Multiple sequence alignment - TraesCS3B01G285800

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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 TraesCS3B01G285800 chr3B 100.000 3888 0 0 1 3888 457577429 457573542 0.000000e+00 7180
1 TraesCS3B01G285800 chr3B 100.000 1741 0 0 4592 6332 457572838 457571098 0.000000e+00 3216
2 TraesCS3B01G285800 chr3B 93.431 274 14 3 127 397 750204410 750204682 2.750000e-108 403
3 TraesCS3B01G285800 chr3B 94.574 129 5 2 6205 6332 126669709 126669582 1.390000e-46 198
4 TraesCS3B01G285800 chr3B 94.531 128 6 1 6205 6332 552111447 552111573 5.010000e-46 196
5 TraesCS3B01G285800 chr3B 94.783 115 6 0 3078 3192 521797757 521797871 5.040000e-41 180
6 TraesCS3B01G285800 chr3B 94.737 76 4 0 1 76 750203844 750203919 1.120000e-22 119
7 TraesCS3B01G285800 chr3A 95.254 3203 97 19 717 3888 475283796 475280618 0.000000e+00 5022
8 TraesCS3B01G285800 chr3A 93.598 1640 45 17 4592 6204 475279406 475277800 0.000000e+00 2392
9 TraesCS3B01G285800 chr3A 89.734 263 24 3 3189 3449 706868065 706867804 3.660000e-87 333
10 TraesCS3B01G285800 chr3A 89.170 277 10 7 395 660 475284062 475283795 1.700000e-85 327
11 TraesCS3B01G285800 chr3D 94.033 2715 89 22 395 3093 356592987 356590330 0.000000e+00 4048
12 TraesCS3B01G285800 chr3D 91.623 1146 59 15 4592 5708 356589534 356588397 0.000000e+00 1550
13 TraesCS3B01G285800 chr3D 87.921 505 37 8 5700 6204 356579702 356579222 1.980000e-159 573
14 TraesCS3B01G285800 chr3D 90.585 393 33 3 3499 3888 356590331 356589940 9.410000e-143 518
15 TraesCS3B01G285800 chr4A 84.539 401 52 7 1 398 196566113 196565720 7.700000e-104 388
16 TraesCS3B01G285800 chr4A 89.313 262 25 3 3190 3449 165816284 165816544 6.120000e-85 326
17 TraesCS3B01G285800 chr4D 82.878 403 58 9 1 397 122706354 122706751 1.010000e-92 351
18 TraesCS3B01G285800 chr4D 96.330 109 2 2 3089 3195 119822903 119822795 1.810000e-40 178
19 TraesCS3B01G285800 chr6B 82.294 401 63 7 1 397 617131207 617130811 2.190000e-89 340
20 TraesCS3B01G285800 chr2D 87.415 294 31 4 3189 3480 630180074 630179785 3.660000e-87 333
21 TraesCS3B01G285800 chr2D 92.969 128 8 1 6205 6332 352915480 352915354 1.080000e-42 185
22 TraesCS3B01G285800 chr5A 89.655 261 24 3 3189 3447 571792405 571792146 4.730000e-86 329
23 TraesCS3B01G285800 chr5A 88.722 266 27 3 3189 3452 566605368 566605104 7.920000e-84 322
24 TraesCS3B01G285800 chr5B 89.098 266 25 3 3187 3449 121249765 121249501 1.700000e-85 327
25 TraesCS3B01G285800 chr5B 94.531 128 7 0 6205 6332 360936449 360936576 1.390000e-46 198
26 TraesCS3B01G285800 chr7A 89.313 262 24 4 3190 3449 314404554 314404295 6.120000e-85 326
27 TraesCS3B01G285800 chr7A 86.260 131 16 2 1825 1954 712494357 712494228 2.380000e-29 141
28 TraesCS3B01G285800 chr2B 89.313 262 25 3 3190 3449 673002426 673002686 6.120000e-85 326
29 TraesCS3B01G285800 chrUn 84.211 285 37 8 3170 3449 287282888 287282607 2.910000e-68 270
30 TraesCS3B01G285800 chrUn 84.028 288 38 8 3167 3449 306566059 306566343 2.910000e-68 270
31 TraesCS3B01G285800 chr4B 94.574 129 5 2 6205 6332 289808711 289808838 1.390000e-46 198
32 TraesCS3B01G285800 chr4B 93.750 128 8 0 6205 6332 568662147 568662274 6.480000e-45 193
33 TraesCS3B01G285800 chr1B 94.531 128 7 0 6205 6332 657167797 657167670 1.390000e-46 198
34 TraesCS3B01G285800 chr1B 93.750 128 8 0 6205 6332 1847486 1847359 6.480000e-45 193
35 TraesCS3B01G285800 chr1B 89.147 129 12 2 3069 3195 518807865 518807993 6.570000e-35 159
36 TraesCS3B01G285800 chr5D 93.798 129 8 0 6204 6332 216062878 216063006 1.800000e-45 195
37 TraesCS3B01G285800 chr6A 96.330 109 2 2 3089 3195 538097835 538097727 1.810000e-40 178
38 TraesCS3B01G285800 chr1A 96.296 108 3 1 3089 3195 459273228 459273335 6.520000e-40 176
39 TraesCS3B01G285800 chr6D 96.262 107 3 1 3090 3195 320698233 320698127 2.350000e-39 174
40 TraesCS3B01G285800 chr6D 95.413 109 3 2 3089 3195 392273230 392273122 8.440000e-39 172
41 TraesCS3B01G285800 chr6D 94.595 111 5 1 3092 3201 426888228 426888338 3.040000e-38 171
42 TraesCS3B01G285800 chr7B 90.698 86 8 0 1869 1954 713595252 713595167 1.440000e-21 115


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 TraesCS3B01G285800 chr3B 457571098 457577429 6331 True 5198.000000 7180 100.000000 1 6332 2 chr3B.!!$R2 6331
1 TraesCS3B01G285800 chr3B 750203844 750204682 838 False 261.000000 403 94.084000 1 397 2 chr3B.!!$F3 396
2 TraesCS3B01G285800 chr3A 475277800 475284062 6262 True 2580.333333 5022 92.674000 395 6204 3 chr3A.!!$R2 5809
3 TraesCS3B01G285800 chr3D 356588397 356592987 4590 True 2038.666667 4048 92.080333 395 5708 3 chr3D.!!$R2 5313

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
85 86 0.232303 CCAAAGAACGTGTCGTGCTC 59.768 55.000 3.21 0.0 45.96 4.26 F
365 807 0.247537 GCGATCGGCAAGGTTTTACG 60.248 55.000 18.30 0.0 42.87 3.18 F
1748 2233 0.169009 GCGACAAACAGGAGCCAATC 59.831 55.000 0.00 0.0 0.00 2.67 F
2884 3369 1.468520 GTGTGATCGGGTGGAAATGTG 59.531 52.381 0.00 0.0 0.00 3.21 F
4798 5806 0.550914 ACACAGCCCAGTTTCCTTGA 59.449 50.000 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1748 2233 0.242825 TGTCCGAGGTAAGTGAAGCG 59.757 55.000 0.0 0.0 0.00 4.68 R
2114 2599 3.246572 TGGGACTGGGAGGTAAAGGAATA 60.247 47.826 0.0 0.0 0.00 1.75 R
3040 3531 2.018355 TGCTAGGGTGTAGTTCCACA 57.982 50.000 0.0 0.0 37.06 4.17 R
4800 5808 1.202348 TGACGTGTGCCTAGTGATCAG 59.798 52.381 0.0 0.0 0.00 2.90 R
5727 6776 0.035458 CCTCTCCCAGCAAACTCGTT 59.965 55.000 0.0 0.0 0.00 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.143183 GCTTCATCCCGGCGAACTA 59.857 57.895 9.30 0.00 0.00 2.24
57 58 4.054671 GGCGAACTAATCCTCAAGATCAG 58.945 47.826 0.00 0.00 32.47 2.90
64 65 2.370445 CCTCAAGATCAGGCCCCGT 61.370 63.158 0.00 0.00 0.00 5.28
76 77 2.428622 CCCCGTCCCAAAGAACGT 59.571 61.111 0.00 0.00 0.00 3.99
78 79 1.227734 CCCGTCCCAAAGAACGTGT 60.228 57.895 0.00 0.00 0.00 4.49
79 80 1.226030 CCCGTCCCAAAGAACGTGTC 61.226 60.000 0.00 0.00 0.00 3.67
85 86 0.232303 CCAAAGAACGTGTCGTGCTC 59.768 55.000 3.21 0.00 45.96 4.26
86 87 0.927537 CAAAGAACGTGTCGTGCTCA 59.072 50.000 3.21 0.00 45.96 4.26
87 88 1.526887 CAAAGAACGTGTCGTGCTCAT 59.473 47.619 3.21 0.00 45.96 2.90
88 89 1.419374 AAGAACGTGTCGTGCTCATC 58.581 50.000 3.21 0.00 45.96 2.92
89 90 0.598562 AGAACGTGTCGTGCTCATCT 59.401 50.000 0.00 0.00 42.77 2.90
90 91 0.985549 GAACGTGTCGTGCTCATCTC 59.014 55.000 0.00 0.00 39.99 2.75
91 92 0.388649 AACGTGTCGTGCTCATCTCC 60.389 55.000 0.00 0.00 39.99 3.71
92 93 1.517257 CGTGTCGTGCTCATCTCCC 60.517 63.158 0.00 0.00 0.00 4.30
93 94 1.153549 GTGTCGTGCTCATCTCCCC 60.154 63.158 0.00 0.00 0.00 4.81
94 95 2.359169 TGTCGTGCTCATCTCCCCC 61.359 63.158 0.00 0.00 0.00 5.40
113 114 2.190578 CCCCCTCAGATGCGTTCC 59.809 66.667 0.00 0.00 0.00 3.62
114 115 2.370445 CCCCCTCAGATGCGTTCCT 61.370 63.158 0.00 0.00 0.00 3.36
115 116 1.604378 CCCCTCAGATGCGTTCCTT 59.396 57.895 0.00 0.00 0.00 3.36
116 117 0.462759 CCCCTCAGATGCGTTCCTTC 60.463 60.000 0.00 0.00 0.00 3.46
117 118 0.539051 CCCTCAGATGCGTTCCTTCT 59.461 55.000 0.00 0.00 0.00 2.85
118 119 1.065854 CCCTCAGATGCGTTCCTTCTT 60.066 52.381 0.00 0.00 0.00 2.52
119 120 2.168521 CCCTCAGATGCGTTCCTTCTTA 59.831 50.000 0.00 0.00 0.00 2.10
120 121 3.190874 CCTCAGATGCGTTCCTTCTTAC 58.809 50.000 0.00 0.00 0.00 2.34
121 122 3.190874 CTCAGATGCGTTCCTTCTTACC 58.809 50.000 0.00 0.00 0.00 2.85
122 123 2.832129 TCAGATGCGTTCCTTCTTACCT 59.168 45.455 0.00 0.00 0.00 3.08
123 124 2.932614 CAGATGCGTTCCTTCTTACCTG 59.067 50.000 0.00 0.00 0.00 4.00
124 125 1.666189 GATGCGTTCCTTCTTACCTGC 59.334 52.381 0.00 0.00 0.00 4.85
125 126 0.669318 TGCGTTCCTTCTTACCTGCG 60.669 55.000 0.00 0.00 0.00 5.18
180 622 2.158769 TGACTTGGCTGCTCTTTTCTCA 60.159 45.455 0.00 0.00 0.00 3.27
189 631 3.744660 TGCTCTTTTCTCAAGAACCCTC 58.255 45.455 0.00 0.00 33.13 4.30
209 651 1.213678 CAGGGGCTTCAGATCCAATCA 59.786 52.381 0.00 0.00 0.00 2.57
228 670 1.392534 CCTCCCCTACACCCAGACT 59.607 63.158 0.00 0.00 0.00 3.24
236 678 2.165845 CCTACACCCAGACTTACTTCCG 59.834 54.545 0.00 0.00 0.00 4.30
257 699 1.529309 GCCATCTCTTCCCCCTGAC 59.471 63.158 0.00 0.00 0.00 3.51
285 727 2.154462 CTTCTGTTGCCTTTGATCCGT 58.846 47.619 0.00 0.00 0.00 4.69
326 768 4.011023 CGACGGGAATAGGTAGATCTCAT 58.989 47.826 0.00 0.00 0.00 2.90
333 775 2.373335 AGGTAGATCTCATCGGCAGT 57.627 50.000 0.00 0.00 0.00 4.40
365 807 0.247537 GCGATCGGCAAGGTTTTACG 60.248 55.000 18.30 0.00 42.87 3.18
368 810 2.070783 GATCGGCAAGGTTTTACGTGA 58.929 47.619 0.00 0.00 0.00 4.35
443 887 3.057104 TGCAATTGCTTCAACAGATCAGG 60.057 43.478 29.37 0.00 42.66 3.86
444 888 3.192001 GCAATTGCTTCAACAGATCAGGA 59.808 43.478 23.21 0.00 38.21 3.86
496 949 1.942776 CCCCCAAGAAAGCTCCATTT 58.057 50.000 0.00 0.00 0.00 2.32
581 1038 5.256474 CCATCAACACTCCCTTTTACATCT 58.744 41.667 0.00 0.00 0.00 2.90
585 1042 4.373156 ACACTCCCTTTTACATCTTGCT 57.627 40.909 0.00 0.00 0.00 3.91
594 1051 6.295292 CCCTTTTACATCTTGCTTTTTAGGCT 60.295 38.462 0.00 0.00 0.00 4.58
653 1110 3.884895 ACGCTCATGGAAATACAATGGA 58.115 40.909 0.00 0.00 0.00 3.41
741 1200 2.553172 CCGTGTTTTCCCCGTGAAATTA 59.447 45.455 0.00 0.00 42.38 1.40
789 1250 4.609113 CGTCCGCATATGCATGTTCTTTAG 60.609 45.833 26.52 6.71 42.21 1.85
802 1263 7.219917 TGCATGTTCTTTAGAAAACAAACTTCG 59.780 33.333 0.00 0.00 38.74 3.79
961 1443 2.606519 CCCACCGTCCTCTTCCCA 60.607 66.667 0.00 0.00 0.00 4.37
962 1444 2.663196 CCACCGTCCTCTTCCCAC 59.337 66.667 0.00 0.00 0.00 4.61
963 1445 2.663196 CACCGTCCTCTTCCCACC 59.337 66.667 0.00 0.00 0.00 4.61
964 1446 2.606826 ACCGTCCTCTTCCCACCC 60.607 66.667 0.00 0.00 0.00 4.61
965 1447 3.771160 CCGTCCTCTTCCCACCCG 61.771 72.222 0.00 0.00 0.00 5.28
966 1448 4.452733 CGTCCTCTTCCCACCCGC 62.453 72.222 0.00 0.00 0.00 6.13
967 1449 4.452733 GTCCTCTTCCCACCCGCG 62.453 72.222 0.00 0.00 0.00 6.46
992 1474 2.243264 GCTGCTGTCAGATAGCGCC 61.243 63.158 18.56 8.33 44.01 6.53
1145 1627 1.656092 ATCCCCTCCTCCTCGTGCTA 61.656 60.000 0.00 0.00 0.00 3.49
1236 1718 8.718734 GTGAGTTTTAATTAGTTACTGGTGGAG 58.281 37.037 0.00 0.00 0.00 3.86
1238 1720 6.657966 AGTTTTAATTAGTTACTGGTGGAGGC 59.342 38.462 0.00 0.00 0.00 4.70
1382 1865 8.067751 ACCTCTTAAATTTTCTTAGAATGGGC 57.932 34.615 0.00 0.00 0.00 5.36
1444 1927 2.286872 CTTCTGCGATTCTGGATGCTT 58.713 47.619 0.00 0.00 0.00 3.91
1486 1969 5.701290 GTGAATTGTCTGGTTTAGCAGTACT 59.299 40.000 8.61 0.00 0.00 2.73
1587 2071 4.395625 ACTTGGGCACTCTAAAAGGTAAC 58.604 43.478 0.00 0.00 0.00 2.50
1644 2129 4.010667 ACACATAGCCCTTTACGTTGAA 57.989 40.909 0.00 0.00 0.00 2.69
1748 2233 0.169009 GCGACAAACAGGAGCCAATC 59.831 55.000 0.00 0.00 0.00 2.67
1793 2278 4.500035 CCGGTCTTAGAAGATACCAAGAGC 60.500 50.000 0.00 0.00 40.43 4.09
2250 2735 8.588290 AAAGGCATGTAAGTAATTGGTGATTA 57.412 30.769 0.00 0.00 0.00 1.75
2302 2787 4.079269 TGATCATCCCCCATACACATTGTT 60.079 41.667 0.00 0.00 0.00 2.83
2421 2906 4.646040 TCATTGGGATGAAAACTAGCCATG 59.354 41.667 0.00 0.00 39.29 3.66
2884 3369 1.468520 GTGTGATCGGGTGGAAATGTG 59.531 52.381 0.00 0.00 0.00 3.21
3001 3489 2.250031 TGTGGAGCCATTTGCAGAATT 58.750 42.857 0.00 0.00 44.83 2.17
3051 3542 6.419791 CCCATTTATAGGTTGTGGAACTACA 58.580 40.000 0.00 0.00 44.49 2.74
3198 3689 9.091220 ACTAAAACATGTCTATATACTCCCTCC 57.909 37.037 0.00 0.00 0.00 4.30
3216 3707 4.174009 CCTCCGTTCCATAATATAGTGCG 58.826 47.826 0.00 0.00 0.00 5.34
3223 3714 8.350722 CCGTTCCATAATATAGTGCGTATAGAT 58.649 37.037 0.00 0.00 0.00 1.98
3254 3745 7.634942 GAAAAGTCAAACTTTGCAATTTTCG 57.365 32.000 12.32 6.22 46.78 3.46
3429 3920 9.646336 CTTTTCAAAACATATATACGCACTACC 57.354 33.333 0.00 0.00 0.00 3.18
3529 4021 3.785887 ACCCCTGCTTTCCTATCAATACA 59.214 43.478 0.00 0.00 0.00 2.29
3533 4025 6.324770 CCCCTGCTTTCCTATCAATACAATTT 59.675 38.462 0.00 0.00 0.00 1.82
3569 4061 5.251932 TGGTTGGGTATCCTTATTCACTTCA 59.748 40.000 0.00 0.00 0.00 3.02
3738 4232 5.010112 TGAGAAATGAAGCTCCGATACTAGG 59.990 44.000 0.00 0.00 0.00 3.02
3790 4284 7.829725 TCTGACAAATATGAAAACAATCTGGG 58.170 34.615 0.00 0.00 0.00 4.45
4649 5657 7.068702 AGGCAAATAATGTCCTGATATTTCCA 58.931 34.615 0.00 0.00 35.21 3.53
4798 5806 0.550914 ACACAGCCCAGTTTCCTTGA 59.449 50.000 0.00 0.00 0.00 3.02
4800 5808 1.338020 CACAGCCCAGTTTCCTTGAAC 59.662 52.381 0.00 0.00 0.00 3.18
4828 5836 2.831685 AGGCACACGTCAGTATTTGA 57.168 45.000 0.00 0.00 0.00 2.69
4920 5935 2.771943 AGCTTAGTAATGCCTGGCTGTA 59.228 45.455 21.03 8.95 0.00 2.74
4977 5995 6.099845 ACCATACACTATAGCTGCCTACTTTT 59.900 38.462 0.00 0.00 0.00 2.27
5404 6437 1.781786 TGATCTACCTGGAGCCAGTC 58.218 55.000 14.97 6.48 42.15 3.51
5466 6499 1.538512 GCTTCAGCTGATGAACTGCAA 59.461 47.619 28.50 6.31 43.09 4.08
5620 6669 9.010029 TCAACTAATTTTGACTGAAGTTATCCC 57.990 33.333 0.00 0.00 30.29 3.85
5666 6715 2.951642 CAACAGTCACCACTCCAATTGT 59.048 45.455 4.43 0.00 0.00 2.71
5726 6775 7.022055 TGTTTATGGGTAATGTTATTCAGCG 57.978 36.000 0.00 0.00 0.00 5.18
5727 6776 6.824196 TGTTTATGGGTAATGTTATTCAGCGA 59.176 34.615 0.00 0.00 0.00 4.93
5728 6777 7.337184 TGTTTATGGGTAATGTTATTCAGCGAA 59.663 33.333 0.00 0.00 0.00 4.70
5729 6778 5.751243 ATGGGTAATGTTATTCAGCGAAC 57.249 39.130 0.00 0.00 0.00 3.95
5730 6779 3.619483 TGGGTAATGTTATTCAGCGAACG 59.381 43.478 0.00 0.00 0.00 3.95
5731 6780 3.866910 GGGTAATGTTATTCAGCGAACGA 59.133 43.478 0.00 0.00 0.00 3.85
5746 6795 0.035458 AACGAGTTTGCTGGGAGAGG 59.965 55.000 0.00 0.00 0.00 3.69
5751 6800 0.329596 GTTTGCTGGGAGAGGATGGT 59.670 55.000 0.00 0.00 0.00 3.55
5752 6801 0.329261 TTTGCTGGGAGAGGATGGTG 59.671 55.000 0.00 0.00 0.00 4.17
5787 6836 8.449397 GTTTTTCATGGCAATTATATTGTGCAA 58.551 29.630 0.00 0.00 40.12 4.08
5794 6843 5.049954 GGCAATTATATTGTGCAAAGCATGG 60.050 40.000 0.00 0.00 41.91 3.66
5811 6860 4.039488 AGCATGGCAATTTCTTCAAGTGAA 59.961 37.500 0.00 0.00 31.74 3.18
5814 6863 5.336150 TGGCAATTTCTTCAAGTGAACAA 57.664 34.783 0.00 0.00 31.74 2.83
5835 6884 9.366216 GAACAAGACTTTTACAACAAATCCTTT 57.634 29.630 0.00 0.00 0.00 3.11
5862 6911 8.885494 TTTGCTAAAAATTGCTATGTGTTTCT 57.115 26.923 0.00 0.00 0.00 2.52
5863 6912 7.872163 TGCTAAAAATTGCTATGTGTTTCTG 57.128 32.000 0.00 0.00 0.00 3.02
5864 6913 7.656412 TGCTAAAAATTGCTATGTGTTTCTGA 58.344 30.769 0.00 0.00 0.00 3.27
5866 6915 8.427774 GCTAAAAATTGCTATGTGTTTCTGAAC 58.572 33.333 0.00 0.00 36.29 3.18
5867 6916 6.991485 AAAATTGCTATGTGTTTCTGAACG 57.009 33.333 0.00 0.00 38.65 3.95
5870 6919 5.493133 TTGCTATGTGTTTCTGAACGTTT 57.507 34.783 0.46 0.00 38.65 3.60
5871 6920 4.843147 TGCTATGTGTTTCTGAACGTTTG 58.157 39.130 0.46 0.00 38.65 2.93
5872 6921 3.664025 GCTATGTGTTTCTGAACGTTTGC 59.336 43.478 0.46 0.00 38.65 3.68
5873 6922 4.554723 GCTATGTGTTTCTGAACGTTTGCT 60.555 41.667 0.46 0.00 38.65 3.91
5874 6923 3.129852 TGTGTTTCTGAACGTTTGCTG 57.870 42.857 0.46 0.00 38.65 4.41
5875 6924 2.744741 TGTGTTTCTGAACGTTTGCTGA 59.255 40.909 0.46 0.00 38.65 4.26
5876 6925 3.189495 TGTGTTTCTGAACGTTTGCTGAA 59.811 39.130 0.46 3.76 38.65 3.02
5877 6926 4.162812 GTGTTTCTGAACGTTTGCTGAAA 58.837 39.130 14.13 14.13 38.65 2.69
5878 6927 4.619336 GTGTTTCTGAACGTTTGCTGAAAA 59.381 37.500 17.62 9.75 38.65 2.29
5879 6928 4.856487 TGTTTCTGAACGTTTGCTGAAAAG 59.144 37.500 17.62 2.82 38.65 2.27
5880 6929 3.691049 TCTGAACGTTTGCTGAAAAGG 57.309 42.857 0.46 0.00 39.14 3.11
5881 6930 3.013921 TCTGAACGTTTGCTGAAAAGGT 58.986 40.909 0.46 0.67 46.18 3.50
5882 6931 3.108144 CTGAACGTTTGCTGAAAAGGTG 58.892 45.455 0.46 0.00 44.08 4.00
5883 6932 2.750166 TGAACGTTTGCTGAAAAGGTGA 59.250 40.909 0.46 0.00 44.08 4.02
5884 6933 3.181501 TGAACGTTTGCTGAAAAGGTGAG 60.182 43.478 0.46 0.00 44.08 3.51
5885 6934 2.365582 ACGTTTGCTGAAAAGGTGAGT 58.634 42.857 5.69 0.00 43.42 3.41
5886 6935 2.097466 ACGTTTGCTGAAAAGGTGAGTG 59.903 45.455 5.69 0.00 43.42 3.51
5887 6936 2.463876 GTTTGCTGAAAAGGTGAGTGC 58.536 47.619 0.00 0.00 0.00 4.40
5888 6937 2.057137 TTGCTGAAAAGGTGAGTGCT 57.943 45.000 0.00 0.00 0.00 4.40
5889 6938 1.311859 TGCTGAAAAGGTGAGTGCTG 58.688 50.000 0.00 0.00 0.00 4.41
5890 6939 1.312815 GCTGAAAAGGTGAGTGCTGT 58.687 50.000 0.00 0.00 0.00 4.40
5891 6940 1.265365 GCTGAAAAGGTGAGTGCTGTC 59.735 52.381 0.00 0.00 0.00 3.51
5892 6941 2.564771 CTGAAAAGGTGAGTGCTGTCA 58.435 47.619 0.00 0.00 0.00 3.58
5893 6942 2.288666 TGAAAAGGTGAGTGCTGTCAC 58.711 47.619 9.75 9.75 45.30 3.67
5898 6947 3.612517 GTGAGTGCTGTCACCATGA 57.387 52.632 7.56 0.00 44.16 3.07
5917 6966 3.979948 TGACTTCCACAACGTTATTCGA 58.020 40.909 0.00 0.00 42.86 3.71
5950 6999 2.099405 TCGCAGATGTCATGTCTACCA 58.901 47.619 0.00 0.00 0.00 3.25
5952 7001 2.800985 CGCAGATGTCATGTCTACCAGG 60.801 54.545 0.00 0.00 0.00 4.45
5964 7013 1.156736 CTACCAGGGAACGTTTGCTG 58.843 55.000 0.46 0.00 0.00 4.41
5984 7033 4.009675 CTGGCTATTGCAGTCCTTGTTTA 58.990 43.478 0.66 0.00 41.91 2.01
5985 7034 4.599041 TGGCTATTGCAGTCCTTGTTTAT 58.401 39.130 0.66 0.00 41.91 1.40
5995 7044 5.065218 GCAGTCCTTGTTTATTCATCATCGT 59.935 40.000 0.00 0.00 0.00 3.73
6015 7064 3.749088 CGTTAAGCCAACACAATGGAGTA 59.251 43.478 0.00 0.00 43.54 2.59
6192 7241 1.368374 CTTCCCACCCCACCTTCTAA 58.632 55.000 0.00 0.00 0.00 2.10
6204 7253 5.246307 CCCACCTTCTAAGTTTCCAGTTAG 58.754 45.833 0.00 0.00 37.29 2.34
6205 7254 5.012768 CCCACCTTCTAAGTTTCCAGTTAGA 59.987 44.000 0.00 0.00 41.42 2.10
6206 7255 6.166982 CCACCTTCTAAGTTTCCAGTTAGAG 58.833 44.000 0.96 0.00 43.13 2.43
6207 7256 6.166982 CACCTTCTAAGTTTCCAGTTAGAGG 58.833 44.000 10.61 10.61 43.13 3.69
6208 7257 6.014499 CACCTTCTAAGTTTCCAGTTAGAGGA 60.014 42.308 15.22 0.00 43.13 3.71
6209 7258 6.014413 ACCTTCTAAGTTTCCAGTTAGAGGAC 60.014 42.308 15.22 0.00 43.13 3.85
6210 7259 5.640189 TCTAAGTTTCCAGTTAGAGGACG 57.360 43.478 0.00 0.00 39.22 4.79
6211 7260 3.679824 AAGTTTCCAGTTAGAGGACGG 57.320 47.619 0.00 0.00 34.19 4.79
6212 7261 1.900486 AGTTTCCAGTTAGAGGACGGG 59.100 52.381 0.00 0.00 36.38 5.28
6213 7262 1.066358 GTTTCCAGTTAGAGGACGGGG 60.066 57.143 0.00 0.00 35.83 5.73
6214 7263 1.262640 TTCCAGTTAGAGGACGGGGC 61.263 60.000 0.00 0.00 35.83 5.80
6215 7264 2.494918 CAGTTAGAGGACGGGGCG 59.505 66.667 0.00 0.00 0.00 6.13
6216 7265 2.036890 AGTTAGAGGACGGGGCGT 59.963 61.111 0.00 0.00 45.10 5.68
6245 7294 3.060615 CTGGGCAGCTGAGGTTGC 61.061 66.667 20.43 0.23 46.58 4.17
6246 7295 3.564345 CTGGGCAGCTGAGGTTGCT 62.564 63.158 20.43 0.00 46.51 3.91
6251 7300 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
6252 7301 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
6253 7302 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
6254 7303 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
6255 7304 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
6256 7305 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
6265 7314 3.636231 CCAGCCCACCCGAGTTCA 61.636 66.667 0.00 0.00 0.00 3.18
6266 7315 2.429930 CAGCCCACCCGAGTTCAA 59.570 61.111 0.00 0.00 0.00 2.69
6267 7316 1.672356 CAGCCCACCCGAGTTCAAG 60.672 63.158 0.00 0.00 0.00 3.02
6268 7317 2.147387 AGCCCACCCGAGTTCAAGT 61.147 57.895 0.00 0.00 0.00 3.16
6269 7318 1.671379 GCCCACCCGAGTTCAAGTC 60.671 63.158 0.00 0.00 0.00 3.01
6270 7319 2.058675 CCCACCCGAGTTCAAGTCT 58.941 57.895 0.00 0.00 0.00 3.24
6271 7320 0.037232 CCCACCCGAGTTCAAGTCTC 60.037 60.000 0.00 0.00 0.00 3.36
6278 7327 1.433534 GAGTTCAAGTCTCGGCTTGG 58.566 55.000 10.97 0.00 44.26 3.61
6279 7328 1.000955 GAGTTCAAGTCTCGGCTTGGA 59.999 52.381 10.97 0.00 44.26 3.53
6280 7329 1.625818 AGTTCAAGTCTCGGCTTGGAT 59.374 47.619 10.97 0.00 44.26 3.41
6281 7330 1.734465 GTTCAAGTCTCGGCTTGGATG 59.266 52.381 10.97 0.00 44.26 3.51
6282 7331 0.976641 TCAAGTCTCGGCTTGGATGT 59.023 50.000 10.97 0.00 44.26 3.06
6283 7332 1.081892 CAAGTCTCGGCTTGGATGTG 58.918 55.000 3.40 0.00 41.41 3.21
6284 7333 0.687354 AAGTCTCGGCTTGGATGTGT 59.313 50.000 0.00 0.00 0.00 3.72
6285 7334 0.036952 AGTCTCGGCTTGGATGTGTG 60.037 55.000 0.00 0.00 0.00 3.82
6286 7335 1.021390 GTCTCGGCTTGGATGTGTGG 61.021 60.000 0.00 0.00 0.00 4.17
6287 7336 1.003355 CTCGGCTTGGATGTGTGGT 60.003 57.895 0.00 0.00 0.00 4.16
6288 7337 1.300971 CTCGGCTTGGATGTGTGGTG 61.301 60.000 0.00 0.00 0.00 4.17
6289 7338 2.964978 GGCTTGGATGTGTGGTGC 59.035 61.111 0.00 0.00 0.00 5.01
6290 7339 1.604593 GGCTTGGATGTGTGGTGCT 60.605 57.895 0.00 0.00 0.00 4.40
6291 7340 1.589716 GGCTTGGATGTGTGGTGCTC 61.590 60.000 0.00 0.00 0.00 4.26
6292 7341 1.915614 GCTTGGATGTGTGGTGCTCG 61.916 60.000 0.00 0.00 0.00 5.03
6293 7342 1.915614 CTTGGATGTGTGGTGCTCGC 61.916 60.000 0.00 0.00 0.00 5.03
6294 7343 3.490759 GGATGTGTGGTGCTCGCG 61.491 66.667 0.00 0.00 0.00 5.87
6295 7344 3.490759 GATGTGTGGTGCTCGCGG 61.491 66.667 6.13 0.00 0.00 6.46
6296 7345 3.932580 GATGTGTGGTGCTCGCGGA 62.933 63.158 6.13 0.00 0.00 5.54
6297 7346 3.939837 ATGTGTGGTGCTCGCGGAG 62.940 63.158 6.13 3.47 0.00 4.63
6298 7347 4.664677 GTGTGGTGCTCGCGGAGT 62.665 66.667 6.13 0.00 31.39 3.85
6299 7348 3.923864 TGTGGTGCTCGCGGAGTT 61.924 61.111 6.13 0.00 31.39 3.01
6300 7349 2.665185 GTGGTGCTCGCGGAGTTT 60.665 61.111 6.13 0.00 31.39 2.66
6301 7350 2.357034 TGGTGCTCGCGGAGTTTC 60.357 61.111 6.13 0.00 31.39 2.78
6302 7351 2.048127 GGTGCTCGCGGAGTTTCT 60.048 61.111 6.13 0.00 31.39 2.52
6303 7352 2.095252 GGTGCTCGCGGAGTTTCTC 61.095 63.158 6.13 0.00 31.39 2.87
6304 7353 2.095252 GTGCTCGCGGAGTTTCTCC 61.095 63.158 6.13 5.79 46.44 3.71
6319 7368 8.691661 GGAGTTTCTCCTATATAAAAATGCCA 57.308 34.615 8.38 0.00 46.41 4.92
6320 7369 9.131791 GGAGTTTCTCCTATATAAAAATGCCAA 57.868 33.333 8.38 0.00 46.41 4.52
6321 7370 9.952188 GAGTTTCTCCTATATAAAAATGCCAAC 57.048 33.333 0.00 0.00 0.00 3.77
6322 7371 8.621286 AGTTTCTCCTATATAAAAATGCCAACG 58.379 33.333 0.00 0.00 0.00 4.10
6323 7372 8.617809 GTTTCTCCTATATAAAAATGCCAACGA 58.382 33.333 0.00 0.00 0.00 3.85
6324 7373 7.962964 TCTCCTATATAAAAATGCCAACGAG 57.037 36.000 0.00 0.00 0.00 4.18
6325 7374 7.506114 TCTCCTATATAAAAATGCCAACGAGT 58.494 34.615 0.00 0.00 0.00 4.18
6326 7375 8.644216 TCTCCTATATAAAAATGCCAACGAGTA 58.356 33.333 0.00 0.00 0.00 2.59
6327 7376 9.436957 CTCCTATATAAAAATGCCAACGAGTAT 57.563 33.333 0.00 0.00 0.00 2.12
6328 7377 9.787435 TCCTATATAAAAATGCCAACGAGTATT 57.213 29.630 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.181329 TGAAGCTACATGGGAAGGAAGA 58.819 45.455 0.00 0.00 0.00 2.87
43 44 0.849417 GGGGCCTGATCTTGAGGATT 59.151 55.000 0.84 0.00 34.33 3.01
57 58 2.675423 GTTCTTTGGGACGGGGCC 60.675 66.667 0.00 0.00 0.00 5.80
64 65 1.155424 GCACGACACGTTCTTTGGGA 61.155 55.000 0.00 0.00 38.32 4.37
76 77 2.359169 GGGGGAGATGAGCACGACA 61.359 63.158 0.00 0.00 0.00 4.35
96 97 1.915078 AAGGAACGCATCTGAGGGGG 61.915 60.000 11.06 3.33 0.00 5.40
97 98 0.462759 GAAGGAACGCATCTGAGGGG 60.463 60.000 4.77 4.77 0.00 4.79
98 99 0.539051 AGAAGGAACGCATCTGAGGG 59.461 55.000 0.00 0.00 0.00 4.30
99 100 2.393271 AAGAAGGAACGCATCTGAGG 57.607 50.000 0.00 0.00 0.00 3.86
100 101 3.118956 AGGTAAGAAGGAACGCATCTGAG 60.119 47.826 0.00 0.00 0.00 3.35
101 102 2.832129 AGGTAAGAAGGAACGCATCTGA 59.168 45.455 0.00 0.00 0.00 3.27
102 103 2.932614 CAGGTAAGAAGGAACGCATCTG 59.067 50.000 0.00 0.00 0.00 2.90
103 104 2.678190 GCAGGTAAGAAGGAACGCATCT 60.678 50.000 0.00 0.00 0.00 2.90
104 105 1.666189 GCAGGTAAGAAGGAACGCATC 59.334 52.381 0.00 0.00 0.00 3.91
105 106 1.739067 GCAGGTAAGAAGGAACGCAT 58.261 50.000 0.00 0.00 0.00 4.73
106 107 0.669318 CGCAGGTAAGAAGGAACGCA 60.669 55.000 0.00 0.00 0.00 5.24
107 108 0.389426 TCGCAGGTAAGAAGGAACGC 60.389 55.000 0.00 0.00 0.00 4.84
108 109 1.630148 CTCGCAGGTAAGAAGGAACG 58.370 55.000 0.00 0.00 0.00 3.95
109 110 1.066787 AGCTCGCAGGTAAGAAGGAAC 60.067 52.381 0.00 0.00 0.00 3.62
110 111 1.267121 AGCTCGCAGGTAAGAAGGAA 58.733 50.000 0.00 0.00 0.00 3.36
111 112 2.139323 TAGCTCGCAGGTAAGAAGGA 57.861 50.000 0.00 0.00 0.00 3.36
112 113 2.362397 TCATAGCTCGCAGGTAAGAAGG 59.638 50.000 0.00 0.00 31.35 3.46
113 114 3.067461 AGTCATAGCTCGCAGGTAAGAAG 59.933 47.826 0.00 0.00 29.39 2.85
114 115 3.024547 AGTCATAGCTCGCAGGTAAGAA 58.975 45.455 0.00 0.00 29.39 2.52
115 116 2.619177 GAGTCATAGCTCGCAGGTAAGA 59.381 50.000 0.00 0.00 31.35 2.10
116 117 2.287909 GGAGTCATAGCTCGCAGGTAAG 60.288 54.545 0.00 0.00 36.41 2.34
117 118 1.681793 GGAGTCATAGCTCGCAGGTAA 59.318 52.381 0.00 0.00 36.41 2.85
118 119 1.319541 GGAGTCATAGCTCGCAGGTA 58.680 55.000 0.00 0.00 36.41 3.08
119 120 1.395826 GGGAGTCATAGCTCGCAGGT 61.396 60.000 0.00 0.00 44.62 4.00
120 121 1.365633 GGGAGTCATAGCTCGCAGG 59.634 63.158 0.00 0.00 44.62 4.85
121 122 1.365633 GGGGAGTCATAGCTCGCAG 59.634 63.158 11.24 0.00 46.29 5.18
122 123 2.134287 GGGGGAGTCATAGCTCGCA 61.134 63.158 11.24 0.00 46.29 5.10
123 124 2.737830 GGGGGAGTCATAGCTCGC 59.262 66.667 0.00 0.00 44.54 5.03
154 595 2.875094 AGAGCAGCCAAGTCAATTCT 57.125 45.000 0.00 0.00 0.00 2.40
189 631 1.213678 TGATTGGATCTGAAGCCCCTG 59.786 52.381 0.00 0.00 0.00 4.45
193 635 2.570135 GAGGTGATTGGATCTGAAGCC 58.430 52.381 0.00 0.00 0.00 4.35
209 651 1.080538 GTCTGGGTGTAGGGGAGGT 59.919 63.158 0.00 0.00 0.00 3.85
228 670 1.143183 GAGATGGCGGCGGAAGTAA 59.857 57.895 9.78 0.00 0.00 2.24
236 678 4.570874 GGGGGAAGAGATGGCGGC 62.571 72.222 0.00 0.00 0.00 6.53
257 699 2.677875 GCAACAGAAGCCAGGGGG 60.678 66.667 0.00 0.00 37.18 5.40
275 717 1.530441 CGCTTGCATGACGGATCAAAG 60.530 52.381 3.33 0.00 38.69 2.77
285 727 2.555782 GCACGTTCGCTTGCATGA 59.444 55.556 3.33 0.00 41.38 3.07
326 768 2.577059 GTTCCATCCGACTGCCGA 59.423 61.111 0.00 0.00 41.76 5.54
386 830 2.960688 GCCTCGCTCACCCTTCCTT 61.961 63.158 0.00 0.00 0.00 3.36
443 887 5.059833 GGTTATGGACAGAGTGATGGATTC 58.940 45.833 0.00 0.00 0.00 2.52
444 888 4.474651 TGGTTATGGACAGAGTGATGGATT 59.525 41.667 0.00 0.00 0.00 3.01
496 949 3.491267 CGGCGGCAATTTTTCACTAAAAA 59.509 39.130 10.53 0.00 45.89 1.94
525 978 0.525311 GAGCAAAGGAAGAGCTTGCC 59.475 55.000 0.76 0.00 45.23 4.52
526 979 0.525311 GGAGCAAAGGAAGAGCTTGC 59.475 55.000 0.00 0.00 44.61 4.01
581 1038 6.150474 AGAGCGTATTTTAGCCTAAAAAGCAA 59.850 34.615 24.05 8.41 40.62 3.91
627 1084 6.404184 CCATTGTATTTCCATGAGCGTTGTTA 60.404 38.462 0.00 0.00 0.00 2.41
631 1088 4.096382 GTCCATTGTATTTCCATGAGCGTT 59.904 41.667 0.00 0.00 0.00 4.84
632 1089 3.627577 GTCCATTGTATTTCCATGAGCGT 59.372 43.478 0.00 0.00 0.00 5.07
633 1090 3.879295 AGTCCATTGTATTTCCATGAGCG 59.121 43.478 0.00 0.00 0.00 5.03
829 1303 4.142293 GCCCAGATGTCAGATTTTTCCTTC 60.142 45.833 0.00 0.00 0.00 3.46
832 1306 2.428530 GGCCCAGATGTCAGATTTTTCC 59.571 50.000 0.00 0.00 0.00 3.13
967 1449 2.833604 ATCTGACAGCAGCAAGGGGC 62.834 60.000 0.00 0.00 42.01 5.80
968 1450 0.543277 TATCTGACAGCAGCAAGGGG 59.457 55.000 0.00 0.00 42.01 4.79
969 1451 1.950828 CTATCTGACAGCAGCAAGGG 58.049 55.000 0.00 0.00 42.01 3.95
970 1452 1.297664 GCTATCTGACAGCAGCAAGG 58.702 55.000 18.64 0.00 42.01 3.61
981 1463 2.782222 GGTCCGTGGCGCTATCTGA 61.782 63.158 7.64 0.00 0.00 3.27
1107 1589 3.394606 GGATTGCCTTGGGATAGGAGTAA 59.605 47.826 0.00 0.00 37.50 2.24
1109 1591 1.777272 GGATTGCCTTGGGATAGGAGT 59.223 52.381 0.00 0.00 37.50 3.85
1236 1718 1.752833 CATACGGGGGACTAAGGCC 59.247 63.158 0.00 0.00 0.00 5.19
1238 1720 2.025636 ATCCATACGGGGGACTAAGG 57.974 55.000 0.00 0.00 37.23 2.69
1372 1855 6.308015 AGTATGTAACTGTGCCCATTCTAA 57.692 37.500 0.00 0.00 36.93 2.10
1373 1856 5.950544 AGTATGTAACTGTGCCCATTCTA 57.049 39.130 0.00 0.00 36.93 2.10
1374 1857 4.844349 AGTATGTAACTGTGCCCATTCT 57.156 40.909 0.00 0.00 36.93 2.40
1375 1858 5.878116 TGTAAGTATGTAACTGTGCCCATTC 59.122 40.000 0.00 0.00 38.88 2.67
1376 1859 5.811190 TGTAAGTATGTAACTGTGCCCATT 58.189 37.500 0.00 0.00 38.88 3.16
1377 1860 5.429681 TGTAAGTATGTAACTGTGCCCAT 57.570 39.130 0.00 0.00 38.88 4.00
1378 1861 4.893829 TGTAAGTATGTAACTGTGCCCA 57.106 40.909 0.00 0.00 38.88 5.36
1379 1862 5.183228 ACATGTAAGTATGTAACTGTGCCC 58.817 41.667 0.00 0.00 39.40 5.36
1380 1863 6.257193 GGTACATGTAAGTATGTAACTGTGCC 59.743 42.308 7.25 0.00 44.20 5.01
1381 1864 7.230466 GGTACATGTAAGTATGTAACTGTGC 57.770 40.000 7.25 0.00 44.20 4.57
1444 1927 7.280428 ACAATTCACTGCAATTTTCATGTTCAA 59.720 29.630 0.00 0.00 0.00 2.69
1486 1969 4.212716 AGATAACCCTGTGTCATACGCTA 58.787 43.478 0.00 0.00 0.00 4.26
1644 2129 6.316890 ACTTGTTCTGTTAACACGTGGTAAAT 59.683 34.615 26.71 6.47 32.45 1.40
1748 2233 0.242825 TGTCCGAGGTAAGTGAAGCG 59.757 55.000 0.00 0.00 0.00 4.68
2114 2599 3.246572 TGGGACTGGGAGGTAAAGGAATA 60.247 47.826 0.00 0.00 0.00 1.75
2884 3369 8.942338 TGACTACCATCTTAACAATGACATAC 57.058 34.615 0.00 0.00 0.00 2.39
3001 3489 9.550406 GCCTACCATGTATGTATAACAACTTAA 57.450 33.333 0.00 0.00 0.00 1.85
3040 3531 2.018355 TGCTAGGGTGTAGTTCCACA 57.982 50.000 0.00 0.00 37.06 4.17
3051 3542 9.660544 AAAGATTATTTTCCATATTGCTAGGGT 57.339 29.630 0.00 0.00 30.63 4.34
3198 3689 9.731819 AATCTATACGCACTATATTATGGAACG 57.268 33.333 0.00 0.57 0.00 3.95
3346 3837 9.508567 GGAGAAAAACATTTACATCTAGAATGC 57.491 33.333 0.00 0.00 34.86 3.56
3363 3854 5.066968 TGACCAAGTTTGTGGAGAAAAAC 57.933 39.130 0.00 0.00 41.65 2.43
3429 3920 3.028850 TGTACTCCCTCCGTTCCATAAG 58.971 50.000 0.00 0.00 0.00 1.73
3696 4190 2.722629 CTCATGTTTGTGCAAGCTTTCG 59.277 45.455 0.00 0.00 0.00 3.46
3822 4317 3.469008 TTATACGGTCATGCCTTCCAG 57.531 47.619 4.92 0.00 34.25 3.86
4661 5669 8.830915 AACCATGTAATATATTGGGTTGTCAA 57.169 30.769 17.54 0.00 35.93 3.18
4798 5806 1.618837 ACGTGTGCCTAGTGATCAGTT 59.381 47.619 8.68 0.00 0.00 3.16
4800 5808 1.202348 TGACGTGTGCCTAGTGATCAG 59.798 52.381 0.00 0.00 0.00 2.90
4920 5935 5.163416 GGCAATCCTTTAATAACAGGCACAT 60.163 40.000 0.00 0.00 0.00 3.21
4977 5995 4.767409 ACAACAGCAGTAGTCATAGTCAGA 59.233 41.667 0.00 0.00 0.00 3.27
5404 6437 9.853555 CTAAAGATAACCTCTGCAGATGTATAG 57.146 37.037 22.73 14.20 33.29 1.31
5444 6477 1.538512 GCAGTTCATCAGCTGAAGCAA 59.461 47.619 22.50 10.74 44.44 3.91
5718 6767 2.683968 AGCAAACTCGTTCGCTGAATA 58.316 42.857 0.00 0.00 32.33 1.75
5720 6769 2.986311 AGCAAACTCGTTCGCTGAA 58.014 47.368 0.00 0.00 32.33 3.02
5721 6770 4.750460 AGCAAACTCGTTCGCTGA 57.250 50.000 0.00 0.00 32.33 4.26
5722 6771 4.806225 CAGCAAACTCGTTCGCTG 57.194 55.556 8.17 8.17 45.17 5.18
5724 6773 1.901650 CTCCCAGCAAACTCGTTCGC 61.902 60.000 0.00 0.00 0.00 4.70
5726 6775 1.433534 CTCTCCCAGCAAACTCGTTC 58.566 55.000 0.00 0.00 0.00 3.95
5727 6776 0.035458 CCTCTCCCAGCAAACTCGTT 59.965 55.000 0.00 0.00 0.00 3.85
5728 6777 0.832135 TCCTCTCCCAGCAAACTCGT 60.832 55.000 0.00 0.00 0.00 4.18
5729 6778 0.539051 ATCCTCTCCCAGCAAACTCG 59.461 55.000 0.00 0.00 0.00 4.18
5730 6779 1.407989 CCATCCTCTCCCAGCAAACTC 60.408 57.143 0.00 0.00 0.00 3.01
5731 6780 0.622665 CCATCCTCTCCCAGCAAACT 59.377 55.000 0.00 0.00 0.00 2.66
5746 6795 6.128849 CCATGAAAAACATTCGTTTCACCATC 60.129 38.462 0.00 0.00 44.65 3.51
5751 6800 4.686972 TGCCATGAAAAACATTCGTTTCA 58.313 34.783 0.00 1.68 44.65 2.69
5752 6801 5.649602 TTGCCATGAAAAACATTCGTTTC 57.350 34.783 0.00 0.00 44.65 2.78
5787 6836 4.039488 TCACTTGAAGAAATTGCCATGCTT 59.961 37.500 0.00 0.00 0.00 3.91
5794 6843 6.268566 AGTCTTGTTCACTTGAAGAAATTGC 58.731 36.000 0.00 0.00 36.96 3.56
5844 6893 6.503524 ACGTTCAGAAACACATAGCAATTTT 58.496 32.000 0.00 0.00 34.93 1.82
5853 6902 3.376859 TCAGCAAACGTTCAGAAACACAT 59.623 39.130 0.00 0.00 34.93 3.21
5857 6906 4.265320 CCTTTTCAGCAAACGTTCAGAAAC 59.735 41.667 0.00 0.00 0.00 2.78
5859 6908 3.442273 ACCTTTTCAGCAAACGTTCAGAA 59.558 39.130 0.00 0.89 0.00 3.02
5860 6909 3.013921 ACCTTTTCAGCAAACGTTCAGA 58.986 40.909 0.00 0.00 0.00 3.27
5861 6910 3.108144 CACCTTTTCAGCAAACGTTCAG 58.892 45.455 0.00 0.00 0.00 3.02
5862 6911 2.750166 TCACCTTTTCAGCAAACGTTCA 59.250 40.909 0.00 0.00 0.00 3.18
5863 6912 3.181500 ACTCACCTTTTCAGCAAACGTTC 60.181 43.478 0.00 0.00 0.00 3.95
5864 6913 2.752903 ACTCACCTTTTCAGCAAACGTT 59.247 40.909 0.00 0.00 0.00 3.99
5866 6915 2.719798 CACTCACCTTTTCAGCAAACG 58.280 47.619 0.00 0.00 0.00 3.60
5867 6916 2.099756 AGCACTCACCTTTTCAGCAAAC 59.900 45.455 0.00 0.00 0.00 2.93
5870 6919 1.311859 CAGCACTCACCTTTTCAGCA 58.688 50.000 0.00 0.00 0.00 4.41
5871 6920 1.265365 GACAGCACTCACCTTTTCAGC 59.735 52.381 0.00 0.00 0.00 4.26
5872 6921 2.289002 GTGACAGCACTCACCTTTTCAG 59.711 50.000 2.99 0.00 41.84 3.02
5873 6922 2.288666 GTGACAGCACTCACCTTTTCA 58.711 47.619 2.99 0.00 41.84 2.69
5890 6939 1.140052 ACGTTGTGGAAGTCATGGTGA 59.860 47.619 0.00 0.00 0.00 4.02
5891 6940 1.593196 ACGTTGTGGAAGTCATGGTG 58.407 50.000 0.00 0.00 0.00 4.17
5892 6941 2.341846 AACGTTGTGGAAGTCATGGT 57.658 45.000 0.00 0.00 0.00 3.55
5893 6942 4.435518 CGAATAACGTTGTGGAAGTCATGG 60.436 45.833 11.99 0.00 37.22 3.66
5894 6943 4.387559 TCGAATAACGTTGTGGAAGTCATG 59.612 41.667 11.99 0.00 43.13 3.07
5895 6944 4.387862 GTCGAATAACGTTGTGGAAGTCAT 59.612 41.667 11.99 0.00 43.13 3.06
5896 6945 3.737266 GTCGAATAACGTTGTGGAAGTCA 59.263 43.478 11.99 0.00 43.13 3.41
5897 6946 3.737266 TGTCGAATAACGTTGTGGAAGTC 59.263 43.478 11.99 0.00 43.13 3.01
5898 6947 3.719924 TGTCGAATAACGTTGTGGAAGT 58.280 40.909 11.99 0.00 43.13 3.01
5901 6950 6.782298 TTTTATGTCGAATAACGTTGTGGA 57.218 33.333 11.99 2.95 43.13 4.02
5935 6984 3.738281 CGTTCCCTGGTAGACATGACATC 60.738 52.174 0.00 0.00 0.00 3.06
5950 6999 0.328258 ATAGCCAGCAAACGTTCCCT 59.672 50.000 0.00 0.00 0.00 4.20
5952 7001 1.732405 GCAATAGCCAGCAAACGTTCC 60.732 52.381 0.00 0.00 33.58 3.62
5964 7013 5.125417 TGAATAAACAAGGACTGCAATAGCC 59.875 40.000 0.00 0.00 41.13 3.93
5984 7033 4.699735 TGTGTTGGCTTAACGATGATGAAT 59.300 37.500 0.00 0.00 42.34 2.57
5985 7034 4.068599 TGTGTTGGCTTAACGATGATGAA 58.931 39.130 0.00 0.00 42.34 2.57
5995 7044 6.909550 AAATACTCCATTGTGTTGGCTTAA 57.090 33.333 0.00 0.00 36.66 1.85
6079 7128 3.570912 AGGGAAAAAGGACGTCAGAAA 57.429 42.857 18.91 0.00 0.00 2.52
6164 7213 1.618586 GGGTGGGAAGGGGTTATGG 59.381 63.158 0.00 0.00 0.00 2.74
6192 7241 1.900486 CCCGTCCTCTAACTGGAAACT 59.100 52.381 0.00 0.00 35.10 2.66
6228 7277 3.060615 GCAACCTCAGCTGCCCAG 61.061 66.667 9.47 0.70 32.18 4.45
6229 7278 3.573229 AGCAACCTCAGCTGCCCA 61.573 61.111 9.47 0.00 41.61 5.36
6234 7283 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
6235 7284 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
6236 7285 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
6237 7286 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
6238 7287 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
6239 7288 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
6248 7297 3.190738 TTGAACTCGGGTGGGCTGG 62.191 63.158 0.00 0.00 0.00 4.85
6249 7298 1.672356 CTTGAACTCGGGTGGGCTG 60.672 63.158 0.00 0.00 0.00 4.85
6250 7299 2.113243 GACTTGAACTCGGGTGGGCT 62.113 60.000 0.00 0.00 0.00 5.19
6251 7300 1.671379 GACTTGAACTCGGGTGGGC 60.671 63.158 0.00 0.00 0.00 5.36
6252 7301 0.037232 GAGACTTGAACTCGGGTGGG 60.037 60.000 0.00 0.00 0.00 4.61
6253 7302 3.516578 GAGACTTGAACTCGGGTGG 57.483 57.895 0.00 0.00 0.00 4.61
6264 7313 1.081892 CACATCCAAGCCGAGACTTG 58.918 55.000 5.99 5.99 45.42 3.16
6265 7314 0.687354 ACACATCCAAGCCGAGACTT 59.313 50.000 0.00 0.00 0.00 3.01
6266 7315 0.036952 CACACATCCAAGCCGAGACT 60.037 55.000 0.00 0.00 0.00 3.24
6267 7316 1.021390 CCACACATCCAAGCCGAGAC 61.021 60.000 0.00 0.00 0.00 3.36
6268 7317 1.296392 CCACACATCCAAGCCGAGA 59.704 57.895 0.00 0.00 0.00 4.04
6269 7318 1.003355 ACCACACATCCAAGCCGAG 60.003 57.895 0.00 0.00 0.00 4.63
6270 7319 1.302431 CACCACACATCCAAGCCGA 60.302 57.895 0.00 0.00 0.00 5.54
6271 7320 2.981560 GCACCACACATCCAAGCCG 61.982 63.158 0.00 0.00 0.00 5.52
6272 7321 1.589716 GAGCACCACACATCCAAGCC 61.590 60.000 0.00 0.00 0.00 4.35
6273 7322 1.878775 GAGCACCACACATCCAAGC 59.121 57.895 0.00 0.00 0.00 4.01
6274 7323 1.915614 GCGAGCACCACACATCCAAG 61.916 60.000 0.00 0.00 0.00 3.61
6275 7324 1.965930 GCGAGCACCACACATCCAA 60.966 57.895 0.00 0.00 0.00 3.53
6276 7325 2.358615 GCGAGCACCACACATCCA 60.359 61.111 0.00 0.00 0.00 3.41
6277 7326 3.490759 CGCGAGCACCACACATCC 61.491 66.667 0.00 0.00 0.00 3.51
6278 7327 3.490759 CCGCGAGCACCACACATC 61.491 66.667 8.23 0.00 0.00 3.06
6279 7328 3.939837 CTCCGCGAGCACCACACAT 62.940 63.158 8.23 0.00 0.00 3.21
6280 7329 4.662961 CTCCGCGAGCACCACACA 62.663 66.667 8.23 0.00 0.00 3.72
6281 7330 4.664677 ACTCCGCGAGCACCACAC 62.665 66.667 8.23 0.00 32.04 3.82
6282 7331 3.454587 AAACTCCGCGAGCACCACA 62.455 57.895 8.23 0.00 32.04 4.17
6283 7332 2.665185 AAACTCCGCGAGCACCAC 60.665 61.111 8.23 0.00 32.04 4.16
6284 7333 2.357034 GAAACTCCGCGAGCACCA 60.357 61.111 8.23 0.00 32.04 4.17
6285 7334 2.048127 AGAAACTCCGCGAGCACC 60.048 61.111 8.23 0.00 32.04 5.01
6286 7335 2.095252 GGAGAAACTCCGCGAGCAC 61.095 63.158 8.23 0.00 41.08 4.40
6287 7336 2.261671 GGAGAAACTCCGCGAGCA 59.738 61.111 8.23 0.00 41.08 4.26
6295 7344 9.952188 GTTGGCATTTTTATATAGGAGAAACTC 57.048 33.333 0.00 0.00 0.00 3.01
6296 7345 8.621286 CGTTGGCATTTTTATATAGGAGAAACT 58.379 33.333 0.00 0.00 0.00 2.66
6297 7346 8.617809 TCGTTGGCATTTTTATATAGGAGAAAC 58.382 33.333 0.00 0.00 0.00 2.78
6298 7347 8.740123 TCGTTGGCATTTTTATATAGGAGAAA 57.260 30.769 0.00 0.00 0.00 2.52
6299 7348 7.990886 ACTCGTTGGCATTTTTATATAGGAGAA 59.009 33.333 6.71 0.00 0.00 2.87
6300 7349 7.506114 ACTCGTTGGCATTTTTATATAGGAGA 58.494 34.615 6.71 0.00 0.00 3.71
6301 7350 7.730364 ACTCGTTGGCATTTTTATATAGGAG 57.270 36.000 0.00 0.00 0.00 3.69
6302 7351 9.787435 AATACTCGTTGGCATTTTTATATAGGA 57.213 29.630 0.00 0.00 0.00 2.94


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

AutoCloner maintained by Alex Coulton.