Multiple sequence alignment - TraesCS3D01G358000

Loading Multiple Alignment...

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 TraesCS3D01G358000 chr3D 100.000 3890 0 0 1 3890 471264633 471268522 0.000000e+00 7184
1 TraesCS3D01G358000 chr3B 87.794 3957 189 113 15 3888 625893175 625896920 0.000000e+00 4361
2 TraesCS3D01G358000 chr3A 88.674 3046 188 79 844 3791 613390942 613393928 0.000000e+00 3568
3 TraesCS3D01G358000 chr3A 83.925 479 20 21 353 805 613390492 613390939 4.680000e-109 405
4 TraesCS3D01G358000 chr3A 88.546 227 15 9 26 247 613390229 613390449 8.290000e-67 265
5 TraesCS3D01G358000 chr6D 74.807 909 118 54 1927 2796 424931413 424930577 1.360000e-79 307
6 TraesCS3D01G358000 chr4A 81.349 252 38 6 1393 1635 701978353 701978604 3.070000e-46 196


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 TraesCS3D01G358000 chr3D 471264633 471268522 3889 False 7184.000000 7184 100.000000 1 3890 1 chr3D.!!$F1 3889
1 TraesCS3D01G358000 chr3B 625893175 625896920 3745 False 4361.000000 4361 87.794000 15 3888 1 chr3B.!!$F1 3873
2 TraesCS3D01G358000 chr3A 613390229 613393928 3699 False 1412.666667 3568 87.048333 26 3791 3 chr3A.!!$F1 3765
3 TraesCS3D01G358000 chr6D 424930577 424931413 836 True 307.000000 307 74.807000 1927 2796 1 chr6D.!!$R1 869

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
160 161 0.030773 TAACGCGCTGATCTGCCTAG 59.969 55.0 17.78 11.75 0.0 3.02 F
833 891 0.108089 CGTCCGGTGAGAGAGAGAGA 60.108 60.0 0.00 0.00 0.0 3.10 F
1325 1395 0.234884 CGTCGCTTCTTGGTTTGGTC 59.765 55.0 0.00 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1697 1774 0.176449 GTTCGGCGGGTACTGGTAAT 59.824 55.0 7.21 0.0 33.56 1.89 R
2341 2450 0.108329 ACGTGCGTAATGAGAAGGGG 60.108 55.0 0.00 0.0 0.00 4.79 R
3059 3284 0.251341 AAACCCAAGGCAGCAGTAGG 60.251 55.0 0.00 0.0 0.00 3.18 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
23 24 3.758715 GCTCTCAAGCTTCCTCCTC 57.241 57.895 0.00 0.00 45.55 3.71
24 25 0.179113 GCTCTCAAGCTTCCTCCTCG 60.179 60.000 0.00 0.00 45.55 4.63
50 51 5.728344 GCCAGCGCGACAGTAATTTAATTAA 60.728 40.000 12.10 0.00 0.00 1.40
52 53 6.910433 CCAGCGCGACAGTAATTTAATTAATT 59.090 34.615 12.10 5.89 39.69 1.40
55 56 7.012044 AGCGCGACAGTAATTTAATTAATTCCT 59.988 33.333 12.10 0.00 37.60 3.36
56 57 8.277713 GCGCGACAGTAATTTAATTAATTCCTA 58.722 33.333 12.10 0.00 37.60 2.94
57 58 9.577003 CGCGACAGTAATTTAATTAATTCCTAC 57.423 33.333 0.00 3.01 37.60 3.18
58 59 9.874215 GCGACAGTAATTTAATTAATTCCTACC 57.126 33.333 3.39 0.00 37.60 3.18
60 61 9.874215 GACAGTAATTTAATTAATTCCTACCGC 57.126 33.333 3.39 0.00 37.60 5.68
66 67 9.930693 AATTTAATTAATTCCTACCGCAAACAA 57.069 25.926 3.39 0.00 30.55 2.83
71 72 3.706600 TTCCTACCGCAAACAATACCT 57.293 42.857 0.00 0.00 0.00 3.08
77 78 3.417101 ACCGCAAACAATACCTGAATGA 58.583 40.909 0.00 0.00 0.00 2.57
115 116 2.556287 GCTGGTTTCCGCGTGAAG 59.444 61.111 4.92 0.00 33.63 3.02
160 161 0.030773 TAACGCGCTGATCTGCCTAG 59.969 55.000 17.78 11.75 0.00 3.02
177 178 3.556513 CCTAGTAGATCGCATGTTCGAC 58.443 50.000 0.00 0.00 41.62 4.20
216 217 2.176798 TGTGAACCCCATGGAACTTTCT 59.823 45.455 15.22 0.00 34.81 2.52
229 230 3.746492 GGAACTTTCTGCTGTTCATACGT 59.254 43.478 0.00 0.00 42.91 3.57
258 259 0.370273 GTCGCACATTAGCTGAACGG 59.630 55.000 0.00 0.00 0.00 4.44
262 263 1.382522 CACATTAGCTGAACGGCCAT 58.617 50.000 2.24 0.00 0.00 4.40
270 271 1.176527 CTGAACGGCCATCCAACAAT 58.823 50.000 2.24 0.00 0.00 2.71
273 274 2.102749 CGGCCATCCAACAATGCG 59.897 61.111 2.24 0.00 0.00 4.73
274 275 2.202783 GGCCATCCAACAATGCGC 60.203 61.111 0.00 0.00 0.00 6.09
275 276 2.202783 GCCATCCAACAATGCGCC 60.203 61.111 4.18 0.00 0.00 6.53
276 277 2.713967 GCCATCCAACAATGCGCCT 61.714 57.895 4.18 0.00 0.00 5.52
277 278 1.140161 CCATCCAACAATGCGCCTG 59.860 57.895 4.18 4.75 0.00 4.85
278 279 1.517694 CATCCAACAATGCGCCTGC 60.518 57.895 4.18 0.00 43.20 4.85
302 303 2.032071 GGTTGGGTCGGGTGAGTG 59.968 66.667 0.00 0.00 0.00 3.51
318 319 2.884012 TGAGTGCCAAAATCACGACATT 59.116 40.909 0.00 0.00 39.31 2.71
319 320 3.236816 GAGTGCCAAAATCACGACATTG 58.763 45.455 0.00 0.00 39.31 2.82
320 321 2.884012 AGTGCCAAAATCACGACATTGA 59.116 40.909 0.00 0.00 39.31 2.57
321 322 3.058016 AGTGCCAAAATCACGACATTGAG 60.058 43.478 0.00 0.00 39.31 3.02
374 375 4.435425 CAGAACAATTATTGGGTGCCATG 58.565 43.478 9.88 0.00 31.53 3.66
394 395 2.158623 TGTCCAGAGGCAAAAGTCACAT 60.159 45.455 0.00 0.00 0.00 3.21
395 396 2.227388 GTCCAGAGGCAAAAGTCACATG 59.773 50.000 0.00 0.00 0.00 3.21
396 397 2.106338 TCCAGAGGCAAAAGTCACATGA 59.894 45.455 0.00 0.00 0.00 3.07
397 398 2.486982 CCAGAGGCAAAAGTCACATGAG 59.513 50.000 0.00 0.00 0.00 2.90
398 399 2.095364 CAGAGGCAAAAGTCACATGAGC 60.095 50.000 0.00 0.00 0.00 4.26
504 537 3.007614 AGCCGTAGAAAAGAGCTGGTTAA 59.992 43.478 0.00 0.00 31.23 2.01
508 541 6.093082 GCCGTAGAAAAGAGCTGGTTAATTTA 59.907 38.462 0.00 0.00 0.00 1.40
531 564 3.887110 GCCATGTTACCATACTTAACCCC 59.113 47.826 0.00 0.00 0.00 4.95
532 565 4.131596 CCATGTTACCATACTTAACCCCG 58.868 47.826 0.00 0.00 0.00 5.73
533 566 3.264998 TGTTACCATACTTAACCCCGC 57.735 47.619 0.00 0.00 0.00 6.13
535 568 0.752054 TACCATACTTAACCCCGCCG 59.248 55.000 0.00 0.00 0.00 6.46
557 590 1.958902 TATTAGAAACGCGGCCCCGT 61.959 55.000 10.28 10.28 44.41 5.28
610 664 0.170116 CACCGCAAACGCAATGGTAT 59.830 50.000 0.00 0.00 38.22 2.73
611 665 0.885196 ACCGCAAACGCAATGGTATT 59.115 45.000 0.00 0.00 38.22 1.89
612 666 2.085320 ACCGCAAACGCAATGGTATTA 58.915 42.857 0.00 0.00 38.22 0.98
613 667 2.488545 ACCGCAAACGCAATGGTATTAA 59.511 40.909 0.00 0.00 38.22 1.40
614 668 2.849473 CCGCAAACGCAATGGTATTAAC 59.151 45.455 0.00 0.00 38.22 2.01
615 669 2.849473 CGCAAACGCAATGGTATTAACC 59.151 45.455 0.00 0.00 46.98 2.85
616 670 3.426963 CGCAAACGCAATGGTATTAACCT 60.427 43.478 0.00 0.00 46.91 3.50
617 671 4.490743 GCAAACGCAATGGTATTAACCTT 58.509 39.130 0.00 0.00 46.91 3.50
618 672 4.926832 GCAAACGCAATGGTATTAACCTTT 59.073 37.500 0.00 0.00 46.91 3.11
619 673 5.407084 GCAAACGCAATGGTATTAACCTTTT 59.593 36.000 0.00 0.00 46.91 2.27
620 674 6.586844 GCAAACGCAATGGTATTAACCTTTTA 59.413 34.615 0.00 0.00 46.91 1.52
621 675 7.411049 GCAAACGCAATGGTATTAACCTTTTAC 60.411 37.037 0.00 0.00 46.91 2.01
654 708 1.855441 AATTCGGCCGGGGGTAACTT 61.855 55.000 27.83 1.70 0.00 2.66
666 720 2.881111 GGTAACTTTTGCCCCTCTCT 57.119 50.000 0.00 0.00 0.00 3.10
667 721 2.712709 GGTAACTTTTGCCCCTCTCTC 58.287 52.381 0.00 0.00 0.00 3.20
668 722 2.618302 GGTAACTTTTGCCCCTCTCTCC 60.618 54.545 0.00 0.00 0.00 3.71
669 723 1.450360 AACTTTTGCCCCTCTCTCCT 58.550 50.000 0.00 0.00 0.00 3.69
674 728 3.773154 GCCCCTCTCTCCTCCCCT 61.773 72.222 0.00 0.00 0.00 4.79
717 771 2.438434 CCGCACATCCACCCCTTC 60.438 66.667 0.00 0.00 0.00 3.46
833 891 0.108089 CGTCCGGTGAGAGAGAGAGA 60.108 60.000 0.00 0.00 0.00 3.10
834 892 1.663695 GTCCGGTGAGAGAGAGAGAG 58.336 60.000 0.00 0.00 0.00 3.20
835 893 1.208535 GTCCGGTGAGAGAGAGAGAGA 59.791 57.143 0.00 0.00 0.00 3.10
836 894 1.484653 TCCGGTGAGAGAGAGAGAGAG 59.515 57.143 0.00 0.00 0.00 3.20
837 895 1.475034 CCGGTGAGAGAGAGAGAGAGG 60.475 61.905 0.00 0.00 0.00 3.69
838 896 1.475034 CGGTGAGAGAGAGAGAGAGGG 60.475 61.905 0.00 0.00 0.00 4.30
839 897 1.843851 GGTGAGAGAGAGAGAGAGGGA 59.156 57.143 0.00 0.00 0.00 4.20
840 898 2.158755 GGTGAGAGAGAGAGAGAGGGAG 60.159 59.091 0.00 0.00 0.00 4.30
841 899 2.771943 GTGAGAGAGAGAGAGAGGGAGA 59.228 54.545 0.00 0.00 0.00 3.71
856 914 6.104094 AGAGAGGGAGAGGAGATAAATACACT 59.896 42.308 0.00 0.00 0.00 3.55
901 962 2.914289 CAGAGGGAGCCATCACCC 59.086 66.667 3.84 0.00 45.88 4.61
905 966 2.190578 GGGAGCCATCACCCTTCG 59.809 66.667 0.00 0.00 42.56 3.79
908 969 3.329542 GAGCCATCACCCTTCGCCA 62.330 63.158 0.00 0.00 0.00 5.69
909 970 3.134127 GCCATCACCCTTCGCCAC 61.134 66.667 0.00 0.00 0.00 5.01
910 971 2.438434 CCATCACCCTTCGCCACC 60.438 66.667 0.00 0.00 0.00 4.61
911 972 2.819595 CATCACCCTTCGCCACCG 60.820 66.667 0.00 0.00 0.00 4.94
934 995 4.041049 CGTACGTGTTGGGCGTAATTATA 58.959 43.478 7.22 0.00 44.73 0.98
993 1054 1.065701 CCTCGCTCGCGCCTATAATAT 59.934 52.381 0.00 0.00 39.59 1.28
994 1055 2.479730 CCTCGCTCGCGCCTATAATATT 60.480 50.000 0.00 0.00 39.59 1.28
995 1056 2.784380 CTCGCTCGCGCCTATAATATTC 59.216 50.000 0.00 0.00 39.59 1.75
996 1057 1.513178 CGCTCGCGCCTATAATATTCG 59.487 52.381 0.00 0.00 0.00 3.34
997 1058 2.527100 GCTCGCGCCTATAATATTCGT 58.473 47.619 0.00 0.00 0.00 3.85
998 1059 2.921754 GCTCGCGCCTATAATATTCGTT 59.078 45.455 0.00 0.00 0.00 3.85
999 1060 3.000971 GCTCGCGCCTATAATATTCGTTC 60.001 47.826 0.00 0.00 0.00 3.95
1000 1061 3.165890 TCGCGCCTATAATATTCGTTCG 58.834 45.455 0.00 0.00 0.00 3.95
1059 1121 3.056832 AGGAGTTGGTTCCTTCTTCCTT 58.943 45.455 0.00 0.00 45.35 3.36
1207 1269 2.098680 GACAGCGACGACGAGGAG 59.901 66.667 12.29 0.00 42.66 3.69
1294 1356 2.953648 CAAGGTTGGTTTTCGGTTACCT 59.046 45.455 0.00 0.00 37.60 3.08
1319 1389 1.081376 CGTCTCGTCGCTTCTTGGT 60.081 57.895 0.00 0.00 0.00 3.67
1325 1395 0.234884 CGTCGCTTCTTGGTTTGGTC 59.765 55.000 0.00 0.00 0.00 4.02
1349 1419 0.392336 TTGGCATCCCTGTTTGTTGC 59.608 50.000 0.00 0.00 0.00 4.17
1378 1452 5.382618 AAGCATCTGATTGTTGTTTCTCC 57.617 39.130 0.00 0.00 0.00 3.71
1781 1858 0.391130 TCTGTCATACACCGCCTTGC 60.391 55.000 0.00 0.00 0.00 4.01
1784 1861 0.953471 GTCATACACCGCCTTGCACA 60.953 55.000 0.00 0.00 0.00 4.57
1785 1862 0.250510 TCATACACCGCCTTGCACAA 60.251 50.000 0.00 0.00 0.00 3.33
1786 1863 0.810648 CATACACCGCCTTGCACAAT 59.189 50.000 0.00 0.00 0.00 2.71
1801 1882 1.126846 CACAATCTGTTCCGCTTCGTC 59.873 52.381 0.00 0.00 0.00 4.20
1807 1888 1.514443 GTTCCGCTTCGTCTCTCCG 60.514 63.158 0.00 0.00 0.00 4.63
1827 1912 3.381949 CGGGGATTATTCTCTGACGTTC 58.618 50.000 0.00 0.00 29.18 3.95
1838 1923 6.951256 TTCTCTGACGTTCTGTATGATTTG 57.049 37.500 0.00 0.00 0.00 2.32
1839 1924 6.025749 TCTCTGACGTTCTGTATGATTTGT 57.974 37.500 0.00 0.00 0.00 2.83
2036 2124 4.101790 ATGCGCGCCGTTTTCCTG 62.102 61.111 30.77 0.00 0.00 3.86
2134 2222 1.065401 CAAGAAGAAACCAAGTGCGCA 59.935 47.619 5.66 5.66 0.00 6.09
2135 2223 1.609208 AGAAGAAACCAAGTGCGCAT 58.391 45.000 15.91 0.00 0.00 4.73
2156 2244 3.853698 TTTTCCGCCCCCACTTCCG 62.854 63.158 0.00 0.00 0.00 4.30
2165 2258 3.365265 CCACTTCCGTTGCCCTGC 61.365 66.667 0.00 0.00 0.00 4.85
2167 2260 4.660938 ACTTCCGTTGCCCTGCCC 62.661 66.667 0.00 0.00 0.00 5.36
2341 2450 4.391830 TCTTGATCACGGTAAGCAATCAAC 59.608 41.667 0.00 0.00 33.37 3.18
2360 2469 0.108329 CCCCTTCTCATTACGCACGT 60.108 55.000 0.00 0.00 0.00 4.49
2364 2473 2.852413 CCTTCTCATTACGCACGTACTG 59.148 50.000 12.68 12.68 34.07 2.74
2394 2503 6.467047 CGGCAATGATAATCGCATCTTTATTC 59.533 38.462 0.00 0.00 0.00 1.75
2430 2543 5.550232 TCCATCAATGACATTTCGAACTG 57.450 39.130 13.40 13.40 0.00 3.16
2434 2554 5.034554 TCAATGACATTTCGAACTGCTTC 57.965 39.130 14.74 7.19 0.00 3.86
2513 2639 2.015627 CACAACGCCAACGCCAATG 61.016 57.895 0.00 0.00 45.53 2.82
2514 2640 3.105157 CAACGCCAACGCCAATGC 61.105 61.111 0.00 0.00 45.53 3.56
2515 2641 4.356442 AACGCCAACGCCAATGCC 62.356 61.111 0.00 0.00 45.53 4.40
2631 2778 2.503775 CCCCCGTTTCCATGGATTG 58.496 57.895 17.06 8.32 0.00 2.67
2654 2801 8.972458 TTGCTGCCATATTTAAGTATTACTCA 57.028 30.769 0.00 0.00 0.00 3.41
2801 2998 1.696063 GTTGGTGATGGATGGATGGG 58.304 55.000 0.00 0.00 0.00 4.00
2884 3086 3.808174 GGAGGAATAATAAGTGTCGTGGC 59.192 47.826 0.00 0.00 0.00 5.01
2894 3103 2.504244 GTCGTGGCTCCGACGAAG 60.504 66.667 12.94 0.00 46.71 3.79
2895 3104 3.744719 TCGTGGCTCCGACGAAGG 61.745 66.667 0.00 0.00 42.63 3.46
2896 3105 3.744719 CGTGGCTCCGACGAAGGA 61.745 66.667 0.00 0.00 39.21 3.36
2923 3132 2.193248 GGAGGTATGGTGCTGCCC 59.807 66.667 0.00 0.00 36.04 5.36
2927 3136 2.897350 GTATGGTGCTGCCCGCTC 60.897 66.667 0.00 0.00 40.11 5.03
2992 3202 1.667212 GGAAAATATCGTCGGCGGTTT 59.333 47.619 10.62 6.04 38.89 3.27
3025 3235 7.358066 CGTCGCTGTAAGATATAAGTAAGGAA 58.642 38.462 0.00 0.00 34.07 3.36
3058 3283 4.521146 AGAGCTCCATGTTTCCATTAGTG 58.479 43.478 10.93 0.00 0.00 2.74
3059 3284 3.019564 AGCTCCATGTTTCCATTAGTGC 58.980 45.455 0.00 0.00 0.00 4.40
3060 3285 2.099756 GCTCCATGTTTCCATTAGTGCC 59.900 50.000 0.00 0.00 0.00 5.01
3061 3286 3.624777 CTCCATGTTTCCATTAGTGCCT 58.375 45.455 0.00 0.00 0.00 4.75
3062 3287 4.780815 CTCCATGTTTCCATTAGTGCCTA 58.219 43.478 0.00 0.00 0.00 3.93
3063 3288 4.523083 TCCATGTTTCCATTAGTGCCTAC 58.477 43.478 0.00 0.00 0.00 3.18
3064 3289 4.227300 TCCATGTTTCCATTAGTGCCTACT 59.773 41.667 0.00 0.00 40.99 2.57
3065 3290 4.336433 CCATGTTTCCATTAGTGCCTACTG 59.664 45.833 0.00 0.00 37.78 2.74
3066 3291 3.343617 TGTTTCCATTAGTGCCTACTGC 58.656 45.455 0.00 0.00 37.78 4.40
3067 3292 3.009033 TGTTTCCATTAGTGCCTACTGCT 59.991 43.478 0.00 0.00 42.00 4.24
3068 3293 2.988010 TCCATTAGTGCCTACTGCTG 57.012 50.000 0.00 0.00 42.00 4.41
3069 3294 1.134401 TCCATTAGTGCCTACTGCTGC 60.134 52.381 0.00 0.00 42.00 5.25
3070 3295 1.303309 CATTAGTGCCTACTGCTGCC 58.697 55.000 0.00 0.00 42.00 4.85
3071 3296 1.134280 CATTAGTGCCTACTGCTGCCT 60.134 52.381 0.00 0.00 42.00 4.75
3075 3300 2.439156 GCCTACTGCTGCCTTGGG 60.439 66.667 0.00 0.00 36.87 4.12
3112 3337 2.244695 TCCACTTCGGTCATGTGTACT 58.755 47.619 0.00 0.00 35.57 2.73
3118 3353 5.460091 CACTTCGGTCATGTGTACTATCATG 59.540 44.000 15.06 15.06 41.64 3.07
3218 3453 3.035727 TTTTTCGGTGCTTCGGCC 58.964 55.556 0.00 0.00 40.91 6.13
3224 3459 4.103103 GGTGCTTCGGCCGAAAGC 62.103 66.667 37.62 36.19 40.91 3.51
3236 3471 1.200252 GCCGAAAGCCTTTTCTTCCTC 59.800 52.381 0.00 0.00 40.43 3.71
3237 3472 1.813178 CCGAAAGCCTTTTCTTCCTCC 59.187 52.381 0.00 0.00 40.43 4.30
3246 3481 4.503817 GCCTTTTCTTCCTCCTTGCATTTT 60.504 41.667 0.00 0.00 0.00 1.82
3247 3482 4.992951 CCTTTTCTTCCTCCTTGCATTTTG 59.007 41.667 0.00 0.00 0.00 2.44
3248 3483 5.453762 CCTTTTCTTCCTCCTTGCATTTTGT 60.454 40.000 0.00 0.00 0.00 2.83
3249 3484 5.612725 TTTCTTCCTCCTTGCATTTTGTT 57.387 34.783 0.00 0.00 0.00 2.83
3250 3485 5.612725 TTCTTCCTCCTTGCATTTTGTTT 57.387 34.783 0.00 0.00 0.00 2.83
3257 3492 6.432472 TCCTCCTTGCATTTTGTTTTGTTTTT 59.568 30.769 0.00 0.00 0.00 1.94
3261 3496 8.137437 TCCTTGCATTTTGTTTTGTTTTTGAAA 58.863 25.926 0.00 0.00 0.00 2.69
3283 3518 9.281371 TGAAATATTTTTGCATGTGAAATTGGA 57.719 25.926 1.43 0.00 0.00 3.53
3285 3520 8.851541 AATATTTTTGCATGTGAAATTGGACT 57.148 26.923 0.00 0.00 0.00 3.85
3294 3529 6.676456 GCATGTGAAATTGGACTAGTGTCATC 60.676 42.308 0.00 0.00 44.61 2.92
3308 3546 4.177026 AGTGTCATCGCTCAGTGATTAAC 58.823 43.478 0.00 0.90 29.68 2.01
3311 3549 5.457148 GTGTCATCGCTCAGTGATTAACTAG 59.543 44.000 0.00 0.00 36.83 2.57
3332 3575 3.325135 AGACTTGGAGTAGGTTGAACAGG 59.675 47.826 0.00 0.00 0.00 4.00
3335 3578 0.035343 GGAGTAGGTTGAACAGGGGC 60.035 60.000 0.00 0.00 0.00 5.80
3354 3597 2.039831 AGGTGAGGTGGTGGGTGT 60.040 61.111 0.00 0.00 0.00 4.16
3368 3611 1.301401 GGTGTACTCCACTTGCGCA 60.301 57.895 5.66 5.66 43.94 6.09
3393 3648 6.089016 ACAAAAGTCTAATCATGTGACGTACG 59.911 38.462 15.01 15.01 36.01 3.67
3405 3660 2.097250 GTGACGTACGGTTGCTTAACAC 60.097 50.000 21.06 10.59 0.00 3.32
3497 3753 1.282157 CAAAGAATCTTCTCCCCCGGT 59.718 52.381 0.00 0.00 36.28 5.28
3621 3879 2.656069 CGAGACCCATCCACCCGTT 61.656 63.158 0.00 0.00 0.00 4.44
3628 3886 3.093814 ACCCATCCACCCGTTTAAAATC 58.906 45.455 0.00 0.00 0.00 2.17
3690 3959 4.003788 CGTTGGTCCCTGTCCGCT 62.004 66.667 0.00 0.00 0.00 5.52
3691 3960 2.047179 GTTGGTCCCTGTCCGCTC 60.047 66.667 0.00 0.00 0.00 5.03
3781 4050 0.689080 ATGGCTCCATCCTGTCGTCT 60.689 55.000 0.00 0.00 29.42 4.18
3798 4067 4.717629 TCGTTGCGCCGAGTCCTG 62.718 66.667 4.18 0.00 32.18 3.86
3804 4073 3.753434 CGCCGAGTCCTGCTGTCT 61.753 66.667 0.00 0.00 0.00 3.41
3805 4074 2.125753 GCCGAGTCCTGCTGTCTG 60.126 66.667 0.00 0.00 0.00 3.51
3806 4075 2.125753 CCGAGTCCTGCTGTCTGC 60.126 66.667 0.00 0.00 43.25 4.26
3807 4076 2.505777 CGAGTCCTGCTGTCTGCG 60.506 66.667 0.00 0.00 46.63 5.18
3808 4077 2.653702 GAGTCCTGCTGTCTGCGT 59.346 61.111 0.00 0.00 46.63 5.24
3809 4078 1.005630 GAGTCCTGCTGTCTGCGTT 60.006 57.895 0.00 0.00 46.63 4.84
3810 4079 1.287730 GAGTCCTGCTGTCTGCGTTG 61.288 60.000 0.00 0.00 46.63 4.10
3811 4080 2.666190 TCCTGCTGTCTGCGTTGC 60.666 61.111 0.00 0.00 46.63 4.17
3812 4081 2.667536 CCTGCTGTCTGCGTTGCT 60.668 61.111 0.00 0.00 46.63 3.91
3813 4082 2.554775 CTGCTGTCTGCGTTGCTG 59.445 61.111 0.00 0.00 46.63 4.41
3814 4083 2.962827 CTGCTGTCTGCGTTGCTGG 61.963 63.158 0.00 0.00 46.63 4.85
3815 4084 2.666190 GCTGTCTGCGTTGCTGGA 60.666 61.111 0.00 0.00 0.00 3.86
3816 4085 2.675056 GCTGTCTGCGTTGCTGGAG 61.675 63.158 0.00 0.00 0.00 3.86
3817 4086 2.666190 TGTCTGCGTTGCTGGAGC 60.666 61.111 0.00 0.00 42.50 4.70
3818 4087 2.358003 GTCTGCGTTGCTGGAGCT 60.358 61.111 0.00 0.00 42.66 4.09
3819 4088 1.963338 GTCTGCGTTGCTGGAGCTT 60.963 57.895 0.00 0.00 42.66 3.74
3820 4089 1.227943 TCTGCGTTGCTGGAGCTTT 60.228 52.632 0.00 0.00 42.66 3.51
3821 4090 1.081641 CTGCGTTGCTGGAGCTTTG 60.082 57.895 0.00 0.00 42.66 2.77
3833 4102 1.670406 AGCTTTGCTGCTCTGACCG 60.670 57.895 0.00 0.00 39.34 4.79
3859 4128 1.006922 GTGGCTGGCTTTGTTCTGC 60.007 57.895 2.00 0.00 0.00 4.26
3863 4132 2.590291 TGGCTTTGTTCTGCGCGA 60.590 55.556 12.10 0.00 0.00 5.87
3879 4148 1.285023 CGACGTCTCCCACTTTCGT 59.715 57.895 14.70 0.00 37.45 3.85
3888 4157 0.949105 CCCACTTTCGTCCTGTTCCG 60.949 60.000 0.00 0.00 0.00 4.30
3889 4158 0.249741 CCACTTTCGTCCTGTTCCGT 60.250 55.000 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.893786 GCGAGGAGGAAGCTTGAGA 59.106 57.895 2.10 0.00 0.00 3.27
9 10 2.573869 CGCGAGGAGGAAGCTTGA 59.426 61.111 2.10 0.00 0.00 3.02
30 31 7.130269 AGGAATTAATTAAATTACTGTCGCGC 58.870 34.615 0.00 0.00 45.46 6.86
35 36 9.398538 TGCGGTAGGAATTAATTAAATTACTGT 57.601 29.630 1.21 0.00 46.42 3.55
50 51 3.945285 CAGGTATTGTTTGCGGTAGGAAT 59.055 43.478 0.00 0.00 0.00 3.01
52 53 2.568062 TCAGGTATTGTTTGCGGTAGGA 59.432 45.455 0.00 0.00 0.00 2.94
55 56 4.580868 TCATTCAGGTATTGTTTGCGGTA 58.419 39.130 0.00 0.00 0.00 4.02
56 57 3.417101 TCATTCAGGTATTGTTTGCGGT 58.583 40.909 0.00 0.00 0.00 5.68
57 58 4.353737 CATCATTCAGGTATTGTTTGCGG 58.646 43.478 0.00 0.00 0.00 5.69
58 59 4.353737 CCATCATTCAGGTATTGTTTGCG 58.646 43.478 0.00 0.00 0.00 4.85
59 60 4.114794 GCCATCATTCAGGTATTGTTTGC 58.885 43.478 0.00 0.00 0.00 3.68
60 61 5.327616 TGCCATCATTCAGGTATTGTTTG 57.672 39.130 0.00 0.00 0.00 2.93
63 64 5.221106 CGAAATGCCATCATTCAGGTATTGT 60.221 40.000 0.00 0.00 41.77 2.71
64 65 5.217393 CGAAATGCCATCATTCAGGTATTG 58.783 41.667 0.00 0.00 41.77 1.90
66 67 3.822735 CCGAAATGCCATCATTCAGGTAT 59.177 43.478 0.00 0.00 41.77 2.73
67 68 3.213506 CCGAAATGCCATCATTCAGGTA 58.786 45.455 0.00 0.00 41.77 3.08
71 72 1.750206 CCACCGAAATGCCATCATTCA 59.250 47.619 0.00 0.00 41.77 2.57
77 78 2.043046 CCCCCACCGAAATGCCAT 60.043 61.111 0.00 0.00 0.00 4.40
160 161 2.037649 CGAGTCGAACATGCGATCTAC 58.962 52.381 6.73 0.00 42.82 2.59
170 171 0.596600 GCACTGAACCGAGTCGAACA 60.597 55.000 15.64 9.78 0.00 3.18
177 178 1.071471 ACCAAGGCACTGAACCGAG 59.929 57.895 0.00 0.00 40.86 4.63
216 217 4.593157 GAAACAACAACGTATGAACAGCA 58.407 39.130 0.00 0.00 0.00 4.41
229 230 2.834574 AATGTGCGACGAAACAACAA 57.165 40.000 0.00 0.00 0.00 2.83
258 259 2.202783 GGCGCATTGTTGGATGGC 60.203 61.111 10.83 0.00 0.00 4.40
262 263 2.596923 TGCAGGCGCATTGTTGGA 60.597 55.556 10.83 0.00 45.36 3.53
275 276 4.954970 ACCCAACCCGCTGTGCAG 62.955 66.667 0.00 0.00 0.00 4.41
276 277 4.947147 GACCCAACCCGCTGTGCA 62.947 66.667 0.00 0.00 0.00 4.57
283 284 4.388499 CTCACCCGACCCAACCCG 62.388 72.222 0.00 0.00 0.00 5.28
299 300 2.884012 TCAATGTCGTGATTTTGGCACT 59.116 40.909 0.00 0.00 34.18 4.40
302 303 3.559238 ACTCAATGTCGTGATTTTGGC 57.441 42.857 0.00 0.00 0.00 4.52
318 319 2.500369 GCGTCGCGTTCGTACTCA 60.500 61.111 21.63 0.00 36.96 3.41
319 320 3.236137 GGCGTCGCGTTCGTACTC 61.236 66.667 21.63 9.54 36.96 2.59
320 321 3.541093 TTGGCGTCGCGTTCGTACT 62.541 57.895 21.63 0.00 36.96 2.73
321 322 2.144808 TTTTGGCGTCGCGTTCGTAC 62.145 55.000 21.63 16.71 36.96 3.67
343 344 5.105228 CCCAATAATTGTTCTGCTTCATGGT 60.105 40.000 0.00 0.00 0.00 3.55
353 354 4.095946 ACATGGCACCCAATAATTGTTCT 58.904 39.130 0.00 0.00 36.95 3.01
354 355 4.432712 GACATGGCACCCAATAATTGTTC 58.567 43.478 0.00 0.00 36.95 3.18
374 375 1.967319 TGTGACTTTTGCCTCTGGAC 58.033 50.000 0.00 0.00 0.00 4.02
394 395 2.827800 CTGAACCTCAACTCAGCTCA 57.172 50.000 0.00 0.00 33.17 4.26
398 399 1.345741 TCTGGCTGAACCTCAACTCAG 59.654 52.381 0.00 0.00 41.71 3.35
437 452 2.526304 TTCAGTTTCACCTCACCTCG 57.474 50.000 0.00 0.00 0.00 4.63
438 453 2.879026 GGTTTCAGTTTCACCTCACCTC 59.121 50.000 0.00 0.00 0.00 3.85
439 454 2.509964 AGGTTTCAGTTTCACCTCACCT 59.490 45.455 0.00 0.00 35.99 4.00
440 455 2.932261 AGGTTTCAGTTTCACCTCACC 58.068 47.619 0.00 0.00 35.99 4.02
531 564 0.043652 CGCGTTTCTAATAACCGGCG 60.044 55.000 0.00 0.00 33.77 6.46
532 565 0.302589 CCGCGTTTCTAATAACCGGC 59.697 55.000 4.92 0.00 36.12 6.13
533 566 0.302589 GCCGCGTTTCTAATAACCGG 59.697 55.000 4.92 0.00 41.07 5.28
535 568 0.659427 GGGCCGCGTTTCTAATAACC 59.341 55.000 4.92 0.00 0.00 2.85
537 570 0.810823 CGGGGCCGCGTTTCTAATAA 60.811 55.000 32.15 0.00 0.00 1.40
538 571 1.227321 CGGGGCCGCGTTTCTAATA 60.227 57.895 32.15 0.00 0.00 0.98
539 572 2.512974 CGGGGCCGCGTTTCTAAT 60.513 61.111 32.15 0.00 0.00 1.73
616 670 8.756864 GCCGAATTGTTCAAAAATGTAGTAAAA 58.243 29.630 0.00 0.00 0.00 1.52
617 671 7.382759 GGCCGAATTGTTCAAAAATGTAGTAAA 59.617 33.333 0.00 0.00 0.00 2.01
618 672 6.864165 GGCCGAATTGTTCAAAAATGTAGTAA 59.136 34.615 0.00 0.00 0.00 2.24
619 673 6.383415 GGCCGAATTGTTCAAAAATGTAGTA 58.617 36.000 0.00 0.00 0.00 1.82
620 674 5.227152 GGCCGAATTGTTCAAAAATGTAGT 58.773 37.500 0.00 0.00 0.00 2.73
621 675 4.323336 CGGCCGAATTGTTCAAAAATGTAG 59.677 41.667 24.07 0.00 0.00 2.74
641 695 2.642254 GGCAAAAGTTACCCCCGGC 61.642 63.158 0.00 0.00 0.00 6.13
654 708 1.616628 GGGAGGAGAGAGGGGCAAA 60.617 63.158 0.00 0.00 0.00 3.68
660 714 2.612251 GGGAGGGGAGGAGAGAGG 59.388 72.222 0.00 0.00 0.00 3.69
661 715 2.018086 AGGGGAGGGGAGGAGAGAG 61.018 68.421 0.00 0.00 0.00 3.20
662 716 2.015726 GAGGGGAGGGGAGGAGAGA 61.016 68.421 0.00 0.00 0.00 3.10
663 717 2.612251 GAGGGGAGGGGAGGAGAG 59.388 72.222 0.00 0.00 0.00 3.20
664 718 3.036959 GGAGGGGAGGGGAGGAGA 61.037 72.222 0.00 0.00 0.00 3.71
665 719 4.179599 GGGAGGGGAGGGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
668 722 3.289454 AAAGGGGAGGGGAGGGGAG 62.289 68.421 0.00 0.00 0.00 4.30
669 723 3.224269 AAAGGGGAGGGGAGGGGA 61.224 66.667 0.00 0.00 0.00 4.81
674 728 4.231195 GGTTTATAAAGAAAGGGGAGGGGA 59.769 45.833 0.00 0.00 0.00 4.81
717 771 2.105128 GAGCCGATGTGGAGGTCG 59.895 66.667 0.00 0.00 42.00 4.79
766 824 4.717313 GAGAAAAGCGGCGGGGGT 62.717 66.667 9.78 0.00 0.00 4.95
798 856 4.471726 CGGAAGACGGACGGACGG 62.472 72.222 6.00 0.00 39.42 4.79
833 891 6.288096 AGTGTATTTATCTCCTCTCCCTCT 57.712 41.667 0.00 0.00 0.00 3.69
834 892 6.987403 AAGTGTATTTATCTCCTCTCCCTC 57.013 41.667 0.00 0.00 0.00 4.30
835 893 7.182930 ACAAAAGTGTATTTATCTCCTCTCCCT 59.817 37.037 0.00 0.00 35.72 4.20
836 894 7.281100 CACAAAAGTGTATTTATCTCCTCTCCC 59.719 40.741 0.00 0.00 35.72 4.30
837 895 7.281100 CCACAAAAGTGTATTTATCTCCTCTCC 59.719 40.741 0.00 0.00 35.72 3.71
838 896 7.281100 CCCACAAAAGTGTATTTATCTCCTCTC 59.719 40.741 0.00 0.00 35.72 3.20
839 897 7.112779 CCCACAAAAGTGTATTTATCTCCTCT 58.887 38.462 0.00 0.00 35.72 3.69
840 898 6.318900 CCCCACAAAAGTGTATTTATCTCCTC 59.681 42.308 0.00 0.00 35.72 3.71
841 899 6.011981 TCCCCACAAAAGTGTATTTATCTCCT 60.012 38.462 0.00 0.00 35.72 3.69
856 914 1.214175 TGCTTCTCACTCCCCACAAAA 59.786 47.619 0.00 0.00 0.00 2.44
863 921 1.576356 CGCTAATGCTTCTCACTCCC 58.424 55.000 0.00 0.00 36.97 4.30
890 951 2.514824 GGCGAAGGGTGATGGCTC 60.515 66.667 0.00 0.00 0.00 4.70
905 966 4.067016 CAACACGTACGCGGTGGC 62.067 66.667 16.72 0.00 43.45 5.01
911 972 1.353609 ATTACGCCCAACACGTACGC 61.354 55.000 16.72 0.00 44.95 4.42
993 1054 1.586028 CCCTACCCGAACGAACGAA 59.414 57.895 0.14 0.00 35.09 3.85
994 1055 2.342650 CCCCTACCCGAACGAACGA 61.343 63.158 0.14 0.00 35.09 3.85
995 1056 2.182537 CCCCTACCCGAACGAACG 59.817 66.667 0.00 0.00 0.00 3.95
996 1057 2.230994 GACCCCCTACCCGAACGAAC 62.231 65.000 0.00 0.00 0.00 3.95
997 1058 1.984026 GACCCCCTACCCGAACGAA 60.984 63.158 0.00 0.00 0.00 3.85
998 1059 2.362889 GACCCCCTACCCGAACGA 60.363 66.667 0.00 0.00 0.00 3.85
999 1060 3.830192 CGACCCCCTACCCGAACG 61.830 72.222 0.00 0.00 0.00 3.95
1000 1061 2.230994 GAACGACCCCCTACCCGAAC 62.231 65.000 0.00 0.00 0.00 3.95
1057 1119 2.749839 TCCGCCATTTCCGCCAAG 60.750 61.111 0.00 0.00 0.00 3.61
1059 1121 4.794648 CCTCCGCCATTTCCGCCA 62.795 66.667 0.00 0.00 0.00 5.69
1319 1389 0.541764 GGATGCCAACCCAGACCAAA 60.542 55.000 0.00 0.00 0.00 3.28
1349 1419 4.021719 ACAACAATCAGATGCTTCCAAAGG 60.022 41.667 0.00 0.00 0.00 3.11
1378 1452 1.797441 CGAGACACGGAGAGACAGG 59.203 63.158 0.00 0.00 38.46 4.00
1539 1613 3.535629 CTCGTGCAGCAGGTCCCAA 62.536 63.158 14.62 0.00 0.00 4.12
1697 1774 0.176449 GTTCGGCGGGTACTGGTAAT 59.824 55.000 7.21 0.00 33.56 1.89
1740 1817 3.414700 CTCACACGGGCGACTTGC 61.415 66.667 0.00 0.00 45.38 4.01
1781 1858 1.126846 GACGAAGCGGAACAGATTGTG 59.873 52.381 0.00 0.00 0.00 3.33
1784 1861 1.546476 AGAGACGAAGCGGAACAGATT 59.454 47.619 0.00 0.00 0.00 2.40
1785 1862 1.133407 GAGAGACGAAGCGGAACAGAT 59.867 52.381 0.00 0.00 0.00 2.90
1786 1863 0.522180 GAGAGACGAAGCGGAACAGA 59.478 55.000 0.00 0.00 0.00 3.41
1801 1882 3.257127 GTCAGAGAATAATCCCCGGAGAG 59.743 52.174 0.73 0.00 0.00 3.20
1807 1888 4.141914 ACAGAACGTCAGAGAATAATCCCC 60.142 45.833 0.00 0.00 0.00 4.81
1827 1912 6.016360 TGGAACTGAAACCACAAATCATACAG 60.016 38.462 0.00 0.00 0.00 2.74
1838 1923 3.077359 CAGGAGATGGAACTGAAACCAC 58.923 50.000 0.00 0.00 39.06 4.16
1839 1924 2.978978 TCAGGAGATGGAACTGAAACCA 59.021 45.455 0.00 0.00 38.22 3.67
2030 2118 3.253838 CCGGGTGGGGTCAGGAAA 61.254 66.667 0.00 0.00 0.00 3.13
2134 2222 1.800229 AAGTGGGGGCGGAAAAGGAT 61.800 55.000 0.00 0.00 0.00 3.24
2135 2223 2.420466 GAAGTGGGGGCGGAAAAGGA 62.420 60.000 0.00 0.00 0.00 3.36
2165 2258 2.919772 AATACTTTTGGGGGACAGGG 57.080 50.000 0.00 0.00 0.00 4.45
2167 2260 5.480422 AGCTAAAAATACTTTTGGGGGACAG 59.520 40.000 0.00 0.00 35.50 3.51
2196 2290 1.518903 GCCAAGCAGAACCACAGGAC 61.519 60.000 0.00 0.00 0.00 3.85
2341 2450 0.108329 ACGTGCGTAATGAGAAGGGG 60.108 55.000 0.00 0.00 0.00 4.79
2360 2469 2.700722 TATCATTGCCGTTGCCAGTA 57.299 45.000 0.00 0.00 36.33 2.74
2364 2473 1.925946 GCGATTATCATTGCCGTTGCC 60.926 52.381 0.00 0.00 33.98 4.52
2371 2480 6.467047 CCGAATAAAGATGCGATTATCATTGC 59.533 38.462 0.00 0.00 36.00 3.56
2394 2503 3.769739 TGATGGATCTTCATAACCCCG 57.230 47.619 0.00 0.00 0.00 5.73
2491 2617 3.649986 GCGTTGGCGTTGTGCTCT 61.650 61.111 0.00 0.00 45.43 4.09
2801 2998 3.213009 TTTGTTCGTTCGTCGGCGC 62.213 57.895 3.52 0.00 40.32 6.53
2811 3008 2.207590 GTTTCTCCTCCGTTTGTTCGT 58.792 47.619 0.00 0.00 0.00 3.85
2813 3010 4.625972 TTTGTTTCTCCTCCGTTTGTTC 57.374 40.909 0.00 0.00 0.00 3.18
2817 3014 4.211920 TGGATTTTGTTTCTCCTCCGTTT 58.788 39.130 0.00 0.00 0.00 3.60
2894 3103 3.118000 ACCATACCTCCGAAATTTCCTCC 60.118 47.826 12.54 0.00 0.00 4.30
2895 3104 3.877508 CACCATACCTCCGAAATTTCCTC 59.122 47.826 12.54 0.00 0.00 3.71
2896 3105 3.886123 CACCATACCTCCGAAATTTCCT 58.114 45.455 12.54 0.00 0.00 3.36
2897 3106 2.357952 GCACCATACCTCCGAAATTTCC 59.642 50.000 12.54 0.00 0.00 3.13
2923 3132 3.127895 ACAGCTAGAAGAACTACTGAGCG 59.872 47.826 0.00 0.00 35.87 5.03
2927 3136 6.071840 ACCTTACACAGCTAGAAGAACTACTG 60.072 42.308 0.00 0.00 36.85 2.74
2992 3202 0.669318 CTTACAGCGACGCCTTTCCA 60.669 55.000 17.79 0.00 0.00 3.53
3025 3235 7.121907 GGAAACATGGAGCTCTTATTTCTTTCT 59.878 37.037 14.64 0.00 0.00 2.52
3058 3283 2.439156 CCCAAGGCAGCAGTAGGC 60.439 66.667 0.00 0.00 45.30 3.93
3059 3284 0.251341 AAACCCAAGGCAGCAGTAGG 60.251 55.000 0.00 0.00 0.00 3.18
3060 3285 0.883833 CAAACCCAAGGCAGCAGTAG 59.116 55.000 0.00 0.00 0.00 2.57
3061 3286 1.178534 GCAAACCCAAGGCAGCAGTA 61.179 55.000 0.00 0.00 0.00 2.74
3062 3287 2.501602 GCAAACCCAAGGCAGCAGT 61.502 57.895 0.00 0.00 0.00 4.40
3063 3288 1.751349 AAGCAAACCCAAGGCAGCAG 61.751 55.000 0.00 0.00 0.00 4.24
3064 3289 1.336632 AAAGCAAACCCAAGGCAGCA 61.337 50.000 0.00 0.00 0.00 4.41
3065 3290 0.881600 CAAAGCAAACCCAAGGCAGC 60.882 55.000 0.00 0.00 0.00 5.25
3066 3291 0.465287 ACAAAGCAAACCCAAGGCAG 59.535 50.000 0.00 0.00 0.00 4.85
3067 3292 0.908198 AACAAAGCAAACCCAAGGCA 59.092 45.000 0.00 0.00 0.00 4.75
3068 3293 1.298602 CAACAAAGCAAACCCAAGGC 58.701 50.000 0.00 0.00 0.00 4.35
3069 3294 1.298602 GCAACAAAGCAAACCCAAGG 58.701 50.000 0.00 0.00 0.00 3.61
3070 3295 2.021355 TGCAACAAAGCAAACCCAAG 57.979 45.000 0.00 0.00 42.46 3.61
3112 3337 4.248174 TGCCAAAAGGGATGACATGATA 57.752 40.909 0.00 0.00 40.01 2.15
3118 3353 1.463674 ACGATGCCAAAAGGGATGAC 58.536 50.000 0.00 0.00 40.01 3.06
3218 3453 2.784347 AGGAGGAAGAAAAGGCTTTCG 58.216 47.619 13.76 0.00 44.83 3.46
3219 3454 3.305676 GCAAGGAGGAAGAAAAGGCTTTC 60.306 47.826 13.76 7.09 41.19 2.62
3220 3455 2.630098 GCAAGGAGGAAGAAAAGGCTTT 59.370 45.455 6.68 6.68 0.00 3.51
3221 3456 2.242926 GCAAGGAGGAAGAAAAGGCTT 58.757 47.619 0.00 0.00 0.00 4.35
3222 3457 1.145738 TGCAAGGAGGAAGAAAAGGCT 59.854 47.619 0.00 0.00 0.00 4.58
3223 3458 1.620822 TGCAAGGAGGAAGAAAAGGC 58.379 50.000 0.00 0.00 0.00 4.35
3224 3459 4.879197 AAATGCAAGGAGGAAGAAAAGG 57.121 40.909 0.00 0.00 0.00 3.11
3225 3460 5.604565 ACAAAATGCAAGGAGGAAGAAAAG 58.395 37.500 0.00 0.00 0.00 2.27
3231 3466 5.096443 ACAAAACAAAATGCAAGGAGGAA 57.904 34.783 0.00 0.00 0.00 3.36
3236 3471 7.864307 TTCAAAAACAAAACAAAATGCAAGG 57.136 28.000 0.00 0.00 0.00 3.61
3257 3492 9.281371 TCCAATTTCACATGCAAAAATATTTCA 57.719 25.926 0.10 0.00 0.00 2.69
3261 3496 9.590451 CTAGTCCAATTTCACATGCAAAAATAT 57.410 29.630 0.00 0.00 0.00 1.28
3283 3518 2.437413 TCACTGAGCGATGACACTAGT 58.563 47.619 0.00 0.00 0.00 2.57
3285 3520 5.125578 AGTTAATCACTGAGCGATGACACTA 59.874 40.000 0.00 0.00 32.83 2.74
3294 3529 4.800993 CCAAGTCTAGTTAATCACTGAGCG 59.199 45.833 0.00 0.00 35.97 5.03
3308 3546 5.336849 CCTGTTCAACCTACTCCAAGTCTAG 60.337 48.000 0.00 0.00 0.00 2.43
3311 3549 3.557264 CCCTGTTCAACCTACTCCAAGTC 60.557 52.174 0.00 0.00 0.00 3.01
3332 3575 4.394712 CACCACCTCACCTCGCCC 62.395 72.222 0.00 0.00 0.00 6.13
3335 3578 2.923035 ACCCACCACCTCACCTCG 60.923 66.667 0.00 0.00 0.00 4.63
3354 3597 1.601903 CTTTTGTGCGCAAGTGGAGTA 59.398 47.619 14.00 0.00 41.68 2.59
3365 3608 5.082059 GTCACATGATTAGACTTTTGTGCG 58.918 41.667 0.00 0.00 35.58 5.34
3368 3611 6.089016 CGTACGTCACATGATTAGACTTTTGT 59.911 38.462 7.22 0.00 0.00 2.83
3393 3648 2.611974 CACCATCGTGTTAAGCAACC 57.388 50.000 0.00 0.00 35.10 3.77
3405 3660 4.810790 AGAAAGAACAGACTACACCATCG 58.189 43.478 0.00 0.00 0.00 3.84
3621 3879 2.619590 GGCCCCGACCTCTTGATTTTAA 60.620 50.000 0.00 0.00 0.00 1.52
3728 3997 0.179097 GAATCTCCACTCGCCTCACC 60.179 60.000 0.00 0.00 0.00 4.02
3781 4050 4.717629 CAGGACTCGGCGCAACGA 62.718 66.667 10.83 9.42 41.13 3.85
3792 4061 1.301244 CAACGCAGACAGCAGGACT 60.301 57.895 0.00 0.00 46.13 3.85
3794 4063 2.666190 GCAACGCAGACAGCAGGA 60.666 61.111 0.00 0.00 46.13 3.86
3796 4065 2.554775 CAGCAACGCAGACAGCAG 59.445 61.111 0.00 0.00 46.13 4.24
3797 4066 2.974148 CCAGCAACGCAGACAGCA 60.974 61.111 0.00 0.00 46.13 4.41
3798 4067 2.666190 TCCAGCAACGCAGACAGC 60.666 61.111 0.00 0.00 40.87 4.40
3799 4068 2.675056 GCTCCAGCAACGCAGACAG 61.675 63.158 0.00 0.00 41.59 3.51
3800 4069 2.665008 AAGCTCCAGCAACGCAGACA 62.665 55.000 0.48 0.00 45.16 3.41
3801 4070 1.510480 AAAGCTCCAGCAACGCAGAC 61.510 55.000 0.48 0.00 45.16 3.51
3802 4071 1.227943 AAAGCTCCAGCAACGCAGA 60.228 52.632 0.48 0.00 45.16 4.26
3803 4072 1.081641 CAAAGCTCCAGCAACGCAG 60.082 57.895 0.48 0.00 45.16 5.18
3804 4073 3.033184 CAAAGCTCCAGCAACGCA 58.967 55.556 0.48 0.00 45.16 5.24
3805 4074 2.429739 GCAAAGCTCCAGCAACGC 60.430 61.111 0.48 0.00 45.16 4.84
3806 4075 1.081641 CAGCAAAGCTCCAGCAACG 60.082 57.895 0.48 0.00 45.16 4.10
3807 4076 1.372623 GCAGCAAAGCTCCAGCAAC 60.373 57.895 0.48 0.00 45.16 4.17
3808 4077 1.529948 AGCAGCAAAGCTCCAGCAA 60.530 52.632 0.48 0.00 42.18 3.91
3809 4078 2.114625 AGCAGCAAAGCTCCAGCA 59.885 55.556 0.48 0.00 42.18 4.41
3816 4085 2.684843 CCGGTCAGAGCAGCAAAGC 61.685 63.158 0.00 0.00 0.00 3.51
3817 4086 2.037136 CCCGGTCAGAGCAGCAAAG 61.037 63.158 0.00 0.00 0.00 2.77
3818 4087 2.032528 CCCGGTCAGAGCAGCAAA 59.967 61.111 0.00 0.00 0.00 3.68
3819 4088 3.240134 GACCCGGTCAGAGCAGCAA 62.240 63.158 13.05 0.00 32.09 3.91
3820 4089 3.695606 GACCCGGTCAGAGCAGCA 61.696 66.667 13.05 0.00 32.09 4.41
3821 4090 2.527951 ATTGACCCGGTCAGAGCAGC 62.528 60.000 19.59 0.00 43.69 5.25
3833 4102 1.187567 AAAGCCAGCCACATTGACCC 61.188 55.000 0.00 0.00 0.00 4.46
3859 4128 2.049433 AAAGTGGGAGACGTCGCG 60.049 61.111 13.27 0.00 38.49 5.87


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

AutoCloner maintained by Alex Coulton.