Multiple sequence alignment - TraesCS2A01G244500

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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 TraesCS2A01G244500 chr2A 100.000 3619 0 0 1 3619 349728481 349724863 0.000000e+00 6684
1 TraesCS2A01G244500 chr2A 96.954 197 6 0 1 197 323353846 323353650 7.490000e-87 331
2 TraesCS2A01G244500 chr2A 96.954 197 6 0 1 197 349747262 349747066 7.490000e-87 331
3 TraesCS2A01G244500 chr2A 96.447 197 7 0 1 197 330863698 330863894 3.480000e-85 326
4 TraesCS2A01G244500 chr2A 95.522 201 9 0 2 202 319799092 319799292 4.510000e-84 322
5 TraesCS2A01G244500 chr2D 98.605 2151 24 4 1376 3526 279050106 279052250 0.000000e+00 3801
6 TraesCS2A01G244500 chr2D 93.504 1093 65 4 198 1290 279048628 279049714 0.000000e+00 1620
7 TraesCS2A01G244500 chr2D 89.782 597 56 3 198 793 626640810 626641402 0.000000e+00 760
8 TraesCS2A01G244500 chr2D 85.930 597 75 7 204 795 38059790 38059198 2.370000e-176 628
9 TraesCS2A01G244500 chr2D 98.507 67 1 0 3553 3619 279052250 279052316 6.350000e-23 119
10 TraesCS2A01G244500 chr2B 97.732 1367 28 2 1367 2732 318147902 318149266 0.000000e+00 2350
11 TraesCS2A01G244500 chr2B 95.956 544 13 4 798 1336 318147371 318147910 0.000000e+00 874
12 TraesCS2A01G244500 chr2B 94.358 514 18 3 2795 3300 318149267 318149777 0.000000e+00 778
13 TraesCS2A01G244500 chr2B 94.118 187 9 2 3294 3480 318150208 318150392 2.130000e-72 283
14 TraesCS2A01G244500 chr1B 86.711 602 75 4 198 795 671544515 671543915 0.000000e+00 664
15 TraesCS2A01G244500 chr1B 85.668 614 81 6 199 808 379627733 379627123 1.100000e-179 640
16 TraesCS2A01G244500 chr1A 86.379 602 77 4 201 798 13970197 13969597 0.000000e+00 652
17 TraesCS2A01G244500 chr1A 95.960 198 8 0 1 198 153861482 153861679 4.510000e-84 322
18 TraesCS2A01G244500 chr4B 86.125 591 77 4 209 795 86132570 86133159 1.830000e-177 632
19 TraesCS2A01G244500 chr3A 85.667 607 80 7 201 802 550471033 550470429 1.830000e-177 632
20 TraesCS2A01G244500 chr7D 85.203 615 79 8 198 803 558090095 558090706 3.970000e-174 621
21 TraesCS2A01G244500 chr5A 96.954 197 6 0 1 197 690383997 690383801 7.490000e-87 331
22 TraesCS2A01G244500 chr7A 96.447 197 7 0 1 197 187181941 187182137 3.480000e-85 326
23 TraesCS2A01G244500 chr7A 96.447 197 7 0 1 197 398217315 398217119 3.480000e-85 326
24 TraesCS2A01G244500 chr6A 96.447 197 7 0 1 197 281885131 281884935 3.480000e-85 326


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 TraesCS2A01G244500 chr2A 349724863 349728481 3618 True 6684.000000 6684 100.000 1 3619 1 chr2A.!!$R2 3618
1 TraesCS2A01G244500 chr2D 279048628 279052316 3688 False 1846.666667 3801 96.872 198 3619 3 chr2D.!!$F2 3421
2 TraesCS2A01G244500 chr2D 626640810 626641402 592 False 760.000000 760 89.782 198 793 1 chr2D.!!$F1 595
3 TraesCS2A01G244500 chr2D 38059198 38059790 592 True 628.000000 628 85.930 204 795 1 chr2D.!!$R1 591
4 TraesCS2A01G244500 chr2B 318147371 318150392 3021 False 1071.250000 2350 95.541 798 3480 4 chr2B.!!$F1 2682
5 TraesCS2A01G244500 chr1B 671543915 671544515 600 True 664.000000 664 86.711 198 795 1 chr1B.!!$R2 597
6 TraesCS2A01G244500 chr1B 379627123 379627733 610 True 640.000000 640 85.668 199 808 1 chr1B.!!$R1 609
7 TraesCS2A01G244500 chr1A 13969597 13970197 600 True 652.000000 652 86.379 201 798 1 chr1A.!!$R1 597
8 TraesCS2A01G244500 chr4B 86132570 86133159 589 False 632.000000 632 86.125 209 795 1 chr4B.!!$F1 586
9 TraesCS2A01G244500 chr3A 550470429 550471033 604 True 632.000000 632 85.667 201 802 1 chr3A.!!$R1 601
10 TraesCS2A01G244500 chr7D 558090095 558090706 611 False 621.000000 621 85.203 198 803 1 chr7D.!!$F1 605

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
160 161 0.036765 GGGCTTGATGTGTCGGTGTA 60.037 55.0 0.00 0.0 0.00 2.90 F
192 193 0.250640 ATGATGGAAGGATGCTCCGC 60.251 55.0 0.00 0.0 42.75 5.54 F
289 294 0.407528 TGCTCCTCCTCTGTCTCAGT 59.592 55.0 0.00 0.0 32.61 3.41 F
1356 1378 0.179127 CCTCGCGCTTTCATCTCTGA 60.179 55.0 5.56 0.0 0.00 3.27 F
1358 1380 0.243636 TCGCGCTTTCATCTCTGACA 59.756 50.0 5.56 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1359 0.179127 TCAGAGATGAAAGCGCGAGG 60.179 55.0 12.10 0.00 0.00 4.63 R
1339 1361 0.243636 TGTCAGAGATGAAAGCGCGA 59.756 50.0 12.10 0.00 0.00 5.87 R
1493 1821 0.248336 CGACAGCATCGCATTGCAAT 60.248 50.0 5.99 5.99 45.52 3.56 R
2189 2517 5.074239 CCTTATTTCTGAATCCTCCCCTGAT 59.926 44.0 0.00 0.00 0.00 2.90 R
3201 3537 5.598417 AGTGAAATAATAGCAAATCACCCCC 59.402 40.0 0.00 0.00 38.29 5.40 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
27 28 3.959573 GTACCTAACGAGACATAGCGT 57.040 47.619 0.00 0.00 43.39 5.07
29 30 5.604010 GTACCTAACGAGACATAGCGTAT 57.396 43.478 0.00 0.00 40.23 3.06
30 31 4.745837 ACCTAACGAGACATAGCGTATC 57.254 45.455 0.00 0.00 40.23 2.24
31 32 4.387598 ACCTAACGAGACATAGCGTATCT 58.612 43.478 0.00 0.00 40.23 1.98
32 33 4.820716 ACCTAACGAGACATAGCGTATCTT 59.179 41.667 0.00 0.00 40.23 2.40
33 34 5.147865 CCTAACGAGACATAGCGTATCTTG 58.852 45.833 0.00 0.00 40.23 3.02
34 35 3.627732 ACGAGACATAGCGTATCTTGG 57.372 47.619 0.00 0.00 39.21 3.61
35 36 2.950309 ACGAGACATAGCGTATCTTGGT 59.050 45.455 0.00 0.00 39.21 3.67
36 37 3.243101 ACGAGACATAGCGTATCTTGGTG 60.243 47.826 0.00 0.00 39.21 4.17
37 38 3.003378 CGAGACATAGCGTATCTTGGTGA 59.997 47.826 0.00 0.00 33.47 4.02
38 39 4.541779 GAGACATAGCGTATCTTGGTGAG 58.458 47.826 0.00 0.00 32.86 3.51
39 40 3.319405 AGACATAGCGTATCTTGGTGAGG 59.681 47.826 0.00 0.00 0.00 3.86
40 41 3.031736 ACATAGCGTATCTTGGTGAGGT 58.968 45.455 0.00 0.00 0.00 3.85
41 42 4.212716 ACATAGCGTATCTTGGTGAGGTA 58.787 43.478 0.00 0.00 0.00 3.08
42 43 4.278669 ACATAGCGTATCTTGGTGAGGTAG 59.721 45.833 0.00 0.00 0.00 3.18
43 44 1.409427 AGCGTATCTTGGTGAGGTAGC 59.591 52.381 0.00 0.00 0.00 3.58
44 45 1.136305 GCGTATCTTGGTGAGGTAGCA 59.864 52.381 0.00 0.00 34.39 3.49
45 46 2.418197 GCGTATCTTGGTGAGGTAGCAA 60.418 50.000 0.00 0.00 43.97 3.91
46 47 3.741388 GCGTATCTTGGTGAGGTAGCAAT 60.741 47.826 0.00 0.00 44.95 3.56
47 48 4.500887 GCGTATCTTGGTGAGGTAGCAATA 60.501 45.833 0.00 0.00 44.95 1.90
48 49 5.597806 CGTATCTTGGTGAGGTAGCAATAA 58.402 41.667 0.00 0.00 44.95 1.40
49 50 6.223852 CGTATCTTGGTGAGGTAGCAATAAT 58.776 40.000 0.00 0.00 44.95 1.28
50 51 6.146184 CGTATCTTGGTGAGGTAGCAATAATG 59.854 42.308 0.00 0.00 44.95 1.90
51 52 5.435686 TCTTGGTGAGGTAGCAATAATGT 57.564 39.130 0.00 0.00 44.95 2.71
52 53 5.815581 TCTTGGTGAGGTAGCAATAATGTT 58.184 37.500 0.00 0.00 44.95 2.71
53 54 5.880332 TCTTGGTGAGGTAGCAATAATGTTC 59.120 40.000 0.00 0.00 44.95 3.18
54 55 4.523083 TGGTGAGGTAGCAATAATGTTCC 58.477 43.478 0.00 0.00 33.01 3.62
55 56 4.018870 TGGTGAGGTAGCAATAATGTTCCA 60.019 41.667 0.00 0.00 33.01 3.53
56 57 5.133221 GGTGAGGTAGCAATAATGTTCCAT 58.867 41.667 0.00 0.00 0.00 3.41
57 58 5.594317 GGTGAGGTAGCAATAATGTTCCATT 59.406 40.000 0.00 0.00 0.00 3.16
58 59 6.238759 GGTGAGGTAGCAATAATGTTCCATTC 60.239 42.308 0.00 0.00 0.00 2.67
59 60 5.527214 TGAGGTAGCAATAATGTTCCATTCG 59.473 40.000 0.00 0.00 0.00 3.34
60 61 5.437060 AGGTAGCAATAATGTTCCATTCGT 58.563 37.500 0.00 0.00 0.00 3.85
61 62 6.588204 AGGTAGCAATAATGTTCCATTCGTA 58.412 36.000 0.00 0.00 0.00 3.43
62 63 7.224297 AGGTAGCAATAATGTTCCATTCGTAT 58.776 34.615 0.00 0.00 0.00 3.06
63 64 7.387948 AGGTAGCAATAATGTTCCATTCGTATC 59.612 37.037 0.00 0.00 0.00 2.24
64 65 6.560253 AGCAATAATGTTCCATTCGTATCC 57.440 37.500 0.00 0.00 0.00 2.59
65 66 6.061441 AGCAATAATGTTCCATTCGTATCCA 58.939 36.000 0.00 0.00 0.00 3.41
66 67 6.716628 AGCAATAATGTTCCATTCGTATCCAT 59.283 34.615 0.00 0.00 0.00 3.41
67 68 7.882791 AGCAATAATGTTCCATTCGTATCCATA 59.117 33.333 0.00 0.00 0.00 2.74
68 69 8.677300 GCAATAATGTTCCATTCGTATCCATAT 58.323 33.333 0.00 0.00 0.00 1.78
69 70 9.992910 CAATAATGTTCCATTCGTATCCATATG 57.007 33.333 0.00 0.00 0.00 1.78
70 71 6.500684 AATGTTCCATTCGTATCCATATGC 57.499 37.500 0.00 0.00 0.00 3.14
71 72 4.967036 TGTTCCATTCGTATCCATATGCA 58.033 39.130 0.00 0.00 0.00 3.96
72 73 5.372373 TGTTCCATTCGTATCCATATGCAA 58.628 37.500 0.00 0.00 0.00 4.08
73 74 5.469760 TGTTCCATTCGTATCCATATGCAAG 59.530 40.000 0.00 0.00 0.00 4.01
74 75 4.002982 TCCATTCGTATCCATATGCAAGC 58.997 43.478 0.00 0.00 0.00 4.01
75 76 4.005650 CCATTCGTATCCATATGCAAGCT 58.994 43.478 0.00 0.00 0.00 3.74
76 77 5.046663 TCCATTCGTATCCATATGCAAGCTA 60.047 40.000 0.00 0.00 0.00 3.32
77 78 5.643348 CCATTCGTATCCATATGCAAGCTAA 59.357 40.000 0.00 0.00 0.00 3.09
78 79 6.183360 CCATTCGTATCCATATGCAAGCTAAG 60.183 42.308 0.00 0.00 0.00 2.18
79 80 5.468540 TCGTATCCATATGCAAGCTAAGT 57.531 39.130 0.00 0.00 0.00 2.24
80 81 6.584185 TCGTATCCATATGCAAGCTAAGTA 57.416 37.500 0.00 0.00 0.00 2.24
81 82 6.621613 TCGTATCCATATGCAAGCTAAGTAG 58.378 40.000 0.00 0.00 0.00 2.57
82 83 5.807520 CGTATCCATATGCAAGCTAAGTAGG 59.192 44.000 0.00 0.00 0.00 3.18
83 84 6.350194 CGTATCCATATGCAAGCTAAGTAGGA 60.350 42.308 0.00 0.00 0.00 2.94
84 85 5.474578 TCCATATGCAAGCTAAGTAGGAG 57.525 43.478 0.00 0.00 0.00 3.69
85 86 4.284490 TCCATATGCAAGCTAAGTAGGAGG 59.716 45.833 0.00 0.00 0.00 4.30
86 87 4.564406 CCATATGCAAGCTAAGTAGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
87 88 2.247699 TGCAAGCTAAGTAGGAGGGA 57.752 50.000 0.00 0.00 0.00 4.20
88 89 2.111384 TGCAAGCTAAGTAGGAGGGAG 58.889 52.381 0.00 0.00 0.00 4.30
89 90 2.112190 GCAAGCTAAGTAGGAGGGAGT 58.888 52.381 0.00 0.00 0.00 3.85
90 91 2.502130 GCAAGCTAAGTAGGAGGGAGTT 59.498 50.000 0.00 0.00 0.00 3.01
91 92 3.431068 GCAAGCTAAGTAGGAGGGAGTTC 60.431 52.174 0.00 0.00 0.00 3.01
92 93 3.759815 AGCTAAGTAGGAGGGAGTTCA 57.240 47.619 0.00 0.00 0.00 3.18
93 94 3.367321 AGCTAAGTAGGAGGGAGTTCAC 58.633 50.000 0.00 0.00 0.00 3.18
94 95 2.431419 GCTAAGTAGGAGGGAGTTCACC 59.569 54.545 0.00 0.00 0.00 4.02
95 96 3.882515 GCTAAGTAGGAGGGAGTTCACCT 60.883 52.174 0.00 0.00 42.18 4.00
101 102 2.545537 GAGGGAGTTCACCTCGTTTT 57.454 50.000 0.00 0.00 44.50 2.43
102 103 2.414806 GAGGGAGTTCACCTCGTTTTC 58.585 52.381 0.00 0.00 44.50 2.29
103 104 1.071857 AGGGAGTTCACCTCGTTTTCC 59.928 52.381 0.00 0.00 41.46 3.13
104 105 1.202722 GGGAGTTCACCTCGTTTTCCA 60.203 52.381 0.00 0.00 41.46 3.53
105 106 2.567985 GGAGTTCACCTCGTTTTCCAA 58.432 47.619 0.00 0.00 41.46 3.53
106 107 2.946990 GGAGTTCACCTCGTTTTCCAAA 59.053 45.455 0.00 0.00 41.46 3.28
107 108 3.003378 GGAGTTCACCTCGTTTTCCAAAG 59.997 47.826 0.00 0.00 41.46 2.77
108 109 3.617284 AGTTCACCTCGTTTTCCAAAGT 58.383 40.909 0.00 0.00 0.00 2.66
109 110 4.773013 AGTTCACCTCGTTTTCCAAAGTA 58.227 39.130 0.00 0.00 0.00 2.24
110 111 4.573607 AGTTCACCTCGTTTTCCAAAGTAC 59.426 41.667 0.00 0.00 0.00 2.73
111 112 3.125316 TCACCTCGTTTTCCAAAGTACG 58.875 45.455 0.00 0.00 35.46 3.67
112 113 2.867975 CACCTCGTTTTCCAAAGTACGT 59.132 45.455 0.00 0.00 35.63 3.57
113 114 2.867975 ACCTCGTTTTCCAAAGTACGTG 59.132 45.455 0.00 0.00 35.63 4.49
114 115 2.349155 CCTCGTTTTCCAAAGTACGTGC 60.349 50.000 0.00 0.00 35.63 5.34
115 116 2.542595 CTCGTTTTCCAAAGTACGTGCT 59.457 45.455 0.00 0.00 35.63 4.40
116 117 2.540931 TCGTTTTCCAAAGTACGTGCTC 59.459 45.455 6.63 0.00 35.63 4.26
117 118 2.542595 CGTTTTCCAAAGTACGTGCTCT 59.457 45.455 6.63 0.00 0.00 4.09
118 119 3.737266 CGTTTTCCAAAGTACGTGCTCTA 59.263 43.478 6.63 0.00 0.00 2.43
119 120 4.143389 CGTTTTCCAAAGTACGTGCTCTAG 60.143 45.833 6.63 0.00 0.00 2.43
120 121 2.649331 TCCAAAGTACGTGCTCTAGC 57.351 50.000 6.63 0.00 42.50 3.42
121 122 2.168496 TCCAAAGTACGTGCTCTAGCT 58.832 47.619 6.63 0.00 42.66 3.32
122 123 2.163815 TCCAAAGTACGTGCTCTAGCTC 59.836 50.000 6.63 0.00 42.66 4.09
123 124 2.164624 CCAAAGTACGTGCTCTAGCTCT 59.835 50.000 6.63 0.00 42.66 4.09
124 125 3.367498 CCAAAGTACGTGCTCTAGCTCTT 60.367 47.826 6.63 0.00 42.66 2.85
125 126 3.495670 AAGTACGTGCTCTAGCTCTTG 57.504 47.619 6.63 0.00 42.66 3.02
126 127 2.438411 AGTACGTGCTCTAGCTCTTGT 58.562 47.619 0.00 0.00 42.66 3.16
127 128 2.820787 AGTACGTGCTCTAGCTCTTGTT 59.179 45.455 0.00 0.00 42.66 2.83
128 129 4.008330 AGTACGTGCTCTAGCTCTTGTTA 58.992 43.478 0.00 0.00 42.66 2.41
129 130 4.641094 AGTACGTGCTCTAGCTCTTGTTAT 59.359 41.667 0.00 0.00 42.66 1.89
130 131 5.821470 AGTACGTGCTCTAGCTCTTGTTATA 59.179 40.000 0.00 0.00 42.66 0.98
131 132 5.176407 ACGTGCTCTAGCTCTTGTTATAG 57.824 43.478 3.26 0.00 42.66 1.31
132 133 4.036971 ACGTGCTCTAGCTCTTGTTATAGG 59.963 45.833 3.26 0.00 42.66 2.57
133 134 4.036971 CGTGCTCTAGCTCTTGTTATAGGT 59.963 45.833 3.26 0.00 42.66 3.08
134 135 5.525199 GTGCTCTAGCTCTTGTTATAGGTC 58.475 45.833 3.26 0.00 42.66 3.85
135 136 4.585162 TGCTCTAGCTCTTGTTATAGGTCC 59.415 45.833 3.26 0.00 42.66 4.46
136 137 4.585162 GCTCTAGCTCTTGTTATAGGTCCA 59.415 45.833 0.00 0.00 38.21 4.02
137 138 5.508320 GCTCTAGCTCTTGTTATAGGTCCAC 60.508 48.000 0.00 0.00 38.21 4.02
138 139 3.802948 AGCTCTTGTTATAGGTCCACG 57.197 47.619 0.00 0.00 0.00 4.94
139 140 3.097614 AGCTCTTGTTATAGGTCCACGT 58.902 45.455 0.00 0.00 0.00 4.49
140 141 3.119101 AGCTCTTGTTATAGGTCCACGTG 60.119 47.826 9.08 9.08 0.00 4.49
141 142 3.782046 CTCTTGTTATAGGTCCACGTGG 58.218 50.000 29.26 29.26 0.00 4.94
142 143 2.498481 TCTTGTTATAGGTCCACGTGGG 59.502 50.000 33.40 15.70 35.41 4.61
143 144 1.196911 TGTTATAGGTCCACGTGGGG 58.803 55.000 33.40 10.49 37.22 4.96
144 145 0.179065 GTTATAGGTCCACGTGGGGC 60.179 60.000 33.40 24.71 42.12 5.80
145 146 0.325860 TTATAGGTCCACGTGGGGCT 60.326 55.000 33.40 16.26 42.62 5.19
146 147 0.325860 TATAGGTCCACGTGGGGCTT 60.326 55.000 33.40 23.45 42.62 4.35
147 148 1.910580 ATAGGTCCACGTGGGGCTTG 61.911 60.000 33.40 7.86 42.62 4.01
148 149 3.948719 GGTCCACGTGGGGCTTGA 61.949 66.667 33.40 11.27 42.62 3.02
149 150 2.351276 GTCCACGTGGGGCTTGAT 59.649 61.111 33.40 0.00 38.65 2.57
150 151 2.040544 GTCCACGTGGGGCTTGATG 61.041 63.158 33.40 5.51 38.65 3.07
151 152 2.034066 CCACGTGGGGCTTGATGT 59.966 61.111 27.57 0.00 0.00 3.06
152 153 2.334946 CCACGTGGGGCTTGATGTG 61.335 63.158 27.57 0.00 0.00 3.21
153 154 1.600636 CACGTGGGGCTTGATGTGT 60.601 57.895 7.95 0.00 0.00 3.72
154 155 1.302511 ACGTGGGGCTTGATGTGTC 60.303 57.895 0.00 0.00 0.00 3.67
155 156 2.390599 CGTGGGGCTTGATGTGTCG 61.391 63.158 0.00 0.00 0.00 4.35
156 157 2.040544 GTGGGGCTTGATGTGTCGG 61.041 63.158 0.00 0.00 0.00 4.79
157 158 2.351276 GGGGCTTGATGTGTCGGT 59.649 61.111 0.00 0.00 0.00 4.69
158 159 2.040544 GGGGCTTGATGTGTCGGTG 61.041 63.158 0.00 0.00 0.00 4.94
159 160 1.302511 GGGCTTGATGTGTCGGTGT 60.303 57.895 0.00 0.00 0.00 4.16
160 161 0.036765 GGGCTTGATGTGTCGGTGTA 60.037 55.000 0.00 0.00 0.00 2.90
161 162 1.359848 GGCTTGATGTGTCGGTGTAG 58.640 55.000 0.00 0.00 0.00 2.74
162 163 1.067142 GGCTTGATGTGTCGGTGTAGA 60.067 52.381 0.00 0.00 0.00 2.59
163 164 2.263077 GCTTGATGTGTCGGTGTAGAG 58.737 52.381 0.00 0.00 0.00 2.43
164 165 2.352814 GCTTGATGTGTCGGTGTAGAGT 60.353 50.000 0.00 0.00 0.00 3.24
165 166 3.502920 CTTGATGTGTCGGTGTAGAGTC 58.497 50.000 0.00 0.00 0.00 3.36
166 167 1.816835 TGATGTGTCGGTGTAGAGTCC 59.183 52.381 0.00 0.00 0.00 3.85
167 168 1.816835 GATGTGTCGGTGTAGAGTCCA 59.183 52.381 0.00 0.00 0.00 4.02
168 169 1.919240 TGTGTCGGTGTAGAGTCCAT 58.081 50.000 0.00 0.00 0.00 3.41
169 170 1.544246 TGTGTCGGTGTAGAGTCCATG 59.456 52.381 0.00 0.00 0.00 3.66
170 171 1.135083 GTGTCGGTGTAGAGTCCATGG 60.135 57.143 4.97 4.97 0.00 3.66
171 172 0.460311 GTCGGTGTAGAGTCCATGGG 59.540 60.000 13.02 0.00 0.00 4.00
172 173 0.686441 TCGGTGTAGAGTCCATGGGG 60.686 60.000 13.02 0.00 0.00 4.96
173 174 0.686441 CGGTGTAGAGTCCATGGGGA 60.686 60.000 13.02 0.00 42.29 4.81
183 184 1.151760 TCCATGGGGATGATGGAAGG 58.848 55.000 13.02 0.00 45.25 3.46
184 185 1.151760 CCATGGGGATGATGGAAGGA 58.848 55.000 2.85 0.00 42.81 3.36
185 186 1.714787 CCATGGGGATGATGGAAGGAT 59.285 52.381 2.85 0.00 42.81 3.24
186 187 2.556782 CCATGGGGATGATGGAAGGATG 60.557 54.545 2.85 0.00 42.81 3.51
187 188 0.479815 TGGGGATGATGGAAGGATGC 59.520 55.000 0.00 0.00 0.00 3.91
188 189 0.776176 GGGGATGATGGAAGGATGCT 59.224 55.000 0.00 0.00 0.00 3.79
189 190 1.271817 GGGGATGATGGAAGGATGCTC 60.272 57.143 0.00 0.00 0.00 4.26
190 191 1.271817 GGGATGATGGAAGGATGCTCC 60.272 57.143 0.00 0.00 36.58 4.70
191 192 1.610102 GGATGATGGAAGGATGCTCCG 60.610 57.143 0.00 0.00 42.75 4.63
192 193 0.250640 ATGATGGAAGGATGCTCCGC 60.251 55.000 0.00 0.00 42.75 5.54
193 194 1.146930 GATGGAAGGATGCTCCGCA 59.853 57.895 0.00 0.00 42.75 5.69
207 208 4.415150 CGCATCACAGCCCCCACT 62.415 66.667 0.00 0.00 0.00 4.00
252 257 1.265454 CGGGGGAACTAGTCCTTGCT 61.265 60.000 0.00 0.00 46.92 3.91
281 286 2.285824 GAGTTGCTGCTCCTCCTCT 58.714 57.895 0.00 0.00 0.00 3.69
289 294 0.407528 TGCTCCTCCTCTGTCTCAGT 59.592 55.000 0.00 0.00 32.61 3.41
301 306 4.504916 CTCAGTCCCGCGAGCAGG 62.505 72.222 8.23 0.00 0.00 4.85
319 324 1.605058 GGTGCTAGCTCCAACCGAGA 61.605 60.000 27.04 0.00 41.63 4.04
415 420 3.881688 GCCTCATATTGCAATGTCTGACT 59.118 43.478 22.27 0.00 0.00 3.41
470 475 0.733150 GCAACTCGGGCTATGTTTCC 59.267 55.000 0.00 0.00 0.00 3.13
489 494 1.578583 CGAAACAAGACCCTCGTTGT 58.421 50.000 0.00 0.00 38.56 3.32
549 557 8.939201 TTTCTGAAACAAAAGATATGTTGCAA 57.061 26.923 0.00 0.00 43.83 4.08
661 674 6.166279 TGCAGAAATCTATCGAAACAAGACT 58.834 36.000 0.00 0.00 0.00 3.24
685 700 2.888834 TTGCAAGAAAAAGACTGGCC 57.111 45.000 0.00 0.00 33.79 5.36
705 720 1.671054 CGCGGGATTGACTTGTGGT 60.671 57.895 0.00 0.00 0.00 4.16
714 729 1.885850 GACTTGTGGTCGGCGTGTT 60.886 57.895 6.85 0.00 35.07 3.32
762 777 4.781959 TAAGCGGCGGACGTTCGG 62.782 66.667 19.64 2.87 46.52 4.30
771 786 1.079681 GGACGTTCGGGTGTGCATA 60.080 57.895 0.00 0.00 0.00 3.14
795 810 1.128692 CGGCTGAAGGTAAGCTTTTCG 59.871 52.381 3.20 1.03 40.64 3.46
866 885 5.904362 AAGGGAGCAGAAATATTGTGTTC 57.096 39.130 6.44 6.44 34.20 3.18
867 886 5.184892 AGGGAGCAGAAATATTGTGTTCT 57.815 39.130 12.03 0.00 35.11 3.01
868 887 6.313519 AGGGAGCAGAAATATTGTGTTCTA 57.686 37.500 12.03 0.00 35.11 2.10
869 888 6.721318 AGGGAGCAGAAATATTGTGTTCTAA 58.279 36.000 12.03 0.00 35.11 2.10
870 889 7.175104 AGGGAGCAGAAATATTGTGTTCTAAA 58.825 34.615 12.03 0.00 35.11 1.85
1292 1314 1.004560 TCTTCCTCAGCAAGCACGG 60.005 57.895 0.00 0.00 0.00 4.94
1318 1340 0.804989 CCACAAGGAAGCCGAATCAC 59.195 55.000 0.00 0.00 36.89 3.06
1327 1349 2.795389 GCCGAATCACGTACCGCAC 61.795 63.158 0.00 0.00 40.78 5.34
1329 1351 1.153901 CGAATCACGTACCGCACCT 60.154 57.895 0.00 0.00 37.22 4.00
1330 1352 1.138047 CGAATCACGTACCGCACCTC 61.138 60.000 0.00 0.00 37.22 3.85
1331 1353 0.804933 GAATCACGTACCGCACCTCC 60.805 60.000 0.00 0.00 0.00 4.30
1332 1354 2.234913 AATCACGTACCGCACCTCCC 62.235 60.000 0.00 0.00 0.00 4.30
1333 1355 3.687102 CACGTACCGCACCTCCCA 61.687 66.667 0.00 0.00 0.00 4.37
1334 1356 2.918802 ACGTACCGCACCTCCCAA 60.919 61.111 0.00 0.00 0.00 4.12
1335 1357 2.344500 CGTACCGCACCTCCCAAA 59.656 61.111 0.00 0.00 0.00 3.28
1336 1358 2.030958 CGTACCGCACCTCCCAAAC 61.031 63.158 0.00 0.00 0.00 2.93
1337 1359 1.673337 GTACCGCACCTCCCAAACC 60.673 63.158 0.00 0.00 0.00 3.27
1338 1360 2.897762 TACCGCACCTCCCAAACCC 61.898 63.158 0.00 0.00 0.00 4.11
1339 1361 3.966543 CCGCACCTCCCAAACCCT 61.967 66.667 0.00 0.00 0.00 4.34
1340 1362 2.359975 CGCACCTCCCAAACCCTC 60.360 66.667 0.00 0.00 0.00 4.30
1341 1363 2.359975 GCACCTCCCAAACCCTCG 60.360 66.667 0.00 0.00 0.00 4.63
1342 1364 2.359975 CACCTCCCAAACCCTCGC 60.360 66.667 0.00 0.00 0.00 5.03
1343 1365 4.016706 ACCTCCCAAACCCTCGCG 62.017 66.667 0.00 0.00 0.00 5.87
1345 1367 4.394712 CTCCCAAACCCTCGCGCT 62.395 66.667 5.56 0.00 0.00 5.92
1346 1368 3.901797 CTCCCAAACCCTCGCGCTT 62.902 63.158 5.56 0.00 0.00 4.68
1347 1369 2.983592 CCCAAACCCTCGCGCTTT 60.984 61.111 5.56 0.00 0.00 3.51
1348 1370 2.561373 CCAAACCCTCGCGCTTTC 59.439 61.111 5.56 0.00 0.00 2.62
1349 1371 2.258013 CCAAACCCTCGCGCTTTCA 61.258 57.895 5.56 0.00 0.00 2.69
1350 1372 1.586154 CCAAACCCTCGCGCTTTCAT 61.586 55.000 5.56 0.00 0.00 2.57
1351 1373 0.179189 CAAACCCTCGCGCTTTCATC 60.179 55.000 5.56 0.00 0.00 2.92
1352 1374 0.321653 AAACCCTCGCGCTTTCATCT 60.322 50.000 5.56 0.00 0.00 2.90
1353 1375 0.741221 AACCCTCGCGCTTTCATCTC 60.741 55.000 5.56 0.00 0.00 2.75
1354 1376 1.142748 CCCTCGCGCTTTCATCTCT 59.857 57.895 5.56 0.00 0.00 3.10
1355 1377 1.150567 CCCTCGCGCTTTCATCTCTG 61.151 60.000 5.56 0.00 0.00 3.35
1356 1378 0.179127 CCTCGCGCTTTCATCTCTGA 60.179 55.000 5.56 0.00 0.00 3.27
1357 1379 0.919981 CTCGCGCTTTCATCTCTGAC 59.080 55.000 5.56 0.00 0.00 3.51
1358 1380 0.243636 TCGCGCTTTCATCTCTGACA 59.756 50.000 5.56 0.00 0.00 3.58
1359 1381 0.644331 CGCGCTTTCATCTCTGACAG 59.356 55.000 5.56 0.00 33.21 3.51
1360 1382 1.719600 GCGCTTTCATCTCTGACAGT 58.280 50.000 0.00 0.00 32.74 3.55
1361 1383 1.658095 GCGCTTTCATCTCTGACAGTC 59.342 52.381 0.00 0.00 32.74 3.51
1362 1384 2.266554 CGCTTTCATCTCTGACAGTCC 58.733 52.381 1.59 0.00 32.74 3.85
1363 1385 2.626840 GCTTTCATCTCTGACAGTCCC 58.373 52.381 1.59 0.00 32.74 4.46
1364 1386 2.679349 GCTTTCATCTCTGACAGTCCCC 60.679 54.545 1.59 0.00 32.74 4.81
1365 1387 1.573108 TTCATCTCTGACAGTCCCCC 58.427 55.000 1.59 0.00 0.00 5.40
1401 1729 0.813184 ATTCGGCAGCCAATCTTGTG 59.187 50.000 13.30 0.00 0.00 3.33
1402 1730 0.537143 TTCGGCAGCCAATCTTGTGT 60.537 50.000 13.30 0.00 0.00 3.72
1413 1741 4.111916 CCAATCTTGTGTTTGGTGTGTTC 58.888 43.478 0.00 0.00 37.93 3.18
1493 1821 6.533723 ACGAATCTTGTAGATTAATTGCGACA 59.466 34.615 11.79 0.00 44.41 4.35
1940 2268 0.409876 AGGCTGTCTCTGGTCTACCA 59.590 55.000 1.13 1.13 45.30 3.25
2189 2517 3.743521 CTTGAATGGTCCTGTCAGAACA 58.256 45.455 0.00 0.00 38.00 3.18
2267 2595 0.179048 TGCCATGGCTTATGACTCCG 60.179 55.000 35.53 0.00 42.51 4.63
2945 3273 6.338214 TGAGGCTCTATTGTCATTAGCTAG 57.662 41.667 16.72 0.00 33.67 3.42
3106 3442 6.268847 CCTCATCTTTGGTAGATTACTAGGCT 59.731 42.308 0.00 0.00 41.78 4.58
3150 3486 6.264832 GTTTTGTGTTTGACATGACTGATGA 58.735 36.000 0.00 0.00 35.80 2.92
3172 3508 5.999600 TGATGATTTGCTGAACTTCTGAAGA 59.000 36.000 23.36 0.85 0.00 2.87
3173 3509 6.657966 TGATGATTTGCTGAACTTCTGAAGAT 59.342 34.615 23.36 12.21 0.00 2.40
3257 3593 6.882678 GGTCTAAAATCCTTAAGTGGCAAGTA 59.117 38.462 0.97 0.00 0.00 2.24
3302 4073 5.413833 ACCTTCTTTGATAGCACACTTGATG 59.586 40.000 0.00 0.00 0.00 3.07
3522 4293 0.256752 TGACAGGCATTGGAGGGATG 59.743 55.000 0.00 0.00 0.00 3.51
3524 4295 1.002069 ACAGGCATTGGAGGGATGAA 58.998 50.000 0.00 0.00 0.00 2.57
3525 4296 1.572415 ACAGGCATTGGAGGGATGAAT 59.428 47.619 0.00 0.00 0.00 2.57
3526 4297 2.023695 ACAGGCATTGGAGGGATGAATT 60.024 45.455 0.00 0.00 0.00 2.17
3527 4298 2.364324 CAGGCATTGGAGGGATGAATTG 59.636 50.000 0.00 0.00 0.00 2.32
3528 4299 1.069668 GGCATTGGAGGGATGAATTGC 59.930 52.381 0.00 0.00 0.00 3.56
3529 4300 2.037144 GCATTGGAGGGATGAATTGCT 58.963 47.619 0.00 0.00 0.00 3.91
3530 4301 2.433239 GCATTGGAGGGATGAATTGCTT 59.567 45.455 0.00 0.00 0.00 3.91
3531 4302 3.118519 GCATTGGAGGGATGAATTGCTTT 60.119 43.478 0.00 0.00 0.00 3.51
3532 4303 4.624604 GCATTGGAGGGATGAATTGCTTTT 60.625 41.667 0.00 0.00 0.00 2.27
3533 4304 5.493809 CATTGGAGGGATGAATTGCTTTTT 58.506 37.500 0.00 0.00 0.00 1.94
3534 4305 4.806640 TGGAGGGATGAATTGCTTTTTC 57.193 40.909 0.00 0.00 0.00 2.29
3535 4306 3.515104 TGGAGGGATGAATTGCTTTTTCC 59.485 43.478 0.00 0.00 0.00 3.13
3536 4307 3.515104 GGAGGGATGAATTGCTTTTTCCA 59.485 43.478 0.00 0.00 0.00 3.53
3537 4308 4.020307 GGAGGGATGAATTGCTTTTTCCAA 60.020 41.667 0.00 0.00 0.00 3.53
3538 4309 5.338626 GGAGGGATGAATTGCTTTTTCCAAT 60.339 40.000 0.00 0.00 34.56 3.16
3539 4310 5.493809 AGGGATGAATTGCTTTTTCCAATG 58.506 37.500 0.00 0.00 33.48 2.82
3540 4311 5.248934 AGGGATGAATTGCTTTTTCCAATGA 59.751 36.000 0.00 0.00 33.48 2.57
3541 4312 5.583457 GGGATGAATTGCTTTTTCCAATGAG 59.417 40.000 0.00 0.00 33.48 2.90
3542 4313 5.583457 GGATGAATTGCTTTTTCCAATGAGG 59.417 40.000 0.00 0.00 33.48 3.86
3589 4360 7.175104 TCTCCATATACCTTTTTGTGCTTCTT 58.825 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.959573 ACGCTATGTCTCGTTAGGTAC 57.040 47.619 0.00 0.00 35.09 3.34
8 9 5.545588 AGATACGCTATGTCTCGTTAGGTA 58.454 41.667 0.00 0.00 39.79 3.08
9 10 4.387598 AGATACGCTATGTCTCGTTAGGT 58.612 43.478 0.00 0.00 39.79 3.08
10 11 5.147865 CAAGATACGCTATGTCTCGTTAGG 58.852 45.833 0.00 0.00 39.79 2.69
11 12 5.147865 CCAAGATACGCTATGTCTCGTTAG 58.852 45.833 0.00 0.00 39.79 2.34
12 13 4.577693 ACCAAGATACGCTATGTCTCGTTA 59.422 41.667 0.00 0.00 39.79 3.18
13 14 3.380637 ACCAAGATACGCTATGTCTCGTT 59.619 43.478 0.00 0.00 39.79 3.85
14 15 2.950309 ACCAAGATACGCTATGTCTCGT 59.050 45.455 0.00 0.00 42.09 4.18
15 16 3.003378 TCACCAAGATACGCTATGTCTCG 59.997 47.826 0.00 0.00 0.00 4.04
16 17 4.541779 CTCACCAAGATACGCTATGTCTC 58.458 47.826 0.00 0.00 0.00 3.36
17 18 3.319405 CCTCACCAAGATACGCTATGTCT 59.681 47.826 0.00 0.00 0.00 3.41
18 19 3.068307 ACCTCACCAAGATACGCTATGTC 59.932 47.826 0.00 0.00 0.00 3.06
19 20 3.031736 ACCTCACCAAGATACGCTATGT 58.968 45.455 0.00 0.00 0.00 2.29
20 21 3.735237 ACCTCACCAAGATACGCTATG 57.265 47.619 0.00 0.00 0.00 2.23
21 22 3.256136 GCTACCTCACCAAGATACGCTAT 59.744 47.826 0.00 0.00 0.00 2.97
22 23 2.621998 GCTACCTCACCAAGATACGCTA 59.378 50.000 0.00 0.00 0.00 4.26
23 24 1.409427 GCTACCTCACCAAGATACGCT 59.591 52.381 0.00 0.00 0.00 5.07
24 25 1.136305 TGCTACCTCACCAAGATACGC 59.864 52.381 0.00 0.00 0.00 4.42
25 26 3.520290 TTGCTACCTCACCAAGATACG 57.480 47.619 0.00 0.00 0.00 3.06
26 27 6.992715 ACATTATTGCTACCTCACCAAGATAC 59.007 38.462 0.00 0.00 0.00 2.24
27 28 7.136822 ACATTATTGCTACCTCACCAAGATA 57.863 36.000 0.00 0.00 0.00 1.98
28 29 6.006275 ACATTATTGCTACCTCACCAAGAT 57.994 37.500 0.00 0.00 0.00 2.40
29 30 5.435686 ACATTATTGCTACCTCACCAAGA 57.564 39.130 0.00 0.00 0.00 3.02
30 31 5.066505 GGAACATTATTGCTACCTCACCAAG 59.933 44.000 0.00 0.00 0.00 3.61
31 32 4.947388 GGAACATTATTGCTACCTCACCAA 59.053 41.667 0.00 0.00 0.00 3.67
32 33 4.018870 TGGAACATTATTGCTACCTCACCA 60.019 41.667 0.00 0.00 0.00 4.17
33 34 4.523083 TGGAACATTATTGCTACCTCACC 58.477 43.478 0.00 0.00 0.00 4.02
39 40 7.172532 TGGATACGAATGGAACATTATTGCTAC 59.827 37.037 0.00 0.00 43.03 3.58
40 41 7.220740 TGGATACGAATGGAACATTATTGCTA 58.779 34.615 0.00 0.00 43.03 3.49
41 42 6.061441 TGGATACGAATGGAACATTATTGCT 58.939 36.000 0.00 0.00 43.03 3.91
42 43 6.312399 TGGATACGAATGGAACATTATTGC 57.688 37.500 0.00 0.00 43.03 3.56
43 44 9.992910 CATATGGATACGAATGGAACATTATTG 57.007 33.333 0.00 0.00 43.03 1.90
44 45 8.677300 GCATATGGATACGAATGGAACATTATT 58.323 33.333 4.56 0.00 43.03 1.40
45 46 7.828717 TGCATATGGATACGAATGGAACATTAT 59.171 33.333 4.56 0.00 43.03 1.28
46 47 7.164803 TGCATATGGATACGAATGGAACATTA 58.835 34.615 4.56 0.00 43.03 1.90
47 48 6.003326 TGCATATGGATACGAATGGAACATT 58.997 36.000 4.56 0.00 43.03 2.71
48 49 5.559770 TGCATATGGATACGAATGGAACAT 58.440 37.500 4.56 0.00 43.03 2.71
49 50 4.967036 TGCATATGGATACGAATGGAACA 58.033 39.130 4.56 0.00 43.15 3.18
50 51 5.617751 GCTTGCATATGGATACGAATGGAAC 60.618 44.000 4.56 0.00 36.95 3.62
51 52 4.455533 GCTTGCATATGGATACGAATGGAA 59.544 41.667 4.56 0.00 38.63 3.53
52 53 4.002982 GCTTGCATATGGATACGAATGGA 58.997 43.478 4.56 0.00 42.51 3.41
53 54 4.005650 AGCTTGCATATGGATACGAATGG 58.994 43.478 4.56 0.00 42.51 3.16
54 55 6.369890 ACTTAGCTTGCATATGGATACGAATG 59.630 38.462 4.56 0.00 42.51 2.67
55 56 6.467677 ACTTAGCTTGCATATGGATACGAAT 58.532 36.000 4.56 0.00 42.51 3.34
56 57 5.853936 ACTTAGCTTGCATATGGATACGAA 58.146 37.500 4.56 0.00 42.51 3.85
57 58 5.468540 ACTTAGCTTGCATATGGATACGA 57.531 39.130 4.56 0.00 42.51 3.43
58 59 5.807520 CCTACTTAGCTTGCATATGGATACG 59.192 44.000 4.56 0.00 42.51 3.06
59 60 6.936279 TCCTACTTAGCTTGCATATGGATAC 58.064 40.000 4.56 0.00 0.00 2.24
60 61 6.155221 CCTCCTACTTAGCTTGCATATGGATA 59.845 42.308 4.56 0.00 0.00 2.59
61 62 5.046014 CCTCCTACTTAGCTTGCATATGGAT 60.046 44.000 4.56 0.00 0.00 3.41
62 63 4.284490 CCTCCTACTTAGCTTGCATATGGA 59.716 45.833 4.56 0.00 0.00 3.41
63 64 4.564406 CCCTCCTACTTAGCTTGCATATGG 60.564 50.000 4.56 0.00 0.00 2.74
64 65 4.284490 TCCCTCCTACTTAGCTTGCATATG 59.716 45.833 0.00 0.00 0.00 1.78
65 66 4.493618 TCCCTCCTACTTAGCTTGCATAT 58.506 43.478 0.00 0.00 0.00 1.78
66 67 3.898123 CTCCCTCCTACTTAGCTTGCATA 59.102 47.826 0.00 0.00 0.00 3.14
67 68 2.703007 CTCCCTCCTACTTAGCTTGCAT 59.297 50.000 0.00 0.00 0.00 3.96
68 69 2.111384 CTCCCTCCTACTTAGCTTGCA 58.889 52.381 0.00 0.00 0.00 4.08
69 70 2.112190 ACTCCCTCCTACTTAGCTTGC 58.888 52.381 0.00 0.00 0.00 4.01
70 71 3.769844 TGAACTCCCTCCTACTTAGCTTG 59.230 47.826 0.00 0.00 0.00 4.01
71 72 3.770388 GTGAACTCCCTCCTACTTAGCTT 59.230 47.826 0.00 0.00 0.00 3.74
72 73 3.367321 GTGAACTCCCTCCTACTTAGCT 58.633 50.000 0.00 0.00 0.00 3.32
73 74 2.431419 GGTGAACTCCCTCCTACTTAGC 59.569 54.545 0.00 0.00 0.00 3.09
74 75 3.955551 GAGGTGAACTCCCTCCTACTTAG 59.044 52.174 0.00 0.00 42.29 2.18
75 76 3.624205 CGAGGTGAACTCCCTCCTACTTA 60.624 52.174 0.00 0.00 44.75 2.24
76 77 2.822697 GAGGTGAACTCCCTCCTACTT 58.177 52.381 0.00 0.00 42.29 2.24
77 78 1.341187 CGAGGTGAACTCCCTCCTACT 60.341 57.143 0.00 0.00 44.75 2.57
78 79 1.104630 CGAGGTGAACTCCCTCCTAC 58.895 60.000 0.00 0.00 44.75 3.18
79 80 0.702902 ACGAGGTGAACTCCCTCCTA 59.297 55.000 0.00 0.00 44.75 2.94
80 81 0.178929 AACGAGGTGAACTCCCTCCT 60.179 55.000 0.00 0.00 44.75 3.69
81 82 0.685660 AAACGAGGTGAACTCCCTCC 59.314 55.000 0.00 0.00 44.75 4.30
82 83 2.414806 GAAAACGAGGTGAACTCCCTC 58.585 52.381 0.00 0.00 43.57 4.30
83 84 1.071857 GGAAAACGAGGTGAACTCCCT 59.928 52.381 0.00 0.00 43.57 4.20
84 85 1.202722 TGGAAAACGAGGTGAACTCCC 60.203 52.381 0.00 0.00 43.57 4.30
85 86 2.249844 TGGAAAACGAGGTGAACTCC 57.750 50.000 0.00 0.00 43.57 3.85
86 87 3.626217 ACTTTGGAAAACGAGGTGAACTC 59.374 43.478 0.00 0.00 43.02 3.01
87 88 3.617284 ACTTTGGAAAACGAGGTGAACT 58.383 40.909 0.00 0.00 0.00 3.01
88 89 4.551410 CGTACTTTGGAAAACGAGGTGAAC 60.551 45.833 0.00 0.00 37.53 3.18
89 90 3.556775 CGTACTTTGGAAAACGAGGTGAA 59.443 43.478 0.00 0.00 37.53 3.18
90 91 3.125316 CGTACTTTGGAAAACGAGGTGA 58.875 45.455 0.00 0.00 37.53 4.02
91 92 2.867975 ACGTACTTTGGAAAACGAGGTG 59.132 45.455 0.23 0.00 38.64 4.00
92 93 2.867975 CACGTACTTTGGAAAACGAGGT 59.132 45.455 0.23 0.00 38.64 3.85
93 94 2.349155 GCACGTACTTTGGAAAACGAGG 60.349 50.000 0.23 0.00 38.64 4.63
94 95 2.542595 AGCACGTACTTTGGAAAACGAG 59.457 45.455 0.23 0.00 38.64 4.18
95 96 2.540931 GAGCACGTACTTTGGAAAACGA 59.459 45.455 0.23 0.00 38.64 3.85
96 97 2.542595 AGAGCACGTACTTTGGAAAACG 59.457 45.455 0.00 0.00 40.99 3.60
97 98 4.377124 GCTAGAGCACGTACTTTGGAAAAC 60.377 45.833 0.00 0.00 41.59 2.43
98 99 3.744426 GCTAGAGCACGTACTTTGGAAAA 59.256 43.478 0.00 0.00 41.59 2.29
99 100 3.006537 AGCTAGAGCACGTACTTTGGAAA 59.993 43.478 4.01 0.00 45.16 3.13
100 101 2.561419 AGCTAGAGCACGTACTTTGGAA 59.439 45.455 4.01 0.00 45.16 3.53
101 102 2.163815 GAGCTAGAGCACGTACTTTGGA 59.836 50.000 4.01 0.00 45.16 3.53
102 103 2.164624 AGAGCTAGAGCACGTACTTTGG 59.835 50.000 4.01 0.00 45.16 3.28
103 104 3.495670 AGAGCTAGAGCACGTACTTTG 57.504 47.619 4.01 0.00 45.16 2.77
104 105 3.256136 ACAAGAGCTAGAGCACGTACTTT 59.744 43.478 4.01 0.00 45.16 2.66
105 106 2.820787 ACAAGAGCTAGAGCACGTACTT 59.179 45.455 4.01 0.00 45.16 2.24
106 107 2.438411 ACAAGAGCTAGAGCACGTACT 58.562 47.619 4.01 0.00 45.16 2.73
107 108 2.923605 ACAAGAGCTAGAGCACGTAC 57.076 50.000 4.01 0.00 45.16 3.67
108 109 5.238868 CCTATAACAAGAGCTAGAGCACGTA 59.761 44.000 4.01 0.00 45.16 3.57
109 110 4.036971 CCTATAACAAGAGCTAGAGCACGT 59.963 45.833 4.01 0.00 45.16 4.49
110 111 4.036971 ACCTATAACAAGAGCTAGAGCACG 59.963 45.833 4.01 0.00 45.16 5.34
111 112 5.508320 GGACCTATAACAAGAGCTAGAGCAC 60.508 48.000 4.01 0.00 45.16 4.40
112 113 4.585162 GGACCTATAACAAGAGCTAGAGCA 59.415 45.833 4.01 0.00 45.16 4.26
113 114 4.585162 TGGACCTATAACAAGAGCTAGAGC 59.415 45.833 0.00 0.00 42.49 4.09
114 115 5.278071 CGTGGACCTATAACAAGAGCTAGAG 60.278 48.000 0.00 0.00 0.00 2.43
115 116 4.579340 CGTGGACCTATAACAAGAGCTAGA 59.421 45.833 0.00 0.00 0.00 2.43
116 117 4.338682 ACGTGGACCTATAACAAGAGCTAG 59.661 45.833 0.00 0.00 0.00 3.42
117 118 4.097437 CACGTGGACCTATAACAAGAGCTA 59.903 45.833 7.95 0.00 0.00 3.32
118 119 3.097614 ACGTGGACCTATAACAAGAGCT 58.902 45.455 0.00 0.00 0.00 4.09
119 120 3.187700 CACGTGGACCTATAACAAGAGC 58.812 50.000 7.95 0.00 0.00 4.09
120 121 3.430374 CCCACGTGGACCTATAACAAGAG 60.430 52.174 36.07 9.74 37.39 2.85
121 122 2.498481 CCCACGTGGACCTATAACAAGA 59.502 50.000 36.07 0.00 37.39 3.02
122 123 2.419574 CCCCACGTGGACCTATAACAAG 60.420 54.545 36.07 13.77 37.39 3.16
123 124 1.555992 CCCCACGTGGACCTATAACAA 59.444 52.381 36.07 0.00 37.39 2.83
124 125 1.196911 CCCCACGTGGACCTATAACA 58.803 55.000 36.07 0.00 37.39 2.41
125 126 0.179065 GCCCCACGTGGACCTATAAC 60.179 60.000 36.07 11.23 37.39 1.89
126 127 0.325860 AGCCCCACGTGGACCTATAA 60.326 55.000 36.07 0.00 37.39 0.98
127 128 0.325860 AAGCCCCACGTGGACCTATA 60.326 55.000 36.07 0.00 37.39 1.31
128 129 1.615424 AAGCCCCACGTGGACCTAT 60.615 57.895 36.07 14.55 37.39 2.57
129 130 2.203877 AAGCCCCACGTGGACCTA 60.204 61.111 36.07 0.00 37.39 3.08
130 131 3.953775 CAAGCCCCACGTGGACCT 61.954 66.667 36.07 25.76 37.39 3.85
131 132 3.268103 ATCAAGCCCCACGTGGACC 62.268 63.158 36.07 23.98 37.39 4.46
132 133 2.040544 CATCAAGCCCCACGTGGAC 61.041 63.158 36.07 25.64 37.39 4.02
133 134 2.350895 CATCAAGCCCCACGTGGA 59.649 61.111 36.07 15.39 37.39 4.02
134 135 2.034066 ACATCAAGCCCCACGTGG 59.966 61.111 28.26 28.26 0.00 4.94
135 136 1.577328 GACACATCAAGCCCCACGTG 61.577 60.000 9.08 9.08 0.00 4.49
136 137 1.302511 GACACATCAAGCCCCACGT 60.303 57.895 0.00 0.00 0.00 4.49
137 138 2.390599 CGACACATCAAGCCCCACG 61.391 63.158 0.00 0.00 0.00 4.94
138 139 2.040544 CCGACACATCAAGCCCCAC 61.041 63.158 0.00 0.00 0.00 4.61
139 140 2.350895 CCGACACATCAAGCCCCA 59.649 61.111 0.00 0.00 0.00 4.96
140 141 2.040544 CACCGACACATCAAGCCCC 61.041 63.158 0.00 0.00 0.00 5.80
141 142 0.036765 TACACCGACACATCAAGCCC 60.037 55.000 0.00 0.00 0.00 5.19
142 143 1.067142 TCTACACCGACACATCAAGCC 60.067 52.381 0.00 0.00 0.00 4.35
143 144 2.263077 CTCTACACCGACACATCAAGC 58.737 52.381 0.00 0.00 0.00 4.01
144 145 3.502920 GACTCTACACCGACACATCAAG 58.497 50.000 0.00 0.00 0.00 3.02
145 146 2.230508 GGACTCTACACCGACACATCAA 59.769 50.000 0.00 0.00 0.00 2.57
146 147 1.816835 GGACTCTACACCGACACATCA 59.183 52.381 0.00 0.00 0.00 3.07
147 148 1.816835 TGGACTCTACACCGACACATC 59.183 52.381 0.00 0.00 0.00 3.06
148 149 1.919240 TGGACTCTACACCGACACAT 58.081 50.000 0.00 0.00 0.00 3.21
149 150 1.544246 CATGGACTCTACACCGACACA 59.456 52.381 0.00 0.00 0.00 3.72
150 151 1.135083 CCATGGACTCTACACCGACAC 60.135 57.143 5.56 0.00 0.00 3.67
151 152 1.182667 CCATGGACTCTACACCGACA 58.817 55.000 5.56 0.00 0.00 4.35
152 153 0.460311 CCCATGGACTCTACACCGAC 59.540 60.000 15.22 0.00 0.00 4.79
153 154 0.686441 CCCCATGGACTCTACACCGA 60.686 60.000 15.22 0.00 0.00 4.69
154 155 0.686441 TCCCCATGGACTCTACACCG 60.686 60.000 15.22 0.00 35.03 4.94
155 156 1.417890 CATCCCCATGGACTCTACACC 59.582 57.143 15.22 0.00 45.58 4.16
156 157 2.398588 TCATCCCCATGGACTCTACAC 58.601 52.381 15.22 0.00 45.58 2.90
157 158 2.866923 TCATCCCCATGGACTCTACA 57.133 50.000 15.22 0.00 45.58 2.74
158 159 2.304180 CCATCATCCCCATGGACTCTAC 59.696 54.545 15.22 0.00 45.58 2.59
159 160 2.182088 TCCATCATCCCCATGGACTCTA 59.818 50.000 15.22 0.00 44.17 2.43
160 161 1.061111 TCCATCATCCCCATGGACTCT 60.061 52.381 15.22 0.00 44.17 3.24
161 162 1.438469 TCCATCATCCCCATGGACTC 58.562 55.000 15.22 0.00 44.17 3.36
162 163 3.681004 TCCATCATCCCCATGGACT 57.319 52.632 15.22 0.00 44.17 3.85
164 165 1.151760 CCTTCCATCATCCCCATGGA 58.848 55.000 15.22 0.00 46.81 3.41
165 166 1.151760 TCCTTCCATCATCCCCATGG 58.848 55.000 4.14 4.14 42.16 3.66
166 167 2.803956 CATCCTTCCATCATCCCCATG 58.196 52.381 0.00 0.00 0.00 3.66
167 168 1.076677 GCATCCTTCCATCATCCCCAT 59.923 52.381 0.00 0.00 0.00 4.00
168 169 0.479815 GCATCCTTCCATCATCCCCA 59.520 55.000 0.00 0.00 0.00 4.96
169 170 0.776176 AGCATCCTTCCATCATCCCC 59.224 55.000 0.00 0.00 0.00 4.81
170 171 2.197283 GAGCATCCTTCCATCATCCC 57.803 55.000 0.00 0.00 0.00 3.85
187 188 4.864334 GGGGGCTGTGATGCGGAG 62.864 72.222 0.00 0.00 0.00 4.63
190 191 3.030168 TAGTGGGGGCTGTGATGCG 62.030 63.158 0.00 0.00 0.00 4.73
191 192 1.452108 GTAGTGGGGGCTGTGATGC 60.452 63.158 0.00 0.00 0.00 3.91
192 193 1.224592 GGTAGTGGGGGCTGTGATG 59.775 63.158 0.00 0.00 0.00 3.07
193 194 2.367202 CGGTAGTGGGGGCTGTGAT 61.367 63.158 0.00 0.00 0.00 3.06
194 195 3.000819 CGGTAGTGGGGGCTGTGA 61.001 66.667 0.00 0.00 0.00 3.58
195 196 4.778143 GCGGTAGTGGGGGCTGTG 62.778 72.222 0.00 0.00 0.00 3.66
207 208 1.672682 TGGCAGCGATTTTGCGGTA 60.673 52.632 0.00 0.00 42.42 4.02
281 286 3.749064 GCTCGCGGGACTGAGACA 61.749 66.667 12.03 0.00 34.04 3.41
301 306 0.246635 TTCTCGGTTGGAGCTAGCAC 59.753 55.000 18.83 11.05 42.82 4.40
319 324 0.109873 GACAGGTCGTCGTCGTCATT 60.110 55.000 1.33 0.00 38.33 2.57
400 405 5.046735 AGAGTGAGTAGTCAGACATTGCAAT 60.047 40.000 5.99 5.99 31.53 3.56
415 420 2.419574 GCCCGGCATTAAAGAGTGAGTA 60.420 50.000 3.91 0.00 0.00 2.59
470 475 1.578583 ACAACGAGGGTCTTGTTTCG 58.421 50.000 0.00 0.00 36.08 3.46
559 567 3.620488 TCTGCAACTGGAGTCTTGTTTT 58.380 40.909 0.00 0.00 34.87 2.43
615 628 7.806690 TGCAACATATGACTAGTTTCAGAAAC 58.193 34.615 17.11 17.11 41.69 2.78
649 662 5.989168 TCTTGCAATAAGAGTCTTGTTTCGA 59.011 36.000 15.90 8.48 0.00 3.71
661 674 5.278957 GGCCAGTCTTTTTCTTGCAATAAGA 60.279 40.000 0.00 4.60 0.00 2.10
685 700 3.118454 ACAAGTCAATCCCGCGCG 61.118 61.111 25.67 25.67 0.00 6.86
694 709 1.885388 CACGCCGACCACAAGTCAA 60.885 57.895 0.00 0.00 46.69 3.18
705 720 0.032815 TGATCAAGTGAACACGCCGA 59.967 50.000 0.00 0.00 36.20 5.54
707 722 0.798776 CCTGATCAAGTGAACACGCC 59.201 55.000 0.00 0.00 36.20 5.68
745 760 4.781959 CCGAACGTCCGCCGCTTA 62.782 66.667 0.00 0.00 41.42 3.09
758 773 1.743623 CGGCTTATGCACACCCGAA 60.744 57.895 10.37 0.00 41.34 4.30
762 777 2.438434 AGCCGGCTTATGCACACC 60.438 61.111 27.08 0.00 41.91 4.16
771 786 1.377333 GCTTACCTTCAGCCGGCTT 60.377 57.895 30.60 15.53 0.00 4.35
1292 1314 0.609406 GGCTTCCTTGTGGAGTTCCC 60.609 60.000 0.00 0.00 44.24 3.97
1329 1351 3.485346 AAAGCGCGAGGGTTTGGGA 62.485 57.895 12.10 0.00 44.23 4.37
1330 1352 2.978018 GAAAGCGCGAGGGTTTGGG 61.978 63.158 12.10 0.00 45.79 4.12
1331 1353 1.586154 ATGAAAGCGCGAGGGTTTGG 61.586 55.000 12.10 0.00 45.79 3.28
1332 1354 0.179189 GATGAAAGCGCGAGGGTTTG 60.179 55.000 12.10 0.00 45.79 2.93
1334 1356 0.741221 GAGATGAAAGCGCGAGGGTT 60.741 55.000 12.10 0.00 38.16 4.11
1335 1357 1.153549 GAGATGAAAGCGCGAGGGT 60.154 57.895 12.10 0.00 0.00 4.34
1336 1358 1.142748 AGAGATGAAAGCGCGAGGG 59.857 57.895 12.10 0.00 0.00 4.30
1337 1359 0.179127 TCAGAGATGAAAGCGCGAGG 60.179 55.000 12.10 0.00 0.00 4.63
1338 1360 0.919981 GTCAGAGATGAAAGCGCGAG 59.080 55.000 12.10 0.00 0.00 5.03
1339 1361 0.243636 TGTCAGAGATGAAAGCGCGA 59.756 50.000 12.10 0.00 0.00 5.87
1340 1362 0.644331 CTGTCAGAGATGAAAGCGCG 59.356 55.000 0.00 0.00 0.00 6.86
1341 1363 1.658095 GACTGTCAGAGATGAAAGCGC 59.342 52.381 6.91 0.00 0.00 5.92
1342 1364 2.266554 GGACTGTCAGAGATGAAAGCG 58.733 52.381 6.91 0.00 0.00 4.68
1343 1365 2.626840 GGGACTGTCAGAGATGAAAGC 58.373 52.381 6.91 0.00 0.00 3.51
1344 1366 2.093235 GGGGGACTGTCAGAGATGAAAG 60.093 54.545 6.91 0.00 0.00 2.62
1345 1367 1.909302 GGGGGACTGTCAGAGATGAAA 59.091 52.381 6.91 0.00 0.00 2.69
1346 1368 1.573108 GGGGGACTGTCAGAGATGAA 58.427 55.000 6.91 0.00 0.00 2.57
1347 1369 3.306902 GGGGGACTGTCAGAGATGA 57.693 57.895 6.91 0.00 0.00 2.92
1367 1389 1.447317 CGAATGGAGCGATTTGGGGG 61.447 60.000 0.00 0.00 0.00 5.40
1368 1390 1.447317 CCGAATGGAGCGATTTGGGG 61.447 60.000 4.14 0.00 37.49 4.96
1401 1729 1.660104 ACGTACACGAACACACCAAAC 59.340 47.619 9.04 0.00 43.02 2.93
1402 1730 2.007360 ACGTACACGAACACACCAAA 57.993 45.000 9.04 0.00 43.02 3.28
1413 1741 4.593597 ATCTTGGCAAAATACGTACACG 57.406 40.909 0.00 0.00 46.33 4.49
1493 1821 0.248336 CGACAGCATCGCATTGCAAT 60.248 50.000 5.99 5.99 45.52 3.56
1940 2268 0.671163 CAATGGCACCGCAGCAATTT 60.671 50.000 0.00 0.00 36.01 1.82
2189 2517 5.074239 CCTTATTTCTGAATCCTCCCCTGAT 59.926 44.000 0.00 0.00 0.00 2.90
2267 2595 6.040729 GGGTAGATAGACTTTCTCCTTGGTAC 59.959 46.154 0.00 0.00 0.00 3.34
3150 3486 8.749026 ATATCTTCAGAAGTTCAGCAAATCAT 57.251 30.769 10.09 0.00 0.00 2.45
3201 3537 5.598417 AGTGAAATAATAGCAAATCACCCCC 59.402 40.000 0.00 0.00 38.29 5.40
3302 4073 6.688578 TCTATAGAGTCAATATTTCACGGGC 58.311 40.000 0.00 0.00 0.00 6.13
3533 4304 6.794493 AGATATAAATGGGAGTCCTCATTGGA 59.206 38.462 20.21 14.26 43.86 3.53
3534 4305 7.025520 AGATATAAATGGGAGTCCTCATTGG 57.974 40.000 20.21 0.00 34.28 3.16
3589 4360 2.224606 ACCTGTTCACGTCTCGAAGTA 58.775 47.619 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.