Multiple sequence alignment - TraesCS4D01G239700

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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 TraesCS4D01G239700 chr4D 100.000 4757 0 0 1 4757 402207357 402212113 0.000000e+00 8785
1 TraesCS4D01G239700 chr4D 96.000 175 6 1 4035 4209 122586115 122586288 2.800000e-72 283
2 TraesCS4D01G239700 chr4D 95.000 180 7 1 4026 4205 455016444 455016621 1.010000e-71 281
3 TraesCS4D01G239700 chr4A 97.391 1763 41 3 1029 2791 59481805 59483562 0.000000e+00 2996
4 TraesCS4D01G239700 chr4A 93.986 1031 47 5 3016 4043 59483790 59484808 0.000000e+00 1546
5 TraesCS4D01G239700 chr4A 98.601 143 2 0 4615 4757 59484837 59484979 2.200000e-63 254
6 TraesCS4D01G239700 chr4B 98.557 1663 24 0 1029 2691 497551776 497553438 0.000000e+00 2939
7 TraesCS4D01G239700 chr4B 95.434 1117 33 8 2932 4043 497553634 497554737 0.000000e+00 1764
8 TraesCS4D01G239700 chr4B 86.806 576 22 17 4202 4757 497554730 497555271 1.140000e-165 593
9 TraesCS4D01G239700 chr6D 99.709 1032 1 2 1 1031 449114396 449113366 0.000000e+00 1888
10 TraesCS4D01G239700 chr6D 76.675 806 162 20 1036 1828 436225221 436224429 1.580000e-114 424
11 TraesCS4D01G239700 chr1D 91.973 1034 64 9 1 1028 401569992 401571012 0.000000e+00 1432
12 TraesCS4D01G239700 chr1D 98.182 165 3 0 4041 4205 490423152 490423316 6.020000e-74 289
13 TraesCS4D01G239700 chr5A 94.053 723 35 3 1 720 39302830 39303547 0.000000e+00 1090
14 TraesCS4D01G239700 chr5A 84.504 413 31 21 55 445 34971200 34971601 1.250000e-100 377
15 TraesCS4D01G239700 chr5A 90.942 276 20 2 753 1028 39303550 39303820 2.700000e-97 366
16 TraesCS4D01G239700 chr5A 97.041 169 4 1 4038 4206 670399155 670399322 2.800000e-72 283
17 TraesCS4D01G239700 chr5A 80.180 222 36 8 3410 3627 413043886 413044103 4.930000e-35 159
18 TraesCS4D01G239700 chr5A 87.000 100 13 0 669 768 34971821 34971920 3.890000e-21 113
19 TraesCS4D01G239700 chr7D 86.700 594 43 12 10 571 520316220 520316809 1.120000e-175 627
20 TraesCS4D01G239700 chr7D 97.024 168 5 0 4039 4206 93090112 93090279 2.800000e-72 283
21 TraesCS4D01G239700 chr6B 76.768 792 162 18 1048 1828 659236414 659235634 1.580000e-114 424
22 TraesCS4D01G239700 chr7A 87.569 362 37 5 669 1028 619046336 619045981 3.430000e-111 412
23 TraesCS4D01G239700 chr7A 84.340 447 34 18 55 476 138312457 138312022 5.730000e-109 405
24 TraesCS4D01G239700 chr3B 84.340 447 33 21 55 476 694763848 694763414 2.060000e-108 403
25 TraesCS4D01G239700 chr3B 84.865 185 17 7 848 1028 694756743 694756566 4.890000e-40 176
26 TraesCS4D01G239700 chr2A 84.746 413 30 17 55 445 27316614 27317015 2.690000e-102 383
27 TraesCS4D01G239700 chr2A 84.504 413 31 17 55 445 25545342 25544941 1.250000e-100 377
28 TraesCS4D01G239700 chr2A 84.262 413 32 20 55 445 26959813 26959412 5.810000e-99 372
29 TraesCS4D01G239700 chr2A 84.262 413 32 20 55 445 52368531 52368932 5.810000e-99 372
30 TraesCS4D01G239700 chr2A 84.262 413 31 18 55 445 134874207 134874607 5.810000e-99 372
31 TraesCS4D01G239700 chr2A 88.000 100 12 0 669 768 26959193 26959094 8.360000e-23 119
32 TraesCS4D01G239700 chr2A 87.000 100 13 0 669 768 52369152 52369251 3.890000e-21 113
33 TraesCS4D01G239700 chr2A 87.000 100 13 0 669 768 134874827 134874926 3.890000e-21 113
34 TraesCS4D01G239700 chr2A 86.735 98 13 0 669 766 27317235 27317332 5.030000e-20 110
35 TraesCS4D01G239700 chr2D 96.067 178 6 1 4032 4208 620615820 620615643 6.020000e-74 289
36 TraesCS4D01G239700 chr1B 96.023 176 6 1 4040 4215 520523917 520523743 7.790000e-73 285
37 TraesCS4D01G239700 chr5B 95.531 179 4 4 4042 4218 584659346 584659522 2.800000e-72 283
38 TraesCS4D01G239700 chr7B 94.536 183 7 3 4033 4213 739630280 739630099 3.630000e-71 279
39 TraesCS4D01G239700 chrUn 97.674 43 1 0 987 1029 43007632 43007674 1.840000e-09 75
40 TraesCS4D01G239700 chrUn 97.674 43 1 0 987 1029 43189636 43189594 1.840000e-09 75
41 TraesCS4D01G239700 chrUn 97.674 43 1 0 987 1029 178612026 178611984 1.840000e-09 75
42 TraesCS4D01G239700 chrUn 97.674 43 1 0 987 1029 364116481 364116439 1.840000e-09 75


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 TraesCS4D01G239700 chr4D 402207357 402212113 4756 False 8785.000000 8785 100.000000 1 4757 1 chr4D.!!$F2 4756
1 TraesCS4D01G239700 chr4A 59481805 59484979 3174 False 1598.666667 2996 96.659333 1029 4757 3 chr4A.!!$F1 3728
2 TraesCS4D01G239700 chr4B 497551776 497555271 3495 False 1765.333333 2939 93.599000 1029 4757 3 chr4B.!!$F1 3728
3 TraesCS4D01G239700 chr6D 449113366 449114396 1030 True 1888.000000 1888 99.709000 1 1031 1 chr6D.!!$R2 1030
4 TraesCS4D01G239700 chr6D 436224429 436225221 792 True 424.000000 424 76.675000 1036 1828 1 chr6D.!!$R1 792
5 TraesCS4D01G239700 chr1D 401569992 401571012 1020 False 1432.000000 1432 91.973000 1 1028 1 chr1D.!!$F1 1027
6 TraesCS4D01G239700 chr5A 39302830 39303820 990 False 728.000000 1090 92.497500 1 1028 2 chr5A.!!$F4 1027
7 TraesCS4D01G239700 chr5A 34971200 34971920 720 False 245.000000 377 85.752000 55 768 2 chr5A.!!$F3 713
8 TraesCS4D01G239700 chr7D 520316220 520316809 589 False 627.000000 627 86.700000 10 571 1 chr7D.!!$F2 561
9 TraesCS4D01G239700 chr6B 659235634 659236414 780 True 424.000000 424 76.768000 1048 1828 1 chr6B.!!$R1 780
10 TraesCS4D01G239700 chr2A 27316614 27317332 718 False 246.500000 383 85.740500 55 766 2 chr2A.!!$F1 711
11 TraesCS4D01G239700 chr2A 26959094 26959813 719 True 245.500000 372 86.131000 55 768 2 chr2A.!!$R2 713
12 TraesCS4D01G239700 chr2A 52368531 52369251 720 False 242.500000 372 85.631000 55 768 2 chr2A.!!$F2 713
13 TraesCS4D01G239700 chr2A 134874207 134874926 719 False 242.500000 372 85.631000 55 768 2 chr2A.!!$F3 713

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
883 984 0.401979 ACCTCGATGGGGATGGGAAT 60.402 55.0 0.00 0.00 41.11 3.01 F
1860 1967 0.739561 AGAGGATCAACGAGGCGTAC 59.260 55.0 0.00 0.00 39.99 3.67 F
3370 3563 0.250295 TTTCACCCTCTTGGCACGAG 60.250 55.0 13.65 13.65 37.83 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2610 2717 0.179137 TCATGAAGTAGCCGTGCTCG 60.179 55.000 0.14 0.14 40.44 5.03 R
3741 3936 1.066587 CTACTACTGCAGCTCGCCC 59.933 63.158 15.27 0.00 41.33 6.13 R
4387 4607 0.106819 ATTGCCTAGAGCTGCCTTGG 60.107 55.000 11.92 11.92 44.23 3.61 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
883 984 0.401979 ACCTCGATGGGGATGGGAAT 60.402 55.000 0.00 0.00 41.11 3.01
1701 1808 3.181436 ACATATTCAAGGGGATCAGCCTG 60.181 47.826 0.00 0.00 36.66 4.85
1860 1967 0.739561 AGAGGATCAACGAGGCGTAC 59.260 55.000 0.00 0.00 39.99 3.67
2487 2594 2.116125 AACAAGAGCCCCACTGCC 59.884 61.111 0.00 0.00 0.00 4.85
2743 2850 1.774254 TCCTTTTCTTGCCTGTCCTCA 59.226 47.619 0.00 0.00 0.00 3.86
2754 2861 3.519510 TGCCTGTCCTCATTAGCTAACTT 59.480 43.478 8.70 0.00 0.00 2.66
2756 2863 5.366768 TGCCTGTCCTCATTAGCTAACTTAT 59.633 40.000 8.70 0.00 0.00 1.73
2758 2865 7.070696 TGCCTGTCCTCATTAGCTAACTTATTA 59.929 37.037 8.70 0.00 0.00 0.98
2759 2866 7.931948 GCCTGTCCTCATTAGCTAACTTATTAA 59.068 37.037 8.70 0.00 0.00 1.40
2782 2889 9.689976 TTAATTGTGAAATGTTATTGGACACTG 57.310 29.630 0.00 0.00 31.30 3.66
2793 2900 9.851686 ATGTTATTGGACACTGTATCATTATGT 57.148 29.630 0.00 0.00 31.30 2.29
2797 2904 8.806429 ATTGGACACTGTATCATTATGTCAAA 57.194 30.769 5.18 0.47 41.18 2.69
2801 2908 9.547753 GGACACTGTATCATTATGTCAAATACT 57.452 33.333 5.18 0.00 41.18 2.12
2843 2950 9.483489 TTTGAACTACTCCTACAATATAGTGGA 57.517 33.333 5.03 0.00 0.00 4.02
2905 3090 6.431234 AGGTTCATATTCAAGTTGAAGTGGAC 59.569 38.462 24.09 24.09 40.05 4.02
2920 3105 3.084786 AGTGGACTAGCATGCCTTTTTC 58.915 45.455 15.66 3.96 0.00 2.29
3028 3221 6.704050 GCCTAGTTCTCTGATGTCTAATTTCC 59.296 42.308 0.00 0.00 0.00 3.13
3341 3534 3.529533 CGCAGGTGAAGAAATCTCTCAT 58.470 45.455 0.00 0.00 0.00 2.90
3343 3536 4.394300 CGCAGGTGAAGAAATCTCTCATTT 59.606 41.667 0.00 0.00 0.00 2.32
3370 3563 0.250295 TTTCACCCTCTTGGCACGAG 60.250 55.000 13.65 13.65 37.83 4.18
3389 3584 1.664649 TCAAGCTTCACCGCTCACG 60.665 57.895 0.00 0.00 39.86 4.35
3486 3681 2.100631 CATGTGCCCGGACTTCGTC 61.101 63.158 0.73 0.00 37.11 4.20
3540 3735 3.181440 ACATGTTCCAGTTCATCACCAGT 60.181 43.478 0.00 0.00 0.00 4.00
3543 3738 1.059098 TCCAGTTCATCACCAGTGCT 58.941 50.000 0.00 0.00 0.00 4.40
3546 3741 2.551721 CCAGTTCATCACCAGTGCTTCT 60.552 50.000 0.00 0.00 0.00 2.85
3645 3840 4.773117 GACGACACGGCGGAGGTC 62.773 72.222 13.24 14.68 35.12 3.85
3764 3959 1.770294 GAGCTGCAGTAGTAGGGAGT 58.230 55.000 16.64 0.00 0.00 3.85
3875 4071 4.035675 GGTGTACATGAGCTATGCTTTTCC 59.964 45.833 0.00 0.00 39.88 3.13
3877 4073 5.007136 GTGTACATGAGCTATGCTTTTCCTC 59.993 44.000 0.00 0.00 39.88 3.71
3936 4132 6.998802 AGTATGAGACTTGCTTTAGAGTGTT 58.001 36.000 0.00 0.00 33.13 3.32
3937 4133 6.870965 AGTATGAGACTTGCTTTAGAGTGTTG 59.129 38.462 0.00 0.00 33.13 3.33
3938 4134 5.023533 TGAGACTTGCTTTAGAGTGTTGT 57.976 39.130 0.00 0.00 0.00 3.32
3939 4135 4.811024 TGAGACTTGCTTTAGAGTGTTGTG 59.189 41.667 0.00 0.00 0.00 3.33
3940 4136 5.023533 AGACTTGCTTTAGAGTGTTGTGA 57.976 39.130 0.00 0.00 0.00 3.58
3941 4137 4.811557 AGACTTGCTTTAGAGTGTTGTGAC 59.188 41.667 0.00 0.00 0.00 3.67
3942 4138 4.770795 ACTTGCTTTAGAGTGTTGTGACT 58.229 39.130 0.00 0.00 0.00 3.41
4042 4242 9.703892 AATGCTAATTTGTGCTGTTAAAACATA 57.296 25.926 0.00 0.00 38.41 2.29
4043 4243 8.514136 TGCTAATTTGTGCTGTTAAAACATAC 57.486 30.769 0.00 0.59 38.41 2.39
4044 4244 8.356657 TGCTAATTTGTGCTGTTAAAACATACT 58.643 29.630 0.00 0.00 38.41 2.12
4045 4245 8.850452 GCTAATTTGTGCTGTTAAAACATACTC 58.150 33.333 0.00 0.00 38.41 2.59
4046 4246 9.341899 CTAATTTGTGCTGTTAAAACATACTCC 57.658 33.333 0.00 0.00 38.41 3.85
4047 4247 5.699097 TTGTGCTGTTAAAACATACTCCC 57.301 39.130 0.00 0.00 38.41 4.30
4048 4248 4.980573 TGTGCTGTTAAAACATACTCCCT 58.019 39.130 0.00 0.00 38.41 4.20
4049 4249 5.001232 TGTGCTGTTAAAACATACTCCCTC 58.999 41.667 0.00 0.00 38.41 4.30
4050 4250 4.395231 GTGCTGTTAAAACATACTCCCTCC 59.605 45.833 0.00 0.00 38.41 4.30
4051 4251 3.621715 GCTGTTAAAACATACTCCCTCCG 59.378 47.826 0.00 0.00 38.41 4.63
4052 4252 3.602483 TGTTAAAACATACTCCCTCCGC 58.398 45.455 0.00 0.00 33.17 5.54
4053 4253 3.262405 TGTTAAAACATACTCCCTCCGCT 59.738 43.478 0.00 0.00 33.17 5.52
4054 4254 2.693267 AAAACATACTCCCTCCGCTC 57.307 50.000 0.00 0.00 0.00 5.03
4055 4255 0.831307 AAACATACTCCCTCCGCTCC 59.169 55.000 0.00 0.00 0.00 4.70
4056 4256 0.032017 AACATACTCCCTCCGCTCCT 60.032 55.000 0.00 0.00 0.00 3.69
4057 4257 0.851469 ACATACTCCCTCCGCTCCTA 59.149 55.000 0.00 0.00 0.00 2.94
4058 4258 1.217183 ACATACTCCCTCCGCTCCTAA 59.783 52.381 0.00 0.00 0.00 2.69
4059 4259 2.317040 CATACTCCCTCCGCTCCTAAA 58.683 52.381 0.00 0.00 0.00 1.85
4060 4260 2.769602 TACTCCCTCCGCTCCTAAAT 57.230 50.000 0.00 0.00 0.00 1.40
4061 4261 2.769602 ACTCCCTCCGCTCCTAAATA 57.230 50.000 0.00 0.00 0.00 1.40
4062 4262 3.261818 ACTCCCTCCGCTCCTAAATAT 57.738 47.619 0.00 0.00 0.00 1.28
4063 4263 3.588569 ACTCCCTCCGCTCCTAAATATT 58.411 45.455 0.00 0.00 0.00 1.28
4064 4264 3.974642 ACTCCCTCCGCTCCTAAATATTT 59.025 43.478 5.89 5.89 0.00 1.40
4065 4265 4.202367 ACTCCCTCCGCTCCTAAATATTTG 60.202 45.833 11.05 1.40 0.00 2.32
4066 4266 3.714798 TCCCTCCGCTCCTAAATATTTGT 59.285 43.478 11.05 0.00 0.00 2.83
4067 4267 4.065789 CCCTCCGCTCCTAAATATTTGTC 58.934 47.826 11.05 0.00 0.00 3.18
4068 4268 4.202367 CCCTCCGCTCCTAAATATTTGTCT 60.202 45.833 11.05 0.00 0.00 3.41
4069 4269 5.368989 CCTCCGCTCCTAAATATTTGTCTT 58.631 41.667 11.05 0.00 0.00 3.01
4070 4270 5.823045 CCTCCGCTCCTAAATATTTGTCTTT 59.177 40.000 11.05 0.00 0.00 2.52
4071 4271 6.017852 CCTCCGCTCCTAAATATTTGTCTTTC 60.018 42.308 11.05 0.00 0.00 2.62
4072 4272 6.650120 TCCGCTCCTAAATATTTGTCTTTCT 58.350 36.000 11.05 0.00 0.00 2.52
4073 4273 7.788026 TCCGCTCCTAAATATTTGTCTTTCTA 58.212 34.615 11.05 0.00 0.00 2.10
4074 4274 7.926555 TCCGCTCCTAAATATTTGTCTTTCTAG 59.073 37.037 11.05 0.00 0.00 2.43
4075 4275 7.926555 CCGCTCCTAAATATTTGTCTTTCTAGA 59.073 37.037 11.05 0.00 0.00 2.43
4092 4292 9.436957 TCTTTCTAGACATTTCAAATGACTACC 57.563 33.333 17.30 1.06 0.00 3.18
4093 4293 9.219603 CTTTCTAGACATTTCAAATGACTACCA 57.780 33.333 17.30 5.07 0.00 3.25
4094 4294 8.547967 TTCTAGACATTTCAAATGACTACCAC 57.452 34.615 17.30 0.12 0.00 4.16
4095 4295 7.676004 TCTAGACATTTCAAATGACTACCACA 58.324 34.615 17.30 0.05 0.00 4.17
4096 4296 8.321353 TCTAGACATTTCAAATGACTACCACAT 58.679 33.333 17.30 0.00 0.00 3.21
4097 4297 9.599866 CTAGACATTTCAAATGACTACCACATA 57.400 33.333 17.30 0.00 0.00 2.29
4098 4298 8.268850 AGACATTTCAAATGACTACCACATAC 57.731 34.615 17.30 0.00 0.00 2.39
4099 4299 7.064609 AGACATTTCAAATGACTACCACATACG 59.935 37.037 17.30 0.00 0.00 3.06
4100 4300 6.093495 ACATTTCAAATGACTACCACATACGG 59.907 38.462 17.30 0.00 0.00 4.02
4101 4301 5.408880 TTCAAATGACTACCACATACGGA 57.591 39.130 0.00 0.00 0.00 4.69
4102 4302 5.607939 TCAAATGACTACCACATACGGAT 57.392 39.130 0.00 0.00 0.00 4.18
4103 4303 5.356426 TCAAATGACTACCACATACGGATG 58.644 41.667 5.94 5.94 39.16 3.51
4105 4305 6.097129 TCAAATGACTACCACATACGGATGTA 59.903 38.462 14.23 0.00 44.82 2.29
4106 4306 6.665992 AATGACTACCACATACGGATGTAT 57.334 37.500 14.23 7.46 44.82 2.29
4145 4345 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
4146 4346 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
4147 4347 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
4148 4348 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
4149 4349 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
4150 4350 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
4151 4351 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
4152 4352 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
4153 4353 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
4154 4354 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
4155 4355 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
4156 4356 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
4157 4357 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
4158 4358 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
4159 4359 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
4160 4360 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
4161 4361 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
4162 4362 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
4163 4363 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
4164 4364 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
4165 4365 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
4166 4366 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
4167 4367 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
4168 4368 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
4169 4369 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
4170 4370 6.147164 CCGTATGTAGTCACTTGTTGAAATGT 59.853 38.462 0.00 0.00 35.39 2.71
4171 4371 7.227461 CGTATGTAGTCACTTGTTGAAATGTC 58.773 38.462 0.00 0.00 35.39 3.06
4172 4372 7.116376 CGTATGTAGTCACTTGTTGAAATGTCT 59.884 37.037 0.00 0.00 35.39 3.41
4173 4373 9.419297 GTATGTAGTCACTTGTTGAAATGTCTA 57.581 33.333 0.00 0.00 35.39 2.59
4174 4374 7.946655 TGTAGTCACTTGTTGAAATGTCTAG 57.053 36.000 0.00 0.00 35.39 2.43
4175 4375 7.722363 TGTAGTCACTTGTTGAAATGTCTAGA 58.278 34.615 0.00 0.00 35.39 2.43
4176 4376 8.201464 TGTAGTCACTTGTTGAAATGTCTAGAA 58.799 33.333 0.00 0.00 35.39 2.10
4177 4377 9.042008 GTAGTCACTTGTTGAAATGTCTAGAAA 57.958 33.333 0.00 0.00 35.39 2.52
4178 4378 8.147642 AGTCACTTGTTGAAATGTCTAGAAAG 57.852 34.615 0.00 0.00 35.39 2.62
4179 4379 7.987458 AGTCACTTGTTGAAATGTCTAGAAAGA 59.013 33.333 0.00 0.00 35.39 2.52
4180 4380 8.064814 GTCACTTGTTGAAATGTCTAGAAAGAC 58.935 37.037 0.00 0.00 43.53 3.01
4199 4399 9.413734 AGAAAGACAAATATTTAGGAATGGAGG 57.586 33.333 0.00 0.00 0.00 4.30
4200 4400 8.539117 AAAGACAAATATTTAGGAATGGAGGG 57.461 34.615 0.00 0.00 0.00 4.30
4201 4401 7.465900 AGACAAATATTTAGGAATGGAGGGA 57.534 36.000 0.00 0.00 0.00 4.20
4202 4402 7.521669 AGACAAATATTTAGGAATGGAGGGAG 58.478 38.462 0.00 0.00 0.00 4.30
4203 4403 7.129504 AGACAAATATTTAGGAATGGAGGGAGT 59.870 37.037 0.00 0.00 0.00 3.85
4204 4404 8.344939 ACAAATATTTAGGAATGGAGGGAGTA 57.655 34.615 0.00 0.00 0.00 2.59
4205 4405 8.218488 ACAAATATTTAGGAATGGAGGGAGTAC 58.782 37.037 0.00 0.00 0.00 2.73
4206 4406 8.440771 CAAATATTTAGGAATGGAGGGAGTACT 58.559 37.037 0.00 0.00 0.00 2.73
4207 4407 8.582891 AATATTTAGGAATGGAGGGAGTACTT 57.417 34.615 0.00 0.00 0.00 2.24
4212 4412 6.253946 AGGAATGGAGGGAGTACTTATTTG 57.746 41.667 0.00 0.00 0.00 2.32
4243 4443 1.686464 GCTTCTTGCACTAAAACCGC 58.314 50.000 0.00 0.00 42.31 5.68
4244 4444 1.001815 GCTTCTTGCACTAAAACCGCA 60.002 47.619 0.00 0.00 42.31 5.69
4245 4445 2.351738 GCTTCTTGCACTAAAACCGCAT 60.352 45.455 0.00 0.00 42.31 4.73
4246 4446 3.857010 GCTTCTTGCACTAAAACCGCATT 60.857 43.478 0.00 0.00 42.31 3.56
4310 4530 9.679661 TGCTTCCTAATAATTCATCAAGTGTTA 57.320 29.630 0.00 0.00 0.00 2.41
4325 4545 3.487372 AGTGTTAGAAAAAGGTGGAGCC 58.513 45.455 0.00 0.00 37.58 4.70
4387 4607 0.600057 CAAAGCCCAAGTGAAGCCTC 59.400 55.000 0.00 0.00 0.00 4.70
4406 4626 0.106819 CCAAGGCAGCTCTAGGCAAT 60.107 55.000 6.07 0.00 44.79 3.56
4413 4633 3.947834 GGCAGCTCTAGGCAATTTTAAGA 59.052 43.478 6.07 0.00 44.79 2.10
4418 4638 7.247019 CAGCTCTAGGCAATTTTAAGAAAGTC 58.753 38.462 6.07 0.00 44.79 3.01
4447 4667 4.198530 CCAAAGAAACCAAAGTTGCCAAT 58.801 39.130 0.00 0.00 35.97 3.16
4449 4669 4.751767 AAGAAACCAAAGTTGCCAATGA 57.248 36.364 0.00 0.00 35.97 2.57
4463 4683 4.143543 TGCCAATGACTCAAAAGATGACA 58.856 39.130 0.00 0.00 33.47 3.58
4479 4699 5.251764 AGATGACACAAAAGGAAGATGGAG 58.748 41.667 0.00 0.00 0.00 3.86
4480 4700 3.754965 TGACACAAAAGGAAGATGGAGG 58.245 45.455 0.00 0.00 0.00 4.30
4481 4701 3.394274 TGACACAAAAGGAAGATGGAGGA 59.606 43.478 0.00 0.00 0.00 3.71
4482 4702 4.006319 GACACAAAAGGAAGATGGAGGAG 58.994 47.826 0.00 0.00 0.00 3.69
4483 4703 2.751806 CACAAAAGGAAGATGGAGGAGC 59.248 50.000 0.00 0.00 0.00 4.70
4484 4704 2.291217 ACAAAAGGAAGATGGAGGAGCC 60.291 50.000 0.00 0.00 37.10 4.70
4598 4818 2.636830 CTAGGCATGGTCCTGTTCAAG 58.363 52.381 2.35 0.00 37.01 3.02
4613 4833 4.406456 TGTTCAAGTTATGGCTCAATGGT 58.594 39.130 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1473 1580 2.838693 GACTCGTAGGGGAGGCCC 60.839 72.222 0.00 0.00 44.51 5.80
1902 2009 2.793322 GCGCTCGTAGAACTGCAGC 61.793 63.158 15.27 0.00 34.09 5.25
2055 2162 1.485895 AGCATGCTCTTCTTCTCCTCC 59.514 52.381 16.30 0.00 0.00 4.30
2373 2480 1.042229 TGTGCTCCATTGCAAGCTTT 58.958 45.000 4.94 0.00 45.12 3.51
2427 2534 1.534175 CCGTCGTAGTCCAGCAGAATC 60.534 57.143 0.00 0.00 0.00 2.52
2487 2594 4.503910 TGTTGAGTATCTGGACCGATTTG 58.496 43.478 4.51 0.00 34.92 2.32
2610 2717 0.179137 TCATGAAGTAGCCGTGCTCG 60.179 55.000 0.14 0.14 40.44 5.03
2756 2863 9.689976 CAGTGTCCAATAACATTTCACAATTAA 57.310 29.630 0.00 0.00 0.00 1.40
2758 2865 7.725251 ACAGTGTCCAATAACATTTCACAATT 58.275 30.769 0.00 0.00 0.00 2.32
2759 2866 7.288810 ACAGTGTCCAATAACATTTCACAAT 57.711 32.000 0.00 0.00 0.00 2.71
2760 2867 6.707440 ACAGTGTCCAATAACATTTCACAA 57.293 33.333 0.00 0.00 0.00 3.33
2761 2868 7.663493 TGATACAGTGTCCAATAACATTTCACA 59.337 33.333 0.00 0.00 0.00 3.58
2762 2869 8.039603 TGATACAGTGTCCAATAACATTTCAC 57.960 34.615 0.00 0.00 0.00 3.18
2814 2921 9.710818 ACTATATTGTAGGAGTAGTTCAAAGGA 57.289 33.333 0.00 0.00 0.00 3.36
2815 2922 9.751542 CACTATATTGTAGGAGTAGTTCAAAGG 57.248 37.037 0.00 0.00 0.00 3.11
2816 2923 9.751542 CCACTATATTGTAGGAGTAGTTCAAAG 57.248 37.037 0.00 0.00 0.00 2.77
2817 2924 9.483489 TCCACTATATTGTAGGAGTAGTTCAAA 57.517 33.333 5.03 0.00 0.00 2.69
2818 2925 9.483489 TTCCACTATATTGTAGGAGTAGTTCAA 57.517 33.333 7.90 0.00 0.00 2.69
2819 2926 8.910944 GTTCCACTATATTGTAGGAGTAGTTCA 58.089 37.037 7.90 0.00 0.00 3.18
2820 2927 8.910944 TGTTCCACTATATTGTAGGAGTAGTTC 58.089 37.037 7.90 0.00 0.00 3.01
2821 2928 8.834004 TGTTCCACTATATTGTAGGAGTAGTT 57.166 34.615 7.90 0.00 0.00 2.24
2822 2929 8.861086 CATGTTCCACTATATTGTAGGAGTAGT 58.139 37.037 7.90 0.00 0.00 2.73
2823 2930 8.861086 ACATGTTCCACTATATTGTAGGAGTAG 58.139 37.037 0.00 0.00 0.00 2.57
2824 2931 8.777578 ACATGTTCCACTATATTGTAGGAGTA 57.222 34.615 0.00 4.12 0.00 2.59
2825 2932 7.676683 ACATGTTCCACTATATTGTAGGAGT 57.323 36.000 0.00 2.80 0.00 3.85
2860 2967 9.391006 TGAACCTATGATGTAAGATACCAAAAC 57.609 33.333 0.00 0.00 0.00 2.43
2873 2980 9.685276 TTCAACTTGAATATGAACCTATGATGT 57.315 29.630 0.00 0.00 30.26 3.06
2905 3090 3.428589 GGCAGAAGAAAAAGGCATGCTAG 60.429 47.826 18.92 0.00 32.89 3.42
2920 3105 5.657474 AGCAACAAAATATCATGGCAGAAG 58.343 37.500 0.00 0.00 0.00 2.85
2950 3142 1.832719 TAACTTAGCAGCCGCCCACA 61.833 55.000 0.00 0.00 39.83 4.17
3028 3221 2.624316 ATTCAGTGCAGCACATTTCG 57.376 45.000 27.35 10.01 36.74 3.46
3118 3311 4.899239 GAGCTCCATGACCGGCCG 62.899 72.222 21.04 21.04 0.00 6.13
3119 3312 2.134287 TAGAGCTCCATGACCGGCC 61.134 63.158 10.93 0.00 0.00 6.13
3341 3534 5.022787 CCAAGAGGGTGAAATGGGATTAAA 58.977 41.667 0.00 0.00 0.00 1.52
3343 3536 3.627237 GCCAAGAGGGTGAAATGGGATTA 60.627 47.826 0.00 0.00 39.65 1.75
3389 3584 5.043248 CCTGTTGTTCAACACAAGAATTCC 58.957 41.667 13.36 0.00 46.49 3.01
3486 3681 3.147595 TCGTCCCCGATGCAGAGG 61.148 66.667 3.41 3.41 38.40 3.69
3540 3735 2.738521 GAGTCGGCGCAAGAAGCA 60.739 61.111 10.83 0.00 46.13 3.91
3543 3738 2.019951 GAACGAGTCGGCGCAAGAA 61.020 57.895 18.30 0.00 43.02 2.52
3606 3801 1.279271 AGGTAGTACTTGGCCTTGCTG 59.721 52.381 3.32 0.00 0.00 4.41
3645 3840 1.153489 CCCCTGCATCAGTCTCACG 60.153 63.158 0.00 0.00 0.00 4.35
3651 3846 4.437587 GCCAGCCCCTGCATCAGT 62.438 66.667 0.00 0.00 41.13 3.41
3741 3936 1.066587 CTACTACTGCAGCTCGCCC 59.933 63.158 15.27 0.00 41.33 6.13
3764 3959 1.678635 CCCCTGCGCTTCATTCCAA 60.679 57.895 9.73 0.00 0.00 3.53
3875 4071 0.097674 GGCAGTGCAGCAAATACGAG 59.902 55.000 18.61 0.00 35.83 4.18
3877 4073 1.226101 CGGCAGTGCAGCAAATACG 60.226 57.895 18.61 4.52 35.83 3.06
3936 4132 0.464036 AACGGAGCTCACAAGTCACA 59.536 50.000 17.19 0.00 0.00 3.58
3937 4133 1.261619 CAAACGGAGCTCACAAGTCAC 59.738 52.381 17.19 0.00 0.00 3.67
3938 4134 1.138069 TCAAACGGAGCTCACAAGTCA 59.862 47.619 17.19 0.00 0.00 3.41
3939 4135 1.865865 TCAAACGGAGCTCACAAGTC 58.134 50.000 17.19 0.00 0.00 3.01
3940 4136 2.325583 TTCAAACGGAGCTCACAAGT 57.674 45.000 17.19 6.80 0.00 3.16
3941 4137 3.363178 GTTTTCAAACGGAGCTCACAAG 58.637 45.455 17.19 6.13 0.00 3.16
3942 4138 2.098443 GGTTTTCAAACGGAGCTCACAA 59.902 45.455 17.19 0.00 39.77 3.33
4042 4242 2.769602 TATTTAGGAGCGGAGGGAGT 57.230 50.000 0.00 0.00 0.00 3.85
4043 4243 4.202367 ACAAATATTTAGGAGCGGAGGGAG 60.202 45.833 0.00 0.00 0.00 4.30
4044 4244 3.714798 ACAAATATTTAGGAGCGGAGGGA 59.285 43.478 0.00 0.00 0.00 4.20
4045 4245 4.065789 GACAAATATTTAGGAGCGGAGGG 58.934 47.826 0.00 0.00 0.00 4.30
4046 4246 4.962155 AGACAAATATTTAGGAGCGGAGG 58.038 43.478 0.00 0.00 0.00 4.30
4047 4247 6.763610 AGAAAGACAAATATTTAGGAGCGGAG 59.236 38.462 0.00 0.00 0.00 4.63
4048 4248 6.650120 AGAAAGACAAATATTTAGGAGCGGA 58.350 36.000 0.00 0.00 0.00 5.54
4049 4249 6.927294 AGAAAGACAAATATTTAGGAGCGG 57.073 37.500 0.00 0.00 0.00 5.52
4050 4250 8.873215 TCTAGAAAGACAAATATTTAGGAGCG 57.127 34.615 0.00 0.00 0.00 5.03
4066 4266 9.436957 GGTAGTCATTTGAAATGTCTAGAAAGA 57.563 33.333 19.92 3.04 0.00 2.52
4067 4267 9.219603 TGGTAGTCATTTGAAATGTCTAGAAAG 57.780 33.333 19.92 0.00 0.00 2.62
4068 4268 8.999431 GTGGTAGTCATTTGAAATGTCTAGAAA 58.001 33.333 19.92 9.72 0.00 2.52
4069 4269 8.154203 TGTGGTAGTCATTTGAAATGTCTAGAA 58.846 33.333 19.92 11.56 0.00 2.10
4070 4270 7.676004 TGTGGTAGTCATTTGAAATGTCTAGA 58.324 34.615 19.92 10.61 0.00 2.43
4071 4271 7.905604 TGTGGTAGTCATTTGAAATGTCTAG 57.094 36.000 19.92 0.00 0.00 2.43
4072 4272 9.378551 GTATGTGGTAGTCATTTGAAATGTCTA 57.621 33.333 16.93 16.93 0.00 2.59
4073 4273 7.064609 CGTATGTGGTAGTCATTTGAAATGTCT 59.935 37.037 18.62 18.62 0.00 3.41
4074 4274 7.180079 CGTATGTGGTAGTCATTTGAAATGTC 58.820 38.462 16.62 11.74 0.00 3.06
4075 4275 6.093495 CCGTATGTGGTAGTCATTTGAAATGT 59.907 38.462 16.62 2.38 0.00 2.71
4076 4276 6.315144 TCCGTATGTGGTAGTCATTTGAAATG 59.685 38.462 11.54 11.54 0.00 2.32
4077 4277 6.411376 TCCGTATGTGGTAGTCATTTGAAAT 58.589 36.000 0.00 0.00 0.00 2.17
4078 4278 5.795972 TCCGTATGTGGTAGTCATTTGAAA 58.204 37.500 0.00 0.00 0.00 2.69
4079 4279 5.408880 TCCGTATGTGGTAGTCATTTGAA 57.591 39.130 0.00 0.00 0.00 2.69
4080 4280 5.105106 ACATCCGTATGTGGTAGTCATTTGA 60.105 40.000 0.00 0.00 44.79 2.69
4081 4281 5.116180 ACATCCGTATGTGGTAGTCATTTG 58.884 41.667 0.00 0.00 44.79 2.32
4082 4282 5.353394 ACATCCGTATGTGGTAGTCATTT 57.647 39.130 0.00 0.00 44.79 2.32
4083 4283 6.455647 CATACATCCGTATGTGGTAGTCATT 58.544 40.000 3.56 0.00 46.70 2.57
4084 4284 6.025749 CATACATCCGTATGTGGTAGTCAT 57.974 41.667 3.56 0.00 46.70 3.06
4085 4285 5.447624 CATACATCCGTATGTGGTAGTCA 57.552 43.478 3.56 0.00 46.70 3.41
4123 4323 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
4124 4324 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
4125 4325 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
4126 4326 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
4127 4327 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
4128 4328 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
4129 4329 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
4130 4330 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
4131 4331 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
4132 4332 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
4133 4333 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
4134 4334 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
4135 4335 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
4136 4336 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
4137 4337 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
4138 4338 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
4139 4339 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
4140 4340 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
4141 4341 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
4142 4342 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
4143 4343 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
4144 4344 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
4145 4345 6.147164 ACATTTCAACAAGTGACTACATACGG 59.853 38.462 0.00 0.00 35.39 4.02
4146 4346 7.116376 AGACATTTCAACAAGTGACTACATACG 59.884 37.037 0.00 0.00 35.39 3.06
4147 4347 8.311650 AGACATTTCAACAAGTGACTACATAC 57.688 34.615 0.00 0.00 35.39 2.39
4148 4348 9.639601 CTAGACATTTCAACAAGTGACTACATA 57.360 33.333 0.00 0.00 35.39 2.29
4149 4349 8.367911 TCTAGACATTTCAACAAGTGACTACAT 58.632 33.333 0.00 0.00 35.39 2.29
4150 4350 7.722363 TCTAGACATTTCAACAAGTGACTACA 58.278 34.615 0.00 0.00 35.39 2.74
4151 4351 8.589335 TTCTAGACATTTCAACAAGTGACTAC 57.411 34.615 0.00 0.00 35.39 2.73
4152 4352 9.261180 CTTTCTAGACATTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 35.39 2.59
4153 4353 7.987458 TCTTTCTAGACATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
4154 4354 8.142994 TCTTTCTAGACATTTCAACAAGTGAC 57.857 34.615 0.00 0.00 35.39 3.67
4173 4373 9.413734 CCTCCATTCCTAAATATTTGTCTTTCT 57.586 33.333 11.05 0.00 0.00 2.52
4174 4374 8.633561 CCCTCCATTCCTAAATATTTGTCTTTC 58.366 37.037 11.05 0.00 0.00 2.62
4175 4375 8.343787 TCCCTCCATTCCTAAATATTTGTCTTT 58.656 33.333 11.05 0.00 0.00 2.52
4176 4376 7.882755 TCCCTCCATTCCTAAATATTTGTCTT 58.117 34.615 11.05 0.00 0.00 3.01
4177 4377 7.129504 ACTCCCTCCATTCCTAAATATTTGTCT 59.870 37.037 11.05 0.00 0.00 3.41
4178 4378 7.290813 ACTCCCTCCATTCCTAAATATTTGTC 58.709 38.462 11.05 0.00 0.00 3.18
4179 4379 7.226059 ACTCCCTCCATTCCTAAATATTTGT 57.774 36.000 11.05 0.00 0.00 2.83
4180 4380 8.440771 AGTACTCCCTCCATTCCTAAATATTTG 58.559 37.037 11.05 1.40 0.00 2.32
4181 4381 8.582891 AGTACTCCCTCCATTCCTAAATATTT 57.417 34.615 5.89 5.89 0.00 1.40
4182 4382 8.582891 AAGTACTCCCTCCATTCCTAAATATT 57.417 34.615 0.00 0.00 0.00 1.28
4183 4383 9.860393 ATAAGTACTCCCTCCATTCCTAAATAT 57.140 33.333 0.00 0.00 0.00 1.28
4184 4384 9.684702 AATAAGTACTCCCTCCATTCCTAAATA 57.315 33.333 0.00 0.00 0.00 1.40
4185 4385 8.582891 AATAAGTACTCCCTCCATTCCTAAAT 57.417 34.615 0.00 0.00 0.00 1.40
4186 4386 8.272173 CAAATAAGTACTCCCTCCATTCCTAAA 58.728 37.037 0.00 0.00 0.00 1.85
4187 4387 7.147373 CCAAATAAGTACTCCCTCCATTCCTAA 60.147 40.741 0.00 0.00 0.00 2.69
4188 4388 6.329197 CCAAATAAGTACTCCCTCCATTCCTA 59.671 42.308 0.00 0.00 0.00 2.94
4189 4389 5.132816 CCAAATAAGTACTCCCTCCATTCCT 59.867 44.000 0.00 0.00 0.00 3.36
4190 4390 5.377478 CCAAATAAGTACTCCCTCCATTCC 58.623 45.833 0.00 0.00 0.00 3.01
4191 4391 4.822350 GCCAAATAAGTACTCCCTCCATTC 59.178 45.833 0.00 0.00 0.00 2.67
4192 4392 4.686122 CGCCAAATAAGTACTCCCTCCATT 60.686 45.833 0.00 0.00 0.00 3.16
4193 4393 3.181454 CGCCAAATAAGTACTCCCTCCAT 60.181 47.826 0.00 0.00 0.00 3.41
4194 4394 2.169769 CGCCAAATAAGTACTCCCTCCA 59.830 50.000 0.00 0.00 0.00 3.86
4195 4395 2.835027 CGCCAAATAAGTACTCCCTCC 58.165 52.381 0.00 0.00 0.00 4.30
4196 4396 2.210961 GCGCCAAATAAGTACTCCCTC 58.789 52.381 0.00 0.00 0.00 4.30
4197 4397 1.134189 GGCGCCAAATAAGTACTCCCT 60.134 52.381 24.80 0.00 0.00 4.20
4198 4398 1.306148 GGCGCCAAATAAGTACTCCC 58.694 55.000 24.80 0.00 0.00 4.30
4199 4399 0.935196 CGGCGCCAAATAAGTACTCC 59.065 55.000 28.98 0.00 0.00 3.85
4200 4400 1.930567 TCGGCGCCAAATAAGTACTC 58.069 50.000 28.98 0.00 0.00 2.59
4201 4401 2.614829 ATCGGCGCCAAATAAGTACT 57.385 45.000 28.98 0.00 0.00 2.73
4202 4402 2.870411 AGAATCGGCGCCAAATAAGTAC 59.130 45.455 28.98 7.15 0.00 2.73
4203 4403 2.869801 CAGAATCGGCGCCAAATAAGTA 59.130 45.455 28.98 0.44 0.00 2.24
4204 4404 1.670811 CAGAATCGGCGCCAAATAAGT 59.329 47.619 28.98 4.71 0.00 2.24
4205 4405 1.597937 GCAGAATCGGCGCCAAATAAG 60.598 52.381 28.98 12.85 0.00 1.73
4206 4406 0.380378 GCAGAATCGGCGCCAAATAA 59.620 50.000 28.98 6.05 0.00 1.40
4207 4407 0.463654 AGCAGAATCGGCGCCAAATA 60.464 50.000 28.98 8.91 36.08 1.40
4212 4412 2.109126 AAGAAGCAGAATCGGCGCC 61.109 57.895 19.07 19.07 36.08 6.53
4235 4435 5.176774 CAGTAGATATCGCAATGCGGTTTTA 59.823 40.000 27.80 14.13 45.69 1.52
4237 4437 3.494626 CAGTAGATATCGCAATGCGGTTT 59.505 43.478 27.80 16.33 45.69 3.27
4238 4438 3.059884 CAGTAGATATCGCAATGCGGTT 58.940 45.455 27.80 17.36 45.69 4.44
4240 4440 3.515630 ATCAGTAGATATCGCAATGCGG 58.484 45.455 27.80 9.24 41.95 5.69
4241 4441 6.632171 TTAATCAGTAGATATCGCAATGCG 57.368 37.500 22.84 22.84 43.04 4.73
4242 4442 7.796838 TGTTTAATCAGTAGATATCGCAATGC 58.203 34.615 0.00 0.00 33.08 3.56
4243 4443 8.982685 ACTGTTTAATCAGTAGATATCGCAATG 58.017 33.333 15.93 0.00 45.31 2.82
4244 4444 8.982685 CACTGTTTAATCAGTAGATATCGCAAT 58.017 33.333 16.81 0.00 45.37 3.56
4245 4445 7.979537 ACACTGTTTAATCAGTAGATATCGCAA 59.020 33.333 16.81 0.00 45.37 4.85
4246 4446 7.489160 ACACTGTTTAATCAGTAGATATCGCA 58.511 34.615 16.81 0.00 45.37 5.10
4265 4465 6.595716 GGAAGCAGTATAATCTTTGACACTGT 59.404 38.462 0.00 0.00 36.59 3.55
4283 4483 8.218338 ACACTTGATGAATTATTAGGAAGCAG 57.782 34.615 0.00 0.00 0.00 4.24
4284 4484 8.579850 AACACTTGATGAATTATTAGGAAGCA 57.420 30.769 0.00 0.00 0.00 3.91
4319 4539 1.097232 CATGAATTTCGCAGGCTCCA 58.903 50.000 0.00 0.00 0.00 3.86
4325 4545 1.135199 AGCCTTGCATGAATTTCGCAG 60.135 47.619 0.00 0.00 36.91 5.18
4387 4607 0.106819 ATTGCCTAGAGCTGCCTTGG 60.107 55.000 11.92 11.92 44.23 3.61
4406 4626 5.878406 TTGGCCCATTGACTTTCTTAAAA 57.122 34.783 0.00 0.00 0.00 1.52
4413 4633 3.181455 GGTTTCTTTGGCCCATTGACTTT 60.181 43.478 0.00 0.00 0.00 2.66
4418 4638 2.926778 TTGGTTTCTTTGGCCCATTG 57.073 45.000 0.00 0.00 0.00 2.82
4447 4667 5.885352 TCCTTTTGTGTCATCTTTTGAGTCA 59.115 36.000 0.00 0.00 34.17 3.41
4449 4669 6.603201 TCTTCCTTTTGTGTCATCTTTTGAGT 59.397 34.615 0.00 0.00 34.17 3.41
4463 4683 2.291217 GGCTCCTCCATCTTCCTTTTGT 60.291 50.000 0.00 0.00 34.01 2.83
4493 4713 1.354368 TCGGCCTCCATCTTCCTTTTT 59.646 47.619 0.00 0.00 0.00 1.94
4494 4714 0.991920 TCGGCCTCCATCTTCCTTTT 59.008 50.000 0.00 0.00 0.00 2.27
4495 4715 0.543749 CTCGGCCTCCATCTTCCTTT 59.456 55.000 0.00 0.00 0.00 3.11
4496 4716 1.341156 CCTCGGCCTCCATCTTCCTT 61.341 60.000 0.00 0.00 0.00 3.36
4497 4717 1.764054 CCTCGGCCTCCATCTTCCT 60.764 63.158 0.00 0.00 0.00 3.36
4498 4718 1.338136 TTCCTCGGCCTCCATCTTCC 61.338 60.000 0.00 0.00 0.00 3.46
4499 4719 0.179070 GTTCCTCGGCCTCCATCTTC 60.179 60.000 0.00 0.00 0.00 2.87
4500 4720 0.909610 TGTTCCTCGGCCTCCATCTT 60.910 55.000 0.00 0.00 0.00 2.40
4501 4721 0.909610 TTGTTCCTCGGCCTCCATCT 60.910 55.000 0.00 0.00 0.00 2.90
4502 4722 0.462759 CTTGTTCCTCGGCCTCCATC 60.463 60.000 0.00 0.00 0.00 3.51
4503 4723 1.604378 CTTGTTCCTCGGCCTCCAT 59.396 57.895 0.00 0.00 0.00 3.41
4504 4724 2.592993 CCTTGTTCCTCGGCCTCCA 61.593 63.158 0.00 0.00 0.00 3.86
4505 4725 2.245438 CTCCTTGTTCCTCGGCCTCC 62.245 65.000 0.00 0.00 0.00 4.30
4506 4726 1.219393 CTCCTTGTTCCTCGGCCTC 59.781 63.158 0.00 0.00 0.00 4.70
4507 4727 1.229209 TCTCCTTGTTCCTCGGCCT 60.229 57.895 0.00 0.00 0.00 5.19
4508 4728 1.219393 CTCTCCTTGTTCCTCGGCC 59.781 63.158 0.00 0.00 0.00 6.13
4598 4818 3.616219 TGGTGTACCATTGAGCCATAAC 58.384 45.455 0.00 0.00 42.01 1.89
4613 4833 7.431249 GGATGATAACGATCTAGTTTGGTGTA 58.569 38.462 0.00 0.00 35.70 2.90


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

AutoCloner maintained by Alex Coulton.