Multiple sequence alignment - TraesCS6B01G336000

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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 TraesCS6B01G336000 chr6B 100.000 3810 0 0 821 4630 591248119 591251928 0.000000e+00 7036
1 TraesCS6B01G336000 chr6B 100.000 316 0 0 1 316 591247299 591247614 6.680000e-163 584
2 TraesCS6B01G336000 chr6A 93.577 3612 135 18 821 4393 541414652 541418205 0.000000e+00 5295
3 TraesCS6B01G336000 chr6A 95.556 135 4 2 4399 4531 222571377 222571243 1.010000e-51 215
4 TraesCS6B01G336000 chr6A 91.558 154 12 1 164 316 541414447 541414600 1.310000e-50 211
5 TraesCS6B01G336000 chr6A 90.625 128 7 5 4417 4542 328255241 328255365 1.030000e-36 165
6 TraesCS6B01G336000 chr6A 96.907 97 2 1 4535 4630 541418283 541418379 1.330000e-35 161
7 TraesCS6B01G336000 chr6D 96.454 1946 51 6 821 2751 394933444 394935386 0.000000e+00 3195
8 TraesCS6B01G336000 chr6D 95.598 1363 29 9 2748 4080 394935792 394937153 0.000000e+00 2156
9 TraesCS6B01G336000 chr6D 94.853 136 5 2 4398 4531 389700571 389700706 1.310000e-50 211
10 TraesCS6B01G336000 chr6D 84.977 213 13 4 122 316 394933192 394933403 1.020000e-46 198
11 TraesCS6B01G336000 chr6D 91.892 111 6 3 4174 4283 395022094 395022202 8.020000e-33 152
12 TraesCS6B01G336000 chr6D 91.892 111 6 3 4174 4283 395032643 395032751 8.020000e-33 152
13 TraesCS6B01G336000 chr6D 94.681 94 5 0 4076 4169 395014736 395014829 3.730000e-31 147
14 TraesCS6B01G336000 chr6D 86.000 100 7 3 4537 4630 395377818 395377916 2.950000e-17 100
15 TraesCS6B01G336000 chr1D 95.588 136 4 2 4399 4532 206955670 206955535 2.810000e-52 217
16 TraesCS6B01G336000 chr1D 94.853 136 5 2 4398 4531 411982136 411982271 1.310000e-50 211
17 TraesCS6B01G336000 chr2B 95.556 135 5 1 4398 4531 18313729 18313595 1.010000e-51 215
18 TraesCS6B01G336000 chr2B 93.220 118 6 2 4415 4530 602756739 602756856 6.160000e-39 172
19 TraesCS6B01G336000 chr2B 91.089 101 3 5 4415 4511 594837083 594837181 1.050000e-26 132
20 TraesCS6B01G336000 chrUn 95.522 134 4 2 4399 4530 100214710 100214843 3.630000e-51 213
21 TraesCS6B01G336000 chrUn 94.853 136 5 2 4398 4531 173546567 173546702 1.310000e-50 211
22 TraesCS6B01G336000 chr7B 93.103 145 6 3 4399 4539 714315973 714316117 4.690000e-50 209
23 TraesCS6B01G336000 chr7B 85.833 120 3 4 4415 4532 437671166 437671059 1.050000e-21 115
24 TraesCS6B01G336000 chr3D 86.631 187 20 3 4349 4530 610161890 610162076 7.860000e-48 202
25 TraesCS6B01G336000 chr2D 84.817 191 8 10 4342 4530 508728798 508728627 6.160000e-39 172
26 TraesCS6B01G336000 chr7D 92.500 120 3 3 4417 4530 562409378 562409497 2.870000e-37 167
27 TraesCS6B01G336000 chr7D 90.909 121 8 3 4412 4530 500622998 500622879 4.790000e-35 159
28 TraesCS6B01G336000 chr7D 81.383 188 12 5 4345 4530 4786277 4786111 1.050000e-26 132
29 TraesCS6B01G336000 chr5B 91.525 118 7 3 4415 4530 305442170 305442054 4.790000e-35 159
30 TraesCS6B01G336000 chr3B 81.407 199 14 11 4337 4533 542727046 542726869 1.740000e-29 141


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 TraesCS6B01G336000 chr6B 591247299 591251928 4629 False 3810.000000 7036 100.000 1 4630 2 chr6B.!!$F1 4629
1 TraesCS6B01G336000 chr6A 541414447 541418379 3932 False 1889.000000 5295 94.014 164 4630 3 chr6A.!!$F2 4466
2 TraesCS6B01G336000 chr6D 394933192 394937153 3961 False 1849.666667 3195 92.343 122 4080 3 chr6D.!!$F6 3958

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
64 65 0.031616 CTGAGAGGGGCTCTAGGGTT 60.032 60.000 0.00 0.0 41.35 4.11 F
99 100 0.167908 CGTTGCTCTTTGCGCCAATA 59.832 50.000 4.18 0.0 46.63 1.90 F
103 104 0.179163 GCTCTTTGCGCCAATACCAC 60.179 55.000 4.18 0.0 0.00 4.16 F
116 117 0.263765 ATACCACTCTTCCCGGCCTA 59.736 55.000 0.00 0.0 0.00 3.93 F
117 118 0.396695 TACCACTCTTCCCGGCCTAG 60.397 60.000 0.00 0.0 0.00 3.02 F
169 180 0.581529 TTGAAGACGTGAAGCAAGCG 59.418 50.000 0.00 0.0 0.00 4.68 F
186 197 0.947180 GCGCAAACAGGACGGACTAA 60.947 55.000 0.30 0.0 0.00 2.24 F
1155 1175 1.219124 GCACTCCCTGAGCGATTCA 59.781 57.895 0.00 0.0 32.04 2.57 F
1208 1228 1.239968 CCAGTGAGTTTGCTCTGGGC 61.240 60.000 0.00 0.0 42.80 5.36 F
1619 1644 1.281419 TTCAGGGATCGCAAGGGTTA 58.719 50.000 12.83 0.0 38.47 2.85 F
1624 1649 2.041216 AGGGATCGCAAGGGTTAAGTTT 59.959 45.455 12.83 0.0 38.47 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1274 0.967380 GCCCCACCAGTCAAATCCTG 60.967 60.000 0.00 0.00 0.00 3.86 R
1592 1617 2.643551 TGCGATCCCTGAATCTTTTCC 58.356 47.619 0.00 0.00 0.00 3.13 R
1610 1635 4.600692 ATCCACAAAACTTAACCCTTGC 57.399 40.909 0.00 0.00 0.00 4.01 R
1758 1783 5.047660 TCCATTCTTTTGGTTTATTGTCCGG 60.048 40.000 0.00 0.00 38.01 5.14 R
2050 2075 7.665561 TTTTACCTTTGAAATTGCTATTGCC 57.334 32.000 0.00 0.00 38.71 4.52 R
2146 2171 2.425143 ATAACCTGAGGTGGCATGTG 57.575 50.000 4.15 0.00 35.34 3.21 R
2333 2358 2.425143 TGGATGCATCAAGGAAGTCC 57.575 50.000 27.25 9.56 0.00 3.85 R
3188 3633 0.811281 AAATACAGAAAGGGCTGCGC 59.189 50.000 8.86 8.86 39.51 6.09 R
3312 3764 5.765182 ACTTGGTTAACAATGAGTCTCCTTG 59.235 40.000 14.31 14.31 38.65 3.61 R
3542 3994 4.082571 AGAGGTGCTTGCATTATGTTCAAC 60.083 41.667 0.00 0.00 0.00 3.18 R
3650 4103 4.351127 AGTAGTTCCACCCGAAGTTATCT 58.649 43.478 0.00 0.00 35.65 1.98 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
21 22 3.942829 TCCTAGGTTCTGACAAGCAATG 58.057 45.455 9.08 0.00 0.00 2.82
22 23 2.421424 CCTAGGTTCTGACAAGCAATGC 59.579 50.000 0.00 0.00 0.00 3.56
23 24 0.877071 AGGTTCTGACAAGCAATGCG 59.123 50.000 0.00 0.00 0.00 4.73
24 25 0.593128 GGTTCTGACAAGCAATGCGT 59.407 50.000 0.00 0.00 0.00 5.24
25 26 1.400242 GGTTCTGACAAGCAATGCGTC 60.400 52.381 0.00 2.79 0.00 5.19
26 27 1.264020 GTTCTGACAAGCAATGCGTCA 59.736 47.619 13.67 13.67 37.33 4.35
27 28 0.867746 TCTGACAAGCAATGCGTCAC 59.132 50.000 11.02 0.50 34.83 3.67
28 29 0.870393 CTGACAAGCAATGCGTCACT 59.130 50.000 11.02 0.00 34.83 3.41
29 30 1.265095 CTGACAAGCAATGCGTCACTT 59.735 47.619 11.02 0.00 34.83 3.16
30 31 2.480037 CTGACAAGCAATGCGTCACTTA 59.520 45.455 11.02 0.00 34.83 2.24
31 32 3.073678 TGACAAGCAATGCGTCACTTAT 58.926 40.909 11.02 0.00 34.83 1.73
32 33 3.125146 TGACAAGCAATGCGTCACTTATC 59.875 43.478 11.02 0.00 34.83 1.75
33 34 2.094258 ACAAGCAATGCGTCACTTATCG 59.906 45.455 0.00 0.00 0.00 2.92
41 42 0.999406 CGTCACTTATCGCAACCAGG 59.001 55.000 0.00 0.00 0.00 4.45
42 43 1.671850 CGTCACTTATCGCAACCAGGT 60.672 52.381 0.00 0.00 0.00 4.00
43 44 2.416296 CGTCACTTATCGCAACCAGGTA 60.416 50.000 0.00 0.00 0.00 3.08
44 45 3.187700 GTCACTTATCGCAACCAGGTAG 58.812 50.000 0.00 0.00 0.00 3.18
45 46 1.933853 CACTTATCGCAACCAGGTAGC 59.066 52.381 0.00 0.00 0.00 3.58
46 47 1.831736 ACTTATCGCAACCAGGTAGCT 59.168 47.619 0.00 0.00 0.00 3.32
47 48 2.205074 CTTATCGCAACCAGGTAGCTG 58.795 52.381 15.13 15.13 0.00 4.24
48 49 1.480789 TATCGCAACCAGGTAGCTGA 58.519 50.000 23.31 2.21 0.00 4.26
49 50 0.176680 ATCGCAACCAGGTAGCTGAG 59.823 55.000 23.31 14.89 0.00 3.35
50 51 0.898326 TCGCAACCAGGTAGCTGAGA 60.898 55.000 23.31 10.82 0.00 3.27
51 52 0.459237 CGCAACCAGGTAGCTGAGAG 60.459 60.000 23.31 12.34 0.00 3.20
52 53 0.107945 GCAACCAGGTAGCTGAGAGG 60.108 60.000 23.31 8.95 0.00 3.69
53 54 0.539051 CAACCAGGTAGCTGAGAGGG 59.461 60.000 23.31 8.56 0.00 4.30
54 55 0.618968 AACCAGGTAGCTGAGAGGGG 60.619 60.000 23.31 7.81 0.00 4.79
55 56 2.439104 CCAGGTAGCTGAGAGGGGC 61.439 68.421 23.31 0.00 0.00 5.80
56 57 1.382420 CAGGTAGCTGAGAGGGGCT 60.382 63.158 17.08 0.00 41.92 5.19
57 58 1.075600 AGGTAGCTGAGAGGGGCTC 60.076 63.158 0.00 0.00 44.21 4.70
58 59 1.075600 GGTAGCTGAGAGGGGCTCT 60.076 63.158 0.00 0.00 44.28 4.09
59 60 0.186386 GGTAGCTGAGAGGGGCTCTA 59.814 60.000 0.00 0.00 41.35 2.43
60 61 1.616159 GTAGCTGAGAGGGGCTCTAG 58.384 60.000 0.00 0.00 41.35 2.43
61 62 0.480690 TAGCTGAGAGGGGCTCTAGG 59.519 60.000 0.00 0.00 41.35 3.02
62 63 1.836604 GCTGAGAGGGGCTCTAGGG 60.837 68.421 0.00 0.00 41.35 3.53
63 64 1.623625 CTGAGAGGGGCTCTAGGGT 59.376 63.158 0.00 0.00 41.35 4.34
64 65 0.031616 CTGAGAGGGGCTCTAGGGTT 60.032 60.000 0.00 0.00 41.35 4.11
65 66 1.218196 CTGAGAGGGGCTCTAGGGTTA 59.782 57.143 0.00 0.00 41.35 2.85
66 67 1.063114 TGAGAGGGGCTCTAGGGTTAC 60.063 57.143 0.00 0.00 41.35 2.50
67 68 0.265254 AGAGGGGCTCTAGGGTTACC 59.735 60.000 0.00 0.00 39.28 2.85
68 69 4.111697 GAGAGGGGCTCTAGGGTTACCT 62.112 59.091 0.00 2.08 41.35 3.08
69 70 0.265254 AGGGGCTCTAGGGTTACCTC 59.735 60.000 0.00 0.00 46.95 3.85
70 71 0.265254 GGGGCTCTAGGGTTACCTCT 59.735 60.000 0.00 0.00 46.95 3.69
71 72 1.344189 GGGGCTCTAGGGTTACCTCTT 60.344 57.143 0.00 0.00 46.95 2.85
72 73 2.090887 GGGGCTCTAGGGTTACCTCTTA 60.091 54.545 0.00 0.00 46.95 2.10
73 74 3.232662 GGGCTCTAGGGTTACCTCTTAG 58.767 54.545 0.00 1.94 46.95 2.18
74 75 3.373987 GGGCTCTAGGGTTACCTCTTAGT 60.374 52.174 0.00 0.00 46.95 2.24
75 76 3.637694 GGCTCTAGGGTTACCTCTTAGTG 59.362 52.174 0.00 4.09 46.95 2.74
76 77 4.534797 GCTCTAGGGTTACCTCTTAGTGA 58.465 47.826 0.00 0.00 46.95 3.41
77 78 5.141910 GCTCTAGGGTTACCTCTTAGTGAT 58.858 45.833 0.00 0.00 46.95 3.06
78 79 5.599242 GCTCTAGGGTTACCTCTTAGTGATT 59.401 44.000 0.00 0.00 46.95 2.57
79 80 6.098552 GCTCTAGGGTTACCTCTTAGTGATTT 59.901 42.308 0.00 0.00 46.95 2.17
80 81 7.657023 TCTAGGGTTACCTCTTAGTGATTTC 57.343 40.000 0.00 0.00 46.95 2.17
81 82 5.340439 AGGGTTACCTCTTAGTGATTTCG 57.660 43.478 0.00 0.00 46.95 3.46
82 83 4.776308 AGGGTTACCTCTTAGTGATTTCGT 59.224 41.667 0.00 0.00 46.95 3.85
83 84 5.247792 AGGGTTACCTCTTAGTGATTTCGTT 59.752 40.000 0.00 0.00 46.95 3.85
84 85 5.350640 GGGTTACCTCTTAGTGATTTCGTTG 59.649 44.000 0.00 0.00 0.00 4.10
85 86 5.163884 GGTTACCTCTTAGTGATTTCGTTGC 60.164 44.000 0.00 0.00 0.00 4.17
86 87 4.273148 ACCTCTTAGTGATTTCGTTGCT 57.727 40.909 0.00 0.00 0.00 3.91
87 88 4.246458 ACCTCTTAGTGATTTCGTTGCTC 58.754 43.478 0.00 0.00 0.00 4.26
88 89 4.021016 ACCTCTTAGTGATTTCGTTGCTCT 60.021 41.667 0.00 0.00 0.00 4.09
89 90 4.932200 CCTCTTAGTGATTTCGTTGCTCTT 59.068 41.667 0.00 0.00 0.00 2.85
90 91 5.409826 CCTCTTAGTGATTTCGTTGCTCTTT 59.590 40.000 0.00 0.00 0.00 2.52
91 92 6.228273 TCTTAGTGATTTCGTTGCTCTTTG 57.772 37.500 0.00 0.00 0.00 2.77
92 93 3.273919 AGTGATTTCGTTGCTCTTTGC 57.726 42.857 0.00 0.00 43.25 3.68
93 94 1.971962 GTGATTTCGTTGCTCTTTGCG 59.028 47.619 0.00 0.00 46.63 4.85
94 95 0.977674 GATTTCGTTGCTCTTTGCGC 59.022 50.000 0.00 0.00 46.63 6.09
95 96 0.387239 ATTTCGTTGCTCTTTGCGCC 60.387 50.000 4.18 0.00 46.63 6.53
96 97 1.719725 TTTCGTTGCTCTTTGCGCCA 61.720 50.000 4.18 0.00 46.63 5.69
97 98 1.719725 TTCGTTGCTCTTTGCGCCAA 61.720 50.000 4.18 0.00 46.63 4.52
98 99 1.081242 CGTTGCTCTTTGCGCCAAT 60.081 52.632 4.18 0.00 46.63 3.16
99 100 0.167908 CGTTGCTCTTTGCGCCAATA 59.832 50.000 4.18 0.00 46.63 1.90
100 101 1.617740 GTTGCTCTTTGCGCCAATAC 58.382 50.000 4.18 0.00 46.63 1.89
101 102 0.525761 TTGCTCTTTGCGCCAATACC 59.474 50.000 4.18 0.00 46.63 2.73
102 103 0.607762 TGCTCTTTGCGCCAATACCA 60.608 50.000 4.18 0.00 46.63 3.25
103 104 0.179163 GCTCTTTGCGCCAATACCAC 60.179 55.000 4.18 0.00 0.00 4.16
104 105 1.453155 CTCTTTGCGCCAATACCACT 58.547 50.000 4.18 0.00 0.00 4.00
105 106 1.398390 CTCTTTGCGCCAATACCACTC 59.602 52.381 4.18 0.00 0.00 3.51
106 107 1.003118 TCTTTGCGCCAATACCACTCT 59.997 47.619 4.18 0.00 0.00 3.24
107 108 1.812571 CTTTGCGCCAATACCACTCTT 59.187 47.619 4.18 0.00 0.00 2.85
108 109 1.448985 TTGCGCCAATACCACTCTTC 58.551 50.000 4.18 0.00 0.00 2.87
109 110 0.392461 TGCGCCAATACCACTCTTCC 60.392 55.000 4.18 0.00 0.00 3.46
110 111 1.095807 GCGCCAATACCACTCTTCCC 61.096 60.000 0.00 0.00 0.00 3.97
111 112 0.810031 CGCCAATACCACTCTTCCCG 60.810 60.000 0.00 0.00 0.00 5.14
112 113 0.463833 GCCAATACCACTCTTCCCGG 60.464 60.000 0.00 0.00 0.00 5.73
113 114 0.463833 CCAATACCACTCTTCCCGGC 60.464 60.000 0.00 0.00 0.00 6.13
114 115 0.463833 CAATACCACTCTTCCCGGCC 60.464 60.000 0.00 0.00 0.00 6.13
115 116 0.620700 AATACCACTCTTCCCGGCCT 60.621 55.000 0.00 0.00 0.00 5.19
116 117 0.263765 ATACCACTCTTCCCGGCCTA 59.736 55.000 0.00 0.00 0.00 3.93
117 118 0.396695 TACCACTCTTCCCGGCCTAG 60.397 60.000 0.00 0.00 0.00 3.02
118 119 2.435693 CCACTCTTCCCGGCCTAGG 61.436 68.421 3.67 3.67 0.00 3.02
119 120 2.764547 ACTCTTCCCGGCCTAGGC 60.765 66.667 26.55 26.55 41.06 3.93
169 180 0.581529 TTGAAGACGTGAAGCAAGCG 59.418 50.000 0.00 0.00 0.00 4.68
172 183 1.436195 AAGACGTGAAGCAAGCGCAA 61.436 50.000 11.47 0.00 42.27 4.85
178 189 1.100463 TGAAGCAAGCGCAAACAGGA 61.100 50.000 11.47 0.00 42.27 3.86
182 193 2.110213 AAGCGCAAACAGGACGGA 59.890 55.556 11.47 0.00 0.00 4.69
184 195 2.660258 AAGCGCAAACAGGACGGACT 62.660 55.000 11.47 0.00 0.00 3.85
185 196 1.373748 GCGCAAACAGGACGGACTA 60.374 57.895 0.30 0.00 0.00 2.59
186 197 0.947180 GCGCAAACAGGACGGACTAA 60.947 55.000 0.30 0.00 0.00 2.24
307 327 2.680312 TCAATCAGAAGCGGAGAAGG 57.320 50.000 0.00 0.00 0.00 3.46
1155 1175 1.219124 GCACTCCCTGAGCGATTCA 59.781 57.895 0.00 0.00 32.04 2.57
1199 1219 2.038295 CTCCAGCTCTTCCAGTGAGTTT 59.962 50.000 0.00 0.00 34.30 2.66
1208 1228 1.239968 CCAGTGAGTTTGCTCTGGGC 61.240 60.000 0.00 0.00 42.80 5.36
1214 1234 2.040278 TGAGTTTGCTCTGGGCTTGTAT 59.960 45.455 0.00 0.00 42.13 2.29
1243 1263 3.194542 TGTATTTGTAACATTGCCCCTGC 59.805 43.478 0.00 0.00 38.26 4.85
1254 1274 3.365265 CCCCTGCCTGCGTGTTTC 61.365 66.667 0.00 0.00 0.00 2.78
1313 1333 1.612950 ACTGATTCGCCATTGTTTGCA 59.387 42.857 0.00 0.00 0.00 4.08
1525 1550 6.914757 GGTATCTTCTTTTATTGATGCAGTGC 59.085 38.462 8.58 8.58 0.00 4.40
1592 1617 8.550376 CATGGAAAACTCAACTGTTAAATTTGG 58.450 33.333 0.00 0.00 0.00 3.28
1610 1635 3.281727 TGGGAAAAGATTCAGGGATCG 57.718 47.619 0.00 0.00 37.29 3.69
1619 1644 1.281419 TTCAGGGATCGCAAGGGTTA 58.719 50.000 12.83 0.00 38.47 2.85
1624 1649 2.041216 AGGGATCGCAAGGGTTAAGTTT 59.959 45.455 12.83 0.00 38.47 2.66
1633 1658 5.364778 GCAAGGGTTAAGTTTTGTGGATTT 58.635 37.500 0.00 0.00 0.00 2.17
1648 1673 4.841813 TGTGGATTTACAAGTAGTGGAGGA 59.158 41.667 0.00 0.00 0.00 3.71
1652 1677 5.187186 GGATTTACAAGTAGTGGAGGACTGA 59.813 44.000 0.00 0.00 35.96 3.41
1664 1689 5.421056 AGTGGAGGACTGATTTAATCGTGTA 59.579 40.000 7.04 0.00 31.75 2.90
1675 1700 8.083462 TGATTTAATCGTGTATATCACTTGGC 57.917 34.615 0.23 0.00 44.16 4.52
2109 2134 4.481072 GGGCTTATAGTCTCCCTACTTCA 58.519 47.826 0.00 0.00 35.87 3.02
2146 2171 6.538189 GCTCTAGCTTGTGATTTCCTATTC 57.462 41.667 0.00 0.00 38.21 1.75
2333 2358 3.247648 CACTCCGGTTATTATCTTTGCCG 59.752 47.826 0.00 0.00 38.99 5.69
2457 2492 7.759489 ATGGCTGAAGTCAACTTATTTTGTA 57.241 32.000 0.00 0.00 36.11 2.41
2459 2494 7.816640 TGGCTGAAGTCAACTTATTTTGTATC 58.183 34.615 0.00 0.00 36.11 2.24
2477 2512 5.862845 TGTATCACCAAAATTGTTTGCCAT 58.137 33.333 0.00 0.00 42.44 4.40
2605 2640 9.685828 GTGCCTTTATGTTAACTTGTGAAATTA 57.314 29.630 7.22 0.00 0.00 1.40
2607 2642 8.860128 GCCTTTATGTTAACTTGTGAAATTAGC 58.140 33.333 7.22 0.13 0.00 3.09
2664 2699 9.562583 TTCAATTGTTTTACAGTGTTAAGTGAC 57.437 29.630 0.00 0.00 0.00 3.67
2665 2700 8.731605 TCAATTGTTTTACAGTGTTAAGTGACA 58.268 29.630 0.00 0.00 0.00 3.58
2695 2730 6.620678 CATTTTGTCAGTTATGGTTACCAGG 58.379 40.000 10.74 0.00 36.75 4.45
3188 3633 3.262420 CGGTACATTTTCTCCTCACCTG 58.738 50.000 0.00 0.00 0.00 4.00
3542 3994 1.842562 AGTGATCCAGAGTTGATGGGG 59.157 52.381 0.00 0.00 38.44 4.96
3650 4103 3.492337 ACCTTAGTTTGCGGGAAAATGA 58.508 40.909 5.18 0.00 0.00 2.57
3695 4148 4.426416 TGGTCGATACAACTGTTTATCCG 58.574 43.478 12.71 6.52 0.00 4.18
3818 4271 7.011857 GCTAGCATATGGGATTTGCTATACTTC 59.988 40.741 10.63 0.00 44.72 3.01
3853 4307 4.455606 AGGGATTTGCTATACTTGACAGC 58.544 43.478 0.00 0.00 35.82 4.40
3919 4388 2.810852 CCAGTCTGCTTCTTTGTCCTTC 59.189 50.000 0.00 0.00 0.00 3.46
3936 4405 2.171448 CCTTCTAGGATCACTTGTGGGG 59.829 54.545 0.00 0.00 37.67 4.96
3965 4434 9.883142 TCAGATCCAAAACTTTGTAAACAAAAT 57.117 25.926 9.39 0.00 44.24 1.82
4007 4483 9.225436 TGTAAATGTTAATAGCAATGAGTGTCA 57.775 29.630 0.00 0.00 0.00 3.58
4040 4516 0.249868 GGCAGCTTGGGGAAACAAAC 60.250 55.000 0.00 0.00 0.00 2.93
4050 4526 6.422701 GCTTGGGGAAACAAACAGTTAAATAC 59.577 38.462 0.00 0.00 40.26 1.89
4098 4574 0.107703 CCACGTGTGATGTAGGGCAT 60.108 55.000 15.65 0.00 41.24 4.40
4099 4575 1.009078 CACGTGTGATGTAGGGCATG 58.991 55.000 7.58 0.00 38.06 4.06
4100 4576 0.744414 ACGTGTGATGTAGGGCATGC 60.744 55.000 9.90 9.90 38.06 4.06
4101 4577 1.765161 CGTGTGATGTAGGGCATGCG 61.765 60.000 12.44 0.00 38.06 4.73
4102 4578 0.744414 GTGTGATGTAGGGCATGCGT 60.744 55.000 12.44 3.79 38.06 5.24
4103 4579 0.744057 TGTGATGTAGGGCATGCGTG 60.744 55.000 12.44 0.09 38.06 5.34
4104 4580 1.153188 TGATGTAGGGCATGCGTGG 60.153 57.895 12.44 0.00 38.06 4.94
4112 4588 2.644418 GCATGCGTGGCAACTGAA 59.356 55.556 8.27 0.00 43.62 3.02
4113 4589 1.443194 GCATGCGTGGCAACTGAAG 60.443 57.895 8.27 0.00 43.62 3.02
4114 4590 1.951510 CATGCGTGGCAACTGAAGT 59.048 52.632 0.00 0.00 43.62 3.01
4115 4591 0.386352 CATGCGTGGCAACTGAAGTG 60.386 55.000 0.00 0.00 43.62 3.16
4116 4592 1.518056 ATGCGTGGCAACTGAAGTGG 61.518 55.000 0.00 0.00 43.62 4.00
4143 4619 0.534427 GGCGGTACTGGGCCTAATTC 60.534 60.000 4.53 0.00 45.93 2.17
4146 4622 2.038033 GCGGTACTGGGCCTAATTCATA 59.962 50.000 4.53 0.00 0.00 2.15
4176 4652 1.871772 CTTGCAGTGTGCTAGGTGC 59.128 57.895 0.00 0.00 45.31 5.01
4177 4653 1.580845 CTTGCAGTGTGCTAGGTGCC 61.581 60.000 0.00 0.00 45.31 5.01
4178 4654 2.055689 TTGCAGTGTGCTAGGTGCCT 62.056 55.000 0.00 0.00 45.31 4.75
4179 4655 1.191489 TGCAGTGTGCTAGGTGCCTA 61.191 55.000 0.00 0.00 45.31 3.93
4180 4656 0.460987 GCAGTGTGCTAGGTGCCTAG 60.461 60.000 18.40 18.40 46.41 3.02
4181 4657 0.176680 CAGTGTGCTAGGTGCCTAGG 59.823 60.000 22.52 3.67 44.48 3.02
4182 4658 0.252284 AGTGTGCTAGGTGCCTAGGT 60.252 55.000 22.52 0.00 44.48 3.08
4202 4678 4.074970 GGTCTGATGCCAAATATGTAGGG 58.925 47.826 0.00 0.00 0.00 3.53
4203 4679 4.446311 GGTCTGATGCCAAATATGTAGGGT 60.446 45.833 0.00 0.00 0.00 4.34
4204 4680 4.516698 GTCTGATGCCAAATATGTAGGGTG 59.483 45.833 0.00 0.00 0.00 4.61
4205 4681 3.221771 TGATGCCAAATATGTAGGGTGC 58.778 45.455 0.00 0.00 0.00 5.01
4206 4682 3.117550 TGATGCCAAATATGTAGGGTGCT 60.118 43.478 0.00 0.00 0.00 4.40
4207 4683 4.103943 TGATGCCAAATATGTAGGGTGCTA 59.896 41.667 0.00 0.00 0.00 3.49
4208 4684 4.511786 TGCCAAATATGTAGGGTGCTAA 57.488 40.909 0.00 0.00 0.00 3.09
4209 4685 5.060427 TGCCAAATATGTAGGGTGCTAAT 57.940 39.130 0.00 0.00 0.00 1.73
4210 4686 5.454062 TGCCAAATATGTAGGGTGCTAATT 58.546 37.500 0.00 0.00 0.00 1.40
4211 4687 5.896678 TGCCAAATATGTAGGGTGCTAATTT 59.103 36.000 0.00 0.00 0.00 1.82
4212 4688 7.063593 TGCCAAATATGTAGGGTGCTAATTTA 58.936 34.615 0.00 0.00 0.00 1.40
4213 4689 7.013846 TGCCAAATATGTAGGGTGCTAATTTAC 59.986 37.037 0.00 0.00 0.00 2.01
4214 4690 7.581476 CCAAATATGTAGGGTGCTAATTTACG 58.419 38.462 0.00 0.00 0.00 3.18
4215 4691 7.227910 CCAAATATGTAGGGTGCTAATTTACGT 59.772 37.037 0.00 0.00 0.00 3.57
4216 4692 7.958053 AATATGTAGGGTGCTAATTTACGTC 57.042 36.000 0.00 0.00 0.00 4.34
4217 4693 5.609533 ATGTAGGGTGCTAATTTACGTCT 57.390 39.130 0.00 0.00 0.00 4.18
4228 4704 8.272866 GTGCTAATTTACGTCTTTTGCAAATTT 58.727 29.630 13.65 0.00 34.01 1.82
4236 4712 6.259638 ACGTCTTTTGCAAATTTTTCGACTA 58.740 32.000 13.65 0.00 0.00 2.59
4266 4742 9.060347 TGATCTAATGTGATGAATTTAGGCTTC 57.940 33.333 0.00 0.00 0.00 3.86
4280 4756 8.658840 AATTTAGGCTTCCCAGTAAACATTTA 57.341 30.769 0.00 0.00 0.00 1.40
4333 4809 2.127118 CGCAGCTCGGTGCAAAAG 60.127 61.111 19.46 1.24 44.21 2.27
4347 4823 3.398954 GCAAAAGGATGCAATGCAATG 57.601 42.857 13.45 6.12 43.62 2.82
4349 4825 3.933955 GCAAAAGGATGCAATGCAATGTA 59.066 39.130 13.45 0.00 43.62 2.29
4351 4827 5.065474 GCAAAAGGATGCAATGCAATGTATT 59.935 36.000 13.45 2.50 43.62 1.89
4352 4828 6.711579 CAAAAGGATGCAATGCAATGTATTC 58.288 36.000 13.45 4.90 43.62 1.75
4353 4829 4.595762 AGGATGCAATGCAATGTATTCC 57.404 40.909 13.45 13.59 43.62 3.01
4354 4830 3.322828 AGGATGCAATGCAATGTATTCCC 59.677 43.478 13.45 4.83 43.62 3.97
4355 4831 3.322828 GGATGCAATGCAATGTATTCCCT 59.677 43.478 13.45 0.00 43.62 4.20
4356 4832 4.553323 GATGCAATGCAATGTATTCCCTC 58.447 43.478 13.45 0.00 43.62 4.30
4358 4834 2.287788 GCAATGCAATGTATTCCCTCCG 60.288 50.000 0.00 0.00 0.00 4.63
4359 4835 2.951642 CAATGCAATGTATTCCCTCCGT 59.048 45.455 0.00 0.00 0.00 4.69
4362 4842 2.238646 TGCAATGTATTCCCTCCGTTCT 59.761 45.455 0.00 0.00 0.00 3.01
4363 4843 3.279434 GCAATGTATTCCCTCCGTTCTT 58.721 45.455 0.00 0.00 0.00 2.52
4364 4844 4.080807 TGCAATGTATTCCCTCCGTTCTTA 60.081 41.667 0.00 0.00 0.00 2.10
4370 4850 9.862149 AATGTATTCCCTCCGTTCTTAAATATT 57.138 29.630 0.00 0.00 0.00 1.28
4371 4851 9.862149 ATGTATTCCCTCCGTTCTTAAATATTT 57.138 29.630 5.89 5.89 0.00 1.40
4373 4853 9.117183 GTATTCCCTCCGTTCTTAAATATTTGT 57.883 33.333 11.05 0.00 0.00 2.83
4375 4855 6.954232 TCCCTCCGTTCTTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
4378 4858 8.182227 CCCTCCGTTCTTAAATATTTGTCTTTC 58.818 37.037 11.05 0.00 0.00 2.62
4441 4921 6.818644 ACTACATACGAAGCAAAATGAGTGAT 59.181 34.615 0.00 0.00 0.00 3.06
4442 4922 6.111768 ACATACGAAGCAAAATGAGTGATC 57.888 37.500 0.00 0.00 0.00 2.92
4443 4923 5.877012 ACATACGAAGCAAAATGAGTGATCT 59.123 36.000 0.00 0.00 0.00 2.75
4444 4924 7.041721 ACATACGAAGCAAAATGAGTGATCTA 58.958 34.615 0.00 0.00 0.00 1.98
4445 4925 5.786401 ACGAAGCAAAATGAGTGATCTAC 57.214 39.130 0.00 0.00 0.00 2.59
4446 4926 5.237815 ACGAAGCAAAATGAGTGATCTACA 58.762 37.500 0.00 0.00 0.00 2.74
4491 4971 8.806429 ACATCTGTATGTGGTAATCATTTGAA 57.194 30.769 0.00 0.00 44.79 2.69
4492 4972 9.241919 ACATCTGTATGTGGTAATCATTTGAAA 57.758 29.630 0.00 0.00 44.79 2.69
4495 4975 9.685276 TCTGTATGTGGTAATCATTTGAAATCT 57.315 29.630 0.00 0.00 0.00 2.40
4496 4976 9.941664 CTGTATGTGGTAATCATTTGAAATCTC 57.058 33.333 0.00 0.00 0.00 2.75
4497 4977 9.685276 TGTATGTGGTAATCATTTGAAATCTCT 57.315 29.630 0.00 0.00 0.00 3.10
4526 5006 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4527 5007 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4528 5008 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
4529 5009 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
4530 5010 7.072076 ACAAATATTTAGGAACGGAGGGAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
4531 5011 7.628501 AATATTTAGGAACGGAGGGAGTATT 57.371 36.000 0.00 0.00 0.00 1.89
4532 5012 4.748277 TTTAGGAACGGAGGGAGTATTG 57.252 45.455 0.00 0.00 0.00 1.90
4533 5013 0.831307 AGGAACGGAGGGAGTATTGC 59.169 55.000 0.00 0.00 0.00 3.56
4544 5024 6.354130 GGAGGGAGTATTGCAGTATAAAACA 58.646 40.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.869912 GCATTGCTTGTCAGAACCTAGGA 60.870 47.826 17.98 0.00 0.00 2.94
2 3 2.094894 CGCATTGCTTGTCAGAACCTAG 59.905 50.000 7.12 0.00 0.00 3.02
4 5 0.877071 CGCATTGCTTGTCAGAACCT 59.123 50.000 7.12 0.00 0.00 3.50
5 6 0.593128 ACGCATTGCTTGTCAGAACC 59.407 50.000 7.12 0.00 0.00 3.62
6 7 1.264020 TGACGCATTGCTTGTCAGAAC 59.736 47.619 13.30 0.00 37.69 3.01
7 8 1.264020 GTGACGCATTGCTTGTCAGAA 59.736 47.619 16.51 0.00 42.77 3.02
8 9 0.867746 GTGACGCATTGCTTGTCAGA 59.132 50.000 16.51 0.00 42.77 3.27
9 10 0.870393 AGTGACGCATTGCTTGTCAG 59.130 50.000 16.51 0.00 42.77 3.51
10 11 1.308047 AAGTGACGCATTGCTTGTCA 58.692 45.000 13.30 13.30 40.12 3.58
11 12 3.674423 GATAAGTGACGCATTGCTTGTC 58.326 45.455 7.12 8.25 0.00 3.18
12 13 2.094258 CGATAAGTGACGCATTGCTTGT 59.906 45.455 7.12 0.00 0.00 3.16
13 14 2.697363 CGATAAGTGACGCATTGCTTG 58.303 47.619 7.12 0.00 0.00 4.01
22 23 0.999406 CCTGGTTGCGATAAGTGACG 59.001 55.000 0.00 0.00 0.00 4.35
23 24 2.094762 ACCTGGTTGCGATAAGTGAC 57.905 50.000 0.00 0.00 0.00 3.67
24 25 2.418197 GCTACCTGGTTGCGATAAGTGA 60.418 50.000 17.01 0.00 0.00 3.41
25 26 1.933853 GCTACCTGGTTGCGATAAGTG 59.066 52.381 17.01 0.00 0.00 3.16
26 27 1.831736 AGCTACCTGGTTGCGATAAGT 59.168 47.619 23.81 6.17 39.09 2.24
27 28 2.159099 TCAGCTACCTGGTTGCGATAAG 60.159 50.000 23.81 14.18 39.09 1.73
28 29 1.828595 TCAGCTACCTGGTTGCGATAA 59.171 47.619 23.81 10.63 39.09 1.75
29 30 1.409064 CTCAGCTACCTGGTTGCGATA 59.591 52.381 23.81 14.01 39.09 2.92
30 31 0.176680 CTCAGCTACCTGGTTGCGAT 59.823 55.000 23.81 8.22 39.09 4.58
31 32 0.898326 TCTCAGCTACCTGGTTGCGA 60.898 55.000 23.81 21.30 39.09 5.10
32 33 0.459237 CTCTCAGCTACCTGGTTGCG 60.459 60.000 23.81 18.86 39.09 4.85
33 34 0.107945 CCTCTCAGCTACCTGGTTGC 60.108 60.000 22.98 22.98 39.61 4.17
34 35 0.539051 CCCTCTCAGCTACCTGGTTG 59.461 60.000 3.84 3.81 39.61 3.77
35 36 0.618968 CCCCTCTCAGCTACCTGGTT 60.619 60.000 3.84 0.00 39.61 3.67
36 37 1.002274 CCCCTCTCAGCTACCTGGT 59.998 63.158 4.05 4.05 39.61 4.00
37 38 2.439104 GCCCCTCTCAGCTACCTGG 61.439 68.421 0.00 0.00 39.61 4.45
38 39 1.382420 AGCCCCTCTCAGCTACCTG 60.382 63.158 0.00 0.00 37.64 4.00
39 40 1.075600 GAGCCCCTCTCAGCTACCT 60.076 63.158 0.00 0.00 40.11 3.08
40 41 0.186386 TAGAGCCCCTCTCAGCTACC 59.814 60.000 0.00 0.00 44.35 3.18
41 42 1.616159 CTAGAGCCCCTCTCAGCTAC 58.384 60.000 0.00 0.00 44.35 3.58
42 43 0.480690 CCTAGAGCCCCTCTCAGCTA 59.519 60.000 0.00 0.00 44.35 3.32
43 44 1.232792 CCTAGAGCCCCTCTCAGCT 59.767 63.158 0.00 0.00 44.35 4.24
44 45 1.836604 CCCTAGAGCCCCTCTCAGC 60.837 68.421 0.00 0.00 44.35 4.26
45 46 0.031616 AACCCTAGAGCCCCTCTCAG 60.032 60.000 0.00 0.00 44.35 3.35
46 47 1.063114 GTAACCCTAGAGCCCCTCTCA 60.063 57.143 0.00 0.00 44.35 3.27
47 48 1.707106 GTAACCCTAGAGCCCCTCTC 58.293 60.000 0.00 0.00 40.34 3.20
48 49 0.265254 GGTAACCCTAGAGCCCCTCT 59.735 60.000 0.00 0.00 43.83 3.69
49 50 0.265254 AGGTAACCCTAGAGCCCCTC 59.735 60.000 0.00 0.00 40.19 4.30
50 51 0.265254 GAGGTAACCCTAGAGCCCCT 59.735 60.000 0.00 0.00 42.86 4.79
51 52 0.265254 AGAGGTAACCCTAGAGCCCC 59.735 60.000 0.00 0.00 42.86 5.80
52 53 2.177811 AAGAGGTAACCCTAGAGCCC 57.822 55.000 0.00 0.00 42.86 5.19
53 54 3.637694 CACTAAGAGGTAACCCTAGAGCC 59.362 52.174 0.00 0.00 42.86 4.70
54 55 4.534797 TCACTAAGAGGTAACCCTAGAGC 58.465 47.826 0.00 0.00 42.86 4.09
55 56 7.468906 CGAAATCACTAAGAGGTAACCCTAGAG 60.469 44.444 0.00 0.00 42.86 2.43
56 57 6.320672 CGAAATCACTAAGAGGTAACCCTAGA 59.679 42.308 0.00 0.00 42.86 2.43
57 58 6.096564 ACGAAATCACTAAGAGGTAACCCTAG 59.903 42.308 0.00 0.00 42.86 3.02
58 59 5.954150 ACGAAATCACTAAGAGGTAACCCTA 59.046 40.000 0.00 0.00 42.86 3.53
59 60 4.776308 ACGAAATCACTAAGAGGTAACCCT 59.224 41.667 0.00 0.00 46.66 4.34
60 61 5.082251 ACGAAATCACTAAGAGGTAACCC 57.918 43.478 0.00 0.00 37.17 4.11
61 62 5.163884 GCAACGAAATCACTAAGAGGTAACC 60.164 44.000 0.00 0.00 37.17 2.85
62 63 5.638234 AGCAACGAAATCACTAAGAGGTAAC 59.362 40.000 0.00 0.00 0.00 2.50
63 64 5.790593 AGCAACGAAATCACTAAGAGGTAA 58.209 37.500 0.00 0.00 0.00 2.85
64 65 5.185249 AGAGCAACGAAATCACTAAGAGGTA 59.815 40.000 0.00 0.00 0.00 3.08
65 66 4.021016 AGAGCAACGAAATCACTAAGAGGT 60.021 41.667 0.00 0.00 0.00 3.85
66 67 4.499183 AGAGCAACGAAATCACTAAGAGG 58.501 43.478 0.00 0.00 0.00 3.69
67 68 6.302615 CAAAGAGCAACGAAATCACTAAGAG 58.697 40.000 0.00 0.00 0.00 2.85
68 69 5.334105 GCAAAGAGCAACGAAATCACTAAGA 60.334 40.000 0.00 0.00 44.79 2.10
69 70 4.848299 GCAAAGAGCAACGAAATCACTAAG 59.152 41.667 0.00 0.00 44.79 2.18
70 71 4.610456 CGCAAAGAGCAACGAAATCACTAA 60.610 41.667 0.00 0.00 46.13 2.24
71 72 3.120683 CGCAAAGAGCAACGAAATCACTA 60.121 43.478 0.00 0.00 46.13 2.74
72 73 2.349817 CGCAAAGAGCAACGAAATCACT 60.350 45.455 0.00 0.00 46.13 3.41
73 74 1.971962 CGCAAAGAGCAACGAAATCAC 59.028 47.619 0.00 0.00 46.13 3.06
74 75 1.662876 GCGCAAAGAGCAACGAAATCA 60.663 47.619 0.30 0.00 46.13 2.57
75 76 0.977674 GCGCAAAGAGCAACGAAATC 59.022 50.000 0.30 0.00 46.13 2.17
76 77 0.387239 GGCGCAAAGAGCAACGAAAT 60.387 50.000 10.83 0.00 46.13 2.17
77 78 1.008995 GGCGCAAAGAGCAACGAAA 60.009 52.632 10.83 0.00 46.13 3.46
78 79 1.719725 TTGGCGCAAAGAGCAACGAA 61.720 50.000 10.83 0.00 46.13 3.85
79 80 1.514678 ATTGGCGCAAAGAGCAACGA 61.515 50.000 10.83 0.00 46.13 3.85
80 81 0.167908 TATTGGCGCAAAGAGCAACG 59.832 50.000 10.83 0.00 46.13 4.10
81 82 1.617740 GTATTGGCGCAAAGAGCAAC 58.382 50.000 10.83 0.00 46.13 4.17
82 83 0.525761 GGTATTGGCGCAAAGAGCAA 59.474 50.000 16.06 6.72 46.13 3.91
83 84 0.607762 TGGTATTGGCGCAAAGAGCA 60.608 50.000 19.40 19.40 46.13 4.26
84 85 0.179163 GTGGTATTGGCGCAAAGAGC 60.179 55.000 14.24 14.24 40.87 4.09
85 86 1.398390 GAGTGGTATTGGCGCAAAGAG 59.602 52.381 10.83 0.00 0.00 2.85
86 87 1.003118 AGAGTGGTATTGGCGCAAAGA 59.997 47.619 10.83 0.00 0.00 2.52
87 88 1.453155 AGAGTGGTATTGGCGCAAAG 58.547 50.000 10.83 0.00 0.00 2.77
88 89 1.810151 GAAGAGTGGTATTGGCGCAAA 59.190 47.619 10.83 3.91 0.00 3.68
89 90 1.448985 GAAGAGTGGTATTGGCGCAA 58.551 50.000 10.83 0.00 0.00 4.85
90 91 0.392461 GGAAGAGTGGTATTGGCGCA 60.392 55.000 10.83 0.00 0.00 6.09
91 92 1.095807 GGGAAGAGTGGTATTGGCGC 61.096 60.000 0.00 0.00 0.00 6.53
92 93 0.810031 CGGGAAGAGTGGTATTGGCG 60.810 60.000 0.00 0.00 0.00 5.69
93 94 0.463833 CCGGGAAGAGTGGTATTGGC 60.464 60.000 0.00 0.00 0.00 4.52
94 95 0.463833 GCCGGGAAGAGTGGTATTGG 60.464 60.000 2.18 0.00 0.00 3.16
95 96 0.463833 GGCCGGGAAGAGTGGTATTG 60.464 60.000 2.18 0.00 0.00 1.90
96 97 0.620700 AGGCCGGGAAGAGTGGTATT 60.621 55.000 2.18 0.00 0.00 1.89
97 98 0.263765 TAGGCCGGGAAGAGTGGTAT 59.736 55.000 2.18 0.00 0.00 2.73
98 99 0.396695 CTAGGCCGGGAAGAGTGGTA 60.397 60.000 2.18 0.00 0.00 3.25
99 100 1.686110 CTAGGCCGGGAAGAGTGGT 60.686 63.158 2.18 0.00 0.00 4.16
100 101 2.435693 CCTAGGCCGGGAAGAGTGG 61.436 68.421 11.67 0.00 0.00 4.00
101 102 3.095347 GCCTAGGCCGGGAAGAGTG 62.095 68.421 24.19 0.00 34.56 3.51
102 103 2.764547 GCCTAGGCCGGGAAGAGT 60.765 66.667 24.19 0.00 34.56 3.24
112 113 2.902343 GAACCATGCGGCCTAGGC 60.902 66.667 26.55 26.55 41.06 3.93
113 114 2.588877 CGAACCATGCGGCCTAGG 60.589 66.667 3.67 3.67 34.57 3.02
114 115 2.588877 CCGAACCATGCGGCCTAG 60.589 66.667 0.00 0.00 42.55 3.02
120 121 1.330521 CCATCTAAACCGAACCATGCG 59.669 52.381 0.00 0.00 0.00 4.73
121 122 1.676006 CCCATCTAAACCGAACCATGC 59.324 52.381 0.00 0.00 0.00 4.06
122 123 1.676006 GCCCATCTAAACCGAACCATG 59.324 52.381 0.00 0.00 0.00 3.66
123 124 1.564348 AGCCCATCTAAACCGAACCAT 59.436 47.619 0.00 0.00 0.00 3.55
124 125 0.988832 AGCCCATCTAAACCGAACCA 59.011 50.000 0.00 0.00 0.00 3.67
125 126 1.065709 TCAGCCCATCTAAACCGAACC 60.066 52.381 0.00 0.00 0.00 3.62
126 127 2.007608 GTCAGCCCATCTAAACCGAAC 58.992 52.381 0.00 0.00 0.00 3.95
162 167 2.896801 CGTCCTGTTTGCGCTTGCT 61.897 57.895 9.73 0.00 40.12 3.91
169 180 2.165319 ACTTAGTCCGTCCTGTTTGC 57.835 50.000 0.00 0.00 0.00 3.68
172 183 1.346722 CCCAACTTAGTCCGTCCTGTT 59.653 52.381 0.00 0.00 0.00 3.16
178 189 1.003718 GCAGCCCAACTTAGTCCGT 60.004 57.895 0.00 0.00 0.00 4.69
182 193 1.296715 CGAGGCAGCCCAACTTAGT 59.703 57.895 8.22 0.00 0.00 2.24
184 195 2.046314 GCGAGGCAGCCCAACTTA 60.046 61.111 8.22 0.00 0.00 2.24
255 266 4.477975 GACGACGAGGCCGGTCTG 62.478 72.222 16.74 8.87 40.78 3.51
979 999 2.581354 CTCGAACCCCAGCTCCTG 59.419 66.667 0.00 0.00 0.00 3.86
1214 1234 6.127479 GGGCAATGTTACAAATACATCAGGAA 60.127 38.462 0.00 0.00 35.26 3.36
1254 1274 0.967380 GCCCCACCAGTCAAATCCTG 60.967 60.000 0.00 0.00 0.00 3.86
1313 1333 4.706842 ACCAATGTAACTCACCTCAAGT 57.293 40.909 0.00 0.00 0.00 3.16
1592 1617 2.643551 TGCGATCCCTGAATCTTTTCC 58.356 47.619 0.00 0.00 0.00 3.13
1610 1635 4.600692 ATCCACAAAACTTAACCCTTGC 57.399 40.909 0.00 0.00 0.00 4.01
1619 1644 7.558444 TCCACTACTTGTAAATCCACAAAACTT 59.442 33.333 0.00 0.00 37.93 2.66
1624 1649 5.308497 TCCTCCACTACTTGTAAATCCACAA 59.692 40.000 0.00 0.00 36.94 3.33
1633 1658 7.786046 TTAAATCAGTCCTCCACTACTTGTA 57.214 36.000 0.00 0.00 32.21 2.41
1664 1689 8.677870 ATTCTAGATTCTAGGCCAAGTGATAT 57.322 34.615 18.43 0.00 0.00 1.63
1675 1700 5.558818 AGCCATGCAATTCTAGATTCTAGG 58.441 41.667 18.43 5.78 0.00 3.02
1758 1783 5.047660 TCCATTCTTTTGGTTTATTGTCCGG 60.048 40.000 0.00 0.00 38.01 5.14
2050 2075 7.665561 TTTTACCTTTGAAATTGCTATTGCC 57.334 32.000 0.00 0.00 38.71 4.52
2146 2171 2.425143 ATAACCTGAGGTGGCATGTG 57.575 50.000 4.15 0.00 35.34 3.21
2333 2358 2.425143 TGGATGCATCAAGGAAGTCC 57.575 50.000 27.25 9.56 0.00 3.85
2457 2492 7.396418 AGATAATGGCAAACAATTTTGGTGAT 58.604 30.769 0.00 0.00 42.22 3.06
2459 2494 6.875195 AGAGATAATGGCAAACAATTTTGGTG 59.125 34.615 0.00 0.00 42.22 4.17
2477 2512 7.423844 TCCAGCAGAATAACAGAAGAGATAA 57.576 36.000 0.00 0.00 0.00 1.75
2664 2699 7.325660 ACCATAACTGACAAAATGCTAGATG 57.674 36.000 0.00 0.00 0.00 2.90
2665 2700 7.944729 AACCATAACTGACAAAATGCTAGAT 57.055 32.000 0.00 0.00 0.00 1.98
2695 2730 2.493675 GTGAAGGGGAAATTTCTGAGGC 59.506 50.000 17.42 6.15 0.00 4.70
2868 3312 9.736023 GATGGCAGGAAAAGTTAAATTAGTATG 57.264 33.333 0.00 0.00 0.00 2.39
3188 3633 0.811281 AAATACAGAAAGGGCTGCGC 59.189 50.000 8.86 8.86 39.51 6.09
3312 3764 5.765182 ACTTGGTTAACAATGAGTCTCCTTG 59.235 40.000 14.31 14.31 38.65 3.61
3542 3994 4.082571 AGAGGTGCTTGCATTATGTTCAAC 60.083 41.667 0.00 0.00 0.00 3.18
3599 4051 6.657541 TCCACACTATATCACCCAAAAACTTC 59.342 38.462 0.00 0.00 0.00 3.01
3650 4103 4.351127 AGTAGTTCCACCCGAAGTTATCT 58.649 43.478 0.00 0.00 35.65 1.98
3695 4148 5.009610 CCAGTAGCTCTAGAGAACTTGGATC 59.990 48.000 24.24 2.06 0.00 3.36
3853 4307 7.381948 TGCAACTGTTTAAGCAATCTTGTATTG 59.618 33.333 2.00 0.00 33.48 1.90
3896 4353 1.202818 GGACAAAGAAGCAGACTGGGT 60.203 52.381 4.26 0.00 0.00 4.51
3919 4388 3.009033 TGAAACCCCACAAGTGATCCTAG 59.991 47.826 0.94 0.00 0.00 3.02
3936 4405 8.696410 TGTTTACAAAGTTTTGGATCTGAAAC 57.304 30.769 9.22 13.23 42.34 2.78
3965 4434 5.762711 ACATTTACATGCGGCACATAGAATA 59.237 36.000 4.03 0.00 36.64 1.75
3977 4446 7.857389 ACTCATTGCTATTAACATTTACATGCG 59.143 33.333 0.00 0.00 33.05 4.73
4007 4483 0.171903 GCTGCCACATGAGCGATTTT 59.828 50.000 0.00 0.00 0.00 1.82
4040 4516 1.940613 GCCAGGAGCGGTATTTAACTG 59.059 52.381 0.00 0.00 37.55 3.16
4090 4566 2.749839 TTGCCACGCATGCCCTAC 60.750 61.111 13.15 0.00 38.76 3.18
4098 4574 2.186160 CCACTTCAGTTGCCACGCA 61.186 57.895 0.00 0.00 36.47 5.24
4099 4575 2.639286 CCACTTCAGTTGCCACGC 59.361 61.111 0.00 0.00 0.00 5.34
4100 4576 1.518056 ATGCCACTTCAGTTGCCACG 61.518 55.000 0.84 0.00 36.02 4.94
4101 4577 1.470098 CTATGCCACTTCAGTTGCCAC 59.530 52.381 0.84 0.00 36.02 5.01
4102 4578 1.073763 ACTATGCCACTTCAGTTGCCA 59.926 47.619 0.84 0.00 36.02 4.92
4103 4579 1.740025 GACTATGCCACTTCAGTTGCC 59.260 52.381 0.84 0.00 36.02 4.52
4104 4580 1.394917 CGACTATGCCACTTCAGTTGC 59.605 52.381 0.00 0.00 37.23 4.17
4105 4581 2.002586 CCGACTATGCCACTTCAGTTG 58.997 52.381 0.00 0.00 0.00 3.16
4106 4582 1.676014 GCCGACTATGCCACTTCAGTT 60.676 52.381 0.00 0.00 0.00 3.16
4107 4583 0.108138 GCCGACTATGCCACTTCAGT 60.108 55.000 0.00 0.00 0.00 3.41
4108 4584 1.148157 CGCCGACTATGCCACTTCAG 61.148 60.000 0.00 0.00 0.00 3.02
4109 4585 1.153647 CGCCGACTATGCCACTTCA 60.154 57.895 0.00 0.00 0.00 3.02
4110 4586 1.883084 CCGCCGACTATGCCACTTC 60.883 63.158 0.00 0.00 0.00 3.01
4111 4587 1.324740 TACCGCCGACTATGCCACTT 61.325 55.000 0.00 0.00 0.00 3.16
4112 4588 1.755395 TACCGCCGACTATGCCACT 60.755 57.895 0.00 0.00 0.00 4.00
4113 4589 1.590792 GTACCGCCGACTATGCCAC 60.591 63.158 0.00 0.00 0.00 5.01
4114 4590 1.755395 AGTACCGCCGACTATGCCA 60.755 57.895 0.00 0.00 0.00 4.92
4115 4591 1.299926 CAGTACCGCCGACTATGCC 60.300 63.158 0.00 0.00 0.00 4.40
4116 4592 1.299926 CCAGTACCGCCGACTATGC 60.300 63.158 0.00 0.00 0.00 3.14
4175 4651 2.355010 ATTTGGCATCAGACCTAGGC 57.645 50.000 9.30 1.39 0.00 3.93
4176 4652 4.978099 ACATATTTGGCATCAGACCTAGG 58.022 43.478 7.41 7.41 0.00 3.02
4177 4653 6.169094 CCTACATATTTGGCATCAGACCTAG 58.831 44.000 0.00 0.00 0.00 3.02
4178 4654 5.013079 CCCTACATATTTGGCATCAGACCTA 59.987 44.000 0.00 0.00 0.00 3.08
4179 4655 4.202503 CCCTACATATTTGGCATCAGACCT 60.203 45.833 0.00 0.00 0.00 3.85
4180 4656 4.074970 CCCTACATATTTGGCATCAGACC 58.925 47.826 0.00 0.00 0.00 3.85
4181 4657 4.516698 CACCCTACATATTTGGCATCAGAC 59.483 45.833 0.00 0.00 0.00 3.51
4182 4658 4.717877 CACCCTACATATTTGGCATCAGA 58.282 43.478 0.00 0.00 0.00 3.27
4202 4678 6.741448 TTTGCAAAAGACGTAAATTAGCAC 57.259 33.333 10.02 0.00 0.00 4.40
4203 4679 7.938563 AATTTGCAAAAGACGTAAATTAGCA 57.061 28.000 17.19 0.08 37.04 3.49
4204 4680 9.644993 AAAAATTTGCAAAAGACGTAAATTAGC 57.355 25.926 17.19 0.00 37.58 3.09
4206 4682 9.836739 CGAAAAATTTGCAAAAGACGTAAATTA 57.163 25.926 17.19 0.00 37.58 1.40
4207 4683 8.596380 TCGAAAAATTTGCAAAAGACGTAAATT 58.404 25.926 17.19 0.00 39.40 1.82
4208 4684 8.053653 GTCGAAAAATTTGCAAAAGACGTAAAT 58.946 29.630 17.19 0.00 31.12 1.40
4209 4685 7.273815 AGTCGAAAAATTTGCAAAAGACGTAAA 59.726 29.630 17.19 0.00 0.00 2.01
4210 4686 6.748198 AGTCGAAAAATTTGCAAAAGACGTAA 59.252 30.769 17.19 0.00 0.00 3.18
4211 4687 6.259638 AGTCGAAAAATTTGCAAAAGACGTA 58.740 32.000 17.19 6.00 0.00 3.57
4212 4688 5.099575 AGTCGAAAAATTTGCAAAAGACGT 58.900 33.333 17.19 0.59 0.00 4.34
4213 4689 5.620098 AGTCGAAAAATTTGCAAAAGACG 57.380 34.783 17.19 16.25 0.00 4.18
4214 4690 8.592155 AGTTTAGTCGAAAAATTTGCAAAAGAC 58.408 29.630 17.19 16.59 0.00 3.01
4215 4691 8.591312 CAGTTTAGTCGAAAAATTTGCAAAAGA 58.409 29.630 17.19 6.38 0.00 2.52
4216 4692 8.591312 TCAGTTTAGTCGAAAAATTTGCAAAAG 58.409 29.630 17.19 4.15 0.00 2.27
4217 4693 8.467402 TCAGTTTAGTCGAAAAATTTGCAAAA 57.533 26.923 17.19 0.00 0.00 2.44
4228 4704 9.087424 CATCACATTAGATCAGTTTAGTCGAAA 57.913 33.333 0.00 0.00 0.00 3.46
4231 4707 8.634475 TTCATCACATTAGATCAGTTTAGTCG 57.366 34.615 0.00 0.00 0.00 4.18
4250 4726 4.591321 ACTGGGAAGCCTAAATTCATCA 57.409 40.909 0.00 0.00 0.00 3.07
4280 4756 8.833493 GCGTACCCAAATTAATAAACTATCAGT 58.167 33.333 0.00 0.00 0.00 3.41
4333 4809 3.322828 AGGGAATACATTGCATTGCATCC 59.677 43.478 12.95 14.38 38.76 3.51
4345 4821 9.862149 AAATATTTAAGAACGGAGGGAATACAT 57.138 29.630 0.00 0.00 0.00 2.29
4346 4822 9.116067 CAAATATTTAAGAACGGAGGGAATACA 57.884 33.333 0.00 0.00 0.00 2.29
4347 4823 9.117183 ACAAATATTTAAGAACGGAGGGAATAC 57.883 33.333 0.00 0.00 0.00 1.89
4349 4825 8.053355 AGACAAATATTTAAGAACGGAGGGAAT 58.947 33.333 0.00 0.00 0.00 3.01
4351 4827 6.954232 AGACAAATATTTAAGAACGGAGGGA 58.046 36.000 0.00 0.00 0.00 4.20
4352 4828 7.625828 AAGACAAATATTTAAGAACGGAGGG 57.374 36.000 0.00 0.00 0.00 4.30
4353 4829 8.947115 AGAAAGACAAATATTTAAGAACGGAGG 58.053 33.333 0.00 0.00 0.00 4.30
4404 4884 9.157104 TGCTTCGTATGTAGTCATTTATTGAAA 57.843 29.630 0.00 0.00 35.70 2.69
4405 4885 8.710835 TGCTTCGTATGTAGTCATTTATTGAA 57.289 30.769 0.00 0.00 35.70 2.69
4406 4886 8.710835 TTGCTTCGTATGTAGTCATTTATTGA 57.289 30.769 0.00 0.00 35.70 2.57
4407 4887 9.767684 TTTTGCTTCGTATGTAGTCATTTATTG 57.232 29.630 0.00 0.00 35.70 1.90
4409 4889 9.935682 CATTTTGCTTCGTATGTAGTCATTTAT 57.064 29.630 0.00 0.00 35.70 1.40
4410 4890 9.157104 TCATTTTGCTTCGTATGTAGTCATTTA 57.843 29.630 0.00 0.00 35.70 1.40
4411 4891 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
4412 4892 7.334421 ACTCATTTTGCTTCGTATGTAGTCATT 59.666 33.333 0.00 0.00 35.70 2.57
4413 4893 6.818644 ACTCATTTTGCTTCGTATGTAGTCAT 59.181 34.615 0.00 0.00 38.00 3.06
4417 4897 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4469 4949 9.685276 AGATTTCAAATGATTACCACATACAGA 57.315 29.630 0.00 0.00 0.00 3.41
4470 4950 9.941664 GAGATTTCAAATGATTACCACATACAG 57.058 33.333 0.00 0.00 0.00 2.74
4471 4951 9.685276 AGAGATTTCAAATGATTACCACATACA 57.315 29.630 0.00 0.00 0.00 2.29
4498 4978 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
4499 4979 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
4500 4980 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4501 4981 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4502 4982 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4503 4983 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4504 4984 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4505 4985 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4506 4986 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4507 4987 7.450903 CAATACTCCCTCCGTTCCTAAATATT 58.549 38.462 0.00 0.00 0.00 1.28
4508 4988 6.520231 GCAATACTCCCTCCGTTCCTAAATAT 60.520 42.308 0.00 0.00 0.00 1.28
4513 4993 2.037144 GCAATACTCCCTCCGTTCCTA 58.963 52.381 0.00 0.00 0.00 2.94
4514 4994 0.831307 GCAATACTCCCTCCGTTCCT 59.169 55.000 0.00 0.00 0.00 3.36
4526 5006 6.095300 TGCTGCATGTTTTATACTGCAATACT 59.905 34.615 0.00 0.00 39.05 2.12
4527 5007 6.264832 TGCTGCATGTTTTATACTGCAATAC 58.735 36.000 0.00 0.00 39.05 1.89
4528 5008 6.448207 TGCTGCATGTTTTATACTGCAATA 57.552 33.333 0.00 0.00 39.05 1.90
4529 5009 5.327616 TGCTGCATGTTTTATACTGCAAT 57.672 34.783 0.00 0.00 39.05 3.56
4530 5010 4.780275 TGCTGCATGTTTTATACTGCAA 57.220 36.364 0.00 0.00 39.05 4.08
4531 5011 4.484236 GTTGCTGCATGTTTTATACTGCA 58.516 39.130 1.84 0.00 38.04 4.41
4532 5012 3.543494 CGTTGCTGCATGTTTTATACTGC 59.457 43.478 1.84 0.00 33.93 4.40
4533 5013 3.543494 GCGTTGCTGCATGTTTTATACTG 59.457 43.478 1.84 0.00 34.15 2.74
4544 5024 1.445410 CTGCATTGCGTTGCTGCAT 60.445 52.632 1.84 0.00 45.78 3.96


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

AutoCloner maintained by Alex Coulton.