Multiple sequence alignment - TraesCS6D01G342800
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 | TraesCS6D01G342800 | chr6D | 100.000 | 4629 | 0 | 0 | 1 | 4629 | 441888540 | 441893168 | 0.000000e+00 | 8549.0 |
1 | TraesCS6D01G342800 | chr6D | 86.486 | 592 | 61 | 9 | 4047 | 4624 | 116356366 | 116356952 | 2.350000e-177 | 632.0 |
2 | TraesCS6D01G342800 | chr6D | 89.352 | 216 | 15 | 7 | 4047 | 4258 | 441893936 | 441893725 | 9.880000e-67 | 265.0 |
3 | TraesCS6D01G342800 | chr6B | 90.966 | 3199 | 193 | 60 | 554 | 3685 | 667884409 | 667887578 | 0.000000e+00 | 4218.0 |
4 | TraesCS6D01G342800 | chr6B | 93.074 | 592 | 29 | 2 | 4047 | 4626 | 539619392 | 539619983 | 0.000000e+00 | 856.0 |
5 | TraesCS6D01G342800 | chr6B | 93.204 | 412 | 18 | 5 | 50 | 455 | 667883853 | 667884260 | 8.570000e-167 | 597.0 |
6 | TraesCS6D01G342800 | chr6A | 88.724 | 2554 | 154 | 60 | 26 | 2504 | 591218458 | 591220952 | 0.000000e+00 | 2998.0 |
7 | TraesCS6D01G342800 | chr6A | 92.321 | 1146 | 75 | 4 | 2660 | 3792 | 591220960 | 591222105 | 0.000000e+00 | 1616.0 |
8 | TraesCS6D01G342800 | chr6A | 91.440 | 257 | 12 | 5 | 3801 | 4050 | 591222079 | 591222332 | 1.230000e-90 | 344.0 |
9 | TraesCS6D01G342800 | chr2B | 92.399 | 592 | 33 | 2 | 4047 | 4626 | 394119688 | 394120279 | 0.000000e+00 | 833.0 |
10 | TraesCS6D01G342800 | chr2B | 87.838 | 222 | 17 | 2 | 4047 | 4258 | 394121085 | 394120864 | 7.690000e-63 | 252.0 |
11 | TraesCS6D01G342800 | chr2B | 100.000 | 29 | 0 | 0 | 3765 | 3793 | 554307402 | 554307374 | 2.000000e-03 | 54.7 |
12 | TraesCS6D01G342800 | chr2D | 91.765 | 595 | 37 | 4 | 4044 | 4626 | 153043688 | 153044282 | 0.000000e+00 | 817.0 |
13 | TraesCS6D01G342800 | chr2D | 86.022 | 186 | 17 | 1 | 4047 | 4223 | 153045091 | 153044906 | 1.700000e-44 | 191.0 |
14 | TraesCS6D01G342800 | chr2D | 83.163 | 196 | 22 | 5 | 4048 | 4233 | 294618784 | 294618590 | 7.970000e-38 | 169.0 |
15 | TraesCS6D01G342800 | chr2D | 100.000 | 28 | 0 | 0 | 3766 | 3793 | 473711827 | 473711800 | 8.000000e-03 | 52.8 |
16 | TraesCS6D01G342800 | chr4D | 91.723 | 592 | 35 | 5 | 4047 | 4626 | 459070589 | 459071178 | 0.000000e+00 | 809.0 |
17 | TraesCS6D01G342800 | chr4D | 84.409 | 186 | 16 | 5 | 4045 | 4219 | 98077214 | 98077031 | 2.210000e-38 | 171.0 |
18 | TraesCS6D01G342800 | chr3D | 88.494 | 591 | 43 | 13 | 4043 | 4625 | 444067618 | 444068191 | 0.000000e+00 | 691.0 |
19 | TraesCS6D01G342800 | chr5A | 83.920 | 597 | 80 | 10 | 4047 | 4629 | 18782064 | 18781470 | 1.450000e-154 | 556.0 |
20 | TraesCS6D01G342800 | chr2A | 88.651 | 467 | 36 | 4 | 4047 | 4496 | 327214525 | 327214059 | 1.880000e-153 | 553.0 |
21 | TraesCS6D01G342800 | chr2A | 89.195 | 435 | 30 | 4 | 4047 | 4464 | 327366573 | 327367007 | 1.140000e-145 | 527.0 |
22 | TraesCS6D01G342800 | chr2A | 86.559 | 186 | 16 | 1 | 4047 | 4223 | 327213151 | 327213336 | 3.650000e-46 | 196.0 |
23 | TraesCS6D01G342800 | chr7D | 81.985 | 544 | 76 | 14 | 4048 | 4577 | 345735656 | 345735121 | 4.250000e-120 | 442.0 |
24 | TraesCS6D01G342800 | chr3B | 92.157 | 306 | 15 | 1 | 4047 | 4343 | 763044426 | 763044121 | 1.540000e-114 | 424.0 |
25 | TraesCS6D01G342800 | chr3B | 92.000 | 300 | 20 | 2 | 4333 | 4629 | 763042030 | 763041732 | 7.160000e-113 | 418.0 |
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 | TraesCS6D01G342800 | chr6D | 441888540 | 441893168 | 4628 | False | 8549.000000 | 8549 | 100.000000 | 1 | 4629 | 1 | chr6D.!!$F2 | 4628 |
1 | TraesCS6D01G342800 | chr6D | 116356366 | 116356952 | 586 | False | 632.000000 | 632 | 86.486000 | 4047 | 4624 | 1 | chr6D.!!$F1 | 577 |
2 | TraesCS6D01G342800 | chr6B | 667883853 | 667887578 | 3725 | False | 2407.500000 | 4218 | 92.085000 | 50 | 3685 | 2 | chr6B.!!$F2 | 3635 |
3 | TraesCS6D01G342800 | chr6B | 539619392 | 539619983 | 591 | False | 856.000000 | 856 | 93.074000 | 4047 | 4626 | 1 | chr6B.!!$F1 | 579 |
4 | TraesCS6D01G342800 | chr6A | 591218458 | 591222332 | 3874 | False | 1652.666667 | 2998 | 90.828333 | 26 | 4050 | 3 | chr6A.!!$F1 | 4024 |
5 | TraesCS6D01G342800 | chr2B | 394119688 | 394120279 | 591 | False | 833.000000 | 833 | 92.399000 | 4047 | 4626 | 1 | chr2B.!!$F1 | 579 |
6 | TraesCS6D01G342800 | chr2D | 153043688 | 153044282 | 594 | False | 817.000000 | 817 | 91.765000 | 4044 | 4626 | 1 | chr2D.!!$F1 | 582 |
7 | TraesCS6D01G342800 | chr4D | 459070589 | 459071178 | 589 | False | 809.000000 | 809 | 91.723000 | 4047 | 4626 | 1 | chr4D.!!$F1 | 579 |
8 | TraesCS6D01G342800 | chr3D | 444067618 | 444068191 | 573 | False | 691.000000 | 691 | 88.494000 | 4043 | 4625 | 1 | chr3D.!!$F1 | 582 |
9 | TraesCS6D01G342800 | chr5A | 18781470 | 18782064 | 594 | True | 556.000000 | 556 | 83.920000 | 4047 | 4629 | 1 | chr5A.!!$R1 | 582 |
10 | TraesCS6D01G342800 | chr7D | 345735121 | 345735656 | 535 | True | 442.000000 | 442 | 81.985000 | 4048 | 4577 | 1 | chr7D.!!$R1 | 529 |
11 | TraesCS6D01G342800 | chr3B | 763041732 | 763044426 | 2694 | True | 421.000000 | 424 | 92.078500 | 4047 | 4629 | 2 | chr3B.!!$R1 | 582 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
501 | 542 | 0.106217 | CACCTCTCTCCCTCTCCCTC | 60.106 | 65.0 | 0.00 | 0.0 | 0.00 | 4.30 | F |
1837 | 1983 | 0.405585 | ACCACAGGAATGGACCCAAG | 59.594 | 55.0 | 0.00 | 0.0 | 43.02 | 3.61 | F |
3532 | 3695 | 0.250295 | ATGTGGTGGACAACGGTGAG | 60.250 | 55.0 | 7.88 | 0.0 | 38.36 | 3.51 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
2174 | 2327 | 0.097150 | GGATCGCAAAAGAAGTCGCC | 59.903 | 55.000 | 0.00 | 0.0 | 0.00 | 5.54 | R |
3584 | 3747 | 0.249489 | GTAGATTCGCCACCATCGCT | 60.249 | 55.000 | 0.00 | 0.0 | 0.00 | 4.93 | R |
4499 | 6795 | 2.124983 | GCTCATGCAAGCCCGAGA | 60.125 | 61.111 | 10.82 | 0.0 | 39.41 | 4.04 | 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 |
---|---|---|---|---|---|---|---|---|---|
17 | 18 | 4.043200 | GCACCTTCCGCAACAGCC | 62.043 | 66.667 | 0.00 | 0.00 | 0.00 | 4.85 |
18 | 19 | 2.281761 | CACCTTCCGCAACAGCCT | 60.282 | 61.111 | 0.00 | 0.00 | 0.00 | 4.58 |
19 | 20 | 2.281761 | ACCTTCCGCAACAGCCTG | 60.282 | 61.111 | 0.00 | 0.00 | 0.00 | 4.85 |
20 | 21 | 3.741476 | CCTTCCGCAACAGCCTGC | 61.741 | 66.667 | 0.00 | 0.00 | 39.04 | 4.85 |
21 | 22 | 2.670934 | CTTCCGCAACAGCCTGCT | 60.671 | 61.111 | 0.00 | 0.00 | 40.33 | 4.24 |
22 | 23 | 1.375908 | CTTCCGCAACAGCCTGCTA | 60.376 | 57.895 | 0.00 | 0.00 | 40.33 | 3.49 |
23 | 24 | 0.745845 | CTTCCGCAACAGCCTGCTAT | 60.746 | 55.000 | 0.00 | 0.00 | 40.33 | 2.97 |
24 | 25 | 1.026182 | TTCCGCAACAGCCTGCTATG | 61.026 | 55.000 | 0.00 | 0.00 | 40.33 | 2.23 |
44 | 45 | 8.822652 | GCTATGTGCATGTATATATATGAGCA | 57.177 | 34.615 | 20.21 | 16.73 | 42.31 | 4.26 |
117 | 123 | 6.442513 | AAAAGTGAGAAGAGGTTTTGACTG | 57.557 | 37.500 | 0.00 | 0.00 | 0.00 | 3.51 |
118 | 124 | 5.359194 | AAGTGAGAAGAGGTTTTGACTGA | 57.641 | 39.130 | 0.00 | 0.00 | 0.00 | 3.41 |
170 | 176 | 1.146485 | TCGTGCACGAAAAAGGGGA | 59.854 | 52.632 | 37.68 | 13.53 | 46.30 | 4.81 |
171 | 177 | 0.882927 | TCGTGCACGAAAAAGGGGAG | 60.883 | 55.000 | 37.68 | 6.55 | 46.30 | 4.30 |
172 | 178 | 0.882927 | CGTGCACGAAAAAGGGGAGA | 60.883 | 55.000 | 34.93 | 0.00 | 43.02 | 3.71 |
173 | 179 | 1.314730 | GTGCACGAAAAAGGGGAGAA | 58.685 | 50.000 | 0.00 | 0.00 | 0.00 | 2.87 |
179 | 185 | 4.793028 | GCACGAAAAAGGGGAGAAAGAAAG | 60.793 | 45.833 | 0.00 | 0.00 | 0.00 | 2.62 |
215 | 223 | 3.948719 | GGGGCACGTGGTTGGAGA | 61.949 | 66.667 | 18.88 | 0.00 | 0.00 | 3.71 |
230 | 238 | 3.680338 | GAGACCGAAGCGTCCGACC | 62.680 | 68.421 | 0.00 | 0.00 | 32.91 | 4.79 |
436 | 445 | 3.866449 | GCAAACTTCCCATCTCGTCTCTT | 60.866 | 47.826 | 0.00 | 0.00 | 0.00 | 2.85 |
440 | 449 | 2.060050 | TCCCATCTCGTCTCTTCTCC | 57.940 | 55.000 | 0.00 | 0.00 | 0.00 | 3.71 |
443 | 469 | 1.384525 | CATCTCGTCTCTTCTCCCGT | 58.615 | 55.000 | 0.00 | 0.00 | 0.00 | 5.28 |
472 | 513 | 4.988598 | CGGGCGCCACAGTTGAGT | 62.989 | 66.667 | 30.85 | 0.00 | 0.00 | 3.41 |
477 | 518 | 1.574702 | GCGCCACAGTTGAGTTACCC | 61.575 | 60.000 | 0.00 | 0.00 | 0.00 | 3.69 |
479 | 520 | 1.610624 | CGCCACAGTTGAGTTACCCAT | 60.611 | 52.381 | 0.00 | 0.00 | 0.00 | 4.00 |
484 | 525 | 4.023193 | CCACAGTTGAGTTACCCATTTCAC | 60.023 | 45.833 | 0.00 | 0.00 | 0.00 | 3.18 |
490 | 531 | 4.168101 | TGAGTTACCCATTTCACCTCTCT | 58.832 | 43.478 | 0.00 | 0.00 | 0.00 | 3.10 |
495 | 536 | 1.488393 | CCCATTTCACCTCTCTCCCTC | 59.512 | 57.143 | 0.00 | 0.00 | 0.00 | 4.30 |
496 | 537 | 2.476199 | CCATTTCACCTCTCTCCCTCT | 58.524 | 52.381 | 0.00 | 0.00 | 0.00 | 3.69 |
497 | 538 | 2.433970 | CCATTTCACCTCTCTCCCTCTC | 59.566 | 54.545 | 0.00 | 0.00 | 0.00 | 3.20 |
498 | 539 | 2.239681 | TTTCACCTCTCTCCCTCTCC | 57.760 | 55.000 | 0.00 | 0.00 | 0.00 | 3.71 |
499 | 540 | 0.336737 | TTCACCTCTCTCCCTCTCCC | 59.663 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
500 | 541 | 0.553862 | TCACCTCTCTCCCTCTCCCT | 60.554 | 60.000 | 0.00 | 0.00 | 0.00 | 4.20 |
501 | 542 | 0.106217 | CACCTCTCTCCCTCTCCCTC | 60.106 | 65.000 | 0.00 | 0.00 | 0.00 | 4.30 |
502 | 543 | 1.150536 | CCTCTCTCCCTCTCCCTCG | 59.849 | 68.421 | 0.00 | 0.00 | 0.00 | 4.63 |
503 | 544 | 1.528309 | CTCTCTCCCTCTCCCTCGC | 60.528 | 68.421 | 0.00 | 0.00 | 0.00 | 5.03 |
521 | 562 | 1.825281 | GCCCTGCGCCATCTCTATCT | 61.825 | 60.000 | 4.18 | 0.00 | 0.00 | 1.98 |
528 | 569 | 1.336332 | CGCCATCTCTATCTTGGGACG | 60.336 | 57.143 | 0.00 | 0.00 | 0.00 | 4.79 |
529 | 570 | 1.606737 | GCCATCTCTATCTTGGGACGC | 60.607 | 57.143 | 0.00 | 0.00 | 0.00 | 5.19 |
530 | 571 | 1.001406 | CCATCTCTATCTTGGGACGCC | 59.999 | 57.143 | 0.00 | 0.00 | 0.00 | 5.68 |
533 | 574 | 2.280186 | CTATCTTGGGACGCCGGC | 60.280 | 66.667 | 19.07 | 19.07 | 0.00 | 6.13 |
534 | 575 | 4.215742 | TATCTTGGGACGCCGGCG | 62.216 | 66.667 | 44.88 | 44.88 | 46.03 | 6.46 |
545 | 586 | 4.803426 | GCCGGCGTCCTGAGACTG | 62.803 | 72.222 | 12.58 | 0.00 | 41.16 | 3.51 |
546 | 587 | 3.062466 | CCGGCGTCCTGAGACTGA | 61.062 | 66.667 | 6.01 | 0.00 | 41.16 | 3.41 |
629 | 713 | 2.884207 | GCCGCGAGTTCCTTACCG | 60.884 | 66.667 | 8.23 | 0.00 | 0.00 | 4.02 |
680 | 764 | 1.376037 | GCCAGGTTCTTCCTCGGTG | 60.376 | 63.158 | 0.00 | 0.00 | 46.24 | 4.94 |
683 | 767 | 1.608283 | CCAGGTTCTTCCTCGGTGAAC | 60.608 | 57.143 | 12.53 | 12.53 | 46.24 | 3.18 |
694 | 778 | 2.135933 | CTCGGTGAACTTCGCTTTCTT | 58.864 | 47.619 | 2.43 | 0.00 | 0.00 | 2.52 |
695 | 779 | 1.864711 | TCGGTGAACTTCGCTTTCTTG | 59.135 | 47.619 | 2.43 | 0.00 | 0.00 | 3.02 |
711 | 795 | 5.174579 | GCTTTCTTGATGTGCTCTGTTTTTC | 59.825 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
714 | 798 | 4.276678 | TCTTGATGTGCTCTGTTTTTCCTG | 59.723 | 41.667 | 0.00 | 0.00 | 0.00 | 3.86 |
736 | 820 | 3.119291 | CTCCGAATGTCATACTCTGCAC | 58.881 | 50.000 | 0.00 | 0.00 | 0.00 | 4.57 |
743 | 827 | 4.558226 | TGTCATACTCTGCACCTCATTT | 57.442 | 40.909 | 0.00 | 0.00 | 0.00 | 2.32 |
763 | 854 | 9.217278 | CTCATTTCGATATCATTTCTTCTGGAT | 57.783 | 33.333 | 3.12 | 0.00 | 0.00 | 3.41 |
768 | 859 | 7.433680 | TCGATATCATTTCTTCTGGATCGAAA | 58.566 | 34.615 | 3.12 | 0.00 | 40.48 | 3.46 |
778 | 869 | 5.598417 | TCTTCTGGATCGAAACCTCATATCA | 59.402 | 40.000 | 12.11 | 0.00 | 0.00 | 2.15 |
779 | 870 | 6.268617 | TCTTCTGGATCGAAACCTCATATCAT | 59.731 | 38.462 | 12.11 | 0.00 | 0.00 | 2.45 |
780 | 871 | 7.451566 | TCTTCTGGATCGAAACCTCATATCATA | 59.548 | 37.037 | 12.11 | 0.00 | 0.00 | 2.15 |
781 | 872 | 7.724490 | TCTGGATCGAAACCTCATATCATAT | 57.276 | 36.000 | 12.11 | 0.00 | 0.00 | 1.78 |
783 | 874 | 8.253810 | TCTGGATCGAAACCTCATATCATATTC | 58.746 | 37.037 | 12.11 | 0.00 | 0.00 | 1.75 |
784 | 875 | 7.906327 | TGGATCGAAACCTCATATCATATTCA | 58.094 | 34.615 | 12.11 | 0.00 | 0.00 | 2.57 |
785 | 876 | 8.542926 | TGGATCGAAACCTCATATCATATTCAT | 58.457 | 33.333 | 12.11 | 0.00 | 0.00 | 2.57 |
808 | 899 | 8.094548 | TCATATACATAGGTGCCTGTTAATGAC | 58.905 | 37.037 | 0.12 | 0.00 | 0.00 | 3.06 |
814 | 905 | 7.499232 | ACATAGGTGCCTGTTAATGACTAATTC | 59.501 | 37.037 | 0.12 | 0.00 | 0.00 | 2.17 |
828 | 924 | 3.836949 | ACTAATTCACTGCAATTTGGCG | 58.163 | 40.909 | 0.00 | 0.00 | 36.28 | 5.69 |
844 | 940 | 3.918102 | GCGCAAAGCCACCTATAAC | 57.082 | 52.632 | 0.30 | 0.00 | 40.81 | 1.89 |
845 | 941 | 1.091537 | GCGCAAAGCCACCTATAACA | 58.908 | 50.000 | 0.30 | 0.00 | 40.81 | 2.41 |
846 | 942 | 1.676006 | GCGCAAAGCCACCTATAACAT | 59.324 | 47.619 | 0.30 | 0.00 | 40.81 | 2.71 |
847 | 943 | 2.099098 | GCGCAAAGCCACCTATAACATT | 59.901 | 45.455 | 0.30 | 0.00 | 40.81 | 2.71 |
865 | 961 | 5.375417 | ACATTCATTCGTTCAGCAAATCA | 57.625 | 34.783 | 0.00 | 0.00 | 0.00 | 2.57 |
867 | 963 | 4.424061 | TTCATTCGTTCAGCAAATCAGG | 57.576 | 40.909 | 0.00 | 0.00 | 0.00 | 3.86 |
868 | 964 | 3.673902 | TCATTCGTTCAGCAAATCAGGA | 58.326 | 40.909 | 0.00 | 0.00 | 0.00 | 3.86 |
869 | 965 | 3.436704 | TCATTCGTTCAGCAAATCAGGAC | 59.563 | 43.478 | 0.00 | 0.00 | 0.00 | 3.85 |
870 | 966 | 2.542020 | TCGTTCAGCAAATCAGGACA | 57.458 | 45.000 | 0.00 | 0.00 | 0.00 | 4.02 |
876 | 991 | 3.159472 | TCAGCAAATCAGGACAGCAATT | 58.841 | 40.909 | 0.00 | 0.00 | 0.00 | 2.32 |
897 | 1020 | 4.574674 | TGGGCAGTCAGAATCAGTTTAT | 57.425 | 40.909 | 0.00 | 0.00 | 0.00 | 1.40 |
912 | 1040 | 8.480643 | AATCAGTTTATAAGTTTCTGTCCTCG | 57.519 | 34.615 | 0.00 | 0.00 | 0.00 | 4.63 |
922 | 1050 | 3.896648 | TTCTGTCCTCGTGCATTTTTC | 57.103 | 42.857 | 0.00 | 0.00 | 0.00 | 2.29 |
925 | 1053 | 2.807967 | CTGTCCTCGTGCATTTTTCAGA | 59.192 | 45.455 | 0.00 | 0.00 | 0.00 | 3.27 |
926 | 1054 | 3.411446 | TGTCCTCGTGCATTTTTCAGAT | 58.589 | 40.909 | 0.00 | 0.00 | 0.00 | 2.90 |
928 | 1056 | 5.000591 | TGTCCTCGTGCATTTTTCAGATAA | 58.999 | 37.500 | 0.00 | 0.00 | 0.00 | 1.75 |
929 | 1057 | 5.106712 | TGTCCTCGTGCATTTTTCAGATAAC | 60.107 | 40.000 | 0.00 | 0.00 | 0.00 | 1.89 |
931 | 1059 | 5.122239 | TCCTCGTGCATTTTTCAGATAACAG | 59.878 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
932 | 1060 | 5.122239 | CCTCGTGCATTTTTCAGATAACAGA | 59.878 | 40.000 | 0.00 | 0.00 | 0.00 | 3.41 |
1035 | 1168 | 2.999928 | TCCTCTAGTTTCCAGGGGTTT | 58.000 | 47.619 | 0.00 | 0.00 | 34.97 | 3.27 |
1074 | 1207 | 2.107141 | GCGGTGCTTATCGGAGCT | 59.893 | 61.111 | 0.00 | 0.00 | 43.11 | 4.09 |
1327 | 1464 | 3.199677 | GTTTATGGTGCCTGTATACGCA | 58.800 | 45.455 | 1.76 | 1.76 | 0.00 | 5.24 |
1617 | 1761 | 3.482156 | TGCCTGCCTGAAGATTCTATC | 57.518 | 47.619 | 0.00 | 0.00 | 0.00 | 2.08 |
1625 | 1769 | 6.197168 | TGCCTGAAGATTCTATCCCATTTTT | 58.803 | 36.000 | 0.00 | 0.00 | 0.00 | 1.94 |
1837 | 1983 | 0.405585 | ACCACAGGAATGGACCCAAG | 59.594 | 55.000 | 0.00 | 0.00 | 43.02 | 3.61 |
1868 | 2014 | 6.585702 | TGTGAGAAATCATTGTAAATTTGCCG | 59.414 | 34.615 | 0.00 | 0.00 | 0.00 | 5.69 |
1952 | 2098 | 4.389687 | CAGTGTTATGGAGCAAATTTTGGC | 59.610 | 41.667 | 10.96 | 3.82 | 0.00 | 4.52 |
1997 | 2143 | 2.109774 | CTCCAGCACCTCTCTGATTCT | 58.890 | 52.381 | 0.00 | 0.00 | 33.54 | 2.40 |
2004 | 2150 | 3.306641 | GCACCTCTCTGATTCTGTTGTCT | 60.307 | 47.826 | 0.00 | 0.00 | 0.00 | 3.41 |
2207 | 2360 | 0.758734 | CGATCCTAATGCACTGGGGA | 59.241 | 55.000 | 0.00 | 0.00 | 0.00 | 4.81 |
2221 | 2374 | 2.431057 | ACTGGGGAAGAGCTTATACACG | 59.569 | 50.000 | 0.00 | 0.00 | 0.00 | 4.49 |
2293 | 2448 | 4.008074 | TCTCACCTGAAACTGGTCAATC | 57.992 | 45.455 | 0.00 | 0.00 | 33.44 | 2.67 |
2310 | 2465 | 5.458015 | GTCAATCACGACGTGGATGATATA | 58.542 | 41.667 | 27.28 | 10.86 | 33.71 | 0.86 |
2319 | 2474 | 5.449314 | CGACGTGGATGATATATCCTTCCTC | 60.449 | 48.000 | 22.72 | 19.57 | 38.95 | 3.71 |
2324 | 2479 | 6.876257 | GTGGATGATATATCCTTCCTCAACAC | 59.124 | 42.308 | 22.72 | 13.74 | 38.95 | 3.32 |
2325 | 2480 | 6.102663 | GGATGATATATCCTTCCTCAACACG | 58.897 | 44.000 | 18.23 | 0.00 | 35.36 | 4.49 |
2341 | 2497 | 6.758416 | CCTCAACACGATTTCAGATGATTCTA | 59.242 | 38.462 | 0.00 | 0.00 | 0.00 | 2.10 |
2348 | 2504 | 8.113062 | CACGATTTCAGATGATTCTAAAGACAC | 58.887 | 37.037 | 0.00 | 0.00 | 0.00 | 3.67 |
2525 | 2681 | 3.261897 | AGCTGATAGGTGCAGTGTACTTT | 59.738 | 43.478 | 11.32 | 3.12 | 35.81 | 2.66 |
2546 | 2702 | 7.224297 | ACTTTTACACATTAGAGAAGCTTGGA | 58.776 | 34.615 | 2.10 | 0.00 | 0.00 | 3.53 |
2549 | 2705 | 5.234466 | ACACATTAGAGAAGCTTGGAACT | 57.766 | 39.130 | 2.10 | 0.00 | 0.00 | 3.01 |
2551 | 2707 | 6.769512 | ACACATTAGAGAAGCTTGGAACTTA | 58.230 | 36.000 | 2.10 | 0.00 | 0.00 | 2.24 |
2586 | 2742 | 9.429109 | AAAAGATTACCTTCAAAAGTTAGGGAA | 57.571 | 29.630 | 0.00 | 0.00 | 36.36 | 3.97 |
2600 | 2756 | 6.128138 | AGTTAGGGAAAGAACATTAGCAGT | 57.872 | 37.500 | 0.00 | 0.00 | 0.00 | 4.40 |
2609 | 2765 | 9.331282 | GGAAAGAACATTAGCAGTCACTATTAT | 57.669 | 33.333 | 0.00 | 0.00 | 0.00 | 1.28 |
2629 | 2785 | 7.787725 | ATTATGAAAATCCGAGTACTTCCAC | 57.212 | 36.000 | 0.00 | 0.00 | 0.00 | 4.02 |
2645 | 2801 | 8.537016 | AGTACTTCCACTATGCATTTAACTACA | 58.463 | 33.333 | 3.54 | 0.00 | 0.00 | 2.74 |
2716 | 2875 | 3.055094 | ACCCTTACATCGCTCTTGTCATT | 60.055 | 43.478 | 0.00 | 0.00 | 0.00 | 2.57 |
2764 | 2923 | 7.699566 | TGTACTGTCTGGTGAAATTTTACAAC | 58.300 | 34.615 | 14.30 | 9.56 | 0.00 | 3.32 |
2782 | 2941 | 1.890876 | ACGCAACACATGAAAGGCTA | 58.109 | 45.000 | 0.00 | 0.00 | 0.00 | 3.93 |
2963 | 3122 | 6.093495 | CGAGGTAAATAGGCAAATCTTGTGAA | 59.907 | 38.462 | 0.00 | 0.00 | 0.00 | 3.18 |
2975 | 3134 | 7.063074 | GGCAAATCTTGTGAATTTGATTGAGAG | 59.937 | 37.037 | 11.62 | 0.00 | 37.44 | 3.20 |
3082 | 3241 | 2.584608 | GTGGAGCCGTACCAGCAT | 59.415 | 61.111 | 5.42 | 0.00 | 38.14 | 3.79 |
3120 | 3279 | 4.436998 | GCACGAGGAGGTGACCCG | 62.437 | 72.222 | 0.00 | 0.00 | 40.38 | 5.28 |
3140 | 3299 | 3.786635 | CGTGAGGAGAGTAAAATGGAGG | 58.213 | 50.000 | 0.00 | 0.00 | 0.00 | 4.30 |
3144 | 3303 | 4.223032 | TGAGGAGAGTAAAATGGAGGTGAC | 59.777 | 45.833 | 0.00 | 0.00 | 0.00 | 3.67 |
3155 | 3314 | 1.218316 | GAGGTGACGGTGGATGTCC | 59.782 | 63.158 | 0.00 | 0.00 | 35.46 | 4.02 |
3167 | 3326 | 1.683790 | GGATGTCCACGACGAAAGCG | 61.684 | 60.000 | 0.00 | 0.00 | 38.71 | 4.68 |
3442 | 3605 | 2.200955 | GGGAAGATCCAGGAGACCTTT | 58.799 | 52.381 | 0.00 | 0.00 | 38.64 | 3.11 |
3445 | 3608 | 3.457749 | GGAAGATCCAGGAGACCTTTCAT | 59.542 | 47.826 | 0.00 | 0.00 | 36.28 | 2.57 |
3476 | 3639 | 0.322906 | GAAGCCAGGGGACAAGAAGG | 60.323 | 60.000 | 0.00 | 0.00 | 0.00 | 3.46 |
3501 | 3664 | 3.062466 | CGTCGAGGTGGAGGAGCA | 61.062 | 66.667 | 0.00 | 0.00 | 0.00 | 4.26 |
3532 | 3695 | 0.250295 | ATGTGGTGGACAACGGTGAG | 60.250 | 55.000 | 7.88 | 0.00 | 38.36 | 3.51 |
3538 | 3701 | 1.227853 | GGACAACGGTGAGGCTGTT | 60.228 | 57.895 | 7.88 | 0.00 | 46.91 | 3.16 |
3559 | 3722 | 2.577059 | GTCGATGCGGAGGTGGAA | 59.423 | 61.111 | 0.00 | 0.00 | 0.00 | 3.53 |
3577 | 3740 | 3.699038 | TGGAAGTTGAAACAAGGGTGAAG | 59.301 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
3584 | 3747 | 3.053991 | TGAAACAAGGGTGAAGGACAAGA | 60.054 | 43.478 | 0.00 | 0.00 | 0.00 | 3.02 |
3619 | 3782 | 3.777465 | TCTACGGAGAGGTTGAAATCG | 57.223 | 47.619 | 0.00 | 0.00 | 0.00 | 3.34 |
3676 | 3839 | 2.158813 | GGAACTGGTCCTTGAGAACACA | 60.159 | 50.000 | 3.98 | 0.00 | 43.98 | 3.72 |
3689 | 3858 | 0.942410 | GAACACAGTACGCTTCCGCA | 60.942 | 55.000 | 0.00 | 0.00 | 38.22 | 5.69 |
3717 | 3886 | 6.313411 | TCGAAAAAGGAAACTGAGTAAAACGA | 59.687 | 34.615 | 0.00 | 0.00 | 42.68 | 3.85 |
3723 | 3895 | 6.464222 | AGGAAACTGAGTAAAACGATGATGA | 58.536 | 36.000 | 0.00 | 0.00 | 41.13 | 2.92 |
3726 | 3898 | 8.879759 | GGAAACTGAGTAAAACGATGATGAATA | 58.120 | 33.333 | 0.00 | 0.00 | 0.00 | 1.75 |
3729 | 3901 | 8.370493 | ACTGAGTAAAACGATGATGAATATGG | 57.630 | 34.615 | 0.00 | 0.00 | 0.00 | 2.74 |
3790 | 3962 | 4.569719 | AACTAGTGGTTGGATGGTTAGG | 57.430 | 45.455 | 0.00 | 0.00 | 36.70 | 2.69 |
3791 | 3963 | 3.798515 | ACTAGTGGTTGGATGGTTAGGA | 58.201 | 45.455 | 0.00 | 0.00 | 0.00 | 2.94 |
3792 | 3964 | 4.172807 | ACTAGTGGTTGGATGGTTAGGAA | 58.827 | 43.478 | 0.00 | 0.00 | 0.00 | 3.36 |
3793 | 3965 | 4.788617 | ACTAGTGGTTGGATGGTTAGGAAT | 59.211 | 41.667 | 0.00 | 0.00 | 0.00 | 3.01 |
3794 | 3966 | 4.675063 | AGTGGTTGGATGGTTAGGAATT | 57.325 | 40.909 | 0.00 | 0.00 | 0.00 | 2.17 |
3795 | 3967 | 5.010708 | AGTGGTTGGATGGTTAGGAATTT | 57.989 | 39.130 | 0.00 | 0.00 | 0.00 | 1.82 |
3796 | 3968 | 5.402630 | AGTGGTTGGATGGTTAGGAATTTT | 58.597 | 37.500 | 0.00 | 0.00 | 0.00 | 1.82 |
3797 | 3969 | 5.480422 | AGTGGTTGGATGGTTAGGAATTTTC | 59.520 | 40.000 | 0.00 | 0.00 | 0.00 | 2.29 |
3798 | 3970 | 5.245075 | GTGGTTGGATGGTTAGGAATTTTCA | 59.755 | 40.000 | 0.00 | 0.00 | 0.00 | 2.69 |
3799 | 3971 | 6.022315 | TGGTTGGATGGTTAGGAATTTTCAT | 58.978 | 36.000 | 0.00 | 0.00 | 0.00 | 2.57 |
3800 | 3972 | 7.123547 | GTGGTTGGATGGTTAGGAATTTTCATA | 59.876 | 37.037 | 0.00 | 0.00 | 0.00 | 2.15 |
3801 | 3973 | 7.676043 | TGGTTGGATGGTTAGGAATTTTCATAA | 59.324 | 33.333 | 0.00 | 0.00 | 31.81 | 1.90 |
3821 | 3993 | 4.569719 | AACTAACTAGGTGTTGGATGGG | 57.430 | 45.455 | 0.00 | 0.00 | 39.15 | 4.00 |
3829 | 4001 | 0.546598 | GTGTTGGATGGGTAGGAGGG | 59.453 | 60.000 | 0.00 | 0.00 | 0.00 | 4.30 |
3838 | 4010 | 1.519246 | GGTAGGAGGGCGGTTGTAC | 59.481 | 63.158 | 0.00 | 0.00 | 0.00 | 2.90 |
3850 | 4022 | 2.527123 | TTGTACCCCGGGCTCACA | 60.527 | 61.111 | 17.73 | 15.49 | 0.00 | 3.58 |
3867 | 4039 | 1.194781 | ACACAGGGATCAAGCCTCGT | 61.195 | 55.000 | 0.00 | 0.00 | 0.00 | 4.18 |
3883 | 4055 | 2.267426 | CTCGTGTCGATATTGTTGCCA | 58.733 | 47.619 | 0.00 | 0.00 | 34.61 | 4.92 |
3970 | 4142 | 2.433868 | TGCTACGTGTCTTTGGTCTC | 57.566 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 |
3987 | 4159 | 0.879765 | CTCTGCTTTCCCTGCACAAG | 59.120 | 55.000 | 0.00 | 0.00 | 36.37 | 3.16 |
4021 | 4193 | 9.391227 | AGTTCCTTTGATCATATATTCTCTCCT | 57.609 | 33.333 | 0.00 | 0.00 | 0.00 | 3.69 |
4237 | 4426 | 4.154918 | GTGGCAAAGACTAATCCAAGTCAG | 59.845 | 45.833 | 6.76 | 0.00 | 46.89 | 3.51 |
4281 | 4472 | 0.615331 | GAGACCCATCAGTCAGCCAA | 59.385 | 55.000 | 0.00 | 0.00 | 39.34 | 4.52 |
4562 | 6858 | 2.526545 | GCTAAGCAGCTAGATGGCG | 58.473 | 57.895 | 10.52 | 0.00 | 44.93 | 5.69 |
4595 | 6891 | 2.172505 | CCATGGTCCCAATACAGTGCTA | 59.827 | 50.000 | 2.57 | 0.00 | 0.00 | 3.49 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
0 | 1 | 4.043200 | GGCTGTTGCGGAAGGTGC | 62.043 | 66.667 | 0.00 | 0.00 | 40.82 | 5.01 |
1 | 2 | 2.281761 | AGGCTGTTGCGGAAGGTG | 60.282 | 61.111 | 0.00 | 0.00 | 40.82 | 4.00 |
2 | 3 | 2.281761 | CAGGCTGTTGCGGAAGGT | 60.282 | 61.111 | 6.28 | 0.00 | 40.82 | 3.50 |
3 | 4 | 3.741476 | GCAGGCTGTTGCGGAAGG | 61.741 | 66.667 | 17.16 | 0.00 | 40.82 | 3.46 |
9 | 10 | 1.138247 | GCACATAGCAGGCTGTTGC | 59.862 | 57.895 | 17.16 | 12.84 | 44.79 | 4.17 |
19 | 20 | 8.822652 | TGCTCATATATATACATGCACATAGC | 57.177 | 34.615 | 9.79 | 5.21 | 45.96 | 2.97 |
22 | 23 | 9.490379 | CAGATGCTCATATATATACATGCACAT | 57.510 | 33.333 | 13.87 | 7.78 | 31.92 | 3.21 |
23 | 24 | 7.440255 | GCAGATGCTCATATATATACATGCACA | 59.560 | 37.037 | 13.87 | 0.00 | 38.21 | 4.57 |
24 | 25 | 7.359014 | CGCAGATGCTCATATATATACATGCAC | 60.359 | 40.741 | 13.87 | 9.96 | 39.32 | 4.57 |
28 | 29 | 8.175925 | AGACGCAGATGCTCATATATATACAT | 57.824 | 34.615 | 2.95 | 0.40 | 39.32 | 2.29 |
40 | 41 | 1.403679 | ACAGTAGAGACGCAGATGCTC | 59.596 | 52.381 | 2.95 | 0.27 | 39.32 | 4.26 |
44 | 45 | 5.386958 | TTTAACACAGTAGAGACGCAGAT | 57.613 | 39.130 | 0.00 | 0.00 | 0.00 | 2.90 |
46 | 47 | 5.900339 | TTTTTAACACAGTAGAGACGCAG | 57.100 | 39.130 | 0.00 | 0.00 | 0.00 | 5.18 |
105 | 111 | 3.978687 | TCTCTTCGTCAGTCAAAACCTC | 58.021 | 45.455 | 0.00 | 0.00 | 0.00 | 3.85 |
117 | 123 | 1.468395 | CGCTTCCCTCTTCTCTTCGTC | 60.468 | 57.143 | 0.00 | 0.00 | 0.00 | 4.20 |
118 | 124 | 0.528470 | CGCTTCCCTCTTCTCTTCGT | 59.472 | 55.000 | 0.00 | 0.00 | 0.00 | 3.85 |
170 | 176 | 3.160269 | CCATGTGCTTCCCTTTCTTTCT | 58.840 | 45.455 | 0.00 | 0.00 | 0.00 | 2.52 |
171 | 177 | 3.157087 | TCCATGTGCTTCCCTTTCTTTC | 58.843 | 45.455 | 0.00 | 0.00 | 0.00 | 2.62 |
172 | 178 | 3.160269 | CTCCATGTGCTTCCCTTTCTTT | 58.840 | 45.455 | 0.00 | 0.00 | 0.00 | 2.52 |
173 | 179 | 2.800250 | CTCCATGTGCTTCCCTTTCTT | 58.200 | 47.619 | 0.00 | 0.00 | 0.00 | 2.52 |
179 | 185 | 1.751927 | CCTGCTCCATGTGCTTCCC | 60.752 | 63.158 | 8.95 | 0.00 | 0.00 | 3.97 |
215 | 223 | 4.353437 | GTGGTCGGACGCTTCGGT | 62.353 | 66.667 | 1.43 | 0.00 | 0.00 | 4.69 |
253 | 261 | 2.437281 | AGAACCATCTGATTCATCCGCT | 59.563 | 45.455 | 0.00 | 0.00 | 33.59 | 5.52 |
463 | 504 | 4.141251 | AGGTGAAATGGGTAACTCAACTGT | 60.141 | 41.667 | 0.00 | 0.00 | 34.57 | 3.55 |
464 | 505 | 4.398319 | AGGTGAAATGGGTAACTCAACTG | 58.602 | 43.478 | 0.00 | 0.00 | 34.57 | 3.16 |
466 | 507 | 4.652822 | AGAGGTGAAATGGGTAACTCAAC | 58.347 | 43.478 | 0.00 | 0.00 | 0.00 | 3.18 |
467 | 508 | 4.597507 | AGAGAGGTGAAATGGGTAACTCAA | 59.402 | 41.667 | 0.00 | 0.00 | 0.00 | 3.02 |
472 | 513 | 2.844348 | GGGAGAGAGGTGAAATGGGTAA | 59.156 | 50.000 | 0.00 | 0.00 | 0.00 | 2.85 |
477 | 518 | 2.433970 | GGAGAGGGAGAGAGGTGAAATG | 59.566 | 54.545 | 0.00 | 0.00 | 0.00 | 2.32 |
479 | 520 | 1.273324 | GGGAGAGGGAGAGAGGTGAAA | 60.273 | 57.143 | 0.00 | 0.00 | 0.00 | 2.69 |
484 | 525 | 1.150536 | CGAGGGAGAGGGAGAGAGG | 59.849 | 68.421 | 0.00 | 0.00 | 0.00 | 3.69 |
490 | 531 | 4.465446 | CAGGGCGAGGGAGAGGGA | 62.465 | 72.222 | 0.00 | 0.00 | 0.00 | 4.20 |
502 | 543 | 1.375268 | GATAGAGATGGCGCAGGGC | 60.375 | 63.158 | 10.83 | 0.00 | 42.51 | 5.19 |
503 | 544 | 0.683973 | AAGATAGAGATGGCGCAGGG | 59.316 | 55.000 | 10.83 | 0.00 | 0.00 | 4.45 |
528 | 569 | 4.803426 | CAGTCTCAGGACGCCGGC | 62.803 | 72.222 | 19.07 | 19.07 | 46.29 | 6.13 |
529 | 570 | 3.057547 | CTCAGTCTCAGGACGCCGG | 62.058 | 68.421 | 0.00 | 0.00 | 46.29 | 6.13 |
530 | 571 | 2.487428 | CTCAGTCTCAGGACGCCG | 59.513 | 66.667 | 0.00 | 0.00 | 46.29 | 6.46 |
533 | 574 | 0.884514 | TCAAGCTCAGTCTCAGGACG | 59.115 | 55.000 | 0.00 | 0.00 | 46.29 | 4.79 |
534 | 575 | 1.204467 | CCTCAAGCTCAGTCTCAGGAC | 59.796 | 57.143 | 0.00 | 0.00 | 42.41 | 3.85 |
535 | 576 | 1.554836 | CCTCAAGCTCAGTCTCAGGA | 58.445 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
536 | 577 | 0.536260 | CCCTCAAGCTCAGTCTCAGG | 59.464 | 60.000 | 0.00 | 0.00 | 0.00 | 3.86 |
537 | 578 | 0.108233 | GCCCTCAAGCTCAGTCTCAG | 60.108 | 60.000 | 0.00 | 0.00 | 0.00 | 3.35 |
538 | 579 | 1.881903 | CGCCCTCAAGCTCAGTCTCA | 61.882 | 60.000 | 0.00 | 0.00 | 0.00 | 3.27 |
539 | 580 | 1.153667 | CGCCCTCAAGCTCAGTCTC | 60.154 | 63.158 | 0.00 | 0.00 | 0.00 | 3.36 |
540 | 581 | 2.977178 | CGCCCTCAAGCTCAGTCT | 59.023 | 61.111 | 0.00 | 0.00 | 0.00 | 3.24 |
542 | 583 | 4.749310 | CGCGCCCTCAAGCTCAGT | 62.749 | 66.667 | 0.00 | 0.00 | 0.00 | 3.41 |
571 | 638 | 2.027625 | CTTGCCGTCGAAGTCACCC | 61.028 | 63.158 | 0.00 | 0.00 | 0.00 | 4.61 |
651 | 735 | 0.951040 | GAACCTGGCAGACAGTTCCG | 60.951 | 60.000 | 17.94 | 0.00 | 46.06 | 4.30 |
680 | 764 | 3.058639 | AGCACATCAAGAAAGCGAAGTTC | 60.059 | 43.478 | 0.00 | 0.00 | 0.00 | 3.01 |
683 | 767 | 2.740981 | AGAGCACATCAAGAAAGCGAAG | 59.259 | 45.455 | 0.00 | 0.00 | 0.00 | 3.79 |
694 | 778 | 2.294233 | GCAGGAAAAACAGAGCACATCA | 59.706 | 45.455 | 0.00 | 0.00 | 0.00 | 3.07 |
695 | 779 | 2.555757 | AGCAGGAAAAACAGAGCACATC | 59.444 | 45.455 | 0.00 | 0.00 | 0.00 | 3.06 |
711 | 795 | 2.363680 | AGAGTATGACATTCGGAGCAGG | 59.636 | 50.000 | 0.00 | 0.00 | 0.00 | 4.85 |
714 | 798 | 2.131183 | GCAGAGTATGACATTCGGAGC | 58.869 | 52.381 | 0.00 | 0.00 | 0.00 | 4.70 |
736 | 820 | 7.658982 | TCCAGAAGAAATGATATCGAAATGAGG | 59.341 | 37.037 | 0.00 | 0.00 | 0.00 | 3.86 |
743 | 827 | 6.575162 | TCGATCCAGAAGAAATGATATCGA | 57.425 | 37.500 | 0.00 | 0.00 | 38.68 | 3.59 |
780 | 871 | 9.453572 | CATTAACAGGCACCTATGTATATGAAT | 57.546 | 33.333 | 0.00 | 0.00 | 0.00 | 2.57 |
781 | 872 | 8.655901 | TCATTAACAGGCACCTATGTATATGAA | 58.344 | 33.333 | 0.00 | 0.00 | 31.71 | 2.57 |
783 | 874 | 8.097038 | AGTCATTAACAGGCACCTATGTATATG | 58.903 | 37.037 | 0.00 | 0.00 | 0.00 | 1.78 |
784 | 875 | 8.207350 | AGTCATTAACAGGCACCTATGTATAT | 57.793 | 34.615 | 0.00 | 0.00 | 0.00 | 0.86 |
785 | 876 | 7.612065 | AGTCATTAACAGGCACCTATGTATA | 57.388 | 36.000 | 0.00 | 0.00 | 0.00 | 1.47 |
786 | 877 | 6.500589 | AGTCATTAACAGGCACCTATGTAT | 57.499 | 37.500 | 0.00 | 0.00 | 0.00 | 2.29 |
787 | 878 | 5.950544 | AGTCATTAACAGGCACCTATGTA | 57.049 | 39.130 | 0.00 | 0.00 | 0.00 | 2.29 |
788 | 879 | 4.844349 | AGTCATTAACAGGCACCTATGT | 57.156 | 40.909 | 0.00 | 0.00 | 0.00 | 2.29 |
789 | 880 | 7.498900 | TGAATTAGTCATTAACAGGCACCTATG | 59.501 | 37.037 | 0.00 | 0.00 | 0.00 | 2.23 |
790 | 881 | 7.499232 | GTGAATTAGTCATTAACAGGCACCTAT | 59.501 | 37.037 | 0.00 | 0.00 | 38.90 | 2.57 |
791 | 882 | 6.821665 | GTGAATTAGTCATTAACAGGCACCTA | 59.178 | 38.462 | 0.00 | 0.00 | 38.90 | 3.08 |
792 | 883 | 5.648092 | GTGAATTAGTCATTAACAGGCACCT | 59.352 | 40.000 | 0.00 | 0.00 | 38.90 | 4.00 |
793 | 884 | 5.648092 | AGTGAATTAGTCATTAACAGGCACC | 59.352 | 40.000 | 0.00 | 0.00 | 38.90 | 5.01 |
794 | 885 | 6.546395 | CAGTGAATTAGTCATTAACAGGCAC | 58.454 | 40.000 | 0.00 | 0.00 | 38.90 | 5.01 |
795 | 886 | 5.123820 | GCAGTGAATTAGTCATTAACAGGCA | 59.876 | 40.000 | 0.00 | 0.00 | 38.90 | 4.75 |
796 | 887 | 5.123820 | TGCAGTGAATTAGTCATTAACAGGC | 59.876 | 40.000 | 0.00 | 0.00 | 38.90 | 4.85 |
797 | 888 | 6.741992 | TGCAGTGAATTAGTCATTAACAGG | 57.258 | 37.500 | 0.00 | 0.00 | 38.90 | 4.00 |
798 | 889 | 9.630098 | AAATTGCAGTGAATTAGTCATTAACAG | 57.370 | 29.630 | 0.00 | 0.00 | 38.90 | 3.16 |
799 | 890 | 9.409312 | CAAATTGCAGTGAATTAGTCATTAACA | 57.591 | 29.630 | 0.00 | 0.00 | 38.90 | 2.41 |
800 | 891 | 8.863049 | CCAAATTGCAGTGAATTAGTCATTAAC | 58.137 | 33.333 | 0.00 | 0.00 | 38.90 | 2.01 |
804 | 895 | 5.413499 | GCCAAATTGCAGTGAATTAGTCAT | 58.587 | 37.500 | 0.00 | 0.00 | 38.90 | 3.06 |
808 | 899 | 2.599973 | GCGCCAAATTGCAGTGAATTAG | 59.400 | 45.455 | 0.00 | 0.00 | 0.00 | 1.73 |
814 | 905 | 0.509499 | CTTTGCGCCAAATTGCAGTG | 59.491 | 50.000 | 4.18 | 0.00 | 42.89 | 3.66 |
828 | 924 | 4.981806 | TGAATGTTATAGGTGGCTTTGC | 57.018 | 40.909 | 0.00 | 0.00 | 0.00 | 3.68 |
842 | 938 | 5.771469 | TGATTTGCTGAACGAATGAATGTT | 58.229 | 33.333 | 0.00 | 0.00 | 32.10 | 2.71 |
843 | 939 | 5.375417 | TGATTTGCTGAACGAATGAATGT | 57.625 | 34.783 | 0.00 | 0.00 | 32.10 | 2.71 |
844 | 940 | 4.796830 | CCTGATTTGCTGAACGAATGAATG | 59.203 | 41.667 | 0.00 | 0.00 | 32.10 | 2.67 |
845 | 941 | 4.701651 | TCCTGATTTGCTGAACGAATGAAT | 59.298 | 37.500 | 0.00 | 0.00 | 32.10 | 2.57 |
846 | 942 | 4.071423 | TCCTGATTTGCTGAACGAATGAA | 58.929 | 39.130 | 0.00 | 0.00 | 32.10 | 2.57 |
847 | 943 | 3.436704 | GTCCTGATTTGCTGAACGAATGA | 59.563 | 43.478 | 0.00 | 0.00 | 32.10 | 2.57 |
865 | 961 | 1.462035 | ACTGCCCAATTGCTGTCCT | 59.538 | 52.632 | 0.00 | 0.00 | 38.85 | 3.85 |
868 | 964 | 0.111061 | TCTGACTGCCCAATTGCTGT | 59.889 | 50.000 | 0.00 | 0.00 | 44.72 | 4.40 |
869 | 965 | 1.250328 | TTCTGACTGCCCAATTGCTG | 58.750 | 50.000 | 0.00 | 0.00 | 36.39 | 4.41 |
870 | 966 | 2.097825 | GATTCTGACTGCCCAATTGCT | 58.902 | 47.619 | 0.00 | 0.00 | 0.00 | 3.91 |
876 | 991 | 2.957402 | AAACTGATTCTGACTGCCCA | 57.043 | 45.000 | 0.00 | 0.00 | 0.00 | 5.36 |
897 | 1020 | 3.678056 | ATGCACGAGGACAGAAACTTA | 57.322 | 42.857 | 0.00 | 0.00 | 0.00 | 2.24 |
906 | 1029 | 5.106712 | TGTTATCTGAAAAATGCACGAGGAC | 60.107 | 40.000 | 0.00 | 0.00 | 0.00 | 3.85 |
912 | 1040 | 8.239314 | TCAGAATCTGTTATCTGAAAAATGCAC | 58.761 | 33.333 | 10.36 | 0.00 | 46.67 | 4.57 |
1035 | 1168 | 1.061546 | GGGTGTGGAGGTTCCTGTAA | 58.938 | 55.000 | 0.00 | 0.00 | 37.46 | 2.41 |
1065 | 1198 | 1.813859 | CACGAACCCAGCTCCGATA | 59.186 | 57.895 | 0.00 | 0.00 | 0.00 | 2.92 |
1327 | 1464 | 5.189180 | GGGCTCAAACTTACAGATTCAGAT | 58.811 | 41.667 | 0.00 | 0.00 | 0.00 | 2.90 |
1477 | 1620 | 8.571461 | TTTGATATGAAAATGAGAGAAGCTGT | 57.429 | 30.769 | 0.00 | 0.00 | 0.00 | 4.40 |
1547 | 1691 | 9.802039 | ATGATAAGGTGGTTTTTCTTACAAGTA | 57.198 | 29.630 | 0.00 | 0.00 | 0.00 | 2.24 |
1617 | 1761 | 8.531146 | AGGTCAACAGTTCAATATAAAAATGGG | 58.469 | 33.333 | 3.47 | 0.00 | 0.00 | 4.00 |
1675 | 1821 | 5.707298 | CACAGCGATATTATCTGGGGAAAAT | 59.293 | 40.000 | 2.36 | 0.00 | 32.42 | 1.82 |
1876 | 2022 | 5.679382 | GCAATGTCCATGCAATTTACTGCTA | 60.679 | 40.000 | 0.00 | 0.00 | 43.07 | 3.49 |
1927 | 2073 | 3.492421 | AATTTGCTCCATAACACTGCG | 57.508 | 42.857 | 0.00 | 0.00 | 0.00 | 5.18 |
1932 | 2078 | 4.888326 | AGCCAAAATTTGCTCCATAACA | 57.112 | 36.364 | 0.00 | 0.00 | 30.33 | 2.41 |
1969 | 2115 | 4.633565 | CAGAGAGGTGCTGGAGTTAATTTC | 59.366 | 45.833 | 0.00 | 0.00 | 0.00 | 2.17 |
1979 | 2125 | 1.554160 | ACAGAATCAGAGAGGTGCTGG | 59.446 | 52.381 | 0.00 | 0.00 | 34.20 | 4.85 |
2053 | 2206 | 1.348036 | CGTTCTCCCCCTGAAAGAGTT | 59.652 | 52.381 | 0.00 | 0.00 | 34.07 | 3.01 |
2174 | 2327 | 0.097150 | GGATCGCAAAAGAAGTCGCC | 59.903 | 55.000 | 0.00 | 0.00 | 0.00 | 5.54 |
2221 | 2374 | 5.587289 | TGCACAAGGCCGAATTTTATAATC | 58.413 | 37.500 | 0.00 | 0.00 | 43.89 | 1.75 |
2293 | 2448 | 4.703645 | AGGATATATCATCCACGTCGTG | 57.296 | 45.455 | 18.54 | 18.54 | 40.61 | 4.35 |
2310 | 2465 | 4.020218 | TCTGAAATCGTGTTGAGGAAGGAT | 60.020 | 41.667 | 0.00 | 0.00 | 0.00 | 3.24 |
2319 | 2474 | 8.659491 | TCTTTAGAATCATCTGAAATCGTGTTG | 58.341 | 33.333 | 0.00 | 0.00 | 37.10 | 3.33 |
2324 | 2479 | 8.417780 | AGTGTCTTTAGAATCATCTGAAATCG | 57.582 | 34.615 | 0.00 | 0.00 | 37.10 | 3.34 |
2325 | 2480 | 9.598517 | AGAGTGTCTTTAGAATCATCTGAAATC | 57.401 | 33.333 | 0.00 | 0.00 | 37.10 | 2.17 |
2341 | 2497 | 3.629398 | CCAAGAAAGCACAGAGTGTCTTT | 59.371 | 43.478 | 14.66 | 14.66 | 40.03 | 2.52 |
2348 | 2504 | 2.555325 | TGAATGCCAAGAAAGCACAGAG | 59.445 | 45.455 | 0.00 | 0.00 | 44.40 | 3.35 |
2525 | 2681 | 6.769512 | AGTTCCAAGCTTCTCTAATGTGTAA | 58.230 | 36.000 | 0.00 | 0.00 | 0.00 | 2.41 |
2586 | 2742 | 9.890629 | TTCATAATAGTGACTGCTAATGTTCTT | 57.109 | 29.630 | 0.00 | 0.00 | 0.00 | 2.52 |
2600 | 2756 | 9.745880 | GAAGTACTCGGATTTTCATAATAGTGA | 57.254 | 33.333 | 0.00 | 0.00 | 0.00 | 3.41 |
2609 | 2765 | 4.884668 | AGTGGAAGTACTCGGATTTTCA | 57.115 | 40.909 | 0.00 | 0.00 | 0.00 | 2.69 |
2629 | 2785 | 6.752351 | ACGAGTCACTGTAGTTAAATGCATAG | 59.248 | 38.462 | 0.00 | 0.00 | 0.00 | 2.23 |
2716 | 2875 | 2.378038 | GCCCATGTCTGGCTGAAATTA | 58.622 | 47.619 | 4.37 | 0.00 | 45.70 | 1.40 |
2764 | 2923 | 1.535028 | TGTAGCCTTTCATGTGTTGCG | 59.465 | 47.619 | 0.00 | 0.00 | 0.00 | 4.85 |
2797 | 2956 | 6.431234 | CCTTGAAACTTATGAACTTGGCTAGT | 59.569 | 38.462 | 0.00 | 0.00 | 39.32 | 2.57 |
2963 | 3122 | 3.958798 | CCAAGGATGGCTCTCAATCAAAT | 59.041 | 43.478 | 0.00 | 0.00 | 40.58 | 2.32 |
3108 | 3267 | 2.283966 | CCTCACGGGTCACCTCCT | 60.284 | 66.667 | 0.00 | 0.00 | 33.28 | 3.69 |
3120 | 3279 | 4.223032 | TCACCTCCATTTTACTCTCCTCAC | 59.777 | 45.833 | 0.00 | 0.00 | 0.00 | 3.51 |
3130 | 3289 | 1.979308 | TCCACCGTCACCTCCATTTTA | 59.021 | 47.619 | 0.00 | 0.00 | 0.00 | 1.52 |
3155 | 3314 | 2.018670 | CGCATCGCTTTCGTCGTG | 59.981 | 61.111 | 0.00 | 0.00 | 36.96 | 4.35 |
3157 | 3316 | 3.179265 | ACCGCATCGCTTTCGTCG | 61.179 | 61.111 | 0.00 | 0.00 | 36.96 | 5.12 |
3184 | 3343 | 3.558931 | TTTGTCTCTTTCTGCTCCACA | 57.441 | 42.857 | 0.00 | 0.00 | 0.00 | 4.17 |
3193 | 3352 | 5.760253 | TGGAGTCTTGACATTTGTCTCTTTC | 59.240 | 40.000 | 11.67 | 4.07 | 44.99 | 2.62 |
3442 | 3605 | 1.008875 | GCTTCAGCGACACGTGATGA | 61.009 | 55.000 | 25.01 | 16.64 | 0.00 | 2.92 |
3445 | 3608 | 2.355837 | GGCTTCAGCGACACGTGA | 60.356 | 61.111 | 25.01 | 0.00 | 43.26 | 4.35 |
3476 | 3639 | 2.126580 | CACCTCGACGTCGGGTTC | 60.127 | 66.667 | 33.99 | 4.19 | 39.62 | 3.62 |
3532 | 3695 | 4.166011 | GCATCGACCGCAACAGCC | 62.166 | 66.667 | 3.85 | 0.00 | 0.00 | 4.85 |
3559 | 3722 | 3.288092 | GTCCTTCACCCTTGTTTCAACT | 58.712 | 45.455 | 0.00 | 0.00 | 0.00 | 3.16 |
3577 | 3740 | 2.109126 | GCCACCATCGCTCTTGTCC | 61.109 | 63.158 | 0.00 | 0.00 | 0.00 | 4.02 |
3584 | 3747 | 0.249489 | GTAGATTCGCCACCATCGCT | 60.249 | 55.000 | 0.00 | 0.00 | 0.00 | 4.93 |
3629 | 3792 | 7.665690 | TCTTGCACTCCTCTTATTATCATCTC | 58.334 | 38.462 | 0.00 | 0.00 | 0.00 | 2.75 |
3689 | 3858 | 9.297586 | GTTTTACTCAGTTTCCTTTTTCGAATT | 57.702 | 29.630 | 0.00 | 0.00 | 0.00 | 2.17 |
3717 | 3886 | 4.391683 | TCATGGTGCCCATATTCATCAT | 57.608 | 40.909 | 6.42 | 0.00 | 43.15 | 2.45 |
3723 | 3895 | 4.140947 | ACTTGGTATCATGGTGCCCATATT | 60.141 | 41.667 | 10.93 | 1.30 | 43.15 | 1.28 |
3726 | 3898 | 1.570501 | ACTTGGTATCATGGTGCCCAT | 59.429 | 47.619 | 10.93 | 1.21 | 46.37 | 4.00 |
3729 | 3901 | 2.128771 | ACACTTGGTATCATGGTGCC | 57.871 | 50.000 | 6.07 | 6.07 | 33.46 | 5.01 |
3745 | 3917 | 7.214467 | TGGTTCTTGATTTTCAGGATAACAC | 57.786 | 36.000 | 0.00 | 0.00 | 32.38 | 3.32 |
3778 | 3950 | 8.893563 | AGTTATGAAAATTCCTAACCATCCAA | 57.106 | 30.769 | 14.00 | 0.00 | 38.34 | 3.53 |
3779 | 3951 | 9.983024 | TTAGTTATGAAAATTCCTAACCATCCA | 57.017 | 29.630 | 14.00 | 0.00 | 38.34 | 3.41 |
3791 | 3963 | 9.802039 | TCCAACACCTAGTTAGTTATGAAAATT | 57.198 | 29.630 | 0.00 | 0.00 | 38.74 | 1.82 |
3792 | 3964 | 9.975218 | ATCCAACACCTAGTTAGTTATGAAAAT | 57.025 | 29.630 | 0.00 | 0.00 | 38.74 | 1.82 |
3793 | 3965 | 9.226606 | CATCCAACACCTAGTTAGTTATGAAAA | 57.773 | 33.333 | 0.00 | 0.00 | 38.74 | 2.29 |
3794 | 3966 | 7.827236 | CCATCCAACACCTAGTTAGTTATGAAA | 59.173 | 37.037 | 0.00 | 0.00 | 38.74 | 2.69 |
3795 | 3967 | 7.335627 | CCATCCAACACCTAGTTAGTTATGAA | 58.664 | 38.462 | 0.00 | 0.00 | 38.74 | 2.57 |
3796 | 3968 | 6.126883 | CCCATCCAACACCTAGTTAGTTATGA | 60.127 | 42.308 | 0.00 | 0.00 | 38.74 | 2.15 |
3797 | 3969 | 6.055588 | CCCATCCAACACCTAGTTAGTTATG | 58.944 | 44.000 | 0.00 | 0.00 | 38.74 | 1.90 |
3798 | 3970 | 5.729718 | ACCCATCCAACACCTAGTTAGTTAT | 59.270 | 40.000 | 0.00 | 0.00 | 38.74 | 1.89 |
3799 | 3971 | 5.095809 | ACCCATCCAACACCTAGTTAGTTA | 58.904 | 41.667 | 0.00 | 0.00 | 38.74 | 2.24 |
3800 | 3972 | 3.914435 | ACCCATCCAACACCTAGTTAGTT | 59.086 | 43.478 | 0.00 | 0.00 | 38.74 | 2.24 |
3801 | 3973 | 3.527937 | ACCCATCCAACACCTAGTTAGT | 58.472 | 45.455 | 0.00 | 0.00 | 38.74 | 2.24 |
3802 | 3974 | 4.101119 | CCTACCCATCCAACACCTAGTTAG | 59.899 | 50.000 | 0.00 | 0.00 | 38.74 | 2.34 |
3803 | 3975 | 4.035112 | CCTACCCATCCAACACCTAGTTA | 58.965 | 47.826 | 0.00 | 0.00 | 38.74 | 2.24 |
3804 | 3976 | 2.844348 | CCTACCCATCCAACACCTAGTT | 59.156 | 50.000 | 0.00 | 0.00 | 42.42 | 2.24 |
3805 | 3977 | 2.045326 | TCCTACCCATCCAACACCTAGT | 59.955 | 50.000 | 0.00 | 0.00 | 0.00 | 2.57 |
3806 | 3978 | 2.700897 | CTCCTACCCATCCAACACCTAG | 59.299 | 54.545 | 0.00 | 0.00 | 0.00 | 3.02 |
3807 | 3979 | 2.628559 | CCTCCTACCCATCCAACACCTA | 60.629 | 54.545 | 0.00 | 0.00 | 0.00 | 3.08 |
3808 | 3980 | 1.584724 | CTCCTACCCATCCAACACCT | 58.415 | 55.000 | 0.00 | 0.00 | 0.00 | 4.00 |
3809 | 3981 | 0.546598 | CCTCCTACCCATCCAACACC | 59.453 | 60.000 | 0.00 | 0.00 | 0.00 | 4.16 |
3810 | 3982 | 0.546598 | CCCTCCTACCCATCCAACAC | 59.453 | 60.000 | 0.00 | 0.00 | 0.00 | 3.32 |
3811 | 3983 | 1.279025 | GCCCTCCTACCCATCCAACA | 61.279 | 60.000 | 0.00 | 0.00 | 0.00 | 3.33 |
3812 | 3984 | 1.532238 | GCCCTCCTACCCATCCAAC | 59.468 | 63.158 | 0.00 | 0.00 | 0.00 | 3.77 |
3813 | 3985 | 2.070039 | CGCCCTCCTACCCATCCAA | 61.070 | 63.158 | 0.00 | 0.00 | 0.00 | 3.53 |
3821 | 3993 | 1.519246 | GGTACAACCGCCCTCCTAC | 59.481 | 63.158 | 0.00 | 0.00 | 0.00 | 3.18 |
3850 | 4022 | 1.194781 | ACACGAGGCTTGATCCCTGT | 61.195 | 55.000 | 9.20 | 0.00 | 31.41 | 4.00 |
3901 | 4073 | 1.881973 | GCTTCATGGCTTCAACACTCA | 59.118 | 47.619 | 0.00 | 0.00 | 0.00 | 3.41 |
3970 | 4142 | 1.537202 | GTACTTGTGCAGGGAAAGCAG | 59.463 | 52.381 | 0.00 | 0.00 | 43.63 | 4.24 |
4020 | 4192 | 5.138125 | ACATTACAACATTGCCTCCAAAG | 57.862 | 39.130 | 0.00 | 0.00 | 34.05 | 2.77 |
4021 | 4193 | 5.772672 | ACTACATTACAACATTGCCTCCAAA | 59.227 | 36.000 | 0.00 | 0.00 | 34.05 | 3.28 |
4022 | 4194 | 5.182950 | CACTACATTACAACATTGCCTCCAA | 59.817 | 40.000 | 0.00 | 0.00 | 35.01 | 3.53 |
4024 | 4196 | 4.941263 | TCACTACATTACAACATTGCCTCC | 59.059 | 41.667 | 0.00 | 0.00 | 0.00 | 4.30 |
4028 | 4207 | 9.840427 | AAATAACTCACTACATTACAACATTGC | 57.160 | 29.630 | 0.00 | 0.00 | 0.00 | 3.56 |
4499 | 6795 | 2.124983 | GCTCATGCAAGCCCGAGA | 60.125 | 61.111 | 10.82 | 0.00 | 39.41 | 4.04 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.