Multiple sequence alignment - TraesCS5A01G022100

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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 TraesCS5A01G022100 chr5A 100.000 4888 0 0 1 4888 17829240 17834127 0.000000e+00 9027.0
1 TraesCS5A01G022100 chr5A 97.778 90 2 0 3668 3757 504543200 504543289 6.550000e-34 156.0
2 TraesCS5A01G022100 chr5A 90.196 102 10 0 4157 4258 17833214 17833315 3.070000e-27 134.0
3 TraesCS5A01G022100 chr5A 90.196 102 10 0 3975 4076 17833396 17833497 3.070000e-27 134.0
4 TraesCS5A01G022100 chr5D 94.216 4564 125 43 1 4494 25312624 25308130 0.000000e+00 6837.0
5 TraesCS5A01G022100 chr5D 88.214 280 4 3 4494 4744 25307344 25307065 1.710000e-79 307.0
6 TraesCS5A01G022100 chr5D 86.268 284 10 13 4491 4745 516962645 516962928 1.040000e-71 281.0
7 TraesCS5A01G022100 chr5D 91.270 126 9 1 3911 4036 25308502 25308379 2.340000e-38 171.0
8 TraesCS5A01G022100 chr5D 90.909 99 9 0 4160 4258 25308635 25308537 3.070000e-27 134.0
9 TraesCS5A01G022100 chr5D 85.246 61 5 3 4754 4814 276704482 276704426 5.280000e-05 60.2
10 TraesCS5A01G022100 chr5B 89.183 2154 139 39 523 2622 17970875 17972988 0.000000e+00 2601.0
11 TraesCS5A01G022100 chr5B 96.806 1440 44 2 2617 4054 17973021 17974460 0.000000e+00 2403.0
12 TraesCS5A01G022100 chr5B 90.538 539 42 8 2 532 17970251 17970788 0.000000e+00 704.0
13 TraesCS5A01G022100 chr5B 91.824 318 20 4 3793 4107 69574319 69574005 5.810000e-119 438.0
14 TraesCS5A01G022100 chr5B 89.571 163 13 2 4259 4421 69573989 69573831 2.310000e-48 204.0
15 TraesCS5A01G022100 chr5B 96.703 91 3 0 3667 3757 192087464 192087554 8.470000e-33 152.0
16 TraesCS5A01G022100 chr5B 95.062 81 3 1 4495 4574 17975359 17975439 5.140000e-25 126.0
17 TraesCS5A01G022100 chr6B 90.123 162 12 2 4259 4420 642296835 642296678 1.780000e-49 207.0
18 TraesCS5A01G022100 chr6B 96.703 91 3 0 3667 3757 183060521 183060431 8.470000e-33 152.0
19 TraesCS5A01G022100 chr6B 93.407 91 6 0 3667 3757 635775273 635775363 8.530000e-28 135.0
20 TraesCS5A01G022100 chr6B 93.407 91 5 1 3667 3756 430964599 430964509 3.070000e-27 134.0
21 TraesCS5A01G022100 chr6B 97.436 78 2 0 3731 3808 642297155 642297078 3.070000e-27 134.0
22 TraesCS5A01G022100 chr3D 92.126 127 7 2 4260 4383 120527397 120527523 5.030000e-40 176.0
23 TraesCS5A01G022100 chr3D 78.761 113 18 5 4782 4888 346337615 346337727 2.440000e-08 71.3
24 TraesCS5A01G022100 chrUn 89.764 127 9 3 4260 4383 379040833 379040708 5.060000e-35 159.0
25 TraesCS5A01G022100 chrUn 86.047 86 6 4 4351 4436 3908015 3908094 2.420000e-13 87.9
26 TraesCS5A01G022100 chr4A 89.764 127 9 3 4260 4383 635820928 635820803 5.060000e-35 159.0
27 TraesCS5A01G022100 chr2B 89.764 127 9 3 4260 4383 758940713 758940588 5.060000e-35 159.0
28 TraesCS5A01G022100 chr2B 98.113 53 1 0 3668 3720 702038712 702038764 5.210000e-15 93.5
29 TraesCS5A01G022100 chr2B 80.870 115 12 7 4750 4858 596079397 596079507 1.130000e-11 82.4
30 TraesCS5A01G022100 chr2A 90.323 124 9 2 4260 4380 724128984 724129107 5.060000e-35 159.0
31 TraesCS5A01G022100 chr6D 88.550 131 11 3 4260 4387 430741275 430741146 6.550000e-34 156.0
32 TraesCS5A01G022100 chr1B 93.407 91 6 0 3667 3757 128745595 128745685 8.530000e-28 135.0
33 TraesCS5A01G022100 chr1B 84.884 86 7 4 4351 4436 90855434 90855513 1.130000e-11 82.4
34 TraesCS5A01G022100 chr1D 100.000 31 0 0 4828 4858 486465182 486465152 1.900000e-04 58.4
35 TraesCS5A01G022100 chr6A 92.683 41 0 3 4783 4821 496587597 496587558 6.830000e-04 56.5


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 TraesCS5A01G022100 chr5A 17829240 17834127 4887 False 3098.333333 9027 93.46400 1 4888 3 chr5A.!!$F2 4887
1 TraesCS5A01G022100 chr5D 25307065 25312624 5559 True 3572.000000 6837 91.21500 1 4744 2 chr5D.!!$R2 4743
2 TraesCS5A01G022100 chr5B 17970251 17975439 5188 False 1458.500000 2601 92.89725 2 4574 4 chr5B.!!$F2 4572

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
742 851 0.100325 TTGAACCTTGTTGCGTGCAG 59.900 50.0 0.0 0.0 0.00 4.41 F
1793 1989 0.318955 AGGAAAAGCAATGCGTGTGC 60.319 50.0 0.0 0.0 42.55 4.57 F
2313 2517 0.829602 TCGAATGCCCCCAAAGCAAA 60.830 50.0 0.0 0.0 44.83 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1994 1.086696 CGACATTGATTCAAGGCCGT 58.913 50.0 10.89 0.0 0.00 5.68 R
3100 3343 1.533187 ATAATGCCCCTGATGGACCA 58.467 50.0 0.00 0.0 35.39 4.02 R
4113 4357 0.178953 AACTCCAGCCCTGCAAACAT 60.179 50.0 0.00 0.0 0.00 2.71 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
48 50 2.840203 CTAGGGGTGGAAGGGAGGCA 62.840 65.000 0.00 0.00 0.00 4.75
144 146 4.436998 GACGACACCAGCCTCGGG 62.437 72.222 0.00 0.00 34.07 5.14
383 387 4.204891 CGTTTAGCGGCGCTTCGG 62.205 66.667 40.77 22.00 40.44 4.30
438 443 4.084287 GGATTTTCCCCGAGTTAAACCTT 58.916 43.478 0.00 0.00 0.00 3.50
443 448 1.268625 CCCCGAGTTAAACCTTGCAAC 59.731 52.381 0.00 0.00 0.00 4.17
457 463 3.249799 CCTTGCAACGTTGTTATCTGTCA 59.750 43.478 27.78 12.75 0.00 3.58
499 510 6.799925 CACGACAACCAATTGGAGTATTTAAC 59.200 38.462 31.22 13.29 40.42 2.01
581 688 4.591321 TGCTTAACCTCCCATGAAATCT 57.409 40.909 0.00 0.00 0.00 2.40
608 715 4.223032 TCTCCCTCAAGATAAACCTCACAC 59.777 45.833 0.00 0.00 0.00 3.82
707 816 6.266558 ACATACATACACACACCCAAACAAAT 59.733 34.615 0.00 0.00 0.00 2.32
742 851 0.100325 TTGAACCTTGTTGCGTGCAG 59.900 50.000 0.00 0.00 0.00 4.41
774 893 6.885922 GACTAGTCCATTGTATGTAAACCCT 58.114 40.000 12.13 0.00 0.00 4.34
777 896 8.483758 ACTAGTCCATTGTATGTAAACCCTAAG 58.516 37.037 0.00 0.00 0.00 2.18
783 902 5.968676 TGTATGTAAACCCTAAGCCTCAT 57.031 39.130 0.00 0.00 0.00 2.90
804 926 2.035832 TGGCTAAGCAAAAAGAGGCAAC 59.964 45.455 0.00 0.00 41.04 4.17
1220 1388 1.300620 GGGGTTTTGGTTGCTTCGC 60.301 57.895 0.00 0.00 0.00 4.70
1281 1449 4.789012 TTGAATGCTTTCTTGGATGTCC 57.211 40.909 12.96 0.00 32.78 4.02
1325 1493 3.491964 GGAATATTTTGCGGGGTTTAGGC 60.492 47.826 0.00 0.00 0.00 3.93
1326 1494 1.096416 TATTTTGCGGGGTTTAGGCG 58.904 50.000 0.00 0.00 0.00 5.52
1327 1495 2.220615 ATTTTGCGGGGTTTAGGCGC 62.221 55.000 0.00 0.00 0.00 6.53
1380 1558 1.202794 TGGGGTTTAGGTTGGTTCGTC 60.203 52.381 0.00 0.00 0.00 4.20
1383 1561 2.486013 GGGTTTAGGTTGGTTCGTCTGT 60.486 50.000 0.00 0.00 0.00 3.41
1411 1589 2.460027 AACCCTAGGTGGTTTCGCT 58.540 52.632 8.29 0.00 46.45 4.93
1440 1618 6.256053 TCTTGCTCCCTTTAGGATGAAATTT 58.744 36.000 0.00 0.00 46.33 1.82
1493 1676 2.086054 AATGTCGACTCTGTTCCTGC 57.914 50.000 17.92 0.00 0.00 4.85
1515 1699 4.668289 CGTTGCTTTTACTGTTTTGGTCT 58.332 39.130 0.00 0.00 0.00 3.85
1562 1746 8.246908 TGTTCACGTTTGTGTCTATTATTAGG 57.753 34.615 0.00 0.00 46.49 2.69
1563 1747 8.089597 TGTTCACGTTTGTGTCTATTATTAGGA 58.910 33.333 0.00 0.00 46.49 2.94
1591 1778 1.301293 GCTCTGGTTGGAGGGAAGG 59.699 63.158 0.00 0.00 34.21 3.46
1592 1779 1.201429 GCTCTGGTTGGAGGGAAGGA 61.201 60.000 0.00 0.00 34.21 3.36
1757 1949 8.047413 GGAAAAGTATTATGTTTCCCTTTCGA 57.953 34.615 3.50 0.00 42.97 3.71
1792 1988 1.267806 AGAGGAAAAGCAATGCGTGTG 59.732 47.619 0.00 0.00 0.00 3.82
1793 1989 0.318955 AGGAAAAGCAATGCGTGTGC 60.319 50.000 0.00 0.00 42.55 4.57
1794 1990 1.284297 GGAAAAGCAATGCGTGTGCC 61.284 55.000 0.00 0.00 43.27 5.01
1795 1991 1.284297 GAAAAGCAATGCGTGTGCCC 61.284 55.000 0.00 0.00 43.27 5.36
1796 1992 1.747325 AAAAGCAATGCGTGTGCCCT 61.747 50.000 0.00 0.00 43.27 5.19
1797 1993 1.747325 AAAGCAATGCGTGTGCCCTT 61.747 50.000 0.00 2.50 43.27 3.95
1798 1994 0.893270 AAGCAATGCGTGTGCCCTTA 60.893 50.000 0.00 0.00 43.27 2.69
1799 1995 1.154035 GCAATGCGTGTGCCCTTAC 60.154 57.895 0.00 0.00 41.78 2.34
1800 1996 1.134487 CAATGCGTGTGCCCTTACG 59.866 57.895 0.00 0.00 41.78 3.18
1801 1997 2.038269 AATGCGTGTGCCCTTACGG 61.038 57.895 0.00 0.00 41.78 4.02
1881 2077 2.157668 GCGCATCCACTGTTAATATCCG 59.842 50.000 0.30 0.00 0.00 4.18
1905 2101 2.584418 CGCTGTGAGAGGATGCGG 60.584 66.667 0.00 0.00 42.46 5.69
1988 2184 3.382048 AGGACTAGAAACGGTGACAAC 57.618 47.619 0.00 0.00 0.00 3.32
1996 2192 2.279851 CGGTGACAACGGCAGTCA 60.280 61.111 4.57 3.21 43.23 3.41
2070 2269 3.701664 AGGATTCAAGGAAACATCCCAC 58.298 45.455 0.00 0.00 0.00 4.61
2089 2288 6.837312 TCCCACCCATTGTATCACTTATTAG 58.163 40.000 0.00 0.00 0.00 1.73
2261 2464 6.470557 TCGTTCCAGTAACTTAATTTTCCG 57.529 37.500 0.00 0.00 35.81 4.30
2271 2474 9.074576 AGTAACTTAATTTTCCGTTGGAATCTT 57.925 29.630 0.00 0.00 41.71 2.40
2277 2480 5.952526 TTTTCCGTTGGAATCTTAACTCC 57.047 39.130 0.00 0.00 41.71 3.85
2313 2517 0.829602 TCGAATGCCCCCAAAGCAAA 60.830 50.000 0.00 0.00 44.83 3.68
2335 2539 8.938906 GCAAATTTTCTATTGATTGATGGTGTT 58.061 29.630 0.00 0.00 0.00 3.32
2542 2746 4.906065 TTATTCATCCTCACATGCTTGC 57.094 40.909 0.00 0.00 0.00 4.01
2550 2754 1.884579 CTCACATGCTTGCTTCTTGGT 59.115 47.619 0.00 0.00 0.00 3.67
2572 2776 5.646793 GGTAAAAACATAGAACAGGACCTCC 59.353 44.000 0.00 0.00 0.00 4.30
3346 3589 2.634940 CAAGAGGAGGACCAAGAAGACA 59.365 50.000 0.00 0.00 38.94 3.41
3451 3694 4.818314 CCTCTAGGGCCCAAGACT 57.182 61.111 27.56 4.81 0.00 3.24
3604 3847 1.515088 CGAGAACGAGCACGAGCAT 60.515 57.895 11.40 0.00 45.49 3.79
3903 4146 1.339631 TGCTATGTTTTCCTGTCCCCG 60.340 52.381 0.00 0.00 0.00 5.73
3988 4232 0.321919 TGATCTTGGCACTGCTGACC 60.322 55.000 0.00 0.00 0.00 4.02
4068 4312 1.415289 CTCTCTACCCAGCATGCATGA 59.585 52.381 30.64 7.11 31.97 3.07
4113 4357 6.374333 GCATCTAAAAACACTGGATCAGGTTA 59.626 38.462 0.00 0.00 35.51 2.85
4245 4508 3.957497 AGAAGTAGTCTCTACCCAGCATG 59.043 47.826 3.69 0.00 0.00 4.06
4246 4509 3.671740 AGTAGTCTCTACCCAGCATGA 57.328 47.619 0.00 0.00 39.69 3.07
4247 4510 3.561143 AGTAGTCTCTACCCAGCATGAG 58.439 50.000 0.00 0.00 39.69 2.90
4249 4512 2.106566 AGTCTCTACCCAGCATGAGTG 58.893 52.381 0.00 0.00 39.69 3.51
4250 4513 2.103373 GTCTCTACCCAGCATGAGTGA 58.897 52.381 0.00 0.00 39.69 3.41
4251 4514 2.697751 GTCTCTACCCAGCATGAGTGAT 59.302 50.000 0.00 0.00 39.69 3.06
4252 4515 2.961741 TCTCTACCCAGCATGAGTGATC 59.038 50.000 0.00 0.00 39.69 2.92
4254 4517 2.432146 TCTACCCAGCATGAGTGATCAC 59.568 50.000 18.47 18.47 39.69 3.06
4296 4559 3.004862 TGTTGTGTATGCTGATGCTCAG 58.995 45.455 8.34 8.34 46.90 3.35
4413 4676 4.661222 TGCAATCTTCAAGTCCCACATAA 58.339 39.130 0.00 0.00 0.00 1.90
4426 4689 4.396166 GTCCCACATAAGTTCCAACATCTG 59.604 45.833 0.00 0.00 0.00 2.90
4475 4738 3.404869 TCTCTCAGGGCCATCTCTTTA 57.595 47.619 6.18 0.00 0.00 1.85
4622 5702 6.130298 TGGTACCTAAAAATCAATGCATCG 57.870 37.500 14.36 0.00 0.00 3.84
4628 5708 5.286797 CCTAAAAATCAATGCATCGTGTGTG 59.713 40.000 0.00 0.00 0.00 3.82
4643 5723 1.068588 TGTGTGCTCCAGTACAGTGAC 59.931 52.381 0.00 0.00 41.15 3.67
4652 5732 3.574396 TCCAGTACAGTGACCAGAAAGAG 59.426 47.826 0.00 0.00 0.00 2.85
4744 5853 4.778579 AGCATCAATGATTCAGCACTACT 58.221 39.130 6.77 0.00 0.00 2.57
4745 5854 5.922053 AGCATCAATGATTCAGCACTACTA 58.078 37.500 6.77 0.00 0.00 1.82
4746 5855 5.757320 AGCATCAATGATTCAGCACTACTAC 59.243 40.000 6.77 0.00 0.00 2.73
4747 5856 5.049818 GCATCAATGATTCAGCACTACTACC 60.050 44.000 0.00 0.00 0.00 3.18
4748 5857 5.675684 TCAATGATTCAGCACTACTACCA 57.324 39.130 0.00 0.00 0.00 3.25
4749 5858 6.048732 TCAATGATTCAGCACTACTACCAA 57.951 37.500 0.00 0.00 0.00 3.67
4750 5859 6.472016 TCAATGATTCAGCACTACTACCAAA 58.528 36.000 0.00 0.00 0.00 3.28
4751 5860 6.595326 TCAATGATTCAGCACTACTACCAAAG 59.405 38.462 0.00 0.00 0.00 2.77
4752 5861 4.832248 TGATTCAGCACTACTACCAAAGG 58.168 43.478 0.00 0.00 0.00 3.11
4753 5862 2.762535 TCAGCACTACTACCAAAGGC 57.237 50.000 0.00 0.00 0.00 4.35
4754 5863 1.278127 TCAGCACTACTACCAAAGGCC 59.722 52.381 0.00 0.00 0.00 5.19
4755 5864 1.003118 CAGCACTACTACCAAAGGCCA 59.997 52.381 5.01 0.00 0.00 5.36
4756 5865 1.702957 AGCACTACTACCAAAGGCCAA 59.297 47.619 5.01 0.00 0.00 4.52
4757 5866 1.810755 GCACTACTACCAAAGGCCAAC 59.189 52.381 5.01 0.00 0.00 3.77
4758 5867 2.552373 GCACTACTACCAAAGGCCAACT 60.552 50.000 5.01 0.00 0.00 3.16
4759 5868 3.751518 CACTACTACCAAAGGCCAACTT 58.248 45.455 5.01 0.00 42.52 2.66
4760 5869 3.751698 CACTACTACCAAAGGCCAACTTC 59.248 47.826 5.01 0.00 38.85 3.01
4761 5870 3.393278 ACTACTACCAAAGGCCAACTTCA 59.607 43.478 5.01 0.00 38.85 3.02
4762 5871 3.306472 ACTACCAAAGGCCAACTTCAA 57.694 42.857 5.01 0.00 38.85 2.69
4763 5872 2.956333 ACTACCAAAGGCCAACTTCAAC 59.044 45.455 5.01 0.00 38.85 3.18
4764 5873 1.859302 ACCAAAGGCCAACTTCAACA 58.141 45.000 5.01 0.00 38.85 3.33
4765 5874 1.480545 ACCAAAGGCCAACTTCAACAC 59.519 47.619 5.01 0.00 38.85 3.32
4766 5875 1.480137 CCAAAGGCCAACTTCAACACA 59.520 47.619 5.01 0.00 38.85 3.72
4767 5876 2.539476 CAAAGGCCAACTTCAACACAC 58.461 47.619 5.01 0.00 38.85 3.82
4768 5877 0.738389 AAGGCCAACTTCAACACACG 59.262 50.000 5.01 0.00 32.85 4.49
4769 5878 0.107410 AGGCCAACTTCAACACACGA 60.107 50.000 5.01 0.00 0.00 4.35
4770 5879 0.028902 GGCCAACTTCAACACACGAC 59.971 55.000 0.00 0.00 0.00 4.34
4771 5880 0.028902 GCCAACTTCAACACACGACC 59.971 55.000 0.00 0.00 0.00 4.79
4772 5881 1.374560 CCAACTTCAACACACGACCA 58.625 50.000 0.00 0.00 0.00 4.02
4773 5882 1.063469 CCAACTTCAACACACGACCAC 59.937 52.381 0.00 0.00 0.00 4.16
4774 5883 1.735018 CAACTTCAACACACGACCACA 59.265 47.619 0.00 0.00 0.00 4.17
4775 5884 2.102070 ACTTCAACACACGACCACAA 57.898 45.000 0.00 0.00 0.00 3.33
4776 5885 2.428491 ACTTCAACACACGACCACAAA 58.572 42.857 0.00 0.00 0.00 2.83
4777 5886 3.013921 ACTTCAACACACGACCACAAAT 58.986 40.909 0.00 0.00 0.00 2.32
4778 5887 4.193090 ACTTCAACACACGACCACAAATA 58.807 39.130 0.00 0.00 0.00 1.40
4779 5888 4.819630 ACTTCAACACACGACCACAAATAT 59.180 37.500 0.00 0.00 0.00 1.28
4780 5889 5.298276 ACTTCAACACACGACCACAAATATT 59.702 36.000 0.00 0.00 0.00 1.28
4781 5890 5.759506 TCAACACACGACCACAAATATTT 57.240 34.783 0.00 0.00 0.00 1.40
4782 5891 5.515184 TCAACACACGACCACAAATATTTG 58.485 37.500 23.60 23.60 43.62 2.32
4783 5892 4.497473 ACACACGACCACAAATATTTGG 57.503 40.909 27.43 16.83 42.34 3.28
4789 5898 1.822371 ACCACAAATATTTGGTCCGGC 59.178 47.619 27.43 0.00 42.86 6.13
4790 5899 1.136110 CCACAAATATTTGGTCCGGCC 59.864 52.381 27.43 1.41 42.34 6.13
4791 5900 1.099689 ACAAATATTTGGTCCGGCCG 58.900 50.000 27.43 21.04 42.34 6.13
4792 5901 0.248866 CAAATATTTGGTCCGGCCGC 60.249 55.000 22.85 6.98 41.21 6.53
4793 5902 1.720694 AAATATTTGGTCCGGCCGCG 61.721 55.000 22.85 13.93 41.21 6.46
4794 5903 2.879813 AATATTTGGTCCGGCCGCGT 62.880 55.000 22.85 1.88 41.21 6.01
4806 5915 4.675029 CCGCGTCCGTTTGAGGGT 62.675 66.667 4.92 0.00 0.00 4.34
4807 5916 2.259204 CGCGTCCGTTTGAGGGTA 59.741 61.111 0.00 0.00 0.00 3.69
4808 5917 1.373246 CGCGTCCGTTTGAGGGTAA 60.373 57.895 0.00 0.00 0.00 2.85
4809 5918 0.945265 CGCGTCCGTTTGAGGGTAAA 60.945 55.000 0.00 0.00 0.00 2.01
4810 5919 0.514255 GCGTCCGTTTGAGGGTAAAC 59.486 55.000 0.00 0.00 37.23 2.01
4811 5920 1.875157 GCGTCCGTTTGAGGGTAAACT 60.875 52.381 0.00 0.00 38.17 2.66
4812 5921 1.796459 CGTCCGTTTGAGGGTAAACTG 59.204 52.381 0.00 0.00 38.17 3.16
4813 5922 2.546373 CGTCCGTTTGAGGGTAAACTGA 60.546 50.000 0.00 0.00 38.17 3.41
4814 5923 2.804527 GTCCGTTTGAGGGTAAACTGAC 59.195 50.000 9.15 9.15 42.88 3.51
4815 5924 2.435069 TCCGTTTGAGGGTAAACTGACA 59.565 45.455 0.00 0.00 38.17 3.58
4816 5925 3.118334 TCCGTTTGAGGGTAAACTGACAA 60.118 43.478 0.00 0.00 38.17 3.18
4817 5926 3.628487 CCGTTTGAGGGTAAACTGACAAA 59.372 43.478 0.00 0.00 38.17 2.83
4818 5927 4.096682 CCGTTTGAGGGTAAACTGACAAAA 59.903 41.667 0.00 0.00 38.17 2.44
4819 5928 5.393243 CCGTTTGAGGGTAAACTGACAAAAA 60.393 40.000 0.00 0.00 38.17 1.94
4820 5929 6.270064 CGTTTGAGGGTAAACTGACAAAAAT 58.730 36.000 0.00 0.00 38.17 1.82
4821 5930 6.416750 CGTTTGAGGGTAAACTGACAAAAATC 59.583 38.462 0.00 0.00 38.17 2.17
4822 5931 5.682943 TGAGGGTAAACTGACAAAAATCG 57.317 39.130 0.00 0.00 0.00 3.34
4823 5932 4.023536 TGAGGGTAAACTGACAAAAATCGC 60.024 41.667 0.00 0.00 0.00 4.58
4824 5933 3.058501 AGGGTAAACTGACAAAAATCGCG 60.059 43.478 0.00 0.00 0.00 5.87
4825 5934 3.231160 GGTAAACTGACAAAAATCGCGG 58.769 45.455 6.13 0.00 0.00 6.46
4826 5935 1.766069 AAACTGACAAAAATCGCGGC 58.234 45.000 6.13 0.00 0.00 6.53
4827 5936 0.039527 AACTGACAAAAATCGCGGCC 60.040 50.000 6.13 0.00 0.00 6.13
4828 5937 1.511887 CTGACAAAAATCGCGGCCG 60.512 57.895 24.05 24.05 0.00 6.13
4829 5938 2.874315 GACAAAAATCGCGGCCGC 60.874 61.111 39.82 39.82 37.85 6.53
4848 5957 1.685302 CGGGAGCAAACGAACAAATG 58.315 50.000 0.00 0.00 0.00 2.32
4849 5958 1.001815 CGGGAGCAAACGAACAAATGT 60.002 47.619 0.00 0.00 0.00 2.71
4850 5959 2.661594 GGGAGCAAACGAACAAATGTC 58.338 47.619 0.00 0.00 0.00 3.06
4851 5960 2.607038 GGGAGCAAACGAACAAATGTCC 60.607 50.000 0.00 0.00 0.00 4.02
4852 5961 2.307049 GAGCAAACGAACAAATGTCCG 58.693 47.619 0.00 0.00 0.00 4.79
4853 5962 1.673920 AGCAAACGAACAAATGTCCGT 59.326 42.857 0.00 0.00 36.77 4.69
4854 5963 2.098443 AGCAAACGAACAAATGTCCGTT 59.902 40.909 4.68 4.68 45.56 4.44
4859 5968 4.358494 ACGAACAAATGTCCGTTTTTCA 57.642 36.364 0.00 0.00 30.41 2.69
4860 5969 4.927422 ACGAACAAATGTCCGTTTTTCAT 58.073 34.783 0.00 0.00 30.41 2.57
4861 5970 5.344884 ACGAACAAATGTCCGTTTTTCATT 58.655 33.333 0.00 0.00 33.94 2.57
4862 5971 5.457473 ACGAACAAATGTCCGTTTTTCATTC 59.543 36.000 0.00 0.00 32.39 2.67
4863 5972 5.385918 CGAACAAATGTCCGTTTTTCATTCG 60.386 40.000 0.00 0.00 32.39 3.34
4864 5973 3.733727 ACAAATGTCCGTTTTTCATTCGC 59.266 39.130 0.00 0.00 32.39 4.70
4865 5974 2.629639 ATGTCCGTTTTTCATTCGCC 57.370 45.000 0.00 0.00 0.00 5.54
4866 5975 0.236187 TGTCCGTTTTTCATTCGCCG 59.764 50.000 0.00 0.00 0.00 6.46
4867 5976 1.063412 GTCCGTTTTTCATTCGCCGC 61.063 55.000 0.00 0.00 0.00 6.53
4868 5977 1.799916 CCGTTTTTCATTCGCCGCC 60.800 57.895 0.00 0.00 0.00 6.13
4869 5978 2.143458 CGTTTTTCATTCGCCGCCG 61.143 57.895 0.00 0.00 0.00 6.46
4870 5979 1.208103 GTTTTTCATTCGCCGCCGA 59.792 52.632 0.00 0.00 42.66 5.54
4871 5980 1.063412 GTTTTTCATTCGCCGCCGAC 61.063 55.000 0.00 0.00 44.30 4.79
4872 5981 2.501607 TTTTTCATTCGCCGCCGACG 62.502 55.000 0.00 0.00 44.30 5.12
4883 5992 3.861263 GCCGACGCATTTCCGGTC 61.861 66.667 0.00 0.00 44.63 4.79
4884 5993 3.192922 CCGACGCATTTCCGGTCC 61.193 66.667 0.00 0.00 38.55 4.46
4885 5994 2.433491 CGACGCATTTCCGGTCCA 60.433 61.111 0.00 0.00 0.00 4.02
4886 5995 2.030401 CGACGCATTTCCGGTCCAA 61.030 57.895 0.00 0.00 0.00 3.53
4887 5996 1.570347 CGACGCATTTCCGGTCCAAA 61.570 55.000 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 2.042261 GCCTCCCTTCCACCCCTA 59.958 66.667 0.00 0.00 0.00 3.53
48 50 0.247736 GTCAGTCCCGACTTGCTGAT 59.752 55.000 0.00 0.00 40.20 2.90
248 250 0.600057 GGTCTGTAAACGTCCGGACT 59.400 55.000 30.92 16.13 37.19 3.85
261 263 1.272147 GCAAATCTGGGGAAGGTCTGT 60.272 52.381 0.00 0.00 0.00 3.41
327 330 4.158209 TCATCCAACGTCATGCATGAAAAT 59.842 37.500 30.24 15.87 38.75 1.82
328 331 3.505293 TCATCCAACGTCATGCATGAAAA 59.495 39.130 30.24 12.61 38.75 2.29
383 387 1.355210 CACCTCCAACGTTGTGCAC 59.645 57.895 25.63 10.75 0.00 4.57
438 443 5.872070 TCATATGACAGATAACAACGTTGCA 59.128 36.000 27.61 16.30 0.00 4.08
443 448 9.463443 TTGTATCTCATATGACAGATAACAACG 57.537 33.333 13.47 0.00 34.17 4.10
457 463 5.106442 TGTCGTGCGTTTTGTATCTCATAT 58.894 37.500 0.00 0.00 0.00 1.78
471 482 0.816018 TCCAATTGGTTGTCGTGCGT 60.816 50.000 23.76 0.00 36.34 5.24
499 510 7.333174 GGTTATGTTTGGGTAAATTTGACATGG 59.667 37.037 0.00 0.00 0.00 3.66
581 688 6.715264 GTGAGGTTTATCTTGAGGGAGAAAAA 59.285 38.462 0.00 0.00 29.99 1.94
608 715 9.589111 CCACATGAGAAGATAAGATGATGATAG 57.411 37.037 0.00 0.00 0.00 2.08
680 789 4.625607 TTGGGTGTGTGTATGTATGTGA 57.374 40.909 0.00 0.00 0.00 3.58
689 798 7.171630 AGTTTTATTTGTTTGGGTGTGTGTA 57.828 32.000 0.00 0.00 0.00 2.90
693 802 5.525745 GGGAAGTTTTATTTGTTTGGGTGTG 59.474 40.000 0.00 0.00 0.00 3.82
695 804 5.060506 GGGGAAGTTTTATTTGTTTGGGTG 58.939 41.667 0.00 0.00 0.00 4.61
738 847 3.449227 CTAGTCCCGTCGGCTGCA 61.449 66.667 5.50 0.00 0.00 4.41
750 859 6.885922 AGGGTTTACATACAATGGACTAGTC 58.114 40.000 14.87 14.87 33.60 2.59
752 861 7.441458 GCTTAGGGTTTACATACAATGGACTAG 59.559 40.741 0.00 0.00 33.60 2.57
753 862 7.277396 GCTTAGGGTTTACATACAATGGACTA 58.723 38.462 0.00 0.00 33.60 2.59
765 878 3.644966 CCATGAGGCTTAGGGTTTACA 57.355 47.619 1.23 0.00 0.00 2.41
783 902 1.993956 TGCCTCTTTTTGCTTAGCCA 58.006 45.000 0.29 0.00 0.00 4.75
804 926 0.593128 CCGTGCTTGGAGGACAAAAG 59.407 55.000 0.71 0.00 36.23 2.27
805 927 0.106918 ACCGTGCTTGGAGGACAAAA 60.107 50.000 1.60 0.00 36.23 2.44
806 928 0.759959 TACCGTGCTTGGAGGACAAA 59.240 50.000 1.60 0.00 36.23 2.83
846 988 2.060004 TACGATTGAGCGGCGAGAGG 62.060 60.000 12.98 0.00 35.12 3.69
847 989 0.248498 TTACGATTGAGCGGCGAGAG 60.248 55.000 12.98 0.00 35.12 3.20
848 990 0.524816 GTTACGATTGAGCGGCGAGA 60.525 55.000 12.98 0.00 35.12 4.04
849 991 1.480219 GGTTACGATTGAGCGGCGAG 61.480 60.000 12.98 0.00 35.12 5.03
850 992 1.517694 GGTTACGATTGAGCGGCGA 60.518 57.895 12.98 0.00 35.12 5.54
851 993 2.522638 GGGTTACGATTGAGCGGCG 61.523 63.158 0.51 0.51 35.12 6.46
852 994 2.178235 GGGGTTACGATTGAGCGGC 61.178 63.158 0.00 0.00 35.12 6.53
853 995 0.391927 TTGGGGTTACGATTGAGCGG 60.392 55.000 0.00 0.00 35.12 5.52
854 996 0.725117 GTTGGGGTTACGATTGAGCG 59.275 55.000 0.00 0.00 37.29 5.03
855 997 0.725117 CGTTGGGGTTACGATTGAGC 59.275 55.000 0.00 0.00 41.33 4.26
968 1123 4.104102 GGAGTGGAGAGAGGAGATAGAGAA 59.896 50.000 0.00 0.00 0.00 2.87
1125 1293 4.038080 CAACCGGAACAAGCGGGC 62.038 66.667 9.46 0.00 0.00 6.13
1201 1369 2.425562 CGAAGCAACCAAAACCCCT 58.574 52.632 0.00 0.00 0.00 4.79
1281 1449 3.788766 CGAAAGCGCAACCCGGAG 61.789 66.667 11.47 0.00 37.44 4.63
1380 1558 5.186198 CACCTAGGGTTCAAGGAATTACAG 58.814 45.833 14.81 0.00 36.66 2.74
1383 1561 4.180723 ACCACCTAGGGTTCAAGGAATTA 58.819 43.478 14.81 0.00 43.89 1.40
1411 1589 2.714250 TCCTAAAGGGAGCAAGAAACCA 59.286 45.455 0.00 0.00 39.58 3.67
1440 1618 6.405731 CCTTTGTGTTCCAAACATTCAAGAGA 60.406 38.462 0.00 0.00 44.35 3.10
1478 1661 0.318699 CAACGCAGGAACAGAGTCGA 60.319 55.000 0.00 0.00 0.00 4.20
1481 1664 0.179045 AAGCAACGCAGGAACAGAGT 60.179 50.000 0.00 0.00 0.00 3.24
1493 1676 4.668289 AGACCAAAACAGTAAAAGCAACG 58.332 39.130 0.00 0.00 0.00 4.10
1562 1746 5.028549 TCCAACCAGAGCAATATTCTCTC 57.971 43.478 11.99 9.25 38.76 3.20
1563 1747 4.141528 CCTCCAACCAGAGCAATATTCTCT 60.142 45.833 10.06 10.06 41.28 3.10
1591 1778 3.915437 TGCTCGGGAAATTGAAAACTC 57.085 42.857 0.00 0.00 0.00 3.01
1592 1779 4.871933 ATTGCTCGGGAAATTGAAAACT 57.128 36.364 0.00 0.00 0.00 2.66
1757 1949 2.179427 TCCTCTTCCGTGACATCACAT 58.821 47.619 12.32 0.00 46.75 3.21
1795 1991 3.242413 CGACATTGATTCAAGGCCGTAAG 60.242 47.826 10.89 0.00 0.00 2.34
1796 1992 2.675844 CGACATTGATTCAAGGCCGTAA 59.324 45.455 10.89 0.00 0.00 3.18
1797 1993 2.093921 TCGACATTGATTCAAGGCCGTA 60.094 45.455 16.97 4.36 0.00 4.02
1798 1994 1.086696 CGACATTGATTCAAGGCCGT 58.913 50.000 10.89 0.00 0.00 5.68
1799 1995 1.368641 TCGACATTGATTCAAGGCCG 58.631 50.000 12.55 12.55 0.00 6.13
1800 1996 2.684881 ACATCGACATTGATTCAAGGCC 59.315 45.455 10.77 0.00 0.00 5.19
1801 1997 3.688272 CACATCGACATTGATTCAAGGC 58.312 45.455 10.77 3.73 0.00 4.35
1802 1998 3.127376 TGCACATCGACATTGATTCAAGG 59.873 43.478 9.38 9.38 0.00 3.61
1881 2077 2.328099 CCTCTCACAGCGGCCAAAC 61.328 63.158 2.24 0.00 0.00 2.93
1905 2101 7.012138 ACAATATCTCTGTCACAATCTTGCATC 59.988 37.037 0.00 0.00 0.00 3.91
1942 2138 6.345096 AGTTTTCCACCCAAATTGATAGTG 57.655 37.500 0.00 0.00 0.00 2.74
1988 2184 1.376543 AATTGAGATGCTGACTGCCG 58.623 50.000 1.50 0.00 42.00 5.69
1996 2192 3.194968 CCTTGAGGCAAAATTGAGATGCT 59.805 43.478 0.00 0.00 39.94 3.79
2070 2269 8.299570 GCATTTCCTAATAAGTGATACAATGGG 58.700 37.037 0.00 0.00 0.00 4.00
2089 2288 5.357878 TGAGGAACATAACTGATGCATTTCC 59.642 40.000 12.61 12.61 39.39 3.13
2261 2464 7.331791 AGTGATACTGGAGTTAAGATTCCAAC 58.668 38.462 5.18 1.53 40.68 3.77
2271 2474 4.901197 TTGGCAAGTGATACTGGAGTTA 57.099 40.909 0.00 0.00 0.00 2.24
2277 2480 4.944962 TTCGAATTGGCAAGTGATACTG 57.055 40.909 4.31 0.00 0.00 2.74
2313 2517 9.028284 AGTCAACACCATCAATCAATAGAAAAT 57.972 29.630 0.00 0.00 0.00 1.82
2444 2648 8.531146 CAATATGGTTCCCAAACAAAGAGTATT 58.469 33.333 0.00 0.00 36.95 1.89
2445 2649 7.363793 GCAATATGGTTCCCAAACAAAGAGTAT 60.364 37.037 0.00 0.00 36.95 2.12
2542 2746 8.290325 GTCCTGTTCTATGTTTTTACCAAGAAG 58.710 37.037 0.00 0.00 0.00 2.85
2550 2754 6.442541 TGGAGGTCCTGTTCTATGTTTTTA 57.557 37.500 0.00 0.00 36.82 1.52
2572 2776 6.917533 ACTGCAAGGAAATCTACTTTTCATG 58.082 36.000 0.00 0.00 39.30 3.07
2635 2877 4.987912 CACGTTTAGACAAAATGGCCAAAT 59.012 37.500 10.96 0.00 38.24 2.32
3100 3343 1.533187 ATAATGCCCCTGATGGACCA 58.467 50.000 0.00 0.00 35.39 4.02
3346 3589 2.040178 GGGACCTCCTCGTTCACATAT 58.960 52.381 0.00 0.00 35.95 1.78
3604 3847 4.335594 CACATATCCGAGTGTGAGTACTCA 59.664 45.833 21.74 21.74 46.58 3.41
3903 4146 2.459934 CCTGCAAACAAAACTCGGAAC 58.540 47.619 0.00 0.00 0.00 3.62
4068 4312 3.842732 CATGTCAATGCTGTGTGTGAT 57.157 42.857 0.00 0.00 0.00 3.06
4113 4357 0.178953 AACTCCAGCCCTGCAAACAT 60.179 50.000 0.00 0.00 0.00 2.71
4242 4505 4.628766 CAGTAACCTGTGTGATCACTCATG 59.371 45.833 26.06 24.53 44.14 3.07
4245 4508 3.258372 TCCAGTAACCTGTGTGATCACTC 59.742 47.826 25.55 22.03 44.14 3.51
4246 4509 3.239449 TCCAGTAACCTGTGTGATCACT 58.761 45.455 25.55 7.77 44.14 3.41
4247 4510 3.006967 ACTCCAGTAACCTGTGTGATCAC 59.993 47.826 19.27 19.27 44.08 3.06
4249 4512 3.368531 GGACTCCAGTAACCTGTGTGATC 60.369 52.174 0.00 0.00 36.95 2.92
4250 4513 2.567615 GGACTCCAGTAACCTGTGTGAT 59.432 50.000 0.00 0.00 36.95 3.06
4251 4514 1.968493 GGACTCCAGTAACCTGTGTGA 59.032 52.381 0.00 0.00 36.95 3.58
4252 4515 1.691976 TGGACTCCAGTAACCTGTGTG 59.308 52.381 0.00 0.00 36.95 3.82
4254 4517 2.303022 ACATGGACTCCAGTAACCTGTG 59.697 50.000 3.62 0.00 36.75 3.66
4426 4689 6.037610 CAGGGAACATCTACTAATCTGCAAAC 59.962 42.308 0.00 0.00 0.00 2.93
4606 5686 4.620609 GCACACACGATGCATTGATTTTTA 59.379 37.500 21.12 0.00 42.88 1.52
4622 5702 1.068588 TCACTGTACTGGAGCACACAC 59.931 52.381 4.66 0.00 0.00 3.82
4628 5708 1.257743 TCTGGTCACTGTACTGGAGC 58.742 55.000 4.66 8.57 0.00 4.70
4643 5723 0.103937 CTCGGCTAGCCTCTTTCTGG 59.896 60.000 30.55 13.07 0.00 3.86
4744 5853 2.691011 GTGTTGAAGTTGGCCTTTGGTA 59.309 45.455 3.32 0.00 32.03 3.25
4745 5854 1.480545 GTGTTGAAGTTGGCCTTTGGT 59.519 47.619 3.32 0.00 32.03 3.67
4746 5855 1.480137 TGTGTTGAAGTTGGCCTTTGG 59.520 47.619 3.32 0.00 32.03 3.28
4747 5856 2.539476 GTGTGTTGAAGTTGGCCTTTG 58.461 47.619 3.32 0.00 32.03 2.77
4748 5857 1.134175 CGTGTGTTGAAGTTGGCCTTT 59.866 47.619 3.32 0.00 32.03 3.11
4749 5858 0.738389 CGTGTGTTGAAGTTGGCCTT 59.262 50.000 3.32 0.00 35.59 4.35
4750 5859 0.107410 TCGTGTGTTGAAGTTGGCCT 60.107 50.000 3.32 0.00 0.00 5.19
4751 5860 0.028902 GTCGTGTGTTGAAGTTGGCC 59.971 55.000 0.00 0.00 0.00 5.36
4752 5861 0.028902 GGTCGTGTGTTGAAGTTGGC 59.971 55.000 0.00 0.00 0.00 4.52
4753 5862 1.063469 GTGGTCGTGTGTTGAAGTTGG 59.937 52.381 0.00 0.00 0.00 3.77
4754 5863 1.735018 TGTGGTCGTGTGTTGAAGTTG 59.265 47.619 0.00 0.00 0.00 3.16
4755 5864 2.102070 TGTGGTCGTGTGTTGAAGTT 57.898 45.000 0.00 0.00 0.00 2.66
4756 5865 2.102070 TTGTGGTCGTGTGTTGAAGT 57.898 45.000 0.00 0.00 0.00 3.01
4757 5866 3.691049 ATTTGTGGTCGTGTGTTGAAG 57.309 42.857 0.00 0.00 0.00 3.02
4758 5867 5.759506 AATATTTGTGGTCGTGTGTTGAA 57.240 34.783 0.00 0.00 0.00 2.69
4759 5868 5.506483 CCAAATATTTGTGGTCGTGTGTTGA 60.506 40.000 23.24 0.00 36.45 3.18
4760 5869 4.679197 CCAAATATTTGTGGTCGTGTGTTG 59.321 41.667 23.24 3.32 36.45 3.33
4761 5870 4.339814 ACCAAATATTTGTGGTCGTGTGTT 59.660 37.500 23.24 0.00 45.18 3.32
4762 5871 3.886505 ACCAAATATTTGTGGTCGTGTGT 59.113 39.130 23.24 10.28 45.18 3.72
4763 5872 4.497473 ACCAAATATTTGTGGTCGTGTG 57.503 40.909 23.24 9.74 45.18 3.82
4770 5879 1.136110 GGCCGGACCAAATATTTGTGG 59.864 52.381 23.24 19.14 41.00 4.17
4771 5880 1.202245 CGGCCGGACCAAATATTTGTG 60.202 52.381 20.10 17.42 39.03 3.33
4772 5881 1.099689 CGGCCGGACCAAATATTTGT 58.900 50.000 20.10 13.36 39.03 2.83
4773 5882 0.248866 GCGGCCGGACCAAATATTTG 60.249 55.000 29.38 19.40 39.03 2.32
4774 5883 1.720694 CGCGGCCGGACCAAATATTT 61.721 55.000 29.38 0.00 39.03 1.40
4775 5884 2.184167 CGCGGCCGGACCAAATATT 61.184 57.895 29.38 0.00 39.03 1.28
4776 5885 2.590575 CGCGGCCGGACCAAATAT 60.591 61.111 29.38 0.00 39.03 1.28
4777 5886 4.085204 ACGCGGCCGGACCAAATA 62.085 61.111 29.38 0.00 39.03 1.40
4789 5898 2.768503 TTACCCTCAAACGGACGCGG 62.769 60.000 12.47 0.00 0.00 6.46
4790 5899 0.945265 TTTACCCTCAAACGGACGCG 60.945 55.000 3.53 3.53 0.00 6.01
4791 5900 0.514255 GTTTACCCTCAAACGGACGC 59.486 55.000 0.00 0.00 0.00 5.19
4792 5901 1.796459 CAGTTTACCCTCAAACGGACG 59.204 52.381 0.00 0.00 42.12 4.79
4793 5902 3.116079 TCAGTTTACCCTCAAACGGAC 57.884 47.619 0.00 0.00 42.12 4.79
4794 5903 2.435069 TGTCAGTTTACCCTCAAACGGA 59.565 45.455 0.00 0.00 42.12 4.69
4795 5904 2.841215 TGTCAGTTTACCCTCAAACGG 58.159 47.619 0.00 0.00 42.12 4.44
4796 5905 4.886247 TTTGTCAGTTTACCCTCAAACG 57.114 40.909 0.00 0.00 42.12 3.60
4797 5906 6.416750 CGATTTTTGTCAGTTTACCCTCAAAC 59.583 38.462 0.00 0.00 38.44 2.93
4798 5907 6.500041 CGATTTTTGTCAGTTTACCCTCAAA 58.500 36.000 0.00 0.00 0.00 2.69
4799 5908 5.506649 GCGATTTTTGTCAGTTTACCCTCAA 60.507 40.000 0.00 0.00 0.00 3.02
4800 5909 4.023536 GCGATTTTTGTCAGTTTACCCTCA 60.024 41.667 0.00 0.00 0.00 3.86
4801 5910 4.473199 GCGATTTTTGTCAGTTTACCCTC 58.527 43.478 0.00 0.00 0.00 4.30
4802 5911 3.058501 CGCGATTTTTGTCAGTTTACCCT 60.059 43.478 0.00 0.00 0.00 4.34
4803 5912 3.231160 CGCGATTTTTGTCAGTTTACCC 58.769 45.455 0.00 0.00 0.00 3.69
4804 5913 3.231160 CCGCGATTTTTGTCAGTTTACC 58.769 45.455 8.23 0.00 0.00 2.85
4805 5914 2.655001 GCCGCGATTTTTGTCAGTTTAC 59.345 45.455 8.23 0.00 0.00 2.01
4806 5915 2.350964 GGCCGCGATTTTTGTCAGTTTA 60.351 45.455 8.23 0.00 0.00 2.01
4807 5916 1.601914 GGCCGCGATTTTTGTCAGTTT 60.602 47.619 8.23 0.00 0.00 2.66
4808 5917 0.039527 GGCCGCGATTTTTGTCAGTT 60.040 50.000 8.23 0.00 0.00 3.16
4809 5918 1.579429 GGCCGCGATTTTTGTCAGT 59.421 52.632 8.23 0.00 0.00 3.41
4810 5919 1.511887 CGGCCGCGATTTTTGTCAG 60.512 57.895 14.67 0.00 0.00 3.51
4811 5920 2.558821 CGGCCGCGATTTTTGTCA 59.441 55.556 14.67 0.00 0.00 3.58
4812 5921 2.874315 GCGGCCGCGATTTTTGTC 60.874 61.111 37.24 5.14 0.00 3.18
4826 5935 4.084888 GTTCGTTTGCTCCCGCGG 62.085 66.667 21.04 21.04 39.65 6.46
4827 5936 2.381665 TTTGTTCGTTTGCTCCCGCG 62.382 55.000 0.00 0.00 39.65 6.46
4828 5937 0.039527 ATTTGTTCGTTTGCTCCCGC 60.040 50.000 0.00 0.00 0.00 6.13
4829 5938 1.001815 ACATTTGTTCGTTTGCTCCCG 60.002 47.619 0.00 0.00 0.00 5.14
4830 5939 2.607038 GGACATTTGTTCGTTTGCTCCC 60.607 50.000 0.00 0.00 0.00 4.30
4831 5940 2.661594 GGACATTTGTTCGTTTGCTCC 58.338 47.619 0.00 0.00 0.00 4.70
4832 5941 2.307049 CGGACATTTGTTCGTTTGCTC 58.693 47.619 3.18 0.00 41.88 4.26
4833 5942 2.399396 CGGACATTTGTTCGTTTGCT 57.601 45.000 3.18 0.00 41.88 3.91
4840 5949 5.609483 GCGAATGAAAAACGGACATTTGTTC 60.609 40.000 0.00 0.00 37.58 3.18
4841 5950 4.208253 GCGAATGAAAAACGGACATTTGTT 59.792 37.500 0.00 0.00 37.58 2.83
4842 5951 3.733727 GCGAATGAAAAACGGACATTTGT 59.266 39.130 0.00 0.00 37.58 2.83
4843 5952 3.121113 GGCGAATGAAAAACGGACATTTG 59.879 43.478 0.00 0.00 38.02 2.32
4844 5953 3.313690 GGCGAATGAAAAACGGACATTT 58.686 40.909 0.00 0.00 34.94 2.32
4845 5954 2.667171 CGGCGAATGAAAAACGGACATT 60.667 45.455 0.00 0.00 37.03 2.71
4846 5955 1.135803 CGGCGAATGAAAAACGGACAT 60.136 47.619 0.00 0.00 0.00 3.06
4847 5956 0.236187 CGGCGAATGAAAAACGGACA 59.764 50.000 0.00 0.00 0.00 4.02
4848 5957 1.063412 GCGGCGAATGAAAAACGGAC 61.063 55.000 12.98 0.00 0.00 4.79
4849 5958 1.208103 GCGGCGAATGAAAAACGGA 59.792 52.632 12.98 0.00 0.00 4.69
4850 5959 1.799916 GGCGGCGAATGAAAAACGG 60.800 57.895 12.98 0.00 0.00 4.44
4851 5960 2.143458 CGGCGGCGAATGAAAAACG 61.143 57.895 29.19 0.00 0.00 3.60
4852 5961 1.063412 GTCGGCGGCGAATGAAAAAC 61.063 55.000 36.31 17.56 0.00 2.43
4853 5962 1.208103 GTCGGCGGCGAATGAAAAA 59.792 52.632 36.31 8.56 0.00 1.94
4854 5963 2.864589 GTCGGCGGCGAATGAAAA 59.135 55.556 36.31 9.43 0.00 2.29
4855 5964 3.483665 CGTCGGCGGCGAATGAAA 61.484 61.111 36.31 10.30 0.00 2.69
4866 5975 3.861263 GACCGGAAATGCGTCGGC 61.861 66.667 9.46 0.00 46.87 5.54
4868 5977 1.570347 TTTGGACCGGAAATGCGTCG 61.570 55.000 9.46 0.00 0.00 5.12
4869 5978 2.249692 TTTGGACCGGAAATGCGTC 58.750 52.632 9.46 0.00 0.00 5.19
4870 5979 4.484987 TTTGGACCGGAAATGCGT 57.515 50.000 9.46 0.00 0.00 5.24


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

AutoCloner maintained by Alex Coulton.