Multiple sequence alignment - TraesCS3B01G456600

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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 TraesCS3B01G456600 chr3B 100.000 1547 0 0 1 1547 697999195 698000741 0.000000e+00 2857.0
1 TraesCS3B01G456600 chr3B 100.000 1001 0 0 1971 2971 698001165 698002165 0.000000e+00 1849.0
2 TraesCS3B01G456600 chr3B 88.249 1251 60 27 359 1547 697982606 697983831 0.000000e+00 1415.0
3 TraesCS3B01G456600 chr3B 91.429 980 51 11 1971 2942 698122896 698123850 0.000000e+00 1314.0
4 TraesCS3B01G456600 chr3B 90.092 979 58 6 1971 2942 697983899 697984845 0.000000e+00 1234.0
5 TraesCS3B01G456600 chr3B 85.531 1168 83 37 437 1547 698121687 698122825 0.000000e+00 1142.0
6 TraesCS3B01G456600 chr3B 87.340 703 52 20 785 1470 698194659 698195341 0.000000e+00 771.0
7 TraesCS3B01G456600 chr3B 94.677 263 13 1 1 262 541061882 541061620 9.910000e-110 407.0
8 TraesCS3B01G456600 chr3B 83.832 334 22 13 433 746 698193460 698193781 3.750000e-74 289.0
9 TraesCS3B01G456600 chr3B 75.405 679 102 40 2146 2762 193212386 193213061 4.880000e-68 268.0
10 TraesCS3B01G456600 chr3B 94.681 94 5 0 261 354 697982466 697982559 2.390000e-31 147.0
11 TraesCS3B01G456600 chr3D 84.110 1095 79 43 433 1468 528094283 528095341 0.000000e+00 970.0
12 TraesCS3B01G456600 chr3D 83.610 1086 85 39 433 1468 527735121 527736163 0.000000e+00 933.0
13 TraesCS3B01G456600 chr3D 80.621 805 70 38 433 1177 528083187 528083965 7.240000e-151 544.0
14 TraesCS3B01G456600 chr3D 89.691 388 22 2 1175 1547 528084506 528084890 2.070000e-131 479.0
15 TraesCS3B01G456600 chr3D 87.470 415 44 4 2533 2939 528087367 528087781 3.470000e-129 472.0
16 TraesCS3B01G456600 chr3D 77.687 856 127 37 2146 2942 488226989 488226139 5.800000e-127 464.0
17 TraesCS3B01G456600 chr3D 87.310 394 42 6 2015 2405 528012060 528012448 7.560000e-121 444.0
18 TraesCS3B01G456600 chr3D 75.518 772 133 34 2215 2942 453661204 453660445 7.940000e-86 327.0
19 TraesCS3B01G456600 chr3D 92.025 163 13 0 1971 2133 527736338 527736500 2.300000e-56 230.0
20 TraesCS3B01G456600 chr3D 87.166 187 20 3 433 615 528011858 528012044 3.000000e-50 209.0
21 TraesCS3B01G456600 chr3D 94.872 78 4 0 1971 2048 528084959 528085036 4.020000e-24 122.0
22 TraesCS3B01G456600 chr3A 83.198 988 86 25 513 1465 662519710 662520652 0.000000e+00 832.0
23 TraesCS3B01G456600 chr3A 76.366 842 134 36 2146 2925 336161956 336162794 2.780000e-105 392.0
24 TraesCS3B01G456600 chr3A 81.600 125 9 5 391 515 662513359 662513469 1.130000e-14 91.6
25 TraesCS3B01G456600 chr1D 80.774 749 94 32 2146 2860 205034678 205033946 9.370000e-150 540.0
26 TraesCS3B01G456600 chr5B 85.311 531 55 15 2430 2942 559630297 559630822 7.290000e-146 527.0
27 TraesCS3B01G456600 chr5B 94.297 263 14 1 1 262 448832685 448832423 4.610000e-108 401.0
28 TraesCS3B01G456600 chr5B 79.856 278 37 10 2146 2404 559629971 559630248 5.060000e-43 185.0
29 TraesCS3B01G456600 chr5D 84.991 533 56 13 2430 2941 457566398 457566927 1.220000e-143 520.0
30 TraesCS3B01G456600 chr4D 78.344 785 109 30 2212 2942 15264257 15263480 4.520000e-123 451.0
31 TraesCS3B01G456600 chr6B 77.997 759 106 24 2223 2931 573837744 573836997 1.270000e-113 420.0
32 TraesCS3B01G456600 chr6B 95.057 263 12 1 1 262 28113048 28112786 2.130000e-111 412.0
33 TraesCS3B01G456600 chr6B 76.443 849 140 35 2146 2939 651864576 651863733 3.570000e-109 405.0
34 TraesCS3B01G456600 chr7A 95.420 262 12 0 1 262 50183183 50182922 4.580000e-113 418.0
35 TraesCS3B01G456600 chr7A 79.562 274 33 8 2152 2404 722119693 722119964 1.090000e-39 174.0
36 TraesCS3B01G456600 chr7A 78.214 280 38 9 2146 2404 722117413 722117690 1.100000e-34 158.0
37 TraesCS3B01G456600 chr1A 95.437 263 11 1 1 262 253314574 253314836 4.580000e-113 418.0
38 TraesCS3B01G456600 chr1A 94.677 263 13 1 1 262 277625861 277625599 9.910000e-110 407.0
39 TraesCS3B01G456600 chr1A 94.677 263 13 1 1 262 281656550 281656812 9.910000e-110 407.0
40 TraesCS3B01G456600 chr4B 94.318 264 13 2 1 262 47854215 47854478 1.280000e-108 403.0
41 TraesCS3B01G456600 chr5A 94.297 263 14 1 1 262 343042930 343042668 4.610000e-108 401.0
42 TraesCS3B01G456600 chr7B 76.112 854 141 34 2146 2939 243003533 243004383 3.590000e-104 388.0
43 TraesCS3B01G456600 chr7B 77.500 280 40 8 2146 2404 726451943 726452220 2.390000e-31 147.0
44 TraesCS3B01G456600 chr7B 77.143 280 41 8 2146 2404 726896288 726896011 1.110000e-29 141.0
45 TraesCS3B01G456600 chr7D 80.071 281 31 9 2146 2404 626451203 626451480 5.060000e-43 185.0
46 TraesCS3B01G456600 chr2B 80.000 270 36 9 2153 2404 397946475 397946744 1.820000e-42 183.0


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 TraesCS3B01G456600 chr3B 697999195 698002165 2970 False 2353.00 2857 100.000000 1 2971 2 chr3B.!!$F3 2970
1 TraesCS3B01G456600 chr3B 698121687 698123850 2163 False 1228.00 1314 88.480000 437 2942 2 chr3B.!!$F4 2505
2 TraesCS3B01G456600 chr3B 697982466 697984845 2379 False 932.00 1415 91.007333 261 2942 3 chr3B.!!$F2 2681
3 TraesCS3B01G456600 chr3B 698193460 698195341 1881 False 530.00 771 85.586000 433 1470 2 chr3B.!!$F5 1037
4 TraesCS3B01G456600 chr3B 193212386 193213061 675 False 268.00 268 75.405000 2146 2762 1 chr3B.!!$F1 616
5 TraesCS3B01G456600 chr3D 528094283 528095341 1058 False 970.00 970 84.110000 433 1468 1 chr3D.!!$F1 1035
6 TraesCS3B01G456600 chr3D 527735121 527736500 1379 False 581.50 933 87.817500 433 2133 2 chr3D.!!$F2 1700
7 TraesCS3B01G456600 chr3D 488226139 488226989 850 True 464.00 464 77.687000 2146 2942 1 chr3D.!!$R2 796
8 TraesCS3B01G456600 chr3D 528083187 528087781 4594 False 404.25 544 88.163500 433 2939 4 chr3D.!!$F4 2506
9 TraesCS3B01G456600 chr3D 453660445 453661204 759 True 327.00 327 75.518000 2215 2942 1 chr3D.!!$R1 727
10 TraesCS3B01G456600 chr3D 528011858 528012448 590 False 326.50 444 87.238000 433 2405 2 chr3D.!!$F3 1972
11 TraesCS3B01G456600 chr3A 662519710 662520652 942 False 832.00 832 83.198000 513 1465 1 chr3A.!!$F3 952
12 TraesCS3B01G456600 chr3A 336161956 336162794 838 False 392.00 392 76.366000 2146 2925 1 chr3A.!!$F1 779
13 TraesCS3B01G456600 chr1D 205033946 205034678 732 True 540.00 540 80.774000 2146 2860 1 chr1D.!!$R1 714
14 TraesCS3B01G456600 chr5B 559629971 559630822 851 False 356.00 527 82.583500 2146 2942 2 chr5B.!!$F1 796
15 TraesCS3B01G456600 chr5D 457566398 457566927 529 False 520.00 520 84.991000 2430 2941 1 chr5D.!!$F1 511
16 TraesCS3B01G456600 chr4D 15263480 15264257 777 True 451.00 451 78.344000 2212 2942 1 chr4D.!!$R1 730
17 TraesCS3B01G456600 chr6B 573836997 573837744 747 True 420.00 420 77.997000 2223 2931 1 chr6B.!!$R2 708
18 TraesCS3B01G456600 chr6B 651863733 651864576 843 True 405.00 405 76.443000 2146 2939 1 chr6B.!!$R3 793
19 TraesCS3B01G456600 chr7B 243003533 243004383 850 False 388.00 388 76.112000 2146 2939 1 chr7B.!!$F1 793

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
63 64 0.036732 TTTCGATGGCTGCTTCCACT 59.963 50.0 0.00 0.0 39.25 4.00 F
65 66 0.175760 TCGATGGCTGCTTCCACTAC 59.824 55.0 0.00 0.0 39.25 2.73 F
73 74 0.320050 TGCTTCCACTACGCATGTGA 59.680 50.0 14.43 0.0 37.60 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 2157 0.687757 CCAGCTACTGCACCTCCCTA 60.688 60.000 0.00 0.0 42.74 3.53 R
1427 3005 1.377202 GCTCATTTGGAGTCGGCCA 60.377 57.895 2.24 0.0 45.88 5.36 R
2058 3668 2.238521 GAATGTTCAGCAAGTTCCCCA 58.761 47.619 0.00 0.0 0.00 4.96 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
20 21 3.398694 CATGCAGGATGGAGGACTG 57.601 57.895 0.00 0.00 42.26 3.51
21 22 0.545171 CATGCAGGATGGAGGACTGT 59.455 55.000 0.00 0.00 42.26 3.55
22 23 0.835941 ATGCAGGATGGAGGACTGTC 59.164 55.000 0.00 0.00 42.42 3.51
23 24 0.545071 TGCAGGATGGAGGACTGTCA 60.545 55.000 10.38 0.00 35.86 3.58
24 25 0.615331 GCAGGATGGAGGACTGTCAA 59.385 55.000 10.38 0.00 35.86 3.18
25 26 1.677217 GCAGGATGGAGGACTGTCAAC 60.677 57.143 10.38 2.73 35.86 3.18
26 27 0.898320 AGGATGGAGGACTGTCAACG 59.102 55.000 10.38 0.00 0.00 4.10
27 28 0.108138 GGATGGAGGACTGTCAACGG 60.108 60.000 10.38 0.00 0.00 4.44
28 29 0.108138 GATGGAGGACTGTCAACGGG 60.108 60.000 10.38 0.00 0.00 5.28
29 30 0.836400 ATGGAGGACTGTCAACGGGT 60.836 55.000 10.38 0.00 0.00 5.28
30 31 1.004918 GGAGGACTGTCAACGGGTG 60.005 63.158 10.38 0.00 0.00 4.61
31 32 1.668151 GAGGACTGTCAACGGGTGC 60.668 63.158 10.38 0.00 0.00 5.01
32 33 3.041940 GGACTGTCAACGGGTGCG 61.042 66.667 10.38 0.00 0.00 5.34
33 34 3.041940 GACTGTCAACGGGTGCGG 61.042 66.667 2.24 0.00 0.00 5.69
36 37 4.858680 TGTCAACGGGTGCGGCAA 62.859 61.111 3.23 0.00 0.00 4.52
37 38 4.322385 GTCAACGGGTGCGGCAAC 62.322 66.667 10.14 10.14 0.00 4.17
49 50 4.955089 GGCAACGGCAATTTTCGA 57.045 50.000 4.46 0.00 43.71 3.71
50 51 3.416955 GGCAACGGCAATTTTCGAT 57.583 47.368 4.46 0.00 43.71 3.59
51 52 0.991344 GGCAACGGCAATTTTCGATG 59.009 50.000 4.46 4.19 43.71 3.84
52 53 0.991344 GCAACGGCAATTTTCGATGG 59.009 50.000 4.46 0.00 40.72 3.51
53 54 0.991344 CAACGGCAATTTTCGATGGC 59.009 50.000 0.46 0.46 38.62 4.40
54 55 0.887933 AACGGCAATTTTCGATGGCT 59.112 45.000 8.43 0.00 39.74 4.75
55 56 0.171007 ACGGCAATTTTCGATGGCTG 59.829 50.000 8.43 0.32 39.74 4.85
56 57 1.141591 CGGCAATTTTCGATGGCTGC 61.142 55.000 8.43 5.37 39.74 5.25
57 58 0.174162 GGCAATTTTCGATGGCTGCT 59.826 50.000 0.00 0.00 38.91 4.24
58 59 1.404583 GGCAATTTTCGATGGCTGCTT 60.405 47.619 0.00 0.00 38.91 3.91
59 60 1.922545 GCAATTTTCGATGGCTGCTTC 59.077 47.619 0.00 0.00 0.00 3.86
60 61 2.533266 CAATTTTCGATGGCTGCTTCC 58.467 47.619 0.00 0.00 0.00 3.46
61 62 1.838112 ATTTTCGATGGCTGCTTCCA 58.162 45.000 0.00 0.12 40.97 3.53
62 63 0.881118 TTTTCGATGGCTGCTTCCAC 59.119 50.000 0.00 0.00 39.25 4.02
63 64 0.036732 TTTCGATGGCTGCTTCCACT 59.963 50.000 0.00 0.00 39.25 4.00
64 65 0.901827 TTCGATGGCTGCTTCCACTA 59.098 50.000 0.00 0.00 39.25 2.74
65 66 0.175760 TCGATGGCTGCTTCCACTAC 59.824 55.000 0.00 0.00 39.25 2.73
66 67 1.148157 CGATGGCTGCTTCCACTACG 61.148 60.000 0.00 3.87 39.25 3.51
67 68 1.432270 GATGGCTGCTTCCACTACGC 61.432 60.000 0.00 0.00 39.25 4.42
68 69 2.047274 GGCTGCTTCCACTACGCA 60.047 61.111 0.00 0.00 0.00 5.24
69 70 1.450312 GGCTGCTTCCACTACGCAT 60.450 57.895 0.00 0.00 32.62 4.73
70 71 1.709147 GGCTGCTTCCACTACGCATG 61.709 60.000 0.00 0.00 32.62 4.06
71 72 1.021390 GCTGCTTCCACTACGCATGT 61.021 55.000 0.00 0.00 32.62 3.21
72 73 0.723414 CTGCTTCCACTACGCATGTG 59.277 55.000 4.30 4.30 32.62 3.21
73 74 0.320050 TGCTTCCACTACGCATGTGA 59.680 50.000 14.43 0.00 37.60 3.58
74 75 1.066215 TGCTTCCACTACGCATGTGAT 60.066 47.619 14.43 0.00 37.60 3.06
75 76 2.009774 GCTTCCACTACGCATGTGATT 58.990 47.619 14.43 0.00 37.60 2.57
76 77 2.420022 GCTTCCACTACGCATGTGATTT 59.580 45.455 14.43 0.00 37.60 2.17
77 78 3.119849 GCTTCCACTACGCATGTGATTTT 60.120 43.478 14.43 0.00 37.60 1.82
78 79 4.094294 GCTTCCACTACGCATGTGATTTTA 59.906 41.667 14.43 0.00 37.60 1.52
79 80 5.220854 GCTTCCACTACGCATGTGATTTTAT 60.221 40.000 14.43 0.00 37.60 1.40
80 81 5.984233 TCCACTACGCATGTGATTTTATC 57.016 39.130 14.43 0.00 37.60 1.75
81 82 5.423886 TCCACTACGCATGTGATTTTATCA 58.576 37.500 14.43 0.00 37.60 2.15
82 83 6.054941 TCCACTACGCATGTGATTTTATCAT 58.945 36.000 14.43 0.00 42.04 2.45
83 84 6.018016 TCCACTACGCATGTGATTTTATCATG 60.018 38.462 14.43 0.00 42.04 3.07
84 85 6.018016 CCACTACGCATGTGATTTTATCATGA 60.018 38.462 14.43 0.00 42.04 3.07
85 86 6.847792 CACTACGCATGTGATTTTATCATGAC 59.152 38.462 14.43 0.00 42.04 3.06
86 87 6.763135 ACTACGCATGTGATTTTATCATGACT 59.237 34.615 14.43 0.00 42.04 3.41
87 88 7.926018 ACTACGCATGTGATTTTATCATGACTA 59.074 33.333 14.43 0.00 42.04 2.59
88 89 7.182361 ACGCATGTGATTTTATCATGACTAG 57.818 36.000 14.43 0.00 42.04 2.57
89 90 6.986231 ACGCATGTGATTTTATCATGACTAGA 59.014 34.615 14.43 0.00 42.04 2.43
90 91 7.658982 ACGCATGTGATTTTATCATGACTAGAT 59.341 33.333 14.43 0.00 42.04 1.98
91 92 8.501580 CGCATGTGATTTTATCATGACTAGATT 58.498 33.333 0.00 0.00 42.04 2.40
92 93 9.823098 GCATGTGATTTTATCATGACTAGATTC 57.177 33.333 0.00 0.00 42.04 2.52
94 95 9.987272 ATGTGATTTTATCATGACTAGATTCGA 57.013 29.630 0.00 0.00 42.04 3.71
95 96 9.816354 TGTGATTTTATCATGACTAGATTCGAA 57.184 29.630 0.00 0.00 42.04 3.71
125 126 9.628500 TGTAATAGAGAGACAAATAGAGTAGCA 57.372 33.333 0.00 0.00 0.00 3.49
126 127 9.887406 GTAATAGAGAGACAAATAGAGTAGCAC 57.113 37.037 0.00 0.00 0.00 4.40
127 128 8.526667 AATAGAGAGACAAATAGAGTAGCACA 57.473 34.615 0.00 0.00 0.00 4.57
128 129 8.704849 ATAGAGAGACAAATAGAGTAGCACAT 57.295 34.615 0.00 0.00 0.00 3.21
129 130 6.804677 AGAGAGACAAATAGAGTAGCACATG 58.195 40.000 0.00 0.00 0.00 3.21
130 131 6.605194 AGAGAGACAAATAGAGTAGCACATGA 59.395 38.462 0.00 0.00 0.00 3.07
131 132 7.123397 AGAGAGACAAATAGAGTAGCACATGAA 59.877 37.037 0.00 0.00 0.00 2.57
132 133 7.038659 AGAGACAAATAGAGTAGCACATGAAC 58.961 38.462 0.00 0.00 0.00 3.18
133 134 6.940739 AGACAAATAGAGTAGCACATGAACT 58.059 36.000 0.00 0.00 0.00 3.01
134 135 7.390027 AGACAAATAGAGTAGCACATGAACTT 58.610 34.615 0.00 0.00 0.00 2.66
135 136 7.332926 AGACAAATAGAGTAGCACATGAACTTG 59.667 37.037 0.00 0.00 0.00 3.16
136 137 6.936900 ACAAATAGAGTAGCACATGAACTTGT 59.063 34.615 0.00 0.00 0.00 3.16
137 138 7.445402 ACAAATAGAGTAGCACATGAACTTGTT 59.555 33.333 0.00 0.00 0.00 2.83
138 139 8.935844 CAAATAGAGTAGCACATGAACTTGTTA 58.064 33.333 0.00 0.00 0.00 2.41
139 140 9.502091 AAATAGAGTAGCACATGAACTTGTTAA 57.498 29.630 0.00 0.00 0.00 2.01
140 141 9.502091 AATAGAGTAGCACATGAACTTGTTAAA 57.498 29.630 0.00 0.00 0.00 1.52
141 142 7.986085 AGAGTAGCACATGAACTTGTTAAAT 57.014 32.000 0.00 0.00 0.00 1.40
142 143 8.396272 AGAGTAGCACATGAACTTGTTAAATT 57.604 30.769 0.00 0.00 0.00 1.82
143 144 9.502091 AGAGTAGCACATGAACTTGTTAAATTA 57.498 29.630 0.00 0.00 0.00 1.40
144 145 9.760660 GAGTAGCACATGAACTTGTTAAATTAG 57.239 33.333 0.00 0.00 0.00 1.73
145 146 8.237267 AGTAGCACATGAACTTGTTAAATTAGC 58.763 33.333 0.00 0.00 0.00 3.09
146 147 7.219484 AGCACATGAACTTGTTAAATTAGCT 57.781 32.000 0.00 0.00 0.00 3.32
147 148 8.335532 AGCACATGAACTTGTTAAATTAGCTA 57.664 30.769 0.00 0.00 0.00 3.32
148 149 8.454106 AGCACATGAACTTGTTAAATTAGCTAG 58.546 33.333 0.00 0.00 0.00 3.42
149 150 8.450964 GCACATGAACTTGTTAAATTAGCTAGA 58.549 33.333 0.00 0.00 0.00 2.43
165 166 9.950496 AATTAGCTAGATTTCTTCAACTTCAGA 57.050 29.630 0.00 0.00 0.00 3.27
167 168 9.950496 TTAGCTAGATTTCTTCAACTTCAGATT 57.050 29.630 0.00 0.00 0.00 2.40
168 169 8.266392 AGCTAGATTTCTTCAACTTCAGATTG 57.734 34.615 0.00 0.00 0.00 2.67
169 170 7.336427 AGCTAGATTTCTTCAACTTCAGATTGG 59.664 37.037 0.00 0.00 0.00 3.16
170 171 7.120432 GCTAGATTTCTTCAACTTCAGATTGGT 59.880 37.037 0.00 0.00 0.00 3.67
171 172 7.830099 AGATTTCTTCAACTTCAGATTGGTT 57.170 32.000 0.00 0.00 0.00 3.67
172 173 7.880105 AGATTTCTTCAACTTCAGATTGGTTC 58.120 34.615 0.00 0.00 0.00 3.62
173 174 5.673337 TTCTTCAACTTCAGATTGGTTCG 57.327 39.130 0.00 0.00 0.00 3.95
174 175 4.956085 TCTTCAACTTCAGATTGGTTCGA 58.044 39.130 0.00 0.00 0.00 3.71
175 176 4.991056 TCTTCAACTTCAGATTGGTTCGAG 59.009 41.667 0.00 0.00 0.00 4.04
176 177 3.664107 TCAACTTCAGATTGGTTCGAGG 58.336 45.455 0.00 0.00 0.00 4.63
177 178 3.323691 TCAACTTCAGATTGGTTCGAGGA 59.676 43.478 0.00 0.00 0.00 3.71
178 179 3.601443 ACTTCAGATTGGTTCGAGGAG 57.399 47.619 0.00 0.00 0.00 3.69
179 180 2.275318 CTTCAGATTGGTTCGAGGAGC 58.725 52.381 0.00 0.00 0.00 4.70
180 181 0.537188 TCAGATTGGTTCGAGGAGCC 59.463 55.000 0.00 0.00 33.44 4.70
181 182 0.539051 CAGATTGGTTCGAGGAGCCT 59.461 55.000 0.28 0.00 33.98 4.58
182 183 1.757118 CAGATTGGTTCGAGGAGCCTA 59.243 52.381 0.28 0.00 33.98 3.93
183 184 2.366916 CAGATTGGTTCGAGGAGCCTAT 59.633 50.000 0.28 0.00 33.98 2.57
184 185 2.630580 AGATTGGTTCGAGGAGCCTATC 59.369 50.000 12.48 12.48 42.05 2.08
185 186 1.860641 TTGGTTCGAGGAGCCTATCA 58.139 50.000 0.28 0.00 33.98 2.15
186 187 1.860641 TGGTTCGAGGAGCCTATCAA 58.139 50.000 0.28 0.00 33.98 2.57
187 188 2.398588 TGGTTCGAGGAGCCTATCAAT 58.601 47.619 0.28 0.00 33.98 2.57
188 189 2.103094 TGGTTCGAGGAGCCTATCAATG 59.897 50.000 0.28 0.00 33.98 2.82
189 190 2.365617 GGTTCGAGGAGCCTATCAATGA 59.634 50.000 0.00 0.00 30.11 2.57
190 191 3.181465 GGTTCGAGGAGCCTATCAATGAA 60.181 47.826 0.00 0.00 30.11 2.57
191 192 4.442706 GTTCGAGGAGCCTATCAATGAAA 58.557 43.478 0.00 0.00 0.00 2.69
192 193 4.963318 TCGAGGAGCCTATCAATGAAAT 57.037 40.909 0.00 0.00 0.00 2.17
193 194 5.296151 TCGAGGAGCCTATCAATGAAATT 57.704 39.130 0.00 0.00 36.63 1.82
194 195 6.419484 TCGAGGAGCCTATCAATGAAATTA 57.581 37.500 0.00 0.00 32.46 1.40
195 196 7.009179 TCGAGGAGCCTATCAATGAAATTAT 57.991 36.000 0.00 0.00 32.46 1.28
196 197 8.134202 TCGAGGAGCCTATCAATGAAATTATA 57.866 34.615 0.00 0.00 32.46 0.98
197 198 8.035394 TCGAGGAGCCTATCAATGAAATTATAC 58.965 37.037 0.00 0.00 32.46 1.47
198 199 8.037758 CGAGGAGCCTATCAATGAAATTATACT 58.962 37.037 0.00 0.00 32.46 2.12
199 200 9.377312 GAGGAGCCTATCAATGAAATTATACTC 57.623 37.037 0.00 0.00 32.46 2.59
200 201 9.110382 AGGAGCCTATCAATGAAATTATACTCT 57.890 33.333 0.00 0.00 32.46 3.24
201 202 9.732130 GGAGCCTATCAATGAAATTATACTCTT 57.268 33.333 0.00 0.00 32.46 2.85
203 204 9.732130 AGCCTATCAATGAAATTATACTCTTCC 57.268 33.333 0.00 0.00 32.46 3.46
204 205 9.732130 GCCTATCAATGAAATTATACTCTTCCT 57.268 33.333 0.00 0.00 32.46 3.36
209 210 9.958180 TCAATGAAATTATACTCTTCCTCACAA 57.042 29.630 0.00 0.00 32.46 3.33
212 213 8.251750 TGAAATTATACTCTTCCTCACAAACG 57.748 34.615 0.00 0.00 0.00 3.60
213 214 8.092068 TGAAATTATACTCTTCCTCACAAACGA 58.908 33.333 0.00 0.00 0.00 3.85
214 215 9.099454 GAAATTATACTCTTCCTCACAAACGAT 57.901 33.333 0.00 0.00 0.00 3.73
215 216 8.425577 AATTATACTCTTCCTCACAAACGATG 57.574 34.615 0.00 0.00 0.00 3.84
216 217 3.753294 ACTCTTCCTCACAAACGATGT 57.247 42.857 0.00 0.00 45.34 3.06
217 218 4.866508 ACTCTTCCTCACAAACGATGTA 57.133 40.909 0.00 0.00 41.46 2.29
218 219 5.407407 ACTCTTCCTCACAAACGATGTAT 57.593 39.130 0.00 0.00 41.46 2.29
219 220 5.794894 ACTCTTCCTCACAAACGATGTATT 58.205 37.500 0.00 0.00 41.46 1.89
220 221 5.639506 ACTCTTCCTCACAAACGATGTATTG 59.360 40.000 0.00 0.00 41.46 1.90
221 222 4.935205 TCTTCCTCACAAACGATGTATTGG 59.065 41.667 0.00 0.00 41.46 3.16
222 223 4.280436 TCCTCACAAACGATGTATTGGT 57.720 40.909 0.00 0.00 41.46 3.67
223 224 4.647611 TCCTCACAAACGATGTATTGGTT 58.352 39.130 0.00 0.00 41.46 3.67
224 225 5.795972 TCCTCACAAACGATGTATTGGTTA 58.204 37.500 0.00 0.00 41.46 2.85
225 226 6.411376 TCCTCACAAACGATGTATTGGTTAT 58.589 36.000 0.00 0.00 41.46 1.89
226 227 6.882140 TCCTCACAAACGATGTATTGGTTATT 59.118 34.615 0.00 0.00 41.46 1.40
227 228 7.392113 TCCTCACAAACGATGTATTGGTTATTT 59.608 33.333 0.00 0.00 41.46 1.40
228 229 7.696453 CCTCACAAACGATGTATTGGTTATTTC 59.304 37.037 0.00 0.00 41.46 2.17
229 230 8.330466 TCACAAACGATGTATTGGTTATTTCT 57.670 30.769 0.00 0.00 41.46 2.52
230 231 9.438228 TCACAAACGATGTATTGGTTATTTCTA 57.562 29.630 0.00 0.00 41.46 2.10
341 342 2.954318 ACGGCGTACTACTGAATATGGT 59.046 45.455 12.58 0.00 0.00 3.55
355 356 7.798596 CTGAATATGGTTCAGTGCTATCTTT 57.201 36.000 12.19 0.00 40.63 2.52
357 358 8.579850 TGAATATGGTTCAGTGCTATCTTTTT 57.420 30.769 0.00 0.00 0.00 1.94
382 425 2.253610 TGGACGAAGGATGTACCAACT 58.746 47.619 0.00 0.00 42.04 3.16
389 432 3.434940 AGGATGTACCAACTCCCAAAC 57.565 47.619 0.00 0.00 42.04 2.93
427 470 5.171476 CACTGAAACGAGACTATCATTGGT 58.829 41.667 0.00 0.00 0.00 3.67
428 471 5.639506 CACTGAAACGAGACTATCATTGGTT 59.360 40.000 0.00 0.00 0.00 3.67
429 472 5.639506 ACTGAAACGAGACTATCATTGGTTG 59.360 40.000 0.00 0.00 0.00 3.77
430 473 4.935205 TGAAACGAGACTATCATTGGTTGG 59.065 41.667 0.00 0.00 0.00 3.77
431 474 2.906354 ACGAGACTATCATTGGTTGGC 58.094 47.619 0.00 0.00 0.00 4.52
682 767 2.490217 CGCCCTACGTGTCTCCTG 59.510 66.667 0.00 0.00 36.87 3.86
837 1798 1.154035 GCAATGCCTTTCCGTTCCG 60.154 57.895 0.00 0.00 0.00 4.30
987 1978 4.826733 CAGTGATCTAGCTAGGACAGACAT 59.173 45.833 20.58 4.77 0.00 3.06
1024 2017 3.399181 GGGTGATCGGTGCCTCCA 61.399 66.667 0.00 0.00 35.57 3.86
1025 2018 2.125106 GGTGATCGGTGCCTCCAC 60.125 66.667 0.00 0.00 41.32 4.02
1051 2044 3.432588 CGCTCGTCCTCGTCCTGT 61.433 66.667 0.00 0.00 38.33 4.00
1177 2170 2.435693 GGCGATAGGGAGGTGCAGT 61.436 63.158 0.00 0.00 0.00 4.40
1187 2723 4.033776 GGTGCAGTAGCTGGGCCA 62.034 66.667 5.85 5.85 42.74 5.36
1271 2819 3.003173 CCGGCTGGAGTTCTCCCA 61.003 66.667 5.28 4.17 37.49 4.37
2068 3678 2.991250 AGATCGACAATGGGGAACTTG 58.009 47.619 0.00 0.00 0.00 3.16
2093 3703 1.988107 ACATTCAGAGAAAGCCCAGGA 59.012 47.619 0.00 0.00 0.00 3.86
2116 3726 4.769688 AGTGCTCGATCATTTTGTGGATA 58.230 39.130 0.00 0.00 0.00 2.59
2120 3730 5.239306 TGCTCGATCATTTTGTGGATATTCC 59.761 40.000 0.00 0.00 36.96 3.01
2323 5840 7.982919 CCATTTCATCAAGGCAAAGATATCAAA 59.017 33.333 5.32 0.00 0.00 2.69
2405 5970 6.921857 GCATCCTCTGGATTGACAAAATTATG 59.078 38.462 0.00 0.00 39.79 1.90
2406 5971 7.201848 GCATCCTCTGGATTGACAAAATTATGA 60.202 37.037 0.00 0.00 39.79 2.15
2407 5972 8.689061 CATCCTCTGGATTGACAAAATTATGAA 58.311 33.333 0.00 0.00 39.79 2.57
2408 5973 8.648698 TCCTCTGGATTGACAAAATTATGAAA 57.351 30.769 0.00 0.00 0.00 2.69
2409 5974 9.087871 TCCTCTGGATTGACAAAATTATGAAAA 57.912 29.630 0.00 0.00 0.00 2.29
2410 5975 9.880157 CCTCTGGATTGACAAAATTATGAAAAT 57.120 29.630 0.00 0.00 0.00 1.82
2544 6122 9.863650 AATCTCATCATAGTCAATTCCTTGATT 57.136 29.630 0.00 0.00 43.08 2.57
2735 6325 2.566010 CGGGCCCATCAACGTTTG 59.434 61.111 24.92 0.00 0.00 2.93
2780 6371 6.655062 TGTTTGTTCAACAACATATCGTCTC 58.345 36.000 1.28 0.00 42.76 3.36
2849 6445 2.930040 TGCAAGTTCGATCGAAATCTCC 59.070 45.455 30.61 20.08 35.75 3.71
2955 6551 7.050377 TGATGAAGAATCATTTGACCTACTCC 58.950 38.462 0.00 0.00 46.30 3.85
2956 6552 6.627087 TGAAGAATCATTTGACCTACTCCT 57.373 37.500 0.00 0.00 0.00 3.69
2957 6553 7.733773 TGAAGAATCATTTGACCTACTCCTA 57.266 36.000 0.00 0.00 0.00 2.94
2958 6554 7.556844 TGAAGAATCATTTGACCTACTCCTAC 58.443 38.462 0.00 0.00 0.00 3.18
2959 6555 6.487299 AGAATCATTTGACCTACTCCTACC 57.513 41.667 0.00 0.00 0.00 3.18
2960 6556 6.206042 AGAATCATTTGACCTACTCCTACCT 58.794 40.000 0.00 0.00 0.00 3.08
2961 6557 5.878406 ATCATTTGACCTACTCCTACCTG 57.122 43.478 0.00 0.00 0.00 4.00
2962 6558 4.942944 TCATTTGACCTACTCCTACCTGA 58.057 43.478 0.00 0.00 0.00 3.86
2963 6559 5.529289 TCATTTGACCTACTCCTACCTGAT 58.471 41.667 0.00 0.00 0.00 2.90
2964 6560 5.964477 TCATTTGACCTACTCCTACCTGATT 59.036 40.000 0.00 0.00 0.00 2.57
2965 6561 7.130099 TCATTTGACCTACTCCTACCTGATTA 58.870 38.462 0.00 0.00 0.00 1.75
2966 6562 7.789831 TCATTTGACCTACTCCTACCTGATTAT 59.210 37.037 0.00 0.00 0.00 1.28
2967 6563 9.090103 CATTTGACCTACTCCTACCTGATTATA 57.910 37.037 0.00 0.00 0.00 0.98
2968 6564 9.845214 ATTTGACCTACTCCTACCTGATTATAT 57.155 33.333 0.00 0.00 0.00 0.86
2969 6565 9.670442 TTTGACCTACTCCTACCTGATTATATT 57.330 33.333 0.00 0.00 0.00 1.28
2970 6566 8.880991 TGACCTACTCCTACCTGATTATATTC 57.119 38.462 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.835941 GACAGTCCTCCATCCTGCAT 59.164 55.000 0.00 0.00 0.00 3.96
8 9 0.108138 CCGTTGACAGTCCTCCATCC 60.108 60.000 0.00 0.00 0.00 3.51
9 10 0.108138 CCCGTTGACAGTCCTCCATC 60.108 60.000 0.00 0.00 0.00 3.51
10 11 0.836400 ACCCGTTGACAGTCCTCCAT 60.836 55.000 0.00 0.00 0.00 3.41
11 12 1.458777 ACCCGTTGACAGTCCTCCA 60.459 57.895 0.00 0.00 0.00 3.86
12 13 1.004918 CACCCGTTGACAGTCCTCC 60.005 63.158 0.00 0.00 0.00 4.30
13 14 1.668151 GCACCCGTTGACAGTCCTC 60.668 63.158 0.00 0.00 0.00 3.71
14 15 2.426023 GCACCCGTTGACAGTCCT 59.574 61.111 0.00 0.00 0.00 3.85
15 16 3.041940 CGCACCCGTTGACAGTCC 61.042 66.667 0.00 0.00 0.00 3.85
16 17 3.041940 CCGCACCCGTTGACAGTC 61.042 66.667 0.00 0.00 0.00 3.51
19 20 4.858680 TTGCCGCACCCGTTGACA 62.859 61.111 0.00 0.00 0.00 3.58
20 21 4.322385 GTTGCCGCACCCGTTGAC 62.322 66.667 0.00 0.00 0.00 3.18
27 28 3.857109 AAATTGCCGTTGCCGCACC 62.857 57.895 0.00 0.00 36.33 5.01
28 29 1.885814 GAAAATTGCCGTTGCCGCAC 61.886 55.000 0.00 0.00 36.33 5.34
29 30 1.663074 GAAAATTGCCGTTGCCGCA 60.663 52.632 0.00 0.00 36.33 5.69
30 31 2.715849 CGAAAATTGCCGTTGCCGC 61.716 57.895 0.00 0.00 36.33 6.53
31 32 0.455972 ATCGAAAATTGCCGTTGCCG 60.456 50.000 0.00 0.00 36.33 5.69
32 33 0.991344 CATCGAAAATTGCCGTTGCC 59.009 50.000 0.00 0.00 36.33 4.52
33 34 0.991344 CCATCGAAAATTGCCGTTGC 59.009 50.000 0.00 0.00 38.26 4.17
34 35 0.991344 GCCATCGAAAATTGCCGTTG 59.009 50.000 0.00 2.87 0.00 4.10
35 36 0.887933 AGCCATCGAAAATTGCCGTT 59.112 45.000 0.00 0.00 0.00 4.44
36 37 0.171007 CAGCCATCGAAAATTGCCGT 59.829 50.000 0.00 0.00 0.00 5.68
37 38 1.141591 GCAGCCATCGAAAATTGCCG 61.142 55.000 0.00 0.00 0.00 5.69
38 39 0.174162 AGCAGCCATCGAAAATTGCC 59.826 50.000 10.47 0.00 32.21 4.52
39 40 1.922545 GAAGCAGCCATCGAAAATTGC 59.077 47.619 7.10 7.10 0.00 3.56
40 41 2.094597 TGGAAGCAGCCATCGAAAATTG 60.095 45.455 0.00 0.00 31.66 2.32
41 42 2.094545 GTGGAAGCAGCCATCGAAAATT 60.095 45.455 0.63 0.00 40.68 1.82
42 43 1.474077 GTGGAAGCAGCCATCGAAAAT 59.526 47.619 0.63 0.00 40.68 1.82
43 44 0.881118 GTGGAAGCAGCCATCGAAAA 59.119 50.000 0.63 0.00 40.68 2.29
44 45 0.036732 AGTGGAAGCAGCCATCGAAA 59.963 50.000 0.63 0.00 40.68 3.46
45 46 0.901827 TAGTGGAAGCAGCCATCGAA 59.098 50.000 0.63 0.00 40.68 3.71
46 47 0.175760 GTAGTGGAAGCAGCCATCGA 59.824 55.000 0.63 0.00 40.68 3.59
47 48 1.148157 CGTAGTGGAAGCAGCCATCG 61.148 60.000 0.63 3.95 40.68 3.84
48 49 1.432270 GCGTAGTGGAAGCAGCCATC 61.432 60.000 0.63 0.00 40.68 3.51
49 50 1.450312 GCGTAGTGGAAGCAGCCAT 60.450 57.895 0.63 0.00 40.68 4.40
50 51 2.047274 GCGTAGTGGAAGCAGCCA 60.047 61.111 0.00 0.00 35.02 4.75
51 52 1.450312 ATGCGTAGTGGAAGCAGCC 60.450 57.895 0.00 0.00 46.09 4.85
52 53 1.021390 ACATGCGTAGTGGAAGCAGC 61.021 55.000 0.00 0.00 46.09 5.25
53 54 0.723414 CACATGCGTAGTGGAAGCAG 59.277 55.000 0.00 0.00 46.09 4.24
54 55 0.320050 TCACATGCGTAGTGGAAGCA 59.680 50.000 0.00 0.00 46.96 3.91
55 56 1.656652 ATCACATGCGTAGTGGAAGC 58.343 50.000 0.00 0.00 37.58 3.86
56 57 4.685169 AAAATCACATGCGTAGTGGAAG 57.315 40.909 0.00 0.00 37.58 3.46
57 58 5.877564 TGATAAAATCACATGCGTAGTGGAA 59.122 36.000 0.00 0.00 37.58 3.53
58 59 5.423886 TGATAAAATCACATGCGTAGTGGA 58.576 37.500 0.00 0.00 37.58 4.02
59 60 5.733226 TGATAAAATCACATGCGTAGTGG 57.267 39.130 0.00 0.00 37.58 4.00
60 61 6.847792 GTCATGATAAAATCACATGCGTAGTG 59.152 38.462 0.00 3.05 43.01 2.74
61 62 6.763135 AGTCATGATAAAATCACATGCGTAGT 59.237 34.615 0.00 0.00 43.01 2.73
62 63 7.182361 AGTCATGATAAAATCACATGCGTAG 57.818 36.000 0.00 0.00 43.01 3.51
63 64 8.141268 TCTAGTCATGATAAAATCACATGCGTA 58.859 33.333 0.00 0.00 43.01 4.42
64 65 6.986231 TCTAGTCATGATAAAATCACATGCGT 59.014 34.615 0.00 0.00 43.01 5.24
65 66 7.412137 TCTAGTCATGATAAAATCACATGCG 57.588 36.000 0.00 0.00 43.01 4.73
66 67 9.823098 GAATCTAGTCATGATAAAATCACATGC 57.177 33.333 0.00 0.00 43.01 4.06
68 69 9.987272 TCGAATCTAGTCATGATAAAATCACAT 57.013 29.630 0.00 0.00 43.01 3.21
69 70 9.816354 TTCGAATCTAGTCATGATAAAATCACA 57.184 29.630 0.00 0.00 43.01 3.58
99 100 9.628500 TGCTACTCTATTTGTCTCTCTATTACA 57.372 33.333 0.00 0.00 0.00 2.41
100 101 9.887406 GTGCTACTCTATTTGTCTCTCTATTAC 57.113 37.037 0.00 0.00 0.00 1.89
101 102 9.628500 TGTGCTACTCTATTTGTCTCTCTATTA 57.372 33.333 0.00 0.00 0.00 0.98
102 103 8.526667 TGTGCTACTCTATTTGTCTCTCTATT 57.473 34.615 0.00 0.00 0.00 1.73
103 104 8.575589 CATGTGCTACTCTATTTGTCTCTCTAT 58.424 37.037 0.00 0.00 0.00 1.98
104 105 7.775561 TCATGTGCTACTCTATTTGTCTCTCTA 59.224 37.037 0.00 0.00 0.00 2.43
105 106 6.605194 TCATGTGCTACTCTATTTGTCTCTCT 59.395 38.462 0.00 0.00 0.00 3.10
106 107 6.800543 TCATGTGCTACTCTATTTGTCTCTC 58.199 40.000 0.00 0.00 0.00 3.20
107 108 6.782082 TCATGTGCTACTCTATTTGTCTCT 57.218 37.500 0.00 0.00 0.00 3.10
108 109 7.038659 AGTTCATGTGCTACTCTATTTGTCTC 58.961 38.462 0.00 0.00 0.00 3.36
109 110 6.940739 AGTTCATGTGCTACTCTATTTGTCT 58.059 36.000 0.00 0.00 0.00 3.41
110 111 7.118390 ACAAGTTCATGTGCTACTCTATTTGTC 59.882 37.037 0.00 0.00 30.82 3.18
111 112 6.936900 ACAAGTTCATGTGCTACTCTATTTGT 59.063 34.615 0.00 0.00 30.82 2.83
112 113 7.369803 ACAAGTTCATGTGCTACTCTATTTG 57.630 36.000 0.00 0.00 30.82 2.32
113 114 7.986085 AACAAGTTCATGTGCTACTCTATTT 57.014 32.000 0.00 0.00 32.81 1.40
114 115 9.502091 TTTAACAAGTTCATGTGCTACTCTATT 57.498 29.630 0.00 0.00 32.81 1.73
115 116 9.672673 ATTTAACAAGTTCATGTGCTACTCTAT 57.327 29.630 0.00 0.00 32.81 1.98
116 117 9.502091 AATTTAACAAGTTCATGTGCTACTCTA 57.498 29.630 0.00 0.00 32.81 2.43
117 118 7.986085 ATTTAACAAGTTCATGTGCTACTCT 57.014 32.000 0.00 0.00 32.81 3.24
118 119 9.760660 CTAATTTAACAAGTTCATGTGCTACTC 57.239 33.333 0.00 0.00 32.81 2.59
119 120 8.237267 GCTAATTTAACAAGTTCATGTGCTACT 58.763 33.333 0.00 0.00 32.81 2.57
120 121 8.237267 AGCTAATTTAACAAGTTCATGTGCTAC 58.763 33.333 0.00 0.00 32.81 3.58
121 122 8.335532 AGCTAATTTAACAAGTTCATGTGCTA 57.664 30.769 0.00 0.00 32.81 3.49
122 123 7.219484 AGCTAATTTAACAAGTTCATGTGCT 57.781 32.000 0.00 0.00 32.81 4.40
123 124 8.450964 TCTAGCTAATTTAACAAGTTCATGTGC 58.549 33.333 0.00 0.00 32.81 4.57
139 140 9.950496 TCTGAAGTTGAAGAAATCTAGCTAATT 57.050 29.630 0.00 0.00 0.00 1.40
141 142 9.950496 AATCTGAAGTTGAAGAAATCTAGCTAA 57.050 29.630 0.00 0.00 0.00 3.09
142 143 9.376075 CAATCTGAAGTTGAAGAAATCTAGCTA 57.624 33.333 0.00 0.00 0.00 3.32
143 144 7.336427 CCAATCTGAAGTTGAAGAAATCTAGCT 59.664 37.037 0.00 0.00 0.00 3.32
144 145 7.120432 ACCAATCTGAAGTTGAAGAAATCTAGC 59.880 37.037 0.00 0.00 0.00 3.42
145 146 8.558973 ACCAATCTGAAGTTGAAGAAATCTAG 57.441 34.615 0.00 0.00 0.00 2.43
146 147 8.924511 AACCAATCTGAAGTTGAAGAAATCTA 57.075 30.769 0.00 0.00 0.00 1.98
147 148 7.308229 CGAACCAATCTGAAGTTGAAGAAATCT 60.308 37.037 0.00 0.00 0.00 2.40
148 149 6.798959 CGAACCAATCTGAAGTTGAAGAAATC 59.201 38.462 0.00 0.00 0.00 2.17
149 150 6.486657 TCGAACCAATCTGAAGTTGAAGAAAT 59.513 34.615 0.00 0.00 0.00 2.17
150 151 5.820423 TCGAACCAATCTGAAGTTGAAGAAA 59.180 36.000 0.00 0.00 0.00 2.52
151 152 5.364778 TCGAACCAATCTGAAGTTGAAGAA 58.635 37.500 0.00 0.00 0.00 2.52
152 153 4.956085 TCGAACCAATCTGAAGTTGAAGA 58.044 39.130 0.00 0.00 0.00 2.87
153 154 4.153117 CCTCGAACCAATCTGAAGTTGAAG 59.847 45.833 0.00 0.00 0.00 3.02
154 155 4.065088 CCTCGAACCAATCTGAAGTTGAA 58.935 43.478 0.00 0.00 0.00 2.69
155 156 3.323691 TCCTCGAACCAATCTGAAGTTGA 59.676 43.478 0.00 0.00 0.00 3.18
156 157 3.664107 TCCTCGAACCAATCTGAAGTTG 58.336 45.455 0.00 0.00 0.00 3.16
157 158 3.866449 GCTCCTCGAACCAATCTGAAGTT 60.866 47.826 0.00 0.00 0.00 2.66
158 159 2.354203 GCTCCTCGAACCAATCTGAAGT 60.354 50.000 0.00 0.00 0.00 3.01
159 160 2.275318 GCTCCTCGAACCAATCTGAAG 58.725 52.381 0.00 0.00 0.00 3.02
160 161 1.066143 GGCTCCTCGAACCAATCTGAA 60.066 52.381 0.00 0.00 0.00 3.02
161 162 0.537188 GGCTCCTCGAACCAATCTGA 59.463 55.000 0.00 0.00 0.00 3.27
162 163 0.539051 AGGCTCCTCGAACCAATCTG 59.461 55.000 0.00 0.00 0.00 2.90
163 164 2.160721 TAGGCTCCTCGAACCAATCT 57.839 50.000 0.00 0.00 0.00 2.40
164 165 2.365617 TGATAGGCTCCTCGAACCAATC 59.634 50.000 0.00 0.00 0.00 2.67
165 166 2.398588 TGATAGGCTCCTCGAACCAAT 58.601 47.619 0.00 0.00 0.00 3.16
166 167 1.860641 TGATAGGCTCCTCGAACCAA 58.139 50.000 0.00 0.00 0.00 3.67
167 168 1.860641 TTGATAGGCTCCTCGAACCA 58.139 50.000 0.00 0.00 0.00 3.67
168 169 2.365617 TCATTGATAGGCTCCTCGAACC 59.634 50.000 0.00 0.00 0.00 3.62
169 170 3.735237 TCATTGATAGGCTCCTCGAAC 57.265 47.619 0.00 0.00 0.00 3.95
170 171 4.753516 TTTCATTGATAGGCTCCTCGAA 57.246 40.909 0.00 0.00 0.00 3.71
171 172 4.963318 ATTTCATTGATAGGCTCCTCGA 57.037 40.909 0.00 0.00 0.00 4.04
172 173 8.037758 AGTATAATTTCATTGATAGGCTCCTCG 58.962 37.037 0.00 0.00 0.00 4.63
173 174 9.377312 GAGTATAATTTCATTGATAGGCTCCTC 57.623 37.037 0.00 0.00 0.00 3.71
174 175 9.110382 AGAGTATAATTTCATTGATAGGCTCCT 57.890 33.333 0.00 0.00 0.00 3.69
175 176 9.732130 AAGAGTATAATTTCATTGATAGGCTCC 57.268 33.333 0.00 0.00 0.00 4.70
177 178 9.732130 GGAAGAGTATAATTTCATTGATAGGCT 57.268 33.333 0.00 0.00 0.00 4.58
178 179 9.732130 AGGAAGAGTATAATTTCATTGATAGGC 57.268 33.333 0.00 0.00 0.00 3.93
183 184 9.958180 TTGTGAGGAAGAGTATAATTTCATTGA 57.042 29.630 0.00 0.00 0.00 2.57
186 187 8.883731 CGTTTGTGAGGAAGAGTATAATTTCAT 58.116 33.333 0.00 0.00 0.00 2.57
187 188 8.092068 TCGTTTGTGAGGAAGAGTATAATTTCA 58.908 33.333 0.00 0.00 0.00 2.69
188 189 8.475331 TCGTTTGTGAGGAAGAGTATAATTTC 57.525 34.615 0.00 0.00 0.00 2.17
189 190 8.883731 CATCGTTTGTGAGGAAGAGTATAATTT 58.116 33.333 0.00 0.00 0.00 1.82
190 191 8.041323 ACATCGTTTGTGAGGAAGAGTATAATT 58.959 33.333 0.00 0.00 37.11 1.40
191 192 7.556844 ACATCGTTTGTGAGGAAGAGTATAAT 58.443 34.615 0.00 0.00 37.11 1.28
192 193 6.931838 ACATCGTTTGTGAGGAAGAGTATAA 58.068 36.000 0.00 0.00 37.11 0.98
193 194 6.525578 ACATCGTTTGTGAGGAAGAGTATA 57.474 37.500 0.00 0.00 37.11 1.47
194 195 5.407407 ACATCGTTTGTGAGGAAGAGTAT 57.593 39.130 0.00 0.00 37.11 2.12
195 196 4.866508 ACATCGTTTGTGAGGAAGAGTA 57.133 40.909 0.00 0.00 37.11 2.59
196 197 3.753294 ACATCGTTTGTGAGGAAGAGT 57.247 42.857 0.00 0.00 37.11 3.24
197 198 5.063944 CCAATACATCGTTTGTGAGGAAGAG 59.936 44.000 4.39 0.00 39.48 2.85
198 199 4.935205 CCAATACATCGTTTGTGAGGAAGA 59.065 41.667 4.39 0.00 39.48 2.87
199 200 4.695455 ACCAATACATCGTTTGTGAGGAAG 59.305 41.667 4.39 0.00 39.48 3.46
200 201 4.647611 ACCAATACATCGTTTGTGAGGAA 58.352 39.130 4.39 0.00 39.48 3.36
201 202 4.280436 ACCAATACATCGTTTGTGAGGA 57.720 40.909 4.39 0.00 39.48 3.71
202 203 6.677781 ATAACCAATACATCGTTTGTGAGG 57.322 37.500 4.39 5.80 39.48 3.86
203 204 8.450964 AGAAATAACCAATACATCGTTTGTGAG 58.549 33.333 4.39 0.00 39.48 3.51
204 205 8.330466 AGAAATAACCAATACATCGTTTGTGA 57.670 30.769 4.39 0.00 39.48 3.58
257 258 7.112452 AGTCAAATACAAGAAGGCAGTTTTT 57.888 32.000 0.00 0.00 0.00 1.94
258 259 6.715347 AGTCAAATACAAGAAGGCAGTTTT 57.285 33.333 0.00 0.00 0.00 2.43
259 260 6.715347 AAGTCAAATACAAGAAGGCAGTTT 57.285 33.333 0.00 0.00 0.00 2.66
382 425 2.988684 GCGCCATGGTGTTTGGGA 60.989 61.111 25.68 0.00 34.66 4.37
411 454 2.501723 AGCCAACCAATGATAGTCTCGT 59.498 45.455 0.00 0.00 0.00 4.18
856 1833 1.802880 CGTGGGCGGCATATATAGAGC 60.803 57.143 12.47 2.21 0.00 4.09
891 1868 3.845259 AGGTGTGTCGTGTGCGGT 61.845 61.111 0.00 0.00 38.89 5.68
892 1869 3.337889 CAGGTGTGTCGTGTGCGG 61.338 66.667 0.00 0.00 38.89 5.69
894 1871 0.031585 TACTCAGGTGTGTCGTGTGC 59.968 55.000 0.00 0.00 34.10 4.57
987 1978 1.438651 GAGCCATTTCACGTGCACTA 58.561 50.000 16.19 0.00 0.00 2.74
1039 2032 1.080705 CCACGAACAGGACGAGGAC 60.081 63.158 0.00 0.00 42.27 3.85
1164 2157 0.687757 CCAGCTACTGCACCTCCCTA 60.688 60.000 0.00 0.00 42.74 3.53
1177 2170 1.756950 CGGAGTACTGGCCCAGCTA 60.757 63.158 11.63 0.00 34.37 3.32
1187 2723 1.961394 TGTGCTCTTCAACGGAGTACT 59.039 47.619 0.00 0.00 45.00 2.73
1427 3005 1.377202 GCTCATTTGGAGTCGGCCA 60.377 57.895 2.24 0.00 45.88 5.36
2010 3620 5.228945 AGTTTGTACTAGAAGCACATGGT 57.771 39.130 0.00 0.00 31.21 3.55
2058 3668 2.238521 GAATGTTCAGCAAGTTCCCCA 58.761 47.619 0.00 0.00 0.00 4.96
2093 3703 3.411446 TCCACAAAATGATCGAGCACTT 58.589 40.909 5.03 0.00 0.00 3.16
2116 3726 3.072476 TCCACGTTTTCTTCTCCTGGAAT 59.928 43.478 0.00 0.00 33.01 3.01
2120 3730 2.833794 TGTCCACGTTTTCTTCTCCTG 58.166 47.619 0.00 0.00 0.00 3.86
2289 3929 6.942532 TGCCTTGATGAAATGGTTAGATAC 57.057 37.500 0.00 0.00 0.00 2.24
2418 5983 9.844257 TGTCAAAAAGAATTCCCATAATTTTGT 57.156 25.926 0.65 0.00 37.48 2.83
2421 5986 9.671279 GGATGTCAAAAAGAATTCCCATAATTT 57.329 29.630 0.65 0.00 0.00 1.82
2422 5987 8.824783 TGGATGTCAAAAAGAATTCCCATAATT 58.175 29.630 0.65 0.00 31.56 1.40
2423 5988 8.378115 TGGATGTCAAAAAGAATTCCCATAAT 57.622 30.769 0.65 0.00 31.56 1.28
2424 5989 7.789202 TGGATGTCAAAAAGAATTCCCATAA 57.211 32.000 0.65 0.00 31.56 1.90
2425 5990 7.840716 AGATGGATGTCAAAAAGAATTCCCATA 59.159 33.333 0.65 0.00 31.56 2.74
2426 5991 6.670902 AGATGGATGTCAAAAAGAATTCCCAT 59.329 34.615 0.65 3.66 31.56 4.00
2427 5992 6.018469 AGATGGATGTCAAAAAGAATTCCCA 58.982 36.000 0.65 0.00 31.56 4.37
2544 6122 9.383519 TGGTTGTTGCAAATAGTTTATGAAAAA 57.616 25.926 0.00 0.00 0.00 1.94
2849 6445 4.219507 ACGGAAGCCTCTACATGAGATATG 59.780 45.833 0.00 0.00 45.39 1.78
2942 6538 9.845214 ATATAATCAGGTAGGAGTAGGTCAAAT 57.155 33.333 0.00 0.00 0.00 2.32
2943 6539 9.670442 AATATAATCAGGTAGGAGTAGGTCAAA 57.330 33.333 0.00 0.00 0.00 2.69
2944 6540 9.310449 GAATATAATCAGGTAGGAGTAGGTCAA 57.690 37.037 0.00 0.00 0.00 3.18
2945 6541 8.880991 GAATATAATCAGGTAGGAGTAGGTCA 57.119 38.462 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.