Multiple sequence alignment - TraesCS6A01G372100

Loading Multiple Alignment...

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 TraesCS6A01G372100 chr6A 100.000 2932 0 0 1 2932 596128766 596131697 0.000000e+00 5415.0
1 TraesCS6A01G372100 chr6A 95.763 236 8 1 2698 2931 176168112 176167877 2.130000e-101 379.0
2 TraesCS6A01G372100 chr6D 92.662 2739 139 22 3 2697 450613608 450616328 0.000000e+00 3888.0
3 TraesCS6A01G372100 chr6D 84.643 280 35 6 2179 2456 201578830 201579103 3.720000e-69 272.0
4 TraesCS6A01G372100 chr6B 93.591 1732 57 18 203 1897 684219411 684221125 0.000000e+00 2534.0
5 TraesCS6A01G372100 chr6B 84.758 702 66 23 2037 2697 684375461 684376162 0.000000e+00 665.0
6 TraesCS6A01G372100 chr6B 90.506 316 16 10 2006 2311 684221286 684221597 3.520000e-109 405.0
7 TraesCS6A01G372100 chr6B 88.433 268 18 3 2304 2558 684245232 684245499 7.890000e-81 311.0
8 TraesCS6A01G372100 chr6B 84.698 281 32 9 2179 2456 470630509 470630781 1.340000e-68 270.0
9 TraesCS6A01G372100 chr6B 84.532 278 35 6 2179 2454 136802448 136802177 4.820000e-68 268.0
10 TraesCS6A01G372100 chr7A 96.596 235 8 0 2697 2931 497025028 497024794 9.850000e-105 390.0
11 TraesCS6A01G372100 chr7A 96.186 236 8 1 2698 2932 463745677 463745442 4.580000e-103 385.0
12 TraesCS6A01G372100 chr7A 95.781 237 7 2 2698 2932 172292526 172292761 2.130000e-101 379.0
13 TraesCS6A01G372100 chr3A 95.781 237 9 1 2697 2932 33033539 33033775 5.930000e-102 381.0
14 TraesCS6A01G372100 chr3A 95.781 237 9 1 2697 2932 612992301 612992537 5.930000e-102 381.0
15 TraesCS6A01G372100 chr2A 95.397 239 9 1 2696 2932 151333014 151333252 2.130000e-101 379.0
16 TraesCS6A01G372100 chr2A 95.021 241 11 1 2692 2931 125306813 125307053 7.670000e-101 377.0
17 TraesCS6A01G372100 chr1A 95.763 236 8 1 2698 2931 483902029 483901794 2.130000e-101 379.0
18 TraesCS6A01G372100 chr3D 86.022 279 29 8 2179 2454 574321694 574321423 1.030000e-74 291.0
19 TraesCS6A01G372100 chr3D 84.752 282 32 9 2179 2456 486913963 486913689 3.720000e-69 272.0
20 TraesCS6A01G372100 chr4D 86.822 258 24 8 2181 2435 19287858 19288108 2.230000e-71 279.0
21 TraesCS6A01G372100 chr4D 88.119 101 9 3 305 403 323534446 323534545 1.850000e-22 117.0
22 TraesCS6A01G372100 chr5A 84.211 285 32 9 2177 2456 18780642 18780366 6.230000e-67 265.0
23 TraesCS6A01G372100 chr4B 86.000 100 11 3 305 403 404107415 404107512 1.440000e-18 104.0
24 TraesCS6A01G372100 chr3B 87.324 71 7 2 334 403 671373655 671373586 2.420000e-11 80.5


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 TraesCS6A01G372100 chr6A 596128766 596131697 2931 False 5415.0 5415 100.0000 1 2932 1 chr6A.!!$F1 2931
1 TraesCS6A01G372100 chr6D 450613608 450616328 2720 False 3888.0 3888 92.6620 3 2697 1 chr6D.!!$F2 2694
2 TraesCS6A01G372100 chr6B 684219411 684221597 2186 False 1469.5 2534 92.0485 203 2311 2 chr6B.!!$F4 2108
3 TraesCS6A01G372100 chr6B 684375461 684376162 701 False 665.0 665 84.7580 2037 2697 1 chr6B.!!$F3 660

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
77 78 0.035458 AAGAAGGTTGCCGAGGACAG 59.965 55.0 0.0 0.0 0.00 3.51 F
615 631 0.103208 GTGGAGTTCGGCATCTCGAT 59.897 55.0 0.0 0.0 39.03 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1556 0.525029 GGTTGTCGCCGTAGTAGAGC 60.525 60.000 0.0 0.0 0.00 4.09 R
2571 2772 1.004862 AGGCTTTTTAGAGGGCTCACC 59.995 52.381 0.0 0.0 40.67 4.02 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
25 26 4.437239 GTCCATCGTCTTCATCATCAACT 58.563 43.478 0.00 0.00 0.00 3.16
27 28 4.872124 TCCATCGTCTTCATCATCAACTTG 59.128 41.667 0.00 0.00 0.00 3.16
39 40 2.509052 TCAACTTGTCCACTGACTCG 57.491 50.000 0.00 0.00 42.28 4.18
40 41 1.068588 TCAACTTGTCCACTGACTCGG 59.931 52.381 0.00 0.00 42.28 4.63
50 51 0.606944 ACTGACTCGGAGAAGCTCGT 60.607 55.000 12.86 0.00 34.09 4.18
53 54 0.241481 GACTCGGAGAAGCTCGTTGT 59.759 55.000 12.86 0.00 34.09 3.32
54 55 0.241481 ACTCGGAGAAGCTCGTTGTC 59.759 55.000 12.86 0.00 34.09 3.18
77 78 0.035458 AAGAAGGTTGCCGAGGACAG 59.965 55.000 0.00 0.00 0.00 3.51
117 118 2.626780 GGCTTCGACTTGGCCAACC 61.627 63.158 16.05 8.83 44.69 3.77
144 145 4.142249 GGGTATATAAATCATTTGGCCCGC 60.142 45.833 0.00 0.00 0.00 6.13
162 163 2.159517 CCGCTCCTGTTTATTTCTGTGC 60.160 50.000 0.00 0.00 0.00 4.57
163 164 2.159517 CGCTCCTGTTTATTTCTGTGCC 60.160 50.000 0.00 0.00 0.00 5.01
168 169 0.885196 GTTTATTTCTGTGCCGGCCA 59.115 50.000 26.77 20.19 0.00 5.36
391 392 2.493675 AGTCTGCGACATATGACAGTGT 59.506 45.455 10.38 0.00 34.60 3.55
404 405 9.481340 ACATATGACAGTGTGTGTATGATATTC 57.519 33.333 10.38 0.00 40.56 1.75
406 407 9.702494 ATATGACAGTGTGTGTATGATATTCTG 57.298 33.333 0.00 0.00 40.56 3.02
417 418 9.895138 TGTGTATGATATTCTGGATATGAATGG 57.105 33.333 0.00 0.00 35.90 3.16
441 449 9.349713 TGGAATGGTCTATATTTGAAATGGTAC 57.650 33.333 0.00 0.00 0.00 3.34
442 450 9.574516 GGAATGGTCTATATTTGAAATGGTACT 57.425 33.333 0.00 0.00 0.00 2.73
444 452 7.801716 TGGTCTATATTTGAAATGGTACTGC 57.198 36.000 0.00 0.00 0.00 4.40
445 453 7.342581 TGGTCTATATTTGAAATGGTACTGCA 58.657 34.615 0.00 0.00 0.00 4.41
446 454 7.998383 TGGTCTATATTTGAAATGGTACTGCAT 59.002 33.333 0.00 0.00 0.00 3.96
447 455 8.850156 GGTCTATATTTGAAATGGTACTGCATT 58.150 33.333 0.00 0.00 0.00 3.56
467 475 6.579666 CATTACTGCATATGGCCTTACAAT 57.420 37.500 3.32 0.00 43.89 2.71
469 477 3.225104 ACTGCATATGGCCTTACAATGG 58.775 45.455 3.32 0.00 43.89 3.16
488 496 2.236146 TGGTAAATCAGCGTCAGATGGT 59.764 45.455 0.00 0.00 33.94 3.55
489 497 2.866762 GGTAAATCAGCGTCAGATGGTC 59.133 50.000 0.00 0.00 33.94 4.02
490 498 2.768253 AAATCAGCGTCAGATGGTCA 57.232 45.000 0.00 0.00 33.94 4.02
491 499 2.015736 AATCAGCGTCAGATGGTCAC 57.984 50.000 0.00 0.00 33.94 3.67
492 500 1.189752 ATCAGCGTCAGATGGTCACT 58.810 50.000 0.00 0.00 33.94 3.41
493 501 0.244721 TCAGCGTCAGATGGTCACTG 59.755 55.000 0.00 0.00 33.94 3.66
494 502 1.079543 AGCGTCAGATGGTCACTGC 60.080 57.895 0.00 0.00 35.61 4.40
598 614 3.192422 TGAGTTTTGACAGGTGTTTGGTG 59.808 43.478 0.00 0.00 0.00 4.17
614 630 1.511305 GTGGAGTTCGGCATCTCGA 59.489 57.895 0.00 0.00 37.38 4.04
615 631 0.103208 GTGGAGTTCGGCATCTCGAT 59.897 55.000 0.00 0.00 39.03 3.59
616 632 0.385751 TGGAGTTCGGCATCTCGATC 59.614 55.000 0.00 0.00 39.03 3.69
617 633 0.661780 GGAGTTCGGCATCTCGATCG 60.662 60.000 9.36 9.36 39.03 3.69
628 644 4.092091 GGCATCTCGATCGGTGATATTTTC 59.908 45.833 16.41 6.94 0.00 2.29
692 708 6.119536 TCAAAATATCGAAACCTGCCAGTAT 58.880 36.000 0.00 0.00 0.00 2.12
738 754 2.234414 AGCAAATTAGTTGTGGCCATGG 59.766 45.455 9.72 7.63 39.63 3.66
742 758 2.889170 TTAGTTGTGGCCATGGCTAA 57.111 45.000 34.70 23.51 41.60 3.09
778 794 1.273606 AGATTGAGGTGTGTGGTCTCG 59.726 52.381 0.00 0.00 0.00 4.04
786 802 0.103390 TGTGTGGTCTCGCGAAGAAA 59.897 50.000 11.33 0.00 35.21 2.52
796 812 1.868498 TCGCGAAGAAACCGACAAAAT 59.132 42.857 6.20 0.00 0.00 1.82
901 927 3.181446 GCCTCATCCTATTCTTCAAGCCT 60.181 47.826 0.00 0.00 0.00 4.58
973 999 1.807755 GCTGCCATCATCACGAGCTAA 60.808 52.381 0.00 0.00 0.00 3.09
1063 1089 2.821366 CCACAGCCAGCCTTAGCG 60.821 66.667 0.00 0.00 46.67 4.26
1112 1144 4.697756 CAGGTTCCTGCCGGCGAA 62.698 66.667 23.90 17.40 0.00 4.70
1371 1412 1.134901 CGACGTCGACTTCCTCCTG 59.865 63.158 33.35 0.00 43.02 3.86
1587 1628 4.783621 GTGGAGGCGCTCATGGCA 62.784 66.667 7.64 0.00 41.91 4.92
1615 1656 4.070552 GCGAGGACGGGAAGCTGT 62.071 66.667 0.00 0.00 40.15 4.40
1785 1826 3.063084 GAGGTCGTCGAGGTGCCT 61.063 66.667 18.52 18.52 0.00 4.75
1869 1910 2.986413 ATCGGCGAGATCCTCCGG 60.986 66.667 17.22 0.00 43.10 5.14
1901 1950 4.504858 GTCAGGGTCACATACTAAACCAG 58.495 47.826 0.00 0.00 33.27 4.00
1931 2077 4.570772 ACCAGCAATGCTTTATGTACGTAG 59.429 41.667 4.36 0.00 36.40 3.51
1932 2078 4.570772 CCAGCAATGCTTTATGTACGTAGT 59.429 41.667 4.36 0.00 40.74 2.73
1933 2079 5.751509 CCAGCAATGCTTTATGTACGTAGTA 59.248 40.000 4.36 0.00 38.56 1.82
2338 2518 5.956642 ACTAAACCAACAAAACGACAACAT 58.043 33.333 0.00 0.00 0.00 2.71
2382 2562 2.751259 ACTATGCCTACGTCGAAAGTGA 59.249 45.455 0.00 0.00 0.00 3.41
2414 2594 1.221840 CGGAGGTTATGCTGCCACT 59.778 57.895 0.00 0.00 0.00 4.00
2423 2603 0.968901 ATGCTGCCACTCATGTTGGG 60.969 55.000 15.26 6.59 0.00 4.12
2467 2648 4.235762 AACCGCCACTCACGCTGT 62.236 61.111 0.00 0.00 0.00 4.40
2489 2670 4.443394 GTCGAGTATTAACATGTAAGCCGG 59.557 45.833 0.00 0.00 0.00 6.13
2571 2772 1.940613 GCTTATGGCTGAGTAAACCGG 59.059 52.381 0.00 0.00 38.06 5.28
2619 2820 6.350277 GGCTTACATATAAGACTCGGCATACT 60.350 42.308 0.00 0.00 42.50 2.12
2621 2822 7.520451 TTACATATAAGACTCGGCATACTGT 57.480 36.000 0.00 0.00 0.00 3.55
2633 2834 3.703420 GGCATACTGTACGGAGTTACTG 58.297 50.000 9.17 0.00 37.78 2.74
2653 2854 3.760693 GCTTACAGCCAATCCTCGA 57.239 52.632 0.00 0.00 34.48 4.04
2697 2898 2.596851 ATGGGAGTTGCAGACGGCT 61.597 57.895 0.00 0.00 45.15 5.52
2698 2899 2.743928 GGGAGTTGCAGACGGCTG 60.744 66.667 15.93 15.93 45.15 4.85
2699 2900 2.343758 GGAGTTGCAGACGGCTGA 59.656 61.111 26.04 4.03 45.17 4.26
2700 2901 1.078848 GGAGTTGCAGACGGCTGAT 60.079 57.895 26.04 3.51 45.17 2.90
2701 2902 0.175760 GGAGTTGCAGACGGCTGATA 59.824 55.000 26.04 7.08 45.17 2.15
2702 2903 1.281899 GAGTTGCAGACGGCTGATAC 58.718 55.000 26.04 18.57 45.17 2.24
2703 2904 0.458543 AGTTGCAGACGGCTGATACG 60.459 55.000 26.04 0.00 45.17 3.06
2709 2910 3.108343 ACGGCTGATACGTCTCCG 58.892 61.111 0.00 1.43 41.25 4.63
2711 2912 1.009900 CGGCTGATACGTCTCCGTC 60.010 63.158 0.00 0.00 46.28 4.79
2712 2913 1.009900 GGCTGATACGTCTCCGTCG 60.010 63.158 0.00 0.00 46.28 5.12
2713 2914 1.712977 GGCTGATACGTCTCCGTCGT 61.713 60.000 0.00 0.00 46.28 4.34
2714 2915 0.933097 GCTGATACGTCTCCGTCGTA 59.067 55.000 0.00 0.00 46.28 3.43
2720 2921 2.593346 ACGTCTCCGTCGTATCTACT 57.407 50.000 0.00 0.00 46.28 2.57
2721 2922 2.898705 ACGTCTCCGTCGTATCTACTT 58.101 47.619 0.00 0.00 46.28 2.24
2722 2923 3.265791 ACGTCTCCGTCGTATCTACTTT 58.734 45.455 0.00 0.00 46.28 2.66
2723 2924 3.686726 ACGTCTCCGTCGTATCTACTTTT 59.313 43.478 0.00 0.00 46.28 2.27
2724 2925 4.201763 ACGTCTCCGTCGTATCTACTTTTC 60.202 45.833 0.00 0.00 46.28 2.29
2725 2926 4.596097 GTCTCCGTCGTATCTACTTTTCC 58.404 47.826 0.00 0.00 0.00 3.13
2726 2927 4.095483 GTCTCCGTCGTATCTACTTTTCCA 59.905 45.833 0.00 0.00 0.00 3.53
2727 2928 4.701651 TCTCCGTCGTATCTACTTTTCCAA 59.298 41.667 0.00 0.00 0.00 3.53
2728 2929 5.183713 TCTCCGTCGTATCTACTTTTCCAAA 59.816 40.000 0.00 0.00 0.00 3.28
2729 2930 5.163513 TCCGTCGTATCTACTTTTCCAAAC 58.836 41.667 0.00 0.00 0.00 2.93
2730 2931 4.925054 CCGTCGTATCTACTTTTCCAAACA 59.075 41.667 0.00 0.00 0.00 2.83
2731 2932 5.164022 CCGTCGTATCTACTTTTCCAAACAC 60.164 44.000 0.00 0.00 0.00 3.32
2732 2933 5.632347 CGTCGTATCTACTTTTCCAAACACT 59.368 40.000 0.00 0.00 0.00 3.55
2733 2934 6.145048 CGTCGTATCTACTTTTCCAAACACTT 59.855 38.462 0.00 0.00 0.00 3.16
2734 2935 7.306983 CGTCGTATCTACTTTTCCAAACACTTT 60.307 37.037 0.00 0.00 0.00 2.66
2735 2936 8.340443 GTCGTATCTACTTTTCCAAACACTTTT 58.660 33.333 0.00 0.00 0.00 2.27
2736 2937 8.339714 TCGTATCTACTTTTCCAAACACTTTTG 58.660 33.333 0.00 0.00 41.71 2.44
2737 2938 7.112984 CGTATCTACTTTTCCAAACACTTTTGC 59.887 37.037 0.00 0.00 40.84 3.68
2738 2939 5.656480 TCTACTTTTCCAAACACTTTTGCC 58.344 37.500 0.00 0.00 40.84 4.52
2739 2940 3.605634 ACTTTTCCAAACACTTTTGCCC 58.394 40.909 0.00 0.00 40.84 5.36
2740 2941 3.263170 ACTTTTCCAAACACTTTTGCCCT 59.737 39.130 0.00 0.00 40.84 5.19
2741 2942 3.990959 TTTCCAAACACTTTTGCCCTT 57.009 38.095 0.00 0.00 40.84 3.95
2742 2943 5.046231 ACTTTTCCAAACACTTTTGCCCTTA 60.046 36.000 0.00 0.00 40.84 2.69
2743 2944 5.622346 TTTCCAAACACTTTTGCCCTTAT 57.378 34.783 0.00 0.00 40.84 1.73
2744 2945 5.622346 TTCCAAACACTTTTGCCCTTATT 57.378 34.783 0.00 0.00 40.84 1.40
2745 2946 5.622346 TCCAAACACTTTTGCCCTTATTT 57.378 34.783 0.00 0.00 40.84 1.40
2746 2947 5.995446 TCCAAACACTTTTGCCCTTATTTT 58.005 33.333 0.00 0.00 40.84 1.82
2747 2948 5.819901 TCCAAACACTTTTGCCCTTATTTTG 59.180 36.000 0.00 0.00 40.84 2.44
2748 2949 5.008514 CCAAACACTTTTGCCCTTATTTTGG 59.991 40.000 0.00 0.00 40.84 3.28
2749 2950 5.622346 AACACTTTTGCCCTTATTTTGGA 57.378 34.783 0.00 0.00 0.00 3.53
2750 2951 4.956085 ACACTTTTGCCCTTATTTTGGAC 58.044 39.130 0.00 0.00 0.00 4.02
2751 2952 4.653801 ACACTTTTGCCCTTATTTTGGACT 59.346 37.500 0.00 0.00 0.00 3.85
2752 2953 5.221441 ACACTTTTGCCCTTATTTTGGACTC 60.221 40.000 0.00 0.00 0.00 3.36
2753 2954 5.011023 CACTTTTGCCCTTATTTTGGACTCT 59.989 40.000 0.00 0.00 0.00 3.24
2754 2955 6.208599 CACTTTTGCCCTTATTTTGGACTCTA 59.791 38.462 0.00 0.00 0.00 2.43
2755 2956 6.780522 ACTTTTGCCCTTATTTTGGACTCTAA 59.219 34.615 0.00 0.00 0.00 2.10
2756 2957 6.584185 TTTGCCCTTATTTTGGACTCTAAC 57.416 37.500 0.00 0.00 0.00 2.34
2757 2958 5.514500 TGCCCTTATTTTGGACTCTAACT 57.486 39.130 0.00 0.00 0.00 2.24
2758 2959 5.887754 TGCCCTTATTTTGGACTCTAACTT 58.112 37.500 0.00 0.00 0.00 2.66
2759 2960 6.311735 TGCCCTTATTTTGGACTCTAACTTT 58.688 36.000 0.00 0.00 0.00 2.66
2760 2961 6.780522 TGCCCTTATTTTGGACTCTAACTTTT 59.219 34.615 0.00 0.00 0.00 2.27
2761 2962 7.945664 TGCCCTTATTTTGGACTCTAACTTTTA 59.054 33.333 0.00 0.00 0.00 1.52
2762 2963 8.967918 GCCCTTATTTTGGACTCTAACTTTTAT 58.032 33.333 0.00 0.00 0.00 1.40
2782 2983 9.586435 CTTTTATGATTTGAATGGAACTAACCC 57.414 33.333 0.00 0.00 0.00 4.11
2783 2984 5.835113 ATGATTTGAATGGAACTAACCCG 57.165 39.130 0.00 0.00 0.00 5.28
2784 2985 4.013728 TGATTTGAATGGAACTAACCCGG 58.986 43.478 0.00 0.00 0.00 5.73
2785 2986 3.791953 TTTGAATGGAACTAACCCGGA 57.208 42.857 0.73 0.00 0.00 5.14
2786 2987 2.773993 TGAATGGAACTAACCCGGAC 57.226 50.000 0.73 0.00 0.00 4.79
2787 2988 2.262637 TGAATGGAACTAACCCGGACT 58.737 47.619 0.73 0.00 0.00 3.85
2788 2989 2.027561 TGAATGGAACTAACCCGGACTG 60.028 50.000 0.73 0.00 0.00 3.51
2789 2990 1.946984 ATGGAACTAACCCGGACTGA 58.053 50.000 0.73 0.00 0.00 3.41
2790 2991 0.971386 TGGAACTAACCCGGACTGAC 59.029 55.000 0.73 0.00 0.00 3.51
2791 2992 0.108945 GGAACTAACCCGGACTGACG 60.109 60.000 0.73 0.00 0.00 4.35
2792 2993 0.735287 GAACTAACCCGGACTGACGC 60.735 60.000 0.73 0.00 0.00 5.19
2793 2994 1.183676 AACTAACCCGGACTGACGCT 61.184 55.000 0.73 0.00 0.00 5.07
2794 2995 1.153823 CTAACCCGGACTGACGCTG 60.154 63.158 0.73 0.00 0.00 5.18
2795 2996 1.874345 CTAACCCGGACTGACGCTGT 61.874 60.000 0.73 0.00 0.00 4.40
2796 2997 1.466025 TAACCCGGACTGACGCTGTT 61.466 55.000 0.73 0.00 33.80 3.16
2797 2998 2.030562 CCCGGACTGACGCTGTTT 59.969 61.111 0.73 0.00 0.00 2.83
2798 2999 1.597027 CCCGGACTGACGCTGTTTT 60.597 57.895 0.73 0.00 0.00 2.43
2799 3000 1.566018 CCCGGACTGACGCTGTTTTC 61.566 60.000 0.73 0.00 0.00 2.29
2800 3001 0.878523 CCGGACTGACGCTGTTTTCA 60.879 55.000 0.00 0.00 0.00 2.69
2821 3022 3.241067 GCAGAATTGCCATGATGTTGT 57.759 42.857 0.00 0.00 44.74 3.32
2822 3023 3.592059 GCAGAATTGCCATGATGTTGTT 58.408 40.909 0.00 0.00 44.74 2.83
2823 3024 3.998341 GCAGAATTGCCATGATGTTGTTT 59.002 39.130 0.00 0.00 44.74 2.83
2824 3025 4.453136 GCAGAATTGCCATGATGTTGTTTT 59.547 37.500 0.00 0.00 44.74 2.43
2825 3026 5.638657 GCAGAATTGCCATGATGTTGTTTTA 59.361 36.000 0.00 0.00 44.74 1.52
2826 3027 6.314400 GCAGAATTGCCATGATGTTGTTTTAT 59.686 34.615 0.00 0.00 44.74 1.40
2827 3028 7.675403 GCAGAATTGCCATGATGTTGTTTTATG 60.675 37.037 0.00 0.00 44.74 1.90
2828 3029 7.332430 CAGAATTGCCATGATGTTGTTTTATGT 59.668 33.333 0.00 0.00 0.00 2.29
2829 3030 6.971527 ATTGCCATGATGTTGTTTTATGTG 57.028 33.333 0.00 0.00 0.00 3.21
2830 3031 5.465532 TGCCATGATGTTGTTTTATGTGT 57.534 34.783 0.00 0.00 0.00 3.72
2831 3032 6.581171 TGCCATGATGTTGTTTTATGTGTA 57.419 33.333 0.00 0.00 0.00 2.90
2832 3033 6.619744 TGCCATGATGTTGTTTTATGTGTAG 58.380 36.000 0.00 0.00 0.00 2.74
2833 3034 6.432472 TGCCATGATGTTGTTTTATGTGTAGA 59.568 34.615 0.00 0.00 0.00 2.59
2834 3035 7.040132 TGCCATGATGTTGTTTTATGTGTAGAA 60.040 33.333 0.00 0.00 0.00 2.10
2835 3036 7.812191 GCCATGATGTTGTTTTATGTGTAGAAA 59.188 33.333 0.00 0.00 0.00 2.52
2836 3037 9.689976 CCATGATGTTGTTTTATGTGTAGAAAA 57.310 29.630 0.00 0.00 0.00 2.29
2857 3058 9.408648 AGAAAACAAATATTATCGGAATGACCT 57.591 29.630 0.00 0.00 36.31 3.85
2865 3066 9.503399 AATATTATCGGAATGACCTAAAACTCC 57.497 33.333 0.00 0.00 36.31 3.85
2866 3067 4.837093 ATCGGAATGACCTAAAACTCCA 57.163 40.909 0.00 0.00 36.31 3.86
2867 3068 3.934068 TCGGAATGACCTAAAACTCCAC 58.066 45.455 0.00 0.00 36.31 4.02
2868 3069 2.671396 CGGAATGACCTAAAACTCCACG 59.329 50.000 0.00 0.00 36.31 4.94
2869 3070 3.007635 GGAATGACCTAAAACTCCACGG 58.992 50.000 0.00 0.00 35.41 4.94
2870 3071 3.307199 GGAATGACCTAAAACTCCACGGA 60.307 47.826 0.00 0.00 35.41 4.69
2871 3072 4.320870 GAATGACCTAAAACTCCACGGAA 58.679 43.478 0.00 0.00 0.00 4.30
2872 3073 3.116079 TGACCTAAAACTCCACGGAAC 57.884 47.619 0.00 0.00 0.00 3.62
2873 3074 2.435069 TGACCTAAAACTCCACGGAACA 59.565 45.455 0.00 0.00 0.00 3.18
2874 3075 3.118334 TGACCTAAAACTCCACGGAACAA 60.118 43.478 0.00 0.00 0.00 2.83
2875 3076 3.208594 ACCTAAAACTCCACGGAACAAC 58.791 45.455 0.00 0.00 0.00 3.32
2876 3077 3.118149 ACCTAAAACTCCACGGAACAACT 60.118 43.478 0.00 0.00 0.00 3.16
2877 3078 3.881089 CCTAAAACTCCACGGAACAACTT 59.119 43.478 0.00 0.00 0.00 2.66
2878 3079 5.058490 CCTAAAACTCCACGGAACAACTTA 58.942 41.667 0.00 0.00 0.00 2.24
2879 3080 5.178809 CCTAAAACTCCACGGAACAACTTAG 59.821 44.000 0.00 0.00 0.00 2.18
2880 3081 4.411256 AAACTCCACGGAACAACTTAGA 57.589 40.909 0.00 0.00 0.00 2.10
2881 3082 4.411256 AACTCCACGGAACAACTTAGAA 57.589 40.909 0.00 0.00 0.00 2.10
2882 3083 4.411256 ACTCCACGGAACAACTTAGAAA 57.589 40.909 0.00 0.00 0.00 2.52
2883 3084 4.773013 ACTCCACGGAACAACTTAGAAAA 58.227 39.130 0.00 0.00 0.00 2.29
2884 3085 5.187687 ACTCCACGGAACAACTTAGAAAAA 58.812 37.500 0.00 0.00 0.00 1.94
2911 3112 4.708726 AAAATCCTCGCCAAAGATGAAG 57.291 40.909 0.00 0.00 0.00 3.02
2912 3113 3.634397 AATCCTCGCCAAAGATGAAGA 57.366 42.857 0.00 0.00 0.00 2.87
2913 3114 2.386661 TCCTCGCCAAAGATGAAGAC 57.613 50.000 0.00 0.00 0.00 3.01
2914 3115 1.066143 TCCTCGCCAAAGATGAAGACC 60.066 52.381 0.00 0.00 0.00 3.85
2915 3116 1.339055 CCTCGCCAAAGATGAAGACCA 60.339 52.381 0.00 0.00 0.00 4.02
2916 3117 2.636830 CTCGCCAAAGATGAAGACCAT 58.363 47.619 0.00 0.00 38.43 3.55
2917 3118 2.353889 CTCGCCAAAGATGAAGACCATG 59.646 50.000 0.00 0.00 35.17 3.66
2918 3119 2.086869 CGCCAAAGATGAAGACCATGT 58.913 47.619 0.00 0.00 35.17 3.21
2919 3120 2.159476 CGCCAAAGATGAAGACCATGTG 60.159 50.000 0.00 0.00 35.17 3.21
2920 3121 2.165030 GCCAAAGATGAAGACCATGTGG 59.835 50.000 0.00 0.00 42.17 4.17
2921 3122 2.165030 CCAAAGATGAAGACCATGTGGC 59.835 50.000 0.00 0.00 39.32 5.01
2922 3123 2.134789 AAGATGAAGACCATGTGGCC 57.865 50.000 0.00 0.00 39.32 5.36
2923 3124 0.257039 AGATGAAGACCATGTGGCCC 59.743 55.000 0.00 0.00 39.32 5.80
2924 3125 0.034186 GATGAAGACCATGTGGCCCA 60.034 55.000 0.00 0.00 39.32 5.36
2925 3126 0.323725 ATGAAGACCATGTGGCCCAC 60.324 55.000 7.01 7.01 39.32 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 4.437239 AGTTGATGATGAAGACGATGGAC 58.563 43.478 0.00 0.00 0.00 4.02
4 5 4.743057 AGTTGATGATGAAGACGATGGA 57.257 40.909 0.00 0.00 0.00 3.41
5 6 4.633126 ACAAGTTGATGATGAAGACGATGG 59.367 41.667 10.54 0.00 0.00 3.51
6 7 5.220548 GGACAAGTTGATGATGAAGACGATG 60.221 44.000 10.54 0.00 0.00 3.84
7 8 4.872691 GGACAAGTTGATGATGAAGACGAT 59.127 41.667 10.54 0.00 0.00 3.73
8 9 4.245660 GGACAAGTTGATGATGAAGACGA 58.754 43.478 10.54 0.00 0.00 4.20
10 11 4.999950 AGTGGACAAGTTGATGATGAAGAC 59.000 41.667 10.54 0.00 0.00 3.01
11 12 4.999311 CAGTGGACAAGTTGATGATGAAGA 59.001 41.667 10.54 0.00 0.00 2.87
16 17 4.573900 GAGTCAGTGGACAAGTTGATGAT 58.426 43.478 10.54 0.00 46.80 2.45
25 26 1.613925 CTTCTCCGAGTCAGTGGACAA 59.386 52.381 0.00 0.00 46.80 3.18
27 28 0.109039 GCTTCTCCGAGTCAGTGGAC 60.109 60.000 0.00 0.00 44.66 4.02
50 51 1.872237 CGGCAACCTTCTTCTCGACAA 60.872 52.381 0.00 0.00 0.00 3.18
53 54 0.243907 CTCGGCAACCTTCTTCTCGA 59.756 55.000 0.00 0.00 0.00 4.04
54 55 0.737715 CCTCGGCAACCTTCTTCTCG 60.738 60.000 0.00 0.00 0.00 4.04
107 108 0.039618 ATACCCACTGGTTGGCCAAG 59.960 55.000 21.21 10.33 44.75 3.61
108 109 1.373536 TATACCCACTGGTTGGCCAA 58.626 50.000 16.05 16.05 44.75 4.52
117 118 6.071391 GGGCCAAATGATTTATATACCCACTG 60.071 42.308 4.39 0.00 33.65 3.66
120 121 5.013547 CGGGCCAAATGATTTATATACCCA 58.986 41.667 4.39 0.00 32.98 4.51
130 131 1.039233 CAGGAGCGGGCCAAATGATT 61.039 55.000 4.39 0.00 0.00 2.57
138 139 0.738975 GAAATAAACAGGAGCGGGCC 59.261 55.000 0.00 0.00 0.00 5.80
139 140 1.401905 CAGAAATAAACAGGAGCGGGC 59.598 52.381 0.00 0.00 0.00 6.13
144 145 2.420022 CCGGCACAGAAATAAACAGGAG 59.580 50.000 0.00 0.00 0.00 3.69
391 392 9.895138 CCATTCATATCCAGAATATCATACACA 57.105 33.333 0.00 0.00 34.14 3.72
416 417 9.574516 AGTACCATTTCAAATATAGACCATTCC 57.425 33.333 0.00 0.00 0.00 3.01
420 428 7.342581 TGCAGTACCATTTCAAATATAGACCA 58.657 34.615 0.00 0.00 0.00 4.02
443 451 3.820467 TGTAAGGCCATATGCAGTAATGC 59.180 43.478 8.51 8.51 43.89 3.56
444 452 6.384224 CATTGTAAGGCCATATGCAGTAATG 58.616 40.000 5.01 0.00 43.89 1.90
445 453 5.477984 CCATTGTAAGGCCATATGCAGTAAT 59.522 40.000 5.01 0.00 43.89 1.89
446 454 4.826733 CCATTGTAAGGCCATATGCAGTAA 59.173 41.667 5.01 0.00 43.89 2.24
447 455 4.141274 ACCATTGTAAGGCCATATGCAGTA 60.141 41.667 5.01 0.00 43.89 2.74
467 475 2.236146 ACCATCTGACGCTGATTTACCA 59.764 45.455 0.00 0.00 0.00 3.25
469 477 3.307242 GTGACCATCTGACGCTGATTTAC 59.693 47.826 0.00 0.00 0.00 2.01
490 498 1.745087 CACCAGTTCACACTTTGCAGT 59.255 47.619 0.00 0.00 0.00 4.40
491 499 1.066002 CCACCAGTTCACACTTTGCAG 59.934 52.381 0.00 0.00 0.00 4.41
492 500 1.102154 CCACCAGTTCACACTTTGCA 58.898 50.000 0.00 0.00 0.00 4.08
493 501 1.065551 GTCCACCAGTTCACACTTTGC 59.934 52.381 0.00 0.00 0.00 3.68
494 502 2.355756 CTGTCCACCAGTTCACACTTTG 59.644 50.000 0.00 0.00 36.37 2.77
598 614 0.661780 CGATCGAGATGCCGAACTCC 60.662 60.000 10.26 0.00 42.22 3.85
614 630 8.980143 AAAACAATTTCGAAAATATCACCGAT 57.020 26.923 15.66 0.00 0.00 4.18
628 644 6.739550 GGTAGGACGAACATAAAACAATTTCG 59.260 38.462 0.00 0.00 43.61 3.46
692 708 0.106167 CTCTCGGGTGATCTGGGGTA 60.106 60.000 0.00 0.00 0.00 3.69
778 794 2.153057 GCAATTTTGTCGGTTTCTTCGC 59.847 45.455 0.00 0.00 0.00 4.70
786 802 1.851658 GCACTTGCAATTTTGTCGGT 58.148 45.000 0.00 0.00 41.59 4.69
919 945 1.437772 GCTGACTGGCTGCTGCTATG 61.438 60.000 15.64 8.23 38.32 2.23
920 946 1.153208 GCTGACTGGCTGCTGCTAT 60.153 57.895 15.64 1.08 38.32 2.97
921 947 2.267006 GCTGACTGGCTGCTGCTA 59.733 61.111 15.64 8.60 38.32 3.49
922 948 3.903616 CTGCTGACTGGCTGCTGCT 62.904 63.158 15.64 0.00 41.53 4.24
923 949 3.432588 CTGCTGACTGGCTGCTGC 61.433 66.667 13.71 7.10 41.53 5.25
924 950 2.746671 CCTGCTGACTGGCTGCTG 60.747 66.667 13.71 12.52 41.53 4.41
949 975 2.242572 CGTGATGATGGCAGCGAGG 61.243 63.158 0.00 0.00 31.73 4.63
1045 1071 2.352805 GCTAAGGCTGGCTGTGGT 59.647 61.111 3.84 0.00 35.22 4.16
1081 1113 3.060615 CCTGACCTTGCTGCTGCC 61.061 66.667 13.47 0.00 38.71 4.85
1371 1412 2.202756 GACTCGTCGCCCATGACC 60.203 66.667 0.00 0.00 35.40 4.02
1411 1452 4.115199 GGTGATGCCCTCCCGCTT 62.115 66.667 0.00 0.00 0.00 4.68
1515 1556 0.525029 GGTTGTCGCCGTAGTAGAGC 60.525 60.000 0.00 0.00 0.00 4.09
1587 1628 2.676822 TCCTCGCCGCTGTTCTCT 60.677 61.111 0.00 0.00 0.00 3.10
1608 1649 1.845809 CGTCCAGCACCAACAGCTTC 61.846 60.000 0.00 0.00 41.14 3.86
1615 1656 4.308458 CCCGACGTCCAGCACCAA 62.308 66.667 10.58 0.00 0.00 3.67
1785 1826 3.245984 TGTCCCTGATGAAGAGGAAGGTA 60.246 47.826 0.00 0.00 31.48 3.08
1845 1886 1.080839 GATCTCGCCGATGAGCTCC 60.081 63.158 12.15 0.00 35.90 4.70
1869 1910 3.001406 ACCCTGACGCCCTGGTAC 61.001 66.667 0.00 0.00 32.48 3.34
1901 1950 2.433664 GCATTGCTGGTGGCTTGC 60.434 61.111 0.16 0.00 41.00 4.01
1931 2077 6.730619 CGAATTCACAAGTATCGTTGTTGTAC 59.269 38.462 6.22 0.00 38.65 2.90
1932 2078 6.128769 CCGAATTCACAAGTATCGTTGTTGTA 60.129 38.462 6.22 0.00 38.65 2.41
1933 2079 5.333798 CCGAATTCACAAGTATCGTTGTTGT 60.334 40.000 6.22 0.00 38.65 3.32
1934 2080 5.079406 CCGAATTCACAAGTATCGTTGTTG 58.921 41.667 6.22 0.00 38.65 3.33
1935 2081 4.378046 GCCGAATTCACAAGTATCGTTGTT 60.378 41.667 6.22 0.00 38.65 2.83
1936 2082 3.124636 GCCGAATTCACAAGTATCGTTGT 59.875 43.478 6.22 0.00 41.47 3.32
1937 2083 3.485216 GGCCGAATTCACAAGTATCGTTG 60.485 47.826 6.22 0.00 0.00 4.10
1938 2084 2.676342 GGCCGAATTCACAAGTATCGTT 59.324 45.455 6.22 0.00 0.00 3.85
2338 2518 4.164796 TGTTGGTCTATAGGACTCTACCGA 59.835 45.833 0.00 0.00 43.97 4.69
2340 2520 5.447757 AGTGTTGGTCTATAGGACTCTACC 58.552 45.833 0.00 0.00 43.97 3.18
2467 2648 4.500205 CCCGGCTTACATGTTAATACTCGA 60.500 45.833 2.30 0.00 0.00 4.04
2489 2670 2.096119 CGAATACCCGTGTTTTGACACC 60.096 50.000 4.29 0.00 37.33 4.16
2571 2772 1.004862 AGGCTTTTTAGAGGGCTCACC 59.995 52.381 0.00 0.00 40.67 4.02
2619 2820 1.636148 AAGCCCAGTAACTCCGTACA 58.364 50.000 0.00 0.00 0.00 2.90
2621 2822 2.756760 CTGTAAGCCCAGTAACTCCGTA 59.243 50.000 0.00 0.00 0.00 4.02
2670 2871 0.820891 GCAACTCCCATGATCGCCAT 60.821 55.000 0.00 0.00 35.44 4.40
2703 2904 4.095483 TGGAAAAGTAGATACGACGGAGAC 59.905 45.833 0.00 0.00 0.00 3.36
2704 2905 4.264253 TGGAAAAGTAGATACGACGGAGA 58.736 43.478 0.00 0.00 0.00 3.71
2705 2906 4.627611 TGGAAAAGTAGATACGACGGAG 57.372 45.455 0.00 0.00 0.00 4.63
2706 2907 5.163513 GTTTGGAAAAGTAGATACGACGGA 58.836 41.667 0.00 0.00 0.00 4.69
2707 2908 4.925054 TGTTTGGAAAAGTAGATACGACGG 59.075 41.667 0.00 0.00 0.00 4.79
2708 2909 5.632347 AGTGTTTGGAAAAGTAGATACGACG 59.368 40.000 0.00 0.00 0.00 5.12
2709 2910 7.417496 AAGTGTTTGGAAAAGTAGATACGAC 57.583 36.000 0.00 0.00 0.00 4.34
2710 2911 8.339714 CAAAAGTGTTTGGAAAAGTAGATACGA 58.660 33.333 0.00 0.00 40.47 3.43
2711 2912 7.112984 GCAAAAGTGTTTGGAAAAGTAGATACG 59.887 37.037 1.72 0.00 43.73 3.06
2712 2913 7.381408 GGCAAAAGTGTTTGGAAAAGTAGATAC 59.619 37.037 1.72 0.00 43.73 2.24
2713 2914 7.430441 GGCAAAAGTGTTTGGAAAAGTAGATA 58.570 34.615 1.72 0.00 43.73 1.98
2714 2915 6.280643 GGCAAAAGTGTTTGGAAAAGTAGAT 58.719 36.000 1.72 0.00 43.73 1.98
2715 2916 5.394773 GGGCAAAAGTGTTTGGAAAAGTAGA 60.395 40.000 1.72 0.00 43.73 2.59
2716 2917 4.808895 GGGCAAAAGTGTTTGGAAAAGTAG 59.191 41.667 1.72 0.00 43.73 2.57
2717 2918 4.468153 AGGGCAAAAGTGTTTGGAAAAGTA 59.532 37.500 1.72 0.00 43.73 2.24
2718 2919 3.263170 AGGGCAAAAGTGTTTGGAAAAGT 59.737 39.130 1.72 0.00 43.73 2.66
2719 2920 3.872696 AGGGCAAAAGTGTTTGGAAAAG 58.127 40.909 1.72 0.00 43.73 2.27
2720 2921 3.990959 AGGGCAAAAGTGTTTGGAAAA 57.009 38.095 1.72 0.00 43.73 2.29
2721 2922 3.990959 AAGGGCAAAAGTGTTTGGAAA 57.009 38.095 1.72 0.00 43.73 3.13
2722 2923 5.622346 AATAAGGGCAAAAGTGTTTGGAA 57.378 34.783 1.72 0.00 43.73 3.53
2723 2924 5.622346 AAATAAGGGCAAAAGTGTTTGGA 57.378 34.783 1.72 0.00 43.73 3.53
2724 2925 5.008514 CCAAAATAAGGGCAAAAGTGTTTGG 59.991 40.000 0.00 0.00 43.73 3.28
2725 2926 5.819901 TCCAAAATAAGGGCAAAAGTGTTTG 59.180 36.000 0.00 0.00 45.88 2.93
2726 2927 5.820423 GTCCAAAATAAGGGCAAAAGTGTTT 59.180 36.000 0.00 0.00 0.00 2.83
2727 2928 5.130311 AGTCCAAAATAAGGGCAAAAGTGTT 59.870 36.000 0.00 0.00 31.65 3.32
2728 2929 4.653801 AGTCCAAAATAAGGGCAAAAGTGT 59.346 37.500 0.00 0.00 31.65 3.55
2729 2930 5.011023 AGAGTCCAAAATAAGGGCAAAAGTG 59.989 40.000 0.00 0.00 31.65 3.16
2730 2931 5.147767 AGAGTCCAAAATAAGGGCAAAAGT 58.852 37.500 0.00 0.00 31.65 2.66
2731 2932 5.728637 AGAGTCCAAAATAAGGGCAAAAG 57.271 39.130 0.00 0.00 31.65 2.27
2732 2933 6.780522 AGTTAGAGTCCAAAATAAGGGCAAAA 59.219 34.615 0.00 0.00 31.65 2.44
2733 2934 6.311735 AGTTAGAGTCCAAAATAAGGGCAAA 58.688 36.000 0.00 0.00 31.65 3.68
2734 2935 5.887754 AGTTAGAGTCCAAAATAAGGGCAA 58.112 37.500 0.00 0.00 31.65 4.52
2735 2936 5.514500 AGTTAGAGTCCAAAATAAGGGCA 57.486 39.130 0.00 0.00 31.65 5.36
2736 2937 6.835819 AAAGTTAGAGTCCAAAATAAGGGC 57.164 37.500 0.00 0.00 0.00 5.19
2756 2957 9.586435 GGGTTAGTTCCATTCAAATCATAAAAG 57.414 33.333 0.00 0.00 0.00 2.27
2757 2958 8.247562 CGGGTTAGTTCCATTCAAATCATAAAA 58.752 33.333 0.00 0.00 0.00 1.52
2758 2959 7.147983 CCGGGTTAGTTCCATTCAAATCATAAA 60.148 37.037 0.00 0.00 0.00 1.40
2759 2960 6.320164 CCGGGTTAGTTCCATTCAAATCATAA 59.680 38.462 0.00 0.00 0.00 1.90
2760 2961 5.825679 CCGGGTTAGTTCCATTCAAATCATA 59.174 40.000 0.00 0.00 0.00 2.15
2761 2962 4.644685 CCGGGTTAGTTCCATTCAAATCAT 59.355 41.667 0.00 0.00 0.00 2.45
2762 2963 4.013728 CCGGGTTAGTTCCATTCAAATCA 58.986 43.478 0.00 0.00 0.00 2.57
2763 2964 4.095932 GTCCGGGTTAGTTCCATTCAAATC 59.904 45.833 0.00 0.00 0.00 2.17
2764 2965 4.014406 GTCCGGGTTAGTTCCATTCAAAT 58.986 43.478 0.00 0.00 0.00 2.32
2765 2966 3.073356 AGTCCGGGTTAGTTCCATTCAAA 59.927 43.478 0.00 0.00 0.00 2.69
2766 2967 2.640826 AGTCCGGGTTAGTTCCATTCAA 59.359 45.455 0.00 0.00 0.00 2.69
2767 2968 2.027561 CAGTCCGGGTTAGTTCCATTCA 60.028 50.000 0.00 0.00 0.00 2.57
2768 2969 2.235402 TCAGTCCGGGTTAGTTCCATTC 59.765 50.000 0.00 0.00 0.00 2.67
2769 2970 2.027469 GTCAGTCCGGGTTAGTTCCATT 60.027 50.000 0.00 0.00 0.00 3.16
2770 2971 1.553704 GTCAGTCCGGGTTAGTTCCAT 59.446 52.381 0.00 0.00 0.00 3.41
2771 2972 0.971386 GTCAGTCCGGGTTAGTTCCA 59.029 55.000 0.00 0.00 0.00 3.53
2772 2973 0.108945 CGTCAGTCCGGGTTAGTTCC 60.109 60.000 0.00 0.00 0.00 3.62
2773 2974 0.735287 GCGTCAGTCCGGGTTAGTTC 60.735 60.000 0.00 0.00 0.00 3.01
2774 2975 1.183676 AGCGTCAGTCCGGGTTAGTT 61.184 55.000 0.00 0.00 0.00 2.24
2775 2976 1.605738 AGCGTCAGTCCGGGTTAGT 60.606 57.895 0.00 0.00 0.00 2.24
2776 2977 1.153823 CAGCGTCAGTCCGGGTTAG 60.154 63.158 0.00 0.00 0.00 2.34
2777 2978 1.466025 AACAGCGTCAGTCCGGGTTA 61.466 55.000 0.00 0.00 0.00 2.85
2778 2979 2.319890 AAACAGCGTCAGTCCGGGTT 62.320 55.000 0.00 0.00 0.00 4.11
2779 2980 2.319890 AAAACAGCGTCAGTCCGGGT 62.320 55.000 0.00 0.00 0.00 5.28
2780 2981 1.566018 GAAAACAGCGTCAGTCCGGG 61.566 60.000 0.00 0.00 0.00 5.73
2781 2982 0.878523 TGAAAACAGCGTCAGTCCGG 60.879 55.000 0.00 0.00 0.00 5.14
2782 2983 0.508641 CTGAAAACAGCGTCAGTCCG 59.491 55.000 0.00 0.00 37.16 4.79
2783 2984 0.235926 GCTGAAAACAGCGTCAGTCC 59.764 55.000 6.46 0.00 42.72 3.85
2784 2985 3.736581 GCTGAAAACAGCGTCAGTC 57.263 52.632 6.46 0.00 42.72 3.51
2802 3003 7.332430 ACATAAAACAACATCATGGCAATTCTG 59.668 33.333 0.00 0.00 0.00 3.02
2803 3004 7.332430 CACATAAAACAACATCATGGCAATTCT 59.668 33.333 0.00 0.00 0.00 2.40
2804 3005 7.118101 ACACATAAAACAACATCATGGCAATTC 59.882 33.333 0.00 0.00 0.00 2.17
2805 3006 6.935771 ACACATAAAACAACATCATGGCAATT 59.064 30.769 0.00 0.00 0.00 2.32
2806 3007 6.465948 ACACATAAAACAACATCATGGCAAT 58.534 32.000 0.00 0.00 0.00 3.56
2807 3008 5.851720 ACACATAAAACAACATCATGGCAA 58.148 33.333 0.00 0.00 0.00 4.52
2808 3009 5.465532 ACACATAAAACAACATCATGGCA 57.534 34.783 0.00 0.00 0.00 4.92
2809 3010 6.851609 TCTACACATAAAACAACATCATGGC 58.148 36.000 0.00 0.00 0.00 4.40
2810 3011 9.689976 TTTTCTACACATAAAACAACATCATGG 57.310 29.630 0.00 0.00 0.00 3.66
2831 3032 9.408648 AGGTCATTCCGATAATATTTGTTTTCT 57.591 29.630 0.00 0.00 41.99 2.52
2839 3040 9.503399 GGAGTTTTAGGTCATTCCGATAATATT 57.497 33.333 0.00 0.00 41.99 1.28
2840 3041 8.656806 TGGAGTTTTAGGTCATTCCGATAATAT 58.343 33.333 0.00 0.00 41.99 1.28
2841 3042 7.929785 GTGGAGTTTTAGGTCATTCCGATAATA 59.070 37.037 0.00 0.00 41.99 0.98
2842 3043 6.766467 GTGGAGTTTTAGGTCATTCCGATAAT 59.234 38.462 0.00 0.00 41.99 1.28
2843 3044 6.110707 GTGGAGTTTTAGGTCATTCCGATAA 58.889 40.000 0.00 0.00 41.99 1.75
2844 3045 5.667466 GTGGAGTTTTAGGTCATTCCGATA 58.333 41.667 0.00 0.00 41.99 2.92
2845 3046 4.514401 GTGGAGTTTTAGGTCATTCCGAT 58.486 43.478 0.00 0.00 41.99 4.18
2846 3047 3.615592 CGTGGAGTTTTAGGTCATTCCGA 60.616 47.826 0.00 0.00 41.99 4.55
2847 3048 2.671396 CGTGGAGTTTTAGGTCATTCCG 59.329 50.000 0.00 0.00 41.99 4.30
2848 3049 3.007635 CCGTGGAGTTTTAGGTCATTCC 58.992 50.000 0.00 0.00 0.00 3.01
2849 3050 3.934068 TCCGTGGAGTTTTAGGTCATTC 58.066 45.455 0.00 0.00 0.00 2.67
2850 3051 4.070009 GTTCCGTGGAGTTTTAGGTCATT 58.930 43.478 0.00 0.00 0.00 2.57
2851 3052 3.071892 TGTTCCGTGGAGTTTTAGGTCAT 59.928 43.478 0.00 0.00 0.00 3.06
2852 3053 2.435069 TGTTCCGTGGAGTTTTAGGTCA 59.565 45.455 0.00 0.00 0.00 4.02
2853 3054 3.116079 TGTTCCGTGGAGTTTTAGGTC 57.884 47.619 0.00 0.00 0.00 3.85
2854 3055 3.118149 AGTTGTTCCGTGGAGTTTTAGGT 60.118 43.478 0.00 0.00 0.00 3.08
2855 3056 3.473625 AGTTGTTCCGTGGAGTTTTAGG 58.526 45.455 0.00 0.00 0.00 2.69
2856 3057 5.987347 TCTAAGTTGTTCCGTGGAGTTTTAG 59.013 40.000 0.00 0.00 0.00 1.85
2857 3058 5.916318 TCTAAGTTGTTCCGTGGAGTTTTA 58.084 37.500 0.00 0.00 0.00 1.52
2858 3059 4.773013 TCTAAGTTGTTCCGTGGAGTTTT 58.227 39.130 0.00 0.00 0.00 2.43
2859 3060 4.411256 TCTAAGTTGTTCCGTGGAGTTT 57.589 40.909 0.00 0.00 0.00 2.66
2860 3061 4.411256 TTCTAAGTTGTTCCGTGGAGTT 57.589 40.909 0.00 0.00 0.00 3.01
2861 3062 4.411256 TTTCTAAGTTGTTCCGTGGAGT 57.589 40.909 0.00 0.00 0.00 3.85
2862 3063 5.744666 TTTTTCTAAGTTGTTCCGTGGAG 57.255 39.130 0.00 0.00 0.00 3.86
2889 3090 4.766891 TCTTCATCTTTGGCGAGGATTTTT 59.233 37.500 0.00 0.00 0.00 1.94
2890 3091 4.156739 GTCTTCATCTTTGGCGAGGATTTT 59.843 41.667 0.00 0.00 0.00 1.82
2891 3092 3.691609 GTCTTCATCTTTGGCGAGGATTT 59.308 43.478 0.00 0.00 0.00 2.17
2892 3093 3.274288 GTCTTCATCTTTGGCGAGGATT 58.726 45.455 0.00 0.00 0.00 3.01
2893 3094 2.420687 GGTCTTCATCTTTGGCGAGGAT 60.421 50.000 0.00 0.00 0.00 3.24
2894 3095 1.066143 GGTCTTCATCTTTGGCGAGGA 60.066 52.381 0.00 0.00 0.00 3.71
2895 3096 1.339055 TGGTCTTCATCTTTGGCGAGG 60.339 52.381 0.00 0.00 0.00 4.63
2896 3097 2.099141 TGGTCTTCATCTTTGGCGAG 57.901 50.000 0.00 0.00 0.00 5.03
2897 3098 2.290260 ACATGGTCTTCATCTTTGGCGA 60.290 45.455 0.00 0.00 32.92 5.54
2898 3099 2.086869 ACATGGTCTTCATCTTTGGCG 58.913 47.619 0.00 0.00 32.92 5.69
2899 3100 2.165030 CCACATGGTCTTCATCTTTGGC 59.835 50.000 0.00 0.00 32.92 4.52
2900 3101 2.165030 GCCACATGGTCTTCATCTTTGG 59.835 50.000 0.00 0.00 37.57 3.28
2901 3102 2.165030 GGCCACATGGTCTTCATCTTTG 59.835 50.000 0.00 0.00 36.72 2.77
2902 3103 2.450476 GGCCACATGGTCTTCATCTTT 58.550 47.619 0.00 0.00 36.72 2.52
2903 3104 1.341383 GGGCCACATGGTCTTCATCTT 60.341 52.381 4.39 0.00 40.38 2.40
2904 3105 0.257039 GGGCCACATGGTCTTCATCT 59.743 55.000 4.39 0.00 40.38 2.90
2905 3106 0.034186 TGGGCCACATGGTCTTCATC 60.034 55.000 0.00 0.00 40.38 2.92
2906 3107 0.323725 GTGGGCCACATGGTCTTCAT 60.324 55.000 31.26 0.00 40.38 2.57
2907 3108 1.074775 GTGGGCCACATGGTCTTCA 59.925 57.895 31.26 0.00 40.38 3.02
2908 3109 1.074775 TGTGGGCCACATGGTCTTC 59.925 57.895 34.67 6.66 39.62 2.87
2909 3110 1.228552 GTGTGGGCCACATGGTCTT 60.229 57.895 39.33 0.00 46.32 3.01
2910 3111 2.436109 GTGTGGGCCACATGGTCT 59.564 61.111 39.33 0.00 46.32 3.85
2911 3112 2.676471 GGTGTGGGCCACATGGTC 60.676 66.667 39.33 26.49 46.32 4.02
2912 3113 4.299796 GGGTGTGGGCCACATGGT 62.300 66.667 39.33 0.00 46.32 3.55
2913 3114 3.528217 AAGGGTGTGGGCCACATGG 62.528 63.158 39.33 0.00 46.32 3.66
2914 3115 2.118076 AAGGGTGTGGGCCACATG 59.882 61.111 39.33 0.00 46.32 3.21


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

AutoCloner maintained by Alex Coulton.