Multiple sequence alignment - TraesCS7B01G480500

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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 TraesCS7B01G480500 chr7B 100.000 2768 0 0 1 2768 734359373 734362140 0.000000e+00 5112.0
1 TraesCS7B01G480500 chr7B 93.023 129 9 0 680 808 128905431 128905303 3.640000e-44 189.0
2 TraesCS7B01G480500 chr7D 92.188 512 40 0 1188 1699 638382059 638381548 0.000000e+00 725.0
3 TraesCS7B01G480500 chr7D 90.182 550 41 9 6 546 638383156 638382611 0.000000e+00 704.0
4 TraesCS7B01G480500 chr7D 87.077 650 30 16 2136 2768 638349236 638348624 0.000000e+00 686.0
5 TraesCS7B01G480500 chr7D 92.748 262 17 2 286 545 638400655 638400394 7.240000e-101 377.0
6 TraesCS7B01G480500 chr7D 88.142 253 23 3 934 1186 638382360 638382115 7.500000e-76 294.0
7 TraesCS7B01G480500 chr7D 76.268 493 90 18 1188 1676 638296801 638296332 1.280000e-58 237.0
8 TraesCS7B01G480500 chr7D 93.289 149 5 2 534 680 638382497 638382352 6.000000e-52 215.0
9 TraesCS7B01G480500 chr7D 92.029 138 9 2 680 817 379095755 379095890 2.810000e-45 193.0
10 TraesCS7B01G480500 chr7D 100.000 29 0 0 563 591 638354792 638354764 1.000000e-03 54.7
11 TraesCS7B01G480500 chr7A 92.188 512 40 0 1188 1699 727532688 727533199 0.000000e+00 725.0
12 TraesCS7B01G480500 chr7A 89.781 548 49 3 6 546 727531588 727532135 0.000000e+00 695.0
13 TraesCS7B01G480500 chr7A 84.190 525 62 14 1188 1711 727692525 727693029 8.910000e-135 490.0
14 TraesCS7B01G480500 chr7A 85.041 488 52 12 1502 1985 727552007 727552477 6.940000e-131 477.0
15 TraesCS7B01G480500 chr7A 85.496 393 19 7 2385 2768 727701596 727701959 2.600000e-100 375.0
16 TraesCS7B01G480500 chr7A 78.317 618 81 22 2000 2602 727553062 727553641 1.580000e-92 350.0
17 TraesCS7B01G480500 chr7A 90.157 254 20 1 934 1187 727532388 727532636 2.660000e-85 326.0
18 TraesCS7B01G480500 chr7A 76.258 497 83 25 1188 1676 727773806 727774275 5.960000e-57 231.0
19 TraesCS7B01G480500 chr7A 90.604 149 11 2 534 680 727532249 727532396 7.820000e-46 195.0
20 TraesCS7B01G480500 chr7A 89.744 156 7 2 2613 2768 727703697 727703843 1.010000e-44 191.0
21 TraesCS7B01G480500 chr5B 91.506 259 16 2 680 932 544182187 544182445 4.390000e-93 351.0
22 TraesCS7B01G480500 chr5B 87.568 185 19 3 748 930 666893599 666893781 7.770000e-51 211.0
23 TraesCS7B01G480500 chr3B 90.041 241 18 3 680 915 69363141 69363380 9.630000e-80 307.0
24 TraesCS7B01G480500 chr3B 87.917 240 19 3 680 914 479986823 479986589 9.770000e-70 274.0
25 TraesCS7B01G480500 chr1B 90.000 240 19 1 680 914 321874090 321873851 3.460000e-79 305.0
26 TraesCS7B01G480500 chr5A 88.288 222 20 2 713 929 680120277 680120497 7.600000e-66 261.0
27 TraesCS7B01G480500 chr5A 92.537 134 5 1 680 808 126953939 126953806 1.310000e-43 187.0
28 TraesCS7B01G480500 chr4B 84.028 288 8 15 676 932 134599471 134599191 2.750000e-60 243.0
29 TraesCS7B01G480500 chr4B 87.019 208 17 6 707 913 14386702 14386900 2.770000e-55 226.0
30 TraesCS7B01G480500 chr2B 85.000 240 20 6 680 914 160755374 160755602 2.140000e-56 230.0
31 TraesCS7B01G480500 chr2B 85.106 188 19 7 751 932 677041386 677041202 1.690000e-42 183.0
32 TraesCS7B01G480500 chr4D 86.765 204 15 6 713 911 111552647 111552843 1.670000e-52 217.0
33 TraesCS7B01G480500 chr6B 88.393 112 11 2 1433 1544 717596712 717596603 1.730000e-27 134.0


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 TraesCS7B01G480500 chr7B 734359373 734362140 2767 False 5112.00 5112 100.00000 1 2768 1 chr7B.!!$F1 2767
1 TraesCS7B01G480500 chr7D 638348624 638349236 612 True 686.00 686 87.07700 2136 2768 1 chr7D.!!$R2 632
2 TraesCS7B01G480500 chr7D 638381548 638383156 1608 True 484.50 725 90.95025 6 1699 4 chr7D.!!$R5 1693
3 TraesCS7B01G480500 chr7A 727692525 727693029 504 False 490.00 490 84.19000 1188 1711 1 chr7A.!!$F1 523
4 TraesCS7B01G480500 chr7A 727531588 727533199 1611 False 485.25 725 90.68250 6 1699 4 chr7A.!!$F3 1693
5 TraesCS7B01G480500 chr7A 727552007 727553641 1634 False 413.50 477 81.67900 1502 2602 2 chr7A.!!$F4 1100
6 TraesCS7B01G480500 chr7A 727701596 727703843 2247 False 283.00 375 87.62000 2385 2768 2 chr7A.!!$F5 383

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
815 951 0.034337 CCCGTCCCGAACTTCAGAAA 59.966 55.0 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2143 0.107606 CAGAGCTTGCATCAGAGCCT 60.108 55.0 4.49 0.0 39.71 4.58 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
38 39 7.720442 TGGAACAAAATCACATGTGTCATTTA 58.280 30.769 24.63 5.41 31.92 1.40
51 52 8.934825 ACATGTGTCATTTATTTACCATTTTGC 58.065 29.630 0.00 0.00 0.00 3.68
54 55 6.035542 GTGTCATTTATTTACCATTTTGCCCG 59.964 38.462 0.00 0.00 0.00 6.13
75 77 5.391523 CCCGTGAATTGTATGTACCTTTGTG 60.392 44.000 0.00 0.00 0.00 3.33
142 144 2.783135 CATAGGATCCACCATTTCGGG 58.217 52.381 15.82 0.00 42.04 5.14
147 149 2.854300 ATCCACCATTTCGGGCCACC 62.854 60.000 4.39 0.00 40.22 4.61
155 157 0.693622 TTTCGGGCCACCAATAGACA 59.306 50.000 4.39 0.00 36.13 3.41
163 165 2.287915 GCCACCAATAGACATGTAAGCG 59.712 50.000 0.00 0.00 0.00 4.68
168 170 6.194463 CACCAATAGACATGTAAGCGATTTG 58.806 40.000 0.00 0.00 0.00 2.32
169 171 5.207768 CCAATAGACATGTAAGCGATTTGC 58.792 41.667 0.00 0.00 46.98 3.68
179 181 2.505447 GCGATTTGCACACAACACC 58.495 52.632 0.00 0.00 45.45 4.16
228 230 9.950680 CATTTATTTCGCTTATGTTTGAGGTAT 57.049 29.630 0.00 0.00 0.00 2.73
239 241 9.396022 CTTATGTTTGAGGTATGATAACCAACT 57.604 33.333 0.00 0.00 42.40 3.16
254 256 9.567776 TGATAACCAACTGTGAATAAGAAAAGA 57.432 29.630 0.00 0.00 0.00 2.52
257 259 8.519799 AACCAACTGTGAATAAGAAAAGAAGA 57.480 30.769 0.00 0.00 0.00 2.87
319 326 2.094182 CCCTCGAATCGACCTCTTTTCA 60.094 50.000 0.00 0.00 0.00 2.69
338 345 9.897744 TCTTTTCATGCTTCACTTTACAATAAG 57.102 29.630 0.00 0.00 0.00 1.73
397 404 1.113788 AAGCACAAGCCAAAAGAGCA 58.886 45.000 0.00 0.00 43.56 4.26
403 410 2.169144 ACAAGCCAAAAGAGCAAAAGCT 59.831 40.909 0.00 0.00 0.00 3.74
412 419 5.526506 AAAGAGCAAAAGCTTGTCTCATT 57.473 34.783 18.89 13.18 37.78 2.57
487 494 3.201290 CCACTGATCATTACCACTCAGC 58.799 50.000 0.00 0.00 38.94 4.26
495 502 1.593196 TTACCACTCAGCACAACAGC 58.407 50.000 0.00 0.00 0.00 4.40
619 755 4.778143 ATGGACCCGTTCTGGCGC 62.778 66.667 0.00 0.00 35.87 6.53
667 803 2.609610 TGTCCTGGGCCCACTACC 60.610 66.667 24.45 9.82 0.00 3.18
668 804 2.285442 GTCCTGGGCCCACTACCT 60.285 66.667 24.45 0.00 0.00 3.08
669 805 1.923909 GTCCTGGGCCCACTACCTT 60.924 63.158 24.45 0.00 0.00 3.50
670 806 1.615424 TCCTGGGCCCACTACCTTC 60.615 63.158 24.45 0.00 0.00 3.46
671 807 2.680370 CCTGGGCCCACTACCTTCC 61.680 68.421 24.45 0.00 0.00 3.46
672 808 1.923395 CTGGGCCCACTACCTTCCA 60.923 63.158 24.45 0.00 0.00 3.53
673 809 2.198304 CTGGGCCCACTACCTTCCAC 62.198 65.000 24.45 0.00 0.00 4.02
674 810 1.923909 GGGCCCACTACCTTCCACT 60.924 63.158 19.95 0.00 0.00 4.00
675 811 1.299976 GGCCCACTACCTTCCACTG 59.700 63.158 0.00 0.00 0.00 3.66
676 812 1.377333 GCCCACTACCTTCCACTGC 60.377 63.158 0.00 0.00 0.00 4.40
677 813 1.299976 CCCACTACCTTCCACTGCC 59.700 63.158 0.00 0.00 0.00 4.85
678 814 1.079127 CCACTACCTTCCACTGCCG 60.079 63.158 0.00 0.00 0.00 5.69
679 815 1.671742 CACTACCTTCCACTGCCGT 59.328 57.895 0.00 0.00 0.00 5.68
680 816 0.892755 CACTACCTTCCACTGCCGTA 59.107 55.000 0.00 0.00 0.00 4.02
681 817 1.480954 CACTACCTTCCACTGCCGTAT 59.519 52.381 0.00 0.00 0.00 3.06
682 818 2.691526 CACTACCTTCCACTGCCGTATA 59.308 50.000 0.00 0.00 0.00 1.47
683 819 2.692041 ACTACCTTCCACTGCCGTATAC 59.308 50.000 0.00 0.00 0.00 1.47
684 820 0.828677 ACCTTCCACTGCCGTATACC 59.171 55.000 0.00 0.00 0.00 2.73
685 821 1.120530 CCTTCCACTGCCGTATACCT 58.879 55.000 0.00 0.00 0.00 3.08
686 822 1.202533 CCTTCCACTGCCGTATACCTG 60.203 57.143 0.00 0.00 0.00 4.00
687 823 0.828022 TTCCACTGCCGTATACCTGG 59.172 55.000 0.00 0.00 0.00 4.45
692 828 4.968370 GCCGTATACCTGGCCAAA 57.032 55.556 7.01 0.00 45.73 3.28
693 829 2.400911 GCCGTATACCTGGCCAAAC 58.599 57.895 7.01 0.00 45.73 2.93
694 830 1.099295 GCCGTATACCTGGCCAAACC 61.099 60.000 7.01 0.00 45.73 3.27
695 831 0.544697 CCGTATACCTGGCCAAACCT 59.455 55.000 7.01 0.00 40.22 3.50
696 832 1.474498 CCGTATACCTGGCCAAACCTC 60.474 57.143 7.01 0.00 40.22 3.85
697 833 1.805120 CGTATACCTGGCCAAACCTCG 60.805 57.143 7.01 4.16 40.22 4.63
698 834 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
699 835 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
737 873 2.272471 GGCCTACCCAAGCCTGAC 59.728 66.667 0.00 0.00 46.14 3.51
738 874 2.602676 GGCCTACCCAAGCCTGACA 61.603 63.158 0.00 0.00 46.14 3.58
739 875 1.377333 GCCTACCCAAGCCTGACAC 60.377 63.158 0.00 0.00 0.00 3.67
740 876 2.066340 CCTACCCAAGCCTGACACA 58.934 57.895 0.00 0.00 0.00 3.72
741 877 0.400213 CCTACCCAAGCCTGACACAA 59.600 55.000 0.00 0.00 0.00 3.33
742 878 1.202879 CCTACCCAAGCCTGACACAAA 60.203 52.381 0.00 0.00 0.00 2.83
743 879 2.582052 CTACCCAAGCCTGACACAAAA 58.418 47.619 0.00 0.00 0.00 2.44
744 880 1.859302 ACCCAAGCCTGACACAAAAA 58.141 45.000 0.00 0.00 0.00 1.94
785 921 3.590824 CCATCGGGCCTGTGTTTC 58.409 61.111 12.43 0.00 0.00 2.78
786 922 1.002134 CCATCGGGCCTGTGTTTCT 60.002 57.895 12.43 0.00 0.00 2.52
787 923 1.308069 CCATCGGGCCTGTGTTTCTG 61.308 60.000 12.43 1.22 0.00 3.02
788 924 1.002134 ATCGGGCCTGTGTTTCTGG 60.002 57.895 12.43 0.00 38.06 3.86
789 925 2.484287 ATCGGGCCTGTGTTTCTGGG 62.484 60.000 12.43 0.00 35.96 4.45
792 928 2.991540 GCCTGTGTTTCTGGGCCC 60.992 66.667 17.59 17.59 38.77 5.80
793 929 2.520458 CCTGTGTTTCTGGGCCCA 59.480 61.111 26.67 26.67 0.00 5.36
794 930 1.152567 CCTGTGTTTCTGGGCCCAA 60.153 57.895 28.29 14.38 0.00 4.12
795 931 1.181098 CCTGTGTTTCTGGGCCCAAG 61.181 60.000 28.29 18.16 0.00 3.61
796 932 1.809567 CTGTGTTTCTGGGCCCAAGC 61.810 60.000 28.29 15.03 38.76 4.01
808 944 4.016706 CCAAGCCCGTCCCGAACT 62.017 66.667 0.00 0.00 0.00 3.01
809 945 2.032071 CAAGCCCGTCCCGAACTT 59.968 61.111 0.00 0.00 0.00 2.66
810 946 2.033194 CAAGCCCGTCCCGAACTTC 61.033 63.158 0.00 0.00 0.00 3.01
811 947 2.513259 AAGCCCGTCCCGAACTTCA 61.513 57.895 0.00 0.00 0.00 3.02
812 948 2.434359 GCCCGTCCCGAACTTCAG 60.434 66.667 0.00 0.00 0.00 3.02
813 949 2.939261 GCCCGTCCCGAACTTCAGA 61.939 63.158 0.00 0.00 0.00 3.27
814 950 1.669440 CCCGTCCCGAACTTCAGAA 59.331 57.895 0.00 0.00 0.00 3.02
815 951 0.034337 CCCGTCCCGAACTTCAGAAA 59.966 55.000 0.00 0.00 0.00 2.52
816 952 1.541670 CCCGTCCCGAACTTCAGAAAA 60.542 52.381 0.00 0.00 0.00 2.29
817 953 2.215196 CCGTCCCGAACTTCAGAAAAA 58.785 47.619 0.00 0.00 0.00 1.94
818 954 2.812011 CCGTCCCGAACTTCAGAAAAAT 59.188 45.455 0.00 0.00 0.00 1.82
819 955 3.364964 CCGTCCCGAACTTCAGAAAAATG 60.365 47.826 0.00 0.00 0.00 2.32
820 956 3.496884 CGTCCCGAACTTCAGAAAAATGA 59.503 43.478 0.00 0.00 0.00 2.57
821 957 4.024387 CGTCCCGAACTTCAGAAAAATGAA 60.024 41.667 0.00 0.00 37.60 2.57
822 958 5.504994 CGTCCCGAACTTCAGAAAAATGAAA 60.505 40.000 0.00 0.00 38.66 2.69
823 959 6.270064 GTCCCGAACTTCAGAAAAATGAAAA 58.730 36.000 0.00 0.00 38.66 2.29
824 960 6.754675 GTCCCGAACTTCAGAAAAATGAAAAA 59.245 34.615 0.00 0.00 38.66 1.94
929 1065 3.743017 GGCTTCCCATGGCCAGGA 61.743 66.667 21.32 15.01 46.84 3.86
930 1066 2.440980 GCTTCCCATGGCCAGGAC 60.441 66.667 21.32 2.25 0.00 3.85
931 1067 2.988839 GCTTCCCATGGCCAGGACT 61.989 63.158 21.32 0.00 0.00 3.85
932 1068 1.077212 CTTCCCATGGCCAGGACTG 60.077 63.158 21.32 8.21 0.00 3.51
950 1086 2.665000 CACTGCCGTGACATCCCT 59.335 61.111 1.41 0.00 43.97 4.20
954 1090 2.225791 CTGCCGTGACATCCCTCGAA 62.226 60.000 0.00 0.00 0.00 3.71
955 1091 1.810030 GCCGTGACATCCCTCGAAC 60.810 63.158 0.00 0.00 0.00 3.95
962 1098 3.322254 GTGACATCCCTCGAACCATCTAT 59.678 47.826 0.00 0.00 0.00 1.98
1001 1137 2.050351 ACGACGCACGGTCAGAAG 60.050 61.111 7.45 0.00 46.42 2.85
1002 1138 2.050351 CGACGCACGGTCAGAAGT 60.050 61.111 0.00 0.00 46.42 3.01
1003 1139 2.081212 CGACGCACGGTCAGAAGTC 61.081 63.158 0.00 0.00 46.42 3.01
1004 1140 1.007734 GACGCACGGTCAGAAGTCA 60.008 57.895 0.00 0.00 45.36 3.41
1005 1141 1.004277 GACGCACGGTCAGAAGTCAG 61.004 60.000 0.00 0.00 45.36 3.51
1006 1142 1.285950 CGCACGGTCAGAAGTCAGA 59.714 57.895 0.00 0.00 0.00 3.27
1007 1143 0.318699 CGCACGGTCAGAAGTCAGAA 60.319 55.000 0.00 0.00 0.00 3.02
1015 1151 3.046390 GTCAGAAGTCAGAACTCACACG 58.954 50.000 0.00 0.00 33.48 4.49
1048 1186 2.634940 TCAGTCAAAGCTCTTAGCCACT 59.365 45.455 0.00 0.00 43.77 4.00
1086 1224 1.298340 CAACACTATGCGGGGTCCA 59.702 57.895 0.00 0.00 0.00 4.02
1088 1226 1.198759 AACACTATGCGGGGTCCAGT 61.199 55.000 0.00 0.00 0.00 4.00
1146 1284 3.749064 GGCGAGCCGTCTCTGTCA 61.749 66.667 0.00 0.00 37.19 3.58
1267 1459 3.111838 CGACGACGCTCTAACTCTACTA 58.888 50.000 0.00 0.00 0.00 1.82
1286 1478 1.227089 CATCCTCCGTGCCTCTTCG 60.227 63.158 0.00 0.00 0.00 3.79
1315 1507 1.340405 GCCTCAAGAAGAAGGCCATCA 60.340 52.381 11.19 0.00 41.28 3.07
1380 1572 1.895231 GCCATCATCATCAGCGGCA 60.895 57.895 1.45 0.00 39.38 5.69
1428 1620 1.557099 TATGCCTCACGGAGTTCACT 58.443 50.000 0.00 0.00 41.61 3.41
1695 1887 8.226819 AGCTTTTATCTTACCCATTTTCTAGC 57.773 34.615 0.00 0.00 0.00 3.42
1701 1893 4.939439 TCTTACCCATTTTCTAGCGTTTCC 59.061 41.667 0.00 0.00 0.00 3.13
1702 1894 3.434940 ACCCATTTTCTAGCGTTTCCT 57.565 42.857 0.00 0.00 0.00 3.36
1706 1898 5.949952 ACCCATTTTCTAGCGTTTCCTTTAT 59.050 36.000 0.00 0.00 0.00 1.40
1707 1899 6.127730 ACCCATTTTCTAGCGTTTCCTTTATG 60.128 38.462 0.00 0.00 0.00 1.90
1708 1900 6.127730 CCCATTTTCTAGCGTTTCCTTTATGT 60.128 38.462 0.00 0.00 0.00 2.29
1709 1901 7.312899 CCATTTTCTAGCGTTTCCTTTATGTT 58.687 34.615 0.00 0.00 0.00 2.71
1710 1902 8.455682 CCATTTTCTAGCGTTTCCTTTATGTTA 58.544 33.333 0.00 0.00 0.00 2.41
1716 1908 6.046290 AGCGTTTCCTTTATGTTAGGTAGT 57.954 37.500 0.00 0.00 34.29 2.73
1717 1909 6.470278 AGCGTTTCCTTTATGTTAGGTAGTT 58.530 36.000 0.00 0.00 34.29 2.24
1725 1917 9.492973 TCCTTTATGTTAGGTAGTTGTGTTAAC 57.507 33.333 0.00 0.00 34.29 2.01
1737 1930 9.702494 GGTAGTTGTGTTAACTAGTATCAGTTT 57.298 33.333 7.22 0.00 39.45 2.66
1740 1933 9.609346 AGTTGTGTTAACTAGTATCAGTTTGTT 57.391 29.630 7.22 0.00 39.45 2.83
1782 1975 7.961325 TTAATCAGGCTTGAAATGTTTTTCC 57.039 32.000 1.33 0.00 40.49 3.13
1793 1986 6.638610 TGAAATGTTTTTCCTGCAAAAGAGA 58.361 32.000 0.00 0.00 40.49 3.10
1821 2014 4.010667 TCCGTACTGTTATTGCACCTTT 57.989 40.909 0.00 0.00 0.00 3.11
1822 2015 4.391155 TCCGTACTGTTATTGCACCTTTT 58.609 39.130 0.00 0.00 0.00 2.27
1823 2016 4.214545 TCCGTACTGTTATTGCACCTTTTG 59.785 41.667 0.00 0.00 0.00 2.44
1850 2043 2.172505 TCAGTGCTCTTCCACCTTTCAA 59.827 45.455 0.00 0.00 36.38 2.69
1913 2106 8.018520 CACGTTAATTTTTGTGGCAACTCTATA 58.981 33.333 0.00 0.00 37.61 1.31
1914 2107 8.569641 ACGTTAATTTTTGTGGCAACTCTATAA 58.430 29.630 0.00 0.00 37.61 0.98
1929 2122 9.495754 GCAACTCTATAAAATAAGACTTGCAAG 57.504 33.333 24.84 24.84 39.41 4.01
1945 2138 8.568794 AGACTTGCAAGGTTTAAGATTTTACTC 58.431 33.333 29.18 12.07 0.00 2.59
1946 2139 8.232913 ACTTGCAAGGTTTAAGATTTTACTCA 57.767 30.769 29.18 0.00 0.00 3.41
1947 2140 8.135529 ACTTGCAAGGTTTAAGATTTTACTCAC 58.864 33.333 29.18 0.00 0.00 3.51
1948 2141 7.817418 TGCAAGGTTTAAGATTTTACTCACT 57.183 32.000 0.00 0.00 0.00 3.41
1949 2142 8.232913 TGCAAGGTTTAAGATTTTACTCACTT 57.767 30.769 0.00 0.00 0.00 3.16
1950 2143 9.344772 TGCAAGGTTTAAGATTTTACTCACTTA 57.655 29.630 0.00 0.00 0.00 2.24
1951 2144 9.827411 GCAAGGTTTAAGATTTTACTCACTTAG 57.173 33.333 0.00 0.00 0.00 2.18
1985 2178 2.050144 CTCTGCACATGGTACCCCTAT 58.950 52.381 10.07 0.00 0.00 2.57
1987 2180 2.969950 TCTGCACATGGTACCCCTATAC 59.030 50.000 10.07 0.00 0.00 1.47
1988 2181 2.703536 CTGCACATGGTACCCCTATACA 59.296 50.000 10.07 0.00 0.00 2.29
1989 2182 2.436542 TGCACATGGTACCCCTATACAC 59.563 50.000 10.07 0.00 0.00 2.90
1995 2755 4.781775 TGGTACCCCTATACACAAATGG 57.218 45.455 10.07 0.00 0.00 3.16
1996 2756 3.117813 TGGTACCCCTATACACAAATGGC 60.118 47.826 10.07 0.00 0.00 4.40
2006 2766 0.169672 CACAAATGGCAGCTCCTTCG 59.830 55.000 0.00 0.00 35.26 3.79
2012 2775 1.219124 GGCAGCTCCTTCGTGATCA 59.781 57.895 0.00 0.00 0.00 2.92
2019 2782 2.288152 GCTCCTTCGTGATCATCCTCTC 60.288 54.545 0.00 0.00 0.00 3.20
2023 2786 3.118992 CCTTCGTGATCATCCTCTCACAA 60.119 47.826 0.00 0.00 41.46 3.33
2044 2807 6.153340 CACAAATCATTGAGGGTTGGTAGAAT 59.847 38.462 10.51 0.00 38.94 2.40
2045 2808 6.153340 ACAAATCATTGAGGGTTGGTAGAATG 59.847 38.462 10.51 0.00 38.94 2.67
2046 2809 4.927267 TCATTGAGGGTTGGTAGAATGT 57.073 40.909 0.00 0.00 0.00 2.71
2047 2810 4.588899 TCATTGAGGGTTGGTAGAATGTG 58.411 43.478 0.00 0.00 0.00 3.21
2048 2811 4.288366 TCATTGAGGGTTGGTAGAATGTGA 59.712 41.667 0.00 0.00 0.00 3.58
2049 2812 4.715534 TTGAGGGTTGGTAGAATGTGAA 57.284 40.909 0.00 0.00 0.00 3.18
2051 2814 6.381498 TTGAGGGTTGGTAGAATGTGAATA 57.619 37.500 0.00 0.00 0.00 1.75
2052 2815 5.989477 TGAGGGTTGGTAGAATGTGAATAG 58.011 41.667 0.00 0.00 0.00 1.73
2056 2819 5.066505 GGGTTGGTAGAATGTGAATAGCTTG 59.933 44.000 0.00 0.00 0.00 4.01
2057 2820 5.449177 GGTTGGTAGAATGTGAATAGCTTGC 60.449 44.000 0.00 0.00 0.00 4.01
2058 2821 4.842574 TGGTAGAATGTGAATAGCTTGCA 58.157 39.130 0.00 0.00 0.00 4.08
2061 2824 7.053498 TGGTAGAATGTGAATAGCTTGCATTA 58.947 34.615 0.00 0.00 30.96 1.90
2128 2891 2.937469 TTGTTTTGTGTGCTCCAGTG 57.063 45.000 0.00 0.00 0.00 3.66
2134 2897 1.408969 TGTGTGCTCCAGTGTACTCA 58.591 50.000 0.00 0.00 0.00 3.41
2157 2920 2.092968 AGACCGCATCCAATGAAGCTTA 60.093 45.455 0.00 0.00 33.11 3.09
2158 2921 2.682856 GACCGCATCCAATGAAGCTTAA 59.317 45.455 0.00 0.00 33.11 1.85
2159 2922 3.290710 ACCGCATCCAATGAAGCTTAAT 58.709 40.909 0.00 0.00 33.11 1.40
2160 2923 3.701040 ACCGCATCCAATGAAGCTTAATT 59.299 39.130 2.89 2.89 33.11 1.40
2209 2972 5.290885 CCATTGATTGAAGCACAACATGATG 59.709 40.000 0.00 0.00 41.52 3.07
2231 2994 3.372897 AGAGCTCAACTGATGGAGATGA 58.627 45.455 17.77 0.00 32.81 2.92
2250 3014 2.671963 GCGGGGGTGGAAAGACAC 60.672 66.667 0.00 0.00 40.60 3.67
2252 3016 1.833787 GCGGGGGTGGAAAGACACTA 61.834 60.000 0.00 0.00 41.09 2.74
2295 3059 6.742718 GGTCACAGTTCATGTTTATTTGATCG 59.257 38.462 0.00 0.00 41.41 3.69
2317 3081 5.238432 TCGCTTTTGTGAATGTGTTGTCTAT 59.762 36.000 0.00 0.00 35.81 1.98
2327 3091 8.745837 GTGAATGTGTTGTCTATCTTGTTTTTG 58.254 33.333 0.00 0.00 0.00 2.44
2367 3133 4.578928 GTGTAGCCGATATGATTGGGTTTT 59.421 41.667 2.85 0.00 41.74 2.43
2371 3137 4.339247 AGCCGATATGATTGGGTTTTTCAG 59.661 41.667 0.00 0.00 41.74 3.02
2398 3179 3.149981 AGCCAACTGAAACTTAAGAGCC 58.850 45.455 10.09 0.00 0.00 4.70
2424 3205 1.067364 TCTACTTTTGCCACACGACGA 59.933 47.619 0.00 0.00 0.00 4.20
2445 3226 1.546834 GAAGATGTACGCGGACTGTC 58.453 55.000 24.23 19.72 0.00 3.51
2535 3316 2.432628 CGTCGAGGACTTGTGGGC 60.433 66.667 0.00 0.00 0.00 5.36
2554 3335 2.034812 GGCCTGTCTCCGTCTGTAATAG 59.965 54.545 0.00 0.00 0.00 1.73
2602 3383 8.842280 TGTTTTACTAGATCGTGGTTGATTTTT 58.158 29.630 0.00 0.00 0.00 1.94
2631 3412 4.378459 GGTGAGATCGTGGTTGATTTTGTC 60.378 45.833 0.00 0.00 0.00 3.18
2675 3456 2.158841 CGTGTGACTTTTATTCCCCACG 59.841 50.000 0.00 0.00 38.48 4.94
2688 3469 2.214216 CCCACGAGACCACCTGGAA 61.214 63.158 0.00 0.00 38.94 3.53
2748 3538 2.126031 GTGCCGAGGAGAACCGAC 60.126 66.667 0.00 0.00 41.83 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.690884 TGTGATTTTGTTCCATGAAACTTAGAA 58.309 29.630 0.00 0.00 0.00 2.10
2 3 8.231692 TGTGATTTTGTTCCATGAAACTTAGA 57.768 30.769 0.00 0.00 0.00 2.10
3 4 8.918658 CATGTGATTTTGTTCCATGAAACTTAG 58.081 33.333 0.00 0.00 35.96 2.18
4 5 8.420222 ACATGTGATTTTGTTCCATGAAACTTA 58.580 29.630 0.00 0.00 37.07 2.24
38 39 4.817318 ATTCACGGGCAAAATGGTAAAT 57.183 36.364 0.00 0.00 0.00 1.40
41 42 2.894126 ACAATTCACGGGCAAAATGGTA 59.106 40.909 0.00 0.00 0.00 3.25
51 52 4.698304 ACAAAGGTACATACAATTCACGGG 59.302 41.667 0.00 0.00 0.00 5.28
54 55 7.273381 GCATTCACAAAGGTACATACAATTCAC 59.727 37.037 0.00 0.00 0.00 3.18
142 144 2.287915 CGCTTACATGTCTATTGGTGGC 59.712 50.000 0.00 0.00 0.00 5.01
147 149 5.678483 GTGCAAATCGCTTACATGTCTATTG 59.322 40.000 0.00 1.13 43.06 1.90
155 157 3.004210 TGTTGTGTGCAAATCGCTTACAT 59.996 39.130 0.00 0.00 43.06 2.29
163 165 3.341857 TTACGGTGTTGTGTGCAAATC 57.658 42.857 0.00 0.00 36.22 2.17
168 170 4.599047 TGTTTTATTACGGTGTTGTGTGC 58.401 39.130 0.00 0.00 0.00 4.57
169 171 7.507672 TTTTGTTTTATTACGGTGTTGTGTG 57.492 32.000 0.00 0.00 0.00 3.82
177 179 9.765795 TGGATGAAATTTTTGTTTTATTACGGT 57.234 25.926 0.00 0.00 0.00 4.83
207 209 7.807977 ATCATACCTCAAACATAAGCGAAAT 57.192 32.000 0.00 0.00 0.00 2.17
228 230 9.567776 TCTTTTCTTATTCACAGTTGGTTATCA 57.432 29.630 0.00 0.00 0.00 2.15
256 258 9.314321 TCGTCTGGTGATCTTTTTCTTATATTC 57.686 33.333 0.00 0.00 0.00 1.75
257 259 9.838339 ATCGTCTGGTGATCTTTTTCTTATATT 57.162 29.630 0.00 0.00 0.00 1.28
280 287 3.089284 AGGGCCCTTTTGACTAAAATCG 58.911 45.455 22.28 0.00 35.39 3.34
319 326 8.409358 ACTTTCCTTATTGTAAAGTGAAGCAT 57.591 30.769 0.00 0.00 40.85 3.79
354 361 7.546250 TTGCTCCCAAAGGAAAAATGTTATA 57.454 32.000 0.00 0.00 43.40 0.98
397 404 7.771183 TGTGTAAAAGAATGAGACAAGCTTTT 58.229 30.769 0.00 0.00 40.59 2.27
476 483 1.593196 GCTGTTGTGCTGAGTGGTAA 58.407 50.000 0.00 0.00 0.00 2.85
487 494 3.579709 AGAATCTAGTGACGCTGTTGTG 58.420 45.455 0.00 0.00 0.00 3.33
495 502 4.024725 CGGTAGGAGAAGAATCTAGTGACG 60.025 50.000 0.00 0.00 35.54 4.35
546 555 5.918576 GTGGCAACTTTGTTTGGAGTATTAC 59.081 40.000 0.00 0.00 37.61 1.89
552 688 1.838913 CGTGGCAACTTTGTTTGGAG 58.161 50.000 0.00 0.00 37.61 3.86
554 690 1.478622 CGCGTGGCAACTTTGTTTGG 61.479 55.000 0.00 0.00 37.61 3.28
558 694 2.407210 CACGCGTGGCAACTTTGT 59.593 55.556 31.15 0.00 37.61 2.83
619 755 1.077501 CCCATGTGGTAGTGGCAGG 60.078 63.158 0.00 0.00 34.08 4.85
667 803 1.202533 CCAGGTATACGGCAGTGGAAG 60.203 57.143 0.00 0.00 0.00 3.46
668 804 0.828022 CCAGGTATACGGCAGTGGAA 59.172 55.000 0.00 0.00 0.00 3.53
669 805 2.511818 CCAGGTATACGGCAGTGGA 58.488 57.895 0.00 0.00 0.00 4.02
676 812 0.544697 AGGTTTGGCCAGGTATACGG 59.455 55.000 5.11 0.00 40.61 4.02
677 813 1.805120 CGAGGTTTGGCCAGGTATACG 60.805 57.143 5.11 5.74 40.61 3.06
678 814 1.474498 CCGAGGTTTGGCCAGGTATAC 60.474 57.143 5.11 0.40 40.61 1.47
679 815 0.834612 CCGAGGTTTGGCCAGGTATA 59.165 55.000 5.11 0.00 40.61 1.47
680 816 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
681 817 2.598787 CCCGAGGTTTGGCCAGGTA 61.599 63.158 5.11 0.00 40.61 3.08
682 818 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
722 858 0.400213 TTGTGTCAGGCTTGGGTAGG 59.600 55.000 0.00 0.00 0.00 3.18
723 859 2.270352 TTTGTGTCAGGCTTGGGTAG 57.730 50.000 0.00 0.00 0.00 3.18
724 860 2.738587 TTTTGTGTCAGGCTTGGGTA 57.261 45.000 0.00 0.00 0.00 3.69
725 861 1.859302 TTTTTGTGTCAGGCTTGGGT 58.141 45.000 0.00 0.00 0.00 4.51
768 904 1.002134 AGAAACACAGGCCCGATGG 60.002 57.895 0.00 0.00 0.00 3.51
769 905 1.308069 CCAGAAACACAGGCCCGATG 61.308 60.000 0.00 0.00 0.00 3.84
770 906 1.002134 CCAGAAACACAGGCCCGAT 60.002 57.895 0.00 0.00 0.00 4.18
771 907 2.429930 CCAGAAACACAGGCCCGA 59.570 61.111 0.00 0.00 0.00 5.14
772 908 2.672996 CCCAGAAACACAGGCCCG 60.673 66.667 0.00 0.00 0.00 6.13
773 909 2.991540 GCCCAGAAACACAGGCCC 60.992 66.667 0.00 0.00 39.60 5.80
775 911 2.991540 GGGCCCAGAAACACAGGC 60.992 66.667 19.95 0.00 44.99 4.85
776 912 1.152567 TTGGGCCCAGAAACACAGG 60.153 57.895 26.87 0.00 0.00 4.00
777 913 1.809567 GCTTGGGCCCAGAAACACAG 61.810 60.000 26.87 18.74 0.00 3.66
778 914 1.832167 GCTTGGGCCCAGAAACACA 60.832 57.895 26.87 7.32 0.00 3.72
779 915 3.051210 GCTTGGGCCCAGAAACAC 58.949 61.111 26.87 8.28 0.00 3.32
797 933 6.990447 TTCATTTTTCTGAAGTTCGGGACGG 61.990 44.000 11.82 0.00 40.44 4.79
798 934 4.024387 TTCATTTTTCTGAAGTTCGGGACG 60.024 41.667 11.82 0.00 40.97 4.79
799 935 5.432885 TTCATTTTTCTGAAGTTCGGGAC 57.567 39.130 11.82 0.00 31.65 4.46
800 936 6.458232 TTTTCATTTTTCTGAAGTTCGGGA 57.542 33.333 11.82 0.00 36.55 5.14
913 1049 2.440980 GTCCTGGCCATGGGAAGC 60.441 66.667 15.05 0.89 33.01 3.86
914 1050 1.077212 CAGTCCTGGCCATGGGAAG 60.077 63.158 15.05 7.66 33.01 3.46
915 1051 3.089838 CAGTCCTGGCCATGGGAA 58.910 61.111 15.05 0.00 33.01 3.97
916 1052 3.731728 GCAGTCCTGGCCATGGGA 61.732 66.667 15.13 8.01 0.00 4.37
917 1053 4.051167 TGCAGTCCTGGCCATGGG 62.051 66.667 15.13 4.96 0.00 4.00
918 1054 2.753043 GTGCAGTCCTGGCCATGG 60.753 66.667 5.51 7.63 0.00 3.66
919 1055 2.044555 CAGTGCAGTCCTGGCCATG 61.045 63.158 5.51 2.84 0.00 3.66
920 1056 2.353958 CAGTGCAGTCCTGGCCAT 59.646 61.111 5.51 0.00 0.00 4.40
921 1057 4.648626 GCAGTGCAGTCCTGGCCA 62.649 66.667 11.09 4.71 0.00 5.36
924 1060 4.320456 ACGGCAGTGCAGTCCTGG 62.320 66.667 18.61 0.00 29.95 4.45
925 1061 3.046087 CACGGCAGTGCAGTCCTG 61.046 66.667 18.45 3.93 41.94 3.86
950 1086 8.201464 TGAGTTTTTATAGCATAGATGGTTCGA 58.799 33.333 0.00 0.00 39.52 3.71
954 1090 6.202954 GCGTGAGTTTTTATAGCATAGATGGT 59.797 38.462 0.00 0.00 41.93 3.55
955 1091 6.593978 GCGTGAGTTTTTATAGCATAGATGG 58.406 40.000 0.00 0.00 0.00 3.51
962 1098 2.343101 AGCGCGTGAGTTTTTATAGCA 58.657 42.857 8.43 0.00 0.00 3.49
1001 1137 0.577269 GTGTGCGTGTGAGTTCTGAC 59.423 55.000 0.00 0.00 0.00 3.51
1002 1138 0.174617 TGTGTGCGTGTGAGTTCTGA 59.825 50.000 0.00 0.00 0.00 3.27
1003 1139 1.193203 GATGTGTGCGTGTGAGTTCTG 59.807 52.381 0.00 0.00 0.00 3.02
1004 1140 1.502231 GATGTGTGCGTGTGAGTTCT 58.498 50.000 0.00 0.00 0.00 3.01
1005 1141 0.512952 GGATGTGTGCGTGTGAGTTC 59.487 55.000 0.00 0.00 0.00 3.01
1006 1142 1.221466 CGGATGTGTGCGTGTGAGTT 61.221 55.000 0.00 0.00 34.19 3.01
1007 1143 1.664649 CGGATGTGTGCGTGTGAGT 60.665 57.895 0.00 0.00 34.19 3.41
1015 1151 0.950555 TTGACTGAGCGGATGTGTGC 60.951 55.000 0.00 0.00 0.00 4.57
1082 1220 0.603975 GTGCAGGAGGTTCACTGGAC 60.604 60.000 0.00 0.00 46.11 4.02
1086 1224 2.743718 CGGTGCAGGAGGTTCACT 59.256 61.111 0.00 0.00 0.00 3.41
1088 1226 3.555324 TGCGGTGCAGGAGGTTCA 61.555 61.111 0.00 0.00 33.32 3.18
1142 1280 2.343758 GCAGCGAGGAAGGTGACA 59.656 61.111 0.04 0.00 41.72 3.58
1163 1301 4.166888 GCTGCTCCGGATGAGGCA 62.167 66.667 14.65 14.65 41.73 4.75
1267 1459 1.901085 GAAGAGGCACGGAGGATGT 59.099 57.895 0.00 0.00 0.00 3.06
1363 1555 1.853114 GCTGCCGCTGATGATGATGG 61.853 60.000 0.73 0.00 0.00 3.51
1380 1572 3.069300 ACTCTAATGACGATGAGCATGCT 59.931 43.478 22.92 22.92 0.00 3.79
1389 1581 0.380733 TCGCGCACTCTAATGACGAT 59.619 50.000 8.75 0.00 0.00 3.73
1398 1590 1.006805 GAGGCATATCGCGCACTCT 60.007 57.895 8.75 0.00 43.84 3.24
1428 1620 4.103103 CGCACGCTCTCTCCGTCA 62.103 66.667 0.00 0.00 36.69 4.35
1590 1782 2.671177 CCTGTTGTTCTCCGCTGCG 61.671 63.158 16.34 16.34 0.00 5.18
1650 1842 2.472695 AAGGCAAGAACGTGCTATCA 57.527 45.000 0.00 0.00 44.31 2.15
1695 1887 7.172019 ACACAACTACCTAACATAAAGGAAACG 59.828 37.037 0.00 0.00 37.57 3.60
1709 1901 9.745018 ACTGATACTAGTTAACACAACTACCTA 57.255 33.333 8.61 0.00 0.00 3.08
1710 1902 8.647256 ACTGATACTAGTTAACACAACTACCT 57.353 34.615 8.61 0.00 0.00 3.08
1717 1909 9.199982 GCTAACAAACTGATACTAGTTAACACA 57.800 33.333 8.61 0.00 39.86 3.72
1730 1922 9.630098 CAATTGATTACAAGCTAACAAACTGAT 57.370 29.630 0.00 0.00 39.46 2.90
1731 1923 8.845227 TCAATTGATTACAAGCTAACAAACTGA 58.155 29.630 3.38 0.00 39.46 3.41
1762 1955 4.740334 GCAGGAAAAACATTTCAAGCCTGA 60.740 41.667 0.00 0.00 32.77 3.86
1766 1959 5.482686 TTTGCAGGAAAAACATTTCAAGC 57.517 34.783 3.97 6.87 34.79 4.01
1798 1991 4.216411 AGGTGCAATAACAGTACGGATT 57.784 40.909 0.00 0.00 0.00 3.01
1799 1992 3.906720 AGGTGCAATAACAGTACGGAT 57.093 42.857 0.00 0.00 0.00 4.18
1800 1993 3.688694 AAGGTGCAATAACAGTACGGA 57.311 42.857 0.00 0.00 0.00 4.69
1801 1994 4.472286 CAAAAGGTGCAATAACAGTACGG 58.528 43.478 0.00 0.00 0.00 4.02
1827 2020 2.557920 AAGGTGGAAGAGCACTGAAG 57.442 50.000 0.00 0.00 0.00 3.02
1828 2021 2.172505 TGAAAGGTGGAAGAGCACTGAA 59.827 45.455 0.00 0.00 0.00 3.02
1830 2023 2.260844 TGAAAGGTGGAAGAGCACTG 57.739 50.000 0.00 0.00 0.00 3.66
1831 2024 3.515602 ATTGAAAGGTGGAAGAGCACT 57.484 42.857 0.00 0.00 0.00 4.40
1832 2025 4.590850 AAATTGAAAGGTGGAAGAGCAC 57.409 40.909 0.00 0.00 0.00 4.40
1833 2026 6.721208 AGATAAAATTGAAAGGTGGAAGAGCA 59.279 34.615 0.00 0.00 0.00 4.26
1834 2027 7.163001 AGATAAAATTGAAAGGTGGAAGAGC 57.837 36.000 0.00 0.00 0.00 4.09
1835 2028 8.897752 CCTAGATAAAATTGAAAGGTGGAAGAG 58.102 37.037 0.00 0.00 0.00 2.85
1836 2029 8.390921 ACCTAGATAAAATTGAAAGGTGGAAGA 58.609 33.333 0.00 0.00 34.64 2.87
1837 2030 8.581253 ACCTAGATAAAATTGAAAGGTGGAAG 57.419 34.615 0.00 0.00 34.64 3.46
1850 2043 9.699410 TTGGATTGACAATGACCTAGATAAAAT 57.301 29.630 5.14 0.00 0.00 1.82
1905 2098 9.740710 ACCTTGCAAGTCTTATTTTATAGAGTT 57.259 29.630 24.35 0.00 35.06 3.01
1906 2099 9.740710 AACCTTGCAAGTCTTATTTTATAGAGT 57.259 29.630 24.35 6.84 0.00 3.24
1929 2122 8.563123 AGCCTAAGTGAGTAAAATCTTAAACC 57.437 34.615 0.00 0.00 0.00 3.27
1945 2138 1.669779 GCTTGCATCAGAGCCTAAGTG 59.330 52.381 0.00 0.00 32.80 3.16
1946 2139 1.558756 AGCTTGCATCAGAGCCTAAGT 59.441 47.619 4.49 0.00 39.71 2.24
1947 2140 2.158928 AGAGCTTGCATCAGAGCCTAAG 60.159 50.000 4.49 0.00 39.71 2.18
1948 2141 1.836166 AGAGCTTGCATCAGAGCCTAA 59.164 47.619 4.49 0.00 39.71 2.69
1949 2142 1.138464 CAGAGCTTGCATCAGAGCCTA 59.862 52.381 4.49 0.00 39.71 3.93
1950 2143 0.107606 CAGAGCTTGCATCAGAGCCT 60.108 55.000 4.49 0.00 39.71 4.58
1951 2144 2.395651 CAGAGCTTGCATCAGAGCC 58.604 57.895 4.49 0.00 39.71 4.70
1985 2178 2.436417 GAAGGAGCTGCCATTTGTGTA 58.564 47.619 0.00 0.00 40.02 2.90
1987 2180 0.169672 CGAAGGAGCTGCCATTTGTG 59.830 55.000 0.00 0.00 40.02 3.33
1988 2181 0.250901 ACGAAGGAGCTGCCATTTGT 60.251 50.000 0.00 0.00 40.02 2.83
1989 2182 0.169672 CACGAAGGAGCTGCCATTTG 59.830 55.000 0.00 0.00 40.02 2.32
1995 2755 1.216122 GATGATCACGAAGGAGCTGC 58.784 55.000 0.00 0.00 0.00 5.25
1996 2756 1.411977 AGGATGATCACGAAGGAGCTG 59.588 52.381 0.00 0.00 0.00 4.24
2006 2766 6.541278 TCAATGATTTGTGAGAGGATGATCAC 59.459 38.462 0.00 0.00 44.88 3.06
2012 2775 4.229123 ACCCTCAATGATTTGTGAGAGGAT 59.771 41.667 9.37 0.00 44.12 3.24
2019 2782 5.009631 TCTACCAACCCTCAATGATTTGTG 58.990 41.667 0.00 0.00 34.32 3.33
2023 2786 5.653769 CACATTCTACCAACCCTCAATGATT 59.346 40.000 0.00 0.00 0.00 2.57
2076 2839 5.406780 CGACAATAGATTCCCTGCTTATGTC 59.593 44.000 0.00 0.00 0.00 3.06
2081 2844 3.914426 ACGACAATAGATTCCCTGCTT 57.086 42.857 0.00 0.00 0.00 3.91
2083 2846 4.965119 AAAACGACAATAGATTCCCTGC 57.035 40.909 0.00 0.00 0.00 4.85
2128 2891 0.530744 TGGATGCGGTCTGTGAGTAC 59.469 55.000 0.00 0.00 0.00 2.73
2134 2897 1.742761 CTTCATTGGATGCGGTCTGT 58.257 50.000 0.00 0.00 0.00 3.41
2158 2921 9.769093 CGAATTAATTCCGTTTGAGACTAAAAT 57.231 29.630 20.01 0.00 33.28 1.82
2159 2922 7.747357 GCGAATTAATTCCGTTTGAGACTAAAA 59.253 33.333 20.01 0.00 33.28 1.52
2160 2923 7.238571 GCGAATTAATTCCGTTTGAGACTAAA 58.761 34.615 20.01 0.00 33.28 1.85
2209 2972 3.384146 TCATCTCCATCAGTTGAGCTCTC 59.616 47.826 16.19 8.27 0.00 3.20
2231 2994 2.434774 GTCTTTCCACCCCCGCTT 59.565 61.111 0.00 0.00 0.00 4.68
2250 3014 5.481824 TGACCAAGCTACCCTGATGATATAG 59.518 44.000 0.00 0.00 0.00 1.31
2252 3016 4.040952 GTGACCAAGCTACCCTGATGATAT 59.959 45.833 0.00 0.00 0.00 1.63
2295 3059 6.672147 AGATAGACAACACATTCACAAAAGC 58.328 36.000 0.00 0.00 0.00 3.51
2317 3081 4.764172 CATTGTGGTTCCCAAAAACAAGA 58.236 39.130 0.00 0.00 34.06 3.02
2327 3091 0.171007 CACATCGCATTGTGGTTCCC 59.829 55.000 7.89 0.00 42.63 3.97
2340 3106 3.614176 CCAATCATATCGGCTACACATCG 59.386 47.826 0.00 0.00 0.00 3.84
2371 3137 5.527582 TCTTAAGTTTCAGTTGGCTCTTGAC 59.472 40.000 1.63 0.00 0.00 3.18
2398 3179 3.242091 CGTGTGGCAAAAGTAGATGATCG 60.242 47.826 0.00 0.00 0.00 3.69
2424 3205 0.456221 CAGTCCGCGTACATCTTCCT 59.544 55.000 4.17 0.00 0.00 3.36
2445 3226 9.956720 AATCATCACTTTTTGTCTTCACTAAAG 57.043 29.630 0.00 0.00 34.46 1.85
2501 3282 2.970639 GAGACCAGTAGCGCCACA 59.029 61.111 9.06 0.00 0.00 4.17
2535 3316 4.673441 CAACTATTACAGACGGAGACAGG 58.327 47.826 0.00 0.00 0.00 4.00
2554 3335 7.133891 ACAGTCATCTAAATTGTACTGCAAC 57.866 36.000 0.00 0.00 40.28 4.17
2571 3352 6.282199 ACCACGATCTAGTAAAACAGTCAT 57.718 37.500 0.00 0.00 0.00 3.06
2602 3383 1.189524 ACCACGATCTCACCCGGAAA 61.190 55.000 0.73 0.00 0.00 3.13
2603 3384 1.189524 AACCACGATCTCACCCGGAA 61.190 55.000 0.73 0.00 0.00 4.30
2604 3385 1.608336 AACCACGATCTCACCCGGA 60.608 57.895 0.73 0.00 0.00 5.14
2605 3386 1.447838 CAACCACGATCTCACCCGG 60.448 63.158 0.00 0.00 0.00 5.73
2606 3387 0.175760 ATCAACCACGATCTCACCCG 59.824 55.000 0.00 0.00 0.00 5.28
2607 3388 2.403252 AATCAACCACGATCTCACCC 57.597 50.000 0.00 0.00 0.00 4.61
2608 3389 3.502211 ACAAAATCAACCACGATCTCACC 59.498 43.478 0.00 0.00 0.00 4.02
2609 3390 4.213270 TGACAAAATCAACCACGATCTCAC 59.787 41.667 0.00 0.00 33.02 3.51
2610 3391 4.384940 TGACAAAATCAACCACGATCTCA 58.615 39.130 0.00 0.00 33.02 3.27
2611 3392 4.670221 GCTGACAAAATCAACCACGATCTC 60.670 45.833 0.00 0.00 36.69 2.75
2612 3393 3.189287 GCTGACAAAATCAACCACGATCT 59.811 43.478 0.00 0.00 36.69 2.75
2613 3394 3.189287 AGCTGACAAAATCAACCACGATC 59.811 43.478 0.00 0.00 36.69 3.69
2614 3395 3.058016 CAGCTGACAAAATCAACCACGAT 60.058 43.478 8.42 0.00 36.69 3.73
2615 3396 2.290367 CAGCTGACAAAATCAACCACGA 59.710 45.455 8.42 0.00 36.69 4.35
2631 3412 2.497138 TCAATCAAGGTCACACAGCTG 58.503 47.619 13.48 13.48 31.27 4.24
2675 3456 1.605712 CGTCAACTTCCAGGTGGTCTC 60.606 57.143 0.00 0.00 32.64 3.36
2688 3469 1.745232 TGAGTGTTTTGGCGTCAACT 58.255 45.000 0.00 0.00 31.78 3.16


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

AutoCloner maintained by Alex Coulton.