Multiple sequence alignment - TraesCS4B01G180000
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 | TraesCS4B01G180000 | chr4B | 100.000 | 2573 | 0 | 0 | 1 | 2573 | 394385694 | 394383122 | 0.000000e+00 | 4752.0 |
1 | TraesCS4B01G180000 | chr4A | 93.626 | 1616 | 63 | 11 | 876 | 2482 | 157561875 | 157563459 | 0.000000e+00 | 2377.0 |
2 | TraesCS4B01G180000 | chr4A | 95.395 | 760 | 25 | 5 | 1 | 750 | 157560877 | 157561636 | 0.000000e+00 | 1201.0 |
3 | TraesCS4B01G180000 | chr4A | 97.059 | 102 | 3 | 0 | 747 | 848 | 157561688 | 157561789 | 3.400000e-39 | 172.0 |
4 | TraesCS4B01G180000 | chr4A | 92.308 | 39 | 2 | 1 | 2288 | 2326 | 690220614 | 690220577 | 1.000000e-03 | 54.7 |
5 | TraesCS4B01G180000 | chr4D | 90.785 | 1617 | 79 | 17 | 903 | 2482 | 317198557 | 317196974 | 0.000000e+00 | 2097.0 |
6 | TraesCS4B01G180000 | chr4D | 92.358 | 759 | 45 | 6 | 1 | 750 | 317199612 | 317198858 | 0.000000e+00 | 1068.0 |
7 | TraesCS4B01G180000 | chr4D | 94.175 | 103 | 5 | 1 | 747 | 848 | 317198806 | 317198704 | 3.430000e-34 | 156.0 |
8 | TraesCS4B01G180000 | chr6B | 84.048 | 746 | 98 | 15 | 892 | 1629 | 50396631 | 50397363 | 0.000000e+00 | 699.0 |
9 | TraesCS4B01G180000 | chr6D | 84.423 | 719 | 99 | 10 | 915 | 1629 | 27521365 | 27520656 | 0.000000e+00 | 695.0 |
10 | TraesCS4B01G180000 | chr6A | 84.254 | 724 | 102 | 8 | 910 | 1629 | 30466997 | 30467712 | 0.000000e+00 | 695.0 |
11 | TraesCS4B01G180000 | chrUn | 84.043 | 94 | 15 | 0 | 2245 | 2338 | 235115315 | 235115222 | 9.800000e-15 | 91.6 |
12 | TraesCS4B01G180000 | chr3D | 89.583 | 48 | 5 | 0 | 2279 | 2326 | 524715656 | 524715703 | 7.690000e-06 | 62.1 |
13 | TraesCS4B01G180000 | chr2D | 100.000 | 28 | 0 | 0 | 2304 | 2331 | 351288369 | 351288342 | 5.000000e-03 | 52.8 |
These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.
query | scaffold | start | end | length | rev.comp | avg.bitscore | max.bitscore | avg.percent.identical | query.start | query.end | num_hsp | groupid | homo_length | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | TraesCS4B01G180000 | chr4B | 394383122 | 394385694 | 2572 | True | 4752 | 4752 | 100.000000 | 1 | 2573 | 1 | chr4B.!!$R1 | 2572 |
1 | TraesCS4B01G180000 | chr4A | 157560877 | 157563459 | 2582 | False | 1250 | 2377 | 95.360000 | 1 | 2482 | 3 | chr4A.!!$F1 | 2481 |
2 | TraesCS4B01G180000 | chr4D | 317196974 | 317199612 | 2638 | True | 1107 | 2097 | 92.439333 | 1 | 2482 | 3 | chr4D.!!$R1 | 2481 |
3 | TraesCS4B01G180000 | chr6B | 50396631 | 50397363 | 732 | False | 699 | 699 | 84.048000 | 892 | 1629 | 1 | chr6B.!!$F1 | 737 |
4 | TraesCS4B01G180000 | chr6D | 27520656 | 27521365 | 709 | True | 695 | 695 | 84.423000 | 915 | 1629 | 1 | chr6D.!!$R1 | 714 |
5 | TraesCS4B01G180000 | chr6A | 30466997 | 30467712 | 715 | False | 695 | 695 | 84.254000 | 910 | 1629 | 1 | chr6A.!!$F1 | 719 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
843 | 915 | 0.034574 | ATAATGCGTTGCCCTCCACA | 60.035 | 50.0 | 0.08 | 0.0 | 0.0 | 4.17 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1885 | 2085 | 0.693049 | CTACCAGAGCCACAAACCCT | 59.307 | 55.0 | 0.0 | 0.0 | 0.0 | 4.34 | 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 |
---|---|---|---|---|---|---|---|---|---|
173 | 180 | 4.148128 | AGAGCTAACATGAACCATGGAG | 57.852 | 45.455 | 21.47 | 3.29 | 45.16 | 3.86 |
225 | 232 | 1.898472 | CTCGAGGGGATATCTGTGCAT | 59.102 | 52.381 | 3.91 | 0.00 | 0.00 | 3.96 |
260 | 267 | 3.092301 | AGTTTATGAAAAGGAGGGCAGC | 58.908 | 45.455 | 0.00 | 0.00 | 0.00 | 5.25 |
324 | 337 | 2.554893 | GCTGACCGGTCAAATTTAACCA | 59.445 | 45.455 | 35.36 | 11.68 | 39.39 | 3.67 |
389 | 402 | 6.259829 | GGCTAGCTTTTTAAGATGAGAAGAGG | 59.740 | 42.308 | 15.72 | 0.00 | 0.00 | 3.69 |
393 | 406 | 8.105097 | AGCTTTTTAAGATGAGAAGAGGAAAC | 57.895 | 34.615 | 0.00 | 0.00 | 0.00 | 2.78 |
472 | 486 | 9.836864 | TGGCTAATCAAGGTAATATATGCTATG | 57.163 | 33.333 | 0.00 | 0.00 | 0.00 | 2.23 |
479 | 493 | 9.739276 | TCAAGGTAATATATGCTATGGGAAAAG | 57.261 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
505 | 522 | 9.696917 | GGTCTCATTGAACAATAACAGAAAAAT | 57.303 | 29.630 | 0.00 | 0.00 | 31.33 | 1.82 |
536 | 553 | 1.974957 | TGAGGATCGTTTGAGTGGGAA | 59.025 | 47.619 | 0.00 | 0.00 | 38.61 | 3.97 |
617 | 634 | 4.156373 | TGATTCACATGTATGGTGCAAGTG | 59.844 | 41.667 | 0.00 | 0.00 | 37.03 | 3.16 |
740 | 757 | 8.492673 | AAAACAAGATCTTAGTTGATGCGATA | 57.507 | 30.769 | 18.05 | 0.00 | 0.00 | 2.92 |
750 | 767 | 7.976175 | TCTTAGTTGATGCGATACATGGATATC | 59.024 | 37.037 | 0.00 | 0.00 | 39.84 | 1.63 |
751 | 768 | 6.041423 | AGTTGATGCGATACATGGATATCA | 57.959 | 37.500 | 4.83 | 0.00 | 39.84 | 2.15 |
752 | 769 | 5.871524 | AGTTGATGCGATACATGGATATCAC | 59.128 | 40.000 | 4.83 | 0.00 | 39.84 | 3.06 |
837 | 909 | 4.033932 | GGAAAATTCAATAATGCGTTGCCC | 59.966 | 41.667 | 0.08 | 0.00 | 0.00 | 5.36 |
843 | 915 | 0.034574 | ATAATGCGTTGCCCTCCACA | 60.035 | 50.000 | 0.08 | 0.00 | 0.00 | 4.17 |
844 | 916 | 0.250945 | TAATGCGTTGCCCTCCACAA | 60.251 | 50.000 | 0.08 | 0.00 | 0.00 | 3.33 |
845 | 917 | 0.899717 | AATGCGTTGCCCTCCACAAT | 60.900 | 50.000 | 0.00 | 0.00 | 0.00 | 2.71 |
846 | 918 | 1.315257 | ATGCGTTGCCCTCCACAATC | 61.315 | 55.000 | 0.00 | 0.00 | 0.00 | 2.67 |
847 | 919 | 2.700773 | GCGTTGCCCTCCACAATCC | 61.701 | 63.158 | 0.00 | 0.00 | 0.00 | 3.01 |
848 | 920 | 1.002134 | CGTTGCCCTCCACAATCCT | 60.002 | 57.895 | 0.00 | 0.00 | 0.00 | 3.24 |
849 | 921 | 1.308069 | CGTTGCCCTCCACAATCCTG | 61.308 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 |
850 | 922 | 1.304381 | TTGCCCTCCACAATCCTGC | 60.304 | 57.895 | 0.00 | 0.00 | 0.00 | 4.85 |
851 | 923 | 2.825836 | GCCCTCCACAATCCTGCG | 60.826 | 66.667 | 0.00 | 0.00 | 0.00 | 5.18 |
852 | 924 | 2.671070 | CCCTCCACAATCCTGCGT | 59.329 | 61.111 | 0.00 | 0.00 | 0.00 | 5.24 |
853 | 925 | 1.002134 | CCCTCCACAATCCTGCGTT | 60.002 | 57.895 | 0.00 | 0.00 | 0.00 | 4.84 |
854 | 926 | 1.308069 | CCCTCCACAATCCTGCGTTG | 61.308 | 60.000 | 0.00 | 0.00 | 0.00 | 4.10 |
867 | 939 | 3.039202 | GCGTTGCCCTCCACAATCG | 62.039 | 63.158 | 0.00 | 0.00 | 0.00 | 3.34 |
874 | 946 | 1.519455 | CCTCCACAATCGAGACGGC | 60.519 | 63.158 | 0.00 | 0.00 | 0.00 | 5.68 |
973 | 1158 | 2.978978 | TGATCAACAAGAGGTGGAGGAA | 59.021 | 45.455 | 0.00 | 0.00 | 31.44 | 3.36 |
1174 | 1361 | 1.384502 | CATGGCCTAGACCCAGGGA | 60.385 | 63.158 | 14.54 | 0.00 | 35.48 | 4.20 |
1184 | 1371 | 0.108019 | GACCCAGGGAACTTCGTTGT | 59.892 | 55.000 | 14.54 | 0.00 | 40.21 | 3.32 |
1296 | 1490 | 2.110627 | GATGGGCAGAGCATCGCT | 59.889 | 61.111 | 0.00 | 0.00 | 43.88 | 4.93 |
1312 | 1506 | 1.657751 | CGCTCTGACATCGGACCTCA | 61.658 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 |
1549 | 1743 | 3.009143 | GGTCATGGAGGAAAGTTACACCT | 59.991 | 47.826 | 0.00 | 0.00 | 36.68 | 4.00 |
1550 | 1744 | 4.506802 | GGTCATGGAGGAAAGTTACACCTT | 60.507 | 45.833 | 0.00 | 0.00 | 33.89 | 3.50 |
1622 | 1818 | 2.358267 | CAGATCTGCATCCTGAAAAGGC | 59.642 | 50.000 | 10.38 | 0.00 | 0.00 | 4.35 |
1651 | 1847 | 3.826157 | TCTTGCTCGTTTGGGATTCATTT | 59.174 | 39.130 | 0.00 | 0.00 | 0.00 | 2.32 |
1765 | 1961 | 9.667107 | TTTTATACGAGGATTCTGAATTGAGTT | 57.333 | 29.630 | 4.11 | 0.00 | 0.00 | 3.01 |
1783 | 1979 | 5.977635 | TGAGTTCTCAGACAAGTTTCAGAA | 58.022 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
1791 | 1987 | 6.611381 | TCAGACAAGTTTCAGAAAAGTGTTG | 58.389 | 36.000 | 12.03 | 9.33 | 28.67 | 3.33 |
1799 | 1995 | 6.868339 | AGTTTCAGAAAAGTGTTGGTTTTCAG | 59.132 | 34.615 | 10.12 | 3.48 | 43.48 | 3.02 |
1815 | 2011 | 4.875544 | TTTCAGCACACAAGTACAAGTC | 57.124 | 40.909 | 0.00 | 0.00 | 0.00 | 3.01 |
1816 | 2012 | 3.535280 | TCAGCACACAAGTACAAGTCA | 57.465 | 42.857 | 0.00 | 0.00 | 0.00 | 3.41 |
1817 | 2013 | 4.071961 | TCAGCACACAAGTACAAGTCAT | 57.928 | 40.909 | 0.00 | 0.00 | 0.00 | 3.06 |
1818 | 2014 | 4.450976 | TCAGCACACAAGTACAAGTCATT | 58.549 | 39.130 | 0.00 | 0.00 | 0.00 | 2.57 |
1819 | 2015 | 4.511454 | TCAGCACACAAGTACAAGTCATTC | 59.489 | 41.667 | 0.00 | 0.00 | 0.00 | 2.67 |
1820 | 2016 | 4.273235 | CAGCACACAAGTACAAGTCATTCA | 59.727 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
1821 | 2017 | 5.049198 | CAGCACACAAGTACAAGTCATTCAT | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1822 | 2018 | 5.049198 | AGCACACAAGTACAAGTCATTCATG | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 3.07 |
1823 | 2019 | 5.049474 | GCACACAAGTACAAGTCATTCATGA | 60.049 | 40.000 | 0.00 | 0.00 | 0.00 | 3.07 |
1824 | 2020 | 6.348786 | GCACACAAGTACAAGTCATTCATGAT | 60.349 | 38.462 | 0.00 | 0.00 | 39.30 | 2.45 |
1825 | 2021 | 7.587629 | CACACAAGTACAAGTCATTCATGATT | 58.412 | 34.615 | 0.00 | 0.00 | 39.30 | 2.57 |
1826 | 2022 | 8.077991 | CACACAAGTACAAGTCATTCATGATTT | 58.922 | 33.333 | 0.00 | 0.00 | 39.30 | 2.17 |
1827 | 2023 | 9.283768 | ACACAAGTACAAGTCATTCATGATTTA | 57.716 | 29.630 | 0.00 | 0.00 | 39.30 | 1.40 |
1841 | 2037 | 5.003160 | TCATGATTTATCAGGCCGTAATGG | 58.997 | 41.667 | 0.00 | 0.00 | 40.64 | 3.16 |
1852 | 2048 | 5.354792 | TCAGGCCGTAATGGTTTATTTACAC | 59.645 | 40.000 | 0.00 | 0.00 | 41.21 | 2.90 |
1873 | 2073 | 1.598685 | GGGTTCAGGTTTTCGCGGA | 60.599 | 57.895 | 6.13 | 0.00 | 0.00 | 5.54 |
1885 | 2085 | 0.248012 | TTCGCGGAGGTGATTTGCTA | 59.752 | 50.000 | 6.13 | 0.00 | 31.66 | 3.49 |
1993 | 2193 | 3.572255 | GGGATGCTTGGTTTTCAGTACAA | 59.428 | 43.478 | 0.00 | 0.00 | 0.00 | 2.41 |
2124 | 2324 | 0.486879 | TGGCTGGGGTTCAAGGATTT | 59.513 | 50.000 | 0.00 | 0.00 | 0.00 | 2.17 |
2125 | 2325 | 1.713647 | TGGCTGGGGTTCAAGGATTTA | 59.286 | 47.619 | 0.00 | 0.00 | 0.00 | 1.40 |
2128 | 2328 | 4.017037 | TGGCTGGGGTTCAAGGATTTATTA | 60.017 | 41.667 | 0.00 | 0.00 | 0.00 | 0.98 |
2131 | 2335 | 6.239317 | GGCTGGGGTTCAAGGATTTATTATTC | 60.239 | 42.308 | 0.00 | 0.00 | 0.00 | 1.75 |
2250 | 2481 | 9.628500 | GAAATACAAAATGTAGTAATCCCTCCT | 57.372 | 33.333 | 0.00 | 0.00 | 36.14 | 3.69 |
2268 | 2499 | 6.781014 | TCCCTCCTATTCATATTACTTGTCGT | 59.219 | 38.462 | 0.00 | 0.00 | 0.00 | 4.34 |
2403 | 2634 | 8.295288 | GCTAAGAATTGCATGCAGAAAGTATAT | 58.705 | 33.333 | 21.50 | 5.92 | 0.00 | 0.86 |
2482 | 2713 | 2.737881 | GGTAGTATGGGGCGGCACA | 61.738 | 63.158 | 19.28 | 19.28 | 0.00 | 4.57 |
2483 | 2714 | 1.450211 | GTAGTATGGGGCGGCACAT | 59.550 | 57.895 | 30.64 | 30.64 | 0.00 | 3.21 |
2484 | 2715 | 0.682852 | GTAGTATGGGGCGGCACATA | 59.317 | 55.000 | 28.29 | 28.29 | 0.00 | 2.29 |
2485 | 2716 | 0.973632 | TAGTATGGGGCGGCACATAG | 59.026 | 55.000 | 31.93 | 0.00 | 30.80 | 2.23 |
2486 | 2717 | 1.054406 | AGTATGGGGCGGCACATAGT | 61.054 | 55.000 | 31.93 | 30.98 | 30.80 | 2.12 |
2487 | 2718 | 0.602905 | GTATGGGGCGGCACATAGTC | 60.603 | 60.000 | 31.93 | 18.66 | 30.80 | 2.59 |
2488 | 2719 | 1.051556 | TATGGGGCGGCACATAGTCA | 61.052 | 55.000 | 28.29 | 10.19 | 0.00 | 3.41 |
2489 | 2720 | 2.203070 | GGGGCGGCACATAGTCAG | 60.203 | 66.667 | 12.47 | 0.00 | 0.00 | 3.51 |
2490 | 2721 | 2.897350 | GGGCGGCACATAGTCAGC | 60.897 | 66.667 | 12.47 | 0.00 | 0.00 | 4.26 |
2491 | 2722 | 2.897350 | GGCGGCACATAGTCAGCC | 60.897 | 66.667 | 3.07 | 0.00 | 44.89 | 4.85 |
2492 | 2723 | 2.187946 | GCGGCACATAGTCAGCCT | 59.812 | 61.111 | 0.00 | 0.00 | 46.14 | 4.58 |
2493 | 2724 | 1.884926 | GCGGCACATAGTCAGCCTC | 60.885 | 63.158 | 0.00 | 0.00 | 46.14 | 4.70 |
2494 | 2725 | 1.819229 | CGGCACATAGTCAGCCTCT | 59.181 | 57.895 | 0.00 | 0.00 | 46.14 | 3.69 |
2495 | 2726 | 0.176680 | CGGCACATAGTCAGCCTCTT | 59.823 | 55.000 | 0.00 | 0.00 | 46.14 | 2.85 |
2496 | 2727 | 1.409064 | CGGCACATAGTCAGCCTCTTA | 59.591 | 52.381 | 0.00 | 0.00 | 46.14 | 2.10 |
2497 | 2728 | 2.544694 | CGGCACATAGTCAGCCTCTTAG | 60.545 | 54.545 | 0.00 | 0.00 | 46.14 | 2.18 |
2498 | 2729 | 2.478831 | GCACATAGTCAGCCTCTTAGC | 58.521 | 52.381 | 0.00 | 0.00 | 0.00 | 3.09 |
2499 | 2730 | 2.102252 | GCACATAGTCAGCCTCTTAGCT | 59.898 | 50.000 | 0.00 | 0.00 | 46.45 | 3.32 |
2500 | 2731 | 3.431486 | GCACATAGTCAGCCTCTTAGCTT | 60.431 | 47.826 | 0.00 | 0.00 | 42.61 | 3.74 |
2501 | 2732 | 4.202161 | GCACATAGTCAGCCTCTTAGCTTA | 60.202 | 45.833 | 0.00 | 0.00 | 42.61 | 3.09 |
2502 | 2733 | 5.682471 | GCACATAGTCAGCCTCTTAGCTTAA | 60.682 | 44.000 | 0.00 | 0.00 | 42.61 | 1.85 |
2503 | 2734 | 5.982516 | CACATAGTCAGCCTCTTAGCTTAAG | 59.017 | 44.000 | 0.00 | 0.00 | 42.61 | 1.85 |
2504 | 2735 | 5.894393 | ACATAGTCAGCCTCTTAGCTTAAGA | 59.106 | 40.000 | 6.67 | 0.00 | 42.61 | 2.10 |
2505 | 2736 | 6.553100 | ACATAGTCAGCCTCTTAGCTTAAGAT | 59.447 | 38.462 | 6.67 | 1.53 | 42.61 | 2.40 |
2506 | 2737 | 7.726291 | ACATAGTCAGCCTCTTAGCTTAAGATA | 59.274 | 37.037 | 6.67 | 0.26 | 42.61 | 1.98 |
2507 | 2738 | 8.580720 | CATAGTCAGCCTCTTAGCTTAAGATAA | 58.419 | 37.037 | 12.36 | 12.36 | 42.61 | 1.75 |
2508 | 2739 | 7.049799 | AGTCAGCCTCTTAGCTTAAGATAAG | 57.950 | 40.000 | 27.22 | 27.22 | 42.61 | 1.73 |
2509 | 2740 | 6.041523 | AGTCAGCCTCTTAGCTTAAGATAAGG | 59.958 | 42.308 | 30.39 | 21.76 | 42.61 | 2.69 |
2510 | 2741 | 5.305644 | TCAGCCTCTTAGCTTAAGATAAGGG | 59.694 | 44.000 | 30.39 | 28.58 | 42.47 | 3.95 |
2513 | 2744 | 4.900684 | CTCTTAGCTTAAGATAAGGGGGC | 58.099 | 47.826 | 30.39 | 5.22 | 43.32 | 5.80 |
2514 | 2745 | 4.303794 | TCTTAGCTTAAGATAAGGGGGCA | 58.696 | 43.478 | 30.39 | 14.96 | 42.47 | 5.36 |
2515 | 2746 | 4.102681 | TCTTAGCTTAAGATAAGGGGGCAC | 59.897 | 45.833 | 30.39 | 1.22 | 42.47 | 5.01 |
2516 | 2747 | 2.205342 | AGCTTAAGATAAGGGGGCACA | 58.795 | 47.619 | 6.67 | 0.00 | 0.00 | 4.57 |
2517 | 2748 | 2.580783 | AGCTTAAGATAAGGGGGCACAA | 59.419 | 45.455 | 6.67 | 0.00 | 0.00 | 3.33 |
2518 | 2749 | 3.205282 | AGCTTAAGATAAGGGGGCACAAT | 59.795 | 43.478 | 6.67 | 0.00 | 0.00 | 2.71 |
2519 | 2750 | 3.960755 | GCTTAAGATAAGGGGGCACAATT | 59.039 | 43.478 | 6.67 | 0.00 | 0.00 | 2.32 |
2520 | 2751 | 4.405680 | GCTTAAGATAAGGGGGCACAATTT | 59.594 | 41.667 | 6.67 | 0.00 | 0.00 | 1.82 |
2521 | 2752 | 5.104941 | GCTTAAGATAAGGGGGCACAATTTT | 60.105 | 40.000 | 6.67 | 0.00 | 0.00 | 1.82 |
2522 | 2753 | 6.576244 | GCTTAAGATAAGGGGGCACAATTTTT | 60.576 | 38.462 | 6.67 | 0.00 | 0.00 | 1.94 |
2552 | 2783 | 8.688747 | ATCAAAGATATGATGACTTTTCCCTC | 57.311 | 34.615 | 0.00 | 0.00 | 38.59 | 4.30 |
2553 | 2784 | 7.056635 | TCAAAGATATGATGACTTTTCCCTCC | 58.943 | 38.462 | 0.00 | 0.00 | 32.59 | 4.30 |
2554 | 2785 | 5.574970 | AGATATGATGACTTTTCCCTCCC | 57.425 | 43.478 | 0.00 | 0.00 | 0.00 | 4.30 |
2555 | 2786 | 4.352298 | AGATATGATGACTTTTCCCTCCCC | 59.648 | 45.833 | 0.00 | 0.00 | 0.00 | 4.81 |
2556 | 2787 | 2.059756 | TGATGACTTTTCCCTCCCCT | 57.940 | 50.000 | 0.00 | 0.00 | 0.00 | 4.79 |
2557 | 2788 | 1.916181 | TGATGACTTTTCCCTCCCCTC | 59.084 | 52.381 | 0.00 | 0.00 | 0.00 | 4.30 |
2558 | 2789 | 1.916181 | GATGACTTTTCCCTCCCCTCA | 59.084 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
2559 | 2790 | 1.827792 | TGACTTTTCCCTCCCCTCAA | 58.172 | 50.000 | 0.00 | 0.00 | 0.00 | 3.02 |
2560 | 2791 | 2.140224 | TGACTTTTCCCTCCCCTCAAA | 58.860 | 47.619 | 0.00 | 0.00 | 0.00 | 2.69 |
2561 | 2792 | 2.516277 | TGACTTTTCCCTCCCCTCAAAA | 59.484 | 45.455 | 0.00 | 0.00 | 0.00 | 2.44 |
2562 | 2793 | 3.052490 | TGACTTTTCCCTCCCCTCAAAAA | 60.052 | 43.478 | 0.00 | 0.00 | 0.00 | 1.94 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
24 | 25 | 2.228925 | CGGTAACTACCTAGGAGCCTC | 58.771 | 57.143 | 17.98 | 1.06 | 44.25 | 4.70 |
239 | 246 | 3.092301 | GCTGCCCTCCTTTTCATAAACT | 58.908 | 45.455 | 0.00 | 0.00 | 0.00 | 2.66 |
283 | 290 | 2.096496 | GCTGGTCATGTACAGATTGCAC | 59.904 | 50.000 | 18.93 | 0.00 | 36.86 | 4.57 |
324 | 337 | 0.032678 | CGATATCCAGCGGCACTTCT | 59.967 | 55.000 | 1.45 | 0.00 | 0.00 | 2.85 |
389 | 402 | 6.833342 | AATGTGAAGCTTGTTTCATGTTTC | 57.167 | 33.333 | 2.10 | 5.69 | 39.13 | 2.78 |
393 | 406 | 5.107607 | GCTGAAATGTGAAGCTTGTTTCATG | 60.108 | 40.000 | 18.39 | 14.95 | 39.13 | 3.07 |
471 | 485 | 4.177537 | TGTTCAATGAGACCTTTTCCCA | 57.822 | 40.909 | 0.00 | 0.00 | 0.00 | 4.37 |
472 | 486 | 5.728637 | ATTGTTCAATGAGACCTTTTCCC | 57.271 | 39.130 | 0.00 | 0.00 | 0.00 | 3.97 |
475 | 489 | 8.463930 | TCTGTTATTGTTCAATGAGACCTTTT | 57.536 | 30.769 | 8.11 | 0.00 | 0.00 | 2.27 |
479 | 493 | 9.696917 | ATTTTTCTGTTATTGTTCAATGAGACC | 57.303 | 29.630 | 8.11 | 0.00 | 0.00 | 3.85 |
505 | 522 | 5.762711 | TCAAACGATCCTCATCTTCAAACAA | 59.237 | 36.000 | 0.00 | 0.00 | 0.00 | 2.83 |
598 | 615 | 3.415457 | TCACTTGCACCATACATGTGA | 57.585 | 42.857 | 9.11 | 8.00 | 44.89 | 3.58 |
617 | 634 | 1.739562 | CGTCTGGCAGGCAGAGTTC | 60.740 | 63.158 | 26.45 | 14.14 | 0.00 | 3.01 |
740 | 757 | 3.473923 | TGCATGTCGTGATATCCATGT | 57.526 | 42.857 | 16.31 | 0.00 | 37.57 | 3.21 |
750 | 767 | 0.316442 | GCGATGGATTGCATGTCGTG | 60.316 | 55.000 | 0.00 | 0.00 | 37.15 | 4.35 |
751 | 768 | 0.462581 | AGCGATGGATTGCATGTCGT | 60.463 | 50.000 | 0.00 | 0.00 | 39.70 | 4.34 |
752 | 769 | 0.659427 | AAGCGATGGATTGCATGTCG | 59.341 | 50.000 | 0.00 | 0.00 | 39.70 | 4.35 |
837 | 909 | 1.503542 | GCAACGCAGGATTGTGGAG | 59.496 | 57.895 | 0.00 | 0.00 | 39.15 | 3.86 |
843 | 915 | 2.044946 | GGAGGGCAACGCAGGATT | 60.045 | 61.111 | 0.00 | 0.00 | 37.60 | 3.01 |
844 | 916 | 3.329889 | TGGAGGGCAACGCAGGAT | 61.330 | 61.111 | 0.00 | 0.00 | 37.60 | 3.24 |
845 | 917 | 4.329545 | GTGGAGGGCAACGCAGGA | 62.330 | 66.667 | 0.00 | 0.00 | 37.60 | 3.86 |
846 | 918 | 4.641645 | TGTGGAGGGCAACGCAGG | 62.642 | 66.667 | 0.00 | 0.00 | 37.60 | 4.85 |
847 | 919 | 1.926511 | GATTGTGGAGGGCAACGCAG | 61.927 | 60.000 | 0.00 | 0.00 | 37.60 | 5.18 |
848 | 920 | 1.971167 | GATTGTGGAGGGCAACGCA | 60.971 | 57.895 | 0.00 | 0.00 | 37.60 | 5.24 |
849 | 921 | 2.877691 | GATTGTGGAGGGCAACGC | 59.122 | 61.111 | 0.00 | 0.00 | 37.60 | 4.84 |
850 | 922 | 1.361668 | CTCGATTGTGGAGGGCAACG | 61.362 | 60.000 | 0.00 | 0.00 | 37.60 | 4.10 |
851 | 923 | 0.036388 | TCTCGATTGTGGAGGGCAAC | 60.036 | 55.000 | 0.00 | 0.00 | 32.34 | 4.17 |
852 | 924 | 0.036388 | GTCTCGATTGTGGAGGGCAA | 60.036 | 55.000 | 0.00 | 0.00 | 32.34 | 4.52 |
853 | 925 | 1.596934 | GTCTCGATTGTGGAGGGCA | 59.403 | 57.895 | 0.00 | 0.00 | 32.34 | 5.36 |
854 | 926 | 1.519455 | CGTCTCGATTGTGGAGGGC | 60.519 | 63.158 | 0.00 | 0.00 | 32.34 | 5.19 |
867 | 939 | 1.453155 | AAATCACCATGTGCCGTCTC | 58.547 | 50.000 | 0.00 | 0.00 | 32.98 | 3.36 |
965 | 1150 | 6.385649 | TCTTGTATTTGTTGTTTCCTCCAC | 57.614 | 37.500 | 0.00 | 0.00 | 0.00 | 4.02 |
1151 | 1338 | 0.548926 | TGGGTCTAGGCCATGGTCAA | 60.549 | 55.000 | 20.74 | 0.00 | 0.00 | 3.18 |
1152 | 1339 | 0.982852 | CTGGGTCTAGGCCATGGTCA | 60.983 | 60.000 | 20.74 | 3.57 | 0.00 | 4.02 |
1184 | 1371 | 5.050227 | CGGTCGATTGTGTTTACCAAGTAAA | 60.050 | 40.000 | 0.00 | 0.00 | 35.92 | 2.01 |
1296 | 1490 | 1.177401 | CAGTGAGGTCCGATGTCAGA | 58.823 | 55.000 | 0.00 | 0.00 | 0.00 | 3.27 |
1297 | 1491 | 0.459237 | GCAGTGAGGTCCGATGTCAG | 60.459 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 |
1549 | 1743 | 0.885150 | TTTGCATACGGGCACGACAA | 60.885 | 50.000 | 19.19 | 11.22 | 44.86 | 3.18 |
1550 | 1744 | 0.675208 | ATTTGCATACGGGCACGACA | 60.675 | 50.000 | 19.19 | 4.42 | 44.86 | 4.35 |
1622 | 1818 | 2.031682 | CCCAAACGAGCAAGAAACAGAG | 60.032 | 50.000 | 0.00 | 0.00 | 0.00 | 3.35 |
1651 | 1847 | 8.868522 | ACAGAAATTCCAGATACATCTCAAAA | 57.131 | 30.769 | 0.00 | 0.00 | 34.22 | 2.44 |
1727 | 1923 | 7.463961 | TCCTCGTATAAAACTCTGAAGTCTT | 57.536 | 36.000 | 0.00 | 0.00 | 33.48 | 3.01 |
1765 | 1961 | 6.173339 | ACACTTTTCTGAAACTTGTCTGAGA | 58.827 | 36.000 | 1.58 | 0.00 | 0.00 | 3.27 |
1783 | 1979 | 3.006323 | TGTGTGCTGAAAACCAACACTTT | 59.994 | 39.130 | 5.90 | 0.00 | 41.26 | 2.66 |
1791 | 1987 | 4.142469 | ACTTGTACTTGTGTGCTGAAAACC | 60.142 | 41.667 | 0.00 | 0.00 | 0.00 | 3.27 |
1799 | 1995 | 4.811555 | TGAATGACTTGTACTTGTGTGC | 57.188 | 40.909 | 0.00 | 0.00 | 0.00 | 4.57 |
1815 | 2011 | 6.558771 | TTACGGCCTGATAAATCATGAATG | 57.441 | 37.500 | 0.00 | 0.00 | 36.02 | 2.67 |
1816 | 2012 | 6.151648 | CCATTACGGCCTGATAAATCATGAAT | 59.848 | 38.462 | 0.00 | 0.00 | 36.02 | 2.57 |
1817 | 2013 | 5.473162 | CCATTACGGCCTGATAAATCATGAA | 59.527 | 40.000 | 0.00 | 0.00 | 36.02 | 2.57 |
1818 | 2014 | 5.003160 | CCATTACGGCCTGATAAATCATGA | 58.997 | 41.667 | 0.00 | 0.00 | 36.02 | 3.07 |
1819 | 2015 | 4.761739 | ACCATTACGGCCTGATAAATCATG | 59.238 | 41.667 | 0.00 | 0.00 | 39.03 | 3.07 |
1820 | 2016 | 4.985538 | ACCATTACGGCCTGATAAATCAT | 58.014 | 39.130 | 0.00 | 0.00 | 39.03 | 2.45 |
1821 | 2017 | 4.431416 | ACCATTACGGCCTGATAAATCA | 57.569 | 40.909 | 0.00 | 0.00 | 39.03 | 2.57 |
1822 | 2018 | 5.767816 | AAACCATTACGGCCTGATAAATC | 57.232 | 39.130 | 0.00 | 0.00 | 39.03 | 2.17 |
1823 | 2019 | 7.833285 | AATAAACCATTACGGCCTGATAAAT | 57.167 | 32.000 | 0.00 | 0.00 | 39.03 | 1.40 |
1824 | 2020 | 7.648039 | AAATAAACCATTACGGCCTGATAAA | 57.352 | 32.000 | 0.00 | 0.00 | 39.03 | 1.40 |
1825 | 2021 | 7.774157 | TGTAAATAAACCATTACGGCCTGATAA | 59.226 | 33.333 | 0.00 | 0.00 | 39.03 | 1.75 |
1826 | 2022 | 7.227116 | GTGTAAATAAACCATTACGGCCTGATA | 59.773 | 37.037 | 0.00 | 0.00 | 39.03 | 2.15 |
1827 | 2023 | 6.038936 | GTGTAAATAAACCATTACGGCCTGAT | 59.961 | 38.462 | 0.00 | 0.00 | 39.03 | 2.90 |
1828 | 2024 | 5.354792 | GTGTAAATAAACCATTACGGCCTGA | 59.645 | 40.000 | 0.00 | 0.00 | 39.03 | 3.86 |
1829 | 2025 | 5.124138 | TGTGTAAATAAACCATTACGGCCTG | 59.876 | 40.000 | 0.00 | 0.00 | 39.03 | 4.85 |
1830 | 2026 | 5.254901 | TGTGTAAATAAACCATTACGGCCT | 58.745 | 37.500 | 0.00 | 0.00 | 39.03 | 5.19 |
1841 | 2037 | 5.074804 | ACCTGAACCCCTGTGTAAATAAAC | 58.925 | 41.667 | 0.00 | 0.00 | 0.00 | 2.01 |
1852 | 2048 | 1.852067 | CGCGAAAACCTGAACCCCTG | 61.852 | 60.000 | 0.00 | 0.00 | 0.00 | 4.45 |
1873 | 2073 | 3.157087 | CACAAACCCTAGCAAATCACCT | 58.843 | 45.455 | 0.00 | 0.00 | 0.00 | 4.00 |
1885 | 2085 | 0.693049 | CTACCAGAGCCACAAACCCT | 59.307 | 55.000 | 0.00 | 0.00 | 0.00 | 4.34 |
1939 | 2139 | 7.165460 | TCTTTGACGTCCAGATAATCTTACA | 57.835 | 36.000 | 14.12 | 0.00 | 0.00 | 2.41 |
1993 | 2193 | 5.810074 | CCAGAACGGAAAACAAGACAAAATT | 59.190 | 36.000 | 0.00 | 0.00 | 36.56 | 1.82 |
2051 | 2251 | 7.228308 | ACTTCTTTCTCAGATCCTTTTCTGTTG | 59.772 | 37.037 | 1.76 | 0.00 | 43.02 | 3.33 |
2052 | 2252 | 7.286313 | ACTTCTTTCTCAGATCCTTTTCTGTT | 58.714 | 34.615 | 1.76 | 0.00 | 43.02 | 3.16 |
2053 | 2253 | 6.836242 | ACTTCTTTCTCAGATCCTTTTCTGT | 58.164 | 36.000 | 1.76 | 0.00 | 43.02 | 3.41 |
2054 | 2254 | 7.583230 | CAACTTCTTTCTCAGATCCTTTTCTG | 58.417 | 38.462 | 0.00 | 0.00 | 43.70 | 3.02 |
2055 | 2255 | 6.206438 | GCAACTTCTTTCTCAGATCCTTTTCT | 59.794 | 38.462 | 0.00 | 0.00 | 0.00 | 2.52 |
2056 | 2256 | 6.377780 | GCAACTTCTTTCTCAGATCCTTTTC | 58.622 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
2057 | 2257 | 5.242615 | GGCAACTTCTTTCTCAGATCCTTTT | 59.757 | 40.000 | 0.00 | 0.00 | 0.00 | 2.27 |
2058 | 2258 | 4.764308 | GGCAACTTCTTTCTCAGATCCTTT | 59.236 | 41.667 | 0.00 | 0.00 | 0.00 | 3.11 |
2059 | 2259 | 4.331108 | GGCAACTTCTTTCTCAGATCCTT | 58.669 | 43.478 | 0.00 | 0.00 | 0.00 | 3.36 |
2060 | 2260 | 3.949132 | GGCAACTTCTTTCTCAGATCCT | 58.051 | 45.455 | 0.00 | 0.00 | 0.00 | 3.24 |
2124 | 2324 | 6.838612 | AGCCCCTTATGCAAACAAGAATAATA | 59.161 | 34.615 | 0.00 | 0.00 | 0.00 | 0.98 |
2125 | 2325 | 5.662657 | AGCCCCTTATGCAAACAAGAATAAT | 59.337 | 36.000 | 0.00 | 0.00 | 0.00 | 1.28 |
2128 | 2328 | 3.444029 | AGCCCCTTATGCAAACAAGAAT | 58.556 | 40.909 | 0.00 | 0.00 | 0.00 | 2.40 |
2131 | 2335 | 2.427095 | GGTAGCCCCTTATGCAAACAAG | 59.573 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
2194 | 2425 | 3.726291 | TTTGTTGGCCTCTGCTTAAAC | 57.274 | 42.857 | 3.32 | 0.00 | 37.74 | 2.01 |
2203 | 2434 | 2.814336 | CTCTACTGGTTTTGTTGGCCTC | 59.186 | 50.000 | 3.32 | 0.00 | 0.00 | 4.70 |
2250 | 2481 | 9.602568 | TTAAAGCCACGACAAGTAATATGAATA | 57.397 | 29.630 | 0.00 | 0.00 | 0.00 | 1.75 |
2252 | 2483 | 7.908827 | TTAAAGCCACGACAAGTAATATGAA | 57.091 | 32.000 | 0.00 | 0.00 | 0.00 | 2.57 |
2268 | 2499 | 6.885952 | TGTACTAAAGTTGCATTAAAGCCA | 57.114 | 33.333 | 0.00 | 0.00 | 0.00 | 4.75 |
2403 | 2634 | 7.339721 | CAGGAAGGACTCACTGTATTCTTAGTA | 59.660 | 40.741 | 0.00 | 0.00 | 0.00 | 1.82 |
2416 | 2647 | 1.633774 | TCTGGTCAGGAAGGACTCAC | 58.366 | 55.000 | 0.00 | 0.00 | 37.91 | 3.51 |
2482 | 2713 | 8.713708 | TTATCTTAAGCTAAGAGGCTGACTAT | 57.286 | 34.615 | 0.00 | 0.00 | 46.90 | 2.12 |
2483 | 2714 | 7.231722 | CCTTATCTTAAGCTAAGAGGCTGACTA | 59.768 | 40.741 | 22.05 | 0.00 | 46.90 | 2.59 |
2484 | 2715 | 6.041523 | CCTTATCTTAAGCTAAGAGGCTGACT | 59.958 | 42.308 | 22.05 | 0.00 | 46.90 | 3.41 |
2485 | 2716 | 6.220201 | CCTTATCTTAAGCTAAGAGGCTGAC | 58.780 | 44.000 | 22.05 | 0.00 | 46.90 | 3.51 |
2486 | 2717 | 5.305644 | CCCTTATCTTAAGCTAAGAGGCTGA | 59.694 | 44.000 | 22.05 | 0.00 | 46.90 | 4.26 |
2487 | 2718 | 5.512232 | CCCCTTATCTTAAGCTAAGAGGCTG | 60.512 | 48.000 | 22.05 | 9.03 | 46.90 | 4.85 |
2488 | 2719 | 4.595350 | CCCCTTATCTTAAGCTAAGAGGCT | 59.405 | 45.833 | 22.05 | 0.00 | 46.90 | 4.58 |
2489 | 2720 | 4.263112 | CCCCCTTATCTTAAGCTAAGAGGC | 60.263 | 50.000 | 22.05 | 0.00 | 46.90 | 4.70 |
2490 | 2721 | 4.263112 | GCCCCCTTATCTTAAGCTAAGAGG | 60.263 | 50.000 | 22.05 | 18.97 | 46.90 | 3.69 |
2491 | 2722 | 4.348168 | TGCCCCCTTATCTTAAGCTAAGAG | 59.652 | 45.833 | 22.05 | 12.44 | 46.90 | 2.85 |
2493 | 2724 | 4.141482 | TGTGCCCCCTTATCTTAAGCTAAG | 60.141 | 45.833 | 16.01 | 16.01 | 37.13 | 2.18 |
2494 | 2725 | 3.783642 | TGTGCCCCCTTATCTTAAGCTAA | 59.216 | 43.478 | 0.00 | 0.00 | 0.00 | 3.09 |
2495 | 2726 | 3.389866 | TGTGCCCCCTTATCTTAAGCTA | 58.610 | 45.455 | 0.00 | 0.00 | 0.00 | 3.32 |
2496 | 2727 | 2.205342 | TGTGCCCCCTTATCTTAAGCT | 58.795 | 47.619 | 0.00 | 0.00 | 0.00 | 3.74 |
2497 | 2728 | 2.729028 | TGTGCCCCCTTATCTTAAGC | 57.271 | 50.000 | 0.00 | 0.00 | 0.00 | 3.09 |
2498 | 2729 | 6.544928 | AAAATTGTGCCCCCTTATCTTAAG | 57.455 | 37.500 | 0.00 | 0.00 | 0.00 | 1.85 |
2499 | 2730 | 6.943899 | AAAAATTGTGCCCCCTTATCTTAA | 57.056 | 33.333 | 0.00 | 0.00 | 0.00 | 1.85 |
2526 | 2757 | 9.784531 | GAGGGAAAAGTCATCATATCTTTGATA | 57.215 | 33.333 | 0.00 | 0.00 | 34.59 | 2.15 |
2527 | 2758 | 7.723172 | GGAGGGAAAAGTCATCATATCTTTGAT | 59.277 | 37.037 | 0.00 | 0.00 | 36.79 | 2.57 |
2528 | 2759 | 7.056635 | GGAGGGAAAAGTCATCATATCTTTGA | 58.943 | 38.462 | 0.00 | 0.00 | 32.74 | 2.69 |
2529 | 2760 | 6.264067 | GGGAGGGAAAAGTCATCATATCTTTG | 59.736 | 42.308 | 0.00 | 0.00 | 32.74 | 2.77 |
2530 | 2761 | 6.368805 | GGGAGGGAAAAGTCATCATATCTTT | 58.631 | 40.000 | 0.00 | 0.00 | 33.61 | 2.52 |
2531 | 2762 | 5.163045 | GGGGAGGGAAAAGTCATCATATCTT | 60.163 | 44.000 | 0.00 | 0.00 | 0.00 | 2.40 |
2532 | 2763 | 4.352298 | GGGGAGGGAAAAGTCATCATATCT | 59.648 | 45.833 | 0.00 | 0.00 | 0.00 | 1.98 |
2533 | 2764 | 4.352298 | AGGGGAGGGAAAAGTCATCATATC | 59.648 | 45.833 | 0.00 | 0.00 | 0.00 | 1.63 |
2534 | 2765 | 4.319515 | AGGGGAGGGAAAAGTCATCATAT | 58.680 | 43.478 | 0.00 | 0.00 | 0.00 | 1.78 |
2535 | 2766 | 3.716872 | GAGGGGAGGGAAAAGTCATCATA | 59.283 | 47.826 | 0.00 | 0.00 | 0.00 | 2.15 |
2536 | 2767 | 2.511637 | GAGGGGAGGGAAAAGTCATCAT | 59.488 | 50.000 | 0.00 | 0.00 | 0.00 | 2.45 |
2537 | 2768 | 1.916181 | GAGGGGAGGGAAAAGTCATCA | 59.084 | 52.381 | 0.00 | 0.00 | 0.00 | 3.07 |
2538 | 2769 | 1.916181 | TGAGGGGAGGGAAAAGTCATC | 59.084 | 52.381 | 0.00 | 0.00 | 0.00 | 2.92 |
2539 | 2770 | 2.059756 | TGAGGGGAGGGAAAAGTCAT | 57.940 | 50.000 | 0.00 | 0.00 | 0.00 | 3.06 |
2540 | 2771 | 1.827792 | TTGAGGGGAGGGAAAAGTCA | 58.172 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
2541 | 2772 | 2.971901 | TTTGAGGGGAGGGAAAAGTC | 57.028 | 50.000 | 0.00 | 0.00 | 0.00 | 3.01 |
2542 | 2773 | 3.699025 | TTTTTGAGGGGAGGGAAAAGT | 57.301 | 42.857 | 0.00 | 0.00 | 0.00 | 2.66 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.