Multiple sequence alignment - TraesCS2A01G146700

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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 TraesCS2A01G146700 chr2A 100.000 2767 0 0 1 2767 92331598 92328832 0.000000e+00 5110
1 TraesCS2A01G146700 chr2A 93.684 190 12 0 2578 2767 613783421 613783232 4.510000e-73 285
2 TraesCS2A01G146700 chr2D 94.025 2594 113 14 4 2582 94331999 94329433 0.000000e+00 3893
3 TraesCS2A01G146700 chr2B 94.602 1834 62 10 781 2582 146454390 146452562 0.000000e+00 2804
4 TraesCS2A01G146700 chr2B 92.248 774 56 3 4 773 146455278 146454505 0.000000e+00 1094
5 TraesCS2A01G146700 chr2B 96.089 179 7 0 2589 2767 239515808 239515986 2.700000e-75 292
6 TraesCS2A01G146700 chr3B 96.667 180 6 0 2588 2767 212447970 212448149 1.610000e-77 300
7 TraesCS2A01G146700 chr3B 96.111 180 7 0 2588 2767 793379863 793380042 7.490000e-76 294
8 TraesCS2A01G146700 chr4A 93.137 204 11 3 2566 2767 448572498 448572296 2.080000e-76 296
9 TraesCS2A01G146700 chr3A 95.109 184 9 0 2584 2767 210511202 210511385 9.690000e-75 291
10 TraesCS2A01G146700 chr5B 95.556 180 8 0 2588 2767 490904010 490904189 3.490000e-74 289
11 TraesCS2A01G146700 chr4B 95.082 183 9 0 2585 2767 111713864 111713682 3.490000e-74 289
12 TraesCS2A01G146700 chr1B 95.556 180 8 0 2588 2767 437281417 437281238 3.490000e-74 289


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 TraesCS2A01G146700 chr2A 92328832 92331598 2766 True 5110 5110 100.000 1 2767 1 chr2A.!!$R1 2766
1 TraesCS2A01G146700 chr2D 94329433 94331999 2566 True 3893 3893 94.025 4 2582 1 chr2D.!!$R1 2578
2 TraesCS2A01G146700 chr2B 146452562 146455278 2716 True 1949 2804 93.425 4 2582 2 chr2B.!!$R1 2578

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
927 1051 0.777678 GGATCCCCTTCCATCCCCAT 60.778 60.0 0.0 0.0 35.72 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2698 2867 0.033228 TTGCTTTTGCCACGGGAATG 59.967 50.0 0.0 0.0 46.87 2.67 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
22 23 1.001597 GGGTACGGCGACAGATCTAAG 60.002 57.143 16.62 0.00 0.00 2.18
28 29 2.792890 CGGCGACAGATCTAAGTGAGTG 60.793 54.545 0.00 0.00 0.00 3.51
37 38 7.939782 ACAGATCTAAGTGAGTGTCTGATATG 58.060 38.462 15.34 0.00 39.38 1.78
39 40 9.061435 CAGATCTAAGTGAGTGTCTGATATGTA 57.939 37.037 0.00 0.00 39.38 2.29
45 46 6.058833 AGTGAGTGTCTGATATGTATCGAGT 58.941 40.000 0.00 0.00 35.48 4.18
49 50 9.720769 TGAGTGTCTGATATGTATCGAGTTATA 57.279 33.333 0.00 0.00 35.48 0.98
51 52 9.168451 AGTGTCTGATATGTATCGAGTTATAGG 57.832 37.037 0.00 0.00 35.48 2.57
81 82 4.494091 ACAAGGAATGGATGTAGTGGAG 57.506 45.455 0.00 0.00 0.00 3.86
83 84 2.481441 AGGAATGGATGTAGTGGAGCA 58.519 47.619 0.00 0.00 0.00 4.26
97 98 4.154942 AGTGGAGCATCTGGTTTGAAATT 58.845 39.130 0.00 0.00 33.73 1.82
105 106 7.899973 AGCATCTGGTTTGAAATTCATAACTT 58.100 30.769 15.26 0.00 0.00 2.66
128 129 8.159447 ACTTCATAAGATATCTGCTAATTGCCA 58.841 33.333 5.86 0.00 42.00 4.92
138 139 6.534475 TCTGCTAATTGCCAAATTCAGAAT 57.466 33.333 0.00 0.00 42.00 2.40
142 143 5.521372 GCTAATTGCCAAATTCAGAATGTCC 59.479 40.000 0.00 0.00 37.23 4.02
157 158 2.113860 TGTCCACTCTTAAGCCATGC 57.886 50.000 0.00 0.00 0.00 4.06
164 165 4.202295 CCACTCTTAAGCCATGCAGATCTA 60.202 45.833 0.00 0.00 0.00 1.98
166 167 3.995705 CTCTTAAGCCATGCAGATCTAGC 59.004 47.826 0.00 2.38 0.00 3.42
169 170 3.399440 AAGCCATGCAGATCTAGCTAC 57.601 47.619 15.20 5.50 0.00 3.58
173 174 3.558746 GCCATGCAGATCTAGCTACCAAT 60.559 47.826 15.20 1.69 0.00 3.16
199 200 5.105997 GCTGGATTATTCAGTGACTTTGCTT 60.106 40.000 2.12 0.00 34.89 3.91
209 211 2.860136 GTGACTTTGCTTGCCACTTTTC 59.140 45.455 0.00 0.00 0.00 2.29
305 310 3.798202 AGAATTGACTTGGATACTCGGC 58.202 45.455 0.00 0.00 37.61 5.54
330 335 4.872124 GGATTCTGGCCAACATTTTCAATC 59.128 41.667 7.01 4.61 0.00 2.67
439 444 1.616159 TAAAAGGGCACTGTGGAAGC 58.384 50.000 10.21 0.00 0.00 3.86
493 498 7.957002 TGGATAGCTAGTGAATTCTTCTAAGG 58.043 38.462 7.05 1.36 0.00 2.69
498 503 5.293079 GCTAGTGAATTCTTCTAAGGTGCTG 59.707 44.000 7.05 0.00 0.00 4.41
550 555 9.030452 ACCTTAGGTTTTAATGCAATGTAATGA 57.970 29.630 0.00 0.00 27.29 2.57
555 560 7.754924 AGGTTTTAATGCAATGTAATGAGTTCG 59.245 33.333 0.00 0.00 0.00 3.95
680 688 7.839200 ACCTTTGGTATTGGATTTGCTTACTAT 59.161 33.333 0.00 0.00 32.11 2.12
704 712 8.833231 ATAATCAGTACTATTTGTGATTCCCG 57.167 34.615 8.54 0.00 39.68 5.14
710 718 5.888982 ACTATTTGTGATTCCCGGATACT 57.111 39.130 0.73 0.00 0.00 2.12
773 896 7.578310 TGACCTAGCAACGACTAAATACTAT 57.422 36.000 0.00 0.00 0.00 2.12
774 897 7.646314 TGACCTAGCAACGACTAAATACTATC 58.354 38.462 0.00 0.00 0.00 2.08
775 898 7.501559 TGACCTAGCAACGACTAAATACTATCT 59.498 37.037 0.00 0.00 0.00 1.98
776 899 8.235359 ACCTAGCAACGACTAAATACTATCTT 57.765 34.615 0.00 0.00 0.00 2.40
777 900 8.136165 ACCTAGCAACGACTAAATACTATCTTG 58.864 37.037 0.00 0.00 0.00 3.02
778 901 7.595502 CCTAGCAACGACTAAATACTATCTTGG 59.404 40.741 0.00 0.00 0.00 3.61
779 902 6.281405 AGCAACGACTAAATACTATCTTGGG 58.719 40.000 0.00 0.00 0.00 4.12
780 903 6.097839 AGCAACGACTAAATACTATCTTGGGA 59.902 38.462 0.00 0.00 0.00 4.37
794 917 8.107196 ACTATCTTGGGATTTCCTTATGTTCT 57.893 34.615 0.00 0.00 36.20 3.01
795 918 7.995488 ACTATCTTGGGATTTCCTTATGTTCTG 59.005 37.037 0.00 0.00 36.20 3.02
821 945 3.489785 CAGTAGAATCATAACGCCCGAAC 59.510 47.826 0.00 0.00 0.00 3.95
927 1051 0.777678 GGATCCCCTTCCATCCCCAT 60.778 60.000 0.00 0.00 35.72 4.00
973 1097 1.140652 CTGGAAGAAGAGATCCCTGCC 59.859 57.143 0.00 0.00 34.07 4.85
1119 1243 1.988406 GTTCCGTGCCTCCTACCCT 60.988 63.158 0.00 0.00 0.00 4.34
1148 1272 5.247792 ACGTTAGTAATCAAACTCCCCTTCT 59.752 40.000 0.00 0.00 0.00 2.85
1165 1289 0.816018 TCTTCTCCTCTCTAGCCGCG 60.816 60.000 0.00 0.00 0.00 6.46
1175 1299 0.466739 TCTAGCCGCGTCCTTCCATA 60.467 55.000 4.92 0.00 0.00 2.74
1187 1311 2.439507 TCCTTCCATAACAGGATCTGGC 59.560 50.000 0.00 0.00 37.56 4.85
1340 1464 2.234908 CGAATCCTCCACACCTTCTTCT 59.765 50.000 0.00 0.00 0.00 2.85
1367 1491 2.663188 GATCCCGTGATCCTGCGC 60.663 66.667 0.00 0.00 41.37 6.09
1543 1667 0.753262 CCCGCAATCTAGCTACAGGT 59.247 55.000 0.00 0.00 0.00 4.00
1561 1685 3.213506 AGGTCGTGAGAGATCTGATGAG 58.786 50.000 0.00 0.00 43.49 2.90
1563 1687 3.003275 GGTCGTGAGAGATCTGATGAGTC 59.997 52.174 0.00 0.00 43.49 3.36
1669 1798 3.042887 GCAGTTCGTTGGATTTTGTGAC 58.957 45.455 0.00 0.00 0.00 3.67
1690 1819 0.765510 GGGAACTCACTCCAACTGGT 59.234 55.000 0.00 0.00 37.20 4.00
1772 1901 3.381908 TCTCCGCAATCCTTTAGAGAGAC 59.618 47.826 0.00 0.00 0.00 3.36
1796 1925 4.574421 TGAAAACTTCTTGAGCATCGAACA 59.426 37.500 0.00 0.00 38.61 3.18
1922 2051 3.959535 TGATTTCTTGGTTTGGGATGC 57.040 42.857 0.00 0.00 0.00 3.91
1943 2072 8.656849 GGATGCTATTCCTGTTATGTATTTACG 58.343 37.037 0.00 0.00 32.68 3.18
1982 2124 4.197750 CAGTTTTCTAGCTGGCTCATCAT 58.802 43.478 0.00 0.00 0.00 2.45
1983 2125 4.035324 CAGTTTTCTAGCTGGCTCATCATG 59.965 45.833 0.00 0.00 0.00 3.07
1984 2126 2.251409 TTCTAGCTGGCTCATCATGC 57.749 50.000 0.00 0.00 0.00 4.06
1985 2127 1.125633 TCTAGCTGGCTCATCATGCA 58.874 50.000 0.00 0.00 0.00 3.96
1986 2128 1.697982 TCTAGCTGGCTCATCATGCAT 59.302 47.619 0.00 0.00 0.00 3.96
1987 2129 2.105993 TCTAGCTGGCTCATCATGCATT 59.894 45.455 0.00 0.00 0.00 3.56
1988 2130 2.651382 AGCTGGCTCATCATGCATTA 57.349 45.000 0.00 0.00 0.00 1.90
1989 2131 3.156288 AGCTGGCTCATCATGCATTAT 57.844 42.857 0.00 0.00 0.00 1.28
1990 2132 4.296621 AGCTGGCTCATCATGCATTATA 57.703 40.909 0.00 0.00 0.00 0.98
1991 2133 4.856509 AGCTGGCTCATCATGCATTATAT 58.143 39.130 0.00 0.00 0.00 0.86
1992 2134 5.262009 AGCTGGCTCATCATGCATTATATT 58.738 37.500 0.00 0.00 0.00 1.28
1993 2135 5.715279 AGCTGGCTCATCATGCATTATATTT 59.285 36.000 0.00 0.00 0.00 1.40
1994 2136 6.888088 AGCTGGCTCATCATGCATTATATTTA 59.112 34.615 0.00 0.00 0.00 1.40
2076 2221 5.716228 TGAGTATGGAAGAAACATGGCAATT 59.284 36.000 0.00 0.00 0.00 2.32
2117 2262 6.112058 TGTGCCTTTTCAAAAGCTAAATTGT 58.888 32.000 4.15 0.00 0.00 2.71
2170 2317 5.357878 TCATTGGCATGGTTTAGAATCTGAC 59.642 40.000 0.00 0.00 0.00 3.51
2182 2329 6.834168 TTAGAATCTGACCATTTTCCAACC 57.166 37.500 0.00 0.00 0.00 3.77
2226 2373 5.126061 TCCTTTAAAGATGAAAGAGCATGCC 59.874 40.000 15.66 6.03 36.22 4.40
2327 2474 3.056328 GTGGTGCGGGAGAAAGCC 61.056 66.667 0.00 0.00 0.00 4.35
2352 2499 2.713863 TGCTGTGGCATGATGTCATA 57.286 45.000 1.91 0.00 44.28 2.15
2354 2501 3.558033 TGCTGTGGCATGATGTCATAAT 58.442 40.909 1.91 0.00 44.28 1.28
2358 2505 3.067040 TGTGGCATGATGTCATAATGTGC 59.933 43.478 1.91 7.18 33.03 4.57
2374 2521 2.083774 TGTGCTGCTAGGGAAAAATCG 58.916 47.619 0.00 0.00 0.00 3.34
2385 2532 6.127897 GCTAGGGAAAAATCGATTATGGATGG 60.128 42.308 11.83 0.20 0.00 3.51
2394 2541 9.745018 AAAATCGATTATGGATGGTCTAATGAT 57.255 29.630 11.83 0.00 0.00 2.45
2512 2681 3.290710 AGTTTTGCTGGAAGACATGTGT 58.709 40.909 1.15 0.00 34.07 3.72
2560 2729 4.848357 AGTATCAACCAGCTTAGCATGTT 58.152 39.130 7.07 6.27 0.00 2.71
2582 2751 8.696410 TGTTTTCAGTTTTAATGAAGTGTTCC 57.304 30.769 0.00 0.00 37.91 3.62
2583 2752 8.527810 TGTTTTCAGTTTTAATGAAGTGTTCCT 58.472 29.630 0.00 0.00 37.91 3.36
2584 2753 9.020813 GTTTTCAGTTTTAATGAAGTGTTCCTC 57.979 33.333 0.00 0.00 37.91 3.71
2585 2754 8.519799 TTTCAGTTTTAATGAAGTGTTCCTCT 57.480 30.769 0.00 0.00 37.91 3.69
2586 2755 8.519799 TTCAGTTTTAATGAAGTGTTCCTCTT 57.480 30.769 0.00 0.00 32.96 2.85
2587 2756 9.621629 TTCAGTTTTAATGAAGTGTTCCTCTTA 57.378 29.630 0.00 0.00 32.96 2.10
2588 2757 9.273016 TCAGTTTTAATGAAGTGTTCCTCTTAG 57.727 33.333 0.00 0.00 32.90 2.18
2589 2758 8.507249 CAGTTTTAATGAAGTGTTCCTCTTAGG 58.493 37.037 0.00 0.00 36.46 2.69
2590 2759 7.665974 AGTTTTAATGAAGTGTTCCTCTTAGGG 59.334 37.037 0.00 0.00 35.59 3.53
2591 2760 6.945636 TTAATGAAGTGTTCCTCTTAGGGA 57.054 37.500 0.00 0.00 35.59 4.20
2592 2761 5.843019 AATGAAGTGTTCCTCTTAGGGAA 57.157 39.130 0.00 0.00 42.39 3.97
2593 2762 5.843019 ATGAAGTGTTCCTCTTAGGGAAA 57.157 39.130 4.23 0.00 45.55 3.13
2594 2763 5.640158 TGAAGTGTTCCTCTTAGGGAAAA 57.360 39.130 4.23 0.00 45.55 2.29
2595 2764 6.200878 TGAAGTGTTCCTCTTAGGGAAAAT 57.799 37.500 4.23 0.00 45.55 1.82
2596 2765 6.610830 TGAAGTGTTCCTCTTAGGGAAAATT 58.389 36.000 4.23 0.00 45.55 1.82
2597 2766 7.066781 TGAAGTGTTCCTCTTAGGGAAAATTT 58.933 34.615 4.23 3.02 45.55 1.82
2598 2767 7.563556 TGAAGTGTTCCTCTTAGGGAAAATTTT 59.436 33.333 2.28 2.28 45.55 1.82
2599 2768 7.290110 AGTGTTCCTCTTAGGGAAAATTTTG 57.710 36.000 8.47 0.00 45.55 2.44
2600 2769 5.926542 GTGTTCCTCTTAGGGAAAATTTTGC 59.073 40.000 13.54 13.54 45.55 3.68
2601 2770 5.838521 TGTTCCTCTTAGGGAAAATTTTGCT 59.161 36.000 20.02 10.07 45.55 3.91
2602 2771 6.326323 TGTTCCTCTTAGGGAAAATTTTGCTT 59.674 34.615 20.02 15.90 45.55 3.91
2603 2772 6.994421 TCCTCTTAGGGAAAATTTTGCTTT 57.006 33.333 20.02 12.19 35.59 3.51
2604 2773 7.373617 TCCTCTTAGGGAAAATTTTGCTTTT 57.626 32.000 20.02 10.09 35.59 2.27
2605 2774 7.216494 TCCTCTTAGGGAAAATTTTGCTTTTG 58.784 34.615 20.02 10.17 35.59 2.44
2606 2775 8.168984 TCCTCTTAGGGAAAATTTTGCTTTTGC 61.169 37.037 20.02 5.18 40.23 3.68
2610 2779 4.898829 GGAAAATTTTGCTTTTGCCACT 57.101 36.364 14.52 0.00 46.87 4.00
2611 2780 4.847633 GGAAAATTTTGCTTTTGCCACTC 58.152 39.130 14.52 0.00 46.87 3.51
2612 2781 4.576053 GGAAAATTTTGCTTTTGCCACTCT 59.424 37.500 14.52 0.00 46.87 3.24
2613 2782 5.757808 GGAAAATTTTGCTTTTGCCACTCTA 59.242 36.000 14.52 0.00 46.87 2.43
2614 2783 6.073602 GGAAAATTTTGCTTTTGCCACTCTAG 60.074 38.462 14.52 0.00 46.87 2.43
2615 2784 5.789643 AATTTTGCTTTTGCCACTCTAGA 57.210 34.783 0.00 0.00 46.87 2.43
2616 2785 5.990120 ATTTTGCTTTTGCCACTCTAGAT 57.010 34.783 0.00 0.00 46.87 1.98
2617 2786 5.789643 TTTTGCTTTTGCCACTCTAGATT 57.210 34.783 0.00 0.00 46.87 2.40
2618 2787 5.789643 TTTGCTTTTGCCACTCTAGATTT 57.210 34.783 0.00 0.00 46.87 2.17
2619 2788 5.789643 TTGCTTTTGCCACTCTAGATTTT 57.210 34.783 0.00 0.00 46.87 1.82
2620 2789 5.125100 TGCTTTTGCCACTCTAGATTTTG 57.875 39.130 0.00 0.00 46.87 2.44
2621 2790 3.922850 GCTTTTGCCACTCTAGATTTTGC 59.077 43.478 0.00 0.00 40.15 3.68
2622 2791 4.488879 CTTTTGCCACTCTAGATTTTGCC 58.511 43.478 0.00 0.00 0.00 4.52
2623 2792 2.877097 TGCCACTCTAGATTTTGCCA 57.123 45.000 0.00 0.00 0.00 4.92
2624 2793 3.153369 TGCCACTCTAGATTTTGCCAA 57.847 42.857 0.00 0.00 0.00 4.52
2625 2794 3.700538 TGCCACTCTAGATTTTGCCAAT 58.299 40.909 0.00 0.00 0.00 3.16
2626 2795 4.088634 TGCCACTCTAGATTTTGCCAATT 58.911 39.130 0.00 0.00 0.00 2.32
2627 2796 4.527816 TGCCACTCTAGATTTTGCCAATTT 59.472 37.500 0.00 0.00 0.00 1.82
2628 2797 5.011943 TGCCACTCTAGATTTTGCCAATTTT 59.988 36.000 0.00 0.00 0.00 1.82
2629 2798 5.578336 GCCACTCTAGATTTTGCCAATTTTC 59.422 40.000 0.00 0.00 0.00 2.29
2630 2799 6.101997 CCACTCTAGATTTTGCCAATTTTCC 58.898 40.000 0.00 0.00 0.00 3.13
2631 2800 6.071165 CCACTCTAGATTTTGCCAATTTTCCT 60.071 38.462 0.00 0.00 0.00 3.36
2632 2801 7.381323 CACTCTAGATTTTGCCAATTTTCCTT 58.619 34.615 0.00 0.00 0.00 3.36
2633 2802 8.522830 CACTCTAGATTTTGCCAATTTTCCTTA 58.477 33.333 0.00 0.00 0.00 2.69
2634 2803 9.259832 ACTCTAGATTTTGCCAATTTTCCTTAT 57.740 29.630 0.00 0.00 0.00 1.73
2635 2804 9.525409 CTCTAGATTTTGCCAATTTTCCTTATG 57.475 33.333 0.00 0.00 0.00 1.90
2636 2805 6.990341 AGATTTTGCCAATTTTCCTTATGC 57.010 33.333 0.00 0.00 0.00 3.14
2637 2806 5.882000 AGATTTTGCCAATTTTCCTTATGCC 59.118 36.000 0.00 0.00 0.00 4.40
2638 2807 4.630644 TTTGCCAATTTTCCTTATGCCA 57.369 36.364 0.00 0.00 0.00 4.92
2639 2808 3.608316 TGCCAATTTTCCTTATGCCAC 57.392 42.857 0.00 0.00 0.00 5.01
2640 2809 3.172339 TGCCAATTTTCCTTATGCCACT 58.828 40.909 0.00 0.00 0.00 4.00
2641 2810 3.195396 TGCCAATTTTCCTTATGCCACTC 59.805 43.478 0.00 0.00 0.00 3.51
2642 2811 3.448660 GCCAATTTTCCTTATGCCACTCT 59.551 43.478 0.00 0.00 0.00 3.24
2643 2812 4.644685 GCCAATTTTCCTTATGCCACTCTA 59.355 41.667 0.00 0.00 0.00 2.43
2644 2813 5.221126 GCCAATTTTCCTTATGCCACTCTAG 60.221 44.000 0.00 0.00 0.00 2.43
2645 2814 6.122277 CCAATTTTCCTTATGCCACTCTAGA 58.878 40.000 0.00 0.00 0.00 2.43
2646 2815 6.774656 CCAATTTTCCTTATGCCACTCTAGAT 59.225 38.462 0.00 0.00 0.00 1.98
2647 2816 7.286316 CCAATTTTCCTTATGCCACTCTAGATT 59.714 37.037 0.00 0.00 0.00 2.40
2648 2817 8.689972 CAATTTTCCTTATGCCACTCTAGATTT 58.310 33.333 0.00 0.00 0.00 2.17
2649 2818 8.829373 ATTTTCCTTATGCCACTCTAGATTTT 57.171 30.769 0.00 0.00 0.00 1.82
2650 2819 7.630242 TTTCCTTATGCCACTCTAGATTTTG 57.370 36.000 0.00 0.00 0.00 2.44
2651 2820 6.560003 TCCTTATGCCACTCTAGATTTTGA 57.440 37.500 0.00 0.00 0.00 2.69
2652 2821 6.349300 TCCTTATGCCACTCTAGATTTTGAC 58.651 40.000 0.00 0.00 0.00 3.18
2653 2822 6.070251 TCCTTATGCCACTCTAGATTTTGACA 60.070 38.462 0.00 0.00 0.00 3.58
2654 2823 6.769822 CCTTATGCCACTCTAGATTTTGACAT 59.230 38.462 0.00 0.00 0.00 3.06
2655 2824 7.284034 CCTTATGCCACTCTAGATTTTGACATT 59.716 37.037 0.00 0.00 0.00 2.71
2656 2825 8.579850 TTATGCCACTCTAGATTTTGACATTT 57.420 30.769 0.00 0.00 0.00 2.32
2657 2826 6.500684 TGCCACTCTAGATTTTGACATTTC 57.499 37.500 0.00 0.00 0.00 2.17
2658 2827 6.003326 TGCCACTCTAGATTTTGACATTTCA 58.997 36.000 0.00 0.00 0.00 2.69
2659 2828 6.072508 TGCCACTCTAGATTTTGACATTTCAC 60.073 38.462 0.00 0.00 0.00 3.18
2660 2829 6.150140 GCCACTCTAGATTTTGACATTTCACT 59.850 38.462 0.00 0.00 0.00 3.41
2661 2830 7.308830 GCCACTCTAGATTTTGACATTTCACTT 60.309 37.037 0.00 0.00 0.00 3.16
2662 2831 8.233190 CCACTCTAGATTTTGACATTTCACTTC 58.767 37.037 0.00 0.00 0.00 3.01
2663 2832 8.997323 CACTCTAGATTTTGACATTTCACTTCT 58.003 33.333 0.00 0.00 0.00 2.85
2664 2833 8.997323 ACTCTAGATTTTGACATTTCACTTCTG 58.003 33.333 0.00 0.00 0.00 3.02
2665 2834 7.810658 TCTAGATTTTGACATTTCACTTCTGC 58.189 34.615 0.00 0.00 0.00 4.26
2666 2835 5.776744 AGATTTTGACATTTCACTTCTGCC 58.223 37.500 0.00 0.00 0.00 4.85
2667 2836 4.998671 TTTTGACATTTCACTTCTGCCA 57.001 36.364 0.00 0.00 0.00 4.92
2668 2837 3.988379 TTGACATTTCACTTCTGCCAC 57.012 42.857 0.00 0.00 0.00 5.01
2669 2838 3.213206 TGACATTTCACTTCTGCCACT 57.787 42.857 0.00 0.00 0.00 4.00
2670 2839 3.141398 TGACATTTCACTTCTGCCACTC 58.859 45.455 0.00 0.00 0.00 3.51
2671 2840 3.181451 TGACATTTCACTTCTGCCACTCT 60.181 43.478 0.00 0.00 0.00 3.24
2672 2841 3.817647 GACATTTCACTTCTGCCACTCTT 59.182 43.478 0.00 0.00 0.00 2.85
2673 2842 4.973168 ACATTTCACTTCTGCCACTCTTA 58.027 39.130 0.00 0.00 0.00 2.10
2674 2843 4.999950 ACATTTCACTTCTGCCACTCTTAG 59.000 41.667 0.00 0.00 0.00 2.18
2675 2844 4.689612 TTTCACTTCTGCCACTCTTAGT 57.310 40.909 0.00 0.00 0.00 2.24
2676 2845 4.689612 TTCACTTCTGCCACTCTTAGTT 57.310 40.909 0.00 0.00 0.00 2.24
2677 2846 4.689612 TCACTTCTGCCACTCTTAGTTT 57.310 40.909 0.00 0.00 0.00 2.66
2678 2847 5.036117 TCACTTCTGCCACTCTTAGTTTT 57.964 39.130 0.00 0.00 0.00 2.43
2679 2848 5.437060 TCACTTCTGCCACTCTTAGTTTTT 58.563 37.500 0.00 0.00 0.00 1.94
2680 2849 5.296780 TCACTTCTGCCACTCTTAGTTTTTG 59.703 40.000 0.00 0.00 0.00 2.44
2681 2850 5.296780 CACTTCTGCCACTCTTAGTTTTTGA 59.703 40.000 0.00 0.00 0.00 2.69
2682 2851 5.297029 ACTTCTGCCACTCTTAGTTTTTGAC 59.703 40.000 0.00 0.00 0.00 3.18
2683 2852 4.776349 TCTGCCACTCTTAGTTTTTGACA 58.224 39.130 0.00 0.00 0.00 3.58
2684 2853 5.189928 TCTGCCACTCTTAGTTTTTGACAA 58.810 37.500 0.00 0.00 0.00 3.18
2685 2854 5.827797 TCTGCCACTCTTAGTTTTTGACAAT 59.172 36.000 0.00 0.00 0.00 2.71
2686 2855 6.321181 TCTGCCACTCTTAGTTTTTGACAATT 59.679 34.615 0.00 0.00 0.00 2.32
2687 2856 7.500892 TCTGCCACTCTTAGTTTTTGACAATTA 59.499 33.333 0.00 0.00 0.00 1.40
2688 2857 8.177119 TGCCACTCTTAGTTTTTGACAATTAT 57.823 30.769 0.00 0.00 0.00 1.28
2689 2858 8.296713 TGCCACTCTTAGTTTTTGACAATTATC 58.703 33.333 0.00 0.00 0.00 1.75
2690 2859 8.296713 GCCACTCTTAGTTTTTGACAATTATCA 58.703 33.333 0.00 0.00 0.00 2.15
2691 2860 9.612620 CCACTCTTAGTTTTTGACAATTATCAC 57.387 33.333 0.00 0.00 0.00 3.06
2705 2874 6.563422 ACAATTATCACAATTGTCATTCCCG 58.437 36.000 8.48 0.00 44.83 5.14
2706 2875 6.152661 ACAATTATCACAATTGTCATTCCCGT 59.847 34.615 8.48 0.00 44.83 5.28
2707 2876 5.559427 TTATCACAATTGTCATTCCCGTG 57.441 39.130 8.48 0.00 0.00 4.94
2708 2877 2.158559 TCACAATTGTCATTCCCGTGG 58.841 47.619 8.48 0.00 0.00 4.94
2709 2878 0.887933 ACAATTGTCATTCCCGTGGC 59.112 50.000 4.92 0.00 0.00 5.01
2710 2879 0.887247 CAATTGTCATTCCCGTGGCA 59.113 50.000 0.00 0.00 30.63 4.92
2711 2880 1.271934 CAATTGTCATTCCCGTGGCAA 59.728 47.619 0.00 0.00 46.47 4.52
2712 2881 1.626686 ATTGTCATTCCCGTGGCAAA 58.373 45.000 0.00 0.00 45.67 3.68
2713 2882 1.403814 TTGTCATTCCCGTGGCAAAA 58.596 45.000 0.00 0.00 40.43 2.44
2714 2883 0.958091 TGTCATTCCCGTGGCAAAAG 59.042 50.000 0.00 0.00 29.34 2.27
2715 2884 0.388520 GTCATTCCCGTGGCAAAAGC 60.389 55.000 0.00 0.00 0.00 3.51
2716 2885 0.825425 TCATTCCCGTGGCAAAAGCA 60.825 50.000 0.00 0.00 0.00 3.91
2717 2886 0.033228 CATTCCCGTGGCAAAAGCAA 59.967 50.000 0.00 0.00 0.00 3.91
2718 2887 0.755686 ATTCCCGTGGCAAAAGCAAA 59.244 45.000 0.00 0.00 0.00 3.68
2719 2888 0.537188 TTCCCGTGGCAAAAGCAAAA 59.463 45.000 0.00 0.00 0.00 2.44
2720 2889 0.755686 TCCCGTGGCAAAAGCAAAAT 59.244 45.000 0.00 0.00 0.00 1.82
2721 2890 1.139853 TCCCGTGGCAAAAGCAAAATT 59.860 42.857 0.00 0.00 0.00 1.82
2722 2891 1.946081 CCCGTGGCAAAAGCAAAATTT 59.054 42.857 0.00 0.00 0.00 1.82
2723 2892 2.357323 CCCGTGGCAAAAGCAAAATTTT 59.643 40.909 0.00 0.00 32.65 1.82
2724 2893 3.547813 CCCGTGGCAAAAGCAAAATTTTC 60.548 43.478 0.00 0.00 30.01 2.29
2725 2894 3.064545 CCGTGGCAAAAGCAAAATTTTCA 59.935 39.130 0.00 0.00 30.01 2.69
2726 2895 4.273274 CGTGGCAAAAGCAAAATTTTCAG 58.727 39.130 0.00 0.00 30.01 3.02
2727 2896 4.033817 CGTGGCAAAAGCAAAATTTTCAGA 59.966 37.500 0.00 0.00 30.01 3.27
2728 2897 5.504392 GTGGCAAAAGCAAAATTTTCAGAG 58.496 37.500 0.00 0.00 30.01 3.35
2729 2898 5.065090 GTGGCAAAAGCAAAATTTTCAGAGT 59.935 36.000 0.00 0.00 30.01 3.24
2730 2899 5.064962 TGGCAAAAGCAAAATTTTCAGAGTG 59.935 36.000 0.00 0.00 30.01 3.51
2731 2900 5.504392 GCAAAAGCAAAATTTTCAGAGTGG 58.496 37.500 0.00 0.00 30.01 4.00
2732 2901 5.504392 CAAAAGCAAAATTTTCAGAGTGGC 58.496 37.500 0.00 0.00 30.01 5.01
2733 2902 4.405116 AAGCAAAATTTTCAGAGTGGCA 57.595 36.364 0.00 0.00 0.00 4.92
2734 2903 4.612264 AGCAAAATTTTCAGAGTGGCAT 57.388 36.364 0.00 0.00 0.00 4.40
2735 2904 4.964593 AGCAAAATTTTCAGAGTGGCATT 58.035 34.783 0.00 0.00 0.00 3.56
2736 2905 5.370679 AGCAAAATTTTCAGAGTGGCATTT 58.629 33.333 0.00 0.00 0.00 2.32
2737 2906 5.237779 AGCAAAATTTTCAGAGTGGCATTTG 59.762 36.000 0.00 0.00 0.00 2.32
2738 2907 5.007921 GCAAAATTTTCAGAGTGGCATTTGT 59.992 36.000 0.00 0.00 0.00 2.83
2739 2908 6.423862 CAAAATTTTCAGAGTGGCATTTGTG 58.576 36.000 0.00 0.00 0.00 3.33
2740 2909 5.534207 AATTTTCAGAGTGGCATTTGTGA 57.466 34.783 0.00 0.00 0.00 3.58
2741 2910 5.733620 ATTTTCAGAGTGGCATTTGTGAT 57.266 34.783 0.00 0.00 0.00 3.06
2742 2911 6.839124 ATTTTCAGAGTGGCATTTGTGATA 57.161 33.333 0.00 0.00 0.00 2.15
2743 2912 6.647334 TTTTCAGAGTGGCATTTGTGATAA 57.353 33.333 0.00 0.00 0.00 1.75
2744 2913 6.839124 TTTCAGAGTGGCATTTGTGATAAT 57.161 33.333 0.00 0.00 0.00 1.28
2745 2914 6.839124 TTCAGAGTGGCATTTGTGATAATT 57.161 33.333 0.00 0.00 0.00 1.40
2746 2915 6.198650 TCAGAGTGGCATTTGTGATAATTG 57.801 37.500 0.00 0.00 0.00 2.32
2747 2916 5.711506 TCAGAGTGGCATTTGTGATAATTGT 59.288 36.000 0.00 0.00 0.00 2.71
2748 2917 6.032094 CAGAGTGGCATTTGTGATAATTGTC 58.968 40.000 0.00 0.00 0.00 3.18
2749 2918 5.711506 AGAGTGGCATTTGTGATAATTGTCA 59.288 36.000 0.03 0.03 0.00 3.58
2750 2919 6.209192 AGAGTGGCATTTGTGATAATTGTCAA 59.791 34.615 6.45 0.00 0.00 3.18
2751 2920 6.757237 AGTGGCATTTGTGATAATTGTCAAA 58.243 32.000 6.45 0.00 34.95 2.69
2752 2921 7.215789 AGTGGCATTTGTGATAATTGTCAAAA 58.784 30.769 6.45 5.05 34.32 2.44
2753 2922 7.385752 AGTGGCATTTGTGATAATTGTCAAAAG 59.614 33.333 6.45 0.00 34.32 2.27
2754 2923 6.649973 TGGCATTTGTGATAATTGTCAAAAGG 59.350 34.615 6.45 11.53 34.32 3.11
2755 2924 6.650390 GGCATTTGTGATAATTGTCAAAAGGT 59.350 34.615 6.45 0.00 34.32 3.50
2756 2925 7.816995 GGCATTTGTGATAATTGTCAAAAGGTA 59.183 33.333 6.45 0.00 34.32 3.08
2757 2926 9.202273 GCATTTGTGATAATTGTCAAAAGGTAA 57.798 29.630 6.45 0.00 34.32 2.85
2761 2930 8.918202 TGTGATAATTGTCAAAAGGTAAGAGT 57.082 30.769 6.45 0.00 0.00 3.24
2764 2933 9.162764 TGATAATTGTCAAAAGGTAAGAGTAGC 57.837 33.333 1.92 0.00 0.00 3.58
2765 2934 9.162764 GATAATTGTCAAAAGGTAAGAGTAGCA 57.837 33.333 0.00 0.00 0.00 3.49
2766 2935 7.817418 AATTGTCAAAAGGTAAGAGTAGCAA 57.183 32.000 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.968901 AGATCTGTCGCCGTACCCAA 60.969 55.000 0.00 0.00 0.00 4.12
1 2 0.107066 TAGATCTGTCGCCGTACCCA 60.107 55.000 5.18 0.00 0.00 4.51
2 3 1.001597 CTTAGATCTGTCGCCGTACCC 60.002 57.143 5.18 0.00 0.00 3.69
10 11 4.393371 TCAGACACTCACTTAGATCTGTCG 59.607 45.833 5.18 0.00 40.21 4.35
22 23 6.307031 ACTCGATACATATCAGACACTCAC 57.693 41.667 0.10 0.00 32.98 3.51
28 29 9.776158 CAACCTATAACTCGATACATATCAGAC 57.224 37.037 0.10 0.00 32.98 3.51
39 40 8.794553 CCTTGTAGATACAACCTATAACTCGAT 58.205 37.037 1.30 0.00 40.93 3.59
41 42 8.162878 TCCTTGTAGATACAACCTATAACTCG 57.837 38.462 1.30 0.00 40.93 4.18
45 46 9.442062 TCCATTCCTTGTAGATACAACCTATAA 57.558 33.333 1.30 0.00 40.93 0.98
49 50 6.158695 ACATCCATTCCTTGTAGATACAACCT 59.841 38.462 1.30 0.00 40.93 3.50
51 52 8.204836 ACTACATCCATTCCTTGTAGATACAAC 58.795 37.037 14.34 0.00 43.47 3.32
60 61 3.370953 GCTCCACTACATCCATTCCTTGT 60.371 47.826 0.00 0.00 0.00 3.16
81 82 7.814107 TGAAGTTATGAATTTCAAACCAGATGC 59.186 33.333 2.68 0.00 34.69 3.91
120 121 6.211184 AGTGGACATTCTGAATTTGGCAATTA 59.789 34.615 0.00 0.00 32.35 1.40
128 129 6.151817 GGCTTAAGAGTGGACATTCTGAATTT 59.848 38.462 6.67 0.00 0.00 1.82
138 139 1.350684 TGCATGGCTTAAGAGTGGACA 59.649 47.619 6.67 0.00 0.00 4.02
142 143 3.806380 AGATCTGCATGGCTTAAGAGTG 58.194 45.455 6.67 2.37 0.00 3.51
157 158 4.063689 CCAGCAATTGGTAGCTAGATCTG 58.936 47.826 10.31 2.88 42.41 2.90
173 174 5.335897 GCAAAGTCACTGAATAATCCAGCAA 60.336 40.000 0.00 0.00 35.14 3.91
179 180 5.098211 GGCAAGCAAAGTCACTGAATAATC 58.902 41.667 0.00 0.00 0.00 1.75
180 181 4.523943 TGGCAAGCAAAGTCACTGAATAAT 59.476 37.500 0.00 0.00 0.00 1.28
190 191 3.067320 AGAGAAAAGTGGCAAGCAAAGTC 59.933 43.478 0.00 0.00 0.00 3.01
199 200 2.760092 AGCAAACAAGAGAAAAGTGGCA 59.240 40.909 0.00 0.00 0.00 4.92
209 211 3.425359 CGGCTTGATACAGCAAACAAGAG 60.425 47.826 0.00 0.00 42.10 2.85
285 288 3.557595 CAGCCGAGTATCCAAGTCAATTC 59.442 47.826 0.00 0.00 0.00 2.17
300 305 2.203126 GGCCAGAATCCAGCCGAG 60.203 66.667 0.00 0.00 36.84 4.63
305 310 3.258872 TGAAAATGTTGGCCAGAATCCAG 59.741 43.478 5.11 0.00 34.66 3.86
493 498 1.927710 GCTAAAGCAACACAGCAGCAC 60.928 52.381 0.00 0.00 41.59 4.40
498 503 4.223320 TGTTAAGCTAAAGCAACACAGC 57.777 40.909 4.54 0.00 45.16 4.40
615 623 6.201615 TGAGCTTTCGCATATATGAACTGAAG 59.798 38.462 17.10 11.95 39.10 3.02
639 647 6.824305 ACCAAAGGTAAGATTTCACAGATG 57.176 37.500 0.00 0.00 32.11 2.90
652 660 6.926630 AAGCAAATCCAATACCAAAGGTAA 57.073 33.333 0.00 0.00 41.85 2.85
680 688 7.070198 TCCGGGAATCACAAATAGTACTGATTA 59.930 37.037 5.39 0.00 34.26 1.75
683 691 4.712829 TCCGGGAATCACAAATAGTACTGA 59.287 41.667 5.39 0.00 0.00 3.41
732 740 7.609918 TGCTAGGTCAAAAATACATTTCTAGCA 59.390 33.333 20.22 20.22 44.21 3.49
740 748 5.938125 AGTCGTTGCTAGGTCAAAAATACAT 59.062 36.000 0.00 0.00 0.00 2.29
773 896 5.015178 ACCAGAACATAAGGAAATCCCAAGA 59.985 40.000 0.00 0.00 37.41 3.02
774 897 5.264395 ACCAGAACATAAGGAAATCCCAAG 58.736 41.667 0.00 0.00 37.41 3.61
775 898 5.269554 ACCAGAACATAAGGAAATCCCAA 57.730 39.130 0.00 0.00 37.41 4.12
776 899 4.946160 ACCAGAACATAAGGAAATCCCA 57.054 40.909 0.00 0.00 37.41 4.37
777 900 5.751586 TGTACCAGAACATAAGGAAATCCC 58.248 41.667 0.00 0.00 36.42 3.85
778 901 6.415573 ACTGTACCAGAACATAAGGAAATCC 58.584 40.000 0.00 0.00 35.18 3.01
779 902 8.475639 TCTACTGTACCAGAACATAAGGAAATC 58.524 37.037 0.00 0.00 35.18 2.17
780 903 8.375493 TCTACTGTACCAGAACATAAGGAAAT 57.625 34.615 0.00 0.00 35.18 2.17
793 916 4.982916 GGCGTTATGATTCTACTGTACCAG 59.017 45.833 0.00 0.00 37.52 4.00
794 917 4.202182 GGGCGTTATGATTCTACTGTACCA 60.202 45.833 0.00 0.00 0.00 3.25
795 918 4.304939 GGGCGTTATGATTCTACTGTACC 58.695 47.826 0.00 0.00 0.00 3.34
875 999 8.677148 CTGCAAGGAAAACCTAAGCTATATTA 57.323 34.615 0.00 0.00 0.00 0.98
973 1097 3.636300 TGTTTGGGTCAATGGAAGTGAAG 59.364 43.478 0.00 0.00 45.34 3.02
1026 1150 1.023502 TCAGGTACACGTCGTTCACA 58.976 50.000 0.00 0.00 0.00 3.58
1119 1243 5.232463 GGAGTTTGATTACTAACGTGGTCA 58.768 41.667 0.00 0.00 36.98 4.02
1148 1272 1.077644 ACGCGGCTAGAGAGGAGAA 60.078 57.895 12.47 0.00 0.00 2.87
1165 1289 3.745797 GCCAGATCCTGTTATGGAAGGAC 60.746 52.174 0.76 0.00 45.26 3.85
1175 1299 1.194781 ACCGTCAGCCAGATCCTGTT 61.195 55.000 0.00 0.00 0.00 3.16
1187 1311 1.522668 TGCCTGAATGAAACCGTCAG 58.477 50.000 0.00 0.00 40.43 3.51
1543 1667 3.876320 CAGACTCATCAGATCTCTCACGA 59.124 47.826 0.00 0.00 0.00 4.35
1561 1685 4.962151 GCAACGTAAACAAAGAGAACAGAC 59.038 41.667 0.00 0.00 0.00 3.51
1563 1687 4.904116 TGCAACGTAAACAAAGAGAACAG 58.096 39.130 0.00 0.00 0.00 3.16
1669 1798 0.320771 CAGTTGGAGTGAGTTCCCCG 60.321 60.000 0.00 0.00 36.35 5.73
1690 1819 0.817634 CCCTGCAAGTGAAACCACGA 60.818 55.000 0.00 0.00 39.45 4.35
1772 1901 4.997905 TCGATGCTCAAGAAGTTTTCAG 57.002 40.909 0.00 0.00 0.00 3.02
1796 1925 7.423844 AGGAAAAACTTCCAACAGAGAAATT 57.576 32.000 6.67 0.00 43.54 1.82
1853 1982 0.373716 GACGCTAATTGACAAGCCCG 59.626 55.000 0.00 0.00 35.22 6.13
1922 2051 9.193133 CTGGACGTAAATACATAACAGGAATAG 57.807 37.037 0.00 0.00 0.00 1.73
1990 2132 9.453572 TTTGTGATTAGAGCTGATGAGTTAAAT 57.546 29.630 0.00 0.00 0.00 1.40
1991 2133 8.846943 TTTGTGATTAGAGCTGATGAGTTAAA 57.153 30.769 0.00 0.00 0.00 1.52
1992 2134 8.846943 TTTTGTGATTAGAGCTGATGAGTTAA 57.153 30.769 0.00 0.00 0.00 2.01
1993 2135 8.846943 TTTTTGTGATTAGAGCTGATGAGTTA 57.153 30.769 0.00 0.00 0.00 2.24
1994 2136 7.750229 TTTTTGTGATTAGAGCTGATGAGTT 57.250 32.000 0.00 0.00 0.00 3.01
2029 2172 1.647346 AAAAGTGAACGACGCTCACA 58.353 45.000 27.64 6.91 44.68 3.58
2076 2221 4.402155 AGGCACAAAGAGAACAAAACATGA 59.598 37.500 0.00 0.00 0.00 3.07
2190 2337 9.965824 TTCATCTTTAAAGGACAATTTCTCAAC 57.034 29.630 15.13 0.00 0.00 3.18
2226 2373 4.035208 CCCTTTAACAGTTAAGCCGCATAG 59.965 45.833 5.88 0.00 0.00 2.23
2231 2378 2.156098 TGCCCTTTAACAGTTAAGCCG 58.844 47.619 5.88 0.29 0.00 5.52
2352 2499 3.129287 CGATTTTTCCCTAGCAGCACATT 59.871 43.478 0.00 0.00 0.00 2.71
2354 2501 2.083774 CGATTTTTCCCTAGCAGCACA 58.916 47.619 0.00 0.00 0.00 4.57
2358 2505 5.997746 TCCATAATCGATTTTTCCCTAGCAG 59.002 40.000 17.19 0.00 0.00 4.24
2394 2541 6.200854 GCACGATCATTGTCATTGTATCAGTA 59.799 38.462 0.00 0.00 0.00 2.74
2411 2558 2.480037 GACACAGACATTTGCACGATCA 59.520 45.455 0.00 0.00 0.00 2.92
2512 2681 4.523943 ACTAATGAAATGAAGCACAGGCAA 59.476 37.500 0.00 0.00 44.61 4.52
2553 2722 7.981225 ACACTTCATTAAAACTGAAAACATGCT 59.019 29.630 0.00 0.00 32.53 3.79
2560 2729 8.519799 AGAGGAACACTTCATTAAAACTGAAA 57.480 30.769 0.00 0.00 32.53 2.69
2582 2751 6.073058 GGCAAAAGCAAAATTTTCCCTAAGAG 60.073 38.462 0.00 0.00 28.93 2.85
2583 2752 5.762711 GGCAAAAGCAAAATTTTCCCTAAGA 59.237 36.000 0.00 0.00 28.93 2.10
2584 2753 5.530543 TGGCAAAAGCAAAATTTTCCCTAAG 59.469 36.000 0.00 0.00 32.18 2.18
2585 2754 5.298026 GTGGCAAAAGCAAAATTTTCCCTAA 59.702 36.000 0.00 0.00 32.18 2.69
2586 2755 4.819088 GTGGCAAAAGCAAAATTTTCCCTA 59.181 37.500 0.00 0.00 32.18 3.53
2587 2756 3.631686 GTGGCAAAAGCAAAATTTTCCCT 59.368 39.130 0.00 0.00 32.18 4.20
2588 2757 3.631686 AGTGGCAAAAGCAAAATTTTCCC 59.368 39.130 0.00 0.00 31.66 3.97
2589 2758 4.576053 AGAGTGGCAAAAGCAAAATTTTCC 59.424 37.500 0.00 0.00 30.01 3.13
2590 2759 5.739752 AGAGTGGCAAAAGCAAAATTTTC 57.260 34.783 0.00 0.00 30.01 2.29
2591 2760 6.581712 TCTAGAGTGGCAAAAGCAAAATTTT 58.418 32.000 0.00 0.00 32.65 1.82
2592 2761 6.160576 TCTAGAGTGGCAAAAGCAAAATTT 57.839 33.333 0.00 0.00 0.00 1.82
2593 2762 5.789643 TCTAGAGTGGCAAAAGCAAAATT 57.210 34.783 0.00 0.00 0.00 1.82
2594 2763 5.990120 ATCTAGAGTGGCAAAAGCAAAAT 57.010 34.783 0.00 0.00 0.00 1.82
2595 2764 5.789643 AATCTAGAGTGGCAAAAGCAAAA 57.210 34.783 0.00 0.00 0.00 2.44
2596 2765 5.789643 AAATCTAGAGTGGCAAAAGCAAA 57.210 34.783 0.00 0.00 0.00 3.68
2597 2766 5.531634 CAAAATCTAGAGTGGCAAAAGCAA 58.468 37.500 0.00 0.00 0.00 3.91
2598 2767 4.559300 GCAAAATCTAGAGTGGCAAAAGCA 60.559 41.667 11.01 0.00 0.00 3.91
2599 2768 3.922850 GCAAAATCTAGAGTGGCAAAAGC 59.077 43.478 11.01 0.00 0.00 3.51
2600 2769 4.022068 TGGCAAAATCTAGAGTGGCAAAAG 60.022 41.667 20.86 0.00 42.78 2.27
2601 2770 3.894427 TGGCAAAATCTAGAGTGGCAAAA 59.106 39.130 20.86 5.26 42.78 2.44
2602 2771 3.495331 TGGCAAAATCTAGAGTGGCAAA 58.505 40.909 20.86 7.34 42.78 3.68
2603 2772 3.153369 TGGCAAAATCTAGAGTGGCAA 57.847 42.857 20.86 8.40 42.78 4.52
2604 2773 2.877097 TGGCAAAATCTAGAGTGGCA 57.123 45.000 19.84 19.84 43.41 4.92
2605 2774 4.725790 AATTGGCAAAATCTAGAGTGGC 57.274 40.909 3.01 16.21 37.09 5.01
2606 2775 6.071165 AGGAAAATTGGCAAAATCTAGAGTGG 60.071 38.462 3.01 0.00 0.00 4.00
2607 2776 6.928520 AGGAAAATTGGCAAAATCTAGAGTG 58.071 36.000 3.01 0.00 0.00 3.51
2608 2777 7.544804 AAGGAAAATTGGCAAAATCTAGAGT 57.455 32.000 3.01 0.00 0.00 3.24
2609 2778 9.525409 CATAAGGAAAATTGGCAAAATCTAGAG 57.475 33.333 3.01 0.00 0.00 2.43
2610 2779 7.981225 GCATAAGGAAAATTGGCAAAATCTAGA 59.019 33.333 3.01 0.00 0.00 2.43
2611 2780 7.225341 GGCATAAGGAAAATTGGCAAAATCTAG 59.775 37.037 3.01 0.00 35.00 2.43
2612 2781 7.047271 GGCATAAGGAAAATTGGCAAAATCTA 58.953 34.615 3.01 0.00 35.00 1.98
2613 2782 5.882000 GGCATAAGGAAAATTGGCAAAATCT 59.118 36.000 3.01 0.00 35.00 2.40
2614 2783 5.647225 TGGCATAAGGAAAATTGGCAAAATC 59.353 36.000 3.01 2.81 41.05 2.17
2615 2784 5.415389 GTGGCATAAGGAAAATTGGCAAAAT 59.585 36.000 3.01 0.00 44.76 1.82
2616 2785 4.759183 GTGGCATAAGGAAAATTGGCAAAA 59.241 37.500 3.01 0.00 44.76 2.44
2617 2786 4.041444 AGTGGCATAAGGAAAATTGGCAAA 59.959 37.500 3.01 0.00 44.76 3.68
2618 2787 3.582208 AGTGGCATAAGGAAAATTGGCAA 59.418 39.130 0.68 0.68 44.76 4.52
2619 2788 3.172339 AGTGGCATAAGGAAAATTGGCA 58.828 40.909 0.00 0.00 41.64 4.92
2620 2789 3.448660 AGAGTGGCATAAGGAAAATTGGC 59.551 43.478 0.00 0.00 35.41 4.52
2621 2790 6.122277 TCTAGAGTGGCATAAGGAAAATTGG 58.878 40.000 0.00 0.00 0.00 3.16
2622 2791 7.814264 ATCTAGAGTGGCATAAGGAAAATTG 57.186 36.000 0.00 0.00 0.00 2.32
2623 2792 8.829373 AAATCTAGAGTGGCATAAGGAAAATT 57.171 30.769 0.00 0.00 0.00 1.82
2624 2793 8.689972 CAAAATCTAGAGTGGCATAAGGAAAAT 58.310 33.333 0.00 0.00 0.00 1.82
2625 2794 7.888021 TCAAAATCTAGAGTGGCATAAGGAAAA 59.112 33.333 0.00 0.00 0.00 2.29
2626 2795 7.336931 GTCAAAATCTAGAGTGGCATAAGGAAA 59.663 37.037 0.00 0.00 0.00 3.13
2627 2796 6.823689 GTCAAAATCTAGAGTGGCATAAGGAA 59.176 38.462 0.00 0.00 0.00 3.36
2628 2797 6.070251 TGTCAAAATCTAGAGTGGCATAAGGA 60.070 38.462 0.00 0.00 0.00 3.36
2629 2798 6.115446 TGTCAAAATCTAGAGTGGCATAAGG 58.885 40.000 0.00 0.00 0.00 2.69
2630 2799 7.798596 ATGTCAAAATCTAGAGTGGCATAAG 57.201 36.000 15.58 0.00 34.66 1.73
2631 2800 8.579850 AAATGTCAAAATCTAGAGTGGCATAA 57.420 30.769 16.82 0.00 35.34 1.90
2632 2801 7.828717 TGAAATGTCAAAATCTAGAGTGGCATA 59.171 33.333 16.82 4.28 35.34 3.14
2633 2802 6.660521 TGAAATGTCAAAATCTAGAGTGGCAT 59.339 34.615 12.72 12.72 37.91 4.40
2634 2803 6.003326 TGAAATGTCAAAATCTAGAGTGGCA 58.997 36.000 9.74 9.74 0.00 4.92
2635 2804 6.150140 AGTGAAATGTCAAAATCTAGAGTGGC 59.850 38.462 0.00 0.00 34.87 5.01
2636 2805 7.678947 AGTGAAATGTCAAAATCTAGAGTGG 57.321 36.000 0.00 0.00 34.87 4.00
2637 2806 8.997323 AGAAGTGAAATGTCAAAATCTAGAGTG 58.003 33.333 0.00 0.00 34.87 3.51
2638 2807 8.997323 CAGAAGTGAAATGTCAAAATCTAGAGT 58.003 33.333 0.00 0.00 34.87 3.24
2639 2808 7.961827 GCAGAAGTGAAATGTCAAAATCTAGAG 59.038 37.037 0.00 0.00 34.87 2.43
2640 2809 7.094634 GGCAGAAGTGAAATGTCAAAATCTAGA 60.095 37.037 0.00 0.00 34.87 2.43
2641 2810 7.025963 GGCAGAAGTGAAATGTCAAAATCTAG 58.974 38.462 0.00 0.00 34.87 2.43
2642 2811 6.489700 TGGCAGAAGTGAAATGTCAAAATCTA 59.510 34.615 0.00 0.00 34.87 1.98
2643 2812 5.302568 TGGCAGAAGTGAAATGTCAAAATCT 59.697 36.000 0.00 0.00 34.87 2.40
2644 2813 5.403466 GTGGCAGAAGTGAAATGTCAAAATC 59.597 40.000 0.00 0.00 34.87 2.17
2645 2814 5.069516 AGTGGCAGAAGTGAAATGTCAAAAT 59.930 36.000 0.00 0.00 34.87 1.82
2646 2815 4.402155 AGTGGCAGAAGTGAAATGTCAAAA 59.598 37.500 0.00 0.00 34.87 2.44
2647 2816 3.953612 AGTGGCAGAAGTGAAATGTCAAA 59.046 39.130 0.00 0.00 34.87 2.69
2648 2817 3.554934 AGTGGCAGAAGTGAAATGTCAA 58.445 40.909 0.00 0.00 34.87 3.18
2649 2818 3.141398 GAGTGGCAGAAGTGAAATGTCA 58.859 45.455 0.00 0.00 0.00 3.58
2650 2819 3.406764 AGAGTGGCAGAAGTGAAATGTC 58.593 45.455 0.00 0.00 0.00 3.06
2651 2820 3.498774 AGAGTGGCAGAAGTGAAATGT 57.501 42.857 0.00 0.00 0.00 2.71
2652 2821 4.999950 ACTAAGAGTGGCAGAAGTGAAATG 59.000 41.667 0.00 0.00 0.00 2.32
2653 2822 5.234466 ACTAAGAGTGGCAGAAGTGAAAT 57.766 39.130 0.00 0.00 0.00 2.17
2654 2823 4.689612 ACTAAGAGTGGCAGAAGTGAAA 57.310 40.909 0.00 0.00 0.00 2.69
2655 2824 4.689612 AACTAAGAGTGGCAGAAGTGAA 57.310 40.909 0.00 0.00 0.00 3.18
2656 2825 4.689612 AAACTAAGAGTGGCAGAAGTGA 57.310 40.909 0.00 0.00 0.00 3.41
2657 2826 5.296780 TCAAAAACTAAGAGTGGCAGAAGTG 59.703 40.000 0.00 0.00 0.00 3.16
2658 2827 5.297029 GTCAAAAACTAAGAGTGGCAGAAGT 59.703 40.000 0.00 0.00 0.00 3.01
2659 2828 5.296780 TGTCAAAAACTAAGAGTGGCAGAAG 59.703 40.000 0.00 0.00 0.00 2.85
2660 2829 5.189928 TGTCAAAAACTAAGAGTGGCAGAA 58.810 37.500 0.00 0.00 0.00 3.02
2661 2830 4.776349 TGTCAAAAACTAAGAGTGGCAGA 58.224 39.130 0.00 0.00 0.00 4.26
2662 2831 5.499139 TTGTCAAAAACTAAGAGTGGCAG 57.501 39.130 0.00 0.00 0.00 4.85
2663 2832 6.463995 AATTGTCAAAAACTAAGAGTGGCA 57.536 33.333 0.00 0.00 0.00 4.92
2664 2833 8.296713 TGATAATTGTCAAAAACTAAGAGTGGC 58.703 33.333 1.92 0.00 0.00 5.01
2665 2834 9.612620 GTGATAATTGTCAAAAACTAAGAGTGG 57.387 33.333 6.45 0.00 0.00 4.00
2682 2851 6.473131 CACGGGAATGACAATTGTGATAATTG 59.527 38.462 17.58 12.26 41.91 2.32
2683 2852 6.405731 CCACGGGAATGACAATTGTGATAATT 60.406 38.462 17.58 10.06 0.00 1.40
2684 2853 5.067674 CCACGGGAATGACAATTGTGATAAT 59.932 40.000 17.58 0.00 0.00 1.28
2685 2854 4.397730 CCACGGGAATGACAATTGTGATAA 59.602 41.667 17.58 0.00 0.00 1.75
2686 2855 3.944650 CCACGGGAATGACAATTGTGATA 59.055 43.478 17.58 2.38 0.00 2.15
2687 2856 2.754552 CCACGGGAATGACAATTGTGAT 59.245 45.455 17.58 10.77 0.00 3.06
2688 2857 2.158559 CCACGGGAATGACAATTGTGA 58.841 47.619 17.58 8.31 0.00 3.58
2689 2858 1.402720 GCCACGGGAATGACAATTGTG 60.403 52.381 17.58 1.77 0.00 3.33
2690 2859 0.887933 GCCACGGGAATGACAATTGT 59.112 50.000 11.78 11.78 0.00 2.71
2691 2860 0.887247 TGCCACGGGAATGACAATTG 59.113 50.000 3.24 3.24 0.00 2.32
2692 2861 1.626686 TTGCCACGGGAATGACAATT 58.373 45.000 0.00 0.00 0.00 2.32
2693 2862 1.626686 TTTGCCACGGGAATGACAAT 58.373 45.000 0.00 0.00 0.00 2.71
2694 2863 1.339610 CTTTTGCCACGGGAATGACAA 59.660 47.619 0.00 0.00 0.00 3.18
2695 2864 0.958091 CTTTTGCCACGGGAATGACA 59.042 50.000 0.00 0.00 0.00 3.58
2696 2865 0.388520 GCTTTTGCCACGGGAATGAC 60.389 55.000 0.00 0.00 40.15 3.06
2697 2866 0.825425 TGCTTTTGCCACGGGAATGA 60.825 50.000 0.00 0.00 46.87 2.57
2698 2867 0.033228 TTGCTTTTGCCACGGGAATG 59.967 50.000 0.00 0.00 46.87 2.67
2699 2868 0.755686 TTTGCTTTTGCCACGGGAAT 59.244 45.000 0.00 0.00 46.87 3.01
2700 2869 0.537188 TTTTGCTTTTGCCACGGGAA 59.463 45.000 0.00 0.00 46.87 3.97
2701 2870 0.755686 ATTTTGCTTTTGCCACGGGA 59.244 45.000 0.00 0.00 46.87 5.14
2702 2871 1.592064 AATTTTGCTTTTGCCACGGG 58.408 45.000 0.00 0.00 46.87 5.28
2703 2872 3.064545 TGAAAATTTTGCTTTTGCCACGG 59.935 39.130 8.47 0.00 46.87 4.94
2704 2873 4.033817 TCTGAAAATTTTGCTTTTGCCACG 59.966 37.500 8.47 0.00 46.87 4.94
2705 2874 5.065090 ACTCTGAAAATTTTGCTTTTGCCAC 59.935 36.000 8.47 0.00 46.87 5.01
2706 2875 5.064962 CACTCTGAAAATTTTGCTTTTGCCA 59.935 36.000 8.47 0.00 46.87 4.92
2707 2876 5.504392 CACTCTGAAAATTTTGCTTTTGCC 58.496 37.500 8.47 0.00 46.87 4.52
2709 2878 5.064962 TGCCACTCTGAAAATTTTGCTTTTG 59.935 36.000 8.47 0.31 0.00 2.44
2710 2879 5.184711 TGCCACTCTGAAAATTTTGCTTTT 58.815 33.333 8.47 0.00 0.00 2.27
2711 2880 4.768583 TGCCACTCTGAAAATTTTGCTTT 58.231 34.783 8.47 0.00 0.00 3.51
2712 2881 4.405116 TGCCACTCTGAAAATTTTGCTT 57.595 36.364 8.47 0.00 0.00 3.91
2713 2882 4.612264 ATGCCACTCTGAAAATTTTGCT 57.388 36.364 8.47 0.00 0.00 3.91
2714 2883 5.007921 ACAAATGCCACTCTGAAAATTTTGC 59.992 36.000 8.47 4.25 0.00 3.68
2715 2884 6.258287 TCACAAATGCCACTCTGAAAATTTTG 59.742 34.615 8.47 0.00 0.00 2.44
2716 2885 6.347696 TCACAAATGCCACTCTGAAAATTTT 58.652 32.000 2.28 2.28 0.00 1.82
2717 2886 5.916318 TCACAAATGCCACTCTGAAAATTT 58.084 33.333 0.00 0.00 0.00 1.82
2718 2887 5.534207 TCACAAATGCCACTCTGAAAATT 57.466 34.783 0.00 0.00 0.00 1.82
2719 2888 5.733620 ATCACAAATGCCACTCTGAAAAT 57.266 34.783 0.00 0.00 0.00 1.82
2720 2889 6.647334 TTATCACAAATGCCACTCTGAAAA 57.353 33.333 0.00 0.00 0.00 2.29
2721 2890 6.839124 ATTATCACAAATGCCACTCTGAAA 57.161 33.333 0.00 0.00 0.00 2.69
2722 2891 6.209192 ACAATTATCACAAATGCCACTCTGAA 59.791 34.615 0.00 0.00 0.00 3.02
2723 2892 5.711506 ACAATTATCACAAATGCCACTCTGA 59.288 36.000 0.00 0.00 0.00 3.27
2724 2893 5.957798 ACAATTATCACAAATGCCACTCTG 58.042 37.500 0.00 0.00 0.00 3.35
2725 2894 5.711506 TGACAATTATCACAAATGCCACTCT 59.288 36.000 0.00 0.00 0.00 3.24
2726 2895 5.953183 TGACAATTATCACAAATGCCACTC 58.047 37.500 0.00 0.00 0.00 3.51
2727 2896 5.981088 TGACAATTATCACAAATGCCACT 57.019 34.783 0.00 0.00 0.00 4.00
2728 2897 7.360269 CCTTTTGACAATTATCACAAATGCCAC 60.360 37.037 0.00 0.00 33.38 5.01
2729 2898 6.649973 CCTTTTGACAATTATCACAAATGCCA 59.350 34.615 0.00 0.00 33.38 4.92
2730 2899 6.650390 ACCTTTTGACAATTATCACAAATGCC 59.350 34.615 0.00 0.00 33.38 4.40
2731 2900 7.656707 ACCTTTTGACAATTATCACAAATGC 57.343 32.000 0.00 0.00 33.38 3.56
2735 2904 9.349713 ACTCTTACCTTTTGACAATTATCACAA 57.650 29.630 0.00 0.00 0.00 3.33
2736 2905 8.918202 ACTCTTACCTTTTGACAATTATCACA 57.082 30.769 0.00 0.00 0.00 3.58
2738 2907 9.162764 GCTACTCTTACCTTTTGACAATTATCA 57.837 33.333 0.00 0.00 0.00 2.15
2739 2908 9.162764 TGCTACTCTTACCTTTTGACAATTATC 57.837 33.333 0.00 0.00 0.00 1.75
2740 2909 9.515226 TTGCTACTCTTACCTTTTGACAATTAT 57.485 29.630 0.00 0.00 0.00 1.28
2741 2910 8.911918 TTGCTACTCTTACCTTTTGACAATTA 57.088 30.769 0.00 0.00 0.00 1.40
2742 2911 7.817418 TTGCTACTCTTACCTTTTGACAATT 57.183 32.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.