Multiple sequence alignment - TraesCS7D01G046500

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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 TraesCS7D01G046500 chr7D 100.000 3188 0 0 1 3188 24022236 24019049 0.000000e+00 5888.0
1 TraesCS7D01G046500 chr7D 92.232 2034 119 26 667 2679 24119148 24117133 0.000000e+00 2844.0
2 TraesCS7D01G046500 chr7D 84.634 1230 175 11 975 2192 24326413 24327640 0.000000e+00 1212.0
3 TraesCS7D01G046500 chr7D 92.868 631 39 4 34 658 24319073 24319703 0.000000e+00 911.0
4 TraesCS7D01G046500 chr7D 80.309 259 33 13 718 974 24325920 24326162 2.530000e-41 180.0
5 TraesCS7D01G046500 chr7D 93.694 111 7 0 356 466 24180212 24180322 1.970000e-37 167.0
6 TraesCS7D01G046500 chr4A 91.166 1664 132 10 975 2625 707674783 707676444 0.000000e+00 2244.0
7 TraesCS7D01G046500 chr4A 88.335 1886 183 29 725 2579 707487283 707489162 0.000000e+00 2230.0
8 TraesCS7D01G046500 chr4A 90.986 1664 135 10 975 2625 707702242 707703903 0.000000e+00 2228.0
9 TraesCS7D01G046500 chr4A 88.804 1706 170 15 892 2582 706089895 706088196 0.000000e+00 2073.0
10 TraesCS7D01G046500 chr4A 88.648 1709 169 16 892 2582 705953919 705952218 0.000000e+00 2058.0
11 TraesCS7D01G046500 chr4A 82.420 1314 199 18 998 2280 707305504 707304192 0.000000e+00 1118.0
12 TraesCS7D01G046500 chr4A 85.737 631 74 10 34 658 705882186 705881566 0.000000e+00 652.0
13 TraesCS7D01G046500 chr4A 85.873 630 70 10 34 658 707691084 707691699 0.000000e+00 652.0
14 TraesCS7D01G046500 chr4A 85.737 631 73 11 34 658 707395659 707395040 0.000000e+00 651.0
15 TraesCS7D01G046500 chr4A 85.714 630 71 10 34 658 707663379 707663994 0.000000e+00 647.0
16 TraesCS7D01G046500 chr4A 83.861 632 81 10 34 658 705877988 705877371 1.650000e-162 582.0
17 TraesCS7D01G046500 chr4A 83.228 632 85 10 34 658 707391373 707390756 7.720000e-156 560.0
18 TraesCS7D01G046500 chr4A 80.198 404 53 13 2713 3112 707494950 707495330 8.710000e-71 278.0
19 TraesCS7D01G046500 chr4A 95.918 98 3 1 743 840 705954098 705954002 1.180000e-34 158.0
20 TraesCS7D01G046500 chr4A 95.918 98 3 1 743 840 706090074 706089978 1.180000e-34 158.0
21 TraesCS7D01G046500 chr4A 93.269 104 7 0 744 847 707509715 707509818 1.530000e-33 154.0
22 TraesCS7D01G046500 chr4A 92.929 99 7 0 750 848 707305617 707305519 9.220000e-31 145.0
23 TraesCS7D01G046500 chrUn 88.739 1705 172 15 892 2582 220049557 220047859 0.000000e+00 2067.0
24 TraesCS7D01G046500 chrUn 95.918 98 3 1 743 840 220049736 220049640 1.180000e-34 158.0
25 TraesCS7D01G046500 chr6A 75.292 514 81 30 2697 3188 445613894 445614383 1.500000e-48 204.0
26 TraesCS7D01G046500 chr5B 90.000 70 7 0 2830 2899 516456909 516456840 1.220000e-14 91.6
27 TraesCS7D01G046500 chr1A 77.848 158 26 7 2832 2982 446247809 446247964 4.380000e-14 89.8
28 TraesCS7D01G046500 chr6B 88.732 71 6 2 2830 2899 155202054 155202123 5.670000e-13 86.1
29 TraesCS7D01G046500 chr5D 88.571 70 8 0 2830 2899 426450046 426449977 5.670000e-13 86.1
30 TraesCS7D01G046500 chr5D 75.135 185 27 12 2833 3012 393910866 393911036 5.710000e-08 69.4
31 TraesCS7D01G046500 chr6D 78.417 139 20 9 2804 2936 25719225 25719359 7.330000e-12 82.4
32 TraesCS7D01G046500 chr6D 78.689 122 22 4 2864 2982 9390539 9390659 9.480000e-11 78.7
33 TraesCS7D01G046500 chr2A 73.106 264 49 16 2868 3118 758367379 758367633 1.230000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G046500 chr7D 24019049 24022236 3187 True 5888.0 5888 100.0000 1 3188 1 chr7D.!!$R1 3187
1 TraesCS7D01G046500 chr7D 24117133 24119148 2015 True 2844.0 2844 92.2320 667 2679 1 chr7D.!!$R2 2012
2 TraesCS7D01G046500 chr7D 24319073 24319703 630 False 911.0 911 92.8680 34 658 1 chr7D.!!$F2 624
3 TraesCS7D01G046500 chr7D 24325920 24327640 1720 False 696.0 1212 82.4715 718 2192 2 chr7D.!!$F3 1474
4 TraesCS7D01G046500 chr4A 707674783 707676444 1661 False 2244.0 2244 91.1660 975 2625 1 chr4A.!!$F5 1650
5 TraesCS7D01G046500 chr4A 707487283 707489162 1879 False 2230.0 2230 88.3350 725 2579 1 chr4A.!!$F1 1854
6 TraesCS7D01G046500 chr4A 707702242 707703903 1661 False 2228.0 2228 90.9860 975 2625 1 chr4A.!!$F7 1650
7 TraesCS7D01G046500 chr4A 706088196 706090074 1878 True 1115.5 2073 92.3610 743 2582 2 chr4A.!!$R3 1839
8 TraesCS7D01G046500 chr4A 705952218 705954098 1880 True 1108.0 2058 92.2830 743 2582 2 chr4A.!!$R2 1839
9 TraesCS7D01G046500 chr4A 707691084 707691699 615 False 652.0 652 85.8730 34 658 1 chr4A.!!$F6 624
10 TraesCS7D01G046500 chr4A 707663379 707663994 615 False 647.0 647 85.7140 34 658 1 chr4A.!!$F4 624
11 TraesCS7D01G046500 chr4A 707304192 707305617 1425 True 631.5 1118 87.6745 750 2280 2 chr4A.!!$R4 1530
12 TraesCS7D01G046500 chr4A 705877371 705882186 4815 True 617.0 652 84.7990 34 658 2 chr4A.!!$R1 624
13 TraesCS7D01G046500 chr4A 707390756 707395659 4903 True 605.5 651 84.4825 34 658 2 chr4A.!!$R5 624
14 TraesCS7D01G046500 chrUn 220047859 220049736 1877 True 1112.5 2067 92.3285 743 2582 2 chrUn.!!$R1 1839

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
22 23 0.179062 CCTTCGCATTCTCCTCCTGG 60.179 60.0 0.0 0.0 0.00 4.45 F
24 25 0.250234 TTCGCATTCTCCTCCTGGTG 59.750 55.0 0.0 0.0 34.23 4.17 F
1728 3104 0.109086 CGCTGTTCGAGATGGTGTCT 60.109 55.0 0.0 0.0 41.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 3104 1.068588 GGTATCACATACTGCGAGGCA 59.931 52.381 0.0 0.0 36.04 4.75 R
2104 5171 0.549950 CCCCAGTCTTCATCATGGCT 59.450 55.000 0.0 0.0 0.00 4.75 R
3122 6362 1.346395 TGAACGACTAGTGGCATTGGT 59.654 47.619 0.0 0.0 0.00 3.67 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
19 20 0.827368 AGTCCTTCGCATTCTCCTCC 59.173 55.000 0.00 0.00 0.00 4.30
20 21 0.827368 GTCCTTCGCATTCTCCTCCT 59.173 55.000 0.00 0.00 0.00 3.69
21 22 0.826715 TCCTTCGCATTCTCCTCCTG 59.173 55.000 0.00 0.00 0.00 3.86
22 23 0.179062 CCTTCGCATTCTCCTCCTGG 60.179 60.000 0.00 0.00 0.00 4.45
23 24 0.539051 CTTCGCATTCTCCTCCTGGT 59.461 55.000 0.00 0.00 34.23 4.00
24 25 0.250234 TTCGCATTCTCCTCCTGGTG 59.750 55.000 0.00 0.00 34.23 4.17
25 26 0.904865 TCGCATTCTCCTCCTGGTGT 60.905 55.000 0.00 0.00 34.23 4.16
26 27 0.742281 CGCATTCTCCTCCTGGTGTG 60.742 60.000 0.00 0.00 34.23 3.82
27 28 0.326264 GCATTCTCCTCCTGGTGTGT 59.674 55.000 0.00 0.00 34.23 3.72
28 29 1.555075 GCATTCTCCTCCTGGTGTGTA 59.445 52.381 0.00 0.00 34.23 2.90
29 30 2.171448 GCATTCTCCTCCTGGTGTGTAT 59.829 50.000 0.00 0.00 34.23 2.29
30 31 3.388024 GCATTCTCCTCCTGGTGTGTATA 59.612 47.826 0.00 0.00 34.23 1.47
31 32 4.040952 GCATTCTCCTCCTGGTGTGTATAT 59.959 45.833 0.00 0.00 34.23 0.86
32 33 5.246203 GCATTCTCCTCCTGGTGTGTATATA 59.754 44.000 0.00 0.00 34.23 0.86
59 60 5.971763 ACTCAACTGAACTAGGATAGCTTG 58.028 41.667 0.00 0.00 44.39 4.01
129 130 5.104562 CGTACTCCATGTATCATGTACGT 57.895 43.478 16.08 0.00 44.27 3.57
155 156 1.934410 AGTTACAGGCTCCGGTAGTT 58.066 50.000 0.00 0.00 0.00 2.24
156 157 2.254508 AGTTACAGGCTCCGGTAGTTT 58.745 47.619 0.00 0.00 0.00 2.66
181 182 1.067776 GTGACGACGATGGAGAACCTT 60.068 52.381 0.00 0.00 37.04 3.50
191 193 2.348472 TGGAGAACCTTTCCTGATGGT 58.652 47.619 0.00 0.00 37.39 3.55
229 236 7.041721 CCGCTAAATATATACCATGAGCTTCA 58.958 38.462 0.00 0.00 0.00 3.02
278 285 6.210984 TGACTTCTACTCCTTACTTTCTTCCC 59.789 42.308 0.00 0.00 0.00 3.97
304 311 4.688966 GATGATCCCTCGCGGCCC 62.689 72.222 6.13 0.00 0.00 5.80
340 347 1.464997 CTGTTTTGCTTAGTCCGGAGC 59.535 52.381 3.06 5.18 39.33 4.70
398 405 1.048601 TGCCTCGAGGTTCTTCACTT 58.951 50.000 31.43 0.00 37.57 3.16
413 420 3.438216 TCACTTCATGCCCAGAAATCA 57.562 42.857 0.00 0.00 0.00 2.57
490 497 2.229062 TGAGAACTGAACGGACTAGCTG 59.771 50.000 0.00 0.00 0.00 4.24
503 510 0.792640 CTAGCTGTTCCAACGCACTG 59.207 55.000 0.00 0.00 33.20 3.66
587 594 5.264395 CATTTGTAACTCTCCCTTGGGATT 58.736 41.667 9.08 3.71 0.00 3.01
654 662 3.005050 CCGCCCGTCTTCACATATAGTTA 59.995 47.826 0.00 0.00 0.00 2.24
658 666 6.047231 GCCCGTCTTCACATATAGTTAAACT 58.953 40.000 0.00 0.00 0.00 2.66
660 668 7.871463 GCCCGTCTTCACATATAGTTAAACTAT 59.129 37.037 0.00 0.00 43.36 2.12
661 669 9.760077 CCCGTCTTCACATATAGTTAAACTATT 57.240 33.333 0.00 0.00 38.17 1.73
705 713 3.913163 GCCTAGACGAGATATTTACACGC 59.087 47.826 0.00 0.00 0.00 5.34
887 1435 0.250513 ATCCAACTCTCGGGTTCAGC 59.749 55.000 0.00 0.00 0.00 4.26
888 1436 0.832135 TCCAACTCTCGGGTTCAGCT 60.832 55.000 0.00 0.00 0.00 4.24
889 1437 0.895530 CCAACTCTCGGGTTCAGCTA 59.104 55.000 0.00 0.00 0.00 3.32
890 1438 1.482593 CCAACTCTCGGGTTCAGCTAT 59.517 52.381 0.00 0.00 0.00 2.97
894 1442 3.482436 ACTCTCGGGTTCAGCTATCTAG 58.518 50.000 0.00 0.00 0.00 2.43
960 1508 5.063564 ACCTAAAGATCGATCGCTTTTCAAC 59.936 40.000 20.74 0.00 35.98 3.18
977 1784 8.324567 GCTTTTCAACGATCTGATTCTACTTAG 58.675 37.037 0.00 0.00 0.00 2.18
1440 2441 2.047274 ACCGATGTCCGCTTGGTG 60.047 61.111 0.00 0.00 36.84 4.17
1728 3104 0.109086 CGCTGTTCGAGATGGTGTCT 60.109 55.000 0.00 0.00 41.67 3.41
1755 3131 2.100916 GCAGTATGTGATACCGGACACT 59.899 50.000 22.86 14.87 39.31 3.55
2104 5171 1.309876 TCCTGAAGGAGAGGGAGCTA 58.690 55.000 0.00 0.00 39.78 3.32
2216 5412 9.463443 AATTAGAAAGAAGGAATGAAAAACACG 57.537 29.630 0.00 0.00 0.00 4.49
2225 5442 4.562394 GGAATGAAAAACACGTGGCATATG 59.438 41.667 21.57 0.00 0.00 1.78
2241 5459 7.424803 GTGGCATATGTATTCAATAAGTGCAA 58.575 34.615 4.29 0.00 0.00 4.08
2419 5642 4.806640 ATTGTAAATTTGGGTCAGCCAG 57.193 40.909 0.00 0.00 36.17 4.85
2427 5650 0.843309 TGGGTCAGCCAGTTTCTTGA 59.157 50.000 0.00 0.00 36.17 3.02
2429 5652 1.202818 GGGTCAGCCAGTTTCTTGACT 60.203 52.381 0.00 0.00 36.17 3.41
2452 5679 6.703165 ACTGTTCATTTTTGCTCTGAAATTCC 59.297 34.615 0.00 0.00 31.21 3.01
2455 5682 6.653526 TCATTTTTGCTCTGAAATTCCTGA 57.346 33.333 0.00 0.00 0.00 3.86
2528 5765 5.627499 ATTTTGCTCAGTCGATTTGCTTA 57.373 34.783 0.00 0.00 0.00 3.09
2552 5789 1.748493 GCCGAAGCCCATTAATTGTGA 59.252 47.619 0.00 0.00 0.00 3.58
2567 5804 1.661463 TGTGAGATCAAGCCCTCCTT 58.339 50.000 0.00 0.00 0.00 3.36
2579 5816 3.532102 AGCCCTCCTTTCTCTTCCTTTA 58.468 45.455 0.00 0.00 0.00 1.85
2589 5829 9.178758 TCCTTTCTCTTCCTTTATTTCTTATGC 57.821 33.333 0.00 0.00 0.00 3.14
2595 5835 9.578439 CTCTTCCTTTATTTCTTATGCCTTTTG 57.422 33.333 0.00 0.00 0.00 2.44
2626 5866 5.732849 TGTGTTTTCGTCTTTGTTTTTCG 57.267 34.783 0.00 0.00 0.00 3.46
2629 5869 6.198591 TGTGTTTTCGTCTTTGTTTTTCGTTT 59.801 30.769 0.00 0.00 0.00 3.60
2630 5870 7.058608 GTGTTTTCGTCTTTGTTTTTCGTTTT 58.941 30.769 0.00 0.00 0.00 2.43
2631 5871 7.262582 GTGTTTTCGTCTTTGTTTTTCGTTTTC 59.737 33.333 0.00 0.00 0.00 2.29
2632 5872 7.167801 TGTTTTCGTCTTTGTTTTTCGTTTTCT 59.832 29.630 0.00 0.00 0.00 2.52
2633 5873 7.626144 TTTCGTCTTTGTTTTTCGTTTTCTT 57.374 28.000 0.00 0.00 0.00 2.52
2634 5874 6.842081 TCGTCTTTGTTTTTCGTTTTCTTC 57.158 33.333 0.00 0.00 0.00 2.87
2656 5896 9.518906 TCTTCGTTAGTTGGTTTTTATTTTTCC 57.481 29.630 0.00 0.00 0.00 3.13
2665 5905 8.898761 GTTGGTTTTTATTTTTCCTTTGTGGAT 58.101 29.630 0.00 0.00 45.68 3.41
2675 5915 8.511604 TTTTTCCTTTGTGGATATTTTTGCAA 57.488 26.923 0.00 0.00 45.68 4.08
2679 5919 6.873076 TCCTTTGTGGATATTTTTGCAATGTC 59.127 34.615 0.00 0.00 40.56 3.06
2680 5920 6.649973 CCTTTGTGGATATTTTTGCAATGTCA 59.350 34.615 0.00 0.00 38.35 3.58
2681 5921 7.360269 CCTTTGTGGATATTTTTGCAATGTCAC 60.360 37.037 0.00 3.62 38.35 3.67
2682 5922 6.343716 TGTGGATATTTTTGCAATGTCACT 57.656 33.333 0.00 0.00 0.00 3.41
2683 5923 7.459795 TGTGGATATTTTTGCAATGTCACTA 57.540 32.000 0.00 0.00 0.00 2.74
2684 5924 8.065473 TGTGGATATTTTTGCAATGTCACTAT 57.935 30.769 0.00 0.00 0.00 2.12
2685 5925 7.975058 TGTGGATATTTTTGCAATGTCACTATG 59.025 33.333 0.00 0.00 0.00 2.23
2686 5926 6.979817 TGGATATTTTTGCAATGTCACTATGC 59.020 34.615 0.00 0.00 40.45 3.14
2694 5934 5.823353 TGCAATGTCACTATGCAATATGTG 58.177 37.500 5.71 0.00 46.23 3.21
2734 5974 6.743575 AAAAGTGCAATATTAGAGCGAAGT 57.256 33.333 0.00 0.00 0.00 3.01
2735 5975 6.743575 AAAGTGCAATATTAGAGCGAAGTT 57.256 33.333 0.00 0.00 0.00 2.66
2736 5976 5.725110 AGTGCAATATTAGAGCGAAGTTG 57.275 39.130 0.00 0.00 0.00 3.16
2737 5977 5.178797 AGTGCAATATTAGAGCGAAGTTGT 58.821 37.500 0.00 0.00 0.00 3.32
2738 5978 5.063944 AGTGCAATATTAGAGCGAAGTTGTG 59.936 40.000 0.00 0.00 0.00 3.33
2739 5979 4.935205 TGCAATATTAGAGCGAAGTTGTGT 59.065 37.500 0.00 0.00 0.00 3.72
2740 5980 5.163864 TGCAATATTAGAGCGAAGTTGTGTG 60.164 40.000 0.00 0.00 0.00 3.82
2741 5981 5.258622 CAATATTAGAGCGAAGTTGTGTGC 58.741 41.667 0.00 0.00 0.00 4.57
2742 5982 2.232756 TTAGAGCGAAGTTGTGTGCA 57.767 45.000 0.00 0.00 0.00 4.57
2743 5983 2.232756 TAGAGCGAAGTTGTGTGCAA 57.767 45.000 0.00 0.00 0.00 4.08
2744 5984 1.378531 AGAGCGAAGTTGTGTGCAAA 58.621 45.000 0.00 0.00 36.22 3.68
2745 5985 1.742831 AGAGCGAAGTTGTGTGCAAAA 59.257 42.857 0.00 0.00 36.22 2.44
2746 5986 2.358898 AGAGCGAAGTTGTGTGCAAAAT 59.641 40.909 0.00 0.00 36.22 1.82
2747 5987 3.115554 GAGCGAAGTTGTGTGCAAAATT 58.884 40.909 0.00 0.00 36.22 1.82
2748 5988 3.520569 AGCGAAGTTGTGTGCAAAATTT 58.479 36.364 0.00 0.00 36.22 1.82
2749 5989 3.932089 AGCGAAGTTGTGTGCAAAATTTT 59.068 34.783 0.00 0.00 36.22 1.82
2750 5990 4.391523 AGCGAAGTTGTGTGCAAAATTTTT 59.608 33.333 0.00 0.00 36.22 1.94
2751 5991 5.578727 AGCGAAGTTGTGTGCAAAATTTTTA 59.421 32.000 0.00 0.00 36.22 1.52
2752 5992 6.091441 AGCGAAGTTGTGTGCAAAATTTTTAA 59.909 30.769 0.00 0.00 36.22 1.52
2753 5993 6.738649 GCGAAGTTGTGTGCAAAATTTTTAAA 59.261 30.769 0.00 0.00 36.22 1.52
2754 5994 7.269297 GCGAAGTTGTGTGCAAAATTTTTAAAA 59.731 29.630 0.00 0.00 36.22 1.52
2755 5995 8.563133 CGAAGTTGTGTGCAAAATTTTTAAAAC 58.437 29.630 0.00 0.00 36.22 2.43
2756 5996 9.387123 GAAGTTGTGTGCAAAATTTTTAAAACA 57.613 25.926 0.00 1.38 36.22 2.83
2757 5997 9.905171 AAGTTGTGTGCAAAATTTTTAAAACAT 57.095 22.222 0.00 0.00 36.22 2.71
2758 5998 9.905171 AGTTGTGTGCAAAATTTTTAAAACATT 57.095 22.222 0.00 1.97 36.22 2.71
2874 6114 6.775594 ATTCTTAGAGGGTAAAACCAATGC 57.224 37.500 0.00 0.00 41.02 3.56
2875 6115 4.595986 TCTTAGAGGGTAAAACCAATGCC 58.404 43.478 0.00 0.00 41.02 4.40
2876 6116 2.990740 AGAGGGTAAAACCAATGCCA 57.009 45.000 0.00 0.00 41.02 4.92
2877 6117 2.525368 AGAGGGTAAAACCAATGCCAC 58.475 47.619 0.00 0.00 41.02 5.01
2878 6118 2.110011 AGAGGGTAAAACCAATGCCACT 59.890 45.455 0.00 0.00 41.02 4.00
2879 6119 3.332485 AGAGGGTAAAACCAATGCCACTA 59.668 43.478 0.00 0.00 41.02 2.74
2880 6120 4.083565 GAGGGTAAAACCAATGCCACTAA 58.916 43.478 0.00 0.00 41.02 2.24
2881 6121 4.683643 AGGGTAAAACCAATGCCACTAAT 58.316 39.130 0.00 0.00 41.02 1.73
2882 6122 5.090845 AGGGTAAAACCAATGCCACTAATT 58.909 37.500 0.00 0.00 41.02 1.40
2883 6123 5.186992 AGGGTAAAACCAATGCCACTAATTC 59.813 40.000 0.00 0.00 41.02 2.17
2884 6124 5.046950 GGGTAAAACCAATGCCACTAATTCA 60.047 40.000 0.00 0.00 41.02 2.57
2885 6125 6.351796 GGGTAAAACCAATGCCACTAATTCAT 60.352 38.462 0.00 0.00 41.02 2.57
2886 6126 7.102993 GGTAAAACCAATGCCACTAATTCATT 58.897 34.615 0.00 0.00 38.42 2.57
2887 6127 7.277760 GGTAAAACCAATGCCACTAATTCATTC 59.722 37.037 0.00 0.00 38.42 2.67
2888 6128 6.610075 AAACCAATGCCACTAATTCATTCT 57.390 33.333 0.00 0.00 0.00 2.40
2889 6129 6.610075 AACCAATGCCACTAATTCATTCTT 57.390 33.333 0.00 0.00 0.00 2.52
2890 6130 6.610075 ACCAATGCCACTAATTCATTCTTT 57.390 33.333 0.00 0.00 0.00 2.52
2891 6131 6.633856 ACCAATGCCACTAATTCATTCTTTC 58.366 36.000 0.00 0.00 0.00 2.62
2892 6132 6.438425 ACCAATGCCACTAATTCATTCTTTCT 59.562 34.615 0.00 0.00 0.00 2.52
2893 6133 7.038799 ACCAATGCCACTAATTCATTCTTTCTT 60.039 33.333 0.00 0.00 0.00 2.52
2894 6134 8.469200 CCAATGCCACTAATTCATTCTTTCTTA 58.531 33.333 0.00 0.00 0.00 2.10
2895 6135 9.512435 CAATGCCACTAATTCATTCTTTCTTAG 57.488 33.333 0.00 0.00 0.00 2.18
2896 6136 7.630242 TGCCACTAATTCATTCTTTCTTAGG 57.370 36.000 0.00 0.00 0.00 2.69
2897 6137 7.402054 TGCCACTAATTCATTCTTTCTTAGGA 58.598 34.615 0.00 0.00 0.00 2.94
2898 6138 7.888021 TGCCACTAATTCATTCTTTCTTAGGAA 59.112 33.333 0.00 0.00 0.00 3.36
2899 6139 8.907885 GCCACTAATTCATTCTTTCTTAGGAAT 58.092 33.333 0.00 0.00 33.09 3.01
2909 6149 9.237846 CATTCTTTCTTAGGAATTATTTTCGCC 57.762 33.333 0.00 0.00 30.81 5.54
2910 6150 7.931578 TCTTTCTTAGGAATTATTTTCGCCA 57.068 32.000 0.00 0.00 0.00 5.69
2911 6151 8.343168 TCTTTCTTAGGAATTATTTTCGCCAA 57.657 30.769 0.00 0.00 0.00 4.52
2912 6152 8.798402 TCTTTCTTAGGAATTATTTTCGCCAAA 58.202 29.630 0.00 0.00 0.00 3.28
2913 6153 9.418045 CTTTCTTAGGAATTATTTTCGCCAAAA 57.582 29.630 0.00 0.00 35.92 2.44
2914 6154 9.765795 TTTCTTAGGAATTATTTTCGCCAAAAA 57.234 25.926 0.00 0.00 40.98 1.94
2972 6212 8.638685 GCATGAGCACATTTTTACTGAATATT 57.361 30.769 0.00 0.00 41.58 1.28
2973 6213 8.537223 GCATGAGCACATTTTTACTGAATATTG 58.463 33.333 0.00 0.00 41.58 1.90
2974 6214 9.577110 CATGAGCACATTTTTACTGAATATTGT 57.423 29.630 0.00 0.00 34.15 2.71
2975 6215 8.969121 TGAGCACATTTTTACTGAATATTGTG 57.031 30.769 0.00 0.00 0.00 3.33
2976 6216 8.575589 TGAGCACATTTTTACTGAATATTGTGT 58.424 29.630 0.00 0.00 0.00 3.72
2977 6217 8.746922 AGCACATTTTTACTGAATATTGTGTG 57.253 30.769 0.00 0.00 37.04 3.82
2979 6219 8.518151 CACATTTTTACTGAATATTGTGTGCA 57.482 30.769 0.00 0.00 0.00 4.57
2980 6220 8.976471 CACATTTTTACTGAATATTGTGTGCAA 58.024 29.630 0.00 0.00 39.16 4.08
2981 6221 9.539825 ACATTTTTACTGAATATTGTGTGCAAA 57.460 25.926 0.00 0.00 38.21 3.68
2996 6236 9.719279 ATTGTGTGCAAAATTTTATGTTCTTTG 57.281 25.926 2.44 0.00 38.21 2.77
2997 6237 8.261492 TGTGTGCAAAATTTTATGTTCTTTGT 57.739 26.923 2.44 0.00 31.19 2.83
2998 6238 8.725148 TGTGTGCAAAATTTTATGTTCTTTGTT 58.275 25.926 2.44 0.00 31.19 2.83
2999 6239 9.553418 GTGTGCAAAATTTTATGTTCTTTGTTT 57.447 25.926 2.44 0.00 31.19 2.83
3036 6276 9.799106 ATTTCTTCCTAGTGGGTAATATCAATG 57.201 33.333 0.00 0.00 36.25 2.82
3037 6277 6.769512 TCTTCCTAGTGGGTAATATCAATGC 58.230 40.000 0.00 0.00 36.25 3.56
3038 6278 5.499004 TCCTAGTGGGTAATATCAATGCC 57.501 43.478 0.00 0.00 36.25 4.40
3039 6279 4.910913 TCCTAGTGGGTAATATCAATGCCA 59.089 41.667 0.00 0.00 36.25 4.92
3040 6280 5.371176 TCCTAGTGGGTAATATCAATGCCAA 59.629 40.000 0.00 0.00 36.25 4.52
3041 6281 6.045459 TCCTAGTGGGTAATATCAATGCCAAT 59.955 38.462 0.00 0.00 36.25 3.16
3042 6282 7.238723 TCCTAGTGGGTAATATCAATGCCAATA 59.761 37.037 0.00 0.00 36.25 1.90
3043 6283 7.888021 CCTAGTGGGTAATATCAATGCCAATAA 59.112 37.037 0.00 0.00 0.00 1.40
3044 6284 9.466497 CTAGTGGGTAATATCAATGCCAATAAT 57.534 33.333 0.00 0.00 0.00 1.28
3045 6285 8.725606 AGTGGGTAATATCAATGCCAATAATT 57.274 30.769 0.00 0.00 0.00 1.40
3046 6286 9.158097 AGTGGGTAATATCAATGCCAATAATTT 57.842 29.630 0.00 0.00 0.00 1.82
3118 6358 8.432110 TTTGATTTTCTTTGTTCTTTAAGGGC 57.568 30.769 0.00 0.00 0.00 5.19
3119 6359 7.118496 TGATTTTCTTTGTTCTTTAAGGGCA 57.882 32.000 0.00 0.00 0.00 5.36
3120 6360 7.209475 TGATTTTCTTTGTTCTTTAAGGGCAG 58.791 34.615 0.00 0.00 0.00 4.85
3121 6361 6.538945 TTTTCTTTGTTCTTTAAGGGCAGT 57.461 33.333 0.00 0.00 0.00 4.40
3122 6362 7.648039 TTTTCTTTGTTCTTTAAGGGCAGTA 57.352 32.000 0.00 0.00 0.00 2.74
3123 6363 6.628919 TTCTTTGTTCTTTAAGGGCAGTAC 57.371 37.500 0.00 0.00 0.00 2.73
3124 6364 5.067954 TCTTTGTTCTTTAAGGGCAGTACC 58.932 41.667 0.00 0.00 37.93 3.34
3125 6365 4.440826 TTGTTCTTTAAGGGCAGTACCA 57.559 40.909 0.00 0.00 42.05 3.25
3126 6366 4.440826 TGTTCTTTAAGGGCAGTACCAA 57.559 40.909 0.00 0.00 42.05 3.67
3127 6367 4.993028 TGTTCTTTAAGGGCAGTACCAAT 58.007 39.130 0.00 0.00 42.05 3.16
3128 6368 4.764823 TGTTCTTTAAGGGCAGTACCAATG 59.235 41.667 0.00 0.00 42.05 2.82
3129 6369 3.352648 TCTTTAAGGGCAGTACCAATGC 58.647 45.455 0.00 0.00 42.05 3.56
3136 6376 2.403252 GCAGTACCAATGCCACTAGT 57.597 50.000 0.00 0.00 37.73 2.57
3137 6377 2.280628 GCAGTACCAATGCCACTAGTC 58.719 52.381 0.00 0.00 37.73 2.59
3138 6378 2.540515 CAGTACCAATGCCACTAGTCG 58.459 52.381 0.00 0.00 0.00 4.18
3139 6379 2.094182 CAGTACCAATGCCACTAGTCGT 60.094 50.000 0.00 0.00 0.00 4.34
3140 6380 2.565834 AGTACCAATGCCACTAGTCGTT 59.434 45.455 0.00 0.00 0.00 3.85
3141 6381 2.094762 ACCAATGCCACTAGTCGTTC 57.905 50.000 0.00 0.00 0.00 3.95
3142 6382 1.346395 ACCAATGCCACTAGTCGTTCA 59.654 47.619 0.00 0.00 0.00 3.18
3143 6383 2.027192 ACCAATGCCACTAGTCGTTCAT 60.027 45.455 0.00 0.00 0.00 2.57
3144 6384 3.009723 CCAATGCCACTAGTCGTTCATT 58.990 45.455 0.00 0.00 30.67 2.57
3145 6385 3.063997 CCAATGCCACTAGTCGTTCATTC 59.936 47.826 0.00 0.00 29.09 2.67
3146 6386 2.380084 TGCCACTAGTCGTTCATTCC 57.620 50.000 0.00 0.00 0.00 3.01
3147 6387 1.899814 TGCCACTAGTCGTTCATTCCT 59.100 47.619 0.00 0.00 0.00 3.36
3148 6388 3.093814 TGCCACTAGTCGTTCATTCCTA 58.906 45.455 0.00 0.00 0.00 2.94
3149 6389 3.130516 TGCCACTAGTCGTTCATTCCTAG 59.869 47.826 0.00 0.00 34.44 3.02
3150 6390 3.491104 GCCACTAGTCGTTCATTCCTAGG 60.491 52.174 0.82 0.82 32.91 3.02
3151 6391 3.952323 CCACTAGTCGTTCATTCCTAGGA 59.048 47.826 7.62 7.62 32.91 2.94
3152 6392 4.401519 CCACTAGTCGTTCATTCCTAGGAA 59.598 45.833 26.24 26.24 38.59 3.36
3153 6393 5.341617 CACTAGTCGTTCATTCCTAGGAAC 58.658 45.833 26.57 13.52 40.66 3.62
3154 6394 5.014858 ACTAGTCGTTCATTCCTAGGAACA 58.985 41.667 26.57 13.32 43.40 3.18
3155 6395 5.657302 ACTAGTCGTTCATTCCTAGGAACAT 59.343 40.000 26.57 9.19 43.40 2.71
3156 6396 6.832384 ACTAGTCGTTCATTCCTAGGAACATA 59.168 38.462 26.57 11.86 43.40 2.29
3157 6397 6.150396 AGTCGTTCATTCCTAGGAACATAG 57.850 41.667 26.57 15.89 43.40 2.23
3158 6398 5.657302 AGTCGTTCATTCCTAGGAACATAGT 59.343 40.000 26.57 7.59 43.40 2.12
3159 6399 6.154706 AGTCGTTCATTCCTAGGAACATAGTT 59.845 38.462 26.57 6.80 43.40 2.24
3160 6400 6.817140 GTCGTTCATTCCTAGGAACATAGTTT 59.183 38.462 26.57 6.01 43.40 2.66
3161 6401 7.010275 GTCGTTCATTCCTAGGAACATAGTTTC 59.990 40.741 26.57 10.10 43.40 2.78
3162 6402 7.042335 CGTTCATTCCTAGGAACATAGTTTCT 58.958 38.462 26.57 4.45 43.40 2.52
3163 6403 7.549488 CGTTCATTCCTAGGAACATAGTTTCTT 59.451 37.037 26.57 3.67 43.40 2.52
3164 6404 8.669243 GTTCATTCCTAGGAACATAGTTTCTTG 58.331 37.037 26.57 15.83 42.90 3.02
3165 6405 8.146053 TCATTCCTAGGAACATAGTTTCTTGA 57.854 34.615 26.57 17.77 36.91 3.02
3166 6406 8.602424 TCATTCCTAGGAACATAGTTTCTTGAA 58.398 33.333 26.57 0.00 36.91 2.69
3167 6407 9.231297 CATTCCTAGGAACATAGTTTCTTGAAA 57.769 33.333 26.57 0.00 36.91 2.69
3168 6408 9.981460 ATTCCTAGGAACATAGTTTCTTGAAAT 57.019 29.630 26.57 1.34 36.91 2.17
3169 6409 9.807921 TTCCTAGGAACATAGTTTCTTGAAATT 57.192 29.630 20.72 0.00 0.00 1.82
3170 6410 9.807921 TCCTAGGAACATAGTTTCTTGAAATTT 57.192 29.630 9.71 0.00 0.00 1.82
3174 6414 9.136323 AGGAACATAGTTTCTTGAAATTTCACT 57.864 29.630 20.35 15.29 36.83 3.41
3175 6415 9.185192 GGAACATAGTTTCTTGAAATTTCACTG 57.815 33.333 20.35 15.44 36.83 3.66
3176 6416 9.736023 GAACATAGTTTCTTGAAATTTCACTGT 57.264 29.630 20.35 9.36 36.83 3.55
3183 6423 9.636965 GTTTCTTGAAATTTCACTGTTATTTGC 57.363 29.630 20.35 1.00 36.83 3.68
3184 6424 9.598517 TTTCTTGAAATTTCACTGTTATTTGCT 57.401 25.926 20.35 0.00 36.83 3.91
3185 6425 9.598517 TTCTTGAAATTTCACTGTTATTTGCTT 57.401 25.926 20.35 0.00 36.83 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.827368 GGAGGAGAATGCGAAGGACT 59.173 55.000 0.00 0.00 0.00 3.85
1 2 0.827368 AGGAGGAGAATGCGAAGGAC 59.173 55.000 0.00 0.00 0.00 3.85
2 3 0.826715 CAGGAGGAGAATGCGAAGGA 59.173 55.000 0.00 0.00 0.00 3.36
3 4 0.179062 CCAGGAGGAGAATGCGAAGG 60.179 60.000 0.00 0.00 36.89 3.46
4 5 0.539051 ACCAGGAGGAGAATGCGAAG 59.461 55.000 0.00 0.00 38.69 3.79
5 6 0.250234 CACCAGGAGGAGAATGCGAA 59.750 55.000 0.00 0.00 38.69 4.70
6 7 0.904865 ACACCAGGAGGAGAATGCGA 60.905 55.000 0.00 0.00 38.69 5.10
7 8 0.742281 CACACCAGGAGGAGAATGCG 60.742 60.000 0.00 0.00 38.69 4.73
8 9 0.326264 ACACACCAGGAGGAGAATGC 59.674 55.000 0.00 0.00 38.69 3.56
9 10 5.815233 ATATACACACCAGGAGGAGAATG 57.185 43.478 0.00 0.00 38.69 2.67
11 12 9.696572 GTATATATATACACACCAGGAGGAGAA 57.303 37.037 22.64 0.00 38.66 2.87
12 13 9.070210 AGTATATATATACACACCAGGAGGAGA 57.930 37.037 27.07 0.00 40.70 3.71
13 14 9.344772 GAGTATATATATACACACCAGGAGGAG 57.655 40.741 27.07 0.00 40.70 3.69
14 15 8.842764 TGAGTATATATATACACACCAGGAGGA 58.157 37.037 27.07 6.44 40.70 3.71
15 16 9.475620 TTGAGTATATATATACACACCAGGAGG 57.524 37.037 27.07 0.00 38.73 4.30
32 33 9.594936 AAGCTATCCTAGTTCAGTTGAGTATAT 57.405 33.333 0.00 0.00 0.00 0.86
59 60 3.347216 AGTACATGTGCATTGTCTTCCC 58.653 45.455 16.62 0.00 0.00 3.97
129 130 0.690762 GGAGCCTGTAACTTGTGGGA 59.309 55.000 0.00 0.00 0.00 4.37
155 156 0.892063 TCCATCGTCGTCACATGGAA 59.108 50.000 10.14 0.00 42.60 3.53
156 157 0.455815 CTCCATCGTCGTCACATGGA 59.544 55.000 11.61 11.61 43.20 3.41
181 182 0.253044 GCTAGGCACACCATCAGGAA 59.747 55.000 0.00 0.00 39.06 3.36
229 236 6.894339 ATATGGAAAACTTCAGGTTTCGTT 57.106 33.333 10.53 4.21 46.18 3.85
278 285 1.539065 CGAGGGATCATCAAACCTCCG 60.539 57.143 7.59 1.32 45.23 4.63
304 311 2.057137 ACAGAGAGAGCTGGCTAGAG 57.943 55.000 0.00 0.00 40.20 2.43
340 347 0.323629 ATACCGCATATTGGTCCGGG 59.676 55.000 0.00 0.00 44.70 5.73
350 357 3.120321 GTGGGATCAACATACCGCATA 57.880 47.619 0.00 0.00 42.66 3.14
398 405 3.405831 GATCGATGATTTCTGGGCATGA 58.594 45.455 0.54 0.00 0.00 3.07
413 420 4.524714 CCATTGTGTACTAGGAGGATCGAT 59.475 45.833 0.00 0.00 34.37 3.59
466 473 3.367498 GCTAGTCCGTTCAGTTCTCATGT 60.367 47.826 0.00 0.00 0.00 3.21
468 475 3.093057 AGCTAGTCCGTTCAGTTCTCAT 58.907 45.455 0.00 0.00 0.00 2.90
490 497 2.604174 CCGACCAGTGCGTTGGAAC 61.604 63.158 12.76 5.94 39.40 3.62
503 510 1.887707 CGAGCTTATTGGGCCGACC 60.888 63.158 0.00 0.00 40.81 4.79
510 517 2.969628 ACAGTCTCCGAGCTTATTGG 57.030 50.000 0.00 0.00 0.00 3.16
587 594 4.288105 ACAAACATTTGGGCCCATAATTGA 59.712 37.500 29.23 6.34 42.34 2.57
654 662 6.434028 TGATTGAAGCCTAGTGCAAATAGTTT 59.566 34.615 0.00 0.00 44.83 2.66
658 666 7.308770 GCATATGATTGAAGCCTAGTGCAAATA 60.309 37.037 6.97 0.00 44.83 1.40
660 668 5.221106 GCATATGATTGAAGCCTAGTGCAAA 60.221 40.000 6.97 0.00 44.83 3.68
661 669 4.276678 GCATATGATTGAAGCCTAGTGCAA 59.723 41.667 6.97 0.00 44.83 4.08
662 670 3.817084 GCATATGATTGAAGCCTAGTGCA 59.183 43.478 6.97 0.00 44.83 4.57
887 1435 9.778741 CTCCTATTCTACCTGATAGCTAGATAG 57.221 40.741 0.00 0.00 0.00 2.08
888 1436 9.286588 ACTCCTATTCTACCTGATAGCTAGATA 57.713 37.037 0.00 0.00 0.00 1.98
889 1437 8.170121 ACTCCTATTCTACCTGATAGCTAGAT 57.830 38.462 0.00 0.00 0.00 1.98
890 1438 7.576978 ACTCCTATTCTACCTGATAGCTAGA 57.423 40.000 0.00 0.00 0.00 2.43
894 1442 7.338449 CCTTCTACTCCTATTCTACCTGATAGC 59.662 44.444 0.00 0.00 0.00 2.97
906 1454 4.237059 ACCCCCTTACCTTCTACTCCTATT 59.763 45.833 0.00 0.00 0.00 1.73
960 1508 8.858186 CATGCAATACTAAGTAGAATCAGATCG 58.142 37.037 0.00 0.00 0.00 3.69
963 1511 7.500141 TGCATGCAATACTAAGTAGAATCAGA 58.500 34.615 20.30 0.00 0.00 3.27
968 1775 6.233905 TCCTGCATGCAATACTAAGTAGAA 57.766 37.500 22.88 0.00 0.00 2.10
977 1784 3.428045 GGTGACTTTCCTGCATGCAATAC 60.428 47.826 22.88 10.91 0.00 1.89
1728 3104 1.068588 GGTATCACATACTGCGAGGCA 59.931 52.381 0.00 0.00 36.04 4.75
2104 5171 0.549950 CCCCAGTCTTCATCATGGCT 59.450 55.000 0.00 0.00 0.00 4.75
2216 5412 6.969366 TGCACTTATTGAATACATATGCCAC 58.031 36.000 1.58 0.00 0.00 5.01
2241 5459 6.887013 TGGAAATATTAATGGTTGCATTGCT 58.113 32.000 10.49 0.00 0.00 3.91
2419 5642 6.753744 AGAGCAAAAATGAACAGTCAAGAAAC 59.246 34.615 0.00 0.00 37.30 2.78
2427 5650 6.703165 GGAATTTCAGAGCAAAAATGAACAGT 59.297 34.615 0.00 0.00 32.91 3.55
2429 5652 6.702723 CAGGAATTTCAGAGCAAAAATGAACA 59.297 34.615 0.00 0.00 32.91 3.18
2552 5789 2.844369 AGAGAAAGGAGGGCTTGATCT 58.156 47.619 0.00 0.00 0.00 2.75
2567 5804 9.533831 AAAGGCATAAGAAATAAAGGAAGAGAA 57.466 29.630 0.00 0.00 0.00 2.87
2589 5829 8.125728 ACGAAAACACATAAAATCACAAAAGG 57.874 30.769 0.00 0.00 0.00 3.11
2595 5835 8.335256 ACAAAGACGAAAACACATAAAATCAC 57.665 30.769 0.00 0.00 0.00 3.06
2625 5865 6.858104 AAAAACCAACTAACGAAGAAAACG 57.142 33.333 0.00 0.00 0.00 3.60
2630 5870 9.518906 GGAAAAATAAAAACCAACTAACGAAGA 57.481 29.630 0.00 0.00 0.00 2.87
2631 5871 9.524106 AGGAAAAATAAAAACCAACTAACGAAG 57.476 29.630 0.00 0.00 0.00 3.79
2632 5872 9.872721 AAGGAAAAATAAAAACCAACTAACGAA 57.127 25.926 0.00 0.00 0.00 3.85
2633 5873 9.872721 AAAGGAAAAATAAAAACCAACTAACGA 57.127 25.926 0.00 0.00 0.00 3.85
2634 5874 9.909043 CAAAGGAAAAATAAAAACCAACTAACG 57.091 29.630 0.00 0.00 0.00 3.18
2655 5895 6.649973 TGACATTGCAAAAATATCCACAAAGG 59.350 34.615 1.71 0.00 39.47 3.11
2656 5896 7.385752 AGTGACATTGCAAAAATATCCACAAAG 59.614 33.333 1.71 0.00 0.00 2.77
2681 5921 9.992910 AATGTAATTATCGCACATATTGCATAG 57.007 29.630 9.52 0.00 43.61 2.23
2710 5950 7.145932 ACTTCGCTCTAATATTGCACTTTTT 57.854 32.000 0.00 0.00 0.00 1.94
2711 5951 6.743575 ACTTCGCTCTAATATTGCACTTTT 57.256 33.333 0.00 0.00 0.00 2.27
2712 5952 6.149474 ACAACTTCGCTCTAATATTGCACTTT 59.851 34.615 0.00 0.00 0.00 2.66
2713 5953 5.643777 ACAACTTCGCTCTAATATTGCACTT 59.356 36.000 0.00 0.00 0.00 3.16
2714 5954 5.063944 CACAACTTCGCTCTAATATTGCACT 59.936 40.000 0.00 0.00 0.00 4.40
2715 5955 5.163854 ACACAACTTCGCTCTAATATTGCAC 60.164 40.000 0.00 0.00 0.00 4.57
2716 5956 4.935205 ACACAACTTCGCTCTAATATTGCA 59.065 37.500 0.00 0.00 0.00 4.08
2717 5957 5.258622 CACACAACTTCGCTCTAATATTGC 58.741 41.667 0.00 0.00 0.00 3.56
2718 5958 5.163864 TGCACACAACTTCGCTCTAATATTG 60.164 40.000 0.00 0.00 0.00 1.90
2719 5959 4.935205 TGCACACAACTTCGCTCTAATATT 59.065 37.500 0.00 0.00 0.00 1.28
2720 5960 4.503910 TGCACACAACTTCGCTCTAATAT 58.496 39.130 0.00 0.00 0.00 1.28
2721 5961 3.920446 TGCACACAACTTCGCTCTAATA 58.080 40.909 0.00 0.00 0.00 0.98
2722 5962 2.766313 TGCACACAACTTCGCTCTAAT 58.234 42.857 0.00 0.00 0.00 1.73
2723 5963 2.232756 TGCACACAACTTCGCTCTAA 57.767 45.000 0.00 0.00 0.00 2.10
2724 5964 2.232756 TTGCACACAACTTCGCTCTA 57.767 45.000 0.00 0.00 0.00 2.43
2725 5965 1.378531 TTTGCACACAACTTCGCTCT 58.621 45.000 0.00 0.00 34.87 4.09
2726 5966 2.187351 TTTTGCACACAACTTCGCTC 57.813 45.000 0.00 0.00 34.87 5.03
2727 5967 2.869233 ATTTTGCACACAACTTCGCT 57.131 40.000 0.00 0.00 34.87 4.93
2728 5968 3.923827 AAATTTTGCACACAACTTCGC 57.076 38.095 0.00 0.00 34.87 4.70
2729 5969 8.563133 GTTTTAAAAATTTTGCACACAACTTCG 58.437 29.630 3.73 0.00 34.87 3.79
2730 5970 9.387123 TGTTTTAAAAATTTTGCACACAACTTC 57.613 25.926 3.73 0.00 34.87 3.01
2731 5971 9.905171 ATGTTTTAAAAATTTTGCACACAACTT 57.095 22.222 3.73 0.00 34.87 2.66
2732 5972 9.905171 AATGTTTTAAAAATTTTGCACACAACT 57.095 22.222 3.73 0.00 34.87 3.16
2848 6088 8.745590 GCATTGGTTTTACCCTCTAAGAATAAA 58.254 33.333 0.00 0.00 37.50 1.40
2849 6089 7.340999 GGCATTGGTTTTACCCTCTAAGAATAA 59.659 37.037 0.00 0.00 37.50 1.40
2850 6090 6.831868 GGCATTGGTTTTACCCTCTAAGAATA 59.168 38.462 0.00 0.00 37.50 1.75
2851 6091 5.656859 GGCATTGGTTTTACCCTCTAAGAAT 59.343 40.000 0.00 0.00 37.50 2.40
2852 6092 5.014202 GGCATTGGTTTTACCCTCTAAGAA 58.986 41.667 0.00 0.00 37.50 2.52
2853 6093 4.043561 TGGCATTGGTTTTACCCTCTAAGA 59.956 41.667 0.00 0.00 37.50 2.10
2854 6094 4.157840 GTGGCATTGGTTTTACCCTCTAAG 59.842 45.833 0.00 0.00 37.50 2.18
2855 6095 4.083565 GTGGCATTGGTTTTACCCTCTAA 58.916 43.478 0.00 0.00 37.50 2.10
2856 6096 3.332485 AGTGGCATTGGTTTTACCCTCTA 59.668 43.478 0.00 0.00 37.50 2.43
2857 6097 2.110011 AGTGGCATTGGTTTTACCCTCT 59.890 45.455 0.00 0.00 37.50 3.69
2858 6098 2.525368 AGTGGCATTGGTTTTACCCTC 58.475 47.619 0.00 0.00 37.50 4.30
2859 6099 2.694616 AGTGGCATTGGTTTTACCCT 57.305 45.000 0.00 0.00 37.50 4.34
2860 6100 5.046950 TGAATTAGTGGCATTGGTTTTACCC 60.047 40.000 0.00 0.00 37.50 3.69
2861 6101 6.031751 TGAATTAGTGGCATTGGTTTTACC 57.968 37.500 0.00 0.00 39.22 2.85
2862 6102 8.034804 AGAATGAATTAGTGGCATTGGTTTTAC 58.965 33.333 0.00 0.00 32.80 2.01
2863 6103 8.133024 AGAATGAATTAGTGGCATTGGTTTTA 57.867 30.769 0.00 0.00 32.80 1.52
2864 6104 7.008021 AGAATGAATTAGTGGCATTGGTTTT 57.992 32.000 0.00 0.00 32.80 2.43
2865 6105 6.610075 AGAATGAATTAGTGGCATTGGTTT 57.390 33.333 0.00 0.00 32.80 3.27
2866 6106 6.610075 AAGAATGAATTAGTGGCATTGGTT 57.390 33.333 0.00 0.00 32.80 3.67
2867 6107 6.438425 AGAAAGAATGAATTAGTGGCATTGGT 59.562 34.615 0.00 0.00 32.80 3.67
2868 6108 6.870769 AGAAAGAATGAATTAGTGGCATTGG 58.129 36.000 0.00 0.00 32.80 3.16
2869 6109 9.512435 CTAAGAAAGAATGAATTAGTGGCATTG 57.488 33.333 0.00 0.00 32.80 2.82
2870 6110 8.689972 CCTAAGAAAGAATGAATTAGTGGCATT 58.310 33.333 0.00 0.00 35.14 3.56
2871 6111 8.055181 TCCTAAGAAAGAATGAATTAGTGGCAT 58.945 33.333 0.00 0.00 0.00 4.40
2872 6112 7.402054 TCCTAAGAAAGAATGAATTAGTGGCA 58.598 34.615 0.00 0.00 0.00 4.92
2873 6113 7.865706 TCCTAAGAAAGAATGAATTAGTGGC 57.134 36.000 0.00 0.00 0.00 5.01
2883 6123 9.237846 GGCGAAAATAATTCCTAAGAAAGAATG 57.762 33.333 0.00 0.00 35.09 2.67
2884 6124 8.966868 TGGCGAAAATAATTCCTAAGAAAGAAT 58.033 29.630 0.00 0.00 35.09 2.40
2885 6125 8.343168 TGGCGAAAATAATTCCTAAGAAAGAA 57.657 30.769 0.00 0.00 35.09 2.52
2886 6126 7.931578 TGGCGAAAATAATTCCTAAGAAAGA 57.068 32.000 0.00 0.00 35.09 2.52
2887 6127 8.980143 TTTGGCGAAAATAATTCCTAAGAAAG 57.020 30.769 0.00 0.00 35.09 2.62
2888 6128 9.765795 TTTTTGGCGAAAATAATTCCTAAGAAA 57.234 25.926 8.57 0.00 32.21 2.52
2947 6187 8.537223 CAATATTCAGTAAAAATGTGCTCATGC 58.463 33.333 1.29 0.00 40.20 4.06
2948 6188 9.577110 ACAATATTCAGTAAAAATGTGCTCATG 57.423 29.630 1.29 0.00 34.19 3.07
2949 6189 9.577110 CACAATATTCAGTAAAAATGTGCTCAT 57.423 29.630 0.00 0.00 35.59 2.90
2950 6190 8.575589 ACACAATATTCAGTAAAAATGTGCTCA 58.424 29.630 0.00 0.00 40.29 4.26
2951 6191 8.853345 CACACAATATTCAGTAAAAATGTGCTC 58.147 33.333 0.00 0.00 40.29 4.26
2952 6192 8.746922 CACACAATATTCAGTAAAAATGTGCT 57.253 30.769 0.00 0.00 40.29 4.40
2954 6194 8.518151 TGCACACAATATTCAGTAAAAATGTG 57.482 30.769 0.00 0.00 41.86 3.21
2955 6195 9.539825 TTTGCACACAATATTCAGTAAAAATGT 57.460 25.926 0.00 0.00 35.21 2.71
2970 6210 9.719279 CAAAGAACATAAAATTTTGCACACAAT 57.281 25.926 13.76 0.00 35.21 2.71
2971 6211 8.725148 ACAAAGAACATAAAATTTTGCACACAA 58.275 25.926 13.76 0.00 33.28 3.33
2972 6212 8.261492 ACAAAGAACATAAAATTTTGCACACA 57.739 26.923 13.76 0.00 33.28 3.72
2973 6213 9.553418 AAACAAAGAACATAAAATTTTGCACAC 57.447 25.926 13.76 3.02 33.28 3.82
3010 6250 9.799106 CATTGATATTACCCACTAGGAAGAAAT 57.201 33.333 0.00 0.00 39.89 2.17
3011 6251 7.719633 GCATTGATATTACCCACTAGGAAGAAA 59.280 37.037 0.00 0.00 39.89 2.52
3012 6252 7.224297 GCATTGATATTACCCACTAGGAAGAA 58.776 38.462 0.00 0.00 39.89 2.52
3013 6253 6.239887 GGCATTGATATTACCCACTAGGAAGA 60.240 42.308 0.00 0.00 39.89 2.87
3014 6254 5.940470 GGCATTGATATTACCCACTAGGAAG 59.060 44.000 0.00 0.00 39.89 3.46
3015 6255 5.371176 TGGCATTGATATTACCCACTAGGAA 59.629 40.000 0.00 0.00 39.89 3.36
3016 6256 4.910913 TGGCATTGATATTACCCACTAGGA 59.089 41.667 0.00 0.00 39.89 2.94
3017 6257 5.241403 TGGCATTGATATTACCCACTAGG 57.759 43.478 0.00 0.00 43.78 3.02
3018 6258 8.862325 TTATTGGCATTGATATTACCCACTAG 57.138 34.615 0.00 0.00 0.00 2.57
3019 6259 9.821240 AATTATTGGCATTGATATTACCCACTA 57.179 29.630 0.00 0.00 0.00 2.74
3020 6260 8.725606 AATTATTGGCATTGATATTACCCACT 57.274 30.769 0.00 0.00 0.00 4.00
3092 6332 9.056005 GCCCTTAAAGAACAAAGAAAATCAAAT 57.944 29.630 0.00 0.00 0.00 2.32
3093 6333 8.043710 TGCCCTTAAAGAACAAAGAAAATCAAA 58.956 29.630 0.00 0.00 0.00 2.69
3094 6334 7.560368 TGCCCTTAAAGAACAAAGAAAATCAA 58.440 30.769 0.00 0.00 0.00 2.57
3095 6335 7.118496 TGCCCTTAAAGAACAAAGAAAATCA 57.882 32.000 0.00 0.00 0.00 2.57
3096 6336 7.210174 ACTGCCCTTAAAGAACAAAGAAAATC 58.790 34.615 0.00 0.00 0.00 2.17
3097 6337 7.124573 ACTGCCCTTAAAGAACAAAGAAAAT 57.875 32.000 0.00 0.00 0.00 1.82
3098 6338 6.538945 ACTGCCCTTAAAGAACAAAGAAAA 57.461 33.333 0.00 0.00 0.00 2.29
3099 6339 6.040054 GGTACTGCCCTTAAAGAACAAAGAAA 59.960 38.462 0.00 0.00 0.00 2.52
3100 6340 5.533528 GGTACTGCCCTTAAAGAACAAAGAA 59.466 40.000 0.00 0.00 0.00 2.52
3101 6341 5.067954 GGTACTGCCCTTAAAGAACAAAGA 58.932 41.667 0.00 0.00 0.00 2.52
3102 6342 4.825085 TGGTACTGCCCTTAAAGAACAAAG 59.175 41.667 0.00 0.00 36.04 2.77
3103 6343 4.794334 TGGTACTGCCCTTAAAGAACAAA 58.206 39.130 0.00 0.00 36.04 2.83
3104 6344 4.440826 TGGTACTGCCCTTAAAGAACAA 57.559 40.909 0.00 0.00 36.04 2.83
3105 6345 4.440826 TTGGTACTGCCCTTAAAGAACA 57.559 40.909 0.00 0.00 36.04 3.18
3106 6346 4.380550 GCATTGGTACTGCCCTTAAAGAAC 60.381 45.833 0.00 0.00 36.04 3.01
3107 6347 3.761752 GCATTGGTACTGCCCTTAAAGAA 59.238 43.478 0.00 0.00 36.04 2.52
3108 6348 3.352648 GCATTGGTACTGCCCTTAAAGA 58.647 45.455 0.00 0.00 36.04 2.52
3109 6349 3.782889 GCATTGGTACTGCCCTTAAAG 57.217 47.619 0.00 0.00 36.04 1.85
3117 6357 2.280628 GACTAGTGGCATTGGTACTGC 58.719 52.381 0.00 0.00 38.93 4.40
3118 6358 2.094182 ACGACTAGTGGCATTGGTACTG 60.094 50.000 0.00 0.00 0.00 2.74
3119 6359 2.176889 ACGACTAGTGGCATTGGTACT 58.823 47.619 0.00 0.00 0.00 2.73
3120 6360 2.667473 ACGACTAGTGGCATTGGTAC 57.333 50.000 0.00 0.00 0.00 3.34
3121 6361 2.563620 TGAACGACTAGTGGCATTGGTA 59.436 45.455 0.00 0.00 0.00 3.25
3122 6362 1.346395 TGAACGACTAGTGGCATTGGT 59.654 47.619 0.00 0.00 0.00 3.67
3123 6363 2.093306 TGAACGACTAGTGGCATTGG 57.907 50.000 0.00 0.00 0.00 3.16
3124 6364 3.063997 GGAATGAACGACTAGTGGCATTG 59.936 47.826 12.96 0.00 38.18 2.82
3125 6365 3.055094 AGGAATGAACGACTAGTGGCATT 60.055 43.478 0.00 5.28 39.66 3.56
3126 6366 2.501723 AGGAATGAACGACTAGTGGCAT 59.498 45.455 0.00 0.00 32.32 4.40
3127 6367 1.899814 AGGAATGAACGACTAGTGGCA 59.100 47.619 0.00 0.00 0.00 4.92
3128 6368 2.674796 AGGAATGAACGACTAGTGGC 57.325 50.000 0.00 0.00 0.00 5.01
3129 6369 3.952323 TCCTAGGAATGAACGACTAGTGG 59.048 47.826 9.71 0.25 32.91 4.00
3130 6370 5.105877 TGTTCCTAGGAATGAACGACTAGTG 60.106 44.000 26.74 0.00 42.93 2.74
3131 6371 5.014858 TGTTCCTAGGAATGAACGACTAGT 58.985 41.667 26.74 0.00 42.93 2.57
3132 6372 5.578005 TGTTCCTAGGAATGAACGACTAG 57.422 43.478 26.74 0.00 42.93 2.57
3133 6373 6.832384 ACTATGTTCCTAGGAATGAACGACTA 59.168 38.462 26.74 7.47 42.93 2.59
3134 6374 5.657302 ACTATGTTCCTAGGAATGAACGACT 59.343 40.000 26.74 6.76 42.93 4.18
3135 6375 5.903810 ACTATGTTCCTAGGAATGAACGAC 58.096 41.667 26.74 13.47 42.93 4.34
3136 6376 6.540438 AACTATGTTCCTAGGAATGAACGA 57.460 37.500 26.74 8.95 42.93 3.85
3137 6377 7.042335 AGAAACTATGTTCCTAGGAATGAACG 58.958 38.462 26.74 15.96 42.93 3.95
3138 6378 8.669243 CAAGAAACTATGTTCCTAGGAATGAAC 58.331 37.037 26.74 15.29 40.94 3.18
3139 6379 8.602424 TCAAGAAACTATGTTCCTAGGAATGAA 58.398 33.333 26.74 15.81 36.45 2.57
3140 6380 8.146053 TCAAGAAACTATGTTCCTAGGAATGA 57.854 34.615 26.74 18.02 36.45 2.57
3141 6381 8.792830 TTCAAGAAACTATGTTCCTAGGAATG 57.207 34.615 26.74 16.13 36.45 2.67
3142 6382 9.981460 ATTTCAAGAAACTATGTTCCTAGGAAT 57.019 29.630 26.74 14.64 33.23 3.01
3143 6383 9.807921 AATTTCAAGAAACTATGTTCCTAGGAA 57.192 29.630 20.72 20.72 32.51 3.36
3144 6384 9.807921 AAATTTCAAGAAACTATGTTCCTAGGA 57.192 29.630 7.62 7.62 32.51 2.94
3148 6388 9.136323 AGTGAAATTTCAAGAAACTATGTTCCT 57.864 29.630 22.07 7.31 39.21 3.36
3149 6389 9.185192 CAGTGAAATTTCAAGAAACTATGTTCC 57.815 33.333 22.07 5.17 39.21 3.62
3150 6390 9.736023 ACAGTGAAATTTCAAGAAACTATGTTC 57.264 29.630 22.07 5.58 39.21 3.18
3157 6397 9.636965 GCAAATAACAGTGAAATTTCAAGAAAC 57.363 29.630 22.07 9.74 39.21 2.78
3158 6398 9.598517 AGCAAATAACAGTGAAATTTCAAGAAA 57.401 25.926 22.07 11.37 39.21 2.52
3159 6399 9.598517 AAGCAAATAACAGTGAAATTTCAAGAA 57.401 25.926 22.07 11.66 39.21 2.52


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

AutoCloner maintained by Alex Coulton.