Multiple sequence alignment - TraesCS7D01G267500

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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 TraesCS7D01G267500 chr7D 100.000 4565 0 0 1 4565 251032287 251036851 0.000000e+00 8431.0
1 TraesCS7D01G267500 chr7D 96.377 138 5 0 3627 3764 6484459 6484596 1.280000e-55 228.0
2 TraesCS7D01G267500 chr7B 97.780 2027 26 4 926 2948 228009387 228011398 0.000000e+00 3476.0
3 TraesCS7D01G267500 chr7B 95.899 634 18 6 3761 4388 228012355 228012986 0.000000e+00 1020.0
4 TraesCS7D01G267500 chr7B 94.343 654 13 5 2987 3640 228011730 228012359 0.000000e+00 981.0
5 TraesCS7D01G267500 chr7B 96.386 83 2 1 4481 4563 228013029 228013110 7.970000e-28 135.0
6 TraesCS7D01G267500 chr7B 98.000 50 0 1 4410 4458 228012977 228013026 8.140000e-13 86.1
7 TraesCS7D01G267500 chr3D 89.341 910 87 7 1 901 347626918 347627826 0.000000e+00 1134.0
8 TraesCS7D01G267500 chr3D 97.761 134 3 0 3634 3767 210622553 210622420 9.880000e-57 231.0
9 TraesCS7D01G267500 chr3D 94.521 146 7 1 3623 3768 610017588 610017732 1.650000e-54 224.0
10 TraesCS7D01G267500 chr1D 88.997 927 74 16 1 901 249345705 249346629 0.000000e+00 1122.0
11 TraesCS7D01G267500 chr1D 90.323 837 61 10 1 819 274258578 274259412 0.000000e+00 1079.0
12 TraesCS7D01G267500 chr1D 97.059 136 3 1 3630 3765 469018551 469018685 1.280000e-55 228.0
13 TraesCS7D01G267500 chr5D 88.575 919 82 12 1 899 502076160 502077075 0.000000e+00 1094.0
14 TraesCS7D01G267500 chr5D 88.499 826 86 7 1 819 563998798 563999621 0.000000e+00 990.0
15 TraesCS7D01G267500 chr5D 88.043 828 85 8 1 819 312600462 312601284 0.000000e+00 968.0
16 TraesCS7D01G267500 chr5D 89.860 286 27 2 1602 1887 449131715 449131432 2.600000e-97 366.0
17 TraesCS7D01G267500 chr5D 98.450 129 2 0 3638 3766 261390287 261390159 1.280000e-55 228.0
18 TraesCS7D01G267500 chr2D 88.474 911 77 21 1 897 405814775 405813879 0.000000e+00 1075.0
19 TraesCS7D01G267500 chr2D 88.488 886 88 11 24 896 481950959 481950075 0.000000e+00 1059.0
20 TraesCS7D01G267500 chr5B 85.573 908 114 14 1 896 170379389 170378487 0.000000e+00 935.0
21 TraesCS7D01G267500 chr6A 83.051 885 117 20 1212 2069 122679566 122680444 0.000000e+00 773.0
22 TraesCS7D01G267500 chr6B 82.198 910 129 21 1212 2094 186692692 186693595 0.000000e+00 752.0
23 TraesCS7D01G267500 chr6B 84.292 643 83 13 1447 2079 284660094 284659460 3.020000e-171 612.0
24 TraesCS7D01G267500 chr6D 82.400 875 124 19 1247 2094 101720843 101721714 0.000000e+00 736.0
25 TraesCS7D01G267500 chr6D 99.242 132 1 0 3634 3765 272859224 272859355 5.900000e-59 239.0
26 TraesCS7D01G267500 chr1B 97.761 134 3 0 3637 3770 623732112 623731979 9.880000e-57 231.0
27 TraesCS7D01G267500 chr4D 96.377 138 5 0 3633 3770 106682383 106682246 1.280000e-55 228.0
28 TraesCS7D01G267500 chr4B 97.059 136 3 1 3633 3768 180671293 180671159 1.280000e-55 228.0
29 TraesCS7D01G267500 chr3A 84.810 79 12 0 818 896 737736140 737736218 3.790000e-11 80.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G267500 chr7D 251032287 251036851 4564 False 8431.00 8431 100.0000 1 4565 1 chr7D.!!$F2 4564
1 TraesCS7D01G267500 chr7B 228009387 228013110 3723 False 1139.62 3476 96.4816 926 4563 5 chr7B.!!$F1 3637
2 TraesCS7D01G267500 chr3D 347626918 347627826 908 False 1134.00 1134 89.3410 1 901 1 chr3D.!!$F1 900
3 TraesCS7D01G267500 chr1D 249345705 249346629 924 False 1122.00 1122 88.9970 1 901 1 chr1D.!!$F1 900
4 TraesCS7D01G267500 chr1D 274258578 274259412 834 False 1079.00 1079 90.3230 1 819 1 chr1D.!!$F2 818
5 TraesCS7D01G267500 chr5D 502076160 502077075 915 False 1094.00 1094 88.5750 1 899 1 chr5D.!!$F2 898
6 TraesCS7D01G267500 chr5D 563998798 563999621 823 False 990.00 990 88.4990 1 819 1 chr5D.!!$F3 818
7 TraesCS7D01G267500 chr5D 312600462 312601284 822 False 968.00 968 88.0430 1 819 1 chr5D.!!$F1 818
8 TraesCS7D01G267500 chr2D 405813879 405814775 896 True 1075.00 1075 88.4740 1 897 1 chr2D.!!$R1 896
9 TraesCS7D01G267500 chr2D 481950075 481950959 884 True 1059.00 1059 88.4880 24 896 1 chr2D.!!$R2 872
10 TraesCS7D01G267500 chr5B 170378487 170379389 902 True 935.00 935 85.5730 1 896 1 chr5B.!!$R1 895
11 TraesCS7D01G267500 chr6A 122679566 122680444 878 False 773.00 773 83.0510 1212 2069 1 chr6A.!!$F1 857
12 TraesCS7D01G267500 chr6B 186692692 186693595 903 False 752.00 752 82.1980 1212 2094 1 chr6B.!!$F1 882
13 TraesCS7D01G267500 chr6B 284659460 284660094 634 True 612.00 612 84.2920 1447 2079 1 chr6B.!!$R1 632
14 TraesCS7D01G267500 chr6D 101720843 101721714 871 False 736.00 736 82.4000 1247 2094 1 chr6D.!!$F1 847

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
944 994 0.107945 CTTGTAGAGTGGCCAGGAGC 60.108 60.0 5.11 0.0 42.6 4.70 F
1644 1716 0.322975 TTCCTCACTCTTCAGCTGCC 59.677 55.0 9.47 0.0 0.0 4.85 F
2976 3068 0.996583 TTGATTGTCCAGGTACCCCC 59.003 55.0 8.74 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2128 3.054679 TGGTGTTGCCAATCTGCAT 57.945 47.368 0.0 0.0 45.94 3.96 R
3177 3562 0.108186 CACGATGCCCTTGTAGCTCA 60.108 55.000 0.0 0.0 0.00 4.26 R
4303 4692 0.033109 GGCCTCCAAAATGCCCTACT 60.033 55.000 0.0 0.0 39.30 2.57 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
40 41 2.619074 GGCACTCCTTCTTTGGTATGCT 60.619 50.000 0.00 0.00 38.31 3.79
58 60 6.992715 GGTATGCTAGGAACTACAATGACATT 59.007 38.462 0.00 0.00 41.75 2.71
77 80 0.109458 TAACGTACTGCAGTGCTCGG 60.109 55.000 29.57 17.04 0.00 4.63
101 104 2.860136 GTCTTTGCCAAGCTTGTTGAAC 59.140 45.455 24.35 11.03 0.00 3.18
146 149 1.421410 GGTCAATGAGCGCCACTACG 61.421 60.000 2.29 0.00 0.00 3.51
165 169 4.785346 ACGACAAGGGATACTACCTAGA 57.215 45.455 0.00 0.00 37.35 2.43
241 245 1.216990 CAGGAGGCAAGAACCCCTAT 58.783 55.000 0.00 0.00 31.42 2.57
284 288 1.379977 AGGAAGGATGTCGAGCGGA 60.380 57.895 0.00 0.00 0.00 5.54
450 455 5.116084 ACACTGAACCATATTACAGGCAT 57.884 39.130 0.00 0.00 35.08 4.40
484 489 3.119101 CCAAGTTGATCACTAGCTACCGT 60.119 47.826 3.87 0.00 32.94 4.83
488 493 4.219944 AGTTGATCACTAGCTACCGTCAAA 59.780 41.667 0.00 0.00 31.97 2.69
534 539 0.263172 AGGAGATCCGAGACCCACAT 59.737 55.000 0.00 0.00 42.08 3.21
541 546 1.371337 CCGAGACCCACATGTGCATG 61.371 60.000 20.81 12.76 44.15 4.06
557 562 1.664016 GCATGAAGAACTGCAACACGG 60.664 52.381 0.00 0.00 38.28 4.94
740 780 3.781341 GTGTCAAGCACGTCGAAATTA 57.219 42.857 0.00 0.00 38.45 1.40
751 792 4.915085 CACGTCGAAATTAAGCCAATTTGT 59.085 37.500 10.46 1.75 44.98 2.83
770 811 1.290639 GCCGAAAATGGGCCGAAAA 59.709 52.632 0.00 0.00 44.97 2.29
781 822 2.038269 GCCGAAAACGATGGCTGGA 61.038 57.895 0.00 0.00 45.40 3.86
833 878 1.564348 AGCCCCACACCGATTTTATCT 59.436 47.619 0.00 0.00 0.00 1.98
846 891 6.604735 CGATTTTATCTTCGGTTGAATCCT 57.395 37.500 0.00 0.00 32.61 3.24
899 949 1.739338 CGGCCGGAGATGCTCTTAGT 61.739 60.000 20.10 0.00 0.00 2.24
900 950 1.329256 GGCCGGAGATGCTCTTAGTA 58.671 55.000 5.05 0.00 0.00 1.82
901 951 1.896465 GGCCGGAGATGCTCTTAGTAT 59.104 52.381 5.05 0.00 0.00 2.12
902 952 2.353208 GGCCGGAGATGCTCTTAGTATG 60.353 54.545 5.05 0.00 0.00 2.39
903 953 2.928731 GCCGGAGATGCTCTTAGTATGC 60.929 54.545 5.05 0.00 0.00 3.14
904 954 2.590073 CGGAGATGCTCTTAGTATGCG 58.410 52.381 0.00 0.00 0.00 4.73
905 955 2.030717 CGGAGATGCTCTTAGTATGCGT 60.031 50.000 0.00 0.00 0.00 5.24
906 956 3.312828 GGAGATGCTCTTAGTATGCGTG 58.687 50.000 0.00 0.00 0.00 5.34
907 957 3.243569 GGAGATGCTCTTAGTATGCGTGT 60.244 47.826 0.00 0.00 0.00 4.49
908 958 4.363999 GAGATGCTCTTAGTATGCGTGTT 58.636 43.478 0.00 0.00 0.00 3.32
909 959 4.115516 AGATGCTCTTAGTATGCGTGTTG 58.884 43.478 0.00 0.00 0.00 3.33
910 960 2.616960 TGCTCTTAGTATGCGTGTTGG 58.383 47.619 0.00 0.00 0.00 3.77
911 961 2.232696 TGCTCTTAGTATGCGTGTTGGA 59.767 45.455 0.00 0.00 0.00 3.53
912 962 2.603560 GCTCTTAGTATGCGTGTTGGAC 59.396 50.000 0.00 0.00 0.00 4.02
913 963 3.187700 CTCTTAGTATGCGTGTTGGACC 58.812 50.000 0.00 0.00 0.00 4.46
914 964 2.563620 TCTTAGTATGCGTGTTGGACCA 59.436 45.455 0.00 0.00 0.00 4.02
915 965 2.665649 TAGTATGCGTGTTGGACCAG 57.334 50.000 0.00 0.00 0.00 4.00
916 966 0.673644 AGTATGCGTGTTGGACCAGC 60.674 55.000 0.49 0.49 0.00 4.85
917 967 1.739929 TATGCGTGTTGGACCAGCG 60.740 57.895 3.68 7.25 0.00 5.18
918 968 2.443260 TATGCGTGTTGGACCAGCGT 62.443 55.000 13.90 9.39 0.00 5.07
919 969 3.276846 GCGTGTTGGACCAGCGTT 61.277 61.111 13.90 0.00 0.00 4.84
920 970 2.830285 GCGTGTTGGACCAGCGTTT 61.830 57.895 13.90 0.00 0.00 3.60
921 971 1.725066 CGTGTTGGACCAGCGTTTT 59.275 52.632 3.68 0.00 0.00 2.43
922 972 0.591236 CGTGTTGGACCAGCGTTTTG 60.591 55.000 3.68 0.00 0.00 2.44
923 973 0.248866 GTGTTGGACCAGCGTTTTGG 60.249 55.000 3.68 1.88 44.09 3.28
944 994 0.107945 CTTGTAGAGTGGCCAGGAGC 60.108 60.000 5.11 0.00 42.60 4.70
969 1019 2.335011 CTCGTCTCACACACGCCA 59.665 61.111 0.00 0.00 37.18 5.69
982 1032 2.255252 CGCCAGTTCGCCCAAAAG 59.745 61.111 0.00 0.00 0.00 2.27
983 1033 2.650778 GCCAGTTCGCCCAAAAGG 59.349 61.111 0.00 0.00 39.47 3.11
993 1043 2.538790 CCCAAAAGGCCAAAACCCT 58.461 52.632 5.01 0.00 0.00 4.34
994 1044 0.396435 CCCAAAAGGCCAAAACCCTC 59.604 55.000 5.01 0.00 0.00 4.30
995 1045 1.423584 CCAAAAGGCCAAAACCCTCT 58.576 50.000 5.01 0.00 0.00 3.69
1037 1087 2.657459 TCCTCTTCTTCTTCCTCCTCCT 59.343 50.000 0.00 0.00 0.00 3.69
1075 1128 4.918360 TGCCCCACCCACTGACCT 62.918 66.667 0.00 0.00 0.00 3.85
1076 1129 4.035102 GCCCCACCCACTGACCTC 62.035 72.222 0.00 0.00 0.00 3.85
1189 1242 4.436998 CCCGGTGTCGCCTGTCTC 62.437 72.222 0.00 0.00 34.25 3.36
1521 1586 3.733960 GTTTCTTGGACGGCGCCC 61.734 66.667 23.46 4.87 0.00 6.13
1644 1716 0.322975 TTCCTCACTCTTCAGCTGCC 59.677 55.000 9.47 0.00 0.00 4.85
2037 2128 3.355378 CTGGAACCAGGAATGCACATAA 58.645 45.455 12.54 0.00 40.17 1.90
2275 2366 4.142093 GGCAACTACTCTGGTAATCGGTTA 60.142 45.833 0.00 0.00 0.00 2.85
2383 2474 7.965718 AGTTTTGGGAATTTTCATCAATGAGA 58.034 30.769 0.00 0.00 38.19 3.27
2423 2514 5.676079 GCGCTTAAGATTAATGAACTTGCCA 60.676 40.000 6.67 0.00 0.00 4.92
2619 2711 4.568956 GAATTCACATTTTGGGGGAACAG 58.431 43.478 0.00 0.00 0.00 3.16
2902 2994 2.377136 ACTGCATTTCGGAGTCCCT 58.623 52.632 2.80 0.00 44.03 4.20
2948 3040 4.332268 GCTTTCTCAGATGCTTTCCTAGTG 59.668 45.833 0.00 0.00 0.00 2.74
2949 3041 5.486526 CTTTCTCAGATGCTTTCCTAGTGT 58.513 41.667 0.00 0.00 0.00 3.55
2950 3042 4.727507 TCTCAGATGCTTTCCTAGTGTC 57.272 45.455 0.00 0.00 0.00 3.67
2951 3043 3.129462 TCTCAGATGCTTTCCTAGTGTCG 59.871 47.826 0.00 0.00 0.00 4.35
2952 3044 3.089284 TCAGATGCTTTCCTAGTGTCGA 58.911 45.455 0.00 0.00 0.00 4.20
2953 3045 3.129462 TCAGATGCTTTCCTAGTGTCGAG 59.871 47.826 0.00 0.00 0.00 4.04
2954 3046 3.129462 CAGATGCTTTCCTAGTGTCGAGA 59.871 47.826 0.00 0.00 0.00 4.04
2955 3047 3.129638 AGATGCTTTCCTAGTGTCGAGAC 59.870 47.826 4.17 4.17 0.00 3.36
2956 3048 1.199327 TGCTTTCCTAGTGTCGAGACG 59.801 52.381 7.10 0.00 0.00 4.18
2957 3049 1.199558 GCTTTCCTAGTGTCGAGACGT 59.800 52.381 7.10 0.00 0.00 4.34
2958 3050 2.351544 GCTTTCCTAGTGTCGAGACGTT 60.352 50.000 7.10 0.00 0.00 3.99
2959 3051 2.983402 TTCCTAGTGTCGAGACGTTG 57.017 50.000 7.10 1.74 0.00 4.10
2960 3052 2.174363 TCCTAGTGTCGAGACGTTGA 57.826 50.000 7.10 2.27 0.00 3.18
2961 3053 2.708051 TCCTAGTGTCGAGACGTTGAT 58.292 47.619 7.10 0.00 0.00 2.57
2962 3054 3.079578 TCCTAGTGTCGAGACGTTGATT 58.920 45.455 7.10 0.00 0.00 2.57
2963 3055 3.119955 TCCTAGTGTCGAGACGTTGATTG 60.120 47.826 7.10 0.00 0.00 2.67
2964 3056 2.795175 AGTGTCGAGACGTTGATTGT 57.205 45.000 7.10 0.00 0.00 2.71
2965 3057 2.662700 AGTGTCGAGACGTTGATTGTC 58.337 47.619 7.10 0.00 36.60 3.18
2966 3058 1.719780 GTGTCGAGACGTTGATTGTCC 59.280 52.381 0.00 0.00 37.04 4.02
2967 3059 1.338655 TGTCGAGACGTTGATTGTCCA 59.661 47.619 0.00 0.00 37.04 4.02
2968 3060 1.986378 GTCGAGACGTTGATTGTCCAG 59.014 52.381 0.00 0.00 37.04 3.86
2969 3061 1.067846 TCGAGACGTTGATTGTCCAGG 60.068 52.381 0.00 0.00 37.04 4.45
2970 3062 1.336887 CGAGACGTTGATTGTCCAGGT 60.337 52.381 0.00 0.00 37.04 4.00
2971 3063 2.094906 CGAGACGTTGATTGTCCAGGTA 60.095 50.000 0.00 0.00 37.04 3.08
2972 3064 3.251571 GAGACGTTGATTGTCCAGGTAC 58.748 50.000 0.00 0.00 37.04 3.34
2973 3065 2.028385 AGACGTTGATTGTCCAGGTACC 60.028 50.000 2.73 2.73 37.04 3.34
2974 3066 1.002773 ACGTTGATTGTCCAGGTACCC 59.997 52.381 8.74 0.00 0.00 3.69
2975 3067 1.677820 CGTTGATTGTCCAGGTACCCC 60.678 57.143 8.74 0.00 0.00 4.95
2976 3068 0.996583 TTGATTGTCCAGGTACCCCC 59.003 55.000 8.74 0.00 0.00 5.40
3076 3461 6.262049 TGTTTGCTGAACTAAATTGCAGTCTA 59.738 34.615 0.00 0.00 39.08 2.59
3077 3462 7.040478 TGTTTGCTGAACTAAATTGCAGTCTAT 60.040 33.333 0.00 0.00 39.08 1.98
3177 3562 3.694566 AGCTCAAGACTTTGTTTTTCCGT 59.305 39.130 0.00 0.00 35.73 4.69
3243 3628 3.369381 GGAGAATGCGCAGAAGCTA 57.631 52.632 18.32 0.00 39.10 3.32
3288 3673 1.551019 AAGACCTGAGTTACCCCGCC 61.551 60.000 0.00 0.00 0.00 6.13
3373 3758 4.443457 GCAAGATGCTATTCAGGACCAGTA 60.443 45.833 0.00 0.00 40.96 2.74
3405 3790 1.146359 GGTGGTACCCCTTTCAACCTT 59.854 52.381 10.07 0.00 32.99 3.50
3429 3814 7.750229 TGCAATGGGAGTAGATTTATCATTC 57.250 36.000 0.00 0.00 0.00 2.67
3470 3855 4.279169 CCACTGAAAGCCTGAAGATTTCAA 59.721 41.667 7.43 0.00 41.11 2.69
3471 3856 5.218139 CACTGAAAGCCTGAAGATTTCAAC 58.782 41.667 7.43 0.00 41.11 3.18
3472 3857 4.023707 ACTGAAAGCCTGAAGATTTCAACG 60.024 41.667 7.43 0.69 41.11 4.10
3473 3858 2.997485 AAGCCTGAAGATTTCAACGC 57.003 45.000 3.57 3.57 39.58 4.84
3474 3859 1.168714 AGCCTGAAGATTTCAACGCC 58.831 50.000 6.82 0.00 39.58 5.68
3475 3860 0.171231 GCCTGAAGATTTCAACGCCC 59.829 55.000 0.00 0.00 39.58 6.13
3476 3861 1.533625 CCTGAAGATTTCAACGCCCA 58.466 50.000 0.00 0.00 39.58 5.36
3477 3862 1.885887 CCTGAAGATTTCAACGCCCAA 59.114 47.619 0.00 0.00 39.58 4.12
3478 3863 2.095059 CCTGAAGATTTCAACGCCCAAG 60.095 50.000 0.00 0.00 39.58 3.61
3479 3864 2.813754 CTGAAGATTTCAACGCCCAAGA 59.186 45.455 0.00 0.00 39.58 3.02
3480 3865 3.420893 TGAAGATTTCAACGCCCAAGAT 58.579 40.909 0.00 0.00 36.59 2.40
3481 3866 3.826157 TGAAGATTTCAACGCCCAAGATT 59.174 39.130 0.00 0.00 36.59 2.40
3482 3867 4.280677 TGAAGATTTCAACGCCCAAGATTT 59.719 37.500 0.00 0.00 36.59 2.17
3483 3868 4.440839 AGATTTCAACGCCCAAGATTTC 57.559 40.909 0.00 0.00 0.00 2.17
3548 3933 9.357161 ACTAGTATCAGTAGCTTTACTTGCTAT 57.643 33.333 0.00 0.00 43.66 2.97
3549 3934 9.834628 CTAGTATCAGTAGCTTTACTTGCTATC 57.165 37.037 0.00 0.00 43.66 2.08
3550 3935 8.239038 AGTATCAGTAGCTTTACTTGCTATCA 57.761 34.615 0.00 0.00 43.66 2.15
3551 3936 8.865090 AGTATCAGTAGCTTTACTTGCTATCAT 58.135 33.333 0.00 0.00 43.66 2.45
3554 3939 8.201554 TCAGTAGCTTTACTTGCTATCATTTG 57.798 34.615 0.00 0.00 43.66 2.32
3555 3940 7.824289 TCAGTAGCTTTACTTGCTATCATTTGT 59.176 33.333 0.00 0.00 43.66 2.83
3556 3941 8.454106 CAGTAGCTTTACTTGCTATCATTTGTT 58.546 33.333 0.00 0.00 43.66 2.83
3557 3942 9.667107 AGTAGCTTTACTTGCTATCATTTGTTA 57.333 29.630 0.00 0.00 43.66 2.41
3558 3943 9.922305 GTAGCTTTACTTGCTATCATTTGTTAG 57.078 33.333 0.00 0.00 43.66 2.34
3559 3944 8.567285 AGCTTTACTTGCTATCATTTGTTAGT 57.433 30.769 0.00 0.00 39.21 2.24
3560 3945 9.667107 AGCTTTACTTGCTATCATTTGTTAGTA 57.333 29.630 0.00 0.00 39.21 1.82
3606 3991 4.002906 TGATAGCTTCAACGAACTTGGT 57.997 40.909 0.00 0.00 0.00 3.67
3608 3993 2.038387 AGCTTCAACGAACTTGGTGT 57.962 45.000 0.00 0.00 0.00 4.16
3619 4004 0.253610 ACTTGGTGTGGTTTCGGTGA 59.746 50.000 0.00 0.00 0.00 4.02
3649 4034 4.827304 GTACATTAGTACTCCCTCCGTC 57.173 50.000 0.00 0.00 45.66 4.79
3650 4035 2.664015 ACATTAGTACTCCCTCCGTCC 58.336 52.381 0.00 0.00 0.00 4.79
3651 4036 1.962100 CATTAGTACTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
3652 4037 1.002069 TTAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
3653 4038 1.002069 TAGTACTCCCTCCGTCCCAA 58.998 55.000 0.00 0.00 0.00 4.12
3654 4039 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
3655 4040 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3656 4041 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3657 4042 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3658 4043 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3659 4044 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3660 4045 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3661 4046 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3662 4047 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3663 4048 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3664 4049 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3665 4050 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3666 4051 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3667 4052 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3668 4053 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3669 4054 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3670 4055 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3671 4056 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3672 4057 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3673 4058 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3674 4059 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3675 4060 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3697 4082 9.803315 TGTCTAAATACAGATGTATCAAGTCAC 57.197 33.333 5.97 3.82 40.10 3.67
3698 4083 8.959058 GTCTAAATACAGATGTATCAAGTCACG 58.041 37.037 5.97 0.00 40.10 4.35
3699 4084 8.683615 TCTAAATACAGATGTATCAAGTCACGT 58.316 33.333 5.97 0.00 40.10 4.49
3700 4085 9.302345 CTAAATACAGATGTATCAAGTCACGTT 57.698 33.333 5.97 0.00 40.10 3.99
3701 4086 8.547967 AAATACAGATGTATCAAGTCACGTTT 57.452 30.769 5.97 0.00 40.10 3.60
3702 4087 8.547967 AATACAGATGTATCAAGTCACGTTTT 57.452 30.769 5.97 0.00 40.10 2.43
3703 4088 9.647797 AATACAGATGTATCAAGTCACGTTTTA 57.352 29.630 5.97 0.00 40.10 1.52
3704 4089 7.582435 ACAGATGTATCAAGTCACGTTTTAG 57.418 36.000 0.00 0.00 0.00 1.85
3705 4090 7.152645 ACAGATGTATCAAGTCACGTTTTAGT 58.847 34.615 0.00 0.00 0.00 2.24
3706 4091 8.301720 ACAGATGTATCAAGTCACGTTTTAGTA 58.698 33.333 0.00 0.00 0.00 1.82
3707 4092 9.302345 CAGATGTATCAAGTCACGTTTTAGTAT 57.698 33.333 0.00 0.00 0.00 2.12
3708 4093 9.871238 AGATGTATCAAGTCACGTTTTAGTATT 57.129 29.630 0.00 0.00 0.00 1.89
3718 4103 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
3719 4104 9.740239 GTCACGTTTTAGTATTAGATACATCCA 57.260 33.333 0.00 0.00 38.21 3.41
3751 4136 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3752 4137 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3753 4138 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3754 4139 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3755 4140 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3756 4141 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3757 4142 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3758 4143 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3759 4144 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3760 4145 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3761 4146 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
3762 4147 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
3763 4148 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3764 4149 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3813 4198 4.595781 AGTTCATGTGGTAGTAACAGGGAA 59.404 41.667 0.00 0.00 30.52 3.97
3877 4262 3.709587 AGTTTCTCCTCGATGGTCCTTA 58.290 45.455 0.00 0.00 37.07 2.69
3926 4314 2.158856 TGCAGCAGGATATCTCACTTGG 60.159 50.000 2.05 0.00 0.00 3.61
3986 4374 3.634910 GGGGCTTTTGAAGAACTGTTACA 59.365 43.478 0.00 0.00 0.00 2.41
4033 4421 1.374758 GTGTGAAGTGGGAGCTCCG 60.375 63.158 26.36 0.00 38.76 4.63
4037 4425 0.537188 TGAAGTGGGAGCTCCGATTC 59.463 55.000 26.36 25.67 38.76 2.52
4057 4445 5.407407 TTCATGGAGGAGTAGAACACTTC 57.593 43.478 0.00 0.00 37.72 3.01
4284 4673 8.532977 AATTTGTGTAGCAACCATAACAAATC 57.467 30.769 10.87 0.00 43.65 2.17
4293 4682 6.437162 AGCAACCATAACAAATCTGTATGGTT 59.563 34.615 17.52 17.52 46.74 3.67
4303 4692 0.174845 CTGTATGGTTTCGCTCGGGA 59.825 55.000 0.00 0.00 0.00 5.14
4305 4694 0.175073 GTATGGTTTCGCTCGGGAGT 59.825 55.000 0.00 0.00 0.00 3.85
4391 4782 5.927281 AAAAAGCTATGCAAGGATGTGAT 57.073 34.783 0.00 0.00 0.00 3.06
4392 4783 4.913335 AAAGCTATGCAAGGATGTGATG 57.087 40.909 0.00 0.00 0.00 3.07
4393 4784 3.572632 AGCTATGCAAGGATGTGATGT 57.427 42.857 0.00 0.00 0.00 3.06
4394 4785 3.211865 AGCTATGCAAGGATGTGATGTG 58.788 45.455 0.00 0.00 0.00 3.21
4395 4786 2.947652 GCTATGCAAGGATGTGATGTGT 59.052 45.455 0.00 0.00 0.00 3.72
4396 4787 4.129380 GCTATGCAAGGATGTGATGTGTA 58.871 43.478 0.00 0.00 0.00 2.90
4397 4788 4.758674 GCTATGCAAGGATGTGATGTGTAT 59.241 41.667 0.00 0.00 0.00 2.29
4398 4789 5.334646 GCTATGCAAGGATGTGATGTGTATG 60.335 44.000 0.00 0.00 0.00 2.39
4399 4790 3.954200 TGCAAGGATGTGATGTGTATGT 58.046 40.909 0.00 0.00 0.00 2.29
4400 4791 3.690628 TGCAAGGATGTGATGTGTATGTG 59.309 43.478 0.00 0.00 0.00 3.21
4401 4792 3.940852 GCAAGGATGTGATGTGTATGTGA 59.059 43.478 0.00 0.00 0.00 3.58
4402 4793 4.034858 GCAAGGATGTGATGTGTATGTGAG 59.965 45.833 0.00 0.00 0.00 3.51
4403 4794 5.181009 CAAGGATGTGATGTGTATGTGAGT 58.819 41.667 0.00 0.00 0.00 3.41
4404 4795 6.340522 CAAGGATGTGATGTGTATGTGAGTA 58.659 40.000 0.00 0.00 0.00 2.59
4405 4796 6.544928 AGGATGTGATGTGTATGTGAGTAA 57.455 37.500 0.00 0.00 0.00 2.24
4406 4797 6.946340 AGGATGTGATGTGTATGTGAGTAAA 58.054 36.000 0.00 0.00 0.00 2.01
4407 4798 7.394016 AGGATGTGATGTGTATGTGAGTAAAA 58.606 34.615 0.00 0.00 0.00 1.52
4408 4799 8.049117 AGGATGTGATGTGTATGTGAGTAAAAT 58.951 33.333 0.00 0.00 0.00 1.82
4409 4800 8.677300 GGATGTGATGTGTATGTGAGTAAAATT 58.323 33.333 0.00 0.00 0.00 1.82
4410 4801 9.494479 GATGTGATGTGTATGTGAGTAAAATTG 57.506 33.333 0.00 0.00 0.00 2.32
4411 4802 7.304735 TGTGATGTGTATGTGAGTAAAATTGC 58.695 34.615 0.00 0.00 0.00 3.56
4412 4803 7.040823 TGTGATGTGTATGTGAGTAAAATTGCA 60.041 33.333 0.00 0.00 0.00 4.08
4413 4804 7.482743 GTGATGTGTATGTGAGTAAAATTGCAG 59.517 37.037 0.00 0.00 0.00 4.41
4414 4805 6.252967 TGTGTATGTGAGTAAAATTGCAGG 57.747 37.500 0.00 0.00 0.00 4.85
4415 4806 6.000840 TGTGTATGTGAGTAAAATTGCAGGA 58.999 36.000 0.00 0.00 0.00 3.86
4416 4807 6.658816 TGTGTATGTGAGTAAAATTGCAGGAT 59.341 34.615 0.00 0.00 0.00 3.24
4417 4808 6.968904 GTGTATGTGAGTAAAATTGCAGGATG 59.031 38.462 0.00 0.00 40.87 3.51
4458 4849 5.612725 TGAGGATGAATAGTACATGTGCA 57.387 39.130 16.62 2.82 0.00 4.57
4463 4854 6.931281 AGGATGAATAGTACATGTGCACATAC 59.069 38.462 30.92 25.12 34.26 2.39
4465 4856 6.902224 TGAATAGTACATGTGCACATACAC 57.098 37.500 30.92 27.39 41.10 2.90
4563 4954 6.020971 CATGTGCATCATGCCATTAAGTAT 57.979 37.500 7.30 0.00 45.69 2.12
4564 4955 7.148355 CATGTGCATCATGCCATTAAGTATA 57.852 36.000 7.30 0.00 45.69 1.47
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.988107 AGGAGTGCCAAATCCAGAGAA 59.012 47.619 0.49 0.00 38.12 2.87
8 9 1.661463 AGGAGTGCCAAATCCAGAGA 58.339 50.000 0.49 0.00 38.12 3.10
40 41 8.742777 AGTACGTTAATGTCATTGTAGTTCCTA 58.257 33.333 8.39 0.00 0.00 2.94
58 60 0.109458 CCGAGCACTGCAGTACGTTA 60.109 55.000 21.20 0.00 0.00 3.18
77 80 3.054878 CAACAAGCTTGGCAAAGACATC 58.945 45.455 29.18 0.00 35.19 3.06
146 149 6.209788 CCATCTTCTAGGTAGTATCCCTTGTC 59.790 46.154 0.00 0.00 33.35 3.18
236 240 2.493278 CCTGACACTTGGCAAAATAGGG 59.507 50.000 0.00 0.00 29.15 3.53
241 245 1.691196 CCTCCTGACACTTGGCAAAA 58.309 50.000 0.00 0.00 29.15 2.44
484 489 1.072331 GAGGAAGGCAGTCCAGTTTGA 59.928 52.381 9.61 0.00 40.48 2.69
488 493 1.366319 ATTGAGGAAGGCAGTCCAGT 58.634 50.000 9.61 0.00 40.48 4.00
541 546 1.014352 ACACCGTGTTGCAGTTCTTC 58.986 50.000 0.00 0.00 0.00 2.87
781 822 1.823899 GCCGATCCAAAATCGCCCT 60.824 57.895 2.01 0.00 39.95 5.19
833 878 1.406887 GCTGCCTAGGATTCAACCGAA 60.407 52.381 14.75 0.00 35.05 4.30
841 886 2.104792 TGAAATAGCGCTGCCTAGGATT 59.895 45.455 22.90 6.86 0.00 3.01
842 887 1.694150 TGAAATAGCGCTGCCTAGGAT 59.306 47.619 22.90 0.00 0.00 3.24
843 888 1.119684 TGAAATAGCGCTGCCTAGGA 58.880 50.000 22.90 0.00 0.00 2.94
846 891 1.299541 GCTTGAAATAGCGCTGCCTA 58.700 50.000 22.90 0.00 0.00 3.93
899 949 1.739929 CGCTGGTCCAACACGCATA 60.740 57.895 0.00 0.00 0.00 3.14
900 950 3.049674 CGCTGGTCCAACACGCAT 61.050 61.111 0.00 0.00 0.00 4.73
901 951 4.539083 ACGCTGGTCCAACACGCA 62.539 61.111 8.18 0.00 0.00 5.24
902 952 2.331019 AAAACGCTGGTCCAACACGC 62.331 55.000 8.18 0.25 0.00 5.34
903 953 0.591236 CAAAACGCTGGTCCAACACG 60.591 55.000 6.98 6.98 0.00 4.49
904 954 0.248866 CCAAAACGCTGGTCCAACAC 60.249 55.000 0.00 0.00 0.00 3.32
905 955 2.111162 CCAAAACGCTGGTCCAACA 58.889 52.632 0.00 0.00 0.00 3.33
912 962 2.480419 CTCTACAAGACCAAAACGCTGG 59.520 50.000 0.00 0.00 42.68 4.85
913 963 3.059597 CACTCTACAAGACCAAAACGCTG 60.060 47.826 0.00 0.00 0.00 5.18
914 964 3.131396 CACTCTACAAGACCAAAACGCT 58.869 45.455 0.00 0.00 0.00 5.07
915 965 2.223377 CCACTCTACAAGACCAAAACGC 59.777 50.000 0.00 0.00 0.00 4.84
916 966 2.223377 GCCACTCTACAAGACCAAAACG 59.777 50.000 0.00 0.00 0.00 3.60
917 967 2.552743 GGCCACTCTACAAGACCAAAAC 59.447 50.000 0.00 0.00 0.00 2.43
918 968 2.173782 TGGCCACTCTACAAGACCAAAA 59.826 45.455 0.00 0.00 0.00 2.44
919 969 1.771854 TGGCCACTCTACAAGACCAAA 59.228 47.619 0.00 0.00 0.00 3.28
920 970 1.347707 CTGGCCACTCTACAAGACCAA 59.652 52.381 0.00 0.00 0.00 3.67
921 971 0.976641 CTGGCCACTCTACAAGACCA 59.023 55.000 0.00 0.00 0.00 4.02
922 972 0.250513 CCTGGCCACTCTACAAGACC 59.749 60.000 0.00 0.00 0.00 3.85
923 973 1.205893 CTCCTGGCCACTCTACAAGAC 59.794 57.143 0.00 0.00 0.00 3.01
924 974 1.561643 CTCCTGGCCACTCTACAAGA 58.438 55.000 0.00 0.00 0.00 3.02
944 994 2.179517 GTGAGACGAGCCTCCACG 59.820 66.667 0.00 0.00 32.32 4.94
955 1005 1.548973 CGAACTGGCGTGTGTGAGAC 61.549 60.000 0.00 0.00 0.00 3.36
982 1032 1.000771 GAGGGAGAGGGTTTTGGCC 60.001 63.158 0.00 0.00 0.00 5.36
983 1033 1.000771 GGAGGGAGAGGGTTTTGGC 60.001 63.158 0.00 0.00 0.00 4.52
984 1034 0.621082 GAGGAGGGAGAGGGTTTTGG 59.379 60.000 0.00 0.00 0.00 3.28
985 1035 0.621082 GGAGGAGGGAGAGGGTTTTG 59.379 60.000 0.00 0.00 0.00 2.44
986 1036 0.910088 CGGAGGAGGGAGAGGGTTTT 60.910 60.000 0.00 0.00 0.00 2.43
987 1037 1.306226 CGGAGGAGGGAGAGGGTTT 60.306 63.158 0.00 0.00 0.00 3.27
988 1038 2.364961 CGGAGGAGGGAGAGGGTT 59.635 66.667 0.00 0.00 0.00 4.11
989 1039 4.467107 GCGGAGGAGGGAGAGGGT 62.467 72.222 0.00 0.00 0.00 4.34
990 1040 3.984186 TTGCGGAGGAGGGAGAGGG 62.984 68.421 0.00 0.00 0.00 4.30
991 1041 1.553690 TTTTGCGGAGGAGGGAGAGG 61.554 60.000 0.00 0.00 0.00 3.69
992 1042 0.324943 TTTTTGCGGAGGAGGGAGAG 59.675 55.000 0.00 0.00 0.00 3.20
993 1043 2.458892 TTTTTGCGGAGGAGGGAGA 58.541 52.632 0.00 0.00 0.00 3.71
1158 1211 2.494918 CGGGAAGGAGGCGTACAG 59.505 66.667 0.00 0.00 0.00 2.74
1189 1242 0.972471 GCAAAGGGAGGGGAATGTGG 60.972 60.000 0.00 0.00 0.00 4.17
2037 2128 3.054679 TGGTGTTGCCAATCTGCAT 57.945 47.368 0.00 0.00 45.94 3.96
2275 2366 4.461781 CAGGACTGCAAGAAAGAAATGGAT 59.538 41.667 0.00 0.00 37.43 3.41
2401 2492 8.598075 CAAATGGCAAGTTCATTAATCTTAAGC 58.402 33.333 0.00 0.00 34.15 3.09
2423 2514 9.872721 TTGCAATTATGTGTTGTATCATCAAAT 57.127 25.926 0.00 0.00 0.00 2.32
2429 2520 9.138062 GTGAAATTGCAATTATGTGTTGTATCA 57.862 29.630 24.35 16.34 0.00 2.15
2619 2711 4.279420 CACTTACGTATTCCCCCTACCTAC 59.721 50.000 0.00 0.00 0.00 3.18
2656 2748 6.361481 CACTACAATGTGCAAAATTCAGACAG 59.639 38.462 0.00 0.00 0.00 3.51
2902 2994 3.091545 GGGAAGCATCTTGATTTCACCA 58.908 45.455 0.00 0.00 0.00 4.17
2929 3021 3.129462 CGACACTAGGAAAGCATCTGAGA 59.871 47.826 0.00 0.00 0.00 3.27
2948 3040 1.986378 CTGGACAATCAACGTCTCGAC 59.014 52.381 0.00 0.00 33.73 4.20
2949 3041 1.067846 CCTGGACAATCAACGTCTCGA 60.068 52.381 0.00 0.00 33.73 4.04
2950 3042 1.336887 ACCTGGACAATCAACGTCTCG 60.337 52.381 0.00 0.00 33.73 4.04
2951 3043 2.457366 ACCTGGACAATCAACGTCTC 57.543 50.000 0.00 0.00 33.73 3.36
2952 3044 2.028385 GGTACCTGGACAATCAACGTCT 60.028 50.000 4.06 0.00 33.73 4.18
2953 3045 2.344025 GGTACCTGGACAATCAACGTC 58.656 52.381 4.06 0.00 0.00 4.34
2954 3046 2.467566 GGTACCTGGACAATCAACGT 57.532 50.000 4.06 0.00 0.00 3.99
2973 3065 1.054406 TGATCTAAAGGAGGCGGGGG 61.054 60.000 0.00 0.00 0.00 5.40
2974 3066 1.002544 GATGATCTAAAGGAGGCGGGG 59.997 57.143 0.00 0.00 0.00 5.73
2975 3067 1.694150 TGATGATCTAAAGGAGGCGGG 59.306 52.381 0.00 0.00 0.00 6.13
2976 3068 2.869636 GCTGATGATCTAAAGGAGGCGG 60.870 54.545 0.00 0.00 0.00 6.13
2977 3069 2.411904 GCTGATGATCTAAAGGAGGCG 58.588 52.381 0.00 0.00 0.00 5.52
2978 3070 2.411904 CGCTGATGATCTAAAGGAGGC 58.588 52.381 0.00 0.00 0.00 4.70
2979 3071 2.036992 AGCGCTGATGATCTAAAGGAGG 59.963 50.000 10.39 0.00 0.00 4.30
2980 3072 3.383620 AGCGCTGATGATCTAAAGGAG 57.616 47.619 10.39 0.00 0.00 3.69
2981 3073 3.636764 TGTAGCGCTGATGATCTAAAGGA 59.363 43.478 22.90 0.00 0.00 3.36
2982 3074 3.982475 TGTAGCGCTGATGATCTAAAGG 58.018 45.455 22.90 0.00 0.00 3.11
2983 3075 5.614231 GCAATGTAGCGCTGATGATCTAAAG 60.614 44.000 22.90 0.00 0.00 1.85
2984 3076 4.212004 GCAATGTAGCGCTGATGATCTAAA 59.788 41.667 22.90 0.00 0.00 1.85
2985 3077 3.742882 GCAATGTAGCGCTGATGATCTAA 59.257 43.478 22.90 0.00 0.00 2.10
3076 3461 1.614241 GCGGGTCCACTAGTGTCCAT 61.614 60.000 25.39 0.00 0.00 3.41
3077 3462 2.280552 GCGGGTCCACTAGTGTCCA 61.281 63.158 25.39 8.84 0.00 4.02
3177 3562 0.108186 CACGATGCCCTTGTAGCTCA 60.108 55.000 0.00 0.00 0.00 4.26
3243 3628 3.052566 TCACCCAGATGTACATCCTCTCT 60.053 47.826 28.26 10.86 38.58 3.10
3288 3673 3.576078 TTGGCACCCATAGATACCTTG 57.424 47.619 0.00 0.00 31.53 3.61
3373 3758 3.451402 GGTACCACCTCCAGGAAATTT 57.549 47.619 7.15 0.00 38.94 1.82
3405 3790 6.427853 CGAATGATAAATCTACTCCCATTGCA 59.572 38.462 0.00 0.00 0.00 4.08
3429 3814 2.125512 CAGAAGAAGGGGTCGGCG 60.126 66.667 0.00 0.00 0.00 6.46
3470 3855 0.537143 TGCAGTGAAATCTTGGGCGT 60.537 50.000 0.00 0.00 0.00 5.68
3471 3856 0.597568 TTGCAGTGAAATCTTGGGCG 59.402 50.000 0.00 0.00 0.00 6.13
3472 3857 2.997986 CAATTGCAGTGAAATCTTGGGC 59.002 45.455 0.00 0.00 0.00 5.36
3473 3858 3.007182 ACCAATTGCAGTGAAATCTTGGG 59.993 43.478 17.18 10.31 0.00 4.12
3474 3859 3.991773 CACCAATTGCAGTGAAATCTTGG 59.008 43.478 12.90 12.90 36.01 3.61
3556 3941 9.467796 CATCATCCAGATACTAACAGGATACTA 57.532 37.037 0.00 0.00 39.67 1.82
3557 3942 8.173412 TCATCATCCAGATACTAACAGGATACT 58.827 37.037 0.00 0.00 41.91 2.12
3558 3943 8.354711 TCATCATCCAGATACTAACAGGATAC 57.645 38.462 0.00 0.00 36.99 2.24
3559 3944 9.552695 AATCATCATCCAGATACTAACAGGATA 57.447 33.333 0.00 0.00 36.99 2.59
3560 3945 8.319881 CAATCATCATCCAGATACTAACAGGAT 58.680 37.037 0.00 0.00 39.58 3.24
3561 3946 7.510343 TCAATCATCATCCAGATACTAACAGGA 59.490 37.037 0.00 0.00 34.43 3.86
3562 3947 7.674120 TCAATCATCATCCAGATACTAACAGG 58.326 38.462 0.00 0.00 34.43 4.00
3606 3991 0.249405 GTACCGTCACCGAAACCACA 60.249 55.000 0.00 0.00 35.63 4.17
3608 3993 0.752054 AAGTACCGTCACCGAAACCA 59.248 50.000 0.00 0.00 35.63 3.67
3634 4019 1.002069 TTGGGACGGAGGGAGTACTA 58.998 55.000 0.00 0.00 0.00 1.82
3640 4025 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3641 4026 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3642 4027 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3643 4028 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3644 4029 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3645 4030 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
3646 4031 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
3647 4032 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
3648 4033 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
3649 4034 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
3671 4056 9.803315 GTGACTTGATACATCTGTATTTAGACA 57.197 33.333 14.44 12.43 40.99 3.41
3672 4057 8.959058 CGTGACTTGATACATCTGTATTTAGAC 58.041 37.037 14.44 10.85 40.99 2.59
3673 4058 8.683615 ACGTGACTTGATACATCTGTATTTAGA 58.316 33.333 14.44 0.00 40.99 2.10
3674 4059 8.858003 ACGTGACTTGATACATCTGTATTTAG 57.142 34.615 4.44 7.42 40.99 1.85
3675 4060 9.647797 AAACGTGACTTGATACATCTGTATTTA 57.352 29.630 4.44 0.00 40.99 1.40
3676 4061 8.547967 AAACGTGACTTGATACATCTGTATTT 57.452 30.769 4.44 0.00 40.99 1.40
3677 4062 8.547967 AAAACGTGACTTGATACATCTGTATT 57.452 30.769 4.44 0.00 40.99 1.89
3678 4063 9.302345 CTAAAACGTGACTTGATACATCTGTAT 57.698 33.333 2.53 2.53 43.38 2.29
3679 4064 8.301720 ACTAAAACGTGACTTGATACATCTGTA 58.698 33.333 0.00 0.00 34.67 2.74
3680 4065 7.152645 ACTAAAACGTGACTTGATACATCTGT 58.847 34.615 0.00 0.00 0.00 3.41
3681 4066 7.582435 ACTAAAACGTGACTTGATACATCTG 57.418 36.000 0.00 0.00 0.00 2.90
3682 4067 9.871238 AATACTAAAACGTGACTTGATACATCT 57.129 29.630 0.00 0.00 0.00 2.90
3692 4077 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
3693 4078 9.740239 TGGATGTATCTAATACTAAAACGTGAC 57.260 33.333 0.00 0.00 36.70 3.67
3725 4110 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
3726 4111 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
3727 4112 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
3728 4113 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
3729 4114 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
3730 4115 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
3731 4116 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
3732 4117 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
3733 4118 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
3734 4119 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3735 4120 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3736 4121 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3737 4122 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3738 4123 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3739 4124 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3740 4125 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
3741 4126 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
3742 4127 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
3743 4128 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
3744 4129 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3745 4130 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3746 4131 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3747 4132 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
3748 4133 0.178926 TTTGTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
3749 4134 0.978907 TTTTGTACTCCCTCCGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
3750 4135 3.055312 AGAATTTTGTACTCCCTCCGTCC 60.055 47.826 0.00 0.00 0.00 4.79
3751 4136 3.933332 CAGAATTTTGTACTCCCTCCGTC 59.067 47.826 0.00 0.00 0.00 4.79
3752 4137 3.581332 TCAGAATTTTGTACTCCCTCCGT 59.419 43.478 0.00 0.00 0.00 4.69
3753 4138 4.202245 TCAGAATTTTGTACTCCCTCCG 57.798 45.455 0.00 0.00 0.00 4.63
3754 4139 6.570571 GCTTTTCAGAATTTTGTACTCCCTCC 60.571 42.308 0.00 0.00 0.00 4.30
3755 4140 6.016276 TGCTTTTCAGAATTTTGTACTCCCTC 60.016 38.462 0.00 0.00 0.00 4.30
3756 4141 5.833131 TGCTTTTCAGAATTTTGTACTCCCT 59.167 36.000 0.00 0.00 0.00 4.20
3757 4142 6.084326 TGCTTTTCAGAATTTTGTACTCCC 57.916 37.500 0.00 0.00 0.00 4.30
3758 4143 7.115378 CACATGCTTTTCAGAATTTTGTACTCC 59.885 37.037 0.00 0.00 0.00 3.85
3759 4144 7.115378 CCACATGCTTTTCAGAATTTTGTACTC 59.885 37.037 0.00 0.00 0.00 2.59
3760 4145 6.925165 CCACATGCTTTTCAGAATTTTGTACT 59.075 34.615 0.00 0.00 0.00 2.73
3761 4146 6.146021 CCCACATGCTTTTCAGAATTTTGTAC 59.854 38.462 0.00 0.00 0.00 2.90
3762 4147 6.183360 ACCCACATGCTTTTCAGAATTTTGTA 60.183 34.615 0.00 0.00 0.00 2.41
3763 4148 5.058490 CCCACATGCTTTTCAGAATTTTGT 58.942 37.500 0.00 0.00 0.00 2.83
3764 4149 5.058490 ACCCACATGCTTTTCAGAATTTTG 58.942 37.500 0.00 0.00 0.00 2.44
3813 4198 3.714144 ACCAGCTCAGGTAATGTCTAGT 58.286 45.455 0.00 0.00 40.98 2.57
3877 4262 7.391148 ACGTTCTATCTAATTTGGTTGCATT 57.609 32.000 0.00 0.00 0.00 3.56
3926 4314 4.034975 GCCAAGTTCACTGATAAGATGAGC 59.965 45.833 0.00 0.00 0.00 4.26
3986 4374 3.523564 ACTGACCCCAACAAGTATATGCT 59.476 43.478 0.00 0.00 0.00 3.79
4033 4421 5.606348 AGTGTTCTACTCCTCCATGAATC 57.394 43.478 0.00 0.00 33.17 2.52
4037 4425 4.221703 ACTGAAGTGTTCTACTCCTCCATG 59.778 45.833 0.00 0.00 39.18 3.66
4044 4432 3.982058 CGGTTCACTGAAGTGTTCTACTC 59.018 47.826 10.14 0.83 45.76 2.59
4057 4445 1.608590 ACTCCAAATTGCGGTTCACTG 59.391 47.619 0.00 0.00 0.00 3.66
4066 4454 3.060339 CGCTTGTGAAAACTCCAAATTGC 60.060 43.478 0.00 0.00 0.00 3.56
4067 4455 3.490526 CCGCTTGTGAAAACTCCAAATTG 59.509 43.478 0.00 0.00 0.00 2.32
4153 4542 0.297820 CGCGCAATAGACCGAAGAAC 59.702 55.000 8.75 0.00 0.00 3.01
4199 4588 6.037281 GTCACTCTCATCTGAATACACGAGTA 59.963 42.308 0.00 0.00 34.10 2.59
4284 4673 0.174845 TCCCGAGCGAAACCATACAG 59.825 55.000 0.00 0.00 0.00 2.74
4293 4682 3.145551 GCCCTACTCCCGAGCGAA 61.146 66.667 0.00 0.00 0.00 4.70
4303 4692 0.033109 GGCCTCCAAAATGCCCTACT 60.033 55.000 0.00 0.00 39.30 2.57
4305 4694 0.709992 AAGGCCTCCAAAATGCCCTA 59.290 50.000 5.23 0.00 46.55 3.53
4375 4766 5.761726 ACATACACATCACATCCTTGCATAG 59.238 40.000 0.00 0.00 0.00 2.23
4388 4779 7.361971 CCTGCAATTTTACTCACATACACATCA 60.362 37.037 0.00 0.00 0.00 3.07
4389 4780 6.968904 CCTGCAATTTTACTCACATACACATC 59.031 38.462 0.00 0.00 0.00 3.06
4390 4781 6.658816 TCCTGCAATTTTACTCACATACACAT 59.341 34.615 0.00 0.00 0.00 3.21
4391 4782 6.000840 TCCTGCAATTTTACTCACATACACA 58.999 36.000 0.00 0.00 0.00 3.72
4392 4783 6.494893 TCCTGCAATTTTACTCACATACAC 57.505 37.500 0.00 0.00 0.00 2.90
4393 4784 6.883756 TCATCCTGCAATTTTACTCACATACA 59.116 34.615 0.00 0.00 0.00 2.29
4394 4785 7.320443 TCATCCTGCAATTTTACTCACATAC 57.680 36.000 0.00 0.00 0.00 2.39
4395 4786 7.936496 TTCATCCTGCAATTTTACTCACATA 57.064 32.000 0.00 0.00 0.00 2.29
4396 4787 6.839124 TTCATCCTGCAATTTTACTCACAT 57.161 33.333 0.00 0.00 0.00 3.21
4397 4788 6.647334 TTTCATCCTGCAATTTTACTCACA 57.353 33.333 0.00 0.00 0.00 3.58
4398 4789 7.945033 TTTTTCATCCTGCAATTTTACTCAC 57.055 32.000 0.00 0.00 0.00 3.51
4405 4796 9.893634 TCATGATTATTTTTCATCCTGCAATTT 57.106 25.926 0.00 0.00 31.50 1.82
4406 4797 9.893634 TTCATGATTATTTTTCATCCTGCAATT 57.106 25.926 0.00 0.00 31.50 2.32
4407 4798 9.321562 GTTCATGATTATTTTTCATCCTGCAAT 57.678 29.630 0.00 0.00 31.50 3.56
4408 4799 7.765360 GGTTCATGATTATTTTTCATCCTGCAA 59.235 33.333 0.00 0.00 31.50 4.08
4409 4800 7.124599 AGGTTCATGATTATTTTTCATCCTGCA 59.875 33.333 0.00 0.00 31.50 4.41
4410 4801 7.495055 AGGTTCATGATTATTTTTCATCCTGC 58.505 34.615 0.00 0.00 31.50 4.85
4411 4802 9.309516 CAAGGTTCATGATTATTTTTCATCCTG 57.690 33.333 0.00 0.00 31.50 3.86
4412 4803 9.258629 TCAAGGTTCATGATTATTTTTCATCCT 57.741 29.630 0.00 0.00 31.50 3.24
4413 4804 9.525409 CTCAAGGTTCATGATTATTTTTCATCC 57.475 33.333 0.00 0.00 31.50 3.51
4414 4805 9.525409 CCTCAAGGTTCATGATTATTTTTCATC 57.475 33.333 0.00 0.00 31.50 2.92
4415 4806 9.258629 TCCTCAAGGTTCATGATTATTTTTCAT 57.741 29.630 0.00 0.00 33.79 2.57
4416 4807 8.648698 TCCTCAAGGTTCATGATTATTTTTCA 57.351 30.769 0.00 0.00 36.34 2.69
4417 4808 9.525409 CATCCTCAAGGTTCATGATTATTTTTC 57.475 33.333 0.00 0.00 36.34 2.29
4516 4907 7.708051 TGTGTAAATTTTCAGGACGAAATTCA 58.292 30.769 0.00 0.00 43.12 2.57


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

AutoCloner maintained by Alex Coulton.