Multiple sequence alignment - TraesCS6D01G186800

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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 TraesCS6D01G186800 chr6D 100.000 9438 0 0 1 9438 249438711 249448148 0.000000e+00 17429.0
1 TraesCS6D01G186800 chr6A 97.939 6163 80 12 889 7018 349527921 349521773 0.000000e+00 10634.0
2 TraesCS6D01G186800 chr6A 96.172 1463 43 8 7200 8660 349521772 349520321 0.000000e+00 2379.0
3 TraesCS6D01G186800 chr6A 90.227 880 62 10 1 861 349530945 349530071 0.000000e+00 1127.0
4 TraesCS6D01G186800 chr6A 96.573 496 16 1 2322 2817 349597611 349597117 0.000000e+00 821.0
5 TraesCS6D01G186800 chr6A 85.152 788 79 21 8661 9438 349520010 349519251 0.000000e+00 773.0
6 TraesCS6D01G186800 chr6A 97.436 78 2 0 7016 7093 507082098 507082021 5.950000e-27 134.0
7 TraesCS6D01G186800 chr6A 100.000 28 0 0 865 892 349527964 349527937 1.700000e-02 52.8
8 TraesCS6D01G186800 chr6B 97.443 4693 77 17 2353 7018 337218714 337223390 0.000000e+00 7962.0
9 TraesCS6D01G186800 chr6B 97.496 1358 30 3 7197 8554 337223388 337224741 0.000000e+00 2316.0
10 TraesCS6D01G186800 chr6B 98.869 1149 12 1 1155 2303 337217569 337218716 0.000000e+00 2049.0
11 TraesCS6D01G186800 chr6B 89.841 817 64 11 1 809 337216089 337216894 0.000000e+00 1031.0
12 TraesCS6D01G186800 chr6B 90.000 260 6 1 824 1063 337216955 337217214 1.530000e-82 318.0
13 TraesCS6D01G186800 chr6B 95.868 121 5 0 9310 9430 337230598 337230718 7.480000e-46 196.0
14 TraesCS6D01G186800 chr6B 94.444 126 7 0 8513 8638 337224742 337224867 2.690000e-45 195.0
15 TraesCS6D01G186800 chr7B 99.074 108 1 0 7091 7198 741544745 741544852 2.690000e-45 195.0
16 TraesCS6D01G186800 chr7B 88.372 129 13 2 7072 7198 513956120 513956248 4.560000e-33 154.0
17 TraesCS6D01G186800 chr2D 97.321 112 3 0 7089 7200 460725348 460725237 3.480000e-44 191.0
18 TraesCS6D01G186800 chr2D 92.913 127 6 3 7073 7198 14813400 14813524 2.090000e-41 182.0
19 TraesCS6D01G186800 chr2D 94.118 85 4 1 7009 7093 145927893 145927810 2.770000e-25 128.0
20 TraesCS6D01G186800 chr4D 97.297 111 3 0 7089 7199 8658848 8658738 1.250000e-43 189.0
21 TraesCS6D01G186800 chr4D 93.204 103 7 0 7016 7118 509649341 509649239 1.640000e-32 152.0
22 TraesCS6D01G186800 chr1D 97.297 111 3 0 7088 7198 110734934 110734824 1.250000e-43 189.0
23 TraesCS6D01G186800 chr5B 95.690 116 5 0 7092 7207 679351644 679351529 4.500000e-43 187.0
24 TraesCS6D01G186800 chr5B 97.403 77 2 0 7017 7093 295178305 295178229 2.140000e-26 132.0
25 TraesCS6D01G186800 chr2B 97.273 110 3 0 7089 7198 770902338 770902447 4.500000e-43 187.0
26 TraesCS6D01G186800 chr2B 88.189 127 13 1 7072 7198 213252501 213252377 5.900000e-32 150.0
27 TraesCS6D01G186800 chr2B 93.258 89 3 3 7006 7093 629108638 629108552 2.770000e-25 128.0
28 TraesCS6D01G186800 chr2B 80.460 174 27 6 7031 7198 715017451 715017279 9.950000e-25 126.0
29 TraesCS6D01G186800 chr5D 98.131 107 1 1 7092 7198 302746275 302746170 1.620000e-42 185.0
30 TraesCS6D01G186800 chr3D 95.652 115 5 0 7092 7206 589199570 589199456 1.620000e-42 185.0
31 TraesCS6D01G186800 chr3D 89.764 127 11 2 7078 7204 522772170 522772294 2.730000e-35 161.0
32 TraesCS6D01G186800 chr3D 90.244 123 11 1 7076 7198 530356868 530356747 9.810000e-35 159.0
33 TraesCS6D01G186800 chr3B 90.833 120 9 2 7079 7198 173580762 173580879 9.810000e-35 159.0
34 TraesCS6D01G186800 chr4A 89.516 124 11 1 7078 7201 647845698 647845577 1.270000e-33 156.0
35 TraesCS6D01G186800 chr4A 97.436 78 2 0 7016 7093 584930961 584931038 5.950000e-27 134.0
36 TraesCS6D01G186800 chr4A 96.154 78 3 0 7016 7093 650040978 650040901 2.770000e-25 128.0
37 TraesCS6D01G186800 chr3A 86.765 136 18 0 7072 7207 661930779 661930644 1.640000e-32 152.0
38 TraesCS6D01G186800 chr1A 86.667 135 17 1 6315 6449 547341810 547341677 2.120000e-31 148.0
39 TraesCS6D01G186800 chr7D 96.203 79 3 0 7015 7093 162222208 162222286 7.690000e-26 130.0


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 TraesCS6D01G186800 chr6D 249438711 249448148 9437 False 17429.000000 17429 100.000000 1 9438 1 chr6D.!!$F1 9437
1 TraesCS6D01G186800 chr6A 349519251 349530945 11694 True 2993.160000 10634 93.898000 1 9438 5 chr6A.!!$R3 9437
2 TraesCS6D01G186800 chr6B 337216089 337224867 8778 False 2311.833333 7962 94.682167 1 8638 6 chr6B.!!$F2 8637

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
806 815 0.454285 ACGAACAATCCAATTGCGCG 60.454 50.000 0.0 0.0 43.98 6.86 F
1442 3887 0.038251 CAGCAACAGGAGTGCGAGTA 60.038 55.000 0.0 0.0 0.00 2.59 F
1535 3980 0.263172 GGGTGAGGATGAGAGGAGGA 59.737 60.000 0.0 0.0 0.00 3.71 F
1536 3981 1.703411 GGTGAGGATGAGAGGAGGAG 58.297 60.000 0.0 0.0 0.00 3.69 F
3466 5923 1.269621 CCGTCTCTCGTTTCTGTTGGT 60.270 52.381 0.0 0.0 37.94 3.67 F
3615 6072 3.548745 AATTGGTCATCAGATCAGCGA 57.451 42.857 0.0 0.0 35.99 4.93 F
4269 6726 5.088739 GCAAATGTATTATATCAGGTGCGC 58.911 41.667 0.0 0.0 0.00 6.09 F
5615 8096 0.749454 AGTCCCATCGGCAAAGCATC 60.749 55.000 0.0 0.0 0.00 3.91 F
7030 9517 0.115745 AACCTACTCCCTCCGTTCCA 59.884 55.000 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 4145 1.197949 AGATATCGCACATCCGTCTCG 59.802 52.381 0.00 0.00 0.00 4.04 R
2343 4792 4.641989 ACTTGCAAGAAACTGACTGACATT 59.358 37.500 32.50 1.12 0.00 2.71 R
3466 5923 0.032130 GAGATCGTGATTAGCCGGCA 59.968 55.000 31.54 9.64 0.00 5.69 R
3586 6043 9.994432 CTGATCTGATGACCAATTTAACTAAAC 57.006 33.333 0.00 0.00 0.00 2.01 R
4491 6948 0.033699 GCCTCTCAAGCCCAATCCTT 60.034 55.000 0.00 0.00 0.00 3.36 R
5432 7913 1.973138 CGCAGAAGACATTGCCAAAG 58.027 50.000 0.00 0.00 37.00 2.77 R
5985 8466 1.140816 GCAGTCCTTCGCGGATATTC 58.859 55.000 6.13 0.00 45.44 1.75 R
7089 9576 0.329261 TTCCGAACGGAGGGAGTAGA 59.671 55.000 15.34 0.00 46.06 2.59 R
8982 11844 0.247576 CTATCTATCGCGTACGCCGG 60.248 60.000 32.64 20.56 39.84 6.13 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
69 70 3.584294 AGGTGTACCACTTACCTCTGTT 58.416 45.455 3.56 0.00 40.73 3.16
76 77 5.562298 ACCACTTACCTCTGTTACATTGT 57.438 39.130 0.00 0.00 0.00 2.71
133 134 3.314357 TCGAGTATTTCCATCGACGTGAT 59.686 43.478 0.00 0.00 40.29 3.06
188 189 1.078759 CAGCGTCCGGTCTTGTCATC 61.079 60.000 0.00 0.00 0.00 2.92
198 199 1.141881 CTTGTCATCCGTCCCTCCG 59.858 63.158 0.00 0.00 0.00 4.63
217 218 1.390123 CGTGGTTGTCGTGATGATGAC 59.610 52.381 0.00 0.00 38.45 3.06
278 284 3.805207 ACCGAGTATTTAATGCCTGGTC 58.195 45.455 0.00 0.00 0.00 4.02
299 305 4.398673 GTCGATGGAGTACTCTACAAGGTT 59.601 45.833 21.88 0.00 38.12 3.50
330 338 4.988598 CGTGTGCCCCGTCTGCTT 62.989 66.667 0.00 0.00 0.00 3.91
332 340 3.555324 TGTGCCCCGTCTGCTTGA 61.555 61.111 0.00 0.00 0.00 3.02
378 387 1.413445 GCTGGCATCATGAGTCTCTCT 59.587 52.381 0.09 0.00 0.00 3.10
430 439 1.429463 GACCCGTTGCTCTGTAGTTG 58.571 55.000 0.00 0.00 0.00 3.16
436 445 1.808945 GTTGCTCTGTAGTTGCTGCAT 59.191 47.619 1.84 0.00 0.00 3.96
442 451 5.053145 GCTCTGTAGTTGCTGCATAAGTAT 58.947 41.667 1.84 0.00 0.00 2.12
490 499 8.218338 ACCATAGTTATCTTTTCTCAATGCTG 57.782 34.615 0.00 0.00 0.00 4.41
491 500 7.831193 ACCATAGTTATCTTTTCTCAATGCTGT 59.169 33.333 0.00 0.00 0.00 4.40
521 530 1.227556 GAGGCGCCGATGTATGGTT 60.228 57.895 23.20 0.00 0.00 3.67
592 601 3.329889 AGGGCAGGCATCGTTCCA 61.330 61.111 0.00 0.00 0.00 3.53
673 682 4.020378 TCGCCGCAAAAACCTCGC 62.020 61.111 0.00 0.00 0.00 5.03
735 744 0.679960 CGGGGAATTCAGGGTGTTCC 60.680 60.000 7.93 0.00 40.50 3.62
788 797 1.934463 CTCCGATATGCACCGCAAC 59.066 57.895 0.00 0.00 43.62 4.17
805 814 1.386412 CAACGAACAATCCAATTGCGC 59.614 47.619 0.00 0.00 43.98 6.09
806 815 0.454285 ACGAACAATCCAATTGCGCG 60.454 50.000 0.00 0.00 43.98 6.86
828 882 1.885871 GCCAAGATCCCTGCAACAC 59.114 57.895 0.00 0.00 0.00 3.32
1442 3887 0.038251 CAGCAACAGGAGTGCGAGTA 60.038 55.000 0.00 0.00 0.00 2.59
1534 3979 1.112315 CGGGTGAGGATGAGAGGAGG 61.112 65.000 0.00 0.00 0.00 4.30
1535 3980 0.263172 GGGTGAGGATGAGAGGAGGA 59.737 60.000 0.00 0.00 0.00 3.71
1536 3981 1.703411 GGTGAGGATGAGAGGAGGAG 58.297 60.000 0.00 0.00 0.00 3.69
1697 4145 3.066064 GGGTTGTGCCATTTTTGTTTTCC 59.934 43.478 0.00 0.00 39.65 3.13
2319 4768 3.054361 CCACAAAGCTTAGGTACCTGGAT 60.054 47.826 25.33 12.82 0.00 3.41
2343 4792 9.798994 GATTTCTATCTTTTCGTACTCCACTAA 57.201 33.333 0.00 0.00 0.00 2.24
2461 4912 2.591429 TCAACCACGTGCAGCCTG 60.591 61.111 10.91 2.25 0.00 4.85
2578 5029 6.294675 CCATGGCTTTTGAGATGAAGTGTAAA 60.295 38.462 0.00 0.00 0.00 2.01
3464 5921 2.135664 ACCGTCTCTCGTTTCTGTTG 57.864 50.000 0.00 0.00 37.94 3.33
3466 5923 1.269621 CCGTCTCTCGTTTCTGTTGGT 60.270 52.381 0.00 0.00 37.94 3.67
3615 6072 3.548745 AATTGGTCATCAGATCAGCGA 57.451 42.857 0.00 0.00 35.99 4.93
4143 6600 6.500684 TCTTTTCAAACCATCAGCTGATAC 57.499 37.500 28.27 0.00 32.63 2.24
4269 6726 5.088739 GCAAATGTATTATATCAGGTGCGC 58.911 41.667 0.00 0.00 0.00 6.09
4309 6766 5.692928 ACCTACGGTCTGTTACTATCTCAT 58.307 41.667 0.00 0.00 0.00 2.90
4318 6775 6.254589 GTCTGTTACTATCTCATGCTTGTCAC 59.745 42.308 0.00 0.00 0.00 3.67
4491 6948 6.765989 GGTGTCAATACTTCCATAATAGTGCA 59.234 38.462 0.00 0.00 0.00 4.57
4674 7131 8.964420 ATTTGTCGGTGTTTCTTGTATATTTG 57.036 30.769 0.00 0.00 0.00 2.32
4782 7239 7.945033 TGCTGAAAACTTCAAAAATATGGAC 57.055 32.000 0.00 0.00 39.58 4.02
4856 7313 6.294675 CCTTCCATGCAGAAACTTGTGAATAA 60.295 38.462 0.00 0.00 0.00 1.40
5382 7863 7.139287 TGGATGAATTCGGGTATAACCTTTA 57.861 36.000 5.01 0.00 38.64 1.85
5605 8086 1.440893 CTCTGCCAGAGTCCCATCG 59.559 63.158 13.74 0.00 37.57 3.84
5615 8096 0.749454 AGTCCCATCGGCAAAGCATC 60.749 55.000 0.00 0.00 0.00 3.91
5638 8119 5.010820 TCTGTGCATTCCAAATCATCAAACA 59.989 36.000 0.00 0.00 0.00 2.83
5664 8145 4.599047 CCAACCTTGGCAATTTTACTGA 57.401 40.909 0.00 0.00 42.21 3.41
5778 8259 9.397280 ACTCTATTTTGCTCCTTTTAAGTATCC 57.603 33.333 0.00 0.00 0.00 2.59
5948 8429 9.627123 TCCTCCAAAGTCCATTTATGTAATTAG 57.373 33.333 0.00 0.00 0.00 1.73
5985 8466 5.353123 TCTTTTTACTTGCAGTATTAGCCCG 59.647 40.000 0.00 0.00 29.64 6.13
6229 8710 7.778185 TTTCCTGGATAGGTAATCTACTAGC 57.222 40.000 0.00 0.00 44.88 3.42
6269 8756 7.048512 GGATGCTCCTTTGTACTTAGTTACAT 58.951 38.462 0.00 0.00 32.53 2.29
6270 8757 7.011482 GGATGCTCCTTTGTACTTAGTTACATG 59.989 40.741 0.00 0.00 32.53 3.21
6271 8758 6.999950 TGCTCCTTTGTACTTAGTTACATGA 58.000 36.000 0.00 0.00 0.00 3.07
6272 8759 7.446769 TGCTCCTTTGTACTTAGTTACATGAA 58.553 34.615 0.00 0.00 0.00 2.57
6273 8760 7.934665 TGCTCCTTTGTACTTAGTTACATGAAA 59.065 33.333 0.00 0.00 0.00 2.69
6274 8761 8.780249 GCTCCTTTGTACTTAGTTACATGAAAA 58.220 33.333 0.00 0.00 0.00 2.29
6276 8763 9.841295 TCCTTTGTACTTAGTTACATGAAAAGT 57.159 29.630 0.00 4.16 34.86 2.66
6281 8768 9.841295 TGTACTTAGTTACATGAAAAGTTTCCT 57.159 29.630 0.00 0.00 36.36 3.36
6469 8956 1.532868 CTTGCAGCTATCGGTAATGGC 59.467 52.381 0.00 0.00 41.93 4.40
6520 9007 6.604171 ACATGATAGAAGGAAACATGCCATA 58.396 36.000 0.00 0.00 40.99 2.74
6849 9336 5.915758 GCCGTGAGTATTCTCTACATTAGTG 59.084 44.000 0.77 0.00 40.98 2.74
7018 9505 7.184022 ACCTTTGGTCCATAATTCTAACCTACT 59.816 37.037 0.00 0.00 0.00 2.57
7019 9506 7.715686 CCTTTGGTCCATAATTCTAACCTACTC 59.284 40.741 0.00 0.00 0.00 2.59
7020 9507 6.742559 TGGTCCATAATTCTAACCTACTCC 57.257 41.667 0.00 0.00 0.00 3.85
7021 9508 5.605488 TGGTCCATAATTCTAACCTACTCCC 59.395 44.000 0.00 0.00 0.00 4.30
7022 9509 5.845065 GGTCCATAATTCTAACCTACTCCCT 59.155 44.000 0.00 0.00 0.00 4.20
7023 9510 6.014413 GGTCCATAATTCTAACCTACTCCCTC 60.014 46.154 0.00 0.00 0.00 4.30
7024 9511 6.014413 GTCCATAATTCTAACCTACTCCCTCC 60.014 46.154 0.00 0.00 0.00 4.30
7025 9512 5.047235 CCATAATTCTAACCTACTCCCTCCG 60.047 48.000 0.00 0.00 0.00 4.63
7026 9513 3.684408 ATTCTAACCTACTCCCTCCGT 57.316 47.619 0.00 0.00 0.00 4.69
7027 9514 3.463048 TTCTAACCTACTCCCTCCGTT 57.537 47.619 0.00 0.00 0.00 4.44
7028 9515 3.010200 TCTAACCTACTCCCTCCGTTC 57.990 52.381 0.00 0.00 0.00 3.95
7029 9516 2.030371 CTAACCTACTCCCTCCGTTCC 58.970 57.143 0.00 0.00 0.00 3.62
7030 9517 0.115745 AACCTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 0.00 3.53
7031 9518 0.115745 ACCTACTCCCTCCGTTCCAA 59.884 55.000 0.00 0.00 0.00 3.53
7032 9519 1.272807 CCTACTCCCTCCGTTCCAAA 58.727 55.000 0.00 0.00 0.00 3.28
7033 9520 1.626825 CCTACTCCCTCCGTTCCAAAA 59.373 52.381 0.00 0.00 0.00 2.44
7034 9521 2.238898 CCTACTCCCTCCGTTCCAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
7035 9522 3.453353 CCTACTCCCTCCGTTCCAAAATA 59.547 47.826 0.00 0.00 0.00 1.40
7036 9523 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
7037 9524 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
7038 9525 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
7039 9526 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
7040 9527 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
7041 9528 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
7042 9529 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
7043 9530 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
7044 9531 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
7045 9532 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
7046 9533 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
7047 9534 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
7048 9535 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
7049 9536 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
7050 9537 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
7051 9538 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
7052 9539 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
7053 9540 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
7054 9541 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
7103 9590 2.830651 AGTCATCTACTCCCTCCGTT 57.169 50.000 0.00 0.00 30.33 4.44
7104 9591 2.657143 AGTCATCTACTCCCTCCGTTC 58.343 52.381 0.00 0.00 30.33 3.95
7105 9592 1.334243 GTCATCTACTCCCTCCGTTCG 59.666 57.143 0.00 0.00 0.00 3.95
7106 9593 0.669077 CATCTACTCCCTCCGTTCGG 59.331 60.000 4.74 4.74 0.00 4.30
7107 9594 0.549950 ATCTACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
7108 9595 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
7109 9596 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
7110 9597 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
7111 9598 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
7112 9599 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
7113 9600 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
7114 9601 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
7115 9602 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
7116 9603 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
7117 9604 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
7118 9605 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
7119 9606 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
7120 9607 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
7121 9608 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
7122 9609 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
7123 9610 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
7124 9611 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
7125 9612 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
7126 9613 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
7127 9614 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
7128 9615 5.808540 CGGAATTACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
7129 9616 6.479001 CGGAATTACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
7130 9617 7.516785 CGGAATTACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
7131 9618 7.280205 GGAATTACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
7132 9619 9.309516 GAATTACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
7133 9620 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
7134 9621 8.642908 TTACTTGTCGTAGAAATGGATGTATG 57.357 34.615 0.00 0.00 39.69 2.39
7135 9622 6.640518 ACTTGTCGTAGAAATGGATGTATGT 58.359 36.000 0.00 0.00 39.69 2.29
7136 9623 7.778083 ACTTGTCGTAGAAATGGATGTATGTA 58.222 34.615 0.00 0.00 39.69 2.29
7137 9624 7.921214 ACTTGTCGTAGAAATGGATGTATGTAG 59.079 37.037 0.00 0.00 39.69 2.74
7138 9625 7.576861 TGTCGTAGAAATGGATGTATGTAGA 57.423 36.000 0.00 0.00 39.69 2.59
7139 9626 7.423199 TGTCGTAGAAATGGATGTATGTAGAC 58.577 38.462 0.00 0.00 39.69 2.59
7140 9627 7.067737 TGTCGTAGAAATGGATGTATGTAGACA 59.932 37.037 0.00 0.00 39.69 3.41
7141 9628 8.082852 GTCGTAGAAATGGATGTATGTAGACAT 58.917 37.037 0.08 0.08 40.04 3.06
7142 9629 8.638873 TCGTAGAAATGGATGTATGTAGACATT 58.361 33.333 0.00 0.00 40.18 2.71
7143 9630 9.261180 CGTAGAAATGGATGTATGTAGACATTT 57.739 33.333 0.00 0.00 40.18 2.32
7170 9657 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
7171 9658 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
7172 9659 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
7173 9660 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
7174 9661 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
7175 9662 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
7176 9663 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
7177 9664 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
7178 9665 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
7179 9666 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
7180 9667 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
7181 9668 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
7182 9669 5.545658 TCCATTTCTGCGACAAGTAATTC 57.454 39.130 0.00 0.00 0.00 2.17
7183 9670 4.092821 TCCATTTCTGCGACAAGTAATTCG 59.907 41.667 0.00 0.00 38.31 3.34
7184 9671 4.334443 CATTTCTGCGACAAGTAATTCGG 58.666 43.478 0.00 0.00 35.73 4.30
7185 9672 3.306917 TTCTGCGACAAGTAATTCGGA 57.693 42.857 0.00 0.00 35.73 4.55
7186 9673 3.306917 TCTGCGACAAGTAATTCGGAA 57.693 42.857 0.00 0.00 35.02 4.30
7187 9674 2.991190 TCTGCGACAAGTAATTCGGAAC 59.009 45.455 0.00 0.00 35.02 3.62
7251 9738 5.845103 AGTGATTGTTTCATGTGCATTTCA 58.155 33.333 0.00 0.00 36.54 2.69
7277 9764 1.078214 TCAGGATGCAAGGAAGCGG 60.078 57.895 0.00 0.00 37.31 5.52
7519 10006 5.278022 GGAAAGATCGTTTCAAAGAGTTGCT 60.278 40.000 15.14 0.00 34.50 3.91
7691 10178 3.740115 ACTGTGTGTGATTAGGGTGTTC 58.260 45.455 0.00 0.00 0.00 3.18
7979 10466 3.446442 ACCATTCTGCACCTCAATTCT 57.554 42.857 0.00 0.00 0.00 2.40
8048 10535 8.816640 AATTACCAGCACAAAACTAAATTCAG 57.183 30.769 0.00 0.00 0.00 3.02
8115 10602 2.354510 CTGTCTTTGTGCGTTCTTTGGA 59.645 45.455 0.00 0.00 0.00 3.53
8451 10939 4.176271 TCACTTTCTGTCGCATACATCAG 58.824 43.478 0.00 0.00 37.50 2.90
8457 10945 5.514274 TCTGTCGCATACATCAGTTCATA 57.486 39.130 0.00 0.00 37.50 2.15
8458 10946 6.089249 TCTGTCGCATACATCAGTTCATAT 57.911 37.500 0.00 0.00 37.50 1.78
8464 10952 6.148811 TCGCATACATCAGTTCATATAGACGA 59.851 38.462 0.00 0.00 0.00 4.20
8476 10964 1.257743 ATAGACGACTGGTGTGTGCT 58.742 50.000 0.00 0.00 0.00 4.40
8504 10992 2.089854 GCATGTCCGATTTGCGTCT 58.910 52.632 0.00 0.00 38.67 4.18
8512 11000 1.556564 CGATTTGCGTCTACACGGAT 58.443 50.000 0.00 0.00 46.68 4.18
8538 11068 1.364171 GTGTCTGCTCGGTGTCAGT 59.636 57.895 0.00 0.00 0.00 3.41
8697 11538 4.814294 CTAGTCACGCGTGGCCCC 62.814 72.222 37.67 22.32 35.39 5.80
8725 11566 0.317160 CAACACTGACCCTAGTCGCA 59.683 55.000 0.00 0.00 46.74 5.10
8737 11578 0.037590 TAGTCGCAATGGGTGGCTTT 59.962 50.000 0.00 0.00 39.37 3.51
8755 11596 2.323968 TTTTTGGCAAGGGAAAGCAC 57.676 45.000 0.00 0.00 0.00 4.40
8756 11597 1.198713 TTTTGGCAAGGGAAAGCACA 58.801 45.000 0.00 0.00 0.00 4.57
8757 11598 1.198713 TTTGGCAAGGGAAAGCACAA 58.801 45.000 0.00 0.00 0.00 3.33
8758 11599 0.463620 TTGGCAAGGGAAAGCACAAC 59.536 50.000 0.00 0.00 0.00 3.32
8759 11600 1.367471 GGCAAGGGAAAGCACAACC 59.633 57.895 0.00 0.00 0.00 3.77
8760 11601 1.398958 GGCAAGGGAAAGCACAACCA 61.399 55.000 0.00 0.00 0.00 3.67
8761 11602 0.249447 GCAAGGGAAAGCACAACCAC 60.249 55.000 0.00 0.00 0.00 4.16
8762 11603 0.030638 CAAGGGAAAGCACAACCACG 59.969 55.000 0.00 0.00 0.00 4.94
8763 11604 1.106944 AAGGGAAAGCACAACCACGG 61.107 55.000 0.00 0.00 0.00 4.94
8764 11605 2.335011 GGAAAGCACAACCACGGC 59.665 61.111 0.00 0.00 0.00 5.68
8809 11650 4.880426 GGGGGAGGGCTCATCGGA 62.880 72.222 0.00 0.00 0.00 4.55
8844 11706 1.461559 AGTACCACTGAGAGTACCGC 58.538 55.000 11.84 0.00 39.76 5.68
8845 11707 1.004511 AGTACCACTGAGAGTACCGCT 59.995 52.381 11.84 0.00 39.76 5.52
8846 11708 2.238144 AGTACCACTGAGAGTACCGCTA 59.762 50.000 11.84 0.00 39.76 4.26
8847 11709 1.461559 ACCACTGAGAGTACCGCTAC 58.538 55.000 0.00 0.00 0.00 3.58
8848 11710 0.739561 CCACTGAGAGTACCGCTACC 59.260 60.000 0.00 0.00 0.00 3.18
8849 11711 1.460504 CACTGAGAGTACCGCTACCA 58.539 55.000 0.00 0.00 0.00 3.25
8870 11732 1.002624 GCCGAATGTCAACCTCCCA 60.003 57.895 0.00 0.00 0.00 4.37
8873 11735 1.340017 CCGAATGTCAACCTCCCACAT 60.340 52.381 0.00 0.00 31.90 3.21
8875 11737 3.198068 CGAATGTCAACCTCCCACATAG 58.802 50.000 0.00 0.00 30.37 2.23
8885 11747 2.092212 CCTCCCACATAGTTGGCATCTT 60.092 50.000 2.98 0.00 35.00 2.40
8894 11756 0.324645 GTTGGCATCTTGACCCCCAT 60.325 55.000 0.00 0.00 0.00 4.00
8901 11763 1.667595 TCTTGACCCCCATCACATCA 58.332 50.000 0.00 0.00 0.00 3.07
8902 11764 1.281867 TCTTGACCCCCATCACATCAC 59.718 52.381 0.00 0.00 0.00 3.06
8903 11765 0.035534 TTGACCCCCATCACATCACG 60.036 55.000 0.00 0.00 0.00 4.35
8904 11766 1.153168 GACCCCCATCACATCACGG 60.153 63.158 0.00 0.00 0.00 4.94
8905 11767 1.910580 GACCCCCATCACATCACGGT 61.911 60.000 0.00 0.00 0.00 4.83
8906 11768 1.451927 CCCCCATCACATCACGGTG 60.452 63.158 0.56 0.56 40.16 4.94
8907 11769 2.114670 CCCCATCACATCACGGTGC 61.115 63.158 2.51 0.00 38.66 5.01
8908 11770 2.114670 CCCATCACATCACGGTGCC 61.115 63.158 2.51 0.00 38.66 5.01
8909 11771 2.463620 CCATCACATCACGGTGCCG 61.464 63.158 9.29 9.29 46.03 5.69
8910 11772 2.819595 ATCACATCACGGTGCCGC 60.820 61.111 10.87 0.00 44.19 6.53
8911 11773 3.604129 ATCACATCACGGTGCCGCA 62.604 57.895 10.87 0.00 44.19 5.69
8912 11774 4.088762 CACATCACGGTGCCGCAC 62.089 66.667 15.50 15.50 44.19 5.34
8913 11775 4.314440 ACATCACGGTGCCGCACT 62.314 61.111 22.41 1.13 44.19 4.40
8934 11796 1.891919 GAGTGGGTGCGTGCAAAGA 60.892 57.895 0.00 0.00 0.00 2.52
8936 11798 1.034838 AGTGGGTGCGTGCAAAGAAA 61.035 50.000 0.00 0.00 0.00 2.52
8948 11810 2.223595 TGCAAAGAAAATCCGCAAACGA 60.224 40.909 0.00 0.00 43.93 3.85
8950 11812 2.309898 AAGAAAATCCGCAAACGACG 57.690 45.000 0.00 0.00 43.93 5.12
8998 11860 3.653009 CCCGGCGTACGCGATAGA 61.653 66.667 31.78 0.00 43.06 1.98
9005 11867 1.202009 GCGTACGCGATAGATAGTCCC 60.202 57.143 26.17 0.00 41.33 4.46
9011 11873 2.351835 CGCGATAGATAGTCCCAACTGG 60.352 54.545 0.00 0.00 35.81 4.00
9026 11888 0.608640 ACTGGGACGTCTGATTCACC 59.391 55.000 16.46 6.66 0.00 4.02
9028 11890 1.208052 CTGGGACGTCTGATTCACCAT 59.792 52.381 16.46 0.00 0.00 3.55
9030 11892 1.207089 GGGACGTCTGATTCACCATGA 59.793 52.381 16.46 0.00 0.00 3.07
9104 11966 1.896660 GCCGCCAGTGGTGAAAAGA 60.897 57.895 24.62 0.00 34.74 2.52
9107 11969 1.021202 CGCCAGTGGTGAAAAGAACA 58.979 50.000 18.34 0.00 34.74 3.18
9108 11970 1.608590 CGCCAGTGGTGAAAAGAACAT 59.391 47.619 18.34 0.00 34.74 2.71
9132 11994 1.432270 GCGAAGGCAGAGTACCATGC 61.432 60.000 10.65 10.65 41.80 4.06
9184 12046 1.315257 GCACACAATGGCCTGTAGGG 61.315 60.000 3.32 0.00 35.18 3.53
9194 12056 3.399181 CTGTAGGGGGCGCTCCAA 61.399 66.667 31.11 13.45 37.22 3.53
9200 12062 4.021925 GGGGCGCTCCAACTCTGT 62.022 66.667 24.98 0.00 37.22 3.41
9201 12063 2.743928 GGGCGCTCCAACTCTGTG 60.744 66.667 7.64 0.00 35.00 3.66
9216 12078 1.794151 CTGTGTGACCGGCAATTGCA 61.794 55.000 30.32 8.07 44.36 4.08
9223 12085 0.751643 ACCGGCAATTGCATCTACCC 60.752 55.000 30.32 11.22 44.36 3.69
9274 12136 1.735920 CACCTGCAGACGTCAGAGC 60.736 63.158 17.39 18.22 33.54 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.706890 ACACCTCGCCGACAATTATTT 58.293 42.857 0.00 0.00 0.00 1.40
40 41 2.598099 TGGTACACCTCGCCGACA 60.598 61.111 0.00 0.00 36.82 4.35
69 70 6.603599 AGTGTCAGCTCATCTACTACAATGTA 59.396 38.462 0.00 0.00 0.00 2.29
76 77 4.380973 GCAACAGTGTCAGCTCATCTACTA 60.381 45.833 12.07 0.00 0.00 1.82
188 189 3.584868 GACAACCACGGAGGGACGG 62.585 68.421 1.11 0.00 43.89 4.79
198 199 1.732259 GGTCATCATCACGACAACCAC 59.268 52.381 0.00 0.00 33.53 4.16
217 218 2.842936 CAGGGCTACGGGTAGGGG 60.843 72.222 7.87 0.00 33.87 4.79
261 267 4.102524 TCCATCGACCAGGCATTAAATACT 59.897 41.667 0.00 0.00 0.00 2.12
278 284 4.158025 ACAACCTTGTAGAGTACTCCATCG 59.842 45.833 19.38 6.80 40.16 3.84
378 387 2.335681 TATGTCACAGAAGGTCCCCA 57.664 50.000 0.00 0.00 0.00 4.96
464 473 9.330063 CAGCATTGAGAAAAGATAACTATGGTA 57.670 33.333 0.00 0.00 0.00 3.25
476 485 9.512435 CTTGGAAATATACAGCATTGAGAAAAG 57.488 33.333 0.00 0.00 0.00 2.27
477 486 8.469200 CCTTGGAAATATACAGCATTGAGAAAA 58.531 33.333 0.00 0.00 0.00 2.29
482 491 6.064060 CCTCCTTGGAAATATACAGCATTGA 58.936 40.000 0.00 0.00 38.35 2.57
490 499 2.152016 GGCGCCTCCTTGGAAATATAC 58.848 52.381 22.15 0.00 38.35 1.47
491 500 1.270625 CGGCGCCTCCTTGGAAATATA 60.271 52.381 26.68 0.00 38.35 0.86
521 530 5.931294 TGGATATCAGGGTATACGCAAAAA 58.069 37.500 20.70 5.33 0.00 1.94
582 591 2.106074 TCATGCGGTGGAACGATGC 61.106 57.895 0.00 0.00 38.12 3.91
664 673 2.271173 GATCCCCGGCGAGGTTTT 59.729 61.111 9.30 0.00 38.74 2.43
716 725 0.679960 GGAACACCCTGAATTCCCCG 60.680 60.000 2.27 0.00 36.64 5.73
724 733 2.214216 CCTCCACGGAACACCCTGA 61.214 63.158 0.00 0.00 33.16 3.86
735 744 1.774894 TTTTCCCCTCACCCTCCACG 61.775 60.000 0.00 0.00 0.00 4.94
788 797 0.454285 ACGCGCAATTGGATTGTTCG 60.454 50.000 5.73 1.27 42.20 3.95
805 814 3.197790 CAGGGATCTTGGCGCACG 61.198 66.667 10.83 0.00 0.00 5.34
806 815 3.512516 GCAGGGATCTTGGCGCAC 61.513 66.667 10.83 0.00 0.00 5.34
1057 3234 2.689034 GTGTGGAGGAGGGGAGGG 60.689 72.222 0.00 0.00 0.00 4.30
1058 3235 2.689034 GGTGTGGAGGAGGGGAGG 60.689 72.222 0.00 0.00 0.00 4.30
1059 3236 2.122729 TGGTGTGGAGGAGGGGAG 59.877 66.667 0.00 0.00 0.00 4.30
1060 3237 2.203938 GTGGTGTGGAGGAGGGGA 60.204 66.667 0.00 0.00 0.00 4.81
1061 3238 2.203998 AGTGGTGTGGAGGAGGGG 60.204 66.667 0.00 0.00 0.00 4.79
1534 3979 1.286553 TCCTCCACTCTCTCCTTCCTC 59.713 57.143 0.00 0.00 0.00 3.71
1535 3980 1.287739 CTCCTCCACTCTCTCCTTCCT 59.712 57.143 0.00 0.00 0.00 3.36
1536 3981 1.286553 TCTCCTCCACTCTCTCCTTCC 59.713 57.143 0.00 0.00 0.00 3.46
1697 4145 1.197949 AGATATCGCACATCCGTCTCG 59.802 52.381 0.00 0.00 0.00 4.04
1744 4192 6.535508 GTGTCACTGAAGTCTTTAGTCAAAGT 59.464 38.462 7.03 0.00 41.66 2.66
2343 4792 4.641989 ACTTGCAAGAAACTGACTGACATT 59.358 37.500 32.50 1.12 0.00 2.71
2578 5029 7.069877 TGACATGTAACCTAAAGTAGTTGGT 57.930 36.000 0.00 0.00 0.00 3.67
3088 5539 6.026947 ACACGTTCCCTATAGCAATCTATC 57.973 41.667 0.00 0.00 36.86 2.08
3464 5921 1.222115 GATCGTGATTAGCCGGCACC 61.222 60.000 31.54 14.60 0.00 5.01
3466 5923 0.032130 GAGATCGTGATTAGCCGGCA 59.968 55.000 31.54 9.64 0.00 5.69
3586 6043 9.994432 CTGATCTGATGACCAATTTAACTAAAC 57.006 33.333 0.00 0.00 0.00 2.01
3615 6072 8.658499 AACTGACAAGAACGACTATTTTACTT 57.342 30.769 0.00 0.00 0.00 2.24
4143 6600 4.163078 ACCTAGAACATCATCAGTTGAGGG 59.837 45.833 0.00 0.00 40.46 4.30
4269 6726 3.340814 AGGTTGTGAGCATAAGACAGG 57.659 47.619 0.00 0.00 0.00 4.00
4309 6766 0.181114 AACCTGAGCTGTGACAAGCA 59.819 50.000 0.00 0.00 46.08 3.91
4318 6775 5.691754 GGTGTTATTTCAAAAACCTGAGCTG 59.308 40.000 0.00 0.00 0.00 4.24
4491 6948 0.033699 GCCTCTCAAGCCCAATCCTT 60.034 55.000 0.00 0.00 0.00 3.36
4653 7110 5.933790 TGCAAATATACAAGAAACACCGAC 58.066 37.500 0.00 0.00 0.00 4.79
4674 7131 9.472361 AGATGATTATGTAATTTGCTTTCATGC 57.528 29.630 0.00 0.00 0.00 4.06
4782 7239 8.454106 CAGTAAATTTCTGGAACCTTCACATAG 58.546 37.037 0.00 0.00 0.00 2.23
4856 7313 5.858381 TCTGTTCTATGTTGCTTGAGAGTT 58.142 37.500 0.00 0.00 0.00 3.01
5432 7913 1.973138 CGCAGAAGACATTGCCAAAG 58.027 50.000 0.00 0.00 37.00 2.77
5615 8096 5.231702 TGTTTGATGATTTGGAATGCACAG 58.768 37.500 0.00 0.00 0.00 3.66
5664 8145 4.125703 GCTGACATAAATAGAGCTGCACT 58.874 43.478 4.73 4.73 0.00 4.40
5778 8259 2.032894 CACGGCTACTGCATTTAATCGG 60.033 50.000 0.00 0.00 41.91 4.18
5985 8466 1.140816 GCAGTCCTTCGCGGATATTC 58.859 55.000 6.13 0.00 45.44 1.75
6269 8756 8.690203 TGTTGATCTCATTAGGAAACTTTTCA 57.310 30.769 4.18 0.00 43.67 2.69
6270 8757 9.399403 GTTGTTGATCTCATTAGGAAACTTTTC 57.601 33.333 0.00 0.00 43.67 2.29
6271 8758 8.076178 CGTTGTTGATCTCATTAGGAAACTTTT 58.924 33.333 0.00 0.00 43.67 2.27
6272 8759 7.584987 CGTTGTTGATCTCATTAGGAAACTTT 58.415 34.615 0.00 0.00 43.67 2.66
6273 8760 6.348540 GCGTTGTTGATCTCATTAGGAAACTT 60.349 38.462 0.00 0.00 43.67 2.66
6275 8762 5.324697 GCGTTGTTGATCTCATTAGGAAAC 58.675 41.667 0.00 0.00 0.00 2.78
6276 8763 4.394920 GGCGTTGTTGATCTCATTAGGAAA 59.605 41.667 0.00 0.00 0.00 3.13
6278 8765 3.531538 GGCGTTGTTGATCTCATTAGGA 58.468 45.455 0.00 0.00 0.00 2.94
6279 8766 2.285220 CGGCGTTGTTGATCTCATTAGG 59.715 50.000 0.00 0.00 0.00 2.69
6280 8767 2.285834 GCGGCGTTGTTGATCTCATTAG 60.286 50.000 9.37 0.00 0.00 1.73
6281 8768 1.663643 GCGGCGTTGTTGATCTCATTA 59.336 47.619 9.37 0.00 0.00 1.90
6469 8956 6.729391 CTGATAGATTGCAGGAATCATGAG 57.271 41.667 16.31 7.89 42.80 2.90
6495 8982 4.883585 TGGCATGTTTCCTTCTATCATGTC 59.116 41.667 0.00 0.00 40.22 3.06
6520 9007 5.072741 AGCAAAACCAGTAGAATGACATGT 58.927 37.500 0.00 0.00 0.00 3.21
7018 9505 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
7019 9506 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
7020 9507 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
7021 9508 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
7022 9509 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
7023 9510 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
7024 9511 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
7025 9512 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
7026 9513 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
7027 9514 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
7028 9515 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
7084 9571 2.657143 GAACGGAGGGAGTAGATGACT 58.343 52.381 0.00 0.00 42.90 3.41
7085 9572 1.334243 CGAACGGAGGGAGTAGATGAC 59.666 57.143 0.00 0.00 0.00 3.06
7086 9573 1.676746 CGAACGGAGGGAGTAGATGA 58.323 55.000 0.00 0.00 0.00 2.92
7087 9574 0.669077 CCGAACGGAGGGAGTAGATG 59.331 60.000 7.53 0.00 37.50 2.90
7088 9575 0.549950 TCCGAACGGAGGGAGTAGAT 59.450 55.000 12.04 0.00 39.76 1.98
7089 9576 0.329261 TTCCGAACGGAGGGAGTAGA 59.671 55.000 15.34 0.00 46.06 2.59
7090 9577 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
7091 9578 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
7092 9579 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
7093 9580 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
7094 9581 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
7095 9582 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
7096 9583 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
7097 9584 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
7098 9585 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
7099 9586 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
7100 9587 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
7101 9588 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
7102 9589 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
7103 9590 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
7104 9591 5.808540 TCCATTTCTACGACAAGTAATTCCG 59.191 40.000 0.00 0.00 34.45 4.30
7105 9592 7.280205 ACATCCATTTCTACGACAAGTAATTCC 59.720 37.037 0.00 0.00 34.45 3.01
7106 9593 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
7107 9594 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
7108 9595 9.261180 CATACATCCATTTCTACGACAAGTAAT 57.739 33.333 0.00 0.00 34.45 1.89
7109 9596 8.255206 ACATACATCCATTTCTACGACAAGTAA 58.745 33.333 0.00 0.00 34.45 2.24
7110 9597 7.778083 ACATACATCCATTTCTACGACAAGTA 58.222 34.615 0.00 0.00 0.00 2.24
7111 9598 6.640518 ACATACATCCATTTCTACGACAAGT 58.359 36.000 0.00 0.00 0.00 3.16
7112 9599 8.135529 TCTACATACATCCATTTCTACGACAAG 58.864 37.037 0.00 0.00 0.00 3.16
7113 9600 7.919091 GTCTACATACATCCATTTCTACGACAA 59.081 37.037 0.00 0.00 0.00 3.18
7114 9601 7.067737 TGTCTACATACATCCATTTCTACGACA 59.932 37.037 0.00 0.00 0.00 4.35
7115 9602 7.423199 TGTCTACATACATCCATTTCTACGAC 58.577 38.462 0.00 0.00 0.00 4.34
7116 9603 7.576861 TGTCTACATACATCCATTTCTACGA 57.423 36.000 0.00 0.00 0.00 3.43
7117 9604 8.818141 AATGTCTACATACATCCATTTCTACG 57.182 34.615 0.00 0.00 39.16 3.51
7144 9631 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
7145 9632 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
7146 9633 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
7147 9634 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
7148 9635 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
7149 9636 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
7150 9637 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
7151 9638 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
7152 9639 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
7153 9640 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
7154 9641 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
7155 9642 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
7156 9643 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
7157 9644 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
7158 9645 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
7159 9646 5.220662 CGAATTACTTGTCGCAGAAATGGAT 60.221 40.000 0.00 0.00 39.69 3.41
7160 9647 4.092821 CGAATTACTTGTCGCAGAAATGGA 59.907 41.667 0.00 0.00 39.69 3.41
7161 9648 4.334443 CGAATTACTTGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
7162 9649 4.092821 TCCGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
7163 9650 4.250464 TCCGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
7164 9651 3.655486 TCCGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
7165 9652 3.306917 TCCGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
7166 9653 2.991190 GTTCCGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 35.93 4.26
7167 9654 2.222508 CGTTCCGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 35.93 5.18
7168 9655 1.722464 CGTTCCGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 35.93 5.10
7169 9656 1.060122 CCGTTCCGAATTACTTGTCGC 59.940 52.381 0.00 0.00 35.93 5.19
7170 9657 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
7171 9658 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
7172 9659 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
7173 9660 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
7174 9661 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
7175 9662 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
7176 9663 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
7177 9664 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
7178 9665 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
7179 9666 1.856629 TTACTCCCTCCGTTCCGAAT 58.143 50.000 0.00 0.00 0.00 3.34
7180 9667 1.631405 TTTACTCCCTCCGTTCCGAA 58.369 50.000 0.00 0.00 0.00 4.30
7181 9668 1.479323 CATTTACTCCCTCCGTTCCGA 59.521 52.381 0.00 0.00 0.00 4.55
7182 9669 1.472728 CCATTTACTCCCTCCGTTCCG 60.473 57.143 0.00 0.00 0.00 4.30
7183 9670 1.558294 ACCATTTACTCCCTCCGTTCC 59.442 52.381 0.00 0.00 0.00 3.62
7184 9671 4.186926 GTTACCATTTACTCCCTCCGTTC 58.813 47.826 0.00 0.00 0.00 3.95
7185 9672 3.368739 CGTTACCATTTACTCCCTCCGTT 60.369 47.826 0.00 0.00 0.00 4.44
7186 9673 2.167075 CGTTACCATTTACTCCCTCCGT 59.833 50.000 0.00 0.00 0.00 4.69
7187 9674 2.817901 CGTTACCATTTACTCCCTCCG 58.182 52.381 0.00 0.00 0.00 4.63
7188 9675 2.558378 GCGTTACCATTTACTCCCTCC 58.442 52.381 0.00 0.00 0.00 4.30
7189 9676 2.169978 AGGCGTTACCATTTACTCCCTC 59.830 50.000 0.00 0.00 43.14 4.30
7190 9677 2.093128 CAGGCGTTACCATTTACTCCCT 60.093 50.000 0.00 0.00 43.14 4.20
7191 9678 2.093341 TCAGGCGTTACCATTTACTCCC 60.093 50.000 0.00 0.00 43.14 4.30
7192 9679 3.195661 CTCAGGCGTTACCATTTACTCC 58.804 50.000 0.00 0.00 43.14 3.85
7193 9680 3.858247 ACTCAGGCGTTACCATTTACTC 58.142 45.455 0.00 0.00 43.14 2.59
7194 9681 3.975168 ACTCAGGCGTTACCATTTACT 57.025 42.857 0.00 0.00 43.14 2.24
7195 9682 5.114081 ACATACTCAGGCGTTACCATTTAC 58.886 41.667 0.00 0.00 43.14 2.01
7196 9683 5.347620 ACATACTCAGGCGTTACCATTTA 57.652 39.130 0.00 0.00 43.14 1.40
7197 9684 4.216411 ACATACTCAGGCGTTACCATTT 57.784 40.909 0.00 0.00 43.14 2.32
7198 9685 3.906720 ACATACTCAGGCGTTACCATT 57.093 42.857 0.00 0.00 43.14 3.16
7251 9738 5.747248 GCTTCCTTGCATCCTGAGGTATAAT 60.747 44.000 0.00 0.00 32.33 1.28
7277 9764 2.262915 CGAGACTGCCTGTCCCAC 59.737 66.667 0.00 0.00 46.46 4.61
7331 9818 5.214417 TCAATGATCTGTGCAAGTTTTTCG 58.786 37.500 0.00 0.00 0.00 3.46
7519 10006 7.176515 ACATATCCAATTGTTTTCTGTACAGCA 59.823 33.333 18.45 4.20 0.00 4.41
7691 10178 1.269448 CCCACCGTGAGACCATTTTTG 59.731 52.381 0.00 0.00 0.00 2.44
7940 10427 2.740447 GGTAGCGAGGTTTACCAAACTG 59.260 50.000 1.13 0.00 41.14 3.16
8048 10535 6.515272 ACAATGGATAAATGGAAGTGTGTC 57.485 37.500 0.00 0.00 0.00 3.67
8115 10602 1.271379 ACGCCAAGCAGGATTTGTAGT 60.271 47.619 0.00 0.00 41.22 2.73
8451 10939 4.798907 CACACACCAGTCGTCTATATGAAC 59.201 45.833 0.00 0.00 0.00 3.18
8457 10945 1.257743 AGCACACACCAGTCGTCTAT 58.742 50.000 0.00 0.00 0.00 1.98
8458 10946 1.037493 AAGCACACACCAGTCGTCTA 58.963 50.000 0.00 0.00 0.00 2.59
8464 10952 1.031571 CCACACAAGCACACACCAGT 61.032 55.000 0.00 0.00 0.00 4.00
8538 11068 3.680786 CGACACACGGGCCTGAGA 61.681 66.667 21.41 0.00 38.46 3.27
8616 11146 1.375908 CGCAGCCTTCCACTTGCTA 60.376 57.895 0.00 0.00 34.50 3.49
8620 11150 2.348998 CTCCGCAGCCTTCCACTT 59.651 61.111 0.00 0.00 0.00 3.16
8644 11175 2.683362 GGGGAAGCCATTAGAAAAGACG 59.317 50.000 0.00 0.00 0.00 4.18
8671 11512 1.577922 GCGTGACTAGACGTGGACA 59.422 57.895 0.00 0.00 41.54 4.02
8697 11538 4.680237 TCAGTGTTGGCCGGCGAG 62.680 66.667 22.54 4.04 0.00 5.03
8737 11578 1.198713 TGTGCTTTCCCTTGCCAAAA 58.801 45.000 0.00 0.00 0.00 2.44
8740 11581 1.398958 GGTTGTGCTTTCCCTTGCCA 61.399 55.000 0.00 0.00 0.00 4.92
8742 11583 0.249447 GTGGTTGTGCTTTCCCTTGC 60.249 55.000 0.00 0.00 0.00 4.01
8792 11633 4.880426 TCCGATGAGCCCTCCCCC 62.880 72.222 0.00 0.00 0.00 5.40
8793 11634 3.551407 GTCCGATGAGCCCTCCCC 61.551 72.222 0.00 0.00 0.00 4.81
8794 11635 2.764128 TGTCCGATGAGCCCTCCC 60.764 66.667 0.00 0.00 0.00 4.30
8835 11697 1.400530 GGCCATGGTAGCGGTACTCT 61.401 60.000 22.84 8.95 0.00 3.24
8836 11698 1.069258 GGCCATGGTAGCGGTACTC 59.931 63.158 22.84 13.99 0.00 2.59
8837 11699 2.792947 CGGCCATGGTAGCGGTACT 61.793 63.158 22.84 2.68 0.00 2.73
8838 11700 2.279918 CGGCCATGGTAGCGGTAC 60.280 66.667 16.33 16.33 0.00 3.34
8839 11701 1.404479 ATTCGGCCATGGTAGCGGTA 61.404 55.000 14.67 0.00 32.81 4.02
8840 11702 2.742116 ATTCGGCCATGGTAGCGGT 61.742 57.895 14.67 0.00 32.81 5.68
8841 11703 2.111043 ATTCGGCCATGGTAGCGG 59.889 61.111 14.67 3.62 0.00 5.52
8842 11704 1.498865 GACATTCGGCCATGGTAGCG 61.499 60.000 14.67 0.02 0.00 4.26
8843 11705 0.463654 TGACATTCGGCCATGGTAGC 60.464 55.000 14.67 0.00 0.00 3.58
8844 11706 1.670811 GTTGACATTCGGCCATGGTAG 59.329 52.381 14.67 7.95 0.00 3.18
8845 11707 1.680555 GGTTGACATTCGGCCATGGTA 60.681 52.381 14.67 0.00 0.00 3.25
8846 11708 0.965363 GGTTGACATTCGGCCATGGT 60.965 55.000 14.67 0.00 0.00 3.55
8847 11709 0.680921 AGGTTGACATTCGGCCATGG 60.681 55.000 7.63 7.63 0.00 3.66
8848 11710 0.734889 GAGGTTGACATTCGGCCATG 59.265 55.000 2.24 1.83 0.00 3.66
8849 11711 0.394352 GGAGGTTGACATTCGGCCAT 60.394 55.000 2.24 0.00 0.00 4.40
8870 11732 2.357154 GGGGTCAAGATGCCAACTATGT 60.357 50.000 0.00 0.00 0.00 2.29
8873 11735 0.623723 GGGGGTCAAGATGCCAACTA 59.376 55.000 0.00 0.00 0.00 2.24
8875 11737 0.324645 ATGGGGGTCAAGATGCCAAC 60.325 55.000 0.00 0.00 0.00 3.77
8885 11747 1.601703 CGTGATGTGATGGGGGTCA 59.398 57.895 0.00 0.00 0.00 4.02
8894 11756 4.306967 TGCGGCACCGTGATGTGA 62.307 61.111 11.27 0.00 42.09 3.58
8910 11772 3.991051 ACGCACCCACTCCGAGTG 61.991 66.667 19.97 19.97 45.53 3.51
8911 11773 3.991051 CACGCACCCACTCCGAGT 61.991 66.667 0.00 0.00 0.00 4.18
8931 11793 1.600485 ACGTCGTTTGCGGATTTTCTT 59.400 42.857 0.00 0.00 38.89 2.52
8934 11796 0.658897 ACACGTCGTTTGCGGATTTT 59.341 45.000 0.00 0.00 38.89 1.82
8936 11798 0.876777 TGACACGTCGTTTGCGGATT 60.877 50.000 0.00 0.00 38.89 3.01
8948 11810 1.213013 GAGCGTGAGGATGACACGT 59.787 57.895 18.66 8.26 0.00 4.49
8950 11812 0.524392 CTCGAGCGTGAGGATGACAC 60.524 60.000 0.00 0.00 32.18 3.67
8982 11844 0.247576 CTATCTATCGCGTACGCCGG 60.248 60.000 32.64 20.56 39.84 6.13
9005 11867 2.069273 GTGAATCAGACGTCCCAGTTG 58.931 52.381 13.01 3.43 0.00 3.16
9011 11873 2.672961 TCATGGTGAATCAGACGTCC 57.327 50.000 13.01 0.00 0.00 4.79
9017 11879 4.082408 ACATTGTGCTTCATGGTGAATCAG 60.082 41.667 0.00 0.00 33.77 2.90
9057 11919 4.162690 GCGGGCCTCGACCTGAAT 62.163 66.667 16.53 0.00 42.43 2.57
9095 11957 2.552315 TCGCCTTCATGTTCTTTTCACC 59.448 45.455 0.00 0.00 0.00 4.02
9104 11966 0.036732 TCTGCCTTCGCCTTCATGTT 59.963 50.000 0.00 0.00 0.00 2.71
9107 11969 1.134670 GTACTCTGCCTTCGCCTTCAT 60.135 52.381 0.00 0.00 0.00 2.57
9108 11970 0.246635 GTACTCTGCCTTCGCCTTCA 59.753 55.000 0.00 0.00 0.00 3.02
9121 11983 2.692557 CTCTAGTGCAGCATGGTACTCT 59.307 50.000 0.00 4.46 35.31 3.24
9130 11992 1.005332 AGAGTCTCCTCTAGTGCAGCA 59.995 52.381 0.00 0.00 46.39 4.41
9179 12041 3.387225 GAGTTGGAGCGCCCCCTAC 62.387 68.421 18.39 18.39 0.00 3.18
9180 12042 3.081409 GAGTTGGAGCGCCCCCTA 61.081 66.667 5.13 0.35 0.00 3.53
9184 12046 2.743928 CACAGAGTTGGAGCGCCC 60.744 66.667 2.29 5.76 0.00 6.13
9194 12056 0.108585 AATTGCCGGTCACACAGAGT 59.891 50.000 1.90 0.00 0.00 3.24
9200 12062 0.608856 AGATGCAATTGCCGGTCACA 60.609 50.000 26.94 7.41 41.18 3.58
9201 12063 1.064060 GTAGATGCAATTGCCGGTCAC 59.936 52.381 26.94 14.28 41.18 3.67
9254 12116 3.108289 CTGACGTCTGCAGGTGCG 61.108 66.667 17.92 17.69 45.83 5.34
9255 12117 1.735920 CTCTGACGTCTGCAGGTGC 60.736 63.158 17.92 3.84 42.50 5.01
9260 12122 2.653115 CCAGCTCTGACGTCTGCA 59.347 61.111 17.92 5.85 0.00 4.41
9264 12126 1.316706 ACTAGCCCAGCTCTGACGTC 61.317 60.000 9.11 9.11 40.44 4.34


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

AutoCloner maintained by Alex Coulton.