Multiple sequence alignment - TraesCS4A01G004600

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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 TraesCS4A01G004600 chr4A 100.000 4816 0 0 1 4816 3113787 3108972 0.000000e+00 8894.0
1 TraesCS4A01G004600 chr4A 100.000 30 0 0 1783 1812 3111932 3111903 6.730000e-04 56.5
2 TraesCS4A01G004600 chr4A 100.000 30 0 0 1856 1885 3112005 3111976 6.730000e-04 56.5
3 TraesCS4A01G004600 chr4D 92.877 4268 226 39 1 4216 468294112 468298353 0.000000e+00 6126.0
4 TraesCS4A01G004600 chr4D 81.458 480 41 25 4298 4751 468298488 468298945 2.760000e-92 350.0
5 TraesCS4A01G004600 chr4D 100.000 30 0 0 1856 1885 468295905 468295934 6.730000e-04 56.5
6 TraesCS4A01G004600 chr4D 100.000 30 0 0 1783 1812 468295978 468296007 6.730000e-04 56.5
7 TraesCS4A01G004600 chr4B 92.383 2442 137 22 1832 4239 586869631 586872057 0.000000e+00 3434.0
8 TraesCS4A01G004600 chr4B 94.439 1870 80 14 1 1856 586867656 586869515 0.000000e+00 2856.0
9 TraesCS4A01G004600 chr4B 95.588 68 2 1 1789 1856 586869507 586869573 1.830000e-19 108.0
10 TraesCS4A01G004600 chr4B 98.361 61 1 0 1789 1849 586869565 586869625 1.830000e-19 108.0
11 TraesCS4A01G004600 chr4B 88.710 62 4 2 1789 1847 586869623 586869684 6.690000e-09 73.1


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 TraesCS4A01G004600 chr4A 3108972 3113787 4815 True 3002.333333 8894 100.00000 1 4816 3 chr4A.!!$R1 4815
1 TraesCS4A01G004600 chr4D 468294112 468298945 4833 False 1647.250000 6126 93.58375 1 4751 4 chr4D.!!$F1 4750
2 TraesCS4A01G004600 chr4B 586867656 586872057 4401 False 1315.820000 3434 93.89620 1 4239 5 chr4B.!!$F1 4238

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
188 189 2.170397 CCTGCAAAAACTTCCCAAACCT 59.830 45.455 0.0 0.0 0.00 3.50 F
642 653 2.877097 TGCTAGATGAACCTTTGCCA 57.123 45.000 0.0 0.0 0.00 4.92 F
1026 1039 0.329596 AGGACAATCTTGAGGTGGGC 59.670 55.000 0.0 0.0 0.00 5.36 F
1473 1492 0.329596 AAGATGGTGCTTCCTGTCCC 59.670 55.000 0.8 0.0 37.07 4.46 F
2157 2318 1.093159 GGCAGAACATGAAGAGGCAG 58.907 55.000 0.0 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1024 0.036010 AGTCGCCCACCTCAAGATTG 60.036 55.000 0.0 0.0 0.00 2.67 R
1605 1624 0.036388 TGTTCAATCTCCTCACGGGC 60.036 55.000 0.0 0.0 34.39 6.13 R
2991 3155 1.268079 CTCGCTCATTCTATCGCAGGA 59.732 52.381 0.0 0.0 0.00 3.86 R
3069 3233 0.035630 AGCATCTCCTGTGCCTTCAC 60.036 55.000 0.0 0.0 43.50 3.18 R
4054 4273 0.107606 ACAGGCACAAACACACGGTA 60.108 50.000 0.0 0.0 0.00 4.02 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
179 180 3.578282 CTCCCCAATACCTGCAAAAACTT 59.422 43.478 0.00 0.00 0.00 2.66
188 189 2.170397 CCTGCAAAAACTTCCCAAACCT 59.830 45.455 0.00 0.00 0.00 3.50
246 247 6.763135 TGAAGATCCTTCATCCTTCAATTACG 59.237 38.462 5.38 0.00 31.29 3.18
334 335 4.256110 CACATGGCTTTCAGATACTGTCA 58.744 43.478 0.00 0.00 32.61 3.58
336 337 5.007430 CACATGGCTTTCAGATACTGTCATC 59.993 44.000 0.00 0.00 32.61 2.92
352 353 3.141398 GTCATCTGTTTGGCTCAGTTGA 58.859 45.455 11.47 11.47 38.49 3.18
369 370 7.225341 GCTCAGTTGAAATCATGTTTTCCTTTT 59.775 33.333 21.09 6.75 35.23 2.27
545 553 9.657419 ACATGGATCAGAAATTAAACCAAAATC 57.343 29.630 0.00 0.00 0.00 2.17
642 653 2.877097 TGCTAGATGAACCTTTGCCA 57.123 45.000 0.00 0.00 0.00 4.92
694 705 5.988561 GGCTTCTCAGATAGTTATGGTTGAG 59.011 44.000 0.00 0.00 34.76 3.02
728 739 5.570320 ACTTGGTTTGCTCTTATACCATGT 58.430 37.500 0.00 0.00 41.47 3.21
868 879 8.439993 TTTGCTGAGTTTATTGTAGTTGTGTA 57.560 30.769 0.00 0.00 0.00 2.90
1011 1024 3.769844 TGACTGGAAGAATGGTAGAGGAC 59.230 47.826 0.00 0.00 37.43 3.85
1020 1033 6.232581 AGAATGGTAGAGGACAATCTTGAG 57.767 41.667 0.00 0.00 0.00 3.02
1026 1039 0.329596 AGGACAATCTTGAGGTGGGC 59.670 55.000 0.00 0.00 0.00 5.36
1032 1045 0.616111 ATCTTGAGGTGGGCGACTCT 60.616 55.000 0.00 0.00 34.84 3.24
1034 1047 0.671781 CTTGAGGTGGGCGACTCTTG 60.672 60.000 0.00 0.00 34.84 3.02
1065 1078 5.916318 TCACCAAAATCTGTGCAAAATTCT 58.084 33.333 0.00 0.00 32.51 2.40
1066 1079 5.754406 TCACCAAAATCTGTGCAAAATTCTG 59.246 36.000 0.00 0.00 32.51 3.02
1076 1089 4.937620 TGTGCAAAATTCTGTAGAGCCTAG 59.062 41.667 0.00 0.00 0.00 3.02
1077 1090 3.941483 TGCAAAATTCTGTAGAGCCTAGC 59.059 43.478 0.00 0.00 0.00 3.42
1104 1117 3.760151 CTGAAGGCACCAATGAAGATGAA 59.240 43.478 0.00 0.00 0.00 2.57
1106 1119 4.219070 TGAAGGCACCAATGAAGATGAAAG 59.781 41.667 0.00 0.00 0.00 2.62
1184 1197 5.198965 ACTTCCTGCAAGCTTGATATTGAT 58.801 37.500 30.39 6.95 35.17 2.57
1231 1244 2.758423 ACTTCGGTTGAACAAAAGGCTT 59.242 40.909 11.80 0.00 0.00 4.35
1302 1321 7.336176 CCATCAATCAAAGAAGATTCTCACAGA 59.664 37.037 0.00 0.00 36.13 3.41
1395 1414 4.157472 TCAGAAGAAAACACACATGCAACA 59.843 37.500 0.00 0.00 0.00 3.33
1471 1490 2.479566 TCAAGATGGTGCTTCCTGTC 57.520 50.000 0.80 0.18 37.07 3.51
1473 1492 0.329596 AAGATGGTGCTTCCTGTCCC 59.670 55.000 0.80 0.00 37.07 4.46
1485 1504 2.536066 TCCTGTCCCGATTCTGAGAAA 58.464 47.619 0.00 0.00 0.00 2.52
1490 1509 2.416893 GTCCCGATTCTGAGAAAACTGC 59.583 50.000 0.00 0.00 0.00 4.40
1497 1516 5.277490 CGATTCTGAGAAAACTGCTTGTGAA 60.277 40.000 0.00 0.00 0.00 3.18
1605 1624 2.094894 CACTAGACAGAAAATGCCTGCG 59.905 50.000 0.00 0.00 35.14 5.18
1608 1627 2.182537 CAGAAAATGCCTGCGCCC 59.817 61.111 4.18 0.00 0.00 6.13
1644 1663 3.775316 ACAGTGGGAATTATTCGAGGACT 59.225 43.478 0.00 0.00 0.00 3.85
1645 1664 4.122776 CAGTGGGAATTATTCGAGGACTG 58.877 47.826 0.00 4.83 0.00 3.51
1646 1665 4.030913 AGTGGGAATTATTCGAGGACTGA 58.969 43.478 0.00 0.00 0.00 3.41
1713 1732 1.180029 CTGCCTCAAGATTTGGTGGG 58.820 55.000 0.00 0.00 0.00 4.61
1924 2082 7.891183 TTTATTGAGACTTACTTGAGCACTC 57.109 36.000 0.00 0.00 0.00 3.51
1933 2091 3.482156 ACTTGAGCACTCACAGACATT 57.518 42.857 0.00 0.00 39.66 2.71
1988 2149 3.360740 TGGTATATCCAGGTGGGTGAT 57.639 47.619 0.00 0.00 41.93 3.06
2091 2252 8.886719 CAAAGCTGTCTGTATTCAATGAGATTA 58.113 33.333 0.00 0.00 0.00 1.75
2129 2290 6.716628 AGCTTATTGAAGACCTGAAACATGAA 59.283 34.615 0.00 0.00 34.25 2.57
2157 2318 1.093159 GGCAGAACATGAAGAGGCAG 58.907 55.000 0.00 0.00 0.00 4.85
2224 2385 1.456705 AGGAAGGAGGAGCTAGCGG 60.457 63.158 9.55 0.00 0.00 5.52
2331 2492 3.977999 TGAGTTAAAAGGGGTTCAGGAGA 59.022 43.478 0.00 0.00 0.00 3.71
2371 2532 4.870123 TTGAACAGGACATTTCCATTGG 57.130 40.909 0.00 0.00 45.72 3.16
2609 2770 4.130118 TCAACAAGAAGCTTTCCTCTGTC 58.870 43.478 0.00 0.00 0.00 3.51
2689 2850 4.349048 AGAGCTAAATGCATATGTGGAGGA 59.651 41.667 0.00 0.00 45.94 3.71
2725 2886 4.462483 AGAAGCACAAGAACAAGGAAACAA 59.538 37.500 0.00 0.00 0.00 2.83
2766 2930 7.120285 TGCAAGAAGAAACCATTCTATCAAGAG 59.880 37.037 0.00 0.00 45.19 2.85
2774 2938 6.497624 ACCATTCTATCAAGAGATGAGCTT 57.502 37.500 0.00 0.00 42.53 3.74
2858 3022 3.396560 TGCATCACTTCAGTCAGAGTTG 58.603 45.455 0.00 0.00 0.00 3.16
2874 3038 6.037610 GTCAGAGTTGAGCAAAGAGAAAGAAA 59.962 38.462 0.00 0.00 32.98 2.52
2936 3100 3.582647 TCACCATTACTTCTCTCAAGGCA 59.417 43.478 0.00 0.00 0.00 4.75
2991 3155 5.163152 ACAGTTCAGTCCAAGGAGAAGAAAT 60.163 40.000 0.00 0.00 0.00 2.17
3065 3229 2.093553 AGCTGATGAGGCAAAGTCTCTC 60.094 50.000 0.01 0.00 35.05 3.20
3069 3233 0.037882 TGAGGCAAAGTCTCTCGCTG 60.038 55.000 0.01 0.00 35.05 5.18
3104 3268 2.831685 TGCTAAGAACGAGCAAGGAA 57.168 45.000 0.00 0.00 46.71 3.36
3155 3319 4.721776 AGTACTATGGAATTCAGGCTCCAA 59.278 41.667 7.93 0.00 44.77 3.53
3284 3448 3.794717 CTCTCCTGGAATGATCACACTG 58.205 50.000 0.00 0.00 0.00 3.66
3291 3455 4.326826 TGGAATGATCACACTGGACTTTC 58.673 43.478 0.00 0.00 0.00 2.62
3299 3463 4.717877 TCACACTGGACTTTCATGAACAT 58.282 39.130 7.89 0.00 0.00 2.71
3423 3587 2.480419 GTCTTAGCAAAGCTCAGCGAAA 59.520 45.455 0.00 4.85 40.44 3.46
3455 3619 0.586319 TGGAAGAACGAAAGCAAGCG 59.414 50.000 0.00 0.00 0.00 4.68
3482 3646 4.056125 GCCCAAAAGCAGGCCGAC 62.056 66.667 0.00 0.00 43.76 4.79
3634 3798 3.076258 TTGAGCGCGATCGGGACAT 62.076 57.895 33.23 18.69 35.95 3.06
3662 3826 1.268899 ACATGCAAAGAAGACAGCTGC 59.731 47.619 15.27 6.85 0.00 5.25
3674 3838 2.034687 AGCTGCGCCTTGGTTCAT 59.965 55.556 4.18 0.00 0.00 2.57
3677 3841 2.745884 TGCGCCTTGGTTCATCCG 60.746 61.111 4.18 0.00 39.52 4.18
3830 3994 0.039437 CGTAACACGGTGTGCTCTCT 60.039 55.000 15.53 0.00 38.08 3.10
3838 4002 0.250467 GGTGTGCTCTCTTTCTGGCA 60.250 55.000 0.00 0.00 0.00 4.92
3841 4005 1.270518 TGTGCTCTCTTTCTGGCAGAC 60.271 52.381 18.55 4.27 35.29 3.51
3861 4025 4.529377 AGACGTGTTAGAACTATTTCCCCA 59.471 41.667 0.00 0.00 31.28 4.96
3865 4029 5.106830 CGTGTTAGAACTATTTCCCCACAAC 60.107 44.000 0.00 0.00 31.28 3.32
3868 4032 6.263617 TGTTAGAACTATTTCCCCACAACAAC 59.736 38.462 0.00 0.00 31.28 3.32
3871 4035 4.929819 ACTATTTCCCCACAACAACAAC 57.070 40.909 0.00 0.00 0.00 3.32
3874 4038 3.320673 TTTCCCCACAACAACAACAAC 57.679 42.857 0.00 0.00 0.00 3.32
3877 4041 2.632996 TCCCCACAACAACAACAACAAA 59.367 40.909 0.00 0.00 0.00 2.83
3878 4042 3.071023 TCCCCACAACAACAACAACAAAA 59.929 39.130 0.00 0.00 0.00 2.44
3879 4043 3.815401 CCCCACAACAACAACAACAAAAA 59.185 39.130 0.00 0.00 0.00 1.94
3904 4104 3.142174 AGCAAGTGTTAGAAGTGCCTTC 58.858 45.455 6.79 6.79 40.45 3.46
3920 4120 0.110328 CTTCTGCTTGCTCAACTGCG 60.110 55.000 0.00 0.00 35.36 5.18
3921 4121 0.532640 TTCTGCTTGCTCAACTGCGA 60.533 50.000 0.00 0.00 35.36 5.10
3936 4136 0.321034 TGCGATGCTGCAGAACTCTT 60.321 50.000 20.43 0.00 40.62 2.85
3937 4137 0.096628 GCGATGCTGCAGAACTCTTG 59.903 55.000 20.43 0.00 34.15 3.02
3969 4169 5.279156 GGCTGTGAAGTCTTCATGGAATTTT 60.279 40.000 18.08 0.00 42.47 1.82
3988 4200 9.760077 GGAATTTTTATATCTACGGAGAAGACA 57.240 33.333 0.00 0.00 34.61 3.41
4001 4213 4.085210 CGGAGAAGACACGAACTTGTAAAC 60.085 45.833 0.00 0.00 0.00 2.01
4009 4228 3.960002 CACGAACTTGTAAACTTGCGAAG 59.040 43.478 0.00 0.00 0.00 3.79
4011 4230 3.001939 CGAACTTGTAAACTTGCGAAGGT 59.998 43.478 0.00 0.00 0.00 3.50
4012 4231 3.963383 ACTTGTAAACTTGCGAAGGTG 57.037 42.857 0.00 0.00 0.00 4.00
4013 4232 3.275999 ACTTGTAAACTTGCGAAGGTGT 58.724 40.909 0.00 0.00 0.00 4.16
4014 4233 4.444536 ACTTGTAAACTTGCGAAGGTGTA 58.555 39.130 0.00 0.00 0.00 2.90
4015 4234 4.271776 ACTTGTAAACTTGCGAAGGTGTAC 59.728 41.667 0.00 0.00 0.00 2.90
4016 4235 3.794717 TGTAAACTTGCGAAGGTGTACA 58.205 40.909 4.57 4.57 0.00 2.90
4017 4236 4.190001 TGTAAACTTGCGAAGGTGTACAA 58.810 39.130 6.22 0.00 0.00 2.41
4018 4237 3.963383 AAACTTGCGAAGGTGTACAAG 57.037 42.857 0.00 0.00 43.99 3.16
4091 4310 3.306780 CCTGTAACTTTGACCGACTCCAT 60.307 47.826 0.00 0.00 0.00 3.41
4117 4336 5.163774 GCTTGATGAACTGGATCTTGAGTTC 60.164 44.000 18.31 18.31 45.60 3.01
4123 4342 6.820470 GAACTGGATCTTGAGTTCGATAAG 57.180 41.667 13.45 0.00 38.93 1.73
4124 4343 5.923733 ACTGGATCTTGAGTTCGATAAGT 57.076 39.130 0.00 0.00 0.00 2.24
4125 4344 7.406031 AACTGGATCTTGAGTTCGATAAGTA 57.594 36.000 0.00 0.00 0.00 2.24
4126 4345 6.797454 ACTGGATCTTGAGTTCGATAAGTAC 58.203 40.000 0.00 0.00 0.00 2.73
4127 4346 6.603997 ACTGGATCTTGAGTTCGATAAGTACT 59.396 38.462 0.00 0.00 32.93 2.73
4128 4347 7.774157 ACTGGATCTTGAGTTCGATAAGTACTA 59.226 37.037 0.00 0.00 30.25 1.82
4129 4348 8.155821 TGGATCTTGAGTTCGATAAGTACTAG 57.844 38.462 0.00 0.00 30.25 2.57
4130 4349 7.774157 TGGATCTTGAGTTCGATAAGTACTAGT 59.226 37.037 0.00 0.00 30.25 2.57
4164 4383 2.602257 TCGTGTGCTGGATAAGATGG 57.398 50.000 0.00 0.00 0.00 3.51
4221 4440 5.449588 GGATCTGATGCTGTTAACATTGTGG 60.450 44.000 9.13 0.00 0.00 4.17
4222 4441 4.650734 TCTGATGCTGTTAACATTGTGGA 58.349 39.130 9.13 0.00 0.00 4.02
4226 4445 3.156293 TGCTGTTAACATTGTGGATGCT 58.844 40.909 9.13 0.00 39.47 3.79
4228 4447 3.674138 GCTGTTAACATTGTGGATGCTGG 60.674 47.826 9.13 0.00 39.47 4.85
4230 4449 3.088532 GTTAACATTGTGGATGCTGGGA 58.911 45.455 0.00 0.00 39.47 4.37
4239 4458 1.425066 TGGATGCTGGGAGTTTCAGTT 59.575 47.619 0.00 0.00 34.89 3.16
4240 4459 2.158475 TGGATGCTGGGAGTTTCAGTTT 60.158 45.455 0.00 0.00 34.89 2.66
4241 4460 3.073798 TGGATGCTGGGAGTTTCAGTTTA 59.926 43.478 0.00 0.00 34.89 2.01
4242 4461 3.440522 GGATGCTGGGAGTTTCAGTTTAC 59.559 47.826 0.00 0.00 34.89 2.01
4243 4462 2.489971 TGCTGGGAGTTTCAGTTTACG 58.510 47.619 0.00 0.00 34.89 3.18
4244 4463 1.804748 GCTGGGAGTTTCAGTTTACGG 59.195 52.381 0.00 0.00 34.89 4.02
4245 4464 2.809299 GCTGGGAGTTTCAGTTTACGGT 60.809 50.000 0.00 0.00 34.89 4.83
4246 4465 2.806244 CTGGGAGTTTCAGTTTACGGTG 59.194 50.000 0.00 0.00 0.00 4.94
4253 4472 0.393820 TCAGTTTACGGTGGTGGGTC 59.606 55.000 0.00 0.00 0.00 4.46
4260 4479 2.551912 CGGTGGTGGGTCTTGCAAC 61.552 63.158 0.00 0.00 0.00 4.17
4263 4482 3.670377 GGTGGGTCTTGCAACGCC 61.670 66.667 0.00 0.00 0.00 5.68
4273 4492 0.667993 TTGCAACGCCCTTTCTTCTG 59.332 50.000 0.00 0.00 0.00 3.02
4280 4573 1.676916 CGCCCTTTCTTCTGATGCTGA 60.677 52.381 0.00 0.00 0.00 4.26
4284 4577 4.081807 GCCCTTTCTTCTGATGCTGAAATT 60.082 41.667 0.00 0.00 0.00 1.82
4327 4630 8.183830 CTGAAGATTCAGCTTGTTCTTACTAG 57.816 38.462 9.50 0.00 46.97 2.57
4330 4633 8.989653 AAGATTCAGCTTGTTCTTACTAGTAC 57.010 34.615 0.91 0.00 30.96 2.73
4331 4634 8.123639 AGATTCAGCTTGTTCTTACTAGTACA 57.876 34.615 0.91 0.00 30.85 2.90
4332 4635 8.754080 AGATTCAGCTTGTTCTTACTAGTACAT 58.246 33.333 0.91 0.00 32.61 2.29
4333 4636 9.372369 GATTCAGCTTGTTCTTACTAGTACATT 57.628 33.333 0.91 0.00 32.61 2.71
4337 4644 6.212791 AGCTTGTTCTTACTAGTACATTGGGA 59.787 38.462 0.91 0.00 32.61 4.37
4339 4646 6.540438 TGTTCTTACTAGTACATTGGGAGG 57.460 41.667 0.91 0.00 28.12 4.30
4370 4677 1.384222 GGCACGGGGAAATCATGGTC 61.384 60.000 0.00 0.00 0.00 4.02
4374 4681 4.579127 GGGAAATCATGGTCCCGG 57.421 61.111 12.51 0.00 44.15 5.73
4376 4683 2.186826 GGAAATCATGGTCCCGGCG 61.187 63.158 0.00 0.00 0.00 6.46
4377 4684 2.828549 AAATCATGGTCCCGGCGC 60.829 61.111 0.00 0.00 0.00 6.53
4414 4722 4.090057 GTTCAGGTTGCGCTCGCC 62.090 66.667 9.73 8.22 41.09 5.54
4507 4825 2.167219 CACACGACGCCTGGCATAG 61.167 63.158 20.29 6.37 0.00 2.23
4508 4826 2.184322 CACGACGCCTGGCATAGT 59.816 61.111 20.29 7.16 0.00 2.12
4509 4827 2.167219 CACGACGCCTGGCATAGTG 61.167 63.158 20.29 16.56 0.00 2.74
4510 4828 2.586079 CGACGCCTGGCATAGTGG 60.586 66.667 20.29 6.16 0.00 4.00
4511 4829 2.897350 GACGCCTGGCATAGTGGC 60.897 66.667 20.29 5.46 44.03 5.01
4572 4890 1.132640 GACATTCCGTGCTCGTTGC 59.867 57.895 7.47 0.00 43.25 4.17
4576 4894 3.807631 TTCCGTGCTCGTTGCTGCT 62.808 57.895 7.47 0.00 43.37 4.24
4586 4904 3.888460 TTGCTGCTGGCCACCTCA 61.888 61.111 0.00 0.00 40.92 3.86
4587 4905 3.433984 TTGCTGCTGGCCACCTCAA 62.434 57.895 0.00 1.56 40.92 3.02
4588 4906 3.060615 GCTGCTGGCCACCTCAAG 61.061 66.667 0.00 0.00 34.27 3.02
4590 4908 3.564345 CTGCTGGCCACCTCAAGCT 62.564 63.158 0.00 0.00 0.00 3.74
4591 4909 3.060615 GCTGGCCACCTCAAGCTG 61.061 66.667 0.00 0.00 0.00 4.24
4592 4910 2.360852 CTGGCCACCTCAAGCTGG 60.361 66.667 0.00 0.00 0.00 4.85
4597 4915 3.575506 CCACCTCAAGCTGGCATAA 57.424 52.632 0.00 0.00 0.00 1.90
4598 4916 1.098050 CCACCTCAAGCTGGCATAAC 58.902 55.000 0.00 0.00 0.00 1.89
4599 4917 0.729116 CACCTCAAGCTGGCATAACG 59.271 55.000 0.00 0.00 0.00 3.18
4600 4918 0.392998 ACCTCAAGCTGGCATAACGG 60.393 55.000 0.00 0.00 0.00 4.44
4601 4919 1.718757 CCTCAAGCTGGCATAACGGC 61.719 60.000 0.00 0.00 43.08 5.68
4639 4957 1.285641 CACGTCGCTGGGCATTTTT 59.714 52.632 0.00 0.00 0.00 1.94
4674 4992 5.090139 TCCTTTTAAATTTCCATGCCCTCA 58.910 37.500 0.00 0.00 0.00 3.86
4714 5032 8.243426 TCATAAGCCATTTCTTTATTCACACAC 58.757 33.333 0.00 0.00 0.00 3.82
4716 5034 6.259550 AGCCATTTCTTTATTCACACACTC 57.740 37.500 0.00 0.00 0.00 3.51
4718 5036 5.631026 CCATTTCTTTATTCACACACTCCG 58.369 41.667 0.00 0.00 0.00 4.63
4720 5038 3.678056 TCTTTATTCACACACTCCGCT 57.322 42.857 0.00 0.00 0.00 5.52
4735 5053 7.227116 ACACACTCCGCTGTTTATTTAGTTAAA 59.773 33.333 0.00 0.00 0.00 1.52
4739 5057 6.912082 TCCGCTGTTTATTTAGTTAAAACCC 58.088 36.000 0.00 0.00 33.21 4.11
4741 5059 5.284424 CGCTGTTTATTTAGTTAAAACCCGC 59.716 40.000 0.00 0.00 33.21 6.13
4747 5065 9.333497 GTTTATTTAGTTAAAACCCGCTGTAAG 57.667 33.333 0.00 0.00 0.00 2.34
4766 5084 8.398491 CTGTAAGCTAATGTAAGGCATTTTTG 57.602 34.615 0.00 0.00 44.82 2.44
4767 5085 8.116651 TGTAAGCTAATGTAAGGCATTTTTGA 57.883 30.769 0.00 0.00 44.82 2.69
4768 5086 8.580720 TGTAAGCTAATGTAAGGCATTTTTGAA 58.419 29.630 0.00 0.00 44.82 2.69
4769 5087 7.889589 AAGCTAATGTAAGGCATTTTTGAAC 57.110 32.000 0.00 0.00 44.82 3.18
4770 5088 7.232118 AGCTAATGTAAGGCATTTTTGAACT 57.768 32.000 0.00 0.00 44.82 3.01
4771 5089 7.092716 AGCTAATGTAAGGCATTTTTGAACTG 58.907 34.615 0.00 0.00 44.82 3.16
4772 5090 6.183360 GCTAATGTAAGGCATTTTTGAACTGC 60.183 38.462 0.00 0.00 44.82 4.40
4773 5091 4.662468 TGTAAGGCATTTTTGAACTGCA 57.338 36.364 0.00 0.00 37.64 4.41
4774 5092 5.016051 TGTAAGGCATTTTTGAACTGCAA 57.984 34.783 0.00 0.00 37.64 4.08
4775 5093 5.423015 TGTAAGGCATTTTTGAACTGCAAA 58.577 33.333 0.00 0.00 44.38 3.68
4789 5107 8.692110 TTGAACTGCAAAAGCATCTTATATTG 57.308 30.769 0.00 0.00 32.46 1.90
4790 5108 8.054152 TGAACTGCAAAAGCATCTTATATTGA 57.946 30.769 0.00 0.00 0.00 2.57
4791 5109 7.970061 TGAACTGCAAAAGCATCTTATATTGAC 59.030 33.333 0.00 0.00 0.00 3.18
4792 5110 6.489675 ACTGCAAAAGCATCTTATATTGACG 58.510 36.000 0.00 0.00 0.00 4.35
4793 5111 6.094048 ACTGCAAAAGCATCTTATATTGACGT 59.906 34.615 0.00 0.00 0.00 4.34
4794 5112 7.279981 ACTGCAAAAGCATCTTATATTGACGTA 59.720 33.333 0.00 0.00 0.00 3.57
4795 5113 7.406553 TGCAAAAGCATCTTATATTGACGTAC 58.593 34.615 0.00 0.00 0.00 3.67
4796 5114 7.065204 TGCAAAAGCATCTTATATTGACGTACA 59.935 33.333 0.00 0.00 0.00 2.90
4797 5115 7.584123 GCAAAAGCATCTTATATTGACGTACAG 59.416 37.037 0.00 0.00 0.00 2.74
4798 5116 8.817100 CAAAAGCATCTTATATTGACGTACAGA 58.183 33.333 0.00 0.00 0.00 3.41
4799 5117 8.581057 AAAGCATCTTATATTGACGTACAGAG 57.419 34.615 0.00 0.00 0.00 3.35
4800 5118 6.682746 AGCATCTTATATTGACGTACAGAGG 58.317 40.000 0.00 0.00 0.00 3.69
4801 5119 6.265649 AGCATCTTATATTGACGTACAGAGGT 59.734 38.462 0.00 0.00 0.00 3.85
4802 5120 7.447545 AGCATCTTATATTGACGTACAGAGGTA 59.552 37.037 0.00 0.00 0.00 3.08
4803 5121 7.751348 GCATCTTATATTGACGTACAGAGGTAG 59.249 40.741 0.00 0.00 0.00 3.18
4804 5122 8.784994 CATCTTATATTGACGTACAGAGGTAGT 58.215 37.037 0.00 0.00 0.00 2.73
4810 5128 5.824904 TGACGTACAGAGGTAGTATTTCC 57.175 43.478 0.00 0.00 0.00 3.13
4811 5129 5.503927 TGACGTACAGAGGTAGTATTTCCT 58.496 41.667 0.00 0.00 36.70 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 2.181196 AGATGGGGAAAAAGGTTTGGGA 59.819 45.455 0.00 0.00 0.00 4.37
188 189 2.308866 GGAGACTGGAGATGGGGAAAAA 59.691 50.000 0.00 0.00 0.00 1.94
246 247 4.299978 GAGACCTCGTGCCTGTATATTTC 58.700 47.826 0.00 0.00 0.00 2.17
269 270 6.852858 AAAGCTGAAACTTACTGAAGAGTC 57.147 37.500 0.00 0.00 36.45 3.36
334 335 4.828939 TGATTTCAACTGAGCCAAACAGAT 59.171 37.500 0.00 0.00 38.55 2.90
336 337 4.572985 TGATTTCAACTGAGCCAAACAG 57.427 40.909 0.00 0.00 40.68 3.16
340 341 5.534207 AAACATGATTTCAACTGAGCCAA 57.466 34.783 0.00 0.00 0.00 4.52
421 429 5.990120 ATCCAACTTCAAGCTAAGCAAAT 57.010 34.783 0.00 0.00 0.00 2.32
463 471 7.168219 ACTGAGGTCTTCATATGTAAGCAAAA 58.832 34.615 1.90 0.00 34.68 2.44
544 552 2.300152 CAAGTTGCAGGACACCTCTAGA 59.700 50.000 0.00 0.00 0.00 2.43
545 553 2.037772 ACAAGTTGCAGGACACCTCTAG 59.962 50.000 1.81 0.00 0.00 2.43
642 653 8.984764 CAAAACATTGACTTGATGATTTGTCAT 58.015 29.630 10.02 0.00 39.95 3.06
694 705 7.260558 AGAGCAAACCAAGTAGTACTTTTTC 57.739 36.000 13.00 0.73 36.03 2.29
763 774 6.306199 TCTCATCCAAGAACATTCAGGAAAA 58.694 36.000 9.12 2.23 37.26 2.29
804 815 6.139679 ACAGATTGTTTAATGAAGGAGGGA 57.860 37.500 0.00 0.00 0.00 4.20
993 1006 5.032846 AGATTGTCCTCTACCATTCTTCCA 58.967 41.667 0.00 0.00 0.00 3.53
1011 1024 0.036010 AGTCGCCCACCTCAAGATTG 60.036 55.000 0.00 0.00 0.00 2.67
1020 1033 0.818040 ACAAACAAGAGTCGCCCACC 60.818 55.000 0.00 0.00 0.00 4.61
1026 1039 3.194861 TGGTGAAGACAAACAAGAGTCG 58.805 45.455 0.00 0.00 39.67 4.18
1032 1045 6.098679 CACAGATTTTGGTGAAGACAAACAA 58.901 36.000 0.00 0.00 37.53 2.83
1034 1047 4.504097 GCACAGATTTTGGTGAAGACAAAC 59.496 41.667 0.00 0.00 37.53 2.93
1065 1078 1.195115 CAGTTGGGCTAGGCTCTACA 58.805 55.000 16.80 2.37 37.24 2.74
1066 1079 1.486211 TCAGTTGGGCTAGGCTCTAC 58.514 55.000 16.80 12.59 35.17 2.59
1077 1090 0.604578 CATTGGTGCCTTCAGTTGGG 59.395 55.000 0.00 0.00 0.00 4.12
1092 1105 6.506500 AGGTTACTGCTTTCATCTTCATTG 57.493 37.500 0.00 0.00 0.00 2.82
1104 1117 4.036852 GCTGTTTTCTCAAGGTTACTGCTT 59.963 41.667 0.00 0.00 0.00 3.91
1106 1119 3.315191 TGCTGTTTTCTCAAGGTTACTGC 59.685 43.478 0.00 0.00 0.00 4.40
1140 1153 1.142667 TCTTGGTGCATTGGTGTCTCA 59.857 47.619 0.00 0.00 0.00 3.27
1184 1197 2.877786 TGCAGATTGCTTTCTTCGTCAA 59.122 40.909 2.48 0.00 45.31 3.18
1206 1219 3.877508 CCTTTTGTTCAACCGAAGTCTCT 59.122 43.478 0.00 0.00 0.00 3.10
1211 1224 3.372060 GAAGCCTTTTGTTCAACCGAAG 58.628 45.455 0.00 0.00 0.00 3.79
1302 1321 4.080863 ACTTCGTTAGAGGCAGATGGAAAT 60.081 41.667 0.00 0.00 0.00 2.17
1364 1383 4.672413 GTGTGTTTTCTTCTGAAGAATGCG 59.328 41.667 27.93 0.05 46.15 4.73
1395 1414 2.965831 TGAGCTAACTGAAGTCTGTGGT 59.034 45.455 0.00 0.00 0.00 4.16
1471 1490 2.704572 AGCAGTTTTCTCAGAATCGGG 58.295 47.619 0.00 0.00 0.00 5.14
1473 1492 4.212004 TCACAAGCAGTTTTCTCAGAATCG 59.788 41.667 0.00 0.00 0.00 3.34
1490 1509 2.949106 CAGGTGGCGCTTCACAAG 59.051 61.111 16.88 6.30 39.27 3.16
1605 1624 0.036388 TGTTCAATCTCCTCACGGGC 60.036 55.000 0.00 0.00 34.39 6.13
1608 1627 2.341257 CCACTGTTCAATCTCCTCACG 58.659 52.381 0.00 0.00 0.00 4.35
1713 1732 1.725931 CGCGTTTTCCAGTTGATGCTC 60.726 52.381 0.00 0.00 0.00 4.26
1988 2149 2.628178 ACTGACCTCGAGTTTGACATGA 59.372 45.455 12.31 0.00 0.00 3.07
2129 2290 0.617413 CATGTTCTGCCCTCTCCAGT 59.383 55.000 0.00 0.00 0.00 4.00
2157 2318 2.442236 TCCAAATCCTCCTTGGCATC 57.558 50.000 0.00 0.00 42.68 3.91
2224 2385 1.002366 CTCGCCTGCAACACTATCAC 58.998 55.000 0.00 0.00 0.00 3.06
2371 2532 2.372264 TGATGGCTGCCTGAGATTTTC 58.628 47.619 21.03 4.71 0.00 2.29
2383 2544 5.862845 ACTCTTTGGATACTATGATGGCTG 58.137 41.667 0.00 0.00 37.61 4.85
2481 2642 1.987770 GTGTTTTTCAGCATCATGGCG 59.012 47.619 0.00 0.00 39.27 5.69
2659 2820 5.586243 ACATATGCATTTAGCTCTTCGTTGT 59.414 36.000 3.54 0.00 45.94 3.32
2689 2850 9.249457 GTTCTTGTGCTTCTTTAATTAGCTTTT 57.751 29.630 0.00 0.00 35.93 2.27
2725 2886 4.025040 TCTTGCATGGTCTCATCAGTTT 57.975 40.909 0.00 0.00 0.00 2.66
2774 2938 1.637338 TGCTCTTCTTCTGCTCCTCA 58.363 50.000 0.00 0.00 0.00 3.86
2858 3022 4.737279 GCAAGTGTTTCTTTCTCTTTGCTC 59.263 41.667 0.00 0.00 33.63 4.26
2874 3038 2.567497 GCTGCATGGTGGCAAGTGT 61.567 57.895 0.00 0.00 44.40 3.55
2936 3100 3.760684 CCTGTTTTGCCAGCTTAATCTCT 59.239 43.478 0.00 0.00 0.00 3.10
2976 3140 2.355108 CGCAGGATTTCTTCTCCTTGGA 60.355 50.000 0.00 0.00 41.29 3.53
2991 3155 1.268079 CTCGCTCATTCTATCGCAGGA 59.732 52.381 0.00 0.00 0.00 3.86
3069 3233 0.035630 AGCATCTCCTGTGCCTTCAC 60.036 55.000 0.00 0.00 43.50 3.18
3103 3267 1.815003 CCTTCGCTTGCTCCATTTCTT 59.185 47.619 0.00 0.00 0.00 2.52
3104 3268 1.457346 CCTTCGCTTGCTCCATTTCT 58.543 50.000 0.00 0.00 0.00 2.52
3135 3299 3.686691 GCTTGGAGCCTGAATTCCATAGT 60.687 47.826 2.27 0.00 42.73 2.12
3155 3319 1.254284 CCGTCTCCTTCAGGACTGCT 61.254 60.000 0.00 0.00 39.78 4.24
3284 3448 2.744202 AGACGCATGTTCATGAAAGTCC 59.256 45.455 10.35 0.00 0.00 3.85
3291 3455 2.218075 CGATGAGAGACGCATGTTCATG 59.782 50.000 8.26 8.26 0.00 3.07
3407 3571 3.253188 TGTAAATTTCGCTGAGCTTTGCT 59.747 39.130 1.78 0.00 43.88 3.91
3634 3798 1.614903 CTTCTTTGCATGTGCCCTTGA 59.385 47.619 2.07 0.00 41.18 3.02
3662 3826 2.436646 AGCGGATGAACCAAGGCG 60.437 61.111 0.00 0.00 38.90 5.52
3677 3841 1.604185 GCTGACATATCCGAGGACAGC 60.604 57.143 13.46 13.46 41.33 4.40
3767 3931 0.309922 CCAGGAACATCATCATGCGC 59.690 55.000 0.00 0.00 32.57 6.09
3830 3994 3.128349 GTTCTAACACGTCTGCCAGAAA 58.872 45.455 0.00 0.00 0.00 2.52
3838 4002 4.529377 TGGGGAAATAGTTCTAACACGTCT 59.471 41.667 2.56 0.00 33.92 4.18
3841 4005 4.571919 TGTGGGGAAATAGTTCTAACACG 58.428 43.478 14.99 0.00 35.89 4.49
3877 4041 5.450550 GGCACTTCTAACACTTGCTTCTTTT 60.451 40.000 0.00 0.00 33.55 2.27
3878 4042 4.036852 GGCACTTCTAACACTTGCTTCTTT 59.963 41.667 0.00 0.00 33.55 2.52
3879 4043 3.565902 GGCACTTCTAACACTTGCTTCTT 59.434 43.478 0.00 0.00 33.55 2.52
3880 4044 3.142174 GGCACTTCTAACACTTGCTTCT 58.858 45.455 0.00 0.00 33.55 2.85
3881 4045 3.142174 AGGCACTTCTAACACTTGCTTC 58.858 45.455 0.00 0.00 27.25 3.86
3882 4046 3.214696 AGGCACTTCTAACACTTGCTT 57.785 42.857 0.00 0.00 27.25 3.91
3883 4047 2.938956 AGGCACTTCTAACACTTGCT 57.061 45.000 0.00 0.00 27.25 3.91
3904 4104 0.179197 CATCGCAGTTGAGCAAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
3910 4110 2.099831 GCAGCATCGCAGTTGAGC 59.900 61.111 0.00 0.00 0.00 4.26
3920 4120 2.105006 TCCAAGAGTTCTGCAGCATC 57.895 50.000 9.47 6.69 0.00 3.91
3921 4121 2.026542 TGATCCAAGAGTTCTGCAGCAT 60.027 45.455 9.47 0.00 0.00 3.79
3969 4169 6.765036 AGTTCGTGTCTTCTCCGTAGATATAA 59.235 38.462 0.00 0.00 0.00 0.98
3973 4173 3.345414 AGTTCGTGTCTTCTCCGTAGAT 58.655 45.455 0.00 0.00 0.00 1.98
3975 4175 3.235195 CAAGTTCGTGTCTTCTCCGTAG 58.765 50.000 0.00 0.00 0.00 3.51
3985 4197 3.000523 TCGCAAGTTTACAAGTTCGTGTC 59.999 43.478 0.00 0.00 39.48 3.67
3988 4200 3.001939 CCTTCGCAAGTTTACAAGTTCGT 59.998 43.478 0.00 0.00 39.48 3.85
4001 4213 4.527564 CTTTTCTTGTACACCTTCGCAAG 58.472 43.478 0.00 0.00 39.52 4.01
4053 4272 0.586319 CAGGCACAAACACACGGTAG 59.414 55.000 0.00 0.00 0.00 3.18
4054 4273 0.107606 ACAGGCACAAACACACGGTA 60.108 50.000 0.00 0.00 0.00 4.02
4055 4274 0.107606 TACAGGCACAAACACACGGT 60.108 50.000 0.00 0.00 0.00 4.83
4091 4310 4.654915 TCAAGATCCAGTTCATCAAGCAA 58.345 39.130 0.00 0.00 0.00 3.91
4122 4341 7.025963 CGAAATTCGTCCAAAGTACTAGTACT 58.974 38.462 26.61 26.61 40.39 2.73
4123 4342 7.202315 CGAAATTCGTCCAAAGTACTAGTAC 57.798 40.000 23.03 23.03 34.72 2.73
4164 4383 2.441532 ATGCATGCAGCTCCCACC 60.442 61.111 26.69 0.00 45.94 4.61
4221 4440 3.125316 CGTAAACTGAAACTCCCAGCATC 59.875 47.826 0.00 0.00 35.14 3.91
4222 4441 3.074412 CGTAAACTGAAACTCCCAGCAT 58.926 45.455 0.00 0.00 35.14 3.79
4226 4445 2.485835 CCACCGTAAACTGAAACTCCCA 60.486 50.000 0.00 0.00 0.00 4.37
4228 4447 2.546789 CACCACCGTAAACTGAAACTCC 59.453 50.000 0.00 0.00 0.00 3.85
4230 4449 2.567985 CCACCACCGTAAACTGAAACT 58.432 47.619 0.00 0.00 0.00 2.66
4239 4458 1.071814 GCAAGACCCACCACCGTAA 59.928 57.895 0.00 0.00 0.00 3.18
4240 4459 1.697082 TTGCAAGACCCACCACCGTA 61.697 55.000 0.00 0.00 0.00 4.02
4241 4460 3.050354 TTGCAAGACCCACCACCGT 62.050 57.895 0.00 0.00 0.00 4.83
4242 4461 2.203280 TTGCAAGACCCACCACCG 60.203 61.111 0.00 0.00 0.00 4.94
4243 4462 2.551912 CGTTGCAAGACCCACCACC 61.552 63.158 0.00 0.00 0.00 4.61
4244 4463 3.030652 CGTTGCAAGACCCACCAC 58.969 61.111 0.00 0.00 0.00 4.16
4245 4464 2.904866 GCGTTGCAAGACCCACCA 60.905 61.111 0.00 0.00 0.00 4.17
4246 4465 3.670377 GGCGTTGCAAGACCCACC 61.670 66.667 0.00 0.00 0.00 4.61
4253 4472 0.954452 AGAAGAAAGGGCGTTGCAAG 59.046 50.000 0.00 0.00 0.00 4.01
4260 4479 0.731417 CAGCATCAGAAGAAAGGGCG 59.269 55.000 0.00 0.00 0.00 6.13
4263 4482 7.376615 AGAAAATTTCAGCATCAGAAGAAAGG 58.623 34.615 8.55 0.00 33.96 3.11
4305 4608 8.585881 TGTACTAGTAAGAACAAGCTGAATCTT 58.414 33.333 3.61 11.48 33.89 2.40
4317 4620 6.541934 ACCTCCCAATGTACTAGTAAGAAC 57.458 41.667 3.61 0.00 0.00 3.01
4325 4628 3.272818 TCCAGGTACCTCCCAATGTACTA 59.727 47.826 12.84 0.00 37.92 1.82
4326 4629 2.045326 TCCAGGTACCTCCCAATGTACT 59.955 50.000 12.84 0.00 37.92 2.73
4327 4630 2.434702 CTCCAGGTACCTCCCAATGTAC 59.565 54.545 12.84 0.00 37.26 2.90
4330 4633 1.879575 TCTCCAGGTACCTCCCAATG 58.120 55.000 12.84 0.00 36.75 2.82
4331 4634 2.482494 CTTCTCCAGGTACCTCCCAAT 58.518 52.381 12.84 0.00 36.75 3.16
4332 4635 1.554822 CCTTCTCCAGGTACCTCCCAA 60.555 57.143 12.84 1.71 37.99 4.12
4333 4636 0.042731 CCTTCTCCAGGTACCTCCCA 59.957 60.000 12.84 0.00 37.99 4.37
4376 4683 3.567797 GAGATGTTGAGCGCCGGC 61.568 66.667 19.07 19.07 40.37 6.13
4377 4684 1.091771 ATTGAGATGTTGAGCGCCGG 61.092 55.000 2.29 0.00 0.00 6.13
4389 4696 1.470098 GCGCAACCTGAACATTGAGAT 59.530 47.619 0.30 0.00 0.00 2.75
4390 4697 0.874390 GCGCAACCTGAACATTGAGA 59.126 50.000 0.30 0.00 0.00 3.27
4464 4782 4.925307 CATGTCGATTGGCGCGCG 62.925 66.667 28.44 28.44 40.61 6.86
4470 4788 1.293924 GTGGAGAGCATGTCGATTGG 58.706 55.000 0.00 0.00 0.00 3.16
4476 4794 0.038251 TCGTGTGTGGAGAGCATGTC 60.038 55.000 0.00 0.00 0.00 3.06
4509 4827 1.308998 CGGAAGGAACATGGTATGCC 58.691 55.000 0.00 0.00 0.00 4.40
4510 4828 0.663153 GCGGAAGGAACATGGTATGC 59.337 55.000 0.00 0.00 0.00 3.14
4511 4829 0.937304 CGCGGAAGGAACATGGTATG 59.063 55.000 0.00 0.00 0.00 2.39
4512 4830 0.179056 CCGCGGAAGGAACATGGTAT 60.179 55.000 24.07 0.00 0.00 2.73
4513 4831 1.219664 CCGCGGAAGGAACATGGTA 59.780 57.895 24.07 0.00 0.00 3.25
4514 4832 2.046314 CCGCGGAAGGAACATGGT 60.046 61.111 24.07 0.00 0.00 3.55
4515 4833 2.046314 ACCGCGGAAGGAACATGG 60.046 61.111 35.90 0.00 34.73 3.66
4572 4890 3.060615 GCTTGAGGTGGCCAGCAG 61.061 66.667 34.87 24.31 0.00 4.24
4583 4901 1.026182 TGCCGTTATGCCAGCTTGAG 61.026 55.000 0.00 0.00 0.00 3.02
4586 4904 1.597742 CTATGCCGTTATGCCAGCTT 58.402 50.000 0.00 0.00 0.00 3.74
4587 4905 0.886490 GCTATGCCGTTATGCCAGCT 60.886 55.000 0.00 0.00 36.14 4.24
4588 4906 1.165907 TGCTATGCCGTTATGCCAGC 61.166 55.000 0.00 0.00 38.25 4.85
4590 4908 1.202746 TCATGCTATGCCGTTATGCCA 60.203 47.619 0.00 0.00 0.00 4.92
4591 4909 1.522668 TCATGCTATGCCGTTATGCC 58.477 50.000 0.00 0.00 0.00 4.40
4592 4910 2.666619 GCTTCATGCTATGCCGTTATGC 60.667 50.000 0.00 0.00 38.95 3.14
4593 4911 3.193157 GCTTCATGCTATGCCGTTATG 57.807 47.619 0.00 0.00 38.95 1.90
4605 4923 3.792047 TGCGCGACAGCTTCATGC 61.792 61.111 12.10 0.00 42.32 4.06
4606 4924 2.097160 GTGCGCGACAGCTTCATG 59.903 61.111 12.10 0.00 42.32 3.07
4607 4925 3.481903 CGTGCGCGACAGCTTCAT 61.482 61.111 16.08 0.00 42.32 2.57
4608 4926 4.942481 ACGTGCGCGACAGCTTCA 62.942 61.111 28.73 0.00 42.32 3.02
4644 4962 9.013229 GGCATGGAAATTTAAAAGGAAATTCTT 57.987 29.630 0.00 0.00 37.91 2.52
4645 4963 7.611467 GGGCATGGAAATTTAAAAGGAAATTCT 59.389 33.333 0.00 0.00 37.91 2.40
4646 4964 7.611467 AGGGCATGGAAATTTAAAAGGAAATTC 59.389 33.333 0.00 0.00 37.91 2.17
4647 4965 7.469343 AGGGCATGGAAATTTAAAAGGAAATT 58.531 30.769 0.00 0.00 40.03 1.82
4648 4966 7.031415 AGGGCATGGAAATTTAAAAGGAAAT 57.969 32.000 0.00 0.00 0.00 2.17
4649 4967 6.043706 TGAGGGCATGGAAATTTAAAAGGAAA 59.956 34.615 0.00 0.00 0.00 3.13
4652 4970 5.419239 TGAGGGCATGGAAATTTAAAAGG 57.581 39.130 0.00 0.00 0.00 3.11
4653 4971 6.913873 CATGAGGGCATGGAAATTTAAAAG 57.086 37.500 0.00 0.00 46.45 2.27
4674 4992 5.748402 TGGCTTATGACAATTCTCACTCAT 58.252 37.500 0.00 0.00 0.00 2.90
4687 5005 8.243426 TGTGTGAATAAAGAAATGGCTTATGAC 58.757 33.333 0.00 0.00 0.00 3.06
4689 5007 8.246180 AGTGTGTGAATAAAGAAATGGCTTATG 58.754 33.333 0.00 0.00 0.00 1.90
4694 5012 5.402398 GGAGTGTGTGAATAAAGAAATGGC 58.598 41.667 0.00 0.00 0.00 4.40
4707 5025 2.831685 ATAAACAGCGGAGTGTGTGA 57.168 45.000 0.00 0.00 0.00 3.58
4714 5032 7.025365 GGGTTTTAACTAAATAAACAGCGGAG 58.975 38.462 0.00 0.00 34.32 4.63
4716 5034 5.796437 CGGGTTTTAACTAAATAAACAGCGG 59.204 40.000 0.00 0.00 34.32 5.52
4718 5036 6.307077 CAGCGGGTTTTAACTAAATAAACAGC 59.693 38.462 0.00 0.00 37.29 4.40
4720 5038 7.274603 ACAGCGGGTTTTAACTAAATAAACA 57.725 32.000 0.00 0.00 34.32 2.83
4739 5057 3.809832 ATGCCTTACATTAGCTTACAGCG 59.190 43.478 0.00 0.00 40.72 5.18
4751 5069 5.212532 TGCAGTTCAAAAATGCCTTACAT 57.787 34.783 9.31 0.00 42.30 2.29
4752 5070 4.662468 TGCAGTTCAAAAATGCCTTACA 57.338 36.364 9.31 0.00 39.22 2.41
4753 5071 5.982465 TTTGCAGTTCAAAAATGCCTTAC 57.018 34.783 9.31 0.00 41.36 2.34
4772 5090 8.817100 TCTGTACGTCAATATAAGATGCTTTTG 58.183 33.333 0.00 0.00 0.00 2.44
4773 5091 8.942338 TCTGTACGTCAATATAAGATGCTTTT 57.058 30.769 0.00 0.00 0.00 2.27
4774 5092 7.653713 CCTCTGTACGTCAATATAAGATGCTTT 59.346 37.037 0.00 0.00 0.00 3.51
4775 5093 7.148641 CCTCTGTACGTCAATATAAGATGCTT 58.851 38.462 0.00 0.00 0.00 3.91
4776 5094 6.265649 ACCTCTGTACGTCAATATAAGATGCT 59.734 38.462 0.00 0.00 0.00 3.79
4777 5095 6.448006 ACCTCTGTACGTCAATATAAGATGC 58.552 40.000 0.00 0.00 0.00 3.91
4778 5096 8.784994 ACTACCTCTGTACGTCAATATAAGATG 58.215 37.037 0.00 0.00 0.00 2.90
4779 5097 8.921353 ACTACCTCTGTACGTCAATATAAGAT 57.079 34.615 0.00 0.00 0.00 2.40
4784 5102 8.574737 GGAAATACTACCTCTGTACGTCAATAT 58.425 37.037 0.00 0.00 0.00 1.28
4785 5103 7.776969 AGGAAATACTACCTCTGTACGTCAATA 59.223 37.037 0.00 0.00 0.00 1.90
4786 5104 6.606395 AGGAAATACTACCTCTGTACGTCAAT 59.394 38.462 0.00 0.00 0.00 2.57
4787 5105 5.948162 AGGAAATACTACCTCTGTACGTCAA 59.052 40.000 0.00 0.00 0.00 3.18
4788 5106 5.503927 AGGAAATACTACCTCTGTACGTCA 58.496 41.667 0.00 0.00 0.00 4.35
4789 5107 6.058827 GAGGAAATACTACCTCTGTACGTC 57.941 45.833 0.00 0.00 46.28 4.34


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

AutoCloner maintained by Alex Coulton.