Multiple sequence alignment - TraesCS1A01G345400

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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 TraesCS1A01G345400 chr1A 100.000 5772 0 0 1 5772 532747220 532741449 0.000000e+00 10659.0
1 TraesCS1A01G345400 chr1A 85.292 1251 149 22 3015 4252 532766172 532764944 0.000000e+00 1258.0
2 TraesCS1A01G345400 chr1A 81.869 1423 207 33 4292 5679 532764943 532763537 0.000000e+00 1151.0
3 TraesCS1A01G345400 chr1A 80.627 893 140 19 1307 2170 532767652 532766764 0.000000e+00 660.0
4 TraesCS1A01G345400 chr1A 73.185 1708 351 64 2584 4242 532617528 532615879 8.570000e-143 518.0
5 TraesCS1A01G345400 chr1A 81.013 553 92 11 1303 1853 532618804 532618263 1.490000e-115 427.0
6 TraesCS1A01G345400 chr1A 76.832 505 94 17 4510 4998 532911908 532912405 4.440000e-66 263.0
7 TraesCS1A01G345400 chr1A 81.818 198 30 5 4325 4520 532911696 532911889 1.660000e-35 161.0
8 TraesCS1A01G345400 chr1A 80.000 150 25 4 4345 4491 532739268 532739415 7.910000e-19 106.0
9 TraesCS1A01G345400 chr1A 98.305 59 1 0 2208 2266 532744956 532744898 2.840000e-18 104.0
10 TraesCS1A01G345400 chr1A 98.305 59 1 0 2265 2323 532745013 532744955 2.840000e-18 104.0
11 TraesCS1A01G345400 chr1A 83.673 98 12 4 501 596 11648138 11648233 7.970000e-14 89.8
12 TraesCS1A01G345400 chr1B 90.128 3525 275 29 2261 5761 588488877 588485402 0.000000e+00 4514.0
13 TraesCS1A01G345400 chr1B 90.973 709 42 7 1176 1867 588490160 588489457 0.000000e+00 935.0
14 TraesCS1A01G345400 chr1B 87.645 518 33 11 624 1140 588490637 588490150 1.800000e-159 573.0
15 TraesCS1A01G345400 chr1B 90.857 350 26 2 1919 2265 588489163 588488817 1.130000e-126 464.0
16 TraesCS1A01G345400 chr1B 81.622 555 85 14 1303 1853 588321946 588321405 1.480000e-120 444.0
17 TraesCS1A01G345400 chr1B 77.424 660 116 26 4361 5007 588318943 588318304 4.250000e-96 363.0
18 TraesCS1A01G345400 chr1B 80.190 525 57 14 81 589 588491128 588490635 3.310000e-92 350.0
19 TraesCS1A01G345400 chr1B 77.374 495 89 22 4514 4998 588648207 588648688 7.370000e-69 272.0
20 TraesCS1A01G345400 chr1B 84.242 165 26 0 4356 4520 588648021 588648185 1.660000e-35 161.0
21 TraesCS1A01G345400 chr1B 81.333 150 25 3 4343 4491 588483502 588483649 1.020000e-22 119.0
22 TraesCS1A01G345400 chr1B 82.828 99 13 4 501 596 397836343 397836440 1.030000e-12 86.1
23 TraesCS1A01G345400 chr1B 80.769 104 14 5 497 596 397860191 397860292 6.200000e-10 76.8
24 TraesCS1A01G345400 chr1D 95.397 2846 103 7 2929 5772 435152641 435149822 0.000000e+00 4505.0
25 TraesCS1A01G345400 chr1D 81.775 631 97 13 1246 1868 435154172 435153552 3.990000e-141 512.0
26 TraesCS1A01G345400 chr1D 92.737 358 18 3 1891 2243 435153454 435153100 1.430000e-140 510.0
27 TraesCS1A01G345400 chr1D 87.668 373 46 0 2560 2932 435153098 435152726 8.880000e-118 435.0
28 TraesCS1A01G345400 chr1D 91.065 291 22 2 1 287 435156308 435156018 1.950000e-104 390.0
29 TraesCS1A01G345400 chr1D 89.583 240 12 8 658 894 435154640 435154411 5.660000e-75 292.0
30 TraesCS1A01G345400 chr1D 83.108 148 22 3 4345 4491 435147458 435147603 1.310000e-26 132.0
31 TraesCS1A01G345400 chr1D 97.297 74 0 1 309 382 435155590 435155519 2.180000e-24 124.0
32 TraesCS1A01G345400 chr1D 91.176 68 2 3 595 662 435155536 435155473 7.970000e-14 89.8
33 TraesCS1A01G345400 chr4A 82.721 272 38 5 2299 2568 47750939 47751203 3.480000e-57 233.0
34 TraesCS1A01G345400 chr4A 81.356 236 36 5 2316 2544 584618672 584618438 9.880000e-43 185.0
35 TraesCS1A01G345400 chr4A 81.116 233 34 7 2299 2525 618848929 618849157 1.650000e-40 178.0
36 TraesCS1A01G345400 chr4A 81.197 117 20 2 383 498 537539691 537539576 6.160000e-15 93.5
37 TraesCS1A01G345400 chr4A 79.167 120 23 2 380 498 511828016 511828134 1.330000e-11 82.4
38 TraesCS1A01G345400 chr3A 84.615 195 30 0 2297 2491 87103576 87103382 1.640000e-45 195.0
39 TraesCS1A01G345400 chr3A 81.081 111 17 4 490 597 50384285 50384394 1.030000e-12 86.1
40 TraesCS1A01G345400 chr6D 80.913 241 46 0 2317 2557 470048981 470049221 2.120000e-44 191.0
41 TraesCS1A01G345400 chr6D 88.571 70 8 0 383 452 463797305 463797236 1.030000e-12 86.1
42 TraesCS1A01G345400 chr2A 80.800 250 34 11 2318 2563 410273804 410273565 3.550000e-42 183.0
43 TraesCS1A01G345400 chr2D 79.916 239 42 4 2318 2554 321780276 321780510 2.770000e-38 171.0
44 TraesCS1A01G345400 chr2D 87.368 95 9 3 504 596 448157356 448157449 7.910000e-19 106.0
45 TraesCS1A01G345400 chr6B 76.077 209 36 11 2304 2510 719952369 719952565 4.760000e-16 97.1
46 TraesCS1A01G345400 chr6B 84.416 77 9 3 393 468 496991513 496991587 8.020000e-09 73.1
47 TraesCS1A01G345400 chr5B 81.905 105 19 0 394 498 328219322 328219426 7.970000e-14 89.8
48 TraesCS1A01G345400 chr3B 85.542 83 12 0 386 468 696985466 696985384 2.870000e-13 87.9
49 TraesCS1A01G345400 chr3B 80.189 106 20 1 394 498 62708076 62708181 1.720000e-10 78.7
50 TraesCS1A01G345400 chr5D 90.625 64 6 0 526 589 501114688 501114625 1.030000e-12 86.1
51 TraesCS1A01G345400 chr7D 80.909 110 17 4 490 596 91118523 91118631 3.710000e-12 84.2
52 TraesCS1A01G345400 chr7A 87.692 65 7 1 490 553 21271229 21271165 2.230000e-09 75.0
53 TraesCS1A01G345400 chr5A 80.808 99 15 4 501 596 529097001 529096904 2.230000e-09 75.0
54 TraesCS1A01G345400 chr7B 76.562 128 26 4 383 508 591203435 591203560 3.730000e-07 67.6


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 TraesCS1A01G345400 chr1A 532741449 532747220 5771 True 3622.333333 10659 98.87000 1 5772 3 chr1A.!!$R2 5771
1 TraesCS1A01G345400 chr1A 532763537 532767652 4115 True 1023.000000 1258 82.59600 1307 5679 3 chr1A.!!$R3 4372
2 TraesCS1A01G345400 chr1A 532615879 532618804 2925 True 472.500000 518 77.09900 1303 4242 2 chr1A.!!$R1 2939
3 TraesCS1A01G345400 chr1A 532911696 532912405 709 False 212.000000 263 79.32500 4325 4998 2 chr1A.!!$F3 673
4 TraesCS1A01G345400 chr1B 588485402 588491128 5726 True 1367.200000 4514 87.95860 81 5761 5 chr1B.!!$R2 5680
5 TraesCS1A01G345400 chr1B 588318304 588321946 3642 True 403.500000 444 79.52300 1303 5007 2 chr1B.!!$R1 3704
6 TraesCS1A01G345400 chr1B 588648021 588648688 667 False 216.500000 272 80.80800 4356 4998 2 chr1B.!!$F4 642
7 TraesCS1A01G345400 chr1D 435149822 435156308 6486 True 857.225000 4505 90.83725 1 5772 8 chr1D.!!$R1 5771

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 2170 0.611200 TATACCACTGGCAAGCGTGT 59.389 50.000 0.59 0.00 0.00 4.49 F
2012 3572 0.036732 TGTGGCTGGACATCTCAACC 59.963 55.000 0.00 0.00 0.00 3.77 F
2725 4315 1.226018 GCGACGCCTTGTACAATGC 60.226 57.895 21.75 21.75 0.00 3.56 F
3044 4801 0.109179 TGCCATCAACGCAATCAAGC 60.109 50.000 0.00 0.00 32.05 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2775 4365 0.102300 GGCGGCAGTGTTGAGTTTTT 59.898 50.0 3.07 0.0 0.00 1.94 R
3018 4775 1.317613 TGCGTTGATGGCAGAAACTT 58.682 45.0 11.79 0.0 35.04 2.66 R
4189 6007 1.187087 GACTGGAGGATTGAGACCGT 58.813 55.0 0.00 0.0 0.00 4.83 R
4804 6686 1.349234 TGTCTTCACATCACGATGCG 58.651 50.0 6.94 0.0 42.39 4.73 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
29 30 4.806247 AGAACAGTTTCAACTCTCTCAACG 59.194 41.667 0.00 0.00 37.08 4.10
47 48 9.098355 CTCTCAACGGAACATTCTAAATTATCA 57.902 33.333 0.00 0.00 0.00 2.15
48 49 9.098355 TCTCAACGGAACATTCTAAATTATCAG 57.902 33.333 0.00 0.00 0.00 2.90
71 72 8.999431 TCAGTAACATCTCAACCAAAAGAATAC 58.001 33.333 0.00 0.00 0.00 1.89
73 74 9.520515 AGTAACATCTCAACCAAAAGAATACAT 57.479 29.630 0.00 0.00 0.00 2.29
75 76 7.765695 ACATCTCAACCAAAAGAATACATGT 57.234 32.000 2.69 2.69 0.00 3.21
144 145 0.958822 ACCGGACAAGAAATTGCCAC 59.041 50.000 9.46 0.00 0.00 5.01
394 818 1.597854 TGTCTCGCAAACCAGCCTG 60.598 57.895 0.00 0.00 0.00 4.85
422 846 3.484953 ATGGTTAGGAGGACAGTGGTA 57.515 47.619 0.00 0.00 0.00 3.25
424 848 3.371965 TGGTTAGGAGGACAGTGGTATC 58.628 50.000 0.00 0.00 0.00 2.24
425 849 2.361438 GGTTAGGAGGACAGTGGTATCG 59.639 54.545 0.00 0.00 0.00 2.92
448 882 3.308688 CCAATCCATCAGGGTTCAAGTCT 60.309 47.826 0.00 0.00 35.53 3.24
451 885 4.826274 TCCATCAGGGTTCAAGTCTTAG 57.174 45.455 0.00 0.00 38.11 2.18
457 891 6.187727 TCAGGGTTCAAGTCTTAGATTTGT 57.812 37.500 15.33 0.00 32.39 2.83
459 893 5.997746 CAGGGTTCAAGTCTTAGATTTGTCA 59.002 40.000 15.33 3.47 32.39 3.58
461 895 7.175641 CAGGGTTCAAGTCTTAGATTTGTCATT 59.824 37.037 15.33 0.00 32.39 2.57
463 897 7.174946 GGGTTCAAGTCTTAGATTTGTCATTGA 59.825 37.037 15.33 2.53 32.39 2.57
466 900 7.755591 TCAAGTCTTAGATTTGTCATTGATGC 58.244 34.615 15.33 0.00 32.39 3.91
468 902 7.551035 AGTCTTAGATTTGTCATTGATGCTC 57.449 36.000 0.00 0.00 0.00 4.26
478 912 6.976636 TGTCATTGATGCTCACGTTATTTA 57.023 33.333 0.00 0.00 0.00 1.40
479 913 6.771076 TGTCATTGATGCTCACGTTATTTAC 58.229 36.000 0.00 0.00 0.00 2.01
497 931 9.447040 GTTATTTACGGATTTATTTCAGGCTTC 57.553 33.333 0.00 0.00 0.00 3.86
505 939 4.640771 TTATTTCAGGCTTCTGAGGTGT 57.359 40.909 0.00 0.00 46.84 4.16
511 945 3.582647 TCAGGCTTCTGAGGTGTTCATAA 59.417 43.478 0.00 0.00 42.13 1.90
513 947 3.584848 AGGCTTCTGAGGTGTTCATAAGT 59.415 43.478 4.82 0.00 40.37 2.24
522 956 5.962031 TGAGGTGTTCATAAGTATAGGGTGT 59.038 40.000 0.00 0.00 0.00 4.16
523 957 6.097839 TGAGGTGTTCATAAGTATAGGGTGTC 59.902 42.308 0.00 0.00 0.00 3.67
526 960 6.183361 GGTGTTCATAAGTATAGGGTGTCCAT 60.183 42.308 0.00 0.00 34.83 3.41
527 961 6.706270 GTGTTCATAAGTATAGGGTGTCCATG 59.294 42.308 0.00 0.00 34.83 3.66
528 962 6.385759 TGTTCATAAGTATAGGGTGTCCATGT 59.614 38.462 0.00 0.00 34.83 3.21
529 963 6.419484 TCATAAGTATAGGGTGTCCATGTG 57.581 41.667 0.00 0.00 34.83 3.21
534 968 0.991146 TAGGGTGTCCATGTGTGCAT 59.009 50.000 0.00 0.00 35.32 3.96
543 977 2.509131 TCCATGTGTGCATTCATAGGGA 59.491 45.455 3.78 3.78 37.14 4.20
553 987 6.269769 TGTGCATTCATAGGGATGAGTGTATA 59.730 38.462 0.00 3.92 46.40 1.47
557 991 8.531982 GCATTCATAGGGATGAGTGTATACTTA 58.468 37.037 0.00 0.00 46.40 2.24
558 992 9.862371 CATTCATAGGGATGAGTGTATACTTAC 57.138 37.037 4.17 0.00 43.03 2.34
568 1002 9.705471 GATGAGTGTATACTTACGTATATGAGC 57.295 37.037 4.17 0.00 39.90 4.26
573 1007 8.226448 GTGTATACTTACGTATATGAGCGACTT 58.774 37.037 4.17 0.00 39.90 3.01
583 1017 6.637254 CGTATATGAGCGACTTTGATTGTACT 59.363 38.462 0.00 0.00 0.00 2.73
584 1018 6.834959 ATATGAGCGACTTTGATTGTACTG 57.165 37.500 0.00 0.00 0.00 2.74
585 1019 3.990092 TGAGCGACTTTGATTGTACTGT 58.010 40.909 0.00 0.00 0.00 3.55
588 1022 4.127171 AGCGACTTTGATTGTACTGTGTT 58.873 39.130 0.00 0.00 0.00 3.32
589 1023 5.294356 AGCGACTTTGATTGTACTGTGTTA 58.706 37.500 0.00 0.00 0.00 2.41
590 1024 5.756347 AGCGACTTTGATTGTACTGTGTTAA 59.244 36.000 0.00 0.00 0.00 2.01
591 1025 6.259167 AGCGACTTTGATTGTACTGTGTTAAA 59.741 34.615 0.00 0.00 0.00 1.52
592 1026 6.908284 GCGACTTTGATTGTACTGTGTTAAAA 59.092 34.615 0.00 0.00 0.00 1.52
593 1027 7.429920 GCGACTTTGATTGTACTGTGTTAAAAA 59.570 33.333 0.00 0.00 0.00 1.94
614 1048 2.853731 ACTACATAGCGTGTCTCAGC 57.146 50.000 0.91 0.00 42.29 4.26
615 1049 2.370349 ACTACATAGCGTGTCTCAGCT 58.630 47.619 0.91 0.00 46.53 4.24
617 1051 2.853731 ACATAGCGTGTCTCAGCTAC 57.146 50.000 0.00 0.00 46.99 3.58
618 1052 2.092323 ACATAGCGTGTCTCAGCTACA 58.908 47.619 0.00 0.00 46.99 2.74
619 1053 2.690497 ACATAGCGTGTCTCAGCTACAT 59.310 45.455 0.00 0.00 46.99 2.29
620 1054 3.883489 ACATAGCGTGTCTCAGCTACATA 59.117 43.478 0.00 0.00 46.99 2.29
621 1055 4.023622 ACATAGCGTGTCTCAGCTACATAG 60.024 45.833 0.00 0.00 46.99 2.23
622 1056 3.057876 ATAGCGTGTCTCAGCTACATAGC 60.058 47.826 2.50 2.50 46.99 2.97
748 2019 2.704065 AGGCCGCACTAATAATGGTACT 59.296 45.455 0.00 0.00 0.00 2.73
749 2020 3.899360 AGGCCGCACTAATAATGGTACTA 59.101 43.478 0.00 0.00 0.00 1.82
750 2021 4.021368 AGGCCGCACTAATAATGGTACTAG 60.021 45.833 0.00 0.00 0.00 2.57
820 2091 3.613671 CGATCAAGTCAACTGCACTCTCT 60.614 47.826 0.00 0.00 0.00 3.10
890 2163 5.365314 TGATGTGTCTATTATACCACTGGCA 59.635 40.000 0.00 0.00 0.00 4.92
891 2164 5.685520 TGTGTCTATTATACCACTGGCAA 57.314 39.130 0.00 0.00 0.00 4.52
892 2165 5.670485 TGTGTCTATTATACCACTGGCAAG 58.330 41.667 0.00 0.00 0.00 4.01
893 2166 4.511826 GTGTCTATTATACCACTGGCAAGC 59.488 45.833 0.00 0.00 0.00 4.01
894 2167 3.741344 GTCTATTATACCACTGGCAAGCG 59.259 47.826 0.00 0.00 0.00 4.68
895 2168 2.710096 ATTATACCACTGGCAAGCGT 57.290 45.000 0.00 0.00 0.00 5.07
896 2169 1.732941 TTATACCACTGGCAAGCGTG 58.267 50.000 0.00 0.00 0.00 5.34
897 2170 0.611200 TATACCACTGGCAAGCGTGT 59.389 50.000 0.59 0.00 0.00 4.49
898 2171 0.955428 ATACCACTGGCAAGCGTGTG 60.955 55.000 0.59 8.42 0.00 3.82
899 2172 2.034048 TACCACTGGCAAGCGTGTGA 62.034 55.000 14.52 0.00 32.72 3.58
900 2173 2.186160 CCACTGGCAAGCGTGTGAA 61.186 57.895 14.52 0.00 32.72 3.18
901 2174 1.009675 CACTGGCAAGCGTGTGAAC 60.010 57.895 0.59 0.00 32.72 3.18
902 2175 2.186826 ACTGGCAAGCGTGTGAACC 61.187 57.895 0.59 0.00 0.00 3.62
903 2176 1.893808 CTGGCAAGCGTGTGAACCT 60.894 57.895 0.59 0.00 0.00 3.50
934 2216 6.918067 AGGCTGAGCACATACTGTATATAA 57.082 37.500 6.82 0.00 0.00 0.98
937 2219 7.821359 AGGCTGAGCACATACTGTATATAAATG 59.179 37.037 6.82 0.00 0.00 2.32
972 2254 0.992072 CGTACGTGGAGCATCTTGTG 59.008 55.000 7.22 0.00 33.73 3.33
987 2269 5.385617 CATCTTGTGCTAGTTACTTGTTGC 58.614 41.667 0.00 0.00 0.00 4.17
988 2270 4.703897 TCTTGTGCTAGTTACTTGTTGCT 58.296 39.130 0.00 0.00 0.00 3.91
1017 2303 4.873129 ATGTGCGCGCGGAGTAGG 62.873 66.667 33.06 1.02 0.00 3.18
1030 2316 2.073037 GAGTAGGATGGACCGGCGAC 62.073 65.000 9.30 1.30 44.74 5.19
1142 2428 2.593346 AGCATCGAAGGTGAGCTTAG 57.407 50.000 0.00 0.00 29.98 2.18
1162 2448 9.526713 AGCTTAGAAGTATTATCATATGCATCG 57.473 33.333 0.19 0.00 0.00 3.84
1163 2449 9.521503 GCTTAGAAGTATTATCATATGCATCGA 57.478 33.333 0.19 1.02 0.00 3.59
1166 2452 8.939201 AGAAGTATTATCATATGCATCGAAGG 57.061 34.615 0.19 0.00 0.00 3.46
1169 2455 7.840931 AGTATTATCATATGCATCGAAGGTGA 58.159 34.615 0.19 0.00 0.00 4.02
1171 2457 2.759191 TCATATGCATCGAAGGTGAGC 58.241 47.619 0.19 0.00 0.00 4.26
1173 2459 2.988010 TATGCATCGAAGGTGAGCTT 57.012 45.000 0.19 0.00 0.00 3.74
1174 2460 2.119801 ATGCATCGAAGGTGAGCTTT 57.880 45.000 0.00 0.00 0.00 3.51
1175 2461 1.159285 TGCATCGAAGGTGAGCTTTG 58.841 50.000 5.28 5.28 0.00 2.77
1176 2462 1.270785 TGCATCGAAGGTGAGCTTTGA 60.271 47.619 15.89 15.89 0.00 2.69
1177 2463 1.806542 GCATCGAAGGTGAGCTTTGAA 59.193 47.619 17.29 2.90 0.00 2.69
1179 2465 2.169832 TCGAAGGTGAGCTTTGAAGG 57.830 50.000 11.65 0.00 0.00 3.46
1181 2467 1.532868 CGAAGGTGAGCTTTGAAGGTG 59.467 52.381 5.73 0.00 36.78 4.00
1182 2468 2.806745 CGAAGGTGAGCTTTGAAGGTGA 60.807 50.000 5.73 0.00 36.78 4.02
1183 2469 2.557920 AGGTGAGCTTTGAAGGTGAG 57.442 50.000 0.00 0.00 36.78 3.51
1185 2471 2.173569 AGGTGAGCTTTGAAGGTGAGTT 59.826 45.455 0.00 0.00 36.78 3.01
1186 2472 2.550180 GGTGAGCTTTGAAGGTGAGTTC 59.450 50.000 0.00 0.00 36.78 3.01
1188 2474 3.002759 GTGAGCTTTGAAGGTGAGTTCAC 59.997 47.826 3.67 3.67 41.86 3.18
1206 2492 7.042797 AGTTCACAATTATTACCATCATGGC 57.957 36.000 2.52 0.00 42.67 4.40
1222 2516 1.007387 GGCTGGTTTGTTTCCGCTG 60.007 57.895 0.00 0.00 0.00 5.18
1224 2518 1.007387 CTGGTTTGTTTCCGCTGGC 60.007 57.895 0.00 0.00 0.00 4.85
1238 2532 1.613925 CGCTGGCTAGGAATGTAGCTA 59.386 52.381 0.00 0.00 44.27 3.32
1242 2536 2.894126 TGGCTAGGAATGTAGCTAGAGC 59.106 50.000 0.00 0.00 44.27 4.09
1243 2537 2.894126 GGCTAGGAATGTAGCTAGAGCA 59.106 50.000 4.01 0.00 44.27 4.26
1278 2572 9.476202 GTTTATTGCTTCTTTTGTCAAACCTAT 57.524 29.630 0.00 0.00 0.00 2.57
1284 2578 6.431198 TTCTTTTGTCAAACCTATATCCGC 57.569 37.500 0.00 0.00 0.00 5.54
1285 2579 4.569162 TCTTTTGTCAAACCTATATCCGCG 59.431 41.667 0.00 0.00 0.00 6.46
1289 2591 1.684450 TCAAACCTATATCCGCGCTCA 59.316 47.619 5.56 0.00 0.00 4.26
1428 2730 2.552155 GGCTACAACCACAACATCTCCA 60.552 50.000 0.00 0.00 0.00 3.86
1445 2747 2.035312 ACCGAGTACGTGAGGCCT 59.965 61.111 3.86 3.86 37.88 5.19
1465 2767 1.202927 TCAGCCCCAACTCTCCAAAAG 60.203 52.381 0.00 0.00 0.00 2.27
1616 2918 2.560542 CCCCATCTTCGATCTCTACCTG 59.439 54.545 0.00 0.00 0.00 4.00
1653 2955 2.035632 GGAGGGTGAACATCTCGAGAT 58.964 52.381 22.32 22.32 34.56 2.75
1857 3159 4.072088 GCGACACGGGCAACTTCG 62.072 66.667 0.00 0.00 0.00 3.79
1869 3171 1.940613 GCAACTTCGCCATTAGGTAGG 59.059 52.381 0.00 0.00 37.19 3.18
1882 3184 5.307196 CCATTAGGTAGGCATACTTACTGGT 59.693 44.000 21.45 0.51 38.47 4.00
1884 3186 7.309867 CCATTAGGTAGGCATACTTACTGGTAG 60.310 44.444 21.45 4.49 38.47 3.18
1885 3187 4.481072 AGGTAGGCATACTTACTGGTAGG 58.519 47.826 8.63 0.00 32.12 3.18
1896 3273 3.329889 TGGTAGGCCTGGGTGCAG 61.330 66.667 17.99 0.00 35.27 4.41
2012 3572 0.036732 TGTGGCTGGACATCTCAACC 59.963 55.000 0.00 0.00 0.00 3.77
2253 3817 7.691993 ACAGTTACACTATAATCCCTCCATT 57.308 36.000 0.00 0.00 0.00 3.16
2254 3818 8.102484 ACAGTTACACTATAATCCCTCCATTT 57.898 34.615 0.00 0.00 0.00 2.32
2255 3819 8.211629 ACAGTTACACTATAATCCCTCCATTTC 58.788 37.037 0.00 0.00 0.00 2.17
2256 3820 8.210946 CAGTTACACTATAATCCCTCCATTTCA 58.789 37.037 0.00 0.00 0.00 2.69
2257 3821 8.778059 AGTTACACTATAATCCCTCCATTTCAA 58.222 33.333 0.00 0.00 0.00 2.69
2258 3822 9.403583 GTTACACTATAATCCCTCCATTTCAAA 57.596 33.333 0.00 0.00 0.00 2.69
2259 3823 9.983024 TTACACTATAATCCCTCCATTTCAAAA 57.017 29.630 0.00 0.00 0.00 2.44
2308 3872 8.792830 ACTACAATTACACTATAATCCCTCCA 57.207 34.615 0.00 0.00 0.00 3.86
2309 3873 9.393786 ACTACAATTACACTATAATCCCTCCAT 57.606 33.333 0.00 0.00 0.00 3.41
2357 3921 7.341446 CTTTTTCAAAAGTCAAACACGTGTTT 58.659 30.769 34.83 34.83 42.66 2.83
2526 4106 6.873076 TCATAAATTTGACTTGCATGGAAACC 59.127 34.615 0.00 0.00 0.00 3.27
2573 4153 6.683537 TGAGGGAGGATAAACTAATGAGAGA 58.316 40.000 0.00 0.00 0.00 3.10
2627 4211 2.188994 GCCGAGCTGCAGATCCTT 59.811 61.111 25.34 0.61 0.00 3.36
2725 4315 1.226018 GCGACGCCTTGTACAATGC 60.226 57.895 21.75 21.75 0.00 3.56
2775 4365 1.339920 ACATCACCATGATCGCCACAA 60.340 47.619 0.00 0.00 34.28 3.33
2776 4366 1.744522 CATCACCATGATCGCCACAAA 59.255 47.619 0.00 0.00 34.28 2.83
2777 4367 1.902938 TCACCATGATCGCCACAAAA 58.097 45.000 0.00 0.00 0.00 2.44
2810 4400 1.705337 CGCCGATCATCAACGCCTTT 61.705 55.000 0.00 0.00 0.00 3.11
2823 4413 3.695830 ACGCCTTTGAGTATTTCTCCA 57.304 42.857 0.00 0.00 42.12 3.86
2843 4433 2.941453 TCATCTCTACAGCCAACGTC 57.059 50.000 0.00 0.00 0.00 4.34
2873 4463 5.567623 CGACCCTCAGGATGGTAAATATCTG 60.568 48.000 0.00 0.00 34.20 2.90
2900 4564 9.204570 CGGGTCCTTATTAAGTTTCACATATAG 57.795 37.037 2.88 0.00 0.00 1.31
2981 4737 5.929058 TGATCTCTGATTACTGCACTTCT 57.071 39.130 0.00 0.00 0.00 2.85
2982 4738 6.291648 TGATCTCTGATTACTGCACTTCTT 57.708 37.500 0.00 0.00 0.00 2.52
2983 4739 7.410120 TGATCTCTGATTACTGCACTTCTTA 57.590 36.000 0.00 0.00 0.00 2.10
2984 4740 7.840931 TGATCTCTGATTACTGCACTTCTTAA 58.159 34.615 0.00 0.00 0.00 1.85
3013 4770 2.096174 TGTGTGTTACTGTCGGCAAAAC 59.904 45.455 7.72 7.72 0.00 2.43
3018 4775 4.621886 GTGTTACTGTCGGCAAAACAAAAA 59.378 37.500 16.50 0.00 34.46 1.94
3044 4801 0.109179 TGCCATCAACGCAATCAAGC 60.109 50.000 0.00 0.00 32.05 4.01
3048 4805 3.688272 CCATCAACGCAATCAAGCTTAG 58.312 45.455 0.00 0.00 0.00 2.18
3199 4956 1.468054 GCGACCATGCACAAGAAATCC 60.468 52.381 0.00 0.00 34.15 3.01
3202 4959 3.119388 CGACCATGCACAAGAAATCCATT 60.119 43.478 0.00 0.00 0.00 3.16
3221 4978 5.011840 TCCATTCAAAATGAGGAAATGCACA 59.988 36.000 0.00 0.00 0.00 4.57
3248 5013 2.092681 CGTCTGAACCATTGTGTGATCG 59.907 50.000 0.00 0.00 0.00 3.69
3271 5040 2.158957 ACAGAAATATGTCATCGGGCGT 60.159 45.455 0.00 0.00 0.00 5.68
3506 5282 7.908082 TGTTGTAAGCGACTTTGAATTATATGC 59.092 33.333 0.00 0.00 0.00 3.14
3528 5304 7.946655 TGCCGTCTTTGATAACTAATATCTG 57.053 36.000 0.00 0.00 40.96 2.90
3558 5355 4.575645 ACCAATGTTTTGATGCCAACTTTG 59.424 37.500 0.00 0.00 37.59 2.77
3560 5357 5.066246 CCAATGTTTTGATGCCAACTTTGTT 59.934 36.000 8.82 0.00 36.78 2.83
3641 5438 1.066573 AGAGAAGTCAAGATGGCACCG 60.067 52.381 0.00 0.00 0.00 4.94
3812 5611 1.410153 ACTCTTGCCAGCCAACAAAAG 59.590 47.619 0.00 0.00 0.00 2.27
4075 5893 0.470341 TGGACAACCACCGATTCACA 59.530 50.000 0.00 0.00 41.77 3.58
4113 5931 5.992217 AGACCATAACAGACAACTTCAAGAC 59.008 40.000 0.00 0.00 0.00 3.01
4189 6007 3.290948 ACCCAAGTTGCAGTCAAGTTA 57.709 42.857 0.00 0.00 42.31 2.24
4252 6070 9.653287 TTGACAGAGGTAAAGTATTATCAACTG 57.347 33.333 0.00 0.00 36.16 3.16
4275 6093 1.858091 CCAGAGCATGGTGTATCGAC 58.142 55.000 0.00 0.00 44.91 4.20
4276 6094 1.136891 CCAGAGCATGGTGTATCGACA 59.863 52.381 0.00 0.00 44.91 4.35
4277 6095 2.224137 CCAGAGCATGGTGTATCGACAT 60.224 50.000 0.00 0.00 44.91 3.06
4278 6096 3.005791 CCAGAGCATGGTGTATCGACATA 59.994 47.826 0.00 0.00 44.91 2.29
4279 6097 4.322273 CCAGAGCATGGTGTATCGACATAT 60.322 45.833 0.00 0.00 44.91 1.78
4280 6098 5.233225 CAGAGCATGGTGTATCGACATATT 58.767 41.667 0.00 0.00 38.04 1.28
4281 6099 6.389906 CAGAGCATGGTGTATCGACATATTA 58.610 40.000 0.00 0.00 38.04 0.98
4282 6100 6.529477 CAGAGCATGGTGTATCGACATATTAG 59.471 42.308 0.00 0.00 38.04 1.73
4283 6101 6.209589 AGAGCATGGTGTATCGACATATTAGT 59.790 38.462 0.00 0.00 38.04 2.24
4284 6102 7.393515 AGAGCATGGTGTATCGACATATTAGTA 59.606 37.037 0.00 0.00 38.04 1.82
4285 6103 7.892609 AGCATGGTGTATCGACATATTAGTAA 58.107 34.615 0.00 0.00 38.04 2.24
4286 6104 8.364894 AGCATGGTGTATCGACATATTAGTAAA 58.635 33.333 0.00 0.00 38.04 2.01
4287 6105 8.984764 GCATGGTGTATCGACATATTAGTAAAA 58.015 33.333 0.00 0.00 38.04 1.52
4403 6221 7.254252 CGAAGATCCATCACAAGAATCTTGTAC 60.254 40.741 25.96 12.32 0.00 2.90
4438 6256 9.474313 GGTTATTGCAAGGATGGGATATATTTA 57.526 33.333 4.94 0.00 0.00 1.40
4491 6309 9.707957 AGGAAATCTAGAAGATAAACTCAGAGA 57.292 33.333 3.79 0.00 32.89 3.10
4559 6406 6.638063 TCATGTTACACACTACTAACGTCAAC 59.362 38.462 0.00 0.00 0.00 3.18
4635 6482 1.206849 TCTGCATCGCACTACAATCCA 59.793 47.619 0.00 0.00 33.79 3.41
4655 6535 9.173021 CAATCCACACAAGGTATACTTTAATCA 57.827 33.333 2.25 0.00 37.29 2.57
4665 6545 9.740710 AAGGTATACTTTAATCAGGATTATGGC 57.259 33.333 2.25 0.00 35.35 4.40
4795 6677 3.677527 GCACAAGTCATGCAGCCT 58.322 55.556 0.00 0.00 42.88 4.58
4804 6686 2.182842 CATGCAGCCTACCCTTCGC 61.183 63.158 0.00 0.00 0.00 4.70
4862 6744 8.415950 TGAATAAAAATCTTGAGGCCAAAGTA 57.584 30.769 5.01 0.00 0.00 2.24
4936 6818 3.443045 GGTGCGGGTGATTGGCAG 61.443 66.667 0.00 0.00 37.36 4.85
5161 7046 1.881973 AGCTTCGGTGTCGTGTTACTA 59.118 47.619 0.00 0.00 37.69 1.82
5260 7145 0.745845 CGGGAGGCAACATTGAGGAG 60.746 60.000 0.00 0.00 41.41 3.69
5412 7297 1.919240 TACTGCCTCGAGTTGGAGAA 58.081 50.000 15.24 0.00 36.08 2.87
5432 7317 2.069273 ACGAAGATCAAAACAGAGGCG 58.931 47.619 0.00 0.00 0.00 5.52
5455 7340 6.018262 GCGATGCTAACAATAACTTCCACATA 60.018 38.462 0.00 0.00 0.00 2.29
5553 7438 0.965363 CTTGTTGGTAGGGCGCCAAT 60.965 55.000 30.85 19.07 46.25 3.16
5596 7481 3.124466 TCTTGGTGCGTGATAAACATTCG 59.876 43.478 0.00 0.00 0.00 3.34
5650 7535 7.899648 TTAATCCCAAACTTGTTCTTTGGTA 57.100 32.000 8.68 0.00 44.33 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 8.918202 TGTATTCTTTTGGTTGAGATGTTACT 57.082 30.769 0.00 0.00 0.00 2.24
48 49 9.559958 CATGTATTCTTTTGGTTGAGATGTTAC 57.440 33.333 0.00 0.00 0.00 2.50
90 91 9.956720 GCTCTTGTATATACAGCAATCAAAATT 57.043 29.630 14.96 0.00 37.52 1.82
144 145 3.989817 GCTCTTTGTTGGTTATTGCAAGG 59.010 43.478 4.94 0.00 0.00 3.61
217 218 1.264295 ACTGTTTACTCCGGAGTCCC 58.736 55.000 39.49 26.49 42.54 4.46
233 234 1.822990 TCAGCTCTTACGGGGTAACTG 59.177 52.381 0.00 0.00 0.00 3.16
234 235 2.226962 TCAGCTCTTACGGGGTAACT 57.773 50.000 0.00 0.00 0.00 2.24
235 236 3.538634 AATCAGCTCTTACGGGGTAAC 57.461 47.619 0.00 0.00 0.00 2.50
306 315 3.867857 TGCTTGAGACACACAACAAGTA 58.132 40.909 0.00 0.00 40.88 2.24
390 814 1.818674 CCTAACCATTCAACCACAGGC 59.181 52.381 0.00 0.00 0.00 4.85
394 818 3.244770 TGTCCTCCTAACCATTCAACCAC 60.245 47.826 0.00 0.00 0.00 4.16
401 825 2.632537 ACCACTGTCCTCCTAACCATT 58.367 47.619 0.00 0.00 0.00 3.16
422 846 0.552848 AACCCTGATGGATTGGCGAT 59.447 50.000 0.00 0.00 38.00 4.58
424 848 0.394216 TGAACCCTGATGGATTGGCG 60.394 55.000 0.00 0.00 38.00 5.69
425 849 1.753073 CTTGAACCCTGATGGATTGGC 59.247 52.381 0.00 0.00 38.00 4.52
429 853 5.032846 TCTAAGACTTGAACCCTGATGGAT 58.967 41.667 0.00 0.00 38.00 3.41
433 857 6.784031 ACAAATCTAAGACTTGAACCCTGAT 58.216 36.000 0.00 0.00 0.00 2.90
434 858 6.183361 TGACAAATCTAAGACTTGAACCCTGA 60.183 38.462 0.00 0.00 0.00 3.86
435 859 5.997746 TGACAAATCTAAGACTTGAACCCTG 59.002 40.000 0.00 0.00 0.00 4.45
436 860 6.187727 TGACAAATCTAAGACTTGAACCCT 57.812 37.500 0.00 0.00 0.00 4.34
478 912 4.843728 TCAGAAGCCTGAAATAAATCCGT 58.156 39.130 0.00 0.00 45.74 4.69
490 924 2.486472 ATGAACACCTCAGAAGCCTG 57.514 50.000 0.00 0.00 37.52 4.85
497 931 6.098409 ACACCCTATACTTATGAACACCTCAG 59.902 42.308 0.00 0.00 37.52 3.35
505 939 6.385759 ACACATGGACACCCTATACTTATGAA 59.614 38.462 0.00 0.00 0.00 2.57
511 945 2.170607 GCACACATGGACACCCTATACT 59.829 50.000 0.00 0.00 0.00 2.12
513 947 2.192263 TGCACACATGGACACCCTATA 58.808 47.619 0.00 0.00 0.00 1.31
522 956 2.509131 TCCCTATGAATGCACACATGGA 59.491 45.455 16.01 12.26 36.36 3.41
523 957 2.934887 TCCCTATGAATGCACACATGG 58.065 47.619 14.98 12.46 36.36 3.66
526 960 3.200605 ACTCATCCCTATGAATGCACACA 59.799 43.478 0.00 0.00 41.57 3.72
527 961 3.562973 CACTCATCCCTATGAATGCACAC 59.437 47.826 0.00 0.00 41.57 3.82
528 962 3.200605 ACACTCATCCCTATGAATGCACA 59.799 43.478 0.00 0.00 41.91 4.57
529 963 3.813443 ACACTCATCCCTATGAATGCAC 58.187 45.455 0.00 0.00 41.91 4.57
534 968 8.107399 CGTAAGTATACACTCATCCCTATGAA 57.893 38.462 5.50 0.00 35.57 2.57
557 991 5.348986 ACAATCAAAGTCGCTCATATACGT 58.651 37.500 0.00 0.00 0.00 3.57
558 992 5.890110 ACAATCAAAGTCGCTCATATACG 57.110 39.130 0.00 0.00 0.00 3.06
563 997 4.389992 CACAGTACAATCAAAGTCGCTCAT 59.610 41.667 0.00 0.00 0.00 2.90
567 1001 4.468095 AACACAGTACAATCAAAGTCGC 57.532 40.909 0.00 0.00 0.00 5.19
568 1002 8.829514 TTTTTAACACAGTACAATCAAAGTCG 57.170 30.769 0.00 0.00 0.00 4.18
591 1025 4.389077 GCTGAGACACGCTATGTAGTTTTT 59.611 41.667 0.00 0.00 43.56 1.94
592 1026 3.927142 GCTGAGACACGCTATGTAGTTTT 59.073 43.478 0.00 0.00 43.56 2.43
593 1027 3.193691 AGCTGAGACACGCTATGTAGTTT 59.806 43.478 0.00 0.00 43.56 2.66
594 1028 2.755655 AGCTGAGACACGCTATGTAGTT 59.244 45.455 0.00 0.00 43.56 2.24
595 1029 2.370349 AGCTGAGACACGCTATGTAGT 58.630 47.619 0.00 0.00 43.56 2.73
596 1030 3.312697 TGTAGCTGAGACACGCTATGTAG 59.687 47.826 0.00 0.00 43.56 2.74
597 1031 3.275999 TGTAGCTGAGACACGCTATGTA 58.724 45.455 0.00 0.00 43.56 2.29
598 1032 7.497071 GCTATGTAGCTGAGACACGCTATGT 62.497 48.000 0.00 0.00 44.82 2.29
599 1033 2.851805 TGTAGCTGAGACACGCTATG 57.148 50.000 0.00 0.00 40.47 2.23
600 1034 3.057876 GCTATGTAGCTGAGACACGCTAT 60.058 47.826 0.00 0.00 45.62 2.97
601 1035 2.290916 GCTATGTAGCTGAGACACGCTA 59.709 50.000 0.00 0.00 45.62 4.26
602 1036 1.066303 GCTATGTAGCTGAGACACGCT 59.934 52.381 0.00 0.00 45.62 5.07
603 1037 1.482278 GCTATGTAGCTGAGACACGC 58.518 55.000 0.00 0.00 45.62 5.34
604 1038 1.064208 ACGCTATGTAGCTGAGACACG 59.936 52.381 10.05 0.00 46.85 4.49
605 1039 2.853731 ACGCTATGTAGCTGAGACAC 57.146 50.000 10.05 0.00 46.85 3.67
606 1040 3.056821 ACAAACGCTATGTAGCTGAGACA 60.057 43.478 10.05 0.00 46.85 3.41
607 1041 3.512680 ACAAACGCTATGTAGCTGAGAC 58.487 45.455 10.05 0.00 46.85 3.36
608 1042 3.192633 TGACAAACGCTATGTAGCTGAGA 59.807 43.478 10.05 0.00 46.85 3.27
609 1043 3.511699 TGACAAACGCTATGTAGCTGAG 58.488 45.455 10.05 0.00 46.85 3.35
610 1044 3.586100 TGACAAACGCTATGTAGCTGA 57.414 42.857 10.05 0.00 46.85 4.26
611 1045 3.679980 ACTTGACAAACGCTATGTAGCTG 59.320 43.478 10.05 4.70 46.85 4.24
612 1046 3.679980 CACTTGACAAACGCTATGTAGCT 59.320 43.478 10.05 0.00 46.85 3.32
613 1047 3.725010 GCACTTGACAAACGCTATGTAGC 60.725 47.826 1.92 1.92 45.62 3.58
614 1048 3.431912 TGCACTTGACAAACGCTATGTAG 59.568 43.478 9.25 0.00 0.00 2.74
615 1049 3.394719 TGCACTTGACAAACGCTATGTA 58.605 40.909 9.25 0.00 0.00 2.29
616 1050 2.217750 TGCACTTGACAAACGCTATGT 58.782 42.857 9.25 0.00 0.00 2.29
617 1051 2.967459 TGCACTTGACAAACGCTATG 57.033 45.000 9.25 0.00 0.00 2.23
618 1052 2.094258 CGATGCACTTGACAAACGCTAT 59.906 45.455 9.25 3.02 0.00 2.97
619 1053 1.459209 CGATGCACTTGACAAACGCTA 59.541 47.619 9.25 0.00 0.00 4.26
620 1054 0.235665 CGATGCACTTGACAAACGCT 59.764 50.000 9.25 0.00 0.00 5.07
621 1055 0.041312 ACGATGCACTTGACAAACGC 60.041 50.000 0.00 2.29 0.00 4.84
622 1056 2.383298 AACGATGCACTTGACAAACG 57.617 45.000 0.00 0.00 0.00 3.60
748 2019 3.055719 GCCGCTGGTTGCAAGCTA 61.056 61.111 27.31 13.95 43.06 3.32
750 2021 4.712425 CTGCCGCTGGTTGCAAGC 62.712 66.667 21.51 21.51 43.06 4.01
820 2091 3.076621 TCTTCTAGTTTGGCGACGACTA 58.923 45.455 0.65 4.49 32.46 2.59
890 2163 2.256117 AAGCTTAGGTTCACACGCTT 57.744 45.000 0.00 0.00 33.32 4.68
891 2164 3.326747 CTTAAGCTTAGGTTCACACGCT 58.673 45.455 6.24 0.00 0.00 5.07
892 2165 2.415512 CCTTAAGCTTAGGTTCACACGC 59.584 50.000 13.90 0.00 0.00 5.34
893 2166 2.415512 GCCTTAAGCTTAGGTTCACACG 59.584 50.000 13.90 0.00 38.99 4.49
972 2254 2.779506 ACCCAGCAACAAGTAACTAGC 58.220 47.619 0.00 0.00 0.00 3.42
977 2259 2.028130 CACCAACCCAGCAACAAGTAA 58.972 47.619 0.00 0.00 0.00 2.24
983 2265 2.209315 ATGCCACCAACCCAGCAAC 61.209 57.895 0.00 0.00 38.99 4.17
985 2267 2.601067 CATGCCACCAACCCAGCA 60.601 61.111 0.00 0.00 40.00 4.41
986 2268 2.601367 ACATGCCACCAACCCAGC 60.601 61.111 0.00 0.00 0.00 4.85
987 2269 2.934570 GCACATGCCACCAACCCAG 61.935 63.158 0.00 0.00 34.31 4.45
988 2270 2.916703 GCACATGCCACCAACCCA 60.917 61.111 0.00 0.00 34.31 4.51
1011 2297 1.826921 TCGCCGGTCCATCCTACTC 60.827 63.158 1.90 0.00 0.00 2.59
1032 2318 3.195698 GACGAACGGGCAGCCATC 61.196 66.667 15.19 7.41 0.00 3.51
1085 2371 3.849953 CTTGAAGTACGCCGCCGC 61.850 66.667 0.00 0.00 38.22 6.53
1088 2374 1.414897 CGAACTTGAAGTACGCCGC 59.585 57.895 0.00 0.00 0.00 6.53
1142 2428 8.598924 CACCTTCGATGCATATGATAATACTTC 58.401 37.037 6.97 0.00 0.00 3.01
1161 2447 1.532868 CACCTTCAAAGCTCACCTTCG 59.467 52.381 0.00 0.00 31.99 3.79
1162 2448 2.810852 CTCACCTTCAAAGCTCACCTTC 59.189 50.000 0.00 0.00 31.99 3.46
1163 2449 2.173569 ACTCACCTTCAAAGCTCACCTT 59.826 45.455 0.00 0.00 34.51 3.50
1164 2450 1.771255 ACTCACCTTCAAAGCTCACCT 59.229 47.619 0.00 0.00 0.00 4.00
1165 2451 2.262423 ACTCACCTTCAAAGCTCACC 57.738 50.000 0.00 0.00 0.00 4.02
1166 2452 3.002759 GTGAACTCACCTTCAAAGCTCAC 59.997 47.826 0.00 0.00 40.85 3.51
1169 2455 3.281727 TGTGAACTCACCTTCAAAGCT 57.718 42.857 7.37 0.00 45.88 3.74
1171 2457 9.612620 GTAATAATTGTGAACTCACCTTCAAAG 57.387 33.333 7.37 0.00 45.88 2.77
1173 2459 7.721842 TGGTAATAATTGTGAACTCACCTTCAA 59.278 33.333 7.37 0.00 45.88 2.69
1174 2460 7.227873 TGGTAATAATTGTGAACTCACCTTCA 58.772 34.615 7.37 0.00 45.88 3.02
1175 2461 7.681939 TGGTAATAATTGTGAACTCACCTTC 57.318 36.000 7.37 0.00 45.88 3.46
1176 2462 7.888021 TGATGGTAATAATTGTGAACTCACCTT 59.112 33.333 7.37 4.19 45.88 3.50
1177 2463 7.402054 TGATGGTAATAATTGTGAACTCACCT 58.598 34.615 7.37 0.00 45.88 4.00
1179 2465 8.131100 CCATGATGGTAATAATTGTGAACTCAC 58.869 37.037 2.54 2.78 38.88 3.51
1181 2467 7.013655 AGCCATGATGGTAATAATTGTGAACTC 59.986 37.037 13.84 0.00 40.46 3.01
1182 2468 6.835488 AGCCATGATGGTAATAATTGTGAACT 59.165 34.615 13.84 0.00 40.46 3.01
1183 2469 6.919662 CAGCCATGATGGTAATAATTGTGAAC 59.080 38.462 13.84 0.00 40.46 3.18
1185 2471 5.535783 CCAGCCATGATGGTAATAATTGTGA 59.464 40.000 13.84 0.00 40.46 3.58
1186 2472 5.775686 CCAGCCATGATGGTAATAATTGTG 58.224 41.667 13.84 0.00 40.46 3.33
1206 2492 1.007387 GCCAGCGGAAACAAACCAG 60.007 57.895 0.00 0.00 0.00 4.00
1222 2516 2.894126 TGCTCTAGCTACATTCCTAGCC 59.106 50.000 3.26 0.00 40.18 3.93
1224 2518 3.566322 ACGTGCTCTAGCTACATTCCTAG 59.434 47.826 3.26 0.00 42.66 3.02
1278 2572 3.272766 CTCAATGTGAGCGCGGATA 57.727 52.632 8.83 0.00 37.72 2.59
1338 2640 4.713824 TGTTCACGTAGCTACTATGCTT 57.286 40.909 21.20 0.00 43.74 3.91
1346 2648 0.314618 TGCGGTTGTTCACGTAGCTA 59.685 50.000 0.00 0.00 0.00 3.32
1428 2730 2.035312 AGGCCTCACGTACTCGGT 59.965 61.111 0.00 0.00 41.85 4.69
1445 2747 0.850100 TTTTGGAGAGTTGGGGCTGA 59.150 50.000 0.00 0.00 0.00 4.26
1454 2756 3.555168 CGTTGAGGTAGCTTTTGGAGAGT 60.555 47.826 0.00 0.00 0.00 3.24
1465 2767 1.805945 CTGCGGACGTTGAGGTAGC 60.806 63.158 0.00 0.00 0.00 3.58
1616 2918 1.104577 TCCACCAAAAGTTGACGCCC 61.105 55.000 0.00 0.00 0.00 6.13
1686 2988 2.194212 CCGAGTCGTCCGGGATCAT 61.194 63.158 12.31 0.00 43.05 2.45
1857 3159 8.154081 ACCAGTAAGTATGCCTACCTAATGGC 62.154 46.154 18.46 0.00 40.94 4.40
1868 3170 2.545537 GGCCTACCAGTAAGTATGCC 57.454 55.000 0.00 2.87 43.68 4.40
1869 3171 2.224305 CCAGGCCTACCAGTAAGTATGC 60.224 54.545 3.98 0.00 39.06 3.14
1875 3177 1.559065 GCACCCAGGCCTACCAGTAA 61.559 60.000 3.98 0.00 39.06 2.24
1876 3178 1.993391 GCACCCAGGCCTACCAGTA 60.993 63.158 3.98 0.00 39.06 2.74
1877 3179 3.330720 GCACCCAGGCCTACCAGT 61.331 66.667 3.98 0.00 39.06 4.00
1878 3180 3.329889 TGCACCCAGGCCTACCAG 61.330 66.667 3.98 0.00 39.06 4.00
1880 3182 3.009115 TCTGCACCCAGGCCTACC 61.009 66.667 3.98 0.00 39.61 3.18
1882 3184 1.229496 TTCTCTGCACCCAGGCCTA 60.229 57.895 3.98 0.00 39.61 3.93
1884 3186 2.360475 GTTCTCTGCACCCAGGCC 60.360 66.667 0.00 0.00 39.61 5.19
1885 3187 1.673665 CAGTTCTCTGCACCCAGGC 60.674 63.158 0.00 0.00 39.61 4.85
1910 3287 3.188460 CAGAACACGTTAGGACCAAATGG 59.812 47.826 0.00 0.00 42.17 3.16
2012 3572 4.566426 ATTCTCTTGGACCTTCTCCTTG 57.434 45.455 0.00 0.00 40.26 3.61
2081 3641 1.173444 AGTCGTTGAGCTCCGTGACT 61.173 55.000 20.04 20.04 32.19 3.41
2089 3649 1.587933 GGACTCGGAGTCGTTGAGCT 61.588 60.000 26.86 0.00 45.96 4.09
2283 3847 8.792830 TGGAGGGATTATAGTGTAATTGTAGT 57.207 34.615 0.00 0.00 0.00 2.73
2286 3850 9.574516 GAAATGGAGGGATTATAGTGTAATTGT 57.425 33.333 0.00 0.00 0.00 2.71
2287 3851 9.573166 TGAAATGGAGGGATTATAGTGTAATTG 57.427 33.333 0.00 0.00 0.00 2.32
2299 3863 8.927411 CACCTTATATTTTGAAATGGAGGGATT 58.073 33.333 13.91 0.00 32.26 3.01
2300 3864 8.067488 ACACCTTATATTTTGAAATGGAGGGAT 58.933 33.333 13.91 4.70 32.26 3.85
2301 3865 7.418378 ACACCTTATATTTTGAAATGGAGGGA 58.582 34.615 13.91 0.00 32.26 4.20
2302 3866 7.660030 ACACCTTATATTTTGAAATGGAGGG 57.340 36.000 13.91 8.25 32.26 4.30
2332 3896 6.872608 AACACGTGTTTGACTTTTGAAAAAG 58.127 32.000 27.70 12.82 42.06 2.27
2351 3915 3.757745 AAACTTGGTCAGACAAACACG 57.242 42.857 2.17 0.00 0.00 4.49
2496 4076 8.095792 TCCATGCAAGTCAAATTTATGAATGTT 58.904 29.630 0.00 0.00 0.00 2.71
2506 4086 4.686191 TGGTTTCCATGCAAGTCAAATT 57.314 36.364 0.00 0.00 0.00 1.82
2511 4091 4.782019 TGTATTGGTTTCCATGCAAGTC 57.218 40.909 0.00 0.00 31.53 3.01
2544 4124 8.337118 TCATTAGTTTATCCTCCCTCAATCTT 57.663 34.615 0.00 0.00 0.00 2.40
2545 4125 7.791766 TCTCATTAGTTTATCCTCCCTCAATCT 59.208 37.037 0.00 0.00 0.00 2.40
2546 4126 7.967908 TCTCATTAGTTTATCCTCCCTCAATC 58.032 38.462 0.00 0.00 0.00 2.67
2557 4137 7.228308 AGCAGGCATTTCTCTCATTAGTTTATC 59.772 37.037 0.00 0.00 0.00 1.75
2573 4153 4.037208 GCAACACATCTATAGCAGGCATTT 59.963 41.667 0.00 0.00 0.00 2.32
2717 4307 1.904287 TGTGGGGTTCAGCATTGTAC 58.096 50.000 0.00 0.00 0.00 2.90
2725 4315 2.270352 TAAGCACTTGTGGGGTTCAG 57.730 50.000 2.81 0.00 0.00 3.02
2775 4365 0.102300 GGCGGCAGTGTTGAGTTTTT 59.898 50.000 3.07 0.00 0.00 1.94
2776 4366 1.733526 GGCGGCAGTGTTGAGTTTT 59.266 52.632 3.07 0.00 0.00 2.43
2777 4367 2.542907 CGGCGGCAGTGTTGAGTTT 61.543 57.895 10.53 0.00 0.00 2.66
2783 4373 1.815421 GATGATCGGCGGCAGTGTT 60.815 57.895 10.53 0.00 0.00 3.32
2810 4400 7.255766 GCTGTAGAGATGATGGAGAAATACTCA 60.256 40.741 0.00 0.00 46.54 3.41
2823 4413 2.223595 CGACGTTGGCTGTAGAGATGAT 60.224 50.000 0.00 0.00 0.00 2.45
2854 4444 4.248859 CCGCAGATATTTACCATCCTGAG 58.751 47.826 0.00 0.00 0.00 3.35
2873 4463 4.004982 TGTGAAACTTAATAAGGACCCGC 58.995 43.478 4.92 0.00 38.04 6.13
2900 4564 5.163281 ACCAGCATAGATGATTGATCTCC 57.837 43.478 0.00 0.00 40.88 3.71
2981 4737 7.403421 CGACAGTAACACACAAGACAAATTAA 58.597 34.615 0.00 0.00 0.00 1.40
2982 4738 6.018588 CCGACAGTAACACACAAGACAAATTA 60.019 38.462 0.00 0.00 0.00 1.40
2983 4739 5.220777 CCGACAGTAACACACAAGACAAATT 60.221 40.000 0.00 0.00 0.00 1.82
2984 4740 4.272504 CCGACAGTAACACACAAGACAAAT 59.727 41.667 0.00 0.00 0.00 2.32
3018 4775 1.317613 TGCGTTGATGGCAGAAACTT 58.682 45.000 11.79 0.00 35.04 2.66
3019 4776 1.317613 TTGCGTTGATGGCAGAAACT 58.682 45.000 11.79 0.00 42.12 2.66
3044 4801 8.844244 CCAATTCCTTTTCATCTGATACCTAAG 58.156 37.037 0.00 0.00 0.00 2.18
3048 4805 7.255730 CCATCCAATTCCTTTTCATCTGATACC 60.256 40.741 0.00 0.00 0.00 2.73
3199 4956 5.697178 TGTGTGCATTTCCTCATTTTGAATG 59.303 36.000 0.00 0.00 0.00 2.67
3202 4959 4.933505 TGTGTGCATTTCCTCATTTTGA 57.066 36.364 0.00 0.00 0.00 2.69
3221 4978 2.807967 CACAATGGTTCAGACGACATGT 59.192 45.455 0.00 0.00 0.00 3.21
3248 5013 3.428870 CGCCCGATGACATATTTCTGTAC 59.571 47.826 0.00 0.00 0.00 2.90
3271 5040 8.908786 ATAAGATGATATCTCGCCTTTCAAAA 57.091 30.769 3.98 0.00 39.08 2.44
3284 5053 8.923609 TGAGATCAGCGAAATAAGATGATATC 57.076 34.615 10.80 10.80 46.55 1.63
3343 5112 8.133627 CCTAGCAGAATTATTGTGAAAATGGAG 58.866 37.037 6.26 0.00 0.00 3.86
3362 5131 4.696479 ATGTGAACCTATTCCCTAGCAG 57.304 45.455 0.00 0.00 33.49 4.24
3558 5355 4.326826 TGTCAAATCTCTGGATGGACAAC 58.673 43.478 9.64 0.00 40.66 3.32
3560 5357 3.054875 CCTGTCAAATCTCTGGATGGACA 60.055 47.826 10.84 10.84 40.99 4.02
3812 5611 6.072119 ACGACAATCTTAGAATTGTTTTCCCC 60.072 38.462 9.93 0.02 46.99 4.81
4027 5845 1.601903 CGGTCTTGTTGTTTGCTGCTA 59.398 47.619 0.00 0.00 0.00 3.49
4075 5893 9.256228 TCTGTTATGGTCTCTAGTTCTTTGTAT 57.744 33.333 0.00 0.00 0.00 2.29
4113 5931 1.975407 CCTCCTTGGCCAAGCACTG 60.975 63.158 35.85 23.51 37.11 3.66
4189 6007 1.187087 GACTGGAGGATTGAGACCGT 58.813 55.000 0.00 0.00 0.00 4.83
4499 6317 5.279206 CCGTATGCTCTTCTTACAGATGGAT 60.279 44.000 0.00 0.00 34.33 3.41
4559 6406 5.969435 GTCGTTCTTTCCTGTAAAAGTTTGG 59.031 40.000 0.00 0.00 37.49 3.28
4655 6535 2.509964 ACGAAAGGAAGGCCATAATCCT 59.490 45.455 5.01 9.66 45.43 3.24
4665 6545 2.206750 TCGACAACAACGAAAGGAAGG 58.793 47.619 0.00 0.00 36.84 3.46
4795 6677 2.011741 ATCACGATGCGCGAAGGGTA 62.012 55.000 12.10 0.00 44.57 3.69
4804 6686 1.349234 TGTCTTCACATCACGATGCG 58.651 50.000 6.94 0.00 42.39 4.73
4862 6744 2.574006 TCATCAAGCCAAAGTCAGCT 57.426 45.000 0.00 0.00 42.40 4.24
5107 6992 3.638160 TCTTTTCATTCAGTTGCAAGGCT 59.362 39.130 0.00 0.00 0.00 4.58
5161 7046 2.572104 GGGTTGTCCTGTGATTACCTCT 59.428 50.000 0.00 0.00 31.20 3.69
5260 7145 4.404098 ATTCGGCCGTCCACCACC 62.404 66.667 27.15 0.00 0.00 4.61
5299 7184 3.965258 ACGGCCTTCCACATGCCA 61.965 61.111 0.00 0.00 45.63 4.92
5412 7297 2.069273 CGCCTCTGTTTTGATCTTCGT 58.931 47.619 0.00 0.00 0.00 3.85
5432 7317 9.669353 CATTATGTGGAAGTTATTGTTAGCATC 57.331 33.333 0.00 0.00 0.00 3.91
5455 7340 4.184629 GGTCACGACTGCTATCTTTCATT 58.815 43.478 0.00 0.00 0.00 2.57
5534 7419 1.602323 TTGGCGCCCTACCAACAAG 60.602 57.895 26.77 0.00 42.23 3.16
5666 7551 6.669125 TGAAGATGGGTCAAAATGAAACAT 57.331 33.333 0.00 0.00 30.75 2.71
5668 7553 5.801947 CGATGAAGATGGGTCAAAATGAAAC 59.198 40.000 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.