Multiple sequence alignment - TraesCS5D01G410900

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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 TraesCS5D01G410900 chr5D 100.000 5209 0 0 973 6181 474200732 474205940 0.000000e+00 9620.0
1 TraesCS5D01G410900 chr5D 100.000 692 0 0 1 692 474199760 474200451 0.000000e+00 1279.0
2 TraesCS5D01G410900 chr5D 92.913 127 9 0 5574 5700 539915851 539915977 1.060000e-42 185.0
3 TraesCS5D01G410900 chr5A 94.686 2672 78 26 1038 3652 593455889 593458553 0.000000e+00 4089.0
4 TraesCS5D01G410900 chr5A 94.059 1902 55 10 3713 5576 593458552 593460433 0.000000e+00 2833.0
5 TraesCS5D01G410900 chr5A 85.200 750 35 20 1 692 593454743 593455474 0.000000e+00 701.0
6 TraesCS5D01G410900 chr5A 89.119 193 19 2 5957 6147 593460738 593460930 8.010000e-59 239.0
7 TraesCS5D01G410900 chr5A 93.805 113 3 1 5820 5932 593460529 593460637 3.830000e-37 167.0
8 TraesCS5D01G410900 chr5B 91.411 2573 99 49 1162 3652 581128372 581130904 0.000000e+00 3415.0
9 TraesCS5D01G410900 chr5B 90.981 1907 93 16 3713 5576 581130903 581132773 0.000000e+00 2495.0
10 TraesCS5D01G410900 chr5B 88.553 463 24 15 240 692 581127597 581128040 9.120000e-148 534.0
11 TraesCS5D01G410900 chr5B 85.714 427 30 9 5770 6181 581133330 581133740 7.410000e-114 422.0
12 TraesCS5D01G410900 chr5B 91.758 182 9 3 1 179 581127421 581127599 1.330000e-61 248.0
13 TraesCS5D01G410900 chr5B 92.308 130 10 0 5571 5700 595395490 595395361 1.060000e-42 185.0
14 TraesCS5D01G410900 chr5B 85.714 77 2 3 5716 5783 581133019 581133095 8.590000e-09 73.1
15 TraesCS5D01G410900 chr3B 93.651 126 8 0 5575 5700 540175090 540174965 8.180000e-44 189.0
16 TraesCS5D01G410900 chr3B 92.308 52 2 2 3669 3719 395075296 395075346 8.590000e-09 73.1
17 TraesCS5D01G410900 chr6A 92.969 128 9 0 5573 5700 10056593 10056720 2.940000e-43 187.0
18 TraesCS5D01G410900 chr6A 89.286 56 3 2 3662 3714 565345076 565345131 4.000000e-07 67.6
19 TraesCS5D01G410900 chr7D 92.969 128 8 1 5573 5700 133235199 133235073 1.060000e-42 185.0
20 TraesCS5D01G410900 chr7D 89.928 139 13 1 5563 5700 580373991 580374129 1.770000e-40 178.0
21 TraesCS5D01G410900 chr2D 92.913 127 9 0 5574 5700 71262200 71262074 1.060000e-42 185.0
22 TraesCS5D01G410900 chr1D 92.366 131 9 1 5570 5700 455801645 455801774 1.060000e-42 185.0
23 TraesCS5D01G410900 chr1D 97.059 34 1 0 1 34 471099768 471099735 2.410000e-04 58.4
24 TraesCS5D01G410900 chrUn 90.441 136 12 1 5566 5700 115041287 115041152 1.770000e-40 178.0
25 TraesCS5D01G410900 chr7B 94.340 53 3 0 3662 3714 495309790 495309738 1.430000e-11 82.4
26 TraesCS5D01G410900 chr6B 95.745 47 0 2 3674 3719 522912809 522912764 2.390000e-09 75.0
27 TraesCS5D01G410900 chr4D 92.157 51 2 2 3669 3718 335044914 335044865 3.090000e-08 71.3
28 TraesCS5D01G410900 chr4B 92.157 51 2 2 3669 3718 467273912 467273961 3.090000e-08 71.3
29 TraesCS5D01G410900 chr3A 88.889 54 5 1 3662 3714 603267332 603267279 1.440000e-06 65.8
30 TraesCS5D01G410900 chr2B 90.385 52 0 4 3670 3718 21936984 21936935 5.170000e-06 63.9
31 TraesCS5D01G410900 chr3D 83.582 67 8 3 3664 3728 598895791 598895726 6.690000e-05 60.2


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 TraesCS5D01G410900 chr5D 474199760 474205940 6180 False 5449.50 9620 100.000000 1 6181 2 chr5D.!!$F2 6180
1 TraesCS5D01G410900 chr5A 593454743 593460930 6187 False 1605.80 4089 91.373800 1 6147 5 chr5A.!!$F1 6146
2 TraesCS5D01G410900 chr5B 581127421 581133740 6319 False 1197.85 3415 89.021833 1 6181 6 chr5B.!!$F1 6180

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
992 1058 1.081108 CCGAGATTCCGCGAGATCC 60.081 63.158 8.23 4.17 37.82 3.36 F
1206 1453 1.200760 CCTCCACCTCCACATCCACA 61.201 60.000 0.00 0.00 0.00 4.17 F
1845 2107 0.799917 CTCACAGAGCACGTCCATCG 60.800 60.000 0.00 0.00 46.00 3.84 F
2308 2570 0.948141 GACTGCAGAGGTGAGTGTGC 60.948 60.000 23.35 0.00 37.24 4.57 F
3465 3788 1.906757 TTTTGAAATATGCGGCGCAG 58.093 45.000 38.27 6.41 43.65 5.18 F
4475 4860 0.324552 TGGATGGTTGGATTGGCTGG 60.325 55.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2077 0.445436 CTCTGTGAGCAACGCCATTC 59.555 55.000 0.00 0.0 0.00 2.67 R
2017 2279 2.037251 GCCTAACTGGTCTGTTGAGTGA 59.963 50.000 3.94 0.0 38.35 3.41 R
3697 4035 0.116342 TGCTACTCCCTCTGTCCCAA 59.884 55.000 0.00 0.0 0.00 4.12 R
3698 4036 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.000 0.00 0.0 0.00 4.37 R
4752 5144 2.026356 ACATGCACCACCATACAAGCTA 60.026 45.455 0.00 0.0 0.00 3.32 R
5914 6820 0.316841 GCCCTCGCCAATGTCAAAAA 59.683 50.000 0.00 0.0 0.00 1.94 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
50 55 9.349713 TGTTTTCTTGACCTCTACAAATGTTAT 57.650 29.630 0.00 0.00 0.00 1.89
98 103 2.349886 GGTGAAACACTCATCGATGCTC 59.650 50.000 20.81 9.76 39.98 4.26
110 115 1.297689 GATGCTCACTGCTCACCCA 59.702 57.895 0.00 0.00 43.37 4.51
224 230 2.332063 AGAATCGGCGATCAAACCAT 57.668 45.000 24.20 5.12 0.00 3.55
227 233 4.389374 AGAATCGGCGATCAAACCATATT 58.611 39.130 24.20 3.53 0.00 1.28
325 355 4.319477 CCAAAGTTTCGTGTGTATGACCAG 60.319 45.833 0.00 0.00 0.00 4.00
374 404 4.497966 GCGACCAAAGACAAAACAAACTAC 59.502 41.667 0.00 0.00 0.00 2.73
375 405 4.726704 CGACCAAAGACAAAACAAACTACG 59.273 41.667 0.00 0.00 0.00 3.51
468 513 1.250154 ACATGCATCCAAACCCCGTG 61.250 55.000 0.00 0.00 0.00 4.94
989 1055 4.251843 CGCCGAGATTCCGCGAGA 62.252 66.667 8.23 0.00 37.82 4.04
990 1056 2.336809 GCCGAGATTCCGCGAGAT 59.663 61.111 8.23 0.00 37.82 2.75
991 1057 1.731257 GCCGAGATTCCGCGAGATC 60.731 63.158 8.23 10.75 37.82 2.75
992 1058 1.081108 CCGAGATTCCGCGAGATCC 60.081 63.158 8.23 4.17 37.82 3.36
993 1059 1.081108 CGAGATTCCGCGAGATCCC 60.081 63.158 8.23 0.00 37.82 3.85
994 1060 1.081108 GAGATTCCGCGAGATCCCG 60.081 63.158 8.23 0.00 0.00 5.14
1003 1069 4.996434 GAGATCCCGCCGCCATGG 62.996 72.222 7.63 7.63 42.50 3.66
1200 1435 1.841556 GTCCACCTCCACCTCCACA 60.842 63.158 0.00 0.00 0.00 4.17
1206 1453 1.200760 CCTCCACCTCCACATCCACA 61.201 60.000 0.00 0.00 0.00 4.17
1563 1825 2.285743 GAGAGGGCCAAGGGGTCT 60.286 66.667 6.18 0.00 39.39 3.85
1572 1834 1.852626 CAAGGGGTCTGAAGGGGGT 60.853 63.158 0.00 0.00 0.00 4.95
1764 2026 1.822990 GGGGACTACTTGATGTCGTCA 59.177 52.381 5.70 0.00 41.46 4.35
1815 2077 3.866582 GAGTCCCAGGATGCCGGG 61.867 72.222 2.18 0.00 38.61 5.73
1845 2107 0.799917 CTCACAGAGCACGTCCATCG 60.800 60.000 0.00 0.00 46.00 3.84
2017 2279 2.358015 TGAACGGGTTTGTTTCGTCTT 58.642 42.857 0.00 0.00 36.01 3.01
2308 2570 0.948141 GACTGCAGAGGTGAGTGTGC 60.948 60.000 23.35 0.00 37.24 4.57
2318 2580 2.371841 AGGTGAGTGTGCCTGTTAATCA 59.628 45.455 0.00 0.00 33.13 2.57
2363 2647 8.665685 GGTATACCAAGTTTCTAATCAGTGTTG 58.334 37.037 17.44 0.00 35.64 3.33
2484 2770 8.919777 ATTTTACCTGATATAAGGCCACTTAC 57.080 34.615 5.01 0.00 41.68 2.34
2628 2924 7.189693 TGCAATAGCTTATAACATAGTGCAC 57.810 36.000 9.40 9.40 42.29 4.57
2674 2982 4.631813 CAGCTTTCACGCTAAAGATAACCT 59.368 41.667 12.81 0.00 38.50 3.50
2769 3077 4.690748 CGCACCAAATATGTAGGATAGTGG 59.309 45.833 0.00 0.00 0.00 4.00
2805 3115 6.705863 AAGAACTGACAGCTTTGAAAATCT 57.294 33.333 1.25 0.00 0.00 2.40
2891 3202 3.149196 TCCCTCTGTTTCTTGCAATGAC 58.851 45.455 0.00 0.00 0.00 3.06
2995 3310 6.660521 AGCATAGATTTGGACAGTCAAAATGA 59.339 34.615 19.15 8.46 39.64 2.57
3001 3316 4.898829 TGGACAGTCAAAATGAACACTG 57.101 40.909 2.17 0.00 41.77 3.66
3461 3784 5.903764 TGCATTATTTTGAAATATGCGGC 57.096 34.783 16.67 0.00 37.73 6.53
3465 3788 1.906757 TTTTGAAATATGCGGCGCAG 58.093 45.000 38.27 6.41 43.65 5.18
3558 3881 4.253685 GGTCAGCTAGCTGTAAACATGAA 58.746 43.478 36.99 17.17 43.96 2.57
3559 3882 4.878397 GGTCAGCTAGCTGTAAACATGAAT 59.122 41.667 36.99 1.35 43.96 2.57
3560 3883 5.355350 GGTCAGCTAGCTGTAAACATGAATT 59.645 40.000 36.99 0.88 43.96 2.17
3561 3884 6.538742 GGTCAGCTAGCTGTAAACATGAATTA 59.461 38.462 36.99 15.79 43.96 1.40
3562 3885 7.402640 GTCAGCTAGCTGTAAACATGAATTAC 58.597 38.462 36.99 22.21 43.96 1.89
3571 3909 7.272084 GCTGTAAACATGAATTACTGCTTTGAG 59.728 37.037 28.58 17.41 46.22 3.02
3608 3946 5.981088 TGCAGTTTGTACAATTGATCCAT 57.019 34.783 13.59 0.00 0.00 3.41
3656 3994 9.951866 ATAATGATTGGGATAATTAATACCCCC 57.048 33.333 17.17 13.97 37.88 5.40
3675 4013 3.059352 CCCCCTAGTGTCTCAACTTTG 57.941 52.381 0.00 0.00 0.00 2.77
3676 4014 2.372172 CCCCCTAGTGTCTCAACTTTGT 59.628 50.000 0.00 0.00 0.00 2.83
3677 4015 3.581332 CCCCCTAGTGTCTCAACTTTGTA 59.419 47.826 0.00 0.00 0.00 2.41
3678 4016 4.562963 CCCCCTAGTGTCTCAACTTTGTAC 60.563 50.000 0.00 0.00 0.00 2.90
3679 4017 4.283722 CCCCTAGTGTCTCAACTTTGTACT 59.716 45.833 0.00 0.00 0.00 2.73
3680 4018 5.479375 CCCCTAGTGTCTCAACTTTGTACTA 59.521 44.000 0.00 0.00 0.00 1.82
3681 4019 6.014840 CCCCTAGTGTCTCAACTTTGTACTAA 60.015 42.308 0.00 0.00 0.00 2.24
3682 4020 6.867293 CCCTAGTGTCTCAACTTTGTACTAAC 59.133 42.308 0.00 0.00 0.00 2.34
3683 4021 7.255871 CCCTAGTGTCTCAACTTTGTACTAACT 60.256 40.741 0.00 0.00 0.00 2.24
3684 4022 8.142551 CCTAGTGTCTCAACTTTGTACTAACTT 58.857 37.037 0.00 0.00 0.00 2.66
3685 4023 9.530633 CTAGTGTCTCAACTTTGTACTAACTTT 57.469 33.333 0.00 0.00 0.00 2.66
3687 4025 9.530633 AGTGTCTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
3688 4026 9.525409 GTGTCTCAACTTTGTACTAACTTTAGA 57.475 33.333 2.95 0.00 34.84 2.10
3689 4027 9.525409 TGTCTCAACTTTGTACTAACTTTAGAC 57.475 33.333 12.38 12.38 34.84 2.59
3690 4028 9.525409 GTCTCAACTTTGTACTAACTTTAGACA 57.475 33.333 13.46 1.25 34.84 3.41
3691 4029 9.525409 TCTCAACTTTGTACTAACTTTAGACAC 57.475 33.333 2.95 1.85 34.84 3.67
3692 4030 9.530633 CTCAACTTTGTACTAACTTTAGACACT 57.469 33.333 2.95 0.00 34.84 3.55
3693 4031 9.880157 TCAACTTTGTACTAACTTTAGACACTT 57.120 29.630 2.95 0.00 34.84 3.16
3703 4041 9.281371 ACTAACTTTAGACACTTATTTTGGGAC 57.719 33.333 2.95 0.00 34.84 4.46
3704 4042 9.280174 CTAACTTTAGACACTTATTTTGGGACA 57.720 33.333 0.00 0.00 32.47 4.02
3705 4043 7.745620 ACTTTAGACACTTATTTTGGGACAG 57.254 36.000 0.00 0.00 42.39 3.51
3706 4044 7.514721 ACTTTAGACACTTATTTTGGGACAGA 58.485 34.615 0.00 0.00 42.39 3.41
3707 4045 7.661847 ACTTTAGACACTTATTTTGGGACAGAG 59.338 37.037 0.00 0.00 42.39 3.35
3708 4046 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
3709 4047 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
3710 4048 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
3711 4049 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
3872 4226 6.159988 ACAGAACTCATAACTACACTGCTTC 58.840 40.000 0.00 0.00 0.00 3.86
3889 4243 7.228108 ACACTGCTTCACAATCATCCATATTAG 59.772 37.037 0.00 0.00 0.00 1.73
3895 4249 7.315066 TCACAATCATCCATATTAGCTGGTA 57.685 36.000 0.00 0.00 35.19 3.25
3962 4318 2.673043 GCACAGCCATCAGGTCATTTTG 60.673 50.000 0.00 0.00 37.19 2.44
4219 4575 9.979270 GTCATGTGTTTCTCTTATGTTGATTAG 57.021 33.333 0.00 0.00 0.00 1.73
4363 4719 5.642063 GCTAAGGTACTGTTTGCTTCACATA 59.358 40.000 0.00 0.00 40.86 2.29
4475 4860 0.324552 TGGATGGTTGGATTGGCTGG 60.325 55.000 0.00 0.00 0.00 4.85
4504 4889 5.398603 TCAGGTGTCAATTTGTTTGTGTT 57.601 34.783 0.00 0.00 36.65 3.32
4514 4899 7.865385 GTCAATTTGTTTGTGTTGATTAGGCTA 59.135 33.333 0.00 0.00 36.65 3.93
4727 5119 7.086376 AGCATCTTGTTAACAAACATTAGCAG 58.914 34.615 20.89 7.09 35.15 4.24
4752 5144 7.013655 AGCATTGTACAGTCAATTCTTTCTTGT 59.986 33.333 0.00 0.00 36.10 3.16
4830 5222 8.857694 AGTATAGAGAGCATAGAACTAGTTCC 57.142 38.462 28.05 15.06 40.33 3.62
4837 5229 6.999272 AGAGCATAGAACTAGTTCCGATAGAA 59.001 38.462 28.05 8.92 40.33 2.10
4843 5235 6.807789 AGAACTAGTTCCGATAGAATGTTCC 58.192 40.000 28.05 2.26 39.79 3.62
4873 5265 9.236691 CAATATTTGTTATGTGGTGCTTCATAC 57.763 33.333 0.00 0.00 0.00 2.39
4880 5272 8.965819 TGTTATGTGGTGCTTCATACATTAATT 58.034 29.630 0.00 0.00 35.55 1.40
5069 5461 8.788813 GTTCAGTTTCATTTTATATGCAACGAG 58.211 33.333 0.00 0.00 32.01 4.18
5221 5613 3.127548 CACTAACCGAAGAGCCTACGTAA 59.872 47.826 0.00 0.00 0.00 3.18
5253 5645 1.123077 TATCTGATGGCTTGCTCGGT 58.877 50.000 0.00 0.00 0.00 4.69
5411 5807 0.035439 AACAGATGTAGGGGGCAACG 60.035 55.000 0.00 0.00 37.60 4.10
5577 5973 7.633193 CTGGTACTCAGTTCTCTTGTATACT 57.367 40.000 4.17 0.00 38.64 2.12
5578 5974 7.627298 TGGTACTCAGTTCTCTTGTATACTC 57.373 40.000 4.17 0.00 0.00 2.59
5579 5975 6.602406 TGGTACTCAGTTCTCTTGTATACTCC 59.398 42.308 4.17 0.00 0.00 3.85
5580 5976 5.821516 ACTCAGTTCTCTTGTATACTCCG 57.178 43.478 4.17 0.00 0.00 4.63
5581 5977 5.254901 ACTCAGTTCTCTTGTATACTCCGT 58.745 41.667 4.17 0.00 0.00 4.69
5582 5978 5.354792 ACTCAGTTCTCTTGTATACTCCGTC 59.645 44.000 4.17 0.00 0.00 4.79
5583 5979 4.639310 TCAGTTCTCTTGTATACTCCGTCC 59.361 45.833 4.17 0.00 0.00 4.79
5584 5980 3.626670 AGTTCTCTTGTATACTCCGTCCG 59.373 47.826 4.17 0.00 0.00 4.79
5585 5981 3.272574 TCTCTTGTATACTCCGTCCGT 57.727 47.619 4.17 0.00 0.00 4.69
5586 5982 3.614092 TCTCTTGTATACTCCGTCCGTT 58.386 45.455 4.17 0.00 0.00 4.44
5587 5983 3.624861 TCTCTTGTATACTCCGTCCGTTC 59.375 47.826 4.17 0.00 0.00 3.95
5588 5984 2.684881 TCTTGTATACTCCGTCCGTTCC 59.315 50.000 4.17 0.00 0.00 3.62
5589 5985 2.425143 TGTATACTCCGTCCGTTCCT 57.575 50.000 4.17 0.00 0.00 3.36
5590 5986 2.019249 TGTATACTCCGTCCGTTCCTG 58.981 52.381 4.17 0.00 0.00 3.86
5591 5987 2.292267 GTATACTCCGTCCGTTCCTGA 58.708 52.381 0.00 0.00 0.00 3.86
5592 5988 1.843368 ATACTCCGTCCGTTCCTGAA 58.157 50.000 0.00 0.00 0.00 3.02
5593 5989 1.843368 TACTCCGTCCGTTCCTGAAT 58.157 50.000 0.00 0.00 0.00 2.57
5594 5990 1.843368 ACTCCGTCCGTTCCTGAATA 58.157 50.000 0.00 0.00 0.00 1.75
5595 5991 2.385803 ACTCCGTCCGTTCCTGAATAT 58.614 47.619 0.00 0.00 0.00 1.28
5596 5992 2.764572 ACTCCGTCCGTTCCTGAATATT 59.235 45.455 0.00 0.00 0.00 1.28
5597 5993 3.956199 ACTCCGTCCGTTCCTGAATATTA 59.044 43.478 0.00 0.00 0.00 0.98
5598 5994 4.037684 ACTCCGTCCGTTCCTGAATATTAG 59.962 45.833 0.00 0.00 0.00 1.73
5599 5995 3.956199 TCCGTCCGTTCCTGAATATTAGT 59.044 43.478 0.00 0.00 0.00 2.24
5600 5996 4.037208 TCCGTCCGTTCCTGAATATTAGTC 59.963 45.833 0.00 0.00 0.00 2.59
5601 5997 4.037684 CCGTCCGTTCCTGAATATTAGTCT 59.962 45.833 0.00 0.00 0.00 3.24
5602 5998 5.451520 CCGTCCGTTCCTGAATATTAGTCTT 60.452 44.000 0.00 0.00 0.00 3.01
5603 5999 6.040878 CGTCCGTTCCTGAATATTAGTCTTT 58.959 40.000 0.00 0.00 0.00 2.52
5604 6000 6.019801 CGTCCGTTCCTGAATATTAGTCTTTG 60.020 42.308 0.00 0.00 0.00 2.77
5605 6001 6.817140 GTCCGTTCCTGAATATTAGTCTTTGT 59.183 38.462 0.00 0.00 0.00 2.83
5606 6002 7.977853 GTCCGTTCCTGAATATTAGTCTTTGTA 59.022 37.037 0.00 0.00 0.00 2.41
5607 6003 8.195436 TCCGTTCCTGAATATTAGTCTTTGTAG 58.805 37.037 0.00 0.00 0.00 2.74
5608 6004 8.195436 CCGTTCCTGAATATTAGTCTTTGTAGA 58.805 37.037 0.00 0.00 0.00 2.59
5609 6005 9.239002 CGTTCCTGAATATTAGTCTTTGTAGAG 57.761 37.037 0.00 0.00 0.00 2.43
5623 6019 9.606631 AGTCTTTGTAGAGATTTCATTATGGAC 57.393 33.333 0.00 0.00 0.00 4.02
5624 6020 9.606631 GTCTTTGTAGAGATTTCATTATGGACT 57.393 33.333 0.00 0.00 0.00 3.85
5632 6028 8.307483 AGAGATTTCATTATGGACTACATACGG 58.693 37.037 0.00 0.00 41.61 4.02
5633 6029 8.190326 AGATTTCATTATGGACTACATACGGA 57.810 34.615 0.00 0.00 41.61 4.69
5634 6030 8.307483 AGATTTCATTATGGACTACATACGGAG 58.693 37.037 0.00 0.00 41.61 4.63
5635 6031 5.386958 TCATTATGGACTACATACGGAGC 57.613 43.478 0.00 0.00 41.61 4.70
5636 6032 4.830600 TCATTATGGACTACATACGGAGCA 59.169 41.667 0.00 0.00 41.61 4.26
5637 6033 5.303333 TCATTATGGACTACATACGGAGCAA 59.697 40.000 0.00 0.00 41.61 3.91
5638 6034 5.601583 TTATGGACTACATACGGAGCAAA 57.398 39.130 0.00 0.00 41.61 3.68
5639 6035 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
5640 6036 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
5641 6037 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
5642 6038 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
5643 6039 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
5644 6040 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
5645 6041 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
5646 6042 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
5647 6043 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
5648 6044 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
5649 6045 5.415701 ACATACGGAGCAAAATGAGTGAATT 59.584 36.000 0.00 0.00 0.00 2.17
5650 6046 4.853924 ACGGAGCAAAATGAGTGAATTT 57.146 36.364 0.00 0.00 0.00 1.82
5651 6047 5.957842 ACGGAGCAAAATGAGTGAATTTA 57.042 34.783 0.00 0.00 0.00 1.40
5652 6048 5.699839 ACGGAGCAAAATGAGTGAATTTAC 58.300 37.500 0.00 0.00 0.00 2.01
5653 6049 5.240623 ACGGAGCAAAATGAGTGAATTTACA 59.759 36.000 2.93 0.00 0.00 2.41
5654 6050 5.569059 CGGAGCAAAATGAGTGAATTTACAC 59.431 40.000 2.93 0.00 40.60 2.90
5668 6064 9.236006 AGTGAATTTACACTCTAAAATGCATCT 57.764 29.630 0.00 0.00 46.36 2.90
5686 6082 9.875691 AATGCATCTATATACATTCGTATGTGT 57.124 29.630 16.91 12.97 44.56 3.72
5687 6083 9.875691 ATGCATCTATATACATTCGTATGTGTT 57.124 29.630 16.91 7.60 44.56 3.32
5688 6084 9.353999 TGCATCTATATACATTCGTATGTGTTC 57.646 33.333 16.91 0.00 44.56 3.18
5689 6085 8.808529 GCATCTATATACATTCGTATGTGTTCC 58.191 37.037 16.91 0.00 44.56 3.62
5690 6086 9.855021 CATCTATATACATTCGTATGTGTTCCA 57.145 33.333 16.91 0.00 44.56 3.53
5695 6091 7.946655 ATACATTCGTATGTGTTCCATAGTG 57.053 36.000 16.91 0.00 44.56 2.74
5696 6092 5.116180 ACATTCGTATGTGTTCCATAGTGG 58.884 41.667 6.89 0.00 43.29 4.00
5697 6093 5.105106 ACATTCGTATGTGTTCCATAGTGGA 60.105 40.000 6.89 0.00 43.30 4.02
5698 6094 6.575451 ACATTCGTATGTGTTCCATAGTGGAA 60.575 38.462 6.89 7.31 46.93 3.53
5699 6095 7.851114 ACATTCGTATGTGTTCCATAGTGGAAT 60.851 37.037 13.96 1.88 45.69 3.01
5718 6355 9.139734 AGTGGAATACATAAGAATAGTACGGAA 57.860 33.333 0.00 0.00 0.00 4.30
5801 6704 6.874134 TCAGTTAAGAAGAGGATAGTTTGTGC 59.126 38.462 0.00 0.00 0.00 4.57
5834 6737 3.031736 ACGGATAGTGCTACAACATCCT 58.968 45.455 0.00 0.00 34.26 3.24
5913 6819 3.010420 GGTGAACCATAGCTTGACTTCC 58.990 50.000 0.00 0.00 35.64 3.46
5914 6820 3.307762 GGTGAACCATAGCTTGACTTCCT 60.308 47.826 0.00 0.00 35.64 3.36
5915 6821 4.327680 GTGAACCATAGCTTGACTTCCTT 58.672 43.478 0.00 0.00 0.00 3.36
5916 6822 4.762251 GTGAACCATAGCTTGACTTCCTTT 59.238 41.667 0.00 0.00 0.00 3.11
5932 6838 1.067635 CCTTTTTGACATTGGCGAGGG 60.068 52.381 0.00 0.00 0.00 4.30
5933 6839 0.316841 TTTTTGACATTGGCGAGGGC 59.683 50.000 0.00 0.00 38.90 5.19
5934 6840 0.825425 TTTTGACATTGGCGAGGGCA 60.825 50.000 0.00 0.00 42.47 5.36
5935 6841 1.243342 TTTGACATTGGCGAGGGCAG 61.243 55.000 0.00 0.00 42.47 4.85
5936 6842 2.123248 TTGACATTGGCGAGGGCAGA 62.123 55.000 0.00 0.00 42.47 4.26
5937 6843 1.377202 GACATTGGCGAGGGCAGAA 60.377 57.895 0.00 0.00 42.47 3.02
5939 6845 1.675310 CATTGGCGAGGGCAGAACA 60.675 57.895 0.00 0.00 42.47 3.18
5940 6846 1.675641 ATTGGCGAGGGCAGAACAC 60.676 57.895 0.00 0.00 42.47 3.32
5941 6847 2.129555 ATTGGCGAGGGCAGAACACT 62.130 55.000 0.00 0.00 42.47 3.55
5942 6848 2.032681 GGCGAGGGCAGAACACTT 59.967 61.111 0.00 0.00 42.47 3.16
5943 6849 1.295423 GGCGAGGGCAGAACACTTA 59.705 57.895 0.00 0.00 42.47 2.24
5944 6850 1.019805 GGCGAGGGCAGAACACTTAC 61.020 60.000 0.00 0.00 42.47 2.34
5945 6851 0.320421 GCGAGGGCAGAACACTTACA 60.320 55.000 0.00 0.00 39.62 2.41
5947 6853 1.429463 GAGGGCAGAACACTTACACG 58.571 55.000 0.00 0.00 0.00 4.49
5948 6854 0.756903 AGGGCAGAACACTTACACGT 59.243 50.000 0.00 0.00 0.00 4.49
5949 6855 0.865769 GGGCAGAACACTTACACGTG 59.134 55.000 15.48 15.48 40.67 4.49
5974 6958 4.453480 TCCTCTTGTTTCAAATGGTCCT 57.547 40.909 0.00 0.00 0.00 3.85
5975 6959 5.576563 TCCTCTTGTTTCAAATGGTCCTA 57.423 39.130 0.00 0.00 0.00 2.94
5993 6977 4.991760 GCAACGAGCATGATGAGC 57.008 55.556 0.00 0.00 44.79 4.26
6049 7033 0.835971 GAAAGGCCCACCCACCAATT 60.836 55.000 0.00 0.00 36.11 2.32
6077 7061 4.361783 TGGATCTCAAGAGGTACCATGAA 58.638 43.478 15.94 7.08 0.00 2.57
6104 7088 3.988379 TCAACATTCACAAGTTGGAGC 57.012 42.857 7.96 0.00 43.91 4.70
6123 7111 2.039480 AGCCAGTCTTTGAGCATCTTCA 59.961 45.455 0.00 0.00 34.92 3.02
6125 7113 3.672808 CCAGTCTTTGAGCATCTTCAGT 58.327 45.455 0.00 0.00 34.92 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 55 3.942115 TCGCAAAAATTCGTGATGGGATA 59.058 39.130 0.00 0.00 0.00 2.59
51 56 2.752354 TCGCAAAAATTCGTGATGGGAT 59.248 40.909 0.00 0.00 0.00 3.85
52 57 2.155279 TCGCAAAAATTCGTGATGGGA 58.845 42.857 0.00 0.00 0.00 4.37
98 103 0.037303 ATGAACCTGGGTGAGCAGTG 59.963 55.000 0.00 0.00 0.00 3.66
110 115 0.981183 TCCCGTGCTAACATGAACCT 59.019 50.000 0.00 0.00 34.49 3.50
173 178 1.679898 AGGCTAGCCTGGACACAAC 59.320 57.895 35.59 3.64 46.22 3.32
224 230 9.261035 AGTCAGAATTACCTTGAGAGAGAAATA 57.739 33.333 0.00 0.00 0.00 1.40
227 233 6.721668 TCAGTCAGAATTACCTTGAGAGAGAA 59.278 38.462 0.00 0.00 0.00 2.87
325 355 3.470645 AACGGCCTATGGAACTATGTC 57.529 47.619 0.00 0.00 0.00 3.06
374 404 5.119931 TGTCATTTCTCATTTTTGGACCG 57.880 39.130 0.00 0.00 0.00 4.79
375 405 7.095102 CCATTTGTCATTTCTCATTTTTGGACC 60.095 37.037 0.00 0.00 0.00 4.46
468 513 1.066071 CCTCTTCTTTCCTTCCGTCCC 60.066 57.143 0.00 0.00 0.00 4.46
565 629 4.024545 GTGGTGGTGGGTACGGGG 62.025 72.222 0.00 0.00 0.00 5.73
973 1039 1.731257 GATCTCGCGGAATCTCGGC 60.731 63.158 6.13 0.00 39.05 5.54
974 1040 1.081108 GGATCTCGCGGAATCTCGG 60.081 63.158 6.13 0.00 0.00 4.63
975 1041 1.081108 GGGATCTCGCGGAATCTCG 60.081 63.158 6.13 0.00 0.00 4.04
976 1042 1.081108 CGGGATCTCGCGGAATCTC 60.081 63.158 0.00 8.88 46.57 2.75
977 1043 3.043419 CGGGATCTCGCGGAATCT 58.957 61.111 0.00 0.00 46.57 2.40
986 1052 4.996434 CCATGGCGGCGGGATCTC 62.996 72.222 9.78 0.00 0.00 2.75
1200 1435 2.158564 GGATGTGGATGTGGATGTGGAT 60.159 50.000 0.00 0.00 0.00 3.41
1206 1453 1.064463 GTGGTGGATGTGGATGTGGAT 60.064 52.381 0.00 0.00 0.00 3.41
1764 2026 2.896044 TGATGACAAGCTCTCTGTGTCT 59.104 45.455 14.78 3.08 41.80 3.41
1815 2077 0.445436 CTCTGTGAGCAACGCCATTC 59.555 55.000 0.00 0.00 0.00 2.67
1845 2107 1.168714 GCACACTCATCCCCTTTGTC 58.831 55.000 0.00 0.00 0.00 3.18
2017 2279 2.037251 GCCTAACTGGTCTGTTGAGTGA 59.963 50.000 3.94 0.00 38.35 3.41
2484 2770 9.781834 TTCAGACTTGTTTTTACACACTAAATG 57.218 29.630 0.00 0.00 0.00 2.32
2541 2832 7.336161 TCAACTCCTGCTATAAGAGAACTAC 57.664 40.000 0.00 0.00 0.00 2.73
2542 2833 8.540507 AATCAACTCCTGCTATAAGAGAACTA 57.459 34.615 0.00 0.00 0.00 2.24
2628 2924 9.683069 GCTGATCCCAGTAAAAATTACATATTG 57.317 33.333 3.37 0.00 42.35 1.90
2632 2928 7.961326 AAGCTGATCCCAGTAAAAATTACAT 57.039 32.000 0.00 0.00 42.35 2.29
2635 2943 7.361713 CGTGAAAGCTGATCCCAGTAAAAATTA 60.362 37.037 0.00 0.00 42.35 1.40
2743 3051 2.992593 TCCTACATATTTGGTGCGCAA 58.007 42.857 14.00 0.00 0.00 4.85
2744 3052 2.700722 TCCTACATATTTGGTGCGCA 57.299 45.000 5.66 5.66 0.00 6.09
2769 3077 7.604545 AGCTGTCAGTTCTTTCTTTTATCCTAC 59.395 37.037 0.93 0.00 0.00 3.18
2805 3115 6.152661 CCTTTATGGCTCCAACATACAGAAAA 59.847 38.462 0.00 0.00 32.85 2.29
2891 3202 9.421806 TGTATTTGTATTCAAAAGCATTCCTTG 57.578 29.630 1.36 0.00 44.97 3.61
2966 3281 5.559770 TGACTGTCCAAATCTATGCTTTGA 58.440 37.500 5.17 0.00 35.99 2.69
2995 3310 5.995282 TCCATCTGTTTCGAAATACAGTGTT 59.005 36.000 22.87 11.24 41.87 3.32
3060 3375 7.503521 TGTATGAATGCACAGTTCAAACTTA 57.496 32.000 5.38 0.00 38.89 2.24
3249 3568 6.866480 AGAAAAGAAGAAATGTCAGCAAACA 58.134 32.000 0.00 0.00 0.00 2.83
3439 3758 4.443725 CGCCGCATATTTCAAAATAATGCA 59.556 37.500 18.79 0.00 36.41 3.96
3465 3788 0.679960 AACTATGCCCGGCAGGAAAC 60.680 55.000 18.96 0.00 43.65 2.78
3558 3881 6.006449 ACTGGAAATCACTCAAAGCAGTAAT 58.994 36.000 0.00 0.00 0.00 1.89
3559 3882 5.376625 ACTGGAAATCACTCAAAGCAGTAA 58.623 37.500 0.00 0.00 0.00 2.24
3560 3883 4.973168 ACTGGAAATCACTCAAAGCAGTA 58.027 39.130 0.00 0.00 0.00 2.74
3561 3884 3.817647 GACTGGAAATCACTCAAAGCAGT 59.182 43.478 0.00 0.00 0.00 4.40
3562 3885 4.070716 AGACTGGAAATCACTCAAAGCAG 58.929 43.478 0.00 0.00 0.00 4.24
3565 3888 5.218139 GCAAAGACTGGAAATCACTCAAAG 58.782 41.667 0.00 0.00 0.00 2.77
3571 3909 4.574599 AACTGCAAAGACTGGAAATCAC 57.425 40.909 0.00 0.00 0.00 3.06
3616 3954 9.496873 TCCCAATCATTATACGAACGAAATAAT 57.503 29.630 0.14 7.30 0.00 1.28
3619 3957 7.979444 ATCCCAATCATTATACGAACGAAAT 57.021 32.000 0.14 0.00 0.00 2.17
3655 3993 2.372172 ACAAAGTTGAGACACTAGGGGG 59.628 50.000 0.00 0.00 0.00 5.40
3656 3994 3.771577 ACAAAGTTGAGACACTAGGGG 57.228 47.619 0.00 0.00 0.00 4.79
3657 3995 5.470047 AGTACAAAGTTGAGACACTAGGG 57.530 43.478 0.00 0.00 0.00 3.53
3658 3996 7.659186 AGTTAGTACAAAGTTGAGACACTAGG 58.341 38.462 0.00 0.00 0.00 3.02
3659 3997 9.530633 AAAGTTAGTACAAAGTTGAGACACTAG 57.469 33.333 0.00 0.00 0.00 2.57
3661 3999 9.530633 CTAAAGTTAGTACAAAGTTGAGACACT 57.469 33.333 0.00 0.00 0.00 3.55
3662 4000 9.525409 TCTAAAGTTAGTACAAAGTTGAGACAC 57.475 33.333 0.00 0.00 28.29 3.67
3663 4001 9.525409 GTCTAAAGTTAGTACAAAGTTGAGACA 57.475 33.333 13.36 0.00 43.75 3.41
3664 4002 9.525409 TGTCTAAAGTTAGTACAAAGTTGAGAC 57.475 33.333 12.07 12.07 44.17 3.36
3665 4003 9.525409 GTGTCTAAAGTTAGTACAAAGTTGAGA 57.475 33.333 0.00 0.00 30.04 3.27
3666 4004 9.530633 AGTGTCTAAAGTTAGTACAAAGTTGAG 57.469 33.333 0.00 0.00 32.61 3.02
3667 4005 9.880157 AAGTGTCTAAAGTTAGTACAAAGTTGA 57.120 29.630 0.00 0.00 32.61 3.18
3677 4015 9.281371 GTCCCAAAATAAGTGTCTAAAGTTAGT 57.719 33.333 0.00 0.00 32.61 2.24
3678 4016 9.280174 TGTCCCAAAATAAGTGTCTAAAGTTAG 57.720 33.333 0.00 0.00 0.00 2.34
3679 4017 9.280174 CTGTCCCAAAATAAGTGTCTAAAGTTA 57.720 33.333 0.00 0.00 0.00 2.24
3680 4018 7.996644 TCTGTCCCAAAATAAGTGTCTAAAGTT 59.003 33.333 0.00 0.00 0.00 2.66
3681 4019 7.514721 TCTGTCCCAAAATAAGTGTCTAAAGT 58.485 34.615 0.00 0.00 0.00 2.66
3682 4020 7.119846 CCTCTGTCCCAAAATAAGTGTCTAAAG 59.880 40.741 0.00 0.00 0.00 1.85
3683 4021 6.940298 CCTCTGTCCCAAAATAAGTGTCTAAA 59.060 38.462 0.00 0.00 0.00 1.85
3684 4022 6.472887 CCTCTGTCCCAAAATAAGTGTCTAA 58.527 40.000 0.00 0.00 0.00 2.10
3685 4023 5.045869 CCCTCTGTCCCAAAATAAGTGTCTA 60.046 44.000 0.00 0.00 0.00 2.59
3686 4024 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
3687 4025 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
3688 4026 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
3689 4027 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
3690 4028 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
3691 4029 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
3692 4030 4.080526 GCTACTCCCTCTGTCCCAAAATAA 60.081 45.833 0.00 0.00 0.00 1.40
3693 4031 3.454812 GCTACTCCCTCTGTCCCAAAATA 59.545 47.826 0.00 0.00 0.00 1.40
3694 4032 2.239907 GCTACTCCCTCTGTCCCAAAAT 59.760 50.000 0.00 0.00 0.00 1.82
3695 4033 1.628846 GCTACTCCCTCTGTCCCAAAA 59.371 52.381 0.00 0.00 0.00 2.44
3696 4034 1.276622 GCTACTCCCTCTGTCCCAAA 58.723 55.000 0.00 0.00 0.00 3.28
3697 4035 0.116342 TGCTACTCCCTCTGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
3698 4036 0.116342 TTGCTACTCCCTCTGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
3699 4037 1.066071 GTTTGCTACTCCCTCTGTCCC 60.066 57.143 0.00 0.00 0.00 4.46
3700 4038 1.903183 AGTTTGCTACTCCCTCTGTCC 59.097 52.381 0.00 0.00 28.23 4.02
3701 4039 2.563179 TCAGTTTGCTACTCCCTCTGTC 59.437 50.000 0.00 0.00 33.85 3.51
3702 4040 2.564947 CTCAGTTTGCTACTCCCTCTGT 59.435 50.000 0.00 0.00 33.85 3.41
3703 4041 2.676463 GCTCAGTTTGCTACTCCCTCTG 60.676 54.545 0.00 0.00 33.85 3.35
3704 4042 1.552792 GCTCAGTTTGCTACTCCCTCT 59.447 52.381 0.00 0.00 33.85 3.69
3705 4043 1.406205 GGCTCAGTTTGCTACTCCCTC 60.406 57.143 0.00 0.00 33.85 4.30
3706 4044 0.615850 GGCTCAGTTTGCTACTCCCT 59.384 55.000 0.00 0.00 33.85 4.20
3707 4045 0.324943 TGGCTCAGTTTGCTACTCCC 59.675 55.000 0.00 0.00 33.85 4.30
3708 4046 2.409948 ATGGCTCAGTTTGCTACTCC 57.590 50.000 0.00 0.00 33.85 3.85
3709 4047 4.479619 CAAAATGGCTCAGTTTGCTACTC 58.520 43.478 12.74 0.00 41.22 2.59
3710 4048 4.510038 CAAAATGGCTCAGTTTGCTACT 57.490 40.909 12.74 0.00 41.22 2.57
3754 4092 0.532115 GAAAGGGCCATGTGCGATTT 59.468 50.000 6.18 0.00 42.61 2.17
3755 4093 0.323725 AGAAAGGGCCATGTGCGATT 60.324 50.000 6.18 0.00 42.61 3.34
3756 4094 0.323725 AAGAAAGGGCCATGTGCGAT 60.324 50.000 6.18 0.00 42.61 4.58
3757 4095 0.326595 TAAGAAAGGGCCATGTGCGA 59.673 50.000 6.18 0.00 42.61 5.10
3758 4096 1.066002 CATAAGAAAGGGCCATGTGCG 59.934 52.381 6.18 0.00 42.61 5.34
3759 4097 1.202452 GCATAAGAAAGGGCCATGTGC 60.202 52.381 6.18 2.82 40.16 4.57
3760 4098 2.101783 TGCATAAGAAAGGGCCATGTG 58.898 47.619 6.18 0.00 0.00 3.21
3761 4099 2.530460 TGCATAAGAAAGGGCCATGT 57.470 45.000 6.18 0.00 0.00 3.21
3762 4100 4.586001 AGTTATGCATAAGAAAGGGCCATG 59.414 41.667 19.41 0.00 0.00 3.66
3864 4218 6.387041 AATATGGATGATTGTGAAGCAGTG 57.613 37.500 0.00 0.00 0.00 3.66
3872 4226 7.984422 TTACCAGCTAATATGGATGATTGTG 57.016 36.000 0.00 0.00 40.51 3.33
3889 4243 9.937175 CTTTATTAAGTCAAAGCTATTACCAGC 57.063 33.333 0.00 0.00 42.12 4.85
4219 4575 6.168270 AGGTAGCAAATAAGGTCTGAGATC 57.832 41.667 0.00 0.00 0.00 2.75
4363 4719 4.142093 GCAAGGAAATGCATTGGTAGACAT 60.142 41.667 13.82 0.00 45.70 3.06
4475 4860 3.684788 ACAAATTGACACCTGATACGCTC 59.315 43.478 0.00 0.00 0.00 5.03
4710 5100 7.593273 TGTACAATGCTGCTAATGTTTGTTAAC 59.407 33.333 0.00 0.00 34.75 2.01
4727 5119 7.141363 ACAAGAAAGAATTGACTGTACAATGC 58.859 34.615 0.00 0.00 39.88 3.56
4752 5144 2.026356 ACATGCACCACCATACAAGCTA 60.026 45.455 0.00 0.00 0.00 3.32
4830 5222 5.845985 ATATTGCACGGAACATTCTATCG 57.154 39.130 0.00 0.00 0.00 2.92
4837 5229 6.751425 CACATAACAAATATTGCACGGAACAT 59.249 34.615 0.00 0.00 0.00 2.71
4843 5235 4.265085 GCACCACATAACAAATATTGCACG 59.735 41.667 0.00 0.00 28.68 5.34
4880 5272 9.941325 ATGACATGAATTAAGCCAAATTAAACA 57.059 25.926 0.00 0.00 0.00 2.83
5069 5461 8.398878 AGGTACAGATTAGAAGTGCTCTATAC 57.601 38.462 0.00 0.00 36.50 1.47
5108 5500 3.746492 GGCTACAGTACTTGACCTGTTTG 59.254 47.826 0.00 0.00 0.00 2.93
5221 5613 3.514706 CCATCAGATATAGCAGCTCCACT 59.485 47.826 0.00 0.00 0.00 4.00
5576 5972 3.454371 AATATTCAGGAACGGACGGAG 57.546 47.619 0.00 0.00 28.33 4.63
5577 5973 3.956199 ACTAATATTCAGGAACGGACGGA 59.044 43.478 0.00 0.00 28.33 4.69
5578 5974 4.037684 AGACTAATATTCAGGAACGGACGG 59.962 45.833 0.00 0.00 28.33 4.79
5579 5975 5.184340 AGACTAATATTCAGGAACGGACG 57.816 43.478 0.00 0.00 28.33 4.79
5580 5976 6.817140 ACAAAGACTAATATTCAGGAACGGAC 59.183 38.462 0.00 0.00 28.33 4.79
5581 5977 6.942976 ACAAAGACTAATATTCAGGAACGGA 58.057 36.000 0.00 0.00 0.00 4.69
5582 5978 8.195436 TCTACAAAGACTAATATTCAGGAACGG 58.805 37.037 0.00 0.00 0.00 4.44
5583 5979 9.239002 CTCTACAAAGACTAATATTCAGGAACG 57.761 37.037 0.00 0.00 0.00 3.95
5597 5993 9.606631 GTCCATAATGAAATCTCTACAAAGACT 57.393 33.333 0.00 0.00 0.00 3.24
5598 5994 9.606631 AGTCCATAATGAAATCTCTACAAAGAC 57.393 33.333 0.00 0.00 0.00 3.01
5606 6002 8.307483 CCGTATGTAGTCCATAATGAAATCTCT 58.693 37.037 0.00 0.00 37.77 3.10
5607 6003 8.304596 TCCGTATGTAGTCCATAATGAAATCTC 58.695 37.037 0.00 0.00 37.77 2.75
5608 6004 8.190326 TCCGTATGTAGTCCATAATGAAATCT 57.810 34.615 0.00 0.00 37.77 2.40
5609 6005 7.063544 GCTCCGTATGTAGTCCATAATGAAATC 59.936 40.741 0.00 0.00 37.77 2.17
5610 6006 6.874134 GCTCCGTATGTAGTCCATAATGAAAT 59.126 38.462 0.00 0.00 37.77 2.17
5611 6007 6.183360 TGCTCCGTATGTAGTCCATAATGAAA 60.183 38.462 0.00 0.00 37.77 2.69
5612 6008 5.303333 TGCTCCGTATGTAGTCCATAATGAA 59.697 40.000 0.00 0.00 37.77 2.57
5613 6009 4.830600 TGCTCCGTATGTAGTCCATAATGA 59.169 41.667 0.00 0.00 37.77 2.57
5614 6010 5.134202 TGCTCCGTATGTAGTCCATAATG 57.866 43.478 0.00 0.00 37.77 1.90
5615 6011 5.801531 TTGCTCCGTATGTAGTCCATAAT 57.198 39.130 0.00 0.00 37.77 1.28
5616 6012 5.601583 TTTGCTCCGTATGTAGTCCATAA 57.398 39.130 0.00 0.00 37.77 1.90
5617 6013 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
5618 6014 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
5619 6015 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
5620 6016 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
5621 6017 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
5622 6018 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
5623 6019 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
5624 6020 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
5625 6021 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
5626 6022 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
5627 6023 6.515272 AAATTCACTCATTTTGCTCCGTAT 57.485 33.333 0.00 0.00 0.00 3.06
5628 6024 5.957842 AAATTCACTCATTTTGCTCCGTA 57.042 34.783 0.00 0.00 0.00 4.02
5629 6025 4.853924 AAATTCACTCATTTTGCTCCGT 57.146 36.364 0.00 0.00 0.00 4.69
5630 6026 5.569059 GTGTAAATTCACTCATTTTGCTCCG 59.431 40.000 0.00 0.00 35.68 4.63
5631 6027 6.681777 AGTGTAAATTCACTCATTTTGCTCC 58.318 36.000 0.00 0.00 44.07 4.70
5661 6057 9.875691 AACACATACGAATGTATATAGATGCAT 57.124 29.630 0.00 0.00 44.70 3.96
5662 6058 9.353999 GAACACATACGAATGTATATAGATGCA 57.646 33.333 0.00 0.00 44.70 3.96
5663 6059 8.808529 GGAACACATACGAATGTATATAGATGC 58.191 37.037 0.00 0.00 44.70 3.91
5664 6060 9.855021 TGGAACACATACGAATGTATATAGATG 57.145 33.333 0.00 0.00 44.70 2.90
5671 6067 7.201965 TCCACTATGGAACACATACGAATGTAT 60.202 37.037 0.00 0.00 45.00 2.29
5672 6068 6.097129 TCCACTATGGAACACATACGAATGTA 59.903 38.462 0.00 0.00 45.00 2.29
5673 6069 5.105106 TCCACTATGGAACACATACGAATGT 60.105 40.000 0.00 0.00 45.00 2.71
5674 6070 5.356426 TCCACTATGGAACACATACGAATG 58.644 41.667 0.00 0.00 45.00 2.67
5675 6071 5.607939 TCCACTATGGAACACATACGAAT 57.392 39.130 0.00 0.00 45.00 3.34
5691 6087 9.797642 TCCGTACTATTCTTATGTATTCCACTA 57.202 33.333 0.00 0.00 0.00 2.74
5692 6088 8.701908 TCCGTACTATTCTTATGTATTCCACT 57.298 34.615 0.00 0.00 0.00 4.00
5693 6089 9.924650 ATTCCGTACTATTCTTATGTATTCCAC 57.075 33.333 0.00 0.00 0.00 4.02
5700 6096 8.867097 ACATGGTATTCCGTACTATTCTTATGT 58.133 33.333 0.00 0.00 32.75 2.29
5701 6097 9.706691 AACATGGTATTCCGTACTATTCTTATG 57.293 33.333 0.00 0.00 32.75 1.90
5703 6099 9.537192 CAAACATGGTATTCCGTACTATTCTTA 57.463 33.333 0.00 0.00 32.75 2.10
5704 6100 7.012044 GCAAACATGGTATTCCGTACTATTCTT 59.988 37.037 0.00 0.00 32.75 2.52
5705 6101 6.482308 GCAAACATGGTATTCCGTACTATTCT 59.518 38.462 0.00 0.00 32.75 2.40
5706 6102 6.482308 AGCAAACATGGTATTCCGTACTATTC 59.518 38.462 0.00 0.00 32.75 1.75
5707 6103 6.354130 AGCAAACATGGTATTCCGTACTATT 58.646 36.000 0.00 0.00 32.75 1.73
5708 6104 5.925509 AGCAAACATGGTATTCCGTACTAT 58.074 37.500 0.00 0.00 35.13 2.12
5709 6105 5.347620 AGCAAACATGGTATTCCGTACTA 57.652 39.130 0.00 0.00 36.30 1.82
5710 6106 4.216411 AGCAAACATGGTATTCCGTACT 57.784 40.909 0.00 0.00 36.30 2.73
5771 6666 9.660180 AAACTATCCTCTTCTTAACTGATGAAC 57.340 33.333 0.00 0.00 0.00 3.18
5801 6704 3.168963 CACTATCCGTGTCGTGTTGTAG 58.831 50.000 0.00 0.00 38.84 2.74
5834 6737 5.858381 AGAGTAGTGAATCTTTGTTGCTCA 58.142 37.500 0.00 0.00 0.00 4.26
5913 6819 1.669795 GCCCTCGCCAATGTCAAAAAG 60.670 52.381 0.00 0.00 0.00 2.27
5914 6820 0.316841 GCCCTCGCCAATGTCAAAAA 59.683 50.000 0.00 0.00 0.00 1.94
5915 6821 0.825425 TGCCCTCGCCAATGTCAAAA 60.825 50.000 0.00 0.00 0.00 2.44
5916 6822 1.228398 TGCCCTCGCCAATGTCAAA 60.228 52.632 0.00 0.00 0.00 2.69
5932 6838 0.934496 TGCACGTGTAAGTGTTCTGC 59.066 50.000 18.38 0.00 43.61 4.26
5933 6839 3.363970 GGAATGCACGTGTAAGTGTTCTG 60.364 47.826 18.38 0.00 43.61 3.02
5934 6840 2.806244 GGAATGCACGTGTAAGTGTTCT 59.194 45.455 18.38 0.00 43.61 3.01
5935 6841 2.806244 AGGAATGCACGTGTAAGTGTTC 59.194 45.455 18.38 12.72 43.61 3.18
5936 6842 2.806244 GAGGAATGCACGTGTAAGTGTT 59.194 45.455 18.38 3.44 43.61 3.32
5937 6843 2.037251 AGAGGAATGCACGTGTAAGTGT 59.963 45.455 18.38 0.00 43.61 3.55
5939 6845 3.067106 CAAGAGGAATGCACGTGTAAGT 58.933 45.455 18.38 5.15 0.00 2.24
5940 6846 3.067106 ACAAGAGGAATGCACGTGTAAG 58.933 45.455 18.38 0.00 0.00 2.34
5941 6847 3.120321 ACAAGAGGAATGCACGTGTAA 57.880 42.857 18.38 6.47 0.00 2.41
5942 6848 2.831685 ACAAGAGGAATGCACGTGTA 57.168 45.000 18.38 14.09 0.00 2.90
5943 6849 1.967319 AACAAGAGGAATGCACGTGT 58.033 45.000 18.38 0.00 0.00 4.49
5944 6850 2.290367 TGAAACAAGAGGAATGCACGTG 59.710 45.455 12.28 12.28 0.00 4.49
5945 6851 2.571212 TGAAACAAGAGGAATGCACGT 58.429 42.857 0.00 0.00 0.00 4.49
5947 6853 4.687483 CCATTTGAAACAAGAGGAATGCAC 59.313 41.667 0.00 0.00 0.00 4.57
5948 6854 4.344679 ACCATTTGAAACAAGAGGAATGCA 59.655 37.500 0.00 0.00 0.00 3.96
5949 6855 4.886579 ACCATTTGAAACAAGAGGAATGC 58.113 39.130 0.00 0.00 0.00 3.56
5974 6958 1.575244 GCTCATCATGCTCGTTGCTA 58.425 50.000 5.00 0.00 43.37 3.49
5975 6959 1.426816 CGCTCATCATGCTCGTTGCT 61.427 55.000 5.00 0.00 43.37 3.91
6049 7033 5.250543 TGGTACCTCTTGAGATCCATCAAAA 59.749 40.000 14.36 0.00 38.66 2.44
6077 7061 6.998074 TCCAACTTGTGAATGTTGATACTTCT 59.002 34.615 7.33 0.00 44.29 2.85
6104 7088 3.672808 ACTGAAGATGCTCAAAGACTGG 58.327 45.455 0.00 0.00 0.00 4.00
6123 7111 6.927381 AGTTGCTACTGTTTCGTATTACAACT 59.073 34.615 0.00 0.00 35.45 3.16
6125 7113 7.112528 CAGTTGCTACTGTTTCGTATTACAA 57.887 36.000 18.65 0.00 45.46 2.41
6150 7138 1.946768 GTACTGCACTTTGTTGGCTCA 59.053 47.619 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.