Multiple sequence alignment - TraesCS2B01G564000

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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 TraesCS2B01G564000 chr2B 100.000 3498 0 0 1 3498 755719801 755716304 0.000000e+00 6460.0
1 TraesCS2B01G564000 chrUn 88.463 2427 179 35 11 2382 278070728 278073108 0.000000e+00 2837.0
2 TraesCS2B01G564000 chrUn 87.019 1795 152 25 933 2687 295592089 295590336 0.000000e+00 1949.0
3 TraesCS2B01G564000 chrUn 83.298 467 37 21 2428 2875 278073110 278073554 3.270000e-105 392.0
4 TraesCS2B01G564000 chrUn 83.554 377 49 10 387 759 295592782 295592415 1.200000e-89 340.0
5 TraesCS2B01G564000 chrUn 79.832 357 44 14 14 355 402417275 402416932 5.840000e-58 235.0
6 TraesCS2B01G564000 chrUn 87.958 191 11 4 732 911 295592406 295592217 7.600000e-52 215.0
7 TraesCS2B01G564000 chr6D 92.750 1862 90 24 943 2796 451854101 451852277 0.000000e+00 2649.0
8 TraesCS2B01G564000 chr6D 84.918 305 45 1 358 661 82194231 82193927 1.220000e-79 307.0
9 TraesCS2B01G564000 chr6D 87.179 156 9 3 735 879 451854418 451854263 2.160000e-37 167.0
10 TraesCS2B01G564000 chr6D 90.217 92 9 0 2950 3041 390793993 390794084 1.710000e-23 121.0
11 TraesCS2B01G564000 chr6B 86.856 2115 184 51 913 2950 5306792 5308889 0.000000e+00 2279.0
12 TraesCS2B01G564000 chr6B 86.274 2120 190 53 913 2950 2827018 2824918 0.000000e+00 2209.0
13 TraesCS2B01G564000 chr6B 84.528 2120 227 49 914 2950 2661206 2659105 0.000000e+00 2004.0
14 TraesCS2B01G564000 chr6B 85.339 1787 191 35 903 2640 5807259 5809023 0.000000e+00 1783.0
15 TraesCS2B01G564000 chr6B 88.052 770 77 6 933 1701 5822319 5823074 0.000000e+00 898.0
16 TraesCS2B01G564000 chr6B 86.778 779 75 7 11 770 5305879 5306648 0.000000e+00 843.0
17 TraesCS2B01G564000 chr6B 86.563 707 75 11 72 770 2662044 2661350 0.000000e+00 761.0
18 TraesCS2B01G564000 chr6B 90.214 562 46 5 1322 1876 5565017 5564458 0.000000e+00 725.0
19 TraesCS2B01G564000 chr6B 86.511 556 57 10 72 618 2837983 2837437 2.320000e-166 595.0
20 TraesCS2B01G564000 chr6B 82.174 460 74 5 2057 2515 5844383 5843931 4.230000e-104 388.0
21 TraesCS2B01G564000 chr6B 80.726 358 45 8 14 358 5575182 5574836 1.250000e-64 257.0
22 TraesCS2B01G564000 chr6B 79.832 357 44 14 14 355 5310378 5310035 5.840000e-58 235.0
23 TraesCS2B01G564000 chr6B 79.444 360 49 11 14 359 5821274 5821622 7.550000e-57 231.0
24 TraesCS2B01G564000 chr6B 92.481 133 9 1 779 911 2827198 2827067 4.610000e-44 189.0
25 TraesCS2B01G564000 chr6B 88.550 131 13 1 119 247 650660465 650660595 1.300000e-34 158.0
26 TraesCS2B01G564000 chr6B 90.741 108 10 0 732 839 5309533 5309426 1.010000e-30 145.0
27 TraesCS2B01G564000 chr6B 89.908 109 11 0 729 837 5844580 5844472 1.310000e-29 141.0
28 TraesCS2B01G564000 chr6B 91.667 96 6 2 2956 3051 5308956 5309049 7.880000e-27 132.0
29 TraesCS2B01G564000 chr6B 85.714 119 9 4 729 839 5806951 5807069 6.130000e-23 119.0
30 TraesCS2B01G564000 chr6B 87.500 96 9 3 2956 3051 2824852 2824760 1.330000e-19 108.0
31 TraesCS2B01G564000 chr6B 95.349 43 1 1 837 879 5306685 5306726 2.250000e-07 67.6
32 TraesCS2B01G564000 chr6A 85.142 2120 222 47 907 2950 56689 58791 0.000000e+00 2084.0
33 TraesCS2B01G564000 chr6A 87.201 711 69 11 69 770 55854 56551 0.000000e+00 789.0
34 TraesCS2B01G564000 chr3A 82.834 367 54 7 363 722 158163327 158163691 1.570000e-83 320.0
35 TraesCS2B01G564000 chr2A 85.906 298 39 3 358 653 564613965 564613669 7.290000e-82 315.0
36 TraesCS2B01G564000 chr2A 90.526 95 6 3 2957 3051 43670611 43670702 4.740000e-24 122.0
37 TraesCS2B01G564000 chr7B 84.091 176 27 1 73 247 11990583 11990408 6.000000e-38 169.0
38 TraesCS2B01G564000 chr7D 89.362 94 10 0 2957 3050 257512536 257512629 6.130000e-23 119.0
39 TraesCS2B01G564000 chr7D 87.879 66 3 4 3047 3109 6091506 6091569 4.840000e-09 73.1
40 TraesCS2B01G564000 chr2D 88.421 95 8 3 2957 3051 41913829 41913920 1.030000e-20 111.0
41 TraesCS2B01G564000 chr2D 83.146 89 12 3 2970 3057 564704644 564704558 1.040000e-10 78.7
42 TraesCS2B01G564000 chr4D 83.908 87 12 2 2965 3051 483203988 483204072 8.050000e-12 82.4
43 TraesCS2B01G564000 chr5B 82.474 97 12 5 2964 3057 439961529 439961435 2.890000e-11 80.5


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 TraesCS2B01G564000 chr2B 755716304 755719801 3497 True 6460.000000 6460 100.000000 1 3498 1 chr2B.!!$R1 3497
1 TraesCS2B01G564000 chrUn 278070728 278073554 2826 False 1614.500000 2837 85.880500 11 2875 2 chrUn.!!$F1 2864
2 TraesCS2B01G564000 chrUn 295590336 295592782 2446 True 834.666667 1949 86.177000 387 2687 3 chrUn.!!$R2 2300
3 TraesCS2B01G564000 chr6D 451852277 451854418 2141 True 1408.000000 2649 89.964500 735 2796 2 chr6D.!!$R2 2061
4 TraesCS2B01G564000 chr6B 2659105 2662044 2939 True 1382.500000 2004 85.545500 72 2950 2 chr6B.!!$R4 2878
5 TraesCS2B01G564000 chr6B 5806951 5809023 2072 False 951.000000 1783 85.526500 729 2640 2 chr6B.!!$F3 1911
6 TraesCS2B01G564000 chr6B 2824760 2827198 2438 True 835.333333 2209 88.751667 779 3051 3 chr6B.!!$R5 2272
7 TraesCS2B01G564000 chr6B 5305879 5309049 3170 False 830.400000 2279 90.162500 11 3051 4 chr6B.!!$F2 3040
8 TraesCS2B01G564000 chr6B 5564458 5565017 559 True 725.000000 725 90.214000 1322 1876 1 chr6B.!!$R2 554
9 TraesCS2B01G564000 chr6B 2837437 2837983 546 True 595.000000 595 86.511000 72 618 1 chr6B.!!$R1 546
10 TraesCS2B01G564000 chr6B 5821274 5823074 1800 False 564.500000 898 83.748000 14 1701 2 chr6B.!!$F4 1687
11 TraesCS2B01G564000 chr6B 5843931 5844580 649 True 264.500000 388 86.041000 729 2515 2 chr6B.!!$R7 1786
12 TraesCS2B01G564000 chr6A 55854 58791 2937 False 1436.500000 2084 86.171500 69 2950 2 chr6A.!!$F1 2881

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
531 647 1.019278 GTTTCCAGCGGATCTTGCGA 61.019 55.0 5.11 0.0 37.44 5.10 F
1033 1484 0.243636 CCTCCAACAATCAAACGCCC 59.756 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2301 2821 0.462759 CCTCCATGACCTCCTTTCGC 60.463 60.000 0.0 0.0 0.0 4.70 R
2860 3412 1.202256 GGACGTAGCATCGATCACACA 60.202 52.381 0.0 0.0 34.7 3.72 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
30 31 3.418047 TCGATGCCTCGGTATGATTCTA 58.582 45.455 11.57 0.00 45.10 2.10
38 39 6.166279 GCCTCGGTATGATTCTATCAATGAA 58.834 40.000 0.00 0.00 43.50 2.57
68 69 2.504367 GCTTCAGGCAAACTACCTTGA 58.496 47.619 0.00 0.00 41.35 3.02
136 146 8.045507 AGAGCTGATCTGTATCATTTTTCTTGA 58.954 33.333 0.00 0.00 41.29 3.02
175 185 4.618227 GCTTGTTTTTGCGTGGGATTATCT 60.618 41.667 0.00 0.00 0.00 1.98
355 372 1.295423 GCTAGGGTTTCTCGTGCCA 59.705 57.895 0.00 0.00 0.00 4.92
379 495 8.347035 CCACCTTCGTTTTTCATACTCTTTTAA 58.653 33.333 0.00 0.00 0.00 1.52
491 607 4.081697 TCTCGGTGATGTTTCTAGCATTGA 60.082 41.667 0.00 0.00 0.00 2.57
514 630 3.157087 GGATGACATGTGGAGGTTTGTT 58.843 45.455 1.15 0.00 0.00 2.83
531 647 1.019278 GTTTCCAGCGGATCTTGCGA 61.019 55.000 5.11 0.00 37.44 5.10
605 725 6.193514 TCGTCCGTGTTTATATGTCTACAA 57.806 37.500 0.00 0.00 0.00 2.41
643 763 1.464734 ACTCTTCTCTTCATCGGCGA 58.535 50.000 13.87 13.87 0.00 5.54
709 829 9.632969 CGATTTTCCGACTGTTTATTACAATAG 57.367 33.333 0.00 0.00 36.02 1.73
879 1116 1.734655 AGGAGCACCCGATGGATAAT 58.265 50.000 0.00 0.00 40.87 1.28
882 1119 1.625818 GAGCACCCGATGGATAATCCT 59.374 52.381 0.00 0.00 37.46 3.24
883 1120 2.832129 GAGCACCCGATGGATAATCCTA 59.168 50.000 0.00 0.00 37.46 2.94
884 1121 3.248024 AGCACCCGATGGATAATCCTAA 58.752 45.455 0.00 0.00 37.46 2.69
885 1122 3.261897 AGCACCCGATGGATAATCCTAAG 59.738 47.826 0.00 0.00 37.46 2.18
886 1123 3.600388 CACCCGATGGATAATCCTAAGC 58.400 50.000 0.00 0.00 37.46 3.09
887 1124 3.261897 CACCCGATGGATAATCCTAAGCT 59.738 47.826 0.00 0.00 37.46 3.74
888 1125 4.466370 CACCCGATGGATAATCCTAAGCTA 59.534 45.833 0.00 0.00 37.46 3.32
889 1126 5.046591 CACCCGATGGATAATCCTAAGCTAA 60.047 44.000 0.00 0.00 37.46 3.09
890 1127 5.046520 ACCCGATGGATAATCCTAAGCTAAC 60.047 44.000 0.00 0.00 37.46 2.34
891 1128 5.420409 CCGATGGATAATCCTAAGCTAACC 58.580 45.833 0.00 0.00 37.46 2.85
931 1369 2.027024 TCTCGGACACACGCACAC 59.973 61.111 0.00 0.00 0.00 3.82
973 1417 3.683822 CGAGTCCACTTCGTACTACTCTT 59.316 47.826 0.00 0.00 32.96 2.85
976 1420 6.699204 CGAGTCCACTTCGTACTACTCTTATA 59.301 42.308 0.00 0.00 32.96 0.98
1004 1455 2.042433 TGTGCCCATAAAGTTAAGCCCT 59.958 45.455 0.00 0.00 0.00 5.19
1005 1456 2.427095 GTGCCCATAAAGTTAAGCCCTG 59.573 50.000 0.00 0.00 0.00 4.45
1033 1484 0.243636 CCTCCAACAATCAAACGCCC 59.756 55.000 0.00 0.00 0.00 6.13
1078 1538 1.153823 GCTCAGGAACTCGCGCTTA 60.154 57.895 5.56 0.00 34.60 3.09
1079 1539 0.736325 GCTCAGGAACTCGCGCTTAA 60.736 55.000 5.56 0.00 34.60 1.85
1080 1540 1.927895 CTCAGGAACTCGCGCTTAAT 58.072 50.000 5.56 0.00 34.60 1.40
1117 1582 1.725557 ATCGTCCGACGCTACTGCAT 61.726 55.000 16.24 0.00 42.21 3.96
1160 1625 1.262417 CCTCGATCGCATTCCAATGTG 59.738 52.381 11.09 6.52 45.74 3.21
1192 1657 2.034221 ACGGCTCTTTTCCTGCCC 59.966 61.111 0.00 0.00 43.42 5.36
1410 1878 2.750637 TCCTGACCTCGTCGGAGC 60.751 66.667 2.12 0.00 41.05 4.70
1449 1918 4.065088 TGAAGACTTCAACGATTGGAAGG 58.935 43.478 15.58 0.00 43.70 3.46
1459 1928 0.460284 GATTGGAAGGAGAAGCGCGA 60.460 55.000 12.10 0.00 0.00 5.87
1464 1933 1.079503 GAAGGAGAAGCGCGACAAAT 58.920 50.000 12.10 0.00 0.00 2.32
1473 1942 3.173668 AGCGCGACAAATACATCCTTA 57.826 42.857 12.10 0.00 0.00 2.69
1496 1965 1.524863 CGTCTGACCCGAGGACTGTT 61.525 60.000 1.55 0.00 0.00 3.16
1595 2065 0.696501 TTAAGCAGGGGAAGGTGGTC 59.303 55.000 0.00 0.00 0.00 4.02
1621 2091 1.448540 CACAGACGGGGCATCTCAC 60.449 63.158 0.00 0.00 0.00 3.51
1653 2123 1.271163 GGGAGGTGATGGTTGTCGAAA 60.271 52.381 0.00 0.00 0.00 3.46
1656 2126 4.258543 GGAGGTGATGGTTGTCGAAAATA 58.741 43.478 0.00 0.00 0.00 1.40
1678 2148 3.566351 ACAAAGTAAGGGCTTTCAGCTT 58.434 40.909 0.00 0.00 41.99 3.74
1781 2251 3.039011 TGAGGTAGGTCTCCCTTATTGC 58.961 50.000 0.00 0.00 42.66 3.56
2029 2546 6.678568 TTTTGTATGGGAATTGGAACATGT 57.321 33.333 0.00 0.00 39.30 3.21
2050 2567 2.683768 TGGTTTGCCAAATACCAGGTT 58.316 42.857 0.00 0.00 42.83 3.50
2087 2607 6.396829 AGGATATTTTATTGTTGAGGCTGC 57.603 37.500 0.00 0.00 0.00 5.25
2160 2680 1.272490 GAGGCGGATCACATCGGATTA 59.728 52.381 0.00 0.00 0.00 1.75
2182 2702 1.510480 GATAATGGCCGCTGCTGGTC 61.510 60.000 0.00 7.93 37.74 4.02
2278 2798 3.498927 TCGGTACTCATCCTTCGTTTC 57.501 47.619 0.00 0.00 0.00 2.78
2286 2806 3.664107 TCATCCTTCGTTTCAGACAAGG 58.336 45.455 0.00 0.00 37.63 3.61
2293 2813 1.805120 CGTTTCAGACAAGGTCACGGT 60.805 52.381 0.00 0.00 34.60 4.83
2301 2821 2.409975 ACAAGGTCACGGTTGTTATCG 58.590 47.619 0.00 0.00 32.93 2.92
2328 2848 1.201429 AGGTCATGGAGGAGGCGTTT 61.201 55.000 0.00 0.00 0.00 3.60
2357 2877 2.225491 ACAAACAAGAACGTATGCGCAT 59.775 40.909 28.23 28.23 42.83 4.73
2376 2896 3.432749 GCATGGAGAAGTGCCAATCTCTA 60.433 47.826 8.24 3.69 41.45 2.43
2408 2928 0.906775 TGGAACGTCCTTGGATACCC 59.093 55.000 0.00 0.00 37.46 3.69
2412 2932 0.612732 ACGTCCTTGGATACCCGTCA 60.613 55.000 0.00 0.00 34.29 4.35
2451 2971 0.243365 TCAATGGCGCAATGACCAAC 59.757 50.000 10.83 0.00 39.96 3.77
2561 3083 3.213264 GGATAACGTCCGGCCTCA 58.787 61.111 0.00 0.00 37.23 3.86
2749 3282 5.809051 ACGTAGATGCTCATACATATGCATG 59.191 40.000 10.16 9.35 44.80 4.06
2760 3293 4.760530 ACATATGCATGTACACTCACCT 57.239 40.909 10.16 0.00 43.74 4.00
2875 3427 5.643348 AGAACAAATTGTGTGATCGATGCTA 59.357 36.000 0.54 0.00 40.60 3.49
2876 3428 5.221891 ACAAATTGTGTGATCGATGCTAC 57.778 39.130 0.54 0.00 39.72 3.58
2879 3431 2.188837 TGTGTGATCGATGCTACGTC 57.811 50.000 0.54 0.00 34.70 4.34
2880 3432 1.202256 TGTGTGATCGATGCTACGTCC 60.202 52.381 0.54 0.00 34.70 4.79
2884 3450 3.379057 TGTGATCGATGCTACGTCCTAAA 59.621 43.478 0.54 0.00 34.70 1.85
2950 3516 6.783708 ATCAACCCACAGTTCACTTTTAAA 57.216 33.333 0.00 0.00 36.18 1.52
2951 3517 5.956642 TCAACCCACAGTTCACTTTTAAAC 58.043 37.500 0.00 0.00 36.18 2.01
2952 3518 5.712917 TCAACCCACAGTTCACTTTTAAACT 59.287 36.000 0.00 0.00 36.18 2.66
2953 3519 6.209788 TCAACCCACAGTTCACTTTTAAACTT 59.790 34.615 0.00 0.00 36.18 2.66
2954 3520 5.961272 ACCCACAGTTCACTTTTAAACTTG 58.039 37.500 0.00 0.00 33.53 3.16
2972 3599 9.579768 TTAAACTTGTAGTCTACGTACAACAAA 57.420 29.630 5.55 0.00 35.84 2.83
2974 3601 9.748708 AAACTTGTAGTCTACGTACAACAAATA 57.251 29.630 5.55 0.00 35.84 1.40
3013 3640 8.990163 ATCCATATCTTTTAAACCATAACCGT 57.010 30.769 0.00 0.00 0.00 4.83
3088 3715 9.855021 ATTCAAAGTGGTACTAAATATTTGTGC 57.145 29.630 11.05 9.78 0.00 4.57
3089 3716 7.523219 TCAAAGTGGTACTAAATATTTGTGCG 58.477 34.615 11.05 0.00 0.00 5.34
3090 3717 7.173562 TCAAAGTGGTACTAAATATTTGTGCGT 59.826 33.333 11.05 5.47 0.00 5.24
3091 3718 6.657836 AGTGGTACTAAATATTTGTGCGTC 57.342 37.500 11.05 7.14 0.00 5.19
3092 3719 5.583457 AGTGGTACTAAATATTTGTGCGTCC 59.417 40.000 11.05 6.51 0.00 4.79
3093 3720 5.352016 GTGGTACTAAATATTTGTGCGTCCA 59.648 40.000 11.05 8.68 0.00 4.02
3094 3721 6.037830 GTGGTACTAAATATTTGTGCGTCCAT 59.962 38.462 11.05 0.00 0.00 3.41
3095 3722 6.259167 TGGTACTAAATATTTGTGCGTCCATC 59.741 38.462 11.05 0.00 0.00 3.51
3096 3723 6.482308 GGTACTAAATATTTGTGCGTCCATCT 59.518 38.462 11.05 0.00 0.00 2.90
3097 3724 6.363577 ACTAAATATTTGTGCGTCCATCTG 57.636 37.500 11.05 0.00 0.00 2.90
3098 3725 5.880332 ACTAAATATTTGTGCGTCCATCTGT 59.120 36.000 11.05 0.00 0.00 3.41
3099 3726 5.643379 AAATATTTGTGCGTCCATCTGTT 57.357 34.783 0.00 0.00 0.00 3.16
3100 3727 6.751514 AAATATTTGTGCGTCCATCTGTTA 57.248 33.333 0.00 0.00 0.00 2.41
3101 3728 5.991328 ATATTTGTGCGTCCATCTGTTAG 57.009 39.130 0.00 0.00 0.00 2.34
3102 3729 3.394674 TTTGTGCGTCCATCTGTTAGA 57.605 42.857 0.00 0.00 0.00 2.10
3103 3730 3.394674 TTGTGCGTCCATCTGTTAGAA 57.605 42.857 0.00 0.00 0.00 2.10
3104 3731 3.394674 TGTGCGTCCATCTGTTAGAAA 57.605 42.857 0.00 0.00 0.00 2.52
3105 3732 3.734463 TGTGCGTCCATCTGTTAGAAAA 58.266 40.909 0.00 0.00 0.00 2.29
3106 3733 3.745975 TGTGCGTCCATCTGTTAGAAAAG 59.254 43.478 0.00 0.00 0.00 2.27
3107 3734 3.994392 GTGCGTCCATCTGTTAGAAAAGA 59.006 43.478 0.00 0.00 0.00 2.52
3108 3735 4.451096 GTGCGTCCATCTGTTAGAAAAGAA 59.549 41.667 0.00 0.00 0.00 2.52
3109 3736 5.122396 GTGCGTCCATCTGTTAGAAAAGAAT 59.878 40.000 0.00 0.00 0.00 2.40
3110 3737 6.312918 GTGCGTCCATCTGTTAGAAAAGAATA 59.687 38.462 0.00 0.00 0.00 1.75
3111 3738 6.876789 TGCGTCCATCTGTTAGAAAAGAATAA 59.123 34.615 0.00 0.00 0.00 1.40
3112 3739 7.552687 TGCGTCCATCTGTTAGAAAAGAATAAT 59.447 33.333 0.00 0.00 0.00 1.28
3113 3740 7.852945 GCGTCCATCTGTTAGAAAAGAATAATG 59.147 37.037 0.00 0.00 0.00 1.90
3114 3741 8.338259 CGTCCATCTGTTAGAAAAGAATAATGG 58.662 37.037 0.00 0.00 0.00 3.16
3115 3742 9.178758 GTCCATCTGTTAGAAAAGAATAATGGT 57.821 33.333 0.00 0.00 0.00 3.55
3116 3743 9.753674 TCCATCTGTTAGAAAAGAATAATGGTT 57.246 29.630 0.00 0.00 0.00 3.67
3121 3748 9.626045 CTGTTAGAAAAGAATAATGGTTTGACC 57.374 33.333 0.00 0.00 39.22 4.02
3132 3759 2.302260 TGGTTTGACCAGAATTTCGCA 58.698 42.857 0.00 0.00 44.79 5.10
3133 3760 2.890311 TGGTTTGACCAGAATTTCGCAT 59.110 40.909 0.00 0.00 44.79 4.73
3134 3761 4.075682 TGGTTTGACCAGAATTTCGCATA 58.924 39.130 0.00 0.00 44.79 3.14
3135 3762 4.704540 TGGTTTGACCAGAATTTCGCATAT 59.295 37.500 0.00 0.00 44.79 1.78
3136 3763 5.036737 GGTTTGACCAGAATTTCGCATATG 58.963 41.667 0.00 0.00 38.42 1.78
3137 3764 4.898829 TTGACCAGAATTTCGCATATGG 57.101 40.909 4.56 1.23 0.00 2.74
3138 3765 3.213506 TGACCAGAATTTCGCATATGGG 58.786 45.455 13.38 13.38 31.95 4.00
3139 3766 1.956477 ACCAGAATTTCGCATATGGGC 59.044 47.619 14.65 0.92 31.95 5.36
3140 3767 1.270550 CCAGAATTTCGCATATGGGCC 59.729 52.381 14.65 0.00 0.00 5.80
3141 3768 1.955778 CAGAATTTCGCATATGGGCCA 59.044 47.619 9.61 9.61 0.00 5.36
3142 3769 1.956477 AGAATTTCGCATATGGGCCAC 59.044 47.619 9.28 0.00 0.00 5.01
3143 3770 0.667993 AATTTCGCATATGGGCCACG 59.332 50.000 9.28 8.41 0.00 4.94
3144 3771 1.795170 ATTTCGCATATGGGCCACGC 61.795 55.000 9.28 11.71 0.00 5.34
3147 3774 3.952675 GCATATGGGCCACGCGTG 61.953 66.667 31.77 31.77 0.00 5.34
3148 3775 3.952675 CATATGGGCCACGCGTGC 61.953 66.667 33.17 26.04 0.00 5.34
3149 3776 4.175337 ATATGGGCCACGCGTGCT 62.175 61.111 33.17 16.09 0.00 4.40
3150 3777 4.830765 TATGGGCCACGCGTGCTC 62.831 66.667 33.17 26.59 0.00 4.26
3183 3810 6.009115 CGAAGCCAACCAACTTAATTTACT 57.991 37.500 0.00 0.00 0.00 2.24
3184 3811 5.856455 CGAAGCCAACCAACTTAATTTACTG 59.144 40.000 0.00 0.00 0.00 2.74
3185 3812 5.134202 AGCCAACCAACTTAATTTACTGC 57.866 39.130 0.00 0.00 0.00 4.40
3186 3813 4.021456 AGCCAACCAACTTAATTTACTGCC 60.021 41.667 0.00 0.00 0.00 4.85
3187 3814 4.262249 GCCAACCAACTTAATTTACTGCCA 60.262 41.667 0.00 0.00 0.00 4.92
3188 3815 5.740513 GCCAACCAACTTAATTTACTGCCAA 60.741 40.000 0.00 0.00 0.00 4.52
3189 3816 5.925969 CCAACCAACTTAATTTACTGCCAAG 59.074 40.000 0.00 0.00 0.00 3.61
3190 3817 5.722021 ACCAACTTAATTTACTGCCAAGG 57.278 39.130 0.00 0.00 0.00 3.61
3191 3818 5.144832 ACCAACTTAATTTACTGCCAAGGT 58.855 37.500 0.00 0.00 0.00 3.50
3192 3819 6.308566 ACCAACTTAATTTACTGCCAAGGTA 58.691 36.000 0.00 0.00 0.00 3.08
3193 3820 6.951778 ACCAACTTAATTTACTGCCAAGGTAT 59.048 34.615 0.00 0.00 0.00 2.73
3194 3821 7.453439 ACCAACTTAATTTACTGCCAAGGTATT 59.547 33.333 0.00 0.00 0.00 1.89
3195 3822 7.973944 CCAACTTAATTTACTGCCAAGGTATTC 59.026 37.037 0.00 0.00 0.00 1.75
3196 3823 7.316544 ACTTAATTTACTGCCAAGGTATTCG 57.683 36.000 0.00 0.00 0.00 3.34
3197 3824 6.317893 ACTTAATTTACTGCCAAGGTATTCGG 59.682 38.462 0.00 0.00 0.00 4.30
3198 3825 2.702592 TTACTGCCAAGGTATTCGGG 57.297 50.000 0.00 0.00 0.00 5.14
3199 3826 1.868713 TACTGCCAAGGTATTCGGGA 58.131 50.000 0.00 0.00 0.00 5.14
3200 3827 0.988832 ACTGCCAAGGTATTCGGGAA 59.011 50.000 0.00 0.00 0.00 3.97
3201 3828 1.353022 ACTGCCAAGGTATTCGGGAAA 59.647 47.619 0.00 0.00 0.00 3.13
3202 3829 2.224917 ACTGCCAAGGTATTCGGGAAAA 60.225 45.455 0.00 0.00 0.00 2.29
3203 3830 2.163613 CTGCCAAGGTATTCGGGAAAAC 59.836 50.000 0.00 0.00 0.00 2.43
3204 3831 2.224917 TGCCAAGGTATTCGGGAAAACT 60.225 45.455 0.00 0.00 0.00 2.66
3205 3832 2.422479 GCCAAGGTATTCGGGAAAACTC 59.578 50.000 0.00 0.00 0.00 3.01
3206 3833 3.872630 GCCAAGGTATTCGGGAAAACTCT 60.873 47.826 0.00 0.00 0.00 3.24
3207 3834 4.624604 GCCAAGGTATTCGGGAAAACTCTA 60.625 45.833 0.00 0.00 0.00 2.43
3208 3835 5.681639 CCAAGGTATTCGGGAAAACTCTAT 58.318 41.667 0.00 0.00 0.00 1.98
3209 3836 6.120220 CCAAGGTATTCGGGAAAACTCTATT 58.880 40.000 0.00 0.00 0.00 1.73
3210 3837 6.602009 CCAAGGTATTCGGGAAAACTCTATTT 59.398 38.462 0.00 0.00 0.00 1.40
3211 3838 7.415206 CCAAGGTATTCGGGAAAACTCTATTTG 60.415 40.741 0.00 0.00 0.00 2.32
3212 3839 6.718294 AGGTATTCGGGAAAACTCTATTTGT 58.282 36.000 0.00 0.00 0.00 2.83
3213 3840 6.822170 AGGTATTCGGGAAAACTCTATTTGTC 59.178 38.462 0.00 0.00 0.00 3.18
3214 3841 5.796350 ATTCGGGAAAACTCTATTTGTCG 57.204 39.130 0.00 0.00 0.00 4.35
3215 3842 2.997986 TCGGGAAAACTCTATTTGTCGC 59.002 45.455 0.00 0.00 0.00 5.19
3216 3843 3.000727 CGGGAAAACTCTATTTGTCGCT 58.999 45.455 0.00 0.00 0.00 4.93
3217 3844 3.062234 CGGGAAAACTCTATTTGTCGCTC 59.938 47.826 0.00 0.00 0.00 5.03
3218 3845 3.062234 GGGAAAACTCTATTTGTCGCTCG 59.938 47.826 0.00 0.00 0.00 5.03
3219 3846 3.062234 GGAAAACTCTATTTGTCGCTCGG 59.938 47.826 0.00 0.00 0.00 4.63
3220 3847 3.314541 AAACTCTATTTGTCGCTCGGT 57.685 42.857 0.00 0.00 0.00 4.69
3221 3848 2.279582 ACTCTATTTGTCGCTCGGTG 57.720 50.000 0.00 0.00 0.00 4.94
3222 3849 0.924090 CTCTATTTGTCGCTCGGTGC 59.076 55.000 0.00 0.00 38.57 5.01
3231 3858 4.354155 GCTCGGTGCGGCATATTA 57.646 55.556 5.72 0.00 0.00 0.98
3232 3859 2.153913 GCTCGGTGCGGCATATTAG 58.846 57.895 5.72 3.15 0.00 1.73
3233 3860 0.600255 GCTCGGTGCGGCATATTAGT 60.600 55.000 5.72 0.00 0.00 2.24
3234 3861 1.419374 CTCGGTGCGGCATATTAGTC 58.581 55.000 5.72 0.00 0.00 2.59
3235 3862 0.747852 TCGGTGCGGCATATTAGTCA 59.252 50.000 5.72 0.00 0.00 3.41
3236 3863 1.139989 CGGTGCGGCATATTAGTCAG 58.860 55.000 5.72 0.00 0.00 3.51
3237 3864 1.512926 GGTGCGGCATATTAGTCAGG 58.487 55.000 5.72 0.00 0.00 3.86
3238 3865 1.512926 GTGCGGCATATTAGTCAGGG 58.487 55.000 5.72 0.00 0.00 4.45
3239 3866 0.250295 TGCGGCATATTAGTCAGGGC 60.250 55.000 0.00 0.00 0.00 5.19
3240 3867 0.955919 GCGGCATATTAGTCAGGGCC 60.956 60.000 0.00 0.00 38.04 5.80
3241 3868 0.687354 CGGCATATTAGTCAGGGCCT 59.313 55.000 0.00 0.00 39.23 5.19
3242 3869 1.338200 CGGCATATTAGTCAGGGCCTC 60.338 57.143 0.95 0.00 39.23 4.70
3243 3870 1.338200 GGCATATTAGTCAGGGCCTCG 60.338 57.143 0.95 0.00 38.37 4.63
3244 3871 1.941668 GCATATTAGTCAGGGCCTCGC 60.942 57.143 0.95 0.00 0.00 5.03
3245 3872 1.344438 CATATTAGTCAGGGCCTCGCA 59.656 52.381 0.95 0.00 0.00 5.10
3246 3873 0.750850 TATTAGTCAGGGCCTCGCAC 59.249 55.000 0.95 0.00 0.00 5.34
3247 3874 1.264749 ATTAGTCAGGGCCTCGCACA 61.265 55.000 0.95 0.00 32.33 4.57
3248 3875 1.264749 TTAGTCAGGGCCTCGCACAT 61.265 55.000 0.95 0.00 32.33 3.21
3249 3876 1.960040 TAGTCAGGGCCTCGCACATG 61.960 60.000 0.95 0.00 32.33 3.21
3250 3877 4.100084 TCAGGGCCTCGCACATGG 62.100 66.667 0.95 0.00 32.33 3.66
3256 3883 4.720902 CCTCGCACATGGCACCCA 62.721 66.667 0.00 0.00 45.17 4.51
3257 3884 2.672651 CTCGCACATGGCACCCAA 60.673 61.111 0.00 0.00 45.17 4.12
3258 3885 2.672651 TCGCACATGGCACCCAAG 60.673 61.111 0.00 0.00 45.17 3.61
3259 3886 2.672651 CGCACATGGCACCCAAGA 60.673 61.111 0.00 0.00 45.17 3.02
3260 3887 2.964978 GCACATGGCACCCAAGAC 59.035 61.111 0.00 0.00 43.97 3.01
3261 3888 1.604593 GCACATGGCACCCAAGACT 60.605 57.895 0.00 0.00 43.97 3.24
3262 3889 1.870055 GCACATGGCACCCAAGACTG 61.870 60.000 0.00 0.00 43.97 3.51
3263 3890 1.075482 ACATGGCACCCAAGACTGG 59.925 57.895 0.00 0.00 43.10 4.00
3264 3891 2.036256 ATGGCACCCAAGACTGGC 59.964 61.111 0.00 0.00 41.99 4.85
3265 3892 3.590466 ATGGCACCCAAGACTGGCC 62.590 63.158 0.00 0.00 41.99 5.36
3268 3895 4.722700 CACCCAAGACTGGCCCGG 62.723 72.222 0.00 0.00 41.99 5.73
3280 3907 2.363147 GCCCGGCCCATTTTGGTA 60.363 61.111 0.00 0.00 35.17 3.25
3281 3908 1.760480 GCCCGGCCCATTTTGGTAT 60.760 57.895 0.00 0.00 35.17 2.73
3282 3909 1.334384 GCCCGGCCCATTTTGGTATT 61.334 55.000 0.00 0.00 35.17 1.89
3283 3910 2.030045 GCCCGGCCCATTTTGGTATTA 61.030 52.381 0.00 0.00 35.17 0.98
3284 3911 2.604139 CCCGGCCCATTTTGGTATTAT 58.396 47.619 0.00 0.00 35.17 1.28
3285 3912 2.560981 CCCGGCCCATTTTGGTATTATC 59.439 50.000 0.00 0.00 35.17 1.75
3286 3913 3.496331 CCGGCCCATTTTGGTATTATCT 58.504 45.455 0.00 0.00 35.17 1.98
3287 3914 3.506067 CCGGCCCATTTTGGTATTATCTC 59.494 47.826 0.00 0.00 35.17 2.75
3288 3915 4.398319 CGGCCCATTTTGGTATTATCTCT 58.602 43.478 0.00 0.00 35.17 3.10
3289 3916 4.216257 CGGCCCATTTTGGTATTATCTCTG 59.784 45.833 0.00 0.00 35.17 3.35
3290 3917 5.140454 GGCCCATTTTGGTATTATCTCTGT 58.860 41.667 0.00 0.00 35.17 3.41
3291 3918 6.303839 GGCCCATTTTGGTATTATCTCTGTA 58.696 40.000 0.00 0.00 35.17 2.74
3292 3919 6.775629 GGCCCATTTTGGTATTATCTCTGTAA 59.224 38.462 0.00 0.00 35.17 2.41
3293 3920 7.451566 GGCCCATTTTGGTATTATCTCTGTAAT 59.548 37.037 0.00 0.00 35.17 1.89
3294 3921 8.860088 GCCCATTTTGGTATTATCTCTGTAATT 58.140 33.333 0.00 0.00 35.17 1.40
3418 4045 9.844257 TCAATATTGGTCAATTTTTCCAAAACT 57.156 25.926 15.36 0.00 43.11 2.66
3422 4049 7.986085 TTGGTCAATTTTTCCAAAACTTTCA 57.014 28.000 4.03 0.00 38.13 2.69
3423 4050 7.371126 TGGTCAATTTTTCCAAAACTTTCAC 57.629 32.000 0.00 0.00 0.00 3.18
3424 4051 6.936900 TGGTCAATTTTTCCAAAACTTTCACA 59.063 30.769 0.00 0.00 0.00 3.58
3425 4052 7.445402 TGGTCAATTTTTCCAAAACTTTCACAA 59.555 29.630 0.00 0.00 0.00 3.33
3426 4053 8.458052 GGTCAATTTTTCCAAAACTTTCACAAT 58.542 29.630 0.00 0.00 0.00 2.71
3427 4054 9.838975 GTCAATTTTTCCAAAACTTTCACAATT 57.161 25.926 0.00 0.00 0.00 2.32
3434 4061 9.670719 TTTCCAAAACTTTCACAATTTTCAAAC 57.329 25.926 0.00 0.00 0.00 2.93
3435 4062 8.383318 TCCAAAACTTTCACAATTTTCAAACA 57.617 26.923 0.00 0.00 0.00 2.83
3436 4063 8.840321 TCCAAAACTTTCACAATTTTCAAACAA 58.160 25.926 0.00 0.00 0.00 2.83
3437 4064 9.455847 CCAAAACTTTCACAATTTTCAAACAAA 57.544 25.926 0.00 0.00 0.00 2.83
3497 4124 6.885735 ATTTTTCTCGTTCCAAAAGTTGTG 57.114 33.333 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.645296 TGATAGAATCATACCGAGGCATCGAAC 62.645 44.444 24.13 4.14 42.18 3.95
8 9 7.745425 TGATAGAATCATACCGAGGCATCGAA 61.745 42.308 24.13 10.42 42.18 3.71
9 10 6.323598 TGATAGAATCATACCGAGGCATCGA 61.324 44.000 24.13 2.90 42.18 3.59
12 13 5.745312 TTGATAGAATCATACCGAGGCAT 57.255 39.130 0.00 0.00 39.39 4.40
30 31 7.279313 GCCTGAAGCATAAACATTTTCATTGAT 59.721 33.333 0.00 0.00 42.97 2.57
64 65 2.552802 CTGACCTGCAGCCTTCAAG 58.447 57.895 8.66 0.00 37.90 3.02
114 124 9.117183 TCCATCAAGAAAAATGATACAGATCAG 57.883 33.333 0.00 0.00 45.29 2.90
136 146 1.630126 AAGCGCATGTCCCTCTCCAT 61.630 55.000 11.47 0.00 0.00 3.41
166 176 7.164803 CAGGACTGAAAGGATAAGATAATCCC 58.835 42.308 0.00 0.00 45.74 3.85
175 185 6.338146 CGACATTACAGGACTGAAAGGATAA 58.662 40.000 6.29 0.00 39.30 1.75
262 279 5.620879 GCGTACAGATCTCTCATGCATATGA 60.621 44.000 6.97 0.00 40.92 2.15
321 338 3.699538 CCCTAGCCAAAACCCAAGATTAC 59.300 47.826 0.00 0.00 0.00 1.89
355 372 9.117183 ACTTAAAAGAGTATGAAAAACGAAGGT 57.883 29.630 0.00 0.00 0.00 3.50
379 495 4.606210 AGGACACAAACCCTAACAAAACT 58.394 39.130 0.00 0.00 0.00 2.66
391 507 2.094649 CCTCTCCGAGTAGGACACAAAC 60.095 54.545 7.71 0.00 45.98 2.93
414 530 1.997874 AGAGAGCCATCGCCCCTTT 60.998 57.895 0.00 0.00 34.57 3.11
491 607 0.984230 AACCTCCACATGTCATCCGT 59.016 50.000 0.00 0.00 0.00 4.69
514 630 2.978000 TCGCAAGATCCGCTGGAA 59.022 55.556 1.44 0.00 45.01 3.53
531 647 3.124921 CAAACGCCGGCCGAATCT 61.125 61.111 30.73 5.16 41.02 2.40
673 793 3.603158 TCGGAAAATCGACATCCTCAA 57.397 42.857 10.28 0.00 33.92 3.02
879 1116 0.323725 ACGTCCCGGTTAGCTTAGGA 60.324 55.000 0.00 0.00 0.00 2.94
882 1119 0.611618 TCCACGTCCCGGTTAGCTTA 60.612 55.000 0.00 0.00 0.00 3.09
883 1120 1.909781 TCCACGTCCCGGTTAGCTT 60.910 57.895 0.00 0.00 0.00 3.74
884 1121 2.283388 TCCACGTCCCGGTTAGCT 60.283 61.111 0.00 0.00 0.00 3.32
885 1122 2.125793 GTCCACGTCCCGGTTAGC 60.126 66.667 0.00 0.00 0.00 3.09
886 1123 1.865788 TTCGTCCACGTCCCGGTTAG 61.866 60.000 0.00 0.00 40.80 2.34
887 1124 1.865788 CTTCGTCCACGTCCCGGTTA 61.866 60.000 0.00 0.00 40.80 2.85
888 1125 3.216944 CTTCGTCCACGTCCCGGTT 62.217 63.158 0.00 0.00 40.80 4.44
889 1126 3.677648 CTTCGTCCACGTCCCGGT 61.678 66.667 0.00 0.00 40.80 5.28
891 1128 4.351938 TGCTTCGTCCACGTCCCG 62.352 66.667 0.00 0.00 40.80 5.14
931 1369 4.940463 TCGGGTTCAATATTCTAAGACGG 58.060 43.478 0.00 0.00 0.00 4.79
939 1383 4.138487 AGTGGACTCGGGTTCAATATTC 57.862 45.455 0.00 0.00 31.99 1.75
973 1417 4.944930 ACTTTATGGGCACAACGCTTTATA 59.055 37.500 0.00 0.00 41.91 0.98
976 1420 1.960689 ACTTTATGGGCACAACGCTTT 59.039 42.857 0.00 0.00 41.91 3.51
1078 1538 3.814504 TCTGGAGCCTGGAGAAAAATT 57.185 42.857 0.00 0.00 0.00 1.82
1079 1539 3.683847 CGATCTGGAGCCTGGAGAAAAAT 60.684 47.826 0.00 0.00 0.00 1.82
1080 1540 2.355108 CGATCTGGAGCCTGGAGAAAAA 60.355 50.000 0.00 0.00 0.00 1.94
1117 1582 1.982395 CGTAGTGTCTGGGCAGGGA 60.982 63.158 0.00 0.00 0.00 4.20
1160 1625 1.595382 CCGTCGGATTGAGCCCATC 60.595 63.158 4.91 0.00 0.00 3.51
1449 1918 2.033662 GGATGTATTTGTCGCGCTTCTC 60.034 50.000 5.56 0.00 0.00 2.87
1459 1928 3.454812 AGACGGGCTAAGGATGTATTTGT 59.545 43.478 0.00 0.00 0.00 2.83
1464 1933 2.029623 GTCAGACGGGCTAAGGATGTA 58.970 52.381 0.00 0.00 0.00 2.29
1621 2091 2.257207 TCACCTCCCAGTTAAGGTCAG 58.743 52.381 0.00 0.00 44.13 3.51
1678 2148 1.281419 TACAATCTTCCCGCCCTTCA 58.719 50.000 0.00 0.00 0.00 3.02
1957 2473 9.143631 GCAATTACTAATTTCAAGAACAATGCT 57.856 29.630 0.00 0.00 0.00 3.79
1958 2474 8.924691 TGCAATTACTAATTTCAAGAACAATGC 58.075 29.630 0.00 0.00 0.00 3.56
1999 2515 7.673641 TCCAATTCCCATACAAAATGCTATT 57.326 32.000 0.00 0.00 0.00 1.73
2003 2520 5.486526 TGTTCCAATTCCCATACAAAATGC 58.513 37.500 0.00 0.00 0.00 3.56
2016 2533 3.498018 GGCAAACCAACATGTTCCAATTC 59.502 43.478 8.48 0.00 35.26 2.17
2045 2562 5.282055 TCCTTGCATACATAGAGAACCTG 57.718 43.478 0.00 0.00 0.00 4.00
2079 2596 5.306419 ACAAGAGATAAGATATGCAGCCTCA 59.694 40.000 0.00 0.00 0.00 3.86
2160 2680 0.956633 CAGCAGCGGCCATTATCATT 59.043 50.000 4.82 0.00 42.56 2.57
2182 2702 1.883084 GGGCTACGCGTGGATTGAG 60.883 63.158 27.75 13.59 0.00 3.02
2185 2705 3.081409 AGGGGCTACGCGTGGATT 61.081 61.111 27.75 4.79 34.23 3.01
2278 2798 1.663695 AACAACCGTGACCTTGTCTG 58.336 50.000 0.00 0.00 33.15 3.51
2286 2806 1.062258 TTCGCGATAACAACCGTGAC 58.938 50.000 10.88 0.00 43.64 3.67
2293 2813 2.028839 TGACCTCCTTTCGCGATAACAA 60.029 45.455 10.88 0.00 0.00 2.83
2301 2821 0.462759 CCTCCATGACCTCCTTTCGC 60.463 60.000 0.00 0.00 0.00 4.70
2328 2848 3.527533 ACGTTCTTGTTTGTACAGCTCA 58.472 40.909 0.00 0.00 35.28 4.26
2357 2877 4.293494 AGATAGAGATTGGCACTTCTCCA 58.707 43.478 18.32 9.31 38.46 3.86
2376 2896 2.434702 GACGTTCCACCATAGGGAAGAT 59.565 50.000 0.00 0.00 44.68 2.40
2408 2928 3.124806 GCAATGGATCATCTAGCATGACG 59.875 47.826 0.00 0.00 0.00 4.35
2412 2932 3.244318 TGACGCAATGGATCATCTAGCAT 60.244 43.478 0.00 0.00 0.00 3.79
2451 2971 5.992217 AGTCTGGCTAACTTTTCTGTTGTAG 59.008 40.000 0.00 0.00 0.00 2.74
2533 3055 3.545078 CGGACGTTATCCTACTTTTCGTG 59.455 47.826 0.00 0.00 46.69 4.35
2561 3083 1.819928 TGTGTGCATCGCTTGGTATT 58.180 45.000 0.00 0.00 0.00 1.89
2710 3243 5.575957 CATCTACGTCTGTACCGTGTTAAT 58.424 41.667 0.00 0.00 39.22 1.40
2749 3282 6.200100 CGTGTATTCATAGAGGTGAGTGTAC 58.800 44.000 0.00 0.00 0.00 2.90
2760 3293 3.555547 GTGTGCATGCGTGTATTCATAGA 59.444 43.478 14.09 0.00 0.00 1.98
2860 3412 1.202256 GGACGTAGCATCGATCACACA 60.202 52.381 0.00 0.00 34.70 3.72
2915 3481 4.798882 TGTGGGTTGATTACCTGAAAGTT 58.201 39.130 0.00 0.00 46.86 2.66
2938 3504 8.811378 ACGTAGACTACAAGTTTAAAAGTGAAC 58.189 33.333 12.99 0.00 0.00 3.18
2950 3516 9.918630 AATATTTGTTGTACGTAGACTACAAGT 57.081 29.630 14.86 14.68 42.92 3.16
3062 3689 9.855021 GCACAAATATTTAGTACCACTTTGAAT 57.145 29.630 0.00 0.00 0.00 2.57
3063 3690 8.018520 CGCACAAATATTTAGTACCACTTTGAA 58.981 33.333 0.00 0.00 0.00 2.69
3064 3691 7.173562 ACGCACAAATATTTAGTACCACTTTGA 59.826 33.333 0.00 0.00 0.00 2.69
3065 3692 7.302524 ACGCACAAATATTTAGTACCACTTTG 58.697 34.615 0.00 0.00 0.00 2.77
3066 3693 7.361457 GGACGCACAAATATTTAGTACCACTTT 60.361 37.037 0.00 0.00 0.00 2.66
3067 3694 6.093082 GGACGCACAAATATTTAGTACCACTT 59.907 38.462 0.00 0.00 0.00 3.16
3068 3695 5.583457 GGACGCACAAATATTTAGTACCACT 59.417 40.000 0.00 0.00 0.00 4.00
3069 3696 5.352016 TGGACGCACAAATATTTAGTACCAC 59.648 40.000 0.00 0.00 0.00 4.16
3070 3697 5.489249 TGGACGCACAAATATTTAGTACCA 58.511 37.500 0.00 4.11 0.00 3.25
3071 3698 6.482308 AGATGGACGCACAAATATTTAGTACC 59.518 38.462 0.00 1.73 0.00 3.34
3072 3699 7.011109 ACAGATGGACGCACAAATATTTAGTAC 59.989 37.037 0.00 1.20 0.00 2.73
3073 3700 7.045416 ACAGATGGACGCACAAATATTTAGTA 58.955 34.615 0.00 0.00 0.00 1.82
3074 3701 5.880332 ACAGATGGACGCACAAATATTTAGT 59.120 36.000 0.00 0.00 0.00 2.24
3075 3702 6.363577 ACAGATGGACGCACAAATATTTAG 57.636 37.500 0.00 0.00 0.00 1.85
3076 3703 6.751514 AACAGATGGACGCACAAATATTTA 57.248 33.333 0.00 0.00 0.00 1.40
3077 3704 5.643379 AACAGATGGACGCACAAATATTT 57.357 34.783 0.00 0.00 0.00 1.40
3078 3705 6.112734 TCTAACAGATGGACGCACAAATATT 58.887 36.000 0.00 0.00 0.00 1.28
3079 3706 5.670485 TCTAACAGATGGACGCACAAATAT 58.330 37.500 0.00 0.00 0.00 1.28
3080 3707 5.079689 TCTAACAGATGGACGCACAAATA 57.920 39.130 0.00 0.00 0.00 1.40
3081 3708 3.937814 TCTAACAGATGGACGCACAAAT 58.062 40.909 0.00 0.00 0.00 2.32
3082 3709 3.394674 TCTAACAGATGGACGCACAAA 57.605 42.857 0.00 0.00 0.00 2.83
3083 3710 3.394674 TTCTAACAGATGGACGCACAA 57.605 42.857 0.00 0.00 0.00 3.33
3084 3711 3.394674 TTTCTAACAGATGGACGCACA 57.605 42.857 0.00 0.00 0.00 4.57
3085 3712 3.994392 TCTTTTCTAACAGATGGACGCAC 59.006 43.478 0.00 0.00 0.00 5.34
3086 3713 4.265904 TCTTTTCTAACAGATGGACGCA 57.734 40.909 0.00 0.00 0.00 5.24
3087 3714 5.803020 ATTCTTTTCTAACAGATGGACGC 57.197 39.130 0.00 0.00 0.00 5.19
3088 3715 8.338259 CCATTATTCTTTTCTAACAGATGGACG 58.662 37.037 0.00 0.00 33.81 4.79
3089 3716 9.178758 ACCATTATTCTTTTCTAACAGATGGAC 57.821 33.333 0.00 0.00 35.48 4.02
3090 3717 9.753674 AACCATTATTCTTTTCTAACAGATGGA 57.246 29.630 0.00 0.00 35.48 3.41
3095 3722 9.626045 GGTCAAACCATTATTCTTTTCTAACAG 57.374 33.333 0.00 0.00 38.42 3.16
3096 3723 9.137459 TGGTCAAACCATTATTCTTTTCTAACA 57.863 29.630 0.00 0.00 44.79 2.41
3113 3740 3.575965 ATGCGAAATTCTGGTCAAACC 57.424 42.857 0.00 0.00 39.22 3.27
3114 3741 5.036737 CCATATGCGAAATTCTGGTCAAAC 58.963 41.667 0.00 0.00 0.00 2.93
3115 3742 4.097741 CCCATATGCGAAATTCTGGTCAAA 59.902 41.667 0.00 0.00 0.00 2.69
3116 3743 3.631686 CCCATATGCGAAATTCTGGTCAA 59.368 43.478 0.00 0.00 0.00 3.18
3117 3744 3.213506 CCCATATGCGAAATTCTGGTCA 58.786 45.455 0.00 0.00 0.00 4.02
3118 3745 2.030805 GCCCATATGCGAAATTCTGGTC 60.031 50.000 0.00 0.00 0.00 4.02
3119 3746 1.956477 GCCCATATGCGAAATTCTGGT 59.044 47.619 0.00 0.00 0.00 4.00
3120 3747 1.270550 GGCCCATATGCGAAATTCTGG 59.729 52.381 0.00 0.00 0.00 3.86
3121 3748 1.955778 TGGCCCATATGCGAAATTCTG 59.044 47.619 0.00 0.00 0.00 3.02
3122 3749 1.956477 GTGGCCCATATGCGAAATTCT 59.044 47.619 0.00 0.00 0.00 2.40
3123 3750 1.334960 CGTGGCCCATATGCGAAATTC 60.335 52.381 0.00 0.00 0.00 2.17
3124 3751 0.667993 CGTGGCCCATATGCGAAATT 59.332 50.000 0.00 0.00 0.00 1.82
3125 3752 1.795170 GCGTGGCCCATATGCGAAAT 61.795 55.000 0.00 0.00 0.00 2.17
3126 3753 2.477176 GCGTGGCCCATATGCGAAA 61.477 57.895 0.00 0.00 0.00 3.46
3127 3754 2.899838 GCGTGGCCCATATGCGAA 60.900 61.111 0.00 0.00 0.00 4.70
3130 3757 3.952675 CACGCGTGGCCCATATGC 61.953 66.667 31.15 0.00 0.00 3.14
3131 3758 3.952675 GCACGCGTGGCCCATATG 61.953 66.667 37.47 12.23 0.00 1.78
3132 3759 4.175337 AGCACGCGTGGCCCATAT 62.175 61.111 37.47 12.89 0.00 1.78
3133 3760 4.830765 GAGCACGCGTGGCCCATA 62.831 66.667 37.47 0.00 0.00 2.74
3155 3782 2.668212 TTGGTTGGCTTCGCTCGG 60.668 61.111 0.00 0.00 0.00 4.63
3156 3783 1.507141 AAGTTGGTTGGCTTCGCTCG 61.507 55.000 0.00 0.00 0.00 5.03
3157 3784 1.519408 TAAGTTGGTTGGCTTCGCTC 58.481 50.000 0.00 0.00 0.00 5.03
3158 3785 1.975660 TTAAGTTGGTTGGCTTCGCT 58.024 45.000 0.00 0.00 0.00 4.93
3159 3786 3.297830 AATTAAGTTGGTTGGCTTCGC 57.702 42.857 0.00 0.00 0.00 4.70
3160 3787 5.856455 CAGTAAATTAAGTTGGTTGGCTTCG 59.144 40.000 0.00 0.00 0.00 3.79
3161 3788 5.633601 GCAGTAAATTAAGTTGGTTGGCTTC 59.366 40.000 0.00 0.00 0.00 3.86
3162 3789 5.510690 GGCAGTAAATTAAGTTGGTTGGCTT 60.511 40.000 0.00 0.00 0.00 4.35
3163 3790 4.021456 GGCAGTAAATTAAGTTGGTTGGCT 60.021 41.667 0.00 0.00 0.00 4.75
3164 3791 4.242475 GGCAGTAAATTAAGTTGGTTGGC 58.758 43.478 0.00 3.08 0.00 4.52
3165 3792 5.461032 TGGCAGTAAATTAAGTTGGTTGG 57.539 39.130 0.00 0.00 0.00 3.77
3166 3793 5.925969 CCTTGGCAGTAAATTAAGTTGGTTG 59.074 40.000 0.00 0.00 0.00 3.77
3167 3794 5.600898 ACCTTGGCAGTAAATTAAGTTGGTT 59.399 36.000 0.00 0.00 0.00 3.67
3168 3795 5.144832 ACCTTGGCAGTAAATTAAGTTGGT 58.855 37.500 0.00 0.00 0.00 3.67
3169 3796 5.722021 ACCTTGGCAGTAAATTAAGTTGG 57.278 39.130 0.00 0.00 0.00 3.77
3170 3797 7.696453 CGAATACCTTGGCAGTAAATTAAGTTG 59.304 37.037 0.00 0.00 0.00 3.16
3171 3798 7.148137 CCGAATACCTTGGCAGTAAATTAAGTT 60.148 37.037 0.00 0.00 0.00 2.66
3172 3799 6.317893 CCGAATACCTTGGCAGTAAATTAAGT 59.682 38.462 0.00 0.00 0.00 2.24
3173 3800 6.238648 CCCGAATACCTTGGCAGTAAATTAAG 60.239 42.308 0.00 0.00 0.00 1.85
3174 3801 5.591067 CCCGAATACCTTGGCAGTAAATTAA 59.409 40.000 0.00 0.00 0.00 1.40
3175 3802 5.104444 TCCCGAATACCTTGGCAGTAAATTA 60.104 40.000 0.00 0.00 0.00 1.40
3176 3803 3.951680 CCCGAATACCTTGGCAGTAAATT 59.048 43.478 0.00 0.00 0.00 1.82
3177 3804 3.201266 TCCCGAATACCTTGGCAGTAAAT 59.799 43.478 0.00 0.00 0.00 1.40
3178 3805 2.572556 TCCCGAATACCTTGGCAGTAAA 59.427 45.455 0.00 0.00 0.00 2.01
3179 3806 2.189676 TCCCGAATACCTTGGCAGTAA 58.810 47.619 0.00 0.00 0.00 2.24
3180 3807 1.868713 TCCCGAATACCTTGGCAGTA 58.131 50.000 0.00 0.00 0.00 2.74
3181 3808 0.988832 TTCCCGAATACCTTGGCAGT 59.011 50.000 0.00 0.00 0.00 4.40
3182 3809 2.122783 TTTCCCGAATACCTTGGCAG 57.877 50.000 0.00 0.00 0.00 4.85
3183 3810 2.164338 GTTTTCCCGAATACCTTGGCA 58.836 47.619 0.00 0.00 0.00 4.92
3184 3811 2.422479 GAGTTTTCCCGAATACCTTGGC 59.578 50.000 0.00 0.00 0.00 4.52
3185 3812 3.951663 AGAGTTTTCCCGAATACCTTGG 58.048 45.455 0.00 0.00 0.00 3.61
3186 3813 7.120726 ACAAATAGAGTTTTCCCGAATACCTTG 59.879 37.037 0.00 0.00 0.00 3.61
3187 3814 7.173032 ACAAATAGAGTTTTCCCGAATACCTT 58.827 34.615 0.00 0.00 0.00 3.50
3188 3815 6.718294 ACAAATAGAGTTTTCCCGAATACCT 58.282 36.000 0.00 0.00 0.00 3.08
3189 3816 6.238022 CGACAAATAGAGTTTTCCCGAATACC 60.238 42.308 0.00 0.00 0.00 2.73
3190 3817 6.702897 CGACAAATAGAGTTTTCCCGAATAC 58.297 40.000 0.00 0.00 0.00 1.89
3191 3818 5.292589 GCGACAAATAGAGTTTTCCCGAATA 59.707 40.000 0.00 0.00 0.00 1.75
3192 3819 4.094442 GCGACAAATAGAGTTTTCCCGAAT 59.906 41.667 0.00 0.00 0.00 3.34
3193 3820 3.434299 GCGACAAATAGAGTTTTCCCGAA 59.566 43.478 0.00 0.00 0.00 4.30
3194 3821 2.997986 GCGACAAATAGAGTTTTCCCGA 59.002 45.455 0.00 0.00 0.00 5.14
3195 3822 3.000727 AGCGACAAATAGAGTTTTCCCG 58.999 45.455 0.00 0.00 0.00 5.14
3196 3823 3.062234 CGAGCGACAAATAGAGTTTTCCC 59.938 47.826 0.00 0.00 0.00 3.97
3197 3824 3.062234 CCGAGCGACAAATAGAGTTTTCC 59.938 47.826 0.00 0.00 0.00 3.13
3198 3825 3.678548 ACCGAGCGACAAATAGAGTTTTC 59.321 43.478 0.00 0.00 0.00 2.29
3199 3826 3.432252 CACCGAGCGACAAATAGAGTTTT 59.568 43.478 0.00 0.00 0.00 2.43
3200 3827 2.993899 CACCGAGCGACAAATAGAGTTT 59.006 45.455 0.00 0.00 0.00 2.66
3201 3828 2.607187 CACCGAGCGACAAATAGAGTT 58.393 47.619 0.00 0.00 0.00 3.01
3202 3829 1.736032 GCACCGAGCGACAAATAGAGT 60.736 52.381 0.00 0.00 0.00 3.24
3203 3830 0.924090 GCACCGAGCGACAAATAGAG 59.076 55.000 0.00 0.00 0.00 2.43
3204 3831 3.044809 GCACCGAGCGACAAATAGA 57.955 52.632 0.00 0.00 0.00 1.98
3214 3841 0.600255 ACTAATATGCCGCACCGAGC 60.600 55.000 0.00 0.00 40.87 5.03
3215 3842 1.269569 TGACTAATATGCCGCACCGAG 60.270 52.381 0.00 0.00 0.00 4.63
3216 3843 0.747852 TGACTAATATGCCGCACCGA 59.252 50.000 0.00 0.00 0.00 4.69
3217 3844 1.139989 CTGACTAATATGCCGCACCG 58.860 55.000 0.00 0.00 0.00 4.94
3218 3845 1.512926 CCTGACTAATATGCCGCACC 58.487 55.000 0.00 0.00 0.00 5.01
3219 3846 1.512926 CCCTGACTAATATGCCGCAC 58.487 55.000 0.00 0.00 0.00 5.34
3220 3847 0.250295 GCCCTGACTAATATGCCGCA 60.250 55.000 0.00 0.00 0.00 5.69
3221 3848 0.955919 GGCCCTGACTAATATGCCGC 60.956 60.000 0.00 0.00 0.00 6.53
3222 3849 0.687354 AGGCCCTGACTAATATGCCG 59.313 55.000 0.00 0.00 43.56 5.69
3223 3850 1.338200 CGAGGCCCTGACTAATATGCC 60.338 57.143 0.00 0.00 39.17 4.40
3224 3851 1.941668 GCGAGGCCCTGACTAATATGC 60.942 57.143 0.00 0.00 0.00 3.14
3225 3852 1.344438 TGCGAGGCCCTGACTAATATG 59.656 52.381 0.00 0.00 0.00 1.78
3226 3853 1.344763 GTGCGAGGCCCTGACTAATAT 59.655 52.381 0.00 0.00 0.00 1.28
3227 3854 0.750850 GTGCGAGGCCCTGACTAATA 59.249 55.000 0.00 0.00 0.00 0.98
3228 3855 1.264749 TGTGCGAGGCCCTGACTAAT 61.265 55.000 0.00 0.00 0.00 1.73
3229 3856 1.264749 ATGTGCGAGGCCCTGACTAA 61.265 55.000 0.00 0.00 0.00 2.24
3230 3857 1.685765 ATGTGCGAGGCCCTGACTA 60.686 57.895 0.00 0.00 0.00 2.59
3231 3858 3.005539 ATGTGCGAGGCCCTGACT 61.006 61.111 0.00 0.00 0.00 3.41
3232 3859 2.821366 CATGTGCGAGGCCCTGAC 60.821 66.667 0.00 0.00 0.00 3.51
3233 3860 4.100084 CCATGTGCGAGGCCCTGA 62.100 66.667 0.00 0.00 0.00 3.86
3239 3866 4.720902 TGGGTGCCATGTGCGAGG 62.721 66.667 0.00 0.00 45.60 4.63
3240 3867 2.672651 TTGGGTGCCATGTGCGAG 60.673 61.111 0.00 0.00 45.60 5.03
3241 3868 2.672651 CTTGGGTGCCATGTGCGA 60.673 61.111 0.00 0.00 45.60 5.10
3242 3869 2.672651 TCTTGGGTGCCATGTGCG 60.673 61.111 0.00 0.00 45.60 5.34
3243 3870 1.604593 AGTCTTGGGTGCCATGTGC 60.605 57.895 0.00 0.00 41.77 4.57
3244 3871 1.246056 CCAGTCTTGGGTGCCATGTG 61.246 60.000 0.00 0.00 41.05 3.21
3245 3872 1.075482 CCAGTCTTGGGTGCCATGT 59.925 57.895 0.00 0.00 41.05 3.21
3246 3873 2.345760 GCCAGTCTTGGGTGCCATG 61.346 63.158 0.00 0.00 45.16 3.66
3247 3874 2.036256 GCCAGTCTTGGGTGCCAT 59.964 61.111 0.00 0.00 45.16 4.40
3248 3875 4.284550 GGCCAGTCTTGGGTGCCA 62.285 66.667 0.00 0.00 45.16 4.92
3251 3878 4.722700 CCGGGCCAGTCTTGGGTG 62.723 72.222 4.39 0.00 45.16 4.61
3263 3890 1.334384 AATACCAAAATGGGCCGGGC 61.334 55.000 22.00 22.00 43.37 6.13
3264 3891 2.074729 TAATACCAAAATGGGCCGGG 57.925 50.000 2.18 0.00 43.37 5.73
3265 3892 3.496331 AGATAATACCAAAATGGGCCGG 58.504 45.455 0.00 0.00 43.37 6.13
3266 3893 4.216257 CAGAGATAATACCAAAATGGGCCG 59.784 45.833 0.00 0.00 43.37 6.13
3267 3894 5.140454 ACAGAGATAATACCAAAATGGGCC 58.860 41.667 0.00 0.00 43.37 5.80
3268 3895 7.817418 TTACAGAGATAATACCAAAATGGGC 57.183 36.000 0.87 0.00 43.37 5.36
3392 4019 9.844257 AGTTTTGGAAAAATTGACCAATATTGA 57.156 25.926 17.23 0.00 42.14 2.57
3396 4023 9.672673 TGAAAGTTTTGGAAAAATTGACCAATA 57.327 25.926 10.56 5.36 42.14 1.90
3397 4024 8.458052 GTGAAAGTTTTGGAAAAATTGACCAAT 58.542 29.630 10.56 0.00 42.14 3.16
3398 4025 7.445402 TGTGAAAGTTTTGGAAAAATTGACCAA 59.555 29.630 0.00 0.00 41.12 3.67
3399 4026 6.936900 TGTGAAAGTTTTGGAAAAATTGACCA 59.063 30.769 0.00 0.00 36.46 4.02
3400 4027 7.371126 TGTGAAAGTTTTGGAAAAATTGACC 57.629 32.000 0.00 0.00 36.46 4.02
3401 4028 9.838975 AATTGTGAAAGTTTTGGAAAAATTGAC 57.161 25.926 0.00 1.11 36.46 3.18
3408 4035 9.670719 GTTTGAAAATTGTGAAAGTTTTGGAAA 57.329 25.926 0.00 0.00 0.00 3.13
3409 4036 8.840321 TGTTTGAAAATTGTGAAAGTTTTGGAA 58.160 25.926 0.00 0.00 0.00 3.53
3410 4037 8.383318 TGTTTGAAAATTGTGAAAGTTTTGGA 57.617 26.923 0.00 0.00 0.00 3.53
3411 4038 9.455847 TTTGTTTGAAAATTGTGAAAGTTTTGG 57.544 25.926 0.00 0.00 0.00 3.28
3471 4098 9.672086 CACAACTTTTGGAACGAGAAAAATATA 57.328 29.630 0.00 0.00 34.12 0.86
3472 4099 8.574196 CACAACTTTTGGAACGAGAAAAATAT 57.426 30.769 0.00 0.00 34.12 1.28
3473 4100 7.979115 CACAACTTTTGGAACGAGAAAAATA 57.021 32.000 0.00 0.00 34.12 1.40
3474 4101 6.885735 CACAACTTTTGGAACGAGAAAAAT 57.114 33.333 0.00 0.00 34.12 1.82


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

AutoCloner maintained by Alex Coulton.