Multiple sequence alignment - TraesCS2D01G110700

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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 TraesCS2D01G110700 chr2D 100.000 6574 0 0 1 6574 61320884 61314311 0.000000e+00 12140.0
1 TraesCS2D01G110700 chr2D 82.765 1555 236 29 4044 5574 61342091 61340545 0.000000e+00 1358.0
2 TraesCS2D01G110700 chr2D 88.809 554 55 6 2234 2787 61347123 61346577 0.000000e+00 673.0
3 TraesCS2D01G110700 chr2A 93.551 2853 139 21 1 2825 61820073 61817238 0.000000e+00 4207.0
4 TraesCS2D01G110700 chr2A 92.686 2297 130 18 3935 6222 61810145 61807878 0.000000e+00 3277.0
5 TraesCS2D01G110700 chr2A 85.181 803 110 7 4778 5574 61959138 61958339 0.000000e+00 815.0
6 TraesCS2D01G110700 chr2A 89.711 554 50 4 2234 2787 61963070 61962524 0.000000e+00 701.0
7 TraesCS2D01G110700 chr2A 91.939 459 33 1 3183 3641 61815527 61815073 2.000000e-179 640.0
8 TraesCS2D01G110700 chr2A 80.836 694 115 13 4044 4724 61959911 61959223 4.510000e-146 529.0
9 TraesCS2D01G110700 chr2A 95.533 291 13 0 3659 3949 61810762 61810472 3.590000e-127 466.0
10 TraesCS2D01G110700 chr2A 90.533 338 28 4 2855 3189 61816930 61816594 1.680000e-120 444.0
11 TraesCS2D01G110700 chr2A 87.187 359 21 11 6226 6573 61806531 61806187 1.030000e-102 385.0
12 TraesCS2D01G110700 chr2A 82.353 255 31 9 5815 6057 13009200 13009452 6.680000e-50 209.0
13 TraesCS2D01G110700 chr2B 92.857 2142 133 10 3638 5768 96086533 96084401 0.000000e+00 3090.0
14 TraesCS2D01G110700 chr2B 86.422 1635 139 37 1 1592 96091788 96090194 0.000000e+00 1712.0
15 TraesCS2D01G110700 chr2B 82.732 1552 236 24 4048 5574 96238099 96236555 0.000000e+00 1352.0
16 TraesCS2D01G110700 chr2B 82.088 1552 241 30 4048 5574 96103491 96101952 0.000000e+00 1291.0
17 TraesCS2D01G110700 chr2B 95.244 757 29 6 2071 2825 96089340 96088589 0.000000e+00 1192.0
18 TraesCS2D01G110700 chr2B 89.362 611 59 3 3033 3641 96088301 96087695 0.000000e+00 763.0
19 TraesCS2D01G110700 chr2B 88.969 553 54 4 2235 2787 96240553 96240008 0.000000e+00 676.0
20 TraesCS2D01G110700 chr2B 87.612 557 61 5 2231 2786 96108976 96108427 2.000000e-179 640.0
21 TraesCS2D01G110700 chr2B 90.437 481 39 5 1590 2065 96089919 96089441 1.560000e-175 627.0
22 TraesCS2D01G110700 chr2B 82.940 551 72 14 913 1445 96242382 96241836 1.660000e-130 477.0
23 TraesCS2D01G110700 chr2B 83.801 463 55 12 913 1358 96242974 96242515 7.880000e-114 422.0
24 TraesCS2D01G110700 chr2B 80.776 541 85 12 934 1462 96110943 96110410 7.940000e-109 405.0
25 TraesCS2D01G110700 chr2B 90.987 233 15 2 2822 3048 96088563 96088331 6.400000e-80 309.0
26 TraesCS2D01G110700 chr2B 82.800 250 29 8 5825 6064 671255750 671255505 1.860000e-50 211.0
27 TraesCS2D01G110700 chr2B 79.612 103 21 0 779 881 96242494 96242392 2.540000e-09 75.0
28 TraesCS2D01G110700 chr2B 79.612 103 21 0 779 881 96243086 96242984 2.540000e-09 75.0
29 TraesCS2D01G110700 chr5D 85.965 228 18 10 5815 6033 248588808 248589030 1.430000e-56 231.0
30 TraesCS2D01G110700 chr5D 82.692 260 31 9 5815 6061 423186600 423186858 1.110000e-52 219.0
31 TraesCS2D01G110700 chr3B 83.206 262 26 9 5815 6061 764100646 764100904 2.390000e-54 224.0
32 TraesCS2D01G110700 chr7A 82.946 258 27 10 5821 6064 419932529 419932275 3.990000e-52 217.0
33 TraesCS2D01G110700 chr7A 75.132 189 39 5 94 277 202714137 202713952 1.520000e-11 82.4
34 TraesCS2D01G110700 chr7D 83.401 247 24 9 5829 6061 141345375 141345618 5.160000e-51 213.0
35 TraesCS2D01G110700 chr7D 78.075 187 37 3 94 277 193187992 193187807 1.500000e-21 115.0
36 TraesCS2D01G110700 chr5A 82.927 246 30 6 5824 6058 643553324 643553568 1.860000e-50 211.0
37 TraesCS2D01G110700 chr3A 79.775 178 31 4 104 277 474969438 474969614 2.490000e-24 124.0
38 TraesCS2D01G110700 chr1A 79.885 174 31 4 104 277 59937240 59937071 2.490000e-24 124.0
39 TraesCS2D01G110700 chr4A 79.191 173 32 4 108 277 579421871 579421700 4.160000e-22 117.0
40 TraesCS2D01G110700 chr4D 79.070 172 31 4 109 277 72239236 72239405 5.390000e-21 113.0
41 TraesCS2D01G110700 chr4D 77.108 166 36 2 108 271 22955885 22956050 1.950000e-15 95.3
42 TraesCS2D01G110700 chrUn 76.796 181 40 2 96 274 7153469 7153649 4.190000e-17 100.0


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 TraesCS2D01G110700 chr2D 61314311 61320884 6573 True 12140.000000 12140 100.000000 1 6574 1 chr2D.!!$R1 6573
1 TraesCS2D01G110700 chr2D 61340545 61342091 1546 True 1358.000000 1358 82.765000 4044 5574 1 chr2D.!!$R2 1530
2 TraesCS2D01G110700 chr2D 61346577 61347123 546 True 673.000000 673 88.809000 2234 2787 1 chr2D.!!$R3 553
3 TraesCS2D01G110700 chr2A 61815073 61820073 5000 True 1763.666667 4207 92.007667 1 3641 3 chr2A.!!$R2 3640
4 TraesCS2D01G110700 chr2A 61806187 61810762 4575 True 1376.000000 3277 91.802000 3659 6573 3 chr2A.!!$R1 2914
5 TraesCS2D01G110700 chr2A 61958339 61963070 4731 True 681.666667 815 85.242667 2234 5574 3 chr2A.!!$R3 3340
6 TraesCS2D01G110700 chr2B 96101952 96103491 1539 True 1291.000000 1291 82.088000 4048 5574 1 chr2B.!!$R1 1526
7 TraesCS2D01G110700 chr2B 96084401 96091788 7387 True 1282.166667 3090 90.884833 1 5768 6 chr2B.!!$R3 5767
8 TraesCS2D01G110700 chr2B 96108427 96110943 2516 True 522.500000 640 84.194000 934 2786 2 chr2B.!!$R4 1852
9 TraesCS2D01G110700 chr2B 96236555 96243086 6531 True 512.833333 1352 82.944333 779 5574 6 chr2B.!!$R5 4795

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
733 763 1.937278 TTCGTTCGTTAACAGCACCA 58.063 45.0 6.39 0.00 35.16 4.17 F
2044 3773 0.109643 GTTGCACATGCTCATGCGAA 60.110 50.0 9.58 0.00 45.13 4.70 F
2048 3777 0.380733 CACATGCTCATGCGAATGCT 59.619 50.0 3.41 0.00 42.39 3.79 F
2049 3778 0.661552 ACATGCTCATGCGAATGCTC 59.338 50.0 3.41 0.00 42.39 4.26 F
3342 7049 0.690192 TCGATGAACACACCATGGGT 59.310 50.0 18.09 8.43 33.89 4.51 F
3656 9768 0.975556 TGTAGCTTCCCGATGCCTCA 60.976 55.0 0.00 0.00 32.53 3.86 F
5057 11662 1.284982 GCCTCATATGCGTGCTACCG 61.285 60.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 3962 0.179100 ATGTCACTTGAGATCGGCCG 60.179 55.000 22.12 22.12 0.00 6.13 R
3118 5750 1.257750 GGAAACTGATTGGGTGGGGC 61.258 60.000 0.00 0.00 0.00 5.80 R
3656 9768 1.348036 GACCTGGCGCCTAAGGATATT 59.652 52.381 33.30 15.29 37.01 1.28 R
3670 9782 4.017126 TCAGTATATATGCGAGGACCTGG 58.983 47.826 0.00 0.00 0.00 4.45 R
5171 11779 0.833287 AATCAGGTACGATGGCTGCT 59.167 50.000 0.00 0.00 0.00 4.24 R
5255 11863 1.564348 GGGAGGTCATTTGGAAGCCTA 59.436 52.381 0.00 0.00 0.00 3.93 R
6363 14338 0.032540 CCAGGTTTCAGGCACAAAGC 59.967 55.000 3.02 3.02 44.65 3.51 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
25 26 2.032620 GTCTCACCCGGTCTCACATAT 58.967 52.381 0.00 0.00 0.00 1.78
175 176 2.026822 AGCCCTAGAGTTGACATTGGTG 60.027 50.000 0.00 0.00 0.00 4.17
277 280 4.926238 GTCTGTGATGACTTCGTCAATCTT 59.074 41.667 2.65 0.00 45.96 2.40
446 468 6.708285 ACTTGTCAACCCTACCAATACTTAG 58.292 40.000 0.00 0.00 0.00 2.18
474 500 2.110990 GTCGTAAACGGTTTGCCAAAC 58.889 47.619 16.05 11.88 40.65 2.93
730 760 4.186241 GAACTTTCGTTCGTTAACAGCA 57.814 40.909 6.39 0.00 40.05 4.41
733 763 1.937278 TTCGTTCGTTAACAGCACCA 58.063 45.000 6.39 0.00 35.16 4.17
735 765 2.485903 TCGTTCGTTAACAGCACCAAT 58.514 42.857 6.39 0.00 35.16 3.16
838 869 2.195389 TAGCGGCGCTAGAAAGGAA 58.805 52.632 35.39 15.26 40.44 3.36
1108 1169 4.889856 CATGGCGCGGATGGTCGA 62.890 66.667 8.83 0.00 0.00 4.20
1218 1898 4.641989 GGTACTACGGAGGTATTTCTCACA 59.358 45.833 0.00 0.00 35.58 3.58
1290 1970 2.240493 TCCTTGATAAGCTTAGCGGC 57.760 50.000 16.41 4.68 0.00 6.53
1400 2081 7.052248 GCTTTCCTACCCTACAAAATAAGCTA 58.948 38.462 0.00 0.00 33.42 3.32
1425 2106 3.338249 ACTTGACATGTTCATCTTCGGG 58.662 45.455 0.00 0.00 32.84 5.14
1429 2110 3.751175 TGACATGTTCATCTTCGGGAAAC 59.249 43.478 0.00 0.00 0.00 2.78
1433 2114 6.180472 ACATGTTCATCTTCGGGAAACTTAT 58.820 36.000 0.00 0.00 0.00 1.73
1453 2134 9.736023 AACTTATACTCAACTTTTTGCTCAAAG 57.264 29.630 6.64 6.64 39.35 2.77
1498 2179 7.220030 ACCCTGTCTAGAAATGCATAACTATG 58.780 38.462 0.00 2.31 36.78 2.23
1519 2200 9.823647 ACTATGTTATCTCAAAAGGAGTACATG 57.176 33.333 0.00 0.00 44.40 3.21
1549 2230 0.388649 CCGATACTGTATCTGCCCGC 60.389 60.000 21.76 0.00 33.01 6.13
1569 2250 3.066760 CGCCCATTATTGAGAAAAGGACC 59.933 47.826 0.00 0.00 0.00 4.46
1692 3078 7.985752 ACTAGGTAACCATAATGTAAAGTGCTC 59.014 37.037 0.00 0.00 37.17 4.26
1824 3215 3.119245 TCCGGAGACCAAGACGATAAAAG 60.119 47.826 0.00 0.00 0.00 2.27
1835 3226 8.883731 ACCAAGACGATAAAAGAAATACATCAG 58.116 33.333 0.00 0.00 0.00 2.90
1975 3701 4.252073 CCAACATGAAAGAGAGTGGAGAG 58.748 47.826 0.00 0.00 0.00 3.20
2040 3769 2.476686 CCGTAAGTTGCACATGCTCATG 60.477 50.000 8.21 8.21 44.15 3.07
2044 3773 0.109643 GTTGCACATGCTCATGCGAA 60.110 50.000 9.58 0.00 45.13 4.70
2045 3774 0.812549 TTGCACATGCTCATGCGAAT 59.187 45.000 9.58 0.00 45.13 3.34
2048 3777 0.380733 CACATGCTCATGCGAATGCT 59.619 50.000 3.41 0.00 42.39 3.79
2049 3778 0.661552 ACATGCTCATGCGAATGCTC 59.338 50.000 3.41 0.00 42.39 4.26
2050 3779 0.945099 CATGCTCATGCGAATGCTCT 59.055 50.000 0.00 0.00 43.34 4.09
2053 3782 1.012086 GCTCATGCGAATGCTCTCAA 58.988 50.000 0.00 0.00 43.34 3.02
2054 3783 1.602851 GCTCATGCGAATGCTCTCAAT 59.397 47.619 0.00 0.00 43.34 2.57
2055 3784 2.349627 GCTCATGCGAATGCTCTCAATC 60.350 50.000 0.00 0.00 43.34 2.67
2056 3785 1.862827 TCATGCGAATGCTCTCAATCG 59.137 47.619 0.00 0.00 45.64 3.34
2058 3787 1.278038 GCGAATGCTCTCAATCGGC 59.722 57.895 5.14 0.00 43.71 5.54
2059 3788 1.156645 GCGAATGCTCTCAATCGGCT 61.157 55.000 5.14 0.00 43.71 5.52
2061 3790 2.057316 CGAATGCTCTCAATCGGCTAG 58.943 52.381 0.00 0.00 40.80 3.42
2062 3791 1.797635 GAATGCTCTCAATCGGCTAGC 59.202 52.381 6.04 6.04 0.00 3.42
2063 3792 1.047002 ATGCTCTCAATCGGCTAGCT 58.953 50.000 15.72 0.00 34.28 3.32
2064 3793 1.692411 TGCTCTCAATCGGCTAGCTA 58.308 50.000 15.72 3.53 34.28 3.32
2065 3794 1.338337 TGCTCTCAATCGGCTAGCTAC 59.662 52.381 15.72 0.00 34.28 3.58
2066 3795 1.336424 GCTCTCAATCGGCTAGCTACC 60.336 57.143 15.72 0.00 0.00 3.18
2068 3797 3.413327 CTCTCAATCGGCTAGCTACCTA 58.587 50.000 15.72 0.00 0.00 3.08
2099 3926 1.637553 ACCAAATCACAGCCCTCTCAT 59.362 47.619 0.00 0.00 0.00 2.90
2135 3962 0.928229 GCCGTCCGTTCACATGATAC 59.072 55.000 0.00 0.00 0.00 2.24
2158 3985 2.544685 CCGATCTCAAGTGACATGACC 58.455 52.381 0.00 0.00 0.00 4.02
2184 4011 5.172934 TGGCTATTAAAGGTTGTCGTACTG 58.827 41.667 0.00 0.00 0.00 2.74
2193 4020 5.979288 AGGTTGTCGTACTGAAATCTACT 57.021 39.130 0.00 0.00 0.00 2.57
2194 4021 6.342338 AGGTTGTCGTACTGAAATCTACTT 57.658 37.500 0.00 0.00 0.00 2.24
2195 4022 7.458409 AGGTTGTCGTACTGAAATCTACTTA 57.542 36.000 0.00 0.00 0.00 2.24
2196 4023 7.311408 AGGTTGTCGTACTGAAATCTACTTAC 58.689 38.462 0.00 0.00 0.00 2.34
2639 4468 2.583319 CGTCATGAGCCGCATCGT 60.583 61.111 0.00 0.00 34.15 3.73
2721 4550 0.976641 TGTTCGAGCTCTTCCATGGT 59.023 50.000 12.58 0.00 0.00 3.55
2742 4571 3.315142 CTGCCTGCTAGCCAACGGA 62.315 63.158 13.29 0.00 0.00 4.69
2787 4616 1.094785 CCAAAGCAATGGAGGTACGG 58.905 55.000 1.70 0.00 43.54 4.02
2881 5146 3.988379 TGTTCTGAAATGTGCCAACTC 57.012 42.857 0.00 0.00 0.00 3.01
2909 5174 1.539827 GGCACATGGGTCACTGTTTAC 59.460 52.381 0.00 0.00 0.00 2.01
2921 5186 5.449041 GGTCACTGTTTACATATGCACATGG 60.449 44.000 10.24 0.00 0.00 3.66
2972 5462 6.922957 TGCATTTCAAACTTTTGATACTGTCC 59.077 34.615 5.26 0.00 45.65 4.02
3008 5498 3.733443 AAAGTTTCATGGACCACTTGC 57.267 42.857 0.00 0.00 29.78 4.01
3100 5731 4.696877 CACAAACTCTCACTCCAATATGCA 59.303 41.667 0.00 0.00 0.00 3.96
3109 5741 4.947388 TCACTCCAATATGCACCTTTAACC 59.053 41.667 0.00 0.00 0.00 2.85
3111 5743 4.949856 ACTCCAATATGCACCTTTAACCTG 59.050 41.667 0.00 0.00 0.00 4.00
3118 5750 2.962421 TGCACCTTTAACCTGGGAAAAG 59.038 45.455 13.26 13.26 0.00 2.27
3154 5786 5.468746 CAGTTTCCCGAACAAATTCTCTACA 59.531 40.000 0.00 0.00 40.84 2.74
3165 5797 8.418597 AACAAATTCTCTACACTAGTAGGTCA 57.581 34.615 1.45 0.00 46.23 4.02
3189 6895 1.475280 CAGTTGAAGGCCACATGGATG 59.525 52.381 5.01 0.00 37.39 3.51
3295 7002 5.568620 ACTCCCTTGTCACTTAGATTTGT 57.431 39.130 0.00 0.00 0.00 2.83
3306 7013 9.739276 TGTCACTTAGATTTGTCAAATTATCCT 57.261 29.630 12.04 7.24 0.00 3.24
3333 7040 2.434702 AGGATTACCCCTCGATGAACAC 59.565 50.000 0.00 0.00 36.73 3.32
3342 7049 0.690192 TCGATGAACACACCATGGGT 59.310 50.000 18.09 8.43 33.89 4.51
3375 7082 3.478857 TGAGCGGAACCTTAGTTTTCA 57.521 42.857 0.00 0.00 35.94 2.69
3389 7096 2.689983 AGTTTTCAAACTGACAGGCCTG 59.310 45.455 31.60 31.60 46.80 4.85
3398 7105 5.968676 AACTGACAGGCCTGGTATTTATA 57.031 39.130 35.42 11.65 34.19 0.98
3469 7176 2.422093 GCCCTCGGAAGGAATCAGATTT 60.422 50.000 0.00 0.00 46.67 2.17
3535 7242 4.183865 CACTTATCCTCGATCAAAGCACA 58.816 43.478 0.00 0.00 0.00 4.57
3616 7323 7.546358 TCCATTGCAAAATATTGTAGAAGGTG 58.454 34.615 1.71 0.00 38.85 4.00
3651 9763 1.942657 CAATGGTGTAGCTTCCCGATG 59.057 52.381 0.00 0.00 0.00 3.84
3656 9768 0.975556 TGTAGCTTCCCGATGCCTCA 60.976 55.000 0.00 0.00 32.53 3.86
3670 9782 1.443802 GCCTCAATATCCTTAGGCGC 58.556 55.000 0.00 0.00 44.63 6.53
3916 10030 3.224884 TCATTTGACGTCAGCGACATA 57.775 42.857 19.11 0.00 41.64 2.29
4096 10654 8.629158 TCTAGATTGTGTACAAAAACAGCAATT 58.371 29.630 1.76 0.00 39.55 2.32
4116 10674 6.806739 GCAATTCTCATTTGGGTAACTTGTAC 59.193 38.462 0.00 0.00 0.00 2.90
4273 10835 8.756927 TCCAATGAAATTCAAAGGCATATACAA 58.243 29.630 0.00 0.00 31.22 2.41
4307 10869 8.432805 TCATAGGAATTTGAGGAAGAATCTACC 58.567 37.037 0.00 0.00 0.00 3.18
4362 10924 2.243736 ACTTTGGTTGGTTCTTCTGGGA 59.756 45.455 0.00 0.00 0.00 4.37
4402 10964 3.243975 ACTGAAATGGAAGCAAGGCAAAG 60.244 43.478 0.00 0.00 0.00 2.77
4409 10974 3.579586 TGGAAGCAAGGCAAAGAAATCAT 59.420 39.130 0.00 0.00 0.00 2.45
4418 10983 6.409524 AGGCAAAGAAATCATGTTTCTTCA 57.590 33.333 23.89 0.00 45.07 3.02
4460 11028 5.408604 ACGCATTAGGTTGAGTTTGAAGTAG 59.591 40.000 0.00 0.00 0.00 2.57
4658 11227 4.039852 GGCACTTTTTCTAACCATTGGGAA 59.960 41.667 7.78 0.00 38.05 3.97
4766 11366 8.208903 ACAACAACTAGTAACAGAATACCACTT 58.791 33.333 0.00 0.00 0.00 3.16
4883 11487 2.639839 CGAGGATATGAAGGTGGGGAAT 59.360 50.000 0.00 0.00 0.00 3.01
4927 11531 8.647143 AATCTACTTTGTGTTTGTGATTTTGG 57.353 30.769 0.00 0.00 0.00 3.28
4939 11543 5.559427 TGTGATTTTGGGTTACATGATCG 57.441 39.130 0.00 0.00 0.00 3.69
4986 11590 3.436243 AGAAAGGAGGAGTGGACACTAG 58.564 50.000 4.73 0.00 42.66 2.57
4988 11593 1.383963 AGGAGGAGTGGACACTAGGA 58.616 55.000 4.73 0.00 42.66 2.94
5045 11650 4.966168 TCAACTGTATACTTGGGCCTCATA 59.034 41.667 4.53 0.00 0.00 2.15
5057 11662 1.284982 GCCTCATATGCGTGCTACCG 61.285 60.000 0.00 0.00 0.00 4.02
5120 11728 7.118535 GGAATAGGACACTTCTTCTTCTTTGTC 59.881 40.741 0.00 0.00 33.99 3.18
5151 11759 1.501169 GGCTTGCACAATGTTGGTTC 58.499 50.000 0.00 0.00 0.00 3.62
5171 11779 6.718912 TGGTTCAAGGTTTGATGATGATTGTA 59.281 34.615 0.00 0.00 39.84 2.41
5255 11863 1.310904 TGCTAAACGCCGGTTTCTTT 58.689 45.000 1.90 0.00 44.91 2.52
5360 11968 7.255801 GGACTGTACAAAAATGAATTCTTGGGA 60.256 37.037 7.05 0.00 0.00 4.37
5498 12109 7.437713 ACTTGGAATGGTCATTATCTACAGA 57.562 36.000 0.00 0.00 0.00 3.41
5533 12144 7.254227 TGGTTATTATAAAGGTTGTCGATGC 57.746 36.000 0.00 0.00 0.00 3.91
5770 12387 5.822519 CCAAGGTAGCTAGCAACAATATCAA 59.177 40.000 24.01 0.00 0.00 2.57
5771 12388 6.318648 CCAAGGTAGCTAGCAACAATATCAAA 59.681 38.462 24.01 0.00 0.00 2.69
5775 12392 8.408601 AGGTAGCTAGCAACAATATCAAATTTG 58.591 33.333 24.01 12.15 0.00 2.32
5800 12417 7.071196 TGTCTAGGAGTGGCATATTTTAGATGT 59.929 37.037 0.00 0.00 0.00 3.06
5801 12418 7.386299 GTCTAGGAGTGGCATATTTTAGATGTG 59.614 40.741 0.00 0.00 0.00 3.21
5803 12420 6.662755 AGGAGTGGCATATTTTAGATGTGAA 58.337 36.000 0.00 0.00 0.00 3.18
5824 12441 2.303175 AGAAGCTAGCTTAGGAGGACG 58.697 52.381 29.39 0.00 36.26 4.79
5834 12452 2.077687 TAGGAGGACGTGTTATCCCC 57.922 55.000 0.00 0.00 36.86 4.81
5838 12456 1.153229 GGACGTGTTATCCCCAGCC 60.153 63.158 0.00 0.00 0.00 4.85
5856 12474 1.481056 CCGACCAGGGTTCAAGTCCT 61.481 60.000 0.00 0.00 35.97 3.85
5861 12479 0.890996 CAGGGTTCAAGTCCTGGTGC 60.891 60.000 0.00 0.00 44.99 5.01
5875 12493 0.597568 TGGTGCTCGCATTTTTCTGG 59.402 50.000 0.00 0.00 0.00 3.86
5877 12495 1.401539 GGTGCTCGCATTTTTCTGGAC 60.402 52.381 0.00 0.00 0.00 4.02
5884 12502 5.513141 GCTCGCATTTTTCTGGACTTATTTC 59.487 40.000 0.00 0.00 0.00 2.17
5895 12513 4.523083 TGGACTTATTTCAGGATTTCCGG 58.477 43.478 0.00 0.00 42.08 5.14
5896 12514 4.018779 TGGACTTATTTCAGGATTTCCGGT 60.019 41.667 0.00 0.00 42.08 5.28
5897 12515 4.335594 GGACTTATTTCAGGATTTCCGGTG 59.664 45.833 0.00 0.00 42.08 4.94
5901 12519 3.712016 TTTCAGGATTTCCGGTGATGA 57.288 42.857 0.00 0.00 42.08 2.92
5902 12520 3.712016 TTCAGGATTTCCGGTGATGAA 57.288 42.857 0.00 2.40 42.08 2.57
5907 12525 2.095372 GGATTTCCGGTGATGAACGTTC 59.905 50.000 21.42 21.42 0.00 3.95
5920 12538 1.550976 GAACGTTCAGTGGGAGGAGAT 59.449 52.381 23.12 0.00 0.00 2.75
5924 12542 2.289694 CGTTCAGTGGGAGGAGATGTTT 60.290 50.000 0.00 0.00 0.00 2.83
5927 12545 1.630369 CAGTGGGAGGAGATGTTTCCA 59.370 52.381 0.00 0.00 39.84 3.53
5943 12561 1.557099 TCCATCGACTACAAGGTGCT 58.443 50.000 0.00 0.00 0.00 4.40
5950 12568 2.930040 CGACTACAAGGTGCTTATGGTG 59.070 50.000 0.00 0.00 0.00 4.17
5964 12582 6.092259 GTGCTTATGGTGACTTCGTAAAATCT 59.908 38.462 0.00 0.00 0.00 2.40
5981 12599 7.277760 CGTAAAATCTCAATATGATATGCCGGA 59.722 37.037 5.05 0.00 0.00 5.14
5982 12600 6.992063 AAATCTCAATATGATATGCCGGAC 57.008 37.500 5.05 0.00 0.00 4.79
5989 12607 1.496060 TGATATGCCGGACCAGTCTT 58.504 50.000 5.05 0.00 0.00 3.01
5993 12611 3.050275 GCCGGACCAGTCTTGTGC 61.050 66.667 5.05 0.00 0.00 4.57
6000 12618 2.234908 GGACCAGTCTTGTGCTCATAGT 59.765 50.000 0.00 0.00 0.00 2.12
6005 12623 4.141846 CCAGTCTTGTGCTCATAGTGGTAT 60.142 45.833 13.52 0.00 31.39 2.73
6008 12626 3.134623 TCTTGTGCTCATAGTGGTATGGG 59.865 47.826 0.00 0.00 39.84 4.00
6009 12627 2.758130 TGTGCTCATAGTGGTATGGGA 58.242 47.619 0.00 0.00 39.26 4.37
6017 12637 2.787473 AGTGGTATGGGATGTGTGTG 57.213 50.000 0.00 0.00 0.00 3.82
6018 12638 1.985159 AGTGGTATGGGATGTGTGTGT 59.015 47.619 0.00 0.00 0.00 3.72
6029 12649 2.559698 TGTGTGTGTGTTCATAGGGG 57.440 50.000 0.00 0.00 0.00 4.79
6040 12660 5.045213 TGTGTTCATAGGGGTGAATGTATGT 60.045 40.000 0.00 0.00 39.99 2.29
6043 12665 6.157123 TGTTCATAGGGGTGAATGTATGTGTA 59.843 38.462 0.00 0.00 39.99 2.90
6052 12674 7.495934 GGGGTGAATGTATGTGTATATATGAGC 59.504 40.741 0.00 0.00 0.00 4.26
6054 12676 7.254117 GGTGAATGTATGTGTATATATGAGCGC 60.254 40.741 0.00 0.00 0.00 5.92
6057 12679 7.761651 ATGTATGTGTATATATGAGCGCTTG 57.238 36.000 13.26 0.00 0.00 4.01
6063 12685 1.208259 TATATGAGCGCTTGCGTGTG 58.792 50.000 13.26 0.00 45.69 3.82
6131 12753 2.913578 CCAAGTGCAGCAGGCCAA 60.914 61.111 5.01 0.00 43.89 4.52
6141 12763 1.752498 CAGCAGGCCAAAATGCAGATA 59.248 47.619 16.24 0.00 45.01 1.98
6144 12766 4.038282 CAGCAGGCCAAAATGCAGATATTA 59.962 41.667 16.24 0.00 45.01 0.98
6151 12773 4.919168 CCAAAATGCAGATATTATGCCGTG 59.081 41.667 10.37 4.68 43.18 4.94
6152 12774 3.837213 AATGCAGATATTATGCCGTGC 57.163 42.857 10.37 0.00 43.18 5.34
6153 12775 2.549064 TGCAGATATTATGCCGTGCT 57.451 45.000 10.37 0.00 43.18 4.40
6154 12776 2.849942 TGCAGATATTATGCCGTGCTT 58.150 42.857 10.37 0.00 43.18 3.91
6155 12777 2.807967 TGCAGATATTATGCCGTGCTTC 59.192 45.455 10.37 0.00 43.18 3.86
6156 12778 2.159787 GCAGATATTATGCCGTGCTTCG 60.160 50.000 3.13 0.00 37.73 3.79
6179 12801 1.141053 GTCTCGGGAGGCATTATGGTT 59.859 52.381 0.00 0.00 32.23 3.67
6234 14199 1.472728 GCTAGGTAGCGCTTGCCTAAA 60.473 52.381 28.53 17.20 39.82 1.85
6239 14204 1.022451 TAGCGCTTGCCTAAAACCGG 61.022 55.000 18.68 0.00 40.41 5.28
6263 14231 4.738541 GCAACCCTAATTGATGCCTGAATG 60.739 45.833 0.00 0.00 0.00 2.67
6265 14233 3.052642 ACCCTAATTGATGCCTGAATGGT 60.053 43.478 0.00 0.00 38.35 3.55
6266 14234 3.319972 CCCTAATTGATGCCTGAATGGTG 59.680 47.826 0.00 0.00 38.35 4.17
6268 14236 2.832643 ATTGATGCCTGAATGGTGGA 57.167 45.000 0.00 0.00 38.35 4.02
6293 14268 8.930846 ATTCTATCCTAGATGGGTGAATTTTG 57.069 34.615 0.00 0.00 34.22 2.44
6300 14275 7.895429 TCCTAGATGGGTGAATTTTGAGATTTT 59.105 33.333 0.00 0.00 36.20 1.82
6303 14278 8.655935 AGATGGGTGAATTTTGAGATTTTACT 57.344 30.769 0.00 0.00 0.00 2.24
6350 14325 6.824958 TCTAGGCCATTTTTAGACATACCT 57.175 37.500 5.01 0.00 0.00 3.08
6352 14327 4.451900 AGGCCATTTTTAGACATACCTCG 58.548 43.478 5.01 0.00 0.00 4.63
6355 14330 5.063880 GCCATTTTTAGACATACCTCGGAT 58.936 41.667 0.00 0.00 0.00 4.18
6356 14331 5.049405 GCCATTTTTAGACATACCTCGGATG 60.049 44.000 0.00 0.00 0.00 3.51
6357 14332 6.055588 CCATTTTTAGACATACCTCGGATGT 58.944 40.000 0.00 0.00 40.25 3.06
6358 14333 6.017934 CCATTTTTAGACATACCTCGGATGTG 60.018 42.308 0.00 0.00 37.65 3.21
6359 14334 3.728076 TTAGACATACCTCGGATGTGC 57.272 47.619 0.00 0.00 37.65 4.57
6360 14335 0.753262 AGACATACCTCGGATGTGCC 59.247 55.000 0.00 0.00 37.65 5.01
6361 14336 0.753262 GACATACCTCGGATGTGCCT 59.247 55.000 0.00 0.00 37.65 4.75
6362 14337 1.961394 GACATACCTCGGATGTGCCTA 59.039 52.381 0.00 0.00 37.65 3.93
6363 14338 1.964223 ACATACCTCGGATGTGCCTAG 59.036 52.381 0.00 0.00 36.18 3.02
6364 14339 0.969894 ATACCTCGGATGTGCCTAGC 59.030 55.000 0.00 0.00 0.00 3.42
6365 14340 0.106167 TACCTCGGATGTGCCTAGCT 60.106 55.000 0.00 0.00 0.00 3.32
6373 14348 0.038744 ATGTGCCTAGCTTTGTGCCT 59.961 50.000 0.00 0.00 44.23 4.75
6449 14425 6.484977 GCTGTTAGAAATAAATGAGCTAGGCT 59.515 38.462 0.00 0.00 43.88 4.58
6488 14464 3.091545 TCAAATTGAGGAGGCCATGAAC 58.908 45.455 5.01 0.00 0.00 3.18
6493 14469 1.425066 TGAGGAGGCCATGAACAACTT 59.575 47.619 5.01 0.00 0.00 2.66
6522 14498 2.640316 ACAAAAGAAGAAGCTCCCGT 57.360 45.000 0.00 0.00 0.00 5.28
6532 14508 2.159085 AGAAGCTCCCGTTCGATAAAGG 60.159 50.000 0.00 0.00 34.33 3.11
6552 14528 0.112995 AAATGCCTGGTCAAGAGCCA 59.887 50.000 0.00 0.00 34.42 4.75
6573 14549 1.140312 AGGAAGTGGAGGTGAAGCAA 58.860 50.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.855110 ACTTTTAAACATGTTGGTGATATGTGA 58.145 29.630 12.82 0.00 38.92 3.58
25 26 8.740906 TGACTTTACTTTTAAACATGTTGGTGA 58.259 29.630 12.82 1.28 0.00 4.02
55 56 5.731957 TTGGTTGGGCCTTAGTTTATTTC 57.268 39.130 4.53 0.00 38.35 2.17
91 92 2.132762 CTGAGGTACACACGGTTTGTC 58.867 52.381 2.74 0.00 35.67 3.18
163 164 0.523072 ATGCGAGCACCAATGTCAAC 59.477 50.000 0.00 0.00 0.00 3.18
277 280 9.555727 GTAGGCCATATCTATTTTTCTAACACA 57.444 33.333 5.01 0.00 0.00 3.72
446 468 1.298602 ACCGTTTACGACAAACCCAC 58.701 50.000 3.46 0.00 43.02 4.61
803 834 4.434330 GCCGCTAGAATAATACGCATGTTC 60.434 45.833 0.00 0.00 0.00 3.18
838 869 8.908903 TGTGTCTTGTTAACAACCAGATATTTT 58.091 29.630 17.01 0.00 35.86 1.82
1119 1180 1.153086 CGGGAAGAAGATGGGGCTG 60.153 63.158 0.00 0.00 0.00 4.85
1311 1991 0.548682 AAGGACCCATGAGAGCCAGT 60.549 55.000 0.00 0.00 0.00 4.00
1400 2081 5.639506 CCGAAGATGAACATGTCAAGTTACT 59.360 40.000 0.00 0.00 40.50 2.24
1425 2106 9.730420 TTGAGCAAAAAGTTGAGTATAAGTTTC 57.270 29.630 0.00 0.00 36.83 2.78
1429 2110 8.567948 TCCTTTGAGCAAAAAGTTGAGTATAAG 58.432 33.333 9.48 0.00 36.83 1.73
1433 2114 6.767524 TTCCTTTGAGCAAAAAGTTGAGTA 57.232 33.333 9.48 0.00 36.83 2.59
1474 2155 7.220030 ACATAGTTATGCATTTCTAGACAGGG 58.780 38.462 3.54 0.00 37.19 4.45
1498 2179 8.997621 TGTACATGTACTCCTTTTGAGATAAC 57.002 34.615 30.69 6.98 44.42 1.89
1510 2191 3.494626 CGGCAATGATGTACATGTACTCC 59.505 47.826 30.69 22.85 39.39 3.85
1515 2196 4.751600 CAGTATCGGCAATGATGTACATGT 59.248 41.667 14.43 2.69 39.39 3.21
1516 2197 4.751600 ACAGTATCGGCAATGATGTACATG 59.248 41.667 14.43 0.83 39.39 3.21
1517 2198 4.960938 ACAGTATCGGCAATGATGTACAT 58.039 39.130 8.43 8.43 41.45 2.29
1518 2199 4.400529 ACAGTATCGGCAATGATGTACA 57.599 40.909 0.00 0.00 0.00 2.90
1519 2200 6.309009 CAGATACAGTATCGGCAATGATGTAC 59.691 42.308 13.89 0.00 40.12 2.90
1549 2230 4.609301 TGGGTCCTTTTCTCAATAATGGG 58.391 43.478 0.00 0.00 0.00 4.00
1569 2250 6.523201 GCAAGTGTACTTCAATTACGAATTGG 59.477 38.462 15.56 7.34 46.40 3.16
1630 2831 7.861629 TGTGGAGACTGGAAGATAATACAAAT 58.138 34.615 0.00 0.00 37.43 2.32
1631 2832 7.252612 TGTGGAGACTGGAAGATAATACAAA 57.747 36.000 0.00 0.00 37.43 2.83
1682 3067 9.221775 CATATGTAATTTTTCCGAGCACTTTAC 57.778 33.333 0.00 0.00 0.00 2.01
1913 3331 8.797438 TGTTTAAGCATACATGTTATGACCAAA 58.203 29.630 2.30 4.69 0.00 3.28
1975 3701 1.003545 CGGCAACCGTTGATCATGATC 60.004 52.381 25.91 25.91 42.73 2.92
2002 3728 1.004745 ACGGAGGTTCTGGATGCAATT 59.995 47.619 0.00 0.00 0.00 2.32
2040 3769 1.156645 AGCCGATTGAGAGCATTCGC 61.157 55.000 0.00 0.00 43.06 4.70
2044 3773 1.047002 AGCTAGCCGATTGAGAGCAT 58.953 50.000 12.13 0.00 35.55 3.79
2045 3774 1.338337 GTAGCTAGCCGATTGAGAGCA 59.662 52.381 12.13 0.00 35.55 4.26
2048 3777 2.366640 AGGTAGCTAGCCGATTGAGA 57.633 50.000 19.06 0.00 0.00 3.27
2049 3778 4.792521 AATAGGTAGCTAGCCGATTGAG 57.207 45.455 19.06 0.00 31.65 3.02
2050 3779 6.659745 TTTAATAGGTAGCTAGCCGATTGA 57.340 37.500 19.06 12.55 34.15 2.57
2053 3782 6.267014 TCAGTTTTAATAGGTAGCTAGCCGAT 59.733 38.462 19.06 10.34 0.00 4.18
2054 3783 5.595542 TCAGTTTTAATAGGTAGCTAGCCGA 59.404 40.000 19.06 8.38 0.00 5.54
2055 3784 5.839621 TCAGTTTTAATAGGTAGCTAGCCG 58.160 41.667 19.06 0.00 0.00 5.52
2056 3785 6.482641 GGTTCAGTTTTAATAGGTAGCTAGCC 59.517 42.308 19.06 11.24 0.00 3.93
2058 3787 9.444600 TTTGGTTCAGTTTTAATAGGTAGCTAG 57.555 33.333 7.83 0.00 0.00 3.42
2059 3788 9.969001 ATTTGGTTCAGTTTTAATAGGTAGCTA 57.031 29.630 3.73 3.73 0.00 3.32
2061 3790 8.736244 TGATTTGGTTCAGTTTTAATAGGTAGC 58.264 33.333 0.00 0.00 0.00 3.58
2063 3792 9.575868 TGTGATTTGGTTCAGTTTTAATAGGTA 57.424 29.630 0.00 0.00 0.00 3.08
2064 3793 8.472007 TGTGATTTGGTTCAGTTTTAATAGGT 57.528 30.769 0.00 0.00 0.00 3.08
2065 3794 7.542130 GCTGTGATTTGGTTCAGTTTTAATAGG 59.458 37.037 0.00 0.00 0.00 2.57
2066 3795 7.542130 GGCTGTGATTTGGTTCAGTTTTAATAG 59.458 37.037 0.00 0.00 0.00 1.73
2068 3797 6.223120 GGCTGTGATTTGGTTCAGTTTTAAT 58.777 36.000 0.00 0.00 0.00 1.40
2099 3926 1.870580 CGGCCAGAAACGTGTAAGTCA 60.871 52.381 2.24 0.00 0.00 3.41
2135 3962 0.179100 ATGTCACTTGAGATCGGCCG 60.179 55.000 22.12 22.12 0.00 6.13
2158 3985 3.869246 ACGACAACCTTTAATAGCCATCG 59.131 43.478 0.00 0.00 0.00 3.84
2206 4033 1.261619 GGAGCATTGCTACACGTATGC 59.738 52.381 16.21 10.09 39.71 3.14
2210 4037 2.295253 GTAGGAGCATTGCTACACGT 57.705 50.000 22.64 9.54 42.99 4.49
2495 4324 1.937546 GCTGATGCCCTTGGAAACGG 61.938 60.000 0.00 0.00 0.00 4.44
2639 4468 2.422803 CCATTCCTTTTGGCTATCCCGA 60.423 50.000 0.00 0.00 40.12 5.14
2646 4475 0.404040 TCGTCCCATTCCTTTTGGCT 59.596 50.000 0.00 0.00 40.12 4.75
2742 4571 1.814394 GGCCCGAAATAAACCGTCTTT 59.186 47.619 0.00 0.00 0.00 2.52
2881 5146 3.214123 CCCATGTGCCCATCGCTG 61.214 66.667 0.00 0.00 38.78 5.18
2909 5174 2.646930 ACAGTGACCCATGTGCATATG 58.353 47.619 15.95 15.95 0.00 1.78
2921 5186 7.758495 TCTTTGAACTTTCTAAAACAGTGACC 58.242 34.615 0.00 0.00 0.00 4.02
3000 5490 4.215109 AGATACCAAACTTTGCAAGTGGT 58.785 39.130 22.07 22.07 41.91 4.16
3002 5492 6.515043 CAAAGATACCAAACTTTGCAAGTG 57.485 37.500 0.00 0.00 43.62 3.16
3051 5602 7.096477 GCATTTTTATCGACATTATGGAACTGC 60.096 37.037 0.00 0.00 0.00 4.40
3100 5731 2.605257 GGCTTTTCCCAGGTTAAAGGT 58.395 47.619 10.87 0.00 31.25 3.50
3118 5750 1.257750 GGAAACTGATTGGGTGGGGC 61.258 60.000 0.00 0.00 0.00 5.80
3154 5786 3.507411 TCAACTGCCTTGACCTACTAGT 58.493 45.455 0.00 0.00 33.65 2.57
3180 5813 3.156293 TCTTTGGTTCACCATCCATGTG 58.844 45.455 0.00 0.00 46.97 3.21
3189 6895 1.524008 CCGCCCTTCTTTGGTTCACC 61.524 60.000 0.00 0.00 0.00 4.02
3272 6979 6.269077 TGACAAATCTAAGTGACAAGGGAGTA 59.731 38.462 0.00 0.00 0.00 2.59
3305 7012 3.573695 TCGAGGGGTAATCCTAAGGAAG 58.426 50.000 0.00 0.00 37.25 3.46
3306 7013 3.693526 TCGAGGGGTAATCCTAAGGAA 57.306 47.619 0.00 0.00 37.25 3.36
3333 7040 7.041098 GCTCAAGATAAATAAGTACCCATGGTG 60.041 40.741 11.73 4.77 36.19 4.17
3342 7049 7.120923 AGGTTCCGCTCAAGATAAATAAGTA 57.879 36.000 0.00 0.00 0.00 2.24
3375 7082 3.525800 AAATACCAGGCCTGTCAGTTT 57.474 42.857 30.63 20.79 0.00 2.66
3384 7091 9.780186 GTATTAGGATCATATAAATACCAGGCC 57.220 37.037 0.00 0.00 30.36 5.19
3421 7128 6.560003 TGCATTCTTCTTGGGTATTCTCTA 57.440 37.500 0.00 0.00 0.00 2.43
3437 7144 2.436646 CGAGGGCGGTTGCATTCT 60.437 61.111 0.00 0.00 45.35 2.40
3535 7242 4.062293 TCCGTTGAACATTCAGTTTCGAT 58.938 39.130 0.00 0.00 41.51 3.59
3616 7323 2.285977 CCATTGGCTTTACCGTACCTC 58.714 52.381 0.00 0.00 43.94 3.85
3656 9768 1.348036 GACCTGGCGCCTAAGGATATT 59.652 52.381 33.30 15.29 37.01 1.28
3670 9782 4.017126 TCAGTATATATGCGAGGACCTGG 58.983 47.826 0.00 0.00 0.00 4.45
3708 9820 7.169982 CACTAAAGATGTCGATCCTAATGGTTC 59.830 40.741 0.00 0.00 34.23 3.62
4091 10649 5.783111 ACAAGTTACCCAAATGAGAATTGC 58.217 37.500 0.00 0.00 0.00 3.56
4096 10654 7.074653 AGAAGTACAAGTTACCCAAATGAGA 57.925 36.000 0.00 0.00 0.00 3.27
4245 10807 3.929094 TGCCTTTGAATTTCATTGGAGC 58.071 40.909 17.22 9.89 0.00 4.70
4362 10924 5.984695 TCAGTGTCTAAGATAGCAACAGT 57.015 39.130 0.00 0.00 0.00 3.55
4437 11002 4.749245 ACTTCAAACTCAACCTAATGCG 57.251 40.909 0.00 0.00 0.00 4.73
4460 11028 7.818446 ACATGAAGCATATGAGTGAGACATATC 59.182 37.037 6.97 0.00 38.40 1.63
4500 11069 2.045524 ACATACTCTCCCTGCAGGATG 58.954 52.381 34.91 27.35 46.33 3.51
4515 11084 5.048713 AGCTTGCCTTTGTTGAACTACATAC 60.049 40.000 0.00 0.00 0.00 2.39
4658 11227 8.735692 ATTGTGACCAACATTGAAGAAAATTT 57.264 26.923 0.00 0.00 38.99 1.82
4724 11293 4.362932 TGTTGTTTTTGTCGCTTCATCA 57.637 36.364 0.00 0.00 0.00 3.07
4766 11366 7.066525 CGTGCCTTAAAGGGTCAAGAAATATAA 59.933 37.037 0.00 0.00 35.37 0.98
4927 11531 9.485591 CTACATTTTACAAACGATCATGTAACC 57.514 33.333 12.66 0.00 40.62 2.85
4986 11590 4.333926 GGCTATGACAAATTCAGTGACTCC 59.666 45.833 0.00 0.00 37.77 3.85
4988 11593 4.910195 TGGCTATGACAAATTCAGTGACT 58.090 39.130 0.00 0.00 37.77 3.41
5057 11662 8.947115 CCAGTTAGGTAATAAGCAATTATAGCC 58.053 37.037 0.00 0.00 32.70 3.93
5120 11728 1.137404 GCAAGCCCATAGTGTTGCG 59.863 57.895 0.00 0.00 36.28 4.85
5151 11759 6.198650 TGCTACAATCATCATCAAACCTTG 57.801 37.500 0.00 0.00 0.00 3.61
5171 11779 0.833287 AATCAGGTACGATGGCTGCT 59.167 50.000 0.00 0.00 0.00 4.24
5255 11863 1.564348 GGGAGGTCATTTGGAAGCCTA 59.436 52.381 0.00 0.00 0.00 3.93
5526 12137 1.933115 ATGGGTTTTGCCGCATCGAC 61.933 55.000 0.00 0.00 38.44 4.20
5533 12144 4.119136 GGATTTTATCATGGGTTTTGCCG 58.881 43.478 0.00 0.00 38.44 5.69
5770 12387 7.961326 AAAATATGCCACTCCTAGACAAATT 57.039 32.000 0.00 0.00 0.00 1.82
5771 12388 8.494433 TCTAAAATATGCCACTCCTAGACAAAT 58.506 33.333 0.00 0.00 0.00 2.32
5775 12392 7.386299 CACATCTAAAATATGCCACTCCTAGAC 59.614 40.741 0.00 0.00 0.00 2.59
5800 12417 4.160626 GTCCTCCTAAGCTAGCTTCTTTCA 59.839 45.833 32.51 14.57 37.47 2.69
5801 12418 4.689071 GTCCTCCTAAGCTAGCTTCTTTC 58.311 47.826 32.51 13.95 37.47 2.62
5803 12420 2.691011 CGTCCTCCTAAGCTAGCTTCTT 59.309 50.000 32.51 13.07 37.47 2.52
5824 12441 1.153229 GGTCGGCTGGGGATAACAC 60.153 63.158 0.00 0.00 0.00 3.32
5834 12452 1.672356 CTTGAACCCTGGTCGGCTG 60.672 63.158 0.00 0.00 0.00 4.85
5838 12456 0.320771 CAGGACTTGAACCCTGGTCG 60.321 60.000 0.00 0.00 44.68 4.79
5847 12465 1.301716 GCGAGCACCAGGACTTGAA 60.302 57.895 0.00 0.00 0.00 2.69
5852 12470 0.598065 AAAAATGCGAGCACCAGGAC 59.402 50.000 0.00 0.00 0.00 3.85
5856 12474 0.597568 CCAGAAAAATGCGAGCACCA 59.402 50.000 0.00 0.00 0.00 4.17
5861 12479 6.611381 TGAAATAAGTCCAGAAAAATGCGAG 58.389 36.000 0.00 0.00 0.00 5.03
5875 12493 5.183228 TCACCGGAAATCCTGAAATAAGTC 58.817 41.667 9.46 0.00 0.00 3.01
5877 12495 5.822519 TCATCACCGGAAATCCTGAAATAAG 59.177 40.000 9.46 0.00 0.00 1.73
5884 12502 1.665679 CGTTCATCACCGGAAATCCTG 59.334 52.381 9.46 0.00 0.00 3.86
5895 12513 2.069273 CTCCCACTGAACGTTCATCAC 58.931 52.381 29.79 4.10 36.46 3.06
5896 12514 1.001974 CCTCCCACTGAACGTTCATCA 59.998 52.381 29.79 9.88 36.46 3.07
5897 12515 1.275291 TCCTCCCACTGAACGTTCATC 59.725 52.381 29.79 4.99 36.46 2.92
5901 12519 1.276421 CATCTCCTCCCACTGAACGTT 59.724 52.381 0.00 0.00 0.00 3.99
5902 12520 0.898320 CATCTCCTCCCACTGAACGT 59.102 55.000 0.00 0.00 0.00 3.99
5907 12525 1.630369 TGGAAACATCTCCTCCCACTG 59.370 52.381 0.00 0.00 36.35 3.66
5924 12542 1.557099 AGCACCTTGTAGTCGATGGA 58.443 50.000 0.00 0.00 0.00 3.41
5927 12545 3.451178 ACCATAAGCACCTTGTAGTCGAT 59.549 43.478 0.00 0.00 0.00 3.59
5936 12554 2.038557 ACGAAGTCACCATAAGCACCTT 59.961 45.455 0.00 0.00 29.74 3.50
5943 12561 8.786826 ATTGAGATTTTACGAAGTCACCATAA 57.213 30.769 0.00 0.00 43.93 1.90
5964 12582 3.582647 ACTGGTCCGGCATATCATATTGA 59.417 43.478 0.00 0.00 0.00 2.57
5981 12599 2.027745 CCACTATGAGCACAAGACTGGT 60.028 50.000 0.00 0.00 0.00 4.00
5982 12600 2.027745 ACCACTATGAGCACAAGACTGG 60.028 50.000 0.00 0.00 0.00 4.00
5989 12607 2.758130 TCCCATACCACTATGAGCACA 58.242 47.619 0.00 0.00 32.66 4.57
5993 12611 4.101585 ACACACATCCCATACCACTATGAG 59.898 45.833 0.00 0.00 32.66 2.90
6000 12618 1.702401 ACACACACACATCCCATACCA 59.298 47.619 0.00 0.00 0.00 3.25
6005 12623 2.655090 ATGAACACACACACATCCCA 57.345 45.000 0.00 0.00 0.00 4.37
6008 12626 3.009723 CCCCTATGAACACACACACATC 58.990 50.000 0.00 0.00 0.00 3.06
6009 12627 2.375174 ACCCCTATGAACACACACACAT 59.625 45.455 0.00 0.00 0.00 3.21
6017 12637 5.296780 CACATACATTCACCCCTATGAACAC 59.703 44.000 0.00 0.00 41.29 3.32
6018 12638 5.045213 ACACATACATTCACCCCTATGAACA 60.045 40.000 0.00 0.00 41.29 3.18
6029 12649 7.489435 AGCGCTCATATATACACATACATTCAC 59.511 37.037 2.64 0.00 0.00 3.18
6040 12660 2.986479 CACGCAAGCGCTCATATATACA 59.014 45.455 12.06 0.00 44.19 2.29
6043 12665 1.794701 CACACGCAAGCGCTCATATAT 59.205 47.619 12.06 0.00 44.19 0.86
6089 12711 4.891168 TCTGGAACGCAGTAGTATTATCCA 59.109 41.667 0.00 0.00 45.00 3.41
6092 12714 4.038883 GGGTCTGGAACGCAGTAGTATTAT 59.961 45.833 0.00 0.00 45.00 1.28
6103 12725 2.617274 GCACTTGGGTCTGGAACGC 61.617 63.158 0.00 0.00 41.08 4.84
6131 12753 3.822735 AGCACGGCATAATATCTGCATTT 59.177 39.130 11.17 0.00 41.47 2.32
6151 12773 2.182030 CTCCCGAGACACCGAAGC 59.818 66.667 0.00 0.00 0.00 3.86
6152 12774 2.885861 CCTCCCGAGACACCGAAG 59.114 66.667 0.00 0.00 0.00 3.79
6153 12775 3.379445 GCCTCCCGAGACACCGAA 61.379 66.667 0.00 0.00 0.00 4.30
6154 12776 3.957435 ATGCCTCCCGAGACACCGA 62.957 63.158 0.00 0.00 0.00 4.69
6155 12777 1.672854 TAATGCCTCCCGAGACACCG 61.673 60.000 0.00 0.00 0.00 4.94
6156 12778 0.759346 ATAATGCCTCCCGAGACACC 59.241 55.000 0.00 0.00 0.00 4.16
6161 12783 1.597742 CAACCATAATGCCTCCCGAG 58.402 55.000 0.00 0.00 0.00 4.63
6222 12844 2.178273 CCGGTTTTAGGCAAGCGC 59.822 61.111 0.00 0.00 44.45 5.92
6223 12845 2.874751 CCCGGTTTTAGGCAAGCG 59.125 61.111 0.00 1.22 45.19 4.68
6311 14286 7.446106 TGGCCTAGATTTAGGTAAAGAATGA 57.554 36.000 10.83 0.00 46.96 2.57
6312 14287 8.697507 AATGGCCTAGATTTAGGTAAAGAATG 57.302 34.615 10.83 0.00 46.96 2.67
6318 14293 9.623000 GTCTAAAAATGGCCTAGATTTAGGTAA 57.377 33.333 20.58 0.56 46.96 2.85
6326 14301 7.394144 AGGTATGTCTAAAAATGGCCTAGAT 57.606 36.000 3.32 0.00 0.00 1.98
6339 14314 2.364324 GGCACATCCGAGGTATGTCTAA 59.636 50.000 4.87 0.00 35.39 2.10
6350 14325 0.613260 ACAAAGCTAGGCACATCCGA 59.387 50.000 0.00 0.00 40.77 4.55
6352 14327 0.453390 GCACAAAGCTAGGCACATCC 59.547 55.000 0.00 0.00 41.15 3.51
6355 14330 0.890542 CAGGCACAAAGCTAGGCACA 60.891 55.000 0.00 0.00 44.79 4.57
6356 14331 0.606401 TCAGGCACAAAGCTAGGCAC 60.606 55.000 0.00 0.00 44.79 5.01
6357 14332 0.110295 TTCAGGCACAAAGCTAGGCA 59.890 50.000 0.00 0.00 44.79 4.75
6358 14333 1.068264 GTTTCAGGCACAAAGCTAGGC 60.068 52.381 0.00 0.00 44.79 3.93
6359 14334 1.541588 GGTTTCAGGCACAAAGCTAGG 59.458 52.381 0.00 0.00 44.79 3.02
6360 14335 2.227388 CAGGTTTCAGGCACAAAGCTAG 59.773 50.000 11.18 0.00 44.79 3.42
6361 14336 2.229792 CAGGTTTCAGGCACAAAGCTA 58.770 47.619 11.18 0.00 44.79 3.32
6362 14337 1.035139 CAGGTTTCAGGCACAAAGCT 58.965 50.000 6.97 6.97 44.79 3.74
6363 14338 0.032540 CCAGGTTTCAGGCACAAAGC 59.967 55.000 3.02 3.02 44.65 3.51
6418 14394 7.559170 AGCTCATTTATTTCTAACAGCAAGGAT 59.441 33.333 0.00 0.00 0.00 3.24
6476 14452 3.751479 AAAAAGTTGTTCATGGCCTCC 57.249 42.857 3.32 0.00 0.00 4.30
6497 14473 4.505039 GGGAGCTTCTTCTTTTGTAGGTCA 60.505 45.833 0.00 0.00 35.61 4.02
6503 14479 2.640316 ACGGGAGCTTCTTCTTTTGT 57.360 45.000 0.00 0.00 0.00 2.83
6522 14498 3.945285 GACCAGGCATTTCCTTTATCGAA 59.055 43.478 0.00 0.00 44.75 3.71
6532 14508 0.813821 GGCTCTTGACCAGGCATTTC 59.186 55.000 0.00 0.00 36.45 2.17
6552 14528 1.494721 TGCTTCACCTCCACTTCCTTT 59.505 47.619 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.