Multiple sequence alignment - TraesCS3D01G241700

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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 TraesCS3D01G241700 chr3D 100.000 8213 0 0 1 8213 336532142 336540354 0.000000e+00 15167.0
1 TraesCS3D01G241700 chr3D 79.714 350 39 15 7384 7707 310678963 310678620 2.980000e-54 224.0
2 TraesCS3D01G241700 chr3D 98.889 90 1 0 7039 7128 583868989 583869078 2.370000e-35 161.0
3 TraesCS3D01G241700 chr3D 91.304 115 7 2 7039 7151 435299690 435299803 3.970000e-33 154.0
4 TraesCS3D01G241700 chr3D 91.429 70 6 0 4695 4764 401303295 401303364 6.780000e-16 97.1
5 TraesCS3D01G241700 chr3D 86.905 84 10 1 4695 4778 546700630 546700548 8.780000e-15 93.5
6 TraesCS3D01G241700 chr3A 96.691 4442 101 20 692 5100 453812843 453817271 0.000000e+00 7347.0
7 TraesCS3D01G241700 chr3A 97.026 1950 47 7 5096 7040 453818692 453820635 0.000000e+00 3269.0
8 TraesCS3D01G241700 chr3A 95.133 1089 29 10 7121 8190 453820633 453821716 0.000000e+00 1696.0
9 TraesCS3D01G241700 chr3A 84.568 162 16 2 7388 7540 168844935 168844774 1.430000e-32 152.0
10 TraesCS3D01G241700 chr3A 92.045 88 6 1 4695 4781 13500132 13500219 1.120000e-23 122.0
11 TraesCS3D01G241700 chr3A 87.379 103 13 0 5741 5843 150715990 150715888 1.450000e-22 119.0
12 TraesCS3D01G241700 chr3B 92.684 1736 97 18 2847 4573 434400074 434401788 0.000000e+00 2475.0
13 TraesCS3D01G241700 chr3B 93.964 1226 58 5 770 1995 434393113 434394322 0.000000e+00 1840.0
14 TraesCS3D01G241700 chr3B 91.964 1232 63 11 5842 7042 434403847 434405073 0.000000e+00 1694.0
15 TraesCS3D01G241700 chr3B 90.619 501 34 9 5180 5670 434402708 434403205 0.000000e+00 652.0
16 TraesCS3D01G241700 chr3B 87.850 535 44 8 2082 2598 434398891 434399422 7.050000e-170 608.0
17 TraesCS3D01G241700 chr3B 90.110 455 36 6 4573 5022 434401871 434402321 4.270000e-162 582.0
18 TraesCS3D01G241700 chr3B 91.852 270 11 5 7949 8213 434405660 434405923 4.680000e-97 366.0
19 TraesCS3D01G241700 chr3B 89.818 275 21 6 7121 7389 434405069 434405342 6.100000e-91 346.0
20 TraesCS3D01G241700 chr3B 93.333 165 10 1 5016 5180 434402281 434402444 8.240000e-60 243.0
21 TraesCS3D01G241700 chr3B 79.320 353 47 12 7378 7707 785616148 785615799 2.980000e-54 224.0
22 TraesCS3D01G241700 chr3B 82.591 247 28 12 7464 7701 520445414 520445654 3.890000e-48 204.0
23 TraesCS3D01G241700 chr3B 98.913 92 1 0 7035 7126 138269215 138269306 1.830000e-36 165.0
24 TraesCS3D01G241700 chr3B 84.472 161 16 2 7388 7539 236120835 236120995 5.130000e-32 150.0
25 TraesCS3D01G241700 chr3B 94.048 84 4 1 4695 4777 180277552 180277635 8.650000e-25 126.0
26 TraesCS3D01G241700 chr3B 89.691 97 9 1 5744 5840 609304995 609305090 1.120000e-23 122.0
27 TraesCS3D01G241700 chr3B 87.379 103 13 0 5741 5843 193611800 193611698 1.450000e-22 119.0
28 TraesCS3D01G241700 chr3B 92.105 76 3 3 5677 5751 434403520 434403593 4.050000e-18 104.0
29 TraesCS3D01G241700 chr3B 82.979 94 7 2 1999 2084 434394381 434394473 8.840000e-10 76.8
30 TraesCS3D01G241700 chr2D 89.571 652 54 8 4 643 623966701 623966052 0.000000e+00 815.0
31 TraesCS3D01G241700 chr2D 79.967 604 36 31 6133 6676 641949165 641949743 4.680000e-97 366.0
32 TraesCS3D01G241700 chr2D 84.071 339 20 11 6318 6626 597895475 597895809 6.230000e-76 296.0
33 TraesCS3D01G241700 chr2D 98.889 90 1 0 7035 7124 278358783 278358694 2.370000e-35 161.0
34 TraesCS3D01G241700 chr2D 92.793 111 4 3 7028 7134 15682887 15682997 3.070000e-34 158.0
35 TraesCS3D01G241700 chr2D 86.076 79 11 0 4695 4773 387905708 387905786 1.470000e-12 86.1
36 TraesCS3D01G241700 chr2D 92.453 53 3 1 6135 6186 597895219 597895271 3.180000e-09 75.0
37 TraesCS3D01G241700 chr2D 100.000 36 0 0 650 685 27654229 27654194 5.320000e-07 67.6
38 TraesCS3D01G241700 chr7B 85.038 655 59 17 1 642 34686770 34687398 1.500000e-176 630.0
39 TraesCS3D01G241700 chr7B 97.895 95 1 1 7032 7125 29304247 29304341 6.600000e-36 163.0
40 TraesCS3D01G241700 chr7B 92.000 100 8 0 5743 5842 245070444 245070345 3.090000e-29 141.0
41 TraesCS3D01G241700 chr7B 79.060 234 27 12 7491 7707 563740720 563740492 3.090000e-29 141.0
42 TraesCS3D01G241700 chr7B 91.566 83 7 0 4695 4777 686630326 686630244 1.870000e-21 115.0
43 TraesCS3D01G241700 chr1A 76.248 661 128 19 4 646 29015929 29015280 2.860000e-84 324.0
44 TraesCS3D01G241700 chr1A 92.000 100 8 0 5741 5840 64714330 64714429 3.090000e-29 141.0
45 TraesCS3D01G241700 chr2B 75.904 664 123 26 4 641 522102622 522103274 1.040000e-78 305.0
46 TraesCS3D01G241700 chr2B 82.621 351 24 14 6249 6566 799970269 799969923 8.120000e-70 276.0
47 TraesCS3D01G241700 chr2B 87.342 79 10 0 4695 4773 459257389 459257467 3.160000e-14 91.6
48 TraesCS3D01G241700 chr2B 100.000 28 0 0 6133 6160 799970783 799970756 1.500000e-02 52.8
49 TraesCS3D01G241700 chr4D 80.580 345 36 11 7389 7707 429121496 429121835 3.830000e-58 237.0
50 TraesCS3D01G241700 chr5A 79.118 340 39 14 7389 7701 659168852 659169186 1.080000e-48 206.0
51 TraesCS3D01G241700 chr5A 79.599 299 40 9 7387 7668 675401666 675401372 2.340000e-45 195.0
52 TraesCS3D01G241700 chr5A 77.810 347 46 14 7388 7708 64754520 64754179 1.410000e-42 185.0
53 TraesCS3D01G241700 chr4A 77.941 340 47 12 7388 7701 64580911 64581248 3.910000e-43 187.0
54 TraesCS3D01G241700 chr7D 80.242 248 25 11 7478 7707 527467576 527467335 1.830000e-36 165.0
55 TraesCS3D01G241700 chr7D 97.059 34 1 0 7391 7424 25873986 25873953 3.200000e-04 58.4
56 TraesCS3D01G241700 chr4B 100.000 88 0 0 7036 7123 507357685 507357772 6.600000e-36 163.0
57 TraesCS3D01G241700 chr1D 97.826 92 2 0 7037 7128 243753385 243753294 8.530000e-35 159.0
58 TraesCS3D01G241700 chr1D 83.648 159 18 1 7389 7539 92321395 92321237 8.590000e-30 143.0
59 TraesCS3D01G241700 chr1D 82.803 157 19 1 7391 7539 92377907 92377751 5.170000e-27 134.0
60 TraesCS3D01G241700 chr1D 81.132 159 22 2 7389 7539 99410934 99410776 4.030000e-23 121.0
61 TraesCS3D01G241700 chr1D 81.609 87 8 7 7628 7707 92377615 92377530 1.910000e-06 65.8
62 TraesCS3D01G241700 chr2A 94.118 102 4 2 7027 7127 36742420 36742320 3.970000e-33 154.0
63 TraesCS3D01G241700 chr2A 100.000 30 0 0 650 679 29830861 29830832 1.000000e-03 56.5
64 TraesCS3D01G241700 chr7A 75.221 339 54 14 7389 7701 719668736 719669070 5.170000e-27 134.0
65 TraesCS3D01G241700 chr7A 81.046 153 28 1 7388 7540 666970882 666970731 4.030000e-23 121.0
66 TraesCS3D01G241700 chr7A 97.059 34 1 0 7385 7418 232756197 232756164 3.200000e-04 58.4
67 TraesCS3D01G241700 chr6A 91.753 97 7 1 5744 5840 34179644 34179549 5.170000e-27 134.0
68 TraesCS3D01G241700 chr6A 89.524 105 7 4 5740 5842 34179544 34179646 6.690000e-26 130.0
69 TraesCS3D01G241700 chr6B 90.722 97 8 1 5744 5840 62403437 62403532 2.410000e-25 128.0
70 TraesCS3D01G241700 chrUn 85.714 112 8 6 7561 7669 341506870 341506764 2.420000e-20 111.0
71 TraesCS3D01G241700 chrUn 85.714 112 8 6 7561 7669 407765417 407765523 2.420000e-20 111.0
72 TraesCS3D01G241700 chr1B 93.750 48 2 1 7387 7434 390427060 390427106 4.110000e-08 71.3


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 TraesCS3D01G241700 chr3D 336532142 336540354 8212 False 15167.000000 15167 100.000000 1 8213 1 chr3D.!!$F1 8212
1 TraesCS3D01G241700 chr3A 453812843 453821716 8873 False 4104.000000 7347 96.283333 692 8190 3 chr3A.!!$F2 7498
2 TraesCS3D01G241700 chr3B 434393113 434394473 1360 False 958.400000 1840 88.471500 770 2084 2 chr3B.!!$F6 1314
3 TraesCS3D01G241700 chr3B 434398891 434405923 7032 False 785.555556 2475 91.148333 2082 8213 9 chr3B.!!$F7 6131
4 TraesCS3D01G241700 chr2D 623966052 623966701 649 True 815.000000 815 89.571000 4 643 1 chr2D.!!$R3 639
5 TraesCS3D01G241700 chr2D 641949165 641949743 578 False 366.000000 366 79.967000 6133 6676 1 chr2D.!!$F3 543
6 TraesCS3D01G241700 chr7B 34686770 34687398 628 False 630.000000 630 85.038000 1 642 1 chr7B.!!$F2 641
7 TraesCS3D01G241700 chr1A 29015280 29015929 649 True 324.000000 324 76.248000 4 646 1 chr1A.!!$R1 642
8 TraesCS3D01G241700 chr2B 522102622 522103274 652 False 305.000000 305 75.904000 4 641 1 chr2B.!!$F2 637

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
742 762 0.037605 GTGCCCCGGATAACTATCGG 60.038 60.000 0.73 0.00 33.52 4.18 F
745 765 0.903454 CCCCGGATAACTATCGGGCT 60.903 60.000 13.88 0.00 46.17 5.19 F
1016 1061 1.209019 AGCAATGCTACCACTCTCCTG 59.791 52.381 5.69 0.00 36.99 3.86 F
2084 2192 1.746787 TGCAGCAATGTGATGTCATCC 59.253 47.619 10.36 2.79 35.94 3.51 F
3245 3787 0.322975 AAAGACAGATGGCTGCTCGT 59.677 50.000 0.00 0.00 46.26 4.18 F
4211 4757 1.192428 AGGAGACACGGTATGGAACC 58.808 55.000 0.00 0.00 45.77 3.62 F
4447 4994 2.617308 GCATGTGTCTGGGATGAATGAG 59.383 50.000 0.00 0.00 0.00 2.90 F
4824 5457 2.738321 GCGGTCATGCTTTAAAATGGGG 60.738 50.000 1.08 0.00 0.00 4.96 F
6186 8996 2.175878 AATCTCAAGCAGACGCACTT 57.824 45.000 0.00 0.00 42.27 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 1994 3.447586 GCATGACACTAGGACTTCCAGTA 59.552 47.826 0.00 0.00 38.89 2.74 R
2387 2514 4.394920 TGTGATAAAAGCAAGATTCCCGTC 59.605 41.667 0.00 0.00 0.00 4.79 R
2969 3509 5.324409 ACAAAAGCTCATCACCCTGATAAA 58.676 37.500 0.00 0.00 34.28 1.40 R
4054 4600 0.400213 TGTGGTGAGCCCCAAACTAG 59.600 55.000 0.00 0.00 35.92 2.57 R
5008 5644 2.721274 CCAAACGAATGGTGCAATCA 57.279 45.000 0.00 0.00 35.65 2.57 R
5528 7864 1.137675 CCGGGTTTACTGGTAGCTACC 59.862 57.143 32.37 32.37 46.62 3.18 R
6180 8986 3.129852 TCAACAAAACAGTGAAGTGCG 57.870 42.857 0.00 0.00 0.00 5.34 R
6319 9134 3.708403 ACTCAAGGATGCTCACATTGA 57.292 42.857 0.00 0.00 36.35 2.57 R
8178 11155 1.407979 CAATGCAATCCAAGGGCTCTC 59.592 52.381 0.00 0.00 0.00 3.20 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
54 55 4.492160 GCTCCGATGGACGCGACA 62.492 66.667 15.93 12.47 41.07 4.35
76 77 6.648192 ACATGATGTTGAACCTTTCCAAAAA 58.352 32.000 0.00 0.00 0.00 1.94
83 84 3.055747 TGAACCTTTCCAAAAACCACACC 60.056 43.478 0.00 0.00 0.00 4.16
90 91 3.866651 TCCAAAAACCACACCATGTTTG 58.133 40.909 0.00 0.00 35.03 2.93
102 103 1.338011 CCATGTTTGCCAACCATCCAC 60.338 52.381 0.00 0.00 31.02 4.02
120 121 0.991920 ACGGACCACCATCCAAGATT 59.008 50.000 0.00 0.00 38.87 2.40
129 130 3.310774 CACCATCCAAGATTCGATCACAC 59.689 47.826 0.00 0.00 0.00 3.82
168 169 7.009174 ACAAAACTAGCAACAAAAACATTCTCG 59.991 33.333 0.00 0.00 0.00 4.04
214 215 4.778143 GATTGCCCCACGCCGAGT 62.778 66.667 0.00 0.00 36.24 4.18
245 246 5.147330 TCTCCAATAGTGTTGACGTGAAT 57.853 39.130 0.00 0.00 0.00 2.57
284 285 2.723586 TTCCCGATCAGTGCGTGCAA 62.724 55.000 0.00 0.00 0.00 4.08
310 311 3.436243 TCCTCCCTCTTCTCTTCTTCAC 58.564 50.000 0.00 0.00 0.00 3.18
396 397 6.293626 CCACTGTTTCTCTGTCCTTTGTATTG 60.294 42.308 0.00 0.00 0.00 1.90
420 421 1.224592 CTTACCTCCCATGGCGCTT 59.775 57.895 6.09 0.00 0.00 4.68
453 457 2.893398 GTCGCCCGACTCCTGATT 59.107 61.111 13.10 0.00 41.57 2.57
551 557 0.385751 GCGAGGATCTGGACAATCGA 59.614 55.000 0.00 0.00 32.13 3.59
554 560 2.099921 CGAGGATCTGGACAATCGAAGT 59.900 50.000 0.00 0.00 32.13 3.01
573 579 4.838152 GCAGGAAGCCGGCGATCA 62.838 66.667 28.65 0.00 34.74 2.92
587 593 1.207329 GCGATCACCAAACCCTAGACT 59.793 52.381 0.00 0.00 0.00 3.24
630 650 3.746940 CCACTCGAAACCCTAGGAAAAA 58.253 45.455 11.48 0.00 0.00 1.94
636 656 4.639755 TCGAAACCCTAGGAAAAACGTTTT 59.360 37.500 20.26 20.26 0.00 2.43
646 666 0.103390 AAAACGTTTTGGGGCTTCCG 59.897 50.000 24.68 0.00 38.76 4.30
647 667 1.038681 AAACGTTTTGGGGCTTCCGT 61.039 50.000 7.96 0.00 38.76 4.69
648 668 1.730451 AACGTTTTGGGGCTTCCGTG 61.730 55.000 0.00 0.00 38.76 4.94
649 669 2.914908 CGTTTTGGGGCTTCCGTGG 61.915 63.158 0.00 0.00 38.76 4.94
650 670 2.203567 TTTTGGGGCTTCCGTGGG 60.204 61.111 0.00 0.00 38.76 4.61
651 671 3.076217 TTTTGGGGCTTCCGTGGGT 62.076 57.895 0.00 0.00 38.76 4.51
652 672 2.591193 TTTTGGGGCTTCCGTGGGTT 62.591 55.000 0.00 0.00 38.76 4.11
653 673 3.801068 TTGGGGCTTCCGTGGGTTG 62.801 63.158 0.00 0.00 38.76 3.77
655 675 4.280019 GGGCTTCCGTGGGTTGGT 62.280 66.667 0.00 0.00 0.00 3.67
656 676 2.751688 GGCTTCCGTGGGTTGGTA 59.248 61.111 0.00 0.00 0.00 3.25
657 677 1.073548 GGCTTCCGTGGGTTGGTAA 59.926 57.895 0.00 0.00 0.00 2.85
658 678 0.537828 GGCTTCCGTGGGTTGGTAAA 60.538 55.000 0.00 0.00 0.00 2.01
659 679 0.879090 GCTTCCGTGGGTTGGTAAAG 59.121 55.000 0.00 0.00 0.00 1.85
660 680 1.816572 GCTTCCGTGGGTTGGTAAAGT 60.817 52.381 0.00 0.00 0.00 2.66
661 681 2.578786 CTTCCGTGGGTTGGTAAAGTT 58.421 47.619 0.00 0.00 0.00 2.66
662 682 1.970092 TCCGTGGGTTGGTAAAGTTG 58.030 50.000 0.00 0.00 0.00 3.16
663 683 0.312729 CCGTGGGTTGGTAAAGTTGC 59.687 55.000 0.00 0.00 0.00 4.17
664 684 1.025812 CGTGGGTTGGTAAAGTTGCA 58.974 50.000 0.00 0.00 0.00 4.08
665 685 1.405821 CGTGGGTTGGTAAAGTTGCAA 59.594 47.619 0.00 0.00 0.00 4.08
666 686 2.796735 CGTGGGTTGGTAAAGTTGCAAC 60.797 50.000 22.17 22.17 0.00 4.17
667 687 1.757699 TGGGTTGGTAAAGTTGCAACC 59.242 47.619 25.62 11.85 43.16 3.77
668 688 2.036387 GGGTTGGTAAAGTTGCAACCT 58.964 47.619 25.62 15.65 43.35 3.50
669 689 2.432874 GGGTTGGTAAAGTTGCAACCTT 59.567 45.455 25.62 21.11 43.35 3.50
670 690 3.453424 GGTTGGTAAAGTTGCAACCTTG 58.547 45.455 25.62 0.00 41.32 3.61
671 691 3.453424 GTTGGTAAAGTTGCAACCTTGG 58.547 45.455 25.62 0.00 34.23 3.61
672 692 2.741145 TGGTAAAGTTGCAACCTTGGT 58.259 42.857 25.62 4.04 34.23 3.67
673 693 2.428890 TGGTAAAGTTGCAACCTTGGTG 59.571 45.455 25.62 0.00 34.23 4.17
674 694 2.691011 GGTAAAGTTGCAACCTTGGTGA 59.309 45.455 25.62 1.42 0.00 4.02
675 695 3.320826 GGTAAAGTTGCAACCTTGGTGAT 59.679 43.478 25.62 1.63 0.00 3.06
676 696 3.457610 AAAGTTGCAACCTTGGTGATG 57.542 42.857 25.62 0.00 0.00 3.07
677 697 2.071778 AGTTGCAACCTTGGTGATGT 57.928 45.000 25.62 0.05 0.00 3.06
678 698 3.222173 AGTTGCAACCTTGGTGATGTA 57.778 42.857 25.62 0.00 0.00 2.29
679 699 3.561143 AGTTGCAACCTTGGTGATGTAA 58.439 40.909 25.62 0.00 0.00 2.41
680 700 3.317993 AGTTGCAACCTTGGTGATGTAAC 59.682 43.478 25.62 13.73 38.25 2.50
681 701 3.222173 TGCAACCTTGGTGATGTAACT 57.778 42.857 0.00 0.00 0.00 2.24
682 702 2.884012 TGCAACCTTGGTGATGTAACTG 59.116 45.455 0.00 0.00 0.00 3.16
683 703 2.884639 GCAACCTTGGTGATGTAACTGT 59.115 45.455 0.00 0.00 0.00 3.55
684 704 3.317993 GCAACCTTGGTGATGTAACTGTT 59.682 43.478 0.00 0.00 0.00 3.16
685 705 4.517453 GCAACCTTGGTGATGTAACTGTTA 59.483 41.667 0.00 0.00 0.00 2.41
686 706 5.183140 GCAACCTTGGTGATGTAACTGTTAT 59.817 40.000 3.23 0.00 0.00 1.89
687 707 6.373216 GCAACCTTGGTGATGTAACTGTTATA 59.627 38.462 3.23 1.22 0.00 0.98
688 708 7.625606 GCAACCTTGGTGATGTAACTGTTATAC 60.626 40.741 3.23 0.00 0.00 1.47
689 709 7.011499 ACCTTGGTGATGTAACTGTTATACA 57.989 36.000 3.23 1.01 37.64 2.29
707 727 2.516225 GCAGTTATCGGGCCCACC 60.516 66.667 24.92 3.61 0.00 4.61
728 748 0.389025 CCTTTTTCAGGTGTGTGCCC 59.611 55.000 0.00 0.00 37.99 5.36
742 762 0.037605 GTGCCCCGGATAACTATCGG 60.038 60.000 0.73 0.00 33.52 4.18
745 765 0.903454 CCCCGGATAACTATCGGGCT 60.903 60.000 13.88 0.00 46.17 5.19
749 769 2.415090 CCGGATAACTATCGGGCTAACG 60.415 54.545 0.00 0.00 43.31 3.18
766 786 2.821366 GGGTGCCAGCGAGTCATG 60.821 66.667 0.00 0.00 0.00 3.07
813 858 4.893424 TTTGACGAAAAGGAAGTTGAGG 57.107 40.909 0.00 0.00 0.00 3.86
896 941 2.046285 CCACATCCGCTCCAAACCC 61.046 63.158 0.00 0.00 0.00 4.11
897 942 2.046285 CACATCCGCTCCAAACCCC 61.046 63.158 0.00 0.00 0.00 4.95
898 943 2.440247 CATCCGCTCCAAACCCCC 60.440 66.667 0.00 0.00 0.00 5.40
899 944 2.938798 ATCCGCTCCAAACCCCCA 60.939 61.111 0.00 0.00 0.00 4.96
900 945 2.316586 ATCCGCTCCAAACCCCCAT 61.317 57.895 0.00 0.00 0.00 4.00
901 946 2.284515 ATCCGCTCCAAACCCCCATC 62.285 60.000 0.00 0.00 0.00 3.51
928 973 2.766828 CCCCACCACTAAACCAAAAACA 59.233 45.455 0.00 0.00 0.00 2.83
1016 1061 1.209019 AGCAATGCTACCACTCTCCTG 59.791 52.381 5.69 0.00 36.99 3.86
1083 1128 2.284112 CACAAGCCCAAGCCCCAT 60.284 61.111 0.00 0.00 41.25 4.00
1404 1449 8.606040 ATCACTTTATTTGTTGGTTCAAATGG 57.394 30.769 12.82 7.18 44.40 3.16
1440 1485 2.553602 CAATGCACACTGTAGCCAGAAA 59.446 45.455 0.00 0.00 41.50 2.52
1678 1723 4.574892 TGATTTCAGTAGGCGAAACATGA 58.425 39.130 0.00 0.00 35.31 3.07
1727 1772 4.658901 TCTCCCCAATCCACTAAGGTTATC 59.341 45.833 0.00 0.00 39.02 1.75
1948 1994 5.823861 AATTTATTTGTTTCTGCCCTGGT 57.176 34.783 0.00 0.00 0.00 4.00
2084 2192 1.746787 TGCAGCAATGTGATGTCATCC 59.253 47.619 10.36 2.79 35.94 3.51
2135 2244 9.383519 CATAGTGATGTAATACAAAACTCCTGT 57.616 33.333 12.64 0.00 32.41 4.00
2154 2263 6.818233 TCCTGTTTTAATGTTTTTACCCACC 58.182 36.000 0.00 0.00 0.00 4.61
2387 2514 5.904802 GCATTTAGTTTGCTTTCCTTTTCG 58.095 37.500 0.00 0.00 37.14 3.46
2969 3509 5.388599 AATCCTTCCGGGTCATTTATCTT 57.611 39.130 0.00 0.00 36.25 2.40
3010 3550 6.257849 GCTTTTGTCTGTCAATGGTATCGATA 59.742 38.462 0.00 0.00 35.84 2.92
3086 3626 8.961092 GGAAACTTTCGTTACAATTAAGGTTTC 58.039 33.333 12.30 12.30 31.86 2.78
3245 3787 0.322975 AAAGACAGATGGCTGCTCGT 59.677 50.000 0.00 0.00 46.26 4.18
3296 3838 8.632906 AAAGAGACAATGAGAATTCATCTGTT 57.367 30.769 8.44 3.03 43.20 3.16
3400 3942 4.929808 TCCTCTTGTCGTTTCTAAATCTGC 59.070 41.667 0.00 0.00 0.00 4.26
3530 4073 6.119144 AGAACATCGCGCAGTTTAAAATAT 57.881 33.333 8.75 0.00 0.00 1.28
3539 4082 4.097892 CGCAGTTTAAAATATTGCCTCCCT 59.902 41.667 0.00 0.00 0.00 4.20
3712 4255 2.704572 GTTACCTGTCTCTTGCAGCAT 58.295 47.619 0.00 0.00 32.93 3.79
4054 4600 8.495949 TCTTGAGTTATTGTGAATTTCTCGAAC 58.504 33.333 0.00 1.51 0.00 3.95
4062 4608 6.539649 TGTGAATTTCTCGAACTAGTTTGG 57.460 37.500 20.51 12.41 0.00 3.28
4211 4757 1.192428 AGGAGACACGGTATGGAACC 58.808 55.000 0.00 0.00 45.77 3.62
4447 4994 2.617308 GCATGTGTCTGGGATGAATGAG 59.383 50.000 0.00 0.00 0.00 2.90
4739 5370 6.538945 TCTTATGGGTTTCAAATTTAGCCC 57.461 37.500 6.04 6.04 36.73 5.19
4824 5457 2.738321 GCGGTCATGCTTTAAAATGGGG 60.738 50.000 1.08 0.00 0.00 4.96
4969 5605 8.954950 TTCCAAATTCTTGTATGCTTCAAAAA 57.045 26.923 0.00 0.00 0.00 1.94
5006 5642 4.473477 TTCGTTTGGTTTTGTTTCCCAT 57.527 36.364 0.00 0.00 0.00 4.00
5008 5644 5.793030 TCGTTTGGTTTTGTTTCCCATAT 57.207 34.783 0.00 0.00 0.00 1.78
5142 7203 6.088016 TGGAACTTTTGATGTCCATTTGAG 57.912 37.500 0.00 0.00 0.00 3.02
5198 7523 6.039047 CAGGAATTAAGTACAATGCATGAGCT 59.961 38.462 0.00 0.00 42.74 4.09
5345 7677 3.619419 TGTTACCATCACCATCACCATG 58.381 45.455 0.00 0.00 0.00 3.66
5528 7864 3.565482 ACCAGCCATTTACATAGCAATCG 59.435 43.478 0.00 0.00 0.00 3.34
5756 8398 6.293571 GCTTCTAGTTAGTACTTCCTCCGATC 60.294 46.154 0.00 0.00 35.78 3.69
5999 8805 8.311109 GGAACTTTGGTGGTGAAATATTTATGT 58.689 33.333 0.00 0.00 0.00 2.29
6180 8986 6.793492 AGTACAAAGAAATCTCAAGCAGAC 57.207 37.500 0.00 0.00 32.26 3.51
6186 8996 2.175878 AATCTCAAGCAGACGCACTT 57.824 45.000 0.00 0.00 42.27 3.16
6212 9022 5.048573 ACTGTTTTGTTGAACCGTGTAAGTT 60.049 36.000 0.00 0.00 0.00 2.66
6329 9144 7.764443 TCCTATACTAAACTTGTCAATGTGAGC 59.236 37.037 0.00 0.00 0.00 4.26
6462 9305 5.617252 CAAGTCCCCTAGTTAACTTGTTGA 58.383 41.667 14.49 7.45 42.20 3.18
6775 9647 6.327279 AGTTTGAACCACCTAAAATAGCAC 57.673 37.500 0.00 0.00 0.00 4.40
6829 9701 5.241949 AGGCTTATAGTATGTCCGTTCTCAG 59.758 44.000 0.00 0.00 0.00 3.35
7048 9922 1.586422 CATGCAATGTACTCCCTCCG 58.414 55.000 0.00 0.00 40.20 4.63
7050 9924 0.535335 TGCAATGTACTCCCTCCGTC 59.465 55.000 0.00 0.00 0.00 4.79
7051 9925 0.179081 GCAATGTACTCCCTCCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
7052 9926 0.464452 CAATGTACTCCCTCCGTCCC 59.536 60.000 0.00 0.00 0.00 4.46
7053 9927 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
7054 9928 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
7055 9929 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
7056 9930 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
7057 9931 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
7058 9932 3.140707 TGTACTCCCTCCGTCCCATAATA 59.859 47.826 0.00 0.00 0.00 0.98
7059 9933 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
7060 9934 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
7061 9935 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
7062 9936 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
7063 9937 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
7064 9938 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
7065 9939 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
7066 9940 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
7067 9941 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
7068 9942 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
7069 9943 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
7070 9944 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
7071 9945 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
7072 9946 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
7073 9947 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
7074 9948 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
7075 9949 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
7076 9950 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
7082 9956 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
7083 9957 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
7084 9958 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
7085 9959 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
7098 9972 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
7099 9973 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
7100 9974 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
7101 9975 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
7102 9976 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
7103 9977 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
7104 9978 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
7110 9984 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
7111 9985 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
7112 9986 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
7147 10021 2.622436 ACTGCTCGGCTGAATTTACTC 58.378 47.619 0.00 0.00 0.00 2.59
7414 10293 3.600694 TTGCCCGTGCGTTGCAAT 61.601 55.556 0.59 0.00 41.47 3.56
7446 10325 0.108138 ATTCTAGCCCGTGACAGCAC 60.108 55.000 0.00 0.00 41.67 4.40
7848 10736 2.289694 ACACTGCGAAGAAATACTGGCT 60.290 45.455 0.00 0.00 32.46 4.75
7864 10752 3.521126 ACTGGCTTGGTGTATGATTCTCT 59.479 43.478 0.00 0.00 0.00 3.10
8083 11060 0.389166 GAGGTGAGACCACAAGCTCG 60.389 60.000 0.00 0.00 44.93 5.03
8088 11065 1.344438 TGAGACCACAAGCTCGACATT 59.656 47.619 0.00 0.00 33.89 2.71
8129 11106 2.546373 GGCATCTGCAGAGATCAGAGTC 60.546 54.545 22.96 3.61 43.02 3.36
8147 11124 2.306805 AGTCAGCATGTCCTTGGATTCA 59.693 45.455 0.00 0.00 37.40 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.691976 CTCAAGATATGGGCACGGGTA 59.308 52.381 0.00 0.00 0.00 3.69
54 55 6.054941 GGTTTTTGGAAAGGTTCAACATCAT 58.945 36.000 0.00 0.00 0.00 2.45
76 77 0.463620 GTTGGCAAACATGGTGTGGT 59.536 50.000 0.00 0.00 36.24 4.16
83 84 1.669502 CGTGGATGGTTGGCAAACATG 60.670 52.381 33.71 16.33 38.10 3.21
90 91 2.750237 GGTCCGTGGATGGTTGGC 60.750 66.667 0.00 0.00 0.00 4.52
102 103 1.668419 GAATCTTGGATGGTGGTCCG 58.332 55.000 0.00 0.00 41.35 4.79
120 121 1.215382 CAAGCGGGAGTGTGATCGA 59.785 57.895 0.00 0.00 0.00 3.59
129 130 1.676006 AGTTTTGTGAACAAGCGGGAG 59.324 47.619 0.00 0.00 37.15 4.30
179 180 4.378459 GCAATCCAAAAGGACTGTACTTCG 60.378 45.833 5.59 0.57 0.00 3.79
245 246 5.214293 GGAAGGTACTCCATAGGAAGGTTA 58.786 45.833 0.00 0.00 38.49 2.85
284 285 1.693799 AGAGAAGAGGGAGGAGGAGT 58.306 55.000 0.00 0.00 0.00 3.85
310 311 4.261578 AGGCAAAACTTGTCATTGATGG 57.738 40.909 0.00 0.00 37.85 3.51
396 397 1.709994 CCATGGGAGGTAAGAGGGGC 61.710 65.000 2.85 0.00 0.00 5.80
420 421 0.247934 CGACGACGATGACGGAATCA 60.248 55.000 0.00 0.00 44.46 2.57
453 457 1.676678 CTCGCGGGAGAAGGGATCAA 61.677 60.000 24.08 0.00 43.27 2.57
551 557 2.269241 GCCGGCTTCCTGCTACTT 59.731 61.111 22.15 0.00 42.39 2.24
554 560 3.151958 GATCGCCGGCTTCCTGCTA 62.152 63.158 26.68 0.00 42.39 3.49
573 579 1.590147 CGCGAGTCTAGGGTTTGGT 59.410 57.895 0.00 0.00 0.00 3.67
630 650 2.190841 CACGGAAGCCCCAAAACGT 61.191 57.895 0.00 0.00 34.61 3.99
636 656 4.278513 CAACCCACGGAAGCCCCA 62.279 66.667 0.00 0.00 34.14 4.96
646 666 2.816689 GTTGCAACTTTACCAACCCAC 58.183 47.619 22.36 0.00 34.32 4.61
650 670 3.118920 ACCAAGGTTGCAACTTTACCAAC 60.119 43.478 27.64 9.58 38.42 3.77
651 671 3.100671 ACCAAGGTTGCAACTTTACCAA 58.899 40.909 27.64 0.00 34.32 3.67
652 672 2.428890 CACCAAGGTTGCAACTTTACCA 59.571 45.455 27.64 0.00 34.32 3.25
653 673 2.691011 TCACCAAGGTTGCAACTTTACC 59.309 45.455 27.64 12.95 0.00 2.85
654 674 4.202111 ACATCACCAAGGTTGCAACTTTAC 60.202 41.667 27.64 12.11 0.00 2.01
655 675 3.957497 ACATCACCAAGGTTGCAACTTTA 59.043 39.130 27.64 12.70 0.00 1.85
656 676 2.765699 ACATCACCAAGGTTGCAACTTT 59.234 40.909 27.64 23.93 0.00 2.66
657 677 2.387757 ACATCACCAAGGTTGCAACTT 58.612 42.857 27.64 19.16 0.00 2.66
658 678 2.071778 ACATCACCAAGGTTGCAACT 57.928 45.000 27.64 12.09 0.00 3.16
659 679 3.317993 AGTTACATCACCAAGGTTGCAAC 59.682 43.478 21.59 21.59 0.00 4.17
660 680 3.317711 CAGTTACATCACCAAGGTTGCAA 59.682 43.478 0.00 0.00 0.00 4.08
661 681 2.884012 CAGTTACATCACCAAGGTTGCA 59.116 45.455 0.00 0.00 0.00 4.08
662 682 2.884639 ACAGTTACATCACCAAGGTTGC 59.115 45.455 0.00 0.00 0.00 4.17
663 683 6.817765 ATAACAGTTACATCACCAAGGTTG 57.182 37.500 0.00 0.00 0.00 3.77
664 684 7.455058 TGTATAACAGTTACATCACCAAGGTT 58.545 34.615 0.00 0.00 0.00 3.50
665 685 7.011499 TGTATAACAGTTACATCACCAAGGT 57.989 36.000 0.00 0.00 0.00 3.50
666 686 7.539712 CTGTATAACAGTTACATCACCAAGG 57.460 40.000 0.00 0.00 41.19 3.61
681 701 3.493699 GGCCCGATAACTGCTGTATAACA 60.494 47.826 0.00 0.00 0.00 2.41
682 702 3.064931 GGCCCGATAACTGCTGTATAAC 58.935 50.000 0.00 0.00 0.00 1.89
683 703 2.038033 GGGCCCGATAACTGCTGTATAA 59.962 50.000 5.69 0.00 0.00 0.98
684 704 1.621814 GGGCCCGATAACTGCTGTATA 59.378 52.381 5.69 0.00 0.00 1.47
685 705 0.396811 GGGCCCGATAACTGCTGTAT 59.603 55.000 5.69 0.00 0.00 2.29
686 706 0.978667 TGGGCCCGATAACTGCTGTA 60.979 55.000 19.37 0.00 0.00 2.74
687 707 2.297895 TGGGCCCGATAACTGCTGT 61.298 57.895 19.37 0.00 0.00 4.40
688 708 1.819632 GTGGGCCCGATAACTGCTG 60.820 63.158 19.37 0.00 0.00 4.41
689 709 2.590092 GTGGGCCCGATAACTGCT 59.410 61.111 19.37 0.00 0.00 4.24
690 710 2.516225 GGTGGGCCCGATAACTGC 60.516 66.667 19.37 0.00 0.00 4.40
700 720 1.471829 CCTGAAAAAGGTGGTGGGCC 61.472 60.000 0.00 0.00 41.74 5.80
720 740 1.414919 GATAGTTATCCGGGGCACACA 59.585 52.381 0.00 0.00 0.00 3.72
728 748 2.415090 CGTTAGCCCGATAGTTATCCGG 60.415 54.545 0.00 0.00 35.19 5.14
745 765 3.291101 GACTCGCTGGCACCCGTTA 62.291 63.158 3.19 0.00 0.00 3.18
749 769 2.821366 CATGACTCGCTGGCACCC 60.821 66.667 0.00 0.00 35.90 4.61
795 815 3.121738 TCCCTCAACTTCCTTTTCGTC 57.878 47.619 0.00 0.00 0.00 4.20
898 943 4.060667 GTGGTGGGGGTGGGGATG 62.061 72.222 0.00 0.00 0.00 3.51
899 944 2.440196 TTAGTGGTGGGGGTGGGGAT 62.440 60.000 0.00 0.00 0.00 3.85
900 945 2.656269 TTTAGTGGTGGGGGTGGGGA 62.656 60.000 0.00 0.00 0.00 4.81
901 946 2.164279 TTTAGTGGTGGGGGTGGGG 61.164 63.158 0.00 0.00 0.00 4.96
1047 1092 3.480133 CTAGGGCTGGGGTTCGGG 61.480 72.222 0.00 0.00 0.00 5.14
1083 1128 1.372997 GAAGAGAAGCACGCACGGA 60.373 57.895 0.00 0.00 0.00 4.69
1135 1180 1.022903 AGGAGGGAGAAGGAGATGGT 58.977 55.000 0.00 0.00 0.00 3.55
1404 1449 3.855950 GTGCATTGAGACTTTATTGCAGC 59.144 43.478 0.00 0.00 40.41 5.25
1440 1485 1.629043 TAGAAGTGAGCGTTCTGGGT 58.371 50.000 0.00 0.00 35.78 4.51
1473 1518 7.964559 TGCATCAAATTAAAATTGAGAGACTCG 59.035 33.333 11.32 0.00 39.92 4.18
1678 1723 8.641541 ACAATAAACATCACTCCAAATTTGAGT 58.358 29.630 19.86 16.33 0.00 3.41
1727 1772 4.081406 TGGATCATGAAGGACAAAAGGTG 58.919 43.478 0.00 0.00 0.00 4.00
1948 1994 3.447586 GCATGACACTAGGACTTCCAGTA 59.552 47.826 0.00 0.00 38.89 2.74
2135 2244 5.068723 TCAGCGGTGGGTAAAAACATTAAAA 59.931 36.000 15.67 0.00 0.00 1.52
2154 2263 7.388712 CAAATAAAAGCAATCAAAGATCAGCG 58.611 34.615 0.00 0.00 0.00 5.18
2387 2514 4.394920 TGTGATAAAAGCAAGATTCCCGTC 59.605 41.667 0.00 0.00 0.00 4.79
2969 3509 5.324409 ACAAAAGCTCATCACCCTGATAAA 58.676 37.500 0.00 0.00 34.28 1.40
3010 3550 6.823689 ACGTCAAATGCAGATTTACCTCTTAT 59.176 34.615 0.00 0.00 30.20 1.73
3559 4102 5.300969 TGAGCAGAAACAATCAATAGTGC 57.699 39.130 0.00 0.00 0.00 4.40
3670 4213 6.144078 ACGTTAAAAGGACAAATCTTGCTT 57.856 33.333 0.00 0.00 0.00 3.91
3712 4255 6.491394 CACCTGAATTTTGTAGACGTTTCAA 58.509 36.000 0.00 0.00 0.00 2.69
3793 4336 9.364989 CGAGGGCATAATTTGAAAAGAAAAATA 57.635 29.630 0.00 0.00 0.00 1.40
4054 4600 0.400213 TGTGGTGAGCCCCAAACTAG 59.600 55.000 0.00 0.00 35.92 2.57
4365 4912 8.118600 ACTTATCCTTCATTTCAGAAAATCCCT 58.881 33.333 0.00 0.00 32.69 4.20
4447 4994 3.753272 TCAAAGCAATCCTAAGCTGACAC 59.247 43.478 0.00 0.00 41.70 3.67
4757 5388 3.684305 ACAACAAAACAAAGCCTTTCAGC 59.316 39.130 0.00 0.00 0.00 4.26
4944 5580 8.954950 TTTTTGAAGCATACAAGAATTTGGAA 57.045 26.923 0.00 0.00 38.66 3.53
4969 5605 4.335400 AACGAATGGTTTCAAATGGCTT 57.665 36.364 0.00 0.00 34.41 4.35
4987 5623 5.533482 TCATATGGGAAACAAAACCAAACG 58.467 37.500 2.13 0.00 37.89 3.60
5006 5642 4.368874 CCAAACGAATGGTGCAATCATA 57.631 40.909 4.49 0.00 35.65 2.15
5008 5644 2.721274 CCAAACGAATGGTGCAATCA 57.279 45.000 0.00 0.00 35.65 2.57
5142 7203 7.173390 ACTGTTTCATGGAAAGTAAGCTTCTAC 59.827 37.037 0.00 0.00 31.87 2.59
5198 7523 3.805066 TGTCCCAACCAAGATTCATGA 57.195 42.857 0.00 0.00 0.00 3.07
5290 7620 3.971150 TGTTAATGTTTTCAACTGCGGG 58.029 40.909 0.00 0.00 0.00 6.13
5386 7719 3.052036 CAACAAAACCACATGCTGCTAC 58.948 45.455 0.00 0.00 0.00 3.58
5431 7765 3.173668 TCCCTTGTATGCACGATACAC 57.826 47.619 0.00 0.00 45.49 2.90
5528 7864 1.137675 CCGGGTTTACTGGTAGCTACC 59.862 57.143 32.37 32.37 46.62 3.18
5756 8398 7.259290 ACTAAACCAGCGACAATTAATATGG 57.741 36.000 0.00 0.00 0.00 2.74
5793 8496 4.271533 TGTCGCTGGTTTAGTACAAAGTTG 59.728 41.667 0.00 0.00 0.00 3.16
5972 8778 6.739331 AAATATTTCACCACCAAAGTTCCA 57.261 33.333 0.00 0.00 0.00 3.53
6180 8986 3.129852 TCAACAAAACAGTGAAGTGCG 57.870 42.857 0.00 0.00 0.00 5.34
6212 9022 8.532186 AATATGTGGGTAAATGCTGTATTCAA 57.468 30.769 0.00 0.00 0.00 2.69
6319 9134 3.708403 ACTCAAGGATGCTCACATTGA 57.292 42.857 0.00 0.00 36.35 2.57
6329 9144 6.320672 AGGAAATAATCTGCAACTCAAGGATG 59.679 38.462 0.00 0.00 0.00 3.51
6462 9305 8.052748 TGGCATGACCTACTAAATTTCAGTAAT 58.947 33.333 0.00 0.00 40.22 1.89
6829 9701 9.045223 TGCAATATCATACACTTGAGTTACATC 57.955 33.333 0.00 0.00 0.00 3.06
7042 9916 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
7043 9917 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
7044 9918 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
7045 9919 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
7046 9920 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
7047 9921 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
7048 9922 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
7050 9924 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
7056 9930 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
7057 9931 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
7058 9932 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
7059 9933 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
7060 9934 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
7061 9935 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
7062 9936 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
7075 9949 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
7076 9950 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
7077 9951 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
7084 9958 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
7085 9959 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
7086 9960 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
7087 9961 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
7088 9962 9.716507 CTGTCCCATAATATAAGAACGTTTTTG 57.283 33.333 13.87 0.00 0.00 2.44
7089 9963 9.675464 TCTGTCCCATAATATAAGAACGTTTTT 57.325 29.630 9.22 9.22 0.00 1.94
7090 9964 9.326413 CTCTGTCCCATAATATAAGAACGTTTT 57.674 33.333 0.46 0.00 0.00 2.43
7091 9965 7.931948 CCTCTGTCCCATAATATAAGAACGTTT 59.068 37.037 0.46 0.00 0.00 3.60
7092 9966 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
7093 9967 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
7094 9968 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
7095 9969 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
7096 9970 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
7097 9971 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
7098 9972 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
7099 9973 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
7100 9974 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
7101 9975 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
7102 9976 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
7103 9977 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
7104 9978 4.348020 AACTACTCCCTCTGTCCCATAA 57.652 45.455 0.00 0.00 0.00 1.90
7105 9979 4.348020 AAACTACTCCCTCTGTCCCATA 57.652 45.455 0.00 0.00 0.00 2.74
7106 9980 2.950990 AACTACTCCCTCTGTCCCAT 57.049 50.000 0.00 0.00 0.00 4.00
7107 9981 2.715763 AAACTACTCCCTCTGTCCCA 57.284 50.000 0.00 0.00 0.00 4.37
7108 9982 3.447944 CAGTAAACTACTCCCTCTGTCCC 59.552 52.174 0.00 0.00 36.76 4.46
7109 9983 3.119065 GCAGTAAACTACTCCCTCTGTCC 60.119 52.174 0.00 0.00 36.76 4.02
7110 9984 3.764972 AGCAGTAAACTACTCCCTCTGTC 59.235 47.826 0.00 0.00 36.76 3.51
7111 9985 3.764972 GAGCAGTAAACTACTCCCTCTGT 59.235 47.826 0.00 0.00 36.76 3.41
7112 9986 3.181495 CGAGCAGTAAACTACTCCCTCTG 60.181 52.174 5.04 0.00 36.76 3.35
7113 9987 3.018149 CGAGCAGTAAACTACTCCCTCT 58.982 50.000 5.04 0.00 36.76 3.69
7114 9988 2.099427 CCGAGCAGTAAACTACTCCCTC 59.901 54.545 5.04 1.32 36.76 4.30
7115 9989 2.100989 CCGAGCAGTAAACTACTCCCT 58.899 52.381 5.04 0.00 36.76 4.20
7116 9990 1.471153 GCCGAGCAGTAAACTACTCCC 60.471 57.143 5.04 0.00 36.76 4.30
7117 9991 1.477295 AGCCGAGCAGTAAACTACTCC 59.523 52.381 5.04 0.00 36.76 3.85
7118 9992 2.163815 TCAGCCGAGCAGTAAACTACTC 59.836 50.000 0.91 0.91 36.76 2.59
7119 9993 2.168496 TCAGCCGAGCAGTAAACTACT 58.832 47.619 0.00 0.00 40.28 2.57
7147 10021 4.094590 GGCTTCATTGAGATCTGTCACAAG 59.905 45.833 0.00 0.00 38.13 3.16
7346 10225 5.299028 TGAGAAATAGTGCAAGCTGTCAAAA 59.701 36.000 0.00 0.00 0.00 2.44
7414 10293 4.039973 CGGGCTAGAATGTTTATACTCCCA 59.960 45.833 0.00 0.00 0.00 4.37
7446 10325 4.917998 AGCGCATCAATGTAATAGTAGACG 59.082 41.667 11.47 0.00 0.00 4.18
7539 10420 9.495572 AAAACATGTTTTCTTTGGTAAGTCAAA 57.504 25.926 27.01 0.00 38.27 2.69
7619 10500 6.183360 CCATCTCTGATTTTTCTCCCATTGAC 60.183 42.308 0.00 0.00 0.00 3.18
7620 10501 5.889853 CCATCTCTGATTTTTCTCCCATTGA 59.110 40.000 0.00 0.00 0.00 2.57
7686 10571 2.486982 TCTCTACTTCGTCCAACCTTCG 59.513 50.000 0.00 0.00 0.00 3.79
7751 10639 9.987272 CAGTGTATGAATCTCTATGATTTACCA 57.013 33.333 0.00 0.00 44.70 3.25
7848 10736 5.030147 ACCCAGTAGAGAATCATACACCAA 58.970 41.667 0.00 0.00 37.82 3.67
7864 10752 5.050126 TGGAAACACATAAACACCCAGTA 57.950 39.130 0.00 0.00 33.40 2.74
8129 11106 2.163010 GTGTGAATCCAAGGACATGCTG 59.837 50.000 0.00 0.00 0.00 4.41
8147 11124 4.681978 GAGCTGCGGAACCGGTGT 62.682 66.667 8.52 0.00 40.19 4.16
8178 11155 1.407979 CAATGCAATCCAAGGGCTCTC 59.592 52.381 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.