Multiple sequence alignment - TraesCS4D01G033600

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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 TraesCS4D01G033600 chr4D 100.000 5103 0 0 1 5103 15367940 15373042 0.000000e+00 9424.0
1 TraesCS4D01G033600 chr4D 97.093 172 3 2 3690 3860 75782050 75782220 6.460000e-74 289.0
2 TraesCS4D01G033600 chr4D 97.093 172 3 2 3694 3864 93338206 93338036 6.460000e-74 289.0
3 TraesCS4D01G033600 chr4B 91.483 2853 144 38 698 3522 25886148 25888929 0.000000e+00 3831.0
4 TraesCS4D01G033600 chr4B 88.953 697 54 11 12 687 25853931 25854625 0.000000e+00 839.0
5 TraesCS4D01G033600 chr4B 89.219 538 27 13 3856 4387 25889032 25889544 1.200000e-180 643.0
6 TraesCS4D01G033600 chr4B 84.950 299 27 9 4569 4866 25889882 25890163 2.330000e-73 287.0
7 TraesCS4D01G033600 chr4B 88.571 210 20 4 4894 5103 25890157 25890362 8.480000e-63 252.0
8 TraesCS4D01G033600 chr4B 87.117 163 11 4 4402 4560 25889517 25889673 5.250000e-40 176.0
9 TraesCS4D01G033600 chr4B 83.051 118 5 2 3578 3695 25888931 25889033 5.440000e-15 93.5
10 TraesCS4D01G033600 chr4A 90.134 2321 136 31 23 2300 585401834 585399564 0.000000e+00 2931.0
11 TraesCS4D01G033600 chr4A 90.977 798 54 10 2893 3684 585398065 585397280 0.000000e+00 1059.0
12 TraesCS4D01G033600 chr4A 89.099 688 44 15 4402 5081 585396799 585396135 0.000000e+00 826.0
13 TraesCS4D01G033600 chr4A 88.960 625 46 11 2285 2897 585398753 585398140 0.000000e+00 750.0
14 TraesCS4D01G033600 chr4A 89.446 578 46 10 2285 2850 585399379 585398805 0.000000e+00 715.0
15 TraesCS4D01G033600 chr4A 90.755 530 29 10 3873 4402 585397266 585396757 0.000000e+00 689.0
16 TraesCS4D01G033600 chr4A 100.000 29 0 0 5073 5101 585396129 585396101 3.000000e-03 54.7
17 TraesCS4D01G033600 chr3B 86.782 923 89 17 1269 2182 69992707 69993605 0.000000e+00 998.0
18 TraesCS4D01G033600 chr3B 87.729 709 51 13 2493 3172 69994297 69994998 0.000000e+00 795.0
19 TraesCS4D01G033600 chr3B 88.435 294 27 4 2173 2465 69994008 69994295 1.050000e-91 348.0
20 TraesCS4D01G033600 chr2B 89.546 507 35 10 2309 2808 183535917 183535422 1.210000e-175 627.0
21 TraesCS4D01G033600 chr2B 96.067 178 4 3 3681 3857 174794997 174794822 2.330000e-73 287.0
22 TraesCS4D01G033600 chr6B 89.621 501 35 9 2309 2803 599818386 599818875 5.610000e-174 621.0
23 TraesCS4D01G033600 chr5B 88.802 509 36 13 2309 2808 672542239 672541743 5.650000e-169 604.0
24 TraesCS4D01G033600 chr5B 97.076 171 3 2 3688 3857 575812800 575812969 2.330000e-73 287.0
25 TraesCS4D01G033600 chr3D 88.340 506 44 7 2302 2803 424218487 424218981 1.220000e-165 593.0
26 TraesCS4D01G033600 chr7B 92.444 225 14 2 2929 3153 708413653 708413432 8.240000e-83 318.0
27 TraesCS4D01G033600 chr1D 97.661 171 3 1 3691 3860 178466303 178466473 5.000000e-75 292.0
28 TraesCS4D01G033600 chr5A 97.093 172 4 1 3694 3864 290391861 290391690 6.460000e-74 289.0
29 TraesCS4D01G033600 chr2D 97.633 169 3 1 3694 3861 560959485 560959653 6.460000e-74 289.0
30 TraesCS4D01G033600 chr6D 96.532 173 5 1 3687 3858 392897146 392896974 8.360000e-73 285.0
31 TraesCS4D01G033600 chr5D 93.085 188 12 1 3677 3863 420206224 420206037 1.810000e-69 274.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G033600 chr4D 15367940 15373042 5102 False 9424.000000 9424 100.000000 1 5103 1 chr4D.!!$F1 5102
1 TraesCS4D01G033600 chr4B 25886148 25890362 4214 False 880.416667 3831 87.398500 698 5103 6 chr4B.!!$F2 4405
2 TraesCS4D01G033600 chr4B 25853931 25854625 694 False 839.000000 839 88.953000 12 687 1 chr4B.!!$F1 675
3 TraesCS4D01G033600 chr4A 585396101 585401834 5733 True 1003.528571 2931 91.338714 23 5101 7 chr4A.!!$R1 5078
4 TraesCS4D01G033600 chr3B 69992707 69994998 2291 False 713.666667 998 87.648667 1269 3172 3 chr3B.!!$F1 1903

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
606 629 0.179192 CACATACACACATGCACGGC 60.179 55.000 0.00 0.0 0.00 5.68 F
813 836 0.393077 CCCTCTCACAAGTCAACCGT 59.607 55.000 0.00 0.0 0.00 4.83 F
1593 1644 0.539051 ACTTCTTCCTCAGCATCCCG 59.461 55.000 0.00 0.0 0.00 5.14 F
1745 1800 0.750911 GATTGGAAGCCCTGCTCCAG 60.751 60.000 7.13 0.0 38.25 3.86 F
3201 4623 1.070134 GACCTAAGTGTGTGTCTGGCA 59.930 52.381 0.00 0.0 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 1773 0.826062 GGGCTTCCAATCCAATGTGG 59.174 55.000 0.00 0.00 39.43 4.17 R
2558 3247 3.973135 CGCGTCATTATGTAGTGTAGGAC 59.027 47.826 0.00 0.00 0.00 3.85 R
3080 4502 1.946768 CAGAACAACCACCACAACGAT 59.053 47.619 0.00 0.00 0.00 3.73 R
3301 4723 2.824689 TCTATTGCCTGAAATGCCCA 57.175 45.000 0.00 0.00 0.00 5.36 R
4931 6579 0.093705 CAAGTAGTTCTTCTGCGCGC 59.906 55.000 27.26 27.26 33.63 6.86 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
48 49 5.314923 TGCAGGAAATTTGTAGAGCATTC 57.685 39.130 0.00 0.00 0.00 2.67
63 64 4.211374 AGAGCATTCGACTACACAACAAAC 59.789 41.667 0.00 0.00 0.00 2.93
66 67 4.449743 GCATTCGACTACACAACAAACCTA 59.550 41.667 0.00 0.00 0.00 3.08
83 84 1.689273 CCTAAATAGCCACGAGGAGCT 59.311 52.381 1.86 0.57 43.20 4.09
232 234 2.744202 ACATGTGCCTTTTAGAGCGAAG 59.256 45.455 0.00 0.00 0.00 3.79
366 369 3.507622 CACATTCCCTTCTTCCTCAAACC 59.492 47.826 0.00 0.00 0.00 3.27
367 370 2.561478 TTCCCTTCTTCCTCAAACCG 57.439 50.000 0.00 0.00 0.00 4.44
427 430 0.240945 GGCACTGTTTGGAATCACCG 59.759 55.000 0.00 0.00 42.61 4.94
438 441 0.802607 GAATCACCGCTCTCGTGTCC 60.803 60.000 0.00 0.00 0.00 4.02
471 474 5.063564 CCGCTAGTAAAAGAAGGAATCACAC 59.936 44.000 0.00 0.00 0.00 3.82
531 534 4.210120 GCATCCTATTCTTACGAGCACTTG 59.790 45.833 0.00 0.00 0.00 3.16
534 537 6.132791 TCCTATTCTTACGAGCACTTGTAG 57.867 41.667 0.00 0.00 31.61 2.74
540 543 0.889306 ACGAGCACTTGTAGGAGTCC 59.111 55.000 0.00 0.00 0.00 3.85
606 629 0.179192 CACATACACACATGCACGGC 60.179 55.000 0.00 0.00 0.00 5.68
656 679 9.046296 CCTACATTATGATCACACCTTAAAGAC 57.954 37.037 0.00 0.00 0.00 3.01
659 682 9.113838 ACATTATGATCACACCTTAAAGACATC 57.886 33.333 0.00 0.00 0.00 3.06
737 760 6.590292 GGTAGATTTTGAGATCGACAAAGTCA 59.410 38.462 27.11 18.16 42.31 3.41
747 770 1.648467 GACAAAGTCATCGCAGCCCC 61.648 60.000 0.00 0.00 32.09 5.80
749 772 2.606587 AAAGTCATCGCAGCCCCCT 61.607 57.895 0.00 0.00 0.00 4.79
750 773 2.142292 AAAGTCATCGCAGCCCCCTT 62.142 55.000 0.00 0.00 0.00 3.95
751 774 2.514824 GTCATCGCAGCCCCCTTC 60.515 66.667 0.00 0.00 0.00 3.46
759 782 2.365237 AGCCCCCTTCGTACCCTC 60.365 66.667 0.00 0.00 0.00 4.30
791 814 4.761739 CCTTCATGGAAGTACTGCAGAAAA 59.238 41.667 23.35 1.97 37.92 2.29
803 826 1.768275 TGCAGAAAAGTCCCTCTCACA 59.232 47.619 0.00 0.00 0.00 3.58
811 834 1.694696 AGTCCCTCTCACAAGTCAACC 59.305 52.381 0.00 0.00 0.00 3.77
813 836 0.393077 CCCTCTCACAAGTCAACCGT 59.607 55.000 0.00 0.00 0.00 4.83
814 837 1.202651 CCCTCTCACAAGTCAACCGTT 60.203 52.381 0.00 0.00 0.00 4.44
829 854 8.683550 AGTCAACCGTTAAAAGAAAAAGAAAG 57.316 30.769 0.00 0.00 0.00 2.62
831 856 9.131416 GTCAACCGTTAAAAGAAAAAGAAAGAA 57.869 29.630 0.00 0.00 0.00 2.52
836 861 9.967245 CCGTTAAAAGAAAAAGAAAGAAAAAGG 57.033 29.630 0.00 0.00 0.00 3.11
839 864 7.938140 AAAAGAAAAAGAAAGAAAAAGGGGG 57.062 32.000 0.00 0.00 0.00 5.40
873 903 4.320608 ACGAAAATCAAAGCAATGGTGT 57.679 36.364 0.00 0.00 0.00 4.16
874 904 4.050553 ACGAAAATCAAAGCAATGGTGTG 58.949 39.130 0.00 0.00 0.00 3.82
875 905 4.202101 ACGAAAATCAAAGCAATGGTGTGA 60.202 37.500 7.84 7.84 31.62 3.58
876 906 4.148696 CGAAAATCAAAGCAATGGTGTGAC 59.851 41.667 7.54 0.00 29.71 3.67
895 928 1.275573 ACGAGCTCCCTCACTTTAACC 59.724 52.381 8.47 0.00 38.00 2.85
899 938 1.405661 GCTCCCTCACTTTAACCTCCG 60.406 57.143 0.00 0.00 0.00 4.63
983 1022 1.600916 GGACAGCTCACCACCAACC 60.601 63.158 1.29 0.00 0.00 3.77
984 1023 1.600916 GACAGCTCACCACCAACCC 60.601 63.158 0.00 0.00 0.00 4.11
985 1024 2.669569 CAGCTCACCACCAACCCG 60.670 66.667 0.00 0.00 0.00 5.28
986 1025 4.643387 AGCTCACCACCAACCCGC 62.643 66.667 0.00 0.00 0.00 6.13
987 1026 4.947147 GCTCACCACCAACCCGCA 62.947 66.667 0.00 0.00 0.00 5.69
988 1027 2.034066 CTCACCACCAACCCGCAT 59.966 61.111 0.00 0.00 0.00 4.73
989 1028 2.033448 TCACCACCAACCCGCATC 59.967 61.111 0.00 0.00 0.00 3.91
990 1029 3.061848 CACCACCAACCCGCATCC 61.062 66.667 0.00 0.00 0.00 3.51
991 1030 4.360405 ACCACCAACCCGCATCCC 62.360 66.667 0.00 0.00 0.00 3.85
992 1031 4.047125 CCACCAACCCGCATCCCT 62.047 66.667 0.00 0.00 0.00 4.20
1122 1170 2.124983 TACGTCCTCCTCGTCCCG 60.125 66.667 0.00 0.00 41.72 5.14
1355 1403 2.126463 CAACCTCTTCGCGCTCGA 60.126 61.111 5.56 0.00 43.89 4.04
1548 1596 1.673808 GGTCCATACCCTTCGACGCT 61.674 60.000 0.00 0.00 40.21 5.07
1588 1639 0.979665 CCTCCACTTCTTCCTCAGCA 59.020 55.000 0.00 0.00 0.00 4.41
1593 1644 0.539051 ACTTCTTCCTCAGCATCCCG 59.461 55.000 0.00 0.00 0.00 5.14
1675 1730 4.395854 ACGCATTGTGAATTAGATTGCTGA 59.604 37.500 3.82 0.00 29.59 4.26
1745 1800 0.750911 GATTGGAAGCCCTGCTCCAG 60.751 60.000 7.13 0.00 38.25 3.86
1886 1953 3.547746 TGGATTGCGATACCTTTAACCC 58.452 45.455 0.00 0.00 0.00 4.11
1892 1959 1.667212 CGATACCTTTAACCCGCCAAC 59.333 52.381 0.00 0.00 0.00 3.77
1893 1960 2.678769 CGATACCTTTAACCCGCCAACT 60.679 50.000 0.00 0.00 0.00 3.16
1941 2012 7.157947 TGGTAATCAGTCTACCAGGAGTATA 57.842 40.000 0.00 0.00 43.11 1.47
1942 2013 7.589081 TGGTAATCAGTCTACCAGGAGTATAA 58.411 38.462 0.00 0.00 43.11 0.98
1943 2014 8.063153 TGGTAATCAGTCTACCAGGAGTATAAA 58.937 37.037 0.00 0.00 43.11 1.40
1944 2015 9.091220 GGTAATCAGTCTACCAGGAGTATAAAT 57.909 37.037 0.00 0.00 38.98 1.40
1996 2067 5.006153 TCCATAGTCACGAATCACGATTT 57.994 39.130 0.00 0.00 45.77 2.17
2046 2117 4.957327 ACCAGTTACCTCTTACATCCTCTC 59.043 45.833 0.00 0.00 0.00 3.20
2050 2121 6.098982 CAGTTACCTCTTACATCCTCTCCATT 59.901 42.308 0.00 0.00 0.00 3.16
2118 2189 9.924650 AACTGGGAAATCGTACTATAATACATC 57.075 33.333 0.00 0.00 0.00 3.06
2203 2686 5.294552 AGGTTCTGTTTTTCTGAACTTCTCG 59.705 40.000 13.90 0.00 46.77 4.04
2205 2688 6.403309 GGTTCTGTTTTTCTGAACTTCTCGTT 60.403 38.462 13.90 0.00 46.77 3.85
2208 2691 7.851508 TCTGTTTTTCTGAACTTCTCGTTATG 58.148 34.615 0.00 0.00 35.56 1.90
2257 2741 7.542130 GCTGGTCCTTGTAAAAATTATTCACAG 59.458 37.037 0.00 0.00 0.00 3.66
2558 3247 4.841422 ACTTGGACCATTCTCATCTTCAG 58.159 43.478 0.00 0.00 0.00 3.02
2735 3430 3.383620 TGGCCATTTTAAACACTGCAG 57.616 42.857 13.48 13.48 0.00 4.41
2846 3544 4.450419 GTGATGCCACTAGCTGATACATTC 59.550 45.833 0.00 0.00 44.23 2.67
3200 4622 1.344763 AGACCTAAGTGTGTGTCTGGC 59.655 52.381 0.00 0.00 36.74 4.85
3201 4623 1.070134 GACCTAAGTGTGTGTCTGGCA 59.930 52.381 0.00 0.00 0.00 4.92
3211 4633 3.936203 GTCTGGCACGGTGTCCCA 61.936 66.667 10.66 8.67 35.30 4.37
3271 4693 4.346418 CCCTTGATAGTGGAACATAGAGCT 59.654 45.833 0.00 0.00 44.52 4.09
3274 4696 4.697514 TGATAGTGGAACATAGAGCTTGC 58.302 43.478 0.00 0.00 44.52 4.01
3276 4698 3.710209 AGTGGAACATAGAGCTTGCTT 57.290 42.857 0.00 0.00 44.52 3.91
3279 4701 4.020218 AGTGGAACATAGAGCTTGCTTGTA 60.020 41.667 0.00 0.00 44.52 2.41
3289 4711 4.119862 GAGCTTGCTTGTATCGTATGGAA 58.880 43.478 0.00 0.00 0.00 3.53
3291 4713 5.126067 AGCTTGCTTGTATCGTATGGAATT 58.874 37.500 0.00 0.00 0.00 2.17
3331 4753 9.736023 CATTTCAGGCAATAGAAACTAATTACC 57.264 33.333 0.00 0.00 36.65 2.85
3334 4756 7.506114 TCAGGCAATAGAAACTAATTACCGAT 58.494 34.615 0.00 0.00 0.00 4.18
3516 4939 2.362889 GATTGTGGTGCCTGGGGG 60.363 66.667 0.00 0.00 0.00 5.40
3530 4957 1.533994 GGGGGCCTGTTTCTTGCTT 60.534 57.895 0.84 0.00 0.00 3.91
3538 4965 5.164233 GGCCTGTTTCTTGCTTCTAATTTC 58.836 41.667 0.00 0.00 0.00 2.17
3539 4966 5.047731 GGCCTGTTTCTTGCTTCTAATTTCT 60.048 40.000 0.00 0.00 0.00 2.52
3546 4973 6.403866 TCTTGCTTCTAATTTCTTTTGCCA 57.596 33.333 0.00 0.00 0.00 4.92
3669 5096 8.877864 TTTTGTTGTTATTCCAGATACCAGAT 57.122 30.769 0.00 0.00 0.00 2.90
3679 5106 7.451731 TTCCAGATACCAGATAGACCAAAAT 57.548 36.000 0.00 0.00 0.00 1.82
3700 5127 2.990740 TGCCCAACAAATTACTCCCT 57.009 45.000 0.00 0.00 0.00 4.20
3701 5128 2.802719 TGCCCAACAAATTACTCCCTC 58.197 47.619 0.00 0.00 0.00 4.30
3702 5129 2.100197 GCCCAACAAATTACTCCCTCC 58.900 52.381 0.00 0.00 0.00 4.30
3703 5130 2.365582 CCCAACAAATTACTCCCTCCG 58.634 52.381 0.00 0.00 0.00 4.63
3704 5131 2.290705 CCCAACAAATTACTCCCTCCGT 60.291 50.000 0.00 0.00 0.00 4.69
3705 5132 3.418047 CCAACAAATTACTCCCTCCGTT 58.582 45.455 0.00 0.00 0.00 4.44
3706 5133 3.439129 CCAACAAATTACTCCCTCCGTTC 59.561 47.826 0.00 0.00 0.00 3.95
3707 5134 3.345508 ACAAATTACTCCCTCCGTTCC 57.654 47.619 0.00 0.00 0.00 3.62
3708 5135 2.910977 ACAAATTACTCCCTCCGTTCCT 59.089 45.455 0.00 0.00 0.00 3.36
3709 5136 4.098894 ACAAATTACTCCCTCCGTTCCTA 58.901 43.478 0.00 0.00 0.00 2.94
3710 5137 4.533311 ACAAATTACTCCCTCCGTTCCTAA 59.467 41.667 0.00 0.00 0.00 2.69
3711 5138 5.013391 ACAAATTACTCCCTCCGTTCCTAAA 59.987 40.000 0.00 0.00 0.00 1.85
3712 5139 5.970501 AATTACTCCCTCCGTTCCTAAAT 57.029 39.130 0.00 0.00 0.00 1.40
3713 5140 7.092757 ACAAATTACTCCCTCCGTTCCTAAATA 60.093 37.037 0.00 0.00 0.00 1.40
3714 5141 7.628501 AATTACTCCCTCCGTTCCTAAATAT 57.371 36.000 0.00 0.00 0.00 1.28
3715 5142 7.628501 ATTACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
3716 5143 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3717 5144 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
3718 5145 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
3719 5146 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
3720 5147 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
3721 5148 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
3722 5149 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
3723 5150 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
3724 5151 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
3740 5167 9.965824 TTTGTCTTTTTAGAGATTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
3741 5168 8.924511 TGTCTTTTTAGAGATTCAAATGGACT 57.075 30.769 0.00 0.00 0.00 3.85
3744 5171 9.449719 TCTTTTTAGAGATTCAAATGGACTACC 57.550 33.333 0.00 0.00 0.00 3.18
3797 5224 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3798 5225 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3799 5226 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3800 5227 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3801 5228 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3802 5229 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3803 5230 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3804 5231 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3805 5232 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3806 5233 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3807 5234 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3808 5235 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3809 5236 4.109766 TCATTTTGCTCCGTATGTAGTCG 58.890 43.478 0.00 0.00 0.00 4.18
3810 5237 1.917273 TTTGCTCCGTATGTAGTCGC 58.083 50.000 0.00 0.00 0.00 5.19
3811 5238 1.100510 TTGCTCCGTATGTAGTCGCT 58.899 50.000 0.00 0.00 0.00 4.93
3812 5239 1.100510 TGCTCCGTATGTAGTCGCTT 58.899 50.000 0.00 0.00 0.00 4.68
3813 5240 1.202256 TGCTCCGTATGTAGTCGCTTG 60.202 52.381 0.00 0.00 0.00 4.01
3814 5241 1.202268 GCTCCGTATGTAGTCGCTTGT 60.202 52.381 0.00 0.00 0.00 3.16
3815 5242 2.734492 GCTCCGTATGTAGTCGCTTGTT 60.734 50.000 0.00 0.00 0.00 2.83
3816 5243 2.852413 CTCCGTATGTAGTCGCTTGTTG 59.148 50.000 0.00 0.00 0.00 3.33
3817 5244 2.488937 TCCGTATGTAGTCGCTTGTTGA 59.511 45.455 0.00 0.00 0.00 3.18
3818 5245 3.057386 TCCGTATGTAGTCGCTTGTTGAA 60.057 43.478 0.00 0.00 0.00 2.69
3819 5246 3.676172 CCGTATGTAGTCGCTTGTTGAAA 59.324 43.478 0.00 0.00 0.00 2.69
3820 5247 4.328983 CCGTATGTAGTCGCTTGTTGAAAT 59.671 41.667 0.00 0.00 0.00 2.17
3821 5248 5.481472 CGTATGTAGTCGCTTGTTGAAATC 58.519 41.667 0.00 0.00 0.00 2.17
3822 5249 5.288712 CGTATGTAGTCGCTTGTTGAAATCT 59.711 40.000 0.00 0.00 0.00 2.40
3823 5250 5.786401 ATGTAGTCGCTTGTTGAAATCTC 57.214 39.130 0.00 0.00 0.00 2.75
3824 5251 4.883083 TGTAGTCGCTTGTTGAAATCTCT 58.117 39.130 0.00 0.00 0.00 3.10
3825 5252 6.020971 TGTAGTCGCTTGTTGAAATCTCTA 57.979 37.500 0.00 0.00 0.00 2.43
3826 5253 6.093404 TGTAGTCGCTTGTTGAAATCTCTAG 58.907 40.000 0.00 0.00 0.00 2.43
3827 5254 5.392767 AGTCGCTTGTTGAAATCTCTAGA 57.607 39.130 0.00 0.00 0.00 2.43
3828 5255 5.784177 AGTCGCTTGTTGAAATCTCTAGAA 58.216 37.500 0.00 0.00 0.00 2.10
3829 5256 6.223852 AGTCGCTTGTTGAAATCTCTAGAAA 58.776 36.000 0.00 0.00 0.00 2.52
3830 5257 6.367422 AGTCGCTTGTTGAAATCTCTAGAAAG 59.633 38.462 0.00 0.00 0.00 2.62
3831 5258 6.366332 GTCGCTTGTTGAAATCTCTAGAAAGA 59.634 38.462 0.00 0.00 0.00 2.52
3832 5259 6.929049 TCGCTTGTTGAAATCTCTAGAAAGAA 59.071 34.615 0.00 0.00 0.00 2.52
3833 5260 7.441157 TCGCTTGTTGAAATCTCTAGAAAGAAA 59.559 33.333 0.00 0.00 0.00 2.52
3834 5261 8.070171 CGCTTGTTGAAATCTCTAGAAAGAAAA 58.930 33.333 0.00 0.00 0.00 2.29
3835 5262 9.736023 GCTTGTTGAAATCTCTAGAAAGAAAAA 57.264 29.630 0.00 0.00 0.00 1.94
3851 5278 8.957466 AGAAAGAAAAATATTTAGGAACGGAGG 58.043 33.333 0.01 0.00 0.00 4.30
3852 5279 7.640597 AAGAAAAATATTTAGGAACGGAGGG 57.359 36.000 0.01 0.00 0.00 4.30
3853 5280 6.965607 AGAAAAATATTTAGGAACGGAGGGA 58.034 36.000 0.01 0.00 0.00 4.20
3854 5281 7.054751 AGAAAAATATTTAGGAACGGAGGGAG 58.945 38.462 0.01 0.00 0.00 4.30
3855 5282 5.970501 AAATATTTAGGAACGGAGGGAGT 57.029 39.130 0.00 0.00 0.00 3.85
3856 5283 7.441903 AAAATATTTAGGAACGGAGGGAGTA 57.558 36.000 0.01 0.00 0.00 2.59
3867 5294 3.518303 ACGGAGGGAGTATATTATTGCCC 59.482 47.826 0.00 0.00 35.79 5.36
3870 5297 4.080299 GGAGGGAGTATATTATTGCCCCAG 60.080 50.000 0.00 0.00 36.19 4.45
3899 5326 9.122613 GTGTTTTTATTCTGCTCTTCTCAATTC 57.877 33.333 0.00 0.00 0.00 2.17
3920 5347 4.040047 TCATGGTCATCATACTGAACCCT 58.960 43.478 0.00 0.00 31.55 4.34
3985 5412 5.128008 TGTTAATCCACACGATCAGACCATA 59.872 40.000 0.00 0.00 0.00 2.74
4049 5476 1.725164 GTTTACCGTCTCAAAGCCGAG 59.275 52.381 0.00 0.00 0.00 4.63
4056 5483 1.069636 GTCTCAAAGCCGAGTGCAAAG 60.070 52.381 0.00 0.00 44.83 2.77
4124 5551 1.727723 CCTCGAGCTATCTTCGCGC 60.728 63.158 6.99 0.00 0.00 6.86
4125 5552 1.009562 CTCGAGCTATCTTCGCGCA 60.010 57.895 8.75 0.00 0.00 6.09
4142 5569 3.964347 CGCGCATGAATCTATTGTTTCAG 59.036 43.478 8.75 1.96 35.95 3.02
4150 5577 3.247006 TCTATTGTTTCAGACCTCGCC 57.753 47.619 0.00 0.00 0.00 5.54
4269 5699 6.459923 GGGTGTTTGTAAATTCTTTGGCATA 58.540 36.000 0.00 0.00 0.00 3.14
4381 5814 3.159213 TGTCATTCTGGATGCTGGTTT 57.841 42.857 0.00 0.00 35.64 3.27
4386 5819 2.205022 TCTGGATGCTGGTTTTCTGG 57.795 50.000 0.00 0.00 0.00 3.86
4387 5820 1.425066 TCTGGATGCTGGTTTTCTGGT 59.575 47.619 0.00 0.00 0.00 4.00
4388 5821 2.158475 TCTGGATGCTGGTTTTCTGGTT 60.158 45.455 0.00 0.00 0.00 3.67
4389 5822 1.962807 TGGATGCTGGTTTTCTGGTTG 59.037 47.619 0.00 0.00 0.00 3.77
4390 5823 1.337167 GGATGCTGGTTTTCTGGTTGC 60.337 52.381 0.00 0.00 0.00 4.17
4391 5824 0.314935 ATGCTGGTTTTCTGGTTGCG 59.685 50.000 0.00 0.00 0.00 4.85
4392 5825 1.007387 GCTGGTTTTCTGGTTGCGG 60.007 57.895 0.00 0.00 0.00 5.69
4393 5826 1.452145 GCTGGTTTTCTGGTTGCGGA 61.452 55.000 0.00 0.00 0.00 5.54
4394 5827 1.247567 CTGGTTTTCTGGTTGCGGAT 58.752 50.000 0.00 0.00 0.00 4.18
4395 5828 1.200020 CTGGTTTTCTGGTTGCGGATC 59.800 52.381 0.00 0.00 0.00 3.36
4396 5829 1.243902 GGTTTTCTGGTTGCGGATCA 58.756 50.000 0.00 0.00 0.00 2.92
4397 5830 1.818674 GGTTTTCTGGTTGCGGATCAT 59.181 47.619 0.00 0.00 0.00 2.45
4398 5831 2.159379 GGTTTTCTGGTTGCGGATCATC 60.159 50.000 0.00 0.00 0.00 2.92
4399 5832 2.749621 GTTTTCTGGTTGCGGATCATCT 59.250 45.455 0.00 0.00 0.00 2.90
4400 5833 2.028420 TTCTGGTTGCGGATCATCTG 57.972 50.000 0.00 0.00 0.00 2.90
4401 5834 1.194218 TCTGGTTGCGGATCATCTGA 58.806 50.000 0.00 0.00 0.00 3.27
4402 5835 1.764723 TCTGGTTGCGGATCATCTGAT 59.235 47.619 0.00 0.00 37.51 2.90
4403 5836 2.171237 TCTGGTTGCGGATCATCTGATT 59.829 45.455 0.00 0.00 34.37 2.57
4404 5837 2.289820 CTGGTTGCGGATCATCTGATTG 59.710 50.000 0.00 0.00 34.37 2.67
4405 5838 2.292267 GGTTGCGGATCATCTGATTGT 58.708 47.619 0.00 0.00 34.37 2.71
4406 5839 2.289002 GGTTGCGGATCATCTGATTGTC 59.711 50.000 0.00 0.00 34.37 3.18
4407 5840 2.938451 GTTGCGGATCATCTGATTGTCA 59.062 45.455 0.00 0.00 34.37 3.58
4408 5841 3.480505 TGCGGATCATCTGATTGTCAT 57.519 42.857 0.00 0.00 34.37 3.06
4409 5842 3.812262 TGCGGATCATCTGATTGTCATT 58.188 40.909 0.00 0.00 34.37 2.57
4410 5843 3.811497 TGCGGATCATCTGATTGTCATTC 59.189 43.478 0.00 0.00 34.37 2.67
4411 5844 4.063689 GCGGATCATCTGATTGTCATTCT 58.936 43.478 0.00 0.00 34.37 2.40
4412 5845 4.152045 GCGGATCATCTGATTGTCATTCTC 59.848 45.833 0.00 0.00 34.37 2.87
4413 5846 4.385146 CGGATCATCTGATTGTCATTCTCG 59.615 45.833 0.00 0.00 34.37 4.04
4414 5847 5.536260 GGATCATCTGATTGTCATTCTCGA 58.464 41.667 0.00 0.00 34.37 4.04
4415 5848 6.164876 GGATCATCTGATTGTCATTCTCGAT 58.835 40.000 0.00 0.00 34.37 3.59
4416 5849 6.091034 GGATCATCTGATTGTCATTCTCGATG 59.909 42.308 14.62 14.62 34.37 3.84
4417 5850 4.748600 TCATCTGATTGTCATTCTCGATGC 59.251 41.667 15.31 0.00 35.64 3.91
4418 5851 4.397481 TCTGATTGTCATTCTCGATGCT 57.603 40.909 0.00 0.00 35.64 3.79
4419 5852 4.117685 TCTGATTGTCATTCTCGATGCTG 58.882 43.478 0.00 0.00 35.64 4.41
4420 5853 3.200483 TGATTGTCATTCTCGATGCTGG 58.800 45.455 0.00 0.00 35.64 4.85
4421 5854 2.768253 TTGTCATTCTCGATGCTGGT 57.232 45.000 0.00 0.00 35.64 4.00
4422 5855 2.768253 TGTCATTCTCGATGCTGGTT 57.232 45.000 0.00 0.00 35.64 3.67
4423 5856 3.057969 TGTCATTCTCGATGCTGGTTT 57.942 42.857 0.00 0.00 35.64 3.27
4424 5857 2.743664 TGTCATTCTCGATGCTGGTTTG 59.256 45.455 0.00 0.00 35.64 2.93
4425 5858 2.744202 GTCATTCTCGATGCTGGTTTGT 59.256 45.455 0.00 0.00 35.64 2.83
4426 5859 3.002791 TCATTCTCGATGCTGGTTTGTC 58.997 45.455 0.00 0.00 35.64 3.18
4427 5860 2.839486 TTCTCGATGCTGGTTTGTCT 57.161 45.000 0.00 0.00 0.00 3.41
4428 5861 2.084610 TCTCGATGCTGGTTTGTCTG 57.915 50.000 0.00 0.00 0.00 3.51
4429 5862 1.081892 CTCGATGCTGGTTTGTCTGG 58.918 55.000 0.00 0.00 0.00 3.86
4430 5863 0.396435 TCGATGCTGGTTTGTCTGGT 59.604 50.000 0.00 0.00 0.00 4.00
4431 5864 1.202758 TCGATGCTGGTTTGTCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
4432 5865 1.069022 CGATGCTGGTTTGTCTGGTTG 60.069 52.381 0.00 0.00 0.00 3.77
4433 5866 0.675633 ATGCTGGTTTGTCTGGTTGC 59.324 50.000 0.00 0.00 0.00 4.17
4472 5910 2.260822 AGGCCATAGCTCATCGGTATT 58.739 47.619 5.01 0.00 39.73 1.89
4532 5974 1.118965 TTCAGGTCGAGCAGGGTCAA 61.119 55.000 18.15 0.00 0.00 3.18
4562 6004 5.221224 TGTCAGCCATTTGTCTGGTTTTTAG 60.221 40.000 0.00 0.00 38.63 1.85
4575 6017 9.787435 TGTCTGGTTTTTAGATACAGTTTACAT 57.213 29.630 0.00 0.00 0.00 2.29
4605 6248 9.150348 GGATCGTTTACATTTTCAATGGATTTT 57.850 29.630 1.72 0.00 0.00 1.82
4620 6263 7.440856 TCAATGGATTTTGCCAAGTTTAAAGAC 59.559 33.333 0.00 0.00 42.16 3.01
4653 6296 6.824305 AGGTCAAACATAGAACTCCAAATG 57.176 37.500 0.00 0.00 0.00 2.32
4673 6316 0.320374 TGGAACGCAGGGAGTAACTG 59.680 55.000 0.00 0.00 38.95 3.16
4765 6408 4.412199 CCCTAATCTGATACCCTTGTGGAA 59.588 45.833 0.00 0.00 38.00 3.53
4807 6452 4.458989 CCAGCTGCTTGGTTACATTCTAAA 59.541 41.667 8.66 0.00 33.38 1.85
4808 6453 5.126061 CCAGCTGCTTGGTTACATTCTAAAT 59.874 40.000 8.66 0.00 33.38 1.40
4809 6454 6.318648 CCAGCTGCTTGGTTACATTCTAAATA 59.681 38.462 8.66 0.00 33.38 1.40
4810 6455 7.148086 CCAGCTGCTTGGTTACATTCTAAATAA 60.148 37.037 8.66 0.00 33.38 1.40
4857 6502 6.148480 GTGCCTGATCATTCTAATGTGGTATC 59.852 42.308 0.00 0.25 37.65 2.24
4880 6525 6.591001 TCACTATGCTGGAAATTATGCTACA 58.409 36.000 0.00 0.00 0.00 2.74
4881 6526 7.226441 TCACTATGCTGGAAATTATGCTACAT 58.774 34.615 0.00 0.00 0.00 2.29
4882 6527 7.720957 TCACTATGCTGGAAATTATGCTACATT 59.279 33.333 0.00 0.00 0.00 2.71
4883 6528 7.806487 CACTATGCTGGAAATTATGCTACATTG 59.194 37.037 0.00 0.00 0.00 2.82
4884 6529 4.935702 TGCTGGAAATTATGCTACATTGC 58.064 39.130 0.00 0.00 0.00 3.56
4922 6570 0.252103 TTGCTACGAGGGAAGGGAGT 60.252 55.000 0.00 0.00 0.00 3.85
4927 6575 0.702902 ACGAGGGAAGGGAGTAGACA 59.297 55.000 0.00 0.00 0.00 3.41
4931 6579 1.205055 GGGAAGGGAGTAGACAAGGG 58.795 60.000 0.00 0.00 0.00 3.95
4932 6580 0.542333 GGAAGGGAGTAGACAAGGGC 59.458 60.000 0.00 0.00 0.00 5.19
4933 6581 0.175989 GAAGGGAGTAGACAAGGGCG 59.824 60.000 0.00 0.00 0.00 6.13
4934 6582 1.900545 AAGGGAGTAGACAAGGGCGC 61.901 60.000 0.00 0.00 0.00 6.53
4947 6595 2.453638 GGGCGCGCAGAAGAACTAC 61.454 63.158 34.42 10.96 0.00 2.73
4970 6618 1.077212 CCTCACTGGCCTTGGATGG 60.077 63.158 3.32 1.69 0.00 3.51
4980 6628 0.819582 CCTTGGATGGTGATGTTGCC 59.180 55.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.987890 GCTCTACAAATTTCCTGCAAAATAAAA 58.012 29.630 0.00 0.00 0.00 1.52
19 20 8.147058 TGCTCTACAAATTTCCTGCAAAATAAA 58.853 29.630 0.00 0.00 0.00 1.40
48 49 6.401796 GGCTATTTAGGTTTGTTGTGTAGTCG 60.402 42.308 0.00 0.00 0.00 4.18
63 64 1.689273 AGCTCCTCGTGGCTATTTAGG 59.311 52.381 0.00 0.00 37.00 2.69
66 67 1.279271 ACAAGCTCCTCGTGGCTATTT 59.721 47.619 0.00 0.00 37.87 1.40
83 84 0.111061 AGCAGGGCAATGTGAGACAA 59.889 50.000 0.00 0.00 0.00 3.18
130 131 3.430042 AGCATGGAGTCACACAATTCT 57.570 42.857 0.00 0.00 0.00 2.40
210 212 3.603158 TCGCTCTAAAAGGCACATGTA 57.397 42.857 0.00 0.00 0.00 2.29
213 215 2.744202 CACTTCGCTCTAAAAGGCACAT 59.256 45.455 0.00 0.00 0.00 3.21
225 227 3.371285 GGATTGTTACCTTCACTTCGCTC 59.629 47.826 0.00 0.00 0.00 5.03
232 234 5.812286 TCCTTTAGGGATTGTTACCTTCAC 58.188 41.667 0.00 0.00 39.58 3.18
274 276 2.167693 TGGCTACATAGGAAAGACGGTG 59.832 50.000 0.00 0.00 0.00 4.94
341 343 2.978978 TGAGGAAGAAGGGAATGTGTCA 59.021 45.455 0.00 0.00 0.00 3.58
366 369 4.188462 TGGAAATAGTGGCAATGTAGACG 58.812 43.478 0.00 0.00 0.00 4.18
367 370 7.573843 GCATATGGAAATAGTGGCAATGTAGAC 60.574 40.741 4.56 0.00 0.00 2.59
427 430 0.456628 GGGAAGTAGGACACGAGAGC 59.543 60.000 0.00 0.00 0.00 4.09
438 441 3.703052 TCTTTTACTAGCGGGGGAAGTAG 59.297 47.826 0.00 0.00 0.00 2.57
497 500 5.301835 AGAATAGGATGCTTGTATGTGCT 57.698 39.130 0.00 0.00 0.00 4.40
498 501 6.346919 CGTAAGAATAGGATGCTTGTATGTGC 60.347 42.308 0.00 0.00 43.02 4.57
531 534 0.818445 TCATCGGCTCGGACTCCTAC 60.818 60.000 0.00 0.00 0.00 3.18
534 537 2.343163 CTGTCATCGGCTCGGACTCC 62.343 65.000 0.00 0.00 32.84 3.85
540 543 3.186909 TCATTTTACTGTCATCGGCTCG 58.813 45.455 0.00 0.00 0.00 5.03
606 629 4.328983 GTGTGTGTATGTTCGTAAGGATGG 59.671 45.833 0.00 0.00 38.47 3.51
737 760 2.762459 TACGAAGGGGGCTGCGAT 60.762 61.111 0.00 0.00 0.00 4.58
747 770 1.067776 GTGACACAGAGGGTACGAAGG 60.068 57.143 0.00 0.00 0.00 3.46
749 772 0.963962 GGTGACACAGAGGGTACGAA 59.036 55.000 8.08 0.00 0.00 3.85
750 773 0.896940 GGGTGACACAGAGGGTACGA 60.897 60.000 8.08 0.00 0.00 3.43
751 774 0.898789 AGGGTGACACAGAGGGTACG 60.899 60.000 8.08 0.00 0.00 3.67
759 782 2.224621 ACTTCCATGAAGGGTGACACAG 60.225 50.000 8.08 0.00 43.25 3.66
803 826 9.135843 CTTTCTTTTTCTTTTAACGGTTGACTT 57.864 29.630 3.07 0.00 0.00 3.01
811 834 9.967245 CCCTTTTTCTTTCTTTTTCTTTTAACG 57.033 29.630 0.00 0.00 0.00 3.18
813 836 9.456147 CCCCCTTTTTCTTTCTTTTTCTTTTAA 57.544 29.630 0.00 0.00 0.00 1.52
854 884 4.148696 CGTCACACCATTGCTTTGATTTTC 59.851 41.667 0.00 0.00 0.00 2.29
859 889 1.872952 CTCGTCACACCATTGCTTTGA 59.127 47.619 0.00 0.00 0.00 2.69
873 903 1.919240 TAAAGTGAGGGAGCTCGTCA 58.081 50.000 12.22 12.22 37.86 4.35
874 904 2.608268 GTTAAAGTGAGGGAGCTCGTC 58.392 52.381 7.83 7.69 0.00 4.20
875 905 1.275573 GGTTAAAGTGAGGGAGCTCGT 59.724 52.381 7.83 0.00 0.00 4.18
876 906 1.550976 AGGTTAAAGTGAGGGAGCTCG 59.449 52.381 7.83 0.00 0.00 5.03
1081 1123 2.804090 GTCGGCGTCGTGGAAGTC 60.804 66.667 10.18 0.00 37.69 3.01
1084 1126 4.688419 GTCGTCGGCGTCGTGGAA 62.688 66.667 24.03 4.06 39.49 3.53
1355 1403 3.812019 CGTCGAGGCGGCTGTAGT 61.812 66.667 19.63 0.00 0.00 2.73
1548 1596 2.745100 CCCTCGACCTCGACGACA 60.745 66.667 0.00 0.00 44.22 4.35
1671 1726 3.157932 AGCGAATTAGAGACAGTCAGC 57.842 47.619 2.66 0.00 0.00 4.26
1675 1730 4.201930 CGAGGTTAGCGAATTAGAGACAGT 60.202 45.833 0.00 0.00 0.00 3.55
1718 1773 0.826062 GGGCTTCCAATCCAATGTGG 59.174 55.000 0.00 0.00 39.43 4.17
1745 1800 4.871993 TTAGACGTCAGATCCTAACGAC 57.128 45.455 19.50 11.23 39.59 4.34
1818 1880 7.857734 TGTAGAGTTGTTTTTCTCACATGAA 57.142 32.000 0.00 0.00 33.63 2.57
1893 1960 9.853555 CCATTACAAAAGTGCTAATCAACATAA 57.146 29.630 0.00 0.00 0.00 1.90
1944 2015 9.330063 CAGAGCATATTTCTTCCAACAGTATTA 57.670 33.333 0.00 0.00 0.00 0.98
2046 2117 8.945057 CCCTAACAAACAATTATGGAAAAATGG 58.055 33.333 0.00 0.00 0.00 3.16
2050 2121 7.071321 ACACCCCTAACAAACAATTATGGAAAA 59.929 33.333 0.00 0.00 0.00 2.29
2203 2686 7.907389 TCAGTTAGGGGATCATCATACATAAC 58.093 38.462 0.00 3.83 0.00 1.89
2205 2688 7.180946 CCTTCAGTTAGGGGATCATCATACATA 59.819 40.741 0.00 0.00 0.00 2.29
2208 2691 5.799213 CCTTCAGTTAGGGGATCATCATAC 58.201 45.833 0.00 0.00 0.00 2.39
2329 3013 7.767198 TGAAAGGGATAACCAGTTAGAAATACG 59.233 37.037 0.00 0.00 43.89 3.06
2332 3016 7.699878 ACTGAAAGGGATAACCAGTTAGAAAT 58.300 34.615 0.00 0.00 43.89 2.17
2558 3247 3.973135 CGCGTCATTATGTAGTGTAGGAC 59.027 47.826 0.00 0.00 0.00 3.85
2735 3430 8.144478 TGATATAGAGGTTTCACTGCATAACTC 58.856 37.037 0.00 0.00 0.00 3.01
2846 3544 5.125097 CCTGAACATGAGAAATTGAGAAGGG 59.875 44.000 0.00 0.00 0.00 3.95
3080 4502 1.946768 CAGAACAACCACCACAACGAT 59.053 47.619 0.00 0.00 0.00 3.73
3156 4578 4.616181 AGAACGAAACAAAACCAGACAG 57.384 40.909 0.00 0.00 0.00 3.51
3208 4630 5.067273 TCACCCAATAGCGTTTAATATGGG 58.933 41.667 6.39 6.39 39.78 4.00
3211 4633 7.875327 AAGTTCACCCAATAGCGTTTAATAT 57.125 32.000 0.00 0.00 0.00 1.28
3301 4723 2.824689 TCTATTGCCTGAAATGCCCA 57.175 45.000 0.00 0.00 0.00 5.36
3331 4753 3.317603 AGGCAAAATGAACCCAAATCG 57.682 42.857 0.00 0.00 0.00 3.34
3334 4756 5.513962 GGGAAATAGGCAAAATGAACCCAAA 60.514 40.000 0.00 0.00 34.43 3.28
3486 4908 3.985279 CACCACAATCTTGTTTGATGCAG 59.015 43.478 0.00 0.00 39.91 4.41
3516 4939 6.018589 AGAAATTAGAAGCAAGAAACAGGC 57.981 37.500 0.00 0.00 0.00 4.85
3522 4945 6.815089 TGGCAAAAGAAATTAGAAGCAAGAA 58.185 32.000 0.00 0.00 0.00 2.52
3524 4947 7.662604 AATGGCAAAAGAAATTAGAAGCAAG 57.337 32.000 0.00 0.00 0.00 4.01
3539 4966 6.162079 TGCGATCTTTTGATTAATGGCAAAA 58.838 32.000 12.12 12.12 40.50 2.44
3546 4973 8.072567 GCTTCAGTATGCGATCTTTTGATTAAT 58.927 33.333 0.00 0.00 35.89 1.40
3643 5070 8.698973 TCTGGTATCTGGAATAACAACAAAAA 57.301 30.769 0.00 0.00 0.00 1.94
3669 5096 5.359194 TTTGTTGGGCAAATTTTGGTCTA 57.641 34.783 10.96 0.00 41.68 2.59
3695 5122 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
3696 5123 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
3697 5124 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
3698 5125 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
3714 5141 9.965824 GTCCATTTGAATCTCTAAAAAGACAAA 57.034 29.630 0.00 0.00 30.50 2.83
3715 5142 9.354673 AGTCCATTTGAATCTCTAAAAAGACAA 57.645 29.630 0.00 0.00 30.54 3.18
3716 5143 8.924511 AGTCCATTTGAATCTCTAAAAAGACA 57.075 30.769 0.00 0.00 30.54 3.41
3718 5145 9.449719 GGTAGTCCATTTGAATCTCTAAAAAGA 57.550 33.333 0.00 0.00 0.00 2.52
3719 5146 9.231297 TGGTAGTCCATTTGAATCTCTAAAAAG 57.769 33.333 0.00 0.00 39.03 2.27
3736 5163 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
3775 5202 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3776 5203 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3777 5204 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3778 5205 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3779 5206 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3780 5207 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3781 5208 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3782 5209 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3783 5210 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3784 5211 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3785 5212 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3786 5213 4.207224 CGACTACATACGGAGCAAAATGAG 59.793 45.833 0.00 0.00 0.00 2.90
3787 5214 4.109766 CGACTACATACGGAGCAAAATGA 58.890 43.478 0.00 0.00 0.00 2.57
3788 5215 3.302480 GCGACTACATACGGAGCAAAATG 60.302 47.826 0.00 0.00 0.00 2.32
3789 5216 2.864343 GCGACTACATACGGAGCAAAAT 59.136 45.455 0.00 0.00 0.00 1.82
3790 5217 2.094390 AGCGACTACATACGGAGCAAAA 60.094 45.455 0.00 0.00 0.00 2.44
3791 5218 1.475280 AGCGACTACATACGGAGCAAA 59.525 47.619 0.00 0.00 0.00 3.68
3792 5219 1.100510 AGCGACTACATACGGAGCAA 58.899 50.000 0.00 0.00 0.00 3.91
3793 5220 1.100510 AAGCGACTACATACGGAGCA 58.899 50.000 0.00 0.00 0.00 4.26
3794 5221 1.202268 ACAAGCGACTACATACGGAGC 60.202 52.381 0.00 0.00 0.00 4.70
3795 5222 2.846039 ACAAGCGACTACATACGGAG 57.154 50.000 0.00 0.00 0.00 4.63
3796 5223 2.488937 TCAACAAGCGACTACATACGGA 59.511 45.455 0.00 0.00 0.00 4.69
3797 5224 2.871133 TCAACAAGCGACTACATACGG 58.129 47.619 0.00 0.00 0.00 4.02
3798 5225 4.896562 TTTCAACAAGCGACTACATACG 57.103 40.909 0.00 0.00 0.00 3.06
3799 5226 6.531948 AGAGATTTCAACAAGCGACTACATAC 59.468 38.462 0.00 0.00 0.00 2.39
3800 5227 6.631016 AGAGATTTCAACAAGCGACTACATA 58.369 36.000 0.00 0.00 0.00 2.29
3801 5228 5.482908 AGAGATTTCAACAAGCGACTACAT 58.517 37.500 0.00 0.00 0.00 2.29
3802 5229 4.883083 AGAGATTTCAACAAGCGACTACA 58.117 39.130 0.00 0.00 0.00 2.74
3803 5230 6.323266 TCTAGAGATTTCAACAAGCGACTAC 58.677 40.000 0.00 0.00 0.00 2.73
3804 5231 6.510879 TCTAGAGATTTCAACAAGCGACTA 57.489 37.500 0.00 0.00 0.00 2.59
3805 5232 5.392767 TCTAGAGATTTCAACAAGCGACT 57.607 39.130 0.00 0.00 0.00 4.18
3806 5233 6.366332 TCTTTCTAGAGATTTCAACAAGCGAC 59.634 38.462 0.00 0.00 0.00 5.19
3807 5234 6.455647 TCTTTCTAGAGATTTCAACAAGCGA 58.544 36.000 0.00 0.00 0.00 4.93
3808 5235 6.712241 TCTTTCTAGAGATTTCAACAAGCG 57.288 37.500 0.00 0.00 0.00 4.68
3809 5236 9.736023 TTTTTCTTTCTAGAGATTTCAACAAGC 57.264 29.630 0.00 0.00 0.00 4.01
3825 5252 8.957466 CCTCCGTTCCTAAATATTTTTCTTTCT 58.043 33.333 5.91 0.00 0.00 2.52
3826 5253 8.188799 CCCTCCGTTCCTAAATATTTTTCTTTC 58.811 37.037 5.91 0.00 0.00 2.62
3827 5254 7.891712 TCCCTCCGTTCCTAAATATTTTTCTTT 59.108 33.333 5.91 0.00 0.00 2.52
3828 5255 7.407729 TCCCTCCGTTCCTAAATATTTTTCTT 58.592 34.615 5.91 0.00 0.00 2.52
3829 5256 6.965607 TCCCTCCGTTCCTAAATATTTTTCT 58.034 36.000 5.91 0.00 0.00 2.52
3830 5257 6.827251 ACTCCCTCCGTTCCTAAATATTTTTC 59.173 38.462 5.91 0.00 0.00 2.29
3831 5258 6.728411 ACTCCCTCCGTTCCTAAATATTTTT 58.272 36.000 5.91 0.00 0.00 1.94
3832 5259 6.323210 ACTCCCTCCGTTCCTAAATATTTT 57.677 37.500 5.91 0.00 0.00 1.82
3833 5260 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
3834 5261 8.912614 ATATACTCCCTCCGTTCCTAAATATT 57.087 34.615 0.00 0.00 0.00 1.28
3835 5262 8.912614 AATATACTCCCTCCGTTCCTAAATAT 57.087 34.615 0.00 0.00 0.00 1.28
3837 5264 8.912614 ATAATATACTCCCTCCGTTCCTAAAT 57.087 34.615 0.00 0.00 0.00 1.40
3838 5265 8.591072 CAATAATATACTCCCTCCGTTCCTAAA 58.409 37.037 0.00 0.00 0.00 1.85
3839 5266 7.310237 GCAATAATATACTCCCTCCGTTCCTAA 60.310 40.741 0.00 0.00 0.00 2.69
3840 5267 6.154021 GCAATAATATACTCCCTCCGTTCCTA 59.846 42.308 0.00 0.00 0.00 2.94
3841 5268 5.046520 GCAATAATATACTCCCTCCGTTCCT 60.047 44.000 0.00 0.00 0.00 3.36
3842 5269 5.176592 GCAATAATATACTCCCTCCGTTCC 58.823 45.833 0.00 0.00 0.00 3.62
3843 5270 5.176592 GGCAATAATATACTCCCTCCGTTC 58.823 45.833 0.00 0.00 0.00 3.95
3844 5271 4.019591 GGGCAATAATATACTCCCTCCGTT 60.020 45.833 0.00 0.00 0.00 4.44
3845 5272 3.518303 GGGCAATAATATACTCCCTCCGT 59.482 47.826 0.00 0.00 0.00 4.69
3846 5273 3.118371 GGGGCAATAATATACTCCCTCCG 60.118 52.174 0.00 0.00 34.28 4.63
3847 5274 3.850173 TGGGGCAATAATATACTCCCTCC 59.150 47.826 0.00 0.00 34.28 4.30
3848 5275 4.626529 GCTGGGGCAATAATATACTCCCTC 60.627 50.000 0.00 0.00 38.54 4.30
3849 5276 3.267031 GCTGGGGCAATAATATACTCCCT 59.733 47.826 0.00 0.00 38.54 4.20
3850 5277 3.010138 TGCTGGGGCAATAATATACTCCC 59.990 47.826 0.00 0.00 46.36 4.30
3851 5278 4.301072 TGCTGGGGCAATAATATACTCC 57.699 45.455 0.00 0.00 46.36 3.85
3920 5347 1.255882 CCCTGCAACAGCCATACAAA 58.744 50.000 0.00 0.00 0.00 2.83
3985 5412 2.292257 TGGATAGCAGTCCTGGTGTACT 60.292 50.000 9.16 0.00 41.87 2.73
4049 5476 4.540824 GTCAGATTCTGGAAACTTTGCAC 58.459 43.478 13.59 0.00 31.51 4.57
4056 5483 4.389374 TGAACAGGTCAGATTCTGGAAAC 58.611 43.478 13.59 4.82 35.47 2.78
4124 5551 6.510799 GCGAGGTCTGAAACAATAGATTCATG 60.511 42.308 0.00 0.00 36.19 3.07
4125 5552 5.525378 GCGAGGTCTGAAACAATAGATTCAT 59.475 40.000 0.00 0.00 36.19 2.57
4142 5569 3.386237 AGCACTCCAGGCGAGGTC 61.386 66.667 0.00 0.00 43.57 3.85
4150 5577 0.466189 AACAACCACCAGCACTCCAG 60.466 55.000 0.00 0.00 0.00 3.86
4269 5699 5.585844 CGGATTTAAACTACGGTATTTGGGT 59.414 40.000 0.00 0.00 0.00 4.51
4381 5814 1.554617 TCAGATGATCCGCAACCAGAA 59.445 47.619 0.00 0.00 0.00 3.02
4386 5819 2.938451 TGACAATCAGATGATCCGCAAC 59.062 45.455 0.00 0.00 32.75 4.17
4387 5820 3.264998 TGACAATCAGATGATCCGCAA 57.735 42.857 0.00 0.00 32.75 4.85
4388 5821 2.985957 TGACAATCAGATGATCCGCA 57.014 45.000 0.00 0.00 32.75 5.69
4389 5822 4.063689 AGAATGACAATCAGATGATCCGC 58.936 43.478 0.00 0.00 32.75 5.54
4390 5823 4.385146 CGAGAATGACAATCAGATGATCCG 59.615 45.833 0.00 0.00 32.75 4.18
4391 5824 5.536260 TCGAGAATGACAATCAGATGATCC 58.464 41.667 0.00 0.00 32.75 3.36
4392 5825 6.401260 GCATCGAGAATGACAATCAGATGATC 60.401 42.308 22.45 9.90 37.59 2.92
4393 5826 5.408909 GCATCGAGAATGACAATCAGATGAT 59.591 40.000 22.45 6.93 37.59 2.45
4394 5827 4.748600 GCATCGAGAATGACAATCAGATGA 59.251 41.667 22.45 5.34 37.59 2.92
4395 5828 4.750598 AGCATCGAGAATGACAATCAGATG 59.249 41.667 17.57 17.57 37.59 2.90
4396 5829 4.750598 CAGCATCGAGAATGACAATCAGAT 59.249 41.667 0.00 0.00 37.59 2.90
4397 5830 4.117685 CAGCATCGAGAATGACAATCAGA 58.882 43.478 0.00 0.00 37.59 3.27
4398 5831 3.247886 CCAGCATCGAGAATGACAATCAG 59.752 47.826 0.00 0.00 37.59 2.90
4399 5832 3.200483 CCAGCATCGAGAATGACAATCA 58.800 45.455 0.00 0.00 37.59 2.57
4400 5833 3.201290 ACCAGCATCGAGAATGACAATC 58.799 45.455 0.00 0.00 37.59 2.67
4401 5834 3.272574 ACCAGCATCGAGAATGACAAT 57.727 42.857 0.00 0.00 37.59 2.71
4402 5835 2.768253 ACCAGCATCGAGAATGACAA 57.232 45.000 0.00 0.00 37.59 3.18
4403 5836 2.743664 CAAACCAGCATCGAGAATGACA 59.256 45.455 0.00 0.00 37.59 3.58
4404 5837 2.744202 ACAAACCAGCATCGAGAATGAC 59.256 45.455 0.00 0.00 37.59 3.06
4405 5838 3.002791 GACAAACCAGCATCGAGAATGA 58.997 45.455 0.00 0.00 37.59 2.57
4406 5839 3.005554 AGACAAACCAGCATCGAGAATG 58.994 45.455 0.00 0.00 38.50 2.67
4407 5840 3.005554 CAGACAAACCAGCATCGAGAAT 58.994 45.455 0.00 0.00 0.00 2.40
4408 5841 2.416747 CAGACAAACCAGCATCGAGAA 58.583 47.619 0.00 0.00 0.00 2.87
4409 5842 1.338105 CCAGACAAACCAGCATCGAGA 60.338 52.381 0.00 0.00 0.00 4.04
4410 5843 1.081892 CCAGACAAACCAGCATCGAG 58.918 55.000 0.00 0.00 0.00 4.04
4411 5844 0.396435 ACCAGACAAACCAGCATCGA 59.604 50.000 0.00 0.00 0.00 3.59
4412 5845 1.069022 CAACCAGACAAACCAGCATCG 60.069 52.381 0.00 0.00 0.00 3.84
4413 5846 1.336240 GCAACCAGACAAACCAGCATC 60.336 52.381 0.00 0.00 0.00 3.91
4414 5847 0.675633 GCAACCAGACAAACCAGCAT 59.324 50.000 0.00 0.00 0.00 3.79
4415 5848 1.723608 CGCAACCAGACAAACCAGCA 61.724 55.000 0.00 0.00 0.00 4.41
4416 5849 1.008538 CGCAACCAGACAAACCAGC 60.009 57.895 0.00 0.00 0.00 4.85
4417 5850 0.817634 TCCGCAACCAGACAAACCAG 60.818 55.000 0.00 0.00 0.00 4.00
4418 5851 0.179004 ATCCGCAACCAGACAAACCA 60.179 50.000 0.00 0.00 0.00 3.67
4419 5852 0.521735 GATCCGCAACCAGACAAACC 59.478 55.000 0.00 0.00 0.00 3.27
4420 5853 1.234821 TGATCCGCAACCAGACAAAC 58.765 50.000 0.00 0.00 0.00 2.93
4421 5854 2.083774 GATGATCCGCAACCAGACAAA 58.916 47.619 0.00 0.00 0.00 2.83
4422 5855 1.278985 AGATGATCCGCAACCAGACAA 59.721 47.619 0.00 0.00 0.00 3.18
4423 5856 0.904649 AGATGATCCGCAACCAGACA 59.095 50.000 0.00 0.00 0.00 3.41
4424 5857 1.134699 TCAGATGATCCGCAACCAGAC 60.135 52.381 0.00 0.00 0.00 3.51
4425 5858 1.134699 GTCAGATGATCCGCAACCAGA 60.135 52.381 0.00 0.00 0.00 3.86
4426 5859 1.293924 GTCAGATGATCCGCAACCAG 58.706 55.000 0.00 0.00 0.00 4.00
4427 5860 0.612744 TGTCAGATGATCCGCAACCA 59.387 50.000 0.00 0.00 0.00 3.67
4428 5861 1.869767 GATGTCAGATGATCCGCAACC 59.130 52.381 0.00 0.00 0.00 3.77
4429 5862 1.524355 CGATGTCAGATGATCCGCAAC 59.476 52.381 0.00 0.00 0.00 4.17
4430 5863 1.408702 TCGATGTCAGATGATCCGCAA 59.591 47.619 0.00 0.00 0.00 4.85
4431 5864 1.032014 TCGATGTCAGATGATCCGCA 58.968 50.000 0.00 0.00 0.00 5.69
4432 5865 2.360553 ATCGATGTCAGATGATCCGC 57.639 50.000 0.00 0.00 0.00 5.54
4433 5866 3.733380 GCCTATCGATGTCAGATGATCCG 60.733 52.174 8.54 0.00 0.00 4.18
4472 5910 0.904649 CACTGGCCCACTGACATCTA 59.095 55.000 0.00 0.00 0.00 1.98
4532 5974 2.107204 AGACAAATGGCTGACAGGAAGT 59.893 45.455 4.26 0.00 27.68 3.01
4562 6004 7.772332 AACGATCCAGAATGTAAACTGTATC 57.228 36.000 0.00 0.00 32.93 2.24
4575 6017 7.175816 TCCATTGAAAATGTAAACGATCCAGAA 59.824 33.333 0.00 0.00 0.00 3.02
4605 6248 4.396790 AGTCAAACGTCTTTAAACTTGGCA 59.603 37.500 0.00 0.00 0.00 4.92
4653 6296 0.320697 AGTTACTCCCTGCGTTCCAC 59.679 55.000 0.00 0.00 0.00 4.02
4663 6306 0.902531 TAGCACTGGCAGTTACTCCC 59.097 55.000 19.43 2.43 44.61 4.30
4673 6316 5.865552 CCAATATGCATATTTTAGCACTGGC 59.134 40.000 25.93 0.00 44.49 4.85
4765 6408 0.598065 GATGCCAAGCCGTTCTTTGT 59.402 50.000 0.00 0.00 31.27 2.83
4774 6417 3.834799 GCAGCTGGATGCCAAGCC 61.835 66.667 17.12 0.00 44.23 4.35
4807 6452 6.406692 AGTACTGCCGTCATGTAGAATTAT 57.593 37.500 0.00 0.00 0.00 1.28
4808 6453 5.847111 AGTACTGCCGTCATGTAGAATTA 57.153 39.130 0.00 0.00 0.00 1.40
4809 6454 4.737855 AGTACTGCCGTCATGTAGAATT 57.262 40.909 0.00 0.00 0.00 2.17
4810 6455 4.888239 ACTAGTACTGCCGTCATGTAGAAT 59.112 41.667 5.39 0.00 0.00 2.40
4857 6502 6.866010 TGTAGCATAATTTCCAGCATAGTG 57.134 37.500 0.00 0.00 0.00 2.74
4880 6525 0.835941 AGCCTAGCAGTAGCAGCAAT 59.164 50.000 0.00 0.00 45.49 3.56
4881 6526 1.137086 GTAGCCTAGCAGTAGCAGCAA 59.863 52.381 0.00 0.00 45.49 3.91
4882 6527 0.747255 GTAGCCTAGCAGTAGCAGCA 59.253 55.000 0.00 0.00 45.49 4.41
4883 6528 0.747255 TGTAGCCTAGCAGTAGCAGC 59.253 55.000 0.00 0.00 45.49 5.25
4884 6529 3.388308 CAATGTAGCCTAGCAGTAGCAG 58.612 50.000 0.00 0.00 45.49 4.24
4922 6570 2.835701 CTTCTGCGCGCCCTTGTCTA 62.836 60.000 30.77 5.88 0.00 2.59
4927 6575 2.167398 TAGTTCTTCTGCGCGCCCTT 62.167 55.000 30.77 7.85 0.00 3.95
4931 6579 0.093705 CAAGTAGTTCTTCTGCGCGC 59.906 55.000 27.26 27.26 33.63 6.86
4932 6580 0.716108 CCAAGTAGTTCTTCTGCGCG 59.284 55.000 0.00 0.00 33.63 6.86
4933 6581 0.444260 GCCAAGTAGTTCTTCTGCGC 59.556 55.000 0.00 0.00 33.63 6.09
4934 6582 1.079503 GGCCAAGTAGTTCTTCTGCG 58.920 55.000 0.00 0.00 34.01 5.18


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

AutoCloner maintained by Alex Coulton.