Multiple sequence alignment - TraesCS7D01G450100

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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 TraesCS7D01G450100 chr7D 100.000 6532 0 0 1 6532 569053253 569046722 0.000000e+00 12063.0
1 TraesCS7D01G450100 chr7D 88.776 98 5 4 6165 6259 569028384 569028290 1.490000e-21 115.0
2 TraesCS7D01G450100 chr7A 91.853 4738 201 76 1820 6445 657905908 657901244 0.000000e+00 6440.0
3 TraesCS7D01G450100 chr7A 93.644 1180 63 6 653 1821 657907168 657905990 0.000000e+00 1753.0
4 TraesCS7D01G450100 chr7A 89.908 654 47 3 4 656 657908066 657907431 0.000000e+00 824.0
5 TraesCS7D01G450100 chr7A 82.313 147 21 4 6187 6330 657890217 657890073 8.890000e-24 122.0
6 TraesCS7D01G450100 chr7B 92.927 4510 172 49 1653 6067 625720262 625715805 0.000000e+00 6425.0
7 TraesCS7D01G450100 chr7B 93.239 1065 57 13 757 1809 625721318 625720257 0.000000e+00 1554.0
8 TraesCS7D01G450100 chr7B 91.127 417 31 5 4 418 625729491 625729079 1.590000e-155 560.0
9 TraesCS7D01G450100 chr7B 89.711 311 32 0 416 726 625728940 625728630 1.320000e-106 398.0
10 TraesCS7D01G450100 chr7B 85.185 216 17 4 6106 6310 625715718 625715507 2.390000e-49 207.0
11 TraesCS7D01G450100 chr7B 80.992 242 25 15 6155 6386 625398877 625398647 8.710000e-39 172.0
12 TraesCS7D01G450100 chr7B 85.149 101 5 7 6292 6392 625711159 625711069 1.940000e-15 95.3
13 TraesCS7D01G450100 chr3D 91.566 83 7 0 306 388 42787845 42787763 1.490000e-21 115.0


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 TraesCS7D01G450100 chr7D 569046722 569053253 6531 True 12063.000000 12063 100.000000 1 6532 1 chr7D.!!$R2 6531
1 TraesCS7D01G450100 chr7A 657901244 657908066 6822 True 3005.666667 6440 91.801667 4 6445 3 chr7A.!!$R2 6441
2 TraesCS7D01G450100 chr7B 625715507 625721318 5811 True 2728.666667 6425 90.450333 757 6310 3 chr7B.!!$R3 5553
3 TraesCS7D01G450100 chr7B 625728630 625729491 861 True 479.000000 560 90.419000 4 726 2 chr7B.!!$R4 722

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
826 1254 0.096976 AAAATCATCCGAGCAACGCG 59.903 50.000 3.53 3.53 41.07 6.01 F
1593 2038 0.032540 GCCAAAATCCATGGATCGGC 59.967 55.000 31.45 31.45 40.56 5.54 F
2497 3189 1.379977 CCTGGAGGGAGTAGTGCGA 60.380 63.158 0.00 0.00 37.23 5.10 F
3425 4117 2.350772 GGGTTGTGCAAAGATGACTTCG 60.351 50.000 0.00 0.00 35.05 3.79 F
4109 4802 1.134175 CATTGTGGGGATACAAACGGC 59.866 52.381 0.00 0.00 43.13 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2608 0.956410 TGTACCGACAATTTGGGCCG 60.956 55.0 0.00 1.82 30.68 6.13 R
3561 4253 0.318699 GAGGACCAAGCGGCAAAAAC 60.319 55.0 1.45 0.00 34.57 2.43 R
3659 4352 0.038744 AGACAGGCTGGACCCAAATG 59.961 55.0 20.34 0.00 40.58 2.32 R
4522 5234 0.872388 GCACCCCTGTTGTTTCTACG 59.128 55.0 0.00 0.00 0.00 3.51 R
6094 6882 0.032678 ATGGCTAGCAGATTCGACCG 59.967 55.0 18.24 0.00 0.00 4.79 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
75 76 2.021068 ATCACTGGGATCCTGTCGCG 62.021 60.000 12.58 0.00 42.37 5.87
127 128 7.316544 ACGATTTGACCAATATCAGTAAACC 57.683 36.000 0.00 0.00 0.00 3.27
128 129 7.110155 ACGATTTGACCAATATCAGTAAACCT 58.890 34.615 0.00 0.00 0.00 3.50
163 164 4.489771 GAGCATCCACCACCCCCG 62.490 72.222 0.00 0.00 0.00 5.73
306 308 1.788229 TCGCCATCCTTCAGGTGATA 58.212 50.000 0.00 0.00 39.36 2.15
307 309 2.115427 TCGCCATCCTTCAGGTGATAA 58.885 47.619 0.00 0.00 39.36 1.75
308 310 2.158957 TCGCCATCCTTCAGGTGATAAC 60.159 50.000 0.00 0.00 39.36 1.89
309 311 2.158900 CGCCATCCTTCAGGTGATAACT 60.159 50.000 0.00 0.00 37.61 2.24
310 312 3.471680 GCCATCCTTCAGGTGATAACTC 58.528 50.000 0.00 0.00 36.34 3.01
311 313 3.118261 GCCATCCTTCAGGTGATAACTCA 60.118 47.826 0.00 0.00 36.34 3.41
312 314 4.626287 GCCATCCTTCAGGTGATAACTCAA 60.626 45.833 0.00 0.00 36.34 3.02
313 315 5.688807 CCATCCTTCAGGTGATAACTCAAT 58.311 41.667 0.00 0.00 36.34 2.57
314 316 5.762218 CCATCCTTCAGGTGATAACTCAATC 59.238 44.000 0.00 0.00 36.34 2.67
315 317 6.351711 CATCCTTCAGGTGATAACTCAATCA 58.648 40.000 0.00 0.00 36.34 2.57
316 318 5.982356 TCCTTCAGGTGATAACTCAATCAG 58.018 41.667 0.00 0.00 36.57 2.90
321 323 3.310303 GTGATAACTCAATCAGCACGC 57.690 47.619 0.00 0.00 36.57 5.34
322 324 2.030946 GTGATAACTCAATCAGCACGCC 59.969 50.000 0.00 0.00 36.57 5.68
409 428 6.266131 ACAATAGCCTTTCATAAGATCCCA 57.734 37.500 0.00 0.00 32.92 4.37
431 591 9.142014 TCCCAATACATTTAATAATTGTCCCAG 57.858 33.333 4.09 0.00 0.00 4.45
444 604 3.237268 TGTCCCAGCACATAGGTTTTT 57.763 42.857 0.00 0.00 0.00 1.94
478 638 6.205464 TGTCTTTGAGCTTGTCTTTCATAAGG 59.795 38.462 0.00 0.00 32.02 2.69
496 656 6.269077 TCATAAGGTCCCTTATTGCTCGAATA 59.731 38.462 14.56 0.00 44.18 1.75
516 676 6.385649 AATACTTGCAACCATATAAACGGG 57.614 37.500 0.00 0.00 0.00 5.28
520 680 0.948678 CAACCATATAAACGGGCGGG 59.051 55.000 0.00 0.00 0.00 6.13
553 713 5.357032 TCTCGAGCTTTTTGACCTTTTCTTT 59.643 36.000 7.81 0.00 0.00 2.52
561 721 9.098355 GCTTTTTGACCTTTTCTTTTCTACATT 57.902 29.630 0.00 0.00 0.00 2.71
577 737 5.109210 TCTACATTAAGATGTTGTGCTCCG 58.891 41.667 0.00 0.00 43.92 4.63
586 746 3.233259 TTGTGCTCCGCATCCACGA 62.233 57.895 0.00 0.00 41.91 4.35
601 761 1.671261 CCACGACAGGAGCTCTTTCTG 60.671 57.143 14.64 14.67 34.91 3.02
618 778 2.290122 CTGTGCTCCCTCCGCTACTG 62.290 65.000 0.00 0.00 0.00 2.74
625 785 0.686769 CCCTCCGCTACTGTAGGGTT 60.687 60.000 24.57 0.00 43.26 4.11
826 1254 0.096976 AAAATCATCCGAGCAACGCG 59.903 50.000 3.53 3.53 41.07 6.01
961 1397 3.358118 ACCCTTCTCTAGTCGAAAGAGG 58.642 50.000 20.32 11.36 43.49 3.69
963 1399 2.691011 CCTTCTCTAGTCGAAAGAGGGG 59.309 54.545 20.32 18.21 43.49 4.79
1389 1834 2.166459 GCTCCCCCAAAGCTATTTGTTC 59.834 50.000 0.00 0.00 43.61 3.18
1425 1870 6.205270 TCGGGAAGTAGTTAATTTTTGTCACC 59.795 38.462 0.00 0.00 0.00 4.02
1457 1902 4.332828 TCGTTCTCACTCTTGGAGATGTA 58.667 43.478 1.31 0.00 40.82 2.29
1508 1953 5.575218 GGCAATTACGATTTGTTAACTTGGG 59.425 40.000 7.22 0.00 0.00 4.12
1518 1963 4.281898 TGTTAACTTGGGAAGCTACCTC 57.718 45.455 7.22 0.00 0.00 3.85
1519 1964 3.259902 GTTAACTTGGGAAGCTACCTCG 58.740 50.000 8.65 2.88 0.00 4.63
1521 1966 1.349067 ACTTGGGAAGCTACCTCGTT 58.651 50.000 8.65 0.00 0.00 3.85
1522 1967 2.532843 ACTTGGGAAGCTACCTCGTTA 58.467 47.619 8.65 0.00 0.00 3.18
1540 1985 4.083003 TCGTTAGGTGTTCATTTCATTGGC 60.083 41.667 0.00 0.00 0.00 4.52
1574 2019 1.542492 AGGCTTTGAGATTGCTGTGG 58.458 50.000 0.00 0.00 0.00 4.17
1593 2038 0.032540 GCCAAAATCCATGGATCGGC 59.967 55.000 31.45 31.45 40.56 5.54
1615 2060 5.297029 GGCCTTCAATTGTTATCCTGTAGTC 59.703 44.000 5.13 0.00 0.00 2.59
1728 2328 2.023673 TGAAGTTGGTTGCAACAGAGG 58.976 47.619 29.55 0.00 37.52 3.69
1734 2334 1.421268 TGGTTGCAACAGAGGATGACT 59.579 47.619 29.55 0.00 0.00 3.41
1735 2335 1.808945 GGTTGCAACAGAGGATGACTG 59.191 52.381 29.55 0.00 40.68 3.51
1742 2342 5.891551 TGCAACAGAGGATGACTGTAGTATA 59.108 40.000 0.00 0.00 46.01 1.47
1754 2354 7.312657 TGACTGTAGTATAACTTGTAGACCG 57.687 40.000 0.00 0.00 0.00 4.79
1783 2383 5.107989 CGATGCAAGATGCTAATTCAAATGC 60.108 40.000 3.78 0.00 45.31 3.56
1806 2406 4.151335 CACTGTGACACTAATGAGCTGTTC 59.849 45.833 7.20 0.00 0.00 3.18
1894 2580 4.323417 GTTGTGTATCTCATGGTGGTTCA 58.677 43.478 0.00 0.00 0.00 3.18
1934 2620 2.970205 CCCTAACGGCCCAAATTGT 58.030 52.632 0.00 0.00 0.00 2.71
1955 2641 2.805671 TCGGTACAAGCATGTCAAGTTG 59.194 45.455 0.00 0.00 41.05 3.16
2009 2695 2.598589 GCAAAGATTTTGCAGATGCGA 58.401 42.857 18.63 0.00 45.83 5.10
2328 3020 2.143925 GGTGTGTGTGGAGTTTCTAGC 58.856 52.381 0.00 0.00 0.00 3.42
2497 3189 1.379977 CCTGGAGGGAGTAGTGCGA 60.380 63.158 0.00 0.00 37.23 5.10
2599 3291 4.434520 GCCTTATAGTTTCTCGCTGACTT 58.565 43.478 0.00 0.00 0.00 3.01
2772 3464 8.192774 ACATAAGTAAATCCAAATGTGCATCAG 58.807 33.333 0.00 0.00 0.00 2.90
3083 3775 5.950549 AGTTCTCTAATTAGTCTCGGGTTCA 59.049 40.000 12.19 0.00 0.00 3.18
3306 3998 8.268850 TCTTTGCTATTTTTCCTGACTATGAC 57.731 34.615 0.00 0.00 0.00 3.06
3307 3999 7.882791 TCTTTGCTATTTTTCCTGACTATGACA 59.117 33.333 0.00 0.00 0.00 3.58
3392 4084 9.868277 AGATGCATATTTAGCTCTAATACTGTC 57.132 33.333 0.00 0.00 0.00 3.51
3425 4117 2.350772 GGGTTGTGCAAAGATGACTTCG 60.351 50.000 0.00 0.00 35.05 3.79
3534 4226 8.333186 GGCTTAAGGTACATGTTTTCTTATACG 58.667 37.037 2.30 3.97 0.00 3.06
3659 4352 4.857037 GTCACGTGGAAATATTTTGCCTTC 59.143 41.667 17.00 0.00 30.81 3.46
3868 4561 8.150945 GCTGTTTGATATCTCCTACATTCCTAA 58.849 37.037 3.98 0.00 0.00 2.69
4103 4796 4.228438 TGAATGTACCATTGTGGGGATACA 59.772 41.667 0.52 1.31 43.37 2.29
4109 4802 1.134175 CATTGTGGGGATACAAACGGC 59.866 52.381 0.00 0.00 43.13 5.68
4181 4874 2.708861 AGAAGTACCATCACACCACCAA 59.291 45.455 0.00 0.00 0.00 3.67
4198 4900 5.163513 CCACCAATGCAGAAGAATTTACAC 58.836 41.667 0.00 0.00 0.00 2.90
4208 4910 7.333423 TGCAGAAGAATTTACACGTATAGCTTT 59.667 33.333 0.00 0.00 0.00 3.51
4226 4928 5.473039 AGCTTTACCATTTTCATTCAGCAC 58.527 37.500 0.00 0.00 0.00 4.40
4241 4943 1.895798 CAGCACCTTGGAGACAGACTA 59.104 52.381 0.00 0.00 44.54 2.59
4300 5002 7.717875 GGTAACCAATAGCCACATGTTAGAATA 59.282 37.037 0.00 0.00 0.00 1.75
4402 5105 9.571816 AAGTCAGTAAGTACTAGGGATACATAC 57.428 37.037 0.00 0.00 34.13 2.39
4522 5234 2.391616 TGCACACATGATGACCTCTC 57.608 50.000 0.00 0.00 0.00 3.20
4529 5241 4.462834 ACACATGATGACCTCTCGTAGAAA 59.537 41.667 0.00 0.00 34.09 2.52
4536 5248 3.005472 TGACCTCTCGTAGAAACAACAGG 59.995 47.826 0.00 0.00 34.09 4.00
4545 5257 1.111277 GAAACAACAGGGGTGCAACT 58.889 50.000 0.00 0.00 36.74 3.16
4565 5277 6.572119 GCAACTCCATTATTTTGTGGTGATCA 60.572 38.462 0.00 0.00 36.84 2.92
4567 5279 5.126061 ACTCCATTATTTTGTGGTGATCAGC 59.874 40.000 18.01 18.01 36.84 4.26
4568 5280 5.015515 TCCATTATTTTGTGGTGATCAGCA 58.984 37.500 23.20 23.20 36.84 4.41
4569 5281 5.125900 TCCATTATTTTGTGGTGATCAGCAG 59.874 40.000 27.11 12.16 39.74 4.24
4570 5282 5.345702 CATTATTTTGTGGTGATCAGCAGG 58.654 41.667 27.11 1.39 39.74 4.85
4571 5283 2.363306 TTTTGTGGTGATCAGCAGGT 57.637 45.000 27.11 0.00 39.74 4.00
4572 5284 1.608055 TTTGTGGTGATCAGCAGGTG 58.392 50.000 27.11 0.00 39.74 4.00
4573 5285 0.764271 TTGTGGTGATCAGCAGGTGA 59.236 50.000 27.11 4.40 39.74 4.02
4647 5369 5.539955 TGTGTATGATAGAATGCTAGCTGGA 59.460 40.000 17.23 0.00 34.18 3.86
4730 5475 1.538512 CACTGTTTGAGGTGATGCCAG 59.461 52.381 0.00 0.00 40.61 4.85
4738 5483 1.077716 GGTGATGCCAGGTGTACCC 60.078 63.158 0.00 0.00 37.17 3.69
4811 5556 3.244700 CCAAGAGAGAAGAGGAAAAGGCA 60.245 47.826 0.00 0.00 0.00 4.75
4826 5571 1.073897 GGCAAAGGGAGTCAGTGCT 59.926 57.895 0.00 0.00 35.53 4.40
4907 5652 3.440127 AGAGGAAAGTGAGGAGGAAGAG 58.560 50.000 0.00 0.00 0.00 2.85
4922 5667 2.232208 GGAAGAGGAAAACAATGGCCAG 59.768 50.000 13.05 0.00 0.00 4.85
4985 5730 1.773054 CTCAGATGCAGATGCCACGC 61.773 60.000 1.72 0.00 41.18 5.34
5219 5964 0.472543 TCGAGATGATGATGGGCCCT 60.473 55.000 25.70 8.64 0.00 5.19
5417 6165 2.203153 AACAACGCCGGCAACTCT 60.203 55.556 28.98 4.09 0.00 3.24
5585 6346 5.380043 GAGACTGATCATCTTCTCCTCTCT 58.620 45.833 14.21 0.00 0.00 3.10
5588 6349 3.637694 CTGATCATCTTCTCCTCTCTGCA 59.362 47.826 0.00 0.00 0.00 4.41
5605 6366 0.319040 GCAGAGACGAGTTGTGCTGA 60.319 55.000 12.17 0.00 33.55 4.26
5802 6564 7.810759 TCATTTTGTGACATGTTGAGATTGATG 59.189 33.333 0.00 0.00 0.00 3.07
5824 6587 3.378427 GGCTTGATCCTGTGGTTGATAAC 59.622 47.826 0.00 0.00 0.00 1.89
5902 6671 4.795268 CGCCGTGTTATATAGTCTGTGAT 58.205 43.478 0.00 0.00 0.00 3.06
5936 6705 0.749454 GACATGGTTAGGCTGGGCTG 60.749 60.000 6.93 0.00 0.00 4.85
5938 6707 0.749454 CATGGTTAGGCTGGGCTGTC 60.749 60.000 6.93 0.33 0.00 3.51
5944 6726 0.972983 TAGGCTGGGCTGTCTCTGTC 60.973 60.000 6.93 0.00 0.00 3.51
5964 6746 0.179051 TCTGTCATGCTGTGTGTGCA 60.179 50.000 0.00 0.00 44.95 4.57
5971 6753 1.227943 GCTGTGTGTGCAAGAGGGA 60.228 57.895 0.00 0.00 0.00 4.20
5980 6762 1.211457 GTGCAAGAGGGACCTGATGAT 59.789 52.381 0.00 0.00 0.00 2.45
5982 6764 3.114606 TGCAAGAGGGACCTGATGATTA 58.885 45.455 0.00 0.00 0.00 1.75
5983 6765 3.718434 TGCAAGAGGGACCTGATGATTAT 59.282 43.478 0.00 0.00 0.00 1.28
5994 6776 7.419057 GGGACCTGATGATTATAGTTCAGTTCA 60.419 40.741 0.00 0.00 35.01 3.18
5997 6779 9.911788 ACCTGATGATTATAGTTCAGTTCATTT 57.088 29.630 0.00 0.00 35.01 2.32
6023 6810 8.349568 TCTTTTAGTACTAGCTCATTCTGTGA 57.650 34.615 2.23 0.00 35.05 3.58
6027 6814 6.142818 AGTACTAGCTCATTCTGTGATCAC 57.857 41.667 19.27 19.27 35.97 3.06
6029 6816 5.008619 ACTAGCTCATTCTGTGATCACTG 57.991 43.478 25.55 24.12 35.97 3.66
6032 6819 2.680221 GCTCATTCTGTGATCACTGCCT 60.680 50.000 25.55 12.86 35.97 4.75
6050 6837 2.476997 GCCTTCTTCTTTCGTGTCTGAC 59.523 50.000 0.00 0.00 0.00 3.51
6051 6838 3.717707 CCTTCTTCTTTCGTGTCTGACA 58.282 45.455 6.36 6.36 0.00 3.58
6053 6840 4.387256 CCTTCTTCTTTCGTGTCTGACATC 59.613 45.833 14.37 7.00 0.00 3.06
6054 6841 4.584327 TCTTCTTTCGTGTCTGACATCA 57.416 40.909 14.37 0.54 0.00 3.07
6064 6851 4.377738 CGTGTCTGACATCAATGGTTTCTG 60.378 45.833 14.37 0.00 0.00 3.02
6067 6854 5.700832 TGTCTGACATCAATGGTTTCTGTAC 59.299 40.000 6.36 0.00 0.00 2.90
6069 6856 4.637276 TGACATCAATGGTTTCTGTACGT 58.363 39.130 0.00 0.00 0.00 3.57
6070 6857 5.060506 TGACATCAATGGTTTCTGTACGTT 58.939 37.500 0.00 0.00 0.00 3.99
6081 6869 6.318144 TGGTTTCTGTACGTTTGTAAATGGAA 59.682 34.615 0.00 0.00 30.94 3.53
6084 6872 8.687301 GTTTCTGTACGTTTGTAAATGGAAATG 58.313 33.333 0.00 0.00 30.94 2.32
6085 6873 6.375377 TCTGTACGTTTGTAAATGGAAATGC 58.625 36.000 0.00 0.00 30.94 3.56
6089 6877 6.088883 GTACGTTTGTAAATGGAAATGCCAAG 59.911 38.462 0.00 0.00 40.58 3.61
6090 6878 8.209482 GTACGTTTGTAAATGGAAATGCCAAGT 61.209 37.037 0.00 0.00 40.58 3.16
6095 6883 2.539003 TGGAAATGCCAAGTCGACG 58.461 52.632 10.46 0.00 45.87 5.12
6096 6884 0.953471 TGGAAATGCCAAGTCGACGG 60.953 55.000 10.46 7.56 45.87 4.79
6097 6885 0.953960 GGAAATGCCAAGTCGACGGT 60.954 55.000 10.46 0.00 36.34 4.83
6098 6886 0.442699 GAAATGCCAAGTCGACGGTC 59.557 55.000 10.46 0.00 0.00 4.79
6099 6887 1.289109 AAATGCCAAGTCGACGGTCG 61.289 55.000 23.73 23.73 42.10 4.79
6108 6947 2.771435 TCGACGGTCGAATCTGCTA 58.229 52.632 28.98 5.49 46.90 3.49
6119 6958 0.833287 AATCTGCTAGCCATGGACGT 59.167 50.000 18.40 0.76 0.00 4.34
6126 6965 2.864097 GCTAGCCATGGACGTATGTGAG 60.864 54.545 18.40 0.00 0.00 3.51
6153 6998 2.576615 GATGGAGTTAGCAATGGACCC 58.423 52.381 0.00 0.00 0.00 4.46
6253 7109 5.046288 AGCCAGAAGGGAATCTATCTTTG 57.954 43.478 0.00 0.00 40.01 2.77
6256 7112 3.812053 CAGAAGGGAATCTATCTTTGGCG 59.188 47.826 0.00 0.00 0.00 5.69
6260 7116 2.687935 GGGAATCTATCTTTGGCGCAAA 59.312 45.455 10.83 0.00 0.00 3.68
6261 7117 3.130340 GGGAATCTATCTTTGGCGCAAAA 59.870 43.478 10.10 10.10 32.75 2.44
6323 7183 4.696078 GCATACAGCGCAACATGG 57.304 55.556 11.47 0.00 0.00 3.66
6369 7229 1.377072 CATCACGGCCATCACCACA 60.377 57.895 2.24 0.00 0.00 4.17
6371 7231 2.819984 ATCACGGCCATCACCACACC 62.820 60.000 2.24 0.00 0.00 4.16
6373 7233 4.343323 CGGCCATCACCACACCCA 62.343 66.667 2.24 0.00 0.00 4.51
6378 7238 0.606401 CCATCACCACACCCACAGAC 60.606 60.000 0.00 0.00 0.00 3.51
6381 7241 3.475494 ACCACACCCACAGACGCA 61.475 61.111 0.00 0.00 0.00 5.24
6382 7242 2.972505 CCACACCCACAGACGCAC 60.973 66.667 0.00 0.00 0.00 5.34
6383 7243 3.337889 CACACCCACAGACGCACG 61.338 66.667 0.00 0.00 0.00 5.34
6386 7246 4.969196 ACCCACAGACGCACGCAG 62.969 66.667 0.00 0.00 0.00 5.18
6387 7247 4.662961 CCCACAGACGCACGCAGA 62.663 66.667 0.00 0.00 0.00 4.26
6388 7248 3.406361 CCACAGACGCACGCAGAC 61.406 66.667 0.00 0.00 0.00 3.51
6411 7294 2.044555 CGCCAGAGACCGACTACCA 61.045 63.158 0.00 0.00 0.00 3.25
6440 7323 2.914695 GCAATCTCCTGCATCTCTCT 57.085 50.000 0.00 0.00 42.17 3.10
6441 7324 2.485903 GCAATCTCCTGCATCTCTCTG 58.514 52.381 0.00 0.00 42.17 3.35
6442 7325 2.158928 GCAATCTCCTGCATCTCTCTGT 60.159 50.000 0.00 0.00 42.17 3.41
6443 7326 3.459145 CAATCTCCTGCATCTCTCTGTG 58.541 50.000 0.00 0.00 0.00 3.66
6446 7329 0.252421 TCCTGCATCTCTCTGTGGGT 60.252 55.000 0.00 0.00 0.00 4.51
6447 7330 0.107800 CCTGCATCTCTCTGTGGGTG 60.108 60.000 0.00 0.00 0.00 4.61
6448 7331 0.612229 CTGCATCTCTCTGTGGGTGT 59.388 55.000 0.00 0.00 0.00 4.16
6449 7332 0.322648 TGCATCTCTCTGTGGGTGTG 59.677 55.000 0.00 0.00 0.00 3.82
6450 7333 0.322975 GCATCTCTCTGTGGGTGTGT 59.677 55.000 0.00 0.00 0.00 3.72
6451 7334 1.271054 GCATCTCTCTGTGGGTGTGTT 60.271 52.381 0.00 0.00 0.00 3.32
6452 7335 2.811873 GCATCTCTCTGTGGGTGTGTTT 60.812 50.000 0.00 0.00 0.00 2.83
6453 7336 2.620251 TCTCTCTGTGGGTGTGTTTG 57.380 50.000 0.00 0.00 0.00 2.93
6454 7337 2.115427 TCTCTCTGTGGGTGTGTTTGA 58.885 47.619 0.00 0.00 0.00 2.69
6455 7338 2.705658 TCTCTCTGTGGGTGTGTTTGAT 59.294 45.455 0.00 0.00 0.00 2.57
6456 7339 3.901222 TCTCTCTGTGGGTGTGTTTGATA 59.099 43.478 0.00 0.00 0.00 2.15
6457 7340 4.021104 TCTCTCTGTGGGTGTGTTTGATAG 60.021 45.833 0.00 0.00 0.00 2.08
6458 7341 3.646162 TCTCTGTGGGTGTGTTTGATAGT 59.354 43.478 0.00 0.00 0.00 2.12
6459 7342 4.836175 TCTCTGTGGGTGTGTTTGATAGTA 59.164 41.667 0.00 0.00 0.00 1.82
6460 7343 5.483937 TCTCTGTGGGTGTGTTTGATAGTAT 59.516 40.000 0.00 0.00 0.00 2.12
6461 7344 5.487433 TCTGTGGGTGTGTTTGATAGTATG 58.513 41.667 0.00 0.00 0.00 2.39
6462 7345 4.006989 TGTGGGTGTGTTTGATAGTATGC 58.993 43.478 0.00 0.00 0.00 3.14
6463 7346 4.006989 GTGGGTGTGTTTGATAGTATGCA 58.993 43.478 0.00 0.00 0.00 3.96
6464 7347 4.640201 GTGGGTGTGTTTGATAGTATGCAT 59.360 41.667 3.79 3.79 0.00 3.96
6465 7348 4.639755 TGGGTGTGTTTGATAGTATGCATG 59.360 41.667 10.16 0.00 0.00 4.06
6466 7349 4.036734 GGGTGTGTTTGATAGTATGCATGG 59.963 45.833 10.16 0.00 0.00 3.66
6467 7350 4.881273 GGTGTGTTTGATAGTATGCATGGA 59.119 41.667 10.16 0.00 0.00 3.41
6468 7351 5.220854 GGTGTGTTTGATAGTATGCATGGAC 60.221 44.000 10.16 0.00 0.00 4.02
6469 7352 4.881273 TGTGTTTGATAGTATGCATGGACC 59.119 41.667 10.16 0.00 0.00 4.46
6470 7353 5.126067 GTGTTTGATAGTATGCATGGACCT 58.874 41.667 10.16 2.45 0.00 3.85
6471 7354 6.126911 TGTGTTTGATAGTATGCATGGACCTA 60.127 38.462 10.16 4.69 0.00 3.08
6472 7355 6.425114 GTGTTTGATAGTATGCATGGACCTAG 59.575 42.308 10.16 0.00 0.00 3.02
6473 7356 4.808414 TGATAGTATGCATGGACCTAGC 57.192 45.455 10.16 7.52 0.00 3.42
6474 7357 3.515502 TGATAGTATGCATGGACCTAGCC 59.484 47.826 10.16 2.23 0.00 3.93
6475 7358 2.109229 AGTATGCATGGACCTAGCCT 57.891 50.000 10.16 0.18 0.00 4.58
6476 7359 3.260269 AGTATGCATGGACCTAGCCTA 57.740 47.619 10.16 0.00 0.00 3.93
6477 7360 3.587498 AGTATGCATGGACCTAGCCTAA 58.413 45.455 10.16 0.00 0.00 2.69
6478 7361 4.171234 AGTATGCATGGACCTAGCCTAAT 58.829 43.478 10.16 0.00 0.00 1.73
6479 7362 4.599241 AGTATGCATGGACCTAGCCTAATT 59.401 41.667 10.16 0.00 0.00 1.40
6480 7363 3.213206 TGCATGGACCTAGCCTAATTG 57.787 47.619 6.32 0.00 0.00 2.32
6481 7364 2.509548 TGCATGGACCTAGCCTAATTGT 59.490 45.455 6.32 0.00 0.00 2.71
6482 7365 3.053693 TGCATGGACCTAGCCTAATTGTT 60.054 43.478 6.32 0.00 0.00 2.83
6483 7366 3.565902 GCATGGACCTAGCCTAATTGTTC 59.434 47.826 0.00 0.00 0.00 3.18
6484 7367 4.687219 GCATGGACCTAGCCTAATTGTTCT 60.687 45.833 0.00 0.00 0.00 3.01
6485 7368 5.440610 CATGGACCTAGCCTAATTGTTCTT 58.559 41.667 0.00 0.00 0.00 2.52
6486 7369 5.099042 TGGACCTAGCCTAATTGTTCTTC 57.901 43.478 0.00 0.00 0.00 2.87
6487 7370 4.783227 TGGACCTAGCCTAATTGTTCTTCT 59.217 41.667 0.00 0.00 0.00 2.85
6488 7371 5.250774 TGGACCTAGCCTAATTGTTCTTCTT 59.749 40.000 0.00 0.00 0.00 2.52
6489 7372 6.181190 GGACCTAGCCTAATTGTTCTTCTTT 58.819 40.000 0.00 0.00 0.00 2.52
6490 7373 6.094186 GGACCTAGCCTAATTGTTCTTCTTTG 59.906 42.308 0.00 0.00 0.00 2.77
6491 7374 6.779860 ACCTAGCCTAATTGTTCTTCTTTGA 58.220 36.000 0.00 0.00 0.00 2.69
6492 7375 7.406104 ACCTAGCCTAATTGTTCTTCTTTGAT 58.594 34.615 0.00 0.00 0.00 2.57
6493 7376 8.548877 ACCTAGCCTAATTGTTCTTCTTTGATA 58.451 33.333 0.00 0.00 0.00 2.15
6494 7377 8.831550 CCTAGCCTAATTGTTCTTCTTTGATAC 58.168 37.037 0.00 0.00 0.00 2.24
6495 7378 9.383519 CTAGCCTAATTGTTCTTCTTTGATACA 57.616 33.333 0.00 0.00 0.00 2.29
6496 7379 8.814038 AGCCTAATTGTTCTTCTTTGATACAT 57.186 30.769 0.00 0.00 0.00 2.29
6497 7380 8.680903 AGCCTAATTGTTCTTCTTTGATACATG 58.319 33.333 0.00 0.00 0.00 3.21
6498 7381 7.433425 GCCTAATTGTTCTTCTTTGATACATGC 59.567 37.037 0.00 0.00 0.00 4.06
6499 7382 8.680903 CCTAATTGTTCTTCTTTGATACATGCT 58.319 33.333 0.00 0.00 0.00 3.79
6500 7383 9.499585 CTAATTGTTCTTCTTTGATACATGCTG 57.500 33.333 0.00 0.00 0.00 4.41
6501 7384 7.692460 ATTGTTCTTCTTTGATACATGCTGA 57.308 32.000 0.00 0.00 0.00 4.26
6502 7385 6.732531 TGTTCTTCTTTGATACATGCTGAG 57.267 37.500 0.00 0.00 0.00 3.35
6503 7386 6.233434 TGTTCTTCTTTGATACATGCTGAGT 58.767 36.000 0.00 0.00 0.00 3.41
6504 7387 6.148315 TGTTCTTCTTTGATACATGCTGAGTG 59.852 38.462 0.00 0.00 0.00 3.51
6505 7388 4.633126 TCTTCTTTGATACATGCTGAGTGC 59.367 41.667 0.00 0.00 43.25 4.40
6506 7389 2.931969 TCTTTGATACATGCTGAGTGCG 59.068 45.455 0.00 0.00 46.63 5.34
6507 7390 1.655484 TTGATACATGCTGAGTGCGG 58.345 50.000 0.00 0.00 46.63 5.69
6508 7391 0.823460 TGATACATGCTGAGTGCGGA 59.177 50.000 0.00 0.00 46.63 5.54
6509 7392 1.212616 GATACATGCTGAGTGCGGAC 58.787 55.000 0.00 0.00 46.63 4.79
6510 7393 0.536724 ATACATGCTGAGTGCGGACA 59.463 50.000 10.52 0.00 46.63 4.02
6511 7394 0.536724 TACATGCTGAGTGCGGACAT 59.463 50.000 10.52 0.00 46.63 3.06
6512 7395 0.536724 ACATGCTGAGTGCGGACATA 59.463 50.000 10.52 0.00 46.63 2.29
6513 7396 1.139654 ACATGCTGAGTGCGGACATAT 59.860 47.619 10.52 0.00 46.63 1.78
6514 7397 1.529865 CATGCTGAGTGCGGACATATG 59.470 52.381 10.52 0.00 46.63 1.78
6515 7398 0.536724 TGCTGAGTGCGGACATATGT 59.463 50.000 8.43 8.43 46.63 2.29
6516 7399 1.066215 TGCTGAGTGCGGACATATGTT 60.066 47.619 10.30 0.00 46.63 2.71
6517 7400 1.594862 GCTGAGTGCGGACATATGTTC 59.405 52.381 10.30 6.98 0.00 3.18
6518 7401 2.892374 CTGAGTGCGGACATATGTTCA 58.108 47.619 14.59 9.73 0.00 3.18
6519 7402 3.461061 CTGAGTGCGGACATATGTTCAT 58.539 45.455 14.59 0.00 0.00 2.57
6520 7403 3.197265 TGAGTGCGGACATATGTTCATG 58.803 45.455 14.59 0.00 0.00 3.07
6521 7404 1.942657 AGTGCGGACATATGTTCATGC 59.057 47.619 14.59 10.50 0.00 4.06
6522 7405 1.670295 GTGCGGACATATGTTCATGCA 59.330 47.619 14.59 12.88 0.00 3.96
6523 7406 2.291465 GTGCGGACATATGTTCATGCAT 59.709 45.455 16.74 0.00 33.25 3.96
6524 7407 2.950975 TGCGGACATATGTTCATGCATT 59.049 40.909 14.59 0.00 0.00 3.56
6525 7408 3.380954 TGCGGACATATGTTCATGCATTT 59.619 39.130 14.59 0.00 0.00 2.32
6526 7409 3.732219 GCGGACATATGTTCATGCATTTG 59.268 43.478 14.59 0.00 35.12 2.32
6527 7410 3.732219 CGGACATATGTTCATGCATTTGC 59.268 43.478 14.59 0.00 42.50 3.68
6528 7411 4.498513 CGGACATATGTTCATGCATTTGCT 60.499 41.667 14.59 0.00 42.66 3.91
6529 7412 4.743151 GGACATATGTTCATGCATTTGCTG 59.257 41.667 10.30 0.54 42.66 4.41
6530 7413 5.333299 ACATATGTTCATGCATTTGCTGT 57.667 34.783 1.41 0.00 42.66 4.40
6531 7414 5.726397 ACATATGTTCATGCATTTGCTGTT 58.274 33.333 1.41 0.00 42.66 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 5.982890 ATTGGTCAAATCGTTTCATTCCT 57.017 34.783 0.00 0.00 0.00 3.36
163 164 2.027625 CCTCTTCAACACGACGGGC 61.028 63.158 0.00 0.00 0.00 6.13
199 200 2.043852 GAGCTCCTCCTCCACCGA 60.044 66.667 0.87 0.00 0.00 4.69
203 204 2.438614 CGACGAGCTCCTCCTCCA 60.439 66.667 8.47 0.00 0.00 3.86
306 308 0.877071 CTTGGCGTGCTGATTGAGTT 59.123 50.000 0.00 0.00 0.00 3.01
307 309 1.580845 GCTTGGCGTGCTGATTGAGT 61.581 55.000 0.00 0.00 0.00 3.41
308 310 1.136147 GCTTGGCGTGCTGATTGAG 59.864 57.895 0.00 0.00 0.00 3.02
309 311 1.171549 TTGCTTGGCGTGCTGATTGA 61.172 50.000 3.39 0.00 0.00 2.57
310 312 0.731514 CTTGCTTGGCGTGCTGATTG 60.732 55.000 3.39 0.00 0.00 2.67
311 313 1.582968 CTTGCTTGGCGTGCTGATT 59.417 52.632 3.39 0.00 0.00 2.57
312 314 2.986306 GCTTGCTTGGCGTGCTGAT 61.986 57.895 3.39 0.00 0.00 2.90
313 315 3.663176 GCTTGCTTGGCGTGCTGA 61.663 61.111 3.39 0.00 0.00 4.26
314 316 3.667282 AGCTTGCTTGGCGTGCTG 61.667 61.111 7.89 0.00 38.02 4.41
315 317 3.667282 CAGCTTGCTTGGCGTGCT 61.667 61.111 0.00 3.97 39.42 4.40
317 319 4.712425 GGCAGCTTGCTTGGCGTG 62.712 66.667 7.85 0.00 44.28 5.34
318 320 4.962836 AGGCAGCTTGCTTGGCGT 62.963 61.111 7.85 0.00 44.28 5.68
319 321 4.112341 GAGGCAGCTTGCTTGGCG 62.112 66.667 7.85 0.00 44.28 5.69
320 322 2.567497 TTGAGGCAGCTTGCTTGGC 61.567 57.895 7.85 1.82 44.28 4.52
321 323 1.288127 GTTGAGGCAGCTTGCTTGG 59.712 57.895 7.85 0.00 44.28 3.61
322 324 1.081641 CGTTGAGGCAGCTTGCTTG 60.082 57.895 7.85 0.00 44.28 4.01
382 401 8.478066 GGGATCTTATGAAAGGCTATTGTTTTT 58.522 33.333 0.00 0.00 33.22 1.94
409 428 8.976353 TGTGCTGGGACAATTATTAAATGTATT 58.024 29.630 0.00 0.00 38.70 1.89
444 604 3.228188 AGCTCAAAGACATTGTCCCAA 57.772 42.857 13.14 0.00 40.11 4.12
446 606 2.887152 ACAAGCTCAAAGACATTGTCCC 59.113 45.455 13.14 0.00 40.11 4.46
478 638 4.024809 GCAAGTATTCGAGCAATAAGGGAC 60.025 45.833 0.00 0.00 0.00 4.46
496 656 2.425668 GCCCGTTTATATGGTTGCAAGT 59.574 45.455 0.00 0.00 0.00 3.16
516 676 2.962253 CGAGAAAGATCCGCCCGC 60.962 66.667 0.00 0.00 0.00 6.13
520 680 1.646189 AAAGCTCGAGAAAGATCCGC 58.354 50.000 18.75 0.00 0.00 5.54
553 713 5.580691 CGGAGCACAACATCTTAATGTAGAA 59.419 40.000 0.00 0.00 45.48 2.10
577 737 1.520342 GAGCTCCTGTCGTGGATGC 60.520 63.158 0.87 0.00 35.30 3.91
586 746 1.055040 AGCACAGAAAGAGCTCCTGT 58.945 50.000 15.81 15.81 40.29 4.00
601 761 1.035932 TACAGTAGCGGAGGGAGCAC 61.036 60.000 0.00 0.00 37.01 4.40
618 778 2.249309 TCTCTTCCCTCCAACCCTAC 57.751 55.000 0.00 0.00 0.00 3.18
625 785 1.361204 TGCAACATCTCTTCCCTCCA 58.639 50.000 0.00 0.00 0.00 3.86
728 1154 9.818270 ATCAACATGTATATCCCTTTCATTGAT 57.182 29.630 0.00 0.00 0.00 2.57
729 1155 9.288576 GATCAACATGTATATCCCTTTCATTGA 57.711 33.333 0.00 0.00 0.00 2.57
730 1156 8.232513 CGATCAACATGTATATCCCTTTCATTG 58.767 37.037 0.00 0.00 0.00 2.82
736 1164 8.924511 ATTTTCGATCAACATGTATATCCCTT 57.075 30.769 0.00 0.00 0.00 3.95
770 1198 1.363885 GGTCCGTACCAAATGTCGGC 61.364 60.000 0.00 0.00 45.98 5.54
826 1254 2.537214 GCGTATTCTTAAGGCGTGGTAC 59.463 50.000 1.85 0.00 0.00 3.34
867 1303 4.790651 CGATCTTTCATATCCGTGATCTCG 59.209 45.833 10.15 10.15 0.00 4.04
961 1397 3.118408 GGTTTGGCAATCTATTTTCCCCC 60.118 47.826 0.00 0.00 0.00 5.40
963 1399 3.774766 AGGGTTTGGCAATCTATTTTCCC 59.225 43.478 0.00 3.83 0.00 3.97
965 1401 6.154534 AGGTTAGGGTTTGGCAATCTATTTTC 59.845 38.462 0.00 0.00 0.00 2.29
1389 1834 5.340439 ACTACTTCCCGACCAAATTAGAG 57.660 43.478 0.00 0.00 0.00 2.43
1425 1870 1.276421 AGTGAGAACGAACCCATCAGG 59.724 52.381 0.00 0.00 43.78 3.86
1442 1887 3.875727 CAGCCATTACATCTCCAAGAGTG 59.124 47.826 0.00 0.00 0.00 3.51
1443 1888 3.776969 TCAGCCATTACATCTCCAAGAGT 59.223 43.478 0.00 0.00 0.00 3.24
1477 1922 8.921670 GTTAACAAATCGTAATTGCCAAATTCT 58.078 29.630 0.00 0.00 37.23 2.40
1487 1932 7.039993 AGCTTCCCAAGTTAACAAATCGTAATT 60.040 33.333 8.61 0.00 0.00 1.40
1518 1963 4.082787 AGCCAATGAAATGAACACCTAACG 60.083 41.667 0.00 0.00 0.00 3.18
1519 1964 5.048083 TCAGCCAATGAAATGAACACCTAAC 60.048 40.000 0.00 0.00 34.02 2.34
1521 1966 4.661222 TCAGCCAATGAAATGAACACCTA 58.339 39.130 0.00 0.00 34.02 3.08
1522 1967 3.499338 TCAGCCAATGAAATGAACACCT 58.501 40.909 0.00 0.00 34.02 4.00
1540 1985 4.711355 TCAAAGCCTAAATTCCCCAATCAG 59.289 41.667 0.00 0.00 0.00 2.90
1574 2019 0.032540 GCCGATCCATGGATTTTGGC 59.967 55.000 32.98 32.98 39.03 4.52
1593 2038 6.414732 TGGACTACAGGATAACAATTGAAGG 58.585 40.000 13.59 0.00 0.00 3.46
1728 2328 8.068977 CGGTCTACAAGTTATACTACAGTCATC 58.931 40.741 0.00 0.00 0.00 2.92
1734 2334 5.945784 ACCACGGTCTACAAGTTATACTACA 59.054 40.000 0.00 0.00 0.00 2.74
1735 2335 6.442513 ACCACGGTCTACAAGTTATACTAC 57.557 41.667 0.00 0.00 0.00 2.73
1742 2342 1.321474 TCGACCACGGTCTACAAGTT 58.679 50.000 14.12 0.00 42.54 2.66
1783 2383 3.657634 ACAGCTCATTAGTGTCACAGTG 58.342 45.455 5.62 0.00 0.00 3.66
1834 2519 8.756927 TGAATGCCTATAATGAACCATTTTTCA 58.243 29.630 0.00 0.00 39.79 2.69
1894 2580 5.140454 GGCAAAATCCCATCTTATACCTGT 58.860 41.667 0.00 0.00 0.00 4.00
1922 2608 0.956410 TGTACCGACAATTTGGGCCG 60.956 55.000 0.00 1.82 30.68 6.13
1934 2620 2.805671 CAACTTGACATGCTTGTACCGA 59.194 45.455 5.05 0.00 35.79 4.69
1955 2641 4.035102 GGAGGTGGTGGTCCAGGC 62.035 72.222 0.00 0.00 45.24 4.85
2207 2893 3.578688 GTTTGTATTTGGCTTCTGCTGG 58.421 45.455 0.00 0.00 39.59 4.85
2328 3020 8.462016 AGTATGCTAAAAGCTTTACAAGATTGG 58.538 33.333 13.10 0.00 42.97 3.16
2635 3327 7.697691 AGATGATAAAAACTGAAACGCATAGG 58.302 34.615 0.00 0.00 0.00 2.57
2636 3328 8.607459 AGAGATGATAAAAACTGAAACGCATAG 58.393 33.333 0.00 0.00 0.00 2.23
2772 3464 5.407084 GCACAATAACCCCAAATACAACAAC 59.593 40.000 0.00 0.00 0.00 3.32
2922 3614 7.601508 CGGTATCCCTTAACCATAACAATAGAC 59.398 40.741 0.00 0.00 35.35 2.59
3392 4084 3.529533 TGCACAACCCTTGAAAAACATG 58.470 40.909 0.00 0.00 0.00 3.21
3425 4117 2.301346 CCAATGTAGCCACCAATCCTC 58.699 52.381 0.00 0.00 0.00 3.71
3534 4226 1.102978 AGCCAACACCAACACAGAAC 58.897 50.000 0.00 0.00 0.00 3.01
3561 4253 0.318699 GAGGACCAAGCGGCAAAAAC 60.319 55.000 1.45 0.00 34.57 2.43
3659 4352 0.038744 AGACAGGCTGGACCCAAATG 59.961 55.000 20.34 0.00 40.58 2.32
3868 4561 8.135529 GCAAAAGTCAAAGGTGAATTAACTAGT 58.864 33.333 0.00 0.00 41.04 2.57
4103 4796 0.746659 AGCTCAAAGCAAAGCCGTTT 59.253 45.000 1.29 0.00 45.56 3.60
4109 4802 5.448360 GCAGGAATACTAGCTCAAAGCAAAG 60.448 44.000 0.00 1.25 45.56 2.77
4181 4874 6.986817 AGCTATACGTGTAAATTCTTCTGCAT 59.013 34.615 0.00 0.00 0.00 3.96
4198 4900 7.587757 GCTGAATGAAAATGGTAAAGCTATACG 59.412 37.037 0.00 0.00 0.00 3.06
4208 4910 4.220382 CCAAGGTGCTGAATGAAAATGGTA 59.780 41.667 0.00 0.00 0.00 3.25
4226 4928 3.829601 AGAACACTAGTCTGTCTCCAAGG 59.170 47.826 0.00 0.00 0.00 3.61
4522 5234 0.872388 GCACCCCTGTTGTTTCTACG 59.128 55.000 0.00 0.00 0.00 3.51
4529 5241 1.152756 GGAGTTGCACCCCTGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
4536 5248 4.244862 CACAAAATAATGGAGTTGCACCC 58.755 43.478 0.00 0.00 0.00 4.61
4545 5257 5.015515 TGCTGATCACCACAAAATAATGGA 58.984 37.500 0.00 0.00 39.46 3.41
4565 5277 8.571336 GCAAAAATAGTATAATGATCACCTGCT 58.429 33.333 0.00 0.00 0.00 4.24
4584 5296 7.500141 ACCACAAACTATCTTCAAGCAAAAAT 58.500 30.769 0.00 0.00 0.00 1.82
4641 5363 2.444421 CTTTCAGCAAAGGATCCAGCT 58.556 47.619 15.82 16.85 36.14 4.24
4699 5443 6.154363 TCACCTCAAACAGTGAAAAGGAAATT 59.846 34.615 0.00 0.00 39.96 1.82
4700 5444 5.656416 TCACCTCAAACAGTGAAAAGGAAAT 59.344 36.000 0.00 0.00 39.96 2.17
4730 5475 1.555075 TCAAGCATCAGAGGGTACACC 59.445 52.381 0.00 0.00 40.67 4.16
4738 5483 2.995283 TCCCATGTTCAAGCATCAGAG 58.005 47.619 0.00 0.00 0.00 3.35
4826 5571 0.880278 GGTTGTCAGCTGCTTCGTCA 60.880 55.000 9.47 0.00 0.00 4.35
4907 5652 2.093500 GGATTCCTGGCCATTGTTTTCC 60.093 50.000 5.51 4.81 0.00 3.13
4985 5730 1.523711 CGGTCCCATCATTGGTCCG 60.524 63.158 0.00 0.00 45.29 4.79
5342 6087 0.986019 ACCTGTCACCCCTGTTGTCA 60.986 55.000 0.00 0.00 0.00 3.58
5393 6141 2.126888 CCGGCGTTGTTGTCATGC 60.127 61.111 6.01 0.00 0.00 4.06
5417 6165 2.583441 CCTGTTCCCGTCTGCTCCA 61.583 63.158 0.00 0.00 0.00 3.86
5486 6234 3.134792 GCCTCCTCGTCGCTCTCA 61.135 66.667 0.00 0.00 0.00 3.27
5585 6346 0.598419 CAGCACAACTCGTCTCTGCA 60.598 55.000 0.00 0.00 0.00 4.41
5588 6349 1.610363 TCTCAGCACAACTCGTCTCT 58.390 50.000 0.00 0.00 0.00 3.10
5594 6355 4.787882 GCTTTTCAGTTCTCAGCACAACTC 60.788 45.833 0.00 0.00 30.06 3.01
5599 6360 1.867233 TCGCTTTTCAGTTCTCAGCAC 59.133 47.619 0.00 0.00 0.00 4.40
5605 6366 1.000163 TCGAGCTCGCTTTTCAGTTCT 60.000 47.619 30.97 0.00 39.60 3.01
5802 6564 2.134789 ATCAACCACAGGATCAAGCC 57.865 50.000 0.00 0.00 0.00 4.35
5902 6671 7.226523 CCTAACCATGTCATTACATCATCGAAA 59.773 37.037 0.00 0.00 44.70 3.46
5912 6681 3.214328 CCCAGCCTAACCATGTCATTAC 58.786 50.000 0.00 0.00 0.00 1.89
5936 6705 2.230992 ACAGCATGACAGAGACAGAGAC 59.769 50.000 0.00 0.00 39.69 3.36
5938 6707 2.029200 ACACAGCATGACAGAGACAGAG 60.029 50.000 0.00 0.00 39.69 3.35
5944 6726 0.516001 GCACACACAGCATGACAGAG 59.484 55.000 0.00 0.00 39.69 3.35
5964 6746 6.846505 TGAACTATAATCATCAGGTCCCTCTT 59.153 38.462 0.00 0.00 0.00 2.85
5971 6753 9.911788 AAATGAACTGAACTATAATCATCAGGT 57.088 29.630 6.58 0.00 42.29 4.00
5997 6779 8.803235 TCACAGAATGAGCTAGTACTAAAAGAA 58.197 33.333 3.76 0.00 39.69 2.52
5999 6781 9.243637 GATCACAGAATGAGCTAGTACTAAAAG 57.756 37.037 3.76 0.00 41.91 2.27
6000 6782 8.749354 TGATCACAGAATGAGCTAGTACTAAAA 58.251 33.333 3.76 0.00 44.50 1.52
6001 6783 8.191446 GTGATCACAGAATGAGCTAGTACTAAA 58.809 37.037 21.07 0.00 44.50 1.85
6003 6785 7.012799 CAGTGATCACAGAATGAGCTAGTACTA 59.987 40.741 27.02 1.89 44.50 1.82
6004 6786 5.890985 AGTGATCACAGAATGAGCTAGTACT 59.109 40.000 27.02 0.00 44.50 2.73
6005 6787 5.976534 CAGTGATCACAGAATGAGCTAGTAC 59.023 44.000 27.02 0.00 44.50 2.73
6006 6788 5.451103 GCAGTGATCACAGAATGAGCTAGTA 60.451 44.000 27.02 0.00 44.50 1.82
6007 6789 4.680172 GCAGTGATCACAGAATGAGCTAGT 60.680 45.833 27.02 0.00 44.50 2.57
6009 6791 3.431346 GGCAGTGATCACAGAATGAGCTA 60.431 47.826 27.02 0.00 44.50 3.32
6010 6792 2.630158 GCAGTGATCACAGAATGAGCT 58.370 47.619 27.02 0.42 44.50 4.09
6011 6793 1.669779 GGCAGTGATCACAGAATGAGC 59.330 52.381 27.02 16.77 44.45 4.26
6023 6810 3.070018 CACGAAAGAAGAAGGCAGTGAT 58.930 45.455 0.00 0.00 0.00 3.06
6027 6814 2.478134 CAGACACGAAAGAAGAAGGCAG 59.522 50.000 0.00 0.00 0.00 4.85
6029 6816 2.476997 GTCAGACACGAAAGAAGAAGGC 59.523 50.000 0.00 0.00 0.00 4.35
6032 6819 4.944048 TGATGTCAGACACGAAAGAAGAA 58.056 39.130 5.05 0.00 0.00 2.52
6050 6837 5.757886 ACAAACGTACAGAAACCATTGATG 58.242 37.500 0.00 0.00 0.00 3.07
6051 6838 7.499321 TTACAAACGTACAGAAACCATTGAT 57.501 32.000 0.00 0.00 0.00 2.57
6053 6840 7.114247 CCATTTACAAACGTACAGAAACCATTG 59.886 37.037 0.00 0.00 0.00 2.82
6054 6841 7.013464 TCCATTTACAAACGTACAGAAACCATT 59.987 33.333 0.00 0.00 0.00 3.16
6064 6851 5.462405 TGGCATTTCCATTTACAAACGTAC 58.538 37.500 0.00 0.00 40.72 3.67
6067 6854 4.987912 ACTTGGCATTTCCATTTACAAACG 59.012 37.500 0.00 0.00 46.04 3.60
6069 6856 5.010112 TCGACTTGGCATTTCCATTTACAAA 59.990 36.000 0.00 0.00 46.04 2.83
6070 6857 4.520874 TCGACTTGGCATTTCCATTTACAA 59.479 37.500 0.00 0.00 46.04 2.41
6081 6869 1.736645 CGACCGTCGACTTGGCATT 60.737 57.895 16.03 0.00 43.74 3.56
6091 6879 0.930742 GCTAGCAGATTCGACCGTCG 60.931 60.000 14.94 14.94 42.10 5.12
6093 6881 1.320344 TGGCTAGCAGATTCGACCGT 61.320 55.000 18.24 0.00 0.00 4.83
6094 6882 0.032678 ATGGCTAGCAGATTCGACCG 59.967 55.000 18.24 0.00 0.00 4.79
6095 6883 1.506493 CATGGCTAGCAGATTCGACC 58.494 55.000 18.24 0.00 0.00 4.79
6096 6884 1.069204 TCCATGGCTAGCAGATTCGAC 59.931 52.381 18.24 0.00 0.00 4.20
6097 6885 1.069204 GTCCATGGCTAGCAGATTCGA 59.931 52.381 18.24 0.65 0.00 3.71
6098 6886 1.506493 GTCCATGGCTAGCAGATTCG 58.494 55.000 18.24 0.00 0.00 3.34
6099 6887 1.202580 ACGTCCATGGCTAGCAGATTC 60.203 52.381 18.24 0.00 0.00 2.52
6100 6888 0.833287 ACGTCCATGGCTAGCAGATT 59.167 50.000 18.24 0.00 0.00 2.40
6101 6889 1.704641 TACGTCCATGGCTAGCAGAT 58.295 50.000 18.24 4.75 0.00 2.90
6102 6890 1.341209 CATACGTCCATGGCTAGCAGA 59.659 52.381 18.24 2.09 0.00 4.26
6103 6891 1.069204 ACATACGTCCATGGCTAGCAG 59.931 52.381 18.24 5.55 0.00 4.24
6104 6892 1.119684 ACATACGTCCATGGCTAGCA 58.880 50.000 18.24 2.97 0.00 3.49
6108 6947 1.134699 CACTCACATACGTCCATGGCT 60.135 52.381 6.96 0.00 0.00 4.75
6119 6958 1.136891 CTCCATCGGTGCACTCACATA 59.863 52.381 17.98 0.00 44.87 2.29
6126 6965 0.391130 TGCTAACTCCATCGGTGCAC 60.391 55.000 8.80 8.80 0.00 4.57
6162 7007 0.877071 AGTACACATTGCACAGCAGC 59.123 50.000 0.00 0.00 40.61 5.25
6163 7008 3.003585 TCAAAGTACACATTGCACAGCAG 59.996 43.478 0.00 0.00 40.61 4.24
6165 7010 3.003689 AGTCAAAGTACACATTGCACAGC 59.996 43.478 0.00 0.00 0.00 4.40
6166 7011 4.530388 CAGTCAAAGTACACATTGCACAG 58.470 43.478 0.00 0.00 0.00 3.66
6169 7014 3.550820 ACCAGTCAAAGTACACATTGCA 58.449 40.909 0.00 0.00 0.00 4.08
6171 7016 4.133820 TGGACCAGTCAAAGTACACATTG 58.866 43.478 0.00 0.00 0.00 2.82
6172 7017 4.431416 TGGACCAGTCAAAGTACACATT 57.569 40.909 0.00 0.00 0.00 2.71
6173 7018 4.389374 CTTGGACCAGTCAAAGTACACAT 58.611 43.478 6.75 0.00 36.20 3.21
6174 7019 3.804036 CTTGGACCAGTCAAAGTACACA 58.196 45.455 6.75 0.00 36.20 3.72
6253 7109 2.434709 CAATGGCCCTTTTGCGCC 60.435 61.111 4.18 0.00 45.92 6.53
6256 7112 1.134995 GTCTAGCAATGGCCCTTTTGC 60.135 52.381 21.31 21.31 46.68 3.68
6260 7116 3.890527 CTGTCTAGCAATGGCCCTT 57.109 52.632 0.00 0.00 42.56 3.95
6350 7210 2.438254 TGGTGATGGCCGTGATGC 60.438 61.111 0.00 0.00 0.00 3.91
6351 7211 1.377072 TGTGGTGATGGCCGTGATG 60.377 57.895 0.00 0.00 0.00 3.07
6352 7212 1.377202 GTGTGGTGATGGCCGTGAT 60.377 57.895 0.00 0.00 0.00 3.06
6353 7213 2.031919 GTGTGGTGATGGCCGTGA 59.968 61.111 0.00 0.00 0.00 4.35
6357 7217 2.676471 GTGGGTGTGGTGATGGCC 60.676 66.667 0.00 0.00 0.00 5.36
6359 7219 0.606401 GTCTGTGGGTGTGGTGATGG 60.606 60.000 0.00 0.00 0.00 3.51
6369 7229 4.969196 CTGCGTGCGTCTGTGGGT 62.969 66.667 0.00 0.00 0.00 4.51
6371 7231 3.406361 GTCTGCGTGCGTCTGTGG 61.406 66.667 0.00 0.00 0.00 4.17
6384 7244 3.443925 TCTCTGGCGAGGCGTCTG 61.444 66.667 0.00 0.00 37.86 3.51
6385 7245 3.444805 GTCTCTGGCGAGGCGTCT 61.445 66.667 4.69 0.00 37.86 4.18
6386 7246 4.500116 GGTCTCTGGCGAGGCGTC 62.500 72.222 0.00 0.00 42.87 5.19
6389 7249 4.500116 GTCGGTCTCTGGCGAGGC 62.500 72.222 0.00 4.80 41.20 4.70
6390 7250 1.451567 TAGTCGGTCTCTGGCGAGG 60.452 63.158 0.00 0.00 37.86 4.63
6391 7251 1.716826 GGTAGTCGGTCTCTGGCGAG 61.717 65.000 0.00 0.00 38.67 5.03
6392 7252 1.748122 GGTAGTCGGTCTCTGGCGA 60.748 63.158 0.00 0.00 0.00 5.54
6393 7253 1.384989 ATGGTAGTCGGTCTCTGGCG 61.385 60.000 0.00 0.00 0.00 5.69
6394 7254 0.103208 CATGGTAGTCGGTCTCTGGC 59.897 60.000 0.00 0.00 0.00 4.85
6395 7255 0.103208 GCATGGTAGTCGGTCTCTGG 59.897 60.000 0.00 0.00 0.00 3.86
6433 7316 2.705658 TCAAACACACCCACAGAGAGAT 59.294 45.455 0.00 0.00 0.00 2.75
6434 7317 2.115427 TCAAACACACCCACAGAGAGA 58.885 47.619 0.00 0.00 0.00 3.10
6435 7318 2.620251 TCAAACACACCCACAGAGAG 57.380 50.000 0.00 0.00 0.00 3.20
6436 7319 3.646162 ACTATCAAACACACCCACAGAGA 59.354 43.478 0.00 0.00 0.00 3.10
6437 7320 4.008074 ACTATCAAACACACCCACAGAG 57.992 45.455 0.00 0.00 0.00 3.35
6438 7321 5.487433 CATACTATCAAACACACCCACAGA 58.513 41.667 0.00 0.00 0.00 3.41
6439 7322 4.094887 GCATACTATCAAACACACCCACAG 59.905 45.833 0.00 0.00 0.00 3.66
6440 7323 4.006989 GCATACTATCAAACACACCCACA 58.993 43.478 0.00 0.00 0.00 4.17
6441 7324 4.006989 TGCATACTATCAAACACACCCAC 58.993 43.478 0.00 0.00 0.00 4.61
6442 7325 4.293662 TGCATACTATCAAACACACCCA 57.706 40.909 0.00 0.00 0.00 4.51
6443 7326 4.036734 CCATGCATACTATCAAACACACCC 59.963 45.833 0.00 0.00 0.00 4.61
6446 7329 4.881273 GGTCCATGCATACTATCAAACACA 59.119 41.667 0.00 0.00 0.00 3.72
6447 7330 5.126067 AGGTCCATGCATACTATCAAACAC 58.874 41.667 0.00 0.00 0.00 3.32
6448 7331 5.372343 AGGTCCATGCATACTATCAAACA 57.628 39.130 0.00 0.00 0.00 2.83
6449 7332 5.409826 GCTAGGTCCATGCATACTATCAAAC 59.590 44.000 0.00 0.00 0.00 2.93
6450 7333 5.513094 GGCTAGGTCCATGCATACTATCAAA 60.513 44.000 0.00 0.00 0.00 2.69
6451 7334 4.020218 GGCTAGGTCCATGCATACTATCAA 60.020 45.833 0.00 0.00 0.00 2.57
6452 7335 3.515502 GGCTAGGTCCATGCATACTATCA 59.484 47.826 0.00 0.00 0.00 2.15
6453 7336 3.772025 AGGCTAGGTCCATGCATACTATC 59.228 47.826 0.00 0.00 0.00 2.08
6454 7337 3.796111 AGGCTAGGTCCATGCATACTAT 58.204 45.455 0.00 0.00 0.00 2.12
6455 7338 3.260269 AGGCTAGGTCCATGCATACTA 57.740 47.619 0.00 0.00 0.00 1.82
6456 7339 2.109229 AGGCTAGGTCCATGCATACT 57.891 50.000 0.00 0.00 0.00 2.12
6457 7340 4.559862 ATTAGGCTAGGTCCATGCATAC 57.440 45.455 0.00 0.00 0.00 2.39
6458 7341 4.350816 ACAATTAGGCTAGGTCCATGCATA 59.649 41.667 0.00 3.06 0.00 3.14
6459 7342 3.139025 ACAATTAGGCTAGGTCCATGCAT 59.861 43.478 0.00 0.00 0.00 3.96
6460 7343 2.509548 ACAATTAGGCTAGGTCCATGCA 59.490 45.455 8.13 0.00 0.00 3.96
6461 7344 3.214696 ACAATTAGGCTAGGTCCATGC 57.785 47.619 0.00 0.00 0.00 4.06
6462 7345 5.041191 AGAACAATTAGGCTAGGTCCATG 57.959 43.478 0.00 0.00 0.00 3.66
6463 7346 5.430089 AGAAGAACAATTAGGCTAGGTCCAT 59.570 40.000 0.00 0.00 0.00 3.41
6464 7347 4.783227 AGAAGAACAATTAGGCTAGGTCCA 59.217 41.667 0.00 0.00 0.00 4.02
6465 7348 5.360649 AGAAGAACAATTAGGCTAGGTCC 57.639 43.478 0.00 0.00 0.00 4.46
6466 7349 6.879458 TCAAAGAAGAACAATTAGGCTAGGTC 59.121 38.462 0.00 0.00 0.00 3.85
6467 7350 6.779860 TCAAAGAAGAACAATTAGGCTAGGT 58.220 36.000 0.00 0.00 0.00 3.08
6468 7351 7.872113 ATCAAAGAAGAACAATTAGGCTAGG 57.128 36.000 0.00 0.00 0.00 3.02
6469 7352 9.383519 TGTATCAAAGAAGAACAATTAGGCTAG 57.616 33.333 0.00 0.00 0.00 3.42
6470 7353 9.905713 ATGTATCAAAGAAGAACAATTAGGCTA 57.094 29.630 0.00 0.00 0.00 3.93
6471 7354 8.680903 CATGTATCAAAGAAGAACAATTAGGCT 58.319 33.333 0.00 0.00 0.00 4.58
6472 7355 7.433425 GCATGTATCAAAGAAGAACAATTAGGC 59.567 37.037 0.00 0.00 0.00 3.93
6473 7356 8.680903 AGCATGTATCAAAGAAGAACAATTAGG 58.319 33.333 0.00 0.00 0.00 2.69
6474 7357 9.499585 CAGCATGTATCAAAGAAGAACAATTAG 57.500 33.333 0.00 0.00 0.00 1.73
6475 7358 9.230122 TCAGCATGTATCAAAGAAGAACAATTA 57.770 29.630 0.00 0.00 37.40 1.40
6476 7359 8.114331 TCAGCATGTATCAAAGAAGAACAATT 57.886 30.769 0.00 0.00 37.40 2.32
6477 7360 7.392673 ACTCAGCATGTATCAAAGAAGAACAAT 59.607 33.333 0.00 0.00 37.40 2.71
6478 7361 6.712095 ACTCAGCATGTATCAAAGAAGAACAA 59.288 34.615 0.00 0.00 37.40 2.83
6479 7362 6.148315 CACTCAGCATGTATCAAAGAAGAACA 59.852 38.462 0.00 0.00 37.40 3.18
6480 7363 6.541086 CACTCAGCATGTATCAAAGAAGAAC 58.459 40.000 0.00 0.00 37.40 3.01
6481 7364 5.122869 GCACTCAGCATGTATCAAAGAAGAA 59.877 40.000 0.00 0.00 44.79 2.52
6482 7365 4.633126 GCACTCAGCATGTATCAAAGAAGA 59.367 41.667 0.00 0.00 44.79 2.87
6483 7366 4.493708 CGCACTCAGCATGTATCAAAGAAG 60.494 45.833 0.00 0.00 46.13 2.85
6484 7367 3.371898 CGCACTCAGCATGTATCAAAGAA 59.628 43.478 0.00 0.00 46.13 2.52
6485 7368 2.931969 CGCACTCAGCATGTATCAAAGA 59.068 45.455 0.00 0.00 46.13 2.52
6486 7369 2.031314 CCGCACTCAGCATGTATCAAAG 59.969 50.000 0.00 0.00 46.13 2.77
6487 7370 2.009051 CCGCACTCAGCATGTATCAAA 58.991 47.619 0.00 0.00 46.13 2.69
6488 7371 1.206849 TCCGCACTCAGCATGTATCAA 59.793 47.619 0.00 0.00 46.13 2.57
6489 7372 0.823460 TCCGCACTCAGCATGTATCA 59.177 50.000 0.00 0.00 46.13 2.15
6490 7373 1.212616 GTCCGCACTCAGCATGTATC 58.787 55.000 0.00 0.00 46.13 2.24
6491 7374 0.536724 TGTCCGCACTCAGCATGTAT 59.463 50.000 0.00 0.00 46.13 2.29
6492 7375 0.536724 ATGTCCGCACTCAGCATGTA 59.463 50.000 0.00 0.00 46.13 2.29
6493 7376 0.536724 TATGTCCGCACTCAGCATGT 59.463 50.000 0.00 0.00 46.13 3.21
6494 7377 1.529865 CATATGTCCGCACTCAGCATG 59.470 52.381 0.00 0.00 46.13 4.06
6495 7378 1.139654 ACATATGTCCGCACTCAGCAT 59.860 47.619 1.41 0.00 46.13 3.79
6496 7379 0.536724 ACATATGTCCGCACTCAGCA 59.463 50.000 1.41 0.00 46.13 4.41
6497 7380 1.594862 GAACATATGTCCGCACTCAGC 59.405 52.381 9.23 0.00 40.87 4.26
6498 7381 2.892374 TGAACATATGTCCGCACTCAG 58.108 47.619 9.23 0.00 0.00 3.35
6499 7382 3.197265 CATGAACATATGTCCGCACTCA 58.803 45.455 9.23 8.41 0.00 3.41
6500 7383 2.032549 GCATGAACATATGTCCGCACTC 60.033 50.000 9.23 2.38 0.00 3.51
6501 7384 1.942657 GCATGAACATATGTCCGCACT 59.057 47.619 9.23 0.00 0.00 4.40
6502 7385 1.670295 TGCATGAACATATGTCCGCAC 59.330 47.619 9.23 0.20 0.00 5.34
6503 7386 2.035530 TGCATGAACATATGTCCGCA 57.964 45.000 9.23 12.26 0.00 5.69
6504 7387 3.631145 AATGCATGAACATATGTCCGC 57.369 42.857 9.23 9.87 0.00 5.54
6505 7388 3.732219 GCAAATGCATGAACATATGTCCG 59.268 43.478 9.23 0.00 41.59 4.79
6506 7389 4.743151 CAGCAAATGCATGAACATATGTCC 59.257 41.667 9.23 0.00 45.16 4.02
6507 7390 5.345702 ACAGCAAATGCATGAACATATGTC 58.654 37.500 9.23 3.74 45.16 3.06
6508 7391 5.333299 ACAGCAAATGCATGAACATATGT 57.667 34.783 1.41 1.41 45.16 2.29


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

AutoCloner maintained by Alex Coulton.