Multiple sequence alignment - TraesCS7A01G232200

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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 TraesCS7A01G232200 chr7A 100.000 4824 0 0 1 4824 203043254 203038431 0.000000e+00 8909.0
1 TraesCS7A01G232200 chr7D 92.846 3299 144 52 139 3390 193588090 193584837 0.000000e+00 4700.0
2 TraesCS7A01G232200 chr7D 90.612 1406 107 9 3441 4824 193584823 193583421 0.000000e+00 1842.0
3 TraesCS7A01G232200 chr7D 94.964 139 7 0 1 139 211761876 211762014 8.130000e-53 219.0
4 TraesCS7A01G232200 chr7D 94.964 139 7 0 1 139 259120405 259120267 8.130000e-53 219.0
5 TraesCS7A01G232200 chr7D 94.964 139 7 0 1 139 282752549 282752411 8.130000e-53 219.0
6 TraesCS7A01G232200 chr7B 88.763 2990 202 62 1863 4824 157218767 157215884 0.000000e+00 3537.0
7 TraesCS7A01G232200 chr7B 91.413 1316 69 26 467 1750 157220104 157218801 0.000000e+00 1764.0
8 TraesCS7A01G232200 chr7B 81.132 371 39 14 139 484 157220491 157220127 7.960000e-68 268.0
9 TraesCS7A01G232200 chr4B 88.998 818 79 8 2653 3468 59233302 59234110 0.000000e+00 1002.0
10 TraesCS7A01G232200 chr4B 91.038 703 53 8 1951 2648 59232528 59233225 0.000000e+00 941.0
11 TraesCS7A01G232200 chr4B 95.536 224 10 0 3683 3906 59234141 59234364 4.590000e-95 359.0
12 TraesCS7A01G232200 chr4B 85.660 265 35 2 1155 1417 59231464 59231727 4.760000e-70 276.0
13 TraesCS7A01G232200 chr4D 91.819 709 52 5 1951 2654 3611496 3610789 0.000000e+00 983.0
14 TraesCS7A01G232200 chr4D 85.578 943 97 25 2653 3589 3610718 3609809 0.000000e+00 952.0
15 TraesCS7A01G232200 chr4D 90.331 393 31 3 3621 4013 3609361 3608976 4.310000e-140 508.0
16 TraesCS7A01G232200 chr4D 87.500 256 29 2 1164 1417 3612748 3612494 4.720000e-75 292.0
17 TraesCS7A01G232200 chr4D 95.683 139 6 0 1 139 312050064 312049926 1.750000e-54 224.0
18 TraesCS7A01G232200 chr4D 100.000 29 0 0 1204 1232 283886819 283886847 2.000000e-03 54.7
19 TraesCS7A01G232200 chr6D 95.683 139 6 0 1 139 410375358 410375220 1.750000e-54 224.0
20 TraesCS7A01G232200 chr6D 95.000 140 5 2 1 139 192920158 192920020 8.130000e-53 219.0
21 TraesCS7A01G232200 chr6D 85.093 161 24 0 1184 1344 360680996 360681156 1.070000e-36 165.0
22 TraesCS7A01G232200 chr6D 100.000 29 0 0 1204 1232 435374028 435374056 2.000000e-03 54.7
23 TraesCS7A01G232200 chr3D 94.964 139 7 0 1 139 121131367 121131229 8.130000e-53 219.0
24 TraesCS7A01G232200 chr3D 94.964 139 7 0 1 139 335484267 335484129 8.130000e-53 219.0
25 TraesCS7A01G232200 chr3D 87.500 72 8 1 311 381 289105828 289105899 1.110000e-11 82.4
26 TraesCS7A01G232200 chr2D 94.964 139 7 0 1 139 319665399 319665261 8.130000e-53 219.0
27 TraesCS7A01G232200 chr6A 85.093 161 24 0 1184 1344 501791976 501792136 1.070000e-36 165.0
28 TraesCS7A01G232200 chr6A 100.000 28 0 0 354 381 30795163 30795190 9.000000e-03 52.8
29 TraesCS7A01G232200 chr6B 83.230 161 27 0 1184 1344 542223767 542223927 1.080000e-31 148.0
30 TraesCS7A01G232200 chr3A 89.062 64 6 1 319 381 379823792 379823855 1.440000e-10 78.7
31 TraesCS7A01G232200 chr3B 86.111 72 8 2 311 381 381756907 381756977 5.180000e-10 76.8


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 TraesCS7A01G232200 chr7A 203038431 203043254 4823 True 8909.000000 8909 100.000000 1 4824 1 chr7A.!!$R1 4823
1 TraesCS7A01G232200 chr7D 193583421 193588090 4669 True 3271.000000 4700 91.729000 139 4824 2 chr7D.!!$R3 4685
2 TraesCS7A01G232200 chr7B 157215884 157220491 4607 True 1856.333333 3537 87.102667 139 4824 3 chr7B.!!$R1 4685
3 TraesCS7A01G232200 chr4B 59231464 59234364 2900 False 644.500000 1002 90.308000 1155 3906 4 chr4B.!!$F1 2751
4 TraesCS7A01G232200 chr4D 3608976 3612748 3772 True 683.750000 983 88.807000 1164 4013 4 chr4D.!!$R2 2849

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
569 647 0.035439 TTGATCCTTCGCCACCCTTC 60.035 55.000 0.00 0.00 0.00 3.46 F
1533 2376 0.031178 GTGAACTTGGCAGCACTTGG 59.969 55.000 0.00 0.00 0.00 3.61 F
2334 3189 1.003696 AGGAACTTCTTGCCTGGCTAC 59.996 52.381 21.03 0.00 27.25 3.58 F
3445 4382 0.671796 CTGATACCGGACCGTATGCA 59.328 55.000 9.46 4.95 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 3024 0.320508 CAGCAGTGAGAAGCAGCTCA 60.321 55.0 0.0 4.61 42.31 4.26 R
3387 4324 0.032952 GACGATACGCCATAAGCCCA 59.967 55.0 0.0 0.00 38.78 5.36 R
3675 5020 0.107643 TCCACATCAGAAACACGGCA 59.892 50.0 0.0 0.00 0.00 5.69 R
4497 5873 0.395586 CGCCCAATGAAATCCCTCCA 60.396 55.0 0.0 0.00 0.00 3.86 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
26 27 8.634335 TTTAATTGTGATTCAACTGATCCTGA 57.366 30.769 0.00 0.00 38.97 3.86
27 28 8.634335 TTAATTGTGATTCAACTGATCCTGAA 57.366 30.769 4.91 4.91 38.97 3.02
28 29 7.713734 AATTGTGATTCAACTGATCCTGAAT 57.286 32.000 12.23 12.23 43.34 2.57
29 30 7.713734 ATTGTGATTCAACTGATCCTGAATT 57.286 32.000 13.15 0.00 41.29 2.17
30 31 6.505044 TGTGATTCAACTGATCCTGAATTG 57.495 37.500 13.15 2.19 41.29 2.32
31 32 6.240145 TGTGATTCAACTGATCCTGAATTGA 58.760 36.000 13.15 4.08 41.29 2.57
32 33 6.716173 TGTGATTCAACTGATCCTGAATTGAA 59.284 34.615 13.15 10.79 41.29 2.69
33 34 7.231115 TGTGATTCAACTGATCCTGAATTGAAA 59.769 33.333 13.15 1.34 41.29 2.69
34 35 8.248945 GTGATTCAACTGATCCTGAATTGAAAT 58.751 33.333 13.15 4.09 41.29 2.17
35 36 8.464404 TGATTCAACTGATCCTGAATTGAAATC 58.536 33.333 13.15 10.19 41.29 2.17
36 37 6.764308 TCAACTGATCCTGAATTGAAATCC 57.236 37.500 0.00 0.00 0.00 3.01
37 38 6.247676 TCAACTGATCCTGAATTGAAATCCA 58.752 36.000 0.00 0.00 0.00 3.41
38 39 6.376299 TCAACTGATCCTGAATTGAAATCCAG 59.624 38.462 0.00 0.00 0.00 3.86
39 40 5.198965 ACTGATCCTGAATTGAAATCCAGG 58.801 41.667 2.03 2.03 45.63 4.45
40 41 3.956199 TGATCCTGAATTGAAATCCAGGC 59.044 43.478 3.54 0.00 44.32 4.85
41 42 2.368439 TCCTGAATTGAAATCCAGGCG 58.632 47.619 3.54 0.00 44.32 5.52
42 43 1.406539 CCTGAATTGAAATCCAGGCGG 59.593 52.381 0.00 0.00 39.59 6.13
43 44 1.406539 CTGAATTGAAATCCAGGCGGG 59.593 52.381 0.00 0.00 38.37 6.13
44 45 0.103026 GAATTGAAATCCAGGCGGGC 59.897 55.000 0.00 0.00 36.21 6.13
45 46 0.324645 AATTGAAATCCAGGCGGGCT 60.325 50.000 0.00 0.00 36.21 5.19
46 47 0.550914 ATTGAAATCCAGGCGGGCTA 59.449 50.000 2.84 0.00 36.21 3.93
47 48 0.393808 TTGAAATCCAGGCGGGCTAC 60.394 55.000 2.84 0.00 36.21 3.58
48 49 1.271840 TGAAATCCAGGCGGGCTACT 61.272 55.000 2.84 0.00 36.21 2.57
49 50 0.815615 GAAATCCAGGCGGGCTACTG 60.816 60.000 2.84 0.00 36.21 2.74
50 51 1.271840 AAATCCAGGCGGGCTACTGA 61.272 55.000 2.84 1.83 36.86 3.41
51 52 1.972660 AATCCAGGCGGGCTACTGAC 61.973 60.000 2.84 0.00 36.86 3.51
52 53 4.162690 CCAGGCGGGCTACTGACC 62.163 72.222 2.84 0.00 36.86 4.02
53 54 3.077556 CAGGCGGGCTACTGACCT 61.078 66.667 2.84 0.00 39.94 3.85
54 55 2.760385 AGGCGGGCTACTGACCTC 60.760 66.667 0.56 0.00 39.94 3.85
55 56 2.760385 GGCGGGCTACTGACCTCT 60.760 66.667 0.00 0.00 39.94 3.69
56 57 1.455217 GGCGGGCTACTGACCTCTA 60.455 63.158 0.00 0.00 39.94 2.43
57 58 1.457009 GGCGGGCTACTGACCTCTAG 61.457 65.000 0.00 0.00 39.94 2.43
58 59 1.457009 GCGGGCTACTGACCTCTAGG 61.457 65.000 0.00 0.00 39.94 3.02
59 60 1.457009 CGGGCTACTGACCTCTAGGC 61.457 65.000 0.00 0.00 39.94 3.93
60 61 0.397254 GGGCTACTGACCTCTAGGCA 60.397 60.000 0.00 0.00 38.69 4.75
61 62 1.486211 GGCTACTGACCTCTAGGCAA 58.514 55.000 0.00 0.00 39.32 4.52
62 63 1.410882 GGCTACTGACCTCTAGGCAAG 59.589 57.143 0.00 0.00 39.32 4.01
63 64 2.379972 GCTACTGACCTCTAGGCAAGA 58.620 52.381 5.74 0.00 39.32 3.02
64 65 2.962421 GCTACTGACCTCTAGGCAAGAT 59.038 50.000 5.74 0.00 39.32 2.40
65 66 3.243704 GCTACTGACCTCTAGGCAAGATG 60.244 52.174 5.74 0.00 39.32 2.90
66 67 3.107402 ACTGACCTCTAGGCAAGATGA 57.893 47.619 5.74 0.00 39.32 2.92
67 68 3.445008 ACTGACCTCTAGGCAAGATGAA 58.555 45.455 5.74 0.00 39.32 2.57
68 69 3.840666 ACTGACCTCTAGGCAAGATGAAA 59.159 43.478 5.74 0.00 39.32 2.69
69 70 4.472833 ACTGACCTCTAGGCAAGATGAAAT 59.527 41.667 5.74 0.00 39.32 2.17
70 71 5.663106 ACTGACCTCTAGGCAAGATGAAATA 59.337 40.000 5.74 0.00 39.32 1.40
71 72 6.166984 TGACCTCTAGGCAAGATGAAATAG 57.833 41.667 0.00 0.00 39.32 1.73
72 73 5.663106 TGACCTCTAGGCAAGATGAAATAGT 59.337 40.000 0.00 0.00 39.32 2.12
73 74 6.839134 TGACCTCTAGGCAAGATGAAATAGTA 59.161 38.462 0.00 0.00 39.32 1.82
74 75 7.344612 TGACCTCTAGGCAAGATGAAATAGTAA 59.655 37.037 0.00 0.00 39.32 2.24
75 76 8.090788 ACCTCTAGGCAAGATGAAATAGTAAA 57.909 34.615 0.00 0.00 39.32 2.01
76 77 8.718656 ACCTCTAGGCAAGATGAAATAGTAAAT 58.281 33.333 0.00 0.00 39.32 1.40
77 78 8.997323 CCTCTAGGCAAGATGAAATAGTAAATG 58.003 37.037 0.00 0.00 32.41 2.32
78 79 8.908786 TCTAGGCAAGATGAAATAGTAAATGG 57.091 34.615 0.00 0.00 0.00 3.16
79 80 6.966534 AGGCAAGATGAAATAGTAAATGGG 57.033 37.500 0.00 0.00 0.00 4.00
80 81 6.672593 AGGCAAGATGAAATAGTAAATGGGA 58.327 36.000 0.00 0.00 0.00 4.37
81 82 6.774656 AGGCAAGATGAAATAGTAAATGGGAG 59.225 38.462 0.00 0.00 0.00 4.30
82 83 6.015940 GGCAAGATGAAATAGTAAATGGGAGG 60.016 42.308 0.00 0.00 0.00 4.30
83 84 6.772716 GCAAGATGAAATAGTAAATGGGAGGA 59.227 38.462 0.00 0.00 0.00 3.71
84 85 7.285401 GCAAGATGAAATAGTAAATGGGAGGAA 59.715 37.037 0.00 0.00 0.00 3.36
85 86 9.189156 CAAGATGAAATAGTAAATGGGAGGAAA 57.811 33.333 0.00 0.00 0.00 3.13
86 87 8.753497 AGATGAAATAGTAAATGGGAGGAAAC 57.247 34.615 0.00 0.00 0.00 2.78
87 88 7.780271 AGATGAAATAGTAAATGGGAGGAAACC 59.220 37.037 0.00 0.00 0.00 3.27
88 89 7.039722 TGAAATAGTAAATGGGAGGAAACCT 57.960 36.000 0.00 0.00 36.03 3.50
89 90 7.475299 TGAAATAGTAAATGGGAGGAAACCTT 58.525 34.615 0.00 0.00 31.76 3.50
90 91 8.616598 TGAAATAGTAAATGGGAGGAAACCTTA 58.383 33.333 0.00 0.00 31.76 2.69
91 92 9.642343 GAAATAGTAAATGGGAGGAAACCTTAT 57.358 33.333 0.00 0.00 31.76 1.73
92 93 8.996651 AATAGTAAATGGGAGGAAACCTTATG 57.003 34.615 0.00 0.00 31.76 1.90
93 94 5.201243 AGTAAATGGGAGGAAACCTTATGC 58.799 41.667 0.00 0.00 31.76 3.14
94 95 3.756082 AATGGGAGGAAACCTTATGCA 57.244 42.857 0.00 0.00 31.76 3.96
95 96 3.979501 ATGGGAGGAAACCTTATGCAT 57.020 42.857 3.79 3.79 31.76 3.96
96 97 3.756082 TGGGAGGAAACCTTATGCATT 57.244 42.857 3.54 0.00 31.76 3.56
97 98 4.059773 TGGGAGGAAACCTTATGCATTT 57.940 40.909 3.54 0.00 31.76 2.32
98 99 5.199982 TGGGAGGAAACCTTATGCATTTA 57.800 39.130 3.54 0.00 31.76 1.40
99 100 5.584913 TGGGAGGAAACCTTATGCATTTAA 58.415 37.500 3.54 0.00 31.76 1.52
100 101 6.201591 TGGGAGGAAACCTTATGCATTTAAT 58.798 36.000 3.54 0.00 31.76 1.40
101 102 7.358263 TGGGAGGAAACCTTATGCATTTAATA 58.642 34.615 3.54 0.00 31.76 0.98
102 103 8.010105 TGGGAGGAAACCTTATGCATTTAATAT 58.990 33.333 3.54 0.00 31.76 1.28
103 104 8.523658 GGGAGGAAACCTTATGCATTTAATATC 58.476 37.037 3.54 0.00 31.76 1.63
104 105 9.077885 GGAGGAAACCTTATGCATTTAATATCA 57.922 33.333 3.54 0.00 31.76 2.15
105 106 9.899226 GAGGAAACCTTATGCATTTAATATCAC 57.101 33.333 3.54 0.00 31.76 3.06
106 107 8.567948 AGGAAACCTTATGCATTTAATATCACG 58.432 33.333 3.54 0.00 0.00 4.35
107 108 8.564574 GGAAACCTTATGCATTTAATATCACGA 58.435 33.333 3.54 0.00 0.00 4.35
108 109 9.944663 GAAACCTTATGCATTTAATATCACGAA 57.055 29.630 3.54 0.00 0.00 3.85
109 110 9.950680 AAACCTTATGCATTTAATATCACGAAG 57.049 29.630 3.54 0.00 0.00 3.79
110 111 8.902540 ACCTTATGCATTTAATATCACGAAGA 57.097 30.769 3.54 0.00 0.00 2.87
111 112 9.337396 ACCTTATGCATTTAATATCACGAAGAA 57.663 29.630 3.54 0.00 0.00 2.52
112 113 9.817365 CCTTATGCATTTAATATCACGAAGAAG 57.183 33.333 3.54 0.00 0.00 2.85
116 117 7.355017 TGCATTTAATATCACGAAGAAGATGC 58.645 34.615 0.00 0.00 0.00 3.91
117 118 7.012232 TGCATTTAATATCACGAAGAAGATGCA 59.988 33.333 0.00 0.00 0.00 3.96
118 119 7.533222 GCATTTAATATCACGAAGAAGATGCAG 59.467 37.037 0.00 0.00 0.00 4.41
119 120 8.554528 CATTTAATATCACGAAGAAGATGCAGT 58.445 33.333 0.00 0.00 0.00 4.40
120 121 9.764363 ATTTAATATCACGAAGAAGATGCAGTA 57.236 29.630 0.00 0.00 0.00 2.74
121 122 9.594478 TTTAATATCACGAAGAAGATGCAGTAA 57.406 29.630 0.00 0.00 0.00 2.24
122 123 7.706281 AATATCACGAAGAAGATGCAGTAAG 57.294 36.000 0.00 0.00 0.00 2.34
123 124 4.783764 TCACGAAGAAGATGCAGTAAGA 57.216 40.909 0.00 0.00 0.00 2.10
124 125 5.134202 TCACGAAGAAGATGCAGTAAGAA 57.866 39.130 0.00 0.00 0.00 2.52
125 126 5.164233 TCACGAAGAAGATGCAGTAAGAAG 58.836 41.667 0.00 0.00 0.00 2.85
126 127 3.929610 ACGAAGAAGATGCAGTAAGAAGC 59.070 43.478 0.00 0.00 0.00 3.86
127 128 3.000277 CGAAGAAGATGCAGTAAGAAGCG 60.000 47.826 0.00 0.00 0.00 4.68
128 129 2.275318 AGAAGATGCAGTAAGAAGCGC 58.725 47.619 0.00 0.00 0.00 5.92
129 130 2.093764 AGAAGATGCAGTAAGAAGCGCT 60.094 45.455 2.64 2.64 0.00 5.92
130 131 1.933247 AGATGCAGTAAGAAGCGCTC 58.067 50.000 12.06 4.30 0.00 5.03
131 132 1.205655 AGATGCAGTAAGAAGCGCTCA 59.794 47.619 12.06 1.00 0.00 4.26
132 133 2.002586 GATGCAGTAAGAAGCGCTCAA 58.997 47.619 12.06 0.00 0.00 3.02
133 134 1.148310 TGCAGTAAGAAGCGCTCAAC 58.852 50.000 12.06 6.84 0.00 3.18
134 135 1.270305 TGCAGTAAGAAGCGCTCAACT 60.270 47.619 12.06 9.29 0.00 3.16
135 136 2.029380 TGCAGTAAGAAGCGCTCAACTA 60.029 45.455 12.06 0.00 0.00 2.24
136 137 2.600867 GCAGTAAGAAGCGCTCAACTAG 59.399 50.000 12.06 8.10 0.00 2.57
137 138 3.839293 CAGTAAGAAGCGCTCAACTAGT 58.161 45.455 12.06 0.04 0.00 2.57
213 216 1.969064 CCGACGGTTGGGCATTTGA 60.969 57.895 5.48 0.00 0.00 2.69
248 251 3.906720 TTTACATCTAGGGTGGTCAGC 57.093 47.619 0.00 0.00 0.00 4.26
255 258 1.556911 CTAGGGTGGTCAGCTGATGTT 59.443 52.381 21.47 5.61 0.00 2.71
257 260 1.145738 AGGGTGGTCAGCTGATGTTTT 59.854 47.619 21.47 1.69 0.00 2.43
313 340 6.748333 ACACATCTTCATCATTCGTTTCAT 57.252 33.333 0.00 0.00 0.00 2.57
314 341 7.149569 ACACATCTTCATCATTCGTTTCATT 57.850 32.000 0.00 0.00 0.00 2.57
315 342 7.246311 ACACATCTTCATCATTCGTTTCATTC 58.754 34.615 0.00 0.00 0.00 2.67
316 343 7.094677 ACACATCTTCATCATTCGTTTCATTCA 60.095 33.333 0.00 0.00 0.00 2.57
362 389 9.689976 CCAAATGATGCATATTTCGGTTATTTA 57.310 29.630 0.00 0.00 0.00 1.40
384 411 9.973450 ATTTATACATCTACATCATCTATCGGC 57.027 33.333 0.00 0.00 0.00 5.54
385 412 4.727507 ACATCTACATCATCTATCGGCC 57.272 45.455 0.00 0.00 0.00 6.13
394 421 3.506398 TCATCTATCGGCCATGGAACTA 58.494 45.455 18.40 0.00 0.00 2.24
400 427 1.140852 TCGGCCATGGAACTATGAAGG 59.859 52.381 18.40 0.00 0.00 3.46
422 449 5.420104 AGGGATGAAAACCAAAGCTAATGAG 59.580 40.000 1.14 0.00 0.00 2.90
427 454 6.503524 TGAAAACCAAAGCTAATGAGTTGAC 58.496 36.000 1.14 3.76 0.00 3.18
453 487 1.826054 TTTGTGCTCCCAACCACCG 60.826 57.895 0.00 0.00 0.00 4.94
496 570 2.013400 ACGCATGACTCACACAAACAA 58.987 42.857 0.00 0.00 0.00 2.83
566 644 2.106683 CGTTGATCCTTCGCCACCC 61.107 63.158 0.00 0.00 0.00 4.61
568 646 0.322546 GTTGATCCTTCGCCACCCTT 60.323 55.000 0.00 0.00 0.00 3.95
569 647 0.035439 TTGATCCTTCGCCACCCTTC 60.035 55.000 0.00 0.00 0.00 3.46
570 648 0.909610 TGATCCTTCGCCACCCTTCT 60.910 55.000 0.00 0.00 0.00 2.85
571 649 0.179070 GATCCTTCGCCACCCTTCTC 60.179 60.000 0.00 0.00 0.00 2.87
606 684 1.519455 CTAGCTAGCCACGGCACAC 60.519 63.158 12.13 0.00 44.88 3.82
634 712 1.740025 CATCTTCTCGCCCACTTTTCC 59.260 52.381 0.00 0.00 0.00 3.13
671 753 0.112412 ACCATCGGCCAAGTCCTTTT 59.888 50.000 2.24 0.00 0.00 2.27
672 754 0.811281 CCATCGGCCAAGTCCTTTTC 59.189 55.000 2.24 0.00 0.00 2.29
673 755 0.811281 CATCGGCCAAGTCCTTTTCC 59.189 55.000 2.24 0.00 0.00 3.13
674 756 0.698818 ATCGGCCAAGTCCTTTTCCT 59.301 50.000 2.24 0.00 0.00 3.36
675 757 1.354101 TCGGCCAAGTCCTTTTCCTA 58.646 50.000 2.24 0.00 0.00 2.94
676 758 1.913419 TCGGCCAAGTCCTTTTCCTAT 59.087 47.619 2.24 0.00 0.00 2.57
677 759 2.093128 TCGGCCAAGTCCTTTTCCTATC 60.093 50.000 2.24 0.00 0.00 2.08
678 760 2.656002 GGCCAAGTCCTTTTCCTATCC 58.344 52.381 0.00 0.00 0.00 2.59
679 761 2.242452 GGCCAAGTCCTTTTCCTATCCT 59.758 50.000 0.00 0.00 0.00 3.24
680 762 3.458487 GGCCAAGTCCTTTTCCTATCCTA 59.542 47.826 0.00 0.00 0.00 2.94
681 763 4.452825 GCCAAGTCCTTTTCCTATCCTAC 58.547 47.826 0.00 0.00 0.00 3.18
732 816 3.756677 CGCACGCGACACACAGAG 61.757 66.667 15.93 0.00 42.83 3.35
935 1030 2.415983 TCACTCCCCTCTTTTCCTCA 57.584 50.000 0.00 0.00 0.00 3.86
953 1048 4.796231 CTCGCCGTTCCCCGTGAG 62.796 72.222 0.00 0.00 32.95 3.51
971 1066 0.035630 AGGTGACTGGCAGATTGCTC 60.036 55.000 23.66 8.38 44.28 4.26
1179 1276 4.036262 TGTTTTGATTTCTGTCTTCCCGTG 59.964 41.667 0.00 0.00 0.00 4.94
1181 1278 1.087501 GATTTCTGTCTTCCCGTGGC 58.912 55.000 0.00 0.00 0.00 5.01
1372 1469 2.739671 GCGGTCGGTACCCAACAC 60.740 66.667 6.25 0.00 43.54 3.32
1386 1484 3.076785 ACCCAACACCATCCCAATTCTTA 59.923 43.478 0.00 0.00 0.00 2.10
1462 2212 4.164294 GCAATTCATGTGCTTCTCTGTTC 58.836 43.478 0.00 0.00 39.00 3.18
1512 2355 7.117236 AGATACAAATCTCAAAACGCTAAACGA 59.883 33.333 0.00 0.00 40.62 3.85
1527 2370 0.663153 AACGAAGTGAACTTGGCAGC 59.337 50.000 0.00 0.00 45.00 5.25
1533 2376 0.031178 GTGAACTTGGCAGCACTTGG 59.969 55.000 0.00 0.00 0.00 3.61
1546 2389 2.985896 GCACTTGGCAGAACCTGTATA 58.014 47.619 0.00 0.00 43.97 1.47
1675 2523 2.751259 TGCTCTGCTTTTTAGCTGATGG 59.249 45.455 0.00 0.00 40.88 3.51
1818 2670 6.713762 TTGACAGACAATTGATGGTTTTCT 57.286 33.333 13.59 0.00 33.18 2.52
1852 2704 5.894393 TCACAATTTCCCAAACTAACTGGAA 59.106 36.000 0.00 0.00 35.85 3.53
1873 2725 5.008415 GGAAGTATCCAAATCATGTGAGCTG 59.992 44.000 0.00 0.00 45.79 4.24
1904 2756 8.233190 GCAGGATCAGTTCAAATGCTTATATAC 58.767 37.037 0.00 0.00 31.05 1.47
2169 3024 6.269940 GAGGATCAAGAAGGCAAAGAACCTT 61.270 44.000 0.00 0.00 42.51 3.50
2184 3039 1.055040 ACCTTGAGCTGCTTCTCACT 58.945 50.000 2.53 0.00 42.27 3.41
2196 3051 1.280133 CTTCTCACTGCTGGGATTGGA 59.720 52.381 0.00 0.00 0.00 3.53
2334 3189 1.003696 AGGAACTTCTTGCCTGGCTAC 59.996 52.381 21.03 0.00 27.25 3.58
2586 3441 6.237154 TCCAAAGTGTGATGTCATTGTGATA 58.763 36.000 0.00 0.00 0.00 2.15
2656 3583 9.681062 TCGGTTCTTTTCCATTATCTTCTAATT 57.319 29.630 0.00 0.00 0.00 1.40
2744 3671 8.031277 GCAAAGATGAAGAAAGGTGTAATCATT 58.969 33.333 0.00 0.00 0.00 2.57
3023 3951 6.823689 AGTACTCAATAATGCCAGTTTGTAGG 59.176 38.462 0.00 0.00 0.00 3.18
3404 4341 1.464608 CATTGGGCTTATGGCGTATCG 59.535 52.381 0.00 0.00 42.94 2.92
3434 4371 1.732259 GCACTTGGTGTTCTGATACCG 59.268 52.381 7.00 0.00 39.73 4.02
3435 4372 2.346803 CACTTGGTGTTCTGATACCGG 58.653 52.381 0.00 0.00 39.73 5.28
3445 4382 0.671796 CTGATACCGGACCGTATGCA 59.328 55.000 9.46 4.95 0.00 3.96
3449 4388 3.057104 TGATACCGGACCGTATGCATTAG 60.057 47.826 9.46 0.00 0.00 1.73
3475 4418 5.446143 AGCTATGGACGAATTCTAGTCAG 57.554 43.478 13.38 5.74 39.01 3.51
3548 4701 7.148171 CCTTTCCTTCATAAGTGGAGAATCAAC 60.148 40.741 0.00 0.00 40.19 3.18
3559 4712 8.649973 AAGTGGAGAATCAACGAATAATCTAC 57.350 34.615 0.00 0.00 46.19 2.59
3571 4724 8.390354 CAACGAATAATCTACATCAAGAGCAAA 58.610 33.333 0.00 0.00 0.00 3.68
3594 4748 8.818057 CAAATACATACAACTAAGACAGTAGGC 58.182 37.037 0.00 0.00 36.04 3.93
3651 4996 8.995027 ATCAGTTTATGCCTGTTTATCCATTA 57.005 30.769 0.00 0.00 0.00 1.90
3655 5000 3.637911 TGCCTGTTTATCCATTACCGT 57.362 42.857 0.00 0.00 0.00 4.83
3672 5017 1.502231 CGTGCTTTGCTACTGACTGT 58.498 50.000 0.00 0.00 0.00 3.55
3675 5020 1.694150 TGCTTTGCTACTGACTGTCCT 59.306 47.619 5.17 0.00 0.00 3.85
3915 5268 6.997655 TGTTGTATGAGTGTTCTCTGAGAAT 58.002 36.000 21.86 7.50 40.98 2.40
3935 5288 5.240183 AGAATGGAAATAATGGATGTCTGCG 59.760 40.000 0.00 0.00 0.00 5.18
4022 5375 9.218359 GTGTGTACTGCTAGTTTTTCTTTTTAC 57.782 33.333 0.00 0.00 0.00 2.01
4023 5376 9.169592 TGTGTACTGCTAGTTTTTCTTTTTACT 57.830 29.630 0.00 0.00 0.00 2.24
4103 5476 3.509388 GGTAACTGACCGGACACAG 57.491 57.895 9.46 16.75 38.87 3.66
4108 5481 2.457366 ACTGACCGGACACAGAATTC 57.543 50.000 25.20 0.00 37.54 2.17
4109 5482 1.971357 ACTGACCGGACACAGAATTCT 59.029 47.619 25.20 0.88 37.54 2.40
4172 5545 0.986019 ACCGGCAACTCCCATATCCA 60.986 55.000 0.00 0.00 0.00 3.41
4173 5546 0.401738 CCGGCAACTCCCATATCCAT 59.598 55.000 0.00 0.00 0.00 3.41
4181 5555 5.132648 GCAACTCCCATATCCATCCCATATA 59.867 44.000 0.00 0.00 0.00 0.86
4217 5591 3.903783 CGCCATGTCGGATTTGGT 58.096 55.556 9.90 0.00 36.56 3.67
4239 5613 2.690510 TGTGGCCCATCCGATCCA 60.691 61.111 0.00 0.00 37.80 3.41
4322 5696 3.261897 ACTCACTTCCCACAGTATCCAAG 59.738 47.826 0.00 0.00 0.00 3.61
4340 5714 2.802106 CTCCTCTCCGGCGAGTTC 59.198 66.667 19.70 0.00 37.40 3.01
4379 5753 3.474570 GCACTGGATCCGGCTCCT 61.475 66.667 24.23 2.92 36.20 3.69
4384 5758 1.711375 ACTGGATCCGGCTCCTAGATA 59.289 52.381 24.23 3.56 36.20 1.98
4405 5779 0.978146 CTGGATCCGAGGACTGGGTT 60.978 60.000 7.39 0.00 0.00 4.11
4437 5811 0.927767 AGTCCCGAGGAGTAGATGGT 59.072 55.000 0.00 0.00 32.96 3.55
4442 5816 1.475392 CCGAGGAGTAGATGGTCGTCT 60.475 57.143 0.00 0.00 0.00 4.18
4443 5817 1.600013 CGAGGAGTAGATGGTCGTCTG 59.400 57.143 3.16 0.00 0.00 3.51
4444 5818 2.645802 GAGGAGTAGATGGTCGTCTGT 58.354 52.381 3.16 0.00 0.00 3.41
4445 5819 2.356382 GAGGAGTAGATGGTCGTCTGTG 59.644 54.545 3.16 0.00 0.00 3.66
4493 5869 0.614697 TCCTCCTGCGGTCTTCATCA 60.615 55.000 0.00 0.00 0.00 3.07
4497 5873 1.833630 TCCTGCGGTCTTCATCAATCT 59.166 47.619 0.00 0.00 0.00 2.40
4507 5883 5.444176 GTCTTCATCAATCTGGAGGGATTT 58.556 41.667 0.00 0.00 34.15 2.17
4522 5898 0.954452 GATTTCATTGGGCGCTAGGG 59.046 55.000 7.64 1.65 0.00 3.53
4534 5910 0.108329 CGCTAGGGTTCCGTTGATGT 60.108 55.000 0.00 0.00 0.00 3.06
4558 5935 2.093711 TGTCATGAGCTTAAGCCGCTTA 60.094 45.455 23.71 8.84 43.38 3.09
4579 5958 0.820871 ACCCTTGTTTGCGCTTCAAA 59.179 45.000 9.73 0.00 42.01 2.69
4629 6008 1.376037 GTCTCCTCAAGGTTGGCGG 60.376 63.158 0.00 0.00 36.34 6.13
4656 6035 2.414293 GCGAGTAAAGCTTCGAGAGTGA 60.414 50.000 9.64 0.00 0.00 3.41
4661 6040 5.646606 AGTAAAGCTTCGAGAGTGATCTTC 58.353 41.667 0.00 0.00 0.00 2.87
4700 6079 5.114785 TCTTCTCTATCTGCATAAGACGC 57.885 43.478 0.00 0.00 37.88 5.19
4701 6080 4.580580 TCTTCTCTATCTGCATAAGACGCA 59.419 41.667 0.00 0.00 37.88 5.24
4711 6090 2.645163 CATAAGACGCACACGCAAAAA 58.355 42.857 0.00 0.00 45.53 1.94
4735 6114 5.244626 AGTGAGGTGAATAAGCAAAGCATTT 59.755 36.000 0.00 0.00 40.26 2.32
4762 6141 4.500265 GCCTCAAGTTTCCTGGCA 57.500 55.556 0.00 0.00 42.79 4.92
4770 6149 3.960102 TCAAGTTTCCTGGCATGTTCTTT 59.040 39.130 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.076781 TCAGGATCAGTTGAATCACAATTAAAA 57.923 29.630 0.00 0.00 40.76 1.52
1 2 8.634335 TCAGGATCAGTTGAATCACAATTAAA 57.366 30.769 0.00 0.00 40.76 1.52
2 3 8.634335 TTCAGGATCAGTTGAATCACAATTAA 57.366 30.769 0.00 0.00 40.76 1.40
3 4 8.812513 ATTCAGGATCAGTTGAATCACAATTA 57.187 30.769 11.40 0.00 39.20 1.40
4 5 7.713734 ATTCAGGATCAGTTGAATCACAATT 57.286 32.000 11.40 0.00 39.20 2.32
5 6 7.395206 TCAATTCAGGATCAGTTGAATCACAAT 59.605 33.333 15.40 2.75 41.76 2.71
6 7 6.716173 TCAATTCAGGATCAGTTGAATCACAA 59.284 34.615 15.40 0.00 41.76 3.33
7 8 6.240145 TCAATTCAGGATCAGTTGAATCACA 58.760 36.000 15.40 4.95 41.76 3.58
8 9 6.748333 TCAATTCAGGATCAGTTGAATCAC 57.252 37.500 15.40 0.00 41.76 3.06
9 10 7.764141 TTTCAATTCAGGATCAGTTGAATCA 57.236 32.000 15.40 6.91 41.76 2.57
10 11 7.919621 GGATTTCAATTCAGGATCAGTTGAATC 59.080 37.037 15.40 9.53 41.76 2.52
11 12 7.398047 TGGATTTCAATTCAGGATCAGTTGAAT 59.602 33.333 11.40 11.40 43.79 2.57
12 13 6.720748 TGGATTTCAATTCAGGATCAGTTGAA 59.279 34.615 8.41 8.41 37.11 2.69
13 14 6.247676 TGGATTTCAATTCAGGATCAGTTGA 58.752 36.000 0.00 0.00 0.00 3.18
14 15 6.519679 TGGATTTCAATTCAGGATCAGTTG 57.480 37.500 0.00 0.00 0.00 3.16
15 16 6.770746 CTGGATTTCAATTCAGGATCAGTT 57.229 37.500 0.25 0.00 38.19 3.16
23 24 1.406539 CCCGCCTGGATTTCAATTCAG 59.593 52.381 0.00 1.19 40.95 3.02
24 25 1.473258 CCCGCCTGGATTTCAATTCA 58.527 50.000 0.00 0.00 37.49 2.57
25 26 0.103026 GCCCGCCTGGATTTCAATTC 59.897 55.000 0.00 0.00 37.49 2.17
26 27 0.324645 AGCCCGCCTGGATTTCAATT 60.325 50.000 0.00 0.00 37.49 2.32
27 28 0.550914 TAGCCCGCCTGGATTTCAAT 59.449 50.000 0.00 0.00 37.49 2.57
28 29 0.393808 GTAGCCCGCCTGGATTTCAA 60.394 55.000 0.00 0.00 37.49 2.69
29 30 1.223487 GTAGCCCGCCTGGATTTCA 59.777 57.895 0.00 0.00 37.49 2.69
30 31 0.815615 CAGTAGCCCGCCTGGATTTC 60.816 60.000 0.00 0.00 37.49 2.17
31 32 1.224592 CAGTAGCCCGCCTGGATTT 59.775 57.895 0.00 0.00 37.49 2.17
32 33 1.689233 TCAGTAGCCCGCCTGGATT 60.689 57.895 0.00 0.00 37.49 3.01
33 34 2.041922 TCAGTAGCCCGCCTGGAT 60.042 61.111 0.00 0.00 37.49 3.41
34 35 3.075005 GTCAGTAGCCCGCCTGGA 61.075 66.667 0.00 0.00 37.49 3.86
35 36 4.162690 GGTCAGTAGCCCGCCTGG 62.163 72.222 0.00 0.00 37.09 4.45
36 37 3.077556 AGGTCAGTAGCCCGCCTG 61.078 66.667 0.00 0.00 0.00 4.85
37 38 1.934459 TAGAGGTCAGTAGCCCGCCT 61.934 60.000 0.00 0.00 0.00 5.52
38 39 1.455217 TAGAGGTCAGTAGCCCGCC 60.455 63.158 0.00 0.00 0.00 6.13
39 40 1.457009 CCTAGAGGTCAGTAGCCCGC 61.457 65.000 0.00 0.00 0.00 6.13
40 41 1.457009 GCCTAGAGGTCAGTAGCCCG 61.457 65.000 0.00 0.00 37.57 6.13
41 42 0.397254 TGCCTAGAGGTCAGTAGCCC 60.397 60.000 0.00 0.00 37.57 5.19
42 43 1.410882 CTTGCCTAGAGGTCAGTAGCC 59.589 57.143 0.00 0.00 37.57 3.93
43 44 2.379972 TCTTGCCTAGAGGTCAGTAGC 58.620 52.381 0.00 0.00 37.57 3.58
44 45 4.211125 TCATCTTGCCTAGAGGTCAGTAG 58.789 47.826 0.00 0.00 36.12 2.57
45 46 4.251103 TCATCTTGCCTAGAGGTCAGTA 57.749 45.455 0.00 0.00 36.12 2.74
46 47 3.107402 TCATCTTGCCTAGAGGTCAGT 57.893 47.619 0.00 0.00 36.12 3.41
47 48 4.478206 TTTCATCTTGCCTAGAGGTCAG 57.522 45.455 0.00 0.00 36.12 3.51
48 49 5.663106 ACTATTTCATCTTGCCTAGAGGTCA 59.337 40.000 0.00 0.00 36.12 4.02
49 50 6.168270 ACTATTTCATCTTGCCTAGAGGTC 57.832 41.667 0.00 0.00 36.12 3.85
50 51 7.676683 TTACTATTTCATCTTGCCTAGAGGT 57.323 36.000 0.00 0.00 36.12 3.85
51 52 8.997323 CATTTACTATTTCATCTTGCCTAGAGG 58.003 37.037 0.00 0.00 36.02 3.69
52 53 8.997323 CCATTTACTATTTCATCTTGCCTAGAG 58.003 37.037 0.00 0.00 36.02 2.43
53 54 7.939039 CCCATTTACTATTTCATCTTGCCTAGA 59.061 37.037 0.00 0.00 37.28 2.43
54 55 7.939039 TCCCATTTACTATTTCATCTTGCCTAG 59.061 37.037 0.00 0.00 0.00 3.02
55 56 7.811282 TCCCATTTACTATTTCATCTTGCCTA 58.189 34.615 0.00 0.00 0.00 3.93
56 57 6.672593 TCCCATTTACTATTTCATCTTGCCT 58.327 36.000 0.00 0.00 0.00 4.75
57 58 6.015940 CCTCCCATTTACTATTTCATCTTGCC 60.016 42.308 0.00 0.00 0.00 4.52
58 59 6.772716 TCCTCCCATTTACTATTTCATCTTGC 59.227 38.462 0.00 0.00 0.00 4.01
59 60 8.752005 TTCCTCCCATTTACTATTTCATCTTG 57.248 34.615 0.00 0.00 0.00 3.02
60 61 9.190317 GTTTCCTCCCATTTACTATTTCATCTT 57.810 33.333 0.00 0.00 0.00 2.40
61 62 7.780271 GGTTTCCTCCCATTTACTATTTCATCT 59.220 37.037 0.00 0.00 0.00 2.90
62 63 7.780271 AGGTTTCCTCCCATTTACTATTTCATC 59.220 37.037 0.00 0.00 0.00 2.92
63 64 7.652554 AGGTTTCCTCCCATTTACTATTTCAT 58.347 34.615 0.00 0.00 0.00 2.57
64 65 7.039722 AGGTTTCCTCCCATTTACTATTTCA 57.960 36.000 0.00 0.00 0.00 2.69
65 66 7.956328 AAGGTTTCCTCCCATTTACTATTTC 57.044 36.000 0.00 0.00 30.89 2.17
66 67 9.421399 CATAAGGTTTCCTCCCATTTACTATTT 57.579 33.333 0.00 0.00 30.89 1.40
67 68 7.505923 GCATAAGGTTTCCTCCCATTTACTATT 59.494 37.037 0.00 0.00 30.89 1.73
68 69 7.004691 GCATAAGGTTTCCTCCCATTTACTAT 58.995 38.462 0.00 0.00 30.89 2.12
69 70 6.069323 TGCATAAGGTTTCCTCCCATTTACTA 60.069 38.462 0.00 0.00 30.89 1.82
70 71 5.201243 GCATAAGGTTTCCTCCCATTTACT 58.799 41.667 0.00 0.00 30.89 2.24
71 72 4.953579 TGCATAAGGTTTCCTCCCATTTAC 59.046 41.667 0.00 0.00 30.89 2.01
72 73 5.199982 TGCATAAGGTTTCCTCCCATTTA 57.800 39.130 0.00 0.00 30.89 1.40
73 74 4.059773 TGCATAAGGTTTCCTCCCATTT 57.940 40.909 0.00 0.00 30.89 2.32
74 75 3.756082 TGCATAAGGTTTCCTCCCATT 57.244 42.857 0.00 0.00 30.89 3.16
75 76 3.979501 ATGCATAAGGTTTCCTCCCAT 57.020 42.857 0.00 0.00 30.89 4.00
76 77 3.756082 AATGCATAAGGTTTCCTCCCA 57.244 42.857 0.00 0.00 30.89 4.37
77 78 6.731292 ATTAAATGCATAAGGTTTCCTCCC 57.269 37.500 0.00 0.00 30.89 4.30
78 79 9.077885 TGATATTAAATGCATAAGGTTTCCTCC 57.922 33.333 0.00 0.00 30.89 4.30
79 80 9.899226 GTGATATTAAATGCATAAGGTTTCCTC 57.101 33.333 0.00 0.00 30.89 3.71
80 81 8.567948 CGTGATATTAAATGCATAAGGTTTCCT 58.432 33.333 0.00 0.00 33.87 3.36
81 82 8.564574 TCGTGATATTAAATGCATAAGGTTTCC 58.435 33.333 0.00 0.00 0.00 3.13
82 83 9.944663 TTCGTGATATTAAATGCATAAGGTTTC 57.055 29.630 0.00 0.00 0.00 2.78
83 84 9.950680 CTTCGTGATATTAAATGCATAAGGTTT 57.049 29.630 0.00 0.00 0.00 3.27
84 85 9.337396 TCTTCGTGATATTAAATGCATAAGGTT 57.663 29.630 0.00 0.00 0.00 3.50
85 86 8.902540 TCTTCGTGATATTAAATGCATAAGGT 57.097 30.769 0.00 0.00 0.00 3.50
86 87 9.817365 CTTCTTCGTGATATTAAATGCATAAGG 57.183 33.333 0.00 0.00 0.00 2.69
90 91 8.019669 GCATCTTCTTCGTGATATTAAATGCAT 58.980 33.333 0.00 0.00 35.79 3.96
91 92 7.012232 TGCATCTTCTTCGTGATATTAAATGCA 59.988 33.333 0.00 0.00 41.41 3.96
92 93 7.355017 TGCATCTTCTTCGTGATATTAAATGC 58.645 34.615 0.00 0.00 36.16 3.56
93 94 8.554528 ACTGCATCTTCTTCGTGATATTAAATG 58.445 33.333 0.00 0.00 0.00 2.32
94 95 8.668510 ACTGCATCTTCTTCGTGATATTAAAT 57.331 30.769 0.00 0.00 0.00 1.40
95 96 9.594478 TTACTGCATCTTCTTCGTGATATTAAA 57.406 29.630 0.00 0.00 0.00 1.52
96 97 9.249457 CTTACTGCATCTTCTTCGTGATATTAA 57.751 33.333 0.00 0.00 0.00 1.40
97 98 8.630037 TCTTACTGCATCTTCTTCGTGATATTA 58.370 33.333 0.00 0.00 0.00 0.98
98 99 7.492524 TCTTACTGCATCTTCTTCGTGATATT 58.507 34.615 0.00 0.00 0.00 1.28
99 100 7.043961 TCTTACTGCATCTTCTTCGTGATAT 57.956 36.000 0.00 0.00 0.00 1.63
100 101 6.451064 TCTTACTGCATCTTCTTCGTGATA 57.549 37.500 0.00 0.00 0.00 2.15
101 102 5.330455 TCTTACTGCATCTTCTTCGTGAT 57.670 39.130 0.00 0.00 0.00 3.06
102 103 4.783764 TCTTACTGCATCTTCTTCGTGA 57.216 40.909 0.00 0.00 0.00 4.35
103 104 4.201666 GCTTCTTACTGCATCTTCTTCGTG 60.202 45.833 0.00 0.00 0.00 4.35
104 105 3.929610 GCTTCTTACTGCATCTTCTTCGT 59.070 43.478 0.00 0.00 0.00 3.85
105 106 3.000277 CGCTTCTTACTGCATCTTCTTCG 60.000 47.826 0.00 0.00 0.00 3.79
106 107 3.242252 GCGCTTCTTACTGCATCTTCTTC 60.242 47.826 0.00 0.00 0.00 2.87
107 108 2.675348 GCGCTTCTTACTGCATCTTCTT 59.325 45.455 0.00 0.00 0.00 2.52
108 109 2.093764 AGCGCTTCTTACTGCATCTTCT 60.094 45.455 2.64 0.00 0.00 2.85
109 110 2.275318 AGCGCTTCTTACTGCATCTTC 58.725 47.619 2.64 0.00 0.00 2.87
110 111 2.275318 GAGCGCTTCTTACTGCATCTT 58.725 47.619 13.26 0.00 0.00 2.40
111 112 1.205655 TGAGCGCTTCTTACTGCATCT 59.794 47.619 13.26 0.00 0.00 2.90
112 113 1.645034 TGAGCGCTTCTTACTGCATC 58.355 50.000 13.26 0.00 0.00 3.91
113 114 1.734465 GTTGAGCGCTTCTTACTGCAT 59.266 47.619 13.26 0.00 0.00 3.96
114 115 1.148310 GTTGAGCGCTTCTTACTGCA 58.852 50.000 13.26 0.00 0.00 4.41
115 116 1.433534 AGTTGAGCGCTTCTTACTGC 58.566 50.000 13.26 0.00 0.00 4.40
116 117 3.839293 ACTAGTTGAGCGCTTCTTACTG 58.161 45.455 13.26 9.84 0.00 2.74
117 118 4.238514 CAACTAGTTGAGCGCTTCTTACT 58.761 43.478 28.17 14.82 42.93 2.24
118 119 3.181529 GCAACTAGTTGAGCGCTTCTTAC 60.182 47.826 34.43 11.81 42.93 2.34
119 120 2.993899 GCAACTAGTTGAGCGCTTCTTA 59.006 45.455 34.43 1.38 42.93 2.10
120 121 1.801178 GCAACTAGTTGAGCGCTTCTT 59.199 47.619 34.43 0.02 42.93 2.52
121 122 1.433534 GCAACTAGTTGAGCGCTTCT 58.566 50.000 34.43 13.37 42.93 2.85
122 123 0.093705 CGCAACTAGTTGAGCGCTTC 59.906 55.000 34.43 16.29 43.80 3.86
123 124 2.153913 CGCAACTAGTTGAGCGCTT 58.846 52.632 34.43 0.00 43.80 4.68
124 125 3.862124 CGCAACTAGTTGAGCGCT 58.138 55.556 34.43 11.27 43.80 5.92
127 128 0.741221 CCCTCCGCAACTAGTTGAGC 60.741 60.000 34.43 21.11 42.93 4.26
128 129 0.895530 TCCCTCCGCAACTAGTTGAG 59.104 55.000 34.43 30.51 42.93 3.02
129 130 0.606604 GTCCCTCCGCAACTAGTTGA 59.393 55.000 34.43 16.05 42.93 3.18
130 131 0.736325 CGTCCCTCCGCAACTAGTTG 60.736 60.000 27.85 27.85 43.14 3.16
131 132 1.590147 CGTCCCTCCGCAACTAGTT 59.410 57.895 1.12 1.12 0.00 2.24
132 133 3.285371 CGTCCCTCCGCAACTAGT 58.715 61.111 0.00 0.00 0.00 2.57
187 190 2.580601 CCAACCGTCGGTTCCTCCT 61.581 63.158 26.61 1.95 43.05 3.69
197 200 1.595093 CCCTCAAATGCCCAACCGTC 61.595 60.000 0.00 0.00 0.00 4.79
213 216 1.493022 TGTAAAACTGACAGCCACCCT 59.507 47.619 1.25 0.00 0.00 4.34
298 325 6.598850 TCTCCAATGAATGAAACGAATGATGA 59.401 34.615 0.00 0.00 0.00 2.92
311 338 7.133891 ACTAAAAACGTCTCTCCAATGAATG 57.866 36.000 0.00 0.00 0.00 2.67
313 340 5.699458 GGACTAAAAACGTCTCTCCAATGAA 59.301 40.000 0.00 0.00 0.00 2.57
314 341 5.221561 TGGACTAAAAACGTCTCTCCAATGA 60.222 40.000 0.00 0.00 0.00 2.57
315 342 4.994852 TGGACTAAAAACGTCTCTCCAATG 59.005 41.667 0.00 0.00 0.00 2.82
316 343 5.223449 TGGACTAAAAACGTCTCTCCAAT 57.777 39.130 0.00 0.00 0.00 3.16
362 389 5.893824 TGGCCGATAGATGATGTAGATGTAT 59.106 40.000 0.00 0.00 39.76 2.29
381 408 1.597742 CCTTCATAGTTCCATGGCCG 58.402 55.000 6.96 0.00 0.00 6.13
384 411 4.712051 TCATCCCTTCATAGTTCCATGG 57.288 45.455 4.97 4.97 0.00 3.66
385 412 6.183360 GGTTTTCATCCCTTCATAGTTCCATG 60.183 42.308 0.00 0.00 0.00 3.66
394 421 4.162651 AGCTTTGGTTTTCATCCCTTCAT 58.837 39.130 0.00 0.00 0.00 2.57
400 427 6.272822 ACTCATTAGCTTTGGTTTTCATCC 57.727 37.500 0.00 0.00 0.00 3.51
422 449 3.695816 GAGCACAAACTCCTTTGTCAAC 58.304 45.455 0.00 0.00 45.81 3.18
453 487 1.524849 GATCTTCAAGCGGGGGAGC 60.525 63.158 0.00 0.00 37.41 4.70
496 570 1.899437 TTTCTTGCCGCCTCGAGGAT 61.899 55.000 35.69 0.00 37.39 3.24
606 684 1.493950 GGCGAGAAGATGCCGTGATG 61.494 60.000 0.00 0.00 42.22 3.07
634 712 1.512926 GTGCCAGTAGTTGTCCACTG 58.487 55.000 0.00 0.00 41.51 3.66
661 743 5.663556 AGGAGTAGGATAGGAAAAGGACTTG 59.336 44.000 0.00 0.00 0.00 3.16
662 744 5.855988 AGGAGTAGGATAGGAAAAGGACTT 58.144 41.667 0.00 0.00 0.00 3.01
671 753 4.730392 TGTTCTGGTAGGAGTAGGATAGGA 59.270 45.833 0.00 0.00 0.00 2.94
672 754 5.063017 TGTTCTGGTAGGAGTAGGATAGG 57.937 47.826 0.00 0.00 0.00 2.57
673 755 7.419711 TTTTGTTCTGGTAGGAGTAGGATAG 57.580 40.000 0.00 0.00 0.00 2.08
674 756 6.127140 GCTTTTGTTCTGGTAGGAGTAGGATA 60.127 42.308 0.00 0.00 0.00 2.59
675 757 5.338463 GCTTTTGTTCTGGTAGGAGTAGGAT 60.338 44.000 0.00 0.00 0.00 3.24
676 758 4.020485 GCTTTTGTTCTGGTAGGAGTAGGA 60.020 45.833 0.00 0.00 0.00 2.94
677 759 4.254492 GCTTTTGTTCTGGTAGGAGTAGG 58.746 47.826 0.00 0.00 0.00 3.18
678 760 4.254492 GGCTTTTGTTCTGGTAGGAGTAG 58.746 47.826 0.00 0.00 0.00 2.57
679 761 3.649023 TGGCTTTTGTTCTGGTAGGAGTA 59.351 43.478 0.00 0.00 0.00 2.59
680 762 2.441750 TGGCTTTTGTTCTGGTAGGAGT 59.558 45.455 0.00 0.00 0.00 3.85
681 763 3.140325 TGGCTTTTGTTCTGGTAGGAG 57.860 47.619 0.00 0.00 0.00 3.69
842 926 4.314440 GCTGACAGGTGGACCGCA 62.314 66.667 7.48 0.00 42.08 5.69
953 1048 1.028868 GGAGCAATCTGCCAGTCACC 61.029 60.000 0.00 0.00 46.52 4.02
958 1053 1.153005 GGGAGGAGCAATCTGCCAG 60.153 63.158 6.63 0.00 46.52 4.85
1420 1520 8.447787 AATTGCATTACAGAATCGTTAACAAC 57.552 30.769 6.39 0.00 0.00 3.32
1512 2355 1.406539 CAAGTGCTGCCAAGTTCACTT 59.593 47.619 0.00 2.01 46.88 3.16
1527 2370 4.471904 TCTATACAGGTTCTGCCAAGTG 57.528 45.455 0.00 0.00 40.61 3.16
1533 2376 7.489757 CAGTAAAGAGTTCTATACAGGTTCTGC 59.510 40.741 0.00 0.00 34.37 4.26
1536 2379 9.356433 GTTCAGTAAAGAGTTCTATACAGGTTC 57.644 37.037 0.00 0.00 0.00 3.62
1675 2523 7.527084 ACAGATGAAAATTACTCTTCGCTAC 57.473 36.000 0.00 0.00 0.00 3.58
1765 2617 1.398390 CAGAACACGGCTGCTTATTCC 59.602 52.381 0.00 0.00 0.00 3.01
1818 2670 9.362151 AGTTTGGGAAATTGTGATAAACTAGAA 57.638 29.630 0.00 0.00 35.75 2.10
1852 2704 4.880120 CACAGCTCACATGATTTGGATACT 59.120 41.667 0.00 0.00 37.61 2.12
1860 2712 0.809385 GCAGCACAGCTCACATGATT 59.191 50.000 0.00 0.00 36.40 2.57
1873 2725 1.527034 TTGAACTGATCCTGCAGCAC 58.473 50.000 8.66 2.04 39.51 4.40
1904 2756 7.988737 TCAAACATACAAGCTAGATTGGAATG 58.011 34.615 24.87 24.87 35.47 2.67
2169 3024 0.320508 CAGCAGTGAGAAGCAGCTCA 60.321 55.000 0.00 4.61 42.31 4.26
2184 3039 1.526887 GTCCGATCCAATCCCAGCA 59.473 57.895 0.00 0.00 0.00 4.41
2196 3051 3.822735 CTGGCAAATCAATATGGTCCGAT 59.177 43.478 0.00 0.00 0.00 4.18
2334 3189 2.841215 TCACCTTTAACGACCTGTTGG 58.159 47.619 0.00 0.00 42.01 3.77
2586 3441 6.415573 AGTTTTCTCAGTAAGAGGTGTGTTT 58.584 36.000 0.00 0.00 44.81 2.83
2656 3583 8.974060 ACCAAACAGAATTTAGAGAACTGTAA 57.026 30.769 0.00 0.00 40.23 2.41
2744 3671 0.174845 CTCCCCGAGCGTTATTCACA 59.825 55.000 0.00 0.00 0.00 3.58
3030 3958 7.869016 TTTTGTCAACACTAAGAGATACTCG 57.131 36.000 0.00 0.00 35.36 4.18
3031 3959 9.042008 TGTTTTTGTCAACACTAAGAGATACTC 57.958 33.333 0.00 0.00 31.48 2.59
3032 3960 8.958119 TGTTTTTGTCAACACTAAGAGATACT 57.042 30.769 0.00 0.00 31.48 2.12
3033 3961 9.997482 TTTGTTTTTGTCAACACTAAGAGATAC 57.003 29.630 0.00 0.00 36.36 2.24
3035 3963 8.190784 CCTTTGTTTTTGTCAACACTAAGAGAT 58.809 33.333 14.71 0.00 36.36 2.75
3036 3964 7.175990 ACCTTTGTTTTTGTCAACACTAAGAGA 59.824 33.333 14.71 0.00 36.36 3.10
3037 3965 7.312899 ACCTTTGTTTTTGTCAACACTAAGAG 58.687 34.615 14.71 9.94 36.36 2.85
3316 4252 0.994247 AGATGTGAGGGGTCATTGCA 59.006 50.000 0.00 0.00 0.00 4.08
3387 4324 0.032952 GACGATACGCCATAAGCCCA 59.967 55.000 0.00 0.00 38.78 5.36
3390 4327 4.446385 TGTAAATGACGATACGCCATAAGC 59.554 41.667 0.00 0.00 28.59 3.09
3395 4332 2.198406 GCTGTAAATGACGATACGCCA 58.802 47.619 0.00 0.00 0.00 5.69
3404 4341 4.275936 AGAACACCAAGTGCTGTAAATGAC 59.724 41.667 0.00 0.00 33.67 3.06
3445 4382 6.058183 AGAATTCGTCCATAGCTTTGCTAAT 58.942 36.000 3.31 0.00 44.62 1.73
3449 4388 4.811557 ACTAGAATTCGTCCATAGCTTTGC 59.188 41.667 0.00 0.00 0.00 3.68
3454 4393 5.189659 ACTGACTAGAATTCGTCCATAGC 57.810 43.478 9.99 0.90 0.00 2.97
3559 4712 9.926751 CTTAGTTGTATGTATTTGCTCTTGATG 57.073 33.333 0.00 0.00 0.00 3.07
3571 4724 6.610020 TGGCCTACTGTCTTAGTTGTATGTAT 59.390 38.462 3.32 0.00 40.89 2.29
3594 4748 4.094294 CGTATGTGTGATGGTTAAGGTTGG 59.906 45.833 0.00 0.00 0.00 3.77
3651 4996 0.393077 AGTCAGTAGCAAAGCACGGT 59.607 50.000 0.00 0.00 0.00 4.83
3655 5000 1.694150 AGGACAGTCAGTAGCAAAGCA 59.306 47.619 2.17 0.00 0.00 3.91
3672 5017 0.396435 ACATCAGAAACACGGCAGGA 59.604 50.000 0.00 0.00 0.00 3.86
3675 5020 0.107643 TCCACATCAGAAACACGGCA 59.892 50.000 0.00 0.00 0.00 5.69
3915 5268 3.627123 CACGCAGACATCCATTATTTCCA 59.373 43.478 0.00 0.00 0.00 3.53
3935 5288 3.747976 GCATGGTCGCAACCCCAC 61.748 66.667 0.00 0.00 45.83 4.61
4028 5393 8.700644 CGGTTATAGATGCTCTATACACAAAAC 58.299 37.037 10.58 8.12 40.53 2.43
4037 5402 4.463186 GGTGTCCGGTTATAGATGCTCTAT 59.537 45.833 0.00 9.63 42.05 1.98
4088 5461 2.368875 AGAATTCTGTGTCCGGTCAGTT 59.631 45.455 7.30 10.01 33.89 3.16
4092 5465 2.338500 GTGAGAATTCTGTGTCCGGTC 58.662 52.381 14.00 0.00 0.00 4.79
4103 5476 1.271163 TGTCCGGTTGGGTGAGAATTC 60.271 52.381 0.00 0.00 37.00 2.17
4108 5481 1.377202 CCATGTCCGGTTGGGTGAG 60.377 63.158 0.00 0.00 37.00 3.51
4109 5482 2.753701 CCATGTCCGGTTGGGTGA 59.246 61.111 0.00 0.00 37.00 4.02
4181 5555 4.101448 GTGCGTCCAGGCATCCCT 62.101 66.667 0.00 0.00 45.99 4.20
4217 5591 3.716195 CGGATGGGCCACAGTGGA 61.716 66.667 24.96 2.33 40.96 4.02
4239 5613 7.671302 AGTGCGGATAGAGTTGAATATATGTT 58.329 34.615 0.00 0.00 0.00 2.71
4269 5643 0.444260 GAGTGCAGCTAAGGTTTCGC 59.556 55.000 0.00 0.00 0.00 4.70
4322 5696 3.418744 GAACTCGCCGGAGAGGAGC 62.419 68.421 34.27 20.77 43.27 4.70
4340 5714 1.048724 TCCATGAAGGACTAGGCCGG 61.049 60.000 9.61 3.73 43.07 6.13
4379 5753 4.324641 CCAGTCCTCGGATCCAGATATCTA 60.325 50.000 13.41 0.00 0.00 1.98
4384 5758 0.470833 CCCAGTCCTCGGATCCAGAT 60.471 60.000 13.41 0.00 0.00 2.90
4405 5779 1.617018 CGGGACTGCAAGGGATGAGA 61.617 60.000 0.00 0.00 39.30 3.27
4437 5811 1.463553 TTGGAGAGCAGCACAGACGA 61.464 55.000 0.00 0.00 0.00 4.20
4442 5816 2.666190 GCGTTGGAGAGCAGCACA 60.666 61.111 0.00 0.00 0.00 4.57
4443 5817 2.358003 AGCGTTGGAGAGCAGCAC 60.358 61.111 0.00 0.00 35.48 4.40
4444 5818 2.047844 GAGCGTTGGAGAGCAGCA 60.048 61.111 0.00 0.00 35.48 4.41
4445 5819 2.817396 GGAGCGTTGGAGAGCAGC 60.817 66.667 0.00 0.00 35.48 5.25
4493 5869 3.919834 CCCAATGAAATCCCTCCAGATT 58.080 45.455 0.00 0.00 38.11 2.40
4497 5873 0.395586 CGCCCAATGAAATCCCTCCA 60.396 55.000 0.00 0.00 0.00 3.86
4507 5883 1.223487 GAACCCTAGCGCCCAATGA 59.777 57.895 2.29 0.00 0.00 2.57
4522 5898 4.242475 TCATGACACTACATCAACGGAAC 58.758 43.478 0.00 0.00 0.00 3.62
4534 5910 2.738643 GCGGCTTAAGCTCATGACACTA 60.739 50.000 25.88 0.00 41.70 2.74
4579 5958 4.464008 TCTTCAACTCTGAACTTTGGCAT 58.536 39.130 0.00 0.00 36.62 4.40
4629 6008 1.360820 GAAGCTTTACTCGCCCTCAC 58.639 55.000 0.00 0.00 0.00 3.51
4656 6035 7.589958 AGAAGATAGTTGTGGATACGAAGAT 57.410 36.000 0.00 0.00 42.51 2.40
4661 6040 7.033530 AGAGAAGAAGATAGTTGTGGATACG 57.966 40.000 0.00 0.00 42.51 3.06
4700 6079 1.400142 TCACCTCACTTTTTGCGTGTG 59.600 47.619 0.00 0.00 34.14 3.82
4701 6080 1.745232 TCACCTCACTTTTTGCGTGT 58.255 45.000 0.00 0.00 34.14 4.49
4711 6090 3.754965 TGCTTTGCTTATTCACCTCACT 58.245 40.909 0.00 0.00 0.00 3.41
4745 6124 0.529378 CATGCCAGGAAACTTGAGGC 59.471 55.000 0.00 0.00 45.00 4.70
4750 6129 6.670695 ATTAAAGAACATGCCAGGAAACTT 57.329 33.333 0.00 0.00 40.21 2.66
4762 6141 7.761249 GCACATCCTAGCAAAATTAAAGAACAT 59.239 33.333 0.00 0.00 0.00 2.71
4770 6149 6.658816 TCAGAAAGCACATCCTAGCAAAATTA 59.341 34.615 0.00 0.00 0.00 1.40
4801 6180 1.772836 AAGTACTCGCCGACCCTAAT 58.227 50.000 0.00 0.00 0.00 1.73
4803 6182 1.549203 AAAAGTACTCGCCGACCCTA 58.451 50.000 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.