Multiple sequence alignment - TraesCS2D01G122000

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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 TraesCS2D01G122000 chr2D 100.000 2864 0 0 1 2864 71256923 71254060 0.000000e+00 5289.0
1 TraesCS2D01G122000 chr2D 93.824 1020 46 6 1862 2864 5216523 5215504 0.000000e+00 1519.0
2 TraesCS2D01G122000 chr2D 91.658 1007 77 7 1862 2864 545350143 545349140 0.000000e+00 1387.0
3 TraesCS2D01G122000 chr2D 93.103 696 39 4 32 723 71383067 71382377 0.000000e+00 1011.0
4 TraesCS2D01G122000 chr2D 82.609 253 44 0 1 253 97231346 97231598 1.030000e-54 224.0
5 TraesCS2D01G122000 chr2D 78.182 275 38 12 1 256 157037661 157037390 3.820000e-34 156.0
6 TraesCS2D01G122000 chr3D 94.412 1020 40 3 1862 2864 444692197 444693216 0.000000e+00 1552.0
7 TraesCS2D01G122000 chr3D 94.398 357 16 3 1860 2215 279338005 279338358 1.940000e-151 545.0
8 TraesCS2D01G122000 chr3D 86.207 232 23 2 1 232 456905803 456906025 2.850000e-60 243.0
9 TraesCS2D01G122000 chr3D 77.679 112 18 5 143 251 478735841 478735948 8.570000e-06 62.1
10 TraesCS2D01G122000 chr1A 93.180 1041 68 3 823 1861 341018986 341020025 0.000000e+00 1526.0
11 TraesCS2D01G122000 chr1A 78.214 280 34 18 1 260 403148670 403148398 1.370000e-33 154.0
12 TraesCS2D01G122000 chr1A 81.176 170 27 5 70 237 548749183 548749017 6.440000e-27 132.0
13 TraesCS2D01G122000 chr7B 91.343 1005 85 2 1861 2864 472617986 472616983 0.000000e+00 1373.0
14 TraesCS2D01G122000 chr5D 91.144 1005 82 3 1862 2864 254252976 254251977 0.000000e+00 1356.0
15 TraesCS2D01G122000 chr5D 84.064 251 32 2 1 251 135233546 135233304 4.770000e-58 235.0
16 TraesCS2D01G122000 chr5D 80.075 266 35 5 1 249 470049868 470049604 6.300000e-42 182.0
17 TraesCS2D01G122000 chr5D 82.412 199 17 6 1 182 445066843 445067040 1.060000e-34 158.0
18 TraesCS2D01G122000 chr6D 90.188 1009 89 7 1862 2864 70416764 70415760 0.000000e+00 1306.0
19 TraesCS2D01G122000 chr6D 86.700 203 26 1 6 207 324594812 324594610 1.030000e-54 224.0
20 TraesCS2D01G122000 chr6D 81.699 153 9 3 1 135 381992427 381992276 3.020000e-20 110.0
21 TraesCS2D01G122000 chr4D 90.159 1006 93 6 1861 2863 438681080 438680078 0.000000e+00 1304.0
22 TraesCS2D01G122000 chr4D 85.514 214 21 3 5 217 507760953 507761157 6.210000e-52 215.0
23 TraesCS2D01G122000 chr4D 80.982 163 26 4 70 229 12416105 12415945 1.080000e-24 124.0
24 TraesCS2D01G122000 chr4A 88.557 1005 111 4 1862 2864 298121450 298122452 0.000000e+00 1216.0
25 TraesCS2D01G122000 chr2A 87.711 1009 114 7 1862 2864 146917271 146918275 0.000000e+00 1168.0
26 TraesCS2D01G122000 chr2A 81.707 246 31 12 1 237 653464198 653463958 2.910000e-45 193.0
27 TraesCS2D01G122000 chr4B 87.657 956 114 3 909 1861 621966699 621967653 0.000000e+00 1109.0
28 TraesCS2D01G122000 chr4B 88.636 176 20 0 2 177 67494595 67494770 6.210000e-52 215.0
29 TraesCS2D01G122000 chr4B 92.308 39 3 0 202 240 57270705 57270667 3.990000e-04 56.5
30 TraesCS2D01G122000 chr3B 85.660 1046 133 12 820 1861 810139474 810140506 0.000000e+00 1085.0
31 TraesCS2D01G122000 chr1B 85.942 1003 120 11 865 1861 394907042 394908029 0.000000e+00 1051.0
32 TraesCS2D01G122000 chr1B 84.564 1043 151 10 824 1860 678554974 678556012 0.000000e+00 1026.0
33 TraesCS2D01G122000 chr1B 91.755 376 27 1 1862 2237 662346967 662347338 1.180000e-143 520.0
34 TraesCS2D01G122000 chr1B 83.004 253 35 1 1 253 645086018 645085774 3.710000e-54 222.0
35 TraesCS2D01G122000 chr1B 85.714 189 27 0 43 231 301038720 301038908 1.740000e-47 200.0
36 TraesCS2D01G122000 chr1B 96.875 32 1 0 267 298 50029766 50029797 1.000000e-03 54.7
37 TraesCS2D01G122000 chr2B 84.586 1038 153 7 828 1861 534244926 534243892 0.000000e+00 1024.0
38 TraesCS2D01G122000 chr2B 87.903 248 30 0 6 253 148249805 148250052 2.790000e-75 292.0
39 TraesCS2D01G122000 chr2B 81.008 258 38 6 2 249 417252261 417252005 8.100000e-46 195.0
40 TraesCS2D01G122000 chr2B 97.500 40 1 0 260 299 88844387 88844348 5.120000e-08 69.4
41 TraesCS2D01G122000 chr5A 81.172 956 160 17 825 1767 396691324 396692272 0.000000e+00 750.0
42 TraesCS2D01G122000 chr1D 85.130 269 38 1 32 298 449488328 449488060 1.010000e-69 274.0
43 TraesCS2D01G122000 chr1D 84.109 258 34 5 1 253 11252955 11252700 2.850000e-60 243.0
44 TraesCS2D01G122000 chr1D 80.258 233 38 7 70 298 37415571 37415343 4.910000e-38 169.0
45 TraesCS2D01G122000 chr1D 79.268 246 35 7 1 230 365300691 365300446 1.060000e-34 158.0
46 TraesCS2D01G122000 chr7D 86.975 238 29 1 13 250 463895896 463895661 1.690000e-67 267.0
47 TraesCS2D01G122000 chr7D 84.649 228 24 4 1 227 579966792 579967009 1.730000e-52 217.0
48 TraesCS2D01G122000 chr6A 82.946 258 31 6 1 256 442040757 442040511 1.340000e-53 220.0


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 TraesCS2D01G122000 chr2D 71254060 71256923 2863 True 5289 5289 100.000 1 2864 1 chr2D.!!$R2 2863
1 TraesCS2D01G122000 chr2D 5215504 5216523 1019 True 1519 1519 93.824 1862 2864 1 chr2D.!!$R1 1002
2 TraesCS2D01G122000 chr2D 545349140 545350143 1003 True 1387 1387 91.658 1862 2864 1 chr2D.!!$R5 1002
3 TraesCS2D01G122000 chr2D 71382377 71383067 690 True 1011 1011 93.103 32 723 1 chr2D.!!$R3 691
4 TraesCS2D01G122000 chr3D 444692197 444693216 1019 False 1552 1552 94.412 1862 2864 1 chr3D.!!$F2 1002
5 TraesCS2D01G122000 chr1A 341018986 341020025 1039 False 1526 1526 93.180 823 1861 1 chr1A.!!$F1 1038
6 TraesCS2D01G122000 chr7B 472616983 472617986 1003 True 1373 1373 91.343 1861 2864 1 chr7B.!!$R1 1003
7 TraesCS2D01G122000 chr5D 254251977 254252976 999 True 1356 1356 91.144 1862 2864 1 chr5D.!!$R2 1002
8 TraesCS2D01G122000 chr6D 70415760 70416764 1004 True 1306 1306 90.188 1862 2864 1 chr6D.!!$R1 1002
9 TraesCS2D01G122000 chr4D 438680078 438681080 1002 True 1304 1304 90.159 1861 2863 1 chr4D.!!$R2 1002
10 TraesCS2D01G122000 chr4A 298121450 298122452 1002 False 1216 1216 88.557 1862 2864 1 chr4A.!!$F1 1002
11 TraesCS2D01G122000 chr2A 146917271 146918275 1004 False 1168 1168 87.711 1862 2864 1 chr2A.!!$F1 1002
12 TraesCS2D01G122000 chr4B 621966699 621967653 954 False 1109 1109 87.657 909 1861 1 chr4B.!!$F2 952
13 TraesCS2D01G122000 chr3B 810139474 810140506 1032 False 1085 1085 85.660 820 1861 1 chr3B.!!$F1 1041
14 TraesCS2D01G122000 chr1B 394907042 394908029 987 False 1051 1051 85.942 865 1861 1 chr1B.!!$F3 996
15 TraesCS2D01G122000 chr1B 678554974 678556012 1038 False 1026 1026 84.564 824 1860 1 chr1B.!!$F5 1036
16 TraesCS2D01G122000 chr2B 534243892 534244926 1034 True 1024 1024 84.586 828 1861 1 chr2B.!!$R3 1033
17 TraesCS2D01G122000 chr5A 396691324 396692272 948 False 750 750 81.172 825 1767 1 chr5A.!!$F1 942

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
645 650 0.036294 CCCTCTTCCGGGTTCAGTTC 60.036 60.0 0.0 0.0 39.51 3.01 F
678 683 0.251916 CTAGTGGATGCGGGTTCCAA 59.748 55.0 0.0 0.0 44.62 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1814 1834 0.610785 GGCATCCCCGTTTCTTCCAA 60.611 55.0 0.0 0.0 0.00 3.53 R
2607 2658 0.798771 CGACGGCAGAGCTAAGTCAC 60.799 60.0 0.0 0.0 31.92 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
18 19 3.231734 CACTGTTGGATGAAGCCGA 57.768 52.632 0.00 0.00 0.00 5.54
19 20 1.522668 CACTGTTGGATGAAGCCGAA 58.477 50.000 0.00 0.00 0.00 4.30
20 21 1.466167 CACTGTTGGATGAAGCCGAAG 59.534 52.381 0.00 0.00 0.00 3.79
34 35 2.767536 CGAAGGGGCAGTATGTGTG 58.232 57.895 0.00 0.00 39.31 3.82
48 49 0.824109 TGTGTGGGACGAGATGATCC 59.176 55.000 0.00 0.00 0.00 3.36
61 62 5.082059 CGAGATGATCCGTTGAAAAACTTG 58.918 41.667 0.00 0.00 0.00 3.16
66 67 4.399618 TGATCCGTTGAAAAACTTGTTGGA 59.600 37.500 0.00 0.00 0.00 3.53
67 68 4.099380 TCCGTTGAAAAACTTGTTGGAC 57.901 40.909 0.00 0.00 0.00 4.02
68 69 3.506455 TCCGTTGAAAAACTTGTTGGACA 59.494 39.130 0.00 0.00 0.00 4.02
69 70 4.158764 TCCGTTGAAAAACTTGTTGGACAT 59.841 37.500 0.00 0.00 0.00 3.06
86 87 5.003160 TGGACATCGAATTTGAGACATTGT 58.997 37.500 1.10 0.22 0.00 2.71
105 106 7.739295 ACATTGTTGTACTAGACTTATTTGCG 58.261 34.615 0.00 0.00 33.16 4.85
113 114 8.030692 TGTACTAGACTTATTTGCGTGTTATGT 58.969 33.333 0.00 0.00 0.00 2.29
130 131 7.436970 CGTGTTATGTATGGATAGTTTGTGCTA 59.563 37.037 0.00 0.00 0.00 3.49
194 195 4.766404 ATTTGGTCCGCTAAGTCAAAAG 57.234 40.909 0.00 0.00 32.23 2.27
198 199 0.319083 TCCGCTAAGTCAAAAGCCGA 59.681 50.000 0.00 0.00 35.22 5.54
310 311 1.202639 TGCCCTTACAGTGTGAGTGTG 60.203 52.381 13.48 3.77 33.15 3.82
317 318 1.202521 ACAGTGTGAGTGTGATTGCGA 60.203 47.619 0.00 0.00 29.04 5.10
326 327 0.107643 TGTGATTGCGACCAGGTCAA 59.892 50.000 20.13 8.27 32.09 3.18
351 352 4.426971 TGCTAGACGCACCCTGTA 57.573 55.556 0.00 0.00 45.47 2.74
422 425 9.661954 ACATATTTCTCTCTACCTCCTTTCATA 57.338 33.333 0.00 0.00 0.00 2.15
430 433 3.438297 ACCTCCTTTCATATCGTCACG 57.562 47.619 0.00 0.00 0.00 4.35
447 450 1.000283 CACGCAAGGCTAGAGGATAGG 60.000 57.143 0.00 0.00 46.39 2.57
448 451 0.037790 CGCAAGGCTAGAGGATAGGC 60.038 60.000 0.00 0.50 40.02 3.93
457 460 3.768757 GCTAGAGGATAGGCTCACATCAT 59.231 47.826 0.00 0.00 0.00 2.45
465 468 1.450134 GCTCACATCATGACCGCCA 60.450 57.895 0.00 0.00 32.37 5.69
495 498 0.613853 TATAGAATCGGGAGGGGCCG 60.614 60.000 0.00 0.00 37.63 6.13
510 513 2.860293 CCGTCACACCGATGTTGC 59.140 61.111 0.00 0.00 36.72 4.17
516 519 2.031245 GTCACACCGATGTTGCAATCAA 60.031 45.455 0.59 0.00 36.72 2.57
561 566 1.508088 GAATGTTGCAAGGCCGAGG 59.492 57.895 0.00 0.00 0.00 4.63
562 567 1.937546 GAATGTTGCAAGGCCGAGGG 61.938 60.000 0.00 0.00 0.00 4.30
580 585 4.007644 CAGGCGGCTCTGACCACA 62.008 66.667 9.32 0.00 36.93 4.17
581 586 3.699894 AGGCGGCTCTGACCACAG 61.700 66.667 5.25 0.00 44.66 3.66
584 589 4.056125 CGGCTCTGACCACAGCGA 62.056 66.667 0.00 0.00 43.17 4.93
585 590 2.125753 GGCTCTGACCACAGCGAG 60.126 66.667 0.00 0.00 43.17 5.03
586 591 2.125753 GCTCTGACCACAGCGAGG 60.126 66.667 0.00 0.00 43.17 4.63
587 592 2.575993 CTCTGACCACAGCGAGGG 59.424 66.667 0.00 0.00 43.17 4.30
600 605 3.009714 GAGGGGCCGAGGGAGTTT 61.010 66.667 0.00 0.00 0.00 2.66
601 606 3.009714 AGGGGCCGAGGGAGTTTC 61.010 66.667 0.00 0.00 0.00 2.78
602 607 4.111053 GGGGCCGAGGGAGTTTCC 62.111 72.222 0.00 0.00 35.23 3.13
603 608 4.468689 GGGCCGAGGGAGTTTCCG 62.469 72.222 0.00 0.00 37.43 4.30
604 609 4.468689 GGCCGAGGGAGTTTCCGG 62.469 72.222 0.00 0.00 44.34 5.14
605 610 4.468689 GCCGAGGGAGTTTCCGGG 62.469 72.222 0.00 0.00 42.02 5.73
606 611 2.682494 CCGAGGGAGTTTCCGGGA 60.682 66.667 0.00 0.00 37.43 5.14
607 612 2.288025 CCGAGGGAGTTTCCGGGAA 61.288 63.158 5.09 5.09 37.43 3.97
608 613 1.675219 CGAGGGAGTTTCCGGGAAA 59.325 57.895 18.03 18.03 37.43 3.13
609 614 0.252197 CGAGGGAGTTTCCGGGAAAT 59.748 55.000 23.98 13.47 37.43 2.17
610 615 1.751437 GAGGGAGTTTCCGGGAAATG 58.249 55.000 23.98 0.00 37.43 2.32
611 616 0.331616 AGGGAGTTTCCGGGAAATGG 59.668 55.000 23.98 0.00 37.43 3.16
612 617 0.683179 GGGAGTTTCCGGGAAATGGG 60.683 60.000 23.98 0.00 37.43 4.00
613 618 0.683179 GGAGTTTCCGGGAAATGGGG 60.683 60.000 23.98 0.00 33.97 4.96
614 619 0.330267 GAGTTTCCGGGAAATGGGGA 59.670 55.000 23.98 0.00 33.97 4.81
615 620 1.007607 AGTTTCCGGGAAATGGGGAT 58.992 50.000 23.98 5.25 33.97 3.85
616 621 1.361197 AGTTTCCGGGAAATGGGGATT 59.639 47.619 23.98 0.00 33.97 3.01
617 622 2.583566 AGTTTCCGGGAAATGGGGATTA 59.416 45.455 23.98 0.00 33.97 1.75
618 623 2.956333 GTTTCCGGGAAATGGGGATTAG 59.044 50.000 23.98 0.00 33.97 1.73
619 624 0.476771 TCCGGGAAATGGGGATTAGC 59.523 55.000 0.00 0.00 0.00 3.09
620 625 0.889186 CCGGGAAATGGGGATTAGCG 60.889 60.000 0.00 0.00 0.00 4.26
621 626 0.107831 CGGGAAATGGGGATTAGCGA 59.892 55.000 0.00 0.00 0.00 4.93
622 627 1.605753 GGGAAATGGGGATTAGCGAC 58.394 55.000 0.00 0.00 0.00 5.19
623 628 1.143073 GGGAAATGGGGATTAGCGACT 59.857 52.381 0.00 0.00 0.00 4.18
624 629 2.370849 GGGAAATGGGGATTAGCGACTA 59.629 50.000 0.00 0.00 0.00 2.59
625 630 3.009143 GGGAAATGGGGATTAGCGACTAT 59.991 47.826 0.00 0.00 0.00 2.12
626 631 4.254492 GGAAATGGGGATTAGCGACTATC 58.746 47.826 0.00 0.00 0.00 2.08
627 632 3.983044 AATGGGGATTAGCGACTATCC 57.017 47.619 0.00 0.00 0.00 2.59
633 638 4.443913 GGATTAGCGACTATCCCTCTTC 57.556 50.000 0.00 0.00 0.00 2.87
634 639 3.193903 GGATTAGCGACTATCCCTCTTCC 59.806 52.174 0.00 0.00 0.00 3.46
635 640 1.893544 TAGCGACTATCCCTCTTCCG 58.106 55.000 0.00 0.00 0.00 4.30
636 641 0.824182 AGCGACTATCCCTCTTCCGG 60.824 60.000 0.00 0.00 0.00 5.14
637 642 1.807495 GCGACTATCCCTCTTCCGGG 61.807 65.000 0.00 0.00 46.13 5.73
638 643 0.467659 CGACTATCCCTCTTCCGGGT 60.468 60.000 0.00 0.00 44.95 5.28
639 644 1.790818 GACTATCCCTCTTCCGGGTT 58.209 55.000 0.00 0.00 44.95 4.11
640 645 1.687660 GACTATCCCTCTTCCGGGTTC 59.312 57.143 0.00 0.00 44.95 3.62
641 646 1.007963 ACTATCCCTCTTCCGGGTTCA 59.992 52.381 0.00 0.00 44.95 3.18
642 647 1.689273 CTATCCCTCTTCCGGGTTCAG 59.311 57.143 0.00 0.00 44.95 3.02
643 648 0.252742 ATCCCTCTTCCGGGTTCAGT 60.253 55.000 0.00 0.00 44.95 3.41
644 649 0.473117 TCCCTCTTCCGGGTTCAGTT 60.473 55.000 0.00 0.00 44.95 3.16
645 650 0.036294 CCCTCTTCCGGGTTCAGTTC 60.036 60.000 0.00 0.00 39.51 3.01
646 651 0.977395 CCTCTTCCGGGTTCAGTTCT 59.023 55.000 0.00 0.00 0.00 3.01
647 652 2.176889 CCTCTTCCGGGTTCAGTTCTA 58.823 52.381 0.00 0.00 0.00 2.10
648 653 2.565834 CCTCTTCCGGGTTCAGTTCTAA 59.434 50.000 0.00 0.00 0.00 2.10
649 654 3.007614 CCTCTTCCGGGTTCAGTTCTAAA 59.992 47.826 0.00 0.00 0.00 1.85
650 655 3.995048 CTCTTCCGGGTTCAGTTCTAAAC 59.005 47.826 0.00 0.00 0.00 2.01
651 656 2.845363 TCCGGGTTCAGTTCTAAACC 57.155 50.000 0.00 0.00 34.65 3.27
652 657 2.048601 TCCGGGTTCAGTTCTAAACCA 58.951 47.619 0.00 0.00 37.05 3.67
653 658 2.640826 TCCGGGTTCAGTTCTAAACCAT 59.359 45.455 0.00 0.00 37.05 3.55
654 659 3.073356 TCCGGGTTCAGTTCTAAACCATT 59.927 43.478 0.00 0.00 37.05 3.16
655 660 3.824443 CCGGGTTCAGTTCTAAACCATTT 59.176 43.478 7.13 0.00 37.05 2.32
656 661 4.082949 CCGGGTTCAGTTCTAAACCATTTC 60.083 45.833 7.13 0.00 37.05 2.17
657 662 4.517453 CGGGTTCAGTTCTAAACCATTTCA 59.483 41.667 7.13 0.00 37.05 2.69
658 663 5.183140 CGGGTTCAGTTCTAAACCATTTCAT 59.817 40.000 7.13 0.00 37.05 2.57
659 664 6.621613 GGGTTCAGTTCTAAACCATTTCATC 58.378 40.000 7.13 0.00 37.05 2.92
660 665 6.434340 GGGTTCAGTTCTAAACCATTTCATCT 59.566 38.462 7.13 0.00 37.05 2.90
661 666 7.610305 GGGTTCAGTTCTAAACCATTTCATCTA 59.390 37.037 7.13 0.00 37.05 1.98
662 667 8.669243 GGTTCAGTTCTAAACCATTTCATCTAG 58.331 37.037 0.39 0.00 35.46 2.43
663 668 9.220767 GTTCAGTTCTAAACCATTTCATCTAGT 57.779 33.333 0.00 0.00 0.00 2.57
664 669 8.777865 TCAGTTCTAAACCATTTCATCTAGTG 57.222 34.615 0.00 0.00 0.00 2.74
665 670 7.824289 TCAGTTCTAAACCATTTCATCTAGTGG 59.176 37.037 0.00 0.00 37.74 4.00
666 671 7.824289 CAGTTCTAAACCATTTCATCTAGTGGA 59.176 37.037 2.03 0.00 35.69 4.02
667 672 8.552296 AGTTCTAAACCATTTCATCTAGTGGAT 58.448 33.333 2.03 0.00 35.69 3.41
675 680 1.871080 CATCTAGTGGATGCGGGTTC 58.129 55.000 3.28 0.00 44.21 3.62
676 681 0.759346 ATCTAGTGGATGCGGGTTCC 59.241 55.000 0.00 0.00 32.69 3.62
677 682 0.616395 TCTAGTGGATGCGGGTTCCA 60.616 55.000 0.00 0.00 40.96 3.53
678 683 0.251916 CTAGTGGATGCGGGTTCCAA 59.748 55.000 0.00 0.00 44.62 3.53
679 684 0.693622 TAGTGGATGCGGGTTCCAAA 59.306 50.000 0.00 0.00 44.62 3.28
680 685 0.893727 AGTGGATGCGGGTTCCAAAC 60.894 55.000 0.00 0.00 44.62 2.93
681 686 1.969064 TGGATGCGGGTTCCAAACG 60.969 57.895 0.00 0.00 40.29 3.60
682 687 2.696759 GGATGCGGGTTCCAAACGG 61.697 63.158 0.00 0.00 33.21 4.44
683 688 2.675075 ATGCGGGTTCCAAACGGG 60.675 61.111 0.00 0.00 38.37 5.28
686 691 2.675075 CGGGTTCCAAACGGGCAT 60.675 61.111 0.00 0.00 36.21 4.40
687 692 2.969827 GGGTTCCAAACGGGCATG 59.030 61.111 0.00 0.00 36.21 4.06
688 693 2.261361 GGTTCCAAACGGGCATGC 59.739 61.111 9.90 9.90 36.21 4.06
689 694 2.261361 GTTCCAAACGGGCATGCC 59.739 61.111 29.47 29.47 36.21 4.40
690 695 3.369400 TTCCAAACGGGCATGCCG 61.369 61.111 29.90 25.34 36.85 5.69
691 696 3.851897 TTCCAAACGGGCATGCCGA 62.852 57.895 29.90 17.50 36.85 5.54
692 697 3.369400 CCAAACGGGCATGCCGAA 61.369 61.111 29.90 0.00 36.85 4.30
693 698 2.647875 CAAACGGGCATGCCGAAA 59.352 55.556 29.90 0.00 36.85 3.46
694 699 1.215117 CAAACGGGCATGCCGAAAT 59.785 52.632 29.90 13.88 36.85 2.17
695 700 1.077645 CAAACGGGCATGCCGAAATG 61.078 55.000 29.90 21.09 36.85 2.32
696 701 2.224495 AAACGGGCATGCCGAAATGG 62.224 55.000 29.90 16.10 42.50 3.16
697 702 3.140141 CGGGCATGCCGAAATGGT 61.140 61.111 29.90 0.00 41.21 3.55
698 703 2.495866 GGGCATGCCGAAATGGTG 59.504 61.111 29.90 0.00 41.21 4.17
699 704 2.051518 GGGCATGCCGAAATGGTGA 61.052 57.895 29.90 0.00 41.21 4.02
700 705 1.434696 GGCATGCCGAAATGGTGAG 59.565 57.895 23.48 0.00 41.21 3.51
701 706 1.226773 GCATGCCGAAATGGTGAGC 60.227 57.895 6.36 0.00 41.21 4.26
702 707 1.063006 CATGCCGAAATGGTGAGCG 59.937 57.895 0.00 0.00 41.21 5.03
703 708 2.114670 ATGCCGAAATGGTGAGCGG 61.115 57.895 0.00 0.00 46.14 5.52
705 710 3.508840 CCGAAATGGTGAGCGGCC 61.509 66.667 0.00 0.00 37.08 6.13
706 711 3.864686 CGAAATGGTGAGCGGCCG 61.865 66.667 24.05 24.05 0.00 6.13
707 712 2.435938 GAAATGGTGAGCGGCCGA 60.436 61.111 33.48 6.95 0.00 5.54
708 713 2.746277 AAATGGTGAGCGGCCGAC 60.746 61.111 33.48 22.24 0.00 4.79
709 714 3.254024 AAATGGTGAGCGGCCGACT 62.254 57.895 33.48 25.56 0.00 4.18
710 715 3.665675 AATGGTGAGCGGCCGACTC 62.666 63.158 33.48 31.55 34.62 3.36
712 717 3.138798 GGTGAGCGGCCGACTCTA 61.139 66.667 33.81 23.55 35.12 2.43
713 718 2.491022 GGTGAGCGGCCGACTCTAT 61.491 63.158 33.81 14.70 35.12 1.98
714 719 1.008309 GTGAGCGGCCGACTCTATC 60.008 63.158 33.81 24.51 35.12 2.08
715 720 2.194212 TGAGCGGCCGACTCTATCC 61.194 63.158 33.81 18.71 35.12 2.59
716 721 1.899534 GAGCGGCCGACTCTATCCT 60.900 63.158 33.48 14.13 0.00 3.24
717 722 2.136196 GAGCGGCCGACTCTATCCTG 62.136 65.000 33.48 0.00 0.00 3.86
718 723 2.336809 CGGCCGACTCTATCCTGC 59.663 66.667 24.07 0.00 0.00 4.85
719 724 2.196925 CGGCCGACTCTATCCTGCT 61.197 63.158 24.07 0.00 0.00 4.24
720 725 1.663173 GGCCGACTCTATCCTGCTC 59.337 63.158 0.00 0.00 0.00 4.26
721 726 1.663173 GCCGACTCTATCCTGCTCC 59.337 63.158 0.00 0.00 0.00 4.70
722 727 1.109920 GCCGACTCTATCCTGCTCCA 61.110 60.000 0.00 0.00 0.00 3.86
723 728 0.958091 CCGACTCTATCCTGCTCCAG 59.042 60.000 0.00 0.00 0.00 3.86
724 729 0.313672 CGACTCTATCCTGCTCCAGC 59.686 60.000 0.00 0.00 42.50 4.85
725 730 1.703411 GACTCTATCCTGCTCCAGCT 58.297 55.000 0.00 0.00 42.66 4.24
726 731 1.613437 GACTCTATCCTGCTCCAGCTC 59.387 57.143 0.00 0.00 42.66 4.09
727 732 1.063341 ACTCTATCCTGCTCCAGCTCA 60.063 52.381 0.00 0.00 42.66 4.26
728 733 2.250031 CTCTATCCTGCTCCAGCTCAT 58.750 52.381 0.00 0.00 42.66 2.90
729 734 3.181424 ACTCTATCCTGCTCCAGCTCATA 60.181 47.826 0.00 0.00 42.66 2.15
730 735 3.831333 CTCTATCCTGCTCCAGCTCATAA 59.169 47.826 0.00 0.00 42.66 1.90
731 736 4.423913 TCTATCCTGCTCCAGCTCATAAT 58.576 43.478 0.00 0.00 42.66 1.28
732 737 4.842948 TCTATCCTGCTCCAGCTCATAATT 59.157 41.667 0.00 0.00 42.66 1.40
733 738 6.019108 TCTATCCTGCTCCAGCTCATAATTA 58.981 40.000 0.00 0.00 42.66 1.40
734 739 5.573380 ATCCTGCTCCAGCTCATAATTAA 57.427 39.130 0.00 0.00 42.66 1.40
735 740 4.708177 TCCTGCTCCAGCTCATAATTAAC 58.292 43.478 0.00 0.00 42.66 2.01
736 741 3.817647 CCTGCTCCAGCTCATAATTAACC 59.182 47.826 0.00 0.00 42.66 2.85
737 742 3.817647 CTGCTCCAGCTCATAATTAACCC 59.182 47.826 0.00 0.00 42.66 4.11
738 743 3.149981 GCTCCAGCTCATAATTAACCCC 58.850 50.000 0.00 0.00 38.21 4.95
739 744 3.756117 CTCCAGCTCATAATTAACCCCC 58.244 50.000 0.00 0.00 0.00 5.40
740 745 3.395941 CTCCAGCTCATAATTAACCCCCT 59.604 47.826 0.00 0.00 0.00 4.79
741 746 3.791545 TCCAGCTCATAATTAACCCCCTT 59.208 43.478 0.00 0.00 0.00 3.95
742 747 4.231890 TCCAGCTCATAATTAACCCCCTTT 59.768 41.667 0.00 0.00 0.00 3.11
743 748 4.584743 CCAGCTCATAATTAACCCCCTTTC 59.415 45.833 0.00 0.00 0.00 2.62
744 749 5.449553 CAGCTCATAATTAACCCCCTTTCT 58.550 41.667 0.00 0.00 0.00 2.52
745 750 5.532779 CAGCTCATAATTAACCCCCTTTCTC 59.467 44.000 0.00 0.00 0.00 2.87
746 751 5.433381 AGCTCATAATTAACCCCCTTTCTCT 59.567 40.000 0.00 0.00 0.00 3.10
747 752 5.532779 GCTCATAATTAACCCCCTTTCTCTG 59.467 44.000 0.00 0.00 0.00 3.35
748 753 6.652205 TCATAATTAACCCCCTTTCTCTGT 57.348 37.500 0.00 0.00 0.00 3.41
749 754 6.659824 TCATAATTAACCCCCTTTCTCTGTC 58.340 40.000 0.00 0.00 0.00 3.51
750 755 6.447084 TCATAATTAACCCCCTTTCTCTGTCT 59.553 38.462 0.00 0.00 0.00 3.41
751 756 7.626084 TCATAATTAACCCCCTTTCTCTGTCTA 59.374 37.037 0.00 0.00 0.00 2.59
752 757 6.713731 AATTAACCCCCTTTCTCTGTCTAA 57.286 37.500 0.00 0.00 0.00 2.10
753 758 5.757099 TTAACCCCCTTTCTCTGTCTAAG 57.243 43.478 0.00 0.00 0.00 2.18
754 759 1.909986 ACCCCCTTTCTCTGTCTAAGC 59.090 52.381 0.00 0.00 0.00 3.09
755 760 2.192263 CCCCCTTTCTCTGTCTAAGCT 58.808 52.381 0.00 0.00 0.00 3.74
756 761 3.246021 ACCCCCTTTCTCTGTCTAAGCTA 60.246 47.826 0.00 0.00 0.00 3.32
757 762 3.775316 CCCCCTTTCTCTGTCTAAGCTAA 59.225 47.826 0.00 0.00 0.00 3.09
758 763 4.383226 CCCCCTTTCTCTGTCTAAGCTAAC 60.383 50.000 0.00 0.00 0.00 2.34
759 764 4.425520 CCCTTTCTCTGTCTAAGCTAACG 58.574 47.826 0.00 0.00 0.00 3.18
760 765 3.860536 CCTTTCTCTGTCTAAGCTAACGC 59.139 47.826 0.00 0.00 0.00 4.84
761 766 3.505464 TTCTCTGTCTAAGCTAACGCC 57.495 47.619 0.00 0.00 36.60 5.68
762 767 2.443416 TCTCTGTCTAAGCTAACGCCA 58.557 47.619 0.00 0.00 36.60 5.69
763 768 2.823747 TCTCTGTCTAAGCTAACGCCAA 59.176 45.455 0.00 0.00 36.60 4.52
764 769 2.924290 CTCTGTCTAAGCTAACGCCAAC 59.076 50.000 0.00 0.00 36.60 3.77
766 771 1.270274 TGTCTAAGCTAACGCCAACGA 59.730 47.619 0.00 0.00 43.93 3.85
767 772 2.288334 TGTCTAAGCTAACGCCAACGAA 60.288 45.455 0.00 0.00 43.93 3.85
768 773 2.733026 GTCTAAGCTAACGCCAACGAAA 59.267 45.455 0.00 0.00 43.93 3.46
769 774 3.370061 GTCTAAGCTAACGCCAACGAAAT 59.630 43.478 0.00 0.00 43.93 2.17
770 775 4.563976 GTCTAAGCTAACGCCAACGAAATA 59.436 41.667 0.00 0.00 43.93 1.40
771 776 5.233689 GTCTAAGCTAACGCCAACGAAATAT 59.766 40.000 0.00 0.00 43.93 1.28
772 777 6.418819 GTCTAAGCTAACGCCAACGAAATATA 59.581 38.462 0.00 0.00 43.93 0.86
773 778 7.115947 GTCTAAGCTAACGCCAACGAAATATAT 59.884 37.037 0.00 0.00 43.93 0.86
774 779 8.298854 TCTAAGCTAACGCCAACGAAATATATA 58.701 33.333 0.00 0.00 43.93 0.86
775 780 7.718272 AAGCTAACGCCAACGAAATATATAA 57.282 32.000 0.00 0.00 43.93 0.98
776 781 7.900782 AGCTAACGCCAACGAAATATATAAT 57.099 32.000 0.00 0.00 43.93 1.28
777 782 7.960793 AGCTAACGCCAACGAAATATATAATC 58.039 34.615 0.00 0.00 43.93 1.75
778 783 7.601130 AGCTAACGCCAACGAAATATATAATCA 59.399 33.333 0.00 0.00 43.93 2.57
779 784 8.225107 GCTAACGCCAACGAAATATATAATCAA 58.775 33.333 0.00 0.00 43.93 2.57
783 788 9.431887 ACGCCAACGAAATATATAATCAATACT 57.568 29.630 0.00 0.00 43.93 2.12
818 823 9.739276 AAATAGATCTCATAGGTAGACTCTGAG 57.261 37.037 0.00 2.45 46.37 3.35
846 851 2.039879 GCTAGGGTTTTGAGTTCCTCCA 59.960 50.000 0.00 0.00 0.00 3.86
870 875 2.853731 CGAGACCGCTGAGAGTAAAT 57.146 50.000 0.00 0.00 0.00 1.40
885 890 8.496534 TGAGAGTAAATTATCTCCATCCATCA 57.503 34.615 10.92 4.15 41.07 3.07
930 944 2.125350 CCAAGGCTCGTCTCTGGC 60.125 66.667 0.00 0.00 0.00 4.85
944 958 0.252881 TCTGGCCTTGGTCTCCTGAT 60.253 55.000 3.32 0.00 0.00 2.90
986 1003 3.808834 CCTCTTGGGTTAGGGTTTCTT 57.191 47.619 0.00 0.00 0.00 2.52
990 1008 3.073946 TCTTGGGTTAGGGTTTCTTGAGG 59.926 47.826 0.00 0.00 0.00 3.86
1023 1041 0.690411 CATCTCAGGAGGAGGCAGGT 60.690 60.000 0.00 0.00 44.19 4.00
1170 1188 0.770590 CGATCGCGAAAGTCCATACG 59.229 55.000 15.24 4.42 40.82 3.06
1260 1278 1.382522 GATGGCGCAGGATTGAAGAA 58.617 50.000 10.83 0.00 0.00 2.52
1293 1311 3.359002 CAGTTTGGCTGTCTGGGC 58.641 61.111 0.00 0.00 40.27 5.36
1410 1428 4.392138 GTGGTGCTTAACAAGATAGTGGTC 59.608 45.833 0.00 0.00 0.00 4.02
1419 1437 1.207791 AGATAGTGGTCTGGGCAAGG 58.792 55.000 0.00 0.00 0.00 3.61
1528 1546 0.539438 TCTTCCAGCGGGTTTTGCAT 60.539 50.000 1.81 0.00 34.93 3.96
1761 1781 0.252696 TGGCAGATGGTGGTAGAGGT 60.253 55.000 0.00 0.00 0.00 3.85
1781 1801 2.120940 TGGGAGAGGCCGTGGTAA 59.879 61.111 0.00 0.00 37.63 2.85
1787 1807 0.907704 AGAGGCCGTGGTAATGGACA 60.908 55.000 0.00 0.00 44.00 4.02
1814 1834 1.552719 GGGAAGAGGTAGAGGTGGTGT 60.553 57.143 0.00 0.00 0.00 4.16
1915 1935 2.302157 GCCGGACTATATACTTTGGCCT 59.698 50.000 5.05 0.00 35.24 5.19
2000 2020 1.898574 CGTGGAAGGCAAGCTTGGT 60.899 57.895 27.10 0.00 0.00 3.67
2237 2287 3.586470 ACCTGGGTAAACATTGTGTCA 57.414 42.857 0.00 0.00 0.00 3.58
2296 2346 1.232216 GACCCCCTACCCGAGATCA 59.768 63.158 0.00 0.00 0.00 2.92
2337 2387 5.069516 ACATTGGTGCTTTCATTGAGAGTTT 59.930 36.000 6.13 0.00 0.00 2.66
2341 2391 4.540824 GTGCTTTCATTGAGAGTTTCACC 58.459 43.478 6.13 0.00 34.94 4.02
2376 2427 1.092345 GGCTTGATGGCTCCTTCGAC 61.092 60.000 0.00 0.00 38.32 4.20
2389 2440 0.652592 CTTCGACCATCGGCAATGAC 59.347 55.000 0.00 0.00 40.88 3.06
2461 2512 2.663196 GTACTGCGGGCCAACTCT 59.337 61.111 4.39 0.00 0.00 3.24
2474 2525 1.093159 CAACTCTCTTGGCCATCTGC 58.907 55.000 6.09 0.00 40.16 4.26
2543 2594 4.737946 GCTTGAACTATACTGCCGACATCT 60.738 45.833 0.00 0.00 0.00 2.90
2607 2658 1.857853 CGTACAGTCACGACGAGCG 60.858 63.158 0.00 0.00 44.69 5.03
2679 2730 3.483869 GGCCCTCAATCCGGAGCT 61.484 66.667 11.34 0.00 33.47 4.09
2813 2864 3.615509 GATTCGTCCCCGGCCACAA 62.616 63.158 2.24 0.00 33.95 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.466167 CTTCGGCTTCATCCAACAGTG 59.534 52.381 0.00 0.00 0.00 3.66
1 2 1.611673 CCTTCGGCTTCATCCAACAGT 60.612 52.381 0.00 0.00 0.00 3.55
2 3 1.089920 CCTTCGGCTTCATCCAACAG 58.910 55.000 0.00 0.00 0.00 3.16
3 4 0.322456 CCCTTCGGCTTCATCCAACA 60.322 55.000 0.00 0.00 0.00 3.33
4 5 1.032114 CCCCTTCGGCTTCATCCAAC 61.032 60.000 0.00 0.00 0.00 3.77
5 6 1.302949 CCCCTTCGGCTTCATCCAA 59.697 57.895 0.00 0.00 0.00 3.53
6 7 2.998097 CCCCTTCGGCTTCATCCA 59.002 61.111 0.00 0.00 0.00 3.41
15 16 0.744414 CACACATACTGCCCCTTCGG 60.744 60.000 0.00 0.00 0.00 4.30
16 17 0.744414 CCACACATACTGCCCCTTCG 60.744 60.000 0.00 0.00 0.00 3.79
17 18 0.394352 CCCACACATACTGCCCCTTC 60.394 60.000 0.00 0.00 0.00 3.46
18 19 0.844661 TCCCACACATACTGCCCCTT 60.845 55.000 0.00 0.00 0.00 3.95
19 20 1.229820 TCCCACACATACTGCCCCT 60.230 57.895 0.00 0.00 0.00 4.79
20 21 1.077716 GTCCCACACATACTGCCCC 60.078 63.158 0.00 0.00 0.00 5.80
21 22 1.449601 CGTCCCACACATACTGCCC 60.450 63.158 0.00 0.00 0.00 5.36
22 23 0.460284 CTCGTCCCACACATACTGCC 60.460 60.000 0.00 0.00 0.00 4.85
23 24 0.530744 TCTCGTCCCACACATACTGC 59.469 55.000 0.00 0.00 0.00 4.40
24 25 2.427095 TCATCTCGTCCCACACATACTG 59.573 50.000 0.00 0.00 0.00 2.74
25 26 2.735151 TCATCTCGTCCCACACATACT 58.265 47.619 0.00 0.00 0.00 2.12
26 27 3.553096 GGATCATCTCGTCCCACACATAC 60.553 52.174 0.00 0.00 0.00 2.39
27 28 2.628178 GGATCATCTCGTCCCACACATA 59.372 50.000 0.00 0.00 0.00 2.29
28 29 1.414181 GGATCATCTCGTCCCACACAT 59.586 52.381 0.00 0.00 0.00 3.21
29 30 0.824109 GGATCATCTCGTCCCACACA 59.176 55.000 0.00 0.00 0.00 3.72
30 31 0.249073 CGGATCATCTCGTCCCACAC 60.249 60.000 0.00 0.00 0.00 3.82
34 35 0.744874 TCAACGGATCATCTCGTCCC 59.255 55.000 2.21 0.00 38.78 4.46
48 49 4.204168 CGATGTCCAACAAGTTTTTCAACG 59.796 41.667 0.00 0.00 38.03 4.10
61 62 5.551760 ATGTCTCAAATTCGATGTCCAAC 57.448 39.130 0.00 0.00 0.00 3.77
66 67 6.317789 ACAACAATGTCTCAAATTCGATGT 57.682 33.333 0.00 0.00 33.41 3.06
67 68 7.521529 AGTACAACAATGTCTCAAATTCGATG 58.478 34.615 0.00 0.00 41.05 3.84
68 69 7.672983 AGTACAACAATGTCTCAAATTCGAT 57.327 32.000 0.00 0.00 41.05 3.59
69 70 8.085909 TCTAGTACAACAATGTCTCAAATTCGA 58.914 33.333 0.00 0.00 41.05 3.71
86 87 8.865978 CATAACACGCAAATAAGTCTAGTACAA 58.134 33.333 0.00 0.00 0.00 2.41
105 106 7.553881 AGCACAAACTATCCATACATAACAC 57.446 36.000 0.00 0.00 0.00 3.32
194 195 2.159627 CCCGCATATATTTCAAGTCGGC 59.840 50.000 0.00 0.00 34.81 5.54
198 199 3.003275 CGTTGCCCGCATATATTTCAAGT 59.997 43.478 0.00 0.00 0.00 3.16
276 277 0.461961 AGGGCATCTCTAACGCTGAC 59.538 55.000 0.00 0.00 0.00 3.51
310 311 0.798776 CAGTTGACCTGGTCGCAATC 59.201 55.000 21.15 9.69 37.54 2.67
348 349 8.231007 AGAGGATAAAGATTGAGGATCTCTACA 58.769 37.037 0.00 0.00 44.41 2.74
351 352 9.842196 ATAAGAGGATAAAGATTGAGGATCTCT 57.158 33.333 0.00 0.00 44.41 3.10
422 425 0.101399 CTCTAGCCTTGCGTGACGAT 59.899 55.000 10.10 0.00 0.00 3.73
430 433 1.275010 GAGCCTATCCTCTAGCCTTGC 59.725 57.143 0.00 0.00 0.00 4.01
448 451 1.091771 GGTGGCGGTCATGATGTGAG 61.092 60.000 0.00 0.00 37.56 3.51
465 468 1.602165 CGATTCTATAAGCGCGGTGGT 60.602 52.381 13.41 6.22 37.72 4.16
474 477 1.555533 GGCCCCTCCCGATTCTATAAG 59.444 57.143 0.00 0.00 0.00 1.73
475 478 1.652947 GGCCCCTCCCGATTCTATAA 58.347 55.000 0.00 0.00 0.00 0.98
495 498 1.535028 TGATTGCAACATCGGTGTGAC 59.465 47.619 0.00 0.00 38.92 3.67
500 503 1.545582 CCCTTTGATTGCAACATCGGT 59.454 47.619 0.00 0.00 32.79 4.69
510 513 2.403259 GTTGTTTCGCCCCTTTGATTG 58.597 47.619 0.00 0.00 0.00 2.67
516 519 1.241315 CGATGGTTGTTTCGCCCCTT 61.241 55.000 0.00 0.00 0.00 3.95
563 568 3.947132 CTGTGGTCAGAGCCGCCTG 62.947 68.421 0.00 3.24 43.76 4.85
564 569 3.699894 CTGTGGTCAGAGCCGCCT 61.700 66.667 0.00 0.00 43.76 5.52
567 572 3.978723 CTCGCTGTGGTCAGAGCCG 62.979 68.421 13.33 9.24 43.95 5.52
568 573 2.125753 CTCGCTGTGGTCAGAGCC 60.126 66.667 13.33 0.00 43.95 4.70
569 574 2.125753 CCTCGCTGTGGTCAGAGC 60.126 66.667 9.68 9.68 43.76 4.09
570 575 2.575993 CCCTCGCTGTGGTCAGAG 59.424 66.667 0.00 0.00 43.76 3.35
571 576 2.997315 CCCCTCGCTGTGGTCAGA 60.997 66.667 0.00 0.00 43.76 3.27
572 577 4.767255 GCCCCTCGCTGTGGTCAG 62.767 72.222 0.00 0.00 43.87 3.51
583 588 3.009714 AAACTCCCTCGGCCCCTC 61.010 66.667 0.00 0.00 0.00 4.30
584 589 3.009714 GAAACTCCCTCGGCCCCT 61.010 66.667 0.00 0.00 0.00 4.79
585 590 4.111053 GGAAACTCCCTCGGCCCC 62.111 72.222 0.00 0.00 0.00 5.80
586 591 4.468689 CGGAAACTCCCTCGGCCC 62.469 72.222 0.00 0.00 31.13 5.80
587 592 4.468689 CCGGAAACTCCCTCGGCC 62.469 72.222 0.00 0.00 35.95 6.13
588 593 4.468689 CCCGGAAACTCCCTCGGC 62.469 72.222 0.73 0.00 41.02 5.54
589 594 1.833787 TTTCCCGGAAACTCCCTCGG 61.834 60.000 8.63 0.00 41.90 4.63
590 595 0.252197 ATTTCCCGGAAACTCCCTCG 59.748 55.000 14.99 0.00 34.23 4.63
591 596 1.682087 CCATTTCCCGGAAACTCCCTC 60.682 57.143 14.99 0.00 34.23 4.30
592 597 0.331616 CCATTTCCCGGAAACTCCCT 59.668 55.000 14.99 0.00 34.23 4.20
593 598 0.683179 CCCATTTCCCGGAAACTCCC 60.683 60.000 14.99 0.00 34.23 4.30
594 599 0.683179 CCCCATTTCCCGGAAACTCC 60.683 60.000 14.99 0.00 34.23 3.85
595 600 0.330267 TCCCCATTTCCCGGAAACTC 59.670 55.000 14.99 0.00 34.23 3.01
596 601 1.007607 ATCCCCATTTCCCGGAAACT 58.992 50.000 14.99 2.30 34.23 2.66
597 602 1.860641 AATCCCCATTTCCCGGAAAC 58.139 50.000 14.99 0.00 34.23 2.78
598 603 2.688515 GCTAATCCCCATTTCCCGGAAA 60.689 50.000 15.04 15.04 35.94 3.13
599 604 1.133606 GCTAATCCCCATTTCCCGGAA 60.134 52.381 0.73 0.00 0.00 4.30
600 605 0.476771 GCTAATCCCCATTTCCCGGA 59.523 55.000 0.73 0.00 0.00 5.14
601 606 0.889186 CGCTAATCCCCATTTCCCGG 60.889 60.000 0.00 0.00 0.00 5.73
602 607 0.107831 TCGCTAATCCCCATTTCCCG 59.892 55.000 0.00 0.00 0.00 5.14
603 608 1.143073 AGTCGCTAATCCCCATTTCCC 59.857 52.381 0.00 0.00 0.00 3.97
604 609 2.640316 AGTCGCTAATCCCCATTTCC 57.360 50.000 0.00 0.00 0.00 3.13
605 610 4.254492 GGATAGTCGCTAATCCCCATTTC 58.746 47.826 0.00 0.00 0.00 2.17
606 611 3.009143 GGGATAGTCGCTAATCCCCATTT 59.991 47.826 14.55 0.00 45.40 2.32
607 612 2.572104 GGGATAGTCGCTAATCCCCATT 59.428 50.000 14.55 0.00 45.40 3.16
608 613 2.188817 GGGATAGTCGCTAATCCCCAT 58.811 52.381 14.55 0.00 45.40 4.00
609 614 1.640917 GGGATAGTCGCTAATCCCCA 58.359 55.000 14.55 0.00 45.40 4.96
612 617 3.193903 GGAAGAGGGATAGTCGCTAATCC 59.806 52.174 9.98 9.98 39.94 3.01
613 618 3.119779 CGGAAGAGGGATAGTCGCTAATC 60.120 52.174 0.00 0.00 39.94 1.75
614 619 2.820787 CGGAAGAGGGATAGTCGCTAAT 59.179 50.000 0.00 0.00 39.94 1.73
615 620 2.228059 CGGAAGAGGGATAGTCGCTAA 58.772 52.381 0.00 0.00 39.94 3.09
616 621 1.544982 CCGGAAGAGGGATAGTCGCTA 60.545 57.143 0.00 0.00 39.94 4.26
617 622 0.824182 CCGGAAGAGGGATAGTCGCT 60.824 60.000 0.00 0.00 42.73 4.93
618 623 1.660917 CCGGAAGAGGGATAGTCGC 59.339 63.158 0.00 0.00 0.00 5.19
627 632 0.977395 AGAACTGAACCCGGAAGAGG 59.023 55.000 0.73 0.00 0.00 3.69
628 633 3.955650 TTAGAACTGAACCCGGAAGAG 57.044 47.619 0.73 0.00 0.00 2.85
629 634 3.244318 GGTTTAGAACTGAACCCGGAAGA 60.244 47.826 14.82 0.00 41.69 2.87
630 635 3.072211 GGTTTAGAACTGAACCCGGAAG 58.928 50.000 14.82 0.00 41.69 3.46
631 636 2.438763 TGGTTTAGAACTGAACCCGGAA 59.561 45.455 20.38 4.70 45.45 4.30
632 637 2.048601 TGGTTTAGAACTGAACCCGGA 58.951 47.619 20.38 4.99 45.45 5.14
633 638 2.554370 TGGTTTAGAACTGAACCCGG 57.446 50.000 20.38 0.00 45.45 5.73
634 639 4.517453 TGAAATGGTTTAGAACTGAACCCG 59.483 41.667 20.38 0.00 45.45 5.28
635 640 6.434340 AGATGAAATGGTTTAGAACTGAACCC 59.566 38.462 20.38 9.54 45.45 4.11
636 641 7.454260 AGATGAAATGGTTTAGAACTGAACC 57.546 36.000 17.69 17.69 46.01 3.62
637 642 9.220767 ACTAGATGAAATGGTTTAGAACTGAAC 57.779 33.333 0.00 1.67 0.00 3.18
638 643 9.219603 CACTAGATGAAATGGTTTAGAACTGAA 57.780 33.333 0.00 0.00 0.00 3.02
639 644 7.824289 CCACTAGATGAAATGGTTTAGAACTGA 59.176 37.037 0.00 0.00 0.00 3.41
640 645 7.824289 TCCACTAGATGAAATGGTTTAGAACTG 59.176 37.037 0.00 0.00 33.67 3.16
641 646 7.918076 TCCACTAGATGAAATGGTTTAGAACT 58.082 34.615 0.00 0.00 33.67 3.01
642 647 8.738645 ATCCACTAGATGAAATGGTTTAGAAC 57.261 34.615 0.00 0.00 32.41 3.01
657 662 0.759346 GGAACCCGCATCCACTAGAT 59.241 55.000 0.00 0.00 36.92 1.98
658 663 0.616395 TGGAACCCGCATCCACTAGA 60.616 55.000 0.00 0.00 41.98 2.43
659 664 0.251916 TTGGAACCCGCATCCACTAG 59.748 55.000 2.00 0.00 46.37 2.57
660 665 0.693622 TTTGGAACCCGCATCCACTA 59.306 50.000 2.00 0.00 46.37 2.74
661 666 0.893727 GTTTGGAACCCGCATCCACT 60.894 55.000 2.00 0.00 46.37 4.00
662 667 1.584495 GTTTGGAACCCGCATCCAC 59.416 57.895 2.00 0.00 46.37 4.02
663 668 1.969064 CGTTTGGAACCCGCATCCA 60.969 57.895 0.00 0.00 45.09 3.41
664 669 2.696759 CCGTTTGGAACCCGCATCC 61.697 63.158 0.00 0.00 37.49 3.51
665 670 2.696759 CCCGTTTGGAACCCGCATC 61.697 63.158 0.00 0.00 37.49 3.91
666 671 2.675075 CCCGTTTGGAACCCGCAT 60.675 61.111 0.00 0.00 37.49 4.73
669 674 2.675075 ATGCCCGTTTGGAACCCG 60.675 61.111 0.00 0.00 37.49 5.28
670 675 2.969827 CATGCCCGTTTGGAACCC 59.030 61.111 0.00 0.00 37.49 4.11
671 676 2.261361 GCATGCCCGTTTGGAACC 59.739 61.111 6.36 0.00 37.49 3.62
672 677 2.261361 GGCATGCCCGTTTGGAAC 59.739 61.111 27.24 0.00 37.49 3.62
681 686 2.008268 CTCACCATTTCGGCATGCCC 62.008 60.000 30.79 13.37 39.03 5.36
682 687 1.434696 CTCACCATTTCGGCATGCC 59.565 57.895 27.67 27.67 39.03 4.40
683 688 1.226773 GCTCACCATTTCGGCATGC 60.227 57.895 9.90 9.90 39.03 4.06
684 689 1.063006 CGCTCACCATTTCGGCATG 59.937 57.895 0.00 0.00 39.03 4.06
685 690 2.114670 CCGCTCACCATTTCGGCAT 61.115 57.895 0.00 0.00 39.03 4.40
686 691 2.745884 CCGCTCACCATTTCGGCA 60.746 61.111 0.00 0.00 39.03 5.69
688 693 3.508840 GGCCGCTCACCATTTCGG 61.509 66.667 0.00 0.00 44.29 4.30
689 694 3.864686 CGGCCGCTCACCATTTCG 61.865 66.667 14.67 0.00 0.00 3.46
690 695 2.435938 TCGGCCGCTCACCATTTC 60.436 61.111 23.51 0.00 0.00 2.17
691 696 2.746277 GTCGGCCGCTCACCATTT 60.746 61.111 23.51 0.00 0.00 2.32
692 697 3.665675 GAGTCGGCCGCTCACCATT 62.666 63.158 31.47 10.31 33.45 3.16
693 698 4.148825 GAGTCGGCCGCTCACCAT 62.149 66.667 31.47 10.06 33.45 3.55
694 699 3.931190 TAGAGTCGGCCGCTCACCA 62.931 63.158 34.89 23.29 35.55 4.17
695 700 2.409241 GATAGAGTCGGCCGCTCACC 62.409 65.000 34.89 24.35 35.55 4.02
696 701 1.008309 GATAGAGTCGGCCGCTCAC 60.008 63.158 34.89 24.33 35.55 3.51
697 702 2.194212 GGATAGAGTCGGCCGCTCA 61.194 63.158 34.89 25.66 35.55 4.26
698 703 1.899534 AGGATAGAGTCGGCCGCTC 60.900 63.158 30.21 30.21 0.00 5.03
699 704 2.196229 AGGATAGAGTCGGCCGCT 59.804 61.111 23.51 21.31 0.00 5.52
700 705 2.336809 CAGGATAGAGTCGGCCGC 59.663 66.667 23.51 16.31 0.00 6.53
701 706 2.136196 GAGCAGGATAGAGTCGGCCG 62.136 65.000 22.12 22.12 0.00 6.13
702 707 1.663173 GAGCAGGATAGAGTCGGCC 59.337 63.158 0.00 0.00 0.00 6.13
703 708 1.109920 TGGAGCAGGATAGAGTCGGC 61.110 60.000 0.00 0.00 0.00 5.54
704 709 0.958091 CTGGAGCAGGATAGAGTCGG 59.042 60.000 0.00 0.00 0.00 4.79
705 710 0.313672 GCTGGAGCAGGATAGAGTCG 59.686 60.000 0.00 0.00 41.59 4.18
706 711 1.613437 GAGCTGGAGCAGGATAGAGTC 59.387 57.143 0.00 0.00 45.16 3.36
707 712 1.063341 TGAGCTGGAGCAGGATAGAGT 60.063 52.381 0.00 0.00 45.16 3.24
708 713 1.702182 TGAGCTGGAGCAGGATAGAG 58.298 55.000 0.00 0.00 45.16 2.43
709 714 2.395336 ATGAGCTGGAGCAGGATAGA 57.605 50.000 0.00 0.00 45.16 1.98
710 715 4.822685 ATTATGAGCTGGAGCAGGATAG 57.177 45.455 0.00 0.00 45.16 2.08
711 716 6.467677 GTTAATTATGAGCTGGAGCAGGATA 58.532 40.000 0.00 0.00 45.16 2.59
712 717 5.312079 GTTAATTATGAGCTGGAGCAGGAT 58.688 41.667 0.00 0.00 45.16 3.24
713 718 4.444876 GGTTAATTATGAGCTGGAGCAGGA 60.445 45.833 0.00 0.00 45.16 3.86
714 719 3.817647 GGTTAATTATGAGCTGGAGCAGG 59.182 47.826 0.00 0.00 45.16 4.85
715 720 3.817647 GGGTTAATTATGAGCTGGAGCAG 59.182 47.826 0.00 0.00 45.16 4.24
716 721 3.435026 GGGGTTAATTATGAGCTGGAGCA 60.435 47.826 0.00 0.00 45.16 4.26
717 722 3.149981 GGGGTTAATTATGAGCTGGAGC 58.850 50.000 0.00 0.00 42.49 4.70
718 723 3.395941 AGGGGGTTAATTATGAGCTGGAG 59.604 47.826 0.00 0.00 0.00 3.86
719 724 3.403322 AGGGGGTTAATTATGAGCTGGA 58.597 45.455 0.00 0.00 0.00 3.86
720 725 3.884037 AGGGGGTTAATTATGAGCTGG 57.116 47.619 0.00 0.00 0.00 4.85
721 726 5.449553 AGAAAGGGGGTTAATTATGAGCTG 58.550 41.667 0.00 0.00 0.00 4.24
722 727 5.433381 AGAGAAAGGGGGTTAATTATGAGCT 59.567 40.000 0.00 0.00 0.00 4.09
723 728 5.532779 CAGAGAAAGGGGGTTAATTATGAGC 59.467 44.000 0.00 0.00 0.00 4.26
724 729 6.663734 ACAGAGAAAGGGGGTTAATTATGAG 58.336 40.000 0.00 0.00 0.00 2.90
725 730 6.447084 AGACAGAGAAAGGGGGTTAATTATGA 59.553 38.462 0.00 0.00 0.00 2.15
726 731 6.663734 AGACAGAGAAAGGGGGTTAATTATG 58.336 40.000 0.00 0.00 0.00 1.90
727 732 6.910259 AGACAGAGAAAGGGGGTTAATTAT 57.090 37.500 0.00 0.00 0.00 1.28
728 733 7.582828 GCTTAGACAGAGAAAGGGGGTTAATTA 60.583 40.741 0.00 0.00 0.00 1.40
729 734 6.713731 TTAGACAGAGAAAGGGGGTTAATT 57.286 37.500 0.00 0.00 0.00 1.40
730 735 5.339282 GCTTAGACAGAGAAAGGGGGTTAAT 60.339 44.000 0.00 0.00 0.00 1.40
731 736 4.019591 GCTTAGACAGAGAAAGGGGGTTAA 60.020 45.833 0.00 0.00 0.00 2.01
732 737 3.518303 GCTTAGACAGAGAAAGGGGGTTA 59.482 47.826 0.00 0.00 0.00 2.85
733 738 2.306219 GCTTAGACAGAGAAAGGGGGTT 59.694 50.000 0.00 0.00 0.00 4.11
734 739 1.909986 GCTTAGACAGAGAAAGGGGGT 59.090 52.381 0.00 0.00 0.00 4.95
735 740 2.192263 AGCTTAGACAGAGAAAGGGGG 58.808 52.381 0.00 0.00 0.00 5.40
736 741 4.678309 CGTTAGCTTAGACAGAGAAAGGGG 60.678 50.000 0.00 0.00 0.00 4.79
737 742 4.425520 CGTTAGCTTAGACAGAGAAAGGG 58.574 47.826 0.00 0.00 0.00 3.95
738 743 3.860536 GCGTTAGCTTAGACAGAGAAAGG 59.139 47.826 0.00 0.00 41.01 3.11
739 744 3.860536 GGCGTTAGCTTAGACAGAGAAAG 59.139 47.826 0.00 0.00 44.37 2.62
740 745 3.257375 TGGCGTTAGCTTAGACAGAGAAA 59.743 43.478 0.00 0.00 44.37 2.52
741 746 2.823747 TGGCGTTAGCTTAGACAGAGAA 59.176 45.455 0.00 0.00 44.37 2.87
742 747 2.443416 TGGCGTTAGCTTAGACAGAGA 58.557 47.619 0.00 0.00 44.37 3.10
743 748 2.924290 GTTGGCGTTAGCTTAGACAGAG 59.076 50.000 0.00 0.00 44.37 3.35
744 749 2.670229 CGTTGGCGTTAGCTTAGACAGA 60.670 50.000 0.00 0.00 44.37 3.41
745 750 1.654105 CGTTGGCGTTAGCTTAGACAG 59.346 52.381 0.00 0.00 44.37 3.51
746 751 1.270274 TCGTTGGCGTTAGCTTAGACA 59.730 47.619 0.00 0.00 44.37 3.41
747 752 1.986698 TCGTTGGCGTTAGCTTAGAC 58.013 50.000 0.00 0.00 44.37 2.59
748 753 2.728690 TTCGTTGGCGTTAGCTTAGA 57.271 45.000 0.00 0.00 44.37 2.10
749 754 5.652744 ATATTTCGTTGGCGTTAGCTTAG 57.347 39.130 0.00 0.00 44.37 2.18
750 755 8.815141 TTATATATTTCGTTGGCGTTAGCTTA 57.185 30.769 0.00 0.00 44.37 3.09
751 756 7.718272 TTATATATTTCGTTGGCGTTAGCTT 57.282 32.000 0.00 0.00 44.37 3.74
752 757 7.601130 TGATTATATATTTCGTTGGCGTTAGCT 59.399 33.333 0.00 0.00 44.37 3.32
753 758 7.735500 TGATTATATATTTCGTTGGCGTTAGC 58.264 34.615 0.00 0.00 44.18 3.09
757 762 9.431887 AGTATTGATTATATATTTCGTTGGCGT 57.568 29.630 0.00 0.00 39.49 5.68
801 806 4.386536 GGGGAACTCAGAGTCTACCTATGA 60.387 50.000 2.72 0.00 39.05 2.15
802 807 3.892588 GGGGAACTCAGAGTCTACCTATG 59.107 52.174 2.72 0.00 33.54 2.23
803 808 3.435313 CGGGGAACTCAGAGTCTACCTAT 60.435 52.174 2.72 0.00 0.00 2.57
804 809 2.092538 CGGGGAACTCAGAGTCTACCTA 60.093 54.545 2.72 0.00 0.00 3.08
805 810 1.341187 CGGGGAACTCAGAGTCTACCT 60.341 57.143 2.72 0.00 0.00 3.08
806 811 1.104630 CGGGGAACTCAGAGTCTACC 58.895 60.000 2.72 8.04 0.00 3.18
807 812 0.456628 GCGGGGAACTCAGAGTCTAC 59.543 60.000 2.72 0.00 0.00 2.59
808 813 0.331954 AGCGGGGAACTCAGAGTCTA 59.668 55.000 2.72 0.00 0.00 2.59
809 814 0.331954 TAGCGGGGAACTCAGAGTCT 59.668 55.000 2.72 0.00 0.00 3.24
810 815 0.741915 CTAGCGGGGAACTCAGAGTC 59.258 60.000 2.72 0.00 0.00 3.36
811 816 0.684805 CCTAGCGGGGAACTCAGAGT 60.685 60.000 0.00 0.00 0.00 3.24
812 817 2.119886 CCTAGCGGGGAACTCAGAG 58.880 63.158 0.00 0.00 0.00 3.35
813 818 4.356979 CCTAGCGGGGAACTCAGA 57.643 61.111 0.00 0.00 0.00 3.27
870 875 6.013032 GGGAGAGAAATGATGGATGGAGATAA 60.013 42.308 0.00 0.00 0.00 1.75
930 944 1.137086 CGTACCATCAGGAGACCAAGG 59.863 57.143 0.00 0.00 38.69 3.61
932 946 1.191535 CCGTACCATCAGGAGACCAA 58.808 55.000 0.00 0.00 38.69 3.67
944 958 0.545787 AGATCAACCCCACCGTACCA 60.546 55.000 0.00 0.00 0.00 3.25
986 1003 3.265221 AGATGCCATCTCAAGTTTCCTCA 59.735 43.478 0.08 0.00 33.42 3.86
1023 1041 3.680620 CTTCCTTGGGCGCGATCCA 62.681 63.158 12.10 14.57 0.00 3.41
1260 1278 4.758165 CCAAACTGTACCGTGAATAGGTTT 59.242 41.667 0.00 0.00 42.81 3.27
1297 1315 1.358725 ATGTTCATCGCCGTGTTCCG 61.359 55.000 0.00 0.00 0.00 4.30
1410 1428 2.490903 CAACTTCAAGATCCTTGCCCAG 59.509 50.000 0.00 1.69 0.00 4.45
1528 1546 1.066454 TCTGACTCGAACAAACTCGCA 59.934 47.619 0.00 0.00 38.73 5.10
1781 1801 2.700897 CCTCTTCCCGTATTCTGTCCAT 59.299 50.000 0.00 0.00 0.00 3.41
1787 1807 3.204831 ACCTCTACCTCTTCCCGTATTCT 59.795 47.826 0.00 0.00 0.00 2.40
1814 1834 0.610785 GGCATCCCCGTTTCTTCCAA 60.611 55.000 0.00 0.00 0.00 3.53
1915 1935 6.850752 TGTATCTTCATAGTCCAACAGTCA 57.149 37.500 0.00 0.00 0.00 3.41
2000 2020 9.241919 GAGAAGGAGATCTACATATCTGAATCA 57.758 37.037 7.93 0.00 36.33 2.57
2237 2287 2.203877 TGGTAACAGGAGGCGGGT 60.204 61.111 0.00 0.00 46.17 5.28
2376 2427 2.162921 GATCGCGTCATTGCCGATGG 62.163 60.000 5.77 0.00 36.37 3.51
2389 2440 2.521958 AAACCTCACCCTGGATCGCG 62.522 60.000 0.00 0.00 0.00 5.87
2461 2512 1.378119 CTGCTGCAGATGGCCAAGA 60.378 57.895 24.88 0.00 43.89 3.02
2543 2594 2.095212 CGTCGAAGATCAAGTCTCCACA 60.095 50.000 0.00 0.00 40.67 4.17
2607 2658 0.798771 CGACGGCAGAGCTAAGTCAC 60.799 60.000 0.00 0.00 31.92 3.67
2679 2730 1.756561 TCCTCGGATGGCACGATCA 60.757 57.895 0.43 0.00 39.89 2.92


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

AutoCloner maintained by Alex Coulton.