Multiple sequence alignment - TraesCS7B01G369400

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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 TraesCS7B01G369400 chr7B 100.000 4845 0 0 1 4845 633320886 633316042 0.000000e+00 8948.0
1 TraesCS7B01G369400 chr7B 92.570 646 32 8 60 704 525227786 525227156 0.000000e+00 913.0
2 TraesCS7B01G369400 chr7A 94.012 2121 70 23 940 3003 663956074 663958194 0.000000e+00 3160.0
3 TraesCS7B01G369400 chr7A 92.703 1617 67 20 3002 4588 663958227 663959822 0.000000e+00 2285.0
4 TraesCS7B01G369400 chr7A 91.667 240 6 9 4619 4845 663960092 663960330 2.180000e-83 320.0
5 TraesCS7B01G369400 chr3B 97.959 637 11 2 60 695 773868061 773867426 0.000000e+00 1103.0
6 TraesCS7B01G369400 chr6D 91.719 640 43 10 60 696 319752837 319752205 0.000000e+00 880.0
7 TraesCS7B01G369400 chr6D 88.697 637 36 18 60 695 63934885 63935486 0.000000e+00 745.0
8 TraesCS7B01G369400 chr1B 91.875 640 31 9 60 695 250576405 250577027 0.000000e+00 874.0
9 TraesCS7B01G369400 chr1B 98.485 132 2 0 812 943 200649171 200649302 2.920000e-57 233.0
10 TraesCS7B01G369400 chr1B 96.947 131 1 2 694 824 200649084 200649211 2.940000e-52 217.0
11 TraesCS7B01G369400 chr1B 90.698 129 9 2 696 824 354545760 354545635 8.340000e-38 169.0
12 TraesCS7B01G369400 chr5D 93.433 533 18 14 164 694 348274190 348274707 0.000000e+00 774.0
13 TraesCS7B01G369400 chr5D 96.970 132 4 0 812 943 77058701 77058832 6.310000e-54 222.0
14 TraesCS7B01G369400 chr5D 96.124 129 2 1 696 824 77058616 77058741 1.770000e-49 207.0
15 TraesCS7B01G369400 chr3D 88.401 638 54 16 60 696 363517287 363517905 0.000000e+00 750.0
16 TraesCS7B01G369400 chr3D 87.558 643 45 19 60 696 13928438 13929051 0.000000e+00 712.0
17 TraesCS7B01G369400 chr3D 86.180 644 58 27 60 695 356929789 356930409 0.000000e+00 667.0
18 TraesCS7B01G369400 chr2A 87.820 665 47 21 37 695 695274641 695274005 0.000000e+00 749.0
19 TraesCS7B01G369400 chr1D 85.971 613 56 23 59 661 317111490 317110898 3.180000e-176 628.0
20 TraesCS7B01G369400 chr1D 93.846 130 4 3 696 824 5628982 5629108 4.950000e-45 193.0
21 TraesCS7B01G369400 chr4A 98.485 132 2 0 812 943 725273483 725273352 2.920000e-57 233.0
22 TraesCS7B01G369400 chr4A 97.674 129 0 2 696 824 725273568 725273443 8.160000e-53 219.0
23 TraesCS7B01G369400 chr2B 97.710 131 3 0 812 942 38372951 38373081 4.880000e-55 226.0
24 TraesCS7B01G369400 chr2B 96.899 129 1 2 696 824 38372866 38372991 3.800000e-51 213.0
25 TraesCS7B01G369400 chr2B 92.188 128 9 1 812 939 774369037 774369163 3.850000e-41 180.0
26 TraesCS7B01G369400 chr2B 89.928 139 10 3 812 948 606482969 606483105 4.980000e-40 176.0
27 TraesCS7B01G369400 chr2B 89.922 129 10 2 696 824 774368952 774369077 3.880000e-36 163.0
28 TraesCS7B01G369400 chr2B 92.241 116 6 3 738 853 606482923 606483035 1.400000e-35 161.0
29 TraesCS7B01G369400 chr5B 96.947 131 4 0 812 942 486034010 486033880 2.270000e-53 220.0
30 TraesCS7B01G369400 chr5B 96.850 127 1 1 698 824 486034093 486033970 4.910000e-50 209.0
31 TraesCS7B01G369400 chr5B 100.000 28 0 0 3988 4015 161067305 161067332 9.000000e-03 52.8
32 TraesCS7B01G369400 chr5A 93.750 128 8 0 812 939 343767254 343767127 4.950000e-45 193.0
33 TraesCS7B01G369400 chr4D 90.909 132 12 0 812 943 14646014 14645883 1.390000e-40 178.0
34 TraesCS7B01G369400 chr6B 80.672 119 21 2 1143 1260 599770474 599770357 1.860000e-14 91.6


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 TraesCS7B01G369400 chr7B 633316042 633320886 4844 True 8948.000000 8948 100.000 1 4845 1 chr7B.!!$R2 4844
1 TraesCS7B01G369400 chr7B 525227156 525227786 630 True 913.000000 913 92.570 60 704 1 chr7B.!!$R1 644
2 TraesCS7B01G369400 chr7A 663956074 663960330 4256 False 1921.666667 3160 92.794 940 4845 3 chr7A.!!$F1 3905
3 TraesCS7B01G369400 chr3B 773867426 773868061 635 True 1103.000000 1103 97.959 60 695 1 chr3B.!!$R1 635
4 TraesCS7B01G369400 chr6D 319752205 319752837 632 True 880.000000 880 91.719 60 696 1 chr6D.!!$R1 636
5 TraesCS7B01G369400 chr6D 63934885 63935486 601 False 745.000000 745 88.697 60 695 1 chr6D.!!$F1 635
6 TraesCS7B01G369400 chr1B 250576405 250577027 622 False 874.000000 874 91.875 60 695 1 chr1B.!!$F1 635
7 TraesCS7B01G369400 chr5D 348274190 348274707 517 False 774.000000 774 93.433 164 694 1 chr5D.!!$F1 530
8 TraesCS7B01G369400 chr3D 363517287 363517905 618 False 750.000000 750 88.401 60 696 1 chr3D.!!$F3 636
9 TraesCS7B01G369400 chr3D 13928438 13929051 613 False 712.000000 712 87.558 60 696 1 chr3D.!!$F1 636
10 TraesCS7B01G369400 chr3D 356929789 356930409 620 False 667.000000 667 86.180 60 695 1 chr3D.!!$F2 635
11 TraesCS7B01G369400 chr2A 695274005 695274641 636 True 749.000000 749 87.820 37 695 1 chr2A.!!$R1 658
12 TraesCS7B01G369400 chr1D 317110898 317111490 592 True 628.000000 628 85.971 59 661 1 chr1D.!!$R1 602

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
712 823 0.670546 CCGTCTTGCCTGTCGATTGT 60.671 55.0 0.00 0.00 0.00 2.71 F
1659 1827 0.175989 GTCATCCCCTCCGACTTCAC 59.824 60.0 0.00 0.00 0.00 3.18 F
1689 1857 0.249322 CACCGACCGTCTTCACAAGT 60.249 55.0 0.00 0.00 0.00 3.16 F
2267 2435 0.319040 CTCGGGTAGCATGTCATCCG 60.319 60.0 12.58 12.58 38.92 4.18 F
2711 2879 0.447801 TACGGTTTCTACGACCTCGC 59.552 55.0 0.00 0.00 44.43 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2435 0.442699 CTCGTAGCGCTTTTGGGTTC 59.557 55.000 18.68 0.0 34.56 3.62 R
3229 3434 0.321122 GCACAAGTCTGGTCCCTCTG 60.321 60.000 0.00 0.0 0.00 3.35 R
3505 3710 0.324738 TTGACAGCACAACCCCCAAA 60.325 50.000 0.00 0.0 0.00 3.28 R
3750 3955 0.836606 TGTTCTCACAAGACAGCCCA 59.163 50.000 0.00 0.0 0.00 5.36 R
4435 4674 1.001181 GTACTTCAGTGCCAACCGGTA 59.999 52.381 8.00 0.0 33.28 4.02 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
201 248 8.387354 TGTGTAATATACGCTGAACAATTTGAG 58.613 33.333 2.79 0.00 39.80 3.02
501 597 7.718334 AAAGAAAAAGGAGAAGGAAAACAGA 57.282 32.000 0.00 0.00 0.00 3.41
502 598 6.951062 AGAAAAAGGAGAAGGAAAACAGAG 57.049 37.500 0.00 0.00 0.00 3.35
503 599 6.663734 AGAAAAAGGAGAAGGAAAACAGAGA 58.336 36.000 0.00 0.00 0.00 3.10
700 811 2.739913 TCAAATAGGAAACGCCGTCTTG 59.260 45.455 0.00 0.00 43.43 3.02
702 813 0.743345 ATAGGAAACGCCGTCTTGCC 60.743 55.000 0.00 0.00 43.43 4.52
703 814 1.823169 TAGGAAACGCCGTCTTGCCT 61.823 55.000 0.00 0.00 43.43 4.75
704 815 2.556287 GAAACGCCGTCTTGCCTG 59.444 61.111 0.00 0.00 0.00 4.85
705 816 2.203153 AAACGCCGTCTTGCCTGT 60.203 55.556 0.00 0.00 0.00 4.00
706 817 2.171489 GAAACGCCGTCTTGCCTGTC 62.171 60.000 0.00 0.00 0.00 3.51
708 819 4.717629 CGCCGTCTTGCCTGTCGA 62.718 66.667 0.00 0.00 0.00 4.20
709 820 2.125512 GCCGTCTTGCCTGTCGAT 60.126 61.111 0.00 0.00 0.00 3.59
710 821 1.741770 GCCGTCTTGCCTGTCGATT 60.742 57.895 0.00 0.00 0.00 3.34
711 822 1.970917 GCCGTCTTGCCTGTCGATTG 61.971 60.000 0.00 0.00 0.00 2.67
712 823 0.670546 CCGTCTTGCCTGTCGATTGT 60.671 55.000 0.00 0.00 0.00 2.71
713 824 1.403647 CCGTCTTGCCTGTCGATTGTA 60.404 52.381 0.00 0.00 0.00 2.41
714 825 1.654105 CGTCTTGCCTGTCGATTGTAC 59.346 52.381 0.00 0.00 0.00 2.90
715 826 2.671351 CGTCTTGCCTGTCGATTGTACT 60.671 50.000 0.00 0.00 0.00 2.73
716 827 3.427098 CGTCTTGCCTGTCGATTGTACTA 60.427 47.826 0.00 0.00 0.00 1.82
717 828 3.858238 GTCTTGCCTGTCGATTGTACTAC 59.142 47.826 0.00 0.00 0.00 2.73
718 829 2.554806 TGCCTGTCGATTGTACTACG 57.445 50.000 0.00 0.00 0.00 3.51
719 830 2.086094 TGCCTGTCGATTGTACTACGA 58.914 47.619 0.00 0.00 0.00 3.43
720 831 2.096980 TGCCTGTCGATTGTACTACGAG 59.903 50.000 9.09 0.00 36.74 4.18
721 832 2.541178 GCCTGTCGATTGTACTACGAGG 60.541 54.545 9.09 9.12 36.74 4.63
722 833 2.541178 CCTGTCGATTGTACTACGAGGC 60.541 54.545 9.09 2.06 36.74 4.70
723 834 2.086094 TGTCGATTGTACTACGAGGCA 58.914 47.619 9.09 4.05 36.74 4.75
724 835 2.159476 TGTCGATTGTACTACGAGGCAC 60.159 50.000 9.09 1.70 36.74 5.01
740 851 4.124943 ACTCCTCCCCGCTCGCTA 62.125 66.667 0.00 0.00 0.00 4.26
741 852 3.291383 CTCCTCCCCGCTCGCTAG 61.291 72.222 0.00 0.00 0.00 3.42
742 853 4.124943 TCCTCCCCGCTCGCTAGT 62.125 66.667 0.00 0.00 0.00 2.57
743 854 3.597728 CCTCCCCGCTCGCTAGTC 61.598 72.222 0.00 0.00 0.00 2.59
744 855 3.955101 CTCCCCGCTCGCTAGTCG 61.955 72.222 0.00 0.00 40.15 4.18
745 856 4.790962 TCCCCGCTCGCTAGTCGT 62.791 66.667 6.49 0.00 39.67 4.34
746 857 4.554363 CCCCGCTCGCTAGTCGTG 62.554 72.222 6.49 5.63 39.67 4.35
751 862 2.577112 CTCGCTAGTCGTGCCGTG 60.577 66.667 6.49 0.00 39.67 4.94
752 863 4.771356 TCGCTAGTCGTGCCGTGC 62.771 66.667 6.49 0.00 39.67 5.34
859 970 4.293648 GGCACGGCCCACAAAACC 62.294 66.667 0.00 0.00 44.06 3.27
860 971 3.532155 GCACGGCCCACAAAACCA 61.532 61.111 0.00 0.00 0.00 3.67
861 972 2.415426 CACGGCCCACAAAACCAC 59.585 61.111 0.00 0.00 0.00 4.16
862 973 3.213402 ACGGCCCACAAAACCACG 61.213 61.111 0.00 0.00 0.00 4.94
863 974 3.213402 CGGCCCACAAAACCACGT 61.213 61.111 0.00 0.00 0.00 4.49
864 975 2.415426 GGCCCACAAAACCACGTG 59.585 61.111 9.08 9.08 0.00 4.49
865 976 2.279186 GCCCACAAAACCACGTGC 60.279 61.111 10.91 0.00 0.00 5.34
866 977 2.415426 CCCACAAAACCACGTGCC 59.585 61.111 10.91 0.00 0.00 5.01
867 978 2.025441 CCACAAAACCACGTGCCG 59.975 61.111 10.91 0.00 0.00 5.69
868 979 2.766400 CCACAAAACCACGTGCCGT 61.766 57.895 10.91 0.00 42.36 5.68
910 1021 4.530857 ACGGGCTATCGTGCTGGC 62.531 66.667 0.00 0.00 42.21 4.85
914 1025 4.221422 GCTATCGTGCTGGCCCGA 62.221 66.667 0.00 1.29 37.51 5.14
915 1026 2.279517 CTATCGTGCTGGCCCGAC 60.280 66.667 0.00 0.00 35.69 4.79
916 1027 3.071837 TATCGTGCTGGCCCGACA 61.072 61.111 0.00 0.00 35.69 4.35
917 1028 2.572095 CTATCGTGCTGGCCCGACAA 62.572 60.000 0.00 0.00 35.69 3.18
918 1029 2.572095 TATCGTGCTGGCCCGACAAG 62.572 60.000 0.00 0.00 35.69 3.16
919 1030 4.680237 CGTGCTGGCCCGACAAGA 62.680 66.667 0.00 0.00 0.00 3.02
920 1031 3.050275 GTGCTGGCCCGACAAGAC 61.050 66.667 0.00 0.00 0.00 3.01
921 1032 4.329545 TGCTGGCCCGACAAGACC 62.330 66.667 0.00 0.00 0.00 3.85
923 1034 4.760047 CTGGCCCGACAAGACCGG 62.760 72.222 0.00 0.00 46.10 5.28
929 1040 4.675029 CGACAAGACCGGCCCGTT 62.675 66.667 0.00 0.00 0.00 4.44
930 1041 2.281276 GACAAGACCGGCCCGTTT 60.281 61.111 0.00 0.00 0.00 3.60
931 1042 2.593436 ACAAGACCGGCCCGTTTG 60.593 61.111 0.00 6.56 0.00 2.93
932 1043 3.361977 CAAGACCGGCCCGTTTGG 61.362 66.667 0.00 0.00 37.09 3.28
933 1044 3.562232 AAGACCGGCCCGTTTGGA 61.562 61.111 0.00 0.00 37.49 3.53
934 1045 3.837570 AAGACCGGCCCGTTTGGAC 62.838 63.158 0.00 0.00 39.70 4.02
935 1046 4.629523 GACCGGCCCGTTTGGACA 62.630 66.667 0.00 0.00 45.87 4.02
936 1047 4.636435 ACCGGCCCGTTTGGACAG 62.636 66.667 0.00 0.00 45.87 3.51
938 1049 4.636435 CGGCCCGTTTGGACAGGT 62.636 66.667 0.00 0.00 45.87 4.00
997 1111 6.449956 TCATATCCTAACAAACCCTAGACCT 58.550 40.000 0.00 0.00 0.00 3.85
1014 1128 3.701604 CTACACCCTCTCACGGCGC 62.702 68.421 6.90 0.00 0.00 6.53
1072 1207 1.519455 CTCCGATGGACGACAAGGC 60.519 63.158 0.00 0.00 45.77 4.35
1170 1305 3.435186 GGCTGCCGTTGAAGGAGC 61.435 66.667 1.35 0.00 35.30 4.70
1295 1430 2.802667 CGCCGCCAAGAAGATGTCG 61.803 63.158 0.00 0.00 0.00 4.35
1313 1448 4.399219 TGTCGAAGAAGAGGAAGAGAAGA 58.601 43.478 0.00 0.00 39.69 2.87
1322 1457 3.960102 AGAGGAAGAGAAGATCGCAGATT 59.040 43.478 0.00 0.00 45.12 2.40
1332 1467 0.829333 ATCGCAGATTGAGGCAGACT 59.171 50.000 0.00 0.00 45.12 3.24
1349 1484 2.026449 AGACTTGCTCCAAGATTCCAGG 60.026 50.000 11.56 0.00 43.42 4.45
1454 1622 1.600107 CTACCTACGGCTGGCCAAA 59.400 57.895 7.01 0.00 35.37 3.28
1472 1640 2.681848 CAAAGCTGATCTCGATTTGGCT 59.318 45.455 14.43 0.00 0.00 4.75
1502 1670 2.105128 CAGCTCGACCGTGGGATC 59.895 66.667 0.00 0.00 0.00 3.36
1544 1712 2.127708 CCCCTTACCACCAAGATAGCT 58.872 52.381 0.00 0.00 0.00 3.32
1547 1715 2.771943 CCTTACCACCAAGATAGCTCCA 59.228 50.000 0.00 0.00 0.00 3.86
1627 1795 0.893270 CCTTCCACATTCACGGCCAA 60.893 55.000 2.24 0.00 0.00 4.52
1659 1827 0.175989 GTCATCCCCTCCGACTTCAC 59.824 60.000 0.00 0.00 0.00 3.18
1676 1844 2.030562 CCACCAGACACCACCGAC 59.969 66.667 0.00 0.00 0.00 4.79
1685 1853 1.663702 CACCACCGACCGTCTTCAC 60.664 63.158 0.00 0.00 0.00 3.18
1689 1857 0.249322 CACCGACCGTCTTCACAAGT 60.249 55.000 0.00 0.00 0.00 3.16
1711 1879 1.280457 CTCCCCACTTTACCTCAGCT 58.720 55.000 0.00 0.00 0.00 4.24
1827 1995 2.750815 CTTGAACTAAGGGCGTCCG 58.249 57.895 0.00 0.00 38.33 4.79
1829 1997 0.393820 TTGAACTAAGGGCGTCCGTT 59.606 50.000 0.00 0.00 38.33 4.44
1868 2036 6.884832 TGGTAAAATCCACAGTATCTACCTG 58.115 40.000 0.00 0.00 31.96 4.00
1881 2049 1.065199 TCTACCTGGAGGCAATTGCAG 60.065 52.381 30.32 18.82 44.36 4.41
1946 2114 2.508526 CTCAAGGCTGGTTACTGCTTT 58.491 47.619 0.00 0.00 40.55 3.51
2111 2279 0.950836 TGACATTTGTTCGTGCCCTG 59.049 50.000 0.00 0.00 0.00 4.45
2159 2327 6.210784 TCGCCATGTTATATCTACTTAAGGCT 59.789 38.462 7.53 0.00 35.23 4.58
2184 2352 1.068333 CCAACCTTCGTGAAGCCATTG 60.068 52.381 4.05 7.91 37.11 2.82
2189 2357 2.322161 CTTCGTGAAGCCATTGCAAAG 58.678 47.619 1.71 0.00 41.13 2.77
2251 2419 2.230940 CGTACAAGATGGCCGCTCG 61.231 63.158 0.00 0.00 0.00 5.03
2267 2435 0.319040 CTCGGGTAGCATGTCATCCG 60.319 60.000 12.58 12.58 38.92 4.18
2313 2481 1.642037 CCTGTCAACTGCGCCATCAG 61.642 60.000 4.18 0.00 39.86 2.90
2324 2492 0.463204 CGCCATCAGTCATGTCCTCT 59.537 55.000 0.00 0.00 0.00 3.69
2327 2495 2.902523 CCATCAGTCATGTCCTCTGTG 58.097 52.381 0.00 0.87 0.00 3.66
2397 2565 1.002430 GTGACATCTCTGCCCTGTTGA 59.998 52.381 0.00 0.00 0.00 3.18
2398 2566 1.911357 TGACATCTCTGCCCTGTTGAT 59.089 47.619 0.00 0.00 0.00 2.57
2442 2610 0.898326 AGTTCCCAAATTGACGCCCC 60.898 55.000 0.00 0.00 0.00 5.80
2485 2653 2.750350 CCAGGCAAGGTTCGAGGT 59.250 61.111 0.00 0.00 0.00 3.85
2588 2756 6.145209 CCAATCGATCTTCACTACTGCTAATG 59.855 42.308 0.00 0.00 0.00 1.90
2619 2787 6.595716 ACTGATTTATTACACTGTCTGCCTTC 59.404 38.462 0.00 0.00 0.00 3.46
2630 2798 1.208293 GTCTGCCTTCTTGTAGGAGGG 59.792 57.143 3.27 0.00 37.50 4.30
2631 2799 1.078823 TCTGCCTTCTTGTAGGAGGGA 59.921 52.381 3.27 0.00 37.50 4.20
2665 2833 7.164803 TCAACTTCATGTTATATGTGGTGTGA 58.835 34.615 0.00 0.00 37.07 3.58
2711 2879 0.447801 TACGGTTTCTACGACCTCGC 59.552 55.000 0.00 0.00 44.43 5.03
2718 2886 1.101635 TCTACGACCTCGCAGATGGG 61.102 60.000 0.00 0.00 44.43 4.00
2846 3014 2.191802 TGAAAATGTGCTGCGTTGTTG 58.808 42.857 0.00 0.00 0.00 3.33
2910 3078 3.129287 GCCTGCTTAAGCTTTCTGCATTA 59.871 43.478 26.90 2.97 45.94 1.90
2953 3121 2.940147 TGCACGCATTCATAAACCAAC 58.060 42.857 0.00 0.00 0.00 3.77
2989 3157 5.245977 AGGCACTGGTTTTTATGTTTGCTAT 59.754 36.000 0.00 0.00 37.18 2.97
3037 3242 3.010420 GGATTGTTAGGCTGTTGTCCTC 58.990 50.000 0.00 0.00 35.21 3.71
3097 3302 9.177608 TGCTGAAACTGTTTTATCTATAAGCAT 57.822 29.630 7.28 0.00 0.00 3.79
3154 3359 5.300792 TGTCATTTAGAAGGTGGTTTTGGTC 59.699 40.000 0.00 0.00 0.00 4.02
3155 3360 5.535030 GTCATTTAGAAGGTGGTTTTGGTCT 59.465 40.000 0.00 0.00 0.00 3.85
3162 3367 2.096248 GGTGGTTTTGGTCTGTTGTGA 58.904 47.619 0.00 0.00 0.00 3.58
3201 3406 4.014847 TCGTTTCTTGTTTTGCTCTGTG 57.985 40.909 0.00 0.00 0.00 3.66
3229 3434 3.054878 CCGTTGTTACCACTGTGAGTAC 58.945 50.000 9.86 4.48 0.00 2.73
3408 3613 8.277197 AGAGGATTCAATCTATTTTGATCCACA 58.723 33.333 0.00 0.00 36.64 4.17
3484 3689 1.200020 CCTGTTCAATCAAACGGGCTC 59.800 52.381 1.92 0.00 45.98 4.70
3568 3773 8.263940 AGTATTTTGAAATATGTACGCTGTGT 57.736 30.769 0.00 0.00 33.79 3.72
3647 3852 4.776743 CCGAACTTGAAACATTCAGACTG 58.223 43.478 0.00 0.00 41.38 3.51
3649 3854 5.465390 CCGAACTTGAAACATTCAGACTGTA 59.535 40.000 1.59 0.00 41.38 2.74
3708 3913 7.981789 CAGAAGTGATAACTGGTTAGCAGATTA 59.018 37.037 18.76 12.36 41.39 1.75
3712 3917 7.124298 AGTGATAACTGGTTAGCAGATTACAGA 59.876 37.037 18.76 0.00 41.39 3.41
3713 3918 7.928706 GTGATAACTGGTTAGCAGATTACAGAT 59.071 37.037 18.76 0.00 41.39 2.90
3714 3919 8.486210 TGATAACTGGTTAGCAGATTACAGATT 58.514 33.333 18.76 1.94 36.64 2.40
3734 3939 8.571336 ACAGATTCACAAAGAGTTCTTTTATGG 58.429 33.333 4.43 0.00 43.07 2.74
3735 3940 7.540055 CAGATTCACAAAGAGTTCTTTTATGGC 59.460 37.037 4.43 2.11 43.07 4.40
3736 3941 6.707440 TTCACAAAGAGTTCTTTTATGGCA 57.293 33.333 4.43 0.00 43.07 4.92
3737 3942 6.072112 TCACAAAGAGTTCTTTTATGGCAC 57.928 37.500 4.43 0.00 43.07 5.01
3738 3943 5.009610 TCACAAAGAGTTCTTTTATGGCACC 59.990 40.000 4.43 0.00 43.07 5.01
3739 3944 4.280929 ACAAAGAGTTCTTTTATGGCACCC 59.719 41.667 4.43 0.00 43.07 4.61
3740 3945 3.087370 AGAGTTCTTTTATGGCACCCC 57.913 47.619 0.00 0.00 0.00 4.95
3741 3946 2.649816 AGAGTTCTTTTATGGCACCCCT 59.350 45.455 0.00 0.00 0.00 4.79
3742 3947 3.076032 AGAGTTCTTTTATGGCACCCCTT 59.924 43.478 0.00 0.00 0.00 3.95
3743 3948 3.165071 AGTTCTTTTATGGCACCCCTTG 58.835 45.455 0.00 0.00 0.00 3.61
3744 3949 2.897326 GTTCTTTTATGGCACCCCTTGT 59.103 45.455 0.00 0.00 0.00 3.16
3745 3950 2.802719 TCTTTTATGGCACCCCTTGTC 58.197 47.619 0.00 0.00 0.00 3.18
3746 3951 2.109128 TCTTTTATGGCACCCCTTGTCA 59.891 45.455 0.00 0.00 46.29 3.58
3747 3952 2.685106 TTTATGGCACCCCTTGTCAA 57.315 45.000 0.00 0.00 45.06 3.18
3748 3953 2.917713 TTATGGCACCCCTTGTCAAT 57.082 45.000 0.00 0.00 45.06 2.57
3749 3954 4.323569 TTTATGGCACCCCTTGTCAATA 57.676 40.909 0.00 0.00 45.06 1.90
3750 3955 4.534647 TTATGGCACCCCTTGTCAATAT 57.465 40.909 0.00 0.00 45.06 1.28
3751 3956 2.142356 TGGCACCCCTTGTCAATATG 57.858 50.000 0.00 0.00 36.68 1.78
3752 3957 1.341877 TGGCACCCCTTGTCAATATGG 60.342 52.381 0.00 0.00 36.68 2.74
3753 3958 1.402787 GCACCCCTTGTCAATATGGG 58.597 55.000 11.55 11.55 42.23 4.00
3758 3963 2.301346 CCCTTGTCAATATGGGCTGTC 58.699 52.381 0.00 0.00 32.49 3.51
3774 3979 3.495001 GGCTGTCTTGTGAGAACAGTAAC 59.505 47.826 3.94 0.00 35.40 2.50
3784 3989 0.608308 GAACAGTAACCCCACCTGGC 60.608 60.000 0.00 0.00 0.00 4.85
3829 4034 4.331968 CATACACTAAGGCCCAAGAACAA 58.668 43.478 8.89 0.00 0.00 2.83
3861 4066 3.243907 CCGTGATCTATGAACTCTTCCCC 60.244 52.174 0.00 0.00 0.00 4.81
3866 4071 6.208599 GTGATCTATGAACTCTTCCCCTCTAG 59.791 46.154 0.00 0.00 0.00 2.43
3880 4085 3.563697 CCCCTCTAGTAGTTCACTGTGGA 60.564 52.174 8.11 0.00 38.24 4.02
3912 4117 7.449704 GGACCAAAGATTTTATCCTGCATCTAT 59.550 37.037 0.00 0.00 0.00 1.98
3913 4118 8.401490 ACCAAAGATTTTATCCTGCATCTATC 57.599 34.615 0.00 0.00 0.00 2.08
3924 4129 3.557898 CCTGCATCTATCGCCTTAATGGT 60.558 47.826 0.00 0.00 38.35 3.55
3960 4171 5.359756 TGTCATTTGTCAAGGATCGATAGG 58.640 41.667 0.00 0.00 0.00 2.57
3978 4189 6.323996 TCGATAGGCTATATAAACCCTCCATG 59.676 42.308 7.08 0.00 0.00 3.66
3981 4192 4.226168 AGGCTATATAAACCCTCCATGAGC 59.774 45.833 0.00 0.00 0.00 4.26
4005 4216 1.611936 GGAGAAGTTTGGAGAGGGTGC 60.612 57.143 0.00 0.00 0.00 5.01
4006 4217 1.349357 GAGAAGTTTGGAGAGGGTGCT 59.651 52.381 0.00 0.00 0.00 4.40
4010 4221 0.322008 GTTTGGAGAGGGTGCTGAGG 60.322 60.000 0.00 0.00 0.00 3.86
4011 4222 0.473694 TTTGGAGAGGGTGCTGAGGA 60.474 55.000 0.00 0.00 0.00 3.71
4012 4223 0.906756 TTGGAGAGGGTGCTGAGGAG 60.907 60.000 0.00 0.00 0.00 3.69
4013 4224 1.305718 GGAGAGGGTGCTGAGGAGT 60.306 63.158 0.00 0.00 0.00 3.85
4014 4225 1.326951 GGAGAGGGTGCTGAGGAGTC 61.327 65.000 0.00 0.00 0.00 3.36
4015 4226 0.324275 GAGAGGGTGCTGAGGAGTCT 60.324 60.000 0.00 0.00 0.00 3.24
4016 4227 0.116143 AGAGGGTGCTGAGGAGTCTT 59.884 55.000 0.00 0.00 0.00 3.01
4035 4246 7.148103 GGAGTCTTGTACAACTTACCCTACTAG 60.148 44.444 3.59 0.00 0.00 2.57
4036 4247 7.237255 AGTCTTGTACAACTTACCCTACTAGT 58.763 38.462 3.59 0.00 0.00 2.57
4037 4248 7.392953 AGTCTTGTACAACTTACCCTACTAGTC 59.607 40.741 3.59 0.00 0.00 2.59
4038 4249 7.392953 GTCTTGTACAACTTACCCTACTAGTCT 59.607 40.741 3.59 0.00 0.00 3.24
4101 4340 4.258702 AGAGTGTCGAATTTGCTAGTGT 57.741 40.909 0.00 0.00 0.00 3.55
4185 4424 2.907910 AGTCTTTGTTGCGATCATGC 57.092 45.000 0.00 0.00 0.00 4.06
4203 4442 3.475566 TGCTACCAATGATACTGCCTC 57.524 47.619 0.00 0.00 0.00 4.70
4216 4455 0.316841 CTGCCTCGAGCCCTAATCTC 59.683 60.000 6.99 0.00 42.71 2.75
4217 4456 1.115930 TGCCTCGAGCCCTAATCTCC 61.116 60.000 6.99 0.00 42.71 3.71
4273 4512 2.128853 AACCATTGTGTGAAGGCGCG 62.129 55.000 0.00 0.00 0.00 6.86
4276 4515 0.247814 CATTGTGTGAAGGCGCGATC 60.248 55.000 12.10 4.99 0.00 3.69
4327 4566 2.945668 GTTTAGGCTGAAGGCGAATCAT 59.054 45.455 0.00 0.00 46.23 2.45
4362 4601 0.818296 AGTGTCGCCACCAGAGTATC 59.182 55.000 0.00 0.00 42.88 2.24
4435 4674 2.240918 TGAAGCCTCCCCAAGCCAT 61.241 57.895 0.00 0.00 0.00 4.40
4441 4680 2.285818 TCCCCAAGCCATACCGGT 60.286 61.111 13.98 13.98 36.97 5.28
4454 4693 1.340088 TACCGGTTGGCACTGAAGTA 58.660 50.000 15.04 0.00 39.70 2.24
4460 4699 2.813908 GGCACTGAAGTACCGCCG 60.814 66.667 0.00 0.00 32.14 6.46
4487 4726 6.491403 ACAAATACAAGCTTCAAATGTCTCCT 59.509 34.615 0.00 0.00 0.00 3.69
4488 4727 7.665559 ACAAATACAAGCTTCAAATGTCTCCTA 59.334 33.333 0.00 0.00 0.00 2.94
4489 4728 8.680903 CAAATACAAGCTTCAAATGTCTCCTAT 58.319 33.333 0.00 0.00 0.00 2.57
4516 4755 1.906333 ACCCGGCCATTCAACCAAC 60.906 57.895 2.24 0.00 0.00 3.77
4538 4777 4.159135 ACTTTGGATGAATCACATGGCTTC 59.841 41.667 0.00 0.00 39.56 3.86
4548 4787 0.329596 ACATGGCTTCAAGGGAGTCC 59.670 55.000 0.00 0.00 0.00 3.85
4588 4827 2.755103 CCTTTGACATTGCTTACTCCCC 59.245 50.000 0.00 0.00 0.00 4.81
4589 4828 2.107950 TTGACATTGCTTACTCCCCG 57.892 50.000 0.00 0.00 0.00 5.73
4590 4829 1.271856 TGACATTGCTTACTCCCCGA 58.728 50.000 0.00 0.00 0.00 5.14
4591 4830 1.626321 TGACATTGCTTACTCCCCGAA 59.374 47.619 0.00 0.00 0.00 4.30
4592 4831 2.007608 GACATTGCTTACTCCCCGAAC 58.992 52.381 0.00 0.00 0.00 3.95
4593 4832 1.349688 ACATTGCTTACTCCCCGAACA 59.650 47.619 0.00 0.00 0.00 3.18
4594 4833 2.026262 ACATTGCTTACTCCCCGAACAT 60.026 45.455 0.00 0.00 0.00 2.71
4595 4834 2.107950 TTGCTTACTCCCCGAACATG 57.892 50.000 0.00 0.00 0.00 3.21
4596 4835 0.251916 TGCTTACTCCCCGAACATGG 59.748 55.000 0.00 0.00 0.00 3.66
4597 4836 1.095807 GCTTACTCCCCGAACATGGC 61.096 60.000 0.00 0.00 0.00 4.40
4598 4837 0.251916 CTTACTCCCCGAACATGGCA 59.748 55.000 0.00 0.00 0.00 4.92
4599 4838 0.035820 TTACTCCCCGAACATGGCAC 60.036 55.000 0.00 0.00 0.00 5.01
4600 4839 1.906105 TACTCCCCGAACATGGCACC 61.906 60.000 0.00 0.00 0.00 5.01
4601 4840 3.253061 TCCCCGAACATGGCACCA 61.253 61.111 0.00 0.00 0.00 4.17
4602 4841 2.282816 CCCCGAACATGGCACCAA 60.283 61.111 0.00 0.00 0.00 3.67
4603 4842 1.905843 CCCCGAACATGGCACCAAA 60.906 57.895 0.00 0.00 0.00 3.28
4604 4843 1.586028 CCCGAACATGGCACCAAAG 59.414 57.895 0.00 0.00 0.00 2.77
4605 4844 1.080569 CCGAACATGGCACCAAAGC 60.081 57.895 0.00 0.00 0.00 3.51
4614 4853 4.382541 CACCAAAGCCCCCTCCCC 62.383 72.222 0.00 0.00 0.00 4.81
4637 5115 4.453892 GCCATGCCTGGAAGCCCT 62.454 66.667 12.80 0.00 46.37 5.19
4675 5153 2.304761 TGGGACTCCACTTCATTGTACC 59.695 50.000 0.00 0.00 38.32 3.34
4676 5154 2.304761 GGGACTCCACTTCATTGTACCA 59.695 50.000 0.00 0.00 32.17 3.25
4687 5166 2.714250 TCATTGTACCACCTCCAAACCT 59.286 45.455 0.00 0.00 0.00 3.50
4736 5224 4.126437 GAGAGCTTAGGAGAAATCAAGGC 58.874 47.826 0.00 0.00 0.00 4.35
4744 5232 0.036732 AGAAATCAAGGCCACTCGCA 59.963 50.000 5.01 0.00 40.31 5.10
4760 5248 1.376466 GCAAGGAGGCCAACTCTCA 59.624 57.895 5.01 0.00 45.83 3.27
4809 5300 0.625849 CCCATAGAGGTTGCACCCTT 59.374 55.000 3.48 0.00 39.75 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 9.593134 TGTTCAATGTGTAGCTAAAATTTGTTT 57.407 25.926 0.00 0.00 0.00 2.83
70 71 7.642071 ATCACAAAAATGTTCAATGTGTAGC 57.358 32.000 4.37 0.00 41.52 3.58
201 248 7.642071 ATCACAAAAATGTTCAATGTGTAGC 57.358 32.000 4.37 0.00 41.52 3.58
700 811 2.541178 CCTCGTAGTACAATCGACAGGC 60.541 54.545 0.38 0.00 0.00 4.85
702 813 2.096980 TGCCTCGTAGTACAATCGACAG 59.903 50.000 0.38 0.00 0.00 3.51
703 814 2.086094 TGCCTCGTAGTACAATCGACA 58.914 47.619 0.38 0.00 0.00 4.35
704 815 2.097142 AGTGCCTCGTAGTACAATCGAC 59.903 50.000 0.38 0.00 0.00 4.20
705 816 2.353889 GAGTGCCTCGTAGTACAATCGA 59.646 50.000 0.38 1.34 0.00 3.59
706 817 2.541178 GGAGTGCCTCGTAGTACAATCG 60.541 54.545 0.38 0.00 0.00 3.34
707 818 2.688958 AGGAGTGCCTCGTAGTACAATC 59.311 50.000 0.38 0.00 42.19 2.67
708 819 2.736347 AGGAGTGCCTCGTAGTACAAT 58.264 47.619 0.38 0.00 42.19 2.71
709 820 2.211250 AGGAGTGCCTCGTAGTACAA 57.789 50.000 0.38 0.00 42.19 2.41
710 821 3.972368 AGGAGTGCCTCGTAGTACA 57.028 52.632 0.38 0.00 42.19 2.90
723 834 4.124943 TAGCGAGCGGGGAGGAGT 62.125 66.667 0.00 0.00 0.00 3.85
724 835 3.291383 CTAGCGAGCGGGGAGGAG 61.291 72.222 0.00 0.00 0.00 3.69
725 836 4.124943 ACTAGCGAGCGGGGAGGA 62.125 66.667 0.00 0.00 0.00 3.71
726 837 3.597728 GACTAGCGAGCGGGGAGG 61.598 72.222 0.00 0.00 0.00 4.30
727 838 3.955101 CGACTAGCGAGCGGGGAG 61.955 72.222 0.00 0.00 44.57 4.30
728 839 4.790962 ACGACTAGCGAGCGGGGA 62.791 66.667 12.46 0.00 44.57 4.81
729 840 4.554363 CACGACTAGCGAGCGGGG 62.554 72.222 12.46 3.96 44.57 5.73
843 954 3.532155 TGGTTTTGTGGGCCGTGC 61.532 61.111 0.00 0.00 0.00 5.34
844 955 2.415426 GTGGTTTTGTGGGCCGTG 59.585 61.111 0.00 0.00 0.00 4.94
845 956 3.213402 CGTGGTTTTGTGGGCCGT 61.213 61.111 0.00 0.00 0.00 5.68
846 957 3.213402 ACGTGGTTTTGTGGGCCG 61.213 61.111 0.00 0.00 0.00 6.13
847 958 2.415426 CACGTGGTTTTGTGGGCC 59.585 61.111 7.95 0.00 32.47 5.80
848 959 2.279186 GCACGTGGTTTTGTGGGC 60.279 61.111 18.88 0.00 36.61 5.36
849 960 2.415426 GGCACGTGGTTTTGTGGG 59.585 61.111 18.88 0.00 36.61 4.61
884 995 4.489771 ATAGCCCGTGTGCCTGGC 62.490 66.667 12.87 12.87 45.70 4.85
885 996 2.203070 GATAGCCCGTGTGCCTGG 60.203 66.667 0.00 0.00 0.00 4.45
886 997 2.586079 CGATAGCCCGTGTGCCTG 60.586 66.667 0.00 0.00 0.00 4.85
887 998 3.075005 ACGATAGCCCGTGTGCCT 61.075 61.111 0.00 0.00 41.70 4.75
893 1004 4.530857 GCCAGCACGATAGCCCGT 62.531 66.667 0.00 0.00 44.43 5.28
902 1013 4.680237 TCTTGTCGGGCCAGCACG 62.680 66.667 8.25 8.25 45.35 5.34
903 1014 3.050275 GTCTTGTCGGGCCAGCAC 61.050 66.667 4.39 1.55 0.00 4.40
904 1015 4.329545 GGTCTTGTCGGGCCAGCA 62.330 66.667 4.39 0.00 0.00 4.41
906 1017 4.760047 CCGGTCTTGTCGGGCCAG 62.760 72.222 4.39 0.00 43.45 4.85
912 1023 4.675029 AACGGGCCGGTCTTGTCG 62.675 66.667 31.78 2.84 0.00 4.35
913 1024 2.281276 AAACGGGCCGGTCTTGTC 60.281 61.111 31.78 0.00 0.00 3.18
914 1025 2.593436 CAAACGGGCCGGTCTTGT 60.593 61.111 31.78 5.20 0.00 3.16
915 1026 3.361977 CCAAACGGGCCGGTCTTG 61.362 66.667 31.78 26.44 0.00 3.02
916 1027 3.562232 TCCAAACGGGCCGGTCTT 61.562 61.111 31.78 17.22 36.21 3.01
917 1028 4.324991 GTCCAAACGGGCCGGTCT 62.325 66.667 31.78 12.05 36.21 3.85
918 1029 4.629523 TGTCCAAACGGGCCGGTC 62.630 66.667 31.78 12.65 36.21 4.79
919 1030 4.636435 CTGTCCAAACGGGCCGGT 62.636 66.667 31.78 24.00 36.21 5.28
925 1036 1.066454 GAACCAAACCTGTCCAAACGG 59.934 52.381 0.00 0.00 0.00 4.44
926 1037 1.066454 GGAACCAAACCTGTCCAAACG 59.934 52.381 0.00 0.00 0.00 3.60
927 1038 1.066454 CGGAACCAAACCTGTCCAAAC 59.934 52.381 0.00 0.00 0.00 2.93
928 1039 1.341187 ACGGAACCAAACCTGTCCAAA 60.341 47.619 0.00 0.00 0.00 3.28
929 1040 0.256464 ACGGAACCAAACCTGTCCAA 59.744 50.000 0.00 0.00 0.00 3.53
930 1041 0.179040 GACGGAACCAAACCTGTCCA 60.179 55.000 0.00 0.00 0.00 4.02
931 1042 0.887836 GGACGGAACCAAACCTGTCC 60.888 60.000 0.00 0.00 40.59 4.02
932 1043 1.226030 CGGACGGAACCAAACCTGTC 61.226 60.000 0.00 0.00 33.64 3.51
933 1044 1.227734 CGGACGGAACCAAACCTGT 60.228 57.895 0.00 0.00 0.00 4.00
934 1045 0.533308 TTCGGACGGAACCAAACCTG 60.533 55.000 0.00 0.00 0.00 4.00
935 1046 0.250166 CTTCGGACGGAACCAAACCT 60.250 55.000 0.00 0.00 0.00 3.50
936 1047 0.533531 ACTTCGGACGGAACCAAACC 60.534 55.000 0.00 0.00 0.00 3.27
937 1048 0.584876 CACTTCGGACGGAACCAAAC 59.415 55.000 0.00 0.00 0.00 2.93
938 1049 1.161563 GCACTTCGGACGGAACCAAA 61.162 55.000 0.00 0.00 0.00 3.28
997 1111 3.755628 GCGCCGTGAGAGGGTGTA 61.756 66.667 0.00 0.00 36.14 2.90
1072 1207 3.782244 GCTGTTGCGGACTGCTCG 61.782 66.667 7.96 0.00 46.26 5.03
1131 1266 1.517257 CGAGCGCCTCCTTGTAGTG 60.517 63.158 2.29 0.00 0.00 2.74
1157 1292 3.435186 GGCAGCTCCTTCAACGGC 61.435 66.667 0.00 0.00 0.00 5.68
1161 1296 2.665000 CTCCGGCAGCTCCTTCAA 59.335 61.111 0.00 0.00 0.00 2.69
1170 1305 4.247380 GGGGATGAGCTCCGGCAG 62.247 72.222 12.15 0.00 46.01 4.85
1278 1413 3.093278 CGACATCTTCTTGGCGGC 58.907 61.111 0.00 0.00 44.46 6.53
1281 1416 3.589988 TCTTCTTCGACATCTTCTTGGC 58.410 45.455 0.00 0.00 0.00 4.52
1295 1430 4.142271 TGCGATCTTCTCTTCCTCTTCTTC 60.142 45.833 0.00 0.00 0.00 2.87
1313 1448 0.829333 AGTCTGCCTCAATCTGCGAT 59.171 50.000 0.00 0.00 0.00 4.58
1332 1467 1.004745 GTCCCTGGAATCTTGGAGCAA 59.995 52.381 0.00 0.00 0.00 3.91
1338 1473 1.815421 CGCCGTCCCTGGAATCTTG 60.815 63.158 0.00 0.00 0.00 3.02
1442 1610 3.574074 ATCAGCTTTGGCCAGCCGT 62.574 57.895 13.08 0.00 41.12 5.68
1454 1622 1.950828 CAGCCAAATCGAGATCAGCT 58.049 50.000 0.00 0.00 0.00 4.24
1502 1670 1.890979 GGAGCAGATGGCCGATGTG 60.891 63.158 0.00 3.07 46.50 3.21
1544 1712 3.599285 GACGGCGGTGGTCAATGGA 62.599 63.158 13.24 0.00 34.56 3.41
1547 1715 2.358247 GTGACGGCGGTGGTCAAT 60.358 61.111 13.24 0.00 45.20 2.57
1659 1827 2.030562 GTCGGTGGTGTCTGGTGG 59.969 66.667 0.00 0.00 0.00 4.61
1676 1844 0.868406 GGAGCAACTTGTGAAGACGG 59.132 55.000 0.00 0.00 0.00 4.79
1685 1853 1.886542 GGTAAAGTGGGGAGCAACTTG 59.113 52.381 0.00 0.00 36.75 3.16
1689 1857 1.351017 CTGAGGTAAAGTGGGGAGCAA 59.649 52.381 0.00 0.00 0.00 3.91
1820 1988 1.805945 CACAGAGCTAACGGACGCC 60.806 63.158 0.00 0.00 0.00 5.68
1829 1997 9.586541 TGGATTTTACCAAGAAGCACAGAGCTA 62.587 40.741 0.00 0.00 44.76 3.32
1844 2012 6.126883 CCAGGTAGATACTGTGGATTTTACCA 60.127 42.308 6.22 0.00 34.32 3.25
1846 2014 7.120923 TCCAGGTAGATACTGTGGATTTTAC 57.879 40.000 9.32 0.00 35.66 2.01
1868 2036 0.813821 GAAGGTCTGCAATTGCCTCC 59.186 55.000 26.94 23.19 41.18 4.30
1881 2049 2.046217 GGCGTCCCTTGGAAGGTC 60.046 66.667 4.72 0.00 44.98 3.85
1946 2114 1.935400 AGGGTCATCAATGGGGCCA 60.935 57.895 4.39 0.00 0.00 5.36
2075 2243 0.609957 TCACAAGGCCAGCCATTGAG 60.610 55.000 20.51 15.20 38.92 3.02
2111 2279 1.446272 CTCGGCGAGTTCAGGGAAC 60.446 63.158 27.92 0.94 42.25 3.62
2159 2327 1.810151 GCTTCACGAAGGTTGGCATTA 59.190 47.619 8.78 0.00 38.80 1.90
2189 2357 2.558378 TGATGATGTTCTAGCTGCAGC 58.442 47.619 31.53 31.53 42.49 5.25
2202 2370 9.163899 CTTATAGGATCCAGACAAATGATGATG 57.836 37.037 15.82 0.00 0.00 3.07
2251 2419 1.583054 GTTCGGATGACATGCTACCC 58.417 55.000 5.35 0.00 0.00 3.69
2267 2435 0.442699 CTCGTAGCGCTTTTGGGTTC 59.557 55.000 18.68 0.00 34.56 3.62
2313 2481 1.134995 TGATCGCACAGAGGACATGAC 60.135 52.381 0.00 0.00 0.00 3.06
2324 2492 6.495892 GTGGTTTTCACAAGTGATCGCACA 62.496 45.833 9.33 0.00 45.16 4.57
2327 2495 2.650608 GTGGTTTTCACAAGTGATCGC 58.349 47.619 3.43 0.00 45.39 4.58
2397 2565 3.158676 GGACTGACGGCCTTAGAGATAT 58.841 50.000 0.00 0.00 0.00 1.63
2398 2566 2.092049 TGGACTGACGGCCTTAGAGATA 60.092 50.000 0.00 0.00 0.00 1.98
2442 2610 2.153247 GTGAGACAAAACTAGACGCACG 59.847 50.000 0.00 0.00 0.00 5.34
2485 2653 6.413526 CGTGTCACGAAAGAAAATTTGATCAA 59.586 34.615 20.75 3.38 46.05 2.57
2588 2756 6.591834 AGACAGTGTAATAAATCAGTGAGCAC 59.408 38.462 0.00 0.00 38.09 4.40
2619 2787 6.485830 TGATACTCAATTCCCTCCTACAAG 57.514 41.667 0.00 0.00 0.00 3.16
2643 2811 7.415541 GCATTCACACCACATATAACATGAAGT 60.416 37.037 0.00 0.00 0.00 3.01
2665 2833 4.460382 CCCATTCTCTGTTACTTGTGCATT 59.540 41.667 0.00 0.00 0.00 3.56
2718 2886 7.727181 AGAAGTTGATATGACAGTATGGGTAC 58.273 38.462 0.00 0.00 43.62 3.34
2787 2955 5.621228 GCTACATTCAACGAAAAACAGAGTG 59.379 40.000 0.00 0.00 0.00 3.51
2865 3033 5.569059 GCACAAGAAAAGTTTACCATCATCG 59.431 40.000 0.00 0.00 0.00 3.84
2910 3078 7.121168 TGCAAAACTAGTAAAGCAGCATCTATT 59.879 33.333 10.81 0.00 0.00 1.73
2953 3121 1.603802 CCAGTGCCTAGTGTTTGTGTG 59.396 52.381 0.00 0.00 0.00 3.82
2989 3157 4.721274 TCAATCAATCATCCACAGAGGGTA 59.279 41.667 0.00 0.00 38.24 3.69
3037 3242 5.410067 CACATAGCACAAAAGGGGTATTTG 58.590 41.667 0.00 0.00 42.18 2.32
3097 3302 8.686397 TCGCGTTAACAGTCAAGTAAATATTA 57.314 30.769 5.77 0.00 0.00 0.98
3100 3305 6.306356 GTCTCGCGTTAACAGTCAAGTAAATA 59.694 38.462 5.77 0.00 0.00 1.40
3154 3359 1.878088 AGCTGCAAGTCATCACAACAG 59.122 47.619 1.02 0.00 35.30 3.16
3155 3360 1.971481 AGCTGCAAGTCATCACAACA 58.029 45.000 1.02 0.00 35.30 3.33
3162 3367 6.540189 AGAAACGATAATTAGCTGCAAGTCAT 59.460 34.615 1.02 0.00 35.30 3.06
3229 3434 0.321122 GCACAAGTCTGGTCCCTCTG 60.321 60.000 0.00 0.00 0.00 3.35
3408 3613 3.517500 ACGGGCAAATTTTATGTCCCATT 59.482 39.130 0.00 0.00 39.45 3.16
3472 3677 2.173669 CGCGATGAGCCCGTTTGAT 61.174 57.895 0.00 0.00 44.76 2.57
3505 3710 0.324738 TTGACAGCACAACCCCCAAA 60.325 50.000 0.00 0.00 0.00 3.28
3554 3759 4.631131 ACATGCATACACAGCGTACATAT 58.369 39.130 0.00 0.00 31.27 1.78
3561 3766 8.634475 ACTATATATAACATGCATACACAGCG 57.366 34.615 0.00 0.00 33.85 5.18
3626 3831 5.409643 ACAGTCTGAATGTTTCAAGTTCG 57.590 39.130 6.91 0.00 39.58 3.95
3708 3913 8.571336 CCATAAAAGAACTCTTTGTGAATCTGT 58.429 33.333 5.49 0.00 44.69 3.41
3712 3917 7.147976 GTGCCATAAAAGAACTCTTTGTGAAT 58.852 34.615 5.49 0.00 44.69 2.57
3713 3918 6.460953 GGTGCCATAAAAGAACTCTTTGTGAA 60.461 38.462 5.49 0.00 44.69 3.18
3714 3919 5.009610 GGTGCCATAAAAGAACTCTTTGTGA 59.990 40.000 5.49 0.00 44.69 3.58
3734 3939 1.402787 CCCATATTGACAAGGGGTGC 58.597 55.000 12.16 0.00 37.66 5.01
3735 3940 1.402787 GCCCATATTGACAAGGGGTG 58.597 55.000 18.47 5.11 41.75 4.61
3736 3941 1.308877 AGCCCATATTGACAAGGGGT 58.691 50.000 18.47 14.39 46.62 4.95
3737 3942 1.063717 ACAGCCCATATTGACAAGGGG 60.064 52.381 14.90 14.90 41.75 4.79
3738 3943 2.092212 AGACAGCCCATATTGACAAGGG 60.092 50.000 6.62 6.62 44.37 3.95
3739 3944 3.287867 AGACAGCCCATATTGACAAGG 57.712 47.619 0.00 0.00 0.00 3.61
3740 3945 4.012374 ACAAGACAGCCCATATTGACAAG 58.988 43.478 0.00 0.00 0.00 3.16
3741 3946 3.758023 CACAAGACAGCCCATATTGACAA 59.242 43.478 0.00 0.00 0.00 3.18
3742 3947 3.008923 TCACAAGACAGCCCATATTGACA 59.991 43.478 0.00 0.00 0.00 3.58
3743 3948 3.609853 TCACAAGACAGCCCATATTGAC 58.390 45.455 0.00 0.00 0.00 3.18
3744 3949 3.519107 TCTCACAAGACAGCCCATATTGA 59.481 43.478 0.00 0.00 0.00 2.57
3745 3950 3.877559 TCTCACAAGACAGCCCATATTG 58.122 45.455 0.00 0.00 0.00 1.90
3746 3951 4.263462 TGTTCTCACAAGACAGCCCATATT 60.263 41.667 0.00 0.00 0.00 1.28
3747 3952 3.264193 TGTTCTCACAAGACAGCCCATAT 59.736 43.478 0.00 0.00 0.00 1.78
3748 3953 2.637382 TGTTCTCACAAGACAGCCCATA 59.363 45.455 0.00 0.00 0.00 2.74
3749 3954 1.421268 TGTTCTCACAAGACAGCCCAT 59.579 47.619 0.00 0.00 0.00 4.00
3750 3955 0.836606 TGTTCTCACAAGACAGCCCA 59.163 50.000 0.00 0.00 0.00 5.36
3751 3956 1.202698 ACTGTTCTCACAAGACAGCCC 60.203 52.381 2.88 0.00 35.67 5.19
3752 3957 2.246719 ACTGTTCTCACAAGACAGCC 57.753 50.000 2.88 0.00 35.67 4.85
3753 3958 3.495001 GGTTACTGTTCTCACAAGACAGC 59.505 47.826 2.88 0.00 35.67 4.40
3758 3963 3.139077 GTGGGGTTACTGTTCTCACAAG 58.861 50.000 0.00 0.00 30.36 3.16
3784 3989 4.154918 GCTTTGATGGGCTAAATAGGATCG 59.845 45.833 0.00 0.00 0.00 3.69
3829 4034 5.661056 TCATAGATCACGGAGACAACTTT 57.339 39.130 0.00 0.00 0.00 2.66
3861 4066 4.337145 AGGTCCACAGTGAACTACTAGAG 58.663 47.826 0.62 0.00 37.60 2.43
3866 4071 3.767673 TCCATAGGTCCACAGTGAACTAC 59.232 47.826 0.62 0.00 37.37 2.73
3880 4085 7.062957 CAGGATAAAATCTTTGGTCCATAGGT 58.937 38.462 9.22 0.00 30.93 3.08
3955 4166 7.676683 TCATGGAGGGTTTATATAGCCTATC 57.323 40.000 13.12 9.62 45.67 2.08
3960 4171 5.165961 TGCTCATGGAGGGTTTATATAGC 57.834 43.478 0.00 0.00 0.00 2.97
3978 4189 4.442753 CCTCTCCAAACTTCTCCTATGCTC 60.443 50.000 0.00 0.00 0.00 4.26
3981 4192 3.777522 ACCCTCTCCAAACTTCTCCTATG 59.222 47.826 0.00 0.00 0.00 2.23
4005 4216 5.471257 GGTAAGTTGTACAAGACTCCTCAG 58.529 45.833 8.98 0.00 0.00 3.35
4006 4217 4.282703 GGGTAAGTTGTACAAGACTCCTCA 59.717 45.833 8.98 0.00 0.00 3.86
4010 4221 6.587206 AGTAGGGTAAGTTGTACAAGACTC 57.413 41.667 8.98 7.70 0.00 3.36
4011 4222 7.237255 ACTAGTAGGGTAAGTTGTACAAGACT 58.763 38.462 8.98 0.79 0.00 3.24
4012 4223 7.392953 AGACTAGTAGGGTAAGTTGTACAAGAC 59.607 40.741 8.98 7.54 0.00 3.01
4013 4224 7.465116 AGACTAGTAGGGTAAGTTGTACAAGA 58.535 38.462 8.98 0.00 0.00 3.02
4014 4225 7.700022 AGACTAGTAGGGTAAGTTGTACAAG 57.300 40.000 8.98 0.00 0.00 3.16
4015 4226 8.386264 AGTAGACTAGTAGGGTAAGTTGTACAA 58.614 37.037 3.59 3.59 0.00 2.41
4016 4227 7.922382 AGTAGACTAGTAGGGTAAGTTGTACA 58.078 38.462 0.00 0.00 0.00 2.90
4101 4340 5.401531 ACCTTAGAGCGAAGTTTGTCATA 57.598 39.130 0.00 0.00 0.00 2.15
4185 4424 3.858877 GCTCGAGGCAGTATCATTGGTAG 60.859 52.174 15.58 0.00 41.35 3.18
4203 4442 1.482593 ACAACTGGAGATTAGGGCTCG 59.517 52.381 0.00 0.00 33.19 5.03
4273 4512 1.341606 GCTATGTAGCTTCGGCGATC 58.658 55.000 11.76 5.94 45.62 3.69
4327 4566 4.768145 CGACACTTTTATTTTGTGAGCGA 58.232 39.130 0.00 0.00 36.25 4.93
4362 4601 5.261370 CGATGATTCGCCTTTTATCTCTG 57.739 43.478 0.00 0.00 38.75 3.35
4402 4641 2.954318 GGCTTCACCAATGCTCATATGT 59.046 45.455 1.90 0.00 38.86 2.29
4435 4674 1.001181 GTACTTCAGTGCCAACCGGTA 59.999 52.381 8.00 0.00 33.28 4.02
4454 4693 1.873165 CTTGTATTTGTGCGGCGGT 59.127 52.632 9.78 0.00 0.00 5.68
4460 4699 5.922544 AGACATTTGAAGCTTGTATTTGTGC 59.077 36.000 2.10 0.00 0.00 4.57
4516 4755 4.158949 TGAAGCCATGTGATTCATCCAAAG 59.841 41.667 9.79 0.00 34.09 2.77
4538 4777 3.771160 CGGGTCCGGACTCCCTTG 61.771 72.222 32.52 13.57 41.40 3.61
4588 4827 4.557942 GCTTTGGTGCCATGTTCG 57.442 55.556 0.00 0.00 0.00 3.95
4597 4836 4.382541 GGGGAGGGGGCTTTGGTG 62.383 72.222 0.00 0.00 0.00 4.17
4663 5141 4.142038 GTTTGGAGGTGGTACAATGAAGT 58.858 43.478 0.00 0.00 44.16 3.01
4675 5153 3.012518 GTCATCATCAGGTTTGGAGGTG 58.987 50.000 0.00 0.00 0.00 4.00
4676 5154 2.915604 AGTCATCATCAGGTTTGGAGGT 59.084 45.455 0.00 0.00 0.00 3.85
4687 5166 2.159184 GGAGTGAGCGAAGTCATCATCA 60.159 50.000 0.00 0.00 0.00 3.07
4736 5224 3.551496 TTGGCCTCCTTGCGAGTGG 62.551 63.158 3.32 3.14 36.82 4.00
4744 5232 0.037447 GCTTGAGAGTTGGCCTCCTT 59.963 55.000 3.32 0.00 41.47 3.36
4760 5248 0.463654 TGTCGGCTCACTTTGTGCTT 60.464 50.000 0.00 0.00 37.09 3.91
4809 5300 6.818644 GCCAAACAATACTCTCATCAAGTAGA 59.181 38.462 0.00 0.00 32.98 2.59


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

AutoCloner maintained by Alex Coulton.