Multiple sequence alignment - TraesCS5A01G282800

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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 TraesCS5A01G282800 chr5A 100.000 3417 0 0 1 3417 491367964 491371380 0.000000e+00 6311.0
1 TraesCS5A01G282800 chr5A 88.734 2441 212 27 329 2722 491521490 491523914 0.000000e+00 2926.0
2 TraesCS5A01G282800 chr5A 87.605 1662 147 32 936 2571 491319265 491317637 0.000000e+00 1873.0
3 TraesCS5A01G282800 chr5A 97.785 316 7 0 1 316 491325946 491325631 2.320000e-151 545.0
4 TraesCS5A01G282800 chr5D 93.559 3105 152 20 341 3415 388330725 388333811 0.000000e+00 4582.0
5 TraesCS5A01G282800 chr5D 89.740 2427 181 29 329 2722 388588420 388590811 0.000000e+00 3040.0
6 TraesCS5A01G282800 chr5D 88.685 1361 105 26 936 2272 388423605 388422270 0.000000e+00 1615.0
7 TraesCS5A01G282800 chr5D 97.785 316 7 0 1 316 170400814 170401129 2.320000e-151 545.0
8 TraesCS5A01G282800 chr6D 90.293 2421 180 18 329 2722 106891315 106893707 0.000000e+00 3118.0
9 TraesCS5A01G282800 chr6D 83.486 109 12 3 3123 3225 391925877 391925985 2.810000e-16 97.1
10 TraesCS5A01G282800 chr6A 89.158 2352 204 22 404 2722 130405139 130407472 0.000000e+00 2883.0
11 TraesCS5A01G282800 chr6A 97.468 316 8 0 1 316 67368094 67367779 1.080000e-149 540.0
12 TraesCS5A01G282800 chr6A 84.956 113 11 3 3125 3231 454678075 454677963 3.610000e-20 110.0
13 TraesCS5A01G282800 chr5B 93.380 1148 53 7 1517 2657 466974255 466975386 0.000000e+00 1677.0
14 TraesCS5A01G282800 chr5B 87.453 1339 95 26 316 1589 466972902 466974232 0.000000e+00 1474.0
15 TraesCS5A01G282800 chr5B 95.480 354 13 1 2656 3006 466975477 466975830 2.300000e-156 562.0
16 TraesCS5A01G282800 chr1D 97.785 316 7 0 1 316 234341900 234341585 2.320000e-151 545.0
17 TraesCS5A01G282800 chr1D 97.468 316 8 0 1 316 234347354 234347039 1.080000e-149 540.0
18 TraesCS5A01G282800 chrUn 97.468 316 8 0 1 316 137819096 137818781 1.080000e-149 540.0
19 TraesCS5A01G282800 chr4D 97.476 317 7 1 1 316 506624462 506624146 1.080000e-149 540.0
20 TraesCS5A01G282800 chr4D 93.103 58 2 2 721 778 378272715 378272660 2.190000e-12 84.2
21 TraesCS5A01G282800 chr3D 97.468 316 8 0 1 316 8256285 8255970 1.080000e-149 540.0
22 TraesCS5A01G282800 chr3D 97.468 316 8 0 1 316 369488992 369488677 1.080000e-149 540.0
23 TraesCS5A01G282800 chr6B 85.981 107 9 3 3125 3225 507471549 507471655 3.610000e-20 110.0
24 TraesCS5A01G282800 chr2A 83.478 115 13 3 3117 3225 727238658 727238772 6.030000e-18 102.0
25 TraesCS5A01G282800 chr2A 81.739 115 13 5 3116 3224 42400387 42400499 4.700000e-14 89.8
26 TraesCS5A01G282800 chr2A 82.407 108 13 3 3131 3232 205917700 205917593 4.700000e-14 89.8
27 TraesCS5A01G282800 chr7A 84.762 105 10 3 316 414 484450836 484450732 2.170000e-17 100.0
28 TraesCS5A01G282800 chr4A 83.486 109 8 4 3124 3226 581333611 581333715 3.630000e-15 93.5
29 TraesCS5A01G282800 chr4A 91.379 58 4 1 723 779 60654297 60654240 1.020000e-10 78.7
30 TraesCS5A01G282800 chr4A 90.385 52 5 0 728 779 477033337 477033286 6.120000e-08 69.4
31 TraesCS5A01G282800 chr2D 80.315 127 14 8 3116 3233 37535848 37535972 6.080000e-13 86.1


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 TraesCS5A01G282800 chr5A 491367964 491371380 3416 False 6311.000000 6311 100.000000 1 3417 1 chr5A.!!$F1 3416
1 TraesCS5A01G282800 chr5A 491521490 491523914 2424 False 2926.000000 2926 88.734000 329 2722 1 chr5A.!!$F2 2393
2 TraesCS5A01G282800 chr5A 491317637 491319265 1628 True 1873.000000 1873 87.605000 936 2571 1 chr5A.!!$R1 1635
3 TraesCS5A01G282800 chr5D 388330725 388333811 3086 False 4582.000000 4582 93.559000 341 3415 1 chr5D.!!$F2 3074
4 TraesCS5A01G282800 chr5D 388588420 388590811 2391 False 3040.000000 3040 89.740000 329 2722 1 chr5D.!!$F3 2393
5 TraesCS5A01G282800 chr5D 388422270 388423605 1335 True 1615.000000 1615 88.685000 936 2272 1 chr5D.!!$R1 1336
6 TraesCS5A01G282800 chr6D 106891315 106893707 2392 False 3118.000000 3118 90.293000 329 2722 1 chr6D.!!$F1 2393
7 TraesCS5A01G282800 chr6A 130405139 130407472 2333 False 2883.000000 2883 89.158000 404 2722 1 chr6A.!!$F1 2318
8 TraesCS5A01G282800 chr5B 466972902 466975830 2928 False 1237.666667 1677 92.104333 316 3006 3 chr5B.!!$F1 2690

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
98 99 0.037697 AGCACGCACGGTATGAAGAA 60.038 50.0 0.00 0.00 0.00 2.52 F
248 249 0.171679 CATGCATGAACGTGCCACAT 59.828 50.0 22.59 1.41 44.43 3.21 F
249 250 0.171679 ATGCATGAACGTGCCACATG 59.828 50.0 14.99 15.76 44.43 3.21 F
1612 1812 0.336737 ACACCCTAGAGAGTGGGAGG 59.663 60.0 4.93 0.00 46.15 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 1812 0.035152 TCAGCACATCCATGGTCACC 60.035 55.000 12.58 0.0 0.00 4.02 R
2148 2364 1.074889 ACTTCTTAAACATGGCCGGGT 59.925 47.619 2.18 0.0 0.00 5.28 R
2263 2479 2.882876 GCCTCTAGTTCGGCGTCA 59.117 61.111 6.85 0.0 36.45 4.35 R
2926 3236 0.887933 CTTGTGGAAAATGGGTCGGG 59.112 55.000 0.00 0.0 0.00 5.14 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
27 28 7.611213 AAATCCTATTAAGTGGTCAGTTTCG 57.389 36.000 0.00 0.00 0.00 3.46
28 29 5.733620 TCCTATTAAGTGGTCAGTTTCGT 57.266 39.130 0.00 0.00 0.00 3.85
29 30 5.717119 TCCTATTAAGTGGTCAGTTTCGTC 58.283 41.667 0.00 0.00 0.00 4.20
30 31 5.479375 TCCTATTAAGTGGTCAGTTTCGTCT 59.521 40.000 0.00 0.00 0.00 4.18
31 32 5.805994 CCTATTAAGTGGTCAGTTTCGTCTC 59.194 44.000 0.00 0.00 0.00 3.36
32 33 2.528041 AAGTGGTCAGTTTCGTCTCC 57.472 50.000 0.00 0.00 0.00 3.71
33 34 0.680061 AGTGGTCAGTTTCGTCTCCC 59.320 55.000 0.00 0.00 0.00 4.30
34 35 0.391597 GTGGTCAGTTTCGTCTCCCA 59.608 55.000 0.00 0.00 0.00 4.37
35 36 1.002087 GTGGTCAGTTTCGTCTCCCAT 59.998 52.381 0.00 0.00 0.00 4.00
36 37 1.697432 TGGTCAGTTTCGTCTCCCATT 59.303 47.619 0.00 0.00 0.00 3.16
37 38 2.901192 TGGTCAGTTTCGTCTCCCATTA 59.099 45.455 0.00 0.00 0.00 1.90
38 39 3.056107 TGGTCAGTTTCGTCTCCCATTAG 60.056 47.826 0.00 0.00 0.00 1.73
39 40 3.056035 GGTCAGTTTCGTCTCCCATTAGT 60.056 47.826 0.00 0.00 0.00 2.24
40 41 4.562963 GGTCAGTTTCGTCTCCCATTAGTT 60.563 45.833 0.00 0.00 0.00 2.24
41 42 4.389077 GTCAGTTTCGTCTCCCATTAGTTG 59.611 45.833 0.00 0.00 0.00 3.16
42 43 3.684788 CAGTTTCGTCTCCCATTAGTTGG 59.315 47.826 0.00 0.00 46.00 3.77
43 44 2.396590 TTCGTCTCCCATTAGTTGGC 57.603 50.000 0.00 0.00 44.97 4.52
44 45 1.271856 TCGTCTCCCATTAGTTGGCA 58.728 50.000 0.00 0.00 44.97 4.92
45 46 1.626321 TCGTCTCCCATTAGTTGGCAA 59.374 47.619 0.00 0.00 44.97 4.52
46 47 2.009774 CGTCTCCCATTAGTTGGCAAG 58.990 52.381 0.00 0.00 44.97 4.01
47 48 2.615493 CGTCTCCCATTAGTTGGCAAGT 60.615 50.000 12.91 12.91 44.97 3.16
48 49 3.010420 GTCTCCCATTAGTTGGCAAGTC 58.990 50.000 11.55 0.00 44.97 3.01
49 50 2.009774 CTCCCATTAGTTGGCAAGTCG 58.990 52.381 11.55 1.61 44.97 4.18
50 51 1.349688 TCCCATTAGTTGGCAAGTCGT 59.650 47.619 11.55 0.00 44.97 4.34
51 52 2.159382 CCCATTAGTTGGCAAGTCGTT 58.841 47.619 11.55 0.00 44.97 3.85
52 53 2.556622 CCCATTAGTTGGCAAGTCGTTT 59.443 45.455 11.55 0.00 44.97 3.60
53 54 3.365969 CCCATTAGTTGGCAAGTCGTTTC 60.366 47.826 11.55 0.00 44.97 2.78
54 55 3.252215 CCATTAGTTGGCAAGTCGTTTCA 59.748 43.478 11.55 0.00 39.09 2.69
55 56 4.261405 CCATTAGTTGGCAAGTCGTTTCAA 60.261 41.667 11.55 0.00 39.09 2.69
56 57 4.545823 TTAGTTGGCAAGTCGTTTCAAG 57.454 40.909 11.55 0.00 0.00 3.02
57 58 2.365582 AGTTGGCAAGTCGTTTCAAGT 58.634 42.857 0.00 0.00 0.00 3.16
58 59 2.752903 AGTTGGCAAGTCGTTTCAAGTT 59.247 40.909 0.00 0.00 0.00 2.66
59 60 3.105937 GTTGGCAAGTCGTTTCAAGTTC 58.894 45.455 0.00 0.00 0.00 3.01
60 61 2.639065 TGGCAAGTCGTTTCAAGTTCT 58.361 42.857 0.00 0.00 0.00 3.01
61 62 3.013921 TGGCAAGTCGTTTCAAGTTCTT 58.986 40.909 0.00 0.00 0.00 2.52
62 63 3.181501 TGGCAAGTCGTTTCAAGTTCTTG 60.182 43.478 6.24 6.24 36.42 3.02
63 64 2.783832 GCAAGTCGTTTCAAGTTCTTGC 59.216 45.455 10.94 10.94 46.25 4.01
64 65 4.014847 CAAGTCGTTTCAAGTTCTTGCA 57.985 40.909 7.58 0.00 0.00 4.08
65 66 4.601019 CAAGTCGTTTCAAGTTCTTGCAT 58.399 39.130 7.58 0.00 0.00 3.96
66 67 4.214980 AGTCGTTTCAAGTTCTTGCATG 57.785 40.909 7.58 0.00 0.00 4.06
67 68 3.876914 AGTCGTTTCAAGTTCTTGCATGA 59.123 39.130 0.00 0.00 0.00 3.07
68 69 3.968724 GTCGTTTCAAGTTCTTGCATGAC 59.031 43.478 1.02 12.05 0.00 3.06
69 70 3.625313 TCGTTTCAAGTTCTTGCATGACA 59.375 39.130 1.02 0.00 0.00 3.58
70 71 4.095632 TCGTTTCAAGTTCTTGCATGACAA 59.904 37.500 1.02 0.00 36.62 3.18
71 72 4.797868 CGTTTCAAGTTCTTGCATGACAAA 59.202 37.500 1.02 0.58 37.96 2.83
72 73 5.288232 CGTTTCAAGTTCTTGCATGACAAAA 59.712 36.000 1.02 0.00 37.96 2.44
73 74 6.019640 CGTTTCAAGTTCTTGCATGACAAAAT 60.020 34.615 1.02 0.00 37.96 1.82
74 75 7.167302 CGTTTCAAGTTCTTGCATGACAAAATA 59.833 33.333 1.02 0.00 37.96 1.40
75 76 8.981647 GTTTCAAGTTCTTGCATGACAAAATAT 58.018 29.630 1.02 0.00 37.96 1.28
76 77 8.523523 TTCAAGTTCTTGCATGACAAAATATG 57.476 30.769 1.02 0.00 37.96 1.78
81 82 5.824429 TCTTGCATGACAAAATATGCTAGC 58.176 37.500 8.10 8.10 45.92 3.42
82 83 5.357596 TCTTGCATGACAAAATATGCTAGCA 59.642 36.000 21.85 21.85 45.92 3.49
83 84 6.678655 TCTTGCATGACAAAATATGCTAGCAC 60.679 38.462 22.07 5.06 45.92 4.40
84 85 3.970610 GCATGACAAAATATGCTAGCACG 59.029 43.478 22.07 7.03 44.70 5.34
85 86 3.673746 TGACAAAATATGCTAGCACGC 57.326 42.857 22.07 3.96 0.00 5.34
86 87 3.006247 TGACAAAATATGCTAGCACGCA 58.994 40.909 22.07 8.86 45.10 5.24
87 88 3.181511 TGACAAAATATGCTAGCACGCAC 60.182 43.478 22.07 7.05 43.61 5.34
88 89 2.223021 ACAAAATATGCTAGCACGCACG 60.223 45.455 22.07 9.81 43.61 5.34
89 90 0.937304 AAATATGCTAGCACGCACGG 59.063 50.000 22.07 0.00 43.61 4.94
90 91 0.179084 AATATGCTAGCACGCACGGT 60.179 50.000 22.07 4.57 43.61 4.83
91 92 0.671796 ATATGCTAGCACGCACGGTA 59.328 50.000 22.07 7.01 43.61 4.02
92 93 0.671796 TATGCTAGCACGCACGGTAT 59.328 50.000 22.07 2.89 43.61 2.73
93 94 0.875908 ATGCTAGCACGCACGGTATG 60.876 55.000 22.07 0.00 43.61 2.39
94 95 1.226859 GCTAGCACGCACGGTATGA 60.227 57.895 10.63 0.00 0.00 2.15
95 96 0.804544 GCTAGCACGCACGGTATGAA 60.805 55.000 10.63 0.00 0.00 2.57
96 97 1.200483 CTAGCACGCACGGTATGAAG 58.800 55.000 0.00 0.00 0.00 3.02
97 98 0.812549 TAGCACGCACGGTATGAAGA 59.187 50.000 0.00 0.00 0.00 2.87
98 99 0.037697 AGCACGCACGGTATGAAGAA 60.038 50.000 0.00 0.00 0.00 2.52
99 100 0.793861 GCACGCACGGTATGAAGAAA 59.206 50.000 0.00 0.00 0.00 2.52
100 101 1.463528 GCACGCACGGTATGAAGAAAC 60.464 52.381 0.00 0.00 0.00 2.78
101 102 1.127951 CACGCACGGTATGAAGAAACC 59.872 52.381 0.00 0.00 0.00 3.27
102 103 1.270412 ACGCACGGTATGAAGAAACCA 60.270 47.619 0.00 0.00 35.35 3.67
103 104 1.801771 CGCACGGTATGAAGAAACCAA 59.198 47.619 0.00 0.00 35.35 3.67
104 105 2.418628 CGCACGGTATGAAGAAACCAAT 59.581 45.455 0.00 0.00 35.35 3.16
105 106 3.727673 CGCACGGTATGAAGAAACCAATG 60.728 47.826 0.00 0.00 35.35 2.82
106 107 3.190535 GCACGGTATGAAGAAACCAATGT 59.809 43.478 0.00 0.00 35.35 2.71
107 108 4.393680 GCACGGTATGAAGAAACCAATGTA 59.606 41.667 0.00 0.00 35.35 2.29
108 109 5.672819 GCACGGTATGAAGAAACCAATGTAC 60.673 44.000 0.00 0.00 35.35 2.90
109 110 5.642063 CACGGTATGAAGAAACCAATGTACT 59.358 40.000 0.00 0.00 35.35 2.73
110 111 6.814644 CACGGTATGAAGAAACCAATGTACTA 59.185 38.462 0.00 0.00 35.35 1.82
111 112 7.332430 CACGGTATGAAGAAACCAATGTACTAA 59.668 37.037 0.00 0.00 35.35 2.24
112 113 8.044908 ACGGTATGAAGAAACCAATGTACTAAT 58.955 33.333 0.00 0.00 35.35 1.73
113 114 8.335356 CGGTATGAAGAAACCAATGTACTAATG 58.665 37.037 0.00 0.00 35.35 1.90
114 115 9.391006 GGTATGAAGAAACCAATGTACTAATGA 57.609 33.333 0.00 0.00 35.73 2.57
117 118 9.739276 ATGAAGAAACCAATGTACTAATGAAGA 57.261 29.630 0.00 0.00 0.00 2.87
118 119 9.567776 TGAAGAAACCAATGTACTAATGAAGAA 57.432 29.630 0.00 0.00 0.00 2.52
126 127 9.573133 CCAATGTACTAATGAAGAAATGAAACC 57.427 33.333 0.00 0.00 0.00 3.27
127 128 9.277565 CAATGTACTAATGAAGAAATGAAACCG 57.722 33.333 0.00 0.00 0.00 4.44
128 129 8.786826 ATGTACTAATGAAGAAATGAAACCGA 57.213 30.769 0.00 0.00 0.00 4.69
129 130 8.610248 TGTACTAATGAAGAAATGAAACCGAA 57.390 30.769 0.00 0.00 0.00 4.30
130 131 9.058174 TGTACTAATGAAGAAATGAAACCGAAA 57.942 29.630 0.00 0.00 0.00 3.46
131 132 9.326339 GTACTAATGAAGAAATGAAACCGAAAC 57.674 33.333 0.00 0.00 0.00 2.78
132 133 7.368059 ACTAATGAAGAAATGAAACCGAAACC 58.632 34.615 0.00 0.00 0.00 3.27
133 134 5.782893 ATGAAGAAATGAAACCGAAACCA 57.217 34.783 0.00 0.00 0.00 3.67
134 135 5.584253 TGAAGAAATGAAACCGAAACCAA 57.416 34.783 0.00 0.00 0.00 3.67
135 136 5.967088 TGAAGAAATGAAACCGAAACCAAA 58.033 33.333 0.00 0.00 0.00 3.28
136 137 6.398918 TGAAGAAATGAAACCGAAACCAAAA 58.601 32.000 0.00 0.00 0.00 2.44
137 138 7.044798 TGAAGAAATGAAACCGAAACCAAAAT 58.955 30.769 0.00 0.00 0.00 1.82
138 139 8.198109 TGAAGAAATGAAACCGAAACCAAAATA 58.802 29.630 0.00 0.00 0.00 1.40
139 140 9.203421 GAAGAAATGAAACCGAAACCAAAATAT 57.797 29.630 0.00 0.00 0.00 1.28
140 141 9.554395 AAGAAATGAAACCGAAACCAAAATATT 57.446 25.926 0.00 0.00 0.00 1.28
141 142 8.987890 AGAAATGAAACCGAAACCAAAATATTG 58.012 29.630 0.00 0.00 36.25 1.90
142 143 8.894768 AAATGAAACCGAAACCAAAATATTGA 57.105 26.923 0.00 0.00 38.94 2.57
143 144 9.500785 AAATGAAACCGAAACCAAAATATTGAT 57.499 25.926 0.00 0.00 38.94 2.57
144 145 7.881643 TGAAACCGAAACCAAAATATTGATG 57.118 32.000 0.00 0.00 38.94 3.07
145 146 6.367422 TGAAACCGAAACCAAAATATTGATGC 59.633 34.615 0.00 0.00 38.94 3.91
146 147 4.754322 ACCGAAACCAAAATATTGATGCC 58.246 39.130 0.00 0.00 38.94 4.40
147 148 4.221703 ACCGAAACCAAAATATTGATGCCA 59.778 37.500 0.00 0.00 38.94 4.92
148 149 5.104982 ACCGAAACCAAAATATTGATGCCAT 60.105 36.000 0.00 0.00 38.94 4.40
149 150 5.463061 CCGAAACCAAAATATTGATGCCATC 59.537 40.000 0.00 0.00 38.94 3.51
150 151 6.041511 CGAAACCAAAATATTGATGCCATCA 58.958 36.000 2.53 2.53 38.94 3.07
159 160 3.937778 TTGATGCCATCAATGAGGAGA 57.062 42.857 15.94 0.00 43.84 3.71
160 161 4.448720 TTGATGCCATCAATGAGGAGAT 57.551 40.909 15.94 0.00 43.84 2.75
161 162 3.751518 TGATGCCATCAATGAGGAGATG 58.248 45.455 4.55 0.00 40.94 2.90
162 163 3.393278 TGATGCCATCAATGAGGAGATGA 59.607 43.478 4.55 0.00 43.28 2.92
163 164 3.937778 TGCCATCAATGAGGAGATGAA 57.062 42.857 0.00 0.00 43.28 2.57
164 165 4.448720 TGCCATCAATGAGGAGATGAAT 57.551 40.909 0.00 0.00 43.28 2.57
165 166 4.142038 TGCCATCAATGAGGAGATGAATG 58.858 43.478 0.00 0.00 43.28 2.67
166 167 4.142790 GCCATCAATGAGGAGATGAATGT 58.857 43.478 0.00 0.00 43.28 2.71
167 168 4.215827 GCCATCAATGAGGAGATGAATGTC 59.784 45.833 0.00 0.00 43.28 3.06
168 169 5.374071 CCATCAATGAGGAGATGAATGTCA 58.626 41.667 0.00 0.00 43.28 3.58
169 170 6.004574 CCATCAATGAGGAGATGAATGTCAT 58.995 40.000 0.00 0.00 43.28 3.06
183 184 7.664552 ATGAATGTCATCATTTACCACCATT 57.335 32.000 0.00 0.00 43.33 3.16
184 185 7.099266 TGAATGTCATCATTTACCACCATTC 57.901 36.000 0.00 0.00 43.33 2.67
185 186 5.756195 ATGTCATCATTTACCACCATTCG 57.244 39.130 0.00 0.00 0.00 3.34
186 187 3.944650 TGTCATCATTTACCACCATTCGG 59.055 43.478 0.00 0.00 38.77 4.30
187 188 7.307777 AATGTCATCATTTACCACCATTCGGT 61.308 38.462 0.00 0.00 43.18 4.69
188 189 4.398044 GTCATCATTTACCACCATTCGGTT 59.602 41.667 0.00 0.00 46.31 4.44
189 190 5.013547 TCATCATTTACCACCATTCGGTTT 58.986 37.500 0.00 0.00 46.31 3.27
190 191 5.124776 TCATCATTTACCACCATTCGGTTTC 59.875 40.000 0.00 0.00 46.31 2.78
191 192 4.399219 TCATTTACCACCATTCGGTTTCA 58.601 39.130 0.00 0.00 46.31 2.69
192 193 5.013547 TCATTTACCACCATTCGGTTTCAT 58.986 37.500 0.00 0.00 46.31 2.57
193 194 5.478679 TCATTTACCACCATTCGGTTTCATT 59.521 36.000 0.00 0.00 46.31 2.57
194 195 5.793030 TTTACCACCATTCGGTTTCATTT 57.207 34.783 0.00 0.00 46.31 2.32
195 196 5.793030 TTACCACCATTCGGTTTCATTTT 57.207 34.783 0.00 0.00 46.31 1.82
196 197 4.251543 ACCACCATTCGGTTTCATTTTC 57.748 40.909 0.00 0.00 46.31 2.29
197 198 3.006430 ACCACCATTCGGTTTCATTTTCC 59.994 43.478 0.00 0.00 46.31 3.13
198 199 3.006323 CCACCATTCGGTTTCATTTTCCA 59.994 43.478 0.00 0.00 46.31 3.53
199 200 3.987220 CACCATTCGGTTTCATTTTCCAC 59.013 43.478 0.00 0.00 46.31 4.02
200 201 3.895041 ACCATTCGGTTTCATTTTCCACT 59.105 39.130 0.00 0.00 46.31 4.00
201 202 5.048364 CACCATTCGGTTTCATTTTCCACTA 60.048 40.000 0.00 0.00 46.31 2.74
202 203 5.183140 ACCATTCGGTTTCATTTTCCACTAG 59.817 40.000 0.00 0.00 46.31 2.57
203 204 4.759516 TTCGGTTTCATTTTCCACTAGC 57.240 40.909 0.00 0.00 0.00 3.42
204 205 2.739913 TCGGTTTCATTTTCCACTAGCG 59.260 45.455 0.00 0.00 0.00 4.26
205 206 2.727916 CGGTTTCATTTTCCACTAGCGC 60.728 50.000 0.00 0.00 0.00 5.92
206 207 2.227865 GGTTTCATTTTCCACTAGCGCA 59.772 45.455 11.47 0.00 0.00 6.09
207 208 3.305064 GGTTTCATTTTCCACTAGCGCAA 60.305 43.478 11.47 0.00 0.00 4.85
208 209 4.295051 GTTTCATTTTCCACTAGCGCAAA 58.705 39.130 11.47 0.00 0.00 3.68
209 210 4.782019 TTCATTTTCCACTAGCGCAAAT 57.218 36.364 11.47 1.45 0.00 2.32
210 211 5.888691 TTCATTTTCCACTAGCGCAAATA 57.111 34.783 11.47 0.00 0.00 1.40
211 212 6.449635 TTCATTTTCCACTAGCGCAAATAT 57.550 33.333 11.47 0.00 0.00 1.28
212 213 6.449635 TCATTTTCCACTAGCGCAAATATT 57.550 33.333 11.47 0.00 0.00 1.28
213 214 6.862209 TCATTTTCCACTAGCGCAAATATTT 58.138 32.000 11.47 0.00 0.00 1.40
214 215 7.319646 TCATTTTCCACTAGCGCAAATATTTT 58.680 30.769 11.47 0.00 0.00 1.82
215 216 8.462811 TCATTTTCCACTAGCGCAAATATTTTA 58.537 29.630 11.47 0.00 0.00 1.52
216 217 9.081997 CATTTTCCACTAGCGCAAATATTTTAA 57.918 29.630 11.47 0.00 0.00 1.52
217 218 8.455598 TTTTCCACTAGCGCAAATATTTTAAC 57.544 30.769 11.47 0.00 0.00 2.01
218 219 6.995511 TCCACTAGCGCAAATATTTTAACT 57.004 33.333 11.47 0.00 0.00 2.24
219 220 7.385778 TCCACTAGCGCAAATATTTTAACTT 57.614 32.000 11.47 0.00 0.00 2.66
220 221 7.469260 TCCACTAGCGCAAATATTTTAACTTC 58.531 34.615 11.47 0.00 0.00 3.01
221 222 7.335924 TCCACTAGCGCAAATATTTTAACTTCT 59.664 33.333 11.47 0.00 0.00 2.85
222 223 7.968405 CCACTAGCGCAAATATTTTAACTTCTT 59.032 33.333 11.47 0.00 0.00 2.52
223 224 9.341899 CACTAGCGCAAATATTTTAACTTCTTT 57.658 29.630 11.47 0.00 0.00 2.52
224 225 9.556030 ACTAGCGCAAATATTTTAACTTCTTTC 57.444 29.630 11.47 0.00 0.00 2.62
225 226 9.774742 CTAGCGCAAATATTTTAACTTCTTTCT 57.225 29.630 11.47 0.00 0.00 2.52
227 228 8.915654 AGCGCAAATATTTTAACTTCTTTCTTG 58.084 29.630 11.47 0.00 0.00 3.02
228 229 8.699749 GCGCAAATATTTTAACTTCTTTCTTGT 58.300 29.630 0.30 0.00 0.00 3.16
236 237 8.578308 TTTTAACTTCTTTCTTGTCATGCATG 57.422 30.769 21.07 21.07 0.00 4.06
237 238 7.509141 TTAACTTCTTTCTTGTCATGCATGA 57.491 32.000 25.42 25.42 0.00 3.07
238 239 6.395426 AACTTCTTTCTTGTCATGCATGAA 57.605 33.333 30.24 15.48 38.75 2.57
239 240 5.766222 ACTTCTTTCTTGTCATGCATGAAC 58.234 37.500 30.24 22.61 39.82 3.18
240 241 4.408993 TCTTTCTTGTCATGCATGAACG 57.591 40.909 30.24 20.03 39.82 3.95
241 242 3.814842 TCTTTCTTGTCATGCATGAACGT 59.185 39.130 30.24 0.00 39.82 3.99
242 243 3.541071 TTCTTGTCATGCATGAACGTG 57.459 42.857 30.24 19.29 38.75 4.49
243 244 1.197492 TCTTGTCATGCATGAACGTGC 59.803 47.619 30.24 17.80 45.25 5.34
244 245 0.240678 TTGTCATGCATGAACGTGCC 59.759 50.000 30.24 17.10 44.43 5.01
245 246 0.888285 TGTCATGCATGAACGTGCCA 60.888 50.000 30.24 19.44 44.43 4.92
246 247 0.454957 GTCATGCATGAACGTGCCAC 60.455 55.000 30.24 12.63 44.43 5.01
247 248 0.888285 TCATGCATGAACGTGCCACA 60.888 50.000 26.87 0.00 44.43 4.17
248 249 0.171679 CATGCATGAACGTGCCACAT 59.828 50.000 22.59 1.41 44.43 3.21
249 250 0.171679 ATGCATGAACGTGCCACATG 59.828 50.000 14.99 15.76 44.43 3.21
250 251 1.153978 GCATGAACGTGCCACATGG 60.154 57.895 19.16 0.00 40.83 3.66
251 252 1.507630 CATGAACGTGCCACATGGG 59.492 57.895 13.61 0.00 38.07 4.00
260 261 3.672913 CCACATGGGCCTATGGGA 58.327 61.111 31.43 0.00 33.20 4.37
261 262 2.167217 CCACATGGGCCTATGGGAT 58.833 57.895 31.43 8.94 33.20 3.85
262 263 0.484212 CCACATGGGCCTATGGGATT 59.516 55.000 31.43 8.55 33.20 3.01
263 264 1.133072 CCACATGGGCCTATGGGATTT 60.133 52.381 31.43 8.15 33.20 2.17
264 265 2.681422 CACATGGGCCTATGGGATTTT 58.319 47.619 30.22 7.88 33.20 1.82
265 266 2.629617 CACATGGGCCTATGGGATTTTC 59.370 50.000 30.22 0.00 33.20 2.29
266 267 2.250924 CATGGGCCTATGGGATTTTCC 58.749 52.381 20.95 0.00 35.23 3.13
267 268 1.619298 TGGGCCTATGGGATTTTCCT 58.381 50.000 4.53 0.00 36.57 3.36
268 269 2.795556 TGGGCCTATGGGATTTTCCTA 58.204 47.619 4.53 0.00 36.57 2.94
269 270 3.135279 TGGGCCTATGGGATTTTCCTAA 58.865 45.455 4.53 0.00 36.57 2.69
270 271 3.533907 TGGGCCTATGGGATTTTCCTAAA 59.466 43.478 4.53 0.00 36.57 1.85
271 272 4.016105 TGGGCCTATGGGATTTTCCTAAAA 60.016 41.667 4.53 0.00 36.57 1.52
272 273 4.966168 GGGCCTATGGGATTTTCCTAAAAA 59.034 41.667 0.84 0.00 38.66 1.94
273 274 5.606749 GGGCCTATGGGATTTTCCTAAAAAT 59.393 40.000 0.84 0.00 45.55 1.82
274 275 6.101150 GGGCCTATGGGATTTTCCTAAAAATT 59.899 38.462 0.84 0.00 43.48 1.82
275 276 7.291416 GGGCCTATGGGATTTTCCTAAAAATTA 59.709 37.037 0.84 0.00 43.48 1.40
276 277 8.880244 GGCCTATGGGATTTTCCTAAAAATTAT 58.120 33.333 0.00 0.00 43.48 1.28
303 304 9.913310 TGGATATAACAGATGGTTTAAATCACA 57.087 29.630 2.56 0.00 40.96 3.58
414 418 8.021396 TCGTACACTAACATATGCATGATACTC 58.979 37.037 10.16 0.00 35.96 2.59
417 421 7.500141 ACACTAACATATGCATGATACTCACA 58.500 34.615 10.16 0.00 35.96 3.58
430 434 8.690884 GCATGATACTCACATATGATACTACCT 58.309 37.037 10.38 0.00 33.22 3.08
514 518 3.718956 CCTCCTCCCACTATTGATTTCCT 59.281 47.826 0.00 0.00 0.00 3.36
538 542 4.911390 TCTCATCTCTGGTTTTTCTTCCC 58.089 43.478 0.00 0.00 0.00 3.97
683 755 5.163416 CCACTTCAAAAGGACATGAGGTTTT 60.163 40.000 0.00 0.00 34.12 2.43
684 756 5.750067 CACTTCAAAAGGACATGAGGTTTTG 59.250 40.000 17.51 17.51 39.96 2.44
690 762 2.447047 AGGACATGAGGTTTTGGTTCCT 59.553 45.455 0.00 0.00 36.70 3.36
837 909 2.236146 AGCAACATAGACCGTTGGATCA 59.764 45.455 5.30 0.00 43.19 2.92
876 948 7.256475 GGGTGAGATCTGTTGGATGTAGATATT 60.256 40.741 0.00 0.00 34.33 1.28
977 1049 8.696374 GCACACCTGAAGCCTATATATATAGAA 58.304 37.037 25.30 9.04 38.30 2.10
1028 1100 5.978322 GGTTTAGAAGACCTATTCTAGCGTG 59.022 44.000 0.00 0.00 41.53 5.34
1127 1199 0.818296 ACGTGCTAAGCGAGGAGAAT 59.182 50.000 0.00 0.00 0.00 2.40
1130 1202 1.103803 TGCTAAGCGAGGAGAATCGT 58.896 50.000 0.00 0.00 44.53 3.73
1163 1235 4.047059 CAGCAAGCCAAGCCGGTG 62.047 66.667 1.90 0.00 36.97 4.94
1407 1479 0.968901 TGAAGGGTACGGCATCGACT 60.969 55.000 0.00 0.00 40.11 4.18
1519 1615 3.420893 CACAAAATCTAAGGCACCCTCA 58.579 45.455 0.00 0.00 30.89 3.86
1581 1679 8.794364 AGATCATATATAATCTGCAGGGATCA 57.206 34.615 15.13 0.00 31.09 2.92
1582 1680 9.222098 AGATCATATATAATCTGCAGGGATCAA 57.778 33.333 15.13 0.00 31.09 2.57
1589 1789 2.256306 TCTGCAGGGATCAACTACACA 58.744 47.619 15.13 0.00 0.00 3.72
1612 1812 0.336737 ACACCCTAGAGAGTGGGAGG 59.663 60.000 4.93 0.00 46.15 4.30
1654 1854 1.206371 GCCATGGCAAAGCTTCTGAAT 59.794 47.619 32.08 0.00 41.49 2.57
2085 2301 2.433318 GAGGCTGTCACTGGCGAC 60.433 66.667 0.00 0.00 36.40 5.19
2295 2511 3.673484 GGCGCATGCAGTGGTTGT 61.673 61.111 19.57 0.00 45.35 3.32
2345 2561 2.093288 TGAGTGCATGATGTTCCTCTCC 60.093 50.000 0.00 0.00 0.00 3.71
2429 2645 8.575649 TCCCTGGAATAAAATAAAGAGTCAAC 57.424 34.615 0.00 0.00 0.00 3.18
2446 2662 7.324178 AGAGTCAACTACATCATTGGTACTTC 58.676 38.462 0.00 0.00 0.00 3.01
2487 2704 7.308169 GGTCACTTTAATACTAAAACTTGCGGT 60.308 37.037 0.00 0.00 0.00 5.68
2607 2824 7.921786 TTCTTTTTGTGTGACCCTCTATATG 57.078 36.000 0.00 0.00 0.00 1.78
2639 2856 1.024271 CGTAGCCATCCCAACCATTG 58.976 55.000 0.00 0.00 0.00 2.82
2738 3047 0.179001 AAAGCCTGCCACTTAACCGT 60.179 50.000 0.00 0.00 0.00 4.83
2926 3236 2.939460 AATAATTGGTTGCAGTCGGC 57.061 45.000 0.00 0.00 45.13 5.54
3221 3534 4.489737 ACAAGTAATATGGATCGGAGGGA 58.510 43.478 0.00 0.00 0.00 4.20
3232 3545 6.852420 TGGATCGGAGGGAGTATAATTTAG 57.148 41.667 0.00 0.00 0.00 1.85
3259 3572 7.440523 AATATTTATTTGAGGATCGGCACTC 57.559 36.000 0.00 0.00 38.61 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.512138 CGAAACTGACCACTTAATAGGATTTTT 58.488 33.333 0.71 0.00 0.00 1.94
2 3 7.664318 ACGAAACTGACCACTTAATAGGATTTT 59.336 33.333 0.00 0.00 0.00 1.82
3 4 7.166167 ACGAAACTGACCACTTAATAGGATTT 58.834 34.615 0.00 0.00 0.00 2.17
4 5 6.708285 ACGAAACTGACCACTTAATAGGATT 58.292 36.000 0.00 0.00 0.00 3.01
5 6 6.154706 AGACGAAACTGACCACTTAATAGGAT 59.845 38.462 0.00 0.00 0.00 3.24
6 7 5.479375 AGACGAAACTGACCACTTAATAGGA 59.521 40.000 0.00 0.00 0.00 2.94
7 8 5.721232 AGACGAAACTGACCACTTAATAGG 58.279 41.667 0.00 0.00 0.00 2.57
8 9 5.805994 GGAGACGAAACTGACCACTTAATAG 59.194 44.000 0.00 0.00 0.00 1.73
9 10 5.337009 GGGAGACGAAACTGACCACTTAATA 60.337 44.000 0.00 0.00 0.00 0.98
10 11 4.562963 GGGAGACGAAACTGACCACTTAAT 60.563 45.833 0.00 0.00 0.00 1.40
11 12 3.243975 GGGAGACGAAACTGACCACTTAA 60.244 47.826 0.00 0.00 0.00 1.85
12 13 2.298163 GGGAGACGAAACTGACCACTTA 59.702 50.000 0.00 0.00 0.00 2.24
13 14 1.070289 GGGAGACGAAACTGACCACTT 59.930 52.381 0.00 0.00 0.00 3.16
14 15 0.680061 GGGAGACGAAACTGACCACT 59.320 55.000 0.00 0.00 0.00 4.00
15 16 0.391597 TGGGAGACGAAACTGACCAC 59.608 55.000 0.00 0.00 0.00 4.16
16 17 1.348064 ATGGGAGACGAAACTGACCA 58.652 50.000 0.00 0.00 0.00 4.02
17 18 2.474410 AATGGGAGACGAAACTGACC 57.526 50.000 0.00 0.00 0.00 4.02
18 19 4.189639 ACTAATGGGAGACGAAACTGAC 57.810 45.455 0.00 0.00 0.00 3.51
19 20 4.562757 CCAACTAATGGGAGACGAAACTGA 60.563 45.833 0.00 0.00 46.27 3.41
20 21 3.684788 CCAACTAATGGGAGACGAAACTG 59.315 47.826 0.00 0.00 46.27 3.16
21 22 3.939066 CCAACTAATGGGAGACGAAACT 58.061 45.455 0.00 0.00 46.27 2.66
33 34 4.481930 TGAAACGACTTGCCAACTAATG 57.518 40.909 0.00 0.00 0.00 1.90
34 35 4.578928 ACTTGAAACGACTTGCCAACTAAT 59.421 37.500 0.00 0.00 0.00 1.73
35 36 3.942748 ACTTGAAACGACTTGCCAACTAA 59.057 39.130 0.00 0.00 0.00 2.24
36 37 3.537580 ACTTGAAACGACTTGCCAACTA 58.462 40.909 0.00 0.00 0.00 2.24
37 38 2.365582 ACTTGAAACGACTTGCCAACT 58.634 42.857 0.00 0.00 0.00 3.16
38 39 2.844122 ACTTGAAACGACTTGCCAAC 57.156 45.000 0.00 0.00 0.00 3.77
39 40 3.013921 AGAACTTGAAACGACTTGCCAA 58.986 40.909 0.00 0.00 0.00 4.52
40 41 2.639065 AGAACTTGAAACGACTTGCCA 58.361 42.857 0.00 0.00 0.00 4.92
41 42 3.363178 CAAGAACTTGAAACGACTTGCC 58.637 45.455 8.65 0.00 42.93 4.52
43 44 4.014847 TGCAAGAACTTGAAACGACTTG 57.985 40.909 17.19 0.00 42.93 3.16
44 45 4.335315 TCATGCAAGAACTTGAAACGACTT 59.665 37.500 17.19 0.00 42.93 3.01
45 46 3.876914 TCATGCAAGAACTTGAAACGACT 59.123 39.130 17.19 0.00 42.93 4.18
46 47 3.968724 GTCATGCAAGAACTTGAAACGAC 59.031 43.478 17.19 13.36 42.93 4.34
47 48 3.625313 TGTCATGCAAGAACTTGAAACGA 59.375 39.130 17.19 6.38 42.93 3.85
48 49 3.951306 TGTCATGCAAGAACTTGAAACG 58.049 40.909 17.19 4.32 42.93 3.60
49 50 6.645700 TTTTGTCATGCAAGAACTTGAAAC 57.354 33.333 17.19 4.90 42.93 2.78
50 51 8.980610 CATATTTTGTCATGCAAGAACTTGAAA 58.019 29.630 17.19 7.89 42.93 2.69
51 52 7.116662 GCATATTTTGTCATGCAAGAACTTGAA 59.883 33.333 17.19 8.14 45.51 2.69
52 53 6.587226 GCATATTTTGTCATGCAAGAACTTGA 59.413 34.615 17.19 4.44 45.51 3.02
53 54 6.758149 GCATATTTTGTCATGCAAGAACTTG 58.242 36.000 9.82 9.82 45.51 3.16
54 55 6.956299 GCATATTTTGTCATGCAAGAACTT 57.044 33.333 0.00 0.00 45.51 2.66
62 63 3.970610 CGTGCTAGCATATTTTGTCATGC 59.029 43.478 22.51 1.68 46.35 4.06
63 64 3.970610 GCGTGCTAGCATATTTTGTCATG 59.029 43.478 22.51 0.00 37.05 3.07
64 65 3.627123 TGCGTGCTAGCATATTTTGTCAT 59.373 39.130 22.51 0.00 42.92 3.06
65 66 3.006247 TGCGTGCTAGCATATTTTGTCA 58.994 40.909 22.51 7.29 42.92 3.58
66 67 3.673746 TGCGTGCTAGCATATTTTGTC 57.326 42.857 22.51 4.04 42.92 3.18
75 76 1.518352 CATACCGTGCGTGCTAGCA 60.518 57.895 14.93 14.93 45.96 3.49
76 77 0.804544 TTCATACCGTGCGTGCTAGC 60.805 55.000 8.10 8.10 37.71 3.42
77 78 1.200483 CTTCATACCGTGCGTGCTAG 58.800 55.000 0.00 0.00 0.00 3.42
78 79 0.812549 TCTTCATACCGTGCGTGCTA 59.187 50.000 0.00 0.00 0.00 3.49
79 80 0.037697 TTCTTCATACCGTGCGTGCT 60.038 50.000 0.00 0.00 0.00 4.40
80 81 0.793861 TTTCTTCATACCGTGCGTGC 59.206 50.000 0.00 0.00 0.00 5.34
81 82 1.127951 GGTTTCTTCATACCGTGCGTG 59.872 52.381 0.00 0.00 0.00 5.34
82 83 1.270412 TGGTTTCTTCATACCGTGCGT 60.270 47.619 0.00 0.00 37.23 5.24
83 84 1.434555 TGGTTTCTTCATACCGTGCG 58.565 50.000 0.00 0.00 37.23 5.34
84 85 3.190535 ACATTGGTTTCTTCATACCGTGC 59.809 43.478 0.00 0.00 37.23 5.34
85 86 5.642063 AGTACATTGGTTTCTTCATACCGTG 59.358 40.000 0.00 0.00 37.23 4.94
86 87 5.801380 AGTACATTGGTTTCTTCATACCGT 58.199 37.500 0.00 0.00 37.23 4.83
87 88 7.837202 TTAGTACATTGGTTTCTTCATACCG 57.163 36.000 0.00 0.00 37.23 4.02
88 89 9.391006 TCATTAGTACATTGGTTTCTTCATACC 57.609 33.333 0.00 0.00 34.93 2.73
91 92 9.739276 TCTTCATTAGTACATTGGTTTCTTCAT 57.261 29.630 0.00 0.00 0.00 2.57
92 93 9.567776 TTCTTCATTAGTACATTGGTTTCTTCA 57.432 29.630 0.00 0.00 0.00 3.02
100 101 9.573133 GGTTTCATTTCTTCATTAGTACATTGG 57.427 33.333 0.00 0.00 0.00 3.16
101 102 9.277565 CGGTTTCATTTCTTCATTAGTACATTG 57.722 33.333 0.00 0.00 0.00 2.82
102 103 9.226606 TCGGTTTCATTTCTTCATTAGTACATT 57.773 29.630 0.00 0.00 0.00 2.71
103 104 8.786826 TCGGTTTCATTTCTTCATTAGTACAT 57.213 30.769 0.00 0.00 0.00 2.29
104 105 8.610248 TTCGGTTTCATTTCTTCATTAGTACA 57.390 30.769 0.00 0.00 0.00 2.90
105 106 9.326339 GTTTCGGTTTCATTTCTTCATTAGTAC 57.674 33.333 0.00 0.00 0.00 2.73
106 107 8.508875 GGTTTCGGTTTCATTTCTTCATTAGTA 58.491 33.333 0.00 0.00 0.00 1.82
107 108 7.013846 TGGTTTCGGTTTCATTTCTTCATTAGT 59.986 33.333 0.00 0.00 0.00 2.24
108 109 7.367285 TGGTTTCGGTTTCATTTCTTCATTAG 58.633 34.615 0.00 0.00 0.00 1.73
109 110 7.278461 TGGTTTCGGTTTCATTTCTTCATTA 57.722 32.000 0.00 0.00 0.00 1.90
110 111 6.155475 TGGTTTCGGTTTCATTTCTTCATT 57.845 33.333 0.00 0.00 0.00 2.57
111 112 5.782893 TGGTTTCGGTTTCATTTCTTCAT 57.217 34.783 0.00 0.00 0.00 2.57
112 113 5.584253 TTGGTTTCGGTTTCATTTCTTCA 57.416 34.783 0.00 0.00 0.00 3.02
113 114 6.895607 TTTTGGTTTCGGTTTCATTTCTTC 57.104 33.333 0.00 0.00 0.00 2.87
114 115 9.554395 AATATTTTGGTTTCGGTTTCATTTCTT 57.446 25.926 0.00 0.00 0.00 2.52
115 116 8.987890 CAATATTTTGGTTTCGGTTTCATTTCT 58.012 29.630 0.00 0.00 0.00 2.52
116 117 8.983724 TCAATATTTTGGTTTCGGTTTCATTTC 58.016 29.630 0.00 0.00 33.44 2.17
117 118 8.894768 TCAATATTTTGGTTTCGGTTTCATTT 57.105 26.923 0.00 0.00 33.44 2.32
118 119 8.934825 CATCAATATTTTGGTTTCGGTTTCATT 58.065 29.630 0.00 0.00 33.44 2.57
119 120 7.064490 GCATCAATATTTTGGTTTCGGTTTCAT 59.936 33.333 0.00 0.00 33.44 2.57
120 121 6.367422 GCATCAATATTTTGGTTTCGGTTTCA 59.633 34.615 0.00 0.00 33.44 2.69
121 122 6.183360 GGCATCAATATTTTGGTTTCGGTTTC 60.183 38.462 0.00 0.00 33.44 2.78
122 123 5.641636 GGCATCAATATTTTGGTTTCGGTTT 59.358 36.000 0.00 0.00 33.44 3.27
123 124 5.175127 GGCATCAATATTTTGGTTTCGGTT 58.825 37.500 0.00 0.00 33.44 4.44
124 125 4.221703 TGGCATCAATATTTTGGTTTCGGT 59.778 37.500 0.00 0.00 33.44 4.69
125 126 4.753233 TGGCATCAATATTTTGGTTTCGG 58.247 39.130 0.00 0.00 33.44 4.30
126 127 6.041511 TGATGGCATCAATATTTTGGTTTCG 58.958 36.000 27.03 0.00 36.11 3.46
127 128 7.846644 TTGATGGCATCAATATTTTGGTTTC 57.153 32.000 33.06 2.84 43.84 2.78
140 141 3.393278 TCATCTCCTCATTGATGGCATCA 59.607 43.478 25.63 25.63 40.13 3.07
141 142 4.017177 TCATCTCCTCATTGATGGCATC 57.983 45.455 20.52 20.52 40.13 3.91
142 143 4.448720 TTCATCTCCTCATTGATGGCAT 57.551 40.909 0.00 0.00 40.13 4.40
143 144 3.937778 TTCATCTCCTCATTGATGGCA 57.062 42.857 0.00 0.00 40.13 4.92
144 145 4.142790 ACATTCATCTCCTCATTGATGGC 58.857 43.478 0.00 0.00 40.13 4.40
145 146 5.374071 TGACATTCATCTCCTCATTGATGG 58.626 41.667 0.00 0.00 40.13 3.51
159 160 7.469043 CGAATGGTGGTAAATGATGACATTCAT 60.469 37.037 0.79 0.00 44.67 2.57
160 161 6.183360 CGAATGGTGGTAAATGATGACATTCA 60.183 38.462 0.79 0.00 44.67 2.57
161 162 6.201517 CGAATGGTGGTAAATGATGACATTC 58.798 40.000 0.00 0.00 44.67 2.67
162 163 5.067674 CCGAATGGTGGTAAATGATGACATT 59.932 40.000 0.00 0.00 46.99 2.71
163 164 4.580167 CCGAATGGTGGTAAATGATGACAT 59.420 41.667 0.00 0.00 38.50 3.06
164 165 3.944650 CCGAATGGTGGTAAATGATGACA 59.055 43.478 0.00 0.00 0.00 3.58
165 166 4.552166 CCGAATGGTGGTAAATGATGAC 57.448 45.455 0.00 0.00 0.00 3.06
179 180 4.519540 AGTGGAAAATGAAACCGAATGG 57.480 40.909 0.00 0.00 42.84 3.16
180 181 5.095490 GCTAGTGGAAAATGAAACCGAATG 58.905 41.667 0.00 0.00 0.00 2.67
181 182 4.142687 CGCTAGTGGAAAATGAAACCGAAT 60.143 41.667 0.00 0.00 0.00 3.34
182 183 3.187637 CGCTAGTGGAAAATGAAACCGAA 59.812 43.478 0.00 0.00 0.00 4.30
183 184 2.739913 CGCTAGTGGAAAATGAAACCGA 59.260 45.455 0.00 0.00 0.00 4.69
184 185 2.727916 GCGCTAGTGGAAAATGAAACCG 60.728 50.000 0.00 0.00 0.00 4.44
185 186 2.227865 TGCGCTAGTGGAAAATGAAACC 59.772 45.455 9.73 0.00 0.00 3.27
186 187 3.552604 TGCGCTAGTGGAAAATGAAAC 57.447 42.857 9.73 0.00 0.00 2.78
187 188 4.576216 TTTGCGCTAGTGGAAAATGAAA 57.424 36.364 19.12 0.00 0.00 2.69
188 189 4.782019 ATTTGCGCTAGTGGAAAATGAA 57.218 36.364 24.02 4.33 32.80 2.57
189 190 6.449635 AATATTTGCGCTAGTGGAAAATGA 57.550 33.333 24.02 14.09 32.80 2.57
190 191 7.524294 AAAATATTTGCGCTAGTGGAAAATG 57.476 32.000 24.02 0.00 32.80 2.32
191 192 9.083080 GTTAAAATATTTGCGCTAGTGGAAAAT 57.917 29.630 24.02 16.03 32.80 1.82
192 193 8.301002 AGTTAAAATATTTGCGCTAGTGGAAAA 58.699 29.630 24.02 14.73 32.80 2.29
193 194 7.822658 AGTTAAAATATTTGCGCTAGTGGAAA 58.177 30.769 22.76 22.76 33.60 3.13
194 195 7.385778 AGTTAAAATATTTGCGCTAGTGGAA 57.614 32.000 9.73 6.09 0.00 3.53
195 196 6.995511 AGTTAAAATATTTGCGCTAGTGGA 57.004 33.333 9.73 0.00 0.00 4.02
196 197 7.472543 AGAAGTTAAAATATTTGCGCTAGTGG 58.527 34.615 9.73 0.00 0.00 4.00
197 198 8.895932 AAGAAGTTAAAATATTTGCGCTAGTG 57.104 30.769 9.73 0.00 0.00 2.74
198 199 9.556030 GAAAGAAGTTAAAATATTTGCGCTAGT 57.444 29.630 9.73 0.00 0.00 2.57
199 200 9.774742 AGAAAGAAGTTAAAATATTTGCGCTAG 57.225 29.630 9.73 0.00 0.00 3.42
201 202 8.915654 CAAGAAAGAAGTTAAAATATTTGCGCT 58.084 29.630 9.73 0.00 0.00 5.92
202 203 8.699749 ACAAGAAAGAAGTTAAAATATTTGCGC 58.300 29.630 0.00 0.00 0.00 6.09
210 211 9.199982 CATGCATGACAAGAAAGAAGTTAAAAT 57.800 29.630 22.59 0.00 0.00 1.82
211 212 8.412456 TCATGCATGACAAGAAAGAAGTTAAAA 58.588 29.630 25.42 0.00 0.00 1.52
212 213 7.939782 TCATGCATGACAAGAAAGAAGTTAAA 58.060 30.769 25.42 0.00 0.00 1.52
213 214 7.509141 TCATGCATGACAAGAAAGAAGTTAA 57.491 32.000 25.42 0.00 0.00 2.01
214 215 7.362662 GTTCATGCATGACAAGAAAGAAGTTA 58.637 34.615 28.72 6.37 37.70 2.24
215 216 6.211515 GTTCATGCATGACAAGAAAGAAGTT 58.788 36.000 28.72 0.00 37.70 2.66
216 217 5.561532 CGTTCATGCATGACAAGAAAGAAGT 60.562 40.000 28.72 0.00 37.70 3.01
217 218 4.849926 CGTTCATGCATGACAAGAAAGAAG 59.150 41.667 28.72 10.24 37.70 2.85
218 219 4.275689 ACGTTCATGCATGACAAGAAAGAA 59.724 37.500 28.72 8.36 37.70 2.52
219 220 3.814842 ACGTTCATGCATGACAAGAAAGA 59.185 39.130 28.72 9.12 37.70 2.52
220 221 3.910170 CACGTTCATGCATGACAAGAAAG 59.090 43.478 28.72 17.55 37.70 2.62
221 222 3.852939 GCACGTTCATGCATGACAAGAAA 60.853 43.478 28.72 10.68 45.39 2.52
222 223 2.350676 GCACGTTCATGCATGACAAGAA 60.351 45.455 28.72 11.45 45.39 2.52
223 224 1.197492 GCACGTTCATGCATGACAAGA 59.803 47.619 28.72 11.86 45.39 3.02
224 225 1.609932 GCACGTTCATGCATGACAAG 58.390 50.000 28.72 22.52 45.39 3.16
225 226 3.771171 GCACGTTCATGCATGACAA 57.229 47.368 28.72 13.03 45.39 3.18
232 233 1.153978 CCATGTGGCACGTTCATGC 60.154 57.895 10.21 1.57 45.34 4.06
233 234 1.507630 CCCATGTGGCACGTTCATG 59.492 57.895 10.21 9.14 38.72 3.07
234 235 4.001248 CCCATGTGGCACGTTCAT 57.999 55.556 10.21 0.00 0.00 2.57
243 244 0.484212 AATCCCATAGGCCCATGTGG 59.516 55.000 10.43 10.71 37.09 4.17
244 245 2.386829 AAATCCCATAGGCCCATGTG 57.613 50.000 10.43 0.00 0.00 3.21
245 246 2.426268 GGAAAATCCCATAGGCCCATGT 60.426 50.000 10.43 0.00 0.00 3.21
246 247 2.158264 AGGAAAATCCCATAGGCCCATG 60.158 50.000 3.86 3.86 37.19 3.66
247 248 2.155563 AGGAAAATCCCATAGGCCCAT 58.844 47.619 0.00 0.00 37.19 4.00
248 249 1.619298 AGGAAAATCCCATAGGCCCA 58.381 50.000 0.00 0.00 37.19 5.36
249 250 3.895704 TTAGGAAAATCCCATAGGCCC 57.104 47.619 0.00 0.00 37.19 5.80
250 251 6.747414 ATTTTTAGGAAAATCCCATAGGCC 57.253 37.500 0.00 0.00 40.54 5.19
277 278 9.913310 TGTGATTTAAACCATCTGTTATATCCA 57.087 29.630 0.00 0.00 35.67 3.41
303 304 9.396022 CCCAAGACACATACTGTTAGAATTATT 57.604 33.333 0.00 0.00 31.03 1.40
304 305 7.499232 GCCCAAGACACATACTGTTAGAATTAT 59.501 37.037 0.00 0.00 31.03 1.28
305 306 6.821665 GCCCAAGACACATACTGTTAGAATTA 59.178 38.462 0.00 0.00 31.03 1.40
306 307 5.648092 GCCCAAGACACATACTGTTAGAATT 59.352 40.000 0.00 0.00 31.03 2.17
307 308 5.186198 GCCCAAGACACATACTGTTAGAAT 58.814 41.667 0.00 0.00 31.03 2.40
308 309 4.041075 TGCCCAAGACACATACTGTTAGAA 59.959 41.667 0.00 0.00 31.03 2.10
309 310 3.580895 TGCCCAAGACACATACTGTTAGA 59.419 43.478 0.00 0.00 31.03 2.10
310 311 3.937814 TGCCCAAGACACATACTGTTAG 58.062 45.455 0.00 0.00 31.03 2.34
311 312 4.359434 TTGCCCAAGACACATACTGTTA 57.641 40.909 0.00 0.00 31.03 2.41
312 313 2.949177 TGCCCAAGACACATACTGTT 57.051 45.000 0.00 0.00 31.03 3.16
313 314 2.949177 TTGCCCAAGACACATACTGT 57.051 45.000 0.00 0.00 34.96 3.55
314 315 5.895636 TTTATTGCCCAAGACACATACTG 57.104 39.130 0.00 0.00 0.00 2.74
354 358 7.117667 TCCGTAACGCGTAGTATCATAGATTAA 59.882 37.037 14.46 0.00 39.32 1.40
370 374 1.682982 GATACCATCTCCGTAACGCG 58.317 55.000 3.53 3.53 40.95 6.01
373 377 4.274459 AGTGTACGATACCATCTCCGTAAC 59.726 45.833 0.00 0.00 38.89 2.50
414 418 8.972127 ACAGCCTAATAGGTAGTATCATATGTG 58.028 37.037 8.28 0.00 37.80 3.21
417 421 8.904834 CGAACAGCCTAATAGGTAGTATCATAT 58.095 37.037 8.28 0.00 37.80 1.78
430 434 3.131577 CACCCACTACGAACAGCCTAATA 59.868 47.826 0.00 0.00 0.00 0.98
471 475 3.923425 GGGAGGGGACAATATAGGGATTT 59.077 47.826 0.00 0.00 0.00 2.17
472 476 3.148795 AGGGAGGGGACAATATAGGGATT 59.851 47.826 0.00 0.00 0.00 3.01
473 477 2.741628 AGGGAGGGGACAATATAGGGAT 59.258 50.000 0.00 0.00 0.00 3.85
481 485 1.004891 GGAGGAGGGAGGGGACAAT 59.995 63.158 0.00 0.00 0.00 2.71
514 518 5.280215 GGGAAGAAAAACCAGAGATGAGAGA 60.280 44.000 0.00 0.00 0.00 3.10
654 726 6.884295 CCTCATGTCCTTTTGAAGTGGTATTA 59.116 38.462 0.00 0.00 0.00 0.98
655 727 5.711976 CCTCATGTCCTTTTGAAGTGGTATT 59.288 40.000 0.00 0.00 0.00 1.89
683 755 2.299297 GGACGAAGAAAGAGAGGAACCA 59.701 50.000 0.00 0.00 0.00 3.67
684 756 2.299297 TGGACGAAGAAAGAGAGGAACC 59.701 50.000 0.00 0.00 0.00 3.62
690 762 8.164733 AGATATAGGTATGGACGAAGAAAGAGA 58.835 37.037 0.00 0.00 0.00 3.10
781 853 6.322491 GCGCTGAATTAATTGTCTTAGGTTT 58.678 36.000 5.17 0.00 0.00 3.27
801 873 0.961019 TTGCTTTGAATCTTGGCGCT 59.039 45.000 7.64 0.00 0.00 5.92
837 909 2.124507 CTCACCCGTCCACCCATGTT 62.125 60.000 0.00 0.00 0.00 2.71
886 958 8.855110 CAGGGTTATCATATCCATACTAGCTAG 58.145 40.741 19.44 19.44 0.00 3.42
887 959 8.344546 ACAGGGTTATCATATCCATACTAGCTA 58.655 37.037 0.00 0.00 0.00 3.32
888 960 7.124901 CACAGGGTTATCATATCCATACTAGCT 59.875 40.741 0.00 0.00 0.00 3.32
889 961 7.268586 CACAGGGTTATCATATCCATACTAGC 58.731 42.308 0.00 0.00 0.00 3.42
977 1049 3.366440 ACGTACTCTTCTCTTTTGCGT 57.634 42.857 0.00 0.00 0.00 5.24
987 1059 6.211515 TCTAAACCAAGTGAACGTACTCTTC 58.788 40.000 0.00 0.00 0.00 2.87
1028 1100 3.397482 CTGATCCCGATGAACCATCTTC 58.603 50.000 5.54 0.00 38.59 2.87
1079 1151 2.904866 GGCGCCACAAGTCCAACA 60.905 61.111 24.80 0.00 0.00 3.33
1159 1231 4.969196 CCGCGATGGGGATCACCG 62.969 72.222 8.23 0.00 41.60 4.94
1163 1235 3.912907 ACGTCCGCGATGGGGATC 61.913 66.667 8.23 0.21 46.03 3.36
1295 1367 0.250166 TCGTCGCCTCGAGGATATCA 60.250 55.000 35.69 12.11 43.93 2.15
1298 1370 4.044721 CTCGTCGCCTCGAGGATA 57.955 61.111 35.69 18.64 46.69 2.59
1318 1390 3.056328 GCGGCAGGTGGAAGAACC 61.056 66.667 0.00 0.00 40.85 3.62
1424 1496 0.891373 CACACCAGTCGAGGATCTGT 59.109 55.000 0.00 0.00 0.00 3.41
1481 1553 0.889306 GTGGCCAGAACTAGAGACGT 59.111 55.000 5.11 0.00 0.00 4.34
1484 1556 4.287067 AGATTTTGTGGCCAGAACTAGAGA 59.713 41.667 16.14 0.00 0.00 3.10
1488 1560 5.253330 CCTTAGATTTTGTGGCCAGAACTA 58.747 41.667 16.14 10.85 0.00 2.24
1581 1679 5.638133 TCTCTAGGGTGTACTTGTGTAGTT 58.362 41.667 0.00 0.00 38.33 2.24
1582 1680 5.222089 ACTCTCTAGGGTGTACTTGTGTAGT 60.222 44.000 0.00 0.00 41.04 2.73
1589 1789 2.653366 TCCCACTCTCTAGGGTGTACTT 59.347 50.000 9.09 0.00 45.64 2.24
1612 1812 0.035152 TCAGCACATCCATGGTCACC 60.035 55.000 12.58 0.00 0.00 4.02
1654 1854 4.420206 TGATGAAGAAGTTCTCCTCCTGA 58.580 43.478 5.70 0.00 33.38 3.86
2085 2301 2.202756 GCTCCGGCTGGTAGAACG 60.203 66.667 12.43 0.00 36.30 3.95
2148 2364 1.074889 ACTTCTTAAACATGGCCGGGT 59.925 47.619 2.18 0.00 0.00 5.28
2263 2479 2.882876 GCCTCTAGTTCGGCGTCA 59.117 61.111 6.85 0.00 36.45 4.35
2429 2645 7.905604 TCAAGTTGAAGTACCAATGATGTAG 57.094 36.000 2.20 0.00 0.00 2.74
2446 2662 8.870160 TTAAAGTGACCATTTCAATCAAGTTG 57.130 30.769 0.00 0.00 35.39 3.16
2487 2704 3.004002 CACGCCCACTAGTTCGATATGTA 59.996 47.826 13.75 0.00 0.00 2.29
2607 2824 2.093983 CTACGCACGCTCGCAAAC 59.906 61.111 0.00 0.00 0.00 2.93
2639 2856 5.751243 ATCCATATTAGACAACAAACGGC 57.249 39.130 0.00 0.00 0.00 5.68
2738 3047 6.993786 TCATTTATAGGCATGAAACGTTCA 57.006 33.333 0.00 1.78 45.01 3.18
2926 3236 0.887933 CTTGTGGAAAATGGGTCGGG 59.112 55.000 0.00 0.00 0.00 5.14
3129 3442 4.129380 CAACAAGCAATATGGATCGGAGA 58.871 43.478 0.00 0.00 45.75 3.71
3232 3545 9.167311 AGTGCCGATCCTCAAATAAATATTATC 57.833 33.333 0.00 0.00 0.00 1.75
3241 3554 3.197766 ACAAGAGTGCCGATCCTCAAATA 59.802 43.478 0.44 0.00 0.00 1.40
3259 3572 3.914426 ATTAGCCTAGTGTCCCACAAG 57.086 47.619 0.00 0.00 36.74 3.16


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

AutoCloner maintained by Alex Coulton.