Multiple sequence alignment - TraesCS4A01G073000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


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 TraesCS4A01G073000 chr4A 100.000 5076 0 0 1 5076 71997303 72002378 0.000000e+00 9374
1 TraesCS4A01G073000 chr4A 93.082 159 11 0 4918 5076 483895496 483895654 3.060000e-57 233
2 TraesCS4A01G073000 chr4A 92.994 157 11 0 4920 5076 59401803 59401647 3.950000e-56 230
3 TraesCS4A01G073000 chr4A 89.143 175 17 2 4903 5076 739882538 739882365 3.080000e-52 217
4 TraesCS4A01G073000 chr4D 96.429 2016 56 9 535 2537 390263998 390266010 0.000000e+00 3310
5 TraesCS4A01G073000 chr4D 91.220 1287 62 22 3649 4920 390268766 390270016 0.000000e+00 1703
6 TraesCS4A01G073000 chr4D 96.548 985 20 4 2672 3649 390266871 390267848 0.000000e+00 1618
7 TraesCS4A01G073000 chr4D 93.678 522 22 3 1 513 390263483 390264002 0.000000e+00 771
8 TraesCS4A01G073000 chr4D 95.890 146 5 1 2530 2674 390266468 390266613 8.500000e-58 235
9 TraesCS4A01G073000 chr4B 91.189 1135 65 15 2530 3649 480052095 480053209 0.000000e+00 1509
10 TraesCS4A01G073000 chr4B 90.622 1045 61 10 1494 2537 480050643 480051651 0.000000e+00 1352
11 TraesCS4A01G073000 chr4B 86.590 962 67 19 288 1225 480049311 480050234 0.000000e+00 1005
12 TraesCS4A01G073000 chr4B 87.196 945 46 26 3649 4550 480054126 480055038 0.000000e+00 1005
13 TraesCS4A01G073000 chr4B 90.706 269 16 4 1233 1494 480050338 480050604 2.910000e-92 350
14 TraesCS4A01G073000 chr4B 84.375 288 25 10 1 277 480048980 480049258 1.080000e-66 265
15 TraesCS4A01G073000 chr4B 93.082 159 11 0 4918 5076 361996966 361997124 3.060000e-57 233
16 TraesCS4A01G073000 chr3B 93.491 169 11 0 415 583 42630983 42630815 8.440000e-63 252
17 TraesCS4A01G073000 chr3A 93.939 165 10 0 415 579 83748186 83748022 3.030000e-62 250
18 TraesCS4A01G073000 chr3A 92.899 169 12 0 415 583 34532614 34532446 3.930000e-61 246
19 TraesCS4A01G073000 chr7B 91.573 178 14 1 415 592 522721478 522721302 1.410000e-60 244
20 TraesCS4A01G073000 chr7A 92.353 170 13 0 415 584 560306158 560305989 5.080000e-60 243
21 TraesCS4A01G073000 chr3D 92.814 167 12 0 415 581 426452024 426451858 5.080000e-60 243
22 TraesCS4A01G073000 chr7D 92.353 170 12 1 415 584 494749949 494749781 1.830000e-59 241
23 TraesCS4A01G073000 chr2A 93.711 159 10 0 4918 5076 773822801 773822643 6.570000e-59 239
24 TraesCS4A01G073000 chr1D 92.262 168 13 0 415 582 175820001 175819834 6.570000e-59 239
25 TraesCS4A01G073000 chr1A 92.453 159 12 0 4918 5076 48782486 48782328 1.420000e-55 228
26 TraesCS4A01G073000 chr2B 91.925 161 13 0 4916 5076 721353100 721353260 5.110000e-55 226
27 TraesCS4A01G073000 chr5B 91.411 163 14 0 4914 5076 587110371 587110533 1.840000e-54 224
28 TraesCS4A01G073000 chr5A 91.925 161 12 1 4917 5076 675642326 675642486 1.840000e-54 224


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 TraesCS4A01G073000 chr4A 71997303 72002378 5075 False 9374.000000 9374 100.000000 1 5076 1 chr4A.!!$F1 5075
1 TraesCS4A01G073000 chr4D 390263483 390270016 6533 False 1527.400000 3310 94.753000 1 4920 5 chr4D.!!$F1 4919
2 TraesCS4A01G073000 chr4B 480048980 480055038 6058 False 914.333333 1509 88.446333 1 4550 6 chr4B.!!$F2 4549

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
447 505 0.603569 CGCAGTGGTGAAGTACTCCT 59.396 55.000 0.0 0.0 33.75 3.69 F
1310 1506 0.035820 GTACGGCTCAAATGACCCCA 60.036 55.000 0.0 0.0 0.00 4.96 F
2357 2599 1.486726 AGCGGAAGTTATTCTGGAGGG 59.513 52.381 0.0 0.0 41.42 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1341 1537 0.768221 TATGGATGCCCCTGAGGACC 60.768 60.0 0.0 0.0 38.24 4.46 R
2716 3692 0.034477 TCAATCCTTTTCTCCCCGGC 60.034 55.0 0.0 0.0 0.00 6.13 R
4131 6098 0.179108 GCAGTGGAAGCTAGTACCGG 60.179 60.0 0.0 0.0 0.00 5.28 R

All possible primers

Listed 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.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 130 4.527564 GAAAGTTGGTTCTGTGAATCACG 58.472 43.478 9.00 4.08 37.14 4.35
140 141 5.610398 TCTGTGAATCACGGCATATGTATT 58.390 37.500 16.93 0.00 40.25 1.89
283 294 8.999895 ACTTGGGGTGATAAAATATACAGTACT 58.000 33.333 0.00 0.00 0.00 2.73
284 295 9.847224 CTTGGGGTGATAAAATATACAGTACTT 57.153 33.333 0.00 0.00 0.00 2.24
285 296 9.841295 TTGGGGTGATAAAATATACAGTACTTC 57.159 33.333 0.00 0.00 0.00 3.01
447 505 0.603569 CGCAGTGGTGAAGTACTCCT 59.396 55.000 0.00 0.00 33.75 3.69
475 533 1.445095 CAAGAGATCCTGGGCTCGG 59.555 63.158 10.43 0.00 36.29 4.63
529 613 4.660168 CAAGGCTTGCCTCATATAATCCT 58.340 43.478 15.25 0.00 0.00 3.24
530 614 5.075493 CAAGGCTTGCCTCATATAATCCTT 58.925 41.667 15.25 0.00 31.98 3.36
531 615 4.916183 AGGCTTGCCTCATATAATCCTTC 58.084 43.478 8.56 0.00 0.00 3.46
532 616 4.013050 GGCTTGCCTCATATAATCCTTCC 58.987 47.826 4.11 0.00 0.00 3.46
533 617 4.263683 GGCTTGCCTCATATAATCCTTCCT 60.264 45.833 4.11 0.00 0.00 3.36
534 618 5.045578 GGCTTGCCTCATATAATCCTTCCTA 60.046 44.000 4.11 0.00 0.00 2.94
535 619 6.476378 GCTTGCCTCATATAATCCTTCCTAA 58.524 40.000 0.00 0.00 0.00 2.69
536 620 6.597280 GCTTGCCTCATATAATCCTTCCTAAG 59.403 42.308 0.00 0.00 0.00 2.18
537 621 7.527868 GCTTGCCTCATATAATCCTTCCTAAGA 60.528 40.741 0.00 0.00 0.00 2.10
538 622 7.246171 TGCCTCATATAATCCTTCCTAAGAC 57.754 40.000 0.00 0.00 0.00 3.01
661 746 8.091449 TGTACATTTCCAGTTGAAACAGTTTTT 58.909 29.630 0.00 0.00 45.38 1.94
664 749 7.117667 ACATTTCCAGTTGAAACAGTTTTTGAC 59.882 33.333 0.00 0.23 45.38 3.18
720 807 6.541278 GGTTGGTATGTAGGGTGTAGAATTTC 59.459 42.308 0.00 0.00 0.00 2.17
850 947 5.962433 TGTTAGTCTAGGTCCTTGATTTCG 58.038 41.667 6.30 0.00 0.00 3.46
938 1035 5.253096 TCTCTTGCTATAAAGGGAAAACCCT 59.747 40.000 1.53 1.53 42.86 4.34
949 1046 2.030540 GGGAAAACCCTGCGTTACTTTC 60.031 50.000 0.00 0.00 33.05 2.62
994 1091 3.714798 AGAGAGGACTAGAGACGAGGAAT 59.285 47.826 0.00 0.00 0.00 3.01
996 1093 4.457466 AGAGGACTAGAGACGAGGAATTC 58.543 47.826 0.00 0.00 0.00 2.17
1085 1182 4.157472 TGTGAACAAACTGAACTGCATGAA 59.843 37.500 0.00 0.00 0.00 2.57
1154 1251 5.124645 ACAGAGTACACCTACTAATCCTCG 58.875 45.833 0.00 0.00 32.96 4.63
1214 1315 8.646004 TCATAGAATGAGACTATCCTTCCTTTG 58.354 37.037 0.00 0.00 34.16 2.77
1310 1506 0.035820 GTACGGCTCAAATGACCCCA 60.036 55.000 0.00 0.00 0.00 4.96
1335 1531 4.378978 CGGCTTATTTTCATTCAACGGTGA 60.379 41.667 0.00 0.00 0.00 4.02
1341 1537 2.455674 TCATTCAACGGTGACTCCAG 57.544 50.000 0.44 0.00 31.90 3.86
1503 1745 5.614324 TGCTAGTTAACTATGGATGTGCT 57.386 39.130 15.57 0.00 0.00 4.40
1513 1755 3.931907 ATGGATGTGCTAGTTAGGCAA 57.068 42.857 0.00 0.00 41.54 4.52
1541 1783 6.719829 CCTTTAACCTTCAGTCATAGGGTTTT 59.280 38.462 0.00 0.00 40.27 2.43
1612 1854 9.628500 GTCTTGGGGAATTAGTATTCTAACATT 57.372 33.333 0.00 0.00 40.07 2.71
1670 1912 2.666207 GGACACCGCCACCATACA 59.334 61.111 0.00 0.00 0.00 2.29
1957 2199 9.713713 GGAAGTTTATTCTTAGAGTCTTTCTGT 57.286 33.333 0.00 0.00 36.61 3.41
1993 2235 1.737793 CGGGTCTGGAAACATTACTGC 59.262 52.381 0.00 0.00 41.51 4.40
2066 2308 7.983363 AGGGATTCATGTTTTAAAATTTCCCA 58.017 30.769 21.68 10.92 33.87 4.37
2182 2424 3.367321 AGGAAGCTTAGGTAGTCTGGAC 58.633 50.000 0.00 0.00 0.00 4.02
2317 2559 7.095439 GGATGAATGACGAGTCCTCAATAATTC 60.095 40.741 8.52 6.35 0.00 2.17
2322 2564 6.436261 TGACGAGTCCTCAATAATTCGATAC 58.564 40.000 0.34 0.00 32.81 2.24
2357 2599 1.486726 AGCGGAAGTTATTCTGGAGGG 59.513 52.381 0.00 0.00 41.42 4.30
2481 2723 6.967199 CAGTCTACTTTTTGTTTCACTGTTCC 59.033 38.462 0.00 0.00 0.00 3.62
2711 3687 2.439156 AGCGCCTCATTGGGAAGC 60.439 61.111 2.29 0.00 36.00 3.86
2714 3690 2.830370 GCCTCATTGGGAAGCGGG 60.830 66.667 0.00 0.00 36.00 6.13
2715 3691 2.124151 CCTCATTGGGAAGCGGGG 60.124 66.667 0.00 0.00 0.00 5.73
2716 3692 2.124151 CTCATTGGGAAGCGGGGG 60.124 66.667 0.00 0.00 0.00 5.40
2717 3693 4.440829 TCATTGGGAAGCGGGGGC 62.441 66.667 0.00 0.00 0.00 5.80
3355 4345 5.308497 TCAGGGTAGTTTGGACTGTTGATAA 59.692 40.000 0.00 0.00 36.60 1.75
3392 4385 6.129179 AGATCAAGTTGGAGAAAAGAACCAA 58.871 36.000 2.34 0.00 40.68 3.67
3470 4463 5.227569 TGACTTCAGATGGACTGCTTAAA 57.772 39.130 0.00 0.00 45.38 1.52
3473 4466 5.376625 ACTTCAGATGGACTGCTTAAAACA 58.623 37.500 0.00 0.00 45.38 2.83
3503 4496 4.527564 GCATTGCGGTAGATTATGACAAC 58.472 43.478 0.00 0.00 0.00 3.32
3507 4500 2.104281 GCGGTAGATTATGACAACCCCT 59.896 50.000 0.00 0.00 0.00 4.79
3522 4515 0.971959 CCCCTTTTGCATAGCCAGCA 60.972 55.000 0.00 0.00 40.85 4.41
3527 4520 3.592059 CTTTTGCATAGCCAGCATTTGT 58.408 40.909 0.00 0.00 42.33 2.83
3563 4556 1.464997 GCTAACCAAGTCTTTCCTGCG 59.535 52.381 0.00 0.00 0.00 5.18
3637 4630 2.253452 GCAACTGCAAGCGACCAG 59.747 61.111 0.00 0.03 41.59 4.00
3720 5649 4.563374 GGACCCAATCCTCCAAAATTTGTG 60.563 45.833 4.92 0.00 45.22 3.33
3987 5950 2.906389 TGTGTAGATCCTCAAAGCTGGT 59.094 45.455 0.00 0.00 0.00 4.00
3988 5951 4.093743 TGTGTAGATCCTCAAAGCTGGTA 58.906 43.478 0.00 0.00 0.00 3.25
3989 5952 4.160439 TGTGTAGATCCTCAAAGCTGGTAG 59.840 45.833 0.00 0.00 0.00 3.18
4131 6098 5.588648 TGCTGATGTAAGGCATAAAACTACC 59.411 40.000 0.00 0.00 38.06 3.18
4132 6099 5.008712 GCTGATGTAAGGCATAAAACTACCC 59.991 44.000 0.00 0.00 38.06 3.69
4185 6152 6.842163 CACGAAACCTAATATTTCTTGCACT 58.158 36.000 0.00 0.00 34.50 4.40
4231 6198 5.721960 ACATGATAGGCCGGAGATAATTAGT 59.278 40.000 5.05 0.00 0.00 2.24
4248 6215 1.795768 AGTAGGTGTTCATGTGTGCG 58.204 50.000 0.00 0.00 0.00 5.34
4308 6275 4.080129 AGGATTCAACATGATGGCTACAGT 60.080 41.667 0.00 0.00 0.00 3.55
4327 6294 4.267928 ACAGTTTCTTCGTCTTCTTTGTCG 59.732 41.667 0.00 0.00 0.00 4.35
4421 6388 3.565902 GCAGTATGTAAAGATCCCCAAGC 59.434 47.826 0.00 0.00 39.31 4.01
4472 6439 7.653713 GCTTATAAGATGCTTGTTGTAGAGCTA 59.346 37.037 16.85 0.00 39.60 3.32
4550 6522 5.907207 ACTAATGTGTATGCTGTACTGAGG 58.093 41.667 3.61 0.00 0.00 3.86
4551 6523 2.672961 TGTGTATGCTGTACTGAGGC 57.327 50.000 3.61 0.00 0.00 4.70
4553 6525 2.271800 GTGTATGCTGTACTGAGGCAC 58.728 52.381 3.61 3.33 38.83 5.01
4574 6547 4.818005 CACTCCTGCTTGCATCATATTACA 59.182 41.667 0.00 0.00 0.00 2.41
4598 6571 7.290014 ACAAAAGGATGGTTTTACAGGAATTCT 59.710 33.333 5.23 0.00 0.00 2.40
4627 6600 8.596271 TCACTAATGTCGTTTCTGAAAATGTA 57.404 30.769 4.09 0.00 33.81 2.29
4634 6607 6.134061 GTCGTTTCTGAAAATGTAAGTGGTC 58.866 40.000 4.09 0.00 33.81 4.02
4644 6619 5.683876 AATGTAAGTGGTCTGAGCTACAT 57.316 39.130 8.47 10.56 0.00 2.29
4654 6629 7.281774 AGTGGTCTGAGCTACATAATTTTCATG 59.718 37.037 8.47 0.00 0.00 3.07
4686 6661 8.060020 TGCAAATTTATGTCAAATATTAGCGC 57.940 30.769 0.00 0.00 0.00 5.92
4687 6662 7.704047 TGCAAATTTATGTCAAATATTAGCGCA 59.296 29.630 11.47 0.00 0.00 6.09
4688 6663 7.998212 GCAAATTTATGTCAAATATTAGCGCAC 59.002 33.333 11.47 0.00 0.00 5.34
4689 6664 7.836358 AATTTATGTCAAATATTAGCGCACG 57.164 32.000 11.47 0.00 0.00 5.34
4690 6665 5.977171 TTATGTCAAATATTAGCGCACGT 57.023 34.783 11.47 0.00 0.00 4.49
4691 6666 3.918258 TGTCAAATATTAGCGCACGTC 57.082 42.857 11.47 0.00 0.00 4.34
4695 6670 0.528901 AATATTAGCGCACGTCGGCA 60.529 50.000 11.47 0.00 38.94 5.69
4698 6673 4.771356 TAGCGCACGTCGGCAGTC 62.771 66.667 11.47 0.00 38.94 3.51
4704 6679 1.442857 CACGTCGGCAGTCTCAGAC 60.443 63.158 0.00 0.00 0.00 3.51
4705 6680 1.897137 ACGTCGGCAGTCTCAGACA 60.897 57.895 7.77 0.00 34.60 3.41
4708 6683 0.664767 GTCGGCAGTCTCAGACACAC 60.665 60.000 7.77 0.00 34.60 3.82
4711 6686 1.606480 CGGCAGTCTCAGACACACAAT 60.606 52.381 7.77 0.00 34.60 2.71
4717 6692 4.447054 CAGTCTCAGACACACAATTCTCAC 59.553 45.833 7.77 0.00 34.60 3.51
4718 6693 4.100035 AGTCTCAGACACACAATTCTCACA 59.900 41.667 7.77 0.00 34.60 3.58
4724 6699 6.758416 TCAGACACACAATTCTCACATATAGC 59.242 38.462 0.00 0.00 0.00 2.97
4725 6700 6.018425 CAGACACACAATTCTCACATATAGCC 60.018 42.308 0.00 0.00 0.00 3.93
4731 6706 5.530171 ACAATTCTCACATATAGCCTGCAAG 59.470 40.000 0.00 0.00 0.00 4.01
4738 6713 5.239306 TCACATATAGCCTGCAAGTTTATGC 59.761 40.000 0.00 0.00 46.58 3.14
4771 6746 4.436852 CCGGTCATTTTCGTACCAATCTTG 60.437 45.833 0.00 0.00 32.55 3.02
4820 6797 0.535335 CAACCGTAGCTCTAGCCCAA 59.465 55.000 0.00 0.00 43.38 4.12
4823 6800 0.039074 CCGTAGCTCTAGCCCAATCG 60.039 60.000 0.00 0.00 43.38 3.34
4830 6807 2.139118 CTCTAGCCCAATCGCTTTAGC 58.861 52.381 0.00 0.00 40.39 3.09
4831 6808 1.202651 TCTAGCCCAATCGCTTTAGCC 60.203 52.381 0.00 0.00 40.39 3.93
4858 6835 9.308318 GATCTATCCACTCTTTTACTTTCTGTC 57.692 37.037 0.00 0.00 0.00 3.51
4859 6836 7.612677 TCTATCCACTCTTTTACTTTCTGTCC 58.387 38.462 0.00 0.00 0.00 4.02
4873 6851 3.492102 TCTGTCCTTTTGGTCTCCAAG 57.508 47.619 1.53 0.00 44.84 3.61
4899 6877 3.084786 ACTTTGGCAGCTTACATTCTCC 58.915 45.455 0.00 0.00 0.00 3.71
4903 6881 2.093288 TGGCAGCTTACATTCTCCTCTG 60.093 50.000 0.00 0.00 0.00 3.35
4914 6892 2.599408 TCTCCTCTGTTTACCCGTCT 57.401 50.000 0.00 0.00 0.00 4.18
4920 6898 4.021719 TCCTCTGTTTACCCGTCTGTTTAG 60.022 45.833 0.00 0.00 0.00 1.85
4921 6899 4.243270 CTCTGTTTACCCGTCTGTTTAGG 58.757 47.826 0.00 0.00 0.00 2.69
4922 6900 2.740447 CTGTTTACCCGTCTGTTTAGGC 59.260 50.000 0.00 0.00 0.00 3.93
4923 6901 2.079158 GTTTACCCGTCTGTTTAGGCC 58.921 52.381 0.00 0.00 0.00 5.19
4924 6902 1.350071 TTACCCGTCTGTTTAGGCCA 58.650 50.000 5.01 0.00 0.00 5.36
4925 6903 1.350071 TACCCGTCTGTTTAGGCCAA 58.650 50.000 5.01 0.00 0.00 4.52
4926 6904 0.250597 ACCCGTCTGTTTAGGCCAAC 60.251 55.000 5.01 1.41 0.00 3.77
4927 6905 0.036306 CCCGTCTGTTTAGGCCAACT 59.964 55.000 5.01 0.00 0.00 3.16
4928 6906 1.439679 CCGTCTGTTTAGGCCAACTC 58.560 55.000 5.01 0.00 0.00 3.01
4929 6907 1.439679 CGTCTGTTTAGGCCAACTCC 58.560 55.000 5.01 0.00 0.00 3.85
4930 6908 1.270625 CGTCTGTTTAGGCCAACTCCA 60.271 52.381 5.01 0.00 0.00 3.86
4931 6909 2.152016 GTCTGTTTAGGCCAACTCCAC 58.848 52.381 5.01 0.00 0.00 4.02
4932 6910 1.073284 TCTGTTTAGGCCAACTCCACC 59.927 52.381 5.01 0.00 0.00 4.61
4933 6911 0.250553 TGTTTAGGCCAACTCCACCG 60.251 55.000 5.01 0.00 0.00 4.94
4934 6912 1.302993 TTTAGGCCAACTCCACCGC 60.303 57.895 5.01 0.00 0.00 5.68
4935 6913 3.599285 TTAGGCCAACTCCACCGCG 62.599 63.158 5.01 0.00 0.00 6.46
4945 6923 4.944372 CCACCGCGCGACCCTATC 62.944 72.222 34.63 0.00 0.00 2.08
4946 6924 4.944372 CACCGCGCGACCCTATCC 62.944 72.222 34.63 0.00 0.00 2.59
4948 6926 4.647615 CCGCGCGACCCTATCCTG 62.648 72.222 34.63 6.11 0.00 3.86
4949 6927 3.900892 CGCGCGACCCTATCCTGT 61.901 66.667 28.94 0.00 0.00 4.00
4950 6928 2.027751 GCGCGACCCTATCCTGTC 59.972 66.667 12.10 0.00 0.00 3.51
4951 6929 2.728817 CGCGACCCTATCCTGTCC 59.271 66.667 0.00 0.00 0.00 4.02
4952 6930 2.728817 GCGACCCTATCCTGTCCG 59.271 66.667 0.00 0.00 0.00 4.79
4953 6931 2.728817 CGACCCTATCCTGTCCGC 59.271 66.667 0.00 0.00 0.00 5.54
4954 6932 2.857744 CGACCCTATCCTGTCCGCC 61.858 68.421 0.00 0.00 0.00 6.13
4955 6933 2.446036 ACCCTATCCTGTCCGCCC 60.446 66.667 0.00 0.00 0.00 6.13
4956 6934 3.242291 CCCTATCCTGTCCGCCCC 61.242 72.222 0.00 0.00 0.00 5.80
4957 6935 3.242291 CCTATCCTGTCCGCCCCC 61.242 72.222 0.00 0.00 0.00 5.40
4958 6936 3.616721 CTATCCTGTCCGCCCCCG 61.617 72.222 0.00 0.00 0.00 5.73
4959 6937 4.468769 TATCCTGTCCGCCCCCGT 62.469 66.667 0.00 0.00 0.00 5.28
4982 6960 6.452494 TCCGTTTGGAGTAAAATGAACAAA 57.548 33.333 0.00 0.00 40.17 2.83
4983 6961 6.267070 TCCGTTTGGAGTAAAATGAACAAAC 58.733 36.000 0.00 0.00 40.17 2.93
4985 6963 6.505039 GTTTGGAGTAAAATGAACAAACGG 57.495 37.500 0.00 0.00 38.51 4.44
4986 6964 4.839668 TGGAGTAAAATGAACAAACGGG 57.160 40.909 0.00 0.00 0.00 5.28
4987 6965 4.462133 TGGAGTAAAATGAACAAACGGGA 58.538 39.130 0.00 0.00 0.00 5.14
4988 6966 5.074115 TGGAGTAAAATGAACAAACGGGAT 58.926 37.500 0.00 0.00 0.00 3.85
4989 6967 5.182380 TGGAGTAAAATGAACAAACGGGATC 59.818 40.000 0.00 0.00 0.00 3.36
4990 6968 5.291293 AGTAAAATGAACAAACGGGATCG 57.709 39.130 0.00 0.00 43.02 3.69
4991 6969 2.629639 AAATGAACAAACGGGATCGC 57.370 45.000 0.00 0.00 40.63 4.58
4992 6970 0.808755 AATGAACAAACGGGATCGCC 59.191 50.000 3.90 0.00 40.63 5.54
5009 6987 3.648982 CCAGCGTGCGAGCACAAA 61.649 61.111 25.18 0.00 46.47 2.83
5010 6988 2.425773 CAGCGTGCGAGCACAAAC 60.426 61.111 25.18 14.88 46.47 2.93
5011 6989 4.000557 AGCGTGCGAGCACAAACG 62.001 61.111 25.18 13.90 46.47 3.60
5013 6991 3.334751 CGTGCGAGCACAAACGGA 61.335 61.111 25.18 0.00 46.47 4.69
5014 6992 2.248431 GTGCGAGCACAAACGGAC 59.752 61.111 21.73 0.00 45.53 4.79
5015 6993 2.202946 TGCGAGCACAAACGGACA 60.203 55.556 0.00 0.00 0.00 4.02
5016 6994 1.815840 TGCGAGCACAAACGGACAA 60.816 52.632 0.00 0.00 0.00 3.18
5017 6995 1.353804 GCGAGCACAAACGGACAAA 59.646 52.632 0.00 0.00 0.00 2.83
5018 6996 0.040425 GCGAGCACAAACGGACAAAT 60.040 50.000 0.00 0.00 0.00 2.32
5019 6997 1.673760 CGAGCACAAACGGACAAATG 58.326 50.000 0.00 0.00 0.00 2.32
5020 6998 1.002900 CGAGCACAAACGGACAAATGT 60.003 47.619 0.00 0.00 0.00 2.71
5021 6999 2.650608 GAGCACAAACGGACAAATGTC 58.349 47.619 4.96 4.96 44.04 3.06
5031 7009 1.734163 GACAAATGTCCGGATTCCGT 58.266 50.000 22.83 1.21 46.80 4.69
5032 7010 1.664151 GACAAATGTCCGGATTCCGTC 59.336 52.381 22.83 15.53 46.80 4.79
5033 7011 1.014352 CAAATGTCCGGATTCCGTCC 58.986 55.000 22.83 13.25 46.80 4.79
5051 7029 3.899395 GTTTTCGACCCATCCCCG 58.101 61.111 0.00 0.00 0.00 5.73
5052 7030 1.747745 GTTTTCGACCCATCCCCGG 60.748 63.158 0.00 0.00 0.00 5.73
5053 7031 3.631952 TTTTCGACCCATCCCCGGC 62.632 63.158 0.00 0.00 0.00 6.13
5060 7038 4.060667 CCATCCCCGGCCCAAACT 62.061 66.667 0.00 0.00 0.00 2.66
5061 7039 2.037208 CATCCCCGGCCCAAACTT 59.963 61.111 0.00 0.00 0.00 2.66
5062 7040 2.037208 ATCCCCGGCCCAAACTTG 59.963 61.111 0.00 0.00 0.00 3.16
5063 7041 4.986708 TCCCCGGCCCAAACTTGC 62.987 66.667 0.00 0.00 0.00 4.01
5067 7045 4.404654 CGGCCCAAACTTGCGCTC 62.405 66.667 9.73 0.00 32.76 5.03
5068 7046 4.404654 GGCCCAAACTTGCGCTCG 62.405 66.667 9.73 1.27 32.76 5.03
5069 7047 4.404654 GCCCAAACTTGCGCTCGG 62.405 66.667 9.73 0.61 0.00 4.63
5070 7048 2.978010 CCCAAACTTGCGCTCGGT 60.978 61.111 9.73 1.34 0.00 4.69
5071 7049 2.551912 CCCAAACTTGCGCTCGGTT 61.552 57.895 9.73 8.16 0.00 4.44
5072 7050 1.358759 CCAAACTTGCGCTCGGTTT 59.641 52.632 9.73 13.79 34.10 3.27
5073 7051 0.934436 CCAAACTTGCGCTCGGTTTG 60.934 55.000 28.50 28.50 45.14 2.93
5074 7052 0.934436 CAAACTTGCGCTCGGTTTGG 60.934 55.000 28.14 17.85 43.19 3.28
5075 7053 2.070654 AAACTTGCGCTCGGTTTGGG 62.071 55.000 19.08 0.36 32.84 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.130516 GCACTATATATACCGCAGAGGCA 59.869 47.826 0.00 0.00 46.52 4.75
129 130 7.875041 ACTCATGTACTCAGAAATACATATGCC 59.125 37.037 1.58 0.00 39.47 4.40
140 141 6.211384 TGATTCTCCAACTCATGTACTCAGAA 59.789 38.462 0.00 0.00 0.00 3.02
235 236 6.537355 AGTGATCTTGTGAGATTTGGAAAGA 58.463 36.000 0.00 0.00 42.66 2.52
281 292 7.397221 TCTCCAATATGACTCAACATTGAAGT 58.603 34.615 14.22 0.00 36.64 3.01
282 293 7.767659 TCTCTCCAATATGACTCAACATTGAAG 59.232 37.037 14.22 7.20 36.64 3.02
283 294 7.623630 TCTCTCCAATATGACTCAACATTGAA 58.376 34.615 14.22 0.00 36.64 2.69
284 295 7.186570 TCTCTCCAATATGACTCAACATTGA 57.813 36.000 14.22 0.00 35.57 2.57
285 296 7.854557 TTCTCTCCAATATGACTCAACATTG 57.145 36.000 8.70 8.70 0.00 2.82
475 533 2.437359 AATGCAGAGAGGCCGCAC 60.437 61.111 9.88 1.52 38.73 5.34
482 540 0.168348 GCACAGTGCAATGCAGAGAG 59.832 55.000 21.22 3.99 44.26 3.20
513 597 7.256691 GGTCTTAGGAAGGATTATATGAGGCAA 60.257 40.741 0.00 0.00 0.00 4.52
514 598 6.213600 GGTCTTAGGAAGGATTATATGAGGCA 59.786 42.308 0.00 0.00 0.00 4.75
515 599 6.352308 GGGTCTTAGGAAGGATTATATGAGGC 60.352 46.154 0.00 0.00 0.00 4.70
516 600 6.157123 GGGGTCTTAGGAAGGATTATATGAGG 59.843 46.154 0.00 0.00 0.00 3.86
517 601 6.730977 TGGGGTCTTAGGAAGGATTATATGAG 59.269 42.308 0.00 0.00 0.00 2.90
518 602 6.500751 GTGGGGTCTTAGGAAGGATTATATGA 59.499 42.308 0.00 0.00 0.00 2.15
519 603 6.296489 GGTGGGGTCTTAGGAAGGATTATATG 60.296 46.154 0.00 0.00 0.00 1.78
520 604 5.791141 GGTGGGGTCTTAGGAAGGATTATAT 59.209 44.000 0.00 0.00 0.00 0.86
521 605 5.102346 AGGTGGGGTCTTAGGAAGGATTATA 60.102 44.000 0.00 0.00 0.00 0.98
522 606 3.981375 GGTGGGGTCTTAGGAAGGATTAT 59.019 47.826 0.00 0.00 0.00 1.28
523 607 3.014807 AGGTGGGGTCTTAGGAAGGATTA 59.985 47.826 0.00 0.00 0.00 1.75
524 608 2.206223 GGTGGGGTCTTAGGAAGGATT 58.794 52.381 0.00 0.00 0.00 3.01
525 609 1.369983 AGGTGGGGTCTTAGGAAGGAT 59.630 52.381 0.00 0.00 0.00 3.24
526 610 0.797579 AGGTGGGGTCTTAGGAAGGA 59.202 55.000 0.00 0.00 0.00 3.36
527 611 0.912486 CAGGTGGGGTCTTAGGAAGG 59.088 60.000 0.00 0.00 0.00 3.46
528 612 0.912486 CCAGGTGGGGTCTTAGGAAG 59.088 60.000 0.00 0.00 0.00 3.46
529 613 1.205460 GCCAGGTGGGGTCTTAGGAA 61.205 60.000 0.00 0.00 37.04 3.36
530 614 1.615424 GCCAGGTGGGGTCTTAGGA 60.615 63.158 0.00 0.00 37.04 2.94
531 615 2.998949 GCCAGGTGGGGTCTTAGG 59.001 66.667 0.00 0.00 37.04 2.69
532 616 2.584608 CGCCAGGTGGGGTCTTAG 59.415 66.667 4.91 0.00 42.54 2.18
720 807 0.320374 TAGAAGCACCGTCAAGTGGG 59.680 55.000 0.00 0.00 38.24 4.61
850 947 7.721286 AGTCCATCAGAAATCAACGATTATC 57.279 36.000 0.00 0.00 31.46 1.75
949 1046 5.740290 TCCTTTCACCTCCTAAGTTACAG 57.260 43.478 0.00 0.00 0.00 2.74
994 1091 5.448654 CACATCTCCCTTTCCCATTATGAA 58.551 41.667 0.00 0.00 0.00 2.57
996 1093 4.147321 CCACATCTCCCTTTCCCATTATG 58.853 47.826 0.00 0.00 0.00 1.90
1154 1251 3.243907 GGACCAGTCAGGATATGCTGTAC 60.244 52.174 21.93 17.72 41.22 2.90
1310 1506 3.119637 CCGTTGAATGAAAATAAGCCGGT 60.120 43.478 1.90 0.00 0.00 5.28
1335 1531 2.452114 CCCCTGAGGACCTGGAGT 59.548 66.667 0.00 0.00 38.24 3.85
1341 1537 0.768221 TATGGATGCCCCTGAGGACC 60.768 60.000 0.00 0.00 38.24 4.46
1416 1612 9.161629 AGTCATTGATTACAACATTATGTCGAA 57.838 29.630 0.00 0.00 38.90 3.71
1513 1755 6.217693 ACCCTATGACTGAAGGTTAAAGGATT 59.782 38.462 0.00 0.00 0.00 3.01
1557 1799 7.764443 TCAGAGGTTGTACTAGCAAATAATGTC 59.236 37.037 9.12 0.00 0.00 3.06
1566 1808 4.833380 AGACTTTCAGAGGTTGTACTAGCA 59.167 41.667 9.12 0.00 0.00 3.49
1612 1854 4.159321 TGCCAGCGGATGAATTCAAATTAA 59.841 37.500 13.09 0.00 0.00 1.40
1670 1912 3.855689 GCCTTGAGCATACATTGTTGT 57.144 42.857 0.00 0.00 42.97 3.32
1957 2199 5.424757 CAGACCCGAAATATAAGGACACAA 58.575 41.667 0.00 0.00 0.00 3.33
1993 2235 9.537848 GTGATAATCGTTAAGTAACAAGTTTGG 57.462 33.333 2.36 0.00 35.99 3.28
2034 2276 6.713762 TTAAAACATGAATCCCTATGCAGG 57.286 37.500 0.00 0.00 42.22 4.85
2182 2424 7.894753 GGCGTTTTATCTTTTACTGTAACTACG 59.105 37.037 0.00 0.00 0.00 3.51
2317 2559 1.655654 CCACTCTCGCTGCGTATCG 60.656 63.158 22.48 11.23 0.00 2.92
2322 2564 3.184683 GCTTCCACTCTCGCTGCG 61.185 66.667 17.25 17.25 0.00 5.18
2357 2599 9.760660 CATACACTTTTAGAATTTGTACTGCTC 57.239 33.333 0.00 0.00 0.00 4.26
2434 2676 7.633789 ACTGTTTGGAATCTGTACCAGAATAT 58.366 34.615 0.00 0.00 44.04 1.28
2481 2723 2.884639 CAAACAAGACCTACAACTGGGG 59.115 50.000 0.00 0.00 0.00 4.96
2546 3262 6.014584 AGGTAAGCATGATGACGGTAATATCA 60.015 38.462 0.00 5.15 35.52 2.15
2641 3357 7.290481 AGAGGAGATTTTAGGACCTACCATTAC 59.710 40.741 0.00 0.00 42.04 1.89
2712 3688 4.442454 CTTTTCTCCCCGGCCCCC 62.442 72.222 0.00 0.00 0.00 5.40
2713 3689 4.442454 CCTTTTCTCCCCGGCCCC 62.442 72.222 0.00 0.00 0.00 5.80
2714 3690 2.224805 AATCCTTTTCTCCCCGGCCC 62.225 60.000 0.00 0.00 0.00 5.80
2715 3691 1.037579 CAATCCTTTTCTCCCCGGCC 61.038 60.000 0.00 0.00 0.00 6.13
2716 3692 0.034477 TCAATCCTTTTCTCCCCGGC 60.034 55.000 0.00 0.00 0.00 6.13
2717 3693 1.408822 CCTCAATCCTTTTCTCCCCGG 60.409 57.143 0.00 0.00 0.00 5.73
2718 3694 1.559682 TCCTCAATCCTTTTCTCCCCG 59.440 52.381 0.00 0.00 0.00 5.73
3355 4345 7.358263 TCCAACTTGATCTCTCCTAGATAAGT 58.642 38.462 0.00 0.00 45.35 2.24
3392 4385 4.263462 TGCAACTAGAGAACCATCACCAAT 60.263 41.667 0.00 0.00 0.00 3.16
3470 4463 1.892474 ACCGCAATGCCAAATACTGTT 59.108 42.857 0.00 0.00 0.00 3.16
3473 4466 3.275617 TCTACCGCAATGCCAAATACT 57.724 42.857 0.00 0.00 0.00 2.12
3503 4496 0.971959 TGCTGGCTATGCAAAAGGGG 60.972 55.000 0.00 0.00 37.51 4.79
3507 4500 3.258872 AGACAAATGCTGGCTATGCAAAA 59.741 39.130 0.00 0.00 43.93 2.44
3527 4520 9.084533 ACTTGGTTAGCAAAATGGTAAAATAGA 57.915 29.630 3.81 0.00 41.29 1.98
3598 4591 4.602995 CTGAACTATACTCCGCTGAACTC 58.397 47.826 0.00 0.00 0.00 3.01
3637 4630 6.189677 ACGAATAGCTAGCAGATCTGATAC 57.810 41.667 27.04 17.31 0.00 2.24
3743 5672 6.844097 AATTTCCATTAAGGCGTCCTTTTA 57.156 33.333 14.87 6.16 41.69 1.52
3962 5925 5.757320 CCAGCTTTGAGGATCTACACAATAG 59.243 44.000 0.00 0.00 34.92 1.73
4131 6098 0.179108 GCAGTGGAAGCTAGTACCGG 60.179 60.000 0.00 0.00 0.00 5.28
4132 6099 0.179108 GGCAGTGGAAGCTAGTACCG 60.179 60.000 0.00 0.00 0.00 4.02
4185 6152 6.361433 TGTCACCTCCAGTTTATCTGAAAAA 58.639 36.000 0.00 0.00 46.27 1.94
4231 6198 2.760634 ATCGCACACATGAACACCTA 57.239 45.000 0.00 0.00 0.00 3.08
4248 6215 6.705863 ACCATCTCAGCCAAAAATCTAATC 57.294 37.500 0.00 0.00 0.00 1.75
4308 6275 3.128349 CCCGACAAAGAAGACGAAGAAA 58.872 45.455 0.00 0.00 0.00 2.52
4337 6304 2.963854 CCATAGAGCACGGCAGCG 60.964 66.667 0.00 0.00 40.15 5.18
4363 6330 2.494073 ACACAAACGCAGGAAAAAGGAA 59.506 40.909 0.00 0.00 0.00 3.36
4364 6331 2.096248 ACACAAACGCAGGAAAAAGGA 58.904 42.857 0.00 0.00 0.00 3.36
4365 6332 2.159310 TCACACAAACGCAGGAAAAAGG 60.159 45.455 0.00 0.00 0.00 3.11
4366 6333 3.108144 CTCACACAAACGCAGGAAAAAG 58.892 45.455 0.00 0.00 0.00 2.27
4367 6334 2.750166 TCTCACACAAACGCAGGAAAAA 59.250 40.909 0.00 0.00 0.00 1.94
4377 6344 5.786401 CTAAGGTAGCATCTCACACAAAC 57.214 43.478 0.00 0.00 0.00 2.93
4421 6388 6.867662 AATCCCGCAAAGTCTCAAATATAG 57.132 37.500 0.00 0.00 0.00 1.31
4472 6439 2.811873 GCATCAGTTCAGGTCAACCAGT 60.812 50.000 1.33 0.00 38.89 4.00
4551 6523 4.818005 TGTAATATGATGCAAGCAGGAGTG 59.182 41.667 0.00 0.00 32.93 3.51
4553 6525 6.381481 TTTGTAATATGATGCAAGCAGGAG 57.619 37.500 0.00 0.00 32.93 3.69
4555 6527 5.981315 CCTTTTGTAATATGATGCAAGCAGG 59.019 40.000 0.00 0.00 32.93 4.85
4556 6528 6.798482 TCCTTTTGTAATATGATGCAAGCAG 58.202 36.000 0.00 0.00 32.93 4.24
4557 6529 6.772360 TCCTTTTGTAATATGATGCAAGCA 57.228 33.333 0.00 0.00 35.55 3.91
4558 6530 6.643770 CCATCCTTTTGTAATATGATGCAAGC 59.356 38.462 0.00 0.00 0.00 4.01
4574 6547 7.670364 CAGAATTCCTGTAAAACCATCCTTTT 58.330 34.615 0.65 0.00 38.10 2.27
4598 6571 4.627058 TCAGAAACGACATTAGTGAAGCA 58.373 39.130 0.00 0.00 0.00 3.91
4599 6572 5.591643 TTCAGAAACGACATTAGTGAAGC 57.408 39.130 0.00 0.00 0.00 3.86
4602 6575 7.490962 ACATTTTCAGAAACGACATTAGTGA 57.509 32.000 0.00 0.00 0.00 3.41
4603 6576 9.318041 CTTACATTTTCAGAAACGACATTAGTG 57.682 33.333 0.00 0.00 0.00 2.74
4604 6577 9.052759 ACTTACATTTTCAGAAACGACATTAGT 57.947 29.630 0.00 0.00 0.00 2.24
4605 6578 9.318041 CACTTACATTTTCAGAAACGACATTAG 57.682 33.333 0.00 0.00 0.00 1.73
4627 6600 7.168219 TGAAAATTATGTAGCTCAGACCACTT 58.832 34.615 0.00 0.00 0.00 3.16
4666 6641 6.954944 ACGTGCGCTAATATTTGACATAAAT 58.045 32.000 9.73 0.00 0.00 1.40
4667 6642 6.352682 ACGTGCGCTAATATTTGACATAAA 57.647 33.333 9.73 0.00 0.00 1.40
4675 6650 0.580104 GCCGACGTGCGCTAATATTT 59.420 50.000 9.73 0.00 39.11 1.40
4676 6651 0.528901 TGCCGACGTGCGCTAATATT 60.529 50.000 9.73 0.00 39.11 1.28
4677 6652 0.939577 CTGCCGACGTGCGCTAATAT 60.940 55.000 9.73 0.00 39.11 1.28
4678 6653 1.587876 CTGCCGACGTGCGCTAATA 60.588 57.895 9.73 0.00 39.11 0.98
4679 6654 2.885644 CTGCCGACGTGCGCTAAT 60.886 61.111 9.73 0.00 39.11 1.73
4680 6655 4.351938 ACTGCCGACGTGCGCTAA 62.352 61.111 9.73 0.00 39.11 3.09
4681 6656 4.771356 GACTGCCGACGTGCGCTA 62.771 66.667 9.73 0.00 39.11 4.26
4684 6659 4.700365 TGAGACTGCCGACGTGCG 62.700 66.667 0.00 0.00 40.47 5.34
4685 6660 2.807045 CTGAGACTGCCGACGTGC 60.807 66.667 0.00 0.00 0.00 5.34
4686 6661 1.442857 GTCTGAGACTGCCGACGTG 60.443 63.158 5.12 0.00 0.00 4.49
4687 6662 1.897137 TGTCTGAGACTGCCGACGT 60.897 57.895 14.42 0.00 33.15 4.34
4688 6663 1.442857 GTGTCTGAGACTGCCGACG 60.443 63.158 14.42 0.00 33.15 5.12
4689 6664 0.664767 GTGTGTCTGAGACTGCCGAC 60.665 60.000 14.42 3.67 33.15 4.79
4690 6665 1.106944 TGTGTGTCTGAGACTGCCGA 61.107 55.000 14.42 0.00 33.15 5.54
4691 6666 0.249447 TTGTGTGTCTGAGACTGCCG 60.249 55.000 14.42 0.00 33.15 5.69
4695 6670 4.100035 TGTGAGAATTGTGTGTCTGAGACT 59.900 41.667 14.42 0.00 33.15 3.24
4698 6673 7.042858 GCTATATGTGAGAATTGTGTGTCTGAG 60.043 40.741 0.00 0.00 0.00 3.35
4704 6679 5.277683 GCAGGCTATATGTGAGAATTGTGTG 60.278 44.000 0.00 0.00 0.00 3.82
4705 6680 4.818546 GCAGGCTATATGTGAGAATTGTGT 59.181 41.667 0.00 0.00 0.00 3.72
4708 6683 5.530171 ACTTGCAGGCTATATGTGAGAATTG 59.470 40.000 0.00 0.00 0.00 2.32
4711 6686 4.760530 ACTTGCAGGCTATATGTGAGAA 57.239 40.909 0.00 0.00 0.00 2.87
4717 6692 4.452114 TCGCATAAACTTGCAGGCTATATG 59.548 41.667 0.00 3.97 42.91 1.78
4718 6693 4.641396 TCGCATAAACTTGCAGGCTATAT 58.359 39.130 0.00 0.00 42.91 0.86
4724 6699 3.281341 TGTTTCGCATAAACTTGCAGG 57.719 42.857 11.64 0.00 42.91 4.85
4725 6700 4.324402 GGAATGTTTCGCATAAACTTGCAG 59.676 41.667 11.64 0.00 42.91 4.41
4731 6706 2.162809 ACCGGGAATGTTTCGCATAAAC 59.837 45.455 6.32 5.02 42.19 2.01
4738 6713 3.498082 GAAAATGACCGGGAATGTTTCG 58.502 45.455 6.32 0.00 0.00 3.46
4771 6746 5.175673 TCAACATGTATCTCGCAATCGATTC 59.824 40.000 7.92 2.75 44.56 2.52
4820 6797 2.826128 TGGATAGATCGGCTAAAGCGAT 59.174 45.455 8.39 8.39 43.26 4.58
4823 6800 3.257127 AGAGTGGATAGATCGGCTAAAGC 59.743 47.826 0.00 0.00 41.14 3.51
4830 6807 7.436673 CAGAAAGTAAAAGAGTGGATAGATCGG 59.563 40.741 0.00 0.00 0.00 4.18
4831 6808 7.976734 ACAGAAAGTAAAAGAGTGGATAGATCG 59.023 37.037 0.00 0.00 0.00 3.69
4858 6835 0.600057 GCTGCTTGGAGACCAAAAGG 59.400 55.000 4.78 0.00 43.44 3.11
4859 6836 1.000938 GTGCTGCTTGGAGACCAAAAG 60.001 52.381 0.00 6.60 43.44 2.27
4889 6867 4.529377 ACGGGTAAACAGAGGAGAATGTAA 59.471 41.667 0.00 0.00 0.00 2.41
4899 6877 4.243270 CCTAAACAGACGGGTAAACAGAG 58.757 47.826 0.00 0.00 0.00 3.35
4903 6881 2.079158 GGCCTAAACAGACGGGTAAAC 58.921 52.381 0.00 0.00 0.00 2.01
4914 6892 0.250553 CGGTGGAGTTGGCCTAAACA 60.251 55.000 3.32 0.00 32.21 2.83
4928 6906 4.944372 GATAGGGTCGCGCGGTGG 62.944 72.222 31.69 0.71 0.00 4.61
4929 6907 4.944372 GGATAGGGTCGCGCGGTG 62.944 72.222 31.69 1.17 0.00 4.94
4931 6909 4.647615 CAGGATAGGGTCGCGCGG 62.648 72.222 31.69 11.75 0.00 6.46
4932 6910 3.825833 GACAGGATAGGGTCGCGCG 62.826 68.421 26.76 26.76 0.00 6.86
4933 6911 2.027751 GACAGGATAGGGTCGCGC 59.972 66.667 0.00 0.00 0.00 6.86
4934 6912 2.728817 GGACAGGATAGGGTCGCG 59.271 66.667 0.00 0.00 34.87 5.87
4935 6913 2.728817 CGGACAGGATAGGGTCGC 59.271 66.667 0.00 0.00 34.87 5.19
4936 6914 2.728817 GCGGACAGGATAGGGTCG 59.271 66.667 0.00 0.00 34.87 4.79
4937 6915 2.508751 GGGCGGACAGGATAGGGTC 61.509 68.421 0.00 0.00 0.00 4.46
4938 6916 2.446036 GGGCGGACAGGATAGGGT 60.446 66.667 0.00 0.00 0.00 4.34
4939 6917 3.242291 GGGGCGGACAGGATAGGG 61.242 72.222 0.00 0.00 0.00 3.53
4940 6918 3.242291 GGGGGCGGACAGGATAGG 61.242 72.222 0.00 0.00 0.00 2.57
4941 6919 3.616721 CGGGGGCGGACAGGATAG 61.617 72.222 0.00 0.00 0.00 2.08
4942 6920 4.468769 ACGGGGGCGGACAGGATA 62.469 66.667 0.00 0.00 0.00 2.59
4953 6931 1.829523 TTACTCCAAACGGACGGGGG 61.830 60.000 0.00 0.00 0.00 5.40
4954 6932 0.035176 TTTACTCCAAACGGACGGGG 59.965 55.000 0.00 0.00 0.00 5.73
4955 6933 1.881591 TTTTACTCCAAACGGACGGG 58.118 50.000 0.00 0.00 0.00 5.28
4956 6934 3.068560 TCATTTTACTCCAAACGGACGG 58.931 45.455 0.00 0.00 0.00 4.79
4957 6935 4.024725 TGTTCATTTTACTCCAAACGGACG 60.025 41.667 0.00 0.00 0.00 4.79
4958 6936 5.427036 TGTTCATTTTACTCCAAACGGAC 57.573 39.130 0.00 0.00 0.00 4.79
4959 6937 6.267070 GTTTGTTCATTTTACTCCAAACGGA 58.733 36.000 0.00 0.00 34.39 4.69
4960 6938 6.505039 GTTTGTTCATTTTACTCCAAACGG 57.495 37.500 0.00 0.00 34.39 4.44
4962 6940 5.460748 CCCGTTTGTTCATTTTACTCCAAAC 59.539 40.000 0.00 0.00 38.67 2.93
4963 6941 5.360144 TCCCGTTTGTTCATTTTACTCCAAA 59.640 36.000 0.00 0.00 0.00 3.28
4964 6942 4.888239 TCCCGTTTGTTCATTTTACTCCAA 59.112 37.500 0.00 0.00 0.00 3.53
4965 6943 4.462133 TCCCGTTTGTTCATTTTACTCCA 58.538 39.130 0.00 0.00 0.00 3.86
4966 6944 5.637809 GATCCCGTTTGTTCATTTTACTCC 58.362 41.667 0.00 0.00 0.00 3.85
4967 6945 5.321516 CGATCCCGTTTGTTCATTTTACTC 58.678 41.667 0.00 0.00 0.00 2.59
4968 6946 4.379082 GCGATCCCGTTTGTTCATTTTACT 60.379 41.667 0.00 0.00 38.24 2.24
4969 6947 3.849708 GCGATCCCGTTTGTTCATTTTAC 59.150 43.478 0.00 0.00 38.24 2.01
4970 6948 3.119779 GGCGATCCCGTTTGTTCATTTTA 60.120 43.478 0.00 0.00 38.24 1.52
4971 6949 2.352323 GGCGATCCCGTTTGTTCATTTT 60.352 45.455 0.00 0.00 38.24 1.82
4972 6950 1.201414 GGCGATCCCGTTTGTTCATTT 59.799 47.619 0.00 0.00 38.24 2.32
4973 6951 0.808755 GGCGATCCCGTTTGTTCATT 59.191 50.000 0.00 0.00 38.24 2.57
4974 6952 1.029947 GGGCGATCCCGTTTGTTCAT 61.030 55.000 0.00 0.00 43.94 2.57
4975 6953 1.673009 GGGCGATCCCGTTTGTTCA 60.673 57.895 0.00 0.00 43.94 3.18
4976 6954 3.184206 GGGCGATCCCGTTTGTTC 58.816 61.111 0.00 0.00 43.94 3.18
4997 6975 2.042520 TTGTCCGTTTGTGCTCGCAC 62.043 55.000 14.75 14.75 46.33 5.34
4998 6976 1.369839 TTTGTCCGTTTGTGCTCGCA 61.370 50.000 0.00 0.00 0.00 5.10
4999 6977 0.040425 ATTTGTCCGTTTGTGCTCGC 60.040 50.000 0.00 0.00 0.00 5.03
5000 6978 1.002900 ACATTTGTCCGTTTGTGCTCG 60.003 47.619 0.00 0.00 0.00 5.03
5001 6979 2.650608 GACATTTGTCCGTTTGTGCTC 58.349 47.619 0.00 0.00 39.07 4.26
5002 6980 2.774439 GACATTTGTCCGTTTGTGCT 57.226 45.000 0.00 0.00 39.07 4.40
5023 7001 0.717784 GTCGAAAACGGACGGAATCC 59.282 55.000 0.00 0.00 45.20 3.01
5024 7002 0.717784 GGTCGAAAACGGACGGAATC 59.282 55.000 0.00 0.00 35.24 2.52
5025 7003 0.671472 GGGTCGAAAACGGACGGAAT 60.671 55.000 0.00 0.00 35.24 3.01
5026 7004 1.300853 GGGTCGAAAACGGACGGAA 60.301 57.895 0.00 0.00 35.24 4.30
5027 7005 1.818959 ATGGGTCGAAAACGGACGGA 61.819 55.000 0.00 0.00 35.24 4.69
5028 7006 1.356527 GATGGGTCGAAAACGGACGG 61.357 60.000 0.00 0.00 35.24 4.79
5029 7007 1.356527 GGATGGGTCGAAAACGGACG 61.357 60.000 0.00 0.00 35.24 4.79
5030 7008 1.022982 GGGATGGGTCGAAAACGGAC 61.023 60.000 0.00 0.00 0.00 4.79
5031 7009 1.297364 GGGATGGGTCGAAAACGGA 59.703 57.895 0.00 0.00 0.00 4.69
5032 7010 1.747745 GGGGATGGGTCGAAAACGG 60.748 63.158 0.00 0.00 0.00 4.44
5033 7011 2.104253 CGGGGATGGGTCGAAAACG 61.104 63.158 0.00 0.00 0.00 3.60
5034 7012 1.747745 CCGGGGATGGGTCGAAAAC 60.748 63.158 0.00 0.00 0.00 2.43
5035 7013 2.672295 CCGGGGATGGGTCGAAAA 59.328 61.111 0.00 0.00 0.00 2.29
5036 7014 4.104183 GCCGGGGATGGGTCGAAA 62.104 66.667 2.18 0.00 0.00 3.46
5043 7021 3.600410 AAGTTTGGGCCGGGGATGG 62.600 63.158 2.18 0.00 0.00 3.51
5044 7022 2.037208 AAGTTTGGGCCGGGGATG 59.963 61.111 2.18 0.00 0.00 3.51
5045 7023 2.037208 CAAGTTTGGGCCGGGGAT 59.963 61.111 2.18 0.00 0.00 3.85
5046 7024 4.986708 GCAAGTTTGGGCCGGGGA 62.987 66.667 2.18 0.00 0.00 4.81
5055 7033 0.934436 CCAAACCGAGCGCAAGTTTG 60.934 55.000 28.51 28.51 46.28 2.93
5056 7034 1.358759 CCAAACCGAGCGCAAGTTT 59.641 52.632 11.47 13.31 41.68 2.66
5057 7035 2.551912 CCCAAACCGAGCGCAAGTT 61.552 57.895 11.47 7.07 41.68 2.66
5058 7036 2.978010 CCCAAACCGAGCGCAAGT 60.978 61.111 11.47 0.00 41.68 3.16


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.