Multiple sequence alignment - TraesCS4B01G085200

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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 TraesCS4B01G085200 chr4B 100.000 7738 0 0 586 8323 85695305 85703042 0.000000e+00 14290.0
1 TraesCS4B01G085200 chr4B 100.000 212 0 0 1 212 85694720 85694931 7.830000e-105 392.0
2 TraesCS4B01G085200 chr4B 83.333 96 11 2 3266 3361 217854105 217854015 5.350000e-12 84.2
3 TraesCS4B01G085200 chr4D 95.514 5796 144 46 2565 8323 57071027 57076743 0.000000e+00 9156.0
4 TraesCS4B01G085200 chr4D 96.072 1731 39 9 856 2564 57069211 57070934 0.000000e+00 2793.0
5 TraesCS4B01G085200 chr4D 89.320 206 18 3 1 206 57068076 57068277 1.070000e-63 255.0
6 TraesCS4B01G085200 chr4D 85.892 241 27 5 586 825 57068717 57068951 4.990000e-62 250.0
7 TraesCS4B01G085200 chr4A 90.219 2556 177 40 4425 6929 539757907 539755374 0.000000e+00 3267.0
8 TraesCS4B01G085200 chr4A 95.581 1720 42 10 871 2564 539761463 539759752 0.000000e+00 2724.0
9 TraesCS4B01G085200 chr4A 96.053 988 34 3 3390 4377 539758880 539757898 0.000000e+00 1604.0
10 TraesCS4B01G085200 chr4A 96.628 771 23 2 2565 3334 539759659 539758891 0.000000e+00 1277.0
11 TraesCS4B01G085200 chr4A 93.861 847 44 5 7478 8323 539754798 539753959 0.000000e+00 1269.0
12 TraesCS4B01G085200 chr5B 81.569 255 29 12 1559 1807 700927661 700927419 2.370000e-45 195.0
13 TraesCS4B01G085200 chr7D 81.855 248 27 10 1559 1800 578156783 578157018 8.530000e-45 193.0
14 TraesCS4B01G085200 chr7D 84.348 115 15 3 3152 3265 500619052 500619164 8.830000e-20 110.0
15 TraesCS4B01G085200 chr7A 80.784 255 37 10 1557 1801 158289725 158289473 1.100000e-43 189.0
16 TraesCS4B01G085200 chr7A 84.211 95 8 5 1410 1503 158289839 158289751 1.490000e-12 86.1
17 TraesCS4B01G085200 chr7A 91.379 58 3 2 1410 1466 668560327 668560383 2.490000e-10 78.7
18 TraesCS4B01G085200 chr6B 81.526 249 28 12 1559 1801 21846562 21846798 1.100000e-43 189.0
19 TraesCS4B01G085200 chr7B 80.400 250 37 8 1562 1801 685044802 685044555 6.640000e-41 180.0
20 TraesCS4B01G085200 chr7B 84.483 116 13 5 3152 3266 135068052 135067941 8.830000e-20 110.0
21 TraesCS4B01G085200 chr6A 79.184 245 39 10 1567 1801 189575501 189575743 8.650000e-35 159.0
22 TraesCS4B01G085200 chr6A 89.655 58 4 2 1410 1466 189575139 189575195 1.160000e-08 73.1
23 TraesCS4B01G085200 chr3A 84.483 116 15 2 3150 3264 53883373 53883260 2.460000e-20 111.0
24 TraesCS4B01G085200 chr2A 85.455 110 13 2 3150 3258 528376210 528376103 2.460000e-20 111.0
25 TraesCS4B01G085200 chr2A 85.455 110 13 2 3150 3258 606574226 606574333 2.460000e-20 111.0
26 TraesCS4B01G085200 chr2A 83.158 95 9 5 1410 1503 186434813 186434725 6.930000e-11 80.5
27 TraesCS4B01G085200 chr1A 85.455 110 13 2 3150 3258 331542589 331542482 2.460000e-20 111.0
28 TraesCS4B01G085200 chr1A 85.455 110 13 2 3150 3258 333917872 333917979 2.460000e-20 111.0
29 TraesCS4B01G085200 chr5D 75.000 228 35 12 3152 3361 417734361 417734584 1.490000e-12 86.1


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 TraesCS4B01G085200 chr4B 85694720 85703042 8322 False 7341.0 14290 100.0000 1 8323 2 chr4B.!!$F1 8322
1 TraesCS4B01G085200 chr4D 57068076 57076743 8667 False 3113.5 9156 91.6995 1 8323 4 chr4D.!!$F1 8322
2 TraesCS4B01G085200 chr4A 539753959 539761463 7504 True 2028.2 3267 94.4684 871 8323 5 chr4A.!!$R1 7452

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
152 153 0.456312 GGCGTCTGTCGAACGAGAAT 60.456 55.000 12.06 0.0 42.62 2.40 F
806 869 1.101331 ATCGAACGGAGGGAGTACAC 58.899 55.000 0.00 0.0 0.00 2.90 F
939 1231 1.593006 GCATGGACCGAAAGATGTACG 59.407 52.381 0.00 0.0 0.00 3.67 F
1234 1529 1.703411 CTTGTGTTGGGGGTTCATGT 58.297 50.000 0.00 0.0 0.00 3.21 F
1324 1619 2.742589 GGATTCTGGTTTCTTCGTCCAC 59.257 50.000 0.00 0.0 0.00 4.02 F
1924 2244 2.936498 CGTCTTTCAGTGTTTCACCTGT 59.064 45.455 0.00 0.0 34.49 4.00 F
3071 3486 4.218417 TGCTCCATAAAAAGCACTTCCTTC 59.782 41.667 0.00 0.0 43.30 3.46 F
5040 5500 0.105964 TCAGTGGTCAAGTGGGAACG 59.894 55.000 0.00 0.0 0.00 3.95 F
6290 6773 0.032815 TGTCAGGATGCGTCAAACGA 59.967 50.000 8.47 0.0 44.57 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1529 0.606096 TAAGTAGCTGCGGAAGTGCA 59.394 50.000 0.00 0.00 43.95 4.57 R
1924 2244 1.556451 AGATATGTGTCACCTGCTGCA 59.444 47.619 0.88 0.88 0.00 4.41 R
2045 2365 1.805945 GACAGTGGGAGCGCTAACG 60.806 63.158 11.50 8.53 44.07 3.18 R
2095 2415 2.068821 GCCCTGAGCATCCTCTCCA 61.069 63.158 0.00 0.00 42.97 3.86 R
2930 3345 3.264450 AGTGCCACTAAGCAGATTACCTT 59.736 43.478 0.00 0.00 45.14 3.50 R
3756 4172 1.879380 TGTGTGTATGGCAAACAGCTC 59.121 47.619 0.00 0.00 40.22 4.09 R
5058 5518 0.106918 TTGCTCGGGTTGTGTTCCTT 60.107 50.000 0.00 0.00 0.00 3.36 R
6902 7388 0.027586 CGCCACGCTAAAGCCATAAC 59.972 55.000 0.00 0.00 37.91 1.89 R
8143 8781 0.462581 GAATCTGAGGATGTGCCGCA 60.463 55.000 0.00 0.00 44.78 5.69 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
25 26 2.614134 TTTGGAGTATTTGGGGTGGG 57.386 50.000 0.00 0.00 0.00 4.61
59 60 2.953648 TGTCTGAGAGGTGTTTGTACGA 59.046 45.455 0.00 0.00 0.00 3.43
62 63 1.342174 TGAGAGGTGTTTGTACGACCC 59.658 52.381 0.00 0.00 0.00 4.46
111 112 2.836667 TGGGAACTACCGAATAACCCT 58.163 47.619 0.00 0.00 40.11 4.34
114 115 3.431346 GGGAACTACCGAATAACCCTGAC 60.431 52.174 0.00 0.00 40.11 3.51
120 121 4.417426 ACCGAATAACCCTGACCATTAG 57.583 45.455 0.00 0.00 0.00 1.73
138 139 2.251642 GGTTGGATATGCGGGCGTC 61.252 63.158 0.00 0.00 0.00 5.19
151 152 1.081641 GGCGTCTGTCGAACGAGAA 60.082 57.895 12.06 0.00 42.62 2.87
152 153 0.456312 GGCGTCTGTCGAACGAGAAT 60.456 55.000 12.06 0.00 42.62 2.40
174 175 5.518848 TTTTCTGTCCGTACACTGTCTAA 57.481 39.130 0.00 0.00 0.00 2.10
176 177 2.486982 TCTGTCCGTACACTGTCTAAGC 59.513 50.000 0.00 0.00 0.00 3.09
180 181 2.486982 TCCGTACACTGTCTAAGCTGTC 59.513 50.000 0.00 0.00 0.00 3.51
195 196 1.335506 GCTGTCCGCTAGAGCATACTC 60.336 57.143 1.89 0.00 43.90 2.59
196 197 4.811102 GCTGTCCGCTAGAGCATACTCG 62.811 59.091 1.89 0.00 43.90 4.18
608 671 6.363577 ACTTTGGCTCGTTGTTCATATATG 57.636 37.500 6.36 6.36 0.00 1.78
609 672 5.880332 ACTTTGGCTCGTTGTTCATATATGT 59.120 36.000 12.42 0.00 0.00 2.29
610 673 5.733226 TTGGCTCGTTGTTCATATATGTG 57.267 39.130 12.42 0.00 0.00 3.21
626 689 9.051679 TCATATATGTGTTAACACTTGTATGCC 57.948 33.333 35.81 17.44 45.16 4.40
689 752 8.526147 CCTCATAACTTTTTGTCATGATTTCCT 58.474 33.333 0.00 0.00 0.00 3.36
700 763 8.450578 TTGTCATGATTTCCTAACATCATACC 57.549 34.615 0.00 0.00 37.93 2.73
701 764 6.998074 TGTCATGATTTCCTAACATCATACCC 59.002 38.462 0.00 0.00 37.93 3.69
704 767 4.981647 TGATTTCCTAACATCATACCCCCT 59.018 41.667 0.00 0.00 0.00 4.79
710 773 1.807814 ACATCATACCCCCTCTGTCC 58.192 55.000 0.00 0.00 0.00 4.02
712 775 1.696336 CATCATACCCCCTCTGTCCAG 59.304 57.143 0.00 0.00 0.00 3.86
723 786 4.383118 CCCCTCTGTCCAGTACTAATTGTG 60.383 50.000 0.00 0.00 0.00 3.33
727 790 4.286032 TCTGTCCAGTACTAATTGTGGCTT 59.714 41.667 0.00 0.00 0.00 4.35
729 792 5.730550 TGTCCAGTACTAATTGTGGCTTAG 58.269 41.667 0.00 0.00 33.36 2.18
736 799 6.979238 AGTACTAATTGTGGCTTAGACGAATC 59.021 38.462 0.00 0.00 31.89 2.52
740 803 8.204836 ACTAATTGTGGCTTAGACGAATCTATT 58.795 33.333 0.00 0.00 37.28 1.73
760 823 9.640963 ATCTATTTAGCCGTATTTTAGTGCTAG 57.359 33.333 0.00 0.00 36.06 3.42
763 826 7.709269 TTTAGCCGTATTTTAGTGCTAGATG 57.291 36.000 0.00 0.00 36.06 2.90
776 839 2.826428 GCTAGATGCATCCGTTTGAGA 58.174 47.619 23.06 0.00 42.31 3.27
779 842 2.898705 AGATGCATCCGTTTGAGAGAC 58.101 47.619 23.06 0.00 0.00 3.36
781 844 2.084610 TGCATCCGTTTGAGAGACAG 57.915 50.000 0.00 0.00 0.00 3.51
789 852 7.306866 GCATCCGTTTGAGAGACAGTTAATATC 60.307 40.741 0.00 0.00 0.00 1.63
790 853 6.263344 TCCGTTTGAGAGACAGTTAATATCG 58.737 40.000 0.00 0.00 0.00 2.92
791 854 6.094464 TCCGTTTGAGAGACAGTTAATATCGA 59.906 38.462 0.00 0.00 0.00 3.59
801 864 4.037684 ACAGTTAATATCGAACGGAGGGAG 59.962 45.833 0.00 0.00 31.85 4.30
804 867 5.240403 AGTTAATATCGAACGGAGGGAGTAC 59.760 44.000 0.00 0.00 31.85 2.73
806 869 1.101331 ATCGAACGGAGGGAGTACAC 58.899 55.000 0.00 0.00 0.00 2.90
812 875 2.165998 ACGGAGGGAGTACACAGTAAC 58.834 52.381 0.00 0.00 0.00 2.50
814 877 2.422832 CGGAGGGAGTACACAGTAACTC 59.577 54.545 6.67 6.67 41.16 3.01
825 888 5.048846 ACACAGTAACTCCCTTCAACAAT 57.951 39.130 0.00 0.00 0.00 2.71
826 889 5.445964 ACACAGTAACTCCCTTCAACAATT 58.554 37.500 0.00 0.00 0.00 2.32
827 890 6.597562 ACACAGTAACTCCCTTCAACAATTA 58.402 36.000 0.00 0.00 0.00 1.40
829 892 7.724061 ACACAGTAACTCCCTTCAACAATTAAT 59.276 33.333 0.00 0.00 0.00 1.40
830 893 9.226606 CACAGTAACTCCCTTCAACAATTAATA 57.773 33.333 0.00 0.00 0.00 0.98
833 896 9.975218 AGTAACTCCCTTCAACAATTAATATGT 57.025 29.630 0.00 0.00 0.00 2.29
836 899 9.975218 AACTCCCTTCAACAATTAATATGTACT 57.025 29.630 0.00 0.00 0.00 2.73
837 900 9.396022 ACTCCCTTCAACAATTAATATGTACTG 57.604 33.333 0.00 0.00 0.00 2.74
838 901 9.396022 CTCCCTTCAACAATTAATATGTACTGT 57.604 33.333 0.00 0.00 0.00 3.55
839 902 9.173021 TCCCTTCAACAATTAATATGTACTGTG 57.827 33.333 0.00 0.00 0.00 3.66
840 903 8.956426 CCCTTCAACAATTAATATGTACTGTGT 58.044 33.333 0.00 0.00 0.00 3.72
841 904 9.773328 CCTTCAACAATTAATATGTACTGTGTG 57.227 33.333 0.00 0.00 0.00 3.82
842 905 9.277565 CTTCAACAATTAATATGTACTGTGTGC 57.722 33.333 0.00 0.00 0.00 4.57
843 906 8.329203 TCAACAATTAATATGTACTGTGTGCA 57.671 30.769 0.00 0.00 32.05 4.57
844 907 8.787852 TCAACAATTAATATGTACTGTGTGCAA 58.212 29.630 0.00 0.00 31.17 4.08
845 908 9.404348 CAACAATTAATATGTACTGTGTGCAAA 57.596 29.630 0.00 0.00 31.17 3.68
846 909 9.973450 AACAATTAATATGTACTGTGTGCAAAA 57.027 25.926 0.00 0.00 31.17 2.44
939 1231 1.593006 GCATGGACCGAAAGATGTACG 59.407 52.381 0.00 0.00 0.00 3.67
972 1264 5.514279 CAAGTACCAAACAGAGAGCAAAAG 58.486 41.667 0.00 0.00 0.00 2.27
982 1274 2.105477 AGAGAGCAAAAGGACAGCAGAA 59.895 45.455 0.00 0.00 0.00 3.02
1099 1392 2.140792 AGCAACCACCTCACCTCGT 61.141 57.895 0.00 0.00 0.00 4.18
1113 1406 3.515502 TCACCTCGTCTCTTTGAATCCAT 59.484 43.478 0.00 0.00 0.00 3.41
1114 1407 4.709886 TCACCTCGTCTCTTTGAATCCATA 59.290 41.667 0.00 0.00 0.00 2.74
1152 1445 9.699703 GCTTCTATAGAACTAGTTTATTCCCTG 57.300 37.037 11.24 0.06 0.00 4.45
1174 1467 2.803386 TCGTGCGCTACAAAAATCTTCA 59.197 40.909 9.73 0.00 0.00 3.02
1234 1529 1.703411 CTTGTGTTGGGGGTTCATGT 58.297 50.000 0.00 0.00 0.00 3.21
1324 1619 2.742589 GGATTCTGGTTTCTTCGTCCAC 59.257 50.000 0.00 0.00 0.00 4.02
1649 1950 7.824289 TCTGGGTAGATGAAAGTGTAAATTCTG 59.176 37.037 0.00 0.00 0.00 3.02
1664 1965 9.109393 GTGTAAATTCTGCACTATGGAAGATTA 57.891 33.333 0.00 0.00 37.64 1.75
1665 1966 9.330063 TGTAAATTCTGCACTATGGAAGATTAG 57.670 33.333 0.00 0.00 0.00 1.73
1666 1967 9.331282 GTAAATTCTGCACTATGGAAGATTAGT 57.669 33.333 0.00 0.00 0.00 2.24
1675 1994 7.329717 GCACTATGGAAGATTAGTAGGATTTCG 59.670 40.741 0.00 0.00 0.00 3.46
1712 2032 9.383519 CTAAAAGTAAATGTCTCTGCAGGAATA 57.616 33.333 15.13 0.76 0.00 1.75
1902 2222 5.006746 CCTTCATTTAGTGACGGTATCTTGC 59.993 44.000 0.00 0.00 40.46 4.01
1924 2244 2.936498 CGTCTTTCAGTGTTTCACCTGT 59.064 45.455 0.00 0.00 34.49 4.00
2784 3197 8.531982 ACTGAAGCAGATAGTATCAAGTTTGTA 58.468 33.333 12.66 1.17 35.18 2.41
2980 3395 6.618287 TCAAACTAGACAACTGGACAAATG 57.382 37.500 0.00 0.00 0.00 2.32
3071 3486 4.218417 TGCTCCATAAAAAGCACTTCCTTC 59.782 41.667 0.00 0.00 43.30 3.46
3160 3575 7.979786 TGATTCTTATCAAAGTACTCCCTCT 57.020 36.000 0.00 0.00 37.83 3.69
3171 3586 7.622081 TCAAAGTACTCCCTCTGTTCCATAATA 59.378 37.037 0.00 0.00 0.00 0.98
3172 3587 8.432805 CAAAGTACTCCCTCTGTTCCATAATAT 58.567 37.037 0.00 0.00 0.00 1.28
3173 3588 9.670442 AAAGTACTCCCTCTGTTCCATAATATA 57.330 33.333 0.00 0.00 0.00 0.86
3382 3798 9.182933 TCAAATGCGGTACAAACTTATTTTTAC 57.817 29.630 0.00 0.00 32.44 2.01
3415 3831 9.434559 GTTTGAAACTATCTACAGTTCAAACAC 57.565 33.333 24.54 8.62 44.00 3.32
3496 3912 5.185828 GGGTGCTAATTTTCTGTTCCAATCT 59.814 40.000 0.00 0.00 0.00 2.40
3579 3995 6.882610 TTTGTAATCTTGCAGTCTGTTCAT 57.117 33.333 0.93 0.00 0.00 2.57
3940 4356 7.200455 TCAATGACATGAGAATGCATGATTTC 58.800 34.615 0.00 0.00 46.64 2.17
4027 4443 5.688807 TCAAATCATCCCTTCTTCTCATCC 58.311 41.667 0.00 0.00 0.00 3.51
4148 4564 2.947652 ACTGGCAATGATGACTATGTGC 59.052 45.455 0.00 0.00 34.75 4.57
4171 4587 4.503714 AGAGTTTTTCCTTCCACTGACA 57.496 40.909 0.00 0.00 0.00 3.58
4380 4796 5.634859 CCAGTGAAGTCAAAATAAATGTGCC 59.365 40.000 0.00 0.00 0.00 5.01
4499 4919 3.446873 TCTCCTCTCTGTCTTCTGATTGC 59.553 47.826 0.00 0.00 0.00 3.56
4524 4944 0.250467 GCTTTCTGTGCTCCAGTCCA 60.250 55.000 4.27 0.00 42.19 4.02
4537 4965 2.105821 TCCAGTCCATAATAAAGGCCCG 59.894 50.000 0.00 0.00 0.00 6.13
4611 5060 7.164803 ACTGAAATTTTGGTCAACAAGGAAAA 58.835 30.769 0.00 0.00 40.82 2.29
4700 5151 2.089201 CCTGCTGCATCATCTTGTCAA 58.911 47.619 1.31 0.00 0.00 3.18
5007 5467 2.716814 TCCTCGAGGAATCCTACGC 58.283 57.895 31.91 0.00 42.18 4.42
5023 5483 1.218047 CGCGAAATGGGAGTCCTCA 59.782 57.895 9.58 5.96 0.00 3.86
5028 5488 1.630878 GAAATGGGAGTCCTCAGTGGT 59.369 52.381 9.58 0.00 37.07 4.16
5040 5500 0.105964 TCAGTGGTCAAGTGGGAACG 59.894 55.000 0.00 0.00 0.00 3.95
5058 5518 2.124529 TGTGACGTTGCTGGCCAA 60.125 55.556 7.01 0.00 0.00 4.52
5568 6045 4.633565 CAGGGAAGAATGTTAGCTTGACTC 59.366 45.833 0.00 0.00 0.00 3.36
5765 6244 6.432783 TCAATGGTTGTTATTCAGTTAGGTGG 59.567 38.462 0.00 0.00 0.00 4.61
5984 6464 7.120138 TCAGAATGTGATAAGTACTGTACACGA 59.880 37.037 19.27 5.04 37.40 4.35
6048 6528 7.888021 TGTATTGTTTCATCTGTTTCCCATACT 59.112 33.333 0.00 0.00 0.00 2.12
6139 6622 5.939447 TCCAACCTGATTATGATGCATACA 58.061 37.500 0.00 0.00 0.00 2.29
6290 6773 0.032815 TGTCAGGATGCGTCAAACGA 59.967 50.000 8.47 0.00 44.57 3.85
6390 6873 9.289782 GTATTGTGGAATTCTATTTCTATGCCT 57.710 33.333 5.23 0.00 0.00 4.75
6537 7020 2.235891 TGCTTGAAGAGTCGACCAGTA 58.764 47.619 13.01 0.00 0.00 2.74
6848 7333 5.475909 CGGGTAGTAGCTTTATATCTGGTCA 59.524 44.000 0.00 0.00 0.00 4.02
6901 7387 6.942532 AACACAGTGTTTTACTCATGACAT 57.057 33.333 13.53 0.00 37.26 3.06
6902 7388 6.304356 ACACAGTGTTTTACTCATGACATG 57.696 37.500 9.28 9.28 37.60 3.21
6904 7390 6.318648 ACACAGTGTTTTACTCATGACATGTT 59.681 34.615 14.98 6.46 37.60 2.71
6972 7542 4.319177 ACAATGTTCCTACTCAAGCTGTC 58.681 43.478 0.00 0.00 0.00 3.51
6976 7546 1.153549 CCTACTCAAGCTGTCGGCC 60.154 63.158 0.00 0.00 43.05 6.13
6989 7559 1.138859 TGTCGGCCATCTGGAACTATG 59.861 52.381 2.24 0.00 37.39 2.23
6991 7561 1.138859 TCGGCCATCTGGAACTATGTG 59.861 52.381 2.24 0.00 37.39 3.21
7010 7580 1.650912 GCTGTTGAGCACACCACTG 59.349 57.895 0.00 0.00 45.46 3.66
7012 7582 1.224075 CTGTTGAGCACACCACTGAG 58.776 55.000 0.00 0.00 0.00 3.35
7013 7583 0.829990 TGTTGAGCACACCACTGAGA 59.170 50.000 0.00 0.00 0.00 3.27
7014 7584 1.209261 TGTTGAGCACACCACTGAGAA 59.791 47.619 0.00 0.00 0.00 2.87
7015 7585 1.869767 GTTGAGCACACCACTGAGAAG 59.130 52.381 0.00 0.00 0.00 2.85
7016 7586 0.394192 TGAGCACACCACTGAGAAGG 59.606 55.000 0.00 0.00 0.00 3.46
7017 7587 0.394565 GAGCACACCACTGAGAAGGT 59.605 55.000 0.00 0.00 39.10 3.50
7018 7588 0.394565 AGCACACCACTGAGAAGGTC 59.605 55.000 0.00 0.00 35.52 3.85
7019 7589 0.394565 GCACACCACTGAGAAGGTCT 59.605 55.000 0.00 0.00 35.52 3.85
7020 7590 1.202698 GCACACCACTGAGAAGGTCTT 60.203 52.381 0.00 0.00 35.52 3.01
7021 7591 2.487934 CACACCACTGAGAAGGTCTTG 58.512 52.381 0.00 0.00 35.52 3.02
7022 7592 1.417890 ACACCACTGAGAAGGTCTTGG 59.582 52.381 0.00 0.00 35.52 3.61
7023 7593 0.398318 ACCACTGAGAAGGTCTTGGC 59.602 55.000 0.00 0.00 34.07 4.52
7024 7594 0.671781 CCACTGAGAAGGTCTTGGCG 60.672 60.000 0.00 0.00 0.00 5.69
7025 7595 1.004440 ACTGAGAAGGTCTTGGCGC 60.004 57.895 0.00 0.00 0.00 6.53
7026 7596 1.004560 CTGAGAAGGTCTTGGCGCA 60.005 57.895 10.83 0.00 0.00 6.09
7027 7597 0.392193 CTGAGAAGGTCTTGGCGCAT 60.392 55.000 10.83 0.00 0.00 4.73
7028 7598 0.036732 TGAGAAGGTCTTGGCGCATT 59.963 50.000 10.83 0.00 0.00 3.56
7029 7599 0.449388 GAGAAGGTCTTGGCGCATTG 59.551 55.000 10.83 0.00 0.00 2.82
7030 7600 0.036732 AGAAGGTCTTGGCGCATTGA 59.963 50.000 10.83 0.00 0.00 2.57
7031 7601 0.449388 GAAGGTCTTGGCGCATTGAG 59.551 55.000 10.83 0.45 0.00 3.02
7032 7602 0.250901 AAGGTCTTGGCGCATTGAGT 60.251 50.000 10.83 0.00 0.00 3.41
7033 7603 0.613260 AGGTCTTGGCGCATTGAGTA 59.387 50.000 10.83 0.00 0.00 2.59
7034 7604 1.009829 GGTCTTGGCGCATTGAGTAG 58.990 55.000 10.83 0.00 0.00 2.57
7100 7685 9.186837 TGGTAGTTTTATTTCACCTTTGTACAA 57.813 29.630 3.59 3.59 0.00 2.41
7125 7710 7.633193 ATTTTTGCCGATGTACCATTAGTAA 57.367 32.000 0.00 0.00 31.05 2.24
7131 7716 6.183360 TGCCGATGTACCATTAGTAATACCAA 60.183 38.462 0.00 0.00 31.05 3.67
7176 7767 4.344968 CACACTTCAAAAAGGGGAAGGATT 59.655 41.667 0.00 0.00 43.70 3.01
7189 7780 3.385111 GGGAAGGATTCTGAGTGTACGAT 59.615 47.826 0.00 0.00 46.56 3.73
7222 7813 7.814264 ATTTCTGAAGTTATTAGGCCATCAG 57.186 36.000 5.01 5.58 35.35 2.90
7223 7814 4.708177 TCTGAAGTTATTAGGCCATCAGC 58.292 43.478 5.01 0.00 42.60 4.26
7231 7827 3.931907 TTAGGCCATCAGCAAGTGTAT 57.068 42.857 5.01 0.00 46.50 2.29
7254 7861 5.555966 TGAGTATGTGGCAGTTTCATGTTA 58.444 37.500 0.00 0.00 0.00 2.41
7255 7862 5.411361 TGAGTATGTGGCAGTTTCATGTTAC 59.589 40.000 0.00 0.00 0.00 2.50
7296 7904 7.494952 GTGGAGTTAGGTGATTACTATTTGACC 59.505 40.741 0.00 0.00 0.00 4.02
7318 7926 3.485216 CGATCGTAGTTCCAATTTGGTGC 60.485 47.826 14.98 9.12 39.03 5.01
7338 7946 3.639561 TGCAGACCTACACAACTCTTACA 59.360 43.478 0.00 0.00 0.00 2.41
7339 7947 3.988517 GCAGACCTACACAACTCTTACAC 59.011 47.826 0.00 0.00 0.00 2.90
7341 7949 5.597806 CAGACCTACACAACTCTTACACAA 58.402 41.667 0.00 0.00 0.00 3.33
7342 7950 5.692204 CAGACCTACACAACTCTTACACAAG 59.308 44.000 0.00 0.00 0.00 3.16
7343 7951 5.363005 AGACCTACACAACTCTTACACAAGT 59.637 40.000 0.00 0.00 33.20 3.16
7388 7996 5.359860 ACTGGTAAGGACTTTTTGGTTCTTG 59.640 40.000 0.00 0.00 35.94 3.02
7391 7999 6.890814 TGGTAAGGACTTTTTGGTTCTTGTAA 59.109 34.615 0.00 0.00 35.94 2.41
7393 8001 7.865889 GGTAAGGACTTTTTGGTTCTTGTAATG 59.134 37.037 0.00 0.00 35.94 1.90
7402 8010 9.757227 TTTTTGGTTCTTGTAATGATTTGTAGG 57.243 29.630 0.00 0.00 0.00 3.18
7422 8030 2.294512 GGAACTGAAGGTCAAGCTTTGG 59.705 50.000 0.00 0.00 0.00 3.28
7424 8032 3.018423 ACTGAAGGTCAAGCTTTGGTT 57.982 42.857 0.00 0.00 0.00 3.67
7740 8378 2.594303 TGACAACAAGGGCTGGCG 60.594 61.111 0.00 0.00 0.00 5.69
7873 8511 1.938585 TGCTTCACACTAGGCCTAGT 58.061 50.000 35.35 35.35 46.52 2.57
7910 8548 5.424895 TGCCAGGCCATTATTTGTAATCTTT 59.575 36.000 9.64 0.00 0.00 2.52
7930 8568 3.574354 TCCACAGCCATGTATATGCAA 57.426 42.857 0.00 0.00 37.65 4.08
7990 8628 3.627395 TCCTTGGTCGCATATGTTTCT 57.373 42.857 4.29 0.00 0.00 2.52
8143 8781 6.118170 CCACCACAGAATCATCAGTAAGATT 58.882 40.000 0.00 0.00 37.19 2.40
8306 8944 1.339438 GGAGAAAGCATGCAGGACTCA 60.339 52.381 21.98 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.130340 CCACCCCAAATACTCCAAAATCG 59.870 47.826 0.00 0.00 0.00 3.34
8 9 1.076350 CAACCCACCCCAAATACTCCA 59.924 52.381 0.00 0.00 0.00 3.86
13 14 1.783979 ACTCACAACCCACCCCAAATA 59.216 47.619 0.00 0.00 0.00 1.40
25 26 2.120232 CTCAGACACGACACTCACAAC 58.880 52.381 0.00 0.00 0.00 3.32
59 60 4.376170 GTGGGGCGGATTTGGGGT 62.376 66.667 0.00 0.00 0.00 4.95
62 63 1.032014 CATAAGTGGGGCGGATTTGG 58.968 55.000 0.00 0.00 0.00 3.28
87 88 3.691118 GGTTATTCGGTAGTTCCCAAACC 59.309 47.826 0.00 0.00 35.92 3.27
90 91 3.054948 CAGGGTTATTCGGTAGTTCCCAA 60.055 47.826 0.00 0.00 36.24 4.12
114 115 2.436417 CCCGCATATCCAACCTAATGG 58.564 52.381 0.00 0.00 42.12 3.16
120 121 2.203153 ACGCCCGCATATCCAACC 60.203 61.111 0.00 0.00 0.00 3.77
138 139 4.143305 GGACAGAAAATTCTCGTTCGACAG 60.143 45.833 0.00 0.00 34.74 3.51
151 152 4.602340 AGACAGTGTACGGACAGAAAAT 57.398 40.909 0.00 0.00 35.82 1.82
152 153 5.518848 TTAGACAGTGTACGGACAGAAAA 57.481 39.130 0.00 0.00 35.82 2.29
174 175 3.648029 GAGTATGCTCTAGCGGACAGCT 61.648 54.545 5.20 5.20 44.81 4.24
176 177 1.069568 CGAGTATGCTCTAGCGGACAG 60.070 57.143 9.26 0.31 45.83 3.51
180 181 0.519519 CTCCGAGTATGCTCTAGCGG 59.480 60.000 9.26 5.83 45.83 5.52
184 185 1.074084 CCCTCCTCCGAGTATGCTCTA 59.926 57.143 9.26 0.00 39.53 2.43
185 186 0.178975 CCCTCCTCCGAGTATGCTCT 60.179 60.000 9.26 0.00 39.53 4.09
188 189 2.210711 CCCCCTCCTCCGAGTATGC 61.211 68.421 0.00 0.00 33.93 3.14
591 654 7.634817 GTGTTAACACATATATGAACAACGAGC 59.365 37.037 29.46 3.93 45.75 5.03
608 671 8.293867 TCTTTTATGGCATACAAGTGTTAACAC 58.706 33.333 27.72 27.72 46.77 3.32
609 672 8.397575 TCTTTTATGGCATACAAGTGTTAACA 57.602 30.769 24.94 3.59 0.00 2.41
646 709 9.047947 AGTTATGAGGTTGTCTTAGAAGGTAAT 57.952 33.333 0.00 0.00 0.00 1.89
654 717 8.836413 TGACAAAAAGTTATGAGGTTGTCTTAG 58.164 33.333 13.61 0.00 43.25 2.18
655 718 8.740123 TGACAAAAAGTTATGAGGTTGTCTTA 57.260 30.769 13.61 0.00 43.25 2.10
658 721 7.648142 TCATGACAAAAAGTTATGAGGTTGTC 58.352 34.615 7.26 7.26 45.16 3.18
659 722 7.581213 TCATGACAAAAAGTTATGAGGTTGT 57.419 32.000 0.00 0.00 45.16 3.32
689 752 3.311028 TGGACAGAGGGGGTATGATGTTA 60.311 47.826 0.00 0.00 0.00 2.41
700 763 3.775316 ACAATTAGTACTGGACAGAGGGG 59.225 47.826 5.39 0.00 0.00 4.79
701 764 4.383118 CCACAATTAGTACTGGACAGAGGG 60.383 50.000 5.39 0.00 0.00 4.30
704 767 3.838317 AGCCACAATTAGTACTGGACAGA 59.162 43.478 5.39 0.00 0.00 3.41
710 773 5.647589 TCGTCTAAGCCACAATTAGTACTG 58.352 41.667 5.39 0.00 33.00 2.74
712 775 6.979238 AGATTCGTCTAAGCCACAATTAGTAC 59.021 38.462 0.00 0.00 33.00 2.73
723 786 4.621886 CGGCTAAATAGATTCGTCTAAGCC 59.378 45.833 13.12 13.12 38.99 4.35
729 792 9.189723 ACTAAAATACGGCTAAATAGATTCGTC 57.810 33.333 0.00 0.00 32.01 4.20
736 799 9.640963 ATCTAGCACTAAAATACGGCTAAATAG 57.359 33.333 0.00 0.00 36.71 1.73
740 803 5.694910 GCATCTAGCACTAAAATACGGCTAA 59.305 40.000 0.00 0.00 44.79 3.09
760 823 2.606725 CTGTCTCTCAAACGGATGCATC 59.393 50.000 18.81 18.81 0.00 3.91
763 826 2.086054 ACTGTCTCTCAAACGGATGC 57.914 50.000 0.00 0.00 0.00 3.91
773 836 6.057627 TCCGTTCGATATTAACTGTCTCTC 57.942 41.667 0.00 0.00 0.00 3.20
776 839 4.037684 CCCTCCGTTCGATATTAACTGTCT 59.962 45.833 0.00 0.00 0.00 3.41
779 842 4.037684 ACTCCCTCCGTTCGATATTAACTG 59.962 45.833 0.00 0.00 0.00 3.16
781 844 4.581077 ACTCCCTCCGTTCGATATTAAC 57.419 45.455 0.00 0.00 0.00 2.01
789 852 0.170561 CTGTGTACTCCCTCCGTTCG 59.829 60.000 0.00 0.00 0.00 3.95
790 853 1.254954 ACTGTGTACTCCCTCCGTTC 58.745 55.000 0.00 0.00 0.00 3.95
791 854 2.560105 GTTACTGTGTACTCCCTCCGTT 59.440 50.000 0.00 0.00 0.00 4.44
801 864 4.952460 TGTTGAAGGGAGTTACTGTGTAC 58.048 43.478 0.00 0.00 0.00 2.90
804 867 7.504924 TTAATTGTTGAAGGGAGTTACTGTG 57.495 36.000 0.00 0.00 0.00 3.66
812 875 9.396022 ACAGTACATATTAATTGTTGAAGGGAG 57.604 33.333 0.00 0.00 0.00 4.30
814 877 8.956426 ACACAGTACATATTAATTGTTGAAGGG 58.044 33.333 0.00 0.00 0.00 3.95
817 880 8.787852 TGCACACAGTACATATTAATTGTTGAA 58.212 29.630 0.00 0.00 0.00 2.69
846 909 7.667219 TCTCCTAAGCTTGTTGATGAGATTTTT 59.333 33.333 9.86 0.00 0.00 1.94
848 911 6.715280 TCTCCTAAGCTTGTTGATGAGATTT 58.285 36.000 9.86 0.00 0.00 2.17
849 912 6.305272 TCTCCTAAGCTTGTTGATGAGATT 57.695 37.500 9.86 0.00 0.00 2.40
850 913 5.946942 TCTCCTAAGCTTGTTGATGAGAT 57.053 39.130 9.86 0.00 0.00 2.75
852 915 6.808008 TTTTCTCCTAAGCTTGTTGATGAG 57.192 37.500 9.86 5.89 0.00 2.90
853 916 7.765695 AATTTTCTCCTAAGCTTGTTGATGA 57.234 32.000 9.86 0.00 0.00 2.92
854 917 9.912634 TTTAATTTTCTCCTAAGCTTGTTGATG 57.087 29.630 9.86 0.00 0.00 3.07
858 921 9.929180 GGATTTTAATTTTCTCCTAAGCTTGTT 57.071 29.630 9.86 0.00 0.00 2.83
939 1231 4.069304 TGTTTGGTACTTGCACATACTCC 58.931 43.478 6.52 0.00 0.00 3.85
940 1232 4.994852 TCTGTTTGGTACTTGCACATACTC 59.005 41.667 6.52 0.00 0.00 2.59
941 1233 4.968259 TCTGTTTGGTACTTGCACATACT 58.032 39.130 6.52 0.00 0.00 2.12
942 1234 4.994852 TCTCTGTTTGGTACTTGCACATAC 59.005 41.667 0.00 0.00 0.00 2.39
972 1264 0.673022 CCACTGCTCTTCTGCTGTCC 60.673 60.000 0.00 0.00 41.89 4.02
982 1274 4.664267 TCCCCCTGCCACTGCTCT 62.664 66.667 0.00 0.00 38.71 4.09
1099 1392 3.181465 GGACCGCTATGGATTCAAAGAGA 60.181 47.826 0.00 0.00 42.00 3.10
1152 1445 2.875080 AGATTTTTGTAGCGCACGAC 57.125 45.000 11.47 5.01 0.00 4.34
1182 1475 6.205464 CCATCATCGCCACTTATTTTCTGTAT 59.795 38.462 0.00 0.00 0.00 2.29
1183 1476 5.527214 CCATCATCGCCACTTATTTTCTGTA 59.473 40.000 0.00 0.00 0.00 2.74
1184 1477 4.336433 CCATCATCGCCACTTATTTTCTGT 59.664 41.667 0.00 0.00 0.00 3.41
1185 1478 4.336433 ACCATCATCGCCACTTATTTTCTG 59.664 41.667 0.00 0.00 0.00 3.02
1186 1479 4.336433 CACCATCATCGCCACTTATTTTCT 59.664 41.667 0.00 0.00 0.00 2.52
1187 1480 4.335315 TCACCATCATCGCCACTTATTTTC 59.665 41.667 0.00 0.00 0.00 2.29
1234 1529 0.606096 TAAGTAGCTGCGGAAGTGCA 59.394 50.000 0.00 0.00 43.95 4.57
1324 1619 2.889045 TCCTCATACCTCGGGTAATTCG 59.111 50.000 6.85 0.00 41.85 3.34
1503 1803 7.260603 CCTTCCAAAAATAAGCGAGATTTCAT 58.739 34.615 0.00 0.00 0.00 2.57
1649 1950 7.329717 CGAAATCCTACTAATCTTCCATAGTGC 59.670 40.741 0.00 0.00 34.37 4.40
1655 1956 8.529424 TCTAACGAAATCCTACTAATCTTCCA 57.471 34.615 0.00 0.00 0.00 3.53
1664 1965 5.978814 AGCAACATCTAACGAAATCCTACT 58.021 37.500 0.00 0.00 0.00 2.57
1665 1966 7.766219 TTAGCAACATCTAACGAAATCCTAC 57.234 36.000 0.00 0.00 0.00 3.18
1666 1967 8.780846 TTTTAGCAACATCTAACGAAATCCTA 57.219 30.769 0.00 0.00 0.00 2.94
1667 1968 7.390718 ACTTTTAGCAACATCTAACGAAATCCT 59.609 33.333 0.00 0.00 0.00 3.24
1712 2032 7.610865 TCTGAACCAAAACACAAAGAATTTCT 58.389 30.769 0.00 0.00 35.03 2.52
1902 2222 2.287915 CAGGTGAAACACTGAAAGACGG 59.712 50.000 0.00 0.00 39.98 4.79
1924 2244 1.556451 AGATATGTGTCACCTGCTGCA 59.444 47.619 0.88 0.88 0.00 4.41
2045 2365 1.805945 GACAGTGGGAGCGCTAACG 60.806 63.158 11.50 8.53 44.07 3.18
2048 2368 3.075005 GGGACAGTGGGAGCGCTA 61.075 66.667 11.50 0.00 0.00 4.26
2081 2401 2.606213 TCCATCAGGGTGACGCCA 60.606 61.111 7.48 0.00 39.65 5.69
2095 2415 2.068821 GCCCTGAGCATCCTCTCCA 61.069 63.158 0.00 0.00 42.97 3.86
2627 3039 4.402793 ACTGTATCAGCTTAATCCGACAGT 59.597 41.667 0.00 0.00 40.97 3.55
2634 3046 8.894768 ACTGGATAAACTGTATCAGCTTAATC 57.105 34.615 0.00 0.00 34.37 1.75
2784 3197 5.627182 AGCACATCACCTCTCTTGATTAT 57.373 39.130 0.00 0.00 30.98 1.28
2825 3238 5.279456 GGGTTCCACTGAGCACATAATTTTT 60.279 40.000 0.00 0.00 0.00 1.94
2930 3345 3.264450 AGTGCCACTAAGCAGATTACCTT 59.736 43.478 0.00 0.00 45.14 3.50
3415 3831 6.589830 ACTAATTTCATCGACTCATTTCCG 57.410 37.500 0.00 0.00 0.00 4.30
3496 3912 6.731292 ACAGATCATATGTGTACAGGCTTA 57.269 37.500 0.00 0.00 34.71 3.09
3579 3995 2.048784 GCTCGCACAGTGCTCAGA 60.049 61.111 23.15 12.13 42.25 3.27
3756 4172 1.879380 TGTGTGTATGGCAAACAGCTC 59.121 47.619 0.00 0.00 40.22 4.09
3895 4311 5.164620 TGATGTAACAGGCAGATTCTTGA 57.835 39.130 0.00 0.00 0.00 3.02
4027 4443 7.705325 TCATGCATATCATATTCTCTCACATCG 59.295 37.037 0.00 0.00 33.19 3.84
4148 4564 5.611374 TGTCAGTGGAAGGAAAAACTCTAG 58.389 41.667 0.00 0.00 0.00 2.43
4398 4814 2.417243 GCCAGTTGCTCAACACTGTTTT 60.417 45.455 14.32 0.00 43.47 2.43
4524 4944 5.376756 TCCAACTTACGGGCCTTTATTAT 57.623 39.130 0.84 0.00 0.00 1.28
4633 5082 5.066505 CAGTACAATACAAGGAAATGAGCCC 59.933 44.000 0.00 0.00 0.00 5.19
4976 5436 5.713792 TCCTCGAGGATTTCTTATAGCAG 57.286 43.478 30.49 0.00 39.78 4.24
5007 5467 1.406069 CCACTGAGGACTCCCATTTCG 60.406 57.143 0.00 0.00 41.22 3.46
5023 5483 0.179056 CACGTTCCCACTTGACCACT 60.179 55.000 0.00 0.00 0.00 4.00
5028 5488 0.528901 CGTCACACGTTCCCACTTGA 60.529 55.000 0.00 0.00 36.74 3.02
5040 5500 1.999071 TTTGGCCAGCAACGTCACAC 61.999 55.000 5.11 0.00 0.00 3.82
5058 5518 0.106918 TTGCTCGGGTTGTGTTCCTT 60.107 50.000 0.00 0.00 0.00 3.36
5379 5856 4.938080 TCAGACTTTGATCCGATAAGAGC 58.062 43.478 0.00 0.00 0.00 4.09
5568 6045 6.457355 CATCAGATGTAGATTCCTGAAGGAG 58.543 44.000 1.74 0.00 46.36 3.69
5765 6244 3.066621 TGGTGTGCTTTGTTCAGATTCAC 59.933 43.478 0.00 0.00 0.00 3.18
5984 6464 9.512588 GATCATATTTTATCACTCCATCCACTT 57.487 33.333 0.00 0.00 0.00 3.16
6048 6528 3.893326 TTCATCATCGAAGGCTCTTCA 57.107 42.857 13.24 3.81 0.00 3.02
6139 6622 4.013050 GCTTGGCCTAGATGTTCTCTTTT 58.987 43.478 19.07 0.00 35.28 2.27
6211 6694 3.388024 CGAGATAACCCTCCAGGATTCAA 59.612 47.826 0.00 0.00 39.89 2.69
6390 6873 7.943079 TTCTATCTCAATTTTCCATTGCTGA 57.057 32.000 0.00 0.00 0.00 4.26
6399 6882 9.818796 GACTTGTCTGTTTCTATCTCAATTTTC 57.181 33.333 0.00 0.00 0.00 2.29
6537 7020 0.393402 TGCTCGCATTGCTTCCATCT 60.393 50.000 7.12 0.00 0.00 2.90
6848 7333 0.469917 CGGCATCACCCTGACCTATT 59.530 55.000 0.00 0.00 33.26 1.73
6901 7387 1.091537 GCCACGCTAAAGCCATAACA 58.908 50.000 0.00 0.00 37.91 2.41
6902 7388 0.027586 CGCCACGCTAAAGCCATAAC 59.972 55.000 0.00 0.00 37.91 1.89
6904 7390 4.118480 CGCCACGCTAAAGCCATA 57.882 55.556 0.00 0.00 37.91 2.74
6972 7542 1.586422 CACATAGTTCCAGATGGCCG 58.414 55.000 0.00 0.00 34.44 6.13
6976 7546 3.272574 ACAGCCACATAGTTCCAGATG 57.727 47.619 0.00 0.00 0.00 2.90
7007 7577 1.004440 GCGCCAAGACCTTCTCAGT 60.004 57.895 0.00 0.00 0.00 3.41
7010 7580 0.449388 CAATGCGCCAAGACCTTCTC 59.551 55.000 4.18 0.00 0.00 2.87
7012 7582 0.449388 CTCAATGCGCCAAGACCTTC 59.551 55.000 4.18 0.00 0.00 3.46
7013 7583 0.250901 ACTCAATGCGCCAAGACCTT 60.251 50.000 4.18 0.00 0.00 3.50
7014 7584 0.613260 TACTCAATGCGCCAAGACCT 59.387 50.000 4.18 0.00 0.00 3.85
7015 7585 1.009829 CTACTCAATGCGCCAAGACC 58.990 55.000 4.18 0.00 0.00 3.85
7016 7586 0.375106 GCTACTCAATGCGCCAAGAC 59.625 55.000 4.18 0.00 0.00 3.01
7017 7587 0.250234 AGCTACTCAATGCGCCAAGA 59.750 50.000 4.18 0.00 0.00 3.02
7018 7588 0.376152 CAGCTACTCAATGCGCCAAG 59.624 55.000 4.18 0.00 0.00 3.61
7019 7589 0.036483 TCAGCTACTCAATGCGCCAA 60.036 50.000 4.18 0.00 0.00 4.52
7020 7590 0.460811 CTCAGCTACTCAATGCGCCA 60.461 55.000 4.18 0.00 0.00 5.69
7021 7591 0.460987 ACTCAGCTACTCAATGCGCC 60.461 55.000 4.18 0.00 0.00 6.53
7022 7592 0.649475 CACTCAGCTACTCAATGCGC 59.351 55.000 0.00 0.00 0.00 6.09
7023 7593 1.284657 CCACTCAGCTACTCAATGCG 58.715 55.000 0.00 0.00 0.00 4.73
7024 7594 1.661341 CCCACTCAGCTACTCAATGC 58.339 55.000 0.00 0.00 0.00 3.56
7025 7595 1.209019 AGCCCACTCAGCTACTCAATG 59.791 52.381 0.00 0.00 39.29 2.82
7026 7596 1.577736 AGCCCACTCAGCTACTCAAT 58.422 50.000 0.00 0.00 39.29 2.57
7027 7597 2.231716 TAGCCCACTCAGCTACTCAA 57.768 50.000 0.00 0.00 41.83 3.02
7028 7598 4.874521 AGCCCACTCAGCTACTCA 57.125 55.556 0.00 0.00 39.29 3.41
7125 7710 5.125417 GTGTACTGCCACAATTCATTGGTAT 59.875 40.000 4.58 0.00 41.96 2.73
7222 7813 3.270027 TGCCACATACTCATACACTTGC 58.730 45.455 0.00 0.00 0.00 4.01
7223 7814 4.507710 ACTGCCACATACTCATACACTTG 58.492 43.478 0.00 0.00 0.00 3.16
7231 7827 4.019792 ACATGAAACTGCCACATACTCA 57.980 40.909 0.00 0.00 0.00 3.41
7296 7904 3.485216 GCACCAAATTGGAACTACGATCG 60.485 47.826 20.25 14.88 40.96 3.69
7318 7926 5.196341 TGTGTAAGAGTTGTGTAGGTCTG 57.804 43.478 0.00 0.00 0.00 3.51
7359 7967 8.631480 AACCAAAAAGTCCTTACCAGTATAAG 57.369 34.615 0.00 0.00 32.78 1.73
7361 7969 7.981142 AGAACCAAAAAGTCCTTACCAGTATA 58.019 34.615 0.00 0.00 0.00 1.47
7370 7978 7.654022 TCATTACAAGAACCAAAAAGTCCTT 57.346 32.000 0.00 0.00 0.00 3.36
7388 7996 7.606456 TGACCTTCAGTTCCTACAAATCATTAC 59.394 37.037 0.00 0.00 0.00 1.89
7391 7999 6.126863 TGACCTTCAGTTCCTACAAATCAT 57.873 37.500 0.00 0.00 0.00 2.45
7393 8001 5.106515 GCTTGACCTTCAGTTCCTACAAATC 60.107 44.000 0.00 0.00 0.00 2.17
7402 8010 2.952310 ACCAAAGCTTGACCTTCAGTTC 59.048 45.455 0.00 0.00 0.00 3.01
7422 8030 2.097680 TCGTAACCATTCCCCGAAAC 57.902 50.000 0.00 0.00 0.00 2.78
7424 8032 2.236644 TGATTCGTAACCATTCCCCGAA 59.763 45.455 0.00 0.00 41.16 4.30
7498 8135 8.565896 AAGTGCTGTCATGAAATTTGATACTA 57.434 30.769 0.00 0.00 0.00 1.82
7500 8137 9.065871 GTAAAGTGCTGTCATGAAATTTGATAC 57.934 33.333 0.00 0.00 0.00 2.24
7698 8336 4.971830 CAGTGTGTTTGTCATTACAGCAAG 59.028 41.667 0.00 0.00 36.83 4.01
7740 8378 3.181487 TGAAGTTTTGACTTGAGCAAGGC 60.181 43.478 14.14 11.79 46.57 4.35
7844 8482 2.880443 AGTGTGAAGCAAATGGTGGAT 58.120 42.857 0.00 0.00 0.00 3.41
7873 8511 1.825090 CCTGGCACTGTTCAGCATTA 58.175 50.000 0.00 0.00 0.00 1.90
7910 8548 3.136260 TCTTGCATATACATGGCTGTGGA 59.864 43.478 0.00 0.00 36.79 4.02
7930 8568 2.031163 GTGTGCGCCTTGAGGTCT 59.969 61.111 4.18 0.00 37.57 3.85
7990 8628 1.960417 TCTTCATGTGAACCGTTGCA 58.040 45.000 0.00 0.00 0.00 4.08
8143 8781 0.462581 GAATCTGAGGATGTGCCGCA 60.463 55.000 0.00 0.00 44.78 5.69


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

AutoCloner maintained by Alex Coulton.