Multiple sequence alignment - TraesCS6B01G417500

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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 TraesCS6B01G417500 chr6B 100.000 2461 0 0 1 2461 689289923 689292383 0.000000e+00 4545.0
1 TraesCS6B01G417500 chr6A 90.387 957 44 24 41 960 600099430 600100375 0.000000e+00 1214.0
2 TraesCS6B01G417500 chr6A 90.030 662 33 16 961 1616 599983528 599984162 0.000000e+00 826.0
3 TraesCS6B01G417500 chr6A 89.449 635 40 18 1145 1775 600102792 600103403 0.000000e+00 776.0
4 TraesCS6B01G417500 chr6A 94.783 345 8 5 361 699 599978532 599978872 1.680000e-146 529.0
5 TraesCS6B01G417500 chr6A 90.610 213 11 7 750 961 599983145 599983349 8.670000e-70 274.0
6 TraesCS6B01G417500 chr6A 92.241 116 9 0 248 363 599956578 599956693 5.440000e-37 165.0
7 TraesCS6B01G417500 chr6A 90.000 130 8 4 959 1085 600100558 600100685 1.960000e-36 163.0
8 TraesCS6B01G417500 chr6A 100.000 35 0 0 1082 1116 600102761 600102795 5.680000e-07 65.8
9 TraesCS6B01G417500 chr6D 90.042 713 27 10 248 960 453940052 453940720 0.000000e+00 883.0
10 TraesCS6B01G417500 chr6D 86.607 672 30 27 966 1616 453940908 453941540 0.000000e+00 688.0
11 TraesCS6B01G417500 chr6D 81.752 411 36 21 1895 2283 453941809 453942202 8.550000e-80 307.0


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 TraesCS6B01G417500 chr6B 689289923 689292383 2460 False 4545.0 4545 100.000000 1 2461 1 chr6B.!!$F1 2460
1 TraesCS6B01G417500 chr6A 600099430 600103403 3973 False 554.7 1214 92.459000 41 1775 4 chr6A.!!$F4 1734
2 TraesCS6B01G417500 chr6A 599983145 599984162 1017 False 550.0 826 90.320000 750 1616 2 chr6A.!!$F3 866
3 TraesCS6B01G417500 chr6D 453940052 453942202 2150 False 626.0 883 86.133667 248 2283 3 chr6D.!!$F1 2035

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
268 296 0.45462 GGCGAGCCATACGACTATCG 60.455 60.0 9.58 0.0 40.03 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 4120 0.030908 GATAGACGGAGGACAAGGCG 59.969 60.0 0.0 0.0 0.0 5.52 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
19 20 2.640316 GGGACCTAATAGCCTTGGTG 57.360 55.000 0.00 0.00 32.30 4.17
20 21 1.477014 GGGACCTAATAGCCTTGGTGC 60.477 57.143 0.00 0.00 39.66 5.01
21 22 1.477014 GGACCTAATAGCCTTGGTGCC 60.477 57.143 0.00 0.00 35.34 5.01
22 23 0.551396 ACCTAATAGCCTTGGTGCCC 59.449 55.000 0.00 0.00 0.00 5.36
23 24 0.846693 CCTAATAGCCTTGGTGCCCT 59.153 55.000 0.00 0.00 0.00 5.19
24 25 1.215423 CCTAATAGCCTTGGTGCCCTT 59.785 52.381 0.00 0.00 0.00 3.95
25 26 2.576615 CTAATAGCCTTGGTGCCCTTC 58.423 52.381 0.00 0.00 0.00 3.46
26 27 1.002857 AATAGCCTTGGTGCCCTTCT 58.997 50.000 0.00 0.00 0.00 2.85
27 28 0.548510 ATAGCCTTGGTGCCCTTCTC 59.451 55.000 0.00 0.00 0.00 2.87
28 29 1.899437 TAGCCTTGGTGCCCTTCTCG 61.899 60.000 0.00 0.00 0.00 4.04
29 30 2.045926 CCTTGGTGCCCTTCTCGG 60.046 66.667 0.00 0.00 0.00 4.63
30 31 2.592993 CCTTGGTGCCCTTCTCGGA 61.593 63.158 0.00 0.00 33.16 4.55
31 32 1.604378 CTTGGTGCCCTTCTCGGAT 59.396 57.895 0.00 0.00 33.16 4.18
32 33 0.830648 CTTGGTGCCCTTCTCGGATA 59.169 55.000 0.00 0.00 33.16 2.59
33 34 0.539986 TTGGTGCCCTTCTCGGATAC 59.460 55.000 0.00 0.00 33.16 2.24
34 35 1.335132 TGGTGCCCTTCTCGGATACC 61.335 60.000 0.00 0.00 38.39 2.73
35 36 1.446366 GTGCCCTTCTCGGATACCC 59.554 63.158 0.00 0.00 33.16 3.69
36 37 1.764854 TGCCCTTCTCGGATACCCC 60.765 63.158 0.00 0.00 33.16 4.95
37 38 1.764854 GCCCTTCTCGGATACCCCA 60.765 63.158 0.00 0.00 33.16 4.96
38 39 1.342672 GCCCTTCTCGGATACCCCAA 61.343 60.000 0.00 0.00 33.16 4.12
39 40 1.435256 CCCTTCTCGGATACCCCAAT 58.565 55.000 0.00 0.00 33.16 3.16
63 64 4.579454 TTTCTTTCTCGGTCTTCTTCGA 57.421 40.909 0.00 0.00 0.00 3.71
141 142 0.895530 CTGGGCTCGGTCAGTTCTTA 59.104 55.000 0.00 0.00 0.00 2.10
145 146 1.672145 GGCTCGGTCAGTTCTTACACC 60.672 57.143 0.00 0.00 0.00 4.16
218 219 0.528470 CTCCGTCTTGGTCACCTCTC 59.472 60.000 0.00 0.00 39.52 3.20
240 242 2.045926 CCCCAGTCTTGGCCTTCG 60.046 66.667 3.32 0.00 43.58 3.79
268 296 0.454620 GGCGAGCCATACGACTATCG 60.455 60.000 9.58 0.00 40.03 2.92
281 309 3.757493 ACGACTATCGACTCCTTGAACTT 59.243 43.478 5.04 0.00 43.74 2.66
312 340 4.381505 GCCTTCTTCTCTAGGTCAGACAAG 60.382 50.000 2.17 0.00 32.20 3.16
314 342 5.245075 CCTTCTTCTCTAGGTCAGACAAGTT 59.755 44.000 2.17 0.00 32.65 2.66
556 585 8.311836 TCCTAATTTTGTCGTCTGAGACTTAAT 58.688 33.333 11.26 0.76 41.47 1.40
557 586 9.582431 CCTAATTTTGTCGTCTGAGACTTAATA 57.418 33.333 11.26 0.00 41.47 0.98
623 657 9.681692 CTGAGTTTGATTTAACACATTTCATGA 57.318 29.630 0.00 0.00 30.22 3.07
629 663 1.909700 AACACATTTCATGAGGGCGT 58.090 45.000 0.00 0.00 0.00 5.68
649 683 8.574737 AGGGCGTTATAAGTACATCTTAGTAAG 58.425 37.037 3.29 3.29 41.22 2.34
922 959 9.117183 TGAGTATCTCACGTACTAATAACACAT 57.883 33.333 0.00 0.00 35.39 3.21
982 1203 6.425417 GGAAGAAGAATAGATTTCCACGATCC 59.575 42.308 0.00 0.00 37.75 3.36
984 1205 6.889198 AGAAGAATAGATTTCCACGATCCAA 58.111 36.000 0.00 0.00 0.00 3.53
985 1206 6.763610 AGAAGAATAGATTTCCACGATCCAAC 59.236 38.462 0.00 0.00 0.00 3.77
986 1207 6.240549 AGAATAGATTTCCACGATCCAACT 57.759 37.500 0.00 0.00 0.00 3.16
1159 3469 2.480037 TCTCGCATTGTGCACTAACAAG 59.520 45.455 19.41 8.65 45.36 3.16
1160 3470 2.217750 TCGCATTGTGCACTAACAAGT 58.782 42.857 19.41 0.00 45.36 3.16
1161 3471 2.616376 TCGCATTGTGCACTAACAAGTT 59.384 40.909 19.41 0.00 45.36 2.66
1162 3472 3.810386 TCGCATTGTGCACTAACAAGTTA 59.190 39.130 19.41 0.00 45.36 2.24
1171 3481 7.825681 TGTGCACTAACAAGTTAATATTGCAT 58.174 30.769 19.41 0.00 0.00 3.96
1218 3528 1.473278 GTCGTCCTGTGGTTAGAGGAG 59.527 57.143 0.00 0.00 46.11 3.69
1219 3529 0.818296 CGTCCTGTGGTTAGAGGAGG 59.182 60.000 0.00 0.00 46.11 4.30
1220 3530 2.233305 GTCCTGTGGTTAGAGGAGGA 57.767 55.000 0.00 0.00 46.11 3.71
1235 3545 0.392327 GAGGAAGCCACCAAGAGAGC 60.392 60.000 0.00 0.00 0.00 4.09
1247 3557 2.557056 CCAAGAGAGCCATGCCAATATG 59.443 50.000 0.00 0.00 0.00 1.78
1291 3601 0.627307 GATTCGTCGTCGTCGTCAAC 59.373 55.000 11.41 0.00 38.33 3.18
1349 3671 3.123050 GGACTGCAACAATCCAAACAAC 58.877 45.455 0.00 0.00 32.35 3.32
1462 3784 2.336945 TGCCATCCTACTTGCTGATG 57.663 50.000 0.00 0.00 36.49 3.07
1463 3785 1.839354 TGCCATCCTACTTGCTGATGA 59.161 47.619 0.00 0.00 38.49 2.92
1464 3786 2.440627 TGCCATCCTACTTGCTGATGAT 59.559 45.455 0.00 0.00 38.49 2.45
1467 3789 5.221986 TGCCATCCTACTTGCTGATGATATT 60.222 40.000 0.00 0.00 38.49 1.28
1504 3830 3.487574 GCTGCGATGTAAAGCTACTAGTG 59.512 47.826 5.39 0.00 34.05 2.74
1519 3845 2.231964 ACTAGTGCGGTGTTATTCGGAA 59.768 45.455 0.00 0.00 0.00 4.30
1565 3893 2.969950 ACACACTAGCTTTCCCACTACA 59.030 45.455 0.00 0.00 0.00 2.74
1566 3894 3.244112 ACACACTAGCTTTCCCACTACAC 60.244 47.826 0.00 0.00 0.00 2.90
1616 3946 9.524106 AAACATGAAATATGTACGATCGAGTTA 57.476 29.630 24.34 8.09 0.00 2.24
1621 3951 5.943706 ATATGTACGATCGAGTTAGTGCT 57.056 39.130 24.34 0.00 0.00 4.40
1648 3978 8.972127 GCCAGTCTGGTAATATCTAGATGAATA 58.028 37.037 20.24 3.03 40.46 1.75
1651 3981 8.898761 AGTCTGGTAATATCTAGATGAATAGCG 58.101 37.037 15.79 10.46 0.00 4.26
1675 4005 8.219769 GCGAGTGTTCATGATTAAAGATATGAG 58.780 37.037 0.00 0.00 31.85 2.90
1682 4012 7.445121 TCATGATTAAAGATATGAGCGAAGGT 58.555 34.615 0.00 0.00 46.54 3.50
1732 4062 5.143376 CATTGTCAATGCCCTCTCTTTTT 57.857 39.130 12.50 0.00 31.20 1.94
1777 4107 9.871238 TCTTTTGTCAATATTGGTCTAGTACTC 57.129 33.333 15.36 0.00 0.00 2.59
1778 4108 9.877178 CTTTTGTCAATATTGGTCTAGTACTCT 57.123 33.333 15.36 0.00 0.00 3.24
1797 4127 4.268720 TTTTTCTGGCCGCCTTGT 57.731 50.000 11.61 0.00 0.00 3.16
1798 4128 2.037871 TTTTTCTGGCCGCCTTGTC 58.962 52.632 11.61 0.00 0.00 3.18
1799 4129 1.460273 TTTTTCTGGCCGCCTTGTCC 61.460 55.000 11.61 0.00 0.00 4.02
1800 4130 2.351924 TTTTCTGGCCGCCTTGTCCT 62.352 55.000 11.61 0.00 0.00 3.85
1801 4131 2.748058 TTTCTGGCCGCCTTGTCCTC 62.748 60.000 11.61 0.00 0.00 3.71
1802 4132 4.785453 CTGGCCGCCTTGTCCTCC 62.785 72.222 11.61 0.00 0.00 4.30
1806 4136 3.382832 CCGCCTTGTCCTCCGTCT 61.383 66.667 0.00 0.00 0.00 4.18
1807 4137 2.050350 CCGCCTTGTCCTCCGTCTA 61.050 63.158 0.00 0.00 0.00 2.59
1808 4138 1.392710 CCGCCTTGTCCTCCGTCTAT 61.393 60.000 0.00 0.00 0.00 1.98
1809 4139 0.030908 CGCCTTGTCCTCCGTCTATC 59.969 60.000 0.00 0.00 0.00 2.08
1810 4140 0.030908 GCCTTGTCCTCCGTCTATCG 59.969 60.000 0.00 0.00 39.52 2.92
1811 4141 1.390565 CCTTGTCCTCCGTCTATCGT 58.609 55.000 0.00 0.00 37.94 3.73
1812 4142 2.569059 CCTTGTCCTCCGTCTATCGTA 58.431 52.381 0.00 0.00 37.94 3.43
1813 4143 2.947652 CCTTGTCCTCCGTCTATCGTAA 59.052 50.000 0.00 0.00 37.94 3.18
1814 4144 3.379372 CCTTGTCCTCCGTCTATCGTAAA 59.621 47.826 0.00 0.00 37.94 2.01
1815 4145 4.349501 CTTGTCCTCCGTCTATCGTAAAC 58.650 47.826 0.00 0.00 37.94 2.01
1816 4146 2.684881 TGTCCTCCGTCTATCGTAAACC 59.315 50.000 0.00 0.00 37.94 3.27
1817 4147 2.033927 GTCCTCCGTCTATCGTAAACCC 59.966 54.545 0.00 0.00 37.94 4.11
1818 4148 2.092212 TCCTCCGTCTATCGTAAACCCT 60.092 50.000 0.00 0.00 37.94 4.34
1819 4149 2.692041 CCTCCGTCTATCGTAAACCCTT 59.308 50.000 0.00 0.00 37.94 3.95
1820 4150 3.243334 CCTCCGTCTATCGTAAACCCTTC 60.243 52.174 0.00 0.00 37.94 3.46
1821 4151 3.355378 TCCGTCTATCGTAAACCCTTCA 58.645 45.455 0.00 0.00 37.94 3.02
1822 4152 3.956199 TCCGTCTATCGTAAACCCTTCAT 59.044 43.478 0.00 0.00 37.94 2.57
1823 4153 4.037208 TCCGTCTATCGTAAACCCTTCATC 59.963 45.833 0.00 0.00 37.94 2.92
1824 4154 4.296690 CGTCTATCGTAAACCCTTCATCC 58.703 47.826 0.00 0.00 34.52 3.51
1825 4155 4.629092 GTCTATCGTAAACCCTTCATCCC 58.371 47.826 0.00 0.00 0.00 3.85
1826 4156 2.614829 ATCGTAAACCCTTCATCCCG 57.385 50.000 0.00 0.00 0.00 5.14
1827 4157 1.559368 TCGTAAACCCTTCATCCCGA 58.441 50.000 0.00 0.00 0.00 5.14
1828 4158 1.205417 TCGTAAACCCTTCATCCCGAC 59.795 52.381 0.00 0.00 0.00 4.79
1829 4159 1.066716 CGTAAACCCTTCATCCCGACA 60.067 52.381 0.00 0.00 0.00 4.35
1830 4160 2.613474 CGTAAACCCTTCATCCCGACAA 60.613 50.000 0.00 0.00 0.00 3.18
1831 4161 2.668144 AAACCCTTCATCCCGACAAA 57.332 45.000 0.00 0.00 0.00 2.83
1832 4162 2.668144 AACCCTTCATCCCGACAAAA 57.332 45.000 0.00 0.00 0.00 2.44
1833 4163 2.668144 ACCCTTCATCCCGACAAAAA 57.332 45.000 0.00 0.00 0.00 1.94
1834 4164 3.169512 ACCCTTCATCCCGACAAAAAT 57.830 42.857 0.00 0.00 0.00 1.82
1835 4165 3.089284 ACCCTTCATCCCGACAAAAATC 58.911 45.455 0.00 0.00 0.00 2.17
1836 4166 2.427095 CCCTTCATCCCGACAAAAATCC 59.573 50.000 0.00 0.00 0.00 3.01
1837 4167 3.356290 CCTTCATCCCGACAAAAATCCT 58.644 45.455 0.00 0.00 0.00 3.24
1847 4177 5.455392 CCGACAAAAATCCTCATATGATGC 58.545 41.667 5.72 0.00 0.00 3.91
1850 4180 6.854892 CGACAAAAATCCTCATATGATGCTTC 59.145 38.462 5.72 0.00 0.00 3.86
1852 4182 6.543465 ACAAAAATCCTCATATGATGCTTCGA 59.457 34.615 5.72 0.00 0.00 3.71
1853 4183 6.798315 AAAATCCTCATATGATGCTTCGAG 57.202 37.500 5.72 0.00 0.00 4.04
1854 4184 5.735285 AATCCTCATATGATGCTTCGAGA 57.265 39.130 5.72 0.00 0.00 4.04
1855 4185 4.780275 TCCTCATATGATGCTTCGAGAG 57.220 45.455 5.72 4.49 0.00 3.20
1856 4186 4.401925 TCCTCATATGATGCTTCGAGAGA 58.598 43.478 5.72 0.00 39.20 3.10
1857 4187 4.217334 TCCTCATATGATGCTTCGAGAGAC 59.783 45.833 5.72 0.00 41.84 3.36
1897 4268 3.181471 ACATAGCTATGCTCAGTTCGCTT 60.181 43.478 29.60 6.46 40.44 4.68
1898 4269 1.933247 AGCTATGCTCAGTTCGCTTC 58.067 50.000 0.00 0.00 30.62 3.86
1899 4270 0.933796 GCTATGCTCAGTTCGCTTCC 59.066 55.000 0.00 0.00 0.00 3.46
1900 4271 1.740380 GCTATGCTCAGTTCGCTTCCA 60.740 52.381 0.00 0.00 0.00 3.53
1901 4272 1.929836 CTATGCTCAGTTCGCTTCCAC 59.070 52.381 0.00 0.00 0.00 4.02
1937 4367 2.665000 GCCTACAGCAGTGCCTCA 59.335 61.111 12.58 0.00 42.97 3.86
1952 4382 2.986979 TCACGCGTGTAGCTGGGA 60.987 61.111 35.74 13.93 45.59 4.37
1960 4390 0.543749 GTGTAGCTGGGAGGCAGATT 59.456 55.000 0.00 0.00 34.17 2.40
1961 4391 1.065126 GTGTAGCTGGGAGGCAGATTT 60.065 52.381 0.00 0.00 34.17 2.17
1972 4402 1.152881 GCAGATTTGGGCGGATCCT 60.153 57.895 10.75 0.00 34.39 3.24
2083 4529 0.679960 AGCCGCCAAAGTTGTATCCC 60.680 55.000 0.00 0.00 0.00 3.85
2087 4533 1.816074 GCCAAAGTTGTATCCCGACA 58.184 50.000 0.00 0.00 0.00 4.35
2130 4577 1.221840 TCCCGCATGAGGAGAAAGC 59.778 57.895 18.16 0.00 0.00 3.51
2138 4585 0.250901 TGAGGAGAAAGCCACCTTGC 60.251 55.000 0.00 0.00 33.89 4.01
2140 4587 2.335712 GGAGAAAGCCACCTTGCCG 61.336 63.158 0.00 0.00 0.00 5.69
2141 4588 2.282462 AGAAAGCCACCTTGCCGG 60.282 61.111 0.00 0.00 39.35 6.13
2151 4598 3.055719 CTTGCCGGCACCGAACAT 61.056 61.111 32.95 0.00 42.83 2.71
2152 4599 3.326889 CTTGCCGGCACCGAACATG 62.327 63.158 32.95 8.01 42.83 3.21
2155 4602 3.055719 CCGGCACCGAACATGCTT 61.056 61.111 11.42 0.00 42.93 3.91
2156 4603 2.480555 CGGCACCGAACATGCTTC 59.519 61.111 2.01 0.00 42.93 3.86
2157 4604 2.324330 CGGCACCGAACATGCTTCA 61.324 57.895 2.01 0.00 42.93 3.02
2158 4605 1.210155 GGCACCGAACATGCTTCAC 59.790 57.895 0.00 0.00 42.93 3.18
2159 4606 1.154413 GCACCGAACATGCTTCACG 60.154 57.895 0.00 0.00 40.08 4.35
2160 4607 1.841663 GCACCGAACATGCTTCACGT 61.842 55.000 0.00 0.00 40.08 4.49
2161 4608 0.110688 CACCGAACATGCTTCACGTG 60.111 55.000 9.94 9.94 41.41 4.49
2166 4613 4.465512 CATGCTTCACGTGGGCGC 62.466 66.667 17.00 15.61 42.83 6.53
2204 4654 2.760385 CGAGGGAGGGGAGTGGAC 60.760 72.222 0.00 0.00 0.00 4.02
2260 4711 3.553095 GAAGCCCGTGCAAGGAGGT 62.553 63.158 21.23 12.63 41.13 3.85
2261 4712 3.133365 AAGCCCGTGCAAGGAGGTT 62.133 57.895 21.23 17.52 41.13 3.50
2284 4735 3.526931 TTTTCCGATCGAGAGCAATCT 57.473 42.857 18.66 0.00 0.00 2.40
2285 4736 2.783828 TTCCGATCGAGAGCAATCTC 57.216 50.000 18.66 0.00 39.65 2.75
2295 4746 3.444703 AGAGCAATCTCTCGCGTATTT 57.555 42.857 5.77 0.00 46.32 1.40
2296 4747 3.786635 AGAGCAATCTCTCGCGTATTTT 58.213 40.909 5.77 0.00 46.32 1.82
2297 4748 4.933330 AGAGCAATCTCTCGCGTATTTTA 58.067 39.130 5.77 0.00 46.32 1.52
2298 4749 4.740695 AGAGCAATCTCTCGCGTATTTTAC 59.259 41.667 5.77 0.00 46.32 2.01
2299 4750 4.683832 AGCAATCTCTCGCGTATTTTACT 58.316 39.130 5.77 0.00 0.00 2.24
2300 4751 5.828747 AGCAATCTCTCGCGTATTTTACTA 58.171 37.500 5.77 0.00 0.00 1.82
2301 4752 6.270815 AGCAATCTCTCGCGTATTTTACTAA 58.729 36.000 5.77 0.00 0.00 2.24
2302 4753 6.755141 AGCAATCTCTCGCGTATTTTACTAAA 59.245 34.615 5.77 0.00 0.00 1.85
2303 4754 7.043325 AGCAATCTCTCGCGTATTTTACTAAAG 60.043 37.037 5.77 0.00 0.00 1.85
2304 4755 7.556433 CAATCTCTCGCGTATTTTACTAAAGG 58.444 38.462 5.77 0.00 0.00 3.11
2305 4756 6.441093 TCTCTCGCGTATTTTACTAAAGGA 57.559 37.500 5.77 0.00 0.00 3.36
2306 4757 6.855836 TCTCTCGCGTATTTTACTAAAGGAA 58.144 36.000 5.77 0.00 0.00 3.36
2307 4758 6.749118 TCTCTCGCGTATTTTACTAAAGGAAC 59.251 38.462 5.77 0.00 0.00 3.62
2308 4759 6.389091 TCTCGCGTATTTTACTAAAGGAACA 58.611 36.000 5.77 0.00 0.00 3.18
2309 4760 6.308766 TCTCGCGTATTTTACTAAAGGAACAC 59.691 38.462 5.77 0.00 0.00 3.32
2310 4761 5.060816 TCGCGTATTTTACTAAAGGAACACG 59.939 40.000 5.77 0.00 0.00 4.49
2311 4762 5.060816 CGCGTATTTTACTAAAGGAACACGA 59.939 40.000 0.00 0.00 0.00 4.35
2312 4763 6.464311 GCGTATTTTACTAAAGGAACACGAG 58.536 40.000 0.00 0.00 0.00 4.18
2313 4764 6.464311 CGTATTTTACTAAAGGAACACGAGC 58.536 40.000 0.00 0.00 0.00 5.03
2314 4765 6.089820 CGTATTTTACTAAAGGAACACGAGCA 59.910 38.462 0.00 0.00 0.00 4.26
2315 4766 5.917541 TTTTACTAAAGGAACACGAGCAG 57.082 39.130 0.00 0.00 0.00 4.24
2316 4767 4.859304 TTACTAAAGGAACACGAGCAGA 57.141 40.909 0.00 0.00 0.00 4.26
2317 4768 3.746045 ACTAAAGGAACACGAGCAGAA 57.254 42.857 0.00 0.00 0.00 3.02
2318 4769 4.067972 ACTAAAGGAACACGAGCAGAAA 57.932 40.909 0.00 0.00 0.00 2.52
2319 4770 3.808174 ACTAAAGGAACACGAGCAGAAAC 59.192 43.478 0.00 0.00 0.00 2.78
2320 4771 2.325583 AAGGAACACGAGCAGAAACA 57.674 45.000 0.00 0.00 0.00 2.83
2321 4772 2.550830 AGGAACACGAGCAGAAACAT 57.449 45.000 0.00 0.00 0.00 2.71
2322 4773 2.146342 AGGAACACGAGCAGAAACATG 58.854 47.619 0.00 0.00 0.00 3.21
2323 4774 2.143122 GGAACACGAGCAGAAACATGA 58.857 47.619 0.00 0.00 0.00 3.07
2324 4775 2.548057 GGAACACGAGCAGAAACATGAA 59.452 45.455 0.00 0.00 0.00 2.57
2325 4776 3.003275 GGAACACGAGCAGAAACATGAAA 59.997 43.478 0.00 0.00 0.00 2.69
2326 4777 4.497340 GGAACACGAGCAGAAACATGAAAA 60.497 41.667 0.00 0.00 0.00 2.29
2327 4778 3.952535 ACACGAGCAGAAACATGAAAAC 58.047 40.909 0.00 0.00 0.00 2.43
2328 4779 2.966708 CACGAGCAGAAACATGAAAACG 59.033 45.455 0.00 0.00 0.00 3.60
2329 4780 2.869801 ACGAGCAGAAACATGAAAACGA 59.130 40.909 0.00 0.00 0.00 3.85
2330 4781 3.311322 ACGAGCAGAAACATGAAAACGAA 59.689 39.130 0.00 0.00 0.00 3.85
2331 4782 4.201871 ACGAGCAGAAACATGAAAACGAAA 60.202 37.500 0.00 0.00 0.00 3.46
2332 4783 4.732923 CGAGCAGAAACATGAAAACGAAAA 59.267 37.500 0.00 0.00 0.00 2.29
2333 4784 5.229052 CGAGCAGAAACATGAAAACGAAAAA 59.771 36.000 0.00 0.00 0.00 1.94
2334 4785 6.558433 CGAGCAGAAACATGAAAACGAAAAAG 60.558 38.462 0.00 0.00 0.00 2.27
2335 4786 6.099341 AGCAGAAACATGAAAACGAAAAAGT 58.901 32.000 0.00 0.00 0.00 2.66
2336 4787 7.254852 AGCAGAAACATGAAAACGAAAAAGTA 58.745 30.769 0.00 0.00 0.00 2.24
2337 4788 7.432252 AGCAGAAACATGAAAACGAAAAAGTAG 59.568 33.333 0.00 0.00 0.00 2.57
2338 4789 7.431084 GCAGAAACATGAAAACGAAAAAGTAGA 59.569 33.333 0.00 0.00 0.00 2.59
2339 4790 9.284594 CAGAAACATGAAAACGAAAAAGTAGAA 57.715 29.630 0.00 0.00 0.00 2.10
2340 4791 9.849166 AGAAACATGAAAACGAAAAAGTAGAAA 57.151 25.926 0.00 0.00 0.00 2.52
2344 4795 9.849166 ACATGAAAACGAAAAAGTAGAAAAAGA 57.151 25.926 0.00 0.00 0.00 2.52
2347 4798 9.769093 TGAAAACGAAAAAGTAGAAAAAGAGAG 57.231 29.630 0.00 0.00 0.00 3.20
2348 4799 9.983804 GAAAACGAAAAAGTAGAAAAAGAGAGA 57.016 29.630 0.00 0.00 0.00 3.10
2352 4803 9.989869 ACGAAAAAGTAGAAAAAGAGAGAAAAG 57.010 29.630 0.00 0.00 0.00 2.27
2353 4804 9.439537 CGAAAAAGTAGAAAAAGAGAGAAAAGG 57.560 33.333 0.00 0.00 0.00 3.11
2358 4809 9.462606 AAGTAGAAAAAGAGAGAAAAGGAAACA 57.537 29.630 0.00 0.00 0.00 2.83
2359 4810 9.114952 AGTAGAAAAAGAGAGAAAAGGAAACAG 57.885 33.333 0.00 0.00 0.00 3.16
2360 4811 6.800543 AGAAAAAGAGAGAAAAGGAAACAGC 58.199 36.000 0.00 0.00 0.00 4.40
2361 4812 6.378280 AGAAAAAGAGAGAAAAGGAAACAGCA 59.622 34.615 0.00 0.00 0.00 4.41
2362 4813 6.530019 AAAAGAGAGAAAAGGAAACAGCAA 57.470 33.333 0.00 0.00 0.00 3.91
2363 4814 6.530019 AAAGAGAGAAAAGGAAACAGCAAA 57.470 33.333 0.00 0.00 0.00 3.68
2364 4815 6.530019 AAGAGAGAAAAGGAAACAGCAAAA 57.470 33.333 0.00 0.00 0.00 2.44
2365 4816 6.141560 AGAGAGAAAAGGAAACAGCAAAAG 57.858 37.500 0.00 0.00 0.00 2.27
2366 4817 4.686972 AGAGAAAAGGAAACAGCAAAAGC 58.313 39.130 0.00 0.00 0.00 3.51
2367 4818 3.797039 AGAAAAGGAAACAGCAAAAGCC 58.203 40.909 0.00 0.00 0.00 4.35
2368 4819 2.620251 AAAGGAAACAGCAAAAGCCC 57.380 45.000 0.00 0.00 0.00 5.19
2369 4820 1.494960 AAGGAAACAGCAAAAGCCCA 58.505 45.000 0.00 0.00 0.00 5.36
2370 4821 1.720781 AGGAAACAGCAAAAGCCCAT 58.279 45.000 0.00 0.00 0.00 4.00
2371 4822 2.888212 AGGAAACAGCAAAAGCCCATA 58.112 42.857 0.00 0.00 0.00 2.74
2372 4823 2.827921 AGGAAACAGCAAAAGCCCATAG 59.172 45.455 0.00 0.00 0.00 2.23
2373 4824 2.094026 GGAAACAGCAAAAGCCCATAGG 60.094 50.000 0.00 0.00 0.00 2.57
2387 4838 2.633481 CCCATAGGCCAGTACTTACTCC 59.367 54.545 5.01 0.00 33.46 3.85
2388 4839 2.296471 CCATAGGCCAGTACTTACTCCG 59.704 54.545 5.01 0.00 33.46 4.63
2389 4840 3.220110 CATAGGCCAGTACTTACTCCGA 58.780 50.000 5.01 0.00 33.46 4.55
2390 4841 1.472188 AGGCCAGTACTTACTCCGAC 58.528 55.000 5.01 0.00 33.46 4.79
2391 4842 1.005687 AGGCCAGTACTTACTCCGACT 59.994 52.381 5.01 0.00 33.46 4.18
2392 4843 1.823610 GGCCAGTACTTACTCCGACTT 59.176 52.381 0.00 0.00 33.46 3.01
2393 4844 2.159268 GGCCAGTACTTACTCCGACTTC 60.159 54.545 0.00 0.00 33.46 3.01
2394 4845 2.490903 GCCAGTACTTACTCCGACTTCA 59.509 50.000 0.00 0.00 33.46 3.02
2395 4846 3.130693 GCCAGTACTTACTCCGACTTCAT 59.869 47.826 0.00 0.00 33.46 2.57
2396 4847 4.337555 GCCAGTACTTACTCCGACTTCATA 59.662 45.833 0.00 0.00 33.46 2.15
2397 4848 5.163581 GCCAGTACTTACTCCGACTTCATAA 60.164 44.000 0.00 0.00 33.46 1.90
2398 4849 6.461231 GCCAGTACTTACTCCGACTTCATAAT 60.461 42.308 0.00 0.00 33.46 1.28
2399 4850 7.255381 GCCAGTACTTACTCCGACTTCATAATA 60.255 40.741 0.00 0.00 33.46 0.98
2400 4851 8.627403 CCAGTACTTACTCCGACTTCATAATAA 58.373 37.037 0.00 0.00 33.46 1.40
2403 4854 9.327529 GTACTTACTCCGACTTCATAATAATCG 57.672 37.037 0.00 0.00 0.00 3.34
2404 4855 8.162878 ACTTACTCCGACTTCATAATAATCGA 57.837 34.615 0.00 0.00 34.77 3.59
2405 4856 8.291032 ACTTACTCCGACTTCATAATAATCGAG 58.709 37.037 0.00 0.00 34.77 4.04
2406 4857 6.879276 ACTCCGACTTCATAATAATCGAGA 57.121 37.500 0.00 0.00 34.77 4.04
2407 4858 7.455641 ACTCCGACTTCATAATAATCGAGAT 57.544 36.000 0.00 0.00 34.77 2.75
2408 4859 8.563123 ACTCCGACTTCATAATAATCGAGATA 57.437 34.615 0.00 0.00 34.77 1.98
2409 4860 9.179909 ACTCCGACTTCATAATAATCGAGATAT 57.820 33.333 0.00 0.00 34.77 1.63
2411 4862 9.788960 TCCGACTTCATAATAATCGAGATATTG 57.211 33.333 13.65 2.83 34.77 1.90
2412 4863 8.535592 CCGACTTCATAATAATCGAGATATTGC 58.464 37.037 13.65 0.00 34.77 3.56
2413 4864 9.295214 CGACTTCATAATAATCGAGATATTGCT 57.705 33.333 13.65 2.45 34.77 3.91
2423 4874 7.849804 AATCGAGATATTGCTTTTGTAGTGT 57.150 32.000 0.00 0.00 0.00 3.55
2424 4875 6.647212 TCGAGATATTGCTTTTGTAGTGTG 57.353 37.500 0.00 0.00 0.00 3.82
2425 4876 5.063438 TCGAGATATTGCTTTTGTAGTGTGC 59.937 40.000 0.00 0.00 0.00 4.57
2426 4877 5.163864 CGAGATATTGCTTTTGTAGTGTGCA 60.164 40.000 0.00 0.00 0.00 4.57
2427 4878 6.573664 AGATATTGCTTTTGTAGTGTGCAA 57.426 33.333 0.00 0.00 45.62 4.08
2449 4900 9.300681 TGCAATATAATTATCTCTTTTCCAGGG 57.699 33.333 0.00 0.00 0.00 4.45
2450 4901 9.520515 GCAATATAATTATCTCTTTTCCAGGGA 57.479 33.333 0.00 0.00 35.97 4.20
2456 4907 8.759481 AATTATCTCTTTTCCAGGGAATCTTC 57.241 34.615 0.83 0.00 34.75 2.87
2457 4908 7.516450 TTATCTCTTTTCCAGGGAATCTTCT 57.484 36.000 0.83 0.00 34.75 2.85
2458 4909 8.624019 TTATCTCTTTTCCAGGGAATCTTCTA 57.376 34.615 0.83 0.00 34.75 2.10
2459 4910 6.301169 TCTCTTTTCCAGGGAATCTTCTAC 57.699 41.667 0.83 0.00 33.79 2.59
2460 4911 6.026186 TCTCTTTTCCAGGGAATCTTCTACT 58.974 40.000 0.83 0.00 33.79 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.477014 GCACCAAGGCTATTAGGTCCC 60.477 57.143 0.00 0.00 30.44 4.46
1 2 1.477014 GGCACCAAGGCTATTAGGTCC 60.477 57.143 0.00 0.00 40.24 4.46
2 3 1.968704 GGCACCAAGGCTATTAGGTC 58.031 55.000 0.00 0.00 40.24 3.85
17 18 1.446366 GGGTATCCGAGAAGGGCAC 59.554 63.158 0.00 0.00 41.52 5.01
18 19 1.764854 GGGGTATCCGAGAAGGGCA 60.765 63.158 0.00 0.00 41.52 5.36
19 20 1.342672 TTGGGGTATCCGAGAAGGGC 61.343 60.000 0.00 0.00 41.52 5.19
20 21 1.072331 CATTGGGGTATCCGAGAAGGG 59.928 57.143 0.00 0.00 41.52 3.95
21 22 2.047061 TCATTGGGGTATCCGAGAAGG 58.953 52.381 0.00 0.00 42.97 3.46
22 23 4.357918 AATCATTGGGGTATCCGAGAAG 57.642 45.455 0.00 0.00 38.76 2.85
23 24 4.412199 AGAAATCATTGGGGTATCCGAGAA 59.588 41.667 0.00 0.00 38.76 2.87
24 25 3.973973 AGAAATCATTGGGGTATCCGAGA 59.026 43.478 0.00 0.00 38.76 4.04
25 26 4.357918 AGAAATCATTGGGGTATCCGAG 57.642 45.455 0.00 0.00 38.76 4.63
26 27 4.788925 AAGAAATCATTGGGGTATCCGA 57.211 40.909 0.00 0.00 38.76 4.55
27 28 5.133221 AGAAAGAAATCATTGGGGTATCCG 58.867 41.667 0.00 0.00 38.76 4.18
28 29 5.239525 CGAGAAAGAAATCATTGGGGTATCC 59.760 44.000 0.00 0.00 0.00 2.59
29 30 5.239525 CCGAGAAAGAAATCATTGGGGTATC 59.760 44.000 0.00 0.00 0.00 2.24
30 31 5.133221 CCGAGAAAGAAATCATTGGGGTAT 58.867 41.667 0.00 0.00 0.00 2.73
31 32 4.018779 ACCGAGAAAGAAATCATTGGGGTA 60.019 41.667 0.00 0.00 0.00 3.69
32 33 3.245264 ACCGAGAAAGAAATCATTGGGGT 60.245 43.478 0.00 0.00 0.00 4.95
33 34 3.356290 ACCGAGAAAGAAATCATTGGGG 58.644 45.455 0.00 0.00 0.00 4.96
34 35 4.265073 AGACCGAGAAAGAAATCATTGGG 58.735 43.478 0.00 0.00 0.00 4.12
35 36 5.645497 AGAAGACCGAGAAAGAAATCATTGG 59.355 40.000 0.00 0.00 0.00 3.16
36 37 6.734104 AGAAGACCGAGAAAGAAATCATTG 57.266 37.500 0.00 0.00 0.00 2.82
37 38 6.091441 CGAAGAAGACCGAGAAAGAAATCATT 59.909 38.462 0.00 0.00 0.00 2.57
38 39 5.578727 CGAAGAAGACCGAGAAAGAAATCAT 59.421 40.000 0.00 0.00 0.00 2.45
39 40 4.923871 CGAAGAAGACCGAGAAAGAAATCA 59.076 41.667 0.00 0.00 0.00 2.57
90 91 1.301293 GCAGTAGCCAAGGAGCCTT 59.699 57.895 0.00 0.00 36.60 4.35
124 125 0.606604 TGTAAGAACTGACCGAGCCC 59.393 55.000 0.00 0.00 0.00 5.19
141 142 2.930826 AGTGAAGGATCAAACGGTGT 57.069 45.000 0.00 0.00 37.30 4.16
145 146 3.941483 AGCCAATAGTGAAGGATCAAACG 59.059 43.478 0.00 0.00 37.30 3.60
146 147 4.336713 GGAGCCAATAGTGAAGGATCAAAC 59.663 45.833 0.00 0.00 39.51 2.93
258 286 4.511527 AGTTCAAGGAGTCGATAGTCGTA 58.488 43.478 0.00 0.00 41.35 3.43
268 296 3.053455 CACTCGACAAGTTCAAGGAGTC 58.947 50.000 0.00 0.00 35.45 3.36
281 309 1.621992 AGAGAAGAAGGCACTCGACA 58.378 50.000 0.00 0.00 38.49 4.35
312 340 2.701107 GAGAGAAACCTAGTGGCCAAC 58.299 52.381 7.24 1.26 36.63 3.77
314 342 0.895530 CGAGAGAAACCTAGTGGCCA 59.104 55.000 0.00 0.00 36.63 5.36
558 587 8.186821 GCTTACTGATGAGCAATTCTACATTTT 58.813 33.333 0.00 0.00 37.40 1.82
559 588 7.337689 TGCTTACTGATGAGCAATTCTACATTT 59.662 33.333 0.00 0.00 43.94 2.32
623 657 6.973460 ACTAAGATGTACTTATAACGCCCT 57.027 37.500 0.00 0.00 39.86 5.19
649 683 5.010617 TGCAAGGGAGTTAAAATCTGGAAAC 59.989 40.000 0.00 0.00 0.00 2.78
764 799 7.446013 ACACTGAAAAGACAATAAATTACGGGA 59.554 33.333 0.00 0.00 0.00 5.14
797 832 5.713389 CCATATTTGCATCAGGGTGACATAT 59.287 40.000 0.00 0.00 0.00 1.78
798 833 5.072055 CCATATTTGCATCAGGGTGACATA 58.928 41.667 0.00 0.00 0.00 2.29
922 959 0.747852 TTGCCGATCACGCATAGGTA 59.252 50.000 5.37 0.00 38.29 3.08
982 1203 6.349115 CCTCTCATGGTTGATCTTCAAAGTTG 60.349 42.308 0.00 0.00 38.22 3.16
984 1205 5.251764 CCTCTCATGGTTGATCTTCAAAGT 58.748 41.667 0.00 0.00 38.22 2.66
985 1206 4.639310 CCCTCTCATGGTTGATCTTCAAAG 59.361 45.833 0.00 0.00 38.22 2.77
986 1207 4.289410 TCCCTCTCATGGTTGATCTTCAAA 59.711 41.667 0.00 0.00 38.22 2.69
1023 1244 1.153349 GAACAGGAGGGCGATCACC 60.153 63.158 0.00 0.00 0.00 4.02
1118 3424 0.973632 ACAACGTACTGGAGGCATCA 59.026 50.000 0.00 0.00 0.00 3.07
1119 3425 2.000447 GAACAACGTACTGGAGGCATC 59.000 52.381 0.00 0.00 0.00 3.91
1120 3426 1.623811 AGAACAACGTACTGGAGGCAT 59.376 47.619 0.00 0.00 0.00 4.40
1218 3528 1.377856 GGCTCTCTTGGTGGCTTCC 60.378 63.158 0.00 0.00 0.00 3.46
1219 3529 0.034670 ATGGCTCTCTTGGTGGCTTC 60.035 55.000 0.00 0.00 35.45 3.86
1220 3530 0.323178 CATGGCTCTCTTGGTGGCTT 60.323 55.000 0.00 0.00 35.45 4.35
1235 3545 1.031235 TTGCGGTCATATTGGCATGG 58.969 50.000 0.00 0.00 35.03 3.66
1291 3601 0.508641 CAACGTCAGTTTGCTCGAGG 59.491 55.000 15.58 0.00 38.79 4.63
1445 3767 7.551974 CCTAAATATCATCAGCAAGTAGGATGG 59.448 40.741 0.00 0.00 39.07 3.51
1462 3784 3.308866 AGCAACGAACACGCCTAAATATC 59.691 43.478 0.00 0.00 0.00 1.63
1463 3785 3.063452 CAGCAACGAACACGCCTAAATAT 59.937 43.478 0.00 0.00 0.00 1.28
1464 3786 2.413796 CAGCAACGAACACGCCTAAATA 59.586 45.455 0.00 0.00 0.00 1.40
1467 3789 1.837538 GCAGCAACGAACACGCCTAA 61.838 55.000 0.00 0.00 0.00 2.69
1504 3830 4.569564 AGTATTTCTTCCGAATAACACCGC 59.430 41.667 0.00 0.00 0.00 5.68
1591 3919 9.181805 CTAACTCGATCGTACATATTTCATGTT 57.818 33.333 15.94 0.00 33.76 2.71
1595 3923 6.635641 GCACTAACTCGATCGTACATATTTCA 59.364 38.462 15.94 0.00 0.00 2.69
1616 3946 0.987294 ATTACCAGACTGGCAGCACT 59.013 50.000 21.95 11.66 42.67 4.40
1621 3951 6.314917 TCATCTAGATATTACCAGACTGGCA 58.685 40.000 21.95 5.73 42.67 4.92
1648 3978 7.928167 TCATATCTTTAATCATGAACACTCGCT 59.072 33.333 0.00 0.00 0.00 4.93
1649 3979 8.076714 TCATATCTTTAATCATGAACACTCGC 57.923 34.615 0.00 0.00 0.00 5.03
1650 3980 8.219769 GCTCATATCTTTAATCATGAACACTCG 58.780 37.037 0.00 0.00 0.00 4.18
1651 3981 8.219769 CGCTCATATCTTTAATCATGAACACTC 58.780 37.037 0.00 0.00 0.00 3.51
1675 4005 5.266242 CACTATTAGCAAATTGACCTTCGC 58.734 41.667 0.00 0.00 0.00 4.70
1682 4012 5.448654 AGATGGGCACTATTAGCAAATTGA 58.551 37.500 0.00 0.00 0.00 2.57
1683 4013 5.779529 AGATGGGCACTATTAGCAAATTG 57.220 39.130 0.00 0.00 0.00 2.32
1688 4018 3.381272 GCAAAAGATGGGCACTATTAGCA 59.619 43.478 0.00 0.00 0.00 3.49
1692 4022 4.223477 ACAATGCAAAAGATGGGCACTATT 59.777 37.500 0.00 0.00 40.83 1.73
1780 4110 1.460273 GGACAAGGCGGCCAGAAAAA 61.460 55.000 23.09 0.00 0.00 1.94
1781 4111 1.901464 GGACAAGGCGGCCAGAAAA 60.901 57.895 23.09 0.00 0.00 2.29
1782 4112 2.282180 GGACAAGGCGGCCAGAAA 60.282 61.111 23.09 0.00 0.00 2.52
1783 4113 3.249189 AGGACAAGGCGGCCAGAA 61.249 61.111 23.09 0.00 0.00 3.02
1784 4114 3.706373 GAGGACAAGGCGGCCAGA 61.706 66.667 23.09 0.00 0.00 3.86
1785 4115 4.785453 GGAGGACAAGGCGGCCAG 62.785 72.222 23.09 15.66 0.00 4.85
1789 4119 1.392710 ATAGACGGAGGACAAGGCGG 61.393 60.000 0.00 0.00 0.00 6.13
1790 4120 0.030908 GATAGACGGAGGACAAGGCG 59.969 60.000 0.00 0.00 0.00 5.52
1791 4121 0.030908 CGATAGACGGAGGACAAGGC 59.969 60.000 0.00 0.00 38.46 4.35
1803 4133 4.629092 GGGATGAAGGGTTTACGATAGAC 58.371 47.826 0.00 0.00 41.38 2.59
1804 4134 3.319972 CGGGATGAAGGGTTTACGATAGA 59.680 47.826 0.00 0.00 41.38 1.98
1805 4135 3.319972 TCGGGATGAAGGGTTTACGATAG 59.680 47.826 0.00 0.00 46.19 2.08
1806 4136 3.068590 GTCGGGATGAAGGGTTTACGATA 59.931 47.826 0.00 0.00 0.00 2.92
1807 4137 2.112998 TCGGGATGAAGGGTTTACGAT 58.887 47.619 0.00 0.00 0.00 3.73
1808 4138 1.205417 GTCGGGATGAAGGGTTTACGA 59.795 52.381 0.00 0.00 0.00 3.43
1809 4139 1.066716 TGTCGGGATGAAGGGTTTACG 60.067 52.381 0.00 0.00 0.00 3.18
1810 4140 2.773993 TGTCGGGATGAAGGGTTTAC 57.226 50.000 0.00 0.00 0.00 2.01
1811 4141 3.791953 TTTGTCGGGATGAAGGGTTTA 57.208 42.857 0.00 0.00 0.00 2.01
1812 4142 2.668144 TTTGTCGGGATGAAGGGTTT 57.332 45.000 0.00 0.00 0.00 3.27
1813 4143 2.668144 TTTTGTCGGGATGAAGGGTT 57.332 45.000 0.00 0.00 0.00 4.11
1814 4144 2.668144 TTTTTGTCGGGATGAAGGGT 57.332 45.000 0.00 0.00 0.00 4.34
1815 4145 2.427095 GGATTTTTGTCGGGATGAAGGG 59.573 50.000 0.00 0.00 0.00 3.95
1816 4146 3.356290 AGGATTTTTGTCGGGATGAAGG 58.644 45.455 0.00 0.00 0.00 3.46
1817 4147 4.009675 TGAGGATTTTTGTCGGGATGAAG 58.990 43.478 0.00 0.00 0.00 3.02
1818 4148 4.027674 TGAGGATTTTTGTCGGGATGAA 57.972 40.909 0.00 0.00 0.00 2.57
1819 4149 3.712016 TGAGGATTTTTGTCGGGATGA 57.288 42.857 0.00 0.00 0.00 2.92
1820 4150 5.764686 TCATATGAGGATTTTTGTCGGGATG 59.235 40.000 0.00 0.00 0.00 3.51
1821 4151 5.940617 TCATATGAGGATTTTTGTCGGGAT 58.059 37.500 0.00 0.00 0.00 3.85
1822 4152 5.366482 TCATATGAGGATTTTTGTCGGGA 57.634 39.130 0.00 0.00 0.00 5.14
1823 4153 5.563475 GCATCATATGAGGATTTTTGTCGGG 60.563 44.000 21.02 0.00 0.00 5.14
1824 4154 5.240183 AGCATCATATGAGGATTTTTGTCGG 59.760 40.000 21.02 0.00 0.00 4.79
1825 4155 6.309712 AGCATCATATGAGGATTTTTGTCG 57.690 37.500 21.02 0.00 0.00 4.35
1826 4156 6.854892 CGAAGCATCATATGAGGATTTTTGTC 59.145 38.462 20.42 8.02 34.47 3.18
1827 4157 6.543465 TCGAAGCATCATATGAGGATTTTTGT 59.457 34.615 20.42 0.00 34.47 2.83
1828 4158 6.962686 TCGAAGCATCATATGAGGATTTTTG 58.037 36.000 20.42 13.84 34.47 2.44
1829 4159 6.994496 TCTCGAAGCATCATATGAGGATTTTT 59.006 34.615 20.42 8.89 34.47 1.94
1830 4160 6.528321 TCTCGAAGCATCATATGAGGATTTT 58.472 36.000 20.42 11.09 34.47 1.82
1831 4161 6.014755 TCTCTCGAAGCATCATATGAGGATTT 60.015 38.462 20.42 13.32 34.47 2.17
1832 4162 5.479724 TCTCTCGAAGCATCATATGAGGATT 59.520 40.000 19.69 19.69 37.15 3.01
1833 4163 5.015515 TCTCTCGAAGCATCATATGAGGAT 58.984 41.667 21.02 12.22 0.00 3.24
1834 4164 4.217334 GTCTCTCGAAGCATCATATGAGGA 59.783 45.833 21.02 5.59 0.00 3.71
1835 4165 4.218200 AGTCTCTCGAAGCATCATATGAGG 59.782 45.833 12.98 12.98 0.00 3.86
1836 4166 5.048852 TCAGTCTCTCGAAGCATCATATGAG 60.049 44.000 11.78 4.86 0.00 2.90
1837 4167 4.823989 TCAGTCTCTCGAAGCATCATATGA 59.176 41.667 8.10 8.10 0.00 2.15
1847 4177 0.248054 GCTCGCTCAGTCTCTCGAAG 60.248 60.000 0.00 0.00 0.00 3.79
1850 4180 1.062365 CTGCTCGCTCAGTCTCTCG 59.938 63.158 0.00 0.00 0.00 4.04
1852 4182 2.884367 GCTGCTCGCTCAGTCTCT 59.116 61.111 0.00 0.00 36.49 3.10
1869 4240 6.307558 CGAACTGAGCATAGCTATGTCAATAG 59.692 42.308 29.62 22.11 39.88 1.73
1876 4247 3.023946 AGCGAACTGAGCATAGCTATG 57.976 47.619 26.42 26.42 39.88 2.23
1884 4255 0.601046 CTGTGGAAGCGAACTGAGCA 60.601 55.000 0.00 0.00 37.01 4.26
1923 4353 2.048222 GCGTGAGGCACTGCTGTA 60.048 61.111 0.00 0.00 41.55 2.74
1937 4367 3.760035 CCTCCCAGCTACACGCGT 61.760 66.667 5.58 5.58 45.59 6.01
1952 4382 1.152881 GATCCGCCCAAATCTGCCT 60.153 57.895 0.00 0.00 0.00 4.75
1960 4390 2.075566 TGGCATAGGATCCGCCCAA 61.076 57.895 22.16 6.00 45.63 4.12
1961 4391 2.447572 TGGCATAGGATCCGCCCA 60.448 61.111 22.16 16.25 45.63 5.36
2005 4435 2.662596 GTCATGGAGGTCGTGGCA 59.337 61.111 0.00 0.00 36.99 4.92
2036 4466 2.052590 CGCGCTAGAGCTCGTCTC 60.053 66.667 16.69 0.00 43.38 3.36
2063 4509 0.733150 GGATACAACTTTGGCGGCTC 59.267 55.000 11.43 0.00 0.00 4.70
2138 4585 3.039202 GAAGCATGTTCGGTGCCGG 62.039 63.158 10.94 0.00 43.50 6.13
2140 4587 1.210155 GTGAAGCATGTTCGGTGCC 59.790 57.895 0.00 0.00 43.50 5.01
2141 4588 1.154413 CGTGAAGCATGTTCGGTGC 60.154 57.895 0.00 0.00 42.81 5.01
2142 4589 0.110688 CACGTGAAGCATGTTCGGTG 60.111 55.000 10.90 6.21 30.47 4.94
2143 4590 1.227999 CCACGTGAAGCATGTTCGGT 61.228 55.000 19.30 0.00 30.47 4.69
2145 4592 1.497278 CCCACGTGAAGCATGTTCG 59.503 57.895 19.30 0.00 30.47 3.95
2146 4593 1.210155 GCCCACGTGAAGCATGTTC 59.790 57.895 19.30 0.00 30.47 3.18
2147 4594 2.616330 CGCCCACGTGAAGCATGTT 61.616 57.895 24.14 0.00 30.47 2.71
2148 4595 3.049674 CGCCCACGTGAAGCATGT 61.050 61.111 24.14 0.00 33.47 3.21
2149 4596 4.465512 GCGCCCACGTGAAGCATG 62.466 66.667 24.14 13.50 42.83 4.06
2166 4613 2.747460 CCACCATGGGCACAGTCG 60.747 66.667 18.09 0.00 32.67 4.18
2188 4635 2.760385 CGTCCACTCCCCTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
2193 4640 4.400251 CCTCCCGTCCACTCCCCT 62.400 72.222 0.00 0.00 0.00 4.79
2218 4668 3.195698 GAACCCTAAGCGCCGCAG 61.196 66.667 13.36 0.00 0.00 5.18
2219 4669 3.659089 GAGAACCCTAAGCGCCGCA 62.659 63.158 13.36 0.00 0.00 5.69
2227 4678 1.628846 GGCTTCACAGGAGAACCCTAA 59.371 52.381 0.00 0.00 45.60 2.69
2283 4734 6.529125 TGTTCCTTTAGTAAAATACGCGAGAG 59.471 38.462 15.93 0.00 0.00 3.20
2284 4735 6.308766 GTGTTCCTTTAGTAAAATACGCGAGA 59.691 38.462 15.93 0.00 0.00 4.04
2285 4736 6.464311 GTGTTCCTTTAGTAAAATACGCGAG 58.536 40.000 15.93 0.00 0.00 5.03
2286 4737 5.060816 CGTGTTCCTTTAGTAAAATACGCGA 59.939 40.000 15.93 0.00 36.94 5.87
2287 4738 5.060816 TCGTGTTCCTTTAGTAAAATACGCG 59.939 40.000 20.19 20.19 36.58 6.01
2288 4739 6.393720 TCGTGTTCCTTTAGTAAAATACGC 57.606 37.500 9.10 7.24 0.00 4.42
2289 4740 6.089820 TGCTCGTGTTCCTTTAGTAAAATACG 59.910 38.462 8.11 8.11 0.00 3.06
2290 4741 7.330208 TCTGCTCGTGTTCCTTTAGTAAAATAC 59.670 37.037 0.00 0.00 0.00 1.89
2291 4742 7.380536 TCTGCTCGTGTTCCTTTAGTAAAATA 58.619 34.615 0.00 0.00 0.00 1.40
2292 4743 6.228258 TCTGCTCGTGTTCCTTTAGTAAAAT 58.772 36.000 0.00 0.00 0.00 1.82
2293 4744 5.603596 TCTGCTCGTGTTCCTTTAGTAAAA 58.396 37.500 0.00 0.00 0.00 1.52
2294 4745 5.204409 TCTGCTCGTGTTCCTTTAGTAAA 57.796 39.130 0.00 0.00 0.00 2.01
2295 4746 4.859304 TCTGCTCGTGTTCCTTTAGTAA 57.141 40.909 0.00 0.00 0.00 2.24
2296 4747 4.859304 TTCTGCTCGTGTTCCTTTAGTA 57.141 40.909 0.00 0.00 0.00 1.82
2297 4748 3.746045 TTCTGCTCGTGTTCCTTTAGT 57.254 42.857 0.00 0.00 0.00 2.24
2298 4749 3.807622 TGTTTCTGCTCGTGTTCCTTTAG 59.192 43.478 0.00 0.00 0.00 1.85
2299 4750 3.799366 TGTTTCTGCTCGTGTTCCTTTA 58.201 40.909 0.00 0.00 0.00 1.85
2300 4751 2.639065 TGTTTCTGCTCGTGTTCCTTT 58.361 42.857 0.00 0.00 0.00 3.11
2301 4752 2.325583 TGTTTCTGCTCGTGTTCCTT 57.674 45.000 0.00 0.00 0.00 3.36
2302 4753 2.146342 CATGTTTCTGCTCGTGTTCCT 58.854 47.619 0.00 0.00 0.00 3.36
2303 4754 2.143122 TCATGTTTCTGCTCGTGTTCC 58.857 47.619 0.00 0.00 0.00 3.62
2304 4755 3.878086 TTCATGTTTCTGCTCGTGTTC 57.122 42.857 0.00 0.00 0.00 3.18
2305 4756 4.351192 GTTTTCATGTTTCTGCTCGTGTT 58.649 39.130 0.00 0.00 0.00 3.32
2306 4757 3.546020 CGTTTTCATGTTTCTGCTCGTGT 60.546 43.478 0.00 0.00 0.00 4.49
2307 4758 2.966708 CGTTTTCATGTTTCTGCTCGTG 59.033 45.455 0.00 0.00 0.00 4.35
2308 4759 2.869801 TCGTTTTCATGTTTCTGCTCGT 59.130 40.909 0.00 0.00 0.00 4.18
2309 4760 3.519908 TCGTTTTCATGTTTCTGCTCG 57.480 42.857 0.00 0.00 0.00 5.03
2310 4761 6.253512 ACTTTTTCGTTTTCATGTTTCTGCTC 59.746 34.615 0.00 0.00 0.00 4.26
2311 4762 6.099341 ACTTTTTCGTTTTCATGTTTCTGCT 58.901 32.000 0.00 0.00 0.00 4.24
2312 4763 6.331170 ACTTTTTCGTTTTCATGTTTCTGC 57.669 33.333 0.00 0.00 0.00 4.26
2313 4764 8.835467 TCTACTTTTTCGTTTTCATGTTTCTG 57.165 30.769 0.00 0.00 0.00 3.02
2314 4765 9.849166 TTTCTACTTTTTCGTTTTCATGTTTCT 57.151 25.926 0.00 0.00 0.00 2.52
2318 4769 9.849166 TCTTTTTCTACTTTTTCGTTTTCATGT 57.151 25.926 0.00 0.00 0.00 3.21
2321 4772 9.769093 CTCTCTTTTTCTACTTTTTCGTTTTCA 57.231 29.630 0.00 0.00 0.00 2.69
2322 4773 9.983804 TCTCTCTTTTTCTACTTTTTCGTTTTC 57.016 29.630 0.00 0.00 0.00 2.29
2326 4777 9.989869 CTTTTCTCTCTTTTTCTACTTTTTCGT 57.010 29.630 0.00 0.00 0.00 3.85
2327 4778 9.439537 CCTTTTCTCTCTTTTTCTACTTTTTCG 57.560 33.333 0.00 0.00 0.00 3.46
2332 4783 9.462606 TGTTTCCTTTTCTCTCTTTTTCTACTT 57.537 29.630 0.00 0.00 0.00 2.24
2333 4784 9.114952 CTGTTTCCTTTTCTCTCTTTTTCTACT 57.885 33.333 0.00 0.00 0.00 2.57
2334 4785 7.858382 GCTGTTTCCTTTTCTCTCTTTTTCTAC 59.142 37.037 0.00 0.00 0.00 2.59
2335 4786 7.556275 TGCTGTTTCCTTTTCTCTCTTTTTCTA 59.444 33.333 0.00 0.00 0.00 2.10
2336 4787 6.378280 TGCTGTTTCCTTTTCTCTCTTTTTCT 59.622 34.615 0.00 0.00 0.00 2.52
2337 4788 6.564328 TGCTGTTTCCTTTTCTCTCTTTTTC 58.436 36.000 0.00 0.00 0.00 2.29
2338 4789 6.530019 TGCTGTTTCCTTTTCTCTCTTTTT 57.470 33.333 0.00 0.00 0.00 1.94
2339 4790 6.530019 TTGCTGTTTCCTTTTCTCTCTTTT 57.470 33.333 0.00 0.00 0.00 2.27
2340 4791 6.530019 TTTGCTGTTTCCTTTTCTCTCTTT 57.470 33.333 0.00 0.00 0.00 2.52
2341 4792 6.530019 TTTTGCTGTTTCCTTTTCTCTCTT 57.470 33.333 0.00 0.00 0.00 2.85
2342 4793 5.451103 GCTTTTGCTGTTTCCTTTTCTCTCT 60.451 40.000 0.00 0.00 43.35 3.10
2343 4794 4.742167 GCTTTTGCTGTTTCCTTTTCTCTC 59.258 41.667 0.00 0.00 43.35 3.20
2344 4795 4.442052 GGCTTTTGCTGTTTCCTTTTCTCT 60.442 41.667 0.00 0.00 46.54 3.10
2345 4796 3.804325 GGCTTTTGCTGTTTCCTTTTCTC 59.196 43.478 0.00 0.00 46.54 2.87
2346 4797 3.432186 GGGCTTTTGCTGTTTCCTTTTCT 60.432 43.478 0.00 0.00 46.54 2.52
2347 4798 2.872245 GGGCTTTTGCTGTTTCCTTTTC 59.128 45.455 0.00 0.00 46.54 2.29
2348 4799 2.238395 TGGGCTTTTGCTGTTTCCTTTT 59.762 40.909 0.00 0.00 46.54 2.27
2349 4800 1.836802 TGGGCTTTTGCTGTTTCCTTT 59.163 42.857 0.00 0.00 46.54 3.11
2350 4801 1.494960 TGGGCTTTTGCTGTTTCCTT 58.505 45.000 0.00 0.00 46.54 3.36
2351 4802 1.720781 ATGGGCTTTTGCTGTTTCCT 58.279 45.000 0.00 0.00 46.54 3.36
2352 4803 2.094026 CCTATGGGCTTTTGCTGTTTCC 60.094 50.000 0.00 0.00 46.54 3.13
2353 4804 3.236632 CCTATGGGCTTTTGCTGTTTC 57.763 47.619 0.00 0.00 46.54 2.78
2365 4816 2.037381 GAGTAAGTACTGGCCTATGGGC 59.963 54.545 12.53 12.53 46.49 5.36
2366 4817 2.633481 GGAGTAAGTACTGGCCTATGGG 59.367 54.545 3.32 0.00 36.50 4.00
2367 4818 2.296471 CGGAGTAAGTACTGGCCTATGG 59.704 54.545 3.32 0.00 36.50 2.74
2368 4819 3.004524 GTCGGAGTAAGTACTGGCCTATG 59.995 52.174 3.32 0.00 36.50 2.23
2369 4820 3.117587 AGTCGGAGTAAGTACTGGCCTAT 60.118 47.826 3.32 0.00 36.50 2.57
2370 4821 2.240667 AGTCGGAGTAAGTACTGGCCTA 59.759 50.000 3.32 0.00 36.50 3.93
2371 4822 1.005687 AGTCGGAGTAAGTACTGGCCT 59.994 52.381 3.32 0.00 36.50 5.19
2372 4823 1.472188 AGTCGGAGTAAGTACTGGCC 58.528 55.000 0.00 0.00 36.50 5.36
2373 4824 2.490903 TGAAGTCGGAGTAAGTACTGGC 59.509 50.000 0.00 0.00 36.50 4.85
2374 4825 4.985538 ATGAAGTCGGAGTAAGTACTGG 57.014 45.455 0.00 0.00 36.50 4.00
2377 4828 9.327529 CGATTATTATGAAGTCGGAGTAAGTAC 57.672 37.037 0.00 0.00 0.00 2.73
2378 4829 9.276590 TCGATTATTATGAAGTCGGAGTAAGTA 57.723 33.333 0.00 0.00 33.46 2.24
2379 4830 8.162878 TCGATTATTATGAAGTCGGAGTAAGT 57.837 34.615 0.00 0.00 33.46 2.24
2380 4831 8.504815 TCTCGATTATTATGAAGTCGGAGTAAG 58.495 37.037 0.00 0.00 33.46 2.34
2381 4832 8.387190 TCTCGATTATTATGAAGTCGGAGTAA 57.613 34.615 0.00 0.00 33.46 2.24
2382 4833 7.974482 TCTCGATTATTATGAAGTCGGAGTA 57.026 36.000 0.00 0.00 33.46 2.59
2383 4834 6.879276 TCTCGATTATTATGAAGTCGGAGT 57.121 37.500 0.00 0.00 33.46 3.85
2385 4836 9.788960 CAATATCTCGATTATTATGAAGTCGGA 57.211 33.333 0.00 0.00 33.46 4.55
2386 4837 8.535592 GCAATATCTCGATTATTATGAAGTCGG 58.464 37.037 0.00 0.00 33.46 4.79
2387 4838 9.295214 AGCAATATCTCGATTATTATGAAGTCG 57.705 33.333 0.00 0.00 0.00 4.18
2397 4848 9.547753 ACACTACAAAAGCAATATCTCGATTAT 57.452 29.630 0.00 0.00 0.00 1.28
2398 4849 8.817100 CACACTACAAAAGCAATATCTCGATTA 58.183 33.333 0.00 0.00 0.00 1.75
2399 4850 7.677276 GCACACTACAAAAGCAATATCTCGATT 60.677 37.037 0.00 0.00 0.00 3.34
2400 4851 6.238211 GCACACTACAAAAGCAATATCTCGAT 60.238 38.462 0.00 0.00 0.00 3.59
2401 4852 5.063438 GCACACTACAAAAGCAATATCTCGA 59.937 40.000 0.00 0.00 0.00 4.04
2402 4853 5.163864 TGCACACTACAAAAGCAATATCTCG 60.164 40.000 0.00 0.00 31.42 4.04
2403 4854 6.182039 TGCACACTACAAAAGCAATATCTC 57.818 37.500 0.00 0.00 31.42 2.75
2404 4855 6.573664 TTGCACACTACAAAAGCAATATCT 57.426 33.333 0.00 0.00 39.95 1.98
2423 4874 9.300681 CCCTGGAAAAGAGATAATTATATTGCA 57.699 33.333 0.00 0.96 0.00 4.08
2424 4875 9.520515 TCCCTGGAAAAGAGATAATTATATTGC 57.479 33.333 0.00 0.00 0.00 3.56
2430 4881 9.853177 GAAGATTCCCTGGAAAAGAGATAATTA 57.147 33.333 2.15 0.00 37.69 1.40
2431 4882 8.564370 AGAAGATTCCCTGGAAAAGAGATAATT 58.436 33.333 2.15 0.00 37.69 1.40
2432 4883 8.111928 AGAAGATTCCCTGGAAAAGAGATAAT 57.888 34.615 2.15 0.00 37.69 1.28
2433 4884 7.516450 AGAAGATTCCCTGGAAAAGAGATAA 57.484 36.000 2.15 0.00 37.69 1.75
2434 4885 7.846823 AGTAGAAGATTCCCTGGAAAAGAGATA 59.153 37.037 2.15 0.00 37.69 1.98
2435 4886 6.676189 AGTAGAAGATTCCCTGGAAAAGAGAT 59.324 38.462 2.15 0.00 37.69 2.75
2436 4887 6.026186 AGTAGAAGATTCCCTGGAAAAGAGA 58.974 40.000 2.15 0.00 37.69 3.10
2437 4888 6.306643 AGTAGAAGATTCCCTGGAAAAGAG 57.693 41.667 2.15 0.00 37.69 2.85


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

AutoCloner maintained by Alex Coulton.