Multiple sequence alignment - TraesCS6A01G338000

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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 TraesCS6A01G338000 chr6A 100.000 4790 0 0 1 4790 571794518 571799307 0.000000e+00 8846.0
1 TraesCS6A01G338000 chr6D 90.293 2215 134 44 1 2177 427087213 427089384 0.000000e+00 2824.0
2 TraesCS6A01G338000 chr6D 91.853 1964 104 27 2470 4404 427089991 427091927 0.000000e+00 2689.0
3 TraesCS6A01G338000 chr6D 93.818 275 13 1 2188 2458 427089669 427089943 1.240000e-110 411.0
4 TraesCS6A01G338000 chr6D 91.477 176 8 3 4439 4614 427091992 427092160 8.010000e-58 235.0
5 TraesCS6A01G338000 chr6D 89.873 158 12 3 1923 2077 427088991 427089147 2.920000e-47 200.0
6 TraesCS6A01G338000 chr6B 90.156 1991 121 30 2480 4432 642917324 642919277 0.000000e+00 2521.0
7 TraesCS6A01G338000 chr6B 90.252 1590 88 28 1 1554 642914713 642916271 0.000000e+00 2015.0
8 TraesCS6A01G338000 chr6B 88.104 807 56 23 1603 2377 642916352 642917150 0.000000e+00 922.0
9 TraesCS6A01G338000 chr6B 90.341 176 10 3 4439 4614 642919330 642919498 1.730000e-54 224.0
10 TraesCS6A01G338000 chr6B 95.238 42 2 0 4653 4694 642919519 642919560 3.090000e-07 67.6
11 TraesCS6A01G338000 chr3A 86.449 214 28 1 1003 1216 116518972 116519184 2.880000e-57 233.0
12 TraesCS6A01G338000 chr3A 87.195 164 15 5 4224 4386 21364460 21364618 1.060000e-41 182.0
13 TraesCS6A01G338000 chr3D 85.981 214 29 1 1003 1216 98871944 98872156 1.340000e-55 228.0
14 TraesCS6A01G338000 chr3D 84.524 84 11 2 4423 4505 182029655 182029573 1.100000e-11 82.4
15 TraesCS6A01G338000 chr3B 85.981 214 29 1 1003 1216 149453773 149453985 1.340000e-55 228.0
16 TraesCS6A01G338000 chr3B 84.091 88 11 3 4423 4509 260316911 260316826 1.100000e-11 82.4
17 TraesCS6A01G338000 chr7A 85.854 205 29 0 1008 1212 519131139 519131343 8.070000e-53 219.0
18 TraesCS6A01G338000 chr7D 85.366 205 30 0 1008 1212 476689884 476689680 3.760000e-51 213.0
19 TraesCS6A01G338000 chr7D 100.000 28 0 0 1 28 49866347 49866374 9.000000e-03 52.8
20 TraesCS6A01G338000 chr7B 85.366 205 30 0 1008 1212 500732710 500732506 3.760000e-51 213.0
21 TraesCS6A01G338000 chr2D 84.343 198 31 0 1015 1212 151325830 151326027 1.360000e-45 195.0
22 TraesCS6A01G338000 chr2D 85.976 164 19 3 4224 4386 571078959 571079119 6.370000e-39 172.0
23 TraesCS6A01G338000 chr4D 86.905 168 17 4 4224 4389 64390472 64390636 2.940000e-42 183.0
24 TraesCS6A01G338000 chr4D 92.500 40 3 0 4420 4459 329302458 329302497 1.860000e-04 58.4
25 TraesCS6A01G338000 chr1D 87.349 166 12 7 4224 4386 462301357 462301516 1.060000e-41 182.0
26 TraesCS6A01G338000 chr5D 84.916 179 20 6 4224 4399 241946445 241946271 1.770000e-39 174.0
27 TraesCS6A01G338000 chr2B 85.714 168 19 4 4221 4386 752669220 752669384 6.370000e-39 172.0
28 TraesCS6A01G338000 chr5A 85.207 169 18 6 4220 4386 136396941 136396778 2.970000e-37 167.0
29 TraesCS6A01G338000 chr5B 79.310 87 16 2 4424 4509 43454713 43454628 5.180000e-05 60.2
30 TraesCS6A01G338000 chrUn 94.444 36 1 1 1 35 50506472 50506507 2.000000e-03 54.7
31 TraesCS6A01G338000 chrUn 92.308 39 2 1 1 38 50544218 50544180 2.000000e-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 TraesCS6A01G338000 chr6A 571794518 571799307 4789 False 8846.00 8846 100.0000 1 4790 1 chr6A.!!$F1 4789
1 TraesCS6A01G338000 chr6D 427087213 427092160 4947 False 1271.80 2824 91.4628 1 4614 5 chr6D.!!$F1 4613
2 TraesCS6A01G338000 chr6B 642914713 642919560 4847 False 1149.92 2521 90.8182 1 4694 5 chr6B.!!$F1 4693

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
983 1021 0.179029 GACGGGAGGAGAGAGAGAGG 60.179 65.000 0.00 0.0 0.00 3.69 F
1274 1312 0.032615 TCTCCTTCCTCTCCTCTGCC 60.033 60.000 0.00 0.0 0.00 4.85 F
1579 1619 0.107703 TCCTTCATGGTGCGGATGAC 60.108 55.000 0.00 0.0 37.07 3.06 F
2120 2206 0.687757 ATAGCTGCGGAGAGAACCCA 60.688 55.000 8.65 0.0 0.00 4.51 F
2463 2856 1.272490 TCATGCGAGAGAAAAGACGGT 59.728 47.619 0.00 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2265 0.243636 AGAAAAGCAAAATCCCGCCG 59.756 50.000 0.00 0.0 0.00 6.46 R
2417 2805 0.392998 CCATCCAAGCACGGCTACTT 60.393 55.000 0.00 0.0 38.25 2.24 R
2971 3425 0.400594 GGGTTGGTACCTTCTGCTGT 59.599 55.000 14.36 0.0 44.38 4.40 R
3120 3610 0.549902 TGAGCCAAGGGATGAGGGAA 60.550 55.000 0.00 0.0 0.00 3.97 R
4129 4628 1.408702 TGCACCAAAAGAGCAAGAACC 59.591 47.619 0.00 0.0 39.28 3.62 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
33 34 6.152932 AGGTAGCATGGCATTTTTCTATTG 57.847 37.500 0.00 0.00 0.00 1.90
38 39 5.577945 AGCATGGCATTTTTCTATTGAAACG 59.422 36.000 0.00 0.00 41.34 3.60
288 313 9.881529 AAAATCATGAATTCCAAATTTTTCGTG 57.118 25.926 13.08 13.08 33.84 4.35
289 314 8.830201 AATCATGAATTCCAAATTTTTCGTGA 57.170 26.923 19.87 19.87 44.03 4.35
291 316 8.830201 TCATGAATTCCAAATTTTTCGTGAAT 57.170 26.923 17.14 6.74 39.74 2.57
582 613 7.133891 AGAATCTAACATCTTCACAAAACCG 57.866 36.000 0.00 0.00 0.00 4.44
628 659 0.970427 TACAGCGAGACAGATGGCCA 60.970 55.000 8.56 8.56 0.00 5.36
687 718 1.527370 GGCCACTCCCACTGATACC 59.473 63.158 0.00 0.00 0.00 2.73
717 749 2.071262 ATCCTCCTCCCAGCTGCAG 61.071 63.158 10.11 10.11 0.00 4.41
805 838 0.533491 TACCGCGCAAGATACCAACT 59.467 50.000 8.75 0.00 43.02 3.16
812 845 2.019156 GCAAGATACCAACTCTGCCCC 61.019 57.143 0.00 0.00 0.00 5.80
823 856 0.189574 CTCTGCCCCTCATCCCTCTA 59.810 60.000 0.00 0.00 0.00 2.43
830 863 1.062886 CCCTCATCCCTCTACTGGACA 60.063 57.143 0.00 0.00 33.94 4.02
933 966 1.536418 CCTCCTCCAGTCCACCACA 60.536 63.158 0.00 0.00 0.00 4.17
934 967 1.674057 CTCCTCCAGTCCACCACAC 59.326 63.158 0.00 0.00 0.00 3.82
971 1009 2.885861 CCGGACTCTTGACGGGAG 59.114 66.667 0.00 0.00 43.69 4.30
979 1017 0.992695 TCTTGACGGGAGGAGAGAGA 59.007 55.000 0.00 0.00 0.00 3.10
980 1018 1.065053 TCTTGACGGGAGGAGAGAGAG 60.065 57.143 0.00 0.00 0.00 3.20
981 1019 0.992695 TTGACGGGAGGAGAGAGAGA 59.007 55.000 0.00 0.00 0.00 3.10
982 1020 0.544223 TGACGGGAGGAGAGAGAGAG 59.456 60.000 0.00 0.00 0.00 3.20
983 1021 0.179029 GACGGGAGGAGAGAGAGAGG 60.179 65.000 0.00 0.00 0.00 3.69
984 1022 1.150536 CGGGAGGAGAGAGAGAGGG 59.849 68.421 0.00 0.00 0.00 4.30
985 1023 1.349542 CGGGAGGAGAGAGAGAGGGA 61.350 65.000 0.00 0.00 0.00 4.20
986 1024 0.478507 GGGAGGAGAGAGAGAGGGAG 59.521 65.000 0.00 0.00 0.00 4.30
987 1025 1.518367 GGAGGAGAGAGAGAGGGAGA 58.482 60.000 0.00 0.00 0.00 3.71
988 1026 1.850345 GGAGGAGAGAGAGAGGGAGAA 59.150 57.143 0.00 0.00 0.00 2.87
1249 1287 0.036388 TCCCTCCGTGCAAACTCATC 60.036 55.000 0.00 0.00 0.00 2.92
1272 1310 2.292192 ACCTTCTCCTTCCTCTCCTCTG 60.292 54.545 0.00 0.00 0.00 3.35
1273 1311 1.756538 CTTCTCCTTCCTCTCCTCTGC 59.243 57.143 0.00 0.00 0.00 4.26
1274 1312 0.032615 TCTCCTTCCTCTCCTCTGCC 60.033 60.000 0.00 0.00 0.00 4.85
1367 1405 0.392193 ATTCTTGCCGAGCTGTGGAG 60.392 55.000 5.77 0.00 0.00 3.86
1449 1489 3.438297 TCCGGATCGAGTGATTTCTTC 57.562 47.619 0.00 0.00 34.09 2.87
1459 1499 6.765403 TCGAGTGATTTCTTCCTTTTTAGGA 58.235 36.000 0.00 0.00 35.93 2.94
1484 1524 4.503991 GGATGGATTGAGCCGTAGATTTCT 60.504 45.833 0.00 0.00 0.00 2.52
1545 1585 9.755804 GATTTCCTTTTCTTGTTGAAATTCTCT 57.244 29.630 0.00 0.00 43.34 3.10
1554 1594 7.365741 TCTTGTTGAAATTCTCTCTTCAATGC 58.634 34.615 1.02 0.00 42.01 3.56
1555 1595 6.638096 TGTTGAAATTCTCTCTTCAATGCA 57.362 33.333 0.00 0.00 42.01 3.96
1556 1596 7.223260 TGTTGAAATTCTCTCTTCAATGCAT 57.777 32.000 0.00 0.00 42.01 3.96
1557 1597 7.088272 TGTTGAAATTCTCTCTTCAATGCATG 58.912 34.615 0.00 0.00 42.01 4.06
1579 1619 0.107703 TCCTTCATGGTGCGGATGAC 60.108 55.000 0.00 0.00 37.07 3.06
1591 1631 2.695314 GGATGACCGTGGAATGAGC 58.305 57.895 0.00 0.00 0.00 4.26
1707 1788 2.121786 GATTGCAGCAATGCGTATTGG 58.878 47.619 25.66 12.14 43.12 3.16
1750 1832 3.883489 AGGAGGTCTGTAAAGTTTTGTGC 59.117 43.478 0.00 0.00 0.00 4.57
1754 1836 5.891451 AGGTCTGTAAAGTTTTGTGCTTTC 58.109 37.500 0.00 0.00 37.37 2.62
1755 1837 5.652452 AGGTCTGTAAAGTTTTGTGCTTTCT 59.348 36.000 0.00 0.00 37.37 2.52
1756 1838 5.971792 GGTCTGTAAAGTTTTGTGCTTTCTC 59.028 40.000 0.00 0.00 37.37 2.87
1760 1842 7.120579 TCTGTAAAGTTTTGTGCTTTCTCTTCA 59.879 33.333 0.00 0.00 37.37 3.02
1762 1844 7.701924 TGTAAAGTTTTGTGCTTTCTCTTCATG 59.298 33.333 0.00 0.00 37.37 3.07
1784 1866 5.116180 TGATGAAGTTAAATCTTCCGCGAT 58.884 37.500 8.23 0.00 41.96 4.58
1786 1868 5.961395 TGAAGTTAAATCTTCCGCGATAC 57.039 39.130 8.23 0.00 41.96 2.24
1816 1898 0.938008 GCCTCGCTATAGTTGTTGGC 59.062 55.000 0.84 9.10 0.00 4.52
1823 1905 2.420687 GCTATAGTTGTTGGCAGCCTCT 60.421 50.000 14.15 6.01 0.00 3.69
1842 1924 2.723746 CGCAATGCTATGGCCACC 59.276 61.111 8.16 0.00 37.74 4.61
1895 1977 4.142902 ACGATCCAAAGTTCAGCAATAACG 60.143 41.667 0.00 0.00 32.00 3.18
1910 1992 6.313905 CAGCAATAACGTACAGAAATCCTCTT 59.686 38.462 0.00 0.00 29.07 2.85
1976 2058 1.595109 CCTCCGCGCAATGCTATGA 60.595 57.895 8.75 0.00 43.27 2.15
2004 2086 1.792367 CGCGAAATGCTCCGAATATCA 59.208 47.619 0.00 0.00 43.27 2.15
2012 2094 2.224042 TGCTCCGAATATCACGCTGAAT 60.224 45.455 0.00 0.00 0.00 2.57
2120 2206 0.687757 ATAGCTGCGGAGAGAACCCA 60.688 55.000 8.65 0.00 0.00 4.51
2133 2219 3.709653 AGAGAACCCACCGCTAAATCATA 59.290 43.478 0.00 0.00 0.00 2.15
2185 2545 3.976701 AATGTGAGGAAGCGGCGGG 62.977 63.158 9.78 0.00 0.00 6.13
2194 2554 2.275380 AAGCGGCGGGATTTTGCTT 61.275 52.632 9.78 0.00 40.79 3.91
2226 2586 6.653989 TGGTCTCTGTTTCTTTTCTTTCTCT 58.346 36.000 0.00 0.00 0.00 3.10
2248 2608 5.240844 TCTTGTCTTTTTAGGCAAGTAAGGC 59.759 40.000 16.41 0.00 39.28 4.35
2259 2619 3.308866 GGCAAGTAAGGCTGTAATGTACG 59.691 47.826 0.00 0.00 0.00 3.67
2298 2659 6.659242 CCTTTCCCTTTTTCAGTTAGCATCTA 59.341 38.462 0.00 0.00 0.00 1.98
2320 2681 2.796593 TGCTATGCATCGAATCTGTTCG 59.203 45.455 0.19 4.32 45.23 3.95
2459 2852 4.527509 AGAGTTCATGCGAGAGAAAAGA 57.472 40.909 0.00 0.00 0.00 2.52
2463 2856 1.272490 TCATGCGAGAGAAAAGACGGT 59.728 47.619 0.00 0.00 0.00 4.83
2464 2857 1.656095 CATGCGAGAGAAAAGACGGTC 59.344 52.381 0.00 0.00 0.00 4.79
2466 2859 1.272490 TGCGAGAGAAAAGACGGTCAT 59.728 47.619 11.27 0.00 0.00 3.06
2468 2861 3.130516 TGCGAGAGAAAAGACGGTCATAT 59.869 43.478 11.27 0.00 0.00 1.78
2600 3036 4.894705 TCTAGAGATGAGCATGCTCTTTCT 59.105 41.667 39.46 36.59 43.12 2.52
2603 3039 5.254901 AGAGATGAGCATGCTCTTTCTTTT 58.745 37.500 39.46 28.11 43.12 2.27
2604 3040 5.711036 AGAGATGAGCATGCTCTTTCTTTTT 59.289 36.000 39.46 26.33 43.12 1.94
2635 3072 2.016318 TCGTGCAATCAGCCTTTATGG 58.984 47.619 0.00 0.00 44.83 2.74
2689 3126 4.752146 ACGGCTGTACTATAAAGGTGTTC 58.248 43.478 0.00 0.00 0.00 3.18
2764 3201 5.363101 GTCATCAGAAATCAGCTGGTATGA 58.637 41.667 15.13 12.52 34.20 2.15
2822 3266 8.356000 ACTAGGCTTGTATCTACATCTAATCC 57.644 38.462 0.00 0.00 35.89 3.01
2829 3273 7.834881 TGTATCTACATCTAATCCCGACTTT 57.165 36.000 0.00 0.00 0.00 2.66
2831 3275 6.978674 ATCTACATCTAATCCCGACTTTCA 57.021 37.500 0.00 0.00 0.00 2.69
2849 3293 7.588143 ACTTTCAGAGTCAATTATCTTGTCG 57.412 36.000 0.00 0.00 31.20 4.35
2938 3392 9.462174 AAAAATACACACACAATTGTCATACTG 57.538 29.630 8.48 0.00 31.66 2.74
2983 3440 2.257207 AGCCTGTAACAGCAGAAGGTA 58.743 47.619 0.00 0.00 38.70 3.08
3328 3821 2.693864 AGGTCCAGCCTCCATGGG 60.694 66.667 13.02 2.26 46.96 4.00
3369 3862 3.668491 GCTACGATGATTACGCCTCTCTC 60.668 52.174 0.00 0.00 0.00 3.20
3835 4332 0.318762 GGAAGCTACCGCCATAGGAG 59.681 60.000 0.00 0.00 36.60 3.69
4027 4524 6.514541 GCATGCTATATGCTGTGAAACTTGAT 60.515 38.462 11.37 0.00 43.37 2.57
4030 4527 6.769341 TGCTATATGCTGTGAAACTTGATCAT 59.231 34.615 0.00 0.00 43.37 2.45
4033 4530 9.486497 CTATATGCTGTGAAACTTGATCATACT 57.514 33.333 0.00 0.00 38.04 2.12
4082 4581 4.126437 TGTCGATCGATTATGTTTGGCAT 58.874 39.130 22.50 0.00 41.42 4.40
4091 4590 5.748152 CGATTATGTTTGGCATTTTGGGTAG 59.252 40.000 0.00 0.00 38.94 3.18
4228 4729 5.446260 TCTTCTCCTGTTTTATAACCCCC 57.554 43.478 0.00 0.00 33.15 5.40
4229 4730 5.105853 TCTTCTCCTGTTTTATAACCCCCT 58.894 41.667 0.00 0.00 33.15 4.79
4231 4732 3.784202 TCTCCTGTTTTATAACCCCCTCC 59.216 47.826 0.00 0.00 33.15 4.30
4232 4733 2.506644 TCCTGTTTTATAACCCCCTCCG 59.493 50.000 0.00 0.00 33.15 4.63
4300 4801 9.471084 CATATGGATGTACATGAACGTAGTTTA 57.529 33.333 14.43 0.00 40.84 2.01
4301 4802 9.692749 ATATGGATGTACATGAACGTAGTTTAG 57.307 33.333 14.43 0.00 39.95 1.85
4348 4849 9.530129 GCTGCGTATGTAGTTCATATTAAAATC 57.470 33.333 1.82 0.00 40.54 2.17
4381 4882 8.755977 AGAAGACTTATATTTACAAACGGAGGA 58.244 33.333 0.00 0.00 0.00 3.71
4405 4906 8.095169 GGAAGTAAAACAGTATCCTCTTCTTCA 58.905 37.037 0.00 0.00 33.14 3.02
4435 4936 3.370527 GCTATCTTGTTTGGGAGCACCTA 60.371 47.826 0.00 0.00 41.11 3.08
4437 4938 3.071874 TCTTGTTTGGGAGCACCTATG 57.928 47.619 0.00 0.00 41.11 2.23
4481 5029 6.877611 TCTTTGTTTCAGTCTATTGTTCCC 57.122 37.500 0.00 0.00 0.00 3.97
4505 5053 6.083098 TGAAACGTTTGATTCACATCCAAT 57.917 33.333 20.10 0.00 32.63 3.16
4554 5102 6.176183 ACTTCCAGTCAATTCCAATACTCAG 58.824 40.000 0.00 0.00 0.00 3.35
4565 5113 2.213499 CAATACTCAGCCCGATCAACC 58.787 52.381 0.00 0.00 0.00 3.77
4566 5114 1.496060 ATACTCAGCCCGATCAACCA 58.504 50.000 0.00 0.00 0.00 3.67
4567 5115 1.271856 TACTCAGCCCGATCAACCAA 58.728 50.000 0.00 0.00 0.00 3.67
4568 5116 0.321653 ACTCAGCCCGATCAACCAAC 60.322 55.000 0.00 0.00 0.00 3.77
4596 5144 3.793801 GCAGACAGGAAGTGCTACTATCG 60.794 52.174 0.00 0.00 34.23 2.92
4614 5162 1.885887 TCGAAGCCCAACCAATCAAAG 59.114 47.619 0.00 0.00 0.00 2.77
4615 5163 1.669795 CGAAGCCCAACCAATCAAAGC 60.670 52.381 0.00 0.00 0.00 3.51
4616 5164 0.686789 AAGCCCAACCAATCAAAGCC 59.313 50.000 0.00 0.00 0.00 4.35
4617 5165 1.194121 AGCCCAACCAATCAAAGCCC 61.194 55.000 0.00 0.00 0.00 5.19
4618 5166 1.479368 GCCCAACCAATCAAAGCCCA 61.479 55.000 0.00 0.00 0.00 5.36
4620 5168 1.270785 CCCAACCAATCAAAGCCCAAC 60.271 52.381 0.00 0.00 0.00 3.77
4623 5171 3.496515 CCAACCAATCAAAGCCCAACAAT 60.497 43.478 0.00 0.00 0.00 2.71
4624 5172 3.683365 ACCAATCAAAGCCCAACAATC 57.317 42.857 0.00 0.00 0.00 2.67
4627 5175 3.747529 CCAATCAAAGCCCAACAATCAAC 59.252 43.478 0.00 0.00 0.00 3.18
4628 5176 4.503643 CCAATCAAAGCCCAACAATCAACT 60.504 41.667 0.00 0.00 0.00 3.16
4630 5178 4.846779 TCAAAGCCCAACAATCAACTAC 57.153 40.909 0.00 0.00 0.00 2.73
4631 5179 3.572255 TCAAAGCCCAACAATCAACTACC 59.428 43.478 0.00 0.00 0.00 3.18
4632 5180 2.215942 AGCCCAACAATCAACTACCC 57.784 50.000 0.00 0.00 0.00 3.69
4637 5185 3.009033 CCCAACAATCAACTACCCAGAGA 59.991 47.826 0.00 0.00 0.00 3.10
4638 5186 4.256920 CCAACAATCAACTACCCAGAGAG 58.743 47.826 0.00 0.00 0.00 3.20
4639 5187 4.256920 CAACAATCAACTACCCAGAGAGG 58.743 47.826 0.00 0.00 37.03 3.69
4640 5188 3.521727 ACAATCAACTACCCAGAGAGGT 58.478 45.455 0.00 0.00 44.37 3.85
4641 5189 4.684724 ACAATCAACTACCCAGAGAGGTA 58.315 43.478 0.00 0.00 41.58 3.08
4642 5190 5.091552 ACAATCAACTACCCAGAGAGGTAA 58.908 41.667 0.00 0.00 41.85 2.85
4643 5191 5.546499 ACAATCAACTACCCAGAGAGGTAAA 59.454 40.000 0.00 0.00 41.85 2.01
4644 5192 6.043938 ACAATCAACTACCCAGAGAGGTAAAA 59.956 38.462 0.00 0.00 41.85 1.52
4645 5193 6.697641 ATCAACTACCCAGAGAGGTAAAAA 57.302 37.500 0.00 0.00 41.85 1.94
4689 5237 7.485810 TGTACATGACCACACACTATACATAC 58.514 38.462 0.00 0.00 0.00 2.39
4694 5242 7.661127 TGACCACACACTATACATACAAAAC 57.339 36.000 0.00 0.00 0.00 2.43
4695 5243 6.366604 TGACCACACACTATACATACAAAACG 59.633 38.462 0.00 0.00 0.00 3.60
4696 5244 5.121142 ACCACACACTATACATACAAAACGC 59.879 40.000 0.00 0.00 0.00 4.84
4697 5245 5.446741 CCACACACTATACATACAAAACGCC 60.447 44.000 0.00 0.00 0.00 5.68
4698 5246 4.632688 ACACACTATACATACAAAACGCCC 59.367 41.667 0.00 0.00 0.00 6.13
4699 5247 4.034742 CACACTATACATACAAAACGCCCC 59.965 45.833 0.00 0.00 0.00 5.80
4700 5248 3.246699 CACTATACATACAAAACGCCCCG 59.753 47.826 0.00 0.00 0.00 5.73
4701 5249 2.406596 ATACATACAAAACGCCCCGT 57.593 45.000 0.00 0.00 43.97 5.28
4702 5250 1.440708 TACATACAAAACGCCCCGTG 58.559 50.000 0.00 0.00 39.99 4.94
4703 5251 0.535553 ACATACAAAACGCCCCGTGT 60.536 50.000 0.00 0.00 39.99 4.49
4704 5252 1.270732 ACATACAAAACGCCCCGTGTA 60.271 47.619 0.00 0.00 39.99 2.90
4705 5253 1.129064 CATACAAAACGCCCCGTGTAC 59.871 52.381 0.00 0.00 39.99 2.90
4706 5254 0.392336 TACAAAACGCCCCGTGTACT 59.608 50.000 0.00 0.00 39.99 2.73
4707 5255 0.464193 ACAAAACGCCCCGTGTACTT 60.464 50.000 0.00 0.00 39.99 2.24
4708 5256 0.664224 CAAAACGCCCCGTGTACTTT 59.336 50.000 0.00 0.00 39.99 2.66
4709 5257 1.065851 CAAAACGCCCCGTGTACTTTT 59.934 47.619 0.00 0.00 39.99 2.27
4710 5258 0.946528 AAACGCCCCGTGTACTTTTC 59.053 50.000 0.00 0.00 39.99 2.29
4711 5259 0.886043 AACGCCCCGTGTACTTTTCC 60.886 55.000 0.00 0.00 39.99 3.13
4712 5260 2.036571 CGCCCCGTGTACTTTTCCC 61.037 63.158 0.00 0.00 0.00 3.97
4713 5261 1.377612 GCCCCGTGTACTTTTCCCT 59.622 57.895 0.00 0.00 0.00 4.20
4714 5262 0.675837 GCCCCGTGTACTTTTCCCTC 60.676 60.000 0.00 0.00 0.00 4.30
4715 5263 0.981943 CCCCGTGTACTTTTCCCTCT 59.018 55.000 0.00 0.00 0.00 3.69
4716 5264 2.181975 CCCCGTGTACTTTTCCCTCTA 58.818 52.381 0.00 0.00 0.00 2.43
4717 5265 2.167900 CCCCGTGTACTTTTCCCTCTAG 59.832 54.545 0.00 0.00 0.00 2.43
4718 5266 2.830321 CCCGTGTACTTTTCCCTCTAGT 59.170 50.000 0.00 0.00 0.00 2.57
4719 5267 3.260128 CCCGTGTACTTTTCCCTCTAGTT 59.740 47.826 0.00 0.00 0.00 2.24
4720 5268 4.463891 CCCGTGTACTTTTCCCTCTAGTTA 59.536 45.833 0.00 0.00 0.00 2.24
4721 5269 5.393896 CCCGTGTACTTTTCCCTCTAGTTAG 60.394 48.000 0.00 0.00 0.00 2.34
4722 5270 5.393896 CCGTGTACTTTTCCCTCTAGTTAGG 60.394 48.000 0.00 0.00 36.30 2.69
4734 5282 5.866207 CCTCTAGTTAGGGTTTTGTGTTCT 58.134 41.667 0.00 0.00 32.55 3.01
4735 5283 5.932883 CCTCTAGTTAGGGTTTTGTGTTCTC 59.067 44.000 0.00 0.00 32.55 2.87
4736 5284 5.861727 TCTAGTTAGGGTTTTGTGTTCTCC 58.138 41.667 0.00 0.00 0.00 3.71
4737 5285 3.828921 AGTTAGGGTTTTGTGTTCTCCC 58.171 45.455 0.00 0.00 38.50 4.30
4738 5286 2.551032 GTTAGGGTTTTGTGTTCTCCCG 59.449 50.000 0.00 0.00 42.57 5.14
4739 5287 0.179001 AGGGTTTTGTGTTCTCCCGG 60.179 55.000 0.00 0.00 42.57 5.73
4740 5288 1.176619 GGGTTTTGTGTTCTCCCGGG 61.177 60.000 16.85 16.85 0.00 5.73
4741 5289 1.176619 GGTTTTGTGTTCTCCCGGGG 61.177 60.000 23.50 12.05 0.00 5.73
4742 5290 1.529713 TTTTGTGTTCTCCCGGGGC 60.530 57.895 23.50 9.48 0.00 5.80
4743 5291 3.835790 TTTGTGTTCTCCCGGGGCG 62.836 63.158 23.50 12.84 0.00 6.13
4745 5293 4.754667 GTGTTCTCCCGGGGCGAC 62.755 72.222 23.50 16.71 0.00 5.19
4747 5295 3.703127 GTTCTCCCGGGGCGACTT 61.703 66.667 23.50 0.00 0.00 3.01
4748 5296 2.926242 TTCTCCCGGGGCGACTTT 60.926 61.111 23.50 0.00 0.00 2.66
4749 5297 2.522367 TTCTCCCGGGGCGACTTTT 61.522 57.895 23.50 0.00 0.00 2.27
4750 5298 2.436115 CTCCCGGGGCGACTTTTC 60.436 66.667 23.50 0.00 0.00 2.29
4759 5307 2.399611 CGACTTTTCGCCGCCATC 59.600 61.111 0.00 0.00 38.71 3.51
4760 5308 2.399611 GACTTTTCGCCGCCATCG 59.600 61.111 0.00 0.00 0.00 3.84
4761 5309 2.047655 ACTTTTCGCCGCCATCGA 60.048 55.556 0.00 0.00 38.10 3.59
4762 5310 2.025359 GACTTTTCGCCGCCATCGAG 62.025 60.000 0.00 0.00 37.26 4.04
4763 5311 2.813179 CTTTTCGCCGCCATCGAGG 61.813 63.158 0.00 0.00 37.26 4.63
4764 5312 3.599285 TTTTCGCCGCCATCGAGGT 62.599 57.895 0.00 0.00 40.61 3.85
4765 5313 3.599285 TTTCGCCGCCATCGAGGTT 62.599 57.895 0.00 0.00 40.61 3.50
4766 5314 3.599285 TTCGCCGCCATCGAGGTTT 62.599 57.895 0.00 0.00 40.61 3.27
4767 5315 3.124921 CGCCGCCATCGAGGTTTT 61.125 61.111 0.00 0.00 40.61 2.43
4768 5316 2.485122 GCCGCCATCGAGGTTTTG 59.515 61.111 0.00 0.00 40.61 2.44
4769 5317 2.485122 CCGCCATCGAGGTTTTGC 59.515 61.111 0.00 0.00 40.61 3.68
4770 5318 2.040544 CCGCCATCGAGGTTTTGCT 61.041 57.895 0.00 0.00 40.61 3.91
4771 5319 1.425428 CGCCATCGAGGTTTTGCTC 59.575 57.895 0.00 0.00 40.61 4.26
4772 5320 1.803289 GCCATCGAGGTTTTGCTCC 59.197 57.895 0.00 0.00 40.61 4.70
4773 5321 1.657751 GCCATCGAGGTTTTGCTCCC 61.658 60.000 0.00 0.00 40.61 4.30
4774 5322 1.032114 CCATCGAGGTTTTGCTCCCC 61.032 60.000 0.00 0.00 0.00 4.81
4775 5323 0.035056 CATCGAGGTTTTGCTCCCCT 60.035 55.000 0.00 0.00 0.00 4.79
4776 5324 1.209504 CATCGAGGTTTTGCTCCCCTA 59.790 52.381 0.00 0.00 0.00 3.53
4777 5325 1.580059 TCGAGGTTTTGCTCCCCTAT 58.420 50.000 0.00 0.00 0.00 2.57
4778 5326 1.485066 TCGAGGTTTTGCTCCCCTATC 59.515 52.381 0.00 0.00 0.00 2.08
4779 5327 1.806623 CGAGGTTTTGCTCCCCTATCG 60.807 57.143 0.00 0.00 0.00 2.92
4780 5328 0.107165 AGGTTTTGCTCCCCTATCGC 60.107 55.000 0.00 0.00 0.00 4.58
4781 5329 1.101635 GGTTTTGCTCCCCTATCGCC 61.102 60.000 0.00 0.00 0.00 5.54
4782 5330 1.153249 TTTTGCTCCCCTATCGCCG 60.153 57.895 0.00 0.00 0.00 6.46
4783 5331 1.618876 TTTTGCTCCCCTATCGCCGA 61.619 55.000 0.00 0.00 0.00 5.54
4784 5332 1.407656 TTTGCTCCCCTATCGCCGAT 61.408 55.000 4.45 4.45 0.00 4.18
4785 5333 1.816863 TTGCTCCCCTATCGCCGATC 61.817 60.000 1.25 0.00 0.00 3.69
4786 5334 2.276116 GCTCCCCTATCGCCGATCA 61.276 63.158 1.25 0.00 0.00 2.92
4787 5335 1.816863 GCTCCCCTATCGCCGATCAA 61.817 60.000 1.25 0.00 0.00 2.57
4788 5336 0.038159 CTCCCCTATCGCCGATCAAC 60.038 60.000 1.25 0.00 0.00 3.18
4789 5337 1.004918 CCCCTATCGCCGATCAACC 60.005 63.158 1.25 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 289 8.830201 TCACGAAAAATTTGGAATTCATGATT 57.170 26.923 7.93 1.09 0.00 2.57
265 290 8.830201 TTCACGAAAAATTTGGAATTCATGAT 57.170 26.923 7.93 0.00 0.00 2.45
280 305 9.825972 TTGCAATTGTTTTTAATTCACGAAAAA 57.174 22.222 7.40 0.00 33.32 1.94
283 308 9.994432 AATTTGCAATTGTTTTTAATTCACGAA 57.006 22.222 7.40 0.00 0.00 3.85
285 310 9.430838 TGAATTTGCAATTGTTTTTAATTCACG 57.569 25.926 19.52 0.00 36.29 4.35
375 403 9.757227 AATTTCGTGAAATTTTCCAAGTTCATA 57.243 25.926 13.39 0.00 45.90 2.15
582 613 1.529309 GGATCCTGTGCTTCCCTCC 59.471 63.158 3.84 0.00 0.00 4.30
586 617 1.522580 GCTCGGATCCTGTGCTTCC 60.523 63.158 10.75 0.00 0.00 3.46
628 659 7.666063 AGAAGATTTATTTTGCTAATGGGCT 57.334 32.000 0.00 0.00 0.00 5.19
671 702 0.175760 CGTGGTATCAGTGGGAGTGG 59.824 60.000 0.00 0.00 0.00 4.00
687 718 4.489771 GAGGATGGTGGGCCCGTG 62.490 72.222 19.37 0.00 35.15 4.94
805 838 0.105453 GTAGAGGGATGAGGGGCAGA 60.105 60.000 0.00 0.00 0.00 4.26
812 845 1.678627 CGTGTCCAGTAGAGGGATGAG 59.321 57.143 0.00 0.00 36.67 2.90
844 877 1.747206 CGATTTTACCTCCCTGCCCTG 60.747 57.143 0.00 0.00 0.00 4.45
852 885 1.093496 CGGGTGGCGATTTTACCTCC 61.093 60.000 0.00 0.00 38.61 4.30
934 967 4.504916 CAGGAGCTCGCGAGGTGG 62.505 72.222 41.93 26.73 39.57 4.61
971 1009 2.243736 TCCTTTCTCCCTCTCTCTCTCC 59.756 54.545 0.00 0.00 0.00 3.71
979 1017 0.341609 CCCCTCTCCTTTCTCCCTCT 59.658 60.000 0.00 0.00 0.00 3.69
980 1018 0.692756 CCCCCTCTCCTTTCTCCCTC 60.693 65.000 0.00 0.00 0.00 4.30
981 1019 1.162951 TCCCCCTCTCCTTTCTCCCT 61.163 60.000 0.00 0.00 0.00 4.20
982 1020 0.029577 ATCCCCCTCTCCTTTCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
983 1021 1.135960 CATCCCCCTCTCCTTTCTCC 58.864 60.000 0.00 0.00 0.00 3.71
984 1022 1.135960 CCATCCCCCTCTCCTTTCTC 58.864 60.000 0.00 0.00 0.00 2.87
985 1023 0.990818 GCCATCCCCCTCTCCTTTCT 60.991 60.000 0.00 0.00 0.00 2.52
986 1024 1.534203 GCCATCCCCCTCTCCTTTC 59.466 63.158 0.00 0.00 0.00 2.62
987 1025 2.378634 CGCCATCCCCCTCTCCTTT 61.379 63.158 0.00 0.00 0.00 3.11
988 1026 2.770048 CGCCATCCCCCTCTCCTT 60.770 66.667 0.00 0.00 0.00 3.36
1225 1263 2.890766 TTTGCACGGAGGGAGGGAC 61.891 63.158 0.00 0.00 0.00 4.46
1249 1287 1.199615 GGAGAGGAAGGAGAAGGTGG 58.800 60.000 0.00 0.00 0.00 4.61
1334 1372 2.776225 GCAAGAATTAATGCACGTACGC 59.224 45.455 16.72 0.00 42.12 4.42
1342 1380 2.098117 ACAGCTCGGCAAGAATTAATGC 59.902 45.455 6.42 6.42 41.82 3.56
1367 1405 1.081774 CGAGACGGGATCAGATCGC 60.082 63.158 15.98 15.98 38.71 4.58
1449 1489 5.010415 GCTCAATCCATCCATCCTAAAAAGG 59.990 44.000 0.00 0.00 0.00 3.11
1459 1499 2.329267 TCTACGGCTCAATCCATCCAT 58.671 47.619 0.00 0.00 0.00 3.41
1484 1524 0.767375 AAAACCAGCTGAGAGGAGCA 59.233 50.000 17.39 0.00 41.83 4.26
1545 1585 3.765381 TGAAGGAACCATGCATTGAAGA 58.235 40.909 4.52 0.00 0.00 2.87
1554 1594 0.452987 CGCACCATGAAGGAACCATG 59.547 55.000 0.00 0.00 41.22 3.66
1555 1595 0.680921 CCGCACCATGAAGGAACCAT 60.681 55.000 0.00 0.00 41.22 3.55
1556 1596 1.303236 CCGCACCATGAAGGAACCA 60.303 57.895 0.00 0.00 41.22 3.67
1557 1597 0.394352 ATCCGCACCATGAAGGAACC 60.394 55.000 0.00 0.00 41.22 3.62
1579 1619 2.930385 ATCGGCAGCTCATTCCACGG 62.930 60.000 0.00 0.00 0.00 4.94
1583 1623 2.020131 CACATCGGCAGCTCATTCC 58.980 57.895 0.00 0.00 0.00 3.01
1650 1727 3.244215 TGGAAACAGGCACACAAACAAAA 60.244 39.130 0.00 0.00 35.01 2.44
1652 1729 1.895798 TGGAAACAGGCACACAAACAA 59.104 42.857 0.00 0.00 35.01 2.83
1707 1788 6.718294 TCCTCACTTAATAAGGGGAAAGAAC 58.282 40.000 2.04 0.00 31.06 3.01
1760 1842 5.116180 TCGCGGAAGATTTAACTTCATCAT 58.884 37.500 6.13 0.00 45.39 2.45
1762 1844 5.659048 ATCGCGGAAGATTTAACTTCATC 57.341 39.130 6.13 0.00 45.39 2.92
1784 1866 1.863662 GCGAGGCTATAGCGGCAGTA 61.864 60.000 21.83 0.00 43.26 2.74
1786 1868 1.587043 TAGCGAGGCTATAGCGGCAG 61.587 60.000 25.89 16.09 43.26 4.85
1816 1898 1.164662 ATAGCATTGCGCAGAGGCTG 61.165 55.000 30.39 17.63 46.13 4.85
1823 1905 2.439883 TGGCCATAGCATTGCGCA 60.440 55.556 5.66 5.66 46.13 6.09
1895 1977 5.179533 GGTCAGGAAAGAGGATTTCTGTAC 58.820 45.833 0.86 0.00 35.91 2.90
1910 1992 3.211045 CGGAAACTTTTCTGGTCAGGAA 58.789 45.455 2.98 0.00 39.36 3.36
1976 2058 2.642700 GCATTTCGCGGTTGTGGT 59.357 55.556 6.13 0.00 0.00 4.16
2004 2086 3.997021 CTGAACTTTAGACCATTCAGCGT 59.003 43.478 0.30 0.00 41.03 5.07
2012 2094 8.318412 TGTAGATTATTGCTGAACTTTAGACCA 58.682 33.333 0.00 0.00 0.00 4.02
2093 2179 0.670706 CTCCGCAGCTATAGCAGTCA 59.329 55.000 26.07 6.14 45.16 3.41
2120 2206 3.813166 CACGGGAAATATGATTTAGCGGT 59.187 43.478 0.00 0.00 0.00 5.68
2133 2219 5.722021 AAAAGCTACAAATCACGGGAAAT 57.278 34.783 0.00 0.00 0.00 2.17
2177 2263 1.815817 AAAAGCAAAATCCCGCCGCT 61.816 50.000 0.00 0.00 33.45 5.52
2178 2264 1.351430 GAAAAGCAAAATCCCGCCGC 61.351 55.000 0.00 0.00 0.00 6.53
2179 2265 0.243636 AGAAAAGCAAAATCCCGCCG 59.756 50.000 0.00 0.00 0.00 6.46
2182 2542 3.989817 CCAAGAAGAAAAGCAAAATCCCG 59.010 43.478 0.00 0.00 0.00 5.14
2185 2545 6.640092 CAGAGACCAAGAAGAAAAGCAAAATC 59.360 38.462 0.00 0.00 0.00 2.17
2186 2546 6.097412 ACAGAGACCAAGAAGAAAAGCAAAAT 59.903 34.615 0.00 0.00 0.00 1.82
2194 2554 7.611855 AGAAAAGAAACAGAGACCAAGAAGAAA 59.388 33.333 0.00 0.00 0.00 2.52
2226 2586 5.009610 CAGCCTTACTTGCCTAAAAAGACAA 59.990 40.000 0.00 0.00 0.00 3.18
2248 2608 4.740695 GCTAGGAGCTTTCGTACATTACAG 59.259 45.833 0.00 0.00 38.45 2.74
2320 2681 0.943835 GTGGCAAATGTTTGGACGGC 60.944 55.000 7.51 0.00 38.57 5.68
2417 2805 0.392998 CCATCCAAGCACGGCTACTT 60.393 55.000 0.00 0.00 38.25 2.24
2459 2852 3.861840 GCACCTGCATATATATGACCGT 58.138 45.455 24.06 13.16 41.59 4.83
2603 3039 5.255710 TGATTGCACGAGAAAAGGAAAAA 57.744 34.783 0.00 0.00 0.00 1.94
2604 3040 4.792704 GCTGATTGCACGAGAAAAGGAAAA 60.793 41.667 0.00 0.00 42.31 2.29
2614 3050 2.032550 CCATAAAGGCTGATTGCACGAG 59.967 50.000 0.00 0.00 45.15 4.18
2635 3072 2.607892 GCTGGCGGTGACACACTTC 61.608 63.158 8.08 0.00 34.40 3.01
2665 3102 3.765511 ACACCTTTATAGTACAGCCGTCA 59.234 43.478 0.00 0.00 0.00 4.35
2764 3201 5.165961 ACATGCATAGTGTGTACTCCTTT 57.834 39.130 0.00 0.00 38.36 3.11
2829 3273 4.105486 CGCGACAAGATAATTGACTCTGA 58.895 43.478 0.00 0.00 0.00 3.27
2831 3275 3.119101 ACCGCGACAAGATAATTGACTCT 60.119 43.478 8.23 0.00 0.00 3.24
2837 3281 6.203915 TGCATATTTACCGCGACAAGATAATT 59.796 34.615 8.23 0.00 0.00 1.40
2849 3293 5.171337 CGAAAGACAAATGCATATTTACCGC 59.829 40.000 0.00 0.00 34.81 5.68
2938 3392 7.227049 TGGAACCCTGAAAAATGAATAAGTC 57.773 36.000 0.00 0.00 0.00 3.01
2968 3422 3.072211 GGTTGGTACCTTCTGCTGTTAC 58.928 50.000 14.36 0.00 41.53 2.50
2971 3425 0.400594 GGGTTGGTACCTTCTGCTGT 59.599 55.000 14.36 0.00 44.38 4.40
3120 3610 0.549902 TGAGCCAAGGGATGAGGGAA 60.550 55.000 0.00 0.00 0.00 3.97
3124 3614 2.363683 GTTCTTGAGCCAAGGGATGAG 58.636 52.381 12.99 0.00 41.33 2.90
3441 3937 3.498676 GGCCGACGATATCTGGAAG 57.501 57.895 0.00 0.00 0.00 3.46
3775 4271 2.005451 GATGATTCAGTTCAGTGCGCT 58.995 47.619 9.73 0.00 0.00 5.92
3781 4277 5.095145 TCTCCCTTGATGATTCAGTTCAG 57.905 43.478 0.00 0.00 32.27 3.02
3835 4332 4.385748 GCCAAAATGGAAATCTGACGAAAC 59.614 41.667 0.00 0.00 40.96 2.78
3887 4384 3.743396 AGTTCTAGCAAAACTGAAGCTCG 59.257 43.478 0.00 0.00 39.68 5.03
3890 4387 5.790547 CGATAGTTCTAGCAAAACTGAAGC 58.209 41.667 5.74 0.00 37.52 3.86
3985 4482 1.979155 GCAGGTTCCCTTCCCTTGC 60.979 63.158 0.00 0.00 0.00 4.01
4006 4503 6.609237 TGATCAAGTTTCACAGCATATAGC 57.391 37.500 0.00 0.00 46.19 2.97
4007 4504 9.486497 AGTATGATCAAGTTTCACAGCATATAG 57.514 33.333 0.00 0.00 0.00 1.31
4008 4505 9.264719 CAGTATGATCAAGTTTCACAGCATATA 57.735 33.333 0.00 0.00 39.69 0.86
4009 4506 7.772292 ACAGTATGATCAAGTTTCACAGCATAT 59.228 33.333 0.00 0.00 39.69 1.78
4010 4507 7.105588 ACAGTATGATCAAGTTTCACAGCATA 58.894 34.615 0.00 0.00 39.69 3.14
4011 4508 5.942236 ACAGTATGATCAAGTTTCACAGCAT 59.058 36.000 0.00 0.00 39.69 3.79
4014 4511 7.425577 TCAACAGTATGATCAAGTTTCACAG 57.574 36.000 0.00 0.00 39.69 3.66
4067 4566 4.502962 ACCCAAAATGCCAAACATAATCG 58.497 39.130 0.00 0.00 38.34 3.34
4082 4581 4.237976 TCACAGGAAACACTACCCAAAA 57.762 40.909 0.00 0.00 0.00 2.44
4091 4590 3.119849 CGGATGGAAATCACAGGAAACAC 60.120 47.826 0.00 0.00 0.00 3.32
4129 4628 1.408702 TGCACCAAAAGAGCAAGAACC 59.591 47.619 0.00 0.00 39.28 3.62
4223 4724 6.331577 ACTTATATTTAAAACGGAGGGGGT 57.668 37.500 0.00 0.00 0.00 4.95
4278 4779 7.094075 ACTCTAAACTACGTTCATGTACATCCA 60.094 37.037 5.07 0.00 0.00 3.41
4289 4790 9.570488 AATGAATCTACACTCTAAACTACGTTC 57.430 33.333 0.00 0.00 0.00 3.95
4300 4801 7.627939 GCAGCAAAATGAATGAATCTACACTCT 60.628 37.037 0.00 0.00 0.00 3.24
4301 4802 6.471519 GCAGCAAAATGAATGAATCTACACTC 59.528 38.462 0.00 0.00 0.00 3.51
4305 4806 5.335127 ACGCAGCAAAATGAATGAATCTAC 58.665 37.500 0.00 0.00 0.00 2.59
4314 4815 5.180304 TGAACTACATACGCAGCAAAATGAA 59.820 36.000 5.79 0.00 0.00 2.57
4357 4858 9.379791 CTTCCTCCGTTTGTAAATATAAGTCTT 57.620 33.333 0.00 0.00 0.00 3.01
4358 4859 8.537858 ACTTCCTCCGTTTGTAAATATAAGTCT 58.462 33.333 0.00 0.00 0.00 3.24
4371 4872 6.128363 GGATACTGTTTTACTTCCTCCGTTTG 60.128 42.308 0.00 0.00 0.00 2.93
4372 4873 5.936372 GGATACTGTTTTACTTCCTCCGTTT 59.064 40.000 0.00 0.00 0.00 3.60
4405 4906 6.264067 GCTCCCAAACAAGATAGCTATGAAAT 59.736 38.462 11.94 0.00 0.00 2.17
4481 5029 5.107109 TGGATGTGAATCAAACGTTTCAG 57.893 39.130 11.37 0.79 32.79 3.02
4531 5079 5.065731 GCTGAGTATTGGAATTGACTGGAAG 59.934 44.000 0.00 0.00 42.29 3.46
4554 5102 3.810896 GGCGTTGGTTGATCGGGC 61.811 66.667 0.00 0.00 0.00 6.13
4565 5113 3.052082 CCTGTCTGCTGGGCGTTG 61.052 66.667 0.00 0.00 0.00 4.10
4566 5114 2.738213 CTTCCTGTCTGCTGGGCGTT 62.738 60.000 0.00 0.00 34.83 4.84
4567 5115 3.241530 TTCCTGTCTGCTGGGCGT 61.242 61.111 0.00 0.00 34.83 5.68
4568 5116 2.435586 CTTCCTGTCTGCTGGGCG 60.436 66.667 0.00 0.00 34.83 6.13
4596 5144 1.338105 GGCTTTGATTGGTTGGGCTTC 60.338 52.381 0.00 0.00 0.00 3.86
4614 5162 1.818674 CTGGGTAGTTGATTGTTGGGC 59.181 52.381 0.00 0.00 0.00 5.36
4615 5163 3.009033 TCTCTGGGTAGTTGATTGTTGGG 59.991 47.826 0.00 0.00 0.00 4.12
4616 5164 4.256920 CTCTCTGGGTAGTTGATTGTTGG 58.743 47.826 0.00 0.00 0.00 3.77
4617 5165 4.256920 CCTCTCTGGGTAGTTGATTGTTG 58.743 47.826 0.00 0.00 0.00 3.33
4618 5166 3.910627 ACCTCTCTGGGTAGTTGATTGTT 59.089 43.478 0.00 0.00 41.11 2.83
4620 5168 5.677319 TTACCTCTCTGGGTAGTTGATTG 57.323 43.478 0.00 0.00 42.04 2.67
4648 5196 9.620660 GGTCATGTACAAAGAAAAATATCGTTT 57.379 29.630 0.00 0.00 0.00 3.60
4649 5197 8.788806 TGGTCATGTACAAAGAAAAATATCGTT 58.211 29.630 0.00 0.00 0.00 3.85
4650 5198 8.234546 GTGGTCATGTACAAAGAAAAATATCGT 58.765 33.333 0.00 0.00 0.00 3.73
4651 5199 8.233868 TGTGGTCATGTACAAAGAAAAATATCG 58.766 33.333 0.00 0.00 0.00 2.92
4652 5200 9.341899 GTGTGGTCATGTACAAAGAAAAATATC 57.658 33.333 0.00 0.00 0.00 1.63
4653 5201 8.855110 TGTGTGGTCATGTACAAAGAAAAATAT 58.145 29.630 0.00 0.00 0.00 1.28
4654 5202 8.132362 GTGTGTGGTCATGTACAAAGAAAAATA 58.868 33.333 0.00 0.00 0.00 1.40
4689 5237 0.664224 AAAGTACACGGGGCGTTTTG 59.336 50.000 0.00 0.00 38.32 2.44
4694 5242 2.036571 GGGAAAAGTACACGGGGCG 61.037 63.158 0.00 0.00 0.00 6.13
4695 5243 0.675837 GAGGGAAAAGTACACGGGGC 60.676 60.000 0.00 0.00 0.00 5.80
4696 5244 0.981943 AGAGGGAAAAGTACACGGGG 59.018 55.000 0.00 0.00 0.00 5.73
4697 5245 2.830321 ACTAGAGGGAAAAGTACACGGG 59.170 50.000 0.00 0.00 0.00 5.28
4698 5246 4.532314 AACTAGAGGGAAAAGTACACGG 57.468 45.455 0.00 0.00 0.00 4.94
4699 5247 5.648572 CCTAACTAGAGGGAAAAGTACACG 58.351 45.833 0.00 0.00 32.39 4.49
4711 5259 5.866207 AGAACACAAAACCCTAACTAGAGG 58.134 41.667 0.00 0.00 36.23 3.69
4712 5260 5.932883 GGAGAACACAAAACCCTAACTAGAG 59.067 44.000 0.00 0.00 0.00 2.43
4713 5261 5.221783 GGGAGAACACAAAACCCTAACTAGA 60.222 44.000 0.00 0.00 37.75 2.43
4714 5262 5.001874 GGGAGAACACAAAACCCTAACTAG 58.998 45.833 0.00 0.00 37.75 2.57
4715 5263 4.503643 CGGGAGAACACAAAACCCTAACTA 60.504 45.833 0.00 0.00 38.51 2.24
4716 5264 3.746432 CGGGAGAACACAAAACCCTAACT 60.746 47.826 0.00 0.00 38.51 2.24
4717 5265 2.551032 CGGGAGAACACAAAACCCTAAC 59.449 50.000 0.00 0.00 38.51 2.34
4718 5266 2.487625 CCGGGAGAACACAAAACCCTAA 60.488 50.000 0.00 0.00 38.51 2.69
4719 5267 1.072648 CCGGGAGAACACAAAACCCTA 59.927 52.381 0.00 0.00 38.51 3.53
4720 5268 0.179001 CCGGGAGAACACAAAACCCT 60.179 55.000 0.00 0.00 38.51 4.34
4721 5269 1.176619 CCCGGGAGAACACAAAACCC 61.177 60.000 18.48 0.00 37.42 4.11
4722 5270 1.176619 CCCCGGGAGAACACAAAACC 61.177 60.000 26.32 0.00 0.00 3.27
4723 5271 1.802337 GCCCCGGGAGAACACAAAAC 61.802 60.000 26.32 0.00 0.00 2.43
4724 5272 1.529713 GCCCCGGGAGAACACAAAA 60.530 57.895 26.32 0.00 0.00 2.44
4725 5273 2.114411 GCCCCGGGAGAACACAAA 59.886 61.111 26.32 0.00 0.00 2.83
4726 5274 4.323477 CGCCCCGGGAGAACACAA 62.323 66.667 26.32 0.00 0.00 3.33
4728 5276 4.754667 GTCGCCCCGGGAGAACAC 62.755 72.222 26.32 7.19 32.47 3.32
4730 5278 2.743126 AAAAGTCGCCCCGGGAGAAC 62.743 60.000 26.32 16.48 32.47 3.01
4731 5279 2.459202 GAAAAGTCGCCCCGGGAGAA 62.459 60.000 26.32 2.66 32.47 2.87
4732 5280 2.926242 AAAAGTCGCCCCGGGAGA 60.926 61.111 26.32 18.83 0.00 3.71
4733 5281 2.436115 GAAAAGTCGCCCCGGGAG 60.436 66.667 26.32 16.47 0.00 4.30
4734 5282 4.382320 CGAAAAGTCGCCCCGGGA 62.382 66.667 26.32 0.00 41.08 5.14
4743 5291 2.025359 CTCGATGGCGGCGAAAAGTC 62.025 60.000 12.98 0.00 37.32 3.01
4744 5292 2.047655 TCGATGGCGGCGAAAAGT 60.048 55.556 12.98 0.00 38.28 2.66
4745 5293 2.703409 CTCGATGGCGGCGAAAAG 59.297 61.111 12.98 0.00 37.32 2.27
4746 5294 2.817834 CCTCGATGGCGGCGAAAA 60.818 61.111 12.98 0.00 37.32 2.29
4747 5295 3.599285 AACCTCGATGGCGGCGAAA 62.599 57.895 12.98 0.00 40.22 3.46
4748 5296 3.599285 AAACCTCGATGGCGGCGAA 62.599 57.895 12.98 0.00 40.22 4.70
4749 5297 3.599285 AAAACCTCGATGGCGGCGA 62.599 57.895 12.98 1.68 40.22 5.54
4750 5298 3.124921 AAAACCTCGATGGCGGCG 61.125 61.111 0.51 0.51 40.22 6.46
4751 5299 2.485122 CAAAACCTCGATGGCGGC 59.515 61.111 0.00 0.00 40.22 6.53
4752 5300 1.982073 GAGCAAAACCTCGATGGCGG 61.982 60.000 0.00 0.00 40.22 6.13
4753 5301 1.425428 GAGCAAAACCTCGATGGCG 59.575 57.895 0.00 0.00 40.22 5.69
4754 5302 1.657751 GGGAGCAAAACCTCGATGGC 61.658 60.000 0.00 0.00 40.22 4.40
4755 5303 1.032114 GGGGAGCAAAACCTCGATGG 61.032 60.000 0.00 0.00 42.93 3.51
4756 5304 0.035056 AGGGGAGCAAAACCTCGATG 60.035 55.000 0.00 0.00 32.37 3.84
4757 5305 1.580059 TAGGGGAGCAAAACCTCGAT 58.420 50.000 0.00 0.00 35.84 3.59
4758 5306 1.485066 GATAGGGGAGCAAAACCTCGA 59.515 52.381 0.00 0.00 35.84 4.04
4759 5307 1.806623 CGATAGGGGAGCAAAACCTCG 60.807 57.143 0.00 0.00 35.84 4.63
4760 5308 1.954927 CGATAGGGGAGCAAAACCTC 58.045 55.000 0.00 0.00 35.84 3.85
4761 5309 0.107165 GCGATAGGGGAGCAAAACCT 60.107 55.000 0.00 0.00 38.40 3.50
4762 5310 1.101635 GGCGATAGGGGAGCAAAACC 61.102 60.000 0.00 0.00 0.00 3.27
4763 5311 1.436983 CGGCGATAGGGGAGCAAAAC 61.437 60.000 0.00 0.00 0.00 2.43
4764 5312 1.153249 CGGCGATAGGGGAGCAAAA 60.153 57.895 0.00 0.00 0.00 2.44
4765 5313 1.407656 ATCGGCGATAGGGGAGCAAA 61.408 55.000 22.68 0.00 0.00 3.68
4766 5314 1.816863 GATCGGCGATAGGGGAGCAA 61.817 60.000 24.05 0.00 0.00 3.91
4767 5315 2.203640 ATCGGCGATAGGGGAGCA 60.204 61.111 22.68 0.00 0.00 4.26
4768 5316 1.816863 TTGATCGGCGATAGGGGAGC 61.817 60.000 24.05 8.97 0.00 4.70
4769 5317 0.038159 GTTGATCGGCGATAGGGGAG 60.038 60.000 24.05 0.00 0.00 4.30
4770 5318 1.469335 GGTTGATCGGCGATAGGGGA 61.469 60.000 24.05 4.26 0.00 4.81
4771 5319 1.004918 GGTTGATCGGCGATAGGGG 60.005 63.158 24.05 0.00 0.00 4.79
4772 5320 4.675404 GGTTGATCGGCGATAGGG 57.325 61.111 24.05 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.