Multiple sequence alignment - TraesCS4D01G227700
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 | TraesCS4D01G227700 | chr4D | 100.000 | 4761 | 0 | 0 | 1 | 4761 | 386998480 | 386993720 | 0.000000e+00 | 8793.0 |
1 | TraesCS4D01G227700 | chr4D | 91.964 | 112 | 9 | 0 | 4650 | 4761 | 128254497 | 128254608 | 1.770000e-34 | 158.0 |
2 | TraesCS4D01G227700 | chr4D | 91.964 | 112 | 9 | 0 | 4650 | 4761 | 405022009 | 405021898 | 1.770000e-34 | 158.0 |
3 | TraesCS4D01G227700 | chr4D | 91.892 | 111 | 9 | 0 | 4650 | 4760 | 117307810 | 117307920 | 6.380000e-34 | 156.0 |
4 | TraesCS4D01G227700 | chr4D | 74.455 | 321 | 64 | 13 | 3291 | 3606 | 428941065 | 428940758 | 6.470000e-24 | 122.0 |
5 | TraesCS4D01G227700 | chr4D | 88.889 | 63 | 5 | 2 | 3433 | 3494 | 8258887 | 8258948 | 5.110000e-10 | 76.8 |
6 | TraesCS4D01G227700 | chr4A | 93.381 | 3913 | 136 | 49 | 3 | 3883 | 68471177 | 68467356 | 0.000000e+00 | 5677.0 |
7 | TraesCS4D01G227700 | chr4A | 86.881 | 747 | 94 | 3 | 4017 | 4760 | 68466768 | 68466023 | 0.000000e+00 | 833.0 |
8 | TraesCS4D01G227700 | chr4A | 74.766 | 321 | 63 | 13 | 3291 | 3606 | 37318250 | 37318557 | 1.390000e-25 | 128.0 |
9 | TraesCS4D01G227700 | chr4A | 89.157 | 83 | 8 | 1 | 3880 | 3961 | 668942398 | 668942316 | 8.430000e-18 | 102.0 |
10 | TraesCS4D01G227700 | chr4B | 91.479 | 3943 | 177 | 70 | 1 | 3886 | 475196604 | 475192764 | 0.000000e+00 | 5273.0 |
11 | TraesCS4D01G227700 | chr4B | 89.072 | 485 | 47 | 5 | 3988 | 4467 | 475192182 | 475191699 | 8.820000e-167 | 597.0 |
12 | TraesCS4D01G227700 | chr4B | 90.236 | 297 | 27 | 2 | 4464 | 4760 | 475170647 | 475170353 | 2.080000e-103 | 387.0 |
13 | TraesCS4D01G227700 | chr4B | 80.447 | 179 | 26 | 8 | 3433 | 3606 | 526275700 | 526275874 | 1.390000e-25 | 128.0 |
14 | TraesCS4D01G227700 | chr4B | 90.123 | 81 | 7 | 1 | 3879 | 3958 | 522554733 | 522554813 | 2.340000e-18 | 104.0 |
15 | TraesCS4D01G227700 | chr4B | 88.095 | 84 | 9 | 1 | 3879 | 3961 | 155718291 | 155718208 | 1.090000e-16 | 99.0 |
16 | TraesCS4D01G227700 | chr4B | 88.095 | 84 | 9 | 1 | 3879 | 3961 | 431286497 | 431286414 | 1.090000e-16 | 99.0 |
17 | TraesCS4D01G227700 | chr4B | 90.476 | 63 | 4 | 2 | 3433 | 3494 | 15753796 | 15753857 | 1.100000e-11 | 82.4 |
18 | TraesCS4D01G227700 | chr1D | 95.536 | 112 | 5 | 0 | 4650 | 4761 | 180716935 | 180717046 | 3.790000e-41 | 180.0 |
19 | TraesCS4D01G227700 | chr3D | 93.750 | 112 | 7 | 0 | 4650 | 4761 | 374065872 | 374065983 | 8.190000e-38 | 169.0 |
20 | TraesCS4D01G227700 | chr5B | 93.519 | 108 | 7 | 0 | 4654 | 4761 | 648137502 | 648137609 | 1.370000e-35 | 161.0 |
21 | TraesCS4D01G227700 | chr7B | 91.892 | 111 | 9 | 0 | 4651 | 4761 | 226322979 | 226322869 | 6.380000e-34 | 156.0 |
22 | TraesCS4D01G227700 | chr7B | 90.000 | 80 | 7 | 1 | 3880 | 3958 | 563739848 | 563739927 | 8.430000e-18 | 102.0 |
23 | TraesCS4D01G227700 | chr6D | 91.358 | 81 | 6 | 1 | 3879 | 3958 | 446533223 | 446533303 | 5.040000e-20 | 110.0 |
24 | TraesCS4D01G227700 | chr5D | 88.372 | 86 | 8 | 2 | 3875 | 3958 | 443091287 | 443091202 | 8.430000e-18 | 102.0 |
25 | TraesCS4D01G227700 | chr3B | 87.640 | 89 | 9 | 2 | 3879 | 3966 | 91503290 | 91503203 | 8.430000e-18 | 102.0 |
26 | TraesCS4D01G227700 | chr2D | 86.813 | 91 | 11 | 1 | 3872 | 3961 | 16331179 | 16331089 | 3.030000e-17 | 100.0 |
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.
query | scaffold | start | end | length | rev.comp | avg.bitscore | max.bitscore | avg.percent.identical | query.start | query.end | num_hsp | groupid | homo_length | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS4D01G227700 | chr4D | 386993720 | 386998480 | 4760 | True | 8793 | 8793 | 100.0000 | 1 | 4761 | 1 | chr4D.!!$R1 | 4760 |
1 | TraesCS4D01G227700 | chr4A | 68466023 | 68471177 | 5154 | True | 3255 | 5677 | 90.1310 | 3 | 4760 | 2 | chr4A.!!$R2 | 4757 |
2 | TraesCS4D01G227700 | chr4B | 475191699 | 475196604 | 4905 | True | 2935 | 5273 | 90.2755 | 1 | 4467 | 2 | chr4B.!!$R4 | 4466 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
605 | 635 | 0.254462 | TCACTCACTGCACCAAACCA | 59.746 | 50.000 | 0.0 | 0.0 | 0.00 | 3.67 | F |
1061 | 1111 | 0.605319 | TTTCTCGTGTGGTGGATGGC | 60.605 | 55.000 | 0.0 | 0.0 | 0.00 | 4.40 | F |
1589 | 1656 | 0.665835 | CGCACCAACCTGCTAAACAA | 59.334 | 50.000 | 0.0 | 0.0 | 34.77 | 2.83 | F |
1590 | 1657 | 1.269448 | CGCACCAACCTGCTAAACAAT | 59.731 | 47.619 | 0.0 | 0.0 | 34.77 | 2.71 | F |
2466 | 2534 | 2.053244 | CAGAATGCTGATAGGACCCCT | 58.947 | 52.381 | 0.0 | 0.0 | 45.17 | 4.79 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1483 | 1550 | 0.108585 | GCACACTGTGGGAGGAAAGA | 59.891 | 55.0 | 15.50 | 0.00 | 33.64 | 2.52 | R |
2100 | 2168 | 0.318955 | CCGTCGTCTTGTACCCGTTT | 60.319 | 55.0 | 0.00 | 0.00 | 0.00 | 3.60 | R |
2517 | 2585 | 0.798776 | CTTTCTGGTGCATCGACCAC | 59.201 | 55.0 | 9.02 | 9.02 | 41.30 | 4.16 | R |
2572 | 2640 | 0.881118 | GGAAGATCAAGTTGGCGCAA | 59.119 | 50.0 | 10.83 | 0.00 | 0.00 | 4.85 | R |
3947 | 4080 | 0.251354 | GAGGGCTGCAGATTCACTCA | 59.749 | 55.0 | 20.43 | 0.00 | 0.00 | 3.41 | 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 |
---|---|---|---|---|---|---|---|---|---|
82 | 83 | 2.250939 | CGGGCGTGTCACATGTTGT | 61.251 | 57.895 | 0.00 | 0.00 | 0.00 | 3.32 |
144 | 148 | 0.806868 | CAACGTCGACCCTAGCTGTA | 59.193 | 55.000 | 10.58 | 0.00 | 0.00 | 2.74 |
164 | 168 | 2.185350 | CTGCAGGGAACGCGATCT | 59.815 | 61.111 | 15.93 | 0.72 | 33.51 | 2.75 |
166 | 170 | 2.956964 | GCAGGGAACGCGATCTCG | 60.957 | 66.667 | 15.93 | 8.48 | 43.27 | 4.04 |
196 | 200 | 2.520979 | GAACGATGAACTCTGGACGAG | 58.479 | 52.381 | 0.00 | 0.00 | 45.56 | 4.18 |
223 | 227 | 3.807622 | GTGCAACAATCCTAGCGCTATTA | 59.192 | 43.478 | 19.19 | 9.50 | 36.32 | 0.98 |
452 | 475 | 1.400846 | GTACGAGACAGCGGAATGAGA | 59.599 | 52.381 | 0.00 | 0.00 | 35.12 | 3.27 |
500 | 524 | 4.202070 | TGTGATTGATACGATCTTACCGCA | 60.202 | 41.667 | 0.00 | 0.00 | 0.00 | 5.69 |
517 | 541 | 3.758172 | ACGCATGTGAACCAACCC | 58.242 | 55.556 | 14.43 | 0.00 | 0.00 | 4.11 |
518 | 542 | 1.152860 | ACGCATGTGAACCAACCCA | 60.153 | 52.632 | 14.43 | 0.00 | 0.00 | 4.51 |
519 | 543 | 1.285641 | CGCATGTGAACCAACCCAC | 59.714 | 57.895 | 0.00 | 0.00 | 0.00 | 4.61 |
520 | 544 | 1.172180 | CGCATGTGAACCAACCCACT | 61.172 | 55.000 | 0.00 | 0.00 | 34.57 | 4.00 |
521 | 545 | 0.314935 | GCATGTGAACCAACCCACTG | 59.685 | 55.000 | 0.00 | 0.00 | 34.57 | 3.66 |
522 | 546 | 0.961019 | CATGTGAACCAACCCACTGG | 59.039 | 55.000 | 0.00 | 0.00 | 42.68 | 4.00 |
585 | 615 | 1.187567 | GGAAAGCACCACAAGGGCAT | 61.188 | 55.000 | 0.00 | 0.00 | 42.05 | 4.40 |
604 | 634 | 1.388547 | TTCACTCACTGCACCAAACC | 58.611 | 50.000 | 0.00 | 0.00 | 0.00 | 3.27 |
605 | 635 | 0.254462 | TCACTCACTGCACCAAACCA | 59.746 | 50.000 | 0.00 | 0.00 | 0.00 | 3.67 |
606 | 636 | 1.102154 | CACTCACTGCACCAAACCAA | 58.898 | 50.000 | 0.00 | 0.00 | 0.00 | 3.67 |
607 | 637 | 1.476085 | CACTCACTGCACCAAACCAAA | 59.524 | 47.619 | 0.00 | 0.00 | 0.00 | 3.28 |
810 | 841 | 2.187163 | GGCCGTCTTCTACCTGGC | 59.813 | 66.667 | 0.00 | 0.00 | 44.98 | 4.85 |
932 | 980 | 1.781786 | CTAGCTAGCTTGTGAGGGGA | 58.218 | 55.000 | 24.88 | 0.00 | 0.00 | 4.81 |
1025 | 1075 | 2.399356 | GCCGTGGTAGCTTTGCTCC | 61.399 | 63.158 | 0.00 | 0.00 | 40.44 | 4.70 |
1061 | 1111 | 0.605319 | TTTCTCGTGTGGTGGATGGC | 60.605 | 55.000 | 0.00 | 0.00 | 0.00 | 4.40 |
1304 | 1365 | 1.743958 | TCCAGTAGTAGCTGCGAGTTC | 59.256 | 52.381 | 0.00 | 0.00 | 35.28 | 3.01 |
1339 | 1400 | 1.270839 | TGGTAGTTTGACAGAGCTGGC | 60.271 | 52.381 | 0.00 | 0.00 | 39.62 | 4.85 |
1376 | 1437 | 1.869132 | CATTGTTTAGCAGCGCGGC | 60.869 | 57.895 | 25.52 | 25.52 | 0.00 | 6.53 |
1392 | 1453 | 1.305213 | GGCCATTGCTCTTGGGGAA | 60.305 | 57.895 | 0.00 | 0.00 | 37.74 | 3.97 |
1409 | 1470 | 2.369394 | GGAACTCATGTCATGGGGTTC | 58.631 | 52.381 | 26.36 | 26.36 | 39.82 | 3.62 |
1410 | 1471 | 2.290896 | GGAACTCATGTCATGGGGTTCA | 60.291 | 50.000 | 30.35 | 10.39 | 40.97 | 3.18 |
1441 | 1502 | 1.511613 | CTAGGAAGAGAATGGGGGCA | 58.488 | 55.000 | 0.00 | 0.00 | 0.00 | 5.36 |
1443 | 1504 | 1.228510 | GGAAGAGAATGGGGGCAGG | 59.771 | 63.158 | 0.00 | 0.00 | 0.00 | 4.85 |
1444 | 1505 | 1.454663 | GAAGAGAATGGGGGCAGGC | 60.455 | 63.158 | 0.00 | 0.00 | 0.00 | 4.85 |
1483 | 1550 | 0.750182 | CCACTGGACCACCAACGTTT | 60.750 | 55.000 | 0.00 | 0.00 | 46.32 | 3.60 |
1547 | 1614 | 3.360867 | TCAGTTTTGTTCCCATGTGTGT | 58.639 | 40.909 | 0.00 | 0.00 | 0.00 | 3.72 |
1587 | 1654 | 1.579429 | CCGCACCAACCTGCTAAAC | 59.421 | 57.895 | 0.00 | 0.00 | 34.77 | 2.01 |
1588 | 1655 | 1.169661 | CCGCACCAACCTGCTAAACA | 61.170 | 55.000 | 0.00 | 0.00 | 34.77 | 2.83 |
1589 | 1656 | 0.665835 | CGCACCAACCTGCTAAACAA | 59.334 | 50.000 | 0.00 | 0.00 | 34.77 | 2.83 |
1590 | 1657 | 1.269448 | CGCACCAACCTGCTAAACAAT | 59.731 | 47.619 | 0.00 | 0.00 | 34.77 | 2.71 |
1591 | 1658 | 2.486203 | CGCACCAACCTGCTAAACAATA | 59.514 | 45.455 | 0.00 | 0.00 | 34.77 | 1.90 |
1592 | 1659 | 3.426159 | CGCACCAACCTGCTAAACAATAG | 60.426 | 47.826 | 0.00 | 0.00 | 34.77 | 1.73 |
1593 | 1660 | 3.756434 | GCACCAACCTGCTAAACAATAGA | 59.244 | 43.478 | 0.00 | 0.00 | 34.06 | 1.98 |
1594 | 1661 | 4.217550 | GCACCAACCTGCTAAACAATAGAA | 59.782 | 41.667 | 0.00 | 0.00 | 34.06 | 2.10 |
1595 | 1662 | 5.278758 | GCACCAACCTGCTAAACAATAGAAA | 60.279 | 40.000 | 0.00 | 0.00 | 34.06 | 2.52 |
1596 | 1663 | 6.572314 | GCACCAACCTGCTAAACAATAGAAAT | 60.572 | 38.462 | 0.00 | 0.00 | 34.06 | 2.17 |
1616 | 1683 | 8.524870 | AGAAATTATCACACAGAAACAAATGC | 57.475 | 30.769 | 0.00 | 0.00 | 0.00 | 3.56 |
1623 | 1690 | 5.301551 | TCACACAGAAACAAATGCCAACTAT | 59.698 | 36.000 | 0.00 | 0.00 | 0.00 | 2.12 |
1627 | 1694 | 7.144661 | CACAGAAACAAATGCCAACTATTGTA | 58.855 | 34.615 | 0.00 | 0.00 | 35.09 | 2.41 |
1629 | 1696 | 8.367156 | ACAGAAACAAATGCCAACTATTGTAAT | 58.633 | 29.630 | 0.00 | 0.00 | 35.09 | 1.89 |
1630 | 1697 | 9.206870 | CAGAAACAAATGCCAACTATTGTAATT | 57.793 | 29.630 | 0.00 | 0.00 | 35.09 | 1.40 |
1631 | 1698 | 9.777297 | AGAAACAAATGCCAACTATTGTAATTT | 57.223 | 25.926 | 0.00 | 0.00 | 35.09 | 1.82 |
1632 | 1699 | 9.810231 | GAAACAAATGCCAACTATTGTAATTTG | 57.190 | 29.630 | 16.67 | 16.67 | 41.91 | 2.32 |
1633 | 1700 | 8.900983 | AACAAATGCCAACTATTGTAATTTGT | 57.099 | 26.923 | 17.48 | 17.48 | 45.97 | 2.83 |
1634 | 1701 | 9.988815 | AACAAATGCCAACTATTGTAATTTGTA | 57.011 | 25.926 | 20.56 | 0.00 | 44.78 | 2.41 |
1635 | 1702 | 9.988815 | ACAAATGCCAACTATTGTAATTTGTAA | 57.011 | 25.926 | 19.69 | 0.00 | 44.30 | 2.41 |
1643 | 1710 | 9.749490 | CAACTATTGTAATTTGTAAGTACCACG | 57.251 | 33.333 | 0.00 | 0.00 | 31.33 | 4.94 |
1665 | 1732 | 4.485163 | GCTTTTCGTGGCATAATTGAAGT | 58.515 | 39.130 | 0.00 | 0.00 | 0.00 | 3.01 |
1666 | 1733 | 5.636837 | GCTTTTCGTGGCATAATTGAAGTA | 58.363 | 37.500 | 0.00 | 0.00 | 0.00 | 2.24 |
1667 | 1734 | 6.265577 | GCTTTTCGTGGCATAATTGAAGTAT | 58.734 | 36.000 | 0.00 | 0.00 | 0.00 | 2.12 |
1668 | 1735 | 6.751888 | GCTTTTCGTGGCATAATTGAAGTATT | 59.248 | 34.615 | 0.00 | 0.00 | 0.00 | 1.89 |
1669 | 1736 | 7.913297 | GCTTTTCGTGGCATAATTGAAGTATTA | 59.087 | 33.333 | 0.00 | 0.00 | 0.00 | 0.98 |
1670 | 1737 | 9.950680 | CTTTTCGTGGCATAATTGAAGTATTAT | 57.049 | 29.630 | 0.00 | 0.00 | 32.30 | 1.28 |
1817 | 1884 | 4.636206 | GCCGACCAAATGATCTTCTTACTT | 59.364 | 41.667 | 0.00 | 0.00 | 0.00 | 2.24 |
1892 | 1960 | 2.936912 | GCTGTCGCTGTCCTGTCCT | 61.937 | 63.158 | 0.00 | 0.00 | 0.00 | 3.85 |
1902 | 1970 | 3.786635 | CTGTCCTGTCCTTATACAGTGC | 58.213 | 50.000 | 3.56 | 0.00 | 44.45 | 4.40 |
2014 | 2082 | 8.544622 | TGGAATAGTGGTGATTAAATCTGTGTA | 58.455 | 33.333 | 0.00 | 0.00 | 0.00 | 2.90 |
2019 | 2087 | 8.044060 | AGTGGTGATTAAATCTGTGTAATGTG | 57.956 | 34.615 | 0.00 | 0.00 | 0.00 | 3.21 |
2371 | 2439 | 4.164796 | TCATCTTCTTCCAGGTGCACATAT | 59.835 | 41.667 | 20.43 | 0.20 | 0.00 | 1.78 |
2372 | 2440 | 5.366477 | TCATCTTCTTCCAGGTGCACATATA | 59.634 | 40.000 | 20.43 | 0.00 | 0.00 | 0.86 |
2466 | 2534 | 2.053244 | CAGAATGCTGATAGGACCCCT | 58.947 | 52.381 | 0.00 | 0.00 | 45.17 | 4.79 |
2571 | 2639 | 1.069906 | GTAGCTGCTTTCGGTGTTGTG | 60.070 | 52.381 | 7.79 | 0.00 | 0.00 | 3.33 |
2572 | 2640 | 0.748005 | AGCTGCTTTCGGTGTTGTGT | 60.748 | 50.000 | 0.00 | 0.00 | 0.00 | 3.72 |
2573 | 2641 | 0.100503 | GCTGCTTTCGGTGTTGTGTT | 59.899 | 50.000 | 0.00 | 0.00 | 0.00 | 3.32 |
2575 | 2643 | 0.179150 | TGCTTTCGGTGTTGTGTTGC | 60.179 | 50.000 | 0.00 | 0.00 | 0.00 | 4.17 |
2624 | 2707 | 5.226396 | TGCGGGTAATTTGATCTGTTTTTG | 58.774 | 37.500 | 0.00 | 0.00 | 0.00 | 2.44 |
2626 | 2709 | 5.778862 | CGGGTAATTTGATCTGTTTTTGGT | 58.221 | 37.500 | 0.00 | 0.00 | 0.00 | 3.67 |
2629 | 2712 | 7.307101 | CGGGTAATTTGATCTGTTTTTGGTTTG | 60.307 | 37.037 | 0.00 | 0.00 | 0.00 | 2.93 |
2740 | 2826 | 1.079057 | GTCCAAGGACTTCCCGCTC | 60.079 | 63.158 | 11.94 | 0.00 | 41.57 | 5.03 |
3361 | 3447 | 2.743928 | CTCGACAAGCTGGCCACC | 60.744 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
3704 | 3790 | 1.004440 | GGCAACTCCTCGAAGCAGT | 60.004 | 57.895 | 0.00 | 0.00 | 0.00 | 4.40 |
3768 | 3854 | 4.021229 | ACCGTTCAGATATGACACTGGTA | 58.979 | 43.478 | 0.00 | 0.00 | 35.20 | 3.25 |
3856 | 3947 | 1.491670 | GCTGACACATATCGTCGCAT | 58.508 | 50.000 | 10.82 | 0.00 | 36.11 | 4.73 |
3857 | 3948 | 2.661594 | GCTGACACATATCGTCGCATA | 58.338 | 47.619 | 10.82 | 0.00 | 36.11 | 3.14 |
3884 | 3975 | 9.270707 | TGTGGGTAGTGGTTACTAAATTATACT | 57.729 | 33.333 | 0.00 | 0.00 | 40.89 | 2.12 |
3886 | 3977 | 8.927411 | TGGGTAGTGGTTACTAAATTATACTCC | 58.073 | 37.037 | 0.00 | 0.00 | 40.89 | 3.85 |
3888 | 3979 | 9.152327 | GGTAGTGGTTACTAAATTATACTCCCT | 57.848 | 37.037 | 0.00 | 0.00 | 40.89 | 4.20 |
3890 | 3981 | 8.260099 | AGTGGTTACTAAATTATACTCCCTCC | 57.740 | 38.462 | 0.00 | 0.00 | 34.74 | 4.30 |
3891 | 3982 | 7.015001 | AGTGGTTACTAAATTATACTCCCTCCG | 59.985 | 40.741 | 0.00 | 0.00 | 34.74 | 4.63 |
3893 | 3984 | 7.345392 | TGGTTACTAAATTATACTCCCTCCGTT | 59.655 | 37.037 | 0.00 | 0.00 | 0.00 | 4.44 |
3894 | 3985 | 8.206867 | GGTTACTAAATTATACTCCCTCCGTTT | 58.793 | 37.037 | 0.00 | 0.00 | 0.00 | 3.60 |
3895 | 3986 | 9.254133 | GTTACTAAATTATACTCCCTCCGTTTC | 57.746 | 37.037 | 0.00 | 0.00 | 0.00 | 2.78 |
3896 | 3987 | 6.824553 | ACTAAATTATACTCCCTCCGTTTCC | 58.175 | 40.000 | 0.00 | 0.00 | 0.00 | 3.13 |
3897 | 3988 | 5.703730 | AAATTATACTCCCTCCGTTTCCA | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 3.53 |
3899 | 3990 | 5.703730 | ATTATACTCCCTCCGTTTCCAAA | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 3.28 |
3900 | 3991 | 5.703730 | TTATACTCCCTCCGTTTCCAAAT | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 2.32 |
3901 | 3992 | 6.811634 | TTATACTCCCTCCGTTTCCAAATA | 57.188 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
3902 | 3993 | 5.906772 | ATACTCCCTCCGTTTCCAAATAT | 57.093 | 39.130 | 0.00 | 0.00 | 0.00 | 1.28 |
3903 | 3994 | 8.495160 | TTATACTCCCTCCGTTTCCAAATATA | 57.505 | 34.615 | 0.00 | 0.00 | 0.00 | 0.86 |
3904 | 3995 | 5.703730 | ACTCCCTCCGTTTCCAAATATAA | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 0.98 |
3909 | 4000 | 6.949463 | TCCCTCCGTTTCCAAATATAAGTTTT | 59.051 | 34.615 | 0.00 | 0.00 | 0.00 | 2.43 |
3910 | 4001 | 7.452189 | TCCCTCCGTTTCCAAATATAAGTTTTT | 59.548 | 33.333 | 0.00 | 0.00 | 0.00 | 1.94 |
3946 | 4079 | 9.566530 | CAACAAATGATTACATACGGATCAAAA | 57.433 | 29.630 | 0.00 | 0.00 | 35.50 | 2.44 |
3949 | 4082 | 9.949174 | CAAATGATTACATACGGATCAAAATGA | 57.051 | 29.630 | 0.00 | 0.00 | 35.50 | 2.57 |
3953 | 4579 | 7.984617 | TGATTACATACGGATCAAAATGAGTGA | 59.015 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
3954 | 4580 | 8.731275 | ATTACATACGGATCAAAATGAGTGAA | 57.269 | 30.769 | 0.00 | 0.00 | 0.00 | 3.18 |
3956 | 4582 | 7.251704 | ACATACGGATCAAAATGAGTGAATC | 57.748 | 36.000 | 0.00 | 0.00 | 0.00 | 2.52 |
3961 | 4587 | 5.579718 | GGATCAAAATGAGTGAATCTGCAG | 58.420 | 41.667 | 7.63 | 7.63 | 0.00 | 4.41 |
3968 | 4594 | 0.990374 | AGTGAATCTGCAGCCCTCTT | 59.010 | 50.000 | 9.47 | 0.00 | 0.00 | 2.85 |
3978 | 4604 | 1.488393 | GCAGCCCTCTTCAAGGTATCT | 59.512 | 52.381 | 0.00 | 0.00 | 44.56 | 1.98 |
3979 | 4605 | 2.744494 | GCAGCCCTCTTCAAGGTATCTG | 60.744 | 54.545 | 0.00 | 0.00 | 44.56 | 2.90 |
3980 | 4606 | 1.488393 | AGCCCTCTTCAAGGTATCTGC | 59.512 | 52.381 | 0.00 | 0.00 | 44.56 | 4.26 |
3981 | 4607 | 1.488393 | GCCCTCTTCAAGGTATCTGCT | 59.512 | 52.381 | 0.00 | 0.00 | 44.56 | 4.24 |
3982 | 4608 | 2.484594 | GCCCTCTTCAAGGTATCTGCTC | 60.485 | 54.545 | 0.00 | 0.00 | 44.56 | 4.26 |
3983 | 4609 | 3.037549 | CCCTCTTCAAGGTATCTGCTCT | 58.962 | 50.000 | 0.00 | 0.00 | 44.56 | 4.09 |
3984 | 4610 | 3.454082 | CCCTCTTCAAGGTATCTGCTCTT | 59.546 | 47.826 | 0.00 | 0.00 | 44.56 | 2.85 |
3985 | 4611 | 4.442753 | CCCTCTTCAAGGTATCTGCTCTTC | 60.443 | 50.000 | 0.00 | 0.00 | 44.56 | 2.87 |
3986 | 4612 | 4.161189 | CCTCTTCAAGGTATCTGCTCTTCA | 59.839 | 45.833 | 0.00 | 0.00 | 40.67 | 3.02 |
3994 | 4620 | 3.065925 | GGTATCTGCTCTTCACAATTGGC | 59.934 | 47.826 | 10.83 | 2.75 | 0.00 | 4.52 |
4013 | 4639 | 4.378774 | TGGCCATTCAAATTTTGTGTCTG | 58.621 | 39.130 | 0.00 | 3.46 | 0.00 | 3.51 |
4024 | 4650 | 9.787532 | TCAAATTTTGTGTCTGTTCTAAAGAAG | 57.212 | 29.630 | 8.89 | 0.00 | 34.27 | 2.85 |
4033 | 4660 | 6.094881 | TGTCTGTTCTAAAGAAGTTGGTTTGG | 59.905 | 38.462 | 0.00 | 0.00 | 34.27 | 3.28 |
4041 | 4668 | 8.923270 | TCTAAAGAAGTTGGTTTGGAATCATTT | 58.077 | 29.630 | 0.00 | 0.00 | 0.00 | 2.32 |
4048 | 4675 | 2.637382 | GGTTTGGAATCATTTGGGGTGT | 59.363 | 45.455 | 0.00 | 0.00 | 0.00 | 4.16 |
4051 | 4678 | 5.234752 | GTTTGGAATCATTTGGGGTGTTAC | 58.765 | 41.667 | 0.00 | 0.00 | 0.00 | 2.50 |
4062 | 4689 | 6.988622 | TTTGGGGTGTTACTATATCAAACG | 57.011 | 37.500 | 0.00 | 0.00 | 0.00 | 3.60 |
4098 | 4725 | 4.290985 | TGGATTTCCTGTTGTTGGGATCTA | 59.709 | 41.667 | 0.00 | 0.00 | 36.82 | 1.98 |
4099 | 4726 | 4.640647 | GGATTTCCTGTTGTTGGGATCTAC | 59.359 | 45.833 | 0.00 | 0.00 | 0.00 | 2.59 |
4101 | 4728 | 4.715534 | TTCCTGTTGTTGGGATCTACAA | 57.284 | 40.909 | 0.00 | 0.00 | 36.55 | 2.41 |
4186 | 4813 | 0.837272 | TCCCGATCCAGAAATCACCC | 59.163 | 55.000 | 0.00 | 0.00 | 0.00 | 4.61 |
4196 | 4823 | 3.571401 | CCAGAAATCACCCATCTTATGCC | 59.429 | 47.826 | 0.00 | 0.00 | 0.00 | 4.40 |
4250 | 4877 | 2.734492 | CGGTCGTTCTTCAGGTGGTATC | 60.734 | 54.545 | 0.00 | 0.00 | 0.00 | 2.24 |
4253 | 4880 | 1.134491 | CGTTCTTCAGGTGGTATCCCC | 60.134 | 57.143 | 0.00 | 0.00 | 0.00 | 4.81 |
4293 | 4920 | 4.219033 | GTTCGAACGCATTGATTCAGTTT | 58.781 | 39.130 | 13.36 | 0.00 | 0.00 | 2.66 |
4314 | 4941 | 7.010923 | CAGTTTATCAGTCAGTTTCTCCTATGC | 59.989 | 40.741 | 0.00 | 0.00 | 0.00 | 3.14 |
4335 | 4962 | 3.564225 | GCTAACTTCCCCCAATAATGTCG | 59.436 | 47.826 | 0.00 | 0.00 | 0.00 | 4.35 |
4376 | 5006 | 1.070786 | GGCGGTTCACTCTTGACCA | 59.929 | 57.895 | 0.00 | 0.00 | 0.00 | 4.02 |
4397 | 5027 | 3.826157 | CAGAATGAGTCTAGGCCTAGGAG | 59.174 | 52.174 | 34.43 | 16.86 | 39.69 | 3.69 |
4407 | 5037 | 2.794028 | GCCTAGGAGTACGGTGGGC | 61.794 | 68.421 | 14.75 | 4.28 | 0.00 | 5.36 |
4424 | 5054 | 0.179108 | GGCGCGTCTAGAATTCAGGT | 60.179 | 55.000 | 8.43 | 0.00 | 0.00 | 4.00 |
4448 | 5078 | 1.745890 | CTTCTGTGTCCGGTGTCCA | 59.254 | 57.895 | 0.00 | 0.00 | 0.00 | 4.02 |
4449 | 5079 | 0.319900 | CTTCTGTGTCCGGTGTCCAG | 60.320 | 60.000 | 0.00 | 4.09 | 0.00 | 3.86 |
4467 | 5097 | 0.768221 | AGTTTCAGGCCACAGGAGGA | 60.768 | 55.000 | 5.01 | 0.00 | 0.00 | 3.71 |
4489 | 5119 | 2.355756 | CCAGTTGCACCAATAGAATCCG | 59.644 | 50.000 | 0.00 | 0.00 | 0.00 | 4.18 |
4543 | 5173 | 9.260002 | CATTGAAGCTAATTGTTGGTTTAAAGT | 57.740 | 29.630 | 0.00 | 0.00 | 0.00 | 2.66 |
4554 | 5184 | 7.954788 | TGTTGGTTTAAAGTGGATAAATTGC | 57.045 | 32.000 | 0.00 | 0.00 | 0.00 | 3.56 |
4556 | 5186 | 7.987458 | TGTTGGTTTAAAGTGGATAAATTGCAA | 59.013 | 29.630 | 0.00 | 0.00 | 0.00 | 4.08 |
4558 | 5188 | 7.731054 | TGGTTTAAAGTGGATAAATTGCAAGT | 58.269 | 30.769 | 4.94 | 0.00 | 0.00 | 3.16 |
4563 | 5193 | 3.834231 | AGTGGATAAATTGCAAGTTGCCT | 59.166 | 39.130 | 24.59 | 9.69 | 44.23 | 4.75 |
4577 | 5207 | 1.075601 | TTGCCTCTTCACCTCCCAAT | 58.924 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
4579 | 5209 | 1.004745 | TGCCTCTTCACCTCCCAATTC | 59.995 | 52.381 | 0.00 | 0.00 | 0.00 | 2.17 |
4597 | 5227 | 1.629043 | TCTAGTCCTCAACTTGCCGT | 58.371 | 50.000 | 0.00 | 0.00 | 39.55 | 5.68 |
4611 | 5241 | 0.459585 | TGCCGTTGGTAATCGAGCTC | 60.460 | 55.000 | 2.73 | 2.73 | 0.00 | 4.09 |
4623 | 5253 | 2.010145 | TCGAGCTCTTTTGGAATCCG | 57.990 | 50.000 | 12.85 | 0.00 | 0.00 | 4.18 |
4635 | 5265 | 0.394352 | GGAATCCGGGCACAATCACT | 60.394 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 |
4646 | 5276 | 2.233271 | CACAATCACTGGTCTTTGCCT | 58.767 | 47.619 | 0.00 | 0.00 | 0.00 | 4.75 |
4652 | 5282 | 1.073722 | CTGGTCTTTGCCTGAGCCA | 59.926 | 57.895 | 0.00 | 0.00 | 38.69 | 4.75 |
4656 | 5286 | 0.877743 | GTCTTTGCCTGAGCCAGAAC | 59.122 | 55.000 | 4.00 | 0.00 | 38.69 | 3.01 |
4666 | 5296 | 0.596600 | GAGCCAGAACACGACAACGA | 60.597 | 55.000 | 0.00 | 0.00 | 42.66 | 3.85 |
4677 | 5307 | 4.369182 | ACACGACAACGAGAAAGAAGAAT | 58.631 | 39.130 | 0.00 | 0.00 | 42.66 | 2.40 |
4689 | 5319 | 7.605309 | ACGAGAAAGAAGAATAAAACCGGTAAT | 59.395 | 33.333 | 8.00 | 1.54 | 0.00 | 1.89 |
4709 | 5339 | 7.536855 | GGTAATGAGGATAACGGTATAGTGAG | 58.463 | 42.308 | 0.00 | 0.00 | 0.00 | 3.51 |
4720 | 5350 | 4.281941 | ACGGTATAGTGAGCATGTGATGAT | 59.718 | 41.667 | 0.00 | 0.00 | 0.00 | 2.45 |
4721 | 5351 | 4.861462 | CGGTATAGTGAGCATGTGATGATC | 59.139 | 45.833 | 0.00 | 0.00 | 45.45 | 2.92 |
4743 | 5373 | 1.707427 | AGGAGGATACCAATGCATCCC | 59.293 | 52.381 | 0.00 | 0.00 | 41.51 | 3.85 |
4746 | 5376 | 0.609131 | GGATACCAATGCATCCCGGG | 60.609 | 60.000 | 16.85 | 16.85 | 35.61 | 5.73 |
4750 | 5380 | 0.544120 | ACCAATGCATCCCGGGTTTT | 60.544 | 50.000 | 22.86 | 3.64 | 0.00 | 2.43 |
4751 | 5381 | 0.108233 | CCAATGCATCCCGGGTTTTG | 60.108 | 55.000 | 22.86 | 17.54 | 0.00 | 2.44 |
4752 | 5382 | 0.607620 | CAATGCATCCCGGGTTTTGT | 59.392 | 50.000 | 22.86 | 2.13 | 0.00 | 2.83 |
4756 | 5386 | 0.243636 | GCATCCCGGGTTTTGTGAAG | 59.756 | 55.000 | 22.86 | 0.00 | 0.00 | 3.02 |
4757 | 5387 | 1.616159 | CATCCCGGGTTTTGTGAAGT | 58.384 | 50.000 | 22.86 | 0.00 | 0.00 | 3.01 |
4758 | 5388 | 2.785562 | CATCCCGGGTTTTGTGAAGTA | 58.214 | 47.619 | 22.86 | 0.00 | 0.00 | 2.24 |
4759 | 5389 | 3.352648 | CATCCCGGGTTTTGTGAAGTAT | 58.647 | 45.455 | 22.86 | 0.00 | 0.00 | 2.12 |
4760 | 5390 | 3.062122 | TCCCGGGTTTTGTGAAGTATC | 57.938 | 47.619 | 22.86 | 0.00 | 0.00 | 2.24 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
32 | 33 | 6.658188 | AGGGAAGCTGATCATTAGTACTAC | 57.342 | 41.667 | 0.91 | 0.00 | 0.00 | 2.73 |
82 | 83 | 3.567585 | TGTGACGCAATTGAGATGGAAAA | 59.432 | 39.130 | 16.56 | 0.00 | 0.00 | 2.29 |
196 | 200 | 2.348666 | CGCTAGGATTGTTGCACTGTAC | 59.651 | 50.000 | 0.00 | 0.00 | 0.00 | 2.90 |
310 | 314 | 1.329599 | GTGCGCGGGTTAAATTCTAGG | 59.670 | 52.381 | 8.83 | 0.00 | 0.00 | 3.02 |
343 | 347 | 2.475111 | TCTCATGTCGTTTCGTTCTTGC | 59.525 | 45.455 | 0.00 | 0.00 | 0.00 | 4.01 |
452 | 475 | 2.513895 | CCTGTGAACAACCCCCGT | 59.486 | 61.111 | 0.00 | 0.00 | 0.00 | 5.28 |
500 | 524 | 1.152860 | TGGGTTGGTTCACATGCGT | 60.153 | 52.632 | 0.00 | 0.00 | 0.00 | 5.24 |
517 | 541 | 3.357079 | GTTCGCCCAGTGCCAGTG | 61.357 | 66.667 | 0.00 | 0.00 | 36.24 | 3.66 |
518 | 542 | 3.832237 | CTGTTCGCCCAGTGCCAGT | 62.832 | 63.158 | 0.00 | 0.00 | 36.24 | 4.00 |
519 | 543 | 3.052082 | CTGTTCGCCCAGTGCCAG | 61.052 | 66.667 | 0.00 | 0.00 | 36.24 | 4.85 |
520 | 544 | 4.641645 | CCTGTTCGCCCAGTGCCA | 62.642 | 66.667 | 1.35 | 0.00 | 36.24 | 4.92 |
560 | 590 | 2.991540 | GTGGTGCTTTCCAGGGCC | 60.992 | 66.667 | 0.00 | 0.00 | 38.23 | 5.80 |
561 | 591 | 1.809567 | CTTGTGGTGCTTTCCAGGGC | 61.810 | 60.000 | 0.00 | 0.00 | 38.23 | 5.19 |
562 | 592 | 1.181098 | CCTTGTGGTGCTTTCCAGGG | 61.181 | 60.000 | 0.00 | 0.00 | 38.23 | 4.45 |
563 | 593 | 1.181098 | CCCTTGTGGTGCTTTCCAGG | 61.181 | 60.000 | 0.00 | 0.00 | 38.23 | 4.45 |
564 | 594 | 1.809567 | GCCCTTGTGGTGCTTTCCAG | 61.810 | 60.000 | 0.00 | 0.00 | 38.23 | 3.86 |
569 | 599 | 0.469705 | TGAATGCCCTTGTGGTGCTT | 60.470 | 50.000 | 0.00 | 0.00 | 36.04 | 3.91 |
585 | 615 | 1.340502 | TGGTTTGGTGCAGTGAGTGAA | 60.341 | 47.619 | 0.00 | 0.00 | 0.00 | 3.18 |
604 | 634 | 1.534729 | CTTCCTTCCTTCCCGGTTTG | 58.465 | 55.000 | 0.00 | 0.00 | 0.00 | 2.93 |
605 | 635 | 0.404426 | CCTTCCTTCCTTCCCGGTTT | 59.596 | 55.000 | 0.00 | 0.00 | 0.00 | 3.27 |
606 | 636 | 2.075837 | CCTTCCTTCCTTCCCGGTT | 58.924 | 57.895 | 0.00 | 0.00 | 0.00 | 4.44 |
607 | 637 | 2.603652 | GCCTTCCTTCCTTCCCGGT | 61.604 | 63.158 | 0.00 | 0.00 | 0.00 | 5.28 |
1090 | 1140 | 1.366319 | AGAAACTGACCAGGAGGCAT | 58.634 | 50.000 | 0.00 | 0.00 | 39.06 | 4.40 |
1304 | 1365 | 2.368875 | ACTACCACACTCTCACCAAAGG | 59.631 | 50.000 | 0.00 | 0.00 | 0.00 | 3.11 |
1339 | 1400 | 3.781079 | TGCAAGAACAGTTGACAAAGG | 57.219 | 42.857 | 0.00 | 0.00 | 0.00 | 3.11 |
1376 | 1437 | 1.272092 | TGAGTTCCCCAAGAGCAATGG | 60.272 | 52.381 | 0.00 | 0.00 | 37.71 | 3.16 |
1392 | 1453 | 1.988107 | ACTGAACCCCATGACATGAGT | 59.012 | 47.619 | 17.24 | 10.68 | 0.00 | 3.41 |
1409 | 1470 | 7.633193 | TTCTCTTCCTAGCTAGTTCTAACTG | 57.367 | 40.000 | 19.31 | 1.76 | 40.07 | 3.16 |
1410 | 1471 | 7.286775 | CCATTCTCTTCCTAGCTAGTTCTAACT | 59.713 | 40.741 | 19.31 | 0.39 | 42.91 | 2.24 |
1421 | 1482 | 0.109532 | GCCCCCATTCTCTTCCTAGC | 59.890 | 60.000 | 0.00 | 0.00 | 0.00 | 3.42 |
1441 | 1502 | 2.332654 | GGGCGTCGTCATTTTGCCT | 61.333 | 57.895 | 0.00 | 0.00 | 45.06 | 4.75 |
1443 | 1504 | 0.318275 | TTTGGGCGTCGTCATTTTGC | 60.318 | 50.000 | 0.00 | 0.00 | 0.00 | 3.68 |
1444 | 1505 | 2.250188 | GATTTGGGCGTCGTCATTTTG | 58.750 | 47.619 | 0.00 | 0.00 | 0.00 | 2.44 |
1483 | 1550 | 0.108585 | GCACACTGTGGGAGGAAAGA | 59.891 | 55.000 | 15.50 | 0.00 | 33.64 | 2.52 |
1547 | 1614 | 3.695606 | GCTCGTGGTCTCCCAGCA | 61.696 | 66.667 | 0.00 | 0.00 | 42.94 | 4.41 |
1590 | 1657 | 9.624697 | GCATTTGTTTCTGTGTGATAATTTCTA | 57.375 | 29.630 | 0.00 | 0.00 | 0.00 | 2.10 |
1591 | 1658 | 7.599998 | GGCATTTGTTTCTGTGTGATAATTTCT | 59.400 | 33.333 | 0.00 | 0.00 | 0.00 | 2.52 |
1592 | 1659 | 7.384660 | TGGCATTTGTTTCTGTGTGATAATTTC | 59.615 | 33.333 | 0.00 | 0.00 | 0.00 | 2.17 |
1593 | 1660 | 7.215789 | TGGCATTTGTTTCTGTGTGATAATTT | 58.784 | 30.769 | 0.00 | 0.00 | 0.00 | 1.82 |
1594 | 1661 | 6.757237 | TGGCATTTGTTTCTGTGTGATAATT | 58.243 | 32.000 | 0.00 | 0.00 | 0.00 | 1.40 |
1595 | 1662 | 6.343716 | TGGCATTTGTTTCTGTGTGATAAT | 57.656 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
1596 | 1663 | 5.781210 | TGGCATTTGTTTCTGTGTGATAA | 57.219 | 34.783 | 0.00 | 0.00 | 0.00 | 1.75 |
1606 | 1673 | 9.810231 | CAAATTACAATAGTTGGCATTTGTTTC | 57.190 | 29.630 | 14.43 | 0.00 | 38.29 | 2.78 |
1623 | 1690 | 6.864360 | AAGCGTGGTACTTACAAATTACAA | 57.136 | 33.333 | 0.00 | 0.00 | 0.00 | 2.41 |
1627 | 1694 | 5.445845 | CGAAAAGCGTGGTACTTACAAATT | 58.554 | 37.500 | 0.00 | 0.00 | 34.64 | 1.82 |
1629 | 1696 | 4.455917 | CGAAAAGCGTGGTACTTACAAA | 57.544 | 40.909 | 0.00 | 0.00 | 34.64 | 2.83 |
1643 | 1710 | 4.485163 | ACTTCAATTATGCCACGAAAAGC | 58.515 | 39.130 | 0.00 | 0.00 | 0.00 | 3.51 |
1840 | 1907 | 7.194962 | AGACTAAAGTTCAGCTAAGCGTATAC | 58.805 | 38.462 | 0.00 | 0.00 | 0.00 | 1.47 |
1892 | 1960 | 5.420725 | ACTTCCATCAGTGCACTGTATAA | 57.579 | 39.130 | 38.41 | 27.04 | 44.12 | 0.98 |
1937 | 2005 | 1.538512 | TCCAGTTTACTCGTCGTCAGG | 59.461 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
2014 | 2082 | 1.891919 | ACTGAACGCCACGCACATT | 60.892 | 52.632 | 0.00 | 0.00 | 0.00 | 2.71 |
2019 | 2087 | 4.374702 | CTGCACTGAACGCCACGC | 62.375 | 66.667 | 0.00 | 0.00 | 0.00 | 5.34 |
2100 | 2168 | 0.318955 | CCGTCGTCTTGTACCCGTTT | 60.319 | 55.000 | 0.00 | 0.00 | 0.00 | 3.60 |
2466 | 2534 | 2.481969 | GCTCGCAGTGGTGATCTTCATA | 60.482 | 50.000 | 0.00 | 0.00 | 32.11 | 2.15 |
2514 | 2582 | 2.358615 | TGGTGCATCGACCACTGC | 60.359 | 61.111 | 15.21 | 9.44 | 41.30 | 4.40 |
2517 | 2585 | 0.798776 | CTTTCTGGTGCATCGACCAC | 59.201 | 55.000 | 9.02 | 9.02 | 41.30 | 4.16 |
2562 | 2630 | 3.402691 | TTGGCGCAACACAACACCG | 62.403 | 57.895 | 10.83 | 0.00 | 0.00 | 4.94 |
2571 | 2639 | 1.401539 | GGAAGATCAAGTTGGCGCAAC | 60.402 | 52.381 | 10.83 | 12.09 | 43.83 | 4.17 |
2572 | 2640 | 0.881118 | GGAAGATCAAGTTGGCGCAA | 59.119 | 50.000 | 10.83 | 0.00 | 0.00 | 4.85 |
2573 | 2641 | 0.960364 | GGGAAGATCAAGTTGGCGCA | 60.960 | 55.000 | 10.83 | 0.00 | 0.00 | 6.09 |
2575 | 2643 | 1.089920 | CAGGGAAGATCAAGTTGGCG | 58.910 | 55.000 | 2.34 | 0.00 | 0.00 | 5.69 |
2624 | 2707 | 4.755266 | TCCTCCTCTGCTTATACAAACC | 57.245 | 45.455 | 0.00 | 0.00 | 0.00 | 3.27 |
2626 | 2709 | 5.129485 | CCTCTTCCTCCTCTGCTTATACAAA | 59.871 | 44.000 | 0.00 | 0.00 | 0.00 | 2.83 |
2629 | 2712 | 4.475345 | TCCTCTTCCTCCTCTGCTTATAC | 58.525 | 47.826 | 0.00 | 0.00 | 0.00 | 1.47 |
3361 | 3447 | 1.077212 | CCAGATGGGCAGGTTGAGG | 60.077 | 63.158 | 0.00 | 0.00 | 0.00 | 3.86 |
3580 | 3666 | 3.972971 | CTGCCACTCCTGGAGCAGC | 62.973 | 68.421 | 23.43 | 23.96 | 45.44 | 5.25 |
3586 | 3672 | 4.087892 | CCCGTCTGCCACTCCTGG | 62.088 | 72.222 | 0.00 | 0.00 | 41.13 | 4.45 |
3692 | 3778 | 0.832135 | AAGGTGGACTGCTTCGAGGA | 60.832 | 55.000 | 0.00 | 0.00 | 0.00 | 3.71 |
3768 | 3854 | 1.276421 | GGCCACTCACATACAGACACT | 59.724 | 52.381 | 0.00 | 0.00 | 0.00 | 3.55 |
3883 | 3974 | 5.681639 | ACTTATATTTGGAAACGGAGGGAG | 58.318 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
3884 | 3975 | 5.703730 | ACTTATATTTGGAAACGGAGGGA | 57.296 | 39.130 | 0.00 | 0.00 | 0.00 | 4.20 |
3913 | 4004 | 9.445786 | CCGTATGTAATCATTTGTTGAAATACC | 57.554 | 33.333 | 0.00 | 0.00 | 38.03 | 2.73 |
3916 | 4007 | 9.950680 | GATCCGTATGTAATCATTTGTTGAAAT | 57.049 | 29.630 | 0.00 | 0.00 | 38.03 | 2.17 |
3918 | 4009 | 8.499403 | TGATCCGTATGTAATCATTTGTTGAA | 57.501 | 30.769 | 0.00 | 0.00 | 38.03 | 2.69 |
3919 | 4010 | 8.499403 | TTGATCCGTATGTAATCATTTGTTGA | 57.501 | 30.769 | 0.00 | 0.00 | 39.12 | 3.18 |
3920 | 4011 | 9.566530 | TTTTGATCCGTATGTAATCATTTGTTG | 57.433 | 29.630 | 0.00 | 0.00 | 35.70 | 3.33 |
3933 | 4066 | 7.350467 | CAGATTCACTCATTTTGATCCGTATG | 58.650 | 38.462 | 0.00 | 0.00 | 0.00 | 2.39 |
3934 | 4067 | 6.017605 | GCAGATTCACTCATTTTGATCCGTAT | 60.018 | 38.462 | 0.00 | 0.00 | 0.00 | 3.06 |
3935 | 4068 | 5.294306 | GCAGATTCACTCATTTTGATCCGTA | 59.706 | 40.000 | 0.00 | 0.00 | 0.00 | 4.02 |
3936 | 4069 | 4.095483 | GCAGATTCACTCATTTTGATCCGT | 59.905 | 41.667 | 0.00 | 0.00 | 0.00 | 4.69 |
3937 | 4070 | 4.095334 | TGCAGATTCACTCATTTTGATCCG | 59.905 | 41.667 | 0.00 | 0.00 | 0.00 | 4.18 |
3938 | 4071 | 5.571784 | TGCAGATTCACTCATTTTGATCC | 57.428 | 39.130 | 0.00 | 0.00 | 0.00 | 3.36 |
3940 | 4073 | 4.142227 | GGCTGCAGATTCACTCATTTTGAT | 60.142 | 41.667 | 20.43 | 0.00 | 0.00 | 2.57 |
3946 | 4079 | 0.917533 | AGGGCTGCAGATTCACTCAT | 59.082 | 50.000 | 20.43 | 0.00 | 0.00 | 2.90 |
3947 | 4080 | 0.251354 | GAGGGCTGCAGATTCACTCA | 59.749 | 55.000 | 20.43 | 0.00 | 0.00 | 3.41 |
3949 | 4082 | 0.990374 | AAGAGGGCTGCAGATTCACT | 59.010 | 50.000 | 20.43 | 6.01 | 0.00 | 3.41 |
3953 | 4579 | 1.340795 | CCTTGAAGAGGGCTGCAGATT | 60.341 | 52.381 | 20.43 | 0.50 | 42.26 | 2.40 |
3954 | 4580 | 0.255318 | CCTTGAAGAGGGCTGCAGAT | 59.745 | 55.000 | 20.43 | 1.27 | 42.26 | 2.90 |
3956 | 4582 | 4.315588 | CCTTGAAGAGGGCTGCAG | 57.684 | 61.111 | 10.11 | 10.11 | 42.26 | 4.41 |
3968 | 4594 | 4.890158 | TTGTGAAGAGCAGATACCTTGA | 57.110 | 40.909 | 0.00 | 0.00 | 0.00 | 3.02 |
3978 | 4604 | 1.927487 | ATGGCCAATTGTGAAGAGCA | 58.073 | 45.000 | 10.96 | 0.00 | 0.00 | 4.26 |
3979 | 4605 | 2.231964 | TGAATGGCCAATTGTGAAGAGC | 59.768 | 45.455 | 10.96 | 0.00 | 0.00 | 4.09 |
3980 | 4606 | 4.524316 | TTGAATGGCCAATTGTGAAGAG | 57.476 | 40.909 | 10.96 | 0.00 | 0.00 | 2.85 |
3981 | 4607 | 4.952071 | TTTGAATGGCCAATTGTGAAGA | 57.048 | 36.364 | 10.96 | 0.00 | 0.00 | 2.87 |
3982 | 4608 | 6.563222 | AAATTTGAATGGCCAATTGTGAAG | 57.437 | 33.333 | 10.96 | 0.00 | 0.00 | 3.02 |
3983 | 4609 | 6.320672 | ACAAAATTTGAATGGCCAATTGTGAA | 59.679 | 30.769 | 19.74 | 7.86 | 30.30 | 3.18 |
3984 | 4610 | 5.826737 | ACAAAATTTGAATGGCCAATTGTGA | 59.173 | 32.000 | 19.74 | 2.96 | 30.30 | 3.58 |
3985 | 4611 | 5.915758 | CACAAAATTTGAATGGCCAATTGTG | 59.084 | 36.000 | 10.96 | 12.68 | 37.78 | 3.33 |
3986 | 4612 | 5.593502 | ACACAAAATTTGAATGGCCAATTGT | 59.406 | 32.000 | 10.96 | 8.45 | 31.04 | 2.71 |
3994 | 4620 | 8.870160 | TTAGAACAGACACAAAATTTGAATGG | 57.130 | 30.769 | 13.19 | 1.87 | 0.00 | 3.16 |
4013 | 4639 | 7.712797 | TGATTCCAAACCAACTTCTTTAGAAC | 58.287 | 34.615 | 0.00 | 0.00 | 0.00 | 3.01 |
4024 | 4650 | 3.072330 | ACCCCAAATGATTCCAAACCAAC | 59.928 | 43.478 | 0.00 | 0.00 | 0.00 | 3.77 |
4033 | 4660 | 8.918202 | TGATATAGTAACACCCCAAATGATTC | 57.082 | 34.615 | 0.00 | 0.00 | 0.00 | 2.52 |
4041 | 4668 | 5.936187 | TCGTTTGATATAGTAACACCCCA | 57.064 | 39.130 | 0.00 | 0.00 | 0.00 | 4.96 |
4051 | 4678 | 9.186323 | CCACACTAAAGAGATCGTTTGATATAG | 57.814 | 37.037 | 6.41 | 0.00 | 34.09 | 1.31 |
4062 | 4689 | 6.410540 | ACAGGAAATCCACACTAAAGAGATC | 58.589 | 40.000 | 1.67 | 0.00 | 38.89 | 2.75 |
4098 | 4725 | 1.448540 | CGAGCGGATCAAGGCTTGT | 60.449 | 57.895 | 25.39 | 13.72 | 40.16 | 3.16 |
4099 | 4726 | 2.817423 | GCGAGCGGATCAAGGCTTG | 61.817 | 63.158 | 21.17 | 21.17 | 40.16 | 4.01 |
4101 | 4728 | 3.729965 | CTGCGAGCGGATCAAGGCT | 62.730 | 63.158 | 5.01 | 5.01 | 43.42 | 4.58 |
4111 | 4738 | 1.868251 | GAACGGTAGTCTGCGAGCG | 60.868 | 63.158 | 0.00 | 0.00 | 44.51 | 5.03 |
4186 | 4813 | 2.868583 | CGAACCACAGAGGCATAAGATG | 59.131 | 50.000 | 0.00 | 0.00 | 43.14 | 2.90 |
4196 | 4823 | 1.374758 | GGGCTCACGAACCACAGAG | 60.375 | 63.158 | 0.00 | 0.00 | 0.00 | 3.35 |
4267 | 4894 | 3.188254 | TGAATCAATGCGTTCGAACACAT | 59.812 | 39.130 | 26.71 | 24.64 | 33.43 | 3.21 |
4293 | 4920 | 7.561722 | AGTTAGCATAGGAGAAACTGACTGATA | 59.438 | 37.037 | 0.00 | 0.00 | 0.00 | 2.15 |
4314 | 4941 | 3.564225 | GCGACATTATTGGGGGAAGTTAG | 59.436 | 47.826 | 0.00 | 0.00 | 0.00 | 2.34 |
4335 | 4962 | 3.837213 | ATCCCGCCCTCCCTAGAGC | 62.837 | 68.421 | 0.00 | 0.00 | 38.96 | 4.09 |
4376 | 5006 | 3.465588 | ACTCCTAGGCCTAGACTCATTCT | 59.534 | 47.826 | 36.80 | 10.34 | 38.51 | 2.40 |
4397 | 5027 | 3.746409 | CTAGACGCGCCCACCGTAC | 62.746 | 68.421 | 5.73 | 0.00 | 39.30 | 3.67 |
4407 | 5037 | 2.455032 | CTCACCTGAATTCTAGACGCG | 58.545 | 52.381 | 3.53 | 3.53 | 0.00 | 6.01 |
4424 | 5054 | 2.583441 | CCGGACACAGAAGGCCTCA | 61.583 | 63.158 | 5.23 | 0.00 | 0.00 | 3.86 |
4448 | 5078 | 0.768221 | TCCTCCTGTGGCCTGAAACT | 60.768 | 55.000 | 3.32 | 0.00 | 0.00 | 2.66 |
4449 | 5079 | 0.606673 | GTCCTCCTGTGGCCTGAAAC | 60.607 | 60.000 | 3.32 | 0.00 | 0.00 | 2.78 |
4467 | 5097 | 3.356290 | GGATTCTATTGGTGCAACTGGT | 58.644 | 45.455 | 2.04 | 0.00 | 36.74 | 4.00 |
4489 | 5119 | 0.392461 | TCTATGACAAGCCCGCCAAC | 60.392 | 55.000 | 0.00 | 0.00 | 0.00 | 3.77 |
4497 | 5127 | 0.183492 | TGGCCCCATCTATGACAAGC | 59.817 | 55.000 | 0.00 | 0.00 | 0.00 | 4.01 |
4558 | 5188 | 1.075601 | ATTGGGAGGTGAAGAGGCAA | 58.924 | 50.000 | 0.00 | 0.00 | 0.00 | 4.52 |
4563 | 5193 | 3.775316 | GGACTAGAATTGGGAGGTGAAGA | 59.225 | 47.826 | 0.00 | 0.00 | 0.00 | 2.87 |
4577 | 5207 | 1.968493 | ACGGCAAGTTGAGGACTAGAA | 59.032 | 47.619 | 7.16 | 0.00 | 37.72 | 2.10 |
4579 | 5209 | 2.457366 | AACGGCAAGTTGAGGACTAG | 57.543 | 50.000 | 7.16 | 0.00 | 42.39 | 2.57 |
4597 | 5227 | 4.280436 | TCCAAAAGAGCTCGATTACCAA | 57.720 | 40.909 | 8.37 | 0.00 | 0.00 | 3.67 |
4603 | 5233 | 2.555199 | CGGATTCCAAAAGAGCTCGAT | 58.445 | 47.619 | 8.37 | 0.00 | 0.00 | 3.59 |
4611 | 5241 | 0.965439 | TTGTGCCCGGATTCCAAAAG | 59.035 | 50.000 | 0.73 | 0.00 | 0.00 | 2.27 |
4623 | 5253 | 1.270550 | CAAAGACCAGTGATTGTGCCC | 59.729 | 52.381 | 0.00 | 0.00 | 0.00 | 5.36 |
4635 | 5265 | 1.073722 | CTGGCTCAGGCAAAGACCA | 59.926 | 57.895 | 1.02 | 0.00 | 37.73 | 4.02 |
4646 | 5276 | 0.874175 | CGTTGTCGTGTTCTGGCTCA | 60.874 | 55.000 | 0.00 | 0.00 | 0.00 | 4.26 |
4652 | 5282 | 3.431922 | TCTTTCTCGTTGTCGTGTTCT | 57.568 | 42.857 | 0.00 | 0.00 | 38.33 | 3.01 |
4656 | 5286 | 4.974103 | ATTCTTCTTTCTCGTTGTCGTG | 57.026 | 40.909 | 0.00 | 0.00 | 38.33 | 4.35 |
4666 | 5296 | 8.857694 | TCATTACCGGTTTTATTCTTCTTTCT | 57.142 | 30.769 | 15.04 | 0.00 | 0.00 | 2.52 |
4677 | 5307 | 5.104982 | ACCGTTATCCTCATTACCGGTTTTA | 60.105 | 40.000 | 15.04 | 0.00 | 0.00 | 1.52 |
4689 | 5319 | 4.466827 | TGCTCACTATACCGTTATCCTCA | 58.533 | 43.478 | 0.00 | 0.00 | 0.00 | 3.86 |
4709 | 5339 | 1.419012 | TCCTCCTGGATCATCACATGC | 59.581 | 52.381 | 0.00 | 0.00 | 37.46 | 4.06 |
4721 | 5351 | 2.787994 | GATGCATTGGTATCCTCCTGG | 58.212 | 52.381 | 0.00 | 0.00 | 30.73 | 4.45 |
4733 | 5363 | 0.607620 | ACAAAACCCGGGATGCATTG | 59.392 | 50.000 | 32.02 | 23.67 | 0.00 | 2.82 |
4734 | 5364 | 0.607620 | CACAAAACCCGGGATGCATT | 59.392 | 50.000 | 32.02 | 7.67 | 0.00 | 3.56 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.