Multiple sequence alignment - TraesCS2B01G350400
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 | TraesCS2B01G350400 | chr2B | 100.000 | 5605 | 0 | 0 | 1 | 5605 | 497794654 | 497800258 | 0.000000e+00 | 10351.0 |
1 | TraesCS2B01G350400 | chr2A | 94.457 | 5015 | 166 | 47 | 1 | 4952 | 564621724 | 564616759 | 0.000000e+00 | 7618.0 |
2 | TraesCS2B01G350400 | chr2A | 84.452 | 283 | 25 | 11 | 5086 | 5367 | 564616629 | 564616365 | 1.550000e-65 | 261.0 |
3 | TraesCS2B01G350400 | chr2A | 87.500 | 128 | 12 | 4 | 5418 | 5541 | 564616356 | 564616229 | 1.630000e-30 | 145.0 |
4 | TraesCS2B01G350400 | chr2A | 100.000 | 32 | 0 | 0 | 5574 | 5605 | 564615874 | 564615843 | 6.060000e-05 | 60.2 |
5 | TraesCS2B01G350400 | chr2D | 93.484 | 5003 | 198 | 64 | 233 | 5186 | 423852695 | 423857618 | 0.000000e+00 | 7315.0 |
6 | TraesCS2B01G350400 | chr2D | 93.820 | 178 | 7 | 2 | 1 | 178 | 423852520 | 423852693 | 1.200000e-66 | 265.0 |
7 | TraesCS2B01G350400 | chr2D | 92.593 | 135 | 8 | 2 | 4947 | 5080 | 423859587 | 423859720 | 5.730000e-45 | 193.0 |
8 | TraesCS2B01G350400 | chr2D | 89.262 | 149 | 8 | 6 | 5217 | 5364 | 423859804 | 423859945 | 4.460000e-41 | 180.0 |
9 | TraesCS2B01G350400 | chr2D | 92.929 | 99 | 1 | 4 | 5217 | 5315 | 423858897 | 423858989 | 7.570000e-29 | 139.0 |
10 | TraesCS2B01G350400 | chr2D | 90.698 | 86 | 8 | 0 | 5520 | 5605 | 423859951 | 423860036 | 1.280000e-21 | 115.0 |
11 | TraesCS2B01G350400 | chr3D | 95.000 | 100 | 2 | 3 | 5238 | 5335 | 610344626 | 610344724 | 2.700000e-33 | 154.0 |
12 | TraesCS2B01G350400 | chr3D | 94.681 | 94 | 4 | 1 | 5238 | 5330 | 610110519 | 610110612 | 1.630000e-30 | 145.0 |
13 | TraesCS2B01G350400 | chr3D | 93.750 | 96 | 4 | 2 | 5238 | 5331 | 610184414 | 610184509 | 5.850000e-30 | 143.0 |
14 | TraesCS2B01G350400 | chr3D | 90.090 | 111 | 6 | 4 | 5235 | 5341 | 610153532 | 610153641 | 7.570000e-29 | 139.0 |
15 | TraesCS2B01G350400 | chr7A | 94.845 | 97 | 2 | 3 | 5249 | 5343 | 209593018 | 209592923 | 1.260000e-31 | 148.0 |
16 | TraesCS2B01G350400 | chr1B | 89.815 | 108 | 8 | 2 | 5226 | 5330 | 534665237 | 534665344 | 9.790000e-28 | 135.0 |
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 | TraesCS2B01G350400 | chr2B | 497794654 | 497800258 | 5604 | False | 10351.000000 | 10351 | 100.00000 | 1 | 5605 | 1 | chr2B.!!$F1 | 5604 |
1 | TraesCS2B01G350400 | chr2A | 564615843 | 564621724 | 5881 | True | 2021.050000 | 7618 | 91.60225 | 1 | 5605 | 4 | chr2A.!!$R1 | 5604 |
2 | TraesCS2B01G350400 | chr2D | 423852520 | 423860036 | 7516 | False | 1367.833333 | 7315 | 92.13100 | 1 | 5605 | 6 | chr2D.!!$F1 | 5604 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
479 | 492 | 0.675208 | TGCGTGCATGTAACCCGATT | 60.675 | 50.0 | 7.93 | 0.0 | 0.00 | 3.34 | F |
1122 | 1153 | 1.065410 | TCAACCCCAAGGCTCCAAGA | 61.065 | 55.0 | 0.00 | 0.0 | 36.11 | 3.02 | F |
1933 | 1975 | 0.240945 | GGTGCATGCACTAACCACAC | 59.759 | 55.0 | 40.86 | 23.3 | 45.52 | 3.82 | F |
2517 | 2612 | 0.179009 | AAGGCTGACTGCTGCAAGAA | 60.179 | 50.0 | 3.02 | 0.0 | 42.39 | 2.52 | F |
2554 | 2649 | 0.247460 | TGCTCCTGTCAACCGATGAG | 59.753 | 55.0 | 0.00 | 0.0 | 39.19 | 2.90 | F |
2919 | 3017 | 0.616371 | TGTAGCCGGTTGGTAAGCAT | 59.384 | 50.0 | 1.90 | 0.0 | 37.67 | 3.79 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1929 | 1971 | 0.036732 | TCTAGCCAGCTTTGGGTGTG | 59.963 | 55.000 | 6.94 | 0.88 | 40.29 | 3.82 | R |
2485 | 2580 | 0.325110 | CAGCCTTCCTCCTCTCCTCA | 60.325 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 | R |
3114 | 3223 | 1.812571 | GAAAGGACATCCACGCATGTT | 59.187 | 47.619 | 0.00 | 0.00 | 37.11 | 2.71 | R |
4158 | 4267 | 0.665369 | ATTTGTTGCTCTTGCTGCGC | 60.665 | 50.000 | 0.00 | 0.00 | 40.48 | 6.09 | R |
4304 | 4416 | 1.364901 | GCTGCCATGTTTGCACAGT | 59.635 | 52.632 | 0.00 | 0.00 | 35.94 | 3.55 | R |
4837 | 4955 | 1.072266 | TGTAAACACCAGGAGCCCAT | 58.928 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 | 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 |
---|---|---|---|---|---|---|---|---|---|
48 | 49 | 6.366061 | GCCAGTTCATTTATTCTTGGTGTTTC | 59.634 | 38.462 | 0.00 | 0.00 | 0.00 | 2.78 |
80 | 81 | 4.392138 | GCCTGTTGACAAGTCTATTGGTAC | 59.608 | 45.833 | 1.53 | 0.00 | 0.00 | 3.34 |
81 | 82 | 4.625742 | CCTGTTGACAAGTCTATTGGTACG | 59.374 | 45.833 | 1.53 | 0.00 | 0.00 | 3.67 |
82 | 83 | 5.204409 | TGTTGACAAGTCTATTGGTACGT | 57.796 | 39.130 | 0.00 | 0.00 | 0.00 | 3.57 |
83 | 84 | 6.330004 | TGTTGACAAGTCTATTGGTACGTA | 57.670 | 37.500 | 1.53 | 0.00 | 0.00 | 3.57 |
207 | 215 | 1.855295 | AGATTGTGCATGCATTGGGA | 58.145 | 45.000 | 25.64 | 8.67 | 0.00 | 4.37 |
303 | 311 | 4.051922 | AGAACACTGCTCAAACGAGTTAG | 58.948 | 43.478 | 0.00 | 0.00 | 32.72 | 2.34 |
305 | 313 | 1.461127 | CACTGCTCAAACGAGTTAGCC | 59.539 | 52.381 | 7.90 | 0.00 | 33.99 | 3.93 |
306 | 314 | 1.070134 | ACTGCTCAAACGAGTTAGCCA | 59.930 | 47.619 | 7.90 | 0.00 | 33.99 | 4.75 |
307 | 315 | 1.728971 | CTGCTCAAACGAGTTAGCCAG | 59.271 | 52.381 | 7.90 | 3.45 | 33.99 | 4.85 |
308 | 316 | 1.343142 | TGCTCAAACGAGTTAGCCAGA | 59.657 | 47.619 | 7.90 | 0.00 | 33.99 | 3.86 |
309 | 317 | 2.224185 | TGCTCAAACGAGTTAGCCAGAA | 60.224 | 45.455 | 7.90 | 0.00 | 33.99 | 3.02 |
310 | 318 | 2.806244 | GCTCAAACGAGTTAGCCAGAAA | 59.194 | 45.455 | 0.00 | 0.00 | 32.72 | 2.52 |
312 | 320 | 4.083271 | GCTCAAACGAGTTAGCCAGAAAAT | 60.083 | 41.667 | 0.00 | 0.00 | 32.72 | 1.82 |
355 | 368 | 9.366216 | CAAACTAATCAAGCACAGTACTATACA | 57.634 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
400 | 413 | 7.148474 | TGGCACTCGATTTAGTTTTCAGATTAC | 60.148 | 37.037 | 0.00 | 0.00 | 0.00 | 1.89 |
479 | 492 | 0.675208 | TGCGTGCATGTAACCCGATT | 60.675 | 50.000 | 7.93 | 0.00 | 0.00 | 3.34 |
482 | 495 | 1.939934 | CGTGCATGTAACCCGATTCAT | 59.060 | 47.619 | 0.00 | 0.00 | 0.00 | 2.57 |
485 | 498 | 4.351192 | GTGCATGTAACCCGATTCATTTC | 58.649 | 43.478 | 0.00 | 0.00 | 0.00 | 2.17 |
486 | 499 | 4.096382 | GTGCATGTAACCCGATTCATTTCT | 59.904 | 41.667 | 0.00 | 0.00 | 0.00 | 2.52 |
487 | 500 | 4.335315 | TGCATGTAACCCGATTCATTTCTC | 59.665 | 41.667 | 0.00 | 0.00 | 0.00 | 2.87 |
488 | 501 | 4.576463 | GCATGTAACCCGATTCATTTCTCT | 59.424 | 41.667 | 0.00 | 0.00 | 0.00 | 3.10 |
489 | 502 | 5.277538 | GCATGTAACCCGATTCATTTCTCTC | 60.278 | 44.000 | 0.00 | 0.00 | 0.00 | 3.20 |
490 | 503 | 5.677319 | TGTAACCCGATTCATTTCTCTCT | 57.323 | 39.130 | 0.00 | 0.00 | 0.00 | 3.10 |
491 | 504 | 5.419542 | TGTAACCCGATTCATTTCTCTCTG | 58.580 | 41.667 | 0.00 | 0.00 | 0.00 | 3.35 |
515 | 528 | 3.151554 | TCTCTACCTGCGTGTTTGACTA | 58.848 | 45.455 | 0.00 | 0.00 | 0.00 | 2.59 |
595 | 608 | 3.074836 | GGGACCATACTCCTAGCTAGACT | 59.925 | 52.174 | 22.70 | 6.21 | 0.00 | 3.24 |
901 | 920 | 3.384668 | GCGAGCAAGTGAATGATAGCTA | 58.615 | 45.455 | 0.00 | 0.00 | 34.99 | 3.32 |
902 | 921 | 3.428198 | GCGAGCAAGTGAATGATAGCTAG | 59.572 | 47.826 | 0.00 | 0.00 | 34.99 | 3.42 |
903 | 922 | 4.794329 | GCGAGCAAGTGAATGATAGCTAGA | 60.794 | 45.833 | 0.00 | 0.00 | 34.99 | 2.43 |
904 | 923 | 4.679197 | CGAGCAAGTGAATGATAGCTAGAC | 59.321 | 45.833 | 0.00 | 0.00 | 31.61 | 2.59 |
905 | 924 | 5.595885 | GAGCAAGTGAATGATAGCTAGACA | 58.404 | 41.667 | 0.00 | 2.67 | 31.61 | 3.41 |
906 | 925 | 5.599732 | AGCAAGTGAATGATAGCTAGACAG | 58.400 | 41.667 | 0.00 | 0.00 | 0.00 | 3.51 |
907 | 926 | 5.362143 | AGCAAGTGAATGATAGCTAGACAGA | 59.638 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
908 | 927 | 5.461737 | GCAAGTGAATGATAGCTAGACAGAC | 59.538 | 44.000 | 0.00 | 1.92 | 0.00 | 3.51 |
909 | 928 | 6.567959 | CAAGTGAATGATAGCTAGACAGACA | 58.432 | 40.000 | 0.00 | 4.52 | 0.00 | 3.41 |
910 | 929 | 6.389830 | AGTGAATGATAGCTAGACAGACAG | 57.610 | 41.667 | 0.00 | 0.00 | 0.00 | 3.51 |
911 | 930 | 6.125719 | AGTGAATGATAGCTAGACAGACAGA | 58.874 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
912 | 931 | 6.039270 | AGTGAATGATAGCTAGACAGACAGAC | 59.961 | 42.308 | 0.00 | 0.00 | 0.00 | 3.51 |
1119 | 1150 | 2.538141 | CCTCAACCCCAAGGCTCCA | 61.538 | 63.158 | 0.00 | 0.00 | 36.11 | 3.86 |
1122 | 1153 | 1.065410 | TCAACCCCAAGGCTCCAAGA | 61.065 | 55.000 | 0.00 | 0.00 | 36.11 | 3.02 |
1149 | 1180 | 1.734420 | TTGGATGGCCCCTTGTTGGA | 61.734 | 55.000 | 0.00 | 0.00 | 38.35 | 3.53 |
1285 | 1322 | 3.496692 | CCACACCTCAAGATTTCTCCACA | 60.497 | 47.826 | 0.00 | 0.00 | 0.00 | 4.17 |
1292 | 1329 | 5.125100 | TCAAGATTTCTCCACAATGCAAC | 57.875 | 39.130 | 0.00 | 0.00 | 0.00 | 4.17 |
1442 | 1479 | 6.229936 | TCTACAGGTTTTGTGTACAGAACT | 57.770 | 37.500 | 15.24 | 0.00 | 41.10 | 3.01 |
1479 | 1517 | 4.957606 | TCACCTATTGTTTTATGGGGGT | 57.042 | 40.909 | 0.00 | 0.00 | 31.85 | 4.95 |
1512 | 1550 | 7.132805 | TGGAAAGATCTCATAAGACCCTCTAA | 58.867 | 38.462 | 0.00 | 0.00 | 33.32 | 2.10 |
1531 | 1569 | 7.147846 | CCCTCTAACAAATGATGGCAACTTAAT | 60.148 | 37.037 | 0.00 | 0.00 | 37.61 | 1.40 |
1794 | 1836 | 3.249189 | GCCCTGGTCACCTCCACA | 61.249 | 66.667 | 0.00 | 0.00 | 33.55 | 4.17 |
1829 | 1871 | 2.935238 | GCTACCTTGGCGACATTGAGAA | 60.935 | 50.000 | 0.00 | 0.00 | 42.32 | 2.87 |
1910 | 1952 | 1.478654 | GGAGGCAAGAAAGGTTGGTCA | 60.479 | 52.381 | 0.00 | 0.00 | 0.00 | 4.02 |
1929 | 1971 | 2.406616 | CCCGGTGCATGCACTAACC | 61.407 | 63.158 | 40.86 | 27.85 | 45.52 | 2.85 |
1933 | 1975 | 0.240945 | GGTGCATGCACTAACCACAC | 59.759 | 55.000 | 40.86 | 23.30 | 45.52 | 3.82 |
2033 | 2075 | 8.202811 | CCTATAGCTACATCATCATGCTGTTAT | 58.797 | 37.037 | 0.00 | 0.00 | 35.47 | 1.89 |
2058 | 2105 | 5.838529 | TGCTGATGCATGGATATTTTTCAG | 58.161 | 37.500 | 2.46 | 4.27 | 45.31 | 3.02 |
2094 | 2141 | 2.350863 | ACCAGGGTCATTCTTCTCCT | 57.649 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
2096 | 2143 | 2.989571 | ACCAGGGTCATTCTTCTCCTTT | 59.010 | 45.455 | 0.00 | 0.00 | 0.00 | 3.11 |
2425 | 2520 | 1.001633 | TCTAACACCGAGGTTCTTGGC | 59.998 | 52.381 | 1.26 | 0.00 | 38.56 | 4.52 |
2482 | 2577 | 0.524862 | CAAGCACTGTGAAGGGCATC | 59.475 | 55.000 | 12.86 | 0.00 | 0.00 | 3.91 |
2485 | 2580 | 1.180029 | GCACTGTGAAGGGCATCATT | 58.820 | 50.000 | 12.86 | 0.00 | 0.00 | 2.57 |
2517 | 2612 | 0.179009 | AAGGCTGACTGCTGCAAGAA | 60.179 | 50.000 | 3.02 | 0.00 | 42.39 | 2.52 |
2554 | 2649 | 0.247460 | TGCTCCTGTCAACCGATGAG | 59.753 | 55.000 | 0.00 | 0.00 | 39.19 | 2.90 |
2629 | 2724 | 3.981212 | TGAGACCACCTCACTCATGATA | 58.019 | 45.455 | 0.00 | 0.00 | 46.38 | 2.15 |
2671 | 2766 | 1.759445 | GGGCAGTCAGCTCAAGATCTA | 59.241 | 52.381 | 0.00 | 0.00 | 45.63 | 1.98 |
2919 | 3017 | 0.616371 | TGTAGCCGGTTGGTAAGCAT | 59.384 | 50.000 | 1.90 | 0.00 | 37.67 | 3.79 |
2950 | 3049 | 9.129532 | CCTTTTTCTTTCTATTATCAGCCATCT | 57.870 | 33.333 | 0.00 | 0.00 | 0.00 | 2.90 |
2981 | 3080 | 2.174639 | TGTGACCCTCCAAAACTGATGT | 59.825 | 45.455 | 0.00 | 0.00 | 0.00 | 3.06 |
2982 | 3081 | 3.222603 | GTGACCCTCCAAAACTGATGTT | 58.777 | 45.455 | 0.00 | 0.00 | 38.16 | 2.71 |
3089 | 3194 | 7.334671 | GGAAGGGTCTCTTAATTTGTTCTGTAG | 59.665 | 40.741 | 0.00 | 0.00 | 35.50 | 2.74 |
3114 | 3223 | 9.253832 | AGTAATTGGAATGGTTCAATGATACAA | 57.746 | 29.630 | 0.00 | 0.00 | 34.28 | 2.41 |
3525 | 3634 | 5.688807 | CAGATGGGAGGTATGTCTGATTTT | 58.311 | 41.667 | 0.00 | 0.00 | 38.81 | 1.82 |
3539 | 3648 | 5.653330 | TGTCTGATTTTCATACCATGTGCAT | 59.347 | 36.000 | 0.00 | 0.00 | 0.00 | 3.96 |
3559 | 3668 | 4.321452 | GCATGGGCATCTATATTTGTGGTG | 60.321 | 45.833 | 0.00 | 0.00 | 40.72 | 4.17 |
3624 | 3733 | 7.062957 | ACATAATATGCTTGTTTAGGGAAGCT | 58.937 | 34.615 | 0.00 | 0.00 | 44.15 | 3.74 |
3834 | 3943 | 1.390565 | ATCTTCAGATGCCAAGCAGC | 58.609 | 50.000 | 0.00 | 0.00 | 45.98 | 5.25 |
3890 | 3999 | 4.446371 | GTCCTAACCATGATTCCTCACTG | 58.554 | 47.826 | 0.00 | 0.00 | 33.22 | 3.66 |
3945 | 4054 | 4.908601 | TCTTAACTCCCTTGATGAAGCA | 57.091 | 40.909 | 0.00 | 0.00 | 0.00 | 3.91 |
3967 | 4076 | 5.048921 | GCAAGCTCATATGCATGACTTGTAT | 60.049 | 40.000 | 20.90 | 3.42 | 43.34 | 2.29 |
3980 | 4089 | 8.905850 | TGCATGACTTGTATAATTGATTGATGT | 58.094 | 29.630 | 0.00 | 0.00 | 0.00 | 3.06 |
4060 | 4169 | 1.047596 | TCTGCCCTGGATCAGAGCTC | 61.048 | 60.000 | 5.27 | 5.27 | 36.19 | 4.09 |
4194 | 4303 | 4.124238 | ACAAATCGGAGAAACGAAGAACA | 58.876 | 39.130 | 0.00 | 0.00 | 46.92 | 3.18 |
4201 | 4310 | 8.888579 | ATCGGAGAAACGAAGAACATAAATAT | 57.111 | 30.769 | 0.00 | 0.00 | 46.92 | 1.28 |
4202 | 4311 | 8.712285 | TCGGAGAAACGAAGAACATAAATATT | 57.288 | 30.769 | 0.00 | 0.00 | 40.34 | 1.28 |
4296 | 4405 | 8.237811 | TGATGCAGTTATCAGTCTCATACTAA | 57.762 | 34.615 | 0.00 | 0.00 | 35.76 | 2.24 |
4418 | 4530 | 5.628193 | CAGATTGTGACAGAAGAAAATGCAC | 59.372 | 40.000 | 0.00 | 0.00 | 0.00 | 4.57 |
4423 | 4535 | 3.149196 | GACAGAAGAAAATGCACCTCCA | 58.851 | 45.455 | 0.00 | 0.00 | 0.00 | 3.86 |
4427 | 4539 | 4.461781 | CAGAAGAAAATGCACCTCCATCTT | 59.538 | 41.667 | 0.00 | 0.00 | 0.00 | 2.40 |
4428 | 4540 | 5.047519 | CAGAAGAAAATGCACCTCCATCTTT | 60.048 | 40.000 | 0.00 | 0.00 | 0.00 | 2.52 |
4429 | 4541 | 5.184671 | AGAAGAAAATGCACCTCCATCTTTC | 59.815 | 40.000 | 0.00 | 0.00 | 0.00 | 2.62 |
4432 | 4544 | 5.184671 | AGAAAATGCACCTCCATCTTTCTTC | 59.815 | 40.000 | 0.00 | 0.00 | 33.69 | 2.87 |
4433 | 4545 | 3.726557 | ATGCACCTCCATCTTTCTTCA | 57.273 | 42.857 | 0.00 | 0.00 | 0.00 | 3.02 |
4434 | 4546 | 3.063510 | TGCACCTCCATCTTTCTTCAG | 57.936 | 47.619 | 0.00 | 0.00 | 0.00 | 3.02 |
4435 | 4547 | 2.639347 | TGCACCTCCATCTTTCTTCAGA | 59.361 | 45.455 | 0.00 | 0.00 | 0.00 | 3.27 |
4437 | 4549 | 3.307339 | GCACCTCCATCTTTCTTCAGACT | 60.307 | 47.826 | 0.00 | 0.00 | 0.00 | 3.24 |
4438 | 4550 | 4.081420 | GCACCTCCATCTTTCTTCAGACTA | 60.081 | 45.833 | 0.00 | 0.00 | 0.00 | 2.59 |
4439 | 4551 | 5.659463 | CACCTCCATCTTTCTTCAGACTAG | 58.341 | 45.833 | 0.00 | 0.00 | 0.00 | 2.57 |
4440 | 4552 | 4.161377 | ACCTCCATCTTTCTTCAGACTAGC | 59.839 | 45.833 | 0.00 | 0.00 | 0.00 | 3.42 |
4441 | 4553 | 4.358851 | CTCCATCTTTCTTCAGACTAGCG | 58.641 | 47.826 | 0.00 | 0.00 | 0.00 | 4.26 |
4443 | 4555 | 4.097135 | TCCATCTTTCTTCAGACTAGCGAG | 59.903 | 45.833 | 0.00 | 0.00 | 0.00 | 5.03 |
4444 | 4556 | 4.097135 | CCATCTTTCTTCAGACTAGCGAGA | 59.903 | 45.833 | 0.00 | 0.00 | 0.00 | 4.04 |
4445 | 4557 | 5.221224 | CCATCTTTCTTCAGACTAGCGAGAT | 60.221 | 44.000 | 0.00 | 0.00 | 0.00 | 2.75 |
4457 | 4570 | 5.008217 | AGACTAGCGAGATAGTAAGTGCTTG | 59.992 | 44.000 | 0.00 | 0.00 | 36.13 | 4.01 |
4466 | 4579 | 6.648192 | AGATAGTAAGTGCTTGCTGAATCTT | 58.352 | 36.000 | 11.80 | 0.00 | 36.24 | 2.40 |
4636 | 4749 | 2.338015 | GCTGCAGACATGGTGGTGG | 61.338 | 63.158 | 20.43 | 0.00 | 0.00 | 4.61 |
4723 | 4841 | 0.714180 | TGGGGTAGCTGAGGAGGTTA | 59.286 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 |
4897 | 5015 | 6.213397 | CAGTATGGGGAGATATGTATGAACCA | 59.787 | 42.308 | 0.00 | 0.00 | 0.00 | 3.67 |
5002 | 5155 | 5.698545 | AGTGAACAGAGAGTGAAGTTATTGC | 59.301 | 40.000 | 0.00 | 0.00 | 0.00 | 3.56 |
5032 | 5188 | 6.958767 | ACTGGCATTAACCTTTAGTGATACT | 58.041 | 36.000 | 0.00 | 0.00 | 0.00 | 2.12 |
5066 | 5223 | 7.751732 | TCCTTCAGAATTCATGTAAATTCGTG | 58.248 | 34.615 | 8.44 | 10.90 | 45.92 | 4.35 |
5081 | 5238 | 2.526888 | TCGTGTGGGGAGATTCTACT | 57.473 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
5082 | 5239 | 3.657398 | TCGTGTGGGGAGATTCTACTA | 57.343 | 47.619 | 0.00 | 0.00 | 0.00 | 1.82 |
5083 | 5240 | 4.180377 | TCGTGTGGGGAGATTCTACTAT | 57.820 | 45.455 | 0.00 | 0.00 | 0.00 | 2.12 |
5084 | 5241 | 3.889538 | TCGTGTGGGGAGATTCTACTATG | 59.110 | 47.826 | 0.00 | 0.00 | 0.00 | 2.23 |
5085 | 5242 | 3.889538 | CGTGTGGGGAGATTCTACTATGA | 59.110 | 47.826 | 0.00 | 0.00 | 0.00 | 2.15 |
5086 | 5243 | 4.524714 | CGTGTGGGGAGATTCTACTATGAT | 59.475 | 45.833 | 0.00 | 0.00 | 0.00 | 2.45 |
5087 | 5244 | 5.336055 | CGTGTGGGGAGATTCTACTATGATC | 60.336 | 48.000 | 0.00 | 0.00 | 0.00 | 2.92 |
5088 | 5245 | 5.540337 | GTGTGGGGAGATTCTACTATGATCA | 59.460 | 44.000 | 0.00 | 0.00 | 0.00 | 2.92 |
5089 | 5246 | 5.777223 | TGTGGGGAGATTCTACTATGATCAG | 59.223 | 44.000 | 0.09 | 0.00 | 0.00 | 2.90 |
5090 | 5247 | 5.777732 | GTGGGGAGATTCTACTATGATCAGT | 59.222 | 44.000 | 0.09 | 0.00 | 0.00 | 3.41 |
5091 | 5248 | 6.268847 | GTGGGGAGATTCTACTATGATCAGTT | 59.731 | 42.308 | 0.09 | 0.00 | 0.00 | 3.16 |
5092 | 5249 | 7.451877 | GTGGGGAGATTCTACTATGATCAGTTA | 59.548 | 40.741 | 0.09 | 0.00 | 0.00 | 2.24 |
5093 | 5250 | 8.180165 | TGGGGAGATTCTACTATGATCAGTTAT | 58.820 | 37.037 | 0.09 | 0.00 | 0.00 | 1.89 |
5094 | 5251 | 9.702253 | GGGGAGATTCTACTATGATCAGTTATA | 57.298 | 37.037 | 0.09 | 0.00 | 0.00 | 0.98 |
5123 | 5280 | 6.619023 | AGATTCTATGAGGGACTTTTGGAGAT | 59.381 | 38.462 | 0.00 | 0.00 | 41.55 | 2.75 |
5128 | 5285 | 3.055385 | TGAGGGACTTTTGGAGATAACGG | 60.055 | 47.826 | 0.00 | 0.00 | 41.55 | 4.44 |
5168 | 5325 | 4.022068 | TCAGTTGAAATTCCCATGCTCAAC | 60.022 | 41.667 | 8.28 | 8.28 | 43.94 | 3.18 |
5186 | 5343 | 3.513119 | TCAACTGGAGAATGACAGGAGAG | 59.487 | 47.826 | 0.00 | 0.00 | 39.00 | 3.20 |
5187 | 5344 | 3.464720 | ACTGGAGAATGACAGGAGAGA | 57.535 | 47.619 | 0.00 | 0.00 | 39.00 | 3.10 |
5188 | 5345 | 3.364549 | ACTGGAGAATGACAGGAGAGAG | 58.635 | 50.000 | 0.00 | 0.00 | 39.00 | 3.20 |
5189 | 5346 | 2.694628 | CTGGAGAATGACAGGAGAGAGG | 59.305 | 54.545 | 0.00 | 0.00 | 0.00 | 3.69 |
5190 | 5347 | 2.313041 | TGGAGAATGACAGGAGAGAGGA | 59.687 | 50.000 | 0.00 | 0.00 | 0.00 | 3.71 |
5191 | 5348 | 2.958355 | GGAGAATGACAGGAGAGAGGAG | 59.042 | 54.545 | 0.00 | 0.00 | 0.00 | 3.69 |
5192 | 5349 | 3.372566 | GGAGAATGACAGGAGAGAGGAGA | 60.373 | 52.174 | 0.00 | 0.00 | 0.00 | 3.71 |
5193 | 5350 | 3.631250 | AGAATGACAGGAGAGAGGAGAC | 58.369 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 |
5339 | 7657 | 3.264450 | AGCTAATAGGCCTTGTGTGAAGT | 59.736 | 43.478 | 12.58 | 0.00 | 0.00 | 3.01 |
5341 | 7659 | 4.095036 | GCTAATAGGCCTTGTGTGAAGTTC | 59.905 | 45.833 | 12.58 | 0.00 | 0.00 | 3.01 |
5353 | 7671 | 5.466819 | TGTGTGAAGTTCGATCGAGTAAAT | 58.533 | 37.500 | 18.54 | 0.00 | 0.00 | 1.40 |
5410 | 7728 | 3.209091 | TTTTTCTTTGCGGGGGACA | 57.791 | 47.368 | 0.00 | 0.00 | 0.00 | 4.02 |
5411 | 7729 | 1.710816 | TTTTTCTTTGCGGGGGACAT | 58.289 | 45.000 | 0.00 | 0.00 | 0.00 | 3.06 |
5412 | 7730 | 2.588464 | TTTTCTTTGCGGGGGACATA | 57.412 | 45.000 | 0.00 | 0.00 | 0.00 | 2.29 |
5413 | 7731 | 1.828979 | TTTCTTTGCGGGGGACATAC | 58.171 | 50.000 | 0.00 | 0.00 | 0.00 | 2.39 |
5414 | 7732 | 0.391927 | TTCTTTGCGGGGGACATACG | 60.392 | 55.000 | 0.00 | 0.00 | 0.00 | 3.06 |
5415 | 7733 | 1.078708 | CTTTGCGGGGGACATACGT | 60.079 | 57.895 | 0.00 | 0.00 | 0.00 | 3.57 |
5416 | 7734 | 0.675522 | CTTTGCGGGGGACATACGTT | 60.676 | 55.000 | 0.00 | 0.00 | 0.00 | 3.99 |
5417 | 7735 | 0.250814 | TTTGCGGGGGACATACGTTT | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 3.60 |
5418 | 7736 | 0.250814 | TTGCGGGGGACATACGTTTT | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 2.43 |
5419 | 7737 | 0.250814 | TGCGGGGGACATACGTTTTT | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 1.94 |
5450 | 7768 | 2.223340 | CCCAATCAGTCAAAGCGTATGC | 60.223 | 50.000 | 0.00 | 0.00 | 43.24 | 3.14 |
5456 | 7774 | 1.009829 | GTCAAAGCGTATGCCCTCTG | 58.990 | 55.000 | 2.51 | 0.00 | 44.31 | 3.35 |
5498 | 7819 | 0.981183 | AGTCAGGGCGTATGTTGGAA | 59.019 | 50.000 | 0.00 | 0.00 | 0.00 | 3.53 |
5499 | 7820 | 1.559682 | AGTCAGGGCGTATGTTGGAAT | 59.440 | 47.619 | 0.00 | 0.00 | 0.00 | 3.01 |
5509 | 7830 | 6.304126 | GGCGTATGTTGGAATAAATATGACG | 58.696 | 40.000 | 0.00 | 0.00 | 0.00 | 4.35 |
5521 | 7842 | 4.465632 | AAATATGACGTACTGGCAGACA | 57.534 | 40.909 | 23.66 | 12.59 | 0.00 | 3.41 |
5528 | 7849 | 3.585862 | ACGTACTGGCAGACAACAATAG | 58.414 | 45.455 | 23.66 | 6.09 | 0.00 | 1.73 |
5551 | 8184 | 3.535561 | CTCGTCCCTAATGACTTGCAAT | 58.464 | 45.455 | 0.00 | 0.00 | 32.97 | 3.56 |
5554 | 8187 | 3.019564 | GTCCCTAATGACTTGCAATGCT | 58.980 | 45.455 | 6.82 | 0.00 | 32.39 | 3.79 |
5557 | 8190 | 5.125417 | GTCCCTAATGACTTGCAATGCTAAA | 59.875 | 40.000 | 6.82 | 0.00 | 32.39 | 1.85 |
5562 | 8195 | 5.648178 | ATGACTTGCAATGCTAAATGTCA | 57.352 | 34.783 | 13.98 | 13.98 | 37.55 | 3.58 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
27 | 28 | 6.868339 | CCCAGAAACACCAAGAATAAATGAAC | 59.132 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
32 | 33 | 6.310941 | TCATCCCAGAAACACCAAGAATAAA | 58.689 | 36.000 | 0.00 | 0.00 | 0.00 | 1.40 |
48 | 49 | 0.325933 | TGTCAACAGGCTCATCCCAG | 59.674 | 55.000 | 0.00 | 0.00 | 34.51 | 4.45 |
80 | 81 | 6.828672 | TCGTTGACTATACATATCTGCTACG | 58.171 | 40.000 | 0.00 | 0.00 | 0.00 | 3.51 |
81 | 82 | 9.923786 | CTATCGTTGACTATACATATCTGCTAC | 57.076 | 37.037 | 0.00 | 0.00 | 0.00 | 3.58 |
82 | 83 | 9.668497 | ACTATCGTTGACTATACATATCTGCTA | 57.332 | 33.333 | 0.00 | 0.00 | 0.00 | 3.49 |
83 | 84 | 8.568676 | ACTATCGTTGACTATACATATCTGCT | 57.431 | 34.615 | 0.00 | 0.00 | 0.00 | 4.24 |
155 | 157 | 5.014858 | ACATGTACCTCTTCTTTCTCGGTA | 58.985 | 41.667 | 0.00 | 0.00 | 0.00 | 4.02 |
207 | 215 | 4.199310 | TGTGCTCAAAACTCAAAGCTACT | 58.801 | 39.130 | 0.00 | 0.00 | 35.76 | 2.57 |
303 | 311 | 7.945033 | TTGTGTGAAATTCTAATTTTCTGGC | 57.055 | 32.000 | 2.41 | 0.00 | 38.64 | 4.85 |
355 | 368 | 0.106519 | AGTTTTGGTCACAGCAGGCT | 60.107 | 50.000 | 0.00 | 0.00 | 0.00 | 4.58 |
400 | 413 | 6.176975 | TGCGTCTGAAATAATAACTTGTGG | 57.823 | 37.500 | 0.00 | 0.00 | 0.00 | 4.17 |
479 | 492 | 5.885352 | CAGGTAGAGAGACAGAGAGAAATGA | 59.115 | 44.000 | 0.00 | 0.00 | 0.00 | 2.57 |
482 | 495 | 4.013728 | GCAGGTAGAGAGACAGAGAGAAA | 58.986 | 47.826 | 0.00 | 0.00 | 0.00 | 2.52 |
485 | 498 | 1.939934 | CGCAGGTAGAGAGACAGAGAG | 59.060 | 57.143 | 0.00 | 0.00 | 0.00 | 3.20 |
486 | 499 | 1.279558 | ACGCAGGTAGAGAGACAGAGA | 59.720 | 52.381 | 0.00 | 0.00 | 0.00 | 3.10 |
487 | 500 | 1.400142 | CACGCAGGTAGAGAGACAGAG | 59.600 | 57.143 | 0.00 | 0.00 | 0.00 | 3.35 |
488 | 501 | 1.271434 | ACACGCAGGTAGAGAGACAGA | 60.271 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
489 | 502 | 1.169577 | ACACGCAGGTAGAGAGACAG | 58.830 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
490 | 503 | 1.617322 | AACACGCAGGTAGAGAGACA | 58.383 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
491 | 504 | 2.030185 | TCAAACACGCAGGTAGAGAGAC | 60.030 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 |
515 | 528 | 1.600076 | CTGCTGCTGCTCAAGGTGT | 60.600 | 57.895 | 17.00 | 0.00 | 40.48 | 4.16 |
901 | 920 | 3.411446 | CTCTCTGTCTGTCTGTCTGTCT | 58.589 | 50.000 | 0.00 | 0.00 | 0.00 | 3.41 |
902 | 921 | 2.487762 | CCTCTCTGTCTGTCTGTCTGTC | 59.512 | 54.545 | 0.00 | 0.00 | 0.00 | 3.51 |
903 | 922 | 2.513753 | CCTCTCTGTCTGTCTGTCTGT | 58.486 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
904 | 923 | 1.202114 | GCCTCTCTGTCTGTCTGTCTG | 59.798 | 57.143 | 0.00 | 0.00 | 0.00 | 3.51 |
905 | 924 | 1.202989 | TGCCTCTCTGTCTGTCTGTCT | 60.203 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
906 | 925 | 1.252175 | TGCCTCTCTGTCTGTCTGTC | 58.748 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
907 | 926 | 1.617850 | CTTGCCTCTCTGTCTGTCTGT | 59.382 | 52.381 | 0.00 | 0.00 | 0.00 | 3.41 |
908 | 927 | 1.067000 | CCTTGCCTCTCTGTCTGTCTG | 60.067 | 57.143 | 0.00 | 0.00 | 0.00 | 3.51 |
909 | 928 | 1.265236 | CCTTGCCTCTCTGTCTGTCT | 58.735 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 |
910 | 929 | 0.390998 | GCCTTGCCTCTCTGTCTGTC | 60.391 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 |
911 | 930 | 1.123861 | TGCCTTGCCTCTCTGTCTGT | 61.124 | 55.000 | 0.00 | 0.00 | 0.00 | 3.41 |
912 | 931 | 0.252479 | ATGCCTTGCCTCTCTGTCTG | 59.748 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
994 | 1021 | 2.421811 | CCACCATCATGCTCATACCACA | 60.422 | 50.000 | 0.00 | 0.00 | 0.00 | 4.17 |
1119 | 1150 | 0.969409 | GCCATCCAAAGCTGCCTCTT | 60.969 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 |
1122 | 1153 | 2.363406 | GGCCATCCAAAGCTGCCT | 60.363 | 61.111 | 0.00 | 0.00 | 39.05 | 4.75 |
1149 | 1180 | 0.787084 | TGAGGAACCTGAGGGTCTCT | 59.213 | 55.000 | 17.37 | 11.76 | 46.67 | 3.10 |
1285 | 1322 | 1.604604 | ACTACGTGCTTGGTTGCATT | 58.395 | 45.000 | 0.00 | 0.00 | 45.23 | 3.56 |
1292 | 1329 | 6.656314 | TGATAAACAATACTACGTGCTTGG | 57.344 | 37.500 | 0.00 | 0.00 | 0.00 | 3.61 |
1459 | 1497 | 4.605183 | TCACCCCCATAAAACAATAGGTG | 58.395 | 43.478 | 0.00 | 0.00 | 43.89 | 4.00 |
1472 | 1510 | 3.077391 | TCTTTCCATCTTTTCACCCCCAT | 59.923 | 43.478 | 0.00 | 0.00 | 0.00 | 4.00 |
1479 | 1517 | 9.388506 | GTCTTATGAGATCTTTCCATCTTTTCA | 57.611 | 33.333 | 0.00 | 0.00 | 32.94 | 2.69 |
1557 | 1596 | 4.340097 | CCATACCTGCACAATCACATCAAT | 59.660 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
1568 | 1607 | 1.229820 | ACCCTCCCATACCTGCACA | 60.230 | 57.895 | 0.00 | 0.00 | 0.00 | 4.57 |
1569 | 1608 | 1.224592 | CACCCTCCCATACCTGCAC | 59.775 | 63.158 | 0.00 | 0.00 | 0.00 | 4.57 |
1829 | 1871 | 1.293924 | GACTATGTGCAGCGCAATCT | 58.706 | 50.000 | 13.81 | 0.00 | 41.47 | 2.40 |
1929 | 1971 | 0.036732 | TCTAGCCAGCTTTGGGTGTG | 59.963 | 55.000 | 6.94 | 0.88 | 40.29 | 3.82 |
1933 | 1975 | 1.386533 | CATGTCTAGCCAGCTTTGGG | 58.613 | 55.000 | 0.00 | 0.00 | 0.00 | 4.12 |
2046 | 2088 | 2.945668 | AGCCAGCGTCTGAAAAATATCC | 59.054 | 45.455 | 8.20 | 0.00 | 32.44 | 2.59 |
2047 | 2089 | 4.622701 | AAGCCAGCGTCTGAAAAATATC | 57.377 | 40.909 | 8.20 | 0.00 | 32.44 | 1.63 |
2048 | 2090 | 4.458989 | TCAAAGCCAGCGTCTGAAAAATAT | 59.541 | 37.500 | 8.20 | 0.00 | 32.44 | 1.28 |
2049 | 2091 | 3.818210 | TCAAAGCCAGCGTCTGAAAAATA | 59.182 | 39.130 | 8.20 | 0.00 | 32.44 | 1.40 |
2058 | 2105 | 0.796927 | GGTAAGTCAAAGCCAGCGTC | 59.203 | 55.000 | 0.00 | 0.00 | 0.00 | 5.19 |
2413 | 2508 | 2.972625 | TCAACATAGCCAAGAACCTCG | 58.027 | 47.619 | 0.00 | 0.00 | 0.00 | 4.63 |
2425 | 2520 | 4.691175 | CCTGTGAGGAGTGATCAACATAG | 58.309 | 47.826 | 0.00 | 1.59 | 37.67 | 2.23 |
2482 | 2577 | 1.140652 | GCCTTCCTCCTCTCCTCAATG | 59.859 | 57.143 | 0.00 | 0.00 | 0.00 | 2.82 |
2485 | 2580 | 0.325110 | CAGCCTTCCTCCTCTCCTCA | 60.325 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 |
2629 | 2724 | 3.033659 | AGGAAGTAGACGACCATGGAT | 57.966 | 47.619 | 21.47 | 1.98 | 0.00 | 3.41 |
2919 | 3017 | 9.125026 | GCTGATAATAGAAAGAAAAAGGATCCA | 57.875 | 33.333 | 15.82 | 0.00 | 0.00 | 3.41 |
3089 | 3194 | 9.868277 | TTTGTATCATTGAACCATTCCAATTAC | 57.132 | 29.630 | 0.00 | 0.00 | 31.25 | 1.89 |
3114 | 3223 | 1.812571 | GAAAGGACATCCACGCATGTT | 59.187 | 47.619 | 0.00 | 0.00 | 37.11 | 2.71 |
3469 | 3578 | 2.564062 | CTGTTGGGCATTTCCATGAAGT | 59.436 | 45.455 | 0.00 | 0.00 | 36.58 | 3.01 |
3539 | 3648 | 4.787135 | TCACCACAAATATAGATGCCCA | 57.213 | 40.909 | 0.00 | 0.00 | 0.00 | 5.36 |
3556 | 3665 | 8.494016 | AACTAAGCTGTATTCATTACTTCACC | 57.506 | 34.615 | 0.00 | 0.00 | 0.00 | 4.02 |
3574 | 3683 | 9.439537 | GTTAAAGCTAATCTGCATAAACTAAGC | 57.560 | 33.333 | 0.00 | 0.00 | 34.99 | 3.09 |
3679 | 3788 | 9.107177 | CAGATAAGCACTTCTGATTTGTTCTAT | 57.893 | 33.333 | 4.33 | 0.00 | 41.53 | 1.98 |
3680 | 3789 | 8.097038 | ACAGATAAGCACTTCTGATTTGTTCTA | 58.903 | 33.333 | 14.40 | 0.00 | 41.53 | 2.10 |
3696 | 3805 | 5.921962 | TCTCTCAAAGCTACAGATAAGCA | 57.078 | 39.130 | 0.00 | 0.00 | 42.62 | 3.91 |
3945 | 4054 | 8.859236 | ATTATACAAGTCATGCATATGAGCTT | 57.141 | 30.769 | 6.97 | 0.00 | 43.66 | 3.74 |
3967 | 4076 | 4.892934 | GGGCCCTGTTACATCAATCAATTA | 59.107 | 41.667 | 17.04 | 0.00 | 0.00 | 1.40 |
4158 | 4267 | 0.665369 | ATTTGTTGCTCTTGCTGCGC | 60.665 | 50.000 | 0.00 | 0.00 | 40.48 | 6.09 |
4296 | 4405 | 3.949754 | CCATGTTTGCACAGTATCTCCAT | 59.050 | 43.478 | 0.00 | 0.00 | 35.94 | 3.41 |
4304 | 4416 | 1.364901 | GCTGCCATGTTTGCACAGT | 59.635 | 52.632 | 0.00 | 0.00 | 35.94 | 3.55 |
4418 | 4530 | 4.692228 | GCTAGTCTGAAGAAAGATGGAGG | 58.308 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
4423 | 4535 | 6.770785 | ACTATCTCGCTAGTCTGAAGAAAGAT | 59.229 | 38.462 | 0.00 | 0.00 | 0.00 | 2.40 |
4427 | 4539 | 7.011576 | CACTTACTATCTCGCTAGTCTGAAGAA | 59.988 | 40.741 | 0.00 | 0.00 | 33.96 | 2.52 |
4428 | 4540 | 6.480651 | CACTTACTATCTCGCTAGTCTGAAGA | 59.519 | 42.308 | 0.00 | 0.00 | 33.96 | 2.87 |
4429 | 4541 | 6.655062 | CACTTACTATCTCGCTAGTCTGAAG | 58.345 | 44.000 | 0.00 | 0.00 | 33.96 | 3.02 |
4432 | 4544 | 4.513692 | AGCACTTACTATCTCGCTAGTCTG | 59.486 | 45.833 | 0.00 | 0.00 | 33.96 | 3.51 |
4433 | 4545 | 4.710324 | AGCACTTACTATCTCGCTAGTCT | 58.290 | 43.478 | 0.00 | 0.00 | 33.96 | 3.24 |
4434 | 4546 | 5.209240 | CAAGCACTTACTATCTCGCTAGTC | 58.791 | 45.833 | 0.00 | 0.00 | 33.96 | 2.59 |
4435 | 4547 | 4.498345 | GCAAGCACTTACTATCTCGCTAGT | 60.498 | 45.833 | 0.00 | 0.00 | 36.04 | 2.57 |
4437 | 4549 | 3.632604 | AGCAAGCACTTACTATCTCGCTA | 59.367 | 43.478 | 0.00 | 0.00 | 0.00 | 4.26 |
4438 | 4550 | 2.428890 | AGCAAGCACTTACTATCTCGCT | 59.571 | 45.455 | 0.00 | 0.00 | 0.00 | 4.93 |
4439 | 4551 | 2.537625 | CAGCAAGCACTTACTATCTCGC | 59.462 | 50.000 | 0.00 | 0.00 | 0.00 | 5.03 |
4440 | 4552 | 4.033990 | TCAGCAAGCACTTACTATCTCG | 57.966 | 45.455 | 0.00 | 0.00 | 0.00 | 4.04 |
4441 | 4553 | 6.279882 | AGATTCAGCAAGCACTTACTATCTC | 58.720 | 40.000 | 0.00 | 0.00 | 0.00 | 2.75 |
4443 | 4555 | 6.917217 | AAGATTCAGCAAGCACTTACTATC | 57.083 | 37.500 | 0.00 | 0.00 | 0.00 | 2.08 |
4444 | 4556 | 8.970859 | ATAAAGATTCAGCAAGCACTTACTAT | 57.029 | 30.769 | 0.00 | 0.00 | 0.00 | 2.12 |
4445 | 4557 | 9.534565 | CTATAAAGATTCAGCAAGCACTTACTA | 57.465 | 33.333 | 0.00 | 0.00 | 0.00 | 1.82 |
4490 | 4603 | 2.050350 | CCATCTGCAGGGTGCCAAG | 61.050 | 63.158 | 15.13 | 0.00 | 44.23 | 3.61 |
4723 | 4841 | 4.293494 | ACACCATGTACAGAGGAGATCAT | 58.707 | 43.478 | 20.54 | 0.00 | 0.00 | 2.45 |
4757 | 4875 | 5.195940 | CCACCTCAAGTAATCACAATGGAT | 58.804 | 41.667 | 0.00 | 0.00 | 0.00 | 3.41 |
4837 | 4955 | 1.072266 | TGTAAACACCAGGAGCCCAT | 58.928 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 |
4897 | 5015 | 4.120589 | GTTTCGAAGTTTCAGTGAGGTCT | 58.879 | 43.478 | 0.00 | 0.00 | 0.00 | 3.85 |
5002 | 5155 | 7.175990 | TCACTAAAGGTTAATGCCAGTTTTAGG | 59.824 | 37.037 | 0.00 | 0.00 | 32.55 | 2.69 |
5046 | 5202 | 6.029607 | CCCACACGAATTTACATGAATTCTG | 58.970 | 40.000 | 14.52 | 13.40 | 41.61 | 3.02 |
5063 | 5220 | 3.889538 | TCATAGTAGAATCTCCCCACACG | 59.110 | 47.826 | 0.00 | 0.00 | 0.00 | 4.49 |
5066 | 5223 | 5.777732 | ACTGATCATAGTAGAATCTCCCCAC | 59.222 | 44.000 | 0.00 | 0.00 | 0.00 | 4.61 |
5085 | 5242 | 9.699410 | CCCTCATAGAATCTCTCTATAACTGAT | 57.301 | 37.037 | 0.00 | 0.00 | 44.23 | 2.90 |
5086 | 5243 | 8.895624 | TCCCTCATAGAATCTCTCTATAACTGA | 58.104 | 37.037 | 0.00 | 0.00 | 44.23 | 3.41 |
5087 | 5244 | 8.956426 | GTCCCTCATAGAATCTCTCTATAACTG | 58.044 | 40.741 | 0.00 | 0.00 | 44.23 | 3.16 |
5088 | 5245 | 8.900802 | AGTCCCTCATAGAATCTCTCTATAACT | 58.099 | 37.037 | 0.00 | 0.00 | 44.23 | 2.24 |
5089 | 5246 | 9.528489 | AAGTCCCTCATAGAATCTCTCTATAAC | 57.472 | 37.037 | 0.00 | 0.00 | 44.23 | 1.89 |
5092 | 5249 | 8.869109 | CAAAAGTCCCTCATAGAATCTCTCTAT | 58.131 | 37.037 | 0.00 | 0.00 | 46.55 | 1.98 |
5093 | 5250 | 7.288852 | CCAAAAGTCCCTCATAGAATCTCTCTA | 59.711 | 40.741 | 0.00 | 0.00 | 41.00 | 2.43 |
5094 | 5251 | 6.099557 | CCAAAAGTCCCTCATAGAATCTCTCT | 59.900 | 42.308 | 0.00 | 0.00 | 38.28 | 3.10 |
5095 | 5252 | 6.098982 | TCCAAAAGTCCCTCATAGAATCTCTC | 59.901 | 42.308 | 0.00 | 0.00 | 0.00 | 3.20 |
5096 | 5253 | 5.966935 | TCCAAAAGTCCCTCATAGAATCTCT | 59.033 | 40.000 | 0.00 | 0.00 | 0.00 | 3.10 |
5097 | 5254 | 6.098982 | TCTCCAAAAGTCCCTCATAGAATCTC | 59.901 | 42.308 | 0.00 | 0.00 | 0.00 | 2.75 |
5098 | 5255 | 5.966935 | TCTCCAAAAGTCCCTCATAGAATCT | 59.033 | 40.000 | 0.00 | 0.00 | 0.00 | 2.40 |
5099 | 5256 | 6.240549 | TCTCCAAAAGTCCCTCATAGAATC | 57.759 | 41.667 | 0.00 | 0.00 | 0.00 | 2.52 |
5100 | 5257 | 6.838401 | ATCTCCAAAAGTCCCTCATAGAAT | 57.162 | 37.500 | 0.00 | 0.00 | 0.00 | 2.40 |
5101 | 5258 | 7.565680 | GTTATCTCCAAAAGTCCCTCATAGAA | 58.434 | 38.462 | 0.00 | 0.00 | 0.00 | 2.10 |
5102 | 5259 | 6.183360 | CGTTATCTCCAAAAGTCCCTCATAGA | 60.183 | 42.308 | 0.00 | 0.00 | 0.00 | 1.98 |
5103 | 5260 | 5.986135 | CGTTATCTCCAAAAGTCCCTCATAG | 59.014 | 44.000 | 0.00 | 0.00 | 0.00 | 2.23 |
5104 | 5261 | 5.163343 | CCGTTATCTCCAAAAGTCCCTCATA | 60.163 | 44.000 | 0.00 | 0.00 | 0.00 | 2.15 |
5105 | 5262 | 4.384208 | CCGTTATCTCCAAAAGTCCCTCAT | 60.384 | 45.833 | 0.00 | 0.00 | 0.00 | 2.90 |
5106 | 5263 | 3.055385 | CCGTTATCTCCAAAAGTCCCTCA | 60.055 | 47.826 | 0.00 | 0.00 | 0.00 | 3.86 |
5107 | 5264 | 3.197116 | TCCGTTATCTCCAAAAGTCCCTC | 59.803 | 47.826 | 0.00 | 0.00 | 0.00 | 4.30 |
5128 | 5285 | 8.553459 | TTCAACTGAATTCTGAAGGACTTATC | 57.447 | 34.615 | 18.13 | 0.00 | 0.00 | 1.75 |
5168 | 5325 | 2.694628 | CCTCTCTCCTGTCATTCTCCAG | 59.305 | 54.545 | 0.00 | 0.00 | 0.00 | 3.86 |
5179 | 5336 | 2.744760 | TCATTGGTCTCCTCTCTCCTG | 58.255 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
5186 | 5343 | 2.224257 | GCCTCTGATCATTGGTCTCCTC | 60.224 | 54.545 | 13.49 | 0.00 | 0.00 | 3.71 |
5187 | 5344 | 1.767681 | GCCTCTGATCATTGGTCTCCT | 59.232 | 52.381 | 13.49 | 0.00 | 0.00 | 3.69 |
5188 | 5345 | 1.767681 | AGCCTCTGATCATTGGTCTCC | 59.232 | 52.381 | 13.49 | 0.68 | 0.00 | 3.71 |
5189 | 5346 | 3.557228 | AAGCCTCTGATCATTGGTCTC | 57.443 | 47.619 | 13.49 | 0.95 | 0.00 | 3.36 |
5190 | 5347 | 3.009916 | ACAAAGCCTCTGATCATTGGTCT | 59.990 | 43.478 | 13.49 | 9.34 | 0.00 | 3.85 |
5191 | 5348 | 3.350833 | ACAAAGCCTCTGATCATTGGTC | 58.649 | 45.455 | 13.49 | 7.72 | 0.00 | 4.02 |
5192 | 5349 | 3.446442 | ACAAAGCCTCTGATCATTGGT | 57.554 | 42.857 | 13.49 | 0.00 | 0.00 | 3.67 |
5193 | 5350 | 3.760151 | TGAACAAAGCCTCTGATCATTGG | 59.240 | 43.478 | 0.00 | 2.62 | 0.00 | 3.16 |
5243 | 7561 | 3.509575 | TGTATGGGCCACAATTTTCTGTC | 59.490 | 43.478 | 9.28 | 0.00 | 0.00 | 3.51 |
5245 | 7563 | 3.119029 | CCTGTATGGGCCACAATTTTCTG | 60.119 | 47.826 | 9.28 | 0.00 | 0.00 | 3.02 |
5247 | 7565 | 2.831526 | ACCTGTATGGGCCACAATTTTC | 59.168 | 45.455 | 9.28 | 0.00 | 41.11 | 2.29 |
5248 | 7566 | 2.831526 | GACCTGTATGGGCCACAATTTT | 59.168 | 45.455 | 9.28 | 0.00 | 38.13 | 1.82 |
5249 | 7567 | 2.456577 | GACCTGTATGGGCCACAATTT | 58.543 | 47.619 | 9.28 | 0.00 | 38.13 | 1.82 |
5250 | 7568 | 2.143876 | GACCTGTATGGGCCACAATT | 57.856 | 50.000 | 9.28 | 0.00 | 38.13 | 2.32 |
5251 | 7569 | 3.903208 | GACCTGTATGGGCCACAAT | 57.097 | 52.632 | 9.28 | 0.00 | 38.13 | 2.71 |
5392 | 7710 | 1.710816 | ATGTCCCCCGCAAAGAAAAA | 58.289 | 45.000 | 0.00 | 0.00 | 0.00 | 1.94 |
5393 | 7711 | 2.164338 | GTATGTCCCCCGCAAAGAAAA | 58.836 | 47.619 | 0.00 | 0.00 | 0.00 | 2.29 |
5394 | 7712 | 1.828979 | GTATGTCCCCCGCAAAGAAA | 58.171 | 50.000 | 0.00 | 0.00 | 0.00 | 2.52 |
5395 | 7713 | 0.391927 | CGTATGTCCCCCGCAAAGAA | 60.392 | 55.000 | 0.00 | 0.00 | 0.00 | 2.52 |
5396 | 7714 | 1.219664 | CGTATGTCCCCCGCAAAGA | 59.780 | 57.895 | 0.00 | 0.00 | 0.00 | 2.52 |
5397 | 7715 | 0.675522 | AACGTATGTCCCCCGCAAAG | 60.676 | 55.000 | 0.00 | 0.00 | 0.00 | 2.77 |
5398 | 7716 | 0.250814 | AAACGTATGTCCCCCGCAAA | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 3.68 |
5399 | 7717 | 0.250814 | AAAACGTATGTCCCCCGCAA | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 4.85 |
5400 | 7718 | 0.250814 | AAAAACGTATGTCCCCCGCA | 60.251 | 50.000 | 0.00 | 0.00 | 0.00 | 5.69 |
5401 | 7719 | 2.558617 | AAAAACGTATGTCCCCCGC | 58.441 | 52.632 | 0.00 | 0.00 | 0.00 | 6.13 |
5416 | 7734 | 6.843752 | TGACTGATTGGGGTACTTAGAAAAA | 58.156 | 36.000 | 0.00 | 0.00 | 0.00 | 1.94 |
5417 | 7735 | 6.442541 | TGACTGATTGGGGTACTTAGAAAA | 57.557 | 37.500 | 0.00 | 0.00 | 0.00 | 2.29 |
5418 | 7736 | 6.442541 | TTGACTGATTGGGGTACTTAGAAA | 57.557 | 37.500 | 0.00 | 0.00 | 0.00 | 2.52 |
5419 | 7737 | 6.442541 | TTTGACTGATTGGGGTACTTAGAA | 57.557 | 37.500 | 0.00 | 0.00 | 0.00 | 2.10 |
5420 | 7738 | 5.570844 | GCTTTGACTGATTGGGGTACTTAGA | 60.571 | 44.000 | 0.00 | 0.00 | 0.00 | 2.10 |
5421 | 7739 | 4.636206 | GCTTTGACTGATTGGGGTACTTAG | 59.364 | 45.833 | 0.00 | 0.00 | 0.00 | 2.18 |
5427 | 7745 | 0.110486 | ACGCTTTGACTGATTGGGGT | 59.890 | 50.000 | 0.00 | 0.00 | 0.00 | 4.95 |
5430 | 7748 | 2.223340 | GGCATACGCTTTGACTGATTGG | 60.223 | 50.000 | 0.00 | 0.00 | 38.60 | 3.16 |
5431 | 7749 | 2.223340 | GGGCATACGCTTTGACTGATTG | 60.223 | 50.000 | 0.00 | 0.00 | 38.60 | 2.67 |
5498 | 7819 | 6.156748 | TGTCTGCCAGTACGTCATATTTAT | 57.843 | 37.500 | 0.00 | 0.00 | 0.00 | 1.40 |
5499 | 7820 | 5.585820 | TGTCTGCCAGTACGTCATATTTA | 57.414 | 39.130 | 0.00 | 0.00 | 0.00 | 1.40 |
5509 | 7830 | 2.678336 | GCCTATTGTTGTCTGCCAGTAC | 59.322 | 50.000 | 0.00 | 0.00 | 0.00 | 2.73 |
5521 | 7842 | 3.709653 | TCATTAGGGACGAGCCTATTGTT | 59.290 | 43.478 | 0.00 | 0.00 | 36.66 | 2.83 |
5528 | 7849 | 1.941325 | CAAGTCATTAGGGACGAGCC | 58.059 | 55.000 | 0.00 | 0.00 | 42.62 | 4.70 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.