Multiple sequence alignment - TraesCS6D01G050000

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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 TraesCS6D01G050000 chr6D 100.000 2477 0 0 1 2477 24218716 24221192 0.000000e+00 4575
1 TraesCS6D01G050000 chr6B 90.067 1188 68 27 707 1850 39180402 39181583 0.000000e+00 1495
2 TraesCS6D01G050000 chr6B 85.980 592 43 16 1847 2436 39181616 39182169 4.560000e-167 597
3 TraesCS6D01G050000 chr6A 89.606 1193 73 24 688 1850 22684321 22685492 0.000000e+00 1469
4 TraesCS6D01G050000 chr6A 89.000 400 28 11 2037 2428 22685666 22686057 4.790000e-132 481
5 TraesCS6D01G050000 chr6A 86.009 436 54 7 136 566 22681895 22682328 6.240000e-126 460
6 TraesCS6D01G050000 chr6A 92.920 113 8 0 1847 1959 22685529 22685641 5.480000e-37 165
7 TraesCS6D01G050000 chr6A 92.135 89 6 1 602 690 22682333 22682420 9.300000e-25 124
8 TraesCS6D01G050000 chr5A 84.389 1089 117 31 694 1762 285395532 285396587 0.000000e+00 1020
9 TraesCS6D01G050000 chr5B 83.956 1097 111 35 694 1762 232293640 232294699 0.000000e+00 990
10 TraesCS6D01G050000 chr5D 82.568 958 86 32 830 1762 216154077 216154978 0.000000e+00 769
11 TraesCS6D01G050000 chr7A 82.625 259 35 8 2219 2472 91662115 91661862 1.150000e-53 220


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 TraesCS6D01G050000 chr6D 24218716 24221192 2476 False 4575.0 4575 100.0000 1 2477 1 chr6D.!!$F1 2476
1 TraesCS6D01G050000 chr6B 39180402 39182169 1767 False 1046.0 1495 88.0235 707 2436 2 chr6B.!!$F1 1729
2 TraesCS6D01G050000 chr6A 22681895 22686057 4162 False 539.8 1469 89.9340 136 2428 5 chr6A.!!$F1 2292
3 TraesCS6D01G050000 chr5A 285395532 285396587 1055 False 1020.0 1020 84.3890 694 1762 1 chr5A.!!$F1 1068
4 TraesCS6D01G050000 chr5B 232293640 232294699 1059 False 990.0 990 83.9560 694 1762 1 chr5B.!!$F1 1068
5 TraesCS6D01G050000 chr5D 216154077 216154978 901 False 769.0 769 82.5680 830 1762 1 chr5D.!!$F1 932

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
56 57 0.033601 GATGTTGGGCCCCACATACA 60.034 55.0 35.11 22.84 30.78 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 3839 0.108472 GCCAAGCCAGAGCCAAAATC 60.108 55.0 0.0 0.0 41.25 2.17 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
20 21 2.331194 GCTAGCAAAAGCACAACATGG 58.669 47.619 10.63 0.00 42.30 3.66
21 22 2.030007 GCTAGCAAAAGCACAACATGGA 60.030 45.455 10.63 0.00 42.30 3.41
22 23 3.367703 GCTAGCAAAAGCACAACATGGAT 60.368 43.478 10.63 0.00 42.30 3.41
23 24 3.756933 AGCAAAAGCACAACATGGATT 57.243 38.095 0.00 0.00 0.00 3.01
24 25 4.870123 AGCAAAAGCACAACATGGATTA 57.130 36.364 0.00 0.00 0.00 1.75
25 26 4.813027 AGCAAAAGCACAACATGGATTAG 58.187 39.130 0.00 0.00 0.00 1.73
26 27 3.928375 GCAAAAGCACAACATGGATTAGG 59.072 43.478 0.00 0.00 0.00 2.69
27 28 3.874392 AAAGCACAACATGGATTAGGC 57.126 42.857 0.00 0.00 0.00 3.93
28 29 1.767759 AGCACAACATGGATTAGGCC 58.232 50.000 0.00 0.00 0.00 5.19
29 30 1.285962 AGCACAACATGGATTAGGCCT 59.714 47.619 11.78 11.78 0.00 5.19
30 31 1.406539 GCACAACATGGATTAGGCCTG 59.593 52.381 17.99 0.00 0.00 4.85
31 32 1.406539 CACAACATGGATTAGGCCTGC 59.593 52.381 17.99 4.33 0.00 4.85
32 33 1.035139 CAACATGGATTAGGCCTGCC 58.965 55.000 17.99 14.78 0.00 4.85
33 34 0.106015 AACATGGATTAGGCCTGCCC 60.106 55.000 17.99 14.07 36.58 5.36
34 35 1.228675 CATGGATTAGGCCTGCCCC 60.229 63.158 17.99 13.69 36.58 5.80
35 36 1.701024 ATGGATTAGGCCTGCCCCA 60.701 57.895 17.99 19.07 36.58 4.96
36 37 1.295915 ATGGATTAGGCCTGCCCCAA 61.296 55.000 17.99 0.16 36.58 4.12
37 38 1.152673 GGATTAGGCCTGCCCCAAG 60.153 63.158 17.99 0.00 36.58 3.61
38 39 1.645402 GGATTAGGCCTGCCCCAAGA 61.645 60.000 17.99 0.00 36.58 3.02
39 40 0.480252 GATTAGGCCTGCCCCAAGAT 59.520 55.000 17.99 0.00 36.58 2.40
40 41 0.186873 ATTAGGCCTGCCCCAAGATG 59.813 55.000 17.99 0.00 36.58 2.90
41 42 1.214305 TTAGGCCTGCCCCAAGATGT 61.214 55.000 17.99 0.00 36.58 3.06
42 43 1.214305 TAGGCCTGCCCCAAGATGTT 61.214 55.000 17.99 0.00 36.58 2.71
43 44 2.353610 GGCCTGCCCCAAGATGTTG 61.354 63.158 0.00 0.00 0.00 3.33
51 52 3.698765 CAAGATGTTGGGCCCCAC 58.301 61.111 22.27 20.63 30.78 4.61
52 53 1.228831 CAAGATGTTGGGCCCCACA 60.229 57.895 29.56 29.56 30.78 4.17
53 54 0.615544 CAAGATGTTGGGCCCCACAT 60.616 55.000 35.51 35.51 30.78 3.21
54 55 1.006813 AAGATGTTGGGCCCCACATA 58.993 50.000 35.11 14.50 30.78 2.29
55 56 0.258774 AGATGTTGGGCCCCACATAC 59.741 55.000 35.11 27.14 30.78 2.39
56 57 0.033601 GATGTTGGGCCCCACATACA 60.034 55.000 35.11 22.84 30.78 2.29
57 58 0.636101 ATGTTGGGCCCCACATACAT 59.364 50.000 34.42 23.38 30.78 2.29
58 59 0.324183 TGTTGGGCCCCACATACATG 60.324 55.000 24.51 0.00 30.78 3.21
59 60 1.381056 TTGGGCCCCACATACATGC 60.381 57.895 22.27 0.00 30.78 4.06
60 61 1.873178 TTGGGCCCCACATACATGCT 61.873 55.000 22.27 0.00 30.78 3.79
61 62 0.990818 TGGGCCCCACATACATGCTA 60.991 55.000 22.27 0.00 0.00 3.49
62 63 0.184933 GGGCCCCACATACATGCTAA 59.815 55.000 12.23 0.00 0.00 3.09
63 64 1.203050 GGGCCCCACATACATGCTAAT 60.203 52.381 12.23 0.00 0.00 1.73
64 65 1.888512 GGCCCCACATACATGCTAATG 59.111 52.381 0.00 0.00 39.89 1.90
66 67 2.958355 GCCCCACATACATGCTAATGTT 59.042 45.455 6.27 0.00 44.94 2.71
67 68 3.384467 GCCCCACATACATGCTAATGTTT 59.616 43.478 6.27 0.00 44.94 2.83
68 69 4.499696 GCCCCACATACATGCTAATGTTTC 60.500 45.833 6.27 0.00 44.94 2.78
69 70 4.037923 CCCCACATACATGCTAATGTTTCC 59.962 45.833 6.27 0.00 44.94 3.13
70 71 4.889409 CCCACATACATGCTAATGTTTCCT 59.111 41.667 6.27 0.00 44.94 3.36
71 72 5.221106 CCCACATACATGCTAATGTTTCCTG 60.221 44.000 6.27 0.00 44.94 3.86
72 73 5.589855 CCACATACATGCTAATGTTTCCTGA 59.410 40.000 6.27 0.00 44.94 3.86
73 74 6.458751 CCACATACATGCTAATGTTTCCTGAC 60.459 42.308 6.27 0.00 44.94 3.51
74 75 5.590259 ACATACATGCTAATGTTTCCTGACC 59.410 40.000 0.00 0.00 44.94 4.02
75 76 4.307032 ACATGCTAATGTTTCCTGACCT 57.693 40.909 0.00 0.00 44.94 3.85
76 77 4.265073 ACATGCTAATGTTTCCTGACCTC 58.735 43.478 0.00 0.00 44.94 3.85
77 78 4.263462 ACATGCTAATGTTTCCTGACCTCA 60.263 41.667 0.00 0.00 44.94 3.86
78 79 4.574674 TGCTAATGTTTCCTGACCTCAT 57.425 40.909 0.00 0.00 0.00 2.90
79 80 5.692115 TGCTAATGTTTCCTGACCTCATA 57.308 39.130 0.00 0.00 0.00 2.15
80 81 5.428253 TGCTAATGTTTCCTGACCTCATAC 58.572 41.667 0.00 0.00 0.00 2.39
81 82 5.189736 TGCTAATGTTTCCTGACCTCATACT 59.810 40.000 0.00 0.00 0.00 2.12
82 83 6.116126 GCTAATGTTTCCTGACCTCATACTT 58.884 40.000 0.00 0.00 0.00 2.24
83 84 7.093068 TGCTAATGTTTCCTGACCTCATACTTA 60.093 37.037 0.00 0.00 0.00 2.24
84 85 7.224949 GCTAATGTTTCCTGACCTCATACTTAC 59.775 40.741 0.00 0.00 0.00 2.34
85 86 6.620877 ATGTTTCCTGACCTCATACTTACA 57.379 37.500 0.00 0.00 0.00 2.41
86 87 6.620877 TGTTTCCTGACCTCATACTTACAT 57.379 37.500 0.00 0.00 0.00 2.29
87 88 6.406370 TGTTTCCTGACCTCATACTTACATG 58.594 40.000 0.00 0.00 0.00 3.21
88 89 4.672587 TCCTGACCTCATACTTACATGC 57.327 45.455 0.00 0.00 0.00 4.06
89 90 4.030216 TCCTGACCTCATACTTACATGCA 58.970 43.478 0.00 0.00 0.00 3.96
90 91 4.122776 CCTGACCTCATACTTACATGCAC 58.877 47.826 0.00 0.00 0.00 4.57
91 92 4.383010 CCTGACCTCATACTTACATGCACA 60.383 45.833 0.00 0.00 0.00 4.57
92 93 5.357742 TGACCTCATACTTACATGCACAT 57.642 39.130 0.00 0.00 0.00 3.21
93 94 6.462909 CCTGACCTCATACTTACATGCACATA 60.463 42.308 0.00 0.00 0.00 2.29
94 95 7.066307 TGACCTCATACTTACATGCACATAT 57.934 36.000 0.00 0.00 0.00 1.78
95 96 6.930722 TGACCTCATACTTACATGCACATATG 59.069 38.462 0.00 0.00 0.00 1.78
96 97 6.233434 ACCTCATACTTACATGCACATATGG 58.767 40.000 7.80 0.00 32.32 2.74
97 98 6.183361 ACCTCATACTTACATGCACATATGGT 60.183 38.462 7.80 0.00 32.32 3.55
98 99 7.016170 ACCTCATACTTACATGCACATATGGTA 59.984 37.037 7.80 0.00 32.32 3.25
99 100 7.547019 CCTCATACTTACATGCACATATGGTAG 59.453 40.741 7.80 0.00 32.32 3.18
100 101 7.386059 TCATACTTACATGCACATATGGTAGG 58.614 38.462 7.80 2.60 32.32 3.18
101 102 4.389374 ACTTACATGCACATATGGTAGGC 58.611 43.478 7.80 5.89 32.32 3.93
102 103 4.103153 ACTTACATGCACATATGGTAGGCT 59.897 41.667 7.80 0.00 32.32 4.58
103 104 2.854963 ACATGCACATATGGTAGGCTG 58.145 47.619 7.80 7.82 32.32 4.85
104 105 2.173356 ACATGCACATATGGTAGGCTGT 59.827 45.455 7.80 8.34 32.32 4.40
105 106 3.216800 CATGCACATATGGTAGGCTGTT 58.783 45.455 7.80 0.00 0.00 3.16
106 107 2.642427 TGCACATATGGTAGGCTGTTG 58.358 47.619 7.80 0.00 0.00 3.33
107 108 1.334869 GCACATATGGTAGGCTGTTGC 59.665 52.381 7.80 0.54 38.76 4.17
119 120 2.070262 GCTGTTGCCATTTCCAACTC 57.930 50.000 5.94 0.00 42.25 3.01
120 121 1.337167 GCTGTTGCCATTTCCAACTCC 60.337 52.381 5.94 0.00 42.25 3.85
121 122 1.962807 CTGTTGCCATTTCCAACTCCA 59.037 47.619 5.94 0.00 42.25 3.86
122 123 1.962807 TGTTGCCATTTCCAACTCCAG 59.037 47.619 5.94 0.00 42.25 3.86
123 124 1.963515 GTTGCCATTTCCAACTCCAGT 59.036 47.619 0.00 0.00 39.47 4.00
124 125 2.365293 GTTGCCATTTCCAACTCCAGTT 59.635 45.455 0.00 0.00 39.47 3.16
125 126 2.238521 TGCCATTTCCAACTCCAGTTC 58.761 47.619 0.00 0.00 35.83 3.01
126 127 1.546029 GCCATTTCCAACTCCAGTTCC 59.454 52.381 0.00 0.00 35.83 3.62
127 128 2.171003 CCATTTCCAACTCCAGTTCCC 58.829 52.381 0.00 0.00 35.83 3.97
128 129 2.225117 CCATTTCCAACTCCAGTTCCCT 60.225 50.000 0.00 0.00 35.83 4.20
129 130 3.500343 CATTTCCAACTCCAGTTCCCTT 58.500 45.455 0.00 0.00 35.83 3.95
130 131 2.951229 TTCCAACTCCAGTTCCCTTC 57.049 50.000 0.00 0.00 35.83 3.46
131 132 1.064825 TCCAACTCCAGTTCCCTTCC 58.935 55.000 0.00 0.00 35.83 3.46
132 133 0.771127 CCAACTCCAGTTCCCTTCCA 59.229 55.000 0.00 0.00 35.83 3.53
133 134 1.144913 CCAACTCCAGTTCCCTTCCAA 59.855 52.381 0.00 0.00 35.83 3.53
134 135 2.230660 CAACTCCAGTTCCCTTCCAAC 58.769 52.381 0.00 0.00 35.83 3.77
137 138 2.230660 CTCCAGTTCCCTTCCAACAAC 58.769 52.381 0.00 0.00 0.00 3.32
143 144 4.037222 AGTTCCCTTCCAACAACCAATTT 58.963 39.130 0.00 0.00 0.00 1.82
154 155 6.989169 TCCAACAACCAATTTAACTCCATTTG 59.011 34.615 0.00 0.00 0.00 2.32
155 156 6.765512 CCAACAACCAATTTAACTCCATTTGT 59.234 34.615 0.00 0.00 0.00 2.83
158 159 6.098982 ACAACCAATTTAACTCCATTTGTCCA 59.901 34.615 0.00 0.00 0.00 4.02
160 161 7.130681 ACCAATTTAACTCCATTTGTCCAAA 57.869 32.000 0.00 0.00 34.46 3.28
189 190 6.155475 TGGTTTTCCCAATAACTTGTTCTG 57.845 37.500 0.00 0.00 41.50 3.02
198 201 6.146021 CCCAATAACTTGTTCTGTGATTTTGC 59.854 38.462 0.00 0.00 0.00 3.68
199 202 6.129115 CCAATAACTTGTTCTGTGATTTTGCG 60.129 38.462 0.00 0.00 0.00 4.85
200 203 4.630894 AACTTGTTCTGTGATTTTGCGA 57.369 36.364 0.00 0.00 0.00 5.10
207 210 5.288232 TGTTCTGTGATTTTGCGAAAGTTTG 59.712 36.000 5.18 0.00 0.00 2.93
215 218 5.765072 TTTTGCGAAAGTTTGGTGTTAAC 57.235 34.783 0.00 0.00 0.00 2.01
220 223 4.268522 CGAAAGTTTGGTGTTAACAGTCG 58.731 43.478 8.98 4.83 32.06 4.18
224 227 6.780706 AAGTTTGGTGTTAACAGTCGATAG 57.219 37.500 8.98 0.00 0.00 2.08
227 230 4.087510 TGGTGTTAACAGTCGATAGTCG 57.912 45.455 8.98 0.00 42.10 4.18
245 249 1.000843 TCGGCCTTCATGATGATACCG 59.999 52.381 19.17 19.17 37.62 4.02
247 251 2.354103 CGGCCTTCATGATGATACCGAT 60.354 50.000 20.05 0.00 38.14 4.18
248 252 3.265791 GGCCTTCATGATGATACCGATC 58.734 50.000 10.07 0.00 0.00 3.69
325 329 4.777140 AACTAAAACGTGTGAACGGTAC 57.223 40.909 3.09 0.00 37.45 3.34
326 330 4.045636 ACTAAAACGTGTGAACGGTACT 57.954 40.909 3.09 0.00 37.45 2.73
333 337 4.726416 ACGTGTGAACGGTACTAGTATTG 58.274 43.478 5.75 4.44 37.45 1.90
342 346 8.186163 TGAACGGTACTAGTATTGTCACTAATG 58.814 37.037 5.75 0.00 30.77 1.90
344 348 5.919141 CGGTACTAGTATTGTCACTAATGCC 59.081 44.000 5.75 0.00 31.92 4.40
364 368 1.536940 CCATCATGTCCAGTGTGCAA 58.463 50.000 0.00 0.00 0.00 4.08
373 377 2.171448 GTCCAGTGTGCAATCCCTCTAT 59.829 50.000 0.00 0.00 0.00 1.98
391 395 4.952845 TCTATCTATCCATGAGGGGAAGG 58.047 47.826 0.00 0.00 41.12 3.46
393 397 1.873049 TCTATCCATGAGGGGAAGGGA 59.127 52.381 0.00 0.00 41.12 4.20
403 408 4.442454 GGAAGGGAAAGGGGGCGG 62.442 72.222 0.00 0.00 0.00 6.13
432 437 8.745837 CATAAAATTAGCGAGCATAAAGGTTTG 58.254 33.333 0.00 0.00 0.00 2.93
435 440 3.831715 AGCGAGCATAAAGGTTTGAAC 57.168 42.857 0.00 0.00 0.00 3.18
436 441 3.412386 AGCGAGCATAAAGGTTTGAACT 58.588 40.909 0.00 0.00 0.00 3.01
437 442 3.189287 AGCGAGCATAAAGGTTTGAACTG 59.811 43.478 0.00 0.00 0.00 3.16
463 468 8.128582 GGATTCAAAATTGCGATTGACTATGTA 58.871 33.333 0.00 0.00 35.42 2.29
468 473 7.552458 AAATTGCGATTGACTATGTATCACA 57.448 32.000 0.00 0.00 0.00 3.58
506 511 7.170151 ACCGTTTTATGAAAAATAGTGTTTGGC 59.830 33.333 0.00 0.00 36.96 4.52
516 521 7.475137 AAAATAGTGTTTGGCTGCCTATTTA 57.525 32.000 21.03 5.56 37.34 1.40
527 532 7.652524 TGGCTGCCTATTTATTTGTTAATCA 57.347 32.000 21.03 0.00 0.00 2.57
559 565 8.777865 TGTAGAACATATATAAGATGCAAGGC 57.222 34.615 0.00 0.00 0.00 4.35
566 572 3.827008 ATAAGATGCAAGGCGAGAGAA 57.173 42.857 0.00 0.00 0.00 2.87
567 573 1.731720 AAGATGCAAGGCGAGAGAAC 58.268 50.000 0.00 0.00 0.00 3.01
568 574 0.610174 AGATGCAAGGCGAGAGAACA 59.390 50.000 0.00 0.00 0.00 3.18
569 575 1.002430 AGATGCAAGGCGAGAGAACAA 59.998 47.619 0.00 0.00 0.00 2.83
570 576 1.129437 GATGCAAGGCGAGAGAACAAC 59.871 52.381 0.00 0.00 0.00 3.32
572 578 1.343142 TGCAAGGCGAGAGAACAACTA 59.657 47.619 0.00 0.00 0.00 2.24
573 579 1.727335 GCAAGGCGAGAGAACAACTAC 59.273 52.381 0.00 0.00 0.00 2.73
575 581 3.367087 GCAAGGCGAGAGAACAACTACTA 60.367 47.826 0.00 0.00 0.00 1.82
576 582 4.806330 CAAGGCGAGAGAACAACTACTAA 58.194 43.478 0.00 0.00 0.00 2.24
578 584 5.061920 AGGCGAGAGAACAACTACTAAAG 57.938 43.478 0.00 0.00 0.00 1.85
579 585 4.765856 AGGCGAGAGAACAACTACTAAAGA 59.234 41.667 0.00 0.00 0.00 2.52
580 586 5.096849 GGCGAGAGAACAACTACTAAAGAG 58.903 45.833 0.00 0.00 0.00 2.85
581 587 5.335819 GGCGAGAGAACAACTACTAAAGAGT 60.336 44.000 0.00 0.00 39.92 3.24
582 588 6.151004 GCGAGAGAACAACTACTAAAGAGTT 58.849 40.000 0.00 0.00 37.64 3.01
583 589 6.641723 GCGAGAGAACAACTACTAAAGAGTTT 59.358 38.462 0.00 0.00 34.90 2.66
584 590 7.358517 GCGAGAGAACAACTACTAAAGAGTTTG 60.359 40.741 0.00 0.00 34.90 2.93
585 591 7.115095 CGAGAGAACAACTACTAAAGAGTTTGG 59.885 40.741 0.00 0.00 34.90 3.28
586 592 7.793036 AGAGAACAACTACTAAAGAGTTTGGT 58.207 34.615 0.00 0.00 34.90 3.67
587 593 8.921205 AGAGAACAACTACTAAAGAGTTTGGTA 58.079 33.333 0.00 0.00 34.90 3.25
588 594 8.883954 AGAACAACTACTAAAGAGTTTGGTAC 57.116 34.615 0.00 0.00 34.90 3.34
589 595 8.480501 AGAACAACTACTAAAGAGTTTGGTACA 58.519 33.333 0.00 0.00 34.90 2.90
590 596 9.269453 GAACAACTACTAAAGAGTTTGGTACAT 57.731 33.333 0.00 0.00 35.89 2.29
591 597 8.828688 ACAACTACTAAAGAGTTTGGTACATC 57.171 34.615 0.00 0.00 35.89 3.06
592 598 8.426489 ACAACTACTAAAGAGTTTGGTACATCA 58.574 33.333 0.00 0.00 35.89 3.07
593 599 9.268268 CAACTACTAAAGAGTTTGGTACATCAA 57.732 33.333 0.00 0.00 35.89 2.57
594 600 8.828688 ACTACTAAAGAGTTTGGTACATCAAC 57.171 34.615 0.00 0.00 35.89 3.18
595 601 7.876582 ACTACTAAAGAGTTTGGTACATCAACC 59.123 37.037 0.00 0.00 35.89 3.77
596 602 6.002082 ACTAAAGAGTTTGGTACATCAACCC 58.998 40.000 0.00 0.00 39.30 4.11
597 603 4.447138 AAGAGTTTGGTACATCAACCCA 57.553 40.909 0.00 0.00 39.30 4.51
598 604 4.021102 AGAGTTTGGTACATCAACCCAG 57.979 45.455 0.00 0.00 39.30 4.45
599 605 3.650942 AGAGTTTGGTACATCAACCCAGA 59.349 43.478 0.00 0.00 39.30 3.86
600 606 3.751518 AGTTTGGTACATCAACCCAGAC 58.248 45.455 0.00 0.00 39.30 3.51
601 607 3.394606 AGTTTGGTACATCAACCCAGACT 59.605 43.478 0.00 0.00 38.48 3.24
602 608 4.141251 AGTTTGGTACATCAACCCAGACTT 60.141 41.667 0.00 0.00 39.83 3.01
603 609 4.447138 TTGGTACATCAACCCAGACTTT 57.553 40.909 0.00 0.00 39.30 2.66
604 610 5.570205 TTGGTACATCAACCCAGACTTTA 57.430 39.130 0.00 0.00 39.30 1.85
605 611 5.772393 TGGTACATCAACCCAGACTTTAT 57.228 39.130 0.00 0.00 38.90 1.40
606 612 6.134535 TGGTACATCAACCCAGACTTTATT 57.865 37.500 0.00 0.00 38.90 1.40
607 613 6.548321 TGGTACATCAACCCAGACTTTATTT 58.452 36.000 0.00 0.00 38.90 1.40
608 614 7.691213 TGGTACATCAACCCAGACTTTATTTA 58.309 34.615 0.00 0.00 38.90 1.40
609 615 8.333235 TGGTACATCAACCCAGACTTTATTTAT 58.667 33.333 0.00 0.00 38.90 1.40
650 656 7.519347 TCCTAATTACTAACCCAAAGGACAT 57.481 36.000 0.00 0.00 36.73 3.06
653 659 2.781681 ACTAACCCAAAGGACATCCG 57.218 50.000 0.00 0.00 42.08 4.18
655 661 1.557832 CTAACCCAAAGGACATCCGGA 59.442 52.381 6.61 6.61 42.08 5.14
663 669 0.460311 AGGACATCCGGATCGTCAAC 59.540 55.000 30.75 21.36 42.08 3.18
665 671 0.174845 GACATCCGGATCGTCAACCA 59.825 55.000 27.79 0.00 0.00 3.67
690 696 6.540914 ACGATCAAAGACAGTAAGGAACAAAA 59.459 34.615 0.00 0.00 0.00 2.44
691 697 7.066525 ACGATCAAAGACAGTAAGGAACAAAAA 59.933 33.333 0.00 0.00 0.00 1.94
727 2638 4.047883 ACTTAGGTAGGCCAAGATCCAAT 58.952 43.478 5.01 0.00 37.19 3.16
739 2650 4.409570 CAAGATCCAATGTCGCTTTCAAG 58.590 43.478 0.00 0.00 0.00 3.02
805 2719 3.316308 GGGCAATGGCAGTAGTGAAATAG 59.684 47.826 9.51 0.00 43.71 1.73
818 2732 9.220767 CAGTAGTGAAATAGGCCCTTAAATATC 57.779 37.037 0.00 0.00 0.00 1.63
856 2771 5.880887 CCCTCAGTTCTTTAAATAGACCACC 59.119 44.000 0.00 0.00 0.00 4.61
898 2821 0.250038 CCCCACTCACACAGACACAG 60.250 60.000 0.00 0.00 0.00 3.66
901 2824 1.136891 CCACTCACACAGACACAGACA 59.863 52.381 0.00 0.00 0.00 3.41
902 2825 2.196749 CACTCACACAGACACAGACAC 58.803 52.381 0.00 0.00 0.00 3.67
903 2826 1.202302 ACTCACACAGACACAGACACG 60.202 52.381 0.00 0.00 0.00 4.49
1140 3080 3.437795 GACTCCTCCGACGCCGAA 61.438 66.667 0.00 0.00 38.22 4.30
1221 3164 1.383248 CCTCCTGTTCCCCTCCGAT 60.383 63.158 0.00 0.00 0.00 4.18
1224 3167 2.370445 CCTGTTCCCCTCCGATGCT 61.370 63.158 0.00 0.00 0.00 3.79
1227 3170 0.539986 TGTTCCCCTCCGATGCTAAC 59.460 55.000 0.00 0.00 0.00 2.34
1408 3351 1.153881 GAGGACGTCGGTTGCTACC 60.154 63.158 9.92 7.33 41.33 3.18
1689 3675 4.770795 AGATAGTCCTGGAAATCAAACGG 58.229 43.478 17.80 0.00 0.00 4.44
1702 3688 6.976349 GGAAATCAAACGGGACAATATAAACC 59.024 38.462 0.00 0.00 0.00 3.27
1779 3782 3.324846 TCACAAGCTCTCAACTACACCAT 59.675 43.478 0.00 0.00 0.00 3.55
1784 3787 6.210784 ACAAGCTCTCAACTACACCATAGTAA 59.789 38.462 0.00 0.00 0.00 2.24
1793 3796 5.081728 ACTACACCATAGTAACACACCAGA 58.918 41.667 0.00 0.00 0.00 3.86
1827 3830 0.610174 AATGACTCCGCTGCTCAAGA 59.390 50.000 0.00 0.00 0.00 3.02
1832 3835 2.619177 GACTCCGCTGCTCAAGATACTA 59.381 50.000 0.00 0.00 0.00 1.82
1836 3839 3.188667 TCCGCTGCTCAAGATACTATACG 59.811 47.826 0.00 0.00 0.00 3.06
1839 3842 5.394802 CGCTGCTCAAGATACTATACGATT 58.605 41.667 0.00 0.00 0.00 3.34
1840 3843 5.859114 CGCTGCTCAAGATACTATACGATTT 59.141 40.000 0.00 0.00 0.00 2.17
1842 3845 7.505646 GCTGCTCAAGATACTATACGATTTTG 58.494 38.462 0.00 0.00 0.00 2.44
1843 3846 7.359598 GCTGCTCAAGATACTATACGATTTTGG 60.360 40.741 0.00 0.00 0.00 3.28
1845 3848 6.647067 GCTCAAGATACTATACGATTTTGGCT 59.353 38.462 0.00 0.00 0.00 4.75
1848 3894 7.867909 TCAAGATACTATACGATTTTGGCTCTG 59.132 37.037 0.00 0.00 0.00 3.35
1851 3897 2.717639 ATACGATTTTGGCTCTGGCT 57.282 45.000 0.00 0.00 38.73 4.75
1868 3914 2.964464 TGGCTTGGCTTCAAAGATGAAA 59.036 40.909 0.00 0.00 44.64 2.69
1871 3917 4.999311 GGCTTGGCTTCAAAGATGAAAAAT 59.001 37.500 0.00 0.00 44.64 1.82
1921 3967 6.854892 CCATAATTAAGCAAGCAGAAGATTCG 59.145 38.462 0.00 0.00 0.00 3.34
1963 4009 4.003648 ACTTGAAGGAAATCGCGAATTCT 58.996 39.130 29.94 16.86 0.00 2.40
1964 4010 4.455877 ACTTGAAGGAAATCGCGAATTCTT 59.544 37.500 29.94 23.13 0.00 2.52
1965 4011 4.340894 TGAAGGAAATCGCGAATTCTTG 57.659 40.909 29.94 0.00 0.00 3.02
1979 4025 5.447818 GCGAATTCTTGATCACCGAATTCTT 60.448 40.000 31.78 17.09 45.28 2.52
1980 4026 6.546395 CGAATTCTTGATCACCGAATTCTTT 58.454 36.000 31.78 16.86 45.28 2.52
1981 4027 6.684555 CGAATTCTTGATCACCGAATTCTTTC 59.315 38.462 31.78 20.65 45.28 2.62
1982 4028 5.880054 TTCTTGATCACCGAATTCTTTCC 57.120 39.130 3.52 0.00 0.00 3.13
1983 4029 5.165961 TCTTGATCACCGAATTCTTTCCT 57.834 39.130 3.52 0.00 0.00 3.36
1984 4030 6.294361 TCTTGATCACCGAATTCTTTCCTA 57.706 37.500 3.52 0.00 0.00 2.94
1985 4031 6.707290 TCTTGATCACCGAATTCTTTCCTAA 58.293 36.000 3.52 0.00 0.00 2.69
2021 4067 5.762825 ATATGCATTGCCAGACTTAAGTG 57.237 39.130 14.14 0.00 0.00 3.16
2055 4101 1.902508 GTGTGATCTCCTTGGAGGACA 59.097 52.381 15.81 12.88 40.06 4.02
2088 4135 0.518636 CAACGCTCCCACAACATCAG 59.481 55.000 0.00 0.00 0.00 2.90
2089 4136 0.108585 AACGCTCCCACAACATCAGT 59.891 50.000 0.00 0.00 0.00 3.41
2152 4199 2.734591 GCCGATCGACCATAGCCA 59.265 61.111 18.66 0.00 0.00 4.75
2197 4247 1.679311 CCAAGTAGCCCTGCTGTCA 59.321 57.895 0.00 0.00 40.10 3.58
2296 4350 1.377594 CACTGCCATGCTGCCACTA 60.378 57.895 0.00 0.00 0.00 2.74
2297 4351 0.961857 CACTGCCATGCTGCCACTAA 60.962 55.000 0.00 0.00 0.00 2.24
2302 4357 2.302445 TGCCATGCTGCCACTAATTTTT 59.698 40.909 0.00 0.00 0.00 1.94
2364 4419 3.495670 TTTGTTGTCTTCACCGGTTTG 57.504 42.857 2.97 0.00 0.00 2.93
2376 4431 0.601057 CCGGTTTGGGTGGATTCAAC 59.399 55.000 0.00 0.00 0.00 3.18
2380 4435 1.950909 GTTTGGGTGGATTCAACACGA 59.049 47.619 0.00 0.00 39.69 4.35
2394 4449 1.002366 ACACGAGCTCGATGAAATGC 58.998 50.000 40.58 0.00 43.02 3.56
2400 4455 2.871022 GAGCTCGATGAAATGCACTCAT 59.129 45.455 11.91 11.91 36.21 2.90
2436 4491 5.316987 ACAAGAACAGAGGATAAAACAGGG 58.683 41.667 0.00 0.00 0.00 4.45
2437 4492 3.956744 AGAACAGAGGATAAAACAGGGC 58.043 45.455 0.00 0.00 0.00 5.19
2438 4493 3.330701 AGAACAGAGGATAAAACAGGGCA 59.669 43.478 0.00 0.00 0.00 5.36
2439 4494 3.806949 ACAGAGGATAAAACAGGGCAA 57.193 42.857 0.00 0.00 0.00 4.52
2440 4495 4.322057 ACAGAGGATAAAACAGGGCAAT 57.678 40.909 0.00 0.00 0.00 3.56
2441 4496 4.019174 ACAGAGGATAAAACAGGGCAATG 58.981 43.478 0.00 0.00 0.00 2.82
2442 4497 4.019174 CAGAGGATAAAACAGGGCAATGT 58.981 43.478 0.00 0.00 33.96 2.71
2443 4498 4.019174 AGAGGATAAAACAGGGCAATGTG 58.981 43.478 0.00 0.00 32.52 3.21
2444 4499 4.016444 GAGGATAAAACAGGGCAATGTGA 58.984 43.478 0.00 0.00 32.52 3.58
2445 4500 3.763897 AGGATAAAACAGGGCAATGTGAC 59.236 43.478 0.00 0.00 32.52 3.67
2446 4501 3.763897 GGATAAAACAGGGCAATGTGACT 59.236 43.478 0.00 0.00 32.52 3.41
2447 4502 4.142381 GGATAAAACAGGGCAATGTGACTC 60.142 45.833 0.00 0.00 32.52 3.36
2448 4503 2.363306 AAACAGGGCAATGTGACTCA 57.637 45.000 0.00 0.00 32.52 3.41
2449 4504 1.901591 AACAGGGCAATGTGACTCAG 58.098 50.000 0.00 0.00 32.52 3.35
2450 4505 0.767375 ACAGGGCAATGTGACTCAGT 59.233 50.000 0.00 0.00 30.46 3.41
2451 4506 1.143684 ACAGGGCAATGTGACTCAGTT 59.856 47.619 0.00 0.00 30.46 3.16
2452 4507 1.538512 CAGGGCAATGTGACTCAGTTG 59.461 52.381 0.00 1.39 0.00 3.16
2453 4508 1.143684 AGGGCAATGTGACTCAGTTGT 59.856 47.619 6.15 0.00 0.00 3.32
2454 4509 1.267806 GGGCAATGTGACTCAGTTGTG 59.732 52.381 6.15 0.00 0.00 3.33
2455 4510 2.221169 GGCAATGTGACTCAGTTGTGA 58.779 47.619 6.15 0.00 0.00 3.58
2456 4511 2.816087 GGCAATGTGACTCAGTTGTGAT 59.184 45.455 6.15 0.00 30.18 3.06
2457 4512 3.120060 GGCAATGTGACTCAGTTGTGATC 60.120 47.826 6.15 0.00 30.18 2.92
2458 4513 3.120060 GCAATGTGACTCAGTTGTGATCC 60.120 47.826 0.00 0.00 30.18 3.36
2459 4514 4.067192 CAATGTGACTCAGTTGTGATCCA 58.933 43.478 0.00 0.00 30.18 3.41
2460 4515 3.391506 TGTGACTCAGTTGTGATCCAG 57.608 47.619 0.00 0.00 30.18 3.86
2461 4516 2.037641 TGTGACTCAGTTGTGATCCAGG 59.962 50.000 0.00 0.00 30.18 4.45
2462 4517 1.002430 TGACTCAGTTGTGATCCAGGC 59.998 52.381 0.00 0.00 30.18 4.85
2463 4518 1.002430 GACTCAGTTGTGATCCAGGCA 59.998 52.381 0.00 0.00 30.18 4.75
2464 4519 1.421268 ACTCAGTTGTGATCCAGGCAA 59.579 47.619 0.00 0.00 30.18 4.52
2465 4520 1.808945 CTCAGTTGTGATCCAGGCAAC 59.191 52.381 9.88 9.88 41.78 4.17
2466 4521 1.142667 TCAGTTGTGATCCAGGCAACA 59.857 47.619 16.33 1.03 43.31 3.33
2467 4522 1.538512 CAGTTGTGATCCAGGCAACAG 59.461 52.381 16.33 8.77 43.31 3.16
2468 4523 1.421268 AGTTGTGATCCAGGCAACAGA 59.579 47.619 16.33 0.00 43.31 3.41
2469 4524 2.040813 AGTTGTGATCCAGGCAACAGAT 59.959 45.455 16.33 0.00 43.31 2.90
2470 4525 2.118313 TGTGATCCAGGCAACAGATG 57.882 50.000 0.00 0.00 41.41 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.928375 GCCTAATCCATGTTGTGCTTTTG 59.072 43.478 0.00 0.00 0.00 2.44
6 7 3.055891 GGCCTAATCCATGTTGTGCTTTT 60.056 43.478 0.00 0.00 0.00 2.27
7 8 2.497273 GGCCTAATCCATGTTGTGCTTT 59.503 45.455 0.00 0.00 0.00 3.51
8 9 2.102578 GGCCTAATCCATGTTGTGCTT 58.897 47.619 0.00 0.00 0.00 3.91
9 10 1.285962 AGGCCTAATCCATGTTGTGCT 59.714 47.619 1.29 0.00 0.00 4.40
10 11 1.406539 CAGGCCTAATCCATGTTGTGC 59.593 52.381 3.98 0.00 0.00 4.57
11 12 1.406539 GCAGGCCTAATCCATGTTGTG 59.593 52.381 3.98 0.00 0.00 3.33
12 13 1.686115 GGCAGGCCTAATCCATGTTGT 60.686 52.381 3.98 0.00 0.00 3.32
13 14 1.035139 GGCAGGCCTAATCCATGTTG 58.965 55.000 3.98 0.00 0.00 3.33
14 15 0.106015 GGGCAGGCCTAATCCATGTT 60.106 55.000 3.98 0.00 36.10 2.71
15 16 1.538666 GGGCAGGCCTAATCCATGT 59.461 57.895 3.98 0.00 36.10 3.21
16 17 1.228675 GGGGCAGGCCTAATCCATG 60.229 63.158 13.81 0.00 36.10 3.66
17 18 1.295915 TTGGGGCAGGCCTAATCCAT 61.296 55.000 13.81 0.00 36.10 3.41
18 19 1.933284 TTGGGGCAGGCCTAATCCA 60.933 57.895 13.81 10.69 36.10 3.41
19 20 1.152673 CTTGGGGCAGGCCTAATCC 60.153 63.158 12.62 7.19 36.10 3.01
20 21 0.480252 ATCTTGGGGCAGGCCTAATC 59.520 55.000 12.62 0.00 36.10 1.75
21 22 0.186873 CATCTTGGGGCAGGCCTAAT 59.813 55.000 12.62 0.00 36.10 1.73
22 23 1.214305 ACATCTTGGGGCAGGCCTAA 61.214 55.000 13.81 12.67 36.10 2.69
23 24 1.214305 AACATCTTGGGGCAGGCCTA 61.214 55.000 13.81 3.26 36.10 3.93
24 25 2.551413 AACATCTTGGGGCAGGCCT 61.551 57.895 13.81 0.00 36.10 5.19
25 26 2.037847 AACATCTTGGGGCAGGCC 59.962 61.111 3.77 3.77 0.00 5.19
26 27 2.353610 CCAACATCTTGGGGCAGGC 61.354 63.158 0.00 0.00 43.19 4.85
27 28 4.023137 CCAACATCTTGGGGCAGG 57.977 61.111 0.00 0.00 43.19 4.85
33 34 1.984026 GTGGGGCCCAACATCTTGG 60.984 63.158 30.70 0.00 46.15 3.61
34 35 0.615544 ATGTGGGGCCCAACATCTTG 60.616 55.000 35.82 0.00 34.18 3.02
35 36 1.006813 TATGTGGGGCCCAACATCTT 58.993 50.000 42.62 26.39 34.18 2.40
36 37 0.258774 GTATGTGGGGCCCAACATCT 59.741 55.000 42.62 27.12 34.18 2.90
37 38 0.033601 TGTATGTGGGGCCCAACATC 60.034 55.000 42.62 32.05 34.18 3.06
38 39 0.636101 ATGTATGTGGGGCCCAACAT 59.364 50.000 40.60 40.60 34.18 2.71
39 40 0.324183 CATGTATGTGGGGCCCAACA 60.324 55.000 34.63 34.63 34.18 3.33
40 41 1.675720 GCATGTATGTGGGGCCCAAC 61.676 60.000 30.70 23.97 34.18 3.77
41 42 1.381056 GCATGTATGTGGGGCCCAA 60.381 57.895 30.70 18.32 34.18 4.12
42 43 0.990818 TAGCATGTATGTGGGGCCCA 60.991 55.000 24.76 24.76 0.00 5.36
43 44 0.184933 TTAGCATGTATGTGGGGCCC 59.815 55.000 18.17 18.17 0.00 5.80
44 45 1.888512 CATTAGCATGTATGTGGGGCC 59.111 52.381 0.00 0.00 0.00 5.80
45 46 2.586425 ACATTAGCATGTATGTGGGGC 58.414 47.619 8.72 0.00 42.24 5.80
46 47 4.037923 GGAAACATTAGCATGTATGTGGGG 59.962 45.833 9.85 0.00 43.34 4.96
47 48 4.889409 AGGAAACATTAGCATGTATGTGGG 59.111 41.667 9.85 0.00 43.34 4.61
48 49 5.589855 TCAGGAAACATTAGCATGTATGTGG 59.410 40.000 9.85 0.00 43.34 4.17
49 50 6.458751 GGTCAGGAAACATTAGCATGTATGTG 60.459 42.308 9.85 1.27 43.34 3.21
50 51 5.590259 GGTCAGGAAACATTAGCATGTATGT 59.410 40.000 0.00 0.00 43.34 2.29
51 52 5.824624 AGGTCAGGAAACATTAGCATGTATG 59.175 40.000 0.00 0.00 43.34 2.39
52 53 6.006275 AGGTCAGGAAACATTAGCATGTAT 57.994 37.500 0.00 0.00 43.34 2.29
53 54 5.045942 TGAGGTCAGGAAACATTAGCATGTA 60.046 40.000 0.00 0.00 43.34 2.29
54 55 4.263462 TGAGGTCAGGAAACATTAGCATGT 60.263 41.667 0.00 0.00 46.34 3.21
55 56 4.264253 TGAGGTCAGGAAACATTAGCATG 58.736 43.478 0.00 0.00 36.34 4.06
56 57 4.574674 TGAGGTCAGGAAACATTAGCAT 57.425 40.909 0.00 0.00 0.00 3.79
57 58 4.574674 ATGAGGTCAGGAAACATTAGCA 57.425 40.909 0.00 0.00 0.00 3.49
58 59 5.675538 AGTATGAGGTCAGGAAACATTAGC 58.324 41.667 0.00 0.00 0.00 3.09
59 60 8.258007 TGTAAGTATGAGGTCAGGAAACATTAG 58.742 37.037 0.00 0.00 0.00 1.73
60 61 8.141298 TGTAAGTATGAGGTCAGGAAACATTA 57.859 34.615 0.00 0.00 0.00 1.90
61 62 7.016153 TGTAAGTATGAGGTCAGGAAACATT 57.984 36.000 0.00 0.00 0.00 2.71
62 63 6.620877 TGTAAGTATGAGGTCAGGAAACAT 57.379 37.500 0.00 0.00 0.00 2.71
63 64 6.406370 CATGTAAGTATGAGGTCAGGAAACA 58.594 40.000 0.00 0.00 0.00 2.83
64 65 5.294552 GCATGTAAGTATGAGGTCAGGAAAC 59.705 44.000 0.00 0.00 0.00 2.78
65 66 5.045942 TGCATGTAAGTATGAGGTCAGGAAA 60.046 40.000 0.00 0.00 0.00 3.13
66 67 4.469586 TGCATGTAAGTATGAGGTCAGGAA 59.530 41.667 0.00 0.00 0.00 3.36
67 68 4.030216 TGCATGTAAGTATGAGGTCAGGA 58.970 43.478 0.00 0.00 0.00 3.86
68 69 4.122776 GTGCATGTAAGTATGAGGTCAGG 58.877 47.826 0.00 0.00 0.00 3.86
69 70 4.758688 TGTGCATGTAAGTATGAGGTCAG 58.241 43.478 0.00 0.00 0.00 3.51
70 71 4.817318 TGTGCATGTAAGTATGAGGTCA 57.183 40.909 0.00 0.00 0.00 4.02
71 72 6.369890 CCATATGTGCATGTAAGTATGAGGTC 59.630 42.308 14.31 0.00 0.00 3.85
72 73 6.183361 ACCATATGTGCATGTAAGTATGAGGT 60.183 38.462 14.31 5.92 0.00 3.85
73 74 6.233434 ACCATATGTGCATGTAAGTATGAGG 58.767 40.000 14.31 5.47 0.00 3.86
74 75 7.547019 CCTACCATATGTGCATGTAAGTATGAG 59.453 40.741 14.31 9.22 0.00 2.90
75 76 7.386059 CCTACCATATGTGCATGTAAGTATGA 58.614 38.462 14.31 0.85 0.00 2.15
76 77 6.092670 GCCTACCATATGTGCATGTAAGTATG 59.907 42.308 1.24 8.70 0.00 2.39
77 78 6.013379 AGCCTACCATATGTGCATGTAAGTAT 60.013 38.462 1.24 0.00 0.00 2.12
78 79 5.306937 AGCCTACCATATGTGCATGTAAGTA 59.693 40.000 1.24 0.00 0.00 2.24
79 80 4.103153 AGCCTACCATATGTGCATGTAAGT 59.897 41.667 1.24 0.00 0.00 2.24
80 81 4.453478 CAGCCTACCATATGTGCATGTAAG 59.547 45.833 1.24 0.00 0.00 2.34
81 82 4.141505 ACAGCCTACCATATGTGCATGTAA 60.142 41.667 1.24 0.00 0.00 2.41
82 83 3.390967 ACAGCCTACCATATGTGCATGTA 59.609 43.478 1.24 0.00 0.00 2.29
83 84 2.173356 ACAGCCTACCATATGTGCATGT 59.827 45.455 1.24 0.00 0.00 3.21
84 85 2.854963 ACAGCCTACCATATGTGCATG 58.145 47.619 1.24 0.00 0.00 4.06
85 86 3.216800 CAACAGCCTACCATATGTGCAT 58.783 45.455 1.24 0.00 0.00 3.96
86 87 2.642427 CAACAGCCTACCATATGTGCA 58.358 47.619 1.24 0.00 0.00 4.57
87 88 1.334869 GCAACAGCCTACCATATGTGC 59.665 52.381 1.24 0.00 0.00 4.57
88 89 1.949525 GGCAACAGCCTACCATATGTG 59.050 52.381 1.24 0.00 45.21 3.21
89 90 2.348411 GGCAACAGCCTACCATATGT 57.652 50.000 1.24 0.00 45.21 2.29
101 102 6.008021 AACTGGAGTTGGAAATGGCAACAG 62.008 45.833 0.00 0.00 43.99 3.16
102 103 4.196923 AACTGGAGTTGGAAATGGCAACA 61.197 43.478 0.00 0.00 44.60 3.33
103 104 1.963515 ACTGGAGTTGGAAATGGCAAC 59.036 47.619 0.00 0.00 0.00 4.17
104 105 2.380064 ACTGGAGTTGGAAATGGCAA 57.620 45.000 0.00 0.00 0.00 4.52
105 106 2.238521 GAACTGGAGTTGGAAATGGCA 58.761 47.619 0.00 0.00 38.56 4.92
106 107 1.546029 GGAACTGGAGTTGGAAATGGC 59.454 52.381 0.00 0.00 38.56 4.40
107 108 2.171003 GGGAACTGGAGTTGGAAATGG 58.829 52.381 0.00 0.00 38.56 3.16
108 109 3.160679 AGGGAACTGGAGTTGGAAATG 57.839 47.619 0.00 0.00 41.13 2.32
109 110 3.500471 GGAAGGGAACTGGAGTTGGAAAT 60.500 47.826 0.00 0.00 42.68 2.17
110 111 2.158519 GGAAGGGAACTGGAGTTGGAAA 60.159 50.000 0.00 0.00 42.68 3.13
111 112 1.423921 GGAAGGGAACTGGAGTTGGAA 59.576 52.381 0.00 0.00 42.68 3.53
112 113 1.064825 GGAAGGGAACTGGAGTTGGA 58.935 55.000 0.00 0.00 42.68 3.53
113 114 0.771127 TGGAAGGGAACTGGAGTTGG 59.229 55.000 0.00 0.00 42.68 3.77
114 115 2.230660 GTTGGAAGGGAACTGGAGTTG 58.769 52.381 0.00 0.00 42.68 3.16
115 116 1.850345 TGTTGGAAGGGAACTGGAGTT 59.150 47.619 0.00 0.00 42.68 3.01
116 117 1.518367 TGTTGGAAGGGAACTGGAGT 58.482 50.000 0.00 0.00 42.68 3.85
117 118 2.230660 GTTGTTGGAAGGGAACTGGAG 58.769 52.381 0.00 0.00 42.68 3.86
118 119 1.133606 GGTTGTTGGAAGGGAACTGGA 60.134 52.381 0.00 0.00 42.68 3.86
119 120 1.328279 GGTTGTTGGAAGGGAACTGG 58.672 55.000 0.00 0.00 42.68 4.00
120 121 2.065899 TGGTTGTTGGAAGGGAACTG 57.934 50.000 0.00 0.00 42.68 3.16
122 123 4.415881 AAATTGGTTGTTGGAAGGGAAC 57.584 40.909 0.00 0.00 0.00 3.62
123 124 5.663556 AGTTAAATTGGTTGTTGGAAGGGAA 59.336 36.000 0.00 0.00 0.00 3.97
124 125 5.212745 AGTTAAATTGGTTGTTGGAAGGGA 58.787 37.500 0.00 0.00 0.00 4.20
125 126 5.510690 GGAGTTAAATTGGTTGTTGGAAGGG 60.511 44.000 0.00 0.00 0.00 3.95
126 127 5.069781 TGGAGTTAAATTGGTTGTTGGAAGG 59.930 40.000 0.00 0.00 0.00 3.46
127 128 6.155475 TGGAGTTAAATTGGTTGTTGGAAG 57.845 37.500 0.00 0.00 0.00 3.46
128 129 6.739331 ATGGAGTTAAATTGGTTGTTGGAA 57.261 33.333 0.00 0.00 0.00 3.53
129 130 6.739331 AATGGAGTTAAATTGGTTGTTGGA 57.261 33.333 0.00 0.00 0.00 3.53
130 131 6.765512 ACAAATGGAGTTAAATTGGTTGTTGG 59.234 34.615 0.00 0.00 0.00 3.77
131 132 7.042119 GGACAAATGGAGTTAAATTGGTTGTTG 60.042 37.037 0.00 0.00 0.00 3.33
132 133 6.989759 GGACAAATGGAGTTAAATTGGTTGTT 59.010 34.615 0.00 0.00 0.00 2.83
133 134 6.098982 TGGACAAATGGAGTTAAATTGGTTGT 59.901 34.615 0.00 0.00 0.00 3.32
134 135 6.520272 TGGACAAATGGAGTTAAATTGGTTG 58.480 36.000 0.00 0.00 0.00 3.77
137 138 8.443953 TTTTTGGACAAATGGAGTTAAATTGG 57.556 30.769 0.00 0.00 0.00 3.16
189 190 3.862845 ACACCAAACTTTCGCAAAATCAC 59.137 39.130 0.00 0.00 0.00 3.06
198 201 4.033129 TCGACTGTTAACACCAAACTTTCG 59.967 41.667 3.59 3.59 35.22 3.46
199 202 5.473796 TCGACTGTTAACACCAAACTTTC 57.526 39.130 3.59 0.00 0.00 2.62
200 203 6.764560 ACTATCGACTGTTAACACCAAACTTT 59.235 34.615 3.59 0.00 0.00 2.66
207 210 3.432782 CCGACTATCGACTGTTAACACC 58.567 50.000 3.59 0.00 43.74 4.16
215 218 0.738975 TGAAGGCCGACTATCGACTG 59.261 55.000 0.00 0.00 43.74 3.51
220 223 3.667497 TCATCATGAAGGCCGACTATC 57.333 47.619 0.00 0.00 0.00 2.08
224 227 2.417719 GGTATCATCATGAAGGCCGAC 58.582 52.381 0.00 0.00 0.00 4.79
227 230 2.839486 TCGGTATCATCATGAAGGCC 57.161 50.000 0.00 0.00 0.00 5.19
230 233 7.387122 ACTTGATTGATCGGTATCATCATGAAG 59.613 37.037 0.00 0.00 41.73 3.02
313 317 5.570589 GTGACAATACTAGTACCGTTCACAC 59.429 44.000 20.50 14.21 0.00 3.82
320 324 5.919141 GGCATTAGTGACAATACTAGTACCG 59.081 44.000 4.31 1.74 34.84 4.02
325 329 5.290493 TGGGGCATTAGTGACAATACTAG 57.710 43.478 0.00 0.00 33.89 2.57
326 330 5.368230 TGATGGGGCATTAGTGACAATACTA 59.632 40.000 0.00 0.00 33.89 1.82
333 337 2.880890 GACATGATGGGGCATTAGTGAC 59.119 50.000 0.00 0.00 0.00 3.67
342 346 1.033746 CACACTGGACATGATGGGGC 61.034 60.000 0.00 0.00 0.00 5.80
344 348 0.322726 TGCACACTGGACATGATGGG 60.323 55.000 0.00 0.00 0.00 4.00
373 377 1.873049 TCCCTTCCCCTCATGGATAGA 59.127 52.381 0.00 0.00 35.39 1.98
386 390 4.442454 CCGCCCCCTTTCCCTTCC 62.442 72.222 0.00 0.00 0.00 3.46
393 397 3.948004 TTTATGCGCCGCCCCCTTT 62.948 57.895 6.63 0.00 0.00 3.11
405 410 6.438763 ACCTTTATGCTCGCTAATTTTATGC 58.561 36.000 0.00 0.00 0.00 3.14
420 425 6.024552 TGAATCCAGTTCAAACCTTTATGC 57.975 37.500 0.00 0.00 43.64 3.14
432 437 5.863397 TCAATCGCAATTTTGAATCCAGTTC 59.137 36.000 0.00 0.00 37.35 3.01
435 440 5.404946 AGTCAATCGCAATTTTGAATCCAG 58.595 37.500 0.00 0.00 33.90 3.86
436 441 5.389859 AGTCAATCGCAATTTTGAATCCA 57.610 34.783 0.00 0.00 33.90 3.41
437 442 6.974622 ACATAGTCAATCGCAATTTTGAATCC 59.025 34.615 0.00 0.00 33.90 3.01
450 455 8.873830 ACTTTCTTTGTGATACATAGTCAATCG 58.126 33.333 0.00 0.00 30.67 3.34
504 509 7.716612 ACTGATTAACAAATAAATAGGCAGCC 58.283 34.615 1.84 1.84 0.00 4.85
552 558 0.106708 AGTTGTTCTCTCGCCTTGCA 59.893 50.000 0.00 0.00 0.00 4.08
557 563 5.056894 TCTTTAGTAGTTGTTCTCTCGCC 57.943 43.478 0.00 0.00 0.00 5.54
559 565 7.115095 CCAAACTCTTTAGTAGTTGTTCTCTCG 59.885 40.741 0.00 0.00 37.26 4.04
566 572 8.426489 TGATGTACCAAACTCTTTAGTAGTTGT 58.574 33.333 0.00 0.00 37.26 3.32
567 573 8.827177 TGATGTACCAAACTCTTTAGTAGTTG 57.173 34.615 0.00 0.00 37.26 3.16
568 574 9.269453 GTTGATGTACCAAACTCTTTAGTAGTT 57.731 33.333 0.00 0.00 38.82 2.24
569 575 7.876582 GGTTGATGTACCAAACTCTTTAGTAGT 59.123 37.037 0.00 0.00 38.12 2.73
570 576 7.333672 GGGTTGATGTACCAAACTCTTTAGTAG 59.666 40.741 0.00 0.00 40.09 2.57
572 578 6.002082 GGGTTGATGTACCAAACTCTTTAGT 58.998 40.000 0.00 0.00 40.09 2.24
573 579 6.001460 TGGGTTGATGTACCAAACTCTTTAG 58.999 40.000 0.00 0.00 40.09 1.85
575 581 4.798882 TGGGTTGATGTACCAAACTCTTT 58.201 39.130 0.00 0.00 40.09 2.52
576 582 4.104102 TCTGGGTTGATGTACCAAACTCTT 59.896 41.667 0.00 0.00 40.09 2.85
578 584 3.751698 GTCTGGGTTGATGTACCAAACTC 59.248 47.826 0.00 0.00 40.09 3.01
579 585 3.394606 AGTCTGGGTTGATGTACCAAACT 59.605 43.478 0.00 0.00 40.09 2.66
580 586 3.751518 AGTCTGGGTTGATGTACCAAAC 58.248 45.455 0.00 0.00 40.09 2.93
581 587 4.447138 AAGTCTGGGTTGATGTACCAAA 57.553 40.909 0.00 0.00 40.09 3.28
582 588 4.447138 AAAGTCTGGGTTGATGTACCAA 57.553 40.909 0.00 0.00 40.09 3.67
583 589 5.772393 ATAAAGTCTGGGTTGATGTACCA 57.228 39.130 0.00 0.00 40.09 3.25
584 590 8.747538 ATAAATAAAGTCTGGGTTGATGTACC 57.252 34.615 0.00 0.00 37.47 3.34
619 625 6.894735 TGGGTTAGTAATTAGGAACCATCA 57.105 37.500 21.69 13.13 42.66 3.07
663 669 4.188247 TCCTTACTGTCTTTGATCGTGG 57.812 45.455 0.00 0.00 0.00 4.94
665 671 5.209818 TGTTCCTTACTGTCTTTGATCGT 57.790 39.130 0.00 0.00 0.00 3.73
690 696 6.766467 CCTACCTAAGTGAAGTGAAGTTGTTT 59.234 38.462 0.00 0.00 0.00 2.83
691 697 6.289064 CCTACCTAAGTGAAGTGAAGTTGTT 58.711 40.000 0.00 0.00 0.00 2.83
727 2638 2.631160 TTCCCTTCTTGAAAGCGACA 57.369 45.000 0.00 0.00 0.00 4.35
805 2719 4.767409 GGAATGTCCAGATATTTAAGGGCC 59.233 45.833 0.00 0.00 36.28 5.80
818 2732 1.765314 CTGAGGGTAGGGAATGTCCAG 59.235 57.143 0.00 0.00 38.64 3.86
856 2771 4.065281 GACGGACGGACCAGTGGG 62.065 72.222 15.21 0.00 38.90 4.61
898 2821 3.712881 GCTCGTTGTGCCCGTGTC 61.713 66.667 0.00 0.00 0.00 3.67
901 2824 3.750373 AAGTGCTCGTTGTGCCCGT 62.750 57.895 0.00 0.00 0.00 5.28
902 2825 2.972505 AAGTGCTCGTTGTGCCCG 60.973 61.111 0.00 0.00 0.00 6.13
903 2826 2.639286 CAAGTGCTCGTTGTGCCC 59.361 61.111 0.00 0.00 0.00 5.36
929 2860 0.456653 GCACGCGCAATGGAAAGATT 60.457 50.000 5.73 0.00 38.36 2.40
956 2891 1.661341 GCAGATTGGTGGTGAGCTAG 58.339 55.000 0.00 0.00 0.00 3.42
1085 3025 3.023116 CCTTGGAGGGGGATGGCA 61.023 66.667 0.00 0.00 0.00 4.92
1124 3064 3.441290 CTTCGGCGTCGGAGGAGT 61.441 66.667 10.65 0.00 38.31 3.85
1205 3148 2.367202 GCATCGGAGGGGAACAGGA 61.367 63.158 0.00 0.00 0.00 3.86
1221 3164 3.118454 GCAGAAGGCGCGTTAGCA 61.118 61.111 25.43 0.00 45.49 3.49
1378 3321 0.534412 ACGTCCTCCTGCTTCTGATG 59.466 55.000 0.00 0.00 0.00 3.07
1560 3531 8.361139 ACCCAACTATGATCTCTATTTTCTACG 58.639 37.037 0.00 0.00 0.00 3.51
1784 3787 8.821686 TTTGATCCAATTAATATCTGGTGTGT 57.178 30.769 4.88 0.00 0.00 3.72
1793 3796 7.667219 AGCGGAGTCATTTGATCCAATTAATAT 59.333 33.333 0.00 0.00 32.31 1.28
1827 3830 5.012148 AGCCAGAGCCAAAATCGTATAGTAT 59.988 40.000 0.00 0.00 41.25 2.12
1832 3835 2.684881 CAAGCCAGAGCCAAAATCGTAT 59.315 45.455 0.00 0.00 41.25 3.06
1836 3839 0.108472 GCCAAGCCAGAGCCAAAATC 60.108 55.000 0.00 0.00 41.25 2.17
1839 3842 1.152483 AAGCCAAGCCAGAGCCAAA 60.152 52.632 0.00 0.00 41.25 3.28
1840 3843 1.604593 GAAGCCAAGCCAGAGCCAA 60.605 57.895 0.00 0.00 41.25 4.52
1842 3845 1.181098 TTTGAAGCCAAGCCAGAGCC 61.181 55.000 0.00 0.00 41.25 4.70
1843 3846 0.243095 CTTTGAAGCCAAGCCAGAGC 59.757 55.000 0.00 0.00 40.32 4.09
1845 3848 2.165167 CATCTTTGAAGCCAAGCCAGA 58.835 47.619 0.00 0.00 33.23 3.86
1848 3894 3.665745 TTTCATCTTTGAAGCCAAGCC 57.334 42.857 0.00 0.00 42.60 4.35
1851 3897 6.819284 AGTCATTTTTCATCTTTGAAGCCAA 58.181 32.000 0.00 0.00 42.60 4.52
1868 3914 4.936411 CAGAGATGTCTTGCAGAGTCATTT 59.064 41.667 0.00 5.19 34.85 2.32
1871 3917 2.353505 GCAGAGATGTCTTGCAGAGTCA 60.354 50.000 8.68 0.00 31.12 3.41
1921 3967 5.104259 AGTAGGTCCAGAATTCATTGACC 57.896 43.478 23.24 23.24 44.64 4.02
1963 4009 6.707290 TCTTAGGAAAGAATTCGGTGATCAA 58.293 36.000 0.00 0.00 38.81 2.57
1964 4010 6.294361 TCTTAGGAAAGAATTCGGTGATCA 57.706 37.500 0.00 0.00 38.81 2.92
1965 4011 7.793927 AATCTTAGGAAAGAATTCGGTGATC 57.206 36.000 0.00 0.00 44.75 2.92
1984 4030 9.918630 GGCAATGCATATTACTTGATAAATCTT 57.081 29.630 7.79 0.00 0.00 2.40
1985 4031 9.081204 TGGCAATGCATATTACTTGATAAATCT 57.919 29.630 7.79 0.00 0.00 2.40
2021 4067 3.944015 AGATCACACAAGAGCCTTTATGC 59.056 43.478 0.00 0.00 0.00 3.14
2138 4185 2.297315 TGATGACTGGCTATGGTCGATC 59.703 50.000 0.00 0.00 35.45 3.69
2152 4199 2.106566 CCACTACTCTGCCTGATGACT 58.893 52.381 0.00 0.00 0.00 3.41
2251 4301 3.939066 AGTAGTTCACCGAGGGAAAATG 58.061 45.455 0.00 0.00 0.00 2.32
2253 4303 5.750352 AATAGTAGTTCACCGAGGGAAAA 57.250 39.130 0.00 0.00 0.00 2.29
2318 4373 4.055360 GGTGGCCAACAGAAACAAATTAC 58.945 43.478 18.33 0.00 0.00 1.89
2364 4419 0.321653 AGCTCGTGTTGAATCCACCC 60.322 55.000 0.00 0.00 0.00 4.61
2376 4431 1.001624 TGCATTTCATCGAGCTCGTG 58.998 50.000 33.33 27.89 40.80 4.35
2380 4435 2.391616 TGAGTGCATTTCATCGAGCT 57.608 45.000 0.00 0.00 0.00 4.09
2394 4449 1.806542 GTTGGCCTGTGTGTATGAGTG 59.193 52.381 3.32 0.00 0.00 3.51
2400 4455 2.294074 GTTCTTGTTGGCCTGTGTGTA 58.706 47.619 3.32 0.00 0.00 2.90
2436 4491 3.120060 GGATCACAACTGAGTCACATTGC 60.120 47.826 10.89 0.00 0.00 3.56
2437 4492 4.067192 TGGATCACAACTGAGTCACATTG 58.933 43.478 9.79 9.79 0.00 2.82
2438 4493 4.321718 CTGGATCACAACTGAGTCACATT 58.678 43.478 0.00 0.00 0.00 2.71
2439 4494 3.307269 CCTGGATCACAACTGAGTCACAT 60.307 47.826 0.00 0.00 0.00 3.21
2440 4495 2.037641 CCTGGATCACAACTGAGTCACA 59.962 50.000 0.00 0.00 0.00 3.58
2441 4496 2.693069 CCTGGATCACAACTGAGTCAC 58.307 52.381 0.00 0.00 0.00 3.67
2442 4497 1.002430 GCCTGGATCACAACTGAGTCA 59.998 52.381 0.00 0.00 0.00 3.41
2443 4498 1.002430 TGCCTGGATCACAACTGAGTC 59.998 52.381 0.00 0.00 0.00 3.36
2444 4499 1.059098 TGCCTGGATCACAACTGAGT 58.941 50.000 0.00 0.00 0.00 3.41
2445 4500 1.808945 GTTGCCTGGATCACAACTGAG 59.191 52.381 0.00 0.00 40.36 3.35
2446 4501 1.142667 TGTTGCCTGGATCACAACTGA 59.857 47.619 16.21 0.00 43.19 3.41
2447 4502 1.538512 CTGTTGCCTGGATCACAACTG 59.461 52.381 16.21 13.26 43.19 3.16
2448 4503 1.421268 TCTGTTGCCTGGATCACAACT 59.579 47.619 16.21 0.00 43.19 3.16
2449 4504 1.896220 TCTGTTGCCTGGATCACAAC 58.104 50.000 0.00 2.78 43.10 3.32
2450 4505 2.439409 CATCTGTTGCCTGGATCACAA 58.561 47.619 0.00 0.00 0.00 3.33
2451 4506 1.951895 GCATCTGTTGCCTGGATCACA 60.952 52.381 0.00 0.00 46.15 3.58
2452 4507 0.737219 GCATCTGTTGCCTGGATCAC 59.263 55.000 0.00 0.00 46.15 3.06
2453 4508 3.179925 GCATCTGTTGCCTGGATCA 57.820 52.632 0.00 0.00 46.15 2.92


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

AutoCloner maintained by Alex Coulton.