Multiple sequence alignment - TraesCS2D01G184100

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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 TraesCS2D01G184100 chr2D 100.000 3557 0 0 1 3557 129343866 129347422 0.000000e+00 6569.0
1 TraesCS2D01G184100 chr2B 95.745 1598 49 5 981 2575 182925918 182927499 0.000000e+00 2556.0
2 TraesCS2D01G184100 chr2B 86.916 963 82 28 2615 3553 182927495 182928437 0.000000e+00 1040.0
3 TraesCS2D01G184100 chr2B 88.095 462 37 9 289 736 182925359 182925816 1.880000e-147 532.0
4 TraesCS2D01G184100 chr2B 94.158 291 13 3 1 288 182925023 182925312 1.170000e-119 440.0
5 TraesCS2D01G184100 chr2A 91.358 243 19 2 289 529 136115958 136116200 7.360000e-87 331.0
6 TraesCS2D01G184100 chr2A 91.509 212 14 1 77 288 136115704 136115911 4.490000e-74 289.0
7 TraesCS2D01G184100 chr2A 88.966 145 3 8 612 754 136116203 136116336 2.200000e-37 167.0
8 TraesCS2D01G184100 chr2A 95.402 87 4 0 772 858 136116321 136116407 4.790000e-29 139.0
9 TraesCS2D01G184100 chr2A 95.522 67 0 1 876 939 136116452 136116518 1.750000e-18 104.0
10 TraesCS2D01G184100 chr2A 100.000 33 0 0 191 223 101846660 101846628 1.070000e-05 62.1
11 TraesCS2D01G184100 chr3A 72.894 819 176 37 1000 1792 30444050 30444848 1.280000e-59 241.0
12 TraesCS2D01G184100 chr3A 74.152 619 128 22 1093 1691 30362561 30363167 9.930000e-56 228.0


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 TraesCS2D01G184100 chr2D 129343866 129347422 3556 False 6569 6569 100.0000 1 3557 1 chr2D.!!$F1 3556
1 TraesCS2D01G184100 chr2B 182925023 182928437 3414 False 1142 2556 91.2285 1 3553 4 chr2B.!!$F1 3552
2 TraesCS2D01G184100 chr2A 136115704 136116518 814 False 206 331 92.5514 77 939 5 chr2A.!!$F1 862
3 TraesCS2D01G184100 chr3A 30444050 30444848 798 False 241 241 72.8940 1000 1792 1 chr3A.!!$F2 792
4 TraesCS2D01G184100 chr3A 30362561 30363167 606 False 228 228 74.1520 1093 1691 1 chr3A.!!$F1 598

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
763 828 0.178921 ACACTCTCTGGCTTCCCTCA 60.179 55.0 0.0 0.0 0.0 3.86 F
979 1074 0.458716 GAGCAGAGCAGGAACCGTAC 60.459 60.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1917 0.038166 TTCCAGTGATCCTTGTGGCC 59.962 55.0 0.0 0.0 0.0 5.36 R
2898 3011 0.179084 TCGCCGTCATCATTTCTCCC 60.179 55.0 0.0 0.0 0.0 4.30 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
44 45 4.202151 GGCAACTTTGTTCCTCAAATGAGT 60.202 41.667 9.43 0.00 43.78 3.41
94 97 6.995091 AGGTGCATAATCAGAAATACTTCTCC 59.005 38.462 0.00 0.00 40.05 3.71
177 181 8.557029 CCTTCACGGAATATTTATTGTAGTTCC 58.443 37.037 0.00 0.00 33.16 3.62
224 228 6.262273 GGTTTCATTAGGACAAGTCTTTGACA 59.738 38.462 0.00 0.00 37.73 3.58
326 376 5.536497 AGAACATTAAATCAGGGTCCCTT 57.464 39.130 8.08 0.00 0.00 3.95
376 427 8.582657 TTTTCCCGTCTATTTCCAATAATCAA 57.417 30.769 0.00 0.00 0.00 2.57
380 431 8.629158 TCCCGTCTATTTCCAATAATCAATTTG 58.371 33.333 0.00 0.00 0.00 2.32
381 432 7.382218 CCCGTCTATTTCCAATAATCAATTTGC 59.618 37.037 0.00 0.00 0.00 3.68
387 440 5.261209 TCCAATAATCAATTTGCGGGAAG 57.739 39.130 0.00 0.00 0.00 3.46
473 532 2.225382 TCCAGGACCATGACTTCGTA 57.775 50.000 0.00 0.00 0.00 3.43
494 553 6.733721 GTATACATACGTGTGTCACATCTG 57.266 41.667 21.83 5.20 39.39 2.90
519 578 5.954296 AGATCACTTCATCACCAAACTTG 57.046 39.130 0.00 0.00 0.00 3.16
521 580 3.554934 TCACTTCATCACCAAACTTGCT 58.445 40.909 0.00 0.00 0.00 3.91
557 616 1.153449 CGTATCCATGGCGGTGTGT 60.153 57.895 6.96 0.00 35.57 3.72
566 625 1.021202 TGGCGGTGTGTTCTTTCTTG 58.979 50.000 0.00 0.00 0.00 3.02
567 626 1.305201 GGCGGTGTGTTCTTTCTTGA 58.695 50.000 0.00 0.00 0.00 3.02
574 633 6.075046 GCGGTGTGTTCTTTCTTGAATTTTAC 60.075 38.462 0.00 0.00 0.00 2.01
575 634 6.416750 CGGTGTGTTCTTTCTTGAATTTTACC 59.583 38.462 0.00 0.00 0.00 2.85
759 824 2.849294 AGAAACACTCTCTGGCTTCC 57.151 50.000 0.00 0.00 0.00 3.46
760 825 1.349357 AGAAACACTCTCTGGCTTCCC 59.651 52.381 0.00 0.00 0.00 3.97
761 826 1.349357 GAAACACTCTCTGGCTTCCCT 59.651 52.381 0.00 0.00 0.00 4.20
762 827 0.980423 AACACTCTCTGGCTTCCCTC 59.020 55.000 0.00 0.00 0.00 4.30
763 828 0.178921 ACACTCTCTGGCTTCCCTCA 60.179 55.000 0.00 0.00 0.00 3.86
764 829 0.979665 CACTCTCTGGCTTCCCTCAA 59.020 55.000 0.00 0.00 0.00 3.02
765 830 1.349026 CACTCTCTGGCTTCCCTCAAA 59.651 52.381 0.00 0.00 0.00 2.69
766 831 2.057922 ACTCTCTGGCTTCCCTCAAAA 58.942 47.619 0.00 0.00 0.00 2.44
767 832 2.443255 ACTCTCTGGCTTCCCTCAAAAA 59.557 45.455 0.00 0.00 0.00 1.94
798 863 1.135546 CACTCTCTGGCAGACACTACG 60.136 57.143 14.43 2.69 0.00 3.51
858 923 6.585695 ATCTTACGACCACTTCACTAAAGA 57.414 37.500 0.00 0.00 38.44 2.52
860 925 6.618811 TCTTACGACCACTTCACTAAAGATC 58.381 40.000 0.00 0.00 38.44 2.75
864 929 3.935828 GACCACTTCACTAAAGATCTGCC 59.064 47.826 0.00 0.00 38.44 4.85
865 930 3.327757 ACCACTTCACTAAAGATCTGCCA 59.672 43.478 0.00 0.00 38.44 4.92
866 931 3.686726 CCACTTCACTAAAGATCTGCCAC 59.313 47.826 0.00 0.00 38.44 5.01
868 933 4.999950 CACTTCACTAAAGATCTGCCACTT 59.000 41.667 0.00 0.00 38.44 3.16
869 934 5.121454 CACTTCACTAAAGATCTGCCACTTC 59.879 44.000 0.00 0.00 38.44 3.01
870 935 4.207891 TCACTAAAGATCTGCCACTTCC 57.792 45.455 0.00 0.00 0.00 3.46
871 936 3.582647 TCACTAAAGATCTGCCACTTCCA 59.417 43.478 0.00 0.00 0.00 3.53
872 937 3.686726 CACTAAAGATCTGCCACTTCCAC 59.313 47.826 0.00 0.00 0.00 4.02
873 938 2.206576 AAAGATCTGCCACTTCCACC 57.793 50.000 0.00 0.00 0.00 4.61
874 939 1.067295 AAGATCTGCCACTTCCACCA 58.933 50.000 0.00 0.00 0.00 4.17
941 1036 5.845985 TGAGACTTTTACTCATCTTTGCG 57.154 39.130 0.00 0.00 39.10 4.85
944 1039 7.097192 TGAGACTTTTACTCATCTTTGCGTAT 58.903 34.615 0.00 0.00 39.10 3.06
946 1041 7.965045 AGACTTTTACTCATCTTTGCGTATTC 58.035 34.615 0.00 0.00 0.00 1.75
949 1044 8.391106 ACTTTTACTCATCTTTGCGTATTCATC 58.609 33.333 0.00 0.00 0.00 2.92
958 1053 5.700832 TCTTTGCGTATTCATCACTTGTCTT 59.299 36.000 0.00 0.00 0.00 3.01
960 1055 5.281693 TGCGTATTCATCACTTGTCTTTG 57.718 39.130 0.00 0.00 0.00 2.77
961 1056 4.994217 TGCGTATTCATCACTTGTCTTTGA 59.006 37.500 0.00 0.00 0.00 2.69
962 1057 5.120674 TGCGTATTCATCACTTGTCTTTGAG 59.879 40.000 0.00 0.00 0.00 3.02
963 1058 5.554636 CGTATTCATCACTTGTCTTTGAGC 58.445 41.667 0.00 0.00 0.00 4.26
964 1059 5.120674 CGTATTCATCACTTGTCTTTGAGCA 59.879 40.000 0.00 0.00 0.00 4.26
965 1060 5.624344 ATTCATCACTTGTCTTTGAGCAG 57.376 39.130 0.00 0.00 0.00 4.24
966 1061 4.341366 TCATCACTTGTCTTTGAGCAGA 57.659 40.909 0.00 0.00 0.00 4.26
967 1062 4.313282 TCATCACTTGTCTTTGAGCAGAG 58.687 43.478 0.00 0.00 0.00 3.35
968 1063 2.487934 TCACTTGTCTTTGAGCAGAGC 58.512 47.619 0.00 0.00 0.00 4.09
969 1064 2.158914 TCACTTGTCTTTGAGCAGAGCA 60.159 45.455 0.00 0.00 0.00 4.26
970 1065 2.223611 CACTTGTCTTTGAGCAGAGCAG 59.776 50.000 0.00 0.00 0.00 4.24
971 1066 1.805345 CTTGTCTTTGAGCAGAGCAGG 59.195 52.381 0.00 0.00 0.00 4.85
972 1067 1.051008 TGTCTTTGAGCAGAGCAGGA 58.949 50.000 0.00 0.00 0.00 3.86
973 1068 1.417517 TGTCTTTGAGCAGAGCAGGAA 59.582 47.619 0.00 0.00 0.00 3.36
974 1069 1.803555 GTCTTTGAGCAGAGCAGGAAC 59.196 52.381 0.00 0.00 0.00 3.62
975 1070 1.163554 CTTTGAGCAGAGCAGGAACC 58.836 55.000 0.00 0.00 0.00 3.62
976 1071 0.603707 TTTGAGCAGAGCAGGAACCG 60.604 55.000 0.00 0.00 0.00 4.44
977 1072 1.758440 TTGAGCAGAGCAGGAACCGT 61.758 55.000 0.00 0.00 0.00 4.83
978 1073 0.898326 TGAGCAGAGCAGGAACCGTA 60.898 55.000 0.00 0.00 0.00 4.02
979 1074 0.458716 GAGCAGAGCAGGAACCGTAC 60.459 60.000 0.00 0.00 0.00 3.67
991 1086 0.963962 AACCGTACGTGTCATCAGGT 59.036 50.000 15.21 0.00 43.60 4.00
992 1087 0.963962 ACCGTACGTGTCATCAGGTT 59.036 50.000 15.21 0.00 41.81 3.50
1017 1115 1.153086 AATGGCGGAGATGGTCAGC 60.153 57.895 0.00 0.00 44.98 4.26
1070 1168 5.538053 AGATCGTATCTGGTCTGATTGACAT 59.462 40.000 0.00 0.00 40.73 3.06
1091 1189 1.206610 GCATGAAGAGAGACCAGAGCA 59.793 52.381 0.00 0.00 0.00 4.26
1095 1193 1.132262 GAAGAGAGACCAGAGCAGACG 59.868 57.143 0.00 0.00 0.00 4.18
1341 1445 2.737376 GCCACCAGGTCGTTCGTC 60.737 66.667 0.00 0.00 37.19 4.20
1347 1451 4.353437 AGGTCGTTCGTCACCGGC 62.353 66.667 0.00 0.00 37.79 6.13
1659 1769 4.559063 CTGGGCTCCATCCTGCGG 62.559 72.222 0.00 0.00 30.82 5.69
1807 1917 3.129502 TGCCGTACCTCGACTCCG 61.130 66.667 0.00 0.00 42.86 4.63
1813 1923 3.572447 TACCTCGACTCCGGCCACA 62.572 63.158 2.24 0.00 36.24 4.17
1974 2084 1.134189 TCTCTAGAGCCGGTCATCGAA 60.134 52.381 15.35 0.00 42.43 3.71
2024 2134 1.189446 CGAGTACAACGTGCACAGAAC 59.811 52.381 18.64 7.14 0.00 3.01
2032 2142 1.159713 CGTGCACAGAACCAAGAGCA 61.160 55.000 18.64 0.00 0.00 4.26
2035 2145 0.590195 GCACAGAACCAAGAGCACTG 59.410 55.000 0.00 0.00 35.14 3.66
2344 2454 1.986575 GAGCTTGGTGAAGATGCCGC 61.987 60.000 0.00 0.00 0.00 6.53
2355 2465 4.286320 ATGCCGCCGACGAGGATC 62.286 66.667 12.49 0.00 45.00 3.36
2368 2478 3.237741 GGATCGGAGAGGCTGGGG 61.238 72.222 0.00 0.00 43.63 4.96
2400 2510 4.194720 ATCCAGCGACGCCGAGAC 62.195 66.667 17.79 0.00 38.22 3.36
2559 2669 9.940166 GAAAGAGCTACTACTTCATACTAGAAC 57.060 37.037 0.00 0.00 0.00 3.01
2569 2679 4.713824 TCATACTAGAACAAGTCCGTGG 57.286 45.455 0.00 0.00 0.00 4.94
2570 2680 4.338012 TCATACTAGAACAAGTCCGTGGA 58.662 43.478 0.00 0.00 0.00 4.02
2571 2681 4.157289 TCATACTAGAACAAGTCCGTGGAC 59.843 45.833 11.14 11.14 44.86 4.02
2572 2682 2.313317 ACTAGAACAAGTCCGTGGACA 58.687 47.619 20.51 0.00 46.76 4.02
2573 2683 2.296471 ACTAGAACAAGTCCGTGGACAG 59.704 50.000 20.51 14.37 46.76 3.51
2574 2684 1.410004 AGAACAAGTCCGTGGACAGA 58.590 50.000 20.51 0.00 46.76 3.41
2575 2685 1.341531 AGAACAAGTCCGTGGACAGAG 59.658 52.381 20.51 11.77 46.76 3.35
2576 2686 1.068741 GAACAAGTCCGTGGACAGAGT 59.931 52.381 20.51 12.35 46.76 3.24
2577 2687 1.120530 ACAAGTCCGTGGACAGAGTT 58.879 50.000 20.51 3.81 46.76 3.01
2578 2688 1.202533 ACAAGTCCGTGGACAGAGTTG 60.203 52.381 20.51 16.79 46.76 3.16
2579 2689 1.068588 CAAGTCCGTGGACAGAGTTGA 59.931 52.381 20.51 0.00 46.76 3.18
2580 2690 0.962489 AGTCCGTGGACAGAGTTGAG 59.038 55.000 20.51 0.00 46.76 3.02
2581 2691 0.959553 GTCCGTGGACAGAGTTGAGA 59.040 55.000 14.10 0.00 44.02 3.27
2582 2692 0.959553 TCCGTGGACAGAGTTGAGAC 59.040 55.000 0.00 0.00 0.00 3.36
2583 2693 0.673985 CCGTGGACAGAGTTGAGACA 59.326 55.000 0.00 0.00 0.00 3.41
2584 2694 1.603172 CCGTGGACAGAGTTGAGACAC 60.603 57.143 0.00 0.00 0.00 3.67
2585 2695 1.338337 CGTGGACAGAGTTGAGACACT 59.662 52.381 0.00 0.00 0.00 3.55
2586 2696 2.223829 CGTGGACAGAGTTGAGACACTT 60.224 50.000 0.00 0.00 0.00 3.16
2587 2697 3.004419 CGTGGACAGAGTTGAGACACTTA 59.996 47.826 0.00 0.00 0.00 2.24
2588 2698 4.321304 CGTGGACAGAGTTGAGACACTTAT 60.321 45.833 0.00 0.00 0.00 1.73
2589 2699 5.164954 GTGGACAGAGTTGAGACACTTATC 58.835 45.833 0.00 0.00 0.00 1.75
2590 2700 4.832823 TGGACAGAGTTGAGACACTTATCA 59.167 41.667 0.00 0.00 0.00 2.15
2591 2701 5.481824 TGGACAGAGTTGAGACACTTATCAT 59.518 40.000 0.00 0.00 0.00 2.45
2592 2702 5.809562 GGACAGAGTTGAGACACTTATCATG 59.190 44.000 0.00 0.00 0.00 3.07
2593 2703 6.350528 GGACAGAGTTGAGACACTTATCATGA 60.351 42.308 0.00 0.00 0.00 3.07
2594 2704 6.629128 ACAGAGTTGAGACACTTATCATGAG 58.371 40.000 0.09 0.00 0.00 2.90
2595 2705 6.435591 ACAGAGTTGAGACACTTATCATGAGA 59.564 38.462 0.09 0.00 0.00 3.27
2596 2706 6.751425 CAGAGTTGAGACACTTATCATGAGAC 59.249 42.308 0.09 0.00 0.00 3.36
2597 2707 5.645624 AGTTGAGACACTTATCATGAGACG 58.354 41.667 0.09 0.00 0.00 4.18
2598 2708 5.416013 AGTTGAGACACTTATCATGAGACGA 59.584 40.000 0.09 0.00 0.00 4.20
2599 2709 5.897377 TGAGACACTTATCATGAGACGAA 57.103 39.130 0.09 0.00 0.00 3.85
2600 2710 5.884771 TGAGACACTTATCATGAGACGAAG 58.115 41.667 0.09 4.89 0.00 3.79
2601 2711 5.163612 TGAGACACTTATCATGAGACGAAGG 60.164 44.000 0.09 0.42 0.00 3.46
2602 2712 4.098654 AGACACTTATCATGAGACGAAGGG 59.901 45.833 0.09 5.92 32.36 3.95
2603 2713 4.023980 ACACTTATCATGAGACGAAGGGA 58.976 43.478 15.00 0.00 31.20 4.20
2604 2714 4.098654 ACACTTATCATGAGACGAAGGGAG 59.901 45.833 15.00 1.23 31.20 4.30
2605 2715 4.098654 CACTTATCATGAGACGAAGGGAGT 59.901 45.833 0.09 0.00 29.09 3.85
2606 2716 4.098654 ACTTATCATGAGACGAAGGGAGTG 59.901 45.833 0.09 0.00 0.00 3.51
2607 2717 1.924731 TCATGAGACGAAGGGAGTGT 58.075 50.000 0.00 0.00 0.00 3.55
2608 2718 1.819288 TCATGAGACGAAGGGAGTGTC 59.181 52.381 0.00 0.00 33.17 3.67
2609 2719 1.546029 CATGAGACGAAGGGAGTGTCA 59.454 52.381 0.00 0.00 44.18 3.58
2610 2720 1.699730 TGAGACGAAGGGAGTGTCAA 58.300 50.000 0.00 0.00 38.65 3.18
2611 2721 2.036387 TGAGACGAAGGGAGTGTCAAA 58.964 47.619 0.00 0.00 38.65 2.69
2612 2722 2.632996 TGAGACGAAGGGAGTGTCAAAT 59.367 45.455 0.00 0.00 38.65 2.32
2613 2723 3.830178 TGAGACGAAGGGAGTGTCAAATA 59.170 43.478 0.00 0.00 38.65 1.40
2650 2760 3.305403 GCTCACTGCTCAGTACTGTTACA 60.305 47.826 21.99 16.41 40.20 2.41
2656 2766 4.368315 TGCTCAGTACTGTTACACACTTG 58.632 43.478 21.99 0.00 0.00 3.16
2691 2801 9.368921 CGTTTGAAAAAGGATTTAAATTCAAGC 57.631 29.630 9.19 11.33 37.28 4.01
2692 2802 9.663904 GTTTGAAAAAGGATTTAAATTCAAGCC 57.336 29.630 9.19 2.34 37.28 4.35
2694 2804 6.648725 TGAAAAAGGATTTAAATTCAAGCCCG 59.351 34.615 9.19 0.00 37.28 6.13
2700 2810 5.355910 GGATTTAAATTCAAGCCCGTGTCTA 59.644 40.000 1.43 0.00 0.00 2.59
2706 2816 3.627395 TCAAGCCCGTGTCTATCAAAT 57.373 42.857 0.00 0.00 0.00 2.32
2789 2902 3.447918 TTAGCGGTGTATAGGCAAGTC 57.552 47.619 0.00 0.00 0.00 3.01
2790 2903 0.464452 AGCGGTGTATAGGCAAGTCC 59.536 55.000 0.00 0.00 0.00 3.85
2791 2904 0.874607 GCGGTGTATAGGCAAGTCCG 60.875 60.000 0.00 0.00 40.77 4.79
2792 2905 0.874607 CGGTGTATAGGCAAGTCCGC 60.875 60.000 0.00 0.00 40.77 5.54
2793 2906 0.177141 GGTGTATAGGCAAGTCCGCA 59.823 55.000 0.00 0.00 40.77 5.69
2794 2907 1.406341 GGTGTATAGGCAAGTCCGCAA 60.406 52.381 0.00 0.00 40.77 4.85
2795 2908 1.933853 GTGTATAGGCAAGTCCGCAAG 59.066 52.381 0.00 0.00 40.77 4.01
2796 2909 1.553248 TGTATAGGCAAGTCCGCAAGT 59.447 47.619 0.00 0.00 40.77 3.16
2797 2910 1.933853 GTATAGGCAAGTCCGCAAGTG 59.066 52.381 0.00 0.00 40.77 3.16
2798 2911 1.026718 ATAGGCAAGTCCGCAAGTGC 61.027 55.000 0.00 0.00 40.77 4.40
2804 2917 1.854126 CAAGTCCGCAAGTGCTTTTTG 59.146 47.619 1.21 0.00 39.32 2.44
2809 2922 0.805322 CGCAAGTGCTTTTTGTGGCA 60.805 50.000 1.21 0.00 39.32 4.92
2814 2927 4.034975 GCAAGTGCTTTTTGTGGCAAAATA 59.965 37.500 7.70 0.00 40.26 1.40
2817 2930 6.940831 AGTGCTTTTTGTGGCAAAATATTT 57.059 29.167 7.70 0.00 40.26 1.40
2818 2931 7.332213 AGTGCTTTTTGTGGCAAAATATTTT 57.668 28.000 7.64 7.64 40.26 1.82
2824 2937 9.545611 CTTTTTGTGGCAAAATATTTTATGCTC 57.454 29.630 19.30 14.48 0.00 4.26
2825 2938 6.884096 TTGTGGCAAAATATTTTATGCTCG 57.116 33.333 19.30 6.96 0.00 5.03
2840 2953 1.029681 GCTCGAAACACCCAACCTTT 58.970 50.000 0.00 0.00 0.00 3.11
2854 2967 3.430453 CAACCTTTGATGTGTGGGGTAT 58.570 45.455 0.00 0.00 0.00 2.73
2862 2975 6.522625 TTGATGTGTGGGGTATATGTTTTG 57.477 37.500 0.00 0.00 0.00 2.44
2875 2988 8.413229 GGGTATATGTTTTGTGAAGCATGTATT 58.587 33.333 0.00 0.00 37.30 1.89
2908 3021 0.396139 GCCTGCATGGGGAGAAATGA 60.396 55.000 0.00 0.00 33.71 2.57
2911 3024 2.423803 CCTGCATGGGGAGAAATGATGA 60.424 50.000 0.00 0.00 33.71 2.92
2914 3027 2.224606 CATGGGGAGAAATGATGACGG 58.775 52.381 0.00 0.00 0.00 4.79
2919 3032 2.288825 GGGAGAAATGATGACGGCGATA 60.289 50.000 16.62 1.21 0.00 2.92
2920 3033 3.589988 GGAGAAATGATGACGGCGATAT 58.410 45.455 16.62 7.18 0.00 1.63
2921 3034 3.997021 GGAGAAATGATGACGGCGATATT 59.003 43.478 16.62 3.50 0.00 1.28
2923 3036 5.637810 GGAGAAATGATGACGGCGATATTTA 59.362 40.000 16.62 1.50 0.00 1.40
2925 3038 7.065216 AGAAATGATGACGGCGATATTTATG 57.935 36.000 16.62 0.00 0.00 1.90
2926 3039 6.650807 AGAAATGATGACGGCGATATTTATGT 59.349 34.615 16.62 1.81 0.00 2.29
2927 3040 5.784750 ATGATGACGGCGATATTTATGTG 57.215 39.130 16.62 0.00 0.00 3.21
2928 3041 3.431912 TGATGACGGCGATATTTATGTGC 59.568 43.478 16.62 0.00 0.00 4.57
2929 3042 3.106242 TGACGGCGATATTTATGTGCT 57.894 42.857 16.62 0.00 0.00 4.40
2931 3044 4.816392 TGACGGCGATATTTATGTGCTAT 58.184 39.130 16.62 0.00 0.00 2.97
2932 3045 4.625311 TGACGGCGATATTTATGTGCTATG 59.375 41.667 16.62 0.00 0.00 2.23
2933 3046 3.932710 ACGGCGATATTTATGTGCTATGG 59.067 43.478 16.62 0.00 0.00 2.74
2938 3053 5.352569 GCGATATTTATGTGCTATGGCTCTT 59.647 40.000 1.68 0.00 39.59 2.85
2939 3054 6.128172 GCGATATTTATGTGCTATGGCTCTTT 60.128 38.462 1.68 0.00 39.59 2.52
2945 3060 4.771590 TGTGCTATGGCTCTTTTTGAAG 57.228 40.909 1.68 0.00 39.59 3.02
2947 3062 5.012239 TGTGCTATGGCTCTTTTTGAAGAT 58.988 37.500 1.68 0.00 39.59 2.40
2962 3077 0.618458 AAGATGTGTGTGCGGGGTAT 59.382 50.000 0.00 0.00 0.00 2.73
2973 3088 1.834896 TGCGGGGTATTCTATGTGTGT 59.165 47.619 0.00 0.00 0.00 3.72
3030 3145 5.776173 TGTGTGAATTAACCGGACAATTT 57.224 34.783 9.46 0.00 0.00 1.82
3056 3171 2.546778 CGCTTAATTAGGACGAGGCAA 58.453 47.619 0.00 0.00 0.00 4.52
3062 3177 3.528597 ATTAGGACGAGGCAAGTCTTC 57.471 47.619 11.19 0.00 38.58 2.87
3077 3192 2.039084 AGTCTTCTGCCTCCGTTTCAAT 59.961 45.455 0.00 0.00 0.00 2.57
3084 3199 6.339587 TCTGCCTCCGTTTCAATAAAAATT 57.660 33.333 0.00 0.00 0.00 1.82
3085 3200 6.155827 TCTGCCTCCGTTTCAATAAAAATTG 58.844 36.000 0.00 0.00 0.00 2.32
3086 3201 5.848406 TGCCTCCGTTTCAATAAAAATTGT 58.152 33.333 0.00 0.00 33.49 2.71
3108 3224 6.815089 TGTTCAAAATGGCTGAGTTACATTT 58.185 32.000 6.23 6.23 44.18 2.32
3166 3282 9.143631 CAATTTGATGAAAGATAAAAGACACCC 57.856 33.333 0.00 0.00 0.00 4.61
3169 3297 8.477419 TTGATGAAAGATAAAAGACACCCTTT 57.523 30.769 0.00 0.00 46.47 3.11
3250 3378 3.624410 TGAATGCATCGAGTGGAATTGAG 59.376 43.478 0.00 0.00 0.00 3.02
3252 3380 3.885724 TGCATCGAGTGGAATTGAGTA 57.114 42.857 0.00 0.00 0.00 2.59
3273 3401 0.183492 ACTTTGGTTCCAGCAGCTCA 59.817 50.000 0.00 0.00 0.00 4.26
3325 3453 3.131396 ACAAGCCTACAACTTTGAGACG 58.869 45.455 0.00 0.00 0.00 4.18
3346 3474 5.039333 ACGTGTTCACTTGTACACTTCTAC 58.961 41.667 14.73 0.00 41.99 2.59
3365 3493 8.860088 ACTTCTACTGCATAAAACATTTCCTTT 58.140 29.630 0.00 0.00 0.00 3.11
3366 3494 9.132521 CTTCTACTGCATAAAACATTTCCTTTG 57.867 33.333 0.00 0.00 0.00 2.77
3430 3563 7.797121 AAAAATCCTATTTCAACCTCCACAT 57.203 32.000 0.00 0.00 0.00 3.21
3463 3596 3.732849 CTGAGGCCCTCAACCCCC 61.733 72.222 15.67 0.00 40.18 5.40
3466 3599 2.941583 AGGCCCTCAACCCCCTTC 60.942 66.667 0.00 0.00 0.00 3.46
3468 3601 2.941583 GCCCTCAACCCCCTTCCT 60.942 66.667 0.00 0.00 0.00 3.36
3501 3634 1.556911 GGTGGTGTCTGAGATGGTCAT 59.443 52.381 0.00 0.00 33.51 3.06
3507 3640 3.109928 TGTCTGAGATGGTCATGATGGT 58.890 45.455 0.00 0.00 33.51 3.55
3513 3646 3.755378 GAGATGGTCATGATGGTAATGGC 59.245 47.826 0.00 0.00 0.00 4.40
3517 3650 2.158623 GGTCATGATGGTAATGGCCAGA 60.159 50.000 13.05 0.00 46.96 3.86
3518 3651 3.144506 GTCATGATGGTAATGGCCAGAG 58.855 50.000 13.05 0.00 42.47 3.35
3519 3652 2.779430 TCATGATGGTAATGGCCAGAGT 59.221 45.455 13.05 0.87 42.47 3.24
3520 3653 3.144506 CATGATGGTAATGGCCAGAGTC 58.855 50.000 13.05 4.03 42.47 3.36
3525 3658 1.065126 GGTAATGGCCAGAGTCAGCTT 60.065 52.381 13.05 0.00 0.00 3.74
3531 3664 1.668294 CCAGAGTCAGCTTGTCGGT 59.332 57.895 0.00 0.00 0.00 4.69
3539 3672 3.128349 GTCAGCTTGTCGGTTCACTAAA 58.872 45.455 0.00 0.00 0.00 1.85
3553 3686 5.217393 GTTCACTAAACCGACCCAAAAATC 58.783 41.667 0.00 0.00 31.20 2.17
3554 3687 3.499157 TCACTAAACCGACCCAAAAATCG 59.501 43.478 0.00 0.00 38.08 3.34
3555 3688 3.499157 CACTAAACCGACCCAAAAATCGA 59.501 43.478 0.00 0.00 40.86 3.59
3556 3689 3.749609 ACTAAACCGACCCAAAAATCGAG 59.250 43.478 0.00 0.00 40.86 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.835978 TCTTTTGGACTCCGGTGAGATTA 59.164 43.478 11.17 0.00 41.42 1.75
94 97 1.423395 GTGACTGTCAAAGCTCTCCG 58.577 55.000 12.81 0.00 0.00 4.63
139 142 3.371034 TCCGTGAAGGACCTGATTGATA 58.629 45.455 0.00 0.00 45.98 2.15
247 251 2.498167 CACTGCATATTAGGCCTCCAC 58.502 52.381 9.68 0.00 0.00 4.02
387 440 7.830739 ACAATTGGTCAAGATTATTGGAACTC 58.169 34.615 10.83 0.00 32.04 3.01
420 473 9.312904 AGAAATTTCTGGAATGAATGGACTTTA 57.687 29.630 19.86 0.00 35.89 1.85
494 553 7.301054 CAAGTTTGGTGATGAAGTGATCTTAC 58.699 38.462 0.00 0.00 33.64 2.34
508 567 4.016444 AGAGTCAAAAGCAAGTTTGGTGA 58.984 39.130 0.00 0.00 39.13 4.02
519 578 2.096516 CGCTCAAGACAGAGTCAAAAGC 60.097 50.000 0.00 4.27 37.94 3.51
521 580 3.179443 ACGCTCAAGACAGAGTCAAAA 57.821 42.857 0.00 0.00 37.94 2.44
584 648 4.693566 TGGTCATCAACACCGAATAAGTTC 59.306 41.667 0.00 0.00 36.61 3.01
595 659 1.802960 CTCTGTGCTGGTCATCAACAC 59.197 52.381 0.00 0.00 41.47 3.32
638 702 9.823647 CAAGACTATAGGTTGACAATGAATAGT 57.176 33.333 14.29 14.29 32.79 2.12
653 717 7.095270 AGTGTTTCGTTTACCAAGACTATAGG 58.905 38.462 4.43 0.00 0.00 2.57
654 718 8.530269 AAGTGTTTCGTTTACCAAGACTATAG 57.470 34.615 0.00 0.00 0.00 1.31
655 719 8.891671 AAAGTGTTTCGTTTACCAAGACTATA 57.108 30.769 0.00 0.00 0.00 1.31
744 809 0.178921 TGAGGGAAGCCAGAGAGTGT 60.179 55.000 0.00 0.00 0.00 3.55
745 810 0.979665 TTGAGGGAAGCCAGAGAGTG 59.020 55.000 0.00 0.00 0.00 3.51
746 811 1.734655 TTTGAGGGAAGCCAGAGAGT 58.265 50.000 0.00 0.00 0.00 3.24
747 812 2.867109 TTTTGAGGGAAGCCAGAGAG 57.133 50.000 0.00 0.00 0.00 3.20
798 863 4.947147 TGGTGGAAGTGCACCGGC 62.947 66.667 14.63 2.66 44.07 6.13
818 883 5.446875 CGTAAGATTACACTCGCTGACTACA 60.447 44.000 3.81 0.00 43.02 2.74
858 923 0.606401 CGTTGGTGGAAGTGGCAGAT 60.606 55.000 0.00 0.00 0.00 2.90
860 925 2.260869 CCGTTGGTGGAAGTGGCAG 61.261 63.158 0.00 0.00 0.00 4.85
864 929 1.202604 ACTGTACCGTTGGTGGAAGTG 60.203 52.381 0.00 0.00 36.19 3.16
865 930 1.125633 ACTGTACCGTTGGTGGAAGT 58.874 50.000 0.00 0.00 36.19 3.01
866 931 2.298163 AGTACTGTACCGTTGGTGGAAG 59.702 50.000 14.05 0.00 36.19 3.46
868 933 1.999648 AGTACTGTACCGTTGGTGGA 58.000 50.000 14.05 0.00 36.19 4.02
869 934 2.557924 TGTAGTACTGTACCGTTGGTGG 59.442 50.000 14.05 0.00 36.19 4.61
870 935 3.921119 TGTAGTACTGTACCGTTGGTG 57.079 47.619 14.05 0.00 36.19 4.17
871 936 5.244626 AGAAATGTAGTACTGTACCGTTGGT 59.755 40.000 14.05 0.00 40.16 3.67
872 937 5.717119 AGAAATGTAGTACTGTACCGTTGG 58.283 41.667 14.05 0.00 0.00 3.77
873 938 7.307694 TGTAGAAATGTAGTACTGTACCGTTG 58.692 38.462 14.05 0.00 0.00 4.10
874 939 7.175641 ACTGTAGAAATGTAGTACTGTACCGTT 59.824 37.037 14.05 5.31 29.93 4.44
939 1034 5.530519 TCAAAGACAAGTGATGAATACGC 57.469 39.130 0.00 0.00 0.00 4.42
940 1035 5.120674 TGCTCAAAGACAAGTGATGAATACG 59.879 40.000 0.00 0.00 0.00 3.06
941 1036 6.369890 TCTGCTCAAAGACAAGTGATGAATAC 59.630 38.462 0.00 0.00 0.00 1.89
944 1039 4.707105 TCTGCTCAAAGACAAGTGATGAA 58.293 39.130 0.00 0.00 0.00 2.57
946 1041 3.120269 GCTCTGCTCAAAGACAAGTGATG 60.120 47.826 0.00 0.00 0.00 3.07
949 1044 2.216046 TGCTCTGCTCAAAGACAAGTG 58.784 47.619 0.00 0.00 0.00 3.16
958 1053 1.004560 CGGTTCCTGCTCTGCTCAA 60.005 57.895 0.00 0.00 0.00 3.02
960 1055 0.458716 GTACGGTTCCTGCTCTGCTC 60.459 60.000 0.00 0.00 0.00 4.26
961 1056 1.592223 GTACGGTTCCTGCTCTGCT 59.408 57.895 0.00 0.00 0.00 4.24
962 1057 1.805945 CGTACGGTTCCTGCTCTGC 60.806 63.158 7.57 0.00 0.00 4.26
963 1058 0.732880 CACGTACGGTTCCTGCTCTG 60.733 60.000 21.06 0.21 0.00 3.35
964 1059 1.177256 ACACGTACGGTTCCTGCTCT 61.177 55.000 21.06 0.00 0.00 4.09
965 1060 0.731855 GACACGTACGGTTCCTGCTC 60.732 60.000 21.06 5.20 0.00 4.26
966 1061 1.288127 GACACGTACGGTTCCTGCT 59.712 57.895 21.06 0.00 0.00 4.24
967 1062 0.389426 ATGACACGTACGGTTCCTGC 60.389 55.000 21.06 5.44 0.00 4.85
968 1063 1.068125 TGATGACACGTACGGTTCCTG 60.068 52.381 21.06 10.70 0.00 3.86
969 1064 1.201647 CTGATGACACGTACGGTTCCT 59.798 52.381 21.06 7.98 0.00 3.36
970 1065 1.625616 CTGATGACACGTACGGTTCC 58.374 55.000 21.06 6.26 0.00 3.62
971 1066 1.068055 ACCTGATGACACGTACGGTTC 60.068 52.381 21.06 15.11 0.00 3.62
972 1067 0.963962 ACCTGATGACACGTACGGTT 59.036 50.000 21.06 5.28 0.00 4.44
973 1068 0.963962 AACCTGATGACACGTACGGT 59.036 50.000 21.06 14.36 0.00 4.83
974 1069 1.201647 AGAACCTGATGACACGTACGG 59.798 52.381 21.06 11.05 0.00 4.02
975 1070 2.631418 AGAACCTGATGACACGTACG 57.369 50.000 15.01 15.01 0.00 3.67
976 1071 5.647589 TGATTAGAACCTGATGACACGTAC 58.352 41.667 0.00 0.00 0.00 3.67
977 1072 5.907866 TGATTAGAACCTGATGACACGTA 57.092 39.130 0.00 0.00 0.00 3.57
978 1073 4.801330 TGATTAGAACCTGATGACACGT 57.199 40.909 0.00 0.00 0.00 4.49
979 1074 5.007039 CCATTGATTAGAACCTGATGACACG 59.993 44.000 0.00 0.00 0.00 4.49
991 1086 3.136443 ACCATCTCCGCCATTGATTAGAA 59.864 43.478 0.00 0.00 0.00 2.10
992 1087 2.705658 ACCATCTCCGCCATTGATTAGA 59.294 45.455 0.00 0.00 0.00 2.10
1070 1168 1.206610 GCTCTGGTCTCTCTTCATGCA 59.793 52.381 0.00 0.00 0.00 3.96
1091 1189 0.754957 CCTCTCCATCTGCTCCGTCT 60.755 60.000 0.00 0.00 0.00 4.18
1095 1193 1.446791 CAGCCTCTCCATCTGCTCC 59.553 63.158 0.00 0.00 30.08 4.70
1276 1380 1.394151 CCCTGACCTCCTCCTCCTT 59.606 63.158 0.00 0.00 0.00 3.36
1347 1451 2.027625 GGTGTCACGGCGGAAGAAG 61.028 63.158 13.24 0.00 0.00 2.85
1378 1482 4.493747 CTCGAACCTCCGGACGGC 62.494 72.222 16.99 3.39 34.68 5.68
1807 1917 0.038166 TTCCAGTGATCCTTGTGGCC 59.962 55.000 0.00 0.00 0.00 5.36
1813 1923 2.356535 GGATGCTGTTCCAGTGATCCTT 60.357 50.000 13.12 0.00 38.47 3.36
1884 1994 4.724602 TGGAGCTCGTCGTGCTGC 62.725 66.667 27.25 27.25 46.71 5.25
1920 2030 4.264638 GTTGTGCGTGTGGTGCCC 62.265 66.667 0.00 0.00 0.00 5.36
1921 2031 4.605967 CGTTGTGCGTGTGGTGCC 62.606 66.667 0.00 0.00 35.54 5.01
1922 2032 3.506312 CTCGTTGTGCGTGTGGTGC 62.506 63.158 0.00 0.00 42.13 5.01
1923 2033 1.880796 TCTCGTTGTGCGTGTGGTG 60.881 57.895 0.00 0.00 42.13 4.17
1924 2034 1.881252 GTCTCGTTGTGCGTGTGGT 60.881 57.895 0.00 0.00 42.13 4.16
1925 2035 2.594962 GGTCTCGTTGTGCGTGTGG 61.595 63.158 0.00 0.00 42.13 4.17
1926 2036 2.927618 CGGTCTCGTTGTGCGTGTG 61.928 63.158 0.00 0.00 42.13 3.82
1927 2037 2.657296 CGGTCTCGTTGTGCGTGT 60.657 61.111 0.00 0.00 42.13 4.49
1953 2063 1.134189 TCGATGACCGGCTCTAGAGAA 60.134 52.381 24.24 1.39 39.14 2.87
1974 2084 4.254709 TGGCGCTGCAGGAACACT 62.255 61.111 17.12 0.00 0.00 3.55
2024 2134 1.239968 GCCTTGGACAGTGCTCTTGG 61.240 60.000 0.00 0.00 0.00 3.61
2032 2142 2.286523 CCCTCTCGCCTTGGACAGT 61.287 63.158 0.00 0.00 0.00 3.55
2035 2145 4.475135 GCCCCTCTCGCCTTGGAC 62.475 72.222 0.00 0.00 0.00 4.02
2109 2219 4.767255 GGCACCAGGTCCTCTGCG 62.767 72.222 10.69 0.00 42.05 5.18
2110 2220 4.767255 CGGCACCAGGTCCTCTGC 62.767 72.222 8.98 8.98 42.05 4.26
2316 2426 0.241213 TCACCAAGCTCGTCTTCTCG 59.759 55.000 0.00 0.00 31.27 4.04
2355 2465 4.479993 CTTGCCCCAGCCTCTCCG 62.480 72.222 0.00 0.00 38.69 4.63
2368 2478 0.960364 TGGATCGCCAACCTTCTTGC 60.960 55.000 0.00 0.00 42.49 4.01
2400 2510 2.581354 CACCTCTCCAGCTTCGGG 59.419 66.667 0.00 0.00 0.00 5.14
2409 2519 1.123928 CCACCTGTATCCACCTCTCC 58.876 60.000 0.00 0.00 0.00 3.71
2484 2594 4.731773 GCCTTGTGAATCCATTCGATGAAC 60.732 45.833 0.00 0.00 39.62 3.18
2533 2643 9.940166 GTTCTAGTATGAAGTAGTAGCTCTTTC 57.060 37.037 0.00 0.00 36.61 2.62
2539 2649 8.130469 GGACTTGTTCTAGTATGAAGTAGTAGC 58.870 40.741 0.00 0.00 36.61 3.58
2545 2655 5.336531 CCACGGACTTGTTCTAGTATGAAGT 60.337 44.000 0.00 0.00 0.00 3.01
2559 2669 1.068588 TCAACTCTGTCCACGGACTTG 59.931 52.381 16.88 12.39 44.80 3.16
2569 2679 6.625362 TCATGATAAGTGTCTCAACTCTGTC 58.375 40.000 0.00 0.00 29.93 3.51
2570 2680 6.435591 TCTCATGATAAGTGTCTCAACTCTGT 59.564 38.462 0.00 0.00 29.93 3.41
2571 2681 6.751425 GTCTCATGATAAGTGTCTCAACTCTG 59.249 42.308 0.00 0.00 29.93 3.35
2572 2682 6.404184 CGTCTCATGATAAGTGTCTCAACTCT 60.404 42.308 0.00 0.00 0.00 3.24
2573 2683 5.741510 CGTCTCATGATAAGTGTCTCAACTC 59.258 44.000 0.00 0.00 0.00 3.01
2574 2684 5.416013 TCGTCTCATGATAAGTGTCTCAACT 59.584 40.000 0.00 0.00 0.00 3.16
2575 2685 5.641709 TCGTCTCATGATAAGTGTCTCAAC 58.358 41.667 0.00 0.00 0.00 3.18
2576 2686 5.897377 TCGTCTCATGATAAGTGTCTCAA 57.103 39.130 0.00 0.00 0.00 3.02
2577 2687 5.163612 CCTTCGTCTCATGATAAGTGTCTCA 60.164 44.000 0.00 0.00 0.00 3.27
2578 2688 5.277825 CCTTCGTCTCATGATAAGTGTCTC 58.722 45.833 0.00 0.00 0.00 3.36
2579 2689 4.098654 CCCTTCGTCTCATGATAAGTGTCT 59.901 45.833 0.00 0.00 0.00 3.41
2580 2690 4.098044 TCCCTTCGTCTCATGATAAGTGTC 59.902 45.833 0.00 0.00 0.00 3.67
2581 2691 4.023980 TCCCTTCGTCTCATGATAAGTGT 58.976 43.478 0.00 0.00 0.00 3.55
2582 2692 4.098654 ACTCCCTTCGTCTCATGATAAGTG 59.901 45.833 0.00 0.00 0.00 3.16
2583 2693 4.098654 CACTCCCTTCGTCTCATGATAAGT 59.901 45.833 0.00 0.00 0.00 2.24
2584 2694 4.098654 ACACTCCCTTCGTCTCATGATAAG 59.901 45.833 0.00 0.00 0.00 1.73
2585 2695 4.023980 ACACTCCCTTCGTCTCATGATAA 58.976 43.478 0.00 0.00 0.00 1.75
2586 2696 3.632333 ACACTCCCTTCGTCTCATGATA 58.368 45.455 0.00 0.00 0.00 2.15
2587 2697 2.428890 GACACTCCCTTCGTCTCATGAT 59.571 50.000 0.00 0.00 0.00 2.45
2588 2698 1.819288 GACACTCCCTTCGTCTCATGA 59.181 52.381 0.00 0.00 0.00 3.07
2589 2699 1.546029 TGACACTCCCTTCGTCTCATG 59.454 52.381 0.00 0.00 0.00 3.07
2590 2700 1.924731 TGACACTCCCTTCGTCTCAT 58.075 50.000 0.00 0.00 0.00 2.90
2591 2701 1.699730 TTGACACTCCCTTCGTCTCA 58.300 50.000 0.00 0.00 0.00 3.27
2592 2702 2.814280 TTTGACACTCCCTTCGTCTC 57.186 50.000 0.00 0.00 0.00 3.36
2593 2703 4.087182 TCTATTTGACACTCCCTTCGTCT 58.913 43.478 0.00 0.00 0.00 4.18
2594 2704 4.451629 TCTATTTGACACTCCCTTCGTC 57.548 45.455 0.00 0.00 0.00 4.20
2595 2705 4.527038 TCTTCTATTTGACACTCCCTTCGT 59.473 41.667 0.00 0.00 0.00 3.85
2596 2706 5.073311 TCTTCTATTTGACACTCCCTTCG 57.927 43.478 0.00 0.00 0.00 3.79
2597 2707 5.352846 GCTTCTTCTATTTGACACTCCCTTC 59.647 44.000 0.00 0.00 0.00 3.46
2598 2708 5.013599 AGCTTCTTCTATTTGACACTCCCTT 59.986 40.000 0.00 0.00 0.00 3.95
2599 2709 4.534103 AGCTTCTTCTATTTGACACTCCCT 59.466 41.667 0.00 0.00 0.00 4.20
2600 2710 4.633565 CAGCTTCTTCTATTTGACACTCCC 59.366 45.833 0.00 0.00 0.00 4.30
2601 2711 4.094146 GCAGCTTCTTCTATTTGACACTCC 59.906 45.833 0.00 0.00 0.00 3.85
2602 2712 4.692625 TGCAGCTTCTTCTATTTGACACTC 59.307 41.667 0.00 0.00 0.00 3.51
2603 2713 4.645535 TGCAGCTTCTTCTATTTGACACT 58.354 39.130 0.00 0.00 0.00 3.55
2604 2714 4.692625 TCTGCAGCTTCTTCTATTTGACAC 59.307 41.667 9.47 0.00 0.00 3.67
2605 2715 4.898320 TCTGCAGCTTCTTCTATTTGACA 58.102 39.130 9.47 0.00 0.00 3.58
2606 2716 4.201802 GCTCTGCAGCTTCTTCTATTTGAC 60.202 45.833 9.47 0.00 43.09 3.18
2607 2717 3.937706 GCTCTGCAGCTTCTTCTATTTGA 59.062 43.478 9.47 0.00 43.09 2.69
2608 2718 4.275838 GCTCTGCAGCTTCTTCTATTTG 57.724 45.455 9.47 0.00 43.09 2.32
2650 2760 0.963355 AAACGTGTGTGGCCAAGTGT 60.963 50.000 7.24 0.00 0.00 3.55
2656 2766 1.923864 CTTTTTCAAACGTGTGTGGCC 59.076 47.619 5.45 0.00 0.00 5.36
2720 2832 9.972106 AGAATCTTCACCATTCTTTTTCTATCT 57.028 29.630 0.00 0.00 37.31 1.98
2763 2876 6.649557 ACTTGCCTATACACCGCTAAAATATC 59.350 38.462 0.00 0.00 0.00 1.63
2772 2885 0.874607 CGGACTTGCCTATACACCGC 60.875 60.000 0.00 0.00 33.03 5.68
2780 2893 1.671054 GCACTTGCGGACTTGCCTA 60.671 57.895 0.00 0.00 0.00 3.93
2791 2904 1.367659 TTGCCACAAAAAGCACTTGC 58.632 45.000 0.00 0.00 39.10 4.01
2792 2905 4.619437 ATTTTGCCACAAAAAGCACTTG 57.381 36.364 9.32 0.00 39.10 3.16
2793 2906 6.940831 AATATTTTGCCACAAAAAGCACTT 57.059 29.167 9.32 0.00 39.10 3.16
2794 2907 6.940831 AAATATTTTGCCACAAAAAGCACT 57.059 29.167 9.32 0.00 39.10 4.40
2795 2908 9.116054 CATAAAATATTTTGCCACAAAAAGCAC 57.884 29.630 21.19 0.00 39.10 4.40
2796 2909 7.806960 GCATAAAATATTTTGCCACAAAAAGCA 59.193 29.630 21.19 0.00 37.48 3.91
2797 2910 8.022550 AGCATAAAATATTTTGCCACAAAAAGC 58.977 29.630 21.19 8.85 42.37 3.51
2798 2911 9.545611 GAGCATAAAATATTTTGCCACAAAAAG 57.454 29.630 21.19 0.00 42.37 2.27
2804 2917 7.062839 TGTTTCGAGCATAAAATATTTTGCCAC 59.937 33.333 21.19 13.70 42.37 5.01
2809 2922 7.607250 TGGGTGTTTCGAGCATAAAATATTTT 58.393 30.769 17.18 17.18 0.00 1.82
2814 2927 4.321675 GGTTGGGTGTTTCGAGCATAAAAT 60.322 41.667 0.00 0.00 0.00 1.82
2817 2930 2.156098 GGTTGGGTGTTTCGAGCATAA 58.844 47.619 0.00 0.00 0.00 1.90
2818 2931 1.349688 AGGTTGGGTGTTTCGAGCATA 59.650 47.619 0.00 0.00 0.00 3.14
2824 2937 2.360801 ACATCAAAGGTTGGGTGTTTCG 59.639 45.455 0.00 0.00 29.80 3.46
2825 2938 3.132111 ACACATCAAAGGTTGGGTGTTTC 59.868 43.478 11.17 0.00 42.57 2.78
2840 2953 5.417266 CACAAAACATATACCCCACACATCA 59.583 40.000 0.00 0.00 0.00 3.07
2862 2975 8.682016 GTTATCGCATAAAAATACATGCTTCAC 58.318 33.333 5.16 0.00 44.30 3.18
2886 2999 2.424842 TTTCTCCCCATGCAGGCGTT 62.425 55.000 0.00 0.00 35.39 4.84
2898 3011 0.179084 TCGCCGTCATCATTTCTCCC 60.179 55.000 0.00 0.00 0.00 4.30
2908 3021 3.664107 AGCACATAAATATCGCCGTCAT 58.336 40.909 0.00 0.00 0.00 3.06
2911 3024 3.932710 CCATAGCACATAAATATCGCCGT 59.067 43.478 0.00 0.00 0.00 5.68
2914 3027 4.872691 AGAGCCATAGCACATAAATATCGC 59.127 41.667 0.00 0.00 43.56 4.58
2919 3032 7.408756 TCAAAAAGAGCCATAGCACATAAAT 57.591 32.000 0.00 0.00 43.56 1.40
2920 3033 6.832520 TCAAAAAGAGCCATAGCACATAAA 57.167 33.333 0.00 0.00 43.56 1.40
2921 3034 6.658816 TCTTCAAAAAGAGCCATAGCACATAA 59.341 34.615 0.00 0.00 43.56 1.90
2923 3036 5.012239 TCTTCAAAAAGAGCCATAGCACAT 58.988 37.500 0.00 0.00 43.56 3.21
2925 3038 5.105997 ACATCTTCAAAAAGAGCCATAGCAC 60.106 40.000 0.00 0.00 44.53 4.40
2926 3039 5.012239 ACATCTTCAAAAAGAGCCATAGCA 58.988 37.500 0.00 0.00 44.53 3.49
2927 3040 5.105997 ACACATCTTCAAAAAGAGCCATAGC 60.106 40.000 0.00 0.00 44.53 2.97
2928 3041 6.072286 ACACACATCTTCAAAAAGAGCCATAG 60.072 38.462 0.00 0.00 44.53 2.23
2929 3042 5.769662 ACACACATCTTCAAAAAGAGCCATA 59.230 36.000 0.00 0.00 44.53 2.74
2931 3044 3.953612 ACACACATCTTCAAAAAGAGCCA 59.046 39.130 0.00 0.00 44.53 4.75
2932 3045 4.293415 CACACACATCTTCAAAAAGAGCC 58.707 43.478 0.00 0.00 44.53 4.70
2933 3046 3.732721 GCACACACATCTTCAAAAAGAGC 59.267 43.478 0.00 0.00 44.53 4.09
2938 3053 1.336440 CCCGCACACACATCTTCAAAA 59.664 47.619 0.00 0.00 0.00 2.44
2939 3054 0.950836 CCCGCACACACATCTTCAAA 59.049 50.000 0.00 0.00 0.00 2.69
2945 3060 1.014352 GAATACCCCGCACACACATC 58.986 55.000 0.00 0.00 0.00 3.06
2947 3062 1.268066 TAGAATACCCCGCACACACA 58.732 50.000 0.00 0.00 0.00 3.72
2962 3077 4.450976 ACTGTTGAGCAACACACATAGAA 58.549 39.130 11.70 0.00 45.42 2.10
3009 3124 6.443792 AGAAAATTGTCCGGTTAATTCACAC 58.556 36.000 15.50 9.54 0.00 3.82
3010 3125 6.642707 AGAAAATTGTCCGGTTAATTCACA 57.357 33.333 15.50 2.94 0.00 3.58
3011 3126 6.584942 GGAAGAAAATTGTCCGGTTAATTCAC 59.415 38.462 15.50 12.86 0.00 3.18
3012 3127 6.683715 GGAAGAAAATTGTCCGGTTAATTCA 58.316 36.000 15.50 0.35 0.00 2.57
3030 3145 4.441079 CCTCGTCCTAATTAAGCGGAAGAA 60.441 45.833 8.50 0.00 35.46 2.52
3056 3171 1.048601 TGAAACGGAGGCAGAAGACT 58.951 50.000 0.00 0.00 33.94 3.24
3062 3177 5.925969 ACAATTTTTATTGAAACGGAGGCAG 59.074 36.000 4.99 0.00 35.60 4.85
3077 3192 8.729805 AACTCAGCCATTTTGAACAATTTTTA 57.270 26.923 0.00 0.00 0.00 1.52
3084 3199 6.403866 AATGTAACTCAGCCATTTTGAACA 57.596 33.333 0.00 0.00 0.00 3.18
3085 3200 7.437862 TGAAAATGTAACTCAGCCATTTTGAAC 59.562 33.333 12.67 2.31 32.47 3.18
3086 3201 7.495901 TGAAAATGTAACTCAGCCATTTTGAA 58.504 30.769 12.67 1.37 32.47 2.69
3161 3277 5.112129 ACTAGAGTTGACAAAAAGGGTGT 57.888 39.130 0.00 0.00 0.00 4.16
3250 3378 1.266989 GCTGCTGGAACCAAAGTGTAC 59.733 52.381 0.00 0.00 0.00 2.90
3252 3380 0.106519 AGCTGCTGGAACCAAAGTGT 60.107 50.000 0.00 0.00 0.00 3.55
3273 3401 4.400567 GCTGGAGAACAAATCAAGGCTTAT 59.599 41.667 0.00 0.00 0.00 1.73
3325 3453 5.050972 GCAGTAGAAGTGTACAAGTGAACAC 60.051 44.000 0.00 0.00 45.06 3.32
3346 3474 7.951530 AGTTCAAAGGAAATGTTTTATGCAG 57.048 32.000 0.00 0.00 34.13 4.41
3404 3537 8.893563 TGTGGAGGTTGAAATAGGATTTTTAT 57.106 30.769 0.00 0.00 0.00 1.40
3406 3539 7.454380 TCATGTGGAGGTTGAAATAGGATTTTT 59.546 33.333 0.00 0.00 0.00 1.94
3419 3552 3.244353 ACTCAAGAGTCATGTGGAGGTTG 60.244 47.826 0.00 0.00 36.92 3.77
3427 3560 3.643320 TCAGTTCCACTCAAGAGTCATGT 59.357 43.478 0.00 0.00 40.20 3.21
3430 3563 2.630098 CCTCAGTTCCACTCAAGAGTCA 59.370 50.000 0.00 0.00 40.20 3.41
3463 3596 1.395826 CCCTAGCCGACTCCAGGAAG 61.396 65.000 0.00 0.00 0.00 3.46
3466 3599 2.042843 ACCCTAGCCGACTCCAGG 60.043 66.667 0.00 0.00 0.00 4.45
3468 3601 2.363795 CCACCCTAGCCGACTCCA 60.364 66.667 0.00 0.00 0.00 3.86
3501 3634 2.171237 CTGACTCTGGCCATTACCATCA 59.829 50.000 5.51 3.99 39.54 3.07
3507 3640 1.630369 ACAAGCTGACTCTGGCCATTA 59.370 47.619 5.51 0.00 0.00 1.90
3513 3646 0.034059 AACCGACAAGCTGACTCTGG 59.966 55.000 0.00 0.00 0.00 3.86
3517 3650 0.753262 AGTGAACCGACAAGCTGACT 59.247 50.000 0.00 0.00 0.00 3.41
3518 3651 2.433868 TAGTGAACCGACAAGCTGAC 57.566 50.000 0.00 0.00 0.00 3.51
3519 3652 3.128349 GTTTAGTGAACCGACAAGCTGA 58.872 45.455 0.00 0.00 31.85 4.26
3520 3653 3.521524 GTTTAGTGAACCGACAAGCTG 57.478 47.619 0.00 0.00 31.85 4.24
3531 3664 4.023878 CGATTTTTGGGTCGGTTTAGTGAA 60.024 41.667 0.00 0.00 34.39 3.18


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

AutoCloner maintained by Alex Coulton.