Multiple sequence alignment - TraesCS5B01G446400

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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 TraesCS5B01G446400 chr5B 100.000 8825 0 0 1 8825 617824121 617832945 0.000000e+00 16297.0
1 TraesCS5B01G446400 chr5A 92.542 5846 265 68 1 5783 622772737 622778474 0.000000e+00 8222.0
2 TraesCS5B01G446400 chr5A 92.563 3012 135 33 5836 8823 622778474 622781420 0.000000e+00 4239.0
3 TraesCS5B01G446400 chr5A 87.013 77 5 4 6505 6581 342045642 342045713 2.040000e-11 82.4
4 TraesCS5B01G446400 chr5D 89.496 2856 167 60 1 2781 498493154 498495951 0.000000e+00 3489.0
5 TraesCS5B01G446400 chr5D 91.484 1233 61 20 4546 5768 498497674 498498872 0.000000e+00 1655.0
6 TraesCS5B01G446400 chr5D 84.464 1017 93 30 6721 7711 498499476 498500453 0.000000e+00 942.0
7 TraesCS5B01G446400 chr5D 87.105 822 46 14 3194 3993 498496278 498497061 0.000000e+00 876.0
8 TraesCS5B01G446400 chr5D 92.762 525 30 6 8246 8767 498554607 498555126 0.000000e+00 752.0
9 TraesCS5B01G446400 chr5D 88.571 595 45 9 5889 6477 498498873 498499450 0.000000e+00 701.0
10 TraesCS5B01G446400 chr5D 84.274 744 62 21 3771 4487 65000735 65001450 0.000000e+00 675.0
11 TraesCS5B01G446400 chr5D 96.591 176 6 0 7372 7547 498550970 498551145 8.670000e-75 292.0
12 TraesCS5B01G446400 chr5D 96.753 154 5 0 5359 5512 65002299 65002452 3.160000e-64 257.0
13 TraesCS5B01G446400 chr5D 85.714 210 14 8 4546 4753 65001446 65001641 3.230000e-49 207.0
14 TraesCS5B01G446400 chr5D 93.846 65 4 0 3129 3193 267759290 267759354 2.030000e-16 99.0
15 TraesCS5B01G446400 chr5D 95.082 61 3 0 6970 7030 498548780 498548840 7.290000e-16 97.1
16 TraesCS5B01G446400 chr5D 100.000 37 0 0 8787 8823 498555119 498555155 1.590000e-07 69.4
17 TraesCS5B01G446400 chr2B 84.816 461 58 8 8361 8820 762518485 762518934 3.760000e-123 453.0
18 TraesCS5B01G446400 chr2B 85.479 303 39 3 8519 8820 762532029 762532327 2.390000e-80 311.0
19 TraesCS5B01G446400 chr2D 84.816 461 57 9 8361 8820 621558194 621558642 1.350000e-122 451.0
20 TraesCS5B01G446400 chr2D 93.333 120 6 2 5774 5891 357698031 357697912 9.110000e-40 176.0
21 TraesCS5B01G446400 chr2D 93.939 66 3 1 3129 3193 392544973 392545038 2.030000e-16 99.0
22 TraesCS5B01G446400 chr2D 91.549 71 4 2 3125 3193 180879398 180879468 7.290000e-16 97.1
23 TraesCS5B01G446400 chr4A 88.199 161 15 2 6561 6717 556761736 556761896 1.170000e-43 189.0
24 TraesCS5B01G446400 chr4D 87.425 167 16 3 6556 6717 365080860 365081026 4.210000e-43 187.0
25 TraesCS5B01G446400 chr4D 93.333 120 6 2 5774 5891 291740469 291740588 9.110000e-40 176.0
26 TraesCS5B01G446400 chr4D 91.549 71 6 0 3124 3194 346123442 346123372 2.030000e-16 99.0
27 TraesCS5B01G446400 chr4D 91.304 69 5 1 3126 3193 253934925 253934993 9.430000e-15 93.5
28 TraesCS5B01G446400 chr6B 87.273 165 17 2 6558 6718 128926002 128925838 1.510000e-42 185.0
29 TraesCS5B01G446400 chr6B 93.333 120 6 2 5774 5891 423542133 423542014 9.110000e-40 176.0
30 TraesCS5B01G446400 chr6B 91.892 74 3 2 3121 3193 345159658 345159587 5.640000e-17 100.0
31 TraesCS5B01G446400 chr1A 86.905 168 16 4 6576 6738 540323922 540324088 5.440000e-42 183.0
32 TraesCS5B01G446400 chr1A 91.549 71 5 1 3124 3193 108906922 108906992 7.290000e-16 97.1
33 TraesCS5B01G446400 chr1A 94.915 59 3 0 3135 3193 254485841 254485783 9.430000e-15 93.5
34 TraesCS5B01G446400 chrUn 84.158 202 16 12 6534 6722 135090755 135090953 1.960000e-41 182.0
35 TraesCS5B01G446400 chrUn 84.158 202 16 12 6534 6722 152687611 152687809 1.960000e-41 182.0
36 TraesCS5B01G446400 chrUn 94.915 59 3 0 3135 3193 11913550 11913492 9.430000e-15 93.5
37 TraesCS5B01G446400 chrUn 92.424 66 4 1 3129 3193 17582083 17582148 9.430000e-15 93.5
38 TraesCS5B01G446400 chrUn 94.915 59 3 0 3135 3193 49494001 49493943 9.430000e-15 93.5
39 TraesCS5B01G446400 chrUn 92.424 66 4 1 3129 3193 86972269 86972334 9.430000e-15 93.5
40 TraesCS5B01G446400 chrUn 95.000 60 2 1 3134 3193 119818324 119818266 9.430000e-15 93.5
41 TraesCS5B01G446400 chrUn 92.424 66 4 1 3129 3193 349855626 349855691 9.430000e-15 93.5
42 TraesCS5B01G446400 chrUn 92.424 66 4 1 3129 3193 356902590 356902525 9.430000e-15 93.5
43 TraesCS5B01G446400 chrUn 92.424 66 4 1 3129 3193 406809136 406809071 9.430000e-15 93.5
44 TraesCS5B01G446400 chrUn 92.308 65 4 1 3129 3192 388759468 388759404 3.390000e-14 91.6
45 TraesCS5B01G446400 chrUn 92.308 65 4 1 3129 3192 390044130 390044194 3.390000e-14 91.6
46 TraesCS5B01G446400 chrUn 92.308 65 4 1 3129 3192 466843347 466843411 3.390000e-14 91.6
47 TraesCS5B01G446400 chr3A 85.714 175 19 3 6549 6717 746316858 746316684 7.040000e-41 180.0
48 TraesCS5B01G446400 chr7A 93.333 120 6 2 5774 5891 15493833 15493952 9.110000e-40 176.0
49 TraesCS5B01G446400 chr7A 94.030 67 2 1 3127 3193 368518696 368518760 5.640000e-17 100.0
50 TraesCS5B01G446400 chr7A 100.000 28 0 0 6507 6534 679191889 679191916 1.600000e-02 52.8
51 TraesCS5B01G446400 chr4B 92.063 126 8 2 5774 5897 340640763 340640638 9.110000e-40 176.0
52 TraesCS5B01G446400 chr4B 96.610 59 2 0 3135 3193 650410746 650410688 2.030000e-16 99.0
53 TraesCS5B01G446400 chr4B 88.608 79 8 1 3116 3193 69316984 69316906 2.620000e-15 95.3
54 TraesCS5B01G446400 chr3D 93.333 120 6 2 5774 5891 323763304 323763185 9.110000e-40 176.0
55 TraesCS5B01G446400 chr3D 93.333 120 6 2 5774 5891 593115345 593115226 9.110000e-40 176.0
56 TraesCS5B01G446400 chr3D 89.474 76 8 0 3118 3193 272504945 272505020 7.290000e-16 97.1
57 TraesCS5B01G446400 chr1D 93.333 120 6 2 5774 5891 158107766 158107647 9.110000e-40 176.0
58 TraesCS5B01G446400 chr1D 84.409 186 19 6 6540 6717 377800787 377800604 3.280000e-39 174.0
59 TraesCS5B01G446400 chr1D 94.915 59 3 0 3135 3193 493220716 493220658 9.430000e-15 93.5
60 TraesCS5B01G446400 chr1D 100.000 28 0 0 6510 6537 76975556 76975529 1.600000e-02 52.8
61 TraesCS5B01G446400 chr3B 93.277 119 6 2 5774 5890 448788838 448788720 3.280000e-39 174.0
62 TraesCS5B01G446400 chr7D 93.939 66 3 1 3129 3193 534470992 534471057 2.030000e-16 99.0
63 TraesCS5B01G446400 chr7D 92.537 67 4 1 3128 3193 511568910 511568976 2.620000e-15 95.3
64 TraesCS5B01G446400 chr7D 92.537 67 4 1 3128 3193 540843474 540843408 2.620000e-15 95.3
65 TraesCS5B01G446400 chr7D 89.706 68 4 3 6514 6580 136315418 136315483 5.680000e-12 84.2
66 TraesCS5B01G446400 chr1B 91.667 72 5 1 3123 3193 24771598 24771527 2.030000e-16 99.0
67 TraesCS5B01G446400 chr6A 92.537 67 3 1 3127 3193 115340514 115340578 2.620000e-15 95.3
68 TraesCS5B01G446400 chr6A 92.537 67 4 1 3128 3193 595187268 595187334 2.620000e-15 95.3
69 TraesCS5B01G446400 chr6A 92.424 66 3 1 3128 3193 63754301 63754364 9.430000e-15 93.5
70 TraesCS5B01G446400 chr6A 85.714 84 8 3 3114 3193 291419086 291419169 1.580000e-12 86.1
71 TraesCS5B01G446400 chr6D 92.424 66 4 1 3129 3193 39376984 39376919 9.430000e-15 93.5
72 TraesCS5B01G446400 chr6D 92.424 66 4 1 3129 3193 115323563 115323628 9.430000e-15 93.5
73 TraesCS5B01G446400 chr6D 92.424 66 4 1 3129 3193 135102314 135102249 9.430000e-15 93.5
74 TraesCS5B01G446400 chr6D 92.424 66 4 1 3129 3193 160204384 160204449 9.430000e-15 93.5


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 TraesCS5B01G446400 chr5B 617824121 617832945 8824 False 16297.000000 16297 100.000000 1 8825 1 chr5B.!!$F1 8824
1 TraesCS5B01G446400 chr5A 622772737 622781420 8683 False 6230.500000 8222 92.552500 1 8823 2 chr5A.!!$F2 8822
2 TraesCS5B01G446400 chr5D 498493154 498500453 7299 False 1532.600000 3489 88.224000 1 7711 5 chr5D.!!$F3 7710
3 TraesCS5B01G446400 chr5D 65000735 65002452 1717 False 379.666667 675 88.913667 3771 5512 3 chr5D.!!$F2 1741
4 TraesCS5B01G446400 chr5D 498548780 498555155 6375 False 302.625000 752 96.108750 6970 8823 4 chr5D.!!$F4 1853

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
607 636 0.672342 AACAAGCAAGCAAGAGCAGG 59.328 50.000 0.00 0.00 45.49 4.85 F
1451 1506 0.532115 GGGCTTGGTTGGTGCTAATG 59.468 55.000 0.00 0.00 0.00 1.90 F
2201 2264 1.095807 GCTTGCGAATGAGGTACCCC 61.096 60.000 8.74 0.00 0.00 4.95 F
2791 2892 0.466189 CTGCAAACTGACCCACACCT 60.466 55.000 0.00 0.00 0.00 4.00 F
2792 2893 0.840617 TGCAAACTGACCCACACCTA 59.159 50.000 0.00 0.00 0.00 3.08 F
4497 4804 1.001487 TCATTCGTGTGCCTTGCTTTG 60.001 47.619 0.00 0.00 0.00 2.77 F
4506 4813 1.446791 CCTTGCTTTGCTTGCCCAA 59.553 52.632 0.00 0.00 0.00 4.12 F
5915 6484 1.958579 ACTGTGTGCATGCAGTGAAAT 59.041 42.857 23.41 2.22 43.45 2.17 F
7649 10076 1.004595 GATACCGGAAACAAGCGACC 58.995 55.000 9.46 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 2368 0.378257 CGGTATGACAATGCTGGTGC 59.622 55.000 0.00 0.0 40.20 5.01 R
2431 2508 0.546122 ATCCTTGGAACGCATAGGCA 59.454 50.000 0.00 0.0 41.24 4.75 R
3155 3262 2.054799 TGGGACTAAAGGCTCTGTTGT 58.945 47.619 0.00 0.0 0.00 3.32 R
4232 4538 1.331756 GACGCATTAAGGCATCACAGG 59.668 52.381 13.17 0.0 0.00 4.00 R
4523 4830 1.339535 GCCAAAGAGGACTGAGAAGGG 60.340 57.143 0.00 0.0 41.22 3.95 R
5932 6501 0.108424 CTCGAGGCAGAGTGGGAAAG 60.108 60.000 3.91 0.0 33.75 2.62 R
6269 6843 1.180029 ACTTGGCATGAGCAATGGAC 58.820 50.000 7.45 0.0 44.61 4.02 R
7792 10223 0.394192 CACACCAAGAGCAGGAGTCA 59.606 55.000 0.00 0.0 0.00 3.41 R
8540 14226 0.030908 GCCGGAGAAGATGAGGTACG 59.969 60.000 5.05 0.0 0.00 3.67 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.773976 TTAAGGCCCTTGTATTTCTCAATG 57.226 37.500 6.16 0.00 0.00 2.82
74 75 5.519566 CACAGAGATGCTAGCTAGAAACTTG 59.480 44.000 25.15 18.31 0.00 3.16
137 138 1.133407 GTCCTGAGCCTGTTCTCGTAG 59.867 57.143 0.00 0.00 35.90 3.51
176 177 3.690460 ACACATTGATCAGAACTTCCCC 58.310 45.455 0.00 0.00 0.00 4.81
209 213 8.792830 AAAGAGTGCAATTCAGCTAATAGTAA 57.207 30.769 0.00 0.00 34.99 2.24
211 215 8.792830 AGAGTGCAATTCAGCTAATAGTAAAA 57.207 30.769 0.00 0.00 34.99 1.52
213 217 7.464358 AGTGCAATTCAGCTAATAGTAAAACG 58.536 34.615 0.00 0.00 34.99 3.60
260 264 2.311463 ACAGTAGGATCCATGTCCTCG 58.689 52.381 15.82 2.40 45.51 4.63
369 383 5.812642 ACGGAGATATTAGTGTTTCAGCAAG 59.187 40.000 0.00 0.00 0.00 4.01
375 389 5.972107 ATTAGTGTTTCAGCAAGCAAGAT 57.028 34.783 0.00 0.00 0.00 2.40
402 416 1.298953 AGGGAGCTCTCTCTCAGACT 58.701 55.000 11.38 0.00 42.40 3.24
403 417 2.487775 AGGGAGCTCTCTCTCAGACTA 58.512 52.381 11.38 0.00 42.40 2.59
542 571 3.031964 CTTTCTTCTGGGCGCTGCG 62.032 63.158 19.17 19.17 0.00 5.18
581 610 1.486310 ACAATCAAGAGCCGGAGCATA 59.514 47.619 5.05 0.00 43.56 3.14
582 611 2.092968 ACAATCAAGAGCCGGAGCATAA 60.093 45.455 5.05 0.00 43.56 1.90
583 612 3.144506 CAATCAAGAGCCGGAGCATAAT 58.855 45.455 5.05 0.00 43.56 1.28
607 636 0.672342 AACAAGCAAGCAAGAGCAGG 59.328 50.000 0.00 0.00 45.49 4.85
639 671 2.667137 GCGAGACGGAAGATGATAAGG 58.333 52.381 0.00 0.00 0.00 2.69
649 681 3.658757 AGATGATAAGGAGAAGCGAGC 57.341 47.619 0.00 0.00 0.00 5.03
953 988 0.724785 GCTTGGTGCGCGTAAGTTTC 60.725 55.000 8.43 0.00 41.68 2.78
1014 1049 2.037772 TGCCTTCGCTTCTCTCTCTTTT 59.962 45.455 0.00 0.00 35.36 2.27
1015 1050 2.670905 GCCTTCGCTTCTCTCTCTTTTC 59.329 50.000 0.00 0.00 0.00 2.29
1016 1051 3.258228 CCTTCGCTTCTCTCTCTTTTCC 58.742 50.000 0.00 0.00 0.00 3.13
1250 1302 4.023279 CAGTTGTTTCGATGTTGGAATGGA 60.023 41.667 0.00 0.00 0.00 3.41
1273 1328 1.523258 GATGATGAGCTGCTGCGGT 60.523 57.895 7.01 3.07 45.42 5.68
1338 1393 0.972983 CCAAGAGGAAGGAGAGGCGA 60.973 60.000 0.00 0.00 36.89 5.54
1344 1399 1.380650 GAAGGAGAGGCGAGGGTCT 60.381 63.158 0.00 0.00 0.00 3.85
1403 1458 4.404654 CTGGTTCGGCGCTTTGGC 62.405 66.667 7.64 0.00 40.44 4.52
1419 1474 2.440980 GCCCCTCCATTGCTGACC 60.441 66.667 0.00 0.00 0.00 4.02
1451 1506 0.532115 GGGCTTGGTTGGTGCTAATG 59.468 55.000 0.00 0.00 0.00 1.90
1468 1523 3.581024 AATGTATTGCTTGCTGTGTGG 57.419 42.857 0.00 0.00 0.00 4.17
1570 1625 3.493028 TCACAAGGTGAGCTTTGCA 57.507 47.368 0.00 0.00 37.67 4.08
1610 1665 6.925610 TCTCAGTTTGGCAATATGACATAC 57.074 37.500 0.00 0.00 33.90 2.39
1611 1666 6.413892 TCTCAGTTTGGCAATATGACATACA 58.586 36.000 0.00 0.00 39.39 2.29
1614 1669 6.658816 TCAGTTTGGCAATATGACATACAAGT 59.341 34.615 0.00 0.00 39.39 3.16
1622 1677 6.652481 GCAATATGACATACAAGTAGGATGCT 59.348 38.462 0.00 0.00 0.00 3.79
1636 1691 3.295973 AGGATGCTACTTCTGGTCTCTC 58.704 50.000 0.00 0.00 0.00 3.20
1684 1739 4.705023 TCTGGATCACTTGTCGACTTATCA 59.295 41.667 17.92 0.00 0.00 2.15
1688 1743 5.463724 GGATCACTTGTCGACTTATCATTCC 59.536 44.000 17.92 10.90 0.00 3.01
1692 1747 5.869344 CACTTGTCGACTTATCATTCCTTGA 59.131 40.000 17.92 0.00 39.12 3.02
1783 1840 8.547894 GTGTGATTATGTAATGTTAATCGCTGA 58.452 33.333 13.97 0.00 42.07 4.26
1852 1911 1.766496 TGAATTACATCCCCGGGACTC 59.234 52.381 26.32 0.00 32.98 3.36
1857 1916 1.961133 ACATCCCCGGGACTCTTTTA 58.039 50.000 26.32 0.00 32.98 1.52
1877 1937 8.784043 TCTTTTAGGATTAGCACTTTGTTTCTC 58.216 33.333 0.00 0.00 0.00 2.87
2125 2186 7.004086 TGAACAAACAGGATTCTTCCATTACT 58.996 34.615 0.00 0.00 45.30 2.24
2201 2264 1.095807 GCTTGCGAATGAGGTACCCC 61.096 60.000 8.74 0.00 0.00 4.95
2227 2290 1.782044 AACGCATGGTTTCATTGCAC 58.218 45.000 0.00 0.00 34.41 4.57
2230 2293 1.722464 CGCATGGTTTCATTGCACAAG 59.278 47.619 0.00 0.00 32.00 3.16
2231 2294 1.461897 GCATGGTTTCATTGCACAAGC 59.538 47.619 0.00 0.00 42.57 4.01
2233 2296 3.395639 CATGGTTTCATTGCACAAGCTT 58.604 40.909 0.00 0.00 42.74 3.74
2256 2326 7.469181 GCTTACAGCATATTTTTCACCTAGCAT 60.469 37.037 0.00 0.00 41.89 3.79
2385 2462 2.562298 CAACTTAGCAAGGGCATCCAAA 59.438 45.455 0.00 0.00 44.61 3.28
2405 2482 1.202818 ACAGGACCTTCTGCAAACCTC 60.203 52.381 0.00 0.00 38.26 3.85
2431 2508 6.187727 TCCTGTGTTATTTGGAGAGAACTT 57.812 37.500 0.00 0.00 0.00 2.66
2505 2582 2.417933 GACGACTCGCAGGTTAGACTTA 59.582 50.000 0.00 0.00 0.00 2.24
2718 2819 3.258872 TGAGGCAATGATTTGGTTCCTTG 59.741 43.478 0.00 0.00 33.22 3.61
2791 2892 0.466189 CTGCAAACTGACCCACACCT 60.466 55.000 0.00 0.00 0.00 4.00
2792 2893 0.840617 TGCAAACTGACCCACACCTA 59.159 50.000 0.00 0.00 0.00 3.08
2793 2894 1.213182 TGCAAACTGACCCACACCTAA 59.787 47.619 0.00 0.00 0.00 2.69
2874 2975 3.119708 CCACAAAGAATGCTGTTAGGCTC 60.120 47.826 0.00 0.00 0.00 4.70
2876 2977 4.006319 ACAAAGAATGCTGTTAGGCTCTC 58.994 43.478 0.00 0.00 0.00 3.20
2877 2978 3.988976 AAGAATGCTGTTAGGCTCTCA 57.011 42.857 0.00 0.00 0.00 3.27
2931 3032 6.458210 AGCTTTTAGTGAATTGATTGTTGGG 58.542 36.000 0.00 0.00 0.00 4.12
2983 3085 7.194278 TGCTATACTTGAGAACTAAAGTAGCG 58.806 38.462 14.60 10.10 41.02 4.26
3062 3169 2.168947 CTCTTGAAGCAGCGCACAT 58.831 52.632 11.47 0.00 0.00 3.21
3133 3240 7.349711 AGCTGTAGTTACATTTGTTTAACACG 58.650 34.615 0.00 0.00 35.36 4.49
3143 3250 6.641314 ACATTTGTTTAACACGACAACAACAA 59.359 30.769 0.00 0.00 39.52 2.83
3144 3251 7.329717 ACATTTGTTTAACACGACAACAACAAT 59.670 29.630 0.00 0.00 39.52 2.71
3145 3252 8.799091 CATTTGTTTAACACGACAACAACAATA 58.201 29.630 0.00 0.00 39.52 1.90
3146 3253 8.738199 TTTGTTTAACACGACAACAACAATAA 57.262 26.923 0.00 0.00 39.52 1.40
3147 3254 7.722647 TGTTTAACACGACAACAACAATAAC 57.277 32.000 0.00 0.00 0.00 1.89
3148 3255 7.303261 TGTTTAACACGACAACAACAATAACA 58.697 30.769 0.00 0.00 0.00 2.41
3149 3256 7.806487 TGTTTAACACGACAACAACAATAACAA 59.194 29.630 0.00 0.00 0.00 2.83
3150 3257 7.722647 TTAACACGACAACAACAATAACAAC 57.277 32.000 0.00 0.00 0.00 3.32
3151 3258 5.298197 ACACGACAACAACAATAACAACA 57.702 34.783 0.00 0.00 0.00 3.33
3152 3259 5.700846 ACACGACAACAACAATAACAACAA 58.299 33.333 0.00 0.00 0.00 2.83
3153 3260 5.569823 ACACGACAACAACAATAACAACAAC 59.430 36.000 0.00 0.00 0.00 3.32
3154 3261 5.797934 CACGACAACAACAATAACAACAACT 59.202 36.000 0.00 0.00 0.00 3.16
3155 3262 6.962116 CACGACAACAACAATAACAACAACTA 59.038 34.615 0.00 0.00 0.00 2.24
3156 3263 6.962678 ACGACAACAACAATAACAACAACTAC 59.037 34.615 0.00 0.00 0.00 2.73
3157 3264 6.962116 CGACAACAACAATAACAACAACTACA 59.038 34.615 0.00 0.00 0.00 2.74
3162 3269 8.046294 ACAACAATAACAACAACTACAACAGA 57.954 30.769 0.00 0.00 0.00 3.41
3345 3461 4.997395 ACAACTGTAGGCATGTAAAGTCAG 59.003 41.667 0.00 0.00 0.00 3.51
3361 3478 8.783093 TGTAAAGTCAGTTGTTCTATGAAATGG 58.217 33.333 0.00 0.00 0.00 3.16
3376 3493 2.399396 AATGGTTTTCAACGAGCACG 57.601 45.000 0.76 0.76 45.75 5.34
3848 3975 2.490903 GCTCTTGATGCACAGGTGAAAT 59.509 45.455 3.10 0.00 0.00 2.17
3940 4082 5.175856 GCTCATAAGTTATGCTTTCGATCGT 59.824 40.000 15.94 0.00 38.57 3.73
4232 4538 6.884295 TGGGCTATATTTGGCAGATGTATTAC 59.116 38.462 0.00 0.00 0.00 1.89
4249 4555 5.530915 TGTATTACCTGTGATGCCTTAATGC 59.469 40.000 0.00 0.00 0.00 3.56
4322 4628 3.023946 CTGCGAGCAGATAATAGCAGT 57.976 47.619 19.40 0.00 46.30 4.40
4497 4804 1.001487 TCATTCGTGTGCCTTGCTTTG 60.001 47.619 0.00 0.00 0.00 2.77
4506 4813 1.446791 CCTTGCTTTGCTTGCCCAA 59.553 52.632 0.00 0.00 0.00 4.12
4523 4830 5.500234 TGCCCAATCTATTAGTATGGCATC 58.500 41.667 1.65 0.00 42.32 3.91
4550 4857 2.373169 TCAGTCCTCTTTGGCTGATGTT 59.627 45.455 0.00 0.00 41.01 2.71
4980 5306 8.116651 TGTATTGGTGTAAATTGTAGCACATT 57.883 30.769 0.00 0.00 33.88 2.71
5074 5400 7.610692 CCAGTAGACAGATCGTAGGGAATATAA 59.389 40.741 0.00 0.00 0.00 0.98
5102 5428 2.863809 CTTTACAGTCAAGGCACCCTT 58.136 47.619 0.00 0.00 45.88 3.95
5189 5749 5.588246 TGCAGTTGTTTCTCTGTTTGACATA 59.412 36.000 0.00 0.00 34.57 2.29
5276 5842 6.038603 TGTGTTATGGAGCTTCTCATTTATGC 59.961 38.462 0.00 0.00 31.08 3.14
5590 6157 7.435488 TCTCTTTACGCTACTATTTTCTCATGC 59.565 37.037 0.00 0.00 0.00 4.06
5782 6350 2.574369 ACTCCACATATTTCCGTCCCAA 59.426 45.455 0.00 0.00 0.00 4.12
5783 6351 3.009695 ACTCCACATATTTCCGTCCCAAA 59.990 43.478 0.00 0.00 0.00 3.28
5784 6352 4.013728 CTCCACATATTTCCGTCCCAAAA 58.986 43.478 0.00 0.00 0.00 2.44
5785 6353 4.605183 TCCACATATTTCCGTCCCAAAAT 58.395 39.130 0.00 0.00 0.00 1.82
5786 6354 5.020132 TCCACATATTTCCGTCCCAAAATT 58.980 37.500 0.00 0.00 0.00 1.82
5787 6355 5.126384 TCCACATATTTCCGTCCCAAAATTC 59.874 40.000 0.00 0.00 0.00 2.17
5788 6356 5.127031 CCACATATTTCCGTCCCAAAATTCT 59.873 40.000 0.00 0.00 0.00 2.40
5789 6357 6.350949 CCACATATTTCCGTCCCAAAATTCTT 60.351 38.462 0.00 0.00 0.00 2.52
5790 6358 6.531240 CACATATTTCCGTCCCAAAATTCTTG 59.469 38.462 0.00 0.00 0.00 3.02
5791 6359 6.210584 ACATATTTCCGTCCCAAAATTCTTGT 59.789 34.615 0.00 0.00 0.00 3.16
5792 6360 4.577834 TTTCCGTCCCAAAATTCTTGTC 57.422 40.909 0.00 0.00 0.00 3.18
5793 6361 3.502123 TCCGTCCCAAAATTCTTGTCT 57.498 42.857 0.00 0.00 0.00 3.41
5794 6362 3.827722 TCCGTCCCAAAATTCTTGTCTT 58.172 40.909 0.00 0.00 0.00 3.01
5795 6363 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
5796 6364 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
5797 6365 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
5798 6366 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
5799 6367 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
5800 6368 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
5801 6369 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
5802 6370 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
5803 6371 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
5804 6372 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
5812 6380 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
5813 6381 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
5814 6382 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
5815 6383 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
5816 6384 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
5817 6385 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
5825 6393 9.740239 TTGTCTAGATACGGATGTATTTAACAC 57.260 33.333 0.00 0.00 41.37 3.32
5826 6394 9.128404 TGTCTAGATACGGATGTATTTAACACT 57.872 33.333 0.00 0.00 41.37 3.55
5879 6448 7.461749 AGACAATCTAAGACAAGAATTTGGGA 58.538 34.615 0.00 0.00 38.66 4.37
5881 6450 7.004086 ACAATCTAAGACAAGAATTTGGGACA 58.996 34.615 0.00 0.00 38.66 4.02
5915 6484 1.958579 ACTGTGTGCATGCAGTGAAAT 59.041 42.857 23.41 2.22 43.45 2.17
5932 6501 7.254218 GCAGTGAAATCTTGGCTATTTTTATGC 60.254 37.037 0.00 0.00 0.00 3.14
6048 6622 9.301153 GCTAATACAATAATTTGACAGGTTTGG 57.699 33.333 0.00 0.00 36.64 3.28
6480 7054 4.940463 TGTTTACACTCGCTAGTTGTCTT 58.060 39.130 0.00 0.00 31.97 3.01
6541 7115 6.834451 TCCCTCTGTTCCTAAATACTCACTAG 59.166 42.308 0.00 0.00 0.00 2.57
6552 7126 9.268268 CCTAAATACTCACTAGTGTCAAAAACA 57.732 33.333 21.99 0.00 36.36 2.83
6612 7186 8.662781 TTTTAGAGATTTCAATATGGACTCCG 57.337 34.615 0.00 0.00 0.00 4.63
6614 7188 5.605534 AGAGATTTCAATATGGACTCCGTG 58.394 41.667 0.00 0.00 0.00 4.94
6684 7262 9.429359 CTGTATATAGTCCATGTTGAAATCTCC 57.571 37.037 0.00 0.00 0.00 3.71
6804 7385 7.010183 CGTTGTTTGAAAGACTCTGTTCTTCTA 59.990 37.037 0.00 0.00 34.60 2.10
6851 7432 5.823353 AGTTTTTGGCTTGCAATTCATTTG 58.177 33.333 0.00 0.00 38.43 2.32
6998 7579 5.165652 AGGGAGAAAGAGGCCATAATCATA 58.834 41.667 5.01 0.00 0.00 2.15
7163 9582 2.829023 AGGAGACGGGAAGTTCCATAA 58.171 47.619 23.33 0.00 38.64 1.90
7245 9666 1.686325 AATATCGGGTGTCTGCGGCT 61.686 55.000 0.00 0.00 0.00 5.52
7366 9793 2.352034 CGAGCGAGCTCTTGTCTAGTTA 59.648 50.000 20.97 0.00 40.69 2.24
7646 10073 1.927174 CAGAGATACCGGAAACAAGCG 59.073 52.381 9.46 0.00 0.00 4.68
7649 10076 1.004595 GATACCGGAAACAAGCGACC 58.995 55.000 9.46 0.00 0.00 4.79
7651 10078 4.084888 CCGGAAACAAGCGACCGC 62.085 66.667 6.25 6.25 43.37 5.68
7672 10099 1.742411 CGACAACACAAGTGGACAGGT 60.742 52.381 5.08 0.00 34.19 4.00
7716 10147 5.505173 GCATACATTGCCACAGAATACTT 57.495 39.130 0.00 0.00 46.15 2.24
7717 10148 5.276270 GCATACATTGCCACAGAATACTTG 58.724 41.667 0.00 0.00 46.15 3.16
7718 10149 3.855689 ACATTGCCACAGAATACTTGC 57.144 42.857 0.00 0.00 0.00 4.01
7719 10150 3.424703 ACATTGCCACAGAATACTTGCT 58.575 40.909 0.00 0.00 0.00 3.91
7720 10151 4.588899 ACATTGCCACAGAATACTTGCTA 58.411 39.130 0.00 0.00 0.00 3.49
7721 10152 4.396166 ACATTGCCACAGAATACTTGCTAC 59.604 41.667 0.00 0.00 0.00 3.58
7722 10153 3.694043 TGCCACAGAATACTTGCTACA 57.306 42.857 0.00 0.00 0.00 2.74
7723 10154 3.599343 TGCCACAGAATACTTGCTACAG 58.401 45.455 0.00 0.00 0.00 2.74
7724 10155 2.352960 GCCACAGAATACTTGCTACAGC 59.647 50.000 0.00 0.00 42.50 4.40
7725 10156 3.866651 CCACAGAATACTTGCTACAGCT 58.133 45.455 2.44 0.00 42.66 4.24
7726 10157 3.620374 CCACAGAATACTTGCTACAGCTG 59.380 47.826 13.48 13.48 42.66 4.24
7727 10158 4.498241 CACAGAATACTTGCTACAGCTGA 58.502 43.478 23.35 2.95 42.66 4.26
7728 10159 4.931601 CACAGAATACTTGCTACAGCTGAA 59.068 41.667 23.35 2.64 42.66 3.02
7729 10160 4.932200 ACAGAATACTTGCTACAGCTGAAC 59.068 41.667 23.35 9.58 42.66 3.18
7730 10161 4.931601 CAGAATACTTGCTACAGCTGAACA 59.068 41.667 23.35 12.29 42.66 3.18
7731 10162 5.409520 CAGAATACTTGCTACAGCTGAACAA 59.590 40.000 23.35 18.71 42.66 2.83
7732 10163 5.641209 AGAATACTTGCTACAGCTGAACAAG 59.359 40.000 29.33 29.33 42.63 3.16
7751 10182 5.460646 ACAAGCATCTGGTTAAATTGTTCG 58.539 37.500 0.00 0.00 33.98 3.95
7764 10195 1.983196 TTGTTCGCCGTGTTGTGTGG 61.983 55.000 0.00 0.00 0.00 4.17
7765 10196 2.174969 GTTCGCCGTGTTGTGTGGA 61.175 57.895 0.00 0.00 0.00 4.02
7777 10208 4.152402 GTGTTGTGTGGAGTATAGCAGTTG 59.848 45.833 0.00 0.00 0.00 3.16
7779 10210 3.925379 TGTGTGGAGTATAGCAGTTGTG 58.075 45.455 0.00 0.00 0.00 3.33
7791 10222 1.392589 CAGTTGTGGCCACTTTGTCT 58.607 50.000 34.75 21.22 0.00 3.41
7792 10223 1.750778 CAGTTGTGGCCACTTTGTCTT 59.249 47.619 34.75 11.88 0.00 3.01
7821 10252 2.796032 GCTCTTGGTGTGAGTTTGTTGC 60.796 50.000 0.00 0.00 34.30 4.17
7853 10284 7.653767 ATTTTTCGGAGACTACAAAGTACAG 57.346 36.000 0.00 0.00 35.56 2.74
7854 10285 5.779529 TTTCGGAGACTACAAAGTACAGT 57.220 39.130 0.00 0.00 35.56 3.55
7855 10286 6.882610 TTTCGGAGACTACAAAGTACAGTA 57.117 37.500 0.00 0.00 35.56 2.74
7856 10287 5.869753 TCGGAGACTACAAAGTACAGTAC 57.130 43.478 2.05 2.05 35.56 2.73
7857 10288 5.555017 TCGGAGACTACAAAGTACAGTACT 58.445 41.667 7.48 7.48 41.73 2.73
7858 10289 6.488006 TTCGGAGACTACAAAGTACAGTACTT 59.512 38.462 18.79 18.79 44.19 2.24
7929 10360 4.952262 TGAATGCGAAGAAAATCTCCAG 57.048 40.909 0.00 0.00 0.00 3.86
7961 10392 6.259550 CCTTTGGGCAGCAGTAAATATATC 57.740 41.667 0.00 0.00 0.00 1.63
7962 10393 5.106555 CCTTTGGGCAGCAGTAAATATATCG 60.107 44.000 0.00 0.00 0.00 2.92
7963 10394 4.882842 TGGGCAGCAGTAAATATATCGA 57.117 40.909 0.00 0.00 0.00 3.59
7964 10395 4.566004 TGGGCAGCAGTAAATATATCGAC 58.434 43.478 0.00 0.00 0.00 4.20
7965 10396 4.039852 TGGGCAGCAGTAAATATATCGACA 59.960 41.667 0.00 0.00 0.00 4.35
7966 10397 5.178797 GGGCAGCAGTAAATATATCGACAT 58.821 41.667 0.00 0.00 0.00 3.06
7968 10399 5.063944 GGCAGCAGTAAATATATCGACATGG 59.936 44.000 0.00 0.00 0.00 3.66
7997 10430 8.219546 TCAAATGTTAAAATGACTGTCTCACA 57.780 30.769 9.51 3.61 0.00 3.58
7998 10431 8.128582 TCAAATGTTAAAATGACTGTCTCACAC 58.871 33.333 9.51 0.00 0.00 3.82
7999 10432 6.560253 ATGTTAAAATGACTGTCTCACACC 57.440 37.500 9.51 0.00 0.00 4.16
8000 10433 4.509970 TGTTAAAATGACTGTCTCACACCG 59.490 41.667 9.51 0.00 0.00 4.94
8055 10488 1.935933 ACGTGCTTCGACAAGAAAGT 58.064 45.000 8.63 0.00 42.86 2.66
8121 10554 5.541845 CACTGGACTAGAAGAATCACAACA 58.458 41.667 0.00 0.00 0.00 3.33
8196 10629 5.438833 TCATCAGCAATACATCAACCATCA 58.561 37.500 0.00 0.00 0.00 3.07
8206 10639 8.939929 CAATACATCAACCATCATAGTACATCC 58.060 37.037 0.00 0.00 0.00 3.51
8252 13927 4.602340 ACCACTCATCGGTAATACATCC 57.398 45.455 0.00 0.00 34.02 3.51
8275 13950 2.223444 CGCGTGTCGAGATCGTATTAG 58.777 52.381 0.00 0.00 41.67 1.73
8315 13990 4.703645 TGACGGTGAATCTGAAGACTAG 57.296 45.455 0.00 0.00 0.00 2.57
8316 13991 4.079970 TGACGGTGAATCTGAAGACTAGT 58.920 43.478 0.00 0.00 0.00 2.57
8317 13992 4.156190 TGACGGTGAATCTGAAGACTAGTC 59.844 45.833 15.41 15.41 0.00 2.59
8321 13996 6.102663 CGGTGAATCTGAAGACTAGTCATTT 58.897 40.000 24.44 11.17 0.00 2.32
8388 14070 6.012745 ACAGTGGAAAAGGAAGAGCAATTAT 58.987 36.000 0.00 0.00 0.00 1.28
8389 14071 6.494835 ACAGTGGAAAAGGAAGAGCAATTATT 59.505 34.615 0.00 0.00 0.00 1.40
8390 14072 7.669722 ACAGTGGAAAAGGAAGAGCAATTATTA 59.330 33.333 0.00 0.00 0.00 0.98
8403 14085 5.465935 AGCAATTATTACCAACACAAACGG 58.534 37.500 0.00 0.00 0.00 4.44
8428 14111 1.749258 GGGCGAACCAATCAGGACC 60.749 63.158 0.00 0.00 41.22 4.46
8464 14147 3.092511 TCCATCCTGCAGAGCCCC 61.093 66.667 17.39 0.00 0.00 5.80
8519 14205 2.771639 CGAGCAGCATGGCAAGCAT 61.772 57.895 17.75 2.01 35.04 3.79
8663 14349 2.172851 TCATGGTTCCCAACGTACAC 57.827 50.000 0.00 0.00 36.95 2.90
8734 14420 4.201951 CACGGTACATGGACTGCC 57.798 61.111 17.33 0.00 0.00 4.85
8751 14437 1.374758 CCGCGGCTGAGGGAATATC 60.375 63.158 14.67 0.00 0.00 1.63
8769 14455 2.584608 GGGACATCAGGGTGGTCG 59.415 66.667 0.00 0.00 32.39 4.79
8823 14509 2.658593 GCCATCCCGATCACGACG 60.659 66.667 0.00 0.00 42.66 5.12
8824 14510 2.805546 CCATCCCGATCACGACGT 59.194 61.111 0.00 0.00 42.66 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.415659 AGCATCTCTGTGCCTGGATAC 59.584 52.381 0.00 0.00 46.19 2.24
74 75 2.516225 GCCAACCCCTATCCGCAC 60.516 66.667 0.00 0.00 0.00 5.34
176 177 3.321682 TGAATTGCACTCTTTCCCTTTGG 59.678 43.478 0.00 0.00 0.00 3.28
189 190 6.687105 CCGTTTTACTATTAGCTGAATTGCAC 59.313 38.462 0.00 0.00 34.99 4.57
190 191 6.676943 GCCGTTTTACTATTAGCTGAATTGCA 60.677 38.462 0.00 0.00 34.99 4.08
209 213 2.335011 GCCGCTTTCTTGCCGTTT 59.665 55.556 0.00 0.00 0.00 3.60
369 383 2.965147 AGCTCCCTTCTCTCTATCTTGC 59.035 50.000 0.00 0.00 0.00 4.01
402 416 1.667830 GTGCAGTTCTGCGGCTGTA 60.668 57.895 17.95 0.00 39.09 2.74
403 417 2.974698 GTGCAGTTCTGCGGCTGT 60.975 61.111 17.95 0.00 39.09 4.40
423 452 3.955771 TTTTCTGTCGCGCTACTTTTT 57.044 38.095 13.63 0.00 0.00 1.94
458 487 3.070748 GAGGAGAAGAAGAACAAGGTGC 58.929 50.000 0.00 0.00 0.00 5.01
542 571 0.459489 TTGGCTGTTGTTGTTGGCTC 59.541 50.000 0.00 0.00 0.00 4.70
581 610 4.746611 GCTCTTGCTTGCTTGTTTGTTATT 59.253 37.500 0.00 0.00 36.03 1.40
582 611 4.202141 TGCTCTTGCTTGCTTGTTTGTTAT 60.202 37.500 0.00 0.00 40.48 1.89
583 612 3.130164 TGCTCTTGCTTGCTTGTTTGTTA 59.870 39.130 0.00 0.00 40.48 2.41
623 655 4.303282 GCTTCTCCTTATCATCTTCCGTC 58.697 47.826 0.00 0.00 0.00 4.79
629 661 2.961741 TGCTCGCTTCTCCTTATCATCT 59.038 45.455 0.00 0.00 0.00 2.90
639 671 1.813337 GCCTCCTTGCTCGCTTCTC 60.813 63.158 0.00 0.00 0.00 2.87
649 681 1.630244 CGAAGAAGTGCGCCTCCTTG 61.630 60.000 4.18 0.00 0.00 3.61
812 844 2.109229 TCCCATCCATCTCCCTCTTC 57.891 55.000 0.00 0.00 0.00 2.87
813 845 2.831607 ATCCCATCCATCTCCCTCTT 57.168 50.000 0.00 0.00 0.00 2.85
814 846 2.831607 AATCCCATCCATCTCCCTCT 57.168 50.000 0.00 0.00 0.00 3.69
816 848 2.260822 CGTAATCCCATCCATCTCCCT 58.739 52.381 0.00 0.00 0.00 4.20
818 850 2.234908 CTCCGTAATCCCATCCATCTCC 59.765 54.545 0.00 0.00 0.00 3.71
936 971 0.863144 GAGAAACTTACGCGCACCAA 59.137 50.000 5.73 0.00 0.00 3.67
953 988 2.111878 CAGCCCGGCCCATTAGAG 59.888 66.667 5.55 0.00 0.00 2.43
1014 1049 1.158466 TCCCACAGCAAGAGGAGGA 59.842 57.895 0.00 0.00 0.00 3.71
1015 1050 1.298014 GTCCCACAGCAAGAGGAGG 59.702 63.158 0.00 0.00 0.00 4.30
1016 1051 1.298014 GGTCCCACAGCAAGAGGAG 59.702 63.158 0.00 0.00 0.00 3.69
1228 1280 4.141287 TCCATTCCAACATCGAAACAACT 58.859 39.130 0.00 0.00 0.00 3.16
1250 1302 0.945099 CAGCAGCTCATCATCGCAAT 59.055 50.000 0.00 0.00 0.00 3.56
1338 1393 1.380302 GTTGGGCATGACAGACCCT 59.620 57.895 14.90 0.00 44.56 4.34
1344 1399 0.478072 ACTTGAGGTTGGGCATGACA 59.522 50.000 0.00 0.00 0.00 3.58
1403 1458 2.276740 GGGTCAGCAATGGAGGGG 59.723 66.667 0.00 0.00 0.00 4.79
1404 1459 2.124570 CGGGTCAGCAATGGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
1405 1460 1.153289 CTCGGGTCAGCAATGGAGG 60.153 63.158 0.00 0.00 0.00 4.30
1435 1490 4.158394 AGCAATACATTAGCACCAACCAAG 59.842 41.667 0.00 0.00 0.00 3.61
1451 1506 1.666888 GCACCACACAGCAAGCAATAC 60.667 52.381 0.00 0.00 0.00 1.89
1468 1523 0.400594 ACTCTACCCACCAAAGGCAC 59.599 55.000 0.00 0.00 0.00 5.01
1570 1625 1.912731 GAGAAGAGGGGAAAGGAAGCT 59.087 52.381 0.00 0.00 0.00 3.74
1614 1669 4.465886 GAGAGACCAGAAGTAGCATCCTA 58.534 47.826 0.00 0.00 0.00 2.94
1622 1677 4.564782 TCCTAACGAGAGACCAGAAGTA 57.435 45.455 0.00 0.00 0.00 2.24
1660 1715 5.360999 TGATAAGTCGACAAGTGATCCAGAT 59.639 40.000 19.50 0.00 0.00 2.90
1684 1739 4.541250 TTTCCATAGCCCATCAAGGAAT 57.459 40.909 0.00 0.00 41.22 3.01
1688 1743 4.891756 AGACAATTTCCATAGCCCATCAAG 59.108 41.667 0.00 0.00 0.00 3.02
1692 1747 4.803329 AGAGACAATTTCCATAGCCCAT 57.197 40.909 0.00 0.00 0.00 4.00
1753 1808 9.773670 CGATTAACATTACATAATCACACGTAC 57.226 33.333 0.00 0.00 38.05 3.67
1756 1813 7.527183 CAGCGATTAACATTACATAATCACACG 59.473 37.037 6.40 0.00 38.05 4.49
1837 1896 1.961133 AAAAGAGTCCCGGGGATGTA 58.039 50.000 23.50 0.00 32.73 2.29
1852 1911 8.787852 AGAGAAACAAAGTGCTAATCCTAAAAG 58.212 33.333 0.00 0.00 0.00 2.27
1857 1916 5.048434 GCAAGAGAAACAAAGTGCTAATCCT 60.048 40.000 0.00 0.00 0.00 3.24
2125 2186 7.606073 TCTTCAGGAATATCATCAAAAACGACA 59.394 33.333 0.00 0.00 0.00 4.35
2208 2271 1.068281 TGTGCAATGAAACCATGCGTT 59.932 42.857 0.00 0.00 35.70 4.84
2209 2272 0.672889 TGTGCAATGAAACCATGCGT 59.327 45.000 0.00 0.00 0.00 5.24
2231 2294 7.320443 TGCTAGGTGAAAAATATGCTGTAAG 57.680 36.000 0.00 0.00 0.00 2.34
2233 2296 7.282585 AGATGCTAGGTGAAAAATATGCTGTA 58.717 34.615 0.00 0.00 0.00 2.74
2291 2368 0.378257 CGGTATGACAATGCTGGTGC 59.622 55.000 0.00 0.00 40.20 5.01
2302 2379 7.713942 ACAAGAGGGATTAATAAACGGTATGAC 59.286 37.037 0.00 0.00 0.00 3.06
2385 2462 0.846693 AGGTTTGCAGAAGGTCCTGT 59.153 50.000 0.00 0.00 36.57 4.00
2405 2482 4.566004 TCTCTCCAAATAACACAGGAACG 58.434 43.478 0.00 0.00 0.00 3.95
2431 2508 0.546122 ATCCTTGGAACGCATAGGCA 59.454 50.000 0.00 0.00 41.24 4.75
2517 2597 1.470098 GAACATAGGCAGCAACACAGG 59.530 52.381 0.00 0.00 0.00 4.00
2750 2851 6.689547 CAGCTTTCATCGCAAAATTGATTAC 58.310 36.000 0.00 0.00 0.00 1.89
2791 2892 2.630580 GCAAGTTGGGTCCCATTTGTTA 59.369 45.455 25.36 5.74 33.72 2.41
2792 2893 1.416030 GCAAGTTGGGTCCCATTTGTT 59.584 47.619 25.36 11.27 33.72 2.83
2793 2894 1.047801 GCAAGTTGGGTCCCATTTGT 58.952 50.000 25.36 7.52 33.72 2.83
2874 2975 3.034635 ACTCCTACAAGGCAGGTATGAG 58.965 50.000 14.61 14.61 38.59 2.90
2876 2977 2.743183 GCACTCCTACAAGGCAGGTATG 60.743 54.545 0.00 0.00 34.61 2.39
2877 2978 1.486726 GCACTCCTACAAGGCAGGTAT 59.513 52.381 0.00 0.00 34.61 2.73
3109 3216 7.319615 GTCGTGTTAAACAAATGTAACTACAGC 59.680 37.037 0.00 0.00 39.92 4.40
3133 3240 8.580431 GTTGTAGTTGTTGTTATTGTTGTTGTC 58.420 33.333 0.00 0.00 0.00 3.18
3143 3250 5.621193 AGGCTCTGTTGTAGTTGTTGTTAT 58.379 37.500 0.00 0.00 0.00 1.89
3144 3251 5.031066 AGGCTCTGTTGTAGTTGTTGTTA 57.969 39.130 0.00 0.00 0.00 2.41
3145 3252 3.886123 AGGCTCTGTTGTAGTTGTTGTT 58.114 40.909 0.00 0.00 0.00 2.83
3146 3253 3.560636 AGGCTCTGTTGTAGTTGTTGT 57.439 42.857 0.00 0.00 0.00 3.32
3147 3254 4.900635 AAAGGCTCTGTTGTAGTTGTTG 57.099 40.909 0.00 0.00 0.00 3.33
3148 3255 5.681639 ACTAAAGGCTCTGTTGTAGTTGTT 58.318 37.500 0.00 0.00 0.00 2.83
3149 3256 5.291905 ACTAAAGGCTCTGTTGTAGTTGT 57.708 39.130 0.00 0.00 0.00 3.32
3150 3257 4.691216 GGACTAAAGGCTCTGTTGTAGTTG 59.309 45.833 0.00 0.00 0.00 3.16
3151 3258 4.262938 GGGACTAAAGGCTCTGTTGTAGTT 60.263 45.833 0.00 0.00 0.00 2.24
3152 3259 3.261137 GGGACTAAAGGCTCTGTTGTAGT 59.739 47.826 0.00 0.00 0.00 2.73
3153 3260 3.260884 TGGGACTAAAGGCTCTGTTGTAG 59.739 47.826 0.00 0.00 0.00 2.74
3154 3261 3.244582 TGGGACTAAAGGCTCTGTTGTA 58.755 45.455 0.00 0.00 0.00 2.41
3155 3262 2.054799 TGGGACTAAAGGCTCTGTTGT 58.945 47.619 0.00 0.00 0.00 3.32
3156 3263 2.859165 TGGGACTAAAGGCTCTGTTG 57.141 50.000 0.00 0.00 0.00 3.33
3157 3264 3.117663 TGTTTGGGACTAAAGGCTCTGTT 60.118 43.478 0.00 0.00 0.00 3.16
3162 3269 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
3214 3321 8.702438 CATAAAAACATCCATTGCGATATTTCC 58.298 33.333 0.00 0.00 0.00 3.13
3222 3330 5.276489 GCATGTCATAAAAACATCCATTGCG 60.276 40.000 0.00 0.00 35.19 4.85
3269 3385 2.455674 TGCTGACACTGGTACATGAC 57.544 50.000 0.00 0.00 38.20 3.06
3361 3478 2.286772 ACAATCCGTGCTCGTTGAAAAC 60.287 45.455 15.59 0.00 45.31 2.43
3370 3487 5.986135 ACATTTCTCTATACAATCCGTGCTC 59.014 40.000 0.00 0.00 0.00 4.26
3683 3800 4.331968 TCCACTTTTGTAAGGGCTACATG 58.668 43.478 0.00 0.00 40.27 3.21
3848 3975 6.045955 GCAAATTGAACAACTTAAACAGGGA 58.954 36.000 0.00 0.00 0.00 4.20
3911 4053 8.662781 TCGAAAGCATAACTTATGAGCTAATT 57.337 30.769 12.26 0.00 37.75 1.40
3940 4082 9.109393 GCAGTGGATGAGTATTGAAGTTAAATA 57.891 33.333 0.00 0.00 0.00 1.40
4080 4369 7.495055 AGGCATAAGCAAATAGGAAAAAGATG 58.505 34.615 0.00 0.00 44.61 2.90
4232 4538 1.331756 GACGCATTAAGGCATCACAGG 59.668 52.381 13.17 0.00 0.00 4.00
4249 4555 7.012044 CCAACTATCATAAGGTTAAAAGGGACG 59.988 40.741 0.00 0.00 0.00 4.79
4322 4628 2.038269 GCGAATGTCTCCGGCCAAA 61.038 57.895 2.24 0.00 0.00 3.28
4497 4804 4.156739 GCCATACTAATAGATTGGGCAAGC 59.843 45.833 12.58 0.00 39.88 4.01
4506 4813 6.962311 TGAGAAGGGATGCCATACTAATAGAT 59.038 38.462 5.86 0.00 0.00 1.98
4523 4830 1.339535 GCCAAAGAGGACTGAGAAGGG 60.340 57.143 0.00 0.00 41.22 3.95
4761 5070 6.015688 CCAGATCAAATGTAATGCCAGCTATT 60.016 38.462 0.00 0.00 0.00 1.73
5040 5366 3.939592 CGATCTGTCTACTGGTGACACTA 59.060 47.826 5.39 0.00 39.23 2.74
5074 5400 4.100808 TGCCTTGACTGTAAAGCCAAAAAT 59.899 37.500 0.00 0.00 0.00 1.82
5102 5428 3.593442 AACCAATCAACCACCAGAAGA 57.407 42.857 0.00 0.00 0.00 2.87
5189 5749 5.931294 TCCAAATCATTATGCATGCCAATT 58.069 33.333 16.68 3.11 32.13 2.32
5228 5788 7.326789 CACAAATGCTACCTTAACAAGAACATG 59.673 37.037 0.00 0.00 0.00 3.21
5590 6157 9.617975 GATCTGAGAATACAAAAGGAAAAACAG 57.382 33.333 0.00 0.00 0.00 3.16
5774 6342 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
5786 6354 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
5787 6355 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
5788 6356 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
5789 6357 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
5790 6358 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
5791 6359 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
5799 6367 9.740239 GTGTTAAATACATCCGTATCTAGACAA 57.260 33.333 0.00 0.00 37.34 3.18
5800 6368 9.128404 AGTGTTAAATACATCCGTATCTAGACA 57.872 33.333 0.00 0.00 37.34 3.41
5809 6377 9.221933 TCATGTTTTAGTGTTAAATACATCCGT 57.778 29.630 0.00 0.00 39.39 4.69
5810 6378 9.485591 GTCATGTTTTAGTGTTAAATACATCCG 57.514 33.333 0.00 0.00 39.39 4.18
5822 6390 9.809096 CAGATGTATCTAGTCATGTTTTAGTGT 57.191 33.333 0.00 0.00 34.85 3.55
5823 6391 9.809096 ACAGATGTATCTAGTCATGTTTTAGTG 57.191 33.333 0.00 0.00 34.85 2.74
5852 6420 8.887717 CCCAAATTCTTGTCTTAGATTGTCTAG 58.112 37.037 0.00 0.00 29.56 2.43
5879 6448 1.768870 ACAGTTTGCTACTCCCTGTGT 59.231 47.619 0.00 0.00 35.20 3.72
5881 6450 1.768870 ACACAGTTTGCTACTCCCTGT 59.231 47.619 0.00 0.00 36.85 4.00
5915 6484 5.719085 TGGGAAAGCATAAAAATAGCCAAGA 59.281 36.000 0.00 0.00 0.00 3.02
5932 6501 0.108424 CTCGAGGCAGAGTGGGAAAG 60.108 60.000 3.91 0.00 33.75 2.62
5978 6552 1.437986 GCCACCAGCTAGTCCTACG 59.562 63.158 0.00 0.00 38.99 3.51
6046 6620 9.391006 GATGGTCTACACTTGAAATAATAACCA 57.609 33.333 0.00 0.00 36.44 3.67
6048 6622 9.614792 AGGATGGTCTACACTTGAAATAATAAC 57.385 33.333 0.00 0.00 0.00 1.89
6199 6773 6.207417 CACTTCTTCCATGTCACACCTAAAAT 59.793 38.462 0.00 0.00 0.00 1.82
6269 6843 1.180029 ACTTGGCATGAGCAATGGAC 58.820 50.000 7.45 0.00 44.61 4.02
6552 7126 6.826727 TCCCTCCATCCCATAATATAAGAGT 58.173 40.000 0.00 0.00 0.00 3.24
6569 7143 8.120538 TCTCTAAAAAGACTTATACTCCCTCCA 58.879 37.037 0.00 0.00 0.00 3.86
6610 7184 1.197721 GATTCACTCACTTTGCCACGG 59.802 52.381 0.00 0.00 0.00 4.94
6612 7186 4.065088 TGTAGATTCACTCACTTTGCCAC 58.935 43.478 0.00 0.00 0.00 5.01
6614 7188 4.319177 AGTGTAGATTCACTCACTTTGCC 58.681 43.478 0.00 0.00 44.07 4.52
6659 7237 8.933653 TGGAGATTTCAACATGGACTATATACA 58.066 33.333 0.00 0.00 0.00 2.29
6706 7284 1.414181 AGCAACATGATACTCCCTCCG 59.586 52.381 0.00 0.00 0.00 4.63
6830 7411 5.589452 AGACAAATGAATTGCAAGCCAAAAA 59.411 32.000 4.94 0.00 43.13 1.94
6872 7453 1.234821 GTTGCACCATCGAAGGAACA 58.765 50.000 14.76 7.96 34.32 3.18
6880 7461 0.802494 GGTTACCTGTTGCACCATCG 59.198 55.000 0.00 0.00 0.00 3.84
6998 7579 2.109834 TGGGTTGGATCTGACCATTGTT 59.890 45.455 16.39 0.00 39.82 2.83
7245 9666 5.576447 TCTGTTCATCGCACATACTTAGA 57.424 39.130 0.00 0.00 0.00 2.10
7292 9719 8.857098 CATGAATCTCCATCTTTTATGTCCAAT 58.143 33.333 0.00 0.00 0.00 3.16
7306 9733 5.618236 CACATAGTGGACATGAATCTCCAT 58.382 41.667 0.00 0.00 38.84 3.41
7384 9811 2.813754 CGACCTGGAGAAGCAAATGAAA 59.186 45.455 0.00 0.00 0.00 2.69
7468 9895 1.138883 TCTCGGCATCGCACACTAC 59.861 57.895 0.00 0.00 36.13 2.73
7646 10073 1.885850 ACTTGTGTTGTCGGCGGTC 60.886 57.895 7.21 1.06 0.00 4.79
7649 10076 1.885388 TCCACTTGTGTTGTCGGCG 60.885 57.895 0.00 0.00 0.00 6.46
7651 10078 0.937304 CTGTCCACTTGTGTTGTCGG 59.063 55.000 0.00 0.00 0.00 4.79
7724 10155 6.449698 ACAATTTAACCAGATGCTTGTTCAG 58.550 36.000 0.00 0.00 0.00 3.02
7725 10156 6.403866 ACAATTTAACCAGATGCTTGTTCA 57.596 33.333 0.00 0.00 0.00 3.18
7726 10157 6.088085 CGAACAATTTAACCAGATGCTTGTTC 59.912 38.462 12.75 12.75 43.50 3.18
7727 10158 5.920273 CGAACAATTTAACCAGATGCTTGTT 59.080 36.000 0.00 0.00 37.87 2.83
7728 10159 5.460646 CGAACAATTTAACCAGATGCTTGT 58.539 37.500 0.00 0.00 0.00 3.16
7729 10160 4.324402 GCGAACAATTTAACCAGATGCTTG 59.676 41.667 0.00 0.00 0.00 4.01
7730 10161 4.485163 GCGAACAATTTAACCAGATGCTT 58.515 39.130 0.00 0.00 0.00 3.91
7731 10162 3.119495 GGCGAACAATTTAACCAGATGCT 60.119 43.478 0.00 0.00 0.00 3.79
7732 10163 3.179048 GGCGAACAATTTAACCAGATGC 58.821 45.455 0.00 0.00 0.00 3.91
7733 10164 3.119990 ACGGCGAACAATTTAACCAGATG 60.120 43.478 16.62 0.00 0.00 2.90
7751 10182 2.268298 CTATACTCCACACAACACGGC 58.732 52.381 0.00 0.00 0.00 5.68
7764 10195 2.093447 AGTGGCCACAACTGCTATACTC 60.093 50.000 36.39 5.31 0.00 2.59
7765 10196 1.909302 AGTGGCCACAACTGCTATACT 59.091 47.619 36.39 9.43 0.00 2.12
7777 10208 1.604278 GAGTCAAGACAAAGTGGCCAC 59.396 52.381 29.22 29.22 0.00 5.01
7779 10210 1.202818 AGGAGTCAAGACAAAGTGGCC 60.203 52.381 0.00 0.00 0.00 5.36
7791 10222 1.131638 ACACCAAGAGCAGGAGTCAA 58.868 50.000 0.00 0.00 0.00 3.18
7792 10223 0.394192 CACACCAAGAGCAGGAGTCA 59.606 55.000 0.00 0.00 0.00 3.41
7907 10338 4.201990 GCTGGAGATTTTCTTCGCATTCAT 60.202 41.667 0.00 0.00 0.00 2.57
7961 10392 9.566530 TCATTTTAACATTTGATTACCATGTCG 57.433 29.630 0.00 0.00 30.58 4.35
7966 10397 9.906660 GACAGTCATTTTAACATTTGATTACCA 57.093 29.630 0.00 0.00 0.00 3.25
7981 10414 3.469008 TCGGTGTGAGACAGTCATTTT 57.531 42.857 2.66 0.00 37.56 1.82
7988 10421 8.425577 AAAAGAATATATTCGGTGTGAGACAG 57.574 34.615 17.69 0.00 41.56 3.51
7990 10423 9.309516 TGTAAAAGAATATATTCGGTGTGAGAC 57.690 33.333 17.69 10.45 41.56 3.36
7993 10426 8.609176 GCTTGTAAAAGAATATATTCGGTGTGA 58.391 33.333 17.69 2.42 41.56 3.58
7997 10430 8.567948 CCATGCTTGTAAAAGAATATATTCGGT 58.432 33.333 17.69 8.87 41.56 4.69
7998 10431 8.567948 ACCATGCTTGTAAAAGAATATATTCGG 58.432 33.333 17.69 11.21 41.56 4.30
8027 10460 0.741574 TCGAAGCACGTTGTTGGTGT 60.742 50.000 0.00 0.00 43.13 4.16
8055 10488 7.940137 TGAATAAAAGCCAGTAGGTTTCTGTAA 59.060 33.333 0.00 0.00 45.29 2.41
8121 10554 4.998671 TCATTGTGGTGTGTTGATTGTT 57.001 36.364 0.00 0.00 0.00 2.83
8196 10629 8.687292 TTACTGATGTCTTACGGATGTACTAT 57.313 34.615 0.00 0.00 0.00 2.12
8206 10639 2.531912 CAGCGCTTACTGATGTCTTACG 59.468 50.000 7.50 0.00 40.25 3.18
8252 13927 2.300597 TACGATCTCGACACGCGGTG 62.301 60.000 12.47 9.20 43.02 4.94
8315 13990 3.609103 AGACACGACAGCAAAAATGAC 57.391 42.857 0.00 0.00 0.00 3.06
8316 13991 4.447724 GTCTAGACACGACAGCAAAAATGA 59.552 41.667 18.20 0.00 0.00 2.57
8317 13992 4.211164 TGTCTAGACACGACAGCAAAAATG 59.789 41.667 21.74 0.00 36.54 2.32
8321 13996 3.660501 ATGTCTAGACACGACAGCAAA 57.339 42.857 27.41 1.00 45.05 3.68
8356 14038 6.126409 TCTTCCTTTTCCACTGTAACACATT 58.874 36.000 0.00 0.00 0.00 2.71
8359 14041 4.023963 GCTCTTCCTTTTCCACTGTAACAC 60.024 45.833 0.00 0.00 0.00 3.32
8388 14070 4.097589 CCTTTTACCCGTTTGTGTTGGTAA 59.902 41.667 0.00 0.00 40.59 2.85
8389 14071 3.631227 CCTTTTACCCGTTTGTGTTGGTA 59.369 43.478 0.00 0.00 32.27 3.25
8390 14072 2.427812 CCTTTTACCCGTTTGTGTTGGT 59.572 45.455 0.00 0.00 34.85 3.67
8403 14085 2.163613 CTGATTGGTTCGCCCTTTTACC 59.836 50.000 0.00 0.00 36.08 2.85
8428 14111 2.432510 GGAGTCCTGTACAAGATGAGGG 59.567 54.545 0.41 0.00 0.00 4.30
8464 14147 6.369799 GCTTTGCTGTTAGAAAGAAGAAGAG 58.630 40.000 0.00 0.00 31.89 2.85
8534 14220 2.758979 GAGAAGATGAGGTACGTGGGAA 59.241 50.000 0.00 0.00 0.00 3.97
8540 14226 0.030908 GCCGGAGAAGATGAGGTACG 59.969 60.000 5.05 0.00 0.00 3.67
8604 14290 2.709475 GAAATACTGGCGCCGCAG 59.291 61.111 23.90 17.51 0.00 5.18
8612 14298 3.561310 CCATGACATGGTCGAAATACTGG 59.439 47.826 24.15 0.00 45.54 4.00
8663 14349 0.610687 GAGGGAGAGGTTGACACTGG 59.389 60.000 0.00 0.00 0.00 4.00
8734 14420 1.734477 CGATATTCCCTCAGCCGCG 60.734 63.158 0.00 0.00 0.00 6.46
8751 14437 2.584608 GACCACCCTGATGTCCCG 59.415 66.667 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.