Multiple sequence alignment - TraesCS7A01G408600

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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 TraesCS7A01G408600 chr7A 100.000 4100 0 0 893 4992 594558009 594553910 0.000000e+00 7572.0
1 TraesCS7A01G408600 chr7A 100.000 544 0 0 1 544 594558901 594558358 0.000000e+00 1005.0
2 TraesCS7A01G408600 chr7B 97.076 1368 32 4 1854 3221 552129026 552127667 0.000000e+00 2298.0
3 TraesCS7A01G408600 chr7B 94.152 1368 38 13 3217 4573 552127618 552126282 0.000000e+00 2045.0
4 TraesCS7A01G408600 chr7B 96.744 952 23 5 906 1856 552130078 552129134 0.000000e+00 1580.0
5 TraesCS7A01G408600 chr7B 93.410 349 9 9 193 533 552130406 552130064 5.770000e-139 505.0
6 TraesCS7A01G408600 chr7B 82.609 69 7 4 3709 3775 522138170 522138235 6.980000e-04 56.5
7 TraesCS7A01G408600 chr7D 96.861 1370 40 2 1852 3221 518796440 518795074 0.000000e+00 2289.0
8 TraesCS7A01G408600 chr7D 94.863 1129 34 6 3217 4335 518795025 518793911 0.000000e+00 1742.0
9 TraesCS7A01G408600 chr7D 97.277 955 22 2 906 1856 518797509 518796555 0.000000e+00 1616.0
10 TraesCS7A01G408600 chr7D 88.177 609 39 15 4326 4910 518793757 518793158 0.000000e+00 695.0
11 TraesCS7A01G408600 chr7D 96.821 346 6 3 193 533 518797840 518797495 1.560000e-159 573.0
12 TraesCS7A01G408600 chr1B 83.636 165 24 2 3057 3221 668913799 668913638 8.660000e-33 152.0
13 TraesCS7A01G408600 chr1B 95.000 40 1 1 3747 3785 662552720 662552681 1.500000e-05 62.1
14 TraesCS7A01G408600 chr1B 94.737 38 1 1 3716 3752 174643546 174643509 1.940000e-04 58.4
15 TraesCS7A01G408600 chrUn 91.803 61 3 2 25 84 94312797 94312856 3.200000e-12 84.2
16 TraesCS7A01G408600 chrUn 91.803 61 3 2 25 84 94453325 94453384 3.200000e-12 84.2
17 TraesCS7A01G408600 chrUn 91.803 61 3 2 25 84 284303141 284303200 3.200000e-12 84.2
18 TraesCS7A01G408600 chrUn 91.803 61 3 2 25 84 384732606 384732547 3.200000e-12 84.2
19 TraesCS7A01G408600 chrUn 91.803 61 3 2 25 84 393590455 393590396 3.200000e-12 84.2
20 TraesCS7A01G408600 chr5A 93.103 58 2 2 3720 3776 29677646 29677702 3.200000e-12 84.2
21 TraesCS7A01G408600 chr4A 94.545 55 2 1 3718 3771 387126062 387126116 3.200000e-12 84.2
22 TraesCS7A01G408600 chr2A 89.474 57 5 1 3719 3774 699875898 699875954 2.490000e-08 71.3
23 TraesCS7A01G408600 chr1A 92.857 42 2 1 3739 3780 132413990 132414030 5.400000e-05 60.2
24 TraesCS7A01G408600 chr1A 82.432 74 3 5 3720 3785 550888529 550888600 6.980000e-04 56.5
25 TraesCS7A01G408600 chr1D 100.000 28 0 0 3716 3743 311357636 311357663 9.000000e-03 52.8


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 TraesCS7A01G408600 chr7A 594553910 594558901 4991 True 4288.5 7572 100.0000 1 4992 2 chr7A.!!$R1 4991
1 TraesCS7A01G408600 chr7B 552126282 552130406 4124 True 1607.0 2298 95.3455 193 4573 4 chr7B.!!$R1 4380
2 TraesCS7A01G408600 chr7D 518793158 518797840 4682 True 1383.0 2289 94.7998 193 4910 5 chr7D.!!$R1 4717

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 0.035820 TTTTCGCCCAATCGCTAGGT 60.036 50.000 0.00 0.0 0.00 3.08 F
146 147 0.179171 CAATCGCTAGGTGACGACGT 60.179 55.000 0.00 0.0 41.76 4.34 F
153 154 1.002684 CTAGGTGACGACGTGGCTATC 60.003 57.143 4.58 0.0 0.00 2.08 F
182 183 1.083806 CGCTCTTGATGCACGCCTTA 61.084 55.000 0.00 0.0 0.00 2.69 F
1228 1242 1.098869 TGCGCTCGATCTCTCTTTCT 58.901 50.000 9.73 0.0 0.00 2.52 F
2375 2512 1.043116 GGCCCATAAGCAAACCTCCC 61.043 60.000 0.00 0.0 0.00 4.30 F
3685 3875 1.201647 CATGGCCAAAGAAGAGCACTG 59.798 52.381 10.96 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1407 0.174617 CTTCCTCGCCCTCTTCTGAC 59.825 60.000 0.00 0.0 0.00 3.51 R
1821 1838 3.996150 GATTTGATCGTCAATGCCCAT 57.004 42.857 2.09 0.0 36.11 4.00 R
1857 1994 9.289782 ACTAAATGGATATGGCTTATGAACTTC 57.710 33.333 0.00 0.0 0.00 3.01 R
2335 2472 1.281867 TGGGACATCAGGGACATTCAC 59.718 52.381 0.00 0.0 0.00 3.18 R
2983 3120 2.696989 ATTCACGACAGGCATCATCA 57.303 45.000 0.00 0.0 0.00 3.07 R
3973 4170 0.388659 ATCAGCAAAACCGCAAAGCA 59.611 45.000 0.00 0.0 0.00 3.91 R
4638 5021 0.036164 AACGGTTGATGCACAGGCTA 59.964 50.000 0.00 0.0 41.91 3.93 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
43 44 5.900339 TTTAAGAGTTCTTGTACACAGCG 57.100 39.130 0.00 0.00 37.40 5.18
44 45 3.728076 AAGAGTTCTTGTACACAGCGA 57.272 42.857 0.00 0.00 34.38 4.93
45 46 3.014604 AGAGTTCTTGTACACAGCGAC 57.985 47.619 0.00 0.28 0.00 5.19
46 47 2.361119 AGAGTTCTTGTACACAGCGACA 59.639 45.455 0.00 0.00 0.00 4.35
47 48 2.726760 GAGTTCTTGTACACAGCGACAG 59.273 50.000 0.00 0.00 0.00 3.51
48 49 1.192534 GTTCTTGTACACAGCGACAGC 59.807 52.381 0.00 0.00 45.58 4.40
60 61 3.782042 GACAGCGTCGTCCAATCC 58.218 61.111 0.00 0.00 0.00 3.01
61 62 1.810030 GACAGCGTCGTCCAATCCC 60.810 63.158 0.00 0.00 0.00 3.85
62 63 2.511600 CAGCGTCGTCCAATCCCC 60.512 66.667 0.00 0.00 0.00 4.81
63 64 2.683933 AGCGTCGTCCAATCCCCT 60.684 61.111 0.00 0.00 0.00 4.79
64 65 2.202892 GCGTCGTCCAATCCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
65 66 2.104331 CGTCGTCCAATCCCCTCG 59.896 66.667 0.00 0.00 0.00 4.63
66 67 2.202892 GTCGTCCAATCCCCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
67 68 2.363795 TCGTCCAATCCCCTCGCT 60.364 61.111 0.00 0.00 0.00 4.93
68 69 2.202932 CGTCCAATCCCCTCGCTG 60.203 66.667 0.00 0.00 0.00 5.18
69 70 2.514824 GTCCAATCCCCTCGCTGC 60.515 66.667 0.00 0.00 0.00 5.25
70 71 3.797353 TCCAATCCCCTCGCTGCC 61.797 66.667 0.00 0.00 0.00 4.85
72 73 4.161295 CAATCCCCTCGCTGCCGA 62.161 66.667 0.00 0.00 42.01 5.54
73 74 3.164269 AATCCCCTCGCTGCCGAT 61.164 61.111 0.00 0.00 43.47 4.18
74 75 2.746375 AATCCCCTCGCTGCCGATT 61.746 57.895 0.00 0.00 43.47 3.34
75 76 2.666596 AATCCCCTCGCTGCCGATTC 62.667 60.000 0.00 0.00 43.47 2.52
76 77 3.854669 CCCCTCGCTGCCGATTCT 61.855 66.667 0.00 0.00 43.47 2.40
77 78 2.498941 CCCCTCGCTGCCGATTCTA 61.499 63.158 0.00 0.00 43.47 2.10
78 79 1.441729 CCCTCGCTGCCGATTCTAA 59.558 57.895 0.00 0.00 43.47 2.10
79 80 0.179084 CCCTCGCTGCCGATTCTAAA 60.179 55.000 0.00 0.00 43.47 1.85
80 81 1.651987 CCTCGCTGCCGATTCTAAAA 58.348 50.000 0.00 0.00 43.47 1.52
81 82 2.006888 CCTCGCTGCCGATTCTAAAAA 58.993 47.619 0.00 0.00 43.47 1.94
100 101 4.841441 AAAAATCCCTCGCTGCCA 57.159 50.000 0.00 0.00 0.00 4.92
101 102 3.050089 AAAAATCCCTCGCTGCCAA 57.950 47.368 0.00 0.00 0.00 4.52
102 103 1.560505 AAAAATCCCTCGCTGCCAAT 58.439 45.000 0.00 0.00 0.00 3.16
103 104 1.560505 AAAATCCCTCGCTGCCAATT 58.439 45.000 0.00 0.00 0.00 2.32
104 105 0.819582 AAATCCCTCGCTGCCAATTG 59.180 50.000 0.00 0.00 0.00 2.32
105 106 1.669999 AATCCCTCGCTGCCAATTGC 61.670 55.000 0.00 0.00 41.77 3.56
106 107 2.563013 ATCCCTCGCTGCCAATTGCT 62.563 55.000 0.00 0.00 42.00 3.91
107 108 1.451927 CCCTCGCTGCCAATTGCTA 60.452 57.895 0.00 0.00 42.00 3.49
108 109 1.442526 CCCTCGCTGCCAATTGCTAG 61.443 60.000 0.00 1.39 42.00 3.42
109 110 1.354506 CTCGCTGCCAATTGCTAGC 59.645 57.895 8.10 8.10 42.00 3.42
110 111 2.056481 CTCGCTGCCAATTGCTAGCC 62.056 60.000 13.29 0.00 39.46 3.93
111 112 2.810403 GCTGCCAATTGCTAGCCC 59.190 61.111 13.29 0.00 42.00 5.19
112 113 3.113745 CTGCCAATTGCTAGCCCG 58.886 61.111 13.29 0.00 42.00 6.13
113 114 1.451927 CTGCCAATTGCTAGCCCGA 60.452 57.895 13.29 0.00 42.00 5.14
114 115 0.820891 CTGCCAATTGCTAGCCCGAT 60.821 55.000 13.29 0.60 42.00 4.18
115 116 0.395586 TGCCAATTGCTAGCCCGATT 60.396 50.000 13.29 7.23 42.00 3.34
116 117 0.312102 GCCAATTGCTAGCCCGATTC 59.688 55.000 13.29 0.00 36.87 2.52
117 118 1.972872 CCAATTGCTAGCCCGATTCT 58.027 50.000 13.29 0.00 0.00 2.40
118 119 2.301346 CCAATTGCTAGCCCGATTCTT 58.699 47.619 13.29 0.00 0.00 2.52
119 120 2.689983 CCAATTGCTAGCCCGATTCTTT 59.310 45.455 13.29 0.00 0.00 2.52
120 121 3.131046 CCAATTGCTAGCCCGATTCTTTT 59.869 43.478 13.29 0.00 0.00 2.27
121 122 4.381932 CCAATTGCTAGCCCGATTCTTTTT 60.382 41.667 13.29 0.00 0.00 1.94
137 138 1.091537 TTTTTCGCCCAATCGCTAGG 58.908 50.000 0.00 0.00 0.00 3.02
138 139 0.035820 TTTTCGCCCAATCGCTAGGT 60.036 50.000 0.00 0.00 0.00 3.08
139 140 0.742990 TTTCGCCCAATCGCTAGGTG 60.743 55.000 0.00 0.00 0.00 4.00
140 141 1.609635 TTCGCCCAATCGCTAGGTGA 61.610 55.000 0.00 0.00 38.39 4.02
141 142 1.883084 CGCCCAATCGCTAGGTGAC 60.883 63.158 0.00 0.00 32.75 3.67
142 143 1.883084 GCCCAATCGCTAGGTGACG 60.883 63.158 0.00 0.00 0.00 4.35
143 144 1.813859 CCCAATCGCTAGGTGACGA 59.186 57.895 0.00 0.00 43.33 4.20
144 145 0.527817 CCCAATCGCTAGGTGACGAC 60.528 60.000 0.00 0.00 41.76 4.34
145 146 0.866061 CCAATCGCTAGGTGACGACG 60.866 60.000 0.00 0.00 41.76 5.12
146 147 0.179171 CAATCGCTAGGTGACGACGT 60.179 55.000 0.00 0.00 41.76 4.34
147 148 0.179171 AATCGCTAGGTGACGACGTG 60.179 55.000 4.58 0.00 41.76 4.49
148 149 1.989966 ATCGCTAGGTGACGACGTGG 61.990 60.000 4.58 0.00 41.76 4.94
149 150 2.506438 GCTAGGTGACGACGTGGC 60.506 66.667 4.58 0.00 37.30 5.01
150 151 2.991076 GCTAGGTGACGACGTGGCT 61.991 63.158 4.58 0.00 40.28 4.75
151 152 1.651240 GCTAGGTGACGACGTGGCTA 61.651 60.000 4.58 0.00 40.28 3.93
152 153 1.022735 CTAGGTGACGACGTGGCTAT 58.977 55.000 4.58 0.00 0.00 2.97
153 154 1.002684 CTAGGTGACGACGTGGCTATC 60.003 57.143 4.58 0.00 0.00 2.08
154 155 1.585521 GGTGACGACGTGGCTATCG 60.586 63.158 4.58 0.00 43.97 2.92
155 156 2.101575 TGACGACGTGGCTATCGC 59.898 61.111 4.58 0.00 42.12 4.58
161 162 4.647615 CGTGGCTATCGCGGGGAG 62.648 72.222 6.13 1.96 44.78 4.30
162 163 4.301027 GTGGCTATCGCGGGGAGG 62.301 72.222 6.13 0.00 36.88 4.30
172 173 3.854669 CGGGGAGGCGCTCTTGAT 61.855 66.667 7.64 0.00 0.00 2.57
173 174 2.203126 GGGGAGGCGCTCTTGATG 60.203 66.667 7.64 0.00 0.00 3.07
174 175 2.899339 GGGAGGCGCTCTTGATGC 60.899 66.667 7.64 0.00 0.00 3.91
175 176 2.124983 GGAGGCGCTCTTGATGCA 60.125 61.111 7.64 0.00 0.00 3.96
176 177 2.467826 GGAGGCGCTCTTGATGCAC 61.468 63.158 7.64 0.00 0.00 4.57
177 178 2.806856 GAGGCGCTCTTGATGCACG 61.807 63.158 7.64 0.00 0.00 5.34
179 180 4.527157 GCGCTCTTGATGCACGCC 62.527 66.667 0.00 0.00 43.58 5.68
180 181 2.816958 CGCTCTTGATGCACGCCT 60.817 61.111 0.00 0.00 0.00 5.52
181 182 2.393768 CGCTCTTGATGCACGCCTT 61.394 57.895 0.00 0.00 0.00 4.35
182 183 1.083806 CGCTCTTGATGCACGCCTTA 61.084 55.000 0.00 0.00 0.00 2.69
183 184 1.303309 GCTCTTGATGCACGCCTTAT 58.697 50.000 0.00 0.00 0.00 1.73
184 185 1.672881 GCTCTTGATGCACGCCTTATT 59.327 47.619 0.00 0.00 0.00 1.40
185 186 2.540361 GCTCTTGATGCACGCCTTATTG 60.540 50.000 0.00 0.00 0.00 1.90
186 187 2.679837 CTCTTGATGCACGCCTTATTGT 59.320 45.455 0.00 0.00 0.00 2.71
187 188 3.081061 TCTTGATGCACGCCTTATTGTT 58.919 40.909 0.00 0.00 0.00 2.83
188 189 3.505680 TCTTGATGCACGCCTTATTGTTT 59.494 39.130 0.00 0.00 0.00 2.83
189 190 3.932545 TGATGCACGCCTTATTGTTTT 57.067 38.095 0.00 0.00 0.00 2.43
190 191 3.573598 TGATGCACGCCTTATTGTTTTG 58.426 40.909 0.00 0.00 0.00 2.44
191 192 2.430546 TGCACGCCTTATTGTTTTGG 57.569 45.000 0.00 0.00 0.00 3.28
400 407 1.379843 GTGACCATCGGCCCCAATT 60.380 57.895 0.00 0.00 0.00 2.32
525 536 2.693250 TTCTGGTGGCTCACGTGACG 62.693 60.000 15.76 12.08 34.83 4.35
526 537 4.961511 TGGTGGCTCACGTGACGC 62.962 66.667 23.39 23.39 34.83 5.19
527 538 4.961511 GGTGGCTCACGTGACGCA 62.962 66.667 28.66 18.01 34.83 5.24
528 539 2.738521 GTGGCTCACGTGACGCAT 60.739 61.111 28.66 0.00 0.00 4.73
529 540 2.432456 TGGCTCACGTGACGCATC 60.432 61.111 28.66 18.58 0.00 3.91
530 541 3.545481 GGCTCACGTGACGCATCG 61.545 66.667 28.66 15.98 0.00 3.84
531 542 2.805353 GCTCACGTGACGCATCGT 60.805 61.111 25.27 0.00 45.10 3.73
1228 1242 1.098869 TGCGCTCGATCTCTCTTTCT 58.901 50.000 9.73 0.00 0.00 2.52
1248 1262 8.634444 TCTTTCTCTCCTAATTTCCTTATCGAG 58.366 37.037 0.00 0.00 0.00 4.04
1317 1331 2.284699 AGAAGGAGACGGGGGTGG 60.285 66.667 0.00 0.00 0.00 4.61
1335 1349 3.265791 GTGGATGATGAAGCGAAGAACT 58.734 45.455 0.00 0.00 0.00 3.01
1437 1451 5.277250 AGAAGGGAAAAGGAAAGGTTTTGA 58.723 37.500 0.00 0.00 0.00 2.69
1789 1806 2.107726 GGTAGTCCCACCTGTTTTTCCT 59.892 50.000 0.00 0.00 35.55 3.36
1821 1838 3.126001 AGTTTGATCTCGTTGAAGCCA 57.874 42.857 0.00 0.00 0.00 4.75
1857 1994 4.402583 TCAAATCGCACAAATTAGCTTCG 58.597 39.130 0.00 0.00 0.00 3.79
2335 2472 8.526147 AGATTTTATGGTGGACTGAAATTCTTG 58.474 33.333 0.00 0.00 0.00 3.02
2340 2477 5.139727 TGGTGGACTGAAATTCTTGTGAAT 58.860 37.500 0.00 0.00 44.08 2.57
2375 2512 1.043116 GGCCCATAAGCAAACCTCCC 61.043 60.000 0.00 0.00 0.00 4.30
2408 2545 7.294473 GTTTTCTCAATCTACTTGCTGAAGTC 58.706 38.462 0.00 0.00 41.75 3.01
2472 2609 3.396276 TGATGTGGGTACAAGAAGGGAAA 59.604 43.478 0.00 0.00 40.84 3.13
2504 2641 4.799564 AAAACCTGTTCTGCACAAGAAA 57.200 36.364 0.00 0.00 46.51 2.52
2507 2644 2.023673 CCTGTTCTGCACAAGAAACCA 58.976 47.619 0.00 0.00 46.51 3.67
2521 2658 4.112634 AGAAACCATGAAAGTTAGGGCA 57.887 40.909 0.00 0.00 0.00 5.36
2561 2698 2.693591 TGTGACAAAATGCCCCGTAAAA 59.306 40.909 0.00 0.00 0.00 1.52
2562 2699 3.132289 TGTGACAAAATGCCCCGTAAAAA 59.868 39.130 0.00 0.00 0.00 1.94
2632 2769 7.203910 AGTAGTATGAATCTCTAGTTTTGCGG 58.796 38.462 0.00 0.00 0.00 5.69
3215 3352 4.736126 TGATCTTACCTGAGCGAATTCA 57.264 40.909 6.22 0.00 0.00 2.57
3339 3529 6.288941 TCTGGACGATTTGGTACTAATTCA 57.711 37.500 12.49 0.00 0.00 2.57
3574 3764 4.823442 AGTGTTTGATCATGTTGCAGAAGA 59.177 37.500 0.00 0.00 0.00 2.87
3586 3776 2.346803 TGCAGAAGATGGCGTAGTTTC 58.653 47.619 0.00 0.00 0.00 2.78
3588 3778 2.349886 GCAGAAGATGGCGTAGTTTCTG 59.650 50.000 17.24 17.24 44.60 3.02
3604 3794 5.773091 AGTTTCTGTTTTTAGGGGGAGAAA 58.227 37.500 0.00 0.00 0.00 2.52
3610 3800 1.755200 TTTAGGGGGAGAAAGTGGCT 58.245 50.000 0.00 0.00 0.00 4.75
3630 3820 6.318900 GTGGCTTAGTTGCTAGGTGATATTTT 59.681 38.462 0.00 0.00 0.00 1.82
3685 3875 1.201647 CATGGCCAAAGAAGAGCACTG 59.798 52.381 10.96 0.00 0.00 3.66
4029 4226 3.510459 TGATCCTTCAGACCTTCACTCA 58.490 45.455 0.00 0.00 0.00 3.41
4200 4400 3.812053 GAGGGAGCTAATATGCTGTTGTG 59.188 47.826 0.00 0.00 44.17 3.33
4212 4412 8.807948 AATATGCTGTTGTGTAGTTTCCTAAT 57.192 30.769 0.00 0.00 0.00 1.73
4230 4430 7.482169 TCCTAATTTATGAGCGATGTATCCT 57.518 36.000 0.00 0.00 0.00 3.24
4231 4431 8.589701 TCCTAATTTATGAGCGATGTATCCTA 57.410 34.615 0.00 0.00 0.00 2.94
4232 4432 9.031537 TCCTAATTTATGAGCGATGTATCCTAA 57.968 33.333 0.00 0.00 0.00 2.69
4468 4830 2.561373 GCGTGCTGGTAGGTTTGC 59.439 61.111 0.00 0.00 0.00 3.68
4490 4852 2.937379 ATCGCTGCAGCTGGATGGAC 62.937 60.000 34.22 4.61 39.32 4.02
4566 4931 1.278985 CACAAGAGTAGATGGTGGGCA 59.721 52.381 0.00 0.00 0.00 5.36
4567 4932 1.279271 ACAAGAGTAGATGGTGGGCAC 59.721 52.381 0.00 0.00 0.00 5.01
4610 4993 5.436175 TGCATTCTCTCCAATTTTATCGGA 58.564 37.500 0.00 0.00 0.00 4.55
4628 5011 1.166129 GAAAAAGCTTCCCCTCGTCC 58.834 55.000 0.00 0.00 0.00 4.79
4638 5021 1.472662 CCCCTCGTCCGGCTGATTAT 61.473 60.000 0.00 0.00 0.00 1.28
4659 5042 0.878416 GCCTGTGCATCAACCGTTTA 59.122 50.000 0.00 0.00 37.47 2.01
4665 5048 0.179163 GCATCAACCGTTTAGGCTGC 60.179 55.000 0.00 0.00 46.52 5.25
4671 5054 0.107831 ACCGTTTAGGCTGCTTGACA 59.892 50.000 0.00 0.00 46.52 3.58
4680 5063 1.069765 CTGCTTGACACGTGTCCCT 59.930 57.895 38.12 11.32 44.15 4.20
4689 5072 2.217038 ACGTGTCCCTGTGAGCCAT 61.217 57.895 0.00 0.00 0.00 4.40
4695 5078 1.826921 CCCTGTGAGCCATGCATCC 60.827 63.158 0.00 0.00 0.00 3.51
4699 5084 0.038599 TGTGAGCCATGCATCCTTGT 59.961 50.000 0.00 0.00 0.00 3.16
4702 5087 0.179119 GAGCCATGCATCCTTGTTGC 60.179 55.000 0.00 0.00 40.55 4.17
4715 5100 2.557452 CCTTGTTGCACCTTATCCCCTT 60.557 50.000 0.00 0.00 0.00 3.95
4727 5112 5.103086 ACCTTATCCCCTTATGCCTTCATTT 60.103 40.000 0.00 0.00 34.22 2.32
4728 5113 5.840693 CCTTATCCCCTTATGCCTTCATTTT 59.159 40.000 0.00 0.00 34.22 1.82
4729 5114 6.327365 CCTTATCCCCTTATGCCTTCATTTTT 59.673 38.462 0.00 0.00 34.22 1.94
4730 5115 5.619132 ATCCCCTTATGCCTTCATTTTTG 57.381 39.130 0.00 0.00 34.22 2.44
4750 5135 1.061570 GAAATCTCAGCAAGCGCCG 59.938 57.895 2.29 0.00 39.83 6.46
4757 5142 4.927782 AGCAAGCGCCGTCAACCA 62.928 61.111 2.29 0.00 39.83 3.67
4775 5160 2.900546 ACCATTCGTCCTTCACTCTCTT 59.099 45.455 0.00 0.00 0.00 2.85
4794 5179 2.961536 TCCTCCCAACTCCCATCTAA 57.038 50.000 0.00 0.00 0.00 2.10
4806 5191 0.102481 CCATCTAACACCGTCGGAGG 59.898 60.000 20.51 12.16 37.30 4.30
4856 5241 4.542525 TCCTCCTCTCTCCTTAACTCTCTT 59.457 45.833 0.00 0.00 0.00 2.85
4857 5242 5.015817 TCCTCCTCTCTCCTTAACTCTCTTT 59.984 44.000 0.00 0.00 0.00 2.52
4858 5243 5.359860 CCTCCTCTCTCCTTAACTCTCTTTC 59.640 48.000 0.00 0.00 0.00 2.62
4859 5244 6.147437 TCCTCTCTCCTTAACTCTCTTTCT 57.853 41.667 0.00 0.00 0.00 2.52
4873 5258 2.428171 CTCTTTCTCTCTCTCCCAGCTG 59.572 54.545 6.78 6.78 0.00 4.24
4883 5268 1.617536 TCCCAGCTGAGCTCCCATT 60.618 57.895 17.39 0.00 36.40 3.16
4886 5271 2.124819 AGCTGAGCTCCCATTGCG 60.125 61.111 12.15 0.00 30.62 4.85
4906 5291 1.870055 CTCCGCTGCCAGCACATTTT 61.870 55.000 18.21 0.00 42.58 1.82
4907 5292 1.444895 CCGCTGCCAGCACATTTTC 60.445 57.895 18.21 0.00 42.58 2.29
4908 5293 1.582968 CGCTGCCAGCACATTTTCT 59.417 52.632 18.21 0.00 42.58 2.52
4909 5294 0.455633 CGCTGCCAGCACATTTTCTC 60.456 55.000 18.21 0.00 42.58 2.87
4910 5295 0.886563 GCTGCCAGCACATTTTCTCT 59.113 50.000 12.82 0.00 41.89 3.10
4911 5296 1.135460 GCTGCCAGCACATTTTCTCTC 60.135 52.381 12.82 0.00 41.89 3.20
4912 5297 1.129998 CTGCCAGCACATTTTCTCTCG 59.870 52.381 0.00 0.00 0.00 4.04
4913 5298 1.160137 GCCAGCACATTTTCTCTCGT 58.840 50.000 0.00 0.00 0.00 4.18
4914 5299 1.537202 GCCAGCACATTTTCTCTCGTT 59.463 47.619 0.00 0.00 0.00 3.85
4915 5300 2.413371 GCCAGCACATTTTCTCTCGTTC 60.413 50.000 0.00 0.00 0.00 3.95
4916 5301 3.070018 CCAGCACATTTTCTCTCGTTCT 58.930 45.455 0.00 0.00 0.00 3.01
4917 5302 3.124297 CCAGCACATTTTCTCTCGTTCTC 59.876 47.826 0.00 0.00 0.00 2.87
4918 5303 3.993081 CAGCACATTTTCTCTCGTTCTCT 59.007 43.478 0.00 0.00 0.00 3.10
4919 5304 4.091220 CAGCACATTTTCTCTCGTTCTCTC 59.909 45.833 0.00 0.00 0.00 3.20
4920 5305 3.990469 GCACATTTTCTCTCGTTCTCTCA 59.010 43.478 0.00 0.00 0.00 3.27
4921 5306 4.449068 GCACATTTTCTCTCGTTCTCTCAA 59.551 41.667 0.00 0.00 0.00 3.02
4922 5307 5.613577 GCACATTTTCTCTCGTTCTCTCAAC 60.614 44.000 0.00 0.00 0.00 3.18
4923 5308 5.463392 CACATTTTCTCTCGTTCTCTCAACA 59.537 40.000 0.00 0.00 0.00 3.33
4924 5309 6.018751 CACATTTTCTCTCGTTCTCTCAACAA 60.019 38.462 0.00 0.00 0.00 2.83
4925 5310 6.538742 ACATTTTCTCTCGTTCTCTCAACAAA 59.461 34.615 0.00 0.00 0.00 2.83
4926 5311 5.968387 TTTCTCTCGTTCTCTCAACAAAC 57.032 39.130 0.00 0.00 0.00 2.93
4927 5312 4.649088 TCTCTCGTTCTCTCAACAAACA 57.351 40.909 0.00 0.00 0.00 2.83
4928 5313 5.006153 TCTCTCGTTCTCTCAACAAACAA 57.994 39.130 0.00 0.00 0.00 2.83
4929 5314 5.043903 TCTCTCGTTCTCTCAACAAACAAG 58.956 41.667 0.00 0.00 0.00 3.16
4930 5315 3.555956 TCTCGTTCTCTCAACAAACAAGC 59.444 43.478 0.00 0.00 0.00 4.01
4931 5316 3.531538 TCGTTCTCTCAACAAACAAGCT 58.468 40.909 0.00 0.00 0.00 3.74
4932 5317 3.555956 TCGTTCTCTCAACAAACAAGCTC 59.444 43.478 0.00 0.00 0.00 4.09
4933 5318 3.557595 CGTTCTCTCAACAAACAAGCTCT 59.442 43.478 0.00 0.00 0.00 4.09
4934 5319 4.034510 CGTTCTCTCAACAAACAAGCTCTT 59.965 41.667 0.00 0.00 0.00 2.85
4935 5320 5.234329 CGTTCTCTCAACAAACAAGCTCTTA 59.766 40.000 0.00 0.00 0.00 2.10
4936 5321 6.073548 CGTTCTCTCAACAAACAAGCTCTTAT 60.074 38.462 0.00 0.00 0.00 1.73
4937 5322 6.791887 TCTCTCAACAAACAAGCTCTTATG 57.208 37.500 0.00 0.00 0.00 1.90
4938 5323 6.524734 TCTCTCAACAAACAAGCTCTTATGA 58.475 36.000 0.00 0.00 0.00 2.15
4939 5324 7.164122 TCTCTCAACAAACAAGCTCTTATGAT 58.836 34.615 0.00 0.00 0.00 2.45
4940 5325 7.118825 TCTCTCAACAAACAAGCTCTTATGATG 59.881 37.037 0.00 0.00 0.00 3.07
4941 5326 5.702865 TCAACAAACAAGCTCTTATGATGC 58.297 37.500 0.00 0.00 0.00 3.91
4942 5327 5.474532 TCAACAAACAAGCTCTTATGATGCT 59.525 36.000 0.00 0.00 38.87 3.79
4943 5328 5.557891 ACAAACAAGCTCTTATGATGCTC 57.442 39.130 0.00 0.00 35.85 4.26
4944 5329 5.251764 ACAAACAAGCTCTTATGATGCTCT 58.748 37.500 0.00 0.00 35.85 4.09
4945 5330 5.709164 ACAAACAAGCTCTTATGATGCTCTT 59.291 36.000 0.00 0.00 35.85 2.85
4946 5331 6.208204 ACAAACAAGCTCTTATGATGCTCTTT 59.792 34.615 0.00 0.00 35.85 2.52
4947 5332 6.830873 AACAAGCTCTTATGATGCTCTTTT 57.169 33.333 0.00 0.00 35.85 2.27
4948 5333 6.434018 ACAAGCTCTTATGATGCTCTTTTC 57.566 37.500 0.00 0.00 35.85 2.29
4949 5334 6.179040 ACAAGCTCTTATGATGCTCTTTTCT 58.821 36.000 0.00 0.00 35.85 2.52
4950 5335 6.658391 ACAAGCTCTTATGATGCTCTTTTCTT 59.342 34.615 0.00 0.00 35.85 2.52
4951 5336 6.680874 AGCTCTTATGATGCTCTTTTCTTG 57.319 37.500 0.00 0.00 30.41 3.02
4952 5337 5.066246 AGCTCTTATGATGCTCTTTTCTTGC 59.934 40.000 0.00 0.00 30.41 4.01
4953 5338 5.475273 TCTTATGATGCTCTTTTCTTGCG 57.525 39.130 0.00 0.00 0.00 4.85
4954 5339 4.937620 TCTTATGATGCTCTTTTCTTGCGT 59.062 37.500 0.00 0.00 0.00 5.24
4955 5340 2.975410 TGATGCTCTTTTCTTGCGTG 57.025 45.000 0.00 0.00 0.00 5.34
4956 5341 1.069022 TGATGCTCTTTTCTTGCGTGC 60.069 47.619 0.00 0.00 0.00 5.34
4957 5342 1.198637 GATGCTCTTTTCTTGCGTGCT 59.801 47.619 0.00 0.00 0.00 4.40
4958 5343 1.024271 TGCTCTTTTCTTGCGTGCTT 58.976 45.000 0.00 0.00 0.00 3.91
4959 5344 1.405105 TGCTCTTTTCTTGCGTGCTTT 59.595 42.857 0.00 0.00 0.00 3.51
4960 5345 2.159254 TGCTCTTTTCTTGCGTGCTTTT 60.159 40.909 0.00 0.00 0.00 2.27
4961 5346 2.469147 GCTCTTTTCTTGCGTGCTTTTC 59.531 45.455 0.00 0.00 0.00 2.29
4962 5347 3.793465 GCTCTTTTCTTGCGTGCTTTTCT 60.793 43.478 0.00 0.00 0.00 2.52
4963 5348 3.694734 TCTTTTCTTGCGTGCTTTTCTG 58.305 40.909 0.00 0.00 0.00 3.02
4964 5349 1.838913 TTTCTTGCGTGCTTTTCTGC 58.161 45.000 0.00 0.00 0.00 4.26
4965 5350 0.737804 TTCTTGCGTGCTTTTCTGCA 59.262 45.000 0.00 0.00 41.05 4.41
4966 5351 0.737804 TCTTGCGTGCTTTTCTGCAA 59.262 45.000 0.00 0.00 45.12 4.08
4967 5352 0.848305 CTTGCGTGCTTTTCTGCAAC 59.152 50.000 0.00 0.00 45.12 4.17
4968 5353 0.172127 TTGCGTGCTTTTCTGCAACA 59.828 45.000 0.00 0.00 45.12 3.33
4969 5354 0.172127 TGCGTGCTTTTCTGCAACAA 59.828 45.000 0.00 0.00 45.12 2.83
4970 5355 0.848305 GCGTGCTTTTCTGCAACAAG 59.152 50.000 0.00 0.00 45.12 3.16
4971 5356 1.533756 GCGTGCTTTTCTGCAACAAGA 60.534 47.619 3.86 0.00 45.12 3.02
4972 5357 2.378806 CGTGCTTTTCTGCAACAAGAG 58.621 47.619 3.86 0.00 45.12 2.85
4973 5358 2.122564 GTGCTTTTCTGCAACAAGAGC 58.877 47.619 11.71 11.71 45.12 4.09
4974 5359 2.026641 TGCTTTTCTGCAACAAGAGCT 58.973 42.857 16.93 0.00 40.29 4.09
4975 5360 3.003689 GTGCTTTTCTGCAACAAGAGCTA 59.996 43.478 16.93 5.79 45.12 3.32
4976 5361 3.822735 TGCTTTTCTGCAACAAGAGCTAT 59.177 39.130 16.93 0.00 40.29 2.97
4977 5362 4.164294 GCTTTTCTGCAACAAGAGCTATG 58.836 43.478 11.46 0.00 0.00 2.23
4978 5363 4.320788 GCTTTTCTGCAACAAGAGCTATGT 60.321 41.667 11.46 0.00 0.00 2.29
4979 5364 5.766222 CTTTTCTGCAACAAGAGCTATGTT 58.234 37.500 10.71 10.71 41.50 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 6.535865 TCGCTGTGTACAAGAACTCTTAAAAA 59.464 34.615 0.00 0.00 34.28 1.94
20 21 6.019318 GTCGCTGTGTACAAGAACTCTTAAAA 60.019 38.462 0.00 0.00 34.28 1.52
21 22 5.461078 GTCGCTGTGTACAAGAACTCTTAAA 59.539 40.000 0.00 0.00 34.28 1.52
22 23 4.980434 GTCGCTGTGTACAAGAACTCTTAA 59.020 41.667 0.00 0.00 34.28 1.85
23 24 4.037089 TGTCGCTGTGTACAAGAACTCTTA 59.963 41.667 0.00 0.00 34.28 2.10
24 25 3.181479 TGTCGCTGTGTACAAGAACTCTT 60.181 43.478 0.00 0.00 36.45 2.85
25 26 2.361119 TGTCGCTGTGTACAAGAACTCT 59.639 45.455 0.00 0.00 0.00 3.24
26 27 2.726760 CTGTCGCTGTGTACAAGAACTC 59.273 50.000 0.00 0.00 0.00 3.01
27 28 2.743938 CTGTCGCTGTGTACAAGAACT 58.256 47.619 0.00 0.00 0.00 3.01
28 29 1.192534 GCTGTCGCTGTGTACAAGAAC 59.807 52.381 0.00 1.52 0.00 3.01
29 30 1.497991 GCTGTCGCTGTGTACAAGAA 58.502 50.000 0.00 0.00 0.00 2.52
30 31 0.663269 CGCTGTCGCTGTGTACAAGA 60.663 55.000 0.00 0.00 0.00 3.02
31 32 0.939577 ACGCTGTCGCTGTGTACAAG 60.940 55.000 0.00 0.00 39.84 3.16
32 33 0.937699 GACGCTGTCGCTGTGTACAA 60.938 55.000 0.00 0.00 39.84 2.41
33 34 1.371267 GACGCTGTCGCTGTGTACA 60.371 57.895 0.00 0.00 39.84 2.90
34 35 3.449042 GACGCTGTCGCTGTGTAC 58.551 61.111 3.71 0.00 39.84 2.90
43 44 1.810030 GGGATTGGACGACGCTGTC 60.810 63.158 0.00 0.00 38.17 3.51
44 45 2.264794 GGGATTGGACGACGCTGT 59.735 61.111 0.00 0.00 0.00 4.40
45 46 2.511600 GGGGATTGGACGACGCTG 60.512 66.667 0.00 0.00 0.00 5.18
46 47 2.683933 AGGGGATTGGACGACGCT 60.684 61.111 0.00 0.00 0.00 5.07
47 48 2.202892 GAGGGGATTGGACGACGC 60.203 66.667 0.00 0.00 0.00 5.19
48 49 2.104331 CGAGGGGATTGGACGACG 59.896 66.667 0.00 0.00 0.00 5.12
49 50 2.202892 GCGAGGGGATTGGACGAC 60.203 66.667 0.00 0.00 0.00 4.34
50 51 2.363795 AGCGAGGGGATTGGACGA 60.364 61.111 0.00 0.00 0.00 4.20
51 52 2.202932 CAGCGAGGGGATTGGACG 60.203 66.667 0.00 0.00 0.00 4.79
52 53 2.514824 GCAGCGAGGGGATTGGAC 60.515 66.667 0.00 0.00 0.00 4.02
53 54 3.797353 GGCAGCGAGGGGATTGGA 61.797 66.667 0.00 0.00 0.00 3.53
55 56 2.947938 AATCGGCAGCGAGGGGATTG 62.948 60.000 0.00 0.00 0.00 2.67
56 57 2.666596 GAATCGGCAGCGAGGGGATT 62.667 60.000 0.00 0.00 0.00 3.01
57 58 3.164269 AATCGGCAGCGAGGGGAT 61.164 61.111 0.00 0.00 0.00 3.85
58 59 2.921853 TAGAATCGGCAGCGAGGGGA 62.922 60.000 0.00 0.00 0.00 4.81
59 60 2.028125 TTAGAATCGGCAGCGAGGGG 62.028 60.000 0.00 0.00 0.00 4.79
60 61 0.179084 TTTAGAATCGGCAGCGAGGG 60.179 55.000 0.00 0.00 0.00 4.30
61 62 1.651987 TTTTAGAATCGGCAGCGAGG 58.348 50.000 0.00 0.00 0.00 4.63
83 84 1.560505 ATTGGCAGCGAGGGATTTTT 58.439 45.000 0.00 0.00 0.00 1.94
84 85 1.205417 CAATTGGCAGCGAGGGATTTT 59.795 47.619 0.00 0.00 0.00 1.82
85 86 0.819582 CAATTGGCAGCGAGGGATTT 59.180 50.000 0.00 0.00 0.00 2.17
86 87 1.669999 GCAATTGGCAGCGAGGGATT 61.670 55.000 7.72 0.00 43.97 3.01
87 88 2.123428 GCAATTGGCAGCGAGGGAT 61.123 57.895 7.72 0.00 43.97 3.85
88 89 2.751436 GCAATTGGCAGCGAGGGA 60.751 61.111 7.72 0.00 43.97 4.20
97 98 0.312102 GAATCGGGCTAGCAATTGGC 59.688 55.000 18.24 1.92 45.30 4.52
98 99 1.972872 AGAATCGGGCTAGCAATTGG 58.027 50.000 18.24 0.14 0.00 3.16
99 100 4.376340 AAAAGAATCGGGCTAGCAATTG 57.624 40.909 18.24 0.00 0.00 2.32
118 119 1.091537 CCTAGCGATTGGGCGAAAAA 58.908 50.000 0.00 0.00 38.18 1.94
119 120 0.035820 ACCTAGCGATTGGGCGAAAA 60.036 50.000 6.05 0.00 38.18 2.29
120 121 0.742990 CACCTAGCGATTGGGCGAAA 60.743 55.000 6.05 0.00 38.18 3.46
121 122 1.153449 CACCTAGCGATTGGGCGAA 60.153 57.895 6.05 0.00 38.18 4.70
122 123 2.055633 TCACCTAGCGATTGGGCGA 61.056 57.895 6.05 0.00 38.18 5.54
123 124 1.883084 GTCACCTAGCGATTGGGCG 60.883 63.158 6.05 0.00 38.18 6.13
124 125 1.883084 CGTCACCTAGCGATTGGGC 60.883 63.158 6.05 0.00 0.00 5.36
125 126 0.527817 GTCGTCACCTAGCGATTGGG 60.528 60.000 6.05 0.00 39.38 4.12
126 127 0.866061 CGTCGTCACCTAGCGATTGG 60.866 60.000 0.00 0.00 39.38 3.16
127 128 0.179171 ACGTCGTCACCTAGCGATTG 60.179 55.000 0.00 0.00 39.38 2.67
128 129 0.179171 CACGTCGTCACCTAGCGATT 60.179 55.000 0.00 0.00 39.38 3.34
129 130 1.428219 CACGTCGTCACCTAGCGAT 59.572 57.895 0.00 0.00 39.38 4.58
130 131 2.683859 CCACGTCGTCACCTAGCGA 61.684 63.158 0.00 0.00 34.54 4.93
131 132 2.202440 CCACGTCGTCACCTAGCG 60.202 66.667 0.00 0.00 0.00 4.26
132 133 1.651240 TAGCCACGTCGTCACCTAGC 61.651 60.000 0.00 0.00 0.00 3.42
133 134 1.002684 GATAGCCACGTCGTCACCTAG 60.003 57.143 0.00 0.00 0.00 3.02
134 135 1.019673 GATAGCCACGTCGTCACCTA 58.980 55.000 0.00 0.00 0.00 3.08
135 136 1.807886 GATAGCCACGTCGTCACCT 59.192 57.895 0.00 0.00 0.00 4.00
136 137 1.585521 CGATAGCCACGTCGTCACC 60.586 63.158 0.00 0.00 33.42 4.02
137 138 3.978373 CGATAGCCACGTCGTCAC 58.022 61.111 0.00 0.00 33.42 3.67
155 156 3.854669 ATCAAGAGCGCCTCCCCG 61.855 66.667 2.29 0.00 0.00 5.73
156 157 2.203126 CATCAAGAGCGCCTCCCC 60.203 66.667 2.29 0.00 0.00 4.81
157 158 2.899339 GCATCAAGAGCGCCTCCC 60.899 66.667 2.29 0.00 0.00 4.30
158 159 2.124983 TGCATCAAGAGCGCCTCC 60.125 61.111 2.29 0.00 33.85 4.30
159 160 2.806856 CGTGCATCAAGAGCGCCTC 61.807 63.158 2.29 0.45 39.23 4.70
160 161 2.816958 CGTGCATCAAGAGCGCCT 60.817 61.111 2.29 0.00 39.23 5.52
161 162 4.527157 GCGTGCATCAAGAGCGCC 62.527 66.667 2.29 0.00 41.93 6.53
162 163 4.527157 GGCGTGCATCAAGAGCGC 62.527 66.667 0.00 0.00 46.24 5.92
163 164 1.083806 TAAGGCGTGCATCAAGAGCG 61.084 55.000 0.00 0.00 33.85 5.03
164 165 1.303309 ATAAGGCGTGCATCAAGAGC 58.697 50.000 0.00 0.00 0.00 4.09
165 166 2.679837 ACAATAAGGCGTGCATCAAGAG 59.320 45.455 0.00 0.00 0.00 2.85
166 167 2.710377 ACAATAAGGCGTGCATCAAGA 58.290 42.857 0.00 0.00 0.00 3.02
167 168 3.492421 AACAATAAGGCGTGCATCAAG 57.508 42.857 0.00 0.00 0.00 3.02
168 169 3.932545 AAACAATAAGGCGTGCATCAA 57.067 38.095 0.00 0.00 0.00 2.57
169 170 3.573598 CAAAACAATAAGGCGTGCATCA 58.426 40.909 0.00 0.00 0.00 3.07
170 171 2.923020 CCAAAACAATAAGGCGTGCATC 59.077 45.455 0.00 0.00 0.00 3.91
171 172 2.560542 TCCAAAACAATAAGGCGTGCAT 59.439 40.909 0.00 0.00 0.00 3.96
172 173 1.957177 TCCAAAACAATAAGGCGTGCA 59.043 42.857 0.00 0.00 0.00 4.57
173 174 2.715737 TCCAAAACAATAAGGCGTGC 57.284 45.000 0.00 0.00 0.00 5.34
174 175 5.560966 ACTATCCAAAACAATAAGGCGTG 57.439 39.130 0.00 0.00 0.00 5.34
175 176 4.331717 CGACTATCCAAAACAATAAGGCGT 59.668 41.667 0.00 0.00 0.00 5.68
176 177 4.331717 ACGACTATCCAAAACAATAAGGCG 59.668 41.667 0.00 0.00 0.00 5.52
177 178 5.585047 AGACGACTATCCAAAACAATAAGGC 59.415 40.000 0.00 0.00 0.00 4.35
178 179 6.258068 GGAGACGACTATCCAAAACAATAAGG 59.742 42.308 0.00 0.00 35.54 2.69
179 180 7.042335 AGGAGACGACTATCCAAAACAATAAG 58.958 38.462 0.00 0.00 38.12 1.73
180 181 6.942976 AGGAGACGACTATCCAAAACAATAA 58.057 36.000 0.00 0.00 38.12 1.40
181 182 6.540438 AGGAGACGACTATCCAAAACAATA 57.460 37.500 0.00 0.00 38.12 1.90
182 183 5.422214 AGGAGACGACTATCCAAAACAAT 57.578 39.130 0.00 0.00 38.12 2.71
183 184 4.884668 AGGAGACGACTATCCAAAACAA 57.115 40.909 0.00 0.00 38.12 2.83
184 185 4.884668 AAGGAGACGACTATCCAAAACA 57.115 40.909 0.00 0.00 38.12 2.83
185 186 6.555812 AAAAAGGAGACGACTATCCAAAAC 57.444 37.500 0.00 0.00 38.12 2.43
400 407 0.818938 TTGGGCTCGACGCTATTGTA 59.181 50.000 6.78 0.00 39.13 2.41
910 921 4.673298 TGCGGTTGGACGATGCGT 62.673 61.111 0.00 0.00 45.10 5.24
911 922 4.147322 GTGCGGTTGGACGATGCG 62.147 66.667 0.00 0.00 35.47 4.73
987 998 2.586792 GCCATGCTCGTCCTCCTT 59.413 61.111 0.00 0.00 0.00 3.36
1039 1050 1.298667 CTTCATCGGGGTCGGGTTT 59.701 57.895 0.00 0.00 36.95 3.27
1107 1121 4.129737 TCTTCTTCCTCGCCGCCG 62.130 66.667 0.00 0.00 0.00 6.46
1108 1122 2.202810 CTCTTCTTCCTCGCCGCC 60.203 66.667 0.00 0.00 0.00 6.13
1228 1242 9.144298 ACAATACTCGATAAGGAAATTAGGAGA 57.856 33.333 0.00 0.00 34.40 3.71
1248 1262 3.247648 CGAATCCCCAATCACGACAATAC 59.752 47.826 0.00 0.00 0.00 1.89
1317 1331 5.807520 TCTTACAGTTCTTCGCTTCATCATC 59.192 40.000 0.00 0.00 0.00 2.92
1335 1349 3.055819 AGCGAATCTTGCTTCCTCTTACA 60.056 43.478 0.00 0.00 40.48 2.41
1393 1407 0.174617 CTTCCTCGCCCTCTTCTGAC 59.825 60.000 0.00 0.00 0.00 3.51
1662 1679 6.208840 ACCTTACAAAATCAGAAAGGGGTA 57.791 37.500 4.58 0.00 40.86 3.69
1664 1681 7.178451 ACAATACCTTACAAAATCAGAAAGGGG 59.822 37.037 4.58 0.00 40.86 4.79
1821 1838 3.996150 GATTTGATCGTCAATGCCCAT 57.004 42.857 2.09 0.00 36.11 4.00
1857 1994 9.289782 ACTAAATGGATATGGCTTATGAACTTC 57.710 33.333 0.00 0.00 0.00 3.01
2335 2472 1.281867 TGGGACATCAGGGACATTCAC 59.718 52.381 0.00 0.00 0.00 3.18
2375 2512 7.116805 GCAAGTAGATTGAGAAAACCATTTTGG 59.883 37.037 0.00 0.00 41.80 3.28
2472 2609 2.713828 ACAGGTTTTTGGGGCCTAAT 57.286 45.000 2.11 0.00 0.00 1.73
2504 2641 3.157087 CTGTTGCCCTAACTTTCATGGT 58.843 45.455 0.00 0.00 40.05 3.55
2507 2644 3.806949 TCCTGTTGCCCTAACTTTCAT 57.193 42.857 0.00 0.00 40.05 2.57
2983 3120 2.696989 ATTCACGACAGGCATCATCA 57.303 45.000 0.00 0.00 0.00 3.07
3215 3352 6.323996 TGATAAGTACGGGATCAGACAAAGAT 59.676 38.462 0.00 0.00 0.00 2.40
3360 3550 3.673866 CGCAACATGCATGATGGAAGAAA 60.674 43.478 32.75 0.00 45.36 2.52
3393 3583 8.872845 CAACTCCACAATATTTAAATTTGCTCC 58.127 33.333 5.91 0.00 0.00 4.70
3574 3764 4.457949 CCCTAAAAACAGAAACTACGCCAT 59.542 41.667 0.00 0.00 0.00 4.40
3586 3776 3.826729 CCACTTTCTCCCCCTAAAAACAG 59.173 47.826 0.00 0.00 0.00 3.16
3588 3778 2.561419 GCCACTTTCTCCCCCTAAAAAC 59.439 50.000 0.00 0.00 0.00 2.43
3604 3794 2.257207 TCACCTAGCAACTAAGCCACT 58.743 47.619 0.00 0.00 34.23 4.00
3630 3820 7.668052 ACTTGGGTAAGCACATTTTAGATAACA 59.332 33.333 0.00 0.00 37.43 2.41
3685 3875 4.574599 ATTGCAACTCTTTCACTTCCAC 57.425 40.909 0.00 0.00 0.00 4.02
3794 3991 2.245582 ACCACACTACCAGAGTACCAC 58.754 52.381 0.00 0.00 35.64 4.16
3877 4074 3.126000 GGATCAGTAACTCAAAGCACTGC 59.874 47.826 0.00 0.00 38.60 4.40
3973 4170 0.388659 ATCAGCAAAACCGCAAAGCA 59.611 45.000 0.00 0.00 0.00 3.91
3985 4182 0.764890 CCCCGGGAGAATATCAGCAA 59.235 55.000 26.32 0.00 0.00 3.91
4200 4400 8.366671 ACATCGCTCATAAATTAGGAAACTAC 57.633 34.615 0.00 0.00 44.30 2.73
4255 4455 3.081804 GGGATTACAAGTGGACAAGTGG 58.918 50.000 0.00 0.00 0.00 4.00
4256 4456 3.081804 GGGGATTACAAGTGGACAAGTG 58.918 50.000 0.00 0.00 0.00 3.16
4257 4457 2.714250 TGGGGATTACAAGTGGACAAGT 59.286 45.455 0.00 0.00 0.00 3.16
4258 4458 3.081804 GTGGGGATTACAAGTGGACAAG 58.918 50.000 0.00 0.00 0.00 3.16
4259 4459 2.443632 TGTGGGGATTACAAGTGGACAA 59.556 45.455 0.00 0.00 0.00 3.18
4260 4460 2.058705 TGTGGGGATTACAAGTGGACA 58.941 47.619 0.00 0.00 0.00 4.02
4261 4461 2.817844 GTTGTGGGGATTACAAGTGGAC 59.182 50.000 0.00 0.00 38.58 4.02
4262 4462 2.443632 TGTTGTGGGGATTACAAGTGGA 59.556 45.455 0.00 0.00 38.58 4.02
4490 4852 3.135530 ACTTTGGATGGAGCTTAGCTAGG 59.864 47.826 6.75 0.00 39.88 3.02
4579 4944 8.680039 AAAATTGGAGAGAATGCATTCAAAAA 57.320 26.923 34.59 22.43 39.23 1.94
4610 4993 0.605589 CGGACGAGGGGAAGCTTTTT 60.606 55.000 0.00 0.00 0.00 1.94
4638 5021 0.036164 AACGGTTGATGCACAGGCTA 59.964 50.000 0.00 0.00 41.91 3.93
4642 5025 1.135689 GCCTAAACGGTTGATGCACAG 60.136 52.381 0.00 0.00 34.25 3.66
4659 5042 1.595382 GACACGTGTCAAGCAGCCT 60.595 57.895 37.16 5.72 44.18 4.58
4665 5048 0.104120 TCACAGGGACACGTGTCAAG 59.896 55.000 40.51 31.55 46.47 3.02
4671 5054 2.217038 ATGGCTCACAGGGACACGT 61.217 57.895 0.00 0.00 0.00 4.49
4680 5063 0.038599 ACAAGGATGCATGGCTCACA 59.961 50.000 2.46 0.00 0.00 3.58
4695 5078 2.514458 AGGGGATAAGGTGCAACAAG 57.486 50.000 3.64 0.00 39.98 3.16
4699 5084 2.424234 GGCATAAGGGGATAAGGTGCAA 60.424 50.000 0.00 0.00 33.05 4.08
4702 5087 3.138283 TGAAGGCATAAGGGGATAAGGTG 59.862 47.826 0.00 0.00 0.00 4.00
4704 5089 4.664688 ATGAAGGCATAAGGGGATAAGG 57.335 45.455 0.00 0.00 31.57 2.69
4715 5100 6.440010 TGAGATTTCCCAAAAATGAAGGCATA 59.560 34.615 0.00 0.00 33.44 3.14
4727 5112 1.541147 CGCTTGCTGAGATTTCCCAAA 59.459 47.619 0.00 0.00 0.00 3.28
4728 5113 1.167851 CGCTTGCTGAGATTTCCCAA 58.832 50.000 0.00 0.00 0.00 4.12
4729 5114 1.308069 GCGCTTGCTGAGATTTCCCA 61.308 55.000 0.00 0.00 35.07 4.37
4730 5115 1.431036 GCGCTTGCTGAGATTTCCC 59.569 57.895 0.00 0.00 35.07 3.97
4750 5135 2.737252 GAGTGAAGGACGAATGGTTGAC 59.263 50.000 0.00 0.00 0.00 3.18
4757 5142 3.436243 AGGAAGAGAGTGAAGGACGAAT 58.564 45.455 0.00 0.00 0.00 3.34
4775 5160 2.225779 TGTTAGATGGGAGTTGGGAGGA 60.226 50.000 0.00 0.00 0.00 3.71
4856 5241 1.959508 GCTCAGCTGGGAGAGAGAGAA 60.960 57.143 20.53 0.00 37.05 2.87
4857 5242 0.395586 GCTCAGCTGGGAGAGAGAGA 60.396 60.000 20.53 0.00 37.05 3.10
4858 5243 0.396139 AGCTCAGCTGGGAGAGAGAG 60.396 60.000 20.53 3.86 37.57 3.20
4859 5244 0.395586 GAGCTCAGCTGGGAGAGAGA 60.396 60.000 20.53 0.00 39.88 3.10
4893 5278 1.159285 CGAGAGAAAATGTGCTGGCA 58.841 50.000 0.00 0.00 0.00 4.92
4900 5285 5.601662 TGTTGAGAGAACGAGAGAAAATGT 58.398 37.500 0.00 0.00 0.00 2.71
4902 5287 6.538742 TGTTTGTTGAGAGAACGAGAGAAAAT 59.461 34.615 0.00 0.00 0.00 1.82
4906 5291 4.649088 TGTTTGTTGAGAGAACGAGAGA 57.351 40.909 0.00 0.00 0.00 3.10
4907 5292 4.318404 GCTTGTTTGTTGAGAGAACGAGAG 60.318 45.833 6.84 0.00 37.08 3.20
4908 5293 3.555956 GCTTGTTTGTTGAGAGAACGAGA 59.444 43.478 6.84 0.00 37.08 4.04
4909 5294 3.557595 AGCTTGTTTGTTGAGAGAACGAG 59.442 43.478 0.00 0.00 37.68 4.18
4910 5295 3.531538 AGCTTGTTTGTTGAGAGAACGA 58.468 40.909 0.00 0.00 0.00 3.85
4911 5296 3.557595 AGAGCTTGTTTGTTGAGAGAACG 59.442 43.478 0.00 0.00 0.00 3.95
4912 5297 5.491635 AAGAGCTTGTTTGTTGAGAGAAC 57.508 39.130 0.00 0.00 0.00 3.01
4913 5298 6.992123 TCATAAGAGCTTGTTTGTTGAGAGAA 59.008 34.615 0.00 0.00 0.00 2.87
4914 5299 6.524734 TCATAAGAGCTTGTTTGTTGAGAGA 58.475 36.000 0.00 0.00 0.00 3.10
4915 5300 6.791887 TCATAAGAGCTTGTTTGTTGAGAG 57.208 37.500 0.00 0.00 0.00 3.20
4916 5301 6.348786 GCATCATAAGAGCTTGTTTGTTGAGA 60.349 38.462 0.00 0.00 0.00 3.27
4917 5302 5.798934 GCATCATAAGAGCTTGTTTGTTGAG 59.201 40.000 0.00 0.00 0.00 3.02
4918 5303 5.474532 AGCATCATAAGAGCTTGTTTGTTGA 59.525 36.000 0.00 0.00 34.37 3.18
4919 5304 5.706916 AGCATCATAAGAGCTTGTTTGTTG 58.293 37.500 0.00 0.00 34.37 3.33
4920 5305 5.709164 AGAGCATCATAAGAGCTTGTTTGTT 59.291 36.000 0.00 0.00 39.02 2.83
4921 5306 5.251764 AGAGCATCATAAGAGCTTGTTTGT 58.748 37.500 0.00 0.00 39.02 2.83
4922 5307 5.814764 AGAGCATCATAAGAGCTTGTTTG 57.185 39.130 0.00 0.00 39.02 2.93
4923 5308 6.830873 AAAGAGCATCATAAGAGCTTGTTT 57.169 33.333 0.00 0.00 39.02 2.83
4924 5309 6.658391 AGAAAAGAGCATCATAAGAGCTTGTT 59.342 34.615 0.00 0.00 39.02 2.83
4925 5310 6.179040 AGAAAAGAGCATCATAAGAGCTTGT 58.821 36.000 0.00 0.00 39.02 3.16
4926 5311 6.680874 AGAAAAGAGCATCATAAGAGCTTG 57.319 37.500 0.00 0.00 39.02 4.01
4927 5312 6.404513 GCAAGAAAAGAGCATCATAAGAGCTT 60.405 38.462 0.00 0.00 39.02 3.74
4928 5313 5.066246 GCAAGAAAAGAGCATCATAAGAGCT 59.934 40.000 0.00 0.00 42.17 4.09
4929 5314 5.272397 GCAAGAAAAGAGCATCATAAGAGC 58.728 41.667 0.00 0.00 37.82 4.09
4930 5315 5.064452 ACGCAAGAAAAGAGCATCATAAGAG 59.936 40.000 0.00 0.00 43.62 2.85
4931 5316 4.937620 ACGCAAGAAAAGAGCATCATAAGA 59.062 37.500 0.00 0.00 43.62 2.10
4932 5317 5.026462 CACGCAAGAAAAGAGCATCATAAG 58.974 41.667 0.00 0.00 43.62 1.73
4933 5318 4.672542 GCACGCAAGAAAAGAGCATCATAA 60.673 41.667 0.00 0.00 43.62 1.90
4934 5319 3.181507 GCACGCAAGAAAAGAGCATCATA 60.182 43.478 0.00 0.00 43.62 2.15
4935 5320 2.415090 GCACGCAAGAAAAGAGCATCAT 60.415 45.455 0.00 0.00 43.62 2.45
4936 5321 1.069022 GCACGCAAGAAAAGAGCATCA 60.069 47.619 0.00 0.00 43.62 3.07
4937 5322 1.198637 AGCACGCAAGAAAAGAGCATC 59.801 47.619 0.00 0.00 43.62 3.91
4938 5323 1.242076 AGCACGCAAGAAAAGAGCAT 58.758 45.000 0.00 0.00 43.62 3.79
4939 5324 1.024271 AAGCACGCAAGAAAAGAGCA 58.976 45.000 0.00 0.00 43.62 4.26
4940 5325 2.125461 AAAGCACGCAAGAAAAGAGC 57.875 45.000 0.00 0.00 43.62 4.09
4941 5326 3.727723 CAGAAAAGCACGCAAGAAAAGAG 59.272 43.478 0.00 0.00 43.62 2.85
4942 5327 3.694734 CAGAAAAGCACGCAAGAAAAGA 58.305 40.909 0.00 0.00 43.62 2.52
4943 5328 2.217167 GCAGAAAAGCACGCAAGAAAAG 59.783 45.455 0.00 0.00 43.62 2.27
4944 5329 2.192624 GCAGAAAAGCACGCAAGAAAA 58.807 42.857 0.00 0.00 43.62 2.29
4945 5330 1.133982 TGCAGAAAAGCACGCAAGAAA 59.866 42.857 0.00 0.00 40.11 2.52
4946 5331 0.737804 TGCAGAAAAGCACGCAAGAA 59.262 45.000 0.00 0.00 40.11 2.52
4947 5332 0.737804 TTGCAGAAAAGCACGCAAGA 59.262 45.000 0.00 0.00 45.61 3.02
4948 5333 0.848305 GTTGCAGAAAAGCACGCAAG 59.152 50.000 0.00 0.00 45.61 4.01
4949 5334 0.172127 TGTTGCAGAAAAGCACGCAA 59.828 45.000 0.00 0.00 45.61 4.85
4950 5335 0.172127 TTGTTGCAGAAAAGCACGCA 59.828 45.000 0.00 0.00 45.61 5.24
4951 5336 0.848305 CTTGTTGCAGAAAAGCACGC 59.152 50.000 0.00 0.00 45.61 5.34
4952 5337 2.378806 CTCTTGTTGCAGAAAAGCACG 58.621 47.619 0.00 0.00 45.61 5.34
4953 5338 2.122564 GCTCTTGTTGCAGAAAAGCAC 58.877 47.619 1.94 0.00 45.61 4.40
4954 5339 2.026641 AGCTCTTGTTGCAGAAAAGCA 58.973 42.857 8.18 0.00 43.99 3.91
4955 5340 2.789491 AGCTCTTGTTGCAGAAAAGC 57.211 45.000 0.00 0.00 0.00 3.51
4956 5341 5.368256 ACATAGCTCTTGTTGCAGAAAAG 57.632 39.130 0.00 0.00 0.00 2.27
4957 5342 5.522456 CAACATAGCTCTTGTTGCAGAAAA 58.478 37.500 22.27 0.00 45.10 2.29
4958 5343 5.112220 CAACATAGCTCTTGTTGCAGAAA 57.888 39.130 22.27 0.00 45.10 2.52
4959 5344 4.754372 CAACATAGCTCTTGTTGCAGAA 57.246 40.909 22.27 0.00 45.10 3.02


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

AutoCloner maintained by Alex Coulton.