Multiple sequence alignment - TraesCS4A01G271000
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 | TraesCS4A01G271000 | chr4A | 100.000 | 3863 | 0 | 0 | 1 | 3863 | 582480578 | 582476716 | 0.000000e+00 | 7134.0 |
1 | TraesCS4A01G271000 | chr4A | 85.232 | 1036 | 132 | 12 | 1882 | 2912 | 729477055 | 729476036 | 0.000000e+00 | 1046.0 |
2 | TraesCS4A01G271000 | chr4A | 81.429 | 140 | 24 | 2 | 1932 | 2070 | 573172934 | 573172796 | 3.150000e-21 | 113.0 |
3 | TraesCS4A01G271000 | chr4D | 91.531 | 3920 | 190 | 80 | 9 | 3859 | 18780089 | 18783935 | 0.000000e+00 | 5269.0 |
4 | TraesCS4A01G271000 | chr4D | 79.720 | 143 | 27 | 2 | 1923 | 2064 | 30005079 | 30005220 | 6.830000e-18 | 102.0 |
5 | TraesCS4A01G271000 | chr4B | 90.370 | 2949 | 120 | 70 | 465 | 3346 | 30860880 | 30863731 | 0.000000e+00 | 3722.0 |
6 | TraesCS4A01G271000 | chr4B | 92.888 | 464 | 21 | 3 | 2028 | 2491 | 389754555 | 389755006 | 0.000000e+00 | 664.0 |
7 | TraesCS4A01G271000 | chr4B | 95.652 | 207 | 8 | 1 | 2456 | 2661 | 389755009 | 389755215 | 8.000000e-87 | 331.0 |
8 | TraesCS4A01G271000 | chr4B | 86.411 | 287 | 13 | 14 | 3485 | 3757 | 30863762 | 30864036 | 1.360000e-74 | 291.0 |
9 | TraesCS4A01G271000 | chr4B | 93.056 | 72 | 3 | 2 | 307 | 378 | 30860789 | 30860858 | 1.900000e-18 | 104.0 |
10 | TraesCS4A01G271000 | chr4B | 79.085 | 153 | 29 | 3 | 1919 | 2070 | 42776335 | 42776185 | 6.830000e-18 | 102.0 |
11 | TraesCS4A01G271000 | chr5A | 94.016 | 635 | 25 | 4 | 2028 | 2661 | 363860115 | 363859493 | 0.000000e+00 | 950.0 |
12 | TraesCS4A01G271000 | chr5A | 81.429 | 350 | 57 | 6 | 79 | 424 | 396747739 | 396748084 | 2.940000e-71 | 279.0 |
13 | TraesCS4A01G271000 | chr7B | 93.534 | 464 | 18 | 3 | 2028 | 2491 | 60629189 | 60629640 | 0.000000e+00 | 680.0 |
14 | TraesCS4A01G271000 | chr7B | 95.652 | 207 | 8 | 1 | 2456 | 2661 | 60629643 | 60629849 | 8.000000e-87 | 331.0 |
15 | TraesCS4A01G271000 | chr1B | 93.534 | 464 | 18 | 3 | 2028 | 2491 | 605938407 | 605937956 | 0.000000e+00 | 680.0 |
16 | TraesCS4A01G271000 | chr1B | 96.517 | 201 | 6 | 1 | 2462 | 2661 | 605937947 | 605937747 | 8.000000e-87 | 331.0 |
17 | TraesCS4A01G271000 | chr6B | 91.879 | 431 | 23 | 3 | 2061 | 2491 | 623993608 | 623994026 | 3.320000e-165 | 592.0 |
18 | TraesCS4A01G271000 | chr6B | 93.720 | 207 | 12 | 1 | 2456 | 2661 | 623994029 | 623994235 | 3.750000e-80 | 309.0 |
19 | TraesCS4A01G271000 | chr6B | 97.368 | 38 | 1 | 0 | 2028 | 2065 | 623987611 | 623987648 | 8.960000e-07 | 65.8 |
20 | TraesCS4A01G271000 | chr7D | 85.658 | 509 | 52 | 12 | 2405 | 2911 | 9093015 | 9093504 | 2.060000e-142 | 516.0 |
21 | TraesCS4A01G271000 | chr7D | 83.333 | 330 | 49 | 5 | 98 | 424 | 537570813 | 537570487 | 2.260000e-77 | 300.0 |
22 | TraesCS4A01G271000 | chr7A | 86.567 | 335 | 27 | 7 | 1427 | 1761 | 562904755 | 562904439 | 1.710000e-93 | 353.0 |
23 | TraesCS4A01G271000 | chr7A | 89.818 | 275 | 25 | 1 | 1148 | 1422 | 563212858 | 563212587 | 2.210000e-92 | 350.0 |
24 | TraesCS4A01G271000 | chr7A | 80.769 | 390 | 57 | 14 | 79 | 456 | 254378129 | 254377746 | 4.880000e-74 | 289.0 |
25 | TraesCS4A01G271000 | chr3D | 83.143 | 350 | 52 | 5 | 79 | 424 | 178186877 | 178186531 | 2.900000e-81 | 313.0 |
26 | TraesCS4A01G271000 | chr3A | 83.046 | 348 | 54 | 4 | 79 | 424 | 510413353 | 510413697 | 1.040000e-80 | 311.0 |
27 | TraesCS4A01G271000 | chr1A | 82.759 | 348 | 55 | 4 | 79 | 424 | 3160081 | 3159737 | 4.850000e-79 | 305.0 |
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 | TraesCS4A01G271000 | chr4A | 582476716 | 582480578 | 3862 | True | 7134.000000 | 7134 | 100.000000 | 1 | 3863 | 1 | chr4A.!!$R2 | 3862 |
1 | TraesCS4A01G271000 | chr4A | 729476036 | 729477055 | 1019 | True | 1046.000000 | 1046 | 85.232000 | 1882 | 2912 | 1 | chr4A.!!$R3 | 1030 |
2 | TraesCS4A01G271000 | chr4D | 18780089 | 18783935 | 3846 | False | 5269.000000 | 5269 | 91.531000 | 9 | 3859 | 1 | chr4D.!!$F1 | 3850 |
3 | TraesCS4A01G271000 | chr4B | 30860789 | 30864036 | 3247 | False | 1372.333333 | 3722 | 89.945667 | 307 | 3757 | 3 | chr4B.!!$F1 | 3450 |
4 | TraesCS4A01G271000 | chr4B | 389754555 | 389755215 | 660 | False | 497.500000 | 664 | 94.270000 | 2028 | 2661 | 2 | chr4B.!!$F2 | 633 |
5 | TraesCS4A01G271000 | chr5A | 363859493 | 363860115 | 622 | True | 950.000000 | 950 | 94.016000 | 2028 | 2661 | 1 | chr5A.!!$R1 | 633 |
6 | TraesCS4A01G271000 | chr7B | 60629189 | 60629849 | 660 | False | 505.500000 | 680 | 94.593000 | 2028 | 2661 | 2 | chr7B.!!$F1 | 633 |
7 | TraesCS4A01G271000 | chr1B | 605937747 | 605938407 | 660 | True | 505.500000 | 680 | 95.025500 | 2028 | 2661 | 2 | chr1B.!!$R1 | 633 |
8 | TraesCS4A01G271000 | chr6B | 623993608 | 623994235 | 627 | False | 450.500000 | 592 | 92.799500 | 2061 | 2661 | 2 | chr6B.!!$F2 | 600 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
863 | 925 | 0.253207 | TTCCTCCTTCTTCCTCCCCC | 60.253 | 60.0 | 0.00 | 0.00 | 0.0 | 5.40 | F |
936 | 998 | 0.665369 | CCGAGGCAAGCAAAAGCTTG | 60.665 | 55.0 | 22.09 | 22.09 | 46.9 | 4.01 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2418 | 2512 | 1.172180 | ATGTGCCGGAGTTGTGGTTG | 61.172 | 55.000 | 5.05 | 0.0 | 0.0 | 3.77 | R |
2962 | 3097 | 6.936335 | TGACATGACATTTAGCTTCTTCTTCA | 59.064 | 34.615 | 0.00 | 0.0 | 0.0 | 3.02 | 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 |
---|---|---|---|---|---|---|---|---|---|
60 | 61 | 3.179795 | CGTGTGTCGCATTAGCTATGTAC | 59.820 | 47.826 | 0.00 | 0.00 | 39.10 | 2.90 |
69 | 70 | 4.376413 | GCATTAGCTATGTACGTGTCATGC | 60.376 | 45.833 | 15.10 | 14.99 | 36.57 | 4.06 |
83 | 84 | 4.345271 | TGTCATGCGAGACAAAATCATG | 57.655 | 40.909 | 8.41 | 0.00 | 44.92 | 3.07 |
84 | 85 | 3.752747 | TGTCATGCGAGACAAAATCATGT | 59.247 | 39.130 | 8.41 | 0.00 | 44.92 | 3.21 |
85 | 86 | 4.934602 | TGTCATGCGAGACAAAATCATGTA | 59.065 | 37.500 | 8.41 | 0.00 | 44.92 | 2.29 |
86 | 87 | 5.063817 | TGTCATGCGAGACAAAATCATGTAG | 59.936 | 40.000 | 8.41 | 0.00 | 44.92 | 2.74 |
88 | 89 | 6.018425 | GTCATGCGAGACAAAATCATGTAGAT | 60.018 | 38.462 | 3.71 | 0.00 | 38.40 | 1.98 |
89 | 90 | 7.169813 | GTCATGCGAGACAAAATCATGTAGATA | 59.830 | 37.037 | 3.71 | 0.00 | 38.40 | 1.98 |
90 | 91 | 7.383300 | TCATGCGAGACAAAATCATGTAGATAG | 59.617 | 37.037 | 0.00 | 0.00 | 35.39 | 2.08 |
92 | 93 | 5.986135 | GCGAGACAAAATCATGTAGATAGGT | 59.014 | 40.000 | 0.00 | 0.00 | 35.39 | 3.08 |
93 | 94 | 6.144724 | GCGAGACAAAATCATGTAGATAGGTC | 59.855 | 42.308 | 0.00 | 0.00 | 35.39 | 3.85 |
94 | 95 | 7.203218 | CGAGACAAAATCATGTAGATAGGTCA | 58.797 | 38.462 | 0.00 | 0.00 | 35.39 | 4.02 |
109 | 110 | 9.005777 | GTAGATAGGTCAAAATGTTGGTTGTTA | 57.994 | 33.333 | 0.00 | 0.00 | 35.29 | 2.41 |
114 | 115 | 7.433680 | AGGTCAAAATGTTGGTTGTTAGATTC | 58.566 | 34.615 | 0.00 | 0.00 | 35.29 | 2.52 |
116 | 117 | 6.362283 | GTCAAAATGTTGGTTGTTAGATTCGG | 59.638 | 38.462 | 0.00 | 0.00 | 35.29 | 4.30 |
144 | 145 | 5.128827 | TCGATAGACAAGTTAGGGCATCTTT | 59.871 | 40.000 | 0.00 | 0.00 | 42.67 | 2.52 |
173 | 174 | 8.620116 | TCACATGATTCTAGAAACACATGAAA | 57.380 | 30.769 | 32.51 | 23.88 | 35.97 | 2.69 |
225 | 226 | 2.544685 | TCATGCACGGTTTTTGGTTTG | 58.455 | 42.857 | 0.00 | 0.00 | 0.00 | 2.93 |
245 | 246 | 1.081774 | TTGCATCGCCGGAAAAACG | 60.082 | 52.632 | 5.05 | 0.00 | 0.00 | 3.60 |
251 | 252 | 1.133869 | CGCCGGAAAAACGTGGATC | 59.866 | 57.895 | 5.05 | 0.00 | 0.00 | 3.36 |
252 | 253 | 1.504900 | GCCGGAAAAACGTGGATCC | 59.495 | 57.895 | 5.05 | 4.20 | 0.00 | 3.36 |
257 | 258 | 3.561503 | CGGAAAAACGTGGATCCTTTTC | 58.438 | 45.455 | 20.78 | 20.78 | 37.15 | 2.29 |
259 | 260 | 4.320935 | CGGAAAAACGTGGATCCTTTTCAT | 60.321 | 41.667 | 26.09 | 9.29 | 38.80 | 2.57 |
263 | 264 | 2.991250 | ACGTGGATCCTTTTCATGAGG | 58.009 | 47.619 | 14.23 | 0.00 | 35.53 | 3.86 |
268 | 269 | 5.619981 | CGTGGATCCTTTTCATGAGGTTTTC | 60.620 | 44.000 | 14.23 | 0.00 | 35.71 | 2.29 |
275 | 276 | 5.507985 | CCTTTTCATGAGGTTTTCAGTGGAC | 60.508 | 44.000 | 0.00 | 0.00 | 39.68 | 4.02 |
276 | 277 | 3.855255 | TCATGAGGTTTTCAGTGGACA | 57.145 | 42.857 | 0.00 | 0.00 | 39.68 | 4.02 |
282 | 283 | 4.407621 | TGAGGTTTTCAGTGGACACTAGAA | 59.592 | 41.667 | 4.41 | 8.53 | 40.20 | 2.10 |
284 | 285 | 5.941788 | AGGTTTTCAGTGGACACTAGAATT | 58.058 | 37.500 | 4.41 | 0.00 | 40.20 | 2.17 |
286 | 287 | 5.181433 | GGTTTTCAGTGGACACTAGAATTCC | 59.819 | 44.000 | 4.41 | 11.36 | 40.20 | 3.01 |
314 | 317 | 6.703165 | GGAATGAATACAAATGAATCCTTGGC | 59.297 | 38.462 | 0.00 | 0.00 | 0.00 | 4.52 |
326 | 329 | 6.357579 | TGAATCCTTGGCAAATATTTGTGT | 57.642 | 33.333 | 25.15 | 6.07 | 40.24 | 3.72 |
367 | 370 | 0.661020 | AACGACCAGCACGGAAAAAG | 59.339 | 50.000 | 0.00 | 0.00 | 38.63 | 2.27 |
369 | 372 | 0.941542 | CGACCAGCACGGAAAAAGAA | 59.058 | 50.000 | 0.00 | 0.00 | 38.63 | 2.52 |
370 | 373 | 1.535462 | CGACCAGCACGGAAAAAGAAT | 59.465 | 47.619 | 0.00 | 0.00 | 38.63 | 2.40 |
371 | 374 | 2.412847 | CGACCAGCACGGAAAAAGAATC | 60.413 | 50.000 | 0.00 | 0.00 | 38.63 | 2.52 |
449 | 460 | 7.147497 | ACCTTCAAAGTCTTGGAATCCATTTTT | 60.147 | 33.333 | 1.39 | 0.00 | 31.53 | 1.94 |
450 | 461 | 7.386025 | CCTTCAAAGTCTTGGAATCCATTTTTC | 59.614 | 37.037 | 1.39 | 0.00 | 31.53 | 2.29 |
459 | 470 | 3.451902 | GGAATCCATTTTTCCCATGAGCA | 59.548 | 43.478 | 0.00 | 0.00 | 37.29 | 4.26 |
510 | 521 | 2.962569 | CGCACGGAGAAGGAGTCA | 59.037 | 61.111 | 0.00 | 0.00 | 0.00 | 3.41 |
527 | 552 | 2.760385 | AGACGTAGCAGAGCCCCC | 60.760 | 66.667 | 0.00 | 0.00 | 0.00 | 5.40 |
528 | 553 | 3.075005 | GACGTAGCAGAGCCCCCA | 61.075 | 66.667 | 0.00 | 0.00 | 0.00 | 4.96 |
529 | 554 | 2.365635 | ACGTAGCAGAGCCCCCAT | 60.366 | 61.111 | 0.00 | 0.00 | 0.00 | 4.00 |
530 | 555 | 2.370647 | GACGTAGCAGAGCCCCCATC | 62.371 | 65.000 | 0.00 | 0.00 | 0.00 | 3.51 |
537 | 562 | 3.249189 | GAGCCCCCATCCCGCATA | 61.249 | 66.667 | 0.00 | 0.00 | 0.00 | 3.14 |
538 | 563 | 3.252284 | AGCCCCCATCCCGCATAG | 61.252 | 66.667 | 0.00 | 0.00 | 0.00 | 2.23 |
540 | 565 | 3.569210 | CCCCCATCCCGCATAGCA | 61.569 | 66.667 | 0.00 | 0.00 | 0.00 | 3.49 |
546 | 573 | 2.890311 | CCCATCCCGCATAGCATTTTTA | 59.110 | 45.455 | 0.00 | 0.00 | 0.00 | 1.52 |
703 | 730 | 4.394712 | CCAGCGACCCACCACTCC | 62.395 | 72.222 | 0.00 | 0.00 | 0.00 | 3.85 |
704 | 731 | 3.625897 | CAGCGACCCACCACTCCA | 61.626 | 66.667 | 0.00 | 0.00 | 0.00 | 3.86 |
708 | 735 | 2.852075 | GACCCACCACTCCACCCA | 60.852 | 66.667 | 0.00 | 0.00 | 0.00 | 4.51 |
710 | 737 | 2.529136 | CCCACCACTCCACCCAGA | 60.529 | 66.667 | 0.00 | 0.00 | 0.00 | 3.86 |
748 | 782 | 2.501128 | CATCACCCGATGCCGTCT | 59.499 | 61.111 | 0.00 | 0.00 | 42.54 | 4.18 |
749 | 783 | 1.592669 | CATCACCCGATGCCGTCTC | 60.593 | 63.158 | 0.00 | 0.00 | 42.54 | 3.36 |
750 | 784 | 3.138930 | ATCACCCGATGCCGTCTCG | 62.139 | 63.158 | 0.00 | 0.00 | 35.92 | 4.04 |
753 | 787 | 4.812476 | CCCGATGCCGTCTCGCAA | 62.812 | 66.667 | 0.00 | 0.00 | 43.24 | 4.85 |
754 | 788 | 2.586079 | CCGATGCCGTCTCGCAAT | 60.586 | 61.111 | 0.00 | 0.00 | 43.24 | 3.56 |
755 | 789 | 2.589492 | CCGATGCCGTCTCGCAATC | 61.589 | 63.158 | 0.00 | 0.00 | 43.24 | 2.67 |
756 | 790 | 1.589993 | CGATGCCGTCTCGCAATCT | 60.590 | 57.895 | 0.00 | 0.00 | 43.24 | 2.40 |
757 | 791 | 1.543941 | CGATGCCGTCTCGCAATCTC | 61.544 | 60.000 | 0.00 | 0.00 | 43.24 | 2.75 |
758 | 792 | 1.218230 | GATGCCGTCTCGCAATCTCC | 61.218 | 60.000 | 0.00 | 0.00 | 43.24 | 3.71 |
759 | 793 | 2.586357 | GCCGTCTCGCAATCTCCC | 60.586 | 66.667 | 0.00 | 0.00 | 0.00 | 4.30 |
760 | 794 | 2.107141 | CCGTCTCGCAATCTCCCC | 59.893 | 66.667 | 0.00 | 0.00 | 0.00 | 4.81 |
761 | 795 | 2.107141 | CGTCTCGCAATCTCCCCC | 59.893 | 66.667 | 0.00 | 0.00 | 0.00 | 5.40 |
826 | 860 | 4.724602 | TCGCTCGCTCGCTGCTTT | 62.725 | 61.111 | 0.00 | 0.00 | 40.11 | 3.51 |
831 | 893 | 3.117171 | CGCTCGCTGCTTTGCTCT | 61.117 | 61.111 | 0.00 | 0.00 | 40.11 | 4.09 |
832 | 894 | 2.783935 | GCTCGCTGCTTTGCTCTC | 59.216 | 61.111 | 0.00 | 0.00 | 38.95 | 3.20 |
839 | 901 | 1.338960 | GCTGCTTTGCTCTCTCTCCTT | 60.339 | 52.381 | 0.00 | 0.00 | 0.00 | 3.36 |
852 | 914 | 4.045334 | TCTCTCTCCTTCTTCTTCCTCCTT | 59.955 | 45.833 | 0.00 | 0.00 | 0.00 | 3.36 |
853 | 915 | 4.349365 | TCTCTCCTTCTTCTTCCTCCTTC | 58.651 | 47.826 | 0.00 | 0.00 | 0.00 | 3.46 |
854 | 916 | 4.045334 | TCTCTCCTTCTTCTTCCTCCTTCT | 59.955 | 45.833 | 0.00 | 0.00 | 0.00 | 2.85 |
855 | 917 | 4.757692 | TCTCCTTCTTCTTCCTCCTTCTT | 58.242 | 43.478 | 0.00 | 0.00 | 0.00 | 2.52 |
857 | 919 | 3.841255 | TCCTTCTTCTTCCTCCTTCTTCC | 59.159 | 47.826 | 0.00 | 0.00 | 0.00 | 3.46 |
858 | 920 | 3.843619 | CCTTCTTCTTCCTCCTTCTTCCT | 59.156 | 47.826 | 0.00 | 0.00 | 0.00 | 3.36 |
859 | 921 | 4.081142 | CCTTCTTCTTCCTCCTTCTTCCTC | 60.081 | 50.000 | 0.00 | 0.00 | 0.00 | 3.71 |
860 | 922 | 3.445987 | TCTTCTTCCTCCTTCTTCCTCC | 58.554 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
861 | 923 | 2.255770 | TCTTCCTCCTTCTTCCTCCC | 57.744 | 55.000 | 0.00 | 0.00 | 0.00 | 4.30 |
862 | 924 | 1.208706 | CTTCCTCCTTCTTCCTCCCC | 58.791 | 60.000 | 0.00 | 0.00 | 0.00 | 4.81 |
863 | 925 | 0.253207 | TTCCTCCTTCTTCCTCCCCC | 60.253 | 60.000 | 0.00 | 0.00 | 0.00 | 5.40 |
864 | 926 | 1.082954 | CCTCCTTCTTCCTCCCCCA | 59.917 | 63.158 | 0.00 | 0.00 | 0.00 | 4.96 |
865 | 927 | 1.275421 | CCTCCTTCTTCCTCCCCCAC | 61.275 | 65.000 | 0.00 | 0.00 | 0.00 | 4.61 |
902 | 964 | 2.231642 | GGATCCAAATCCCGACCCT | 58.768 | 57.895 | 6.95 | 0.00 | 45.11 | 4.34 |
936 | 998 | 0.665369 | CCGAGGCAAGCAAAAGCTTG | 60.665 | 55.000 | 22.09 | 22.09 | 46.90 | 4.01 |
952 | 1014 | 0.871163 | CTTGGCGCAATTATTGGCCG | 60.871 | 55.000 | 22.69 | 13.77 | 44.71 | 6.13 |
960 | 1022 | 2.749621 | GCAATTATTGGCCGGAGATAGG | 59.250 | 50.000 | 5.05 | 0.00 | 0.00 | 2.57 |
967 | 1029 | 1.497716 | TGGCCGGAGATAGGTAGAGAA | 59.502 | 52.381 | 5.05 | 0.00 | 0.00 | 2.87 |
974 | 1036 | 2.486592 | GAGATAGGTAGAGAAGCGAGGC | 59.513 | 54.545 | 0.00 | 0.00 | 0.00 | 4.70 |
1026 | 1088 | 4.509737 | GAGTACCAGGACGCCGGC | 62.510 | 72.222 | 19.07 | 19.07 | 0.00 | 6.13 |
1422 | 1496 | 3.200887 | CTTCGATCTCCCGCCCTCG | 62.201 | 68.421 | 0.00 | 0.00 | 0.00 | 4.63 |
1449 | 1523 | 4.082523 | TCCTGCAGCACCTACGCC | 62.083 | 66.667 | 8.66 | 0.00 | 0.00 | 5.68 |
1617 | 1697 | 2.527624 | TCTGTGGTGGAGGCTGCT | 60.528 | 61.111 | 7.74 | 0.00 | 0.00 | 4.24 |
2418 | 2512 | 4.416738 | GTGGTGGAGCAGGAGGCC | 62.417 | 72.222 | 0.00 | 0.00 | 46.50 | 5.19 |
2541 | 2674 | 4.554036 | GTCTCATCGGGGGCTGCC | 62.554 | 72.222 | 11.05 | 11.05 | 0.00 | 4.85 |
2802 | 2935 | 2.204059 | AAGGAGGGCTGCCTGACT | 60.204 | 61.111 | 19.68 | 7.18 | 35.50 | 3.41 |
2805 | 2938 | 2.730524 | GGAGGGCTGCCTGACTCTC | 61.731 | 68.421 | 19.68 | 15.19 | 0.00 | 3.20 |
2990 | 3133 | 7.615403 | AGAAGAAGCTAAATGTCATGTCAGTA | 58.385 | 34.615 | 0.00 | 0.00 | 0.00 | 2.74 |
3024 | 3167 | 2.052414 | GACCGGCTACGATCGACG | 60.052 | 66.667 | 24.34 | 18.65 | 44.60 | 5.12 |
3112 | 3260 | 4.149922 | CACCGGCATGTAGTAATGTAATCG | 59.850 | 45.833 | 0.00 | 0.00 | 0.00 | 3.34 |
3134 | 3282 | 0.974383 | TCTTCGTTCCCAGTTCTCCC | 59.026 | 55.000 | 0.00 | 0.00 | 0.00 | 4.30 |
3135 | 3283 | 0.389948 | CTTCGTTCCCAGTTCTCCCG | 60.390 | 60.000 | 0.00 | 0.00 | 0.00 | 5.14 |
3137 | 3285 | 2.747686 | GTTCCCAGTTCTCCCGCA | 59.252 | 61.111 | 0.00 | 0.00 | 0.00 | 5.69 |
3164 | 3312 | 3.604875 | TGATCACCCGTAAAACTCCTC | 57.395 | 47.619 | 0.00 | 0.00 | 0.00 | 3.71 |
3165 | 3313 | 2.235402 | TGATCACCCGTAAAACTCCTCC | 59.765 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
3166 | 3314 | 2.019807 | TCACCCGTAAAACTCCTCCT | 57.980 | 50.000 | 0.00 | 0.00 | 0.00 | 3.69 |
3167 | 3315 | 3.173953 | TCACCCGTAAAACTCCTCCTA | 57.826 | 47.619 | 0.00 | 0.00 | 0.00 | 2.94 |
3168 | 3316 | 3.509442 | TCACCCGTAAAACTCCTCCTAA | 58.491 | 45.455 | 0.00 | 0.00 | 0.00 | 2.69 |
3169 | 3317 | 3.512724 | TCACCCGTAAAACTCCTCCTAAG | 59.487 | 47.826 | 0.00 | 0.00 | 0.00 | 2.18 |
3170 | 3318 | 2.235650 | ACCCGTAAAACTCCTCCTAAGC | 59.764 | 50.000 | 0.00 | 0.00 | 0.00 | 3.09 |
3171 | 3319 | 2.419713 | CCCGTAAAACTCCTCCTAAGCC | 60.420 | 54.545 | 0.00 | 0.00 | 0.00 | 4.35 |
3173 | 3321 | 2.419713 | CGTAAAACTCCTCCTAAGCCCC | 60.420 | 54.545 | 0.00 | 0.00 | 0.00 | 5.80 |
3175 | 3323 | 1.987080 | AAACTCCTCCTAAGCCCCAT | 58.013 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 |
3178 | 3326 | 3.368921 | ACTCCTCCTAAGCCCCATTAT | 57.631 | 47.619 | 0.00 | 0.00 | 0.00 | 1.28 |
3286 | 3443 | 1.338200 | CGGACTTTGTTAGCAGCTCCT | 60.338 | 52.381 | 0.00 | 0.00 | 0.00 | 3.69 |
3311 | 3474 | 5.153513 | TGAGAATGAATTTTGTACGCAAGC | 58.846 | 37.500 | 0.00 | 0.00 | 45.62 | 4.01 |
3315 | 3478 | 2.359214 | TGAATTTTGTACGCAAGCCACA | 59.641 | 40.909 | 0.00 | 0.00 | 45.62 | 4.17 |
3323 | 3486 | 0.968405 | ACGCAAGCCACATCCAAAAT | 59.032 | 45.000 | 0.00 | 0.00 | 45.62 | 1.82 |
3346 | 3509 | 1.609072 | GGCTGACCTTTGTTCTGTTCC | 59.391 | 52.381 | 0.00 | 0.00 | 0.00 | 3.62 |
3349 | 3512 | 2.943033 | CTGACCTTTGTTCTGTTCCGTT | 59.057 | 45.455 | 0.00 | 0.00 | 0.00 | 4.44 |
3350 | 3513 | 2.940410 | TGACCTTTGTTCTGTTCCGTTC | 59.060 | 45.455 | 0.00 | 0.00 | 0.00 | 3.95 |
3351 | 3514 | 3.203716 | GACCTTTGTTCTGTTCCGTTCT | 58.796 | 45.455 | 0.00 | 0.00 | 0.00 | 3.01 |
3352 | 3515 | 3.617284 | ACCTTTGTTCTGTTCCGTTCTT | 58.383 | 40.909 | 0.00 | 0.00 | 0.00 | 2.52 |
3353 | 3516 | 3.377172 | ACCTTTGTTCTGTTCCGTTCTTG | 59.623 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
3354 | 3517 | 3.625764 | CCTTTGTTCTGTTCCGTTCTTGA | 59.374 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
3355 | 3518 | 4.275936 | CCTTTGTTCTGTTCCGTTCTTGAT | 59.724 | 41.667 | 0.00 | 0.00 | 0.00 | 2.57 |
3356 | 3519 | 5.418310 | TTTGTTCTGTTCCGTTCTTGATC | 57.582 | 39.130 | 0.00 | 0.00 | 0.00 | 2.92 |
3357 | 3520 | 4.066646 | TGTTCTGTTCCGTTCTTGATCA | 57.933 | 40.909 | 0.00 | 0.00 | 0.00 | 2.92 |
3358 | 3521 | 4.058124 | TGTTCTGTTCCGTTCTTGATCAG | 58.942 | 43.478 | 0.00 | 0.00 | 33.03 | 2.90 |
3359 | 3522 | 4.058817 | GTTCTGTTCCGTTCTTGATCAGT | 58.941 | 43.478 | 0.00 | 0.00 | 33.36 | 3.41 |
3360 | 3523 | 3.653344 | TCTGTTCCGTTCTTGATCAGTG | 58.347 | 45.455 | 0.00 | 0.00 | 33.36 | 3.66 |
3361 | 3524 | 2.738846 | CTGTTCCGTTCTTGATCAGTGG | 59.261 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 |
3362 | 3525 | 2.104111 | TGTTCCGTTCTTGATCAGTGGT | 59.896 | 45.455 | 0.00 | 0.00 | 0.00 | 4.16 |
3363 | 3526 | 3.322541 | TGTTCCGTTCTTGATCAGTGGTA | 59.677 | 43.478 | 0.00 | 0.00 | 0.00 | 3.25 |
3364 | 3527 | 4.020573 | TGTTCCGTTCTTGATCAGTGGTAT | 60.021 | 41.667 | 0.00 | 0.00 | 0.00 | 2.73 |
3365 | 3528 | 5.186215 | TGTTCCGTTCTTGATCAGTGGTATA | 59.814 | 40.000 | 0.00 | 0.00 | 0.00 | 1.47 |
3366 | 3529 | 5.925506 | TCCGTTCTTGATCAGTGGTATAA | 57.074 | 39.130 | 0.00 | 0.00 | 0.00 | 0.98 |
3367 | 3530 | 5.902681 | TCCGTTCTTGATCAGTGGTATAAG | 58.097 | 41.667 | 0.00 | 0.00 | 0.00 | 1.73 |
3368 | 3531 | 4.508124 | CCGTTCTTGATCAGTGGTATAAGC | 59.492 | 45.833 | 0.00 | 0.00 | 0.00 | 3.09 |
3369 | 3532 | 5.352284 | CGTTCTTGATCAGTGGTATAAGCT | 58.648 | 41.667 | 0.00 | 0.00 | 0.00 | 3.74 |
3370 | 3533 | 5.812642 | CGTTCTTGATCAGTGGTATAAGCTT | 59.187 | 40.000 | 3.48 | 3.48 | 0.00 | 3.74 |
3371 | 3534 | 6.237942 | CGTTCTTGATCAGTGGTATAAGCTTG | 60.238 | 42.308 | 9.86 | 0.00 | 0.00 | 4.01 |
3383 | 3546 | 5.530915 | TGGTATAAGCTTGTATGTTCATGGC | 59.469 | 40.000 | 9.86 | 0.00 | 0.00 | 4.40 |
3396 | 3559 | 0.035317 | TCATGGCGTTCACTGCTCTT | 59.965 | 50.000 | 0.00 | 0.00 | 0.00 | 2.85 |
3421 | 3599 | 2.352388 | ACATGATGGCTTTGCAATTGC | 58.648 | 42.857 | 23.69 | 23.69 | 42.50 | 3.56 |
3425 | 3603 | 1.997606 | GATGGCTTTGCAATTGCTGAC | 59.002 | 47.619 | 29.37 | 21.16 | 42.66 | 3.51 |
3429 | 3607 | 1.689959 | CTTTGCAATTGCTGACCGTC | 58.310 | 50.000 | 29.37 | 0.24 | 42.66 | 4.79 |
3432 | 3610 | 0.250252 | TGCAATTGCTGACCGTCTGA | 60.250 | 50.000 | 29.37 | 3.82 | 42.66 | 3.27 |
3451 | 3629 | 1.286305 | ACTTGGGGACTTGGTGGTGT | 61.286 | 55.000 | 0.00 | 0.00 | 0.00 | 4.16 |
3452 | 3630 | 0.823356 | CTTGGGGACTTGGTGGTGTG | 60.823 | 60.000 | 0.00 | 0.00 | 0.00 | 3.82 |
3453 | 3631 | 2.597510 | GGGGACTTGGTGGTGTGC | 60.598 | 66.667 | 0.00 | 0.00 | 0.00 | 4.57 |
3491 | 3669 | 4.687948 | CACATCACGGATTAGATTAGCCTG | 59.312 | 45.833 | 0.00 | 0.00 | 0.00 | 4.85 |
3540 | 3718 | 3.094572 | ACGAAGTTTCCCGATCTAGGAA | 58.905 | 45.455 | 9.41 | 9.41 | 37.78 | 3.36 |
3591 | 3769 | 0.606604 | TCTCGTGTAGTTTCCCCTGC | 59.393 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
3592 | 3770 | 0.608640 | CTCGTGTAGTTTCCCCTGCT | 59.391 | 55.000 | 0.00 | 0.00 | 0.00 | 4.24 |
3598 | 3776 | 2.463589 | TAGTTTCCCCTGCTGTGCCG | 62.464 | 60.000 | 0.00 | 0.00 | 0.00 | 5.69 |
3671 | 3850 | 0.320421 | TGCACGTTAGTTGGAGAGGC | 60.320 | 55.000 | 0.00 | 0.00 | 0.00 | 4.70 |
3673 | 3852 | 1.080025 | ACGTTAGTTGGAGAGGCGC | 60.080 | 57.895 | 0.00 | 0.00 | 0.00 | 6.53 |
3674 | 3853 | 1.080093 | CGTTAGTTGGAGAGGCGCA | 60.080 | 57.895 | 10.83 | 0.00 | 0.00 | 6.09 |
3675 | 3854 | 0.460284 | CGTTAGTTGGAGAGGCGCAT | 60.460 | 55.000 | 10.83 | 0.00 | 0.00 | 4.73 |
3676 | 3855 | 1.291132 | GTTAGTTGGAGAGGCGCATC | 58.709 | 55.000 | 15.45 | 15.45 | 0.00 | 3.91 |
3677 | 3856 | 0.901827 | TTAGTTGGAGAGGCGCATCA | 59.098 | 50.000 | 25.38 | 0.38 | 0.00 | 3.07 |
3678 | 3857 | 0.175760 | TAGTTGGAGAGGCGCATCAC | 59.824 | 55.000 | 25.38 | 18.28 | 0.00 | 3.06 |
3679 | 3858 | 2.109126 | GTTGGAGAGGCGCATCACC | 61.109 | 63.158 | 28.11 | 28.11 | 0.00 | 4.02 |
3680 | 3859 | 2.293318 | TTGGAGAGGCGCATCACCT | 61.293 | 57.895 | 32.59 | 11.00 | 41.41 | 4.00 |
3734 | 3930 | 3.242543 | GCCGTAGCAATCAGTTGATCAAG | 60.243 | 47.826 | 8.80 | 0.00 | 37.53 | 3.02 |
3751 | 3947 | 4.002906 | TCAAGCCGAATACTGTTTCTGT | 57.997 | 40.909 | 0.00 | 0.00 | 0.00 | 3.41 |
3777 | 3976 | 3.853330 | CCGTCTGAATGCCGCACG | 61.853 | 66.667 | 0.00 | 0.00 | 0.00 | 5.34 |
3794 | 3993 | 1.237285 | ACGGCCACAGCAATCAGTTC | 61.237 | 55.000 | 2.24 | 0.00 | 42.56 | 3.01 |
3795 | 3994 | 1.885871 | GGCCACAGCAATCAGTTCC | 59.114 | 57.895 | 0.00 | 0.00 | 42.56 | 3.62 |
3803 | 4002 | 3.693085 | ACAGCAATCAGTTCCATGATCAC | 59.307 | 43.478 | 0.00 | 0.00 | 39.00 | 3.06 |
3807 | 4006 | 3.928005 | ATCAGTTCCATGATCACAGCT | 57.072 | 42.857 | 0.00 | 0.00 | 34.84 | 4.24 |
3808 | 4007 | 3.708403 | TCAGTTCCATGATCACAGCTT | 57.292 | 42.857 | 0.00 | 0.00 | 0.00 | 3.74 |
3809 | 4008 | 4.025040 | TCAGTTCCATGATCACAGCTTT | 57.975 | 40.909 | 0.00 | 0.00 | 0.00 | 3.51 |
3811 | 4010 | 4.937620 | TCAGTTCCATGATCACAGCTTTAC | 59.062 | 41.667 | 0.00 | 0.00 | 0.00 | 2.01 |
3812 | 4011 | 4.696877 | CAGTTCCATGATCACAGCTTTACA | 59.303 | 41.667 | 0.00 | 0.00 | 0.00 | 2.41 |
3813 | 4012 | 4.697352 | AGTTCCATGATCACAGCTTTACAC | 59.303 | 41.667 | 0.00 | 0.00 | 0.00 | 2.90 |
3840 | 4044 | 3.482809 | CACTGCTGATCGGTGCTG | 58.517 | 61.111 | 2.89 | 6.91 | 44.30 | 4.41 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
11 | 12 | 0.031917 | TACGGGTCAAGCCATAGGGA | 60.032 | 55.000 | 0.00 | 0.00 | 39.65 | 4.20 |
24 | 25 | 1.826720 | ACACACGGTTATGATACGGGT | 59.173 | 47.619 | 0.00 | 0.00 | 46.33 | 5.28 |
60 | 61 | 2.157474 | TGATTTTGTCTCGCATGACACG | 59.843 | 45.455 | 8.09 | 0.00 | 45.32 | 4.49 |
69 | 70 | 7.203218 | TGACCTATCTACATGATTTTGTCTCG | 58.797 | 38.462 | 0.00 | 0.00 | 36.65 | 4.04 |
81 | 82 | 7.669722 | ACAACCAACATTTTGACCTATCTACAT | 59.330 | 33.333 | 0.00 | 0.00 | 34.24 | 2.29 |
82 | 83 | 7.001674 | ACAACCAACATTTTGACCTATCTACA | 58.998 | 34.615 | 0.00 | 0.00 | 34.24 | 2.74 |
83 | 84 | 7.448748 | ACAACCAACATTTTGACCTATCTAC | 57.551 | 36.000 | 0.00 | 0.00 | 34.24 | 2.59 |
84 | 85 | 9.226606 | CTAACAACCAACATTTTGACCTATCTA | 57.773 | 33.333 | 0.00 | 0.00 | 34.24 | 1.98 |
85 | 86 | 6.976934 | AACAACCAACATTTTGACCTATCT | 57.023 | 33.333 | 0.00 | 0.00 | 34.24 | 1.98 |
86 | 87 | 8.106247 | TCTAACAACCAACATTTTGACCTATC | 57.894 | 34.615 | 0.00 | 0.00 | 34.24 | 2.08 |
88 | 89 | 8.472007 | AATCTAACAACCAACATTTTGACCTA | 57.528 | 30.769 | 0.00 | 0.00 | 34.24 | 3.08 |
89 | 90 | 6.976934 | ATCTAACAACCAACATTTTGACCT | 57.023 | 33.333 | 0.00 | 0.00 | 34.24 | 3.85 |
90 | 91 | 6.362283 | CGAATCTAACAACCAACATTTTGACC | 59.638 | 38.462 | 0.00 | 0.00 | 34.24 | 4.02 |
92 | 93 | 6.039941 | ACCGAATCTAACAACCAACATTTTGA | 59.960 | 34.615 | 0.00 | 0.00 | 34.24 | 2.69 |
93 | 94 | 6.212955 | ACCGAATCTAACAACCAACATTTTG | 58.787 | 36.000 | 0.00 | 0.00 | 0.00 | 2.44 |
94 | 95 | 6.039941 | TGACCGAATCTAACAACCAACATTTT | 59.960 | 34.615 | 0.00 | 0.00 | 0.00 | 1.82 |
114 | 115 | 4.537965 | CCTAACTTGTCTATCGATGACCG | 58.462 | 47.826 | 18.87 | 14.20 | 40.25 | 4.79 |
116 | 117 | 4.202121 | TGCCCTAACTTGTCTATCGATGAC | 60.202 | 45.833 | 8.54 | 13.59 | 35.21 | 3.06 |
123 | 124 | 6.313519 | TCAAAGATGCCCTAACTTGTCTAT | 57.686 | 37.500 | 0.00 | 0.00 | 0.00 | 1.98 |
144 | 145 | 8.671028 | CATGTGTTTCTAGAATCATGTGAATCA | 58.329 | 33.333 | 23.10 | 14.88 | 0.00 | 2.57 |
173 | 174 | 4.923281 | GGCGTAACTTTGCAATCTTTTCAT | 59.077 | 37.500 | 0.00 | 0.00 | 0.00 | 2.57 |
175 | 176 | 3.673338 | GGGCGTAACTTTGCAATCTTTTC | 59.327 | 43.478 | 0.00 | 0.00 | 0.00 | 2.29 |
190 | 191 | 2.757314 | TGCATGATTCAAATGGGCGTAA | 59.243 | 40.909 | 0.00 | 0.00 | 0.00 | 3.18 |
193 | 194 | 1.563111 | GTGCATGATTCAAATGGGCG | 58.437 | 50.000 | 0.00 | 0.00 | 0.00 | 6.13 |
225 | 226 | 1.006825 | GTTTTTCCGGCGATGCAACC | 61.007 | 55.000 | 9.30 | 0.00 | 0.00 | 3.77 |
245 | 246 | 5.243730 | TGAAAACCTCATGAAAAGGATCCAC | 59.756 | 40.000 | 15.82 | 2.97 | 37.35 | 4.02 |
251 | 252 | 4.584325 | TCCACTGAAAACCTCATGAAAAGG | 59.416 | 41.667 | 0.00 | 0.00 | 39.96 | 3.11 |
252 | 253 | 5.067674 | TGTCCACTGAAAACCTCATGAAAAG | 59.932 | 40.000 | 0.00 | 0.00 | 32.14 | 2.27 |
257 | 258 | 3.480470 | AGTGTCCACTGAAAACCTCATG | 58.520 | 45.455 | 0.00 | 0.00 | 40.75 | 3.07 |
259 | 260 | 3.964688 | TCTAGTGTCCACTGAAAACCTCA | 59.035 | 43.478 | 10.15 | 0.00 | 42.52 | 3.86 |
263 | 264 | 5.998363 | AGGAATTCTAGTGTCCACTGAAAAC | 59.002 | 40.000 | 10.15 | 9.19 | 42.52 | 2.43 |
268 | 269 | 4.020218 | TCCAAGGAATTCTAGTGTCCACTG | 60.020 | 45.833 | 10.15 | 1.15 | 42.52 | 3.66 |
275 | 276 | 8.737168 | TGTATTCATTCCAAGGAATTCTAGTG | 57.263 | 34.615 | 11.54 | 1.96 | 42.30 | 2.74 |
276 | 277 | 9.753674 | TTTGTATTCATTCCAAGGAATTCTAGT | 57.246 | 29.630 | 11.54 | 1.36 | 42.30 | 2.57 |
284 | 285 | 7.840716 | AGGATTCATTTGTATTCATTCCAAGGA | 59.159 | 33.333 | 0.00 | 0.00 | 0.00 | 3.36 |
286 | 287 | 9.309516 | CAAGGATTCATTTGTATTCATTCCAAG | 57.690 | 33.333 | 0.00 | 0.00 | 0.00 | 3.61 |
370 | 373 | 4.183916 | AGGAGTCTTTTAATCCTTGGGGA | 58.816 | 43.478 | 0.00 | 0.00 | 40.65 | 4.81 |
371 | 374 | 4.592997 | AGGAGTCTTTTAATCCTTGGGG | 57.407 | 45.455 | 0.00 | 0.00 | 40.65 | 4.96 |
386 | 389 | 2.933260 | GCCTCTTTGAATCGAAGGAGTC | 59.067 | 50.000 | 10.14 | 0.00 | 37.76 | 3.36 |
387 | 390 | 2.355209 | GGCCTCTTTGAATCGAAGGAGT | 60.355 | 50.000 | 10.14 | 0.00 | 0.00 | 3.85 |
449 | 460 | 1.676635 | GCTTGCAGTGCTCATGGGA | 60.677 | 57.895 | 17.60 | 0.00 | 0.00 | 4.37 |
450 | 461 | 2.707849 | GGCTTGCAGTGCTCATGGG | 61.708 | 63.158 | 17.60 | 0.00 | 0.00 | 4.00 |
459 | 470 | 1.374190 | CCTCTCTGTGGCTTGCAGT | 59.626 | 57.895 | 0.00 | 0.00 | 35.60 | 4.40 |
503 | 514 | 1.745232 | CTCTGCTACGTCTGACTCCT | 58.255 | 55.000 | 6.21 | 0.00 | 0.00 | 3.69 |
510 | 521 | 2.760385 | GGGGGCTCTGCTACGTCT | 60.760 | 66.667 | 0.00 | 0.00 | 0.00 | 4.18 |
527 | 552 | 8.761575 | ATTAAATAAAAATGCTATGCGGGATG | 57.238 | 30.769 | 0.00 | 0.00 | 0.00 | 3.51 |
528 | 553 | 9.777297 | AAATTAAATAAAAATGCTATGCGGGAT | 57.223 | 25.926 | 0.00 | 0.00 | 0.00 | 3.85 |
529 | 554 | 9.039870 | CAAATTAAATAAAAATGCTATGCGGGA | 57.960 | 29.630 | 0.00 | 0.00 | 0.00 | 5.14 |
530 | 555 | 7.798052 | GCAAATTAAATAAAAATGCTATGCGGG | 59.202 | 33.333 | 0.00 | 0.00 | 32.72 | 6.13 |
533 | 558 | 7.798052 | CCCGCAAATTAAATAAAAATGCTATGC | 59.202 | 33.333 | 0.00 | 0.00 | 33.08 | 3.14 |
534 | 559 | 8.281893 | CCCCGCAAATTAAATAAAAATGCTATG | 58.718 | 33.333 | 0.00 | 0.00 | 33.08 | 2.23 |
535 | 560 | 8.207545 | TCCCCGCAAATTAAATAAAAATGCTAT | 58.792 | 29.630 | 0.00 | 0.00 | 33.08 | 2.97 |
536 | 561 | 7.556844 | TCCCCGCAAATTAAATAAAAATGCTA | 58.443 | 30.769 | 0.00 | 0.00 | 33.08 | 3.49 |
537 | 562 | 6.410540 | TCCCCGCAAATTAAATAAAAATGCT | 58.589 | 32.000 | 0.00 | 0.00 | 33.08 | 3.79 |
538 | 563 | 6.670077 | TCCCCGCAAATTAAATAAAAATGC | 57.330 | 33.333 | 0.00 | 0.00 | 32.34 | 3.56 |
539 | 564 | 9.715123 | GAAATCCCCGCAAATTAAATAAAAATG | 57.285 | 29.630 | 0.00 | 0.00 | 0.00 | 2.32 |
540 | 565 | 9.679661 | AGAAATCCCCGCAAATTAAATAAAAAT | 57.320 | 25.926 | 0.00 | 0.00 | 0.00 | 1.82 |
546 | 573 | 4.141733 | CCCAGAAATCCCCGCAAATTAAAT | 60.142 | 41.667 | 0.00 | 0.00 | 0.00 | 1.40 |
702 | 729 | 2.273449 | GCATCTGGGTCTGGGTGG | 59.727 | 66.667 | 0.00 | 0.00 | 0.00 | 4.61 |
703 | 730 | 1.856539 | AAGGCATCTGGGTCTGGGTG | 61.857 | 60.000 | 0.00 | 0.00 | 0.00 | 4.61 |
704 | 731 | 1.542375 | AAGGCATCTGGGTCTGGGT | 60.542 | 57.895 | 0.00 | 0.00 | 0.00 | 4.51 |
708 | 735 | 2.003548 | GGGGAAGGCATCTGGGTCT | 61.004 | 63.158 | 0.00 | 0.00 | 0.00 | 3.85 |
710 | 737 | 3.023735 | GGGGGAAGGCATCTGGGT | 61.024 | 66.667 | 0.00 | 0.00 | 0.00 | 4.51 |
758 | 792 | 3.382864 | TAGGGGAAGGGGAGGGGG | 61.383 | 72.222 | 0.00 | 0.00 | 0.00 | 5.40 |
759 | 793 | 2.039724 | GTAGGGGAAGGGGAGGGG | 60.040 | 72.222 | 0.00 | 0.00 | 0.00 | 4.79 |
760 | 794 | 1.084084 | TTGTAGGGGAAGGGGAGGG | 59.916 | 63.158 | 0.00 | 0.00 | 0.00 | 4.30 |
761 | 795 | 0.253207 | AGTTGTAGGGGAAGGGGAGG | 60.253 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
762 | 796 | 2.117051 | GTAGTTGTAGGGGAAGGGGAG | 58.883 | 57.143 | 0.00 | 0.00 | 0.00 | 4.30 |
763 | 797 | 1.726352 | AGTAGTTGTAGGGGAAGGGGA | 59.274 | 52.381 | 0.00 | 0.00 | 0.00 | 4.81 |
764 | 798 | 2.265526 | AGTAGTTGTAGGGGAAGGGG | 57.734 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
765 | 799 | 3.991683 | AGTAGTAGTTGTAGGGGAAGGG | 58.008 | 50.000 | 0.00 | 0.00 | 0.00 | 3.95 |
766 | 800 | 5.764432 | AGTAGTAGTAGTTGTAGGGGAAGG | 58.236 | 45.833 | 0.00 | 0.00 | 0.00 | 3.46 |
767 | 801 | 5.526846 | CGAGTAGTAGTAGTTGTAGGGGAAG | 59.473 | 48.000 | 0.00 | 0.00 | 0.00 | 3.46 |
768 | 802 | 5.431765 | CGAGTAGTAGTAGTTGTAGGGGAA | 58.568 | 45.833 | 0.00 | 0.00 | 0.00 | 3.97 |
769 | 803 | 4.684485 | GCGAGTAGTAGTAGTTGTAGGGGA | 60.684 | 50.000 | 0.00 | 0.00 | 0.00 | 4.81 |
770 | 804 | 3.563390 | GCGAGTAGTAGTAGTTGTAGGGG | 59.437 | 52.174 | 0.00 | 0.00 | 0.00 | 4.79 |
771 | 805 | 4.450053 | AGCGAGTAGTAGTAGTTGTAGGG | 58.550 | 47.826 | 0.00 | 0.00 | 0.00 | 3.53 |
772 | 806 | 4.511082 | GGAGCGAGTAGTAGTAGTTGTAGG | 59.489 | 50.000 | 0.00 | 0.00 | 0.00 | 3.18 |
773 | 807 | 4.511082 | GGGAGCGAGTAGTAGTAGTTGTAG | 59.489 | 50.000 | 0.00 | 0.00 | 0.00 | 2.74 |
815 | 849 | 1.694955 | GAGAGAGCAAAGCAGCGAGC | 61.695 | 60.000 | 0.00 | 0.00 | 46.19 | 5.03 |
816 | 850 | 0.108709 | AGAGAGAGCAAAGCAGCGAG | 60.109 | 55.000 | 0.00 | 0.00 | 40.15 | 5.03 |
817 | 851 | 0.108898 | GAGAGAGAGCAAAGCAGCGA | 60.109 | 55.000 | 0.00 | 0.00 | 40.15 | 4.93 |
818 | 852 | 1.083242 | GGAGAGAGAGCAAAGCAGCG | 61.083 | 60.000 | 0.00 | 0.00 | 40.15 | 5.18 |
822 | 856 | 3.055891 | AGAAGAAGGAGAGAGAGCAAAGC | 60.056 | 47.826 | 0.00 | 0.00 | 0.00 | 3.51 |
823 | 857 | 4.806640 | AGAAGAAGGAGAGAGAGCAAAG | 57.193 | 45.455 | 0.00 | 0.00 | 0.00 | 2.77 |
824 | 858 | 4.020662 | GGAAGAAGAAGGAGAGAGAGCAAA | 60.021 | 45.833 | 0.00 | 0.00 | 0.00 | 3.68 |
826 | 860 | 3.096092 | GGAAGAAGAAGGAGAGAGAGCA | 58.904 | 50.000 | 0.00 | 0.00 | 0.00 | 4.26 |
831 | 893 | 4.045334 | AGAAGGAGGAAGAAGAAGGAGAGA | 59.955 | 45.833 | 0.00 | 0.00 | 0.00 | 3.10 |
832 | 894 | 4.352893 | AGAAGGAGGAAGAAGAAGGAGAG | 58.647 | 47.826 | 0.00 | 0.00 | 0.00 | 3.20 |
839 | 901 | 3.445987 | GGAGGAAGAAGGAGGAAGAAGA | 58.554 | 50.000 | 0.00 | 0.00 | 0.00 | 2.87 |
852 | 914 | 4.364686 | GGGGGTGGGGGAGGAAGA | 62.365 | 72.222 | 0.00 | 0.00 | 0.00 | 2.87 |
902 | 964 | 3.315949 | CGGTTCCGGTTCTGGGGA | 61.316 | 66.667 | 0.00 | 0.00 | 0.00 | 4.81 |
936 | 998 | 2.027460 | CCGGCCAATAATTGCGCC | 59.973 | 61.111 | 4.18 | 0.00 | 41.01 | 6.53 |
952 | 1014 | 3.078837 | CCTCGCTTCTCTACCTATCTCC | 58.921 | 54.545 | 0.00 | 0.00 | 0.00 | 3.71 |
960 | 1022 | 0.248866 | GAGCTGCCTCGCTTCTCTAC | 60.249 | 60.000 | 0.00 | 0.00 | 41.08 | 2.59 |
984 | 1046 | 1.953138 | CATGATCTCGCCTCACCGC | 60.953 | 63.158 | 0.00 | 0.00 | 0.00 | 5.68 |
985 | 1047 | 0.103026 | TTCATGATCTCGCCTCACCG | 59.897 | 55.000 | 0.00 | 0.00 | 0.00 | 4.94 |
986 | 1048 | 1.863267 | CTTCATGATCTCGCCTCACC | 58.137 | 55.000 | 0.00 | 0.00 | 0.00 | 4.02 |
987 | 1049 | 1.216122 | GCTTCATGATCTCGCCTCAC | 58.784 | 55.000 | 0.00 | 0.00 | 0.00 | 3.51 |
988 | 1050 | 0.249197 | CGCTTCATGATCTCGCCTCA | 60.249 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
1059 | 1124 | 2.094026 | CGACACCATCATCTTGTCCTCA | 60.094 | 50.000 | 0.00 | 0.00 | 37.01 | 3.86 |
1398 | 1472 | 1.389609 | GCGGGAGATCGAAGTACCCA | 61.390 | 60.000 | 16.47 | 0.00 | 40.45 | 4.51 |
1422 | 1496 | 1.376553 | GCTGCAGGAGGAGTCAACC | 60.377 | 63.158 | 17.12 | 0.00 | 35.34 | 3.77 |
1425 | 1499 | 2.587247 | GGTGCTGCAGGAGGAGTCA | 61.587 | 63.158 | 17.12 | 0.00 | 35.34 | 3.41 |
2418 | 2512 | 1.172180 | ATGTGCCGGAGTTGTGGTTG | 61.172 | 55.000 | 5.05 | 0.00 | 0.00 | 3.77 |
2959 | 3094 | 7.333921 | ACATGACATTTAGCTTCTTCTTCAGAG | 59.666 | 37.037 | 0.00 | 0.00 | 31.12 | 3.35 |
2960 | 3095 | 7.164122 | ACATGACATTTAGCTTCTTCTTCAGA | 58.836 | 34.615 | 0.00 | 0.00 | 0.00 | 3.27 |
2961 | 3096 | 7.118825 | TGACATGACATTTAGCTTCTTCTTCAG | 59.881 | 37.037 | 0.00 | 0.00 | 0.00 | 3.02 |
2962 | 3097 | 6.936335 | TGACATGACATTTAGCTTCTTCTTCA | 59.064 | 34.615 | 0.00 | 0.00 | 0.00 | 3.02 |
3024 | 3167 | 4.105553 | GGAACCACCCGTAGCCCC | 62.106 | 72.222 | 0.00 | 0.00 | 0.00 | 5.80 |
3112 | 3260 | 2.070028 | GAGAACTGGGAACGAAGAAGC | 58.930 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
3134 | 3282 | 1.524621 | GGGTGATCATGGAGGTGCG | 60.525 | 63.158 | 0.00 | 0.00 | 0.00 | 5.34 |
3135 | 3283 | 1.524621 | CGGGTGATCATGGAGGTGC | 60.525 | 63.158 | 0.00 | 0.00 | 0.00 | 5.01 |
3137 | 3285 | 1.874129 | TTACGGGTGATCATGGAGGT | 58.126 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
3164 | 3312 | 7.793948 | AGTAGTAGTAATAATGGGGCTTAGG | 57.206 | 40.000 | 0.00 | 0.00 | 0.00 | 2.69 |
3165 | 3313 | 9.531158 | AGTAGTAGTAGTAATAATGGGGCTTAG | 57.469 | 37.037 | 0.00 | 0.00 | 0.00 | 2.18 |
3219 | 3376 | 5.050091 | GCGATTGGAGGAATTACACATACAG | 60.050 | 44.000 | 0.00 | 0.00 | 0.00 | 2.74 |
3220 | 3377 | 4.814234 | GCGATTGGAGGAATTACACATACA | 59.186 | 41.667 | 0.00 | 0.00 | 0.00 | 2.29 |
3221 | 3378 | 5.057149 | AGCGATTGGAGGAATTACACATAC | 58.943 | 41.667 | 0.00 | 0.00 | 0.00 | 2.39 |
3222 | 3379 | 5.163353 | TGAGCGATTGGAGGAATTACACATA | 60.163 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
3223 | 3380 | 4.130118 | GAGCGATTGGAGGAATTACACAT | 58.870 | 43.478 | 0.00 | 0.00 | 0.00 | 3.21 |
3286 | 3443 | 6.966632 | GCTTGCGTACAAAATTCATTCTCATA | 59.033 | 34.615 | 0.00 | 0.00 | 34.74 | 2.15 |
3323 | 3486 | 1.064017 | ACAGAACAAAGGTCAGCCCAA | 60.064 | 47.619 | 0.00 | 0.00 | 34.66 | 4.12 |
3332 | 3495 | 3.625764 | TCAAGAACGGAACAGAACAAAGG | 59.374 | 43.478 | 0.00 | 0.00 | 0.00 | 3.11 |
3346 | 3509 | 5.352284 | AGCTTATACCACTGATCAAGAACG | 58.648 | 41.667 | 0.00 | 0.00 | 0.00 | 3.95 |
3349 | 3512 | 6.299805 | ACAAGCTTATACCACTGATCAAGA | 57.700 | 37.500 | 0.00 | 0.00 | 0.00 | 3.02 |
3350 | 3513 | 7.712639 | ACATACAAGCTTATACCACTGATCAAG | 59.287 | 37.037 | 0.00 | 0.00 | 0.00 | 3.02 |
3351 | 3514 | 7.564793 | ACATACAAGCTTATACCACTGATCAA | 58.435 | 34.615 | 0.00 | 0.00 | 0.00 | 2.57 |
3352 | 3515 | 7.124573 | ACATACAAGCTTATACCACTGATCA | 57.875 | 36.000 | 0.00 | 0.00 | 0.00 | 2.92 |
3353 | 3516 | 7.710907 | TGAACATACAAGCTTATACCACTGATC | 59.289 | 37.037 | 0.00 | 0.00 | 0.00 | 2.92 |
3354 | 3517 | 7.564793 | TGAACATACAAGCTTATACCACTGAT | 58.435 | 34.615 | 0.00 | 0.00 | 0.00 | 2.90 |
3355 | 3518 | 6.941857 | TGAACATACAAGCTTATACCACTGA | 58.058 | 36.000 | 0.00 | 0.00 | 0.00 | 3.41 |
3356 | 3519 | 7.254898 | CCATGAACATACAAGCTTATACCACTG | 60.255 | 40.741 | 0.00 | 0.00 | 0.00 | 3.66 |
3357 | 3520 | 6.767902 | CCATGAACATACAAGCTTATACCACT | 59.232 | 38.462 | 0.00 | 0.00 | 0.00 | 4.00 |
3358 | 3521 | 6.513393 | GCCATGAACATACAAGCTTATACCAC | 60.513 | 42.308 | 0.00 | 0.00 | 0.00 | 4.16 |
3359 | 3522 | 5.530915 | GCCATGAACATACAAGCTTATACCA | 59.469 | 40.000 | 0.00 | 0.00 | 0.00 | 3.25 |
3360 | 3523 | 5.334105 | CGCCATGAACATACAAGCTTATACC | 60.334 | 44.000 | 0.00 | 0.00 | 0.00 | 2.73 |
3361 | 3524 | 5.236478 | ACGCCATGAACATACAAGCTTATAC | 59.764 | 40.000 | 0.00 | 0.00 | 0.00 | 1.47 |
3362 | 3525 | 5.364778 | ACGCCATGAACATACAAGCTTATA | 58.635 | 37.500 | 0.00 | 0.00 | 0.00 | 0.98 |
3363 | 3526 | 4.199310 | ACGCCATGAACATACAAGCTTAT | 58.801 | 39.130 | 0.00 | 0.00 | 0.00 | 1.73 |
3364 | 3527 | 3.605634 | ACGCCATGAACATACAAGCTTA | 58.394 | 40.909 | 0.00 | 0.00 | 0.00 | 3.09 |
3365 | 3528 | 2.436417 | ACGCCATGAACATACAAGCTT | 58.564 | 42.857 | 0.00 | 0.00 | 0.00 | 3.74 |
3366 | 3529 | 2.113860 | ACGCCATGAACATACAAGCT | 57.886 | 45.000 | 0.00 | 0.00 | 0.00 | 3.74 |
3367 | 3530 | 2.161410 | TGAACGCCATGAACATACAAGC | 59.839 | 45.455 | 0.00 | 0.00 | 0.00 | 4.01 |
3368 | 3531 | 3.436704 | AGTGAACGCCATGAACATACAAG | 59.563 | 43.478 | 0.00 | 0.00 | 0.00 | 3.16 |
3369 | 3532 | 3.188254 | CAGTGAACGCCATGAACATACAA | 59.812 | 43.478 | 0.00 | 0.00 | 0.00 | 2.41 |
3370 | 3533 | 2.741517 | CAGTGAACGCCATGAACATACA | 59.258 | 45.455 | 0.00 | 0.00 | 0.00 | 2.29 |
3371 | 3534 | 2.476185 | GCAGTGAACGCCATGAACATAC | 60.476 | 50.000 | 0.00 | 0.00 | 0.00 | 2.39 |
3396 | 3559 | 5.601583 | ATTGCAAAGCCATCATGTTCATA | 57.398 | 34.783 | 1.71 | 0.00 | 0.00 | 2.15 |
3421 | 3599 | 1.185618 | TCCCCAAGTCAGACGGTCAG | 61.186 | 60.000 | 11.27 | 2.08 | 0.00 | 3.51 |
3425 | 3603 | 0.320771 | CAAGTCCCCAAGTCAGACGG | 60.321 | 60.000 | 0.00 | 0.00 | 35.65 | 4.79 |
3429 | 3607 | 0.250901 | CCACCAAGTCCCCAAGTCAG | 60.251 | 60.000 | 0.00 | 0.00 | 0.00 | 3.51 |
3432 | 3610 | 1.286305 | ACACCACCAAGTCCCCAAGT | 61.286 | 55.000 | 0.00 | 0.00 | 0.00 | 3.16 |
3451 | 3629 | 1.634973 | TGTGAATCTCTTCCCATGGCA | 59.365 | 47.619 | 6.09 | 0.00 | 0.00 | 4.92 |
3452 | 3630 | 2.425143 | TGTGAATCTCTTCCCATGGC | 57.575 | 50.000 | 6.09 | 0.00 | 0.00 | 4.40 |
3453 | 3631 | 3.881688 | GTGATGTGAATCTCTTCCCATGG | 59.118 | 47.826 | 4.14 | 4.14 | 30.76 | 3.66 |
3461 | 3639 | 6.662865 | ATCTAATCCGTGATGTGAATCTCT | 57.337 | 37.500 | 0.00 | 0.00 | 0.00 | 3.10 |
3491 | 3669 | 0.519077 | CTCTCAAAGACGGCAAAGGC | 59.481 | 55.000 | 0.00 | 0.00 | 40.13 | 4.35 |
3570 | 3748 | 2.893637 | CAGGGGAAACTACACGAGATG | 58.106 | 52.381 | 0.00 | 0.00 | 0.00 | 2.90 |
3635 | 3813 | 4.759693 | ACGTGCAGGTTCATTTTTAGATGA | 59.240 | 37.500 | 6.15 | 0.00 | 34.37 | 2.92 |
3636 | 3814 | 5.046910 | ACGTGCAGGTTCATTTTTAGATG | 57.953 | 39.130 | 6.15 | 0.00 | 0.00 | 2.90 |
3671 | 3850 | 1.077501 | ATTGGTGGGAGGTGATGCG | 60.078 | 57.895 | 0.00 | 0.00 | 0.00 | 4.73 |
3673 | 3852 | 0.464373 | CCGATTGGTGGGAGGTGATG | 60.464 | 60.000 | 0.00 | 0.00 | 0.00 | 3.07 |
3674 | 3853 | 1.915228 | CCGATTGGTGGGAGGTGAT | 59.085 | 57.895 | 0.00 | 0.00 | 0.00 | 3.06 |
3675 | 3854 | 3.399046 | CCGATTGGTGGGAGGTGA | 58.601 | 61.111 | 0.00 | 0.00 | 0.00 | 4.02 |
3734 | 3930 | 4.433805 | CGTTGTACAGAAACAGTATTCGGC | 60.434 | 45.833 | 0.00 | 0.00 | 34.46 | 5.54 |
3751 | 3947 | 0.390603 | CATTCAGACGGGCCGTTGTA | 60.391 | 55.000 | 34.58 | 24.02 | 41.37 | 2.41 |
3777 | 3976 | 0.895100 | TGGAACTGATTGCTGTGGCC | 60.895 | 55.000 | 0.00 | 0.00 | 37.74 | 5.36 |
3782 | 3981 | 3.692593 | TGTGATCATGGAACTGATTGCTG | 59.307 | 43.478 | 0.00 | 0.00 | 36.01 | 4.41 |
3794 | 3993 | 3.181503 | GCAGTGTAAAGCTGTGATCATGG | 60.182 | 47.826 | 0.00 | 0.00 | 36.42 | 3.66 |
3795 | 3994 | 3.437741 | TGCAGTGTAAAGCTGTGATCATG | 59.562 | 43.478 | 0.00 | 0.00 | 36.42 | 3.07 |
3803 | 4002 | 1.001378 | GGTTGGTGCAGTGTAAAGCTG | 60.001 | 52.381 | 0.00 | 0.00 | 37.06 | 4.24 |
3807 | 4006 | 2.020720 | CAGTGGTTGGTGCAGTGTAAA | 58.979 | 47.619 | 0.00 | 0.00 | 0.00 | 2.01 |
3808 | 4007 | 1.674359 | CAGTGGTTGGTGCAGTGTAA | 58.326 | 50.000 | 0.00 | 0.00 | 0.00 | 2.41 |
3809 | 4008 | 0.817634 | GCAGTGGTTGGTGCAGTGTA | 60.818 | 55.000 | 0.00 | 0.00 | 39.62 | 2.90 |
3811 | 4010 | 1.825191 | AGCAGTGGTTGGTGCAGTG | 60.825 | 57.895 | 0.00 | 0.00 | 42.47 | 3.66 |
3812 | 4011 | 2.597340 | AGCAGTGGTTGGTGCAGT | 59.403 | 55.556 | 0.00 | 0.00 | 42.47 | 4.40 |
3840 | 4044 | 5.485662 | AGTATCTTTTGTTATGGCTTCGC | 57.514 | 39.130 | 0.00 | 0.00 | 0.00 | 4.70 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.