Multiple sequence alignment - TraesCS6D01G195700

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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 TraesCS6D01G195700 chr6D 100.000 6572 0 0 1 6572 271293401 271299972 0.000000e+00 12137.0
1 TraesCS6D01G195700 chr6D 100.000 36 0 0 4593 4628 271298028 271297993 4.250000e-07 67.6
2 TraesCS6D01G195700 chr6A 97.097 5684 98 24 1 5662 384733583 384727945 0.000000e+00 9520.0
3 TraesCS6D01G195700 chr6A 91.935 248 15 4 5653 5895 384727917 384727670 6.310000e-90 342.0
4 TraesCS6D01G195700 chr6A 89.640 222 17 2 6307 6525 384725421 384725203 1.800000e-70 278.0
5 TraesCS6D01G195700 chr6A 84.015 269 37 6 2919 3183 603803607 603803873 3.040000e-63 254.0
6 TraesCS6D01G195700 chr6A 78.853 279 49 7 3472 3743 603779965 603779690 5.240000e-41 180.0
7 TraesCS6D01G195700 chr6A 87.879 132 14 2 6113 6243 384727443 384727313 3.170000e-33 154.0
8 TraesCS6D01G195700 chr6A 96.203 79 3 0 5995 6073 384727669 384727591 5.350000e-26 130.0
9 TraesCS6D01G195700 chr6A 91.667 84 6 1 2205 2288 603803004 603803086 1.500000e-21 115.0
10 TraesCS6D01G195700 chr6A 100.000 36 0 0 4593 4628 384728975 384729010 4.250000e-07 67.6
11 TraesCS6D01G195700 chr6A 94.595 37 2 0 6243 6279 384725464 384725428 2.560000e-04 58.4
12 TraesCS6D01G195700 chr6A 100.000 28 0 0 5984 6011 384727619 384727592 1.200000e-02 52.8
13 TraesCS6D01G195700 chr6B 97.413 4407 77 16 1 4388 432356876 432361264 0.000000e+00 7472.0
14 TraesCS6D01G195700 chr6B 97.653 767 13 4 4385 5150 432361386 432362148 0.000000e+00 1312.0
15 TraesCS6D01G195700 chr6B 96.895 773 22 2 5140 5910 432371022 432371794 0.000000e+00 1293.0
16 TraesCS6D01G195700 chr3B 95.059 425 17 2 1362 1786 46803533 46803113 0.000000e+00 665.0
17 TraesCS6D01G195700 chr3B 94.578 166 5 2 1493 1658 158153210 158153371 3.040000e-63 254.0
18 TraesCS6D01G195700 chr3B 100.000 81 0 0 1706 1786 158153372 158153452 4.110000e-32 150.0
19 TraesCS6D01G195700 chr3B 93.590 78 5 0 1362 1439 158153135 158153212 4.160000e-22 117.0
20 TraesCS6D01G195700 chr3B 97.917 48 1 0 1235 1282 158152976 158153023 4.220000e-12 84.2
21 TraesCS6D01G195700 chr3B 97.917 48 1 0 1235 1282 158153031 158153078 4.220000e-12 84.2
22 TraesCS6D01G195700 chr3B 95.000 40 2 0 1841 1880 158153450 158153489 5.500000e-06 63.9
23 TraesCS6D01G195700 chr5A 94.737 342 14 2 1343 1684 591606968 591607305 4.510000e-146 529.0
24 TraesCS6D01G195700 chr5A 95.902 244 9 1 1343 1586 296677306 296677548 1.720000e-105 394.0
25 TraesCS6D01G195700 chr5A 96.491 114 3 1 1235 1348 296677162 296677274 3.130000e-43 187.0
26 TraesCS6D01G195700 chr5A 92.982 114 7 1 1235 1348 591606824 591606936 1.470000e-36 165.0
27 TraesCS6D01G195700 chr5A 94.845 97 4 1 1235 1330 12879947 12880043 4.110000e-32 150.0
28 TraesCS6D01G195700 chr5A 92.784 97 6 1 1235 1330 52509660 52509756 8.890000e-29 139.0
29 TraesCS6D01G195700 chr7D 93.162 117 6 2 1235 1350 134507950 134508065 3.150000e-38 171.0
30 TraesCS6D01G195700 chrUn 97.059 68 2 0 2600 2667 25906171 25906104 1.500000e-21 115.0
31 TraesCS6D01G195700 chr2B 93.506 77 5 0 2588 2664 516724232 516724308 1.500000e-21 115.0
32 TraesCS6D01G195700 chr2A 97.059 68 2 0 2600 2667 549969010 549968943 1.500000e-21 115.0
33 TraesCS6D01G195700 chr2A 100.000 28 0 0 6477 6504 82342057 82342084 1.200000e-02 52.8
34 TraesCS6D01G195700 chr4A 100.000 29 0 0 4057 4085 363126525 363126497 3.000000e-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 TraesCS6D01G195700 chr6D 271293401 271299972 6571 False 12137.000000 12137 100.000 1 6572 1 chr6D.!!$F1 6571
1 TraesCS6D01G195700 chr6A 384725203 384733583 8380 True 1505.028571 9520 93.907 1 6525 7 chr6A.!!$R2 6524
2 TraesCS6D01G195700 chr6B 432356876 432362148 5272 False 4392.000000 7472 97.533 1 5150 2 chr6B.!!$F2 5149
3 TraesCS6D01G195700 chr6B 432371022 432371794 772 False 1293.000000 1293 96.895 5140 5910 1 chr6B.!!$F1 770

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
140 141 1.277557 CCTCTTGTTGGGTCTGAGGAG 59.722 57.143 0.00 0.0 45.07 3.69 F
547 558 1.758841 GCATATGGGGGAGCCATGTTT 60.759 52.381 4.56 0.0 0.00 2.83 F
1294 1306 5.391523 CCCAAATGTAAACCGTACATGACTG 60.392 44.000 0.00 0.0 38.10 3.51 F
1603 1615 6.795144 ATATGATGAAAATGCTGGTTCCAA 57.205 33.333 0.00 0.0 0.00 3.53 F
3867 3895 7.411588 GCGACAAAAGAGTCTTACGACATTATT 60.412 37.037 5.65 0.0 42.73 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1278 0.594110 ACGGTTTACATTTGGGTGCG 59.406 50.000 0.0 0.0 0.0 5.34 R
2523 2538 5.471797 TGAAATGCTCCAACTATTCGAACAA 59.528 36.000 0.0 0.0 0.0 2.83 R
3867 3895 3.106827 TCAGGAATGTGATGCAGGACTA 58.893 45.455 0.0 0.0 0.0 2.59 R
3889 3917 3.338818 AGAAACCGCATCGCAAATATG 57.661 42.857 0.0 0.0 0.0 1.78 R
5936 6145 0.178891 TGCCCCTCTTCTCTTCCACT 60.179 55.000 0.0 0.0 0.0 4.00 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
138 139 1.352083 TCCTCTTGTTGGGTCTGAGG 58.648 55.000 0.00 0.00 44.00 3.86
139 140 1.352083 CCTCTTGTTGGGTCTGAGGA 58.648 55.000 0.00 0.00 45.07 3.71
140 141 1.277557 CCTCTTGTTGGGTCTGAGGAG 59.722 57.143 0.00 0.00 45.07 3.69
150 151 2.018515 GGTCTGAGGAGTCCTTAGTCG 58.981 57.143 25.79 6.61 38.26 4.18
163 164 2.894240 TTAGTCGATTCACCGGCCGC 62.894 60.000 22.85 3.39 34.19 6.53
389 396 9.010029 TCCTCTGAACACAGATATTTTTAAACC 57.990 33.333 0.00 0.00 39.48 3.27
458 467 7.995463 TTTTATTTATATGAAACGCTTGCCC 57.005 32.000 0.00 0.00 0.00 5.36
475 484 3.904717 TGCCCTTTCAAGGTTCTACAAA 58.095 40.909 4.86 0.00 44.98 2.83
476 485 3.888930 TGCCCTTTCAAGGTTCTACAAAG 59.111 43.478 4.86 0.00 44.98 2.77
477 486 3.889538 GCCCTTTCAAGGTTCTACAAAGT 59.110 43.478 4.86 0.00 44.98 2.66
478 487 4.261614 GCCCTTTCAAGGTTCTACAAAGTG 60.262 45.833 4.86 0.00 44.98 3.16
479 488 5.130350 CCCTTTCAAGGTTCTACAAAGTGA 58.870 41.667 4.86 0.00 44.98 3.41
480 489 5.239525 CCCTTTCAAGGTTCTACAAAGTGAG 59.760 44.000 4.86 0.00 44.98 3.51
481 490 6.055588 CCTTTCAAGGTTCTACAAAGTGAGA 58.944 40.000 0.00 0.00 41.41 3.27
518 529 4.820897 ACAGATCTGAAGTCGCAATTGTA 58.179 39.130 29.27 0.00 0.00 2.41
547 558 1.758841 GCATATGGGGGAGCCATGTTT 60.759 52.381 4.56 0.00 0.00 2.83
565 576 7.370383 CCATGTTTCAATGCAGTTAGTTACTT 58.630 34.615 0.00 0.00 33.85 2.24
796 807 6.662865 TTTTATTCTGTGATGGCCTTCAAA 57.337 33.333 21.99 16.36 0.00 2.69
967 979 6.100424 ACCTCTCCATTCTTAGGTTATCTTGG 59.900 42.308 0.00 0.00 39.32 3.61
1294 1306 5.391523 CCCAAATGTAAACCGTACATGACTG 60.392 44.000 0.00 0.00 38.10 3.51
1602 1614 9.585369 TTATATATGATGAAAATGCTGGTTCCA 57.415 29.630 0.00 0.00 0.00 3.53
1603 1615 6.795144 ATATGATGAAAATGCTGGTTCCAA 57.205 33.333 0.00 0.00 0.00 3.53
3458 3483 9.547753 TTCTTGCATCTCCTTAAATCATACTAC 57.452 33.333 0.00 0.00 0.00 2.73
3459 3484 8.928448 TCTTGCATCTCCTTAAATCATACTACT 58.072 33.333 0.00 0.00 0.00 2.57
3867 3895 7.411588 GCGACAAAAGAGTCTTACGACATTATT 60.412 37.037 5.65 0.00 42.73 1.40
3889 3917 2.012673 GTCCTGCATCACATTCCTGAC 58.987 52.381 0.00 0.00 0.00 3.51
4252 4280 3.181465 ACTCCCCACTATAAATCTGTGCG 60.181 47.826 0.00 0.00 0.00 5.34
4320 4348 3.153676 CGTGTAATGACGTGATACCCA 57.846 47.619 0.00 0.00 34.56 4.51
4325 4353 6.074516 CGTGTAATGACGTGATACCCATAAAG 60.075 42.308 0.00 0.00 34.56 1.85
4342 4370 2.464157 AAGTGAGCACAGAACCTAGC 57.536 50.000 3.19 0.00 0.00 3.42
4497 4650 5.175859 GCTTATGCCTGTTTAGTACTGACA 58.824 41.667 5.39 9.46 0.00 3.58
4752 4908 3.977427 AGCACCGAAGTTGAATTTTTCC 58.023 40.909 0.00 0.00 0.00 3.13
5169 5325 1.136891 GCCCTTTACCCATCAATGCAC 59.863 52.381 0.00 0.00 0.00 4.57
5233 5389 6.391227 TCTGAAAGAACAAACATTCTTCCC 57.609 37.500 1.47 0.00 46.02 3.97
5339 5501 6.753107 AGGTTTGTACACCATAGCATTTAC 57.247 37.500 0.00 0.00 39.62 2.01
5357 5519 1.317613 ACATCCGTGCTTCTTTTGCA 58.682 45.000 0.00 0.00 38.19 4.08
5831 6038 2.256117 AACCTAGCAAGCGTCAGTTT 57.744 45.000 0.00 0.00 0.00 2.66
5910 6119 4.357918 TTTGCCTCTCTTCTGCTAAACT 57.642 40.909 0.00 0.00 0.00 2.66
5911 6120 3.325293 TGCCTCTCTTCTGCTAAACTG 57.675 47.619 0.00 0.00 0.00 3.16
5912 6121 2.634940 TGCCTCTCTTCTGCTAAACTGT 59.365 45.455 0.00 0.00 0.00 3.55
5913 6122 3.832490 TGCCTCTCTTCTGCTAAACTGTA 59.168 43.478 0.00 0.00 0.00 2.74
5914 6123 4.177783 GCCTCTCTTCTGCTAAACTGTAC 58.822 47.826 0.00 0.00 0.00 2.90
5915 6124 4.416620 CCTCTCTTCTGCTAAACTGTACG 58.583 47.826 0.00 0.00 0.00 3.67
5916 6125 4.416620 CTCTCTTCTGCTAAACTGTACGG 58.583 47.826 0.00 0.00 0.00 4.02
5917 6126 2.924290 CTCTTCTGCTAAACTGTACGGC 59.076 50.000 0.23 0.00 0.00 5.68
5918 6127 2.000447 CTTCTGCTAAACTGTACGGCC 59.000 52.381 0.23 0.00 0.00 6.13
5919 6128 1.263356 TCTGCTAAACTGTACGGCCT 58.737 50.000 0.00 0.00 0.00 5.19
5920 6129 1.621814 TCTGCTAAACTGTACGGCCTT 59.378 47.619 0.00 0.00 0.00 4.35
5921 6130 1.732259 CTGCTAAACTGTACGGCCTTG 59.268 52.381 0.00 0.00 0.00 3.61
5922 6131 1.084289 GCTAAACTGTACGGCCTTGG 58.916 55.000 0.00 0.00 0.00 3.61
5923 6132 1.084289 CTAAACTGTACGGCCTTGGC 58.916 55.000 0.00 2.49 0.00 4.52
5924 6133 0.397187 TAAACTGTACGGCCTTGGCA 59.603 50.000 14.04 0.00 0.00 4.92
5925 6134 1.170290 AAACTGTACGGCCTTGGCAC 61.170 55.000 14.04 3.94 0.00 5.01
5926 6135 2.052047 AACTGTACGGCCTTGGCACT 62.052 55.000 14.04 0.00 0.00 4.40
5927 6136 1.189524 ACTGTACGGCCTTGGCACTA 61.190 55.000 14.04 0.00 0.00 2.74
5928 6137 0.460284 CTGTACGGCCTTGGCACTAG 60.460 60.000 14.04 4.33 0.00 2.57
5929 6138 0.901114 TGTACGGCCTTGGCACTAGA 60.901 55.000 14.04 0.00 0.00 2.43
5930 6139 0.248289 GTACGGCCTTGGCACTAGAA 59.752 55.000 14.04 0.00 0.00 2.10
5931 6140 0.978151 TACGGCCTTGGCACTAGAAA 59.022 50.000 14.04 0.00 0.00 2.52
5932 6141 0.605589 ACGGCCTTGGCACTAGAAAC 60.606 55.000 14.04 0.00 0.00 2.78
5933 6142 0.321653 CGGCCTTGGCACTAGAAACT 60.322 55.000 14.04 0.00 0.00 2.66
5934 6143 1.066430 CGGCCTTGGCACTAGAAACTA 60.066 52.381 14.04 0.00 0.00 2.24
5935 6144 2.420129 CGGCCTTGGCACTAGAAACTAT 60.420 50.000 14.04 0.00 0.00 2.12
5936 6145 3.181469 CGGCCTTGGCACTAGAAACTATA 60.181 47.826 14.04 0.00 0.00 1.31
5937 6146 4.381411 GGCCTTGGCACTAGAAACTATAG 58.619 47.826 14.04 0.00 0.00 1.31
5938 6147 4.141688 GGCCTTGGCACTAGAAACTATAGT 60.142 45.833 14.04 0.00 33.74 2.12
5940 6149 5.360591 CCTTGGCACTAGAAACTATAGTGG 58.639 45.833 6.06 0.00 46.68 4.00
5941 6150 5.128827 CCTTGGCACTAGAAACTATAGTGGA 59.871 44.000 6.06 0.00 46.68 4.02
5942 6151 6.351881 CCTTGGCACTAGAAACTATAGTGGAA 60.352 42.308 6.06 0.00 46.68 3.53
5943 6152 6.222038 TGGCACTAGAAACTATAGTGGAAG 57.778 41.667 6.06 4.89 46.68 3.46
5944 6153 5.955959 TGGCACTAGAAACTATAGTGGAAGA 59.044 40.000 6.06 0.00 46.68 2.87
5945 6154 6.096987 TGGCACTAGAAACTATAGTGGAAGAG 59.903 42.308 6.06 3.66 46.68 2.85
5946 6155 6.321690 GGCACTAGAAACTATAGTGGAAGAGA 59.678 42.308 6.06 0.00 46.68 3.10
5947 6156 7.147880 GGCACTAGAAACTATAGTGGAAGAGAA 60.148 40.741 6.06 0.00 46.68 2.87
5948 6157 7.918562 GCACTAGAAACTATAGTGGAAGAGAAG 59.081 40.741 6.06 0.00 46.68 2.85
5949 6158 9.179909 CACTAGAAACTATAGTGGAAGAGAAGA 57.820 37.037 6.06 0.00 44.16 2.87
5950 6159 9.403583 ACTAGAAACTATAGTGGAAGAGAAGAG 57.596 37.037 6.06 0.00 32.27 2.85
5951 6160 7.654022 AGAAACTATAGTGGAAGAGAAGAGG 57.346 40.000 6.06 0.00 0.00 3.69
5952 6161 6.609616 AGAAACTATAGTGGAAGAGAAGAGGG 59.390 42.308 6.06 0.00 0.00 4.30
5953 6162 4.810345 ACTATAGTGGAAGAGAAGAGGGG 58.190 47.826 4.10 0.00 0.00 4.79
5954 6163 1.867363 TAGTGGAAGAGAAGAGGGGC 58.133 55.000 0.00 0.00 0.00 5.80
5955 6164 0.178891 AGTGGAAGAGAAGAGGGGCA 60.179 55.000 0.00 0.00 0.00 5.36
5956 6165 0.693049 GTGGAAGAGAAGAGGGGCAA 59.307 55.000 0.00 0.00 0.00 4.52
5957 6166 1.073923 GTGGAAGAGAAGAGGGGCAAA 59.926 52.381 0.00 0.00 0.00 3.68
5958 6167 1.995542 TGGAAGAGAAGAGGGGCAAAT 59.004 47.619 0.00 0.00 0.00 2.32
5959 6168 2.379907 TGGAAGAGAAGAGGGGCAAATT 59.620 45.455 0.00 0.00 0.00 1.82
5960 6169 3.181418 TGGAAGAGAAGAGGGGCAAATTT 60.181 43.478 0.00 0.00 0.00 1.82
5961 6170 3.445450 GGAAGAGAAGAGGGGCAAATTTC 59.555 47.826 0.00 0.00 0.00 2.17
5962 6171 4.339748 GAAGAGAAGAGGGGCAAATTTCT 58.660 43.478 0.00 0.00 0.00 2.52
5963 6172 3.961849 AGAGAAGAGGGGCAAATTTCTC 58.038 45.455 10.96 10.96 42.42 2.87
5964 6173 3.591079 AGAGAAGAGGGGCAAATTTCTCT 59.409 43.478 14.06 14.06 45.50 3.10
5965 6174 5.104259 GAGAAGAGGGGCAAATTTCTCTA 57.896 43.478 7.37 0.00 40.19 2.43
5966 6175 5.689835 GAGAAGAGGGGCAAATTTCTCTAT 58.310 41.667 7.37 1.45 40.19 1.98
5967 6176 6.831664 AGAAGAGGGGCAAATTTCTCTATA 57.168 37.500 7.37 0.00 35.76 1.31
5968 6177 7.213178 AGAAGAGGGGCAAATTTCTCTATAA 57.787 36.000 7.37 0.00 35.76 0.98
5969 6178 7.820532 AGAAGAGGGGCAAATTTCTCTATAAT 58.179 34.615 7.37 0.00 35.76 1.28
5970 6179 8.949421 AGAAGAGGGGCAAATTTCTCTATAATA 58.051 33.333 7.37 0.00 35.76 0.98
5971 6180 9.225436 GAAGAGGGGCAAATTTCTCTATAATAG 57.775 37.037 7.37 0.00 35.76 1.73
5972 6181 8.511748 AGAGGGGCAAATTTCTCTATAATAGA 57.488 34.615 5.56 0.00 35.13 1.98
5973 6182 8.379331 AGAGGGGCAAATTTCTCTATAATAGAC 58.621 37.037 5.56 0.00 35.13 2.59
5974 6183 8.281529 AGGGGCAAATTTCTCTATAATAGACT 57.718 34.615 0.00 0.00 0.00 3.24
5975 6184 8.728098 AGGGGCAAATTTCTCTATAATAGACTT 58.272 33.333 0.00 0.00 0.00 3.01
5976 6185 9.355916 GGGGCAAATTTCTCTATAATAGACTTT 57.644 33.333 0.00 0.00 0.00 2.66
6098 6307 6.724893 TCAAGAGAACATCCGATATAACCA 57.275 37.500 0.00 0.00 0.00 3.67
6099 6308 6.749139 TCAAGAGAACATCCGATATAACCAG 58.251 40.000 0.00 0.00 0.00 4.00
6101 6310 7.233553 TCAAGAGAACATCCGATATAACCAGAT 59.766 37.037 0.00 0.00 0.00 2.90
6103 6312 8.057536 AGAGAACATCCGATATAACCAGATAC 57.942 38.462 0.00 0.00 0.00 2.24
6104 6313 6.853720 AGAACATCCGATATAACCAGATACG 58.146 40.000 0.00 0.00 0.00 3.06
6105 6314 5.578005 ACATCCGATATAACCAGATACGG 57.422 43.478 0.00 0.00 40.16 4.02
6107 6316 4.305539 TCCGATATAACCAGATACGGGA 57.694 45.455 0.00 0.00 39.44 5.14
6108 6317 4.665451 TCCGATATAACCAGATACGGGAA 58.335 43.478 0.00 0.00 39.44 3.97
6109 6318 5.078949 TCCGATATAACCAGATACGGGAAA 58.921 41.667 0.00 0.00 39.44 3.13
6110 6319 5.047802 TCCGATATAACCAGATACGGGAAAC 60.048 44.000 0.00 0.00 39.44 2.78
6111 6320 5.047519 CCGATATAACCAGATACGGGAAACT 60.048 44.000 0.00 0.00 36.08 2.66
6125 6442 3.736720 GGGAAACTGAACCTAAAGACGT 58.263 45.455 0.00 0.00 0.00 4.34
6129 6446 5.404667 GGAAACTGAACCTAAAGACGTACAG 59.595 44.000 0.00 0.00 0.00 2.74
6162 6479 4.569719 AACGAAGGGAGATACAACCAAT 57.430 40.909 0.00 0.00 0.00 3.16
6175 6492 3.334691 ACAACCAATACCACATGACTCG 58.665 45.455 0.00 0.00 0.00 4.18
6176 6493 2.677836 CAACCAATACCACATGACTCGG 59.322 50.000 0.00 0.00 0.00 4.63
6185 6502 5.160607 ACCACATGACTCGGAAATTCTTA 57.839 39.130 0.00 0.00 0.00 2.10
6192 6509 7.607991 ACATGACTCGGAAATTCTTATCAAAGT 59.392 33.333 0.00 0.00 34.13 2.66
6207 6524 0.582005 AAAGTCGCAACTGAACTCGC 59.418 50.000 0.00 0.00 35.36 5.03
6209 6526 1.664965 GTCGCAACTGAACTCGCCT 60.665 57.895 0.00 0.00 0.00 5.52
6215 6533 1.002468 CAACTGAACTCGCCTTGTTGG 60.002 52.381 0.00 0.00 39.35 3.77
6247 8414 1.468985 TTTACCGGCAATGGTGATGG 58.531 50.000 0.00 0.00 43.68 3.51
6279 8446 3.085208 CGCCAAGCATATCTGGTGT 57.915 52.632 0.00 0.00 32.27 4.16
6281 8448 1.755179 GCCAAGCATATCTGGTGTGT 58.245 50.000 0.00 0.00 32.27 3.72
6284 8451 2.019249 CAAGCATATCTGGTGTGTGGG 58.981 52.381 0.00 0.00 32.27 4.61
6285 8452 1.289160 AGCATATCTGGTGTGTGGGT 58.711 50.000 0.00 0.00 0.00 4.51
6286 8453 1.065199 AGCATATCTGGTGTGTGGGTG 60.065 52.381 0.00 0.00 0.00 4.61
6287 8454 1.340017 GCATATCTGGTGTGTGGGTGT 60.340 52.381 0.00 0.00 0.00 4.16
6288 8455 2.358957 CATATCTGGTGTGTGGGTGTG 58.641 52.381 0.00 0.00 0.00 3.82
6289 8456 1.429930 TATCTGGTGTGTGGGTGTGT 58.570 50.000 0.00 0.00 0.00 3.72
6290 8457 0.179020 ATCTGGTGTGTGGGTGTGTG 60.179 55.000 0.00 0.00 0.00 3.82
6291 8458 1.823470 CTGGTGTGTGGGTGTGTGG 60.823 63.158 0.00 0.00 0.00 4.17
6292 8459 2.518349 GGTGTGTGGGTGTGTGGG 60.518 66.667 0.00 0.00 0.00 4.61
6293 8460 2.274104 GTGTGTGGGTGTGTGGGT 59.726 61.111 0.00 0.00 0.00 4.51
6294 8461 2.118404 GTGTGTGGGTGTGTGGGTG 61.118 63.158 0.00 0.00 0.00 4.61
6295 8462 2.274104 GTGTGGGTGTGTGGGTGT 59.726 61.111 0.00 0.00 0.00 4.16
6296 8463 2.118404 GTGTGGGTGTGTGGGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
6297 8464 2.274104 GTGGGTGTGTGGGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
6298 8465 2.118404 GTGGGTGTGTGGGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
6299 8466 2.274104 GGGTGTGTGGGTGTGTGT 59.726 61.111 0.00 0.00 0.00 3.72
6300 8467 2.118404 GGGTGTGTGGGTGTGTGTG 61.118 63.158 0.00 0.00 0.00 3.82
6301 8468 1.377987 GGTGTGTGGGTGTGTGTGT 60.378 57.895 0.00 0.00 0.00 3.72
6302 8469 1.653094 GGTGTGTGGGTGTGTGTGTG 61.653 60.000 0.00 0.00 0.00 3.82
6303 8470 0.958382 GTGTGTGGGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
6304 8471 0.957888 TGTGTGGGTGTGTGTGTGTG 60.958 55.000 0.00 0.00 0.00 3.82
6305 8472 0.958382 GTGTGGGTGTGTGTGTGTGT 60.958 55.000 0.00 0.00 0.00 3.72
6336 8503 3.362706 TCTAGGTAGGTAAGCACACCAG 58.637 50.000 9.20 0.00 41.40 4.00
6373 8540 3.696051 GCCATCACCTTGCTCATAAAGAA 59.304 43.478 0.00 0.00 0.00 2.52
6374 8541 4.201990 GCCATCACCTTGCTCATAAAGAAG 60.202 45.833 0.00 0.00 0.00 2.85
6376 8543 5.826737 CCATCACCTTGCTCATAAAGAAGAT 59.173 40.000 0.00 0.00 0.00 2.40
6377 8544 6.320672 CCATCACCTTGCTCATAAAGAAGATT 59.679 38.462 0.00 0.00 0.00 2.40
6378 8545 6.748333 TCACCTTGCTCATAAAGAAGATTG 57.252 37.500 0.00 0.00 0.00 2.67
6382 8549 8.248945 CACCTTGCTCATAAAGAAGATTGAAAT 58.751 33.333 0.00 0.00 0.00 2.17
6415 8585 1.648467 GAAGACGGCCATCACCTTGC 61.648 60.000 0.00 0.00 0.00 4.01
6421 8591 1.310933 GGCCATCACCTTGCTCACAG 61.311 60.000 0.00 0.00 0.00 3.66
6427 8597 3.325293 TCACCTTGCTCACAGAGATTC 57.675 47.619 0.00 0.00 0.00 2.52
6434 8604 3.329386 TGCTCACAGAGATTCGAAAAGG 58.671 45.455 0.00 0.00 0.00 3.11
6458 8628 8.978472 AGGAATTGATGAAGAAAATGATGATGT 58.022 29.630 0.00 0.00 0.00 3.06
6467 8637 0.742505 AATGATGATGTTGCCCGCAG 59.257 50.000 0.00 0.00 0.00 5.18
6482 8652 1.709147 CGCAGTGCCTATGAAGCCAC 61.709 60.000 10.11 0.00 0.00 5.01
6507 8677 4.423732 CAACTTGACACAAAGAACCAAGG 58.576 43.478 0.00 0.00 38.70 3.61
6510 8680 0.310854 GACACAAAGAACCAAGGGCG 59.689 55.000 0.00 0.00 0.00 6.13
6525 8695 0.935196 GGGCGTCGTCCATGAATAAC 59.065 55.000 11.94 0.00 0.00 1.89
6526 8696 1.647346 GGCGTCGTCCATGAATAACA 58.353 50.000 0.00 0.00 0.00 2.41
6527 8697 1.593006 GGCGTCGTCCATGAATAACAG 59.407 52.381 0.00 0.00 0.00 3.16
6528 8698 1.004927 GCGTCGTCCATGAATAACAGC 60.005 52.381 0.00 0.00 0.00 4.40
6529 8699 2.267426 CGTCGTCCATGAATAACAGCA 58.733 47.619 0.00 0.00 0.00 4.41
6530 8700 2.282555 CGTCGTCCATGAATAACAGCAG 59.717 50.000 0.00 0.00 0.00 4.24
6531 8701 3.521560 GTCGTCCATGAATAACAGCAGA 58.478 45.455 0.00 0.00 0.00 4.26
6532 8702 3.553511 GTCGTCCATGAATAACAGCAGAG 59.446 47.826 0.00 0.00 0.00 3.35
6533 8703 3.447229 TCGTCCATGAATAACAGCAGAGA 59.553 43.478 0.00 0.00 0.00 3.10
6534 8704 3.801050 CGTCCATGAATAACAGCAGAGAG 59.199 47.826 0.00 0.00 0.00 3.20
6535 8705 4.440663 CGTCCATGAATAACAGCAGAGAGA 60.441 45.833 0.00 0.00 0.00 3.10
6536 8706 5.423015 GTCCATGAATAACAGCAGAGAGAA 58.577 41.667 0.00 0.00 0.00 2.87
6537 8707 5.877012 GTCCATGAATAACAGCAGAGAGAAA 59.123 40.000 0.00 0.00 0.00 2.52
6538 8708 6.372659 GTCCATGAATAACAGCAGAGAGAAAA 59.627 38.462 0.00 0.00 0.00 2.29
6539 8709 6.942005 TCCATGAATAACAGCAGAGAGAAAAA 59.058 34.615 0.00 0.00 0.00 1.94
6540 8710 7.025963 CCATGAATAACAGCAGAGAGAAAAAC 58.974 38.462 0.00 0.00 0.00 2.43
6541 8711 7.094463 CCATGAATAACAGCAGAGAGAAAAACT 60.094 37.037 0.00 0.00 0.00 2.66
6542 8712 7.194607 TGAATAACAGCAGAGAGAAAAACTG 57.805 36.000 0.00 0.00 35.14 3.16
6548 8718 3.632855 CAGAGAGAAAAACTGCCAACC 57.367 47.619 0.00 0.00 0.00 3.77
6549 8719 3.217626 CAGAGAGAAAAACTGCCAACCT 58.782 45.455 0.00 0.00 0.00 3.50
6550 8720 3.251972 CAGAGAGAAAAACTGCCAACCTC 59.748 47.826 0.00 0.00 0.00 3.85
6551 8721 2.554462 GAGAGAAAAACTGCCAACCTCC 59.446 50.000 0.00 0.00 0.00 4.30
6552 8722 2.175715 AGAGAAAAACTGCCAACCTCCT 59.824 45.455 0.00 0.00 0.00 3.69
6553 8723 2.554462 GAGAAAAACTGCCAACCTCCTC 59.446 50.000 0.00 0.00 0.00 3.71
6554 8724 2.091885 AGAAAAACTGCCAACCTCCTCA 60.092 45.455 0.00 0.00 0.00 3.86
6555 8725 1.986882 AAAACTGCCAACCTCCTCAG 58.013 50.000 0.00 0.00 0.00 3.35
6556 8726 0.538287 AAACTGCCAACCTCCTCAGC 60.538 55.000 0.00 0.00 0.00 4.26
6557 8727 1.708993 AACTGCCAACCTCCTCAGCA 61.709 55.000 0.00 0.00 0.00 4.41
6558 8728 1.073722 CTGCCAACCTCCTCAGCAA 59.926 57.895 0.00 0.00 32.14 3.91
6559 8729 1.228245 TGCCAACCTCCTCAGCAAC 60.228 57.895 0.00 0.00 0.00 4.17
6560 8730 2.328099 GCCAACCTCCTCAGCAACG 61.328 63.158 0.00 0.00 0.00 4.10
6561 8731 1.672356 CCAACCTCCTCAGCAACGG 60.672 63.158 0.00 0.00 0.00 4.44
6562 8732 2.032681 AACCTCCTCAGCAACGGC 59.967 61.111 0.00 0.00 41.61 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.201429 GCTTGACTTGGGGAGGAGGA 61.201 60.000 0.00 0.00 0.00 3.71
138 139 2.223525 CCGGTGAATCGACTAAGGACTC 60.224 54.545 0.00 0.00 0.00 3.36
139 140 1.749634 CCGGTGAATCGACTAAGGACT 59.250 52.381 0.00 0.00 0.00 3.85
140 141 1.801765 GCCGGTGAATCGACTAAGGAC 60.802 57.143 1.90 0.00 0.00 3.85
150 151 4.162690 AGAGGCGGCCGGTGAATC 62.163 66.667 29.38 8.67 0.00 2.52
163 164 3.787001 GGGGACGGGAAGCAGAGG 61.787 72.222 0.00 0.00 0.00 3.69
350 351 4.079443 TGTTCAGAGGAGGAAAAGGGAAAA 60.079 41.667 0.00 0.00 0.00 2.29
389 396 0.241749 GTAAAACCGGGCCGAAAAGG 59.758 55.000 30.79 13.10 44.97 3.11
458 467 7.736447 ATCTCACTTTGTAGAACCTTGAAAG 57.264 36.000 0.00 0.00 0.00 2.62
475 484 7.161404 TCTGTTGCATACACTAAAATCTCACT 58.839 34.615 0.00 0.00 32.10 3.41
476 485 7.364522 TCTGTTGCATACACTAAAATCTCAC 57.635 36.000 0.00 0.00 32.10 3.51
477 486 8.043113 AGATCTGTTGCATACACTAAAATCTCA 58.957 33.333 0.00 0.00 32.10 3.27
478 487 8.333908 CAGATCTGTTGCATACACTAAAATCTC 58.666 37.037 14.95 0.00 32.10 2.75
479 488 8.043113 TCAGATCTGTTGCATACACTAAAATCT 58.957 33.333 21.92 0.00 32.10 2.40
480 489 8.201554 TCAGATCTGTTGCATACACTAAAATC 57.798 34.615 21.92 0.00 32.10 2.17
481 490 8.565896 TTCAGATCTGTTGCATACACTAAAAT 57.434 30.769 21.92 0.00 32.10 1.82
518 529 1.214175 TCCCCCATATGCGTGAACATT 59.786 47.619 0.00 0.00 0.00 2.71
547 558 5.298026 TGTGCAAAGTAACTAACTGCATTGA 59.702 36.000 0.00 0.00 38.81 2.57
565 576 8.462811 TCAAGTTAAAAATTACTGTCTGTGCAA 58.537 29.630 0.00 0.00 0.00 4.08
782 793 5.410924 GGAACTAAATTTGAAGGCCATCAC 58.589 41.667 10.89 0.00 0.00 3.06
967 979 3.194968 TCTGTATGGTTTCTCCGTCCTTC 59.805 47.826 0.00 0.00 39.52 3.46
1266 1278 0.594110 ACGGTTTACATTTGGGTGCG 59.406 50.000 0.00 0.00 0.00 5.34
1455 1467 5.665459 CGTTCTCTTAACCCTTCATCAGAT 58.335 41.667 0.00 0.00 0.00 2.90
2407 2422 5.648092 GTGTCCTAACAACCTAAGATTGCAT 59.352 40.000 0.00 0.00 37.08 3.96
2523 2538 5.471797 TGAAATGCTCCAACTATTCGAACAA 59.528 36.000 0.00 0.00 0.00 2.83
3867 3895 3.106827 TCAGGAATGTGATGCAGGACTA 58.893 45.455 0.00 0.00 0.00 2.59
3889 3917 3.338818 AGAAACCGCATCGCAAATATG 57.661 42.857 0.00 0.00 0.00 1.78
4252 4280 3.696051 ACACATTGGGCATGTTCTACATC 59.304 43.478 0.00 0.00 44.40 3.06
4320 4348 4.508662 GCTAGGTTCTGTGCTCACTTTAT 58.491 43.478 1.47 0.00 0.00 1.40
4325 4353 0.243907 TCGCTAGGTTCTGTGCTCAC 59.756 55.000 0.00 0.00 0.00 3.51
4752 4908 9.107177 ACACAGAGCTATTTTGATTCAATAGAG 57.893 33.333 10.03 8.55 36.64 2.43
4938 5094 3.799917 GCCCAAAGTCATCAAGTTTGTGG 60.800 47.826 5.03 6.56 43.83 4.17
5087 5243 2.842496 AGCAGAAGATGAAGGATGGACA 59.158 45.455 0.00 0.00 0.00 4.02
5169 5325 2.501723 AGGTTATATATGGCGCCTCCTG 59.498 50.000 29.70 0.00 35.26 3.86
5233 5389 4.145807 AGGTATCGGTGAGTAGATTGAGG 58.854 47.826 0.00 0.00 0.00 3.86
5339 5501 1.267806 ACTGCAAAAGAAGCACGGATG 59.732 47.619 0.00 0.00 37.02 3.51
5357 5519 5.010012 GTCATGTTCCCAACAGAAATTCACT 59.990 40.000 0.00 0.00 45.95 3.41
5486 5648 1.900351 CTCAACTCATCGGCCTCCA 59.100 57.895 0.00 0.00 0.00 3.86
5556 5718 1.953686 AGCGGCTAAAACTTTGCAAGA 59.046 42.857 0.00 0.00 0.00 3.02
5749 5954 1.089920 GCTGAGCGGAATGTGTGAAT 58.910 50.000 0.00 0.00 0.00 2.57
5867 6076 5.678955 ATTTCTCTATAATAGACCCGGGC 57.321 43.478 24.08 14.21 0.00 6.13
5910 6119 0.901114 TCTAGTGCCAAGGCCGTACA 60.901 55.000 8.89 0.00 41.09 2.90
5911 6120 0.248289 TTCTAGTGCCAAGGCCGTAC 59.752 55.000 8.89 0.00 41.09 3.67
5912 6121 0.978151 TTTCTAGTGCCAAGGCCGTA 59.022 50.000 8.89 0.00 41.09 4.02
5913 6122 0.605589 GTTTCTAGTGCCAAGGCCGT 60.606 55.000 8.89 0.00 41.09 5.68
5914 6123 0.321653 AGTTTCTAGTGCCAAGGCCG 60.322 55.000 8.89 0.00 41.09 6.13
5915 6124 2.781681 TAGTTTCTAGTGCCAAGGCC 57.218 50.000 8.89 0.00 41.09 5.19
5916 6125 4.811557 CACTATAGTTTCTAGTGCCAAGGC 59.188 45.833 1.56 3.61 39.57 4.35
5917 6126 5.128827 TCCACTATAGTTTCTAGTGCCAAGG 59.871 44.000 1.56 0.00 43.03 3.61
5918 6127 6.222038 TCCACTATAGTTTCTAGTGCCAAG 57.778 41.667 1.56 0.00 43.03 3.61
5919 6128 6.439375 TCTTCCACTATAGTTTCTAGTGCCAA 59.561 38.462 1.56 0.92 43.03 4.52
5920 6129 5.955959 TCTTCCACTATAGTTTCTAGTGCCA 59.044 40.000 1.56 0.00 43.03 4.92
5921 6130 6.321690 TCTCTTCCACTATAGTTTCTAGTGCC 59.678 42.308 1.56 0.00 43.03 5.01
5922 6131 7.336161 TCTCTTCCACTATAGTTTCTAGTGC 57.664 40.000 1.56 0.00 43.03 4.40
5923 6132 9.179909 TCTTCTCTTCCACTATAGTTTCTAGTG 57.820 37.037 1.56 3.96 43.67 2.74
5924 6133 9.403583 CTCTTCTCTTCCACTATAGTTTCTAGT 57.596 37.037 1.56 0.00 0.00 2.57
5925 6134 8.846211 CCTCTTCTCTTCCACTATAGTTTCTAG 58.154 40.741 1.56 0.00 0.00 2.43
5926 6135 7.780745 CCCTCTTCTCTTCCACTATAGTTTCTA 59.219 40.741 1.56 0.00 0.00 2.10
5927 6136 6.609616 CCCTCTTCTCTTCCACTATAGTTTCT 59.390 42.308 1.56 0.00 0.00 2.52
5928 6137 6.183360 CCCCTCTTCTCTTCCACTATAGTTTC 60.183 46.154 1.56 0.00 0.00 2.78
5929 6138 5.663556 CCCCTCTTCTCTTCCACTATAGTTT 59.336 44.000 1.56 0.00 0.00 2.66
5930 6139 5.212745 CCCCTCTTCTCTTCCACTATAGTT 58.787 45.833 1.56 0.00 0.00 2.24
5931 6140 4.810345 CCCCTCTTCTCTTCCACTATAGT 58.190 47.826 0.00 0.00 0.00 2.12
5932 6141 3.576550 GCCCCTCTTCTCTTCCACTATAG 59.423 52.174 0.00 0.00 0.00 1.31
5933 6142 3.052109 TGCCCCTCTTCTCTTCCACTATA 60.052 47.826 0.00 0.00 0.00 1.31
5934 6143 2.293184 TGCCCCTCTTCTCTTCCACTAT 60.293 50.000 0.00 0.00 0.00 2.12
5935 6144 1.078823 TGCCCCTCTTCTCTTCCACTA 59.921 52.381 0.00 0.00 0.00 2.74
5936 6145 0.178891 TGCCCCTCTTCTCTTCCACT 60.179 55.000 0.00 0.00 0.00 4.00
5937 6146 0.693049 TTGCCCCTCTTCTCTTCCAC 59.307 55.000 0.00 0.00 0.00 4.02
5938 6147 1.444933 TTTGCCCCTCTTCTCTTCCA 58.555 50.000 0.00 0.00 0.00 3.53
5939 6148 2.816777 ATTTGCCCCTCTTCTCTTCC 57.183 50.000 0.00 0.00 0.00 3.46
5940 6149 4.339748 AGAAATTTGCCCCTCTTCTCTTC 58.660 43.478 0.00 0.00 0.00 2.87
5941 6150 4.043938 AGAGAAATTTGCCCCTCTTCTCTT 59.956 41.667 6.79 0.00 46.38 2.85
5942 6151 3.591079 AGAGAAATTTGCCCCTCTTCTCT 59.409 43.478 6.79 6.79 44.68 3.10
5943 6152 3.961849 AGAGAAATTTGCCCCTCTTCTC 58.038 45.455 0.00 2.60 41.43 2.87
5944 6153 5.723860 ATAGAGAAATTTGCCCCTCTTCT 57.276 39.130 11.20 0.00 37.25 2.85
5945 6154 9.225436 CTATTATAGAGAAATTTGCCCCTCTTC 57.775 37.037 11.20 0.00 37.25 2.87
5946 6155 8.949421 TCTATTATAGAGAAATTTGCCCCTCTT 58.051 33.333 11.20 4.49 37.25 2.85
5947 6156 8.379331 GTCTATTATAGAGAAATTTGCCCCTCT 58.621 37.037 1.66 10.84 39.17 3.69
5948 6157 8.379331 AGTCTATTATAGAGAAATTTGCCCCTC 58.621 37.037 1.66 0.00 35.04 4.30
5949 6158 8.281529 AGTCTATTATAGAGAAATTTGCCCCT 57.718 34.615 1.66 0.00 35.04 4.79
5950 6159 8.926092 AAGTCTATTATAGAGAAATTTGCCCC 57.074 34.615 1.66 0.00 35.04 5.80
6009 6218 2.762535 ACGAAGGGACATACAACCAG 57.237 50.000 0.00 0.00 0.00 4.00
6073 6282 7.735917 TGGTTATATCGGATGTTCTCTTGATT 58.264 34.615 0.00 0.00 0.00 2.57
6074 6283 7.233553 TCTGGTTATATCGGATGTTCTCTTGAT 59.766 37.037 0.00 0.00 0.00 2.57
6075 6284 6.549736 TCTGGTTATATCGGATGTTCTCTTGA 59.450 38.462 0.00 0.00 0.00 3.02
6077 6286 6.978674 TCTGGTTATATCGGATGTTCTCTT 57.021 37.500 0.00 0.00 0.00 2.85
6078 6287 7.148222 CGTATCTGGTTATATCGGATGTTCTCT 60.148 40.741 0.00 0.00 32.92 3.10
6079 6288 6.967767 CGTATCTGGTTATATCGGATGTTCTC 59.032 42.308 0.00 0.00 32.92 2.87
6080 6289 6.127703 CCGTATCTGGTTATATCGGATGTTCT 60.128 42.308 0.00 0.00 38.96 3.01
6081 6290 6.034591 CCGTATCTGGTTATATCGGATGTTC 58.965 44.000 0.00 0.00 38.96 3.18
6082 6291 5.105473 CCCGTATCTGGTTATATCGGATGTT 60.105 44.000 0.00 0.00 38.96 2.71
6083 6292 4.401519 CCCGTATCTGGTTATATCGGATGT 59.598 45.833 0.00 0.00 38.96 3.06
6085 6294 4.863548 TCCCGTATCTGGTTATATCGGAT 58.136 43.478 0.00 0.00 38.96 4.18
6086 6295 4.305539 TCCCGTATCTGGTTATATCGGA 57.694 45.455 0.00 0.00 38.96 4.55
6087 6296 5.047519 AGTTTCCCGTATCTGGTTATATCGG 60.048 44.000 0.00 0.00 36.85 4.18
6088 6297 5.862323 CAGTTTCCCGTATCTGGTTATATCG 59.138 44.000 0.00 0.00 0.00 2.92
6090 6299 6.989155 TCAGTTTCCCGTATCTGGTTATAT 57.011 37.500 0.00 0.00 0.00 0.86
6092 6301 5.425630 GTTCAGTTTCCCGTATCTGGTTAT 58.574 41.667 0.00 0.00 0.00 1.89
6094 6303 3.558533 GGTTCAGTTTCCCGTATCTGGTT 60.559 47.826 0.00 0.00 0.00 3.67
6095 6304 2.027469 GGTTCAGTTTCCCGTATCTGGT 60.027 50.000 0.00 0.00 0.00 4.00
6096 6305 2.236395 AGGTTCAGTTTCCCGTATCTGG 59.764 50.000 0.00 0.00 0.00 3.86
6098 6307 5.482878 TCTTTAGGTTCAGTTTCCCGTATCT 59.517 40.000 0.00 0.00 0.00 1.98
6099 6308 5.579904 GTCTTTAGGTTCAGTTTCCCGTATC 59.420 44.000 0.00 0.00 0.00 2.24
6101 6310 4.559300 CGTCTTTAGGTTCAGTTTCCCGTA 60.559 45.833 0.00 0.00 0.00 4.02
6103 6312 2.735134 CGTCTTTAGGTTCAGTTTCCCG 59.265 50.000 0.00 0.00 0.00 5.14
6104 6313 3.736720 ACGTCTTTAGGTTCAGTTTCCC 58.263 45.455 0.00 0.00 0.00 3.97
6105 6314 5.291971 TGTACGTCTTTAGGTTCAGTTTCC 58.708 41.667 0.00 0.00 0.00 3.13
6107 6316 6.152932 TCTGTACGTCTTTAGGTTCAGTTT 57.847 37.500 0.00 0.00 38.94 2.66
6108 6317 5.779529 TCTGTACGTCTTTAGGTTCAGTT 57.220 39.130 0.00 0.00 38.94 3.16
6109 6318 5.779529 TTCTGTACGTCTTTAGGTTCAGT 57.220 39.130 0.00 0.00 38.94 3.41
6110 6319 6.866770 TCATTTCTGTACGTCTTTAGGTTCAG 59.133 38.462 0.00 0.00 39.11 3.02
6111 6320 6.643770 GTCATTTCTGTACGTCTTTAGGTTCA 59.356 38.462 0.00 0.00 0.00 3.18
6125 6442 5.484715 CCTTCGTTTAGGGTCATTTCTGTA 58.515 41.667 0.00 0.00 0.00 2.74
6158 6475 2.979814 TCCGAGTCATGTGGTATTGG 57.020 50.000 0.00 0.00 0.00 3.16
6162 6479 4.819105 AGAATTTCCGAGTCATGTGGTA 57.181 40.909 0.00 0.00 0.00 3.25
6175 6492 6.524586 CAGTTGCGACTTTGATAAGAATTTCC 59.475 38.462 3.02 0.00 35.30 3.13
6176 6493 7.298122 TCAGTTGCGACTTTGATAAGAATTTC 58.702 34.615 3.02 0.00 35.30 2.17
6185 6502 2.476619 CGAGTTCAGTTGCGACTTTGAT 59.523 45.455 3.02 0.00 32.54 2.57
6192 6509 1.069090 AAGGCGAGTTCAGTTGCGA 59.931 52.632 0.00 0.00 0.00 5.10
6207 6524 1.120795 ACAATGGTGGCCCAACAAGG 61.121 55.000 5.08 3.10 46.04 3.61
6209 6526 1.207791 AAACAATGGTGGCCCAACAA 58.792 45.000 5.08 0.00 46.04 2.83
6215 6533 1.337354 CCGGTAAAAACAATGGTGGCC 60.337 52.381 0.00 0.00 0.00 5.36
6217 6535 1.341531 TGCCGGTAAAAACAATGGTGG 59.658 47.619 1.90 0.00 0.00 4.61
6226 6544 2.232452 CCATCACCATTGCCGGTAAAAA 59.768 45.455 9.67 0.00 37.07 1.94
6228 6546 1.004862 TCCATCACCATTGCCGGTAAA 59.995 47.619 9.67 0.94 37.07 2.01
6231 6549 1.077501 CTCCATCACCATTGCCGGT 60.078 57.895 1.90 0.00 41.07 5.28
6276 8443 2.118404 CACCCACACACCCACACAC 61.118 63.158 0.00 0.00 0.00 3.82
6279 8446 2.273776 CACACCCACACACCCACA 59.726 61.111 0.00 0.00 0.00 4.17
6281 8448 2.273776 CACACACCCACACACCCA 59.726 61.111 0.00 0.00 0.00 4.51
6284 8451 0.958382 ACACACACACACCCACACAC 60.958 55.000 0.00 0.00 0.00 3.82
6285 8452 0.957888 CACACACACACACCCACACA 60.958 55.000 0.00 0.00 0.00 3.72
6286 8453 0.958382 ACACACACACACACCCACAC 60.958 55.000 0.00 0.00 0.00 3.82
6287 8454 0.957888 CACACACACACACACCCACA 60.958 55.000 0.00 0.00 0.00 4.17
6288 8455 1.800032 CACACACACACACACCCAC 59.200 57.895 0.00 0.00 0.00 4.61
6289 8456 2.043405 GCACACACACACACACCCA 61.043 57.895 0.00 0.00 0.00 4.51
6290 8457 2.043405 TGCACACACACACACACCC 61.043 57.895 0.00 0.00 0.00 4.61
6291 8458 1.136565 GTGCACACACACACACACC 59.863 57.895 13.17 0.00 46.61 4.16
6292 8459 4.763593 GTGCACACACACACACAC 57.236 55.556 13.17 0.00 46.61 3.82
6300 8467 1.469940 CCTAGATCGAGGTGCACACAC 60.470 57.143 20.43 8.07 46.66 3.82
6301 8468 0.817654 CCTAGATCGAGGTGCACACA 59.182 55.000 20.43 0.00 0.00 3.72
6302 8469 3.650409 CCTAGATCGAGGTGCACAC 57.350 57.895 20.43 11.06 0.00 3.82
6325 8492 4.382685 GGTCTAGCAATACTGGTGTGCTTA 60.383 45.833 15.33 5.85 46.25 3.09
6336 8503 2.104792 TGATGGCCTGGTCTAGCAATAC 59.895 50.000 3.32 0.00 0.00 1.89
6373 8540 9.933723 CTTCAACAATCCCTTTTATTTCAATCT 57.066 29.630 0.00 0.00 0.00 2.40
6374 8541 9.927668 TCTTCAACAATCCCTTTTATTTCAATC 57.072 29.630 0.00 0.00 0.00 2.67
6376 8543 7.865385 CGTCTTCAACAATCCCTTTTATTTCAA 59.135 33.333 0.00 0.00 0.00 2.69
6377 8544 7.367285 CGTCTTCAACAATCCCTTTTATTTCA 58.633 34.615 0.00 0.00 0.00 2.69
6378 8545 6.806739 CCGTCTTCAACAATCCCTTTTATTTC 59.193 38.462 0.00 0.00 0.00 2.17
6382 8549 3.504520 GCCGTCTTCAACAATCCCTTTTA 59.495 43.478 0.00 0.00 0.00 1.52
6384 8551 1.886542 GCCGTCTTCAACAATCCCTTT 59.113 47.619 0.00 0.00 0.00 3.11
6415 8585 6.369890 TCAATTCCTTTTCGAATCTCTGTGAG 59.630 38.462 0.00 0.00 31.14 3.51
6421 8591 7.978982 TCTTCATCAATTCCTTTTCGAATCTC 58.021 34.615 0.00 0.00 31.14 2.75
6427 8597 8.746922 TCATTTTCTTCATCAATTCCTTTTCG 57.253 30.769 0.00 0.00 0.00 3.46
6455 8625 2.556840 ATAGGCACTGCGGGCAACAT 62.557 55.000 0.00 0.00 41.52 2.71
6456 8626 3.266686 ATAGGCACTGCGGGCAACA 62.267 57.895 0.00 0.00 41.52 3.33
6458 8628 2.438254 CATAGGCACTGCGGGCAA 60.438 61.111 0.00 0.00 41.52 4.52
6482 8652 2.450160 GTTCTTTGTGTCAAGTTGGCG 58.550 47.619 2.48 0.00 0.00 5.69
6507 8677 1.593006 CTGTTATTCATGGACGACGCC 59.407 52.381 0.00 0.00 0.00 5.68
6510 8680 3.521560 TCTGCTGTTATTCATGGACGAC 58.478 45.455 0.00 0.00 0.00 4.34
6528 8698 3.217626 AGGTTGGCAGTTTTTCTCTCTG 58.782 45.455 0.00 0.00 0.00 3.35
6529 8699 3.481453 GAGGTTGGCAGTTTTTCTCTCT 58.519 45.455 0.00 0.00 0.00 3.10
6530 8700 2.554462 GGAGGTTGGCAGTTTTTCTCTC 59.446 50.000 0.00 0.00 0.00 3.20
6531 8701 2.175715 AGGAGGTTGGCAGTTTTTCTCT 59.824 45.455 0.00 0.00 0.00 3.10
6532 8702 2.554462 GAGGAGGTTGGCAGTTTTTCTC 59.446 50.000 0.00 0.00 0.00 2.87
6533 8703 2.091885 TGAGGAGGTTGGCAGTTTTTCT 60.092 45.455 0.00 0.00 0.00 2.52
6534 8704 2.294512 CTGAGGAGGTTGGCAGTTTTTC 59.705 50.000 0.00 0.00 0.00 2.29
6535 8705 2.310538 CTGAGGAGGTTGGCAGTTTTT 58.689 47.619 0.00 0.00 0.00 1.94
6536 8706 1.986882 CTGAGGAGGTTGGCAGTTTT 58.013 50.000 0.00 0.00 0.00 2.43
6537 8707 0.538287 GCTGAGGAGGTTGGCAGTTT 60.538 55.000 0.00 0.00 0.00 2.66
6538 8708 1.073897 GCTGAGGAGGTTGGCAGTT 59.926 57.895 0.00 0.00 0.00 3.16
6539 8709 1.708993 TTGCTGAGGAGGTTGGCAGT 61.709 55.000 0.00 0.00 34.37 4.40
6540 8710 1.073722 TTGCTGAGGAGGTTGGCAG 59.926 57.895 0.00 0.00 34.37 4.85
6541 8711 1.228245 GTTGCTGAGGAGGTTGGCA 60.228 57.895 0.00 0.00 0.00 4.92
6542 8712 2.328099 CGTTGCTGAGGAGGTTGGC 61.328 63.158 0.00 0.00 0.00 4.52
6543 8713 1.672356 CCGTTGCTGAGGAGGTTGG 60.672 63.158 0.00 0.00 0.00 3.77
6544 8714 2.328099 GCCGTTGCTGAGGAGGTTG 61.328 63.158 0.00 0.00 33.53 3.77
6545 8715 2.032681 GCCGTTGCTGAGGAGGTT 59.967 61.111 0.00 0.00 33.53 3.50
6546 8716 4.379243 CGCCGTTGCTGAGGAGGT 62.379 66.667 0.00 0.00 34.43 3.85
6548 8718 4.069232 TCCGCCGTTGCTGAGGAG 62.069 66.667 0.00 0.00 34.43 3.69
6549 8719 4.373116 GTCCGCCGTTGCTGAGGA 62.373 66.667 0.00 0.00 30.88 3.71
6551 8721 4.680237 TGGTCCGCCGTTGCTGAG 62.680 66.667 0.00 0.00 37.67 3.35
6552 8722 2.173758 TATTGGTCCGCCGTTGCTGA 62.174 55.000 0.00 0.00 37.67 4.26
6553 8723 1.743623 TATTGGTCCGCCGTTGCTG 60.744 57.895 0.00 0.00 37.67 4.41
6554 8724 2.666207 TATTGGTCCGCCGTTGCT 59.334 55.556 0.00 0.00 37.67 3.91


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

AutoCloner maintained by Alex Coulton.