Multiple sequence alignment - TraesCS2B01G444000

Loading Multiple Alignment...

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 TraesCS2B01G444000 chr2B 100.000 4433 0 0 1 4433 636776194 636780626 0.000000e+00 8187.0
1 TraesCS2B01G444000 chr2A 92.884 4300 196 57 1 4244 678671752 678675997 0.000000e+00 6144.0
2 TraesCS2B01G444000 chr2A 81.505 319 43 13 3760 4065 164709703 164709388 9.520000e-62 248.0
3 TraesCS2B01G444000 chr2D 92.903 4241 201 51 1 4193 535572122 535576310 0.000000e+00 6072.0
4 TraesCS2B01G444000 chr2D 93.011 186 8 3 4076 4259 535576436 535576618 2.630000e-67 267.0
5 TraesCS2B01G444000 chr2D 92.373 118 6 1 4076 4193 535576316 535576430 9.860000e-37 165.0
6 TraesCS2B01G444000 chr7B 78.208 413 67 19 3664 4066 479873472 479873073 4.430000e-60 243.0
7 TraesCS2B01G444000 chr7B 78.208 413 67 19 3664 4066 479896683 479896284 4.430000e-60 243.0
8 TraesCS2B01G444000 chr7B 81.410 156 21 6 3853 4008 540790522 540790375 2.170000e-23 121.0
9 TraesCS2B01G444000 chr4A 91.765 170 11 2 4264 4433 593349203 593349037 2.670000e-57 233.0
10 TraesCS2B01G444000 chr4A 77.696 408 58 15 3665 4063 720377532 720377915 7.470000e-53 219.0
11 TraesCS2B01G444000 chr7D 82.143 280 30 12 3738 4006 36789353 36789083 5.770000e-54 222.0
12 TraesCS2B01G444000 chr1B 88.824 170 18 1 4264 4433 595338271 595338439 1.620000e-49 207.0
13 TraesCS2B01G444000 chr1B 78.140 215 34 8 3853 4059 561301944 561301735 1.670000e-24 124.0
14 TraesCS2B01G444000 chrUn 85.946 185 19 7 3659 3839 87945854 87946035 1.630000e-44 191.0
15 TraesCS2B01G444000 chr1A 78.369 282 46 7 3692 3970 583366127 583366396 7.630000e-38 169.0
16 TraesCS2B01G444000 chr3A 83.721 172 26 2 4258 4428 171350811 171350981 1.280000e-35 161.0
17 TraesCS2B01G444000 chr3B 85.938 128 15 1 3853 3980 809044573 809044449 2.780000e-27 134.0
18 TraesCS2B01G444000 chr6A 79.195 149 28 3 4264 4410 29693425 29693572 2.820000e-17 100.0
19 TraesCS2B01G444000 chr5D 82.203 118 14 7 3734 3849 467260927 467261039 1.310000e-15 95.3
20 TraesCS2B01G444000 chr5A 85.263 95 7 6 4236 4328 635463801 635463712 1.700000e-14 91.6
21 TraesCS2B01G444000 chr5A 90.385 52 5 0 3793 3844 378524122 378524071 7.960000e-08 69.4


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 TraesCS2B01G444000 chr2B 636776194 636780626 4432 False 8187 8187 100.000000 1 4433 1 chr2B.!!$F1 4432
1 TraesCS2B01G444000 chr2A 678671752 678675997 4245 False 6144 6144 92.884000 1 4244 1 chr2A.!!$F1 4243
2 TraesCS2B01G444000 chr2D 535572122 535576618 4496 False 2168 6072 92.762333 1 4259 3 chr2D.!!$F1 4258

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
866 899 0.179067 AAGCAAACAGGACGTTCCGA 60.179 50.000 0.0 0.0 42.75 4.55 F
978 1031 1.719378 GGAGAGAGGAGGGGGATGATA 59.281 57.143 0.0 0.0 0.00 2.15 F
2376 2450 0.035152 ACTCGATGGCAAATGCAGGA 60.035 50.000 7.8 0.0 44.36 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2169 1.001641 CCTTCACAAGCCCCTCCAG 60.002 63.158 0.00 0.0 0.00 3.86 R
2931 3005 0.976641 CCAGGTAGTTGAGGAGCACA 59.023 55.000 0.00 0.0 0.00 4.57 R
4367 4688 0.040425 AAAGCACGCTTTAACGCTGG 60.040 50.000 15.13 0.0 43.58 4.85 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
92 93 4.933330 ACGTATGTGCTTCAGTACCATAG 58.067 43.478 0.00 0.00 0.00 2.23
261 268 2.105993 TCTCCTGATGGGAATGCTGATG 59.894 50.000 0.00 0.00 44.58 3.07
262 269 0.959553 CCTGATGGGAATGCTGATGC 59.040 55.000 0.00 0.00 37.23 3.91
297 304 2.416836 GCATGCAACATGAGCTCAATGT 60.417 45.455 22.50 20.73 0.00 2.71
298 305 3.179048 CATGCAACATGAGCTCAATGTG 58.821 45.455 22.50 17.12 0.00 3.21
322 329 8.138712 GTGCAGTTATAAGCTAGACAGAACTAT 58.861 37.037 0.00 0.00 0.00 2.12
340 347 8.933807 CAGAACTATCATGGTTGCAGATATTAG 58.066 37.037 0.00 0.00 0.00 1.73
387 394 2.674852 AGCAAACACAGCTCATATGACG 59.325 45.455 0.00 0.00 38.01 4.35
419 426 2.766263 TGACTTCGCTACCCAATCTGAT 59.234 45.455 0.00 0.00 0.00 2.90
429 436 3.724478 ACCCAATCTGATCTGACCTACA 58.276 45.455 4.21 0.00 0.00 2.74
431 438 5.467738 ACCCAATCTGATCTGACCTACATA 58.532 41.667 4.21 0.00 0.00 2.29
460 467 4.276678 CCAAACTCAGAATTTCAGAGTGCA 59.723 41.667 20.93 0.00 41.50 4.57
465 478 7.175347 ACTCAGAATTTCAGAGTGCAGTATA 57.825 36.000 19.92 0.00 40.94 1.47
471 484 8.649591 AGAATTTCAGAGTGCAGTATATGAGAT 58.350 33.333 0.00 0.00 0.00 2.75
481 494 8.093307 AGTGCAGTATATGAGATTCCATACTTG 58.907 37.037 0.00 0.00 33.08 3.16
488 501 5.871396 TGAGATTCCATACTTGTCTACCC 57.129 43.478 0.00 0.00 0.00 3.69
500 513 1.714787 TGTCTACCCCTACAGTCCACT 59.285 52.381 0.00 0.00 0.00 4.00
501 514 2.111255 TGTCTACCCCTACAGTCCACTT 59.889 50.000 0.00 0.00 0.00 3.16
505 518 0.618981 CCCCTACAGTCCACTTTCCC 59.381 60.000 0.00 0.00 0.00 3.97
537 557 1.086696 CACACAGGATAAACGCCCAG 58.913 55.000 0.00 0.00 0.00 4.45
548 568 3.069946 CGCCCAGTACCCACGGTA 61.070 66.667 0.00 0.00 37.09 4.02
560 580 2.494870 ACCCACGGTAGTACTGATTCAC 59.505 50.000 16.20 0.00 32.11 3.18
571 591 3.134127 GATTCACAGGCACGGGGC 61.134 66.667 1.25 1.25 43.74 5.80
592 612 4.403453 GCGAGCAATTACTGAACGAAATT 58.597 39.130 0.00 0.00 0.00 1.82
607 627 2.661594 GAAATTGAGCGTCAAACCACC 58.338 47.619 4.87 0.00 40.12 4.61
608 628 0.591170 AATTGAGCGTCAAACCACCG 59.409 50.000 4.87 0.00 40.12 4.94
610 630 3.723348 GAGCGTCAAACCACCGGC 61.723 66.667 0.00 0.00 0.00 6.13
622 655 2.032681 ACCGGCAAGCTCTCCAAC 59.967 61.111 0.00 0.00 0.00 3.77
631 664 2.990479 CTCTCCAACCCCTTCCCG 59.010 66.667 0.00 0.00 0.00 5.14
650 683 2.767505 CGAAGGTTGAAGCTACCAAGT 58.232 47.619 6.91 0.00 38.16 3.16
654 687 4.918810 AGGTTGAAGCTACCAAGTTTTG 57.081 40.909 6.91 0.00 38.16 2.44
659 692 4.523083 TGAAGCTACCAAGTTTTGACAGT 58.477 39.130 0.00 0.00 0.00 3.55
661 694 3.131396 AGCTACCAAGTTTTGACAGTCG 58.869 45.455 0.00 0.00 0.00 4.18
662 695 2.223377 GCTACCAAGTTTTGACAGTCGG 59.777 50.000 0.00 0.00 0.00 4.79
665 698 1.675552 CAAGTTTTGACAGTCGGGGT 58.324 50.000 0.00 0.00 0.00 4.95
745 778 7.391833 GGATCAATCAACCTAGAAAAACAGAGT 59.608 37.037 0.00 0.00 0.00 3.24
750 783 8.834749 ATCAACCTAGAAAAACAGAGTCTAAC 57.165 34.615 0.00 0.00 0.00 2.34
752 785 7.926555 TCAACCTAGAAAAACAGAGTCTAACTG 59.073 37.037 0.00 0.00 40.68 3.16
844 877 1.065126 AGCTTACTTGATCTGGTGCCC 60.065 52.381 0.00 0.00 0.00 5.36
858 891 2.282180 GCCCCGAAGCAAACAGGA 60.282 61.111 0.00 0.00 0.00 3.86
861 894 1.597027 CCCGAAGCAAACAGGACGT 60.597 57.895 0.00 0.00 0.00 4.34
865 898 0.234884 GAAGCAAACAGGACGTTCCG 59.765 55.000 0.00 0.00 42.75 4.30
866 899 0.179067 AAGCAAACAGGACGTTCCGA 60.179 50.000 0.00 0.00 42.75 4.55
876 909 3.245315 CGTTCCGACGCACCGATC 61.245 66.667 0.00 0.00 43.03 3.69
877 910 2.181021 GTTCCGACGCACCGATCT 59.819 61.111 0.00 0.00 0.00 2.75
878 911 2.158959 GTTCCGACGCACCGATCTG 61.159 63.158 0.00 0.00 0.00 2.90
879 912 3.350909 TTCCGACGCACCGATCTGG 62.351 63.158 2.55 2.55 46.41 3.86
880 913 3.822192 CCGACGCACCGATCTGGA 61.822 66.667 10.05 0.00 42.00 3.86
881 914 2.278206 CGACGCACCGATCTGGAG 60.278 66.667 10.05 4.11 42.00 3.86
882 915 2.105128 GACGCACCGATCTGGAGG 59.895 66.667 10.05 0.00 42.00 4.30
883 916 4.148825 ACGCACCGATCTGGAGGC 62.149 66.667 10.05 10.97 42.00 4.70
885 918 3.838271 GCACCGATCTGGAGGCGA 61.838 66.667 10.05 0.00 42.00 5.54
886 919 2.105128 CACCGATCTGGAGGCGAC 59.895 66.667 10.05 0.00 42.00 5.19
888 921 2.415010 CCGATCTGGAGGCGACTG 59.585 66.667 0.00 0.00 44.43 3.51
889 922 2.415010 CGATCTGGAGGCGACTGG 59.585 66.667 0.00 0.00 44.43 4.00
890 923 2.418910 CGATCTGGAGGCGACTGGT 61.419 63.158 0.00 0.00 44.43 4.00
940 993 3.043419 CGGAGGCGGATAGGAGTG 58.957 66.667 0.00 0.00 0.00 3.51
946 999 2.028190 CGGATAGGAGTGGCAGCG 59.972 66.667 0.00 0.00 0.00 5.18
962 1015 2.660064 GCGAAGAAGCCAGGGGAGA 61.660 63.158 0.00 0.00 0.00 3.71
978 1031 1.719378 GGAGAGAGGAGGGGGATGATA 59.281 57.143 0.00 0.00 0.00 2.15
1010 1063 2.398498 CGAGATTTAGATGGCTCGGTG 58.602 52.381 0.00 0.00 44.58 4.94
1011 1064 2.760374 GAGATTTAGATGGCTCGGTGG 58.240 52.381 0.00 0.00 0.00 4.61
1089 1154 4.346049 CCGAGAAGGGCTGAGAGA 57.654 61.111 0.00 0.00 35.97 3.10
1763 1837 2.363795 CCTCCAGACGCCCACCTA 60.364 66.667 0.00 0.00 0.00 3.08
1788 1862 2.578128 CTCCTCTCGCTGCTGCTT 59.422 61.111 14.03 0.00 36.97 3.91
1953 2027 3.453868 TGAAATGAGACAGAGGGATGGA 58.546 45.455 0.00 0.00 0.00 3.41
1998 2072 3.949113 TGTACAGCACTATGGTCGATGTA 59.051 43.478 0.00 5.94 0.00 2.29
2095 2169 3.807538 CTGTGAGCACCGCCATGC 61.808 66.667 0.00 0.00 46.50 4.06
2156 2230 0.254178 GAGCTTTGGGAGGAGATGCA 59.746 55.000 0.00 0.00 0.00 3.96
2376 2450 0.035152 ACTCGATGGCAAATGCAGGA 60.035 50.000 7.80 0.00 44.36 3.86
2523 2597 4.572389 GCGAGTGACCTGTTGATGATTTAT 59.428 41.667 0.00 0.00 0.00 1.40
2709 2783 2.205074 GCGAAGGTGGACATGATACTG 58.795 52.381 0.00 0.00 0.00 2.74
2784 2858 3.548770 GGCAATCATGAACATCCTGAGA 58.451 45.455 0.00 0.00 0.00 3.27
2931 3005 1.722011 CGGCGAGGTACTTTGTGAAT 58.278 50.000 0.00 0.00 41.55 2.57
3075 3149 1.153628 GGACATCCGGAACCTGTCG 60.154 63.158 23.69 5.17 40.11 4.35
3127 3201 1.371183 CTGCACCGGTTCAGGAAGA 59.629 57.895 24.63 0.00 34.73 2.87
3207 3281 3.192630 ATGGTGGTGGCCCAGGTT 61.193 61.111 0.00 0.00 42.94 3.50
3429 3503 2.359850 TCCCTTGGCATGTCACGC 60.360 61.111 0.00 0.00 0.00 5.34
3453 3527 1.510383 GTGCCAGTGTGTGCAAACA 59.490 52.632 5.33 5.33 39.57 2.83
3574 3648 6.525629 TGGTTTGTGGTACCATAATTTTTGG 58.474 36.000 22.97 4.53 40.65 3.28
3631 3705 1.556564 CGAAGAGTGTGACGTGTTGT 58.443 50.000 0.00 0.00 0.00 3.32
3655 3729 6.935741 ACTTATTTGCGGCATATAGTTGAA 57.064 33.333 2.28 0.00 0.00 2.69
3779 3853 3.628942 TGGCATGTAAGATGATTGAGTGC 59.371 43.478 0.00 0.00 0.00 4.40
3788 3862 0.392706 TGATTGAGTGCGTGAGGTGT 59.607 50.000 0.00 0.00 0.00 4.16
3831 3905 5.117406 TGGACATCTTAGTAGCTCTCAGA 57.883 43.478 0.00 0.00 31.98 3.27
3832 3906 5.510430 TGGACATCTTAGTAGCTCTCAGAA 58.490 41.667 0.00 0.00 31.32 3.02
3862 3936 0.951558 AATCGGGTCTGCACAAACAC 59.048 50.000 0.00 0.00 0.00 3.32
3893 3967 9.649167 CTTTTTCATAGATCTCAAATTTGCCTT 57.351 29.630 13.54 0.02 0.00 4.35
3952 4026 2.625314 TGAAATTTGGCACGGACATCAA 59.375 40.909 0.00 0.00 0.00 2.57
3953 4027 3.068732 TGAAATTTGGCACGGACATCAAA 59.931 39.130 0.00 0.00 34.28 2.69
3976 4050 1.070134 CTCAGTCGTCTTTCCCCACAA 59.930 52.381 0.00 0.00 0.00 3.33
3980 4054 3.317993 CAGTCGTCTTTCCCCACAAAAAT 59.682 43.478 0.00 0.00 0.00 1.82
3994 4069 9.114952 TCCCCACAAAAATAAACAGAATTTTTC 57.885 29.630 4.09 0.00 41.99 2.29
4131 4330 6.060028 TGCATTGTTACTGTCTCAGAAAAC 57.940 37.500 3.70 7.88 35.18 2.43
4146 4345 3.188460 CAGAAAACCCATTCCAGTGTACG 59.812 47.826 0.00 0.00 0.00 3.67
4150 4349 1.001633 ACCCATTCCAGTGTACGTCAC 59.998 52.381 0.00 0.00 46.46 3.67
4166 4485 4.765273 ACGTCACAAACATATATGCAGGA 58.235 39.130 12.79 1.45 0.00 3.86
4171 4490 7.042119 CGTCACAAACATATATGCAGGATACAA 60.042 37.037 12.79 0.00 41.41 2.41
4279 4600 9.384764 AGAGTATATGTTTTTCTAGGCAAACTC 57.615 33.333 14.87 0.00 34.52 3.01
4280 4601 9.162764 GAGTATATGTTTTTCTAGGCAAACTCA 57.837 33.333 14.87 6.89 34.52 3.41
4281 4602 8.947115 AGTATATGTTTTTCTAGGCAAACTCAC 58.053 33.333 14.87 9.37 34.52 3.51
4282 4603 7.759489 ATATGTTTTTCTAGGCAAACTCACA 57.241 32.000 14.87 6.55 34.52 3.58
4283 4604 5.906113 TGTTTTTCTAGGCAAACTCACAA 57.094 34.783 14.87 0.00 34.52 3.33
4284 4605 6.274157 TGTTTTTCTAGGCAAACTCACAAA 57.726 33.333 14.87 0.00 34.52 2.83
4285 4606 6.329496 TGTTTTTCTAGGCAAACTCACAAAG 58.671 36.000 14.87 0.00 34.52 2.77
4286 4607 4.568152 TTTCTAGGCAAACTCACAAAGC 57.432 40.909 0.00 0.00 0.00 3.51
4287 4608 3.492102 TCTAGGCAAACTCACAAAGCT 57.508 42.857 0.00 0.00 0.00 3.74
4288 4609 3.820557 TCTAGGCAAACTCACAAAGCTT 58.179 40.909 0.00 0.00 0.00 3.74
4289 4610 4.207165 TCTAGGCAAACTCACAAAGCTTT 58.793 39.130 5.69 5.69 0.00 3.51
4290 4611 3.893326 AGGCAAACTCACAAAGCTTTT 57.107 38.095 9.53 0.00 0.00 2.27
4291 4612 4.206477 AGGCAAACTCACAAAGCTTTTT 57.794 36.364 9.53 0.00 0.00 1.94
4292 4613 5.337578 AGGCAAACTCACAAAGCTTTTTA 57.662 34.783 9.53 0.00 0.00 1.52
4293 4614 5.917462 AGGCAAACTCACAAAGCTTTTTAT 58.083 33.333 9.53 0.00 0.00 1.40
4294 4615 6.348498 AGGCAAACTCACAAAGCTTTTTATT 58.652 32.000 9.53 0.00 0.00 1.40
4295 4616 6.479990 AGGCAAACTCACAAAGCTTTTTATTC 59.520 34.615 9.53 0.00 0.00 1.75
4296 4617 6.257630 GGCAAACTCACAAAGCTTTTTATTCA 59.742 34.615 9.53 0.00 0.00 2.57
4297 4618 7.041848 GGCAAACTCACAAAGCTTTTTATTCAT 60.042 33.333 9.53 0.00 0.00 2.57
4298 4619 8.006027 GCAAACTCACAAAGCTTTTTATTCATC 58.994 33.333 9.53 0.00 0.00 2.92
4299 4620 8.490355 CAAACTCACAAAGCTTTTTATTCATCC 58.510 33.333 9.53 0.00 0.00 3.51
4300 4621 6.381801 ACTCACAAAGCTTTTTATTCATCCG 58.618 36.000 9.53 0.00 0.00 4.18
4301 4622 6.016276 ACTCACAAAGCTTTTTATTCATCCGT 60.016 34.615 9.53 0.00 0.00 4.69
4302 4623 6.378582 TCACAAAGCTTTTTATTCATCCGTC 58.621 36.000 9.53 0.00 0.00 4.79
4303 4624 6.016693 TCACAAAGCTTTTTATTCATCCGTCA 60.017 34.615 9.53 0.00 0.00 4.35
4304 4625 6.088085 CACAAAGCTTTTTATTCATCCGTCAC 59.912 38.462 9.53 0.00 0.00 3.67
4305 4626 5.957842 AAGCTTTTTATTCATCCGTCACA 57.042 34.783 0.00 0.00 0.00 3.58
4306 4627 5.296813 AGCTTTTTATTCATCCGTCACAC 57.703 39.130 0.00 0.00 0.00 3.82
4307 4628 4.759693 AGCTTTTTATTCATCCGTCACACA 59.240 37.500 0.00 0.00 0.00 3.72
4308 4629 5.088739 GCTTTTTATTCATCCGTCACACAG 58.911 41.667 0.00 0.00 0.00 3.66
4309 4630 5.334879 GCTTTTTATTCATCCGTCACACAGT 60.335 40.000 0.00 0.00 0.00 3.55
4310 4631 6.627395 TTTTTATTCATCCGTCACACAGTT 57.373 33.333 0.00 0.00 0.00 3.16
4311 4632 6.627395 TTTTATTCATCCGTCACACAGTTT 57.373 33.333 0.00 0.00 0.00 2.66
4312 4633 7.731882 TTTTATTCATCCGTCACACAGTTTA 57.268 32.000 0.00 0.00 0.00 2.01
4313 4634 7.731882 TTTATTCATCCGTCACACAGTTTAA 57.268 32.000 0.00 0.00 0.00 1.52
4314 4635 7.731882 TTATTCATCCGTCACACAGTTTAAA 57.268 32.000 0.00 0.00 0.00 1.52
4315 4636 5.666969 TTCATCCGTCACACAGTTTAAAG 57.333 39.130 0.00 0.00 0.00 1.85
4316 4637 4.062293 TCATCCGTCACACAGTTTAAAGG 58.938 43.478 0.00 0.00 0.00 3.11
4317 4638 2.841215 TCCGTCACACAGTTTAAAGGG 58.159 47.619 0.00 0.00 0.00 3.95
4318 4639 2.435069 TCCGTCACACAGTTTAAAGGGA 59.565 45.455 0.00 0.00 0.00 4.20
4319 4640 2.546789 CCGTCACACAGTTTAAAGGGAC 59.453 50.000 0.00 0.00 0.00 4.46
4320 4641 2.220133 CGTCACACAGTTTAAAGGGACG 59.780 50.000 13.42 13.42 40.45 4.79
4321 4642 3.460103 GTCACACAGTTTAAAGGGACGA 58.540 45.455 0.00 0.00 0.00 4.20
4322 4643 3.872771 GTCACACAGTTTAAAGGGACGAA 59.127 43.478 0.00 0.00 0.00 3.85
4323 4644 4.025145 GTCACACAGTTTAAAGGGACGAAG 60.025 45.833 0.00 0.00 0.00 3.79
4324 4645 2.876550 ACACAGTTTAAAGGGACGAAGC 59.123 45.455 0.00 0.00 0.00 3.86
4325 4646 2.875933 CACAGTTTAAAGGGACGAAGCA 59.124 45.455 0.00 0.00 0.00 3.91
4326 4647 3.314080 CACAGTTTAAAGGGACGAAGCAA 59.686 43.478 0.00 0.00 0.00 3.91
4327 4648 3.949113 ACAGTTTAAAGGGACGAAGCAAA 59.051 39.130 0.00 0.00 0.00 3.68
4328 4649 4.036380 ACAGTTTAAAGGGACGAAGCAAAG 59.964 41.667 0.00 0.00 0.00 2.77
4329 4650 4.274950 CAGTTTAAAGGGACGAAGCAAAGA 59.725 41.667 0.00 0.00 0.00 2.52
4330 4651 5.048713 CAGTTTAAAGGGACGAAGCAAAGAT 60.049 40.000 0.00 0.00 0.00 2.40
4331 4652 5.181433 AGTTTAAAGGGACGAAGCAAAGATC 59.819 40.000 0.00 0.00 0.00 2.75
4332 4653 3.425162 AAAGGGACGAAGCAAAGATCT 57.575 42.857 0.00 0.00 0.00 2.75
4333 4654 2.682155 AGGGACGAAGCAAAGATCTC 57.318 50.000 0.00 0.00 0.00 2.75
4334 4655 1.208293 AGGGACGAAGCAAAGATCTCC 59.792 52.381 0.00 0.00 0.00 3.71
4335 4656 1.066143 GGGACGAAGCAAAGATCTCCA 60.066 52.381 0.00 0.00 0.00 3.86
4336 4657 2.420687 GGGACGAAGCAAAGATCTCCAT 60.421 50.000 0.00 0.00 0.00 3.41
4337 4658 2.611292 GGACGAAGCAAAGATCTCCATG 59.389 50.000 0.00 0.00 0.00 3.66
4338 4659 2.611292 GACGAAGCAAAGATCTCCATGG 59.389 50.000 4.97 4.97 0.00 3.66
4339 4660 2.026822 ACGAAGCAAAGATCTCCATGGT 60.027 45.455 12.58 0.00 0.00 3.55
4340 4661 2.353889 CGAAGCAAAGATCTCCATGGTG 59.646 50.000 12.58 9.91 0.00 4.17
4341 4662 3.614092 GAAGCAAAGATCTCCATGGTGA 58.386 45.455 18.39 18.39 0.00 4.02
4342 4663 2.996631 AGCAAAGATCTCCATGGTGAC 58.003 47.619 18.45 12.21 0.00 3.67
4343 4664 2.019984 GCAAAGATCTCCATGGTGACC 58.980 52.381 18.45 9.49 0.00 4.02
4344 4665 2.356535 GCAAAGATCTCCATGGTGACCT 60.357 50.000 18.45 11.90 0.00 3.85
4345 4666 3.118261 GCAAAGATCTCCATGGTGACCTA 60.118 47.826 18.45 0.00 0.00 3.08
4346 4667 4.701765 CAAAGATCTCCATGGTGACCTAG 58.298 47.826 18.45 7.32 0.00 3.02
4347 4668 2.324541 AGATCTCCATGGTGACCTAGC 58.675 52.381 18.45 6.52 0.00 3.42
4348 4669 1.346068 GATCTCCATGGTGACCTAGCC 59.654 57.143 18.45 1.50 0.00 3.93
4349 4670 0.042581 TCTCCATGGTGACCTAGCCA 59.957 55.000 12.58 0.00 39.33 4.75
4350 4671 0.911769 CTCCATGGTGACCTAGCCAA 59.088 55.000 12.58 0.00 38.38 4.52
4351 4672 1.281867 CTCCATGGTGACCTAGCCAAA 59.718 52.381 12.58 0.00 38.38 3.28
4352 4673 1.004277 TCCATGGTGACCTAGCCAAAC 59.996 52.381 12.58 0.00 38.38 2.93
4353 4674 1.271871 CCATGGTGACCTAGCCAAACA 60.272 52.381 2.57 0.00 38.38 2.83
4354 4675 2.621407 CCATGGTGACCTAGCCAAACAT 60.621 50.000 2.57 0.00 38.38 2.71
4355 4676 2.198827 TGGTGACCTAGCCAAACATG 57.801 50.000 2.11 0.00 0.00 3.21
4356 4677 1.702401 TGGTGACCTAGCCAAACATGA 59.298 47.619 2.11 0.00 0.00 3.07
4357 4678 2.308570 TGGTGACCTAGCCAAACATGAT 59.691 45.455 2.11 0.00 0.00 2.45
4358 4679 2.684881 GGTGACCTAGCCAAACATGATG 59.315 50.000 0.00 0.00 0.00 3.07
4359 4680 2.684881 GTGACCTAGCCAAACATGATGG 59.315 50.000 15.23 15.23 41.08 3.51
4364 4685 4.016838 CCAAACATGATGGCCGGT 57.983 55.556 1.90 0.00 0.00 5.28
4365 4686 1.809207 CCAAACATGATGGCCGGTC 59.191 57.895 0.00 0.00 0.00 4.79
4366 4687 1.666209 CCAAACATGATGGCCGGTCC 61.666 60.000 2.12 5.67 0.00 4.46
4367 4688 1.379843 AAACATGATGGCCGGTCCC 60.380 57.895 2.12 0.00 0.00 4.46
4368 4689 2.854300 AAACATGATGGCCGGTCCCC 62.854 60.000 2.12 0.00 0.00 4.81
4369 4690 3.807839 CATGATGGCCGGTCCCCA 61.808 66.667 2.12 1.71 36.66 4.96
4370 4691 3.492353 ATGATGGCCGGTCCCCAG 61.492 66.667 2.12 0.00 35.48 4.45
4376 4697 4.397832 GCCGGTCCCCAGCGTTAA 62.398 66.667 1.90 0.00 42.17 2.01
4377 4698 2.348243 CCGGTCCCCAGCGTTAAA 59.652 61.111 0.00 0.00 42.17 1.52
4378 4699 1.743995 CCGGTCCCCAGCGTTAAAG 60.744 63.158 0.00 0.00 42.17 1.85
4379 4700 2.396157 CGGTCCCCAGCGTTAAAGC 61.396 63.158 5.12 5.12 38.76 3.51
4380 4701 2.396157 GGTCCCCAGCGTTAAAGCG 61.396 63.158 7.75 3.40 43.00 4.68
4381 4702 1.670083 GTCCCCAGCGTTAAAGCGT 60.670 57.895 7.75 0.00 43.00 5.07
4382 4703 1.669760 TCCCCAGCGTTAAAGCGTG 60.670 57.895 7.75 6.76 43.00 5.34
4383 4704 2.175811 CCCAGCGTTAAAGCGTGC 59.824 61.111 7.75 0.00 43.00 5.34
4384 4705 2.325082 CCCAGCGTTAAAGCGTGCT 61.325 57.895 7.75 0.00 43.00 4.40
4385 4706 1.574428 CCAGCGTTAAAGCGTGCTT 59.426 52.632 7.75 0.24 43.00 3.91
4386 4707 0.040425 CCAGCGTTAAAGCGTGCTTT 60.040 50.000 21.99 21.99 46.56 3.51
4387 4708 1.044725 CAGCGTTAAAGCGTGCTTTG 58.955 50.000 25.69 12.95 44.84 2.77
4388 4709 0.660300 AGCGTTAAAGCGTGCTTTGC 60.660 50.000 25.69 20.54 44.84 3.68
4389 4710 0.932585 GCGTTAAAGCGTGCTTTGCA 60.933 50.000 25.69 12.22 44.84 4.08
4390 4711 1.471964 CGTTAAAGCGTGCTTTGCAA 58.528 45.000 25.69 12.93 44.84 4.08
4391 4712 1.447938 CGTTAAAGCGTGCTTTGCAAG 59.552 47.619 25.69 12.92 44.84 4.01
4392 4713 2.459934 GTTAAAGCGTGCTTTGCAAGT 58.540 42.857 25.69 4.95 44.84 3.16
4393 4714 2.857748 GTTAAAGCGTGCTTTGCAAGTT 59.142 40.909 25.69 4.28 44.84 2.66
4394 4715 2.008752 AAAGCGTGCTTTGCAAGTTT 57.991 40.000 18.32 4.84 43.72 2.66
4395 4716 1.280066 AAGCGTGCTTTGCAAGTTTG 58.720 45.000 0.24 0.00 39.38 2.93
4396 4717 0.173255 AGCGTGCTTTGCAAGTTTGT 59.827 45.000 0.00 0.00 41.47 2.83
4397 4718 0.298411 GCGTGCTTTGCAAGTTTGTG 59.702 50.000 0.00 0.00 41.47 3.33
4398 4719 0.922717 CGTGCTTTGCAAGTTTGTGG 59.077 50.000 0.00 0.00 41.47 4.17
4399 4720 1.289276 GTGCTTTGCAAGTTTGTGGG 58.711 50.000 0.00 0.00 41.47 4.61
4400 4721 0.461693 TGCTTTGCAAGTTTGTGGGC 60.462 50.000 0.00 0.00 34.76 5.36
4401 4722 1.159713 GCTTTGCAAGTTTGTGGGCC 61.160 55.000 0.00 0.00 0.00 5.80
4402 4723 0.465287 CTTTGCAAGTTTGTGGGCCT 59.535 50.000 4.53 0.00 0.00 5.19
4403 4724 0.908198 TTTGCAAGTTTGTGGGCCTT 59.092 45.000 4.53 0.00 0.00 4.35
4404 4725 1.781786 TTGCAAGTTTGTGGGCCTTA 58.218 45.000 4.53 0.00 0.00 2.69
4405 4726 1.781786 TGCAAGTTTGTGGGCCTTAA 58.218 45.000 4.53 0.00 0.00 1.85
4406 4727 1.410882 TGCAAGTTTGTGGGCCTTAAC 59.589 47.619 4.53 6.48 0.00 2.01
4407 4728 1.410882 GCAAGTTTGTGGGCCTTAACA 59.589 47.619 4.53 2.07 0.00 2.41
4408 4729 2.037121 GCAAGTTTGTGGGCCTTAACAT 59.963 45.455 4.53 0.00 0.00 2.71
4409 4730 3.494223 GCAAGTTTGTGGGCCTTAACATT 60.494 43.478 4.53 0.00 0.00 2.71
4410 4731 4.702831 CAAGTTTGTGGGCCTTAACATTT 58.297 39.130 4.53 0.00 0.00 2.32
4411 4732 4.335400 AGTTTGTGGGCCTTAACATTTG 57.665 40.909 4.53 0.00 0.00 2.32
4412 4733 3.964031 AGTTTGTGGGCCTTAACATTTGA 59.036 39.130 4.53 0.00 0.00 2.69
4413 4734 4.039124 AGTTTGTGGGCCTTAACATTTGAG 59.961 41.667 4.53 0.00 0.00 3.02
4414 4735 2.524306 TGTGGGCCTTAACATTTGAGG 58.476 47.619 4.53 0.00 0.00 3.86
4415 4736 2.158385 TGTGGGCCTTAACATTTGAGGT 60.158 45.455 4.53 0.00 33.03 3.85
4416 4737 2.897326 GTGGGCCTTAACATTTGAGGTT 59.103 45.455 4.53 0.00 33.03 3.50
4417 4738 3.056821 GTGGGCCTTAACATTTGAGGTTC 60.057 47.826 4.53 0.00 33.03 3.62
4418 4739 3.181423 TGGGCCTTAACATTTGAGGTTCT 60.181 43.478 4.53 0.00 33.03 3.01
4419 4740 4.043561 TGGGCCTTAACATTTGAGGTTCTA 59.956 41.667 4.53 0.00 33.03 2.10
4420 4741 5.014202 GGGCCTTAACATTTGAGGTTCTAA 58.986 41.667 0.84 0.00 33.03 2.10
4421 4742 5.479027 GGGCCTTAACATTTGAGGTTCTAAA 59.521 40.000 0.84 0.00 33.03 1.85
4422 4743 6.154534 GGGCCTTAACATTTGAGGTTCTAAAT 59.845 38.462 0.84 0.00 33.03 1.40
4423 4744 7.310423 GGGCCTTAACATTTGAGGTTCTAAATT 60.310 37.037 0.84 0.00 33.03 1.82
4424 4745 7.759886 GGCCTTAACATTTGAGGTTCTAAATTC 59.240 37.037 0.00 0.00 33.03 2.17
4425 4746 8.303876 GCCTTAACATTTGAGGTTCTAAATTCA 58.696 33.333 0.00 0.00 33.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.083630 CGTTCATACGGAAATGATGTTTTGT 58.916 36.000 0.00 0.00 43.94 2.83
49 50 6.538894 CGTTCATACGGAAATGATGTTTTG 57.461 37.500 0.00 0.00 43.94 2.44
100 101 9.499479 CTCCTTCTACATTATGTTATGCTTGAT 57.501 33.333 2.23 0.00 0.00 2.57
101 102 7.442364 GCTCCTTCTACATTATGTTATGCTTGA 59.558 37.037 2.23 0.00 0.00 3.02
102 103 7.227314 TGCTCCTTCTACATTATGTTATGCTTG 59.773 37.037 2.23 0.00 0.00 4.01
106 108 8.437360 TGTTGCTCCTTCTACATTATGTTATG 57.563 34.615 2.23 0.00 0.00 1.90
261 268 1.004200 ATGCTTGCCTTGCCTTTGC 60.004 52.632 0.00 0.00 38.26 3.68
262 269 1.296056 GCATGCTTGCCTTGCCTTTG 61.296 55.000 11.37 0.00 43.38 2.77
273 280 1.201414 TGAGCTCATGTTGCATGCTTG 59.799 47.619 20.33 11.19 33.83 4.01
283 290 2.195741 ACTGCACATTGAGCTCATGT 57.804 45.000 19.04 19.44 0.00 3.21
285 292 5.008415 GCTTATAACTGCACATTGAGCTCAT 59.992 40.000 19.04 4.99 0.00 2.90
297 304 6.531503 AGTTCTGTCTAGCTTATAACTGCA 57.468 37.500 0.00 0.00 0.00 4.41
298 305 8.353684 TGATAGTTCTGTCTAGCTTATAACTGC 58.646 37.037 0.00 0.00 0.00 4.40
322 329 5.471116 GCACATCTAATATCTGCAACCATGA 59.529 40.000 0.00 0.00 0.00 3.07
340 347 3.747099 AAGATGTTTACTGCGCACATC 57.253 42.857 23.22 23.22 44.88 3.06
387 394 0.790814 GCGAAGTCACAGTTGTAGCC 59.209 55.000 0.00 0.00 0.00 3.93
419 426 3.699025 TGGGTGGATATGTAGGTCAGA 57.301 47.619 0.00 0.00 0.00 3.27
429 436 6.493166 TGAAATTCTGAGTTTGGGTGGATAT 58.507 36.000 2.68 0.00 0.00 1.63
431 438 4.739793 TGAAATTCTGAGTTTGGGTGGAT 58.260 39.130 2.68 0.00 0.00 3.41
465 478 5.308237 GGGGTAGACAAGTATGGAATCTCAT 59.692 44.000 0.00 0.00 0.00 2.90
471 484 4.950361 TGTAGGGGTAGACAAGTATGGAA 58.050 43.478 0.00 0.00 0.00 3.53
481 494 2.528673 AGTGGACTGTAGGGGTAGAC 57.471 55.000 0.00 0.00 0.00 2.59
487 500 0.618981 GGGGAAAGTGGACTGTAGGG 59.381 60.000 0.00 0.00 0.00 3.53
488 501 0.618981 GGGGGAAAGTGGACTGTAGG 59.381 60.000 0.00 0.00 0.00 3.18
505 518 0.675837 CTGTGTGATGTGCTCTGGGG 60.676 60.000 0.00 0.00 0.00 4.96
519 532 0.690762 ACTGGGCGTTTATCCTGTGT 59.309 50.000 0.00 0.00 34.60 3.72
537 557 3.696051 TGAATCAGTACTACCGTGGGTAC 59.304 47.826 0.00 7.93 37.09 3.34
547 567 2.165641 CCGTGCCTGTGAATCAGTACTA 59.834 50.000 0.00 0.00 42.19 1.82
548 568 1.066858 CCGTGCCTGTGAATCAGTACT 60.067 52.381 0.00 0.00 42.19 2.73
571 591 5.617609 TCAATTTCGTTCAGTAATTGCTCG 58.382 37.500 0.00 0.00 43.16 5.03
576 596 5.178623 TGACGCTCAATTTCGTTCAGTAATT 59.821 36.000 0.00 0.00 39.22 1.40
592 612 2.280524 CCGGTGGTTTGACGCTCA 60.281 61.111 0.00 0.00 0.00 4.26
607 627 2.747855 GGGTTGGAGAGCTTGCCG 60.748 66.667 0.00 0.00 0.00 5.69
608 628 2.361737 GGGGTTGGAGAGCTTGCC 60.362 66.667 0.00 0.00 0.00 4.52
610 630 0.322906 GGAAGGGGTTGGAGAGCTTG 60.323 60.000 0.00 0.00 0.00 4.01
631 664 5.067283 TCAAAACTTGGTAGCTTCAACCTTC 59.933 40.000 5.75 0.00 37.91 3.46
649 682 1.345415 TCCTACCCCGACTGTCAAAAC 59.655 52.381 8.73 0.00 0.00 2.43
650 683 1.345415 GTCCTACCCCGACTGTCAAAA 59.655 52.381 8.73 0.00 0.00 2.44
654 687 1.064832 AGTAGTCCTACCCCGACTGTC 60.065 57.143 0.00 0.00 40.75 3.51
659 692 3.658725 AGTAGTAGTAGTCCTACCCCGA 58.341 50.000 0.89 0.00 46.15 5.14
661 694 6.785466 AGTAGTAGTAGTAGTAGTCCTACCCC 59.215 46.154 10.17 0.00 46.15 4.95
662 695 7.849322 AGTAGTAGTAGTAGTAGTCCTACCC 57.151 44.000 10.17 0.00 46.15 3.69
688 721 8.670135 CCTCGATTAGATGATTGGTAGTAGTAG 58.330 40.741 0.00 0.00 0.00 2.57
689 722 8.380867 TCCTCGATTAGATGATTGGTAGTAGTA 58.619 37.037 0.00 0.00 0.00 1.82
690 723 7.175293 GTCCTCGATTAGATGATTGGTAGTAGT 59.825 40.741 0.00 0.00 0.00 2.73
691 724 7.392113 AGTCCTCGATTAGATGATTGGTAGTAG 59.608 40.741 0.00 0.00 0.00 2.57
692 725 7.232188 AGTCCTCGATTAGATGATTGGTAGTA 58.768 38.462 0.00 0.00 0.00 1.82
693 726 6.071984 AGTCCTCGATTAGATGATTGGTAGT 58.928 40.000 0.00 0.00 0.00 2.73
694 727 6.582677 AGTCCTCGATTAGATGATTGGTAG 57.417 41.667 0.00 0.00 0.00 3.18
695 728 6.576662 GAGTCCTCGATTAGATGATTGGTA 57.423 41.667 0.00 0.00 0.00 3.25
696 729 5.461032 GAGTCCTCGATTAGATGATTGGT 57.539 43.478 0.00 0.00 0.00 3.67
711 744 2.432510 AGGTTGATTGATCCGAGTCCTC 59.567 50.000 0.00 0.00 0.00 3.71
720 753 8.329203 ACTCTGTTTTTCTAGGTTGATTGATC 57.671 34.615 0.00 0.00 0.00 2.92
745 778 1.751351 CTCCACCGAGATGCAGTTAGA 59.249 52.381 0.00 0.00 38.52 2.10
750 783 3.359194 CTTCTCCACCGAGATGCAG 57.641 57.895 0.00 0.00 44.68 4.41
782 815 1.315981 TTGGTGTTGTTTGGCGAGCA 61.316 50.000 0.00 0.00 0.00 4.26
844 877 0.234884 GAACGTCCTGTTTGCTTCGG 59.765 55.000 0.00 0.00 42.09 4.30
861 894 2.180769 CAGATCGGTGCGTCGGAA 59.819 61.111 0.00 0.00 0.00 4.30
865 898 2.105128 CCTCCAGATCGGTGCGTC 59.895 66.667 3.97 0.00 35.57 5.19
866 899 4.148825 GCCTCCAGATCGGTGCGT 62.149 66.667 3.97 0.00 35.57 5.24
875 908 1.228894 AGAACCAGTCGCCTCCAGA 60.229 57.895 0.00 0.00 0.00 3.86
876 909 1.079543 CAGAACCAGTCGCCTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
877 910 2.583441 CCAGAACCAGTCGCCTCCA 61.583 63.158 0.00 0.00 0.00 3.86
878 911 2.232298 CTCCAGAACCAGTCGCCTCC 62.232 65.000 0.00 0.00 0.00 4.30
879 912 1.216710 CTCCAGAACCAGTCGCCTC 59.783 63.158 0.00 0.00 0.00 4.70
880 913 2.286523 CCTCCAGAACCAGTCGCCT 61.287 63.158 0.00 0.00 0.00 5.52
881 914 2.266055 CCTCCAGAACCAGTCGCC 59.734 66.667 0.00 0.00 0.00 5.54
882 915 2.435059 GCCTCCAGAACCAGTCGC 60.435 66.667 0.00 0.00 0.00 5.19
883 916 2.125912 CGCCTCCAGAACCAGTCG 60.126 66.667 0.00 0.00 0.00 4.18
884 917 2.266055 CCGCCTCCAGAACCAGTC 59.734 66.667 0.00 0.00 0.00 3.51
885 918 3.322466 CCCGCCTCCAGAACCAGT 61.322 66.667 0.00 0.00 0.00 4.00
886 919 3.316573 GACCCGCCTCCAGAACCAG 62.317 68.421 0.00 0.00 0.00 4.00
887 920 3.319198 GACCCGCCTCCAGAACCA 61.319 66.667 0.00 0.00 0.00 3.67
888 921 4.452733 CGACCCGCCTCCAGAACC 62.453 72.222 0.00 0.00 0.00 3.62
889 922 4.452733 CCGACCCGCCTCCAGAAC 62.453 72.222 0.00 0.00 0.00 3.01
925 978 2.093537 CTGCCACTCCTATCCGCCTC 62.094 65.000 0.00 0.00 0.00 4.70
929 982 2.016393 TTCGCTGCCACTCCTATCCG 62.016 60.000 0.00 0.00 0.00 4.18
930 983 0.249657 CTTCGCTGCCACTCCTATCC 60.250 60.000 0.00 0.00 0.00 2.59
932 985 1.137872 CTTCTTCGCTGCCACTCCTAT 59.862 52.381 0.00 0.00 0.00 2.57
940 993 3.130160 CCTGGCTTCTTCGCTGCC 61.130 66.667 0.00 0.00 46.26 4.85
946 999 0.829990 CTCTCTCCCCTGGCTTCTTC 59.170 60.000 0.00 0.00 0.00 2.87
956 1009 2.416923 ATCCCCCTCCTCTCTCCCC 61.417 68.421 0.00 0.00 0.00 4.81
962 1015 1.563616 AGGTATCATCCCCCTCCTCT 58.436 55.000 0.00 0.00 0.00 3.69
978 1031 2.586648 AAATCTCGAGCCCAAAAGGT 57.413 45.000 7.81 0.00 38.26 3.50
1010 1063 0.375803 AAACGTCAACGAGCAACACC 59.624 50.000 9.88 0.00 43.02 4.16
1011 1064 1.452717 CAAACGTCAACGAGCAACAC 58.547 50.000 9.88 0.00 43.02 3.32
1198 1272 1.268589 CGTGTCTATCCATTCGACGCT 60.269 52.381 0.00 0.00 36.36 5.07
1763 1837 1.992277 AGCGAGAGGAGGGCATTGT 60.992 57.895 0.00 0.00 0.00 2.71
1851 1925 1.218316 GTAGGTGCCCTTGTCGAGG 59.782 63.158 0.00 0.00 45.86 4.63
1866 1940 2.447887 CGGCACAGCAAGCTCGTAG 61.448 63.158 0.00 0.00 0.00 3.51
1896 1970 2.956964 GCGTCGATCCTTCCAGCG 60.957 66.667 0.00 0.00 0.00 5.18
1998 2072 1.693640 CCTCCCTGATTTGGCCAGT 59.306 57.895 5.11 0.00 0.00 4.00
2095 2169 1.001641 CCTTCACAAGCCCCTCCAG 60.002 63.158 0.00 0.00 0.00 3.86
2376 2450 2.437897 CTCAGCCCTGGCCTTGTT 59.562 61.111 3.32 0.00 43.17 2.83
2523 2597 2.361119 CTCCGTCGACCCATCTTTGATA 59.639 50.000 10.58 0.00 0.00 2.15
2691 2765 5.105310 AGTGTACAGTATCATGTCCACCTTC 60.105 44.000 0.00 0.00 39.96 3.46
2709 2783 2.683968 TGTGCGAGGATTGAAGTGTAC 58.316 47.619 0.00 0.00 0.00 2.90
2784 2858 2.282040 GCCTTGTGCCTGCTCACT 60.282 61.111 0.00 0.00 37.81 3.41
2931 3005 0.976641 CCAGGTAGTTGAGGAGCACA 59.023 55.000 0.00 0.00 0.00 4.57
2985 3059 3.007506 TGTTCTCATAAGCGACCTTCCAA 59.992 43.478 0.00 0.00 32.47 3.53
3127 3201 0.556747 ACCCCGTAGTAGAGCATCCT 59.443 55.000 0.00 0.00 33.66 3.24
3186 3260 1.379044 CTGGGCCACCACCATCTTC 60.379 63.158 0.00 0.00 43.37 2.87
3276 3350 0.756294 TCGGCTTCTTGAACCACTCA 59.244 50.000 0.00 0.00 0.00 3.41
3318 3392 1.012086 CGGACTTCGACGGTATCTCA 58.988 55.000 0.00 0.00 42.43 3.27
3429 3503 1.859427 GCACACACTGGCACCATCAG 61.859 60.000 0.00 0.00 38.16 2.90
3574 3648 6.437094 GCATTTGCATTATCTCTCCTTTCTC 58.563 40.000 0.00 0.00 41.59 2.87
3631 3705 7.929245 TCTTCAACTATATGCCGCAAATAAGTA 59.071 33.333 0.00 0.00 0.00 2.24
3663 3737 3.131933 CCGGGCACAAAATTGGATATTCA 59.868 43.478 0.00 0.00 0.00 2.57
3745 3819 7.599621 TCATCTTACATGCCAAACAAAATTCAG 59.400 33.333 0.00 0.00 0.00 3.02
3746 3820 7.440198 TCATCTTACATGCCAAACAAAATTCA 58.560 30.769 0.00 0.00 0.00 2.57
3747 3821 7.887996 TCATCTTACATGCCAAACAAAATTC 57.112 32.000 0.00 0.00 0.00 2.17
3748 3822 8.723311 CAATCATCTTACATGCCAAACAAAATT 58.277 29.630 0.00 0.00 0.00 1.82
3750 3824 7.440198 TCAATCATCTTACATGCCAAACAAAA 58.560 30.769 0.00 0.00 0.00 2.44
3754 3828 6.032094 CACTCAATCATCTTACATGCCAAAC 58.968 40.000 0.00 0.00 0.00 2.93
3779 3853 0.667993 AATTTGGCACACACCTCACG 59.332 50.000 0.00 0.00 39.29 4.35
3840 3914 2.223688 TGTTTGTGCAGACCCGATTTTG 60.224 45.455 0.00 0.00 0.00 2.44
3952 4026 1.070289 GGGGAAAGACGACTGAGTGTT 59.930 52.381 0.00 0.00 0.00 3.32
3953 4027 0.680061 GGGGAAAGACGACTGAGTGT 59.320 55.000 0.00 0.00 0.00 3.55
4131 4330 1.722011 GTGACGTACACTGGAATGGG 58.278 55.000 9.86 0.00 45.13 4.00
4146 4345 7.728847 TGTATCCTGCATATATGTTTGTGAC 57.271 36.000 14.14 7.13 0.00 3.67
4171 4490 7.093552 TGTGCTTAATTTGGCCTAATGTATTGT 60.094 33.333 13.37 0.00 0.00 2.71
4259 4580 7.575414 TTGTGAGTTTGCCTAGAAAAACATA 57.425 32.000 17.32 7.31 38.48 2.29
4260 4581 6.463995 TTGTGAGTTTGCCTAGAAAAACAT 57.536 33.333 17.32 7.16 38.48 2.71
4261 4582 5.906113 TTGTGAGTTTGCCTAGAAAAACA 57.094 34.783 17.32 6.46 38.48 2.83
4262 4583 5.232202 GCTTTGTGAGTTTGCCTAGAAAAAC 59.768 40.000 10.58 10.58 36.69 2.43
4263 4584 5.127031 AGCTTTGTGAGTTTGCCTAGAAAAA 59.873 36.000 0.00 0.00 0.00 1.94
4264 4585 4.644685 AGCTTTGTGAGTTTGCCTAGAAAA 59.355 37.500 0.00 0.00 0.00 2.29
4265 4586 4.207165 AGCTTTGTGAGTTTGCCTAGAAA 58.793 39.130 0.00 0.00 0.00 2.52
4266 4587 3.820557 AGCTTTGTGAGTTTGCCTAGAA 58.179 40.909 0.00 0.00 0.00 2.10
4267 4588 3.492102 AGCTTTGTGAGTTTGCCTAGA 57.508 42.857 0.00 0.00 0.00 2.43
4268 4589 4.574599 AAAGCTTTGTGAGTTTGCCTAG 57.425 40.909 11.80 0.00 0.00 3.02
4269 4590 5.337578 AAAAAGCTTTGTGAGTTTGCCTA 57.662 34.783 13.54 0.00 0.00 3.93
4270 4591 3.893326 AAAAGCTTTGTGAGTTTGCCT 57.107 38.095 13.54 0.00 0.00 4.75
4271 4592 6.257630 TGAATAAAAAGCTTTGTGAGTTTGCC 59.742 34.615 13.54 0.00 0.00 4.52
4272 4593 7.232945 TGAATAAAAAGCTTTGTGAGTTTGC 57.767 32.000 13.54 0.00 0.00 3.68
4273 4594 8.490355 GGATGAATAAAAAGCTTTGTGAGTTTG 58.510 33.333 13.54 0.00 0.00 2.93
4274 4595 7.382218 CGGATGAATAAAAAGCTTTGTGAGTTT 59.618 33.333 13.54 4.61 0.00 2.66
4275 4596 6.863126 CGGATGAATAAAAAGCTTTGTGAGTT 59.137 34.615 13.54 5.37 0.00 3.01
4276 4597 6.016276 ACGGATGAATAAAAAGCTTTGTGAGT 60.016 34.615 13.54 0.00 0.00 3.41
4277 4598 6.381801 ACGGATGAATAAAAAGCTTTGTGAG 58.618 36.000 13.54 0.00 0.00 3.51
4278 4599 6.016693 TGACGGATGAATAAAAAGCTTTGTGA 60.017 34.615 13.54 1.21 0.00 3.58
4279 4600 6.088085 GTGACGGATGAATAAAAAGCTTTGTG 59.912 38.462 13.54 0.00 0.00 3.33
4280 4601 6.149633 GTGACGGATGAATAAAAAGCTTTGT 58.850 36.000 13.54 10.19 0.00 2.83
4281 4602 6.088085 GTGTGACGGATGAATAAAAAGCTTTG 59.912 38.462 13.54 0.00 0.00 2.77
4282 4603 6.149633 GTGTGACGGATGAATAAAAAGCTTT 58.850 36.000 5.69 5.69 0.00 3.51
4283 4604 5.240623 TGTGTGACGGATGAATAAAAAGCTT 59.759 36.000 0.00 0.00 0.00 3.74
4284 4605 4.759693 TGTGTGACGGATGAATAAAAAGCT 59.240 37.500 0.00 0.00 0.00 3.74
4285 4606 5.041951 TGTGTGACGGATGAATAAAAAGC 57.958 39.130 0.00 0.00 0.00 3.51
4286 4607 6.241207 ACTGTGTGACGGATGAATAAAAAG 57.759 37.500 0.00 0.00 0.00 2.27
4287 4608 6.627395 AACTGTGTGACGGATGAATAAAAA 57.373 33.333 0.00 0.00 0.00 1.94
4288 4609 6.627395 AAACTGTGTGACGGATGAATAAAA 57.373 33.333 0.00 0.00 0.00 1.52
4289 4610 7.731882 TTAAACTGTGTGACGGATGAATAAA 57.268 32.000 0.00 0.00 0.00 1.40
4290 4611 7.094975 CCTTTAAACTGTGTGACGGATGAATAA 60.095 37.037 0.00 0.00 0.00 1.40
4291 4612 6.370442 CCTTTAAACTGTGTGACGGATGAATA 59.630 38.462 0.00 0.00 0.00 1.75
4292 4613 5.181245 CCTTTAAACTGTGTGACGGATGAAT 59.819 40.000 0.00 0.00 0.00 2.57
4293 4614 4.513692 CCTTTAAACTGTGTGACGGATGAA 59.486 41.667 0.00 0.00 0.00 2.57
4294 4615 4.062293 CCTTTAAACTGTGTGACGGATGA 58.938 43.478 0.00 0.00 0.00 2.92
4295 4616 3.188460 CCCTTTAAACTGTGTGACGGATG 59.812 47.826 0.00 0.00 0.00 3.51
4296 4617 3.071892 TCCCTTTAAACTGTGTGACGGAT 59.928 43.478 0.00 0.00 0.00 4.18
4297 4618 2.435069 TCCCTTTAAACTGTGTGACGGA 59.565 45.455 0.00 0.00 0.00 4.69
4298 4619 2.546789 GTCCCTTTAAACTGTGTGACGG 59.453 50.000 0.00 0.00 0.00 4.79
4299 4620 2.220133 CGTCCCTTTAAACTGTGTGACG 59.780 50.000 0.00 0.00 38.42 4.35
4300 4621 3.460103 TCGTCCCTTTAAACTGTGTGAC 58.540 45.455 0.00 0.00 0.00 3.67
4301 4622 3.823281 TCGTCCCTTTAAACTGTGTGA 57.177 42.857 0.00 0.00 0.00 3.58
4302 4623 3.303791 GCTTCGTCCCTTTAAACTGTGTG 60.304 47.826 0.00 0.00 0.00 3.82
4303 4624 2.876550 GCTTCGTCCCTTTAAACTGTGT 59.123 45.455 0.00 0.00 0.00 3.72
4304 4625 2.875933 TGCTTCGTCCCTTTAAACTGTG 59.124 45.455 0.00 0.00 0.00 3.66
4305 4626 3.202829 TGCTTCGTCCCTTTAAACTGT 57.797 42.857 0.00 0.00 0.00 3.55
4306 4627 4.274950 TCTTTGCTTCGTCCCTTTAAACTG 59.725 41.667 0.00 0.00 0.00 3.16
4307 4628 4.457466 TCTTTGCTTCGTCCCTTTAAACT 58.543 39.130 0.00 0.00 0.00 2.66
4308 4629 4.823790 TCTTTGCTTCGTCCCTTTAAAC 57.176 40.909 0.00 0.00 0.00 2.01
4309 4630 5.313712 AGATCTTTGCTTCGTCCCTTTAAA 58.686 37.500 0.00 0.00 0.00 1.52
4310 4631 4.906618 AGATCTTTGCTTCGTCCCTTTAA 58.093 39.130 0.00 0.00 0.00 1.52
4311 4632 4.504858 GAGATCTTTGCTTCGTCCCTTTA 58.495 43.478 0.00 0.00 0.00 1.85
4312 4633 3.339141 GAGATCTTTGCTTCGTCCCTTT 58.661 45.455 0.00 0.00 0.00 3.11
4313 4634 2.355209 GGAGATCTTTGCTTCGTCCCTT 60.355 50.000 0.00 0.00 0.00 3.95
4314 4635 1.208293 GGAGATCTTTGCTTCGTCCCT 59.792 52.381 0.00 0.00 0.00 4.20
4315 4636 1.066143 TGGAGATCTTTGCTTCGTCCC 60.066 52.381 0.00 0.00 0.00 4.46
4316 4637 2.386661 TGGAGATCTTTGCTTCGTCC 57.613 50.000 0.00 0.00 0.00 4.79
4317 4638 2.611292 CCATGGAGATCTTTGCTTCGTC 59.389 50.000 5.56 0.00 0.00 4.20
4318 4639 2.026822 ACCATGGAGATCTTTGCTTCGT 60.027 45.455 21.47 0.00 0.00 3.85
4319 4640 2.353889 CACCATGGAGATCTTTGCTTCG 59.646 50.000 21.47 0.00 0.00 3.79
4320 4641 3.376546 GTCACCATGGAGATCTTTGCTTC 59.623 47.826 21.47 0.00 0.00 3.86
4321 4642 3.350833 GTCACCATGGAGATCTTTGCTT 58.649 45.455 21.47 0.00 0.00 3.91
4322 4643 2.356535 GGTCACCATGGAGATCTTTGCT 60.357 50.000 21.47 0.00 0.00 3.91
4323 4644 2.019984 GGTCACCATGGAGATCTTTGC 58.980 52.381 21.47 2.52 0.00 3.68
4324 4645 3.641434 AGGTCACCATGGAGATCTTTG 57.359 47.619 21.47 4.07 0.00 2.77
4325 4646 3.135530 GCTAGGTCACCATGGAGATCTTT 59.864 47.826 27.16 9.51 29.48 2.52
4326 4647 2.703007 GCTAGGTCACCATGGAGATCTT 59.297 50.000 27.16 13.29 29.48 2.40
4327 4648 2.324541 GCTAGGTCACCATGGAGATCT 58.675 52.381 25.64 25.64 31.48 2.75
4328 4649 1.346068 GGCTAGGTCACCATGGAGATC 59.654 57.143 21.47 17.37 0.00 2.75
4329 4650 1.344393 TGGCTAGGTCACCATGGAGAT 60.344 52.381 21.47 4.48 0.00 2.75
4330 4651 0.042581 TGGCTAGGTCACCATGGAGA 59.957 55.000 21.47 14.37 0.00 3.71
4331 4652 0.911769 TTGGCTAGGTCACCATGGAG 59.088 55.000 21.47 11.61 35.42 3.86
4332 4653 1.004277 GTTTGGCTAGGTCACCATGGA 59.996 52.381 21.47 0.00 35.42 3.41
4333 4654 1.271871 TGTTTGGCTAGGTCACCATGG 60.272 52.381 11.19 11.19 35.42 3.66
4334 4655 2.198827 TGTTTGGCTAGGTCACCATG 57.801 50.000 0.00 0.00 35.42 3.66
4335 4656 2.308570 TCATGTTTGGCTAGGTCACCAT 59.691 45.455 0.00 0.00 35.42 3.55
4336 4657 1.702401 TCATGTTTGGCTAGGTCACCA 59.298 47.619 0.00 0.00 0.00 4.17
4337 4658 2.489938 TCATGTTTGGCTAGGTCACC 57.510 50.000 0.00 0.00 0.00 4.02
4338 4659 2.684881 CCATCATGTTTGGCTAGGTCAC 59.315 50.000 4.82 0.00 0.00 3.67
4339 4660 3.003394 CCATCATGTTTGGCTAGGTCA 57.997 47.619 4.82 0.00 0.00 4.02
4347 4668 1.666209 GGACCGGCCATCATGTTTGG 61.666 60.000 0.00 11.62 37.31 3.28
4348 4669 1.666209 GGGACCGGCCATCATGTTTG 61.666 60.000 15.49 0.00 38.95 2.93
4349 4670 1.379843 GGGACCGGCCATCATGTTT 60.380 57.895 15.49 0.00 38.95 2.83
4350 4671 2.275418 GGGACCGGCCATCATGTT 59.725 61.111 15.49 0.00 38.95 2.71
4351 4672 3.809013 GGGGACCGGCCATCATGT 61.809 66.667 15.49 0.00 40.86 3.21
4363 4684 1.670083 ACGCTTTAACGCTGGGGAC 60.670 57.895 2.20 0.00 36.19 4.46
4364 4685 1.669760 CACGCTTTAACGCTGGGGA 60.670 57.895 2.20 0.00 36.19 4.81
4365 4686 2.867472 CACGCTTTAACGCTGGGG 59.133 61.111 2.20 0.00 36.19 4.96
4366 4687 1.852067 AAGCACGCTTTAACGCTGGG 61.852 55.000 0.00 0.00 34.26 4.45
4367 4688 0.040425 AAAGCACGCTTTAACGCTGG 60.040 50.000 15.13 0.00 43.58 4.85
4368 4689 1.044725 CAAAGCACGCTTTAACGCTG 58.955 50.000 16.18 0.90 43.56 5.18
4369 4690 0.660300 GCAAAGCACGCTTTAACGCT 60.660 50.000 16.18 0.00 43.56 5.07
4370 4691 0.932585 TGCAAAGCACGCTTTAACGC 60.933 50.000 16.18 15.42 43.56 4.84
4371 4692 1.447938 CTTGCAAAGCACGCTTTAACG 59.552 47.619 16.18 6.36 43.56 3.18
4384 4705 0.908198 AAGGCCCACAAACTTGCAAA 59.092 45.000 0.00 0.00 0.00 3.68
4385 4706 1.781786 TAAGGCCCACAAACTTGCAA 58.218 45.000 0.00 0.00 0.00 4.08
4386 4707 1.410882 GTTAAGGCCCACAAACTTGCA 59.589 47.619 0.00 0.00 0.00 4.08
4387 4708 1.410882 TGTTAAGGCCCACAAACTTGC 59.589 47.619 0.00 0.00 0.00 4.01
4388 4709 4.335400 AATGTTAAGGCCCACAAACTTG 57.665 40.909 0.00 0.00 0.00 3.16
4389 4710 4.407296 TCAAATGTTAAGGCCCACAAACTT 59.593 37.500 0.00 0.00 0.00 2.66
4390 4711 3.964031 TCAAATGTTAAGGCCCACAAACT 59.036 39.130 0.00 0.00 0.00 2.66
4391 4712 4.306600 CTCAAATGTTAAGGCCCACAAAC 58.693 43.478 0.00 0.00 0.00 2.93
4392 4713 3.323403 CCTCAAATGTTAAGGCCCACAAA 59.677 43.478 0.00 0.00 0.00 2.83
4393 4714 2.896685 CCTCAAATGTTAAGGCCCACAA 59.103 45.455 0.00 0.00 0.00 3.33
4394 4715 2.158385 ACCTCAAATGTTAAGGCCCACA 60.158 45.455 0.00 0.00 33.21 4.17
4395 4716 2.525368 ACCTCAAATGTTAAGGCCCAC 58.475 47.619 0.00 0.00 33.21 4.61
4396 4717 2.990740 ACCTCAAATGTTAAGGCCCA 57.009 45.000 0.00 0.00 33.21 5.36
4397 4718 3.431415 AGAACCTCAAATGTTAAGGCCC 58.569 45.455 0.00 0.00 33.21 5.80
4398 4719 6.584185 TTTAGAACCTCAAATGTTAAGGCC 57.416 37.500 0.00 0.00 33.21 5.19
4399 4720 8.303876 TGAATTTAGAACCTCAAATGTTAAGGC 58.696 33.333 0.00 0.00 33.21 4.35


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

AutoCloner maintained by Alex Coulton.