Multiple sequence alignment - TraesCS6A01G220900

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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 TraesCS6A01G220900 chr6A 100.000 5097 0 0 988 6084 410584143 410579047 0.000000e+00 9413
1 TraesCS6A01G220900 chr6A 100.000 578 0 0 1 578 410585130 410584553 0.000000e+00 1068
2 TraesCS6A01G220900 chr6D 94.744 4585 150 36 988 5514 304735476 304740027 0.000000e+00 7047
3 TraesCS6A01G220900 chr6D 84.422 597 35 26 3 578 304734508 304735067 8.980000e-148 534
4 TraesCS6A01G220900 chr6D 81.013 158 13 12 5717 5872 304740025 304740167 6.450000e-20 110
5 TraesCS6A01G220900 chr6B 97.033 2022 57 3 3065 5084 472612062 472610042 0.000000e+00 3398
6 TraesCS6A01G220900 chr6B 92.485 2129 77 34 988 3067 472614237 472612143 0.000000e+00 2968
7 TraesCS6A01G220900 chr6B 90.092 757 30 21 5116 5855 472610041 472609313 0.000000e+00 941
8 TraesCS6A01G220900 chr6B 89.863 365 16 9 158 515 472615194 472614844 3.340000e-122 449
9 TraesCS6A01G220900 chr6B 91.257 183 6 5 5904 6084 472609304 472609130 2.190000e-59 241
10 TraesCS6A01G220900 chr2B 86.774 310 41 0 1138 1447 559193249 559192940 4.510000e-91 346
11 TraesCS6A01G220900 chr2B 83.974 312 50 0 1136 1447 557990213 557990524 3.560000e-77 300
12 TraesCS6A01G220900 chr2B 83.596 317 44 8 1135 1447 559306331 559306643 2.150000e-74 291
13 TraesCS6A01G220900 chr2A 85.806 310 43 1 1138 1447 619628311 619628003 1.640000e-85 327
14 TraesCS6A01G220900 chr2A 83.912 317 43 8 1135 1447 619755074 619755386 4.610000e-76 296
15 TraesCS6A01G220900 chr2D 85.484 310 45 0 1138 1447 477264759 477264450 2.120000e-84 324
16 TraesCS6A01G220900 chr2D 84.488 303 39 8 1149 1447 477394150 477394448 5.960000e-75 292


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 TraesCS6A01G220900 chr6A 410579047 410585130 6083 True 5240.500000 9413 100.000000 1 6084 2 chr6A.!!$R1 6083
1 TraesCS6A01G220900 chr6D 304734508 304740167 5659 False 2563.666667 7047 86.726333 3 5872 3 chr6D.!!$F1 5869
2 TraesCS6A01G220900 chr6B 472609130 472615194 6064 True 1599.400000 3398 92.146000 158 6084 5 chr6B.!!$R1 5926

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
61 62 0.032912 AAAAACGGTTGGTCCCTGGT 60.033 50.000 0.00 0.0 0.00 4.00 F
100 111 0.036388 TCCACTCGGGAGATGCAAAC 60.036 55.000 2.08 0.0 42.15 2.93 F
226 245 0.468648 ATAACCAAGGAGGCTACGGC 59.531 55.000 0.00 0.0 43.14 5.68 F
2000 2181 0.247736 AGCTGTTGGAGACGATGGTC 59.752 55.000 0.00 0.0 43.76 4.02 F
2021 2202 0.534877 TTGCGTGCACCTGACTGAAT 60.535 50.000 12.15 0.0 0.00 2.57 F
3778 4080 0.536460 CGTGGGGTATAATGTGGCCC 60.536 60.000 0.00 0.0 40.35 5.80 F
4306 4609 1.743772 GCCTATGTGGTAGCACCTGTG 60.744 57.143 21.65 9.5 39.58 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2164 0.898320 AGGACCATCGTCTCCAACAG 59.102 55.000 0.00 0.00 39.15 3.16 R
2000 2181 2.281070 AGTCAGGTGCACGCAAGG 60.281 61.111 11.45 0.00 46.39 3.61 R
2185 2370 1.525765 TGAAAGCAAGCACGCTCCA 60.526 52.632 0.00 0.19 42.89 3.86 R
3927 4230 1.134175 CTTGGTCGCAAAACTGTTGGT 59.866 47.619 0.00 0.00 0.00 3.67 R
4054 4357 7.894753 TTTATGAACCATTGATATGAAGCCA 57.105 32.000 0.00 0.00 33.37 4.75 R
4952 5255 0.178981 ATCCCATCCCCGCAAATCAG 60.179 55.000 0.00 0.00 0.00 2.90 R
5998 6349 0.255033 AAAATACGACTGGGGGAGGC 59.745 55.000 0.00 0.00 0.00 4.70 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
24 25 3.309582 TCCGAGATGGGAGGCAAC 58.690 61.111 0.00 0.00 38.76 4.17
30 31 1.810030 GATGGGAGGCAACGACGAC 60.810 63.158 0.00 0.00 46.39 4.34
31 32 3.642778 ATGGGAGGCAACGACGACG 62.643 63.158 5.58 5.58 46.39 5.12
32 33 4.047059 GGGAGGCAACGACGACGA 62.047 66.667 15.32 0.00 46.39 4.20
33 34 2.504244 GGAGGCAACGACGACGAG 60.504 66.667 15.32 7.19 46.39 4.18
34 35 3.173240 GAGGCAACGACGACGAGC 61.173 66.667 15.32 16.30 46.39 5.03
51 52 2.852180 GCCTGGGCGAAAAACGGTT 61.852 57.895 0.00 0.00 42.83 4.44
53 54 1.007849 CTGGGCGAAAAACGGTTGG 60.008 57.895 0.00 0.00 42.83 3.77
54 55 1.730451 CTGGGCGAAAAACGGTTGGT 61.730 55.000 0.00 0.00 42.83 3.67
56 57 1.008194 GGCGAAAAACGGTTGGTCC 60.008 57.895 0.00 0.00 42.83 4.46
57 58 1.008194 GCGAAAAACGGTTGGTCCC 60.008 57.895 0.00 0.00 42.83 4.46
58 59 1.449726 GCGAAAAACGGTTGGTCCCT 61.450 55.000 0.00 0.00 42.83 4.20
59 60 0.309612 CGAAAAACGGTTGGTCCCTG 59.690 55.000 0.00 0.00 38.46 4.45
60 61 0.671796 GAAAAACGGTTGGTCCCTGG 59.328 55.000 0.00 0.00 0.00 4.45
61 62 0.032912 AAAAACGGTTGGTCCCTGGT 60.033 50.000 0.00 0.00 0.00 4.00
62 63 0.466739 AAAACGGTTGGTCCCTGGTC 60.467 55.000 0.00 0.00 0.00 4.02
63 64 2.347691 AAACGGTTGGTCCCTGGTCC 62.348 60.000 0.00 0.00 0.00 4.46
64 65 3.246112 CGGTTGGTCCCTGGTCCA 61.246 66.667 0.00 0.00 0.00 4.02
65 66 2.602676 CGGTTGGTCCCTGGTCCAT 61.603 63.158 2.94 0.00 33.70 3.41
66 67 1.268992 CGGTTGGTCCCTGGTCCATA 61.269 60.000 2.94 0.00 33.70 2.74
67 68 0.996583 GGTTGGTCCCTGGTCCATAA 59.003 55.000 2.94 0.00 33.70 1.90
68 69 1.340697 GGTTGGTCCCTGGTCCATAAC 60.341 57.143 2.94 0.13 33.70 1.89
69 70 0.616371 TTGGTCCCTGGTCCATAACG 59.384 55.000 2.94 0.00 33.70 3.18
71 72 1.525442 GTCCCTGGTCCATAACGGG 59.475 63.158 7.49 7.49 36.21 5.28
72 73 0.979187 GTCCCTGGTCCATAACGGGA 60.979 60.000 11.78 11.78 41.47 5.14
73 74 0.252789 TCCCTGGTCCATAACGGGAA 60.253 55.000 13.16 0.00 40.81 3.97
74 75 0.107361 CCCTGGTCCATAACGGGAAC 60.107 60.000 8.02 0.00 45.29 3.62
90 101 2.907897 GAACGGCTGATCCACTCGGG 62.908 65.000 0.00 0.00 38.37 5.14
100 111 0.036388 TCCACTCGGGAGATGCAAAC 60.036 55.000 2.08 0.00 42.15 2.93
105 116 2.223829 ACTCGGGAGATGCAAACGATAG 60.224 50.000 2.08 0.00 38.80 2.08
169 188 4.371855 TTTCAAACACCATGTTGCGTTA 57.628 36.364 0.00 0.00 40.14 3.18
212 231 1.609555 AGATGGCTCGACGAGATAACC 59.390 52.381 28.43 18.90 0.00 2.85
222 241 2.957006 GACGAGATAACCAAGGAGGCTA 59.043 50.000 0.00 0.00 43.14 3.93
223 242 2.694109 ACGAGATAACCAAGGAGGCTAC 59.306 50.000 0.00 0.00 43.14 3.58
224 243 2.287668 CGAGATAACCAAGGAGGCTACG 60.288 54.545 0.00 0.00 43.14 3.51
225 244 2.036089 GAGATAACCAAGGAGGCTACGG 59.964 54.545 0.00 0.00 43.14 4.02
226 245 0.468648 ATAACCAAGGAGGCTACGGC 59.531 55.000 0.00 0.00 43.14 5.68
227 246 0.616679 TAACCAAGGAGGCTACGGCT 60.617 55.000 0.00 0.00 43.14 5.52
287 310 3.306818 AGAAAAGAGACTGCGTACGAAC 58.693 45.455 21.65 2.16 0.00 3.95
308 331 2.350616 GTTACACGCGCAAATGATACG 58.649 47.619 5.73 0.00 0.00 3.06
313 336 1.298339 GCGCAAATGATACGGCCAC 60.298 57.895 0.30 0.00 0.00 5.01
370 394 1.268899 AGTTCTCCCAAGACGTACGTG 59.731 52.381 28.16 11.71 0.00 4.49
462 486 3.264193 AGCTGGGATCAAGTACATCACAA 59.736 43.478 0.00 0.00 33.17 3.33
463 487 3.375299 GCTGGGATCAAGTACATCACAAC 59.625 47.826 0.00 0.00 33.17 3.32
464 488 4.578871 CTGGGATCAAGTACATCACAACA 58.421 43.478 0.00 0.00 33.17 3.33
485 509 6.743575 ACATCACCAGCTAACATAAGAAAC 57.256 37.500 0.00 0.00 0.00 2.78
518 545 9.703892 TGTAATAGTACTAGATCGTTCCTCTAC 57.296 37.037 8.85 0.00 0.00 2.59
519 546 9.150348 GTAATAGTACTAGATCGTTCCTCTACC 57.850 40.741 8.85 0.00 0.00 3.18
520 547 5.892524 AGTACTAGATCGTTCCTCTACCT 57.107 43.478 0.00 0.00 0.00 3.08
521 548 5.857268 AGTACTAGATCGTTCCTCTACCTC 58.143 45.833 0.00 0.00 0.00 3.85
523 550 6.782000 AGTACTAGATCGTTCCTCTACCTCTA 59.218 42.308 0.00 0.00 0.00 2.43
524 551 6.691255 ACTAGATCGTTCCTCTACCTCTAT 57.309 41.667 0.00 0.00 0.00 1.98
526 553 4.658063 AGATCGTTCCTCTACCTCTATGG 58.342 47.826 0.00 0.00 42.93 2.74
528 555 4.726035 TCGTTCCTCTACCTCTATGGAT 57.274 45.455 0.00 0.00 39.71 3.41
529 556 5.063017 TCGTTCCTCTACCTCTATGGATT 57.937 43.478 0.00 0.00 39.71 3.01
570 729 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
571 730 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
572 731 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
573 732 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
574 733 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
576 735 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
577 736 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
1161 1332 1.071471 CTCGGTGGAGCAGGTGTTT 59.929 57.895 0.00 0.00 32.61 2.83
1201 1372 4.154347 GGAGGGAGCAGCTCACGG 62.154 72.222 24.09 0.00 39.19 4.94
1203 1374 3.363844 GAGGGAGCAGCTCACGGTC 62.364 68.421 24.09 11.31 39.19 4.79
1492 1664 3.308438 ACGCTCGGTTACAGTTACAAT 57.692 42.857 0.00 0.00 0.00 2.71
1494 1666 4.808558 ACGCTCGGTTACAGTTACAATTA 58.191 39.130 0.00 0.00 0.00 1.40
1495 1667 4.860907 ACGCTCGGTTACAGTTACAATTAG 59.139 41.667 0.00 0.00 0.00 1.73
1527 1699 2.550978 CGTGCTACTAGGAACATTGGG 58.449 52.381 0.00 0.00 0.00 4.12
1547 1721 3.489416 GGGTTTTGCGAATGTCAAGTTTC 59.511 43.478 0.00 0.00 0.00 2.78
1550 1724 2.686558 TGCGAATGTCAAGTTTCAGC 57.313 45.000 0.00 0.00 0.00 4.26
1606 1780 7.227910 TGCTCTTACCTTCGTATGAAAAGTTTT 59.772 33.333 0.00 0.00 32.66 2.43
1607 1781 8.715088 GCTCTTACCTTCGTATGAAAAGTTTTA 58.285 33.333 0.00 0.00 32.66 1.52
1643 1817 4.120589 GACCAGTAGACGAATCCATTTCC 58.879 47.826 0.00 0.00 0.00 3.13
1749 1923 1.062121 AGGAGCTAGAGGTGGGCATAA 60.062 52.381 0.00 0.00 0.00 1.90
1815 1994 2.678190 CGTTGTTTCTTTTGCCCCCAAA 60.678 45.455 0.00 0.00 39.08 3.28
1858 2038 3.611025 TTCAAATCCTCCAAAGTGGGT 57.389 42.857 0.00 0.00 38.32 4.51
1963 2144 1.134946 ACTGCAGTGTGCCTTTTGTTC 59.865 47.619 20.97 0.00 44.23 3.18
1965 2146 1.405105 TGCAGTGTGCCTTTTGTTCTC 59.595 47.619 0.00 0.00 44.23 2.87
1983 2164 6.281405 TGTTCTCCTAATCTTCCGAAATAGC 58.719 40.000 0.00 0.00 0.00 2.97
2000 2181 0.247736 AGCTGTTGGAGACGATGGTC 59.752 55.000 0.00 0.00 43.76 4.02
2021 2202 0.534877 TTGCGTGCACCTGACTGAAT 60.535 50.000 12.15 0.00 0.00 2.57
2029 2210 2.880890 GCACCTGACTGAATTGTGAAGT 59.119 45.455 0.00 0.00 0.00 3.01
2067 2252 6.472016 GGACCATTTTTGGTTGGTTCATTAT 58.528 36.000 0.00 0.00 46.14 1.28
2068 2253 7.310734 GGGACCATTTTTGGTTGGTTCATTATA 60.311 37.037 0.00 0.00 46.14 0.98
2083 2268 7.770433 TGGTTCATTATAGGTGAATGAGTGAAG 59.230 37.037 6.08 0.00 42.63 3.02
2084 2269 7.227512 GGTTCATTATAGGTGAATGAGTGAAGG 59.772 40.741 6.08 0.00 42.63 3.46
2087 2272 7.987458 TCATTATAGGTGAATGAGTGAAGGAAC 59.013 37.037 0.00 0.00 38.17 3.62
2185 2370 3.228188 TGAGGACAAGCTGAAAATGGT 57.772 42.857 0.00 0.00 0.00 3.55
2198 2383 2.146073 AAATGGTGGAGCGTGCTTGC 62.146 55.000 0.00 0.00 0.00 4.01
2412 2597 7.032377 GTGATAGTCACTGATGTCATACAGA 57.968 40.000 15.11 0.00 43.73 3.41
2413 2598 7.138081 GTGATAGTCACTGATGTCATACAGAG 58.862 42.308 15.11 9.73 43.73 3.35
2414 2599 7.012799 GTGATAGTCACTGATGTCATACAGAGA 59.987 40.741 15.11 11.30 43.73 3.10
2415 2600 5.833406 AGTCACTGATGTCATACAGAGAG 57.167 43.478 15.11 7.78 35.29 3.20
2417 2602 3.065925 TCACTGATGTCATACAGAGAGCG 59.934 47.826 15.11 0.00 37.54 5.03
2421 2615 1.946650 GTCATACAGAGAGCGCCGC 60.947 63.158 2.29 0.00 0.00 6.53
2422 2616 2.104928 CATACAGAGAGCGCCGCA 59.895 61.111 13.36 0.00 0.00 5.69
2510 2707 3.696051 TGTGGAAATTCTTATCAGCAGCC 59.304 43.478 0.00 0.00 0.00 4.85
2514 2711 5.590259 TGGAAATTCTTATCAGCAGCCTTAC 59.410 40.000 0.00 0.00 0.00 2.34
2515 2712 5.590259 GGAAATTCTTATCAGCAGCCTTACA 59.410 40.000 0.00 0.00 0.00 2.41
2516 2713 6.264067 GGAAATTCTTATCAGCAGCCTTACAT 59.736 38.462 0.00 0.00 0.00 2.29
2517 2714 7.201857 GGAAATTCTTATCAGCAGCCTTACATT 60.202 37.037 0.00 0.00 0.00 2.71
2518 2715 7.651027 AATTCTTATCAGCAGCCTTACATTT 57.349 32.000 0.00 0.00 0.00 2.32
2519 2716 7.651027 ATTCTTATCAGCAGCCTTACATTTT 57.349 32.000 0.00 0.00 0.00 1.82
2520 2717 7.466746 TTCTTATCAGCAGCCTTACATTTTT 57.533 32.000 0.00 0.00 0.00 1.94
2656 2872 3.996921 ATGTGATCATAGGATGAGGGC 57.003 47.619 0.00 0.00 43.53 5.19
2824 3041 9.941325 AATAAATTTGGCTAATTGACATGTTGA 57.059 25.926 7.65 0.00 36.57 3.18
3426 3727 6.166279 TGAAGCTTACAAGAATAGGTCAGTG 58.834 40.000 0.00 0.00 0.00 3.66
3482 3783 8.640063 TGATTATGATTTGTCCAATATCTGGG 57.360 34.615 4.69 0.00 46.44 4.45
3485 3786 6.966534 ATGATTTGTCCAATATCTGGGAAC 57.033 37.500 4.69 0.00 46.44 3.62
3491 3792 6.381498 TGTCCAATATCTGGGAACAACTTA 57.619 37.500 4.69 0.00 46.44 2.24
3657 3959 9.939424 AGTCTCCTATACTGAACCTAACTTATT 57.061 33.333 0.00 0.00 0.00 1.40
3670 3972 6.849151 ACCTAACTTATTGTCTTCCAGGTTT 58.151 36.000 0.00 0.00 29.68 3.27
3778 4080 0.536460 CGTGGGGTATAATGTGGCCC 60.536 60.000 0.00 0.00 40.35 5.80
3796 4098 3.323751 CCCCTCATTGGCAAGAAAAAG 57.676 47.619 5.96 0.00 0.00 2.27
3887 4189 3.001414 CTGATCTTGCCACTGTCTTCAG 58.999 50.000 0.00 0.00 46.18 3.02
3909 4211 8.099364 TCAGTTTTGTCTAAGCTAAAATCCAG 57.901 34.615 0.00 0.00 0.00 3.86
4306 4609 1.743772 GCCTATGTGGTAGCACCTGTG 60.744 57.143 21.65 9.50 39.58 3.66
4579 4882 1.811965 TCAATGGGCTGTGTCATTTCG 59.188 47.619 0.00 0.00 31.95 3.46
4744 5047 5.105392 CCTGACTCTCTGCTACATCTTCTTT 60.105 44.000 0.00 0.00 0.00 2.52
4750 5053 2.745821 CTGCTACATCTTCTTTGCTGCA 59.254 45.455 0.00 0.00 0.00 4.41
4758 5061 3.415212 TCTTCTTTGCTGCAGCTATTGT 58.585 40.909 36.61 0.00 42.66 2.71
4783 5086 5.060662 TCAACCTGATAAGAGACTTGACG 57.939 43.478 0.00 0.00 0.00 4.35
4846 5149 4.562767 TGGCCATACCTTTCTACATAGGA 58.437 43.478 0.00 0.00 40.22 2.94
4894 5197 3.084786 GGGCAGCTTCATACTCTTTGTT 58.915 45.455 0.00 0.00 0.00 2.83
4904 5207 6.433847 TCATACTCTTTGTTTGGGAGAAGA 57.566 37.500 0.00 0.00 0.00 2.87
4952 5255 3.123620 CTGCTGTCGCTTCAGGGC 61.124 66.667 7.03 0.00 36.12 5.19
4966 5269 2.123726 GGGCTGATTTGCGGGGAT 60.124 61.111 0.00 0.00 0.00 3.85
5053 5356 4.698575 AGTTCTTGACAAGAGGAGACAAC 58.301 43.478 17.06 11.04 39.03 3.32
5087 5390 4.019174 CAAATTCCTTGGTGGCTAGTCAT 58.981 43.478 0.00 0.00 35.26 3.06
5088 5391 2.787473 TTCCTTGGTGGCTAGTCATG 57.213 50.000 0.00 0.00 35.26 3.07
5089 5392 0.911769 TCCTTGGTGGCTAGTCATGG 59.088 55.000 0.00 1.30 35.26 3.66
5090 5393 0.620556 CCTTGGTGGCTAGTCATGGT 59.379 55.000 0.00 0.00 0.00 3.55
5091 5394 1.407437 CCTTGGTGGCTAGTCATGGTC 60.407 57.143 0.00 0.00 0.00 4.02
5092 5395 1.278985 CTTGGTGGCTAGTCATGGTCA 59.721 52.381 0.00 0.00 0.00 4.02
5093 5396 0.904649 TGGTGGCTAGTCATGGTCAG 59.095 55.000 0.00 0.00 0.00 3.51
5094 5397 0.905357 GGTGGCTAGTCATGGTCAGT 59.095 55.000 0.00 0.00 0.00 3.41
5095 5398 1.134670 GGTGGCTAGTCATGGTCAGTC 60.135 57.143 0.00 0.00 0.00 3.51
5096 5399 1.134670 GTGGCTAGTCATGGTCAGTCC 60.135 57.143 0.00 0.00 0.00 3.85
5249 5553 9.853177 AGAATTATCCCTACGAATCAAATTTCT 57.147 29.630 0.00 0.00 0.00 2.52
5256 5560 6.021596 CCTACGAATCAAATTTCTGAAACGG 58.978 40.000 4.73 0.00 34.54 4.44
5280 5584 5.222079 TGTAGCTGTTCCTTCACAATGTA 57.778 39.130 0.00 0.00 0.00 2.29
5329 5633 5.009811 AGGCAGAACGACATAGTATTAGGTC 59.990 44.000 0.36 0.36 37.26 3.85
5386 5709 1.672356 GGCGGCTGTGAGTTGTGAT 60.672 57.895 0.00 0.00 0.00 3.06
5403 5726 7.577303 AGTTGTGATATGTTCCTCCATAACAT 58.423 34.615 6.67 6.67 46.49 2.71
5500 5838 1.662044 CAAAACACCAGCTCCAGCC 59.338 57.895 0.00 0.00 43.38 4.85
5598 5936 1.671261 GCTCTATCATGCGGGTGCTAG 60.671 57.143 0.00 0.00 43.34 3.42
5600 5938 1.006220 TATCATGCGGGTGCTAGCG 60.006 57.895 10.77 0.00 43.34 4.26
5603 5941 3.536917 ATGCGGGTGCTAGCGCTA 61.537 61.111 26.36 17.75 43.34 4.26
5605 5943 2.735100 GCGGGTGCTAGCGCTATC 60.735 66.667 26.36 14.96 38.39 2.08
5606 5944 3.043419 CGGGTGCTAGCGCTATCT 58.957 61.111 26.36 0.00 36.97 1.98
5608 5946 0.664767 CGGGTGCTAGCGCTATCTTC 60.665 60.000 26.36 10.94 36.97 2.87
5609 5947 0.676736 GGGTGCTAGCGCTATCTTCT 59.323 55.000 26.36 0.00 36.97 2.85
5610 5948 1.069358 GGGTGCTAGCGCTATCTTCTT 59.931 52.381 26.36 0.00 36.97 2.52
5611 5949 2.483889 GGGTGCTAGCGCTATCTTCTTT 60.484 50.000 26.36 0.00 36.97 2.52
5612 5950 2.541762 GGTGCTAGCGCTATCTTCTTTG 59.458 50.000 26.36 4.56 36.97 2.77
5650 5988 0.941542 GTGCGTTGGAACTGCACTTA 59.058 50.000 21.51 0.00 46.10 2.24
5668 6006 4.201758 CACTTATTAGTTCGTCGTGCGTAG 59.798 45.833 0.00 0.00 35.58 3.51
5673 6011 0.701303 GTTCGTCGTGCGTAGAACTG 59.299 55.000 18.81 0.31 39.66 3.16
5674 6012 1.000233 TTCGTCGTGCGTAGAACTGC 61.000 55.000 0.00 0.00 42.13 4.40
5675 6013 1.728074 CGTCGTGCGTAGAACTGCA 60.728 57.895 0.00 0.00 39.13 4.41
5681 6019 2.455674 TGCGTAGAACTGCACTCATT 57.544 45.000 0.00 0.00 35.90 2.57
5682 6020 3.586100 TGCGTAGAACTGCACTCATTA 57.414 42.857 0.00 0.00 35.90 1.90
5683 6021 4.123497 TGCGTAGAACTGCACTCATTAT 57.877 40.909 0.00 0.00 35.90 1.28
5684 6022 4.503910 TGCGTAGAACTGCACTCATTATT 58.496 39.130 0.00 0.00 35.90 1.40
5685 6023 4.935205 TGCGTAGAACTGCACTCATTATTT 59.065 37.500 0.00 0.00 35.90 1.40
5686 6024 5.063438 TGCGTAGAACTGCACTCATTATTTC 59.937 40.000 0.00 0.00 35.90 2.17
5687 6025 5.063438 GCGTAGAACTGCACTCATTATTTCA 59.937 40.000 0.00 0.00 0.00 2.69
5688 6026 6.470160 CGTAGAACTGCACTCATTATTTCAC 58.530 40.000 0.00 0.00 0.00 3.18
5689 6027 5.536554 AGAACTGCACTCATTATTTCACG 57.463 39.130 0.00 0.00 0.00 4.35
5690 6028 4.997395 AGAACTGCACTCATTATTTCACGT 59.003 37.500 0.00 0.00 0.00 4.49
5691 6029 4.668576 ACTGCACTCATTATTTCACGTG 57.331 40.909 9.94 9.94 0.00 4.49
5692 6030 4.314961 ACTGCACTCATTATTTCACGTGA 58.685 39.130 15.76 15.76 0.00 4.35
5693 6031 4.389992 ACTGCACTCATTATTTCACGTGAG 59.610 41.667 19.11 6.11 42.80 3.51
5694 6032 3.125146 TGCACTCATTATTTCACGTGAGC 59.875 43.478 19.11 14.41 41.28 4.26
5695 6033 3.125146 GCACTCATTATTTCACGTGAGCA 59.875 43.478 19.11 10.14 41.28 4.26
5696 6034 4.201851 GCACTCATTATTTCACGTGAGCAT 60.202 41.667 19.11 16.49 41.28 3.79
5872 6223 2.030562 ACCCTTCGGTGCTGTTCG 59.969 61.111 0.00 0.00 42.48 3.95
5873 6224 3.423154 CCCTTCGGTGCTGTTCGC 61.423 66.667 0.00 0.00 39.77 4.70
5874 6225 3.423154 CCTTCGGTGCTGTTCGCC 61.423 66.667 0.00 0.00 41.96 5.54
5875 6226 2.664851 CTTCGGTGCTGTTCGCCA 60.665 61.111 0.00 0.00 45.70 5.69
5876 6227 2.954753 CTTCGGTGCTGTTCGCCAC 61.955 63.158 0.00 0.00 45.70 5.01
5905 6256 4.680237 CCCACCGAGCTCGCAACA 62.680 66.667 30.49 0.00 38.18 3.33
5906 6257 3.414700 CCACCGAGCTCGCAACAC 61.415 66.667 30.49 0.00 38.18 3.32
5907 6258 3.767230 CACCGAGCTCGCAACACG 61.767 66.667 30.49 17.62 45.62 4.49
5931 6282 0.544357 CCCATACCTCGCCATCCCTA 60.544 60.000 0.00 0.00 0.00 3.53
5984 6335 4.035102 GTCCCCGCCAAGCTCCTT 62.035 66.667 0.00 0.00 0.00 3.36
5985 6336 2.285069 TCCCCGCCAAGCTCCTTA 60.285 61.111 0.00 0.00 0.00 2.69
5986 6337 2.190578 CCCCGCCAAGCTCCTTAG 59.809 66.667 0.00 0.00 0.00 2.18
5987 6338 2.367202 CCCCGCCAAGCTCCTTAGA 61.367 63.158 0.00 0.00 0.00 2.10
5988 6339 1.700042 CCCCGCCAAGCTCCTTAGAT 61.700 60.000 0.00 0.00 0.00 1.98
5990 6341 0.465705 CCGCCAAGCTCCTTAGATCA 59.534 55.000 0.00 0.00 0.00 2.92
5991 6342 1.539929 CCGCCAAGCTCCTTAGATCAG 60.540 57.143 0.00 0.00 0.00 2.90
5992 6343 1.592064 GCCAAGCTCCTTAGATCAGC 58.408 55.000 0.00 0.00 0.00 4.26
5993 6344 1.140652 GCCAAGCTCCTTAGATCAGCT 59.859 52.381 0.00 0.00 45.69 4.24
5997 6348 2.756907 AGCTCCTTAGATCAGCTTCCA 58.243 47.619 0.00 0.00 40.77 3.53
5998 6349 2.699846 AGCTCCTTAGATCAGCTTCCAG 59.300 50.000 0.00 0.00 40.77 3.86
5999 6350 2.806382 GCTCCTTAGATCAGCTTCCAGC 60.806 54.545 0.00 0.00 42.84 4.85
6044 6396 4.826500 GCAGTTTTACATCATCTGCTACG 58.173 43.478 7.98 0.00 45.14 3.51
6069 6421 6.142139 GCAAAAATAATCTGGTGCCAAAAAC 58.858 36.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.047002 CTCCCATCTCGGAGCTTGAT 58.953 55.000 0.00 0.00 43.01 2.57
1 2 2.509512 CTCCCATCTCGGAGCTTGA 58.490 57.895 0.00 0.00 43.01 3.02
11 12 1.982395 TCGTCGTTGCCTCCCATCT 60.982 57.895 0.00 0.00 0.00 2.90
30 31 2.561373 GTTTTTCGCCCAGGCTCG 59.439 61.111 7.17 0.33 39.32 5.03
31 32 2.561373 CGTTTTTCGCCCAGGCTC 59.439 61.111 7.17 0.00 39.32 4.70
32 33 2.983592 CCGTTTTTCGCCCAGGCT 60.984 61.111 7.17 0.00 39.32 4.58
33 34 2.852180 AACCGTTTTTCGCCCAGGC 61.852 57.895 0.00 0.00 38.35 4.85
34 35 1.007849 CAACCGTTTTTCGCCCAGG 60.008 57.895 0.00 0.00 38.35 4.45
35 36 1.007849 CCAACCGTTTTTCGCCCAG 60.008 57.895 0.00 0.00 38.35 4.45
42 43 0.032912 ACCAGGGACCAACCGTTTTT 60.033 50.000 0.00 0.00 40.11 1.94
47 48 1.268992 TATGGACCAGGGACCAACCG 61.269 60.000 13.31 0.00 42.50 4.44
51 52 1.268992 CCGTTATGGACCAGGGACCA 61.269 60.000 11.80 11.80 43.27 4.02
53 54 0.979187 TCCCGTTATGGACCAGGGAC 60.979 60.000 14.00 5.12 45.44 4.46
54 55 4.060065 CCCGTTATGGACCAGGGA 57.940 61.111 10.49 0.00 44.70 4.20
56 57 0.461339 CGTTCCCGTTATGGACCAGG 60.461 60.000 0.00 0.00 42.00 4.45
57 58 0.461339 CCGTTCCCGTTATGGACCAG 60.461 60.000 0.00 0.00 42.00 4.00
58 59 1.597989 CCGTTCCCGTTATGGACCA 59.402 57.895 0.00 0.00 42.00 4.02
59 60 1.816679 GCCGTTCCCGTTATGGACC 60.817 63.158 0.00 0.00 42.00 4.46
60 61 1.087771 CAGCCGTTCCCGTTATGGAC 61.088 60.000 0.00 0.00 42.00 4.02
61 62 1.219664 CAGCCGTTCCCGTTATGGA 59.780 57.895 0.00 0.00 42.00 3.41
62 63 0.179056 ATCAGCCGTTCCCGTTATGG 60.179 55.000 0.00 0.00 37.55 2.74
63 64 1.217882 GATCAGCCGTTCCCGTTATG 58.782 55.000 0.00 0.00 0.00 1.90
64 65 0.106149 GGATCAGCCGTTCCCGTTAT 59.894 55.000 0.00 0.00 0.00 1.89
65 66 1.259142 TGGATCAGCCGTTCCCGTTA 61.259 55.000 0.00 0.00 40.66 3.18
66 67 2.267961 GGATCAGCCGTTCCCGTT 59.732 61.111 0.00 0.00 0.00 4.44
67 68 3.000819 TGGATCAGCCGTTCCCGT 61.001 61.111 0.00 0.00 40.66 5.28
68 69 2.511600 GTGGATCAGCCGTTCCCG 60.512 66.667 0.00 0.00 40.66 5.14
69 70 1.153349 GAGTGGATCAGCCGTTCCC 60.153 63.158 0.00 0.00 40.66 3.97
71 72 1.519455 CCGAGTGGATCAGCCGTTC 60.519 63.158 0.00 0.00 40.66 3.95
72 73 2.579201 CCGAGTGGATCAGCCGTT 59.421 61.111 0.00 0.00 40.66 4.44
73 74 3.461773 CCCGAGTGGATCAGCCGT 61.462 66.667 0.00 0.00 40.66 5.68
74 75 3.144120 CTCCCGAGTGGATCAGCCG 62.144 68.421 0.00 0.00 44.07 5.52
90 101 5.854157 TCGAAAAACTATCGTTTGCATCTC 58.146 37.500 0.00 0.00 42.28 2.75
100 111 2.535984 AGCGCATCTCGAAAAACTATCG 59.464 45.455 11.47 0.00 41.67 2.92
105 116 0.796312 TGGAGCGCATCTCGAAAAAC 59.204 50.000 11.47 0.00 42.82 2.43
108 119 1.665679 GAAATGGAGCGCATCTCGAAA 59.334 47.619 11.47 0.00 42.82 3.46
109 120 1.290203 GAAATGGAGCGCATCTCGAA 58.710 50.000 11.47 0.00 42.82 3.71
111 122 1.561730 CGAAATGGAGCGCATCTCG 59.438 57.895 11.47 5.03 42.82 4.04
212 231 2.185310 AACCAGCCGTAGCCTCCTTG 62.185 60.000 0.00 0.00 41.25 3.61
225 244 2.042831 ATTGCGAGGCAGAACCAGC 61.043 57.895 0.00 0.00 40.61 4.85
226 245 0.674581 TCATTGCGAGGCAGAACCAG 60.675 55.000 0.00 0.00 40.61 4.00
227 246 0.035152 ATCATTGCGAGGCAGAACCA 60.035 50.000 0.00 0.00 40.61 3.67
292 315 1.651132 GCCGTATCATTTGCGCGTG 60.651 57.895 8.43 1.36 31.38 5.34
293 316 2.707039 GCCGTATCATTTGCGCGT 59.293 55.556 8.43 0.00 31.38 6.01
308 331 0.953471 TGTGTGCTATGTTCGTGGCC 60.953 55.000 0.00 0.00 0.00 5.36
313 336 2.263077 GAGGTCTGTGTGCTATGTTCG 58.737 52.381 0.00 0.00 0.00 3.95
314 337 3.257393 CTGAGGTCTGTGTGCTATGTTC 58.743 50.000 0.00 0.00 0.00 3.18
353 377 1.267806 GTTCACGTACGTCTTGGGAGA 59.732 52.381 19.94 8.15 0.00 3.71
462 486 5.648092 GGTTTCTTATGTTAGCTGGTGATGT 59.352 40.000 0.00 0.00 0.00 3.06
463 487 5.220662 CGGTTTCTTATGTTAGCTGGTGATG 60.221 44.000 0.00 0.00 0.00 3.07
464 488 4.876107 CGGTTTCTTATGTTAGCTGGTGAT 59.124 41.667 0.00 0.00 0.00 3.06
485 509 7.082602 ACGATCTAGTACTATTACATTTGCGG 58.917 38.462 2.33 0.00 0.00 5.69
517 544 5.372363 TCTCTCTCTCTCAATCCATAGAGGT 59.628 44.000 0.00 0.00 39.79 3.85
518 545 5.879763 TCTCTCTCTCTCAATCCATAGAGG 58.120 45.833 0.00 0.00 39.79 3.69
519 546 6.772605 TCTCTCTCTCTCTCAATCCATAGAG 58.227 44.000 0.00 0.00 40.54 2.43
520 547 6.558394 TCTCTCTCTCTCTCTCAATCCATAGA 59.442 42.308 0.00 0.00 0.00 1.98
521 548 6.772605 TCTCTCTCTCTCTCTCAATCCATAG 58.227 44.000 0.00 0.00 0.00 2.23
523 550 5.370584 TCTCTCTCTCTCTCTCTCAATCCAT 59.629 44.000 0.00 0.00 0.00 3.41
524 551 4.721274 TCTCTCTCTCTCTCTCTCAATCCA 59.279 45.833 0.00 0.00 0.00 3.41
526 553 6.041409 TCTCTCTCTCTCTCTCTCTCTCAATC 59.959 46.154 0.00 0.00 0.00 2.67
528 555 5.272402 TCTCTCTCTCTCTCTCTCTCTCAA 58.728 45.833 0.00 0.00 0.00 3.02
529 556 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
1201 1372 4.754667 GACGACCAAGGCCCGGAC 62.755 72.222 15.70 8.40 0.00 4.79
1203 1374 4.760047 CTGACGACCAAGGCCCGG 62.760 72.222 7.28 7.28 0.00 5.73
1492 1664 5.475719 AGTAGCACGCTTCAATTGTACTAA 58.524 37.500 5.13 0.00 0.00 2.24
1494 1666 3.926616 AGTAGCACGCTTCAATTGTACT 58.073 40.909 5.13 0.55 0.00 2.73
1495 1667 4.267928 CCTAGTAGCACGCTTCAATTGTAC 59.732 45.833 5.13 0.00 0.00 2.90
1527 1699 4.317348 GCTGAAACTTGACATTCGCAAAAC 60.317 41.667 0.00 0.00 0.00 2.43
1550 1724 1.438710 CGTTGAAGCAAAGCCGACG 60.439 57.895 0.00 0.00 0.00 5.12
1606 1780 8.135529 CGTCTACTGGTCAATTTATGTCAGATA 58.864 37.037 0.00 0.00 36.23 1.98
1607 1781 6.980978 CGTCTACTGGTCAATTTATGTCAGAT 59.019 38.462 0.00 0.00 36.23 2.90
1608 1782 6.152154 TCGTCTACTGGTCAATTTATGTCAGA 59.848 38.462 0.00 0.00 36.23 3.27
1609 1783 6.330278 TCGTCTACTGGTCAATTTATGTCAG 58.670 40.000 0.00 0.00 37.39 3.51
1610 1784 6.275494 TCGTCTACTGGTCAATTTATGTCA 57.725 37.500 0.00 0.00 0.00 3.58
1643 1817 1.545759 ATCGACATACACGCACGAAG 58.454 50.000 0.00 0.00 36.62 3.79
1734 1908 2.981859 AACGTTATGCCCACCTCTAG 57.018 50.000 0.00 0.00 0.00 2.43
1749 1923 2.047002 ACCCACTAGTGCAAAAACGT 57.953 45.000 17.86 1.49 0.00 3.99
1858 2038 5.304357 TCCCTATCGTTGCTCTCATCATAAA 59.696 40.000 0.00 0.00 0.00 1.40
1963 2144 5.848406 ACAGCTATTTCGGAAGATTAGGAG 58.152 41.667 0.00 0.00 41.60 3.69
1965 2146 5.237344 CCAACAGCTATTTCGGAAGATTAGG 59.763 44.000 0.00 0.00 41.60 2.69
1983 2164 0.898320 AGGACCATCGTCTCCAACAG 59.102 55.000 0.00 0.00 39.15 3.16
2000 2181 2.281070 AGTCAGGTGCACGCAAGG 60.281 61.111 11.45 0.00 46.39 3.61
2029 2210 7.147983 CCAAAAATGGTCCCTAATTTCGTGATA 60.148 37.037 0.00 0.00 0.00 2.15
2067 2252 5.422331 CCTAGTTCCTTCACTCATTCACCTA 59.578 44.000 0.00 0.00 0.00 3.08
2068 2253 4.223923 CCTAGTTCCTTCACTCATTCACCT 59.776 45.833 0.00 0.00 0.00 4.00
2083 2268 2.488153 GTTGACCATTGCACCTAGTTCC 59.512 50.000 0.00 0.00 0.00 3.62
2084 2269 3.146066 TGTTGACCATTGCACCTAGTTC 58.854 45.455 0.00 0.00 0.00 3.01
2087 2272 2.884012 TGTTGTTGACCATTGCACCTAG 59.116 45.455 0.00 0.00 0.00 3.02
2185 2370 1.525765 TGAAAGCAAGCACGCTCCA 60.526 52.632 0.00 0.19 42.89 3.86
2403 2588 1.946650 GCGGCGCTCTCTGTATGAC 60.947 63.158 26.86 0.00 0.00 3.06
2408 2593 4.299547 TGTTGCGGCGCTCTCTGT 62.300 61.111 33.26 0.00 0.00 3.41
2409 2594 3.485431 CTGTTGCGGCGCTCTCTG 61.485 66.667 33.26 20.37 0.00 3.35
2410 2595 3.996124 ACTGTTGCGGCGCTCTCT 61.996 61.111 33.26 8.63 0.00 3.10
2411 2596 3.782244 CACTGTTGCGGCGCTCTC 61.782 66.667 33.26 21.53 0.00 3.20
2421 2615 0.179250 GCGACGTATGTGCACTGTTG 60.179 55.000 19.41 14.94 0.00 3.33
2422 2616 0.319555 AGCGACGTATGTGCACTGTT 60.320 50.000 19.41 5.59 0.00 3.16
2431 2625 6.020984 TCAATTTTCAAATCAGCGACGTATG 58.979 36.000 0.00 0.00 0.00 2.39
2433 2627 5.050023 TGTCAATTTTCAAATCAGCGACGTA 60.050 36.000 0.00 0.00 0.00 3.57
2434 2628 4.219033 GTCAATTTTCAAATCAGCGACGT 58.781 39.130 0.00 0.00 0.00 4.34
2438 2632 3.982701 TGCTGTCAATTTTCAAATCAGCG 59.017 39.130 14.76 0.00 42.23 5.18
2519 2716 7.288810 AGAGAAACAGGAACATATGCAAAAA 57.711 32.000 1.58 0.00 0.00 1.94
2520 2717 6.899393 AGAGAAACAGGAACATATGCAAAA 57.101 33.333 1.58 0.00 0.00 2.44
2521 2718 6.680810 CAAGAGAAACAGGAACATATGCAAA 58.319 36.000 1.58 0.00 0.00 3.68
2522 2719 5.335897 GCAAGAGAAACAGGAACATATGCAA 60.336 40.000 1.58 0.00 0.00 4.08
2523 2720 4.156556 GCAAGAGAAACAGGAACATATGCA 59.843 41.667 1.58 0.00 0.00 3.96
2524 2721 4.156556 TGCAAGAGAAACAGGAACATATGC 59.843 41.667 1.58 0.00 0.00 3.14
2533 2730 2.412421 GCAGTTGCAAGAGAAACAGG 57.588 50.000 0.00 0.00 41.59 4.00
2558 2755 3.285484 CTCACCATCCTGGAAATTCCTG 58.715 50.000 13.78 12.52 40.96 3.86
2607 2816 3.304928 GCGAATCATCCCATGACCAATTC 60.305 47.826 0.00 0.00 43.01 2.17
2824 3041 8.898761 TGAACCAATCGTAACAAATAAGCATAT 58.101 29.630 0.00 0.00 0.00 1.78
3098 3398 3.247173 GTCGACAATCATGATCTGGAAGC 59.753 47.826 11.55 0.00 0.00 3.86
3127 3427 1.702401 TGTGCCACTTGGATAGGTCAA 59.298 47.619 0.00 0.00 37.39 3.18
3426 3727 3.887716 AGCAGAACCAAGATAATGCCATC 59.112 43.478 0.00 0.00 34.24 3.51
3517 3818 9.944376 AGAAGAAAAACATAGTGTAGCAAGATA 57.056 29.630 0.00 0.00 0.00 1.98
3559 3861 6.942005 TGCAGCAGGTACATAAGCATAAATAT 59.058 34.615 0.00 0.00 0.00 1.28
3573 3875 4.446371 AGACATTATCTTGCAGCAGGTAC 58.554 43.478 4.15 0.00 31.62 3.34
3578 3880 5.089970 ACACTAGACATTATCTTGCAGCA 57.910 39.130 0.00 0.00 39.04 4.41
3657 3959 7.559897 AGAAATCAAAGTAAAACCTGGAAGACA 59.440 33.333 0.00 0.00 34.07 3.41
3778 4080 2.027837 CCCCTTTTTCTTGCCAATGAGG 60.028 50.000 0.00 0.00 41.84 3.86
3887 4189 6.677913 TGCTGGATTTTAGCTTAGACAAAAC 58.322 36.000 0.00 0.00 41.66 2.43
3927 4230 1.134175 CTTGGTCGCAAAACTGTTGGT 59.866 47.619 0.00 0.00 0.00 3.67
4054 4357 7.894753 TTTATGAACCATTGATATGAAGCCA 57.105 32.000 0.00 0.00 33.37 4.75
4306 4609 2.183555 GCATTGCAGAAGGCCAGC 59.816 61.111 5.01 3.73 43.89 4.85
4567 4870 0.518636 CACAGGGCGAAATGACACAG 59.481 55.000 0.00 0.00 0.00 3.66
4579 4882 1.673665 CAGCCAGAAGACACAGGGC 60.674 63.158 0.00 0.00 44.92 5.19
4744 5047 2.406596 TGATGACAATAGCTGCAGCA 57.593 45.000 38.24 24.73 45.16 4.41
4750 5053 7.070447 TCTCTTATCAGGTTGATGACAATAGCT 59.930 37.037 1.94 0.00 37.70 3.32
4758 5061 6.625960 CGTCAAGTCTCTTATCAGGTTGATGA 60.626 42.308 1.94 0.00 37.70 2.92
4783 5086 1.082104 CCTCGAAAACTTGTGCGGC 60.082 57.895 0.00 0.00 0.00 6.53
4846 5149 4.371786 ACATGTCGATCGCAAAGTATGAT 58.628 39.130 11.09 0.00 0.00 2.45
4894 5197 2.108075 TGCCTTGTTCATCTTCTCCCAA 59.892 45.455 0.00 0.00 0.00 4.12
4904 5207 3.863400 GCATCTGCTTTTGCCTTGTTCAT 60.863 43.478 0.00 0.00 46.87 2.57
4952 5255 0.178981 ATCCCATCCCCGCAAATCAG 60.179 55.000 0.00 0.00 0.00 2.90
4966 5269 2.692368 GGCAGGGTCCAGATCCCA 60.692 66.667 3.79 0.00 46.82 4.37
5087 5390 2.526432 GTAGAAGACCAGGACTGACCA 58.474 52.381 0.00 0.00 42.04 4.02
5088 5391 1.473278 CGTAGAAGACCAGGACTGACC 59.527 57.143 0.00 0.00 39.35 4.02
5089 5392 1.473278 CCGTAGAAGACCAGGACTGAC 59.527 57.143 0.00 0.00 0.00 3.51
5090 5393 1.353358 TCCGTAGAAGACCAGGACTGA 59.647 52.381 0.00 0.00 0.00 3.41
5091 5394 1.746220 CTCCGTAGAAGACCAGGACTG 59.254 57.143 0.00 0.00 0.00 3.51
5092 5395 1.341187 CCTCCGTAGAAGACCAGGACT 60.341 57.143 0.00 0.00 0.00 3.85
5093 5396 1.104630 CCTCCGTAGAAGACCAGGAC 58.895 60.000 0.00 0.00 0.00 3.85
5094 5397 0.997363 TCCTCCGTAGAAGACCAGGA 59.003 55.000 0.00 0.00 0.00 3.86
5095 5398 1.104630 GTCCTCCGTAGAAGACCAGG 58.895 60.000 0.00 0.00 28.59 4.45
5096 5399 1.835494 TGTCCTCCGTAGAAGACCAG 58.165 55.000 0.00 0.00 33.21 4.00
5249 5553 2.158871 AGGAACAGCTACAACCGTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
5256 5560 4.275936 ACATTGTGAAGGAACAGCTACAAC 59.724 41.667 0.00 0.00 31.75 3.32
5329 5633 5.571741 CAGACAAAATGTGAAATGCTGCTAG 59.428 40.000 0.00 0.00 0.00 3.42
5386 5709 6.645306 TCGAACAATGTTATGGAGGAACATA 58.355 36.000 0.00 0.00 44.75 2.29
5500 5838 5.478332 GGAGCTAAAATTTGGGGATCATAGG 59.522 44.000 0.00 0.00 0.00 2.57
5598 5936 5.212194 TGACAAAAACAAAGAAGATAGCGC 58.788 37.500 0.00 0.00 0.00 5.92
5600 5938 7.915397 TCAGTTGACAAAAACAAAGAAGATAGC 59.085 33.333 0.00 0.00 32.21 2.97
5601 5939 9.787532 TTCAGTTGACAAAAACAAAGAAGATAG 57.212 29.630 0.00 0.00 32.21 2.08
5602 5940 9.787532 CTTCAGTTGACAAAAACAAAGAAGATA 57.212 29.630 0.67 0.00 40.23 1.98
5603 5941 8.306761 ACTTCAGTTGACAAAAACAAAGAAGAT 58.693 29.630 20.12 9.66 40.23 2.40
5605 5943 7.201266 CGACTTCAGTTGACAAAAACAAAGAAG 60.201 37.037 3.33 3.33 41.64 2.85
5606 5944 6.580791 CGACTTCAGTTGACAAAAACAAAGAA 59.419 34.615 0.00 0.00 33.12 2.52
5608 5946 5.856455 ACGACTTCAGTTGACAAAAACAAAG 59.144 36.000 0.89 0.00 34.14 2.77
5609 5947 5.627367 CACGACTTCAGTTGACAAAAACAAA 59.373 36.000 0.89 0.00 33.65 2.83
5610 5948 5.150683 CACGACTTCAGTTGACAAAAACAA 58.849 37.500 0.89 0.00 33.65 2.83
5611 5949 4.717991 CACGACTTCAGTTGACAAAAACA 58.282 39.130 0.89 0.00 33.65 2.83
5612 5950 3.542310 GCACGACTTCAGTTGACAAAAAC 59.458 43.478 0.89 0.00 33.65 2.43
5668 6006 5.082059 CACGTGAAATAATGAGTGCAGTTC 58.918 41.667 10.90 0.00 0.00 3.01
5673 6011 3.125146 TGCTCACGTGAAATAATGAGTGC 59.875 43.478 20.49 15.00 40.61 4.40
5674 6012 4.926860 TGCTCACGTGAAATAATGAGTG 57.073 40.909 20.49 4.74 40.61 3.51
5675 6013 5.178061 TGATGCTCACGTGAAATAATGAGT 58.822 37.500 20.49 0.00 40.61 3.41
5676 6014 5.723492 TGATGCTCACGTGAAATAATGAG 57.277 39.130 20.49 6.26 41.29 2.90
5677 6015 6.314018 GTTTGATGCTCACGTGAAATAATGA 58.686 36.000 20.49 2.34 0.00 2.57
5678 6016 5.512788 GGTTTGATGCTCACGTGAAATAATG 59.487 40.000 20.49 7.79 0.00 1.90
5679 6017 5.182950 TGGTTTGATGCTCACGTGAAATAAT 59.817 36.000 20.49 10.33 0.00 1.28
5680 6018 4.517075 TGGTTTGATGCTCACGTGAAATAA 59.483 37.500 20.49 6.77 0.00 1.40
5681 6019 4.068599 TGGTTTGATGCTCACGTGAAATA 58.931 39.130 20.49 9.02 0.00 1.40
5682 6020 2.884012 TGGTTTGATGCTCACGTGAAAT 59.116 40.909 20.49 15.75 0.00 2.17
5683 6021 2.293170 TGGTTTGATGCTCACGTGAAA 58.707 42.857 20.49 11.35 0.00 2.69
5684 6022 1.960417 TGGTTTGATGCTCACGTGAA 58.040 45.000 20.49 5.99 0.00 3.18
5685 6023 2.076100 GATGGTTTGATGCTCACGTGA 58.924 47.619 18.88 18.88 0.00 4.35
5686 6024 1.131126 GGATGGTTTGATGCTCACGTG 59.869 52.381 9.94 9.94 0.00 4.49
5687 6025 1.271325 TGGATGGTTTGATGCTCACGT 60.271 47.619 0.00 0.00 0.00 4.49
5688 6026 1.452110 TGGATGGTTTGATGCTCACG 58.548 50.000 0.00 0.00 0.00 4.35
5689 6027 3.947196 TGTATGGATGGTTTGATGCTCAC 59.053 43.478 0.00 0.00 0.00 3.51
5690 6028 3.947196 GTGTATGGATGGTTTGATGCTCA 59.053 43.478 0.00 0.00 0.00 4.26
5691 6029 3.947196 TGTGTATGGATGGTTTGATGCTC 59.053 43.478 0.00 0.00 0.00 4.26
5692 6030 3.696051 GTGTGTATGGATGGTTTGATGCT 59.304 43.478 0.00 0.00 0.00 3.79
5693 6031 3.443329 TGTGTGTATGGATGGTTTGATGC 59.557 43.478 0.00 0.00 0.00 3.91
5694 6032 4.458642 TGTGTGTGTATGGATGGTTTGATG 59.541 41.667 0.00 0.00 0.00 3.07
5695 6033 4.661222 TGTGTGTGTATGGATGGTTTGAT 58.339 39.130 0.00 0.00 0.00 2.57
5696 6034 4.092116 TGTGTGTGTATGGATGGTTTGA 57.908 40.909 0.00 0.00 0.00 2.69
5708 6046 5.731957 TGGTATAGAAGCTTGTGTGTGTA 57.268 39.130 2.10 0.00 0.00 2.90
5888 6239 4.680237 TGTTGCGAGCTCGGTGGG 62.680 66.667 35.10 9.75 40.23 4.61
5889 6240 3.414700 GTGTTGCGAGCTCGGTGG 61.415 66.667 35.10 10.14 40.23 4.61
5890 6241 3.767230 CGTGTTGCGAGCTCGGTG 61.767 66.667 35.10 10.53 44.77 4.94
5900 6251 2.360600 TATGGGTGGCCGTGTTGC 60.361 61.111 0.00 0.00 0.00 4.17
5901 6252 2.043980 GGTATGGGTGGCCGTGTTG 61.044 63.158 0.00 0.00 0.00 3.33
5902 6253 2.193087 GAGGTATGGGTGGCCGTGTT 62.193 60.000 0.00 0.00 0.00 3.32
5903 6254 2.609610 AGGTATGGGTGGCCGTGT 60.610 61.111 0.00 0.00 0.00 4.49
5904 6255 2.189521 GAGGTATGGGTGGCCGTG 59.810 66.667 0.00 0.00 0.00 4.94
5905 6256 3.467226 CGAGGTATGGGTGGCCGT 61.467 66.667 0.00 0.00 0.00 5.68
5906 6257 4.910585 GCGAGGTATGGGTGGCCG 62.911 72.222 0.00 0.00 0.00 6.13
5907 6258 4.564110 GGCGAGGTATGGGTGGCC 62.564 72.222 0.00 0.00 0.00 5.36
5908 6259 3.120086 ATGGCGAGGTATGGGTGGC 62.120 63.158 0.00 0.00 0.00 5.01
5909 6260 1.071471 GATGGCGAGGTATGGGTGG 59.929 63.158 0.00 0.00 0.00 4.61
5910 6261 1.071471 GGATGGCGAGGTATGGGTG 59.929 63.158 0.00 0.00 0.00 4.61
5911 6262 2.147387 GGGATGGCGAGGTATGGGT 61.147 63.158 0.00 0.00 0.00 4.51
5931 6282 1.209019 CAGTGATAGTGGCAGGAGCTT 59.791 52.381 0.00 0.00 41.70 3.74
5992 6343 2.612115 ACTGGGGGAGGCTGGAAG 60.612 66.667 0.00 0.00 0.00 3.46
5993 6344 2.610859 GACTGGGGGAGGCTGGAA 60.611 66.667 0.00 0.00 0.00 3.53
5995 6346 3.976490 TACGACTGGGGGAGGCTGG 62.976 68.421 0.00 0.00 0.00 4.85
5996 6347 1.338136 AATACGACTGGGGGAGGCTG 61.338 60.000 0.00 0.00 0.00 4.85
5997 6348 0.620700 AAATACGACTGGGGGAGGCT 60.621 55.000 0.00 0.00 0.00 4.58
5998 6349 0.255033 AAAATACGACTGGGGGAGGC 59.745 55.000 0.00 0.00 0.00 4.70
5999 6350 1.408266 CCAAAATACGACTGGGGGAGG 60.408 57.143 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.