Multiple sequence alignment - TraesCS6D01G049500

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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 TraesCS6D01G049500 chr6D 100.000 4079 0 0 1 4079 24021473 24025551 0.000000e+00 7533.0
1 TraesCS6D01G049500 chr6D 92.040 402 31 1 3562 3963 24024954 24025354 7.650000e-157 564.0
2 TraesCS6D01G049500 chr6D 92.040 402 31 1 3482 3882 24025034 24025435 7.650000e-157 564.0
3 TraesCS6D01G049500 chr6A 96.627 2935 76 13 239 3164 22546256 22549176 0.000000e+00 4850.0
4 TraesCS6D01G049500 chr6A 96.809 94 2 1 3960 4053 588556428 588556336 5.460000e-34 156.0
5 TraesCS6D01G049500 chr6B 96.651 2538 50 11 638 3150 38925234 38927761 0.000000e+00 4183.0
6 TraesCS6D01G049500 chr1D 93.737 495 30 1 3562 4056 357456640 357457133 0.000000e+00 741.0
7 TraesCS6D01G049500 chr1D 97.349 415 11 0 3468 3882 357456626 357457040 0.000000e+00 706.0
8 TraesCS6D01G049500 chr1D 96.460 339 9 3 3468 3804 365432973 365432636 1.280000e-154 556.0
9 TraesCS6D01G049500 chr1D 91.316 380 29 4 3643 4020 365432959 365432582 2.170000e-142 516.0
10 TraesCS6D01G049500 chr1D 96.000 300 5 5 3164 3463 365433425 365433133 7.930000e-132 481.0
11 TraesCS6D01G049500 chr1D 91.975 324 25 1 3482 3804 357456720 357457043 1.730000e-123 453.0
12 TraesCS6D01G049500 chr1D 90.491 326 27 4 3562 3885 365432959 365432636 1.050000e-115 427.0
13 TraesCS6D01G049500 chr1D 89.198 324 34 1 3643 3966 357456640 357456962 1.770000e-108 403.0
14 TraesCS6D01G049500 chr1D 94.340 265 8 6 3200 3463 357456208 357456466 2.280000e-107 399.0
15 TraesCS6D01G049500 chr1D 91.057 246 18 4 3482 3724 365432879 365432635 3.040000e-86 329.0
16 TraesCS6D01G049500 chr1D 89.344 244 25 1 3482 3724 357456801 357457044 5.120000e-79 305.0
17 TraesCS6D01G049500 chr1D 87.967 241 26 3 3725 3964 365432958 365432720 8.630000e-72 281.0
18 TraesCS6D01G049500 chr2A 73.082 1642 384 46 1409 3030 680262003 680263606 7.760000e-147 531.0
19 TraesCS6D01G049500 chr2A 92.982 57 4 0 1528 1584 758881632 758881688 2.610000e-12 84.2
20 TraesCS6D01G049500 chr2D 73.082 1642 375 52 1409 3030 537929120 537930714 4.670000e-144 521.0
21 TraesCS6D01G049500 chr2D 77.616 344 74 3 239 580 420747264 420747606 5.340000e-49 206.0
22 TraesCS6D01G049500 chr2D 74.129 402 94 10 239 635 94726667 94726271 1.520000e-34 158.0
23 TraesCS6D01G049500 chr2D 77.323 269 47 12 319 580 505625558 505625819 3.290000e-31 147.0
24 TraesCS6D01G049500 chr2D 95.714 70 1 1 3165 3234 569955362 569955295 1.200000e-20 111.0
25 TraesCS6D01G049500 chr2D 94.737 57 3 0 1528 1584 629074954 629075010 5.620000e-14 89.8
26 TraesCS6D01G049500 chr4A 90.152 396 39 0 239 634 496113106 496112711 2.170000e-142 516.0
27 TraesCS6D01G049500 chr4A 91.064 235 21 0 3 237 690119830 690119596 6.580000e-83 318.0
28 TraesCS6D01G049500 chr2B 86.650 397 46 4 239 634 245121606 245121216 2.250000e-117 433.0
29 TraesCS6D01G049500 chr2B 75.480 469 103 12 1409 1871 640599476 640599938 6.860000e-53 219.0
30 TraesCS6D01G049500 chr2B 75.949 395 91 4 242 634 560880933 560880541 2.490000e-47 200.0
31 TraesCS6D01G049500 chr5D 82.576 396 65 2 239 634 398887295 398886904 3.020000e-91 346.0
32 TraesCS6D01G049500 chr3D 92.704 233 16 1 1 233 516859548 516859779 6.530000e-88 335.0
33 TraesCS6D01G049500 chr3D 91.810 232 19 0 1 232 590230724 590230955 1.410000e-84 324.0
34 TraesCS6D01G049500 chr7B 91.342 231 20 0 2 232 627051451 627051681 2.370000e-82 316.0
35 TraesCS6D01G049500 chr3B 91.342 231 20 0 3 233 656736541 656736771 2.370000e-82 316.0
36 TraesCS6D01G049500 chr3B 91.630 227 19 0 2 228 396732284 396732510 8.510000e-82 315.0
37 TraesCS6D01G049500 chr5B 90.987 233 21 0 2 234 331650289 331650521 8.510000e-82 315.0
38 TraesCS6D01G049500 chr4B 90.948 232 21 0 1 232 490649038 490648807 3.060000e-81 313.0
39 TraesCS6D01G049500 chr7A 90.598 234 22 0 1 234 493654715 493654482 1.100000e-80 311.0
40 TraesCS6D01G049500 chr7A 92.632 95 4 2 3367 3460 27519825 27519917 2.560000e-27 134.0
41 TraesCS6D01G049500 chr7D 93.103 116 2 3 3165 3275 576898659 576898773 9.070000e-37 165.0
42 TraesCS6D01G049500 chr3A 74.185 368 91 4 270 635 64342210 64342575 2.540000e-32 150.0
43 TraesCS6D01G049500 chr3A 95.506 89 4 0 3965 4053 637916076 637916164 4.250000e-30 143.0
44 TraesCS6D01G049500 chr4D 91.753 97 6 2 3960 4056 53230530 53230436 2.560000e-27 134.0
45 TraesCS6D01G049500 chrUn 83.784 111 11 6 3200 3309 101232616 101232512 9.330000e-17 99.0


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 TraesCS6D01G049500 chr6D 24021473 24025551 4078 False 2887.000000 7533 94.693333 1 4079 3 chr6D.!!$F1 4078
1 TraesCS6D01G049500 chr6A 22546256 22549176 2920 False 4850.000000 4850 96.627000 239 3164 1 chr6A.!!$F1 2925
2 TraesCS6D01G049500 chr6B 38925234 38927761 2527 False 4183.000000 4183 96.651000 638 3150 1 chr6B.!!$F1 2512
3 TraesCS6D01G049500 chr1D 357456208 357457133 925 False 501.166667 741 92.657167 3200 4056 6 chr1D.!!$F1 856
4 TraesCS6D01G049500 chr1D 365432582 365433425 843 True 431.666667 556 92.215167 3164 4020 6 chr1D.!!$R1 856
5 TraesCS6D01G049500 chr2A 680262003 680263606 1603 False 531.000000 531 73.082000 1409 3030 1 chr2A.!!$F1 1621
6 TraesCS6D01G049500 chr2D 537929120 537930714 1594 False 521.000000 521 73.082000 1409 3030 1 chr2D.!!$F3 1621

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
87 88 0.033504 TGACTCACGAGAAACTGCCC 59.966 55.0 0.0 0.0 0.00 5.36 F
161 162 0.038343 CAGGCCCAACAATGAAACCG 60.038 55.0 0.0 0.0 0.00 4.44 F
271 272 0.105964 TGTAGGCAACAAGTCGCTGT 59.894 50.0 0.0 0.0 34.29 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1953 1979 1.625818 GAGAGGAAGTTGAAGAGGCCA 59.374 52.381 5.01 0.0 0.00 5.36 R
2169 2195 0.956633 GGATGTAGACGCCGATGGTA 59.043 55.000 0.00 0.0 0.00 3.25 R
3159 3188 9.855021 CGGTTGATTTTAATACTTTTCCAAGAT 57.145 29.630 0.00 0.0 33.72 2.40 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
18 19 2.900528 CGTAATCACCTCGCATCCC 58.099 57.895 0.00 0.00 0.00 3.85
19 20 0.389391 CGTAATCACCTCGCATCCCT 59.611 55.000 0.00 0.00 0.00 4.20
20 21 1.603172 CGTAATCACCTCGCATCCCTC 60.603 57.143 0.00 0.00 0.00 4.30
21 22 1.048601 TAATCACCTCGCATCCCTCC 58.951 55.000 0.00 0.00 0.00 4.30
22 23 1.700042 AATCACCTCGCATCCCTCCC 61.700 60.000 0.00 0.00 0.00 4.30
23 24 4.227134 CACCTCGCATCCCTCCCG 62.227 72.222 0.00 0.00 0.00 5.14
24 25 4.779733 ACCTCGCATCCCTCCCGT 62.780 66.667 0.00 0.00 0.00 5.28
25 26 3.917760 CCTCGCATCCCTCCCGTC 61.918 72.222 0.00 0.00 0.00 4.79
26 27 2.835431 CTCGCATCCCTCCCGTCT 60.835 66.667 0.00 0.00 0.00 4.18
27 28 2.833582 TCGCATCCCTCCCGTCTC 60.834 66.667 0.00 0.00 0.00 3.36
28 29 3.917760 CGCATCCCTCCCGTCTCC 61.918 72.222 0.00 0.00 0.00 3.71
29 30 2.764128 GCATCCCTCCCGTCTCCA 60.764 66.667 0.00 0.00 0.00 3.86
30 31 3.095347 GCATCCCTCCCGTCTCCAC 62.095 68.421 0.00 0.00 0.00 4.02
31 32 1.381872 CATCCCTCCCGTCTCCACT 60.382 63.158 0.00 0.00 0.00 4.00
32 33 1.075896 ATCCCTCCCGTCTCCACTC 60.076 63.158 0.00 0.00 0.00 3.51
33 34 1.875422 ATCCCTCCCGTCTCCACTCA 61.875 60.000 0.00 0.00 0.00 3.41
34 35 1.381872 CCCTCCCGTCTCCACTCAT 60.382 63.158 0.00 0.00 0.00 2.90
35 36 1.680522 CCCTCCCGTCTCCACTCATG 61.681 65.000 0.00 0.00 0.00 3.07
36 37 1.142748 CTCCCGTCTCCACTCATGC 59.857 63.158 0.00 0.00 0.00 4.06
37 38 1.607801 CTCCCGTCTCCACTCATGCA 61.608 60.000 0.00 0.00 0.00 3.96
38 39 1.191489 TCCCGTCTCCACTCATGCAA 61.191 55.000 0.00 0.00 0.00 4.08
39 40 0.742281 CCCGTCTCCACTCATGCAAG 60.742 60.000 0.00 0.00 0.00 4.01
40 41 0.742281 CCGTCTCCACTCATGCAAGG 60.742 60.000 0.00 0.00 0.00 3.61
41 42 0.742281 CGTCTCCACTCATGCAAGGG 60.742 60.000 0.00 0.00 0.00 3.95
42 43 1.028868 GTCTCCACTCATGCAAGGGC 61.029 60.000 0.00 0.00 41.68 5.19
43 44 1.751927 CTCCACTCATGCAAGGGCC 60.752 63.158 0.00 0.00 40.13 5.80
44 45 2.757099 CCACTCATGCAAGGGCCC 60.757 66.667 16.46 16.46 40.13 5.80
45 46 3.136123 CACTCATGCAAGGGCCCG 61.136 66.667 18.44 3.70 40.13 6.13
47 48 4.809496 CTCATGCAAGGGCCCGCT 62.809 66.667 18.44 4.49 40.13 5.52
73 74 4.200283 CTCGCCTCGGCCTGACTC 62.200 72.222 0.00 0.00 37.98 3.36
75 76 4.803426 CGCCTCGGCCTGACTCAC 62.803 72.222 0.00 0.00 37.98 3.51
76 77 4.803426 GCCTCGGCCTGACTCACG 62.803 72.222 0.00 0.00 34.56 4.35
77 78 3.062466 CCTCGGCCTGACTCACGA 61.062 66.667 0.00 0.00 0.00 4.35
78 79 2.487428 CTCGGCCTGACTCACGAG 59.513 66.667 0.00 0.00 45.34 4.18
79 80 2.033602 TCGGCCTGACTCACGAGA 59.966 61.111 0.00 0.00 0.00 4.04
80 81 1.602605 TCGGCCTGACTCACGAGAA 60.603 57.895 0.00 0.00 0.00 2.87
81 82 1.176619 TCGGCCTGACTCACGAGAAA 61.177 55.000 0.00 0.00 0.00 2.52
82 83 1.009389 CGGCCTGACTCACGAGAAAC 61.009 60.000 0.00 0.00 0.00 2.78
83 84 0.318762 GGCCTGACTCACGAGAAACT 59.681 55.000 0.00 0.00 0.00 2.66
84 85 1.423395 GCCTGACTCACGAGAAACTG 58.577 55.000 0.00 0.00 0.00 3.16
85 86 1.423395 CCTGACTCACGAGAAACTGC 58.577 55.000 0.00 0.00 0.00 4.40
86 87 1.423395 CTGACTCACGAGAAACTGCC 58.577 55.000 0.00 0.00 0.00 4.85
87 88 0.033504 TGACTCACGAGAAACTGCCC 59.966 55.000 0.00 0.00 0.00 5.36
88 89 0.033504 GACTCACGAGAAACTGCCCA 59.966 55.000 0.00 0.00 0.00 5.36
89 90 0.687354 ACTCACGAGAAACTGCCCAT 59.313 50.000 0.00 0.00 0.00 4.00
90 91 1.072331 ACTCACGAGAAACTGCCCATT 59.928 47.619 0.00 0.00 0.00 3.16
91 92 1.734465 CTCACGAGAAACTGCCCATTC 59.266 52.381 0.00 0.00 0.00 2.67
92 93 1.071542 TCACGAGAAACTGCCCATTCA 59.928 47.619 0.00 0.00 0.00 2.57
93 94 1.879380 CACGAGAAACTGCCCATTCAA 59.121 47.619 0.00 0.00 0.00 2.69
94 95 2.095567 CACGAGAAACTGCCCATTCAAG 60.096 50.000 0.00 0.00 0.00 3.02
95 96 1.135575 CGAGAAACTGCCCATTCAAGC 60.136 52.381 0.00 0.00 0.00 4.01
96 97 0.883833 AGAAACTGCCCATTCAAGCG 59.116 50.000 0.00 0.00 0.00 4.68
97 98 0.598065 GAAACTGCCCATTCAAGCGT 59.402 50.000 0.00 0.00 0.00 5.07
98 99 1.000274 GAAACTGCCCATTCAAGCGTT 60.000 47.619 0.00 0.00 0.00 4.84
99 100 1.039856 AACTGCCCATTCAAGCGTTT 58.960 45.000 0.00 0.00 0.00 3.60
100 101 0.598065 ACTGCCCATTCAAGCGTTTC 59.402 50.000 0.00 0.00 0.00 2.78
101 102 0.109132 CTGCCCATTCAAGCGTTTCC 60.109 55.000 0.00 0.00 0.00 3.13
102 103 0.825425 TGCCCATTCAAGCGTTTCCA 60.825 50.000 0.00 0.00 0.00 3.53
103 104 0.109132 GCCCATTCAAGCGTTTCCAG 60.109 55.000 0.00 0.00 0.00 3.86
104 105 0.109132 CCCATTCAAGCGTTTCCAGC 60.109 55.000 0.00 0.00 0.00 4.85
105 106 0.454957 CCATTCAAGCGTTTCCAGCG 60.455 55.000 0.00 0.00 40.04 5.18
106 107 0.516877 CATTCAAGCGTTTCCAGCGA 59.483 50.000 0.00 0.00 40.04 4.93
107 108 0.798776 ATTCAAGCGTTTCCAGCGAG 59.201 50.000 0.00 0.00 40.04 5.03
108 109 1.841663 TTCAAGCGTTTCCAGCGAGC 61.842 55.000 0.00 0.00 40.04 5.03
109 110 3.050275 AAGCGTTTCCAGCGAGCC 61.050 61.111 0.00 0.00 40.04 4.70
110 111 3.825160 AAGCGTTTCCAGCGAGCCA 62.825 57.895 0.00 0.00 40.04 4.75
111 112 3.353836 GCGTTTCCAGCGAGCCAA 61.354 61.111 0.00 0.00 0.00 4.52
112 113 2.556287 CGTTTCCAGCGAGCCAAC 59.444 61.111 0.00 0.00 0.00 3.77
113 114 2.954611 GTTTCCAGCGAGCCAACC 59.045 61.111 0.00 0.00 0.00 3.77
114 115 1.600916 GTTTCCAGCGAGCCAACCT 60.601 57.895 0.00 0.00 0.00 3.50
115 116 0.321298 GTTTCCAGCGAGCCAACCTA 60.321 55.000 0.00 0.00 0.00 3.08
116 117 0.618458 TTTCCAGCGAGCCAACCTAT 59.382 50.000 0.00 0.00 0.00 2.57
117 118 0.107703 TTCCAGCGAGCCAACCTATG 60.108 55.000 0.00 0.00 0.00 2.23
126 127 3.288099 CCAACCTATGGGCTGCTTT 57.712 52.632 0.00 0.00 46.27 3.51
127 128 2.435372 CCAACCTATGGGCTGCTTTA 57.565 50.000 0.00 0.00 46.27 1.85
128 129 2.733956 CCAACCTATGGGCTGCTTTAA 58.266 47.619 0.00 0.00 46.27 1.52
129 130 2.689983 CCAACCTATGGGCTGCTTTAAG 59.310 50.000 0.00 0.00 46.27 1.85
130 131 3.620488 CAACCTATGGGCTGCTTTAAGA 58.380 45.455 0.00 0.00 35.63 2.10
131 132 4.016444 CAACCTATGGGCTGCTTTAAGAA 58.984 43.478 0.00 0.00 35.63 2.52
132 133 3.891049 ACCTATGGGCTGCTTTAAGAAG 58.109 45.455 0.00 0.00 35.63 2.85
133 134 3.937311 ACCTATGGGCTGCTTTAAGAAGC 60.937 47.826 16.30 16.30 46.48 3.86
142 143 1.802839 CTTTAAGAAGCGTGCGATGC 58.197 50.000 0.00 0.00 0.00 3.91
143 144 1.128507 CTTTAAGAAGCGTGCGATGCA 59.871 47.619 0.00 0.00 35.60 3.96
144 145 0.721154 TTAAGAAGCGTGCGATGCAG 59.279 50.000 0.00 0.00 40.08 4.41
145 146 1.083806 TAAGAAGCGTGCGATGCAGG 61.084 55.000 7.09 7.09 45.60 4.85
151 152 4.120331 GTGCGATGCAGGCCCAAC 62.120 66.667 0.00 0.00 40.08 3.77
152 153 4.657408 TGCGATGCAGGCCCAACA 62.657 61.111 0.00 0.00 33.32 3.33
153 154 3.372730 GCGATGCAGGCCCAACAA 61.373 61.111 0.00 0.00 0.00 2.83
154 155 2.713967 GCGATGCAGGCCCAACAAT 61.714 57.895 0.00 0.00 0.00 2.71
155 156 1.140161 CGATGCAGGCCCAACAATG 59.860 57.895 0.00 0.00 0.00 2.82
156 157 1.314534 CGATGCAGGCCCAACAATGA 61.315 55.000 0.00 0.00 0.00 2.57
157 158 0.896923 GATGCAGGCCCAACAATGAA 59.103 50.000 0.00 0.00 0.00 2.57
158 159 1.275856 GATGCAGGCCCAACAATGAAA 59.724 47.619 0.00 0.00 0.00 2.69
159 160 0.392336 TGCAGGCCCAACAATGAAAC 59.608 50.000 0.00 0.00 0.00 2.78
160 161 0.320683 GCAGGCCCAACAATGAAACC 60.321 55.000 0.00 0.00 0.00 3.27
161 162 0.038343 CAGGCCCAACAATGAAACCG 60.038 55.000 0.00 0.00 0.00 4.44
162 163 1.184970 AGGCCCAACAATGAAACCGG 61.185 55.000 0.00 0.00 0.00 5.28
163 164 1.291906 GCCCAACAATGAAACCGGG 59.708 57.895 6.32 0.00 36.71 5.73
164 165 1.291906 CCCAACAATGAAACCGGGC 59.708 57.895 6.32 0.00 0.00 6.13
165 166 1.467678 CCCAACAATGAAACCGGGCA 61.468 55.000 6.32 0.45 0.00 5.36
166 167 0.390860 CCAACAATGAAACCGGGCAA 59.609 50.000 6.32 0.00 0.00 4.52
167 168 1.496934 CAACAATGAAACCGGGCAAC 58.503 50.000 6.32 0.00 0.00 4.17
179 180 3.051210 GGCAACCAAACAGGCCTC 58.949 61.111 0.00 0.00 43.09 4.70
180 181 1.531602 GGCAACCAAACAGGCCTCT 60.532 57.895 0.00 0.00 43.09 3.69
181 182 1.115326 GGCAACCAAACAGGCCTCTT 61.115 55.000 0.00 0.00 43.09 2.85
182 183 0.315251 GCAACCAAACAGGCCTCTTC 59.685 55.000 0.00 0.00 43.14 2.87
183 184 0.961753 CAACCAAACAGGCCTCTTCC 59.038 55.000 0.00 0.00 43.14 3.46
184 185 0.853530 AACCAAACAGGCCTCTTCCT 59.146 50.000 0.00 0.00 43.14 3.36
185 186 0.853530 ACCAAACAGGCCTCTTCCTT 59.146 50.000 0.00 0.00 43.14 3.36
186 187 1.202940 ACCAAACAGGCCTCTTCCTTC 60.203 52.381 0.00 0.00 43.14 3.46
187 188 1.539157 CAAACAGGCCTCTTCCTTCC 58.461 55.000 0.00 0.00 33.25 3.46
188 189 0.405973 AAACAGGCCTCTTCCTTCCC 59.594 55.000 0.00 0.00 33.25 3.97
189 190 1.842381 AACAGGCCTCTTCCTTCCCG 61.842 60.000 0.00 0.00 33.25 5.14
190 191 2.122954 AGGCCTCTTCCTTCCCGT 59.877 61.111 0.00 0.00 30.82 5.28
191 192 2.269241 GGCCTCTTCCTTCCCGTG 59.731 66.667 0.00 0.00 0.00 4.94
192 193 2.436824 GCCTCTTCCTTCCCGTGC 60.437 66.667 0.00 0.00 0.00 5.34
193 194 2.125512 CCTCTTCCTTCCCGTGCG 60.126 66.667 0.00 0.00 0.00 5.34
194 195 2.125512 CTCTTCCTTCCCGTGCGG 60.126 66.667 3.25 3.25 0.00 5.69
213 214 2.825836 CCTGGTTGGGCTCGATGC 60.826 66.667 0.00 0.00 41.94 3.91
214 215 3.197790 CTGGTTGGGCTCGATGCG 61.198 66.667 0.00 0.00 44.05 4.73
215 216 4.776322 TGGTTGGGCTCGATGCGG 62.776 66.667 0.00 0.00 44.05 5.69
232 233 3.223589 GGCAACCAAACACGCCCT 61.224 61.111 0.00 0.00 38.67 5.19
233 234 2.791868 GGCAACCAAACACGCCCTT 61.792 57.895 0.00 0.00 38.67 3.95
234 235 1.299850 GCAACCAAACACGCCCTTC 60.300 57.895 0.00 0.00 0.00 3.46
235 236 1.008995 CAACCAAACACGCCCTTCG 60.009 57.895 0.00 0.00 45.38 3.79
271 272 0.105964 TGTAGGCAACAAGTCGCTGT 59.894 50.000 0.00 0.00 34.29 4.40
290 291 5.163784 CGCTGTCAATCATCAAACTCTTCAT 60.164 40.000 0.00 0.00 0.00 2.57
315 316 4.101448 AGAGCGCCGGAAAGCCAT 62.101 61.111 5.05 0.00 0.00 4.40
395 396 4.213482 AGAAAAGCGTAGTAAAAGCCACAG 59.787 41.667 0.00 0.00 32.28 3.66
418 419 2.249139 AGGGTAGTCTCTCCACACAAC 58.751 52.381 0.00 0.00 0.00 3.32
419 420 1.275573 GGGTAGTCTCTCCACACAACC 59.724 57.143 0.00 0.00 0.00 3.77
422 423 1.794714 AGTCTCTCCACACAACCAGT 58.205 50.000 0.00 0.00 0.00 4.00
468 469 4.244862 CCATTGCCAACCACAAATCTAAC 58.755 43.478 0.00 0.00 0.00 2.34
469 470 4.262377 CCATTGCCAACCACAAATCTAACA 60.262 41.667 0.00 0.00 0.00 2.41
496 497 6.554334 TCTTTAAAATGAGGTCGGACTTTG 57.446 37.500 8.23 0.00 0.00 2.77
510 511 4.065088 CGGACTTTGACAAGATCTTTCCA 58.935 43.478 16.56 10.44 33.72 3.53
837 842 2.755103 GCTTCCTAACCACCAAATGAGG 59.245 50.000 0.00 0.00 0.00 3.86
853 858 1.995542 TGAGGCTCTTCCCCATTTTCT 59.004 47.619 16.72 0.00 34.51 2.52
944 963 0.950555 ACACACATGCACGTGCCTAG 60.951 55.000 35.72 26.24 40.73 3.02
969 990 4.168760 GCCAAGAAATTCCTCAATCAACG 58.831 43.478 0.00 0.00 0.00 4.10
971 992 5.393962 CCAAGAAATTCCTCAATCAACGAC 58.606 41.667 0.00 0.00 0.00 4.34
972 993 5.182001 CCAAGAAATTCCTCAATCAACGACT 59.818 40.000 0.00 0.00 0.00 4.18
997 1019 5.227152 TGAATTTCTTGTGAAGATCGACGA 58.773 37.500 0.00 0.00 37.38 4.20
998 1020 5.346011 TGAATTTCTTGTGAAGATCGACGAG 59.654 40.000 3.01 4.30 37.38 4.18
1249 1275 2.435693 ATCCGGCTGCTGGAGTACC 61.436 63.158 31.73 0.00 42.74 3.34
1600 1626 2.036098 CCACCCATGCCAAGCTGA 59.964 61.111 0.00 0.00 0.00 4.26
1953 1979 0.540597 TCTCCATGATCCTCGCCGAT 60.541 55.000 0.00 0.00 0.00 4.18
2167 2193 1.064758 GGGACAGCATACCCAACATGA 60.065 52.381 0.00 0.00 44.96 3.07
2169 2195 3.290710 GGACAGCATACCCAACATGATT 58.709 45.455 0.00 0.00 0.00 2.57
2595 2621 0.395312 ACAAGGTGTACAAGACGGGG 59.605 55.000 0.00 0.00 0.00 5.73
2676 2705 3.842923 CTGAGCGTCGGCCAGGAT 61.843 66.667 2.24 0.00 41.24 3.24
2970 2999 4.838486 CTCGGCTCGCTCGTGTCC 62.838 72.222 0.00 0.00 0.00 4.02
3156 3185 7.602644 CCGTGTACAAACTATTCAGGCATATAT 59.397 37.037 0.00 0.00 0.00 0.86
3193 3222 8.937634 AAGTATTAAAATCAACCGACGTATCT 57.062 30.769 0.00 0.00 0.00 1.98
3194 3223 8.571461 AGTATTAAAATCAACCGACGTATCTC 57.429 34.615 0.00 0.00 0.00 2.75
3275 3304 4.315941 CCCCCGCGAGCCTTATCC 62.316 72.222 8.23 0.00 0.00 2.59
3276 3305 3.234730 CCCCGCGAGCCTTATCCT 61.235 66.667 8.23 0.00 0.00 3.24
3277 3306 2.340443 CCCGCGAGCCTTATCCTC 59.660 66.667 8.23 0.00 0.00 3.71
3283 3312 0.236187 CGAGCCTTATCCTCGTCTCG 59.764 60.000 2.90 0.00 45.17 4.04
3284 3313 1.310904 GAGCCTTATCCTCGTCTCGT 58.689 55.000 0.00 0.00 0.00 4.18
3285 3314 1.264826 GAGCCTTATCCTCGTCTCGTC 59.735 57.143 0.00 0.00 0.00 4.20
3319 3348 1.202817 GTCCACTCGTTCTTCCTCTCC 59.797 57.143 0.00 0.00 0.00 3.71
3463 3492 0.984230 TCCTCAAGATCCACACCACC 59.016 55.000 0.00 0.00 0.00 4.61
3464 3493 0.987294 CCTCAAGATCCACACCACCT 59.013 55.000 0.00 0.00 0.00 4.00
3465 3494 1.339438 CCTCAAGATCCACACCACCTG 60.339 57.143 0.00 0.00 0.00 4.00
3466 3495 0.036732 TCAAGATCCACACCACCTGC 59.963 55.000 0.00 0.00 0.00 4.85
3794 3979 2.812609 CTGCACTGACGCGCTGAT 60.813 61.111 5.73 0.00 33.35 2.90
3795 3980 2.796425 CTGCACTGACGCGCTGATC 61.796 63.158 5.73 0.40 33.35 2.92
3796 3981 3.906649 GCACTGACGCGCTGATCG 61.907 66.667 5.73 0.00 42.12 3.69
3821 4006 2.932663 ACGGAGTTGCAATGGAGTG 58.067 52.632 0.59 0.00 37.78 3.51
3822 4007 1.237285 ACGGAGTTGCAATGGAGTGC 61.237 55.000 0.59 0.00 37.78 4.40
3823 4008 1.885871 GGAGTTGCAATGGAGTGCC 59.114 57.895 0.59 0.00 44.26 5.01
3824 4009 1.503542 GAGTTGCAATGGAGTGCCG 59.496 57.895 0.59 0.00 44.26 5.69
3825 4010 2.126346 GTTGCAATGGAGTGCCGC 60.126 61.111 0.59 0.00 44.26 6.53
3826 4011 2.282391 TTGCAATGGAGTGCCGCT 60.282 55.556 0.00 0.00 44.26 5.52
3827 4012 2.334946 TTGCAATGGAGTGCCGCTC 61.335 57.895 0.00 0.00 44.26 5.03
3828 4013 3.869272 GCAATGGAGTGCCGCTCG 61.869 66.667 0.00 0.00 45.03 5.03
3829 4014 3.869272 CAATGGAGTGCCGCTCGC 61.869 66.667 0.00 0.00 45.03 5.03
3848 4033 3.807538 GCCGGTGATGCAGTGCAG 61.808 66.667 24.20 9.66 43.65 4.41
3849 4034 3.807538 CCGGTGATGCAGTGCAGC 61.808 66.667 26.04 26.04 45.81 5.25
3872 4057 3.038417 GAGCTGCACTGACGCGTT 61.038 61.111 15.53 0.00 33.35 4.84
3873 4058 3.287121 GAGCTGCACTGACGCGTTG 62.287 63.158 15.53 9.50 33.35 4.10
3874 4059 3.337889 GCTGCACTGACGCGTTGA 61.338 61.111 15.53 1.78 33.35 3.18
3875 4060 2.671177 GCTGCACTGACGCGTTGAT 61.671 57.895 15.53 0.00 33.35 2.57
3876 4061 1.417592 CTGCACTGACGCGTTGATC 59.582 57.895 15.53 0.00 33.35 2.92
3877 4062 2.271024 CTGCACTGACGCGTTGATCG 62.271 60.000 15.53 2.43 43.12 3.69
3886 4071 3.902063 CGTTGATCGCCGCTGACG 61.902 66.667 0.00 0.00 39.67 4.35
3902 4087 2.932663 ACGGAGTTGCAATGGAGTG 58.067 52.632 0.59 0.00 37.78 3.51
3903 4088 1.237285 ACGGAGTTGCAATGGAGTGC 61.237 55.000 0.59 0.00 37.78 4.40
3904 4089 0.957395 CGGAGTTGCAATGGAGTGCT 60.957 55.000 0.59 0.00 45.17 4.40
3905 4090 1.675714 CGGAGTTGCAATGGAGTGCTA 60.676 52.381 0.59 0.00 45.17 3.49
3906 4091 1.740025 GGAGTTGCAATGGAGTGCTAC 59.260 52.381 0.59 5.68 46.44 3.58
3909 4094 1.394917 GTTGCAATGGAGTGCTACTCG 59.605 52.381 0.59 0.00 45.96 4.18
3910 4095 0.740868 TGCAATGGAGTGCTACTCGC 60.741 55.000 0.32 7.96 45.96 5.03
3911 4096 1.432270 GCAATGGAGTGCTACTCGCC 61.432 60.000 9.29 0.00 45.96 5.54
3912 4097 1.141881 AATGGAGTGCTACTCGCCG 59.858 57.895 9.29 0.00 45.96 6.46
3913 4098 2.907897 AATGGAGTGCTACTCGCCGC 62.908 60.000 9.29 0.00 45.96 6.53
3914 4099 4.874977 GGAGTGCTACTCGCCGCC 62.875 72.222 9.29 0.00 45.96 6.13
3920 4105 3.900892 CTACTCGCCGCCGGTGAT 61.901 66.667 21.11 12.66 41.66 3.06
3921 4106 4.201679 TACTCGCCGCCGGTGATG 62.202 66.667 21.11 15.97 41.66 3.07
3929 4114 3.807538 GCCGGTGATGCAGTGCAG 61.808 66.667 24.20 9.66 43.65 4.41
3930 4115 3.807538 CCGGTGATGCAGTGCAGC 61.808 66.667 26.04 26.04 45.81 5.25
4057 4323 3.486263 CCGACGGGCTTTGTGATC 58.514 61.111 5.81 0.00 0.00 2.92
4058 4324 1.079127 CCGACGGGCTTTGTGATCT 60.079 57.895 5.81 0.00 0.00 2.75
4059 4325 1.361668 CCGACGGGCTTTGTGATCTG 61.362 60.000 5.81 0.00 0.00 2.90
4060 4326 1.796796 GACGGGCTTTGTGATCTGC 59.203 57.895 0.00 0.00 0.00 4.26
4061 4327 1.970917 GACGGGCTTTGTGATCTGCG 61.971 60.000 0.00 0.00 0.00 5.18
4062 4328 2.486966 GGGCTTTGTGATCTGCGC 59.513 61.111 0.00 0.00 0.00 6.09
4063 4329 2.042831 GGGCTTTGTGATCTGCGCT 61.043 57.895 9.73 0.00 35.85 5.92
4064 4330 1.589716 GGGCTTTGTGATCTGCGCTT 61.590 55.000 9.73 0.00 35.85 4.68
4065 4331 0.242017 GGCTTTGTGATCTGCGCTTT 59.758 50.000 9.73 0.00 0.00 3.51
4066 4332 1.468520 GGCTTTGTGATCTGCGCTTTA 59.531 47.619 9.73 0.00 0.00 1.85
4067 4333 2.509870 GCTTTGTGATCTGCGCTTTAC 58.490 47.619 9.73 1.12 0.00 2.01
4068 4334 2.095768 GCTTTGTGATCTGCGCTTTACA 60.096 45.455 9.73 3.99 0.00 2.41
4069 4335 3.426695 GCTTTGTGATCTGCGCTTTACAT 60.427 43.478 9.73 0.00 0.00 2.29
4070 4336 4.337763 CTTTGTGATCTGCGCTTTACATC 58.662 43.478 9.73 3.41 0.00 3.06
4071 4337 1.926510 TGTGATCTGCGCTTTACATCG 59.073 47.619 9.73 0.00 0.00 3.84
4072 4338 1.258982 GTGATCTGCGCTTTACATCGG 59.741 52.381 9.73 0.00 0.00 4.18
4073 4339 1.136110 TGATCTGCGCTTTACATCGGA 59.864 47.619 9.73 0.00 0.00 4.55
4074 4340 1.523095 GATCTGCGCTTTACATCGGAC 59.477 52.381 9.73 0.00 0.00 4.79
4075 4341 0.800683 TCTGCGCTTTACATCGGACG 60.801 55.000 9.73 0.00 0.00 4.79
4076 4342 1.752501 CTGCGCTTTACATCGGACGG 61.753 60.000 9.73 0.00 0.00 4.79
4077 4343 3.003478 CGCTTTACATCGGACGGC 58.997 61.111 0.00 0.00 0.00 5.68
4078 4344 2.522638 CGCTTTACATCGGACGGCC 61.523 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.389391 AGGGATGCGAGGTGATTACG 59.611 55.000 0.00 0.00 0.00 3.18
1 2 1.270358 GGAGGGATGCGAGGTGATTAC 60.270 57.143 0.00 0.00 0.00 1.89
2 3 1.048601 GGAGGGATGCGAGGTGATTA 58.951 55.000 0.00 0.00 0.00 1.75
3 4 1.700042 GGGAGGGATGCGAGGTGATT 61.700 60.000 0.00 0.00 0.00 2.57
4 5 2.143419 GGGAGGGATGCGAGGTGAT 61.143 63.158 0.00 0.00 0.00 3.06
5 6 2.764128 GGGAGGGATGCGAGGTGA 60.764 66.667 0.00 0.00 0.00 4.02
6 7 4.227134 CGGGAGGGATGCGAGGTG 62.227 72.222 0.00 0.00 0.00 4.00
7 8 4.779733 ACGGGAGGGATGCGAGGT 62.780 66.667 0.00 0.00 0.00 3.85
8 9 3.917760 GACGGGAGGGATGCGAGG 61.918 72.222 0.00 0.00 0.00 4.63
9 10 2.835431 AGACGGGAGGGATGCGAG 60.835 66.667 0.00 0.00 0.00 5.03
10 11 2.833582 GAGACGGGAGGGATGCGA 60.834 66.667 0.00 0.00 0.00 5.10
11 12 3.917760 GGAGACGGGAGGGATGCG 61.918 72.222 0.00 0.00 0.00 4.73
12 13 2.764128 TGGAGACGGGAGGGATGC 60.764 66.667 0.00 0.00 0.00 3.91
13 14 1.381872 AGTGGAGACGGGAGGGATG 60.382 63.158 0.00 0.00 0.00 3.51
14 15 1.075896 GAGTGGAGACGGGAGGGAT 60.076 63.158 0.00 0.00 0.00 3.85
15 16 1.875422 ATGAGTGGAGACGGGAGGGA 61.875 60.000 0.00 0.00 0.00 4.20
16 17 1.381872 ATGAGTGGAGACGGGAGGG 60.382 63.158 0.00 0.00 0.00 4.30
17 18 1.819229 CATGAGTGGAGACGGGAGG 59.181 63.158 0.00 0.00 0.00 4.30
18 19 1.142748 GCATGAGTGGAGACGGGAG 59.857 63.158 0.00 0.00 0.00 4.30
19 20 1.191489 TTGCATGAGTGGAGACGGGA 61.191 55.000 0.00 0.00 0.00 5.14
20 21 0.742281 CTTGCATGAGTGGAGACGGG 60.742 60.000 0.00 0.00 0.00 5.28
21 22 0.742281 CCTTGCATGAGTGGAGACGG 60.742 60.000 0.00 0.00 0.00 4.79
22 23 0.742281 CCCTTGCATGAGTGGAGACG 60.742 60.000 0.00 0.00 0.00 4.18
23 24 1.028868 GCCCTTGCATGAGTGGAGAC 61.029 60.000 0.00 0.00 37.47 3.36
24 25 1.300963 GCCCTTGCATGAGTGGAGA 59.699 57.895 0.00 0.00 37.47 3.71
25 26 1.751927 GGCCCTTGCATGAGTGGAG 60.752 63.158 0.00 0.00 40.13 3.86
26 27 2.356278 GGCCCTTGCATGAGTGGA 59.644 61.111 0.00 0.00 40.13 4.02
27 28 2.757099 GGGCCCTTGCATGAGTGG 60.757 66.667 17.04 0.00 40.13 4.00
28 29 3.136123 CGGGCCCTTGCATGAGTG 61.136 66.667 22.43 0.00 40.13 3.51
30 31 4.809496 AGCGGGCCCTTGCATGAG 62.809 66.667 22.43 1.78 40.13 2.90
56 57 4.200283 GAGTCAGGCCGAGGCGAG 62.200 72.222 8.14 3.13 43.06 5.03
58 59 4.803426 GTGAGTCAGGCCGAGGCG 62.803 72.222 8.14 0.00 43.06 5.52
59 60 4.803426 CGTGAGTCAGGCCGAGGC 62.803 72.222 5.37 5.37 41.06 4.70
60 61 3.057547 CTCGTGAGTCAGGCCGAGG 62.058 68.421 18.91 5.62 42.21 4.63
61 62 1.587043 TTCTCGTGAGTCAGGCCGAG 61.587 60.000 20.06 20.06 46.06 4.63
62 63 1.176619 TTTCTCGTGAGTCAGGCCGA 61.177 55.000 7.98 6.09 0.00 5.54
63 64 1.009389 GTTTCTCGTGAGTCAGGCCG 61.009 60.000 7.98 1.61 0.00 6.13
64 65 0.318762 AGTTTCTCGTGAGTCAGGCC 59.681 55.000 7.98 0.00 0.00 5.19
65 66 1.423395 CAGTTTCTCGTGAGTCAGGC 58.577 55.000 7.98 0.00 0.00 4.85
66 67 1.423395 GCAGTTTCTCGTGAGTCAGG 58.577 55.000 6.49 6.49 0.00 3.86
67 68 1.423395 GGCAGTTTCTCGTGAGTCAG 58.577 55.000 0.00 0.00 0.00 3.51
68 69 0.033504 GGGCAGTTTCTCGTGAGTCA 59.966 55.000 0.00 0.00 0.00 3.41
69 70 0.033504 TGGGCAGTTTCTCGTGAGTC 59.966 55.000 0.00 0.00 0.00 3.36
70 71 0.687354 ATGGGCAGTTTCTCGTGAGT 59.313 50.000 0.00 0.00 0.00 3.41
71 72 1.734465 GAATGGGCAGTTTCTCGTGAG 59.266 52.381 0.00 0.00 0.00 3.51
72 73 1.071542 TGAATGGGCAGTTTCTCGTGA 59.928 47.619 0.00 0.00 0.00 4.35
73 74 1.522668 TGAATGGGCAGTTTCTCGTG 58.477 50.000 0.00 0.00 0.00 4.35
74 75 2.154462 CTTGAATGGGCAGTTTCTCGT 58.846 47.619 0.00 0.00 0.00 4.18
75 76 1.135575 GCTTGAATGGGCAGTTTCTCG 60.136 52.381 0.00 0.00 0.00 4.04
76 77 1.135575 CGCTTGAATGGGCAGTTTCTC 60.136 52.381 0.00 0.00 0.00 2.87
77 78 0.883833 CGCTTGAATGGGCAGTTTCT 59.116 50.000 0.00 0.00 0.00 2.52
78 79 0.598065 ACGCTTGAATGGGCAGTTTC 59.402 50.000 0.00 0.00 0.00 2.78
79 80 1.039856 AACGCTTGAATGGGCAGTTT 58.960 45.000 0.00 0.00 0.00 2.66
80 81 1.000274 GAAACGCTTGAATGGGCAGTT 60.000 47.619 0.00 0.00 0.00 3.16
81 82 0.598065 GAAACGCTTGAATGGGCAGT 59.402 50.000 0.00 0.00 0.00 4.40
82 83 0.109132 GGAAACGCTTGAATGGGCAG 60.109 55.000 0.00 0.00 0.00 4.85
83 84 0.825425 TGGAAACGCTTGAATGGGCA 60.825 50.000 0.00 0.00 0.00 5.36
84 85 0.109132 CTGGAAACGCTTGAATGGGC 60.109 55.000 0.00 0.00 0.00 5.36
85 86 0.109132 GCTGGAAACGCTTGAATGGG 60.109 55.000 0.00 0.00 0.00 4.00
86 87 0.454957 CGCTGGAAACGCTTGAATGG 60.455 55.000 0.00 0.00 0.00 3.16
87 88 0.516877 TCGCTGGAAACGCTTGAATG 59.483 50.000 0.00 0.00 0.00 2.67
88 89 0.798776 CTCGCTGGAAACGCTTGAAT 59.201 50.000 0.00 0.00 0.00 2.57
89 90 1.841663 GCTCGCTGGAAACGCTTGAA 61.842 55.000 0.00 0.00 0.00 2.69
90 91 2.317609 GCTCGCTGGAAACGCTTGA 61.318 57.895 0.00 0.00 0.00 3.02
91 92 2.174349 GCTCGCTGGAAACGCTTG 59.826 61.111 0.00 0.00 0.00 4.01
92 93 3.050275 GGCTCGCTGGAAACGCTT 61.050 61.111 0.00 0.00 0.00 4.68
93 94 3.825160 TTGGCTCGCTGGAAACGCT 62.825 57.895 0.00 0.00 0.00 5.07
94 95 3.353836 TTGGCTCGCTGGAAACGC 61.354 61.111 0.00 0.00 0.00 4.84
95 96 2.556287 GTTGGCTCGCTGGAAACG 59.444 61.111 0.00 0.00 0.00 3.60
96 97 0.321298 TAGGTTGGCTCGCTGGAAAC 60.321 55.000 0.00 0.00 0.00 2.78
97 98 0.618458 ATAGGTTGGCTCGCTGGAAA 59.382 50.000 0.00 0.00 0.00 3.13
98 99 0.107703 CATAGGTTGGCTCGCTGGAA 60.108 55.000 0.00 0.00 0.00 3.53
99 100 1.522092 CATAGGTTGGCTCGCTGGA 59.478 57.895 0.00 0.00 0.00 3.86
100 101 1.524621 CCATAGGTTGGCTCGCTGG 60.525 63.158 0.00 0.00 39.09 4.85
101 102 1.524621 CCCATAGGTTGGCTCGCTG 60.525 63.158 0.00 0.00 44.97 5.18
102 103 2.911143 CCCATAGGTTGGCTCGCT 59.089 61.111 0.00 0.00 44.97 4.93
103 104 2.902343 GCCCATAGGTTGGCTCGC 60.902 66.667 0.00 0.00 44.97 5.03
107 108 0.972471 AAAGCAGCCCATAGGTTGGC 60.972 55.000 0.00 0.00 44.23 4.52
108 109 2.435372 TAAAGCAGCCCATAGGTTGG 57.565 50.000 0.00 0.00 44.23 3.77
109 110 3.620488 TCTTAAAGCAGCCCATAGGTTG 58.380 45.455 0.00 0.00 46.67 3.77
110 111 4.273318 CTTCTTAAAGCAGCCCATAGGTT 58.727 43.478 0.00 0.00 34.57 3.50
111 112 3.891049 CTTCTTAAAGCAGCCCATAGGT 58.109 45.455 0.00 0.00 34.57 3.08
122 123 4.616192 TGCATCGCACGCTTCTTAAAGC 62.616 50.000 0.05 0.05 43.39 3.51
123 124 1.128507 TGCATCGCACGCTTCTTAAAG 59.871 47.619 0.00 0.00 31.71 1.85
124 125 1.128507 CTGCATCGCACGCTTCTTAAA 59.871 47.619 0.00 0.00 33.79 1.52
125 126 0.721154 CTGCATCGCACGCTTCTTAA 59.279 50.000 0.00 0.00 33.79 1.85
126 127 1.083806 CCTGCATCGCACGCTTCTTA 61.084 55.000 0.00 0.00 33.79 2.10
127 128 2.393768 CCTGCATCGCACGCTTCTT 61.394 57.895 0.00 0.00 33.79 2.52
128 129 2.816958 CCTGCATCGCACGCTTCT 60.817 61.111 0.00 0.00 33.79 2.85
129 130 4.527157 GCCTGCATCGCACGCTTC 62.527 66.667 1.21 0.00 37.54 3.86
134 135 4.120331 GTTGGGCCTGCATCGCAC 62.120 66.667 4.53 4.85 33.79 5.34
135 136 4.657408 TGTTGGGCCTGCATCGCA 62.657 61.111 4.53 5.20 36.92 5.10
136 137 2.713967 ATTGTTGGGCCTGCATCGC 61.714 57.895 4.53 0.00 0.00 4.58
137 138 1.140161 CATTGTTGGGCCTGCATCG 59.860 57.895 4.53 0.00 0.00 3.84
138 139 0.896923 TTCATTGTTGGGCCTGCATC 59.103 50.000 4.53 0.00 0.00 3.91
139 140 1.002315 GTTTCATTGTTGGGCCTGCAT 59.998 47.619 4.53 0.00 0.00 3.96
140 141 0.392336 GTTTCATTGTTGGGCCTGCA 59.608 50.000 4.53 0.00 0.00 4.41
141 142 0.320683 GGTTTCATTGTTGGGCCTGC 60.321 55.000 4.53 0.00 0.00 4.85
142 143 0.038343 CGGTTTCATTGTTGGGCCTG 60.038 55.000 4.53 0.00 0.00 4.85
143 144 1.184970 CCGGTTTCATTGTTGGGCCT 61.185 55.000 4.53 0.00 0.00 5.19
144 145 1.291906 CCGGTTTCATTGTTGGGCC 59.708 57.895 0.00 0.00 0.00 5.80
145 146 1.291906 CCCGGTTTCATTGTTGGGC 59.708 57.895 0.00 0.00 0.00 5.36
146 147 1.291906 GCCCGGTTTCATTGTTGGG 59.708 57.895 0.00 0.00 39.72 4.12
147 148 0.390860 TTGCCCGGTTTCATTGTTGG 59.609 50.000 0.00 0.00 0.00 3.77
148 149 1.496934 GTTGCCCGGTTTCATTGTTG 58.503 50.000 0.00 0.00 0.00 3.33
149 150 0.391228 GGTTGCCCGGTTTCATTGTT 59.609 50.000 0.00 0.00 0.00 2.83
150 151 0.757188 TGGTTGCCCGGTTTCATTGT 60.757 50.000 0.00 0.00 0.00 2.71
151 152 0.390860 TTGGTTGCCCGGTTTCATTG 59.609 50.000 0.00 0.00 0.00 2.82
152 153 1.123928 TTTGGTTGCCCGGTTTCATT 58.876 45.000 0.00 0.00 0.00 2.57
153 154 0.391228 GTTTGGTTGCCCGGTTTCAT 59.609 50.000 0.00 0.00 0.00 2.57
154 155 0.970937 TGTTTGGTTGCCCGGTTTCA 60.971 50.000 0.00 0.00 0.00 2.69
155 156 0.249280 CTGTTTGGTTGCCCGGTTTC 60.249 55.000 0.00 0.00 0.00 2.78
156 157 1.681486 CCTGTTTGGTTGCCCGGTTT 61.681 55.000 0.00 0.00 0.00 3.27
157 158 2.131067 CCTGTTTGGTTGCCCGGTT 61.131 57.895 0.00 0.00 0.00 4.44
158 159 2.520741 CCTGTTTGGTTGCCCGGT 60.521 61.111 0.00 0.00 0.00 5.28
159 160 3.989787 GCCTGTTTGGTTGCCCGG 61.990 66.667 0.00 0.00 38.35 5.73
160 161 3.989787 GGCCTGTTTGGTTGCCCG 61.990 66.667 0.00 0.00 37.94 6.13
161 162 2.524148 AGGCCTGTTTGGTTGCCC 60.524 61.111 3.11 0.00 45.14 5.36
162 163 1.115326 AAGAGGCCTGTTTGGTTGCC 61.115 55.000 12.00 0.00 44.35 4.52
163 164 0.315251 GAAGAGGCCTGTTTGGTTGC 59.685 55.000 17.52 0.00 38.35 4.17
164 165 0.961753 GGAAGAGGCCTGTTTGGTTG 59.038 55.000 17.52 0.00 38.35 3.77
165 166 0.853530 AGGAAGAGGCCTGTTTGGTT 59.146 50.000 17.52 0.00 36.76 3.67
166 167 0.853530 AAGGAAGAGGCCTGTTTGGT 59.146 50.000 17.52 1.48 38.58 3.67
167 168 1.539157 GAAGGAAGAGGCCTGTTTGG 58.461 55.000 17.52 0.00 38.58 3.28
168 169 1.539157 GGAAGGAAGAGGCCTGTTTG 58.461 55.000 17.52 0.00 38.58 2.93
169 170 0.405973 GGGAAGGAAGAGGCCTGTTT 59.594 55.000 17.52 7.76 38.58 2.83
170 171 1.842381 CGGGAAGGAAGAGGCCTGTT 61.842 60.000 16.35 16.35 38.58 3.16
171 172 2.294078 CGGGAAGGAAGAGGCCTGT 61.294 63.158 12.00 1.36 38.58 4.00
172 173 2.294078 ACGGGAAGGAAGAGGCCTG 61.294 63.158 12.00 0.00 38.58 4.85
173 174 2.122954 ACGGGAAGGAAGAGGCCT 59.877 61.111 3.86 3.86 40.93 5.19
174 175 2.269241 CACGGGAAGGAAGAGGCC 59.731 66.667 0.00 0.00 0.00 5.19
175 176 2.436824 GCACGGGAAGGAAGAGGC 60.437 66.667 0.00 0.00 0.00 4.70
176 177 2.125512 CGCACGGGAAGGAAGAGG 60.126 66.667 0.00 0.00 0.00 3.69
177 178 2.125512 CCGCACGGGAAGGAAGAG 60.126 66.667 0.00 0.00 38.47 2.85
196 197 2.825836 GCATCGAGCCCAACCAGG 60.826 66.667 0.00 0.00 37.23 4.45
197 198 3.197790 CGCATCGAGCCCAACCAG 61.198 66.667 0.00 0.00 41.38 4.00
198 199 4.776322 CCGCATCGAGCCCAACCA 62.776 66.667 0.00 0.00 41.38 3.67
206 207 2.331893 TTTGGTTGCCCGCATCGAG 61.332 57.895 0.00 0.00 0.00 4.04
207 208 2.281831 TTTGGTTGCCCGCATCGA 60.282 55.556 0.00 0.00 0.00 3.59
208 209 2.126502 GTTTGGTTGCCCGCATCG 60.127 61.111 0.00 0.00 0.00 3.84
209 210 1.372872 GTGTTTGGTTGCCCGCATC 60.373 57.895 0.00 0.00 0.00 3.91
210 211 2.733945 GTGTTTGGTTGCCCGCAT 59.266 55.556 0.00 0.00 0.00 4.73
211 212 3.893763 CGTGTTTGGTTGCCCGCA 61.894 61.111 0.00 0.00 0.00 5.69
213 214 4.639171 GGCGTGTTTGGTTGCCCG 62.639 66.667 0.00 0.00 41.70 6.13
215 216 2.693250 GAAGGGCGTGTTTGGTTGCC 62.693 60.000 0.00 0.00 46.82 4.52
216 217 1.299850 GAAGGGCGTGTTTGGTTGC 60.300 57.895 0.00 0.00 0.00 4.17
217 218 1.008995 CGAAGGGCGTGTTTGGTTG 60.009 57.895 0.00 0.00 34.64 3.77
218 219 3.427670 CGAAGGGCGTGTTTGGTT 58.572 55.556 0.00 0.00 34.64 3.67
228 229 2.095252 GTGCTCTCGAACGAAGGGC 61.095 63.158 10.02 10.02 0.00 5.19
229 230 1.801913 CGTGCTCTCGAACGAAGGG 60.802 63.158 1.14 0.00 42.32 3.95
230 231 1.801913 CCGTGCTCTCGAACGAAGG 60.802 63.158 8.86 0.00 42.32 3.46
231 232 1.801913 CCCGTGCTCTCGAACGAAG 60.802 63.158 8.86 0.00 42.32 3.79
232 233 1.798234 TTCCCGTGCTCTCGAACGAA 61.798 55.000 8.86 0.00 42.32 3.85
233 234 1.592400 ATTCCCGTGCTCTCGAACGA 61.592 55.000 8.86 0.00 42.32 3.85
234 235 1.153823 ATTCCCGTGCTCTCGAACG 60.154 57.895 0.41 0.41 39.48 3.95
235 236 0.389948 ACATTCCCGTGCTCTCGAAC 60.390 55.000 0.00 0.00 0.00 3.95
236 237 1.134367 CTACATTCCCGTGCTCTCGAA 59.866 52.381 0.00 0.00 0.00 3.71
237 238 0.738975 CTACATTCCCGTGCTCTCGA 59.261 55.000 0.00 0.00 0.00 4.04
250 251 1.806542 CAGCGACTTGTTGCCTACATT 59.193 47.619 9.17 0.00 36.44 2.71
271 272 7.163441 TGTCTCATGAAGAGTTTGATGATTGA 58.837 34.615 0.00 0.00 44.98 2.57
290 291 3.443925 CCGGCGCTCTCTGTCTCA 61.444 66.667 7.64 0.00 0.00 3.27
315 316 3.321111 GCTCTCCGATAATAACTGGGACA 59.679 47.826 0.00 0.00 0.00 4.02
356 357 3.463048 TTTCTCTTACTACCCGGACCT 57.537 47.619 0.73 0.00 0.00 3.85
395 396 1.066787 GTGTGGAGAGACTACCCTTGC 60.067 57.143 0.00 0.00 0.00 4.01
468 469 6.540189 AGTCCGACCTCATTTTAAAGATCATG 59.460 38.462 0.00 0.00 0.00 3.07
469 470 6.653989 AGTCCGACCTCATTTTAAAGATCAT 58.346 36.000 0.00 0.00 0.00 2.45
482 483 2.036387 TCTTGTCAAAGTCCGACCTCA 58.964 47.619 0.00 0.00 34.78 3.86
483 484 2.814280 TCTTGTCAAAGTCCGACCTC 57.186 50.000 0.00 0.00 34.78 3.85
496 497 4.006319 CCCAGTTCTGGAAAGATCTTGTC 58.994 47.826 19.12 8.65 0.00 3.18
510 511 2.920912 TCGGCGGTTCCCAGTTCT 60.921 61.111 7.21 0.00 0.00 3.01
592 593 1.920835 GAAGAGTGGGGTGGGCTCT 60.921 63.158 0.00 0.00 40.89 4.09
716 721 4.491676 ACTCATGCAAGCAAAAATAGCAG 58.508 39.130 0.00 0.00 38.75 4.24
837 842 3.013219 GAGTGAGAAAATGGGGAAGAGC 58.987 50.000 0.00 0.00 0.00 4.09
853 858 0.397675 ATGATGCCGGGAGAGAGTGA 60.398 55.000 2.18 0.00 0.00 3.41
944 963 0.887933 TTGAGGAATTTCTTGGCGCC 59.112 50.000 22.73 22.73 0.00 6.53
969 990 6.587990 TCGATCTTCACAAGAAATTCAGAGTC 59.412 38.462 0.00 0.00 41.63 3.36
971 992 6.453527 CGTCGATCTTCACAAGAAATTCAGAG 60.454 42.308 0.00 0.00 41.63 3.35
972 993 5.346011 CGTCGATCTTCACAAGAAATTCAGA 59.654 40.000 0.00 0.00 41.63 3.27
997 1019 1.406069 GCATGTGTCCGACTCCATTCT 60.406 52.381 0.00 0.00 0.00 2.40
998 1020 1.009829 GCATGTGTCCGACTCCATTC 58.990 55.000 0.00 0.00 0.00 2.67
1600 1626 2.233271 CTTGAACAGCATGGACACCTT 58.767 47.619 0.00 0.00 43.62 3.50
1953 1979 1.625818 GAGAGGAAGTTGAAGAGGCCA 59.374 52.381 5.01 0.00 0.00 5.36
2167 2193 2.029290 GGATGTAGACGCCGATGGTAAT 60.029 50.000 0.00 0.00 0.00 1.89
2169 2195 0.956633 GGATGTAGACGCCGATGGTA 59.043 55.000 0.00 0.00 0.00 3.25
3159 3188 9.855021 CGGTTGATTTTAATACTTTTCCAAGAT 57.145 29.630 0.00 0.00 33.72 2.40
3161 3190 9.124807 GTCGGTTGATTTTAATACTTTTCCAAG 57.875 33.333 0.00 0.00 35.92 3.61
3162 3191 7.804129 CGTCGGTTGATTTTAATACTTTTCCAA 59.196 33.333 0.00 0.00 0.00 3.53
3193 3222 2.008329 GAGAGGTTTACGCGAGAGAGA 58.992 52.381 15.93 0.00 33.96 3.10
3194 3223 1.064357 GGAGAGGTTTACGCGAGAGAG 59.936 57.143 15.93 0.00 0.00 3.20
3235 3264 4.980805 GTGGACTCGCGTGGGCAA 62.981 66.667 13.32 0.00 39.92 4.52
3275 3304 4.813526 CCGCGTGGACGAGACGAG 62.814 72.222 10.20 6.20 41.67 4.18
3319 3348 2.829120 AGACGAGGAGAGGGAAAAAGAG 59.171 50.000 0.00 0.00 0.00 2.85
3463 3492 2.684843 GGCCTTCGTCTTGCAGCAG 61.685 63.158 0.00 0.00 0.00 4.24
3464 3493 2.669569 GGCCTTCGTCTTGCAGCA 60.670 61.111 0.00 0.00 0.00 4.41
3465 3494 3.793144 CGGCCTTCGTCTTGCAGC 61.793 66.667 0.00 0.00 0.00 5.25
3466 3495 3.121030 CCGGCCTTCGTCTTGCAG 61.121 66.667 0.00 0.00 37.11 4.41
3610 3794 3.485431 CGCTTCAGTGCAGCTCCG 61.485 66.667 12.97 0.00 34.88 4.63
3638 3822 1.970917 CTCCATTGCAACTCCGTCGC 61.971 60.000 0.00 0.00 0.00 5.19
3723 3908 0.895100 GGCACTCCATTGCAACTCCA 60.895 55.000 0.00 0.00 44.94 3.86
3798 3983 3.118454 ATTGCAACTCCGTCGGCG 61.118 61.111 6.34 0.29 37.95 6.46
3799 3984 2.480555 CATTGCAACTCCGTCGGC 59.519 61.111 6.34 0.00 0.00 5.54
3800 3985 1.361668 CTCCATTGCAACTCCGTCGG 61.362 60.000 4.39 4.39 0.00 4.79
3801 3986 0.670546 ACTCCATTGCAACTCCGTCG 60.671 55.000 0.00 0.00 0.00 5.12
3802 3987 0.798776 CACTCCATTGCAACTCCGTC 59.201 55.000 0.00 0.00 0.00 4.79
3803 3988 1.237285 GCACTCCATTGCAACTCCGT 61.237 55.000 0.00 0.00 42.49 4.69
3804 3989 1.503542 GCACTCCATTGCAACTCCG 59.496 57.895 0.00 0.00 42.49 4.63
3805 3990 1.885871 GGCACTCCATTGCAACTCC 59.114 57.895 0.00 0.00 44.94 3.85
3806 3991 1.503542 CGGCACTCCATTGCAACTC 59.496 57.895 0.00 0.00 44.94 3.01
3807 3992 2.629656 GCGGCACTCCATTGCAACT 61.630 57.895 0.00 0.00 44.94 3.16
3808 3993 2.126346 GCGGCACTCCATTGCAAC 60.126 61.111 0.00 0.00 44.94 4.17
3809 3994 2.282391 AGCGGCACTCCATTGCAA 60.282 55.556 0.00 0.00 44.94 4.08
3810 3995 2.747460 GAGCGGCACTCCATTGCA 60.747 61.111 1.45 0.00 44.94 4.08
3811 3996 3.869272 CGAGCGGCACTCCATTGC 61.869 66.667 1.45 0.00 43.01 3.56
3812 3997 3.869272 GCGAGCGGCACTCCATTG 61.869 66.667 1.45 0.00 43.01 2.82
3831 4016 3.807538 CTGCACTGCATCACCGGC 61.808 66.667 3.64 0.00 38.13 6.13
3832 4017 3.807538 GCTGCACTGCATCACCGG 61.808 66.667 3.64 0.00 38.13 5.28
3833 4018 3.051479 TGCTGCACTGCATCACCG 61.051 61.111 3.64 0.00 38.13 4.94
3834 4019 2.564975 GTGCTGCACTGCATCACC 59.435 61.111 24.68 8.58 45.96 4.02
3836 4021 3.729698 GCGTGCTGCACTGCATCA 61.730 61.111 30.18 3.50 45.23 3.07
3837 4022 4.806481 CGCGTGCTGCACTGCATC 62.806 66.667 32.10 17.24 46.97 3.91
3855 4040 3.038417 AACGCGTCAGTGCAGCTC 61.038 61.111 14.44 0.00 34.15 4.09
3856 4041 3.341043 CAACGCGTCAGTGCAGCT 61.341 61.111 14.44 0.00 34.15 4.24
3857 4042 2.554365 GATCAACGCGTCAGTGCAGC 62.554 60.000 14.44 0.00 34.15 5.25
3858 4043 1.417592 GATCAACGCGTCAGTGCAG 59.582 57.895 14.44 0.00 34.15 4.41
3859 4044 2.371923 CGATCAACGCGTCAGTGCA 61.372 57.895 14.44 0.00 34.51 4.57
3860 4045 2.391821 CGATCAACGCGTCAGTGC 59.608 61.111 14.44 0.06 34.51 4.40
3869 4054 3.902063 CGTCAGCGGCGATCAACG 61.902 66.667 12.98 13.53 45.66 4.10
3879 4064 1.133253 CATTGCAACTCCGTCAGCG 59.867 57.895 0.00 0.00 37.95 5.18
3880 4065 0.955428 TCCATTGCAACTCCGTCAGC 60.955 55.000 0.00 0.00 0.00 4.26
3881 4066 1.081892 CTCCATTGCAACTCCGTCAG 58.918 55.000 0.00 0.00 0.00 3.51
3882 4067 0.396435 ACTCCATTGCAACTCCGTCA 59.604 50.000 0.00 0.00 0.00 4.35
3883 4068 0.798776 CACTCCATTGCAACTCCGTC 59.201 55.000 0.00 0.00 0.00 4.79
3884 4069 1.237285 GCACTCCATTGCAACTCCGT 61.237 55.000 0.00 0.00 42.49 4.69
3885 4070 0.957395 AGCACTCCATTGCAACTCCG 60.957 55.000 0.00 0.00 45.62 4.63
3886 4071 1.740025 GTAGCACTCCATTGCAACTCC 59.260 52.381 0.00 0.00 45.62 3.85
3887 4072 2.675348 GAGTAGCACTCCATTGCAACTC 59.325 50.000 0.00 0.00 45.62 3.01
3888 4073 2.704572 GAGTAGCACTCCATTGCAACT 58.295 47.619 0.00 0.00 45.62 3.16
3889 4074 1.394917 CGAGTAGCACTCCATTGCAAC 59.605 52.381 0.00 0.00 45.62 4.17
3890 4075 1.725641 CGAGTAGCACTCCATTGCAA 58.274 50.000 0.00 0.00 45.62 4.08
3891 4076 0.740868 GCGAGTAGCACTCCATTGCA 60.741 55.000 9.71 0.00 45.62 4.08
3903 4088 3.900892 ATCACCGGCGGCGAGTAG 61.901 66.667 34.49 18.45 0.00 2.57
3904 4089 4.201679 CATCACCGGCGGCGAGTA 62.202 66.667 34.49 17.18 0.00 2.59
3912 4097 3.807538 CTGCACTGCATCACCGGC 61.808 66.667 3.64 0.00 38.13 6.13
3913 4098 3.807538 GCTGCACTGCATCACCGG 61.808 66.667 3.64 0.00 38.13 5.28
3914 4099 3.051479 TGCTGCACTGCATCACCG 61.051 61.111 3.64 0.00 38.13 4.94
3915 4100 2.564975 GTGCTGCACTGCATCACC 59.435 61.111 24.68 8.58 45.96 4.02
3917 4102 3.729698 GCGTGCTGCACTGCATCA 61.730 61.111 30.18 3.50 45.23 3.07
3918 4103 4.806481 CGCGTGCTGCACTGCATC 62.806 66.667 32.10 17.24 46.97 3.91
4056 4322 0.800683 CGTCCGATGTAAAGCGCAGA 60.801 55.000 11.47 0.00 0.00 4.26
4057 4323 1.631072 CGTCCGATGTAAAGCGCAG 59.369 57.895 11.47 0.00 0.00 5.18
4058 4324 1.807981 CCGTCCGATGTAAAGCGCA 60.808 57.895 11.47 0.00 0.00 6.09
4059 4325 3.003478 CCGTCCGATGTAAAGCGC 58.997 61.111 0.00 0.00 0.00 5.92
4060 4326 2.522638 GGCCGTCCGATGTAAAGCG 61.523 63.158 0.00 0.00 0.00 4.68
4061 4327 3.406559 GGCCGTCCGATGTAAAGC 58.593 61.111 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.