Multiple sequence alignment - TraesCS1B01G098200

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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 TraesCS1B01G098200 chr1B 100.000 5003 0 0 1 5003 104774651 104769649 0.000000e+00 9239.0
1 TraesCS1B01G098200 chr1D 93.261 4808 241 40 1 4790 63952264 63947522 0.000000e+00 7007.0
2 TraesCS1B01G098200 chr1D 87.179 195 12 7 4791 4978 63947565 63947377 5.080000e-50 209.0
3 TraesCS1B01G098200 chr1A 93.358 4381 215 33 1 4371 63054584 63050270 0.000000e+00 6408.0
4 TraesCS1B01G098200 chr1A 86.387 382 24 12 4303 4679 63050272 63049914 4.700000e-105 392.0
5 TraesCS1B01G098200 chr1A 85.981 107 7 3 4791 4890 63049884 63049779 1.900000e-19 108.0
6 TraesCS1B01G098200 chr1A 93.151 73 5 0 4718 4790 63049913 63049841 1.900000e-19 108.0
7 TraesCS1B01G098200 chr6A 84.530 181 22 1 4791 4965 34187749 34187569 1.850000e-39 174.0
8 TraesCS1B01G098200 chr3A 84.444 180 22 1 4791 4964 107603093 107602914 6.660000e-39 172.0
9 TraesCS1B01G098200 chr3A 82.723 191 26 2 4791 4975 107609713 107609524 4.010000e-36 163.0
10 TraesCS1B01G098200 chr4A 83.425 181 24 1 4791 4965 201794042 201793862 4.010000e-36 163.0
11 TraesCS1B01G098200 chr5D 91.837 98 8 0 4691 4788 27262758 27262661 2.430000e-28 137.0
12 TraesCS1B01G098200 chr5D 93.651 63 3 1 4728 4790 85910791 85910730 5.330000e-15 93.5
13 TraesCS1B01G098200 chr5D 89.286 56 5 1 4728 4783 85922088 85922034 8.990000e-08 69.4
14 TraesCS1B01G098200 chr2A 87.611 113 14 0 4852 4964 44037224 44037112 1.130000e-26 132.0
15 TraesCS1B01G098200 chr5B 89.796 98 10 0 4691 4788 36187021 36186924 5.260000e-25 126.0


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 TraesCS1B01G098200 chr1B 104769649 104774651 5002 True 9239 9239 100.00000 1 5003 1 chr1B.!!$R1 5002
1 TraesCS1B01G098200 chr1D 63947377 63952264 4887 True 3608 7007 90.22000 1 4978 2 chr1D.!!$R1 4977
2 TraesCS1B01G098200 chr1A 63049779 63054584 4805 True 1754 6408 89.71925 1 4890 4 chr1A.!!$R1 4889

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
511 518 0.101040 CCGCCGTTTGATTCATGCAT 59.899 50.000 0.00 0.00 0.00 3.96 F
1031 1059 0.548031 TTCCCCATCCATGTCTCAGC 59.452 55.000 0.00 0.00 0.00 4.26 F
2488 2517 0.805711 TGACCGATGTGCGCACTATG 60.806 55.000 37.59 25.97 39.11 2.23 F
3240 3272 1.202245 GCTAGAGTCGTCTGCCAGAAG 60.202 57.143 0.00 0.00 33.84 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2538 0.976641 CCCAGGAAGCAGTACACTGA 59.023 55.000 13.5 0.00 46.59 3.41 R
2927 2959 1.003718 GGGTTGGTCTTCAGGACGG 60.004 63.158 0.0 0.00 45.35 4.79 R
3345 3377 0.179043 TGTCACGGCAAACCTTAGCA 60.179 50.000 0.0 0.00 0.00 3.49 R
4671 4787 0.258194 AGTACAGGGGGAGTACTCCG 59.742 60.000 31.0 21.12 46.80 4.63 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
27 33 3.746492 CGAAAACAAACACAAAACCCCAA 59.254 39.130 0.00 0.00 0.00 4.12
28 34 4.213482 CGAAAACAAACACAAAACCCCAAA 59.787 37.500 0.00 0.00 0.00 3.28
206 212 1.512734 CAAAATCCGCGCTCTGCAC 60.513 57.895 5.56 0.00 46.97 4.57
249 255 2.770589 CGGGCGCCAGGGTAAATTG 61.771 63.158 30.85 0.00 0.00 2.32
251 257 1.680989 GGCGCCAGGGTAAATTGGT 60.681 57.895 24.80 0.00 36.81 3.67
265 271 2.346597 TTGGTTTCCAATCCCACGC 58.653 52.632 0.00 0.00 38.75 5.34
267 273 2.348104 GGTTTCCAATCCCACGCCC 61.348 63.158 0.00 0.00 0.00 6.13
281 287 4.002797 GCCCGAGGCTGAAAATGT 57.997 55.556 7.58 0.00 46.69 2.71
286 292 1.339055 CCGAGGCTGAAAATGTCTCCA 60.339 52.381 0.00 0.00 33.01 3.86
296 302 1.843368 AATGTCTCCAGTTGCCATGG 58.157 50.000 7.63 7.63 39.33 3.66
318 324 1.669999 TTAGTTAGGGGCGGCGAGAC 61.670 60.000 12.98 0.00 0.00 3.36
336 342 0.247736 ACGATTCTTGCGAGGCTTCT 59.752 50.000 0.00 0.00 0.00 2.85
372 378 3.829728 AGTTACTCAGGGTAGAGGTGT 57.170 47.619 0.00 0.00 39.97 4.16
417 423 4.642429 ACCTGGTTGACTTTAGCTTGTAG 58.358 43.478 0.00 0.00 0.00 2.74
418 424 4.102681 ACCTGGTTGACTTTAGCTTGTAGT 59.897 41.667 0.00 0.00 0.00 2.73
419 425 5.306160 ACCTGGTTGACTTTAGCTTGTAGTA 59.694 40.000 0.00 0.00 0.00 1.82
427 433 7.027760 TGACTTTAGCTTGTAGTATCTTGACG 58.972 38.462 0.00 0.00 0.00 4.35
433 439 4.537965 CTTGTAGTATCTTGACGATCCCG 58.462 47.826 0.00 0.00 42.50 5.14
447 454 1.122019 ATCCCGTACCATCCTGCCTC 61.122 60.000 0.00 0.00 0.00 4.70
463 470 1.097232 CCTCGCCTCATGAATTTGCA 58.903 50.000 0.00 0.00 0.00 4.08
477 484 2.743636 TTTGCACCTAGGAAGAGACG 57.256 50.000 17.98 0.00 0.00 4.18
493 500 4.047142 AGAGACGTTTTGTTTACTCGACC 58.953 43.478 0.00 0.00 0.00 4.79
510 517 1.240641 ACCGCCGTTTGATTCATGCA 61.241 50.000 0.00 0.00 0.00 3.96
511 518 0.101040 CCGCCGTTTGATTCATGCAT 59.899 50.000 0.00 0.00 0.00 3.96
566 573 4.325204 CAGTTCGATTCGGTTTCGATGTAA 59.675 41.667 6.18 0.00 44.32 2.41
568 575 5.579511 AGTTCGATTCGGTTTCGATGTAATT 59.420 36.000 6.18 0.00 44.32 1.40
572 579 5.556382 CGATTCGGTTTCGATGTAATTCCAG 60.556 44.000 0.00 0.00 45.51 3.86
577 584 5.445939 CGGTTTCGATGTAATTCCAGTTCTG 60.446 44.000 0.00 0.00 39.00 3.02
602 609 3.188254 CCAGTTGTGTGATTTGCATCGTA 59.812 43.478 0.00 0.00 31.08 3.43
670 677 8.743085 AATAACAATTCTGCACATATCTCTGT 57.257 30.769 0.00 0.00 0.00 3.41
693 700 6.972328 TGTTTTTCTCAACTTTTCGGAGATTG 59.028 34.615 0.00 0.00 37.51 2.67
781 792 4.194640 ACATGGTTGATCACTAGTCATGC 58.805 43.478 14.91 0.00 35.34 4.06
818 829 8.362639 ACAAACTAGACCGAAGTTTCATACTTA 58.637 33.333 0.00 0.00 47.00 2.24
824 835 7.497595 AGACCGAAGTTTCATACTTATGCATA 58.502 34.615 1.16 1.16 47.00 3.14
862 873 4.640201 GCCATGGCTCACTTGTATTTAGAA 59.360 41.667 29.98 0.00 38.26 2.10
866 877 8.253113 CCATGGCTCACTTGTATTTAGAATTTT 58.747 33.333 0.00 0.00 0.00 1.82
918 929 6.636850 AGATCACAAATTACACTTGAAAACGC 59.363 34.615 0.00 0.00 0.00 4.84
924 935 4.440851 TTACACTTGAAAACGCGTGTAG 57.559 40.909 14.98 3.91 41.95 2.74
936 947 1.452025 CGCGTGTAGAACAAGACACAG 59.548 52.381 0.00 0.70 45.08 3.66
939 950 3.855895 GCGTGTAGAACAAGACACAGCTA 60.856 47.826 6.04 0.00 45.08 3.32
996 1024 1.557099 GACCAAAACTTCCCCATCCC 58.443 55.000 0.00 0.00 0.00 3.85
997 1025 1.077169 GACCAAAACTTCCCCATCCCT 59.923 52.381 0.00 0.00 0.00 4.20
998 1026 1.203174 ACCAAAACTTCCCCATCCCTG 60.203 52.381 0.00 0.00 0.00 4.45
999 1027 1.077005 CCAAAACTTCCCCATCCCTGA 59.923 52.381 0.00 0.00 0.00 3.86
1000 1028 2.492567 CCAAAACTTCCCCATCCCTGAA 60.493 50.000 0.00 0.00 0.00 3.02
1001 1029 3.444029 CAAAACTTCCCCATCCCTGAAT 58.556 45.455 0.00 0.00 0.00 2.57
1002 1030 2.834638 AACTTCCCCATCCCTGAATG 57.165 50.000 0.00 0.00 0.00 2.67
1003 1031 0.929244 ACTTCCCCATCCCTGAATGG 59.071 55.000 0.00 0.00 44.96 3.16
1011 1039 3.874392 CATCCCTGAATGGACCAAAAC 57.126 47.619 0.00 0.00 37.20 2.43
1012 1040 3.434309 CATCCCTGAATGGACCAAAACT 58.566 45.455 0.00 0.00 37.20 2.66
1013 1041 3.611025 TCCCTGAATGGACCAAAACTT 57.389 42.857 0.00 0.00 38.35 2.66
1014 1042 3.496331 TCCCTGAATGGACCAAAACTTC 58.504 45.455 0.00 0.00 38.35 3.01
1015 1043 2.562738 CCCTGAATGGACCAAAACTTCC 59.437 50.000 0.00 0.00 38.35 3.46
1031 1059 0.548031 TTCCCCATCCATGTCTCAGC 59.452 55.000 0.00 0.00 0.00 4.26
1072 1101 5.680619 ACATTGTGATCTTCCGGCTATTTA 58.319 37.500 0.00 0.00 0.00 1.40
1075 1104 4.945246 TGTGATCTTCCGGCTATTTAGAC 58.055 43.478 0.00 0.00 0.00 2.59
1086 1115 7.332557 TCCGGCTATTTAGACTTGTTTTCATA 58.667 34.615 0.00 0.00 0.00 2.15
1140 1169 5.102953 TGACTAGGTGGGATGAAATTCTG 57.897 43.478 0.00 0.00 0.00 3.02
1239 1268 0.957395 ACTCAATGGACAGGCTTGCG 60.957 55.000 0.00 0.00 0.00 4.85
1289 1318 6.624352 TTTTGTCAGAGGAGAATCAAACAG 57.376 37.500 0.00 0.00 36.25 3.16
1485 1514 4.522405 TGATGCTTTTGGCTTTAGCTGTTA 59.478 37.500 0.00 0.00 42.39 2.41
1486 1515 4.927978 TGCTTTTGGCTTTAGCTGTTAA 57.072 36.364 0.00 0.00 42.39 2.01
1568 1597 3.057806 GGTATTGGTGTTCTTTTGGTCCG 60.058 47.826 0.00 0.00 0.00 4.79
1835 1864 7.063544 GCACCTTACATATCGGATGAATTACTC 59.936 40.741 0.00 0.00 0.00 2.59
1874 1903 5.435686 TGCTCTATGTTGGTATTCCTGTT 57.564 39.130 0.00 0.00 34.23 3.16
2204 2233 5.041287 GGAACAAACAAGTTAAAGGTCTGC 58.959 41.667 0.00 0.00 0.00 4.26
2275 2304 8.575565 TGCTTGATTTCATAGTAGTATCGTTC 57.424 34.615 0.00 0.00 0.00 3.95
2374 2403 5.957842 TCATCACTCCCAATTTTACACAC 57.042 39.130 0.00 0.00 0.00 3.82
2384 2413 5.588648 CCCAATTTTACACACGGTGAGATAT 59.411 40.000 16.29 0.00 36.96 1.63
2413 2442 3.181471 GGATGGGTGCTCTATATGATCGG 60.181 52.174 0.00 0.00 0.00 4.18
2488 2517 0.805711 TGACCGATGTGCGCACTATG 60.806 55.000 37.59 25.97 39.11 2.23
2721 2750 4.142609 TCTGCAGAGGAAATGGTGATAC 57.857 45.455 13.74 0.00 0.00 2.24
2841 2873 3.444029 ACCTTGCTTTTCTGGCCATATT 58.556 40.909 5.51 0.00 0.00 1.28
2927 2959 3.731728 TCCAGGGGCATGGACAGC 61.732 66.667 6.58 0.00 44.56 4.40
3089 3121 4.702131 GGGTACGAAGGTTCACTCTTACTA 59.298 45.833 0.00 0.00 0.00 1.82
3240 3272 1.202245 GCTAGAGTCGTCTGCCAGAAG 60.202 57.143 0.00 0.00 33.84 2.85
3511 3543 2.224079 ACACAGTTAGATGCGTTGCTTG 59.776 45.455 0.00 0.00 0.00 4.01
3575 3607 2.290641 GTCCACAATCAACCAGTGACAC 59.709 50.000 0.00 0.00 39.72 3.67
3590 3622 1.416401 TGACACTGAACCCAGAGAACC 59.584 52.381 0.00 0.00 43.02 3.62
3617 3649 1.611491 TCGGGAAGCCAACATTGAAAC 59.389 47.619 0.00 0.00 0.00 2.78
3651 3683 1.000283 CCCGCTGATGAGGATAGTGAC 60.000 57.143 0.00 0.00 34.95 3.67
3674 3706 0.673022 GACAGTCCTGCCTGCAAGAG 60.673 60.000 0.00 0.00 35.83 2.85
3678 3710 0.676151 GTCCTGCCTGCAAGAGAAGG 60.676 60.000 0.00 0.00 44.35 3.46
3682 3714 0.767375 TGCCTGCAAGAGAAGGAAGT 59.233 50.000 0.00 0.00 44.27 3.01
3690 3722 3.132111 GCAAGAGAAGGAAGTCTAGAGGG 59.868 52.174 0.00 0.00 0.00 4.30
3691 3723 3.680777 AGAGAAGGAAGTCTAGAGGGG 57.319 52.381 0.00 0.00 0.00 4.79
3697 3729 2.022527 AGGAAGTCTAGAGGGGCATCTT 60.023 50.000 0.00 0.00 0.00 2.40
3705 3737 5.047377 GTCTAGAGGGGCATCTTATGAAGAG 60.047 48.000 0.00 0.00 41.61 2.85
3710 3742 3.885901 GGGGCATCTTATGAAGAGGAAAC 59.114 47.826 5.13 0.00 41.61 2.78
3715 3747 3.861840 TCTTATGAAGAGGAAACCGCTG 58.138 45.455 0.00 0.00 33.05 5.18
3762 3794 0.669932 AAGCTGAGAGCAGTCAAGCG 60.670 55.000 0.00 0.00 45.56 4.68
3785 3817 3.576982 ACTTCTGTACGGGAACTTGATCA 59.423 43.478 0.85 0.00 0.00 2.92
3786 3818 3.587797 TCTGTACGGGAACTTGATCAC 57.412 47.619 0.85 0.00 0.00 3.06
3797 3829 5.112686 GGAACTTGATCACTGTCAGGATAC 58.887 45.833 4.53 0.95 0.00 2.24
3840 3872 3.595691 CAGAGAAACTGCTGACGGT 57.404 52.632 0.00 0.00 39.86 4.83
3841 3873 1.143305 CAGAGAAACTGCTGACGGTG 58.857 55.000 0.00 0.00 39.86 4.94
3893 3925 1.412710 TGACGAGGAAGAAACTGCAGT 59.587 47.619 15.25 15.25 0.00 4.40
3896 3928 1.270305 CGAGGAAGAAACTGCAGTGGA 60.270 52.381 22.49 0.00 0.00 4.02
3939 3971 1.140816 GTGAGAACAGTCAAGCGACC 58.859 55.000 0.00 0.00 43.73 4.79
3960 3992 1.202639 TGTGTGCAGGAACTTGATCGT 60.203 47.619 0.00 0.00 34.60 3.73
3961 3993 1.195448 GTGTGCAGGAACTTGATCGTG 59.805 52.381 0.00 0.00 34.60 4.35
3975 4007 1.271102 GATCGTGCTCAGGATAGTCCC 59.729 57.143 5.21 0.00 37.19 4.46
3980 4012 1.109920 GCTCAGGATAGTCCCGCTCA 61.110 60.000 0.00 0.00 37.19 4.26
3992 4024 1.674057 CCGCTCACCAGGAAAGAGT 59.326 57.895 0.00 0.00 0.00 3.24
4014 4046 0.733150 GCAGATAAACTTGGGACGGC 59.267 55.000 0.00 0.00 0.00 5.68
4019 4051 0.609151 TAAACTTGGGACGGCGATGA 59.391 50.000 16.62 0.00 0.00 2.92
4068 4100 1.576421 CGACAAGGAAACTGCAGCC 59.424 57.895 15.27 7.24 42.68 4.85
4070 4102 1.152963 ACAAGGAAACTGCAGCCGT 60.153 52.632 15.27 2.15 42.68 5.68
4071 4103 1.283793 CAAGGAAACTGCAGCCGTG 59.716 57.895 15.27 11.81 42.68 4.94
4095 4127 3.641434 AGGAACTGATGGACTGAATGG 57.359 47.619 0.00 0.00 37.18 3.16
4096 4128 2.915604 AGGAACTGATGGACTGAATGGT 59.084 45.455 0.00 0.00 37.18 3.55
4097 4129 3.331889 AGGAACTGATGGACTGAATGGTT 59.668 43.478 0.00 0.00 37.18 3.67
4098 4130 3.691609 GGAACTGATGGACTGAATGGTTC 59.308 47.826 0.00 0.00 33.41 3.62
4139 4171 1.566211 AGCTGATCGGATAGATGGGG 58.434 55.000 5.48 0.00 40.26 4.96
4204 4236 5.274718 CAGTTTGTTTGTGCGGTTTGTATA 58.725 37.500 0.00 0.00 0.00 1.47
4213 4245 4.102649 GTGCGGTTTGTATATTTTCAGCC 58.897 43.478 0.00 0.00 0.00 4.85
4217 4249 4.668289 GGTTTGTATATTTTCAGCCACCG 58.332 43.478 0.00 0.00 0.00 4.94
4233 4265 2.161609 CCACCGAAACTTCATGCTTACC 59.838 50.000 0.00 0.00 0.00 2.85
4351 4454 3.751175 ACGTGGTTTACAATCACATGAGG 59.249 43.478 0.00 0.00 0.00 3.86
4388 4491 4.442472 CCCTGTATTACGACGATTTTCCCT 60.442 45.833 0.00 0.00 0.00 4.20
4451 4554 0.615331 AATCTTCTCTTCCCGCAGCA 59.385 50.000 0.00 0.00 0.00 4.41
4452 4555 0.615331 ATCTTCTCTTCCCGCAGCAA 59.385 50.000 0.00 0.00 0.00 3.91
4488 4593 2.892425 CAAGCTCGTGCCCCGATC 60.892 66.667 5.73 0.00 46.23 3.69
4535 4640 7.456684 CAAGAGTGCATTACATCTACAGTAC 57.543 40.000 0.00 0.00 0.00 2.73
4536 4641 7.261325 CAAGAGTGCATTACATCTACAGTACT 58.739 38.462 0.00 0.00 0.00 2.73
4537 4642 8.406297 CAAGAGTGCATTACATCTACAGTACTA 58.594 37.037 0.00 0.00 0.00 1.82
4538 4643 8.521170 AGAGTGCATTACATCTACAGTACTAA 57.479 34.615 0.00 0.00 0.00 2.24
4539 4644 8.967918 AGAGTGCATTACATCTACAGTACTAAA 58.032 33.333 0.00 0.00 0.00 1.85
4540 4645 9.751542 GAGTGCATTACATCTACAGTACTAAAT 57.248 33.333 0.00 0.00 0.00 1.40
4591 4707 1.281656 CTTTCGTGGGCGTGAAACC 59.718 57.895 0.00 0.00 39.49 3.27
4601 4717 3.550656 GTGAAACCACGAGCCTCG 58.449 61.111 13.52 13.52 46.93 4.63
4602 4718 2.357034 TGAAACCACGAGCCTCGC 60.357 61.111 15.20 0.00 45.12 5.03
4603 4719 3.479269 GAAACCACGAGCCTCGCG 61.479 66.667 15.20 4.23 45.12 5.87
4622 4738 1.433879 CTGTTCTACCCGAGCTCCG 59.566 63.158 8.47 0.80 38.18 4.63
4652 4768 6.760770 CCAAACACCAACAAAATCAGTACAAT 59.239 34.615 0.00 0.00 0.00 2.71
4671 4787 4.220602 ACAATTCCCTCAACCAATACTTGC 59.779 41.667 0.00 0.00 0.00 4.01
4683 4799 1.411041 ATACTTGCGGAGTACTCCCC 58.589 55.000 31.78 25.14 46.96 4.81
4685 4801 1.686110 CTTGCGGAGTACTCCCCCT 60.686 63.158 31.78 0.00 46.96 4.79
4726 4842 4.639135 TGTATCGACAGAGACAATGGAG 57.361 45.455 0.00 0.00 44.54 3.86
4783 4899 8.204160 TGAATGAACACTTATATACAGTGGGAG 58.796 37.037 19.95 3.14 45.20 4.30
4790 4906 2.139323 TATACAGTGGGAGCAGTCGT 57.861 50.000 0.00 0.00 0.00 4.34
4791 4907 1.267121 ATACAGTGGGAGCAGTCGTT 58.733 50.000 0.00 0.00 0.00 3.85
4793 4909 0.532862 ACAGTGGGAGCAGTCGTTTG 60.533 55.000 0.00 0.00 0.00 2.93
4795 4911 0.180406 AGTGGGAGCAGTCGTTTGTT 59.820 50.000 0.00 0.00 0.00 2.83
4796 4912 0.307760 GTGGGAGCAGTCGTTTGTTG 59.692 55.000 0.00 0.00 0.00 3.33
4797 4913 0.179234 TGGGAGCAGTCGTTTGTTGA 59.821 50.000 0.00 0.00 0.00 3.18
4798 4914 1.202758 TGGGAGCAGTCGTTTGTTGAT 60.203 47.619 0.00 0.00 0.00 2.57
4799 4915 1.197721 GGGAGCAGTCGTTTGTTGATG 59.802 52.381 0.00 0.00 0.00 3.07
4800 4916 2.143122 GGAGCAGTCGTTTGTTGATGA 58.857 47.619 0.00 0.00 0.00 2.92
4801 4917 2.744202 GGAGCAGTCGTTTGTTGATGAT 59.256 45.455 0.00 0.00 0.00 2.45
4802 4918 3.425359 GGAGCAGTCGTTTGTTGATGATG 60.425 47.826 0.00 0.00 0.00 3.07
4803 4919 3.402110 AGCAGTCGTTTGTTGATGATGA 58.598 40.909 0.00 0.00 0.00 2.92
4804 4920 3.814842 AGCAGTCGTTTGTTGATGATGAA 59.185 39.130 0.00 0.00 0.00 2.57
4805 4921 4.456911 AGCAGTCGTTTGTTGATGATGAAT 59.543 37.500 0.00 0.00 0.00 2.57
4806 4922 4.556135 GCAGTCGTTTGTTGATGATGAATG 59.444 41.667 0.00 0.00 0.00 2.67
4807 4923 5.617529 GCAGTCGTTTGTTGATGATGAATGA 60.618 40.000 0.00 0.00 0.00 2.57
4808 4924 6.372981 CAGTCGTTTGTTGATGATGAATGAA 58.627 36.000 0.00 0.00 0.00 2.57
4809 4925 6.303970 CAGTCGTTTGTTGATGATGAATGAAC 59.696 38.462 0.00 0.00 33.39 3.18
4810 4926 6.017192 AGTCGTTTGTTGATGATGAATGAACA 60.017 34.615 0.00 0.00 40.15 3.18
4811 4927 6.086765 GTCGTTTGTTGATGATGAATGAACAC 59.913 38.462 0.00 0.00 41.36 3.32
4812 4928 6.017192 TCGTTTGTTGATGATGAATGAACACT 60.017 34.615 0.00 0.00 41.36 3.55
4813 4929 6.638063 CGTTTGTTGATGATGAATGAACACTT 59.362 34.615 0.00 0.00 41.36 3.16
4814 4930 7.802720 CGTTTGTTGATGATGAATGAACACTTA 59.197 33.333 0.00 0.00 41.36 2.24
4815 4931 9.462174 GTTTGTTGATGATGAATGAACACTTAA 57.538 29.630 0.00 0.00 41.36 1.85
4817 4933 9.628746 TTGTTGATGATGAATGAACACTTAATG 57.371 29.630 0.00 0.00 41.36 1.90
4818 4934 8.245491 TGTTGATGATGAATGAACACTTAATGG 58.755 33.333 0.00 0.00 37.45 3.16
4819 4935 7.337480 TGATGATGAATGAACACTTAATGGG 57.663 36.000 0.00 0.00 0.00 4.00
4820 4936 7.118060 TGATGATGAATGAACACTTAATGGGA 58.882 34.615 0.00 0.00 0.00 4.37
4821 4937 7.614974 TGATGATGAATGAACACTTAATGGGAA 59.385 33.333 0.00 0.00 0.00 3.97
4822 4938 7.156876 TGATGAATGAACACTTAATGGGAAC 57.843 36.000 0.00 0.00 0.00 3.62
4833 4949 3.691342 TGGGAACAGTCGCCTCCG 61.691 66.667 0.00 0.00 35.87 4.63
4902 5018 0.682532 TTGCTGGAAGTGTGCAACCA 60.683 50.000 0.00 0.00 41.06 3.67
4903 5019 0.682532 TGCTGGAAGTGTGCAACCAA 60.683 50.000 0.00 0.00 35.30 3.67
4919 5035 3.864789 ACCAAACATGTGAGAAGGAGT 57.135 42.857 0.00 0.00 0.00 3.85
4920 5036 4.170468 ACCAAACATGTGAGAAGGAGTT 57.830 40.909 0.00 0.00 0.00 3.01
4923 5039 4.136796 CAAACATGTGAGAAGGAGTTGGA 58.863 43.478 0.00 0.00 0.00 3.53
4924 5040 4.437682 AACATGTGAGAAGGAGTTGGAA 57.562 40.909 0.00 0.00 0.00 3.53
4967 5083 8.667463 GCAAGGGTTATCTATTTTTAACACGTA 58.333 33.333 0.00 0.00 36.93 3.57
4984 5100 7.675962 AACACGTACCATAATTTATGTGTGT 57.324 32.000 18.31 18.31 44.18 3.72
4985 5101 7.067532 ACACGTACCATAATTTATGTGTGTG 57.932 36.000 20.81 19.17 43.60 3.82
4986 5102 6.651643 ACACGTACCATAATTTATGTGTGTGT 59.348 34.615 20.81 19.57 43.60 3.72
4987 5103 6.958752 CACGTACCATAATTTATGTGTGTGTG 59.041 38.462 13.87 16.13 34.36 3.82
4988 5104 6.651643 ACGTACCATAATTTATGTGTGTGTGT 59.348 34.615 13.87 6.57 34.36 3.72
4989 5105 6.958752 CGTACCATAATTTATGTGTGTGTGTG 59.041 38.462 13.87 0.46 34.36 3.82
4990 5106 6.892658 ACCATAATTTATGTGTGTGTGTGT 57.107 33.333 13.87 0.98 34.36 3.72
4991 5107 6.676950 ACCATAATTTATGTGTGTGTGTGTG 58.323 36.000 13.87 0.00 34.36 3.82
4992 5108 6.264292 ACCATAATTTATGTGTGTGTGTGTGT 59.736 34.615 13.87 0.00 34.36 3.72
4993 5109 6.581919 CCATAATTTATGTGTGTGTGTGTGTG 59.418 38.462 13.87 0.00 34.36 3.82
4994 5110 5.574891 AATTTATGTGTGTGTGTGTGTGT 57.425 34.783 0.00 0.00 0.00 3.72
4995 5111 4.348198 TTTATGTGTGTGTGTGTGTGTG 57.652 40.909 0.00 0.00 0.00 3.82
4996 5112 1.819928 ATGTGTGTGTGTGTGTGTGT 58.180 45.000 0.00 0.00 0.00 3.72
4997 5113 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
4998 5114 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
4999 5115 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5000 5116 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
5001 5117 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
5002 5118 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 22 2.436544 GGGGCGTTTGGGGTTTTGT 61.437 57.895 0.00 0.00 0.00 2.83
27 33 2.203582 GTTTGGGAAGGGGGCGTT 60.204 61.111 0.00 0.00 0.00 4.84
28 34 4.295199 GGTTTGGGAAGGGGGCGT 62.295 66.667 0.00 0.00 0.00 5.68
183 189 3.044059 GAGCGCGGATTTTGCAGCT 62.044 57.895 8.83 4.51 42.04 4.24
191 197 2.510238 GAGTGCAGAGCGCGGATT 60.510 61.111 8.83 0.00 46.97 3.01
192 198 4.521062 GGAGTGCAGAGCGCGGAT 62.521 66.667 8.83 0.00 46.97 4.18
232 238 2.423064 CCAATTTACCCTGGCGCCC 61.423 63.158 26.77 6.44 0.00 6.13
249 255 2.348104 GGGCGTGGGATTGGAAACC 61.348 63.158 0.00 0.00 0.00 3.27
251 257 2.360600 CGGGCGTGGGATTGGAAA 60.361 61.111 0.00 0.00 0.00 3.13
265 271 1.373570 GAGACATTTTCAGCCTCGGG 58.626 55.000 0.00 0.00 0.00 5.14
267 273 2.005451 CTGGAGACATTTTCAGCCTCG 58.995 52.381 0.00 0.00 41.51 4.63
275 281 2.564062 CCATGGCAACTGGAGACATTTT 59.436 45.455 0.00 0.00 41.51 1.82
281 287 2.380064 AAAACCATGGCAACTGGAGA 57.620 45.000 13.04 0.00 37.22 3.71
286 292 4.086457 CCCTAACTAAAACCATGGCAACT 58.914 43.478 13.04 0.00 37.61 3.16
296 302 0.391528 TCGCCGCCCCTAACTAAAAC 60.392 55.000 0.00 0.00 0.00 2.43
336 342 9.667107 CCTGAGTAACTAAACAAAATCTCCATA 57.333 33.333 0.00 0.00 0.00 2.74
372 378 1.071987 CCTCACTGGTGCTGCTCAA 59.928 57.895 0.00 0.00 0.00 3.02
396 402 4.642429 ACTACAAGCTAAAGTCAACCAGG 58.358 43.478 0.00 0.00 0.00 4.45
427 433 1.122019 AGGCAGGATGGTACGGGATC 61.122 60.000 0.00 0.00 35.86 3.36
433 439 2.109181 GGCGAGGCAGGATGGTAC 59.891 66.667 0.00 0.00 35.86 3.34
434 440 2.041922 AGGCGAGGCAGGATGGTA 60.042 61.111 0.00 0.00 35.86 3.25
435 441 3.474570 GAGGCGAGGCAGGATGGT 61.475 66.667 0.00 0.00 35.86 3.55
436 442 2.815945 ATGAGGCGAGGCAGGATGG 61.816 63.158 0.00 0.00 35.86 3.51
447 454 0.813184 AGGTGCAAATTCATGAGGCG 59.187 50.000 0.00 0.00 0.00 5.52
463 470 4.684484 AACAAAACGTCTCTTCCTAGGT 57.316 40.909 9.08 0.00 0.00 3.08
477 484 1.397567 CGGCGGTCGAGTAAACAAAAC 60.398 52.381 0.00 0.00 42.43 2.43
493 500 1.584761 CAATGCATGAATCAAACGGCG 59.415 47.619 4.80 4.80 0.00 6.46
510 517 9.167311 GACATCCTAAACAACACTAAGATCAAT 57.833 33.333 0.00 0.00 0.00 2.57
511 518 8.154203 TGACATCCTAAACAACACTAAGATCAA 58.846 33.333 0.00 0.00 0.00 2.57
577 584 1.202394 TGCAAATCACACAACTGGCAC 60.202 47.619 0.00 0.00 0.00 5.01
602 609 1.160137 GCATTCTCGCAAACAGAGGT 58.840 50.000 0.00 0.00 36.45 3.85
656 663 6.712095 AGTTGAGAAAAACAGAGATATGTGCA 59.288 34.615 0.00 0.00 32.52 4.57
670 677 6.503524 CCAATCTCCGAAAAGTTGAGAAAAA 58.496 36.000 0.00 0.00 38.53 1.94
693 700 2.676471 ACACGGCAATCAAGGGCC 60.676 61.111 0.00 0.00 46.80 5.80
781 792 6.449698 TCGGTCTAGTTTGTAACAACTTAGG 58.550 40.000 0.00 0.00 0.00 2.69
818 829 2.216046 CTTCACGCACTGGATATGCAT 58.784 47.619 3.79 3.79 43.57 3.96
824 835 2.045926 GGCCTTCACGCACTGGAT 60.046 61.111 0.00 0.00 0.00 3.41
862 873 6.996509 ACAAGACCATAGTTGCATTCAAAAT 58.003 32.000 0.00 0.00 33.37 1.82
866 877 4.458989 GGAACAAGACCATAGTTGCATTCA 59.541 41.667 0.00 0.00 34.32 2.57
936 947 2.684881 AGCCATGCATGTTACAGTTAGC 59.315 45.455 24.58 16.57 0.00 3.09
939 950 4.525996 TCATAGCCATGCATGTTACAGTT 58.474 39.130 24.58 9.82 31.73 3.16
996 1024 2.562738 GGGGAAGTTTTGGTCCATTCAG 59.437 50.000 0.00 0.00 35.44 3.02
997 1025 2.091055 TGGGGAAGTTTTGGTCCATTCA 60.091 45.455 0.00 0.00 35.44 2.57
998 1026 2.604139 TGGGGAAGTTTTGGTCCATTC 58.396 47.619 0.00 0.00 35.44 2.67
999 1027 2.785357 TGGGGAAGTTTTGGTCCATT 57.215 45.000 0.00 0.00 35.44 3.16
1000 1028 2.559705 GGATGGGGAAGTTTTGGTCCAT 60.560 50.000 0.00 0.00 37.66 3.41
1001 1029 1.203125 GGATGGGGAAGTTTTGGTCCA 60.203 52.381 0.00 0.00 35.44 4.02
1002 1030 1.203125 TGGATGGGGAAGTTTTGGTCC 60.203 52.381 0.00 0.00 0.00 4.46
1003 1031 2.302587 TGGATGGGGAAGTTTTGGTC 57.697 50.000 0.00 0.00 0.00 4.02
1004 1032 2.158173 ACATGGATGGGGAAGTTTTGGT 60.158 45.455 0.00 0.00 0.00 3.67
1005 1033 2.497273 GACATGGATGGGGAAGTTTTGG 59.503 50.000 0.00 0.00 0.00 3.28
1006 1034 3.434309 AGACATGGATGGGGAAGTTTTG 58.566 45.455 0.00 0.00 0.00 2.44
1007 1035 3.075882 TGAGACATGGATGGGGAAGTTTT 59.924 43.478 0.00 0.00 0.00 2.43
1008 1036 2.649312 TGAGACATGGATGGGGAAGTTT 59.351 45.455 0.00 0.00 0.00 2.66
1009 1037 2.240667 CTGAGACATGGATGGGGAAGTT 59.759 50.000 0.00 0.00 0.00 2.66
1010 1038 1.842562 CTGAGACATGGATGGGGAAGT 59.157 52.381 0.00 0.00 0.00 3.01
1011 1039 1.476471 GCTGAGACATGGATGGGGAAG 60.476 57.143 0.00 0.00 0.00 3.46
1012 1040 0.548031 GCTGAGACATGGATGGGGAA 59.452 55.000 0.00 0.00 0.00 3.97
1013 1041 1.689243 CGCTGAGACATGGATGGGGA 61.689 60.000 0.00 0.00 0.00 4.81
1014 1042 1.227764 CGCTGAGACATGGATGGGG 60.228 63.158 0.00 0.00 0.00 4.96
1015 1043 0.178767 TTCGCTGAGACATGGATGGG 59.821 55.000 0.00 0.00 0.00 4.00
1031 1059 8.659491 TCACAATGTCAGATCTATTTCTTTTCG 58.341 33.333 0.00 0.00 0.00 3.46
1086 1115 5.645497 GCACAGAGTCATCATCCTTAAAAGT 59.355 40.000 0.00 0.00 0.00 2.66
1140 1169 1.271434 GGGTTCTGAACTGGAAGGGTC 60.271 57.143 19.05 0.48 39.30 4.46
1239 1268 2.678336 CACCCTAGAAAACGGAATGAGC 59.322 50.000 0.00 0.00 0.00 4.26
1486 1515 9.944376 TGTTTAAATTCTAGCATCTCAACTAGT 57.056 29.630 0.00 0.00 37.67 2.57
1524 1553 1.745115 ATGGAATGGTGTCGCCGTG 60.745 57.895 0.00 0.00 41.21 4.94
1568 1597 4.762251 GCACCACCCTTTCTATAATCATCC 59.238 45.833 0.00 0.00 0.00 3.51
1835 1864 7.335422 ACATAGAGCAAAGACATAACTTCAAGG 59.665 37.037 0.00 0.00 0.00 3.61
1874 1903 5.600069 AGTATGTCTCTGCATTATGGTCTCA 59.400 40.000 0.00 0.00 0.00 3.27
2374 2403 5.835819 ACCCATCCATCTATATATCTCACCG 59.164 44.000 0.00 0.00 0.00 4.94
2384 2413 7.595488 TCATATAGAGCACCCATCCATCTATA 58.405 38.462 0.00 0.00 38.89 1.31
2413 2442 1.794701 GTCGGGTCTTTTGTACGAACC 59.205 52.381 0.00 0.00 35.17 3.62
2488 2517 5.479306 TGACACAGAAGCATTAGTTACCTC 58.521 41.667 0.00 0.00 0.00 3.85
2506 2535 2.408050 CAGGAAGCAGTACACTGACAC 58.592 52.381 13.50 3.19 46.59 3.67
2509 2538 0.976641 CCCAGGAAGCAGTACACTGA 59.023 55.000 13.50 0.00 46.59 3.41
2869 2901 6.993902 ACGGTTCAATAAGAGAACTTACCAAA 59.006 34.615 6.09 0.00 43.67 3.28
2870 2902 6.527423 ACGGTTCAATAAGAGAACTTACCAA 58.473 36.000 6.09 0.00 43.67 3.67
2871 2903 6.105397 ACGGTTCAATAAGAGAACTTACCA 57.895 37.500 6.09 0.00 43.67 3.25
2888 2920 8.433421 TGGAAGATATTGAGATTAAACGGTTC 57.567 34.615 0.00 0.00 0.00 3.62
2927 2959 1.003718 GGGTTGGTCTTCAGGACGG 60.004 63.158 0.00 0.00 45.35 4.79
3089 3121 3.834231 CCCAGAAAATTCATCCAACCAGT 59.166 43.478 0.00 0.00 0.00 4.00
3216 3248 0.243907 GGCAGACGACTCTAGCACAA 59.756 55.000 0.00 0.00 0.00 3.33
3240 3272 1.457346 CATGGGACTTCTCCTTGTGC 58.543 55.000 0.00 0.00 36.68 4.57
3345 3377 0.179043 TGTCACGGCAAACCTTAGCA 60.179 50.000 0.00 0.00 0.00 3.49
3575 3607 2.304180 ACATCAGGTTCTCTGGGTTCAG 59.696 50.000 0.00 0.00 43.53 3.02
3590 3622 0.804989 GTTGGCTTCCCGAACATCAG 59.195 55.000 0.00 0.00 0.00 2.90
3617 3649 2.328099 GCGGGAACTTCACTGCCAG 61.328 63.158 0.00 0.00 32.90 4.85
3651 3683 2.575993 CAGGCAGGACTGTCCTCG 59.424 66.667 26.11 20.64 45.66 4.63
3666 3698 4.142182 CCTCTAGACTTCCTTCTCTTGCAG 60.142 50.000 0.00 0.00 0.00 4.41
3674 3706 1.867363 TGCCCCTCTAGACTTCCTTC 58.133 55.000 0.00 0.00 0.00 3.46
3678 3710 4.835615 TCATAAGATGCCCCTCTAGACTTC 59.164 45.833 0.00 0.00 0.00 3.01
3682 3714 5.079998 TCTTCATAAGATGCCCCTCTAGA 57.920 43.478 0.00 0.00 31.20 2.43
3690 3722 3.561725 CGGTTTCCTCTTCATAAGATGCC 59.438 47.826 0.00 0.00 36.82 4.40
3691 3723 3.002759 GCGGTTTCCTCTTCATAAGATGC 59.997 47.826 0.00 0.00 36.82 3.91
3697 3729 1.277842 TGCAGCGGTTTCCTCTTCATA 59.722 47.619 0.00 0.00 0.00 2.15
3727 3759 3.314388 CTTCAGAAACCTGCGCGGC 62.314 63.158 11.81 0.00 35.61 6.53
3728 3760 2.863153 CTTCAGAAACCTGCGCGG 59.137 61.111 9.96 9.96 39.35 6.46
3729 3761 2.174349 GCTTCAGAAACCTGCGCG 59.826 61.111 0.00 0.00 0.00 6.86
3730 3762 1.208614 CAGCTTCAGAAACCTGCGC 59.791 57.895 0.00 0.00 0.00 6.09
3731 3763 0.795085 CTCAGCTTCAGAAACCTGCG 59.205 55.000 5.86 0.00 0.00 5.18
3732 3764 2.075338 CTCTCAGCTTCAGAAACCTGC 58.925 52.381 5.86 0.00 0.00 4.85
3733 3765 2.075338 GCTCTCAGCTTCAGAAACCTG 58.925 52.381 4.72 4.72 38.45 4.00
3734 3766 1.696336 TGCTCTCAGCTTCAGAAACCT 59.304 47.619 0.00 0.00 42.97 3.50
3735 3767 2.075338 CTGCTCTCAGCTTCAGAAACC 58.925 52.381 0.00 0.00 42.97 3.27
3762 3794 3.655276 TCAAGTTCCCGTACAGAAGTC 57.345 47.619 4.01 0.00 0.00 3.01
3769 3801 3.251571 GACAGTGATCAAGTTCCCGTAC 58.748 50.000 0.00 0.00 0.00 3.67
3805 3837 2.669569 GCGCACTCTTTCCTGGCA 60.670 61.111 0.30 0.00 0.00 4.92
3806 3838 2.669569 TGCGCACTCTTTCCTGGC 60.670 61.111 5.66 0.00 0.00 4.85
3832 3864 1.079503 GTTCCTTCATCACCGTCAGC 58.920 55.000 0.00 0.00 0.00 4.26
3840 3872 2.880268 CAACACTGCAGTTCCTTCATCA 59.120 45.455 18.94 0.00 0.00 3.07
3841 3873 2.227388 CCAACACTGCAGTTCCTTCATC 59.773 50.000 18.94 0.00 0.00 2.92
3859 3891 4.905429 TCCTCGTCATCAGAAATTTCCAA 58.095 39.130 14.61 3.66 0.00 3.53
3893 3925 0.537143 AGGTTGCGTGATTTGCTCCA 60.537 50.000 0.00 0.00 32.48 3.86
3896 3928 1.267806 CAGAAGGTTGCGTGATTTGCT 59.732 47.619 0.00 0.00 0.00 3.91
3939 3971 1.462283 CGATCAAGTTCCTGCACACAG 59.538 52.381 0.00 0.00 44.05 3.66
3952 3984 3.551863 GGACTATCCTGAGCACGATCAAG 60.552 52.174 0.00 0.00 32.53 3.02
3960 3992 1.075970 AGCGGGACTATCCTGAGCA 60.076 57.895 7.92 0.00 45.95 4.26
3961 3993 1.109920 TGAGCGGGACTATCCTGAGC 61.110 60.000 7.92 5.34 45.95 4.26
3962 3994 0.671251 GTGAGCGGGACTATCCTGAG 59.329 60.000 7.92 0.00 45.95 3.35
3975 4007 0.671781 CCACTCTTTCCTGGTGAGCG 60.672 60.000 11.71 5.21 33.32 5.03
3980 4012 0.768221 TCTGCCCACTCTTTCCTGGT 60.768 55.000 0.00 0.00 0.00 4.00
3992 4024 1.339631 CGTCCCAAGTTTATCTGCCCA 60.340 52.381 0.00 0.00 0.00 5.36
4014 4046 2.802667 CGCCGCAGTTCCTTCATCG 61.803 63.158 0.00 0.00 0.00 3.84
4037 4069 2.301902 CTTGTCGCCATCGCAAGCTC 62.302 60.000 0.00 0.00 40.22 4.09
4042 4074 1.302112 TTTCCTTGTCGCCATCGCA 60.302 52.632 0.00 0.00 35.26 5.10
4068 4100 1.197721 GTCCATCAGTTCCTTTGCACG 59.802 52.381 0.00 0.00 0.00 5.34
4070 4102 2.106338 TCAGTCCATCAGTTCCTTTGCA 59.894 45.455 0.00 0.00 0.00 4.08
4071 4103 2.783135 TCAGTCCATCAGTTCCTTTGC 58.217 47.619 0.00 0.00 0.00 3.68
4072 4104 4.157289 CCATTCAGTCCATCAGTTCCTTTG 59.843 45.833 0.00 0.00 0.00 2.77
4077 4109 4.583871 AGAACCATTCAGTCCATCAGTTC 58.416 43.478 0.00 0.00 34.09 3.01
4095 4127 5.373981 TCTAACCTCGACAGAAGAAGAAC 57.626 43.478 0.00 0.00 0.00 3.01
4096 4128 6.591750 AATCTAACCTCGACAGAAGAAGAA 57.408 37.500 0.00 0.00 0.00 2.52
4097 4129 6.183360 GCTAATCTAACCTCGACAGAAGAAGA 60.183 42.308 0.00 0.00 0.00 2.87
4098 4130 5.974751 GCTAATCTAACCTCGACAGAAGAAG 59.025 44.000 0.00 0.00 0.00 2.85
4204 4236 2.955660 TGAAGTTTCGGTGGCTGAAAAT 59.044 40.909 4.89 1.69 39.92 1.82
4213 4245 2.159707 CGGTAAGCATGAAGTTTCGGTG 60.160 50.000 0.00 0.00 0.00 4.94
4217 4249 5.545658 TCATTCGGTAAGCATGAAGTTTC 57.454 39.130 0.00 0.00 29.76 2.78
4233 4265 3.624410 TGACTTCCAGATGCATTCATTCG 59.376 43.478 0.00 0.00 31.96 3.34
4351 4454 1.699730 ACAGGGGGCAAAGTAACAAC 58.300 50.000 0.00 0.00 0.00 3.32
4388 4491 6.050432 GCAATTCAGATTTGCCCATCATTTA 58.950 36.000 16.22 0.00 0.00 1.40
4488 4593 4.595116 CCATGAAGCAGCTTCTTATTTCG 58.405 43.478 30.82 14.95 40.73 3.46
4537 4642 8.116753 CGAGTCGTATCAGCTGAAATTTAATTT 58.883 33.333 22.50 2.23 34.64 1.82
4538 4643 7.491372 TCGAGTCGTATCAGCTGAAATTTAATT 59.509 33.333 22.50 3.74 0.00 1.40
4539 4644 6.978659 TCGAGTCGTATCAGCTGAAATTTAAT 59.021 34.615 22.50 4.57 0.00 1.40
4540 4645 6.327154 TCGAGTCGTATCAGCTGAAATTTAA 58.673 36.000 22.50 1.53 0.00 1.52
4552 4657 6.432607 AAGTTCAGTTATCGAGTCGTATCA 57.567 37.500 13.12 0.00 0.00 2.15
4596 4712 2.886124 GGTAGAACAGCGCGAGGC 60.886 66.667 12.10 0.00 44.05 4.70
4598 4714 2.579787 CGGGTAGAACAGCGCGAG 60.580 66.667 12.10 3.23 42.39 5.03
4599 4715 3.047718 CTCGGGTAGAACAGCGCGA 62.048 63.158 12.10 0.00 45.27 5.87
4600 4716 2.579787 CTCGGGTAGAACAGCGCG 60.580 66.667 0.00 0.00 41.40 6.86
4601 4717 2.886124 GCTCGGGTAGAACAGCGC 60.886 66.667 0.00 0.00 0.00 5.92
4602 4718 1.226717 GAGCTCGGGTAGAACAGCG 60.227 63.158 0.00 0.00 0.00 5.18
4603 4719 1.142097 GGAGCTCGGGTAGAACAGC 59.858 63.158 7.83 0.00 0.00 4.40
4604 4720 1.433879 CGGAGCTCGGGTAGAACAG 59.566 63.158 13.25 0.00 34.75 3.16
4622 4738 2.100605 TTTGTTGGTGTTTGGGTTGC 57.899 45.000 0.00 0.00 0.00 4.17
4671 4787 0.258194 AGTACAGGGGGAGTACTCCG 59.742 60.000 31.00 21.12 46.80 4.63
4683 4799 9.770097 ATACAATTCTATTCATCACAGTACAGG 57.230 33.333 0.00 0.00 0.00 4.00
4685 4801 9.463443 CGATACAATTCTATTCATCACAGTACA 57.537 33.333 0.00 0.00 0.00 2.90
4690 4806 8.413229 TCTGTCGATACAATTCTATTCATCACA 58.587 33.333 0.00 0.00 34.49 3.58
4726 4842 8.368126 CAATAAAGAACTGTTCGAATCATTTGC 58.632 33.333 14.35 0.00 34.02 3.68
4783 4899 3.811722 TCATCATCAACAAACGACTGC 57.188 42.857 0.00 0.00 0.00 4.40
4791 4907 9.628746 CATTAAGTGTTCATTCATCATCAACAA 57.371 29.630 0.00 0.00 25.81 2.83
4793 4909 7.703621 CCCATTAAGTGTTCATTCATCATCAAC 59.296 37.037 0.00 0.00 0.00 3.18
4795 4911 7.118060 TCCCATTAAGTGTTCATTCATCATCA 58.882 34.615 0.00 0.00 0.00 3.07
4796 4912 7.572523 TCCCATTAAGTGTTCATTCATCATC 57.427 36.000 0.00 0.00 0.00 2.92
4797 4913 7.396907 TGTTCCCATTAAGTGTTCATTCATCAT 59.603 33.333 0.00 0.00 0.00 2.45
4798 4914 6.718912 TGTTCCCATTAAGTGTTCATTCATCA 59.281 34.615 0.00 0.00 0.00 3.07
4799 4915 7.094205 ACTGTTCCCATTAAGTGTTCATTCATC 60.094 37.037 0.00 0.00 0.00 2.92
4800 4916 6.721208 ACTGTTCCCATTAAGTGTTCATTCAT 59.279 34.615 0.00 0.00 0.00 2.57
4801 4917 6.068010 ACTGTTCCCATTAAGTGTTCATTCA 58.932 36.000 0.00 0.00 0.00 2.57
4802 4918 6.575162 ACTGTTCCCATTAAGTGTTCATTC 57.425 37.500 0.00 0.00 0.00 2.67
4803 4919 5.181245 CGACTGTTCCCATTAAGTGTTCATT 59.819 40.000 0.00 0.00 0.00 2.57
4804 4920 4.695455 CGACTGTTCCCATTAAGTGTTCAT 59.305 41.667 0.00 0.00 0.00 2.57
4805 4921 4.062293 CGACTGTTCCCATTAAGTGTTCA 58.938 43.478 0.00 0.00 0.00 3.18
4806 4922 3.120304 GCGACTGTTCCCATTAAGTGTTC 60.120 47.826 0.00 0.00 0.00 3.18
4807 4923 2.812011 GCGACTGTTCCCATTAAGTGTT 59.188 45.455 0.00 0.00 0.00 3.32
4808 4924 2.423577 GCGACTGTTCCCATTAAGTGT 58.576 47.619 0.00 0.00 0.00 3.55
4809 4925 1.737793 GGCGACTGTTCCCATTAAGTG 59.262 52.381 0.00 0.00 0.00 3.16
4810 4926 1.628846 AGGCGACTGTTCCCATTAAGT 59.371 47.619 0.00 0.00 41.13 2.24
4811 4927 2.280628 GAGGCGACTGTTCCCATTAAG 58.719 52.381 0.00 0.00 44.43 1.85
4812 4928 1.065709 GGAGGCGACTGTTCCCATTAA 60.066 52.381 0.00 0.00 44.43 1.40
4813 4929 0.539986 GGAGGCGACTGTTCCCATTA 59.460 55.000 0.00 0.00 44.43 1.90
4814 4930 1.299976 GGAGGCGACTGTTCCCATT 59.700 57.895 0.00 0.00 44.43 3.16
4815 4931 2.990479 GGAGGCGACTGTTCCCAT 59.010 61.111 0.00 0.00 44.43 4.00
4816 4932 3.691342 CGGAGGCGACTGTTCCCA 61.691 66.667 0.00 0.00 44.43 4.37
4817 4933 3.358076 CTCGGAGGCGACTGTTCCC 62.358 68.421 0.00 0.00 44.43 3.97
4818 4934 2.182030 CTCGGAGGCGACTGTTCC 59.818 66.667 0.00 0.00 44.43 3.62
4819 4935 2.182030 CCTCGGAGGCGACTGTTC 59.818 66.667 11.83 0.00 44.43 3.18
4820 4936 3.382832 CCCTCGGAGGCGACTGTT 61.383 66.667 18.91 0.00 44.43 3.16
4821 4937 4.361971 TCCCTCGGAGGCGACTGT 62.362 66.667 18.91 0.00 44.43 3.55
4822 4938 3.827898 GTCCCTCGGAGGCGACTG 61.828 72.222 25.76 12.55 44.43 3.51
4828 4944 4.271816 CATCGCGTCCCTCGGAGG 62.272 72.222 17.41 17.41 40.18 4.30
4829 4945 4.271816 CCATCGCGTCCCTCGGAG 62.272 72.222 5.77 0.00 40.26 4.63
4831 4947 4.143333 AACCATCGCGTCCCTCGG 62.143 66.667 5.77 1.23 40.26 4.63
4832 4948 2.582498 GAACCATCGCGTCCCTCG 60.582 66.667 5.77 0.00 43.12 4.63
4833 4949 0.387929 TATGAACCATCGCGTCCCTC 59.612 55.000 5.77 0.00 0.00 4.30
4902 5018 4.437682 TCCAACTCCTTCTCACATGTTT 57.562 40.909 0.00 0.00 0.00 2.83
4903 5019 4.437682 TTCCAACTCCTTCTCACATGTT 57.562 40.909 0.00 0.00 0.00 2.71
4919 5035 5.163077 TGCGGTTATTAGGGGATAATTCCAA 60.163 40.000 0.00 0.00 44.60 3.53
4920 5036 4.351407 TGCGGTTATTAGGGGATAATTCCA 59.649 41.667 0.00 0.00 44.60 3.53
4923 5039 5.321927 CCTTGCGGTTATTAGGGGATAATT 58.678 41.667 0.00 0.00 35.63 1.40
4924 5040 4.263771 CCCTTGCGGTTATTAGGGGATAAT 60.264 45.833 0.00 0.00 43.04 1.28
4967 5083 6.264292 ACACACACACACACATAAATTATGGT 59.736 34.615 16.36 9.01 40.47 3.55
4975 5091 3.126000 CACACACACACACACACACATAA 59.874 43.478 0.00 0.00 0.00 1.90
4977 5093 1.468127 CACACACACACACACACACAT 59.532 47.619 0.00 0.00 0.00 3.21
4978 5094 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4979 5095 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4980 5096 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4981 5097 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4982 5098 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4983 5099 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4984 5100 3.314083 ACACACACACACACACACA 57.686 47.368 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.