Multiple sequence alignment - TraesCS4D01G224800

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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 TraesCS4D01G224800 chr4D 100.000 7073 0 0 1 7073 381877762 381884834 0.000000e+00 13062
1 TraesCS4D01G224800 chr4D 95.402 87 4 0 4834 4920 509646354 509646440 9.570000e-29 139
2 TraesCS4D01G224800 chr4A 96.164 3259 71 16 1603 4838 81821556 81818329 0.000000e+00 5276
3 TraesCS4D01G224800 chr4A 92.308 1911 100 21 4919 6826 81818330 81816464 0.000000e+00 2671
4 TraesCS4D01G224800 chr4A 95.346 1633 54 9 1 1625 81823242 81821624 0.000000e+00 2575
5 TraesCS4D01G224800 chr4A 86.341 205 7 5 6882 7065 81816456 81816252 3.340000e-48 204
6 TraesCS4D01G224800 chr4B 94.619 2063 71 13 192 2234 469010610 469012652 0.000000e+00 3158
7 TraesCS4D01G224800 chr4B 95.368 1727 67 9 2269 3984 469012650 469014374 0.000000e+00 2734
8 TraesCS4D01G224800 chr4B 94.459 1119 51 8 4919 6034 469015578 469016688 0.000000e+00 1712
9 TraesCS4D01G224800 chr4B 94.894 705 24 8 3983 4676 469014536 469015239 0.000000e+00 1092
10 TraesCS4D01G224800 chr4B 87.838 592 28 13 6227 6816 469016682 469017231 0.000000e+00 654
11 TraesCS4D01G224800 chr4B 93.043 230 6 6 6837 7065 469025628 469025848 1.900000e-85 327
12 TraesCS4D01G224800 chr4B 92.500 160 8 1 4679 4838 469015424 469015579 7.140000e-55 226
13 TraesCS4D01G224800 chr4B 94.845 97 5 0 4833 4929 670403247 670403343 1.230000e-32 152
14 TraesCS4D01G224800 chr5D 92.139 1412 92 15 3261 4659 497781843 497780438 0.000000e+00 1975
15 TraesCS4D01G224800 chr3B 98.824 85 1 0 4836 4920 556504501 556504585 1.230000e-32 152
16 TraesCS4D01G224800 chr1D 98.810 84 1 0 4837 4920 348128524 348128607 4.420000e-32 150
17 TraesCS4D01G224800 chr1A 95.349 86 4 0 4835 4920 7287086 7287171 3.440000e-28 137
18 TraesCS4D01G224800 chr1B 95.294 85 4 0 4836 4920 688114421 688114505 1.240000e-27 135
19 TraesCS4D01G224800 chr6A 92.473 93 7 0 4831 4923 472952757 472952665 4.450000e-27 134
20 TraesCS4D01G224800 chr3A 95.238 84 4 0 4837 4920 741249639 741249556 4.450000e-27 134
21 TraesCS4D01G224800 chr2B 94.253 87 5 0 4837 4923 255054248 255054162 4.450000e-27 134


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 TraesCS4D01G224800 chr4D 381877762 381884834 7072 False 13062.0 13062 100.000000 1 7073 1 chr4D.!!$F1 7072
1 TraesCS4D01G224800 chr4A 81816252 81823242 6990 True 2681.5 5276 92.539750 1 7065 4 chr4A.!!$R1 7064
2 TraesCS4D01G224800 chr4B 469010610 469017231 6621 False 1596.0 3158 93.279667 192 6816 6 chr4B.!!$F3 6624
3 TraesCS4D01G224800 chr5D 497780438 497781843 1405 True 1975.0 1975 92.139000 3261 4659 1 chr5D.!!$R1 1398

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
681 693 0.950836 TGGTTGCTGATCGGTGTTTG 59.049 50.000 2.89 0.00 0.00 2.93 F
1323 1337 0.321210 TCACGGTGTGCTGTATTGGG 60.321 55.000 8.17 0.00 32.98 4.12 F
1626 1738 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32 F
1627 1739 2.480802 GTGTGTGTGTGTGTGTGTGTTA 59.519 45.455 0.00 0.00 0.00 2.41 F
1889 2001 2.703675 CTTGGCTTCCTGGTGCTGGT 62.704 60.000 12.41 0.00 0.00 4.00 F
3455 3580 4.345257 AGCACCTTCTGTCTTTCTCTTACA 59.655 41.667 0.00 0.00 0.00 2.41 F
4358 4668 2.362397 TCAGTTGCTGAAGTCTCTTCGT 59.638 45.455 0.00 0.00 37.57 3.85 F
5489 6007 1.365368 TACATGCGGCATTCACCACG 61.365 55.000 13.81 2.58 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2165 2281 2.229784 CTGATGAAGGGTGTTTCTTGCC 59.770 50.000 0.00 0.00 0.00 4.52 R
2171 2287 3.181429 ACATGGACTGATGAAGGGTGTTT 60.181 43.478 0.00 0.00 0.00 2.83 R
2778 2900 3.756434 TGCAAAGCAAAGGATACAGGTAC 59.244 43.478 0.00 0.00 34.76 3.34 R
3432 3557 4.345257 TGTAAGAGAAAGACAGAAGGTGCT 59.655 41.667 0.00 0.00 0.00 4.40 R
3742 3867 5.642491 CCAGATGCCACATGAGTATTATCTG 59.358 44.000 0.00 10.34 37.25 2.90 R
4387 4697 1.946768 GTTAAGTGTTGCACTGCCTCA 59.053 47.619 2.31 0.00 44.62 3.86 R
5532 6050 0.888619 TAGTGTTCTGACCAGCCTCG 59.111 55.000 0.00 0.00 0.00 4.63 R
6447 6968 0.242825 CAACTCATGTGCCTTGCCAG 59.757 55.000 0.00 0.00 0.00 4.85 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
44 45 7.618117 AGGAAACGAACAAATTATTATCCCCTT 59.382 33.333 0.00 0.00 0.00 3.95
67 68 1.270147 CGTACGATTCCTTCCATCCCC 60.270 57.143 10.44 0.00 0.00 4.81
317 326 4.467107 GACTCCGCCCCTCCCTCT 62.467 72.222 0.00 0.00 0.00 3.69
351 361 7.201530 CCGCTCACGACTCTTTTTCTATTTATT 60.202 37.037 0.00 0.00 43.93 1.40
352 362 8.169268 CGCTCACGACTCTTTTTCTATTTATTT 58.831 33.333 0.00 0.00 43.93 1.40
396 406 8.818141 TTATTATGAGATTAAACCGAGCTCTG 57.182 34.615 12.85 8.03 0.00 3.35
401 411 1.808411 TTAAACCGAGCTCTGGCAAG 58.192 50.000 20.11 1.31 41.70 4.01
587 597 2.689553 TGCTCCGCTGATGATAACAA 57.310 45.000 0.00 0.00 0.00 2.83
612 622 2.659063 CGTGGGAGGAGATGGTGCA 61.659 63.158 0.00 0.00 0.00 4.57
681 693 0.950836 TGGTTGCTGATCGGTGTTTG 59.049 50.000 2.89 0.00 0.00 2.93
692 704 4.150980 TGATCGGTGTTTGTAAGCTTAACG 59.849 41.667 7.99 1.21 0.00 3.18
701 713 7.644945 GTGTTTGTAAGCTTAACGTTGGTTAAT 59.355 33.333 11.99 0.00 45.03 1.40
714 727 3.667497 TGGTTAATTTGATTTGCGCCA 57.333 38.095 4.18 0.00 0.00 5.69
730 743 2.606795 GCGCCAAACTGTTTGATGCTTA 60.607 45.455 29.47 0.00 43.26 3.09
747 761 5.878332 TGCTTATATGTTCACTGTGTTGG 57.122 39.130 7.79 0.00 0.00 3.77
752 766 7.362056 GCTTATATGTTCACTGTGTTGGAATGT 60.362 37.037 7.79 0.00 0.00 2.71
782 796 9.284968 TCCAATATACTTGCCTTATTAAGCTTC 57.715 33.333 0.00 0.00 0.00 3.86
827 841 1.762370 CCAGGTGGGGAAAATATTGCC 59.238 52.381 0.00 0.00 45.73 4.52
932 946 4.268884 GTGAGTCATTAACATCCTCTTCGC 59.731 45.833 0.00 0.00 0.00 4.70
940 954 3.518634 ACATCCTCTTCGCTCTCTTTC 57.481 47.619 0.00 0.00 0.00 2.62
1038 1052 3.723764 CGAAGGACACAAATTCACAAACG 59.276 43.478 0.00 0.00 0.00 3.60
1158 1172 0.687354 GTTCTGGAAGTGAGAGCCCA 59.313 55.000 0.00 0.00 33.76 5.36
1162 1176 2.023984 TCTGGAAGTGAGAGCCCATCTA 60.024 50.000 0.00 0.00 34.52 1.98
1164 1178 1.691434 GGAAGTGAGAGCCCATCTAGG 59.309 57.143 0.00 0.00 38.84 3.02
1246 1260 7.066887 TCGAAAGGCTTTATGAATATTTCTGCA 59.933 33.333 13.37 0.00 0.00 4.41
1251 1265 7.977853 AGGCTTTATGAATATTTCTGCACAAAG 59.022 33.333 2.73 2.73 0.00 2.77
1267 1281 4.564821 GCACAAAGGGACTAAGGTGTATCA 60.565 45.833 0.00 0.00 38.49 2.15
1323 1337 0.321210 TCACGGTGTGCTGTATTGGG 60.321 55.000 8.17 0.00 32.98 4.12
1626 1738 1.265635 GTGTGTGTGTGTGTGTGTGTT 59.734 47.619 0.00 0.00 0.00 3.32
1627 1739 2.480802 GTGTGTGTGTGTGTGTGTGTTA 59.519 45.455 0.00 0.00 0.00 2.41
1889 2001 2.703675 CTTGGCTTCCTGGTGCTGGT 62.704 60.000 12.41 0.00 0.00 4.00
2003 2115 6.710744 AGAGTATGTTTGACAGGTAAACTTGG 59.289 38.462 0.00 0.00 38.50 3.61
2165 2281 6.484643 TGCTCCTGCTTTTTATATAAGCTCAG 59.515 38.462 16.52 8.74 46.30 3.35
2171 2287 6.828273 TGCTTTTTATATAAGCTCAGGCAAGA 59.172 34.615 16.52 0.00 46.30 3.02
2308 2427 4.448210 ACCGGCTACCAAATATGTAGTTG 58.552 43.478 0.00 0.00 38.34 3.16
2514 2635 8.601845 TCATATTCCTGTTGTGTATTTATCCG 57.398 34.615 0.00 0.00 0.00 4.18
2778 2900 5.612709 GCGAACTTTAGTTACTTGCACTGAG 60.613 44.000 0.00 0.00 38.56 3.35
3061 3183 8.662781 TGCATAACTCATTAATTCTAGTCACC 57.337 34.615 0.00 0.00 0.00 4.02
3432 3557 5.163248 TGAGGGTCATGTAAGTTCTTTGTCA 60.163 40.000 0.00 0.00 0.00 3.58
3440 3565 4.574828 TGTAAGTTCTTTGTCAGCACCTTC 59.425 41.667 0.00 0.00 0.00 3.46
3455 3580 4.345257 AGCACCTTCTGTCTTTCTCTTACA 59.655 41.667 0.00 0.00 0.00 2.41
3763 3891 7.605309 TGATTCAGATAATACTCATGTGGCATC 59.395 37.037 0.00 0.00 0.00 3.91
3880 4010 7.015195 TCCCGATAGAGATATGACAATGTTGAA 59.985 37.037 0.00 0.00 39.76 2.69
3999 4299 5.250082 TGCTTCCTAGATATCATCTGCCATT 59.750 40.000 5.32 0.00 40.51 3.16
4247 4557 4.882671 ACAGTTTTGTAACAGCTGTGAG 57.117 40.909 22.49 1.03 38.74 3.51
4358 4668 2.362397 TCAGTTGCTGAAGTCTCTTCGT 59.638 45.455 0.00 0.00 37.57 3.85
4370 4680 8.475331 TGAAGTCTCTTCGTAATTTATGTTCC 57.525 34.615 5.28 0.00 0.00 3.62
4387 4697 5.160607 TGTTCCGACCATCTATCTTTGTT 57.839 39.130 0.00 0.00 0.00 2.83
4388 4698 4.935205 TGTTCCGACCATCTATCTTTGTTG 59.065 41.667 0.00 0.00 0.00 3.33
4389 4699 5.175859 GTTCCGACCATCTATCTTTGTTGA 58.824 41.667 0.00 0.00 0.00 3.18
4390 4700 5.011090 TCCGACCATCTATCTTTGTTGAG 57.989 43.478 0.00 0.00 0.00 3.02
4391 4701 4.122776 CCGACCATCTATCTTTGTTGAGG 58.877 47.826 0.00 0.00 0.00 3.86
4392 4702 3.557595 CGACCATCTATCTTTGTTGAGGC 59.442 47.826 0.00 0.00 0.00 4.70
4393 4703 4.517285 GACCATCTATCTTTGTTGAGGCA 58.483 43.478 0.00 0.00 0.00 4.75
4394 4704 4.521146 ACCATCTATCTTTGTTGAGGCAG 58.479 43.478 0.00 0.00 0.00 4.85
4446 4764 8.850454 TGTGTTTCAATAGTTTAAGCTTGTTC 57.150 30.769 9.86 0.00 0.00 3.18
4461 4779 3.743396 GCTTGTTCGACTTCAGAAGACAT 59.257 43.478 17.56 0.00 0.00 3.06
4596 4915 6.209986 TGCTTCTTACTAGCTTGGTGTACTTA 59.790 38.462 0.00 0.00 39.38 2.24
4663 4997 6.349300 TCTTGGAAGTATGTATTTCCTCTGC 58.651 40.000 13.37 0.00 41.22 4.26
4664 4998 5.957771 TGGAAGTATGTATTTCCTCTGCT 57.042 39.130 13.37 0.00 41.22 4.24
4684 5200 3.118482 GCTGTCCCATTCTCAGAAGATGA 60.118 47.826 0.00 0.00 36.21 2.92
4763 5280 6.551736 AGCTAACTTGTTAAAACAGTGTGTG 58.448 36.000 0.00 0.00 40.50 3.82
4808 5325 5.933617 TGAGGCAATTCAATATAGCAGAGT 58.066 37.500 0.00 0.00 0.00 3.24
4810 5327 4.518211 AGGCAATTCAATATAGCAGAGTGC 59.482 41.667 0.00 0.00 45.46 4.40
4836 5353 8.085296 CGCTTTTCTCCTAAGACATGATATACT 58.915 37.037 0.00 0.00 0.00 2.12
4848 5365 9.509956 AAGACATGATATACTACTACTCTGTCC 57.490 37.037 0.00 0.00 31.89 4.02
4849 5366 8.104566 AGACATGATATACTACTACTCTGTCCC 58.895 40.741 0.00 0.00 31.89 4.46
4850 5367 7.756614 ACATGATATACTACTACTCTGTCCCA 58.243 38.462 0.00 0.00 0.00 4.37
4851 5368 8.394822 ACATGATATACTACTACTCTGTCCCAT 58.605 37.037 0.00 0.00 0.00 4.00
4852 5369 9.907229 CATGATATACTACTACTCTGTCCCATA 57.093 37.037 0.00 0.00 0.00 2.74
4859 5376 8.466617 ACTACTACTCTGTCCCATAATGTAAG 57.533 38.462 0.00 0.00 0.00 2.34
4860 5377 8.280084 ACTACTACTCTGTCCCATAATGTAAGA 58.720 37.037 0.00 0.00 0.00 2.10
4861 5378 7.349412 ACTACTCTGTCCCATAATGTAAGAC 57.651 40.000 0.00 0.00 0.00 3.01
4862 5379 5.263968 ACTCTGTCCCATAATGTAAGACG 57.736 43.478 0.00 0.00 0.00 4.18
4863 5380 4.710375 ACTCTGTCCCATAATGTAAGACGT 59.290 41.667 0.00 0.00 0.00 4.34
4864 5381 5.187186 ACTCTGTCCCATAATGTAAGACGTT 59.813 40.000 0.00 0.00 0.00 3.99
4865 5382 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
4866 5383 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
4867 5384 6.938030 TCTGTCCCATAATGTAAGACGTTTTT 59.062 34.615 0.00 0.00 0.00 1.94
4868 5385 6.904498 TGTCCCATAATGTAAGACGTTTTTG 58.096 36.000 0.00 0.00 0.00 2.44
4869 5386 5.798434 GTCCCATAATGTAAGACGTTTTTGC 59.202 40.000 0.00 0.00 0.00 3.68
4870 5387 5.473846 TCCCATAATGTAAGACGTTTTTGCA 59.526 36.000 0.00 1.87 0.00 4.08
4871 5388 5.799936 CCCATAATGTAAGACGTTTTTGCAG 59.200 40.000 0.00 0.00 0.00 4.41
4872 5389 6.378582 CCATAATGTAAGACGTTTTTGCAGT 58.621 36.000 0.00 3.59 0.00 4.40
4873 5390 6.861055 CCATAATGTAAGACGTTTTTGCAGTT 59.139 34.615 9.23 7.12 0.00 3.16
4874 5391 7.060633 CCATAATGTAAGACGTTTTTGCAGTTC 59.939 37.037 9.23 0.00 0.00 3.01
4875 5392 4.948608 TGTAAGACGTTTTTGCAGTTCA 57.051 36.364 0.00 0.00 0.00 3.18
4876 5393 5.298197 TGTAAGACGTTTTTGCAGTTCAA 57.702 34.783 0.00 0.00 0.00 2.69
4877 5394 5.885881 TGTAAGACGTTTTTGCAGTTCAAT 58.114 33.333 0.00 0.00 34.12 2.57
4878 5395 6.326375 TGTAAGACGTTTTTGCAGTTCAATT 58.674 32.000 0.00 0.00 34.12 2.32
4879 5396 6.809196 TGTAAGACGTTTTTGCAGTTCAATTT 59.191 30.769 0.00 0.00 34.12 1.82
4880 5397 7.968956 TGTAAGACGTTTTTGCAGTTCAATTTA 59.031 29.630 0.00 0.00 34.12 1.40
4881 5398 7.820044 AAGACGTTTTTGCAGTTCAATTTAA 57.180 28.000 0.00 0.00 34.12 1.52
4882 5399 7.820044 AGACGTTTTTGCAGTTCAATTTAAA 57.180 28.000 0.00 0.00 34.12 1.52
4883 5400 7.671827 AGACGTTTTTGCAGTTCAATTTAAAC 58.328 30.769 0.00 0.00 33.11 2.01
4884 5401 7.544217 AGACGTTTTTGCAGTTCAATTTAAACT 59.456 29.630 0.00 0.00 37.44 2.66
4893 5410 7.859891 CAGTTCAATTTAAACTGCAAAAACG 57.140 32.000 14.40 0.00 44.94 3.60
4894 5411 7.452231 CAGTTCAATTTAAACTGCAAAAACGT 58.548 30.769 14.40 0.00 44.94 3.99
4895 5412 7.630606 CAGTTCAATTTAAACTGCAAAAACGTC 59.369 33.333 14.40 0.00 44.94 4.34
4896 5413 6.576551 TCAATTTAAACTGCAAAAACGTCC 57.423 33.333 0.00 0.00 0.00 4.79
4897 5414 6.334202 TCAATTTAAACTGCAAAAACGTCCT 58.666 32.000 0.00 0.00 0.00 3.85
4898 5415 7.481642 TCAATTTAAACTGCAAAAACGTCCTA 58.518 30.769 0.00 0.00 0.00 2.94
4899 5416 8.138712 TCAATTTAAACTGCAAAAACGTCCTAT 58.861 29.630 0.00 0.00 0.00 2.57
4900 5417 9.400638 CAATTTAAACTGCAAAAACGTCCTATA 57.599 29.630 0.00 0.00 0.00 1.31
4906 5423 7.259290 ACTGCAAAAACGTCCTATATTATGG 57.741 36.000 0.00 0.00 0.00 2.74
4907 5424 6.262273 ACTGCAAAAACGTCCTATATTATGGG 59.738 38.462 0.00 0.00 0.00 4.00
4908 5425 6.358178 TGCAAAAACGTCCTATATTATGGGA 58.642 36.000 4.74 4.74 37.61 4.37
4915 5432 4.959522 TCCTATATTATGGGACGGAGGA 57.040 45.455 4.74 0.00 34.71 3.71
4916 5433 5.279562 TCCTATATTATGGGACGGAGGAA 57.720 43.478 4.74 0.00 34.71 3.36
4917 5434 5.269991 TCCTATATTATGGGACGGAGGAAG 58.730 45.833 4.74 0.00 34.71 3.46
4974 5491 8.994500 TGTTATCATTCTGTTAGTATTACCCCA 58.006 33.333 0.00 0.00 0.00 4.96
4975 5492 9.841295 GTTATCATTCTGTTAGTATTACCCCAA 57.159 33.333 0.00 0.00 0.00 4.12
5069 5586 4.870426 TGATCCTGTGATTTTCGAAGCTAC 59.130 41.667 0.00 0.00 0.00 3.58
5073 5590 4.396166 CCTGTGATTTTCGAAGCTACCATT 59.604 41.667 0.00 0.00 0.00 3.16
5074 5591 5.447818 CCTGTGATTTTCGAAGCTACCATTC 60.448 44.000 0.00 0.00 0.00 2.67
5075 5592 5.000591 TGTGATTTTCGAAGCTACCATTCA 58.999 37.500 0.00 0.00 0.00 2.57
5077 5594 5.122396 GTGATTTTCGAAGCTACCATTCACT 59.878 40.000 0.00 0.00 0.00 3.41
5082 5599 5.607119 TCGAAGCTACCATTCACTTTTTC 57.393 39.130 0.00 0.00 0.00 2.29
5084 5601 4.455877 CGAAGCTACCATTCACTTTTTCCT 59.544 41.667 0.00 0.00 0.00 3.36
5085 5602 5.642063 CGAAGCTACCATTCACTTTTTCCTA 59.358 40.000 0.00 0.00 0.00 2.94
5087 5604 6.819397 AGCTACCATTCACTTTTTCCTAAC 57.181 37.500 0.00 0.00 0.00 2.34
5088 5605 6.543735 AGCTACCATTCACTTTTTCCTAACT 58.456 36.000 0.00 0.00 0.00 2.24
5094 5611 8.877195 ACCATTCACTTTTTCCTAACTACTAGA 58.123 33.333 0.00 0.00 0.00 2.43
5096 5613 9.706691 CATTCACTTTTTCCTAACTACTAGACA 57.293 33.333 0.00 0.00 0.00 3.41
5178 5696 9.013490 CAGTATTACATAATTGCTTGCAGTTTC 57.987 33.333 8.54 0.00 0.00 2.78
5183 5701 5.010922 ACATAATTGCTTGCAGTTTCCAGAA 59.989 36.000 8.54 0.00 0.00 3.02
5207 5725 6.151663 TGTTTATCCATCATTGGCATCAAG 57.848 37.500 0.00 0.00 43.29 3.02
5406 5924 3.117512 CCTTCCCACCTGCTGGTTATAAT 60.118 47.826 13.36 0.00 46.05 1.28
5478 5996 3.738982 TCTGGATTGGTATTACATGCGG 58.261 45.455 0.00 0.00 0.00 5.69
5489 6007 1.365368 TACATGCGGCATTCACCACG 61.365 55.000 13.81 2.58 0.00 4.94
5532 6050 2.098117 CCATTTTGACGAAGCATCCCTC 59.902 50.000 0.00 0.00 0.00 4.30
5550 6068 0.827925 TCGAGGCTGGTCAGAACACT 60.828 55.000 0.00 0.00 0.00 3.55
5708 6226 2.981859 AACGAAGACAGTTCCACAGT 57.018 45.000 0.00 0.00 0.00 3.55
5806 6324 6.548251 TGGATATCATAATATGGCAGGCAATG 59.452 38.462 0.00 0.00 0.00 2.82
5807 6325 6.774170 GGATATCATAATATGGCAGGCAATGA 59.226 38.462 10.58 10.58 0.00 2.57
5808 6326 5.909621 ATCATAATATGGCAGGCAATGAC 57.090 39.130 10.42 0.00 37.50 3.06
5809 6327 4.989277 TCATAATATGGCAGGCAATGACT 58.011 39.130 0.00 0.00 38.04 3.41
6024 6542 2.813474 GCGTACGACAGCATGCCA 60.813 61.111 21.65 0.00 42.53 4.92
6086 6604 2.996621 CAGTGTAGGCTCGAAAAAGGAG 59.003 50.000 0.00 0.00 34.62 3.69
6118 6636 8.947055 AAACTGACAAAAATAGTTGATGCTTT 57.053 26.923 0.00 0.00 35.06 3.51
6132 6650 2.171940 CTTTGCTCGTGCGCTGTC 59.828 61.111 9.73 0.00 43.34 3.51
6138 6656 1.442184 CTCGTGCGCTGTCGTAACT 60.442 57.895 9.73 0.00 38.14 2.24
6160 6678 4.134623 GTGTGAACCACGCCTTCA 57.865 55.556 0.00 0.00 38.73 3.02
6162 6680 0.517316 GTGTGAACCACGCCTTCATC 59.483 55.000 0.00 0.00 38.73 2.92
6163 6681 0.107643 TGTGAACCACGCCTTCATCA 59.892 50.000 0.00 0.00 37.14 3.07
6315 6833 1.375140 ACGCAGTGCATCTGTCTGG 60.375 57.895 16.83 0.00 45.23 3.86
6317 6835 0.108662 CGCAGTGCATCTGTCTGGTA 60.109 55.000 16.83 0.00 45.23 3.25
6318 6836 1.472201 CGCAGTGCATCTGTCTGGTAT 60.472 52.381 16.83 0.00 45.23 2.73
6319 6837 1.938577 GCAGTGCATCTGTCTGGTATG 59.061 52.381 11.09 0.00 45.23 2.39
6345 6863 0.820891 CCTCACAAGTTGGCTGTGCT 60.821 55.000 7.96 0.00 33.93 4.40
6360 6878 2.360165 CTGTGCTAGGCCAAATCAATCC 59.640 50.000 5.01 0.00 0.00 3.01
6366 6884 0.668535 GGCCAAATCAATCCGCTACC 59.331 55.000 0.00 0.00 0.00 3.18
6380 6898 2.285977 CGCTACCCAACATACTTTCCC 58.714 52.381 0.00 0.00 0.00 3.97
6385 6903 2.027469 ACCCAACATACTTTCCCGAGAC 60.027 50.000 0.00 0.00 0.00 3.36
6392 6910 4.161001 ACATACTTTCCCGAGACGGTTTAT 59.839 41.667 9.28 0.00 46.80 1.40
6401 6919 4.022589 CCCGAGACGGTTTATCATTAGCTA 60.023 45.833 9.28 0.00 46.80 3.32
6402 6920 4.916249 CCGAGACGGTTTATCATTAGCTAC 59.084 45.833 0.00 0.00 42.73 3.58
6411 6929 8.656849 CGGTTTATCATTAGCTACCACATAATC 58.343 37.037 0.00 0.00 0.00 1.75
6426 6947 8.752005 ACCACATAATCAGTATAAATGTTGCT 57.248 30.769 0.00 0.00 0.00 3.91
6427 6948 8.840321 ACCACATAATCAGTATAAATGTTGCTC 58.160 33.333 0.00 0.00 0.00 4.26
6428 6949 8.839343 CCACATAATCAGTATAAATGTTGCTCA 58.161 33.333 0.00 0.00 0.00 4.26
6431 6952 9.338291 CATAATCAGTATAAATGTTGCTCATGC 57.662 33.333 0.00 0.00 36.81 4.06
6432 6953 7.578310 AATCAGTATAAATGTTGCTCATGCT 57.422 32.000 0.00 0.00 40.48 3.79
6433 6954 6.367686 TCAGTATAAATGTTGCTCATGCTG 57.632 37.500 0.00 0.00 40.48 4.41
6434 6955 4.974275 CAGTATAAATGTTGCTCATGCTGC 59.026 41.667 0.00 0.00 40.48 5.25
6435 6956 2.945447 TAAATGTTGCTCATGCTGCC 57.055 45.000 0.00 0.00 40.48 4.85
6436 6957 0.970640 AAATGTTGCTCATGCTGCCA 59.029 45.000 0.00 1.41 40.48 4.92
6437 6958 1.191535 AATGTTGCTCATGCTGCCAT 58.808 45.000 0.00 3.33 40.48 4.40
6445 6966 2.921435 ATGCTGCCATGATCCCGT 59.079 55.556 0.00 0.00 0.00 5.28
6446 6967 1.228063 ATGCTGCCATGATCCCGTC 60.228 57.895 0.00 0.00 0.00 4.79
6447 6968 2.592861 GCTGCCATGATCCCGTCC 60.593 66.667 0.00 0.00 0.00 4.79
6448 6969 3.112205 GCTGCCATGATCCCGTCCT 62.112 63.158 0.00 0.00 0.00 3.85
6449 6970 1.227764 CTGCCATGATCCCGTCCTG 60.228 63.158 0.00 0.00 0.00 3.86
6450 6971 2.111878 GCCATGATCCCGTCCTGG 59.888 66.667 0.00 0.00 43.34 4.45
6451 6972 2.111878 CCATGATCCCGTCCTGGC 59.888 66.667 0.00 0.00 36.10 4.85
6452 6973 2.745308 CCATGATCCCGTCCTGGCA 61.745 63.158 0.00 0.00 36.10 4.92
6453 6974 1.224315 CATGATCCCGTCCTGGCAA 59.776 57.895 0.00 0.00 35.87 4.52
6454 6975 0.816825 CATGATCCCGTCCTGGCAAG 60.817 60.000 0.00 0.00 35.87 4.01
6455 6976 1.987807 ATGATCCCGTCCTGGCAAGG 61.988 60.000 0.00 0.00 46.06 3.61
6456 6977 4.115199 ATCCCGTCCTGGCAAGGC 62.115 66.667 0.56 0.00 44.11 4.35
6489 7027 2.165998 GAGCTGTCATTTTGAAGGCCT 58.834 47.619 0.00 0.00 30.16 5.19
6508 7046 3.434596 GCCTCCGGGAATTAATTGGTAGT 60.435 47.826 5.17 0.00 33.58 2.73
6510 7048 5.548406 CCTCCGGGAATTAATTGGTAGTAG 58.452 45.833 5.17 0.00 33.58 2.57
6527 7065 4.661247 AGTAGGTTCTGGAGTACACTCT 57.339 45.455 9.15 0.00 42.48 3.24
6543 7081 0.108424 CTCTTCTTGAGGGCCAGACG 60.108 60.000 6.18 0.00 39.08 4.18
6775 7313 3.443045 GCCACTCAATGCCACCCG 61.443 66.667 0.00 0.00 0.00 5.28
6799 7337 1.821136 CTAGTACGAACGGTTTCCCCT 59.179 52.381 0.00 0.00 0.00 4.79
6803 7341 0.758123 ACGAACGGTTTCCCCTAACA 59.242 50.000 0.00 0.00 0.00 2.41
6816 7354 1.138266 CCCTAACACACGATCCGGATT 59.862 52.381 20.22 3.66 0.00 3.01
6826 7364 4.527038 ACACGATCCGGATTTACATATCCT 59.473 41.667 20.22 0.00 41.65 3.24
6827 7365 5.011738 ACACGATCCGGATTTACATATCCTT 59.988 40.000 20.22 0.00 41.65 3.36
6829 7367 6.426937 CACGATCCGGATTTACATATCCTTTT 59.573 38.462 20.22 0.00 41.65 2.27
6830 7368 6.996282 ACGATCCGGATTTACATATCCTTTTT 59.004 34.615 20.22 0.00 41.65 1.94
6853 7391 7.517614 TTTTTAATCCAGTGTGTAATGAGCA 57.482 32.000 0.00 0.00 0.00 4.26
6854 7392 6.741992 TTTAATCCAGTGTGTAATGAGCAG 57.258 37.500 0.00 0.00 0.00 4.24
6855 7393 2.768253 TCCAGTGTGTAATGAGCAGG 57.232 50.000 0.00 0.00 0.00 4.85
6856 7394 1.089920 CCAGTGTGTAATGAGCAGGC 58.910 55.000 0.00 0.00 0.00 4.85
6857 7395 1.089920 CAGTGTGTAATGAGCAGGCC 58.910 55.000 0.00 0.00 0.00 5.19
6858 7396 0.987294 AGTGTGTAATGAGCAGGCCT 59.013 50.000 0.00 0.00 0.00 5.19
6859 7397 2.093500 CAGTGTGTAATGAGCAGGCCTA 60.093 50.000 3.98 0.00 0.00 3.93
6860 7398 2.774234 AGTGTGTAATGAGCAGGCCTAT 59.226 45.455 3.98 0.00 0.00 2.57
6861 7399 3.200825 AGTGTGTAATGAGCAGGCCTATT 59.799 43.478 3.98 3.98 0.00 1.73
6862 7400 3.561725 GTGTGTAATGAGCAGGCCTATTC 59.438 47.826 3.98 6.86 0.00 1.75
6863 7401 2.802816 GTGTAATGAGCAGGCCTATTCG 59.197 50.000 3.98 0.00 0.00 3.34
6864 7402 1.801178 GTAATGAGCAGGCCTATTCGC 59.199 52.381 3.98 4.38 0.00 4.70
6865 7403 0.471617 AATGAGCAGGCCTATTCGCT 59.528 50.000 14.80 14.80 37.44 4.93
6866 7404 4.352386 GAGCAGGCCTATTCGCTC 57.648 61.111 22.76 22.76 43.60 5.03
6867 7405 3.634202 AGCAGGCCTATTCGCTCA 58.366 55.556 3.98 0.00 0.00 4.26
6868 7406 1.907739 AGCAGGCCTATTCGCTCAA 59.092 52.632 3.98 0.00 0.00 3.02
6869 7407 0.471617 AGCAGGCCTATTCGCTCAAT 59.528 50.000 3.98 0.00 0.00 2.57
6870 7408 1.133976 AGCAGGCCTATTCGCTCAATT 60.134 47.619 3.98 0.00 0.00 2.32
6871 7409 1.265365 GCAGGCCTATTCGCTCAATTC 59.735 52.381 3.98 0.00 0.00 2.17
6872 7410 2.843701 CAGGCCTATTCGCTCAATTCT 58.156 47.619 3.98 0.00 0.00 2.40
6873 7411 3.803715 GCAGGCCTATTCGCTCAATTCTA 60.804 47.826 3.98 0.00 0.00 2.10
6874 7412 3.743396 CAGGCCTATTCGCTCAATTCTAC 59.257 47.826 3.98 0.00 0.00 2.59
6875 7413 3.067833 GGCCTATTCGCTCAATTCTACC 58.932 50.000 0.00 0.00 0.00 3.18
6876 7414 3.494398 GGCCTATTCGCTCAATTCTACCA 60.494 47.826 0.00 0.00 0.00 3.25
6877 7415 4.127171 GCCTATTCGCTCAATTCTACCAA 58.873 43.478 0.00 0.00 0.00 3.67
6880 7418 4.558538 ATTCGCTCAATTCTACCAATGC 57.441 40.909 0.00 0.00 0.00 3.56
6884 7422 4.035558 TCGCTCAATTCTACCAATGCAATC 59.964 41.667 0.00 0.00 0.00 2.67
6918 7456 8.355272 GTAACCAACCACGATTTTACATTTTT 57.645 30.769 0.00 0.00 0.00 1.94
6955 7499 2.103094 CCATGACAGTGGTACGATCCAT 59.897 50.000 0.00 0.00 39.81 3.41
6956 7500 3.384668 CATGACAGTGGTACGATCCATC 58.615 50.000 6.61 2.42 39.81 3.51
6966 7510 3.922190 CGATCCATCGCAATTTGCA 57.078 47.368 20.56 8.76 45.36 4.08
6979 7529 2.559668 CAATTTGCAGAGAGGCCTTTCA 59.440 45.455 24.25 4.42 0.00 2.69
7017 7576 9.405587 ACTTGTGGTTGATTGATTAATTAAACG 57.594 29.630 1.21 0.00 33.49 3.60
7065 7624 1.869767 CCATTTCCTCGCTCATGCTAC 59.130 52.381 0.00 0.00 36.97 3.58
7066 7625 1.869767 CATTTCCTCGCTCATGCTACC 59.130 52.381 0.00 0.00 36.97 3.18
7067 7626 0.901827 TTTCCTCGCTCATGCTACCA 59.098 50.000 0.00 0.00 36.97 3.25
7068 7627 0.175760 TTCCTCGCTCATGCTACCAC 59.824 55.000 0.00 0.00 36.97 4.16
7069 7628 0.970427 TCCTCGCTCATGCTACCACA 60.970 55.000 0.00 0.00 36.97 4.17
7070 7629 0.807667 CCTCGCTCATGCTACCACAC 60.808 60.000 0.00 0.00 36.97 3.82
7071 7630 0.108662 CTCGCTCATGCTACCACACA 60.109 55.000 0.00 0.00 36.97 3.72
7072 7631 0.389817 TCGCTCATGCTACCACACAC 60.390 55.000 0.00 0.00 36.97 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.684983 GATGGAAGGAATCGTACGGGA 59.315 52.381 16.52 0.00 0.00 5.14
67 68 1.654954 AAGAGACGTGACGGGATCGG 61.655 60.000 10.66 0.00 41.39 4.18
108 109 0.747852 GACGATGAGAGGGGGAAGAC 59.252 60.000 0.00 0.00 0.00 3.01
113 114 1.403687 GGGAAGACGATGAGAGGGGG 61.404 65.000 0.00 0.00 0.00 5.40
317 326 1.941294 GAGTCGTGAGCGGATAAGAGA 59.059 52.381 0.00 0.00 38.89 3.10
383 393 0.673644 GCTTGCCAGAGCTCGGTTTA 60.674 55.000 20.69 9.21 39.57 2.01
396 406 1.065126 ACCTAGATCAACTGGCTTGCC 60.065 52.381 4.43 4.43 0.00 4.52
401 411 2.290960 ACCCAAACCTAGATCAACTGGC 60.291 50.000 0.00 0.00 0.00 4.85
493 503 3.712016 TGTAGCAAAATCCCTACAGCA 57.288 42.857 0.00 0.00 39.05 4.41
556 566 4.542075 GGAGCAATCCGGTTCTCC 57.458 61.111 14.63 14.63 38.40 3.71
587 597 2.700897 CCATCTCCTCCCACGTATTCTT 59.299 50.000 0.00 0.00 0.00 2.52
612 622 0.394352 CCAAGAGGCCCAGCGTAATT 60.394 55.000 0.00 0.00 0.00 1.40
681 693 8.959734 ATCAAATTAACCAACGTTAAGCTTAC 57.040 30.769 5.45 0.99 45.29 2.34
692 704 3.743396 TGGCGCAAATCAAATTAACCAAC 59.257 39.130 10.83 0.00 0.00 3.77
701 713 2.593346 ACAGTTTGGCGCAAATCAAA 57.407 40.000 10.83 7.66 35.74 2.69
714 727 8.796475 AGTGAACATATAAGCATCAAACAGTTT 58.204 29.630 0.00 0.00 0.00 2.66
730 743 6.899393 AACATTCCAACACAGTGAACATAT 57.101 33.333 7.81 0.00 0.00 1.78
782 796 0.964358 CCCAAGGGCAAGCTCTGAAG 60.964 60.000 0.00 0.00 0.00 3.02
827 841 6.311445 AGAAACTGAAGTAATGTCATACGCAG 59.689 38.462 0.00 0.00 38.20 5.18
932 946 6.105333 CACAGGAAATGACCTAGAAAGAGAG 58.895 44.000 0.00 0.00 38.32 3.20
940 954 2.787473 TGCCACAGGAAATGACCTAG 57.213 50.000 0.00 0.00 38.32 3.02
1038 1052 5.944007 TCTTCTCCAAGGCCACTTAAATAAC 59.056 40.000 5.01 0.00 34.49 1.89
1095 1109 5.458041 ACAACTCAATTTCAGGTGGAATG 57.542 39.130 4.57 0.00 34.91 2.67
1158 1172 2.950781 TCACCATCGAGAAGCCTAGAT 58.049 47.619 0.00 0.00 35.53 1.98
1162 1176 0.539051 CCTTCACCATCGAGAAGCCT 59.461 55.000 6.62 0.00 39.85 4.58
1164 1178 1.424493 CGCCTTCACCATCGAGAAGC 61.424 60.000 6.62 2.90 39.85 3.86
1171 1185 0.036388 TCCTTGACGCCTTCACCATC 60.036 55.000 0.00 0.00 32.26 3.51
1246 1260 6.388619 AATGATACACCTTAGTCCCTTTGT 57.611 37.500 0.00 0.00 0.00 2.83
1251 1265 5.881923 TGGTAATGATACACCTTAGTCCC 57.118 43.478 0.00 0.00 35.73 4.46
1284 1298 6.405953 CCGTGAACAGTACATTAAGGATCTCT 60.406 42.308 0.00 0.00 0.00 3.10
1305 1319 0.605319 ACCCAATACAGCACACCGTG 60.605 55.000 0.00 0.00 36.51 4.94
1651 1763 4.202080 GGCTACGAAAGAAAAACAAGGGTT 60.202 41.667 0.00 0.00 39.43 4.11
1668 1780 7.426410 TCAAGATCTGTAATCTTAAGGCTACG 58.574 38.462 1.85 2.65 36.68 3.51
1889 2001 5.863965 TGTACATGAGATTTGACAGTTGGA 58.136 37.500 0.00 0.00 0.00 3.53
2165 2281 2.229784 CTGATGAAGGGTGTTTCTTGCC 59.770 50.000 0.00 0.00 0.00 4.52
2171 2287 3.181429 ACATGGACTGATGAAGGGTGTTT 60.181 43.478 0.00 0.00 0.00 2.83
2499 2620 4.146745 AGGGGACGGATAAATACACAAC 57.853 45.455 0.00 0.00 0.00 3.32
2778 2900 3.756434 TGCAAAGCAAAGGATACAGGTAC 59.244 43.478 0.00 0.00 34.76 3.34
3105 3230 7.383300 GCCACATAAATCATGAAAATAAGAGGC 59.617 37.037 0.00 6.60 38.10 4.70
3191 3316 7.765360 TGAGTTTTAGAGACAACGAAGGTAAAA 59.235 33.333 0.00 0.00 0.00 1.52
3432 3557 4.345257 TGTAAGAGAAAGACAGAAGGTGCT 59.655 41.667 0.00 0.00 0.00 4.40
3440 3565 9.499585 CATAAAATGCATGTAAGAGAAAGACAG 57.500 33.333 0.00 0.00 0.00 3.51
3742 3867 5.642491 CCAGATGCCACATGAGTATTATCTG 59.358 44.000 0.00 10.34 37.25 2.90
3854 3984 6.493458 TCAACATTGTCATATCTCTATCGGGA 59.507 38.462 0.00 0.00 0.00 5.14
3999 4299 4.759693 ACCACTGACGAAAATCTAATGCAA 59.240 37.500 0.00 0.00 0.00 4.08
4247 4557 9.769093 ATCAACACGCTGTAAATTTATAAGAAC 57.231 29.630 12.62 0.00 0.00 3.01
4370 4680 3.557595 GCCTCAACAAAGATAGATGGTCG 59.442 47.826 0.00 0.00 0.00 4.79
4387 4697 1.946768 GTTAAGTGTTGCACTGCCTCA 59.053 47.619 2.31 0.00 44.62 3.86
4388 4698 1.946768 TGTTAAGTGTTGCACTGCCTC 59.053 47.619 2.31 0.00 44.62 4.70
4389 4699 2.051334 TGTTAAGTGTTGCACTGCCT 57.949 45.000 2.31 0.00 44.62 4.75
4390 4700 2.293122 TGATGTTAAGTGTTGCACTGCC 59.707 45.455 2.31 0.00 44.62 4.85
4391 4701 3.624326 TGATGTTAAGTGTTGCACTGC 57.376 42.857 2.31 0.00 44.62 4.40
4392 4702 4.383649 GCAATGATGTTAAGTGTTGCACTG 59.616 41.667 2.31 0.00 44.62 3.66
4394 4704 4.549458 AGCAATGATGTTAAGTGTTGCAC 58.451 39.130 10.06 0.00 43.08 4.57
4446 4764 2.084610 TGCCATGTCTTCTGAAGTCG 57.915 50.000 16.43 4.66 0.00 4.18
4663 4997 4.750021 TCATCTTCTGAGAATGGGACAG 57.250 45.455 0.00 0.00 35.93 3.51
4664 4998 4.718276 TCATCATCTTCTGAGAATGGGACA 59.282 41.667 0.00 0.00 39.62 4.02
4715 5232 8.170553 GCTAACATTTTCCATATTTTGCACAAG 58.829 33.333 0.00 0.00 0.00 3.16
4781 5298 8.241497 TCTGCTATATTGAATTGCCTCAAATT 57.759 30.769 0.00 0.00 38.75 1.82
4808 5325 2.831685 TGTCTTAGGAGAAAAGCGCA 57.168 45.000 11.47 0.00 32.66 6.09
4810 5327 8.085296 AGTATATCATGTCTTAGGAGAAAAGCG 58.915 37.037 0.00 0.00 32.66 4.68
4845 5362 5.798434 GCAAAAACGTCTTACATTATGGGAC 59.202 40.000 0.00 1.75 0.00 4.46
4846 5363 5.473846 TGCAAAAACGTCTTACATTATGGGA 59.526 36.000 0.00 0.00 0.00 4.37
4847 5364 5.704888 TGCAAAAACGTCTTACATTATGGG 58.295 37.500 0.00 0.00 0.00 4.00
4848 5365 6.378582 ACTGCAAAAACGTCTTACATTATGG 58.621 36.000 0.00 0.00 0.00 2.74
4849 5366 7.589587 TGAACTGCAAAAACGTCTTACATTATG 59.410 33.333 0.00 0.00 0.00 1.90
4850 5367 7.644490 TGAACTGCAAAAACGTCTTACATTAT 58.356 30.769 0.00 0.00 0.00 1.28
4851 5368 7.017498 TGAACTGCAAAAACGTCTTACATTA 57.983 32.000 0.00 0.00 0.00 1.90
4852 5369 5.885881 TGAACTGCAAAAACGTCTTACATT 58.114 33.333 0.00 0.00 0.00 2.71
4853 5370 5.493133 TGAACTGCAAAAACGTCTTACAT 57.507 34.783 0.00 0.00 0.00 2.29
4854 5371 4.948608 TGAACTGCAAAAACGTCTTACA 57.051 36.364 0.00 0.00 0.00 2.41
4855 5372 6.806120 AATTGAACTGCAAAAACGTCTTAC 57.194 33.333 0.00 0.00 40.48 2.34
4856 5373 8.912787 TTAAATTGAACTGCAAAAACGTCTTA 57.087 26.923 0.00 0.00 40.48 2.10
4857 5374 7.820044 TTAAATTGAACTGCAAAAACGTCTT 57.180 28.000 0.00 0.00 40.48 3.01
4858 5375 7.544217 AGTTTAAATTGAACTGCAAAAACGTCT 59.456 29.630 2.22 0.00 38.67 4.18
4859 5376 7.630606 CAGTTTAAATTGAACTGCAAAAACGTC 59.369 33.333 15.89 0.00 45.02 4.34
4860 5377 7.452231 CAGTTTAAATTGAACTGCAAAAACGT 58.548 30.769 15.89 0.00 45.02 3.99
4861 5378 7.859891 CAGTTTAAATTGAACTGCAAAAACG 57.140 32.000 15.89 0.00 45.02 3.60
4870 5387 7.201487 GGACGTTTTTGCAGTTTAAATTGAACT 60.201 33.333 14.30 0.00 37.82 3.01
4871 5388 6.897663 GGACGTTTTTGCAGTTTAAATTGAAC 59.102 34.615 14.30 8.43 0.00 3.18
4872 5389 6.814146 AGGACGTTTTTGCAGTTTAAATTGAA 59.186 30.769 14.30 0.78 0.00 2.69
4873 5390 6.334202 AGGACGTTTTTGCAGTTTAAATTGA 58.666 32.000 14.30 0.00 0.00 2.57
4874 5391 6.582437 AGGACGTTTTTGCAGTTTAAATTG 57.418 33.333 6.35 6.35 0.00 2.32
4880 5397 8.188139 CCATAATATAGGACGTTTTTGCAGTTT 58.812 33.333 0.00 0.00 0.00 2.66
4881 5398 7.201785 CCCATAATATAGGACGTTTTTGCAGTT 60.202 37.037 0.00 0.00 0.00 3.16
4882 5399 6.262273 CCCATAATATAGGACGTTTTTGCAGT 59.738 38.462 0.00 0.00 0.00 4.40
4883 5400 6.485313 TCCCATAATATAGGACGTTTTTGCAG 59.515 38.462 0.00 0.00 0.00 4.41
4884 5401 6.261381 GTCCCATAATATAGGACGTTTTTGCA 59.739 38.462 2.27 0.00 40.65 4.08
4885 5402 6.665465 GTCCCATAATATAGGACGTTTTTGC 58.335 40.000 2.27 0.00 40.65 3.68
4893 5410 4.607239 TCCTCCGTCCCATAATATAGGAC 58.393 47.826 7.65 7.65 45.49 3.85
4894 5411 4.959522 TCCTCCGTCCCATAATATAGGA 57.040 45.455 0.00 0.00 0.00 2.94
4895 5412 5.024118 ACTTCCTCCGTCCCATAATATAGG 58.976 45.833 0.00 0.00 0.00 2.57
4896 5413 7.713734 TTACTTCCTCCGTCCCATAATATAG 57.286 40.000 0.00 0.00 0.00 1.31
4897 5414 8.674925 AATTACTTCCTCCGTCCCATAATATA 57.325 34.615 0.00 0.00 0.00 0.86
4898 5415 7.569599 AATTACTTCCTCCGTCCCATAATAT 57.430 36.000 0.00 0.00 0.00 1.28
4899 5416 7.383156 AAATTACTTCCTCCGTCCCATAATA 57.617 36.000 0.00 0.00 0.00 0.98
4900 5417 5.906772 AATTACTTCCTCCGTCCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
4901 5418 5.703730 AAATTACTTCCTCCGTCCCATAA 57.296 39.130 0.00 0.00 0.00 1.90
4902 5419 5.703730 AAAATTACTTCCTCCGTCCCATA 57.296 39.130 0.00 0.00 0.00 2.74
4903 5420 4.586306 AAAATTACTTCCTCCGTCCCAT 57.414 40.909 0.00 0.00 0.00 4.00
4904 5421 4.376225 AAAAATTACTTCCTCCGTCCCA 57.624 40.909 0.00 0.00 0.00 4.37
4905 5422 6.827251 AGATTAAAAATTACTTCCTCCGTCCC 59.173 38.462 0.00 0.00 0.00 4.46
4906 5423 7.860918 AGATTAAAAATTACTTCCTCCGTCC 57.139 36.000 0.00 0.00 0.00 4.79
4907 5424 8.727910 ACAAGATTAAAAATTACTTCCTCCGTC 58.272 33.333 0.00 0.00 0.00 4.79
4908 5425 8.631480 ACAAGATTAAAAATTACTTCCTCCGT 57.369 30.769 0.00 0.00 0.00 4.69
5069 5586 9.152595 GTCTAGTAGTTAGGAAAAAGTGAATGG 57.847 37.037 0.00 0.00 0.00 3.16
5073 5590 8.529476 GGATGTCTAGTAGTTAGGAAAAAGTGA 58.471 37.037 0.00 0.00 0.00 3.41
5074 5591 8.311836 TGGATGTCTAGTAGTTAGGAAAAAGTG 58.688 37.037 0.00 0.00 0.00 3.16
5075 5592 8.431910 TGGATGTCTAGTAGTTAGGAAAAAGT 57.568 34.615 0.00 0.00 0.00 2.66
5077 5594 9.886132 GAATGGATGTCTAGTAGTTAGGAAAAA 57.114 33.333 0.00 0.00 0.00 1.94
5082 5599 7.068839 AGTGTGAATGGATGTCTAGTAGTTAGG 59.931 40.741 0.00 0.00 0.00 2.69
5084 5601 7.614192 TCAGTGTGAATGGATGTCTAGTAGTTA 59.386 37.037 0.00 0.00 0.00 2.24
5085 5602 6.437477 TCAGTGTGAATGGATGTCTAGTAGTT 59.563 38.462 0.00 0.00 0.00 2.24
5087 5604 6.127619 TGTCAGTGTGAATGGATGTCTAGTAG 60.128 42.308 0.00 0.00 0.00 2.57
5088 5605 5.714806 TGTCAGTGTGAATGGATGTCTAGTA 59.285 40.000 0.00 0.00 0.00 1.82
5094 5611 3.141398 GTGTGTCAGTGTGAATGGATGT 58.859 45.455 0.00 0.00 0.00 3.06
5096 5613 3.490439 TGTGTGTCAGTGTGAATGGAT 57.510 42.857 0.00 0.00 0.00 3.41
5097 5614 2.998316 TGTGTGTCAGTGTGAATGGA 57.002 45.000 0.00 0.00 0.00 3.41
5168 5686 6.095377 GGATAAACATTCTGGAAACTGCAAG 58.905 40.000 0.00 0.00 42.29 4.01
5223 5741 9.485206 TTGAACTTCTGTAGGTTATGTAAGAAC 57.515 33.333 0.00 0.00 0.00 3.01
5489 6007 2.197577 GAGCTTCAGTTCTATCCACGC 58.802 52.381 0.00 0.00 0.00 5.34
5491 6009 2.158885 GGGGAGCTTCAGTTCTATCCAC 60.159 54.545 0.00 0.00 0.00 4.02
5500 6018 2.519013 GTCAAAATGGGGAGCTTCAGT 58.481 47.619 0.00 0.00 0.00 3.41
5532 6050 0.888619 TAGTGTTCTGACCAGCCTCG 59.111 55.000 0.00 0.00 0.00 4.63
5550 6068 4.967084 TGTTTCCCTTGCTAGTTGACTA 57.033 40.909 0.00 0.00 0.00 2.59
5682 6200 2.728318 GGAACTGTCTTCGTTACCGTTC 59.272 50.000 10.75 10.75 39.16 3.95
5806 6324 2.012673 GTGATGGCTGGAATGACAGTC 58.987 52.381 0.00 0.00 43.24 3.51
5807 6325 1.352017 TGTGATGGCTGGAATGACAGT 59.648 47.619 0.00 0.00 40.59 3.55
5808 6326 2.014857 CTGTGATGGCTGGAATGACAG 58.985 52.381 0.00 0.00 41.41 3.51
5809 6327 1.352017 ACTGTGATGGCTGGAATGACA 59.648 47.619 0.00 0.00 0.00 3.58
6024 6542 2.990479 CTTACGGGAAGGCCAGCT 59.010 61.111 5.01 0.00 35.15 4.24
6093 6611 8.819974 CAAAGCATCAACTATTTTTGTCAGTTT 58.180 29.630 0.00 0.00 30.20 2.66
6094 6612 7.042523 GCAAAGCATCAACTATTTTTGTCAGTT 60.043 33.333 0.00 0.00 32.82 3.16
6095 6613 6.421801 GCAAAGCATCAACTATTTTTGTCAGT 59.578 34.615 0.00 0.00 0.00 3.41
6096 6614 6.643770 AGCAAAGCATCAACTATTTTTGTCAG 59.356 34.615 0.00 0.00 0.00 3.51
6097 6615 6.514947 AGCAAAGCATCAACTATTTTTGTCA 58.485 32.000 0.00 0.00 0.00 3.58
6098 6616 6.183359 CGAGCAAAGCATCAACTATTTTTGTC 60.183 38.462 0.00 0.00 0.00 3.18
6099 6617 5.630680 CGAGCAAAGCATCAACTATTTTTGT 59.369 36.000 0.00 0.00 0.00 2.83
6100 6618 5.630680 ACGAGCAAAGCATCAACTATTTTTG 59.369 36.000 0.00 0.00 0.00 2.44
6118 6636 3.545707 TTACGACAGCGCACGAGCA 62.546 57.895 23.27 9.03 42.27 4.26
6132 6650 2.281517 TGGTTCACACAACCAGTTACG 58.718 47.619 1.93 0.00 44.74 3.18
6162 6680 4.707030 TTTGCCAGCTTATCATGAAGTG 57.293 40.909 0.00 0.00 0.00 3.16
6163 6681 4.098960 CCATTTGCCAGCTTATCATGAAGT 59.901 41.667 0.00 0.00 0.00 3.01
6312 6830 6.227298 ACTTGTGAGGAAGTATCATACCAG 57.773 41.667 0.00 0.00 34.29 4.00
6315 6833 5.294552 GCCAACTTGTGAGGAAGTATCATAC 59.705 44.000 0.00 0.00 35.01 2.39
6317 6835 4.018960 AGCCAACTTGTGAGGAAGTATCAT 60.019 41.667 0.00 0.00 35.01 2.45
6318 6836 3.327757 AGCCAACTTGTGAGGAAGTATCA 59.672 43.478 0.00 0.00 35.01 2.15
6319 6837 3.686726 CAGCCAACTTGTGAGGAAGTATC 59.313 47.826 0.00 0.00 35.01 2.24
6345 6863 2.486548 GGTAGCGGATTGATTTGGCCTA 60.487 50.000 3.32 0.00 0.00 3.93
6350 6868 2.752354 TGTTGGGTAGCGGATTGATTTG 59.248 45.455 0.00 0.00 0.00 2.32
6360 6878 2.285977 GGGAAAGTATGTTGGGTAGCG 58.714 52.381 0.00 0.00 0.00 4.26
6366 6884 2.268298 CGTCTCGGGAAAGTATGTTGG 58.732 52.381 0.00 0.00 0.00 3.77
6380 6898 4.916249 GGTAGCTAATGATAAACCGTCTCG 59.084 45.833 0.00 0.00 0.00 4.04
6385 6903 7.956420 TTATGTGGTAGCTAATGATAAACCG 57.044 36.000 0.00 0.00 0.00 4.44
6401 6919 8.752005 AGCAACATTTATACTGATTATGTGGT 57.248 30.769 0.00 0.00 30.43 4.16
6402 6920 8.839343 TGAGCAACATTTATACTGATTATGTGG 58.161 33.333 0.00 0.00 30.43 4.17
6411 6929 4.974275 GCAGCATGAGCAACATTTATACTG 59.026 41.667 0.00 0.00 45.49 2.74
6416 6937 2.169330 TGGCAGCATGAGCAACATTTA 58.831 42.857 11.88 0.00 45.49 1.40
6417 6938 0.970640 TGGCAGCATGAGCAACATTT 59.029 45.000 11.88 0.00 45.49 2.32
6420 6941 0.609681 TCATGGCAGCATGAGCAACA 60.610 50.000 11.88 3.21 45.49 3.33
6421 6942 0.744874 ATCATGGCAGCATGAGCAAC 59.255 50.000 10.74 0.00 43.79 4.17
6422 6943 1.029681 GATCATGGCAGCATGAGCAA 58.970 50.000 14.03 1.81 44.62 3.91
6424 6945 1.524863 GGGATCATGGCAGCATGAGC 61.525 60.000 11.40 11.40 43.79 4.26
6425 6946 1.235281 CGGGATCATGGCAGCATGAG 61.235 60.000 10.74 0.00 43.79 2.90
6426 6947 1.228033 CGGGATCATGGCAGCATGA 60.228 57.895 7.92 7.92 44.54 3.07
6427 6948 1.512996 GACGGGATCATGGCAGCATG 61.513 60.000 0.00 0.00 40.87 4.06
6428 6949 1.228063 GACGGGATCATGGCAGCAT 60.228 57.895 0.00 0.00 0.00 3.79
6429 6950 2.190313 GACGGGATCATGGCAGCA 59.810 61.111 0.00 0.00 0.00 4.41
6430 6951 2.592861 GGACGGGATCATGGCAGC 60.593 66.667 0.00 0.00 0.00 5.25
6431 6952 1.227764 CAGGACGGGATCATGGCAG 60.228 63.158 0.00 0.00 35.39 4.85
6432 6953 2.910360 CAGGACGGGATCATGGCA 59.090 61.111 0.00 0.00 35.39 4.92
6435 6956 0.816825 CTTGCCAGGACGGGATCATG 60.817 60.000 0.00 0.00 38.90 3.07
6436 6957 1.528824 CTTGCCAGGACGGGATCAT 59.471 57.895 0.00 0.00 33.48 2.45
6437 6958 2.669133 CCTTGCCAGGACGGGATCA 61.669 63.158 0.00 0.00 44.19 2.92
6438 6959 2.190578 CCTTGCCAGGACGGGATC 59.809 66.667 0.00 0.00 44.19 3.36
6439 6960 4.115199 GCCTTGCCAGGACGGGAT 62.115 66.667 8.31 0.00 44.19 3.85
6442 6963 3.925630 ATGTGCCTTGCCAGGACGG 62.926 63.158 8.31 0.00 44.19 4.79
6443 6964 2.360350 ATGTGCCTTGCCAGGACG 60.360 61.111 8.31 0.00 44.19 4.79
6444 6965 1.303561 TCATGTGCCTTGCCAGGAC 60.304 57.895 8.31 3.92 44.19 3.85
6445 6966 1.001764 CTCATGTGCCTTGCCAGGA 60.002 57.895 8.31 0.00 44.19 3.86
6446 6967 0.896940 AACTCATGTGCCTTGCCAGG 60.897 55.000 0.00 0.00 44.28 4.45
6447 6968 0.242825 CAACTCATGTGCCTTGCCAG 59.757 55.000 0.00 0.00 0.00 4.85
6448 6969 0.467844 ACAACTCATGTGCCTTGCCA 60.468 50.000 0.00 0.00 41.93 4.92
6449 6970 2.344535 ACAACTCATGTGCCTTGCC 58.655 52.632 0.00 0.00 41.93 4.52
6457 6978 1.417517 TGACAGCTCCACAACTCATGT 59.582 47.619 0.00 0.00 45.34 3.21
6489 7027 4.970640 ACCTACTACCAATTAATTCCCGGA 59.029 41.667 0.73 0.00 0.00 5.14
6508 7046 5.258216 AGAAGAGTGTACTCCAGAACCTA 57.742 43.478 8.34 0.00 43.88 3.08
6510 7048 4.281182 TCAAGAAGAGTGTACTCCAGAACC 59.719 45.833 8.34 0.00 43.88 3.62
6527 7065 0.541998 TCTCGTCTGGCCCTCAAGAA 60.542 55.000 0.00 0.00 0.00 2.52
6543 7081 4.135153 TGAGGCCGCTCGCTTCTC 62.135 66.667 8.34 0.00 43.82 2.87
6624 7162 3.312709 GCGTATGCAACCTGCTTTC 57.687 52.632 0.89 0.00 45.31 2.62
6775 7313 3.245797 GGAAACCGTTCGTACTAGGAAC 58.754 50.000 10.41 10.41 39.02 3.62
6799 7337 4.453177 TGTAAATCCGGATCGTGTGTTA 57.547 40.909 19.43 8.67 0.00 2.41
6803 7341 4.817517 GGATATGTAAATCCGGATCGTGT 58.182 43.478 19.43 5.05 36.34 4.49
6829 7367 7.309133 CCTGCTCATTACACACTGGATTAAAAA 60.309 37.037 0.00 0.00 0.00 1.94
6830 7368 6.150976 CCTGCTCATTACACACTGGATTAAAA 59.849 38.462 0.00 0.00 0.00 1.52
6831 7369 5.647658 CCTGCTCATTACACACTGGATTAAA 59.352 40.000 0.00 0.00 0.00 1.52
6832 7370 5.185454 CCTGCTCATTACACACTGGATTAA 58.815 41.667 0.00 0.00 0.00 1.40
6833 7371 4.769688 CCTGCTCATTACACACTGGATTA 58.230 43.478 0.00 0.00 0.00 1.75
6834 7372 3.614092 CCTGCTCATTACACACTGGATT 58.386 45.455 0.00 0.00 0.00 3.01
6835 7373 2.681976 GCCTGCTCATTACACACTGGAT 60.682 50.000 0.00 0.00 0.00 3.41
6836 7374 1.339055 GCCTGCTCATTACACACTGGA 60.339 52.381 0.00 0.00 0.00 3.86
6837 7375 1.089920 GCCTGCTCATTACACACTGG 58.910 55.000 0.00 0.00 0.00 4.00
6838 7376 1.089920 GGCCTGCTCATTACACACTG 58.910 55.000 0.00 0.00 0.00 3.66
6839 7377 0.987294 AGGCCTGCTCATTACACACT 59.013 50.000 3.11 0.00 0.00 3.55
6840 7378 2.691409 TAGGCCTGCTCATTACACAC 57.309 50.000 17.99 0.00 0.00 3.82
6841 7379 3.741075 CGAATAGGCCTGCTCATTACACA 60.741 47.826 17.99 0.00 0.00 3.72
6842 7380 2.802816 CGAATAGGCCTGCTCATTACAC 59.197 50.000 17.99 0.00 0.00 2.90
6843 7381 2.806745 GCGAATAGGCCTGCTCATTACA 60.807 50.000 17.99 0.00 0.00 2.41
6844 7382 1.801178 GCGAATAGGCCTGCTCATTAC 59.199 52.381 17.99 0.00 0.00 1.89
6845 7383 1.694150 AGCGAATAGGCCTGCTCATTA 59.306 47.619 17.99 0.00 30.37 1.90
6846 7384 0.471617 AGCGAATAGGCCTGCTCATT 59.528 50.000 17.99 6.89 30.37 2.57
6847 7385 2.140405 AGCGAATAGGCCTGCTCAT 58.860 52.632 17.99 0.00 30.37 2.90
6848 7386 3.634202 AGCGAATAGGCCTGCTCA 58.366 55.556 17.99 0.00 30.37 4.26
6849 7387 4.352386 GAGCGAATAGGCCTGCTC 57.648 61.111 22.76 22.76 45.95 4.26
6850 7388 0.471617 ATTGAGCGAATAGGCCTGCT 59.528 50.000 17.99 16.18 41.11 4.24
6851 7389 1.265365 GAATTGAGCGAATAGGCCTGC 59.735 52.381 17.99 10.59 0.00 4.85
6852 7390 2.843701 AGAATTGAGCGAATAGGCCTG 58.156 47.619 17.99 0.00 0.00 4.85
6853 7391 3.244249 GGTAGAATTGAGCGAATAGGCCT 60.244 47.826 11.78 11.78 0.00 5.19
6854 7392 3.067833 GGTAGAATTGAGCGAATAGGCC 58.932 50.000 0.00 0.00 0.00 5.19
6855 7393 3.728845 TGGTAGAATTGAGCGAATAGGC 58.271 45.455 0.00 0.00 0.00 3.93
6856 7394 5.334414 GCATTGGTAGAATTGAGCGAATAGG 60.334 44.000 0.00 0.00 0.00 2.57
6857 7395 5.237127 TGCATTGGTAGAATTGAGCGAATAG 59.763 40.000 0.00 0.00 0.00 1.73
6858 7396 5.122519 TGCATTGGTAGAATTGAGCGAATA 58.877 37.500 0.00 0.00 0.00 1.75
6859 7397 3.947196 TGCATTGGTAGAATTGAGCGAAT 59.053 39.130 0.00 0.00 0.00 3.34
6860 7398 3.342719 TGCATTGGTAGAATTGAGCGAA 58.657 40.909 0.00 0.00 0.00 4.70
6861 7399 2.984562 TGCATTGGTAGAATTGAGCGA 58.015 42.857 0.00 0.00 0.00 4.93
6862 7400 3.763097 TTGCATTGGTAGAATTGAGCG 57.237 42.857 0.00 0.00 0.00 5.03
6863 7401 4.614946 GGATTGCATTGGTAGAATTGAGC 58.385 43.478 0.00 0.00 0.00 4.26
6864 7402 4.790766 GCGGATTGCATTGGTAGAATTGAG 60.791 45.833 0.00 0.00 45.45 3.02
6865 7403 3.066621 GCGGATTGCATTGGTAGAATTGA 59.933 43.478 0.00 0.00 45.45 2.57
6866 7404 3.374745 GCGGATTGCATTGGTAGAATTG 58.625 45.455 0.00 0.00 45.45 2.32
6867 7405 3.715628 GCGGATTGCATTGGTAGAATT 57.284 42.857 0.00 0.00 45.45 2.17
6880 7418 2.036958 TGGTTACCATCAGCGGATTG 57.963 50.000 0.00 0.00 0.00 2.67
6884 7422 2.477880 GGTTGGTTACCATCAGCGG 58.522 57.895 4.38 0.00 46.92 5.52
6966 7510 0.474660 ACTGGGTGAAAGGCCTCTCT 60.475 55.000 5.23 0.00 0.00 3.10
6979 7529 1.005450 ACCACAAGTTGACAACTGGGT 59.995 47.619 23.64 23.63 41.91 4.51
7017 7576 2.171725 GTCGGCAGCCATCGTTACC 61.172 63.158 13.30 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.