTAAAGACAGAGCAATGCACA 59.500 43.478 8.35 0.00 0.00 4.57
8426 10821 8.575589 ACACATTTGCATTTCTCATACAGTAAA 58.424 29.630 0.00 0.00 0.00 2.01
8430 10830 8.453320 TCTTACACATTTGCATTTCTCATACAG 58.547 33.333 0.00 0.00 0.00 2.74
8431 10831 8.236586 GTCTTACACATTTGCATTTCTCATACA 58.763 33.333 0.00 0.00 0.00 2.29
8432 10832 8.454106 AGTCTTACACATTTGCATTTCTCATAC 58.546 33.333 0.00 0.00 0.00 2.39
8433 10833 8.565896 AGTCTTACACATTTGCATTTCTCATA 57.434 30.769 0.00 0.00 0.00 2.15
8435 10835 6.882610 AGTCTTACACATTTGCATTTCTCA 57.117 33.333 0.00 0.00 0.00 3.27
8436 10836 7.244192 GGTAGTCTTACACATTTGCATTTCTC 58.756 38.462 0.00 0.00 0.00 2.87
8437 10837 6.128282 CGGTAGTCTTACACATTTGCATTTCT 60.128 38.462 0.00 0.00 0.00 2.52
8438 10838 6.021596 CGGTAGTCTTACACATTTGCATTTC 58.978 40.000 0.00 0.00 0.00 2.17
8439 10839 5.472137 ACGGTAGTCTTACACATTTGCATTT 59.528 36.000 0.00 0.00 0.00 2.32
8440 10840 5.001232 ACGGTAGTCTTACACATTTGCATT 58.999 37.500 0.00 0.00 0.00 3.56
8449 10849 2.603953 GCCTCAACGGTAGTCTTACAC 58.396 52.381 0.00 0.00 34.25 2.90
8571 10975 6.867662 ATCCCATGCTAAGAAATACGAAAG 57.132 37.500 0.00 0.00 0.00 2.62
8584 10988 7.038729 TGGTTTTCAAATGTTAATCCCATGCTA 60.039 33.333 0.00 0.00 0.00 3.49
8628 11034 6.214191 TGTTGTAAAGTGGAAATGCAAAGA 57.786 33.333 0.00 0.00 0.00 2.52
8728 11137 9.209048 TCTGCCTACTCTAGTGGAAAAATAATA 57.791 33.333 0.00 0.00 0.00 0.98
8731 11140 6.405508 CGTCTGCCTACTCTAGTGGAAAAATA 60.406 42.308 0.00 0.00 0.00 1.40
9149 11591 5.314529 AGATCTCATATGGCATTCAACAGG 58.685 41.667 4.78 0.00 0.00 4.00
9151 11593 6.598503 AGAAGATCTCATATGGCATTCAACA 58.401 36.000 4.78 0.00 0.00 3.33
9152 11594 7.507733 AAGAAGATCTCATATGGCATTCAAC 57.492 36.000 4.78 0.00 0.00 3.18
9156 11598 5.699915 CACGAAGAAGATCTCATATGGCATT 59.300 40.000 4.78 0.00 0.00 3.56
9165 11607 2.493675 CCTGGACACGAAGAAGATCTCA 59.506 50.000 0.00 0.00 0.00 3.27
9177 11619 1.890894 CACCTACTCCCTGGACACG 59.109 63.158 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.