Multiple sequence alignment - TraesCS4A01G063100

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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 TraesCS4A01G063100 chr4A 100.000 7540 0 0 1 7540 59679073 59671534 0.000000e+00 13924.0
1 TraesCS4A01G063100 chr4B 94.093 4131 150 26 1 4091 497868879 497864803 0.000000e+00 6191.0
2 TraesCS4A01G063100 chr4B 95.521 2590 74 17 4755 7341 497864447 497861897 0.000000e+00 4102.0
3 TraesCS4A01G063100 chr4B 92.935 368 15 5 4162 4527 497864804 497864446 6.700000e-145 525.0
4 TraesCS4A01G063100 chr4D 95.017 2649 70 14 4162 6788 402237116 402234508 0.000000e+00 4104.0
5 TraesCS4A01G063100 chr4D 95.351 2151 72 13 1964 4091 402239260 402237115 0.000000e+00 3393.0
6 TraesCS4A01G063100 chr4D 94.115 1954 67 23 1 1936 402241181 402239258 0.000000e+00 2928.0
7 TraesCS4A01G063100 chr4D 87.299 685 38 22 6884 7540 402234475 402233812 0.000000e+00 737.0
8 TraesCS4A01G063100 chr4D 84.270 89 12 2 4086 4172 416070712 416070624 1.350000e-12 86.1
9 TraesCS4A01G063100 chr7A 91.026 78 6 1 4086 4163 606561447 606561523 3.720000e-18 104.0
10 TraesCS4A01G063100 chr7A 90.123 81 2 5 4086 4164 19955495 19955419 4.810000e-17 100.0
11 TraesCS4A01G063100 chr7D 89.610 77 5 3 4090 4163 177987451 177987527 2.240000e-15 95.3
12 TraesCS4A01G063100 chr6B 87.952 83 5 4 4083 4164 541936647 541936725 8.060000e-15 93.5
13 TraesCS4A01G063100 chr3B 89.474 76 5 3 4090 4163 727322080 727322006 8.060000e-15 93.5
14 TraesCS4A01G063100 chr3B 84.884 86 12 1 4087 4171 823942405 823942490 1.350000e-12 86.1
15 TraesCS4A01G063100 chr3B 94.286 35 2 0 5076 5110 541523922 541523888 4.000000e-03 54.7
16 TraesCS4A01G063100 chr1B 89.333 75 4 3 4090 4163 421421293 421421364 2.900000e-14 91.6
17 TraesCS4A01G063100 chr2D 84.000 100 5 6 4070 4165 15196259 15196351 1.350000e-12 86.1
18 TraesCS4A01G063100 chr3A 87.500 64 6 2 4969 5031 493130077 493130015 1.050000e-08 73.1
19 TraesCS4A01G063100 chr3A 96.875 32 1 0 5076 5107 534997868 534997899 4.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G063100 chr4A 59671534 59679073 7539 True 13924.0 13924 100.0000 1 7540 1 chr4A.!!$R1 7539
1 TraesCS4A01G063100 chr4B 497861897 497868879 6982 True 3606.0 6191 94.1830 1 7341 3 chr4B.!!$R1 7340
2 TraesCS4A01G063100 chr4D 402233812 402241181 7369 True 2790.5 4104 92.9455 1 7540 4 chr4D.!!$R2 7539

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
313 314 0.179148 CGTGTATGCAGCTCGTACCA 60.179 55.000 0.00 0.00 36.55 3.25 F
316 317 1.068588 TGTATGCAGCTCGTACCATCC 59.931 52.381 0.00 0.00 36.55 3.51 F
1342 1349 1.413077 CTAGGGGATTCTCAACGGTCC 59.587 57.143 0.00 0.00 0.00 4.46 F
1825 1850 0.038166 GAGTGTTTCCCTGGGATGCA 59.962 55.000 17.93 15.33 0.00 3.96 F
1842 1867 0.179163 GCACGCTCAACCCAATTAGC 60.179 55.000 0.00 0.00 0.00 3.09 F
2360 2385 1.003580 TCCAAAGGTCAGTCCAGCATC 59.996 52.381 0.00 0.00 39.02 3.91 F
2539 2566 1.033746 CATCCTTGGCGGCTTGACAT 61.034 55.000 11.43 0.00 33.63 3.06 F
2575 2602 1.344226 CTCGCTCGTGTTGCAATCGA 61.344 55.000 21.71 21.71 0.00 3.59 F
2830 2874 1.650912 CGCTCAATGCATGGTAGCC 59.349 57.895 17.67 5.57 43.06 3.93 F
3660 3708 2.084610 TGTCTGCTGATTCAAGGACG 57.915 50.000 0.00 0.00 0.00 4.79 F
4815 4867 0.999406 CTGTGCATCCCGTTAGTTCG 59.001 55.000 0.00 0.00 0.00 3.95 F
5658 5713 0.955428 TTCAATGAGCGCACTGGGTC 60.955 55.000 11.47 0.00 35.07 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1567 0.093026 GAAACTCGCGTGAATCACCG 59.907 55.000 16.04 12.09 32.42 4.94 R
1819 1839 1.315257 ATTGGGTTGAGCGTGCATCC 61.315 55.000 0.00 0.00 0.00 3.51 R
2921 2965 0.036952 CAAGCTCCACGGAGTCACAT 60.037 55.000 14.48 0.00 41.61 3.21 R
2931 2975 0.038159 ACAGACGCTACAAGCTCCAC 60.038 55.000 0.00 0.00 39.60 4.02 R
3160 3204 1.380650 GGAGCTCTCGGGGAAGAGT 60.381 63.158 14.64 0.00 43.92 3.24 R
4147 4195 1.934480 TGTACTACTCCCTCCATCCCA 59.066 52.381 0.00 0.00 0.00 4.37 R
4148 4196 2.769602 TGTACTACTCCCTCCATCCC 57.230 55.000 0.00 0.00 0.00 3.85 R
4521 4573 4.742012 AGGATTCTTCGAGCTAGGGATAA 58.258 43.478 0.00 0.00 0.00 1.75 R
4796 4848 0.999406 CGAACTAACGGGATGCACAG 59.001 55.000 0.00 0.00 0.00 3.66 R
5301 5356 0.321122 GCACTAGAAGCAGGCACACT 60.321 55.000 0.00 0.00 0.00 3.55 R
6255 6310 0.326264 GAAGACCAGCCACCTGTGAT 59.674 55.000 0.00 0.00 37.38 3.06 R
7445 7587 0.610174 TGGCCAGAAGTGACTAGCAG 59.390 55.000 0.00 0.00 0.00 4.24 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
92 93 7.094508 TCATTTTGTGTTAGACTTCAAAGCA 57.905 32.000 0.00 0.00 32.67 3.91
95 96 4.552166 TGTGTTAGACTTCAAAGCAAGC 57.448 40.909 0.00 0.00 0.00 4.01
119 120 1.133181 TGATGGGGTTGAGGCAGTCA 61.133 55.000 0.00 0.00 0.00 3.41
238 239 2.004808 TACGTGGATGCAGCTCGGAG 62.005 60.000 19.50 0.00 0.00 4.63
313 314 0.179148 CGTGTATGCAGCTCGTACCA 60.179 55.000 0.00 0.00 36.55 3.25
316 317 1.068588 TGTATGCAGCTCGTACCATCC 59.931 52.381 0.00 0.00 36.55 3.51
388 389 1.865788 GCCACGCTTCAAATCCAGCA 61.866 55.000 0.00 0.00 35.60 4.41
409 410 5.413213 AGCAAATATTAACAGCCGTTACACA 59.587 36.000 0.00 0.00 37.33 3.72
412 413 6.417191 AATATTAACAGCCGTTACACAGTG 57.583 37.500 0.00 0.00 37.33 3.66
413 414 1.504359 TAACAGCCGTTACACAGTGC 58.496 50.000 0.00 0.00 36.52 4.40
416 417 1.597027 AGCCGTTACACAGTGCACC 60.597 57.895 14.63 0.00 0.00 5.01
469 470 4.427793 GGCGAAAAGGCGTAAACG 57.572 55.556 0.00 0.00 43.27 3.60
517 519 8.090214 TGGAAAGAAATCAGTGGAAAATCAATC 58.910 33.333 0.00 0.00 0.00 2.67
688 690 5.346281 GGAATCATTAACTCCTAATCGCTCG 59.654 44.000 0.00 0.00 0.00 5.03
689 691 3.639538 TCATTAACTCCTAATCGCTCGC 58.360 45.455 0.00 0.00 0.00 5.03
989 993 4.432741 GGGGGCTGGTGAGGCTTC 62.433 72.222 0.00 0.00 44.36 3.86
1165 1169 4.742201 TCCCGTCTCGCTTGCTGC 62.742 66.667 0.00 0.00 38.57 5.25
1342 1349 1.413077 CTAGGGGATTCTCAACGGTCC 59.587 57.143 0.00 0.00 0.00 4.46
1415 1422 3.887716 GTCTGGGGAATGGATTTCTGATG 59.112 47.826 0.00 0.00 34.56 3.07
1525 1543 7.499563 TGCTAATTCGCAATACTTTACCCATTA 59.500 33.333 1.54 0.00 36.89 1.90
1529 1547 4.573201 TCGCAATACTTTACCCATTAGCAC 59.427 41.667 0.00 0.00 0.00 4.40
1549 1567 6.926313 AGCACGAGTATTAGGATTAGATTCC 58.074 40.000 0.00 0.00 35.90 3.01
1581 1599 3.001330 CGCGAGTTTCCAGTTATGATTCC 59.999 47.826 0.00 0.00 0.00 3.01
1588 1606 5.957771 TTCCAGTTATGATTCCAGCTAGT 57.042 39.130 0.00 0.00 0.00 2.57
1634 1652 7.094592 TGTCTCTAGGAATAGATAGTTGATGCG 60.095 40.741 0.00 0.00 0.00 4.73
1709 1727 5.856455 CCGAAAATGGTTGATGTACAGTTTC 59.144 40.000 0.33 0.00 42.41 2.78
1825 1850 0.038166 GAGTGTTTCCCTGGGATGCA 59.962 55.000 17.93 15.33 0.00 3.96
1842 1867 0.179163 GCACGCTCAACCCAATTAGC 60.179 55.000 0.00 0.00 0.00 3.09
1844 1869 1.745087 CACGCTCAACCCAATTAGCAT 59.255 47.619 0.00 0.00 34.60 3.79
1863 1888 4.861462 AGCATCGATGTATCTATTTGCTCG 59.139 41.667 25.47 0.00 0.00 5.03
1878 1903 1.281899 GCTCGACTGTAATGCCTGTC 58.718 55.000 0.00 0.00 0.00 3.51
1958 1983 7.016072 GCTCATATGTATCCCTTGCCTATAGAT 59.984 40.741 0.00 0.00 0.00 1.98
1965 1990 7.616150 TGTATCCCTTGCCTATAGATTCTACTC 59.384 40.741 0.00 0.00 0.00 2.59
2009 2034 8.429641 ACACATACATAGGGAAATAGTGTAAGG 58.570 37.037 0.00 0.00 36.09 2.69
2043 2068 5.156355 GCTCCTGATTGTGTTGTATTGTTG 58.844 41.667 0.00 0.00 0.00 3.33
2228 2253 3.377154 AATATGTGGGGAGGGGACATA 57.623 47.619 0.00 0.00 37.07 2.29
2308 2333 7.068226 TGGACTCGATTGTCTTATCTGATGTTA 59.932 37.037 0.00 0.00 37.16 2.41
2311 2336 9.121658 ACTCGATTGTCTTATCTGATGTTACTA 57.878 33.333 0.00 0.00 0.00 1.82
2360 2385 1.003580 TCCAAAGGTCAGTCCAGCATC 59.996 52.381 0.00 0.00 39.02 3.91
2409 2436 3.119814 TGCTTGTGTCGCAACTAAACAAA 60.120 39.130 0.00 0.00 33.87 2.83
2413 2440 3.181505 TGTGTCGCAACTAAACAAAGTGG 60.182 43.478 0.00 0.00 0.00 4.00
2512 2539 1.869132 GTTGGTACCGTTTCGAAAGCT 59.131 47.619 11.66 0.00 0.00 3.74
2539 2566 1.033746 CATCCTTGGCGGCTTGACAT 61.034 55.000 11.43 0.00 33.63 3.06
2575 2602 1.344226 CTCGCTCGTGTTGCAATCGA 61.344 55.000 21.71 21.71 0.00 3.59
2707 2734 4.549793 TTGCTTCTCAACCGCACA 57.450 50.000 0.00 0.00 32.71 4.57
2741 2768 9.938280 ATGATCCATTTGCCTCATTATATTTTG 57.062 29.630 0.00 0.00 0.00 2.44
2758 2785 3.631145 TTTGTGCAGCAAGATCTTCAC 57.369 42.857 14.90 14.90 38.47 3.18
2762 2789 4.520179 TGTGCAGCAAGATCTTCACATAT 58.480 39.130 18.71 0.00 35.80 1.78
2763 2790 4.334481 TGTGCAGCAAGATCTTCACATATG 59.666 41.667 18.71 0.00 35.80 1.78
2794 2821 9.226606 CCCACTTGTACTTATTTCAGTGAAATA 57.773 33.333 27.12 27.12 41.64 1.40
2816 2843 2.817396 GTCCTGCCTTCTGCGCTC 60.817 66.667 9.73 0.00 45.60 5.03
2830 2874 1.650912 CGCTCAATGCATGGTAGCC 59.349 57.895 17.67 5.57 43.06 3.93
2931 2975 2.174334 CCAAAGGCATGTGACTCCG 58.826 57.895 0.00 0.00 29.30 4.63
2973 3017 5.044558 TGACGTTTTTATTTGGCAAGGTTC 58.955 37.500 0.00 0.00 0.00 3.62
3160 3204 2.853542 TTGGCTGCCTGGAGGACA 60.854 61.111 21.03 0.00 37.39 4.02
3220 3267 4.128643 CTCAAAACATTTTGCACACCCAT 58.871 39.130 11.46 0.00 45.35 4.00
3246 3293 2.210116 TCTTGAAACGTTCTGTCTGGC 58.790 47.619 0.00 0.00 0.00 4.85
3261 3308 8.577296 GTTCTGTCTGGCTATACATGACTTATA 58.423 37.037 0.00 0.00 0.00 0.98
3274 3321 5.069914 ACATGACTTATACATTCGGTAGGCA 59.930 40.000 0.00 0.00 34.92 4.75
3294 3341 3.689161 GCACATTATACTGTCACTGCCAA 59.311 43.478 0.00 0.00 0.00 4.52
3579 3627 8.625651 TCGAGAAAAAGATTCTACTATCTCCTG 58.374 37.037 10.57 2.71 33.81 3.86
3660 3708 2.084610 TGTCTGCTGATTCAAGGACG 57.915 50.000 0.00 0.00 0.00 4.79
3776 3824 4.159506 TGTGAGGAAAAAGTTTGGTGGAAG 59.840 41.667 0.00 0.00 0.00 3.46
3831 3879 5.886474 TGATACAGATCGGAACAGACTAACT 59.114 40.000 0.00 0.00 34.49 2.24
3942 3990 3.897239 TGACAGTGAATTGGAAAGTGGT 58.103 40.909 0.00 0.00 0.00 4.16
3969 4017 8.678593 ATCCTTCTAATAATTCGAAGAAACCC 57.321 34.615 3.35 0.00 45.90 4.11
4094 4142 9.444600 TCTATCAACTTTGGTGTTTATTACTCC 57.555 33.333 0.00 0.00 40.18 3.85
4095 4143 6.887626 TCAACTTTGGTGTTTATTACTCCC 57.112 37.500 0.00 0.00 39.23 4.30
4096 4144 6.607019 TCAACTTTGGTGTTTATTACTCCCT 58.393 36.000 0.00 0.00 39.23 4.20
4097 4145 6.713450 TCAACTTTGGTGTTTATTACTCCCTC 59.287 38.462 0.00 0.00 39.23 4.30
4098 4146 5.567430 ACTTTGGTGTTTATTACTCCCTCC 58.433 41.667 0.00 0.00 39.23 4.30
4099 4147 3.899052 TGGTGTTTATTACTCCCTCCG 57.101 47.619 0.00 0.00 39.23 4.63
4100 4148 3.175594 TGGTGTTTATTACTCCCTCCGT 58.824 45.455 0.00 0.00 39.23 4.69
4101 4149 3.196254 TGGTGTTTATTACTCCCTCCGTC 59.804 47.826 0.00 0.00 39.23 4.79
4102 4150 3.431346 GGTGTTTATTACTCCCTCCGTCC 60.431 52.174 0.00 0.00 34.91 4.79
4103 4151 2.767960 TGTTTATTACTCCCTCCGTCCC 59.232 50.000 0.00 0.00 0.00 4.46
4104 4152 2.767960 GTTTATTACTCCCTCCGTCCCA 59.232 50.000 0.00 0.00 0.00 4.37
4105 4153 3.339713 TTATTACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
4106 4154 4.474303 TTATTACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
4107 4155 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
4108 4156 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
4109 4157 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
4110 4158 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
4111 4159 3.870559 ACTCCCTCCGTCCCATAATATT 58.129 45.455 0.00 0.00 0.00 1.28
4112 4160 3.583086 ACTCCCTCCGTCCCATAATATTG 59.417 47.826 0.00 0.00 0.00 1.90
4113 4161 3.838317 CTCCCTCCGTCCCATAATATTGA 59.162 47.826 0.00 0.00 0.00 2.57
4114 4162 3.581332 TCCCTCCGTCCCATAATATTGAC 59.419 47.826 0.00 0.00 0.00 3.18
4115 4163 3.326588 CCCTCCGTCCCATAATATTGACA 59.673 47.826 0.00 0.00 0.00 3.58
4116 4164 4.315803 CCTCCGTCCCATAATATTGACAC 58.684 47.826 0.00 0.00 0.00 3.67
4117 4165 4.040461 CCTCCGTCCCATAATATTGACACT 59.960 45.833 0.00 0.00 0.00 3.55
4118 4166 5.245301 CCTCCGTCCCATAATATTGACACTA 59.755 44.000 0.00 0.00 0.00 2.74
4119 4167 6.340962 TCCGTCCCATAATATTGACACTAG 57.659 41.667 0.00 0.00 0.00 2.57
4120 4168 5.836898 TCCGTCCCATAATATTGACACTAGT 59.163 40.000 0.00 0.00 0.00 2.57
4121 4169 5.926542 CCGTCCCATAATATTGACACTAGTG 59.073 44.000 21.44 21.44 0.00 2.74
4123 4171 7.255695 CCGTCCCATAATATTGACACTAGTGTA 60.256 40.741 27.98 14.56 45.05 2.90
4124 4172 7.808381 CGTCCCATAATATTGACACTAGTGTAG 59.192 40.741 27.98 2.52 45.05 2.74
4125 4173 8.639761 GTCCCATAATATTGACACTAGTGTAGT 58.360 37.037 27.98 18.09 45.05 2.73
4154 4202 7.687941 AAAACGCTCTTATATTATGGGATGG 57.312 36.000 0.00 0.00 0.00 3.51
4155 4203 6.620877 AACGCTCTTATATTATGGGATGGA 57.379 37.500 0.00 0.00 0.00 3.41
4156 4204 6.227298 ACGCTCTTATATTATGGGATGGAG 57.773 41.667 0.00 0.00 0.00 3.86
4157 4205 5.129485 ACGCTCTTATATTATGGGATGGAGG 59.871 44.000 0.00 0.00 0.00 4.30
4158 4206 5.453903 CGCTCTTATATTATGGGATGGAGGG 60.454 48.000 0.00 0.00 0.00 4.30
4159 4207 5.667626 GCTCTTATATTATGGGATGGAGGGA 59.332 44.000 0.00 0.00 0.00 4.20
4160 4208 6.183361 GCTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
4270 4320 5.574188 AGTATGCCAATTCTCTCCACTTTT 58.426 37.500 0.00 0.00 0.00 2.27
4271 4321 4.796038 ATGCCAATTCTCTCCACTTTTG 57.204 40.909 0.00 0.00 0.00 2.44
4399 4451 7.092079 TGCAGGTTTGATTATTGTCTTCAATG 58.908 34.615 4.06 0.00 43.17 2.82
4402 4454 9.132521 CAGGTTTGATTATTGTCTTCAATGTTC 57.867 33.333 4.06 2.33 43.17 3.18
4500 4552 3.521947 ACGCTCCTGGATGTTAGTAAC 57.478 47.619 6.06 6.06 0.00 2.50
4521 4573 8.154856 AGTAACTGTGTACATTTTACACCTCAT 58.845 33.333 18.74 0.00 45.18 2.90
4542 4594 5.186021 TCATTATCCCTAGCTCGAAGAATCC 59.814 44.000 0.00 0.00 34.09 3.01
4576 4628 6.901081 AGTTAGCAATATGAATTAAGGGCC 57.099 37.500 0.00 0.00 0.00 5.80
4715 4767 8.867112 AATATTGTGAGAACATGAATGAATGC 57.133 30.769 0.00 0.00 0.00 3.56
4716 4768 5.970317 TTGTGAGAACATGAATGAATGCT 57.030 34.783 0.00 0.00 0.00 3.79
4717 4769 5.970317 TGTGAGAACATGAATGAATGCTT 57.030 34.783 0.00 0.00 0.00 3.91
4718 4770 6.335471 TGTGAGAACATGAATGAATGCTTT 57.665 33.333 0.00 0.00 0.00 3.51
4719 4771 6.384224 TGTGAGAACATGAATGAATGCTTTC 58.616 36.000 0.00 5.41 0.00 2.62
4720 4772 5.803967 GTGAGAACATGAATGAATGCTTTCC 59.196 40.000 9.63 0.00 0.00 3.13
4721 4773 5.477637 TGAGAACATGAATGAATGCTTTCCA 59.522 36.000 9.63 1.73 0.00 3.53
4729 4781 9.929722 CATGAATGAATGCTTTCCAATATTTTG 57.070 29.630 9.63 2.82 0.00 2.44
4796 4848 4.038522 TGCTGACATGCTAGTTATCTCCTC 59.961 45.833 0.00 0.00 0.00 3.71
4804 4856 4.038522 TGCTAGTTATCTCCTCTGTGCATC 59.961 45.833 0.00 0.00 0.00 3.91
4807 4859 1.332195 TATCTCCTCTGTGCATCCCG 58.668 55.000 0.00 0.00 0.00 5.14
4815 4867 0.999406 CTGTGCATCCCGTTAGTTCG 59.001 55.000 0.00 0.00 0.00 3.95
4857 4909 5.755409 TGTCTTCTGAGCCCAAAACTATA 57.245 39.130 0.00 0.00 0.00 1.31
4895 4947 8.690884 CAGATTCATCATATACTCCTTCCGTAT 58.309 37.037 0.00 0.00 0.00 3.06
4905 4957 5.007385 ACTCCTTCCGTATCACACATAAC 57.993 43.478 0.00 0.00 0.00 1.89
4963 5015 9.871238 TTTAAACCTGACTACAGATAATCAGAC 57.129 33.333 1.71 0.00 46.03 3.51
5106 5161 5.763204 GGTCAAAGTTACATCTTGAAGACCA 59.237 40.000 0.00 0.00 40.39 4.02
5658 5713 0.955428 TTCAATGAGCGCACTGGGTC 60.955 55.000 11.47 0.00 35.07 4.46
5807 5862 7.770897 CAGTCATTAAATACTTTCCCAGCTAGT 59.229 37.037 0.00 0.00 0.00 2.57
6255 6310 5.415701 GGTTTTCTGCAGAGTCCAAATGATA 59.584 40.000 17.43 0.00 0.00 2.15
6353 6408 4.521256 AGTTCGTCTAGCTTTCAGAGTTCT 59.479 41.667 0.00 0.00 0.00 3.01
6365 6420 2.573462 TCAGAGTTCTAATGCAGCCCTT 59.427 45.455 0.00 0.00 0.00 3.95
6377 6432 0.906282 CAGCCCTTGGGAAATTGCCT 60.906 55.000 10.36 0.00 0.00 4.75
6585 6640 5.812642 AGGTAAGCATCATTTCGTAGTCAAG 59.187 40.000 0.00 0.00 0.00 3.02
6594 6652 7.079182 TCATTTCGTAGTCAAGTTTGTTGTT 57.921 32.000 0.00 0.00 0.00 2.83
6599 6657 6.900189 TCGTAGTCAAGTTTGTTGTTTTCAA 58.100 32.000 0.00 0.00 37.48 2.69
6773 6845 6.201226 TCACATACTCTTCAAGCTAGTCTG 57.799 41.667 0.00 0.00 0.00 3.51
6796 6868 4.575885 GCCGTAGCCCATTAGATTTATCA 58.424 43.478 0.00 0.00 0.00 2.15
6797 6869 5.001232 GCCGTAGCCCATTAGATTTATCAA 58.999 41.667 0.00 0.00 0.00 2.57
6798 6870 5.106673 GCCGTAGCCCATTAGATTTATCAAC 60.107 44.000 0.00 0.00 0.00 3.18
6799 6871 6.231211 CCGTAGCCCATTAGATTTATCAACT 58.769 40.000 0.00 0.00 0.00 3.16
6800 6872 6.710744 CCGTAGCCCATTAGATTTATCAACTT 59.289 38.462 0.00 0.00 0.00 2.66
6801 6873 7.095187 CCGTAGCCCATTAGATTTATCAACTTC 60.095 40.741 0.00 0.00 0.00 3.01
6802 6874 7.441157 CGTAGCCCATTAGATTTATCAACTTCA 59.559 37.037 0.00 0.00 0.00 3.02
6803 6875 7.573968 AGCCCATTAGATTTATCAACTTCAC 57.426 36.000 0.00 0.00 0.00 3.18
6804 6876 7.118723 AGCCCATTAGATTTATCAACTTCACA 58.881 34.615 0.00 0.00 0.00 3.58
6805 6877 7.781693 AGCCCATTAGATTTATCAACTTCACAT 59.218 33.333 0.00 0.00 0.00 3.21
6862 6934 6.808008 TTGATTACTCTCTTTTCTTGCCTG 57.192 37.500 0.00 0.00 0.00 4.85
6863 6935 6.114187 TGATTACTCTCTTTTCTTGCCTGA 57.886 37.500 0.00 0.00 0.00 3.86
6864 6936 6.715280 TGATTACTCTCTTTTCTTGCCTGAT 58.285 36.000 0.00 0.00 0.00 2.90
6865 6937 6.596888 TGATTACTCTCTTTTCTTGCCTGATG 59.403 38.462 0.00 0.00 0.00 3.07
6866 6938 3.080319 ACTCTCTTTTCTTGCCTGATGC 58.920 45.455 0.00 0.00 41.77 3.91
6946 7018 4.521256 TGTTTACTTTGTGCAGGGTAATCC 59.479 41.667 0.00 0.00 0.00 3.01
7167 7241 5.347907 GTGTTCGTTTAGTCCCATCTAACAG 59.652 44.000 0.00 0.00 30.87 3.16
7168 7242 4.730949 TCGTTTAGTCCCATCTAACAGG 57.269 45.455 0.00 0.00 30.87 4.00
7170 7244 4.159135 TCGTTTAGTCCCATCTAACAGGTC 59.841 45.833 0.00 0.00 30.87 3.85
7231 7306 0.674534 GCCGTCTCCGATACTGGAAT 59.325 55.000 0.00 0.00 37.64 3.01
7297 7373 8.814038 AGTTTAGAGGATTAACAATTGCATCT 57.186 30.769 5.05 4.01 0.00 2.90
7341 7457 4.173036 GCTGTAAAGCCTGTAAATTGCA 57.827 40.909 0.00 0.00 0.00 4.08
7343 7459 4.800471 GCTGTAAAGCCTGTAAATTGCATC 59.200 41.667 0.00 0.00 0.00 3.91
7344 7460 5.393461 GCTGTAAAGCCTGTAAATTGCATCT 60.393 40.000 0.00 0.00 0.00 2.90
7345 7461 6.183360 GCTGTAAAGCCTGTAAATTGCATCTA 60.183 38.462 0.00 0.00 0.00 1.98
7346 7462 7.320443 TGTAAAGCCTGTAAATTGCATCTAG 57.680 36.000 0.00 0.00 0.00 2.43
7347 7463 6.884295 TGTAAAGCCTGTAAATTGCATCTAGT 59.116 34.615 0.00 0.00 0.00 2.57
7348 7464 6.840780 AAAGCCTGTAAATTGCATCTAGTT 57.159 33.333 0.00 0.00 0.00 2.24
7349 7465 5.824904 AGCCTGTAAATTGCATCTAGTTG 57.175 39.130 0.00 0.00 0.00 3.16
7350 7466 5.500234 AGCCTGTAAATTGCATCTAGTTGA 58.500 37.500 4.94 0.00 0.00 3.18
7351 7467 5.945784 AGCCTGTAAATTGCATCTAGTTGAA 59.054 36.000 4.94 0.00 0.00 2.69
7352 7468 6.604795 AGCCTGTAAATTGCATCTAGTTGAAT 59.395 34.615 4.94 0.14 0.00 2.57
7353 7469 7.775093 AGCCTGTAAATTGCATCTAGTTGAATA 59.225 33.333 4.94 0.00 0.00 1.75
7354 7470 8.571336 GCCTGTAAATTGCATCTAGTTGAATAT 58.429 33.333 4.94 0.00 0.00 1.28
7360 7476 8.874744 AATTGCATCTAGTTGAATATATGGCT 57.125 30.769 4.94 0.00 0.00 4.75
7361 7477 7.677454 TTGCATCTAGTTGAATATATGGCTG 57.323 36.000 4.94 0.00 0.00 4.85
7362 7478 6.772605 TGCATCTAGTTGAATATATGGCTGT 58.227 36.000 4.94 0.00 0.00 4.40
7363 7479 7.906327 TGCATCTAGTTGAATATATGGCTGTA 58.094 34.615 4.94 0.00 0.00 2.74
7364 7480 8.374743 TGCATCTAGTTGAATATATGGCTGTAA 58.625 33.333 4.94 0.00 0.00 2.41
7365 7481 9.219603 GCATCTAGTTGAATATATGGCTGTAAA 57.780 33.333 4.94 0.00 0.00 2.01
7367 7483 8.833231 TCTAGTTGAATATATGGCTGTAAAGC 57.167 34.615 0.00 0.00 0.00 3.51
7378 7494 3.203161 GCTGTAAAGCCTGTAAGTTGC 57.797 47.619 0.00 0.00 0.00 4.17
7379 7495 2.095212 GCTGTAAAGCCTGTAAGTTGCC 60.095 50.000 0.00 0.00 0.00 4.52
7380 7496 3.412386 CTGTAAAGCCTGTAAGTTGCCT 58.588 45.455 0.00 0.00 0.00 4.75
7381 7497 3.821033 CTGTAAAGCCTGTAAGTTGCCTT 59.179 43.478 0.00 0.00 34.56 4.35
7386 7502 1.271379 GCCTGTAAGTTGCCTTCCTGA 60.271 52.381 0.00 0.00 31.89 3.86
7428 7544 6.849085 ATACAATTTTGTCCATGTAGCCAA 57.151 33.333 0.00 0.00 42.35 4.52
7429 7545 5.138125 ACAATTTTGTCCATGTAGCCAAG 57.862 39.130 0.00 0.00 36.50 3.61
7431 7547 1.544724 TTTGTCCATGTAGCCAAGCC 58.455 50.000 0.00 0.00 0.00 4.35
7433 7549 0.035152 TGTCCATGTAGCCAAGCCTG 60.035 55.000 0.00 0.00 0.00 4.85
7434 7550 0.035056 GTCCATGTAGCCAAGCCTGT 60.035 55.000 0.00 0.00 0.00 4.00
7445 7587 2.810852 GCCAAGCCTGTCTTAGATATGC 59.189 50.000 0.00 0.00 32.74 3.14
7463 7605 0.742635 GCTGCTAGTCACTTCTGGCC 60.743 60.000 0.00 0.00 40.40 5.36
7498 7640 1.281925 AAGCCATCCACCCCAGTAGG 61.282 60.000 0.00 0.00 0.00 3.18
7510 7652 3.224269 CCCCAGTAGGAGTACTAGAAGC 58.776 54.545 0.00 0.00 37.40 3.86
7516 7658 4.582656 AGTAGGAGTACTAGAAGCAGCATG 59.417 45.833 0.00 0.00 37.76 4.06
7528 7670 0.801251 GCAGCATGTTCACAGTCCTC 59.199 55.000 0.00 0.00 39.31 3.71
7532 7674 2.079925 GCATGTTCACAGTCCTCTTCC 58.920 52.381 0.00 0.00 0.00 3.46
7535 7677 2.964209 TGTTCACAGTCCTCTTCCTCT 58.036 47.619 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.682209 TCCCCTTCGCTAGTTACGCT 60.682 55.000 0.00 0.00 0.00 5.07
7 8 0.174162 TTCCCCTTCGCTAGTTACGC 59.826 55.000 0.00 0.00 0.00 4.42
75 76 3.304726 GGGCTTGCTTTGAAGTCTAACAC 60.305 47.826 0.00 0.00 0.00 3.32
86 87 2.018542 CCATCAATGGGCTTGCTTTG 57.981 50.000 0.75 0.00 44.31 2.77
119 120 2.161012 CGCATGCTTGACAAATCTGAGT 59.839 45.455 17.13 0.00 0.00 3.41
238 239 1.823169 TAGACAACTGGCGTGACCCC 61.823 60.000 0.00 0.00 37.83 4.95
313 314 1.209747 GGACTAGAAAACTGGCGGGAT 59.790 52.381 0.00 0.00 0.00 3.85
316 317 2.474410 AAGGACTAGAAAACTGGCGG 57.526 50.000 0.00 0.00 0.00 6.13
349 350 4.649218 TGGCCATAAATTTCCTAAGAAGGC 59.351 41.667 0.00 0.00 43.31 4.35
357 358 2.143876 AGCGTGGCCATAAATTTCCT 57.856 45.000 9.72 0.00 0.00 3.36
416 417 3.615509 TTTCCTAAGGCCGGGCGTG 62.616 63.158 26.28 17.39 0.00 5.34
423 424 6.379988 TGGAATTGATTAACTTTCCTAAGGCC 59.620 38.462 0.00 0.00 38.73 5.19
427 428 9.189156 CCAGATGGAATTGATTAACTTTCCTAA 57.811 33.333 0.00 0.00 38.73 2.69
428 429 7.285401 GCCAGATGGAATTGATTAACTTTCCTA 59.715 37.037 2.18 0.00 38.73 2.94
469 470 7.470192 TCCATAATTCTATGATTTCCTTCCCC 58.530 38.462 0.00 0.00 37.68 4.81
517 519 3.871006 GCTTCCTTTTGAAAACAGGTTGG 59.129 43.478 0.00 0.00 31.06 3.77
634 636 2.370189 CTCTCTCTCTCCTCTCTCTCCC 59.630 59.091 0.00 0.00 0.00 4.30
637 639 1.414181 CGCTCTCTCTCTCCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
639 641 0.179045 GCGCTCTCTCTCTCCTCTCT 60.179 60.000 0.00 0.00 0.00 3.10
640 642 1.166531 GGCGCTCTCTCTCTCCTCTC 61.167 65.000 7.64 0.00 0.00 3.20
641 643 1.152963 GGCGCTCTCTCTCTCCTCT 60.153 63.158 7.64 0.00 0.00 3.69
642 644 2.193536 GGGCGCTCTCTCTCTCCTC 61.194 68.421 7.64 0.00 0.00 3.71
643 645 2.123897 GGGCGCTCTCTCTCTCCT 60.124 66.667 7.64 0.00 0.00 3.69
644 646 3.223589 GGGGCGCTCTCTCTCTCC 61.224 72.222 7.48 0.00 0.00 3.71
645 647 3.591835 CGGGGCGCTCTCTCTCTC 61.592 72.222 7.48 0.00 0.00 3.20
688 690 2.959030 GGATTAAATTCTGTCAGGGGGC 59.041 50.000 0.00 0.00 0.00 5.80
689 691 3.566351 GGGATTAAATTCTGTCAGGGGG 58.434 50.000 0.00 0.00 0.00 5.40
774 778 2.364317 CTGCGGAGGAGGGAAGGA 60.364 66.667 0.00 0.00 44.33 3.36
1047 1051 0.670546 CGACGACCAGCACCTTCATT 60.671 55.000 0.00 0.00 0.00 2.57
1165 1169 3.337889 CAGCACGACACCACACCG 61.338 66.667 0.00 0.00 0.00 4.94
1208 1215 1.226211 CGCCAGACCTACGTACGTG 60.226 63.158 30.25 17.12 0.00 4.49
1342 1349 4.106029 TCTCGAAAACGGAGGATTACAG 57.894 45.455 0.00 0.00 32.34 2.74
1415 1422 6.870971 TTACCAGTCCTTAATCAAACACAC 57.129 37.500 0.00 0.00 0.00 3.82
1507 1525 4.551990 CGTGCTAATGGGTAAAGTATTGCG 60.552 45.833 0.00 0.00 0.00 4.85
1513 1531 3.975168 ACTCGTGCTAATGGGTAAAGT 57.025 42.857 0.00 0.00 0.00 2.66
1517 1535 5.387788 TCCTAATACTCGTGCTAATGGGTA 58.612 41.667 0.00 0.00 32.73 3.69
1519 1537 4.866508 TCCTAATACTCGTGCTAATGGG 57.133 45.455 0.00 0.00 0.00 4.00
1525 1543 6.349445 CGGAATCTAATCCTAATACTCGTGCT 60.349 42.308 0.00 0.00 37.34 4.40
1529 1547 6.150641 TCACCGGAATCTAATCCTAATACTCG 59.849 42.308 9.46 0.00 37.34 4.18
1549 1567 0.093026 GAAACTCGCGTGAATCACCG 59.907 55.000 16.04 12.09 32.42 4.94
1581 1599 3.186909 TGCGCTGTTTATGTACTAGCTG 58.813 45.455 9.73 0.00 32.43 4.24
1588 1606 3.128415 ACATTGCATGCGCTGTTTATGTA 59.872 39.130 16.66 0.00 39.64 2.29
1613 1631 5.105554 AGGCGCATCAACTATCTATTCCTAG 60.106 44.000 10.83 0.00 0.00 3.02
1709 1727 6.796705 AACTTACTGTTCCCAAATAGAACG 57.203 37.500 0.00 0.00 45.33 3.95
1819 1839 1.315257 ATTGGGTTGAGCGTGCATCC 61.315 55.000 0.00 0.00 0.00 3.51
1825 1850 2.017049 GATGCTAATTGGGTTGAGCGT 58.983 47.619 0.00 0.00 37.77 5.07
1842 1867 6.033302 CAGTCGAGCAAATAGATACATCGATG 59.967 42.308 23.68 23.68 39.55 3.84
1844 1869 5.008712 ACAGTCGAGCAAATAGATACATCGA 59.991 40.000 0.00 0.00 35.56 3.59
1863 1888 8.894768 AATAAATAGAGACAGGCATTACAGTC 57.105 34.615 0.00 0.00 0.00 3.51
1878 1903 7.915397 ACATTAAGGTTGCGCAAATAAATAGAG 59.085 33.333 26.87 12.38 0.00 2.43
1958 1983 1.737838 CATTTGCGCCCAGAGTAGAA 58.262 50.000 4.18 0.00 0.00 2.10
2009 2034 1.494960 ATCAGGAGCCTGGTTCTCTC 58.505 55.000 16.06 0.67 43.75 3.20
2043 2068 6.101997 AGGAAAATTAAGCAATAGCAGCAAC 58.898 36.000 0.00 0.00 45.49 4.17
2121 2146 5.254115 GGTTGTAACCTTCAAGCTTCCTAT 58.746 41.667 6.54 0.00 45.75 2.57
2169 2194 3.624861 AGCATTCATAGCACACTTACTGC 59.375 43.478 0.00 0.00 34.63 4.40
2308 2333 5.473504 AGCGGAAAAATCATTCAACTGTAGT 59.526 36.000 0.00 0.00 0.00 2.73
2311 2336 4.853924 AGCGGAAAAATCATTCAACTGT 57.146 36.364 0.00 0.00 0.00 3.55
2360 2385 3.403057 CGTCGCCACGTGTCAAGG 61.403 66.667 15.65 0.00 41.42 3.61
2409 2436 5.888161 GGATAAGACAATCAAATCCACCACT 59.112 40.000 0.00 0.00 36.83 4.00
2413 2440 7.775120 ACATTGGATAAGACAATCAAATCCAC 58.225 34.615 10.17 0.00 44.35 4.02
2512 2539 1.675310 CGCCAAGGATGCTGAACCA 60.675 57.895 0.00 0.00 0.00 3.67
2575 2602 3.530535 GAAAAACCATGCACACCTTGTT 58.469 40.909 0.00 0.00 0.00 2.83
2696 2723 5.233957 TCATTATTTGATGTGCGGTTGAG 57.766 39.130 0.00 0.00 0.00 3.02
2701 2728 4.834357 TGGATCATTATTTGATGTGCGG 57.166 40.909 0.00 0.00 45.29 5.69
2741 2768 4.334759 ACATATGTGAAGATCTTGCTGCAC 59.665 41.667 14.00 14.56 43.47 4.57
2758 2785 9.832445 AAATAAGTACAAGTGGGTCTACATATG 57.168 33.333 0.00 0.00 0.00 1.78
2762 2789 7.015877 ACTGAAATAAGTACAAGTGGGTCTACA 59.984 37.037 0.00 0.00 0.00 2.74
2763 2790 7.331193 CACTGAAATAAGTACAAGTGGGTCTAC 59.669 40.741 0.00 0.00 0.00 2.59
2794 2821 1.073897 GCAGAAGGCAGGACCACTT 59.926 57.895 0.00 0.00 43.14 3.16
2816 2843 1.037493 ATGCTGGCTACCATGCATTG 58.963 50.000 14.04 0.00 41.72 2.82
2830 2874 4.366586 AGACGACATGAGATGTAATGCTG 58.633 43.478 0.00 0.00 45.03 4.41
2921 2965 0.036952 CAAGCTCCACGGAGTCACAT 60.037 55.000 14.48 0.00 41.61 3.21
2931 2975 0.038159 ACAGACGCTACAAGCTCCAC 60.038 55.000 0.00 0.00 39.60 4.02
2973 3017 5.446143 TTGTGCAGTTATTACCCAAAGTG 57.554 39.130 0.00 0.00 0.00 3.16
3160 3204 1.380650 GGAGCTCTCGGGGAAGAGT 60.381 63.158 14.64 0.00 43.92 3.24
3220 3267 5.006649 CAGACAGAACGTTTCAAGATGTTCA 59.993 40.000 0.46 0.00 44.30 3.18
3261 3308 5.163343 ACAGTATAATGTGCCTACCGAATGT 60.163 40.000 4.77 0.00 30.46 2.71
3272 3319 3.270027 TGGCAGTGACAGTATAATGTGC 58.730 45.455 11.11 7.69 32.25 4.57
3274 3321 4.261801 GGTTGGCAGTGACAGTATAATGT 58.738 43.478 5.33 5.33 35.68 2.71
3294 3341 4.263462 TGGATAGAGCAACATTTCACTGGT 60.263 41.667 0.00 0.00 0.00 4.00
3550 3598 9.790389 GAGATAGTAGAATCTTTTTCTCGAACA 57.210 33.333 0.00 0.00 36.33 3.18
3776 3824 2.159282 CCTGAATGCTCATGTTCCTTGC 60.159 50.000 0.00 0.00 0.00 4.01
3942 3990 9.326413 GGTTTCTTCGAATTATTAGAAGGATCA 57.674 33.333 21.49 5.70 41.07 2.92
3969 4017 3.242870 GCTCAACTGACCAAACAACTCTG 60.243 47.826 0.00 0.00 0.00 3.35
4069 4117 8.674607 GGGAGTAATAAACACCAAAGTTGATAG 58.325 37.037 0.00 0.00 40.39 2.08
4089 4137 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
4090 4138 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
4091 4139 3.838317 TCAATATTATGGGACGGAGGGAG 59.162 47.826 0.00 0.00 0.00 4.30
4092 4140 3.581332 GTCAATATTATGGGACGGAGGGA 59.419 47.826 0.00 0.00 0.00 4.20
4093 4141 3.326588 TGTCAATATTATGGGACGGAGGG 59.673 47.826 0.00 0.00 33.04 4.30
4094 4142 4.040461 AGTGTCAATATTATGGGACGGAGG 59.960 45.833 0.00 0.00 33.04 4.30
4095 4143 5.215252 AGTGTCAATATTATGGGACGGAG 57.785 43.478 0.00 0.00 33.04 4.63
4096 4144 5.836898 ACTAGTGTCAATATTATGGGACGGA 59.163 40.000 0.00 0.00 33.04 4.69
4097 4145 5.926542 CACTAGTGTCAATATTATGGGACGG 59.073 44.000 15.06 0.00 33.04 4.79
4098 4146 6.513180 ACACTAGTGTCAATATTATGGGACG 58.487 40.000 22.95 0.00 40.24 4.79
4099 4147 8.639761 ACTACACTAGTGTCAATATTATGGGAC 58.360 37.037 31.11 0.00 43.74 4.46
4100 4148 8.777578 ACTACACTAGTGTCAATATTATGGGA 57.222 34.615 31.11 8.80 43.74 4.37
4129 4177 7.942341 TCCATCCCATAATATAAGAGCGTTTTT 59.058 33.333 0.00 0.00 0.00 1.94
4130 4178 7.458397 TCCATCCCATAATATAAGAGCGTTTT 58.542 34.615 0.00 0.00 0.00 2.43
4131 4179 7.016153 TCCATCCCATAATATAAGAGCGTTT 57.984 36.000 0.00 0.00 0.00 3.60
4132 4180 6.352222 CCTCCATCCCATAATATAAGAGCGTT 60.352 42.308 0.00 0.00 0.00 4.84
4133 4181 5.129485 CCTCCATCCCATAATATAAGAGCGT 59.871 44.000 0.00 0.00 0.00 5.07
4134 4182 5.453903 CCCTCCATCCCATAATATAAGAGCG 60.454 48.000 0.00 0.00 0.00 5.03
4135 4183 5.667626 TCCCTCCATCCCATAATATAAGAGC 59.332 44.000 0.00 0.00 0.00 4.09
4136 4184 6.905776 ACTCCCTCCATCCCATAATATAAGAG 59.094 42.308 0.00 0.00 0.00 2.85
4137 4185 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
4138 4186 7.846823 ACTACTCCCTCCATCCCATAATATAAG 59.153 40.741 0.00 0.00 0.00 1.73
4139 4187 7.729350 ACTACTCCCTCCATCCCATAATATAA 58.271 38.462 0.00 0.00 0.00 0.98
4140 4188 7.312162 ACTACTCCCTCCATCCCATAATATA 57.688 40.000 0.00 0.00 0.00 0.86
4141 4189 6.185677 ACTACTCCCTCCATCCCATAATAT 57.814 41.667 0.00 0.00 0.00 1.28
4142 4190 5.633473 ACTACTCCCTCCATCCCATAATA 57.367 43.478 0.00 0.00 0.00 0.98
4143 4191 4.510303 ACTACTCCCTCCATCCCATAAT 57.490 45.455 0.00 0.00 0.00 1.28
4144 4192 4.171243 TGTACTACTCCCTCCATCCCATAA 59.829 45.833 0.00 0.00 0.00 1.90
4145 4193 3.730594 TGTACTACTCCCTCCATCCCATA 59.269 47.826 0.00 0.00 0.00 2.74
4146 4194 2.522705 TGTACTACTCCCTCCATCCCAT 59.477 50.000 0.00 0.00 0.00 4.00
4147 4195 1.934480 TGTACTACTCCCTCCATCCCA 59.066 52.381 0.00 0.00 0.00 4.37
4148 4196 2.769602 TGTACTACTCCCTCCATCCC 57.230 55.000 0.00 0.00 0.00 3.85
4149 4197 5.244178 CAGTAATGTACTACTCCCTCCATCC 59.756 48.000 0.00 0.00 37.23 3.51
4150 4198 5.834204 ACAGTAATGTACTACTCCCTCCATC 59.166 44.000 0.00 0.00 37.23 3.51
4151 4199 5.778542 ACAGTAATGTACTACTCCCTCCAT 58.221 41.667 0.00 0.00 37.23 3.41
4152 4200 5.202746 ACAGTAATGTACTACTCCCTCCA 57.797 43.478 0.00 0.00 37.23 3.86
4153 4201 6.832900 ACTTACAGTAATGTACTACTCCCTCC 59.167 42.308 1.81 0.00 37.23 4.30
4154 4202 7.878547 ACTTACAGTAATGTACTACTCCCTC 57.121 40.000 1.81 0.00 37.23 4.30
4155 4203 7.997803 CCTACTTACAGTAATGTACTACTCCCT 59.002 40.741 1.81 0.00 37.23 4.20
4156 4204 7.995488 TCCTACTTACAGTAATGTACTACTCCC 59.005 40.741 1.81 0.00 37.23 4.30
4157 4205 8.970859 TCCTACTTACAGTAATGTACTACTCC 57.029 38.462 1.81 0.00 37.23 3.85
4200 4248 7.800380 CAGACAACACTTGCTTGATAAAACTAG 59.200 37.037 0.00 0.00 0.00 2.57
4221 4269 7.676004 TCTAAATCATAGGTGTTCAACAGACA 58.324 34.615 0.00 0.00 0.00 3.41
4289 4341 7.432148 TGGGAACAGCTTCTGTAGAAATATA 57.568 36.000 0.00 0.00 44.62 0.86
4500 4552 8.612619 GGATAATGAGGTGTAAAATGTACACAG 58.387 37.037 14.93 0.00 46.96 3.66
4521 4573 4.742012 AGGATTCTTCGAGCTAGGGATAA 58.258 43.478 0.00 0.00 0.00 1.75
4656 4708 3.485394 TCTACAACTTGAGGCAATTGCA 58.515 40.909 30.32 8.86 44.36 4.08
4694 4746 5.970317 AGCATTCATTCATGTTCTCACAA 57.030 34.783 0.00 0.00 36.16 3.33
4729 4781 6.203723 GGAATGCTTCTTGTCATACATCTACC 59.796 42.308 0.00 0.00 0.00 3.18
4760 4812 4.673580 GCATGTCAGCATCAAACCACTAAG 60.674 45.833 0.00 0.00 31.99 2.18
4796 4848 0.999406 CGAACTAACGGGATGCACAG 59.001 55.000 0.00 0.00 0.00 3.66
4807 4859 6.537660 AGGCAATATAACCTGTTCGAACTAAC 59.462 38.462 27.32 3.80 34.07 2.34
4895 4947 4.876679 TCCAAAAACGTCAGTTATGTGTGA 59.123 37.500 0.00 0.00 40.18 3.58
4905 4957 1.608590 AGGCATGTCCAAAAACGTCAG 59.391 47.619 8.58 0.00 37.29 3.51
5073 5128 8.950210 CAAGATGTAACTTTGACCACTGATTAT 58.050 33.333 0.00 0.00 0.00 1.28
5074 5129 8.154203 TCAAGATGTAACTTTGACCACTGATTA 58.846 33.333 0.00 0.00 0.00 1.75
5106 5161 1.320344 TATTCCCTCGCAGCTGACGT 61.320 55.000 20.43 6.15 0.00 4.34
5171 5226 7.859325 ATAACTGACATAAAGTTACCGCAAT 57.141 32.000 0.00 0.00 41.59 3.56
5301 5356 0.321122 GCACTAGAAGCAGGCACACT 60.321 55.000 0.00 0.00 0.00 3.55
5813 5868 7.922382 TCAAGGAATTTTGATTAGGAGAGAGT 58.078 34.615 0.00 0.00 32.39 3.24
6255 6310 0.326264 GAAGACCAGCCACCTGTGAT 59.674 55.000 0.00 0.00 37.38 3.06
6353 6408 2.500910 CAATTTCCCAAGGGCTGCATTA 59.499 45.455 0.50 0.00 34.68 1.90
6365 6420 2.042842 TCCTTGATCAGGCAATTTCCCA 59.957 45.455 0.00 0.00 43.55 4.37
6585 6640 7.597369 AGAAACAGTACCTTGAAAACAACAAAC 59.403 33.333 0.00 0.00 0.00 2.93
6594 6652 6.434652 TGTCCAAAAGAAACAGTACCTTGAAA 59.565 34.615 0.00 0.00 0.00 2.69
6599 6657 8.706322 ATTATTGTCCAAAAGAAACAGTACCT 57.294 30.769 0.00 0.00 0.00 3.08
6701 6773 9.700831 AGCTACCAAGTGAAAATAAATAGGATT 57.299 29.630 0.00 0.00 0.00 3.01
6802 6874 8.766994 AATTAGCATAATTCACAAGGGTATGT 57.233 30.769 0.00 0.00 0.00 2.29
6857 6929 4.561979 AACACATGTTCTTGCATCAGGCA 61.562 43.478 0.00 0.00 42.36 4.75
6858 6930 1.542915 ACACATGTTCTTGCATCAGGC 59.457 47.619 0.00 0.00 45.13 4.85
6859 6931 3.928727 AACACATGTTCTTGCATCAGG 57.071 42.857 0.00 0.00 31.64 3.86
6946 7018 6.155475 TCAAACCACTAAATTGTTTCCAGG 57.845 37.500 0.00 0.00 30.19 4.45
7231 7306 7.430844 ACCAGATAATATATAGCCTCCCTGAA 58.569 38.462 0.00 0.00 0.00 3.02
7287 7363 6.093633 TCAAGACAAGATCTCAGATGCAATTG 59.906 38.462 0.00 0.00 36.27 2.32
7297 7373 5.819379 GCCATATGTTCAAGACAAGATCTCA 59.181 40.000 0.00 0.00 42.62 3.27
7341 7457 9.442047 GCTTTACAGCCATATATTCAACTAGAT 57.558 33.333 0.00 0.00 40.61 1.98
7358 7474 2.095212 GGCAACTTACAGGCTTTACAGC 60.095 50.000 0.00 0.00 46.52 4.40
7359 7475 3.831715 GGCAACTTACAGGCTTTACAG 57.168 47.619 0.00 0.00 0.00 2.74
7373 7489 2.854253 TCCACTCAGGAAGGCAACT 58.146 52.632 0.00 0.00 45.65 3.16
7381 7497 4.993705 ATTTTTGTAGGTCCACTCAGGA 57.006 40.909 0.00 0.00 46.75 3.86
7410 7526 2.497273 GGCTTGGCTACATGGACAAAAT 59.503 45.455 0.00 0.00 33.44 1.82
7421 7537 3.828875 ATCTAAGACAGGCTTGGCTAC 57.171 47.619 3.81 0.00 43.74 3.58
7426 7542 3.497640 GCAGCATATCTAAGACAGGCTTG 59.502 47.826 0.00 0.00 37.42 4.01
7428 7544 2.971330 AGCAGCATATCTAAGACAGGCT 59.029 45.455 0.00 0.00 0.00 4.58
7429 7545 3.399440 AGCAGCATATCTAAGACAGGC 57.601 47.619 0.00 0.00 0.00 4.85
7431 7547 6.016360 AGTGACTAGCAGCATATCTAAGACAG 60.016 42.308 0.00 0.00 0.00 3.51
7433 7549 6.325919 AGTGACTAGCAGCATATCTAAGAC 57.674 41.667 0.00 0.00 0.00 3.01
7434 7550 6.775142 AGAAGTGACTAGCAGCATATCTAAGA 59.225 38.462 0.00 0.00 0.00 2.10
7445 7587 0.610174 TGGCCAGAAGTGACTAGCAG 59.390 55.000 0.00 0.00 0.00 4.24
7463 7605 1.404583 GGCTTAAACCAGGCATTGCTG 60.405 52.381 8.82 5.00 39.20 4.41
7498 7640 4.564769 GTGAACATGCTGCTTCTAGTACTC 59.435 45.833 0.00 0.00 0.00 2.59
7510 7652 2.469274 AGAGGACTGTGAACATGCTG 57.531 50.000 0.00 0.00 0.00 4.41
7516 7658 2.028567 CCAGAGGAAGAGGACTGTGAAC 60.029 54.545 0.00 0.00 30.23 3.18


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

AutoCloner maintained by Alex Coulton.