Multiple sequence alignment - TraesCS2D01G080900

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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 TraesCS2D01G080900 chr2D 100.000 4261 0 0 1 4261 34980830 34985090 0.000000e+00 7869.0
1 TraesCS2D01G080900 chr2D 93.906 1165 49 10 2141 3301 34894206 34895352 0.000000e+00 1738.0
2 TraesCS2D01G080900 chr2D 84.552 1327 113 42 875 2147 34892732 34894020 0.000000e+00 1230.0
3 TraesCS2D01G080900 chr2D 89.474 285 21 7 377 657 34892322 34892601 6.780000e-93 351.0
4 TraesCS2D01G080900 chr2B 95.642 2547 77 13 943 3459 57652791 57655333 0.000000e+00 4058.0
5 TraesCS2D01G080900 chr2B 92.857 1162 67 8 2141 3301 57421310 57422456 0.000000e+00 1672.0
6 TraesCS2D01G080900 chr2B 89.319 852 54 13 875 1712 57420018 57420846 0.000000e+00 1035.0
7 TraesCS2D01G080900 chr2B 90.743 713 35 11 58 770 57651816 57652497 0.000000e+00 922.0
8 TraesCS2D01G080900 chr2B 89.643 280 22 5 377 652 57419607 57419883 2.440000e-92 350.0
9 TraesCS2D01G080900 chr2B 97.727 132 3 0 830 961 57652478 57652609 1.190000e-55 228.0
10 TraesCS2D01G080900 chr2B 93.617 94 6 0 58 151 57651682 57651775 1.600000e-29 141.0
11 TraesCS2D01G080900 chr2B 97.015 67 2 0 191 257 57651764 57651830 3.480000e-21 113.0
12 TraesCS2D01G080900 chr2B 95.312 64 1 1 193 254 57651630 57651693 2.710000e-17 100.0
13 TraesCS2D01G080900 chr2B 97.826 46 1 0 3951 3996 57655632 57655677 3.530000e-11 80.5
14 TraesCS2D01G080900 chr2B 92.308 52 4 0 695 746 49315650 49315701 1.640000e-09 75.0
15 TraesCS2D01G080900 chr2A 94.462 1246 56 6 2137 3372 38305980 38307222 0.000000e+00 1906.0
16 TraesCS2D01G080900 chr2A 93.385 1164 50 9 2141 3301 38219158 38220297 0.000000e+00 1698.0
17 TraesCS2D01G080900 chr2A 89.486 856 42 17 1005 1824 38218100 38218943 0.000000e+00 1038.0
18 TraesCS2D01G080900 chr2A 91.455 749 33 10 862 1590 38304767 38305504 0.000000e+00 1000.0
19 TraesCS2D01G080900 chr2A 88.384 594 47 10 62 654 487646364 487646936 0.000000e+00 695.0
20 TraesCS2D01G080900 chr2A 86.136 440 44 9 256 691 38304284 38304710 3.880000e-125 459.0
21 TraesCS2D01G080900 chr2A 86.817 311 32 7 345 652 38217494 38217798 5.280000e-89 339.0
22 TraesCS2D01G080900 chr2A 90.795 239 20 1 1 239 38304064 38304300 6.880000e-83 318.0
23 TraesCS2D01G080900 chr2A 84.281 299 21 11 3949 4236 38308127 38308410 7.020000e-68 268.0
24 TraesCS2D01G080900 chr2A 90.411 73 3 4 744 816 38304692 38304760 4.540000e-15 93.5
25 TraesCS2D01G080900 chr2A 95.833 48 2 0 191 238 487646304 487646351 1.270000e-10 78.7
26 TraesCS2D01G080900 chr5D 90.130 922 90 1 2140 3061 483227800 483226880 0.000000e+00 1197.0
27 TraesCS2D01G080900 chr5D 89.956 916 92 0 2149 3064 483371408 483370493 0.000000e+00 1182.0
28 TraesCS2D01G080900 chr5D 88.383 637 61 11 1050 1683 483372433 483371807 0.000000e+00 754.0
29 TraesCS2D01G080900 chr5D 93.083 506 32 3 1071 1575 483228778 483228275 0.000000e+00 737.0
30 TraesCS2D01G080900 chr5A 89.924 923 93 0 2142 3064 604311664 604310742 0.000000e+00 1190.0
31 TraesCS2D01G080900 chr5A 89.044 931 101 1 2132 3061 603794351 603793421 0.000000e+00 1153.0
32 TraesCS2D01G080900 chr5A 88.394 629 58 12 1051 1675 604312728 604312111 0.000000e+00 743.0
33 TraesCS2D01G080900 chr5A 95.918 49 2 0 701 749 535571647 535571695 3.530000e-11 80.5
34 TraesCS2D01G080900 chr5A 89.655 58 5 1 701 757 68817794 68817737 5.910000e-09 73.1
35 TraesCS2D01G080900 chr5B 91.941 546 38 6 1050 1593 593945346 593944805 0.000000e+00 760.0
36 TraesCS2D01G080900 chr6D 89.412 595 38 11 62 654 67714995 67714424 0.000000e+00 726.0
37 TraesCS2D01G080900 chr6D 88.384 594 37 16 62 654 452249777 452250339 0.000000e+00 686.0
38 TraesCS2D01G080900 chr3A 88.644 590 43 12 79 667 42410357 42409791 0.000000e+00 697.0
39 TraesCS2D01G080900 chr3A 92.453 53 3 1 701 753 277498643 277498694 1.640000e-09 75.0
40 TraesCS2D01G080900 chr3A 92.308 52 4 0 701 752 316571907 316571958 1.640000e-09 75.0
41 TraesCS2D01G080900 chr1D 97.826 46 1 0 701 746 225403956 225404001 3.530000e-11 80.5
42 TraesCS2D01G080900 chr7A 85.075 67 8 2 701 765 42966036 42965970 2.750000e-07 67.6
43 TraesCS2D01G080900 chr4D 97.436 39 1 0 701 739 164880555 164880593 2.750000e-07 67.6


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 TraesCS2D01G080900 chr2D 34980830 34985090 4260 False 7869.000000 7869 100.000000 1 4261 1 chr2D.!!$F1 4260
1 TraesCS2D01G080900 chr2D 34892322 34895352 3030 False 1106.333333 1738 89.310667 377 3301 3 chr2D.!!$F2 2924
2 TraesCS2D01G080900 chr2B 57419607 57422456 2849 False 1019.000000 1672 90.606333 377 3301 3 chr2B.!!$F2 2924
3 TraesCS2D01G080900 chr2B 57651630 57655677 4047 False 806.071429 4058 95.411714 58 3996 7 chr2B.!!$F3 3938
4 TraesCS2D01G080900 chr2A 38217494 38220297 2803 False 1025.000000 1698 89.896000 345 3301 3 chr2A.!!$F1 2956
5 TraesCS2D01G080900 chr2A 38304064 38308410 4346 False 674.083333 1906 89.590000 1 4236 6 chr2A.!!$F2 4235
6 TraesCS2D01G080900 chr2A 487646304 487646936 632 False 386.850000 695 92.108500 62 654 2 chr2A.!!$F3 592
7 TraesCS2D01G080900 chr5D 483370493 483372433 1940 True 968.000000 1182 89.169500 1050 3064 2 chr5D.!!$R2 2014
8 TraesCS2D01G080900 chr5D 483226880 483228778 1898 True 967.000000 1197 91.606500 1071 3061 2 chr5D.!!$R1 1990
9 TraesCS2D01G080900 chr5A 603793421 603794351 930 True 1153.000000 1153 89.044000 2132 3061 1 chr5A.!!$R2 929
10 TraesCS2D01G080900 chr5A 604310742 604312728 1986 True 966.500000 1190 89.159000 1051 3064 2 chr5A.!!$R3 2013
11 TraesCS2D01G080900 chr5B 593944805 593945346 541 True 760.000000 760 91.941000 1050 1593 1 chr5B.!!$R1 543
12 TraesCS2D01G080900 chr6D 67714424 67714995 571 True 726.000000 726 89.412000 62 654 1 chr6D.!!$R1 592
13 TraesCS2D01G080900 chr6D 452249777 452250339 562 False 686.000000 686 88.384000 62 654 1 chr6D.!!$F1 592
14 TraesCS2D01G080900 chr3A 42409791 42410357 566 True 697.000000 697 88.644000 79 667 1 chr3A.!!$R1 588

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
535 670 0.255890 GCTCTGGCCCTGAATTACCA 59.744 55.000 0.00 0.0 0.00 3.25 F
846 1048 2.235898 TGGGGATTTAGTTTTGCATGCC 59.764 45.455 16.68 0.0 0.00 4.40 F
1780 2255 2.229675 TGCTATCCACTTGATGCGAG 57.770 50.000 0.00 0.0 34.76 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2231 3.562973 CGCATCAAGTGGATAGCAAAGAT 59.437 43.478 0.00 0.00 33.95 2.40 R
2588 3738 1.001974 CCGACATTGTCACCAGGAAGA 59.998 52.381 16.61 0.00 32.09 2.87 R
3496 4742 0.038599 ACAGGGATTGCAGTGCATCA 59.961 50.000 20.50 5.07 38.76 3.07 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
19 20 3.392431 CGAGGCTGTCGCATGAAG 58.608 61.111 0.00 0.00 43.03 3.02
36 37 4.901197 TGAAGTGCCTGTATTGGTTCTA 57.099 40.909 0.00 0.00 0.00 2.10
77 78 2.079158 ACTGTCGCATGATGAACTTGG 58.921 47.619 0.00 0.00 0.00 3.61
136 268 2.368105 CCGCGCGCTGTGATAGATC 61.368 63.158 30.48 0.00 0.00 2.75
137 269 1.371022 CGCGCGCTGTGATAGATCT 60.371 57.895 30.48 0.00 0.00 2.75
161 293 2.858344 CGATCTGCTCGGTTTCGTATTT 59.142 45.455 0.00 0.00 43.82 1.40
162 294 4.039703 CGATCTGCTCGGTTTCGTATTTA 58.960 43.478 0.00 0.00 43.82 1.40
295 427 2.408271 TGCATGTCTCTTGGGCTAAG 57.592 50.000 3.92 3.92 37.76 2.18
436 570 5.980116 CCATCGTCTAATGGTAAAGACTGAG 59.020 44.000 0.00 0.00 41.18 3.35
471 605 2.093658 GGCCTTCTCATGTAGGTTCGAA 60.094 50.000 0.00 0.00 33.82 3.71
522 657 2.097036 TGCATCTCCAATTTGCTCTGG 58.903 47.619 1.13 0.00 37.28 3.86
535 670 0.255890 GCTCTGGCCCTGAATTACCA 59.744 55.000 0.00 0.00 0.00 3.25
616 751 5.568620 ACTTGACAAGGTATTCTGGTCTT 57.431 39.130 19.16 0.00 44.85 3.01
625 760 7.881751 ACAAGGTATTCTGGTCTTTAGGTTTAC 59.118 37.037 0.00 0.00 0.00 2.01
672 809 9.614792 GTTGGATGTAGATCTAATTTTACCTGT 57.385 33.333 3.40 0.00 32.27 4.00
691 828 7.745620 ACCTGTTAGTCAGATTTAGTTTTGG 57.254 36.000 0.00 0.00 46.27 3.28
692 829 7.287810 ACCTGTTAGTCAGATTTAGTTTTGGT 58.712 34.615 0.00 0.00 46.27 3.67
693 830 7.778382 ACCTGTTAGTCAGATTTAGTTTTGGTT 59.222 33.333 0.00 0.00 46.27 3.67
694 831 8.290325 CCTGTTAGTCAGATTTAGTTTTGGTTC 58.710 37.037 0.00 0.00 46.27 3.62
695 832 8.974060 TGTTAGTCAGATTTAGTTTTGGTTCT 57.026 30.769 0.00 0.00 0.00 3.01
696 833 8.836413 TGTTAGTCAGATTTAGTTTTGGTTCTG 58.164 33.333 0.00 0.00 33.55 3.02
697 834 8.837389 GTTAGTCAGATTTAGTTTTGGTTCTGT 58.163 33.333 0.00 0.00 33.88 3.41
698 835 7.497925 AGTCAGATTTAGTTTTGGTTCTGTC 57.502 36.000 0.00 0.00 33.88 3.51
699 836 7.283329 AGTCAGATTTAGTTTTGGTTCTGTCT 58.717 34.615 0.00 0.00 33.88 3.41
700 837 7.442666 AGTCAGATTTAGTTTTGGTTCTGTCTC 59.557 37.037 0.00 0.00 33.88 3.36
701 838 7.226720 GTCAGATTTAGTTTTGGTTCTGTCTCA 59.773 37.037 0.00 0.00 33.88 3.27
702 839 7.773224 TCAGATTTAGTTTTGGTTCTGTCTCAA 59.227 33.333 0.00 0.00 33.88 3.02
703 840 7.857885 CAGATTTAGTTTTGGTTCTGTCTCAAC 59.142 37.037 0.00 0.00 0.00 3.18
704 841 7.775561 AGATTTAGTTTTGGTTCTGTCTCAACT 59.224 33.333 0.00 0.00 0.00 3.16
705 842 7.696992 TTTAGTTTTGGTTCTGTCTCAACTT 57.303 32.000 0.00 0.00 0.00 2.66
706 843 5.567138 AGTTTTGGTTCTGTCTCAACTTG 57.433 39.130 0.00 0.00 0.00 3.16
707 844 5.010282 AGTTTTGGTTCTGTCTCAACTTGT 58.990 37.500 0.00 0.00 0.00 3.16
708 845 6.177610 AGTTTTGGTTCTGTCTCAACTTGTA 58.822 36.000 0.00 0.00 0.00 2.41
709 846 6.828785 AGTTTTGGTTCTGTCTCAACTTGTAT 59.171 34.615 0.00 0.00 0.00 2.29
710 847 6.618287 TTTGGTTCTGTCTCAACTTGTATG 57.382 37.500 0.00 0.00 0.00 2.39
711 848 4.641396 TGGTTCTGTCTCAACTTGTATGG 58.359 43.478 0.00 0.00 0.00 2.74
712 849 4.003648 GGTTCTGTCTCAACTTGTATGGG 58.996 47.826 0.00 0.00 0.00 4.00
713 850 4.262894 GGTTCTGTCTCAACTTGTATGGGA 60.263 45.833 0.00 0.00 0.00 4.37
714 851 4.537135 TCTGTCTCAACTTGTATGGGAC 57.463 45.455 0.00 0.00 46.34 4.46
715 852 4.160329 TCTGTCTCAACTTGTATGGGACT 58.840 43.478 7.92 0.00 46.31 3.85
716 853 5.330233 TCTGTCTCAACTTGTATGGGACTA 58.670 41.667 7.92 0.00 46.31 2.59
717 854 5.778241 TCTGTCTCAACTTGTATGGGACTAA 59.222 40.000 7.92 0.00 46.31 2.24
718 855 6.269077 TCTGTCTCAACTTGTATGGGACTAAA 59.731 38.462 7.92 0.00 46.31 1.85
719 856 6.464222 TGTCTCAACTTGTATGGGACTAAAG 58.536 40.000 7.92 0.00 46.31 1.85
720 857 5.875359 GTCTCAACTTGTATGGGACTAAAGG 59.125 44.000 0.00 0.00 43.49 3.11
721 858 4.585879 TCAACTTGTATGGGACTAAAGGC 58.414 43.478 0.00 0.00 0.00 4.35
722 859 4.288626 TCAACTTGTATGGGACTAAAGGCT 59.711 41.667 0.00 0.00 0.00 4.58
723 860 4.929146 ACTTGTATGGGACTAAAGGCTT 57.071 40.909 0.00 0.00 0.00 4.35
724 861 5.256806 ACTTGTATGGGACTAAAGGCTTT 57.743 39.130 17.76 17.76 0.00 3.51
725 862 5.010282 ACTTGTATGGGACTAAAGGCTTTG 58.990 41.667 22.32 13.97 0.00 2.77
726 863 4.650972 TGTATGGGACTAAAGGCTTTGT 57.349 40.909 22.32 16.86 0.00 2.83
727 864 4.993028 TGTATGGGACTAAAGGCTTTGTT 58.007 39.130 22.32 8.73 0.00 2.83
728 865 4.764823 TGTATGGGACTAAAGGCTTTGTTG 59.235 41.667 22.32 13.85 0.00 3.33
729 866 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
730 867 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
731 868 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
732 869 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
733 870 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
734 871 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
735 872 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
736 873 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
737 874 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
738 875 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
739 876 4.792521 AGGCTTTGTTGTTGTTGTTGTA 57.207 36.364 0.00 0.00 0.00 2.41
740 877 4.743493 AGGCTTTGTTGTTGTTGTTGTAG 58.257 39.130 0.00 0.00 0.00 2.74
741 878 4.219725 AGGCTTTGTTGTTGTTGTTGTAGT 59.780 37.500 0.00 0.00 0.00 2.73
742 879 5.416326 AGGCTTTGTTGTTGTTGTTGTAGTA 59.584 36.000 0.00 0.00 0.00 1.82
797 999 8.525316 TCTGATGAATTTGAATAATTGCAGTGT 58.475 29.630 0.00 0.00 0.00 3.55
816 1018 6.198966 GCAGTGTTATTTCTTTCCAGTGTTTG 59.801 38.462 0.00 0.00 0.00 2.93
839 1041 7.142995 TGGAACAAATTGGGGATTTAGTTTT 57.857 32.000 0.00 0.00 35.79 2.43
840 1042 6.995091 TGGAACAAATTGGGGATTTAGTTTTG 59.005 34.615 0.00 0.00 35.79 2.44
842 1044 5.934781 ACAAATTGGGGATTTAGTTTTGCA 58.065 33.333 0.00 0.00 35.79 4.08
843 1045 6.541907 ACAAATTGGGGATTTAGTTTTGCAT 58.458 32.000 0.00 0.00 35.79 3.96
844 1046 6.430616 ACAAATTGGGGATTTAGTTTTGCATG 59.569 34.615 0.00 0.00 35.79 4.06
845 1047 3.608316 TGGGGATTTAGTTTTGCATGC 57.392 42.857 11.82 11.82 0.00 4.06
846 1048 2.235898 TGGGGATTTAGTTTTGCATGCC 59.764 45.455 16.68 0.00 0.00 4.40
847 1049 2.501316 GGGGATTTAGTTTTGCATGCCT 59.499 45.455 16.68 7.36 0.00 4.75
889 1104 5.649557 TGTGGAATTGTTGTTTCAAGTCTG 58.350 37.500 6.78 0.00 40.65 3.51
997 1454 4.218200 TCACCATCGTTCAATCATTTGCTT 59.782 37.500 0.00 0.00 32.61 3.91
1014 1475 9.944663 TCATTTGCTTAAGTTTAAACTGTAGTG 57.055 29.630 21.22 13.88 39.66 2.74
1067 1528 5.992217 CCTAATTTGGTCTATGCAGGTAGTC 59.008 44.000 0.00 0.00 0.00 2.59
1069 1530 2.848678 TGGTCTATGCAGGTAGTCCT 57.151 50.000 10.63 0.00 46.37 3.85
1296 1769 5.485353 TGAGAGGGGTATCACCATTGATATC 59.515 44.000 0.00 0.00 44.77 1.63
1622 2097 6.359804 TGCTATCAATTTGATAAGGCTCAGT 58.640 36.000 21.62 1.39 38.72 3.41
1718 2193 6.016360 TCCACTTGATGTTAAGGTTGTCAATG 60.016 38.462 0.00 0.00 31.94 2.82
1723 2198 7.340122 TGATGTTAAGGTTGTCAATGTTCAA 57.660 32.000 0.00 0.00 0.00 2.69
1724 2199 7.950512 TGATGTTAAGGTTGTCAATGTTCAAT 58.049 30.769 0.00 0.00 0.00 2.57
1756 2231 4.787551 ACATCCTGTAAACTGGTTTGACA 58.212 39.130 8.73 8.06 36.48 3.58
1769 2244 4.661222 TGGTTTGACATCTTTGCTATCCA 58.339 39.130 0.00 0.00 0.00 3.41
1780 2255 2.229675 TGCTATCCACTTGATGCGAG 57.770 50.000 0.00 0.00 34.76 5.03
2648 3798 1.404717 GCTGTCAAGGATCTCAAGCGA 60.405 52.381 0.00 0.00 0.00 4.93
3138 4294 1.227060 GCGGTATACGGTGGTGGTC 60.227 63.158 11.59 0.00 44.51 4.02
3223 4380 4.327357 CGAACTGCTTATTACTGTGGTCAG 59.673 45.833 0.00 0.00 46.18 3.51
3224 4381 3.600388 ACTGCTTATTACTGTGGTCAGC 58.400 45.455 0.00 0.00 44.77 4.26
3225 4382 3.007940 ACTGCTTATTACTGTGGTCAGCA 59.992 43.478 6.45 6.45 44.77 4.41
3237 4394 3.181479 TGTGGTCAGCATAGTATCGTTCC 60.181 47.826 0.00 0.00 0.00 3.62
3307 4479 1.009829 GTATTTGGAGTCGCTGCCTG 58.990 55.000 0.00 0.00 0.00 4.85
3309 4481 0.957395 ATTTGGAGTCGCTGCCTGTG 60.957 55.000 0.00 0.00 0.00 3.66
3322 4494 1.205179 TGCCTGTGCAAGCATATTTGG 59.795 47.619 0.00 0.00 46.66 3.28
3405 4651 9.908152 AACTTACCTGTGCTGAAAATTTATTAC 57.092 29.630 0.00 0.00 0.00 1.89
3459 4705 5.738783 GCTTTGTTTTTCCAGGTTGCATCTA 60.739 40.000 0.00 0.00 0.00 1.98
3470 4716 6.375455 TCCAGGTTGCATCTAAGAAAATCTTC 59.625 38.462 0.00 0.00 37.89 2.87
3482 4728 3.585732 AGAAAATCTTCCAACCCGGACTA 59.414 43.478 0.73 0.00 46.36 2.59
3484 4730 2.249309 ATCTTCCAACCCGGACTACT 57.751 50.000 0.73 0.00 46.36 2.57
3485 4731 2.019807 TCTTCCAACCCGGACTACTT 57.980 50.000 0.73 0.00 46.36 2.24
3486 4732 1.897802 TCTTCCAACCCGGACTACTTC 59.102 52.381 0.73 0.00 46.36 3.01
3487 4733 1.900486 CTTCCAACCCGGACTACTTCT 59.100 52.381 0.73 0.00 46.36 2.85
3488 4734 2.019807 TCCAACCCGGACTACTTCTT 57.980 50.000 0.73 0.00 39.64 2.52
3489 4735 1.897802 TCCAACCCGGACTACTTCTTC 59.102 52.381 0.73 0.00 39.64 2.87
3490 4736 1.066358 CCAACCCGGACTACTTCTTCC 60.066 57.143 0.73 0.00 36.56 3.46
3491 4737 1.066358 CAACCCGGACTACTTCTTCCC 60.066 57.143 0.73 0.00 0.00 3.97
3492 4738 0.616964 ACCCGGACTACTTCTTCCCC 60.617 60.000 0.73 0.00 0.00 4.81
3493 4739 0.616679 CCCGGACTACTTCTTCCCCA 60.617 60.000 0.73 0.00 0.00 4.96
3494 4740 1.272807 CCGGACTACTTCTTCCCCAA 58.727 55.000 0.00 0.00 0.00 4.12
3495 4741 1.838077 CCGGACTACTTCTTCCCCAAT 59.162 52.381 0.00 0.00 0.00 3.16
3496 4742 2.238898 CCGGACTACTTCTTCCCCAATT 59.761 50.000 0.00 0.00 0.00 2.32
3497 4743 3.270877 CGGACTACTTCTTCCCCAATTG 58.729 50.000 0.00 0.00 0.00 2.32
3498 4744 3.055385 CGGACTACTTCTTCCCCAATTGA 60.055 47.826 7.12 0.00 0.00 2.57
3499 4745 4.384208 CGGACTACTTCTTCCCCAATTGAT 60.384 45.833 7.12 0.00 0.00 2.57
3505 4751 2.449464 TCTTCCCCAATTGATGCACTG 58.551 47.619 7.12 0.00 0.00 3.66
3518 4764 0.983467 TGCACTGCAATCCCTGTCTA 59.017 50.000 0.00 0.00 34.76 2.59
3524 4770 1.134007 TGCAATCCCTGTCTAGCCATG 60.134 52.381 0.00 0.00 0.00 3.66
3525 4771 1.602311 CAATCCCTGTCTAGCCATGC 58.398 55.000 0.00 0.00 0.00 4.06
3526 4772 1.142465 CAATCCCTGTCTAGCCATGCT 59.858 52.381 0.00 0.00 43.41 3.79
3527 4773 1.055040 ATCCCTGTCTAGCCATGCTC 58.945 55.000 0.00 0.00 40.44 4.26
3528 4774 1.068753 CCCTGTCTAGCCATGCTCG 59.931 63.158 0.00 0.00 40.44 5.03
3529 4775 1.680522 CCCTGTCTAGCCATGCTCGT 61.681 60.000 0.00 0.00 40.44 4.18
3530 4776 0.249238 CCTGTCTAGCCATGCTCGTC 60.249 60.000 0.00 0.00 40.44 4.20
3531 4777 0.743688 CTGTCTAGCCATGCTCGTCT 59.256 55.000 0.00 0.00 40.44 4.18
3534 4780 1.135139 GTCTAGCCATGCTCGTCTGAA 59.865 52.381 0.00 0.00 40.44 3.02
3535 4781 1.135139 TCTAGCCATGCTCGTCTGAAC 59.865 52.381 0.00 0.00 40.44 3.18
3536 4782 1.135915 CTAGCCATGCTCGTCTGAACT 59.864 52.381 0.00 0.00 40.44 3.01
3537 4783 0.390866 AGCCATGCTCGTCTGAACTG 60.391 55.000 0.00 0.00 30.62 3.16
3538 4784 0.671781 GCCATGCTCGTCTGAACTGT 60.672 55.000 0.00 0.00 0.00 3.55
3539 4785 1.354040 CCATGCTCGTCTGAACTGTC 58.646 55.000 0.00 0.00 0.00 3.51
3540 4786 1.354040 CATGCTCGTCTGAACTGTCC 58.646 55.000 0.00 0.00 0.00 4.02
3541 4787 0.109086 ATGCTCGTCTGAACTGTCCG 60.109 55.000 0.00 0.00 0.00 4.79
3542 4788 2.089349 GCTCGTCTGAACTGTCCGC 61.089 63.158 0.00 0.00 0.00 5.54
3545 4791 0.388520 TCGTCTGAACTGTCCGCATG 60.389 55.000 0.00 0.00 0.00 4.06
3546 4792 0.388520 CGTCTGAACTGTCCGCATGA 60.389 55.000 0.00 0.00 0.00 3.07
3548 4794 2.479560 CGTCTGAACTGTCCGCATGATA 60.480 50.000 0.00 0.00 0.00 2.15
3549 4795 3.722147 GTCTGAACTGTCCGCATGATAT 58.278 45.455 0.00 0.00 0.00 1.63
3550 4796 4.556699 CGTCTGAACTGTCCGCATGATATA 60.557 45.833 0.00 0.00 0.00 0.86
3552 4798 4.340950 TCTGAACTGTCCGCATGATATACA 59.659 41.667 0.00 0.00 0.00 2.29
3553 4799 5.017294 TGAACTGTCCGCATGATATACAA 57.983 39.130 0.00 0.00 0.00 2.41
3554 4800 5.423886 TGAACTGTCCGCATGATATACAAA 58.576 37.500 0.00 0.00 0.00 2.83
3555 4801 6.054941 TGAACTGTCCGCATGATATACAAAT 58.945 36.000 0.00 0.00 0.00 2.32
3556 4802 5.929697 ACTGTCCGCATGATATACAAATG 57.070 39.130 0.00 0.00 0.00 2.32
3557 4803 4.214119 ACTGTCCGCATGATATACAAATGC 59.786 41.667 0.00 6.18 42.59 3.56
3558 4804 4.388485 TGTCCGCATGATATACAAATGCT 58.612 39.130 0.00 0.00 43.59 3.79
3559 4805 4.213906 TGTCCGCATGATATACAAATGCTG 59.786 41.667 0.00 7.47 43.59 4.41
3561 4807 4.452114 TCCGCATGATATACAAATGCTGTC 59.548 41.667 0.00 0.00 43.59 3.51
3562 4808 4.213906 CCGCATGATATACAAATGCTGTCA 59.786 41.667 0.00 0.00 43.59 3.58
3564 4810 5.178067 CGCATGATATACAAATGCTGTCAGA 59.822 40.000 3.32 0.00 43.59 3.27
3566 4812 7.572539 CGCATGATATACAAATGCTGTCAGATT 60.573 37.037 3.32 0.00 43.59 2.40
3567 4813 8.080417 GCATGATATACAAATGCTGTCAGATTT 58.920 33.333 3.32 4.48 42.70 2.17
3568 4814 9.961265 CATGATATACAAATGCTGTCAGATTTT 57.039 29.630 3.32 0.00 39.64 1.82
3589 4835 4.599047 TTTCCCCTGTATTTGCTGTTTG 57.401 40.909 0.00 0.00 0.00 2.93
3605 4851 6.737254 GCTGTTTGCATACTCCTTACTTAA 57.263 37.500 8.78 0.00 42.31 1.85
3609 4855 8.911918 TGTTTGCATACTCCTTACTTAAAGAA 57.088 30.769 8.78 0.00 37.38 2.52
3642 4888 9.474249 GAACGTTTACATCACTTTTATTAGAGC 57.526 33.333 0.46 0.00 0.00 4.09
3643 4889 7.971455 ACGTTTACATCACTTTTATTAGAGCC 58.029 34.615 0.00 0.00 0.00 4.70
3644 4890 7.117454 CGTTTACATCACTTTTATTAGAGCCG 58.883 38.462 0.00 0.00 0.00 5.52
3645 4891 7.009815 CGTTTACATCACTTTTATTAGAGCCGA 59.990 37.037 0.00 0.00 0.00 5.54
3646 4892 8.662141 GTTTACATCACTTTTATTAGAGCCGAA 58.338 33.333 0.00 0.00 0.00 4.30
3649 4895 6.313905 ACATCACTTTTATTAGAGCCGAACAG 59.686 38.462 0.00 0.00 0.00 3.16
3651 4897 6.927416 TCACTTTTATTAGAGCCGAACAGTA 58.073 36.000 0.00 0.00 0.00 2.74
3652 4898 7.380536 TCACTTTTATTAGAGCCGAACAGTAA 58.619 34.615 0.00 0.00 0.00 2.24
3653 4899 7.874016 TCACTTTTATTAGAGCCGAACAGTAAA 59.126 33.333 0.00 0.00 0.00 2.01
3655 4901 9.227777 ACTTTTATTAGAGCCGAACAGTAAAAT 57.772 29.630 0.00 0.00 0.00 1.82
3659 4905 7.923414 ATTAGAGCCGAACAGTAAAATTCTT 57.077 32.000 0.00 0.00 0.00 2.52
3660 4906 5.613358 AGAGCCGAACAGTAAAATTCTTG 57.387 39.130 0.00 0.00 0.00 3.02
3662 4908 5.940470 AGAGCCGAACAGTAAAATTCTTGAT 59.060 36.000 0.00 0.00 0.00 2.57
3665 4911 7.103641 AGCCGAACAGTAAAATTCTTGATAGA 58.896 34.615 0.00 0.00 0.00 1.98
3666 4912 7.278868 AGCCGAACAGTAAAATTCTTGATAGAG 59.721 37.037 0.00 0.00 0.00 2.43
3667 4913 7.277981 GCCGAACAGTAAAATTCTTGATAGAGA 59.722 37.037 0.00 0.00 0.00 3.10
3669 4915 9.574458 CGAACAGTAAAATTCTTGATAGAGAGA 57.426 33.333 0.00 0.00 0.00 3.10
3694 5001 7.951347 AAGGCTTCATCAAAAGATTAGTGAT 57.049 32.000 0.00 0.00 32.17 3.06
3714 5021 8.718158 AGTGATAAGATGAGGAGATAACATGA 57.282 34.615 0.00 0.00 0.00 3.07
3715 5022 9.152327 AGTGATAAGATGAGGAGATAACATGAA 57.848 33.333 0.00 0.00 0.00 2.57
3717 5024 8.927411 TGATAAGATGAGGAGATAACATGAACA 58.073 33.333 0.00 0.00 0.00 3.18
3719 5026 9.722184 ATAAGATGAGGAGATAACATGAACATG 57.278 33.333 12.43 12.43 44.15 3.21
3721 5028 4.454678 TGAGGAGATAACATGAACATGGC 58.545 43.478 17.25 5.71 42.91 4.40
3722 5029 3.817647 GAGGAGATAACATGAACATGGCC 59.182 47.826 17.25 0.00 42.91 5.36
3723 5030 2.549754 GGAGATAACATGAACATGGCCG 59.450 50.000 17.25 0.00 42.91 6.13
3724 5031 1.949525 AGATAACATGAACATGGCCGC 59.050 47.619 17.25 6.00 42.91 6.53
3725 5032 1.001378 GATAACATGAACATGGCCGCC 60.001 52.381 17.25 1.04 42.91 6.13
3728 5035 2.037049 ATGAACATGGCCGCCCAA 59.963 55.556 7.03 0.00 46.14 4.12
3729 5036 1.608918 ATGAACATGGCCGCCCAAA 60.609 52.632 7.03 0.00 46.14 3.28
3730 5037 1.190833 ATGAACATGGCCGCCCAAAA 61.191 50.000 7.03 0.00 46.14 2.44
3731 5038 1.369321 GAACATGGCCGCCCAAAAA 59.631 52.632 7.03 0.00 46.14 1.94
3825 5136 4.729868 AGAGGTAGTTTTTGAAGGCACAT 58.270 39.130 0.00 0.00 0.00 3.21
3838 5149 3.756082 AGGCACATCAAATTAAGGGGA 57.244 42.857 0.00 0.00 0.00 4.81
3839 5150 4.059773 AGGCACATCAAATTAAGGGGAA 57.940 40.909 0.00 0.00 0.00 3.97
3840 5151 4.424842 AGGCACATCAAATTAAGGGGAAA 58.575 39.130 0.00 0.00 0.00 3.13
3841 5152 4.843516 AGGCACATCAAATTAAGGGGAAAA 59.156 37.500 0.00 0.00 0.00 2.29
3865 5176 5.686159 AAAGCAGAGAAGACACTTGATTG 57.314 39.130 0.00 0.00 0.00 2.67
3897 5208 4.454678 TGGTAGATGCATGGTGAGAAATC 58.545 43.478 2.46 0.00 0.00 2.17
3898 5209 4.164796 TGGTAGATGCATGGTGAGAAATCT 59.835 41.667 2.46 0.00 0.00 2.40
3899 5210 4.514441 GGTAGATGCATGGTGAGAAATCTG 59.486 45.833 2.46 0.00 0.00 2.90
3900 5211 4.498894 AGATGCATGGTGAGAAATCTGA 57.501 40.909 2.46 0.00 0.00 3.27
3901 5212 4.197750 AGATGCATGGTGAGAAATCTGAC 58.802 43.478 2.46 0.00 0.00 3.51
3908 5219 2.611518 GTGAGAAATCTGACCACGGAG 58.388 52.381 0.00 0.00 34.70 4.63
3910 5221 0.250513 AGAAATCTGACCACGGAGGC 59.749 55.000 0.00 0.00 43.14 4.70
3911 5222 1.079127 AAATCTGACCACGGAGGCG 60.079 57.895 0.00 0.00 43.14 5.52
3912 5223 2.521958 AAATCTGACCACGGAGGCGG 62.522 60.000 0.00 0.00 43.14 6.13
3935 5358 2.355126 CACACACGTCTCGCTGCT 60.355 61.111 0.00 0.00 0.00 4.24
4027 5589 1.364626 GCGGACAGTGGCAGATCTTG 61.365 60.000 0.00 0.00 0.00 3.02
4032 5594 1.211457 ACAGTGGCAGATCTTGGATCC 59.789 52.381 4.20 4.20 0.00 3.36
4054 5616 0.843984 ACACTAGGGTGCCACTGTTT 59.156 50.000 0.00 0.00 46.57 2.83
4181 5745 7.897864 AGCACATAGTAAAAACTACTCTCTGT 58.102 34.615 0.00 0.00 0.00 3.41
4182 5746 7.815068 AGCACATAGTAAAAACTACTCTCTGTG 59.185 37.037 9.99 9.99 36.60 3.66
4183 5747 7.599245 GCACATAGTAAAAACTACTCTCTGTGT 59.401 37.037 13.51 0.00 36.30 3.72
4253 5819 9.802039 AGAAGTCTTATATTACTCTACAGAGGG 57.198 37.037 10.86 0.00 46.13 4.30
4254 5820 9.796180 GAAGTCTTATATTACTCTACAGAGGGA 57.204 37.037 10.86 0.00 46.13 4.20
4255 5821 9.802039 AAGTCTTATATTACTCTACAGAGGGAG 57.198 37.037 10.86 0.00 46.13 4.30
4256 5822 8.951541 AGTCTTATATTACTCTACAGAGGGAGT 58.048 37.037 10.86 0.00 46.13 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 4.473477 AGTCTAGAACCAATACAGGCAC 57.527 45.455 0.00 0.00 0.00 5.01
36 37 4.523558 AGTAAGGACTCGCAAAACTAGTCT 59.476 41.667 0.00 0.00 40.19 3.24
77 78 2.475487 GCATACGGGCGAGAGAAATAAC 59.525 50.000 0.00 0.00 0.00 1.89
161 293 4.058124 CAAGCTAAGGCGACATGCTTATA 58.942 43.478 13.56 0.00 45.43 0.98
162 294 2.874701 CAAGCTAAGGCGACATGCTTAT 59.125 45.455 13.56 0.00 45.43 1.73
295 427 3.368236 CAGTAAGGACTCGCAAAACTAGC 59.632 47.826 0.00 0.00 31.73 3.42
471 605 2.355010 GCAGAAGCACCCAATAGGAT 57.645 50.000 0.00 0.00 41.58 3.24
522 657 7.582667 AATACTTAACATGGTAATTCAGGGC 57.417 36.000 3.09 0.00 0.00 5.19
535 670 4.381932 GCAGGCAAGGCAAATACTTAACAT 60.382 41.667 0.00 0.00 0.00 2.71
625 760 7.829211 TCCAACTGATTCTTAACAGGAATAAGG 59.171 37.037 0.00 0.00 36.47 2.69
646 783 9.614792 ACAGGTAAAATTAGATCTACATCCAAC 57.385 33.333 0.67 0.00 0.00 3.77
672 809 8.974060 ACAGAACCAAAACTAAATCTGACTAA 57.026 30.769 7.51 0.00 38.10 2.24
673 810 8.429641 AGACAGAACCAAAACTAAATCTGACTA 58.570 33.333 7.51 0.00 37.86 2.59
674 811 7.283329 AGACAGAACCAAAACTAAATCTGACT 58.717 34.615 7.51 4.04 38.10 3.41
675 812 7.226720 TGAGACAGAACCAAAACTAAATCTGAC 59.773 37.037 7.51 1.85 38.10 3.51
676 813 7.279615 TGAGACAGAACCAAAACTAAATCTGA 58.720 34.615 7.51 0.00 38.10 3.27
677 814 7.496529 TGAGACAGAACCAAAACTAAATCTG 57.503 36.000 0.00 0.00 40.01 2.90
678 815 7.775561 AGTTGAGACAGAACCAAAACTAAATCT 59.224 33.333 0.00 0.00 0.00 2.40
679 816 7.931275 AGTTGAGACAGAACCAAAACTAAATC 58.069 34.615 0.00 0.00 0.00 2.17
680 817 7.881775 AGTTGAGACAGAACCAAAACTAAAT 57.118 32.000 0.00 0.00 0.00 1.40
681 818 7.175990 ACAAGTTGAGACAGAACCAAAACTAAA 59.824 33.333 10.54 0.00 0.00 1.85
682 819 6.657541 ACAAGTTGAGACAGAACCAAAACTAA 59.342 34.615 10.54 0.00 0.00 2.24
683 820 6.177610 ACAAGTTGAGACAGAACCAAAACTA 58.822 36.000 10.54 0.00 0.00 2.24
684 821 5.010282 ACAAGTTGAGACAGAACCAAAACT 58.990 37.500 10.54 0.00 0.00 2.66
685 822 5.310720 ACAAGTTGAGACAGAACCAAAAC 57.689 39.130 10.54 0.00 0.00 2.43
686 823 6.039270 CCATACAAGTTGAGACAGAACCAAAA 59.961 38.462 10.54 0.00 0.00 2.44
687 824 5.530915 CCATACAAGTTGAGACAGAACCAAA 59.469 40.000 10.54 0.00 0.00 3.28
688 825 5.063204 CCATACAAGTTGAGACAGAACCAA 58.937 41.667 10.54 0.00 0.00 3.67
689 826 4.504864 CCCATACAAGTTGAGACAGAACCA 60.505 45.833 10.54 0.00 0.00 3.67
690 827 4.003648 CCCATACAAGTTGAGACAGAACC 58.996 47.826 10.54 0.00 0.00 3.62
691 828 4.691216 GTCCCATACAAGTTGAGACAGAAC 59.309 45.833 10.54 0.00 0.00 3.01
692 829 4.593206 AGTCCCATACAAGTTGAGACAGAA 59.407 41.667 10.54 0.00 0.00 3.02
693 830 4.160329 AGTCCCATACAAGTTGAGACAGA 58.840 43.478 10.54 0.00 0.00 3.41
694 831 4.543590 AGTCCCATACAAGTTGAGACAG 57.456 45.455 10.54 0.00 0.00 3.51
695 832 6.428083 TTTAGTCCCATACAAGTTGAGACA 57.572 37.500 10.54 0.00 0.00 3.41
696 833 5.875359 CCTTTAGTCCCATACAAGTTGAGAC 59.125 44.000 10.54 8.01 0.00 3.36
697 834 5.570844 GCCTTTAGTCCCATACAAGTTGAGA 60.571 44.000 10.54 0.00 0.00 3.27
698 835 4.636206 GCCTTTAGTCCCATACAAGTTGAG 59.364 45.833 10.54 0.00 0.00 3.02
699 836 4.288626 AGCCTTTAGTCCCATACAAGTTGA 59.711 41.667 10.54 0.00 0.00 3.18
700 837 4.589908 AGCCTTTAGTCCCATACAAGTTG 58.410 43.478 0.00 0.00 0.00 3.16
701 838 4.929146 AGCCTTTAGTCCCATACAAGTT 57.071 40.909 0.00 0.00 0.00 2.66
702 839 4.929146 AAGCCTTTAGTCCCATACAAGT 57.071 40.909 0.00 0.00 0.00 3.16
703 840 5.010282 ACAAAGCCTTTAGTCCCATACAAG 58.990 41.667 0.00 0.00 0.00 3.16
704 841 4.993028 ACAAAGCCTTTAGTCCCATACAA 58.007 39.130 0.00 0.00 0.00 2.41
705 842 4.650972 ACAAAGCCTTTAGTCCCATACA 57.349 40.909 0.00 0.00 0.00 2.29
706 843 4.765339 ACAACAAAGCCTTTAGTCCCATAC 59.235 41.667 0.00 0.00 0.00 2.39
707 844 4.993028 ACAACAAAGCCTTTAGTCCCATA 58.007 39.130 0.00 0.00 0.00 2.74
708 845 3.844640 ACAACAAAGCCTTTAGTCCCAT 58.155 40.909 0.00 0.00 0.00 4.00
709 846 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
710 847 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
711 848 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
712 849 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
713 850 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
714 851 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
715 852 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
716 853 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
717 854 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
718 855 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
719 856 4.490743 ACTACAACAACAACAACAAAGCC 58.509 39.130 0.00 0.00 0.00 4.35
720 857 7.749539 AATACTACAACAACAACAACAAAGC 57.250 32.000 0.00 0.00 0.00 3.51
721 858 9.997482 ACTAATACTACAACAACAACAACAAAG 57.003 29.630 0.00 0.00 0.00 2.77
722 859 9.991388 GACTAATACTACAACAACAACAACAAA 57.009 29.630 0.00 0.00 0.00 2.83
723 860 9.163899 TGACTAATACTACAACAACAACAACAA 57.836 29.630 0.00 0.00 0.00 2.83
724 861 8.719560 TGACTAATACTACAACAACAACAACA 57.280 30.769 0.00 0.00 0.00 3.33
725 862 9.037737 TCTGACTAATACTACAACAACAACAAC 57.962 33.333 0.00 0.00 0.00 3.32
726 863 9.772973 ATCTGACTAATACTACAACAACAACAA 57.227 29.630 0.00 0.00 0.00 2.83
727 864 9.772973 AATCTGACTAATACTACAACAACAACA 57.227 29.630 0.00 0.00 0.00 3.33
740 877 9.226345 GCATGCAAAACTAAATCTGACTAATAC 57.774 33.333 14.21 0.00 0.00 1.89
741 878 8.405531 GGCATGCAAAACTAAATCTGACTAATA 58.594 33.333 21.36 0.00 0.00 0.98
742 879 7.123247 AGGCATGCAAAACTAAATCTGACTAAT 59.877 33.333 21.36 0.00 0.00 1.73
816 1018 6.072728 GCAAAACTAAATCCCCAATTTGTTCC 60.073 38.462 0.00 0.00 38.08 3.62
818 1020 6.360618 TGCAAAACTAAATCCCCAATTTGTT 58.639 32.000 0.00 0.00 38.08 2.83
819 1021 5.934781 TGCAAAACTAAATCCCCAATTTGT 58.065 33.333 0.00 0.00 38.08 2.83
820 1022 6.623331 GCATGCAAAACTAAATCCCCAATTTG 60.623 38.462 14.21 0.00 38.08 2.32
821 1023 5.415389 GCATGCAAAACTAAATCCCCAATTT 59.585 36.000 14.21 0.00 40.67 1.82
822 1024 4.943093 GCATGCAAAACTAAATCCCCAATT 59.057 37.500 14.21 0.00 0.00 2.32
823 1025 4.516323 GCATGCAAAACTAAATCCCCAAT 58.484 39.130 14.21 0.00 0.00 3.16
825 1027 2.235898 GGCATGCAAAACTAAATCCCCA 59.764 45.455 21.36 0.00 0.00 4.96
826 1028 2.501316 AGGCATGCAAAACTAAATCCCC 59.499 45.455 21.36 0.00 0.00 4.81
829 1031 6.365050 CAAACAAGGCATGCAAAACTAAATC 58.635 36.000 21.36 0.00 0.00 2.17
831 1033 4.574013 CCAAACAAGGCATGCAAAACTAAA 59.426 37.500 21.36 0.00 0.00 1.85
833 1035 3.494048 CCCAAACAAGGCATGCAAAACTA 60.494 43.478 21.36 0.00 0.00 2.24
834 1036 2.563702 CCAAACAAGGCATGCAAAACT 58.436 42.857 21.36 3.93 0.00 2.66
835 1037 1.603326 CCCAAACAAGGCATGCAAAAC 59.397 47.619 21.36 1.15 0.00 2.43
837 1039 1.126488 TCCCAAACAAGGCATGCAAA 58.874 45.000 21.36 0.00 0.00 3.68
839 1041 0.469705 AGTCCCAAACAAGGCATGCA 60.470 50.000 21.36 0.00 0.00 3.96
840 1042 1.544724 TAGTCCCAAACAAGGCATGC 58.455 50.000 9.90 9.90 0.00 4.06
842 1044 4.223144 ACTTTTAGTCCCAAACAAGGCAT 58.777 39.130 0.00 0.00 0.00 4.40
843 1045 3.634910 GACTTTTAGTCCCAAACAAGGCA 59.365 43.478 0.00 0.00 39.28 4.75
844 1046 3.889538 AGACTTTTAGTCCCAAACAAGGC 59.110 43.478 3.33 0.00 46.18 4.35
845 1047 4.887655 ACAGACTTTTAGTCCCAAACAAGG 59.112 41.667 3.33 0.00 46.18 3.61
846 1048 5.221048 CCACAGACTTTTAGTCCCAAACAAG 60.221 44.000 3.33 0.00 46.18 3.16
847 1049 4.642885 CCACAGACTTTTAGTCCCAAACAA 59.357 41.667 3.33 0.00 46.18 2.83
963 1378 6.435430 TGAACGATGGTGATAATTTGGAAG 57.565 37.500 0.00 0.00 0.00 3.46
978 1393 7.801547 AACTTAAGCAAATGATTGAACGATG 57.198 32.000 1.29 0.00 38.94 3.84
1067 1528 0.106819 CTTCTCCTTGCCCATGGAGG 60.107 60.000 22.59 12.78 46.81 4.30
1069 1530 1.492176 GATCTTCTCCTTGCCCATGGA 59.508 52.381 15.22 0.00 34.06 3.41
1296 1769 0.241213 TCTCGAACTTCCACAGAGCG 59.759 55.000 0.00 0.00 0.00 5.03
1675 2150 4.946157 AGTGGATAGCAAAAGGATGTCAAG 59.054 41.667 0.00 0.00 0.00 3.02
1756 2231 3.562973 CGCATCAAGTGGATAGCAAAGAT 59.437 43.478 0.00 0.00 33.95 2.40
1769 2244 3.883830 ATTCTGAGTCTCGCATCAAGT 57.116 42.857 0.00 0.00 0.00 3.16
2072 2984 5.478407 TGCACAGAATAAGAGATCACGAAA 58.522 37.500 0.00 0.00 0.00 3.46
2073 2985 5.072040 TGCACAGAATAAGAGATCACGAA 57.928 39.130 0.00 0.00 0.00 3.85
2078 3018 5.877012 TGGAAGTTGCACAGAATAAGAGATC 59.123 40.000 0.00 0.00 0.00 2.75
2588 3738 1.001974 CCGACATTGTCACCAGGAAGA 59.998 52.381 16.61 0.00 32.09 2.87
2648 3798 1.183676 AGTTGGAAGCGACGTACCCT 61.184 55.000 0.00 0.00 0.00 4.34
3078 4228 3.708734 GAACCACCAACGACGCCG 61.709 66.667 0.00 0.00 42.50 6.46
3118 4274 2.278989 CACCACCGTATACCGCCG 60.279 66.667 0.00 0.00 34.38 6.46
3138 4294 3.302480 GCAAATCCGCTAACACGACTATG 60.302 47.826 0.00 0.00 34.06 2.23
3223 4380 4.034048 CCAACACAAGGAACGATACTATGC 59.966 45.833 0.00 0.00 0.00 3.14
3224 4381 5.063438 CACCAACACAAGGAACGATACTATG 59.937 44.000 0.00 0.00 0.00 2.23
3225 4382 5.046878 TCACCAACACAAGGAACGATACTAT 60.047 40.000 0.00 0.00 0.00 2.12
3237 4394 3.757745 ACGAAGTTTCACCAACACAAG 57.242 42.857 0.00 0.00 37.78 3.16
3288 4446 1.009829 CAGGCAGCGACTCCAAATAC 58.990 55.000 0.00 0.00 0.00 1.89
3307 4479 5.009854 ACCATTACCAAATATGCTTGCAC 57.990 39.130 0.00 0.00 0.00 4.57
3309 4481 6.983474 AAAACCATTACCAAATATGCTTGC 57.017 33.333 0.00 0.00 0.00 4.01
3371 4617 2.816087 AGCACAGGTAAGTTTCAGCATG 59.184 45.455 0.00 0.00 37.54 4.06
3418 4664 3.576004 CAGCTGCTGCAACTCTCC 58.424 61.111 17.73 0.00 42.74 3.71
3440 4686 5.705609 TCTTAGATGCAACCTGGAAAAAC 57.294 39.130 0.00 0.00 0.00 2.43
3459 4705 3.518992 TCCGGGTTGGAAGATTTTCTT 57.481 42.857 0.00 0.00 46.38 2.52
3470 4716 1.066358 GGAAGAAGTAGTCCGGGTTGG 60.066 57.143 0.00 0.00 40.09 3.77
3482 4728 2.827921 GTGCATCAATTGGGGAAGAAGT 59.172 45.455 5.42 0.00 0.00 3.01
3484 4730 2.827322 CAGTGCATCAATTGGGGAAGAA 59.173 45.455 5.42 0.00 0.00 2.52
3485 4731 2.449464 CAGTGCATCAATTGGGGAAGA 58.551 47.619 5.42 0.00 0.00 2.87
3486 4732 1.134907 GCAGTGCATCAATTGGGGAAG 60.135 52.381 11.09 0.00 0.00 3.46
3487 4733 0.896923 GCAGTGCATCAATTGGGGAA 59.103 50.000 11.09 0.00 0.00 3.97
3488 4734 0.251698 TGCAGTGCATCAATTGGGGA 60.252 50.000 15.37 0.00 31.71 4.81
3489 4735 0.609151 TTGCAGTGCATCAATTGGGG 59.391 50.000 20.50 0.00 38.76 4.96
3490 4736 2.546778 GATTGCAGTGCATCAATTGGG 58.453 47.619 20.50 0.00 38.76 4.12
3491 4737 2.546778 GGATTGCAGTGCATCAATTGG 58.453 47.619 20.50 0.00 38.76 3.16
3492 4738 2.167693 AGGGATTGCAGTGCATCAATTG 59.832 45.455 20.50 0.00 38.76 2.32
3493 4739 2.167693 CAGGGATTGCAGTGCATCAATT 59.832 45.455 20.50 2.26 38.76 2.32
3494 4740 1.754803 CAGGGATTGCAGTGCATCAAT 59.245 47.619 20.50 9.81 38.76 2.57
3495 4741 1.179152 CAGGGATTGCAGTGCATCAA 58.821 50.000 20.50 4.19 38.76 2.57
3496 4742 0.038599 ACAGGGATTGCAGTGCATCA 59.961 50.000 20.50 5.07 38.76 3.07
3497 4743 0.737219 GACAGGGATTGCAGTGCATC 59.263 55.000 20.50 17.19 38.76 3.91
3498 4744 0.330604 AGACAGGGATTGCAGTGCAT 59.669 50.000 20.50 9.23 38.76 3.96
3499 4745 0.983467 TAGACAGGGATTGCAGTGCA 59.017 50.000 15.37 15.37 36.47 4.57
3505 4751 1.602311 CATGGCTAGACAGGGATTGC 58.398 55.000 3.72 0.00 0.00 3.56
3518 4764 0.390866 CAGTTCAGACGAGCATGGCT 60.391 55.000 0.00 0.00 43.88 4.75
3524 4770 2.089349 GCGGACAGTTCAGACGAGC 61.089 63.158 0.00 0.00 0.00 5.03
3525 4771 0.109086 ATGCGGACAGTTCAGACGAG 60.109 55.000 0.00 0.00 0.00 4.18
3526 4772 0.388520 CATGCGGACAGTTCAGACGA 60.389 55.000 0.00 0.00 0.00 4.20
3527 4773 0.388520 TCATGCGGACAGTTCAGACG 60.389 55.000 0.00 0.00 0.00 4.18
3528 4774 2.015736 ATCATGCGGACAGTTCAGAC 57.984 50.000 0.00 0.00 0.00 3.51
3529 4775 4.340950 TGTATATCATGCGGACAGTTCAGA 59.659 41.667 0.00 0.00 0.00 3.27
3530 4776 4.620982 TGTATATCATGCGGACAGTTCAG 58.379 43.478 0.00 0.00 0.00 3.02
3531 4777 4.664150 TGTATATCATGCGGACAGTTCA 57.336 40.909 0.00 0.00 0.00 3.18
3534 4780 4.214119 GCATTTGTATATCATGCGGACAGT 59.786 41.667 0.00 0.00 0.00 3.55
3535 4781 4.453478 AGCATTTGTATATCATGCGGACAG 59.547 41.667 7.65 0.00 42.51 3.51
3536 4782 4.213906 CAGCATTTGTATATCATGCGGACA 59.786 41.667 7.61 0.00 42.51 4.02
3537 4783 4.214119 ACAGCATTTGTATATCATGCGGAC 59.786 41.667 15.70 0.00 42.51 4.79
3538 4784 4.388485 ACAGCATTTGTATATCATGCGGA 58.612 39.130 15.70 0.00 42.51 5.54
3539 4785 4.213906 TGACAGCATTTGTATATCATGCGG 59.786 41.667 10.33 10.33 41.05 5.69
3540 4786 5.178067 TCTGACAGCATTTGTATATCATGCG 59.822 40.000 0.00 6.26 41.05 4.73
3541 4787 6.549912 TCTGACAGCATTTGTATATCATGC 57.450 37.500 0.00 5.88 41.05 4.06
3542 4788 9.961265 AAAATCTGACAGCATTTGTATATCATG 57.039 29.630 11.28 0.00 41.05 3.07
3566 4812 5.363939 CAAACAGCAAATACAGGGGAAAAA 58.636 37.500 0.00 0.00 0.00 1.94
3567 4813 4.742138 GCAAACAGCAAATACAGGGGAAAA 60.742 41.667 0.00 0.00 44.79 2.29
3568 4814 3.244044 GCAAACAGCAAATACAGGGGAAA 60.244 43.478 0.00 0.00 44.79 3.13
3569 4815 2.298729 GCAAACAGCAAATACAGGGGAA 59.701 45.455 0.00 0.00 44.79 3.97
3570 4816 1.892474 GCAAACAGCAAATACAGGGGA 59.108 47.619 0.00 0.00 44.79 4.81
3571 4817 2.368655 GCAAACAGCAAATACAGGGG 57.631 50.000 0.00 0.00 44.79 4.79
3583 4829 8.547967 TCTTTAAGTAAGGAGTATGCAAACAG 57.452 34.615 0.00 0.00 34.46 3.16
3616 4862 9.474249 GCTCTAATAAAAGTGATGTAAACGTTC 57.526 33.333 0.00 0.00 0.00 3.95
3619 4865 7.009815 TCGGCTCTAATAAAAGTGATGTAAACG 59.990 37.037 0.00 0.00 0.00 3.60
3622 4868 7.820386 TGTTCGGCTCTAATAAAAGTGATGTAA 59.180 33.333 0.00 0.00 0.00 2.41
3623 4869 7.324935 TGTTCGGCTCTAATAAAAGTGATGTA 58.675 34.615 0.00 0.00 0.00 2.29
3626 4872 6.407202 ACTGTTCGGCTCTAATAAAAGTGAT 58.593 36.000 0.00 0.00 0.00 3.06
3633 4879 9.444600 AAGAATTTTACTGTTCGGCTCTAATAA 57.555 29.630 0.00 0.00 0.00 1.40
3636 4882 6.932400 TCAAGAATTTTACTGTTCGGCTCTAA 59.068 34.615 0.00 0.00 0.00 2.10
3637 4883 6.460781 TCAAGAATTTTACTGTTCGGCTCTA 58.539 36.000 0.00 0.00 0.00 2.43
3641 4887 7.277981 TCTCTATCAAGAATTTTACTGTTCGGC 59.722 37.037 0.00 0.00 0.00 5.54
3642 4888 8.703604 TCTCTATCAAGAATTTTACTGTTCGG 57.296 34.615 0.00 0.00 0.00 4.30
3643 4889 9.574458 TCTCTCTATCAAGAATTTTACTGTTCG 57.426 33.333 0.00 0.00 0.00 3.95
3649 4895 9.389755 AGCCTTTCTCTCTATCAAGAATTTTAC 57.610 33.333 0.00 0.00 31.89 2.01
3651 4897 8.876303 AAGCCTTTCTCTCTATCAAGAATTTT 57.124 30.769 0.00 0.00 31.89 1.82
3652 4898 8.105829 TGAAGCCTTTCTCTCTATCAAGAATTT 58.894 33.333 0.00 0.00 34.31 1.82
3653 4899 7.628234 TGAAGCCTTTCTCTCTATCAAGAATT 58.372 34.615 0.00 0.00 34.31 2.17
3655 4901 6.611613 TGAAGCCTTTCTCTCTATCAAGAA 57.388 37.500 0.00 0.00 34.31 2.52
3656 4902 6.382282 TGATGAAGCCTTTCTCTCTATCAAGA 59.618 38.462 0.00 0.00 34.31 3.02
3659 4905 6.550938 TTGATGAAGCCTTTCTCTCTATCA 57.449 37.500 0.00 0.00 34.31 2.15
3660 4906 7.768120 TCTTTTGATGAAGCCTTTCTCTCTATC 59.232 37.037 0.00 0.00 34.31 2.08
3662 4908 7.009179 TCTTTTGATGAAGCCTTTCTCTCTA 57.991 36.000 0.00 0.00 34.31 2.43
3665 4911 7.887495 ACTAATCTTTTGATGAAGCCTTTCTCT 59.113 33.333 0.00 0.00 39.48 3.10
3666 4912 7.967303 CACTAATCTTTTGATGAAGCCTTTCTC 59.033 37.037 0.00 0.00 39.48 2.87
3667 4913 7.667219 TCACTAATCTTTTGATGAAGCCTTTCT 59.333 33.333 0.00 0.00 39.48 2.52
3669 4915 7.765695 TCACTAATCTTTTGATGAAGCCTTT 57.234 32.000 0.00 0.00 39.48 3.11
3670 4916 7.951347 ATCACTAATCTTTTGATGAAGCCTT 57.049 32.000 0.00 0.00 39.48 4.35
3671 4917 9.118300 CTTATCACTAATCTTTTGATGAAGCCT 57.882 33.333 0.00 0.00 39.48 4.58
3694 5001 8.152898 CCATGTTCATGTTATCTCCTCATCTTA 58.847 37.037 11.13 0.00 0.00 2.10
3699 5006 4.454678 GCCATGTTCATGTTATCTCCTCA 58.545 43.478 11.13 0.00 0.00 3.86
3702 5009 2.549754 CGGCCATGTTCATGTTATCTCC 59.450 50.000 2.24 3.12 0.00 3.71
3706 5013 1.032014 GGCGGCCATGTTCATGTTAT 58.968 50.000 15.62 0.00 0.00 1.89
3707 5014 1.034838 GGGCGGCCATGTTCATGTTA 61.035 55.000 25.33 0.00 0.00 2.41
3708 5015 2.350458 GGGCGGCCATGTTCATGTT 61.350 57.895 25.33 0.00 0.00 2.71
3710 5017 1.886253 TTTGGGCGGCCATGTTCATG 61.886 55.000 33.19 5.88 0.00 3.07
3711 5018 1.190833 TTTTGGGCGGCCATGTTCAT 61.191 50.000 33.19 0.00 0.00 2.57
3713 5020 1.369321 TTTTTGGGCGGCCATGTTC 59.631 52.632 33.19 1.99 0.00 3.18
3714 5021 3.555967 TTTTTGGGCGGCCATGTT 58.444 50.000 33.19 0.00 0.00 2.71
3738 5045 9.696572 GGGGACTACATGTATATAGAACTCATA 57.303 37.037 5.91 0.00 0.00 2.15
3739 5046 8.177456 TGGGGACTACATGTATATAGAACTCAT 58.823 37.037 5.91 0.00 0.00 2.90
3740 5047 7.532199 TGGGGACTACATGTATATAGAACTCA 58.468 38.462 5.91 0.00 0.00 3.41
3741 5048 8.596781 ATGGGGACTACATGTATATAGAACTC 57.403 38.462 5.91 0.00 0.00 3.01
3795 5102 7.255486 GCCTTCAAAAACTACCTCTTACATTGT 60.255 37.037 0.00 0.00 0.00 2.71
3796 5103 7.084486 GCCTTCAAAAACTACCTCTTACATTG 58.916 38.462 0.00 0.00 0.00 2.82
3798 5105 6.206829 GTGCCTTCAAAAACTACCTCTTACAT 59.793 38.462 0.00 0.00 0.00 2.29
3799 5106 5.529800 GTGCCTTCAAAAACTACCTCTTACA 59.470 40.000 0.00 0.00 0.00 2.41
3800 5107 5.529800 TGTGCCTTCAAAAACTACCTCTTAC 59.470 40.000 0.00 0.00 0.00 2.34
3803 5110 4.164843 TGTGCCTTCAAAAACTACCTCT 57.835 40.909 0.00 0.00 0.00 3.69
3804 5111 4.518970 TGATGTGCCTTCAAAAACTACCTC 59.481 41.667 0.00 0.00 0.00 3.85
3805 5112 4.469657 TGATGTGCCTTCAAAAACTACCT 58.530 39.130 0.00 0.00 0.00 3.08
3807 5114 7.713764 AATTTGATGTGCCTTCAAAAACTAC 57.286 32.000 15.23 0.00 43.94 2.73
3808 5115 9.474920 CTTAATTTGATGTGCCTTCAAAAACTA 57.525 29.630 15.23 8.43 43.94 2.24
3809 5116 7.442062 CCTTAATTTGATGTGCCTTCAAAAACT 59.558 33.333 15.23 9.04 43.94 2.66
3810 5117 7.307930 CCCTTAATTTGATGTGCCTTCAAAAAC 60.308 37.037 15.23 0.00 43.94 2.43
3811 5118 6.709846 CCCTTAATTTGATGTGCCTTCAAAAA 59.290 34.615 15.23 8.86 43.94 1.94
3813 5120 5.279910 CCCCTTAATTTGATGTGCCTTCAAA 60.280 40.000 14.25 14.25 44.60 2.69
3815 5122 3.768757 CCCCTTAATTTGATGTGCCTTCA 59.231 43.478 0.00 0.00 0.00 3.02
3816 5123 4.023291 TCCCCTTAATTTGATGTGCCTTC 58.977 43.478 0.00 0.00 0.00 3.46
3841 5152 6.319658 TCAATCAAGTGTCTTCTCTGCTTTTT 59.680 34.615 0.00 0.00 0.00 1.94
3865 5176 8.043113 TCACCATGCATCTACCATAATTATCTC 58.957 37.037 0.00 0.00 0.00 2.75
3875 5186 3.998913 TTTCTCACCATGCATCTACCA 57.001 42.857 0.00 0.00 0.00 3.25
3911 5222 4.626081 AGACGTGTGTGGCCTGCC 62.626 66.667 3.32 0.00 0.00 4.85
3912 5223 3.044305 GAGACGTGTGTGGCCTGC 61.044 66.667 3.32 0.00 0.00 4.85
3913 5224 2.734723 CGAGACGTGTGTGGCCTG 60.735 66.667 3.32 0.00 0.00 4.85
3914 5225 4.664677 GCGAGACGTGTGTGGCCT 62.665 66.667 3.32 0.00 0.00 5.19
3919 5319 2.355126 CAGCAGCGAGACGTGTGT 60.355 61.111 0.00 0.00 0.00 3.72
4019 5581 3.641434 AGTGTTGGGATCCAAGATCTG 57.359 47.619 15.23 0.00 44.82 2.90
4032 5594 0.606401 CAGTGGCACCCTAGTGTTGG 60.606 60.000 15.27 0.00 46.35 3.77
4157 5721 7.599245 ACACAGAGAGTAGTTTTTACTATGTGC 59.401 37.037 16.33 0.00 38.62 4.57
4174 5738 9.915629 AAGTCTTATGTTACTTTACACAGAGAG 57.084 33.333 0.00 0.00 32.00 3.20


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

AutoCloner maintained by Alex Coulton.