Multiple sequence alignment - TraesCS5D01G533200

Loading Multiple Alignment...

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 TraesCS5D01G533200 chr5D 100.000 3315 0 0 1 3315 547885115 547881801 0.000000e+00 6122.0
1 TraesCS5D01G533200 chr5D 84.634 1614 160 49 1017 2597 547841202 547839644 0.000000e+00 1526.0
2 TraesCS5D01G533200 chr5D 82.794 1639 184 48 977 2574 547892913 547891332 0.000000e+00 1375.0
3 TraesCS5D01G533200 chr5D 89.130 782 78 6 1821 2599 547925523 547924746 0.000000e+00 966.0
4 TraesCS5D01G533200 chr5D 84.540 718 59 23 1031 1706 547926297 547925590 0.000000e+00 664.0
5 TraesCS5D01G533200 chr5D 76.336 262 33 12 483 743 547842495 547842262 2.700000e-21 113.0
6 TraesCS5D01G533200 chr5D 97.778 45 1 0 2646 2690 547891338 547891294 9.860000e-11 78.7
7 TraesCS5D01G533200 chr5B 88.030 1746 139 37 891 2597 691773907 691772193 0.000000e+00 2002.0
8 TraesCS5D01G533200 chr5B 81.861 2117 209 76 494 2545 691799005 691796999 0.000000e+00 1620.0
9 TraesCS5D01G533200 chr5B 84.005 1713 194 54 900 2579 691825468 691823803 0.000000e+00 1572.0
10 TraesCS5D01G533200 chr5B 87.817 788 91 5 1821 2606 691942175 691941391 0.000000e+00 918.0
11 TraesCS5D01G533200 chr5B 92.272 427 23 6 9 432 691802819 691802400 6.120000e-167 597.0
12 TraesCS5D01G533200 chr5B 82.416 745 66 30 1017 1706 691942999 691942265 1.020000e-164 590.0
13 TraesCS5D01G533200 chr5B 83.585 463 47 18 443 899 691774371 691773932 1.110000e-109 407.0
14 TraesCS5D01G533200 chr5B 100.000 48 0 0 2643 2690 691796950 691796903 4.560000e-14 89.8
15 TraesCS5D01G533200 chr4A 87.622 1737 130 33 906 2575 618419188 618417470 0.000000e+00 1938.0
16 TraesCS5D01G533200 chr4A 86.151 1242 122 13 1359 2597 618412596 618411402 0.000000e+00 1295.0
17 TraesCS5D01G533200 chr4A 87.406 802 91 8 1814 2613 618529024 618528231 0.000000e+00 913.0
18 TraesCS5D01G533200 chr4A 87.368 760 85 8 1824 2579 618463771 618463019 0.000000e+00 861.0
19 TraesCS5D01G533200 chr4A 82.647 801 69 28 977 1732 618464601 618463826 0.000000e+00 645.0
20 TraesCS5D01G533200 chr4A 84.211 703 69 24 1031 1706 618529790 618529103 0.000000e+00 645.0
21 TraesCS5D01G533200 chr4A 90.952 210 17 2 2707 2915 643090434 643090226 7.000000e-72 281.0
22 TraesCS5D01G533200 chr4A 78.769 325 42 12 960 1257 618412982 618412658 3.370000e-45 193.0
23 TraesCS5D01G533200 chr4A 81.377 247 26 16 488 733 618413423 618413196 2.030000e-42 183.0
24 TraesCS5D01G533200 chr4A 88.000 75 7 2 2806 2880 730624683 730624611 1.640000e-13 87.9
25 TraesCS5D01G533200 chr4A 82.716 81 7 4 569 649 618419519 618419446 7.680000e-07 65.8
26 TraesCS5D01G533200 chr4A 100.000 32 0 0 815 846 618419309 618419278 3.570000e-05 60.2
27 TraesCS5D01G533200 chr7D 91.703 229 19 0 2915 3143 54793502 54793730 5.340000e-83 318.0
28 TraesCS5D01G533200 chr7D 90.870 230 16 5 2689 2915 54793208 54793435 1.490000e-78 303.0
29 TraesCS5D01G533200 chr7D 78.338 397 78 3 2918 3307 519600249 519600644 1.970000e-62 250.0
30 TraesCS5D01G533200 chr6D 92.000 225 15 3 2693 2915 464967121 464967344 2.480000e-81 313.0
31 TraesCS5D01G533200 chr2A 86.667 210 20 3 2707 2915 775940418 775940620 3.330000e-55 226.0
32 TraesCS5D01G533200 chr7B 78.986 276 46 6 2918 3192 287944220 287943956 9.450000e-41 178.0
33 TraesCS5D01G533200 chr4D 78.421 190 27 9 2696 2879 400176805 400176624 9.720000e-21 111.0
34 TraesCS5D01G533200 chr1D 89.286 84 7 2 2798 2881 463429671 463429752 1.630000e-18 104.0
35 TraesCS5D01G533200 chr1A 78.616 159 26 7 2727 2881 555544997 555545151 7.570000e-17 99.0
36 TraesCS5D01G533200 chr2B 88.571 70 6 2 2812 2881 2636725 2636658 2.120000e-12 84.2


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 TraesCS5D01G533200 chr5D 547881801 547885115 3314 True 6122.000000 6122 100.000000 1 3315 1 chr5D.!!$R1 3314
1 TraesCS5D01G533200 chr5D 547839644 547842495 2851 True 819.500000 1526 80.485000 483 2597 2 chr5D.!!$R2 2114
2 TraesCS5D01G533200 chr5D 547924746 547926297 1551 True 815.000000 966 86.835000 1031 2599 2 chr5D.!!$R4 1568
3 TraesCS5D01G533200 chr5D 547891294 547892913 1619 True 726.850000 1375 90.286000 977 2690 2 chr5D.!!$R3 1713
4 TraesCS5D01G533200 chr5B 691823803 691825468 1665 True 1572.000000 1572 84.005000 900 2579 1 chr5B.!!$R1 1679
5 TraesCS5D01G533200 chr5B 691772193 691774371 2178 True 1204.500000 2002 85.807500 443 2597 2 chr5B.!!$R2 2154
6 TraesCS5D01G533200 chr5B 691796903 691802819 5916 True 768.933333 1620 91.377667 9 2690 3 chr5B.!!$R3 2681
7 TraesCS5D01G533200 chr5B 691941391 691942999 1608 True 754.000000 918 85.116500 1017 2606 2 chr5B.!!$R4 1589
8 TraesCS5D01G533200 chr4A 618528231 618529790 1559 True 779.000000 913 85.808500 1031 2613 2 chr4A.!!$R6 1582
9 TraesCS5D01G533200 chr4A 618463019 618464601 1582 True 753.000000 861 85.007500 977 2579 2 chr4A.!!$R5 1602
10 TraesCS5D01G533200 chr4A 618417470 618419519 2049 True 688.000000 1938 90.112667 569 2575 3 chr4A.!!$R4 2006
11 TraesCS5D01G533200 chr4A 618411402 618413423 2021 True 557.000000 1295 82.099000 488 2597 3 chr4A.!!$R3 2109
12 TraesCS5D01G533200 chr7D 54793208 54793730 522 False 310.500000 318 91.286500 2689 3143 2 chr7D.!!$F2 454

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
81 82 0.318955 AACATGTGCAAAAGCTCGGC 60.319 50.0 0.0 0.0 0.0 5.54 F
998 5142 0.534203 TTCTTGTTCCCACCAGCGAC 60.534 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 6300 0.604243 TACATGGTTGGTGTCCGTGC 60.604 55.0 0.0 0.0 43.47 5.34 R
2842 7242 0.028902 GCGTTGTTGCGGAAGAAGTT 59.971 50.0 0.0 0.0 0.00 2.66 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
24 25 2.903547 CGGTGCTTGTCAAACCCCG 61.904 63.158 0.00 0.00 0.00 5.73
58 59 5.279910 CCTCTAGGAGAGATAAAAGCCCATG 60.280 48.000 5.03 0.00 45.07 3.66
81 82 0.318955 AACATGTGCAAAAGCTCGGC 60.319 50.000 0.00 0.00 0.00 5.54
84 85 3.660111 GTGCAAAAGCTCGGCGGT 61.660 61.111 7.21 0.00 0.00 5.68
97 98 1.503542 GGCGGTCAAGCACTGATTG 59.496 57.895 0.26 0.26 36.14 2.67
160 161 9.162793 CATTCTTAATCAAAATGATAGTGACGC 57.837 33.333 0.00 0.00 35.76 5.19
184 185 2.615912 GCCATCTCAGCATCCAACTTAC 59.384 50.000 0.00 0.00 0.00 2.34
242 243 2.027837 AGGCCCAGATCATTTGCAAAAC 60.028 45.455 17.19 8.25 0.00 2.43
252 253 2.307934 TTTGCAAAACAAGGCCTCAC 57.692 45.000 10.02 0.00 40.06 3.51
272 273 2.997303 ACGACGCTGTTAATGCACATAA 59.003 40.909 0.00 0.00 0.00 1.90
293 294 1.228429 GTGTGCCTGCCCCAAACTA 60.228 57.895 0.00 0.00 0.00 2.24
300 301 1.549203 CTGCCCCAAACTAGTTGCAT 58.451 50.000 16.12 0.00 35.74 3.96
319 320 5.348418 GCATAATGCGATGAACATACACT 57.652 39.130 0.00 0.00 31.71 3.55
320 321 5.751680 GCATAATGCGATGAACATACACTT 58.248 37.500 0.00 0.00 31.71 3.16
321 322 5.622448 GCATAATGCGATGAACATACACTTG 59.378 40.000 0.00 0.00 31.71 3.16
322 323 6.511605 GCATAATGCGATGAACATACACTTGA 60.512 38.462 0.00 0.00 31.71 3.02
327 328 7.552458 TGCGATGAACATACACTTGATTAAT 57.448 32.000 0.00 0.00 0.00 1.40
339 340 5.716228 ACACTTGATTAATGCCTTTGATGGA 59.284 36.000 0.00 0.00 0.00 3.41
345 346 7.064866 TGATTAATGCCTTTGATGGAGATTCT 58.935 34.615 0.00 0.00 0.00 2.40
350 351 4.471025 TGCCTTTGATGGAGATTCTAGACA 59.529 41.667 0.00 0.00 0.00 3.41
352 353 5.700373 GCCTTTGATGGAGATTCTAGACATC 59.300 44.000 11.51 11.51 38.65 3.06
374 375 9.942850 ACATCGATGTTGTATGGATTGAATATA 57.057 29.630 25.18 0.00 37.90 0.86
389 390 9.394767 GGATTGAATATATGTGGCATATGTGTA 57.605 33.333 7.02 0.00 0.00 2.90
413 414 4.959631 TCGTCGTTTGTCTATGTTGTTC 57.040 40.909 0.00 0.00 0.00 3.18
416 417 4.607557 CGTCGTTTGTCTATGTTGTTCCAC 60.608 45.833 0.00 0.00 0.00 4.02
456 460 9.636879 TTTGACATAATGTTGTTCCATATGTTG 57.363 29.630 1.24 0.00 0.00 3.33
463 3762 6.723298 TGTTGTTCCATATGTTGGTTTTCT 57.277 33.333 1.24 0.00 46.52 2.52
465 3764 7.560368 TGTTGTTCCATATGTTGGTTTTCTTT 58.440 30.769 1.24 0.00 46.52 2.52
466 3765 8.043710 TGTTGTTCCATATGTTGGTTTTCTTTT 58.956 29.630 1.24 0.00 46.52 2.27
468 3767 7.786030 TGTTCCATATGTTGGTTTTCTTTTCA 58.214 30.769 1.24 0.00 46.52 2.69
469 3768 8.428063 TGTTCCATATGTTGGTTTTCTTTTCAT 58.572 29.630 1.24 0.00 46.52 2.57
470 3769 8.711457 GTTCCATATGTTGGTTTTCTTTTCATG 58.289 33.333 1.24 0.00 46.52 3.07
471 3770 6.873076 TCCATATGTTGGTTTTCTTTTCATGC 59.127 34.615 1.24 0.00 46.52 4.06
473 3772 7.388500 CCATATGTTGGTTTTCTTTTCATGCTT 59.612 33.333 1.24 0.00 40.99 3.91
475 3774 6.660887 TGTTGGTTTTCTTTTCATGCTTTC 57.339 33.333 0.00 0.00 0.00 2.62
476 3775 5.290643 TGTTGGTTTTCTTTTCATGCTTTCG 59.709 36.000 0.00 0.00 0.00 3.46
477 3776 4.367450 TGGTTTTCTTTTCATGCTTTCGG 58.633 39.130 0.00 0.00 0.00 4.30
478 3777 4.098654 TGGTTTTCTTTTCATGCTTTCGGA 59.901 37.500 0.00 0.00 0.00 4.55
663 4727 1.001974 GCCGCCCCTTTGAAAAAGAAT 59.998 47.619 1.31 0.00 0.00 2.40
664 4728 2.549992 GCCGCCCCTTTGAAAAAGAATT 60.550 45.455 1.31 0.00 0.00 2.17
665 4729 3.738982 CCGCCCCTTTGAAAAAGAATTT 58.261 40.909 1.31 0.00 42.41 1.82
756 4833 1.624312 TCGCCATTTATATACCGCCCA 59.376 47.619 0.00 0.00 0.00 5.36
846 4926 1.613630 GCACCTCCCCCTCTTCTCA 60.614 63.158 0.00 0.00 0.00 3.27
868 4954 5.604650 TCATCTTCCTCTTCTTCCCCTATTC 59.395 44.000 0.00 0.00 0.00 1.75
998 5142 0.534203 TTCTTGTTCCCACCAGCGAC 60.534 55.000 0.00 0.00 0.00 5.19
1011 5155 1.338105 CCAGCGACCATGTCTTCTTCA 60.338 52.381 0.00 0.00 0.00 3.02
1051 5249 1.420138 GGAAGGTGGTGAAGAAGGTGA 59.580 52.381 0.00 0.00 0.00 4.02
1057 5255 1.079503 GGTGAAGAAGGTGATGTCGC 58.920 55.000 0.00 0.00 0.00 5.19
1059 5257 2.094182 GGTGAAGAAGGTGATGTCGCTA 60.094 50.000 0.00 0.00 0.00 4.26
1065 5263 1.496060 AGGTGATGTCGCTATCCCAA 58.504 50.000 0.00 0.00 0.00 4.12
1066 5264 1.414181 AGGTGATGTCGCTATCCCAAG 59.586 52.381 0.00 0.00 0.00 3.61
1399 5705 3.365767 GCTGAAATGCTGTTCTGTCTTCC 60.366 47.826 8.04 0.00 0.00 3.46
1445 5752 0.764890 CTTCACCCACCAGGACTTCA 59.235 55.000 0.00 0.00 39.89 3.02
1447 5754 0.692756 TCACCCACCAGGACTTCACA 60.693 55.000 0.00 0.00 39.89 3.58
1946 6300 1.443872 GTGCGGTCACCAGTCTACG 60.444 63.158 0.00 0.00 37.24 3.51
2076 6430 2.305607 TATTTGGCAGGGAGGGCGT 61.306 57.895 0.00 0.00 35.84 5.68
2274 6628 3.623703 TGCAGGACTATTACTACGGACA 58.376 45.455 0.00 0.00 0.00 4.02
2362 6716 2.422832 TGATCAACATTGCAGCGCATTA 59.577 40.909 11.47 0.00 38.76 1.90
2367 6721 2.209273 ACATTGCAGCGCATTATCGTA 58.791 42.857 11.47 0.00 38.76 3.43
2442 6804 2.745821 TGTGTAGAGTGCCGTAGTAGTG 59.254 50.000 0.00 0.00 0.00 2.74
2443 6805 1.741706 TGTAGAGTGCCGTAGTAGTGC 59.258 52.381 0.00 0.00 0.00 4.40
2450 6812 2.157085 GTGCCGTAGTAGTGCTGTTTTC 59.843 50.000 0.00 0.00 0.00 2.29
2451 6813 2.036733 TGCCGTAGTAGTGCTGTTTTCT 59.963 45.455 0.00 0.00 0.00 2.52
2454 6816 4.610680 GCCGTAGTAGTGCTGTTTTCTTTG 60.611 45.833 0.00 0.00 0.00 2.77
2455 6817 4.748102 CCGTAGTAGTGCTGTTTTCTTTGA 59.252 41.667 0.00 0.00 0.00 2.69
2536 6908 9.981460 ATGAGGAGGAAGTTAGTAATCATTTTT 57.019 29.630 0.00 0.00 0.00 1.94
2537 6909 9.449719 TGAGGAGGAAGTTAGTAATCATTTTTC 57.550 33.333 0.00 0.00 0.00 2.29
2538 6910 8.494016 AGGAGGAAGTTAGTAATCATTTTTCG 57.506 34.615 0.00 0.00 0.00 3.46
2539 6911 7.553044 AGGAGGAAGTTAGTAATCATTTTTCGG 59.447 37.037 0.00 0.00 0.00 4.30
2540 6912 7.336176 GGAGGAAGTTAGTAATCATTTTTCGGT 59.664 37.037 0.00 0.00 0.00 4.69
2541 6913 8.265165 AGGAAGTTAGTAATCATTTTTCGGTC 57.735 34.615 0.00 0.00 0.00 4.79
2599 6998 6.207417 GGCAAGCAGAGCAAGGATAAATAATA 59.793 38.462 0.00 0.00 0.00 0.98
2603 7002 7.164803 AGCAGAGCAAGGATAAATAATAGGTC 58.835 38.462 0.00 0.00 0.00 3.85
2606 7005 7.329717 CAGAGCAAGGATAAATAATAGGTCGAC 59.670 40.741 7.13 7.13 0.00 4.20
2609 7008 7.604164 AGCAAGGATAAATAATAGGTCGACATG 59.396 37.037 18.91 0.00 0.00 3.21
2610 7009 7.624344 GCAAGGATAAATAATAGGTCGACATGC 60.624 40.741 18.91 4.05 0.00 4.06
2611 7010 7.004555 AGGATAAATAATAGGTCGACATGCA 57.995 36.000 18.91 0.00 0.00 3.96
2613 7012 7.039011 AGGATAAATAATAGGTCGACATGCAGA 60.039 37.037 18.91 0.00 0.00 4.26
2614 7013 7.766278 GGATAAATAATAGGTCGACATGCAGAT 59.234 37.037 18.91 0.00 0.00 2.90
2615 7014 9.155975 GATAAATAATAGGTCGACATGCAGATT 57.844 33.333 18.91 9.39 0.00 2.40
2616 7015 7.807977 AAATAATAGGTCGACATGCAGATTT 57.192 32.000 18.91 12.00 0.00 2.17
2617 7016 7.426929 AATAATAGGTCGACATGCAGATTTC 57.573 36.000 18.91 0.00 0.00 2.17
2618 7017 4.679373 ATAGGTCGACATGCAGATTTCT 57.321 40.909 18.91 3.41 0.00 2.52
2619 7018 5.791336 ATAGGTCGACATGCAGATTTCTA 57.209 39.130 18.91 5.65 0.00 2.10
2620 7019 4.052159 AGGTCGACATGCAGATTTCTAG 57.948 45.455 18.91 0.00 0.00 2.43
2621 7020 3.449018 AGGTCGACATGCAGATTTCTAGT 59.551 43.478 18.91 0.00 0.00 2.57
2622 7021 3.553511 GGTCGACATGCAGATTTCTAGTG 59.446 47.826 18.91 0.00 0.00 2.74
2623 7022 3.000724 GTCGACATGCAGATTTCTAGTGC 59.999 47.826 11.55 0.00 37.73 4.40
2624 7023 3.118992 TCGACATGCAGATTTCTAGTGCT 60.119 43.478 0.00 0.00 38.09 4.40
2625 7024 3.001026 CGACATGCAGATTTCTAGTGCTG 59.999 47.826 0.00 0.00 38.09 4.41
2640 7039 1.836802 TGCTGCTGCATGGTTAATCA 58.163 45.000 14.93 0.00 45.31 2.57
2641 7040 2.380941 TGCTGCTGCATGGTTAATCAT 58.619 42.857 14.93 0.00 45.31 2.45
2705 7104 9.784531 TGAGCCACCAAATTTATTTATTTTTGA 57.215 25.926 0.00 0.00 32.17 2.69
2723 7122 2.573463 TGAAAAAGGAGGATAGCCCCT 58.427 47.619 0.00 0.00 39.77 4.79
2725 7124 2.286935 AAAAGGAGGATAGCCCCTGA 57.713 50.000 7.70 0.00 36.49 3.86
2758 7157 5.465056 TCGAGCGATGCATACAATCAATTTA 59.535 36.000 0.00 0.00 0.00 1.40
2764 7164 9.778993 GCGATGCATACAATCAATTTATTAGAT 57.221 29.630 0.00 0.00 0.00 1.98
2842 7242 5.779529 AAGAAACACCTACGACTAAGTCA 57.220 39.130 0.00 0.00 32.09 3.41
2871 7271 1.758783 GCAACAACGCCTTCAAGAAG 58.241 50.000 2.83 2.83 38.14 2.85
2888 7288 5.941058 TCAAGAAGGAATAAACGCCATTGTA 59.059 36.000 0.00 0.00 0.00 2.41
2889 7289 6.601613 TCAAGAAGGAATAAACGCCATTGTAT 59.398 34.615 0.00 0.00 0.00 2.29
2901 7301 3.120889 CGCCATTGTATCATCGTCATCAC 60.121 47.826 0.00 0.00 0.00 3.06
2928 7395 4.320057 CGACCAAAGAGTAGTAGACAACGT 60.320 45.833 0.00 0.00 0.00 3.99
2940 7407 1.940613 AGACAACGTCTTCAACAAGGC 59.059 47.619 0.00 0.00 40.28 4.35
2946 7413 2.290641 ACGTCTTCAACAAGGCAATGAC 59.709 45.455 0.00 0.00 33.36 3.06
2947 7414 2.290367 CGTCTTCAACAAGGCAATGACA 59.710 45.455 0.00 0.00 33.36 3.58
2951 7418 4.159321 TCTTCAACAAGGCAATGACACAAA 59.841 37.500 0.00 0.00 0.00 2.83
2958 7425 2.884012 AGGCAATGACACAAATTCGTCA 59.116 40.909 7.51 7.51 45.62 4.35
2959 7426 2.979813 GGCAATGACACAAATTCGTCAC 59.020 45.455 7.29 0.00 44.45 3.67
2965 7432 2.287915 GACACAAATTCGTCACTGCTGT 59.712 45.455 0.00 0.00 32.24 4.40
2967 7434 1.002468 ACAAATTCGTCACTGCTGTGC 60.002 47.619 18.11 12.24 43.49 4.57
3026 7493 3.256631 GGACATGAAGCAGTGTTCCAATT 59.743 43.478 0.00 0.00 0.00 2.32
3039 7506 7.414540 GCAGTGTTCCAATTAGTATCTTGAAGG 60.415 40.741 0.00 0.00 0.00 3.46
3050 7517 3.981071 ATCTTGAAGGTGGATCGTTCA 57.019 42.857 0.00 0.00 45.28 3.18
3061 7528 2.223735 TGGATCGTTCAATAGTCGCCTC 60.224 50.000 0.00 0.00 0.00 4.70
3075 7542 2.893398 CCTCCGCCAGTACTCCAC 59.107 66.667 0.00 0.00 0.00 4.02
3076 7543 1.982395 CCTCCGCCAGTACTCCACA 60.982 63.158 0.00 0.00 0.00 4.17
3107 7574 5.068198 CCAAAAGGCACTAGCATATTGATGT 59.932 40.000 0.00 0.00 44.61 3.06
3114 7581 5.106791 GCACTAGCATATTGATGTGATGTCC 60.107 44.000 0.00 0.00 41.58 4.02
3131 7598 1.069775 TCCTCCCACCTTAAACCACC 58.930 55.000 0.00 0.00 0.00 4.61
3143 7610 3.894547 AACCACCGTCATGGCCGTC 62.895 63.158 0.00 0.00 44.33 4.79
3144 7611 4.386951 CCACCGTCATGGCCGTCA 62.387 66.667 0.00 0.00 43.94 4.35
3145 7612 2.815211 CACCGTCATGGCCGTCAG 60.815 66.667 0.00 0.00 43.94 3.51
3146 7613 4.082523 ACCGTCATGGCCGTCAGG 62.083 66.667 0.00 0.84 43.94 3.86
3147 7614 4.082523 CCGTCATGGCCGTCAGGT 62.083 66.667 0.00 0.00 40.50 4.00
3148 7615 2.815211 CGTCATGGCCGTCAGGTG 60.815 66.667 0.00 0.00 40.50 4.00
3149 7616 2.436646 GTCATGGCCGTCAGGTGG 60.437 66.667 0.00 0.00 40.50 4.61
3150 7617 2.606213 TCATGGCCGTCAGGTGGA 60.606 61.111 0.00 0.00 40.50 4.02
3151 7618 2.436646 CATGGCCGTCAGGTGGAC 60.437 66.667 0.00 0.00 43.36 4.02
3158 7625 2.436646 GTCAGGTGGACGCCCATG 60.437 66.667 0.00 0.00 45.68 3.66
3159 7626 2.927856 TCAGGTGGACGCCCATGT 60.928 61.111 0.00 0.00 45.68 3.21
3160 7627 2.436646 CAGGTGGACGCCCATGTC 60.437 66.667 0.00 0.00 45.68 3.06
3161 7628 2.607750 AGGTGGACGCCCATGTCT 60.608 61.111 0.00 0.00 45.68 3.41
3162 7629 2.125106 GGTGGACGCCCATGTCTC 60.125 66.667 0.00 0.00 45.68 3.36
3163 7630 2.662596 GTGGACGCCCATGTCTCA 59.337 61.111 0.00 0.00 45.68 3.27
3164 7631 1.448540 GTGGACGCCCATGTCTCAG 60.449 63.158 0.00 0.00 45.68 3.35
3165 7632 2.512515 GGACGCCCATGTCTCAGC 60.513 66.667 0.00 0.00 38.91 4.26
3170 7637 4.147449 CCCATGTCTCAGCGGCGA 62.147 66.667 12.98 0.00 0.00 5.54
3171 7638 2.125552 CCATGTCTCAGCGGCGAA 60.126 61.111 12.98 0.00 0.00 4.70
3172 7639 2.456119 CCATGTCTCAGCGGCGAAC 61.456 63.158 12.98 0.06 0.00 3.95
3173 7640 1.446792 CATGTCTCAGCGGCGAACT 60.447 57.895 12.98 0.00 0.00 3.01
3174 7641 1.446792 ATGTCTCAGCGGCGAACTG 60.447 57.895 12.98 9.95 36.44 3.16
3175 7642 2.811317 GTCTCAGCGGCGAACTGG 60.811 66.667 12.98 4.00 35.78 4.00
3176 7643 4.742201 TCTCAGCGGCGAACTGGC 62.742 66.667 12.98 0.00 35.78 4.85
3177 7644 4.749310 CTCAGCGGCGAACTGGCT 62.749 66.667 12.98 0.00 42.02 4.75
3193 7660 3.200593 CTGCTGCCGCTCCACATC 61.201 66.667 0.70 0.00 36.97 3.06
3195 7662 4.819761 GCTGCCGCTCCACATCGA 62.820 66.667 0.00 0.00 0.00 3.59
3196 7663 2.107750 CTGCCGCTCCACATCGAT 59.892 61.111 0.00 0.00 0.00 3.59
3197 7664 2.202919 TGCCGCTCCACATCGATG 60.203 61.111 23.68 23.68 0.00 3.84
3198 7665 3.643978 GCCGCTCCACATCGATGC 61.644 66.667 25.11 9.91 0.00 3.91
3199 7666 3.333189 CCGCTCCACATCGATGCG 61.333 66.667 25.11 20.78 45.22 4.73
3201 7668 4.108902 GCTCCACATCGATGCGAA 57.891 55.556 25.11 9.43 39.99 4.70
3202 7669 2.609825 GCTCCACATCGATGCGAAT 58.390 52.632 25.11 2.57 39.99 3.34
3203 7670 0.510359 GCTCCACATCGATGCGAATC 59.490 55.000 25.11 11.10 39.99 2.52
3204 7671 1.856802 CTCCACATCGATGCGAATCA 58.143 50.000 25.11 2.91 39.99 2.57
3205 7672 1.524355 CTCCACATCGATGCGAATCAC 59.476 52.381 25.11 0.00 39.99 3.06
3206 7673 1.134848 TCCACATCGATGCGAATCACA 60.135 47.619 25.11 0.00 39.99 3.58
3207 7674 1.004610 CCACATCGATGCGAATCACAC 60.005 52.381 25.11 0.00 39.99 3.82
3208 7675 1.929169 CACATCGATGCGAATCACACT 59.071 47.619 25.11 0.00 39.99 3.55
3209 7676 2.349580 CACATCGATGCGAATCACACTT 59.650 45.455 25.11 0.00 39.99 3.16
3210 7677 3.002791 ACATCGATGCGAATCACACTTT 58.997 40.909 25.11 0.00 39.99 2.66
3211 7678 3.181517 ACATCGATGCGAATCACACTTTG 60.182 43.478 25.11 0.00 39.99 2.77
3212 7679 1.731709 TCGATGCGAATCACACTTTGG 59.268 47.619 3.80 0.00 31.06 3.28
3213 7680 1.464608 CGATGCGAATCACACTTTGGT 59.535 47.619 3.80 0.00 0.00 3.67
3214 7681 2.670905 CGATGCGAATCACACTTTGGTA 59.329 45.455 3.80 0.00 0.00 3.25
3215 7682 3.309682 CGATGCGAATCACACTTTGGTAT 59.690 43.478 3.80 0.00 0.00 2.73
3216 7683 4.550831 CGATGCGAATCACACTTTGGTATC 60.551 45.833 3.80 0.00 0.00 2.24
3217 7684 3.006940 TGCGAATCACACTTTGGTATCC 58.993 45.455 0.00 0.00 0.00 2.59
3218 7685 3.006940 GCGAATCACACTTTGGTATCCA 58.993 45.455 0.00 0.00 0.00 3.41
3219 7686 3.181510 GCGAATCACACTTTGGTATCCAC 60.182 47.826 0.00 0.00 30.78 4.02
3220 7687 3.374058 CGAATCACACTTTGGTATCCACC 59.626 47.826 0.00 0.00 46.00 4.61
3233 7700 4.608948 GTATCCACCATACCCTTCAGAG 57.391 50.000 0.00 0.00 32.34 3.35
3234 7701 1.204146 TCCACCATACCCTTCAGAGC 58.796 55.000 0.00 0.00 0.00 4.09
3235 7702 0.181350 CCACCATACCCTTCAGAGCC 59.819 60.000 0.00 0.00 0.00 4.70
3236 7703 0.181350 CACCATACCCTTCAGAGCCC 59.819 60.000 0.00 0.00 0.00 5.19
3237 7704 0.988678 ACCATACCCTTCAGAGCCCC 60.989 60.000 0.00 0.00 0.00 5.80
3238 7705 0.695803 CCATACCCTTCAGAGCCCCT 60.696 60.000 0.00 0.00 0.00 4.79
3239 7706 0.471617 CATACCCTTCAGAGCCCCTG 59.528 60.000 0.00 0.00 44.27 4.45
3240 7707 1.348775 ATACCCTTCAGAGCCCCTGC 61.349 60.000 0.00 0.00 42.62 4.85
3251 7718 3.854669 CCCCTGCTCCGGTGCTAG 61.855 72.222 27.24 21.00 0.00 3.42
3252 7719 2.759973 CCCTGCTCCGGTGCTAGA 60.760 66.667 27.24 8.35 0.00 2.43
3253 7720 2.359169 CCCTGCTCCGGTGCTAGAA 61.359 63.158 27.24 7.99 0.00 2.10
3254 7721 1.142748 CCTGCTCCGGTGCTAGAAG 59.857 63.158 27.24 16.56 0.00 2.85
3255 7722 1.520342 CTGCTCCGGTGCTAGAAGC 60.520 63.158 27.24 15.35 42.82 3.86
3256 7723 2.202946 GCTCCGGTGCTAGAAGCC 60.203 66.667 20.97 0.00 41.51 4.35
3257 7724 3.019003 GCTCCGGTGCTAGAAGCCA 62.019 63.158 20.97 0.00 41.51 4.75
3258 7725 1.142748 CTCCGGTGCTAGAAGCCAG 59.857 63.158 0.00 0.00 41.51 4.85
3259 7726 2.512515 CCGGTGCTAGAAGCCAGC 60.513 66.667 0.00 0.00 41.51 4.85
3260 7727 2.887568 CGGTGCTAGAAGCCAGCG 60.888 66.667 5.51 5.51 41.51 5.18
3261 7728 2.512515 GGTGCTAGAAGCCAGCGG 60.513 66.667 0.00 0.00 41.51 5.52
3262 7729 2.512515 GTGCTAGAAGCCAGCGGG 60.513 66.667 0.00 0.00 41.51 6.13
3263 7730 3.785859 TGCTAGAAGCCAGCGGGG 61.786 66.667 4.64 0.00 41.51 5.73
3264 7731 3.470888 GCTAGAAGCCAGCGGGGA 61.471 66.667 4.64 0.00 40.01 4.81
3265 7732 3.031417 GCTAGAAGCCAGCGGGGAA 62.031 63.158 4.64 0.00 40.01 3.97
3266 7733 1.153349 CTAGAAGCCAGCGGGGAAC 60.153 63.158 4.64 0.00 40.01 3.62
3281 7748 2.636768 GGAACCATTAGTGTGCTTGC 57.363 50.000 0.00 0.00 0.00 4.01
3282 7749 1.135689 GGAACCATTAGTGTGCTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
3283 7750 0.240945 AACCATTAGTGTGCTTGCGC 59.759 50.000 0.00 0.00 0.00 6.09
3284 7751 0.888736 ACCATTAGTGTGCTTGCGCA 60.889 50.000 5.66 5.66 45.60 6.09
3301 7768 2.184385 GCATCAATGCGAAACTCTGG 57.816 50.000 0.00 0.00 44.67 3.86
3302 7769 1.796617 GCATCAATGCGAAACTCTGGC 60.797 52.381 0.00 0.00 44.67 4.85
3303 7770 0.729116 ATCAATGCGAAACTCTGGCG 59.271 50.000 0.00 0.00 0.00 5.69
3307 7774 2.738521 GCGAAACTCTGGCGCTGA 60.739 61.111 7.64 5.34 46.53 4.26
3308 7775 3.016474 GCGAAACTCTGGCGCTGAC 62.016 63.158 7.64 0.00 46.53 3.51
3309 7776 1.664649 CGAAACTCTGGCGCTGACA 60.665 57.895 7.64 0.00 0.00 3.58
3310 7777 1.862806 GAAACTCTGGCGCTGACAC 59.137 57.895 7.64 0.00 0.00 3.67
3311 7778 1.891060 GAAACTCTGGCGCTGACACG 61.891 60.000 7.64 0.00 0.00 4.49
3312 7779 2.644555 AAACTCTGGCGCTGACACGT 62.645 55.000 7.64 0.00 34.88 4.49
3313 7780 2.807045 CTCTGGCGCTGACACGTC 60.807 66.667 7.64 0.00 38.39 4.34
3314 7781 3.558099 CTCTGGCGCTGACACGTCA 62.558 63.158 7.64 0.00 46.99 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.589803 GGTTTGACAAGCACCGTAGT 58.410 50.000 4.34 0.00 0.00 2.73
3 4 0.872388 GGGTTTGACAAGCACCGTAG 59.128 55.000 4.34 0.00 31.46 3.51
5 6 1.826487 GGGGTTTGACAAGCACCGT 60.826 57.895 7.64 0.00 31.46 4.83
7 8 3.039134 CGGGGTTTGACAAGCACC 58.961 61.111 13.05 13.05 29.07 5.01
24 25 2.289569 CTCTCCTAGAGGGCAATCATGC 60.290 54.545 0.00 0.00 41.64 4.06
81 82 3.261580 TGTATCAATCAGTGCTTGACCG 58.738 45.455 11.41 0.00 38.99 4.79
84 85 6.882610 AAAGTTGTATCAATCAGTGCTTGA 57.117 33.333 11.56 11.56 40.85 3.02
97 98 3.189618 CCTCGGGGGTAAAGTTGTATC 57.810 52.381 0.00 0.00 0.00 2.24
160 161 2.281345 GGATGCTGAGATGGCCGG 60.281 66.667 0.00 0.00 0.00 6.13
184 185 5.104109 TCCATCTCCCCCTTATGTTTAACTG 60.104 44.000 0.00 0.00 0.00 3.16
228 229 3.667360 AGGCCTTGTTTTGCAAATGATC 58.333 40.909 13.65 5.14 36.53 2.92
242 243 3.114616 CAGCGTCGTGAGGCCTTG 61.115 66.667 6.77 0.00 42.66 3.61
252 253 3.649870 TTATGTGCATTAACAGCGTCG 57.350 42.857 0.00 0.00 32.52 5.12
272 273 3.465218 TTTGGGGCAGGCACACCAT 62.465 57.895 0.00 0.00 39.06 3.55
283 284 3.737972 GCATTATGCAACTAGTTTGGGGC 60.738 47.826 12.80 7.05 44.26 5.80
293 294 4.906065 ATGTTCATCGCATTATGCAACT 57.094 36.364 17.75 0.00 45.36 3.16
300 301 7.552458 AATCAAGTGTATGTTCATCGCATTA 57.448 32.000 0.00 0.00 0.00 1.90
316 317 6.095860 TCTCCATCAAAGGCATTAATCAAGTG 59.904 38.462 0.00 0.00 0.00 3.16
317 318 6.189859 TCTCCATCAAAGGCATTAATCAAGT 58.810 36.000 0.00 0.00 0.00 3.16
318 319 6.704289 TCTCCATCAAAGGCATTAATCAAG 57.296 37.500 0.00 0.00 0.00 3.02
319 320 7.562454 AGAATCTCCATCAAAGGCATTAATCAA 59.438 33.333 0.00 0.00 0.00 2.57
320 321 7.064866 AGAATCTCCATCAAAGGCATTAATCA 58.935 34.615 0.00 0.00 0.00 2.57
321 322 7.521871 AGAATCTCCATCAAAGGCATTAATC 57.478 36.000 0.00 0.00 0.00 1.75
322 323 8.443176 TCTAGAATCTCCATCAAAGGCATTAAT 58.557 33.333 0.00 0.00 0.00 1.40
327 328 4.471025 TGTCTAGAATCTCCATCAAAGGCA 59.529 41.667 0.00 0.00 0.00 4.75
339 340 7.231519 TCCATACAACATCGATGTCTAGAATCT 59.768 37.037 30.06 10.29 40.80 2.40
345 346 7.049799 TCAATCCATACAACATCGATGTCTA 57.950 36.000 30.06 21.39 40.80 2.59
352 353 9.977762 CACATATATTCAATCCATACAACATCG 57.022 33.333 0.00 0.00 0.00 3.84
374 375 4.211164 CGACGAAATACACATATGCCACAT 59.789 41.667 1.58 0.00 0.00 3.21
389 390 5.917541 ACAACATAGACAAACGACGAAAT 57.082 34.783 0.00 0.00 0.00 2.17
456 460 4.616953 TCCGAAAGCATGAAAAGAAAACC 58.383 39.130 0.00 0.00 0.00 3.27
463 3762 2.604373 CGCAACTCCGAAAGCATGAAAA 60.604 45.455 0.00 0.00 0.00 2.29
465 3764 0.516877 CGCAACTCCGAAAGCATGAA 59.483 50.000 0.00 0.00 0.00 2.57
466 3765 0.320334 TCGCAACTCCGAAAGCATGA 60.320 50.000 0.00 0.00 33.77 3.07
468 3767 1.298859 GGTCGCAACTCCGAAAGCAT 61.299 55.000 0.00 0.00 39.17 3.79
469 3768 1.959226 GGTCGCAACTCCGAAAGCA 60.959 57.895 0.00 0.00 39.17 3.91
470 3769 1.503818 TTGGTCGCAACTCCGAAAGC 61.504 55.000 0.00 0.00 39.17 3.51
471 3770 1.156736 ATTGGTCGCAACTCCGAAAG 58.843 50.000 0.00 0.00 39.17 2.62
473 3772 0.871722 CAATTGGTCGCAACTCCGAA 59.128 50.000 0.00 0.00 39.17 4.30
475 3774 0.591170 AACAATTGGTCGCAACTCCG 59.409 50.000 10.83 0.00 0.00 4.63
476 3775 3.561503 GTTAACAATTGGTCGCAACTCC 58.438 45.455 10.83 0.00 0.00 3.85
477 3776 3.252458 AGGTTAACAATTGGTCGCAACTC 59.748 43.478 10.83 0.12 0.00 3.01
478 3777 3.219281 AGGTTAACAATTGGTCGCAACT 58.781 40.909 10.83 0.00 0.00 3.16
528 3869 6.204882 GCCCCACGATAATTTATATGGCTATC 59.795 42.308 11.36 0.00 0.00 2.08
645 4699 8.541133 TTATAAAATTCTTTTTCAAAGGGGCG 57.459 30.769 0.00 0.00 36.47 6.13
669 4733 7.490725 GCTGCTTTCTTTCTTTCTTTCTTTCTT 59.509 33.333 0.00 0.00 0.00 2.52
670 4734 6.977502 GCTGCTTTCTTTCTTTCTTTCTTTCT 59.022 34.615 0.00 0.00 0.00 2.52
671 4735 6.199908 GGCTGCTTTCTTTCTTTCTTTCTTTC 59.800 38.462 0.00 0.00 0.00 2.62
672 4736 6.045318 GGCTGCTTTCTTTCTTTCTTTCTTT 58.955 36.000 0.00 0.00 0.00 2.52
673 4737 5.595885 GGCTGCTTTCTTTCTTTCTTTCTT 58.404 37.500 0.00 0.00 0.00 2.52
674 4738 4.261363 CGGCTGCTTTCTTTCTTTCTTTCT 60.261 41.667 0.00 0.00 0.00 2.52
675 4739 3.977579 CGGCTGCTTTCTTTCTTTCTTTC 59.022 43.478 0.00 0.00 0.00 2.62
679 4743 1.691127 GCGGCTGCTTTCTTTCTTTC 58.309 50.000 11.21 0.00 38.39 2.62
715 4791 1.145759 CGGGATGATGGTCGTTGACG 61.146 60.000 0.00 0.00 41.45 4.35
756 4833 0.921166 TGCTGGATCATGGTGGATGT 59.079 50.000 0.00 0.00 33.29 3.06
806 4886 1.813513 CCTCAGCATCTTTGGTTCGT 58.186 50.000 0.00 0.00 0.00 3.85
807 4887 0.449388 GCCTCAGCATCTTTGGTTCG 59.551 55.000 0.00 0.00 39.53 3.95
808 4888 1.538047 TGCCTCAGCATCTTTGGTTC 58.462 50.000 0.00 0.00 46.52 3.62
809 4889 3.751767 TGCCTCAGCATCTTTGGTT 57.248 47.368 0.00 0.00 46.52 3.67
846 4926 5.542743 TGAATAGGGGAAGAAGAGGAAGAT 58.457 41.667 0.00 0.00 0.00 2.40
998 5142 2.881074 ACGACGATGAAGAAGACATGG 58.119 47.619 0.00 0.00 0.00 3.66
1029 5227 2.136026 ACCTTCTTCACCACCTTCCTT 58.864 47.619 0.00 0.00 0.00 3.36
1051 5249 1.069765 CGGCTTGGGATAGCGACAT 59.930 57.895 0.00 0.00 42.15 3.06
1445 5752 4.603535 GGTGCCCTTGTGCCCTGT 62.604 66.667 0.00 0.00 0.00 4.00
1447 5754 3.590466 GATGGTGCCCTTGTGCCCT 62.590 63.158 0.00 0.00 0.00 5.19
1486 5793 2.307686 ACAAATTGGATGGGTAGGTCGT 59.692 45.455 0.00 0.00 0.00 4.34
1946 6300 0.604243 TACATGGTTGGTGTCCGTGC 60.604 55.000 0.00 0.00 43.47 5.34
1971 6325 0.604578 CCCTGGTTGCATTGTGAAGG 59.395 55.000 0.00 0.00 0.00 3.46
2119 6473 4.662961 CACACGCTGAGCCCGTCA 62.663 66.667 0.00 0.00 36.69 4.35
2155 6509 2.048503 GCCAGCACGAACCGTAGT 60.049 61.111 0.00 0.00 38.32 2.73
2274 6628 1.668151 GCCTTCTCGAAGCCGTTGT 60.668 57.895 1.13 0.00 37.11 3.32
2337 6691 2.732912 GCGCTGCAATGTTGATCATCAA 60.733 45.455 10.41 0.00 35.48 2.57
2351 6705 1.646189 TTGTACGATAATGCGCTGCA 58.354 45.000 9.73 5.73 44.86 4.41
2362 6716 4.658063 TCCTTCCCAATGTTTTGTACGAT 58.342 39.130 0.00 0.00 0.00 3.73
2367 6721 3.390967 CCCTTTCCTTCCCAATGTTTTGT 59.609 43.478 0.00 0.00 0.00 2.83
2442 6804 6.908870 AAGGAACAAATCAAAGAAAACAGC 57.091 33.333 0.00 0.00 0.00 4.40
2550 6922 7.653311 GCCCAAATCTATGATGAAACAATTACC 59.347 37.037 0.00 0.00 0.00 2.85
2551 6923 8.196771 TGCCCAAATCTATGATGAAACAATTAC 58.803 33.333 0.00 0.00 0.00 1.89
2552 6924 8.303780 TGCCCAAATCTATGATGAAACAATTA 57.696 30.769 0.00 0.00 0.00 1.40
2599 6998 3.449018 ACTAGAAATCTGCATGTCGACCT 59.551 43.478 14.12 0.00 0.00 3.85
2603 7002 3.001026 CAGCACTAGAAATCTGCATGTCG 59.999 47.826 0.00 0.00 33.06 4.35
2622 7021 3.447918 AATGATTAACCATGCAGCAGC 57.552 42.857 0.00 0.00 42.57 5.25
2623 7022 5.001237 TGAAATGATTAACCATGCAGCAG 57.999 39.130 0.00 0.00 0.00 4.24
2624 7023 4.705991 TCTGAAATGATTAACCATGCAGCA 59.294 37.500 0.00 0.00 33.48 4.41
2625 7024 5.252969 TCTGAAATGATTAACCATGCAGC 57.747 39.130 7.69 0.00 33.48 5.25
2626 7025 7.977293 TCAAATCTGAAATGATTAACCATGCAG 59.023 33.333 6.60 6.60 35.82 4.41
2627 7026 7.838884 TCAAATCTGAAATGATTAACCATGCA 58.161 30.769 0.00 0.00 35.82 3.96
2628 7027 8.598075 GTTCAAATCTGAAATGATTAACCATGC 58.402 33.333 0.00 0.00 43.18 4.06
2629 7028 9.642327 TGTTCAAATCTGAAATGATTAACCATG 57.358 29.630 0.00 0.00 43.18 3.66
2630 7029 9.865321 CTGTTCAAATCTGAAATGATTAACCAT 57.135 29.630 0.00 0.00 43.18 3.55
2631 7030 8.306038 CCTGTTCAAATCTGAAATGATTAACCA 58.694 33.333 0.00 0.00 43.18 3.67
2632 7031 8.306761 ACCTGTTCAAATCTGAAATGATTAACC 58.693 33.333 0.00 0.00 43.18 2.85
2633 7032 9.132521 CACCTGTTCAAATCTGAAATGATTAAC 57.867 33.333 0.00 0.00 43.18 2.01
2634 7033 9.076781 TCACCTGTTCAAATCTGAAATGATTAA 57.923 29.630 0.00 0.00 43.18 1.40
2635 7034 8.634335 TCACCTGTTCAAATCTGAAATGATTA 57.366 30.769 0.00 0.00 43.18 1.75
2636 7035 7.528996 TCACCTGTTCAAATCTGAAATGATT 57.471 32.000 0.00 0.00 43.18 2.57
2637 7036 7.528996 TTCACCTGTTCAAATCTGAAATGAT 57.471 32.000 0.00 0.00 43.18 2.45
2638 7037 6.957920 TTCACCTGTTCAAATCTGAAATGA 57.042 33.333 0.00 0.00 43.18 2.57
2639 7038 8.597662 ATTTTCACCTGTTCAAATCTGAAATG 57.402 30.769 0.00 0.00 43.18 2.32
2694 7093 9.890629 GGCTATCCTCCTTTTTCAAAAATAAAT 57.109 29.630 0.00 0.00 0.00 1.40
2695 7094 8.318412 GGGCTATCCTCCTTTTTCAAAAATAAA 58.682 33.333 0.00 0.00 0.00 1.40
2696 7095 7.093068 GGGGCTATCCTCCTTTTTCAAAAATAA 60.093 37.037 0.00 0.00 35.33 1.40
2698 7097 5.189736 GGGGCTATCCTCCTTTTTCAAAAAT 59.810 40.000 0.00 0.00 35.33 1.82
2704 7103 2.509964 TCAGGGGCTATCCTCCTTTTTC 59.490 50.000 0.00 0.00 34.31 2.29
2705 7104 2.242452 GTCAGGGGCTATCCTCCTTTTT 59.758 50.000 0.00 0.00 34.31 1.94
2723 7122 1.387295 ATCGCTCGATGCAGAGGTCA 61.387 55.000 3.76 0.00 43.06 4.02
2725 7124 1.067084 CATCGCTCGATGCAGAGGT 59.933 57.895 17.66 0.00 44.27 3.85
2764 7164 6.039941 GCCTTTAGTCTCTACTCTGCTCAATA 59.960 42.308 0.00 0.00 37.15 1.90
2766 7166 4.158764 GCCTTTAGTCTCTACTCTGCTCAA 59.841 45.833 0.00 0.00 37.15 3.02
2768 7168 3.697045 TGCCTTTAGTCTCTACTCTGCTC 59.303 47.826 0.00 0.00 37.15 4.26
2842 7242 0.028902 GCGTTGTTGCGGAAGAAGTT 59.971 50.000 0.00 0.00 0.00 2.66
2871 7271 5.049680 ACGATGATACAATGGCGTTTATTCC 60.050 40.000 0.00 0.00 0.00 3.01
2901 7301 3.005554 TCTACTACTCTTTGGTCGGACG 58.994 50.000 1.43 0.00 0.00 4.79
2928 7395 3.286353 TGTGTCATTGCCTTGTTGAAGA 58.714 40.909 0.00 0.00 0.00 2.87
2947 7414 4.205879 GGCACAGCAGTGACGAATTTGT 62.206 50.000 14.14 0.00 45.35 2.83
2951 7418 3.972227 GGCACAGCAGTGACGAAT 58.028 55.556 14.14 0.00 45.35 3.34
2958 7425 2.127232 GTTGGTTGGGCACAGCAGT 61.127 57.895 4.80 0.00 0.00 4.40
2959 7426 1.674764 TTGTTGGTTGGGCACAGCAG 61.675 55.000 4.80 0.00 0.00 4.24
2965 7432 1.698506 CTACCTTTGTTGGTTGGGCA 58.301 50.000 0.00 0.00 41.22 5.36
3007 7474 5.633830 ACTAATTGGAACACTGCTTCATG 57.366 39.130 0.00 0.00 39.29 3.07
3026 7493 5.655090 TGAACGATCCACCTTCAAGATACTA 59.345 40.000 0.00 0.00 0.00 1.82
3039 7506 1.859080 GGCGACTATTGAACGATCCAC 59.141 52.381 0.00 0.00 0.00 4.02
3061 7528 2.264794 GGTGTGGAGTACTGGCGG 59.735 66.667 0.00 0.00 0.00 6.13
3107 7574 2.307686 GGTTTAAGGTGGGAGGACATCA 59.692 50.000 0.00 0.00 0.00 3.07
3114 7581 0.399075 ACGGTGGTTTAAGGTGGGAG 59.601 55.000 0.00 0.00 0.00 4.30
3131 7598 2.815211 CACCTGACGGCCATGACG 60.815 66.667 2.24 8.00 41.40 4.35
3148 7615 2.512515 GCTGAGACATGGGCGTCC 60.513 66.667 0.00 0.00 36.52 4.79
3149 7616 2.887568 CGCTGAGACATGGGCGTC 60.888 66.667 0.00 0.00 42.23 5.19
3150 7617 4.457496 CCGCTGAGACATGGGCGT 62.457 66.667 14.33 0.00 45.11 5.68
3153 7620 3.664025 TTCGCCGCTGAGACATGGG 62.664 63.158 0.00 0.00 0.00 4.00
3154 7621 2.125552 TTCGCCGCTGAGACATGG 60.126 61.111 0.00 0.00 0.00 3.66
3155 7622 1.446792 AGTTCGCCGCTGAGACATG 60.447 57.895 0.00 0.00 0.00 3.21
3156 7623 1.446792 CAGTTCGCCGCTGAGACAT 60.447 57.895 0.00 0.00 36.12 3.06
3157 7624 2.049156 CAGTTCGCCGCTGAGACA 60.049 61.111 0.00 0.00 36.12 3.41
3158 7625 2.811317 CCAGTTCGCCGCTGAGAC 60.811 66.667 0.00 0.00 36.12 3.36
3159 7626 4.742201 GCCAGTTCGCCGCTGAGA 62.742 66.667 0.00 0.00 36.12 3.27
3160 7627 4.749310 AGCCAGTTCGCCGCTGAG 62.749 66.667 0.00 0.00 36.12 3.35
3178 7645 4.819761 TCGATGTGGAGCGGCAGC 62.820 66.667 0.00 0.00 45.58 5.25
3179 7646 2.107750 ATCGATGTGGAGCGGCAG 59.892 61.111 1.45 0.00 0.00 4.85
3180 7647 2.202919 CATCGATGTGGAGCGGCA 60.203 61.111 17.50 0.00 0.00 5.69
3181 7648 3.643978 GCATCGATGTGGAGCGGC 61.644 66.667 25.47 5.81 0.00 6.53
3182 7649 3.333189 CGCATCGATGTGGAGCGG 61.333 66.667 27.52 6.59 44.20 5.52
3184 7651 0.510359 GATTCGCATCGATGTGGAGC 59.490 55.000 32.37 26.18 38.75 4.70
3185 7652 1.524355 GTGATTCGCATCGATGTGGAG 59.476 52.381 32.37 18.74 38.75 3.86
3186 7653 1.134848 TGTGATTCGCATCGATGTGGA 60.135 47.619 32.37 27.56 38.75 4.02
3187 7654 1.004610 GTGTGATTCGCATCGATGTGG 60.005 52.381 32.37 21.64 38.75 4.17
3188 7655 1.929169 AGTGTGATTCGCATCGATGTG 59.071 47.619 28.90 28.90 39.55 3.21
3189 7656 2.299993 AGTGTGATTCGCATCGATGT 57.700 45.000 25.47 6.61 35.23 3.06
3190 7657 3.348309 CAAAGTGTGATTCGCATCGATG 58.652 45.455 21.27 21.27 35.23 3.84
3191 7658 2.352651 CCAAAGTGTGATTCGCATCGAT 59.647 45.455 2.78 0.00 35.23 3.59
3192 7659 1.731709 CCAAAGTGTGATTCGCATCGA 59.268 47.619 2.78 0.00 31.08 3.59
3193 7660 1.464608 ACCAAAGTGTGATTCGCATCG 59.535 47.619 2.78 0.00 31.08 3.84
3194 7661 4.260784 GGATACCAAAGTGTGATTCGCATC 60.261 45.833 2.78 0.00 0.00 3.91
3195 7662 3.627577 GGATACCAAAGTGTGATTCGCAT 59.372 43.478 2.78 0.00 0.00 4.73
3196 7663 3.006940 GGATACCAAAGTGTGATTCGCA 58.993 45.455 0.00 0.00 0.00 5.10
3197 7664 3.006940 TGGATACCAAAGTGTGATTCGC 58.993 45.455 0.00 0.00 0.00 4.70
3198 7665 3.374058 GGTGGATACCAAAGTGTGATTCG 59.626 47.826 0.00 0.00 46.71 3.34
3199 7666 4.965119 GGTGGATACCAAAGTGTGATTC 57.035 45.455 0.00 0.00 46.71 2.52
3212 7679 3.244249 GCTCTGAAGGGTATGGTGGATAC 60.244 52.174 0.00 0.00 36.87 2.24
3213 7680 2.972713 GCTCTGAAGGGTATGGTGGATA 59.027 50.000 0.00 0.00 0.00 2.59
3214 7681 1.771255 GCTCTGAAGGGTATGGTGGAT 59.229 52.381 0.00 0.00 0.00 3.41
3215 7682 1.204146 GCTCTGAAGGGTATGGTGGA 58.796 55.000 0.00 0.00 0.00 4.02
3216 7683 0.181350 GGCTCTGAAGGGTATGGTGG 59.819 60.000 0.00 0.00 0.00 4.61
3217 7684 0.181350 GGGCTCTGAAGGGTATGGTG 59.819 60.000 0.00 0.00 0.00 4.17
3218 7685 0.988678 GGGGCTCTGAAGGGTATGGT 60.989 60.000 0.00 0.00 0.00 3.55
3219 7686 0.695803 AGGGGCTCTGAAGGGTATGG 60.696 60.000 0.00 0.00 0.00 2.74
3220 7687 0.471617 CAGGGGCTCTGAAGGGTATG 59.528 60.000 9.31 0.00 46.18 2.39
3221 7688 1.348775 GCAGGGGCTCTGAAGGGTAT 61.349 60.000 20.97 0.00 46.18 2.73
3222 7689 1.995626 GCAGGGGCTCTGAAGGGTA 60.996 63.158 20.97 0.00 46.18 3.69
3223 7690 3.334054 GCAGGGGCTCTGAAGGGT 61.334 66.667 20.97 0.00 46.18 4.34
3234 7701 3.854669 CTAGCACCGGAGCAGGGG 61.855 72.222 26.04 8.60 37.86 4.79
3235 7702 2.303549 CTTCTAGCACCGGAGCAGGG 62.304 65.000 26.04 14.36 36.85 4.45
3236 7703 1.142748 CTTCTAGCACCGGAGCAGG 59.857 63.158 26.04 16.77 36.85 4.85
3237 7704 1.520342 GCTTCTAGCACCGGAGCAG 60.520 63.158 26.04 19.17 41.89 4.24
3238 7705 2.579201 GCTTCTAGCACCGGAGCA 59.421 61.111 26.04 10.83 41.89 4.26
3239 7706 2.202946 GGCTTCTAGCACCGGAGC 60.203 66.667 16.88 16.88 44.75 4.70
3240 7707 1.142748 CTGGCTTCTAGCACCGGAG 59.857 63.158 9.46 0.00 44.75 4.63
3241 7708 3.019003 GCTGGCTTCTAGCACCGGA 62.019 63.158 9.46 0.00 44.75 5.14
3242 7709 2.512515 GCTGGCTTCTAGCACCGG 60.513 66.667 0.00 0.00 44.75 5.28
3243 7710 2.887568 CGCTGGCTTCTAGCACCG 60.888 66.667 0.67 0.00 44.75 4.94
3244 7711 2.512515 CCGCTGGCTTCTAGCACC 60.513 66.667 0.67 0.00 44.75 5.01
3245 7712 2.512515 CCCGCTGGCTTCTAGCAC 60.513 66.667 0.67 0.00 44.75 4.40
3246 7713 3.785859 CCCCGCTGGCTTCTAGCA 61.786 66.667 0.67 0.00 44.75 3.49
3247 7714 3.031417 TTCCCCGCTGGCTTCTAGC 62.031 63.158 0.00 0.00 41.46 3.42
3248 7715 1.153349 GTTCCCCGCTGGCTTCTAG 60.153 63.158 0.00 0.00 0.00 2.43
3249 7716 2.666098 GGTTCCCCGCTGGCTTCTA 61.666 63.158 0.00 0.00 0.00 2.10
3250 7717 4.035102 GGTTCCCCGCTGGCTTCT 62.035 66.667 0.00 0.00 0.00 2.85
3251 7718 3.645268 ATGGTTCCCCGCTGGCTTC 62.645 63.158 0.00 0.00 0.00 3.86
3252 7719 1.858739 TAATGGTTCCCCGCTGGCTT 61.859 55.000 0.00 0.00 0.00 4.35
3253 7720 2.270874 CTAATGGTTCCCCGCTGGCT 62.271 60.000 0.00 0.00 0.00 4.75
3254 7721 1.823899 CTAATGGTTCCCCGCTGGC 60.824 63.158 0.00 0.00 0.00 4.85
3255 7722 0.748005 CACTAATGGTTCCCCGCTGG 60.748 60.000 0.00 0.00 0.00 4.85
3256 7723 0.035439 ACACTAATGGTTCCCCGCTG 60.035 55.000 0.00 0.00 0.00 5.18
3257 7724 0.035439 CACACTAATGGTTCCCCGCT 60.035 55.000 0.00 0.00 0.00 5.52
3258 7725 1.654023 GCACACTAATGGTTCCCCGC 61.654 60.000 0.00 0.00 0.00 6.13
3259 7726 0.035439 AGCACACTAATGGTTCCCCG 60.035 55.000 0.00 0.00 0.00 5.73
3260 7727 1.818674 CAAGCACACTAATGGTTCCCC 59.181 52.381 0.00 0.00 38.21 4.81
3261 7728 1.202348 GCAAGCACACTAATGGTTCCC 59.798 52.381 0.00 0.00 38.21 3.97
3262 7729 1.135689 CGCAAGCACACTAATGGTTCC 60.136 52.381 0.00 0.00 38.21 3.62
3263 7730 2.247311 CGCAAGCACACTAATGGTTC 57.753 50.000 0.00 0.00 38.21 3.62
3283 7750 1.530441 CGCCAGAGTTTCGCATTGATG 60.530 52.381 0.00 0.00 0.00 3.07
3284 7751 0.729116 CGCCAGAGTTTCGCATTGAT 59.271 50.000 0.00 0.00 0.00 2.57
3285 7752 2.161831 CGCCAGAGTTTCGCATTGA 58.838 52.632 0.00 0.00 0.00 2.57
3286 7753 4.751539 CGCCAGAGTTTCGCATTG 57.248 55.556 0.00 0.00 0.00 2.82
3291 7758 1.664649 TGTCAGCGCCAGAGTTTCG 60.665 57.895 2.29 0.00 0.00 3.46
3292 7759 1.862806 GTGTCAGCGCCAGAGTTTC 59.137 57.895 2.29 0.00 0.00 2.78
3293 7760 1.956170 CGTGTCAGCGCCAGAGTTT 60.956 57.895 2.29 0.00 0.00 2.66
3294 7761 2.356313 CGTGTCAGCGCCAGAGTT 60.356 61.111 2.29 0.00 0.00 3.01
3295 7762 3.559657 GACGTGTCAGCGCCAGAGT 62.560 63.158 2.29 0.00 34.88 3.24
3296 7763 2.807045 GACGTGTCAGCGCCAGAG 60.807 66.667 2.29 0.00 34.88 3.35
3297 7764 3.601685 TGACGTGTCAGCGCCAGA 61.602 61.111 2.29 0.00 34.14 3.86


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

AutoCloner maintained by Alex Coulton.