Multiple sequence alignment - TraesCS1A01G328900

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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 TraesCS1A01G328900 chr1A 100.000 2270 0 0 1 2270 517588016 517585747 0.000000e+00 4193
1 TraesCS1A01G328900 chr1A 97.301 1334 34 2 272 1603 517621153 517619820 0.000000e+00 2263
2 TraesCS1A01G328900 chr1A 96.904 646 19 1 273 917 517622191 517621546 0.000000e+00 1081
3 TraesCS1A01G328900 chr1A 97.368 266 7 0 1 266 517595074 517594809 9.560000e-124 453
4 TraesCS1A01G328900 chr1A 80.962 520 79 16 927 1430 353279799 353280314 5.880000e-106 394
5 TraesCS1A01G328900 chr1A 86.905 168 14 3 1440 1603 518668343 518668506 4.980000e-42 182
6 TraesCS1A01G328900 chr5A 94.239 677 33 3 1596 2270 443921114 443920442 0.000000e+00 1029
7 TraesCS1A01G328900 chr5A 93.443 671 43 1 1599 2268 543002737 543003407 0.000000e+00 994
8 TraesCS1A01G328900 chr5A 93.433 670 42 2 1601 2268 480686191 480685522 0.000000e+00 992
9 TraesCS1A01G328900 chr4A 93.814 679 36 5 1597 2270 139854660 139853983 0.000000e+00 1016
10 TraesCS1A01G328900 chr4A 93.304 672 43 2 1601 2270 189197976 189197305 0.000000e+00 990
11 TraesCS1A01G328900 chr7A 93.510 678 39 3 1596 2268 685814782 685815459 0.000000e+00 1003
12 TraesCS1A01G328900 chr7A 93.225 679 42 3 1596 2270 505672470 505671792 0.000000e+00 996
13 TraesCS1A01G328900 chr7A 93.343 676 42 2 1596 2268 685719530 685720205 0.000000e+00 996
14 TraesCS1A01G328900 chr7A 93.205 677 41 4 1596 2268 685725659 685726334 0.000000e+00 990
15 TraesCS1A01G328900 chr3A 87.467 750 60 23 267 997 717914031 717914765 0.000000e+00 833
16 TraesCS1A01G328900 chr3A 89.434 265 22 2 982 1240 717915244 717915508 1.680000e-86 329
17 TraesCS1A01G328900 chr1D 91.716 338 18 5 900 1228 469824688 469825024 5.710000e-126 460
18 TraesCS1A01G328900 chr1D 91.716 338 18 5 900 1228 474305270 474305606 5.710000e-126 460
19 TraesCS1A01G328900 chr1D 86.758 438 27 14 267 698 469824074 469824486 2.050000e-125 459
20 TraesCS1A01G328900 chr1D 86.758 438 27 14 267 698 474304656 474305068 2.050000e-125 459
21 TraesCS1A01G328900 chr1D 93.158 190 13 0 684 873 469824505 469824694 1.720000e-71 279
22 TraesCS1A01G328900 chr1D 93.158 190 13 0 684 873 474305087 474305276 1.720000e-71 279
23 TraesCS1A01G328900 chrUn 97.348 264 6 1 3 266 115185654 115185392 4.450000e-122 448
24 TraesCS1A01G328900 chrUn 96.591 264 7 2 3 266 115199203 115198942 9.630000e-119 436
25 TraesCS1A01G328900 chr7D 96.970 264 7 1 3 266 336789257 336789519 2.070000e-120 442
26 TraesCS1A01G328900 chr7D 81.423 253 39 6 673 922 41370951 41371198 1.380000e-47 200
27 TraesCS1A01G328900 chr5D 96.591 264 8 1 3 266 184353609 184353871 9.630000e-119 436
28 TraesCS1A01G328900 chr5D 95.833 264 10 1 3 266 184345858 184346120 2.080000e-115 425
29 TraesCS1A01G328900 chr6D 96.212 264 9 1 3 266 207369797 207370059 4.480000e-117 431
30 TraesCS1A01G328900 chr4D 95.849 265 8 3 3 266 216763182 216763444 2.080000e-115 425
31 TraesCS1A01G328900 chr4D 95.506 267 9 3 1 266 199937599 199937863 7.500000e-115 424
32 TraesCS1A01G328900 chr4D 82.864 391 57 6 923 1304 398867727 398868116 2.160000e-90 342
33 TraesCS1A01G328900 chr7B 78.652 534 80 26 927 1429 686804808 686805338 7.820000e-85 324
34 TraesCS1A01G328900 chr6B 80.045 446 74 9 1000 1433 11281386 11281828 1.310000e-82 316
35 TraesCS1A01G328900 chr4B 80.662 393 58 10 927 1304 349156581 349156192 2.850000e-74 289
36 TraesCS1A01G328900 chr3B 80.407 393 59 10 927 1304 788007427 788007816 1.330000e-72 283
37 TraesCS1A01G328900 chr1B 80.153 393 60 10 927 1304 584458608 584458997 6.180000e-71 278
38 TraesCS1A01G328900 chr1B 78.736 174 37 0 677 850 448344964 448344791 1.420000e-22 117
39 TraesCS1A01G328900 chr3D 78.437 371 66 9 1072 1430 590749736 590749368 1.750000e-56 230
40 TraesCS1A01G328900 chr2B 77.419 217 43 4 704 917 644610804 644611017 8.510000e-25 124
41 TraesCS1A01G328900 chr6A 83.051 118 20 0 679 796 610214970 610215087 8.570000e-20 108


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 TraesCS1A01G328900 chr1A 517585747 517588016 2269 True 4193.000000 4193 100.0000 1 2270 1 chr1A.!!$R1 2269
1 TraesCS1A01G328900 chr1A 517619820 517622191 2371 True 1672.000000 2263 97.1025 272 1603 2 chr1A.!!$R3 1331
2 TraesCS1A01G328900 chr1A 353279799 353280314 515 False 394.000000 394 80.9620 927 1430 1 chr1A.!!$F1 503
3 TraesCS1A01G328900 chr5A 443920442 443921114 672 True 1029.000000 1029 94.2390 1596 2270 1 chr5A.!!$R1 674
4 TraesCS1A01G328900 chr5A 543002737 543003407 670 False 994.000000 994 93.4430 1599 2268 1 chr5A.!!$F1 669
5 TraesCS1A01G328900 chr5A 480685522 480686191 669 True 992.000000 992 93.4330 1601 2268 1 chr5A.!!$R2 667
6 TraesCS1A01G328900 chr4A 139853983 139854660 677 True 1016.000000 1016 93.8140 1597 2270 1 chr4A.!!$R1 673
7 TraesCS1A01G328900 chr4A 189197305 189197976 671 True 990.000000 990 93.3040 1601 2270 1 chr4A.!!$R2 669
8 TraesCS1A01G328900 chr7A 685814782 685815459 677 False 1003.000000 1003 93.5100 1596 2268 1 chr7A.!!$F3 672
9 TraesCS1A01G328900 chr7A 505671792 505672470 678 True 996.000000 996 93.2250 1596 2270 1 chr7A.!!$R1 674
10 TraesCS1A01G328900 chr7A 685719530 685720205 675 False 996.000000 996 93.3430 1596 2268 1 chr7A.!!$F1 672
11 TraesCS1A01G328900 chr7A 685725659 685726334 675 False 990.000000 990 93.2050 1596 2268 1 chr7A.!!$F2 672
12 TraesCS1A01G328900 chr3A 717914031 717915508 1477 False 581.000000 833 88.4505 267 1240 2 chr3A.!!$F1 973
13 TraesCS1A01G328900 chr1D 469824074 469825024 950 False 399.333333 460 90.5440 267 1228 3 chr1D.!!$F1 961
14 TraesCS1A01G328900 chr1D 474304656 474305606 950 False 399.333333 460 90.5440 267 1228 3 chr1D.!!$F2 961
15 TraesCS1A01G328900 chr7B 686804808 686805338 530 False 324.000000 324 78.6520 927 1429 1 chr7B.!!$F1 502

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
203 204 0.032952 TTCCCCTCGTGTTCTTCGTG 59.967 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1938 3578 0.61782 AAGTACGTCAGGGGAGCCAT 60.618 55.0 0.0 0.0 0.0 4.4 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
30 31 2.043953 GGTGGCCCCATCAAGACC 60.044 66.667 0.00 0.00 0.00 3.85
31 32 2.616458 GGTGGCCCCATCAAGACCT 61.616 63.158 0.00 0.00 0.00 3.85
32 33 1.077429 GTGGCCCCATCAAGACCTC 60.077 63.158 0.00 0.00 0.00 3.85
33 34 2.308722 TGGCCCCATCAAGACCTCC 61.309 63.158 0.00 0.00 0.00 4.30
34 35 2.003548 GGCCCCATCAAGACCTCCT 61.004 63.158 0.00 0.00 0.00 3.69
35 36 1.575447 GGCCCCATCAAGACCTCCTT 61.575 60.000 0.00 0.00 34.91 3.36
36 37 1.213296 GCCCCATCAAGACCTCCTTA 58.787 55.000 0.00 0.00 32.86 2.69
37 38 1.134068 GCCCCATCAAGACCTCCTTAC 60.134 57.143 0.00 0.00 32.86 2.34
38 39 1.139058 CCCCATCAAGACCTCCTTACG 59.861 57.143 0.00 0.00 32.86 3.18
39 40 1.139058 CCCATCAAGACCTCCTTACGG 59.861 57.143 0.00 0.00 32.86 4.02
40 41 2.108168 CCATCAAGACCTCCTTACGGA 58.892 52.381 0.00 0.00 37.82 4.69
51 52 2.885616 TCCTTACGGAGAAGAACTGGT 58.114 47.619 0.00 0.00 33.30 4.00
52 53 3.236896 TCCTTACGGAGAAGAACTGGTT 58.763 45.455 0.00 0.00 33.30 3.67
53 54 4.410099 TCCTTACGGAGAAGAACTGGTTA 58.590 43.478 0.00 0.00 33.30 2.85
54 55 4.219288 TCCTTACGGAGAAGAACTGGTTAC 59.781 45.833 0.00 0.00 33.30 2.50
55 56 4.492611 CTTACGGAGAAGAACTGGTTACC 58.507 47.826 0.00 0.00 0.00 2.85
56 57 1.271656 ACGGAGAAGAACTGGTTACCG 59.728 52.381 0.00 0.00 43.79 4.02
57 58 1.271656 CGGAGAAGAACTGGTTACCGT 59.728 52.381 0.00 0.00 35.40 4.83
58 59 2.288640 CGGAGAAGAACTGGTTACCGTT 60.289 50.000 10.38 10.38 35.40 4.44
59 60 3.736720 GGAGAAGAACTGGTTACCGTTT 58.263 45.455 11.50 0.71 0.00 3.60
60 61 3.497262 GGAGAAGAACTGGTTACCGTTTG 59.503 47.826 11.50 0.00 0.00 2.93
61 62 4.124970 GAGAAGAACTGGTTACCGTTTGT 58.875 43.478 11.50 4.84 0.00 2.83
62 63 5.280654 AGAAGAACTGGTTACCGTTTGTA 57.719 39.130 11.50 0.00 0.00 2.41
63 64 5.861727 AGAAGAACTGGTTACCGTTTGTAT 58.138 37.500 11.50 0.95 0.00 2.29
64 65 5.930569 AGAAGAACTGGTTACCGTTTGTATC 59.069 40.000 11.50 8.53 0.00 2.24
65 66 4.240096 AGAACTGGTTACCGTTTGTATCG 58.760 43.478 11.50 0.00 0.00 2.92
66 67 3.665745 ACTGGTTACCGTTTGTATCGT 57.334 42.857 0.00 0.00 0.00 3.73
67 68 3.578688 ACTGGTTACCGTTTGTATCGTC 58.421 45.455 0.00 0.00 0.00 4.20
68 69 2.925563 CTGGTTACCGTTTGTATCGTCC 59.074 50.000 0.00 0.00 0.00 4.79
69 70 2.562298 TGGTTACCGTTTGTATCGTCCT 59.438 45.455 0.00 0.00 0.00 3.85
70 71 3.006752 TGGTTACCGTTTGTATCGTCCTT 59.993 43.478 0.00 0.00 0.00 3.36
71 72 3.996363 GGTTACCGTTTGTATCGTCCTTT 59.004 43.478 0.00 0.00 0.00 3.11
72 73 5.167845 GGTTACCGTTTGTATCGTCCTTTA 58.832 41.667 0.00 0.00 0.00 1.85
73 74 5.812127 GGTTACCGTTTGTATCGTCCTTTAT 59.188 40.000 0.00 0.00 0.00 1.40
74 75 6.313658 GGTTACCGTTTGTATCGTCCTTTATT 59.686 38.462 0.00 0.00 0.00 1.40
75 76 5.789710 ACCGTTTGTATCGTCCTTTATTG 57.210 39.130 0.00 0.00 0.00 1.90
76 77 4.632688 ACCGTTTGTATCGTCCTTTATTGG 59.367 41.667 0.00 0.00 0.00 3.16
77 78 4.871557 CCGTTTGTATCGTCCTTTATTGGA 59.128 41.667 0.00 0.00 0.00 3.53
78 79 5.352016 CCGTTTGTATCGTCCTTTATTGGAA 59.648 40.000 0.00 0.00 37.93 3.53
79 80 6.037830 CCGTTTGTATCGTCCTTTATTGGAAT 59.962 38.462 0.00 0.00 37.93 3.01
80 81 7.414762 CCGTTTGTATCGTCCTTTATTGGAATT 60.415 37.037 0.00 0.00 37.93 2.17
81 82 7.428183 CGTTTGTATCGTCCTTTATTGGAATTG 59.572 37.037 0.00 0.00 37.93 2.32
82 83 6.935741 TGTATCGTCCTTTATTGGAATTGG 57.064 37.500 0.00 0.00 37.93 3.16
83 84 6.654959 TGTATCGTCCTTTATTGGAATTGGA 58.345 36.000 0.00 0.00 37.93 3.53
84 85 7.287061 TGTATCGTCCTTTATTGGAATTGGAT 58.713 34.615 0.00 0.00 37.93 3.41
85 86 6.884280 ATCGTCCTTTATTGGAATTGGATC 57.116 37.500 0.00 0.00 37.93 3.36
86 87 6.001449 TCGTCCTTTATTGGAATTGGATCT 57.999 37.500 0.00 0.00 37.93 2.75
87 88 6.423182 TCGTCCTTTATTGGAATTGGATCTT 58.577 36.000 0.00 0.00 37.93 2.40
88 89 6.318648 TCGTCCTTTATTGGAATTGGATCTTG 59.681 38.462 0.00 0.00 37.93 3.02
89 90 6.095440 CGTCCTTTATTGGAATTGGATCTTGT 59.905 38.462 0.00 0.00 37.93 3.16
90 91 7.282224 CGTCCTTTATTGGAATTGGATCTTGTA 59.718 37.037 0.00 0.00 37.93 2.41
91 92 9.136323 GTCCTTTATTGGAATTGGATCTTGTAT 57.864 33.333 0.00 0.00 37.93 2.29
92 93 9.354673 TCCTTTATTGGAATTGGATCTTGTATC 57.645 33.333 0.00 0.00 32.39 2.24
93 94 9.359653 CCTTTATTGGAATTGGATCTTGTATCT 57.640 33.333 0.00 0.00 0.00 1.98
95 96 9.919416 TTTATTGGAATTGGATCTTGTATCTCA 57.081 29.630 0.00 0.00 0.00 3.27
96 97 7.814264 ATTGGAATTGGATCTTGTATCTCAC 57.186 36.000 0.00 0.00 0.00 3.51
97 98 5.684704 TGGAATTGGATCTTGTATCTCACC 58.315 41.667 0.00 0.00 0.00 4.02
98 99 5.429762 TGGAATTGGATCTTGTATCTCACCT 59.570 40.000 0.00 0.00 0.00 4.00
99 100 6.069440 TGGAATTGGATCTTGTATCTCACCTT 60.069 38.462 0.00 0.00 0.00 3.50
100 101 6.830838 GGAATTGGATCTTGTATCTCACCTTT 59.169 38.462 0.00 0.00 0.00 3.11
101 102 7.201767 GGAATTGGATCTTGTATCTCACCTTTG 60.202 40.741 0.00 0.00 0.00 2.77
102 103 5.762179 TGGATCTTGTATCTCACCTTTGT 57.238 39.130 0.00 0.00 0.00 2.83
103 104 5.491070 TGGATCTTGTATCTCACCTTTGTG 58.509 41.667 0.00 0.00 44.18 3.33
104 105 5.013079 TGGATCTTGTATCTCACCTTTGTGT 59.987 40.000 0.00 0.00 43.26 3.72
105 106 5.940470 GGATCTTGTATCTCACCTTTGTGTT 59.060 40.000 0.00 0.00 43.26 3.32
106 107 6.092807 GGATCTTGTATCTCACCTTTGTGTTC 59.907 42.308 0.00 0.00 43.26 3.18
107 108 5.924356 TCTTGTATCTCACCTTTGTGTTCA 58.076 37.500 0.00 0.00 43.26 3.18
108 109 6.533730 TCTTGTATCTCACCTTTGTGTTCAT 58.466 36.000 0.00 0.00 43.26 2.57
109 110 6.650807 TCTTGTATCTCACCTTTGTGTTCATC 59.349 38.462 0.00 0.00 43.26 2.92
110 111 4.929211 TGTATCTCACCTTTGTGTTCATCG 59.071 41.667 0.00 0.00 43.26 3.84
111 112 3.744238 TCTCACCTTTGTGTTCATCGA 57.256 42.857 0.00 0.00 43.26 3.59
112 113 4.271696 TCTCACCTTTGTGTTCATCGAT 57.728 40.909 0.00 0.00 43.26 3.59
113 114 4.245660 TCTCACCTTTGTGTTCATCGATC 58.754 43.478 0.00 0.00 43.26 3.69
114 115 4.021104 TCTCACCTTTGTGTTCATCGATCT 60.021 41.667 0.00 0.00 43.26 2.75
115 116 5.185056 TCTCACCTTTGTGTTCATCGATCTA 59.815 40.000 0.00 0.00 43.26 1.98
116 117 5.410924 TCACCTTTGTGTTCATCGATCTAG 58.589 41.667 0.00 0.00 43.26 2.43
117 118 4.033358 CACCTTTGTGTTCATCGATCTAGC 59.967 45.833 0.00 0.00 37.72 3.42
118 119 3.243877 CCTTTGTGTTCATCGATCTAGCG 59.756 47.826 0.00 0.00 0.00 4.26
119 120 1.840181 TGTGTTCATCGATCTAGCGC 58.160 50.000 0.00 0.00 0.00 5.92
120 121 1.134175 TGTGTTCATCGATCTAGCGCA 59.866 47.619 11.47 0.00 0.00 6.09
121 122 2.223805 TGTGTTCATCGATCTAGCGCAT 60.224 45.455 11.47 0.00 0.00 4.73
122 123 2.154580 GTGTTCATCGATCTAGCGCATG 59.845 50.000 11.47 2.20 0.00 4.06
123 124 2.223805 TGTTCATCGATCTAGCGCATGT 60.224 45.455 11.47 0.00 0.00 3.21
124 125 2.056094 TCATCGATCTAGCGCATGTG 57.944 50.000 11.47 0.66 0.00 3.21
125 126 1.338020 TCATCGATCTAGCGCATGTGT 59.662 47.619 11.47 0.00 0.00 3.72
126 127 1.454653 CATCGATCTAGCGCATGTGTG 59.545 52.381 11.47 0.00 0.00 3.82
127 128 0.738389 TCGATCTAGCGCATGTGTGA 59.262 50.000 11.47 4.83 0.00 3.58
128 129 1.338020 TCGATCTAGCGCATGTGTGAT 59.662 47.619 11.47 9.28 0.00 3.06
129 130 1.718178 CGATCTAGCGCATGTGTGATC 59.282 52.381 11.47 19.46 0.00 2.92
130 131 2.606551 CGATCTAGCGCATGTGTGATCT 60.607 50.000 23.14 11.26 0.00 2.75
131 132 3.365364 CGATCTAGCGCATGTGTGATCTA 60.365 47.826 23.14 11.66 0.00 1.98
132 133 4.673841 CGATCTAGCGCATGTGTGATCTAT 60.674 45.833 23.14 8.24 0.00 1.98
133 134 4.590850 TCTAGCGCATGTGTGATCTATT 57.409 40.909 11.47 0.00 0.00 1.73
134 135 4.550422 TCTAGCGCATGTGTGATCTATTC 58.450 43.478 11.47 0.00 0.00 1.75
135 136 3.465742 AGCGCATGTGTGATCTATTCT 57.534 42.857 11.47 0.00 0.00 2.40
136 137 3.801698 AGCGCATGTGTGATCTATTCTT 58.198 40.909 11.47 0.00 0.00 2.52
137 138 3.558829 AGCGCATGTGTGATCTATTCTTG 59.441 43.478 11.47 0.00 0.00 3.02
138 139 3.310774 GCGCATGTGTGATCTATTCTTGT 59.689 43.478 0.30 0.00 0.00 3.16
139 140 4.201851 GCGCATGTGTGATCTATTCTTGTT 60.202 41.667 0.30 0.00 0.00 2.83
140 141 5.260900 CGCATGTGTGATCTATTCTTGTTG 58.739 41.667 0.00 0.00 0.00 3.33
141 142 5.575957 GCATGTGTGATCTATTCTTGTTGG 58.424 41.667 0.00 0.00 0.00 3.77
142 143 5.124457 GCATGTGTGATCTATTCTTGTTGGT 59.876 40.000 0.00 0.00 0.00 3.67
143 144 6.349611 GCATGTGTGATCTATTCTTGTTGGTT 60.350 38.462 0.00 0.00 0.00 3.67
144 145 6.558771 TGTGTGATCTATTCTTGTTGGTTG 57.441 37.500 0.00 0.00 0.00 3.77
145 146 6.295249 TGTGTGATCTATTCTTGTTGGTTGA 58.705 36.000 0.00 0.00 0.00 3.18
146 147 6.427853 TGTGTGATCTATTCTTGTTGGTTGAG 59.572 38.462 0.00 0.00 0.00 3.02
147 148 6.428159 GTGTGATCTATTCTTGTTGGTTGAGT 59.572 38.462 0.00 0.00 0.00 3.41
148 149 6.427853 TGTGATCTATTCTTGTTGGTTGAGTG 59.572 38.462 0.00 0.00 0.00 3.51
149 150 6.650807 GTGATCTATTCTTGTTGGTTGAGTGA 59.349 38.462 0.00 0.00 0.00 3.41
150 151 7.335422 GTGATCTATTCTTGTTGGTTGAGTGAT 59.665 37.037 0.00 0.00 0.00 3.06
151 152 7.884877 TGATCTATTCTTGTTGGTTGAGTGATT 59.115 33.333 0.00 0.00 0.00 2.57
152 153 7.672983 TCTATTCTTGTTGGTTGAGTGATTC 57.327 36.000 0.00 0.00 0.00 2.52
153 154 7.453393 TCTATTCTTGTTGGTTGAGTGATTCT 58.547 34.615 0.00 0.00 0.00 2.40
154 155 6.566197 ATTCTTGTTGGTTGAGTGATTCTC 57.434 37.500 0.00 0.00 43.03 2.87
155 156 5.296151 TCTTGTTGGTTGAGTGATTCTCT 57.704 39.130 0.00 0.00 43.13 3.10
156 157 5.300752 TCTTGTTGGTTGAGTGATTCTCTC 58.699 41.667 8.48 8.48 43.13 3.20
157 158 3.653344 TGTTGGTTGAGTGATTCTCTCG 58.347 45.455 10.30 0.00 43.13 4.04
158 159 2.370281 TGGTTGAGTGATTCTCTCGC 57.630 50.000 10.30 6.47 43.13 5.03
159 160 1.272781 GGTTGAGTGATTCTCTCGCG 58.727 55.000 0.00 0.00 43.13 5.87
160 161 1.402984 GGTTGAGTGATTCTCTCGCGT 60.403 52.381 5.77 0.00 43.13 6.01
161 162 2.329379 GTTGAGTGATTCTCTCGCGTT 58.671 47.619 5.77 0.00 43.13 4.84
162 163 2.724977 TGAGTGATTCTCTCGCGTTT 57.275 45.000 5.77 0.00 43.13 3.60
163 164 2.596452 TGAGTGATTCTCTCGCGTTTC 58.404 47.619 5.77 0.00 43.13 2.78
164 165 1.921230 GAGTGATTCTCTCGCGTTTCC 59.079 52.381 5.77 0.00 39.46 3.13
165 166 1.546476 AGTGATTCTCTCGCGTTTCCT 59.454 47.619 5.77 0.00 39.46 3.36
166 167 1.921230 GTGATTCTCTCGCGTTTCCTC 59.079 52.381 5.77 0.00 0.00 3.71
167 168 1.819288 TGATTCTCTCGCGTTTCCTCT 59.181 47.619 5.77 0.00 0.00 3.69
168 169 2.231478 TGATTCTCTCGCGTTTCCTCTT 59.769 45.455 5.77 0.00 0.00 2.85
169 170 2.065993 TTCTCTCGCGTTTCCTCTTG 57.934 50.000 5.77 0.00 0.00 3.02
170 171 0.959553 TCTCTCGCGTTTCCTCTTGT 59.040 50.000 5.77 0.00 0.00 3.16
171 172 1.063806 CTCTCGCGTTTCCTCTTGTG 58.936 55.000 5.77 0.00 0.00 3.33
172 173 0.387929 TCTCGCGTTTCCTCTTGTGT 59.612 50.000 5.77 0.00 0.00 3.72
173 174 1.202486 TCTCGCGTTTCCTCTTGTGTT 60.202 47.619 5.77 0.00 0.00 3.32
174 175 1.597663 CTCGCGTTTCCTCTTGTGTTT 59.402 47.619 5.77 0.00 0.00 2.83
175 176 2.011222 TCGCGTTTCCTCTTGTGTTTT 58.989 42.857 5.77 0.00 0.00 2.43
176 177 2.031191 TCGCGTTTCCTCTTGTGTTTTC 59.969 45.455 5.77 0.00 0.00 2.29
177 178 2.727777 GCGTTTCCTCTTGTGTTTTCC 58.272 47.619 0.00 0.00 0.00 3.13
178 179 2.543031 GCGTTTCCTCTTGTGTTTTCCC 60.543 50.000 0.00 0.00 0.00 3.97
179 180 2.949644 CGTTTCCTCTTGTGTTTTCCCT 59.050 45.455 0.00 0.00 0.00 4.20
180 181 3.003378 CGTTTCCTCTTGTGTTTTCCCTC 59.997 47.826 0.00 0.00 0.00 4.30
181 182 2.543777 TCCTCTTGTGTTTTCCCTCG 57.456 50.000 0.00 0.00 0.00 4.63
182 183 1.766496 TCCTCTTGTGTTTTCCCTCGT 59.234 47.619 0.00 0.00 0.00 4.18
183 184 2.171870 TCCTCTTGTGTTTTCCCTCGTT 59.828 45.455 0.00 0.00 0.00 3.85
184 185 2.949644 CCTCTTGTGTTTTCCCTCGTTT 59.050 45.455 0.00 0.00 0.00 3.60
185 186 3.380320 CCTCTTGTGTTTTCCCTCGTTTT 59.620 43.478 0.00 0.00 0.00 2.43
186 187 4.497507 CCTCTTGTGTTTTCCCTCGTTTTC 60.498 45.833 0.00 0.00 0.00 2.29
187 188 3.379057 TCTTGTGTTTTCCCTCGTTTTCC 59.621 43.478 0.00 0.00 0.00 3.13
188 189 2.025898 TGTGTTTTCCCTCGTTTTCCC 58.974 47.619 0.00 0.00 0.00 3.97
189 190 1.338973 GTGTTTTCCCTCGTTTTCCCC 59.661 52.381 0.00 0.00 0.00 4.81
190 191 1.215924 TGTTTTCCCTCGTTTTCCCCT 59.784 47.619 0.00 0.00 0.00 4.79
191 192 1.884579 GTTTTCCCTCGTTTTCCCCTC 59.115 52.381 0.00 0.00 0.00 4.30
192 193 0.035739 TTTCCCTCGTTTTCCCCTCG 59.964 55.000 0.00 0.00 0.00 4.63
193 194 1.123246 TTCCCTCGTTTTCCCCTCGT 61.123 55.000 0.00 0.00 0.00 4.18
194 195 1.375523 CCCTCGTTTTCCCCTCGTG 60.376 63.158 0.00 0.00 0.00 4.35
195 196 1.370064 CCTCGTTTTCCCCTCGTGT 59.630 57.895 0.00 0.00 0.00 4.49
196 197 0.250166 CCTCGTTTTCCCCTCGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
197 198 1.145803 CTCGTTTTCCCCTCGTGTTC 58.854 55.000 0.00 0.00 0.00 3.18
198 199 0.754472 TCGTTTTCCCCTCGTGTTCT 59.246 50.000 0.00 0.00 0.00 3.01
199 200 1.139455 TCGTTTTCCCCTCGTGTTCTT 59.861 47.619 0.00 0.00 0.00 2.52
200 201 1.529865 CGTTTTCCCCTCGTGTTCTTC 59.470 52.381 0.00 0.00 0.00 2.87
201 202 1.529865 GTTTTCCCCTCGTGTTCTTCG 59.470 52.381 0.00 0.00 0.00 3.79
202 203 0.754472 TTTCCCCTCGTGTTCTTCGT 59.246 50.000 0.00 0.00 0.00 3.85
203 204 0.032952 TTCCCCTCGTGTTCTTCGTG 59.967 55.000 0.00 0.00 0.00 4.35
204 205 1.111116 TCCCCTCGTGTTCTTCGTGT 61.111 55.000 0.00 0.00 0.00 4.49
205 206 0.666577 CCCCTCGTGTTCTTCGTGTC 60.667 60.000 0.00 0.00 0.00 3.67
206 207 0.666577 CCCTCGTGTTCTTCGTGTCC 60.667 60.000 0.00 0.00 0.00 4.02
207 208 0.314302 CCTCGTGTTCTTCGTGTCCT 59.686 55.000 0.00 0.00 0.00 3.85
208 209 1.269621 CCTCGTGTTCTTCGTGTCCTT 60.270 52.381 0.00 0.00 0.00 3.36
209 210 2.030540 CCTCGTGTTCTTCGTGTCCTTA 60.031 50.000 0.00 0.00 0.00 2.69
210 211 3.235195 CTCGTGTTCTTCGTGTCCTTAG 58.765 50.000 0.00 0.00 0.00 2.18
211 212 2.620115 TCGTGTTCTTCGTGTCCTTAGT 59.380 45.455 0.00 0.00 0.00 2.24
212 213 3.067180 TCGTGTTCTTCGTGTCCTTAGTT 59.933 43.478 0.00 0.00 0.00 2.24
213 214 3.181774 CGTGTTCTTCGTGTCCTTAGTTG 59.818 47.826 0.00 0.00 0.00 3.16
214 215 3.493503 GTGTTCTTCGTGTCCTTAGTTGG 59.506 47.826 0.00 0.00 0.00 3.77
215 216 3.064931 GTTCTTCGTGTCCTTAGTTGGG 58.935 50.000 0.00 0.00 0.00 4.12
216 217 2.600790 TCTTCGTGTCCTTAGTTGGGA 58.399 47.619 0.00 0.00 0.00 4.37
217 218 3.170717 TCTTCGTGTCCTTAGTTGGGAT 58.829 45.455 0.00 0.00 35.15 3.85
218 219 3.194968 TCTTCGTGTCCTTAGTTGGGATC 59.805 47.826 0.00 0.00 35.15 3.36
219 220 1.829222 TCGTGTCCTTAGTTGGGATCC 59.171 52.381 1.92 1.92 35.15 3.36
220 221 1.470979 CGTGTCCTTAGTTGGGATCCG 60.471 57.143 5.45 0.00 35.15 4.18
221 222 0.539986 TGTCCTTAGTTGGGATCCGC 59.460 55.000 5.45 0.00 35.15 5.54
222 223 0.831307 GTCCTTAGTTGGGATCCGCT 59.169 55.000 5.45 6.51 35.15 5.52
223 224 1.120530 TCCTTAGTTGGGATCCGCTC 58.879 55.000 5.45 0.00 0.00 5.03
224 225 0.106894 CCTTAGTTGGGATCCGCTCC 59.893 60.000 5.45 0.00 44.11 4.70
225 226 1.123928 CTTAGTTGGGATCCGCTCCT 58.876 55.000 5.45 1.45 44.28 3.69
226 227 1.486726 CTTAGTTGGGATCCGCTCCTT 59.513 52.381 5.45 0.00 44.28 3.36
227 228 1.580059 TAGTTGGGATCCGCTCCTTT 58.420 50.000 5.45 0.00 44.28 3.11
228 229 0.253327 AGTTGGGATCCGCTCCTTTC 59.747 55.000 5.45 0.00 44.28 2.62
229 230 1.090052 GTTGGGATCCGCTCCTTTCG 61.090 60.000 5.45 0.00 44.28 3.46
230 231 1.550130 TTGGGATCCGCTCCTTTCGT 61.550 55.000 5.45 0.00 44.28 3.85
231 232 1.521681 GGGATCCGCTCCTTTCGTG 60.522 63.158 5.45 0.00 44.28 4.35
232 233 1.515954 GGATCCGCTCCTTTCGTGA 59.484 57.895 0.00 0.00 41.29 4.35
233 234 0.108329 GGATCCGCTCCTTTCGTGAA 60.108 55.000 0.00 0.00 41.29 3.18
234 235 1.674817 GGATCCGCTCCTTTCGTGAAA 60.675 52.381 0.00 0.00 41.29 2.69
235 236 1.661112 GATCCGCTCCTTTCGTGAAAG 59.339 52.381 14.05 14.05 45.47 2.62
243 244 2.451693 TTTCGTGAAAGATCGGCCG 58.548 52.632 22.12 22.12 0.00 6.13
244 245 0.320073 TTTCGTGAAAGATCGGCCGT 60.320 50.000 27.15 12.96 0.00 5.68
245 246 0.527113 TTCGTGAAAGATCGGCCGTA 59.473 50.000 27.15 12.70 0.00 4.02
246 247 0.179156 TCGTGAAAGATCGGCCGTAC 60.179 55.000 27.15 19.65 0.00 3.67
247 248 1.469126 CGTGAAAGATCGGCCGTACG 61.469 60.000 27.15 19.30 0.00 3.67
248 249 1.140161 TGAAAGATCGGCCGTACGG 59.860 57.895 30.06 30.06 38.57 4.02
249 250 1.314534 TGAAAGATCGGCCGTACGGA 61.315 55.000 37.62 17.89 37.50 4.69
250 251 0.594284 GAAAGATCGGCCGTACGGAG 60.594 60.000 37.62 27.76 37.50 4.63
252 253 1.318158 AAGATCGGCCGTACGGAGTT 61.318 55.000 37.62 23.07 37.78 3.01
253 254 1.298938 GATCGGCCGTACGGAGTTC 60.299 63.158 37.62 26.20 37.78 3.01
254 255 2.674461 GATCGGCCGTACGGAGTTCC 62.674 65.000 37.62 25.92 37.78 3.62
255 256 3.751246 CGGCCGTACGGAGTTCCA 61.751 66.667 37.62 0.00 37.78 3.53
256 257 2.125793 GGCCGTACGGAGTTCCAC 60.126 66.667 37.62 17.33 37.78 4.02
257 258 2.643232 GGCCGTACGGAGTTCCACT 61.643 63.158 37.62 0.00 37.78 4.00
258 259 1.153881 GCCGTACGGAGTTCCACTC 60.154 63.158 37.62 12.69 37.78 3.51
407 427 0.598680 GATCTGACCAATCCGAGGCG 60.599 60.000 0.00 0.00 0.00 5.52
579 607 5.679734 ATATGCATCTTGTAGCGAAAAGG 57.320 39.130 0.19 0.00 0.00 3.11
581 609 3.407698 TGCATCTTGTAGCGAAAAGGAA 58.592 40.909 0.00 0.00 0.00 3.36
593 621 4.100963 AGCGAAAAGGAAAAGGGAAACAAT 59.899 37.500 0.00 0.00 0.00 2.71
617 645 6.475504 TGTGTGGTTGTCTTCATAGAATCAT 58.524 36.000 0.00 0.00 30.65 2.45
625 653 9.979578 GTTGTCTTCATAGAATCATAGAGACAT 57.020 33.333 0.00 0.00 33.48 3.06
834 1905 7.878547 TTCATTGGATGCACATTTATAGTCA 57.121 32.000 0.00 0.00 0.00 3.41
851 1922 4.273148 AGTCACCTAGTGTTCATGAACC 57.727 45.455 30.66 22.45 40.46 3.62
891 1963 7.954835 TGATATTTATGCTCCAAGAAATTGGG 58.045 34.615 7.15 0.16 42.32 4.12
892 1964 5.619132 ATTTATGCTCCAAGAAATTGGGG 57.381 39.130 7.15 4.86 45.45 4.96
1107 2707 2.205074 GTCGCATCGATTGGATCAAGT 58.795 47.619 0.00 0.00 38.42 3.16
1158 2758 8.723942 ACTATTTAGGATCAACAATGACTCAC 57.276 34.615 0.00 0.00 38.69 3.51
1240 2848 4.019591 ACCCCCTCATAAGTGACTTTACAC 60.020 45.833 1.97 0.00 40.60 2.90
1310 2920 3.715618 TGAATACTGCTTTTGTACGCG 57.284 42.857 3.53 3.53 0.00 6.01
1400 3034 1.003233 CTGACTTTTAGTTCCGCCCCT 59.997 52.381 0.00 0.00 0.00 4.79
1469 3103 2.365095 GATGGAGGAGTAACCGGCCG 62.365 65.000 21.04 21.04 44.74 6.13
1494 3128 2.126031 GGACAAGACGAGGCCGAC 60.126 66.667 0.00 0.00 39.50 4.79
1518 3152 1.451567 CCAGCAGGTCATGGCTCAG 60.452 63.158 0.00 0.00 38.56 3.35
1569 3203 1.144936 GCTCGCCCTTGAGTAGCAT 59.855 57.895 0.00 0.00 38.28 3.79
1657 3292 8.860780 TGTGCCATGCTATTATATTATCAACA 57.139 30.769 0.00 0.00 0.00 3.33
1724 3359 8.683776 TTTGGGACTAACCTATTAACCTAGAA 57.316 34.615 0.00 0.00 38.98 2.10
1810 3446 5.388654 AGTCCAATTGACCTGAAACTTCAT 58.611 37.500 7.12 0.00 45.68 2.57
1825 3461 9.748708 CTGAAACTTCATGGAACTTATTTTTGA 57.251 29.630 0.00 0.00 36.46 2.69
1877 3513 1.275291 TGTAAGGGAAGCAACGAGGAG 59.725 52.381 0.00 0.00 0.00 3.69
1880 3516 2.665603 GGAAGCAACGAGGAGGCT 59.334 61.111 0.00 0.00 40.14 4.58
2033 3673 0.036858 GAGTTCCGCCTTCAGAAGCT 60.037 55.000 4.41 0.00 0.00 3.74
2120 3760 1.144503 GGTGGCCATCTTCATCATCCT 59.855 52.381 9.72 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.043953 GGTCTTGATGGGGCCACC 60.044 66.667 0.20 2.19 40.81 4.61
14 15 1.077429 GAGGTCTTGATGGGGCCAC 60.077 63.158 4.39 0.00 0.00 5.01
15 16 2.308722 GGAGGTCTTGATGGGGCCA 61.309 63.158 4.39 0.00 0.00 5.36
16 17 1.575447 AAGGAGGTCTTGATGGGGCC 61.575 60.000 0.00 0.00 33.76 5.80
17 18 1.134068 GTAAGGAGGTCTTGATGGGGC 60.134 57.143 0.00 0.00 36.93 5.80
18 19 1.139058 CGTAAGGAGGTCTTGATGGGG 59.861 57.143 0.00 0.00 36.93 4.96
19 20 2.604046 CGTAAGGAGGTCTTGATGGG 57.396 55.000 0.00 0.00 36.93 4.00
33 34 4.492611 GGTAACCAGTTCTTCTCCGTAAG 58.507 47.826 0.00 0.00 0.00 2.34
34 35 3.057315 CGGTAACCAGTTCTTCTCCGTAA 60.057 47.826 0.00 0.00 33.39 3.18
35 36 2.489329 CGGTAACCAGTTCTTCTCCGTA 59.511 50.000 0.00 0.00 33.39 4.02
36 37 1.271656 CGGTAACCAGTTCTTCTCCGT 59.728 52.381 0.00 0.00 33.39 4.69
37 38 1.271656 ACGGTAACCAGTTCTTCTCCG 59.728 52.381 0.00 0.00 41.95 4.63
38 39 3.397849 AACGGTAACCAGTTCTTCTCC 57.602 47.619 0.00 0.00 0.00 3.71
39 40 4.124970 ACAAACGGTAACCAGTTCTTCTC 58.875 43.478 0.00 0.00 0.00 2.87
40 41 4.146745 ACAAACGGTAACCAGTTCTTCT 57.853 40.909 0.00 0.00 0.00 2.85
41 42 5.164022 CGATACAAACGGTAACCAGTTCTTC 60.164 44.000 0.00 0.00 35.14 2.87
42 43 4.687483 CGATACAAACGGTAACCAGTTCTT 59.313 41.667 0.00 0.00 35.14 2.52
43 44 4.240096 CGATACAAACGGTAACCAGTTCT 58.760 43.478 0.00 0.00 35.14 3.01
44 45 3.989817 ACGATACAAACGGTAACCAGTTC 59.010 43.478 0.00 0.00 35.14 3.01
45 46 3.989817 GACGATACAAACGGTAACCAGTT 59.010 43.478 0.00 0.00 35.14 3.16
46 47 3.578688 GACGATACAAACGGTAACCAGT 58.421 45.455 0.00 0.00 35.14 4.00
47 48 2.925563 GGACGATACAAACGGTAACCAG 59.074 50.000 0.00 0.00 35.14 4.00
48 49 2.562298 AGGACGATACAAACGGTAACCA 59.438 45.455 0.00 0.00 35.14 3.67
49 50 3.236632 AGGACGATACAAACGGTAACC 57.763 47.619 0.00 0.00 35.14 2.85
50 51 6.892310 ATAAAGGACGATACAAACGGTAAC 57.108 37.500 0.00 0.00 35.14 2.50
51 52 6.313411 CCAATAAAGGACGATACAAACGGTAA 59.687 38.462 0.00 0.00 35.14 2.85
52 53 5.811613 CCAATAAAGGACGATACAAACGGTA 59.188 40.000 0.00 0.00 36.16 4.02
53 54 4.632688 CCAATAAAGGACGATACAAACGGT 59.367 41.667 0.00 0.00 34.93 4.83
54 55 4.871557 TCCAATAAAGGACGATACAAACGG 59.128 41.667 0.00 0.00 31.23 4.44
55 56 6.411630 TTCCAATAAAGGACGATACAAACG 57.588 37.500 0.00 0.00 37.42 3.60
56 57 7.700656 CCAATTCCAATAAAGGACGATACAAAC 59.299 37.037 0.00 0.00 37.42 2.93
57 58 7.612244 TCCAATTCCAATAAAGGACGATACAAA 59.388 33.333 0.00 0.00 37.42 2.83
58 59 7.113437 TCCAATTCCAATAAAGGACGATACAA 58.887 34.615 0.00 0.00 37.42 2.41
59 60 6.654959 TCCAATTCCAATAAAGGACGATACA 58.345 36.000 0.00 0.00 37.42 2.29
60 61 7.661847 AGATCCAATTCCAATAAAGGACGATAC 59.338 37.037 0.00 0.00 37.42 2.24
61 62 7.745717 AGATCCAATTCCAATAAAGGACGATA 58.254 34.615 0.00 0.00 37.42 2.92
62 63 6.605119 AGATCCAATTCCAATAAAGGACGAT 58.395 36.000 0.00 0.00 37.42 3.73
63 64 6.001449 AGATCCAATTCCAATAAAGGACGA 57.999 37.500 0.00 0.00 37.42 4.20
64 65 6.095440 ACAAGATCCAATTCCAATAAAGGACG 59.905 38.462 0.00 0.00 37.42 4.79
65 66 7.410120 ACAAGATCCAATTCCAATAAAGGAC 57.590 36.000 0.00 0.00 37.42 3.85
66 67 9.354673 GATACAAGATCCAATTCCAATAAAGGA 57.645 33.333 0.00 0.00 35.41 3.36
67 68 9.359653 AGATACAAGATCCAATTCCAATAAAGG 57.640 33.333 0.00 0.00 0.00 3.11
69 70 9.919416 TGAGATACAAGATCCAATTCCAATAAA 57.081 29.630 0.00 0.00 0.00 1.40
70 71 9.342308 GTGAGATACAAGATCCAATTCCAATAA 57.658 33.333 0.00 0.00 0.00 1.40
71 72 7.939039 GGTGAGATACAAGATCCAATTCCAATA 59.061 37.037 0.00 0.00 0.00 1.90
72 73 6.774656 GGTGAGATACAAGATCCAATTCCAAT 59.225 38.462 0.00 0.00 0.00 3.16
73 74 6.069440 AGGTGAGATACAAGATCCAATTCCAA 60.069 38.462 0.00 0.00 0.00 3.53
74 75 5.429762 AGGTGAGATACAAGATCCAATTCCA 59.570 40.000 0.00 0.00 0.00 3.53
75 76 5.934781 AGGTGAGATACAAGATCCAATTCC 58.065 41.667 0.00 0.00 0.00 3.01
76 77 7.337942 ACAAAGGTGAGATACAAGATCCAATTC 59.662 37.037 0.00 0.00 0.00 2.17
77 78 7.177878 ACAAAGGTGAGATACAAGATCCAATT 58.822 34.615 0.00 0.00 0.00 2.32
78 79 6.725364 ACAAAGGTGAGATACAAGATCCAAT 58.275 36.000 0.00 0.00 0.00 3.16
79 80 6.126863 ACAAAGGTGAGATACAAGATCCAA 57.873 37.500 0.00 0.00 0.00 3.53
80 81 5.762179 ACAAAGGTGAGATACAAGATCCA 57.238 39.130 0.00 0.00 0.00 3.41
95 96 4.184629 GCTAGATCGATGAACACAAAGGT 58.815 43.478 0.54 0.00 0.00 3.50
96 97 3.243877 CGCTAGATCGATGAACACAAAGG 59.756 47.826 0.54 0.00 0.00 3.11
97 98 3.302092 GCGCTAGATCGATGAACACAAAG 60.302 47.826 0.54 0.00 0.00 2.77
98 99 2.603110 GCGCTAGATCGATGAACACAAA 59.397 45.455 0.54 0.00 0.00 2.83
99 100 2.193447 GCGCTAGATCGATGAACACAA 58.807 47.619 0.54 0.00 0.00 3.33
100 101 1.134175 TGCGCTAGATCGATGAACACA 59.866 47.619 9.73 0.00 0.00 3.72
101 102 1.840181 TGCGCTAGATCGATGAACAC 58.160 50.000 9.73 0.00 0.00 3.32
102 103 2.223805 ACATGCGCTAGATCGATGAACA 60.224 45.455 9.73 0.00 0.00 3.18
103 104 2.154580 CACATGCGCTAGATCGATGAAC 59.845 50.000 9.73 0.00 0.00 3.18
104 105 2.223805 ACACATGCGCTAGATCGATGAA 60.224 45.455 9.73 0.00 0.00 2.57
105 106 1.338020 ACACATGCGCTAGATCGATGA 59.662 47.619 9.73 0.00 0.00 2.92
106 107 1.454653 CACACATGCGCTAGATCGATG 59.545 52.381 9.73 4.32 0.00 3.84
107 108 1.338020 TCACACATGCGCTAGATCGAT 59.662 47.619 9.73 0.00 0.00 3.59
108 109 0.738389 TCACACATGCGCTAGATCGA 59.262 50.000 9.73 0.00 0.00 3.59
109 110 1.718178 GATCACACATGCGCTAGATCG 59.282 52.381 9.73 0.00 0.00 3.69
110 111 3.023946 AGATCACACATGCGCTAGATC 57.976 47.619 9.73 11.77 33.79 2.75
111 112 4.797800 ATAGATCACACATGCGCTAGAT 57.202 40.909 9.73 2.72 0.00 1.98
112 113 4.279420 AGAATAGATCACACATGCGCTAGA 59.721 41.667 9.73 0.00 0.00 2.43
113 114 4.554292 AGAATAGATCACACATGCGCTAG 58.446 43.478 9.73 3.08 0.00 3.42
114 115 4.590850 AGAATAGATCACACATGCGCTA 57.409 40.909 9.73 0.00 0.00 4.26
115 116 3.465742 AGAATAGATCACACATGCGCT 57.534 42.857 9.73 0.00 0.00 5.92
116 117 3.310774 ACAAGAATAGATCACACATGCGC 59.689 43.478 0.00 0.00 0.00 6.09
117 118 5.260900 CAACAAGAATAGATCACACATGCG 58.739 41.667 0.00 0.00 0.00 4.73
118 119 5.124457 ACCAACAAGAATAGATCACACATGC 59.876 40.000 0.00 0.00 0.00 4.06
119 120 6.748333 ACCAACAAGAATAGATCACACATG 57.252 37.500 0.00 0.00 0.00 3.21
120 121 6.942005 TCAACCAACAAGAATAGATCACACAT 59.058 34.615 0.00 0.00 0.00 3.21
121 122 6.295249 TCAACCAACAAGAATAGATCACACA 58.705 36.000 0.00 0.00 0.00 3.72
122 123 6.428159 ACTCAACCAACAAGAATAGATCACAC 59.572 38.462 0.00 0.00 0.00 3.82
123 124 6.427853 CACTCAACCAACAAGAATAGATCACA 59.572 38.462 0.00 0.00 0.00 3.58
124 125 6.650807 TCACTCAACCAACAAGAATAGATCAC 59.349 38.462 0.00 0.00 0.00 3.06
125 126 6.768483 TCACTCAACCAACAAGAATAGATCA 58.232 36.000 0.00 0.00 0.00 2.92
126 127 7.856145 ATCACTCAACCAACAAGAATAGATC 57.144 36.000 0.00 0.00 0.00 2.75
127 128 8.105829 AGAATCACTCAACCAACAAGAATAGAT 58.894 33.333 0.00 0.00 0.00 1.98
128 129 7.453393 AGAATCACTCAACCAACAAGAATAGA 58.547 34.615 0.00 0.00 0.00 1.98
129 130 7.678947 AGAATCACTCAACCAACAAGAATAG 57.321 36.000 0.00 0.00 0.00 1.73
130 131 7.672983 GAGAATCACTCAACCAACAAGAATA 57.327 36.000 0.00 0.00 44.36 1.75
131 132 6.566197 GAGAATCACTCAACCAACAAGAAT 57.434 37.500 0.00 0.00 44.36 2.40
144 145 1.921230 GGAAACGCGAGAGAATCACTC 59.079 52.381 15.93 0.00 45.22 3.51
145 146 1.546476 AGGAAACGCGAGAGAATCACT 59.454 47.619 15.93 0.00 37.82 3.41
146 147 1.921230 GAGGAAACGCGAGAGAATCAC 59.079 52.381 15.93 0.00 37.82 3.06
147 148 1.819288 AGAGGAAACGCGAGAGAATCA 59.181 47.619 15.93 0.00 33.43 2.57
148 149 2.570442 AGAGGAAACGCGAGAGAATC 57.430 50.000 15.93 3.31 34.13 2.52
149 150 2.028930 ACAAGAGGAAACGCGAGAGAAT 60.029 45.455 15.93 0.00 34.13 2.40
150 151 1.340248 ACAAGAGGAAACGCGAGAGAA 59.660 47.619 15.93 0.00 34.13 2.87
151 152 0.959553 ACAAGAGGAAACGCGAGAGA 59.040 50.000 15.93 0.00 34.13 3.10
152 153 1.063806 CACAAGAGGAAACGCGAGAG 58.936 55.000 15.93 0.00 34.13 3.20
153 154 0.387929 ACACAAGAGGAAACGCGAGA 59.612 50.000 15.93 0.00 34.13 4.04
154 155 1.217882 AACACAAGAGGAAACGCGAG 58.782 50.000 15.93 0.00 34.13 5.03
155 156 1.658994 AAACACAAGAGGAAACGCGA 58.341 45.000 15.93 0.00 34.13 5.87
156 157 2.372350 GAAAACACAAGAGGAAACGCG 58.628 47.619 3.53 3.53 34.13 6.01
157 158 2.543031 GGGAAAACACAAGAGGAAACGC 60.543 50.000 0.00 0.00 0.00 4.84
158 159 2.949644 AGGGAAAACACAAGAGGAAACG 59.050 45.455 0.00 0.00 0.00 3.60
159 160 3.003378 CGAGGGAAAACACAAGAGGAAAC 59.997 47.826 0.00 0.00 0.00 2.78
160 161 3.211045 CGAGGGAAAACACAAGAGGAAA 58.789 45.455 0.00 0.00 0.00 3.13
161 162 2.171870 ACGAGGGAAAACACAAGAGGAA 59.828 45.455 0.00 0.00 0.00 3.36
162 163 1.766496 ACGAGGGAAAACACAAGAGGA 59.234 47.619 0.00 0.00 0.00 3.71
163 164 2.256117 ACGAGGGAAAACACAAGAGG 57.744 50.000 0.00 0.00 0.00 3.69
164 165 4.497507 GGAAAACGAGGGAAAACACAAGAG 60.498 45.833 0.00 0.00 0.00 2.85
165 166 3.379057 GGAAAACGAGGGAAAACACAAGA 59.621 43.478 0.00 0.00 0.00 3.02
166 167 3.490249 GGGAAAACGAGGGAAAACACAAG 60.490 47.826 0.00 0.00 0.00 3.16
167 168 2.427812 GGGAAAACGAGGGAAAACACAA 59.572 45.455 0.00 0.00 0.00 3.33
168 169 2.025898 GGGAAAACGAGGGAAAACACA 58.974 47.619 0.00 0.00 0.00 3.72
169 170 1.338973 GGGGAAAACGAGGGAAAACAC 59.661 52.381 0.00 0.00 0.00 3.32
170 171 1.215924 AGGGGAAAACGAGGGAAAACA 59.784 47.619 0.00 0.00 0.00 2.83
171 172 1.884579 GAGGGGAAAACGAGGGAAAAC 59.115 52.381 0.00 0.00 0.00 2.43
172 173 1.543871 CGAGGGGAAAACGAGGGAAAA 60.544 52.381 0.00 0.00 0.00 2.29
173 174 0.035739 CGAGGGGAAAACGAGGGAAA 59.964 55.000 0.00 0.00 0.00 3.13
174 175 1.123246 ACGAGGGGAAAACGAGGGAA 61.123 55.000 0.00 0.00 0.00 3.97
175 176 1.534717 ACGAGGGGAAAACGAGGGA 60.535 57.895 0.00 0.00 0.00 4.20
176 177 1.375523 CACGAGGGGAAAACGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
177 178 0.250166 AACACGAGGGGAAAACGAGG 60.250 55.000 0.00 0.00 0.00 4.63
178 179 1.145803 GAACACGAGGGGAAAACGAG 58.854 55.000 0.00 0.00 0.00 4.18
179 180 0.754472 AGAACACGAGGGGAAAACGA 59.246 50.000 0.00 0.00 0.00 3.85
180 181 1.529865 GAAGAACACGAGGGGAAAACG 59.470 52.381 0.00 0.00 0.00 3.60
181 182 1.529865 CGAAGAACACGAGGGGAAAAC 59.470 52.381 0.00 0.00 0.00 2.43
182 183 1.139455 ACGAAGAACACGAGGGGAAAA 59.861 47.619 0.00 0.00 34.70 2.29
183 184 0.754472 ACGAAGAACACGAGGGGAAA 59.246 50.000 0.00 0.00 34.70 3.13
184 185 0.032952 CACGAAGAACACGAGGGGAA 59.967 55.000 0.00 0.00 34.70 3.97
185 186 1.111116 ACACGAAGAACACGAGGGGA 61.111 55.000 0.00 0.00 34.70 4.81
186 187 0.666577 GACACGAAGAACACGAGGGG 60.667 60.000 0.00 0.00 34.70 4.79
187 188 0.666577 GGACACGAAGAACACGAGGG 60.667 60.000 0.00 0.00 34.70 4.30
188 189 0.314302 AGGACACGAAGAACACGAGG 59.686 55.000 0.00 0.00 34.70 4.63
189 190 2.135664 AAGGACACGAAGAACACGAG 57.864 50.000 0.00 0.00 34.70 4.18
190 191 2.620115 ACTAAGGACACGAAGAACACGA 59.380 45.455 0.00 0.00 34.70 4.35
191 192 3.009301 ACTAAGGACACGAAGAACACG 57.991 47.619 0.00 0.00 0.00 4.49
192 193 3.493503 CCAACTAAGGACACGAAGAACAC 59.506 47.826 0.00 0.00 0.00 3.32
193 194 3.493699 CCCAACTAAGGACACGAAGAACA 60.494 47.826 0.00 0.00 0.00 3.18
194 195 3.064931 CCCAACTAAGGACACGAAGAAC 58.935 50.000 0.00 0.00 0.00 3.01
195 196 2.967201 TCCCAACTAAGGACACGAAGAA 59.033 45.455 0.00 0.00 0.00 2.52
196 197 2.600790 TCCCAACTAAGGACACGAAGA 58.399 47.619 0.00 0.00 0.00 2.87
197 198 3.522553 GATCCCAACTAAGGACACGAAG 58.477 50.000 0.00 0.00 35.85 3.79
198 199 2.235402 GGATCCCAACTAAGGACACGAA 59.765 50.000 0.00 0.00 35.85 3.85
199 200 1.829222 GGATCCCAACTAAGGACACGA 59.171 52.381 0.00 0.00 35.85 4.35
200 201 1.470979 CGGATCCCAACTAAGGACACG 60.471 57.143 6.06 0.00 35.85 4.49
201 202 1.742750 GCGGATCCCAACTAAGGACAC 60.743 57.143 6.06 0.00 35.85 3.67
202 203 0.539986 GCGGATCCCAACTAAGGACA 59.460 55.000 6.06 0.00 35.85 4.02
203 204 0.831307 AGCGGATCCCAACTAAGGAC 59.169 55.000 6.06 0.00 35.85 3.85
204 205 1.120530 GAGCGGATCCCAACTAAGGA 58.879 55.000 6.06 0.00 37.93 3.36
205 206 0.106894 GGAGCGGATCCCAACTAAGG 59.893 60.000 6.06 0.00 43.01 2.69
206 207 3.688553 GGAGCGGATCCCAACTAAG 57.311 57.895 6.06 0.00 43.01 2.18
215 216 1.661112 CTTTCACGAAAGGAGCGGATC 59.339 52.381 11.02 0.00 42.96 3.36
216 217 1.275291 TCTTTCACGAAAGGAGCGGAT 59.725 47.619 17.23 0.00 45.80 4.18
217 218 0.677288 TCTTTCACGAAAGGAGCGGA 59.323 50.000 17.23 0.00 45.80 5.54
218 219 1.661112 GATCTTTCACGAAAGGAGCGG 59.339 52.381 17.23 0.00 45.80 5.52
219 220 1.321743 CGATCTTTCACGAAAGGAGCG 59.678 52.381 17.23 14.23 45.80 5.03
220 221 1.661112 CCGATCTTTCACGAAAGGAGC 59.339 52.381 17.23 7.95 45.80 4.70
221 222 1.661112 GCCGATCTTTCACGAAAGGAG 59.339 52.381 17.23 9.96 45.80 3.69
222 223 1.674817 GGCCGATCTTTCACGAAAGGA 60.675 52.381 17.23 6.84 45.80 3.36
223 224 0.727398 GGCCGATCTTTCACGAAAGG 59.273 55.000 17.23 5.63 45.80 3.11
224 225 0.370273 CGGCCGATCTTTCACGAAAG 59.630 55.000 24.07 12.40 46.82 2.62
225 226 0.320073 ACGGCCGATCTTTCACGAAA 60.320 50.000 35.90 0.00 0.00 3.46
226 227 0.527113 TACGGCCGATCTTTCACGAA 59.473 50.000 35.90 0.00 0.00 3.85
227 228 0.179156 GTACGGCCGATCTTTCACGA 60.179 55.000 35.90 0.00 0.00 4.35
228 229 1.469126 CGTACGGCCGATCTTTCACG 61.469 60.000 35.90 22.24 0.00 4.35
229 230 1.143969 CCGTACGGCCGATCTTTCAC 61.144 60.000 35.90 15.27 0.00 3.18
230 231 1.140161 CCGTACGGCCGATCTTTCA 59.860 57.895 35.90 4.20 0.00 2.69
231 232 0.594284 CTCCGTACGGCCGATCTTTC 60.594 60.000 35.90 13.34 34.68 2.62
232 233 1.318158 ACTCCGTACGGCCGATCTTT 61.318 55.000 35.90 12.08 34.68 2.52
233 234 1.318158 AACTCCGTACGGCCGATCTT 61.318 55.000 35.90 12.54 34.68 2.40
234 235 1.722636 GAACTCCGTACGGCCGATCT 61.723 60.000 35.90 12.99 34.68 2.75
235 236 1.298938 GAACTCCGTACGGCCGATC 60.299 63.158 35.90 22.11 34.68 3.69
236 237 2.779033 GGAACTCCGTACGGCCGAT 61.779 63.158 35.90 18.92 34.68 4.18
237 238 3.443045 GGAACTCCGTACGGCCGA 61.443 66.667 35.90 13.31 34.68 5.54
238 239 3.751246 TGGAACTCCGTACGGCCG 61.751 66.667 29.64 26.86 39.43 6.13
239 240 2.125793 GTGGAACTCCGTACGGCC 60.126 66.667 29.64 23.47 39.43 6.13
250 251 2.012673 GATGCTGATGTGGAGTGGAAC 58.987 52.381 0.00 0.00 0.00 3.62
251 252 1.911357 AGATGCTGATGTGGAGTGGAA 59.089 47.619 0.00 0.00 0.00 3.53
252 253 1.483827 GAGATGCTGATGTGGAGTGGA 59.516 52.381 0.00 0.00 0.00 4.02
253 254 1.474677 GGAGATGCTGATGTGGAGTGG 60.475 57.143 0.00 0.00 0.00 4.00
254 255 1.474677 GGGAGATGCTGATGTGGAGTG 60.475 57.143 0.00 0.00 0.00 3.51
255 256 0.835941 GGGAGATGCTGATGTGGAGT 59.164 55.000 0.00 0.00 0.00 3.85
256 257 0.835276 TGGGAGATGCTGATGTGGAG 59.165 55.000 0.00 0.00 0.00 3.86
257 258 0.835276 CTGGGAGATGCTGATGTGGA 59.165 55.000 0.00 0.00 0.00 4.02
258 259 0.818445 GCTGGGAGATGCTGATGTGG 60.818 60.000 0.00 0.00 0.00 4.17
259 260 1.158484 CGCTGGGAGATGCTGATGTG 61.158 60.000 0.00 0.00 0.00 3.21
260 261 1.145598 CGCTGGGAGATGCTGATGT 59.854 57.895 0.00 0.00 0.00 3.06
261 262 1.597302 CCGCTGGGAGATGCTGATG 60.597 63.158 0.00 0.00 34.06 3.07
262 263 2.827423 CCGCTGGGAGATGCTGAT 59.173 61.111 0.00 0.00 34.06 2.90
263 264 4.166888 GCCGCTGGGAGATGCTGA 62.167 66.667 0.00 0.00 34.06 4.26
264 265 4.172512 AGCCGCTGGGAGATGCTG 62.173 66.667 0.00 0.00 34.06 4.41
265 266 3.859414 GAGCCGCTGGGAGATGCT 61.859 66.667 0.00 0.00 34.06 3.79
392 412 0.104120 CATACGCCTCGGATTGGTCA 59.896 55.000 0.00 0.00 0.00 4.02
407 427 7.880195 ACTTAATCTGCAGGGAATACATCATAC 59.120 37.037 15.13 0.00 0.00 2.39
548 574 5.689068 GCTACAAGATGCATATTTTTGGAGC 59.311 40.000 23.08 23.08 45.29 4.70
579 607 4.400529 ACCACACATTGTTTCCCTTTTC 57.599 40.909 0.00 0.00 0.00 2.29
581 609 3.517500 ACAACCACACATTGTTTCCCTTT 59.482 39.130 0.00 0.00 36.93 3.11
593 621 5.863965 TGATTCTATGAAGACAACCACACA 58.136 37.500 0.00 0.00 0.00 3.72
625 653 9.661563 ACTCGTAAATAAAATGTCAATAGGTCA 57.338 29.630 0.00 0.00 0.00 4.02
829 1900 5.084519 AGGTTCATGAACACTAGGTGACTA 58.915 41.667 33.42 0.00 42.85 2.59
834 1905 6.875972 AATAGAGGTTCATGAACACTAGGT 57.124 37.500 33.42 23.14 42.85 3.08
891 1963 4.454728 TTGCTTTAATGTCAGGATTGCC 57.545 40.909 0.00 0.00 0.00 4.52
892 1964 6.158598 TCTTTTGCTTTAATGTCAGGATTGC 58.841 36.000 0.00 0.00 0.00 3.56
965 2071 5.296780 ACGCCATATGACTAAGTGAATTTGG 59.703 40.000 3.65 0.00 0.00 3.28
1158 2758 7.371159 TGCATAATACTCCATTTAGTCTCTCG 58.629 38.462 0.00 0.00 0.00 4.04
1240 2848 7.965107 CCTTCGAATTTTCTTTACATTCCTCAG 59.035 37.037 0.00 0.00 0.00 3.35
1307 2917 6.991655 TGTTACCAATAAACACTTATACGCG 58.008 36.000 3.53 3.53 32.07 6.01
1381 3015 1.061546 AGGGGCGGAACTAAAAGTCA 58.938 50.000 0.00 0.00 0.00 3.41
1400 3034 1.149782 TCCTGGTATTTTGGGGGCCA 61.150 55.000 4.39 0.00 0.00 5.36
1469 3103 2.673833 CCTCGTCTTGTCCTTGTACAC 58.326 52.381 0.00 0.00 0.00 2.90
1635 3270 9.740239 CCAATGTTGATAATATAATAGCATGGC 57.260 33.333 0.00 0.00 0.00 4.40
1657 3292 9.462174 CATATAAATGCGTACAAAACATCCAAT 57.538 29.630 0.00 0.00 0.00 3.16
1759 3395 6.567687 TTGATTTTCCTTTTCTGCGATACA 57.432 33.333 0.00 0.00 0.00 2.29
1810 3446 7.560368 TGCTTTCCTTTCAAAAATAAGTTCCA 58.440 30.769 0.00 0.00 0.00 3.53
1825 3461 1.420138 TCTCTCGGGTTGCTTTCCTTT 59.580 47.619 0.00 0.00 0.00 3.11
1938 3578 0.617820 AAGTACGTCAGGGGAGCCAT 60.618 55.000 0.00 0.00 0.00 4.40
2033 3673 3.985019 TGGTTTTCGGTGGCTATAGAA 57.015 42.857 3.21 0.00 0.00 2.10
2120 3760 0.835276 CCTCATCATGGAGAGCACCA 59.165 55.000 9.11 0.00 44.41 4.17
2182 3822 7.833682 AGAGAGAGAGAGAGATCAAACACATAA 59.166 37.037 0.00 0.00 0.00 1.90
2242 3886 5.914033 TCCAACTATAATAGCAAAGCTCGT 58.086 37.500 0.00 0.00 40.44 4.18


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

AutoCloner maintained by Alex Coulton.