Multiple sequence alignment - TraesCS6B01G185600

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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 TraesCS6B01G185600 chr6B 100.000 2618 0 0 1 2618 211208773 211211390 0.000000e+00 4835.0
1 TraesCS6B01G185600 chr6D 89.785 2418 143 40 1 2378 119291013 119293366 0.000000e+00 3001.0
2 TraesCS6B01G185600 chr6A 89.717 1624 89 35 759 2332 147469604 147471199 0.000000e+00 2002.0
3 TraesCS6B01G185600 chr6A 86.474 658 70 14 1 651 147468961 147469606 0.000000e+00 704.0
4 TraesCS6B01G185600 chr6A 81.449 345 51 4 30 370 140207285 140206950 1.190000e-68 270.0
5 TraesCS6B01G185600 chr6A 100.000 28 0 0 2351 2378 147471195 147471222 5.000000e-03 52.8
6 TraesCS6B01G185600 chr7A 86.828 372 39 5 1 364 198476336 198476705 8.720000e-110 407.0
7 TraesCS6B01G185600 chr2D 86.685 368 43 3 1 364 650649078 650649443 1.130000e-108 403.0
8 TraesCS6B01G185600 chr4A 85.507 345 46 4 1 342 741539366 741539023 8.910000e-95 357.0
9 TraesCS6B01G185600 chr5A 86.325 234 27 4 122 351 706933593 706933825 1.560000e-62 250.0
10 TraesCS6B01G185600 chr4D 84.274 248 34 2 121 364 508821163 508821409 1.210000e-58 237.0
11 TraesCS6B01G185600 chr4D 90.278 144 13 1 1 143 472517953 472517810 1.240000e-43 187.0
12 TraesCS6B01G185600 chr3D 86.000 200 22 5 160 355 6980189 6979992 2.640000e-50 209.0
13 TraesCS6B01G185600 chr7D 80.505 277 42 9 1 268 160555952 160556225 4.420000e-48 202.0
14 TraesCS6B01G185600 chr7B 81.884 138 15 9 1387 1516 642831307 642831172 9.910000e-20 108.0
15 TraesCS6B01G185600 chr1D 100.000 40 0 0 2415 2454 354771417 354771378 1.000000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G185600 chr6B 211208773 211211390 2617 False 4835.0 4835 100.000000 1 2618 1 chr6B.!!$F1 2617
1 TraesCS6B01G185600 chr6D 119291013 119293366 2353 False 3001.0 3001 89.785000 1 2378 1 chr6D.!!$F1 2377
2 TraesCS6B01G185600 chr6A 147468961 147471222 2261 False 919.6 2002 92.063667 1 2378 3 chr6A.!!$F1 2377

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
897 907 0.030092 AATCTTCCCTCCCCCGATGA 60.03 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2561 0.033109 CATTTCCCTCCCCCTGTTCC 60.033 60.0 0.0 0.0 0.0 3.62 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
28 29 4.253685 TCAAGAACCCGAAATTCTAGCAG 58.746 43.478 0.00 0.00 35.31 4.24
34 35 6.884836 AGAACCCGAAATTCTAGCAGTAAAAT 59.115 34.615 0.00 0.00 34.59 1.82
59 60 4.454728 GCTTAGCTAGCTCATCTGCTAT 57.545 45.455 23.26 0.00 46.77 2.97
81 82 3.008594 TCTGATTAGCTTCCCGGAAACAA 59.991 43.478 0.73 0.00 0.00 2.83
145 147 3.429085 CATTTAGAGACCAATGCAACGC 58.571 45.455 0.00 0.00 0.00 4.84
229 235 2.437281 TCACATTGTTGCACCCCAAATT 59.563 40.909 0.00 0.00 34.68 1.82
236 242 0.108207 TGCACCCCAAATTTTGCCAG 59.892 50.000 9.48 0.00 33.86 4.85
237 243 0.108396 GCACCCCAAATTTTGCCAGT 59.892 50.000 3.50 0.00 0.00 4.00
271 277 3.650281 TTCTAATTGCCATGAGCTCCA 57.350 42.857 12.15 0.00 44.23 3.86
314 321 3.135994 GCGGAAGAAACCAAGTCACTTA 58.864 45.455 0.00 0.00 0.00 2.24
317 324 4.755123 CGGAAGAAACCAAGTCACTTATGT 59.245 41.667 0.00 0.00 0.00 2.29
323 330 9.574516 AAGAAACCAAGTCACTTATGTTAGAAT 57.425 29.630 5.33 0.00 0.00 2.40
355 362 2.293955 TCATCACGAACAACAGTACCGA 59.706 45.455 0.00 0.00 0.00 4.69
369 376 3.751175 CAGTACCGAAAGCTCCAAATCAA 59.249 43.478 0.00 0.00 0.00 2.57
421 429 1.633774 TCTTCAGAGTCGGGAGCTTT 58.366 50.000 0.00 0.00 0.00 3.51
426 434 1.219393 GAGTCGGGAGCTTTGGAGG 59.781 63.158 0.00 0.00 0.00 4.30
434 442 1.224965 GAGCTTTGGAGGCATCGATC 58.775 55.000 0.00 0.00 0.00 3.69
445 453 4.180057 GAGGCATCGATCCTGATGTAATC 58.820 47.826 17.66 5.03 45.98 1.75
455 463 5.713792 TCCTGATGTAATCTGTAGCTAGC 57.286 43.478 6.62 6.62 45.81 3.42
457 465 5.777223 TCCTGATGTAATCTGTAGCTAGCAT 59.223 40.000 18.83 4.67 45.81 3.79
472 480 2.680312 AGCATGCGAATAGACAGTGT 57.320 45.000 13.01 0.00 0.00 3.55
482 490 5.599715 CGAATAGACAGTGTTGTTTTCTCG 58.400 41.667 0.00 0.00 37.76 4.04
496 504 4.586841 TGTTTTCTCGGGGTTTTGAATCAT 59.413 37.500 0.00 0.00 0.00 2.45
506 514 5.876460 GGGGTTTTGAATCATGATTCCTTTG 59.124 40.000 34.65 0.00 44.93 2.77
514 522 8.634335 TGAATCATGATTCCTTTGACAAGTTA 57.366 30.769 34.65 16.05 44.93 2.24
533 541 0.250124 ATCGTCGTTGCCACCAAAGA 60.250 50.000 0.00 0.00 37.16 2.52
571 579 1.079127 CCAGTTCGGCCACAGGTAG 60.079 63.158 2.24 0.00 0.00 3.18
577 585 0.907704 TCGGCCACAGGTAGTCCATT 60.908 55.000 2.24 0.00 35.89 3.16
588 596 4.695455 CAGGTAGTCCATTCGAAACAACAT 59.305 41.667 0.00 0.00 35.89 2.71
589 597 4.935808 AGGTAGTCCATTCGAAACAACATC 59.064 41.667 0.00 0.00 35.89 3.06
590 598 4.693566 GGTAGTCCATTCGAAACAACATCA 59.306 41.667 0.00 0.00 0.00 3.07
593 601 5.519722 AGTCCATTCGAAACAACATCAAAC 58.480 37.500 0.00 0.00 0.00 2.93
594 602 5.299279 AGTCCATTCGAAACAACATCAAACT 59.701 36.000 0.00 0.00 0.00 2.66
597 605 6.475076 TCCATTCGAAACAACATCAAACTTTG 59.525 34.615 0.00 0.00 0.00 2.77
598 606 6.475076 CCATTCGAAACAACATCAAACTTTGA 59.525 34.615 0.00 6.67 45.01 2.69
600 608 7.875316 TTCGAAACAACATCAAACTTTGAAA 57.125 28.000 8.28 0.00 43.95 2.69
601 609 7.504922 TCGAAACAACATCAAACTTTGAAAG 57.495 32.000 8.28 2.89 43.95 2.62
603 611 7.973388 TCGAAACAACATCAAACTTTGAAAGAT 59.027 29.630 12.53 0.00 43.95 2.40
604 612 8.261908 CGAAACAACATCAAACTTTGAAAGATC 58.738 33.333 12.53 0.00 43.95 2.75
606 614 9.657419 AAACAACATCAAACTTTGAAAGATCTT 57.343 25.926 12.53 0.88 43.95 2.40
607 615 8.862550 ACAACATCAAACTTTGAAAGATCTTC 57.137 30.769 12.53 3.35 43.95 2.87
608 616 8.469200 ACAACATCAAACTTTGAAAGATCTTCA 58.531 29.630 12.53 6.00 43.95 3.02
609 617 9.472361 CAACATCAAACTTTGAAAGATCTTCAT 57.528 29.630 12.53 0.00 43.95 2.57
619 629 9.381033 CTTTGAAAGATCTTCATAGTGACTGAT 57.619 33.333 8.78 0.00 0.00 2.90
621 631 7.495901 TGAAAGATCTTCATAGTGACTGATCC 58.504 38.462 8.78 0.00 37.34 3.36
624 634 5.539574 AGATCTTCATAGTGACTGATCCTGG 59.460 44.000 0.00 0.00 37.34 4.45
626 636 4.646945 TCTTCATAGTGACTGATCCTGGTC 59.353 45.833 0.00 0.00 0.00 4.02
634 644 0.743688 CTGATCCTGGTCTGTCCTCG 59.256 60.000 0.00 0.00 37.07 4.63
635 645 1.323271 TGATCCTGGTCTGTCCTCGC 61.323 60.000 0.00 0.00 37.07 5.03
653 663 1.536766 CGCCAGTTGCTCTTTGAATGA 59.463 47.619 0.00 0.00 38.05 2.57
660 670 6.183360 CCAGTTGCTCTTTGAATGACATCTAG 60.183 42.308 0.00 0.00 0.00 2.43
668 678 6.441924 TCTTTGAATGACATCTAGAAGTCCCT 59.558 38.462 21.93 11.14 33.89 4.20
675 685 2.151502 TCTAGAAGTCCCTGCTGAGG 57.848 55.000 0.00 0.00 39.42 3.86
691 701 0.868406 GAGGCCACACTTCTTTCACG 59.132 55.000 5.01 0.00 0.00 4.35
728 738 1.792301 CAGTGCTGCAAGTCATCGG 59.208 57.895 2.77 0.00 35.30 4.18
732 742 3.044059 GCTGCAAGTCATCGGCACC 62.044 63.158 0.00 0.00 35.30 5.01
733 743 2.359850 TGCAAGTCATCGGCACCC 60.360 61.111 0.00 0.00 31.58 4.61
734 744 2.359850 GCAAGTCATCGGCACCCA 60.360 61.111 0.00 0.00 0.00 4.51
735 745 1.750399 GCAAGTCATCGGCACCCAT 60.750 57.895 0.00 0.00 0.00 4.00
736 746 1.718757 GCAAGTCATCGGCACCCATC 61.719 60.000 0.00 0.00 0.00 3.51
737 747 1.153369 AAGTCATCGGCACCCATCG 60.153 57.895 0.00 0.00 0.00 3.84
738 748 1.613317 AAGTCATCGGCACCCATCGA 61.613 55.000 0.00 0.00 39.79 3.59
739 749 1.153449 GTCATCGGCACCCATCGAA 60.153 57.895 0.00 0.00 38.92 3.71
740 750 1.153449 TCATCGGCACCCATCGAAC 60.153 57.895 0.00 0.00 38.92 3.95
741 751 2.202878 ATCGGCACCCATCGAACG 60.203 61.111 0.00 0.00 38.92 3.95
742 752 3.733344 ATCGGCACCCATCGAACGG 62.733 63.158 0.00 0.00 38.92 4.44
745 755 2.824041 GCACCCATCGAACGGCAT 60.824 61.111 0.00 0.00 0.00 4.40
746 756 3.101209 CACCCATCGAACGGCATG 58.899 61.111 0.00 0.00 0.00 4.06
747 757 2.124736 ACCCATCGAACGGCATGG 60.125 61.111 0.00 7.61 39.58 3.66
749 759 3.585990 CCATCGAACGGCATGGGC 61.586 66.667 0.00 0.00 36.62 5.36
750 760 2.823593 CATCGAACGGCATGGGCA 60.824 61.111 0.00 0.00 43.71 5.36
751 761 2.188829 CATCGAACGGCATGGGCAT 61.189 57.895 0.00 0.00 43.71 4.40
752 762 1.893808 ATCGAACGGCATGGGCATC 60.894 57.895 0.00 0.00 43.71 3.91
753 763 3.585990 CGAACGGCATGGGCATCC 61.586 66.667 0.00 0.00 43.71 3.51
897 907 0.030092 AATCTTCCCTCCCCCGATGA 60.030 55.000 0.00 0.00 0.00 2.92
899 909 1.075226 CTTCCCTCCCCCGATGAGA 60.075 63.158 0.00 0.00 31.26 3.27
962 972 2.653702 GAGACTGCACTGCTCCGT 59.346 61.111 1.98 0.00 0.00 4.69
963 973 1.735920 GAGACTGCACTGCTCCGTG 60.736 63.158 1.98 0.00 37.94 4.94
964 974 2.740055 GACTGCACTGCTCCGTGG 60.740 66.667 1.98 0.00 35.47 4.94
965 975 4.996434 ACTGCACTGCTCCGTGGC 62.996 66.667 1.98 0.00 35.47 5.01
988 1006 3.777925 CGCCTCAGTTCGCCAACG 61.778 66.667 0.00 0.00 37.61 4.10
1073 1095 1.314730 CCTACCAACAACCCACACAC 58.685 55.000 0.00 0.00 0.00 3.82
1074 1096 0.941542 CTACCAACAACCCACACACG 59.058 55.000 0.00 0.00 0.00 4.49
1075 1097 1.096386 TACCAACAACCCACACACGC 61.096 55.000 0.00 0.00 0.00 5.34
1076 1098 2.024022 CAACAACCCACACACGCG 59.976 61.111 3.53 3.53 0.00 6.01
1077 1099 3.883180 AACAACCCACACACGCGC 61.883 61.111 5.73 0.00 0.00 6.86
1156 1194 4.500116 GCGGAGAGGCGAGGACAC 62.500 72.222 0.00 0.00 0.00 3.67
1166 1214 2.283676 GAGGACACAGACGGGGGA 60.284 66.667 0.00 0.00 0.00 4.81
1661 1709 2.452505 CTTTCTCTCTCCTCGGGTTCT 58.547 52.381 0.00 0.00 0.00 3.01
1681 1729 3.580458 TCTCTTTTCCTCAACCTCTGGAG 59.420 47.826 0.00 0.00 0.00 3.86
1699 1747 0.892814 AGTGGAAAGGCAGCAGCTTC 60.893 55.000 0.00 0.00 41.70 3.86
1700 1748 1.151221 TGGAAAGGCAGCAGCTTCA 59.849 52.632 0.00 0.00 41.70 3.02
1705 1753 3.428589 GGAAAGGCAGCAGCTTCATTTAG 60.429 47.826 4.63 0.00 41.70 1.85
1708 1756 3.160269 AGGCAGCAGCTTCATTTAGTTT 58.840 40.909 0.00 0.00 41.70 2.66
1775 1825 8.827677 AGAAGACGATGCTTGTAAATTAATACC 58.172 33.333 0.00 0.00 0.00 2.73
1784 1834 9.520204 TGCTTGTAAATTAATACCGTAGTACTC 57.480 33.333 0.00 0.00 0.00 2.59
1853 1908 2.910479 ATGCCATGCCATGCTCGG 60.910 61.111 0.00 0.00 0.00 4.63
1864 1919 0.936764 CATGCTCGGTCGGATTCTCG 60.937 60.000 0.00 0.00 0.00 4.04
1919 1975 3.257873 CGAGGATAGGGTCGAGAGTACTA 59.742 52.174 0.00 0.00 38.50 1.82
1929 1985 4.918583 GGTCGAGAGTACTATAATTGCAGC 59.081 45.833 0.00 0.00 0.00 5.25
1959 2019 1.074471 ATGGGCAGGGAGGACGTAT 60.074 57.895 0.00 0.00 0.00 3.06
1960 2020 0.190069 ATGGGCAGGGAGGACGTATA 59.810 55.000 0.00 0.00 0.00 1.47
1963 2023 0.178970 GGCAGGGAGGACGTATAGGA 60.179 60.000 0.00 0.00 0.00 2.94
1968 2028 1.271817 GGGAGGACGTATAGGACCGAT 60.272 57.143 8.02 0.00 0.00 4.18
2035 2095 4.284550 GCTGGCACTGGGTGGGAA 62.285 66.667 0.00 0.00 33.64 3.97
2128 2188 2.579787 CGTCCGTGATCTGTCGCC 60.580 66.667 0.00 0.00 0.00 5.54
2249 2326 2.519302 GGCATTATGGTGCGCCCT 60.519 61.111 15.15 6.58 45.97 5.19
2282 2359 3.259374 GGAATCCTCGGATCTGATGCTTA 59.741 47.826 4.28 0.00 33.08 3.09
2301 2378 4.100084 CCAGGCTGATGGGACGCA 62.100 66.667 17.94 0.00 36.64 5.24
2378 2456 5.221224 TGCTGTTTTTACTTTCACTGGGATG 60.221 40.000 0.00 0.00 0.00 3.51
2379 2457 5.221244 GCTGTTTTTACTTTCACTGGGATGT 60.221 40.000 0.00 0.00 0.00 3.06
2380 2458 6.142818 TGTTTTTACTTTCACTGGGATGTG 57.857 37.500 0.00 0.00 39.15 3.21
2381 2459 5.654650 TGTTTTTACTTTCACTGGGATGTGT 59.345 36.000 0.00 0.00 38.90 3.72
2382 2460 5.766150 TTTTACTTTCACTGGGATGTGTG 57.234 39.130 0.00 0.00 38.90 3.82
2383 2461 4.431416 TTACTTTCACTGGGATGTGTGT 57.569 40.909 0.00 0.00 38.90 3.72
2384 2462 2.575532 ACTTTCACTGGGATGTGTGTG 58.424 47.619 0.00 0.00 38.90 3.82
2385 2463 2.092429 ACTTTCACTGGGATGTGTGTGT 60.092 45.455 0.00 0.00 38.90 3.72
2386 2464 2.727123 TTCACTGGGATGTGTGTGTT 57.273 45.000 0.00 0.00 38.90 3.32
2387 2465 1.965935 TCACTGGGATGTGTGTGTTG 58.034 50.000 0.00 0.00 38.90 3.33
2388 2466 1.488393 TCACTGGGATGTGTGTGTTGA 59.512 47.619 0.00 0.00 38.90 3.18
2389 2467 1.875514 CACTGGGATGTGTGTGTTGAG 59.124 52.381 0.00 0.00 33.61 3.02
2390 2468 0.877071 CTGGGATGTGTGTGTTGAGC 59.123 55.000 0.00 0.00 0.00 4.26
2391 2469 0.182299 TGGGATGTGTGTGTTGAGCA 59.818 50.000 0.00 0.00 0.00 4.26
2392 2470 0.877071 GGGATGTGTGTGTTGAGCAG 59.123 55.000 0.00 0.00 0.00 4.24
2393 2471 1.543208 GGGATGTGTGTGTTGAGCAGA 60.543 52.381 0.00 0.00 0.00 4.26
2394 2472 1.532868 GGATGTGTGTGTTGAGCAGAC 59.467 52.381 0.00 0.00 41.26 3.51
2395 2473 1.193203 GATGTGTGTGTTGAGCAGACG 59.807 52.381 0.00 0.00 43.52 4.18
2396 2474 1.276844 GTGTGTGTTGAGCAGACGC 59.723 57.895 0.00 0.00 43.52 5.19
2407 2485 2.507992 CAGACGCTCCTGCTTCGG 60.508 66.667 0.00 0.00 41.59 4.30
2408 2486 2.992114 AGACGCTCCTGCTTCGGT 60.992 61.111 0.00 0.00 41.59 4.69
2409 2487 2.811317 GACGCTCCTGCTTCGGTG 60.811 66.667 0.00 0.00 36.97 4.94
2411 2489 4.749310 CGCTCCTGCTTCGGTGCT 62.749 66.667 10.81 0.00 40.46 4.40
2412 2490 2.359230 GCTCCTGCTTCGGTGCTT 60.359 61.111 6.94 0.00 39.73 3.91
2413 2491 2.394563 GCTCCTGCTTCGGTGCTTC 61.395 63.158 6.94 0.00 39.73 3.86
2414 2492 1.004560 CTCCTGCTTCGGTGCTTCA 60.005 57.895 2.64 0.00 0.00 3.02
2415 2493 0.392193 CTCCTGCTTCGGTGCTTCAT 60.392 55.000 2.64 0.00 0.00 2.57
2416 2494 0.036732 TCCTGCTTCGGTGCTTCATT 59.963 50.000 2.64 0.00 0.00 2.57
2417 2495 1.277842 TCCTGCTTCGGTGCTTCATTA 59.722 47.619 2.64 0.00 0.00 1.90
2418 2496 1.667724 CCTGCTTCGGTGCTTCATTAG 59.332 52.381 2.64 0.00 0.00 1.73
2419 2497 2.621338 CTGCTTCGGTGCTTCATTAGA 58.379 47.619 2.64 0.00 0.00 2.10
2420 2498 2.606725 CTGCTTCGGTGCTTCATTAGAG 59.393 50.000 2.64 0.00 0.00 2.43
2421 2499 1.328986 GCTTCGGTGCTTCATTAGAGC 59.671 52.381 0.00 0.00 0.00 4.09
2422 2500 2.621338 CTTCGGTGCTTCATTAGAGCA 58.379 47.619 0.00 0.00 36.09 4.26
2423 2501 2.988010 TCGGTGCTTCATTAGAGCAT 57.012 45.000 1.84 0.00 40.84 3.79
2424 2502 2.826428 TCGGTGCTTCATTAGAGCATC 58.174 47.619 1.84 0.60 40.84 3.91
2448 2526 9.932207 ATCTTCAATACAAGATGCAAATTTGAA 57.068 25.926 22.31 12.38 40.88 2.69
2449 2527 9.414295 TCTTCAATACAAGATGCAAATTTGAAG 57.586 29.630 22.31 19.00 0.00 3.02
2450 2528 9.414295 CTTCAATACAAGATGCAAATTTGAAGA 57.586 29.630 22.31 4.98 31.24 2.87
2451 2529 9.932207 TTCAATACAAGATGCAAATTTGAAGAT 57.068 25.926 22.31 9.59 0.00 2.40
2452 2530 9.361315 TCAATACAAGATGCAAATTTGAAGATG 57.639 29.630 22.31 13.40 0.00 2.90
2453 2531 9.146984 CAATACAAGATGCAAATTTGAAGATGT 57.853 29.630 22.31 17.84 0.00 3.06
2457 2535 9.545105 ACAAGATGCAAATTTGAAGATGTAAAA 57.455 25.926 22.31 0.00 0.00 1.52
2480 2558 8.990163 AAAAATGTTTTACAGACTAGGAGGAA 57.010 30.769 0.00 0.00 0.00 3.36
2481 2559 8.622948 AAAATGTTTTACAGACTAGGAGGAAG 57.377 34.615 0.00 0.00 0.00 3.46
2482 2560 7.554959 AATGTTTTACAGACTAGGAGGAAGA 57.445 36.000 0.00 0.00 0.00 2.87
2483 2561 6.591750 TGTTTTACAGACTAGGAGGAAGAG 57.408 41.667 0.00 0.00 0.00 2.85
2484 2562 5.480772 TGTTTTACAGACTAGGAGGAAGAGG 59.519 44.000 0.00 0.00 0.00 3.69
2485 2563 5.531753 TTTACAGACTAGGAGGAAGAGGA 57.468 43.478 0.00 0.00 0.00 3.71
2486 2564 5.531753 TTACAGACTAGGAGGAAGAGGAA 57.468 43.478 0.00 0.00 0.00 3.36
2487 2565 3.703921 ACAGACTAGGAGGAAGAGGAAC 58.296 50.000 0.00 0.00 0.00 3.62
2488 2566 3.076182 ACAGACTAGGAGGAAGAGGAACA 59.924 47.826 0.00 0.00 0.00 3.18
2489 2567 3.699038 CAGACTAGGAGGAAGAGGAACAG 59.301 52.174 0.00 0.00 0.00 3.16
2490 2568 3.028130 GACTAGGAGGAAGAGGAACAGG 58.972 54.545 0.00 0.00 0.00 4.00
2491 2569 2.292587 ACTAGGAGGAAGAGGAACAGGG 60.293 54.545 0.00 0.00 0.00 4.45
2492 2570 0.252927 AGGAGGAAGAGGAACAGGGG 60.253 60.000 0.00 0.00 0.00 4.79
2493 2571 1.275421 GGAGGAAGAGGAACAGGGGG 61.275 65.000 0.00 0.00 0.00 5.40
2494 2572 0.252742 GAGGAAGAGGAACAGGGGGA 60.253 60.000 0.00 0.00 0.00 4.81
2495 2573 0.252927 AGGAAGAGGAACAGGGGGAG 60.253 60.000 0.00 0.00 0.00 4.30
2496 2574 1.275421 GGAAGAGGAACAGGGGGAGG 61.275 65.000 0.00 0.00 0.00 4.30
2497 2575 1.229984 AAGAGGAACAGGGGGAGGG 60.230 63.158 0.00 0.00 0.00 4.30
2498 2576 1.761780 AAGAGGAACAGGGGGAGGGA 61.762 60.000 0.00 0.00 0.00 4.20
2499 2577 1.229853 GAGGAACAGGGGGAGGGAA 60.230 63.158 0.00 0.00 0.00 3.97
2500 2578 0.845102 GAGGAACAGGGGGAGGGAAA 60.845 60.000 0.00 0.00 0.00 3.13
2501 2579 0.178801 AGGAACAGGGGGAGGGAAAT 60.179 55.000 0.00 0.00 0.00 2.17
2502 2580 0.033109 GGAACAGGGGGAGGGAAATG 60.033 60.000 0.00 0.00 0.00 2.32
2503 2581 0.999712 GAACAGGGGGAGGGAAATGA 59.000 55.000 0.00 0.00 0.00 2.57
2504 2582 1.357761 GAACAGGGGGAGGGAAATGAA 59.642 52.381 0.00 0.00 0.00 2.57
2505 2583 1.466858 ACAGGGGGAGGGAAATGAAA 58.533 50.000 0.00 0.00 0.00 2.69
2506 2584 2.010699 ACAGGGGGAGGGAAATGAAAT 58.989 47.619 0.00 0.00 0.00 2.17
2507 2585 2.292455 ACAGGGGGAGGGAAATGAAATG 60.292 50.000 0.00 0.00 0.00 2.32
2508 2586 2.024080 CAGGGGGAGGGAAATGAAATGA 60.024 50.000 0.00 0.00 0.00 2.57
2509 2587 2.659521 AGGGGGAGGGAAATGAAATGAA 59.340 45.455 0.00 0.00 0.00 2.57
2510 2588 3.078918 AGGGGGAGGGAAATGAAATGAAA 59.921 43.478 0.00 0.00 0.00 2.69
2511 2589 3.452264 GGGGGAGGGAAATGAAATGAAAG 59.548 47.826 0.00 0.00 0.00 2.62
2512 2590 3.118629 GGGGAGGGAAATGAAATGAAAGC 60.119 47.826 0.00 0.00 0.00 3.51
2513 2591 3.118629 GGGAGGGAAATGAAATGAAAGCC 60.119 47.826 0.00 0.00 0.00 4.35
2514 2592 3.515104 GGAGGGAAATGAAATGAAAGCCA 59.485 43.478 0.00 0.00 0.00 4.75
2515 2593 4.020307 GGAGGGAAATGAAATGAAAGCCAA 60.020 41.667 0.00 0.00 0.00 4.52
2516 2594 4.898320 AGGGAAATGAAATGAAAGCCAAC 58.102 39.130 0.00 0.00 0.00 3.77
2517 2595 4.594491 AGGGAAATGAAATGAAAGCCAACT 59.406 37.500 0.00 0.00 0.00 3.16
2518 2596 4.692155 GGGAAATGAAATGAAAGCCAACTG 59.308 41.667 0.00 0.00 0.00 3.16
2519 2597 5.511202 GGGAAATGAAATGAAAGCCAACTGA 60.511 40.000 0.00 0.00 0.00 3.41
2520 2598 6.168389 GGAAATGAAATGAAAGCCAACTGAT 58.832 36.000 0.00 0.00 0.00 2.90
2521 2599 6.091713 GGAAATGAAATGAAAGCCAACTGATG 59.908 38.462 0.00 0.00 0.00 3.07
2529 2607 3.578456 CCAACTGATGGTCGGCAC 58.422 61.111 0.00 0.00 44.85 5.01
2545 2623 4.992511 ACGCGGCCGCCAGTTTTA 62.993 61.111 42.07 0.00 38.22 1.52
2546 2624 4.454717 CGCGGCCGCCAGTTTTAC 62.455 66.667 42.07 14.11 37.98 2.01
2547 2625 3.358707 GCGGCCGCCAGTTTTACA 61.359 61.111 39.89 0.00 34.56 2.41
2548 2626 2.696759 GCGGCCGCCAGTTTTACAT 61.697 57.895 39.89 0.00 34.56 2.29
2549 2627 1.427819 CGGCCGCCAGTTTTACATC 59.572 57.895 14.67 0.00 0.00 3.06
2550 2628 1.024579 CGGCCGCCAGTTTTACATCT 61.025 55.000 14.67 0.00 0.00 2.90
2551 2629 0.733150 GGCCGCCAGTTTTACATCTC 59.267 55.000 3.91 0.00 0.00 2.75
2552 2630 0.733150 GCCGCCAGTTTTACATCTCC 59.267 55.000 0.00 0.00 0.00 3.71
2553 2631 1.948611 GCCGCCAGTTTTACATCTCCA 60.949 52.381 0.00 0.00 0.00 3.86
2554 2632 2.009774 CCGCCAGTTTTACATCTCCAG 58.990 52.381 0.00 0.00 0.00 3.86
2555 2633 2.354704 CCGCCAGTTTTACATCTCCAGA 60.355 50.000 0.00 0.00 0.00 3.86
2556 2634 3.535561 CGCCAGTTTTACATCTCCAGAT 58.464 45.455 0.00 0.00 34.56 2.90
2567 2645 3.557228 ATCTCCAGATGAAGGAAGTGC 57.443 47.619 0.00 0.00 34.08 4.40
2568 2646 2.259917 TCTCCAGATGAAGGAAGTGCA 58.740 47.619 0.00 0.00 34.08 4.57
2569 2647 2.639347 TCTCCAGATGAAGGAAGTGCAA 59.361 45.455 0.00 0.00 34.08 4.08
2570 2648 3.072915 TCTCCAGATGAAGGAAGTGCAAA 59.927 43.478 0.00 0.00 34.08 3.68
2571 2649 4.015084 CTCCAGATGAAGGAAGTGCAAAT 58.985 43.478 0.00 0.00 34.08 2.32
2572 2650 4.410099 TCCAGATGAAGGAAGTGCAAATT 58.590 39.130 0.00 0.00 30.71 1.82
2573 2651 4.834496 TCCAGATGAAGGAAGTGCAAATTT 59.166 37.500 0.00 0.00 30.71 1.82
2574 2652 4.927425 CCAGATGAAGGAAGTGCAAATTTG 59.073 41.667 14.03 14.03 0.00 2.32
2575 2653 8.675883 TCCAGATGAAGGAAGTGCAAATTTGC 62.676 42.308 31.67 31.67 42.53 3.68
2589 2667 5.937165 CAAATTTGCATCATAAGGTGTCG 57.063 39.130 5.01 0.00 0.00 4.35
2590 2668 5.401550 CAAATTTGCATCATAAGGTGTCGT 58.598 37.500 5.01 0.00 0.00 4.34
2591 2669 6.550843 CAAATTTGCATCATAAGGTGTCGTA 58.449 36.000 5.01 0.00 0.00 3.43
2592 2670 5.991328 ATTTGCATCATAAGGTGTCGTAG 57.009 39.130 0.00 0.00 0.00 3.51
2593 2671 4.465632 TTGCATCATAAGGTGTCGTAGT 57.534 40.909 0.00 0.00 0.00 2.73
2594 2672 4.465632 TGCATCATAAGGTGTCGTAGTT 57.534 40.909 0.00 0.00 0.00 2.24
2595 2673 4.827692 TGCATCATAAGGTGTCGTAGTTT 58.172 39.130 0.00 0.00 0.00 2.66
2596 2674 5.968254 TGCATCATAAGGTGTCGTAGTTTA 58.032 37.500 0.00 0.00 0.00 2.01
2597 2675 5.808540 TGCATCATAAGGTGTCGTAGTTTAC 59.191 40.000 0.00 0.00 0.00 2.01
2598 2676 5.808540 GCATCATAAGGTGTCGTAGTTTACA 59.191 40.000 0.00 0.00 0.00 2.41
2599 2677 6.479001 GCATCATAAGGTGTCGTAGTTTACAT 59.521 38.462 0.00 0.00 0.00 2.29
2600 2678 7.306632 GCATCATAAGGTGTCGTAGTTTACATC 60.307 40.741 0.00 0.00 0.00 3.06
2601 2679 7.400599 TCATAAGGTGTCGTAGTTTACATCT 57.599 36.000 0.00 0.00 38.71 2.90
2602 2680 7.833786 TCATAAGGTGTCGTAGTTTACATCTT 58.166 34.615 6.27 6.27 46.20 2.40
2603 2681 7.972277 TCATAAGGTGTCGTAGTTTACATCTTC 59.028 37.037 4.37 0.00 42.02 2.87
2604 2682 4.730657 AGGTGTCGTAGTTTACATCTTCG 58.269 43.478 0.00 0.00 33.23 3.79
2605 2683 3.855950 GGTGTCGTAGTTTACATCTTCGG 59.144 47.826 0.00 0.00 0.00 4.30
2606 2684 4.379813 GGTGTCGTAGTTTACATCTTCGGA 60.380 45.833 0.00 0.00 0.00 4.55
2607 2685 5.156355 GTGTCGTAGTTTACATCTTCGGAA 58.844 41.667 0.00 0.00 0.00 4.30
2608 2686 5.285607 GTGTCGTAGTTTACATCTTCGGAAG 59.714 44.000 11.54 11.54 0.00 3.46
2609 2687 4.797349 GTCGTAGTTTACATCTTCGGAAGG 59.203 45.833 17.19 5.30 0.00 3.46
2610 2688 3.550678 CGTAGTTTACATCTTCGGAAGGC 59.449 47.826 17.19 1.04 0.00 4.35
2611 2689 2.618053 AGTTTACATCTTCGGAAGGCG 58.382 47.619 17.19 11.00 0.00 5.52
2612 2690 2.232941 AGTTTACATCTTCGGAAGGCGA 59.767 45.455 17.19 0.00 0.00 5.54
2613 2691 2.997986 GTTTACATCTTCGGAAGGCGAA 59.002 45.455 17.19 4.89 0.00 4.70
2614 2692 3.322211 TTACATCTTCGGAAGGCGAAA 57.678 42.857 17.19 5.41 0.00 3.46
2615 2693 2.178912 ACATCTTCGGAAGGCGAAAA 57.821 45.000 17.19 0.00 0.00 2.29
2616 2694 2.711542 ACATCTTCGGAAGGCGAAAAT 58.288 42.857 17.19 0.09 0.00 1.82
2617 2695 3.869065 ACATCTTCGGAAGGCGAAAATA 58.131 40.909 17.19 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.964476 AGCTAAGCATTATTTTACTGCTAGAA 57.036 30.769 0.00 0.00 45.10 2.10
59 60 2.569853 TGTTTCCGGGAAGCTAATCAGA 59.430 45.455 21.85 0.00 0.00 3.27
81 82 9.737844 AACTTGGCCAAAATATCATTTAAACAT 57.262 25.926 20.91 0.00 0.00 2.71
143 145 2.088674 CTCTTATCCAGGACCCGGCG 62.089 65.000 0.00 0.00 0.00 6.46
145 147 1.041437 GACTCTTATCCAGGACCCGG 58.959 60.000 0.00 0.00 0.00 5.73
154 156 6.501781 CAATTCAGCAAATGGACTCTTATCC 58.498 40.000 0.00 0.00 39.45 2.59
271 277 5.635280 CGCATATCCGAGATGTTTATTCAGT 59.365 40.000 4.97 0.00 0.00 3.41
314 321 3.008594 TGAACGGGGTGACATTCTAACAT 59.991 43.478 0.00 0.00 0.00 2.71
317 324 3.262151 TGATGAACGGGGTGACATTCTAA 59.738 43.478 0.00 0.00 0.00 2.10
342 349 2.158871 TGGAGCTTTCGGTACTGTTGTT 60.159 45.455 0.64 0.00 0.00 2.83
347 354 3.334691 TGATTTGGAGCTTTCGGTACTG 58.665 45.455 0.00 0.00 0.00 2.74
355 362 5.126707 GTCTCATGGATTGATTTGGAGCTTT 59.873 40.000 0.00 0.00 32.72 3.51
396 404 3.368948 GCTCCCGACTCTGAAGAAAGAAT 60.369 47.826 0.00 0.00 0.00 2.40
407 415 1.261238 CCTCCAAAGCTCCCGACTCT 61.261 60.000 0.00 0.00 0.00 3.24
421 429 0.683412 CATCAGGATCGATGCCTCCA 59.317 55.000 13.85 4.35 36.64 3.86
426 434 4.564041 ACAGATTACATCAGGATCGATGC 58.436 43.478 9.16 9.16 45.56 3.91
434 442 5.459536 TGCTAGCTACAGATTACATCAGG 57.540 43.478 17.23 0.00 0.00 3.86
445 453 3.917380 GTCTATTCGCATGCTAGCTACAG 59.083 47.826 17.13 5.44 0.00 2.74
455 463 4.668576 AACAACACTGTCTATTCGCATG 57.331 40.909 0.00 0.00 33.45 4.06
457 465 4.814234 AGAAAACAACACTGTCTATTCGCA 59.186 37.500 0.00 0.00 33.45 5.10
472 480 4.402793 TGATTCAAAACCCCGAGAAAACAA 59.597 37.500 0.00 0.00 0.00 2.83
482 490 5.682234 AAGGAATCATGATTCAAAACCCC 57.318 39.130 36.93 24.33 46.77 4.95
496 504 5.347635 CGACGATAACTTGTCAAAGGAATCA 59.652 40.000 0.00 0.00 37.76 2.57
506 514 2.063266 TGGCAACGACGATAACTTGTC 58.937 47.619 0.00 0.00 42.51 3.18
514 522 0.250124 TCTTTGGTGGCAACGACGAT 60.250 50.000 0.00 0.00 42.51 3.73
533 541 2.744709 GTTGTGGCGGCGTGGTAT 60.745 61.111 9.37 0.00 0.00 2.73
571 579 5.519722 AGTTTGATGTTGTTTCGAATGGAC 58.480 37.500 0.00 0.00 0.00 4.02
577 585 7.309177 TCTTTCAAAGTTTGATGTTGTTTCGA 58.691 30.769 18.69 0.00 39.84 3.71
588 596 9.559732 TCACTATGAAGATCTTTCAAAGTTTGA 57.440 29.630 14.35 14.35 38.04 2.69
589 597 9.604626 GTCACTATGAAGATCTTTCAAAGTTTG 57.395 33.333 9.87 9.44 31.55 2.93
590 598 9.566432 AGTCACTATGAAGATCTTTCAAAGTTT 57.434 29.630 9.87 0.00 31.55 2.66
593 601 8.768957 TCAGTCACTATGAAGATCTTTCAAAG 57.231 34.615 9.87 7.78 31.55 2.77
594 602 9.376075 GATCAGTCACTATGAAGATCTTTCAAA 57.624 33.333 9.87 0.00 37.29 2.69
597 605 7.652909 CAGGATCAGTCACTATGAAGATCTTTC 59.347 40.741 9.87 3.85 38.83 2.62
598 606 7.418827 CCAGGATCAGTCACTATGAAGATCTTT 60.419 40.741 9.87 0.00 38.83 2.52
600 608 5.539574 CCAGGATCAGTCACTATGAAGATCT 59.460 44.000 16.06 0.00 38.83 2.75
601 609 5.304101 ACCAGGATCAGTCACTATGAAGATC 59.696 44.000 0.00 11.35 38.45 2.75
603 611 4.614475 ACCAGGATCAGTCACTATGAAGA 58.386 43.478 0.00 0.00 0.00 2.87
604 612 4.648762 AGACCAGGATCAGTCACTATGAAG 59.351 45.833 11.08 0.00 35.38 3.02
606 614 3.956848 CAGACCAGGATCAGTCACTATGA 59.043 47.826 11.08 0.00 35.38 2.15
607 615 3.703556 ACAGACCAGGATCAGTCACTATG 59.296 47.826 11.08 4.66 35.38 2.23
608 616 3.957497 GACAGACCAGGATCAGTCACTAT 59.043 47.826 11.08 0.00 35.71 2.12
609 617 3.357203 GACAGACCAGGATCAGTCACTA 58.643 50.000 11.08 0.00 35.71 2.74
619 629 2.680352 GGCGAGGACAGACCAGGA 60.680 66.667 0.00 0.00 42.04 3.86
621 631 2.575993 CTGGCGAGGACAGACCAG 59.424 66.667 0.00 0.00 42.14 4.00
624 634 2.029844 GCAACTGGCGAGGACAGAC 61.030 63.158 5.30 0.00 42.14 3.51
634 644 2.294233 TGTCATTCAAAGAGCAACTGGC 59.706 45.455 0.00 0.00 45.30 4.85
635 645 4.458295 AGATGTCATTCAAAGAGCAACTGG 59.542 41.667 0.00 0.00 0.00 4.00
653 663 3.030291 CTCAGCAGGGACTTCTAGATGT 58.970 50.000 10.86 10.86 34.60 3.06
660 670 2.270527 GGCCTCAGCAGGGACTTC 59.729 66.667 0.00 0.00 40.75 3.01
668 678 0.183492 AAAGAAGTGTGGCCTCAGCA 59.817 50.000 7.99 0.00 42.56 4.41
675 685 1.082756 CGCGTGAAAGAAGTGTGGC 60.083 57.895 0.00 0.00 0.00 5.01
691 701 0.095417 GCCTCTTCAAATGTCGTCGC 59.905 55.000 0.00 0.00 0.00 5.19
728 738 2.824041 ATGCCGTTCGATGGGTGC 60.824 61.111 6.37 0.00 0.00 5.01
732 742 3.585990 GCCCATGCCGTTCGATGG 61.586 66.667 6.11 6.11 39.18 3.51
733 743 2.121564 GATGCCCATGCCGTTCGATG 62.122 60.000 0.00 0.00 36.33 3.84
734 744 1.893808 GATGCCCATGCCGTTCGAT 60.894 57.895 0.00 0.00 36.33 3.59
735 745 2.513666 GATGCCCATGCCGTTCGA 60.514 61.111 0.00 0.00 36.33 3.71
736 746 3.585990 GGATGCCCATGCCGTTCG 61.586 66.667 0.00 0.00 36.33 3.95
737 747 3.585990 CGGATGCCCATGCCGTTC 61.586 66.667 0.00 0.00 40.17 3.95
743 753 4.873810 TTCGCCCGGATGCCCATG 62.874 66.667 0.73 0.00 0.00 3.66
744 754 4.875713 GTTCGCCCGGATGCCCAT 62.876 66.667 0.73 0.00 0.00 4.00
747 757 3.508840 CTTGTTCGCCCGGATGCC 61.509 66.667 0.73 0.00 0.00 4.40
748 758 2.862674 TACCTTGTTCGCCCGGATGC 62.863 60.000 0.73 0.00 0.00 3.91
749 759 0.179056 ATACCTTGTTCGCCCGGATG 60.179 55.000 0.73 0.00 0.00 3.51
750 760 0.179056 CATACCTTGTTCGCCCGGAT 60.179 55.000 0.73 0.00 0.00 4.18
751 761 1.219664 CATACCTTGTTCGCCCGGA 59.780 57.895 0.73 0.00 0.00 5.14
752 762 0.176219 TACATACCTTGTTCGCCCGG 59.824 55.000 0.00 0.00 39.87 5.73
753 763 1.864711 CATACATACCTTGTTCGCCCG 59.135 52.381 0.00 0.00 39.87 6.13
754 764 3.188159 TCATACATACCTTGTTCGCCC 57.812 47.619 0.00 0.00 39.87 6.13
755 765 5.554822 TTTTCATACATACCTTGTTCGCC 57.445 39.130 0.00 0.00 39.87 5.54
756 766 6.837992 TCTTTTTCATACATACCTTGTTCGC 58.162 36.000 0.00 0.00 39.87 4.70
757 767 9.672086 TTTTCTTTTTCATACATACCTTGTTCG 57.328 29.630 0.00 0.00 39.87 3.95
877 887 0.398318 CATCGGGGGAGGGAAGATTC 59.602 60.000 0.00 0.00 0.00 2.52
878 888 0.030092 TCATCGGGGGAGGGAAGATT 60.030 55.000 0.00 0.00 0.00 2.40
888 898 2.187946 GTGCACTCTCATCGGGGG 59.812 66.667 10.32 0.00 0.00 5.40
897 907 1.608717 GGATGAGACCCGTGCACTCT 61.609 60.000 16.19 11.16 0.00 3.24
899 909 1.608717 GAGGATGAGACCCGTGCACT 61.609 60.000 16.19 0.00 0.00 4.40
965 975 2.278857 CGAACTGAGGCGATCCGG 60.279 66.667 0.00 0.00 37.47 5.14
966 976 2.956964 GCGAACTGAGGCGATCCG 60.957 66.667 1.24 0.00 37.47 4.18
967 977 2.586357 GGCGAACTGAGGCGATCC 60.586 66.667 1.24 0.00 0.00 3.36
968 978 1.447838 TTGGCGAACTGAGGCGATC 60.448 57.895 1.24 0.00 36.92 3.69
969 979 1.741770 GTTGGCGAACTGAGGCGAT 60.742 57.895 4.11 0.00 36.92 4.58
988 1006 2.926420 AACCCATTCGCGCAAACCC 61.926 57.895 8.75 0.00 0.00 4.11
1083 1105 2.425592 CTGTGGGACTTGTGCCGA 59.574 61.111 6.81 0.00 0.00 5.54
1166 1214 2.797278 CCTTCTACCATCGCCGCCT 61.797 63.158 0.00 0.00 0.00 5.52
1200 1248 4.111016 CGGCAGGTCGACGTAGCA 62.111 66.667 23.80 0.00 43.08 3.49
1392 1440 3.760035 AGCGGGTCGTACTGGCAG 61.760 66.667 14.16 14.16 0.00 4.85
1629 1677 3.767131 GAGAGAGAAAGGGAAGCTACTGT 59.233 47.826 0.00 0.00 0.00 3.55
1661 1709 3.071602 CACTCCAGAGGTTGAGGAAAAGA 59.928 47.826 0.00 0.00 32.80 2.52
1681 1729 1.174712 TGAAGCTGCTGCCTTTCCAC 61.175 55.000 12.44 0.00 40.80 4.02
1719 1767 4.820173 CGAACTTTCCCCTACAGAAAAGTT 59.180 41.667 10.80 10.80 33.06 2.66
1721 1769 3.751698 CCGAACTTTCCCCTACAGAAAAG 59.248 47.826 0.00 0.00 33.06 2.27
1727 1776 0.604578 CGACCGAACTTTCCCCTACA 59.395 55.000 0.00 0.00 0.00 2.74
1784 1834 6.415280 GCGTTCTTCTCACATACAGTACATAG 59.585 42.308 0.00 0.00 0.00 2.23
1788 1838 3.858238 GGCGTTCTTCTCACATACAGTAC 59.142 47.826 0.00 0.00 0.00 2.73
1789 1839 3.508402 TGGCGTTCTTCTCACATACAGTA 59.492 43.478 0.00 0.00 0.00 2.74
1790 1840 2.299013 TGGCGTTCTTCTCACATACAGT 59.701 45.455 0.00 0.00 0.00 3.55
1791 1841 2.959516 TGGCGTTCTTCTCACATACAG 58.040 47.619 0.00 0.00 0.00 2.74
1792 1842 3.610040 ATGGCGTTCTTCTCACATACA 57.390 42.857 0.00 0.00 0.00 2.29
1853 1908 1.355916 CGGTCCTCGAGAATCCGAC 59.644 63.158 26.44 18.84 43.22 4.79
1951 2011 2.617532 GCCTATCGGTCCTATACGTCCT 60.618 54.545 0.00 0.00 0.00 3.85
1959 2019 1.228769 ATGGCGCCTATCGGTCCTA 60.229 57.895 29.70 2.45 38.94 2.94
1960 2020 2.524394 ATGGCGCCTATCGGTCCT 60.524 61.111 29.70 0.00 38.94 3.85
1963 2023 0.603707 CATTCATGGCGCCTATCGGT 60.604 55.000 29.70 6.48 38.94 4.69
2018 2078 4.284550 TTCCCACCCAGTGCCAGC 62.285 66.667 0.00 0.00 31.34 4.85
2019 2079 2.282462 GTTCCCACCCAGTGCCAG 60.282 66.667 0.00 0.00 31.34 4.85
2035 2095 4.446413 GACCGTCGCCCATTCCGT 62.446 66.667 0.00 0.00 0.00 4.69
2070 2130 3.307506 TCCATTTCCAGGGCCAATAATG 58.692 45.455 6.18 9.72 0.00 1.90
2073 2133 3.704545 ATTCCATTTCCAGGGCCAATA 57.295 42.857 6.18 0.00 0.00 1.90
2176 2240 0.757188 GGCATCTTCTCCTCCTCCGA 60.757 60.000 0.00 0.00 0.00 4.55
2177 2241 0.758685 AGGCATCTTCTCCTCCTCCG 60.759 60.000 0.00 0.00 0.00 4.63
2249 2326 1.573108 GAGGATTCCTGAGGGTGACA 58.427 55.000 10.74 0.00 31.76 3.58
2256 2333 2.591923 TCAGATCCGAGGATTCCTGAG 58.408 52.381 10.74 3.87 33.43 3.35
2263 2340 2.564947 GGTAAGCATCAGATCCGAGGAT 59.435 50.000 3.97 3.97 37.59 3.24
2301 2378 3.728373 GGGTCCAGTGGCCGGAAT 61.728 66.667 5.05 0.00 33.29 3.01
2340 2417 0.981183 ACAGCACCGGAATCCTGTAA 59.019 50.000 9.46 0.00 36.82 2.41
2378 2456 1.276844 GCGTCTGCTCAACACACAC 59.723 57.895 0.00 0.00 38.39 3.82
2379 2457 3.717899 GCGTCTGCTCAACACACA 58.282 55.556 0.00 0.00 38.39 3.72
2390 2468 2.507992 CCGAAGCAGGAGCGTCTG 60.508 66.667 5.20 5.20 45.44 3.51
2391 2469 2.992114 ACCGAAGCAGGAGCGTCT 60.992 61.111 0.00 0.00 45.44 4.18
2395 2473 2.359230 AAGCACCGAAGCAGGAGC 60.359 61.111 7.09 7.09 46.17 4.70
2396 2474 0.392193 ATGAAGCACCGAAGCAGGAG 60.392 55.000 0.00 0.00 36.85 3.69
2397 2475 0.036732 AATGAAGCACCGAAGCAGGA 59.963 50.000 0.00 0.00 36.85 3.86
2398 2476 1.667724 CTAATGAAGCACCGAAGCAGG 59.332 52.381 2.02 0.00 36.85 4.85
2399 2477 2.606725 CTCTAATGAAGCACCGAAGCAG 59.393 50.000 2.02 0.00 36.85 4.24
2400 2478 2.621338 CTCTAATGAAGCACCGAAGCA 58.379 47.619 2.02 0.00 36.85 3.91
2401 2479 1.328986 GCTCTAATGAAGCACCGAAGC 59.671 52.381 0.00 0.00 0.00 3.86
2402 2480 2.621338 TGCTCTAATGAAGCACCGAAG 58.379 47.619 0.00 0.00 33.24 3.79
2403 2481 2.760634 TGCTCTAATGAAGCACCGAA 57.239 45.000 0.00 0.00 33.24 4.30
2404 2482 2.432146 AGATGCTCTAATGAAGCACCGA 59.568 45.455 0.00 0.00 41.61 4.69
2405 2483 2.831333 AGATGCTCTAATGAAGCACCG 58.169 47.619 0.00 0.00 41.61 4.94
2406 2484 4.194640 TGAAGATGCTCTAATGAAGCACC 58.805 43.478 0.00 0.00 41.61 5.01
2407 2485 5.808042 TTGAAGATGCTCTAATGAAGCAC 57.192 39.130 0.00 0.00 41.61 4.40
2408 2486 7.049754 TGTATTGAAGATGCTCTAATGAAGCA 58.950 34.615 0.00 0.00 43.04 3.91
2409 2487 7.488187 TGTATTGAAGATGCTCTAATGAAGC 57.512 36.000 0.00 0.00 0.00 3.86
2410 2488 9.322773 TCTTGTATTGAAGATGCTCTAATGAAG 57.677 33.333 0.00 0.00 0.00 3.02
2411 2489 9.842775 ATCTTGTATTGAAGATGCTCTAATGAA 57.157 29.630 0.00 0.00 40.49 2.57
2422 2500 9.932207 TTCAAATTTGCATCTTGTATTGAAGAT 57.068 25.926 13.54 0.00 42.34 2.40
2424 2502 9.414295 TCTTCAAATTTGCATCTTGTATTGAAG 57.586 29.630 13.54 19.00 46.90 3.02
2425 2503 9.932207 ATCTTCAAATTTGCATCTTGTATTGAA 57.068 25.926 13.54 0.00 35.14 2.69
2426 2504 9.361315 CATCTTCAAATTTGCATCTTGTATTGA 57.639 29.630 13.54 0.00 0.00 2.57
2427 2505 9.146984 ACATCTTCAAATTTGCATCTTGTATTG 57.853 29.630 13.54 3.13 0.00 1.90
2431 2509 9.545105 TTTTACATCTTCAAATTTGCATCTTGT 57.455 25.926 13.54 13.78 0.00 3.16
2455 2533 8.990163 TTCCTCCTAGTCTGTAAAACATTTTT 57.010 30.769 0.00 0.00 0.00 1.94
2456 2534 8.437575 TCTTCCTCCTAGTCTGTAAAACATTTT 58.562 33.333 0.00 0.00 0.00 1.82
2457 2535 7.974504 TCTTCCTCCTAGTCTGTAAAACATTT 58.025 34.615 0.00 0.00 0.00 2.32
2458 2536 7.310734 CCTCTTCCTCCTAGTCTGTAAAACATT 60.311 40.741 0.00 0.00 0.00 2.71
2459 2537 6.155393 CCTCTTCCTCCTAGTCTGTAAAACAT 59.845 42.308 0.00 0.00 0.00 2.71
2460 2538 5.480772 CCTCTTCCTCCTAGTCTGTAAAACA 59.519 44.000 0.00 0.00 0.00 2.83
2461 2539 5.715753 TCCTCTTCCTCCTAGTCTGTAAAAC 59.284 44.000 0.00 0.00 0.00 2.43
2462 2540 5.900437 TCCTCTTCCTCCTAGTCTGTAAAA 58.100 41.667 0.00 0.00 0.00 1.52
2463 2541 5.531753 TCCTCTTCCTCCTAGTCTGTAAA 57.468 43.478 0.00 0.00 0.00 2.01
2464 2542 5.222275 TGTTCCTCTTCCTCCTAGTCTGTAA 60.222 44.000 0.00 0.00 0.00 2.41
2465 2543 4.291513 TGTTCCTCTTCCTCCTAGTCTGTA 59.708 45.833 0.00 0.00 0.00 2.74
2466 2544 3.076182 TGTTCCTCTTCCTCCTAGTCTGT 59.924 47.826 0.00 0.00 0.00 3.41
2467 2545 3.699038 CTGTTCCTCTTCCTCCTAGTCTG 59.301 52.174 0.00 0.00 0.00 3.51
2468 2546 3.309556 CCTGTTCCTCTTCCTCCTAGTCT 60.310 52.174 0.00 0.00 0.00 3.24
2469 2547 3.028130 CCTGTTCCTCTTCCTCCTAGTC 58.972 54.545 0.00 0.00 0.00 2.59
2470 2548 2.292587 CCCTGTTCCTCTTCCTCCTAGT 60.293 54.545 0.00 0.00 0.00 2.57
2471 2549 2.393646 CCCTGTTCCTCTTCCTCCTAG 58.606 57.143 0.00 0.00 0.00 3.02
2472 2550 1.008449 CCCCTGTTCCTCTTCCTCCTA 59.992 57.143 0.00 0.00 0.00 2.94
2473 2551 0.252927 CCCCTGTTCCTCTTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
2474 2552 1.275421 CCCCCTGTTCCTCTTCCTCC 61.275 65.000 0.00 0.00 0.00 4.30
2475 2553 0.252742 TCCCCCTGTTCCTCTTCCTC 60.253 60.000 0.00 0.00 0.00 3.71
2476 2554 0.252927 CTCCCCCTGTTCCTCTTCCT 60.253 60.000 0.00 0.00 0.00 3.36
2477 2555 1.275421 CCTCCCCCTGTTCCTCTTCC 61.275 65.000 0.00 0.00 0.00 3.46
2478 2556 1.275421 CCCTCCCCCTGTTCCTCTTC 61.275 65.000 0.00 0.00 0.00 2.87
2479 2557 1.229984 CCCTCCCCCTGTTCCTCTT 60.230 63.158 0.00 0.00 0.00 2.85
2480 2558 1.761780 TTCCCTCCCCCTGTTCCTCT 61.762 60.000 0.00 0.00 0.00 3.69
2481 2559 0.845102 TTTCCCTCCCCCTGTTCCTC 60.845 60.000 0.00 0.00 0.00 3.71
2482 2560 0.178801 ATTTCCCTCCCCCTGTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
2483 2561 0.033109 CATTTCCCTCCCCCTGTTCC 60.033 60.000 0.00 0.00 0.00 3.62
2484 2562 0.999712 TCATTTCCCTCCCCCTGTTC 59.000 55.000 0.00 0.00 0.00 3.18
2485 2563 1.466858 TTCATTTCCCTCCCCCTGTT 58.533 50.000 0.00 0.00 0.00 3.16
2486 2564 1.466858 TTTCATTTCCCTCCCCCTGT 58.533 50.000 0.00 0.00 0.00 4.00
2487 2565 2.024080 TCATTTCATTTCCCTCCCCCTG 60.024 50.000 0.00 0.00 0.00 4.45
2488 2566 2.297044 TCATTTCATTTCCCTCCCCCT 58.703 47.619 0.00 0.00 0.00 4.79
2489 2567 2.846665 TCATTTCATTTCCCTCCCCC 57.153 50.000 0.00 0.00 0.00 5.40
2490 2568 3.118629 GCTTTCATTTCATTTCCCTCCCC 60.119 47.826 0.00 0.00 0.00 4.81
2491 2569 3.118629 GGCTTTCATTTCATTTCCCTCCC 60.119 47.826 0.00 0.00 0.00 4.30
2492 2570 3.515104 TGGCTTTCATTTCATTTCCCTCC 59.485 43.478 0.00 0.00 0.00 4.30
2493 2571 4.806640 TGGCTTTCATTTCATTTCCCTC 57.193 40.909 0.00 0.00 0.00 4.30
2494 2572 4.594491 AGTTGGCTTTCATTTCATTTCCCT 59.406 37.500 0.00 0.00 0.00 4.20
2495 2573 4.692155 CAGTTGGCTTTCATTTCATTTCCC 59.308 41.667 0.00 0.00 0.00 3.97
2496 2574 5.540911 TCAGTTGGCTTTCATTTCATTTCC 58.459 37.500 0.00 0.00 0.00 3.13
2497 2575 6.091713 CCATCAGTTGGCTTTCATTTCATTTC 59.908 38.462 0.00 0.00 39.09 2.17
2498 2576 5.935789 CCATCAGTTGGCTTTCATTTCATTT 59.064 36.000 0.00 0.00 39.09 2.32
2499 2577 5.484715 CCATCAGTTGGCTTTCATTTCATT 58.515 37.500 0.00 0.00 39.09 2.57
2500 2578 5.080969 CCATCAGTTGGCTTTCATTTCAT 57.919 39.130 0.00 0.00 39.09 2.57
2501 2579 4.524316 CCATCAGTTGGCTTTCATTTCA 57.476 40.909 0.00 0.00 39.09 2.69
2513 2591 3.027170 GCGTGCCGACCATCAGTTG 62.027 63.158 0.00 0.00 0.00 3.16
2514 2592 2.742372 GCGTGCCGACCATCAGTT 60.742 61.111 0.00 0.00 0.00 3.16
2528 2606 4.992511 TAAAACTGGCGGCCGCGT 62.993 61.111 41.05 31.74 43.06 6.01
2529 2607 4.454717 GTAAAACTGGCGGCCGCG 62.455 66.667 41.05 31.04 43.06 6.46
2530 2608 2.592623 GATGTAAAACTGGCGGCCGC 62.593 60.000 41.63 41.63 41.06 6.53
2531 2609 1.024579 AGATGTAAAACTGGCGGCCG 61.025 55.000 24.05 24.05 0.00 6.13
2532 2610 0.733150 GAGATGTAAAACTGGCGGCC 59.267 55.000 13.32 13.32 0.00 6.13
2533 2611 0.733150 GGAGATGTAAAACTGGCGGC 59.267 55.000 0.00 0.00 0.00 6.53
2534 2612 2.009774 CTGGAGATGTAAAACTGGCGG 58.990 52.381 0.00 0.00 0.00 6.13
2535 2613 2.972625 TCTGGAGATGTAAAACTGGCG 58.027 47.619 0.00 0.00 0.00 5.69
2536 2614 4.889832 CATCTGGAGATGTAAAACTGGC 57.110 45.455 8.28 0.00 45.10 4.85
2547 2625 2.842496 TGCACTTCCTTCATCTGGAGAT 59.158 45.455 0.00 0.00 34.76 2.75
2548 2626 2.259917 TGCACTTCCTTCATCTGGAGA 58.740 47.619 0.00 0.00 34.76 3.71
2549 2627 2.775911 TGCACTTCCTTCATCTGGAG 57.224 50.000 0.00 0.00 34.76 3.86
2550 2628 3.507162 TTTGCACTTCCTTCATCTGGA 57.493 42.857 0.00 0.00 0.00 3.86
2551 2629 4.796038 AATTTGCACTTCCTTCATCTGG 57.204 40.909 0.00 0.00 0.00 3.86
2567 2645 5.401550 ACGACACCTTATGATGCAAATTTG 58.598 37.500 14.03 14.03 0.00 2.32
2568 2646 5.643379 ACGACACCTTATGATGCAAATTT 57.357 34.783 0.00 0.00 0.00 1.82
2569 2647 5.880332 ACTACGACACCTTATGATGCAAATT 59.120 36.000 0.00 0.00 0.00 1.82
2570 2648 5.428253 ACTACGACACCTTATGATGCAAAT 58.572 37.500 0.00 0.00 0.00 2.32
2571 2649 4.827692 ACTACGACACCTTATGATGCAAA 58.172 39.130 0.00 0.00 0.00 3.68
2572 2650 4.465632 ACTACGACACCTTATGATGCAA 57.534 40.909 0.00 0.00 0.00 4.08
2573 2651 4.465632 AACTACGACACCTTATGATGCA 57.534 40.909 0.00 0.00 0.00 3.96
2574 2652 5.808540 TGTAAACTACGACACCTTATGATGC 59.191 40.000 0.00 0.00 0.00 3.91
2575 2653 7.921214 AGATGTAAACTACGACACCTTATGATG 59.079 37.037 0.00 0.00 0.00 3.07
2576 2654 8.008513 AGATGTAAACTACGACACCTTATGAT 57.991 34.615 0.00 0.00 0.00 2.45
2577 2655 7.400599 AGATGTAAACTACGACACCTTATGA 57.599 36.000 0.00 0.00 0.00 2.15
2578 2656 7.044249 CGAAGATGTAAACTACGACACCTTATG 60.044 40.741 0.00 0.00 0.00 1.90
2579 2657 6.971184 CGAAGATGTAAACTACGACACCTTAT 59.029 38.462 0.00 0.00 0.00 1.73
2580 2658 6.317088 CGAAGATGTAAACTACGACACCTTA 58.683 40.000 0.00 0.00 0.00 2.69
2581 2659 5.159209 CGAAGATGTAAACTACGACACCTT 58.841 41.667 0.00 0.00 0.00 3.50
2582 2660 4.380233 CCGAAGATGTAAACTACGACACCT 60.380 45.833 0.00 0.00 0.00 4.00
2583 2661 3.855950 CCGAAGATGTAAACTACGACACC 59.144 47.826 0.00 0.00 0.00 4.16
2584 2662 4.726416 TCCGAAGATGTAAACTACGACAC 58.274 43.478 0.00 0.00 0.00 3.67
2585 2663 5.375417 TTCCGAAGATGTAAACTACGACA 57.625 39.130 0.00 0.00 0.00 4.35
2586 2664 4.797349 CCTTCCGAAGATGTAAACTACGAC 59.203 45.833 9.87 0.00 0.00 4.34
2587 2665 4.676196 GCCTTCCGAAGATGTAAACTACGA 60.676 45.833 9.87 0.00 0.00 3.43
2588 2666 3.550678 GCCTTCCGAAGATGTAAACTACG 59.449 47.826 9.87 0.00 0.00 3.51
2589 2667 3.550678 CGCCTTCCGAAGATGTAAACTAC 59.449 47.826 9.87 0.00 40.02 2.73
2590 2668 3.444742 TCGCCTTCCGAAGATGTAAACTA 59.555 43.478 9.87 0.00 44.21 2.24
2591 2669 2.232941 TCGCCTTCCGAAGATGTAAACT 59.767 45.455 9.87 0.00 44.21 2.66
2592 2670 2.613691 TCGCCTTCCGAAGATGTAAAC 58.386 47.619 9.87 0.00 44.21 2.01


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

AutoCloner maintained by Alex Coulton.