Multiple sequence alignment - TraesCS2D01G422300

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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 TraesCS2D01G422300 chr2D 100.000 3876 0 0 1 3876 535583358 535579483 0.000000e+00 7158.0
1 TraesCS2D01G422300 chr2D 84.765 978 125 16 1000 1960 542127714 542126744 0.000000e+00 959.0
2 TraesCS2D01G422300 chr2D 81.184 946 139 28 992 1913 536479811 536480741 0.000000e+00 725.0
3 TraesCS2D01G422300 chr2D 81.991 633 114 0 2246 2878 542126491 542125859 4.410000e-149 538.0
4 TraesCS2D01G422300 chr2D 89.474 133 8 1 3347 3473 535579946 535579814 3.100000e-36 163.0
5 TraesCS2D01G422300 chr2D 89.474 133 8 1 3413 3545 535580012 535579886 3.100000e-36 163.0
6 TraesCS2D01G422300 chr2D 89.313 131 9 4 3743 3871 576451154 576451281 4.010000e-35 159.0
7 TraesCS2D01G422300 chr2A 94.804 2733 81 22 670 3358 678679361 678676646 0.000000e+00 4204.0
8 TraesCS2D01G422300 chr2A 84.624 930 122 13 1000 1914 684915848 684914925 0.000000e+00 905.0
9 TraesCS2D01G422300 chr2A 90.893 571 50 2 11 581 678679943 678679375 0.000000e+00 765.0
10 TraesCS2D01G422300 chr2A 81.112 953 142 21 986 1913 678994549 678995488 0.000000e+00 728.0
11 TraesCS2D01G422300 chr2A 81.065 676 127 1 2246 2920 684913915 684913240 4.410000e-149 538.0
12 TraesCS2D01G422300 chr2A 83.677 582 77 14 11 582 717177220 717177793 2.050000e-147 532.0
13 TraesCS2D01G422300 chr2A 95.726 117 5 0 3347 3463 678676466 678676350 5.110000e-44 189.0
14 TraesCS2D01G422300 chr2A 89.313 131 9 4 3747 3875 774591900 774591773 4.010000e-35 159.0
15 TraesCS2D01G422300 chr2A 92.473 93 7 0 579 671 487366051 487365959 2.430000e-27 134.0
16 TraesCS2D01G422300 chr2A 91.209 91 7 1 579 668 100916022 100915932 5.260000e-24 122.0
17 TraesCS2D01G422300 chr2B 93.977 1295 58 10 1964 3255 636822052 636820775 0.000000e+00 1941.0
18 TraesCS2D01G422300 chr2B 96.144 1167 33 8 825 1986 636823382 636822223 0.000000e+00 1895.0
19 TraesCS2D01G422300 chr2B 88.759 1023 77 20 926 1936 638751509 638752505 0.000000e+00 1218.0
20 TraesCS2D01G422300 chr2B 88.288 777 87 2 2146 2918 638752872 638753648 0.000000e+00 928.0
21 TraesCS2D01G422300 chr2B 81.633 931 143 16 992 1913 637791397 637792308 0.000000e+00 747.0
22 TraesCS2D01G422300 chr2B 81.649 752 120 10 992 1739 637797431 637798168 3.310000e-170 608.0
23 TraesCS2D01G422300 chr2B 80.886 722 112 15 1209 1914 646996100 646995389 2.630000e-151 545.0
24 TraesCS2D01G422300 chr2B 79.209 683 139 3 2240 2920 646994380 646993699 4.530000e-129 472.0
25 TraesCS2D01G422300 chr2B 90.027 371 19 6 3383 3744 636820696 636820335 7.590000e-127 464.0
26 TraesCS2D01G422300 chr2B 92.969 128 9 0 3347 3474 636820666 636820539 1.840000e-43 187.0
27 TraesCS2D01G422300 chr2B 88.489 139 9 5 3737 3875 178863037 178862906 1.110000e-35 161.0
28 TraesCS2D01G422300 chr2B 91.398 93 5 1 580 669 141154165 141154257 1.460000e-24 124.0
29 TraesCS2D01G422300 chr2B 87.850 107 8 3 1810 1913 637798731 637798835 1.890000e-23 121.0
30 TraesCS2D01G422300 chr2B 88.660 97 5 2 3449 3545 636820696 636820606 3.170000e-21 113.0
31 TraesCS2D01G422300 chr2B 92.593 54 4 0 1540 1593 646996397 646996450 1.150000e-10 78.7
32 TraesCS2D01G422300 chr7D 78.805 1038 165 32 993 1991 568066900 568067921 0.000000e+00 647.0
33 TraesCS2D01G422300 chr7D 82.300 661 115 2 2246 2905 568067986 568068645 4.340000e-159 571.0
34 TraesCS2D01G422300 chr7D 86.822 516 57 6 11 520 603661800 603662310 2.020000e-157 566.0
35 TraesCS2D01G422300 chr7D 85.740 547 60 13 14 550 159709688 159709150 2.610000e-156 562.0
36 TraesCS2D01G422300 chr7D 89.796 98 4 3 579 672 30369452 30369357 1.890000e-23 121.0
37 TraesCS2D01G422300 chr7D 90.323 93 5 3 579 668 238363923 238364014 6.800000e-23 119.0
38 TraesCS2D01G422300 chr3D 86.460 517 62 5 11 526 514849972 514850481 9.400000e-156 560.0
39 TraesCS2D01G422300 chr3D 77.862 926 167 23 998 1913 43738715 43739612 1.230000e-149 540.0
40 TraesCS2D01G422300 chr3D 75.991 933 164 37 998 1913 43719361 43720250 9.950000e-116 427.0
41 TraesCS2D01G422300 chr1D 84.055 577 80 8 11 582 239565067 239565636 2.630000e-151 545.0
42 TraesCS2D01G422300 chr4B 85.824 522 62 6 11 520 577009627 577010148 9.470000e-151 544.0
43 TraesCS2D01G422300 chr6D 85.632 522 65 7 12 526 157154664 157154146 1.230000e-149 540.0
44 TraesCS2D01G422300 chr4D 83.677 582 75 14 11 581 83270676 83271248 7.370000e-147 531.0
45 TraesCS2D01G422300 chr4D 76.350 926 178 25 1001 1899 448395032 448394121 3.530000e-125 459.0
46 TraesCS2D01G422300 chr3A 78.659 820 147 20 1105 1913 55707888 55707086 1.600000e-143 520.0
47 TraesCS2D01G422300 chr3A 78.053 565 117 6 2247 2806 667306994 667306432 2.220000e-92 350.0
48 TraesCS2D01G422300 chr3B 78.546 564 116 4 2247 2806 704261716 704261154 2.200000e-97 366.0
49 TraesCS2D01G422300 chr3B 89.922 129 10 2 3747 3875 31124988 31124863 3.100000e-36 163.0
50 TraesCS2D01G422300 chr3B 88.148 135 13 2 3741 3875 588755504 588755635 1.440000e-34 158.0
51 TraesCS2D01G422300 chr3B 96.875 32 1 0 3414 3445 489362896 489362927 2.000000e-03 54.7
52 TraesCS2D01G422300 chr7B 90.076 131 8 4 3742 3871 637303972 637304098 8.620000e-37 165.0
53 TraesCS2D01G422300 chr7B 90.909 99 4 4 579 674 144522170 144522266 1.130000e-25 128.0
54 TraesCS2D01G422300 chr7B 88.235 102 7 4 571 669 39817941 39818040 2.450000e-22 117.0
55 TraesCS2D01G422300 chr5D 89.922 129 10 2 3747 3875 558724630 558724505 3.100000e-36 163.0
56 TraesCS2D01G422300 chr5D 88.889 135 9 4 3741 3875 518749382 518749510 1.110000e-35 161.0
57 TraesCS2D01G422300 chr5D 89.231 130 10 3 3747 3875 163993963 163994089 4.010000e-35 159.0
58 TraesCS2D01G422300 chr6A 91.489 94 7 1 579 672 23963371 23963279 1.130000e-25 128.0
59 TraesCS2D01G422300 chr1A 88.776 98 7 2 579 672 583582490 583582393 2.450000e-22 117.0
60 TraesCS2D01G422300 chr5B 92.857 42 3 0 3308 3349 43956871 43956912 1.160000e-05 62.1


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 TraesCS2D01G422300 chr2D 535579483 535583358 3875 True 2494.666667 7158 92.982667 1 3876 3 chr2D.!!$R1 3875
1 TraesCS2D01G422300 chr2D 542125859 542127714 1855 True 748.500000 959 83.378000 1000 2878 2 chr2D.!!$R2 1878
2 TraesCS2D01G422300 chr2D 536479811 536480741 930 False 725.000000 725 81.184000 992 1913 1 chr2D.!!$F1 921
3 TraesCS2D01G422300 chr2A 678676350 678679943 3593 True 1719.333333 4204 93.807667 11 3463 3 chr2A.!!$R4 3452
4 TraesCS2D01G422300 chr2A 678994549 678995488 939 False 728.000000 728 81.112000 986 1913 1 chr2A.!!$F1 927
5 TraesCS2D01G422300 chr2A 684913240 684915848 2608 True 721.500000 905 82.844500 1000 2920 2 chr2A.!!$R5 1920
6 TraesCS2D01G422300 chr2A 717177220 717177793 573 False 532.000000 532 83.677000 11 582 1 chr2A.!!$F2 571
7 TraesCS2D01G422300 chr2B 638751509 638753648 2139 False 1073.000000 1218 88.523500 926 2918 2 chr2B.!!$F5 1992
8 TraesCS2D01G422300 chr2B 636820335 636823382 3047 True 920.000000 1941 92.355400 825 3744 5 chr2B.!!$R2 2919
9 TraesCS2D01G422300 chr2B 637791397 637792308 911 False 747.000000 747 81.633000 992 1913 1 chr2B.!!$F2 921
10 TraesCS2D01G422300 chr2B 646993699 646996100 2401 True 508.500000 545 80.047500 1209 2920 2 chr2B.!!$R3 1711
11 TraesCS2D01G422300 chr2B 637797431 637798835 1404 False 364.500000 608 84.749500 992 1913 2 chr2B.!!$F4 921
12 TraesCS2D01G422300 chr7D 568066900 568068645 1745 False 609.000000 647 80.552500 993 2905 2 chr7D.!!$F3 1912
13 TraesCS2D01G422300 chr7D 603661800 603662310 510 False 566.000000 566 86.822000 11 520 1 chr7D.!!$F2 509
14 TraesCS2D01G422300 chr7D 159709150 159709688 538 True 562.000000 562 85.740000 14 550 1 chr7D.!!$R2 536
15 TraesCS2D01G422300 chr3D 514849972 514850481 509 False 560.000000 560 86.460000 11 526 1 chr3D.!!$F3 515
16 TraesCS2D01G422300 chr3D 43738715 43739612 897 False 540.000000 540 77.862000 998 1913 1 chr3D.!!$F2 915
17 TraesCS2D01G422300 chr3D 43719361 43720250 889 False 427.000000 427 75.991000 998 1913 1 chr3D.!!$F1 915
18 TraesCS2D01G422300 chr1D 239565067 239565636 569 False 545.000000 545 84.055000 11 582 1 chr1D.!!$F1 571
19 TraesCS2D01G422300 chr4B 577009627 577010148 521 False 544.000000 544 85.824000 11 520 1 chr4B.!!$F1 509
20 TraesCS2D01G422300 chr6D 157154146 157154664 518 True 540.000000 540 85.632000 12 526 1 chr6D.!!$R1 514
21 TraesCS2D01G422300 chr4D 83270676 83271248 572 False 531.000000 531 83.677000 11 581 1 chr4D.!!$F1 570
22 TraesCS2D01G422300 chr4D 448394121 448395032 911 True 459.000000 459 76.350000 1001 1899 1 chr4D.!!$R1 898
23 TraesCS2D01G422300 chr3A 55707086 55707888 802 True 520.000000 520 78.659000 1105 1913 1 chr3A.!!$R1 808
24 TraesCS2D01G422300 chr3A 667306432 667306994 562 True 350.000000 350 78.053000 2247 2806 1 chr3A.!!$R2 559
25 TraesCS2D01G422300 chr3B 704261154 704261716 562 True 366.000000 366 78.546000 2247 2806 1 chr3B.!!$R2 559

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
882 901 0.458669 TGCCGTATCCCGAGAAGAAC 59.541 55.0 0.0 0.0 39.56 3.01 F
1921 3248 0.693049 AGTGGTAAGTGCTCCAAGGG 59.307 55.0 0.0 0.0 35.38 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 4645 1.794437 GCGTCGCTACTAGGTGAAGTG 60.794 57.143 10.68 0.0 0.00 3.16 R
3828 5782 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.000 0.00 0.0 31.08 4.20 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
30 34 2.038975 TCCTCCAACTCCTCCGGG 59.961 66.667 0.00 0.00 0.00 5.73
89 93 4.365505 GCGCCTAGCCCCGATCTC 62.366 72.222 0.00 0.00 40.81 2.75
146 150 4.796231 CTCGTTCCTCACCCGGCG 62.796 72.222 0.00 0.00 0.00 6.46
181 185 2.898920 TACTAGGCGGACGGGTGGAG 62.899 65.000 0.00 0.00 0.00 3.86
192 196 0.602905 CGGGTGGAGTGGAAAGTGAC 60.603 60.000 0.00 0.00 0.00 3.67
196 200 2.027625 GGAGTGGAAAGTGACGGCG 61.028 63.158 4.80 4.80 0.00 6.46
224 228 3.054139 CAGGAGGAGGAAAATGTGGATGA 60.054 47.826 0.00 0.00 0.00 2.92
233 237 4.342092 GGAAAATGTGGATGAATGGTAGGG 59.658 45.833 0.00 0.00 0.00 3.53
258 262 2.884207 GCCGCGGGTCGACTTAAG 60.884 66.667 29.38 0.00 41.67 1.85
279 283 3.145551 CCGGGCTAGGCACTACGT 61.146 66.667 19.14 0.00 41.75 3.57
325 329 2.675423 CACCGGTCCGACAGAGGA 60.675 66.667 14.39 0.00 38.11 3.71
377 381 2.125147 CCGGCTGGAATCGCTTCA 60.125 61.111 5.28 0.00 37.49 3.02
441 445 4.210331 GCCCCATATTTAGGCTGGATATG 58.790 47.826 17.93 17.93 43.62 1.78
445 449 5.398353 CCCATATTTAGGCTGGATATGAGGG 60.398 48.000 22.87 16.55 36.37 4.30
470 474 1.079503 GTCAGCTCAGGCGTTTAAGG 58.920 55.000 0.00 0.00 44.37 2.69
471 475 0.673644 TCAGCTCAGGCGTTTAAGGC 60.674 55.000 0.53 0.53 44.37 4.35
504 508 4.708601 CGTTTGTCTGGGTTAAAAGATCG 58.291 43.478 0.00 0.00 0.00 3.69
510 514 3.325425 TCTGGGTTAAAAGATCGTGACCA 59.675 43.478 9.27 0.00 0.00 4.02
519 523 1.542030 AGATCGTGACCAGTCAGTGAC 59.458 52.381 15.78 15.78 40.75 3.67
537 541 4.410400 GGGCGGGCAACTACAGCT 62.410 66.667 3.27 0.00 0.00 4.24
542 546 2.820037 GGCAACTACAGCTCGGGC 60.820 66.667 0.00 0.00 39.06 6.13
569 573 1.823899 CCTATTTGGGGCACTCGGC 60.824 63.158 0.00 0.00 43.74 5.54
581 585 0.814457 CACTCGGCTGTAGAGCTCTT 59.186 55.000 23.84 6.22 45.44 2.85
582 586 0.814457 ACTCGGCTGTAGAGCTCTTG 59.186 55.000 23.84 13.54 45.44 3.02
583 587 1.098869 CTCGGCTGTAGAGCTCTTGA 58.901 55.000 23.84 7.90 45.44 3.02
584 588 1.680735 CTCGGCTGTAGAGCTCTTGAT 59.319 52.381 23.84 0.00 45.44 2.57
585 589 2.881513 CTCGGCTGTAGAGCTCTTGATA 59.118 50.000 23.84 0.00 45.44 2.15
586 590 3.491342 TCGGCTGTAGAGCTCTTGATAT 58.509 45.455 23.84 0.00 45.44 1.63
587 591 3.891977 TCGGCTGTAGAGCTCTTGATATT 59.108 43.478 23.84 0.00 45.44 1.28
589 593 5.053145 CGGCTGTAGAGCTCTTGATATTTT 58.947 41.667 23.84 0.00 45.44 1.82
590 594 5.525378 CGGCTGTAGAGCTCTTGATATTTTT 59.475 40.000 23.84 0.00 45.44 1.94
712 716 8.176814 TGTACTATAATTTTCGTGTACACAGC 57.823 34.615 24.98 0.00 36.42 4.40
783 787 5.833340 ACCAGCCCACCATTATTTAAGTTA 58.167 37.500 0.00 0.00 0.00 2.24
854 873 1.001974 CCTGATGACTTCGTCAACCCA 59.998 52.381 0.36 0.15 45.96 4.51
882 901 0.458669 TGCCGTATCCCGAGAAGAAC 59.541 55.000 0.00 0.00 39.56 3.01
920 939 3.116356 ACCAAATCTTTCCCCTCCCTTTT 60.116 43.478 0.00 0.00 0.00 2.27
921 940 3.909995 CCAAATCTTTCCCCTCCCTTTTT 59.090 43.478 0.00 0.00 0.00 1.94
949 968 4.143740 AGGCACTTCCTGCTAGCT 57.856 55.556 17.23 0.00 45.54 3.32
950 969 3.306902 AGGCACTTCCTGCTAGCTA 57.693 52.632 17.23 1.31 45.54 3.32
951 970 1.118838 AGGCACTTCCTGCTAGCTAG 58.881 55.000 16.84 16.84 45.54 3.42
996 1023 5.046878 AGCTTCAAATTTGATCAAGCCATCA 60.047 36.000 27.80 9.69 38.63 3.07
1099 1147 1.527433 GACAGCAAGTTCCAAGGGGC 61.527 60.000 0.00 0.00 0.00 5.80
1921 3248 0.693049 AGTGGTAAGTGCTCCAAGGG 59.307 55.000 0.00 0.00 35.38 3.95
2057 3724 3.131046 GGGGTGGTGCTAAATGATCTTTG 59.869 47.826 0.00 0.00 0.00 2.77
2193 3869 4.226168 CAGGGGGATAATCTTCCATCCTAC 59.774 50.000 0.97 0.00 40.57 3.18
2216 3900 7.873739 ACAAAGAAAGTTATATTGTTGCAGC 57.126 32.000 0.00 0.00 30.50 5.25
2634 4330 4.142026 TGAGGACATTACCGTGGATTACAG 60.142 45.833 0.00 0.00 34.73 2.74
2829 4645 3.502595 GCAACACTAAGAAGAAGGAACCC 59.497 47.826 0.00 0.00 0.00 4.11
2921 4738 6.778069 TGTTTATGATGGTGGGTTAACTTTCA 59.222 34.615 5.42 0.00 0.00 2.69
3046 4864 9.981114 ACCTAAAGGATTGTTCTACAAAAATTG 57.019 29.630 2.23 0.00 39.06 2.32
3068 4886 8.603242 ATTGATAAATTAGTAATTCGGCGAGT 57.397 30.769 10.46 3.76 0.00 4.18
3117 4936 4.393062 CGTCCTTATTCACTTGCAATGAGT 59.607 41.667 0.00 5.93 0.00 3.41
3125 4944 3.578282 TCACTTGCAATGAGTGGAGTAGA 59.422 43.478 15.28 0.00 43.61 2.59
3148 4967 8.286191 AGAGCTGGAATTAAAAATCTCGAAAT 57.714 30.769 0.00 0.00 0.00 2.17
3277 5097 8.364894 TGAGTGAAGCTAACAAGTTACTCATTA 58.635 33.333 8.94 0.00 0.00 1.90
3337 5157 7.162761 TCTTCGTCCCAAAATAAGTGTCATTA 58.837 34.615 0.00 0.00 0.00 1.90
3369 5314 9.724839 GCACAACTTTGTACTAAATAAAAGACA 57.275 29.630 7.81 0.00 39.91 3.41
3399 5344 7.394016 TCTTGAAAGAGAGTGTGCCAATATTA 58.606 34.615 0.00 0.00 0.00 0.98
3463 5408 4.997395 TCTTGAAAGAGAGTGTGCCAATAC 59.003 41.667 0.00 0.00 0.00 1.89
3545 5499 5.124457 AGAGTGTGCCAATATTGTTGTCATC 59.876 40.000 14.25 5.91 0.00 2.92
3550 5504 5.008980 TGCCAATATTGTTGTCATCTGTGA 58.991 37.500 14.25 0.00 0.00 3.58
3571 5525 5.182001 GTGATGTGCACCAAGTATCTCTTTT 59.818 40.000 15.69 0.00 41.78 2.27
3572 5526 6.371548 GTGATGTGCACCAAGTATCTCTTTTA 59.628 38.462 15.69 0.00 41.78 1.52
3573 5527 6.595326 TGATGTGCACCAAGTATCTCTTTTAG 59.405 38.462 15.69 0.00 33.63 1.85
3607 5561 1.468395 GCTAGCTCAGTCAACGGAGAC 60.468 57.143 7.70 5.78 39.97 3.36
3632 5586 7.603024 ACTTAATTAGTCTCAGTTGGCTAACAC 59.397 37.037 15.86 4.44 33.72 3.32
3652 5606 4.766891 ACACCAGTGCATAAATTTGTAGCT 59.233 37.500 0.00 0.00 0.00 3.32
3655 5609 6.968904 CACCAGTGCATAAATTTGTAGCTTAG 59.031 38.462 0.00 0.00 0.00 2.18
3681 5635 9.952188 GAATTTTCCATTAAGCCAGTATACTTC 57.048 33.333 1.56 0.00 0.00 3.01
3683 5637 8.732746 TTTTCCATTAAGCCAGTATACTTCTC 57.267 34.615 1.56 0.00 0.00 2.87
3717 5671 9.939802 GTAATTAATCGATTACCTGTATCCCTT 57.060 33.333 17.33 0.00 36.80 3.95
3744 5698 9.515226 TTTTAGGCAAATCACTACTTGTATCTT 57.485 29.630 0.00 0.00 0.00 2.40
3745 5699 8.718102 TTAGGCAAATCACTACTTGTATCTTC 57.282 34.615 0.00 0.00 0.00 2.87
3746 5700 6.951971 AGGCAAATCACTACTTGTATCTTCT 58.048 36.000 0.00 0.00 0.00 2.85
3747 5701 7.398024 AGGCAAATCACTACTTGTATCTTCTT 58.602 34.615 0.00 0.00 0.00 2.52
3748 5702 7.885399 AGGCAAATCACTACTTGTATCTTCTTT 59.115 33.333 0.00 0.00 0.00 2.52
3749 5703 8.515414 GGCAAATCACTACTTGTATCTTCTTTT 58.485 33.333 0.00 0.00 0.00 2.27
3750 5704 9.899226 GCAAATCACTACTTGTATCTTCTTTTT 57.101 29.630 0.00 0.00 0.00 1.94
3765 5719 7.459394 TCTTCTTTTTAACACAGTACAGACG 57.541 36.000 0.00 0.00 0.00 4.18
3766 5720 5.646467 TCTTTTTAACACAGTACAGACGC 57.354 39.130 0.00 0.00 0.00 5.19
3767 5721 5.110598 TCTTTTTAACACAGTACAGACGCA 58.889 37.500 0.00 0.00 0.00 5.24
3768 5722 5.581479 TCTTTTTAACACAGTACAGACGCAA 59.419 36.000 0.00 0.00 0.00 4.85
3782 5736 2.736890 CGCAAGTCGCTCACATACA 58.263 52.632 0.00 0.00 39.08 2.29
3783 5737 0.366871 CGCAAGTCGCTCACATACAC 59.633 55.000 0.00 0.00 39.08 2.90
3784 5738 1.428448 GCAAGTCGCTCACATACACA 58.572 50.000 0.00 0.00 37.77 3.72
3785 5739 1.126846 GCAAGTCGCTCACATACACAC 59.873 52.381 0.00 0.00 37.77 3.82
3786 5740 1.386748 CAAGTCGCTCACATACACACG 59.613 52.381 0.00 0.00 0.00 4.49
3787 5741 0.732880 AGTCGCTCACATACACACGC 60.733 55.000 0.00 0.00 0.00 5.34
3788 5742 1.006825 GTCGCTCACATACACACGCA 61.007 55.000 0.00 0.00 0.00 5.24
3789 5743 0.108851 TCGCTCACATACACACGCAT 60.109 50.000 0.00 0.00 0.00 4.73
3790 5744 1.133407 TCGCTCACATACACACGCATA 59.867 47.619 0.00 0.00 0.00 3.14
3791 5745 1.255342 CGCTCACATACACACGCATAC 59.745 52.381 0.00 0.00 0.00 2.39
3792 5746 2.267426 GCTCACATACACACGCATACA 58.733 47.619 0.00 0.00 0.00 2.29
3793 5747 2.029244 GCTCACATACACACGCATACAC 59.971 50.000 0.00 0.00 0.00 2.90
3794 5748 3.511699 CTCACATACACACGCATACACT 58.488 45.455 0.00 0.00 0.00 3.55
3795 5749 3.507786 TCACATACACACGCATACACTC 58.492 45.455 0.00 0.00 0.00 3.51
3796 5750 3.057174 TCACATACACACGCATACACTCA 60.057 43.478 0.00 0.00 0.00 3.41
3797 5751 3.865164 CACATACACACGCATACACTCAT 59.135 43.478 0.00 0.00 0.00 2.90
3798 5752 4.026558 CACATACACACGCATACACTCATC 60.027 45.833 0.00 0.00 0.00 2.92
3799 5753 2.010145 ACACACGCATACACTCATCC 57.990 50.000 0.00 0.00 0.00 3.51
3800 5754 1.290203 CACACGCATACACTCATCCC 58.710 55.000 0.00 0.00 0.00 3.85
3801 5755 1.134699 CACACGCATACACTCATCCCT 60.135 52.381 0.00 0.00 0.00 4.20
3802 5756 2.100749 CACACGCATACACTCATCCCTA 59.899 50.000 0.00 0.00 0.00 3.53
3803 5757 2.965831 ACACGCATACACTCATCCCTAT 59.034 45.455 0.00 0.00 0.00 2.57
3804 5758 3.243873 ACACGCATACACTCATCCCTATG 60.244 47.826 0.00 0.00 0.00 2.23
3805 5759 3.005791 CACGCATACACTCATCCCTATGA 59.994 47.826 0.00 0.00 39.87 2.15
3806 5760 3.641436 ACGCATACACTCATCCCTATGAA 59.359 43.478 0.00 0.00 41.57 2.57
3807 5761 4.284490 ACGCATACACTCATCCCTATGAAT 59.716 41.667 0.00 0.00 41.57 2.57
3808 5762 4.628766 CGCATACACTCATCCCTATGAATG 59.371 45.833 0.00 0.00 43.41 2.67
3816 5770 8.713737 CACTCATCCCTATGAATGTATACATG 57.286 38.462 18.94 6.18 41.57 3.21
3817 5771 8.316946 CACTCATCCCTATGAATGTATACATGT 58.683 37.037 18.94 2.69 41.57 3.21
3818 5772 9.547279 ACTCATCCCTATGAATGTATACATGTA 57.453 33.333 18.94 8.27 41.57 2.29
3819 5773 9.809096 CTCATCCCTATGAATGTATACATGTAC 57.191 37.037 18.94 13.33 41.57 2.90
3820 5774 9.320295 TCATCCCTATGAATGTATACATGTACA 57.680 33.333 18.94 17.75 39.20 2.90
3821 5775 9.371136 CATCCCTATGAATGTATACATGTACAC 57.629 37.037 18.94 7.63 34.96 2.90
3822 5776 8.485578 TCCCTATGAATGTATACATGTACACA 57.514 34.615 18.71 18.71 37.40 3.72
3823 5777 8.364894 TCCCTATGAATGTATACATGTACACAC 58.635 37.037 18.79 12.07 37.40 3.82
3824 5778 7.602644 CCCTATGAATGTATACATGTACACACC 59.397 40.741 18.79 13.74 37.40 4.16
3825 5779 7.602644 CCTATGAATGTATACATGTACACACCC 59.397 40.741 18.79 13.42 37.40 4.61
3826 5780 6.553953 TGAATGTATACATGTACACACCCT 57.446 37.500 18.79 7.05 37.40 4.34
3827 5781 7.663043 TGAATGTATACATGTACACACCCTA 57.337 36.000 18.79 4.05 37.40 3.53
3828 5782 8.257602 TGAATGTATACATGTACACACCCTAT 57.742 34.615 18.79 0.32 37.40 2.57
3829 5783 8.364894 TGAATGTATACATGTACACACCCTATC 58.635 37.037 18.79 12.20 37.40 2.08
3830 5784 6.659745 TGTATACATGTACACACCCTATCC 57.340 41.667 12.91 0.00 30.00 2.59
3831 5785 5.541101 TGTATACATGTACACACCCTATCCC 59.459 44.000 12.91 0.00 30.00 3.85
3832 5786 3.130734 ACATGTACACACCCTATCCCT 57.869 47.619 0.00 0.00 0.00 4.20
3833 5787 4.274794 ACATGTACACACCCTATCCCTA 57.725 45.455 0.00 0.00 0.00 3.53
3834 5788 4.827789 ACATGTACACACCCTATCCCTAT 58.172 43.478 0.00 0.00 0.00 2.57
3835 5789 4.593206 ACATGTACACACCCTATCCCTATG 59.407 45.833 0.00 0.00 0.00 2.23
3836 5790 4.546224 TGTACACACCCTATCCCTATGA 57.454 45.455 0.00 0.00 0.00 2.15
3837 5791 4.480115 TGTACACACCCTATCCCTATGAG 58.520 47.826 0.00 0.00 0.00 2.90
3838 5792 2.330216 ACACACCCTATCCCTATGAGC 58.670 52.381 0.00 0.00 0.00 4.26
3839 5793 2.329267 CACACCCTATCCCTATGAGCA 58.671 52.381 0.00 0.00 0.00 4.26
3840 5794 2.037772 CACACCCTATCCCTATGAGCAC 59.962 54.545 0.00 0.00 0.00 4.40
3841 5795 1.625818 CACCCTATCCCTATGAGCACC 59.374 57.143 0.00 0.00 0.00 5.01
3842 5796 1.509961 ACCCTATCCCTATGAGCACCT 59.490 52.381 0.00 0.00 0.00 4.00
3843 5797 2.183679 CCCTATCCCTATGAGCACCTC 58.816 57.143 0.00 0.00 0.00 3.85
3844 5798 2.183679 CCTATCCCTATGAGCACCTCC 58.816 57.143 0.00 0.00 0.00 4.30
3845 5799 1.821753 CTATCCCTATGAGCACCTCCG 59.178 57.143 0.00 0.00 0.00 4.63
3846 5800 0.188587 ATCCCTATGAGCACCTCCGA 59.811 55.000 0.00 0.00 0.00 4.55
3847 5801 0.032515 TCCCTATGAGCACCTCCGAA 60.033 55.000 0.00 0.00 0.00 4.30
3848 5802 0.830648 CCCTATGAGCACCTCCGAAA 59.169 55.000 0.00 0.00 0.00 3.46
3849 5803 1.202580 CCCTATGAGCACCTCCGAAAG 60.203 57.143 0.00 0.00 0.00 2.62
3850 5804 1.757118 CCTATGAGCACCTCCGAAAGA 59.243 52.381 0.00 0.00 0.00 2.52
3851 5805 2.482142 CCTATGAGCACCTCCGAAAGAC 60.482 54.545 0.00 0.00 0.00 3.01
3852 5806 1.270907 ATGAGCACCTCCGAAAGACT 58.729 50.000 0.00 0.00 0.00 3.24
3853 5807 1.919240 TGAGCACCTCCGAAAGACTA 58.081 50.000 0.00 0.00 0.00 2.59
3854 5808 2.244695 TGAGCACCTCCGAAAGACTAA 58.755 47.619 0.00 0.00 0.00 2.24
3855 5809 2.231478 TGAGCACCTCCGAAAGACTAAG 59.769 50.000 0.00 0.00 0.00 2.18
3856 5810 1.066787 AGCACCTCCGAAAGACTAAGC 60.067 52.381 0.00 0.00 0.00 3.09
3857 5811 2.007547 GCACCTCCGAAAGACTAAGCC 61.008 57.143 0.00 0.00 0.00 4.35
3858 5812 0.531200 ACCTCCGAAAGACTAAGCCG 59.469 55.000 0.00 0.00 0.00 5.52
3859 5813 0.179108 CCTCCGAAAGACTAAGCCGG 60.179 60.000 0.00 0.00 41.36 6.13
3860 5814 0.806492 CTCCGAAAGACTAAGCCGGC 60.806 60.000 21.89 21.89 39.96 6.13
3861 5815 1.079405 CCGAAAGACTAAGCCGGCA 60.079 57.895 31.54 7.98 33.47 5.69
3862 5816 0.462047 CCGAAAGACTAAGCCGGCAT 60.462 55.000 31.54 21.32 33.47 4.40
3863 5817 1.202486 CCGAAAGACTAAGCCGGCATA 60.202 52.381 31.54 21.29 33.47 3.14
3864 5818 2.548067 CCGAAAGACTAAGCCGGCATAT 60.548 50.000 31.54 17.05 33.47 1.78
3865 5819 2.731976 CGAAAGACTAAGCCGGCATATC 59.268 50.000 31.54 19.70 0.00 1.63
3866 5820 3.728845 GAAAGACTAAGCCGGCATATCA 58.271 45.455 31.54 7.27 0.00 2.15
3867 5821 4.319177 GAAAGACTAAGCCGGCATATCAT 58.681 43.478 31.54 10.54 0.00 2.45
3868 5822 3.601443 AGACTAAGCCGGCATATCATC 57.399 47.619 31.54 17.82 0.00 2.92
3869 5823 3.169099 AGACTAAGCCGGCATATCATCT 58.831 45.455 31.54 19.69 0.00 2.90
3870 5824 3.580458 AGACTAAGCCGGCATATCATCTT 59.420 43.478 31.54 14.07 0.00 2.40
3871 5825 4.772624 AGACTAAGCCGGCATATCATCTTA 59.227 41.667 31.54 14.48 0.00 2.10
3872 5826 5.246203 AGACTAAGCCGGCATATCATCTTAA 59.754 40.000 31.54 0.00 0.00 1.85
3873 5827 5.865085 ACTAAGCCGGCATATCATCTTAAA 58.135 37.500 31.54 0.00 0.00 1.52
3874 5828 6.296026 ACTAAGCCGGCATATCATCTTAAAA 58.704 36.000 31.54 0.00 0.00 1.52
3875 5829 5.438761 AAGCCGGCATATCATCTTAAAAC 57.561 39.130 31.54 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.944177 TGGAGGAGGACTTTGAGGAG 58.056 55.000 0.00 0.00 0.00 3.69
3 4 2.027653 GGAGTTGGAGGAGGACTTTGAG 60.028 54.545 0.00 0.00 0.00 3.02
4 5 1.978580 GGAGTTGGAGGAGGACTTTGA 59.021 52.381 0.00 0.00 0.00 2.69
5 6 1.981495 AGGAGTTGGAGGAGGACTTTG 59.019 52.381 0.00 0.00 0.00 2.77
6 7 2.261729 GAGGAGTTGGAGGAGGACTTT 58.738 52.381 0.00 0.00 0.00 2.66
7 8 1.553651 GGAGGAGTTGGAGGAGGACTT 60.554 57.143 0.00 0.00 0.00 3.01
9 10 1.324005 CGGAGGAGTTGGAGGAGGAC 61.324 65.000 0.00 0.00 0.00 3.85
30 34 1.327690 TACCTCCGGATGCAGTGGAC 61.328 60.000 3.57 0.00 0.00 4.02
89 93 2.498726 GGCTCGAGCTCCTTGAGG 59.501 66.667 34.46 0.00 41.12 3.86
117 121 0.034896 GGAACGAGCCCTTTCTGACA 59.965 55.000 0.00 0.00 0.00 3.58
146 150 4.223125 TAGCCATGCCCCCATGCC 62.223 66.667 0.00 0.00 45.97 4.40
181 185 3.723348 GCCGCCGTCACTTTCCAC 61.723 66.667 0.00 0.00 0.00 4.02
196 200 1.838073 TTTTCCTCCTCCTGTCCGCC 61.838 60.000 0.00 0.00 0.00 6.13
208 212 5.300286 CCTACCATTCATCCACATTTTCCTC 59.700 44.000 0.00 0.00 0.00 3.71
212 216 4.946646 ACCCTACCATTCATCCACATTTT 58.053 39.130 0.00 0.00 0.00 1.82
224 228 0.323087 GGCACCGAAACCCTACCATT 60.323 55.000 0.00 0.00 0.00 3.16
311 315 2.751913 CGTCTCCTCTGTCGGACCG 61.752 68.421 7.84 7.84 0.00 4.79
312 316 1.370587 CTCGTCTCCTCTGTCGGACC 61.371 65.000 5.55 0.00 0.00 4.46
350 354 1.536907 TCCAGCCGGAAACACCCTA 60.537 57.895 5.05 0.00 38.83 3.53
351 355 2.852075 TCCAGCCGGAAACACCCT 60.852 61.111 5.05 0.00 38.83 4.34
370 374 1.136774 CGTCCGACTGATGAAGCGA 59.863 57.895 0.00 0.00 31.07 4.93
372 376 1.078759 CCACGTCCGACTGATGAAGC 61.079 60.000 0.00 0.00 33.92 3.86
373 377 1.078759 GCCACGTCCGACTGATGAAG 61.079 60.000 0.00 0.00 33.92 3.02
377 381 4.129737 CCGCCACGTCCGACTGAT 62.130 66.667 6.70 0.00 0.00 2.90
408 412 0.926293 ATATGGGGCGAATATGGGGG 59.074 55.000 0.00 0.00 0.00 5.40
409 413 2.826674 AATATGGGGCGAATATGGGG 57.173 50.000 0.00 0.00 0.00 4.96
410 414 4.207165 CCTAAATATGGGGCGAATATGGG 58.793 47.826 0.00 0.00 0.00 4.00
441 445 4.459089 GAGCTGACCGGCACCCTC 62.459 72.222 0.00 0.00 34.17 4.30
459 463 1.228337 AAACGGGCCTTAAACGCCT 60.228 52.632 0.84 0.00 46.24 5.52
470 474 2.050442 CAAACGCCTCAAACGGGC 60.050 61.111 0.00 0.00 45.57 6.13
471 475 1.164041 AGACAAACGCCTCAAACGGG 61.164 55.000 0.00 0.00 34.00 5.28
504 508 1.006102 CCCGTCACTGACTGGTCAC 60.006 63.158 10.71 0.00 33.28 3.67
522 526 3.188786 CGAGCTGTAGTTGCCCGC 61.189 66.667 0.00 0.00 0.00 6.13
542 546 1.102978 CCCCAAATAGGCCTCAAACG 58.897 55.000 9.68 0.00 35.39 3.60
551 555 1.823899 GCCGAGTGCCCCAAATAGG 60.824 63.158 0.00 0.00 37.03 2.57
652 656 7.493645 CGAAATAATAGTACTCCCTCCGTTTTT 59.506 37.037 0.00 0.00 0.00 1.94
653 657 6.982724 CGAAATAATAGTACTCCCTCCGTTTT 59.017 38.462 0.00 0.00 0.00 2.43
654 658 6.097412 ACGAAATAATAGTACTCCCTCCGTTT 59.903 38.462 0.00 0.00 0.00 3.60
655 659 5.595952 ACGAAATAATAGTACTCCCTCCGTT 59.404 40.000 0.00 0.00 0.00 4.44
656 660 5.136105 ACGAAATAATAGTACTCCCTCCGT 58.864 41.667 0.00 0.00 0.00 4.69
657 661 5.702349 ACGAAATAATAGTACTCCCTCCG 57.298 43.478 0.00 0.00 0.00 4.63
658 662 7.516198 TGTACGAAATAATAGTACTCCCTCC 57.484 40.000 0.00 0.00 40.77 4.30
659 663 7.864882 GGTTGTACGAAATAATAGTACTCCCTC 59.135 40.741 0.00 0.00 40.77 4.30
660 664 7.342799 TGGTTGTACGAAATAATAGTACTCCCT 59.657 37.037 0.00 0.00 40.77 4.20
661 665 7.491682 TGGTTGTACGAAATAATAGTACTCCC 58.508 38.462 0.00 6.56 40.77 4.30
662 666 8.975439 CATGGTTGTACGAAATAATAGTACTCC 58.025 37.037 0.00 8.73 40.77 3.85
663 667 9.525409 ACATGGTTGTACGAAATAATAGTACTC 57.475 33.333 0.00 0.00 40.77 2.59
693 697 8.030692 TGTACTAGCTGTGTACACGAAAATTAT 58.969 33.333 22.32 5.31 43.36 1.28
711 715 6.150396 ACCACTATTCTCATGTGTACTAGC 57.850 41.667 0.00 0.00 0.00 3.42
882 901 2.519377 TGGTTACCACTCGTTGTCTG 57.481 50.000 0.00 0.00 0.00 3.51
948 967 2.159028 GCTTGGGGTGAAGAGCTACTAG 60.159 54.545 0.00 0.00 32.54 2.57
949 968 1.831736 GCTTGGGGTGAAGAGCTACTA 59.168 52.381 0.00 0.00 32.54 1.82
950 969 0.615850 GCTTGGGGTGAAGAGCTACT 59.384 55.000 0.00 0.00 32.54 2.57
951 970 0.324943 TGCTTGGGGTGAAGAGCTAC 59.675 55.000 0.00 0.00 36.16 3.58
996 1023 4.844420 GCGCTTAGCTCCATGAGT 57.156 55.556 0.00 0.00 44.04 3.41
1921 3248 2.861462 ACTATTCAGAGAGCAGACGC 57.139 50.000 0.00 0.00 38.99 5.19
2057 3724 4.370917 TCAACTTAACCACCTTCACGTAC 58.629 43.478 0.00 0.00 0.00 3.67
2193 3869 6.033831 CGGCTGCAACAATATAACTTTCTTTG 59.966 38.462 0.50 0.00 0.00 2.77
2634 4330 2.872370 AGTACTCGAATTGTGTACCGC 58.128 47.619 8.71 0.00 44.72 5.68
2829 4645 1.794437 GCGTCGCTACTAGGTGAAGTG 60.794 57.143 10.68 0.00 0.00 3.16
2921 4738 8.345724 TGAGTTAACGATAAAGAGAACCTAGT 57.654 34.615 0.00 0.00 0.00 2.57
3046 4864 9.189723 AGTTACTCGCCGAATTACTAATTTATC 57.810 33.333 0.00 0.00 0.00 1.75
3051 4869 7.031226 TGTAGTTACTCGCCGAATTACTAAT 57.969 36.000 0.00 0.00 0.00 1.73
3052 4870 6.435430 TGTAGTTACTCGCCGAATTACTAA 57.565 37.500 0.00 0.00 0.00 2.24
3053 4871 6.624352 ATGTAGTTACTCGCCGAATTACTA 57.376 37.500 0.00 0.00 0.00 1.82
3054 4872 4.970662 TGTAGTTACTCGCCGAATTACT 57.029 40.909 0.00 0.00 0.00 2.24
3055 4873 6.579491 AAATGTAGTTACTCGCCGAATTAC 57.421 37.500 0.00 0.00 0.00 1.89
3056 4874 7.706159 TCTAAATGTAGTTACTCGCCGAATTA 58.294 34.615 0.00 0.00 0.00 1.40
3057 4875 6.567050 TCTAAATGTAGTTACTCGCCGAATT 58.433 36.000 0.00 0.00 0.00 2.17
3058 4876 6.140303 TCTAAATGTAGTTACTCGCCGAAT 57.860 37.500 0.00 0.00 0.00 3.34
3093 4911 3.126858 TCATTGCAAGTGAATAAGGACGC 59.873 43.478 4.94 0.00 0.00 5.19
3117 4936 7.633789 AGATTTTTAATTCCAGCTCTACTCCA 58.366 34.615 0.00 0.00 0.00 3.86
3125 4944 8.522830 TGAATTTCGAGATTTTTAATTCCAGCT 58.477 29.630 11.83 0.00 35.42 4.24
3169 4988 1.354337 CGAGCTGAACCATGTCACGG 61.354 60.000 0.00 0.00 0.00 4.94
3255 5075 9.555727 AGTTTAATGAGTAACTTGTTAGCTTCA 57.444 29.630 0.00 0.00 30.72 3.02
3277 5097 9.884465 CTTCTTATCAACGATCTGAAAAAGTTT 57.116 29.630 0.00 0.00 0.00 2.66
3298 5118 7.419711 TGGGACGAAGAAAGTATATCTTCTT 57.580 36.000 12.78 10.71 46.81 2.52
3311 5131 5.369833 TGACACTTATTTTGGGACGAAGAA 58.630 37.500 0.00 0.00 0.00 2.52
3312 5132 4.963373 TGACACTTATTTTGGGACGAAGA 58.037 39.130 0.00 0.00 0.00 2.87
3315 5135 7.931578 ATTAATGACACTTATTTTGGGACGA 57.068 32.000 0.00 0.00 0.00 4.20
3369 5314 5.221722 TGGCACACTCTCTTTCAAGATAAGT 60.222 40.000 0.00 0.00 33.66 2.24
3379 5324 7.944729 ACAATAATATTGGCACACTCTCTTT 57.055 32.000 16.36 0.00 39.29 2.52
3506 5451 5.470098 GGCACACTCTGTTTCAAGATAAAGA 59.530 40.000 0.00 0.00 0.00 2.52
3507 5452 5.239306 TGGCACACTCTGTTTCAAGATAAAG 59.761 40.000 0.00 0.00 0.00 1.85
3508 5453 5.129634 TGGCACACTCTGTTTCAAGATAAA 58.870 37.500 0.00 0.00 0.00 1.40
3509 5454 4.713553 TGGCACACTCTGTTTCAAGATAA 58.286 39.130 0.00 0.00 0.00 1.75
3510 5455 4.350368 TGGCACACTCTGTTTCAAGATA 57.650 40.909 0.00 0.00 0.00 1.98
3511 5456 3.213206 TGGCACACTCTGTTTCAAGAT 57.787 42.857 0.00 0.00 0.00 2.40
3545 5499 7.514697 AAAGAGATACTTGGTGCACATCACAG 61.515 42.308 20.43 8.64 41.63 3.66
3550 5504 6.372659 CACTAAAAGAGATACTTGGTGCACAT 59.627 38.462 20.43 2.21 38.98 3.21
3571 5525 4.030913 AGCTAGCCAGACCATTTACACTA 58.969 43.478 12.13 0.00 0.00 2.74
3572 5526 2.840651 AGCTAGCCAGACCATTTACACT 59.159 45.455 12.13 0.00 0.00 3.55
3573 5527 3.198872 GAGCTAGCCAGACCATTTACAC 58.801 50.000 12.13 0.00 0.00 2.90
3607 5561 7.064728 GGTGTTAGCCAACTGAGACTAATTAAG 59.935 40.741 0.00 0.00 35.56 1.85
3621 5575 1.247567 ATGCACTGGTGTTAGCCAAC 58.752 50.000 0.00 0.00 38.18 3.77
3623 5577 2.869101 TTATGCACTGGTGTTAGCCA 57.131 45.000 0.00 0.00 36.97 4.75
3632 5586 7.320443 TCTAAGCTACAAATTTATGCACTGG 57.680 36.000 0.00 2.32 0.00 4.00
3655 5609 9.952188 GAAGTATACTGGCTTAATGGAAAATTC 57.048 33.333 6.06 0.00 0.00 2.17
3717 5671 9.515226 AGATACAAGTAGTGATTTGCCTAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
3744 5698 5.110598 TGCGTCTGTACTGTGTTAAAAAGA 58.889 37.500 0.00 0.00 0.00 2.52
3745 5699 5.398176 TGCGTCTGTACTGTGTTAAAAAG 57.602 39.130 0.00 0.00 0.00 2.27
3746 5700 5.352016 ACTTGCGTCTGTACTGTGTTAAAAA 59.648 36.000 0.00 0.00 0.00 1.94
3747 5701 4.871557 ACTTGCGTCTGTACTGTGTTAAAA 59.128 37.500 0.00 0.00 0.00 1.52
3748 5702 4.435425 ACTTGCGTCTGTACTGTGTTAAA 58.565 39.130 0.00 0.00 0.00 1.52
3749 5703 4.046462 GACTTGCGTCTGTACTGTGTTAA 58.954 43.478 0.00 0.00 37.19 2.01
3750 5704 3.635331 GACTTGCGTCTGTACTGTGTTA 58.365 45.455 0.00 0.00 37.19 2.41
3751 5705 2.470821 GACTTGCGTCTGTACTGTGTT 58.529 47.619 0.00 0.00 37.19 3.32
3752 5706 1.599667 CGACTTGCGTCTGTACTGTGT 60.600 52.381 0.00 0.00 38.03 3.72
3753 5707 1.053048 CGACTTGCGTCTGTACTGTG 58.947 55.000 0.00 0.00 38.03 3.66
3754 5708 0.663568 GCGACTTGCGTCTGTACTGT 60.664 55.000 0.00 0.00 43.41 3.55
3755 5709 2.062779 GCGACTTGCGTCTGTACTG 58.937 57.895 0.00 0.00 43.41 2.74
3756 5710 4.554163 GCGACTTGCGTCTGTACT 57.446 55.556 0.00 0.00 43.41 2.73
3765 5719 1.126846 GTGTGTATGTGAGCGACTTGC 59.873 52.381 0.00 0.00 46.98 4.01
3766 5720 1.386748 CGTGTGTATGTGAGCGACTTG 59.613 52.381 0.00 0.00 0.00 3.16
3767 5721 1.698165 CGTGTGTATGTGAGCGACTT 58.302 50.000 0.00 0.00 0.00 3.01
3768 5722 0.732880 GCGTGTGTATGTGAGCGACT 60.733 55.000 0.00 0.00 0.00 4.18
3769 5723 1.006825 TGCGTGTGTATGTGAGCGAC 61.007 55.000 0.00 0.00 0.00 5.19
3770 5724 0.108851 ATGCGTGTGTATGTGAGCGA 60.109 50.000 0.00 0.00 0.00 4.93
3771 5725 1.255342 GTATGCGTGTGTATGTGAGCG 59.745 52.381 0.00 0.00 0.00 5.03
3772 5726 2.029244 GTGTATGCGTGTGTATGTGAGC 59.971 50.000 0.00 0.00 0.00 4.26
3773 5727 3.511699 AGTGTATGCGTGTGTATGTGAG 58.488 45.455 0.00 0.00 0.00 3.51
3774 5728 3.057174 TGAGTGTATGCGTGTGTATGTGA 60.057 43.478 0.00 0.00 0.00 3.58
3775 5729 3.249917 TGAGTGTATGCGTGTGTATGTG 58.750 45.455 0.00 0.00 0.00 3.21
3776 5730 3.586100 TGAGTGTATGCGTGTGTATGT 57.414 42.857 0.00 0.00 0.00 2.29
3777 5731 3.490896 GGATGAGTGTATGCGTGTGTATG 59.509 47.826 0.00 0.00 0.00 2.39
3778 5732 3.492656 GGGATGAGTGTATGCGTGTGTAT 60.493 47.826 0.00 0.00 0.00 2.29
3779 5733 2.159156 GGGATGAGTGTATGCGTGTGTA 60.159 50.000 0.00 0.00 0.00 2.90
3780 5734 1.405526 GGGATGAGTGTATGCGTGTGT 60.406 52.381 0.00 0.00 0.00 3.72
3781 5735 1.134699 AGGGATGAGTGTATGCGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
3782 5736 1.195115 AGGGATGAGTGTATGCGTGT 58.805 50.000 0.00 0.00 0.00 4.49
3783 5737 3.005791 TCATAGGGATGAGTGTATGCGTG 59.994 47.826 0.00 0.00 37.15 5.34
3784 5738 3.230976 TCATAGGGATGAGTGTATGCGT 58.769 45.455 0.00 0.00 37.15 5.24
3785 5739 3.942130 TCATAGGGATGAGTGTATGCG 57.058 47.619 0.00 0.00 37.15 4.73
3792 5746 8.441311 ACATGTATACATTCATAGGGATGAGT 57.559 34.615 15.85 3.54 43.03 3.41
3793 5747 9.809096 GTACATGTATACATTCATAGGGATGAG 57.191 37.037 15.85 2.93 43.03 2.90
3794 5748 9.320295 TGTACATGTATACATTCATAGGGATGA 57.680 33.333 15.85 0.00 35.57 2.92
3795 5749 9.371136 GTGTACATGTATACATTCATAGGGATG 57.629 37.037 23.33 5.06 37.40 3.51
3796 5750 9.100197 TGTGTACATGTATACATTCATAGGGAT 57.900 33.333 26.07 0.00 37.40 3.85
3797 5751 8.364894 GTGTGTACATGTATACATTCATAGGGA 58.635 37.037 30.38 8.02 38.94 4.20
3798 5752 7.602644 GGTGTGTACATGTATACATTCATAGGG 59.397 40.741 30.38 5.68 38.94 3.53
3799 5753 7.602644 GGGTGTGTACATGTATACATTCATAGG 59.397 40.741 30.38 6.37 38.94 2.57
3800 5754 8.367911 AGGGTGTGTACATGTATACATTCATAG 58.632 37.037 30.38 7.07 38.94 2.23
3801 5755 8.257602 AGGGTGTGTACATGTATACATTCATA 57.742 34.615 30.38 10.56 38.94 2.15
3802 5756 7.136822 AGGGTGTGTACATGTATACATTCAT 57.863 36.000 30.38 22.00 38.94 2.57
3803 5757 6.553953 AGGGTGTGTACATGTATACATTCA 57.446 37.500 30.38 12.08 38.94 2.57
3804 5758 7.817962 GGATAGGGTGTGTACATGTATACATTC 59.182 40.741 30.38 24.74 38.94 2.67
3805 5759 7.256547 GGGATAGGGTGTGTACATGTATACATT 60.257 40.741 30.38 22.30 38.94 2.71
3806 5760 6.212791 GGGATAGGGTGTGTACATGTATACAT 59.787 42.308 30.38 20.38 38.94 2.29
3807 5761 5.541101 GGGATAGGGTGTGTACATGTATACA 59.459 44.000 26.07 26.07 35.31 2.29
3808 5762 5.778750 AGGGATAGGGTGTGTACATGTATAC 59.221 44.000 21.98 21.98 0.00 1.47
3809 5763 5.972698 AGGGATAGGGTGTGTACATGTATA 58.027 41.667 9.18 3.08 0.00 1.47
3810 5764 4.827789 AGGGATAGGGTGTGTACATGTAT 58.172 43.478 9.18 0.00 0.00 2.29
3811 5765 4.274794 AGGGATAGGGTGTGTACATGTA 57.725 45.455 0.08 0.08 0.00 2.29
3812 5766 3.130734 AGGGATAGGGTGTGTACATGT 57.869 47.619 2.69 2.69 0.00 3.21
3813 5767 4.838423 TCATAGGGATAGGGTGTGTACATG 59.162 45.833 0.00 0.00 0.00 3.21
3814 5768 5.087323 CTCATAGGGATAGGGTGTGTACAT 58.913 45.833 0.00 0.00 0.00 2.29
3815 5769 4.480115 CTCATAGGGATAGGGTGTGTACA 58.520 47.826 0.00 0.00 0.00 2.90
3816 5770 3.258622 GCTCATAGGGATAGGGTGTGTAC 59.741 52.174 0.00 0.00 0.00 2.90
3817 5771 3.116900 TGCTCATAGGGATAGGGTGTGTA 60.117 47.826 0.00 0.00 0.00 2.90
3818 5772 2.330216 GCTCATAGGGATAGGGTGTGT 58.670 52.381 0.00 0.00 0.00 3.72
3819 5773 2.037772 GTGCTCATAGGGATAGGGTGTG 59.962 54.545 0.00 0.00 0.00 3.82
3820 5774 2.330216 GTGCTCATAGGGATAGGGTGT 58.670 52.381 0.00 0.00 0.00 4.16
3821 5775 1.625818 GGTGCTCATAGGGATAGGGTG 59.374 57.143 0.00 0.00 0.00 4.61
3822 5776 1.509961 AGGTGCTCATAGGGATAGGGT 59.490 52.381 0.00 0.00 0.00 4.34
3823 5777 2.183679 GAGGTGCTCATAGGGATAGGG 58.816 57.143 0.00 0.00 0.00 3.53
3824 5778 2.183679 GGAGGTGCTCATAGGGATAGG 58.816 57.143 0.00 0.00 31.08 2.57
3825 5779 1.821753 CGGAGGTGCTCATAGGGATAG 59.178 57.143 0.00 0.00 31.08 2.08
3826 5780 1.427753 TCGGAGGTGCTCATAGGGATA 59.572 52.381 0.00 0.00 31.08 2.59
3827 5781 0.188587 TCGGAGGTGCTCATAGGGAT 59.811 55.000 0.00 0.00 31.08 3.85
3828 5782 0.032515 TTCGGAGGTGCTCATAGGGA 60.033 55.000 0.00 0.00 31.08 4.20
3829 5783 0.830648 TTTCGGAGGTGCTCATAGGG 59.169 55.000 0.00 0.00 31.08 3.53
3830 5784 1.757118 TCTTTCGGAGGTGCTCATAGG 59.243 52.381 0.00 0.00 31.08 2.57
3831 5785 2.428890 AGTCTTTCGGAGGTGCTCATAG 59.571 50.000 0.00 0.00 31.08 2.23
3832 5786 2.457598 AGTCTTTCGGAGGTGCTCATA 58.542 47.619 0.00 0.00 31.08 2.15
3833 5787 1.270907 AGTCTTTCGGAGGTGCTCAT 58.729 50.000 0.00 0.00 31.08 2.90
3834 5788 1.919240 TAGTCTTTCGGAGGTGCTCA 58.081 50.000 0.00 0.00 31.08 4.26
3835 5789 2.882324 CTTAGTCTTTCGGAGGTGCTC 58.118 52.381 0.00 0.00 0.00 4.26
3836 5790 1.066787 GCTTAGTCTTTCGGAGGTGCT 60.067 52.381 0.00 0.00 0.00 4.40
3837 5791 1.360820 GCTTAGTCTTTCGGAGGTGC 58.639 55.000 0.00 0.00 0.00 5.01
3838 5792 1.736032 CGGCTTAGTCTTTCGGAGGTG 60.736 57.143 0.00 0.00 0.00 4.00
3839 5793 0.531200 CGGCTTAGTCTTTCGGAGGT 59.469 55.000 0.00 0.00 0.00 3.85
3840 5794 0.179108 CCGGCTTAGTCTTTCGGAGG 60.179 60.000 0.00 0.00 42.94 4.30
3841 5795 0.806492 GCCGGCTTAGTCTTTCGGAG 60.806 60.000 22.15 0.00 42.94 4.63
3842 5796 1.217244 GCCGGCTTAGTCTTTCGGA 59.783 57.895 22.15 0.00 42.94 4.55
3843 5797 0.462047 ATGCCGGCTTAGTCTTTCGG 60.462 55.000 29.70 0.00 43.13 4.30
3844 5798 2.218953 TATGCCGGCTTAGTCTTTCG 57.781 50.000 29.70 0.00 0.00 3.46
3845 5799 3.728845 TGATATGCCGGCTTAGTCTTTC 58.271 45.455 29.70 18.59 0.00 2.62
3846 5800 3.838244 TGATATGCCGGCTTAGTCTTT 57.162 42.857 29.70 10.12 0.00 2.52
3847 5801 3.580458 AGATGATATGCCGGCTTAGTCTT 59.420 43.478 29.70 19.48 0.00 3.01
3848 5802 3.169099 AGATGATATGCCGGCTTAGTCT 58.831 45.455 29.70 23.43 0.00 3.24
3849 5803 3.601443 AGATGATATGCCGGCTTAGTC 57.399 47.619 29.70 21.82 0.00 2.59
3850 5804 5.483685 TTAAGATGATATGCCGGCTTAGT 57.516 39.130 29.70 15.20 0.00 2.24
3851 5805 6.603095 GTTTTAAGATGATATGCCGGCTTAG 58.397 40.000 29.70 0.00 0.00 2.18
3852 5806 6.554334 GTTTTAAGATGATATGCCGGCTTA 57.446 37.500 29.70 25.95 0.00 3.09
3853 5807 5.438761 GTTTTAAGATGATATGCCGGCTT 57.561 39.130 29.70 24.47 0.00 4.35


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

AutoCloner maintained by Alex Coulton.