Multiple sequence alignment - TraesCS7A01G496000
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 | TraesCS7A01G496000 | chr7A | 100.000 | 4115 | 0 | 0 | 1 | 4115 | 686112140 | 686108026 | 0.000000e+00 | 7600 |
1 | TraesCS7A01G496000 | chr7A | 94.624 | 93 | 5 | 0 | 1790 | 1882 | 138960740 | 138960832 | 1.190000e-30 | 145 |
2 | TraesCS7A01G496000 | chr7A | 93.750 | 96 | 6 | 0 | 1789 | 1884 | 213151353 | 213151258 | 1.190000e-30 | 145 |
3 | TraesCS7A01G496000 | chr7D | 85.660 | 1827 | 155 | 50 | 1 | 1797 | 593274440 | 593272691 | 0.000000e+00 | 1823 |
4 | TraesCS7A01G496000 | chr7D | 92.274 | 1126 | 62 | 9 | 2822 | 3928 | 593271814 | 593270695 | 0.000000e+00 | 1574 |
5 | TraesCS7A01G496000 | chr7D | 91.694 | 927 | 48 | 14 | 1872 | 2796 | 593272699 | 593271800 | 0.000000e+00 | 1258 |
6 | TraesCS7A01G496000 | chr7D | 90.441 | 136 | 11 | 1 | 3982 | 4115 | 593270585 | 593270450 | 1.180000e-40 | 178 |
7 | TraesCS7A01G496000 | chr7D | 94.624 | 93 | 5 | 0 | 1793 | 1885 | 599718525 | 599718433 | 1.190000e-30 | 145 |
8 | TraesCS7A01G496000 | chr7B | 93.340 | 1081 | 65 | 4 | 2873 | 3950 | 667629751 | 667630827 | 0.000000e+00 | 1591 |
9 | TraesCS7A01G496000 | chr7B | 96.120 | 902 | 32 | 3 | 1872 | 2771 | 667628831 | 667629731 | 0.000000e+00 | 1469 |
10 | TraesCS7A01G496000 | chr7B | 83.051 | 1121 | 83 | 50 | 713 | 1794 | 667627784 | 667628836 | 0.000000e+00 | 918 |
11 | TraesCS7A01G496000 | chr7B | 81.414 | 608 | 81 | 15 | 122 | 701 | 667627126 | 667627729 | 6.230000e-128 | 468 |
12 | TraesCS7A01G496000 | chr7B | 91.129 | 124 | 8 | 2 | 3995 | 4115 | 667630932 | 667631055 | 9.150000e-37 | 165 |
13 | TraesCS7A01G496000 | chr7B | 94.949 | 99 | 4 | 1 | 1783 | 1881 | 8925276 | 8925179 | 1.980000e-33 | 154 |
14 | TraesCS7A01G496000 | chr7B | 91.667 | 84 | 7 | 0 | 53 | 136 | 667627018 | 667627101 | 2.600000e-22 | 117 |
15 | TraesCS7A01G496000 | chr3D | 95.556 | 90 | 4 | 0 | 1790 | 1879 | 71371433 | 71371522 | 1.190000e-30 | 145 |
16 | TraesCS7A01G496000 | chr6B | 93.750 | 96 | 5 | 1 | 1789 | 1884 | 320551121 | 320551027 | 4.290000e-30 | 143 |
17 | TraesCS7A01G496000 | chr1B | 93.684 | 95 | 6 | 0 | 1793 | 1887 | 234252674 | 234252580 | 4.290000e-30 | 143 |
18 | TraesCS7A01G496000 | chrUn | 93.617 | 94 | 6 | 0 | 1785 | 1878 | 22143251 | 22143158 | 1.540000e-29 | 141 |
19 | TraesCS7A01G496000 | chr6A | 88.991 | 109 | 10 | 2 | 1773 | 1880 | 614304773 | 614304666 | 2.580000e-27 | 134 |
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 | TraesCS7A01G496000 | chr7A | 686108026 | 686112140 | 4114 | True | 7600.00 | 7600 | 100.00000 | 1 | 4115 | 1 | chr7A.!!$R2 | 4114 |
1 | TraesCS7A01G496000 | chr7D | 593270450 | 593274440 | 3990 | True | 1208.25 | 1823 | 90.01725 | 1 | 4115 | 4 | chr7D.!!$R2 | 4114 |
2 | TraesCS7A01G496000 | chr7B | 667627018 | 667631055 | 4037 | False | 788.00 | 1591 | 89.45350 | 53 | 4115 | 6 | chr7B.!!$F1 | 4062 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
169 | 209 | 0.749818 | TGGTGCAAACGAAGGCTTGA | 60.750 | 50.000 | 3.46 | 0.0 | 0.00 | 3.02 | F |
1312 | 1466 | 0.397564 | TGTGAGCCAGTGATGCTTCA | 59.602 | 50.000 | 0.00 | 0.0 | 39.69 | 3.02 | F |
1313 | 1467 | 1.003928 | TGTGAGCCAGTGATGCTTCAT | 59.996 | 47.619 | 5.49 | 0.0 | 39.69 | 2.57 | F |
2584 | 2771 | 0.238289 | GTTCACATTGTCCGTGGCTG | 59.762 | 55.000 | 0.00 | 0.0 | 35.03 | 4.85 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1591 | 1772 | 0.106719 | TACCCCAGCCTAATTGCAGC | 60.107 | 55.000 | 0.0 | 0.0 | 0.00 | 5.25 | R |
2367 | 2552 | 0.178967 | TGCCCCATTTCAGCTTGACA | 60.179 | 50.000 | 0.0 | 0.0 | 0.00 | 3.58 | R |
3081 | 3284 | 0.895530 | GAATGTCCGTGTCCTCCTCA | 59.104 | 55.000 | 0.0 | 0.0 | 0.00 | 3.86 | R |
3784 | 3988 | 1.131126 | CATGGTCAGCAATTCCACGAC | 59.869 | 52.381 | 0.0 | 0.0 | 33.91 | 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 |
---|---|---|---|---|---|---|---|---|---|
38 | 39 | 9.056005 | TCTAAAGGATAACATTACATGTCATGC | 57.944 | 33.333 | 17.93 | 3.90 | 44.07 | 4.06 |
39 | 40 | 6.639632 | AAGGATAACATTACATGTCATGCC | 57.360 | 37.500 | 17.93 | 11.69 | 44.07 | 4.40 |
40 | 41 | 5.945310 | AGGATAACATTACATGTCATGCCT | 58.055 | 37.500 | 17.93 | 13.46 | 44.07 | 4.75 |
41 | 42 | 6.000219 | AGGATAACATTACATGTCATGCCTC | 59.000 | 40.000 | 17.93 | 12.19 | 44.07 | 4.70 |
42 | 43 | 5.106948 | GGATAACATTACATGTCATGCCTCG | 60.107 | 44.000 | 17.93 | 2.44 | 44.07 | 4.63 |
43 | 44 | 3.266510 | ACATTACATGTCATGCCTCGT | 57.733 | 42.857 | 17.93 | 3.05 | 39.92 | 4.18 |
44 | 45 | 3.198068 | ACATTACATGTCATGCCTCGTC | 58.802 | 45.455 | 17.93 | 0.00 | 39.92 | 4.20 |
45 | 46 | 3.197265 | CATTACATGTCATGCCTCGTCA | 58.803 | 45.455 | 12.91 | 0.00 | 0.00 | 4.35 |
46 | 47 | 3.326836 | TTACATGTCATGCCTCGTCAA | 57.673 | 42.857 | 12.91 | 0.00 | 0.00 | 3.18 |
117 | 118 | 3.393278 | TGTTAAGTTGTACCTCCAAGCCT | 59.607 | 43.478 | 0.00 | 0.00 | 0.00 | 4.58 |
128 | 129 | 2.572104 | CCTCCAAGCCTAGTAACCAAGT | 59.428 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
136 | 176 | 2.481449 | CCTAGTAACCAAGTGCCTAGCG | 60.481 | 54.545 | 0.00 | 0.00 | 0.00 | 4.26 |
169 | 209 | 0.749818 | TGGTGCAAACGAAGGCTTGA | 60.750 | 50.000 | 3.46 | 0.00 | 0.00 | 3.02 |
179 | 219 | 6.541969 | CAAACGAAGGCTTGAAAACATTTTT | 58.458 | 32.000 | 3.46 | 0.00 | 0.00 | 1.94 |
227 | 287 | 2.262637 | ACCCACGGACCAGAGATAAAA | 58.737 | 47.619 | 0.00 | 0.00 | 0.00 | 1.52 |
328 | 388 | 5.529289 | AGACTGGATCCATTCAAGTAGGTA | 58.471 | 41.667 | 28.23 | 0.00 | 38.84 | 3.08 |
357 | 417 | 7.193595 | GCTTAAGAGTTTTTGTAAGCTCACAA | 58.806 | 34.615 | 6.67 | 0.00 | 43.24 | 3.33 |
387 | 447 | 9.535878 | TTTCTTGTGTTTGGGTAAAATACATTC | 57.464 | 29.630 | 1.98 | 0.00 | 45.69 | 2.67 |
516 | 593 | 9.912634 | TTTCCTTGAAACACATGAATATTTCTC | 57.087 | 29.630 | 0.00 | 0.00 | 33.21 | 2.87 |
785 | 918 | 4.202567 | ACCAAGAGCCTCCAATTTCTGTTA | 60.203 | 41.667 | 0.00 | 0.00 | 0.00 | 2.41 |
790 | 923 | 7.200434 | AGAGCCTCCAATTTCTGTTATCTAA | 57.800 | 36.000 | 0.00 | 0.00 | 0.00 | 2.10 |
792 | 925 | 8.109634 | AGAGCCTCCAATTTCTGTTATCTAAAA | 58.890 | 33.333 | 0.00 | 0.00 | 0.00 | 1.52 |
793 | 926 | 8.286191 | AGCCTCCAATTTCTGTTATCTAAAAG | 57.714 | 34.615 | 0.00 | 0.00 | 0.00 | 2.27 |
795 | 928 | 8.523658 | GCCTCCAATTTCTGTTATCTAAAAGTT | 58.476 | 33.333 | 0.00 | 0.00 | 0.00 | 2.66 |
799 | 932 | 9.846248 | CCAATTTCTGTTATCTAAAAGTTCTGG | 57.154 | 33.333 | 0.00 | 0.00 | 0.00 | 3.86 |
800 | 933 | 9.346725 | CAATTTCTGTTATCTAAAAGTTCTGGC | 57.653 | 33.333 | 0.00 | 0.00 | 0.00 | 4.85 |
801 | 934 | 7.448748 | TTTCTGTTATCTAAAAGTTCTGGCC | 57.551 | 36.000 | 0.00 | 0.00 | 0.00 | 5.36 |
895 | 1030 | 2.105128 | CCCTAGTCTCGCTTGCGG | 59.895 | 66.667 | 15.10 | 6.20 | 0.00 | 5.69 |
896 | 1031 | 2.711922 | CCCTAGTCTCGCTTGCGGT | 61.712 | 63.158 | 15.10 | 0.91 | 0.00 | 5.68 |
906 | 1041 | 2.032071 | CTTGCGGTTCGAACCCCT | 59.968 | 61.111 | 35.50 | 0.00 | 46.53 | 4.79 |
930 | 1065 | 1.457455 | CAGCCTCTCCTCCTCCTCC | 60.457 | 68.421 | 0.00 | 0.00 | 0.00 | 4.30 |
1093 | 1231 | 2.494073 | CAGATAGATAGGCGGAGAACCC | 59.506 | 54.545 | 0.00 | 0.00 | 0.00 | 4.11 |
1094 | 1232 | 2.380590 | AGATAGATAGGCGGAGAACCCT | 59.619 | 50.000 | 0.00 | 0.00 | 35.22 | 4.34 |
1095 | 1233 | 3.592427 | AGATAGATAGGCGGAGAACCCTA | 59.408 | 47.826 | 0.00 | 0.00 | 38.04 | 3.53 |
1096 | 1234 | 2.296073 | AGATAGGCGGAGAACCCTAG | 57.704 | 55.000 | 0.00 | 0.00 | 37.15 | 3.02 |
1141 | 1279 | 2.112297 | TCCTGCGGCGGACTTTTT | 59.888 | 55.556 | 11.13 | 0.00 | 0.00 | 1.94 |
1161 | 1299 | 6.892658 | TTTTGCTAGTATTGGTTGTGTGAT | 57.107 | 33.333 | 0.00 | 0.00 | 0.00 | 3.06 |
1178 | 1326 | 1.049402 | GATGGGTCCAGTAGGTAGGC | 58.951 | 60.000 | 0.00 | 0.00 | 35.89 | 3.93 |
1182 | 1330 | 0.974525 | GGTCCAGTAGGTAGGCCGTT | 60.975 | 60.000 | 0.00 | 0.00 | 40.50 | 4.44 |
1188 | 1336 | 2.431057 | CAGTAGGTAGGCCGTTGATTCT | 59.569 | 50.000 | 0.00 | 0.00 | 40.50 | 2.40 |
1191 | 1339 | 1.906574 | AGGTAGGCCGTTGATTCTTGA | 59.093 | 47.619 | 0.00 | 0.00 | 40.50 | 3.02 |
1275 | 1429 | 1.208165 | CCAGCCAGTAACCCCTTCCT | 61.208 | 60.000 | 0.00 | 0.00 | 0.00 | 3.36 |
1283 | 1437 | 4.223953 | CAGTAACCCCTTCCTATCTGCTA | 58.776 | 47.826 | 0.00 | 0.00 | 0.00 | 3.49 |
1299 | 1453 | 4.697514 | TCTGCTATTATTCTGGTGTGAGC | 58.302 | 43.478 | 0.00 | 0.00 | 0.00 | 4.26 |
1308 | 1462 | 1.302752 | TGGTGTGAGCCAGTGATGC | 60.303 | 57.895 | 0.00 | 0.00 | 33.97 | 3.91 |
1309 | 1463 | 1.002868 | GGTGTGAGCCAGTGATGCT | 60.003 | 57.895 | 0.00 | 0.00 | 43.03 | 3.79 |
1310 | 1464 | 0.607489 | GGTGTGAGCCAGTGATGCTT | 60.607 | 55.000 | 0.00 | 0.00 | 39.69 | 3.91 |
1311 | 1465 | 0.801251 | GTGTGAGCCAGTGATGCTTC | 59.199 | 55.000 | 0.00 | 0.00 | 39.69 | 3.86 |
1312 | 1466 | 0.397564 | TGTGAGCCAGTGATGCTTCA | 59.602 | 50.000 | 0.00 | 0.00 | 39.69 | 3.02 |
1313 | 1467 | 1.003928 | TGTGAGCCAGTGATGCTTCAT | 59.996 | 47.619 | 5.49 | 0.00 | 39.69 | 2.57 |
1324 | 1478 | 3.656457 | TGCTTCATCTGCATGGTGT | 57.344 | 47.368 | 0.00 | 0.00 | 35.31 | 4.16 |
1347 | 1501 | 4.347453 | CTGCAAACGTGGCCTGCC | 62.347 | 66.667 | 11.08 | 0.00 | 35.13 | 4.85 |
1351 | 1505 | 4.572571 | AAACGTGGCCTGCCCGAA | 62.573 | 61.111 | 20.69 | 0.00 | 35.87 | 4.30 |
1382 | 1536 | 1.811266 | CTGCCGTCGAGATTGTGGG | 60.811 | 63.158 | 0.00 | 0.00 | 0.00 | 4.61 |
1387 | 1541 | 1.068474 | CGTCGAGATTGTGGGTTGTC | 58.932 | 55.000 | 0.00 | 0.00 | 0.00 | 3.18 |
1419 | 1573 | 5.513849 | GTCTGTCCGTTTTTGTTAGGTTTTG | 59.486 | 40.000 | 0.00 | 0.00 | 0.00 | 2.44 |
1425 | 1579 | 4.259490 | CGTTTTTGTTAGGTTTTGGCGAAC | 60.259 | 41.667 | 0.00 | 0.00 | 0.00 | 3.95 |
1464 | 1621 | 3.181465 | GCTAGATGGGTCGAGATTTTGGA | 60.181 | 47.826 | 0.00 | 0.00 | 29.49 | 3.53 |
1475 | 1632 | 5.980715 | GTCGAGATTTTGGATCTAGAAGGTC | 59.019 | 44.000 | 0.00 | 0.00 | 32.93 | 3.85 |
1490 | 1647 | 2.158959 | GGTCGCGACATCGTCAAGG | 61.159 | 63.158 | 37.26 | 0.00 | 42.22 | 3.61 |
1522 | 1703 | 1.340889 | GTTGCCAATGTCTCCTGCAAA | 59.659 | 47.619 | 0.00 | 0.00 | 42.86 | 3.68 |
1558 | 1739 | 5.416083 | TGGATTTGTCGTATCACTAGTTGG | 58.584 | 41.667 | 0.00 | 0.00 | 0.00 | 3.77 |
1603 | 1784 | 1.354506 | CAGAGCGCTGCAATTAGGC | 59.645 | 57.895 | 18.48 | 0.00 | 34.95 | 3.93 |
1682 | 1865 | 3.426695 | GGTCACAGCACAGAATTGTATGC | 60.427 | 47.826 | 0.00 | 0.00 | 35.25 | 3.14 |
1686 | 1869 | 2.009774 | AGCACAGAATTGTATGCGTCC | 58.990 | 47.619 | 0.00 | 0.00 | 35.25 | 4.79 |
1765 | 1948 | 4.098196 | CCTAGTGTTGTCTTACCTCTAGCC | 59.902 | 50.000 | 0.00 | 0.00 | 0.00 | 3.93 |
1792 | 1975 | 4.040952 | ACTTGTGGTAGCTGATTCAGAACT | 59.959 | 41.667 | 17.87 | 8.26 | 32.44 | 3.01 |
1793 | 1976 | 5.246203 | ACTTGTGGTAGCTGATTCAGAACTA | 59.754 | 40.000 | 17.87 | 9.28 | 32.44 | 2.24 |
1794 | 1977 | 5.073311 | TGTGGTAGCTGATTCAGAACTAC | 57.927 | 43.478 | 17.87 | 19.17 | 34.03 | 2.73 |
1795 | 1978 | 4.772624 | TGTGGTAGCTGATTCAGAACTACT | 59.227 | 41.667 | 23.68 | 13.29 | 34.30 | 2.57 |
1796 | 1979 | 5.246203 | TGTGGTAGCTGATTCAGAACTACTT | 59.754 | 40.000 | 23.68 | 5.68 | 34.30 | 2.24 |
1797 | 1980 | 5.808030 | GTGGTAGCTGATTCAGAACTACTTC | 59.192 | 44.000 | 17.87 | 11.82 | 32.01 | 3.01 |
1798 | 1981 | 5.105310 | TGGTAGCTGATTCAGAACTACTTCC | 60.105 | 44.000 | 17.87 | 11.24 | 32.01 | 3.46 |
1799 | 1982 | 5.128008 | GGTAGCTGATTCAGAACTACTTCCT | 59.872 | 44.000 | 17.87 | 4.19 | 32.01 | 3.36 |
1800 | 1983 | 5.337578 | AGCTGATTCAGAACTACTTCCTC | 57.662 | 43.478 | 17.87 | 0.00 | 32.44 | 3.71 |
1801 | 1984 | 4.161377 | AGCTGATTCAGAACTACTTCCTCC | 59.839 | 45.833 | 17.87 | 0.00 | 32.44 | 4.30 |
1802 | 1985 | 4.677584 | CTGATTCAGAACTACTTCCTCCG | 58.322 | 47.826 | 8.00 | 0.00 | 32.44 | 4.63 |
1803 | 1986 | 4.087182 | TGATTCAGAACTACTTCCTCCGT | 58.913 | 43.478 | 0.00 | 0.00 | 0.00 | 4.69 |
1804 | 1987 | 5.258841 | TGATTCAGAACTACTTCCTCCGTA | 58.741 | 41.667 | 0.00 | 0.00 | 0.00 | 4.02 |
1805 | 1988 | 5.713389 | TGATTCAGAACTACTTCCTCCGTAA | 59.287 | 40.000 | 0.00 | 0.00 | 0.00 | 3.18 |
1806 | 1989 | 6.209986 | TGATTCAGAACTACTTCCTCCGTAAA | 59.790 | 38.462 | 0.00 | 0.00 | 0.00 | 2.01 |
1807 | 1990 | 5.382618 | TCAGAACTACTTCCTCCGTAAAC | 57.617 | 43.478 | 0.00 | 0.00 | 0.00 | 2.01 |
1808 | 1991 | 5.075493 | TCAGAACTACTTCCTCCGTAAACT | 58.925 | 41.667 | 0.00 | 0.00 | 0.00 | 2.66 |
1809 | 1992 | 6.240894 | TCAGAACTACTTCCTCCGTAAACTA | 58.759 | 40.000 | 0.00 | 0.00 | 0.00 | 2.24 |
1810 | 1993 | 6.716628 | TCAGAACTACTTCCTCCGTAAACTAA | 59.283 | 38.462 | 0.00 | 0.00 | 0.00 | 2.24 |
1811 | 1994 | 7.395489 | TCAGAACTACTTCCTCCGTAAACTAAT | 59.605 | 37.037 | 0.00 | 0.00 | 0.00 | 1.73 |
1812 | 1995 | 8.680903 | CAGAACTACTTCCTCCGTAAACTAATA | 58.319 | 37.037 | 0.00 | 0.00 | 0.00 | 0.98 |
1813 | 1996 | 9.418839 | AGAACTACTTCCTCCGTAAACTAATAT | 57.581 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
1819 | 2002 | 9.418839 | ACTTCCTCCGTAAACTAATATAAGAGT | 57.581 | 33.333 | 0.00 | 0.00 | 0.00 | 3.24 |
1820 | 2003 | 9.680315 | CTTCCTCCGTAAACTAATATAAGAGTG | 57.320 | 37.037 | 0.00 | 0.00 | 0.00 | 3.51 |
1821 | 2004 | 8.757982 | TCCTCCGTAAACTAATATAAGAGTGT | 57.242 | 34.615 | 0.00 | 0.00 | 0.00 | 3.55 |
1822 | 2005 | 9.193806 | TCCTCCGTAAACTAATATAAGAGTGTT | 57.806 | 33.333 | 0.00 | 0.00 | 0.00 | 3.32 |
1823 | 2006 | 9.813446 | CCTCCGTAAACTAATATAAGAGTGTTT | 57.187 | 33.333 | 0.00 | 0.00 | 0.00 | 2.83 |
1891 | 2074 | 8.091449 | ACAGAGGAAGTAGTTTTCATGAGTAAG | 58.909 | 37.037 | 0.00 | 0.00 | 0.00 | 2.34 |
1914 | 2097 | 7.121974 | AGTATGAATCGAGGATTATTTTGCG | 57.878 | 36.000 | 0.00 | 0.00 | 31.89 | 4.85 |
1916 | 2099 | 4.447290 | TGAATCGAGGATTATTTTGCGGA | 58.553 | 39.130 | 0.00 | 0.00 | 31.89 | 5.54 |
1957 | 2140 | 6.035327 | GCTGTATTTGAATTGGTCTGAATTGC | 59.965 | 38.462 | 0.00 | 0.00 | 0.00 | 3.56 |
2003 | 2187 | 6.928520 | TCCTGTTAAGGTTACTACTTAGTGC | 58.071 | 40.000 | 0.00 | 0.00 | 44.82 | 4.40 |
2005 | 2189 | 6.812160 | CCTGTTAAGGTTACTACTTAGTGCTG | 59.188 | 42.308 | 0.00 | 0.00 | 38.96 | 4.41 |
2205 | 2390 | 7.480760 | AATTGCCCTAACTGTATTGAACATT | 57.519 | 32.000 | 0.00 | 0.00 | 37.50 | 2.71 |
2367 | 2552 | 5.520748 | ACTTAACAGGGAAGATGGTCATT | 57.479 | 39.130 | 0.00 | 0.00 | 0.00 | 2.57 |
2475 | 2662 | 6.875726 | TCCTTTACAGATGTCTCATTCTTGTG | 59.124 | 38.462 | 0.00 | 0.00 | 0.00 | 3.33 |
2577 | 2764 | 3.568007 | TGCAGGTAAAGTTCACATTGTCC | 59.432 | 43.478 | 0.00 | 0.00 | 0.00 | 4.02 |
2584 | 2771 | 0.238289 | GTTCACATTGTCCGTGGCTG | 59.762 | 55.000 | 0.00 | 0.00 | 35.03 | 4.85 |
2595 | 2782 | 1.510844 | CGTGGCTGCCCATTTTACC | 59.489 | 57.895 | 17.53 | 0.00 | 44.51 | 2.85 |
2606 | 2793 | 3.825328 | CCCATTTTACCTGATGGAGGAG | 58.175 | 50.000 | 4.02 | 0.00 | 46.33 | 3.69 |
2656 | 2843 | 7.132213 | CCACACTATTTTGTTACTCACACTTG | 58.868 | 38.462 | 0.00 | 0.00 | 33.98 | 3.16 |
2661 | 2848 | 8.120465 | ACTATTTTGTTACTCACACTTGAAACG | 58.880 | 33.333 | 0.00 | 0.00 | 33.98 | 3.60 |
2681 | 2868 | 2.351726 | CGAATTGCAGCTAAGTGGTACC | 59.648 | 50.000 | 4.43 | 4.43 | 0.00 | 3.34 |
2927 | 3129 | 4.130857 | CTCCTATAGCTCGACAAGTCAGA | 58.869 | 47.826 | 0.00 | 0.00 | 0.00 | 3.27 |
2961 | 3163 | 3.990959 | TGTGGCAGTGTCATATGGTTA | 57.009 | 42.857 | 0.00 | 0.00 | 0.00 | 2.85 |
2967 | 3169 | 5.365314 | TGGCAGTGTCATATGGTTACTGATA | 59.635 | 40.000 | 25.47 | 16.07 | 40.80 | 2.15 |
3010 | 3212 | 2.877786 | CACATATGCGAGTTAATGGCCA | 59.122 | 45.455 | 8.56 | 8.56 | 0.00 | 5.36 |
3036 | 3239 | 4.142403 | TGCCATAACTATCTGTTTTGCTGC | 60.142 | 41.667 | 0.00 | 0.00 | 39.89 | 5.25 |
3038 | 3241 | 5.393461 | GCCATAACTATCTGTTTTGCTGCTT | 60.393 | 40.000 | 0.00 | 0.00 | 39.89 | 3.91 |
3041 | 3244 | 4.756084 | ACTATCTGTTTTGCTGCTTGTC | 57.244 | 40.909 | 0.00 | 0.00 | 0.00 | 3.18 |
3042 | 3245 | 2.693797 | ATCTGTTTTGCTGCTTGTCG | 57.306 | 45.000 | 0.00 | 0.00 | 0.00 | 4.35 |
3129 | 3332 | 1.612726 | GCCTGAAGAGCACATGGACTT | 60.613 | 52.381 | 0.00 | 0.00 | 0.00 | 3.01 |
3257 | 3461 | 5.423015 | TCTAGTTCTGCATCCTGAATGAAC | 58.577 | 41.667 | 3.68 | 3.68 | 37.59 | 3.18 |
3263 | 3467 | 2.097954 | TGCATCCTGAATGAACGAATGC | 59.902 | 45.455 | 0.00 | 0.00 | 37.59 | 3.56 |
3287 | 3491 | 1.139163 | CTTGCATGTTTGAAACGGCC | 58.861 | 50.000 | 17.78 | 0.00 | 34.57 | 6.13 |
3288 | 3492 | 0.461548 | TTGCATGTTTGAAACGGCCA | 59.538 | 45.000 | 17.78 | 7.80 | 34.57 | 5.36 |
3307 | 3511 | 3.639538 | CCAATTGCTGATTGCTGATAGC | 58.360 | 45.455 | 0.00 | 0.00 | 43.11 | 2.97 |
3366 | 3570 | 7.188834 | TGTCTGAATTGCAATGATCGTATTTC | 58.811 | 34.615 | 13.82 | 4.72 | 0.00 | 2.17 |
3544 | 3748 | 3.303593 | CGTTCATAGGTTGATGCATGCTC | 60.304 | 47.826 | 20.33 | 13.98 | 33.34 | 4.26 |
3660 | 3864 | 4.867047 | GCATATCACCGTATCCTGAATGAG | 59.133 | 45.833 | 0.00 | 0.00 | 0.00 | 2.90 |
3743 | 3947 | 5.807011 | GGCTGTTGGATATGTTTTGATGTTC | 59.193 | 40.000 | 0.00 | 0.00 | 0.00 | 3.18 |
3749 | 3953 | 9.781834 | GTTGGATATGTTTTGATGTTCGAAATA | 57.218 | 29.630 | 0.00 | 0.00 | 32.83 | 1.40 |
3780 | 3984 | 7.148656 | GGTTGTATTTGCGCAATTTGAACTATT | 60.149 | 33.333 | 25.64 | 0.00 | 0.00 | 1.73 |
3784 | 3988 | 9.833894 | GTATTTGCGCAATTTGAACTATTTATG | 57.166 | 29.630 | 25.64 | 0.00 | 0.00 | 1.90 |
3842 | 4046 | 4.024641 | TGTTGCATGATCGAAGACATATGC | 60.025 | 41.667 | 1.58 | 0.00 | 44.84 | 3.14 |
3848 | 4053 | 5.205759 | TGATCGAAGACATATGCAGTGAT | 57.794 | 39.130 | 1.58 | 0.35 | 42.51 | 3.06 |
3928 | 4139 | 2.229784 | GCATTGAACTAGCAAGCCAAGT | 59.770 | 45.455 | 0.00 | 0.00 | 0.00 | 3.16 |
3929 | 4140 | 3.305608 | GCATTGAACTAGCAAGCCAAGTT | 60.306 | 43.478 | 9.37 | 9.37 | 36.20 | 2.66 |
3930 | 4141 | 4.797275 | GCATTGAACTAGCAAGCCAAGTTT | 60.797 | 41.667 | 10.53 | 0.00 | 33.72 | 2.66 |
3931 | 4142 | 3.988379 | TGAACTAGCAAGCCAAGTTTG | 57.012 | 42.857 | 10.53 | 0.00 | 33.72 | 2.93 |
3932 | 4143 | 3.287222 | TGAACTAGCAAGCCAAGTTTGT | 58.713 | 40.909 | 10.53 | 0.00 | 33.72 | 2.83 |
3933 | 4144 | 3.066621 | TGAACTAGCAAGCCAAGTTTGTG | 59.933 | 43.478 | 10.53 | 0.00 | 33.72 | 3.33 |
3950 | 4161 | 5.416952 | AGTTTGTGGATCAGACCATTGATTC | 59.583 | 40.000 | 0.00 | 0.00 | 42.17 | 2.52 |
3952 | 4163 | 5.955961 | TGTGGATCAGACCATTGATTCTA | 57.044 | 39.130 | 0.00 | 0.00 | 42.17 | 2.10 |
3953 | 4164 | 6.312141 | TGTGGATCAGACCATTGATTCTAA | 57.688 | 37.500 | 0.00 | 0.00 | 42.17 | 2.10 |
3955 | 4166 | 6.825213 | TGTGGATCAGACCATTGATTCTAAAG | 59.175 | 38.462 | 0.00 | 0.00 | 42.17 | 1.85 |
3956 | 4167 | 6.825721 | GTGGATCAGACCATTGATTCTAAAGT | 59.174 | 38.462 | 0.00 | 0.00 | 42.17 | 2.66 |
3957 | 4168 | 6.825213 | TGGATCAGACCATTGATTCTAAAGTG | 59.175 | 38.462 | 0.00 | 0.00 | 37.90 | 3.16 |
3971 | 4210 | 7.334421 | TGATTCTAAAGTGTAAGTTCAGGCATC | 59.666 | 37.037 | 0.00 | 0.00 | 0.00 | 3.91 |
3972 | 4211 | 5.168569 | TCTAAAGTGTAAGTTCAGGCATCG | 58.831 | 41.667 | 0.00 | 0.00 | 0.00 | 3.84 |
3973 | 4212 | 3.402628 | AAGTGTAAGTTCAGGCATCGT | 57.597 | 42.857 | 0.00 | 0.00 | 0.00 | 3.73 |
3974 | 4213 | 3.402628 | AGTGTAAGTTCAGGCATCGTT | 57.597 | 42.857 | 0.00 | 0.00 | 0.00 | 3.85 |
3976 | 4215 | 2.092211 | GTGTAAGTTCAGGCATCGTTCG | 59.908 | 50.000 | 0.00 | 0.00 | 0.00 | 3.95 |
3977 | 4216 | 1.659098 | GTAAGTTCAGGCATCGTTCGG | 59.341 | 52.381 | 0.00 | 0.00 | 0.00 | 4.30 |
3978 | 4217 | 0.034896 | AAGTTCAGGCATCGTTCGGT | 59.965 | 50.000 | 0.00 | 0.00 | 0.00 | 4.69 |
3980 | 4219 | 0.872388 | GTTCAGGCATCGTTCGGTTT | 59.128 | 50.000 | 0.00 | 0.00 | 0.00 | 3.27 |
3984 | 4257 | 2.167693 | TCAGGCATCGTTCGGTTTCTAT | 59.832 | 45.455 | 0.00 | 0.00 | 0.00 | 1.98 |
4035 | 4311 | 7.214467 | TCCGAGATAAAGAAAAACAAGCAAT | 57.786 | 32.000 | 0.00 | 0.00 | 0.00 | 3.56 |
4046 | 4322 | 8.842358 | AGAAAAACAAGCAATGAATCATGAAT | 57.158 | 26.923 | 0.00 | 0.00 | 0.00 | 2.57 |
4098 | 4374 | 3.131755 | TGCCATGTTGAATGTTGACACAA | 59.868 | 39.130 | 0.00 | 0.00 | 36.16 | 3.33 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
29 | 30 | 1.259770 | CGATTGACGAGGCATGACATG | 59.740 | 52.381 | 11.27 | 11.27 | 45.77 | 3.21 |
30 | 31 | 1.134699 | ACGATTGACGAGGCATGACAT | 60.135 | 47.619 | 0.00 | 0.00 | 45.77 | 3.06 |
32 | 33 | 0.924090 | GACGATTGACGAGGCATGAC | 59.076 | 55.000 | 0.00 | 0.00 | 45.77 | 3.06 |
33 | 34 | 0.530288 | TGACGATTGACGAGGCATGA | 59.470 | 50.000 | 0.00 | 0.00 | 45.77 | 3.07 |
34 | 35 | 1.524355 | GATGACGATTGACGAGGCATG | 59.476 | 52.381 | 0.00 | 0.00 | 45.77 | 4.06 |
35 | 36 | 1.410517 | AGATGACGATTGACGAGGCAT | 59.589 | 47.619 | 0.00 | 0.00 | 45.77 | 4.40 |
36 | 37 | 0.817654 | AGATGACGATTGACGAGGCA | 59.182 | 50.000 | 0.00 | 0.00 | 45.77 | 4.75 |
37 | 38 | 1.927895 | AAGATGACGATTGACGAGGC | 58.072 | 50.000 | 0.00 | 0.00 | 45.77 | 4.70 |
38 | 39 | 2.029728 | GCAAAGATGACGATTGACGAGG | 59.970 | 50.000 | 0.00 | 0.00 | 45.77 | 4.63 |
39 | 40 | 2.926200 | AGCAAAGATGACGATTGACGAG | 59.074 | 45.455 | 0.00 | 0.00 | 45.77 | 4.18 |
40 | 41 | 2.959516 | AGCAAAGATGACGATTGACGA | 58.040 | 42.857 | 0.00 | 0.00 | 45.77 | 4.20 |
42 | 43 | 4.433615 | TCCTAGCAAAGATGACGATTGAC | 58.566 | 43.478 | 0.00 | 0.00 | 0.00 | 3.18 |
43 | 44 | 4.402474 | TCTCCTAGCAAAGATGACGATTGA | 59.598 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
44 | 45 | 4.686972 | TCTCCTAGCAAAGATGACGATTG | 58.313 | 43.478 | 0.00 | 0.00 | 0.00 | 2.67 |
45 | 46 | 5.543507 | ATCTCCTAGCAAAGATGACGATT | 57.456 | 39.130 | 0.00 | 0.00 | 31.09 | 3.34 |
46 | 47 | 5.163364 | ACAATCTCCTAGCAAAGATGACGAT | 60.163 | 40.000 | 0.00 | 0.00 | 32.62 | 3.73 |
117 | 118 | 2.449464 | TCGCTAGGCACTTGGTTACTA | 58.551 | 47.619 | 0.00 | 0.00 | 41.75 | 1.82 |
128 | 129 | 0.323302 | TTGTCACCATTCGCTAGGCA | 59.677 | 50.000 | 0.00 | 0.00 | 0.00 | 4.75 |
136 | 176 | 3.383620 | TGCACCATTTTGTCACCATTC | 57.616 | 42.857 | 0.00 | 0.00 | 0.00 | 2.67 |
179 | 219 | 8.625651 | TGTAGATCGTTTCAATTCCAAAAGAAA | 58.374 | 29.630 | 0.00 | 0.00 | 38.21 | 2.52 |
180 | 220 | 8.160521 | TGTAGATCGTTTCAATTCCAAAAGAA | 57.839 | 30.769 | 0.92 | 0.00 | 39.32 | 2.52 |
181 | 221 | 7.737972 | TGTAGATCGTTTCAATTCCAAAAGA | 57.262 | 32.000 | 0.00 | 0.00 | 0.00 | 2.52 |
182 | 222 | 9.490663 | GTATGTAGATCGTTTCAATTCCAAAAG | 57.509 | 33.333 | 0.00 | 0.00 | 0.00 | 2.27 |
188 | 233 | 6.292168 | CGTGGGTATGTAGATCGTTTCAATTC | 60.292 | 42.308 | 0.00 | 0.00 | 0.00 | 2.17 |
227 | 287 | 7.738437 | AAATTCCATTCTCAAATACACCCAT | 57.262 | 32.000 | 0.00 | 0.00 | 0.00 | 4.00 |
328 | 388 | 5.828328 | AGCTTACAAAAACTCTTAAGCCACT | 59.172 | 36.000 | 8.25 | 0.00 | 45.01 | 4.00 |
387 | 447 | 8.592105 | ATGGGCATTCGTTTTATGAAAATATG | 57.408 | 30.769 | 0.00 | 0.00 | 32.22 | 1.78 |
557 | 634 | 8.759641 | TCAAAATAAAATTTCATTCCACACACG | 58.240 | 29.630 | 0.00 | 0.00 | 0.00 | 4.49 |
696 | 828 | 8.795842 | AGGTTGTGTGATATACCGATTAAAAA | 57.204 | 30.769 | 0.00 | 0.00 | 35.80 | 1.94 |
697 | 829 | 8.795842 | AAGGTTGTGTGATATACCGATTAAAA | 57.204 | 30.769 | 0.00 | 0.00 | 35.80 | 1.52 |
698 | 830 | 8.795842 | AAAGGTTGTGTGATATACCGATTAAA | 57.204 | 30.769 | 0.00 | 0.00 | 35.80 | 1.52 |
699 | 831 | 7.496591 | GGAAAGGTTGTGTGATATACCGATTAA | 59.503 | 37.037 | 0.00 | 0.00 | 35.80 | 1.40 |
700 | 832 | 6.987992 | GGAAAGGTTGTGTGATATACCGATTA | 59.012 | 38.462 | 0.00 | 0.00 | 35.80 | 1.75 |
701 | 833 | 5.820947 | GGAAAGGTTGTGTGATATACCGATT | 59.179 | 40.000 | 0.00 | 0.00 | 35.80 | 3.34 |
702 | 834 | 5.365619 | GGAAAGGTTGTGTGATATACCGAT | 58.634 | 41.667 | 0.00 | 0.00 | 35.80 | 4.18 |
703 | 835 | 4.678574 | CGGAAAGGTTGTGTGATATACCGA | 60.679 | 45.833 | 0.00 | 0.00 | 38.09 | 4.69 |
704 | 836 | 3.554324 | CGGAAAGGTTGTGTGATATACCG | 59.446 | 47.826 | 0.00 | 0.00 | 35.80 | 4.02 |
705 | 837 | 4.510571 | ACGGAAAGGTTGTGTGATATACC | 58.489 | 43.478 | 0.00 | 0.00 | 0.00 | 2.73 |
706 | 838 | 6.101332 | TGTACGGAAAGGTTGTGTGATATAC | 58.899 | 40.000 | 0.00 | 0.00 | 0.00 | 1.47 |
707 | 839 | 6.283544 | TGTACGGAAAGGTTGTGTGATATA | 57.716 | 37.500 | 0.00 | 0.00 | 0.00 | 0.86 |
708 | 840 | 5.155278 | TGTACGGAAAGGTTGTGTGATAT | 57.845 | 39.130 | 0.00 | 0.00 | 0.00 | 1.63 |
709 | 841 | 4.603989 | TGTACGGAAAGGTTGTGTGATA | 57.396 | 40.909 | 0.00 | 0.00 | 0.00 | 2.15 |
710 | 842 | 3.478857 | TGTACGGAAAGGTTGTGTGAT | 57.521 | 42.857 | 0.00 | 0.00 | 0.00 | 3.06 |
711 | 843 | 2.983907 | TGTACGGAAAGGTTGTGTGA | 57.016 | 45.000 | 0.00 | 0.00 | 0.00 | 3.58 |
717 | 849 | 2.172851 | TTCGCATGTACGGAAAGGTT | 57.827 | 45.000 | 0.00 | 0.00 | 0.00 | 3.50 |
785 | 918 | 4.568592 | CCCAGAAGGCCAGAACTTTTAGAT | 60.569 | 45.833 | 5.01 | 0.00 | 0.00 | 1.98 |
790 | 923 | 3.753787 | CCCAGAAGGCCAGAACTTT | 57.246 | 52.632 | 5.01 | 0.00 | 0.00 | 2.66 |
800 | 933 | 0.323629 | TCGGTTACAAGCCCAGAAGG | 59.676 | 55.000 | 0.00 | 0.00 | 39.47 | 3.46 |
801 | 934 | 1.439679 | GTCGGTTACAAGCCCAGAAG | 58.560 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 |
832 | 965 | 2.645394 | TATTGATGGGCTGGGCTGGC | 62.645 | 60.000 | 0.00 | 0.00 | 0.00 | 4.85 |
833 | 966 | 0.106066 | TTATTGATGGGCTGGGCTGG | 60.106 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
834 | 967 | 1.410153 | GTTTATTGATGGGCTGGGCTG | 59.590 | 52.381 | 0.00 | 0.00 | 0.00 | 4.85 |
835 | 968 | 1.689258 | GGTTTATTGATGGGCTGGGCT | 60.689 | 52.381 | 0.00 | 0.00 | 0.00 | 5.19 |
906 | 1041 | 3.071206 | GAGGAGAGGCTGCCGTGA | 61.071 | 66.667 | 13.96 | 0.00 | 0.00 | 4.35 |
985 | 1123 | 2.725008 | CATCGGAGGAGACGAGCC | 59.275 | 66.667 | 0.00 | 0.00 | 44.24 | 4.70 |
1009 | 1147 | 0.840729 | GTACAGAGAGCGCGAAATCG | 59.159 | 55.000 | 12.10 | 0.00 | 43.27 | 3.34 |
1138 | 1276 | 6.294453 | CCATCACACAACCAATACTAGCAAAA | 60.294 | 38.462 | 0.00 | 0.00 | 0.00 | 2.44 |
1141 | 1279 | 4.260985 | CCATCACACAACCAATACTAGCA | 58.739 | 43.478 | 0.00 | 0.00 | 0.00 | 3.49 |
1161 | 1299 | 1.002533 | GGCCTACCTACTGGACCCA | 59.997 | 63.158 | 0.00 | 0.00 | 37.04 | 4.51 |
1178 | 1326 | 1.734465 | GTGGCTCTCAAGAATCAACGG | 59.266 | 52.381 | 0.00 | 0.00 | 0.00 | 4.44 |
1182 | 1330 | 1.280133 | CCCAGTGGCTCTCAAGAATCA | 59.720 | 52.381 | 2.61 | 0.00 | 0.00 | 2.57 |
1188 | 1336 | 1.548357 | GCTCTCCCAGTGGCTCTCAA | 61.548 | 60.000 | 2.61 | 0.00 | 0.00 | 3.02 |
1191 | 1339 | 3.073735 | CGCTCTCCCAGTGGCTCT | 61.074 | 66.667 | 2.61 | 0.00 | 0.00 | 4.09 |
1256 | 1406 | 1.208165 | AGGAAGGGGTTACTGGCTGG | 61.208 | 60.000 | 0.00 | 0.00 | 0.00 | 4.85 |
1275 | 1429 | 6.459066 | GCTCACACCAGAATAATAGCAGATA | 58.541 | 40.000 | 0.00 | 0.00 | 0.00 | 1.98 |
1299 | 1453 | 1.746470 | TGCAGATGAAGCATCACTGG | 58.254 | 50.000 | 17.25 | 3.47 | 42.72 | 4.00 |
1308 | 1462 | 1.471287 | CACCACACCATGCAGATGAAG | 59.529 | 52.381 | 0.00 | 0.00 | 0.00 | 3.02 |
1309 | 1463 | 1.536940 | CACCACACCATGCAGATGAA | 58.463 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
1310 | 1464 | 0.322726 | CCACCACACCATGCAGATGA | 60.323 | 55.000 | 0.00 | 0.00 | 0.00 | 2.92 |
1311 | 1465 | 1.940883 | GCCACCACACCATGCAGATG | 61.941 | 60.000 | 0.00 | 0.00 | 0.00 | 2.90 |
1312 | 1466 | 1.679977 | GCCACCACACCATGCAGAT | 60.680 | 57.895 | 0.00 | 0.00 | 0.00 | 2.90 |
1313 | 1467 | 2.282391 | GCCACCACACCATGCAGA | 60.282 | 61.111 | 0.00 | 0.00 | 0.00 | 4.26 |
1324 | 1478 | 3.215568 | CCACGTTTGCAGCCACCA | 61.216 | 61.111 | 0.00 | 0.00 | 0.00 | 4.17 |
1346 | 1500 | 2.202676 | GACGCTCAGAGCTTCGGG | 60.203 | 66.667 | 20.39 | 6.77 | 39.60 | 5.14 |
1347 | 1501 | 2.202676 | GGACGCTCAGAGCTTCGG | 60.203 | 66.667 | 20.39 | 7.15 | 40.03 | 4.30 |
1348 | 1502 | 1.515952 | CAGGACGCTCAGAGCTTCG | 60.516 | 63.158 | 20.39 | 7.51 | 40.03 | 3.79 |
1349 | 1503 | 1.809209 | GCAGGACGCTCAGAGCTTC | 60.809 | 63.158 | 20.39 | 19.44 | 39.60 | 3.86 |
1350 | 1504 | 2.264166 | GCAGGACGCTCAGAGCTT | 59.736 | 61.111 | 20.39 | 11.34 | 39.60 | 3.74 |
1351 | 1505 | 3.768922 | GGCAGGACGCTCAGAGCT | 61.769 | 66.667 | 20.39 | 7.43 | 39.60 | 4.09 |
1353 | 1507 | 3.691744 | GACGGCAGGACGCTCAGAG | 62.692 | 68.421 | 0.00 | 0.00 | 41.91 | 3.35 |
1354 | 1508 | 3.749064 | GACGGCAGGACGCTCAGA | 61.749 | 66.667 | 0.00 | 0.00 | 41.91 | 3.27 |
1357 | 1511 | 4.838486 | CTCGACGGCAGGACGCTC | 62.838 | 72.222 | 0.00 | 0.00 | 41.91 | 5.03 |
1361 | 1515 | 1.078759 | CACAATCTCGACGGCAGGAC | 61.079 | 60.000 | 0.00 | 0.00 | 0.00 | 3.85 |
1363 | 1517 | 1.811266 | CCACAATCTCGACGGCAGG | 60.811 | 63.158 | 0.00 | 0.00 | 0.00 | 4.85 |
1368 | 1522 | 1.068474 | GACAACCCACAATCTCGACG | 58.932 | 55.000 | 0.00 | 0.00 | 0.00 | 5.12 |
1371 | 1525 | 2.698803 | TGATGACAACCCACAATCTCG | 58.301 | 47.619 | 0.00 | 0.00 | 0.00 | 4.04 |
1382 | 1536 | 3.560068 | ACGGACAGACTTTTGATGACAAC | 59.440 | 43.478 | 0.00 | 0.00 | 35.63 | 3.32 |
1387 | 1541 | 5.339990 | ACAAAAACGGACAGACTTTTGATG | 58.660 | 37.500 | 17.33 | 0.94 | 38.40 | 3.07 |
1419 | 1573 | 2.676471 | ACCCAGCAATGGTTCGCC | 60.676 | 61.111 | 0.00 | 0.00 | 29.75 | 5.54 |
1425 | 1579 | 0.901580 | AGCCAAAGACCCAGCAATGG | 60.902 | 55.000 | 0.00 | 0.00 | 0.00 | 3.16 |
1464 | 1621 | 1.264557 | CGATGTCGCGACCTTCTAGAT | 59.735 | 52.381 | 34.34 | 20.04 | 0.00 | 1.98 |
1475 | 1632 | 3.554692 | GCCCTTGACGATGTCGCG | 61.555 | 66.667 | 0.00 | 0.00 | 44.43 | 5.87 |
1558 | 1739 | 4.637534 | TGGAGCAGCAGATACAGAATTTTC | 59.362 | 41.667 | 0.00 | 0.00 | 0.00 | 2.29 |
1587 | 1768 | 1.354506 | CAGCCTAATTGCAGCGCTC | 59.645 | 57.895 | 7.13 | 2.98 | 0.00 | 5.03 |
1588 | 1769 | 2.117156 | CCAGCCTAATTGCAGCGCT | 61.117 | 57.895 | 2.64 | 2.64 | 0.00 | 5.92 |
1589 | 1770 | 2.410469 | CCAGCCTAATTGCAGCGC | 59.590 | 61.111 | 0.00 | 0.00 | 0.00 | 5.92 |
1590 | 1771 | 2.484062 | CCCCAGCCTAATTGCAGCG | 61.484 | 63.158 | 0.00 | 0.00 | 0.00 | 5.18 |
1591 | 1772 | 0.106719 | TACCCCAGCCTAATTGCAGC | 60.107 | 55.000 | 0.00 | 0.00 | 0.00 | 5.25 |
1603 | 1784 | 5.780793 | AGGATTAGTAATAGCACTACCCCAG | 59.219 | 44.000 | 0.00 | 0.00 | 30.76 | 4.45 |
1639 | 1822 | 9.313118 | GTGACCAAAAGAACAGTTCAAAATATT | 57.687 | 29.630 | 15.85 | 0.00 | 0.00 | 1.28 |
1640 | 1823 | 8.474025 | TGTGACCAAAAGAACAGTTCAAAATAT | 58.526 | 29.630 | 15.85 | 0.00 | 0.00 | 1.28 |
1643 | 1826 | 6.090483 | TGTGACCAAAAGAACAGTTCAAAA | 57.910 | 33.333 | 15.85 | 0.00 | 0.00 | 2.44 |
1647 | 1830 | 3.128589 | TGCTGTGACCAAAAGAACAGTTC | 59.871 | 43.478 | 5.00 | 5.00 | 41.65 | 3.01 |
1663 | 1846 | 2.160219 | ACGCATACAATTCTGTGCTGTG | 59.840 | 45.455 | 1.36 | 0.00 | 36.96 | 3.66 |
1682 | 1865 | 1.671328 | TCAGCAGAGAAGTATCGGACG | 59.329 | 52.381 | 0.00 | 0.00 | 0.00 | 4.79 |
1686 | 1869 | 5.886715 | CTGAATTCAGCAGAGAAGTATCG | 57.113 | 43.478 | 21.96 | 0.00 | 37.15 | 2.92 |
1725 | 1908 | 6.291377 | ACACTAGGCTTATACCAACATGATG | 58.709 | 40.000 | 0.00 | 0.00 | 0.00 | 3.07 |
1793 | 1976 | 9.418839 | ACTCTTATATTAGTTTACGGAGGAAGT | 57.581 | 33.333 | 0.00 | 0.00 | 0.00 | 3.01 |
1794 | 1977 | 9.680315 | CACTCTTATATTAGTTTACGGAGGAAG | 57.320 | 37.037 | 0.00 | 0.00 | 0.00 | 3.46 |
1795 | 1978 | 9.193806 | ACACTCTTATATTAGTTTACGGAGGAA | 57.806 | 33.333 | 0.00 | 0.00 | 0.00 | 3.36 |
1796 | 1979 | 8.757982 | ACACTCTTATATTAGTTTACGGAGGA | 57.242 | 34.615 | 0.00 | 0.00 | 0.00 | 3.71 |
1797 | 1980 | 9.813446 | AAACACTCTTATATTAGTTTACGGAGG | 57.187 | 33.333 | 0.00 | 0.00 | 0.00 | 4.30 |
1859 | 2042 | 9.706691 | CATGAAAACTACTTCCTCTGTAAACTA | 57.293 | 33.333 | 0.00 | 0.00 | 0.00 | 2.24 |
1860 | 2043 | 8.429641 | TCATGAAAACTACTTCCTCTGTAAACT | 58.570 | 33.333 | 0.00 | 0.00 | 0.00 | 2.66 |
1861 | 2044 | 8.603242 | TCATGAAAACTACTTCCTCTGTAAAC | 57.397 | 34.615 | 0.00 | 0.00 | 0.00 | 2.01 |
1862 | 2045 | 8.429641 | ACTCATGAAAACTACTTCCTCTGTAAA | 58.570 | 33.333 | 0.00 | 0.00 | 0.00 | 2.01 |
1863 | 2046 | 7.963532 | ACTCATGAAAACTACTTCCTCTGTAA | 58.036 | 34.615 | 0.00 | 0.00 | 0.00 | 2.41 |
1864 | 2047 | 7.540474 | ACTCATGAAAACTACTTCCTCTGTA | 57.460 | 36.000 | 0.00 | 0.00 | 0.00 | 2.74 |
1865 | 2048 | 6.426646 | ACTCATGAAAACTACTTCCTCTGT | 57.573 | 37.500 | 0.00 | 0.00 | 0.00 | 3.41 |
1866 | 2049 | 8.091449 | ACTTACTCATGAAAACTACTTCCTCTG | 58.909 | 37.037 | 0.00 | 0.00 | 0.00 | 3.35 |
1867 | 2050 | 8.196378 | ACTTACTCATGAAAACTACTTCCTCT | 57.804 | 34.615 | 0.00 | 0.00 | 0.00 | 3.69 |
1869 | 2052 | 9.877178 | CATACTTACTCATGAAAACTACTTCCT | 57.123 | 33.333 | 0.00 | 0.00 | 0.00 | 3.36 |
1870 | 2053 | 9.871238 | TCATACTTACTCATGAAAACTACTTCC | 57.129 | 33.333 | 0.00 | 0.00 | 0.00 | 3.46 |
1891 | 2074 | 6.147164 | TCCGCAAAATAATCCTCGATTCATAC | 59.853 | 38.462 | 0.00 | 0.00 | 33.95 | 2.39 |
1912 | 2095 | 4.883354 | CCCAGCAATCCCCTCCGC | 62.883 | 72.222 | 0.00 | 0.00 | 0.00 | 5.54 |
1914 | 2097 | 1.380380 | CAACCCAGCAATCCCCTCC | 60.380 | 63.158 | 0.00 | 0.00 | 0.00 | 4.30 |
1916 | 2099 | 2.037847 | GCAACCCAGCAATCCCCT | 59.962 | 61.111 | 0.00 | 0.00 | 0.00 | 4.79 |
2003 | 2187 | 2.288579 | TGCAAATCAAGGAAGCAAGCAG | 60.289 | 45.455 | 0.00 | 0.00 | 31.42 | 4.24 |
2005 | 2189 | 2.443887 | TGCAAATCAAGGAAGCAAGC | 57.556 | 45.000 | 0.00 | 0.00 | 31.42 | 4.01 |
2367 | 2552 | 0.178967 | TGCCCCATTTCAGCTTGACA | 60.179 | 50.000 | 0.00 | 0.00 | 0.00 | 3.58 |
2475 | 2662 | 2.945447 | TTAGCACAATTGAGGCATGC | 57.055 | 45.000 | 22.28 | 9.90 | 36.52 | 4.06 |
2577 | 2764 | 0.965363 | AGGTAAAATGGGCAGCCACG | 60.965 | 55.000 | 15.19 | 0.00 | 0.00 | 4.94 |
2584 | 2771 | 2.091885 | TCCTCCATCAGGTAAAATGGGC | 60.092 | 50.000 | 1.80 | 0.00 | 43.95 | 5.36 |
2606 | 2793 | 4.918810 | AATTGACAAAACACAGGGAGTC | 57.081 | 40.909 | 0.00 | 0.00 | 0.00 | 3.36 |
2613 | 2800 | 4.926238 | GTGTGGTGAAATTGACAAAACACA | 59.074 | 37.500 | 17.74 | 12.36 | 36.62 | 3.72 |
2656 | 2843 | 3.058224 | ACCACTTAGCTGCAATTCGTTTC | 60.058 | 43.478 | 1.02 | 0.00 | 0.00 | 2.78 |
2661 | 2848 | 2.351726 | CGGTACCACTTAGCTGCAATTC | 59.648 | 50.000 | 13.54 | 0.00 | 0.00 | 2.17 |
2681 | 2868 | 2.849942 | TGCCCATCAATGTATTCCTCG | 58.150 | 47.619 | 0.00 | 0.00 | 0.00 | 4.63 |
2833 | 3021 | 9.699703 | GGGAGTTTTAGTGTGCAATTTTAAATA | 57.300 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
2834 | 3022 | 8.207545 | TGGGAGTTTTAGTGTGCAATTTTAAAT | 58.792 | 29.630 | 0.00 | 0.00 | 0.00 | 1.40 |
2835 | 3023 | 7.556844 | TGGGAGTTTTAGTGTGCAATTTTAAA | 58.443 | 30.769 | 0.00 | 0.00 | 0.00 | 1.52 |
2836 | 3024 | 7.113658 | TGGGAGTTTTAGTGTGCAATTTTAA | 57.886 | 32.000 | 0.00 | 0.00 | 0.00 | 1.52 |
2837 | 3025 | 6.716934 | TGGGAGTTTTAGTGTGCAATTTTA | 57.283 | 33.333 | 0.00 | 0.00 | 0.00 | 1.52 |
2838 | 3026 | 5.606348 | TGGGAGTTTTAGTGTGCAATTTT | 57.394 | 34.783 | 0.00 | 0.00 | 0.00 | 1.82 |
2849 | 3037 | 8.025445 | CAGAAAATGAGACAATGGGAGTTTTAG | 58.975 | 37.037 | 0.00 | 0.00 | 0.00 | 1.85 |
2927 | 3129 | 2.501723 | CTGCCACATCTACAGTACCCTT | 59.498 | 50.000 | 0.00 | 0.00 | 0.00 | 3.95 |
2976 | 3178 | 7.489160 | ACTCGCATATGTGATGTAAGACTAAA | 58.511 | 34.615 | 18.88 | 0.00 | 33.67 | 1.85 |
2978 | 3180 | 6.635030 | ACTCGCATATGTGATGTAAGACTA | 57.365 | 37.500 | 18.88 | 0.00 | 33.67 | 2.59 |
3010 | 3212 | 6.039047 | CAGCAAAACAGATAGTTATGGCATCT | 59.961 | 38.462 | 1.65 | 0.00 | 40.26 | 2.90 |
3081 | 3284 | 0.895530 | GAATGTCCGTGTCCTCCTCA | 59.104 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
3129 | 3332 | 1.614903 | CAGCAAGCATCAACCAGGAAA | 59.385 | 47.619 | 0.00 | 0.00 | 0.00 | 3.13 |
3214 | 3418 | 7.161404 | ACTAGAGTTAACATGAGTTCAATGCA | 58.839 | 34.615 | 8.61 | 0.00 | 39.15 | 3.96 |
3217 | 3421 | 9.429359 | CAGAACTAGAGTTAACATGAGTTCAAT | 57.571 | 33.333 | 29.00 | 17.45 | 43.29 | 2.57 |
3263 | 3467 | 4.085107 | GCCGTTTCAAACATGCAAGTTAAG | 60.085 | 41.667 | 7.88 | 4.43 | 0.00 | 1.85 |
3295 | 3499 | 3.261390 | AGGATCAGGAGCTATCAGCAATC | 59.739 | 47.826 | 0.38 | 0.00 | 45.56 | 2.67 |
3307 | 3511 | 1.153289 | CCAACGGCAGGATCAGGAG | 60.153 | 63.158 | 0.00 | 0.00 | 0.00 | 3.69 |
3366 | 3570 | 5.921976 | TCAGCAAATACAGTTCAAATTGCAG | 59.078 | 36.000 | 10.45 | 3.16 | 44.08 | 4.41 |
3544 | 3748 | 5.846473 | GCGAAGTTGTTCTTTAGCAGTAAAG | 59.154 | 40.000 | 0.00 | 0.16 | 44.61 | 1.85 |
3649 | 3853 | 6.249911 | AGTTGATCATCACTCATTCAGGAT | 57.750 | 37.500 | 6.55 | 0.00 | 0.00 | 3.24 |
3660 | 3864 | 7.062605 | CCTTAAAACATGCAAGTTGATCATCAC | 59.937 | 37.037 | 8.27 | 0.00 | 0.00 | 3.06 |
3743 | 3947 | 5.115472 | GCGCAAATACAACCATCATATTTCG | 59.885 | 40.000 | 0.30 | 0.00 | 0.00 | 3.46 |
3749 | 3953 | 3.865011 | TTGCGCAAATACAACCATCAT | 57.135 | 38.095 | 22.78 | 0.00 | 0.00 | 2.45 |
3780 | 3984 | 3.006940 | GGTCAGCAATTCCACGACATAA | 58.993 | 45.455 | 0.00 | 0.00 | 0.00 | 1.90 |
3784 | 3988 | 1.131126 | CATGGTCAGCAATTCCACGAC | 59.869 | 52.381 | 0.00 | 0.00 | 33.91 | 4.34 |
3842 | 4046 | 4.406069 | CCAAGTTCATGCGTTAATCACTG | 58.594 | 43.478 | 0.00 | 0.00 | 0.00 | 3.66 |
3848 | 4053 | 2.606795 | GCAAGCCAAGTTCATGCGTTAA | 60.607 | 45.455 | 0.00 | 0.00 | 0.00 | 2.01 |
3928 | 4139 | 5.573219 | AGAATCAATGGTCTGATCCACAAA | 58.427 | 37.500 | 1.87 | 0.00 | 40.51 | 2.83 |
3929 | 4140 | 5.183530 | AGAATCAATGGTCTGATCCACAA | 57.816 | 39.130 | 1.87 | 0.00 | 40.51 | 3.33 |
3930 | 4141 | 4.849813 | AGAATCAATGGTCTGATCCACA | 57.150 | 40.909 | 1.87 | 0.00 | 40.51 | 4.17 |
3931 | 4142 | 6.825721 | ACTTTAGAATCAATGGTCTGATCCAC | 59.174 | 38.462 | 1.87 | 0.00 | 40.51 | 4.02 |
3932 | 4143 | 6.825213 | CACTTTAGAATCAATGGTCTGATCCA | 59.175 | 38.462 | 0.00 | 2.26 | 42.01 | 3.41 |
3933 | 4144 | 6.825721 | ACACTTTAGAATCAATGGTCTGATCC | 59.174 | 38.462 | 0.00 | 0.00 | 34.90 | 3.36 |
3950 | 4161 | 4.929808 | ACGATGCCTGAACTTACACTTTAG | 59.070 | 41.667 | 0.00 | 0.00 | 0.00 | 1.85 |
3952 | 4163 | 3.740115 | ACGATGCCTGAACTTACACTTT | 58.260 | 40.909 | 0.00 | 0.00 | 0.00 | 2.66 |
3953 | 4164 | 3.402628 | ACGATGCCTGAACTTACACTT | 57.597 | 42.857 | 0.00 | 0.00 | 0.00 | 3.16 |
3955 | 4166 | 2.092211 | CGAACGATGCCTGAACTTACAC | 59.908 | 50.000 | 0.00 | 0.00 | 0.00 | 2.90 |
3956 | 4167 | 2.333926 | CGAACGATGCCTGAACTTACA | 58.666 | 47.619 | 0.00 | 0.00 | 0.00 | 2.41 |
3957 | 4168 | 1.659098 | CCGAACGATGCCTGAACTTAC | 59.341 | 52.381 | 0.00 | 0.00 | 0.00 | 2.34 |
3971 | 4210 | 3.978687 | AGGATAGCATAGAAACCGAACG | 58.021 | 45.455 | 0.00 | 0.00 | 0.00 | 3.95 |
4007 | 4280 | 6.088217 | GCTTGTTTTTCTTTATCTCGGAAAGC | 59.912 | 38.462 | 0.00 | 0.00 | 34.51 | 3.51 |
4035 | 4311 | 4.420522 | TCCATCCACGATTCATGATTCA | 57.579 | 40.909 | 15.82 | 0.00 | 0.00 | 2.57 |
4046 | 4322 | 1.945354 | GCGGTCTCTTCCATCCACGA | 61.945 | 60.000 | 0.00 | 0.00 | 0.00 | 4.35 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.