Multiple sequence alignment - TraesCS5D01G037800

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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 TraesCS5D01G037800 chr5D 100.000 5414 0 0 1 5414 36760646 36766059 0.000000e+00 9998.0
1 TraesCS5D01G037800 chr5B 90.930 3440 180 57 543 3931 27506047 27509405 0.000000e+00 4503.0
2 TraesCS5D01G037800 chr5B 92.477 1183 59 18 3928 5105 27509477 27510634 0.000000e+00 1664.0
3 TraesCS5D01G037800 chr5B 82.100 419 25 19 79 484 27505399 27505780 4.070000e-81 313.0
4 TraesCS5D01G037800 chr5B 91.089 101 7 2 5123 5222 27510866 27510965 9.460000e-28 135.0
5 TraesCS5D01G037800 chr5A 91.578 1781 80 37 98 1867 25887018 25888739 0.000000e+00 2394.0
6 TraesCS5D01G037800 chr5A 91.266 1603 83 31 3661 5224 25890692 25892276 0.000000e+00 2132.0
7 TraesCS5D01G037800 chr5A 94.986 1037 49 3 2291 3324 25889125 25890161 0.000000e+00 1624.0
8 TraesCS5D01G037800 chr5A 92.327 391 23 1 1820 2210 25888739 25889122 2.850000e-152 549.0
9 TraesCS5D01G037800 chr5A 86.992 369 20 8 2352 2716 554347670 554348014 1.830000e-104 390.0
10 TraesCS5D01G037800 chr5A 87.316 339 14 10 3321 3659 25890286 25890595 1.430000e-95 361.0
11 TraesCS5D01G037800 chr5A 98.750 80 1 0 2882 2961 554348030 554348109 5.650000e-30 143.0
12 TraesCS5D01G037800 chr5A 92.857 56 1 2 5226 5279 25892361 25892415 1.620000e-10 78.7
13 TraesCS5D01G037800 chr6B 88.598 956 87 11 999 1948 670366591 670367530 0.000000e+00 1142.0
14 TraesCS5D01G037800 chr6B 87.579 636 43 13 2328 2958 670367912 670368516 0.000000e+00 704.0
15 TraesCS5D01G037800 chr6B 91.641 323 21 2 1943 2264 670367608 670367925 4.980000e-120 442.0
16 TraesCS5D01G037800 chr6B 99.029 103 1 0 1 103 507467061 507467163 9.260000e-43 185.0
17 TraesCS5D01G037800 chr6B 98.058 103 2 0 1 103 50401290 50401188 4.310000e-41 180.0
18 TraesCS5D01G037800 chr6B 98.058 103 2 0 1 103 672494098 672493996 4.310000e-41 180.0
19 TraesCS5D01G037800 chr6D 91.858 786 48 9 1170 1949 196357138 196357913 0.000000e+00 1083.0
20 TraesCS5D01G037800 chr6D 87.534 369 18 7 2352 2716 196358049 196358393 8.450000e-108 401.0
21 TraesCS5D01G037800 chr6D 93.069 101 4 3 2863 2961 196358389 196358488 1.570000e-30 145.0
22 TraesCS5D01G037800 chr7A 90.382 811 57 14 1170 1972 724635749 724636546 0.000000e+00 1046.0
23 TraesCS5D01G037800 chr7A 92.079 101 5 3 2863 2961 724636958 724637057 7.310000e-29 139.0
24 TraesCS5D01G037800 chr3A 90.828 785 56 9 1170 1948 657438927 657439701 0.000000e+00 1037.0
25 TraesCS5D01G037800 chr3A 90.446 785 58 10 1170 1948 50434749 50435522 0.000000e+00 1018.0
26 TraesCS5D01G037800 chr3A 86.179 369 22 8 2352 2716 50435658 50436001 6.620000e-99 372.0
27 TraesCS5D01G037800 chr3A 99.029 103 1 0 1 103 707924237 707924339 9.260000e-43 185.0
28 TraesCS5D01G037800 chr3A 90.476 105 5 5 2859 2961 50435994 50436095 3.400000e-27 134.0
29 TraesCS5D01G037800 chr1A 90.828 785 56 11 1170 1948 527084786 527084012 0.000000e+00 1037.0
30 TraesCS5D01G037800 chr1A 85.908 369 24 13 2352 2716 527083876 527083532 8.570000e-98 368.0
31 TraesCS5D01G037800 chr1A 98.077 104 2 0 1 104 261748607 261748504 1.200000e-41 182.0
32 TraesCS5D01G037800 chr6A 89.936 785 61 10 1170 1948 349779059 349779831 0.000000e+00 996.0
33 TraesCS5D01G037800 chr6A 89.822 786 63 12 1170 1948 508000090 508000865 0.000000e+00 992.0
34 TraesCS5D01G037800 chr6A 91.429 105 5 4 2859 2961 508001338 508001440 2.030000e-29 141.0
35 TraesCS5D01G037800 chr7B 87.132 645 43 16 879 1520 630364458 630365065 0.000000e+00 695.0
36 TraesCS5D01G037800 chr7B 100.000 53 0 0 1 53 732704489 732704437 1.240000e-16 99.0
37 TraesCS5D01G037800 chr1B 88.975 517 52 3 879 1394 78446241 78445729 7.650000e-178 634.0
38 TraesCS5D01G037800 chr1B 88.781 517 53 4 879 1394 78426160 78425648 3.560000e-176 628.0
39 TraesCS5D01G037800 chr1B 86.796 515 41 19 1766 2261 127645475 127645981 2.850000e-152 549.0
40 TraesCS5D01G037800 chr1B 92.857 224 12 2 879 1101 127645253 127645473 6.760000e-84 322.0
41 TraesCS5D01G037800 chr1B 86.517 89 12 0 15 103 179506513 179506425 1.240000e-16 99.0
42 TraesCS5D01G037800 chr2A 87.534 369 18 12 2352 2716 65084955 65085299 8.450000e-108 401.0
43 TraesCS5D01G037800 chr2A 92.381 105 4 4 2859 2961 94222583 94222685 4.370000e-31 147.0
44 TraesCS5D01G037800 chr3B 86.757 370 20 6 2352 2716 61518769 61519114 8.510000e-103 385.0
45 TraesCS5D01G037800 chr4D 98.058 103 2 0 1 103 475120570 475120468 4.310000e-41 180.0
46 TraesCS5D01G037800 chr4A 98.058 103 2 0 1 103 603492962 603493064 4.310000e-41 180.0


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 TraesCS5D01G037800 chr5D 36760646 36766059 5413 False 9998.000000 9998 100.000000 1 5414 1 chr5D.!!$F1 5413
1 TraesCS5D01G037800 chr5B 27505399 27510965 5566 False 1653.750000 4503 89.149000 79 5222 4 chr5B.!!$F1 5143
2 TraesCS5D01G037800 chr5A 25887018 25892415 5397 False 1189.783333 2394 91.721667 98 5279 6 chr5A.!!$F1 5181
3 TraesCS5D01G037800 chr6B 670366591 670368516 1925 False 762.666667 1142 89.272667 999 2958 3 chr6B.!!$F2 1959
4 TraesCS5D01G037800 chr6D 196357138 196358488 1350 False 543.000000 1083 90.820333 1170 2961 3 chr6D.!!$F1 1791
5 TraesCS5D01G037800 chr7A 724635749 724637057 1308 False 592.500000 1046 91.230500 1170 2961 2 chr7A.!!$F1 1791
6 TraesCS5D01G037800 chr3A 657438927 657439701 774 False 1037.000000 1037 90.828000 1170 1948 1 chr3A.!!$F1 778
7 TraesCS5D01G037800 chr3A 50434749 50436095 1346 False 508.000000 1018 89.033667 1170 2961 3 chr3A.!!$F3 1791
8 TraesCS5D01G037800 chr1A 527083532 527084786 1254 True 702.500000 1037 88.368000 1170 2716 2 chr1A.!!$R2 1546
9 TraesCS5D01G037800 chr6A 349779059 349779831 772 False 996.000000 996 89.936000 1170 1948 1 chr6A.!!$F1 778
10 TraesCS5D01G037800 chr6A 508000090 508001440 1350 False 566.500000 992 90.625500 1170 2961 2 chr6A.!!$F2 1791
11 TraesCS5D01G037800 chr7B 630364458 630365065 607 False 695.000000 695 87.132000 879 1520 1 chr7B.!!$F1 641
12 TraesCS5D01G037800 chr1B 78445729 78446241 512 True 634.000000 634 88.975000 879 1394 1 chr1B.!!$R2 515
13 TraesCS5D01G037800 chr1B 78425648 78426160 512 True 628.000000 628 88.781000 879 1394 1 chr1B.!!$R1 515
14 TraesCS5D01G037800 chr1B 127645253 127645981 728 False 435.500000 549 89.826500 879 2261 2 chr1B.!!$F1 1382

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
410 436 0.035881 CATCACCTCACAGGCACAGT 59.964 55.000 0.00 0.00 39.63 3.55 F
482 508 0.673985 GTGAGTGGCCTTTGGTTTCC 59.326 55.000 3.32 0.00 0.00 3.13 F
2090 2506 0.534652 GTCATGCTGGATGAGGGCTC 60.535 60.000 12.37 0.00 42.00 4.70 F
2091 2507 0.693430 TCATGCTGGATGAGGGCTCT 60.693 55.000 7.83 0.00 36.06 4.09 F
2563 2980 1.004560 AGACGTGGCATGACACCAG 60.005 57.895 25.94 15.22 38.04 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2477 2.121129 TCCAGCATGACTCATCATCCA 58.879 47.619 0.00 0.00 44.13 3.41 R
2276 2692 2.582636 ACAGGCTTCCACCCAAATCTAT 59.417 45.455 0.00 0.00 0.00 1.98 R
3866 4514 0.837691 TCTCCTTCTCTGCCTTGGCA 60.838 55.000 14.10 14.10 0.00 4.92 R
3912 4560 2.311688 ATACTTGAGAAGGCGGGCCG 62.312 60.000 24.35 24.35 41.95 6.13 R
4513 5243 1.448540 CACGGACAGCCAGATGACC 60.449 63.158 0.00 0.00 0.00 4.02 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
17 18 2.639286 CGCAGCGCCTTCACTTTT 59.361 55.556 2.29 0.00 0.00 2.27
18 19 1.008538 CGCAGCGCCTTCACTTTTT 60.009 52.632 2.29 0.00 0.00 1.94
19 20 1.270777 CGCAGCGCCTTCACTTTTTG 61.271 55.000 2.29 0.00 0.00 2.44
20 21 1.551503 GCAGCGCCTTCACTTTTTGC 61.552 55.000 2.29 0.00 0.00 3.68
21 22 0.248990 CAGCGCCTTCACTTTTTGCA 60.249 50.000 2.29 0.00 0.00 4.08
22 23 0.675633 AGCGCCTTCACTTTTTGCAT 59.324 45.000 2.29 0.00 0.00 3.96
23 24 0.785979 GCGCCTTCACTTTTTGCATG 59.214 50.000 0.00 0.00 0.00 4.06
24 25 1.421382 CGCCTTCACTTTTTGCATGG 58.579 50.000 0.00 0.00 0.00 3.66
25 26 1.150827 GCCTTCACTTTTTGCATGGC 58.849 50.000 0.00 0.00 0.00 4.40
26 27 1.421382 CCTTCACTTTTTGCATGGCG 58.579 50.000 0.00 0.00 0.00 5.69
27 28 0.785979 CTTCACTTTTTGCATGGCGC 59.214 50.000 0.00 0.00 42.89 6.53
28 29 0.599728 TTCACTTTTTGCATGGCGCC 60.600 50.000 22.73 22.73 41.33 6.53
29 30 2.028733 CACTTTTTGCATGGCGCCC 61.029 57.895 26.77 9.46 41.33 6.13
30 31 2.810458 CTTTTTGCATGGCGCCCG 60.810 61.111 26.77 16.90 41.33 6.13
31 32 3.279974 CTTTTTGCATGGCGCCCGA 62.280 57.895 26.77 6.41 41.33 5.14
32 33 3.279974 TTTTTGCATGGCGCCCGAG 62.280 57.895 26.77 14.98 41.33 4.63
50 51 3.827634 GGAGCGGCCCTGTAAATG 58.172 61.111 0.00 0.00 0.00 2.32
51 52 1.077716 GGAGCGGCCCTGTAAATGT 60.078 57.895 0.00 0.00 0.00 2.71
52 53 1.376609 GGAGCGGCCCTGTAAATGTG 61.377 60.000 0.00 0.00 0.00 3.21
53 54 1.376609 GAGCGGCCCTGTAAATGTGG 61.377 60.000 0.00 0.00 0.00 4.17
54 55 1.677633 GCGGCCCTGTAAATGTGGT 60.678 57.895 0.00 0.00 0.00 4.16
55 56 0.393267 GCGGCCCTGTAAATGTGGTA 60.393 55.000 0.00 0.00 0.00 3.25
56 57 1.375551 CGGCCCTGTAAATGTGGTAC 58.624 55.000 0.00 0.00 0.00 3.34
57 58 1.375551 GGCCCTGTAAATGTGGTACG 58.624 55.000 0.00 0.00 0.00 3.67
58 59 1.065998 GGCCCTGTAAATGTGGTACGA 60.066 52.381 0.00 0.00 0.00 3.43
59 60 2.616001 GGCCCTGTAAATGTGGTACGAA 60.616 50.000 0.00 0.00 0.00 3.85
60 61 2.417586 GCCCTGTAAATGTGGTACGAAC 59.582 50.000 0.00 0.00 0.00 3.95
61 62 2.669434 CCCTGTAAATGTGGTACGAACG 59.331 50.000 0.00 0.00 0.00 3.95
62 63 3.319755 CCTGTAAATGTGGTACGAACGT 58.680 45.455 5.03 5.03 0.00 3.99
63 64 3.122278 CCTGTAAATGTGGTACGAACGTG 59.878 47.826 10.14 0.00 0.00 4.49
64 65 2.475864 TGTAAATGTGGTACGAACGTGC 59.524 45.455 10.14 8.45 0.00 5.34
65 66 0.509499 AAATGTGGTACGAACGTGCG 59.491 50.000 16.06 16.06 37.29 5.34
66 67 1.286354 AATGTGGTACGAACGTGCGG 61.286 55.000 22.16 2.02 35.12 5.69
67 68 3.770424 GTGGTACGAACGTGCGGC 61.770 66.667 22.16 12.49 35.12 6.53
68 69 4.281947 TGGTACGAACGTGCGGCA 62.282 61.111 22.16 4.41 35.12 5.69
69 70 3.770424 GGTACGAACGTGCGGCAC 61.770 66.667 22.16 22.78 35.12 5.01
70 71 3.770424 GTACGAACGTGCGGCACC 61.770 66.667 26.00 12.15 35.12 5.01
196 204 7.095060 GGCAAAGAGGAAAAGGAAAAATCATTC 60.095 37.037 0.00 0.00 0.00 2.67
214 222 0.753479 TCGGGCTTTGCAGTTTTGGA 60.753 50.000 0.00 0.00 0.00 3.53
215 223 0.318955 CGGGCTTTGCAGTTTTGGAG 60.319 55.000 0.00 0.00 0.00 3.86
216 224 0.752658 GGGCTTTGCAGTTTTGGAGT 59.247 50.000 0.00 0.00 0.00 3.85
217 225 1.538849 GGGCTTTGCAGTTTTGGAGTG 60.539 52.381 0.00 0.00 0.00 3.51
218 226 1.538849 GGCTTTGCAGTTTTGGAGTGG 60.539 52.381 0.00 0.00 0.00 4.00
219 227 1.408702 GCTTTGCAGTTTTGGAGTGGA 59.591 47.619 0.00 0.00 0.00 4.02
220 228 2.159114 GCTTTGCAGTTTTGGAGTGGAA 60.159 45.455 0.00 0.00 37.26 3.53
221 229 3.709987 CTTTGCAGTTTTGGAGTGGAAG 58.290 45.455 0.00 0.00 39.71 3.46
222 230 1.691196 TGCAGTTTTGGAGTGGAAGG 58.309 50.000 0.00 0.00 0.00 3.46
223 231 1.214175 TGCAGTTTTGGAGTGGAAGGA 59.786 47.619 0.00 0.00 0.00 3.36
324 347 2.554272 GCCCATTTATACGCGCCG 59.446 61.111 5.73 0.00 0.00 6.46
346 369 1.977544 CCGTCCCGTCTTGTCCTCT 60.978 63.158 0.00 0.00 0.00 3.69
347 370 1.507174 CGTCCCGTCTTGTCCTCTC 59.493 63.158 0.00 0.00 0.00 3.20
354 377 2.014128 CGTCTTGTCCTCTCTCTCTCC 58.986 57.143 0.00 0.00 0.00 3.71
355 378 2.355716 CGTCTTGTCCTCTCTCTCTCCT 60.356 54.545 0.00 0.00 0.00 3.69
357 380 2.241176 TCTTGTCCTCTCTCTCTCCTCC 59.759 54.545 0.00 0.00 0.00 4.30
358 381 1.979809 TGTCCTCTCTCTCTCCTCCT 58.020 55.000 0.00 0.00 0.00 3.69
410 436 0.035881 CATCACCTCACAGGCACAGT 59.964 55.000 0.00 0.00 39.63 3.55
431 457 4.103153 AGTTCTTCTTGTTGTCCTCATCCA 59.897 41.667 0.00 0.00 0.00 3.41
482 508 0.673985 GTGAGTGGCCTTTGGTTTCC 59.326 55.000 3.32 0.00 0.00 3.13
496 523 0.912006 GTTTCCTCCCCTGCTCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
511 538 2.015726 TCCTCCCTCCTCCCTCCTC 61.016 68.421 0.00 0.00 0.00 3.71
515 542 2.641746 CCCTCCTCCCTCCTCCTGT 61.642 68.421 0.00 0.00 0.00 4.00
519 546 2.365586 CCTCCCTCCTCCTGTGCTG 61.366 68.421 0.00 0.00 0.00 4.41
524 551 1.375652 CTCCTCCTGTGCTGTGCTG 60.376 63.158 0.00 0.00 0.00 4.41
525 552 3.054503 CCTCCTGTGCTGTGCTGC 61.055 66.667 0.00 0.00 0.00 5.25
526 553 3.420606 CTCCTGTGCTGTGCTGCG 61.421 66.667 0.00 0.00 35.36 5.18
529 556 4.086178 CTGTGCTGTGCTGCGCTC 62.086 66.667 14.92 6.89 43.17 5.03
530 557 4.614112 TGTGCTGTGCTGCGCTCT 62.614 61.111 14.92 0.00 43.17 4.09
531 558 4.086178 GTGCTGTGCTGCGCTCTG 62.086 66.667 14.92 5.98 40.01 3.35
559 792 2.636830 CATGTCTTGGATCCTTTCGCT 58.363 47.619 14.23 0.00 0.00 4.93
612 849 0.739462 CGCACATTCACGGGCTCTTA 60.739 55.000 0.00 0.00 0.00 2.10
641 878 3.423154 CCCTGCGTTGCGAGTTCC 61.423 66.667 0.00 0.00 0.00 3.62
643 880 1.080093 CCTGCGTTGCGAGTTCCTA 60.080 57.895 0.00 0.00 0.00 2.94
651 888 2.806237 CGAGTTCCTACCGGCTCC 59.194 66.667 0.00 0.00 0.00 4.70
652 889 2.050350 CGAGTTCCTACCGGCTCCA 61.050 63.158 0.00 0.00 0.00 3.86
670 912 2.439156 GGCGCTGCTGAAATCCCT 60.439 61.111 7.64 0.00 0.00 4.20
694 936 6.548321 TGTGGATTTTGGGTACTGTAAATCT 58.452 36.000 17.95 2.28 37.24 2.40
757 1002 2.632512 TCAGTTCTTGGGGAATTTTGCC 59.367 45.455 0.00 0.00 36.24 4.52
779 1029 3.367498 CCTCTCTCGGTTTCTTGATTCGT 60.367 47.826 0.00 0.00 0.00 3.85
781 1031 4.628074 TCTCTCGGTTTCTTGATTCGTTT 58.372 39.130 0.00 0.00 0.00 3.60
794 1044 7.867752 TCTTGATTCGTTTCGGTTTTTAATCT 58.132 30.769 0.00 0.00 0.00 2.40
796 1046 6.604930 TGATTCGTTTCGGTTTTTAATCTCC 58.395 36.000 0.00 0.00 0.00 3.71
797 1047 6.428771 TGATTCGTTTCGGTTTTTAATCTCCT 59.571 34.615 0.00 0.00 0.00 3.69
799 1049 4.692155 TCGTTTCGGTTTTTAATCTCCTCC 59.308 41.667 0.00 0.00 0.00 4.30
800 1050 4.694037 CGTTTCGGTTTTTAATCTCCTCCT 59.306 41.667 0.00 0.00 0.00 3.69
821 1072 2.276309 CTCTCACCCTGCATTCCCCC 62.276 65.000 0.00 0.00 0.00 5.40
1597 1882 3.181438 TGCACATAGTAGGGTGGTGTTTT 60.181 43.478 6.82 0.00 35.58 2.43
1766 2051 5.353394 TGGTTCAGCTCTCGGTAATTTAT 57.647 39.130 0.00 0.00 0.00 1.40
1767 2052 6.474140 TGGTTCAGCTCTCGGTAATTTATA 57.526 37.500 0.00 0.00 0.00 0.98
1768 2053 7.062749 TGGTTCAGCTCTCGGTAATTTATAT 57.937 36.000 0.00 0.00 0.00 0.86
1788 2073 6.849085 ATATGGTTCAGTACAAATTTGGCA 57.151 33.333 21.74 6.87 0.00 4.92
1811 2096 6.364261 CACTATCTGTACCTATTTCTCGACG 58.636 44.000 0.00 0.00 0.00 5.12
1905 2237 3.350612 TGCTTACCGCACCGCAAC 61.351 61.111 0.00 0.00 45.47 4.17
2032 2448 6.200097 GGTAATTTTGAACAAATCTTGCACGT 59.800 34.615 0.82 0.00 0.00 4.49
2061 2477 7.334421 GTGGAATCTGTATATGTTGTGACAAGT 59.666 37.037 0.00 0.00 39.66 3.16
2090 2506 0.534652 GTCATGCTGGATGAGGGCTC 60.535 60.000 12.37 0.00 42.00 4.70
2091 2507 0.693430 TCATGCTGGATGAGGGCTCT 60.693 55.000 7.83 0.00 36.06 4.09
2193 2609 7.040686 ACAGATATTTTTGTACCGCTTTCACTT 60.041 33.333 0.00 0.00 0.00 3.16
2245 2661 8.204160 TGAATACTACTACATCAAGGGTCAATG 58.796 37.037 0.00 0.00 0.00 2.82
2473 2890 1.299850 GAAAAACACCCCAGCGCAC 60.300 57.895 11.47 0.00 0.00 5.34
2563 2980 1.004560 AGACGTGGCATGACACCAG 60.005 57.895 25.94 15.22 38.04 4.00
2606 3023 5.485662 AATACGCCTTGTAGAAAATCTGC 57.514 39.130 0.00 0.00 36.25 4.26
2740 3160 2.030007 TCCACAGCTTTTTAGCACATGC 60.030 45.455 0.00 0.00 42.49 4.06
2761 3181 4.640201 TGCTCTTAGGAAATGTAATGCCAC 59.360 41.667 0.00 0.00 0.00 5.01
2876 3296 3.244422 TGGCGGATTTCAAAGTACAGACT 60.244 43.478 0.00 0.00 37.59 3.24
2877 3297 4.020928 TGGCGGATTTCAAAGTACAGACTA 60.021 41.667 0.00 0.00 33.58 2.59
2878 3298 4.567159 GGCGGATTTCAAAGTACAGACTAG 59.433 45.833 0.00 0.00 33.58 2.57
2879 3299 5.408356 GCGGATTTCAAAGTACAGACTAGA 58.592 41.667 0.00 0.00 33.58 2.43
2880 3300 5.867716 GCGGATTTCAAAGTACAGACTAGAA 59.132 40.000 0.00 0.00 33.58 2.10
2964 3385 2.947532 TTCTGAGCACTCTGCCCCG 61.948 63.158 0.00 0.00 46.52 5.73
3181 3603 4.638865 TGAGTTCATCAATGCCTTCTGATG 59.361 41.667 5.83 5.83 46.83 3.07
3219 3641 5.016831 TCCAACTACTACTCTGATCAGCAA 58.983 41.667 18.36 0.52 0.00 3.91
3270 3692 4.881273 AGATCAGCGGTAATGTGCATTTAA 59.119 37.500 2.56 0.00 32.50 1.52
3378 3928 5.911280 CACAGTTTGAACAATCTAGCACAAG 59.089 40.000 0.00 0.00 0.00 3.16
3445 3997 4.898829 TTTCTGAACATGAAGTGTGTGG 57.101 40.909 0.00 0.00 41.14 4.17
3450 4002 4.013050 TGAACATGAAGTGTGTGGTTGAA 58.987 39.130 0.00 0.00 41.14 2.69
3659 4212 9.391006 TCACTGACACCAAAAAGGATATATAAC 57.609 33.333 0.00 0.00 41.22 1.89
3912 4560 1.073284 TGGTCAAGGCCAGAAAGGTAC 59.927 52.381 5.01 0.00 40.61 3.34
4263 4988 4.256920 AGGTGACAAGCTTGTATGATCAC 58.743 43.478 31.20 29.06 42.43 3.06
4504 5234 4.247380 GCTCCAGGGCAGGGATCG 62.247 72.222 0.00 0.00 33.04 3.69
4506 5236 2.764128 TCCAGGGCAGGGATCGTC 60.764 66.667 0.00 0.00 0.00 4.20
4591 5321 1.134670 GCTCATCGCCTACTTGTCCTT 60.135 52.381 0.00 0.00 0.00 3.36
4627 5357 1.073923 GTTTCCAGGATCCTGTGGTGT 59.926 52.381 34.49 0.89 42.15 4.16
4696 5428 1.133976 ACTGCTTGCTACCATCATCCC 60.134 52.381 0.00 0.00 0.00 3.85
4716 5448 3.849953 CGTTTCGCGGTAGCAGGC 61.850 66.667 6.13 0.00 45.49 4.85
4776 5508 5.990668 ACTAGTTGGAATGGTACTGGAATC 58.009 41.667 0.00 0.00 0.00 2.52
4876 5609 5.938125 TGTAATAGTTGGCTTGAAGGTTCTC 59.062 40.000 0.00 0.00 0.00 2.87
4966 5712 6.265196 TGAAATTCTTTATGCTGTGGTCTGTT 59.735 34.615 0.00 0.00 0.00 3.16
4967 5713 7.446931 TGAAATTCTTTATGCTGTGGTCTGTTA 59.553 33.333 0.00 0.00 0.00 2.41
4968 5714 6.992063 ATTCTTTATGCTGTGGTCTGTTAG 57.008 37.500 0.00 0.00 0.00 2.34
4969 5715 4.832248 TCTTTATGCTGTGGTCTGTTAGG 58.168 43.478 0.00 0.00 0.00 2.69
4970 5716 4.286032 TCTTTATGCTGTGGTCTGTTAGGT 59.714 41.667 0.00 0.00 0.00 3.08
4971 5717 2.479566 ATGCTGTGGTCTGTTAGGTG 57.520 50.000 0.00 0.00 0.00 4.00
4975 5721 2.949644 GCTGTGGTCTGTTAGGTGTTTT 59.050 45.455 0.00 0.00 0.00 2.43
4976 5722 3.243068 GCTGTGGTCTGTTAGGTGTTTTG 60.243 47.826 0.00 0.00 0.00 2.44
4977 5723 2.685897 TGTGGTCTGTTAGGTGTTTTGC 59.314 45.455 0.00 0.00 0.00 3.68
4979 5725 3.380320 GTGGTCTGTTAGGTGTTTTGCTT 59.620 43.478 0.00 0.00 0.00 3.91
4980 5726 4.020543 TGGTCTGTTAGGTGTTTTGCTTT 58.979 39.130 0.00 0.00 0.00 3.51
4981 5727 4.464597 TGGTCTGTTAGGTGTTTTGCTTTT 59.535 37.500 0.00 0.00 0.00 2.27
4982 5728 5.046950 TGGTCTGTTAGGTGTTTTGCTTTTT 60.047 36.000 0.00 0.00 0.00 1.94
4985 5731 6.253512 GTCTGTTAGGTGTTTTGCTTTTTCTG 59.746 38.462 0.00 0.00 0.00 3.02
4987 5733 5.186021 TGTTAGGTGTTTTGCTTTTTCTGGA 59.814 36.000 0.00 0.00 0.00 3.86
5043 5800 3.666274 CCAATTTGCAAGAAGGCATTGA 58.334 40.909 17.00 0.00 44.48 2.57
5085 5842 6.863275 ACTCGAGGAAAGTGAATTTGTTTTT 58.137 32.000 18.41 0.00 0.00 1.94
5091 5848 7.555965 AGGAAAGTGAATTTGTTTTTGCTAGT 58.444 30.769 0.00 0.00 29.44 2.57
5110 5867 7.375834 TGCTAGTTCTTTGTGATATATACGGG 58.624 38.462 0.00 0.00 0.00 5.28
5112 5869 7.755822 GCTAGTTCTTTGTGATATATACGGGAG 59.244 40.741 0.00 0.00 0.00 4.30
5128 5885 5.211174 ACGGGAGTAAATAGTAATCCTGC 57.789 43.478 8.26 0.00 44.60 4.85
5186 6167 5.643379 AACAAACACCAAGCATAGGTATG 57.357 39.130 0.00 0.00 37.23 2.39
5311 6376 8.401046 TGAAGTTTTTAAAAGAAATCACCACG 57.599 30.769 0.14 0.00 0.00 4.94
5312 6377 7.489757 TGAAGTTTTTAAAAGAAATCACCACGG 59.510 33.333 0.14 0.00 0.00 4.94
5313 6378 6.277605 AGTTTTTAAAAGAAATCACCACGGG 58.722 36.000 0.14 0.00 0.00 5.28
5314 6379 3.926821 TTAAAAGAAATCACCACGGGC 57.073 42.857 0.00 0.00 0.00 6.13
5315 6380 1.995376 AAAAGAAATCACCACGGGCT 58.005 45.000 0.00 0.00 0.00 5.19
5316 6381 1.995376 AAAGAAATCACCACGGGCTT 58.005 45.000 0.00 0.00 0.00 4.35
5317 6382 1.534729 AAGAAATCACCACGGGCTTC 58.465 50.000 0.00 0.00 0.00 3.86
5318 6383 0.400213 AGAAATCACCACGGGCTTCA 59.600 50.000 0.00 0.00 0.00 3.02
5319 6384 1.004745 AGAAATCACCACGGGCTTCAT 59.995 47.619 0.00 0.00 0.00 2.57
5320 6385 2.238646 AGAAATCACCACGGGCTTCATA 59.761 45.455 0.00 0.00 0.00 2.15
5321 6386 2.799126 AATCACCACGGGCTTCATAA 57.201 45.000 0.00 0.00 0.00 1.90
5322 6387 2.799126 ATCACCACGGGCTTCATAAA 57.201 45.000 0.00 0.00 0.00 1.40
5323 6388 1.816074 TCACCACGGGCTTCATAAAC 58.184 50.000 0.00 0.00 0.00 2.01
5324 6389 1.349688 TCACCACGGGCTTCATAAACT 59.650 47.619 0.00 0.00 0.00 2.66
5325 6390 2.159382 CACCACGGGCTTCATAAACTT 58.841 47.619 0.00 0.00 0.00 2.66
5326 6391 3.008157 TCACCACGGGCTTCATAAACTTA 59.992 43.478 0.00 0.00 0.00 2.24
5327 6392 3.126343 CACCACGGGCTTCATAAACTTAC 59.874 47.826 0.00 0.00 0.00 2.34
5328 6393 2.681344 CCACGGGCTTCATAAACTTACC 59.319 50.000 0.00 0.00 0.00 2.85
5329 6394 2.350498 CACGGGCTTCATAAACTTACCG 59.650 50.000 0.00 0.00 45.06 4.02
5330 6395 2.624636 CGGGCTTCATAAACTTACCGT 58.375 47.619 0.00 0.00 35.67 4.83
5331 6396 2.606272 CGGGCTTCATAAACTTACCGTC 59.394 50.000 0.00 0.00 35.67 4.79
5332 6397 3.602483 GGGCTTCATAAACTTACCGTCA 58.398 45.455 0.00 0.00 0.00 4.35
5333 6398 4.196971 GGGCTTCATAAACTTACCGTCAT 58.803 43.478 0.00 0.00 0.00 3.06
5334 6399 4.638865 GGGCTTCATAAACTTACCGTCATT 59.361 41.667 0.00 0.00 0.00 2.57
5335 6400 5.818857 GGGCTTCATAAACTTACCGTCATTA 59.181 40.000 0.00 0.00 0.00 1.90
5336 6401 6.485648 GGGCTTCATAAACTTACCGTCATTAT 59.514 38.462 0.00 0.00 0.00 1.28
5337 6402 7.352739 GGCTTCATAAACTTACCGTCATTATG 58.647 38.462 0.00 0.00 36.02 1.90
5338 6403 7.225931 GGCTTCATAAACTTACCGTCATTATGA 59.774 37.037 0.00 0.00 39.76 2.15
5339 6404 8.774586 GCTTCATAAACTTACCGTCATTATGAT 58.225 33.333 0.00 0.00 40.61 2.45
5351 6416 8.912787 ACCGTCATTATGATATCTATTCGTTC 57.087 34.615 3.98 0.00 0.00 3.95
5352 6417 7.974501 ACCGTCATTATGATATCTATTCGTTCC 59.025 37.037 3.98 0.00 0.00 3.62
5353 6418 7.165977 CCGTCATTATGATATCTATTCGTTCCG 59.834 40.741 3.98 0.00 0.00 4.30
5354 6419 7.908601 CGTCATTATGATATCTATTCGTTCCGA 59.091 37.037 3.98 0.00 0.00 4.55
5355 6420 9.737427 GTCATTATGATATCTATTCGTTCCGAT 57.263 33.333 3.98 0.00 35.23 4.18
5358 6423 8.926715 TTATGATATCTATTCGTTCCGATTGG 57.073 34.615 3.98 0.00 35.23 3.16
5359 6424 6.340962 TGATATCTATTCGTTCCGATTGGT 57.659 37.500 3.98 0.00 35.23 3.67
5360 6425 6.156519 TGATATCTATTCGTTCCGATTGGTG 58.843 40.000 3.98 0.00 35.23 4.17
5361 6426 2.546778 TCTATTCGTTCCGATTGGTGC 58.453 47.619 0.00 0.00 35.23 5.01
5362 6427 2.167693 TCTATTCGTTCCGATTGGTGCT 59.832 45.455 0.00 0.00 35.23 4.40
5363 6428 1.821216 ATTCGTTCCGATTGGTGCTT 58.179 45.000 0.00 0.00 35.23 3.91
5364 6429 2.459060 TTCGTTCCGATTGGTGCTTA 57.541 45.000 0.00 0.00 35.23 3.09
5365 6430 2.459060 TCGTTCCGATTGGTGCTTAA 57.541 45.000 0.00 0.00 36.30 1.85
5366 6431 2.768698 TCGTTCCGATTGGTGCTTAAA 58.231 42.857 0.00 0.00 36.30 1.52
5367 6432 2.481185 TCGTTCCGATTGGTGCTTAAAC 59.519 45.455 0.00 0.00 36.30 2.01
5368 6433 2.482721 CGTTCCGATTGGTGCTTAAACT 59.517 45.455 0.00 0.00 36.30 2.66
5369 6434 3.058501 CGTTCCGATTGGTGCTTAAACTT 60.059 43.478 0.00 0.00 36.30 2.66
5370 6435 4.555906 CGTTCCGATTGGTGCTTAAACTTT 60.556 41.667 0.00 0.00 36.30 2.66
5371 6436 5.334260 CGTTCCGATTGGTGCTTAAACTTTA 60.334 40.000 0.00 0.00 36.30 1.85
5372 6437 6.440436 GTTCCGATTGGTGCTTAAACTTTAA 58.560 36.000 0.00 0.00 36.30 1.52
5373 6438 6.636562 TCCGATTGGTGCTTAAACTTTAAA 57.363 33.333 0.00 0.00 36.30 1.52
5374 6439 6.440436 TCCGATTGGTGCTTAAACTTTAAAC 58.560 36.000 0.00 0.00 36.30 2.01
5375 6440 6.039493 TCCGATTGGTGCTTAAACTTTAAACA 59.961 34.615 0.00 0.00 36.30 2.83
5376 6441 6.866248 CCGATTGGTGCTTAAACTTTAAACAT 59.134 34.615 1.65 0.00 0.00 2.71
5377 6442 8.024285 CCGATTGGTGCTTAAACTTTAAACATA 58.976 33.333 1.65 0.00 0.00 2.29
5378 6443 9.567848 CGATTGGTGCTTAAACTTTAAACATAT 57.432 29.630 1.65 0.00 0.00 1.78
5380 6445 9.651913 ATTGGTGCTTAAACTTTAAACATATGG 57.348 29.630 7.80 0.00 0.00 2.74
5381 6446 8.410673 TGGTGCTTAAACTTTAAACATATGGA 57.589 30.769 7.80 0.00 0.00 3.41
5382 6447 8.301002 TGGTGCTTAAACTTTAAACATATGGAC 58.699 33.333 7.80 0.00 0.00 4.02
5383 6448 8.520351 GGTGCTTAAACTTTAAACATATGGACT 58.480 33.333 7.80 0.00 0.00 3.85
5384 6449 9.908152 GTGCTTAAACTTTAAACATATGGACTT 57.092 29.630 7.80 0.22 0.00 3.01
5385 6450 9.906660 TGCTTAAACTTTAAACATATGGACTTG 57.093 29.630 7.80 0.00 0.00 3.16
5386 6451 9.908152 GCTTAAACTTTAAACATATGGACTTGT 57.092 29.630 7.80 0.00 0.00 3.16
5389 6454 7.833285 AACTTTAAACATATGGACTTGTGGT 57.167 32.000 7.80 0.00 0.00 4.16
5390 6455 7.448748 ACTTTAAACATATGGACTTGTGGTC 57.551 36.000 7.80 0.00 43.79 4.02
5391 6456 7.001674 ACTTTAAACATATGGACTTGTGGTCA 58.998 34.615 7.80 0.00 46.16 4.02
5392 6457 7.669722 ACTTTAAACATATGGACTTGTGGTCAT 59.330 33.333 7.80 0.00 46.16 3.06
5393 6458 7.624360 TTAAACATATGGACTTGTGGTCATC 57.376 36.000 7.80 0.00 46.16 2.92
5394 6459 4.156455 ACATATGGACTTGTGGTCATCC 57.844 45.455 7.80 0.00 46.16 3.51
5395 6460 3.523157 ACATATGGACTTGTGGTCATCCA 59.477 43.478 7.80 0.00 46.16 3.41
5396 6461 4.018506 ACATATGGACTTGTGGTCATCCAA 60.019 41.667 7.80 0.00 46.15 3.53
5397 6462 2.270352 TGGACTTGTGGTCATCCAAC 57.730 50.000 0.00 0.00 46.15 3.77
5398 6463 1.774254 TGGACTTGTGGTCATCCAACT 59.226 47.619 0.00 0.00 46.15 3.16
5399 6464 2.174639 TGGACTTGTGGTCATCCAACTT 59.825 45.455 0.00 0.00 46.15 2.66
5400 6465 2.554032 GGACTTGTGGTCATCCAACTTG 59.446 50.000 0.00 0.00 46.15 3.16
5401 6466 1.956477 ACTTGTGGTCATCCAACTTGC 59.044 47.619 0.00 0.00 46.15 4.01
5402 6467 0.950836 TTGTGGTCATCCAACTTGCG 59.049 50.000 0.00 0.00 46.15 4.85
5403 6468 0.179032 TGTGGTCATCCAACTTGCGT 60.179 50.000 0.00 0.00 46.15 5.24
5404 6469 0.517316 GTGGTCATCCAACTTGCGTC 59.483 55.000 0.00 0.00 46.15 5.19
5405 6470 0.605319 TGGTCATCCAACTTGCGTCC 60.605 55.000 0.00 0.00 41.25 4.79
5406 6471 0.321653 GGTCATCCAACTTGCGTCCT 60.322 55.000 0.00 0.00 0.00 3.85
5407 6472 1.079503 GTCATCCAACTTGCGTCCTC 58.920 55.000 0.00 0.00 0.00 3.71
5408 6473 0.389817 TCATCCAACTTGCGTCCTCG 60.390 55.000 0.00 0.00 40.37 4.63
5409 6474 0.670546 CATCCAACTTGCGTCCTCGT 60.671 55.000 0.00 0.00 39.49 4.18
5410 6475 0.670546 ATCCAACTTGCGTCCTCGTG 60.671 55.000 0.00 0.00 39.49 4.35
5411 6476 2.551270 CAACTTGCGTCCTCGTGC 59.449 61.111 0.00 0.00 39.49 5.34
5412 6477 2.108157 AACTTGCGTCCTCGTGCA 59.892 55.556 0.00 0.00 39.81 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.551503 GCAAAAAGTGAAGGCGCTGC 61.552 55.000 7.64 0.37 34.49 5.25
2 3 0.248990 TGCAAAAAGTGAAGGCGCTG 60.249 50.000 7.64 0.00 34.49 5.18
4 5 0.785979 CATGCAAAAAGTGAAGGCGC 59.214 50.000 0.00 0.00 0.00 6.53
5 6 1.421382 CCATGCAAAAAGTGAAGGCG 58.579 50.000 0.00 0.00 0.00 5.52
6 7 1.150827 GCCATGCAAAAAGTGAAGGC 58.849 50.000 0.00 0.00 34.30 4.35
7 8 1.421382 CGCCATGCAAAAAGTGAAGG 58.579 50.000 0.00 0.00 0.00 3.46
8 9 0.785979 GCGCCATGCAAAAAGTGAAG 59.214 50.000 0.00 0.00 45.45 3.02
9 10 2.897780 GCGCCATGCAAAAAGTGAA 58.102 47.368 0.00 0.00 45.45 3.18
10 11 4.651585 GCGCCATGCAAAAAGTGA 57.348 50.000 0.00 0.00 45.45 3.41
33 34 1.077716 ACATTTACAGGGCCGCTCC 60.078 57.895 0.00 0.00 0.00 4.70
34 35 1.376609 CCACATTTACAGGGCCGCTC 61.377 60.000 0.00 0.00 0.00 5.03
35 36 1.378514 CCACATTTACAGGGCCGCT 60.379 57.895 0.00 0.00 0.00 5.52
36 37 0.393267 TACCACATTTACAGGGCCGC 60.393 55.000 0.00 0.00 0.00 6.53
37 38 1.375551 GTACCACATTTACAGGGCCG 58.624 55.000 0.00 0.00 0.00 6.13
38 39 1.065998 TCGTACCACATTTACAGGGCC 60.066 52.381 0.00 0.00 0.00 5.80
39 40 2.389962 TCGTACCACATTTACAGGGC 57.610 50.000 0.00 0.00 0.00 5.19
40 41 2.669434 CGTTCGTACCACATTTACAGGG 59.331 50.000 0.00 0.00 0.00 4.45
41 42 3.122278 CACGTTCGTACCACATTTACAGG 59.878 47.826 0.00 0.00 0.00 4.00
42 43 3.422603 GCACGTTCGTACCACATTTACAG 60.423 47.826 0.00 0.00 0.00 2.74
43 44 2.475864 GCACGTTCGTACCACATTTACA 59.524 45.455 0.00 0.00 0.00 2.41
44 45 2.471103 CGCACGTTCGTACCACATTTAC 60.471 50.000 0.00 0.00 0.00 2.01
45 46 1.720316 CGCACGTTCGTACCACATTTA 59.280 47.619 0.00 0.00 0.00 1.40
46 47 0.509499 CGCACGTTCGTACCACATTT 59.491 50.000 0.00 0.00 0.00 2.32
47 48 1.286354 CCGCACGTTCGTACCACATT 61.286 55.000 6.88 0.00 0.00 2.71
48 49 1.735198 CCGCACGTTCGTACCACAT 60.735 57.895 6.88 0.00 0.00 3.21
49 50 2.354891 CCGCACGTTCGTACCACA 60.355 61.111 6.88 0.00 0.00 4.17
50 51 3.770424 GCCGCACGTTCGTACCAC 61.770 66.667 6.88 0.00 0.00 4.16
51 52 4.281947 TGCCGCACGTTCGTACCA 62.282 61.111 6.88 0.00 0.00 3.25
52 53 3.770424 GTGCCGCACGTTCGTACC 61.770 66.667 7.96 0.00 0.00 3.34
53 54 3.770424 GGTGCCGCACGTTCGTAC 61.770 66.667 17.13 5.35 34.83 3.67
65 66 1.844544 TTTTAGGTCCCCTCGGTGCC 61.845 60.000 0.00 0.00 34.61 5.01
66 67 0.037160 TTTTTAGGTCCCCTCGGTGC 59.963 55.000 0.00 0.00 34.61 5.01
67 68 1.612462 GGTTTTTAGGTCCCCTCGGTG 60.612 57.143 0.00 0.00 34.61 4.94
68 69 0.694771 GGTTTTTAGGTCCCCTCGGT 59.305 55.000 0.00 0.00 34.61 4.69
69 70 0.034767 GGGTTTTTAGGTCCCCTCGG 60.035 60.000 0.00 0.00 34.61 4.63
70 71 0.392060 CGGGTTTTTAGGTCCCCTCG 60.392 60.000 0.00 0.00 38.09 4.63
71 72 0.034767 CCGGGTTTTTAGGTCCCCTC 60.035 60.000 0.00 0.00 38.09 4.30
72 73 0.476219 TCCGGGTTTTTAGGTCCCCT 60.476 55.000 0.00 0.00 38.09 4.79
73 74 0.322816 GTCCGGGTTTTTAGGTCCCC 60.323 60.000 0.00 0.00 38.09 4.81
74 75 0.674581 CGTCCGGGTTTTTAGGTCCC 60.675 60.000 0.00 0.00 37.98 4.46
75 76 0.674581 CCGTCCGGGTTTTTAGGTCC 60.675 60.000 0.00 0.00 0.00 4.46
76 77 0.321346 TCCGTCCGGGTTTTTAGGTC 59.679 55.000 0.00 0.00 37.00 3.85
77 78 0.322648 CTCCGTCCGGGTTTTTAGGT 59.677 55.000 0.00 0.00 37.00 3.08
78 79 0.392060 CCTCCGTCCGGGTTTTTAGG 60.392 60.000 0.00 0.19 37.00 2.69
79 80 0.322648 ACCTCCGTCCGGGTTTTTAG 59.677 55.000 0.00 0.00 37.00 1.85
80 81 1.550072 CTACCTCCGTCCGGGTTTTTA 59.450 52.381 0.00 0.00 37.07 1.52
81 82 0.322648 CTACCTCCGTCCGGGTTTTT 59.677 55.000 0.00 0.00 37.07 1.94
82 83 0.833409 ACTACCTCCGTCCGGGTTTT 60.833 55.000 0.00 0.00 37.07 2.43
160 164 6.765512 CCTTTTCCTCTTTGCCAAAAACATAA 59.234 34.615 0.00 0.00 0.00 1.90
196 204 0.318955 CTCCAAAACTGCAAAGCCCG 60.319 55.000 0.00 0.00 0.00 6.13
214 222 6.272558 ACATTTTACTACTCCTTCCTTCCACT 59.727 38.462 0.00 0.00 0.00 4.00
215 223 6.371825 CACATTTTACTACTCCTTCCTTCCAC 59.628 42.308 0.00 0.00 0.00 4.02
216 224 6.271391 TCACATTTTACTACTCCTTCCTTCCA 59.729 38.462 0.00 0.00 0.00 3.53
217 225 6.708285 TCACATTTTACTACTCCTTCCTTCC 58.292 40.000 0.00 0.00 0.00 3.46
218 226 8.617290 TTTCACATTTTACTACTCCTTCCTTC 57.383 34.615 0.00 0.00 0.00 3.46
219 227 7.175119 GCTTTCACATTTTACTACTCCTTCCTT 59.825 37.037 0.00 0.00 0.00 3.36
220 228 6.655425 GCTTTCACATTTTACTACTCCTTCCT 59.345 38.462 0.00 0.00 0.00 3.36
221 229 6.430000 TGCTTTCACATTTTACTACTCCTTCC 59.570 38.462 0.00 0.00 0.00 3.46
222 230 7.435068 TGCTTTCACATTTTACTACTCCTTC 57.565 36.000 0.00 0.00 0.00 3.46
223 231 7.817418 TTGCTTTCACATTTTACTACTCCTT 57.183 32.000 0.00 0.00 0.00 3.36
256 271 3.732849 CCTTCCCCAGCTCCACCC 61.733 72.222 0.00 0.00 0.00 4.61
346 369 0.047176 AGGGAGGAGGAGGAGAGAGA 59.953 60.000 0.00 0.00 0.00 3.10
347 370 0.478507 GAGGGAGGAGGAGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
354 377 2.612251 GGGAGGAGGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
355 378 3.036959 GGGGAGGAGGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
357 380 2.277126 ATTGGGGGAGGAGGGAGGAG 62.277 65.000 0.00 0.00 0.00 3.69
358 381 2.271493 GATTGGGGGAGGAGGGAGGA 62.271 65.000 0.00 0.00 0.00 3.71
410 436 4.389374 GTGGATGAGGACAACAAGAAGAA 58.611 43.478 0.00 0.00 0.00 2.52
482 508 2.445654 GGGAGGAGAGCAGGGGAG 60.446 72.222 0.00 0.00 0.00 4.30
496 523 2.133201 AGGAGGAGGGAGGAGGGA 59.867 66.667 0.00 0.00 0.00 4.20
531 558 1.731433 ATCCAAGACATGCATGCGGC 61.731 55.000 26.53 15.65 45.13 6.53
532 559 0.309922 GATCCAAGACATGCATGCGG 59.690 55.000 26.53 20.10 0.00 5.69
533 560 0.309922 GGATCCAAGACATGCATGCG 59.690 55.000 26.53 12.20 0.00 4.73
559 792 1.004560 CAGCAAGAGACCAAGGCGA 60.005 57.895 0.00 0.00 0.00 5.54
612 849 2.118294 GCAGGGCAGGGGACTTTT 59.882 61.111 0.00 0.00 40.21 2.27
638 875 3.081409 GCCTGGAGCCGGTAGGAA 61.081 66.667 16.85 0.00 41.02 3.36
651 888 2.768492 GGGATTTCAGCAGCGCCTG 61.768 63.158 2.29 5.38 34.12 4.85
652 889 2.439156 GGGATTTCAGCAGCGCCT 60.439 61.111 2.29 0.00 0.00 5.52
670 912 6.548321 AGATTTACAGTACCCAAAATCCACA 58.452 36.000 15.45 0.00 38.51 4.17
757 1002 3.182967 CGAATCAAGAAACCGAGAGAGG 58.817 50.000 0.00 0.00 37.30 3.69
779 1029 5.013808 AGGAGGAGGAGATTAAAAACCGAAA 59.986 40.000 0.00 0.00 0.00 3.46
781 1031 4.101856 AGGAGGAGGAGATTAAAAACCGA 58.898 43.478 0.00 0.00 0.00 4.69
794 1044 1.700368 CAGGGTGAGAGGAGGAGGA 59.300 63.158 0.00 0.00 0.00 3.71
796 1046 0.690411 ATGCAGGGTGAGAGGAGGAG 60.690 60.000 0.00 0.00 0.00 3.69
797 1047 0.252881 AATGCAGGGTGAGAGGAGGA 60.253 55.000 0.00 0.00 0.00 3.71
799 1049 0.179936 GGAATGCAGGGTGAGAGGAG 59.820 60.000 0.00 0.00 0.00 3.69
800 1050 1.274703 GGGAATGCAGGGTGAGAGGA 61.275 60.000 0.00 0.00 0.00 3.71
821 1072 1.269309 CGGAGGATGTCGCTAAAGAGG 60.269 57.143 0.00 0.00 0.00 3.69
822 1073 2.126914 CGGAGGATGTCGCTAAAGAG 57.873 55.000 0.00 0.00 0.00 2.85
830 1081 0.179100 ACAGAATGCGGAGGATGTCG 60.179 55.000 0.00 0.00 37.86 4.35
831 1082 2.029838 AACAGAATGCGGAGGATGTC 57.970 50.000 0.00 0.00 37.86 3.06
832 1083 2.026822 AGAAACAGAATGCGGAGGATGT 60.027 45.455 0.00 0.00 37.86 3.06
833 1084 2.353889 CAGAAACAGAATGCGGAGGATG 59.646 50.000 0.00 0.00 37.86 3.51
1597 1882 9.601810 TCTTGTAATAGCCCTATTATCTGAGAA 57.398 33.333 10.10 0.00 39.40 2.87
1766 2051 5.772672 AGTGCCAAATTTGTACTGAACCATA 59.227 36.000 18.89 0.00 0.00 2.74
1767 2052 4.588528 AGTGCCAAATTTGTACTGAACCAT 59.411 37.500 18.89 0.79 0.00 3.55
1768 2053 3.957497 AGTGCCAAATTTGTACTGAACCA 59.043 39.130 18.89 2.77 0.00 3.67
1788 2073 6.054295 ACGTCGAGAAATAGGTACAGATAGT 58.946 40.000 0.00 0.00 0.00 2.12
1811 2096 6.628919 ACAACACCAAATTTGTCTACCTAC 57.371 37.500 16.73 0.00 29.75 3.18
1968 2301 7.344913 ACCAAAGAGCAAAGATAATCATCTCT 58.655 34.615 0.00 0.00 40.81 3.10
1969 2302 7.565323 ACCAAAGAGCAAAGATAATCATCTC 57.435 36.000 0.00 0.00 40.81 2.75
2032 2448 7.125053 TGTCACAACATATACAGATTCCACCTA 59.875 37.037 0.00 0.00 0.00 3.08
2061 2477 2.121129 TCCAGCATGACTCATCATCCA 58.879 47.619 0.00 0.00 44.13 3.41
2245 2661 8.819643 TTTGTAGCCATAAATTTAAACACCAC 57.180 30.769 1.21 0.00 0.00 4.16
2276 2692 2.582636 ACAGGCTTCCACCCAAATCTAT 59.417 45.455 0.00 0.00 0.00 1.98
2348 2764 5.366482 TGGCAATACTTATGCTAGAACCA 57.634 39.130 0.00 0.00 43.34 3.67
2415 2831 6.035975 GCATAATTGTGCAGTATGGTTTTTCC 59.964 38.462 20.86 0.00 44.43 3.13
2473 2890 3.235195 GCACGTGTCTACAGACTAGTTG 58.765 50.000 18.38 0.07 44.99 3.16
2530 2947 6.403049 TGCCACGTCTGAATAGAAGAAAATA 58.597 36.000 0.00 0.00 36.16 1.40
2547 2964 0.603707 CTTCTGGTGTCATGCCACGT 60.604 55.000 0.03 0.00 36.16 4.49
2563 2980 9.890352 CGTATTAGGTTACATACTAGGTTCTTC 57.110 37.037 0.00 0.00 0.00 2.87
2693 3113 2.562298 TGAACCCATGGCAATTTGACTC 59.438 45.455 6.09 0.00 0.00 3.36
2740 3160 4.876107 ACGTGGCATTACATTTCCTAAGAG 59.124 41.667 0.00 0.00 0.00 2.85
2746 3166 4.523813 CGATTACGTGGCATTACATTTCC 58.476 43.478 0.00 0.00 34.56 3.13
2821 3241 5.714333 AGTTGCTAGAGAGAGAAAGTCATGA 59.286 40.000 0.00 0.00 0.00 3.07
2876 3296 9.581289 TTTCCAAGATCCATAAAAACAGTTCTA 57.419 29.630 0.00 0.00 0.00 2.10
2877 3297 8.477419 TTTCCAAGATCCATAAAAACAGTTCT 57.523 30.769 0.00 0.00 0.00 3.01
2878 3298 9.143631 CATTTCCAAGATCCATAAAAACAGTTC 57.856 33.333 0.00 0.00 0.00 3.01
2879 3299 8.650490 ACATTTCCAAGATCCATAAAAACAGTT 58.350 29.630 0.00 0.00 0.00 3.16
2880 3300 8.090214 CACATTTCCAAGATCCATAAAAACAGT 58.910 33.333 0.00 0.00 0.00 3.55
2964 3385 2.687700 ATGGTGACTGCAGAGTGATC 57.312 50.000 23.35 7.59 30.16 2.92
3181 3603 7.511959 AGTAGTTGGAGGAAATCTGAAAAAC 57.488 36.000 0.00 0.00 0.00 2.43
3219 3641 7.633018 TCCATAAGAAGAAAGTAGGCCATAT 57.367 36.000 5.01 0.00 0.00 1.78
3325 3875 7.297936 TCAGATGAACACTGGACTAAAGTTA 57.702 36.000 0.00 0.00 36.22 2.24
3378 3928 6.319399 CACTATGAACCATTTTACGGAAACC 58.681 40.000 0.00 0.00 0.00 3.27
3421 3973 5.221106 CCACACACTTCATGTTCAGAAATGT 60.221 40.000 0.00 0.00 40.64 2.71
3445 3997 8.328146 GCACTAAAAGAAATCAAAAGGTTCAAC 58.672 33.333 0.00 0.00 0.00 3.18
3450 4002 8.962884 ATTTGCACTAAAAGAAATCAAAAGGT 57.037 26.923 0.00 0.00 0.00 3.50
3636 4189 8.840321 CCTGTTATATATCCTTTTTGGTGTCAG 58.160 37.037 0.00 0.00 37.07 3.51
3659 4212 7.084486 GCTTACAAACTCAAAGATAAACCCTG 58.916 38.462 0.00 0.00 0.00 4.45
3866 4514 0.837691 TCTCCTTCTCTGCCTTGGCA 60.838 55.000 14.10 14.10 0.00 4.92
3912 4560 2.311688 ATACTTGAGAAGGCGGGCCG 62.312 60.000 24.35 24.35 41.95 6.13
3916 4564 4.755411 TCTGTTTATACTTGAGAAGGCGG 58.245 43.478 0.00 0.00 0.00 6.13
3974 4699 4.940046 ACATGAGTGCGAAAGAAAGATGAT 59.060 37.500 0.00 0.00 0.00 2.45
4263 4988 1.548719 TGGTAGTGGTCCACATCTTCG 59.451 52.381 24.02 0.00 36.74 3.79
4504 5234 2.187946 CAGATGACCGGCAGGGAC 59.812 66.667 8.08 1.45 43.47 4.46
4511 5241 2.187946 GGACAGCCAGATGACCGG 59.812 66.667 0.00 0.00 0.00 5.28
4513 5243 1.448540 CACGGACAGCCAGATGACC 60.449 63.158 0.00 0.00 0.00 4.02
4627 5357 1.456705 GCAAAGGGGGTGTTCCACA 60.457 57.895 0.00 0.00 42.98 4.17
4671 5403 4.655762 TGATGGTAGCAAGCAGTAGTAG 57.344 45.455 0.00 0.00 36.36 2.57
4776 5508 7.170998 GGGATACAATACTTCATACAAACTCCG 59.829 40.741 0.00 0.00 39.74 4.63
4876 5609 3.541632 ACACCAAACCAAGTCTACACAG 58.458 45.455 0.00 0.00 0.00 3.66
4966 5712 5.923733 TTCCAGAAAAAGCAAAACACCTA 57.076 34.783 0.00 0.00 0.00 3.08
4967 5713 4.817318 TTCCAGAAAAAGCAAAACACCT 57.183 36.364 0.00 0.00 0.00 4.00
4968 5714 4.332543 CCTTTCCAGAAAAAGCAAAACACC 59.667 41.667 0.00 0.00 35.37 4.16
4969 5715 4.935205 ACCTTTCCAGAAAAAGCAAAACAC 59.065 37.500 0.00 0.00 35.37 3.32
4970 5716 5.159273 ACCTTTCCAGAAAAAGCAAAACA 57.841 34.783 0.00 0.00 35.37 2.83
4971 5717 7.603963 TTTACCTTTCCAGAAAAAGCAAAAC 57.396 32.000 0.00 0.00 35.37 2.43
4975 5721 6.098982 TGGAATTTACCTTTCCAGAAAAAGCA 59.901 34.615 1.11 0.00 45.91 3.91
4976 5722 6.521162 TGGAATTTACCTTTCCAGAAAAAGC 58.479 36.000 1.11 0.00 45.91 3.51
5006 5763 1.451504 TGGCAGTTCCAGGTGTGAG 59.548 57.895 0.00 0.00 40.72 3.51
5043 5800 5.475719 TCGAGTTTCCGATCAAGTAAACAT 58.524 37.500 10.15 0.00 34.92 2.71
5085 5842 7.231925 TCCCGTATATATCACAAAGAACTAGCA 59.768 37.037 0.00 0.00 0.00 3.49
5105 5862 5.834742 TGCAGGATTACTATTTACTCCCGTA 59.165 40.000 0.00 0.00 0.00 4.02
5107 5864 5.010719 TCTGCAGGATTACTATTTACTCCCG 59.989 44.000 15.13 0.00 0.00 5.14
5108 5865 6.420913 TCTGCAGGATTACTATTTACTCCC 57.579 41.667 15.13 0.00 0.00 4.30
5170 6140 8.454106 GCTAATTTATCATACCTATGCTTGGTG 58.546 37.037 6.20 0.00 38.42 4.17
5224 6205 8.593945 ATTGGAGGTATAATGCTCTTTTTGAA 57.406 30.769 0.00 0.00 0.00 2.69
5225 6206 9.866655 ATATTGGAGGTATAATGCTCTTTTTGA 57.133 29.630 0.00 0.00 0.00 2.69
5226 6207 9.903682 CATATTGGAGGTATAATGCTCTTTTTG 57.096 33.333 0.00 0.00 0.00 2.44
5227 6208 9.866655 TCATATTGGAGGTATAATGCTCTTTTT 57.133 29.630 0.00 0.00 0.00 1.94
5229 6210 9.458727 CATCATATTGGAGGTATAATGCTCTTT 57.541 33.333 0.00 0.00 0.00 2.52
5230 6211 8.609483 ACATCATATTGGAGGTATAATGCTCTT 58.391 33.333 0.00 0.00 28.68 2.85
5231 6212 8.155620 ACATCATATTGGAGGTATAATGCTCT 57.844 34.615 0.00 0.00 28.68 4.09
5232 6213 7.497249 GGACATCATATTGGAGGTATAATGCTC 59.503 40.741 0.00 0.00 31.00 4.26
5285 6350 9.030301 CGTGGTGATTTCTTTTAAAAACTTCAT 57.970 29.630 1.66 0.00 0.00 2.57
5286 6351 7.489757 CCGTGGTGATTTCTTTTAAAAACTTCA 59.510 33.333 1.66 1.15 0.00 3.02
5287 6352 7.042992 CCCGTGGTGATTTCTTTTAAAAACTTC 60.043 37.037 1.66 0.00 0.00 3.01
5288 6353 6.759356 CCCGTGGTGATTTCTTTTAAAAACTT 59.241 34.615 1.66 0.00 0.00 2.66
5289 6354 6.277605 CCCGTGGTGATTTCTTTTAAAAACT 58.722 36.000 1.66 0.00 0.00 2.66
5290 6355 5.050634 GCCCGTGGTGATTTCTTTTAAAAAC 60.051 40.000 1.66 0.00 0.00 2.43
5291 6356 5.051153 GCCCGTGGTGATTTCTTTTAAAAA 58.949 37.500 1.66 0.00 0.00 1.94
5292 6357 4.342665 AGCCCGTGGTGATTTCTTTTAAAA 59.657 37.500 0.00 0.00 0.00 1.52
5293 6358 3.892588 AGCCCGTGGTGATTTCTTTTAAA 59.107 39.130 0.00 0.00 0.00 1.52
5294 6359 3.492337 AGCCCGTGGTGATTTCTTTTAA 58.508 40.909 0.00 0.00 0.00 1.52
5295 6360 3.149005 AGCCCGTGGTGATTTCTTTTA 57.851 42.857 0.00 0.00 0.00 1.52
5296 6361 1.995376 AGCCCGTGGTGATTTCTTTT 58.005 45.000 0.00 0.00 0.00 2.27
5297 6362 1.886542 GAAGCCCGTGGTGATTTCTTT 59.113 47.619 0.00 0.00 0.00 2.52
5298 6363 1.202879 TGAAGCCCGTGGTGATTTCTT 60.203 47.619 0.00 0.00 0.00 2.52
5299 6364 0.400213 TGAAGCCCGTGGTGATTTCT 59.600 50.000 0.00 0.00 0.00 2.52
5300 6365 1.463674 ATGAAGCCCGTGGTGATTTC 58.536 50.000 0.00 0.00 0.00 2.17
5301 6366 2.799126 TATGAAGCCCGTGGTGATTT 57.201 45.000 0.00 0.00 0.00 2.17
5302 6367 2.752903 GTTTATGAAGCCCGTGGTGATT 59.247 45.455 0.00 0.00 0.00 2.57
5303 6368 2.026262 AGTTTATGAAGCCCGTGGTGAT 60.026 45.455 0.00 0.00 0.00 3.06
5304 6369 1.349688 AGTTTATGAAGCCCGTGGTGA 59.650 47.619 0.00 0.00 0.00 4.02
5305 6370 1.821216 AGTTTATGAAGCCCGTGGTG 58.179 50.000 0.00 0.00 0.00 4.17
5306 6371 2.579410 AAGTTTATGAAGCCCGTGGT 57.421 45.000 0.00 0.00 0.00 4.16
5307 6372 2.681344 GGTAAGTTTATGAAGCCCGTGG 59.319 50.000 0.00 0.00 0.00 4.94
5308 6373 2.350498 CGGTAAGTTTATGAAGCCCGTG 59.650 50.000 0.00 0.00 0.00 4.94
5309 6374 2.027837 ACGGTAAGTTTATGAAGCCCGT 60.028 45.455 0.00 0.00 42.15 5.28
5310 6375 2.606272 GACGGTAAGTTTATGAAGCCCG 59.394 50.000 0.00 0.00 39.96 6.13
5311 6376 3.602483 TGACGGTAAGTTTATGAAGCCC 58.398 45.455 0.00 0.00 0.00 5.19
5312 6377 5.813080 AATGACGGTAAGTTTATGAAGCC 57.187 39.130 0.00 0.00 0.00 4.35
5313 6378 8.138365 TCATAATGACGGTAAGTTTATGAAGC 57.862 34.615 9.93 0.00 38.55 3.86
5325 6390 9.999009 GAACGAATAGATATCATAATGACGGTA 57.001 33.333 5.32 0.00 0.00 4.02
5326 6391 7.974501 GGAACGAATAGATATCATAATGACGGT 59.025 37.037 5.32 4.64 0.00 4.83
5327 6392 8.341477 GGAACGAATAGATATCATAATGACGG 57.659 38.462 5.32 0.00 0.00 4.79
5348 6413 4.499037 AAGTTTAAGCACCAATCGGAAC 57.501 40.909 0.00 0.00 35.59 3.62
5349 6414 6.636562 TTAAAGTTTAAGCACCAATCGGAA 57.363 33.333 3.88 0.00 35.59 4.30
5350 6415 6.039493 TGTTTAAAGTTTAAGCACCAATCGGA 59.961 34.615 17.79 0.00 35.59 4.55
5351 6416 6.210078 TGTTTAAAGTTTAAGCACCAATCGG 58.790 36.000 17.79 0.00 38.77 4.18
5352 6417 7.867445 ATGTTTAAAGTTTAAGCACCAATCG 57.133 32.000 22.31 0.00 0.00 3.34
5354 6419 9.651913 CCATATGTTTAAAGTTTAAGCACCAAT 57.348 29.630 22.31 14.91 0.00 3.16
5355 6420 8.861086 TCCATATGTTTAAAGTTTAAGCACCAA 58.139 29.630 22.31 13.66 0.00 3.67
5356 6421 8.301002 GTCCATATGTTTAAAGTTTAAGCACCA 58.699 33.333 22.31 15.35 0.00 4.17
5357 6422 8.520351 AGTCCATATGTTTAAAGTTTAAGCACC 58.480 33.333 22.31 9.81 0.00 5.01
5358 6423 9.908152 AAGTCCATATGTTTAAAGTTTAAGCAC 57.092 29.630 22.31 13.15 0.00 4.40
5359 6424 9.906660 CAAGTCCATATGTTTAAAGTTTAAGCA 57.093 29.630 22.17 22.17 0.00 3.91
5360 6425 9.908152 ACAAGTCCATATGTTTAAAGTTTAAGC 57.092 29.630 13.55 13.55 0.00 3.09
5363 6428 9.357161 ACCACAAGTCCATATGTTTAAAGTTTA 57.643 29.630 1.24 0.00 0.00 2.01
5364 6429 8.245195 ACCACAAGTCCATATGTTTAAAGTTT 57.755 30.769 1.24 0.00 0.00 2.66
5365 6430 7.504238 TGACCACAAGTCCATATGTTTAAAGTT 59.496 33.333 1.24 0.00 45.68 2.66
5366 6431 7.001674 TGACCACAAGTCCATATGTTTAAAGT 58.998 34.615 1.24 0.00 45.68 2.66
5367 6432 7.447374 TGACCACAAGTCCATATGTTTAAAG 57.553 36.000 1.24 0.00 45.68 1.85
5368 6433 7.122055 GGATGACCACAAGTCCATATGTTTAAA 59.878 37.037 1.24 0.00 45.68 1.52
5369 6434 6.601613 GGATGACCACAAGTCCATATGTTTAA 59.398 38.462 1.24 0.00 45.68 1.52
5370 6435 6.119536 GGATGACCACAAGTCCATATGTTTA 58.880 40.000 1.24 0.00 45.68 2.01
5371 6436 4.949856 GGATGACCACAAGTCCATATGTTT 59.050 41.667 1.24 0.00 45.68 2.83
5372 6437 4.018506 TGGATGACCACAAGTCCATATGTT 60.019 41.667 1.24 0.00 45.68 2.71
5373 6438 3.523157 TGGATGACCACAAGTCCATATGT 59.477 43.478 1.24 0.00 45.68 2.29
5374 6439 4.155063 TGGATGACCACAAGTCCATATG 57.845 45.455 0.00 0.00 45.68 1.78
5375 6440 4.228210 AGTTGGATGACCACAAGTCCATAT 59.772 41.667 0.00 0.00 46.80 1.78
5376 6441 3.587061 AGTTGGATGACCACAAGTCCATA 59.413 43.478 0.00 0.00 46.80 2.74
5377 6442 2.376518 AGTTGGATGACCACAAGTCCAT 59.623 45.455 0.00 0.00 46.80 3.41
5378 6443 1.774254 AGTTGGATGACCACAAGTCCA 59.226 47.619 0.00 0.00 46.80 4.02
5379 6444 2.554032 CAAGTTGGATGACCACAAGTCC 59.446 50.000 0.00 0.00 46.80 3.85
5380 6445 2.030805 GCAAGTTGGATGACCACAAGTC 60.031 50.000 4.75 0.00 46.80 3.01
5381 6446 1.956477 GCAAGTTGGATGACCACAAGT 59.044 47.619 4.75 0.00 46.80 3.16
5382 6447 1.069022 CGCAAGTTGGATGACCACAAG 60.069 52.381 4.75 0.00 46.80 3.16
5383 6448 0.950836 CGCAAGTTGGATGACCACAA 59.049 50.000 4.75 0.00 46.80 3.33
5384 6449 2.627791 CGCAAGTTGGATGACCACA 58.372 52.632 4.75 0.00 46.80 4.17


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

AutoCloner maintained by Alex Coulton.