Multiple sequence alignment - TraesCS3A01G100300

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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 TraesCS3A01G100300 chr3A 100.000 5809 0 0 1 5809 65348784 65342976 0.000000e+00 10728.0
1 TraesCS3A01G100300 chr3A 91.781 73 6 0 3050 3122 65355868 65355796 1.030000e-17 102.0
2 TraesCS3A01G100300 chr3A 100.000 28 0 0 2893 2920 65355909 65355882 1.100000e-02 52.8
3 TraesCS3A01G100300 chr3B 94.854 2332 90 12 3313 5635 84731487 84729177 0.000000e+00 3615.0
4 TraesCS3A01G100300 chr3B 92.852 1385 62 13 1542 2920 84733459 84732106 0.000000e+00 1975.0
5 TraesCS3A01G100300 chr3B 92.082 783 22 12 752 1508 84734224 84733456 0.000000e+00 1066.0
6 TraesCS3A01G100300 chr3B 89.019 683 65 5 1 678 84734951 84734274 0.000000e+00 837.0
7 TraesCS3A01G100300 chr3B 88.704 301 14 6 3024 3312 84732107 84731815 3.330000e-92 350.0
8 TraesCS3A01G100300 chr3D 95.817 2008 66 11 3024 5017 54367887 54365884 0.000000e+00 3227.0
9 TraesCS3A01G100300 chr3D 95.300 1085 39 4 1840 2920 54368962 54367886 0.000000e+00 1711.0
10 TraesCS3A01G100300 chr3D 92.324 951 44 11 824 1762 54370187 54369254 0.000000e+00 1325.0
11 TraesCS3A01G100300 chr3D 91.286 700 19 5 5083 5779 54365884 54365224 0.000000e+00 917.0
12 TraesCS3A01G100300 chr3D 90.149 335 32 1 207 541 54370914 54370581 8.940000e-118 435.0
13 TraesCS3A01G100300 chr3D 96.639 119 2 1 2910 3026 230765762 230765644 4.590000e-46 196.0
14 TraesCS3A01G100300 chr3D 82.791 215 29 7 1 210 54371150 54370939 9.940000e-43 185.0
15 TraesCS3A01G100300 chr7A 99.107 112 0 1 2914 3025 242621653 242621543 3.550000e-47 200.0
16 TraesCS3A01G100300 chr2A 97.414 116 3 0 2916 3031 685627219 685627334 1.280000e-46 198.0
17 TraesCS3A01G100300 chr4A 97.391 115 3 0 2919 3033 655433839 655433725 4.590000e-46 196.0
18 TraesCS3A01G100300 chr7B 96.581 117 4 0 2916 3032 327689820 327689704 1.650000e-45 195.0
19 TraesCS3A01G100300 chr4B 93.798 129 5 3 2899 3027 646113947 646113822 2.140000e-44 191.0
20 TraesCS3A01G100300 chr2B 94.400 125 5 2 2903 3025 691451450 691451326 2.140000e-44 191.0
21 TraesCS3A01G100300 chr2B 90.400 125 10 2 2902 3026 17431107 17430985 4.660000e-36 163.0
22 TraesCS3A01G100300 chr5B 97.297 111 3 0 2919 3029 473290745 473290855 7.680000e-44 189.0
23 TraesCS3A01G100300 chr5A 93.077 130 6 2 2919 3045 436986806 436986935 2.760000e-43 187.0


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 TraesCS3A01G100300 chr3A 65342976 65348784 5808 True 10728.0 10728 100.000000 1 5809 1 chr3A.!!$R1 5808
1 TraesCS3A01G100300 chr3B 84729177 84734951 5774 True 1568.6 3615 91.502200 1 5635 5 chr3B.!!$R1 5634
2 TraesCS3A01G100300 chr3D 54365224 54371150 5926 True 1300.0 3227 91.277833 1 5779 6 chr3D.!!$R2 5778

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
838 1034 0.036671 GCCAAACTACGTAGTGGGCT 60.037 55.000 38.70 22.11 45.86 5.19 F
1536 1757 0.250338 CGTGGGGATTTAGGCTAGGC 60.250 60.000 8.55 8.55 0.00 3.93 F
2207 2668 0.325110 CTGGAGGAGCAAGAGGAGGA 60.325 60.000 0.00 0.00 0.00 3.71 F
2315 2782 0.907704 AAGGTGACGGTGGCTATGGA 60.908 55.000 0.00 0.00 0.00 3.41 F
3026 3493 0.038744 TTCCGAACGGAGGGAGTAGT 59.961 55.000 15.34 0.00 46.06 2.73 F
3028 3495 0.455005 CCGAACGGAGGGAGTAGTTC 59.545 60.000 7.53 0.00 39.46 3.01 F
3029 3496 1.461559 CGAACGGAGGGAGTAGTTCT 58.538 55.000 5.78 0.00 40.36 3.01 F
3503 4318 1.754107 GCACCCCCATTGCTTTTGT 59.246 52.632 0.00 0.00 37.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2650 0.341258 ATCCTCCTCTTGCTCCTCCA 59.659 55.000 0.00 0.00 0.00 3.86 R
3007 3474 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30 R
3009 3476 0.455005 GAACTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30 R
3479 4294 1.686800 GCAATGGGGGTGCCATCTT 60.687 57.895 0.00 0.00 35.91 2.40 R
4458 5280 0.385029 CTCCTCCATCTCTGCGTCTG 59.615 60.000 0.00 0.00 0.00 3.51 R
4611 5433 4.641094 CAGACAACCTACCTTACGATCTCT 59.359 45.833 0.00 0.00 0.00 3.10 R
4678 5500 4.946772 TCACTTCTGACAAACAAACATCCA 59.053 37.500 0.00 0.00 0.00 3.41 R
5387 6212 5.278907 CCATAAGTTGCTCAAAACATCACCA 60.279 40.000 0.00 0.00 32.21 4.17 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
34 35 3.708403 TCTTCATGTGAGCTTGGTGAT 57.292 42.857 0.00 0.00 0.00 3.06
63 65 2.940410 ACTTCGACACGTTTGTTCCAAT 59.060 40.909 0.00 0.00 35.47 3.16
106 108 3.049912 TCATAACACGCGCTATGATCAC 58.950 45.455 17.40 0.00 31.17 3.06
120 123 6.311200 CGCTATGATCACATATTTTCATCGGA 59.689 38.462 0.00 0.00 38.17 4.55
122 125 9.317936 GCTATGATCACATATTTTCATCGGATA 57.682 33.333 0.00 0.00 38.17 2.59
142 145 3.632080 TGGGGTGGTTCGTGCGAT 61.632 61.111 0.00 0.00 0.00 4.58
157 160 5.918082 TCGTGCGATTTTTCGAAATCTTTA 58.082 33.333 12.12 0.00 37.10 1.85
247 281 7.411486 TTCTTCACTAATGTTTTGGTGGAAA 57.589 32.000 2.97 0.00 42.71 3.13
267 301 6.830324 TGGAAAGCAGATATGCTAAAAGTGAT 59.170 34.615 16.50 0.00 45.54 3.06
298 332 1.235724 CCGACTTCAAAGAACCCCAC 58.764 55.000 0.00 0.00 0.00 4.61
306 340 3.207778 TCAAAGAACCCCACGTAACTTG 58.792 45.455 0.00 0.00 0.00 3.16
324 358 9.314321 CGTAACTTGTAGTCATGGATCTTTATT 57.686 33.333 0.00 0.00 0.00 1.40
378 412 6.053005 TCCCTAACATTCACTAAATAAGCCG 58.947 40.000 0.00 0.00 0.00 5.52
432 466 4.161565 AGACCCGATATGAAGTTGCACTAA 59.838 41.667 0.00 0.00 0.00 2.24
471 505 4.217754 TGCCGTGTAAGTGAAAAATGTC 57.782 40.909 0.00 0.00 0.00 3.06
472 506 3.223157 GCCGTGTAAGTGAAAAATGTCG 58.777 45.455 0.00 0.00 0.00 4.35
476 510 5.494618 CGTGTAAGTGAAAAATGTCGTTCA 58.505 37.500 0.00 0.00 0.00 3.18
480 514 4.900635 AGTGAAAAATGTCGTTCAGCTT 57.099 36.364 0.00 0.00 34.52 3.74
483 517 4.672413 GTGAAAAATGTCGTTCAGCTTCAG 59.328 41.667 0.00 0.00 34.52 3.02
489 523 6.371809 AATGTCGTTCAGCTTCAGTAAAAA 57.628 33.333 0.00 0.00 0.00 1.94
491 525 4.034742 TGTCGTTCAGCTTCAGTAAAAACC 59.965 41.667 0.00 0.00 0.00 3.27
492 526 4.034742 GTCGTTCAGCTTCAGTAAAAACCA 59.965 41.667 0.00 0.00 0.00 3.67
493 527 4.034742 TCGTTCAGCTTCAGTAAAAACCAC 59.965 41.667 0.00 0.00 0.00 4.16
494 528 4.201871 CGTTCAGCTTCAGTAAAAACCACA 60.202 41.667 0.00 0.00 0.00 4.17
495 529 5.505654 CGTTCAGCTTCAGTAAAAACCACAT 60.506 40.000 0.00 0.00 0.00 3.21
574 635 3.274095 AGAGAAATGCTAAGGCTCACC 57.726 47.619 0.00 0.00 39.59 4.02
597 658 4.182339 TCACGGTTGCTATATTGCGTTAA 58.818 39.130 4.70 0.00 35.36 2.01
706 881 7.441890 TTTTTGAGAAGACAGTAACACACAA 57.558 32.000 0.00 0.00 0.00 3.33
707 882 7.624360 TTTTGAGAAGACAGTAACACACAAT 57.376 32.000 0.00 0.00 0.00 2.71
708 883 7.624360 TTTGAGAAGACAGTAACACACAATT 57.376 32.000 0.00 0.00 0.00 2.32
709 884 7.624360 TTGAGAAGACAGTAACACACAATTT 57.376 32.000 0.00 0.00 0.00 1.82
710 885 7.624360 TGAGAAGACAGTAACACACAATTTT 57.376 32.000 0.00 0.00 0.00 1.82
711 886 8.050778 TGAGAAGACAGTAACACACAATTTTT 57.949 30.769 0.00 0.00 0.00 1.94
734 909 9.862371 TTTTTCTACACAAATAAACACACACAT 57.138 25.926 0.00 0.00 0.00 3.21
735 910 9.862371 TTTTCTACACAAATAAACACACACATT 57.138 25.926 0.00 0.00 0.00 2.71
738 913 9.862371 TCTACACAAATAAACACACACATTTTT 57.138 25.926 0.00 0.00 0.00 1.94
784 959 6.482308 ACAAATAGATTGGACGGTTATGTAGC 59.518 38.462 0.00 0.00 43.66 3.58
811 992 5.395486 GCTTCACACGTCAAAACATCTAAAC 59.605 40.000 0.00 0.00 0.00 2.01
838 1034 0.036671 GCCAAACTACGTAGTGGGCT 60.037 55.000 38.70 22.11 45.86 5.19
889 1085 4.717629 CGGAGTCGGTCAGCGCAA 62.718 66.667 11.47 0.00 0.00 4.85
890 1086 3.112709 GGAGTCGGTCAGCGCAAC 61.113 66.667 11.47 7.37 0.00 4.17
891 1087 3.112709 GAGTCGGTCAGCGCAACC 61.113 66.667 19.05 19.05 0.00 3.77
940 1141 4.256090 GGCCCATGTTCGCGATGC 62.256 66.667 10.88 6.97 0.00 3.91
944 1145 1.368345 CCCATGTTCGCGATGCTTCA 61.368 55.000 10.88 5.29 0.00 3.02
1303 1508 1.695989 GGTGGAGGATATGGAGGTGGT 60.696 57.143 0.00 0.00 0.00 4.16
1351 1556 4.202030 AGAGGGGGTGGTGGTGGT 62.202 66.667 0.00 0.00 0.00 4.16
1517 1738 2.135933 CCGTGGTCTTCTGAACTTGTC 58.864 52.381 0.00 0.00 0.00 3.18
1518 1739 1.787155 CGTGGTCTTCTGAACTTGTCG 59.213 52.381 0.00 0.00 0.00 4.35
1523 1744 1.070134 TCTTCTGAACTTGTCGTGGGG 59.930 52.381 0.00 0.00 0.00 4.96
1533 1754 1.868713 TGTCGTGGGGATTTAGGCTA 58.131 50.000 0.00 0.00 0.00 3.93
1536 1757 0.250338 CGTGGGGATTTAGGCTAGGC 60.250 60.000 8.55 8.55 0.00 3.93
1699 1922 6.205464 CGATCCTATTCCTGTGTGCAATTTAT 59.795 38.462 0.00 0.00 0.00 1.40
1704 1927 8.849168 CCTATTCCTGTGTGCAATTTATATTCA 58.151 33.333 0.00 0.00 0.00 2.57
1737 1960 5.817816 GTGCTGGGCTATATGTTGATATACC 59.182 44.000 0.00 0.00 0.00 2.73
1741 1964 5.487131 TGGGCTATATGTTGATATACCAGCA 59.513 40.000 0.00 0.00 30.88 4.41
1762 1985 6.155475 GCATATTTGCCCTGGTTATTTACA 57.845 37.500 0.00 0.00 43.38 2.41
1763 1986 6.758254 GCATATTTGCCCTGGTTATTTACAT 58.242 36.000 0.00 0.00 43.38 2.29
1764 1987 7.216494 GCATATTTGCCCTGGTTATTTACATT 58.784 34.615 0.00 0.00 43.38 2.71
1765 1988 7.384932 GCATATTTGCCCTGGTTATTTACATTC 59.615 37.037 0.00 0.00 43.38 2.67
1766 1989 4.974368 TTGCCCTGGTTATTTACATTCG 57.026 40.909 0.00 0.00 0.00 3.34
1767 1990 4.223556 TGCCCTGGTTATTTACATTCGA 57.776 40.909 0.00 0.00 0.00 3.71
1769 1992 5.010933 TGCCCTGGTTATTTACATTCGAAA 58.989 37.500 0.00 0.00 0.00 3.46
1770 1993 5.477291 TGCCCTGGTTATTTACATTCGAAAA 59.523 36.000 0.00 0.00 0.00 2.29
1771 1994 6.153680 TGCCCTGGTTATTTACATTCGAAAAT 59.846 34.615 0.00 0.00 0.00 1.82
1772 1995 7.339721 TGCCCTGGTTATTTACATTCGAAAATA 59.660 33.333 0.00 0.00 0.00 1.40
1773 1996 8.357402 GCCCTGGTTATTTACATTCGAAAATAT 58.643 33.333 0.00 0.00 30.01 1.28
1786 2009 9.071276 ACATTCGAAAATATTGATGCTATTCCT 57.929 29.630 0.00 0.00 0.00 3.36
1787 2010 9.338291 CATTCGAAAATATTGATGCTATTCCTG 57.662 33.333 0.00 0.00 0.00 3.86
1788 2011 8.450578 TTCGAAAATATTGATGCTATTCCTGT 57.549 30.769 0.00 0.00 0.00 4.00
1789 2012 9.554395 TTCGAAAATATTGATGCTATTCCTGTA 57.446 29.630 0.00 0.00 0.00 2.74
1790 2013 9.208022 TCGAAAATATTGATGCTATTCCTGTAG 57.792 33.333 0.00 0.00 0.00 2.74
1856 2315 6.440436 ACGGTTTTATGTGTTACCAATGTTC 58.560 36.000 0.00 0.00 0.00 3.18
1877 2336 6.489700 TGTTCTGCTCTTATTGGAAACATTGA 59.510 34.615 0.00 0.00 42.32 2.57
1881 2340 5.716228 TGCTCTTATTGGAAACATTGATGGT 59.284 36.000 0.00 0.00 42.32 3.55
1909 2370 6.431198 AGTTTGTAAACACTACCAGTTGTG 57.569 37.500 10.23 10.23 41.30 3.33
1979 2440 2.042686 TGAACTCTTGTTGCAGCTGT 57.957 45.000 16.64 0.00 36.39 4.40
2101 2562 0.838987 GGTGGAGGTGGAGGGTACAA 60.839 60.000 0.00 0.00 0.00 2.41
2189 2650 2.347490 GGTCGTGATGGTGGTGCT 59.653 61.111 0.00 0.00 0.00 4.40
2192 2653 2.213513 TCGTGATGGTGGTGCTGGA 61.214 57.895 0.00 0.00 0.00 3.86
2207 2668 0.325110 CTGGAGGAGCAAGAGGAGGA 60.325 60.000 0.00 0.00 0.00 3.71
2210 2671 2.180973 TGGAGGAGCAAGAGGAGGATAT 59.819 50.000 0.00 0.00 0.00 1.63
2225 2686 4.223032 GGAGGATATAATCGTGATGGTGGT 59.777 45.833 0.00 0.00 0.00 4.16
2315 2782 0.907704 AAGGTGACGGTGGCTATGGA 60.908 55.000 0.00 0.00 0.00 3.41
2615 3082 2.846206 TGCTCCACCTTCTTATCATGGT 59.154 45.455 0.00 0.00 0.00 3.55
2744 3211 1.067295 ACATCTCAAACCTGCCTCCA 58.933 50.000 0.00 0.00 0.00 3.86
2856 3323 2.438392 TCCTAGAGATCTCCGTGCTGTA 59.562 50.000 19.30 2.49 0.00 2.74
2886 3353 8.325421 TGTGCGTCCTCTAAAAACATATTTTA 57.675 30.769 0.00 0.00 37.01 1.52
2926 3393 9.614792 AATTTGAACTGTATGTATTACTCCCTC 57.385 33.333 0.00 0.00 0.00 4.30
2927 3394 6.726490 TGAACTGTATGTATTACTCCCTCC 57.274 41.667 0.00 0.00 0.00 4.30
2928 3395 5.301045 TGAACTGTATGTATTACTCCCTCCG 59.699 44.000 0.00 0.00 0.00 4.63
2930 3397 5.206587 ACTGTATGTATTACTCCCTCCGTT 58.793 41.667 0.00 0.00 0.00 4.44
2932 3399 4.276678 TGTATGTATTACTCCCTCCGTTCG 59.723 45.833 0.00 0.00 0.00 3.95
2933 3400 2.026641 TGTATTACTCCCTCCGTTCGG 58.973 52.381 4.74 4.74 0.00 4.30
2934 3401 2.301346 GTATTACTCCCTCCGTTCGGA 58.699 52.381 13.34 13.34 0.00 4.55
2935 3402 1.856629 ATTACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.04 33.41 4.30
2936 3403 1.856629 TTACTCCCTCCGTTCGGAAT 58.143 50.000 14.79 2.09 33.41 3.01
2937 3404 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2938 3405 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2939 3406 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2940 3407 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2941 3408 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2942 3409 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2943 3410 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2944 3411 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2945 3412 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2946 3413 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2947 3414 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2948 3415 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2949 3416 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2950 3417 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2951 3418 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2952 3419 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
2953 3420 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
2954 3421 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
2955 3422 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
2956 3423 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
2957 3424 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
2958 3425 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
2959 3426 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
2960 3427 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
2961 3428 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
2962 3429 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
2963 3430 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
2964 3431 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
2965 3432 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
2966 3433 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
2967 3434 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
2968 3435 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
2969 3436 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
2970 3437 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
2971 3438 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
2972 3439 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
2998 3465 6.603237 TGTCTAGATACATCCATTTTTGCG 57.397 37.500 0.00 0.00 0.00 4.85
2999 3466 6.345298 TGTCTAGATACATCCATTTTTGCGA 58.655 36.000 0.00 0.00 0.00 5.10
3000 3467 6.257849 TGTCTAGATACATCCATTTTTGCGAC 59.742 38.462 0.00 0.00 0.00 5.19
3001 3468 6.257849 GTCTAGATACATCCATTTTTGCGACA 59.742 38.462 0.00 0.00 0.00 4.35
3002 3469 5.895636 AGATACATCCATTTTTGCGACAA 57.104 34.783 0.00 0.00 0.00 3.18
3003 3470 5.883661 AGATACATCCATTTTTGCGACAAG 58.116 37.500 0.00 0.00 0.00 3.16
3004 3471 5.415701 AGATACATCCATTTTTGCGACAAGT 59.584 36.000 0.00 0.00 0.00 3.16
3005 3472 6.597672 AGATACATCCATTTTTGCGACAAGTA 59.402 34.615 0.00 0.00 0.00 2.24
3006 3473 5.446143 ACATCCATTTTTGCGACAAGTAA 57.554 34.783 0.00 0.00 0.00 2.24
3007 3474 6.024552 ACATCCATTTTTGCGACAAGTAAT 57.975 33.333 0.00 0.00 0.00 1.89
3008 3475 6.454795 ACATCCATTTTTGCGACAAGTAATT 58.545 32.000 0.00 0.00 0.00 1.40
3009 3476 6.586082 ACATCCATTTTTGCGACAAGTAATTC 59.414 34.615 0.00 0.00 0.00 2.17
3010 3477 5.465935 TCCATTTTTGCGACAAGTAATTCC 58.534 37.500 0.00 0.00 0.00 3.01
3011 3478 4.323336 CCATTTTTGCGACAAGTAATTCCG 59.677 41.667 0.00 0.00 0.00 4.30
3012 3479 4.815040 TTTTTGCGACAAGTAATTCCGA 57.185 36.364 0.00 0.00 0.00 4.55
3013 3480 4.815040 TTTTGCGACAAGTAATTCCGAA 57.185 36.364 0.00 0.00 0.00 4.30
3014 3481 3.799137 TTGCGACAAGTAATTCCGAAC 57.201 42.857 0.00 0.00 0.00 3.95
3015 3482 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3016 3483 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3017 3484 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3018 3485 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3019 3486 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3020 3487 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3021 3488 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3022 3489 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3023 3490 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3024 3491 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3025 3492 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
3026 3493 0.038744 TTCCGAACGGAGGGAGTAGT 59.961 55.000 15.34 0.00 46.06 2.73
3027 3494 0.038744 TCCGAACGGAGGGAGTAGTT 59.961 55.000 12.04 0.00 39.76 2.24
3028 3495 0.455005 CCGAACGGAGGGAGTAGTTC 59.545 60.000 7.53 0.00 39.46 3.01
3029 3496 1.461559 CGAACGGAGGGAGTAGTTCT 58.538 55.000 5.78 0.00 40.36 3.01
3030 3497 1.817447 CGAACGGAGGGAGTAGTTCTT 59.183 52.381 5.78 0.00 40.36 2.52
3031 3498 2.230750 CGAACGGAGGGAGTAGTTCTTT 59.769 50.000 5.78 0.00 40.36 2.52
3032 3499 3.441572 CGAACGGAGGGAGTAGTTCTTTA 59.558 47.826 5.78 0.00 40.36 1.85
3033 3500 4.097589 CGAACGGAGGGAGTAGTTCTTTAT 59.902 45.833 5.78 0.00 40.36 1.40
3034 3501 5.297776 CGAACGGAGGGAGTAGTTCTTTATA 59.702 44.000 5.78 0.00 40.36 0.98
3035 3502 6.016443 CGAACGGAGGGAGTAGTTCTTTATAT 60.016 42.308 5.78 0.00 40.36 0.86
3036 3503 7.469732 CGAACGGAGGGAGTAGTTCTTTATATT 60.470 40.741 5.78 0.00 40.36 1.28
3037 3504 7.052142 ACGGAGGGAGTAGTTCTTTATATTG 57.948 40.000 0.00 0.00 0.00 1.90
3038 3505 5.927115 CGGAGGGAGTAGTTCTTTATATTGC 59.073 44.000 0.00 0.00 0.00 3.56
3039 3506 6.231951 GGAGGGAGTAGTTCTTTATATTGCC 58.768 44.000 0.00 0.00 0.00 4.52
3040 3507 6.043358 GGAGGGAGTAGTTCTTTATATTGCCT 59.957 42.308 0.00 0.00 33.15 4.75
3041 3508 6.831976 AGGGAGTAGTTCTTTATATTGCCTG 58.168 40.000 0.00 0.00 30.03 4.85
3042 3509 6.615726 AGGGAGTAGTTCTTTATATTGCCTGA 59.384 38.462 0.00 0.00 30.03 3.86
3048 3515 7.651027 AGTTCTTTATATTGCCTGAAATGCT 57.349 32.000 0.00 0.00 0.00 3.79
3171 3650 7.554118 AGTTCATATTAAGTGTGTAAGCTGCAT 59.446 33.333 1.02 0.00 0.00 3.96
3223 3702 2.440147 CTGCATGGTTGGACCCCA 59.560 61.111 0.00 0.00 37.50 4.96
3351 4165 3.259123 TCAGCTTGACTCTGCTCACATAA 59.741 43.478 0.00 0.00 37.44 1.90
3354 4168 5.814188 CAGCTTGACTCTGCTCACATAATTA 59.186 40.000 0.00 0.00 37.44 1.40
3475 4290 4.701956 AACATATCTTTGCCCAAGAACG 57.298 40.909 0.00 0.00 45.06 3.95
3479 4294 3.192954 CTTTGCCCAAGAACGCGCA 62.193 57.895 5.73 0.00 33.80 6.09
3503 4318 1.754107 GCACCCCCATTGCTTTTGT 59.246 52.632 0.00 0.00 37.00 2.83
3596 4411 9.170584 GTTCTTTCAATACTTGCAACTACTTTC 57.829 33.333 0.00 0.00 0.00 2.62
3806 4622 9.409312 TGCATCACATTTTTCTATTTAACACTG 57.591 29.630 0.00 0.00 0.00 3.66
3833 4649 7.501892 TGTGCTTTCCACTTCATAATGCATATA 59.498 33.333 0.00 0.00 44.92 0.86
3921 4740 1.892474 CCTAGAGCTCCTACATCTGGC 59.108 57.143 10.93 0.00 0.00 4.85
3944 4763 4.576463 CCATGGGTAAGTACATCTTGCTTC 59.424 45.833 2.85 0.00 38.50 3.86
3945 4764 4.901197 TGGGTAAGTACATCTTGCTTCA 57.099 40.909 0.00 0.00 38.50 3.02
3950 4771 8.710239 TGGGTAAGTACATCTTGCTTCATTATA 58.290 33.333 0.00 0.00 38.50 0.98
4044 4865 9.374838 GTTTGATATCTCAATTTGCATTTTCCT 57.625 29.630 3.98 0.00 40.95 3.36
4290 5112 4.699735 CCAAGTACAGTTGACCAATATGCA 59.300 41.667 0.00 0.00 0.00 3.96
4333 5155 8.557592 CTGAGCCTTTAAATCAGCATATATCA 57.442 34.615 4.75 1.17 34.55 2.15
4458 5280 4.564110 GGTGGCTATGGCGGGGAC 62.564 72.222 0.00 0.00 39.81 4.46
4611 5433 6.246163 TCTCTCTGGACTTGTACTCATACAA 58.754 40.000 0.00 0.36 46.76 2.41
4642 5464 2.441750 AGGTAGGTTGTCTGCTTTTCCA 59.558 45.455 0.00 0.00 0.00 3.53
4678 5500 4.497291 TTGTCTTACTCCAGTGTTGGTT 57.503 40.909 0.00 0.00 45.26 3.67
4695 5517 4.383850 TGGTTGGATGTTTGTTTGTCAG 57.616 40.909 0.00 0.00 0.00 3.51
4791 5613 2.967362 TGTTATTACAGGTGAGTGCCG 58.033 47.619 0.00 0.00 0.00 5.69
4793 5615 3.007074 TGTTATTACAGGTGAGTGCCGAA 59.993 43.478 0.00 0.00 0.00 4.30
5016 5838 5.237815 AGCGATGTGTTTCTGTGAATCTTA 58.762 37.500 0.00 0.00 0.00 2.10
5017 5839 5.349817 AGCGATGTGTTTCTGTGAATCTTAG 59.650 40.000 0.00 0.00 0.00 2.18
5018 5840 5.348724 GCGATGTGTTTCTGTGAATCTTAGA 59.651 40.000 0.00 0.00 0.00 2.10
5019 5841 6.036517 GCGATGTGTTTCTGTGAATCTTAGAT 59.963 38.462 0.00 0.00 0.00 1.98
5020 5842 7.397194 CGATGTGTTTCTGTGAATCTTAGATG 58.603 38.462 0.00 0.00 0.00 2.90
5021 5843 7.063898 CGATGTGTTTCTGTGAATCTTAGATGT 59.936 37.037 0.00 0.00 0.00 3.06
5022 5844 9.371136 GATGTGTTTCTGTGAATCTTAGATGTA 57.629 33.333 0.00 0.00 0.00 2.29
5023 5845 9.896645 ATGTGTTTCTGTGAATCTTAGATGTAT 57.103 29.630 0.00 0.00 0.00 2.29
5024 5846 9.371136 TGTGTTTCTGTGAATCTTAGATGTATC 57.629 33.333 0.00 0.00 0.00 2.24
5057 5879 7.243479 TTCGTAGACTTGCACCTCAGTGATT 62.243 44.000 0.00 0.00 41.59 2.57
5455 6280 8.951243 ACTTATTTCTTCAGAAGAATTGTAGCC 58.049 33.333 23.54 0.00 46.15 3.93
5457 6282 7.765695 ATTTCTTCAGAAGAATTGTAGCCAA 57.234 32.000 23.54 8.23 46.15 4.52
5471 6296 9.120538 GAATTGTAGCCAATAGAAGGTCAAATA 57.879 33.333 0.00 0.00 40.42 1.40
5497 6322 7.610305 ACGATTTATGTGTTACCAAGAGGATTT 59.390 33.333 0.00 0.00 38.69 2.17
5535 6360 7.450074 TCAGTTTATGTTGGTACTCTCATTGT 58.550 34.615 0.00 0.00 0.00 2.71
5581 6408 0.799534 GCGTGCGTCTACGTTACCAT 60.800 55.000 0.00 0.00 45.36 3.55
5703 6530 5.730802 CCACAACGTACGTGCAAAATTATAG 59.269 40.000 23.57 3.17 32.85 1.31
5753 6580 7.214467 TGATTTTGTGAGAATACAACCTTCC 57.786 36.000 0.00 0.00 40.04 3.46
5769 6596 1.488705 TTCCAGGGCATCTCCAACGT 61.489 55.000 0.00 0.00 36.21 3.99
5775 6602 1.745489 GCATCTCCAACGTGGACCC 60.745 63.158 0.00 0.00 42.67 4.46
5779 6606 1.149627 CTCCAACGTGGACCCCAAA 59.850 57.895 0.00 0.00 42.67 3.28
5780 6607 0.466555 CTCCAACGTGGACCCCAAAA 60.467 55.000 0.00 0.00 42.67 2.44
5781 6608 0.752376 TCCAACGTGGACCCCAAAAC 60.752 55.000 0.00 0.00 42.67 2.43
5782 6609 1.737201 CAACGTGGACCCCAAAACC 59.263 57.895 0.00 0.00 34.18 3.27
5783 6610 1.038130 CAACGTGGACCCCAAAACCA 61.038 55.000 0.00 0.00 34.18 3.67
5785 6612 3.865071 GTGGACCCCAAAACCACC 58.135 61.111 0.00 0.00 45.53 4.61
5786 6613 2.196229 TGGACCCCAAAACCACCG 59.804 61.111 0.00 0.00 0.00 4.94
5787 6614 2.599281 GGACCCCAAAACCACCGG 60.599 66.667 0.00 0.00 0.00 5.28
5788 6615 3.299977 GACCCCAAAACCACCGGC 61.300 66.667 0.00 0.00 0.00 6.13
5789 6616 4.144727 ACCCCAAAACCACCGGCA 62.145 61.111 0.00 0.00 0.00 5.69
5790 6617 2.840102 CCCCAAAACCACCGGCAA 60.840 61.111 0.00 0.00 0.00 4.52
5791 6618 2.419620 CCCAAAACCACCGGCAAC 59.580 61.111 0.00 0.00 0.00 4.17
5792 6619 2.419620 CCAAAACCACCGGCAACC 59.580 61.111 0.00 0.00 0.00 3.77
5794 6621 2.440613 AAAACCACCGGCAACCGT 60.441 55.556 0.00 0.00 46.80 4.83
5795 6622 2.776913 AAAACCACCGGCAACCGTG 61.777 57.895 0.00 3.80 46.80 4.94
5796 6623 3.999297 AAACCACCGGCAACCGTGT 62.999 57.895 0.00 0.00 46.80 4.49
5798 6625 4.920112 CCACCGGCAACCGTGTGA 62.920 66.667 21.40 0.00 46.80 3.58
5799 6626 2.668212 CACCGGCAACCGTGTGAT 60.668 61.111 17.30 0.00 46.80 3.06
5800 6627 2.112297 ACCGGCAACCGTGTGATT 59.888 55.556 0.00 0.00 46.80 2.57
5801 6628 1.527380 ACCGGCAACCGTGTGATTT 60.527 52.632 0.00 0.00 46.80 2.17
5802 6629 1.104577 ACCGGCAACCGTGTGATTTT 61.105 50.000 0.00 0.00 46.80 1.82
5803 6630 0.875728 CCGGCAACCGTGTGATTTTA 59.124 50.000 5.17 0.00 46.80 1.52
5804 6631 1.400500 CCGGCAACCGTGTGATTTTAC 60.400 52.381 5.17 0.00 46.80 2.01
5805 6632 1.264557 CGGCAACCGTGTGATTTTACA 59.735 47.619 0.00 0.00 42.73 2.41
5806 6633 2.095466 CGGCAACCGTGTGATTTTACAT 60.095 45.455 0.00 0.00 42.73 2.29
5807 6634 3.125487 CGGCAACCGTGTGATTTTACATA 59.875 43.478 0.00 0.00 42.73 2.29
5808 6635 4.658071 GGCAACCGTGTGATTTTACATAG 58.342 43.478 0.00 0.00 32.43 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.430042 ACTTCATCACCAAGCTCACAT 57.570 42.857 0.00 0.00 0.00 3.21
21 22 3.433615 GTGTACTTCATCACCAAGCTCAC 59.566 47.826 0.00 0.00 0.00 3.51
34 35 6.356695 AACAAACGTGTCGAAGTGTACTTCA 61.357 40.000 20.92 8.55 43.86 3.02
63 65 3.075283 ACCAAATACACATCCCTTGACCA 59.925 43.478 0.00 0.00 0.00 4.02
106 108 4.943705 CCCCACCTATCCGATGAAAATATG 59.056 45.833 0.00 0.00 0.00 1.78
120 123 1.988015 CACGAACCACCCCACCTAT 59.012 57.895 0.00 0.00 0.00 2.57
122 125 4.265056 GCACGAACCACCCCACCT 62.265 66.667 0.00 0.00 0.00 4.00
157 160 5.011023 GCCTGCATAAAACCATATTAGCCTT 59.989 40.000 0.00 0.00 0.00 4.35
258 292 6.592607 GTCGGTGTCTCCAATTATCACTTTTA 59.407 38.462 0.00 0.00 35.57 1.52
267 301 4.610605 TTGAAGTCGGTGTCTCCAATTA 57.389 40.909 0.00 0.00 35.57 1.40
298 332 8.873215 ATAAAGATCCATGACTACAAGTTACG 57.127 34.615 0.00 0.00 0.00 3.18
306 340 8.649973 AACGAAGAATAAAGATCCATGACTAC 57.350 34.615 0.00 0.00 0.00 2.73
324 358 7.279090 TGTCTAGATTGAACAAACAAACGAAGA 59.721 33.333 0.00 0.00 33.44 2.87
378 412 3.632189 GACACACCTGTCAAAGATTTGC 58.368 45.455 0.30 0.00 45.57 3.68
432 466 4.098349 ACGGCATGCATTAATGAACAAGAT 59.902 37.500 21.36 0.00 0.00 2.40
471 505 4.201871 TGTGGTTTTTACTGAAGCTGAACG 60.202 41.667 0.00 0.00 0.00 3.95
472 506 5.243426 TGTGGTTTTTACTGAAGCTGAAC 57.757 39.130 0.00 0.00 0.00 3.18
476 510 8.421002 ACAAATTATGTGGTTTTTACTGAAGCT 58.579 29.630 0.00 0.00 41.93 3.74
574 635 2.201732 ACGCAATATAGCAACCGTGAG 58.798 47.619 0.00 0.00 0.00 3.51
708 883 9.862371 ATGTGTGTGTTTATTTGTGTAGAAAAA 57.138 25.926 0.00 0.00 0.00 1.94
709 884 9.862371 AATGTGTGTGTTTATTTGTGTAGAAAA 57.138 25.926 0.00 0.00 0.00 2.29
710 885 9.862371 AAATGTGTGTGTTTATTTGTGTAGAAA 57.138 25.926 0.00 0.00 0.00 2.52
711 886 9.862371 AAAATGTGTGTGTTTATTTGTGTAGAA 57.138 25.926 0.00 0.00 0.00 2.10
735 910 8.791675 TGTGTGTTTATATGATGCTCAGAAAAA 58.208 29.630 0.00 0.00 0.00 1.94
738 913 7.920160 TTGTGTGTTTATATGATGCTCAGAA 57.080 32.000 0.00 0.00 0.00 3.02
739 914 7.920160 TTTGTGTGTTTATATGATGCTCAGA 57.080 32.000 0.00 0.00 0.00 3.27
740 915 9.874215 CTATTTGTGTGTTTATATGATGCTCAG 57.126 33.333 0.00 0.00 0.00 3.35
741 916 9.612066 TCTATTTGTGTGTTTATATGATGCTCA 57.388 29.630 0.00 0.00 0.00 4.26
748 923 9.650371 CGTCCAATCTATTTGTGTGTTTATATG 57.350 33.333 0.00 0.00 33.15 1.78
749 924 8.836413 CCGTCCAATCTATTTGTGTGTTTATAT 58.164 33.333 0.00 0.00 33.15 0.86
750 925 7.825270 ACCGTCCAATCTATTTGTGTGTTTATA 59.175 33.333 0.00 0.00 33.15 0.98
784 959 0.316689 GTTTTGACGTGTGAAGCCCG 60.317 55.000 0.00 0.00 0.00 6.13
838 1034 1.059584 TGACTGGGGAGTTGCCTGAA 61.060 55.000 0.00 0.00 36.66 3.02
848 1044 1.194781 GCCTTCTGACTGACTGGGGA 61.195 60.000 0.00 0.00 0.00 4.81
889 1085 6.053005 TGTAAAGAGTTCTGTTTGATTCGGT 58.947 36.000 5.41 0.00 0.00 4.69
890 1086 6.539649 TGTAAAGAGTTCTGTTTGATTCGG 57.460 37.500 5.41 0.00 0.00 4.30
940 1141 1.135315 CGCGATTGCAAGGGTGAAG 59.865 57.895 0.00 0.00 42.97 3.02
944 1145 3.118454 CGACGCGATTGCAAGGGT 61.118 61.111 15.93 6.70 42.97 4.34
1083 1285 1.490693 TAGTCGTCGGATCCGTACGC 61.491 60.000 34.32 29.79 40.15 4.42
1249 1451 2.895424 GCCATATCCTCCCCCACCG 61.895 68.421 0.00 0.00 0.00 4.94
1255 1457 2.348998 CTGCCGCCATATCCTCCC 59.651 66.667 0.00 0.00 0.00 4.30
1517 1738 0.250338 GCCTAGCCTAAATCCCCACG 60.250 60.000 0.00 0.00 0.00 4.94
1518 1739 0.843984 TGCCTAGCCTAAATCCCCAC 59.156 55.000 0.00 0.00 0.00 4.61
1523 1744 5.186198 TGAAAGTTCTGCCTAGCCTAAATC 58.814 41.667 0.00 0.00 0.00 2.17
1533 1754 7.961326 ATAAAATACCATGAAAGTTCTGCCT 57.039 32.000 0.00 0.00 0.00 4.75
1576 1797 1.577328 AAATTCCAGTCACGGCGCTG 61.577 55.000 16.39 16.39 0.00 5.18
1618 1839 6.674278 GCATCTAGCAGAAGTTGAAACTAAGC 60.674 42.308 0.00 1.85 44.79 3.09
1619 1840 6.770076 GCATCTAGCAGAAGTTGAAACTAAG 58.230 40.000 0.00 0.00 44.79 2.18
1678 1901 8.849168 TGAATATAAATTGCACACAGGAATAGG 58.151 33.333 0.00 0.00 37.28 2.57
1709 1932 5.567037 TCAACATATAGCCCAGCACTATT 57.433 39.130 0.00 0.00 32.63 1.73
1712 1935 5.768980 ATATCAACATATAGCCCAGCACT 57.231 39.130 0.00 0.00 0.00 4.40
1713 1936 5.817816 GGTATATCAACATATAGCCCAGCAC 59.182 44.000 0.00 0.00 38.95 4.40
1741 1964 7.504238 TCGAATGTAAATAACCAGGGCAAATAT 59.496 33.333 0.00 0.00 0.00 1.28
1762 1985 9.071276 ACAGGAATAGCATCAATATTTTCGAAT 57.929 29.630 0.00 0.00 0.00 3.34
1763 1986 8.450578 ACAGGAATAGCATCAATATTTTCGAA 57.549 30.769 0.00 0.00 0.00 3.71
1764 1987 9.208022 CTACAGGAATAGCATCAATATTTTCGA 57.792 33.333 0.00 0.00 0.00 3.71
1765 1988 8.993121 ACTACAGGAATAGCATCAATATTTTCG 58.007 33.333 0.00 0.00 0.00 3.46
1777 2000 9.337396 CCAACAAAATATACTACAGGAATAGCA 57.663 33.333 0.00 0.00 0.00 3.49
1778 2001 9.338622 ACCAACAAAATATACTACAGGAATAGC 57.661 33.333 0.00 0.00 0.00 2.97
1781 2004 9.528489 ACAACCAACAAAATATACTACAGGAAT 57.472 29.630 0.00 0.00 0.00 3.01
1782 2005 8.927675 ACAACCAACAAAATATACTACAGGAA 57.072 30.769 0.00 0.00 0.00 3.36
1783 2006 8.927675 AACAACCAACAAAATATACTACAGGA 57.072 30.769 0.00 0.00 0.00 3.86
1787 2010 9.830294 GGTGTAACAACCAACAAAATATACTAC 57.170 33.333 0.00 0.00 39.98 2.73
1844 2303 6.374333 TCCAATAAGAGCAGAACATTGGTAAC 59.626 38.462 10.52 0.00 43.93 2.50
1856 2315 6.127535 ACCATCAATGTTTCCAATAAGAGCAG 60.128 38.462 0.00 0.00 0.00 4.24
1877 2336 7.015877 TGGTAGTGTTTACAAACTAGAGACCAT 59.984 37.037 0.00 0.00 39.59 3.55
1881 2340 7.592885 ACTGGTAGTGTTTACAAACTAGAGA 57.407 36.000 13.38 0.00 39.59 3.10
1909 2370 6.529220 AGAAGATAATACCCTCAGCATCAAC 58.471 40.000 0.00 0.00 0.00 3.18
1912 2373 7.124901 TCCATAGAAGATAATACCCTCAGCATC 59.875 40.741 0.00 0.00 0.00 3.91
1979 2440 5.241506 CCTCCTTGCAAAGTTCACATTAAGA 59.758 40.000 0.00 0.00 44.25 2.10
2101 2562 0.911769 ATGATCACCACCACCACGAT 59.088 50.000 0.00 0.00 0.00 3.73
2189 2650 0.341258 ATCCTCCTCTTGCTCCTCCA 59.659 55.000 0.00 0.00 0.00 3.86
2192 2653 4.709397 CGATTATATCCTCCTCTTGCTCCT 59.291 45.833 0.00 0.00 0.00 3.69
2207 2668 4.381612 CCGCTACCACCATCACGATTATAT 60.382 45.833 0.00 0.00 0.00 0.86
2210 2671 1.067974 CCGCTACCACCATCACGATTA 59.932 52.381 0.00 0.00 0.00 1.75
2225 2686 1.003112 ATCAAAACCACGGCCGCTA 60.003 52.632 28.58 1.52 0.00 4.26
2315 2782 2.309504 GCCTTTAGGGGGAGCCTGT 61.310 63.158 0.00 0.00 35.18 4.00
2350 2817 0.965866 TGCGTAGTCACCTGGAGGAG 60.966 60.000 0.00 0.00 38.94 3.69
2604 3071 0.758734 CCGCCTCCACCATGATAAGA 59.241 55.000 0.00 0.00 0.00 2.10
2744 3211 3.805108 GCAGTTCCTCAACAGTCACATCT 60.805 47.826 0.00 0.00 34.60 2.90
2843 3310 2.360483 CACAGATCTACAGCACGGAGAT 59.640 50.000 0.00 0.64 32.57 2.75
2846 3313 0.173481 GCACAGATCTACAGCACGGA 59.827 55.000 0.00 0.00 0.00 4.69
2847 3314 1.142185 CGCACAGATCTACAGCACGG 61.142 60.000 12.06 0.00 0.00 4.94
2849 3316 1.272781 GACGCACAGATCTACAGCAC 58.727 55.000 12.06 3.94 0.00 4.40
2856 3323 4.246458 GTTTTTAGAGGACGCACAGATCT 58.754 43.478 0.00 0.00 0.00 2.75
2920 3387 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2922 3389 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2924 3391 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2926 3393 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2927 3394 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
2928 3395 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2930 3397 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2932 3399 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
2933 3400 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
2934 3401 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
2935 3402 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
2936 3403 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
2937 3404 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2938 3405 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2939 3406 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2940 3407 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2941 3408 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
2942 3409 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
2943 3410 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
2944 3411 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
2945 3412 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
2946 3413 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
2972 3439 8.939929 CGCAAAAATGGATGTATCTAGACATAT 58.060 33.333 0.00 0.00 40.18 1.78
2973 3440 8.147704 TCGCAAAAATGGATGTATCTAGACATA 58.852 33.333 0.00 0.00 40.18 2.29
2974 3441 6.992123 TCGCAAAAATGGATGTATCTAGACAT 59.008 34.615 0.00 0.00 42.82 3.06
2975 3442 6.257849 GTCGCAAAAATGGATGTATCTAGACA 59.742 38.462 0.00 0.00 0.00 3.41
2976 3443 6.257849 TGTCGCAAAAATGGATGTATCTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
2977 3444 6.345298 TGTCGCAAAAATGGATGTATCTAGA 58.655 36.000 0.00 0.00 0.00 2.43
2978 3445 6.603237 TGTCGCAAAAATGGATGTATCTAG 57.397 37.500 0.00 0.00 0.00 2.43
2979 3446 6.597672 ACTTGTCGCAAAAATGGATGTATCTA 59.402 34.615 0.00 0.00 0.00 1.98
2980 3447 5.415701 ACTTGTCGCAAAAATGGATGTATCT 59.584 36.000 0.00 0.00 0.00 1.98
2981 3448 5.640732 ACTTGTCGCAAAAATGGATGTATC 58.359 37.500 0.00 0.00 0.00 2.24
2982 3449 5.643379 ACTTGTCGCAAAAATGGATGTAT 57.357 34.783 0.00 0.00 0.00 2.29
2983 3450 6.561737 TTACTTGTCGCAAAAATGGATGTA 57.438 33.333 0.00 0.00 0.00 2.29
2984 3451 5.446143 TTACTTGTCGCAAAAATGGATGT 57.554 34.783 0.00 0.00 0.00 3.06
2985 3452 6.034898 GGAATTACTTGTCGCAAAAATGGATG 59.965 38.462 0.00 0.00 0.00 3.51
2986 3453 6.099341 GGAATTACTTGTCGCAAAAATGGAT 58.901 36.000 0.00 0.00 0.00 3.41
2987 3454 5.465935 GGAATTACTTGTCGCAAAAATGGA 58.534 37.500 0.00 0.00 0.00 3.41
2988 3455 4.323336 CGGAATTACTTGTCGCAAAAATGG 59.677 41.667 0.00 0.00 0.00 3.16
2989 3456 5.150683 TCGGAATTACTTGTCGCAAAAATG 58.849 37.500 0.00 0.00 0.00 2.32
2990 3457 5.365403 TCGGAATTACTTGTCGCAAAAAT 57.635 34.783 0.00 0.00 0.00 1.82
2991 3458 4.815040 TCGGAATTACTTGTCGCAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
2992 3459 4.529446 GTTCGGAATTACTTGTCGCAAAA 58.471 39.130 0.00 0.00 0.00 2.44
2993 3460 3.363182 CGTTCGGAATTACTTGTCGCAAA 60.363 43.478 0.00 0.00 0.00 3.68
2994 3461 2.156117 CGTTCGGAATTACTTGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
2995 3462 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2996 3463 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
2997 3464 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2998 3465 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2999 3466 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3000 3467 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3001 3468 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3002 3469 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3003 3470 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3004 3471 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3005 3472 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3006 3473 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
3007 3474 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
3008 3475 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
3009 3476 0.455005 GAACTACTCCCTCCGTTCGG 59.545 60.000 4.74 4.74 0.00 4.30
3010 3477 1.461559 AGAACTACTCCCTCCGTTCG 58.538 55.000 0.00 0.00 40.36 3.95
3011 3478 3.957591 AAAGAACTACTCCCTCCGTTC 57.042 47.619 0.00 0.00 36.81 3.95
3012 3479 7.498443 CAATATAAAGAACTACTCCCTCCGTT 58.502 38.462 0.00 0.00 0.00 4.44
3013 3480 6.462628 GCAATATAAAGAACTACTCCCTCCGT 60.463 42.308 0.00 0.00 0.00 4.69
3014 3481 5.927115 GCAATATAAAGAACTACTCCCTCCG 59.073 44.000 0.00 0.00 0.00 4.63
3015 3482 6.043358 AGGCAATATAAAGAACTACTCCCTCC 59.957 42.308 0.00 0.00 0.00 4.30
3016 3483 6.931840 CAGGCAATATAAAGAACTACTCCCTC 59.068 42.308 0.00 0.00 0.00 4.30
3017 3484 6.615726 TCAGGCAATATAAAGAACTACTCCCT 59.384 38.462 0.00 0.00 0.00 4.20
3018 3485 6.827727 TCAGGCAATATAAAGAACTACTCCC 58.172 40.000 0.00 0.00 0.00 4.30
3019 3486 8.732746 TTTCAGGCAATATAAAGAACTACTCC 57.267 34.615 0.00 0.00 0.00 3.85
3021 3488 8.624776 GCATTTCAGGCAATATAAAGAACTACT 58.375 33.333 0.00 0.00 0.00 2.57
3022 3489 8.624776 AGCATTTCAGGCAATATAAAGAACTAC 58.375 33.333 0.00 0.00 0.00 2.73
3023 3490 8.752005 AGCATTTCAGGCAATATAAAGAACTA 57.248 30.769 0.00 0.00 0.00 2.24
3024 3491 7.651027 AGCATTTCAGGCAATATAAAGAACT 57.349 32.000 0.00 0.00 0.00 3.01
3025 3492 7.223387 CCAAGCATTTCAGGCAATATAAAGAAC 59.777 37.037 0.00 0.00 0.00 3.01
3026 3493 7.093377 ACCAAGCATTTCAGGCAATATAAAGAA 60.093 33.333 0.00 0.00 0.00 2.52
3027 3494 6.380846 ACCAAGCATTTCAGGCAATATAAAGA 59.619 34.615 0.00 0.00 0.00 2.52
3028 3495 6.576185 ACCAAGCATTTCAGGCAATATAAAG 58.424 36.000 0.00 0.00 0.00 1.85
3029 3496 6.543430 ACCAAGCATTTCAGGCAATATAAA 57.457 33.333 0.00 0.00 0.00 1.40
3030 3497 7.287466 ACATACCAAGCATTTCAGGCAATATAA 59.713 33.333 0.00 0.00 0.00 0.98
3031 3498 6.777091 ACATACCAAGCATTTCAGGCAATATA 59.223 34.615 0.00 0.00 0.00 0.86
3032 3499 5.599656 ACATACCAAGCATTTCAGGCAATAT 59.400 36.000 0.00 0.00 0.00 1.28
3033 3500 4.955450 ACATACCAAGCATTTCAGGCAATA 59.045 37.500 0.00 0.00 0.00 1.90
3034 3501 3.770933 ACATACCAAGCATTTCAGGCAAT 59.229 39.130 0.00 0.00 0.00 3.56
3035 3502 3.056678 CACATACCAAGCATTTCAGGCAA 60.057 43.478 0.00 0.00 0.00 4.52
3036 3503 2.492881 CACATACCAAGCATTTCAGGCA 59.507 45.455 0.00 0.00 0.00 4.75
3037 3504 2.493278 ACACATACCAAGCATTTCAGGC 59.507 45.455 0.00 0.00 0.00 4.85
3038 3505 4.380867 GGAACACATACCAAGCATTTCAGG 60.381 45.833 0.00 0.00 0.00 3.86
3039 3506 4.460382 AGGAACACATACCAAGCATTTCAG 59.540 41.667 0.00 0.00 0.00 3.02
3040 3507 4.406456 AGGAACACATACCAAGCATTTCA 58.594 39.130 0.00 0.00 0.00 2.69
3041 3508 4.702131 AGAGGAACACATACCAAGCATTTC 59.298 41.667 0.00 0.00 0.00 2.17
3042 3509 4.666512 AGAGGAACACATACCAAGCATTT 58.333 39.130 0.00 0.00 0.00 2.32
3259 3746 2.970609 CACACGTAAACTTCGCATTTGG 59.029 45.455 0.00 0.00 0.00 3.28
3354 4168 9.660544 AGAAAATATTGGCCTATTTTGGAGTAT 57.339 29.630 21.33 2.57 39.95 2.12
3379 4194 9.784531 ACATATATTGAGGTAACAGGAATCAAG 57.215 33.333 0.00 0.00 41.41 3.02
3479 4294 1.686800 GCAATGGGGGTGCCATCTT 60.687 57.895 0.00 0.00 35.91 2.40
3596 4411 4.335416 TGCTTGATCCTTCCAACCTTTAG 58.665 43.478 0.00 0.00 0.00 1.85
3739 4555 7.039882 CACTAAACATACCGTTGTAGAATCCT 58.960 38.462 0.00 0.00 38.07 3.24
3806 4622 4.168760 GCATTATGAAGTGGAAAGCACAC 58.831 43.478 0.00 0.00 39.10 3.82
3833 4649 8.324306 TCATGTCATAATCTGAAAAGGAAGAGT 58.676 33.333 0.00 0.00 35.07 3.24
3921 4740 4.156455 AGCAAGATGTACTTACCCATGG 57.844 45.455 4.14 4.14 37.03 3.66
3969 4790 4.227300 TGGCCCAGAGTAGACATTACATTT 59.773 41.667 0.00 0.00 0.00 2.32
4010 4831 8.133627 GCAAATTGAGATATCAAACTGTAGCAT 58.866 33.333 6.89 0.00 32.94 3.79
4044 4865 9.407380 ACAGGACAAAATAATATGACAATGCTA 57.593 29.630 0.00 0.00 0.00 3.49
4290 5112 5.284864 GCTCAGCTGCTTAAAAGAAAAACT 58.715 37.500 9.47 0.00 0.00 2.66
4389 5211 3.761752 AGTAATGCGGCAAACAGGTTATT 59.238 39.130 6.82 0.00 0.00 1.40
4443 5265 3.479203 CTGTCCCCGCCATAGCCA 61.479 66.667 0.00 0.00 34.57 4.75
4458 5280 0.385029 CTCCTCCATCTCTGCGTCTG 59.615 60.000 0.00 0.00 0.00 3.51
4611 5433 4.641094 CAGACAACCTACCTTACGATCTCT 59.359 45.833 0.00 0.00 0.00 3.10
4678 5500 4.946772 TCACTTCTGACAAACAAACATCCA 59.053 37.500 0.00 0.00 0.00 3.41
5016 5838 8.908903 AGTCTACGAAGATTCTTTGATACATCT 58.091 33.333 18.61 7.48 33.30 2.90
5017 5839 9.522804 AAGTCTACGAAGATTCTTTGATACATC 57.477 33.333 18.61 5.76 33.30 3.06
5018 5840 9.307121 CAAGTCTACGAAGATTCTTTGATACAT 57.693 33.333 18.61 5.55 33.30 2.29
5019 5841 7.275779 GCAAGTCTACGAAGATTCTTTGATACA 59.724 37.037 18.61 2.48 33.30 2.29
5020 5842 7.275779 TGCAAGTCTACGAAGATTCTTTGATAC 59.724 37.037 18.61 12.70 33.30 2.24
5021 5843 7.275779 GTGCAAGTCTACGAAGATTCTTTGATA 59.724 37.037 18.61 7.80 33.30 2.15
5022 5844 6.091441 GTGCAAGTCTACGAAGATTCTTTGAT 59.909 38.462 18.61 7.16 33.30 2.57
5023 5845 5.405571 GTGCAAGTCTACGAAGATTCTTTGA 59.594 40.000 18.61 4.90 33.30 2.69
5024 5846 5.389935 GGTGCAAGTCTACGAAGATTCTTTG 60.390 44.000 11.44 11.44 33.30 2.77
5101 5923 7.715249 AGCTGCTAATTTCCTCGTATTCATAAA 59.285 33.333 0.00 0.00 0.00 1.40
5104 5926 5.615289 AGCTGCTAATTTCCTCGTATTCAT 58.385 37.500 0.00 0.00 0.00 2.57
5387 6212 5.278907 CCATAAGTTGCTCAAAACATCACCA 60.279 40.000 0.00 0.00 32.21 4.17
5457 6282 9.832445 ACACATAAATCGTATTTGACCTTCTAT 57.168 29.630 0.00 0.00 0.00 1.98
5535 6360 1.000771 CGTCCTGTCCTGAGGAGGA 60.001 63.158 0.00 2.84 46.70 3.71
5581 6408 1.225376 GATGGTTCAACGTCCACGCA 61.225 55.000 0.00 0.00 44.43 5.24
5626 6453 7.386025 ACTCTATTTTACGTGTACAGAAAACCC 59.614 37.037 0.00 0.00 0.00 4.11
5685 6512 5.556470 AGTTGCTATAATTTTGCACGTACG 58.444 37.500 15.01 15.01 36.37 3.67
5703 6530 2.222596 CGTATCGCTGTGAAAGAGTTGC 60.223 50.000 0.00 0.00 0.00 4.17
5753 6580 1.746615 CCACGTTGGAGATGCCCTG 60.747 63.158 0.00 0.00 40.96 4.45
5769 6596 2.196229 CGGTGGTTTTGGGGTCCA 59.804 61.111 0.00 0.00 0.00 4.02
5775 6602 2.419620 GGTTGCCGGTGGTTTTGG 59.580 61.111 1.90 0.00 0.00 3.28
5786 6613 3.569250 ATGTAAAATCACACGGTTGCC 57.431 42.857 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.