Multiple sequence alignment - TraesCS7D01G196000

Loading Multiple Alignment...

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 TraesCS7D01G196000 chr7D 100.000 5068 0 0 4259 9326 152131684 152126617 0.000000e+00 9359.0
1 TraesCS7D01G196000 chr7D 100.000 3896 0 0 1 3896 152135942 152132047 0.000000e+00 7195.0
2 TraesCS7D01G196000 chr7B 92.762 4034 164 51 5121 9109 114184248 114180298 0.000000e+00 5714.0
3 TraesCS7D01G196000 chr7B 92.883 1658 57 16 2249 3894 114186481 114184873 0.000000e+00 2351.0
4 TraesCS7D01G196000 chr7B 93.266 995 40 8 830 1815 114194085 114193109 0.000000e+00 1441.0
5 TraesCS7D01G196000 chr7B 95.890 584 18 6 4261 4839 114184825 114184243 0.000000e+00 941.0
6 TraesCS7D01G196000 chr7B 88.535 157 10 5 9177 9326 657622764 657622609 5.750000e-42 183.0
7 TraesCS7D01G196000 chr7A 94.428 3015 92 32 6232 9179 152545239 152542234 0.000000e+00 4567.0
8 TraesCS7D01G196000 chr7A 96.457 2738 51 26 4261 6988 152547179 152544478 0.000000e+00 4477.0
9 TraesCS7D01G196000 chr7A 95.897 2681 91 10 842 3517 152550450 152547784 0.000000e+00 4324.0
10 TraesCS7D01G196000 chr7A 97.644 382 7 2 3516 3896 152547625 152547245 0.000000e+00 654.0
11 TraesCS7D01G196000 chr7A 92.994 157 4 1 9177 9326 10982729 10982573 1.220000e-53 222.0
12 TraesCS7D01G196000 chr3D 92.614 853 50 7 1 844 547515097 547514249 0.000000e+00 1214.0
13 TraesCS7D01G196000 chr3D 85.185 243 30 4 1807 2046 508323730 508323969 2.600000e-60 244.0
14 TraesCS7D01G196000 chr3D 87.264 212 21 3 1806 2014 81373507 81373715 4.350000e-58 237.0
15 TraesCS7D01G196000 chr5D 91.958 858 63 6 8 862 430918799 430917945 0.000000e+00 1197.0
16 TraesCS7D01G196000 chr5D 91.489 846 69 3 1 844 353646286 353645442 0.000000e+00 1160.0
17 TraesCS7D01G196000 chr1D 91.745 848 65 5 1 845 38372189 38373034 0.000000e+00 1173.0
18 TraesCS7D01G196000 chr1D 91.720 157 6 1 9177 9326 120038639 120038483 2.640000e-50 211.0
19 TraesCS7D01G196000 chr1D 90.265 113 4 1 9221 9326 470796746 470796858 3.510000e-29 141.0
20 TraesCS7D01G196000 chr2B 91.726 846 67 3 1 844 385531667 385532511 0.000000e+00 1171.0
21 TraesCS7D01G196000 chr2B 86.607 224 22 5 1828 2047 296022849 296023068 3.370000e-59 241.0
22 TraesCS7D01G196000 chr2B 91.083 157 7 1 9177 9326 575367953 575368109 1.230000e-48 206.0
23 TraesCS7D01G196000 chr2A 91.173 861 69 5 1 858 779602075 779602931 0.000000e+00 1162.0
24 TraesCS7D01G196000 chr2A 90.825 861 75 4 1 858 779494441 779495300 0.000000e+00 1149.0
25 TraesCS7D01G196000 chr4B 91.479 845 69 3 1 843 660245457 660246300 0.000000e+00 1158.0
26 TraesCS7D01G196000 chr2D 91.489 846 65 7 4 846 589513040 589512199 0.000000e+00 1157.0
27 TraesCS7D01G196000 chr4D 84.774 243 32 4 1808 2047 102147829 102148069 1.210000e-58 239.0
28 TraesCS7D01G196000 chr1B 84.898 245 28 5 1809 2047 429010871 429011112 1.210000e-58 239.0
29 TraesCS7D01G196000 chr1A 87.037 216 23 4 1835 2047 398062621 398062834 1.210000e-58 239.0
30 TraesCS7D01G196000 chr1A 91.083 157 7 1 9177 9326 125100354 125100198 1.230000e-48 206.0
31 TraesCS7D01G196000 chr3A 84.274 248 24 10 1812 2047 9747710 9747466 2.620000e-55 228.0
32 TraesCS7D01G196000 chr6B 83.951 243 30 7 1808 2047 680323787 680323551 3.390000e-54 224.0
33 TraesCS7D01G196000 chrUn 92.994 157 4 1 9177 9326 87197556 87197400 1.220000e-53 222.0
34 TraesCS7D01G196000 chr3B 91.083 157 7 1 9177 9326 770655689 770655533 1.230000e-48 206.0
35 TraesCS7D01G196000 chr4A 90.446 157 8 1 9177 9326 229497795 229497639 5.710000e-47 200.0
36 TraesCS7D01G196000 chr6D 100.000 29 0 0 5869 5897 419613434 419613406 5.000000e-03 54.7


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 TraesCS7D01G196000 chr7D 152126617 152135942 9325 True 8277.0 9359 100.0000 1 9326 2 chr7D.!!$R1 9325
1 TraesCS7D01G196000 chr7B 114180298 114186481 6183 True 3002.0 5714 93.8450 2249 9109 3 chr7B.!!$R3 6860
2 TraesCS7D01G196000 chr7B 114193109 114194085 976 True 1441.0 1441 93.2660 830 1815 1 chr7B.!!$R1 985
3 TraesCS7D01G196000 chr7A 152542234 152550450 8216 True 3505.5 4567 96.1065 842 9179 4 chr7A.!!$R2 8337
4 TraesCS7D01G196000 chr3D 547514249 547515097 848 True 1214.0 1214 92.6140 1 844 1 chr3D.!!$R1 843
5 TraesCS7D01G196000 chr5D 430917945 430918799 854 True 1197.0 1197 91.9580 8 862 1 chr5D.!!$R2 854
6 TraesCS7D01G196000 chr5D 353645442 353646286 844 True 1160.0 1160 91.4890 1 844 1 chr5D.!!$R1 843
7 TraesCS7D01G196000 chr1D 38372189 38373034 845 False 1173.0 1173 91.7450 1 845 1 chr1D.!!$F1 844
8 TraesCS7D01G196000 chr2B 385531667 385532511 844 False 1171.0 1171 91.7260 1 844 1 chr2B.!!$F2 843
9 TraesCS7D01G196000 chr2A 779602075 779602931 856 False 1162.0 1162 91.1730 1 858 1 chr2A.!!$F2 857
10 TraesCS7D01G196000 chr2A 779494441 779495300 859 False 1149.0 1149 90.8250 1 858 1 chr2A.!!$F1 857
11 TraesCS7D01G196000 chr4B 660245457 660246300 843 False 1158.0 1158 91.4790 1 843 1 chr4B.!!$F1 842
12 TraesCS7D01G196000 chr2D 589512199 589513040 841 True 1157.0 1157 91.4890 4 846 1 chr2D.!!$R1 842

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
513 520 0.175989 GCTCGAACGGAGGGAGAATT 59.824 55.000 0.00 0.00 43.36 2.17 F
1294 1311 0.403271 ATTCACAGCCAGGACAAGCT 59.597 50.000 0.00 0.00 40.89 3.74 F
2536 2573 0.038983 TTTCGTCCTGATCGCAACGA 60.039 50.000 10.93 10.93 41.89 3.85 F
2873 2912 1.254026 CTACGTCTTCTGGGGTCACA 58.746 55.000 0.00 0.00 0.00 3.58 F
3012 3051 4.220602 ACATGGCAGGTATTTCAAAGAACC 59.779 41.667 1.47 0.00 0.00 3.62 F
4895 5101 2.224314 GCATTCTGCCTATTAAGTCCGC 59.776 50.000 0.00 0.00 37.42 5.54 F
6277 6486 0.032813 CCAAGGCCCACATTCTCCAT 60.033 55.000 0.00 0.00 0.00 3.41 F
7145 7391 4.095036 GGGTAACTGCAATAGCTGAAACTC 59.905 45.833 0.00 0.00 41.71 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1548 0.413832 AGTAGGGAGCAGGGAACAGA 59.586 55.000 0.00 0.00 0.00 3.41 R
2564 2601 0.883833 AAAGACAATCTGGCCAAGCG 59.116 50.000 7.01 0.00 0.00 4.68 R
3696 3896 4.970662 TTGCTGCTAATGAAATCAGACC 57.029 40.909 0.00 0.00 0.00 3.85 R
4599 4805 0.958382 GCATCACGGGTAAAGGCACA 60.958 55.000 0.00 0.00 0.00 4.57 R
4956 5162 2.665165 AGGTGAGCAAATTGTTCCACA 58.335 42.857 7.35 0.00 0.00 4.17 R
6821 7034 0.610232 CCACCTTTTCAGCTCCCTGG 60.610 60.000 0.00 0.00 39.61 4.45 R
7283 7529 2.226330 ACATCGCACAAAGCCTTTACA 58.774 42.857 0.00 0.00 41.38 2.41 R
8455 8710 2.732001 ACACGAGCAGAAACGTTTTC 57.268 45.000 15.89 7.65 40.76 2.29 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
29 34 6.041423 TCACATGGTTCATCGCTATCATAT 57.959 37.500 0.00 0.00 0.00 1.78
37 42 7.607607 TGGTTCATCGCTATCATATTAAGCATT 59.392 33.333 0.00 0.00 35.98 3.56
257 263 5.104817 TCAACCATATGAGCTCACAGATCAA 60.105 40.000 20.97 0.00 44.44 2.57
294 300 5.012458 CCATGCATCTAGATCAAACCCTAGA 59.988 44.000 1.03 0.00 43.62 2.43
378 385 1.984570 CAGCTCAAGGACGAGGGGA 60.985 63.158 0.00 0.00 33.36 4.81
405 412 0.179108 GTAGAAGATCAACGCCGGCT 60.179 55.000 26.68 8.92 0.00 5.52
418 425 4.379243 CGGCTGGTGAAGGAGCGT 62.379 66.667 0.00 0.00 35.95 5.07
455 462 2.890109 GCTGATGAAGATGCGCCGG 61.890 63.158 4.18 0.00 0.00 6.13
513 520 0.175989 GCTCGAACGGAGGGAGAATT 59.824 55.000 0.00 0.00 43.36 2.17
628 636 2.202851 AAGCTCGCGCCATCTCTG 60.203 61.111 0.00 0.00 36.60 3.35
707 716 1.681793 GAGCTACTACCGATTCAGGCA 59.318 52.381 0.00 0.00 33.69 4.75
724 733 2.537959 ATTTCCCCTGGGCCTGGT 60.538 61.111 25.76 6.21 34.68 4.00
854 863 2.225068 ACACGCCCTAATCGAATCAG 57.775 50.000 0.00 0.00 0.00 2.90
878 887 5.175673 GCAAGTGCACAGAAATTTAAACTCC 59.824 40.000 21.04 0.00 41.59 3.85
1294 1311 0.403271 ATTCACAGCCAGGACAAGCT 59.597 50.000 0.00 0.00 40.89 3.74
1412 1429 3.900892 CGCTACATCGTCCCGGCT 61.901 66.667 0.00 0.00 0.00 5.52
1549 1569 0.909610 TGTTCCCTGCTCCCTACTGG 60.910 60.000 0.00 0.00 0.00 4.00
1585 1605 4.033358 CGAAATACTCTGACTGTTGATGCC 59.967 45.833 0.00 0.00 0.00 4.40
1600 1620 5.112686 GTTGATGCCTAGTGTTCCTTAGAG 58.887 45.833 0.00 0.00 0.00 2.43
1603 1623 5.360144 TGATGCCTAGTGTTCCTTAGAGTAC 59.640 44.000 0.00 0.00 0.00 2.73
1617 1637 1.407618 AGAGTACGTGCACAGTGTTGA 59.592 47.619 18.64 0.00 0.00 3.18
1618 1638 1.521423 GAGTACGTGCACAGTGTTGAC 59.479 52.381 18.64 10.28 0.00 3.18
1619 1639 0.580104 GTACGTGCACAGTGTTGACC 59.420 55.000 18.64 0.00 0.00 4.02
1620 1640 0.175989 TACGTGCACAGTGTTGACCA 59.824 50.000 18.64 0.00 0.00 4.02
1621 1641 1.351707 CGTGCACAGTGTTGACCAC 59.648 57.895 18.64 0.42 44.89 4.16
1634 1661 0.322648 TGACCACTGACCAGCTGATG 59.677 55.000 17.39 1.02 0.00 3.07
1655 1682 4.643463 TGGCGTGATTTCCTAGTTACAAA 58.357 39.130 0.00 0.00 0.00 2.83
1688 1716 1.596934 GAGTGAATGCCCCTGACGA 59.403 57.895 0.00 0.00 0.00 4.20
1731 1759 2.556189 TGCACGCAACCATCTTTATTGT 59.444 40.909 0.00 0.00 0.00 2.71
1732 1760 3.005261 TGCACGCAACCATCTTTATTGTT 59.995 39.130 0.00 0.00 0.00 2.83
1922 1952 8.556194 GCGACAATAATATCATTGGAAACTACA 58.444 33.333 3.61 0.00 39.71 2.74
1933 1963 8.554835 TCATTGGAAACTACATTCAAATACGA 57.445 30.769 0.00 0.00 32.41 3.43
1943 1973 8.234546 ACTACATTCAAATACGAATCCAACAAC 58.765 33.333 0.00 0.00 33.27 3.32
1970 2000 7.982761 AATTTTTGGTGACATGCATTAACAT 57.017 28.000 0.00 0.00 42.32 2.71
1981 2011 8.791675 TGACATGCATTAACATTTTTCTAGTCA 58.208 29.630 0.00 0.00 0.00 3.41
1982 2012 9.624697 GACATGCATTAACATTTTTCTAGTCAA 57.375 29.630 0.00 0.00 0.00 3.18
2036 2066 4.847990 TTGGTGACTAATAAACCCGGAT 57.152 40.909 0.73 0.00 32.70 4.18
2047 2077 2.789323 AACCCGGATGGAGGTAGTAT 57.211 50.000 0.73 0.00 37.49 2.12
2048 2078 3.909427 AACCCGGATGGAGGTAGTATA 57.091 47.619 0.73 0.00 37.49 1.47
2122 2152 7.977789 ATTGTGGTCAAAATTTATTGGGTTC 57.022 32.000 0.00 0.00 37.11 3.62
2141 2171 3.435186 GGGAAACTGCTGGAGCGC 61.435 66.667 0.00 0.00 45.83 5.92
2173 2203 5.996644 TGTCAATTTCCCCTATACGTGATT 58.003 37.500 0.00 0.00 0.00 2.57
2174 2204 6.419791 TGTCAATTTCCCCTATACGTGATTT 58.580 36.000 0.00 0.00 0.00 2.17
2175 2205 6.887545 TGTCAATTTCCCCTATACGTGATTTT 59.112 34.615 0.00 0.00 0.00 1.82
2176 2206 7.394923 TGTCAATTTCCCCTATACGTGATTTTT 59.605 33.333 0.00 0.00 0.00 1.94
2215 2245 0.178533 AGCTGCTGGAGATGCTCTTC 59.821 55.000 0.00 0.00 0.00 2.87
2233 2263 5.055265 TCTTCGAGACTAGAGAATCCCAT 57.945 43.478 0.00 0.00 33.66 4.00
2245 2275 3.704231 ATCCCATGCCTCCACACGC 62.704 63.158 0.00 0.00 0.00 5.34
2270 2300 2.038557 AGTAAGCACCACATTCGGTTCT 59.961 45.455 0.00 0.00 37.07 3.01
2279 2309 3.426159 CCACATTCGGTTCTTATGTGTGC 60.426 47.826 11.97 0.00 44.72 4.57
2389 2426 2.427506 CACCTGAGCCTTTAGTTGTCC 58.572 52.381 0.00 0.00 0.00 4.02
2536 2573 0.038983 TTTCGTCCTGATCGCAACGA 60.039 50.000 10.93 10.93 41.89 3.85
2564 2601 4.036616 ACTTTTTGTTGCCATTCCAATTGC 59.963 37.500 0.00 0.00 0.00 3.56
2761 2800 6.542821 TGTTTTGAGAGTTGGTATCTGGAAT 58.457 36.000 0.00 0.00 0.00 3.01
2873 2912 1.254026 CTACGTCTTCTGGGGTCACA 58.746 55.000 0.00 0.00 0.00 3.58
3012 3051 4.220602 ACATGGCAGGTATTTCAAAGAACC 59.779 41.667 1.47 0.00 0.00 3.62
3071 3110 6.896021 AGCTCTTGTAAGACAACTAGTGTA 57.104 37.500 0.00 0.00 41.96 2.90
3191 3230 9.765795 AACAAGGTTAGATATCTAATGTAGTGC 57.234 33.333 24.42 11.93 40.20 4.40
4476 4680 7.242079 GCTTACTATATGATTGCATGCTTGAG 58.758 38.462 20.33 7.22 35.94 3.02
4599 4805 4.803098 AGTTAGTCGCTCACAAACCTAT 57.197 40.909 0.00 0.00 0.00 2.57
4670 4876 6.206395 ACAGTTGACATTGTGTTTGAATCA 57.794 33.333 0.00 0.00 0.00 2.57
4833 5039 4.145807 TCCACATTGTTTGGTTATCGGTT 58.854 39.130 0.00 0.00 35.42 4.44
4834 5040 4.022762 TCCACATTGTTTGGTTATCGGTTG 60.023 41.667 0.00 0.00 35.42 3.77
4835 5041 4.261825 CCACATTGTTTGGTTATCGGTTGT 60.262 41.667 0.00 0.00 0.00 3.32
4895 5101 2.224314 GCATTCTGCCTATTAAGTCCGC 59.776 50.000 0.00 0.00 37.42 5.54
4897 5103 3.620427 TTCTGCCTATTAAGTCCGCAA 57.380 42.857 0.00 0.00 0.00 4.85
4956 5162 6.590656 TTTTTAGATGGGTCCAGATATGGT 57.409 37.500 6.21 0.00 0.00 3.55
4989 5195 6.952773 TTTGCTCACCTACATGTTTACTTT 57.047 33.333 2.30 0.00 0.00 2.66
5039 5245 3.630312 TCTCAGGTTTAAACACTGTTGGC 59.370 43.478 24.10 7.46 32.55 4.52
5915 6123 7.727186 AGTCGACCTAACATATTCCTATGGTTA 59.273 37.037 13.01 0.00 39.29 2.85
6213 6422 2.827800 TGAGTTGTCTCTCCAAGCAG 57.172 50.000 0.00 0.00 40.98 4.24
6214 6423 1.345741 TGAGTTGTCTCTCCAAGCAGG 59.654 52.381 0.00 0.00 40.98 4.85
6215 6424 1.346068 GAGTTGTCTCTCCAAGCAGGT 59.654 52.381 0.00 0.00 39.02 4.00
6216 6425 1.071385 AGTTGTCTCTCCAAGCAGGTG 59.929 52.381 0.00 0.00 39.02 4.00
6217 6426 1.131638 TTGTCTCTCCAAGCAGGTGT 58.868 50.000 0.00 0.00 39.02 4.16
6218 6427 0.394192 TGTCTCTCCAAGCAGGTGTG 59.606 55.000 0.00 0.00 39.02 3.82
6227 6436 2.281208 GCAGGTGTGCCGGTTGTA 60.281 61.111 1.90 0.00 44.72 2.41
6228 6437 2.325082 GCAGGTGTGCCGGTTGTAG 61.325 63.158 1.90 0.00 44.72 2.74
6229 6438 1.671054 CAGGTGTGCCGGTTGTAGG 60.671 63.158 1.90 0.00 40.50 3.18
6236 6445 3.074281 CCGGTTGTAGGCCTCCAA 58.926 61.111 9.68 7.94 0.00 3.53
6237 6446 1.078426 CCGGTTGTAGGCCTCCAAG 60.078 63.158 11.62 0.46 0.00 3.61
6238 6447 1.745489 CGGTTGTAGGCCTCCAAGC 60.745 63.158 25.64 25.64 36.10 4.01
6239 6448 1.378762 GGTTGTAGGCCTCCAAGCA 59.621 57.895 29.12 11.58 38.57 3.91
6277 6486 0.032813 CCAAGGCCCACATTCTCCAT 60.033 55.000 0.00 0.00 0.00 3.41
6328 6537 8.746052 TGGGAATTGTCGATTAGAAAATGTAT 57.254 30.769 0.00 0.00 36.91 2.29
6331 6540 8.958043 GGAATTGTCGATTAGAAAATGTATTGC 58.042 33.333 0.00 0.00 36.91 3.56
6549 6758 7.681939 TTGGTACTTTATTTGACATGGACTC 57.318 36.000 0.00 0.00 0.00 3.36
6762 6975 6.161855 TGATACCTCACATGAGTTCCATAC 57.838 41.667 0.00 0.00 40.48 2.39
7045 7291 7.009357 GCTGTACTTCAGAAACTATTAGTTCCG 59.991 40.741 9.45 2.34 46.27 4.30
7051 7297 9.151471 CTTCAGAAACTATTAGTTCCGATGAAA 57.849 33.333 9.45 0.00 37.47 2.69
7066 7312 6.027131 TCCGATGAAATTTTTGTCATTAGCG 58.973 36.000 0.00 0.00 34.61 4.26
7145 7391 4.095036 GGGTAACTGCAATAGCTGAAACTC 59.905 45.833 0.00 0.00 41.71 3.01
7185 7431 7.170998 AGTGCTGACAACAGTAAGTAAACATAC 59.829 37.037 0.00 0.00 45.04 2.39
7242 7488 6.652481 CACTTCCACTGATTCAGAATGTTACT 59.348 38.462 20.33 0.00 37.40 2.24
7461 7709 0.249447 TGTGTCAGGTGCAGAGTTCG 60.249 55.000 0.00 0.00 0.00 3.95
7691 7939 8.421249 AATCACTTGACCTTGGATTTAATGAA 57.579 30.769 0.00 0.00 0.00 2.57
8099 8353 5.874810 GTGGATGTTTCTGCATAGTTGACTA 59.125 40.000 0.00 0.00 0.00 2.59
8427 8682 1.751924 AGTAGAGTCATCGTCAAGCCC 59.248 52.381 0.00 0.00 0.00 5.19
8455 8710 1.221635 TGTTATGGGGTCATCTGGGG 58.778 55.000 0.00 0.00 34.96 4.96
8540 8796 2.765689 TCAACCCCACAATTTCCACT 57.234 45.000 0.00 0.00 0.00 4.00
8580 8837 9.612066 AAGTTTCATGTGGTACATTTCAAATTT 57.388 25.926 0.00 0.00 44.52 1.82
8718 8975 5.544682 TCTGTTAGGGGTGGGTAGATAAAT 58.455 41.667 0.00 0.00 0.00 1.40
8942 9226 2.352651 CACATAGGTCATTGCTTCCACG 59.647 50.000 0.00 0.00 0.00 4.94
8973 9257 4.737855 TCCATGCTACCTAAGAACAGAC 57.262 45.455 0.00 0.00 0.00 3.51
9068 9352 2.488153 GACCGGCTTTTATTCACAGCTT 59.512 45.455 0.00 0.00 33.76 3.74
9115 9399 9.809096 ATCTGACTGTAGATAGTACACAATTTG 57.191 33.333 0.00 0.00 35.70 2.32
9117 9401 9.295214 CTGACTGTAGATAGTACACAATTTGAG 57.705 37.037 2.79 0.00 0.00 3.02
9179 9463 8.023128 TCATTTTTCTTGTTTCTTGATCGATCC 58.977 33.333 22.31 6.55 0.00 3.36
9180 9464 6.875948 TTTTCTTGTTTCTTGATCGATCCA 57.124 33.333 22.31 11.00 0.00 3.41
9181 9465 5.862924 TTCTTGTTTCTTGATCGATCCAC 57.137 39.130 22.31 11.33 0.00 4.02
9182 9466 4.253685 TCTTGTTTCTTGATCGATCCACC 58.746 43.478 22.31 5.48 0.00 4.61
9183 9467 3.981071 TGTTTCTTGATCGATCCACCT 57.019 42.857 22.31 0.00 0.00 4.00
9184 9468 3.861840 TGTTTCTTGATCGATCCACCTC 58.138 45.455 22.31 9.25 0.00 3.85
9185 9469 3.515502 TGTTTCTTGATCGATCCACCTCT 59.484 43.478 22.31 0.00 0.00 3.69
9186 9470 4.020218 TGTTTCTTGATCGATCCACCTCTT 60.020 41.667 22.31 0.00 0.00 2.85
9187 9471 4.392921 TTCTTGATCGATCCACCTCTTC 57.607 45.455 22.31 0.00 0.00 2.87
9188 9472 2.359214 TCTTGATCGATCCACCTCTTCG 59.641 50.000 22.31 0.00 0.00 3.79
9189 9473 1.763968 TGATCGATCCACCTCTTCGT 58.236 50.000 22.31 0.00 34.60 3.85
9190 9474 1.676529 TGATCGATCCACCTCTTCGTC 59.323 52.381 22.31 0.00 34.60 4.20
9191 9475 1.676529 GATCGATCCACCTCTTCGTCA 59.323 52.381 14.76 0.00 34.60 4.35
9192 9476 1.541379 TCGATCCACCTCTTCGTCAA 58.459 50.000 0.00 0.00 34.60 3.18
9193 9477 1.890489 TCGATCCACCTCTTCGTCAAA 59.110 47.619 0.00 0.00 34.60 2.69
9194 9478 2.496070 TCGATCCACCTCTTCGTCAAAT 59.504 45.455 0.00 0.00 34.60 2.32
9195 9479 2.604914 CGATCCACCTCTTCGTCAAATG 59.395 50.000 0.00 0.00 0.00 2.32
9196 9480 1.808411 TCCACCTCTTCGTCAAATGC 58.192 50.000 0.00 0.00 0.00 3.56
9197 9481 0.804989 CCACCTCTTCGTCAAATGCC 59.195 55.000 0.00 0.00 0.00 4.40
9198 9482 0.443869 CACCTCTTCGTCAAATGCCG 59.556 55.000 0.00 0.00 0.00 5.69
9199 9483 0.034896 ACCTCTTCGTCAAATGCCGT 59.965 50.000 0.00 0.00 0.00 5.68
9200 9484 1.156736 CCTCTTCGTCAAATGCCGTT 58.843 50.000 0.00 0.00 0.00 4.44
9201 9485 1.535462 CCTCTTCGTCAAATGCCGTTT 59.465 47.619 0.00 0.00 0.00 3.60
9202 9486 2.412847 CCTCTTCGTCAAATGCCGTTTC 60.413 50.000 0.00 0.00 0.00 2.78
9203 9487 2.214347 TCTTCGTCAAATGCCGTTTCA 58.786 42.857 0.00 0.00 0.00 2.69
9204 9488 2.032377 TCTTCGTCAAATGCCGTTTCAC 60.032 45.455 0.00 0.00 0.00 3.18
9205 9489 0.589223 TCGTCAAATGCCGTTTCACC 59.411 50.000 0.00 0.00 0.00 4.02
9206 9490 0.309302 CGTCAAATGCCGTTTCACCA 59.691 50.000 0.00 0.00 0.00 4.17
9207 9491 1.068610 CGTCAAATGCCGTTTCACCAT 60.069 47.619 0.00 0.00 0.00 3.55
9208 9492 2.595386 GTCAAATGCCGTTTCACCATC 58.405 47.619 0.00 0.00 0.00 3.51
9209 9493 2.030363 GTCAAATGCCGTTTCACCATCA 60.030 45.455 0.00 0.00 0.00 3.07
9210 9494 2.228582 TCAAATGCCGTTTCACCATCAG 59.771 45.455 0.00 0.00 0.00 2.90
9211 9495 1.176527 AATGCCGTTTCACCATCAGG 58.823 50.000 0.00 0.00 42.21 3.86
9212 9496 1.315257 ATGCCGTTTCACCATCAGGC 61.315 55.000 0.00 0.00 44.38 4.85
9213 9497 1.675641 GCCGTTTCACCATCAGGCT 60.676 57.895 0.00 0.00 41.21 4.58
9214 9498 1.244019 GCCGTTTCACCATCAGGCTT 61.244 55.000 0.00 0.00 41.21 4.35
9215 9499 1.247567 CCGTTTCACCATCAGGCTTT 58.752 50.000 0.00 0.00 39.06 3.51
9216 9500 1.068333 CCGTTTCACCATCAGGCTTTG 60.068 52.381 0.00 0.00 39.06 2.77
9217 9501 1.068333 CGTTTCACCATCAGGCTTTGG 60.068 52.381 10.92 10.92 39.06 3.28
9218 9502 2.238521 GTTTCACCATCAGGCTTTGGA 58.761 47.619 17.84 0.00 39.06 3.53
9219 9503 2.627699 GTTTCACCATCAGGCTTTGGAA 59.372 45.455 17.84 2.59 39.06 3.53
9220 9504 1.909700 TCACCATCAGGCTTTGGAAC 58.090 50.000 17.84 0.00 39.06 3.62
9221 9505 1.144708 TCACCATCAGGCTTTGGAACA 59.855 47.619 17.84 1.23 39.06 3.18
9222 9506 2.173519 CACCATCAGGCTTTGGAACAT 58.826 47.619 17.84 0.00 36.70 2.71
9223 9507 2.094390 CACCATCAGGCTTTGGAACATG 60.094 50.000 17.84 4.28 36.70 3.21
9224 9508 1.479323 CCATCAGGCTTTGGAACATGG 59.521 52.381 7.35 0.00 39.30 3.66
9225 9509 2.173519 CATCAGGCTTTGGAACATGGT 58.826 47.619 0.00 0.00 39.30 3.55
9226 9510 1.909700 TCAGGCTTTGGAACATGGTC 58.090 50.000 0.73 0.73 39.30 4.02
9227 9511 1.144708 TCAGGCTTTGGAACATGGTCA 59.855 47.619 13.90 0.00 39.30 4.02
9228 9512 2.173519 CAGGCTTTGGAACATGGTCAT 58.826 47.619 13.90 0.00 39.30 3.06
9229 9513 2.564062 CAGGCTTTGGAACATGGTCATT 59.436 45.455 13.90 0.00 39.30 2.57
9230 9514 2.564062 AGGCTTTGGAACATGGTCATTG 59.436 45.455 13.90 0.58 39.30 2.82
9231 9515 2.340337 GCTTTGGAACATGGTCATTGC 58.660 47.619 13.90 7.26 39.30 3.56
9232 9516 2.288948 GCTTTGGAACATGGTCATTGCA 60.289 45.455 13.90 0.00 39.30 4.08
9233 9517 3.803021 GCTTTGGAACATGGTCATTGCAA 60.803 43.478 13.90 0.00 39.30 4.08
9234 9518 3.663995 TTGGAACATGGTCATTGCAAG 57.336 42.857 13.90 0.00 39.30 4.01
9235 9519 2.874014 TGGAACATGGTCATTGCAAGA 58.126 42.857 13.90 0.00 0.00 3.02
9236 9520 3.433343 TGGAACATGGTCATTGCAAGAT 58.567 40.909 13.90 0.00 0.00 2.40
9237 9521 4.598022 TGGAACATGGTCATTGCAAGATA 58.402 39.130 13.90 0.00 0.00 1.98
9238 9522 5.202765 TGGAACATGGTCATTGCAAGATAT 58.797 37.500 13.90 0.15 0.00 1.63
9239 9523 5.068067 TGGAACATGGTCATTGCAAGATATG 59.932 40.000 13.90 12.66 0.00 1.78
9240 9524 5.508489 GGAACATGGTCATTGCAAGATATGG 60.508 44.000 13.90 0.00 0.00 2.74
9241 9525 3.893200 ACATGGTCATTGCAAGATATGGG 59.107 43.478 4.94 0.00 0.00 4.00
9242 9526 2.309613 TGGTCATTGCAAGATATGGGC 58.690 47.619 4.94 0.00 0.00 5.36
9243 9527 2.091720 TGGTCATTGCAAGATATGGGCT 60.092 45.455 4.94 0.00 0.00 5.19
9244 9528 2.961062 GGTCATTGCAAGATATGGGCTT 59.039 45.455 4.94 0.00 0.00 4.35
9245 9529 3.243636 GGTCATTGCAAGATATGGGCTTG 60.244 47.826 4.94 0.00 44.22 4.01
9246 9530 3.382546 GTCATTGCAAGATATGGGCTTGT 59.617 43.478 4.94 0.00 43.50 3.16
9247 9531 3.382227 TCATTGCAAGATATGGGCTTGTG 59.618 43.478 4.94 0.00 43.50 3.33
9248 9532 1.105457 TGCAAGATATGGGCTTGTGC 58.895 50.000 0.00 0.00 43.50 4.57
9249 9533 1.105457 GCAAGATATGGGCTTGTGCA 58.895 50.000 0.00 0.00 43.50 4.57
9250 9534 1.202336 GCAAGATATGGGCTTGTGCAC 60.202 52.381 10.75 10.75 43.50 4.57
9256 9540 4.023137 GGGCTTGTGCACATGGAT 57.977 55.556 28.02 0.00 43.35 3.41
9257 9541 3.189568 GGGCTTGTGCACATGGATA 57.810 52.632 28.02 10.94 43.35 2.59
9258 9542 0.740737 GGGCTTGTGCACATGGATAC 59.259 55.000 28.02 14.72 43.35 2.24
9259 9543 0.740737 GGCTTGTGCACATGGATACC 59.259 55.000 28.02 18.86 41.91 2.73
9260 9544 1.462616 GCTTGTGCACATGGATACCA 58.537 50.000 28.02 8.87 39.41 3.25
9261 9545 1.133025 GCTTGTGCACATGGATACCAC 59.867 52.381 28.02 10.62 36.18 4.16
9262 9546 1.745087 CTTGTGCACATGGATACCACC 59.255 52.381 22.39 0.00 35.80 4.61
9263 9547 0.392327 TGTGCACATGGATACCACCG 60.392 55.000 17.42 0.00 35.80 4.94
9264 9548 0.392461 GTGCACATGGATACCACCGT 60.392 55.000 13.17 0.00 35.80 4.83
9265 9549 0.326595 TGCACATGGATACCACCGTT 59.673 50.000 0.00 0.00 35.80 4.44
9266 9550 1.271652 TGCACATGGATACCACCGTTT 60.272 47.619 0.00 0.00 35.80 3.60
9267 9551 1.132262 GCACATGGATACCACCGTTTG 59.868 52.381 0.00 0.00 35.80 2.93
9276 9560 2.639970 CCACCGTTTGGCATCTTCA 58.360 52.632 0.00 0.00 39.07 3.02
9277 9561 0.240945 CCACCGTTTGGCATCTTCAC 59.759 55.000 0.00 0.00 39.07 3.18
9278 9562 0.110238 CACCGTTTGGCATCTTCACG 60.110 55.000 0.00 0.00 39.70 4.35
9279 9563 0.250124 ACCGTTTGGCATCTTCACGA 60.250 50.000 0.00 0.00 39.70 4.35
9280 9564 0.443869 CCGTTTGGCATCTTCACGAG 59.556 55.000 0.00 0.00 32.51 4.18
9281 9565 1.148310 CGTTTGGCATCTTCACGAGT 58.852 50.000 0.00 0.00 32.51 4.18
9282 9566 1.126846 CGTTTGGCATCTTCACGAGTC 59.873 52.381 0.00 0.00 32.51 3.36
9283 9567 1.126846 GTTTGGCATCTTCACGAGTCG 59.873 52.381 11.85 11.85 0.00 4.18
9284 9568 0.601057 TTGGCATCTTCACGAGTCGA 59.399 50.000 21.50 0.00 0.00 4.20
9285 9569 0.817654 TGGCATCTTCACGAGTCGAT 59.182 50.000 21.50 0.00 0.00 3.59
9286 9570 1.204704 TGGCATCTTCACGAGTCGATT 59.795 47.619 21.50 0.00 0.00 3.34
9287 9571 1.590238 GGCATCTTCACGAGTCGATTG 59.410 52.381 21.50 8.28 0.00 2.67
9288 9572 1.590238 GCATCTTCACGAGTCGATTGG 59.410 52.381 21.50 5.76 0.00 3.16
9289 9573 2.881074 CATCTTCACGAGTCGATTGGT 58.119 47.619 21.50 0.00 0.00 3.67
9290 9574 2.347697 TCTTCACGAGTCGATTGGTG 57.652 50.000 21.50 15.43 0.00 4.17
9291 9575 1.067846 TCTTCACGAGTCGATTGGTGG 60.068 52.381 21.50 7.82 0.00 4.61
9292 9576 0.037697 TTCACGAGTCGATTGGTGGG 60.038 55.000 21.50 0.00 0.00 4.61
9293 9577 0.896479 TCACGAGTCGATTGGTGGGA 60.896 55.000 21.50 2.36 0.00 4.37
9294 9578 0.175760 CACGAGTCGATTGGTGGGAT 59.824 55.000 21.50 0.00 0.00 3.85
9295 9579 1.407618 CACGAGTCGATTGGTGGGATA 59.592 52.381 21.50 0.00 0.00 2.59
9296 9580 1.681793 ACGAGTCGATTGGTGGGATAG 59.318 52.381 21.50 0.00 0.00 2.08
9297 9581 1.000163 CGAGTCGATTGGTGGGATAGG 60.000 57.143 6.73 0.00 0.00 2.57
9298 9582 2.317040 GAGTCGATTGGTGGGATAGGA 58.683 52.381 0.00 0.00 0.00 2.94
9299 9583 2.297597 GAGTCGATTGGTGGGATAGGAG 59.702 54.545 0.00 0.00 0.00 3.69
9300 9584 2.091278 AGTCGATTGGTGGGATAGGAGA 60.091 50.000 0.00 0.00 0.00 3.71
9301 9585 2.698797 GTCGATTGGTGGGATAGGAGAA 59.301 50.000 0.00 0.00 0.00 2.87
9302 9586 2.698797 TCGATTGGTGGGATAGGAGAAC 59.301 50.000 0.00 0.00 0.00 3.01
9303 9587 2.224305 CGATTGGTGGGATAGGAGAACC 60.224 54.545 0.00 0.00 0.00 3.62
9304 9588 1.200519 TTGGTGGGATAGGAGAACCG 58.799 55.000 0.00 0.00 41.83 4.44
9305 9589 0.337082 TGGTGGGATAGGAGAACCGA 59.663 55.000 0.00 0.00 41.83 4.69
9306 9590 0.751452 GGTGGGATAGGAGAACCGAC 59.249 60.000 0.00 0.00 41.83 4.79
9307 9591 1.481871 GTGGGATAGGAGAACCGACA 58.518 55.000 0.00 0.00 41.83 4.35
9308 9592 2.040178 GTGGGATAGGAGAACCGACAT 58.960 52.381 0.00 0.00 41.83 3.06
9309 9593 2.039418 TGGGATAGGAGAACCGACATG 58.961 52.381 0.00 0.00 41.83 3.21
9310 9594 2.317040 GGGATAGGAGAACCGACATGA 58.683 52.381 0.00 0.00 41.83 3.07
9311 9595 2.036089 GGGATAGGAGAACCGACATGAC 59.964 54.545 0.00 0.00 41.83 3.06
9312 9596 2.693591 GGATAGGAGAACCGACATGACA 59.306 50.000 0.00 0.00 41.83 3.58
9313 9597 3.132289 GGATAGGAGAACCGACATGACAA 59.868 47.826 0.00 0.00 41.83 3.18
9314 9598 4.382685 GGATAGGAGAACCGACATGACAAA 60.383 45.833 0.00 0.00 41.83 2.83
9315 9599 3.703001 AGGAGAACCGACATGACAAAT 57.297 42.857 0.00 0.00 41.83 2.32
9316 9600 3.600388 AGGAGAACCGACATGACAAATC 58.400 45.455 0.00 0.00 41.83 2.17
9317 9601 2.678336 GGAGAACCGACATGACAAATCC 59.322 50.000 0.00 0.00 0.00 3.01
9318 9602 3.600388 GAGAACCGACATGACAAATCCT 58.400 45.455 0.00 0.00 0.00 3.24
9319 9603 4.382685 GGAGAACCGACATGACAAATCCTA 60.383 45.833 0.00 0.00 0.00 2.94
9320 9604 5.160607 AGAACCGACATGACAAATCCTAA 57.839 39.130 0.00 0.00 0.00 2.69
9321 9605 4.935808 AGAACCGACATGACAAATCCTAAC 59.064 41.667 0.00 0.00 0.00 2.34
9322 9606 4.280436 ACCGACATGACAAATCCTAACA 57.720 40.909 0.00 0.00 0.00 2.41
9323 9607 4.253685 ACCGACATGACAAATCCTAACAG 58.746 43.478 0.00 0.00 0.00 3.16
9324 9608 3.623060 CCGACATGACAAATCCTAACAGG 59.377 47.826 0.00 0.00 36.46 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.817709 TGATAGCGATGAACCATGTGA 57.182 42.857 0.00 0.00 0.00 3.58
29 34 5.924356 TCATAGATTGTCCGGAATGCTTAA 58.076 37.500 5.23 0.00 0.00 1.85
37 42 1.067060 CGTGCTCATAGATTGTCCGGA 59.933 52.381 0.00 0.00 0.00 5.14
124 130 4.261698 CCTTGTGCTTGTGTTGATTCATGA 60.262 41.667 0.00 0.00 0.00 3.07
257 263 4.603131 AGATGCATGGTTGATTAGTGGTT 58.397 39.130 2.46 0.00 0.00 3.67
320 327 5.665360 TGAGTTCAATCCCCCTTTTTCTTTT 59.335 36.000 0.00 0.00 0.00 2.27
322 329 4.588951 GTGAGTTCAATCCCCCTTTTTCTT 59.411 41.667 0.00 0.00 0.00 2.52
326 333 3.140144 TCTGTGAGTTCAATCCCCCTTTT 59.860 43.478 0.00 0.00 0.00 2.27
378 385 3.426426 GCGTTGATCTTCTACGACTGTCT 60.426 47.826 14.01 0.00 45.71 3.41
405 412 2.649034 GTCGACGCTCCTTCACCA 59.351 61.111 0.00 0.00 0.00 4.17
439 446 0.176910 TAACCGGCGCATCTTCATCA 59.823 50.000 10.83 0.00 0.00 3.07
455 462 2.092882 GCACCGACGAGCAGGTAAC 61.093 63.158 0.00 0.00 39.00 2.50
578 585 1.847328 AAAATCGGCGGGAGGATTTT 58.153 45.000 7.21 8.71 44.02 1.82
628 636 0.599204 TTCTTTCCTCGTGCGACCAC 60.599 55.000 0.00 0.00 38.62 4.16
695 704 0.395724 GGGGAAATGCCTGAATCGGT 60.396 55.000 0.00 0.00 36.66 4.69
707 716 2.537959 ACCAGGCCCAGGGGAAAT 60.538 61.111 15.74 0.00 37.50 2.17
724 733 2.762745 GGAACTTAAAGCACGTCCAGA 58.237 47.619 0.00 0.00 0.00 3.86
827 836 1.883926 GATTAGGGCGTGTTTGGTTGT 59.116 47.619 0.00 0.00 0.00 3.32
854 863 5.175673 GGAGTTTAAATTTCTGTGCACTTGC 59.824 40.000 19.41 0.00 42.50 4.01
926 935 1.759445 ACTGCGACATGATAGAGCCTT 59.241 47.619 0.00 0.00 0.00 4.35
1496 1513 5.273944 TCGTGATGATAAGATGACTGTTCG 58.726 41.667 0.00 0.00 0.00 3.95
1528 1548 0.413832 AGTAGGGAGCAGGGAACAGA 59.586 55.000 0.00 0.00 0.00 3.41
1549 1569 4.038162 AGAGTATTTCGTAGGAGATGTGCC 59.962 45.833 0.00 0.00 0.00 5.01
1585 1605 4.155462 TGCACGTACTCTAAGGAACACTAG 59.845 45.833 0.00 0.00 0.00 2.57
1600 1620 0.580104 GGTCAACACTGTGCACGTAC 59.420 55.000 13.13 7.90 0.00 3.67
1603 1623 1.351707 GTGGTCAACACTGTGCACG 59.648 57.895 13.13 9.67 46.72 5.34
1617 1637 1.681666 CCATCAGCTGGTCAGTGGT 59.318 57.895 15.13 0.00 40.49 4.16
1618 1638 4.631773 CCATCAGCTGGTCAGTGG 57.368 61.111 15.13 10.71 40.49 4.00
1634 1661 5.813080 ATTTGTAACTAGGAAATCACGCC 57.187 39.130 0.00 0.00 0.00 5.68
1655 1682 1.708551 TCACTCCTTTTCGGGGGAAAT 59.291 47.619 0.00 0.00 37.70 2.17
1688 1716 2.700371 TCAATCGATGCATAGGTCAGGT 59.300 45.455 0.00 0.00 0.00 4.00
1889 1919 7.931407 TCCAATGATATTATTGTCGCTACAGTT 59.069 33.333 16.48 0.00 36.83 3.16
1890 1920 7.441836 TCCAATGATATTATTGTCGCTACAGT 58.558 34.615 16.48 0.00 36.83 3.55
1933 1963 7.989741 TGTCACCAAAAATTATGTTGTTGGATT 59.010 29.630 17.06 0.00 41.05 3.01
1943 1973 8.933807 TGTTAATGCATGTCACCAAAAATTATG 58.066 29.630 0.00 0.00 0.00 1.90
1953 1983 8.028938 ACTAGAAAAATGTTAATGCATGTCACC 58.971 33.333 0.00 0.00 0.00 4.02
2014 2044 4.847990 TCCGGGTTTATTAGTCACCAAT 57.152 40.909 0.00 0.00 31.50 3.16
2015 2045 4.519213 CATCCGGGTTTATTAGTCACCAA 58.481 43.478 0.00 0.00 31.50 3.67
2036 2066 4.959839 TGCATCAGTTGTATACTACCTCCA 59.040 41.667 12.93 2.88 34.56 3.86
2068 2098 0.911769 TGTCCTGGTCCAGCAATAGG 59.088 55.000 13.99 0.00 0.00 2.57
2122 2152 2.037136 CGCTCCAGCAGTTTCCCTG 61.037 63.158 0.00 0.00 44.53 4.45
2141 2171 4.438148 AGGGGAAATTGACAACAAAAACG 58.562 39.130 0.00 0.00 39.54 3.60
2192 2222 2.744243 GCATCTCCAGCAGCTCCCT 61.744 63.158 0.00 0.00 0.00 4.20
2215 2245 2.029470 GGCATGGGATTCTCTAGTCTCG 60.029 54.545 0.00 0.00 0.00 4.04
2233 2263 4.994471 CTGCAGCGTGTGGAGGCA 62.994 66.667 0.00 0.00 40.89 4.75
2279 2309 2.026641 CCTGCAGGTTATTCATGTGGG 58.973 52.381 25.53 0.00 0.00 4.61
2389 2426 2.818751 TTGGCTACCTGGGGTAAATG 57.181 50.000 0.00 0.00 37.76 2.32
2564 2601 0.883833 AAAGACAATCTGGCCAAGCG 59.116 50.000 7.01 0.00 0.00 4.68
2761 2800 6.605471 TCTGAAACAGAGAATTAGTAGCCA 57.395 37.500 0.00 0.00 35.39 4.75
2873 2912 2.361610 CCGGCAGCAAAGGACCAT 60.362 61.111 0.00 0.00 0.00 3.55
3191 3230 8.738645 AACCTTGTTATAGGCTAAGATTCAAG 57.261 34.615 0.00 9.22 38.99 3.02
3696 3896 4.970662 TTGCTGCTAATGAAATCAGACC 57.029 40.909 0.00 0.00 0.00 3.85
4258 4459 5.692204 CACAAAAGGTAAACACACACACAAA 59.308 36.000 0.00 0.00 0.00 2.83
4259 4460 5.009710 TCACAAAAGGTAAACACACACACAA 59.990 36.000 0.00 0.00 0.00 3.33
4277 4478 8.659925 AAAGAAATTGCATGTTACATCACAAA 57.340 26.923 12.41 0.00 0.00 2.83
4599 4805 0.958382 GCATCACGGGTAAAGGCACA 60.958 55.000 0.00 0.00 0.00 4.57
4956 5162 2.665165 AGGTGAGCAAATTGTTCCACA 58.335 42.857 7.35 0.00 0.00 4.17
4962 5168 5.789643 AAACATGTAGGTGAGCAAATTGT 57.210 34.783 0.00 0.00 0.00 2.71
4970 5176 9.665264 GAAAAAGAAAGTAAACATGTAGGTGAG 57.335 33.333 0.00 0.00 0.00 3.51
4989 5195 9.796120 AAACGAAAACAGATACATTGAAAAAGA 57.204 25.926 0.00 0.00 0.00 2.52
5812 6020 3.388024 GGTATAGCTCCACATGTTCCAGA 59.612 47.826 0.00 0.00 0.00 3.86
5915 6123 6.192970 TCAGTTCAAAAGGAGAGGAAGAAT 57.807 37.500 0.00 0.00 0.00 2.40
5959 6167 6.665680 CAGGGTAGTAGATTCACTATATGCCT 59.334 42.308 0.00 0.00 33.71 4.75
6213 6422 3.053896 GCCTACAACCGGCACACC 61.054 66.667 0.00 0.00 46.77 4.16
6218 6427 3.262448 TTGGAGGCCTACAACCGGC 62.262 63.158 27.41 0.00 46.83 6.13
6219 6428 1.078426 CTTGGAGGCCTACAACCGG 60.078 63.158 27.41 13.74 28.90 5.28
6220 6429 1.745489 GCTTGGAGGCCTACAACCG 60.745 63.158 27.41 18.85 28.90 4.44
6221 6430 0.678048 CTGCTTGGAGGCCTACAACC 60.678 60.000 27.41 20.92 28.90 3.77
6222 6431 0.678048 CCTGCTTGGAGGCCTACAAC 60.678 60.000 27.41 21.95 38.35 3.32
6223 6432 1.133809 ACCTGCTTGGAGGCCTACAA 61.134 55.000 28.95 28.95 36.46 2.41
6224 6433 1.538876 ACCTGCTTGGAGGCCTACA 60.539 57.895 15.85 15.85 36.46 2.74
6225 6434 1.078143 CACCTGCTTGGAGGCCTAC 60.078 63.158 8.55 8.55 36.46 3.18
6226 6435 1.538876 ACACCTGCTTGGAGGCCTA 60.539 57.895 4.42 0.00 36.46 3.93
6227 6436 2.856000 ACACCTGCTTGGAGGCCT 60.856 61.111 3.86 3.86 36.46 5.19
6228 6437 2.674380 CACACCTGCTTGGAGGCC 60.674 66.667 8.11 0.00 36.46 5.19
6229 6438 3.368571 GCACACCTGCTTGGAGGC 61.369 66.667 8.11 0.95 40.63 4.70
6230 6439 2.674380 GGCACACCTGCTTGGAGG 60.674 66.667 6.63 6.63 43.66 4.30
6231 6440 3.052082 CGGCACACCTGCTTGGAG 61.052 66.667 3.40 0.00 43.66 3.86
6232 6441 4.641645 CCGGCACACCTGCTTGGA 62.642 66.667 0.00 0.00 43.66 3.53
6237 6446 4.697756 TACAGCCGGCACACCTGC 62.698 66.667 31.54 0.00 45.96 4.85
6238 6447 2.434884 CTACAGCCGGCACACCTG 60.435 66.667 31.54 20.36 33.22 4.00
6239 6448 3.706373 CCTACAGCCGGCACACCT 61.706 66.667 31.54 3.61 0.00 4.00
6277 6486 1.287217 AAAAATGGGCATGCCATGGA 58.713 45.000 36.56 18.18 37.98 3.41
6316 6525 9.585099 GATTTCATGGTGCAATACATTTTCTAA 57.415 29.630 0.00 0.00 0.00 2.10
6328 6537 3.189080 CGTCTTGAGATTTCATGGTGCAA 59.811 43.478 0.00 0.00 32.27 4.08
6331 6540 4.929211 TGTACGTCTTGAGATTTCATGGTG 59.071 41.667 0.00 0.00 32.27 4.17
6549 6758 4.946157 AGTTCCAAGCAATTACATCTCCAG 59.054 41.667 0.00 0.00 0.00 3.86
6821 7034 0.610232 CCACCTTTTCAGCTCCCTGG 60.610 60.000 0.00 0.00 39.61 4.45
7045 7291 6.630676 TGCGCTAATGACAAAAATTTCATC 57.369 33.333 9.73 0.00 30.96 2.92
7051 7297 4.082571 AGCTCTTGCGCTAATGACAAAAAT 60.083 37.500 9.73 0.00 45.42 1.82
7066 7312 2.470983 AGGAACTTCAGAGCTCTTGC 57.529 50.000 15.27 4.43 27.25 4.01
7145 7391 3.683822 GTCAGCACTTCATTCTCCTTCAG 59.316 47.826 0.00 0.00 0.00 3.02
7185 7431 6.114089 TCATGCAATAAAATGGTTTGGATGG 58.886 36.000 13.81 0.40 44.45 3.51
7242 7488 7.093068 TGGATTATAACTCAACTCCAGCTACAA 60.093 37.037 0.04 0.00 0.00 2.41
7283 7529 2.226330 ACATCGCACAAAGCCTTTACA 58.774 42.857 0.00 0.00 41.38 2.41
7461 7709 7.860373 TGTGTTATACTTCAAACAATCAGCAAC 59.140 33.333 0.00 0.00 37.35 4.17
8027 8275 3.441572 GCTACAGTGCAATGAGAAACCAT 59.558 43.478 22.73 0.00 0.00 3.55
8099 8353 3.172339 TGCCCAAAAGCCTCAATTACAT 58.828 40.909 0.00 0.00 0.00 2.29
8404 8659 4.038162 GGGCTTGACGATGACTCTACTTAT 59.962 45.833 0.00 0.00 0.00 1.73
8427 8682 5.532406 AGATGACCCCATAACAAAATCATCG 59.468 40.000 0.00 0.00 43.61 3.84
8455 8710 2.732001 ACACGAGCAGAAACGTTTTC 57.268 45.000 15.89 7.65 40.76 2.29
8718 8975 4.080413 TGTCCAAGTGATATTGCCTCATCA 60.080 41.667 0.00 0.00 0.00 3.07
8881 9141 5.420409 GACAAAAACGATATCCTGTCCTCT 58.580 41.667 0.00 0.00 0.00 3.69
9092 9376 8.803235 ACTCAAATTGTGTACTATCTACAGTCA 58.197 33.333 0.00 0.00 0.00 3.41
9126 9410 9.778993 CAAATCAGAATGTGAATAGTACCAAAG 57.221 33.333 0.00 0.00 39.19 2.77
9129 9413 8.100164 TGACAAATCAGAATGTGAATAGTACCA 58.900 33.333 0.00 0.00 39.19 3.25
9130 9414 8.492673 TGACAAATCAGAATGTGAATAGTACC 57.507 34.615 0.00 0.00 39.19 3.34
9139 9423 9.037737 ACAAGAAAAATGACAAATCAGAATGTG 57.962 29.630 0.00 0.00 38.57 3.21
9188 9472 2.030363 TGATGGTGAAACGGCATTTGAC 60.030 45.455 0.00 0.00 38.12 3.18
9189 9473 2.228582 CTGATGGTGAAACGGCATTTGA 59.771 45.455 0.00 0.00 38.12 2.69
9190 9474 2.598589 CTGATGGTGAAACGGCATTTG 58.401 47.619 0.00 0.00 38.12 2.32
9191 9475 1.545582 CCTGATGGTGAAACGGCATTT 59.454 47.619 0.00 0.00 38.12 2.32
9192 9476 1.176527 CCTGATGGTGAAACGGCATT 58.823 50.000 0.00 0.00 38.12 3.56
9193 9477 1.315257 GCCTGATGGTGAAACGGCAT 61.315 55.000 0.00 0.00 38.12 4.40
9194 9478 1.971167 GCCTGATGGTGAAACGGCA 60.971 57.895 0.00 0.00 38.12 5.69
9195 9479 1.244019 AAGCCTGATGGTGAAACGGC 61.244 55.000 0.00 0.00 38.12 5.68
9196 9480 1.068333 CAAAGCCTGATGGTGAAACGG 60.068 52.381 0.00 0.00 38.12 4.44
9197 9481 1.068333 CCAAAGCCTGATGGTGAAACG 60.068 52.381 0.00 0.00 38.12 3.60
9198 9482 2.238521 TCCAAAGCCTGATGGTGAAAC 58.761 47.619 0.00 0.00 37.94 2.78
9199 9483 2.627699 GTTCCAAAGCCTGATGGTGAAA 59.372 45.455 0.00 0.00 37.94 2.69
9200 9484 2.238521 GTTCCAAAGCCTGATGGTGAA 58.761 47.619 0.00 0.00 37.94 3.18
9201 9485 1.144708 TGTTCCAAAGCCTGATGGTGA 59.855 47.619 0.00 0.00 37.94 4.02
9202 9486 1.619654 TGTTCCAAAGCCTGATGGTG 58.380 50.000 0.00 0.00 37.94 4.17
9203 9487 2.173519 CATGTTCCAAAGCCTGATGGT 58.826 47.619 0.00 0.00 37.94 3.55
9204 9488 1.479323 CCATGTTCCAAAGCCTGATGG 59.521 52.381 0.00 0.00 38.09 3.51
9205 9489 2.165030 GACCATGTTCCAAAGCCTGATG 59.835 50.000 0.00 0.00 0.00 3.07
9206 9490 2.225091 TGACCATGTTCCAAAGCCTGAT 60.225 45.455 0.00 0.00 0.00 2.90
9207 9491 1.144708 TGACCATGTTCCAAAGCCTGA 59.855 47.619 0.00 0.00 0.00 3.86
9208 9492 1.619654 TGACCATGTTCCAAAGCCTG 58.380 50.000 0.00 0.00 0.00 4.85
9209 9493 2.564062 CAATGACCATGTTCCAAAGCCT 59.436 45.455 0.00 0.00 0.00 4.58
9210 9494 2.932187 GCAATGACCATGTTCCAAAGCC 60.932 50.000 0.00 0.00 0.00 4.35
9211 9495 2.288948 TGCAATGACCATGTTCCAAAGC 60.289 45.455 0.00 0.00 0.00 3.51
9212 9496 3.663995 TGCAATGACCATGTTCCAAAG 57.336 42.857 0.00 0.00 0.00 2.77
9213 9497 3.640498 TCTTGCAATGACCATGTTCCAAA 59.360 39.130 0.00 0.00 0.00 3.28
9214 9498 3.229293 TCTTGCAATGACCATGTTCCAA 58.771 40.909 0.00 0.00 0.00 3.53
9215 9499 2.874014 TCTTGCAATGACCATGTTCCA 58.126 42.857 0.00 0.00 0.00 3.53
9216 9500 5.508489 CCATATCTTGCAATGACCATGTTCC 60.508 44.000 0.00 0.00 0.00 3.62
9217 9501 5.508489 CCCATATCTTGCAATGACCATGTTC 60.508 44.000 0.00 0.00 0.00 3.18
9218 9502 4.342951 CCCATATCTTGCAATGACCATGTT 59.657 41.667 0.00 0.00 0.00 2.71
9219 9503 3.893200 CCCATATCTTGCAATGACCATGT 59.107 43.478 0.00 0.00 0.00 3.21
9220 9504 3.305813 GCCCATATCTTGCAATGACCATG 60.306 47.826 0.00 7.30 0.00 3.66
9221 9505 2.895404 GCCCATATCTTGCAATGACCAT 59.105 45.455 0.00 0.00 0.00 3.55
9222 9506 2.091720 AGCCCATATCTTGCAATGACCA 60.092 45.455 0.00 0.00 0.00 4.02
9223 9507 2.590821 AGCCCATATCTTGCAATGACC 58.409 47.619 0.00 0.00 0.00 4.02
9224 9508 3.382546 ACAAGCCCATATCTTGCAATGAC 59.617 43.478 0.00 0.00 43.40 3.06
9225 9509 3.382227 CACAAGCCCATATCTTGCAATGA 59.618 43.478 0.00 0.00 43.40 2.57
9226 9510 3.713288 CACAAGCCCATATCTTGCAATG 58.287 45.455 0.00 0.00 43.40 2.82
9227 9511 2.101917 GCACAAGCCCATATCTTGCAAT 59.898 45.455 0.00 0.00 43.40 3.56
9228 9512 1.477700 GCACAAGCCCATATCTTGCAA 59.522 47.619 0.00 0.00 43.40 4.08
9229 9513 1.105457 GCACAAGCCCATATCTTGCA 58.895 50.000 2.97 0.00 43.40 4.08
9230 9514 1.105457 TGCACAAGCCCATATCTTGC 58.895 50.000 2.97 0.00 43.40 4.01
9231 9515 2.093890 TGTGCACAAGCCCATATCTTG 58.906 47.619 19.28 1.63 44.71 3.02
9232 9516 2.512692 TGTGCACAAGCCCATATCTT 57.487 45.000 19.28 0.00 41.13 2.40
9233 9517 2.304092 CATGTGCACAAGCCCATATCT 58.696 47.619 25.72 0.00 36.68 1.98
9234 9518 1.338973 CCATGTGCACAAGCCCATATC 59.661 52.381 25.72 0.00 36.68 1.63
9235 9519 1.063792 TCCATGTGCACAAGCCCATAT 60.064 47.619 25.72 0.68 36.68 1.78
9236 9520 0.330941 TCCATGTGCACAAGCCCATA 59.669 50.000 25.72 2.45 36.68 2.74
9237 9521 0.324923 ATCCATGTGCACAAGCCCAT 60.325 50.000 25.72 8.47 39.54 4.00
9238 9522 0.330941 TATCCATGTGCACAAGCCCA 59.669 50.000 25.72 6.67 41.13 5.36
9239 9523 0.740737 GTATCCATGTGCACAAGCCC 59.259 55.000 25.72 6.24 41.13 5.19
9240 9524 0.740737 GGTATCCATGTGCACAAGCC 59.259 55.000 25.72 12.00 41.13 4.35
9241 9525 1.133025 GTGGTATCCATGTGCACAAGC 59.867 52.381 25.72 16.76 37.25 4.01
9242 9526 1.745087 GGTGGTATCCATGTGCACAAG 59.255 52.381 25.72 20.04 35.28 3.16
9243 9527 1.832883 GGTGGTATCCATGTGCACAA 58.167 50.000 25.72 8.09 35.28 3.33
9244 9528 0.392327 CGGTGGTATCCATGTGCACA 60.392 55.000 24.08 24.08 35.28 4.57
9245 9529 0.392461 ACGGTGGTATCCATGTGCAC 60.392 55.000 10.75 10.75 35.28 4.57
9246 9530 0.326595 AACGGTGGTATCCATGTGCA 59.673 50.000 0.00 0.00 35.28 4.57
9247 9531 1.132262 CAAACGGTGGTATCCATGTGC 59.868 52.381 0.00 0.00 35.28 4.57
9248 9532 1.742831 CCAAACGGTGGTATCCATGTG 59.257 52.381 0.00 0.00 43.20 3.21
9249 9533 2.122783 CCAAACGGTGGTATCCATGT 57.877 50.000 0.00 0.00 43.20 3.21
9259 9543 0.110238 CGTGAAGATGCCAAACGGTG 60.110 55.000 0.00 0.00 0.00 4.94
9260 9544 0.250124 TCGTGAAGATGCCAAACGGT 60.250 50.000 0.00 0.00 35.08 4.83
9261 9545 0.443869 CTCGTGAAGATGCCAAACGG 59.556 55.000 0.00 0.00 35.08 4.44
9262 9546 1.126846 GACTCGTGAAGATGCCAAACG 59.873 52.381 0.00 0.00 35.64 3.60
9263 9547 1.126846 CGACTCGTGAAGATGCCAAAC 59.873 52.381 0.00 0.00 0.00 2.93
9264 9548 1.000394 TCGACTCGTGAAGATGCCAAA 60.000 47.619 0.00 0.00 0.00 3.28
9265 9549 0.601057 TCGACTCGTGAAGATGCCAA 59.399 50.000 0.00 0.00 0.00 4.52
9266 9550 0.817654 ATCGACTCGTGAAGATGCCA 59.182 50.000 0.00 0.00 0.00 4.92
9267 9551 1.590238 CAATCGACTCGTGAAGATGCC 59.410 52.381 0.00 0.00 0.00 4.40
9268 9552 1.590238 CCAATCGACTCGTGAAGATGC 59.410 52.381 0.00 0.00 0.00 3.91
9269 9553 2.600420 CACCAATCGACTCGTGAAGATG 59.400 50.000 0.00 0.00 0.00 2.90
9270 9554 2.417379 CCACCAATCGACTCGTGAAGAT 60.417 50.000 8.69 0.00 0.00 2.40
9271 9555 1.067846 CCACCAATCGACTCGTGAAGA 60.068 52.381 8.69 0.00 0.00 2.87
9272 9556 1.350193 CCACCAATCGACTCGTGAAG 58.650 55.000 8.69 0.00 0.00 3.02
9273 9557 0.037697 CCCACCAATCGACTCGTGAA 60.038 55.000 8.69 0.00 0.00 3.18
9274 9558 0.896479 TCCCACCAATCGACTCGTGA 60.896 55.000 8.69 0.00 0.00 4.35
9275 9559 0.175760 ATCCCACCAATCGACTCGTG 59.824 55.000 0.00 0.00 0.00 4.35
9276 9560 1.681793 CTATCCCACCAATCGACTCGT 59.318 52.381 0.00 0.00 0.00 4.18
9277 9561 1.000163 CCTATCCCACCAATCGACTCG 60.000 57.143 0.00 0.00 0.00 4.18
9278 9562 2.297597 CTCCTATCCCACCAATCGACTC 59.702 54.545 0.00 0.00 0.00 3.36
9279 9563 2.091278 TCTCCTATCCCACCAATCGACT 60.091 50.000 0.00 0.00 0.00 4.18
9280 9564 2.317040 TCTCCTATCCCACCAATCGAC 58.683 52.381 0.00 0.00 0.00 4.20
9281 9565 2.698797 GTTCTCCTATCCCACCAATCGA 59.301 50.000 0.00 0.00 0.00 3.59
9282 9566 2.224305 GGTTCTCCTATCCCACCAATCG 60.224 54.545 0.00 0.00 0.00 3.34
9283 9567 2.224305 CGGTTCTCCTATCCCACCAATC 60.224 54.545 0.00 0.00 0.00 2.67
9284 9568 1.768870 CGGTTCTCCTATCCCACCAAT 59.231 52.381 0.00 0.00 0.00 3.16
9285 9569 1.200519 CGGTTCTCCTATCCCACCAA 58.799 55.000 0.00 0.00 0.00 3.67
9286 9570 0.337082 TCGGTTCTCCTATCCCACCA 59.663 55.000 0.00 0.00 0.00 4.17
9287 9571 0.751452 GTCGGTTCTCCTATCCCACC 59.249 60.000 0.00 0.00 0.00 4.61
9288 9572 1.481871 TGTCGGTTCTCCTATCCCAC 58.518 55.000 0.00 0.00 0.00 4.61
9289 9573 2.039418 CATGTCGGTTCTCCTATCCCA 58.961 52.381 0.00 0.00 0.00 4.37
9290 9574 2.036089 GTCATGTCGGTTCTCCTATCCC 59.964 54.545 0.00 0.00 0.00 3.85
9291 9575 2.693591 TGTCATGTCGGTTCTCCTATCC 59.306 50.000 0.00 0.00 0.00 2.59
9292 9576 4.386867 TTGTCATGTCGGTTCTCCTATC 57.613 45.455 0.00 0.00 0.00 2.08
9293 9577 4.819105 TTTGTCATGTCGGTTCTCCTAT 57.181 40.909 0.00 0.00 0.00 2.57
9294 9578 4.382685 GGATTTGTCATGTCGGTTCTCCTA 60.383 45.833 0.00 0.00 0.00 2.94
9295 9579 3.600388 GATTTGTCATGTCGGTTCTCCT 58.400 45.455 0.00 0.00 0.00 3.69
9296 9580 2.678336 GGATTTGTCATGTCGGTTCTCC 59.322 50.000 0.00 0.00 0.00 3.71
9297 9581 3.600388 AGGATTTGTCATGTCGGTTCTC 58.400 45.455 0.00 0.00 0.00 2.87
9298 9582 3.703001 AGGATTTGTCATGTCGGTTCT 57.297 42.857 0.00 0.00 0.00 3.01
9299 9583 4.693566 TGTTAGGATTTGTCATGTCGGTTC 59.306 41.667 0.00 0.00 0.00 3.62
9300 9584 4.647611 TGTTAGGATTTGTCATGTCGGTT 58.352 39.130 0.00 0.00 0.00 4.44
9301 9585 4.253685 CTGTTAGGATTTGTCATGTCGGT 58.746 43.478 0.00 0.00 0.00 4.69
9302 9586 3.623060 CCTGTTAGGATTTGTCATGTCGG 59.377 47.826 0.00 0.00 37.67 4.79
9303 9587 4.503910 TCCTGTTAGGATTTGTCATGTCG 58.496 43.478 0.00 0.00 40.06 4.35


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

AutoCloner maintained by Alex Coulton.