Multiple sequence alignment - TraesCS1D01G379600

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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 TraesCS1D01G379600 chr1D 100.000 4753 0 0 1 4753 455751931 455756683 0.000000e+00 8778.0
1 TraesCS1D01G379600 chr1B 94.917 3856 158 14 909 4753 626091005 626094833 0.000000e+00 6000.0
2 TraesCS1D01G379600 chr1B 88.262 443 30 11 135 568 626088473 626088902 1.180000e-140 510.0
3 TraesCS1D01G379600 chr1B 87.375 301 28 9 618 916 626090558 626090850 2.120000e-88 337.0
4 TraesCS1D01G379600 chr6B 85.297 2326 319 18 945 3253 130301741 130304060 0.000000e+00 2379.0
5 TraesCS1D01G379600 chr6D 85.146 2336 322 19 935 3253 58042981 58045308 0.000000e+00 2368.0
6 TraesCS1D01G379600 chr2A 81.908 2620 422 36 853 3458 762801284 762803865 0.000000e+00 2165.0
7 TraesCS1D01G379600 chr2A 81.988 2354 381 34 932 3255 762759133 762761473 0.000000e+00 1958.0
8 TraesCS1D01G379600 chr2A 83.231 2111 347 5 922 3027 762947588 762949696 0.000000e+00 1930.0
9 TraesCS1D01G379600 chr2A 80.275 218 38 5 3478 3692 762702600 762702815 4.920000e-35 159.0
10 TraesCS1D01G379600 chr2A 80.208 192 31 6 3482 3667 762886881 762887071 2.310000e-28 137.0
11 TraesCS1D01G379600 chr2A 81.935 155 27 1 3511 3664 762761867 762762021 3.860000e-26 130.0
12 TraesCS1D01G379600 chr2A 79.532 171 32 3 3478 3646 762739254 762739423 8.360000e-23 119.0
13 TraesCS1D01G379600 chr2A 97.436 39 1 0 682 720 762770535 762770573 3.070000e-07 67.6
14 TraesCS1D01G379600 chr2B 82.954 2417 377 28 853 3254 794630714 794628318 0.000000e+00 2148.0
15 TraesCS1D01G379600 chr2B 83.544 158 23 3 3481 3636 794425815 794425659 1.380000e-30 145.0
16 TraesCS1D01G379600 chr2B 81.366 161 26 4 3478 3636 794595784 794595942 1.390000e-25 128.0
17 TraesCS1D01G379600 chr2B 94.000 50 3 0 3876 3925 774704494 774704445 5.100000e-10 76.8
18 TraesCS1D01G379600 chrUn 80.879 2547 421 37 910 3435 234394466 234396967 0.000000e+00 1945.0
19 TraesCS1D01G379600 chrUn 95.349 43 2 0 3876 3918 359482822 359482780 8.530000e-08 69.4
20 TraesCS1D01G379600 chrUn 95.349 43 2 0 3876 3918 359503812 359503770 8.530000e-08 69.4
21 TraesCS1D01G379600 chr2D 81.721 2347 407 20 914 3248 636795586 636793250 0.000000e+00 1938.0
22 TraesCS1D01G379600 chr2D 95.918 49 2 0 4168 4216 580395197 580395245 3.940000e-11 80.5
23 TraesCS1D01G379600 chr2D 97.436 39 1 0 682 720 636738422 636738384 3.070000e-07 67.6
24 TraesCS1D01G379600 chr1A 88.223 484 49 7 3478 3958 549293055 549293533 5.340000e-159 571.0
25 TraesCS1D01G379600 chr1A 91.429 70 3 2 4434 4503 549294014 549294080 5.060000e-15 93.5
26 TraesCS1D01G379600 chr7B 80.645 217 35 7 3481 3692 746154051 746153837 1.370000e-35 161.0
27 TraesCS1D01G379600 chr7B 90.000 70 7 0 3876 3945 746112479 746112410 1.820000e-14 91.6
28 TraesCS1D01G379600 chr7B 88.571 70 8 0 3876 3945 746141550 746141481 8.470000e-13 86.1
29 TraesCS1D01G379600 chr6A 86.400 125 17 0 3487 3611 13970010 13970134 2.310000e-28 137.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G379600 chr1D 455751931 455756683 4752 False 8778.000000 8778 100.000000 1 4753 1 chr1D.!!$F1 4752
1 TraesCS1D01G379600 chr1B 626088473 626094833 6360 False 2282.333333 6000 90.184667 135 4753 3 chr1B.!!$F1 4618
2 TraesCS1D01G379600 chr6B 130301741 130304060 2319 False 2379.000000 2379 85.297000 945 3253 1 chr6B.!!$F1 2308
3 TraesCS1D01G379600 chr6D 58042981 58045308 2327 False 2368.000000 2368 85.146000 935 3253 1 chr6D.!!$F1 2318
4 TraesCS1D01G379600 chr2A 762801284 762803865 2581 False 2165.000000 2165 81.908000 853 3458 1 chr2A.!!$F4 2605
5 TraesCS1D01G379600 chr2A 762947588 762949696 2108 False 1930.000000 1930 83.231000 922 3027 1 chr2A.!!$F6 2105
6 TraesCS1D01G379600 chr2A 762759133 762762021 2888 False 1044.000000 1958 81.961500 932 3664 2 chr2A.!!$F7 2732
7 TraesCS1D01G379600 chr2B 794628318 794630714 2396 True 2148.000000 2148 82.954000 853 3254 1 chr2B.!!$R3 2401
8 TraesCS1D01G379600 chrUn 234394466 234396967 2501 False 1945.000000 1945 80.879000 910 3435 1 chrUn.!!$F1 2525
9 TraesCS1D01G379600 chr2D 636793250 636795586 2336 True 1938.000000 1938 81.721000 914 3248 1 chr2D.!!$R2 2334
10 TraesCS1D01G379600 chr1A 549293055 549294080 1025 False 332.250000 571 89.826000 3478 4503 2 chr1A.!!$F1 1025

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
577 585 0.034477 CCGCTTTCCACATACCCCTT 60.034 55.000 0.00 0.00 0.00 3.95 F
751 2387 0.321653 ACGTGATTTCTGGTCAGGGC 60.322 55.000 0.00 0.00 36.18 5.19 F
1398 3216 0.896923 TTCATACCGCCGTACAAGGT 59.103 50.000 8.63 8.63 41.73 3.50 F
1728 3552 1.069978 GTTGGAATTGGTGGTGTTGGG 59.930 52.381 0.00 0.00 0.00 4.12 F
2026 3850 2.288213 GCACCTTTTAGAAGTGCCCAAC 60.288 50.000 3.01 0.00 35.62 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 3459 0.730840 TGCTTGATGATGAGCTTGCG 59.269 50.000 0.00 0.00 39.60 4.85 R
1728 3552 2.858745 TGTTGGGCCAAAGTAGTCTTC 58.141 47.619 22.82 5.61 32.90 2.87 R
3386 5226 1.115326 AAACCAACTTGGGAGCCAGC 61.115 55.000 12.62 0.00 43.37 4.85 R
3554 5562 6.010294 TGGATATCTCGACGGTCTTTATTC 57.990 41.667 6.57 0.00 0.00 1.75 R
3785 5795 0.884704 GAGGCAAAGGCACGAAGTCA 60.885 55.000 0.00 0.00 41.61 3.41 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 3.784412 CAAATCGGCGGCGTTCGT 61.784 61.111 31.06 11.71 41.72 3.85
18 19 3.045492 AAATCGGCGGCGTTCGTT 61.045 55.556 31.06 17.81 41.72 3.85
19 20 2.609759 AAATCGGCGGCGTTCGTTT 61.610 52.632 31.06 21.97 41.72 3.60
20 21 2.503034 AAATCGGCGGCGTTCGTTTC 62.503 55.000 31.06 0.00 41.72 2.78
21 22 4.946266 TCGGCGGCGTTCGTTTCA 62.946 61.111 31.06 6.10 41.72 2.69
22 23 4.712873 CGGCGGCGTTCGTTTCAC 62.713 66.667 24.74 0.00 41.72 3.18
23 24 4.379143 GGCGGCGTTCGTTTCACC 62.379 66.667 9.37 0.00 41.72 4.02
24 25 3.343421 GCGGCGTTCGTTTCACCT 61.343 61.111 9.37 0.00 41.72 4.00
25 26 2.888998 GCGGCGTTCGTTTCACCTT 61.889 57.895 9.37 0.00 41.72 3.50
26 27 1.083015 CGGCGTTCGTTTCACCTTG 60.083 57.895 0.00 0.00 0.00 3.61
27 28 1.768112 CGGCGTTCGTTTCACCTTGT 61.768 55.000 0.00 0.00 0.00 3.16
28 29 0.379316 GGCGTTCGTTTCACCTTGTT 59.621 50.000 0.00 0.00 0.00 2.83
29 30 1.598601 GGCGTTCGTTTCACCTTGTTA 59.401 47.619 0.00 0.00 0.00 2.41
30 31 2.031930 GGCGTTCGTTTCACCTTGTTAA 59.968 45.455 0.00 0.00 0.00 2.01
31 32 3.285745 GCGTTCGTTTCACCTTGTTAAG 58.714 45.455 0.00 0.00 0.00 1.85
32 33 3.285745 CGTTCGTTTCACCTTGTTAAGC 58.714 45.455 0.00 0.00 0.00 3.09
33 34 3.242478 CGTTCGTTTCACCTTGTTAAGCA 60.242 43.478 0.00 0.00 0.00 3.91
34 35 4.553938 CGTTCGTTTCACCTTGTTAAGCAT 60.554 41.667 0.00 0.00 0.00 3.79
35 36 5.278604 GTTCGTTTCACCTTGTTAAGCATT 58.721 37.500 0.00 0.00 0.00 3.56
36 37 5.103290 TCGTTTCACCTTGTTAAGCATTC 57.897 39.130 0.00 0.00 0.00 2.67
37 38 3.906008 CGTTTCACCTTGTTAAGCATTCG 59.094 43.478 0.00 0.00 0.00 3.34
38 39 4.319190 CGTTTCACCTTGTTAAGCATTCGA 60.319 41.667 0.00 0.00 0.00 3.71
39 40 5.616866 CGTTTCACCTTGTTAAGCATTCGAT 60.617 40.000 0.00 0.00 0.00 3.59
40 41 5.545658 TTCACCTTGTTAAGCATTCGATC 57.454 39.130 0.00 0.00 0.00 3.69
41 42 3.938963 TCACCTTGTTAAGCATTCGATCC 59.061 43.478 0.00 0.00 0.00 3.36
42 43 3.065371 CACCTTGTTAAGCATTCGATCCC 59.935 47.826 0.00 0.00 0.00 3.85
43 44 2.618709 CCTTGTTAAGCATTCGATCCCC 59.381 50.000 0.00 0.00 0.00 4.81
44 45 3.545703 CTTGTTAAGCATTCGATCCCCT 58.454 45.455 0.00 0.00 0.00 4.79
45 46 3.644966 TGTTAAGCATTCGATCCCCTT 57.355 42.857 0.00 0.00 0.00 3.95
46 47 3.278574 TGTTAAGCATTCGATCCCCTTG 58.721 45.455 0.00 0.00 0.00 3.61
47 48 2.618709 GTTAAGCATTCGATCCCCTTGG 59.381 50.000 0.00 0.00 0.00 3.61
48 49 0.753111 AAGCATTCGATCCCCTTGGC 60.753 55.000 0.00 0.00 0.00 4.52
49 50 2.196245 GCATTCGATCCCCTTGGCC 61.196 63.158 0.00 0.00 0.00 5.36
50 51 1.533711 CATTCGATCCCCTTGGCCT 59.466 57.895 3.32 0.00 0.00 5.19
51 52 0.106519 CATTCGATCCCCTTGGCCTT 60.107 55.000 3.32 0.00 0.00 4.35
52 53 0.106519 ATTCGATCCCCTTGGCCTTG 60.107 55.000 3.32 0.00 0.00 3.61
53 54 1.204786 TTCGATCCCCTTGGCCTTGA 61.205 55.000 3.32 0.00 0.00 3.02
54 55 0.988145 TCGATCCCCTTGGCCTTGAT 60.988 55.000 3.32 0.00 0.00 2.57
55 56 0.536006 CGATCCCCTTGGCCTTGATC 60.536 60.000 3.32 7.32 0.00 2.92
56 57 0.552848 GATCCCCTTGGCCTTGATCA 59.447 55.000 3.32 0.00 33.64 2.92
57 58 1.146566 GATCCCCTTGGCCTTGATCAT 59.853 52.381 3.32 0.00 33.64 2.45
58 59 0.552848 TCCCCTTGGCCTTGATCATC 59.447 55.000 3.32 0.00 0.00 2.92
59 60 0.820891 CCCCTTGGCCTTGATCATCG 60.821 60.000 3.32 0.00 0.00 3.84
60 61 0.181114 CCCTTGGCCTTGATCATCGA 59.819 55.000 3.32 0.00 0.00 3.59
61 62 1.408683 CCCTTGGCCTTGATCATCGAA 60.409 52.381 3.32 0.00 0.00 3.71
62 63 2.368439 CCTTGGCCTTGATCATCGAAA 58.632 47.619 3.32 0.00 0.00 3.46
63 64 2.357009 CCTTGGCCTTGATCATCGAAAG 59.643 50.000 3.32 0.00 0.00 2.62
64 65 2.042686 TGGCCTTGATCATCGAAAGG 57.957 50.000 3.32 8.24 42.86 3.11
65 66 1.559219 TGGCCTTGATCATCGAAAGGA 59.441 47.619 15.49 2.41 42.65 3.36
66 67 2.026356 TGGCCTTGATCATCGAAAGGAA 60.026 45.455 15.49 1.71 42.65 3.36
67 68 3.217626 GGCCTTGATCATCGAAAGGAAT 58.782 45.455 15.49 0.00 42.65 3.01
68 69 3.251972 GGCCTTGATCATCGAAAGGAATC 59.748 47.826 15.49 3.61 42.65 2.52
69 70 3.059325 GCCTTGATCATCGAAAGGAATCG 60.059 47.826 15.49 0.00 42.65 3.34
76 77 2.010145 TCGAAAGGAATCGAGCTTGG 57.990 50.000 0.00 0.00 46.12 3.61
77 78 0.375106 CGAAAGGAATCGAGCTTGGC 59.625 55.000 0.00 0.00 45.48 4.52
78 79 0.375106 GAAAGGAATCGAGCTTGGCG 59.625 55.000 0.00 0.00 0.00 5.69
79 80 0.321653 AAAGGAATCGAGCTTGGCGT 60.322 50.000 0.00 0.00 0.00 5.68
80 81 0.321653 AAGGAATCGAGCTTGGCGTT 60.322 50.000 0.00 0.00 0.00 4.84
81 82 0.321653 AGGAATCGAGCTTGGCGTTT 60.322 50.000 0.00 0.00 0.00 3.60
82 83 0.521735 GGAATCGAGCTTGGCGTTTT 59.478 50.000 0.00 0.00 0.00 2.43
83 84 1.068541 GGAATCGAGCTTGGCGTTTTT 60.069 47.619 0.00 0.00 0.00 1.94
84 85 1.978782 GAATCGAGCTTGGCGTTTTTG 59.021 47.619 0.00 0.00 0.00 2.44
85 86 0.387239 ATCGAGCTTGGCGTTTTTGC 60.387 50.000 0.00 0.00 0.00 3.68
95 96 1.864565 GCGTTTTTGCCCATTTCTGT 58.135 45.000 0.00 0.00 0.00 3.41
96 97 2.209273 GCGTTTTTGCCCATTTCTGTT 58.791 42.857 0.00 0.00 0.00 3.16
97 98 2.032979 GCGTTTTTGCCCATTTCTGTTG 60.033 45.455 0.00 0.00 0.00 3.33
98 99 2.032979 CGTTTTTGCCCATTTCTGTTGC 60.033 45.455 0.00 0.00 0.00 4.17
99 100 3.205338 GTTTTTGCCCATTTCTGTTGCT 58.795 40.909 0.00 0.00 0.00 3.91
100 101 4.376146 GTTTTTGCCCATTTCTGTTGCTA 58.624 39.130 0.00 0.00 0.00 3.49
101 102 3.658757 TTTGCCCATTTCTGTTGCTAC 57.341 42.857 0.00 0.00 0.00 3.58
102 103 2.584835 TGCCCATTTCTGTTGCTACT 57.415 45.000 0.00 0.00 0.00 2.57
103 104 2.161855 TGCCCATTTCTGTTGCTACTG 58.838 47.619 0.00 0.00 0.00 2.74
104 105 1.474077 GCCCATTTCTGTTGCTACTGG 59.526 52.381 5.45 1.55 0.00 4.00
105 106 2.879756 GCCCATTTCTGTTGCTACTGGA 60.880 50.000 5.32 0.00 0.00 3.86
106 107 3.012518 CCCATTTCTGTTGCTACTGGAG 58.987 50.000 5.32 0.00 0.00 3.86
107 108 3.560025 CCCATTTCTGTTGCTACTGGAGT 60.560 47.826 5.32 0.00 0.00 3.85
108 109 3.438087 CCATTTCTGTTGCTACTGGAGTG 59.562 47.826 5.45 4.08 0.00 3.51
109 110 2.839486 TTCTGTTGCTACTGGAGTGG 57.161 50.000 5.45 0.00 0.00 4.00
119 120 4.691860 CTACTGGAGTGGCATTCTTTTG 57.308 45.455 9.98 1.21 0.00 2.44
120 121 1.615392 ACTGGAGTGGCATTCTTTTGC 59.385 47.619 9.98 0.00 42.01 3.68
121 122 1.891150 CTGGAGTGGCATTCTTTTGCT 59.109 47.619 9.98 0.00 42.38 3.91
122 123 3.084039 CTGGAGTGGCATTCTTTTGCTA 58.916 45.455 9.98 0.00 42.38 3.49
127 128 4.773323 GTGGCATTCTTTTGCTACTCTT 57.227 40.909 5.78 0.00 46.84 2.85
128 129 5.880054 GTGGCATTCTTTTGCTACTCTTA 57.120 39.130 5.78 0.00 46.84 2.10
129 130 5.631992 GTGGCATTCTTTTGCTACTCTTAC 58.368 41.667 5.78 0.00 46.84 2.34
130 131 5.412904 GTGGCATTCTTTTGCTACTCTTACT 59.587 40.000 5.78 0.00 46.84 2.24
131 132 5.412594 TGGCATTCTTTTGCTACTCTTACTG 59.587 40.000 0.00 0.00 42.38 2.74
132 133 5.163713 GGCATTCTTTTGCTACTCTTACTGG 60.164 44.000 0.00 0.00 42.38 4.00
133 134 5.412904 GCATTCTTTTGCTACTCTTACTGGT 59.587 40.000 0.00 0.00 39.57 4.00
163 164 9.221933 TCAGTAACTAAAGAAAACAGTTTGTCA 57.778 29.630 0.00 0.00 34.48 3.58
170 171 7.681939 AAAGAAAACAGTTTGTCAGTACTCA 57.318 32.000 0.00 0.00 0.00 3.41
174 175 4.408182 ACAGTTTGTCAGTACTCAGCTT 57.592 40.909 0.00 0.00 0.00 3.74
178 179 3.475566 TTGTCAGTACTCAGCTTGCTT 57.524 42.857 0.00 0.00 0.00 3.91
314 317 2.730382 TGCATGGCATCTCACTTCATT 58.270 42.857 0.00 0.00 31.71 2.57
327 330 0.592637 CTTCATTGTTGTCGCAGGCA 59.407 50.000 0.00 0.00 45.30 4.75
347 350 3.058160 CAAAGCTGTGAGGCCGGG 61.058 66.667 2.18 0.00 0.00 5.73
393 396 6.759497 GCCTAGAATTGGCTTTTTCTAAGA 57.241 37.500 0.00 0.00 46.38 2.10
394 397 6.556212 GCCTAGAATTGGCTTTTTCTAAGAC 58.444 40.000 0.00 0.00 46.38 3.01
395 398 6.151144 GCCTAGAATTGGCTTTTTCTAAGACA 59.849 38.462 0.00 0.00 46.38 3.41
407 415 7.539022 GCTTTTTCTAAGACATTGTTAAGCTCC 59.461 37.037 0.00 0.00 33.42 4.70
410 418 6.374417 TCTAAGACATTGTTAAGCTCCCTT 57.626 37.500 0.00 0.00 35.05 3.95
412 420 5.966742 AAGACATTGTTAAGCTCCCTTTC 57.033 39.130 0.00 0.00 32.47 2.62
414 422 4.043435 AGACATTGTTAAGCTCCCTTTCCT 59.957 41.667 0.00 0.00 32.47 3.36
426 434 1.075374 CCCTTTCCTTCACACCCATCA 59.925 52.381 0.00 0.00 0.00 3.07
434 442 5.886609 TCCTTCACACCCATCAAAGATTTA 58.113 37.500 0.00 0.00 0.00 1.40
437 445 6.377996 CCTTCACACCCATCAAAGATTTATCA 59.622 38.462 0.00 0.00 0.00 2.15
438 446 6.757897 TCACACCCATCAAAGATTTATCAC 57.242 37.500 0.00 0.00 0.00 3.06
439 447 5.652014 TCACACCCATCAAAGATTTATCACC 59.348 40.000 0.00 0.00 0.00 4.02
440 448 5.653769 CACACCCATCAAAGATTTATCACCT 59.346 40.000 0.00 0.00 0.00 4.00
441 449 5.888161 ACACCCATCAAAGATTTATCACCTC 59.112 40.000 0.00 0.00 0.00 3.85
442 450 6.125029 CACCCATCAAAGATTTATCACCTCT 58.875 40.000 0.00 0.00 0.00 3.69
447 455 7.013083 CCATCAAAGATTTATCACCTCTTCCTG 59.987 40.741 0.00 0.00 0.00 3.86
448 456 5.882557 TCAAAGATTTATCACCTCTTCCTGC 59.117 40.000 0.00 0.00 0.00 4.85
450 458 5.033589 AGATTTATCACCTCTTCCTGCTG 57.966 43.478 0.00 0.00 0.00 4.41
453 461 0.252479 ATCACCTCTTCCTGCTGCTG 59.748 55.000 0.00 0.00 0.00 4.41
456 464 1.745864 CCTCTTCCTGCTGCTGCTG 60.746 63.158 17.00 15.58 40.48 4.41
471 479 2.962569 CTGCTGCTGCTGCACATT 59.037 55.556 27.01 0.00 45.31 2.71
476 484 0.728129 CTGCTGCTGCACATTTGACG 60.728 55.000 14.93 0.00 45.31 4.35
481 489 0.310543 GCTGCACATTTGACGGTGAA 59.689 50.000 0.00 0.00 37.18 3.18
483 491 2.855180 CTGCACATTTGACGGTGAATC 58.145 47.619 0.00 0.00 37.18 2.52
521 529 2.930562 ACTGGTCCAGGTGAGCCC 60.931 66.667 23.06 0.00 40.88 5.19
523 531 2.607750 TGGTCCAGGTGAGCCCTC 60.608 66.667 0.00 0.00 43.86 4.30
541 549 4.593956 CCCTCAACCTTGCTTTCTTCTAT 58.406 43.478 0.00 0.00 0.00 1.98
544 552 4.985538 TCAACCTTGCTTTCTTCTATGGT 58.014 39.130 0.00 0.00 0.00 3.55
559 567 7.112779 TCTTCTATGGTTTCATTTCTCCTTCC 58.887 38.462 0.00 0.00 34.96 3.46
562 570 2.224769 TGGTTTCATTTCTCCTTCCGCT 60.225 45.455 0.00 0.00 0.00 5.52
563 571 2.820197 GGTTTCATTTCTCCTTCCGCTT 59.180 45.455 0.00 0.00 0.00 4.68
564 572 3.255888 GGTTTCATTTCTCCTTCCGCTTT 59.744 43.478 0.00 0.00 0.00 3.51
565 573 4.476862 GTTTCATTTCTCCTTCCGCTTTC 58.523 43.478 0.00 0.00 0.00 2.62
566 574 2.711542 TCATTTCTCCTTCCGCTTTCC 58.288 47.619 0.00 0.00 0.00 3.13
567 575 2.039746 TCATTTCTCCTTCCGCTTTCCA 59.960 45.455 0.00 0.00 0.00 3.53
568 576 1.892209 TTTCTCCTTCCGCTTTCCAC 58.108 50.000 0.00 0.00 0.00 4.02
569 577 0.762418 TTCTCCTTCCGCTTTCCACA 59.238 50.000 0.00 0.00 0.00 4.17
570 578 0.984230 TCTCCTTCCGCTTTCCACAT 59.016 50.000 0.00 0.00 0.00 3.21
571 579 2.184533 TCTCCTTCCGCTTTCCACATA 58.815 47.619 0.00 0.00 0.00 2.29
572 580 2.093658 TCTCCTTCCGCTTTCCACATAC 60.094 50.000 0.00 0.00 0.00 2.39
573 581 1.065709 TCCTTCCGCTTTCCACATACC 60.066 52.381 0.00 0.00 0.00 2.73
574 582 1.379527 CTTCCGCTTTCCACATACCC 58.620 55.000 0.00 0.00 0.00 3.69
575 583 0.034863 TTCCGCTTTCCACATACCCC 60.035 55.000 0.00 0.00 0.00 4.95
576 584 0.912487 TCCGCTTTCCACATACCCCT 60.912 55.000 0.00 0.00 0.00 4.79
577 585 0.034477 CCGCTTTCCACATACCCCTT 60.034 55.000 0.00 0.00 0.00 3.95
578 586 1.615919 CCGCTTTCCACATACCCCTTT 60.616 52.381 0.00 0.00 0.00 3.11
579 587 1.472480 CGCTTTCCACATACCCCTTTG 59.528 52.381 0.00 0.00 0.00 2.77
580 588 2.525368 GCTTTCCACATACCCCTTTGT 58.475 47.619 0.00 0.00 0.00 2.83
581 589 2.897326 GCTTTCCACATACCCCTTTGTT 59.103 45.455 0.00 0.00 0.00 2.83
582 590 3.323691 GCTTTCCACATACCCCTTTGTTT 59.676 43.478 0.00 0.00 0.00 2.83
583 591 4.202315 GCTTTCCACATACCCCTTTGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
584 592 5.686387 GCTTTCCACATACCCCTTTGTTTTT 60.686 40.000 0.00 0.00 0.00 1.94
614 622 5.234752 GTTTTGTTCAAAACAGAACCCAGT 58.765 37.500 26.08 0.00 45.53 4.00
615 623 6.391537 GTTTTGTTCAAAACAGAACCCAGTA 58.608 36.000 26.08 0.00 45.53 2.74
616 624 6.591750 TTTGTTCAAAACAGAACCCAGTAA 57.408 33.333 4.58 0.00 45.62 2.24
623 2259 8.335532 TCAAAACAGAACCCAGTAATCTATTG 57.664 34.615 0.00 0.00 0.00 1.90
637 2273 9.755804 CAGTAATCTATTGTAGCTCTGAAATCA 57.244 33.333 0.00 0.00 0.00 2.57
673 2309 7.856492 TCGCATGCATAAATCATAATCAAAC 57.144 32.000 19.57 0.00 0.00 2.93
711 2347 9.342308 TGTGAATAAATCTCACTTGAATATCCC 57.658 33.333 4.74 0.00 43.03 3.85
730 2366 9.630098 AATATCCCAGTGTATATTTTACGTACG 57.370 33.333 15.01 15.01 0.00 3.67
731 2367 6.449635 TCCCAGTGTATATTTTACGTACGT 57.550 37.500 25.98 25.98 0.00 3.57
732 2368 7.561021 TCCCAGTGTATATTTTACGTACGTA 57.439 36.000 23.60 23.60 0.00 3.57
733 2369 7.414436 TCCCAGTGTATATTTTACGTACGTAC 58.586 38.462 26.83 16.74 0.00 3.67
751 2387 0.321653 ACGTGATTTCTGGTCAGGGC 60.322 55.000 0.00 0.00 36.18 5.19
757 2393 1.886886 TTTCTGGTCAGGGCGTTAAC 58.113 50.000 0.00 0.00 0.00 2.01
777 2413 7.271653 CGTTAACACTTAACAGTTGCAAAGAAA 59.728 33.333 0.00 0.00 44.40 2.52
820 2456 8.121708 GCTAATTCTCACTTCATGACATTTCTC 58.878 37.037 0.00 0.00 32.37 2.87
823 2459 8.715191 ATTCTCACTTCATGACATTTCTCTAC 57.285 34.615 0.00 0.00 32.37 2.59
824 2460 7.473735 TCTCACTTCATGACATTTCTCTACT 57.526 36.000 0.00 0.00 32.37 2.57
835 2471 6.816640 TGACATTTCTCTACTTTATCCGTTGG 59.183 38.462 0.00 0.00 0.00 3.77
848 2484 7.664318 ACTTTATCCGTTGGAACTAACTTCATT 59.336 33.333 0.00 0.00 34.34 2.57
849 2485 9.158233 CTTTATCCGTTGGAACTAACTTCATTA 57.842 33.333 0.00 0.00 34.34 1.90
851 2487 5.484715 TCCGTTGGAACTAACTTCATTAGG 58.515 41.667 0.00 0.00 44.17 2.69
852 2488 5.246656 TCCGTTGGAACTAACTTCATTAGGA 59.753 40.000 0.00 0.00 44.17 2.94
855 2491 7.120726 CCGTTGGAACTAACTTCATTAGGATTT 59.879 37.037 0.00 0.00 44.17 2.17
859 2495 8.802267 TGGAACTAACTTCATTAGGATTTTTGG 58.198 33.333 0.00 0.00 44.17 3.28
912 2548 8.098286 ACTACAATAGTTGGCTTGTTGTATACA 58.902 33.333 0.08 0.08 38.78 2.29
999 2801 1.324383 TGCTCGCAGGACGGATATAA 58.676 50.000 0.00 0.00 43.89 0.98
1398 3216 0.896923 TTCATACCGCCGTACAAGGT 59.103 50.000 8.63 8.63 41.73 3.50
1402 3220 1.666209 TACCGCCGTACAAGGTAGCC 61.666 60.000 6.93 0.00 39.31 3.93
1426 3244 5.830912 TCAACAAACTGAATGATGTCCAAC 58.169 37.500 0.00 0.00 0.00 3.77
1570 3391 1.197036 GTGACAAGGAACTAAAGCGGC 59.803 52.381 0.00 0.00 38.49 6.53
1573 3394 2.671888 GACAAGGAACTAAAGCGGCTAC 59.328 50.000 1.35 0.00 38.49 3.58
1593 3414 3.873910 ACTGGGATTTCTCAATGTACCG 58.126 45.455 0.00 0.00 0.00 4.02
1638 3459 4.697352 ACAACTAGTTCAGTCAATGCATCC 59.303 41.667 4.77 0.00 36.04 3.51
1678 3502 4.496341 GCAATCATGTTGGTAGTGAATCGG 60.496 45.833 9.19 0.00 0.00 4.18
1728 3552 1.069978 GTTGGAATTGGTGGTGTTGGG 59.930 52.381 0.00 0.00 0.00 4.12
1828 3652 3.599343 TCGGATGACTTTGATGTGAAGG 58.401 45.455 0.00 0.00 0.00 3.46
1900 3724 8.954350 CAACTGATAATTTGGATTCTCTTCAGT 58.046 33.333 0.00 0.00 0.00 3.41
1922 3746 5.126869 AGTGTGATCTCTCTAACCATGTGAG 59.873 44.000 0.00 0.00 0.00 3.51
1933 3757 3.874392 ACCATGTGAGCAATAAAAGGC 57.126 42.857 0.00 0.00 0.00 4.35
2026 3850 2.288213 GCACCTTTTAGAAGTGCCCAAC 60.288 50.000 3.01 0.00 35.62 3.77
2175 3999 6.258068 CGTTTGGATCTGAGGGTTCTAATAAC 59.742 42.308 0.00 0.00 0.00 1.89
2380 4204 4.868734 GGTTGAGCTACATGTACTTACCAC 59.131 45.833 20.50 10.90 0.00 4.16
2543 4367 6.547880 TGCCAGTATTTTGAAGACCTTGTAAA 59.452 34.615 0.00 0.00 0.00 2.01
3115 4943 3.907474 TGGTCCAGATAACAAGTGGAGAA 59.093 43.478 0.00 0.00 41.11 2.87
3117 4945 4.938226 GGTCCAGATAACAAGTGGAGAAAG 59.062 45.833 0.00 0.00 41.11 2.62
3174 5014 3.181493 GGCACTTGGAGCTTATTGATGTG 60.181 47.826 0.00 0.00 0.00 3.21
3316 5156 7.687445 TGAGTTTGATATCGACAACAATGATG 58.313 34.615 12.35 0.00 0.00 3.07
3386 5226 6.338146 TGTTCCTCCAAAACTATGACGATAG 58.662 40.000 0.00 0.00 38.06 2.08
3442 5282 8.041323 ACCTACCAAGATTAACATCACTTACTG 58.959 37.037 0.00 0.00 0.00 2.74
3699 5708 4.924625 TCGAAATTCCCAATAGTCCCAAA 58.075 39.130 0.00 0.00 0.00 3.28
3760 5770 3.511934 AGGCACCGGAGATAAATAGCTAG 59.488 47.826 9.46 0.00 0.00 3.42
3766 5776 6.967767 CACCGGAGATAAATAGCTAGATTACG 59.032 42.308 9.46 2.11 0.00 3.18
3785 5795 3.486383 ACGTGGAAAATGAGGACAACAT 58.514 40.909 0.00 0.00 0.00 2.71
3798 5808 1.873591 GACAACATGACTTCGTGCCTT 59.126 47.619 0.00 0.00 36.36 4.35
3801 5811 0.593128 ACATGACTTCGTGCCTTTGC 59.407 50.000 0.00 0.00 36.36 3.68
3808 5818 0.250684 TTCGTGCCTTTGCCTCATCA 60.251 50.000 0.00 0.00 36.33 3.07
3823 5833 6.015282 TGCCTCATCATCTATATGTCTGTCT 58.985 40.000 0.00 0.00 34.50 3.41
3835 5845 3.599730 TGTCTGTCTGTGGCTGATTAG 57.400 47.619 0.00 0.00 0.00 1.73
3844 5854 5.064452 GTCTGTGGCTGATTAGTGATTTCTG 59.936 44.000 0.00 0.00 0.00 3.02
3958 5969 2.432206 TGAAACGACAGAGAATCGCA 57.568 45.000 0.00 0.00 43.46 5.10
3959 5970 2.749776 TGAAACGACAGAGAATCGCAA 58.250 42.857 0.00 0.00 43.46 4.85
3986 6030 5.915196 GTGTTTTGGTTCATCTTAACTCTGC 59.085 40.000 0.00 0.00 0.00 4.26
3989 6033 5.689383 TTGGTTCATCTTAACTCTGCAAC 57.311 39.130 0.00 0.00 0.00 4.17
4045 6092 4.142160 GCCTGTTTGTGATATTTCCCCTTC 60.142 45.833 0.00 0.00 0.00 3.46
4046 6093 5.264395 CCTGTTTGTGATATTTCCCCTTCT 58.736 41.667 0.00 0.00 0.00 2.85
4047 6094 5.358160 CCTGTTTGTGATATTTCCCCTTCTC 59.642 44.000 0.00 0.00 0.00 2.87
4113 6160 5.049060 GTCTTTCTTCTTTGGCTTCTCCTTC 60.049 44.000 0.00 0.00 35.26 3.46
4140 6187 2.224769 TGGTTCTTGGCTTGTAAGAGGG 60.225 50.000 0.00 0.00 35.74 4.30
4150 6197 2.163818 TGTAAGAGGGCACGTTTCAG 57.836 50.000 0.00 0.00 0.00 3.02
4238 6368 4.444876 CCTCTGATGATTATTCCCAACCGT 60.445 45.833 0.00 0.00 0.00 4.83
4250 6380 2.944349 TCCCAACCGTCACAAAGTTAAC 59.056 45.455 0.00 0.00 0.00 2.01
4265 6395 5.638596 AAGTTAACCTAAATGCCCTTTCG 57.361 39.130 0.88 0.00 0.00 3.46
4304 6434 0.964358 AAGGCTGCACTTCCAGATGC 60.964 55.000 0.50 0.00 42.40 3.91
4311 6441 1.153628 ACTTCCAGATGCGGCGTAC 60.154 57.895 9.37 0.00 0.00 3.67
4313 6443 0.739462 CTTCCAGATGCGGCGTACAA 60.739 55.000 9.37 0.00 0.00 2.41
4315 6445 1.017177 TCCAGATGCGGCGTACAAAC 61.017 55.000 9.37 0.00 0.00 2.93
4321 6451 2.961669 GCGGCGTACAAACTGTGGG 61.962 63.158 9.37 0.00 0.00 4.61
4322 6452 1.301087 CGGCGTACAAACTGTGGGA 60.301 57.895 0.00 0.00 0.00 4.37
4334 6464 4.463050 AACTGTGGGATTTGGGAGTAAA 57.537 40.909 0.00 0.00 0.00 2.01
4349 6479 5.014123 TGGGAGTAAATCAGGATCAGTTTGT 59.986 40.000 0.00 0.00 0.00 2.83
4415 6545 1.068954 GTGTGCAGCAGAGTAAAAGGC 60.069 52.381 0.00 0.00 0.00 4.35
4426 6556 5.542779 CAGAGTAAAAGGCAGTGTACTTCT 58.457 41.667 0.00 0.00 0.00 2.85
4524 6654 5.826601 GCTAGAGAAGCCTGCTTATTTTT 57.173 39.130 4.03 0.00 46.25 1.94
4537 6667 6.128172 CCTGCTTATTTTTCGAGACATTGTCT 60.128 38.462 19.05 19.05 46.42 3.41
4545 6675 2.901192 TCGAGACATTGTCTGGGGTTTA 59.099 45.455 23.57 3.77 43.53 2.01
4562 6692 7.523415 TGGGGTTTATGAAGGGAAATAGATAC 58.477 38.462 0.00 0.00 0.00 2.24
4563 6693 7.129660 TGGGGTTTATGAAGGGAAATAGATACA 59.870 37.037 0.00 0.00 0.00 2.29
4619 6749 4.980339 AGGGCCTTGTTTCATTTTTCAT 57.020 36.364 0.00 0.00 0.00 2.57
4626 6756 7.099120 GCCTTGTTTCATTTTTCATGTATCCT 58.901 34.615 0.00 0.00 0.00 3.24
4698 6828 4.228567 GACTAGCCCGCCCTCTGC 62.229 72.222 0.00 0.00 0.00 4.26
4708 6838 1.087501 CGCCCTCTGCTTTAGGTTTC 58.912 55.000 0.00 0.00 38.05 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.773767 AAACGAACGCCGCCGATTTG 62.774 55.000 6.50 0.00 43.32 2.32
2 3 3.018840 GAAACGAACGCCGCCGATT 62.019 57.895 6.50 0.92 43.32 3.34
8 9 1.083015 CAAGGTGAAACGAACGCCG 60.083 57.895 0.00 0.00 42.03 6.46
9 10 0.379316 AACAAGGTGAAACGAACGCC 59.621 50.000 0.00 0.00 38.12 5.68
10 11 3.285745 CTTAACAAGGTGAAACGAACGC 58.714 45.455 0.00 0.00 38.12 4.84
11 12 3.242478 TGCTTAACAAGGTGAAACGAACG 60.242 43.478 0.00 0.00 38.12 3.95
12 13 4.281525 TGCTTAACAAGGTGAAACGAAC 57.718 40.909 0.00 0.00 38.12 3.95
13 14 5.508200 AATGCTTAACAAGGTGAAACGAA 57.492 34.783 0.00 0.00 38.12 3.85
14 15 4.319190 CGAATGCTTAACAAGGTGAAACGA 60.319 41.667 0.00 0.00 38.12 3.85
15 16 3.906008 CGAATGCTTAACAAGGTGAAACG 59.094 43.478 0.00 0.00 38.12 3.60
16 17 5.103290 TCGAATGCTTAACAAGGTGAAAC 57.897 39.130 0.00 0.00 0.00 2.78
17 18 5.106317 GGATCGAATGCTTAACAAGGTGAAA 60.106 40.000 0.00 0.00 0.00 2.69
18 19 4.394920 GGATCGAATGCTTAACAAGGTGAA 59.605 41.667 0.00 0.00 0.00 3.18
19 20 3.938963 GGATCGAATGCTTAACAAGGTGA 59.061 43.478 0.00 0.00 0.00 4.02
20 21 3.065371 GGGATCGAATGCTTAACAAGGTG 59.935 47.826 0.00 0.00 0.00 4.00
21 22 3.279434 GGGATCGAATGCTTAACAAGGT 58.721 45.455 0.00 0.00 0.00 3.50
22 23 2.618709 GGGGATCGAATGCTTAACAAGG 59.381 50.000 0.00 0.00 0.00 3.61
23 24 3.545703 AGGGGATCGAATGCTTAACAAG 58.454 45.455 0.00 0.00 0.00 3.16
24 25 3.644966 AGGGGATCGAATGCTTAACAA 57.355 42.857 0.00 0.00 0.00 2.83
25 26 3.278574 CAAGGGGATCGAATGCTTAACA 58.721 45.455 0.00 0.00 0.00 2.41
26 27 2.618709 CCAAGGGGATCGAATGCTTAAC 59.381 50.000 0.00 0.00 35.59 2.01
27 28 2.930950 CCAAGGGGATCGAATGCTTAA 58.069 47.619 0.00 0.00 35.59 1.85
28 29 1.476833 GCCAAGGGGATCGAATGCTTA 60.477 52.381 0.00 0.00 35.59 3.09
29 30 0.753111 GCCAAGGGGATCGAATGCTT 60.753 55.000 0.00 0.00 35.59 3.91
30 31 1.152881 GCCAAGGGGATCGAATGCT 60.153 57.895 0.00 0.00 35.59 3.79
31 32 2.196245 GGCCAAGGGGATCGAATGC 61.196 63.158 0.00 0.00 35.59 3.56
32 33 0.106519 AAGGCCAAGGGGATCGAATG 60.107 55.000 5.01 0.00 35.59 2.67
33 34 0.106519 CAAGGCCAAGGGGATCGAAT 60.107 55.000 5.01 0.00 35.59 3.34
34 35 1.204786 TCAAGGCCAAGGGGATCGAA 61.205 55.000 5.01 0.00 35.59 3.71
35 36 0.988145 ATCAAGGCCAAGGGGATCGA 60.988 55.000 5.01 0.00 35.59 3.59
36 37 0.536006 GATCAAGGCCAAGGGGATCG 60.536 60.000 5.01 0.00 35.59 3.69
37 38 0.552848 TGATCAAGGCCAAGGGGATC 59.447 55.000 5.01 10.08 35.59 3.36
38 39 1.146566 GATGATCAAGGCCAAGGGGAT 59.853 52.381 5.01 0.00 35.59 3.85
39 40 0.552848 GATGATCAAGGCCAAGGGGA 59.447 55.000 5.01 0.00 35.59 4.81
40 41 0.820891 CGATGATCAAGGCCAAGGGG 60.821 60.000 5.01 0.00 37.18 4.79
41 42 0.181114 TCGATGATCAAGGCCAAGGG 59.819 55.000 5.01 0.00 0.00 3.95
42 43 2.042686 TTCGATGATCAAGGCCAAGG 57.957 50.000 5.01 0.00 0.00 3.61
43 44 2.357009 CCTTTCGATGATCAAGGCCAAG 59.643 50.000 5.01 0.00 30.94 3.61
44 45 2.026356 TCCTTTCGATGATCAAGGCCAA 60.026 45.455 5.01 0.00 37.57 4.52
45 46 1.559219 TCCTTTCGATGATCAAGGCCA 59.441 47.619 5.01 0.00 37.57 5.36
46 47 2.332063 TCCTTTCGATGATCAAGGCC 57.668 50.000 0.00 0.00 37.57 5.19
47 48 3.059325 CGATTCCTTTCGATGATCAAGGC 60.059 47.826 0.00 0.00 41.62 4.35
48 49 4.371786 TCGATTCCTTTCGATGATCAAGG 58.628 43.478 0.00 6.51 42.81 3.61
49 50 4.084641 GCTCGATTCCTTTCGATGATCAAG 60.085 45.833 0.00 0.00 46.16 3.02
50 51 3.804325 GCTCGATTCCTTTCGATGATCAA 59.196 43.478 0.00 0.00 46.16 2.57
51 52 3.068732 AGCTCGATTCCTTTCGATGATCA 59.931 43.478 0.00 0.00 46.16 2.92
52 53 3.648009 AGCTCGATTCCTTTCGATGATC 58.352 45.455 0.00 0.00 46.16 2.92
53 54 3.742433 AGCTCGATTCCTTTCGATGAT 57.258 42.857 0.00 0.00 46.16 2.45
54 55 3.190079 CAAGCTCGATTCCTTTCGATGA 58.810 45.455 0.00 0.00 46.16 2.92
55 56 2.286294 CCAAGCTCGATTCCTTTCGATG 59.714 50.000 0.00 0.00 46.16 3.84
56 57 2.555199 CCAAGCTCGATTCCTTTCGAT 58.445 47.619 0.00 0.00 46.16 3.59
57 58 2.007049 GCCAAGCTCGATTCCTTTCGA 61.007 52.381 0.00 0.00 45.27 3.71
58 59 0.375106 GCCAAGCTCGATTCCTTTCG 59.625 55.000 0.00 0.00 40.46 3.46
59 60 0.375106 CGCCAAGCTCGATTCCTTTC 59.625 55.000 0.00 0.00 0.00 2.62
60 61 0.321653 ACGCCAAGCTCGATTCCTTT 60.322 50.000 0.00 0.00 0.00 3.11
61 62 0.321653 AACGCCAAGCTCGATTCCTT 60.322 50.000 0.00 0.00 0.00 3.36
62 63 0.321653 AAACGCCAAGCTCGATTCCT 60.322 50.000 0.00 0.00 0.00 3.36
63 64 0.521735 AAAACGCCAAGCTCGATTCC 59.478 50.000 0.00 0.00 0.00 3.01
64 65 1.978782 CAAAAACGCCAAGCTCGATTC 59.021 47.619 0.00 0.00 0.00 2.52
65 66 1.930371 GCAAAAACGCCAAGCTCGATT 60.930 47.619 0.00 0.00 0.00 3.34
66 67 0.387239 GCAAAAACGCCAAGCTCGAT 60.387 50.000 0.00 0.00 0.00 3.59
67 68 1.008995 GCAAAAACGCCAAGCTCGA 60.009 52.632 0.00 0.00 0.00 4.04
68 69 3.526029 GCAAAAACGCCAAGCTCG 58.474 55.556 0.00 0.00 0.00 5.03
76 77 1.864565 ACAGAAATGGGCAAAAACGC 58.135 45.000 0.00 0.00 0.00 4.84
77 78 2.032979 GCAACAGAAATGGGCAAAAACG 60.033 45.455 0.00 0.00 0.00 3.60
78 79 3.205338 AGCAACAGAAATGGGCAAAAAC 58.795 40.909 0.00 0.00 0.00 2.43
79 80 3.557228 AGCAACAGAAATGGGCAAAAA 57.443 38.095 0.00 0.00 0.00 1.94
80 81 3.640967 AGTAGCAACAGAAATGGGCAAAA 59.359 39.130 0.00 0.00 0.00 2.44
81 82 3.005684 CAGTAGCAACAGAAATGGGCAAA 59.994 43.478 0.00 0.00 0.00 3.68
82 83 2.557924 CAGTAGCAACAGAAATGGGCAA 59.442 45.455 0.00 0.00 0.00 4.52
83 84 2.161855 CAGTAGCAACAGAAATGGGCA 58.838 47.619 0.00 0.00 0.00 5.36
84 85 1.474077 CCAGTAGCAACAGAAATGGGC 59.526 52.381 0.00 0.00 0.00 5.36
85 86 3.012518 CTCCAGTAGCAACAGAAATGGG 58.987 50.000 0.00 0.00 0.00 4.00
86 87 3.438087 CACTCCAGTAGCAACAGAAATGG 59.562 47.826 0.00 0.00 0.00 3.16
87 88 3.438087 CCACTCCAGTAGCAACAGAAATG 59.562 47.826 0.00 0.00 0.00 2.32
88 89 3.679389 CCACTCCAGTAGCAACAGAAAT 58.321 45.455 0.00 0.00 0.00 2.17
89 90 2.810400 GCCACTCCAGTAGCAACAGAAA 60.810 50.000 0.00 0.00 32.91 2.52
90 91 1.270839 GCCACTCCAGTAGCAACAGAA 60.271 52.381 0.00 0.00 32.91 3.02
91 92 0.321671 GCCACTCCAGTAGCAACAGA 59.678 55.000 0.00 0.00 32.91 3.41
92 93 0.035317 TGCCACTCCAGTAGCAACAG 59.965 55.000 0.00 0.00 39.56 3.16
93 94 0.692476 ATGCCACTCCAGTAGCAACA 59.308 50.000 3.88 0.00 44.98 3.33
94 95 1.740025 GAATGCCACTCCAGTAGCAAC 59.260 52.381 3.88 0.00 44.98 4.17
95 96 1.630369 AGAATGCCACTCCAGTAGCAA 59.370 47.619 3.88 0.00 44.98 3.91
96 97 1.279496 AGAATGCCACTCCAGTAGCA 58.721 50.000 2.19 2.19 45.80 3.49
97 98 2.409948 AAGAATGCCACTCCAGTAGC 57.590 50.000 0.00 0.00 33.28 3.58
98 99 3.119708 GCAAAAGAATGCCACTCCAGTAG 60.120 47.826 0.00 0.00 40.49 2.57
99 100 2.819608 GCAAAAGAATGCCACTCCAGTA 59.180 45.455 0.00 0.00 40.49 2.74
100 101 1.615392 GCAAAAGAATGCCACTCCAGT 59.385 47.619 0.00 0.00 40.49 4.00
101 102 2.358939 GCAAAAGAATGCCACTCCAG 57.641 50.000 0.00 0.00 40.49 3.86
102 103 3.498481 AGTAGCAAAAGAATGCCACTCCA 60.498 43.478 0.00 0.00 43.31 3.86
103 104 3.084786 AGTAGCAAAAGAATGCCACTCC 58.915 45.455 0.00 0.00 43.31 3.85
109 110 5.412904 ACCAGTAAGAGTAGCAAAAGAATGC 59.587 40.000 0.00 0.00 46.78 3.56
110 111 6.428159 ACACCAGTAAGAGTAGCAAAAGAATG 59.572 38.462 0.00 0.00 0.00 2.67
111 112 6.534634 ACACCAGTAAGAGTAGCAAAAGAAT 58.465 36.000 0.00 0.00 0.00 2.40
112 113 5.925509 ACACCAGTAAGAGTAGCAAAAGAA 58.074 37.500 0.00 0.00 0.00 2.52
113 114 5.546621 ACACCAGTAAGAGTAGCAAAAGA 57.453 39.130 0.00 0.00 0.00 2.52
114 115 6.260050 TGAAACACCAGTAAGAGTAGCAAAAG 59.740 38.462 0.00 0.00 0.00 2.27
115 116 6.116806 TGAAACACCAGTAAGAGTAGCAAAA 58.883 36.000 0.00 0.00 0.00 2.44
116 117 5.676552 TGAAACACCAGTAAGAGTAGCAAA 58.323 37.500 0.00 0.00 0.00 3.68
117 118 5.163343 ACTGAAACACCAGTAAGAGTAGCAA 60.163 40.000 0.00 0.00 44.82 3.91
118 119 4.344102 ACTGAAACACCAGTAAGAGTAGCA 59.656 41.667 0.00 0.00 44.82 3.49
119 120 4.884247 ACTGAAACACCAGTAAGAGTAGC 58.116 43.478 0.00 0.00 44.82 3.58
127 128 9.669887 TTTTCTTTAGTTACTGAAACACCAGTA 57.330 29.630 0.00 0.00 44.82 2.74
129 130 8.455682 TGTTTTCTTTAGTTACTGAAACACCAG 58.544 33.333 0.00 0.00 40.83 4.00
130 131 8.338072 TGTTTTCTTTAGTTACTGAAACACCA 57.662 30.769 0.00 0.00 40.83 4.17
131 132 8.456471 ACTGTTTTCTTTAGTTACTGAAACACC 58.544 33.333 0.00 0.00 40.83 4.16
132 133 9.836076 AACTGTTTTCTTTAGTTACTGAAACAC 57.164 29.630 0.00 0.22 40.83 3.32
162 163 5.409520 TGAATACAAAGCAAGCTGAGTACTG 59.590 40.000 0.00 0.00 0.00 2.74
163 164 5.551233 TGAATACAAAGCAAGCTGAGTACT 58.449 37.500 0.00 0.00 0.00 2.73
167 168 6.384224 TGAATTGAATACAAAGCAAGCTGAG 58.616 36.000 0.00 0.00 39.54 3.35
170 171 7.658575 ACAAATGAATTGAATACAAAGCAAGCT 59.341 29.630 0.00 0.00 41.85 3.74
200 201 1.069765 CAAGCTGGACACGGTCACT 59.930 57.895 6.41 0.00 33.68 3.41
309 312 0.592637 CTGCCTGCGACAACAATGAA 59.407 50.000 0.00 0.00 0.00 2.57
314 317 1.153269 TTGTCTGCCTGCGACAACA 60.153 52.632 18.55 4.32 44.03 3.33
327 330 1.302033 CGGCCTCACAGCTTTGTCT 60.302 57.895 0.00 0.00 0.00 3.41
389 392 5.944007 GGAAAGGGAGCTTAACAATGTCTTA 59.056 40.000 0.00 0.00 0.00 2.10
391 394 4.043435 AGGAAAGGGAGCTTAACAATGTCT 59.957 41.667 0.00 0.00 0.00 3.41
392 395 4.336280 AGGAAAGGGAGCTTAACAATGTC 58.664 43.478 0.00 0.00 0.00 3.06
393 396 4.388577 AGGAAAGGGAGCTTAACAATGT 57.611 40.909 0.00 0.00 0.00 2.71
394 397 4.766891 TGAAGGAAAGGGAGCTTAACAATG 59.233 41.667 0.00 0.00 0.00 2.82
395 398 4.767409 GTGAAGGAAAGGGAGCTTAACAAT 59.233 41.667 0.00 0.00 0.00 2.71
402 410 0.402121 GGTGTGAAGGAAAGGGAGCT 59.598 55.000 0.00 0.00 0.00 4.09
407 415 2.584835 TGATGGGTGTGAAGGAAAGG 57.415 50.000 0.00 0.00 0.00 3.11
410 418 3.874383 TCTTTGATGGGTGTGAAGGAA 57.126 42.857 0.00 0.00 0.00 3.36
412 420 6.377996 TGATAAATCTTTGATGGGTGTGAAGG 59.622 38.462 0.00 0.00 0.00 3.46
414 422 6.152661 GGTGATAAATCTTTGATGGGTGTGAA 59.847 38.462 0.00 0.00 0.00 3.18
426 434 5.884792 CAGCAGGAAGAGGTGATAAATCTTT 59.115 40.000 0.00 0.00 36.64 2.52
434 442 0.252479 CAGCAGCAGGAAGAGGTGAT 59.748 55.000 0.00 0.00 36.64 3.06
437 445 2.222727 AGCAGCAGCAGGAAGAGGT 61.223 57.895 3.17 0.00 45.49 3.85
438 446 1.745864 CAGCAGCAGCAGGAAGAGG 60.746 63.158 3.17 0.00 45.49 3.69
439 447 2.400158 GCAGCAGCAGCAGGAAGAG 61.400 63.158 4.63 0.00 45.49 2.85
440 448 2.359602 GCAGCAGCAGCAGGAAGA 60.360 61.111 4.63 0.00 45.49 2.87
441 449 2.360100 AGCAGCAGCAGCAGGAAG 60.360 61.111 12.92 0.00 45.49 3.46
442 450 2.671963 CAGCAGCAGCAGCAGGAA 60.672 61.111 12.92 0.00 45.49 3.36
467 475 1.732259 GAGCGATTCACCGTCAAATGT 59.268 47.619 0.00 0.00 0.00 2.71
471 479 0.319211 AACGAGCGATTCACCGTCAA 60.319 50.000 0.00 0.00 33.84 3.18
476 484 1.683790 CCGTCAACGAGCGATTCACC 61.684 60.000 3.71 0.00 43.02 4.02
481 489 2.048597 TTGCCGTCAACGAGCGAT 60.049 55.556 3.71 0.00 43.02 4.58
483 491 4.430423 GCTTGCCGTCAACGAGCG 62.430 66.667 3.71 0.00 43.02 5.03
521 529 5.006386 ACCATAGAAGAAAGCAAGGTTGAG 58.994 41.667 0.00 0.00 0.00 3.02
523 531 5.712152 AACCATAGAAGAAAGCAAGGTTG 57.288 39.130 0.00 0.00 36.80 3.77
526 534 5.964958 TGAAACCATAGAAGAAAGCAAGG 57.035 39.130 0.00 0.00 0.00 3.61
541 549 2.159382 GCGGAAGGAGAAATGAAACCA 58.841 47.619 0.00 0.00 0.00 3.67
544 552 3.506067 GGAAAGCGGAAGGAGAAATGAAA 59.494 43.478 0.00 0.00 0.00 2.69
559 567 1.472480 CAAAGGGGTATGTGGAAAGCG 59.528 52.381 0.00 0.00 0.00 4.68
562 570 5.959583 AAAAACAAAGGGGTATGTGGAAA 57.040 34.783 0.00 0.00 0.00 3.13
604 612 6.821388 AGCTACAATAGATTACTGGGTTCTG 58.179 40.000 0.00 0.00 0.00 3.02
607 615 6.611642 TCAGAGCTACAATAGATTACTGGGTT 59.388 38.462 0.00 0.00 0.00 4.11
615 623 9.896645 TCTTTGATTTCAGAGCTACAATAGATT 57.103 29.630 0.00 0.00 0.00 2.40
647 2283 9.558648 GTTTGATTATGATTTATGCATGCGATA 57.441 29.630 14.09 9.25 0.00 2.92
651 2287 8.806177 TCAGTTTGATTATGATTTATGCATGC 57.194 30.769 11.82 11.82 0.00 4.06
706 2342 8.165239 ACGTACGTAAAATATACACTGGGATA 57.835 34.615 21.41 0.00 0.00 2.59
726 2362 3.825308 TGACCAGAAATCACGTACGTAC 58.175 45.455 22.34 15.90 0.00 3.67
727 2363 3.119743 CCTGACCAGAAATCACGTACGTA 60.120 47.826 22.34 10.16 0.00 3.57
729 2365 2.259618 CCTGACCAGAAATCACGTACG 58.740 52.381 15.01 15.01 0.00 3.67
730 2366 2.618053 CCCTGACCAGAAATCACGTAC 58.382 52.381 0.00 0.00 0.00 3.67
731 2367 1.066430 GCCCTGACCAGAAATCACGTA 60.066 52.381 0.00 0.00 0.00 3.57
732 2368 0.321653 GCCCTGACCAGAAATCACGT 60.322 55.000 0.00 0.00 0.00 4.49
733 2369 1.361668 CGCCCTGACCAGAAATCACG 61.362 60.000 0.00 0.00 0.00 4.35
751 2387 6.252281 TCTTTGCAACTGTTAAGTGTTAACG 58.748 36.000 0.00 3.59 46.53 3.18
786 2422 9.322773 TCATGAAGTGAGAATTAGCTGATAAAG 57.677 33.333 0.00 0.00 31.80 1.85
794 2430 7.983307 AGAAATGTCATGAAGTGAGAATTAGC 58.017 34.615 0.00 0.00 37.56 3.09
805 2441 8.759641 CGGATAAAGTAGAGAAATGTCATGAAG 58.240 37.037 0.00 0.00 0.00 3.02
820 2456 7.816031 TGAAGTTAGTTCCAACGGATAAAGTAG 59.184 37.037 0.00 0.00 33.75 2.57
822 2458 6.527423 TGAAGTTAGTTCCAACGGATAAAGT 58.473 36.000 0.00 0.00 33.75 2.66
823 2459 7.611213 ATGAAGTTAGTTCCAACGGATAAAG 57.389 36.000 0.00 0.00 33.75 1.85
824 2460 7.989416 AATGAAGTTAGTTCCAACGGATAAA 57.011 32.000 0.00 0.00 33.75 1.40
828 2464 5.246656 TCCTAATGAAGTTAGTTCCAACGGA 59.753 40.000 0.00 0.00 38.50 4.69
835 2471 9.626045 CACCAAAAATCCTAATGAAGTTAGTTC 57.374 33.333 0.00 0.00 38.50 3.01
848 2484 8.748412 CAAGATATGTTTCCACCAAAAATCCTA 58.252 33.333 0.00 0.00 0.00 2.94
849 2485 7.454380 TCAAGATATGTTTCCACCAAAAATCCT 59.546 33.333 0.00 0.00 0.00 3.24
851 2487 8.522830 TCTCAAGATATGTTTCCACCAAAAATC 58.477 33.333 0.00 0.00 0.00 2.17
852 2488 8.421249 TCTCAAGATATGTTTCCACCAAAAAT 57.579 30.769 0.00 0.00 0.00 1.82
855 2491 7.831691 TTTCTCAAGATATGTTTCCACCAAA 57.168 32.000 0.00 0.00 0.00 3.28
999 2801 5.363562 TCATGCTGACTGGAATAGACATT 57.636 39.130 0.00 0.00 30.91 2.71
1398 3216 5.316167 ACATCATTCAGTTTGTTGAGGCTA 58.684 37.500 0.00 0.00 0.00 3.93
1402 3220 5.694231 TGGACATCATTCAGTTTGTTGAG 57.306 39.130 0.00 0.00 0.00 3.02
1426 3244 4.823989 ACTTGAAAGATGGTTCAACCTCAG 59.176 41.667 8.40 0.39 41.45 3.35
1506 3324 1.271597 GGCAAAGATGTGGTCTCTGGT 60.272 52.381 0.00 0.00 35.67 4.00
1570 3391 5.050490 CGGTACATTGAGAAATCCCAGTAG 58.950 45.833 0.00 0.00 0.00 2.57
1573 3394 3.871594 GTCGGTACATTGAGAAATCCCAG 59.128 47.826 0.00 0.00 0.00 4.45
1593 3414 5.514914 TGTTCTCTTGCGTTTTGAAATTGTC 59.485 36.000 0.00 0.00 0.00 3.18
1638 3459 0.730840 TGCTTGATGATGAGCTTGCG 59.269 50.000 0.00 0.00 39.60 4.85
1645 3466 4.707934 ACCAACATGATTGCTTGATGATGA 59.292 37.500 0.00 0.00 0.00 2.92
1678 3502 5.812127 GCAAAACATGAAGACCCAATATTCC 59.188 40.000 0.00 0.00 0.00 3.01
1728 3552 2.858745 TGTTGGGCCAAAGTAGTCTTC 58.141 47.619 22.82 5.61 32.90 2.87
1828 3652 8.044908 TGATTGTATCACCTCTTTAGTTAACCC 58.955 37.037 0.88 0.00 33.59 4.11
1900 3724 4.142071 GCTCACATGGTTAGAGAGATCACA 60.142 45.833 0.00 0.00 0.00 3.58
1922 3746 7.360438 CGAGGACTATCAATAGCCTTTTATTGC 60.360 40.741 11.70 0.00 39.67 3.56
1933 3757 6.805760 CACATGTCATCGAGGACTATCAATAG 59.194 42.308 28.17 12.55 38.61 1.73
2026 3850 3.058016 GTGACCAACATCACACTTCCATG 60.058 47.826 1.08 0.00 46.89 3.66
2175 3999 4.297510 CAATGCTCTCTAACTCAGGATCG 58.702 47.826 0.00 0.00 0.00 3.69
2520 4344 7.589954 CGTTTTACAAGGTCTTCAAAATACTGG 59.410 37.037 4.23 0.00 0.00 4.00
3004 4832 1.243342 CCAAAGTCATCGGGCAAGCA 61.243 55.000 0.00 0.00 0.00 3.91
3117 4945 8.879759 TGGTTCAGATTCTTCATTAACGTAATC 58.120 33.333 0.00 0.00 0.00 1.75
3174 5014 5.269313 GCATGATCTTTACTTAGCAAGTGC 58.731 41.667 0.00 0.00 42.84 4.40
3316 5156 5.734855 TGTAGAACTTCAAGCACTTCAAC 57.265 39.130 0.00 0.00 0.00 3.18
3318 5158 3.809832 GCTGTAGAACTTCAAGCACTTCA 59.190 43.478 6.36 0.00 0.00 3.02
3386 5226 1.115326 AAACCAACTTGGGAGCCAGC 61.115 55.000 12.62 0.00 43.37 4.85
3554 5562 6.010294 TGGATATCTCGACGGTCTTTATTC 57.990 41.667 6.57 0.00 0.00 1.75
3760 5770 5.180492 TGTTGTCCTCATTTTCCACGTAATC 59.820 40.000 0.00 0.00 0.00 1.75
3766 5776 4.520492 AGTCATGTTGTCCTCATTTTCCAC 59.480 41.667 0.00 0.00 0.00 4.02
3785 5795 0.884704 GAGGCAAAGGCACGAAGTCA 60.885 55.000 0.00 0.00 41.61 3.41
3798 5808 6.496218 AGACAGACATATAGATGATGAGGCAA 59.504 38.462 3.93 0.00 36.48 4.52
3801 5811 7.314393 CACAGACAGACATATAGATGATGAGG 58.686 42.308 3.93 1.67 36.48 3.86
3808 5818 5.143369 TCAGCCACAGACAGACATATAGAT 58.857 41.667 0.00 0.00 0.00 1.98
3823 5833 3.691118 GCAGAAATCACTAATCAGCCACA 59.309 43.478 0.00 0.00 0.00 4.17
3835 5845 3.569701 TGAAACTCAAGGGCAGAAATCAC 59.430 43.478 0.00 0.00 0.00 3.06
3844 5854 3.620488 TGATGGTATGAAACTCAAGGGC 58.380 45.455 0.00 0.00 0.00 5.19
3958 5969 7.228706 AGAGTTAAGATGAACCAAAACACGATT 59.771 33.333 0.00 0.00 0.00 3.34
3959 5970 6.710744 AGAGTTAAGATGAACCAAAACACGAT 59.289 34.615 0.00 0.00 0.00 3.73
3986 6030 4.852134 TCAATGGAAGGTGAACATGTTG 57.148 40.909 17.58 0.00 0.00 3.33
3989 6033 4.439700 GCTCATCAATGGAAGGTGAACATG 60.440 45.833 0.00 0.00 0.00 3.21
4045 6092 5.471257 AGCTAAGAACGAAAACTACAGGAG 58.529 41.667 0.00 0.00 0.00 3.69
4046 6093 5.243283 AGAGCTAAGAACGAAAACTACAGGA 59.757 40.000 0.00 0.00 0.00 3.86
4047 6094 5.346281 CAGAGCTAAGAACGAAAACTACAGG 59.654 44.000 0.00 0.00 0.00 4.00
4113 6160 1.072965 ACAAGCCAAGAACCAGAGAGG 59.927 52.381 0.00 0.00 45.67 3.69
4140 6187 2.354821 ACTTCTGAAACCTGAAACGTGC 59.645 45.455 0.00 0.00 0.00 5.34
4238 6368 5.390387 AGGGCATTTAGGTTAACTTTGTGA 58.610 37.500 5.42 0.00 0.00 3.58
4250 6380 2.872858 GAGCTACGAAAGGGCATTTAGG 59.127 50.000 9.42 2.12 36.64 2.69
4265 6395 0.598680 CTGCCAGCCATACGAGCTAC 60.599 60.000 0.00 0.00 38.95 3.58
4297 6427 1.019278 AGTTTGTACGCCGCATCTGG 61.019 55.000 0.00 0.00 0.00 3.86
4304 6434 0.672401 ATCCCACAGTTTGTACGCCG 60.672 55.000 0.00 0.00 0.00 6.46
4311 6441 2.597455 ACTCCCAAATCCCACAGTTTG 58.403 47.619 0.00 0.00 35.60 2.93
4313 6443 4.463050 TTTACTCCCAAATCCCACAGTT 57.537 40.909 0.00 0.00 0.00 3.16
4315 6445 4.599041 TGATTTACTCCCAAATCCCACAG 58.401 43.478 6.21 0.00 42.00 3.66
4321 6451 6.360618 ACTGATCCTGATTTACTCCCAAATC 58.639 40.000 2.38 2.38 42.67 2.17
4322 6452 6.332976 ACTGATCCTGATTTACTCCCAAAT 57.667 37.500 0.00 0.00 0.00 2.32
4334 6464 6.660521 TGCTCATTTTACAAACTGATCCTGAT 59.339 34.615 0.00 0.00 29.02 2.90
4373 6503 6.155827 CACCGCAATAAATTCCTTTTGAGAA 58.844 36.000 0.00 0.00 0.00 2.87
4375 6505 5.345741 CACACCGCAATAAATTCCTTTTGAG 59.654 40.000 0.00 0.00 0.00 3.02
4415 6545 2.036475 ACTGGTGAGCAGAAGTACACTG 59.964 50.000 19.57 13.37 38.27 3.66
4426 6556 3.134442 TCACATGCATATACTGGTGAGCA 59.866 43.478 10.33 0.00 36.34 4.26
4524 6654 1.348064 AACCCCAGACAATGTCTCGA 58.652 50.000 13.72 0.00 41.37 4.04
4537 6667 6.606241 ATCTATTTCCCTTCATAAACCCCA 57.394 37.500 0.00 0.00 0.00 4.96
4545 6675 9.533831 AAAAGTGTTGTATCTATTTCCCTTCAT 57.466 29.630 0.00 0.00 0.00 2.57
4562 6692 4.819630 TGTACCTAGCCTTGAAAAGTGTTG 59.180 41.667 0.00 0.00 44.25 3.33
4563 6693 5.043737 TGTACCTAGCCTTGAAAAGTGTT 57.956 39.130 0.00 0.00 44.25 3.32
4619 6749 1.064240 TGACGACTAGCCCAGGATACA 60.064 52.381 0.00 0.00 41.41 2.29
4626 6756 2.017623 GCTCTACTGACGACTAGCCCA 61.018 57.143 0.00 0.00 0.00 5.36
4708 6838 9.665264 GTACAAGGAAAACAAAGAAGTAGAATG 57.335 33.333 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.