Multiple sequence alignment - TraesCS2A01G076800

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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 TraesCS2A01G076800 chr2A 100.000 6262 0 0 1 6262 34504408 34498147 0.000000e+00 11564.0
1 TraesCS2A01G076800 chr2A 94.926 946 40 4 1 939 88285324 88286268 0.000000e+00 1474.0
2 TraesCS2A01G076800 chr2A 79.455 404 44 32 3504 3878 459472617 459472224 3.750000e-62 250.0
3 TraesCS2A01G076800 chr2A 78.302 424 43 37 3504 3884 459364683 459364266 1.760000e-55 228.0
4 TraesCS2A01G076800 chr2A 92.308 156 12 0 6107 6262 617668994 617668839 8.170000e-54 222.0
5 TraesCS2A01G076800 chr2A 77.284 405 55 26 3492 3868 459525463 459525068 2.960000e-48 204.0
6 TraesCS2A01G076800 chr2A 89.431 123 9 4 5984 6105 34486484 34486603 1.090000e-32 152.0
7 TraesCS2A01G076800 chr2D 96.704 4915 97 15 1247 6105 32280077 32284982 0.000000e+00 8118.0
8 TraesCS2A01G076800 chr2D 82.081 519 64 13 3173 3666 35203405 35202891 3.490000e-112 416.0
9 TraesCS2A01G076800 chr2D 87.967 241 16 2 1008 1247 32279609 32279837 8.000000e-69 272.0
10 TraesCS2A01G076800 chr2D 87.755 147 15 3 3865 4009 74160169 74160314 1.080000e-37 169.0
11 TraesCS2A01G076800 chr2D 95.122 82 2 2 940 1021 32204828 32204907 1.830000e-25 128.0
12 TraesCS2A01G076800 chr2B 91.068 2060 136 19 1504 3518 52906787 52908843 0.000000e+00 2741.0
13 TraesCS2A01G076800 chr2B 92.157 867 53 6 4542 5395 52909792 52910656 0.000000e+00 1210.0
14 TraesCS2A01G076800 chr2B 84.699 915 65 28 3465 4325 52908830 52909723 0.000000e+00 845.0
15 TraesCS2A01G076800 chr2B 79.915 941 134 24 1750 2639 53401013 53401949 1.900000e-179 640.0
16 TraesCS2A01G076800 chr2B 87.469 407 48 3 4785 5189 53401945 53402350 3.420000e-127 466.0
17 TraesCS2A01G076800 chr2B 82.933 375 56 6 1978 2349 53439443 53439812 1.300000e-86 331.0
18 TraesCS2A01G076800 chr2B 93.671 158 10 0 6105 6262 772379361 772379204 2.920000e-58 237.0
19 TraesCS2A01G076800 chr2B 92.405 158 12 0 6105 6262 481892101 481891944 6.320000e-55 226.0
20 TraesCS2A01G076800 chr2B 91.608 143 11 1 4785 4926 53441832 53441974 4.950000e-46 196.0
21 TraesCS2A01G076800 chr2B 89.474 133 11 3 3865 3995 667127396 667127265 1.400000e-36 165.0
22 TraesCS2A01G076800 chr2B 92.308 39 3 0 2734 2772 52907934 52907972 8.770000e-04 56.5
23 TraesCS2A01G076800 chr3A 95.785 949 35 4 1 945 729355391 729356338 0.000000e+00 1526.0
24 TraesCS2A01G076800 chr3A 95.504 912 31 4 1 902 737433415 737434326 0.000000e+00 1448.0
25 TraesCS2A01G076800 chr3A 91.772 158 13 0 6105 6262 12941507 12941664 2.940000e-53 220.0
26 TraesCS2A01G076800 chr3A 79.389 131 17 6 4326 4452 325284395 325284519 4.020000e-12 84.2
27 TraesCS2A01G076800 chr5A 95.772 946 34 2 1 940 22604694 22603749 0.000000e+00 1520.0
28 TraesCS2A01G076800 chr5A 94.099 949 41 5 2 937 429257972 429257026 0.000000e+00 1428.0
29 TraesCS2A01G076800 chr5A 88.526 950 87 17 1 937 411879852 411880792 0.000000e+00 1131.0
30 TraesCS2A01G076800 chr5A 77.072 567 72 25 3151 3664 11037358 11036797 2.220000e-69 274.0
31 TraesCS2A01G076800 chr4A 95.860 942 36 2 1 939 598151619 598152560 0.000000e+00 1520.0
32 TraesCS2A01G076800 chr4A 79.706 340 40 16 3326 3643 502867216 502866884 1.060000e-52 219.0
33 TraesCS2A01G076800 chr4A 94.000 100 5 1 6007 6105 467155517 467155616 3.910000e-32 150.0
34 TraesCS2A01G076800 chr4A 93.407 91 6 0 6013 6103 146562699 146562789 1.090000e-27 135.0
35 TraesCS2A01G076800 chr1A 95.356 926 38 2 1 921 525046859 525047784 0.000000e+00 1467.0
36 TraesCS2A01G076800 chr1A 94.655 898 38 3 1 888 124186631 124185734 0.000000e+00 1384.0
37 TraesCS2A01G076800 chr7A 77.132 809 93 47 3145 3876 146754136 146754929 9.850000e-103 385.0
38 TraesCS2A01G076800 chr5D 83.085 402 37 13 3146 3518 531657631 531657232 2.800000e-88 337.0
39 TraesCS2A01G076800 chr5D 87.313 134 13 4 3861 3992 110798916 110798785 3.910000e-32 150.0
40 TraesCS2A01G076800 chr4B 80.134 448 56 18 3158 3591 466691253 466690825 2.840000e-78 303.0
41 TraesCS2A01G076800 chr4B 93.750 96 6 0 6010 6105 495070347 495070252 1.820000e-30 145.0
42 TraesCS2A01G076800 chr6A 80.153 393 56 15 3145 3518 67532873 67533262 2.220000e-69 274.0
43 TraesCS2A01G076800 chr3D 79.894 378 68 7 3144 3518 511740464 511740092 2.880000e-68 270.0
44 TraesCS2A01G076800 chr3D 94.937 158 8 0 6105 6262 50871808 50871651 1.350000e-61 248.0
45 TraesCS2A01G076800 chr3D 81.659 229 34 7 3440 3665 4350854 4350631 3.860000e-42 183.0
46 TraesCS2A01G076800 chr3D 91.579 95 8 0 6011 6105 24660947 24660853 1.420000e-26 132.0
47 TraesCS2A01G076800 chr3D 80.153 131 17 5 4326 4452 264699114 264699239 8.650000e-14 89.8
48 TraesCS2A01G076800 chr1D 77.291 502 78 21 3160 3632 41491617 41491123 4.810000e-66 263.0
49 TraesCS2A01G076800 chr1D 94.304 158 9 0 6105 6262 71758698 71758855 6.270000e-60 243.0
50 TraesCS2A01G076800 chr1D 93.038 158 11 0 6105 6262 362331769 362331926 1.360000e-56 231.0
51 TraesCS2A01G076800 chr1D 84.932 146 20 2 3866 4009 445363175 445363030 5.060000e-31 147.0
52 TraesCS2A01G076800 chr1B 93.038 158 11 0 6105 6262 56327918 56328075 1.360000e-56 231.0
53 TraesCS2A01G076800 chr1B 88.889 126 11 3 3871 3994 607128443 607128319 1.090000e-32 152.0
54 TraesCS2A01G076800 chr1B 91.919 99 7 1 6008 6105 678003455 678003553 3.040000e-28 137.0
55 TraesCS2A01G076800 chr4D 91.139 158 14 0 6105 6262 137729372 137729529 1.370000e-51 215.0
56 TraesCS2A01G076800 chr3B 84.568 162 19 6 3866 4025 171165803 171165646 8.410000e-34 156.0
57 TraesCS2A01G076800 chr3B 89.516 124 10 3 3884 4005 443760951 443760829 3.020000e-33 154.0
58 TraesCS2A01G076800 chr3B 83.721 86 8 3 4368 4452 335839292 335839372 6.730000e-10 76.8
59 TraesCS2A01G076800 chr6B 76.923 234 42 12 3271 3497 717861028 717860800 8.520000e-24 122.0
60 TraesCS2A01G076800 chr6D 76.871 147 24 9 3493 3631 148159501 148159645 2.420000e-09 75.0


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 TraesCS2A01G076800 chr2A 34498147 34504408 6261 True 11564.000 11564 100.0000 1 6262 1 chr2A.!!$R1 6261
1 TraesCS2A01G076800 chr2A 88285324 88286268 944 False 1474.000 1474 94.9260 1 939 1 chr2A.!!$F2 938
2 TraesCS2A01G076800 chr2D 32279609 32284982 5373 False 4195.000 8118 92.3355 1008 6105 2 chr2D.!!$F3 5097
3 TraesCS2A01G076800 chr2D 35202891 35203405 514 True 416.000 416 82.0810 3173 3666 1 chr2D.!!$R1 493
4 TraesCS2A01G076800 chr2B 52906787 52910656 3869 False 1213.125 2741 90.0580 1504 5395 4 chr2B.!!$F1 3891
5 TraesCS2A01G076800 chr2B 53401013 53402350 1337 False 553.000 640 83.6920 1750 5189 2 chr2B.!!$F2 3439
6 TraesCS2A01G076800 chr2B 53439443 53441974 2531 False 263.500 331 87.2705 1978 4926 2 chr2B.!!$F3 2948
7 TraesCS2A01G076800 chr3A 729355391 729356338 947 False 1526.000 1526 95.7850 1 945 1 chr3A.!!$F3 944
8 TraesCS2A01G076800 chr3A 737433415 737434326 911 False 1448.000 1448 95.5040 1 902 1 chr3A.!!$F4 901
9 TraesCS2A01G076800 chr5A 22603749 22604694 945 True 1520.000 1520 95.7720 1 940 1 chr5A.!!$R2 939
10 TraesCS2A01G076800 chr5A 429257026 429257972 946 True 1428.000 1428 94.0990 2 937 1 chr5A.!!$R3 935
11 TraesCS2A01G076800 chr5A 411879852 411880792 940 False 1131.000 1131 88.5260 1 937 1 chr5A.!!$F1 936
12 TraesCS2A01G076800 chr5A 11036797 11037358 561 True 274.000 274 77.0720 3151 3664 1 chr5A.!!$R1 513
13 TraesCS2A01G076800 chr4A 598151619 598152560 941 False 1520.000 1520 95.8600 1 939 1 chr4A.!!$F3 938
14 TraesCS2A01G076800 chr1A 525046859 525047784 925 False 1467.000 1467 95.3560 1 921 1 chr1A.!!$F1 920
15 TraesCS2A01G076800 chr1A 124185734 124186631 897 True 1384.000 1384 94.6550 1 888 1 chr1A.!!$R1 887
16 TraesCS2A01G076800 chr7A 146754136 146754929 793 False 385.000 385 77.1320 3145 3876 1 chr7A.!!$F1 731

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
538 539 0.442310 CATTCGGCGTCAATCAACGT 59.558 50.000 6.85 0.0 44.38 3.99 F
1170 1201 0.099436 GTTCCAGTGATTGCATCGGC 59.901 55.000 0.00 0.0 41.68 5.54 F
1817 2100 0.179048 CCTATCCAACCAGCGCATCA 60.179 55.000 11.47 0.0 0.00 3.07 F
2011 2297 1.275666 ATGTGGTGATTCCCGAGACA 58.724 50.000 0.00 0.0 34.77 3.41 F
3107 5106 5.065988 GCTATGACCATAAACGGACAAACAT 59.934 40.000 0.00 0.0 34.41 2.71 F
4144 6308 1.740025 GAGCATGGCTGGTTGTTACTC 59.260 52.381 0.00 0.0 39.88 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1916 2199 0.751452 TCAAGGCAACAGCAATGCAA 59.249 45.000 8.35 0.0 45.60 4.08 R
2011 2297 2.398498 GCGATCATAGAGTGCAACGAT 58.602 47.619 0.00 0.0 45.86 3.73 R
3710 5847 6.323482 TGTCAATTCAGAAGATGTTTGGGAAA 59.677 34.615 0.00 0.0 0.00 3.13 R
4047 6208 7.712264 TTTCAAGAAAATAGCACATTTGTGG 57.288 32.000 12.32 0.0 45.72 4.17 R
4401 6574 0.790339 AGGCCCCCTTGTATTTTGGT 59.210 50.000 0.00 0.0 0.00 3.67 R
6063 8278 0.037326 GGAGCGATCCACAAGTCACA 60.037 55.000 16.44 0.0 0.00 3.58 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
143 144 2.031245 CGGTGCAGTTTGTAGCAAATGA 60.031 45.455 0.00 0.00 43.20 2.57
160 161 5.743398 GCAAATGACCGTACGTACAACTATA 59.257 40.000 24.50 6.67 0.00 1.31
331 332 4.891756 CCCAATTTGCTATTGTGAGAGGAT 59.108 41.667 10.03 0.00 0.00 3.24
437 438 4.504858 CGTGGCCAAGATTTAGACTACTT 58.495 43.478 14.14 0.00 0.00 2.24
454 455 7.897864 AGACTACTTACAGTATGAGCTTTTGT 58.102 34.615 0.51 0.00 39.69 2.83
538 539 0.442310 CATTCGGCGTCAATCAACGT 59.558 50.000 6.85 0.00 44.38 3.99
842 871 0.945743 CATTATAGCGCGGCTGCTGA 60.946 55.000 22.96 12.07 46.70 4.26
941 971 2.559440 CTGTTGGAGATGCTCTAAGGC 58.441 52.381 0.00 0.00 31.92 4.35
943 973 2.305635 TGTTGGAGATGCTCTAAGGCAA 59.694 45.455 0.00 0.00 45.68 4.52
944 974 2.941720 GTTGGAGATGCTCTAAGGCAAG 59.058 50.000 0.00 0.00 45.68 4.01
945 975 1.487976 TGGAGATGCTCTAAGGCAAGG 59.512 52.381 0.00 0.00 45.68 3.61
946 976 1.765314 GGAGATGCTCTAAGGCAAGGA 59.235 52.381 0.00 0.00 45.68 3.36
947 977 2.224257 GGAGATGCTCTAAGGCAAGGAG 60.224 54.545 0.00 0.00 45.68 3.69
948 978 2.697751 GAGATGCTCTAAGGCAAGGAGA 59.302 50.000 5.13 0.00 45.68 3.71
949 979 3.316501 AGATGCTCTAAGGCAAGGAGAT 58.683 45.455 5.13 0.00 45.68 2.75
950 980 3.324556 AGATGCTCTAAGGCAAGGAGATC 59.675 47.826 5.13 0.00 45.68 2.75
951 981 2.756907 TGCTCTAAGGCAAGGAGATCT 58.243 47.619 0.00 0.00 39.43 2.75
952 982 3.916035 TGCTCTAAGGCAAGGAGATCTA 58.084 45.455 0.00 0.00 39.43 1.98
953 983 4.290093 TGCTCTAAGGCAAGGAGATCTAA 58.710 43.478 0.00 0.00 39.43 2.10
954 984 4.100189 TGCTCTAAGGCAAGGAGATCTAAC 59.900 45.833 0.00 0.00 39.43 2.34
955 985 4.502431 GCTCTAAGGCAAGGAGATCTAACC 60.502 50.000 0.00 0.00 0.00 2.85
956 986 3.967987 TCTAAGGCAAGGAGATCTAACCC 59.032 47.826 0.00 0.00 0.00 4.11
957 987 1.123928 AGGCAAGGAGATCTAACCCG 58.876 55.000 0.00 0.00 0.00 5.28
958 988 1.120530 GGCAAGGAGATCTAACCCGA 58.879 55.000 0.00 0.00 0.00 5.14
959 989 1.202545 GGCAAGGAGATCTAACCCGAC 60.203 57.143 0.00 0.00 0.00 4.79
960 990 1.757699 GCAAGGAGATCTAACCCGACT 59.242 52.381 0.00 0.00 0.00 4.18
961 991 2.223852 GCAAGGAGATCTAACCCGACTC 60.224 54.545 0.00 0.00 0.00 3.36
962 992 2.362717 CAAGGAGATCTAACCCGACTCC 59.637 54.545 0.00 0.00 44.97 3.85
963 993 2.368311 GGAGATCTAACCCGACTCCT 57.632 55.000 0.00 0.00 42.41 3.69
964 994 2.232399 GGAGATCTAACCCGACTCCTC 58.768 57.143 0.00 0.00 42.41 3.71
965 995 2.232399 GAGATCTAACCCGACTCCTCC 58.768 57.143 0.00 0.00 0.00 4.30
966 996 0.953003 GATCTAACCCGACTCCTCCG 59.047 60.000 0.00 0.00 0.00 4.63
967 997 1.108132 ATCTAACCCGACTCCTCCGC 61.108 60.000 0.00 0.00 0.00 5.54
968 998 2.757099 TAACCCGACTCCTCCGCC 60.757 66.667 0.00 0.00 0.00 6.13
992 1022 4.351054 CCACCTCTGCGCCCCTTT 62.351 66.667 4.18 0.00 0.00 3.11
993 1023 2.747855 CACCTCTGCGCCCCTTTC 60.748 66.667 4.18 0.00 0.00 2.62
994 1024 4.394712 ACCTCTGCGCCCCTTTCG 62.395 66.667 4.18 0.00 0.00 3.46
995 1025 4.394712 CCTCTGCGCCCCTTTCGT 62.395 66.667 4.18 0.00 0.00 3.85
996 1026 2.815647 CTCTGCGCCCCTTTCGTC 60.816 66.667 4.18 0.00 0.00 4.20
997 1027 3.589654 CTCTGCGCCCCTTTCGTCA 62.590 63.158 4.18 0.00 0.00 4.35
998 1028 3.423154 CTGCGCCCCTTTCGTCAC 61.423 66.667 4.18 0.00 0.00 3.67
1001 1031 3.047877 CGCCCCTTTCGTCACCAC 61.048 66.667 0.00 0.00 0.00 4.16
1002 1032 2.671963 GCCCCTTTCGTCACCACC 60.672 66.667 0.00 0.00 0.00 4.61
1003 1033 3.157680 CCCCTTTCGTCACCACCT 58.842 61.111 0.00 0.00 0.00 4.00
1004 1034 1.454539 CCCCTTTCGTCACCACCTT 59.545 57.895 0.00 0.00 0.00 3.50
1005 1035 0.605589 CCCCTTTCGTCACCACCTTC 60.606 60.000 0.00 0.00 0.00 3.46
1006 1036 0.107831 CCCTTTCGTCACCACCTTCA 59.892 55.000 0.00 0.00 0.00 3.02
1017 1047 4.660938 ACCTTCACTTGGCCGGCC 62.661 66.667 39.40 39.40 0.00 6.13
1020 1050 1.903404 CTTCACTTGGCCGGCCTTT 60.903 57.895 43.34 25.90 36.94 3.11
1049 1080 1.151587 ATCCCCCAACCCACACTCT 60.152 57.895 0.00 0.00 0.00 3.24
1089 1120 4.587189 GTATCGGCGGCGGCTTCT 62.587 66.667 31.73 16.90 39.81 2.85
1108 1139 3.296709 GACCTGAAGCCGAAGCCGA 62.297 63.158 0.00 0.00 41.25 5.54
1109 1140 2.047274 CCTGAAGCCGAAGCCGAA 60.047 61.111 0.00 0.00 41.25 4.30
1110 1141 2.103042 CCTGAAGCCGAAGCCGAAG 61.103 63.158 0.00 0.00 41.25 3.79
1111 1142 2.742372 TGAAGCCGAAGCCGAAGC 60.742 61.111 0.00 0.00 41.25 3.86
1112 1143 3.500642 GAAGCCGAAGCCGAAGCC 61.501 66.667 0.00 0.00 41.25 4.35
1116 1147 3.188786 CCGAAGCCGAAGCCGAAG 61.189 66.667 0.00 0.00 41.25 3.79
1117 1148 3.854459 CGAAGCCGAAGCCGAAGC 61.854 66.667 0.00 0.00 41.25 3.86
1118 1149 3.500642 GAAGCCGAAGCCGAAGCC 61.501 66.667 0.00 0.00 41.25 4.35
1170 1201 0.099436 GTTCCAGTGATTGCATCGGC 59.901 55.000 0.00 0.00 41.68 5.54
1179 1210 4.569023 TGCATCGGCGGAGTAGCG 62.569 66.667 7.21 0.00 45.35 4.26
1192 1223 2.678934 TAGCGGAGGCGTTGAGGT 60.679 61.111 0.00 0.00 46.35 3.85
1200 1231 3.730761 GCGTTGAGGTGGCTGCTG 61.731 66.667 0.00 0.00 0.00 4.41
1228 1259 1.988982 GCCCTCCCTGGAGTTGGATC 61.989 65.000 12.09 0.00 40.44 3.36
1242 1273 5.414765 GGAGTTGGATCCGTGTCTTTTAATT 59.585 40.000 7.39 0.00 0.00 1.40
1268 1539 6.426328 GGTATGAGCTATCACTTCCAAGAATG 59.574 42.308 0.00 0.00 38.57 2.67
1289 1560 1.731433 TATGTAGCGGTGGACGGAGC 61.731 60.000 0.00 0.00 44.51 4.70
1349 1620 6.238703 GGAGCAGTAGCCGGACTATATTATAC 60.239 46.154 5.05 0.00 43.56 1.47
1350 1621 6.424883 AGCAGTAGCCGGACTATATTATACT 58.575 40.000 5.05 0.00 43.56 2.12
1351 1622 6.319152 AGCAGTAGCCGGACTATATTATACTG 59.681 42.308 5.05 11.33 43.56 2.74
1352 1623 6.095160 GCAGTAGCCGGACTATATTATACTGT 59.905 42.308 5.05 0.00 40.46 3.55
1392 1667 1.537202 GCAGTCAGCCTTTGTTCGATT 59.463 47.619 0.00 0.00 37.23 3.34
1395 1670 3.499918 CAGTCAGCCTTTGTTCGATTTCT 59.500 43.478 0.00 0.00 0.00 2.52
1400 1675 4.082125 AGCCTTTGTTCGATTTCTTGGAT 58.918 39.130 0.00 0.00 0.00 3.41
1409 1684 4.069304 TCGATTTCTTGGATTTTCACCGT 58.931 39.130 0.00 0.00 0.00 4.83
1422 1697 4.661993 TTTCACCGTTTCATCAAGATCG 57.338 40.909 0.00 0.00 0.00 3.69
1426 1702 3.000727 ACCGTTTCATCAAGATCGAACC 58.999 45.455 0.00 0.00 0.00 3.62
1435 1711 2.126228 GATCGAACCGCGTCCACA 60.126 61.111 4.92 0.00 41.80 4.17
1459 1735 4.346418 ACGATCCAAGGCAGAATTAGATCT 59.654 41.667 0.00 0.00 0.00 2.75
1490 1766 3.868200 CTGCCTGACACCCCAACCC 62.868 68.421 0.00 0.00 0.00 4.11
1491 1767 4.678743 GCCTGACACCCCAACCCC 62.679 72.222 0.00 0.00 0.00 4.95
1675 1954 0.613260 TAGACCTTGACGGCAGCAAT 59.387 50.000 0.00 0.00 35.61 3.56
1690 1969 3.818180 CAGCAATAGGAATCTTGGCTCT 58.182 45.455 0.00 0.00 0.00 4.09
1727 2006 1.299648 CGCATCCTTTCCTCCCACA 59.700 57.895 0.00 0.00 0.00 4.17
1743 2022 1.766059 ACAGCGATGGGCCTATCCA 60.766 57.895 22.24 2.35 45.17 3.41
1744 2023 1.302033 CAGCGATGGGCCTATCCAC 60.302 63.158 22.24 14.90 45.17 4.02
1817 2100 0.179048 CCTATCCAACCAGCGCATCA 60.179 55.000 11.47 0.00 0.00 3.07
1849 2132 2.680913 GCTCAAGTTCGTGCCGCAT 61.681 57.895 0.00 0.00 0.00 4.73
1915 2198 4.394920 GCTAATGTTCTCCGACATTTGGAA 59.605 41.667 8.35 0.00 45.38 3.53
1916 2199 5.066505 GCTAATGTTCTCCGACATTTGGAAT 59.933 40.000 8.35 0.00 45.38 3.01
2011 2297 1.275666 ATGTGGTGATTCCCGAGACA 58.724 50.000 0.00 0.00 34.77 3.41
2323 2623 7.208080 ACTTTGTGATTACGCCTAAGGTATAG 58.792 38.462 0.00 0.00 0.00 1.31
2372 4343 6.123651 TGTGGGGTTCCATGTGTATATAAAC 58.876 40.000 0.00 0.00 46.09 2.01
2649 4648 7.981102 AGTTTTCCTTAAATCACCACTAGAC 57.019 36.000 0.00 0.00 0.00 2.59
3050 5049 5.232838 GGAAAGAAAATTCAGTGCACAAGTG 59.767 40.000 21.04 9.05 0.00 3.16
3099 5098 5.123186 TCAGTTTTGCTATGACCATAAACGG 59.877 40.000 0.00 0.00 0.00 4.44
3107 5106 5.065988 GCTATGACCATAAACGGACAAACAT 59.934 40.000 0.00 0.00 34.41 2.71
4144 6308 1.740025 GAGCATGGCTGGTTGTTACTC 59.260 52.381 0.00 0.00 39.88 2.59
4401 6574 5.568685 TTTGTTGATGGTCAAAGTTCGAA 57.431 34.783 0.00 0.00 38.22 3.71
4469 6642 2.026262 ACACGCCTTACATCTTGGGATT 60.026 45.455 0.00 0.00 0.00 3.01
4540 6713 2.821991 AGAGTGCTTTAGTGCGAACT 57.178 45.000 0.00 0.00 35.36 3.01
4675 6854 3.761218 TGTAATGTCATGCCGTTCCAAAT 59.239 39.130 0.00 0.00 0.00 2.32
5411 7599 1.135083 CACAGTACATCCGGGTGTCTC 60.135 57.143 26.97 18.61 33.62 3.36
5449 7637 9.144747 GATAGATTCACTCGTTATATGCATGTT 57.855 33.333 10.16 0.00 0.00 2.71
5516 7706 3.254014 CTGCCAAAACCGACGGCTG 62.254 63.158 15.39 9.01 46.39 4.85
5532 7723 5.115021 CGACGGCTGTTTTCTTTAATTTGTC 59.885 40.000 0.00 0.00 0.00 3.18
5536 7727 5.696270 GGCTGTTTTCTTTAATTTGTCTGGG 59.304 40.000 0.00 0.00 0.00 4.45
5566 7777 7.282450 AGCTGCATGTATATATGATGTGATTGG 59.718 37.037 13.18 0.00 0.00 3.16
5801 8012 2.128035 GCTGTAAGGATCGGACATTCG 58.872 52.381 0.00 0.00 0.00 3.34
5874 8085 3.372206 CGCCTTGACTTCTGGTTTATCTG 59.628 47.826 0.00 0.00 0.00 2.90
5948 8159 2.803956 CAACATTGCAAAAGCAAGAGGG 59.196 45.455 1.71 1.73 32.97 4.30
5953 8164 2.387757 TGCAAAAGCAAGAGGGACTTT 58.612 42.857 0.00 0.00 41.55 2.66
5981 8192 8.991243 ATGGTTATTCACATCACTTTTTCATG 57.009 30.769 0.00 0.00 0.00 3.07
6008 8219 6.522054 ACTTGAATACCCATACGTCCTATTG 58.478 40.000 0.00 0.00 0.00 1.90
6032 8243 2.028748 AGTAAATTACACGCACGGTCCT 60.029 45.455 5.89 0.00 0.00 3.85
6039 8254 2.432628 CGCACGGTCCTGGAACTC 60.433 66.667 10.54 0.00 0.00 3.01
6051 8266 2.507324 GAACTCGTCGGCCTGCTC 60.507 66.667 0.00 0.00 0.00 4.26
6052 8267 3.991536 GAACTCGTCGGCCTGCTCC 62.992 68.421 0.00 0.00 0.00 4.70
6063 8278 0.538287 GCCTGCTCCAAAACAGTCCT 60.538 55.000 0.00 0.00 31.76 3.85
6083 8298 1.078759 GTGACTTGTGGATCGCTCCG 61.079 60.000 0.03 0.00 45.37 4.63
6105 8320 0.537188 ACGGTCCTCATACTTGCCAG 59.463 55.000 0.00 0.00 0.00 4.85
6106 8321 0.824109 CGGTCCTCATACTTGCCAGA 59.176 55.000 0.00 0.00 0.00 3.86
6107 8322 1.471676 CGGTCCTCATACTTGCCAGAC 60.472 57.143 0.00 0.00 0.00 3.51
6108 8323 1.555075 GGTCCTCATACTTGCCAGACA 59.445 52.381 0.00 0.00 0.00 3.41
6109 8324 2.419297 GGTCCTCATACTTGCCAGACAG 60.419 54.545 0.00 0.00 0.00 3.51
6110 8325 2.234908 GTCCTCATACTTGCCAGACAGT 59.765 50.000 0.00 0.00 0.00 3.55
6111 8326 2.497675 TCCTCATACTTGCCAGACAGTC 59.502 50.000 0.00 0.00 0.00 3.51
6112 8327 2.534298 CTCATACTTGCCAGACAGTCG 58.466 52.381 0.00 0.00 0.00 4.18
6113 8328 1.204704 TCATACTTGCCAGACAGTCGG 59.795 52.381 6.98 6.98 0.00 4.79
6114 8329 1.204704 CATACTTGCCAGACAGTCGGA 59.795 52.381 13.67 0.00 0.00 4.55
6115 8330 1.557099 TACTTGCCAGACAGTCGGAT 58.443 50.000 13.67 1.42 0.00 4.18
6116 8331 0.687354 ACTTGCCAGACAGTCGGATT 59.313 50.000 13.67 0.00 0.00 3.01
6117 8332 1.338200 ACTTGCCAGACAGTCGGATTC 60.338 52.381 13.67 0.00 0.00 2.52
6118 8333 0.036388 TTGCCAGACAGTCGGATTCC 60.036 55.000 13.67 0.00 0.00 3.01
6119 8334 1.191489 TGCCAGACAGTCGGATTCCA 61.191 55.000 13.67 1.97 0.00 3.53
6120 8335 0.460987 GCCAGACAGTCGGATTCCAG 60.461 60.000 13.67 0.00 0.00 3.86
6121 8336 0.898320 CCAGACAGTCGGATTCCAGT 59.102 55.000 1.69 0.00 0.00 4.00
6122 8337 1.134965 CCAGACAGTCGGATTCCAGTC 60.135 57.143 1.69 5.19 0.00 3.51
6123 8338 0.811915 AGACAGTCGGATTCCAGTCG 59.188 55.000 3.09 0.00 0.00 4.18
6124 8339 0.802607 GACAGTCGGATTCCAGTCGC 60.803 60.000 3.09 0.00 0.00 5.19
6125 8340 1.215382 CAGTCGGATTCCAGTCGCA 59.785 57.895 3.09 0.00 0.00 5.10
6126 8341 1.078759 CAGTCGGATTCCAGTCGCAC 61.079 60.000 3.09 0.00 0.00 5.34
6127 8342 2.158959 GTCGGATTCCAGTCGCACG 61.159 63.158 3.09 0.00 0.00 5.34
6128 8343 2.126071 CGGATTCCAGTCGCACGT 60.126 61.111 3.09 0.00 0.00 4.49
6129 8344 2.444624 CGGATTCCAGTCGCACGTG 61.445 63.158 12.28 12.28 0.00 4.49
6130 8345 2.740714 GGATTCCAGTCGCACGTGC 61.741 63.158 30.42 30.42 37.78 5.34
6140 8355 3.479269 GCACGTGCGTGTAGCCTC 61.479 66.667 26.77 4.62 46.90 4.70
6147 8362 1.446272 GCGTGTAGCCTCGAAGCTT 60.446 57.895 14.83 0.00 41.41 3.74
6148 8363 1.414527 GCGTGTAGCCTCGAAGCTTC 61.415 60.000 14.83 16.84 41.41 3.86
6158 8373 2.653742 CGAAGCTTCGCGAAGATGA 58.346 52.632 43.98 15.21 44.26 2.92
6159 8374 0.296056 CGAAGCTTCGCGAAGATGAC 59.704 55.000 43.98 33.07 44.26 3.06
6160 8375 0.296056 GAAGCTTCGCGAAGATGACG 59.704 55.000 43.98 23.48 40.79 4.35
6167 8382 3.918220 CGAAGATGACGCCTGCGC 61.918 66.667 12.03 0.00 44.19 6.09
6177 8392 2.583593 GCCTGCGCGTAAGGAGAG 60.584 66.667 27.55 3.22 36.91 3.20
6178 8393 2.583593 CCTGCGCGTAAGGAGAGC 60.584 66.667 21.25 0.00 36.91 4.09
6179 8394 2.181777 CTGCGCGTAAGGAGAGCA 59.818 61.111 8.43 0.00 41.82 4.26
6180 8395 2.126071 TGCGCGTAAGGAGAGCAC 60.126 61.111 8.43 0.00 39.36 4.40
6181 8396 2.182030 GCGCGTAAGGAGAGCACT 59.818 61.111 8.43 0.00 34.56 4.40
6182 8397 1.446272 GCGCGTAAGGAGAGCACTT 60.446 57.895 8.43 0.00 34.56 3.16
6183 8398 1.414527 GCGCGTAAGGAGAGCACTTC 61.415 60.000 8.43 0.00 34.56 3.01
6184 8399 0.109272 CGCGTAAGGAGAGCACTTCA 60.109 55.000 0.00 0.00 38.28 3.02
6185 8400 1.634702 GCGTAAGGAGAGCACTTCAG 58.365 55.000 0.00 0.00 38.28 3.02
6186 8401 1.634702 CGTAAGGAGAGCACTTCAGC 58.365 55.000 0.00 0.00 0.00 4.26
6187 8402 1.067565 CGTAAGGAGAGCACTTCAGCA 60.068 52.381 0.00 0.00 36.85 4.41
6188 8403 2.610479 CGTAAGGAGAGCACTTCAGCAA 60.610 50.000 0.00 0.00 36.85 3.91
6189 8404 2.875094 AAGGAGAGCACTTCAGCAAT 57.125 45.000 0.00 0.00 36.85 3.56
6190 8405 2.110901 AGGAGAGCACTTCAGCAATG 57.889 50.000 0.00 0.00 36.85 2.82
6191 8406 1.627329 AGGAGAGCACTTCAGCAATGA 59.373 47.619 0.00 0.00 36.85 2.57
6192 8407 2.039480 AGGAGAGCACTTCAGCAATGAA 59.961 45.455 0.00 0.00 36.85 2.57
6193 8408 2.816087 GGAGAGCACTTCAGCAATGAAA 59.184 45.455 0.00 0.00 36.85 2.69
6194 8409 3.119919 GGAGAGCACTTCAGCAATGAAAG 60.120 47.826 0.00 0.00 36.85 2.62
6195 8410 2.818432 AGAGCACTTCAGCAATGAAAGG 59.182 45.455 0.00 0.00 36.85 3.11
6196 8411 2.816087 GAGCACTTCAGCAATGAAAGGA 59.184 45.455 0.00 0.00 36.85 3.36
6197 8412 3.428532 AGCACTTCAGCAATGAAAGGAT 58.571 40.909 0.00 0.00 36.85 3.24
6198 8413 3.442977 AGCACTTCAGCAATGAAAGGATC 59.557 43.478 0.00 0.00 36.85 3.36
6199 8414 3.428589 GCACTTCAGCAATGAAAGGATCC 60.429 47.826 2.48 2.48 0.00 3.36
6200 8415 3.012518 ACTTCAGCAATGAAAGGATCCG 58.987 45.455 5.98 0.00 0.00 4.18
6201 8416 2.787473 TCAGCAATGAAAGGATCCGT 57.213 45.000 5.98 0.00 0.00 4.69
6202 8417 2.358957 TCAGCAATGAAAGGATCCGTG 58.641 47.619 5.98 0.47 0.00 4.94
6203 8418 2.027285 TCAGCAATGAAAGGATCCGTGA 60.027 45.455 5.98 0.00 0.00 4.35
6204 8419 2.096496 CAGCAATGAAAGGATCCGTGAC 59.904 50.000 5.98 2.23 0.00 3.67
6205 8420 1.401905 GCAATGAAAGGATCCGTGACC 59.598 52.381 5.98 0.00 0.00 4.02
6206 8421 2.017049 CAATGAAAGGATCCGTGACCC 58.983 52.381 5.98 0.00 0.00 4.46
6207 8422 0.546598 ATGAAAGGATCCGTGACCCC 59.453 55.000 5.98 0.00 0.00 4.95
6208 8423 0.838554 TGAAAGGATCCGTGACCCCA 60.839 55.000 5.98 0.00 0.00 4.96
6209 8424 0.326927 GAAAGGATCCGTGACCCCAA 59.673 55.000 5.98 0.00 0.00 4.12
6210 8425 0.328258 AAAGGATCCGTGACCCCAAG 59.672 55.000 5.98 0.00 0.00 3.61
6211 8426 0.546747 AAGGATCCGTGACCCCAAGA 60.547 55.000 5.98 0.00 0.00 3.02
6212 8427 0.326618 AGGATCCGTGACCCCAAGAT 60.327 55.000 5.98 0.00 0.00 2.40
6213 8428 0.179045 GGATCCGTGACCCCAAGATG 60.179 60.000 0.00 0.00 0.00 2.90
6214 8429 0.179045 GATCCGTGACCCCAAGATGG 60.179 60.000 0.00 0.00 37.25 3.51
6224 8439 1.974543 CCAAGATGGGGTTTGCACC 59.025 57.895 0.00 0.00 43.37 5.01
6238 8453 2.440796 CACCATGCGCCCAGGAAT 60.441 61.111 15.60 0.00 0.00 3.01
6239 8454 2.440796 ACCATGCGCCCAGGAATG 60.441 61.111 15.60 6.53 0.00 2.67
6240 8455 2.440796 CCATGCGCCCAGGAATGT 60.441 61.111 4.18 0.00 0.00 2.71
6241 8456 2.484062 CCATGCGCCCAGGAATGTC 61.484 63.158 4.18 0.00 0.00 3.06
6242 8457 2.514592 ATGCGCCCAGGAATGTCG 60.515 61.111 4.18 0.00 0.00 4.35
6243 8458 3.030168 ATGCGCCCAGGAATGTCGA 62.030 57.895 4.18 0.00 0.00 4.20
6244 8459 2.892425 GCGCCCAGGAATGTCGAG 60.892 66.667 0.00 0.00 0.00 4.04
6245 8460 2.202932 CGCCCAGGAATGTCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
6246 8461 2.721167 CGCCCAGGAATGTCGAGGA 61.721 63.158 0.00 0.00 0.00 3.71
6247 8462 1.602237 GCCCAGGAATGTCGAGGAA 59.398 57.895 0.00 0.00 0.00 3.36
6248 8463 0.462759 GCCCAGGAATGTCGAGGAAG 60.463 60.000 0.00 0.00 0.00 3.46
6249 8464 1.195115 CCCAGGAATGTCGAGGAAGA 58.805 55.000 0.00 0.00 0.00 2.87
6250 8465 1.137872 CCCAGGAATGTCGAGGAAGAG 59.862 57.143 0.00 0.00 0.00 2.85
6251 8466 1.472376 CCAGGAATGTCGAGGAAGAGC 60.472 57.143 0.00 0.00 0.00 4.09
6252 8467 0.457851 AGGAATGTCGAGGAAGAGCG 59.542 55.000 0.00 0.00 0.00 5.03
6253 8468 0.528684 GGAATGTCGAGGAAGAGCGG 60.529 60.000 0.00 0.00 0.00 5.52
6254 8469 0.528684 GAATGTCGAGGAAGAGCGGG 60.529 60.000 0.00 0.00 0.00 6.13
6255 8470 2.579684 AATGTCGAGGAAGAGCGGGC 62.580 60.000 0.00 0.00 0.00 6.13
6256 8471 3.453679 GTCGAGGAAGAGCGGGCT 61.454 66.667 0.00 0.00 0.00 5.19
6257 8472 2.119655 GTCGAGGAAGAGCGGGCTA 61.120 63.158 0.00 0.00 0.00 3.93
6258 8473 2.119655 TCGAGGAAGAGCGGGCTAC 61.120 63.158 0.00 0.00 0.00 3.58
6259 8474 2.122167 CGAGGAAGAGCGGGCTACT 61.122 63.158 0.00 0.00 0.00 2.57
6260 8475 1.737201 GAGGAAGAGCGGGCTACTC 59.263 63.158 0.00 0.00 0.00 2.59
6261 8476 1.740332 GAGGAAGAGCGGGCTACTCC 61.740 65.000 10.95 10.95 34.56 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 6.867662 AATAGCTATAGTTGTACGTACGGT 57.132 37.500 21.06 11.83 0.00 4.83
160 161 9.934784 ATAGATGTCATCCACTAGATAATAGCT 57.065 33.333 9.29 0.00 32.37 3.32
331 332 3.924114 TTGATCCCAAAATCTAGCCGA 57.076 42.857 0.00 0.00 0.00 5.54
437 438 6.374333 GGGATTTCACAAAAGCTCATACTGTA 59.626 38.462 0.00 0.00 31.41 2.74
450 451 0.871722 CTCGCACGGGATTTCACAAA 59.128 50.000 0.00 0.00 0.00 2.83
454 455 2.032634 GCACTCGCACGGGATTTCA 61.033 57.895 0.00 0.00 38.36 2.69
861 890 2.250939 CGCTTCGACTGGTTTGGCA 61.251 57.895 0.00 0.00 0.00 4.92
941 971 2.362717 GGAGTCGGGTTAGATCTCCTTG 59.637 54.545 0.00 0.00 40.78 3.61
943 973 1.854280 AGGAGTCGGGTTAGATCTCCT 59.146 52.381 0.00 6.25 46.68 3.69
944 974 2.232399 GAGGAGTCGGGTTAGATCTCC 58.768 57.143 0.00 0.00 43.29 3.71
945 975 2.232399 GGAGGAGTCGGGTTAGATCTC 58.768 57.143 0.00 0.00 0.00 2.75
946 976 1.477195 CGGAGGAGTCGGGTTAGATCT 60.477 57.143 0.00 0.00 0.00 2.75
947 977 0.953003 CGGAGGAGTCGGGTTAGATC 59.047 60.000 0.00 0.00 0.00 2.75
948 978 1.108132 GCGGAGGAGTCGGGTTAGAT 61.108 60.000 0.00 0.00 0.00 1.98
949 979 1.751927 GCGGAGGAGTCGGGTTAGA 60.752 63.158 0.00 0.00 0.00 2.10
950 980 2.783288 GGCGGAGGAGTCGGGTTAG 61.783 68.421 0.00 0.00 0.00 2.34
951 981 2.757099 GGCGGAGGAGTCGGGTTA 60.757 66.667 0.00 0.00 0.00 2.85
975 1005 4.351054 AAAGGGGCGCAGAGGTGG 62.351 66.667 10.83 0.00 0.00 4.61
976 1006 2.747855 GAAAGGGGCGCAGAGGTG 60.748 66.667 10.83 0.00 0.00 4.00
977 1007 4.394712 CGAAAGGGGCGCAGAGGT 62.395 66.667 10.83 0.00 0.00 3.85
978 1008 4.394712 ACGAAAGGGGCGCAGAGG 62.395 66.667 10.83 0.00 0.00 3.69
979 1009 2.815647 GACGAAAGGGGCGCAGAG 60.816 66.667 10.83 0.00 0.00 3.35
980 1010 3.621805 TGACGAAAGGGGCGCAGA 61.622 61.111 10.83 0.00 0.00 4.26
981 1011 3.423154 GTGACGAAAGGGGCGCAG 61.423 66.667 10.83 0.00 0.00 5.18
984 1014 3.047877 GTGGTGACGAAAGGGGCG 61.048 66.667 0.00 0.00 0.00 6.13
985 1015 2.671963 GGTGGTGACGAAAGGGGC 60.672 66.667 0.00 0.00 0.00 5.80
986 1016 0.605589 GAAGGTGGTGACGAAAGGGG 60.606 60.000 0.00 0.00 0.00 4.79
987 1017 0.107831 TGAAGGTGGTGACGAAAGGG 59.892 55.000 0.00 0.00 0.00 3.95
988 1018 1.202651 AGTGAAGGTGGTGACGAAAGG 60.203 52.381 0.00 0.00 0.00 3.11
989 1019 2.240493 AGTGAAGGTGGTGACGAAAG 57.760 50.000 0.00 0.00 0.00 2.62
990 1020 2.285083 CAAGTGAAGGTGGTGACGAAA 58.715 47.619 0.00 0.00 0.00 3.46
991 1021 1.474320 CCAAGTGAAGGTGGTGACGAA 60.474 52.381 0.00 0.00 0.00 3.85
992 1022 0.105964 CCAAGTGAAGGTGGTGACGA 59.894 55.000 0.00 0.00 0.00 4.20
993 1023 1.507141 GCCAAGTGAAGGTGGTGACG 61.507 60.000 0.00 0.00 37.23 4.35
994 1024 1.172812 GGCCAAGTGAAGGTGGTGAC 61.173 60.000 0.00 0.00 37.23 3.67
995 1025 1.150536 GGCCAAGTGAAGGTGGTGA 59.849 57.895 0.00 0.00 37.23 4.02
996 1026 2.260869 CGGCCAAGTGAAGGTGGTG 61.261 63.158 2.24 0.00 37.23 4.17
997 1027 2.113139 CGGCCAAGTGAAGGTGGT 59.887 61.111 2.24 0.00 37.23 4.16
998 1028 2.672996 CCGGCCAAGTGAAGGTGG 60.673 66.667 2.24 0.00 38.00 4.61
999 1029 3.365265 GCCGGCCAAGTGAAGGTG 61.365 66.667 18.11 0.00 0.00 4.00
1000 1030 4.660938 GGCCGGCCAAGTGAAGGT 62.661 66.667 40.73 0.00 35.81 3.50
1001 1031 3.868200 AAGGCCGGCCAAGTGAAGG 62.868 63.158 45.13 0.00 38.92 3.46
1002 1032 1.463553 AAAAGGCCGGCCAAGTGAAG 61.464 55.000 45.13 0.00 38.92 3.02
1003 1033 1.456705 AAAAGGCCGGCCAAGTGAA 60.457 52.632 45.13 0.00 38.92 3.18
1004 1034 1.901464 GAAAAGGCCGGCCAAGTGA 60.901 57.895 45.13 0.00 38.92 3.41
1005 1035 2.650778 GAAAAGGCCGGCCAAGTG 59.349 61.111 45.13 0.00 38.92 3.16
1006 1036 2.983592 CGAAAAGGCCGGCCAAGT 60.984 61.111 45.13 29.69 38.92 3.16
1017 1047 1.090052 GGGGATGCGACCTCGAAAAG 61.090 60.000 0.00 0.00 43.02 2.27
1020 1050 3.467226 GGGGGATGCGACCTCGAA 61.467 66.667 0.00 0.00 43.02 3.71
1049 1080 4.331992 CGTCTCCGTGTAGATCTAAAGACA 59.668 45.833 19.61 10.13 33.23 3.41
1089 1120 2.347490 GGCTTCGGCTTCAGGTCA 59.653 61.111 0.00 0.00 41.44 4.02
1161 1192 2.202878 GCTACTCCGCCGATGCAA 60.203 61.111 0.00 0.00 37.32 4.08
1162 1193 4.569023 CGCTACTCCGCCGATGCA 62.569 66.667 0.00 0.00 37.32 3.96
1170 1201 3.823330 AACGCCTCCGCTACTCCG 61.823 66.667 0.00 0.00 38.22 4.63
1179 1210 4.021925 AGCCACCTCAACGCCTCC 62.022 66.667 0.00 0.00 0.00 4.30
1184 1215 3.730761 GCAGCAGCCACCTCAACG 61.731 66.667 0.00 0.00 33.58 4.10
1228 1259 5.354234 AGCTCATACCAATTAAAAGACACGG 59.646 40.000 0.00 0.00 0.00 4.94
1242 1273 4.962362 TCTTGGAAGTGATAGCTCATACCA 59.038 41.667 0.00 0.00 32.98 3.25
1268 1539 0.956633 TCCGTCCACCGCTACATATC 59.043 55.000 0.00 0.00 34.38 1.63
1376 1647 3.253188 CCAAGAAATCGAACAAAGGCTGA 59.747 43.478 0.00 0.00 0.00 4.26
1392 1667 5.300539 TGATGAAACGGTGAAAATCCAAGAA 59.699 36.000 0.00 0.00 0.00 2.52
1395 1670 5.300539 TCTTGATGAAACGGTGAAAATCCAA 59.699 36.000 0.00 0.00 0.00 3.53
1400 1675 4.752604 TCGATCTTGATGAAACGGTGAAAA 59.247 37.500 0.00 0.00 32.54 2.29
1409 1684 1.658596 CGCGGTTCGATCTTGATGAAA 59.341 47.619 0.00 0.00 41.67 2.69
1435 1711 4.487714 TCTAATTCTGCCTTGGATCGTT 57.512 40.909 0.00 0.00 0.00 3.85
1459 1735 0.758685 CAGGCAGGGGGAACAAAACA 60.759 55.000 0.00 0.00 0.00 2.83
1490 1766 3.361977 CGTCGTTGGCCCCAAAGG 61.362 66.667 12.01 0.00 37.70 3.11
1491 1767 1.674322 ATCGTCGTTGGCCCCAAAG 60.674 57.895 0.00 3.95 37.70 2.77
1675 1954 1.757118 CCGTCAGAGCCAAGATTCCTA 59.243 52.381 0.00 0.00 0.00 2.94
1727 2006 2.520536 GGTGGATAGGCCCATCGCT 61.521 63.158 5.01 0.00 38.66 4.93
1777 2056 3.855503 TTGCAGCCAGCTGGAGGTG 62.856 63.158 37.21 27.43 44.76 4.00
1783 2062 1.607628 GATAGGATTTGCAGCCAGCTG 59.392 52.381 15.34 15.34 45.94 4.24
1891 2174 3.689161 CCAAATGTCGGAGAACATTAGCA 59.311 43.478 2.94 0.00 39.69 3.49
1915 2198 1.345089 TCAAGGCAACAGCAATGCAAT 59.655 42.857 8.35 0.00 45.60 3.56
1916 2199 0.751452 TCAAGGCAACAGCAATGCAA 59.249 45.000 8.35 0.00 45.60 4.08
1981 2264 2.727123 TCACCACATTGGACAAGTGT 57.273 45.000 0.00 0.00 40.96 3.55
2011 2297 2.398498 GCGATCATAGAGTGCAACGAT 58.602 47.619 0.00 0.00 45.86 3.73
2323 2623 7.736447 AATCAAAGCTAAGCATGTAGGTATC 57.264 36.000 0.00 0.00 31.65 2.24
3050 5049 8.843885 ATAAGGTTAAGTAGTTTCAACAGACC 57.156 34.615 0.00 0.00 0.00 3.85
3710 5847 6.323482 TGTCAATTCAGAAGATGTTTGGGAAA 59.677 34.615 0.00 0.00 0.00 3.13
4047 6208 7.712264 TTTCAAGAAAATAGCACATTTGTGG 57.288 32.000 12.32 0.00 45.72 4.17
4144 6308 1.937223 TCGTTAATAACCATGCGCCTG 59.063 47.619 4.18 5.00 0.00 4.85
4401 6574 0.790339 AGGCCCCCTTGTATTTTGGT 59.210 50.000 0.00 0.00 0.00 3.67
4494 6667 1.834540 ACTCCCTCCTTCCCAAAACT 58.165 50.000 0.00 0.00 0.00 2.66
4540 6713 6.183360 GGAACAACCCTTGTAACAGATTTTCA 60.183 38.462 0.00 0.00 44.59 2.69
4675 6854 9.631257 AGTTTAACTTAGGTAACCAGCTAAAAA 57.369 29.630 0.00 0.00 42.56 1.94
5411 7599 7.020602 CGAGTGAATCTATCTATGCACAGTAG 58.979 42.308 0.00 0.00 37.81 2.57
5449 7637 2.565391 TGTGCAGCAACTAAGCCTAGTA 59.435 45.455 0.00 0.00 37.39 1.82
5516 7706 8.761497 GCTAAACCCAGACAAATTAAAGAAAAC 58.239 33.333 0.00 0.00 0.00 2.43
5532 7723 7.105588 TCATATATACATGCAGCTAAACCCAG 58.894 38.462 0.00 0.00 0.00 4.45
5536 7727 9.154847 TCACATCATATATACATGCAGCTAAAC 57.845 33.333 0.00 0.00 0.00 2.01
5566 7777 4.757554 GCGTAAATCACCGCCAAC 57.242 55.556 0.00 0.00 43.96 3.77
5801 8012 8.123445 ACGTGGTTTATTCATCGATTAACTAC 57.877 34.615 0.00 3.35 0.00 2.73
5840 8051 2.203625 AAGGCGGTTGGGCACAAT 60.204 55.556 3.81 0.00 45.36 2.71
5874 8085 1.732259 CATTACGGTGAGCCAACAGTC 59.268 52.381 0.00 0.00 30.82 3.51
5981 8192 5.910614 AGGACGTATGGGTATTCAAGTTAC 58.089 41.667 0.00 0.00 0.00 2.50
6008 8219 1.662122 CCGTGCGTGTAATTTACTCCC 59.338 52.381 7.99 0.00 0.00 4.30
6032 8243 4.373116 GCAGGCCGACGAGTTCCA 62.373 66.667 0.00 0.00 0.00 3.53
6039 8254 2.668212 TTTTGGAGCAGGCCGACG 60.668 61.111 0.00 0.00 0.00 5.12
6063 8278 0.037326 GGAGCGATCCACAAGTCACA 60.037 55.000 16.44 0.00 0.00 3.58
6065 8280 1.215382 CGGAGCGATCCACAAGTCA 59.785 57.895 21.44 0.00 0.00 3.41
6083 8298 2.007608 GGCAAGTATGAGGACCGTTTC 58.992 52.381 0.00 0.00 0.00 2.78
6091 8306 2.736719 CGACTGTCTGGCAAGTATGAGG 60.737 54.545 6.21 0.00 0.00 3.86
6105 8320 0.802607 GCGACTGGAATCCGACTGTC 60.803 60.000 0.00 0.00 33.76 3.51
6106 8321 1.215647 GCGACTGGAATCCGACTGT 59.784 57.895 0.00 0.00 0.00 3.55
6107 8322 1.078759 GTGCGACTGGAATCCGACTG 61.079 60.000 0.00 0.00 0.00 3.51
6108 8323 1.215647 GTGCGACTGGAATCCGACT 59.784 57.895 0.00 0.00 0.00 4.18
6109 8324 2.158959 CGTGCGACTGGAATCCGAC 61.159 63.158 0.00 0.00 0.00 4.79
6110 8325 2.180769 CGTGCGACTGGAATCCGA 59.819 61.111 0.00 0.00 0.00 4.55
6111 8326 2.126071 ACGTGCGACTGGAATCCG 60.126 61.111 0.00 0.00 0.00 4.18
6112 8327 2.740714 GCACGTGCGACTGGAATCC 61.741 63.158 26.77 0.00 0.00 3.01
6113 8328 2.778679 GCACGTGCGACTGGAATC 59.221 61.111 26.77 0.00 0.00 2.52
6125 8340 2.797866 CTTCGAGGCTACACGCACGT 62.798 60.000 0.00 0.00 41.67 4.49
6126 8341 2.126618 TTCGAGGCTACACGCACG 60.127 61.111 0.00 0.00 41.67 5.34
6127 8342 2.445438 GCTTCGAGGCTACACGCAC 61.445 63.158 12.94 0.00 41.67 5.34
6128 8343 2.126071 GCTTCGAGGCTACACGCA 60.126 61.111 12.94 0.00 41.67 5.24
6129 8344 1.414527 GAAGCTTCGAGGCTACACGC 61.415 60.000 23.37 6.50 42.24 5.34
6130 8345 2.654939 GAAGCTTCGAGGCTACACG 58.345 57.895 23.37 0.00 42.24 4.49
6150 8365 3.918220 GCGCAGGCGTCATCTTCG 61.918 66.667 15.64 0.00 42.09 3.79
6160 8375 2.583593 CTCTCCTTACGCGCAGGC 60.584 66.667 18.17 0.00 0.00 4.85
6161 8376 2.583593 GCTCTCCTTACGCGCAGG 60.584 66.667 17.12 17.12 0.00 4.85
6162 8377 2.161486 GTGCTCTCCTTACGCGCAG 61.161 63.158 5.73 1.59 34.52 5.18
6163 8378 2.126071 GTGCTCTCCTTACGCGCA 60.126 61.111 5.73 0.00 34.52 6.09
6164 8379 1.414527 GAAGTGCTCTCCTTACGCGC 61.415 60.000 5.73 0.00 34.58 6.86
6165 8380 0.109272 TGAAGTGCTCTCCTTACGCG 60.109 55.000 3.53 3.53 0.00 6.01
6166 8381 1.634702 CTGAAGTGCTCTCCTTACGC 58.365 55.000 0.00 0.00 0.00 4.42
6167 8382 1.067565 TGCTGAAGTGCTCTCCTTACG 60.068 52.381 0.00 0.00 0.00 3.18
6168 8383 2.751166 TGCTGAAGTGCTCTCCTTAC 57.249 50.000 0.00 0.00 0.00 2.34
6169 8384 3.261643 TCATTGCTGAAGTGCTCTCCTTA 59.738 43.478 0.00 0.00 0.00 2.69
6170 8385 2.039480 TCATTGCTGAAGTGCTCTCCTT 59.961 45.455 0.00 0.00 0.00 3.36
6171 8386 1.627329 TCATTGCTGAAGTGCTCTCCT 59.373 47.619 0.00 0.00 0.00 3.69
6172 8387 2.105006 TCATTGCTGAAGTGCTCTCC 57.895 50.000 0.00 0.00 0.00 3.71
6173 8388 3.119919 CCTTTCATTGCTGAAGTGCTCTC 60.120 47.826 0.00 0.00 42.19 3.20
6174 8389 2.818432 CCTTTCATTGCTGAAGTGCTCT 59.182 45.455 0.00 0.00 42.19 4.09
6175 8390 2.816087 TCCTTTCATTGCTGAAGTGCTC 59.184 45.455 0.00 0.00 42.19 4.26
6176 8391 2.867624 TCCTTTCATTGCTGAAGTGCT 58.132 42.857 0.00 0.00 42.19 4.40
6177 8392 3.428589 GGATCCTTTCATTGCTGAAGTGC 60.429 47.826 3.84 0.00 42.19 4.40
6178 8393 3.181503 CGGATCCTTTCATTGCTGAAGTG 60.182 47.826 10.75 0.00 42.19 3.16
6179 8394 3.012518 CGGATCCTTTCATTGCTGAAGT 58.987 45.455 10.75 0.00 42.19 3.01
6180 8395 3.012518 ACGGATCCTTTCATTGCTGAAG 58.987 45.455 10.75 0.00 42.19 3.02
6181 8396 2.749076 CACGGATCCTTTCATTGCTGAA 59.251 45.455 10.75 0.00 39.62 3.02
6182 8397 2.027285 TCACGGATCCTTTCATTGCTGA 60.027 45.455 10.75 0.00 0.00 4.26
6183 8398 2.096496 GTCACGGATCCTTTCATTGCTG 59.904 50.000 10.75 0.00 0.00 4.41
6184 8399 2.359900 GTCACGGATCCTTTCATTGCT 58.640 47.619 10.75 0.00 0.00 3.91
6185 8400 1.401905 GGTCACGGATCCTTTCATTGC 59.598 52.381 10.75 0.00 0.00 3.56
6186 8401 2.017049 GGGTCACGGATCCTTTCATTG 58.983 52.381 10.75 0.00 28.56 2.82
6187 8402 1.064685 GGGGTCACGGATCCTTTCATT 60.065 52.381 10.75 0.00 32.50 2.57
6188 8403 0.546598 GGGGTCACGGATCCTTTCAT 59.453 55.000 10.75 0.00 32.50 2.57
6189 8404 0.838554 TGGGGTCACGGATCCTTTCA 60.839 55.000 10.75 0.00 32.50 2.69
6190 8405 0.326927 TTGGGGTCACGGATCCTTTC 59.673 55.000 10.75 0.00 32.50 2.62
6191 8406 0.328258 CTTGGGGTCACGGATCCTTT 59.672 55.000 10.75 0.00 32.50 3.11
6192 8407 0.546747 TCTTGGGGTCACGGATCCTT 60.547 55.000 10.75 0.00 32.50 3.36
6193 8408 0.326618 ATCTTGGGGTCACGGATCCT 60.327 55.000 10.75 0.00 32.50 3.24
6194 8409 0.179045 CATCTTGGGGTCACGGATCC 60.179 60.000 0.00 0.00 30.73 3.36
6195 8410 0.179045 CCATCTTGGGGTCACGGATC 60.179 60.000 0.00 0.00 32.67 3.36
6196 8411 1.915228 CCATCTTGGGGTCACGGAT 59.085 57.895 0.00 0.00 32.67 4.18
6197 8412 3.399046 CCATCTTGGGGTCACGGA 58.601 61.111 0.00 0.00 32.67 4.69
6206 8421 0.831288 TGGTGCAAACCCCATCTTGG 60.831 55.000 0.00 0.00 37.25 3.61
6207 8422 1.066716 CATGGTGCAAACCCCATCTTG 60.067 52.381 3.65 0.00 39.44 3.02
6208 8423 1.269012 CATGGTGCAAACCCCATCTT 58.731 50.000 3.65 0.00 39.44 2.40
6209 8424 1.259840 GCATGGTGCAAACCCCATCT 61.260 55.000 3.65 0.00 44.26 2.90
6210 8425 1.218854 GCATGGTGCAAACCCCATC 59.781 57.895 3.65 0.00 44.26 3.51
6211 8426 2.648143 CGCATGGTGCAAACCCCAT 61.648 57.895 0.79 0.79 45.36 4.00
6212 8427 3.301554 CGCATGGTGCAAACCCCA 61.302 61.111 2.63 0.00 45.36 4.96
6213 8428 4.740431 GCGCATGGTGCAAACCCC 62.740 66.667 0.30 0.00 45.36 4.95
6214 8429 4.740431 GGCGCATGGTGCAAACCC 62.740 66.667 10.83 0.00 45.36 4.11
6215 8430 4.740431 GGGCGCATGGTGCAAACC 62.740 66.667 10.83 0.00 45.36 3.27
6216 8431 3.919973 CTGGGCGCATGGTGCAAAC 62.920 63.158 10.83 0.00 45.36 2.93
6217 8432 3.682885 CTGGGCGCATGGTGCAAA 61.683 61.111 10.83 0.00 45.36 3.68
6221 8436 2.440796 ATTCCTGGGCGCATGGTG 60.441 61.111 10.83 0.00 0.00 4.17
6222 8437 2.440796 CATTCCTGGGCGCATGGT 60.441 61.111 10.83 0.00 0.00 3.55
6223 8438 2.440796 ACATTCCTGGGCGCATGG 60.441 61.111 10.83 8.08 0.00 3.66
6224 8439 2.827051 CGACATTCCTGGGCGCATG 61.827 63.158 10.83 5.57 0.00 4.06
6225 8440 2.514592 CGACATTCCTGGGCGCAT 60.515 61.111 10.83 0.00 0.00 4.73
6226 8441 3.664025 CTCGACATTCCTGGGCGCA 62.664 63.158 10.83 2.47 0.00 6.09
6227 8442 2.892425 CTCGACATTCCTGGGCGC 60.892 66.667 0.00 0.00 0.00 6.53
6228 8443 2.202932 CCTCGACATTCCTGGGCG 60.203 66.667 0.00 0.00 0.00 6.13
6229 8444 0.462759 CTTCCTCGACATTCCTGGGC 60.463 60.000 0.00 0.00 0.00 5.36
6230 8445 1.137872 CTCTTCCTCGACATTCCTGGG 59.862 57.143 0.00 0.00 0.00 4.45
6231 8446 1.472376 GCTCTTCCTCGACATTCCTGG 60.472 57.143 0.00 0.00 0.00 4.45
6232 8447 1.800655 CGCTCTTCCTCGACATTCCTG 60.801 57.143 0.00 0.00 0.00 3.86
6233 8448 0.457851 CGCTCTTCCTCGACATTCCT 59.542 55.000 0.00 0.00 0.00 3.36
6234 8449 0.528684 CCGCTCTTCCTCGACATTCC 60.529 60.000 0.00 0.00 0.00 3.01
6235 8450 0.528684 CCCGCTCTTCCTCGACATTC 60.529 60.000 0.00 0.00 0.00 2.67
6236 8451 1.517832 CCCGCTCTTCCTCGACATT 59.482 57.895 0.00 0.00 0.00 2.71
6237 8452 3.082579 GCCCGCTCTTCCTCGACAT 62.083 63.158 0.00 0.00 0.00 3.06
6238 8453 2.831894 TAGCCCGCTCTTCCTCGACA 62.832 60.000 0.00 0.00 0.00 4.35
6239 8454 2.119655 TAGCCCGCTCTTCCTCGAC 61.120 63.158 0.00 0.00 0.00 4.20
6240 8455 2.119655 GTAGCCCGCTCTTCCTCGA 61.120 63.158 0.00 0.00 0.00 4.04
6241 8456 2.065906 GAGTAGCCCGCTCTTCCTCG 62.066 65.000 0.00 0.00 0.00 4.63
6242 8457 1.737201 GAGTAGCCCGCTCTTCCTC 59.263 63.158 0.00 0.00 0.00 3.71
6243 8458 1.758906 GGAGTAGCCCGCTCTTCCT 60.759 63.158 10.58 0.00 33.73 3.36
6244 8459 2.816012 GGAGTAGCCCGCTCTTCC 59.184 66.667 0.00 0.00 33.73 3.46


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

AutoCloner maintained by Alex Coulton.