Multiple sequence alignment - TraesCS4D01G222200
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 | TraesCS4D01G222200 | chr4D | 100.000 | 3058 | 0 | 0 | 500 | 3557 | 379260895 | 379257838 | 0.000000e+00 | 5648.0 |
1 | TraesCS4D01G222200 | chr4D | 100.000 | 107 | 0 | 0 | 1 | 107 | 379261394 | 379261288 | 7.790000e-47 | 198.0 |
2 | TraesCS4D01G222200 | chr4B | 95.164 | 2316 | 80 | 15 | 500 | 2795 | 466060448 | 466058145 | 0.000000e+00 | 3627.0 |
3 | TraesCS4D01G222200 | chr4B | 88.095 | 462 | 26 | 15 | 2901 | 3342 | 466058111 | 466057659 | 4.070000e-144 | 521.0 |
4 | TraesCS4D01G222200 | chr4B | 93.671 | 79 | 5 | 0 | 3479 | 3557 | 466057377 | 466057299 | 6.240000e-23 | 119.0 |
5 | TraesCS4D01G222200 | chr4A | 95.557 | 1958 | 59 | 8 | 873 | 2805 | 85568682 | 85570636 | 0.000000e+00 | 3109.0 |
6 | TraesCS4D01G222200 | chr6B | 86.872 | 358 | 22 | 16 | 501 | 840 | 602204408 | 602204758 | 9.320000e-101 | 377.0 |
7 | TraesCS4D01G222200 | chr5B | 81.690 | 284 | 39 | 9 | 1504 | 1779 | 554808832 | 554808554 | 1.290000e-54 | 224.0 |
8 | TraesCS4D01G222200 | chr5A | 80.756 | 291 | 43 | 9 | 1504 | 1786 | 573086443 | 573086158 | 7.730000e-52 | 215.0 |
9 | TraesCS4D01G222200 | chr2D | 77.273 | 308 | 43 | 15 | 1240 | 1547 | 26327151 | 26326871 | 4.750000e-34 | 156.0 |
10 | TraesCS4D01G222200 | chr2D | 78.673 | 211 | 22 | 11 | 1244 | 1454 | 26470410 | 26470597 | 6.240000e-23 | 119.0 |
11 | TraesCS4D01G222200 | chr2D | 77.626 | 219 | 26 | 15 | 1237 | 1455 | 26035952 | 26036147 | 1.040000e-20 | 111.0 |
12 | TraesCS4D01G222200 | chr7D | 77.992 | 259 | 39 | 9 | 1291 | 1547 | 29934882 | 29934640 | 2.860000e-31 | 147.0 |
13 | TraesCS4D01G222200 | chr2B | 86.131 | 137 | 10 | 2 | 1415 | 1547 | 41435975 | 41435844 | 4.790000e-29 | 139.0 |
14 | TraesCS4D01G222200 | chr2B | 92.157 | 51 | 4 | 0 | 1497 | 1547 | 41476195 | 41476145 | 4.930000e-09 | 73.1 |
15 | TraesCS4D01G222200 | chr2A | 78.531 | 177 | 21 | 10 | 1323 | 1494 | 28212859 | 28213023 | 2.260000e-17 | 100.0 |
16 | TraesCS4D01G222200 | chr1D | 87.500 | 80 | 5 | 2 | 2831 | 2905 | 208240413 | 208240334 | 1.760000e-13 | 87.9 |
17 | TraesCS4D01G222200 | chr6D | 89.796 | 49 | 5 | 0 | 681 | 729 | 313280716 | 313280668 | 2.960000e-06 | 63.9 |
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 | TraesCS4D01G222200 | chr4D | 379257838 | 379261394 | 3556 | True | 2923.000000 | 5648 | 100.000 | 1 | 3557 | 2 | chr4D.!!$R1 | 3556 |
1 | TraesCS4D01G222200 | chr4B | 466057299 | 466060448 | 3149 | True | 1422.333333 | 3627 | 92.310 | 500 | 3557 | 3 | chr4B.!!$R1 | 3057 |
2 | TraesCS4D01G222200 | chr4A | 85568682 | 85570636 | 1954 | False | 3109.000000 | 3109 | 95.557 | 873 | 2805 | 1 | chr4A.!!$F1 | 1932 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
32 | 33 | 0.032130 | TCACCGGCTGAAGCGATATC | 59.968 | 55.0 | 0.0 | 0.0 | 43.26 | 1.63 | F |
556 | 557 | 0.178767 | TCATCATCTCGGCTTGGTGG | 59.821 | 55.0 | 0.0 | 0.0 | 0.00 | 4.61 | F |
558 | 559 | 0.179000 | ATCATCTCGGCTTGGTGGTC | 59.821 | 55.0 | 0.0 | 0.0 | 0.00 | 4.02 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1500 | 1526 | 1.519455 | GAATGGGTGGTCGAGCGAG | 60.519 | 63.158 | 10.46 | 0.0 | 0.00 | 5.03 | R |
2484 | 2513 | 1.741706 | CAACTCATCAGCTTGCGGAAT | 59.258 | 47.619 | 0.00 | 0.0 | 0.00 | 3.01 | R |
2626 | 2665 | 2.946785 | CGACCCCTTCCACTCTATAGT | 58.053 | 52.381 | 0.00 | 0.0 | 35.91 | 2.12 | R |
All possible primersListed 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. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
28 | 29 | 4.717629 | CGTCACCGGCTGAAGCGA | 62.718 | 66.667 | 0.00 | 0.00 | 43.26 | 4.93 |
29 | 30 | 2.125512 | GTCACCGGCTGAAGCGAT | 60.126 | 61.111 | 0.00 | 0.00 | 43.26 | 4.58 |
30 | 31 | 1.141019 | GTCACCGGCTGAAGCGATA | 59.859 | 57.895 | 0.00 | 0.00 | 43.26 | 2.92 |
31 | 32 | 0.249489 | GTCACCGGCTGAAGCGATAT | 60.249 | 55.000 | 0.00 | 0.00 | 43.26 | 1.63 |
32 | 33 | 0.032130 | TCACCGGCTGAAGCGATATC | 59.968 | 55.000 | 0.00 | 0.00 | 43.26 | 1.63 |
33 | 34 | 1.007271 | ACCGGCTGAAGCGATATCG | 60.007 | 57.895 | 20.79 | 20.79 | 43.26 | 2.92 |
43 | 44 | 2.030562 | CGATATCGCCCACCACCC | 59.969 | 66.667 | 12.95 | 0.00 | 0.00 | 4.61 |
44 | 45 | 2.030562 | GATATCGCCCACCACCCG | 59.969 | 66.667 | 0.00 | 0.00 | 0.00 | 5.28 |
45 | 46 | 4.250305 | ATATCGCCCACCACCCGC | 62.250 | 66.667 | 0.00 | 0.00 | 0.00 | 6.13 |
51 | 52 | 4.904590 | CCCACCACCCGCAACCAA | 62.905 | 66.667 | 0.00 | 0.00 | 0.00 | 3.67 |
52 | 53 | 3.601685 | CCACCACCCGCAACCAAC | 61.602 | 66.667 | 0.00 | 0.00 | 0.00 | 3.77 |
53 | 54 | 2.830827 | CACCACCCGCAACCAACA | 60.831 | 61.111 | 0.00 | 0.00 | 0.00 | 3.33 |
54 | 55 | 2.197324 | ACCACCCGCAACCAACAT | 59.803 | 55.556 | 0.00 | 0.00 | 0.00 | 2.71 |
55 | 56 | 0.891449 | CACCACCCGCAACCAACATA | 60.891 | 55.000 | 0.00 | 0.00 | 0.00 | 2.29 |
56 | 57 | 0.608035 | ACCACCCGCAACCAACATAG | 60.608 | 55.000 | 0.00 | 0.00 | 0.00 | 2.23 |
57 | 58 | 1.506262 | CACCCGCAACCAACATAGC | 59.494 | 57.895 | 0.00 | 0.00 | 0.00 | 2.97 |
58 | 59 | 1.677633 | ACCCGCAACCAACATAGCC | 60.678 | 57.895 | 0.00 | 0.00 | 0.00 | 3.93 |
59 | 60 | 1.677300 | CCCGCAACCAACATAGCCA | 60.677 | 57.895 | 0.00 | 0.00 | 0.00 | 4.75 |
60 | 61 | 1.037030 | CCCGCAACCAACATAGCCAT | 61.037 | 55.000 | 0.00 | 0.00 | 0.00 | 4.40 |
61 | 62 | 0.381801 | CCGCAACCAACATAGCCATC | 59.618 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
62 | 63 | 1.093972 | CGCAACCAACATAGCCATCA | 58.906 | 50.000 | 0.00 | 0.00 | 0.00 | 3.07 |
63 | 64 | 1.202177 | CGCAACCAACATAGCCATCAC | 60.202 | 52.381 | 0.00 | 0.00 | 0.00 | 3.06 |
64 | 65 | 1.818060 | GCAACCAACATAGCCATCACA | 59.182 | 47.619 | 0.00 | 0.00 | 0.00 | 3.58 |
65 | 66 | 2.428171 | GCAACCAACATAGCCATCACAT | 59.572 | 45.455 | 0.00 | 0.00 | 0.00 | 3.21 |
66 | 67 | 3.119029 | GCAACCAACATAGCCATCACATT | 60.119 | 43.478 | 0.00 | 0.00 | 0.00 | 2.71 |
67 | 68 | 4.426416 | CAACCAACATAGCCATCACATTG | 58.574 | 43.478 | 0.00 | 0.00 | 0.00 | 2.82 |
68 | 69 | 3.025978 | ACCAACATAGCCATCACATTGG | 58.974 | 45.455 | 0.00 | 0.00 | 40.76 | 3.16 |
74 | 75 | 4.230603 | CCATCACATTGGCTCGCT | 57.769 | 55.556 | 0.00 | 0.00 | 0.00 | 4.93 |
75 | 76 | 1.725665 | CCATCACATTGGCTCGCTG | 59.274 | 57.895 | 0.00 | 0.00 | 0.00 | 5.18 |
76 | 77 | 1.063649 | CATCACATTGGCTCGCTGC | 59.936 | 57.895 | 0.00 | 0.00 | 41.94 | 5.25 |
88 | 89 | 4.632974 | CGCTGCCCCTGCCCTATC | 62.633 | 72.222 | 0.00 | 0.00 | 36.33 | 2.08 |
89 | 90 | 4.277009 | GCTGCCCCTGCCCTATCC | 62.277 | 72.222 | 0.00 | 0.00 | 36.33 | 2.59 |
90 | 91 | 2.449322 | CTGCCCCTGCCCTATCCT | 60.449 | 66.667 | 0.00 | 0.00 | 36.33 | 3.24 |
91 | 92 | 2.448542 | TGCCCCTGCCCTATCCTC | 60.449 | 66.667 | 0.00 | 0.00 | 36.33 | 3.71 |
92 | 93 | 3.631046 | GCCCCTGCCCTATCCTCG | 61.631 | 72.222 | 0.00 | 0.00 | 0.00 | 4.63 |
93 | 94 | 3.631046 | CCCCTGCCCTATCCTCGC | 61.631 | 72.222 | 0.00 | 0.00 | 0.00 | 5.03 |
94 | 95 | 3.996124 | CCCTGCCCTATCCTCGCG | 61.996 | 72.222 | 0.00 | 0.00 | 0.00 | 5.87 |
95 | 96 | 3.227276 | CCTGCCCTATCCTCGCGT | 61.227 | 66.667 | 5.77 | 0.00 | 0.00 | 6.01 |
96 | 97 | 2.797278 | CCTGCCCTATCCTCGCGTT | 61.797 | 63.158 | 5.77 | 0.00 | 0.00 | 4.84 |
97 | 98 | 1.300233 | CTGCCCTATCCTCGCGTTC | 60.300 | 63.158 | 5.77 | 0.00 | 0.00 | 3.95 |
98 | 99 | 1.739338 | CTGCCCTATCCTCGCGTTCT | 61.739 | 60.000 | 5.77 | 0.00 | 0.00 | 3.01 |
99 | 100 | 1.007154 | GCCCTATCCTCGCGTTCTC | 60.007 | 63.158 | 5.77 | 0.00 | 0.00 | 2.87 |
100 | 101 | 1.457009 | GCCCTATCCTCGCGTTCTCT | 61.457 | 60.000 | 5.77 | 0.00 | 0.00 | 3.10 |
101 | 102 | 1.033574 | CCCTATCCTCGCGTTCTCTT | 58.966 | 55.000 | 5.77 | 0.00 | 0.00 | 2.85 |
102 | 103 | 1.001158 | CCCTATCCTCGCGTTCTCTTC | 60.001 | 57.143 | 5.77 | 0.00 | 0.00 | 2.87 |
103 | 104 | 1.001158 | CCTATCCTCGCGTTCTCTTCC | 60.001 | 57.143 | 5.77 | 0.00 | 0.00 | 3.46 |
104 | 105 | 0.661552 | TATCCTCGCGTTCTCTTCCG | 59.338 | 55.000 | 5.77 | 0.00 | 0.00 | 4.30 |
105 | 106 | 2.615262 | ATCCTCGCGTTCTCTTCCGC | 62.615 | 60.000 | 5.77 | 0.00 | 46.10 | 5.54 |
106 | 107 | 2.881352 | CTCGCGTTCTCTTCCGCC | 60.881 | 66.667 | 5.77 | 0.00 | 46.83 | 6.13 |
519 | 520 | 1.968540 | GTCAACCCTCCTGCACTGC | 60.969 | 63.158 | 0.00 | 0.00 | 0.00 | 4.40 |
527 | 528 | 4.624364 | CCTGCACTGCCGGTGTCA | 62.624 | 66.667 | 1.90 | 3.31 | 46.86 | 3.58 |
536 | 537 | 2.125512 | CCGGTGTCACAGCTAGCC | 60.126 | 66.667 | 12.13 | 0.00 | 0.00 | 3.93 |
556 | 557 | 0.178767 | TCATCATCTCGGCTTGGTGG | 59.821 | 55.000 | 0.00 | 0.00 | 0.00 | 4.61 |
558 | 559 | 0.179000 | ATCATCTCGGCTTGGTGGTC | 59.821 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 |
652 | 654 | 6.524101 | AAATACAGACAATTTACGCCCATT | 57.476 | 33.333 | 0.00 | 0.00 | 0.00 | 3.16 |
688 | 690 | 7.387397 | CCATTTCTTATTGGCAGATACTCTCTC | 59.613 | 40.741 | 0.00 | 0.00 | 29.16 | 3.20 |
689 | 691 | 6.412362 | TTCTTATTGGCAGATACTCTCTCC | 57.588 | 41.667 | 0.00 | 0.00 | 29.16 | 3.71 |
694 | 696 | 3.413327 | TGGCAGATACTCTCTCCGTATC | 58.587 | 50.000 | 0.00 | 0.00 | 42.11 | 2.24 |
700 | 702 | 6.419413 | GCAGATACTCTCTCCGTATCAAAAAG | 59.581 | 42.308 | 11.41 | 0.34 | 43.48 | 2.27 |
701 | 703 | 7.484975 | CAGATACTCTCTCCGTATCAAAAAGT | 58.515 | 38.462 | 11.41 | 0.00 | 43.48 | 2.66 |
825 | 840 | 1.173913 | GGTCCATTTACAGTGGCCAC | 58.826 | 55.000 | 29.22 | 29.22 | 36.66 | 5.01 |
826 | 841 | 1.173913 | GTCCATTTACAGTGGCCACC | 58.826 | 55.000 | 32.29 | 14.56 | 36.66 | 4.61 |
904 | 926 | 2.575262 | GCTTCATTCTGCGCGCAC | 60.575 | 61.111 | 33.09 | 14.58 | 0.00 | 5.34 |
964 | 986 | 3.876914 | TCACACACAGACTCCAAACAATC | 59.123 | 43.478 | 0.00 | 0.00 | 0.00 | 2.67 |
1500 | 1526 | 2.815298 | CGAGTCTCGCGTCCTCTCC | 61.815 | 68.421 | 9.74 | 0.00 | 31.14 | 3.71 |
1530 | 1556 | 2.751436 | CCATTCGTGCCCACCCTG | 60.751 | 66.667 | 0.00 | 0.00 | 0.00 | 4.45 |
2481 | 2510 | 4.753662 | TACGAGGAGCGGCAGGGT | 62.754 | 66.667 | 1.45 | 0.00 | 46.49 | 4.34 |
2484 | 2513 | 3.075005 | GAGGAGCGGCAGGGTGTA | 61.075 | 66.667 | 1.45 | 0.00 | 0.00 | 2.90 |
2624 | 2663 | 1.068127 | GGGTTCGTGGCGTGTATAGAT | 59.932 | 52.381 | 0.00 | 0.00 | 0.00 | 1.98 |
2625 | 2664 | 2.391879 | GGTTCGTGGCGTGTATAGATC | 58.608 | 52.381 | 0.00 | 0.00 | 0.00 | 2.75 |
2626 | 2665 | 2.223641 | GGTTCGTGGCGTGTATAGATCA | 60.224 | 50.000 | 0.00 | 0.00 | 0.00 | 2.92 |
2669 | 2709 | 4.803426 | GACCGGCGAGGCTGTGAG | 62.803 | 72.222 | 9.30 | 0.00 | 46.52 | 3.51 |
2799 | 2854 | 7.420002 | TGTTCACTGAGATTTGTTTTCTCATG | 58.580 | 34.615 | 4.03 | 5.66 | 46.26 | 3.07 |
2805 | 2860 | 5.049474 | TGAGATTTGTTTTCTCATGACGGTG | 60.049 | 40.000 | 0.00 | 0.00 | 43.49 | 4.94 |
2807 | 2862 | 1.234821 | TGTTTTCTCATGACGGTGCC | 58.765 | 50.000 | 0.00 | 0.00 | 0.00 | 5.01 |
2812 | 2867 | 0.530744 | TCTCATGACGGTGCCAGTAC | 59.469 | 55.000 | 0.00 | 0.00 | 0.00 | 2.73 |
2815 | 2870 | 1.346395 | TCATGACGGTGCCAGTACTTT | 59.654 | 47.619 | 0.00 | 0.00 | 0.00 | 2.66 |
2816 | 2871 | 2.563620 | TCATGACGGTGCCAGTACTTTA | 59.436 | 45.455 | 0.00 | 0.00 | 0.00 | 1.85 |
2817 | 2872 | 2.736144 | TGACGGTGCCAGTACTTTAG | 57.264 | 50.000 | 0.00 | 0.00 | 0.00 | 1.85 |
2818 | 2873 | 1.274167 | TGACGGTGCCAGTACTTTAGG | 59.726 | 52.381 | 0.00 | 0.00 | 0.00 | 2.69 |
2819 | 2874 | 0.611714 | ACGGTGCCAGTACTTTAGGG | 59.388 | 55.000 | 0.00 | 0.00 | 0.00 | 3.53 |
2820 | 2875 | 0.611714 | CGGTGCCAGTACTTTAGGGT | 59.388 | 55.000 | 0.00 | 0.00 | 0.00 | 4.34 |
2821 | 2876 | 1.826720 | CGGTGCCAGTACTTTAGGGTA | 59.173 | 52.381 | 0.00 | 0.00 | 0.00 | 3.69 |
2823 | 2878 | 2.836372 | GGTGCCAGTACTTTAGGGTAGT | 59.164 | 50.000 | 0.00 | 0.00 | 0.00 | 2.73 |
2824 | 2879 | 4.026052 | GGTGCCAGTACTTTAGGGTAGTA | 58.974 | 47.826 | 0.00 | 0.00 | 0.00 | 1.82 |
2825 | 2880 | 4.142071 | GGTGCCAGTACTTTAGGGTAGTAC | 60.142 | 50.000 | 0.00 | 0.00 | 45.27 | 2.73 |
2833 | 2888 | 7.818493 | GTACTTTAGGGTAGTACTTTTTCCG | 57.182 | 40.000 | 0.00 | 0.00 | 42.88 | 4.30 |
2834 | 2889 | 6.425210 | ACTTTAGGGTAGTACTTTTTCCGT | 57.575 | 37.500 | 0.00 | 3.91 | 0.00 | 4.69 |
2835 | 2890 | 6.459066 | ACTTTAGGGTAGTACTTTTTCCGTC | 58.541 | 40.000 | 0.00 | 0.00 | 0.00 | 4.79 |
2836 | 2891 | 3.969287 | AGGGTAGTACTTTTTCCGTCC | 57.031 | 47.619 | 0.00 | 0.00 | 0.00 | 4.79 |
2837 | 2892 | 2.568956 | AGGGTAGTACTTTTTCCGTCCC | 59.431 | 50.000 | 0.00 | 1.38 | 0.00 | 4.46 |
2838 | 2893 | 2.302733 | GGGTAGTACTTTTTCCGTCCCA | 59.697 | 50.000 | 0.00 | 0.00 | 33.33 | 4.37 |
2839 | 2894 | 3.054875 | GGGTAGTACTTTTTCCGTCCCAT | 60.055 | 47.826 | 0.00 | 0.00 | 33.33 | 4.00 |
2840 | 2895 | 3.937079 | GGTAGTACTTTTTCCGTCCCATG | 59.063 | 47.826 | 0.00 | 0.00 | 0.00 | 3.66 |
2841 | 2896 | 4.322953 | GGTAGTACTTTTTCCGTCCCATGA | 60.323 | 45.833 | 0.00 | 0.00 | 0.00 | 3.07 |
2842 | 2897 | 4.569719 | AGTACTTTTTCCGTCCCATGAT | 57.430 | 40.909 | 0.00 | 0.00 | 0.00 | 2.45 |
2843 | 2898 | 5.687166 | AGTACTTTTTCCGTCCCATGATA | 57.313 | 39.130 | 0.00 | 0.00 | 0.00 | 2.15 |
2844 | 2899 | 6.248569 | AGTACTTTTTCCGTCCCATGATAT | 57.751 | 37.500 | 0.00 | 0.00 | 0.00 | 1.63 |
2845 | 2900 | 7.369551 | AGTACTTTTTCCGTCCCATGATATA | 57.630 | 36.000 | 0.00 | 0.00 | 0.00 | 0.86 |
2846 | 2901 | 7.798071 | AGTACTTTTTCCGTCCCATGATATAA | 58.202 | 34.615 | 0.00 | 0.00 | 0.00 | 0.98 |
2847 | 2902 | 8.269317 | AGTACTTTTTCCGTCCCATGATATAAA | 58.731 | 33.333 | 0.00 | 0.00 | 0.00 | 1.40 |
2848 | 2903 | 7.948034 | ACTTTTTCCGTCCCATGATATAAAA | 57.052 | 32.000 | 0.00 | 0.00 | 0.00 | 1.52 |
2849 | 2904 | 7.996385 | ACTTTTTCCGTCCCATGATATAAAAG | 58.004 | 34.615 | 0.00 | 0.00 | 36.59 | 2.27 |
2850 | 2905 | 6.385649 | TTTTCCGTCCCATGATATAAAAGC | 57.614 | 37.500 | 0.00 | 0.00 | 0.00 | 3.51 |
2851 | 2906 | 3.659786 | TCCGTCCCATGATATAAAAGCG | 58.340 | 45.455 | 0.00 | 0.00 | 0.00 | 4.68 |
2852 | 2907 | 3.070446 | TCCGTCCCATGATATAAAAGCGT | 59.930 | 43.478 | 0.00 | 0.00 | 0.00 | 5.07 |
2853 | 2908 | 3.813166 | CCGTCCCATGATATAAAAGCGTT | 59.187 | 43.478 | 0.00 | 0.00 | 0.00 | 4.84 |
2854 | 2909 | 4.274950 | CCGTCCCATGATATAAAAGCGTTT | 59.725 | 41.667 | 2.53 | 2.53 | 0.00 | 3.60 |
2855 | 2910 | 5.220970 | CCGTCCCATGATATAAAAGCGTTTT | 60.221 | 40.000 | 2.19 | 1.29 | 36.67 | 2.43 |
2856 | 2911 | 6.262601 | CGTCCCATGATATAAAAGCGTTTTT | 58.737 | 36.000 | 14.50 | 14.50 | 39.69 | 1.94 |
2897 | 2952 | 8.976986 | AACGCTTTTATATTATAGTACGGAGG | 57.023 | 34.615 | 0.00 | 0.00 | 0.00 | 4.30 |
2898 | 2953 | 7.542025 | ACGCTTTTATATTATAGTACGGAGGG | 58.458 | 38.462 | 0.00 | 0.00 | 0.00 | 4.30 |
2899 | 2954 | 7.394359 | ACGCTTTTATATTATAGTACGGAGGGA | 59.606 | 37.037 | 0.00 | 0.00 | 0.00 | 4.20 |
2945 | 3003 | 0.518636 | CAGATTGACCAGTTGCCGTG | 59.481 | 55.000 | 0.00 | 0.00 | 0.00 | 4.94 |
2971 | 3029 | 2.749621 | GTTAAATGTCAGCAGTCCAGGG | 59.250 | 50.000 | 0.00 | 0.00 | 0.00 | 4.45 |
2972 | 3030 | 0.038744 | AAATGTCAGCAGTCCAGGGG | 59.961 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
3002 | 3065 | 5.585047 | GTCTTTGACCAACAACAAGTAGAGT | 59.415 | 40.000 | 0.00 | 0.00 | 38.29 | 3.24 |
3023 | 3086 | 6.773200 | AGAGTATCCGATATCTTGAACACTGA | 59.227 | 38.462 | 0.34 | 0.00 | 33.66 | 3.41 |
3024 | 3087 | 7.450014 | AGAGTATCCGATATCTTGAACACTGAT | 59.550 | 37.037 | 0.34 | 0.00 | 33.66 | 2.90 |
3025 | 3088 | 7.957002 | AGTATCCGATATCTTGAACACTGATT | 58.043 | 34.615 | 0.34 | 0.00 | 0.00 | 2.57 |
3026 | 3089 | 8.085296 | AGTATCCGATATCTTGAACACTGATTC | 58.915 | 37.037 | 0.34 | 0.00 | 0.00 | 2.52 |
3049 | 3112 | 6.841119 | TCGTATTGAATTTGAACATCTGTGG | 58.159 | 36.000 | 0.00 | 0.00 | 0.00 | 4.17 |
3141 | 3210 | 1.619807 | GCCCATGCCATGCCTTTCTT | 61.620 | 55.000 | 0.00 | 0.00 | 0.00 | 2.52 |
3168 | 3237 | 0.682292 | TGCACTGTACGGGTTGATCA | 59.318 | 50.000 | 6.65 | 0.00 | 0.00 | 2.92 |
3176 | 3245 | 4.562082 | TGTACGGGTTGATCACTACTTTG | 58.438 | 43.478 | 0.00 | 0.00 | 0.00 | 2.77 |
3182 | 3251 | 4.505039 | GGGTTGATCACTACTTTGGTCTGT | 60.505 | 45.833 | 0.00 | 0.00 | 0.00 | 3.41 |
3183 | 3252 | 4.691216 | GGTTGATCACTACTTTGGTCTGTC | 59.309 | 45.833 | 0.00 | 0.00 | 0.00 | 3.51 |
3184 | 3253 | 5.511545 | GGTTGATCACTACTTTGGTCTGTCT | 60.512 | 44.000 | 0.00 | 0.00 | 0.00 | 3.41 |
3185 | 3254 | 6.295123 | GGTTGATCACTACTTTGGTCTGTCTA | 60.295 | 42.308 | 0.00 | 0.00 | 0.00 | 2.59 |
3186 | 3255 | 6.516739 | TGATCACTACTTTGGTCTGTCTAG | 57.483 | 41.667 | 0.00 | 0.00 | 0.00 | 2.43 |
3187 | 3256 | 6.010850 | TGATCACTACTTTGGTCTGTCTAGT | 58.989 | 40.000 | 0.00 | 0.00 | 0.00 | 2.57 |
3188 | 3257 | 7.173032 | TGATCACTACTTTGGTCTGTCTAGTA | 58.827 | 38.462 | 0.00 | 0.00 | 0.00 | 1.82 |
3219 | 3291 | 3.931468 | CCAGAGCATTAACAGTGTCTCAG | 59.069 | 47.826 | 10.54 | 3.79 | 0.00 | 3.35 |
3221 | 3293 | 3.260380 | AGAGCATTAACAGTGTCTCAGCT | 59.740 | 43.478 | 11.51 | 11.51 | 0.00 | 4.24 |
3222 | 3294 | 4.464244 | AGAGCATTAACAGTGTCTCAGCTA | 59.536 | 41.667 | 11.62 | 0.00 | 0.00 | 3.32 |
3223 | 3295 | 5.047021 | AGAGCATTAACAGTGTCTCAGCTAA | 60.047 | 40.000 | 11.62 | 0.33 | 0.00 | 3.09 |
3224 | 3296 | 4.932200 | AGCATTAACAGTGTCTCAGCTAAC | 59.068 | 41.667 | 10.37 | 0.00 | 0.00 | 2.34 |
3225 | 3297 | 4.932200 | GCATTAACAGTGTCTCAGCTAACT | 59.068 | 41.667 | 0.00 | 0.00 | 0.00 | 2.24 |
3226 | 3298 | 5.409826 | GCATTAACAGTGTCTCAGCTAACTT | 59.590 | 40.000 | 0.00 | 0.00 | 0.00 | 2.66 |
3227 | 3299 | 6.590292 | GCATTAACAGTGTCTCAGCTAACTTA | 59.410 | 38.462 | 0.00 | 0.00 | 0.00 | 2.24 |
3231 | 3306 | 5.403246 | ACAGTGTCTCAGCTAACTTATTCG | 58.597 | 41.667 | 0.00 | 0.00 | 0.00 | 3.34 |
3236 | 3311 | 6.365247 | GTGTCTCAGCTAACTTATTCGACAAA | 59.635 | 38.462 | 0.00 | 0.00 | 31.63 | 2.83 |
3238 | 3313 | 7.063426 | TGTCTCAGCTAACTTATTCGACAAATG | 59.937 | 37.037 | 0.00 | 0.00 | 0.00 | 2.32 |
3250 | 3325 | 9.536558 | CTTATTCGACAAATGATTTTACACGAA | 57.463 | 29.630 | 14.95 | 14.95 | 37.29 | 3.85 |
3266 | 3341 | 7.962964 | TTACACGAAGATTCTTCATGAAACT | 57.037 | 32.000 | 24.72 | 8.54 | 39.09 | 2.66 |
3267 | 3342 | 6.473397 | ACACGAAGATTCTTCATGAAACTC | 57.527 | 37.500 | 24.72 | 6.54 | 36.89 | 3.01 |
3269 | 3344 | 5.409520 | CACGAAGATTCTTCATGAAACTCCA | 59.590 | 40.000 | 22.75 | 0.00 | 36.89 | 3.86 |
3281 | 3356 | 2.953648 | TGAAACTCCACACGTCAGTAGA | 59.046 | 45.455 | 0.00 | 0.00 | 0.00 | 2.59 |
3288 | 3363 | 3.108881 | CCACACGTCAGTAGAATGATCG | 58.891 | 50.000 | 0.00 | 0.00 | 33.16 | 3.69 |
3290 | 3365 | 4.498177 | CCACACGTCAGTAGAATGATCGAT | 60.498 | 45.833 | 0.00 | 0.00 | 32.12 | 3.59 |
3305 | 3380 | 5.806654 | TGATCGATCAGATTTGATACCCA | 57.193 | 39.130 | 23.99 | 0.00 | 44.01 | 4.51 |
3308 | 3383 | 7.906327 | TGATCGATCAGATTTGATACCCAATA | 58.094 | 34.615 | 23.99 | 0.00 | 44.01 | 1.90 |
3310 | 3385 | 9.388506 | GATCGATCAGATTTGATACCCAATATT | 57.611 | 33.333 | 20.52 | 0.00 | 44.01 | 1.28 |
3311 | 3386 | 9.745018 | ATCGATCAGATTTGATACCCAATATTT | 57.255 | 29.630 | 0.00 | 0.00 | 44.01 | 1.40 |
3312 | 3387 | 9.573166 | TCGATCAGATTTGATACCCAATATTTT | 57.427 | 29.630 | 0.00 | 0.00 | 44.01 | 1.82 |
3386 | 3651 | 1.142465 | CACCCAAGAGCTCCTATGCAT | 59.858 | 52.381 | 10.93 | 3.79 | 34.99 | 3.96 |
3422 | 3689 | 4.772886 | AAAGAATAACCTCGGCCTATGT | 57.227 | 40.909 | 0.00 | 0.00 | 0.00 | 2.29 |
3425 | 3692 | 6.435292 | AAGAATAACCTCGGCCTATGTATT | 57.565 | 37.500 | 0.00 | 0.00 | 0.00 | 1.89 |
3431 | 3698 | 6.675413 | AACCTCGGCCTATGTATTATACAA | 57.325 | 37.500 | 9.24 | 0.00 | 42.76 | 2.41 |
3432 | 3699 | 6.869206 | ACCTCGGCCTATGTATTATACAAT | 57.131 | 37.500 | 9.24 | 1.63 | 42.76 | 2.71 |
3433 | 3700 | 6.640518 | ACCTCGGCCTATGTATTATACAATG | 58.359 | 40.000 | 9.24 | 5.29 | 42.76 | 2.82 |
3434 | 3701 | 5.523916 | CCTCGGCCTATGTATTATACAATGC | 59.476 | 44.000 | 9.24 | 11.25 | 42.76 | 3.56 |
3435 | 3702 | 6.043854 | TCGGCCTATGTATTATACAATGCA | 57.956 | 37.500 | 9.24 | 0.00 | 42.76 | 3.96 |
3436 | 3703 | 5.872617 | TCGGCCTATGTATTATACAATGCAC | 59.127 | 40.000 | 9.24 | 6.06 | 42.76 | 4.57 |
3437 | 3704 | 5.641636 | CGGCCTATGTATTATACAATGCACA | 59.358 | 40.000 | 9.24 | 0.00 | 42.76 | 4.57 |
3438 | 3705 | 6.402118 | CGGCCTATGTATTATACAATGCACAC | 60.402 | 42.308 | 9.24 | 0.69 | 42.76 | 3.82 |
3439 | 3706 | 6.429692 | GGCCTATGTATTATACAATGCACACA | 59.570 | 38.462 | 9.24 | 0.00 | 42.76 | 3.72 |
3440 | 3707 | 7.040755 | GGCCTATGTATTATACAATGCACACAA | 60.041 | 37.037 | 9.24 | 0.00 | 42.76 | 3.33 |
3441 | 3708 | 7.803189 | GCCTATGTATTATACAATGCACACAAC | 59.197 | 37.037 | 9.24 | 0.00 | 42.76 | 3.32 |
3442 | 3709 | 8.289618 | CCTATGTATTATACAATGCACACAACC | 58.710 | 37.037 | 9.24 | 0.00 | 42.76 | 3.77 |
3443 | 3710 | 7.637631 | ATGTATTATACAATGCACACAACCA | 57.362 | 32.000 | 9.24 | 0.00 | 42.76 | 3.67 |
3444 | 3711 | 7.637631 | TGTATTATACAATGCACACAACCAT | 57.362 | 32.000 | 2.16 | 0.00 | 35.38 | 3.55 |
3445 | 3712 | 8.060931 | TGTATTATACAATGCACACAACCATT | 57.939 | 30.769 | 2.16 | 0.00 | 35.38 | 3.16 |
3446 | 3713 | 8.526978 | TGTATTATACAATGCACACAACCATTT | 58.473 | 29.630 | 2.16 | 0.00 | 35.38 | 2.32 |
3447 | 3714 | 9.364989 | GTATTATACAATGCACACAACCATTTT | 57.635 | 29.630 | 0.00 | 0.00 | 29.71 | 1.82 |
3448 | 3715 | 8.845413 | ATTATACAATGCACACAACCATTTTT | 57.155 | 26.923 | 0.00 | 0.00 | 29.71 | 1.94 |
3468 | 3735 | 2.065899 | TTTTTGTGTGTGAGAGGGGG | 57.934 | 50.000 | 0.00 | 0.00 | 0.00 | 5.40 |
3469 | 3736 | 0.923358 | TTTTGTGTGTGAGAGGGGGT | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 4.95 |
3470 | 3737 | 0.923358 | TTTGTGTGTGAGAGGGGGTT | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 4.11 |
3471 | 3738 | 0.923358 | TTGTGTGTGAGAGGGGGTTT | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 3.27 |
3472 | 3739 | 0.182537 | TGTGTGTGAGAGGGGGTTTG | 59.817 | 55.000 | 0.00 | 0.00 | 0.00 | 2.93 |
3473 | 3740 | 1.150536 | TGTGTGAGAGGGGGTTTGC | 59.849 | 57.895 | 0.00 | 0.00 | 0.00 | 3.68 |
3474 | 3741 | 1.150536 | GTGTGAGAGGGGGTTTGCA | 59.849 | 57.895 | 0.00 | 0.00 | 0.00 | 4.08 |
3475 | 3742 | 0.467290 | GTGTGAGAGGGGGTTTGCAA | 60.467 | 55.000 | 0.00 | 0.00 | 0.00 | 4.08 |
3476 | 3743 | 0.178992 | TGTGAGAGGGGGTTTGCAAG | 60.179 | 55.000 | 0.00 | 0.00 | 0.00 | 4.01 |
3477 | 3744 | 0.895559 | GTGAGAGGGGGTTTGCAAGG | 60.896 | 60.000 | 0.00 | 0.00 | 0.00 | 3.61 |
3501 | 3768 | 8.320617 | AGGATGCACACAACCATTTTATTAAAT | 58.679 | 29.630 | 0.00 | 0.00 | 41.12 | 1.40 |
3502 | 3769 | 8.945057 | GGATGCACACAACCATTTTATTAAATT | 58.055 | 29.630 | 0.00 | 0.00 | 38.58 | 1.82 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
12 | 13 | 0.249489 | ATATCGCTTCAGCCGGTGAC | 60.249 | 55.000 | 1.90 | 0.00 | 37.91 | 3.67 |
13 | 14 | 0.032130 | GATATCGCTTCAGCCGGTGA | 59.968 | 55.000 | 1.90 | 2.59 | 37.91 | 4.02 |
14 | 15 | 1.278172 | CGATATCGCTTCAGCCGGTG | 61.278 | 60.000 | 12.95 | 0.00 | 37.91 | 4.94 |
15 | 16 | 1.007271 | CGATATCGCTTCAGCCGGT | 60.007 | 57.895 | 12.95 | 0.00 | 37.91 | 5.28 |
16 | 17 | 3.848142 | CGATATCGCTTCAGCCGG | 58.152 | 61.111 | 12.95 | 0.00 | 37.91 | 6.13 |
26 | 27 | 2.030562 | GGGTGGTGGGCGATATCG | 59.969 | 66.667 | 20.79 | 20.79 | 43.27 | 2.92 |
27 | 28 | 2.030562 | CGGGTGGTGGGCGATATC | 59.969 | 66.667 | 0.00 | 0.00 | 0.00 | 1.63 |
28 | 29 | 4.250305 | GCGGGTGGTGGGCGATAT | 62.250 | 66.667 | 0.00 | 0.00 | 0.00 | 1.63 |
34 | 35 | 4.904590 | TTGGTTGCGGGTGGTGGG | 62.905 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
35 | 36 | 3.601685 | GTTGGTTGCGGGTGGTGG | 61.602 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
36 | 37 | 0.891449 | TATGTTGGTTGCGGGTGGTG | 60.891 | 55.000 | 0.00 | 0.00 | 0.00 | 4.17 |
37 | 38 | 0.608035 | CTATGTTGGTTGCGGGTGGT | 60.608 | 55.000 | 0.00 | 0.00 | 0.00 | 4.16 |
38 | 39 | 1.933115 | GCTATGTTGGTTGCGGGTGG | 61.933 | 60.000 | 0.00 | 0.00 | 0.00 | 4.61 |
39 | 40 | 1.506262 | GCTATGTTGGTTGCGGGTG | 59.494 | 57.895 | 0.00 | 0.00 | 0.00 | 4.61 |
40 | 41 | 1.677633 | GGCTATGTTGGTTGCGGGT | 60.678 | 57.895 | 0.00 | 0.00 | 0.00 | 5.28 |
41 | 42 | 1.037030 | ATGGCTATGTTGGTTGCGGG | 61.037 | 55.000 | 0.00 | 0.00 | 0.00 | 6.13 |
42 | 43 | 0.381801 | GATGGCTATGTTGGTTGCGG | 59.618 | 55.000 | 0.00 | 0.00 | 0.00 | 5.69 |
43 | 44 | 1.093972 | TGATGGCTATGTTGGTTGCG | 58.906 | 50.000 | 0.00 | 0.00 | 0.00 | 4.85 |
44 | 45 | 1.818060 | TGTGATGGCTATGTTGGTTGC | 59.182 | 47.619 | 0.00 | 0.00 | 0.00 | 4.17 |
45 | 46 | 4.426416 | CAATGTGATGGCTATGTTGGTTG | 58.574 | 43.478 | 0.00 | 0.00 | 0.00 | 3.77 |
46 | 47 | 3.448301 | CCAATGTGATGGCTATGTTGGTT | 59.552 | 43.478 | 0.00 | 0.00 | 32.78 | 3.67 |
47 | 48 | 3.025978 | CCAATGTGATGGCTATGTTGGT | 58.974 | 45.455 | 0.00 | 0.00 | 32.78 | 3.67 |
48 | 49 | 3.720949 | CCAATGTGATGGCTATGTTGG | 57.279 | 47.619 | 0.00 | 0.00 | 32.78 | 3.77 |
57 | 58 | 1.725665 | CAGCGAGCCAATGTGATGG | 59.274 | 57.895 | 0.00 | 0.00 | 43.70 | 3.51 |
58 | 59 | 1.063649 | GCAGCGAGCCAATGTGATG | 59.936 | 57.895 | 0.00 | 0.00 | 37.23 | 3.07 |
59 | 60 | 3.506108 | GCAGCGAGCCAATGTGAT | 58.494 | 55.556 | 0.00 | 0.00 | 37.23 | 3.06 |
71 | 72 | 4.632974 | GATAGGGCAGGGGCAGCG | 62.633 | 72.222 | 0.00 | 0.00 | 43.71 | 5.18 |
72 | 73 | 4.277009 | GGATAGGGCAGGGGCAGC | 62.277 | 72.222 | 0.00 | 0.00 | 43.71 | 5.25 |
73 | 74 | 2.449322 | AGGATAGGGCAGGGGCAG | 60.449 | 66.667 | 0.00 | 0.00 | 43.71 | 4.85 |
74 | 75 | 2.448542 | GAGGATAGGGCAGGGGCA | 60.449 | 66.667 | 0.00 | 0.00 | 43.71 | 5.36 |
75 | 76 | 3.631046 | CGAGGATAGGGCAGGGGC | 61.631 | 72.222 | 0.00 | 0.00 | 40.13 | 5.80 |
76 | 77 | 3.631046 | GCGAGGATAGGGCAGGGG | 61.631 | 72.222 | 0.00 | 0.00 | 0.00 | 4.79 |
77 | 78 | 3.996124 | CGCGAGGATAGGGCAGGG | 61.996 | 72.222 | 0.00 | 0.00 | 0.00 | 4.45 |
78 | 79 | 2.701163 | GAACGCGAGGATAGGGCAGG | 62.701 | 65.000 | 15.93 | 0.00 | 0.00 | 4.85 |
79 | 80 | 1.300233 | GAACGCGAGGATAGGGCAG | 60.300 | 63.158 | 15.93 | 0.00 | 0.00 | 4.85 |
80 | 81 | 1.735376 | GAGAACGCGAGGATAGGGCA | 61.735 | 60.000 | 15.93 | 0.00 | 0.00 | 5.36 |
81 | 82 | 1.007154 | GAGAACGCGAGGATAGGGC | 60.007 | 63.158 | 15.93 | 0.00 | 0.00 | 5.19 |
82 | 83 | 1.001158 | GAAGAGAACGCGAGGATAGGG | 60.001 | 57.143 | 15.93 | 0.00 | 0.00 | 3.53 |
83 | 84 | 1.001158 | GGAAGAGAACGCGAGGATAGG | 60.001 | 57.143 | 15.93 | 0.00 | 0.00 | 2.57 |
84 | 85 | 1.334239 | CGGAAGAGAACGCGAGGATAG | 60.334 | 57.143 | 15.93 | 0.00 | 0.00 | 2.08 |
85 | 86 | 0.661552 | CGGAAGAGAACGCGAGGATA | 59.338 | 55.000 | 15.93 | 0.00 | 0.00 | 2.59 |
86 | 87 | 1.433879 | CGGAAGAGAACGCGAGGAT | 59.566 | 57.895 | 15.93 | 0.00 | 0.00 | 3.24 |
87 | 88 | 2.875485 | CGGAAGAGAACGCGAGGA | 59.125 | 61.111 | 15.93 | 0.00 | 0.00 | 3.71 |
88 | 89 | 2.881352 | GCGGAAGAGAACGCGAGG | 60.881 | 66.667 | 15.93 | 0.00 | 46.58 | 4.63 |
515 | 516 | 2.159819 | CTAGCTGTGACACCGGCAGT | 62.160 | 60.000 | 18.44 | 0.00 | 33.18 | 4.40 |
519 | 520 | 2.125512 | GGCTAGCTGTGACACCGG | 60.126 | 66.667 | 15.72 | 0.00 | 0.00 | 5.28 |
527 | 528 | 1.612950 | CGAGATGATGAGGCTAGCTGT | 59.387 | 52.381 | 15.72 | 1.74 | 0.00 | 4.40 |
536 | 537 | 1.579698 | CACCAAGCCGAGATGATGAG | 58.420 | 55.000 | 0.00 | 0.00 | 0.00 | 2.90 |
556 | 557 | 1.040646 | TATGGGACTGAGATGCGGAC | 58.959 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
558 | 559 | 1.541233 | GGTTATGGGACTGAGATGCGG | 60.541 | 57.143 | 0.00 | 0.00 | 0.00 | 5.69 |
652 | 654 | 0.326595 | TAAGAAATGGCGCCAGGTGA | 59.673 | 50.000 | 35.36 | 11.21 | 0.00 | 4.02 |
682 | 684 | 6.787085 | ACAAACTTTTTGATACGGAGAGAG | 57.213 | 37.500 | 5.67 | 0.00 | 0.00 | 3.20 |
728 | 730 | 8.671384 | TCCGAATGTATCTAATACCAAAAAGG | 57.329 | 34.615 | 0.00 | 0.00 | 45.67 | 3.11 |
780 | 795 | 4.800023 | TCCGATCTATTACCTCTGTCCAA | 58.200 | 43.478 | 0.00 | 0.00 | 0.00 | 3.53 |
782 | 797 | 4.095185 | CGATCCGATCTATTACCTCTGTCC | 59.905 | 50.000 | 6.81 | 0.00 | 0.00 | 4.02 |
825 | 840 | 0.745845 | CAGCTGGAGGGTTCATTCGG | 60.746 | 60.000 | 5.57 | 0.00 | 0.00 | 4.30 |
826 | 841 | 0.745845 | CCAGCTGGAGGGTTCATTCG | 60.746 | 60.000 | 29.88 | 0.00 | 37.39 | 3.34 |
964 | 986 | 2.360585 | GGGCAAAGGAAGGGAGGG | 59.639 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 |
1206 | 1232 | 1.682684 | GGAGGAGAAGGACGGCAGA | 60.683 | 63.158 | 0.00 | 0.00 | 0.00 | 4.26 |
1500 | 1526 | 1.519455 | GAATGGGTGGTCGAGCGAG | 60.519 | 63.158 | 10.46 | 0.00 | 0.00 | 5.03 |
2481 | 2510 | 2.093500 | ACTCATCAGCTTGCGGAATACA | 60.093 | 45.455 | 0.00 | 0.00 | 0.00 | 2.29 |
2484 | 2513 | 1.741706 | CAACTCATCAGCTTGCGGAAT | 59.258 | 47.619 | 0.00 | 0.00 | 0.00 | 3.01 |
2626 | 2665 | 2.946785 | CGACCCCTTCCACTCTATAGT | 58.053 | 52.381 | 0.00 | 0.00 | 35.91 | 2.12 |
2669 | 2709 | 0.912006 | AAAGCTCCTCCTCCTCCACC | 60.912 | 60.000 | 0.00 | 0.00 | 0.00 | 4.61 |
2670 | 2710 | 0.251634 | CAAAGCTCCTCCTCCTCCAC | 59.748 | 60.000 | 0.00 | 0.00 | 0.00 | 4.02 |
2671 | 2711 | 0.178891 | ACAAAGCTCCTCCTCCTCCA | 60.179 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
2799 | 2854 | 1.405121 | CCCTAAAGTACTGGCACCGTC | 60.405 | 57.143 | 0.00 | 0.00 | 0.00 | 4.79 |
2812 | 2867 | 5.871524 | GGACGGAAAAAGTACTACCCTAAAG | 59.128 | 44.000 | 0.00 | 0.00 | 0.00 | 1.85 |
2815 | 2870 | 3.769300 | GGGACGGAAAAAGTACTACCCTA | 59.231 | 47.826 | 0.00 | 0.00 | 32.93 | 3.53 |
2816 | 2871 | 2.568956 | GGGACGGAAAAAGTACTACCCT | 59.431 | 50.000 | 0.00 | 0.00 | 32.93 | 4.34 |
2817 | 2872 | 2.302733 | TGGGACGGAAAAAGTACTACCC | 59.697 | 50.000 | 0.00 | 0.00 | 35.82 | 3.69 |
2818 | 2873 | 3.683365 | TGGGACGGAAAAAGTACTACC | 57.317 | 47.619 | 0.00 | 0.00 | 0.00 | 3.18 |
2819 | 2874 | 4.824289 | TCATGGGACGGAAAAAGTACTAC | 58.176 | 43.478 | 0.00 | 0.00 | 0.00 | 2.73 |
2820 | 2875 | 5.687166 | ATCATGGGACGGAAAAAGTACTA | 57.313 | 39.130 | 0.00 | 0.00 | 0.00 | 1.82 |
2821 | 2876 | 4.569719 | ATCATGGGACGGAAAAAGTACT | 57.430 | 40.909 | 0.00 | 0.00 | 0.00 | 2.73 |
2823 | 2878 | 9.116067 | CTTTTATATCATGGGACGGAAAAAGTA | 57.884 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
2824 | 2879 | 7.416326 | GCTTTTATATCATGGGACGGAAAAAGT | 60.416 | 37.037 | 0.00 | 0.00 | 0.00 | 2.66 |
2825 | 2880 | 6.918022 | GCTTTTATATCATGGGACGGAAAAAG | 59.082 | 38.462 | 0.00 | 0.00 | 0.00 | 2.27 |
2826 | 2881 | 6.459024 | CGCTTTTATATCATGGGACGGAAAAA | 60.459 | 38.462 | 0.00 | 0.00 | 0.00 | 1.94 |
2827 | 2882 | 5.008217 | CGCTTTTATATCATGGGACGGAAAA | 59.992 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
2828 | 2883 | 4.513692 | CGCTTTTATATCATGGGACGGAAA | 59.486 | 41.667 | 0.00 | 0.00 | 0.00 | 3.13 |
2829 | 2884 | 4.062293 | CGCTTTTATATCATGGGACGGAA | 58.938 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
2830 | 2885 | 3.070446 | ACGCTTTTATATCATGGGACGGA | 59.930 | 43.478 | 0.00 | 0.00 | 0.00 | 4.69 |
2831 | 2886 | 3.399330 | ACGCTTTTATATCATGGGACGG | 58.601 | 45.455 | 0.00 | 0.00 | 0.00 | 4.79 |
2832 | 2887 | 5.418310 | AAACGCTTTTATATCATGGGACG | 57.582 | 39.130 | 0.00 | 0.00 | 0.00 | 4.79 |
2871 | 2926 | 9.415544 | CCTCCGTACTATAATATAAAAGCGTTT | 57.584 | 33.333 | 2.53 | 2.53 | 0.00 | 3.60 |
2872 | 2927 | 8.031277 | CCCTCCGTACTATAATATAAAAGCGTT | 58.969 | 37.037 | 0.00 | 0.00 | 0.00 | 4.84 |
2873 | 2928 | 7.394359 | TCCCTCCGTACTATAATATAAAAGCGT | 59.606 | 37.037 | 0.00 | 0.00 | 0.00 | 5.07 |
2874 | 2929 | 7.765307 | TCCCTCCGTACTATAATATAAAAGCG | 58.235 | 38.462 | 0.00 | 0.00 | 0.00 | 4.68 |
2875 | 2930 | 8.747471 | ACTCCCTCCGTACTATAATATAAAAGC | 58.253 | 37.037 | 0.00 | 0.00 | 0.00 | 3.51 |
2886 | 2941 | 9.051259 | TGTAATATACTACTCCCTCCGTACTAT | 57.949 | 37.037 | 0.00 | 0.00 | 0.00 | 2.12 |
2887 | 2942 | 8.435931 | TGTAATATACTACTCCCTCCGTACTA | 57.564 | 38.462 | 0.00 | 0.00 | 0.00 | 1.82 |
2888 | 2943 | 7.017056 | ACTGTAATATACTACTCCCTCCGTACT | 59.983 | 40.741 | 0.00 | 0.00 | 0.00 | 2.73 |
2889 | 2944 | 7.118971 | CACTGTAATATACTACTCCCTCCGTAC | 59.881 | 44.444 | 0.00 | 0.00 | 0.00 | 3.67 |
2890 | 2945 | 7.164122 | CACTGTAATATACTACTCCCTCCGTA | 58.836 | 42.308 | 0.00 | 0.00 | 0.00 | 4.02 |
2891 | 2946 | 6.002704 | CACTGTAATATACTACTCCCTCCGT | 58.997 | 44.000 | 0.00 | 0.00 | 0.00 | 4.69 |
2892 | 2947 | 5.415077 | CCACTGTAATATACTACTCCCTCCG | 59.585 | 48.000 | 0.00 | 0.00 | 0.00 | 4.63 |
2893 | 2948 | 5.715753 | CCCACTGTAATATACTACTCCCTCC | 59.284 | 48.000 | 0.00 | 0.00 | 0.00 | 4.30 |
2894 | 2949 | 6.313324 | ACCCACTGTAATATACTACTCCCTC | 58.687 | 44.000 | 0.00 | 0.00 | 0.00 | 4.30 |
2895 | 2950 | 6.290870 | ACCCACTGTAATATACTACTCCCT | 57.709 | 41.667 | 0.00 | 0.00 | 0.00 | 4.20 |
2896 | 2951 | 6.781507 | AGAACCCACTGTAATATACTACTCCC | 59.218 | 42.308 | 0.00 | 0.00 | 0.00 | 4.30 |
2897 | 2952 | 7.724951 | AGAGAACCCACTGTAATATACTACTCC | 59.275 | 40.741 | 0.00 | 0.00 | 0.00 | 3.85 |
2898 | 2953 | 8.569641 | CAGAGAACCCACTGTAATATACTACTC | 58.430 | 40.741 | 0.00 | 0.00 | 0.00 | 2.59 |
2899 | 2954 | 8.280084 | TCAGAGAACCCACTGTAATATACTACT | 58.720 | 37.037 | 0.00 | 0.00 | 35.84 | 2.57 |
2945 | 3003 | 3.366374 | GGACTGCTGACATTTAACTTGCC | 60.366 | 47.826 | 0.00 | 0.00 | 0.00 | 4.52 |
2971 | 3029 | 2.489971 | TGTTGGTCAAAGACGTGATCC | 58.510 | 47.619 | 0.00 | 0.00 | 32.65 | 3.36 |
2972 | 3030 | 3.311322 | TGTTGTTGGTCAAAGACGTGATC | 59.689 | 43.478 | 0.00 | 0.00 | 37.81 | 2.92 |
3002 | 3065 | 7.084486 | CGAATCAGTGTTCAAGATATCGGATA | 58.916 | 38.462 | 0.00 | 0.00 | 0.00 | 2.59 |
3023 | 3086 | 7.970061 | CCACAGATGTTCAAATTCAATACGAAT | 59.030 | 33.333 | 0.00 | 0.00 | 46.70 | 3.34 |
3024 | 3087 | 7.174080 | TCCACAGATGTTCAAATTCAATACGAA | 59.826 | 33.333 | 0.00 | 0.00 | 38.22 | 3.85 |
3025 | 3088 | 6.652900 | TCCACAGATGTTCAAATTCAATACGA | 59.347 | 34.615 | 0.00 | 0.00 | 0.00 | 3.43 |
3026 | 3089 | 6.841119 | TCCACAGATGTTCAAATTCAATACG | 58.159 | 36.000 | 0.00 | 0.00 | 0.00 | 3.06 |
3062 | 3131 | 8.924511 | TGTTCAGAAGAGGAAATGTTAGAAAT | 57.075 | 30.769 | 0.00 | 0.00 | 0.00 | 2.17 |
3063 | 3132 | 8.924511 | ATGTTCAGAAGAGGAAATGTTAGAAA | 57.075 | 30.769 | 0.00 | 0.00 | 0.00 | 2.52 |
3141 | 3210 | 1.670730 | CGTACAGTGCATGTGGGCA | 60.671 | 57.895 | 10.77 | 0.00 | 43.80 | 5.36 |
3203 | 3275 | 8.709386 | ATAAGTTAGCTGAGACACTGTTAATG | 57.291 | 34.615 | 0.00 | 0.00 | 0.00 | 1.90 |
3222 | 3294 | 9.325150 | CGTGTAAAATCATTTGTCGAATAAGTT | 57.675 | 29.630 | 0.00 | 0.00 | 0.00 | 2.66 |
3223 | 3295 | 8.714179 | TCGTGTAAAATCATTTGTCGAATAAGT | 58.286 | 29.630 | 0.00 | 0.00 | 0.00 | 2.24 |
3224 | 3296 | 9.536558 | TTCGTGTAAAATCATTTGTCGAATAAG | 57.463 | 29.630 | 0.00 | 0.00 | 34.62 | 1.73 |
3225 | 3297 | 9.536558 | CTTCGTGTAAAATCATTTGTCGAATAA | 57.463 | 29.630 | 10.23 | 0.00 | 36.58 | 1.40 |
3226 | 3298 | 8.927721 | TCTTCGTGTAAAATCATTTGTCGAATA | 58.072 | 29.630 | 10.23 | 4.23 | 36.58 | 1.75 |
3227 | 3299 | 7.802738 | TCTTCGTGTAAAATCATTTGTCGAAT | 58.197 | 30.769 | 10.23 | 0.00 | 36.58 | 3.34 |
3231 | 3306 | 9.612620 | AAGAATCTTCGTGTAAAATCATTTGTC | 57.387 | 29.630 | 0.00 | 0.00 | 0.00 | 3.18 |
3236 | 3311 | 9.166173 | TCATGAAGAATCTTCGTGTAAAATCAT | 57.834 | 29.630 | 32.15 | 11.60 | 36.92 | 2.45 |
3238 | 3313 | 9.825972 | TTTCATGAAGAATCTTCGTGTAAAATC | 57.174 | 29.630 | 32.15 | 5.00 | 36.92 | 2.17 |
3245 | 3320 | 5.409520 | TGGAGTTTCATGAAGAATCTTCGTG | 59.590 | 40.000 | 29.72 | 29.72 | 36.62 | 4.35 |
3250 | 3325 | 4.692625 | CGTGTGGAGTTTCATGAAGAATCT | 59.307 | 41.667 | 8.41 | 6.29 | 38.63 | 2.40 |
3266 | 3341 | 3.181500 | CGATCATTCTACTGACGTGTGGA | 60.181 | 47.826 | 0.00 | 0.00 | 0.00 | 4.02 |
3267 | 3342 | 3.108881 | CGATCATTCTACTGACGTGTGG | 58.891 | 50.000 | 0.00 | 0.00 | 0.00 | 4.17 |
3269 | 3344 | 4.335594 | TGATCGATCATTCTACTGACGTGT | 59.664 | 41.667 | 23.99 | 0.00 | 0.00 | 4.49 |
3281 | 3356 | 6.772605 | TGGGTATCAAATCTGATCGATCATT | 58.227 | 36.000 | 27.43 | 17.33 | 41.57 | 2.57 |
3342 | 3417 | 7.001674 | TGCCCGTGAAACCTATATGAATATTT | 58.998 | 34.615 | 0.00 | 0.00 | 0.00 | 1.40 |
3343 | 3418 | 6.430000 | GTGCCCGTGAAACCTATATGAATATT | 59.570 | 38.462 | 0.00 | 0.00 | 0.00 | 1.28 |
3344 | 3419 | 5.938125 | GTGCCCGTGAAACCTATATGAATAT | 59.062 | 40.000 | 0.00 | 0.00 | 0.00 | 1.28 |
3357 | 3622 | 1.228124 | CTCTTGGGTGCCCGTGAAA | 60.228 | 57.895 | 2.44 | 0.00 | 39.42 | 2.69 |
3401 | 3668 | 4.772886 | ACATAGGCCGAGGTTATTCTTT | 57.227 | 40.909 | 0.00 | 0.00 | 0.00 | 2.52 |
3403 | 3670 | 7.735326 | ATAATACATAGGCCGAGGTTATTCT | 57.265 | 36.000 | 8.85 | 0.00 | 0.00 | 2.40 |
3405 | 3672 | 8.370266 | TGTATAATACATAGGCCGAGGTTATT | 57.630 | 34.615 | 8.85 | 9.02 | 32.89 | 1.40 |
3406 | 3673 | 7.966339 | TGTATAATACATAGGCCGAGGTTAT | 57.034 | 36.000 | 8.85 | 4.38 | 32.89 | 1.89 |
3407 | 3674 | 7.779754 | TTGTATAATACATAGGCCGAGGTTA | 57.220 | 36.000 | 8.85 | 0.00 | 38.68 | 2.85 |
3408 | 3675 | 6.675413 | TTGTATAATACATAGGCCGAGGTT | 57.325 | 37.500 | 8.85 | 0.00 | 38.68 | 3.50 |
3410 | 3677 | 5.523916 | GCATTGTATAATACATAGGCCGAGG | 59.476 | 44.000 | 0.00 | 0.00 | 38.68 | 4.63 |
3412 | 3679 | 5.872617 | GTGCATTGTATAATACATAGGCCGA | 59.127 | 40.000 | 0.00 | 0.00 | 38.68 | 5.54 |
3414 | 3681 | 6.429692 | TGTGTGCATTGTATAATACATAGGCC | 59.570 | 38.462 | 0.00 | 0.00 | 38.68 | 5.19 |
3419 | 3686 | 7.637631 | TGGTTGTGTGCATTGTATAATACAT | 57.362 | 32.000 | 0.00 | 0.00 | 38.68 | 2.29 |
3422 | 3689 | 9.935241 | AAAAATGGTTGTGTGCATTGTATAATA | 57.065 | 25.926 | 0.00 | 0.00 | 0.00 | 0.98 |
3449 | 3716 | 1.286553 | ACCCCCTCTCACACACAAAAA | 59.713 | 47.619 | 0.00 | 0.00 | 0.00 | 1.94 |
3450 | 3717 | 0.923358 | ACCCCCTCTCACACACAAAA | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 2.44 |
3451 | 3718 | 0.923358 | AACCCCCTCTCACACACAAA | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 2.83 |
3452 | 3719 | 0.923358 | AAACCCCCTCTCACACACAA | 59.077 | 50.000 | 0.00 | 0.00 | 0.00 | 3.33 |
3453 | 3720 | 0.182537 | CAAACCCCCTCTCACACACA | 59.817 | 55.000 | 0.00 | 0.00 | 0.00 | 3.72 |
3454 | 3721 | 1.172812 | GCAAACCCCCTCTCACACAC | 61.173 | 60.000 | 0.00 | 0.00 | 0.00 | 3.82 |
3455 | 3722 | 1.150536 | GCAAACCCCCTCTCACACA | 59.849 | 57.895 | 0.00 | 0.00 | 0.00 | 3.72 |
3456 | 3723 | 0.467290 | TTGCAAACCCCCTCTCACAC | 60.467 | 55.000 | 0.00 | 0.00 | 0.00 | 3.82 |
3457 | 3724 | 0.178992 | CTTGCAAACCCCCTCTCACA | 60.179 | 55.000 | 0.00 | 0.00 | 0.00 | 3.58 |
3458 | 3725 | 0.895559 | CCTTGCAAACCCCCTCTCAC | 60.896 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 |
3459 | 3726 | 1.065410 | TCCTTGCAAACCCCCTCTCA | 61.065 | 55.000 | 0.00 | 0.00 | 0.00 | 3.27 |
3460 | 3727 | 0.332972 | ATCCTTGCAAACCCCCTCTC | 59.667 | 55.000 | 0.00 | 0.00 | 0.00 | 3.20 |
3461 | 3728 | 0.040204 | CATCCTTGCAAACCCCCTCT | 59.960 | 55.000 | 0.00 | 0.00 | 0.00 | 3.69 |
3462 | 3729 | 2.583472 | CATCCTTGCAAACCCCCTC | 58.417 | 57.895 | 0.00 | 0.00 | 0.00 | 4.30 |
3463 | 3730 | 4.872293 | CATCCTTGCAAACCCCCT | 57.128 | 55.556 | 0.00 | 0.00 | 0.00 | 4.79 |
3473 | 3740 | 3.389925 | AAATGGTTGTGTGCATCCTTG | 57.610 | 42.857 | 0.00 | 0.00 | 35.89 | 3.61 |
3474 | 3741 | 5.743636 | ATAAAATGGTTGTGTGCATCCTT | 57.256 | 34.783 | 0.00 | 0.00 | 35.89 | 3.36 |
3475 | 3742 | 5.743636 | AATAAAATGGTTGTGTGCATCCT | 57.256 | 34.783 | 0.00 | 0.00 | 35.89 | 3.24 |
3476 | 3743 | 7.897575 | TTTAATAAAATGGTTGTGTGCATCC | 57.102 | 32.000 | 0.00 | 0.00 | 35.54 | 3.51 |
3501 | 3768 | 7.957002 | TCAACAAGGAAAATGCATAGGTTAAA | 58.043 | 30.769 | 0.00 | 0.00 | 0.00 | 1.52 |
3502 | 3769 | 7.531857 | TCAACAAGGAAAATGCATAGGTTAA | 57.468 | 32.000 | 0.00 | 0.00 | 0.00 | 2.01 |
3506 | 3773 | 8.253113 | AGTATTTCAACAAGGAAAATGCATAGG | 58.747 | 33.333 | 0.00 | 0.00 | 39.94 | 2.57 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.