Multiple sequence alignment - TraesCS3A01G373100

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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 TraesCS3A01G373100 chr3A 100.000 2894 0 0 1 2894 623339363 623342256 0.000000e+00 5345
1 TraesCS3A01G373100 chr3A 92.686 1381 82 8 936 2309 623229543 623230911 0.000000e+00 1973
2 TraesCS3A01G373100 chr3A 91.165 1313 107 2 986 2291 623354490 623355800 0.000000e+00 1773
3 TraesCS3A01G373100 chr3A 89.911 1348 121 8 976 2311 623362229 623363573 0.000000e+00 1722
4 TraesCS3A01G373100 chr3A 89.458 332 33 1 2565 2894 623355818 623356149 4.460000e-113 418
5 TraesCS3A01G373100 chr3A 92.177 294 20 2 624 914 623229260 623229553 2.080000e-111 412
6 TraesCS3A01G373100 chr3A 88.166 338 36 4 2559 2894 623230913 623231248 1.620000e-107 399
7 TraesCS3A01G373100 chr3A 82.124 386 44 16 229 607 623228910 623229277 1.010000e-79 307
8 TraesCS3A01G373100 chr3A 77.604 192 35 8 229 414 179503203 179503014 3.050000e-20 110
9 TraesCS3A01G373100 chr3B 92.867 1388 85 6 936 2311 640693454 640694839 0.000000e+00 2002
10 TraesCS3A01G373100 chr3B 91.660 1343 103 3 976 2311 640700686 640702026 0.000000e+00 1851
11 TraesCS3A01G373100 chr3B 89.440 1411 112 16 976 2375 640708314 640709698 0.000000e+00 1746
12 TraesCS3A01G373100 chr3B 88.539 349 37 2 2548 2894 640694838 640695185 1.240000e-113 420
13 TraesCS3A01G373100 chr3B 83.333 348 31 10 2548 2893 640702025 640702347 2.180000e-76 296
14 TraesCS3A01G373100 chr3B 83.923 311 34 8 1 307 640674307 640674605 1.700000e-72 283
15 TraesCS3A01G373100 chr3D 93.434 1325 70 7 994 2311 480157922 480159236 0.000000e+00 1949
16 TraesCS3A01G373100 chr3D 91.366 1332 99 6 986 2309 480357995 480359318 0.000000e+00 1808
17 TraesCS3A01G373100 chr3D 89.387 1338 110 11 976 2303 480366710 480368025 0.000000e+00 1655
18 TraesCS3A01G373100 chr3D 92.366 917 68 2 980 1895 480375800 480376715 0.000000e+00 1304
19 TraesCS3A01G373100 chr3D 84.236 609 54 16 1 597 480157214 480157792 3.260000e-154 555
20 TraesCS3A01G373100 chr3D 89.685 349 31 4 2548 2894 480371402 480371747 9.520000e-120 440
21 TraesCS3A01G373100 chr3D 88.669 353 34 5 2546 2894 480359316 480359666 2.670000e-115 425
22 TraesCS3A01G373100 chr3D 87.500 312 30 4 1996 2300 480310690 480310999 4.590000e-93 351
23 TraesCS3A01G373100 chr3D 81.897 348 31 12 2548 2893 480311206 480311523 6.150000e-67 265
24 TraesCS3A01G373100 chr3D 93.827 162 10 0 1 162 480310530 480310691 8.010000e-61 244
25 TraesCS3A01G373100 chr3D 88.571 140 16 0 624 763 480157785 480157924 1.380000e-38 171
26 TraesCS3A01G373100 chr2D 88.115 244 24 5 2309 2549 56196742 56196983 4.720000e-73 285
27 TraesCS3A01G373100 chr7D 88.235 238 23 5 2315 2549 484439880 484439645 2.200000e-71 279
28 TraesCS3A01G373100 chr7D 85.317 252 33 4 2309 2558 29684297 29684546 1.030000e-64 257
29 TraesCS3A01G373100 chr4D 87.149 249 26 6 2313 2558 398549797 398549552 7.900000e-71 278
30 TraesCS3A01G373100 chr4A 87.342 237 27 3 2316 2550 625241549 625241784 4.750000e-68 268
31 TraesCS3A01G373100 chr4A 85.597 243 33 2 2313 2554 624756208 624755967 1.330000e-63 254
32 TraesCS3A01G373100 chr1D 86.420 243 32 1 2308 2549 467628311 467628069 6.150000e-67 265
33 TraesCS3A01G373100 chr1D 81.699 153 21 7 226 374 445248154 445248005 1.410000e-23 121
34 TraesCS3A01G373100 chr6A 86.066 244 30 4 2309 2549 588601128 588600886 2.860000e-65 259
35 TraesCS3A01G373100 chr2A 85.477 241 30 5 2313 2550 737498284 737498046 2.230000e-61 246
36 TraesCS3A01G373100 chr2A 78.788 231 34 14 222 443 444796136 444796360 1.080000e-29 141
37 TraesCS3A01G373100 chr2B 79.221 231 33 14 222 443 402374968 402375192 2.320000e-31 147
38 TraesCS3A01G373100 chr7B 79.612 206 31 9 230 428 19251681 19251480 1.400000e-28 137
39 TraesCS3A01G373100 chr1A 83.660 153 18 7 226 374 541148482 541148333 1.400000e-28 137
40 TraesCS3A01G373100 chr6D 85.149 101 14 1 229 328 402882111 402882211 5.100000e-18 102
41 TraesCS3A01G373100 chr7A 76.636 214 31 13 222 429 668019467 668019267 1.830000e-17 100


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 TraesCS3A01G373100 chr3A 623339363 623342256 2893 False 5345.000000 5345 100.000000 1 2894 1 chr3A.!!$F1 2893
1 TraesCS3A01G373100 chr3A 623362229 623363573 1344 False 1722.000000 1722 89.911000 976 2311 1 chr3A.!!$F2 1335
2 TraesCS3A01G373100 chr3A 623354490 623356149 1659 False 1095.500000 1773 90.311500 986 2894 2 chr3A.!!$F4 1908
3 TraesCS3A01G373100 chr3A 623228910 623231248 2338 False 772.750000 1973 88.788250 229 2894 4 chr3A.!!$F3 2665
4 TraesCS3A01G373100 chr3B 640708314 640709698 1384 False 1746.000000 1746 89.440000 976 2375 1 chr3B.!!$F2 1399
5 TraesCS3A01G373100 chr3B 640693454 640695185 1731 False 1211.000000 2002 90.703000 936 2894 2 chr3B.!!$F3 1958
6 TraesCS3A01G373100 chr3B 640700686 640702347 1661 False 1073.500000 1851 87.496500 976 2893 2 chr3B.!!$F4 1917
7 TraesCS3A01G373100 chr3D 480375800 480376715 915 False 1304.000000 1304 92.366000 980 1895 1 chr3D.!!$F1 915
8 TraesCS3A01G373100 chr3D 480357995 480359666 1671 False 1116.500000 1808 90.017500 986 2894 2 chr3D.!!$F4 1908
9 TraesCS3A01G373100 chr3D 480366710 480371747 5037 False 1047.500000 1655 89.536000 976 2894 2 chr3D.!!$F5 1918
10 TraesCS3A01G373100 chr3D 480157214 480159236 2022 False 891.666667 1949 88.747000 1 2311 3 chr3D.!!$F2 2310
11 TraesCS3A01G373100 chr3D 480310530 480311523 993 False 286.666667 351 87.741333 1 2893 3 chr3D.!!$F3 2892

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
920 935 0.312102 GCAGAGCGCACCTTCTTTTT 59.688 50.0 11.47 0.0 41.79 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2225 0.652592 CGAGGATTCATGTTGTCGGC 59.347 55.0 0.0 0.0 0.0 5.54 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
122 124 2.410785 TGTCGGTTCGAGTAACACAG 57.589 50.000 0.00 0.00 40.08 3.66
123 125 1.058404 GTCGGTTCGAGTAACACAGC 58.942 55.000 0.00 0.00 40.08 4.40
124 126 0.386352 TCGGTTCGAGTAACACAGCG 60.386 55.000 0.00 0.00 40.08 5.18
125 127 1.779683 GGTTCGAGTAACACAGCGC 59.220 57.895 0.00 0.00 40.08 5.92
126 128 0.942410 GGTTCGAGTAACACAGCGCA 60.942 55.000 11.47 0.00 40.08 6.09
135 137 1.992233 AACACAGCGCACACTTGTGG 61.992 55.000 24.82 11.34 44.87 4.17
181 184 2.084546 AGGAACATTTTACTGCTCCGC 58.915 47.619 0.00 0.00 36.66 5.54
184 187 2.989422 ACATTTTACTGCTCCGCAAC 57.011 45.000 0.00 0.00 38.41 4.17
193 196 4.730949 ACTGCTCCGCAACTAAACTATA 57.269 40.909 0.00 0.00 38.41 1.31
200 203 5.606505 TCCGCAACTAAACTATATGCATCA 58.393 37.500 0.19 0.00 36.84 3.07
202 205 5.377358 CGCAACTAAACTATATGCATCAGC 58.623 41.667 0.19 0.00 42.57 4.26
203 206 5.377358 GCAACTAAACTATATGCATCAGCG 58.623 41.667 0.19 0.00 46.23 5.18
219 222 5.518847 GCATCAGCGTCACAATAAACTAGTA 59.481 40.000 0.00 0.00 0.00 1.82
224 227 7.699391 TCAGCGTCACAATAAACTAGTACATAC 59.301 37.037 0.00 0.00 0.00 2.39
279 285 5.904362 ATAAGATTTGTCTGGAGCCAAAC 57.096 39.130 0.00 0.00 33.73 2.93
282 288 4.218312 AGATTTGTCTGGAGCCAAACTTT 58.782 39.130 0.00 0.00 33.73 2.66
283 289 3.799281 TTTGTCTGGAGCCAAACTTTG 57.201 42.857 0.00 0.00 0.00 2.77
396 404 4.041049 TGTTGATTTCGTGTTGTGAATGC 58.959 39.130 0.00 0.00 0.00 3.56
477 486 9.358406 TCTTATATATGACGTAGGAAAGACCAA 57.642 33.333 0.00 0.00 42.04 3.67
479 488 9.976511 TTATATATGACGTAGGAAAGACCAAAG 57.023 33.333 0.00 0.00 42.04 2.77
491 500 5.648526 GGAAAGACCAAAGGGAGTAAGATTC 59.351 44.000 0.00 0.00 38.79 2.52
516 526 2.426842 ATAGGCCCAGAAAACAGAGC 57.573 50.000 0.00 0.00 0.00 4.09
520 531 1.620323 GGCCCAGAAAACAGAGCAAAT 59.380 47.619 0.00 0.00 0.00 2.32
525 536 2.722629 CAGAAAACAGAGCAAATGCACG 59.277 45.455 8.28 1.31 45.16 5.34
537 548 1.732941 AATGCACGGTTTCTATCGCA 58.267 45.000 0.00 0.00 0.00 5.10
538 549 1.006832 ATGCACGGTTTCTATCGCAC 58.993 50.000 0.00 0.00 31.22 5.34
539 550 1.343821 GCACGGTTTCTATCGCACG 59.656 57.895 0.00 0.00 0.00 5.34
540 551 1.349259 GCACGGTTTCTATCGCACGT 61.349 55.000 0.00 0.00 34.61 4.49
541 552 1.898938 CACGGTTTCTATCGCACGTA 58.101 50.000 0.00 0.00 32.85 3.57
542 553 2.456989 CACGGTTTCTATCGCACGTAT 58.543 47.619 0.00 0.00 32.85 3.06
543 554 2.855963 CACGGTTTCTATCGCACGTATT 59.144 45.455 0.00 0.00 32.85 1.89
544 555 2.855963 ACGGTTTCTATCGCACGTATTG 59.144 45.455 0.00 0.00 32.30 1.90
578 592 3.826524 TGTTTTGGTTGAGTATGGAGCA 58.173 40.909 0.00 0.00 0.00 4.26
598 612 3.641648 CATTTGTGATTTGGACGCACTT 58.358 40.909 0.00 0.00 33.83 3.16
599 613 3.791973 TTTGTGATTTGGACGCACTTT 57.208 38.095 0.00 0.00 33.83 2.66
600 614 3.791973 TTGTGATTTGGACGCACTTTT 57.208 38.095 0.00 0.00 33.83 2.27
601 615 4.902443 TTGTGATTTGGACGCACTTTTA 57.098 36.364 0.00 0.00 33.83 1.52
602 616 5.446143 TTGTGATTTGGACGCACTTTTAT 57.554 34.783 0.00 0.00 33.83 1.40
603 617 5.446143 TGTGATTTGGACGCACTTTTATT 57.554 34.783 0.00 0.00 33.83 1.40
604 618 5.837437 TGTGATTTGGACGCACTTTTATTT 58.163 33.333 0.00 0.00 33.83 1.40
605 619 6.276847 TGTGATTTGGACGCACTTTTATTTT 58.723 32.000 0.00 0.00 33.83 1.82
606 620 6.758886 TGTGATTTGGACGCACTTTTATTTTT 59.241 30.769 0.00 0.00 33.83 1.94
607 621 7.062848 GTGATTTGGACGCACTTTTATTTTTG 58.937 34.615 0.00 0.00 0.00 2.44
608 622 5.396750 TTTGGACGCACTTTTATTTTTGC 57.603 34.783 0.00 0.00 0.00 3.68
613 627 3.786657 GCACTTTTATTTTTGCGGGTG 57.213 42.857 0.00 0.00 0.00 4.61
614 628 3.385577 GCACTTTTATTTTTGCGGGTGA 58.614 40.909 0.00 0.00 0.00 4.02
615 629 3.183574 GCACTTTTATTTTTGCGGGTGAC 59.816 43.478 0.00 0.00 0.00 3.67
616 630 4.616953 CACTTTTATTTTTGCGGGTGACT 58.383 39.130 0.00 0.00 0.00 3.41
617 631 4.444056 CACTTTTATTTTTGCGGGTGACTG 59.556 41.667 0.00 0.00 40.79 3.51
618 632 3.651803 TTTATTTTTGCGGGTGACTGG 57.348 42.857 0.00 0.00 37.13 4.00
619 633 1.540267 TATTTTTGCGGGTGACTGGG 58.460 50.000 0.00 0.00 37.13 4.45
620 634 0.469144 ATTTTTGCGGGTGACTGGGT 60.469 50.000 0.00 0.00 37.13 4.51
621 635 1.388065 TTTTTGCGGGTGACTGGGTG 61.388 55.000 0.00 0.00 37.13 4.61
622 636 2.272230 TTTTGCGGGTGACTGGGTGA 62.272 55.000 0.00 0.00 37.13 4.02
623 637 2.674563 TTTGCGGGTGACTGGGTGAG 62.675 60.000 0.00 0.00 37.13 3.51
624 638 4.394712 GCGGGTGACTGGGTGAGG 62.395 72.222 0.00 0.00 37.13 3.86
625 639 2.603473 CGGGTGACTGGGTGAGGA 60.603 66.667 0.00 0.00 0.00 3.71
626 640 2.943978 CGGGTGACTGGGTGAGGAC 61.944 68.421 0.00 0.00 0.00 3.85
627 641 2.657237 GGTGACTGGGTGAGGACG 59.343 66.667 0.00 0.00 0.00 4.79
628 642 2.048127 GTGACTGGGTGAGGACGC 60.048 66.667 0.00 0.00 35.59 5.19
629 643 2.203640 TGACTGGGTGAGGACGCT 60.204 61.111 0.00 0.00 36.03 5.07
652 666 3.405689 TTTTTAGGGCACGCAGTCA 57.594 47.368 0.00 0.00 41.61 3.41
744 758 2.857152 TGCAACGAAATTTGTTCTGCAC 59.143 40.909 8.26 0.00 0.00 4.57
755 769 1.002430 TGTTCTGCACCTCAGCCTTAG 59.998 52.381 0.00 0.00 42.56 2.18
764 779 1.066430 CCTCAGCCTTAGTTAACCGCA 60.066 52.381 0.88 0.00 0.00 5.69
768 783 2.812011 CAGCCTTAGTTAACCGCAAACT 59.188 45.455 0.88 0.00 40.25 2.66
787 802 4.546829 ACTTTGCCGGTAGATTTAGACA 57.453 40.909 1.90 0.00 0.00 3.41
789 804 2.973694 TGCCGGTAGATTTAGACACC 57.026 50.000 1.90 0.00 0.00 4.16
807 822 3.110178 GGAACGGACAAGCGACGG 61.110 66.667 0.00 0.00 0.00 4.79
844 859 3.745975 CACTAAAGAAAGCGTCCATGACA 59.254 43.478 0.00 0.00 32.09 3.58
850 865 0.320771 AAGCGTCCATGACACTCCAC 60.321 55.000 0.00 0.00 32.09 4.02
858 873 1.000843 CATGACACTCCACCGAGACAA 59.999 52.381 0.00 0.00 38.52 3.18
897 912 4.526970 ACCCAATATCCATCACAACTCAC 58.473 43.478 0.00 0.00 0.00 3.51
901 916 6.460537 CCCAATATCCATCACAACTCACAATG 60.461 42.308 0.00 0.00 0.00 2.82
903 918 2.861274 TCCATCACAACTCACAATGCA 58.139 42.857 0.00 0.00 0.00 3.96
904 919 2.815503 TCCATCACAACTCACAATGCAG 59.184 45.455 0.00 0.00 0.00 4.41
905 920 2.815503 CCATCACAACTCACAATGCAGA 59.184 45.455 0.00 0.00 0.00 4.26
906 921 3.119955 CCATCACAACTCACAATGCAGAG 60.120 47.826 0.00 0.00 37.87 3.35
907 922 1.875514 TCACAACTCACAATGCAGAGC 59.124 47.619 0.00 0.00 35.28 4.09
908 923 0.870393 ACAACTCACAATGCAGAGCG 59.130 50.000 0.00 0.00 35.28 5.03
909 924 0.453950 CAACTCACAATGCAGAGCGC 60.454 55.000 0.00 0.00 42.89 5.92
918 933 3.660621 GCAGAGCGCACCTTCTTT 58.339 55.556 11.47 0.00 41.79 2.52
919 934 1.952263 GCAGAGCGCACCTTCTTTT 59.048 52.632 11.47 0.00 41.79 2.27
920 935 0.312102 GCAGAGCGCACCTTCTTTTT 59.688 50.000 11.47 0.00 41.79 1.94
946 961 1.227853 AAACGGAAGAGCGCACCTT 60.228 52.632 11.47 12.84 0.00 3.50
984 999 0.386113 GCAGCTAGCTAGGTACGCTT 59.614 55.000 24.28 0.00 41.15 4.68
1026 1041 1.827789 CCGAGCTCTCCCTCTCCTG 60.828 68.421 12.85 0.00 0.00 3.86
1391 1406 2.257207 CCTCTGGAACAACTACCTGGA 58.743 52.381 0.00 0.00 38.70 3.86
1860 1875 5.940470 GTCCAAGTTCTATGATGACCAAACT 59.060 40.000 0.00 0.00 0.00 2.66
1919 1934 7.120923 AGTTCTCTCTAGTGTGTTTGGTTTA 57.879 36.000 0.00 0.00 0.00 2.01
1951 1966 6.883129 TGTTATTATTGTGTGTCTTGTGTCG 58.117 36.000 0.00 0.00 0.00 4.35
2112 2141 5.704978 TCATGCACTACACTGCTTTTGATTA 59.295 36.000 0.00 0.00 38.07 1.75
2115 2144 7.680442 TGCACTACACTGCTTTTGATTATAA 57.320 32.000 0.00 0.00 38.07 0.98
2151 2180 7.805542 CGTGTGTACAATATTTGGTCAATCAAA 59.194 33.333 0.00 0.00 40.37 2.69
2161 2190 5.867903 TTGGTCAATCAAATGTGGTTCTT 57.132 34.783 0.00 0.00 0.00 2.52
2165 2194 6.322456 TGGTCAATCAAATGTGGTTCTTGTTA 59.678 34.615 0.00 0.00 0.00 2.41
2177 2206 7.007723 TGTGGTTCTTGTTAAATATTGGTCCT 58.992 34.615 0.00 0.00 0.00 3.85
2181 2210 8.581578 GGTTCTTGTTAAATATTGGTCCTTCAA 58.418 33.333 0.00 0.00 0.00 2.69
2196 2225 8.292444 TGGTCCTTCAATTTGAATACCATTAG 57.708 34.615 26.85 10.96 42.44 1.73
2209 2238 3.066291 ACCATTAGCCGACAACATGAA 57.934 42.857 0.00 0.00 0.00 2.57
2323 5934 7.277405 AGAAGAAAGTTAATCCCTCCATTCT 57.723 36.000 0.00 0.00 0.00 2.40
2327 5938 8.393959 AGAAAGTTAATCCCTCCATTCTCTTA 57.606 34.615 0.00 0.00 0.00 2.10
2328 5939 9.008584 AGAAAGTTAATCCCTCCATTCTCTTAT 57.991 33.333 0.00 0.00 0.00 1.73
2399 6011 9.880157 TTACCAGTAAAAGGTGAGTTATATGTC 57.120 33.333 0.00 0.00 40.26 3.06
2400 6012 7.039882 ACCAGTAAAAGGTGAGTTATATGTCG 58.960 38.462 0.00 0.00 38.13 4.35
2401 6013 6.018994 CCAGTAAAAGGTGAGTTATATGTCGC 60.019 42.308 0.00 0.00 0.00 5.19
2402 6014 6.533723 CAGTAAAAGGTGAGTTATATGTCGCA 59.466 38.462 0.00 0.00 0.00 5.10
2403 6015 7.064134 CAGTAAAAGGTGAGTTATATGTCGCAA 59.936 37.037 0.00 0.00 0.00 4.85
2404 6016 6.811253 AAAAGGTGAGTTATATGTCGCAAA 57.189 33.333 0.00 0.00 0.00 3.68
2405 6017 6.811253 AAAGGTGAGTTATATGTCGCAAAA 57.189 33.333 0.00 0.00 0.00 2.44
2406 6018 6.811253 AAGGTGAGTTATATGTCGCAAAAA 57.189 33.333 0.00 0.00 0.00 1.94
2407 6019 6.422776 AGGTGAGTTATATGTCGCAAAAAG 57.577 37.500 0.00 0.00 0.00 2.27
2408 6020 5.938125 AGGTGAGTTATATGTCGCAAAAAGT 59.062 36.000 0.00 0.00 0.00 2.66
2409 6021 7.101054 AGGTGAGTTATATGTCGCAAAAAGTA 58.899 34.615 0.00 0.00 0.00 2.24
2410 6022 7.769044 AGGTGAGTTATATGTCGCAAAAAGTAT 59.231 33.333 0.00 0.00 0.00 2.12
2411 6023 8.395633 GGTGAGTTATATGTCGCAAAAAGTATT 58.604 33.333 0.00 0.00 0.00 1.89
2412 6024 9.769093 GTGAGTTATATGTCGCAAAAAGTATTT 57.231 29.630 0.00 0.00 42.41 1.40
2429 6041 8.856490 AAAGTATTTTATCGGATGCACATTTC 57.144 30.769 0.00 0.00 31.62 2.17
2430 6042 7.566760 AGTATTTTATCGGATGCACATTTCA 57.433 32.000 0.00 0.00 0.00 2.69
2431 6043 7.995289 AGTATTTTATCGGATGCACATTTCAA 58.005 30.769 0.00 0.00 0.00 2.69
2432 6044 8.465999 AGTATTTTATCGGATGCACATTTCAAA 58.534 29.630 0.00 0.00 0.00 2.69
2433 6045 7.760131 ATTTTATCGGATGCACATTTCAAAG 57.240 32.000 0.00 0.00 0.00 2.77
2434 6046 6.507958 TTTATCGGATGCACATTTCAAAGA 57.492 33.333 0.00 0.00 0.00 2.52
2435 6047 6.507958 TTATCGGATGCACATTTCAAAGAA 57.492 33.333 0.00 0.00 0.00 2.52
2436 6048 4.159377 TCGGATGCACATTTCAAAGAAC 57.841 40.909 0.00 0.00 0.00 3.01
2437 6049 3.820467 TCGGATGCACATTTCAAAGAACT 59.180 39.130 0.00 0.00 0.00 3.01
2438 6050 5.000591 TCGGATGCACATTTCAAAGAACTA 58.999 37.500 0.00 0.00 0.00 2.24
2439 6051 5.647658 TCGGATGCACATTTCAAAGAACTAT 59.352 36.000 0.00 0.00 0.00 2.12
2440 6052 6.150976 TCGGATGCACATTTCAAAGAACTATT 59.849 34.615 0.00 0.00 0.00 1.73
2441 6053 6.470235 CGGATGCACATTTCAAAGAACTATTC 59.530 38.462 0.00 0.00 0.00 1.75
2442 6054 6.470235 GGATGCACATTTCAAAGAACTATTCG 59.530 38.462 0.00 0.00 34.02 3.34
2443 6055 6.312399 TGCACATTTCAAAGAACTATTCGT 57.688 33.333 0.00 0.00 34.02 3.85
2444 6056 6.734137 TGCACATTTCAAAGAACTATTCGTT 58.266 32.000 0.00 0.00 38.91 3.85
2445 6057 6.636447 TGCACATTTCAAAGAACTATTCGTTG 59.364 34.615 9.95 9.95 46.15 4.10
2446 6058 6.088085 GCACATTTCAAAGAACTATTCGTTGG 59.912 38.462 14.44 4.41 45.28 3.77
2447 6059 7.138736 CACATTTCAAAGAACTATTCGTTGGT 58.861 34.615 14.44 4.89 45.28 3.67
2448 6060 8.286800 CACATTTCAAAGAACTATTCGTTGGTA 58.713 33.333 14.44 6.20 45.28 3.25
2449 6061 9.010029 ACATTTCAAAGAACTATTCGTTGGTAT 57.990 29.630 14.44 7.72 45.28 2.73
2461 6073 9.477484 ACTATTCGTTGGTATATCTTTGATGAC 57.523 33.333 0.00 0.00 0.00 3.06
2462 6074 9.476202 CTATTCGTTGGTATATCTTTGATGACA 57.524 33.333 0.00 0.00 0.00 3.58
2463 6075 8.908786 ATTCGTTGGTATATCTTTGATGACAT 57.091 30.769 0.00 0.00 0.00 3.06
2464 6076 9.996554 ATTCGTTGGTATATCTTTGATGACATA 57.003 29.630 0.00 0.00 0.00 2.29
2465 6077 9.996554 TTCGTTGGTATATCTTTGATGACATAT 57.003 29.630 0.00 0.00 0.00 1.78
2518 6130 9.447157 AAGTCAAATTTTGAGATGAAAACCAAA 57.553 25.926 12.02 0.00 41.01 3.28
2519 6131 9.101655 AGTCAAATTTTGAGATGAAAACCAAAG 57.898 29.630 12.02 0.00 41.01 2.77
2520 6132 8.882736 GTCAAATTTTGAGATGAAAACCAAAGT 58.117 29.630 12.02 0.00 41.01 2.66
2521 6133 8.881743 TCAAATTTTGAGATGAAAACCAAAGTG 58.118 29.630 7.74 0.00 34.08 3.16
2522 6134 7.790823 AATTTTGAGATGAAAACCAAAGTGG 57.209 32.000 0.00 0.00 45.02 4.00
2523 6135 4.320608 TTGAGATGAAAACCAAAGTGGC 57.679 40.909 0.00 0.00 42.67 5.01
2524 6136 2.627699 TGAGATGAAAACCAAAGTGGCC 59.372 45.455 0.00 0.00 42.67 5.36
2525 6137 2.893489 GAGATGAAAACCAAAGTGGCCT 59.107 45.455 3.32 0.00 42.67 5.19
2526 6138 3.308401 AGATGAAAACCAAAGTGGCCTT 58.692 40.909 3.32 0.00 42.67 4.35
2527 6139 2.977772 TGAAAACCAAAGTGGCCTTG 57.022 45.000 3.32 0.00 42.67 3.61
2528 6140 2.183679 TGAAAACCAAAGTGGCCTTGT 58.816 42.857 3.32 0.00 42.67 3.16
2529 6141 3.366396 TGAAAACCAAAGTGGCCTTGTA 58.634 40.909 3.32 0.00 42.67 2.41
2530 6142 3.964031 TGAAAACCAAAGTGGCCTTGTAT 59.036 39.130 3.32 0.00 42.67 2.29
2531 6143 5.141182 TGAAAACCAAAGTGGCCTTGTATA 58.859 37.500 3.32 0.00 42.67 1.47
2532 6144 5.598830 TGAAAACCAAAGTGGCCTTGTATAA 59.401 36.000 3.32 0.00 42.67 0.98
2533 6145 5.722021 AAACCAAAGTGGCCTTGTATAAG 57.278 39.130 3.32 0.00 42.67 1.73
2546 6158 5.234466 CTTGTATAAGGGAATGGAGGGAG 57.766 47.826 0.00 0.00 0.00 4.30
2547 6159 4.295905 TGTATAAGGGAATGGAGGGAGT 57.704 45.455 0.00 0.00 0.00 3.85
2594 6208 5.853936 ACTTTTTGGAAAATACTTCCCTGC 58.146 37.500 1.18 0.00 37.79 4.85
2595 6209 5.602561 ACTTTTTGGAAAATACTTCCCTGCT 59.397 36.000 1.18 0.00 37.79 4.24
2596 6210 6.099701 ACTTTTTGGAAAATACTTCCCTGCTT 59.900 34.615 1.18 0.00 37.79 3.91
2650 6264 6.192234 AGAGATCAACAAGTCATTTGCATC 57.808 37.500 0.00 0.00 40.59 3.91
2708 6324 1.375326 GAAGGGAGAACAACCGGCT 59.625 57.895 0.00 0.00 0.00 5.52
2756 6373 9.195411 CGGAGTACAAAGTTTACAATACAACTA 57.805 33.333 0.00 0.00 32.74 2.24
2767 6384 9.821662 GTTTACAATACAACTAAACTAGCCAAG 57.178 33.333 0.00 0.00 30.75 3.61
2771 6388 9.297037 ACAATACAACTAAACTAGCCAAGAAAT 57.703 29.630 0.00 0.00 0.00 2.17
2838 6466 5.939764 ATGTAAGAGAACATGAGTGGCTA 57.060 39.130 0.00 0.00 38.65 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 85 5.240183 CGACAAAATATCAATCCTGCCATCT 59.760 40.000 0.00 0.00 0.00 2.90
99 101 4.121317 TGTGTTACTCGAACCGACAAAAT 58.879 39.130 0.00 0.00 37.22 1.82
122 124 3.595758 AAGCCCACAAGTGTGCGC 61.596 61.111 12.16 12.16 46.88 6.09
123 125 1.723608 TTCAAGCCCACAAGTGTGCG 61.724 55.000 5.89 0.00 44.34 5.34
124 126 0.031178 CTTCAAGCCCACAAGTGTGC 59.969 55.000 5.89 0.00 44.34 4.57
125 127 1.679139 TCTTCAAGCCCACAAGTGTG 58.321 50.000 4.38 4.38 45.23 3.82
126 128 2.664402 ATCTTCAAGCCCACAAGTGT 57.336 45.000 0.00 0.00 0.00 3.55
135 137 6.151817 ACAGAACCTTTTGATATCTTCAAGCC 59.848 38.462 3.98 0.00 44.90 4.35
137 139 8.887717 CCTACAGAACCTTTTGATATCTTCAAG 58.112 37.037 3.98 3.64 44.90 3.02
158 160 4.250464 CGGAGCAGTAAAATGTTCCTACA 58.750 43.478 10.80 0.00 45.55 2.74
181 184 6.200854 TGACGCTGATGCATATAGTTTAGTTG 59.799 38.462 0.00 0.00 39.64 3.16
184 187 5.691754 TGTGACGCTGATGCATATAGTTTAG 59.308 40.000 0.00 0.00 39.64 1.85
193 196 3.691118 AGTTTATTGTGACGCTGATGCAT 59.309 39.130 0.00 0.00 39.64 3.96
200 203 7.769220 AGTATGTACTAGTTTATTGTGACGCT 58.231 34.615 0.00 0.00 34.13 5.07
219 222 7.700022 AAAACGGAGAGAGTACTAAGTATGT 57.300 36.000 0.00 0.00 0.00 2.29
269 275 1.234821 CGCTACAAAGTTTGGCTCCA 58.765 50.000 19.45 0.00 34.12 3.86
372 380 5.175491 GCATTCACAACACGAAATCAACATT 59.825 36.000 0.00 0.00 0.00 2.71
457 466 5.396436 CCCTTTGGTCTTTCCTACGTCATAT 60.396 44.000 0.00 0.00 37.07 1.78
462 471 2.302157 CTCCCTTTGGTCTTTCCTACGT 59.698 50.000 0.00 0.00 37.07 3.57
463 472 2.302157 ACTCCCTTTGGTCTTTCCTACG 59.698 50.000 0.00 0.00 37.07 3.51
467 476 4.635699 TCTTACTCCCTTTGGTCTTTCC 57.364 45.455 0.00 0.00 0.00 3.13
468 477 6.372937 CAGAATCTTACTCCCTTTGGTCTTTC 59.627 42.308 0.00 0.00 0.00 2.62
477 486 7.400627 GGCCTATATACAGAATCTTACTCCCTT 59.599 40.741 0.00 0.00 0.00 3.95
479 488 6.098552 GGGCCTATATACAGAATCTTACTCCC 59.901 46.154 0.84 0.00 0.00 4.30
491 500 6.174720 TCTGTTTTCTGGGCCTATATACAG 57.825 41.667 16.99 16.99 33.58 2.74
516 526 2.159585 TGCGATAGAAACCGTGCATTTG 60.160 45.455 0.00 0.00 39.76 2.32
520 531 1.348538 CGTGCGATAGAAACCGTGCA 61.349 55.000 0.00 0.00 39.76 4.57
525 536 3.061403 CGTCAATACGTGCGATAGAAACC 60.061 47.826 0.00 0.00 44.21 3.27
539 550 7.806014 ACCAAAACATCAACAATACGTCAATAC 59.194 33.333 0.00 0.00 0.00 1.89
540 551 7.877003 ACCAAAACATCAACAATACGTCAATA 58.123 30.769 0.00 0.00 0.00 1.90
541 552 6.744112 ACCAAAACATCAACAATACGTCAAT 58.256 32.000 0.00 0.00 0.00 2.57
542 553 6.137794 ACCAAAACATCAACAATACGTCAA 57.862 33.333 0.00 0.00 0.00 3.18
543 554 5.759506 ACCAAAACATCAACAATACGTCA 57.240 34.783 0.00 0.00 0.00 4.35
544 555 6.202937 TCAACCAAAACATCAACAATACGTC 58.797 36.000 0.00 0.00 0.00 4.34
578 592 4.320608 AAAGTGCGTCCAAATCACAAAT 57.679 36.364 0.00 0.00 33.44 2.32
598 612 2.297597 CCCAGTCACCCGCAAAAATAAA 59.702 45.455 0.00 0.00 0.00 1.40
599 613 1.889829 CCCAGTCACCCGCAAAAATAA 59.110 47.619 0.00 0.00 0.00 1.40
600 614 1.202952 ACCCAGTCACCCGCAAAAATA 60.203 47.619 0.00 0.00 0.00 1.40
601 615 0.469144 ACCCAGTCACCCGCAAAAAT 60.469 50.000 0.00 0.00 0.00 1.82
602 616 1.076632 ACCCAGTCACCCGCAAAAA 60.077 52.632 0.00 0.00 0.00 1.94
603 617 1.826054 CACCCAGTCACCCGCAAAA 60.826 57.895 0.00 0.00 0.00 2.44
604 618 2.203280 CACCCAGTCACCCGCAAA 60.203 61.111 0.00 0.00 0.00 3.68
605 619 3.164977 TCACCCAGTCACCCGCAA 61.165 61.111 0.00 0.00 0.00 4.85
606 620 3.625897 CTCACCCAGTCACCCGCA 61.626 66.667 0.00 0.00 0.00 5.69
607 621 4.394712 CCTCACCCAGTCACCCGC 62.395 72.222 0.00 0.00 0.00 6.13
608 622 2.603473 TCCTCACCCAGTCACCCG 60.603 66.667 0.00 0.00 0.00 5.28
609 623 2.943978 CGTCCTCACCCAGTCACCC 61.944 68.421 0.00 0.00 0.00 4.61
610 624 2.657237 CGTCCTCACCCAGTCACC 59.343 66.667 0.00 0.00 0.00 4.02
611 625 2.048127 GCGTCCTCACCCAGTCAC 60.048 66.667 0.00 0.00 0.00 3.67
612 626 2.203640 AGCGTCCTCACCCAGTCA 60.204 61.111 0.00 0.00 0.00 3.41
613 627 1.536943 AAGAGCGTCCTCACCCAGTC 61.537 60.000 0.00 0.00 40.68 3.51
614 628 1.122019 AAAGAGCGTCCTCACCCAGT 61.122 55.000 0.00 0.00 40.68 4.00
615 629 0.035458 AAAAGAGCGTCCTCACCCAG 59.965 55.000 0.00 0.00 40.68 4.45
616 630 0.472471 AAAAAGAGCGTCCTCACCCA 59.528 50.000 0.00 0.00 40.68 4.51
617 631 3.324207 AAAAAGAGCGTCCTCACCC 57.676 52.632 0.00 0.00 40.68 4.61
643 657 3.990469 AGATTAGTGAAAGTGACTGCGTG 59.010 43.478 0.00 0.00 0.00 5.34
649 663 8.017946 GGTTCATCAAAGATTAGTGAAAGTGAC 58.982 37.037 0.00 0.00 31.38 3.67
652 666 6.710744 ACGGTTCATCAAAGATTAGTGAAAGT 59.289 34.615 0.00 0.00 31.38 2.66
744 758 1.066430 TGCGGTTAACTAAGGCTGAGG 60.066 52.381 3.36 0.00 0.00 3.86
764 779 5.180680 GTGTCTAAATCTACCGGCAAAGTTT 59.819 40.000 0.00 0.00 0.00 2.66
768 783 3.602483 GGTGTCTAAATCTACCGGCAAA 58.398 45.455 0.00 0.00 0.00 3.68
789 804 3.467119 CGTCGCTTGTCCGTTCCG 61.467 66.667 0.00 0.00 0.00 4.30
807 822 3.799137 TTAGTGGATTTCGTTTCGTGC 57.201 42.857 0.00 0.00 0.00 5.34
814 829 4.062991 ACGCTTTCTTTAGTGGATTTCGT 58.937 39.130 0.00 0.00 0.00 3.85
844 859 6.126883 TGGATTTTATATTGTCTCGGTGGAGT 60.127 38.462 0.00 0.00 41.26 3.85
850 865 9.878599 GTATGTTTGGATTTTATATTGTCTCGG 57.121 33.333 0.00 0.00 0.00 4.63
901 916 0.312102 AAAAAGAAGGTGCGCTCTGC 59.688 50.000 9.73 4.97 46.70 4.26
922 937 1.402259 TGCGCTCTTCCGTTTCAAAAA 59.598 42.857 9.73 0.00 0.00 1.94
923 938 1.018148 TGCGCTCTTCCGTTTCAAAA 58.982 45.000 9.73 0.00 0.00 2.44
924 939 0.306533 GTGCGCTCTTCCGTTTCAAA 59.693 50.000 9.73 0.00 0.00 2.69
925 940 1.503818 GGTGCGCTCTTCCGTTTCAA 61.504 55.000 9.73 0.00 0.00 2.69
926 941 1.959226 GGTGCGCTCTTCCGTTTCA 60.959 57.895 9.73 0.00 0.00 2.69
927 942 1.228657 AAGGTGCGCTCTTCCGTTTC 61.229 55.000 9.73 0.00 0.00 2.78
928 943 1.227853 AAGGTGCGCTCTTCCGTTT 60.228 52.632 9.73 0.00 0.00 3.60
929 944 1.668151 GAAGGTGCGCTCTTCCGTT 60.668 57.895 23.84 9.81 35.76 4.44
930 945 2.048127 GAAGGTGCGCTCTTCCGT 60.048 61.111 23.84 13.58 35.76 4.69
931 946 1.807573 GAGAAGGTGCGCTCTTCCG 60.808 63.158 27.69 0.00 40.94 4.30
932 947 1.016653 GTGAGAAGGTGCGCTCTTCC 61.017 60.000 27.69 21.86 40.94 3.46
933 948 0.037790 AGTGAGAAGGTGCGCTCTTC 60.038 55.000 25.64 25.64 40.49 2.87
934 949 1.067495 GTAGTGAGAAGGTGCGCTCTT 60.067 52.381 9.73 12.71 32.44 2.85
946 961 1.464734 CTTCCGAGGCAGTAGTGAGA 58.535 55.000 0.42 0.00 0.00 3.27
984 999 1.153107 CATGGCTGGGATCAAGCGA 60.153 57.895 12.08 9.50 0.00 4.93
1391 1406 3.667282 CGGACGAGGACACACCGT 61.667 66.667 0.00 0.00 44.74 4.83
1797 1812 4.382685 CCGTACTTTGAAGAGCCCTTGATA 60.383 45.833 0.00 0.00 31.62 2.15
1889 1904 5.804692 ACACACTAGAGAGAACTATCACG 57.195 43.478 0.00 0.00 0.00 4.35
1919 1934 8.677148 AGACACACAATAATAACAACTCAACT 57.323 30.769 0.00 0.00 0.00 3.16
2027 2056 7.447545 GGGACTTGGTTCAAAGAAACTATACTT 59.552 37.037 0.00 0.00 0.00 2.24
2115 2144 9.872757 CAAATATTGTACACACGTACTTTTCTT 57.127 29.630 0.00 0.00 46.88 2.52
2125 2154 6.836953 TGATTGACCAAATATTGTACACACG 58.163 36.000 0.00 0.00 0.00 4.49
2126 2155 9.638239 ATTTGATTGACCAAATATTGTACACAC 57.362 29.630 0.00 0.00 42.87 3.82
2127 2156 9.636879 CATTTGATTGACCAAATATTGTACACA 57.363 29.630 0.00 0.00 42.83 3.72
2151 2180 7.673926 AGGACCAATATTTAACAAGAACCACAT 59.326 33.333 0.00 0.00 0.00 3.21
2177 2206 6.375736 TGTCGGCTAATGGTATTCAAATTGAA 59.624 34.615 11.10 11.10 41.09 2.69
2181 2210 5.650266 TGTTGTCGGCTAATGGTATTCAAAT 59.350 36.000 0.00 0.00 0.00 2.32
2196 2225 0.652592 CGAGGATTCATGTTGTCGGC 59.347 55.000 0.00 0.00 0.00 5.54
2209 2238 9.238368 TGGTGAAAGTTATAAAAATTCGAGGAT 57.762 29.630 0.00 0.00 0.00 3.24
2329 5940 9.686683 AGACATAAAAATATGAAGTAGCCTTGT 57.313 29.630 3.03 0.00 0.00 3.16
2375 5987 7.039882 CGACATATAACTCACCTTTTACTGGT 58.960 38.462 0.00 0.00 38.53 4.00
2376 5988 6.018994 GCGACATATAACTCACCTTTTACTGG 60.019 42.308 0.00 0.00 0.00 4.00
2377 5989 6.533723 TGCGACATATAACTCACCTTTTACTG 59.466 38.462 0.00 0.00 0.00 2.74
2378 5990 6.636705 TGCGACATATAACTCACCTTTTACT 58.363 36.000 0.00 0.00 0.00 2.24
2379 5991 6.897259 TGCGACATATAACTCACCTTTTAC 57.103 37.500 0.00 0.00 0.00 2.01
2380 5992 7.908827 TTTGCGACATATAACTCACCTTTTA 57.091 32.000 0.00 0.00 0.00 1.52
2381 5993 6.811253 TTTGCGACATATAACTCACCTTTT 57.189 33.333 0.00 0.00 0.00 2.27
2382 5994 6.811253 TTTTGCGACATATAACTCACCTTT 57.189 33.333 0.00 0.00 0.00 3.11
2383 5995 6.430000 ACTTTTTGCGACATATAACTCACCTT 59.570 34.615 0.00 0.00 0.00 3.50
2384 5996 5.938125 ACTTTTTGCGACATATAACTCACCT 59.062 36.000 0.00 0.00 0.00 4.00
2385 5997 6.178239 ACTTTTTGCGACATATAACTCACC 57.822 37.500 0.00 0.00 0.00 4.02
2386 5998 9.769093 AAATACTTTTTGCGACATATAACTCAC 57.231 29.630 0.00 0.00 0.00 3.51
2393 6005 8.832521 TCCGATAAAATACTTTTTGCGACATAT 58.167 29.630 0.00 0.00 36.70 1.78
2394 6006 8.199176 TCCGATAAAATACTTTTTGCGACATA 57.801 30.769 0.00 0.00 36.70 2.29
2395 6007 7.079182 TCCGATAAAATACTTTTTGCGACAT 57.921 32.000 0.00 0.00 36.70 3.06
2396 6008 6.483385 TCCGATAAAATACTTTTTGCGACA 57.517 33.333 0.00 0.00 36.70 4.35
2397 6009 6.075572 GCATCCGATAAAATACTTTTTGCGAC 60.076 38.462 0.00 0.00 36.70 5.19
2398 6010 5.968848 GCATCCGATAAAATACTTTTTGCGA 59.031 36.000 0.00 0.00 36.70 5.10
2399 6011 5.741510 TGCATCCGATAAAATACTTTTTGCG 59.258 36.000 0.00 0.00 35.82 4.85
2400 6012 6.529829 TGTGCATCCGATAAAATACTTTTTGC 59.470 34.615 0.00 0.00 35.82 3.68
2401 6013 8.633075 ATGTGCATCCGATAAAATACTTTTTG 57.367 30.769 0.00 0.00 35.82 2.44
2402 6014 9.651913 AAATGTGCATCCGATAAAATACTTTTT 57.348 25.926 0.00 0.00 38.56 1.94
2403 6015 9.301153 GAAATGTGCATCCGATAAAATACTTTT 57.699 29.630 0.00 0.00 36.67 2.27
2404 6016 8.465999 TGAAATGTGCATCCGATAAAATACTTT 58.534 29.630 0.00 0.00 0.00 2.66
2405 6017 7.995289 TGAAATGTGCATCCGATAAAATACTT 58.005 30.769 0.00 0.00 0.00 2.24
2406 6018 7.566760 TGAAATGTGCATCCGATAAAATACT 57.433 32.000 0.00 0.00 0.00 2.12
2407 6019 8.627487 TTTGAAATGTGCATCCGATAAAATAC 57.373 30.769 0.00 0.00 0.00 1.89
2408 6020 8.681806 TCTTTGAAATGTGCATCCGATAAAATA 58.318 29.630 0.00 0.00 0.00 1.40
2409 6021 7.546358 TCTTTGAAATGTGCATCCGATAAAAT 58.454 30.769 0.00 0.00 0.00 1.82
2410 6022 6.918626 TCTTTGAAATGTGCATCCGATAAAA 58.081 32.000 0.00 0.00 0.00 1.52
2411 6023 6.507958 TCTTTGAAATGTGCATCCGATAAA 57.492 33.333 0.00 0.00 0.00 1.40
2412 6024 6.150976 AGTTCTTTGAAATGTGCATCCGATAA 59.849 34.615 0.00 0.00 0.00 1.75
2413 6025 5.647658 AGTTCTTTGAAATGTGCATCCGATA 59.352 36.000 0.00 0.00 0.00 2.92
2414 6026 4.460382 AGTTCTTTGAAATGTGCATCCGAT 59.540 37.500 0.00 0.00 0.00 4.18
2415 6027 3.820467 AGTTCTTTGAAATGTGCATCCGA 59.180 39.130 0.00 0.00 0.00 4.55
2416 6028 4.164822 AGTTCTTTGAAATGTGCATCCG 57.835 40.909 0.00 0.00 0.00 4.18
2417 6029 6.470235 CGAATAGTTCTTTGAAATGTGCATCC 59.530 38.462 0.00 0.00 0.00 3.51
2418 6030 7.023575 ACGAATAGTTCTTTGAAATGTGCATC 58.976 34.615 0.00 0.00 0.00 3.91
2419 6031 6.913170 ACGAATAGTTCTTTGAAATGTGCAT 58.087 32.000 0.00 0.00 0.00 3.96
2420 6032 6.312399 ACGAATAGTTCTTTGAAATGTGCA 57.688 33.333 0.00 0.00 0.00 4.57
2421 6033 6.088085 CCAACGAATAGTTCTTTGAAATGTGC 59.912 38.462 9.61 0.00 42.02 4.57
2422 6034 7.138736 ACCAACGAATAGTTCTTTGAAATGTG 58.861 34.615 9.61 0.00 42.02 3.21
2423 6035 7.272037 ACCAACGAATAGTTCTTTGAAATGT 57.728 32.000 9.61 0.00 42.02 2.71
2435 6047 9.477484 GTCATCAAAGATATACCAACGAATAGT 57.523 33.333 0.00 0.00 0.00 2.12
2436 6048 9.476202 TGTCATCAAAGATATACCAACGAATAG 57.524 33.333 0.00 0.00 0.00 1.73
2437 6049 9.996554 ATGTCATCAAAGATATACCAACGAATA 57.003 29.630 0.00 0.00 0.00 1.75
2438 6050 8.908786 ATGTCATCAAAGATATACCAACGAAT 57.091 30.769 0.00 0.00 0.00 3.34
2439 6051 9.996554 ATATGTCATCAAAGATATACCAACGAA 57.003 29.630 0.00 0.00 0.00 3.85
2492 6104 9.447157 TTTGGTTTTCATCTCAAAATTTGACTT 57.553 25.926 4.03 0.00 35.46 3.01
2493 6105 9.101655 CTTTGGTTTTCATCTCAAAATTTGACT 57.898 29.630 4.03 0.00 35.46 3.41
2494 6106 8.882736 ACTTTGGTTTTCATCTCAAAATTTGAC 58.117 29.630 4.03 0.00 35.46 3.18
2495 6107 8.881743 CACTTTGGTTTTCATCTCAAAATTTGA 58.118 29.630 8.25 8.25 38.17 2.69
2496 6108 8.124199 CCACTTTGGTTTTCATCTCAAAATTTG 58.876 33.333 0.00 0.00 31.35 2.32
2497 6109 7.201723 GCCACTTTGGTTTTCATCTCAAAATTT 60.202 33.333 0.00 0.00 40.46 1.82
2498 6110 6.260714 GCCACTTTGGTTTTCATCTCAAAATT 59.739 34.615 0.00 0.00 40.46 1.82
2499 6111 5.759763 GCCACTTTGGTTTTCATCTCAAAAT 59.240 36.000 0.00 0.00 40.46 1.82
2500 6112 5.115480 GCCACTTTGGTTTTCATCTCAAAA 58.885 37.500 0.00 0.00 40.46 2.44
2501 6113 4.442753 GGCCACTTTGGTTTTCATCTCAAA 60.443 41.667 0.00 0.00 40.46 2.69
2502 6114 3.069443 GGCCACTTTGGTTTTCATCTCAA 59.931 43.478 0.00 0.00 40.46 3.02
2503 6115 2.627699 GGCCACTTTGGTTTTCATCTCA 59.372 45.455 0.00 0.00 40.46 3.27
2504 6116 2.893489 AGGCCACTTTGGTTTTCATCTC 59.107 45.455 5.01 0.00 40.46 2.75
2505 6117 2.962859 AGGCCACTTTGGTTTTCATCT 58.037 42.857 5.01 0.00 40.46 2.90
2506 6118 3.181466 ACAAGGCCACTTTGGTTTTCATC 60.181 43.478 5.01 0.00 40.46 2.92
2507 6119 2.771372 ACAAGGCCACTTTGGTTTTCAT 59.229 40.909 5.01 0.00 40.46 2.57
2508 6120 2.183679 ACAAGGCCACTTTGGTTTTCA 58.816 42.857 5.01 0.00 40.46 2.69
2509 6121 2.979814 ACAAGGCCACTTTGGTTTTC 57.020 45.000 5.01 0.00 40.46 2.29
2510 6122 5.011635 CCTTATACAAGGCCACTTTGGTTTT 59.988 40.000 5.01 0.00 44.90 2.43
2511 6123 4.526650 CCTTATACAAGGCCACTTTGGTTT 59.473 41.667 5.01 0.00 44.90 3.27
2512 6124 4.086457 CCTTATACAAGGCCACTTTGGTT 58.914 43.478 5.01 0.00 44.90 3.67
2513 6125 3.697166 CCTTATACAAGGCCACTTTGGT 58.303 45.455 5.01 0.00 44.90 3.67
2524 6136 4.660771 ACTCCCTCCATTCCCTTATACAAG 59.339 45.833 0.00 0.00 0.00 3.16
2525 6137 4.641868 ACTCCCTCCATTCCCTTATACAA 58.358 43.478 0.00 0.00 0.00 2.41
2526 6138 4.295905 ACTCCCTCCATTCCCTTATACA 57.704 45.455 0.00 0.00 0.00 2.29
2527 6139 6.954352 AATACTCCCTCCATTCCCTTATAC 57.046 41.667 0.00 0.00 0.00 1.47
2528 6140 9.280456 GAATAATACTCCCTCCATTCCCTTATA 57.720 37.037 0.00 0.00 0.00 0.98
2529 6141 7.970061 AGAATAATACTCCCTCCATTCCCTTAT 59.030 37.037 0.00 0.00 0.00 1.73
2530 6142 7.321530 AGAATAATACTCCCTCCATTCCCTTA 58.678 38.462 0.00 0.00 0.00 2.69
2531 6143 6.161167 AGAATAATACTCCCTCCATTCCCTT 58.839 40.000 0.00 0.00 0.00 3.95
2532 6144 5.742743 AGAATAATACTCCCTCCATTCCCT 58.257 41.667 0.00 0.00 0.00 4.20
2533 6145 6.455690 AAGAATAATACTCCCTCCATTCCC 57.544 41.667 0.00 0.00 0.00 3.97
2534 6146 8.768501 AAAAAGAATAATACTCCCTCCATTCC 57.231 34.615 0.00 0.00 0.00 3.01
2594 6208 6.470235 GCACAGGAATAATCGAATCACAAAAG 59.530 38.462 0.00 0.00 0.00 2.27
2595 6209 6.072230 TGCACAGGAATAATCGAATCACAAAA 60.072 34.615 0.00 0.00 0.00 2.44
2596 6210 5.414144 TGCACAGGAATAATCGAATCACAAA 59.586 36.000 0.00 0.00 0.00 2.83
2627 6241 5.944599 AGATGCAAATGACTTGTTGATCTCT 59.055 36.000 0.00 0.00 37.36 3.10
2630 6244 6.128090 TGAGAGATGCAAATGACTTGTTGATC 60.128 38.462 0.00 0.00 37.36 2.92
2767 6384 7.475771 TGTTTGAATAGTGTTTTGGCATTTC 57.524 32.000 0.00 0.00 0.00 2.17
2771 6388 5.724328 TGTTGTTTGAATAGTGTTTTGGCA 58.276 33.333 0.00 0.00 0.00 4.92
2812 6439 7.341805 AGCCACTCATGTTCTCTTACATTATT 58.658 34.615 0.00 0.00 36.64 1.40
2818 6445 7.617041 AAAATAGCCACTCATGTTCTCTTAC 57.383 36.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.