Multiple sequence alignment - TraesCS6A01G302800

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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 TraesCS6A01G302800 chr6A 100.000 6041 0 0 1 6041 536218854 536212814 0.000000e+00 11156.0
1 TraesCS6A01G302800 chr6A 87.075 147 15 4 3745 3889 570921217 570921361 4.840000e-36 163.0
2 TraesCS6A01G302800 chr6D 91.220 2460 142 42 310 2755 389704786 389702387 0.000000e+00 3278.0
3 TraesCS6A01G302800 chr6D 94.985 1615 66 6 2755 4368 389702303 389700703 0.000000e+00 2519.0
4 TraesCS6A01G302800 chr6D 89.275 1697 107 32 4366 6041 389700542 389698900 0.000000e+00 2056.0
5 TraesCS6A01G302800 chr6D 88.435 147 13 4 3745 3889 426058308 426058452 2.240000e-39 174.0
6 TraesCS6A01G302800 chr6B 94.798 1711 73 7 2670 4365 583447854 583446145 0.000000e+00 2652.0
7 TraesCS6A01G302800 chr6B 87.664 2132 176 54 27 2115 583450803 583448716 0.000000e+00 2399.0
8 TraesCS6A01G302800 chr6B 88.021 1678 106 34 4387 6041 583445981 583444376 0.000000e+00 1897.0
9 TraesCS6A01G302800 chr6B 98.052 616 11 1 2037 2652 583448721 583448107 0.000000e+00 1070.0
10 TraesCS6A01G302800 chr6B 87.324 142 14 4 3745 3884 641283668 641283807 6.270000e-35 159.0
11 TraesCS6A01G302800 chr6B 87.931 116 12 2 3746 3859 185678558 185678673 1.060000e-27 135.0
12 TraesCS6A01G302800 chr7D 89.051 137 12 3 3748 3882 602904868 602905003 3.750000e-37 167.0
13 TraesCS6A01G302800 chr7D 95.455 44 2 0 1311 1354 553013211 553013168 3.020000e-08 71.3
14 TraesCS6A01G302800 chr7D 94.872 39 2 0 1316 1354 553012882 553012844 1.820000e-05 62.1
15 TraesCS6A01G302800 chr7D 92.857 42 3 0 1313 1354 553013993 553013952 1.820000e-05 62.1
16 TraesCS6A01G302800 chr3B 92.308 117 7 2 1235 1351 19049969 19050083 1.350000e-36 165.0
17 TraesCS6A01G302800 chr3B 84.722 144 18 4 3748 3889 416128174 416128315 2.270000e-29 141.0
18 TraesCS6A01G302800 chr3B 86.607 112 12 2 1097 1208 19049865 19049973 2.960000e-23 121.0
19 TraesCS6A01G302800 chr7B 87.500 136 14 3 3749 3882 683516274 683516408 2.920000e-33 154.0


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 TraesCS6A01G302800 chr6A 536212814 536218854 6040 True 11156.000000 11156 100.000000 1 6041 1 chr6A.!!$R1 6040
1 TraesCS6A01G302800 chr6D 389698900 389704786 5886 True 2617.666667 3278 91.826667 310 6041 3 chr6D.!!$R1 5731
2 TraesCS6A01G302800 chr6B 583444376 583450803 6427 True 2004.500000 2652 92.133750 27 6041 4 chr6B.!!$R1 6014

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
728 743 0.246635 TCTGCTAAGCGGGACTCAAC 59.753 55.000 0.0 0.0 35.34 3.18 F
1409 1454 1.137282 GCTCTACCAGACCCAGTTAGC 59.863 57.143 0.0 0.0 0.00 3.09 F
2825 3266 0.590195 GGCATGACGGATGATGCTTC 59.410 55.000 0.0 0.0 43.77 3.86 F
4189 4646 0.661187 GCATGTGTGGTGCGAACTTG 60.661 55.000 0.0 0.0 32.29 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 1837 0.325933 AGCATGTGCAAGCCTCTACA 59.674 50.0 7.83 0.0 45.16 2.74 R
3178 3619 0.817654 CACGGATGTCAGTGGAGCTA 59.182 55.0 5.53 0.0 38.19 3.32 R
4314 4771 0.095935 GCGCTGTGAGCACATTACAG 59.904 55.0 0.00 0.0 42.58 2.74 R
5094 5725 0.306533 CCGAAACAGGTGACAAACGG 59.693 55.0 0.00 0.0 0.00 4.44 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
23 24 4.627035 GGAAATTCTCCCATTTTGCTTTCG 59.373 41.667 0.00 0.00 38.44 3.46
24 25 5.467035 AAATTCTCCCATTTTGCTTTCGA 57.533 34.783 0.00 0.00 0.00 3.71
25 26 5.467035 AATTCTCCCATTTTGCTTTCGAA 57.533 34.783 0.00 0.00 0.00 3.71
101 102 5.103290 GAACCGCTTTGTTCATTTCTACA 57.897 39.130 5.95 0.00 43.27 2.74
110 111 6.480524 TTGTTCATTTCTACATGGAACTCG 57.519 37.500 0.00 0.00 0.00 4.18
147 148 9.546428 CCGTTAAGATATTATGCATCCATGATA 57.454 33.333 0.19 0.00 35.28 2.15
188 190 6.501805 ACATATGACTTATCCTCTTATGGGCA 59.498 38.462 10.38 0.00 33.26 5.36
189 191 4.963318 TGACTTATCCTCTTATGGGCAG 57.037 45.455 0.00 0.00 0.00 4.85
195 197 2.840511 TCCTCTTATGGGCAGTTACCA 58.159 47.619 0.00 0.00 43.22 3.25
203 205 2.051692 TGGGCAGTTACCAGTTACACT 58.948 47.619 0.00 0.00 33.23 3.55
205 207 2.038033 GGGCAGTTACCAGTTACACTCA 59.962 50.000 0.00 0.00 0.00 3.41
206 208 3.064931 GGCAGTTACCAGTTACACTCAC 58.935 50.000 0.00 0.00 0.00 3.51
211 213 5.006358 CAGTTACCAGTTACACTCACACAAC 59.994 44.000 0.00 0.00 0.00 3.32
213 215 3.945346 ACCAGTTACACTCACACAACAA 58.055 40.909 0.00 0.00 0.00 2.83
215 217 4.947388 ACCAGTTACACTCACACAACAAAT 59.053 37.500 0.00 0.00 0.00 2.32
225 227 8.128582 ACACTCACACAACAAATAATACACAAG 58.871 33.333 0.00 0.00 0.00 3.16
246 248 6.013639 ACAAGGGTGTTTGAGTAGCTAGTATT 60.014 38.462 0.00 0.00 32.58 1.89
249 251 5.358090 GGTGTTTGAGTAGCTAGTATTCCC 58.642 45.833 0.00 0.00 0.00 3.97
251 253 6.351966 GGTGTTTGAGTAGCTAGTATTCCCTT 60.352 42.308 0.00 0.00 0.00 3.95
374 379 2.495084 GCTTTCCCCGATCCACTAATC 58.505 52.381 0.00 0.00 0.00 1.75
432 437 0.443088 CAGAGAACGTAGCGACTCGT 59.557 55.000 0.00 0.00 42.12 4.18
468 473 2.156891 GCACACGTTTAGAATGCTTCGA 59.843 45.455 0.00 0.00 33.55 3.71
494 501 7.490402 ACTCTCAATTTATGCAAGCAAAATAGC 59.510 33.333 0.00 0.00 0.00 2.97
509 516 5.183140 GCAAAATAGCCAAGAAACACCTAGA 59.817 40.000 0.00 0.00 0.00 2.43
526 533 4.430441 CCTAGAGAAGGCCCCTAATATGT 58.570 47.826 0.00 0.00 38.97 2.29
540 547 6.294955 CCCCTAATATGTCGGTTAGTCCTTAC 60.295 46.154 0.00 0.00 0.00 2.34
541 548 6.266103 CCCTAATATGTCGGTTAGTCCTTACA 59.734 42.308 0.00 0.00 35.35 2.41
542 549 7.368833 CCTAATATGTCGGTTAGTCCTTACAG 58.631 42.308 0.00 0.00 34.71 2.74
543 550 6.786967 AATATGTCGGTTAGTCCTTACAGT 57.213 37.500 0.00 0.00 34.71 3.55
544 551 3.928727 TGTCGGTTAGTCCTTACAGTG 57.071 47.619 0.00 0.00 0.00 3.66
545 552 3.225104 TGTCGGTTAGTCCTTACAGTGT 58.775 45.455 0.00 0.00 0.00 3.55
547 554 4.099881 TGTCGGTTAGTCCTTACAGTGTTT 59.900 41.667 0.00 0.00 0.00 2.83
548 555 5.052481 GTCGGTTAGTCCTTACAGTGTTTT 58.948 41.667 0.00 0.00 0.00 2.43
591 598 0.984230 TTGCGGGAAAGAGATGGTCT 59.016 50.000 0.00 0.00 36.94 3.85
592 599 0.250234 TGCGGGAAAGAGATGGTCTG 59.750 55.000 0.00 0.00 34.84 3.51
599 606 6.058183 CGGGAAAGAGATGGTCTGATTTTAT 58.942 40.000 0.00 0.00 34.84 1.40
630 637 8.892723 CCAGTAGATTAGTATCAACATGCAAAA 58.107 33.333 0.00 0.00 32.95 2.44
636 643 7.744087 TTAGTATCAACATGCAAAAGTGACT 57.256 32.000 0.00 0.00 0.00 3.41
641 648 6.486253 TCAACATGCAAAAGTGACTATCTC 57.514 37.500 0.00 0.00 0.00 2.75
642 649 5.997129 TCAACATGCAAAAGTGACTATCTCA 59.003 36.000 0.00 0.00 0.00 3.27
643 650 6.486320 TCAACATGCAAAAGTGACTATCTCAA 59.514 34.615 0.00 0.00 0.00 3.02
644 651 6.882610 ACATGCAAAAGTGACTATCTCAAA 57.117 33.333 0.00 0.00 0.00 2.69
681 696 4.290155 AGCATAAAAGTGACAAAACTGCG 58.710 39.130 0.00 0.00 0.00 5.18
728 743 0.246635 TCTGCTAAGCGGGACTCAAC 59.753 55.000 0.00 0.00 35.34 3.18
736 751 2.433436 AGCGGGACTCAACCAAAATAC 58.567 47.619 0.00 0.00 0.00 1.89
782 798 3.430790 GCAAAACTGCCAAAACCTTCTCT 60.431 43.478 0.00 0.00 0.00 3.10
830 846 2.842801 CCACCATCACCACCACCA 59.157 61.111 0.00 0.00 0.00 4.17
831 847 1.603455 CCACCATCACCACCACCAC 60.603 63.158 0.00 0.00 0.00 4.16
832 848 1.603455 CACCATCACCACCACCACC 60.603 63.158 0.00 0.00 0.00 4.61
833 849 2.081787 ACCATCACCACCACCACCA 61.082 57.895 0.00 0.00 0.00 4.17
834 850 1.603455 CCATCACCACCACCACCAC 60.603 63.158 0.00 0.00 0.00 4.16
835 851 1.603455 CATCACCACCACCACCACC 60.603 63.158 0.00 0.00 0.00 4.61
933 972 1.256812 CAAACAAACCCTAGCCCCAG 58.743 55.000 0.00 0.00 0.00 4.45
1233 1278 2.477176 CCAGCTCCTCTCCGTCTCG 61.477 68.421 0.00 0.00 0.00 4.04
1325 1370 4.760047 CCCGGCCGTCTGGTCTTG 62.760 72.222 26.12 4.67 37.90 3.02
1396 1441 6.319911 AGAAGCTTATTTTCCAATGCTCTACC 59.680 38.462 0.00 0.00 0.00 3.18
1409 1454 1.137282 GCTCTACCAGACCCAGTTAGC 59.863 57.143 0.00 0.00 0.00 3.09
1423 1468 8.275040 AGACCCAGTTAGCTTTACATCATATTT 58.725 33.333 0.00 0.00 0.00 1.40
1424 1469 9.555727 GACCCAGTTAGCTTTACATCATATTTA 57.444 33.333 0.00 0.00 0.00 1.40
1472 1517 4.725790 AGAGAAGTTGCTTTGCTTTGTT 57.274 36.364 0.00 0.00 0.00 2.83
1515 1560 7.341030 ACATTGTGAAGTGAATCTATGATGGA 58.659 34.615 0.00 0.00 0.00 3.41
1518 1563 4.747108 GTGAAGTGAATCTATGATGGACCG 59.253 45.833 0.00 0.00 0.00 4.79
1546 1591 7.442666 AGCTTAGCTTTACTGATTACTAATGGC 59.557 37.037 0.00 0.00 33.89 4.40
1552 1597 7.517893 GCTTTACTGATTACTAATGGCGTTACC 60.518 40.741 0.00 0.00 39.84 2.85
1553 1598 4.700700 ACTGATTACTAATGGCGTTACCC 58.299 43.478 0.00 0.00 37.83 3.69
1792 1837 3.093814 TCAATTTGACCAGATGCATGCT 58.906 40.909 20.33 4.11 0.00 3.79
1809 1855 0.731417 GCTGTAGAGGCTTGCACATG 59.269 55.000 0.00 0.00 0.00 3.21
1872 1919 6.710597 AACTCCTTTCTCCCAAAGTAAAAC 57.289 37.500 0.00 0.00 0.00 2.43
1873 1920 5.762279 ACTCCTTTCTCCCAAAGTAAAACA 58.238 37.500 0.00 0.00 0.00 2.83
1926 1973 4.914312 TTGAAGAAACTAATACACGGCG 57.086 40.909 4.80 4.80 0.00 6.46
1945 1992 2.654789 GCGTGTACGTTTCGACTGTTTC 60.655 50.000 6.27 0.00 42.22 2.78
2003 2052 5.451937 GGAGACGATTCACATAGATGTCCAA 60.452 44.000 0.00 0.00 39.39 3.53
2019 2068 4.020543 TGTCCAAGTTAGTTTTGCACCTT 58.979 39.130 0.00 0.00 0.00 3.50
2029 2078 4.215109 AGTTTTGCACCTTTGATACCACT 58.785 39.130 0.00 0.00 0.00 4.00
2030 2079 4.037923 AGTTTTGCACCTTTGATACCACTG 59.962 41.667 0.00 0.00 0.00 3.66
2526 2648 7.054751 GGCTTCAGTCATTATAGGGTAAGTTT 58.945 38.462 0.00 0.00 0.00 2.66
2601 2723 4.880759 TGGCAAATAACAGTCACAATTGG 58.119 39.130 10.83 0.00 0.00 3.16
2658 2965 2.030805 GCTTGTTTTCTGCTGTGGGTAG 60.031 50.000 0.00 0.00 0.00 3.18
2798 3239 5.809001 TCCTTCTATGCACTCTTGAAACAT 58.191 37.500 0.00 0.00 0.00 2.71
2802 3243 8.680903 CCTTCTATGCACTCTTGAAACATAATT 58.319 33.333 0.00 0.00 0.00 1.40
2808 3249 5.119125 GCACTCTTGAAACATAATTGTTGGC 59.881 40.000 0.00 0.00 45.30 4.52
2825 3266 0.590195 GGCATGACGGATGATGCTTC 59.410 55.000 0.00 0.00 43.77 3.86
3066 3507 9.552695 AAGGAATATTCTGGGAGAATTTTCTTT 57.447 29.630 19.82 17.45 44.64 2.52
3156 3597 4.524328 CCTTGGAATGGTCTTTAGTTGCTT 59.476 41.667 0.00 0.00 0.00 3.91
3167 3608 7.387948 TGGTCTTTAGTTGCTTTAGTGATTCTC 59.612 37.037 0.00 0.00 0.00 2.87
3178 3619 9.507329 TGCTTTAGTGATTCTCAAGTTATTTCT 57.493 29.630 0.00 0.00 31.96 2.52
3201 3642 2.611971 GCTCCACTGACATCCGTGTTTA 60.612 50.000 3.24 0.00 39.09 2.01
3235 3676 7.023575 CCAGTCAAACTTATGCTGTTAATGTC 58.976 38.462 0.00 0.00 0.00 3.06
3322 3763 2.996631 ACATCATTCACAGCTCTTCCC 58.003 47.619 0.00 0.00 0.00 3.97
3493 3934 4.695455 TCTTTTGAATACTGCTACAGTGCC 59.305 41.667 10.42 0.70 45.01 5.01
3522 3963 3.126001 TCCGAATTCTGACTGCACTTT 57.874 42.857 3.52 0.00 0.00 2.66
3632 4073 6.707161 ACGTGCCAACTGTAACTCTTAATTTA 59.293 34.615 0.00 0.00 0.00 1.40
3681 4122 6.035220 CGTTAATCCTACAATTGTACGCAAGA 59.965 38.462 14.35 7.01 38.10 3.02
3743 4184 4.984161 GCAAGTTATGTTGTGTTCATTGCT 59.016 37.500 0.00 0.00 0.00 3.91
3761 4202 6.377996 TCATTGCTGAGCATTGTTTATAAGGT 59.622 34.615 23.56 0.00 39.79 3.50
3842 4296 1.451936 GTCAAGGTGCTGACAGGGT 59.548 57.895 4.26 0.00 44.32 4.34
4149 4606 7.338710 TGCTAGGCTCATCTATTAAAAGTTGT 58.661 34.615 0.00 0.00 0.00 3.32
4188 4645 1.100463 TGCATGTGTGGTGCGAACTT 61.100 50.000 0.00 0.00 45.37 2.66
4189 4646 0.661187 GCATGTGTGGTGCGAACTTG 60.661 55.000 0.00 0.00 32.29 3.16
4314 4771 1.538950 CTTTTGACAGCTGAGCCCTTC 59.461 52.381 23.35 6.77 0.00 3.46
4320 4777 1.912043 ACAGCTGAGCCCTTCTGTAAT 59.088 47.619 23.35 0.00 37.94 1.89
4347 4804 1.737793 ACAGCGCATAAACTTACTGCC 59.262 47.619 11.47 0.00 32.24 4.85
4393 5013 5.860941 TGATACAAAACCCACATGTTTGT 57.139 34.783 15.19 15.19 38.41 2.83
4394 5014 6.961360 TGATACAAAACCCACATGTTTGTA 57.039 33.333 17.83 17.83 38.41 2.41
4395 5015 6.740110 TGATACAAAACCCACATGTTTGTAC 58.260 36.000 17.87 13.44 38.41 2.90
4396 5016 6.321435 TGATACAAAACCCACATGTTTGTACA 59.679 34.615 17.87 15.10 38.41 2.90
4397 5017 4.749976 ACAAAACCCACATGTTTGTACAC 58.250 39.130 10.40 0.00 38.41 2.90
4398 5018 4.220821 ACAAAACCCACATGTTTGTACACA 59.779 37.500 10.40 0.00 38.41 3.72
4399 5019 5.171476 CAAAACCCACATGTTTGTACACAA 58.829 37.500 0.00 0.00 38.41 3.33
4400 5020 5.407407 AAACCCACATGTTTGTACACAAA 57.593 34.783 0.00 3.44 42.90 2.83
4401 5021 5.407407 AACCCACATGTTTGTACACAAAA 57.593 34.783 9.01 1.65 46.08 2.44
4402 5022 5.004922 ACCCACATGTTTGTACACAAAAG 57.995 39.130 9.01 5.62 46.08 2.27
4418 5038 5.051816 CACAAAAGGCAGATGTGTCATTTT 58.948 37.500 0.00 1.02 39.60 1.82
4429 5049 7.597743 GCAGATGTGTCATTTTGAGAGAAAAAT 59.402 33.333 0.00 0.00 39.71 1.82
4482 5104 0.096454 GTTTTGCGGCTCGGTGATAC 59.904 55.000 0.00 0.00 0.00 2.24
4561 5188 3.135530 AGTCACCAGAGCCTATTGGAATC 59.864 47.826 0.00 0.00 37.89 2.52
4592 5219 5.007682 GTGAGTGCTTTAATCCTGGGTTAA 58.992 41.667 8.07 8.07 0.00 2.01
4593 5220 5.007682 TGAGTGCTTTAATCCTGGGTTAAC 58.992 41.667 11.62 1.69 0.00 2.01
4594 5221 4.993028 AGTGCTTTAATCCTGGGTTAACA 58.007 39.130 11.62 5.30 0.00 2.41
4595 5222 5.580022 AGTGCTTTAATCCTGGGTTAACAT 58.420 37.500 11.62 0.00 0.00 2.71
4596 5223 5.418840 AGTGCTTTAATCCTGGGTTAACATG 59.581 40.000 11.62 6.75 0.00 3.21
4598 5225 6.376018 GTGCTTTAATCCTGGGTTAACATGTA 59.624 38.462 11.62 3.03 0.00 2.29
4649 5276 0.106149 GCTTACCTGGTATCCGTGGG 59.894 60.000 7.50 0.00 0.00 4.61
4725 5352 2.722201 GGGCTGGTACCGGTCTGAG 61.722 68.421 24.33 6.31 0.00 3.35
4745 5372 6.328641 TGAGTGTAAGTCAGAAACTAGTCC 57.671 41.667 0.00 0.00 42.42 3.85
4756 5383 6.905609 GTCAGAAACTAGTCCAAAAAGAAACG 59.094 38.462 0.00 0.00 0.00 3.60
4757 5384 6.819649 TCAGAAACTAGTCCAAAAAGAAACGA 59.180 34.615 0.00 0.00 0.00 3.85
4766 5396 7.423199 AGTCCAAAAAGAAACGAATTTACCTC 58.577 34.615 0.00 0.00 0.00 3.85
4770 5400 6.718522 AAAAGAAACGAATTTACCTCCCAA 57.281 33.333 0.00 0.00 0.00 4.12
4774 5404 6.007703 AGAAACGAATTTACCTCCCAATCAA 58.992 36.000 0.00 0.00 0.00 2.57
4784 5414 4.887367 ACCTCCCAATCAATCCATGAAAT 58.113 39.130 0.00 0.00 42.54 2.17
4785 5415 4.652421 ACCTCCCAATCAATCCATGAAATG 59.348 41.667 0.00 0.00 46.21 2.32
4795 5425 5.647658 TCAATCCATGAAATGTTAACGCTCT 59.352 36.000 0.26 0.00 44.81 4.09
4796 5426 5.741388 ATCCATGAAATGTTAACGCTCTC 57.259 39.130 0.26 0.00 44.81 3.20
4976 5607 1.469595 CGGGCCGTCGAACTTACATAA 60.470 52.381 19.97 0.00 0.00 1.90
4997 5628 0.792640 CTACTCGCCAACTGTTGCTG 59.207 55.000 14.94 9.12 0.00 4.41
5066 5697 5.705441 TCAGCAACTGAATAAACCTAACTGG 59.295 40.000 0.00 0.00 37.57 4.00
5094 5725 3.679083 GCCCCTGTATATCGCATAAGTCC 60.679 52.174 0.00 0.00 0.00 3.85
5098 5729 4.321750 CCTGTATATCGCATAAGTCCCGTT 60.322 45.833 0.00 0.00 0.00 4.44
5104 5735 1.127951 CGCATAAGTCCCGTTTGTCAC 59.872 52.381 0.00 0.00 0.00 3.67
5156 5789 0.324460 AGGGGTAGAACTCCACTCCG 60.324 60.000 0.00 0.00 42.77 4.63
5178 5811 2.264480 CGAATGGGTCACTCGCCA 59.736 61.111 0.00 0.00 0.00 5.69
5207 5840 6.037786 TCGTCACCAATCTTAGAAGAACAT 57.962 37.500 0.00 0.00 38.77 2.71
5209 5842 6.934645 TCGTCACCAATCTTAGAAGAACATTT 59.065 34.615 0.00 0.00 38.77 2.32
5210 5843 7.117812 TCGTCACCAATCTTAGAAGAACATTTC 59.882 37.037 0.00 0.00 38.77 2.17
5211 5844 7.095229 CGTCACCAATCTTAGAAGAACATTTCA 60.095 37.037 0.00 0.00 38.77 2.69
5212 5845 8.017946 GTCACCAATCTTAGAAGAACATTTCAC 58.982 37.037 0.00 0.00 38.77 3.18
5213 5846 7.939039 TCACCAATCTTAGAAGAACATTTCACT 59.061 33.333 0.00 0.00 38.77 3.41
5214 5847 8.571336 CACCAATCTTAGAAGAACATTTCACTT 58.429 33.333 0.00 0.00 38.77 3.16
5215 5848 9.136323 ACCAATCTTAGAAGAACATTTCACTTT 57.864 29.630 0.00 0.00 38.77 2.66
5232 5865 2.558359 ACTTTACAGATGGGTTTGCTGC 59.442 45.455 0.00 0.00 33.03 5.25
5233 5866 2.584835 TTACAGATGGGTTTGCTGCT 57.415 45.000 0.00 0.00 33.03 4.24
5237 5870 2.558359 ACAGATGGGTTTGCTGCTAAAC 59.442 45.455 14.92 14.92 39.28 2.01
5238 5871 2.557924 CAGATGGGTTTGCTGCTAAACA 59.442 45.455 20.81 13.95 41.23 2.83
5239 5872 3.194116 CAGATGGGTTTGCTGCTAAACAT 59.806 43.478 20.81 16.90 41.23 2.71
5251 5884 4.551603 GCTGCTAAACATCATCACGACATC 60.552 45.833 0.00 0.00 0.00 3.06
5274 5907 2.355716 GCCCATAGTTTCCTGTGCTACA 60.356 50.000 0.00 0.00 0.00 2.74
5330 5965 3.437931 GGATAGGAAGAGGAGGAAGAGCT 60.438 52.174 0.00 0.00 0.00 4.09
5345 5980 0.671781 GAGCTTGTCCGTGCAGTCAT 60.672 55.000 0.00 0.00 0.00 3.06
5346 5981 0.671781 AGCTTGTCCGTGCAGTCATC 60.672 55.000 0.00 0.00 0.00 2.92
5347 5982 1.639298 GCTTGTCCGTGCAGTCATCC 61.639 60.000 0.00 0.00 0.00 3.51
5348 5983 1.354337 CTTGTCCGTGCAGTCATCCG 61.354 60.000 0.00 0.00 0.00 4.18
5400 6035 1.202348 GTGCGAATCCCTTTTTCCCAG 59.798 52.381 0.00 0.00 0.00 4.45
5403 6038 1.195115 GAATCCCTTTTTCCCAGGCC 58.805 55.000 0.00 0.00 0.00 5.19
5408 6043 1.603455 CTTTTTCCCAGGCCGCAGA 60.603 57.895 0.00 0.00 0.00 4.26
5569 6211 0.244721 TCGTCAGTCACATGAGGCTG 59.755 55.000 17.49 17.49 35.54 4.85
5570 6212 0.738762 CGTCAGTCACATGAGGCTGG 60.739 60.000 22.13 5.86 0.00 4.85
5571 6213 1.023513 GTCAGTCACATGAGGCTGGC 61.024 60.000 22.13 18.14 0.00 4.85
5572 6214 1.196766 TCAGTCACATGAGGCTGGCT 61.197 55.000 22.13 2.24 0.00 4.75
5638 6280 2.572284 CGTCACTTCTCCCCGACC 59.428 66.667 0.00 0.00 0.00 4.79
5639 6281 1.977544 CGTCACTTCTCCCCGACCT 60.978 63.158 0.00 0.00 0.00 3.85
5640 6282 1.891616 GTCACTTCTCCCCGACCTC 59.108 63.158 0.00 0.00 0.00 3.85
5641 6283 1.305046 TCACTTCTCCCCGACCTCC 60.305 63.158 0.00 0.00 0.00 4.30
5642 6284 1.305381 CACTTCTCCCCGACCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
5682 6329 1.597854 CCTCCACACACACACGCAT 60.598 57.895 0.00 0.00 0.00 4.73
5751 6398 0.321671 TTCTCCAGGTCGCCTTTGAG 59.678 55.000 12.30 12.30 33.60 3.02
5813 6460 0.931202 CGTGCCATTATGCATGCACG 60.931 55.000 33.47 33.47 46.76 5.34
5816 6463 0.381445 GCCATTATGCATGCACGACA 59.619 50.000 25.37 7.50 0.00 4.35
5819 6466 2.540157 CCATTATGCATGCACGACACAG 60.540 50.000 25.37 9.26 0.00 3.66
5863 6510 0.892358 CAGGCAGGCTTCTTGCTTCA 60.892 55.000 0.00 0.00 41.27 3.02
5864 6511 0.892814 AGGCAGGCTTCTTGCTTCAC 60.893 55.000 0.00 0.00 41.27 3.18
5934 6581 0.672401 GCGTTCGTTCTCCATGGGAA 60.672 55.000 13.02 11.54 0.00 3.97
6013 6666 3.121030 CAAGAAGGAGGGCACGCG 61.121 66.667 3.53 3.53 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.627035 CGAAAGCAAAATGGGAGAATTTCC 59.373 41.667 0.00 0.00 46.00 3.13
1 2 5.469479 TCGAAAGCAAAATGGGAGAATTTC 58.531 37.500 0.00 0.00 0.00 2.17
2 3 5.467035 TCGAAAGCAAAATGGGAGAATTT 57.533 34.783 0.00 0.00 0.00 1.82
3 4 5.221422 TGTTCGAAAGCAAAATGGGAGAATT 60.221 36.000 0.00 0.00 0.00 2.17
4 5 4.280677 TGTTCGAAAGCAAAATGGGAGAAT 59.719 37.500 0.00 0.00 0.00 2.40
5 6 3.634448 TGTTCGAAAGCAAAATGGGAGAA 59.366 39.130 0.00 0.00 0.00 2.87
6 7 3.218453 TGTTCGAAAGCAAAATGGGAGA 58.782 40.909 0.00 0.00 0.00 3.71
7 8 3.641437 TGTTCGAAAGCAAAATGGGAG 57.359 42.857 0.00 0.00 0.00 4.30
8 9 4.038522 TGAATGTTCGAAAGCAAAATGGGA 59.961 37.500 0.00 0.00 0.00 4.37
9 10 4.305769 TGAATGTTCGAAAGCAAAATGGG 58.694 39.130 0.00 0.00 0.00 4.00
10 11 5.903764 TTGAATGTTCGAAAGCAAAATGG 57.096 34.783 0.00 0.00 0.00 3.16
11 12 7.346695 ACATTTGAATGTTCGAAAGCAAAATG 58.653 30.769 21.08 21.08 46.95 2.32
12 13 7.481275 ACATTTGAATGTTCGAAAGCAAAAT 57.519 28.000 15.25 9.33 46.95 1.82
13 14 6.900568 ACATTTGAATGTTCGAAAGCAAAA 57.099 29.167 15.25 7.86 46.95 2.44
116 117 9.952030 TGGATGCATAATATCTTAACGGATTTA 57.048 29.630 0.00 0.00 0.00 1.40
160 161 8.766476 CCCATAAGAGGATAAGTCATATGTCAT 58.234 37.037 1.90 0.00 0.00 3.06
161 162 7.310671 GCCCATAAGAGGATAAGTCATATGTCA 60.311 40.741 1.90 0.00 0.00 3.58
162 163 7.044798 GCCCATAAGAGGATAAGTCATATGTC 58.955 42.308 1.90 0.00 0.00 3.06
179 181 4.634443 GTGTAACTGGTAACTGCCCATAAG 59.366 45.833 0.00 0.00 39.52 1.73
183 185 2.554370 GTGTAACTGGTAACTGCCCA 57.446 50.000 0.00 0.00 39.52 5.36
203 205 6.547880 ACCCTTGTGTATTATTTGTTGTGTGA 59.452 34.615 0.00 0.00 0.00 3.58
205 207 6.744112 CACCCTTGTGTATTATTTGTTGTGT 58.256 36.000 0.00 0.00 37.72 3.72
225 227 5.358090 GGAATACTAGCTACTCAAACACCC 58.642 45.833 0.00 0.00 0.00 4.61
232 234 9.209048 TCAAATTAAGGGAATACTAGCTACTCA 57.791 33.333 0.00 0.00 0.00 3.41
395 400 2.111669 CATGGGCCGCTCTGCATA 59.888 61.111 0.00 0.00 0.00 3.14
458 463 5.906285 GCATAAATTGAGAGTCGAAGCATTC 59.094 40.000 0.00 0.00 43.09 2.67
468 473 7.490402 GCTATTTTGCTTGCATAAATTGAGAGT 59.510 33.333 17.99 1.89 0.00 3.24
494 501 3.339141 GCCTTCTCTAGGTGTTTCTTGG 58.661 50.000 0.00 0.00 46.61 3.61
509 516 1.978580 CCGACATATTAGGGGCCTTCT 59.021 52.381 0.84 3.25 0.00 2.85
514 521 3.306571 GGACTAACCGACATATTAGGGGC 60.307 52.174 0.00 0.00 33.47 5.80
521 528 5.655532 ACACTGTAAGGACTAACCGACATAT 59.344 40.000 0.00 0.00 44.74 1.78
526 533 4.942761 AAACACTGTAAGGACTAACCGA 57.057 40.909 0.00 0.00 44.74 4.69
570 577 2.159382 GACCATCTCTTTCCCGCAAAA 58.841 47.619 0.00 0.00 0.00 2.44
572 579 0.984230 AGACCATCTCTTTCCCGCAA 59.016 50.000 0.00 0.00 0.00 4.85
573 580 0.250234 CAGACCATCTCTTTCCCGCA 59.750 55.000 0.00 0.00 0.00 5.69
574 581 0.537188 TCAGACCATCTCTTTCCCGC 59.463 55.000 0.00 0.00 0.00 6.13
575 582 3.550437 AATCAGACCATCTCTTTCCCG 57.450 47.619 0.00 0.00 0.00 5.14
576 583 7.888250 AATAAAATCAGACCATCTCTTTCCC 57.112 36.000 0.00 0.00 0.00 3.97
578 585 9.943163 GCTAAATAAAATCAGACCATCTCTTTC 57.057 33.333 0.00 0.00 0.00 2.62
579 586 8.907885 GGCTAAATAAAATCAGACCATCTCTTT 58.092 33.333 0.00 0.00 0.00 2.52
580 587 8.055181 TGGCTAAATAAAATCAGACCATCTCTT 58.945 33.333 0.00 0.00 0.00 2.85
584 591 7.573968 ACTGGCTAAATAAAATCAGACCATC 57.426 36.000 0.00 0.00 0.00 3.51
599 606 9.764363 CATGTTGATACTAATCTACTGGCTAAA 57.236 33.333 2.58 0.00 38.30 1.85
615 622 7.978982 AGATAGTCACTTTTGCATGTTGATAC 58.021 34.615 0.00 0.00 0.00 2.24
657 664 5.108254 CGCAGTTTTGTCACTTTTATGCTTC 60.108 40.000 0.00 0.00 0.00 3.86
663 670 3.242478 CGGTCGCAGTTTTGTCACTTTTA 60.242 43.478 0.00 0.00 0.00 1.52
677 684 3.019003 ATTGGTCCCTCGGTCGCAG 62.019 63.158 0.00 0.00 0.00 5.18
681 696 0.108138 CACTCATTGGTCCCTCGGTC 60.108 60.000 0.00 0.00 0.00 4.79
728 743 5.278957 CCACTGAAGAAACCCTGTATTTTGG 60.279 44.000 0.00 0.00 0.00 3.28
736 751 0.178992 TGGCCACTGAAGAAACCCTG 60.179 55.000 0.00 0.00 0.00 4.45
782 798 0.944311 GCGCAGAAAAGAGGACGACA 60.944 55.000 0.30 0.00 0.00 4.35
905 944 1.227527 GGTTTGTTTGCTGGGTGGC 60.228 57.895 0.00 0.00 0.00 5.01
1074 1119 2.509336 CGGTGCACCATCCTCGTC 60.509 66.667 34.16 5.28 35.14 4.20
1318 1363 0.401356 TGAGGAATGCAGCAAGACCA 59.599 50.000 0.00 0.00 0.00 4.02
1356 1401 5.869753 AAGCTTCTGCATTAACAGTACAG 57.130 39.130 0.00 0.00 42.74 2.74
1396 1441 4.832248 TGATGTAAAGCTAACTGGGTCTG 58.168 43.478 0.00 0.00 0.00 3.51
1440 1485 8.483218 GCAAAGCAACTTCTCTTTTTCTAATTC 58.517 33.333 0.00 0.00 30.79 2.17
1472 1517 1.003233 TGTAACACACACACACACCCA 59.997 47.619 0.00 0.00 30.04 4.51
1546 1591 0.670546 CTGCACAGACAGGGGTAACG 60.671 60.000 0.00 0.00 33.85 3.18
1596 1641 2.418976 GACCATAAAGGAAGTGTTCGGC 59.581 50.000 0.00 0.00 41.22 5.54
1792 1837 0.325933 AGCATGTGCAAGCCTCTACA 59.674 50.000 7.83 0.00 45.16 2.74
1809 1855 9.537848 CATCATTTCTTTTCTTTTTGCAATAGC 57.462 29.630 0.00 0.00 42.57 2.97
1926 1973 3.060740 CAGGAAACAGTCGAAACGTACAC 60.061 47.826 0.00 0.00 0.00 2.90
1945 1992 7.334921 TGAATGGAACGTTAATTAAGTACCAGG 59.665 37.037 0.00 0.00 0.00 4.45
2003 2052 5.830991 TGGTATCAAAGGTGCAAAACTAACT 59.169 36.000 0.00 0.00 0.00 2.24
2019 2068 6.491745 TCAATTAAAAGTGGCAGTGGTATCAA 59.508 34.615 0.00 0.00 0.00 2.57
2060 2109 2.798976 TTGGAAATTGTGCAGCTCAC 57.201 45.000 0.00 8.75 45.82 3.51
2366 2488 3.027419 GCTTGAACAGCCTGAACCT 57.973 52.632 0.00 0.00 43.65 3.50
2526 2648 2.038952 AGAGCAATGACAGCTGGTACAA 59.961 45.455 19.93 0.00 43.58 2.41
2577 2699 5.757320 CCAATTGTGACTGTTATTTGCCAAA 59.243 36.000 4.43 0.00 0.00 3.28
2601 2723 1.400500 CCACACGCGGGAAAAACATAC 60.400 52.381 19.19 0.00 0.00 2.39
2658 2965 1.806542 CAGGTGGACACAGTATGCAAC 59.193 52.381 4.69 0.00 42.53 4.17
2798 3239 3.615155 TCATCCGTCATGCCAACAATTA 58.385 40.909 0.00 0.00 31.70 1.40
2802 3243 1.381522 CATCATCCGTCATGCCAACA 58.618 50.000 0.00 0.00 31.70 3.33
2808 3249 2.558378 ACAGAAGCATCATCCGTCATG 58.442 47.619 0.00 0.00 0.00 3.07
2825 3266 5.641709 TGCGACTAGAATTCTTCAGTACAG 58.358 41.667 14.36 5.45 0.00 2.74
3066 3507 2.832129 GGTAGACACTCCTTGATCACCA 59.168 50.000 0.00 0.00 0.00 4.17
3167 3608 6.166279 TGTCAGTGGAGCTAGAAATAACTTG 58.834 40.000 0.00 0.00 0.00 3.16
3178 3619 0.817654 CACGGATGTCAGTGGAGCTA 59.182 55.000 5.53 0.00 38.19 3.32
3201 3642 5.185828 GCATAAGTTTGACTGGGAGGAAAAT 59.814 40.000 0.00 0.00 0.00 1.82
3235 3676 1.336440 TGGCCAACACAAGATTTGTCG 59.664 47.619 0.61 0.00 43.23 4.35
3322 3763 3.820467 TGACAGCCTTGTAAACATTCAGG 59.180 43.478 0.00 0.00 37.76 3.86
3493 3934 4.627467 CAGTCAGAATTCGGAAGTTACCTG 59.373 45.833 9.99 8.25 0.00 4.00
3522 3963 0.485543 TCCTGGTGAGTGGTGACCTA 59.514 55.000 2.11 0.00 32.98 3.08
3571 4012 5.071788 AGAGGACTGAAATCACAAACCAGTA 59.928 40.000 0.00 0.00 38.10 2.74
3632 4073 3.255149 CCTGAAAGCTCTTGTTTGCAGAT 59.745 43.478 2.78 0.00 41.03 2.90
3718 4159 5.406175 GCAATGAACACAACATAACTTGCAT 59.594 36.000 0.00 0.00 31.95 3.96
3736 4177 6.377996 ACCTTATAAACAATGCTCAGCAATGA 59.622 34.615 21.90 0.00 41.42 2.57
3743 4184 6.601613 CCTTACCACCTTATAAACAATGCTCA 59.398 38.462 0.00 0.00 0.00 4.26
3761 4202 1.902556 GCCTTAGGTCGCCTTACCA 59.097 57.895 0.00 0.00 42.40 3.25
3809 4263 1.203052 CTTGACATCATGCCCGCTTTT 59.797 47.619 0.00 0.00 0.00 2.27
3905 4359 2.560504 TGGAGTCGATTTGCGCATAAT 58.439 42.857 12.75 14.08 40.61 1.28
3910 4364 1.135689 ACAAATGGAGTCGATTTGCGC 60.136 47.619 29.69 0.00 42.26 6.09
4048 4504 5.592688 AGCCATTTTACGCACCAACTATATT 59.407 36.000 0.00 0.00 0.00 1.28
4061 4517 1.463056 TCGCAGTTGAGCCATTTTACG 59.537 47.619 0.00 0.00 0.00 3.18
4149 4606 7.609918 ACATGCAAACTCCACATTACACTATAA 59.390 33.333 0.00 0.00 0.00 0.98
4188 4645 7.575532 GCATAGAAACAATTGATGACAGGTTCA 60.576 37.037 13.59 0.00 39.11 3.18
4189 4646 6.749118 GCATAGAAACAATTGATGACAGGTTC 59.251 38.462 13.59 0.00 0.00 3.62
4314 4771 0.095935 GCGCTGTGAGCACATTACAG 59.904 55.000 0.00 0.00 42.58 2.74
4395 5015 3.928727 ATGACACATCTGCCTTTTGTG 57.071 42.857 1.02 1.02 44.85 3.33
4396 5016 4.942761 AAATGACACATCTGCCTTTTGT 57.057 36.364 0.00 0.00 0.00 2.83
4397 5017 5.291178 TCAAAATGACACATCTGCCTTTTG 58.709 37.500 0.00 0.00 34.86 2.44
4398 5018 5.302568 TCTCAAAATGACACATCTGCCTTTT 59.697 36.000 0.00 0.00 0.00 2.27
4399 5019 4.828939 TCTCAAAATGACACATCTGCCTTT 59.171 37.500 0.00 0.00 0.00 3.11
4400 5020 4.401022 TCTCAAAATGACACATCTGCCTT 58.599 39.130 0.00 0.00 0.00 4.35
4401 5021 4.008330 CTCTCAAAATGACACATCTGCCT 58.992 43.478 0.00 0.00 0.00 4.75
4402 5022 4.005650 TCTCTCAAAATGACACATCTGCC 58.994 43.478 0.00 0.00 0.00 4.85
4482 5104 5.221185 CCCTGAACATTAGCAAATGAGATGG 60.221 44.000 5.18 2.82 44.50 3.51
4561 5188 4.437390 GGATTAAAGCACTCACGTCCAATG 60.437 45.833 0.00 0.00 0.00 2.82
4627 5254 2.696707 CCACGGATACCAGGTAAGCTAA 59.303 50.000 2.53 0.00 0.00 3.09
4636 5263 1.153369 CTGCACCCACGGATACCAG 60.153 63.158 0.00 0.00 0.00 4.00
4649 5276 2.411904 CAGTCAGGAAGTTCTCTGCAC 58.588 52.381 13.53 12.36 0.00 4.57
4725 5352 7.781548 TTTTGGACTAGTTTCTGACTTACAC 57.218 36.000 0.00 0.00 39.86 2.90
4742 5369 6.639686 GGAGGTAAATTCGTTTCTTTTTGGAC 59.360 38.462 0.00 0.00 0.00 4.02
4745 5372 6.508777 TGGGAGGTAAATTCGTTTCTTTTTG 58.491 36.000 0.00 0.00 0.00 2.44
4756 5383 6.550854 TCATGGATTGATTGGGAGGTAAATTC 59.449 38.462 0.00 0.00 0.00 2.17
4757 5384 6.442961 TCATGGATTGATTGGGAGGTAAATT 58.557 36.000 0.00 0.00 0.00 1.82
4766 5396 6.476380 CGTTAACATTTCATGGATTGATTGGG 59.524 38.462 6.39 0.00 33.34 4.12
4770 5400 6.319658 AGAGCGTTAACATTTCATGGATTGAT 59.680 34.615 6.39 0.00 33.34 2.57
4774 5404 5.431765 AGAGAGCGTTAACATTTCATGGAT 58.568 37.500 6.39 0.00 33.60 3.41
4784 5414 1.968493 ACAAGGGAGAGAGCGTTAACA 59.032 47.619 6.39 0.00 0.00 2.41
4785 5415 2.745515 ACAAGGGAGAGAGCGTTAAC 57.254 50.000 0.00 0.00 0.00 2.01
4795 5425 2.656069 GGCCTGCGTACAAGGGAGA 61.656 63.158 12.36 0.00 0.00 3.71
4796 5426 2.125106 GGCCTGCGTACAAGGGAG 60.125 66.667 12.36 0.00 0.00 4.30
4954 5585 3.376078 TAAGTTCGACGGCCCGCT 61.376 61.111 1.23 0.00 0.00 5.52
4997 5628 0.807496 GATGGTCAGAAACAGCAGCC 59.193 55.000 0.00 0.00 0.00 4.85
5066 5697 2.496070 TGCGATATACAGGGGCTATCAC 59.504 50.000 0.00 0.00 0.00 3.06
5094 5725 0.306533 CCGAAACAGGTGACAAACGG 59.693 55.000 0.00 0.00 0.00 4.44
5098 5729 1.305201 GCTTCCGAAACAGGTGACAA 58.695 50.000 0.00 0.00 0.00 3.18
5104 5735 1.497722 GAAGCGCTTCCGAAACAGG 59.502 57.895 34.88 0.00 36.29 4.00
5156 5789 2.045926 AGTGACCCATTCGCTGGC 60.046 61.111 0.00 0.00 43.84 4.85
5178 5811 2.386661 AAGATTGGTGACGAGCGATT 57.613 45.000 0.00 0.00 34.48 3.34
5207 5840 4.892934 AGCAAACCCATCTGTAAAGTGAAA 59.107 37.500 0.00 0.00 0.00 2.69
5209 5842 3.820467 CAGCAAACCCATCTGTAAAGTGA 59.180 43.478 0.00 0.00 0.00 3.41
5210 5843 3.612479 GCAGCAAACCCATCTGTAAAGTG 60.612 47.826 0.00 0.00 0.00 3.16
5211 5844 2.558359 GCAGCAAACCCATCTGTAAAGT 59.442 45.455 0.00 0.00 0.00 2.66
5212 5845 2.821969 AGCAGCAAACCCATCTGTAAAG 59.178 45.455 0.00 0.00 0.00 1.85
5213 5846 2.875296 AGCAGCAAACCCATCTGTAAA 58.125 42.857 0.00 0.00 0.00 2.01
5214 5847 2.584835 AGCAGCAAACCCATCTGTAA 57.415 45.000 0.00 0.00 0.00 2.41
5215 5848 3.712016 TTAGCAGCAAACCCATCTGTA 57.288 42.857 0.00 0.00 0.00 2.74
5232 5865 4.025396 GGCAGATGTCGTGATGATGTTTAG 60.025 45.833 0.00 0.00 0.00 1.85
5233 5866 3.871006 GGCAGATGTCGTGATGATGTTTA 59.129 43.478 0.00 0.00 0.00 2.01
5237 5870 1.224075 GGGCAGATGTCGTGATGATG 58.776 55.000 0.00 0.00 0.00 3.07
5238 5871 0.832626 TGGGCAGATGTCGTGATGAT 59.167 50.000 0.00 0.00 0.00 2.45
5239 5872 0.832626 ATGGGCAGATGTCGTGATGA 59.167 50.000 0.00 0.00 0.00 2.92
5251 5884 1.098050 GCACAGGAAACTATGGGCAG 58.902 55.000 0.00 0.00 45.36 4.85
5274 5907 1.550976 TGGTTTTTGCACCGTTTCCTT 59.449 42.857 0.00 0.00 40.09 3.36
5313 5948 1.905894 ACAAGCTCTTCCTCCTCTTCC 59.094 52.381 0.00 0.00 0.00 3.46
5330 5965 1.374125 CGGATGACTGCACGGACAA 60.374 57.895 0.00 0.00 0.00 3.18
5387 6022 2.438795 CGGCCTGGGAAAAAGGGA 59.561 61.111 0.00 0.00 35.17 4.20
5408 6043 1.733389 CGCAAGAAATCGCCTGCAAAT 60.733 47.619 0.00 0.00 43.02 2.32
5569 6211 2.133641 GGCCTCTCCTCTCAGAGCC 61.134 68.421 0.00 0.00 38.98 4.70
5570 6212 1.076044 AGGCCTCTCCTCTCAGAGC 60.076 63.158 0.00 0.00 43.20 4.09
5629 6271 0.753848 GAAGAGAGGAGGTCGGGGAG 60.754 65.000 0.00 0.00 0.00 4.30
5638 6280 1.750193 AGAGAGCACGAAGAGAGGAG 58.250 55.000 0.00 0.00 0.00 3.69
5639 6281 1.815613 CAAGAGAGCACGAAGAGAGGA 59.184 52.381 0.00 0.00 0.00 3.71
5640 6282 1.543802 ACAAGAGAGCACGAAGAGAGG 59.456 52.381 0.00 0.00 0.00 3.69
5641 6283 2.227626 TGACAAGAGAGCACGAAGAGAG 59.772 50.000 0.00 0.00 0.00 3.20
5642 6284 2.227626 CTGACAAGAGAGCACGAAGAGA 59.772 50.000 0.00 0.00 0.00 3.10
5736 6383 2.032528 TGCTCAAAGGCGACCTGG 59.967 61.111 0.00 0.00 32.13 4.45
5828 6475 2.365635 TGAGTGGAGGGCCTAGGC 60.366 66.667 26.55 26.55 41.06 3.93
5863 6510 1.604755 GTGACGAGTGAGTGAGTGAGT 59.395 52.381 0.00 0.00 0.00 3.41
5864 6511 1.876799 AGTGACGAGTGAGTGAGTGAG 59.123 52.381 0.00 0.00 0.00 3.51
5910 6557 3.479269 GGAGAACGAACGCAGCGG 61.479 66.667 21.15 3.58 0.00 5.52
5917 6564 1.087501 GCTTCCCATGGAGAACGAAC 58.912 55.000 15.22 0.00 31.21 3.95
5918 6565 0.391130 CGCTTCCCATGGAGAACGAA 60.391 55.000 15.22 6.76 31.21 3.85
5919 6566 1.218047 CGCTTCCCATGGAGAACGA 59.782 57.895 15.22 0.00 31.21 3.85
5920 6567 1.815421 CCGCTTCCCATGGAGAACG 60.815 63.158 15.22 17.96 31.21 3.95
5921 6568 2.115291 GCCGCTTCCCATGGAGAAC 61.115 63.158 15.22 8.84 31.21 3.01
5994 6641 2.750350 CGTGCCCTCCTTCTTGGT 59.250 61.111 0.00 0.00 37.07 3.67


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

AutoCloner maintained by Alex Coulton.