Multiple sequence alignment - TraesCS3D01G419300

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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 TraesCS3D01G419300 chr3D 100.000 3447 0 0 1 3447 531849830 531846384 0.000000e+00 6366.0
1 TraesCS3D01G419300 chr3D 96.875 64 2 0 2565 2628 531847202 531847139 1.310000e-19 108.0
2 TraesCS3D01G419300 chr3D 96.875 64 2 0 2629 2692 531847266 531847203 1.310000e-19 108.0
3 TraesCS3D01G419300 chr3D 100.000 45 0 0 2872 2916 531846914 531846870 2.200000e-12 84.2
4 TraesCS3D01G419300 chr3D 90.741 54 5 0 1153 1206 531706931 531706878 4.770000e-09 73.1
5 TraesCS3D01G419300 chr3B 91.955 1939 102 25 691 2617 703595658 703593762 0.000000e+00 2667.0
6 TraesCS3D01G419300 chr3B 89.639 637 55 4 1 626 703596313 703595677 0.000000e+00 800.0
7 TraesCS3D01G419300 chr3B 96.133 181 6 1 3267 3447 703592914 703592735 9.360000e-76 294.0
8 TraesCS3D01G419300 chr3B 87.288 236 23 3 2629 2860 703593814 703593582 2.640000e-66 263.0
9 TraesCS3D01G419300 chr3B 98.305 59 1 0 2923 2981 45782663 45782721 1.690000e-18 104.0
10 TraesCS3D01G419300 chr3B 98.305 59 1 0 2923 2981 45851053 45851111 1.690000e-18 104.0
11 TraesCS3D01G419300 chr3B 90.741 54 5 0 1153 1206 703333285 703333232 4.770000e-09 73.1
12 TraesCS3D01G419300 chr3A 92.065 1903 102 21 728 2612 666637394 666635523 0.000000e+00 2632.0
13 TraesCS3D01G419300 chr3A 89.560 546 38 11 182 722 666637903 666637372 0.000000e+00 675.0
14 TraesCS3D01G419300 chr3A 91.457 199 14 2 2986 3182 666635369 666635172 1.580000e-68 270.0
15 TraesCS3D01G419300 chr3A 92.222 180 14 0 3203 3382 666635182 666635003 4.410000e-64 255.0
16 TraesCS3D01G419300 chr3A 89.604 202 20 1 1 202 666654974 666654774 4.410000e-64 255.0
17 TraesCS3D01G419300 chr3A 92.079 101 7 1 2729 2829 666635528 666635429 1.290000e-29 141.0
18 TraesCS3D01G419300 chr3A 96.875 64 2 0 3384 3447 666634962 666634899 1.310000e-19 108.0
19 TraesCS3D01G419300 chr3A 98.305 59 1 0 2923 2981 198296942 198297000 1.690000e-18 104.0
20 TraesCS3D01G419300 chr3A 78.261 138 28 2 57 193 16638942 16638806 1.700000e-13 87.9
21 TraesCS3D01G419300 chr3A 78.261 138 28 2 57 193 16642139 16642003 1.700000e-13 87.9
22 TraesCS3D01G419300 chr3A 78.261 138 28 2 57 193 16644095 16643959 1.700000e-13 87.9
23 TraesCS3D01G419300 chr3A 78.261 138 28 2 57 193 16646304 16646168 1.700000e-13 87.9
24 TraesCS3D01G419300 chr5D 84.259 324 34 13 1425 1738 27232161 27231845 2.010000e-77 300.0
25 TraesCS3D01G419300 chr1B 82.445 319 39 13 1430 1738 519302315 519302626 2.640000e-66 263.0
26 TraesCS3D01G419300 chr1A 80.247 324 46 13 1426 1738 562582596 562582912 9.620000e-56 228.0
27 TraesCS3D01G419300 chr1A 98.387 62 1 0 2923 2984 75096526 75096465 3.640000e-20 110.0
28 TraesCS3D01G419300 chr1A 95.238 42 2 0 2878 2919 10231972 10231931 2.220000e-07 67.6
29 TraesCS3D01G419300 chr1A 95.238 42 2 0 2878 2919 354945737 354945696 2.220000e-07 67.6
30 TraesCS3D01G419300 chr7D 98.387 62 1 0 2923 2984 41935328 41935267 3.640000e-20 110.0
31 TraesCS3D01G419300 chr7D 98.387 62 1 0 2923 2984 427888618 427888557 3.640000e-20 110.0
32 TraesCS3D01G419300 chr7D 100.000 39 0 0 2878 2916 41935328 41935290 4.770000e-09 73.1
33 TraesCS3D01G419300 chr7D 100.000 39 0 0 2878 2916 427888618 427888580 4.770000e-09 73.1
34 TraesCS3D01G419300 chr7D 100.000 38 0 0 2840 2877 41935388 41935351 1.720000e-08 71.3
35 TraesCS3D01G419300 chr2D 96.774 62 2 0 2923 2984 380830953 380831014 1.690000e-18 104.0
36 TraesCS3D01G419300 chr7B 93.939 66 4 0 2916 2981 89658061 89658126 2.190000e-17 100.0
37 TraesCS3D01G419300 chr7B 93.333 45 3 0 2872 2916 89658062 89658106 2.220000e-07 67.6
38 TraesCS3D01G419300 chr5B 89.157 83 5 3 2906 2984 631220123 631220041 2.190000e-17 100.0
39 TraesCS3D01G419300 chr7A 95.161 62 3 0 2923 2984 732841360 732841299 7.870000e-17 99.0
40 TraesCS3D01G419300 chr4B 95.161 62 3 0 2923 2984 105342389 105342328 7.870000e-17 99.0
41 TraesCS3D01G419300 chr4B 95.238 42 2 0 2878 2919 105342389 105342348 2.220000e-07 67.6
42 TraesCS3D01G419300 chr4B 88.235 51 5 1 2828 2877 576400385 576400435 3.720000e-05 60.2
43 TraesCS3D01G419300 chr4B 85.714 56 5 3 2824 2877 483046118 483046064 4.810000e-04 56.5
44 TraesCS3D01G419300 chr4A 86.250 80 6 3 2842 2916 474495704 474495783 7.930000e-12 82.4
45 TraesCS3D01G419300 chr2B 83.529 85 9 5 3179 3260 631261483 631261401 1.330000e-09 75.0
46 TraesCS3D01G419300 chr2A 100.000 36 0 0 2842 2877 16133631 16133596 2.220000e-07 67.6
47 TraesCS3D01G419300 chr2A 93.182 44 3 0 2834 2877 442518892 442518935 7.990000e-07 65.8
48 TraesCS3D01G419300 chr1D 97.436 39 1 0 2878 2916 256545405 256545443 2.220000e-07 67.6
49 TraesCS3D01G419300 chr6A 97.368 38 1 0 2840 2877 522197987 522197950 7.990000e-07 65.8


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 TraesCS3D01G419300 chr3D 531846384 531849830 3446 True 1666.550000 6366 98.437500 1 3447 4 chr3D.!!$R2 3446
1 TraesCS3D01G419300 chr3B 703592735 703596313 3578 True 1006.000000 2667 91.253750 1 3447 4 chr3B.!!$R2 3446
2 TraesCS3D01G419300 chr3A 666634899 666637903 3004 True 680.166667 2632 92.376333 182 3447 6 chr3A.!!$R3 3265

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
275 276 0.965866 TTGGTTTGTGTCCGGTTGCA 60.966 50.0 0.0 0.0 0.0 4.08 F
1234 1250 0.037734 TCCGCCTTCCCCTCTTTTTC 59.962 55.0 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1293 1309 0.034896 AGCTGGAAACTACCACACCG 59.965 55.0 0.00 0.0 35.91 4.94 R
2653 2725 0.034337 CCTTTTGGCACTGCTGCAAT 59.966 50.0 3.02 0.0 46.28 3.56 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
18 19 2.934570 TACCCACGGTCAGGCGAAC 61.935 63.158 0.00 0.00 37.09 3.95
19 20 4.308458 CCCACGGTCAGGCGAACA 62.308 66.667 0.00 0.00 0.00 3.18
24 25 1.952133 CGGTCAGGCGAACAAACGA 60.952 57.895 0.00 0.00 35.09 3.85
39 40 3.621715 ACAAACGAACACCTCTCTTCAAC 59.378 43.478 0.00 0.00 0.00 3.18
148 149 1.328680 CTCTGGCCGTCATCAATTTCG 59.671 52.381 0.00 0.00 0.00 3.46
179 180 1.599047 CGTTCTGGAGTGGCCTGAT 59.401 57.895 3.32 0.00 43.22 2.90
182 183 1.617018 TTCTGGAGTGGCCTGATCGG 61.617 60.000 3.32 0.00 43.22 4.18
215 216 1.542915 TCGTGTAGAGAGGGTTTTCGG 59.457 52.381 0.00 0.00 0.00 4.30
253 254 2.593128 GGTCTCCCGCTTACCTTCT 58.407 57.895 0.00 0.00 0.00 2.85
275 276 0.965866 TTGGTTTGTGTCCGGTTGCA 60.966 50.000 0.00 0.00 0.00 4.08
307 308 2.728383 CGAACGCGTGAACGGACT 60.728 61.111 14.98 0.00 40.23 3.85
359 361 1.044611 TTGATCACGTGGTCCAGACA 58.955 50.000 25.41 4.60 0.00 3.41
365 367 1.227999 ACGTGGTCCAGACATTTGCG 61.228 55.000 0.00 0.00 0.00 4.85
388 390 3.070015 AGCATTTTGAGGGTTCACTTTGG 59.930 43.478 0.00 0.00 31.71 3.28
418 420 4.051922 CTGATACATGAGTTCCCGCTAAC 58.948 47.826 0.00 0.00 0.00 2.34
421 423 3.350219 ACATGAGTTCCCGCTAACAAT 57.650 42.857 0.00 0.00 0.00 2.71
466 474 2.692041 AGCTTAGCCTGCATTTCATTCC 59.308 45.455 0.00 0.00 0.00 3.01
489 498 4.271049 CGCTGAGGATTTTCGTATCACAAT 59.729 41.667 0.00 0.00 0.00 2.71
522 531 5.757808 GGCCAATTGTACACTCAAATGTTTT 59.242 36.000 4.43 0.00 33.85 2.43
548 560 9.862371 TGCCGTATGTGATGTTTAAATAAAAAT 57.138 25.926 0.00 0.00 0.00 1.82
566 578 5.461032 AAAATAAAATGCCTTGACGGACA 57.539 34.783 0.00 0.00 33.16 4.02
629 642 7.481798 ACAATCTCGCAAAAGAATAAATTCGTC 59.518 33.333 0.00 0.00 41.56 4.20
671 685 7.071071 TGTTTGAAGGGAGAAGAAATTCCAAAT 59.929 33.333 0.00 0.00 35.09 2.32
673 687 7.703058 TGAAGGGAGAAGAAATTCCAAATAC 57.297 36.000 0.00 0.00 35.09 1.89
675 689 8.611257 TGAAGGGAGAAGAAATTCCAAATACTA 58.389 33.333 0.00 0.00 35.09 1.82
677 691 9.634021 AAGGGAGAAGAAATTCCAAATACTATC 57.366 33.333 0.00 0.00 35.09 2.08
678 692 8.781951 AGGGAGAAGAAATTCCAAATACTATCA 58.218 33.333 0.00 0.00 35.09 2.15
679 693 9.579932 GGGAGAAGAAATTCCAAATACTATCAT 57.420 33.333 0.00 0.00 35.09 2.45
728 742 1.135083 AGAGTCATGCGTACCCGAAAG 60.135 52.381 0.00 0.00 35.63 2.62
850 864 1.219522 AAGTACGCGCACTTCACACC 61.220 55.000 18.85 0.00 33.41 4.16
862 876 1.465200 TTCACACCCGATCCGTGTCA 61.465 55.000 9.68 0.00 42.49 3.58
1068 1082 2.409984 TACCCTGCTCCTCACCCCAA 62.410 60.000 0.00 0.00 0.00 4.12
1219 1235 0.249868 TGATCCAATCCGATGTCCGC 60.250 55.000 0.00 0.00 36.84 5.54
1234 1250 0.037734 TCCGCCTTCCCCTCTTTTTC 59.962 55.000 0.00 0.00 0.00 2.29
1259 1275 3.056821 TCGATGGAGTACTGGTTCTGTTG 60.057 47.826 0.00 0.00 0.00 3.33
1293 1309 0.977395 CGGATCCTAGGATTGGGGTC 59.023 60.000 25.25 12.17 34.60 4.46
1329 1345 1.355971 GCTCCGTGCTGTCGATTTAA 58.644 50.000 0.00 0.00 38.95 1.52
1348 1364 6.753107 TTTAAAATCCGGATCTCTGTTTCC 57.247 37.500 19.43 0.00 0.00 3.13
1395 1411 1.179174 TGCGTGGCTCTGTAGTCTGT 61.179 55.000 0.00 0.00 0.00 3.41
1415 1431 0.898320 AGATGCGTGTGCCTAGTCTT 59.102 50.000 0.00 0.00 41.78 3.01
1419 1435 1.005037 CGTGTGCCTAGTCTTGCCA 60.005 57.895 0.00 0.00 0.00 4.92
1458 1484 3.123620 CGCACTTGAGGCTCCTGC 61.124 66.667 12.86 14.41 38.76 4.85
1483 1509 4.379243 CGGTTGCTCTGTCGGCCT 62.379 66.667 0.00 0.00 0.00 5.19
1493 1519 2.032681 GTCGGCCTGCTTCACCTT 59.967 61.111 0.00 0.00 0.00 3.50
1496 1522 0.618458 TCGGCCTGCTTCACCTTTAT 59.382 50.000 0.00 0.00 0.00 1.40
1519 1545 2.724174 GGCGCTGTGTTTGTAATGTTTC 59.276 45.455 7.64 0.00 0.00 2.78
1559 1585 4.623002 GATCTGTAGGCCTACTTAACAGC 58.377 47.826 36.49 18.34 37.94 4.40
1630 1677 3.104512 TGGTCAGTATAGTGAACCAGGG 58.895 50.000 20.52 0.00 32.70 4.45
1659 1709 3.326747 AGTACTAGGCAAAACTTGAGCG 58.673 45.455 0.00 0.00 0.00 5.03
1712 1762 9.545105 TGATCTTGTTTTCTAATTTTGCATTGT 57.455 25.926 0.00 0.00 0.00 2.71
1808 1864 7.829378 AATTATTCCTCGTAGTCAGTTTCAC 57.171 36.000 0.00 0.00 0.00 3.18
1815 1871 5.048224 CCTCGTAGTCAGTTTCACTCCTAAA 60.048 44.000 0.00 0.00 0.00 1.85
1886 1943 2.436417 ACATGTGTGTACTGAATGCCC 58.564 47.619 0.00 0.00 36.63 5.36
1891 1948 2.884639 GTGTGTACTGAATGCCCAGTTT 59.115 45.455 8.47 0.00 44.32 2.66
1899 1956 2.102252 TGAATGCCCAGTTTTTGACACC 59.898 45.455 0.00 0.00 0.00 4.16
1904 1961 2.654863 CCCAGTTTTTGACACCTGTCT 58.345 47.619 6.97 0.00 44.99 3.41
1905 1962 3.023832 CCCAGTTTTTGACACCTGTCTT 58.976 45.455 6.97 0.00 44.99 3.01
2091 2148 3.891366 AGGTATGCTGTTCAACTTTTGCT 59.109 39.130 0.00 0.00 0.00 3.91
2100 2158 3.483235 AACTTTTGCTGGCACGCCG 62.483 57.895 3.13 0.00 39.42 6.46
2127 2185 8.494016 ACATTAGAACCTTAACATTCACTAGC 57.506 34.615 0.00 0.00 0.00 3.42
2149 2207 0.108992 GATGGTCTGTGCCGTCGTTA 60.109 55.000 0.00 0.00 35.16 3.18
2201 2259 0.970937 TGGAGGAAGGCGACGAGATT 60.971 55.000 0.00 0.00 0.00 2.40
2329 2388 8.634475 AAAATGTAAGAAGTGAAAGAACTTGC 57.366 30.769 0.00 0.00 40.48 4.01
2339 2398 3.262420 GAAAGAACTTGCGAGGCTATGA 58.738 45.455 5.79 0.00 0.00 2.15
2454 2513 1.411977 CATGCCTTGTTGTGTTCCCAA 59.588 47.619 0.00 0.00 0.00 4.12
2488 2547 4.631813 ACTCATTTGGTTTCTCATCGTAGC 59.368 41.667 0.00 0.00 0.00 3.58
2521 2593 5.794687 TTTCTGTCTTGTGTACTGTTGTG 57.205 39.130 0.00 0.00 0.00 3.33
2522 2594 4.465632 TCTGTCTTGTGTACTGTTGTGT 57.534 40.909 0.00 0.00 0.00 3.72
2523 2595 4.180817 TCTGTCTTGTGTACTGTTGTGTG 58.819 43.478 0.00 0.00 0.00 3.82
2524 2596 3.932710 CTGTCTTGTGTACTGTTGTGTGT 59.067 43.478 0.00 0.00 0.00 3.72
2525 2597 5.074584 TGTCTTGTGTACTGTTGTGTGTA 57.925 39.130 0.00 0.00 0.00 2.90
2526 2598 4.865925 TGTCTTGTGTACTGTTGTGTGTAC 59.134 41.667 0.00 0.00 39.37 2.90
2527 2599 5.107133 GTCTTGTGTACTGTTGTGTGTACT 58.893 41.667 0.00 0.00 39.57 2.73
2528 2600 5.005394 GTCTTGTGTACTGTTGTGTGTACTG 59.995 44.000 0.00 0.00 39.57 2.74
2529 2601 4.459390 TGTGTACTGTTGTGTGTACTGT 57.541 40.909 0.00 0.00 39.57 3.55
2530 2602 4.823157 TGTGTACTGTTGTGTGTACTGTT 58.177 39.130 0.00 0.00 39.57 3.16
2531 2603 4.627900 TGTGTACTGTTGTGTGTACTGTTG 59.372 41.667 0.00 0.00 39.57 3.33
2532 2604 4.628333 GTGTACTGTTGTGTGTACTGTTGT 59.372 41.667 0.00 0.00 39.57 3.32
2617 2689 0.598419 GTGCCAAAAGGTTCAGCAGC 60.598 55.000 0.00 0.00 33.37 5.25
2618 2690 1.005748 GCCAAAAGGTTCAGCAGCC 60.006 57.895 0.00 0.00 0.00 4.85
2619 2691 1.747325 GCCAAAAGGTTCAGCAGCCA 61.747 55.000 0.00 0.00 0.00 4.75
2620 2692 0.316204 CCAAAAGGTTCAGCAGCCAG 59.684 55.000 0.00 0.00 0.00 4.85
2621 2693 0.319297 CAAAAGGTTCAGCAGCCAGC 60.319 55.000 0.00 0.00 46.19 4.85
2630 2702 4.465413 GCAGCCAGCAAATCGAAC 57.535 55.556 0.00 0.00 44.79 3.95
2631 2703 1.580942 GCAGCCAGCAAATCGAACA 59.419 52.632 0.00 0.00 44.79 3.18
2632 2704 0.455633 GCAGCCAGCAAATCGAACAG 60.456 55.000 0.00 0.00 44.79 3.16
2633 2705 0.877071 CAGCCAGCAAATCGAACAGT 59.123 50.000 0.00 0.00 0.00 3.55
2634 2706 0.877071 AGCCAGCAAATCGAACAGTG 59.123 50.000 0.00 0.00 0.00 3.66
2636 2708 1.001378 GCCAGCAAATCGAACAGTGTT 60.001 47.619 8.61 8.61 0.00 3.32
2637 2709 2.543653 GCCAGCAAATCGAACAGTGTTT 60.544 45.455 10.45 0.00 0.00 2.83
2638 2710 3.044986 CCAGCAAATCGAACAGTGTTTG 58.955 45.455 16.06 16.06 35.30 2.93
2639 2711 3.044986 CAGCAAATCGAACAGTGTTTGG 58.955 45.455 20.79 11.57 33.39 3.28
2640 2712 2.687935 AGCAAATCGAACAGTGTTTGGT 59.312 40.909 20.79 12.94 37.43 3.67
2641 2713 3.130340 AGCAAATCGAACAGTGTTTGGTT 59.870 39.130 20.79 17.94 38.64 3.67
2642 2714 3.242712 GCAAATCGAACAGTGTTTGGTTG 59.757 43.478 20.21 22.03 33.39 3.77
2643 2715 2.774439 ATCGAACAGTGTTTGGTTGC 57.226 45.000 20.79 2.13 0.00 4.17
2644 2716 0.736053 TCGAACAGTGTTTGGTTGCC 59.264 50.000 20.79 1.44 0.00 4.52
2645 2717 0.591236 CGAACAGTGTTTGGTTGCCG 60.591 55.000 14.61 6.05 0.00 5.69
2646 2718 0.736053 GAACAGTGTTTGGTTGCCGA 59.264 50.000 10.45 0.00 0.00 5.54
2647 2719 1.336755 GAACAGTGTTTGGTTGCCGAT 59.663 47.619 10.45 0.00 0.00 4.18
2648 2720 2.264005 ACAGTGTTTGGTTGCCGATA 57.736 45.000 0.00 0.00 0.00 2.92
2649 2721 2.577700 ACAGTGTTTGGTTGCCGATAA 58.422 42.857 0.00 0.00 0.00 1.75
2650 2722 2.292292 ACAGTGTTTGGTTGCCGATAAC 59.708 45.455 0.00 0.00 0.00 1.89
2651 2723 2.292016 CAGTGTTTGGTTGCCGATAACA 59.708 45.455 4.55 0.00 32.22 2.41
2652 2724 2.292292 AGTGTTTGGTTGCCGATAACAC 59.708 45.455 16.10 16.10 45.39 3.32
2653 2725 2.033550 GTGTTTGGTTGCCGATAACACA 59.966 45.455 17.65 1.61 44.77 3.72
2654 2726 2.887783 TGTTTGGTTGCCGATAACACAT 59.112 40.909 4.55 0.00 32.22 3.21
2655 2727 3.319405 TGTTTGGTTGCCGATAACACATT 59.681 39.130 4.55 0.00 32.22 2.71
2656 2728 3.567576 TTGGTTGCCGATAACACATTG 57.432 42.857 4.55 0.00 32.22 2.82
2657 2729 1.201181 TGGTTGCCGATAACACATTGC 59.799 47.619 4.55 0.00 32.22 3.56
2658 2730 1.201181 GGTTGCCGATAACACATTGCA 59.799 47.619 4.55 0.00 32.22 4.08
2659 2731 2.518949 GTTGCCGATAACACATTGCAG 58.481 47.619 0.00 0.00 0.00 4.41
2660 2732 0.451383 TGCCGATAACACATTGCAGC 59.549 50.000 0.00 0.00 0.00 5.25
2661 2733 0.451383 GCCGATAACACATTGCAGCA 59.549 50.000 0.00 0.00 0.00 4.41
2662 2734 1.532505 GCCGATAACACATTGCAGCAG 60.533 52.381 0.00 0.00 0.00 4.24
2663 2735 1.739466 CCGATAACACATTGCAGCAGT 59.261 47.619 0.00 0.00 0.00 4.40
2664 2736 2.476686 CCGATAACACATTGCAGCAGTG 60.477 50.000 16.00 16.00 39.12 3.66
2673 2745 2.341176 GCAGCAGTGCCAAAAGGG 59.659 61.111 12.58 0.00 44.72 3.95
2674 2746 2.501602 GCAGCAGTGCCAAAAGGGT 61.502 57.895 12.58 0.00 44.72 4.34
2675 2747 1.662044 CAGCAGTGCCAAAAGGGTC 59.338 57.895 12.58 0.00 39.65 4.46
2676 2748 1.108727 CAGCAGTGCCAAAAGGGTCA 61.109 55.000 12.58 0.00 39.65 4.02
2677 2749 0.825010 AGCAGTGCCAAAAGGGTCAG 60.825 55.000 12.58 0.00 39.65 3.51
2678 2750 1.662044 CAGTGCCAAAAGGGTCAGC 59.338 57.895 0.00 0.00 39.65 4.26
2679 2751 1.108727 CAGTGCCAAAAGGGTCAGCA 61.109 55.000 0.00 0.00 39.65 4.41
2680 2752 0.825010 AGTGCCAAAAGGGTCAGCAG 60.825 55.000 0.00 0.00 39.65 4.24
2681 2753 2.202395 TGCCAAAAGGGTCAGCAGC 61.202 57.895 0.00 0.00 39.65 5.25
2682 2754 2.935740 GCCAAAAGGGTCAGCAGCC 61.936 63.158 0.00 0.00 40.97 4.85
2683 2755 1.531365 CCAAAAGGGTCAGCAGCCA 60.531 57.895 0.00 0.00 43.42 4.75
2684 2756 1.530013 CCAAAAGGGTCAGCAGCCAG 61.530 60.000 0.00 0.00 43.42 4.85
2685 2757 1.905354 AAAAGGGTCAGCAGCCAGC 60.905 57.895 0.00 0.00 43.42 4.85
2694 2766 4.157817 GCAGCCAGCAAATCGTTG 57.842 55.556 0.00 0.00 44.79 4.10
2695 2767 1.580942 GCAGCCAGCAAATCGTTGA 59.419 52.632 0.00 0.00 44.79 3.18
2696 2768 0.171903 GCAGCCAGCAAATCGTTGAT 59.828 50.000 0.00 0.00 44.79 2.57
2697 2769 1.796617 GCAGCCAGCAAATCGTTGATC 60.797 52.381 0.00 0.00 44.79 2.92
2698 2770 1.469703 CAGCCAGCAAATCGTTGATCA 59.530 47.619 0.00 0.00 36.83 2.92
2699 2771 2.095110 CAGCCAGCAAATCGTTGATCAA 60.095 45.455 3.38 3.38 36.83 2.57
2700 2772 2.095059 AGCCAGCAAATCGTTGATCAAC 60.095 45.455 25.68 25.68 36.83 3.18
2701 2773 2.095059 GCCAGCAAATCGTTGATCAACT 60.095 45.455 30.45 14.61 39.08 3.16
2702 2774 3.612479 GCCAGCAAATCGTTGATCAACTT 60.612 43.478 30.45 19.11 39.08 2.66
2726 2798 2.679450 TCCTTGTTAATCGGACACACG 58.321 47.619 0.00 0.00 0.00 4.49
2796 2868 2.645510 GCGTGACTCACCGACAACG 61.646 63.158 3.50 0.00 39.43 4.10
2844 2923 4.816925 GGTTTGGAGGATGCAGATTAGTAC 59.183 45.833 0.00 0.00 38.09 2.73
2846 2925 5.537300 TTGGAGGATGCAGATTAGTACTC 57.463 43.478 0.00 0.00 38.09 2.59
2847 2926 3.898123 TGGAGGATGCAGATTAGTACTCC 59.102 47.826 7.01 7.01 42.68 3.85
2848 2927 3.259625 GGAGGATGCAGATTAGTACTCCC 59.740 52.174 0.00 0.00 37.80 4.30
2849 2928 4.156477 GAGGATGCAGATTAGTACTCCCT 58.844 47.826 0.00 0.00 0.00 4.20
2851 2930 3.259625 GGATGCAGATTAGTACTCCCTCC 59.740 52.174 0.00 0.00 0.00 4.30
2852 2931 2.307768 TGCAGATTAGTACTCCCTCCG 58.692 52.381 0.00 0.00 0.00 4.63
2853 2932 2.308690 GCAGATTAGTACTCCCTCCGT 58.691 52.381 0.00 0.00 0.00 4.69
2854 2933 2.694109 GCAGATTAGTACTCCCTCCGTT 59.306 50.000 0.00 0.00 0.00 4.44
2869 2956 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2870 2957 4.865365 CCTCCGTTCTGAATTACTTGTCTC 59.135 45.833 0.00 0.00 0.00 3.36
2872 2959 5.470368 TCCGTTCTGAATTACTTGTCTCAG 58.530 41.667 0.00 0.00 37.28 3.35
2874 2961 6.071334 TCCGTTCTGAATTACTTGTCTCAGAT 60.071 38.462 1.75 0.00 42.81 2.90
2876 2963 7.118390 CCGTTCTGAATTACTTGTCTCAGATTT 59.882 37.037 1.75 0.00 42.81 2.17
2877 2964 9.140286 CGTTCTGAATTACTTGTCTCAGATTTA 57.860 33.333 1.75 0.00 42.81 1.40
2880 2967 9.862371 TCTGAATTACTTGTCTCAGATTTACTC 57.138 33.333 0.00 0.00 39.43 2.59
2881 2968 9.645059 CTGAATTACTTGTCTCAGATTTACTCA 57.355 33.333 0.00 0.00 38.02 3.41
2904 3003 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
2946 3045 9.982651 TTACTCATTTTAGTGCTAGATACATCC 57.017 33.333 0.00 0.00 0.00 3.51
2947 3046 7.148641 ACTCATTTTAGTGCTAGATACATCCG 58.851 38.462 0.00 0.00 0.00 4.18
2949 3048 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
2967 3066 9.005777 ACATCCGTATCTAGAGAAATCTAAGAC 57.994 37.037 0.00 0.00 0.00 3.01
2968 3067 9.004717 CATCCGTATCTAGAGAAATCTAAGACA 57.995 37.037 0.00 0.00 0.00 3.41
2970 3069 9.058174 TCCGTATCTAGAGAAATCTAAGACAAG 57.942 37.037 0.00 0.00 0.00 3.16
2971 3070 8.842280 CCGTATCTAGAGAAATCTAAGACAAGT 58.158 37.037 0.00 0.00 0.00 3.16
2998 3265 2.621338 GAATGGCAAGATGAGACGACA 58.379 47.619 0.00 0.00 0.00 4.35
3007 3490 0.894141 ATGAGACGACAGCTGCTCTT 59.106 50.000 15.27 7.58 0.00 2.85
3019 3502 5.251764 ACAGCTGCTCTTTGAAGAATACAT 58.748 37.500 15.27 0.00 34.03 2.29
3055 3540 9.634021 AATAAGGTTCCTGAAATCTATTCCTTC 57.366 33.333 0.00 0.00 35.03 3.46
3057 3542 7.996758 AGGTTCCTGAAATCTATTCCTTCTA 57.003 36.000 0.00 0.00 0.00 2.10
3130 3615 3.897505 CCTTTGTCCCAGTTTCAATTCCT 59.102 43.478 0.00 0.00 0.00 3.36
3175 3660 5.105797 TGTGGTTGAATAATTGATGCCAGTC 60.106 40.000 0.00 0.00 0.00 3.51
3177 3662 5.716228 TGGTTGAATAATTGATGCCAGTCTT 59.284 36.000 0.00 0.00 0.00 3.01
3203 3688 6.036408 CGCATATGAGATTTTGTCTGAAGTCA 59.964 38.462 6.97 0.00 37.29 3.41
3209 3694 8.055279 TGAGATTTTGTCTGAAGTCAAACTTT 57.945 30.769 2.80 0.00 36.45 2.66
3219 3704 8.283291 GTCTGAAGTCAAACTTTATAAGTGTGG 58.717 37.037 9.27 0.00 45.07 4.17
3434 3958 8.573885 GGTGCTAAGTTCTACCAACTAATTTTT 58.426 33.333 0.00 0.00 33.42 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.241880 CGTTTGTTCGCCTGACCGT 61.242 57.895 0.00 0.00 0.00 4.83
18 19 3.302480 CGTTGAAGAGAGGTGTTCGTTTG 60.302 47.826 0.00 0.00 0.00 2.93
19 20 2.864343 CGTTGAAGAGAGGTGTTCGTTT 59.136 45.455 0.00 0.00 0.00 3.60
24 25 1.222115 GCGCGTTGAAGAGAGGTGTT 61.222 55.000 8.43 0.00 0.00 3.32
55 56 1.597461 GCACCCGAGAAGCCTACTT 59.403 57.895 0.00 0.00 39.43 2.24
148 149 1.673033 CCAGAACGGACATGACTCCAC 60.673 57.143 0.00 0.00 36.56 4.02
179 180 0.179121 ACGAAGCGTATTCATGCCGA 60.179 50.000 0.00 0.00 38.73 5.54
182 183 3.113322 TCTACACGAAGCGTATTCATGC 58.887 45.455 0.00 0.00 38.32 4.06
191 192 0.526662 AACCCTCTCTACACGAAGCG 59.473 55.000 0.00 0.00 0.00 4.68
253 254 0.256464 AACCGGACACAAACCAAGGA 59.744 50.000 9.46 0.00 0.00 3.36
275 276 1.227321 TTCGCGTGTCCGAAACCTT 60.227 52.632 5.77 0.00 43.43 3.50
340 341 1.044611 TGTCTGGACCACGTGATCAA 58.955 50.000 19.30 0.37 0.00 2.57
341 342 1.266178 ATGTCTGGACCACGTGATCA 58.734 50.000 19.30 10.89 0.00 2.92
359 361 1.895131 ACCCTCAAAATGCTCGCAAAT 59.105 42.857 0.00 0.00 0.00 2.32
365 367 4.301628 CAAAGTGAACCCTCAAAATGCTC 58.698 43.478 0.00 0.00 31.88 4.26
388 390 4.314121 GAACTCATGTATCAGGGCATCTC 58.686 47.826 0.00 0.00 0.00 2.75
448 456 1.405105 GCGGAATGAAATGCAGGCTAA 59.595 47.619 0.00 0.00 0.00 3.09
466 474 3.186909 TGTGATACGAAAATCCTCAGCG 58.813 45.455 0.00 0.00 0.00 5.18
489 498 4.279671 AGTGTACAATTGGCCAATCGAAAA 59.720 37.500 30.74 14.28 0.00 2.29
522 531 9.862371 ATTTTTATTTAAACATCACATACGGCA 57.138 25.926 0.00 0.00 0.00 5.69
548 560 4.331968 AGAATGTCCGTCAAGGCATTTTA 58.668 39.130 1.98 0.00 42.55 1.52
629 642 7.224557 CCCTTCAAACAAAAGTTGGATTACAAG 59.775 37.037 0.00 0.00 40.38 3.16
680 694 1.252904 TAGTGTCTTCCCGGGGAACG 61.253 60.000 24.64 19.06 36.71 3.95
681 695 0.535797 CTAGTGTCTTCCCGGGGAAC 59.464 60.000 24.64 17.05 36.71 3.62
734 748 1.071299 TGTGTGCGCATGACTCCTT 59.929 52.632 15.91 0.00 0.00 3.36
735 749 1.669115 GTGTGTGCGCATGACTCCT 60.669 57.895 15.91 0.00 0.00 3.69
850 864 2.579787 GCTCGTGACACGGATCGG 60.580 66.667 26.55 13.05 42.81 4.18
1092 1108 4.200283 CGCCGACTCCTCTCTGCC 62.200 72.222 0.00 0.00 0.00 4.85
1096 1112 1.527380 ATCTCCGCCGACTCCTCTC 60.527 63.158 0.00 0.00 0.00 3.20
1219 1235 2.567615 TCGAGAGAAAAAGAGGGGAAGG 59.432 50.000 0.00 0.00 37.03 3.46
1234 1250 3.066064 CAGAACCAGTACTCCATCGAGAG 59.934 52.174 0.00 0.37 38.52 3.20
1293 1309 0.034896 AGCTGGAAACTACCACACCG 59.965 55.000 0.00 0.00 35.91 4.94
1361 1377 3.305110 CCACGCATCTAAACAAACCAAC 58.695 45.455 0.00 0.00 0.00 3.77
1395 1411 1.763968 AGACTAGGCACACGCATCTA 58.236 50.000 0.00 0.00 41.24 1.98
1415 1431 2.776526 AGGGGACACCAGTTGGCA 60.777 61.111 0.00 0.00 43.89 4.92
1419 1435 0.974383 CTAACGAGGGGACACCAGTT 59.026 55.000 11.57 11.57 43.89 3.16
1483 1509 0.525761 GCGCCAATAAAGGTGAAGCA 59.474 50.000 0.00 0.00 41.75 3.91
1493 1519 4.022762 ACATTACAAACACAGCGCCAATAA 60.023 37.500 2.29 0.00 0.00 1.40
1496 1522 1.678627 ACATTACAAACACAGCGCCAA 59.321 42.857 2.29 0.00 0.00 4.52
1519 1545 1.297967 CGATGACGGAGCAGACTCG 60.298 63.158 0.00 0.00 44.48 4.18
1559 1585 4.402155 TGGCTAAAGAATGCACCTTTATGG 59.598 41.667 18.05 11.64 36.06 2.74
1630 1677 1.861982 TTGCCTAGTACTCAGGGGAC 58.138 55.000 15.79 4.91 33.44 4.46
1637 1684 3.368236 CGCTCAAGTTTTGCCTAGTACTC 59.632 47.826 0.00 0.00 0.00 2.59
1659 1709 8.451908 AATCACTAATAAACAGGATTACAGGC 57.548 34.615 0.00 0.00 0.00 4.85
1752 1802 7.928167 TCTGATCTTGCACTAGTTATGTATTGG 59.072 37.037 0.00 0.00 0.00 3.16
1879 1936 2.365293 AGGTGTCAAAAACTGGGCATTC 59.635 45.455 0.00 0.00 0.00 2.67
2091 2148 0.320858 TTCTAATGTTCGGCGTGCCA 60.321 50.000 12.06 2.31 35.37 4.92
2127 2185 1.354337 CGACGGCACAGACCATCAAG 61.354 60.000 0.00 0.00 0.00 3.02
2149 2207 8.284693 GCTGAAACAATTTGCAAAGAATACATT 58.715 29.630 18.19 2.02 0.00 2.71
2201 2259 1.672030 CTGGTGAAGCATGGCGTCA 60.672 57.895 0.00 0.00 43.82 4.35
2329 2388 1.202568 TGGCACAGAATCATAGCCTCG 60.203 52.381 10.31 0.00 45.42 4.63
2454 2513 6.993902 AGAAACCAAATGAGTTTGCAAATCAT 59.006 30.769 16.21 19.59 42.66 2.45
2488 2547 3.438087 ACAAGACAGAAAATGATGCCTCG 59.562 43.478 0.00 0.00 0.00 4.63
2606 2678 0.541296 ATTTGCTGGCTGCTGAACCT 60.541 50.000 17.45 0.00 43.37 3.50
2617 2689 3.044986 CAAACACTGTTCGATTTGCTGG 58.955 45.455 0.00 0.00 0.00 4.85
2618 2690 3.044986 CCAAACACTGTTCGATTTGCTG 58.955 45.455 0.00 0.00 31.95 4.41
2619 2691 2.687935 ACCAAACACTGTTCGATTTGCT 59.312 40.909 0.00 0.00 31.95 3.91
2620 2692 3.078594 ACCAAACACTGTTCGATTTGC 57.921 42.857 0.00 0.00 31.95 3.68
2621 2693 3.242712 GCAACCAAACACTGTTCGATTTG 59.757 43.478 0.00 0.89 32.89 2.32
2622 2694 3.443976 GCAACCAAACACTGTTCGATTT 58.556 40.909 0.00 0.00 0.00 2.17
2624 2696 1.336755 GGCAACCAAACACTGTTCGAT 59.663 47.619 0.00 0.00 0.00 3.59
2625 2697 0.736053 GGCAACCAAACACTGTTCGA 59.264 50.000 0.00 0.00 0.00 3.71
2626 2698 0.591236 CGGCAACCAAACACTGTTCG 60.591 55.000 0.00 0.00 0.00 3.95
2627 2699 0.736053 TCGGCAACCAAACACTGTTC 59.264 50.000 0.00 0.00 0.00 3.18
2628 2700 1.398692 ATCGGCAACCAAACACTGTT 58.601 45.000 0.00 0.00 0.00 3.16
2630 2702 2.292016 TGTTATCGGCAACCAAACACTG 59.708 45.455 0.00 0.00 0.00 3.66
2631 2703 2.292292 GTGTTATCGGCAACCAAACACT 59.708 45.455 14.55 0.00 44.02 3.55
2632 2704 2.033550 TGTGTTATCGGCAACCAAACAC 59.966 45.455 14.79 14.79 46.32 3.32
2633 2705 2.298610 TGTGTTATCGGCAACCAAACA 58.701 42.857 0.00 0.00 0.00 2.83
2634 2706 3.569250 ATGTGTTATCGGCAACCAAAC 57.431 42.857 0.00 0.00 0.00 2.93
2636 2708 2.352225 GCAATGTGTTATCGGCAACCAA 60.352 45.455 0.00 0.00 0.00 3.67
2637 2709 1.201181 GCAATGTGTTATCGGCAACCA 59.799 47.619 0.00 0.00 0.00 3.67
2638 2710 1.201181 TGCAATGTGTTATCGGCAACC 59.799 47.619 0.00 0.00 0.00 3.77
2639 2711 2.518949 CTGCAATGTGTTATCGGCAAC 58.481 47.619 0.00 0.00 0.00 4.17
2640 2712 1.135431 GCTGCAATGTGTTATCGGCAA 60.135 47.619 0.00 0.00 0.00 4.52
2641 2713 0.451383 GCTGCAATGTGTTATCGGCA 59.549 50.000 0.00 0.00 0.00 5.69
2642 2714 0.451383 TGCTGCAATGTGTTATCGGC 59.549 50.000 0.00 0.00 0.00 5.54
2643 2715 1.739466 ACTGCTGCAATGTGTTATCGG 59.261 47.619 3.02 0.00 0.00 4.18
2644 2716 2.777494 CACTGCTGCAATGTGTTATCG 58.223 47.619 12.39 0.00 0.00 2.92
2645 2717 2.523015 GCACTGCTGCAATGTGTTATC 58.477 47.619 19.19 3.65 43.62 1.75
2646 2718 1.203052 GGCACTGCTGCAATGTGTTAT 59.797 47.619 19.19 0.00 46.28 1.89
2647 2719 0.597568 GGCACTGCTGCAATGTGTTA 59.402 50.000 19.19 0.00 46.28 2.41
2648 2720 1.364901 GGCACTGCTGCAATGTGTT 59.635 52.632 19.19 0.00 46.28 3.32
2649 2721 1.393487 TTGGCACTGCTGCAATGTGT 61.393 50.000 19.19 5.33 46.28 3.72
2650 2722 0.249531 TTTGGCACTGCTGCAATGTG 60.250 50.000 12.99 14.31 46.28 3.21
2651 2723 0.464870 TTTTGGCACTGCTGCAATGT 59.535 45.000 12.99 0.47 46.28 2.71
2652 2724 1.144969 CTTTTGGCACTGCTGCAATG 58.855 50.000 6.74 6.74 46.28 2.82
2653 2725 0.034337 CCTTTTGGCACTGCTGCAAT 59.966 50.000 3.02 0.00 46.28 3.56
2654 2726 1.442567 CCTTTTGGCACTGCTGCAA 59.557 52.632 3.02 0.00 46.28 4.08
2655 2727 2.500714 CCCTTTTGGCACTGCTGCA 61.501 57.895 0.88 0.88 46.28 4.41
2656 2728 2.341176 CCCTTTTGGCACTGCTGC 59.659 61.111 0.00 0.00 43.41 5.25
2657 2729 1.108727 TGACCCTTTTGGCACTGCTG 61.109 55.000 0.00 0.00 37.83 4.41
2658 2730 0.825010 CTGACCCTTTTGGCACTGCT 60.825 55.000 0.00 0.00 37.83 4.24
2659 2731 1.662044 CTGACCCTTTTGGCACTGC 59.338 57.895 0.00 0.00 37.83 4.40
2660 2732 1.108727 TGCTGACCCTTTTGGCACTG 61.109 55.000 0.00 0.00 37.83 3.66
2661 2733 0.825010 CTGCTGACCCTTTTGGCACT 60.825 55.000 0.00 0.00 37.83 4.40
2662 2734 1.662044 CTGCTGACCCTTTTGGCAC 59.338 57.895 0.00 0.00 37.83 5.01
2663 2735 2.202395 GCTGCTGACCCTTTTGGCA 61.202 57.895 0.00 0.00 37.83 4.92
2664 2736 2.653115 GCTGCTGACCCTTTTGGC 59.347 61.111 0.00 0.00 37.83 4.52
2665 2737 1.530013 CTGGCTGCTGACCCTTTTGG 61.530 60.000 0.00 0.00 41.37 3.28
2666 2738 1.962144 CTGGCTGCTGACCCTTTTG 59.038 57.895 0.00 0.00 0.00 2.44
2667 2739 1.905354 GCTGGCTGCTGACCCTTTT 60.905 57.895 9.31 0.00 38.95 2.27
2668 2740 2.282745 GCTGGCTGCTGACCCTTT 60.283 61.111 9.31 0.00 38.95 3.11
2669 2741 2.645394 TTTGCTGGCTGCTGACCCTT 62.645 55.000 17.45 0.00 43.37 3.95
2670 2742 2.436596 ATTTGCTGGCTGCTGACCCT 62.437 55.000 17.45 0.00 43.37 4.34
2671 2743 1.941999 GATTTGCTGGCTGCTGACCC 61.942 60.000 17.45 0.08 43.37 4.46
2672 2744 1.509923 GATTTGCTGGCTGCTGACC 59.490 57.895 17.45 0.00 43.37 4.02
2673 2745 1.136147 CGATTTGCTGGCTGCTGAC 59.864 57.895 17.45 0.00 43.37 3.51
2674 2746 0.890542 AACGATTTGCTGGCTGCTGA 60.891 50.000 17.45 6.34 43.37 4.26
2675 2747 0.731514 CAACGATTTGCTGGCTGCTG 60.732 55.000 17.45 1.74 43.37 4.41
2676 2748 0.890542 TCAACGATTTGCTGGCTGCT 60.891 50.000 17.45 0.00 43.37 4.24
2677 2749 0.171903 ATCAACGATTTGCTGGCTGC 59.828 50.000 9.67 9.67 43.25 5.25
2678 2750 1.469703 TGATCAACGATTTGCTGGCTG 59.530 47.619 0.00 0.00 32.17 4.85
2679 2751 1.825090 TGATCAACGATTTGCTGGCT 58.175 45.000 0.00 0.00 32.17 4.75
2680 2752 2.095059 AGTTGATCAACGATTTGCTGGC 60.095 45.455 28.18 4.76 45.50 4.85
2681 2753 3.837213 AGTTGATCAACGATTTGCTGG 57.163 42.857 28.18 0.00 45.50 4.85
2682 2754 3.362831 GCAAGTTGATCAACGATTTGCTG 59.637 43.478 34.32 23.41 45.50 4.41
2683 2755 3.254166 AGCAAGTTGATCAACGATTTGCT 59.746 39.130 36.53 36.53 46.31 3.91
2684 2756 3.568538 AGCAAGTTGATCAACGATTTGC 58.431 40.909 34.50 34.50 43.91 3.68
2685 2757 4.618489 GGAAGCAAGTTGATCAACGATTTG 59.382 41.667 28.18 25.97 45.50 2.32
2686 2758 4.520492 AGGAAGCAAGTTGATCAACGATTT 59.480 37.500 28.18 21.13 45.50 2.17
2687 2759 4.074970 AGGAAGCAAGTTGATCAACGATT 58.925 39.130 28.18 20.97 45.50 3.34
2688 2760 3.679389 AGGAAGCAAGTTGATCAACGAT 58.321 40.909 28.18 20.10 45.50 3.73
2689 2761 3.126001 AGGAAGCAAGTTGATCAACGA 57.874 42.857 28.18 0.00 45.50 3.85
2690 2762 3.003689 ACAAGGAAGCAAGTTGATCAACG 59.996 43.478 28.18 18.28 45.50 4.10
2691 2763 4.574599 ACAAGGAAGCAAGTTGATCAAC 57.425 40.909 27.69 27.69 41.45 3.18
2692 2764 6.707440 TTAACAAGGAAGCAAGTTGATCAA 57.293 33.333 7.16 3.38 0.00 2.57
2693 2765 6.348458 CGATTAACAAGGAAGCAAGTTGATCA 60.348 38.462 7.16 0.00 37.03 2.92
2694 2766 6.024049 CGATTAACAAGGAAGCAAGTTGATC 58.976 40.000 7.16 3.81 35.13 2.92
2695 2767 5.106157 CCGATTAACAAGGAAGCAAGTTGAT 60.106 40.000 7.16 0.00 0.00 2.57
2696 2768 4.215399 CCGATTAACAAGGAAGCAAGTTGA 59.785 41.667 7.16 0.00 0.00 3.18
2697 2769 4.215399 TCCGATTAACAAGGAAGCAAGTTG 59.785 41.667 0.00 0.00 0.00 3.16
2698 2770 4.215613 GTCCGATTAACAAGGAAGCAAGTT 59.784 41.667 0.00 0.00 35.60 2.66
2699 2771 3.751698 GTCCGATTAACAAGGAAGCAAGT 59.248 43.478 0.00 0.00 35.60 3.16
2700 2772 3.751175 TGTCCGATTAACAAGGAAGCAAG 59.249 43.478 0.00 0.00 35.60 4.01
2701 2773 3.500680 GTGTCCGATTAACAAGGAAGCAA 59.499 43.478 0.00 0.00 35.60 3.91
2702 2774 3.071479 GTGTCCGATTAACAAGGAAGCA 58.929 45.455 0.00 0.00 35.60 3.91
2726 2798 4.222366 ACTTTCTACCCTACAGCAACCTAC 59.778 45.833 0.00 0.00 0.00 3.18
2809 2881 2.830827 CAAACCACCGCACCCACA 60.831 61.111 0.00 0.00 0.00 4.17
2844 2923 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2846 2925 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2847 2926 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
2848 2927 5.470368 TGAGACAAGTAATTCAGAACGGAG 58.530 41.667 0.00 0.00 0.00 4.63
2849 2928 5.243060 TCTGAGACAAGTAATTCAGAACGGA 59.757 40.000 0.89 0.00 42.08 4.69
2851 2930 7.588143 AATCTGAGACAAGTAATTCAGAACG 57.412 36.000 7.08 0.00 46.31 3.95
2854 2933 9.862371 GAGTAAATCTGAGACAAGTAATTCAGA 57.138 33.333 5.61 5.61 46.98 3.27
2876 2963 8.297426 CGGATGTATCTAGCACTAAAATGAGTA 58.703 37.037 0.00 0.00 0.00 2.59
2877 2964 7.148641 CGGATGTATCTAGCACTAAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
2878 2965 7.148641 ACGGATGTATCTAGCACTAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
2879 2966 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
2880 2967 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
2920 3019 9.982651 GGATGTATCTAGCACTAAAATGAGTAA 57.017 33.333 0.00 0.00 0.00 2.24
2921 3020 8.297426 CGGATGTATCTAGCACTAAAATGAGTA 58.703 37.037 0.00 0.00 0.00 2.59
2922 3021 7.148641 CGGATGTATCTAGCACTAAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
2923 3022 7.148641 ACGGATGTATCTAGCACTAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
2924 3023 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
2925 3024 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
2945 3044 8.842280 ACTTGTCTTAGATTTCTCTAGATACGG 58.158 37.037 0.00 0.00 35.43 4.02
2958 3057 8.470002 GCCATTCCAAATTACTTGTCTTAGATT 58.530 33.333 0.00 0.00 32.65 2.40
2960 3059 6.945435 TGCCATTCCAAATTACTTGTCTTAGA 59.055 34.615 0.00 0.00 32.65 2.10
2961 3060 7.156876 TGCCATTCCAAATTACTTGTCTTAG 57.843 36.000 0.00 0.00 32.65 2.18
2962 3061 7.450014 TCTTGCCATTCCAAATTACTTGTCTTA 59.550 33.333 0.00 0.00 32.65 2.10
2963 3062 6.267471 TCTTGCCATTCCAAATTACTTGTCTT 59.733 34.615 0.00 0.00 32.65 3.01
2965 3064 6.024552 TCTTGCCATTCCAAATTACTTGTC 57.975 37.500 0.00 0.00 32.65 3.18
2966 3065 6.211184 TCATCTTGCCATTCCAAATTACTTGT 59.789 34.615 0.00 0.00 32.65 3.16
2967 3066 6.632909 TCATCTTGCCATTCCAAATTACTTG 58.367 36.000 0.00 0.00 34.52 3.16
2968 3067 6.664816 TCTCATCTTGCCATTCCAAATTACTT 59.335 34.615 0.00 0.00 0.00 2.24
2970 3069 6.268566 GTCTCATCTTGCCATTCCAAATTAC 58.731 40.000 0.00 0.00 0.00 1.89
2971 3070 5.066375 CGTCTCATCTTGCCATTCCAAATTA 59.934 40.000 0.00 0.00 0.00 1.40
2974 3073 2.749076 CGTCTCATCTTGCCATTCCAAA 59.251 45.455 0.00 0.00 0.00 3.28
2978 3077 2.606725 CTGTCGTCTCATCTTGCCATTC 59.393 50.000 0.00 0.00 0.00 2.67
2979 3078 2.625737 CTGTCGTCTCATCTTGCCATT 58.374 47.619 0.00 0.00 0.00 3.16
2998 3265 5.251764 ACATGTATTCTTCAAAGAGCAGCT 58.748 37.500 0.00 0.00 36.22 4.24
3019 3502 6.373005 TCAGGAACCTTATTTGATGAGACA 57.627 37.500 0.00 0.00 0.00 3.41
3096 3581 1.338200 GGACAAAGGTGCTCGATCTGT 60.338 52.381 0.00 0.00 31.82 3.41
3148 3633 5.657745 TGGCATCAATTATTCAACCACAGAT 59.342 36.000 0.00 0.00 0.00 2.90
3175 3660 6.594284 TCAGACAAAATCTCATATGCGAAG 57.406 37.500 0.00 0.00 34.41 3.79
3177 3662 6.108687 ACTTCAGACAAAATCTCATATGCGA 58.891 36.000 0.00 0.00 34.41 5.10


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

AutoCloner maintained by Alex Coulton.