Multiple sequence alignment - TraesCS2A01G314800
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 | TraesCS2A01G314800 | chr2A | 100.000 | 5471 | 0 | 0 | 1 | 5471 | 539963806 | 539969276 | 0.000000e+00 | 10104.0 |
1 | TraesCS2A01G314800 | chr2A | 83.099 | 142 | 21 | 3 | 4698 | 4838 | 25602170 | 25602309 | 5.750000e-25 | 126.0 |
2 | TraesCS2A01G314800 | chr2A | 83.673 | 98 | 15 | 1 | 525 | 621 | 57887662 | 57887565 | 2.100000e-14 | 91.6 |
3 | TraesCS2A01G314800 | chr2D | 94.064 | 2948 | 125 | 25 | 1 | 2929 | 402708904 | 402711820 | 0.000000e+00 | 4429.0 |
4 | TraesCS2A01G314800 | chr2D | 95.771 | 1608 | 51 | 7 | 2930 | 4529 | 402711866 | 402713464 | 0.000000e+00 | 2577.0 |
5 | TraesCS2A01G314800 | chr2D | 93.023 | 86 | 6 | 0 | 4586 | 4671 | 402713645 | 402713730 | 5.750000e-25 | 126.0 |
6 | TraesCS2A01G314800 | chr2B | 92.217 | 2955 | 160 | 29 | 1 | 2929 | 476556370 | 476559280 | 0.000000e+00 | 4119.0 |
7 | TraesCS2A01G314800 | chr2B | 93.157 | 1476 | 62 | 20 | 3071 | 4529 | 476559635 | 476561088 | 0.000000e+00 | 2130.0 |
8 | TraesCS2A01G314800 | chr2B | 85.035 | 715 | 68 | 13 | 4705 | 5415 | 698101829 | 698101150 | 0.000000e+00 | 691.0 |
9 | TraesCS2A01G314800 | chr2B | 96.795 | 156 | 5 | 0 | 2930 | 3085 | 476559326 | 476559481 | 1.510000e-65 | 261.0 |
10 | TraesCS2A01G314800 | chr2B | 77.841 | 176 | 26 | 8 | 4532 | 4704 | 476561119 | 476561284 | 4.510000e-16 | 97.1 |
11 | TraesCS2A01G314800 | chr6B | 90.130 | 770 | 64 | 7 | 4707 | 5471 | 677567876 | 677568638 | 0.000000e+00 | 990.0 |
12 | TraesCS2A01G314800 | chr6B | 83.826 | 711 | 75 | 14 | 4707 | 5415 | 49874356 | 49873684 | 1.660000e-179 | 640.0 |
13 | TraesCS2A01G314800 | chr6D | 85.795 | 711 | 62 | 14 | 4707 | 5415 | 27201380 | 27200707 | 0.000000e+00 | 717.0 |
14 | TraesCS2A01G314800 | chr7A | 84.432 | 713 | 69 | 18 | 4707 | 5415 | 624886815 | 624886141 | 0.000000e+00 | 664.0 |
15 | TraesCS2A01G314800 | chr7A | 85.556 | 90 | 11 | 2 | 528 | 616 | 25942767 | 25942679 | 5.840000e-15 | 93.5 |
16 | TraesCS2A01G314800 | chr6A | 83.934 | 722 | 74 | 22 | 4700 | 5415 | 45863202 | 45862517 | 0.000000e+00 | 652.0 |
17 | TraesCS2A01G314800 | chr6A | 88.889 | 108 | 10 | 2 | 510 | 616 | 574399238 | 574399344 | 1.240000e-26 | 132.0 |
18 | TraesCS2A01G314800 | chr7B | 84.034 | 714 | 65 | 14 | 4707 | 5412 | 56922106 | 56922778 | 4.620000e-180 | 641.0 |
19 | TraesCS2A01G314800 | chr1A | 92.548 | 416 | 29 | 2 | 5001 | 5415 | 540058747 | 540058333 | 3.650000e-166 | 595.0 |
20 | TraesCS2A01G314800 | chr1A | 82.969 | 640 | 65 | 21 | 4707 | 5342 | 249773030 | 249772431 | 6.240000e-149 | 538.0 |
21 | TraesCS2A01G314800 | chr1A | 85.556 | 90 | 11 | 2 | 533 | 621 | 22078375 | 22078287 | 5.840000e-15 | 93.5 |
22 | TraesCS2A01G314800 | chr1A | 93.443 | 61 | 4 | 0 | 5353 | 5413 | 249772442 | 249772382 | 2.100000e-14 | 91.6 |
23 | TraesCS2A01G314800 | chr1D | 85.075 | 134 | 19 | 1 | 4699 | 4832 | 414249269 | 414249401 | 9.560000e-28 | 135.0 |
24 | TraesCS2A01G314800 | chr1D | 87.097 | 93 | 11 | 1 | 525 | 616 | 307337374 | 307337466 | 2.700000e-18 | 104.0 |
25 | TraesCS2A01G314800 | chr7D | 84.211 | 133 | 18 | 2 | 4700 | 4832 | 163549521 | 163549650 | 5.750000e-25 | 126.0 |
26 | TraesCS2A01G314800 | chrUn | 82.353 | 136 | 22 | 2 | 4698 | 4832 | 228439468 | 228439602 | 3.460000e-22 | 117.0 |
27 | TraesCS2A01G314800 | chrUn | 84.259 | 108 | 15 | 2 | 510 | 616 | 110684354 | 110684248 | 2.700000e-18 | 104.0 |
28 | TraesCS2A01G314800 | chr3D | 85.714 | 91 | 10 | 3 | 520 | 609 | 98940955 | 98941043 | 5.840000e-15 | 93.5 |
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 | TraesCS2A01G314800 | chr2A | 539963806 | 539969276 | 5470 | False | 10104.000000 | 10104 | 100.0000 | 1 | 5471 | 1 | chr2A.!!$F2 | 5470 |
1 | TraesCS2A01G314800 | chr2D | 402708904 | 402713730 | 4826 | False | 2377.333333 | 4429 | 94.2860 | 1 | 4671 | 3 | chr2D.!!$F1 | 4670 |
2 | TraesCS2A01G314800 | chr2B | 476556370 | 476561284 | 4914 | False | 1651.775000 | 4119 | 90.0025 | 1 | 4704 | 4 | chr2B.!!$F1 | 4703 |
3 | TraesCS2A01G314800 | chr2B | 698101150 | 698101829 | 679 | True | 691.000000 | 691 | 85.0350 | 4705 | 5415 | 1 | chr2B.!!$R1 | 710 |
4 | TraesCS2A01G314800 | chr6B | 677567876 | 677568638 | 762 | False | 990.000000 | 990 | 90.1300 | 4707 | 5471 | 1 | chr6B.!!$F1 | 764 |
5 | TraesCS2A01G314800 | chr6B | 49873684 | 49874356 | 672 | True | 640.000000 | 640 | 83.8260 | 4707 | 5415 | 1 | chr6B.!!$R1 | 708 |
6 | TraesCS2A01G314800 | chr6D | 27200707 | 27201380 | 673 | True | 717.000000 | 717 | 85.7950 | 4707 | 5415 | 1 | chr6D.!!$R1 | 708 |
7 | TraesCS2A01G314800 | chr7A | 624886141 | 624886815 | 674 | True | 664.000000 | 664 | 84.4320 | 4707 | 5415 | 1 | chr7A.!!$R2 | 708 |
8 | TraesCS2A01G314800 | chr6A | 45862517 | 45863202 | 685 | True | 652.000000 | 652 | 83.9340 | 4700 | 5415 | 1 | chr6A.!!$R1 | 715 |
9 | TraesCS2A01G314800 | chr7B | 56922106 | 56922778 | 672 | False | 641.000000 | 641 | 84.0340 | 4707 | 5412 | 1 | chr7B.!!$F1 | 705 |
10 | TraesCS2A01G314800 | chr1A | 249772382 | 249773030 | 648 | True | 314.800000 | 538 | 88.2060 | 4707 | 5413 | 2 | chr1A.!!$R3 | 706 |
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 |
---|---|---|---|---|---|---|---|---|---|---|
95 | 96 | 0.107508 | AGCATCGGGTTGTCATCTGG | 60.108 | 55.0 | 0.0 | 0.0 | 0.0 | 3.86 | F |
1108 | 1120 | 0.035056 | CTCGAAGCATCCAAACCCCT | 60.035 | 55.0 | 0.0 | 0.0 | 0.0 | 4.79 | F |
1684 | 1703 | 0.320073 | CGTTCTCGGTGCTTGGGTTA | 60.320 | 55.0 | 0.0 | 0.0 | 0.0 | 2.85 | F |
3228 | 3467 | 0.397941 | TGGAAGTGAGAACCAGGCAG | 59.602 | 55.0 | 0.0 | 0.0 | 0.0 | 4.85 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1991 | 2010 | 1.117150 | ATGGCTTGCACAATGGGATC | 58.883 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 | R |
2473 | 2498 | 0.538057 | GCCAATAGCCCATGCAGCTA | 60.538 | 55.000 | 15.52 | 15.52 | 46.32 | 3.32 | R |
3640 | 3879 | 1.736126 | GAACTTACCCAGCCTAAACGC | 59.264 | 52.381 | 0.00 | 0.00 | 0.00 | 4.84 | R |
4816 | 5198 | 0.250234 | CGAGGAAGGAGTGGATGCAA | 59.750 | 55.000 | 0.00 | 0.00 | 0.00 | 4.08 | 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 |
---|---|---|---|---|---|---|---|---|---|
80 | 81 | 5.471456 | CCTCACACTAGACTTGAAAAAGCAT | 59.529 | 40.000 | 0.00 | 0.00 | 0.00 | 3.79 |
95 | 96 | 0.107508 | AGCATCGGGTTGTCATCTGG | 60.108 | 55.000 | 0.00 | 0.00 | 0.00 | 3.86 |
133 | 137 | 1.984026 | CAGGAATGTTGGGGCCACC | 60.984 | 63.158 | 0.20 | 2.19 | 40.81 | 4.61 |
142 | 146 | 1.724148 | TTGGGGCCACCTTGATGTCA | 61.724 | 55.000 | 0.20 | 0.00 | 41.11 | 3.58 |
170 | 174 | 6.475596 | AATTTGATGAATGGGAACTGGATC | 57.524 | 37.500 | 0.00 | 0.00 | 0.00 | 3.36 |
179 | 183 | 3.934068 | TGGGAACTGGATCTTAAACGTC | 58.066 | 45.455 | 0.00 | 0.00 | 0.00 | 4.34 |
210 | 214 | 2.673368 | CCTCTGTCGCAATCAGTAAACC | 59.327 | 50.000 | 0.00 | 0.00 | 34.86 | 3.27 |
216 | 220 | 5.483811 | TGTCGCAATCAGTAAACCATAAGA | 58.516 | 37.500 | 0.00 | 0.00 | 0.00 | 2.10 |
247 | 251 | 6.428083 | AGATCTCTCTGTCGAATACCTCTA | 57.572 | 41.667 | 0.00 | 0.00 | 0.00 | 2.43 |
341 | 345 | 4.525912 | ATTTCAATCCAAGGTTGAGCAC | 57.474 | 40.909 | 0.00 | 0.00 | 36.96 | 4.40 |
375 | 379 | 4.775236 | GCCATAATAGCCTGGAGATAAGG | 58.225 | 47.826 | 0.00 | 0.00 | 37.91 | 2.69 |
392 | 396 | 4.730487 | GCCACTCAAGCCTGTCAT | 57.270 | 55.556 | 0.00 | 0.00 | 0.00 | 3.06 |
401 | 405 | 4.197750 | CTCAAGCCTGTCATATGCTTTCT | 58.802 | 43.478 | 0.00 | 0.00 | 42.37 | 2.52 |
411 | 415 | 9.149225 | CCTGTCATATGCTTTCTTCATATCTAC | 57.851 | 37.037 | 0.00 | 0.00 | 35.57 | 2.59 |
418 | 422 | 7.055667 | TGCTTTCTTCATATCTACCTACAGG | 57.944 | 40.000 | 0.00 | 0.00 | 42.17 | 4.00 |
534 | 538 | 3.777925 | CAACGCACCTTCGGCTCG | 61.778 | 66.667 | 0.00 | 0.00 | 0.00 | 5.03 |
539 | 543 | 2.507992 | CACCTTCGGCTCGCTCAG | 60.508 | 66.667 | 0.00 | 0.00 | 0.00 | 3.35 |
551 | 555 | 0.958822 | TCGCTCAGTGCTTGTAGTCA | 59.041 | 50.000 | 0.00 | 0.00 | 40.11 | 3.41 |
556 | 560 | 1.002366 | CAGTGCTTGTAGTCATCGCC | 58.998 | 55.000 | 0.00 | 0.00 | 0.00 | 5.54 |
633 | 638 | 7.870826 | TCTCTTGATATTTTTGTTGCGAGAAA | 58.129 | 30.769 | 0.00 | 0.00 | 0.00 | 2.52 |
638 | 643 | 8.894409 | TGATATTTTTGTTGCGAGAAATACTG | 57.106 | 30.769 | 0.00 | 0.00 | 29.68 | 2.74 |
649 | 654 | 5.753438 | TGCGAGAAATACTGCCTTATAGTTG | 59.247 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
862 | 874 | 4.082136 | GGCACCGTGGAAAACCAAAATATA | 60.082 | 41.667 | 0.00 | 0.00 | 0.00 | 0.86 |
863 | 875 | 5.394773 | GGCACCGTGGAAAACCAAAATATAT | 60.395 | 40.000 | 0.00 | 0.00 | 0.00 | 0.86 |
864 | 876 | 6.183360 | GGCACCGTGGAAAACCAAAATATATA | 60.183 | 38.462 | 0.00 | 0.00 | 0.00 | 0.86 |
865 | 877 | 6.693978 | GCACCGTGGAAAACCAAAATATATAC | 59.306 | 38.462 | 0.00 | 0.00 | 0.00 | 1.47 |
866 | 878 | 7.628794 | GCACCGTGGAAAACCAAAATATATACA | 60.629 | 37.037 | 0.00 | 0.00 | 0.00 | 2.29 |
867 | 879 | 7.913297 | CACCGTGGAAAACCAAAATATATACAG | 59.087 | 37.037 | 0.00 | 0.00 | 0.00 | 2.74 |
868 | 880 | 7.067737 | ACCGTGGAAAACCAAAATATATACAGG | 59.932 | 37.037 | 0.00 | 0.00 | 0.00 | 4.00 |
869 | 881 | 6.915843 | CGTGGAAAACCAAAATATATACAGGC | 59.084 | 38.462 | 0.00 | 0.00 | 0.00 | 4.85 |
870 | 882 | 7.207383 | GTGGAAAACCAAAATATATACAGGCC | 58.793 | 38.462 | 0.00 | 0.00 | 0.00 | 5.19 |
871 | 883 | 6.325286 | TGGAAAACCAAAATATATACAGGCCC | 59.675 | 38.462 | 0.00 | 0.00 | 0.00 | 5.80 |
872 | 884 | 6.325286 | GGAAAACCAAAATATATACAGGCCCA | 59.675 | 38.462 | 0.00 | 0.00 | 0.00 | 5.36 |
873 | 885 | 6.976934 | AAACCAAAATATATACAGGCCCAG | 57.023 | 37.500 | 0.00 | 0.00 | 0.00 | 4.45 |
874 | 886 | 4.998051 | ACCAAAATATATACAGGCCCAGG | 58.002 | 43.478 | 0.00 | 0.00 | 0.00 | 4.45 |
875 | 887 | 3.763897 | CCAAAATATATACAGGCCCAGGC | 59.236 | 47.826 | 0.00 | 0.00 | 41.06 | 4.85 |
891 | 903 | 3.612681 | GCGCCCAGCCCGACTATA | 61.613 | 66.667 | 0.00 | 0.00 | 40.81 | 1.31 |
896 | 908 | 1.056660 | CCCAGCCCGACTATAACCAT | 58.943 | 55.000 | 0.00 | 0.00 | 0.00 | 3.55 |
957 | 969 | 0.184451 | AGGCCCATCCTGCAATACTG | 59.816 | 55.000 | 0.00 | 0.00 | 45.54 | 2.74 |
970 | 982 | 2.101415 | GCAATACTGAAGGCCCAAATCC | 59.899 | 50.000 | 0.00 | 0.00 | 0.00 | 3.01 |
971 | 983 | 2.695147 | CAATACTGAAGGCCCAAATCCC | 59.305 | 50.000 | 0.00 | 0.00 | 0.00 | 3.85 |
972 | 984 | 1.377690 | TACTGAAGGCCCAAATCCCA | 58.622 | 50.000 | 0.00 | 0.00 | 0.00 | 4.37 |
973 | 985 | 0.712380 | ACTGAAGGCCCAAATCCCAT | 59.288 | 50.000 | 0.00 | 0.00 | 0.00 | 4.00 |
974 | 986 | 1.117150 | CTGAAGGCCCAAATCCCATG | 58.883 | 55.000 | 0.00 | 0.00 | 0.00 | 3.66 |
975 | 987 | 0.977108 | TGAAGGCCCAAATCCCATGC | 60.977 | 55.000 | 0.00 | 0.00 | 0.00 | 4.06 |
976 | 988 | 2.019897 | GAAGGCCCAAATCCCATGCG | 62.020 | 60.000 | 0.00 | 0.00 | 0.00 | 4.73 |
1001 | 1013 | 1.751536 | GCACAAGTTGGTTGCGTTGC | 61.752 | 55.000 | 7.96 | 2.22 | 40.15 | 4.17 |
1057 | 1069 | 3.905437 | TTAGGGTTTGTCGCCGCCC | 62.905 | 63.158 | 0.00 | 0.00 | 41.36 | 6.13 |
1108 | 1120 | 0.035056 | CTCGAAGCATCCAAACCCCT | 60.035 | 55.000 | 0.00 | 0.00 | 0.00 | 4.79 |
1179 | 1192 | 1.061131 | CATCGGCACATTCGTTGAGTC | 59.939 | 52.381 | 0.00 | 0.00 | 31.34 | 3.36 |
1296 | 1310 | 4.766088 | GCTTGGCCGCTTGCTTCG | 62.766 | 66.667 | 0.00 | 0.00 | 40.92 | 3.79 |
1297 | 1311 | 4.766088 | CTTGGCCGCTTGCTTCGC | 62.766 | 66.667 | 0.00 | 0.00 | 40.92 | 4.70 |
1300 | 1314 | 4.766088 | GGCCGCTTGCTTCGCTTG | 62.766 | 66.667 | 0.00 | 0.00 | 40.92 | 4.01 |
1547 | 1566 | 1.597461 | GTGGAGAAGGGGAAGACGG | 59.403 | 63.158 | 0.00 | 0.00 | 0.00 | 4.79 |
1609 | 1628 | 1.613925 | GTGTATCTCTGCGCCCTGATA | 59.386 | 52.381 | 4.18 | 7.08 | 0.00 | 2.15 |
1634 | 1653 | 1.069765 | CAGTCGGTGACTTGCCACT | 59.930 | 57.895 | 0.00 | 0.00 | 41.37 | 4.00 |
1642 | 1661 | 0.550914 | TGACTTGCCACTTGGACCTT | 59.449 | 50.000 | 0.00 | 0.00 | 37.39 | 3.50 |
1683 | 1702 | 1.597027 | CGTTCTCGGTGCTTGGGTT | 60.597 | 57.895 | 0.00 | 0.00 | 0.00 | 4.11 |
1684 | 1703 | 0.320073 | CGTTCTCGGTGCTTGGGTTA | 60.320 | 55.000 | 0.00 | 0.00 | 0.00 | 2.85 |
1720 | 1739 | 2.484947 | GGCTGGCTACTATGTTGGGTAC | 60.485 | 54.545 | 0.00 | 0.00 | 0.00 | 3.34 |
1742 | 1761 | 4.096833 | ACCCTTTGTTTCGTTTCTGTTACC | 59.903 | 41.667 | 0.00 | 0.00 | 0.00 | 2.85 |
1749 | 1768 | 9.857957 | TTTGTTTCGTTTCTGTTACCTATTTTT | 57.142 | 25.926 | 0.00 | 0.00 | 0.00 | 1.94 |
1750 | 1769 | 9.505995 | TTGTTTCGTTTCTGTTACCTATTTTTC | 57.494 | 29.630 | 0.00 | 0.00 | 0.00 | 2.29 |
1754 | 1773 | 9.940166 | TTCGTTTCTGTTACCTATTTTTCTTTC | 57.060 | 29.630 | 0.00 | 0.00 | 0.00 | 2.62 |
1755 | 1774 | 9.111613 | TCGTTTCTGTTACCTATTTTTCTTTCA | 57.888 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
1756 | 1775 | 9.893305 | CGTTTCTGTTACCTATTTTTCTTTCAT | 57.107 | 29.630 | 0.00 | 0.00 | 0.00 | 2.57 |
1759 | 1778 | 8.934023 | TCTGTTACCTATTTTTCTTTCATGGT | 57.066 | 30.769 | 0.00 | 0.00 | 0.00 | 3.55 |
1760 | 1779 | 8.792633 | TCTGTTACCTATTTTTCTTTCATGGTG | 58.207 | 33.333 | 0.00 | 0.00 | 0.00 | 4.17 |
1775 | 1794 | 8.896744 | TCTTTCATGGTGAATTGATGATAGTTC | 58.103 | 33.333 | 0.00 | 0.00 | 36.11 | 3.01 |
1825 | 1844 | 2.752903 | AGTTGTTGTCAGTGTGGTTTCC | 59.247 | 45.455 | 0.00 | 0.00 | 0.00 | 3.13 |
1835 | 1854 | 5.535030 | GTCAGTGTGGTTTCCTTTCCTTAAT | 59.465 | 40.000 | 0.00 | 0.00 | 0.00 | 1.40 |
1917 | 1936 | 3.118298 | TCAAGGCTCCGATGATGATTTCA | 60.118 | 43.478 | 0.00 | 0.00 | 39.12 | 2.69 |
1991 | 2010 | 7.144661 | TGAACACAGGTATGCTTGTAAATTTG | 58.855 | 34.615 | 0.00 | 0.00 | 32.90 | 2.32 |
2112 | 2131 | 6.111669 | TCAGAGGATGATGAGGATTTGATC | 57.888 | 41.667 | 0.00 | 0.00 | 31.12 | 2.92 |
2174 | 2193 | 2.489528 | TCCATTTCCTAGGTCCCGAT | 57.510 | 50.000 | 9.08 | 0.00 | 0.00 | 4.18 |
2175 | 2194 | 2.047061 | TCCATTTCCTAGGTCCCGATG | 58.953 | 52.381 | 9.08 | 7.06 | 0.00 | 3.84 |
2223 | 2242 | 4.701651 | TGTTGGAAAATGTGCATAGGAGAG | 59.298 | 41.667 | 0.00 | 0.00 | 0.00 | 3.20 |
2226 | 2245 | 3.314635 | GGAAAATGTGCATAGGAGAGCTG | 59.685 | 47.826 | 0.00 | 0.00 | 0.00 | 4.24 |
2243 | 2262 | 4.767409 | AGAGCTGTTGTACATAGTCAGTCA | 59.233 | 41.667 | 0.00 | 0.00 | 0.00 | 3.41 |
2271 | 2290 | 2.622436 | GCCTAGTAAGTGCTTGTCTGG | 58.378 | 52.381 | 0.00 | 0.00 | 0.00 | 3.86 |
2293 | 2318 | 5.602561 | TGGATGTGTATATCAGGTTAGCACT | 59.397 | 40.000 | 0.00 | 0.00 | 0.00 | 4.40 |
2312 | 2337 | 5.128171 | AGCACTGATTAGTATTTCACCGGTA | 59.872 | 40.000 | 6.87 | 0.00 | 34.74 | 4.02 |
2357 | 2382 | 5.630304 | GCCAGTTTCTTAGGCCTAGATTCTT | 60.630 | 44.000 | 13.36 | 0.00 | 42.58 | 2.52 |
2428 | 2453 | 7.027874 | TGTTAATCCTGTCCTTATTTGTCCT | 57.972 | 36.000 | 0.00 | 0.00 | 0.00 | 3.85 |
2430 | 2455 | 7.610305 | TGTTAATCCTGTCCTTATTTGTCCTTC | 59.390 | 37.037 | 0.00 | 0.00 | 0.00 | 3.46 |
2473 | 2498 | 2.611722 | GCCATTTGTGGTATTGGCGTTT | 60.612 | 45.455 | 0.00 | 0.00 | 44.58 | 3.60 |
2570 | 2596 | 6.598457 | CAGTTGTCATTGAGGAGATTCAAGAT | 59.402 | 38.462 | 0.00 | 0.00 | 40.16 | 2.40 |
2710 | 2736 | 5.161943 | TCTAAAGGTAGTTCCAAGAAGGC | 57.838 | 43.478 | 0.00 | 0.00 | 39.02 | 4.35 |
2788 | 2814 | 6.480320 | GCTATTAATGATCCTCACAAGTCGTT | 59.520 | 38.462 | 0.00 | 0.00 | 0.00 | 3.85 |
2924 | 2950 | 7.934120 | TGTGGTTTCAAAGAAAAAGAAAAAGGA | 59.066 | 29.630 | 0.00 | 0.00 | 33.54 | 3.36 |
3025 | 3096 | 6.010850 | AGTACTTCTGAAGGTGACACTGATA | 58.989 | 40.000 | 20.61 | 0.00 | 0.00 | 2.15 |
3039 | 3110 | 6.092670 | GTGACACTGATAAGCAAGCTGATAAA | 59.907 | 38.462 | 0.00 | 0.00 | 0.00 | 1.40 |
3041 | 3112 | 7.081526 | ACACTGATAAGCAAGCTGATAAAAG | 57.918 | 36.000 | 0.00 | 0.00 | 0.00 | 2.27 |
3228 | 3467 | 0.397941 | TGGAAGTGAGAACCAGGCAG | 59.602 | 55.000 | 0.00 | 0.00 | 0.00 | 4.85 |
3229 | 3468 | 0.957888 | GGAAGTGAGAACCAGGCAGC | 60.958 | 60.000 | 0.00 | 0.00 | 0.00 | 5.25 |
3640 | 3879 | 1.028905 | TGTTGGTCGGAAGCCTTTTG | 58.971 | 50.000 | 0.00 | 0.00 | 0.00 | 2.44 |
3681 | 3920 | 2.866762 | CTGATGTTTTACCCTCTAGCGC | 59.133 | 50.000 | 0.00 | 0.00 | 0.00 | 5.92 |
3685 | 3924 | 2.038033 | TGTTTTACCCTCTAGCGCACTT | 59.962 | 45.455 | 11.47 | 0.00 | 0.00 | 3.16 |
3690 | 3929 | 1.831736 | ACCCTCTAGCGCACTTGTATT | 59.168 | 47.619 | 11.47 | 0.00 | 0.00 | 1.89 |
3729 | 3968 | 7.367285 | GTTTTAATGTCACTTTCATGCAGGTA | 58.633 | 34.615 | 0.00 | 0.00 | 0.00 | 3.08 |
3836 | 4075 | 7.734924 | ATTGCATATGTTGTACTACTCCATG | 57.265 | 36.000 | 8.88 | 9.56 | 0.00 | 3.66 |
3981 | 4220 | 4.389077 | ACTGCTTCTACATCGCTTTTACAC | 59.611 | 41.667 | 0.00 | 0.00 | 0.00 | 2.90 |
4100 | 4339 | 4.465632 | TGTGGAGCTAATGAACGTACAT | 57.534 | 40.909 | 0.00 | 0.00 | 0.00 | 2.29 |
4114 | 4353 | 2.259618 | CGTACATTGAAGAGGTGACCG | 58.740 | 52.381 | 0.00 | 0.00 | 0.00 | 4.79 |
4225 | 4464 | 4.175787 | ACAACATCCTACAGTCGTCTTC | 57.824 | 45.455 | 0.00 | 0.00 | 0.00 | 2.87 |
4241 | 4480 | 6.018180 | AGTCGTCTTCATGTACCTTGTTTTTC | 60.018 | 38.462 | 0.00 | 0.00 | 0.00 | 2.29 |
4315 | 4555 | 2.598394 | GCCTGGGCTGCAACTGAA | 60.598 | 61.111 | 0.50 | 0.00 | 38.26 | 3.02 |
4325 | 4565 | 2.286654 | GCTGCAACTGAACTTGTCACTC | 60.287 | 50.000 | 0.00 | 0.00 | 31.13 | 3.51 |
4341 | 4581 | 3.084039 | TCACTCTGATGATTTTGTGGCC | 58.916 | 45.455 | 0.00 | 0.00 | 0.00 | 5.36 |
4386 | 4637 | 6.380079 | AGACTTGTTATGAAGGAATGGAGT | 57.620 | 37.500 | 0.00 | 0.00 | 0.00 | 3.85 |
4438 | 4694 | 2.293399 | AGTTGCTCCATTTTCCGTTCAC | 59.707 | 45.455 | 0.00 | 0.00 | 0.00 | 3.18 |
4450 | 4706 | 2.267426 | TCCGTTCACGCATTCTGTATG | 58.733 | 47.619 | 0.00 | 0.00 | 38.18 | 2.39 |
4462 | 4718 | 4.641989 | GCATTCTGTATGTTGGTTGGATCT | 59.358 | 41.667 | 0.00 | 0.00 | 36.57 | 2.75 |
4466 | 4722 | 5.430886 | TCTGTATGTTGGTTGGATCTCATG | 58.569 | 41.667 | 0.00 | 0.00 | 0.00 | 3.07 |
4467 | 4723 | 5.045651 | TCTGTATGTTGGTTGGATCTCATGT | 60.046 | 40.000 | 0.00 | 0.00 | 0.00 | 3.21 |
4509 | 4765 | 0.961753 | CCACCTTTTGGCTGAAGTCC | 59.038 | 55.000 | 0.00 | 0.00 | 45.59 | 3.85 |
4511 | 4767 | 2.031120 | CACCTTTTGGCTGAAGTCCAA | 58.969 | 47.619 | 3.13 | 3.13 | 45.59 | 3.53 |
4513 | 4769 | 2.893489 | ACCTTTTGGCTGAAGTCCAATC | 59.107 | 45.455 | 6.93 | 0.00 | 42.57 | 2.67 |
4515 | 4771 | 3.057033 | CCTTTTGGCTGAAGTCCAATCTG | 60.057 | 47.826 | 6.93 | 2.69 | 42.57 | 2.90 |
4517 | 4773 | 1.067295 | TGGCTGAAGTCCAATCTGGT | 58.933 | 50.000 | 0.00 | 0.00 | 39.03 | 4.00 |
4518 | 4774 | 1.425066 | TGGCTGAAGTCCAATCTGGTT | 59.575 | 47.619 | 0.00 | 0.00 | 39.03 | 3.67 |
4519 | 4775 | 1.815003 | GGCTGAAGTCCAATCTGGTTG | 59.185 | 52.381 | 0.00 | 0.00 | 39.03 | 3.77 |
4521 | 4777 | 1.815003 | CTGAAGTCCAATCTGGTTGCC | 59.185 | 52.381 | 0.00 | 0.00 | 39.03 | 4.52 |
4522 | 4778 | 1.177401 | GAAGTCCAATCTGGTTGCCC | 58.823 | 55.000 | 0.00 | 0.00 | 39.03 | 5.36 |
4523 | 4779 | 0.251787 | AAGTCCAATCTGGTTGCCCC | 60.252 | 55.000 | 0.00 | 0.00 | 39.03 | 5.80 |
4527 | 4808 | 1.203288 | TCCAATCTGGTTGCCCCAAAT | 60.203 | 47.619 | 0.00 | 0.00 | 44.65 | 2.32 |
4544 | 4825 | 4.580167 | CCCAAATCGCAGGAGAAAATATCA | 59.420 | 41.667 | 0.00 | 0.00 | 0.00 | 2.15 |
4553 | 4834 | 5.757808 | GCAGGAGAAAATATCAGGAGAGAAC | 59.242 | 44.000 | 0.00 | 0.00 | 0.00 | 3.01 |
4676 | 5053 | 7.381766 | TCATCATTATACATTGCTGCATACC | 57.618 | 36.000 | 1.84 | 0.00 | 0.00 | 2.73 |
4678 | 5055 | 7.666804 | TCATCATTATACATTGCTGCATACCTT | 59.333 | 33.333 | 1.84 | 0.00 | 0.00 | 3.50 |
4679 | 5056 | 7.205737 | TCATTATACATTGCTGCATACCTTG | 57.794 | 36.000 | 1.84 | 0.00 | 0.00 | 3.61 |
4681 | 5058 | 7.501892 | TCATTATACATTGCTGCATACCTTGAA | 59.498 | 33.333 | 1.84 | 0.00 | 0.00 | 2.69 |
4682 | 5059 | 3.855689 | ACATTGCTGCATACCTTGAAC | 57.144 | 42.857 | 1.84 | 0.00 | 0.00 | 3.18 |
4683 | 5060 | 3.424703 | ACATTGCTGCATACCTTGAACT | 58.575 | 40.909 | 1.84 | 0.00 | 0.00 | 3.01 |
4684 | 5061 | 4.588899 | ACATTGCTGCATACCTTGAACTA | 58.411 | 39.130 | 1.84 | 0.00 | 0.00 | 2.24 |
4685 | 5062 | 4.637534 | ACATTGCTGCATACCTTGAACTAG | 59.362 | 41.667 | 1.84 | 0.00 | 0.00 | 2.57 |
4688 | 5065 | 4.755411 | TGCTGCATACCTTGAACTAGTAC | 58.245 | 43.478 | 0.00 | 0.00 | 0.00 | 2.73 |
4726 | 5103 | 1.267533 | GGGAAACATTTACGCACGGTT | 59.732 | 47.619 | 0.00 | 0.00 | 0.00 | 4.44 |
4802 | 5184 | 6.597672 | CAGAAAGGCAACATGTGTACCTTATA | 59.402 | 38.462 | 21.29 | 0.00 | 41.24 | 0.98 |
4814 | 5196 | 5.968167 | TGTGTACCTTATATTCTCCCCAACT | 59.032 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
4816 | 5198 | 6.326843 | GTGTACCTTATATTCTCCCCAACTCT | 59.673 | 42.308 | 0.00 | 0.00 | 0.00 | 3.24 |
4858 | 5244 | 3.140814 | GTGGCATCGCTTTCCCCC | 61.141 | 66.667 | 0.00 | 0.00 | 0.00 | 5.40 |
4859 | 5245 | 3.656280 | TGGCATCGCTTTCCCCCA | 61.656 | 61.111 | 0.00 | 0.00 | 0.00 | 4.96 |
4861 | 5247 | 2.196245 | GGCATCGCTTTCCCCCATC | 61.196 | 63.158 | 0.00 | 0.00 | 0.00 | 3.51 |
4863 | 5249 | 2.203209 | ATCGCTTTCCCCCATCGC | 60.203 | 61.111 | 0.00 | 0.00 | 0.00 | 4.58 |
4864 | 5250 | 2.746375 | ATCGCTTTCCCCCATCGCT | 61.746 | 57.895 | 0.00 | 0.00 | 0.00 | 4.93 |
4865 | 5251 | 2.270874 | ATCGCTTTCCCCCATCGCTT | 62.271 | 55.000 | 0.00 | 0.00 | 0.00 | 4.68 |
4866 | 5252 | 2.046285 | CGCTTTCCCCCATCGCTTT | 61.046 | 57.895 | 0.00 | 0.00 | 0.00 | 3.51 |
4867 | 5253 | 1.809869 | GCTTTCCCCCATCGCTTTC | 59.190 | 57.895 | 0.00 | 0.00 | 0.00 | 2.62 |
4868 | 5254 | 1.667154 | GCTTTCCCCCATCGCTTTCC | 61.667 | 60.000 | 0.00 | 0.00 | 0.00 | 3.13 |
4869 | 5255 | 1.376609 | CTTTCCCCCATCGCTTTCCG | 61.377 | 60.000 | 0.00 | 0.00 | 38.61 | 4.30 |
4924 | 5310 | 0.610687 | CTTCGAGCACTCCTCCCTTT | 59.389 | 55.000 | 0.00 | 0.00 | 37.27 | 3.11 |
4965 | 5354 | 4.052518 | GGGGTGCTGCTCCCATGT | 62.053 | 66.667 | 33.55 | 0.00 | 46.26 | 3.21 |
4966 | 5355 | 2.753043 | GGGTGCTGCTCCCATGTG | 60.753 | 66.667 | 29.70 | 0.00 | 44.05 | 3.21 |
4967 | 5356 | 2.034687 | GGTGCTGCTCCCATGTGT | 59.965 | 61.111 | 9.55 | 0.00 | 0.00 | 3.72 |
4968 | 5357 | 2.042831 | GGTGCTGCTCCCATGTGTC | 61.043 | 63.158 | 9.55 | 0.00 | 0.00 | 3.67 |
4969 | 5358 | 2.046988 | TGCTGCTCCCATGTGTCG | 60.047 | 61.111 | 0.00 | 0.00 | 0.00 | 4.35 |
4970 | 5359 | 2.046892 | GCTGCTCCCATGTGTCGT | 60.047 | 61.111 | 0.00 | 0.00 | 0.00 | 4.34 |
4971 | 5360 | 2.103042 | GCTGCTCCCATGTGTCGTC | 61.103 | 63.158 | 0.00 | 0.00 | 0.00 | 4.20 |
4972 | 5361 | 1.293179 | CTGCTCCCATGTGTCGTCA | 59.707 | 57.895 | 0.00 | 0.00 | 0.00 | 4.35 |
4973 | 5362 | 1.005037 | TGCTCCCATGTGTCGTCAC | 60.005 | 57.895 | 5.81 | 5.81 | 44.08 | 3.67 |
4974 | 5363 | 1.741770 | GCTCCCATGTGTCGTCACC | 60.742 | 63.158 | 10.28 | 0.00 | 43.26 | 4.02 |
4975 | 5364 | 1.079127 | CTCCCATGTGTCGTCACCC | 60.079 | 63.158 | 10.28 | 0.00 | 43.26 | 4.61 |
4976 | 5365 | 2.046314 | CCCATGTGTCGTCACCCC | 60.046 | 66.667 | 10.28 | 0.00 | 43.26 | 4.95 |
4977 | 5366 | 2.434185 | CCATGTGTCGTCACCCCG | 60.434 | 66.667 | 10.28 | 0.00 | 43.26 | 5.73 |
4978 | 5367 | 2.654289 | CATGTGTCGTCACCCCGA | 59.346 | 61.111 | 10.28 | 0.00 | 43.26 | 5.14 |
4979 | 5368 | 1.446099 | CATGTGTCGTCACCCCGAG | 60.446 | 63.158 | 10.28 | 0.00 | 43.26 | 4.63 |
4980 | 5369 | 2.646175 | ATGTGTCGTCACCCCGAGG | 61.646 | 63.158 | 10.28 | 0.00 | 43.26 | 4.63 |
4981 | 5370 | 4.736896 | GTGTCGTCACCCCGAGGC | 62.737 | 72.222 | 0.96 | 0.00 | 37.56 | 4.70 |
4992 | 5381 | 4.227134 | CCGAGGCGCTGCTACCAT | 62.227 | 66.667 | 7.64 | 0.00 | 0.00 | 3.55 |
4993 | 5382 | 2.728180 | CGAGGCGCTGCTACCATA | 59.272 | 61.111 | 7.64 | 0.00 | 0.00 | 2.74 |
4994 | 5383 | 1.372251 | CGAGGCGCTGCTACCATAG | 60.372 | 63.158 | 7.64 | 0.00 | 0.00 | 2.23 |
4995 | 5384 | 1.005630 | GAGGCGCTGCTACCATAGG | 60.006 | 63.158 | 7.64 | 0.00 | 0.00 | 2.57 |
4996 | 5385 | 2.031163 | GGCGCTGCTACCATAGGG | 59.969 | 66.667 | 7.64 | 0.00 | 41.29 | 3.53 |
5004 | 5425 | 1.672356 | CTACCATAGGGCGCCATGC | 60.672 | 63.158 | 30.85 | 11.48 | 45.38 | 4.06 |
5092 | 5514 | 0.318441 | GAGCTGCTATGGACGCCATA | 59.682 | 55.000 | 0.15 | 15.01 | 43.19 | 2.74 |
5223 | 5646 | 2.433436 | GACACCTCCCATGTTACAACC | 58.567 | 52.381 | 0.00 | 0.00 | 0.00 | 3.77 |
5238 | 5661 | 0.951558 | CAACCGGTGTTCAAGGAAGG | 59.048 | 55.000 | 8.52 | 0.00 | 30.42 | 3.46 |
5270 | 5693 | 1.548132 | CGCAAAAAGCTTCAACCGGC | 61.548 | 55.000 | 0.00 | 0.00 | 42.61 | 6.13 |
5272 | 5695 | 0.248866 | CAAAAAGCTTCAACCGGCGT | 60.249 | 50.000 | 6.01 | 0.00 | 0.00 | 5.68 |
5275 | 5698 | 3.802418 | AAGCTTCAACCGGCGTCGT | 62.802 | 57.895 | 9.28 | 0.00 | 33.95 | 4.34 |
5317 | 5740 | 2.230992 | TGCCATCGCAAAAAGCTACAAT | 59.769 | 40.909 | 0.00 | 0.00 | 43.74 | 2.71 |
5341 | 5764 | 0.306533 | GTCGCAAAAAGCTTCGACCA | 59.693 | 50.000 | 21.46 | 0.00 | 43.67 | 4.02 |
5344 | 5767 | 0.998727 | GCAAAAAGCTTCGACCAGCG | 60.999 | 55.000 | 0.00 | 0.00 | 45.24 | 5.18 |
5347 | 5770 | 0.531974 | AAAAGCTTCGACCAGCGTCA | 60.532 | 50.000 | 0.00 | 0.00 | 45.24 | 4.35 |
5382 | 5805 | 1.134367 | CACGACGACATATGTCAGGGT | 59.866 | 52.381 | 30.15 | 21.50 | 44.99 | 4.34 |
5392 | 5815 | 0.035056 | ATGTCAGGGTTGGCTACTGC | 60.035 | 55.000 | 0.00 | 0.00 | 38.76 | 4.40 |
5431 | 5854 | 2.979813 | CAACCACATCGCAAAAAGCTAC | 59.020 | 45.455 | 0.00 | 0.00 | 42.61 | 3.58 |
5438 | 5861 | 3.878086 | TCGCAAAAAGCTACAACTGAG | 57.122 | 42.857 | 0.00 | 0.00 | 42.61 | 3.35 |
5452 | 5875 | 1.680338 | ACTGAGGTCGCAAAAAGCTT | 58.320 | 45.000 | 0.00 | 0.00 | 42.61 | 3.74 |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability |
---|---|---|---|---|---|---|---|---|---|
3 | 4 | 1.670811 | CATATTGTGGTGCTTCCCGAC | 59.329 | 52.381 | 0.00 | 0.00 | 34.77 | 4.79 |
32 | 33 | 8.109634 | AGGGGGCAGTTATAGTATCAAAATATG | 58.890 | 37.037 | 0.00 | 0.00 | 0.00 | 1.78 |
51 | 52 | 0.178903 | AAGTCTAGTGTGAGGGGGCA | 60.179 | 55.000 | 0.00 | 0.00 | 0.00 | 5.36 |
80 | 81 | 2.940994 | TTTTCCAGATGACAACCCGA | 57.059 | 45.000 | 0.00 | 0.00 | 0.00 | 5.14 |
133 | 137 | 6.028146 | TCATCAAATTTGGGTGACATCAAG | 57.972 | 37.500 | 17.90 | 0.00 | 0.00 | 3.02 |
142 | 146 | 4.845796 | AGTTCCCATTCATCAAATTTGGGT | 59.154 | 37.500 | 17.90 | 4.89 | 33.89 | 4.51 |
170 | 174 | 1.196127 | GGGCCTTTCGTGACGTTTAAG | 59.804 | 52.381 | 4.40 | 7.48 | 0.00 | 1.85 |
179 | 183 | 1.738099 | CGACAGAGGGCCTTTCGTG | 60.738 | 63.158 | 19.46 | 12.70 | 39.51 | 4.35 |
226 | 230 | 5.514136 | CCCTAGAGGTATTCGACAGAGAGAT | 60.514 | 48.000 | 0.00 | 0.00 | 0.00 | 2.75 |
247 | 251 | 7.883833 | GGAGAGACTTGAATAGTTTAAAACCCT | 59.116 | 37.037 | 0.00 | 0.00 | 37.17 | 4.34 |
302 | 306 | 9.342308 | GATTGAAATAGTGATGGGAATAGTCAA | 57.658 | 33.333 | 0.00 | 0.00 | 0.00 | 3.18 |
307 | 311 | 7.725397 | CCTTGGATTGAAATAGTGATGGGAATA | 59.275 | 37.037 | 0.00 | 0.00 | 0.00 | 1.75 |
375 | 379 | 1.945394 | CATATGACAGGCTTGAGTGGC | 59.055 | 52.381 | 1.40 | 0.00 | 0.00 | 5.01 |
392 | 396 | 8.807118 | CCTGTAGGTAGATATGAAGAAAGCATA | 58.193 | 37.037 | 0.00 | 0.00 | 33.20 | 3.14 |
401 | 405 | 4.552674 | TGTGCCCTGTAGGTAGATATGAA | 58.447 | 43.478 | 0.00 | 0.00 | 38.26 | 2.57 |
411 | 415 | 3.350219 | ACAACTATTGTGCCCTGTAGG | 57.650 | 47.619 | 0.00 | 0.00 | 43.48 | 3.18 |
534 | 538 | 1.923204 | CGATGACTACAAGCACTGAGC | 59.077 | 52.381 | 0.00 | 0.00 | 46.19 | 4.26 |
539 | 543 | 1.438651 | TTGGCGATGACTACAAGCAC | 58.561 | 50.000 | 0.00 | 0.00 | 36.17 | 4.40 |
551 | 555 | 2.277084 | GTCCGTAGACAATTTGGCGAT | 58.723 | 47.619 | 0.78 | 0.00 | 42.99 | 4.58 |
556 | 560 | 3.328382 | TCCAGGTCCGTAGACAATTTG | 57.672 | 47.619 | 0.00 | 0.00 | 45.48 | 2.32 |
606 | 611 | 6.650807 | TCTCGCAACAAAAATATCAAGAGAGT | 59.349 | 34.615 | 0.00 | 0.00 | 0.00 | 3.24 |
618 | 623 | 4.037446 | AGGCAGTATTTCTCGCAACAAAAA | 59.963 | 37.500 | 0.00 | 0.00 | 0.00 | 1.94 |
619 | 624 | 3.568007 | AGGCAGTATTTCTCGCAACAAAA | 59.432 | 39.130 | 0.00 | 0.00 | 0.00 | 2.44 |
620 | 625 | 3.146066 | AGGCAGTATTTCTCGCAACAAA | 58.854 | 40.909 | 0.00 | 0.00 | 0.00 | 2.83 |
623 | 628 | 5.753921 | ACTATAAGGCAGTATTTCTCGCAAC | 59.246 | 40.000 | 0.00 | 0.00 | 0.00 | 4.17 |
649 | 654 | 7.383572 | TGCGAGAAAGCTTCTAATCTATTCATC | 59.616 | 37.037 | 0.00 | 0.00 | 40.87 | 2.92 |
725 | 730 | 8.087136 | AGATTTCTCCATTGCTTTTCTTTTCTC | 58.913 | 33.333 | 0.00 | 0.00 | 0.00 | 2.87 |
732 | 737 | 7.951530 | TTTTCAGATTTCTCCATTGCTTTTC | 57.048 | 32.000 | 0.00 | 0.00 | 0.00 | 2.29 |
874 | 886 | 3.159858 | TTATAGTCGGGCTGGGCGC | 62.160 | 63.158 | 0.00 | 0.00 | 38.15 | 6.53 |
875 | 887 | 1.300697 | GTTATAGTCGGGCTGGGCG | 60.301 | 63.158 | 0.00 | 0.00 | 0.00 | 6.13 |
879 | 891 | 4.056050 | GTTGTATGGTTATAGTCGGGCTG | 58.944 | 47.826 | 0.00 | 0.00 | 0.00 | 4.85 |
880 | 892 | 3.243636 | CGTTGTATGGTTATAGTCGGGCT | 60.244 | 47.826 | 0.00 | 0.00 | 0.00 | 5.19 |
891 | 903 | 4.760683 | CGTTAAAACGTCGTTGTATGGTT | 58.239 | 39.130 | 12.12 | 3.59 | 46.63 | 3.67 |
917 | 929 | 3.153919 | TCCAAAGAGAACGGGGAATTTG | 58.846 | 45.455 | 0.00 | 0.00 | 0.00 | 2.32 |
957 | 969 | 1.825341 | GCATGGGATTTGGGCCTTC | 59.175 | 57.895 | 4.53 | 0.00 | 0.00 | 3.46 |
975 | 987 | 2.043411 | CAACCAACTTGTGCGATTTCG | 58.957 | 47.619 | 0.00 | 0.00 | 43.27 | 3.46 |
976 | 988 | 1.786579 | GCAACCAACTTGTGCGATTTC | 59.213 | 47.619 | 0.00 | 0.00 | 31.73 | 2.17 |
1001 | 1013 | 4.856607 | GCGGAGAGGAAGGACGCG | 62.857 | 72.222 | 3.53 | 3.53 | 40.84 | 6.01 |
1108 | 1120 | 3.054655 | AGGAGATTGGCTTAAAACGGCTA | 60.055 | 43.478 | 0.00 | 0.00 | 0.00 | 3.93 |
1228 | 1241 | 3.095898 | GAGAAATTGACGGCGGCGG | 62.096 | 63.158 | 35.05 | 17.25 | 0.00 | 6.13 |
1320 | 1334 | 1.805945 | GTGCGTGTAGGGCTTCTCG | 60.806 | 63.158 | 0.00 | 0.00 | 0.00 | 4.04 |
1634 | 1653 | 1.618837 | CTCCTCGAACTCAAGGTCCAA | 59.381 | 52.381 | 0.00 | 0.00 | 34.12 | 3.53 |
1642 | 1661 | 2.031069 | CACGAACTTCTCCTCGAACTCA | 60.031 | 50.000 | 0.00 | 0.00 | 38.43 | 3.41 |
1683 | 1702 | 1.192146 | AGCCAAGTGGACGCTCCTTA | 61.192 | 55.000 | 0.18 | 0.00 | 37.46 | 2.69 |
1684 | 1703 | 2.032681 | GCCAAGTGGACGCTCCTT | 59.967 | 61.111 | 0.18 | 0.00 | 37.46 | 3.36 |
1720 | 1739 | 4.337274 | AGGTAACAGAAACGAAACAAAGGG | 59.663 | 41.667 | 0.00 | 0.00 | 41.41 | 3.95 |
1749 | 1768 | 8.812513 | AACTATCATCAATTCACCATGAAAGA | 57.187 | 30.769 | 0.00 | 0.00 | 40.12 | 2.52 |
1750 | 1769 | 8.680001 | TGAACTATCATCAATTCACCATGAAAG | 58.320 | 33.333 | 0.00 | 0.00 | 40.12 | 2.62 |
1753 | 1772 | 8.756486 | AATGAACTATCATCAATTCACCATGA | 57.244 | 30.769 | 0.00 | 0.00 | 45.60 | 3.07 |
1754 | 1773 | 9.888878 | GTAATGAACTATCATCAATTCACCATG | 57.111 | 33.333 | 0.00 | 0.00 | 45.60 | 3.66 |
1755 | 1774 | 9.857656 | AGTAATGAACTATCATCAATTCACCAT | 57.142 | 29.630 | 0.00 | 0.00 | 45.60 | 3.55 |
1756 | 1775 | 9.112725 | CAGTAATGAACTATCATCAATTCACCA | 57.887 | 33.333 | 0.00 | 0.00 | 45.60 | 4.17 |
1757 | 1776 | 8.562892 | CCAGTAATGAACTATCATCAATTCACC | 58.437 | 37.037 | 0.00 | 0.00 | 45.60 | 4.02 |
1758 | 1777 | 8.562892 | CCCAGTAATGAACTATCATCAATTCAC | 58.437 | 37.037 | 0.00 | 0.00 | 45.60 | 3.18 |
1759 | 1778 | 8.493607 | TCCCAGTAATGAACTATCATCAATTCA | 58.506 | 33.333 | 0.00 | 0.00 | 45.60 | 2.57 |
1760 | 1779 | 8.908786 | TCCCAGTAATGAACTATCATCAATTC | 57.091 | 34.615 | 0.00 | 0.00 | 45.60 | 2.17 |
1775 | 1794 | 7.041780 | CGACCAGAGAAAATAATCCCAGTAATG | 60.042 | 40.741 | 0.00 | 0.00 | 0.00 | 1.90 |
1835 | 1854 | 6.367695 | CCTCGTACACATCACTGACAAAATAA | 59.632 | 38.462 | 0.00 | 0.00 | 0.00 | 1.40 |
1871 | 1890 | 6.063496 | AGTGACTCACTACCAGTATCACTA | 57.937 | 41.667 | 10.13 | 0.00 | 43.46 | 2.74 |
1917 | 1936 | 3.244457 | ACATCATCGTCATCAGATGCCAT | 60.244 | 43.478 | 5.41 | 0.00 | 43.68 | 4.40 |
1991 | 2010 | 1.117150 | ATGGCTTGCACAATGGGATC | 58.883 | 50.000 | 0.00 | 0.00 | 0.00 | 3.36 |
2112 | 2131 | 1.568504 | TGCCTCTACCCTGGTTGTAG | 58.431 | 55.000 | 0.00 | 4.32 | 37.60 | 2.74 |
2175 | 2194 | 8.437742 | CAAAAGAAATTGCTTACATCATGGAAC | 58.562 | 33.333 | 0.00 | 0.00 | 0.00 | 3.62 |
2223 | 2242 | 6.980978 | ACATATGACTGACTATGTACAACAGC | 59.019 | 38.462 | 10.38 | 12.27 | 36.93 | 4.40 |
2226 | 2245 | 7.595502 | GCCTACATATGACTGACTATGTACAAC | 59.404 | 40.741 | 10.38 | 0.00 | 38.94 | 3.32 |
2243 | 2262 | 5.602978 | ACAAGCACTTACTAGGCCTACATAT | 59.397 | 40.000 | 8.91 | 0.00 | 0.00 | 1.78 |
2271 | 2290 | 6.749139 | TCAGTGCTAACCTGATATACACATC | 58.251 | 40.000 | 0.00 | 0.00 | 34.12 | 3.06 |
2293 | 2318 | 6.764085 | CCAACATACCGGTGAAATACTAATCA | 59.236 | 38.462 | 19.93 | 0.00 | 0.00 | 2.57 |
2312 | 2337 | 7.031415 | TGGCATATACCATCTAATCCAACAT | 57.969 | 36.000 | 0.00 | 0.00 | 33.75 | 2.71 |
2428 | 2453 | 9.638239 | GGCAACATGACTTCTATTTTATTTGAA | 57.362 | 29.630 | 0.00 | 0.00 | 0.00 | 2.69 |
2430 | 2455 | 8.984891 | TGGCAACATGACTTCTATTTTATTTG | 57.015 | 30.769 | 0.00 | 0.00 | 46.17 | 2.32 |
2473 | 2498 | 0.538057 | GCCAATAGCCCATGCAGCTA | 60.538 | 55.000 | 15.52 | 15.52 | 46.32 | 3.32 |
2570 | 2596 | 3.986996 | TCATCAACAGGCTTCTCATCA | 57.013 | 42.857 | 0.00 | 0.00 | 0.00 | 3.07 |
2788 | 2814 | 4.350245 | ACAGTGAACTAGCATGTACCCTA | 58.650 | 43.478 | 0.00 | 0.00 | 0.00 | 3.53 |
2924 | 2950 | 2.027653 | GCTAGCTTCACCTCCTTCTTGT | 60.028 | 50.000 | 7.70 | 0.00 | 0.00 | 3.16 |
2961 | 3032 | 1.761449 | TCTTCTGTTTGGCTGCAACA | 58.239 | 45.000 | 0.50 | 3.60 | 33.09 | 3.33 |
3004 | 3075 | 5.788450 | CTTATCAGTGTCACCTTCAGAAGT | 58.212 | 41.667 | 9.41 | 0.00 | 0.00 | 3.01 |
3025 | 3096 | 5.990120 | ATGGTTCTTTTATCAGCTTGCTT | 57.010 | 34.783 | 0.00 | 0.00 | 0.00 | 3.91 |
3039 | 3110 | 7.009540 | GCTTAACATACGTACGTTATGGTTCTT | 59.990 | 37.037 | 27.92 | 17.10 | 0.00 | 2.52 |
3041 | 3112 | 6.473455 | AGCTTAACATACGTACGTTATGGTTC | 59.527 | 38.462 | 27.92 | 16.11 | 32.70 | 3.62 |
3228 | 3467 | 4.272018 | AGCTGAATTCATAACATCAGTCGC | 59.728 | 41.667 | 8.96 | 4.27 | 41.03 | 5.19 |
3229 | 3468 | 5.980698 | AGCTGAATTCATAACATCAGTCG | 57.019 | 39.130 | 8.96 | 0.00 | 41.03 | 4.18 |
3430 | 3669 | 6.882610 | ACTGATTACACTGAGCATTGAAAA | 57.117 | 33.333 | 0.00 | 0.00 | 0.00 | 2.29 |
3640 | 3879 | 1.736126 | GAACTTACCCAGCCTAAACGC | 59.264 | 52.381 | 0.00 | 0.00 | 0.00 | 4.84 |
3729 | 3968 | 4.956075 | CCAGCCTTTAATAACCTGTCCAAT | 59.044 | 41.667 | 0.00 | 0.00 | 0.00 | 3.16 |
3836 | 4075 | 2.240493 | ACTAACCGCATGTATCAGGC | 57.760 | 50.000 | 0.00 | 0.00 | 37.83 | 4.85 |
3880 | 4119 | 4.514506 | CGCATACCTATAACAAGCAAACG | 58.485 | 43.478 | 0.00 | 0.00 | 0.00 | 3.60 |
3981 | 4220 | 0.603707 | TCGAAACAAGCAGCTCCTGG | 60.604 | 55.000 | 0.00 | 0.00 | 31.21 | 4.45 |
4100 | 4339 | 1.057851 | AACCCCGGTCACCTCTTCAA | 61.058 | 55.000 | 0.00 | 0.00 | 0.00 | 2.69 |
4114 | 4353 | 0.401356 | TCGTCCCTTTTGGTAACCCC | 59.599 | 55.000 | 0.00 | 0.00 | 38.10 | 4.95 |
4225 | 4464 | 5.047802 | AGCTGATGGAAAAACAAGGTACATG | 60.048 | 40.000 | 0.00 | 0.00 | 0.00 | 3.21 |
4241 | 4480 | 4.134379 | AGTTGACATGTAGAGCTGATGG | 57.866 | 45.455 | 0.00 | 0.00 | 0.00 | 3.51 |
4315 | 4555 | 5.240183 | CCACAAAATCATCAGAGTGACAAGT | 59.760 | 40.000 | 0.00 | 0.00 | 0.00 | 3.16 |
4325 | 4565 | 1.176527 | ACGGGCCACAAAATCATCAG | 58.823 | 50.000 | 4.39 | 0.00 | 0.00 | 2.90 |
4341 | 4581 | 4.829064 | TTCCAGAAGAATGTCAAAACGG | 57.171 | 40.909 | 0.00 | 0.00 | 0.00 | 4.44 |
4438 | 4694 | 2.746904 | TCCAACCAACATACAGAATGCG | 59.253 | 45.455 | 0.00 | 0.00 | 42.53 | 4.73 |
4450 | 4706 | 3.119708 | GCAGAACATGAGATCCAACCAAC | 60.120 | 47.826 | 0.00 | 0.00 | 0.00 | 3.77 |
4462 | 4718 | 3.754850 | CAGATTCAACCAGCAGAACATGA | 59.245 | 43.478 | 0.00 | 0.00 | 0.00 | 3.07 |
4466 | 4722 | 5.382618 | AAATCAGATTCAACCAGCAGAAC | 57.617 | 39.130 | 0.00 | 0.00 | 0.00 | 3.01 |
4467 | 4723 | 5.047802 | GGAAAATCAGATTCAACCAGCAGAA | 60.048 | 40.000 | 0.00 | 0.00 | 0.00 | 3.02 |
4517 | 4773 | 1.678635 | CTCCTGCGATTTGGGGCAA | 60.679 | 57.895 | 0.00 | 0.00 | 38.94 | 4.52 |
4518 | 4774 | 2.045045 | CTCCTGCGATTTGGGGCA | 60.045 | 61.111 | 0.00 | 0.00 | 37.63 | 5.36 |
4519 | 4775 | 0.965363 | TTTCTCCTGCGATTTGGGGC | 60.965 | 55.000 | 0.00 | 0.00 | 0.00 | 5.80 |
4521 | 4777 | 4.580167 | TGATATTTTCTCCTGCGATTTGGG | 59.420 | 41.667 | 0.00 | 0.00 | 0.00 | 4.12 |
4522 | 4778 | 5.278169 | CCTGATATTTTCTCCTGCGATTTGG | 60.278 | 44.000 | 0.00 | 0.00 | 0.00 | 3.28 |
4523 | 4779 | 5.528690 | TCCTGATATTTTCTCCTGCGATTTG | 59.471 | 40.000 | 0.00 | 0.00 | 0.00 | 2.32 |
4527 | 4808 | 3.960755 | TCTCCTGATATTTTCTCCTGCGA | 59.039 | 43.478 | 0.00 | 0.00 | 0.00 | 5.10 |
4544 | 4825 | 3.012518 | CGAAATTGCATGGTTCTCTCCT | 58.987 | 45.455 | 0.00 | 0.00 | 0.00 | 3.69 |
4553 | 4834 | 7.579589 | TTAGTTTGAATTCGAAATTGCATGG | 57.420 | 32.000 | 13.26 | 0.00 | 0.00 | 3.66 |
4622 | 4999 | 8.958119 | TTTCATTTTCGCTACTATTATGACCT | 57.042 | 30.769 | 0.00 | 0.00 | 0.00 | 3.85 |
4713 | 5090 | 3.171056 | GGCGAACCGTGCGTAAAT | 58.829 | 55.556 | 0.00 | 0.00 | 0.00 | 1.40 |
4726 | 5103 | 1.741401 | CCAAGCATTCTGTCGGCGA | 60.741 | 57.895 | 4.99 | 4.99 | 0.00 | 5.54 |
4732 | 5109 | 2.361610 | CCGGCCCAAGCATTCTGT | 60.362 | 61.111 | 0.00 | 0.00 | 42.56 | 3.41 |
4734 | 5111 | 2.044946 | GACCGGCCCAAGCATTCT | 60.045 | 61.111 | 0.00 | 0.00 | 42.56 | 2.40 |
4780 | 5162 | 7.834181 | AGAATATAAGGTACACATGTTGCCTTT | 59.166 | 33.333 | 24.13 | 17.46 | 40.28 | 3.11 |
4802 | 5184 | 2.357569 | GGATGCAAGAGTTGGGGAGAAT | 60.358 | 50.000 | 0.00 | 0.00 | 0.00 | 2.40 |
4814 | 5196 | 1.556911 | GAGGAAGGAGTGGATGCAAGA | 59.443 | 52.381 | 0.00 | 0.00 | 0.00 | 3.02 |
4816 | 5198 | 0.250234 | CGAGGAAGGAGTGGATGCAA | 59.750 | 55.000 | 0.00 | 0.00 | 0.00 | 4.08 |
4844 | 5229 | 2.546494 | CGATGGGGGAAAGCGATGC | 61.546 | 63.158 | 0.00 | 0.00 | 0.00 | 3.91 |
4846 | 5231 | 2.203209 | GCGATGGGGGAAAGCGAT | 60.203 | 61.111 | 0.00 | 0.00 | 0.00 | 4.58 |
4869 | 5255 | 2.509561 | GAAGAGGCGAGGCGGAAC | 60.510 | 66.667 | 0.00 | 0.00 | 0.00 | 3.62 |
4907 | 5293 | 1.975327 | CAAAGGGAGGAGTGCTCGA | 59.025 | 57.895 | 5.49 | 0.00 | 0.00 | 4.04 |
4975 | 5364 | 2.755542 | CTATGGTAGCAGCGCCTCGG | 62.756 | 65.000 | 2.29 | 0.00 | 0.00 | 4.63 |
4976 | 5365 | 1.372251 | CTATGGTAGCAGCGCCTCG | 60.372 | 63.158 | 2.29 | 0.00 | 0.00 | 4.63 |
4977 | 5366 | 1.005630 | CCTATGGTAGCAGCGCCTC | 60.006 | 63.158 | 2.29 | 0.00 | 0.00 | 4.70 |
4978 | 5367 | 2.511452 | CCCTATGGTAGCAGCGCCT | 61.511 | 63.158 | 2.29 | 0.00 | 0.00 | 5.52 |
4979 | 5368 | 2.031163 | CCCTATGGTAGCAGCGCC | 59.969 | 66.667 | 2.29 | 2.47 | 0.00 | 6.53 |
4980 | 5369 | 2.666526 | GCCCTATGGTAGCAGCGC | 60.667 | 66.667 | 0.00 | 0.00 | 0.00 | 5.92 |
4981 | 5370 | 2.356313 | CGCCCTATGGTAGCAGCG | 60.356 | 66.667 | 11.11 | 11.11 | 39.46 | 5.18 |
4982 | 5371 | 2.666526 | GCGCCCTATGGTAGCAGC | 60.667 | 66.667 | 0.00 | 0.00 | 37.36 | 5.25 |
4983 | 5372 | 2.031163 | GGCGCCCTATGGTAGCAG | 59.969 | 66.667 | 18.11 | 0.00 | 38.57 | 4.24 |
4984 | 5373 | 2.146724 | ATGGCGCCCTATGGTAGCA | 61.147 | 57.895 | 26.77 | 0.00 | 38.57 | 3.49 |
4985 | 5374 | 1.672356 | CATGGCGCCCTATGGTAGC | 60.672 | 63.158 | 26.77 | 0.00 | 36.91 | 3.58 |
4986 | 5375 | 1.672356 | GCATGGCGCCCTATGGTAG | 60.672 | 63.158 | 26.77 | 1.54 | 32.94 | 3.18 |
4987 | 5376 | 2.429930 | GCATGGCGCCCTATGGTA | 59.570 | 61.111 | 26.77 | 2.60 | 32.94 | 3.25 |
5004 | 5425 | 2.125350 | GACCTTGAGCTCGCAGGG | 60.125 | 66.667 | 27.43 | 19.46 | 40.57 | 4.45 |
5105 | 5527 | 4.052229 | CGTCGTCGTTCTGCCCCT | 62.052 | 66.667 | 0.00 | 0.00 | 0.00 | 4.79 |
5167 | 5590 | 1.144936 | CCGGTGAGATTCTCCCAGC | 59.855 | 63.158 | 11.12 | 3.22 | 0.00 | 4.85 |
5223 | 5646 | 1.071071 | TGGTACCTTCCTTGAACACCG | 59.929 | 52.381 | 14.36 | 0.00 | 0.00 | 4.94 |
5270 | 5693 | 0.165944 | GGTTCCAGCATTTGACGACG | 59.834 | 55.000 | 0.00 | 0.00 | 0.00 | 5.12 |
5272 | 5695 | 1.573829 | GCGGTTCCAGCATTTGACGA | 61.574 | 55.000 | 0.00 | 0.00 | 34.19 | 4.20 |
5275 | 5698 | 0.250684 | TGAGCGGTTCCAGCATTTGA | 60.251 | 50.000 | 0.00 | 0.00 | 37.01 | 2.69 |
5341 | 5764 | 2.479560 | GGTTGAAGCTTTTTGTGACGCT | 60.480 | 45.455 | 0.00 | 0.00 | 0.00 | 5.07 |
5344 | 5767 | 2.851824 | CGTGGTTGAAGCTTTTTGTGAC | 59.148 | 45.455 | 0.00 | 0.00 | 0.00 | 3.67 |
5347 | 5770 | 2.477189 | CGTCGTGGTTGAAGCTTTTTGT | 60.477 | 45.455 | 0.00 | 0.00 | 0.00 | 2.83 |
5431 | 5854 | 1.758783 | GCTTTTTGCGACCTCAGTTG | 58.241 | 50.000 | 0.00 | 0.00 | 0.00 | 3.16 |
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.