Multiple sequence alignment - TraesCS1A01G080200

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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 TraesCS1A01G080200 chr1A 100.000 4894 0 0 1 4894 63054515 63049622 0.000000e+00 9038.0
1 TraesCS1A01G080200 chr1A 100.000 69 0 0 4178 4246 63050272 63050204 1.430000e-25 128.0
2 TraesCS1A01G080200 chr1A 100.000 69 0 0 4244 4312 63050338 63050270 1.430000e-25 128.0
3 TraesCS1A01G080200 chr1A 92.188 64 3 2 4832 4894 510937502 510937564 6.750000e-14 89.8
4 TraesCS1A01G080200 chr1A 90.000 60 6 0 4800 4859 135910990 135910931 1.460000e-10 78.7
5 TraesCS1A01G080200 chr1A 90.909 55 5 0 4800 4854 21608750 21608804 1.890000e-09 75.0
6 TraesCS1A01G080200 chr1D 94.902 4296 159 23 1 4246 63952200 63947915 0.000000e+00 6665.0
7 TraesCS1A01G080200 chr1D 84.169 379 19 12 4244 4602 63947989 63947632 3.650000e-86 329.0
8 TraesCS1A01G080200 chr1B 93.435 4311 213 30 1 4246 104774586 104770281 0.000000e+00 6329.0
9 TraesCS1A01G080200 chr1B 86.387 382 24 12 4244 4602 104770349 104769973 4.590000e-105 392.0
10 TraesCS1A01G080200 chr1B 85.981 107 7 3 4632 4737 104769861 104769762 1.860000e-19 108.0
11 TraesCS1A01G080200 chr1B 93.151 73 5 0 4603 4675 104769934 104769862 1.860000e-19 108.0
12 TraesCS1A01G080200 chr1B 98.148 54 1 0 4841 4894 462802693 462802640 1.450000e-15 95.3
13 TraesCS1A01G080200 chr7B 96.552 58 2 0 4837 4894 606405915 606405972 4.030000e-16 97.1
14 TraesCS1A01G080200 chrUn 98.148 54 1 0 4841 4894 41958236 41958183 1.450000e-15 95.3
15 TraesCS1A01G080200 chr4D 98.148 54 1 0 4841 4894 333460718 333460771 1.450000e-15 95.3
16 TraesCS1A01G080200 chr5A 96.491 57 1 1 4838 4894 156905241 156905296 5.220000e-15 93.5
17 TraesCS1A01G080200 chr5A 94.915 59 2 1 4836 4894 659831963 659832020 1.880000e-14 91.6
18 TraesCS1A01G080200 chr2D 100.000 49 0 0 4846 4894 6237089 6237041 1.880000e-14 91.6
19 TraesCS1A01G080200 chr5B 86.250 80 6 5 4816 4894 434912023 434912098 1.130000e-11 82.4
20 TraesCS1A01G080200 chr5B 90.909 55 4 1 4785 4839 57496850 57496903 6.800000e-09 73.1
21 TraesCS1A01G080200 chr7A 92.308 52 4 0 4795 4846 572668385 572668334 1.890000e-09 75.0
22 TraesCS1A01G080200 chr7A 85.938 64 8 1 4800 4863 608875152 608875214 3.160000e-07 67.6
23 TraesCS1A01G080200 chr7D 89.474 57 6 0 4800 4856 25322357 25322301 6.800000e-09 73.1
24 TraesCS1A01G080200 chr4B 85.294 68 10 0 4800 4867 221059750 221059683 2.440000e-08 71.3
25 TraesCS1A01G080200 chr3D 95.455 44 2 0 4799 4842 497873815 497873772 2.440000e-08 71.3


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 TraesCS1A01G080200 chr1A 63049622 63054515 4893 True 9038.00 9038 100.0000 1 4894 1 chr1A.!!$R1 4893
1 TraesCS1A01G080200 chr1D 63947632 63952200 4568 True 3497.00 6665 89.5355 1 4602 2 chr1D.!!$R1 4601
2 TraesCS1A01G080200 chr1B 104769762 104774586 4824 True 1734.25 6329 89.7385 1 4737 4 chr1B.!!$R2 4736

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
751 782 0.465460 TTTTCCAGTGCGTGAAGGCT 60.465 50.000 0.0 0.0 0.00 4.58 F
1023 1081 1.085091 CTCTGTGCTTGCAGATGACC 58.915 55.000 0.0 0.0 43.61 4.02 F
2335 2393 1.453148 GTTCGTACAAAAGACCCGACG 59.547 52.381 0.0 0.0 0.00 5.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 2393 2.521708 AAGCCACCCAACTGCCAC 60.522 61.111 0.00 0.0 0.00 5.01 R
2930 2992 0.174389 AGTCTGCACGCTGGTAGATG 59.826 55.000 0.00 0.0 32.12 2.90 R
4238 4325 0.326595 TGCGCTTTATTCACAGGGGA 59.673 50.000 9.73 0.0 0.00 4.81 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
163 176 3.706373 GACCTCTCCAGGCGCCAA 61.706 66.667 31.54 12.89 45.05 4.52
174 187 1.676006 CAGGCGCCAAGGTAAATTAGG 59.324 52.381 31.54 0.00 0.00 2.69
196 209 1.519455 CAATCCGACGTCTGAGGCC 60.519 63.158 14.70 0.00 0.00 5.19
201 214 2.182030 GACGTCTGAGGCCGGAAG 59.818 66.667 5.05 2.40 34.05 3.46
202 215 3.991536 GACGTCTGAGGCCGGAAGC 62.992 68.421 5.05 0.00 42.60 3.86
219 232 4.776322 CGCCTCCGGTTGCCATGA 62.776 66.667 0.00 0.00 0.00 3.07
220 233 3.134127 GCCTCCGGTTGCCATGAC 61.134 66.667 0.00 0.00 0.00 3.06
250 263 1.502163 GGCGGCGAGATGATTCTTGG 61.502 60.000 12.98 0.00 34.37 3.61
269 282 1.202867 GGGAGGCTTCCATGGAGATTC 60.203 57.143 17.76 11.14 45.98 2.52
279 292 6.404074 GCTTCCATGGAGATTCTGTTTAGTTG 60.404 42.308 15.53 0.00 0.00 3.16
323 336 1.066858 CGCCAGTGAGGTGTTATCTGT 60.067 52.381 0.00 0.00 43.15 3.41
445 461 8.599055 TTGATTCATGCTATGATCTTAGTGTC 57.401 34.615 15.05 2.34 39.39 3.67
466 482 0.693622 TTTAGGATGTCACGCCCCAA 59.306 50.000 0.00 0.00 0.00 4.12
481 508 0.655733 CCCAATTCGATTCGGTTCCG 59.344 55.000 6.18 4.74 0.00 4.30
486 513 1.930567 TTCGATTCGGTTCCGATTCC 58.069 50.000 21.97 11.77 38.30 3.01
490 517 1.873591 GATTCGGTTCCGATTCCATGG 59.126 52.381 14.70 4.97 38.30 3.66
494 521 1.728490 GGTTCCGATTCCATGGCAGC 61.728 60.000 6.96 0.00 0.00 5.25
512 539 1.198408 AGCTGTGTGATTTGCATCGTG 59.802 47.619 0.00 0.00 31.08 4.35
531 558 1.160137 GCCTCTGTTTGCGAGAATGT 58.840 50.000 0.00 0.00 0.00 2.71
539 566 1.452110 TTGCGAGAATGTCATGTGGG 58.548 50.000 0.00 0.00 0.00 4.61
559 586 5.352569 GTGGGAACAGAGTCATGTTGAATAG 59.647 44.000 11.22 0.00 43.32 1.73
589 616 4.025896 CGCACATATCTCTGCTTTTCTCAG 60.026 45.833 0.00 0.00 0.00 3.35
599 626 2.948979 TGCTTTTCTCAGCTTTTCGGAA 59.051 40.909 0.00 0.00 40.79 4.30
638 665 5.116983 GCCGTGTCTGACAAACATTTTATTG 59.883 40.000 12.81 0.00 0.00 1.90
678 709 3.652057 AGGGACAATCTACATGGTTGG 57.348 47.619 0.00 0.00 0.00 3.77
716 747 7.325579 GTCTAAGTTGTTACAAACTAGACCGAG 59.674 40.741 23.48 6.08 39.48 4.63
731 762 3.833070 AGACCGAGGTTTCATACTTCTGT 59.167 43.478 0.00 0.00 33.93 3.41
732 763 4.283722 AGACCGAGGTTTCATACTTCTGTT 59.716 41.667 0.00 0.00 31.93 3.16
751 782 0.465460 TTTTCCAGTGCGTGAAGGCT 60.465 50.000 0.00 0.00 0.00 4.58
752 783 1.165907 TTTCCAGTGCGTGAAGGCTG 61.166 55.000 0.00 0.00 0.00 4.85
772 803 4.878397 GCTGTGGCTCACTTGTATTTAGAT 59.122 41.667 6.83 0.00 35.11 1.98
813 844 6.612306 GGTCTTGTTCCATTAGATCACAAAC 58.388 40.000 0.00 0.00 0.00 2.93
832 863 3.668596 ACTACACTTGAAAACGTGTGC 57.331 42.857 5.40 0.00 43.59 4.57
916 947 5.310409 TCTCTGAATGGACCAAAACTTCT 57.690 39.130 0.00 0.00 0.00 2.85
931 988 4.916041 AACTTCTCCATCCATGTCTCAA 57.084 40.909 0.00 0.00 0.00 3.02
933 990 6.566079 AACTTCTCCATCCATGTCTCAATA 57.434 37.500 0.00 0.00 0.00 1.90
964 1022 9.107177 GAAATAGATGTGACATTGTCATCTTCT 57.893 33.333 21.78 23.16 44.63 2.85
974 1032 8.260114 TGACATTGTCATCTTCTAGCTATTTGA 58.740 33.333 15.41 0.00 37.67 2.69
975 1033 9.270640 GACATTGTCATCTTCTAGCTATTTGAT 57.729 33.333 11.93 0.00 32.09 2.57
997 1055 8.900983 TGATTTTGTTTTCATCCTTTTAAGGG 57.099 30.769 8.60 0.00 46.47 3.95
998 1056 7.443879 TGATTTTGTTTTCATCCTTTTAAGGGC 59.556 33.333 8.60 0.00 46.47 5.19
1023 1081 1.085091 CTCTGTGCTTGCAGATGACC 58.915 55.000 0.00 0.00 43.61 4.02
1071 1129 4.158394 CCAGTTCAGAACCCAACCATATTG 59.842 45.833 9.85 0.00 0.00 1.90
2335 2393 1.453148 GTTCGTACAAAAGACCCGACG 59.547 52.381 0.00 0.00 0.00 5.12
2378 2436 6.680148 TTATTGATGATCCCTTGACCGATA 57.320 37.500 0.00 0.00 0.00 2.92
2605 2663 2.224719 GGAGGCAATATCCAGCATCTGT 60.225 50.000 8.60 0.00 40.98 3.41
2696 2754 4.123506 GGACTACTTCAAAGCTCTATGGC 58.876 47.826 0.00 0.00 0.00 4.40
2719 2777 1.888512 CCAAGACTTGGTTGGTCCATG 59.111 52.381 23.92 0.00 46.60 3.66
2734 2792 4.042311 TGGTCCATGTACCTTGCTTTTCTA 59.958 41.667 9.11 0.00 40.44 2.10
2766 2824 8.980481 ATATCTGGATTTTACTTGTTACAGGG 57.020 34.615 0.00 0.00 0.00 4.45
2768 2826 7.319052 TCTGGATTTTACTTGTTACAGGGTA 57.681 36.000 0.00 0.00 0.00 3.69
2773 2835 9.016438 GGATTTTACTTGTTACAGGGTATTTGA 57.984 33.333 0.00 0.00 0.00 2.69
2827 2889 4.731853 TCCAGGGGCATGGACGGA 62.732 66.667 6.58 0.00 44.56 4.69
2829 2891 3.716195 CAGGGGCATGGACGGACA 61.716 66.667 0.00 0.00 0.00 4.02
2832 2894 2.746375 GGGGCATGGACGGACATCT 61.746 63.158 0.00 0.00 0.00 2.90
2882 2944 3.517100 AGGTAGCTTCAGCAATTGAGAGA 59.483 43.478 10.34 0.00 45.16 3.10
2906 2968 2.420022 CCATCACCTGCTAAAACTTCGG 59.580 50.000 0.00 0.00 0.00 4.30
2930 2992 3.192001 TGTTGAATGAGGCAGATGAAAGC 59.808 43.478 0.00 0.00 0.00 3.51
2984 3046 0.599558 TGGGTACGAAGGTTCACTCG 59.400 55.000 0.00 0.00 0.00 4.18
2994 3056 1.014564 GGTTCACTCGTACTGCTGGC 61.015 60.000 0.00 0.00 0.00 4.85
3020 3082 3.157087 TGAATTTTCTGGGAAGGACAGC 58.843 45.455 0.00 0.00 35.94 4.40
3056 3118 2.104963 GAGGAGTGAGTGGAAAACTGGT 59.895 50.000 0.00 0.00 40.07 4.00
3200 3262 0.313043 AGCTTGCATTGTGTGACTGC 59.687 50.000 0.00 0.00 36.45 4.40
3275 3337 2.350895 CGTGACAGGGGATTGGCA 59.649 61.111 0.00 0.00 32.48 4.92
3539 3601 1.569479 GCAGTGAAGTTCCCGCTGAC 61.569 60.000 17.75 2.90 42.89 3.51
3548 3610 1.735376 TTCCCGCTGACGAGGATAGC 61.735 60.000 0.00 0.00 43.93 2.97
3660 3731 3.321968 TGAGAGCAGTCAAGCAACTTCTA 59.678 43.478 0.00 0.00 36.85 2.10
3679 3750 5.624344 TCTATACGGGAACTTGATCGATC 57.376 43.478 18.72 18.72 0.00 3.69
3787 3858 0.603975 GAGGAAGAAACTGCAGCGGT 60.604 55.000 15.27 0.00 0.00 5.68
3843 3914 0.882042 AGCGACTTGTGTGCAGGAAG 60.882 55.000 0.00 0.00 0.00 3.46
3894 3965 1.847088 AGGAAAGAGGGGGCAGATAAC 59.153 52.381 0.00 0.00 0.00 1.89
4190 4277 2.797491 GGAACCATGTGAATAAAGCGC 58.203 47.619 0.00 0.00 0.00 5.92
4191 4278 2.163412 GGAACCATGTGAATAAAGCGCA 59.837 45.455 11.47 0.00 0.00 6.09
4192 4279 3.366883 GGAACCATGTGAATAAAGCGCAA 60.367 43.478 11.47 0.00 0.00 4.85
4193 4280 3.216147 ACCATGTGAATAAAGCGCAAC 57.784 42.857 11.47 0.00 0.00 4.17
4194 4281 2.556189 ACCATGTGAATAAAGCGCAACA 59.444 40.909 11.47 2.36 0.00 3.33
4195 4282 3.005261 ACCATGTGAATAAAGCGCAACAA 59.995 39.130 11.47 0.00 0.00 2.83
4196 4283 4.175516 CCATGTGAATAAAGCGCAACAAT 58.824 39.130 11.47 0.00 0.00 2.71
4197 4284 4.266029 CCATGTGAATAAAGCGCAACAATC 59.734 41.667 11.47 2.56 0.00 2.67
4198 4285 4.764679 TGTGAATAAAGCGCAACAATCT 57.235 36.364 11.47 0.00 0.00 2.40
4199 4286 4.722194 TGTGAATAAAGCGCAACAATCTC 58.278 39.130 11.47 3.98 0.00 2.75
4200 4287 4.215185 TGTGAATAAAGCGCAACAATCTCA 59.785 37.500 11.47 6.67 0.00 3.27
4201 4288 5.106197 TGTGAATAAAGCGCAACAATCTCAT 60.106 36.000 11.47 0.00 0.00 2.90
4202 4289 5.228635 GTGAATAAAGCGCAACAATCTCATG 59.771 40.000 11.47 0.00 0.00 3.07
4203 4290 4.970662 ATAAAGCGCAACAATCTCATGT 57.029 36.364 11.47 0.00 34.24 3.21
4204 4291 6.093357 TGAATAAAGCGCAACAATCTCATGTA 59.907 34.615 11.47 0.00 32.02 2.29
4205 4292 3.747099 AAGCGCAACAATCTCATGTAC 57.253 42.857 11.47 0.00 32.02 2.90
4206 4293 1.660607 AGCGCAACAATCTCATGTACG 59.339 47.619 11.47 0.00 36.58 3.67
4207 4294 1.393539 GCGCAACAATCTCATGTACGT 59.606 47.619 0.30 0.00 36.17 3.57
4208 4295 2.784327 GCGCAACAATCTCATGTACGTG 60.784 50.000 8.90 8.90 36.17 4.49
4209 4296 2.222796 CGCAACAATCTCATGTACGTGG 60.223 50.000 15.02 6.27 32.02 4.94
4210 4297 2.742053 GCAACAATCTCATGTACGTGGT 59.258 45.455 15.02 1.90 32.02 4.16
4211 4298 3.188460 GCAACAATCTCATGTACGTGGTT 59.812 43.478 15.02 7.85 32.02 3.67
4212 4299 4.320202 GCAACAATCTCATGTACGTGGTTT 60.320 41.667 15.02 4.13 32.02 3.27
4213 4300 5.106869 GCAACAATCTCATGTACGTGGTTTA 60.107 40.000 15.02 0.00 32.02 2.01
4214 4301 6.304126 CAACAATCTCATGTACGTGGTTTAC 58.696 40.000 15.02 0.00 32.02 2.01
4215 4302 5.543714 ACAATCTCATGTACGTGGTTTACA 58.456 37.500 15.02 0.00 34.00 2.41
4216 4303 5.992829 ACAATCTCATGTACGTGGTTTACAA 59.007 36.000 15.02 0.00 33.22 2.41
4217 4304 6.653320 ACAATCTCATGTACGTGGTTTACAAT 59.347 34.615 15.02 0.00 33.22 2.71
4218 4305 6.903883 ATCTCATGTACGTGGTTTACAATC 57.096 37.500 15.02 0.00 33.22 2.67
4219 4306 5.785243 TCTCATGTACGTGGTTTACAATCA 58.215 37.500 15.02 0.00 33.22 2.57
4220 4307 5.636121 TCTCATGTACGTGGTTTACAATCAC 59.364 40.000 15.02 0.00 33.22 3.06
4221 4308 5.298347 TCATGTACGTGGTTTACAATCACA 58.702 37.500 15.02 0.00 33.22 3.58
4222 4309 5.935206 TCATGTACGTGGTTTACAATCACAT 59.065 36.000 15.02 0.00 33.22 3.21
4223 4310 5.599359 TGTACGTGGTTTACAATCACATG 57.401 39.130 0.00 0.00 0.00 3.21
4224 4311 5.298347 TGTACGTGGTTTACAATCACATGA 58.702 37.500 0.00 0.00 0.00 3.07
4225 4312 5.407084 TGTACGTGGTTTACAATCACATGAG 59.593 40.000 0.00 0.00 0.00 2.90
4226 4313 3.188460 ACGTGGTTTACAATCACATGAGC 59.812 43.478 0.00 0.00 0.00 4.26
4227 4314 3.436704 CGTGGTTTACAATCACATGAGCT 59.563 43.478 0.00 0.00 0.00 4.09
4228 4315 4.083324 CGTGGTTTACAATCACATGAGCTT 60.083 41.667 0.00 0.00 0.00 3.74
4229 4316 5.156355 GTGGTTTACAATCACATGAGCTTG 58.844 41.667 0.00 1.93 0.00 4.01
4230 4317 4.826733 TGGTTTACAATCACATGAGCTTGT 59.173 37.500 15.06 15.06 33.42 3.16
4231 4318 5.301551 TGGTTTACAATCACATGAGCTTGTT 59.698 36.000 15.75 3.36 31.84 2.83
4232 4319 6.488344 TGGTTTACAATCACATGAGCTTGTTA 59.512 34.615 15.75 6.15 31.84 2.41
4233 4320 6.801862 GGTTTACAATCACATGAGCTTGTTAC 59.198 38.462 15.75 13.66 31.84 2.50
4234 4321 7.308589 GGTTTACAATCACATGAGCTTGTTACT 60.309 37.037 15.75 0.00 31.84 2.24
4235 4322 7.744087 TTACAATCACATGAGCTTGTTACTT 57.256 32.000 15.75 0.00 31.84 2.24
4236 4323 6.639632 ACAATCACATGAGCTTGTTACTTT 57.360 33.333 6.55 0.00 0.00 2.66
4237 4324 6.441274 ACAATCACATGAGCTTGTTACTTTG 58.559 36.000 6.55 0.00 0.00 2.77
4238 4325 6.039717 ACAATCACATGAGCTTGTTACTTTGT 59.960 34.615 6.55 0.00 0.00 2.83
4239 4326 5.673337 TCACATGAGCTTGTTACTTTGTC 57.327 39.130 0.00 0.00 0.00 3.18
4240 4327 4.515191 TCACATGAGCTTGTTACTTTGTCC 59.485 41.667 0.00 0.00 0.00 4.02
4241 4328 3.821033 ACATGAGCTTGTTACTTTGTCCC 59.179 43.478 0.00 0.00 0.00 4.46
4242 4329 2.858745 TGAGCTTGTTACTTTGTCCCC 58.141 47.619 0.00 0.00 0.00 4.81
4243 4330 2.441750 TGAGCTTGTTACTTTGTCCCCT 59.558 45.455 0.00 0.00 0.00 4.79
4244 4331 2.814336 GAGCTTGTTACTTTGTCCCCTG 59.186 50.000 0.00 0.00 0.00 4.45
4245 4332 2.174854 AGCTTGTTACTTTGTCCCCTGT 59.825 45.455 0.00 0.00 0.00 4.00
4246 4333 2.293399 GCTTGTTACTTTGTCCCCTGTG 59.707 50.000 0.00 0.00 0.00 3.66
4247 4334 3.815809 CTTGTTACTTTGTCCCCTGTGA 58.184 45.455 0.00 0.00 0.00 3.58
4248 4335 3.935818 TGTTACTTTGTCCCCTGTGAA 57.064 42.857 0.00 0.00 0.00 3.18
4249 4336 4.447138 TGTTACTTTGTCCCCTGTGAAT 57.553 40.909 0.00 0.00 0.00 2.57
4250 4337 5.570205 TGTTACTTTGTCCCCTGTGAATA 57.430 39.130 0.00 0.00 0.00 1.75
4251 4338 5.942961 TGTTACTTTGTCCCCTGTGAATAA 58.057 37.500 0.00 0.00 0.00 1.40
4304 4396 6.039717 ACAATCACATGAGCTTGTTACTTTGT 59.960 34.615 6.55 0.00 0.00 2.83
4431 4536 2.162408 AGCAAGCTCGAAATAACAAGCC 59.838 45.455 0.00 0.00 35.32 4.35
4474 4590 7.569591 GCATACATCTACTAAATTTCAGCCGAC 60.570 40.741 0.00 0.00 0.00 4.79
4488 4605 0.172803 GCCGACACGACTCATAACCT 59.827 55.000 0.00 0.00 0.00 3.50
4494 4611 2.631062 ACACGACTCATAACCTTCACCA 59.369 45.455 0.00 0.00 0.00 4.17
4507 4624 4.340617 ACCTTCACCAAACTGAACTTTCA 58.659 39.130 0.00 0.00 35.57 2.69
4584 4707 7.781324 ACAAAATCAGTACAAATCCCTCAAT 57.219 32.000 0.00 0.00 0.00 2.57
4611 4772 3.070446 ACTTGTGGAGTACGACAATGGAA 59.930 43.478 8.12 0.00 42.06 3.53
4651 4812 9.218359 CAGTTCTTTATTGATGATGAATGAACG 57.782 33.333 0.00 0.00 32.79 3.95
4662 4823 9.487790 TGATGATGAATGAACGCTTATATACAA 57.512 29.630 0.00 0.00 0.00 2.41
4666 4827 6.898041 TGAATGAACGCTTATATACAATGGC 58.102 36.000 0.00 0.00 0.00 4.40
4713 4913 3.523157 TGGTTCATAGAGATGCCTTCCAA 59.477 43.478 0.00 0.00 32.62 3.53
4714 4914 4.018506 TGGTTCATAGAGATGCCTTCCAAA 60.019 41.667 0.00 0.00 32.62 3.28
4726 4926 1.613437 CCTTCCAAAAACTGCCGTGAT 59.387 47.619 0.00 0.00 0.00 3.06
4727 4927 2.351738 CCTTCCAAAAACTGCCGTGATC 60.352 50.000 0.00 0.00 0.00 2.92
4738 4938 3.499737 CGTGATCGGTTGCTGGCC 61.500 66.667 0.00 0.00 0.00 5.36
4739 4939 2.359850 GTGATCGGTTGCTGGCCA 60.360 61.111 4.71 4.71 0.00 5.36
4740 4940 2.359850 TGATCGGTTGCTGGCCAC 60.360 61.111 0.00 0.00 0.00 5.01
4741 4941 2.359850 GATCGGTTGCTGGCCACA 60.360 61.111 0.00 1.92 0.00 4.17
4742 4942 2.672996 ATCGGTTGCTGGCCACAC 60.673 61.111 0.00 0.00 0.00 3.82
4743 4943 3.490031 ATCGGTTGCTGGCCACACA 62.490 57.895 0.00 0.00 0.00 3.72
4744 4944 2.769652 ATCGGTTGCTGGCCACACAT 62.770 55.000 0.00 0.00 0.00 3.21
4745 4945 2.652530 GGTTGCTGGCCACACATG 59.347 61.111 0.00 0.00 0.00 3.21
4746 4946 2.202395 GGTTGCTGGCCACACATGT 61.202 57.895 0.00 0.00 0.00 3.21
4747 4947 1.007038 GTTGCTGGCCACACATGTG 60.007 57.895 24.25 24.25 45.23 3.21
4758 4958 2.469274 ACACATGTGAGAAGGAGCAG 57.531 50.000 31.94 1.10 0.00 4.24
4759 4959 1.002888 ACACATGTGAGAAGGAGCAGG 59.997 52.381 31.94 0.88 0.00 4.85
4760 4960 0.617413 ACATGTGAGAAGGAGCAGGG 59.383 55.000 0.00 0.00 0.00 4.45
4761 4961 0.907486 CATGTGAGAAGGAGCAGGGA 59.093 55.000 0.00 0.00 0.00 4.20
4762 4962 0.908198 ATGTGAGAAGGAGCAGGGAC 59.092 55.000 0.00 0.00 0.00 4.46
4763 4963 0.178921 TGTGAGAAGGAGCAGGGACT 60.179 55.000 0.00 0.00 43.88 3.85
4764 4964 1.077169 TGTGAGAAGGAGCAGGGACTA 59.923 52.381 0.00 0.00 36.02 2.59
4765 4965 2.292521 TGTGAGAAGGAGCAGGGACTAT 60.293 50.000 0.00 0.00 36.02 2.12
4766 4966 2.364002 GTGAGAAGGAGCAGGGACTATC 59.636 54.545 0.00 0.00 36.02 2.08
4767 4967 1.967779 GAGAAGGAGCAGGGACTATCC 59.032 57.143 0.00 0.00 42.05 2.59
4783 4983 7.400599 GGACTATCCCCTAAAAATCGTTTTT 57.599 36.000 11.37 11.37 44.43 1.94
4784 4984 8.510243 GGACTATCCCCTAAAAATCGTTTTTA 57.490 34.615 4.70 9.21 42.43 1.52
4785 4985 8.959548 GGACTATCCCCTAAAAATCGTTTTTAA 58.040 33.333 4.70 0.00 42.58 1.52
4786 4986 9.778993 GACTATCCCCTAAAAATCGTTTTTAAC 57.221 33.333 4.70 0.00 42.58 2.01
4787 4987 9.299465 ACTATCCCCTAAAAATCGTTTTTAACA 57.701 29.630 4.70 0.00 42.58 2.41
4789 4989 8.996024 ATCCCCTAAAAATCGTTTTTAACATG 57.004 30.769 4.70 0.00 42.58 3.21
4790 4990 7.953752 TCCCCTAAAAATCGTTTTTAACATGT 58.046 30.769 4.70 0.00 42.58 3.21
4791 4991 9.075678 TCCCCTAAAAATCGTTTTTAACATGTA 57.924 29.630 0.00 0.00 42.58 2.29
4792 4992 9.131416 CCCCTAAAAATCGTTTTTAACATGTAC 57.869 33.333 0.00 0.00 42.58 2.90
4793 4993 9.902196 CCCTAAAAATCGTTTTTAACATGTACT 57.098 29.630 0.00 0.00 42.58 2.73
4817 5017 8.553696 ACTGTACTAATTTGAACTAAAACCACG 58.446 33.333 0.00 0.00 0.00 4.94
4818 5018 8.659925 TGTACTAATTTGAACTAAAACCACGA 57.340 30.769 0.00 0.00 0.00 4.35
4819 5019 8.550376 TGTACTAATTTGAACTAAAACCACGAC 58.450 33.333 0.00 0.00 0.00 4.34
4820 5020 6.652245 ACTAATTTGAACTAAAACCACGACG 58.348 36.000 0.00 0.00 0.00 5.12
4821 5021 5.738118 AATTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 0.00 4.20
4822 5022 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
4823 5023 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
4824 5024 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
4825 5025 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
4826 5026 5.531634 TGAACTAAAACCACGACGAGTAAT 58.468 37.500 0.00 0.00 0.00 1.89
4827 5027 5.984926 TGAACTAAAACCACGACGAGTAATT 59.015 36.000 0.00 1.08 0.00 1.40
4828 5028 6.479660 TGAACTAAAACCACGACGAGTAATTT 59.520 34.615 0.00 0.34 0.00 1.82
4829 5029 6.219302 ACTAAAACCACGACGAGTAATTTG 57.781 37.500 0.00 2.39 0.00 2.32
4830 5030 4.477302 AAAACCACGACGAGTAATTTGG 57.523 40.909 0.00 0.00 0.00 3.28
4831 5031 3.389925 AACCACGACGAGTAATTTGGA 57.610 42.857 0.00 0.00 0.00 3.53
4832 5032 3.389925 ACCACGACGAGTAATTTGGAA 57.610 42.857 0.00 0.00 0.00 3.53
4833 5033 3.934068 ACCACGACGAGTAATTTGGAAT 58.066 40.909 0.00 0.00 0.00 3.01
4834 5034 3.682858 ACCACGACGAGTAATTTGGAATG 59.317 43.478 0.00 0.00 0.00 2.67
4835 5035 3.930229 CCACGACGAGTAATTTGGAATGA 59.070 43.478 0.00 0.00 0.00 2.57
4836 5036 4.390603 CCACGACGAGTAATTTGGAATGAA 59.609 41.667 0.00 0.00 0.00 2.57
4837 5037 5.445939 CCACGACGAGTAATTTGGAATGAAG 60.446 44.000 0.00 0.00 0.00 3.02
4838 5038 4.630069 ACGACGAGTAATTTGGAATGAAGG 59.370 41.667 0.00 0.00 0.00 3.46
4839 5039 4.868171 CGACGAGTAATTTGGAATGAAGGA 59.132 41.667 0.00 0.00 0.00 3.36
4840 5040 5.350365 CGACGAGTAATTTGGAATGAAGGAA 59.650 40.000 0.00 0.00 0.00 3.36
4841 5041 6.455646 CGACGAGTAATTTGGAATGAAGGAAG 60.456 42.308 0.00 0.00 0.00 3.46
4842 5042 5.648092 ACGAGTAATTTGGAATGAAGGAAGG 59.352 40.000 0.00 0.00 0.00 3.46
4843 5043 5.880332 CGAGTAATTTGGAATGAAGGAAGGA 59.120 40.000 0.00 0.00 0.00 3.36
4844 5044 6.543831 CGAGTAATTTGGAATGAAGGAAGGAT 59.456 38.462 0.00 0.00 0.00 3.24
4845 5045 7.067494 CGAGTAATTTGGAATGAAGGAAGGATT 59.933 37.037 0.00 0.00 0.00 3.01
4846 5046 8.670521 AGTAATTTGGAATGAAGGAAGGATTT 57.329 30.769 0.00 0.00 0.00 2.17
4847 5047 9.104713 AGTAATTTGGAATGAAGGAAGGATTTT 57.895 29.630 0.00 0.00 0.00 1.82
4848 5048 9.725019 GTAATTTGGAATGAAGGAAGGATTTTT 57.275 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 176 5.434408 GTCGGATTGGAACCTAATTTACCT 58.566 41.667 0.00 0.00 0.00 3.08
174 187 1.630148 CTCAGACGTCGGATTGGAAC 58.370 55.000 18.73 0.00 0.00 3.62
219 232 1.219935 CGCCGCCCCTAACTAAAGT 59.780 57.895 0.00 0.00 0.00 2.66
220 233 0.529992 CTCGCCGCCCCTAACTAAAG 60.530 60.000 0.00 0.00 0.00 1.85
250 263 1.773653 AGAATCTCCATGGAAGCCTCC 59.226 52.381 17.00 0.00 42.81 4.30
269 282 4.499183 CTCTACCCTGAGCAACTAAACAG 58.501 47.826 0.00 0.00 0.00 3.16
279 292 0.972983 TCAGCACCTCTACCCTGAGC 60.973 60.000 0.00 0.00 33.02 4.26
304 317 2.770164 ACAGATAACACCTCACTGGC 57.230 50.000 0.00 0.00 40.22 4.85
323 336 8.445275 TTGTCAAGATACAAGCTAAAGTCAAA 57.555 30.769 0.00 0.00 34.50 2.69
445 461 1.087771 GGGGCGTGACATCCTAAACG 61.088 60.000 0.00 0.00 39.00 3.60
481 508 0.454600 CACACAGCTGCCATGGAATC 59.545 55.000 18.40 0.00 0.00 2.52
486 513 1.990799 CAAATCACACAGCTGCCATG 58.009 50.000 15.27 9.90 0.00 3.66
490 517 1.625616 GATGCAAATCACACAGCTGC 58.374 50.000 15.27 0.00 0.00 5.25
494 521 1.609932 GCACGATGCAAATCACACAG 58.390 50.000 0.00 0.00 44.26 3.66
512 539 1.129437 GACATTCTCGCAAACAGAGGC 59.871 52.381 0.00 0.00 36.45 4.70
531 558 2.639347 ACATGACTCTGTTCCCACATGA 59.361 45.455 0.00 0.00 38.55 3.07
539 566 6.486253 TTGCTATTCAACATGACTCTGTTC 57.514 37.500 0.00 0.00 37.25 3.18
559 586 2.350197 GCAGAGATATGTGCGGAATTGC 60.350 50.000 0.00 0.00 0.00 3.56
589 616 3.192633 TCAAGGGCTAATTTCCGAAAAGC 59.807 43.478 8.48 8.48 0.00 3.51
599 626 1.750778 CACGGCAATCAAGGGCTAATT 59.249 47.619 0.00 0.00 0.00 1.40
638 665 4.884164 CCCTTTTCCTCCATCTATGTCAAC 59.116 45.833 0.00 0.00 0.00 3.18
678 709 8.080417 TGTAACAACTTAGACATGACTAGTGAC 58.920 37.037 0.00 1.61 0.00 3.67
716 747 6.918022 CACTGGAAAAACAGAAGTATGAAACC 59.082 38.462 0.00 0.00 40.97 3.27
731 762 0.383949 GCCTTCACGCACTGGAAAAA 59.616 50.000 0.00 0.00 0.00 1.94
732 763 0.465460 AGCCTTCACGCACTGGAAAA 60.465 50.000 0.00 0.00 0.00 2.29
751 782 7.309133 CCAAAATCTAAATACAAGTGAGCCACA 60.309 37.037 7.86 0.00 36.74 4.17
752 783 7.029563 CCAAAATCTAAATACAAGTGAGCCAC 58.970 38.462 0.00 0.00 34.10 5.01
772 803 3.482436 AGACCGTAGTTGCATTCCAAAA 58.518 40.909 0.00 0.00 34.68 2.44
832 863 3.873361 ACAGTCAGATGTGTCTTGTTGTG 59.127 43.478 0.00 0.00 30.42 3.33
916 947 8.648698 TTTCTTTTTATTGAGACATGGATGGA 57.351 30.769 0.00 0.00 0.00 3.41
947 1005 8.333908 CAAATAGCTAGAAGATGACAATGTCAC 58.666 37.037 19.17 12.29 45.65 3.67
965 1023 9.783081 AAAGGATGAAAACAAAATCAAATAGCT 57.217 25.926 0.00 0.00 0.00 3.32
987 1045 2.939103 CAGAGTCATCGCCCTTAAAAGG 59.061 50.000 1.47 1.47 46.06 3.11
997 1055 1.293963 TGCAAGCACAGAGTCATCGC 61.294 55.000 0.00 0.00 0.00 4.58
998 1056 0.720027 CTGCAAGCACAGAGTCATCG 59.280 55.000 0.00 0.00 40.25 3.84
1023 1081 3.019564 GGTGAGAATTTCATCCCACCTG 58.980 50.000 16.27 0.00 40.48 4.00
1071 1129 4.034975 GTGATATCTGCTGCTGAAAACTCC 59.965 45.833 13.26 1.69 0.00 3.85
1982 2040 5.827797 GCCCAAGACAAAGGTATCATTATCA 59.172 40.000 0.00 0.00 0.00 2.15
2162 2220 7.675962 AAATGGCAAACAACGATACTACTAA 57.324 32.000 0.00 0.00 0.00 2.24
2335 2393 2.521708 AAGCCACCCAACTGCCAC 60.522 61.111 0.00 0.00 0.00 5.01
2378 2436 5.408604 GCATTAGTTACCTTATAGTGCGCAT 59.591 40.000 15.91 5.37 0.00 4.73
2734 2792 8.366359 ACAAGTAAAATCCAGATATTTTGGCT 57.634 30.769 5.12 1.74 38.98 4.75
2740 2798 9.408648 CCCTGTAACAAGTAAAATCCAGATATT 57.591 33.333 0.00 0.00 0.00 1.28
2787 2849 9.135189 TGGAAGATATTGAGATTAAATGGTTGG 57.865 33.333 0.00 0.00 0.00 3.77
2793 2855 6.950619 GCCCCTGGAAGATATTGAGATTAAAT 59.049 38.462 0.00 0.00 34.07 1.40
2825 2887 2.437413 GGGTTGGTCTTCAAGATGTCC 58.563 52.381 0.00 0.00 35.80 4.02
2827 2889 1.420138 ACGGGTTGGTCTTCAAGATGT 59.580 47.619 0.00 0.00 35.80 3.06
2829 2891 2.504367 CAACGGGTTGGTCTTCAAGAT 58.496 47.619 3.63 0.00 35.80 2.40
2882 2944 4.876107 CGAAGTTTTAGCAGGTGATGGTAT 59.124 41.667 0.00 0.00 41.36 2.73
2906 2968 2.362736 TCATCTGCCTCATTCAACAGC 58.637 47.619 0.00 0.00 0.00 4.40
2930 2992 0.174389 AGTCTGCACGCTGGTAGATG 59.826 55.000 0.00 0.00 32.12 2.90
2984 3046 2.338577 ATTCATCCAGCCAGCAGTAC 57.661 50.000 0.00 0.00 0.00 2.73
2994 3056 4.400567 GTCCTTCCCAGAAAATTCATCCAG 59.599 45.833 0.00 0.00 0.00 3.86
3020 3082 3.127895 CACTCCTCCAGTAACGAGAGAAG 59.872 52.174 0.00 0.00 32.21 2.85
3056 3118 1.607178 CTGCTGCCATGGGTTTGGA 60.607 57.895 15.13 0.00 39.25 3.53
3200 3262 0.401738 TTCCCTTCCTTGACCAGCTG 59.598 55.000 6.78 6.78 0.00 4.24
3230 3292 1.246649 TTGCCGACTTCATTGCATGT 58.753 45.000 0.00 0.00 33.08 3.21
3248 3310 1.106944 CCCTGTCACGGCAAACCTTT 61.107 55.000 0.00 0.00 0.00 3.11
3539 3601 1.198867 CTGTCCTCATCGCTATCCTCG 59.801 57.143 0.00 0.00 0.00 4.63
3548 3610 0.534412 AAGCAGGACTGTCCTCATCG 59.466 55.000 26.11 15.90 45.66 3.84
3660 3731 3.889538 TGAGATCGATCAAGTTCCCGTAT 59.110 43.478 26.47 1.56 0.00 3.06
3787 3858 3.286353 TCAGAAGGTTGTGTGATTTGCA 58.714 40.909 0.00 0.00 0.00 4.08
3797 3868 4.843728 TGTTCTCACTTTCAGAAGGTTGT 58.156 39.130 0.00 0.00 37.19 3.32
3843 3914 3.743396 GGACTATCCTGATTGCGATCAAC 59.257 47.826 17.39 4.05 41.55 3.18
3894 3965 1.221840 CTCCATCACCGTCCCAAGG 59.778 63.158 0.00 0.00 0.00 3.61
3921 3992 1.811266 CATCGCTAGCTTGCACCGT 60.811 57.895 19.99 0.00 0.00 4.83
4187 4274 1.393539 ACGTACATGAGATTGTTGCGC 59.606 47.619 0.00 0.00 33.25 6.09
4188 4275 2.222796 CCACGTACATGAGATTGTTGCG 60.223 50.000 0.00 0.00 34.88 4.85
4189 4276 2.742053 ACCACGTACATGAGATTGTTGC 59.258 45.455 0.00 0.00 0.00 4.17
4190 4277 5.356882 AAACCACGTACATGAGATTGTTG 57.643 39.130 0.00 0.00 0.00 3.33
4191 4278 5.992829 TGTAAACCACGTACATGAGATTGTT 59.007 36.000 0.00 0.00 0.00 2.83
4192 4279 5.543714 TGTAAACCACGTACATGAGATTGT 58.456 37.500 0.00 0.00 0.00 2.71
4193 4280 6.474819 TTGTAAACCACGTACATGAGATTG 57.525 37.500 0.00 0.00 31.72 2.67
4194 4281 6.876789 TGATTGTAAACCACGTACATGAGATT 59.123 34.615 0.00 0.00 31.72 2.40
4195 4282 6.312918 GTGATTGTAAACCACGTACATGAGAT 59.687 38.462 0.00 0.00 25.47 2.75
4196 4283 5.636121 GTGATTGTAAACCACGTACATGAGA 59.364 40.000 0.00 0.00 25.47 3.27
4197 4284 5.407084 TGTGATTGTAAACCACGTACATGAG 59.593 40.000 0.00 0.00 45.87 2.90
4198 4285 5.298347 TGTGATTGTAAACCACGTACATGA 58.702 37.500 0.00 0.00 45.87 3.07
4199 4286 5.599359 TGTGATTGTAAACCACGTACATG 57.401 39.130 0.00 0.00 45.87 3.21
4200 4287 5.935206 TCATGTGATTGTAAACCACGTACAT 59.065 36.000 0.00 0.00 45.87 2.29
4201 4288 5.298347 TCATGTGATTGTAAACCACGTACA 58.702 37.500 0.00 0.00 45.87 2.90
4202 4289 5.670341 GCTCATGTGATTGTAAACCACGTAC 60.670 44.000 0.00 0.00 45.87 3.67
4203 4290 4.390603 GCTCATGTGATTGTAAACCACGTA 59.609 41.667 0.00 0.00 45.87 3.57
4204 4291 3.188460 GCTCATGTGATTGTAAACCACGT 59.812 43.478 0.00 0.00 45.87 4.49
4205 4292 3.436704 AGCTCATGTGATTGTAAACCACG 59.563 43.478 0.00 0.00 45.87 4.94
4206 4293 5.156355 CAAGCTCATGTGATTGTAAACCAC 58.844 41.667 15.68 0.00 42.14 4.16
4207 4294 4.826733 ACAAGCTCATGTGATTGTAAACCA 59.173 37.500 25.10 0.00 34.26 3.67
4208 4295 5.376854 ACAAGCTCATGTGATTGTAAACC 57.623 39.130 25.10 0.00 34.26 3.27
4209 4296 7.584987 AGTAACAAGCTCATGTGATTGTAAAC 58.415 34.615 26.15 24.43 34.92 2.01
4210 4297 7.744087 AGTAACAAGCTCATGTGATTGTAAA 57.256 32.000 26.15 16.98 34.92 2.01
4211 4298 7.744087 AAGTAACAAGCTCATGTGATTGTAA 57.256 32.000 26.15 3.89 34.92 2.41
4212 4299 7.228507 ACAAAGTAACAAGCTCATGTGATTGTA 59.771 33.333 26.15 14.60 34.92 2.41
4213 4300 6.039717 ACAAAGTAACAAGCTCATGTGATTGT 59.960 34.615 21.94 21.94 37.47 2.71
4214 4301 6.441274 ACAAAGTAACAAGCTCATGTGATTG 58.559 36.000 20.74 20.74 32.81 2.67
4215 4302 6.294176 GGACAAAGTAACAAGCTCATGTGATT 60.294 38.462 0.00 0.00 32.81 2.57
4216 4303 5.182001 GGACAAAGTAACAAGCTCATGTGAT 59.818 40.000 0.00 0.00 32.81 3.06
4217 4304 4.515191 GGACAAAGTAACAAGCTCATGTGA 59.485 41.667 0.00 0.00 32.81 3.58
4218 4305 4.320494 GGGACAAAGTAACAAGCTCATGTG 60.320 45.833 0.00 0.00 32.81 3.21
4219 4306 3.821033 GGGACAAAGTAACAAGCTCATGT 59.179 43.478 0.00 0.00 34.24 3.21
4220 4307 3.191371 GGGGACAAAGTAACAAGCTCATG 59.809 47.826 0.00 0.00 0.00 3.07
4221 4308 3.074538 AGGGGACAAAGTAACAAGCTCAT 59.925 43.478 0.00 0.00 0.00 2.90
4222 4309 2.441750 AGGGGACAAAGTAACAAGCTCA 59.558 45.455 0.00 0.00 0.00 4.26
4223 4310 2.814336 CAGGGGACAAAGTAACAAGCTC 59.186 50.000 0.00 0.00 0.00 4.09
4224 4311 2.174854 ACAGGGGACAAAGTAACAAGCT 59.825 45.455 0.00 0.00 0.00 3.74
4225 4312 2.293399 CACAGGGGACAAAGTAACAAGC 59.707 50.000 0.00 0.00 0.00 4.01
4226 4313 3.815809 TCACAGGGGACAAAGTAACAAG 58.184 45.455 0.00 0.00 0.00 3.16
4227 4314 3.935818 TCACAGGGGACAAAGTAACAA 57.064 42.857 0.00 0.00 0.00 2.83
4228 4315 3.935818 TTCACAGGGGACAAAGTAACA 57.064 42.857 0.00 0.00 0.00 2.41
4229 4316 6.569801 GCTTTATTCACAGGGGACAAAGTAAC 60.570 42.308 6.65 0.00 0.00 2.50
4230 4317 5.475564 GCTTTATTCACAGGGGACAAAGTAA 59.524 40.000 6.65 0.00 0.00 2.24
4231 4318 5.007682 GCTTTATTCACAGGGGACAAAGTA 58.992 41.667 6.65 0.00 0.00 2.24
4232 4319 3.826729 GCTTTATTCACAGGGGACAAAGT 59.173 43.478 6.65 0.00 0.00 2.66
4233 4320 3.119849 CGCTTTATTCACAGGGGACAAAG 60.120 47.826 2.07 2.07 0.00 2.77
4234 4321 2.817258 CGCTTTATTCACAGGGGACAAA 59.183 45.455 0.00 0.00 0.00 2.83
4235 4322 2.432444 CGCTTTATTCACAGGGGACAA 58.568 47.619 0.00 0.00 0.00 3.18
4236 4323 1.948611 GCGCTTTATTCACAGGGGACA 60.949 52.381 0.00 0.00 0.00 4.02
4237 4324 0.733150 GCGCTTTATTCACAGGGGAC 59.267 55.000 0.00 0.00 0.00 4.46
4238 4325 0.326595 TGCGCTTTATTCACAGGGGA 59.673 50.000 9.73 0.00 0.00 4.81
4239 4326 1.135402 GTTGCGCTTTATTCACAGGGG 60.135 52.381 9.73 0.00 0.00 4.79
4240 4327 1.539388 TGTTGCGCTTTATTCACAGGG 59.461 47.619 9.73 0.00 0.00 4.45
4241 4328 2.987413 TGTTGCGCTTTATTCACAGG 57.013 45.000 9.73 0.00 0.00 4.00
4242 4329 4.726416 AGATTGTTGCGCTTTATTCACAG 58.274 39.130 9.73 0.00 0.00 3.66
4243 4330 4.215185 TGAGATTGTTGCGCTTTATTCACA 59.785 37.500 9.73 2.71 0.00 3.58
4244 4331 4.722194 TGAGATTGTTGCGCTTTATTCAC 58.278 39.130 9.73 0.00 0.00 3.18
4245 4332 5.106197 ACATGAGATTGTTGCGCTTTATTCA 60.106 36.000 9.73 4.55 0.00 2.57
4246 4333 5.335127 ACATGAGATTGTTGCGCTTTATTC 58.665 37.500 9.73 0.14 0.00 1.75
4247 4334 5.314923 ACATGAGATTGTTGCGCTTTATT 57.685 34.783 9.73 0.00 0.00 1.40
4248 4335 4.970662 ACATGAGATTGTTGCGCTTTAT 57.029 36.364 9.73 0.00 0.00 1.40
4249 4336 4.201676 CGTACATGAGATTGTTGCGCTTTA 60.202 41.667 9.73 0.00 0.00 1.85
4250 4337 3.424829 CGTACATGAGATTGTTGCGCTTT 60.425 43.478 9.73 0.00 0.00 3.51
4251 4338 2.094258 CGTACATGAGATTGTTGCGCTT 59.906 45.455 9.73 0.00 0.00 4.68
4304 4396 4.441913 GGAAAATCGTCGTAATACAGGGGA 60.442 45.833 0.00 0.00 0.00 4.81
4398 4490 1.811679 GCTTGCTCGCTCCCAGTAC 60.812 63.158 0.00 0.00 0.00 2.73
4431 4536 1.136147 GCACTCTTGCCATGAAGCG 59.864 57.895 0.00 0.00 43.66 4.68
4456 4561 4.031426 GTCGTGTCGGCTGAAATTTAGTAG 59.969 45.833 0.00 0.00 0.00 2.57
4458 4563 2.735134 GTCGTGTCGGCTGAAATTTAGT 59.265 45.455 0.00 0.00 0.00 2.24
4474 4590 3.313012 TGGTGAAGGTTATGAGTCGTG 57.687 47.619 0.00 0.00 0.00 4.35
4488 4605 4.099266 CCCATGAAAGTTCAGTTTGGTGAA 59.901 41.667 10.00 0.00 41.08 3.18
4494 4611 2.034558 CACGCCCATGAAAGTTCAGTTT 59.965 45.455 0.00 0.00 41.08 2.66
4507 4624 2.746277 GGCTCGTTTCACGCCCAT 60.746 61.111 0.00 0.00 42.21 4.00
4527 4644 1.516423 GGGAGCTCGGGTAGAACAC 59.484 63.158 7.83 0.00 0.00 3.32
4611 4772 9.398170 CAATAAAGAACTGTTCGAATCATTTGT 57.602 29.630 14.35 4.88 34.02 2.83
4651 4812 5.679906 CGACTGTTGCCATTGTATATAAGC 58.320 41.667 0.00 0.00 0.00 3.09
4666 4827 0.895530 TCCCTTAGAGGCGACTGTTG 59.104 55.000 0.00 0.00 44.43 3.33
4679 4878 0.828022 ATGAACCATCGCGTCCCTTA 59.172 50.000 5.77 0.00 0.00 2.69
4680 4879 0.828022 TATGAACCATCGCGTCCCTT 59.172 50.000 5.77 0.00 0.00 3.95
4726 4926 3.490031 ATGTGTGGCCAGCAACCGA 62.490 57.895 5.11 0.00 0.00 4.69
4727 4927 2.985282 ATGTGTGGCCAGCAACCG 60.985 61.111 5.11 0.00 0.00 4.44
4729 4929 1.007038 CACATGTGTGGCCAGCAAC 60.007 57.895 18.03 5.86 42.10 4.17
4731 4931 1.601477 CTCACATGTGTGGCCAGCA 60.601 57.895 24.63 9.42 45.65 4.41
4732 4932 0.890542 TTCTCACATGTGTGGCCAGC 60.891 55.000 24.63 2.20 45.65 4.85
4733 4933 1.162698 CTTCTCACATGTGTGGCCAG 58.837 55.000 24.63 14.52 45.65 4.85
4734 4934 0.250858 CCTTCTCACATGTGTGGCCA 60.251 55.000 24.63 0.00 45.65 5.36
4736 4936 1.446907 CTCCTTCTCACATGTGTGGC 58.553 55.000 24.63 0.00 45.65 5.01
4737 4937 1.271001 TGCTCCTTCTCACATGTGTGG 60.271 52.381 24.63 20.25 45.65 4.17
4738 4938 2.074576 CTGCTCCTTCTCACATGTGTG 58.925 52.381 24.63 21.95 46.91 3.82
4739 4939 1.002888 CCTGCTCCTTCTCACATGTGT 59.997 52.381 24.63 0.00 0.00 3.72
4740 4940 1.678123 CCCTGCTCCTTCTCACATGTG 60.678 57.143 20.18 20.18 0.00 3.21
4741 4941 0.617413 CCCTGCTCCTTCTCACATGT 59.383 55.000 0.00 0.00 0.00 3.21
4742 4942 0.907486 TCCCTGCTCCTTCTCACATG 59.093 55.000 0.00 0.00 0.00 3.21
4743 4943 0.908198 GTCCCTGCTCCTTCTCACAT 59.092 55.000 0.00 0.00 0.00 3.21
4744 4944 0.178921 AGTCCCTGCTCCTTCTCACA 60.179 55.000 0.00 0.00 0.00 3.58
4745 4945 1.853963 TAGTCCCTGCTCCTTCTCAC 58.146 55.000 0.00 0.00 0.00 3.51
4746 4946 2.672098 GATAGTCCCTGCTCCTTCTCA 58.328 52.381 0.00 0.00 0.00 3.27
4747 4947 1.967779 GGATAGTCCCTGCTCCTTCTC 59.032 57.143 0.00 0.00 0.00 2.87
4748 4948 2.095604 GGATAGTCCCTGCTCCTTCT 57.904 55.000 0.00 0.00 0.00 2.85
4757 4957 7.751026 AAAAACGATTTTTAGGGGATAGTCCCT 60.751 37.037 14.35 9.62 46.84 4.20
4758 4958 5.889853 AAAACGATTTTTAGGGGATAGTCCC 59.110 40.000 6.47 6.47 43.48 4.46
4759 4959 7.400599 AAAAACGATTTTTAGGGGATAGTCC 57.599 36.000 0.00 0.00 40.80 3.85
4760 4960 9.778993 GTTAAAAACGATTTTTAGGGGATAGTC 57.221 33.333 8.77 0.00 43.58 2.59
4761 4961 9.299465 TGTTAAAAACGATTTTTAGGGGATAGT 57.701 29.630 8.77 0.00 43.58 2.12
4764 4964 8.590204 ACATGTTAAAAACGATTTTTAGGGGAT 58.410 29.630 8.77 2.38 43.58 3.85
4765 4965 7.953752 ACATGTTAAAAACGATTTTTAGGGGA 58.046 30.769 8.77 0.00 43.58 4.81
4766 4966 9.131416 GTACATGTTAAAAACGATTTTTAGGGG 57.869 33.333 2.30 0.48 43.58 4.79
4767 4967 9.902196 AGTACATGTTAAAAACGATTTTTAGGG 57.098 29.630 2.30 6.34 43.58 3.53
4791 4991 8.553696 CGTGGTTTTAGTTCAAATTAGTACAGT 58.446 33.333 0.00 0.00 0.00 3.55
4792 4992 8.767085 TCGTGGTTTTAGTTCAAATTAGTACAG 58.233 33.333 0.00 0.00 0.00 2.74
4793 4993 8.550376 GTCGTGGTTTTAGTTCAAATTAGTACA 58.450 33.333 0.00 0.00 0.00 2.90
4794 4994 7.737311 CGTCGTGGTTTTAGTTCAAATTAGTAC 59.263 37.037 0.00 0.00 0.00 2.73
4795 4995 7.651304 TCGTCGTGGTTTTAGTTCAAATTAGTA 59.349 33.333 0.00 0.00 0.00 1.82
4796 4996 6.479660 TCGTCGTGGTTTTAGTTCAAATTAGT 59.520 34.615 0.00 0.00 0.00 2.24
4797 4997 6.879962 TCGTCGTGGTTTTAGTTCAAATTAG 58.120 36.000 0.00 0.00 0.00 1.73
4798 4998 6.479660 ACTCGTCGTGGTTTTAGTTCAAATTA 59.520 34.615 0.00 0.00 0.00 1.40
4799 4999 5.295045 ACTCGTCGTGGTTTTAGTTCAAATT 59.705 36.000 0.00 0.00 0.00 1.82
4800 5000 4.812626 ACTCGTCGTGGTTTTAGTTCAAAT 59.187 37.500 0.00 0.00 0.00 2.32
4801 5001 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
4802 5002 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
4803 5003 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
4804 5004 6.457851 AATTACTCGTCGTGGTTTTAGTTC 57.542 37.500 0.00 0.00 0.00 3.01
4805 5005 6.293027 CCAAATTACTCGTCGTGGTTTTAGTT 60.293 38.462 0.00 0.00 0.00 2.24
4806 5006 5.178067 CCAAATTACTCGTCGTGGTTTTAGT 59.822 40.000 0.00 0.00 0.00 2.24
4807 5007 5.406175 TCCAAATTACTCGTCGTGGTTTTAG 59.594 40.000 0.00 0.00 0.00 1.85
4808 5008 5.295950 TCCAAATTACTCGTCGTGGTTTTA 58.704 37.500 0.00 0.00 0.00 1.52
4809 5009 4.128643 TCCAAATTACTCGTCGTGGTTTT 58.871 39.130 0.00 0.00 0.00 2.43
4810 5010 3.731089 TCCAAATTACTCGTCGTGGTTT 58.269 40.909 0.00 0.00 0.00 3.27
4811 5011 3.389925 TCCAAATTACTCGTCGTGGTT 57.610 42.857 0.00 0.00 0.00 3.67
4812 5012 3.389925 TTCCAAATTACTCGTCGTGGT 57.610 42.857 0.00 0.00 0.00 4.16
4813 5013 3.930229 TCATTCCAAATTACTCGTCGTGG 59.070 43.478 0.00 0.00 0.00 4.94
4814 5014 5.445939 CCTTCATTCCAAATTACTCGTCGTG 60.446 44.000 0.00 0.00 0.00 4.35
4815 5015 4.630069 CCTTCATTCCAAATTACTCGTCGT 59.370 41.667 0.00 0.00 0.00 4.34
4816 5016 4.868171 TCCTTCATTCCAAATTACTCGTCG 59.132 41.667 0.00 0.00 0.00 5.12
4817 5017 6.183360 CCTTCCTTCATTCCAAATTACTCGTC 60.183 42.308 0.00 0.00 0.00 4.20
4818 5018 5.648092 CCTTCCTTCATTCCAAATTACTCGT 59.352 40.000 0.00 0.00 0.00 4.18
4819 5019 5.880332 TCCTTCCTTCATTCCAAATTACTCG 59.120 40.000 0.00 0.00 0.00 4.18
4820 5020 7.888250 ATCCTTCCTTCATTCCAAATTACTC 57.112 36.000 0.00 0.00 0.00 2.59
4821 5021 8.670521 AAATCCTTCCTTCATTCCAAATTACT 57.329 30.769 0.00 0.00 0.00 2.24
4822 5022 9.725019 AAAAATCCTTCCTTCATTCCAAATTAC 57.275 29.630 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.