Multiple sequence alignment - TraesCS3B01G355800

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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 TraesCS3B01G355800 chr3B 100.000 3173 0 0 1 3173 566182030 566185202 0.000000e+00 5860.0
1 TraesCS3B01G355800 chr3A 91.613 2623 175 22 107 2702 571795105 571797709 0.000000e+00 3583.0
2 TraesCS3B01G355800 chr3A 86.207 406 33 11 2775 3173 571797708 571798097 4.900000e-113 418.0
3 TraesCS3B01G355800 chr3A 87.755 98 12 0 2996 3093 359357330 359357233 7.190000e-22 115.0
4 TraesCS3B01G355800 chr3D 89.474 2337 169 34 107 2397 433420489 433422794 0.000000e+00 2881.0
5 TraesCS3B01G355800 chr3D 87.937 315 34 2 2389 2702 433423582 433423893 5.000000e-98 368.0
6 TraesCS3B01G355800 chr3D 88.235 102 12 0 2 103 152204521 152204622 4.300000e-24 122.0
7 TraesCS3B01G355800 chr3D 91.011 89 8 0 2 90 301424374 301424462 1.550000e-23 121.0
8 TraesCS3B01G355800 chr3D 87.129 101 12 1 2993 3093 279905096 279905195 2.590000e-21 113.0
9 TraesCS3B01G355800 chr3D 89.474 57 5 1 2689 2745 25966479 25966534 1.580000e-08 71.3
10 TraesCS3B01G355800 chr7D 94.118 85 5 0 6 90 502883063 502882979 2.570000e-26 130.0
11 TraesCS3B01G355800 chr7D 87.963 108 12 1 5 112 502973017 502972911 3.320000e-25 126.0
12 TraesCS3B01G355800 chr7D 86.275 102 14 0 2 103 484698463 484698564 9.300000e-21 111.0
13 TraesCS3B01G355800 chr7D 95.745 47 2 0 2698 2744 389080424 389080470 3.390000e-10 76.8
14 TraesCS3B01G355800 chr7B 90.000 100 10 0 2996 3095 327453234 327453135 2.570000e-26 130.0
15 TraesCS3B01G355800 chr1B 90.816 98 7 2 2995 3090 610355112 610355015 2.570000e-26 130.0
16 TraesCS3B01G355800 chr1A 90.722 97 9 0 2997 3093 481924517 481924421 2.570000e-26 130.0
17 TraesCS3B01G355800 chr6A 89.796 98 9 1 2996 3093 457088796 457088892 1.200000e-24 124.0
18 TraesCS3B01G355800 chr6B 90.323 93 9 0 2 94 385364775 385364867 4.300000e-24 122.0
19 TraesCS3B01G355800 chr5D 90.323 93 9 0 5 97 218897777 218897685 4.300000e-24 122.0
20 TraesCS3B01G355800 chr5D 97.727 44 1 0 2701 2744 330393518 330393561 3.390000e-10 76.8
21 TraesCS3B01G355800 chr5D 80.000 90 9 6 2698 2778 392072085 392072174 1.230000e-04 58.4
22 TraesCS3B01G355800 chr1D 89.691 97 9 1 2998 3093 446426962 446426866 4.300000e-24 122.0
23 TraesCS3B01G355800 chr4D 88.119 101 12 0 2997 3097 210457864 210457764 1.550000e-23 121.0
24 TraesCS3B01G355800 chr4D 85.185 108 16 0 5 112 374344168 374344061 9.300000e-21 111.0
25 TraesCS3B01G355800 chr4B 88.119 101 12 0 2997 3097 253704021 253703921 1.550000e-23 121.0
26 TraesCS3B01G355800 chr2A 89.247 93 10 0 5 97 316554983 316554891 2.000000e-22 117.0
27 TraesCS3B01G355800 chr5B 97.727 44 1 0 2701 2744 383512935 383512978 3.390000e-10 76.8
28 TraesCS3B01G355800 chr5B 97.727 44 1 0 2701 2744 386391916 386391959 3.390000e-10 76.8
29 TraesCS3B01G355800 chr5A 97.727 44 1 0 2701 2744 426531412 426531369 3.390000e-10 76.8
30 TraesCS3B01G355800 chr2D 93.617 47 2 1 2697 2743 99733141 99733186 5.680000e-08 69.4
31 TraesCS3B01G355800 chr7A 80.899 89 8 6 2699 2778 117238166 117238078 9.500000e-06 62.1


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 TraesCS3B01G355800 chr3B 566182030 566185202 3172 False 5860.0 5860 100.0000 1 3173 1 chr3B.!!$F1 3172
1 TraesCS3B01G355800 chr3A 571795105 571798097 2992 False 2000.5 3583 88.9100 107 3173 2 chr3A.!!$F1 3066
2 TraesCS3B01G355800 chr3D 433420489 433423893 3404 False 1624.5 2881 88.7055 107 2702 2 chr3D.!!$F5 2595

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
401 415 0.104304 CCCCTCGGATTCTGTAACGG 59.896 60.0 0.00 0.00 0.00 4.44 F
405 419 0.179156 TCGGATTCTGTAACGGCGAC 60.179 55.0 16.62 1.95 0.00 5.19 F
1812 1838 0.183971 TGGCCAAGAAAGGGACGAAA 59.816 50.0 0.61 0.00 35.62 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2042 1.180456 TCGAGAAGCACGGTACCCAA 61.180 55.0 6.25 0.0 0.00 4.12 R
2025 2051 2.370281 TCTTCATGGTCGAGAAGCAC 57.630 50.0 7.15 0.0 40.72 4.40 R
3069 3958 0.179001 CCCTCCGCCCCGAAATAAAT 60.179 55.0 0.00 0.0 0.00 1.40 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.037208 CGGGGATGGGCCAAACTT 59.963 61.111 11.89 0.00 38.95 2.66
18 19 2.052104 CGGGGATGGGCCAAACTTC 61.052 63.158 11.89 2.61 38.95 3.01
19 20 1.078347 GGGGATGGGCCAAACTTCA 59.922 57.895 11.89 0.00 38.95 3.02
20 21 0.544120 GGGGATGGGCCAAACTTCAA 60.544 55.000 11.89 0.00 38.95 2.69
21 22 1.347062 GGGATGGGCCAAACTTCAAA 58.653 50.000 11.89 0.00 38.95 2.69
22 23 1.276138 GGGATGGGCCAAACTTCAAAG 59.724 52.381 11.89 0.00 38.95 2.77
23 24 2.247358 GGATGGGCCAAACTTCAAAGA 58.753 47.619 11.89 0.00 36.34 2.52
24 25 2.833943 GGATGGGCCAAACTTCAAAGAT 59.166 45.455 11.89 0.00 36.34 2.40
25 26 3.368739 GGATGGGCCAAACTTCAAAGATG 60.369 47.826 11.89 0.00 36.34 2.90
26 27 2.676748 TGGGCCAAACTTCAAAGATGT 58.323 42.857 2.13 0.00 0.00 3.06
27 28 3.037549 TGGGCCAAACTTCAAAGATGTT 58.962 40.909 2.13 0.00 32.56 2.71
28 29 3.069443 TGGGCCAAACTTCAAAGATGTTC 59.931 43.478 2.13 0.00 30.49 3.18
29 30 3.069443 GGGCCAAACTTCAAAGATGTTCA 59.931 43.478 4.39 0.00 30.49 3.18
30 31 4.262592 GGGCCAAACTTCAAAGATGTTCAT 60.263 41.667 4.39 0.00 30.49 2.57
31 32 4.687483 GGCCAAACTTCAAAGATGTTCATG 59.313 41.667 0.00 0.00 30.49 3.07
32 33 5.291971 GCCAAACTTCAAAGATGTTCATGT 58.708 37.500 0.00 0.00 30.49 3.21
33 34 5.403466 GCCAAACTTCAAAGATGTTCATGTC 59.597 40.000 0.00 0.00 30.49 3.06
34 35 5.626543 CCAAACTTCAAAGATGTTCATGTCG 59.373 40.000 0.00 0.00 30.49 4.35
35 36 6.429624 CAAACTTCAAAGATGTTCATGTCGA 58.570 36.000 0.00 0.00 30.49 4.20
36 37 5.597813 ACTTCAAAGATGTTCATGTCGAC 57.402 39.130 9.11 9.11 0.00 4.20
37 38 5.056480 ACTTCAAAGATGTTCATGTCGACA 58.944 37.500 22.48 22.48 0.00 4.35
38 39 4.990543 TCAAAGATGTTCATGTCGACAC 57.009 40.909 22.71 8.79 0.00 3.67
39 40 3.745975 TCAAAGATGTTCATGTCGACACC 59.254 43.478 22.71 9.76 0.00 4.16
40 41 3.401033 AAGATGTTCATGTCGACACCA 57.599 42.857 22.71 15.18 0.00 4.17
41 42 2.688507 AGATGTTCATGTCGACACCAC 58.311 47.619 22.71 17.36 0.00 4.16
42 43 1.390123 GATGTTCATGTCGACACCACG 59.610 52.381 22.71 9.99 0.00 4.94
43 44 0.386113 TGTTCATGTCGACACCACGA 59.614 50.000 22.71 12.28 40.00 4.35
44 45 1.202428 TGTTCATGTCGACACCACGAA 60.202 47.619 22.71 17.36 43.75 3.85
45 46 1.862201 GTTCATGTCGACACCACGAAA 59.138 47.619 22.71 6.22 43.75 3.46
46 47 1.493772 TCATGTCGACACCACGAAAC 58.506 50.000 22.71 0.00 43.75 2.78
47 48 1.067974 TCATGTCGACACCACGAAACT 59.932 47.619 22.71 0.00 43.75 2.66
48 49 1.864711 CATGTCGACACCACGAAACTT 59.135 47.619 22.71 0.00 43.75 2.66
49 50 2.012937 TGTCGACACCACGAAACTTT 57.987 45.000 15.76 0.00 43.75 2.66
50 51 2.348660 TGTCGACACCACGAAACTTTT 58.651 42.857 15.76 0.00 43.75 2.27
51 52 2.743126 TGTCGACACCACGAAACTTTTT 59.257 40.909 15.76 0.00 43.75 1.94
52 53 3.181518 TGTCGACACCACGAAACTTTTTC 60.182 43.478 15.76 0.00 43.75 2.29
53 54 3.001414 TCGACACCACGAAACTTTTTCA 58.999 40.909 0.00 0.00 39.34 2.69
54 55 3.623960 TCGACACCACGAAACTTTTTCAT 59.376 39.130 0.00 0.00 39.34 2.57
55 56 3.723764 CGACACCACGAAACTTTTTCATG 59.276 43.478 0.00 0.00 35.09 3.07
56 57 4.668289 GACACCACGAAACTTTTTCATGT 58.332 39.130 0.00 0.00 0.00 3.21
57 58 5.502706 CGACACCACGAAACTTTTTCATGTA 60.503 40.000 0.00 0.00 35.09 2.29
58 59 5.816919 ACACCACGAAACTTTTTCATGTAG 58.183 37.500 0.00 0.00 0.00 2.74
59 60 5.587043 ACACCACGAAACTTTTTCATGTAGA 59.413 36.000 0.00 0.00 0.00 2.59
60 61 6.262273 ACACCACGAAACTTTTTCATGTAGAT 59.738 34.615 0.00 0.00 0.00 1.98
61 62 6.797033 CACCACGAAACTTTTTCATGTAGATC 59.203 38.462 0.00 0.00 0.00 2.75
62 63 6.485313 ACCACGAAACTTTTTCATGTAGATCA 59.515 34.615 0.00 0.00 0.00 2.92
63 64 7.174946 ACCACGAAACTTTTTCATGTAGATCAT 59.825 33.333 0.00 0.00 37.22 2.45
64 65 8.023128 CCACGAAACTTTTTCATGTAGATCATT 58.977 33.333 0.00 0.00 34.09 2.57
65 66 9.398170 CACGAAACTTTTTCATGTAGATCATTT 57.602 29.630 0.00 0.00 34.09 2.32
66 67 9.612620 ACGAAACTTTTTCATGTAGATCATTTC 57.387 29.630 0.00 0.00 34.09 2.17
67 68 9.831737 CGAAACTTTTTCATGTAGATCATTTCT 57.168 29.630 0.00 0.00 38.57 2.52
70 71 8.868522 ACTTTTTCATGTAGATCATTTCTCCA 57.131 30.769 0.00 0.00 35.79 3.86
71 72 9.471702 ACTTTTTCATGTAGATCATTTCTCCAT 57.528 29.630 0.00 0.00 31.61 3.41
75 76 9.465199 TTTCATGTAGATCATTTCTCCATTTGA 57.535 29.630 0.00 0.00 29.15 2.69
76 77 8.672823 TCATGTAGATCATTTCTCCATTTGAG 57.327 34.615 0.00 0.00 37.25 3.02
77 78 7.718314 TCATGTAGATCATTTCTCCATTTGAGG 59.282 37.037 0.00 0.00 36.85 3.86
78 79 6.962182 TGTAGATCATTTCTCCATTTGAGGT 58.038 36.000 0.00 0.00 41.76 3.85
79 80 7.050377 TGTAGATCATTTCTCCATTTGAGGTC 58.950 38.462 0.00 0.00 41.76 3.85
80 81 6.070951 AGATCATTTCTCCATTTGAGGTCA 57.929 37.500 0.00 0.00 41.76 4.02
81 82 6.670617 AGATCATTTCTCCATTTGAGGTCAT 58.329 36.000 0.00 0.00 41.76 3.06
82 83 6.771749 AGATCATTTCTCCATTTGAGGTCATC 59.228 38.462 0.00 0.00 41.76 2.92
83 84 6.070951 TCATTTCTCCATTTGAGGTCATCT 57.929 37.500 0.00 0.00 41.76 2.90
84 85 6.487828 TCATTTCTCCATTTGAGGTCATCTT 58.512 36.000 0.00 0.00 41.76 2.40
85 86 7.632861 TCATTTCTCCATTTGAGGTCATCTTA 58.367 34.615 0.00 0.00 41.76 2.10
86 87 8.108999 TCATTTCTCCATTTGAGGTCATCTTAA 58.891 33.333 0.00 0.00 41.76 1.85
87 88 8.910944 CATTTCTCCATTTGAGGTCATCTTAAT 58.089 33.333 0.00 0.00 41.76 1.40
88 89 8.884124 TTTCTCCATTTGAGGTCATCTTAATT 57.116 30.769 0.00 0.00 41.76 1.40
89 90 7.870509 TCTCCATTTGAGGTCATCTTAATTG 57.129 36.000 0.00 0.00 41.76 2.32
90 91 7.632861 TCTCCATTTGAGGTCATCTTAATTGA 58.367 34.615 0.00 0.00 41.76 2.57
91 92 7.772292 TCTCCATTTGAGGTCATCTTAATTGAG 59.228 37.037 0.00 0.00 41.76 3.02
92 93 7.405292 TCCATTTGAGGTCATCTTAATTGAGT 58.595 34.615 0.00 0.00 29.34 3.41
93 94 7.890127 TCCATTTGAGGTCATCTTAATTGAGTT 59.110 33.333 0.00 0.00 29.34 3.01
94 95 8.526147 CCATTTGAGGTCATCTTAATTGAGTTT 58.474 33.333 0.00 0.00 29.34 2.66
95 96 9.918630 CATTTGAGGTCATCTTAATTGAGTTTT 57.081 29.630 0.00 0.00 29.34 2.43
121 122 6.964807 TCCATTCCTCAATCCATACAATTG 57.035 37.500 3.24 3.24 35.81 2.32
159 161 8.245195 ACCAAACACAAACATTAAAGACCTAT 57.755 30.769 0.00 0.00 0.00 2.57
165 167 9.189156 ACACAAACATTAAAGACCTATATGCAT 57.811 29.630 3.79 3.79 0.00 3.96
175 187 7.603180 AAGACCTATATGCATTAGTGAGTGA 57.397 36.000 3.54 0.00 0.00 3.41
194 206 7.552687 GTGAGTGAATGTGAATATTTGTAGGGA 59.447 37.037 0.00 0.00 0.00 4.20
234 246 2.434884 CAGCGCCGATGTTGAGGT 60.435 61.111 2.29 0.00 0.00 3.85
248 260 3.181422 TGTTGAGGTCCTAGAGTTCTCCA 60.181 47.826 0.00 0.00 0.00 3.86
257 269 0.761187 AGAGTTCTCCAGTGCTGCAA 59.239 50.000 2.77 0.00 0.00 4.08
260 272 0.819259 GTTCTCCAGTGCTGCAACCA 60.819 55.000 2.77 0.00 0.00 3.67
288 300 0.970427 TCATGTAGTGAGCTCGCCCA 60.970 55.000 23.37 19.66 31.80 5.36
294 306 3.321648 TGAGCTCGCCCATGGTGT 61.322 61.111 11.73 0.00 34.40 4.16
305 317 1.338674 CCCATGGTGTTTGCTACGAGA 60.339 52.381 11.73 0.00 0.00 4.04
346 359 0.392998 GCAGGAACCATGACCACGAT 60.393 55.000 0.00 0.00 0.00 3.73
358 371 2.036604 TGACCACGATGAGCTACAACAA 59.963 45.455 0.00 0.00 0.00 2.83
396 410 2.990479 GCACCCCTCGGATTCTGT 59.010 61.111 0.00 0.00 0.00 3.41
401 415 0.104304 CCCCTCGGATTCTGTAACGG 59.896 60.000 0.00 0.00 0.00 4.44
405 419 0.179156 TCGGATTCTGTAACGGCGAC 60.179 55.000 16.62 1.95 0.00 5.19
425 439 2.195567 ACGACGAGTTGGAACCGGA 61.196 57.895 9.46 0.00 0.00 5.14
426 440 1.007038 CGACGAGTTGGAACCGGAA 60.007 57.895 9.46 0.00 0.00 4.30
427 441 1.007336 CGACGAGTTGGAACCGGAAG 61.007 60.000 9.46 0.00 0.00 3.46
428 442 0.316204 GACGAGTTGGAACCGGAAGA 59.684 55.000 9.46 0.00 0.00 2.87
434 448 0.533308 TTGGAACCGGAAGAACCACG 60.533 55.000 9.46 0.00 38.90 4.94
442 456 1.759236 GAAGAACCACGGGGGAGTT 59.241 57.895 9.50 0.00 41.15 3.01
450 464 3.315949 CGGGGGAGTTGTCGGGAA 61.316 66.667 0.00 0.00 0.00 3.97
457 471 2.746277 GTTGTCGGGAAGCCGCAT 60.746 61.111 0.00 0.00 0.00 4.73
479 493 2.363807 GAGTCGGTCGACATTGCAG 58.636 57.895 22.81 1.18 46.76 4.41
493 508 2.401195 GCAGGAAATGCGAGCGAC 59.599 61.111 0.00 0.00 46.99 5.19
502 517 1.374343 ATGCGAGCGACGGAGACTTA 61.374 55.000 0.00 0.00 46.59 2.24
509 524 3.543665 AGCGACGGAGACTTACTAGAAT 58.456 45.455 0.00 0.00 0.00 2.40
510 525 3.312973 AGCGACGGAGACTTACTAGAATG 59.687 47.826 0.00 0.00 0.00 2.67
512 527 3.548415 CGACGGAGACTTACTAGAATGGC 60.548 52.174 0.00 0.00 0.00 4.40
513 528 2.358267 ACGGAGACTTACTAGAATGGCG 59.642 50.000 0.00 0.00 0.00 5.69
515 530 2.957006 GGAGACTTACTAGAATGGCGGA 59.043 50.000 0.00 0.00 0.00 5.54
518 540 2.357009 GACTTACTAGAATGGCGGACGA 59.643 50.000 0.00 0.00 0.00 4.20
528 550 0.604073 TGGCGGACGACTACATCAAA 59.396 50.000 0.00 0.00 0.00 2.69
567 589 1.302949 GCCTGGTGCCCAATCTACA 59.697 57.895 0.00 0.00 30.80 2.74
577 599 5.296748 GTGCCCAATCTACAAACAACATTT 58.703 37.500 0.00 0.00 0.00 2.32
595 617 3.345808 GCGAGCTGCAACCAACGA 61.346 61.111 1.02 0.00 45.45 3.85
629 651 3.431725 GCCTACAACGCTGGTGCC 61.432 66.667 0.00 0.00 35.36 5.01
632 654 4.308458 TACAACGCTGGTGCCGCT 62.308 61.111 0.00 0.00 35.36 5.52
676 699 2.360350 CACCATGCCTTGCGAGGT 60.360 61.111 21.55 0.00 45.44 3.85
677 700 2.360350 ACCATGCCTTGCGAGGTG 60.360 61.111 21.55 12.33 45.44 4.00
705 728 2.925170 AGGAGAAGCGTGCAGGGT 60.925 61.111 5.06 5.06 0.00 4.34
706 729 1.605058 GAGGAGAAGCGTGCAGGGTA 61.605 60.000 12.00 0.00 0.00 3.69
759 783 2.992089 AGCACGTGTTGGTGAGAAG 58.008 52.632 18.38 0.00 40.38 2.85
816 840 2.091541 ACCCATATCAAACGGCTTGTG 58.908 47.619 0.00 0.00 36.34 3.33
820 844 1.448985 TATCAAACGGCTTGTGAGGC 58.551 50.000 0.00 0.00 44.55 4.70
828 852 2.672996 CTTGTGAGGCCCCCGTTG 60.673 66.667 0.00 0.00 0.00 4.10
844 868 2.534396 TTGTGGATCCTGGCCGGTT 61.534 57.895 14.23 3.79 0.00 4.44
875 899 0.828022 ATGTCGCGAGAAATGGGGTA 59.172 50.000 10.24 0.00 45.01 3.69
876 900 0.609151 TGTCGCGAGAAATGGGGTAA 59.391 50.000 10.24 0.00 45.01 2.85
877 901 1.208535 TGTCGCGAGAAATGGGGTAAT 59.791 47.619 10.24 0.00 45.01 1.89
878 902 2.285977 GTCGCGAGAAATGGGGTAATT 58.714 47.619 10.24 0.00 45.01 1.40
879 903 2.681344 GTCGCGAGAAATGGGGTAATTT 59.319 45.455 10.24 0.00 45.01 1.82
880 904 2.940410 TCGCGAGAAATGGGGTAATTTC 59.060 45.455 3.71 2.19 43.79 2.17
953 977 4.216366 AGAAAGCTTTCTCGTTTTCAGC 57.784 40.909 31.56 6.92 43.72 4.26
977 1003 1.482182 TGTCGATCATTCCCACTCCTG 59.518 52.381 0.00 0.00 0.00 3.86
995 1021 1.377612 GAACCCTAAACCCAGCCGT 59.622 57.895 0.00 0.00 0.00 5.68
1086 1112 2.308722 GGCCTCCATCCTCAACCCA 61.309 63.158 0.00 0.00 0.00 4.51
1293 1319 1.000771 CTCCCTCCGAGACCTCACA 60.001 63.158 0.00 0.00 41.63 3.58
1389 1415 2.630889 TCTCCACCTTCCAGTCATCT 57.369 50.000 0.00 0.00 0.00 2.90
1701 1727 1.023513 AGCTCATGAAGAAGCACGGC 61.024 55.000 7.34 0.00 0.00 5.68
1812 1838 0.183971 TGGCCAAGAAAGGGACGAAA 59.816 50.000 0.61 0.00 35.62 3.46
2163 2189 3.967987 GGAAAGAGGTAGAGGAGGCATTA 59.032 47.826 0.00 0.00 0.00 1.90
2184 2210 7.095607 GCATTACCTCAATAGAATAACCACTCG 60.096 40.741 0.00 0.00 0.00 4.18
2204 2230 4.901868 TCGCAGGTATTGTTTTCCTACTT 58.098 39.130 0.00 0.00 0.00 2.24
2205 2231 4.933400 TCGCAGGTATTGTTTTCCTACTTC 59.067 41.667 0.00 0.00 0.00 3.01
2222 2249 9.621629 TTCCTACTTCATGTTCTTAGAAACAAA 57.378 29.630 0.00 0.00 42.10 2.83
2265 2306 8.072321 AGAATACTGATGTCTGAGTATGTTGT 57.928 34.615 0.00 0.00 35.89 3.32
2266 2307 8.194104 AGAATACTGATGTCTGAGTATGTTGTC 58.806 37.037 0.00 0.00 35.89 3.18
2267 2308 5.991933 ACTGATGTCTGAGTATGTTGTCT 57.008 39.130 0.00 0.00 0.00 3.41
2268 2309 5.718146 ACTGATGTCTGAGTATGTTGTCTG 58.282 41.667 0.00 0.00 0.00 3.51
2269 2310 5.077134 TGATGTCTGAGTATGTTGTCTGG 57.923 43.478 0.00 0.00 0.00 3.86
2294 2344 8.676401 GGCTTATTAAATTTGCCATTTCACATT 58.324 29.630 10.71 0.00 42.79 2.71
2295 2345 9.706846 GCTTATTAAATTTGCCATTTCACATTC 57.293 29.630 0.00 0.00 0.00 2.67
2374 2428 6.701145 TGTTGCAGTTCAATGGTAAAGTAA 57.299 33.333 0.00 0.00 36.99 2.24
2448 3299 7.090953 TGTTTTTCCGTTTCACTTCAGTATT 57.909 32.000 0.00 0.00 0.00 1.89
2495 3346 1.592081 GAACTGCATCTTAGAGCTGCG 59.408 52.381 0.00 2.07 40.00 5.18
2672 3523 8.906693 CACAATAGTCGTGTATATTAGCAAGAG 58.093 37.037 0.00 0.00 0.00 2.85
2706 3557 8.958119 TCATTAGTTTGATGTATGTTACTCCC 57.042 34.615 0.00 0.00 0.00 4.30
2707 3558 8.768397 TCATTAGTTTGATGTATGTTACTCCCT 58.232 33.333 0.00 0.00 0.00 4.20
2708 3559 9.046296 CATTAGTTTGATGTATGTTACTCCCTC 57.954 37.037 0.00 0.00 0.00 4.30
2709 3560 5.990668 AGTTTGATGTATGTTACTCCCTCC 58.009 41.667 0.00 0.00 0.00 4.30
2710 3561 5.487488 AGTTTGATGTATGTTACTCCCTCCA 59.513 40.000 0.00 0.00 0.00 3.86
2711 3562 6.158695 AGTTTGATGTATGTTACTCCCTCCAT 59.841 38.462 0.00 0.00 0.00 3.41
2712 3563 5.808366 TGATGTATGTTACTCCCTCCATC 57.192 43.478 0.00 0.00 0.00 3.51
2713 3564 4.593206 TGATGTATGTTACTCCCTCCATCC 59.407 45.833 0.00 0.00 0.00 3.51
2714 3565 3.314693 TGTATGTTACTCCCTCCATCCC 58.685 50.000 0.00 0.00 0.00 3.85
2715 3566 2.587060 ATGTTACTCCCTCCATCCCA 57.413 50.000 0.00 0.00 0.00 4.37
2716 3567 2.587060 TGTTACTCCCTCCATCCCAT 57.413 50.000 0.00 0.00 0.00 4.00
2717 3568 3.717507 TGTTACTCCCTCCATCCCATA 57.282 47.619 0.00 0.00 0.00 2.74
2718 3569 4.015617 TGTTACTCCCTCCATCCCATAA 57.984 45.455 0.00 0.00 0.00 1.90
2719 3570 4.577096 TGTTACTCCCTCCATCCCATAAT 58.423 43.478 0.00 0.00 0.00 1.28
2720 3571 5.733000 TGTTACTCCCTCCATCCCATAATA 58.267 41.667 0.00 0.00 0.00 0.98
2721 3572 6.339220 TGTTACTCCCTCCATCCCATAATAT 58.661 40.000 0.00 0.00 0.00 1.28
2722 3573 7.492552 TGTTACTCCCTCCATCCCATAATATA 58.507 38.462 0.00 0.00 0.00 0.86
2723 3574 7.964867 TGTTACTCCCTCCATCCCATAATATAA 59.035 37.037 0.00 0.00 0.00 0.98
2724 3575 8.487028 GTTACTCCCTCCATCCCATAATATAAG 58.513 40.741 0.00 0.00 0.00 1.73
2725 3576 6.826727 ACTCCCTCCATCCCATAATATAAGA 58.173 40.000 0.00 0.00 0.00 2.10
2726 3577 7.442655 ACTCCCTCCATCCCATAATATAAGAT 58.557 38.462 0.00 0.00 0.00 2.40
2727 3578 7.570607 ACTCCCTCCATCCCATAATATAAGATC 59.429 40.741 0.00 0.00 0.00 2.75
2728 3579 7.675591 TCCCTCCATCCCATAATATAAGATCT 58.324 38.462 0.00 0.00 0.00 2.75
2729 3580 8.138239 TCCCTCCATCCCATAATATAAGATCTT 58.862 37.037 13.56 13.56 0.00 2.40
2730 3581 9.452517 CCCTCCATCCCATAATATAAGATCTTA 57.547 37.037 17.32 17.32 0.00 2.10
2767 3618 6.919721 TGAAAGATCTTAAATTTTGGGTCGG 58.080 36.000 8.75 0.00 0.00 4.79
2768 3619 6.717540 TGAAAGATCTTAAATTTTGGGTCGGA 59.282 34.615 8.75 0.00 0.00 4.55
2769 3620 6.759497 AAGATCTTAAATTTTGGGTCGGAG 57.241 37.500 6.06 0.00 0.00 4.63
2770 3621 5.193679 AGATCTTAAATTTTGGGTCGGAGG 58.806 41.667 0.00 0.00 0.00 4.30
2771 3622 3.692690 TCTTAAATTTTGGGTCGGAGGG 58.307 45.455 0.00 0.00 0.00 4.30
2772 3623 2.517998 TAAATTTTGGGTCGGAGGGG 57.482 50.000 0.00 0.00 0.00 4.79
2773 3624 0.252057 AAATTTTGGGTCGGAGGGGG 60.252 55.000 0.00 0.00 0.00 5.40
2796 3647 7.093245 GGGGTAGTATAGGATCTGAAAGGAATC 60.093 44.444 0.00 0.00 0.00 2.52
2802 3653 2.092375 GGATCTGAAAGGAATCGGGGTT 60.092 50.000 0.00 0.00 0.00 4.11
2827 3679 3.459232 TTTATCCGGACAGCTGATCAG 57.541 47.619 23.35 18.84 0.00 2.90
2858 3710 7.678837 TCAAATTTGTAAGGAAAAGGATGCAT 58.321 30.769 17.47 0.00 0.00 3.96
2862 3714 5.902613 TGTAAGGAAAAGGATGCATTCTG 57.097 39.130 8.69 0.00 0.00 3.02
2872 3724 6.737720 AAGGATGCATTCTGTAGTAGATCA 57.262 37.500 8.69 0.00 34.80 2.92
2873 3725 6.737720 AGGATGCATTCTGTAGTAGATCAA 57.262 37.500 6.73 0.00 34.80 2.57
2876 3728 6.933521 GGATGCATTCTGTAGTAGATCAACAT 59.066 38.462 0.00 0.00 34.80 2.71
2885 3737 9.719355 TCTGTAGTAGATCAACATTGCTTTTAA 57.281 29.630 0.00 0.00 0.00 1.52
2900 3752 7.636259 TTGCTTTTAATGAGAAATTGGAACG 57.364 32.000 0.00 0.00 0.00 3.95
2989 3841 4.968971 TTTTATTCCCCTCGGAGGTATC 57.031 45.455 22.07 0.00 40.10 2.24
3005 3894 5.782845 GGAGGTATCAAATCATACTCCCTCT 59.217 44.000 0.00 0.00 30.93 3.69
3008 3897 6.617371 AGGTATCAAATCATACTCCCTCTGTT 59.383 38.462 0.00 0.00 30.93 3.16
3023 3912 5.070001 CCCTCTGTTCCAAAATAAGTGTCA 58.930 41.667 0.00 0.00 0.00 3.58
3035 3924 8.287503 CCAAAATAAGTGTCACTGGTTTAGTAC 58.712 37.037 6.18 0.00 37.60 2.73
3036 3925 8.832521 CAAAATAAGTGTCACTGGTTTAGTACA 58.167 33.333 6.18 0.00 37.60 2.90
3037 3926 8.967664 AAATAAGTGTCACTGGTTTAGTACAA 57.032 30.769 6.18 0.00 37.60 2.41
3038 3927 8.967664 AATAAGTGTCACTGGTTTAGTACAAA 57.032 30.769 6.18 0.00 37.60 2.83
3040 3929 7.875327 AAGTGTCACTGGTTTAGTACAAATT 57.125 32.000 6.18 0.00 37.60 1.82
3041 3930 7.875327 AGTGTCACTGGTTTAGTACAAATTT 57.125 32.000 4.21 0.00 37.60 1.82
3042 3931 8.967664 AGTGTCACTGGTTTAGTACAAATTTA 57.032 30.769 4.21 0.00 37.60 1.40
3043 3932 9.052759 AGTGTCACTGGTTTAGTACAAATTTAG 57.947 33.333 4.21 0.00 37.60 1.85
3044 3933 8.833493 GTGTCACTGGTTTAGTACAAATTTAGT 58.167 33.333 0.00 0.00 37.60 2.24
3068 3957 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
3069 3958 5.756347 ACAAAGTTGTACTAAATCAGCGACA 59.244 36.000 0.00 0.00 40.16 4.35
3070 3959 6.426937 ACAAAGTTGTACTAAATCAGCGACAT 59.573 34.615 0.00 0.00 40.16 3.06
3071 3960 7.041372 ACAAAGTTGTACTAAATCAGCGACATT 60.041 33.333 0.00 0.00 40.16 2.71
3072 3961 7.435068 AAGTTGTACTAAATCAGCGACATTT 57.565 32.000 0.00 0.00 0.00 2.32
3073 3962 8.542497 AAGTTGTACTAAATCAGCGACATTTA 57.458 30.769 0.00 0.00 0.00 1.40
3074 3963 8.718102 AGTTGTACTAAATCAGCGACATTTAT 57.282 30.769 0.00 0.00 0.00 1.40
3075 3964 9.162764 AGTTGTACTAAATCAGCGACATTTATT 57.837 29.630 0.00 0.00 0.00 1.40
3076 3965 9.769093 GTTGTACTAAATCAGCGACATTTATTT 57.231 29.630 0.00 0.00 0.00 1.40
3077 3966 9.982291 TTGTACTAAATCAGCGACATTTATTTC 57.018 29.630 0.00 0.00 0.00 2.17
3078 3967 8.325282 TGTACTAAATCAGCGACATTTATTTCG 58.675 33.333 0.00 0.00 38.31 3.46
3079 3968 6.715464 ACTAAATCAGCGACATTTATTTCGG 58.285 36.000 1.10 0.00 35.73 4.30
3080 3969 4.552166 AATCAGCGACATTTATTTCGGG 57.448 40.909 1.10 0.00 35.73 5.14
3081 3970 2.285083 TCAGCGACATTTATTTCGGGG 58.715 47.619 1.10 0.00 35.73 5.73
3111 4000 8.925338 AGGGAGTACATAACTAATAGGAAGTTG 58.075 37.037 0.00 0.00 39.07 3.16
3117 4006 3.821421 ACTAATAGGAAGTTGGAGGCG 57.179 47.619 0.00 0.00 0.00 5.52
3123 4012 1.896660 GAAGTTGGAGGCGCACCAA 60.897 57.895 26.48 26.48 43.84 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.037208 AAGTTTGGCCCATCCCCG 59.963 61.111 0.00 0.00 0.00 5.73
1 2 0.544120 TTGAAGTTTGGCCCATCCCC 60.544 55.000 0.00 0.00 0.00 4.81
2 3 1.276138 CTTTGAAGTTTGGCCCATCCC 59.724 52.381 0.00 0.00 0.00 3.85
3 4 2.247358 TCTTTGAAGTTTGGCCCATCC 58.753 47.619 0.00 0.00 0.00 3.51
4 5 3.259123 ACATCTTTGAAGTTTGGCCCATC 59.741 43.478 0.00 0.00 0.00 3.51
5 6 3.242011 ACATCTTTGAAGTTTGGCCCAT 58.758 40.909 0.00 0.00 0.00 4.00
6 7 2.676748 ACATCTTTGAAGTTTGGCCCA 58.323 42.857 0.00 0.00 0.00 5.36
7 8 3.069443 TGAACATCTTTGAAGTTTGGCCC 59.931 43.478 0.00 0.00 0.00 5.80
8 9 4.320608 TGAACATCTTTGAAGTTTGGCC 57.679 40.909 0.00 0.00 0.00 5.36
9 10 5.291971 ACATGAACATCTTTGAAGTTTGGC 58.708 37.500 0.00 0.00 0.00 4.52
10 11 5.626543 CGACATGAACATCTTTGAAGTTTGG 59.373 40.000 0.00 0.00 0.00 3.28
11 12 6.358030 GTCGACATGAACATCTTTGAAGTTTG 59.642 38.462 11.55 0.00 0.00 2.93
12 13 6.038161 TGTCGACATGAACATCTTTGAAGTTT 59.962 34.615 15.76 0.00 0.00 2.66
13 14 5.527214 TGTCGACATGAACATCTTTGAAGTT 59.473 36.000 15.76 0.00 0.00 2.66
14 15 5.050091 GTGTCGACATGAACATCTTTGAAGT 60.050 40.000 23.12 0.00 0.00 3.01
15 16 5.377358 GTGTCGACATGAACATCTTTGAAG 58.623 41.667 23.12 0.00 0.00 3.02
16 17 4.213270 GGTGTCGACATGAACATCTTTGAA 59.787 41.667 23.12 0.00 0.00 2.69
17 18 3.745975 GGTGTCGACATGAACATCTTTGA 59.254 43.478 23.12 0.00 0.00 2.69
18 19 3.498018 TGGTGTCGACATGAACATCTTTG 59.502 43.478 23.12 0.00 0.00 2.77
19 20 3.498397 GTGGTGTCGACATGAACATCTTT 59.502 43.478 23.12 0.00 0.00 2.52
20 21 3.067106 GTGGTGTCGACATGAACATCTT 58.933 45.455 23.12 0.00 0.00 2.40
21 22 2.688507 GTGGTGTCGACATGAACATCT 58.311 47.619 23.12 0.00 0.00 2.90
22 23 1.390123 CGTGGTGTCGACATGAACATC 59.610 52.381 23.12 6.52 0.00 3.06
23 24 1.000394 TCGTGGTGTCGACATGAACAT 60.000 47.619 23.12 0.00 34.85 2.71
24 25 0.386113 TCGTGGTGTCGACATGAACA 59.614 50.000 23.12 15.27 34.85 3.18
25 26 1.493772 TTCGTGGTGTCGACATGAAC 58.506 50.000 23.12 17.95 38.53 3.18
26 27 1.862201 GTTTCGTGGTGTCGACATGAA 59.138 47.619 23.12 18.93 40.87 2.57
27 28 1.067974 AGTTTCGTGGTGTCGACATGA 59.932 47.619 23.12 14.26 39.58 3.07
28 29 1.497991 AGTTTCGTGGTGTCGACATG 58.502 50.000 23.12 12.14 39.58 3.21
29 30 2.234300 AAGTTTCGTGGTGTCGACAT 57.766 45.000 23.12 0.00 39.58 3.06
30 31 2.012937 AAAGTTTCGTGGTGTCGACA 57.987 45.000 15.76 15.76 39.58 4.35
31 32 3.181518 TGAAAAAGTTTCGTGGTGTCGAC 60.182 43.478 9.11 9.11 39.58 4.20
32 33 3.001414 TGAAAAAGTTTCGTGGTGTCGA 58.999 40.909 0.00 0.00 38.08 4.20
33 34 3.392769 TGAAAAAGTTTCGTGGTGTCG 57.607 42.857 0.00 0.00 0.00 4.35
34 35 4.668289 ACATGAAAAAGTTTCGTGGTGTC 58.332 39.130 21.07 0.00 39.18 3.67
35 36 4.712122 ACATGAAAAAGTTTCGTGGTGT 57.288 36.364 21.07 9.89 39.18 4.16
36 37 6.055231 TCTACATGAAAAAGTTTCGTGGTG 57.945 37.500 21.07 14.82 39.18 4.17
37 38 6.485313 TGATCTACATGAAAAAGTTTCGTGGT 59.515 34.615 21.07 12.35 39.18 4.16
38 39 6.898041 TGATCTACATGAAAAAGTTTCGTGG 58.102 36.000 21.07 9.22 39.18 4.94
39 40 8.955061 AATGATCTACATGAAAAAGTTTCGTG 57.045 30.769 17.34 17.34 39.39 4.35
40 41 9.612620 GAAATGATCTACATGAAAAAGTTTCGT 57.387 29.630 0.00 0.00 39.39 3.85
41 42 9.831737 AGAAATGATCTACATGAAAAAGTTTCG 57.168 29.630 0.00 0.00 39.39 3.46
44 45 9.300681 TGGAGAAATGATCTACATGAAAAAGTT 57.699 29.630 0.00 0.00 44.42 2.66
45 46 8.868522 TGGAGAAATGATCTACATGAAAAAGT 57.131 30.769 0.00 0.00 44.42 2.66
66 67 7.555554 ACTCAATTAAGATGACCTCAAATGGAG 59.444 37.037 7.86 7.86 43.65 3.86
67 68 7.405292 ACTCAATTAAGATGACCTCAAATGGA 58.595 34.615 0.00 0.00 0.00 3.41
68 69 7.636150 ACTCAATTAAGATGACCTCAAATGG 57.364 36.000 0.00 0.00 0.00 3.16
69 70 9.918630 AAAACTCAATTAAGATGACCTCAAATG 57.081 29.630 0.00 0.00 0.00 2.32
94 95 7.789202 TTGTATGGATTGAGGAATGGAAAAA 57.211 32.000 0.00 0.00 0.00 1.94
95 96 7.976414 ATTGTATGGATTGAGGAATGGAAAA 57.024 32.000 0.00 0.00 0.00 2.29
96 97 7.399765 ACAATTGTATGGATTGAGGAATGGAAA 59.600 33.333 9.97 0.00 37.79 3.13
97 98 6.896860 ACAATTGTATGGATTGAGGAATGGAA 59.103 34.615 9.97 0.00 37.79 3.53
98 99 6.434302 ACAATTGTATGGATTGAGGAATGGA 58.566 36.000 9.97 0.00 37.79 3.41
99 100 6.720112 ACAATTGTATGGATTGAGGAATGG 57.280 37.500 9.97 0.00 37.79 3.16
121 122 8.079203 TGTTTGTGTTTGGTATTGATGACATAC 58.921 33.333 0.00 0.00 0.00 2.39
159 161 9.783081 ATATTCACATTCACTCACTAATGCATA 57.217 29.630 0.00 0.00 36.72 3.14
167 169 7.554118 CCCTACAAATATTCACATTCACTCACT 59.446 37.037 0.00 0.00 0.00 3.41
168 170 7.552687 TCCCTACAAATATTCACATTCACTCAC 59.447 37.037 0.00 0.00 0.00 3.51
172 184 8.682936 AGATCCCTACAAATATTCACATTCAC 57.317 34.615 0.00 0.00 0.00 3.18
194 206 3.452627 CCAGTTCAAGGCCACTACTAGAT 59.547 47.826 5.01 0.00 0.00 1.98
220 232 0.249073 CTAGGACCTCAACATCGGCG 60.249 60.000 0.00 0.00 0.00 6.46
234 246 2.451490 CAGCACTGGAGAACTCTAGGA 58.549 52.381 16.96 0.00 41.76 2.94
260 272 2.739932 GCTCACTACATGACCATTCGCT 60.740 50.000 0.00 0.00 32.37 4.93
266 278 0.173481 GCGAGCTCACTACATGACCA 59.827 55.000 15.40 0.00 32.37 4.02
274 286 1.685765 ACCATGGGCGAGCTCACTA 60.686 57.895 18.09 4.11 0.00 2.74
275 287 3.005539 ACCATGGGCGAGCTCACT 61.006 61.111 18.09 0.00 0.00 3.41
288 300 2.612972 CCACTCTCGTAGCAAACACCAT 60.613 50.000 0.00 0.00 0.00 3.55
294 306 0.246635 GGCTCCACTCTCGTAGCAAA 59.753 55.000 0.00 0.00 36.68 3.68
329 342 1.208052 CTCATCGTGGTCATGGTTCCT 59.792 52.381 0.00 0.00 0.00 3.36
330 343 1.656652 CTCATCGTGGTCATGGTTCC 58.343 55.000 0.00 0.00 0.00 3.62
346 359 2.412870 CGTGACCATTGTTGTAGCTCA 58.587 47.619 0.00 0.00 0.00 4.26
358 371 2.942796 TTCAGCTCGCCGTGACCAT 61.943 57.895 0.00 0.00 0.00 3.55
388 402 0.108520 TGGTCGCCGTTACAGAATCC 60.109 55.000 0.00 0.00 0.00 3.01
392 406 2.256158 CGTGGTCGCCGTTACAGA 59.744 61.111 0.00 0.00 0.00 3.41
396 410 3.313007 CTCGTCGTGGTCGCCGTTA 62.313 63.158 0.00 0.00 39.43 3.18
401 415 3.103911 CCAACTCGTCGTGGTCGC 61.104 66.667 0.00 0.00 36.96 5.19
405 419 2.019951 CGGTTCCAACTCGTCGTGG 61.020 63.158 0.00 0.00 0.00 4.94
425 439 1.350310 ACAACTCCCCCGTGGTTCTT 61.350 55.000 0.00 0.00 34.77 2.52
426 440 1.765597 GACAACTCCCCCGTGGTTCT 61.766 60.000 0.00 0.00 34.77 3.01
427 441 1.302271 GACAACTCCCCCGTGGTTC 60.302 63.158 0.00 0.00 34.77 3.62
428 442 2.833957 GACAACTCCCCCGTGGTT 59.166 61.111 0.00 0.00 34.77 3.67
434 448 2.669240 CTTCCCGACAACTCCCCC 59.331 66.667 0.00 0.00 0.00 5.40
457 471 2.632544 AATGTCGACCGACTCGCCA 61.633 57.895 21.01 3.48 44.80 5.69
479 493 2.508439 TCCGTCGCTCGCATTTCC 60.508 61.111 0.00 0.00 38.35 3.13
487 501 2.548875 TCTAGTAAGTCTCCGTCGCTC 58.451 52.381 0.00 0.00 0.00 5.03
488 502 2.687700 TCTAGTAAGTCTCCGTCGCT 57.312 50.000 0.00 0.00 0.00 4.93
492 507 2.358267 CGCCATTCTAGTAAGTCTCCGT 59.642 50.000 0.00 0.00 0.00 4.69
493 508 2.287668 CCGCCATTCTAGTAAGTCTCCG 60.288 54.545 0.00 0.00 0.00 4.63
502 517 1.674962 GTAGTCGTCCGCCATTCTAGT 59.325 52.381 0.00 0.00 0.00 2.57
509 524 0.604073 TTTGATGTAGTCGTCCGCCA 59.396 50.000 0.00 0.00 0.00 5.69
510 525 1.278238 CTTTGATGTAGTCGTCCGCC 58.722 55.000 0.00 0.00 0.00 6.13
512 527 2.527100 GTCCTTTGATGTAGTCGTCCG 58.473 52.381 0.00 0.00 0.00 4.79
513 528 2.094854 ACGTCCTTTGATGTAGTCGTCC 60.095 50.000 0.00 0.00 38.97 4.79
515 530 2.413765 CGACGTCCTTTGATGTAGTCGT 60.414 50.000 10.58 0.00 40.84 4.34
518 540 1.203994 CCCGACGTCCTTTGATGTAGT 59.796 52.381 10.58 0.00 40.84 2.73
528 550 1.904865 TTGTAGCACCCGACGTCCT 60.905 57.895 10.58 3.11 0.00 3.85
558 580 5.218885 TCGCAAATGTTGTTTGTAGATTGG 58.781 37.500 2.90 0.00 0.00 3.16
562 584 3.563808 AGCTCGCAAATGTTGTTTGTAGA 59.436 39.130 2.90 2.79 0.00 2.59
567 589 1.490621 GCAGCTCGCAAATGTTGTTT 58.509 45.000 3.64 0.00 41.79 2.83
591 613 2.185350 CTCTCGCCTGCCATCGTT 59.815 61.111 0.00 0.00 0.00 3.85
613 635 3.118454 CGGCACCAGCGTTGTAGG 61.118 66.667 0.00 0.00 43.41 3.18
632 654 1.174078 TCGTCAGTGTTACGCCCTCA 61.174 55.000 0.00 0.00 40.12 3.86
676 699 3.158537 TTCTCCTCCAACGCGCACA 62.159 57.895 5.73 0.00 0.00 4.57
677 700 2.357034 TTCTCCTCCAACGCGCAC 60.357 61.111 5.73 0.00 0.00 5.34
681 704 2.048127 ACGCTTCTCCTCCAACGC 60.048 61.111 0.00 0.00 0.00 4.84
683 706 1.294659 CTGCACGCTTCTCCTCCAAC 61.295 60.000 0.00 0.00 0.00 3.77
705 728 0.750546 ATCAGCTAGTCGCCACCGTA 60.751 55.000 0.00 0.00 40.39 4.02
706 729 0.750546 TATCAGCTAGTCGCCACCGT 60.751 55.000 0.00 0.00 40.39 4.83
743 767 1.867233 CTTCCTTCTCACCAACACGTG 59.133 52.381 15.48 15.48 34.93 4.49
757 781 3.647636 TCCCTCTCGATTCATCTTCCTT 58.352 45.455 0.00 0.00 0.00 3.36
759 783 4.562552 GGATTCCCTCTCGATTCATCTTCC 60.563 50.000 0.00 0.00 0.00 3.46
801 825 1.448985 GCCTCACAAGCCGTTTGATA 58.551 50.000 1.53 0.00 39.21 2.15
816 840 3.699134 GATCCACAACGGGGGCCTC 62.699 68.421 0.84 0.00 34.36 4.70
820 844 2.272146 CAGGATCCACAACGGGGG 59.728 66.667 15.82 0.00 34.36 5.40
828 852 2.438434 CAACCGGCCAGGATCCAC 60.438 66.667 15.82 2.41 45.00 4.02
858 882 1.949465 ATTACCCCATTTCTCGCGAC 58.051 50.000 3.71 0.00 0.00 5.19
869 893 6.494952 TGGTAGCAAATTAGAAATTACCCCA 58.505 36.000 0.00 0.00 0.00 4.96
875 899 4.405680 GCCCCTGGTAGCAAATTAGAAATT 59.594 41.667 0.00 0.00 0.00 1.82
876 900 3.960755 GCCCCTGGTAGCAAATTAGAAAT 59.039 43.478 0.00 0.00 0.00 2.17
877 901 3.011257 AGCCCCTGGTAGCAAATTAGAAA 59.989 43.478 8.46 0.00 0.00 2.52
878 902 2.580783 AGCCCCTGGTAGCAAATTAGAA 59.419 45.455 8.46 0.00 0.00 2.10
879 903 2.092429 CAGCCCCTGGTAGCAAATTAGA 60.092 50.000 8.46 0.00 0.00 2.10
880 904 2.092429 TCAGCCCCTGGTAGCAAATTAG 60.092 50.000 8.46 0.00 31.51 1.73
881 905 1.919654 TCAGCCCCTGGTAGCAAATTA 59.080 47.619 8.46 0.00 31.51 1.40
953 977 1.208052 AGTGGGAATGATCGACACTGG 59.792 52.381 2.17 0.00 40.64 4.00
977 1003 0.675837 GACGGCTGGGTTTAGGGTTC 60.676 60.000 0.00 0.00 0.00 3.62
1086 1112 4.817909 GGGGTGGTCGGGGAGGAT 62.818 72.222 0.00 0.00 0.00 3.24
1115 1141 3.764466 CGAGGCGGGTCTTCTGCT 61.764 66.667 0.00 0.00 46.69 4.24
1212 1238 1.835712 ACGGTCGAGGTGGGTCTTT 60.836 57.895 0.00 0.00 0.00 2.52
1293 1319 1.582624 TGGGGGATGAGAAGAGAGGAT 59.417 52.381 0.00 0.00 0.00 3.24
1701 1727 1.563435 CTTGCAGTGACTCGCCACAG 61.563 60.000 0.00 0.00 39.42 3.66
1775 1801 2.843701 CCATCTCACTCAGTAATGCCC 58.156 52.381 0.00 0.00 0.00 5.36
1959 1985 3.876914 CAGTATCAAAATCGCCAGCCTTA 59.123 43.478 0.00 0.00 0.00 2.69
2016 2042 1.180456 TCGAGAAGCACGGTACCCAA 61.180 55.000 6.25 0.00 0.00 4.12
2025 2051 2.370281 TCTTCATGGTCGAGAAGCAC 57.630 50.000 7.15 0.00 40.72 4.40
2130 2156 2.637165 ACCTCTTTCCACCCTTCATCT 58.363 47.619 0.00 0.00 0.00 2.90
2163 2189 4.161565 TGCGAGTGGTTATTCTATTGAGGT 59.838 41.667 0.00 0.00 0.00 3.85
2184 2210 6.151144 ACATGAAGTAGGAAAACAATACCTGC 59.849 38.462 0.00 0.00 36.83 4.85
2204 2230 9.944663 GTTGTGTATTTGTTTCTAAGAACATGA 57.055 29.630 0.00 0.00 39.12 3.07
2205 2231 9.950680 AGTTGTGTATTTGTTTCTAAGAACATG 57.049 29.630 0.00 0.00 39.12 3.21
2229 2256 8.944029 CAGACATCAGTATTCTCAAATTGAAGT 58.056 33.333 0.00 0.00 0.00 3.01
2268 2309 7.608308 TGTGAAATGGCAAATTTAATAAGCC 57.392 32.000 11.94 11.94 45.41 4.35
2269 2310 9.706846 GAATGTGAAATGGCAAATTTAATAAGC 57.293 29.630 0.00 0.00 0.00 3.09
2295 2345 9.357652 GCATATTGTAATATTGCAGGTTTATGG 57.642 33.333 18.25 6.91 31.59 2.74
2331 2381 6.516718 CAACATCTTCCGGATATAGAACAGT 58.483 40.000 4.15 3.59 32.64 3.55
2448 3299 2.224209 GGACTCGAACCAAGAGGAACAA 60.224 50.000 3.80 0.00 39.90 2.83
2495 3346 2.844122 AACACTGGAACGCAGAAAAC 57.156 45.000 0.00 0.00 0.00 2.43
2672 3523 9.669353 CATACATCAAACTAATGAATACAAGGC 57.331 33.333 0.00 0.00 32.06 4.35
2702 3553 7.793709 AGATCTTATATTATGGGATGGAGGGAG 59.206 40.741 0.00 0.00 0.00 4.30
2703 3554 7.675591 AGATCTTATATTATGGGATGGAGGGA 58.324 38.462 0.00 0.00 0.00 4.20
2704 3555 7.944414 AGATCTTATATTATGGGATGGAGGG 57.056 40.000 0.00 0.00 0.00 4.30
2741 3592 8.682710 CCGACCCAAAATTTAAGATCTTTCATA 58.317 33.333 14.36 0.00 0.00 2.15
2742 3593 7.396055 TCCGACCCAAAATTTAAGATCTTTCAT 59.604 33.333 14.36 3.28 0.00 2.57
2743 3594 6.717540 TCCGACCCAAAATTTAAGATCTTTCA 59.282 34.615 14.36 0.69 0.00 2.69
2744 3595 7.153217 TCCGACCCAAAATTTAAGATCTTTC 57.847 36.000 14.36 0.00 0.00 2.62
2745 3596 6.152831 CCTCCGACCCAAAATTTAAGATCTTT 59.847 38.462 14.36 0.00 0.00 2.52
2746 3597 5.652452 CCTCCGACCCAAAATTTAAGATCTT 59.348 40.000 13.56 13.56 0.00 2.40
2747 3598 5.193679 CCTCCGACCCAAAATTTAAGATCT 58.806 41.667 0.00 0.00 0.00 2.75
2748 3599 4.338400 CCCTCCGACCCAAAATTTAAGATC 59.662 45.833 0.00 0.00 0.00 2.75
2749 3600 4.278310 CCCTCCGACCCAAAATTTAAGAT 58.722 43.478 0.00 0.00 0.00 2.40
2750 3601 3.562609 CCCCTCCGACCCAAAATTTAAGA 60.563 47.826 0.00 0.00 0.00 2.10
2751 3602 2.758423 CCCCTCCGACCCAAAATTTAAG 59.242 50.000 0.00 0.00 0.00 1.85
2752 3603 2.557901 CCCCCTCCGACCCAAAATTTAA 60.558 50.000 0.00 0.00 0.00 1.52
2753 3604 1.006162 CCCCCTCCGACCCAAAATTTA 59.994 52.381 0.00 0.00 0.00 1.40
2754 3605 0.252057 CCCCCTCCGACCCAAAATTT 60.252 55.000 0.00 0.00 0.00 1.82
2755 3606 1.386550 CCCCCTCCGACCCAAAATT 59.613 57.895 0.00 0.00 0.00 1.82
2756 3607 0.550638 TACCCCCTCCGACCCAAAAT 60.551 55.000 0.00 0.00 0.00 1.82
2757 3608 1.151855 TACCCCCTCCGACCCAAAA 60.152 57.895 0.00 0.00 0.00 2.44
2758 3609 1.614226 CTACCCCCTCCGACCCAAA 60.614 63.158 0.00 0.00 0.00 3.28
2759 3610 1.517538 TACTACCCCCTCCGACCCAA 61.518 60.000 0.00 0.00 0.00 4.12
2760 3611 1.298906 ATACTACCCCCTCCGACCCA 61.299 60.000 0.00 0.00 0.00 4.51
2761 3612 0.779997 TATACTACCCCCTCCGACCC 59.220 60.000 0.00 0.00 0.00 4.46
2762 3613 1.272369 CCTATACTACCCCCTCCGACC 60.272 61.905 0.00 0.00 0.00 4.79
2763 3614 1.707427 TCCTATACTACCCCCTCCGAC 59.293 57.143 0.00 0.00 0.00 4.79
2764 3615 2.138535 TCCTATACTACCCCCTCCGA 57.861 55.000 0.00 0.00 0.00 4.55
2765 3616 2.581709 AGATCCTATACTACCCCCTCCG 59.418 54.545 0.00 0.00 0.00 4.63
2766 3617 3.596956 TCAGATCCTATACTACCCCCTCC 59.403 52.174 0.00 0.00 0.00 4.30
2767 3618 4.949966 TCAGATCCTATACTACCCCCTC 57.050 50.000 0.00 0.00 0.00 4.30
2768 3619 5.461317 CCTTTCAGATCCTATACTACCCCCT 60.461 48.000 0.00 0.00 0.00 4.79
2769 3620 4.778427 CCTTTCAGATCCTATACTACCCCC 59.222 50.000 0.00 0.00 0.00 5.40
2770 3621 5.652324 TCCTTTCAGATCCTATACTACCCC 58.348 45.833 0.00 0.00 0.00 4.95
2771 3622 7.363094 CGATTCCTTTCAGATCCTATACTACCC 60.363 44.444 0.00 0.00 0.00 3.69
2772 3623 7.363094 CCGATTCCTTTCAGATCCTATACTACC 60.363 44.444 0.00 0.00 0.00 3.18
2773 3624 7.363094 CCCGATTCCTTTCAGATCCTATACTAC 60.363 44.444 0.00 0.00 0.00 2.73
2796 3647 1.414919 TCCGGATAAATGAGAACCCCG 59.585 52.381 0.00 0.00 35.68 5.73
2802 3653 3.031013 TCAGCTGTCCGGATAAATGAGA 58.969 45.455 14.67 0.00 0.00 3.27
2827 3679 9.554395 TCCTTTTCCTTACAAATTTGAAAATCC 57.446 29.630 24.64 0.00 35.21 3.01
2858 3710 8.621532 AAAAGCAATGTTGATCTACTACAGAA 57.378 30.769 8.74 0.00 37.61 3.02
2872 3724 9.558396 TTCCAATTTCTCATTAAAAGCAATGTT 57.442 25.926 0.00 0.00 37.23 2.71
2873 3725 8.992073 GTTCCAATTTCTCATTAAAAGCAATGT 58.008 29.630 0.00 0.00 37.23 2.71
2876 3728 6.644592 CCGTTCCAATTTCTCATTAAAAGCAA 59.355 34.615 0.00 0.00 0.00 3.91
2885 3737 6.894339 ACTTAAACCGTTCCAATTTCTCAT 57.106 33.333 0.00 0.00 0.00 2.90
2886 3738 6.993902 ACTACTTAAACCGTTCCAATTTCTCA 59.006 34.615 0.00 0.00 0.00 3.27
2887 3739 7.430992 ACTACTTAAACCGTTCCAATTTCTC 57.569 36.000 0.00 0.00 0.00 2.87
2956 3808 4.102681 AGGGGAATAAAATCTACCTCACGG 59.897 45.833 0.00 0.00 0.00 4.94
2957 3809 5.291905 AGGGGAATAAAATCTACCTCACG 57.708 43.478 0.00 0.00 0.00 4.35
2958 3810 5.298347 CGAGGGGAATAAAATCTACCTCAC 58.702 45.833 0.00 0.00 40.40 3.51
2959 3811 4.347000 CCGAGGGGAATAAAATCTACCTCA 59.653 45.833 0.00 0.00 40.40 3.86
2960 3812 4.591924 TCCGAGGGGAATAAAATCTACCTC 59.408 45.833 0.00 0.00 40.15 3.85
2961 3813 4.563782 TCCGAGGGGAATAAAATCTACCT 58.436 43.478 0.00 0.00 40.15 3.08
2962 3814 4.262938 CCTCCGAGGGGAATAAAATCTACC 60.263 50.000 6.53 0.00 43.27 3.18
2989 3841 5.102953 TGGAACAGAGGGAGTATGATTTG 57.897 43.478 0.00 0.00 0.00 2.32
3005 3894 5.197451 ACCAGTGACACTTATTTTGGAACA 58.803 37.500 14.36 0.00 0.00 3.18
3008 3897 7.057894 ACTAAACCAGTGACACTTATTTTGGA 58.942 34.615 15.58 2.33 35.62 3.53
3044 3933 6.924612 TGTCGCTGATTTAGTACAACTTTGTA 59.075 34.615 0.00 0.00 42.35 2.41
3045 3934 5.756347 TGTCGCTGATTTAGTACAACTTTGT 59.244 36.000 0.00 0.00 44.86 2.83
3046 3935 6.223138 TGTCGCTGATTTAGTACAACTTTG 57.777 37.500 0.00 0.00 0.00 2.77
3047 3936 7.435068 AATGTCGCTGATTTAGTACAACTTT 57.565 32.000 0.00 0.00 31.32 2.66
3048 3937 7.435068 AAATGTCGCTGATTTAGTACAACTT 57.565 32.000 0.00 0.00 31.32 2.66
3049 3938 8.718102 ATAAATGTCGCTGATTTAGTACAACT 57.282 30.769 0.00 0.00 30.69 3.16
3050 3939 9.769093 AAATAAATGTCGCTGATTTAGTACAAC 57.231 29.630 0.00 0.00 30.69 3.32
3051 3940 9.982291 GAAATAAATGTCGCTGATTTAGTACAA 57.018 29.630 0.00 0.00 30.69 2.41
3052 3941 8.325282 CGAAATAAATGTCGCTGATTTAGTACA 58.675 33.333 0.00 0.00 30.69 2.90
3053 3942 7.792508 CCGAAATAAATGTCGCTGATTTAGTAC 59.207 37.037 0.00 0.00 35.93 2.73
3054 3943 7.042321 CCCGAAATAAATGTCGCTGATTTAGTA 60.042 37.037 0.00 0.00 35.93 1.82
3055 3944 6.238374 CCCGAAATAAATGTCGCTGATTTAGT 60.238 38.462 0.00 0.00 35.93 2.24
3056 3945 6.136071 CCCGAAATAAATGTCGCTGATTTAG 58.864 40.000 0.00 0.00 35.93 1.85
3057 3946 5.008217 CCCCGAAATAAATGTCGCTGATTTA 59.992 40.000 0.00 0.00 35.93 1.40
3058 3947 4.202010 CCCCGAAATAAATGTCGCTGATTT 60.202 41.667 0.00 0.00 35.93 2.17
3059 3948 3.315191 CCCCGAAATAAATGTCGCTGATT 59.685 43.478 0.00 0.00 35.93 2.57
3060 3949 2.878406 CCCCGAAATAAATGTCGCTGAT 59.122 45.455 0.00 0.00 35.93 2.90
3061 3950 2.285083 CCCCGAAATAAATGTCGCTGA 58.715 47.619 0.00 0.00 35.93 4.26
3062 3951 1.268539 GCCCCGAAATAAATGTCGCTG 60.269 52.381 0.00 0.00 35.93 5.18
3063 3952 1.021968 GCCCCGAAATAAATGTCGCT 58.978 50.000 0.00 0.00 35.93 4.93
3064 3953 0.316689 CGCCCCGAAATAAATGTCGC 60.317 55.000 0.00 0.00 35.93 5.19
3065 3954 0.306533 CCGCCCCGAAATAAATGTCG 59.693 55.000 0.00 0.00 37.01 4.35
3066 3955 1.602377 CTCCGCCCCGAAATAAATGTC 59.398 52.381 0.00 0.00 0.00 3.06
3067 3956 1.675552 CTCCGCCCCGAAATAAATGT 58.324 50.000 0.00 0.00 0.00 2.71
3068 3957 0.951558 CCTCCGCCCCGAAATAAATG 59.048 55.000 0.00 0.00 0.00 2.32
3069 3958 0.179001 CCCTCCGCCCCGAAATAAAT 60.179 55.000 0.00 0.00 0.00 1.40
3070 3959 1.225148 CCCTCCGCCCCGAAATAAA 59.775 57.895 0.00 0.00 0.00 1.40
3071 3960 1.689932 TCCCTCCGCCCCGAAATAA 60.690 57.895 0.00 0.00 0.00 1.40
3072 3961 2.041715 TCCCTCCGCCCCGAAATA 60.042 61.111 0.00 0.00 0.00 1.40
3073 3962 2.884179 TACTCCCTCCGCCCCGAAAT 62.884 60.000 0.00 0.00 0.00 2.17
3074 3963 3.605412 TACTCCCTCCGCCCCGAAA 62.605 63.158 0.00 0.00 0.00 3.46
3075 3964 4.064768 TACTCCCTCCGCCCCGAA 62.065 66.667 0.00 0.00 0.00 4.30
3076 3965 4.828296 GTACTCCCTCCGCCCCGA 62.828 72.222 0.00 0.00 0.00 5.14
3077 3966 2.989173 TATGTACTCCCTCCGCCCCG 62.989 65.000 0.00 0.00 0.00 5.73
3078 3967 0.761702 TTATGTACTCCCTCCGCCCC 60.762 60.000 0.00 0.00 0.00 5.80
3079 3968 0.391966 GTTATGTACTCCCTCCGCCC 59.608 60.000 0.00 0.00 0.00 6.13
3080 3969 1.411041 AGTTATGTACTCCCTCCGCC 58.589 55.000 0.00 0.00 28.23 6.13
3081 3970 4.868314 ATTAGTTATGTACTCCCTCCGC 57.132 45.455 0.00 0.00 38.33 5.54
3111 4000 3.050275 GTCTGTTGGTGCGCCTCC 61.050 66.667 18.96 8.52 35.27 4.30
3117 4006 4.946784 AATCTAAATCGTCTGTTGGTGC 57.053 40.909 0.00 0.00 0.00 5.01
3123 4012 9.877178 ATGAAACTCTAAATCTAAATCGTCTGT 57.123 29.630 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.