Multiple sequence alignment - TraesCS5A01G192500

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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 TraesCS5A01G192500 chr5A 100.000 4147 0 0 1 4147 395918845 395922991 0.000000e+00 7659.0
1 TraesCS5A01G192500 chr5A 100.000 30 0 0 2041 2070 395920844 395920873 5.790000e-04 56.5
2 TraesCS5A01G192500 chr5A 100.000 30 0 0 2000 2029 395920885 395920914 5.790000e-04 56.5
3 TraesCS5A01G192500 chr5D 96.433 2635 68 15 936 3558 301571766 301569146 0.000000e+00 4322.0
4 TraesCS5A01G192500 chr5D 93.111 929 47 8 1 919 301572777 301571856 0.000000e+00 1345.0
5 TraesCS5A01G192500 chr5D 81.677 322 22 11 3575 3870 301569163 301568853 2.490000e-57 233.0
6 TraesCS5A01G192500 chr5D 100.000 30 0 0 2000 2029 301570658 301570629 5.790000e-04 56.5
7 TraesCS5A01G192500 chr5D 100.000 30 0 0 2041 2070 301570700 301570671 5.790000e-04 56.5
8 TraesCS5A01G192500 chr5B 92.018 1992 102 22 25 1994 344613649 344611693 0.000000e+00 2745.0
9 TraesCS5A01G192500 chr5B 89.555 1551 105 24 2041 3551 344611486 344609953 0.000000e+00 1914.0
10 TraesCS5A01G192500 chr5B 84.286 280 12 7 3575 3827 344609965 344609691 1.150000e-60 244.0
11 TraesCS5A01G192500 chrUn 100.000 422 0 0 1520 1941 476732137 476731716 0.000000e+00 780.0
12 TraesCS5A01G192500 chr2D 93.333 75 5 0 3785 3859 376701188 376701262 1.220000e-20 111.0
13 TraesCS5A01G192500 chr2A 96.875 64 2 0 3785 3848 754039013 754039076 1.580000e-19 108.0
14 TraesCS5A01G192500 chr7B 89.610 77 7 1 3787 3863 744208515 744208440 3.410000e-16 97.1
15 TraesCS5A01G192500 chr4D 89.744 78 4 1 3786 3859 21876135 21876058 3.410000e-16 97.1
16 TraesCS5A01G192500 chr1B 89.610 77 7 1 3786 3862 305291326 305291401 3.410000e-16 97.1
17 TraesCS5A01G192500 chr1B 86.905 84 8 2 3783 3866 32476723 32476643 1.590000e-14 91.6
18 TraesCS5A01G192500 chr6A 89.474 76 7 1 3787 3862 609572180 609572254 1.230000e-15 95.3


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 TraesCS5A01G192500 chr5A 395918845 395922991 4146 False 2590.666667 7659 100.000000 1 4147 3 chr5A.!!$F1 4146
1 TraesCS5A01G192500 chr5D 301568853 301572777 3924 True 1202.600000 4322 94.244200 1 3870 5 chr5D.!!$R1 3869
2 TraesCS5A01G192500 chr5B 344609691 344613649 3958 True 1634.333333 2745 88.619667 25 3827 3 chr5B.!!$R1 3802

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
278 280 0.582005 GGCGGTTGATAACGAGATGC 59.418 55.0 0.00 0.0 0.00 3.91 F
938 1023 0.957395 CCTGTCACTGACATGTGGGC 60.957 60.0 12.34 0.0 41.94 5.36 F
1380 1485 0.109319 GGGTAGTTCGTCGCGGTTAA 60.109 55.0 6.13 0.0 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1384 1.266989 CCATGTACGAGCGATCTAGCA 59.733 52.381 0.00 0.0 40.15 3.49 R
2875 3176 2.438021 ACAGAGCACTACCAAAGAACCA 59.562 45.455 0.00 0.0 0.00 3.67 R
3153 3455 1.736645 ACAGTGTACACGATGCGCC 60.737 57.895 19.93 0.0 36.20 6.53 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
23 24 3.396260 TCCGTTACTTGTTGAGGAAGG 57.604 47.619 0.00 0.00 34.51 3.46
27 28 3.006537 CGTTACTTGTTGAGGAAGGGAGA 59.993 47.826 0.00 0.00 31.72 3.71
55 56 1.417890 ACTGGCAGTGCAAGAAGTAGT 59.582 47.619 26.61 10.04 33.12 2.73
88 89 2.688446 AGCGTCGATGAGGATGTTAGAA 59.312 45.455 9.31 0.00 0.00 2.10
109 110 2.178273 CGAGACGGCGTGACATGA 59.822 61.111 21.19 0.00 0.00 3.07
220 221 3.027170 GCCAACATCACACCGAGCG 62.027 63.158 0.00 0.00 0.00 5.03
251 253 3.378112 TGTGAGAAAGCAGAACAAAGTGG 59.622 43.478 0.00 0.00 0.00 4.00
278 280 0.582005 GGCGGTTGATAACGAGATGC 59.418 55.000 0.00 0.00 0.00 3.91
394 396 2.184322 GACTTCCGCGGCTCATCA 59.816 61.111 23.51 0.00 0.00 3.07
422 424 2.995872 GCCGAGGAAGAGACAGCGT 61.996 63.158 0.00 0.00 0.00 5.07
467 469 3.537206 AAGAAGCGCGCTGGAAGGT 62.537 57.895 37.24 18.86 0.00 3.50
831 833 4.235762 ACGCTGGCCACTTGTCGT 62.236 61.111 0.00 4.21 0.00 4.34
834 844 2.743718 CTGGCCACTTGTCGTCCT 59.256 61.111 0.00 0.00 0.00 3.85
837 847 3.112709 GCCACTTGTCGTCCTCGC 61.113 66.667 0.00 0.00 36.96 5.03
838 848 2.805353 CCACTTGTCGTCCTCGCG 60.805 66.667 0.00 0.00 36.96 5.87
938 1023 0.957395 CCTGTCACTGACATGTGGGC 60.957 60.000 12.34 0.00 41.94 5.36
959 1044 2.392662 CAATAGTCCAGAGAGCCCTGA 58.607 52.381 0.00 0.00 36.29 3.86
960 1045 2.080654 ATAGTCCAGAGAGCCCTGAC 57.919 55.000 0.00 0.00 36.29 3.51
1010 1095 2.083774 TGGGCTTTACATGAGCTTTCG 58.916 47.619 0.00 0.00 40.01 3.46
1071 1156 1.776662 TCCCTTCCTGTCCTATCGTG 58.223 55.000 0.00 0.00 0.00 4.35
1088 1181 1.026718 GTGTCCTCTCCCAATTGCCG 61.027 60.000 0.00 0.00 0.00 5.69
1095 1188 2.361610 CCCAATTGCCGCAGTCCT 60.362 61.111 0.00 0.00 0.00 3.85
1201 1306 3.070748 CGCGAATCTATCTCTCTCTCCA 58.929 50.000 0.00 0.00 0.00 3.86
1203 1308 4.873259 CGCGAATCTATCTCTCTCTCCATA 59.127 45.833 0.00 0.00 0.00 2.74
1228 1333 3.796717 CCGCTCTGTTTCAAAAACTTTCC 59.203 43.478 4.40 0.00 0.00 3.13
1307 1412 0.941463 GCTCGTACATGGGATCAGCG 60.941 60.000 0.00 0.00 0.00 5.18
1312 1417 0.686789 TACATGGGATCAGCGGATGG 59.313 55.000 3.36 0.00 32.67 3.51
1315 1420 0.617413 ATGGGATCAGCGGATGGATC 59.383 55.000 3.36 0.72 39.31 3.36
1329 1434 6.998074 AGCGGATGGATCATTAACATTTCTTA 59.002 34.615 0.00 0.00 0.00 2.10
1380 1485 0.109319 GGGTAGTTCGTCGCGGTTAA 60.109 55.000 6.13 0.00 0.00 2.01
1515 1620 2.777459 ACCTCTTGATCTCGGGGTAT 57.223 50.000 4.77 0.00 0.00 2.73
2032 2296 6.028987 GCTTTTCAATTCTTGAGAGCTCATC 58.971 40.000 17.77 11.03 42.45 2.92
2247 2516 6.127026 ACCTTGTTGAGAAGAGTAGTGTTCTT 60.127 38.462 11.02 0.00 36.45 2.52
2789 3090 9.739276 CAATAAGGATACAAGAAGGGCATAATA 57.261 33.333 0.00 0.00 41.41 0.98
2875 3176 6.374417 ACTTTCCTCATACATGGTAGTTGT 57.626 37.500 0.00 0.00 0.00 3.32
3168 3470 3.550992 CGGGCGCATCGTGTACAC 61.551 66.667 16.32 16.32 0.00 2.90
3180 3482 2.946990 TCGTGTACACTGTGTCTTCAGA 59.053 45.455 23.01 9.02 38.63 3.27
3237 3539 2.544277 CCAGGTGGATGCATTATTTGCG 60.544 50.000 0.00 0.00 46.33 4.85
3248 3550 5.107109 GCATTATTTGCGTCATATCCACA 57.893 39.130 0.00 0.00 42.54 4.17
3254 3556 1.941975 TGCGTCATATCCACATGCAAG 59.058 47.619 0.00 0.00 0.00 4.01
3290 3592 0.375106 GCCAAACTCTATCGCTGCAC 59.625 55.000 0.00 0.00 0.00 4.57
3397 3702 4.122046 GTGTTTGAATTGCCAAGAAGCTT 58.878 39.130 0.00 0.00 0.00 3.74
3437 3743 2.034558 ACACTTTTGTCATTTGCTCGGG 59.965 45.455 0.00 0.00 0.00 5.14
3517 3823 2.481289 TTGATACAATGGTGTGGCGA 57.519 45.000 0.00 0.00 38.82 5.54
3537 3844 3.733380 CGATGTCTCAGAACTGTAGCTGG 60.733 52.174 0.00 0.00 33.05 4.85
3538 3845 1.895798 TGTCTCAGAACTGTAGCTGGG 59.104 52.381 0.00 7.26 33.89 4.45
3605 3912 3.265791 AGAGATTTTAGCAGCTTGGTCG 58.734 45.455 0.00 0.00 0.00 4.79
3611 3918 2.111999 TAGCAGCTTGGTCGCCTTGT 62.112 55.000 0.00 0.00 0.00 3.16
3736 4069 4.927267 AATTCAAGACCACATCCCAGTA 57.073 40.909 0.00 0.00 0.00 2.74
3743 4076 3.967987 AGACCACATCCCAGTATAGGTTC 59.032 47.826 0.00 0.00 0.00 3.62
3870 4203 9.649167 TTACAAAGGAAGTAGCAAGTTATCTAC 57.351 33.333 6.43 6.43 36.35 2.59
3871 4204 7.908453 ACAAAGGAAGTAGCAAGTTATCTACT 58.092 34.615 9.84 9.84 45.20 2.57
3872 4205 7.819900 ACAAAGGAAGTAGCAAGTTATCTACTG 59.180 37.037 14.25 7.29 43.21 2.74
3873 4206 6.472686 AGGAAGTAGCAAGTTATCTACTGG 57.527 41.667 14.25 0.00 43.21 4.00
3874 4207 6.195700 AGGAAGTAGCAAGTTATCTACTGGA 58.804 40.000 14.25 0.00 43.21 3.86
3875 4208 6.322712 AGGAAGTAGCAAGTTATCTACTGGAG 59.677 42.308 14.25 0.00 43.21 3.86
3876 4209 6.461788 GGAAGTAGCAAGTTATCTACTGGAGG 60.462 46.154 14.25 0.00 43.21 4.30
3877 4210 3.828875 AGCAAGTTATCTACTGGAGGC 57.171 47.619 0.00 0.00 37.12 4.70
3878 4211 2.436173 AGCAAGTTATCTACTGGAGGCC 59.564 50.000 0.00 0.00 37.12 5.19
3879 4212 2.436173 GCAAGTTATCTACTGGAGGCCT 59.564 50.000 3.86 3.86 37.12 5.19
3880 4213 3.493524 GCAAGTTATCTACTGGAGGCCTC 60.494 52.174 25.59 25.59 37.12 4.70
3898 4231 4.656117 CCCGCCGCCACCAAAAAC 62.656 66.667 0.00 0.00 0.00 2.43
3899 4232 3.905678 CCGCCGCCACCAAAAACA 61.906 61.111 0.00 0.00 0.00 2.83
3900 4233 2.105128 CGCCGCCACCAAAAACAA 59.895 55.556 0.00 0.00 0.00 2.83
3901 4234 1.300542 CGCCGCCACCAAAAACAAT 60.301 52.632 0.00 0.00 0.00 2.71
3902 4235 1.281566 CGCCGCCACCAAAAACAATC 61.282 55.000 0.00 0.00 0.00 2.67
3903 4236 0.033366 GCCGCCACCAAAAACAATCT 59.967 50.000 0.00 0.00 0.00 2.40
3904 4237 1.934849 GCCGCCACCAAAAACAATCTC 60.935 52.381 0.00 0.00 0.00 2.75
3905 4238 1.339610 CCGCCACCAAAAACAATCTCA 59.660 47.619 0.00 0.00 0.00 3.27
3906 4239 2.393764 CGCCACCAAAAACAATCTCAC 58.606 47.619 0.00 0.00 0.00 3.51
3907 4240 2.754472 GCCACCAAAAACAATCTCACC 58.246 47.619 0.00 0.00 0.00 4.02
3908 4241 2.547855 GCCACCAAAAACAATCTCACCC 60.548 50.000 0.00 0.00 0.00 4.61
3909 4242 2.697751 CCACCAAAAACAATCTCACCCA 59.302 45.455 0.00 0.00 0.00 4.51
3910 4243 3.492482 CCACCAAAAACAATCTCACCCAC 60.492 47.826 0.00 0.00 0.00 4.61
3911 4244 2.698274 ACCAAAAACAATCTCACCCACC 59.302 45.455 0.00 0.00 0.00 4.61
3912 4245 2.288152 CCAAAAACAATCTCACCCACCG 60.288 50.000 0.00 0.00 0.00 4.94
3913 4246 0.958822 AAAACAATCTCACCCACCGC 59.041 50.000 0.00 0.00 0.00 5.68
3914 4247 0.893727 AAACAATCTCACCCACCGCC 60.894 55.000 0.00 0.00 0.00 6.13
3915 4248 2.063015 AACAATCTCACCCACCGCCA 62.063 55.000 0.00 0.00 0.00 5.69
3916 4249 1.303236 CAATCTCACCCACCGCCAA 60.303 57.895 0.00 0.00 0.00 4.52
3917 4250 0.893270 CAATCTCACCCACCGCCAAA 60.893 55.000 0.00 0.00 0.00 3.28
3918 4251 0.039618 AATCTCACCCACCGCCAAAT 59.960 50.000 0.00 0.00 0.00 2.32
3919 4252 0.394352 ATCTCACCCACCGCCAAATC 60.394 55.000 0.00 0.00 0.00 2.17
3920 4253 2.034999 TCACCCACCGCCAAATCC 59.965 61.111 0.00 0.00 0.00 3.01
3921 4254 2.282816 CACCCACCGCCAAATCCA 60.283 61.111 0.00 0.00 0.00 3.41
3922 4255 2.282887 ACCCACCGCCAAATCCAC 60.283 61.111 0.00 0.00 0.00 4.02
3923 4256 3.068064 CCCACCGCCAAATCCACC 61.068 66.667 0.00 0.00 0.00 4.61
3924 4257 2.035626 CCACCGCCAAATCCACCT 59.964 61.111 0.00 0.00 0.00 4.00
3925 4258 2.342650 CCACCGCCAAATCCACCTG 61.343 63.158 0.00 0.00 0.00 4.00
3926 4259 2.676471 ACCGCCAAATCCACCTGC 60.676 61.111 0.00 0.00 0.00 4.85
3927 4260 3.451894 CCGCCAAATCCACCTGCC 61.452 66.667 0.00 0.00 0.00 4.85
3928 4261 3.814268 CGCCAAATCCACCTGCCG 61.814 66.667 0.00 0.00 0.00 5.69
3929 4262 4.133796 GCCAAATCCACCTGCCGC 62.134 66.667 0.00 0.00 0.00 6.53
3930 4263 3.451894 CCAAATCCACCTGCCGCC 61.452 66.667 0.00 0.00 0.00 6.13
3931 4264 3.814268 CAAATCCACCTGCCGCCG 61.814 66.667 0.00 0.00 0.00 6.46
3950 4283 2.045926 CGGAGGAAGCCACCAAGG 60.046 66.667 0.00 0.00 33.80 3.61
3959 4292 3.136123 CCACCAAGGCTGATGGCG 61.136 66.667 5.11 0.00 41.89 5.69
3960 4293 3.136123 CACCAAGGCTGATGGCGG 61.136 66.667 5.11 0.00 41.89 6.13
3993 4326 4.426313 CGCCCCCACTTTCCCCTC 62.426 72.222 0.00 0.00 0.00 4.30
3994 4327 2.941583 GCCCCCACTTTCCCCTCT 60.942 66.667 0.00 0.00 0.00 3.69
3995 4328 2.985116 GCCCCCACTTTCCCCTCTC 61.985 68.421 0.00 0.00 0.00 3.20
3996 4329 2.309504 CCCCCACTTTCCCCTCTCC 61.310 68.421 0.00 0.00 0.00 3.71
3997 4330 2.309504 CCCCACTTTCCCCTCTCCC 61.310 68.421 0.00 0.00 0.00 4.30
3998 4331 2.309504 CCCACTTTCCCCTCTCCCC 61.310 68.421 0.00 0.00 0.00 4.81
3999 4332 1.541368 CCACTTTCCCCTCTCCCCA 60.541 63.158 0.00 0.00 0.00 4.96
4000 4333 1.685820 CACTTTCCCCTCTCCCCAC 59.314 63.158 0.00 0.00 0.00 4.61
4001 4334 1.541620 ACTTTCCCCTCTCCCCACC 60.542 63.158 0.00 0.00 0.00 4.61
4002 4335 2.204244 TTTCCCCTCTCCCCACCC 60.204 66.667 0.00 0.00 0.00 4.61
4003 4336 3.902927 TTTCCCCTCTCCCCACCCC 62.903 68.421 0.00 0.00 0.00 4.95
4006 4339 4.371231 CCCTCTCCCCACCCCCTT 62.371 72.222 0.00 0.00 0.00 3.95
4007 4340 2.204306 CCTCTCCCCACCCCCTTT 60.204 66.667 0.00 0.00 0.00 3.11
4008 4341 1.857348 CCTCTCCCCACCCCCTTTT 60.857 63.158 0.00 0.00 0.00 2.27
4009 4342 1.691823 CTCTCCCCACCCCCTTTTC 59.308 63.158 0.00 0.00 0.00 2.29
4010 4343 0.846870 CTCTCCCCACCCCCTTTTCT 60.847 60.000 0.00 0.00 0.00 2.52
4011 4344 0.845102 TCTCCCCACCCCCTTTTCTC 60.845 60.000 0.00 0.00 0.00 2.87
4012 4345 0.846870 CTCCCCACCCCCTTTTCTCT 60.847 60.000 0.00 0.00 0.00 3.10
4013 4346 0.845102 TCCCCACCCCCTTTTCTCTC 60.845 60.000 0.00 0.00 0.00 3.20
4014 4347 1.691823 CCCACCCCCTTTTCTCTCC 59.308 63.158 0.00 0.00 0.00 3.71
4015 4348 1.691823 CCACCCCCTTTTCTCTCCC 59.308 63.158 0.00 0.00 0.00 4.30
4016 4349 1.140134 CCACCCCCTTTTCTCTCCCA 61.140 60.000 0.00 0.00 0.00 4.37
4017 4350 1.002857 CACCCCCTTTTCTCTCCCAT 58.997 55.000 0.00 0.00 0.00 4.00
4018 4351 1.002857 ACCCCCTTTTCTCTCCCATG 58.997 55.000 0.00 0.00 0.00 3.66
4019 4352 1.002857 CCCCCTTTTCTCTCCCATGT 58.997 55.000 0.00 0.00 0.00 3.21
4020 4353 1.064389 CCCCCTTTTCTCTCCCATGTC 60.064 57.143 0.00 0.00 0.00 3.06
4021 4354 1.407437 CCCCTTTTCTCTCCCATGTCG 60.407 57.143 0.00 0.00 0.00 4.35
4022 4355 1.279271 CCCTTTTCTCTCCCATGTCGT 59.721 52.381 0.00 0.00 0.00 4.34
4023 4356 2.622436 CCTTTTCTCTCCCATGTCGTC 58.378 52.381 0.00 0.00 0.00 4.20
4024 4357 2.263077 CTTTTCTCTCCCATGTCGTCG 58.737 52.381 0.00 0.00 0.00 5.12
4025 4358 1.541379 TTTCTCTCCCATGTCGTCGA 58.459 50.000 0.00 0.00 0.00 4.20
4026 4359 1.763968 TTCTCTCCCATGTCGTCGAT 58.236 50.000 0.00 0.00 0.00 3.59
4027 4360 1.309950 TCTCTCCCATGTCGTCGATC 58.690 55.000 0.00 0.00 0.00 3.69
4028 4361 1.134068 TCTCTCCCATGTCGTCGATCT 60.134 52.381 0.00 0.00 0.00 2.75
4029 4362 2.104281 TCTCTCCCATGTCGTCGATCTA 59.896 50.000 0.00 0.00 0.00 1.98
4030 4363 2.219458 TCTCCCATGTCGTCGATCTAC 58.781 52.381 0.00 0.00 0.00 2.59
4031 4364 1.947456 CTCCCATGTCGTCGATCTACA 59.053 52.381 0.00 0.00 0.00 2.74
4032 4365 2.554462 CTCCCATGTCGTCGATCTACAT 59.446 50.000 0.00 4.87 33.61 2.29
4033 4366 2.956333 TCCCATGTCGTCGATCTACATT 59.044 45.455 0.00 0.00 31.46 2.71
4034 4367 3.383505 TCCCATGTCGTCGATCTACATTT 59.616 43.478 0.00 0.00 31.46 2.32
4035 4368 3.736252 CCCATGTCGTCGATCTACATTTC 59.264 47.826 0.00 0.00 31.46 2.17
4036 4369 4.359706 CCATGTCGTCGATCTACATTTCA 58.640 43.478 0.00 0.00 31.46 2.69
4037 4370 4.984785 CCATGTCGTCGATCTACATTTCAT 59.015 41.667 0.00 0.00 31.46 2.57
4038 4371 5.117745 CCATGTCGTCGATCTACATTTCATC 59.882 44.000 0.00 0.00 31.46 2.92
4039 4372 5.500645 TGTCGTCGATCTACATTTCATCT 57.499 39.130 0.00 0.00 0.00 2.90
4040 4373 5.891451 TGTCGTCGATCTACATTTCATCTT 58.109 37.500 0.00 0.00 0.00 2.40
4041 4374 6.330278 TGTCGTCGATCTACATTTCATCTTT 58.670 36.000 0.00 0.00 0.00 2.52
4042 4375 7.477494 TGTCGTCGATCTACATTTCATCTTTA 58.523 34.615 0.00 0.00 0.00 1.85
4043 4376 7.644157 TGTCGTCGATCTACATTTCATCTTTAG 59.356 37.037 0.00 0.00 0.00 1.85
4044 4377 7.113684 GTCGTCGATCTACATTTCATCTTTAGG 59.886 40.741 0.00 0.00 0.00 2.69
4045 4378 6.129062 CGTCGATCTACATTTCATCTTTAGGC 60.129 42.308 0.00 0.00 0.00 3.93
4046 4379 6.146347 GTCGATCTACATTTCATCTTTAGGCC 59.854 42.308 0.00 0.00 0.00 5.19
4047 4380 5.119279 CGATCTACATTTCATCTTTAGGCCG 59.881 44.000 0.00 0.00 0.00 6.13
4048 4381 4.703897 TCTACATTTCATCTTTAGGCCGG 58.296 43.478 0.00 0.00 0.00 6.13
4049 4382 2.024414 ACATTTCATCTTTAGGCCGGC 58.976 47.619 21.18 21.18 0.00 6.13
4050 4383 1.338020 CATTTCATCTTTAGGCCGGCC 59.662 52.381 39.29 39.29 0.00 6.13
4051 4384 0.746563 TTTCATCTTTAGGCCGGCCG 60.747 55.000 38.88 25.13 41.95 6.13
4052 4385 3.279875 CATCTTTAGGCCGGCCGC 61.280 66.667 38.88 17.88 41.95 6.53
4053 4386 3.792736 ATCTTTAGGCCGGCCGCA 61.793 61.111 38.88 28.10 41.95 5.69
4054 4387 3.120086 ATCTTTAGGCCGGCCGCAT 62.120 57.895 38.88 25.12 41.95 4.73
4055 4388 2.624674 ATCTTTAGGCCGGCCGCATT 62.625 55.000 38.88 24.73 41.95 3.56
4056 4389 2.826738 TTTAGGCCGGCCGCATTC 60.827 61.111 38.88 15.37 41.95 2.67
4063 4396 3.202001 CGGCCGCATTCGTCCATT 61.202 61.111 14.67 0.00 32.38 3.16
4064 4397 2.408835 GGCCGCATTCGTCCATTG 59.591 61.111 0.00 0.00 33.24 2.82
4065 4398 2.408835 GCCGCATTCGTCCATTGG 59.591 61.111 0.00 0.00 0.00 3.16
4066 4399 2.406616 GCCGCATTCGTCCATTGGT 61.407 57.895 1.86 0.00 0.00 3.67
4067 4400 1.429021 CCGCATTCGTCCATTGGTG 59.571 57.895 1.86 0.00 0.00 4.17
4069 4402 1.305219 CGCATTCGTCCATTGGTGGT 61.305 55.000 1.86 0.00 46.16 4.16
4070 4403 0.171007 GCATTCGTCCATTGGTGGTG 59.829 55.000 1.86 2.18 46.16 4.17
4071 4404 0.171007 CATTCGTCCATTGGTGGTGC 59.829 55.000 1.86 0.00 46.16 5.01
4072 4405 0.251121 ATTCGTCCATTGGTGGTGCA 60.251 50.000 1.86 0.00 46.16 4.57
4073 4406 0.251121 TTCGTCCATTGGTGGTGCAT 60.251 50.000 1.86 0.00 46.16 3.96
4074 4407 0.676466 TCGTCCATTGGTGGTGCATC 60.676 55.000 1.86 0.00 46.16 3.91
4075 4408 1.802636 GTCCATTGGTGGTGCATCG 59.197 57.895 1.86 0.00 46.16 3.84
4076 4409 1.378382 TCCATTGGTGGTGCATCGG 60.378 57.895 1.86 0.00 46.16 4.18
4077 4410 1.378382 CCATTGGTGGTGCATCGGA 60.378 57.895 0.00 0.00 40.83 4.55
4078 4411 0.752743 CCATTGGTGGTGCATCGGAT 60.753 55.000 0.00 0.00 40.83 4.18
4079 4412 0.382873 CATTGGTGGTGCATCGGATG 59.617 55.000 13.63 13.63 0.00 3.51
4080 4413 0.255604 ATTGGTGGTGCATCGGATGA 59.744 50.000 21.69 4.28 0.00 2.92
4081 4414 0.676466 TTGGTGGTGCATCGGATGAC 60.676 55.000 21.69 14.99 0.00 3.06
4082 4415 1.221840 GGTGGTGCATCGGATGACT 59.778 57.895 21.69 0.00 0.00 3.41
4083 4416 0.392998 GGTGGTGCATCGGATGACTT 60.393 55.000 21.69 0.00 0.00 3.01
4084 4417 1.009829 GTGGTGCATCGGATGACTTC 58.990 55.000 21.69 4.41 0.00 3.01
4085 4418 0.904649 TGGTGCATCGGATGACTTCT 59.095 50.000 21.69 0.00 0.00 2.85
4086 4419 1.134699 TGGTGCATCGGATGACTTCTC 60.135 52.381 21.69 3.34 0.00 2.87
4087 4420 1.203928 GTGCATCGGATGACTTCTCG 58.796 55.000 21.69 0.00 0.00 4.04
4088 4421 0.528466 TGCATCGGATGACTTCTCGC 60.528 55.000 21.69 4.07 0.00 5.03
4089 4422 1.543941 GCATCGGATGACTTCTCGCG 61.544 60.000 21.69 0.00 0.00 5.87
4090 4423 0.936764 CATCGGATGACTTCTCGCGG 60.937 60.000 12.67 0.00 0.00 6.46
4091 4424 2.076622 ATCGGATGACTTCTCGCGGG 62.077 60.000 6.13 1.01 0.00 6.13
4092 4425 2.586357 GGATGACTTCTCGCGGGC 60.586 66.667 6.13 0.00 0.00 6.13
4093 4426 2.184322 GATGACTTCTCGCGGGCA 59.816 61.111 6.13 0.00 0.00 5.36
4094 4427 2.125512 ATGACTTCTCGCGGGCAC 60.126 61.111 6.13 0.00 0.00 5.01
4095 4428 2.835701 GATGACTTCTCGCGGGCACA 62.836 60.000 6.13 1.10 0.00 4.57
4096 4429 2.125512 GACTTCTCGCGGGCACAT 60.126 61.111 6.13 0.00 0.00 3.21
4097 4430 2.434884 ACTTCTCGCGGGCACATG 60.435 61.111 6.13 0.00 0.00 3.21
4098 4431 2.125552 CTTCTCGCGGGCACATGA 60.126 61.111 6.13 0.00 0.00 3.07
4099 4432 2.434185 TTCTCGCGGGCACATGAC 60.434 61.111 6.13 0.00 0.00 3.06
4100 4433 3.950794 TTCTCGCGGGCACATGACC 62.951 63.158 6.13 0.00 40.84 4.02
4117 4450 3.977244 CCCGCCGCTGTTGCTTTT 61.977 61.111 0.00 0.00 36.97 2.27
4118 4451 2.730604 CCGCCGCTGTTGCTTTTG 60.731 61.111 0.00 0.00 36.97 2.44
4119 4452 2.730604 CGCCGCTGTTGCTTTTGG 60.731 61.111 0.00 0.00 36.97 3.28
4120 4453 2.356194 GCCGCTGTTGCTTTTGGG 60.356 61.111 0.00 0.00 36.97 4.12
4121 4454 2.356194 CCGCTGTTGCTTTTGGGC 60.356 61.111 0.00 0.00 36.97 5.36
4122 4455 2.730094 CGCTGTTGCTTTTGGGCT 59.270 55.556 0.00 0.00 36.97 5.19
4123 4456 1.372128 CGCTGTTGCTTTTGGGCTC 60.372 57.895 0.00 0.00 36.97 4.70
4124 4457 1.741525 GCTGTTGCTTTTGGGCTCA 59.258 52.632 0.00 0.00 36.03 4.26
4125 4458 0.319297 GCTGTTGCTTTTGGGCTCAG 60.319 55.000 0.00 0.00 37.64 3.35
4126 4459 0.319297 CTGTTGCTTTTGGGCTCAGC 60.319 55.000 0.00 0.00 32.46 4.26
4127 4460 0.756442 TGTTGCTTTTGGGCTCAGCT 60.756 50.000 0.00 0.00 34.42 4.24
4128 4461 0.038801 GTTGCTTTTGGGCTCAGCTC 60.039 55.000 0.00 0.00 34.42 4.09
4129 4462 0.178981 TTGCTTTTGGGCTCAGCTCT 60.179 50.000 0.00 0.00 34.42 4.09
4130 4463 0.607489 TGCTTTTGGGCTCAGCTCTC 60.607 55.000 0.00 0.00 34.42 3.20
4131 4464 1.311651 GCTTTTGGGCTCAGCTCTCC 61.312 60.000 0.00 0.00 0.00 3.71
4132 4465 0.327591 CTTTTGGGCTCAGCTCTCCT 59.672 55.000 0.00 0.00 0.00 3.69
4133 4466 0.326264 TTTTGGGCTCAGCTCTCCTC 59.674 55.000 0.00 0.00 0.00 3.71
4134 4467 0.546267 TTTGGGCTCAGCTCTCCTCT 60.546 55.000 0.00 0.00 0.00 3.69
4135 4468 1.263342 TTGGGCTCAGCTCTCCTCTG 61.263 60.000 0.00 0.00 0.00 3.35
4136 4469 1.381056 GGGCTCAGCTCTCCTCTGA 60.381 63.158 0.00 0.00 38.16 3.27
4137 4470 0.975040 GGGCTCAGCTCTCCTCTGAA 60.975 60.000 0.00 0.00 39.77 3.02
4138 4471 0.175531 GGCTCAGCTCTCCTCTGAAC 59.824 60.000 0.00 0.00 39.77 3.18
4139 4472 0.175531 GCTCAGCTCTCCTCTGAACC 59.824 60.000 0.00 0.00 39.77 3.62
4140 4473 0.823460 CTCAGCTCTCCTCTGAACCC 59.177 60.000 0.00 0.00 39.77 4.11
4141 4474 0.967887 TCAGCTCTCCTCTGAACCCG 60.968 60.000 0.00 0.00 37.61 5.28
4142 4475 2.185608 GCTCTCCTCTGAACCCGC 59.814 66.667 0.00 0.00 0.00 6.13
4143 4476 2.492090 CTCTCCTCTGAACCCGCG 59.508 66.667 0.00 0.00 0.00 6.46
4144 4477 3.708220 CTCTCCTCTGAACCCGCGC 62.708 68.421 0.00 0.00 0.00 6.86
4145 4478 4.821589 CTCCTCTGAACCCGCGCC 62.822 72.222 0.00 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 1.163554 CTGCCAGTTGCTTCTTCTCC 58.836 55.000 0.00 0.00 42.00 3.71
27 28 0.752743 TGCACTGCCAGTTGCTTCTT 60.753 50.000 16.45 0.00 42.00 2.52
88 89 4.702081 GTCACGCCGTCTCGCACT 62.702 66.667 0.00 0.00 0.00 4.40
109 110 1.194781 ACACCTCCATTCTCCTGCGT 61.195 55.000 0.00 0.00 0.00 5.24
220 221 1.905922 GCTTTCTCACAGTGCTCGCC 61.906 60.000 0.00 0.00 0.00 5.54
251 253 2.524951 TTATCAACCGCCGGTGGACC 62.525 60.000 40.02 2.94 38.63 4.46
278 280 1.686325 CCCGTATGACCCTCCACCTG 61.686 65.000 0.00 0.00 0.00 4.00
467 469 0.844661 ATGCCTGTACCCCTGGTGAA 60.845 55.000 0.00 0.00 36.19 3.18
474 476 0.529119 CGACGTAATGCCTGTACCCC 60.529 60.000 0.00 0.00 0.00 4.95
576 578 4.200283 CGCTCTCCTCACGCCTCC 62.200 72.222 0.00 0.00 0.00 4.30
730 732 1.000359 TCTCCCGATGTCTGGAGCA 60.000 57.895 13.73 3.19 44.14 4.26
733 735 2.121538 CGCTCTCCCGATGTCTGGA 61.122 63.158 0.00 0.00 0.00 3.86
882 894 1.130613 CGGCTTTTCTTGAGCGTCG 59.869 57.895 0.00 0.00 41.03 5.12
887 899 2.202222 CGCGCGGCTTTTCTTGAG 60.202 61.111 24.84 0.00 0.00 3.02
938 1023 1.415659 CAGGGCTCTCTGGACTATTGG 59.584 57.143 0.00 0.00 0.00 3.16
1071 1156 2.115291 GCGGCAATTGGGAGAGGAC 61.115 63.158 7.72 0.00 0.00 3.85
1088 1181 1.406860 GGGGGAGAGATGAGGACTGC 61.407 65.000 0.00 0.00 0.00 4.40
1095 1188 2.609339 CGGGAGGGGGAGAGATGA 59.391 66.667 0.00 0.00 0.00 2.92
1181 1274 6.017109 GGATATGGAGAGAGAGATAGATTCGC 60.017 46.154 0.00 0.00 0.00 4.70
1201 1306 5.010282 AGTTTTTGAAACAGAGCGGGATAT 58.990 37.500 6.35 0.00 0.00 1.63
1203 1308 3.222603 AGTTTTTGAAACAGAGCGGGAT 58.777 40.909 6.35 0.00 0.00 3.85
1228 1333 1.927895 GTGAAGTACGAGGATGGCAG 58.072 55.000 0.00 0.00 0.00 4.85
1279 1384 1.266989 CCATGTACGAGCGATCTAGCA 59.733 52.381 0.00 0.00 40.15 3.49
1307 1412 7.228706 ACGGTAAGAAATGTTAATGATCCATCC 59.771 37.037 0.00 0.00 0.00 3.51
1312 1417 8.649973 AGAGACGGTAAGAAATGTTAATGATC 57.350 34.615 0.00 0.00 0.00 2.92
1315 1420 8.808529 CACTAGAGACGGTAAGAAATGTTAATG 58.191 37.037 0.00 0.00 0.00 1.90
1349 1454 3.000727 CGAACTACCCTTTAGGCAACAG 58.999 50.000 0.00 0.00 40.58 3.16
1380 1485 2.663196 GCTTACTGCGGTCCCAGT 59.337 61.111 0.00 14.93 46.98 4.00
1515 1620 5.422650 AGGGTTAACTGTAAAAAGCACCAAA 59.577 36.000 5.42 0.00 0.00 3.28
2032 2296 6.664515 TGAAAAGCTAAAACTTGTGATACGG 58.335 36.000 0.00 0.00 0.00 4.02
2247 2516 7.335627 TCTCAGAAGACAAAACTCCTTTACAA 58.664 34.615 0.00 0.00 0.00 2.41
2789 3090 8.087303 AGGTTTTAAAGGAGGTACGATTATCT 57.913 34.615 0.00 0.00 0.00 1.98
2875 3176 2.438021 ACAGAGCACTACCAAAGAACCA 59.562 45.455 0.00 0.00 0.00 3.67
3027 3329 3.181475 ACAGGCGTGTCCTCACTTATATG 60.181 47.826 6.15 0.00 45.52 1.78
3153 3455 1.736645 ACAGTGTACACGATGCGCC 60.737 57.895 19.93 0.00 36.20 6.53
3168 3470 5.755813 CCACTGAAAATTCTGAAGACACAG 58.244 41.667 6.99 12.40 39.02 3.66
3180 3482 5.343307 AGTTTTCACAGCCACTGAAAATT 57.657 34.783 13.79 9.06 45.04 1.82
3237 3539 4.142315 ACAAAGCTTGCATGTGGATATGAC 60.142 41.667 0.00 0.00 0.00 3.06
3254 3556 4.745837 TTGGCAATGCAAAATACAAAGC 57.254 36.364 7.79 0.00 0.00 3.51
3397 3702 9.979578 AAAAGTGTCAAGTGATAAATTGCATAA 57.020 25.926 0.00 0.00 0.00 1.90
3437 3743 2.344025 CCTAGAAGGTTTACGGTGTGC 58.656 52.381 0.00 0.00 0.00 4.57
3517 3823 2.499289 CCCAGCTACAGTTCTGAGACAT 59.501 50.000 6.83 0.00 32.26 3.06
3564 3871 4.822026 TCTTTCTTTTTCACCCGCAAAAA 58.178 34.783 0.00 0.00 32.93 1.94
3565 3872 4.158764 TCTCTTTCTTTTTCACCCGCAAAA 59.841 37.500 0.00 0.00 0.00 2.44
3566 3873 3.697045 TCTCTTTCTTTTTCACCCGCAAA 59.303 39.130 0.00 0.00 0.00 3.68
3567 3874 3.283751 TCTCTTTCTTTTTCACCCGCAA 58.716 40.909 0.00 0.00 0.00 4.85
3568 3875 2.925724 TCTCTTTCTTTTTCACCCGCA 58.074 42.857 0.00 0.00 0.00 5.69
3569 3876 4.505313 AATCTCTTTCTTTTTCACCCGC 57.495 40.909 0.00 0.00 0.00 6.13
3570 3877 6.582672 GCTAAAATCTCTTTCTTTTTCACCCG 59.417 38.462 0.00 0.00 0.00 5.28
3571 3878 7.433680 TGCTAAAATCTCTTTCTTTTTCACCC 58.566 34.615 0.00 0.00 0.00 4.61
3572 3879 7.115520 GCTGCTAAAATCTCTTTCTTTTTCACC 59.884 37.037 0.00 0.00 0.00 4.02
3573 3880 7.864882 AGCTGCTAAAATCTCTTTCTTTTTCAC 59.135 33.333 0.00 0.00 0.00 3.18
3574 3881 7.945134 AGCTGCTAAAATCTCTTTCTTTTTCA 58.055 30.769 0.00 0.00 0.00 2.69
3575 3882 8.697960 CAAGCTGCTAAAATCTCTTTCTTTTTC 58.302 33.333 0.90 0.00 0.00 2.29
3576 3883 7.654923 CCAAGCTGCTAAAATCTCTTTCTTTTT 59.345 33.333 0.90 0.00 0.00 1.94
3577 3884 7.150640 CCAAGCTGCTAAAATCTCTTTCTTTT 58.849 34.615 0.90 0.00 0.00 2.27
3578 3885 6.266330 ACCAAGCTGCTAAAATCTCTTTCTTT 59.734 34.615 0.90 0.00 0.00 2.52
3579 3886 5.772169 ACCAAGCTGCTAAAATCTCTTTCTT 59.228 36.000 0.90 0.00 0.00 2.52
3580 3887 5.320277 ACCAAGCTGCTAAAATCTCTTTCT 58.680 37.500 0.90 0.00 0.00 2.52
3581 3888 5.635417 ACCAAGCTGCTAAAATCTCTTTC 57.365 39.130 0.90 0.00 0.00 2.62
3582 3889 4.154918 CGACCAAGCTGCTAAAATCTCTTT 59.845 41.667 0.90 0.00 0.00 2.52
3583 3890 3.686726 CGACCAAGCTGCTAAAATCTCTT 59.313 43.478 0.90 0.00 0.00 2.85
3584 3891 3.265791 CGACCAAGCTGCTAAAATCTCT 58.734 45.455 0.90 0.00 0.00 3.10
3585 3892 2.223135 GCGACCAAGCTGCTAAAATCTC 60.223 50.000 0.90 0.00 0.00 2.75
3605 3912 2.793278 ATCGACCAAACAAACAAGGC 57.207 45.000 0.00 0.00 0.00 4.35
3611 3918 4.634184 TTCCGAAAATCGACCAAACAAA 57.366 36.364 0.58 0.00 43.74 2.83
3736 4069 7.182817 TGAATTAGTGCTACACTGAACCTAT 57.817 36.000 10.42 0.00 45.01 2.57
3842 4175 9.220767 AGATAACTTGCTACTTCCTTTGTAAAG 57.779 33.333 0.00 0.00 35.79 1.85
3847 4180 7.278868 CCAGTAGATAACTTGCTACTTCCTTTG 59.721 40.741 0.00 0.00 43.44 2.77
3849 4182 6.668283 TCCAGTAGATAACTTGCTACTTCCTT 59.332 38.462 0.00 0.00 43.44 3.36
3853 4186 5.163395 GCCTCCAGTAGATAACTTGCTACTT 60.163 44.000 0.00 0.00 43.44 2.24
3855 4188 4.501743 GGCCTCCAGTAGATAACTTGCTAC 60.502 50.000 0.00 0.00 35.76 3.58
3881 4214 4.656117 GTTTTTGGTGGCGGCGGG 62.656 66.667 9.78 0.00 0.00 6.13
3882 4215 2.707529 ATTGTTTTTGGTGGCGGCGG 62.708 55.000 9.78 0.00 0.00 6.13
3883 4216 1.281566 GATTGTTTTTGGTGGCGGCG 61.282 55.000 0.51 0.51 0.00 6.46
3884 4217 0.033366 AGATTGTTTTTGGTGGCGGC 59.967 50.000 0.00 0.00 0.00 6.53
3885 4218 1.339610 TGAGATTGTTTTTGGTGGCGG 59.660 47.619 0.00 0.00 0.00 6.13
3886 4219 2.393764 GTGAGATTGTTTTTGGTGGCG 58.606 47.619 0.00 0.00 0.00 5.69
3887 4220 2.547855 GGGTGAGATTGTTTTTGGTGGC 60.548 50.000 0.00 0.00 0.00 5.01
3888 4221 2.697751 TGGGTGAGATTGTTTTTGGTGG 59.302 45.455 0.00 0.00 0.00 4.61
3889 4222 3.492482 GGTGGGTGAGATTGTTTTTGGTG 60.492 47.826 0.00 0.00 0.00 4.17
3890 4223 2.698274 GGTGGGTGAGATTGTTTTTGGT 59.302 45.455 0.00 0.00 0.00 3.67
3891 4224 2.288152 CGGTGGGTGAGATTGTTTTTGG 60.288 50.000 0.00 0.00 0.00 3.28
3892 4225 2.862140 GCGGTGGGTGAGATTGTTTTTG 60.862 50.000 0.00 0.00 0.00 2.44
3893 4226 1.339929 GCGGTGGGTGAGATTGTTTTT 59.660 47.619 0.00 0.00 0.00 1.94
3894 4227 0.958822 GCGGTGGGTGAGATTGTTTT 59.041 50.000 0.00 0.00 0.00 2.43
3895 4228 0.893727 GGCGGTGGGTGAGATTGTTT 60.894 55.000 0.00 0.00 0.00 2.83
3896 4229 1.303317 GGCGGTGGGTGAGATTGTT 60.303 57.895 0.00 0.00 0.00 2.83
3897 4230 2.063015 TTGGCGGTGGGTGAGATTGT 62.063 55.000 0.00 0.00 0.00 2.71
3898 4231 0.893270 TTTGGCGGTGGGTGAGATTG 60.893 55.000 0.00 0.00 0.00 2.67
3899 4232 0.039618 ATTTGGCGGTGGGTGAGATT 59.960 50.000 0.00 0.00 0.00 2.40
3900 4233 0.394352 GATTTGGCGGTGGGTGAGAT 60.394 55.000 0.00 0.00 0.00 2.75
3901 4234 1.002624 GATTTGGCGGTGGGTGAGA 60.003 57.895 0.00 0.00 0.00 3.27
3902 4235 2.046285 GGATTTGGCGGTGGGTGAG 61.046 63.158 0.00 0.00 0.00 3.51
3903 4236 2.034999 GGATTTGGCGGTGGGTGA 59.965 61.111 0.00 0.00 0.00 4.02
3904 4237 2.282816 TGGATTTGGCGGTGGGTG 60.283 61.111 0.00 0.00 0.00 4.61
3905 4238 2.282887 GTGGATTTGGCGGTGGGT 60.283 61.111 0.00 0.00 0.00 4.51
3906 4239 3.068064 GGTGGATTTGGCGGTGGG 61.068 66.667 0.00 0.00 0.00 4.61
3907 4240 2.035626 AGGTGGATTTGGCGGTGG 59.964 61.111 0.00 0.00 0.00 4.61
3908 4241 2.993471 GCAGGTGGATTTGGCGGTG 61.993 63.158 0.00 0.00 0.00 4.94
3909 4242 2.676471 GCAGGTGGATTTGGCGGT 60.676 61.111 0.00 0.00 0.00 5.68
3910 4243 3.451894 GGCAGGTGGATTTGGCGG 61.452 66.667 0.00 0.00 0.00 6.13
3912 4245 4.133796 GCGGCAGGTGGATTTGGC 62.134 66.667 0.00 0.00 36.60 4.52
3913 4246 3.451894 GGCGGCAGGTGGATTTGG 61.452 66.667 3.07 0.00 0.00 3.28
3914 4247 3.814268 CGGCGGCAGGTGGATTTG 61.814 66.667 10.53 0.00 0.00 2.32
3931 4264 4.344865 TTGGTGGCTTCCTCCGGC 62.345 66.667 0.00 0.00 39.80 6.13
3932 4265 2.045926 CTTGGTGGCTTCCTCCGG 60.046 66.667 0.00 0.00 39.80 5.14
3933 4266 2.045926 CCTTGGTGGCTTCCTCCG 60.046 66.667 0.23 0.00 39.80 4.63
3943 4276 3.136123 CCGCCATCAGCCTTGGTG 61.136 66.667 4.23 4.23 43.04 4.17
3976 4309 4.426313 GAGGGGAAAGTGGGGGCG 62.426 72.222 0.00 0.00 0.00 6.13
3977 4310 2.941583 AGAGGGGAAAGTGGGGGC 60.942 66.667 0.00 0.00 0.00 5.80
3978 4311 2.309504 GGAGAGGGGAAAGTGGGGG 61.310 68.421 0.00 0.00 0.00 5.40
3979 4312 2.309504 GGGAGAGGGGAAAGTGGGG 61.310 68.421 0.00 0.00 0.00 4.96
3980 4313 2.309504 GGGGAGAGGGGAAAGTGGG 61.310 68.421 0.00 0.00 0.00 4.61
3981 4314 1.541368 TGGGGAGAGGGGAAAGTGG 60.541 63.158 0.00 0.00 0.00 4.00
3982 4315 1.685820 GTGGGGAGAGGGGAAAGTG 59.314 63.158 0.00 0.00 0.00 3.16
3983 4316 1.541620 GGTGGGGAGAGGGGAAAGT 60.542 63.158 0.00 0.00 0.00 2.66
3984 4317 2.309504 GGGTGGGGAGAGGGGAAAG 61.310 68.421 0.00 0.00 0.00 2.62
3985 4318 2.204244 GGGTGGGGAGAGGGGAAA 60.204 66.667 0.00 0.00 0.00 3.13
3986 4319 4.364686 GGGGTGGGGAGAGGGGAA 62.365 72.222 0.00 0.00 0.00 3.97
3989 4322 3.910646 AAAGGGGGTGGGGAGAGGG 62.911 68.421 0.00 0.00 0.00 4.30
3990 4323 1.857348 AAAAGGGGGTGGGGAGAGG 60.857 63.158 0.00 0.00 0.00 3.69
3991 4324 0.846870 AGAAAAGGGGGTGGGGAGAG 60.847 60.000 0.00 0.00 0.00 3.20
3992 4325 0.845102 GAGAAAAGGGGGTGGGGAGA 60.845 60.000 0.00 0.00 0.00 3.71
3993 4326 0.846870 AGAGAAAAGGGGGTGGGGAG 60.847 60.000 0.00 0.00 0.00 4.30
3994 4327 0.845102 GAGAGAAAAGGGGGTGGGGA 60.845 60.000 0.00 0.00 0.00 4.81
3995 4328 1.691823 GAGAGAAAAGGGGGTGGGG 59.308 63.158 0.00 0.00 0.00 4.96
3996 4329 1.691823 GGAGAGAAAAGGGGGTGGG 59.308 63.158 0.00 0.00 0.00 4.61
3997 4330 1.140134 TGGGAGAGAAAAGGGGGTGG 61.140 60.000 0.00 0.00 0.00 4.61
3998 4331 1.002857 ATGGGAGAGAAAAGGGGGTG 58.997 55.000 0.00 0.00 0.00 4.61
3999 4332 1.002857 CATGGGAGAGAAAAGGGGGT 58.997 55.000 0.00 0.00 0.00 4.95
4000 4333 1.002857 ACATGGGAGAGAAAAGGGGG 58.997 55.000 0.00 0.00 0.00 5.40
4001 4334 1.407437 CGACATGGGAGAGAAAAGGGG 60.407 57.143 0.00 0.00 0.00 4.79
4002 4335 1.279271 ACGACATGGGAGAGAAAAGGG 59.721 52.381 0.00 0.00 0.00 3.95
4003 4336 2.622436 GACGACATGGGAGAGAAAAGG 58.378 52.381 0.00 0.00 0.00 3.11
4004 4337 2.094700 TCGACGACATGGGAGAGAAAAG 60.095 50.000 0.00 0.00 0.00 2.27
4005 4338 1.890489 TCGACGACATGGGAGAGAAAA 59.110 47.619 0.00 0.00 0.00 2.29
4006 4339 1.541379 TCGACGACATGGGAGAGAAA 58.459 50.000 0.00 0.00 0.00 2.52
4007 4340 1.676529 GATCGACGACATGGGAGAGAA 59.323 52.381 0.00 0.00 0.00 2.87
4008 4341 1.134068 AGATCGACGACATGGGAGAGA 60.134 52.381 0.00 0.00 0.00 3.10
4009 4342 1.313772 AGATCGACGACATGGGAGAG 58.686 55.000 0.00 0.00 0.00 3.20
4010 4343 2.219458 GTAGATCGACGACATGGGAGA 58.781 52.381 0.00 0.00 0.00 3.71
4011 4344 1.947456 TGTAGATCGACGACATGGGAG 59.053 52.381 0.00 0.00 0.00 4.30
4012 4345 2.047002 TGTAGATCGACGACATGGGA 57.953 50.000 0.00 0.00 0.00 4.37
4013 4346 3.371102 AATGTAGATCGACGACATGGG 57.629 47.619 0.00 0.00 42.33 4.00
4014 4347 4.359706 TGAAATGTAGATCGACGACATGG 58.640 43.478 0.00 0.00 42.33 3.66
4015 4348 5.917447 AGATGAAATGTAGATCGACGACATG 59.083 40.000 0.00 0.00 42.33 3.21
4016 4349 6.078202 AGATGAAATGTAGATCGACGACAT 57.922 37.500 0.00 0.00 44.35 3.06
4017 4350 5.500645 AGATGAAATGTAGATCGACGACA 57.499 39.130 0.00 0.00 38.37 4.35
4018 4351 6.814076 AAAGATGAAATGTAGATCGACGAC 57.186 37.500 0.00 0.00 0.00 4.34
4019 4352 7.139392 CCTAAAGATGAAATGTAGATCGACGA 58.861 38.462 0.00 0.00 0.00 4.20
4020 4353 6.129062 GCCTAAAGATGAAATGTAGATCGACG 60.129 42.308 1.33 0.00 0.00 5.12
4021 4354 6.146347 GGCCTAAAGATGAAATGTAGATCGAC 59.854 42.308 0.00 0.00 0.00 4.20
4022 4355 6.223852 GGCCTAAAGATGAAATGTAGATCGA 58.776 40.000 0.00 0.00 0.00 3.59
4023 4356 5.119279 CGGCCTAAAGATGAAATGTAGATCG 59.881 44.000 0.00 0.00 0.00 3.69
4024 4357 5.409826 CCGGCCTAAAGATGAAATGTAGATC 59.590 44.000 0.00 0.00 0.00 2.75
4025 4358 5.308825 CCGGCCTAAAGATGAAATGTAGAT 58.691 41.667 0.00 0.00 0.00 1.98
4026 4359 4.703897 CCGGCCTAAAGATGAAATGTAGA 58.296 43.478 0.00 0.00 0.00 2.59
4027 4360 3.251004 GCCGGCCTAAAGATGAAATGTAG 59.749 47.826 18.11 0.00 0.00 2.74
4028 4361 3.211045 GCCGGCCTAAAGATGAAATGTA 58.789 45.455 18.11 0.00 0.00 2.29
4029 4362 2.024414 GCCGGCCTAAAGATGAAATGT 58.976 47.619 18.11 0.00 0.00 2.71
4030 4363 1.338020 GGCCGGCCTAAAGATGAAATG 59.662 52.381 38.76 0.00 0.00 2.32
4031 4364 1.692411 GGCCGGCCTAAAGATGAAAT 58.308 50.000 38.76 0.00 0.00 2.17
4032 4365 0.746563 CGGCCGGCCTAAAGATGAAA 60.747 55.000 41.01 0.00 0.00 2.69
4033 4366 1.153249 CGGCCGGCCTAAAGATGAA 60.153 57.895 41.01 0.00 0.00 2.57
4034 4367 2.504032 CGGCCGGCCTAAAGATGA 59.496 61.111 41.01 0.00 0.00 2.92
4035 4368 3.279875 GCGGCCGGCCTAAAGATG 61.280 66.667 41.01 25.35 34.80 2.90
4036 4369 2.624674 AATGCGGCCGGCCTAAAGAT 62.625 55.000 41.01 22.25 42.61 2.40
4037 4370 3.338275 AATGCGGCCGGCCTAAAGA 62.338 57.895 41.01 21.01 42.61 2.52
4038 4371 2.828549 AATGCGGCCGGCCTAAAG 60.829 61.111 41.01 27.25 42.61 1.85
4039 4372 2.826738 GAATGCGGCCGGCCTAAA 60.827 61.111 41.01 26.88 42.61 1.85
4049 4382 1.429021 CACCAATGGACGAATGCGG 59.571 57.895 6.16 0.00 43.17 5.69
4060 4393 0.382873 CATCCGATGCACCACCAATG 59.617 55.000 0.00 0.00 0.00 2.82
4061 4394 0.255604 TCATCCGATGCACCACCAAT 59.744 50.000 3.25 0.00 0.00 3.16
4062 4395 0.676466 GTCATCCGATGCACCACCAA 60.676 55.000 3.25 0.00 0.00 3.67
4063 4396 1.078497 GTCATCCGATGCACCACCA 60.078 57.895 3.25 0.00 0.00 4.17
4064 4397 0.392998 AAGTCATCCGATGCACCACC 60.393 55.000 3.25 0.00 0.00 4.61
4065 4398 1.009829 GAAGTCATCCGATGCACCAC 58.990 55.000 3.25 0.00 0.00 4.16
4066 4399 0.904649 AGAAGTCATCCGATGCACCA 59.095 50.000 3.25 0.00 0.00 4.17
4067 4400 1.576356 GAGAAGTCATCCGATGCACC 58.424 55.000 3.25 0.00 0.00 5.01
4068 4401 1.203928 CGAGAAGTCATCCGATGCAC 58.796 55.000 3.25 3.65 0.00 4.57
4069 4402 0.528466 GCGAGAAGTCATCCGATGCA 60.528 55.000 3.25 0.00 0.00 3.96
4070 4403 1.543941 CGCGAGAAGTCATCCGATGC 61.544 60.000 0.00 0.00 0.00 3.91
4071 4404 0.936764 CCGCGAGAAGTCATCCGATG 60.937 60.000 8.23 1.55 0.00 3.84
4072 4405 1.360551 CCGCGAGAAGTCATCCGAT 59.639 57.895 8.23 0.00 0.00 4.18
4073 4406 2.771639 CCCGCGAGAAGTCATCCGA 61.772 63.158 8.23 0.00 0.00 4.55
4074 4407 2.278857 CCCGCGAGAAGTCATCCG 60.279 66.667 8.23 0.00 0.00 4.18
4075 4408 2.586357 GCCCGCGAGAAGTCATCC 60.586 66.667 8.23 0.00 0.00 3.51
4076 4409 2.167861 GTGCCCGCGAGAAGTCATC 61.168 63.158 8.23 0.00 0.00 2.92
4077 4410 2.125512 GTGCCCGCGAGAAGTCAT 60.126 61.111 8.23 0.00 0.00 3.06
4078 4411 2.942796 ATGTGCCCGCGAGAAGTCA 61.943 57.895 8.23 0.00 0.00 3.41
4079 4412 2.125512 ATGTGCCCGCGAGAAGTC 60.126 61.111 8.23 0.00 0.00 3.01
4080 4413 2.434884 CATGTGCCCGCGAGAAGT 60.435 61.111 8.23 0.00 0.00 3.01
4081 4414 2.125552 TCATGTGCCCGCGAGAAG 60.126 61.111 8.23 0.00 0.00 2.85
4082 4415 2.434185 GTCATGTGCCCGCGAGAA 60.434 61.111 8.23 0.00 0.00 2.87
4083 4416 4.451150 GGTCATGTGCCCGCGAGA 62.451 66.667 8.23 0.00 0.00 4.04
4100 4433 3.977244 AAAAGCAACAGCGGCGGG 61.977 61.111 9.78 0.00 36.08 6.13
4101 4434 2.730604 CAAAAGCAACAGCGGCGG 60.731 61.111 9.78 0.00 36.08 6.13
4102 4435 2.730604 CCAAAAGCAACAGCGGCG 60.731 61.111 0.51 0.51 36.08 6.46
4103 4436 2.356194 CCCAAAAGCAACAGCGGC 60.356 61.111 0.00 0.00 0.00 6.53
4104 4437 2.356194 GCCCAAAAGCAACAGCGG 60.356 61.111 0.00 0.00 0.00 5.52
4105 4438 1.372128 GAGCCCAAAAGCAACAGCG 60.372 57.895 0.00 0.00 34.23 5.18
4106 4439 0.319297 CTGAGCCCAAAAGCAACAGC 60.319 55.000 0.00 0.00 34.53 4.40
4107 4440 0.319297 GCTGAGCCCAAAAGCAACAG 60.319 55.000 0.00 0.00 40.15 3.16
4108 4441 0.756442 AGCTGAGCCCAAAAGCAACA 60.756 50.000 0.00 0.00 39.47 3.33
4109 4442 0.038801 GAGCTGAGCCCAAAAGCAAC 60.039 55.000 0.00 0.00 39.47 4.17
4110 4443 0.178981 AGAGCTGAGCCCAAAAGCAA 60.179 50.000 0.00 0.00 39.47 3.91
4111 4444 0.607489 GAGAGCTGAGCCCAAAAGCA 60.607 55.000 0.00 0.00 39.47 3.91
4112 4445 1.311651 GGAGAGCTGAGCCCAAAAGC 61.312 60.000 0.00 0.00 37.20 3.51
4113 4446 0.327591 AGGAGAGCTGAGCCCAAAAG 59.672 55.000 0.00 0.00 0.00 2.27
4114 4447 0.326264 GAGGAGAGCTGAGCCCAAAA 59.674 55.000 0.00 0.00 0.00 2.44
4115 4448 0.546267 AGAGGAGAGCTGAGCCCAAA 60.546 55.000 0.00 0.00 0.00 3.28
4116 4449 1.079987 AGAGGAGAGCTGAGCCCAA 59.920 57.895 0.00 0.00 0.00 4.12
4117 4450 1.685077 CAGAGGAGAGCTGAGCCCA 60.685 63.158 0.00 0.00 35.39 5.36
4118 4451 0.975040 TTCAGAGGAGAGCTGAGCCC 60.975 60.000 0.00 0.00 42.74 5.19
4119 4452 0.175531 GTTCAGAGGAGAGCTGAGCC 59.824 60.000 0.00 0.00 42.74 4.70
4120 4453 0.175531 GGTTCAGAGGAGAGCTGAGC 59.824 60.000 0.00 0.00 42.74 4.26
4121 4454 0.823460 GGGTTCAGAGGAGAGCTGAG 59.177 60.000 0.00 0.00 42.74 3.35
4122 4455 0.967887 CGGGTTCAGAGGAGAGCTGA 60.968 60.000 0.00 0.00 40.41 4.26
4123 4456 1.515020 CGGGTTCAGAGGAGAGCTG 59.485 63.158 0.00 0.00 34.71 4.24
4124 4457 2.355193 GCGGGTTCAGAGGAGAGCT 61.355 63.158 0.00 0.00 0.00 4.09
4125 4458 2.185608 GCGGGTTCAGAGGAGAGC 59.814 66.667 0.00 0.00 0.00 4.09
4126 4459 2.492090 CGCGGGTTCAGAGGAGAG 59.508 66.667 0.00 0.00 0.00 3.20
4127 4460 3.760035 GCGCGGGTTCAGAGGAGA 61.760 66.667 8.83 0.00 0.00 3.71
4128 4461 4.821589 GGCGCGGGTTCAGAGGAG 62.822 72.222 8.83 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.