Multiple sequence alignment - TraesCS6B01G145500

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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 TraesCS6B01G145500 chr6B 100.000 3579 0 0 1 3579 145577223 145573645 0.000000e+00 6610.0
1 TraesCS6B01G145500 chr6B 93.564 202 12 1 1 202 108258356 108258156 2.090000e-77 300.0
2 TraesCS6B01G145500 chr6B 91.133 203 16 2 1 202 108262568 108262367 1.270000e-69 274.0
3 TraesCS6B01G145500 chr6B 92.593 108 5 3 2986 3090 495435813 495435920 6.190000e-33 152.0
4 TraesCS6B01G145500 chr6B 96.875 32 1 0 3406 3437 145573564 145573595 2.000000e-03 54.7
5 TraesCS6B01G145500 chr6D 95.542 2759 89 14 245 2984 71054049 71051306 0.000000e+00 4383.0
6 TraesCS6B01G145500 chr6D 93.750 320 17 2 3262 3578 71051148 71050829 8.990000e-131 477.0
7 TraesCS6B01G145500 chr6D 96.774 155 3 1 3071 3225 71051299 71051147 1.270000e-64 257.0
8 TraesCS6B01G145500 chr6D 96.875 32 1 0 3406 3437 71050745 71050776 2.000000e-03 54.7
9 TraesCS6B01G145500 chr2B 89.231 520 46 7 209 724 786503820 786504333 3.010000e-180 641.0
10 TraesCS6B01G145500 chr2B 88.910 523 47 7 209 724 786566099 786566617 5.040000e-178 634.0
11 TraesCS6B01G145500 chr2B 96.875 96 1 2 2986 3079 785216424 785216329 3.700000e-35 159.0
12 TraesCS6B01G145500 chr5B 95.074 203 5 5 1 202 26356517 26356715 7.460000e-82 315.0
13 TraesCS6B01G145500 chr5B 91.089 202 13 3 1 202 708772538 708772734 5.890000e-68 268.0
14 TraesCS6B01G145500 chr5B 79.216 255 45 7 1095 1345 626251032 626250782 1.710000e-38 171.0
15 TraesCS6B01G145500 chr5B 96.809 94 2 1 2987 3079 25333595 25333688 4.780000e-34 156.0
16 TraesCS6B01G145500 chr5B 93.396 106 4 2 2990 3092 605826344 605826449 1.720000e-33 154.0
17 TraesCS6B01G145500 chr1B 91.626 203 11 4 1 202 345512735 345512538 3.520000e-70 276.0
18 TraesCS6B01G145500 chr1B 91.176 204 14 4 1 202 591462652 591462451 1.270000e-69 274.0
19 TraesCS6B01G145500 chr1B 90.732 205 15 4 1 202 556846681 556846884 1.640000e-68 270.0
20 TraesCS6B01G145500 chr1B 90.732 205 15 4 1 202 556876113 556876316 1.640000e-68 270.0
21 TraesCS6B01G145500 chr1B 80.631 222 39 4 1014 1233 113567839 113567620 6.150000e-38 169.0
22 TraesCS6B01G145500 chr1B 81.429 210 35 4 1026 1233 113818076 113817869 6.150000e-38 169.0
23 TraesCS6B01G145500 chr1B 79.741 232 39 7 1097 1324 112865988 112865761 1.030000e-35 161.0
24 TraesCS6B01G145500 chr1B 97.802 91 2 0 2990 3080 301949514 301949424 1.330000e-34 158.0
25 TraesCS6B01G145500 chr1B 73.143 525 104 28 1994 2493 112865052 112864540 1.720000e-33 154.0
26 TraesCS6B01G145500 chr1B 83.974 156 25 0 2255 2410 113212626 113212471 2.230000e-32 150.0
27 TraesCS6B01G145500 chr1B 83.974 156 25 0 2255 2410 113314987 113314832 2.230000e-32 150.0
28 TraesCS6B01G145500 chr1B 83.974 156 25 0 2255 2410 113497775 113497620 2.230000e-32 150.0
29 TraesCS6B01G145500 chr1B 89.655 116 8 3 2990 3103 229258721 229258834 1.040000e-30 145.0
30 TraesCS6B01G145500 chr1B 94.872 39 1 1 2949 2987 165762352 165762389 3.860000e-05 60.2
31 TraesCS6B01G145500 chr7B 91.542 201 10 4 1 200 281963916 281964110 1.640000e-68 270.0
32 TraesCS6B01G145500 chr1D 81.991 211 34 4 1025 1233 72501931 72501723 3.670000e-40 176.0
33 TraesCS6B01G145500 chr1D 74.533 428 80 23 1994 2402 71638788 71638371 3.700000e-35 159.0
34 TraesCS6B01G145500 chr1D 77.647 255 49 7 1095 1345 71639735 71639485 8.010000e-32 148.0
35 TraesCS6B01G145500 chr1D 82.051 156 28 0 2255 2410 72434286 72434131 2.240000e-27 134.0
36 TraesCS6B01G145500 chr1A 81.991 211 34 4 1025 1233 71790101 71789893 3.670000e-40 176.0
37 TraesCS6B01G145500 chr1A 73.714 525 101 28 1994 2493 71724011 71723499 1.710000e-38 171.0
38 TraesCS6B01G145500 chr1A 78.824 255 46 7 1095 1345 71724973 71724723 7.950000e-37 165.0
39 TraesCS6B01G145500 chr1A 96.000 100 3 1 2987 3085 460560019 460559920 1.030000e-35 161.0
40 TraesCS6B01G145500 chr1A 93.023 43 3 0 2949 2991 248432188 248432230 2.980000e-06 63.9
41 TraesCS6B01G145500 chr2A 96.875 96 1 2 2987 3081 199398880 199398974 3.700000e-35 159.0
42 TraesCS6B01G145500 chrUn 85.034 147 22 0 2255 2401 372933798 372933944 2.230000e-32 150.0
43 TraesCS6B01G145500 chr3B 93.269 104 3 4 2987 3087 42629625 42629523 2.230000e-32 150.0
44 TraesCS6B01G145500 chr3B 85.345 116 11 4 529 641 43550789 43550677 8.120000e-22 115.0
45 TraesCS6B01G145500 chr3B 100.000 31 0 0 2908 2938 667663772 667663802 1.390000e-04 58.4


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 TraesCS6B01G145500 chr6B 145573645 145577223 3578 True 6610.000000 6610 100.000000 1 3579 1 chr6B.!!$R3 3578
1 TraesCS6B01G145500 chr6D 71050829 71054049 3220 True 1705.666667 4383 95.355333 245 3578 3 chr6D.!!$R1 3333
2 TraesCS6B01G145500 chr2B 786503820 786504333 513 False 641.000000 641 89.231000 209 724 1 chr2B.!!$F1 515
3 TraesCS6B01G145500 chr2B 786566099 786566617 518 False 634.000000 634 88.910000 209 724 1 chr2B.!!$F2 515

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
138 139 0.037697 TTACTAGTGGCGCACTGTGG 60.038 55.0 18.70 12.34 45.01 4.17 F
350 357 0.104120 CGCATCCCAACCATCTACGA 59.896 55.0 0.00 0.00 0.00 3.43 F
1791 1809 0.246635 GGTTGCTGCTACCTTCTCGA 59.753 55.0 23.12 0.00 32.75 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1640 0.106819 CTCCAAGGCCTTGCAGCTAT 60.107 55.000 35.85 0.93 39.16 2.97 R
1818 1836 0.748005 CCAGTTTAGGTGCCCGGATG 60.748 60.000 0.73 0.00 0.00 3.51 R
3309 3337 1.135859 CGGAGTTGCTTTCATGCAGAC 60.136 52.381 0.00 0.00 44.27 3.51 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
17 18 2.660206 TAATGGCGCACCGTGAGT 59.340 55.556 10.83 0.00 39.70 3.41
42 43 6.563222 TGGTGCACCATTACTAGTTTTAAC 57.437 37.500 34.74 2.50 42.01 2.01
43 44 6.300703 TGGTGCACCATTACTAGTTTTAACT 58.699 36.000 34.74 0.29 42.01 2.24
44 45 7.451732 TGGTGCACCATTACTAGTTTTAACTA 58.548 34.615 34.74 5.01 42.01 2.24
58 59 7.435068 AGTTTTAACTAGTAATGGTGCACAG 57.565 36.000 20.43 7.89 37.52 3.66
59 60 5.873179 TTTAACTAGTAATGGTGCACAGC 57.127 39.130 20.43 2.20 0.00 4.40
60 61 3.417069 AACTAGTAATGGTGCACAGCA 57.583 42.857 20.43 8.86 43.48 4.41
69 70 3.208383 TGCACAGCACCCACGTTG 61.208 61.111 0.00 0.00 31.71 4.10
70 71 4.629115 GCACAGCACCCACGTTGC 62.629 66.667 2.43 2.43 0.00 4.17
71 72 4.312231 CACAGCACCCACGTTGCG 62.312 66.667 5.13 3.64 0.00 4.85
76 77 3.669344 CACCCACGTTGCGCCATT 61.669 61.111 4.18 0.00 0.00 3.16
77 78 2.032834 ACCCACGTTGCGCCATTA 59.967 55.556 4.18 0.00 0.00 1.90
78 79 2.329614 ACCCACGTTGCGCCATTAC 61.330 57.895 4.18 0.00 0.00 1.89
79 80 2.038269 CCCACGTTGCGCCATTACT 61.038 57.895 4.18 0.00 0.00 2.24
80 81 0.741574 CCCACGTTGCGCCATTACTA 60.742 55.000 4.18 0.00 0.00 1.82
81 82 1.080298 CCACGTTGCGCCATTACTAA 58.920 50.000 4.18 0.00 0.00 2.24
82 83 1.201987 CCACGTTGCGCCATTACTAAC 60.202 52.381 4.18 0.00 0.00 2.34
83 84 1.730064 CACGTTGCGCCATTACTAACT 59.270 47.619 4.18 0.00 0.00 2.24
84 85 2.158841 CACGTTGCGCCATTACTAACTT 59.841 45.455 4.18 0.00 0.00 2.66
85 86 2.809696 ACGTTGCGCCATTACTAACTTT 59.190 40.909 4.18 0.00 0.00 2.66
86 87 3.160545 CGTTGCGCCATTACTAACTTTG 58.839 45.455 4.18 0.00 0.00 2.77
87 88 3.498082 GTTGCGCCATTACTAACTTTGG 58.502 45.455 4.18 0.00 0.00 3.28
88 89 3.060736 TGCGCCATTACTAACTTTGGA 57.939 42.857 4.18 0.00 0.00 3.53
89 90 3.413327 TGCGCCATTACTAACTTTGGAA 58.587 40.909 4.18 0.00 0.00 3.53
90 91 3.821600 TGCGCCATTACTAACTTTGGAAA 59.178 39.130 4.18 0.00 0.00 3.13
91 92 4.278669 TGCGCCATTACTAACTTTGGAAAA 59.721 37.500 4.18 0.00 0.00 2.29
92 93 5.221263 TGCGCCATTACTAACTTTGGAAAAA 60.221 36.000 4.18 0.00 0.00 1.94
136 137 2.536761 TTTTACTAGTGGCGCACTGT 57.463 45.000 18.70 16.10 45.01 3.55
137 138 1.790755 TTTACTAGTGGCGCACTGTG 58.209 50.000 18.70 2.76 45.01 3.66
138 139 0.037697 TTACTAGTGGCGCACTGTGG 60.038 55.000 18.70 12.34 45.01 4.17
139 140 0.896479 TACTAGTGGCGCACTGTGGA 60.896 55.000 18.70 8.47 45.01 4.02
140 141 1.219124 CTAGTGGCGCACTGTGGAT 59.781 57.895 18.70 0.00 45.01 3.41
141 142 1.079197 TAGTGGCGCACTGTGGATG 60.079 57.895 18.70 0.00 45.01 3.51
142 143 1.826340 TAGTGGCGCACTGTGGATGT 61.826 55.000 18.70 0.00 45.01 3.06
143 144 2.669229 TGGCGCACTGTGGATGTG 60.669 61.111 10.83 0.00 38.36 3.21
144 145 3.434319 GGCGCACTGTGGATGTGG 61.434 66.667 10.83 0.00 36.08 4.17
145 146 2.669569 GCGCACTGTGGATGTGGT 60.670 61.111 10.21 0.00 36.08 4.16
146 147 2.969806 GCGCACTGTGGATGTGGTG 61.970 63.158 10.21 0.00 36.08 4.17
147 148 2.956987 GCACTGTGGATGTGGTGC 59.043 61.111 10.21 0.00 45.93 5.01
148 149 2.969806 GCACTGTGGATGTGGTGCG 61.970 63.158 10.21 0.00 43.91 5.34
149 150 2.669569 ACTGTGGATGTGGTGCGC 60.670 61.111 0.00 0.00 0.00 6.09
150 151 3.434319 CTGTGGATGTGGTGCGCC 61.434 66.667 10.11 10.11 0.00 6.53
151 152 4.262089 TGTGGATGTGGTGCGCCA 62.262 61.111 16.89 16.89 43.73 5.69
161 162 2.483014 TGGTGCGCCATTACTAGTTT 57.517 45.000 16.89 0.00 40.46 2.66
162 163 3.613494 TGGTGCGCCATTACTAGTTTA 57.387 42.857 16.89 0.00 40.46 2.01
163 164 3.940319 TGGTGCGCCATTACTAGTTTAA 58.060 40.909 16.89 0.00 40.46 1.52
164 165 3.685756 TGGTGCGCCATTACTAGTTTAAC 59.314 43.478 16.89 0.00 40.46 2.01
165 166 3.937079 GGTGCGCCATTACTAGTTTAACT 59.063 43.478 12.58 2.32 34.09 2.24
166 167 5.111293 GGTGCGCCATTACTAGTTTAACTA 58.889 41.667 12.58 4.66 34.09 2.24
167 168 5.233689 GGTGCGCCATTACTAGTTTAACTAG 59.766 44.000 25.34 25.34 42.99 2.57
168 169 7.122950 GGTGCGCCATTACTAGTTTAACTAGT 61.123 42.308 31.86 31.86 46.99 2.57
169 170 7.894934 GGTGCGCCATTACTAGTTTAACTAGTA 60.895 40.741 30.12 30.12 45.46 1.82
178 179 6.270096 CTAGTTTAACTAGTAATGGCGCAC 57.730 41.667 20.54 0.00 42.41 5.34
179 180 4.828829 AGTTTAACTAGTAATGGCGCACT 58.171 39.130 10.83 6.53 0.00 4.40
180 181 5.969423 AGTTTAACTAGTAATGGCGCACTA 58.031 37.500 10.83 7.49 0.00 2.74
181 182 6.579865 AGTTTAACTAGTAATGGCGCACTAT 58.420 36.000 10.83 0.00 0.00 2.12
182 183 6.700520 AGTTTAACTAGTAATGGCGCACTATC 59.299 38.462 10.83 0.00 0.00 2.08
183 184 3.662247 ACTAGTAATGGCGCACTATCC 57.338 47.619 10.83 0.00 0.00 2.59
184 185 2.299297 ACTAGTAATGGCGCACTATCCC 59.701 50.000 10.83 0.00 0.00 3.85
185 186 0.396811 AGTAATGGCGCACTATCCCC 59.603 55.000 10.83 0.00 0.00 4.81
186 187 0.396811 GTAATGGCGCACTATCCCCT 59.603 55.000 10.83 0.00 0.00 4.79
187 188 0.396435 TAATGGCGCACTATCCCCTG 59.604 55.000 10.83 0.00 0.00 4.45
188 189 2.343475 AATGGCGCACTATCCCCTGG 62.343 60.000 10.83 0.00 0.00 4.45
189 190 3.480133 GGCGCACTATCCCCTGGT 61.480 66.667 10.83 0.00 0.00 4.00
190 191 2.203070 GCGCACTATCCCCTGGTG 60.203 66.667 0.30 0.00 39.24 4.17
193 194 2.203070 CACTATCCCCTGGTGCGC 60.203 66.667 0.00 0.00 28.87 6.09
194 195 3.480133 ACTATCCCCTGGTGCGCC 61.480 66.667 10.11 10.11 0.00 6.53
195 196 3.479203 CTATCCCCTGGTGCGCCA 61.479 66.667 19.93 19.93 43.73 5.69
196 197 2.772191 TATCCCCTGGTGCGCCAT 60.772 61.111 21.54 7.06 45.05 4.40
197 198 2.343475 CTATCCCCTGGTGCGCCATT 62.343 60.000 21.54 5.33 45.05 3.16
198 199 1.057275 TATCCCCTGGTGCGCCATTA 61.057 55.000 21.54 5.96 45.05 1.90
199 200 2.624674 ATCCCCTGGTGCGCCATTAC 62.625 60.000 21.54 0.00 45.05 1.89
200 201 2.272146 CCCTGGTGCGCCATTACT 59.728 61.111 21.54 0.00 45.05 2.24
201 202 1.524961 CCCTGGTGCGCCATTACTA 59.475 57.895 21.54 0.00 45.05 1.82
202 203 0.108585 CCCTGGTGCGCCATTACTAT 59.891 55.000 21.54 0.00 45.05 2.12
203 204 1.512926 CCTGGTGCGCCATTACTATC 58.487 55.000 21.54 0.00 45.05 2.08
204 205 1.512926 CTGGTGCGCCATTACTATCC 58.487 55.000 21.54 0.00 45.05 2.59
205 206 0.107831 TGGTGCGCCATTACTATCCC 59.892 55.000 16.89 0.00 40.46 3.85
206 207 0.605589 GGTGCGCCATTACTATCCCC 60.606 60.000 12.58 0.00 34.09 4.81
207 208 0.396811 GTGCGCCATTACTATCCCCT 59.603 55.000 4.18 0.00 0.00 4.79
212 213 1.056660 CCATTACTATCCCCTGCCGT 58.943 55.000 0.00 0.00 0.00 5.68
243 246 2.125147 GCAGGTGGCGCTGATGTA 60.125 61.111 7.64 0.00 0.00 2.29
335 342 1.662608 CTCCTCTCCATACGCGCAT 59.337 57.895 5.73 0.00 0.00 4.73
350 357 0.104120 CGCATCCCAACCATCTACGA 59.896 55.000 0.00 0.00 0.00 3.43
387 394 2.027561 CCAACACCTGAAATCCCGAGTA 60.028 50.000 0.00 0.00 0.00 2.59
439 446 3.138798 GCATGAGCCCTGCACCTG 61.139 66.667 0.00 0.00 39.46 4.00
447 454 1.133482 AGCCCTGCACCTGTTAAAACT 60.133 47.619 0.00 0.00 0.00 2.66
457 464 2.227194 CTGTTAAAACTGGAACCGGCT 58.773 47.619 0.00 0.00 0.00 5.52
488 495 1.375908 GCAGCCGATGACAACAGGA 60.376 57.895 0.00 0.00 0.00 3.86
527 534 2.768527 CCCACCTCTCATAGACACACAT 59.231 50.000 0.00 0.00 0.00 3.21
539 546 2.626266 AGACACACATGACGGTAGAACA 59.374 45.455 0.00 0.00 0.00 3.18
541 548 2.101750 ACACACATGACGGTAGAACACA 59.898 45.455 0.00 0.00 0.00 3.72
544 551 3.006430 ACACATGACGGTAGAACACATGA 59.994 43.478 0.00 0.00 40.13 3.07
554 562 3.602390 AGAACACATGAAAAACGACGG 57.398 42.857 0.00 0.00 0.00 4.79
588 596 4.578871 TGATTGTCACATCAACTCCGATT 58.421 39.130 0.00 0.00 0.00 3.34
612 620 1.271762 CGGCCAGGATCATTCCATCAT 60.272 52.381 2.24 0.00 45.30 2.45
619 627 6.463897 GCCAGGATCATTCCATCATGAAAAAT 60.464 38.462 0.00 0.00 45.30 1.82
649 657 4.082125 AGGATTCGTTTGGAAGCTCAATT 58.918 39.130 0.00 0.00 40.84 2.32
783 796 0.761187 GGGTAAATCCTACCCGGACC 59.239 60.000 0.73 0.00 46.80 4.46
784 797 1.499368 GGTAAATCCTACCCGGACCA 58.501 55.000 0.73 0.00 46.80 4.02
796 809 2.345991 GGACCAGCGTGCCTAACA 59.654 61.111 0.00 0.00 0.00 2.41
829 842 4.137116 TCGGCCCATATATTATGTGAGC 57.863 45.455 0.00 0.72 0.00 4.26
837 850 5.578336 CCATATATTATGTGAGCCGTGTCTG 59.422 44.000 2.27 0.00 0.00 3.51
953 971 1.226888 CGGTCCCGATTTCCTCGTC 60.227 63.158 0.00 0.00 46.18 4.20
1074 1092 2.746277 GGCATTCCACGGAAGCGT 60.746 61.111 4.58 0.00 37.56 5.07
1299 1317 2.159028 CCTCTCCAAAATCCTCTCCGAC 60.159 54.545 0.00 0.00 0.00 4.79
1419 1437 0.323816 TCCAGGAGCTCGACATCAGT 60.324 55.000 7.83 0.00 0.00 3.41
1428 1446 1.057636 TCGACATCAGTTTCGTTCGC 58.942 50.000 0.00 0.00 36.60 4.70
1498 1516 2.606213 TGGCATCCACCCTCGTCA 60.606 61.111 0.00 0.00 0.00 4.35
1597 1615 3.565482 ACTACACTACGTTTCCTTGTCGA 59.435 43.478 0.00 0.00 0.00 4.20
1622 1640 3.041211 AGTTCCTACATGGCATGCTCTA 58.959 45.455 26.70 11.30 35.26 2.43
1791 1809 0.246635 GGTTGCTGCTACCTTCTCGA 59.753 55.000 23.12 0.00 32.75 4.04
1818 1836 1.653151 GCGGTGGGACTATTCAGTTC 58.347 55.000 0.00 0.00 34.21 3.01
1944 1962 5.871465 TGCAGAATACATTTTTACGCTCA 57.129 34.783 0.00 0.00 0.00 4.26
1990 2009 4.631377 CCGATCAGCTTGACAAACTTGATA 59.369 41.667 8.07 0.00 0.00 2.15
2028 2047 1.548357 GCTCTCACTTCTGGCCCTCA 61.548 60.000 0.00 0.00 0.00 3.86
2121 2140 8.618702 ATTCATCCTTGCTATTCTCAACATAG 57.381 34.615 0.00 0.00 0.00 2.23
2162 2184 8.757982 AGAATCTAGTTGATTGGCATGTAATT 57.242 30.769 4.47 0.00 44.70 1.40
2197 2219 2.240667 ACCAGCTTTGACATATGCCTCT 59.759 45.455 1.58 0.00 0.00 3.69
2234 2256 6.092955 AGCTGCAGAAAAATTCAAAGATGA 57.907 33.333 20.43 0.00 0.00 2.92
2254 2276 4.051237 TGAATGTGAAAGACGTGTCTCTG 58.949 43.478 2.48 0.00 39.39 3.35
2260 2282 2.656560 AAGACGTGTCTCTGTATGGC 57.343 50.000 2.48 0.00 39.39 4.40
2281 2303 3.126831 CCCACTAGATTCAGTCGAATGC 58.873 50.000 8.24 0.00 42.06 3.56
2303 2325 3.500289 CCTTGGGACCCATCTCAAAGAAA 60.500 47.826 15.83 0.00 44.92 2.52
2331 2353 3.678056 ACTGAATTACGAAGGCTGTGA 57.322 42.857 0.00 0.00 0.00 3.58
2335 2357 2.472695 ATTACGAAGGCTGTGAGCAA 57.527 45.000 0.00 0.00 44.75 3.91
2523 2545 6.039382 GGTTTGGATGATGTCATTAACTACCC 59.961 42.308 0.00 0.00 36.57 3.69
2525 2547 4.407621 TGGATGATGTCATTAACTACCCGT 59.592 41.667 0.00 0.00 36.57 5.28
2528 2550 5.918426 TGATGTCATTAACTACCCGTGTA 57.082 39.130 0.00 0.00 0.00 2.90
2582 2604 4.037208 ACTGCTTGTTTTCTGAATGAGGTG 59.963 41.667 0.00 0.00 0.00 4.00
2590 2612 6.652481 TGTTTTCTGAATGAGGTGATTCTCTC 59.348 38.462 0.00 0.00 34.04 3.20
2666 2691 6.592607 CGTTTTGTAGATGGAGTTAAAGCCTA 59.407 38.462 0.00 0.00 0.00 3.93
2689 2714 8.768955 CCTAAAGATCATATTGTCTTTTCCTCG 58.231 37.037 14.16 0.00 40.71 4.63
2699 2724 4.894784 TGTCTTTTCCTCGCTTTGTAGAT 58.105 39.130 0.00 0.00 0.00 1.98
2870 2895 5.948162 ACATGATCAGGCTACACAATTCTTT 59.052 36.000 7.40 0.00 0.00 2.52
2872 2897 6.899393 TGATCAGGCTACACAATTCTTTTT 57.101 33.333 0.00 0.00 0.00 1.94
2910 2936 1.165270 AGGCATGGCTTGTTCGTTAC 58.835 50.000 17.44 0.00 0.00 2.50
2918 2944 2.614779 GCTTGTTCGTTACTACTCCCC 58.385 52.381 0.00 0.00 0.00 4.81
2984 3010 5.751990 ACGTCTTATATTTCTTTACAGCGGG 59.248 40.000 0.00 0.00 0.00 6.13
2985 3011 5.981315 CGTCTTATATTTCTTTACAGCGGGA 59.019 40.000 0.00 0.00 0.00 5.14
2989 3015 8.867097 TCTTATATTTCTTTACAGCGGGAGTAT 58.133 33.333 0.00 0.00 0.00 2.12
2990 3016 9.141400 CTTATATTTCTTTACAGCGGGAGTATC 57.859 37.037 0.00 0.00 0.00 2.24
3004 3030 3.622166 GAGTATCCCTCCGTTCCAAAA 57.378 47.619 0.00 0.00 33.79 2.44
3005 3031 4.152284 GAGTATCCCTCCGTTCCAAAAT 57.848 45.455 0.00 0.00 33.79 1.82
3006 3032 5.286267 GAGTATCCCTCCGTTCCAAAATA 57.714 43.478 0.00 0.00 33.79 1.40
3007 3033 5.291905 AGTATCCCTCCGTTCCAAAATAG 57.708 43.478 0.00 0.00 0.00 1.73
3008 3034 4.966805 AGTATCCCTCCGTTCCAAAATAGA 59.033 41.667 0.00 0.00 0.00 1.98
3009 3035 5.607171 AGTATCCCTCCGTTCCAAAATAGAT 59.393 40.000 0.00 0.00 0.00 1.98
3010 3036 4.150897 TCCCTCCGTTCCAAAATAGATG 57.849 45.455 0.00 0.00 0.00 2.90
3011 3037 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3012 3038 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3013 3039 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
3014 3040 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
3015 3041 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
3016 3042 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
3017 3043 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
3018 3044 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
3019 3045 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
3020 3046 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
3021 3047 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
3022 3048 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
3023 3049 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
3024 3050 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3025 3051 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
3048 3074 7.567458 ACTAACTTTAGTACAAAGTTGGGTCA 58.433 34.615 28.62 17.50 46.38 4.02
3049 3075 8.215736 ACTAACTTTAGTACAAAGTTGGGTCAT 58.784 33.333 28.62 17.19 46.38 3.06
3050 3076 7.506328 AACTTTAGTACAAAGTTGGGTCATC 57.494 36.000 23.48 0.00 45.58 2.92
3051 3077 6.838382 ACTTTAGTACAAAGTTGGGTCATCT 58.162 36.000 14.04 0.00 37.18 2.90
3052 3078 7.970102 ACTTTAGTACAAAGTTGGGTCATCTA 58.030 34.615 14.04 0.00 37.18 1.98
3053 3079 8.603304 ACTTTAGTACAAAGTTGGGTCATCTAT 58.397 33.333 14.04 0.00 37.18 1.98
3054 3080 9.449719 CTTTAGTACAAAGTTGGGTCATCTATT 57.550 33.333 0.00 0.00 0.00 1.73
3055 3081 9.802039 TTTAGTACAAAGTTGGGTCATCTATTT 57.198 29.630 0.00 0.00 0.00 1.40
3056 3082 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
3057 3083 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
3058 3084 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
3059 3085 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
3060 3086 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
3061 3087 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
3062 3088 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
3063 3089 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
3064 3090 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
3065 3091 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
3066 3092 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
3067 3093 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3068 3094 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
3069 3095 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
3070 3096 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
3071 3097 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
3072 3098 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
3073 3099 4.586306 ATTTTGGAACGGAGGGAGTATT 57.414 40.909 0.00 0.00 0.00 1.89
3074 3100 4.376225 TTTTGGAACGGAGGGAGTATTT 57.624 40.909 0.00 0.00 0.00 1.40
3075 3101 5.502089 TTTTGGAACGGAGGGAGTATTTA 57.498 39.130 0.00 0.00 0.00 1.40
3076 3102 5.703730 TTTGGAACGGAGGGAGTATTTAT 57.296 39.130 0.00 0.00 0.00 1.40
3077 3103 5.703730 TTGGAACGGAGGGAGTATTTATT 57.296 39.130 0.00 0.00 0.00 1.40
3078 3104 6.811634 TTGGAACGGAGGGAGTATTTATTA 57.188 37.500 0.00 0.00 0.00 0.98
3079 3105 6.415206 TGGAACGGAGGGAGTATTTATTAG 57.585 41.667 0.00 0.00 0.00 1.73
3104 3130 8.495260 AGGCTATTACCTATTAGTCAGCTTTTT 58.505 33.333 0.00 0.00 38.67 1.94
3152 3178 8.477419 TGTTGAAATTAAAGGGAGAGAAATGT 57.523 30.769 0.00 0.00 0.00 2.71
3179 3205 9.630098 AACAAAATCTTTAGTTCAGTGCATATG 57.370 29.630 0.00 0.00 0.00 1.78
3225 3251 7.497579 GGTCAATTTTGGGAGTTGTTTTACATT 59.502 33.333 0.00 0.00 0.00 2.71
3226 3252 8.888716 GTCAATTTTGGGAGTTGTTTTACATTT 58.111 29.630 0.00 0.00 0.00 2.32
3227 3253 9.103861 TCAATTTTGGGAGTTGTTTTACATTTC 57.896 29.630 0.00 0.00 0.00 2.17
3228 3254 9.108284 CAATTTTGGGAGTTGTTTTACATTTCT 57.892 29.630 0.00 0.00 0.00 2.52
3229 3255 9.679661 AATTTTGGGAGTTGTTTTACATTTCTT 57.320 25.926 0.00 0.00 0.00 2.52
3230 3256 8.485976 TTTTGGGAGTTGTTTTACATTTCTTG 57.514 30.769 0.00 0.00 0.00 3.02
3231 3257 5.596845 TGGGAGTTGTTTTACATTTCTTGC 58.403 37.500 0.00 0.00 0.00 4.01
3232 3258 5.362430 TGGGAGTTGTTTTACATTTCTTGCT 59.638 36.000 0.00 0.00 0.00 3.91
3233 3259 5.691754 GGGAGTTGTTTTACATTTCTTGCTG 59.308 40.000 0.00 0.00 0.00 4.41
3234 3260 5.691754 GGAGTTGTTTTACATTTCTTGCTGG 59.308 40.000 0.00 0.00 0.00 4.85
3235 3261 6.460953 GGAGTTGTTTTACATTTCTTGCTGGA 60.461 38.462 0.00 0.00 0.00 3.86
3236 3262 6.872920 AGTTGTTTTACATTTCTTGCTGGAA 58.127 32.000 0.00 0.00 0.00 3.53
3237 3263 6.980397 AGTTGTTTTACATTTCTTGCTGGAAG 59.020 34.615 2.09 2.09 0.00 3.46
3238 3264 5.841810 TGTTTTACATTTCTTGCTGGAAGG 58.158 37.500 9.11 0.00 31.85 3.46
3239 3265 5.362430 TGTTTTACATTTCTTGCTGGAAGGT 59.638 36.000 9.11 1.87 31.85 3.50
3240 3266 5.452078 TTTACATTTCTTGCTGGAAGGTG 57.548 39.130 9.11 8.31 31.85 4.00
3241 3267 2.949447 ACATTTCTTGCTGGAAGGTGT 58.051 42.857 9.11 8.87 31.85 4.16
3242 3268 3.299503 ACATTTCTTGCTGGAAGGTGTT 58.700 40.909 9.11 0.00 31.85 3.32
3243 3269 3.319122 ACATTTCTTGCTGGAAGGTGTTC 59.681 43.478 9.11 0.00 31.85 3.18
3328 3357 1.881973 TGTCTGCATGAAAGCAACTCC 59.118 47.619 0.00 0.00 45.13 3.85
3365 3394 4.497473 TGCTAACTTGCCATTTACACAC 57.503 40.909 0.00 0.00 0.00 3.82
3366 3395 3.254657 TGCTAACTTGCCATTTACACACC 59.745 43.478 0.00 0.00 0.00 4.16
3437 3466 8.559536 TCGATTGAAATCTAAAATCTATGCACC 58.440 33.333 0.00 0.00 33.24 5.01
3479 3508 0.178967 TTTCACTTCCCATGGCAGCA 60.179 50.000 6.09 0.00 0.00 4.41
3481 3510 0.609957 TCACTTCCCATGGCAGCAAG 60.610 55.000 6.09 7.74 0.00 4.01
3524 3553 8.020253 TCAGGATAGGTTATGGAGGGTTAAATA 58.980 37.037 0.00 0.00 0.00 1.40
3553 3582 4.401837 TGCAATATTGTATGGAAGCAGCAA 59.598 37.500 16.61 0.00 0.00 3.91
3554 3583 4.741676 GCAATATTGTATGGAAGCAGCAAC 59.258 41.667 16.61 0.00 0.00 4.17
3555 3584 4.818534 ATATTGTATGGAAGCAGCAACG 57.181 40.909 0.00 0.00 0.00 4.10
3578 3607 2.994186 TAAATGTTAGCCGGACCCTC 57.006 50.000 5.05 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.739929 CACTCACGGTGCGCCATTA 60.740 57.895 18.18 0.00 39.22 1.90
1 2 3.049674 CACTCACGGTGCGCCATT 61.050 61.111 18.18 0.00 39.22 3.16
9 10 2.203015 GTGCACCACACTCACGGT 60.203 61.111 5.22 0.00 46.41 4.83
17 18 8.122366 AGTTAAAACTAGTAATGGTGCACCACA 61.122 37.037 39.95 27.28 42.83 4.17
18 19 6.206048 AGTTAAAACTAGTAATGGTGCACCAC 59.794 38.462 39.95 26.88 42.83 4.16
19 20 6.300703 AGTTAAAACTAGTAATGGTGCACCA 58.699 36.000 39.23 39.23 43.64 4.17
20 21 6.812879 AGTTAAAACTAGTAATGGTGCACC 57.187 37.500 29.67 29.67 37.52 5.01
33 34 7.118680 GCTGTGCACCATTACTAGTTAAAACTA 59.881 37.037 15.69 2.76 40.37 2.24
34 35 6.072673 GCTGTGCACCATTACTAGTTAAAACT 60.073 38.462 15.69 0.39 42.91 2.66
35 36 6.084277 GCTGTGCACCATTACTAGTTAAAAC 58.916 40.000 15.69 0.00 0.00 2.43
36 37 5.765677 TGCTGTGCACCATTACTAGTTAAAA 59.234 36.000 15.69 0.00 31.71 1.52
37 38 5.309638 TGCTGTGCACCATTACTAGTTAAA 58.690 37.500 15.69 0.00 31.71 1.52
38 39 4.900684 TGCTGTGCACCATTACTAGTTAA 58.099 39.130 15.69 0.00 31.71 2.01
39 40 4.545208 TGCTGTGCACCATTACTAGTTA 57.455 40.909 15.69 0.00 31.71 2.24
40 41 3.417069 TGCTGTGCACCATTACTAGTT 57.583 42.857 15.69 0.00 31.71 2.24
52 53 3.208383 CAACGTGGGTGCTGTGCA 61.208 61.111 0.00 0.00 35.60 4.57
53 54 4.629115 GCAACGTGGGTGCTGTGC 62.629 66.667 3.46 0.00 0.00 4.57
54 55 4.312231 CGCAACGTGGGTGCTGTG 62.312 66.667 8.90 0.00 0.00 3.66
59 60 2.328856 TAATGGCGCAACGTGGGTG 61.329 57.895 10.83 0.00 32.36 4.61
60 61 2.032834 TAATGGCGCAACGTGGGT 59.967 55.556 10.83 0.00 32.36 4.51
61 62 0.741574 TAGTAATGGCGCAACGTGGG 60.742 55.000 10.83 0.00 0.00 4.61
62 63 1.080298 TTAGTAATGGCGCAACGTGG 58.920 50.000 10.83 0.00 0.00 4.94
63 64 1.730064 AGTTAGTAATGGCGCAACGTG 59.270 47.619 10.83 0.00 0.00 4.49
64 65 2.088950 AGTTAGTAATGGCGCAACGT 57.911 45.000 10.83 0.00 0.00 3.99
65 66 3.160545 CAAAGTTAGTAATGGCGCAACG 58.839 45.455 10.83 0.00 0.00 4.10
66 67 3.189702 TCCAAAGTTAGTAATGGCGCAAC 59.810 43.478 10.83 2.61 32.87 4.17
67 68 3.413327 TCCAAAGTTAGTAATGGCGCAA 58.587 40.909 10.83 0.00 32.87 4.85
68 69 3.060736 TCCAAAGTTAGTAATGGCGCA 57.939 42.857 10.83 0.00 32.87 6.09
69 70 4.428615 TTTCCAAAGTTAGTAATGGCGC 57.571 40.909 0.00 0.00 32.87 6.53
116 117 2.546368 CACAGTGCGCCACTAGTAAAAA 59.454 45.455 4.18 0.00 43.43 1.94
117 118 2.139917 CACAGTGCGCCACTAGTAAAA 58.860 47.619 4.18 0.00 43.43 1.52
118 119 1.606994 CCACAGTGCGCCACTAGTAAA 60.607 52.381 4.18 0.00 43.43 2.01
119 120 0.037697 CCACAGTGCGCCACTAGTAA 60.038 55.000 4.18 0.00 43.43 2.24
120 121 0.896479 TCCACAGTGCGCCACTAGTA 60.896 55.000 4.18 0.00 43.43 1.82
121 122 1.544825 ATCCACAGTGCGCCACTAGT 61.545 55.000 4.18 7.03 43.43 2.57
122 123 1.086067 CATCCACAGTGCGCCACTAG 61.086 60.000 4.18 6.44 43.43 2.57
123 124 1.079197 CATCCACAGTGCGCCACTA 60.079 57.895 4.18 0.00 43.43 2.74
124 125 2.359107 CATCCACAGTGCGCCACT 60.359 61.111 4.18 5.73 46.51 4.00
125 126 2.669569 ACATCCACAGTGCGCCAC 60.670 61.111 4.18 3.02 34.10 5.01
126 127 2.669229 CACATCCACAGTGCGCCA 60.669 61.111 4.18 0.00 0.00 5.69
127 128 3.434319 CCACATCCACAGTGCGCC 61.434 66.667 4.18 0.00 35.69 6.53
128 129 2.669569 ACCACATCCACAGTGCGC 60.670 61.111 0.00 0.00 35.69 6.09
129 130 2.969806 GCACCACATCCACAGTGCG 61.970 63.158 0.00 0.00 45.28 5.34
131 132 2.969806 GCGCACCACATCCACAGTG 61.970 63.158 0.30 0.00 36.76 3.66
132 133 2.669569 GCGCACCACATCCACAGT 60.670 61.111 0.30 0.00 0.00 3.55
133 134 3.434319 GGCGCACCACATCCACAG 61.434 66.667 10.83 0.00 35.26 3.66
134 135 4.262089 TGGCGCACCACATCCACA 62.262 61.111 10.83 0.00 42.67 4.17
141 142 9.043444 CTAGTTAAACTAGTAATGGCGCACCAC 62.043 44.444 10.83 0.54 44.86 4.16
142 143 7.122483 CTAGTTAAACTAGTAATGGCGCACCA 61.122 42.308 10.83 0.00 45.47 4.17
143 144 3.937079 AGTTAAACTAGTAATGGCGCACC 59.063 43.478 10.83 0.00 0.00 5.01
144 145 6.270096 CTAGTTAAACTAGTAATGGCGCAC 57.730 41.667 10.83 0.00 42.41 5.34
156 157 5.969423 AGTGCGCCATTACTAGTTAAACTA 58.031 37.500 4.18 0.00 0.00 2.24
157 158 4.828829 AGTGCGCCATTACTAGTTAAACT 58.171 39.130 4.18 0.00 0.00 2.66
158 159 6.073927 GGATAGTGCGCCATTACTAGTTAAAC 60.074 42.308 4.18 0.00 33.32 2.01
159 160 5.987347 GGATAGTGCGCCATTACTAGTTAAA 59.013 40.000 4.18 0.00 33.32 1.52
160 161 5.510179 GGGATAGTGCGCCATTACTAGTTAA 60.510 44.000 4.18 0.00 33.32 2.01
161 162 4.021719 GGGATAGTGCGCCATTACTAGTTA 60.022 45.833 4.18 0.00 33.32 2.24
162 163 3.244112 GGGATAGTGCGCCATTACTAGTT 60.244 47.826 4.18 0.00 33.32 2.24
163 164 2.299297 GGGATAGTGCGCCATTACTAGT 59.701 50.000 4.18 0.00 33.32 2.57
164 165 2.353803 GGGGATAGTGCGCCATTACTAG 60.354 54.545 4.18 0.00 40.36 2.57
165 166 1.621814 GGGGATAGTGCGCCATTACTA 59.378 52.381 4.18 6.34 40.36 1.82
166 167 0.396811 GGGGATAGTGCGCCATTACT 59.603 55.000 4.18 3.74 40.36 2.24
167 168 0.396811 AGGGGATAGTGCGCCATTAC 59.603 55.000 4.18 0.00 42.86 1.89
168 169 0.396435 CAGGGGATAGTGCGCCATTA 59.604 55.000 4.18 0.00 42.86 1.90
169 170 1.149174 CAGGGGATAGTGCGCCATT 59.851 57.895 4.18 0.00 42.86 3.16
170 171 2.822637 CCAGGGGATAGTGCGCCAT 61.823 63.158 4.18 0.00 42.86 4.40
171 172 3.479203 CCAGGGGATAGTGCGCCA 61.479 66.667 4.18 0.00 42.86 5.69
172 173 3.480133 ACCAGGGGATAGTGCGCC 61.480 66.667 4.18 0.00 40.90 6.53
173 174 2.203070 CACCAGGGGATAGTGCGC 60.203 66.667 0.00 0.00 0.00 6.09
174 175 2.203070 GCACCAGGGGATAGTGCG 60.203 66.667 0.00 0.00 46.43 5.34
176 177 2.203070 GCGCACCAGGGGATAGTG 60.203 66.667 0.30 0.00 34.58 2.74
177 178 3.480133 GGCGCACCAGGGGATAGT 61.480 66.667 10.83 0.00 35.26 2.12
178 179 3.479203 TGGCGCACCAGGGGATAG 61.479 66.667 10.83 0.00 42.67 2.08
187 188 0.605589 GGGGATAGTAATGGCGCACC 60.606 60.000 10.83 0.00 0.00 5.01
188 189 0.396811 AGGGGATAGTAATGGCGCAC 59.603 55.000 10.83 0.00 0.00 5.34
189 190 0.396435 CAGGGGATAGTAATGGCGCA 59.604 55.000 10.83 0.00 0.00 6.09
190 191 0.955919 GCAGGGGATAGTAATGGCGC 60.956 60.000 0.00 0.00 0.00 6.53
191 192 0.321653 GGCAGGGGATAGTAATGGCG 60.322 60.000 0.00 0.00 0.00 5.69
192 193 0.321653 CGGCAGGGGATAGTAATGGC 60.322 60.000 0.00 0.00 0.00 4.40
193 194 1.002087 GACGGCAGGGGATAGTAATGG 59.998 57.143 0.00 0.00 0.00 3.16
194 195 1.336887 CGACGGCAGGGGATAGTAATG 60.337 57.143 0.00 0.00 0.00 1.90
195 196 0.966920 CGACGGCAGGGGATAGTAAT 59.033 55.000 0.00 0.00 0.00 1.89
196 197 0.396139 ACGACGGCAGGGGATAGTAA 60.396 55.000 0.00 0.00 0.00 2.24
197 198 1.105167 CACGACGGCAGGGGATAGTA 61.105 60.000 0.00 0.00 0.00 1.82
198 199 2.043248 ACGACGGCAGGGGATAGT 60.043 61.111 0.00 0.00 0.00 2.12
199 200 2.417516 CACGACGGCAGGGGATAG 59.582 66.667 0.00 0.00 0.00 2.08
200 201 3.151710 CCACGACGGCAGGGGATA 61.152 66.667 0.00 0.00 0.00 2.59
228 231 2.903357 CCTACATCAGCGCCACCT 59.097 61.111 2.29 0.00 0.00 4.00
335 342 1.673626 GCGTTTCGTAGATGGTTGGGA 60.674 52.381 0.00 0.00 35.04 4.37
435 442 2.578786 CCGGTTCCAGTTTTAACAGGT 58.421 47.619 0.00 0.00 36.54 4.00
439 446 3.434641 GTCTAGCCGGTTCCAGTTTTAAC 59.565 47.826 1.90 0.00 0.00 2.01
447 454 0.912487 AATGGGTCTAGCCGGTTCCA 60.912 55.000 1.90 0.08 38.44 3.53
457 464 0.107703 CGGCTGCAGAAATGGGTCTA 60.108 55.000 20.43 0.00 0.00 2.59
527 534 4.025563 CGTTTTTCATGTGTTCTACCGTCA 60.026 41.667 0.00 0.00 0.00 4.35
539 546 0.309612 GTGCCCGTCGTTTTTCATGT 59.690 50.000 0.00 0.00 0.00 3.21
541 548 2.172851 TAGTGCCCGTCGTTTTTCAT 57.827 45.000 0.00 0.00 0.00 2.57
544 551 2.496111 TGAATAGTGCCCGTCGTTTTT 58.504 42.857 0.00 0.00 0.00 1.94
554 562 5.565592 TGTGACAATCAATGAATAGTGCC 57.434 39.130 0.00 0.00 0.00 5.01
588 596 0.107214 GGAATGATCCTGGCCGTTGA 60.107 55.000 0.00 0.00 42.93 3.18
599 607 7.618964 CGTCATTTTTCATGATGGAATGATC 57.381 36.000 21.61 16.54 38.52 2.92
612 620 2.214376 ATCCTGGCCGTCATTTTTCA 57.786 45.000 0.00 0.00 0.00 2.69
619 627 0.953471 CAAACGAATCCTGGCCGTCA 60.953 55.000 0.00 0.00 35.28 4.35
649 657 0.757561 TGTGTTCTCTGGACCGTCCA 60.758 55.000 19.39 19.39 45.98 4.02
699 707 9.528489 ACTTTGTACTATCCCATTGTTACATTT 57.472 29.630 0.00 0.00 0.00 2.32
783 796 1.226101 CGCATTGTTAGGCACGCTG 60.226 57.895 0.00 0.00 0.00 5.18
784 797 3.039202 GCGCATTGTTAGGCACGCT 62.039 57.895 0.30 0.00 42.81 5.07
883 901 1.081833 AGACCTGGACAGATGGGCT 59.918 57.895 0.00 0.00 33.68 5.19
1074 1092 1.123077 AGCAGTTGTCACTCTGACCA 58.877 50.000 8.01 0.00 46.40 4.02
1386 1404 2.121963 TGGAGGTTGGTGAGGGCT 60.122 61.111 0.00 0.00 0.00 5.19
1534 1552 1.732259 GAAATTCGACAGTGGCACGAT 59.268 47.619 12.71 3.93 36.02 3.73
1597 1615 2.684927 GCATGCCATGTAGGAACTCCTT 60.685 50.000 6.36 0.00 46.09 3.36
1622 1640 0.106819 CTCCAAGGCCTTGCAGCTAT 60.107 55.000 35.85 0.93 39.16 2.97
1818 1836 0.748005 CCAGTTTAGGTGCCCGGATG 60.748 60.000 0.73 0.00 0.00 3.51
1944 1962 4.822026 CATCGTTCCCTAGAGAAAACACT 58.178 43.478 0.00 0.00 0.00 3.55
1990 2009 2.158755 AGCTAAAGCCTTCACAGTGTGT 60.159 45.455 22.29 4.41 43.38 3.72
2028 2047 5.829924 AGGATGTCAAGAACAACATTCAGTT 59.170 36.000 0.00 0.00 42.37 3.16
2162 2184 5.541101 TCAAAGCTGGTGGTAACTAGACTAA 59.459 40.000 0.00 0.00 37.06 2.24
2197 2219 4.960938 TCTGCAGCTAGAAACAGAAAGAA 58.039 39.130 9.47 0.00 36.27 2.52
2234 2256 4.060038 ACAGAGACACGTCTTTCACATT 57.940 40.909 0.38 0.00 40.61 2.71
2254 2276 3.553096 CGACTGAATCTAGTGGGCCATAC 60.553 52.174 10.70 2.57 0.00 2.39
2260 2282 3.126831 GCATTCGACTGAATCTAGTGGG 58.873 50.000 6.99 0.00 42.94 4.61
2281 2303 1.635487 TCTTTGAGATGGGTCCCAAGG 59.365 52.381 16.55 0.00 36.95 3.61
2303 2325 5.057149 GCCTTCGTAATTCAGTATCACCAT 58.943 41.667 0.00 0.00 0.00 3.55
2331 2353 3.900446 GCAAAGCCAACATCTTGCT 57.100 47.368 0.00 0.00 0.00 3.91
2582 2604 7.092716 GGATATGCTTCTTCTCAGAGAGAATC 58.907 42.308 9.64 3.96 45.84 2.52
2590 2612 7.747155 AAATCATGGATATGCTTCTTCTCAG 57.253 36.000 0.00 0.00 34.21 3.35
2666 2691 6.825721 AGCGAGGAAAAGACAATATGATCTTT 59.174 34.615 8.13 8.13 45.03 2.52
2689 2714 7.923888 TCAAGCATTAATCTCATCTACAAAGC 58.076 34.615 0.00 0.00 0.00 3.51
2699 2724 8.456471 CAAGACAATCTTCAAGCATTAATCTCA 58.544 33.333 0.00 0.00 33.78 3.27
2735 2760 8.739972 AGCAGTCATAATAAGTTTAGGTTTTGG 58.260 33.333 0.00 0.00 0.00 3.28
2756 2781 7.065563 CAGAGTTTAGAATGCAAATAGAGCAGT 59.934 37.037 0.00 0.00 46.36 4.40
2788 2813 3.170717 ACCCTGTCGGAAATTACAGAGA 58.829 45.455 7.52 0.00 44.79 3.10
2832 2857 2.975732 TCATGTTGCAACTTTTGGCA 57.024 40.000 28.61 8.58 38.46 4.92
2870 2895 8.927675 TGCCTAAGTAGGAAGATAAAACAAAA 57.072 30.769 8.64 0.00 46.63 2.44
2872 2897 7.556275 CCATGCCTAAGTAGGAAGATAAAACAA 59.444 37.037 8.64 0.00 46.63 2.83
2874 2899 6.017026 GCCATGCCTAAGTAGGAAGATAAAAC 60.017 42.308 8.64 0.00 46.63 2.43
2910 2936 8.711170 TCTTATATTTGTTTACAGGGGGAGTAG 58.289 37.037 0.00 0.00 0.00 2.57
2961 2987 5.981315 TCCCGCTGTAAAGAAATATAAGACG 59.019 40.000 0.00 0.00 0.00 4.18
2984 3010 3.622166 TTTTGGAACGGAGGGATACTC 57.378 47.619 0.00 0.00 45.84 2.59
2985 3011 4.966805 TCTATTTTGGAACGGAGGGATACT 59.033 41.667 0.00 0.00 0.00 2.12
2989 3015 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2990 3016 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2991 3017 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2992 3018 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2994 3020 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2995 3021 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2996 3022 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2998 3024 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2999 3025 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
3022 3048 8.703743 TGACCCAACTTTGTACTAAAGTTAGTA 58.296 33.333 23.56 6.81 45.57 1.82
3023 3049 7.567458 TGACCCAACTTTGTACTAAAGTTAGT 58.433 34.615 23.56 22.58 45.57 2.24
3024 3050 8.617290 ATGACCCAACTTTGTACTAAAGTTAG 57.383 34.615 23.56 20.79 45.57 2.34
3025 3051 8.434392 AGATGACCCAACTTTGTACTAAAGTTA 58.566 33.333 23.56 14.79 45.57 2.24
3027 3053 6.838382 AGATGACCCAACTTTGTACTAAAGT 58.162 36.000 14.04 14.04 41.82 2.66
3028 3054 9.449719 AATAGATGACCCAACTTTGTACTAAAG 57.550 33.333 13.08 13.08 0.00 1.85
3029 3055 9.802039 AAATAGATGACCCAACTTTGTACTAAA 57.198 29.630 0.00 0.00 0.00 1.85
3030 3056 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
3031 3057 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
3032 3058 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
3033 3059 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
3034 3060 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
3035 3061 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
3036 3062 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
3037 3063 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3038 3064 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
3039 3065 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
3040 3066 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
3041 3067 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
3042 3068 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
3043 3069 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3044 3070 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3045 3071 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3046 3072 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
3047 3073 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3048 3074 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3049 3075 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3050 3076 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3051 3077 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
3052 3078 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
3053 3079 4.376225 AAATACTCCCTCCGTTCCAAAA 57.624 40.909 0.00 0.00 0.00 2.44
3054 3080 5.703730 ATAAATACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
3055 3081 5.703730 AATAAATACTCCCTCCGTTCCAA 57.296 39.130 0.00 0.00 0.00 3.53
3056 3082 5.306160 CCTAATAAATACTCCCTCCGTTCCA 59.694 44.000 0.00 0.00 0.00 3.53
3057 3083 5.791666 CCTAATAAATACTCCCTCCGTTCC 58.208 45.833 0.00 0.00 0.00 3.62
3058 3084 5.011840 AGCCTAATAAATACTCCCTCCGTTC 59.988 44.000 0.00 0.00 0.00 3.95
3059 3085 4.906060 AGCCTAATAAATACTCCCTCCGTT 59.094 41.667 0.00 0.00 0.00 4.44
3060 3086 4.490706 AGCCTAATAAATACTCCCTCCGT 58.509 43.478 0.00 0.00 0.00 4.69
3061 3087 6.793505 ATAGCCTAATAAATACTCCCTCCG 57.206 41.667 0.00 0.00 0.00 4.63
3062 3088 8.484575 GGTAATAGCCTAATAAATACTCCCTCC 58.515 40.741 0.00 0.00 0.00 4.30
3063 3089 9.269494 AGGTAATAGCCTAATAAATACTCCCTC 57.731 37.037 0.00 0.00 37.04 4.30
3074 3100 9.992442 AGCTGACTAATAGGTAATAGCCTAATA 57.008 33.333 0.00 0.00 43.58 0.98
3075 3101 8.903059 AGCTGACTAATAGGTAATAGCCTAAT 57.097 34.615 0.00 0.00 43.58 1.73
3076 3102 8.722622 AAGCTGACTAATAGGTAATAGCCTAA 57.277 34.615 0.00 0.00 43.58 2.69
3077 3103 8.722622 AAAGCTGACTAATAGGTAATAGCCTA 57.277 34.615 0.00 0.00 44.37 3.93
3078 3104 7.619512 AAAGCTGACTAATAGGTAATAGCCT 57.380 36.000 0.00 0.00 42.43 4.58
3079 3105 8.678593 AAAAAGCTGACTAATAGGTAATAGCC 57.321 34.615 0.00 0.00 0.00 3.93
3225 3251 1.981256 GGAACACCTTCCAGCAAGAA 58.019 50.000 0.00 0.00 45.11 2.52
3226 3252 3.725754 GGAACACCTTCCAGCAAGA 57.274 52.632 0.00 0.00 45.11 3.02
3288 3314 4.077108 ACATGACACTGACTTGCATTCAT 58.923 39.130 0.00 0.00 0.00 2.57
3294 3320 1.196354 GCAGACATGACACTGACTTGC 59.804 52.381 17.87 5.78 36.38 4.01
3308 3336 1.881973 GGAGTTGCTTTCATGCAGACA 59.118 47.619 0.00 0.00 44.27 3.41
3309 3337 1.135859 CGGAGTTGCTTTCATGCAGAC 60.136 52.381 0.00 0.00 44.27 3.51
3328 3357 1.588667 GCAACCAACTGCCACAACG 60.589 57.895 0.00 0.00 36.25 4.10
3365 3394 4.342772 GCAGTAAGCAAAACGATACATGG 58.657 43.478 0.00 0.00 44.79 3.66
3437 3466 7.602517 AAGGAGTTTCTAATTCATGAAGTCG 57.397 36.000 12.35 6.37 0.00 4.18
3481 3510 9.979578 CCTATCCTGAATATAGAACTATGCATC 57.020 37.037 0.19 0.00 0.00 3.91
3495 3524 5.989717 ACCCTCCATAACCTATCCTGAATA 58.010 41.667 0.00 0.00 0.00 1.75
3524 3553 8.236585 TGCTTCCATACAATATTGCAAGTAAT 57.763 30.769 15.48 0.00 0.00 1.89
3528 3557 4.980434 GCTGCTTCCATACAATATTGCAAG 59.020 41.667 15.48 10.32 0.00 4.01
3539 3568 3.764885 ATTTCGTTGCTGCTTCCATAC 57.235 42.857 0.00 0.00 0.00 2.39
3553 3582 3.624410 GGTCCGGCTAACATTTATTTCGT 59.376 43.478 0.00 0.00 0.00 3.85
3554 3583 3.002965 GGGTCCGGCTAACATTTATTTCG 59.997 47.826 0.00 0.00 0.00 3.46
3555 3584 4.204799 AGGGTCCGGCTAACATTTATTTC 58.795 43.478 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.