Multiple sequence alignment - TraesCS2A01G224400

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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 TraesCS2A01G224400 chr2A 100.000 3159 0 0 1 3159 224329230 224332388 0.000000e+00 5834.0
1 TraesCS2A01G224400 chr2A 92.287 1504 88 7 1595 3077 224395514 224397010 0.000000e+00 2109.0
2 TraesCS2A01G224400 chr2A 95.628 732 30 2 2428 3159 166452156 166451427 0.000000e+00 1173.0
3 TraesCS2A01G224400 chr2A 93.460 734 38 4 2428 3159 216287405 216288130 0.000000e+00 1081.0
4 TraesCS2A01G224400 chr2A 90.868 668 54 5 2486 3150 387964972 387964309 0.000000e+00 889.0
5 TraesCS2A01G224400 chr2A 91.304 460 37 2 1107 1564 224395055 224395513 2.680000e-175 625.0
6 TraesCS2A01G224400 chr2A 91.830 306 22 3 1379 1684 216320741 216321043 1.050000e-114 424.0
7 TraesCS2A01G224400 chr2A 86.087 115 13 3 995 1106 297363346 297363232 1.540000e-23 121.0
8 TraesCS2A01G224400 chr2A 95.455 66 2 1 1934 1998 220344618 220344683 1.550000e-18 104.0
9 TraesCS2A01G224400 chr6A 93.976 996 59 1 1 996 471813543 471812549 0.000000e+00 1506.0
10 TraesCS2A01G224400 chr6A 93.058 994 68 1 1 994 397170500 397169508 0.000000e+00 1452.0
11 TraesCS2A01G224400 chr6A 92.764 995 72 0 1 995 142753652 142752658 0.000000e+00 1439.0
12 TraesCS2A01G224400 chr6A 92.161 995 78 0 1 995 205746445 205745451 0.000000e+00 1406.0
13 TraesCS2A01G224400 chr6A 90.650 246 21 1 1753 1996 373943438 373943683 3.040000e-85 326.0
14 TraesCS2A01G224400 chr6A 90.686 204 19 0 1187 1390 378280656 378280453 4.010000e-69 272.0
15 TraesCS2A01G224400 chr6A 86.585 246 31 2 1753 1996 373968801 373969046 1.440000e-68 270.0
16 TraesCS2A01G224400 chr6A 88.462 208 24 0 1181 1388 508617818 508617611 5.230000e-63 252.0
17 TraesCS2A01G224400 chr6A 89.691 194 20 0 1195 1388 508576200 508576007 6.770000e-62 248.0
18 TraesCS2A01G224400 chr6A 87.432 183 20 2 1131 1312 233513645 233513825 1.150000e-49 207.0
19 TraesCS2A01G224400 chr5A 93.079 997 69 0 1 997 168028062 168027066 0.000000e+00 1459.0
20 TraesCS2A01G224400 chr5A 92.153 994 78 0 1 994 257664544 257665537 0.000000e+00 1404.0
21 TraesCS2A01G224400 chr5A 93.460 734 33 10 2428 3159 378682541 378681821 0.000000e+00 1075.0
22 TraesCS2A01G224400 chr5A 87.455 279 27 7 1990 2265 185923362 185923635 6.580000e-82 315.0
23 TraesCS2A01G224400 chr5A 85.921 277 37 2 1989 2265 185893095 185893369 8.570000e-76 294.0
24 TraesCS2A01G224400 chr5A 92.810 153 10 1 2113 2265 97773874 97773723 1.480000e-53 220.0
25 TraesCS2A01G224400 chr5A 91.729 133 11 0 1753 1885 362677387 362677255 5.380000e-43 185.0
26 TraesCS2A01G224400 chr5A 90.741 108 9 1 995 1102 323694874 323694980 3.280000e-30 143.0
27 TraesCS2A01G224400 chr5A 87.500 64 5 3 2290 2352 167885997 167885936 1.570000e-08 71.3
28 TraesCS2A01G224400 chr4A 92.269 996 76 1 1 996 381517012 381518006 0.000000e+00 1411.0
29 TraesCS2A01G224400 chr4A 95.474 685 30 1 2475 3159 428706823 428707506 0.000000e+00 1092.0
30 TraesCS2A01G224400 chr4A 94.536 604 33 0 2475 3078 428712822 428713425 0.000000e+00 933.0
31 TraesCS2A01G224400 chr4A 89.498 638 60 5 1132 1769 368551768 368552398 0.000000e+00 800.0
32 TraesCS2A01G224400 chr4A 88.307 573 63 4 1197 1769 389395971 389395403 0.000000e+00 684.0
33 TraesCS2A01G224400 chr4A 92.113 355 25 3 1325 1679 166506992 166507343 6.080000e-137 497.0
34 TraesCS2A01G224400 chr4A 88.649 370 35 6 1322 1691 166498777 166499139 8.040000e-121 444.0
35 TraesCS2A01G224400 chr4A 88.152 211 21 3 1181 1388 359967623 359967832 6.770000e-62 248.0
36 TraesCS2A01G224400 chr4A 90.991 111 9 1 995 1105 443956236 443956127 7.060000e-32 148.0
37 TraesCS2A01G224400 chr4A 86.486 111 14 1 995 1105 443948529 443948420 1.540000e-23 121.0
38 TraesCS2A01G224400 chr7A 92.153 994 78 0 1 994 292135595 292136588 0.000000e+00 1404.0
39 TraesCS2A01G224400 chr7A 94.923 650 33 0 2428 3077 576564973 576565622 0.000000e+00 1018.0
40 TraesCS2A01G224400 chr7A 94.769 650 34 0 2428 3077 658495947 658495298 0.000000e+00 1013.0
41 TraesCS2A01G224400 chr7A 89.101 367 32 6 1325 1691 325548200 325548558 1.730000e-122 449.0
42 TraesCS2A01G224400 chr7A 88.556 367 38 3 1325 1691 325556330 325556692 2.890000e-120 442.0
43 TraesCS2A01G224400 chr7A 88.258 264 27 4 2440 2701 490042373 490042634 2.370000e-81 313.0
44 TraesCS2A01G224400 chr7A 89.423 208 22 0 1181 1388 307999410 307999617 2.420000e-66 263.0
45 TraesCS2A01G224400 chr7A 89.447 199 21 0 1190 1388 307980447 307980645 5.230000e-63 252.0
46 TraesCS2A01G224400 chr7A 85.047 214 32 0 1177 1390 182523337 182523124 5.310000e-53 219.0
47 TraesCS2A01G224400 chr7A 91.667 120 6 3 2147 2265 165395505 165395621 2.520000e-36 163.0
48 TraesCS2A01G224400 chr7A 84.667 150 21 1 2348 2495 109554597 109554746 7.060000e-32 148.0
49 TraesCS2A01G224400 chr7A 88.462 104 10 2 995 1097 258546142 258546244 1.190000e-24 124.0
50 TraesCS2A01G224400 chr7A 95.122 41 2 0 1845 1885 394887401 394887361 7.310000e-07 65.8
51 TraesCS2A01G224400 chr3A 92.153 994 78 0 1 994 136875599 136876592 0.000000e+00 1404.0
52 TraesCS2A01G224400 chr3A 90.323 248 22 1 1753 1998 228263021 228262774 1.090000e-84 324.0
53 TraesCS2A01G224400 chr3A 89.516 248 24 1 1753 1998 228271203 228270956 2.370000e-81 313.0
54 TraesCS2A01G224400 chr3A 88.608 158 15 3 1155 1311 304940373 304940528 4.160000e-44 189.0
55 TraesCS2A01G224400 chr3A 85.119 168 23 2 1989 2156 297356790 297356625 1.510000e-38 171.0
56 TraesCS2A01G224400 chr3A 95.146 103 5 0 995 1097 464592488 464592386 2.520000e-36 163.0
57 TraesCS2A01G224400 chr3A 94.048 84 5 0 1915 1998 363421829 363421746 9.200000e-26 128.0
58 TraesCS2A01G224400 chr3D 92.276 246 19 0 1753 1998 221073971 221073726 1.800000e-92 350.0
59 TraesCS2A01G224400 chr3D 90.244 246 24 0 1753 1998 221063035 221062790 3.930000e-84 322.0
60 TraesCS2A01G224400 chr3D 87.313 268 27 3 1995 2256 121081108 121081374 1.840000e-77 300.0
61 TraesCS2A01G224400 chr3D 83.630 281 31 6 1982 2255 121072778 121073050 1.880000e-62 250.0
62 TraesCS2A01G224400 chr7B 88.519 270 30 1 1415 1684 207844785 207845053 3.040000e-85 326.0
63 TraesCS2A01G224400 chr7D 87.833 263 29 3 1423 1684 360473994 360474254 3.960000e-79 305.0
64 TraesCS2A01G224400 chr7D 85.586 111 14 2 995 1104 9200914 9200805 7.160000e-22 115.0
65 TraesCS2A01G224400 chr4D 86.545 275 27 7 1989 2255 228754375 228754647 8.570000e-76 294.0
66 TraesCS2A01G224400 chr1A 85.806 155 19 3 1130 1283 141266969 141266817 9.070000e-36 161.0
67 TraesCS2A01G224400 chr1A 90.625 96 6 2 2153 2248 123880361 123880269 1.190000e-24 124.0
68 TraesCS2A01G224400 chr1A 86.916 107 12 2 995 1100 299751956 299752061 5.540000e-23 119.0
69 TraesCS2A01G224400 chr3B 86.486 111 13 2 995 1104 585821224 585821333 1.540000e-23 121.0


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 TraesCS2A01G224400 chr2A 224329230 224332388 3158 False 5834 5834 100.0000 1 3159 1 chr2A.!!$F4 3158
1 TraesCS2A01G224400 chr2A 224395055 224397010 1955 False 1367 2109 91.7955 1107 3077 2 chr2A.!!$F5 1970
2 TraesCS2A01G224400 chr2A 166451427 166452156 729 True 1173 1173 95.6280 2428 3159 1 chr2A.!!$R1 731
3 TraesCS2A01G224400 chr2A 216287405 216288130 725 False 1081 1081 93.4600 2428 3159 1 chr2A.!!$F1 731
4 TraesCS2A01G224400 chr2A 387964309 387964972 663 True 889 889 90.8680 2486 3150 1 chr2A.!!$R3 664
5 TraesCS2A01G224400 chr6A 471812549 471813543 994 True 1506 1506 93.9760 1 996 1 chr6A.!!$R5 995
6 TraesCS2A01G224400 chr6A 397169508 397170500 992 True 1452 1452 93.0580 1 994 1 chr6A.!!$R4 993
7 TraesCS2A01G224400 chr6A 142752658 142753652 994 True 1439 1439 92.7640 1 995 1 chr6A.!!$R1 994
8 TraesCS2A01G224400 chr6A 205745451 205746445 994 True 1406 1406 92.1610 1 995 1 chr6A.!!$R2 994
9 TraesCS2A01G224400 chr5A 168027066 168028062 996 True 1459 1459 93.0790 1 997 1 chr5A.!!$R3 996
10 TraesCS2A01G224400 chr5A 257664544 257665537 993 False 1404 1404 92.1530 1 994 1 chr5A.!!$F3 993
11 TraesCS2A01G224400 chr5A 378681821 378682541 720 True 1075 1075 93.4600 2428 3159 1 chr5A.!!$R5 731
12 TraesCS2A01G224400 chr4A 381517012 381518006 994 False 1411 1411 92.2690 1 996 1 chr4A.!!$F5 995
13 TraesCS2A01G224400 chr4A 428706823 428707506 683 False 1092 1092 95.4740 2475 3159 1 chr4A.!!$F6 684
14 TraesCS2A01G224400 chr4A 428712822 428713425 603 False 933 933 94.5360 2475 3078 1 chr4A.!!$F7 603
15 TraesCS2A01G224400 chr4A 368551768 368552398 630 False 800 800 89.4980 1132 1769 1 chr4A.!!$F4 637
16 TraesCS2A01G224400 chr4A 389395403 389395971 568 True 684 684 88.3070 1197 1769 1 chr4A.!!$R1 572
17 TraesCS2A01G224400 chr7A 292135595 292136588 993 False 1404 1404 92.1530 1 994 1 chr7A.!!$F4 993
18 TraesCS2A01G224400 chr7A 576564973 576565622 649 False 1018 1018 94.9230 2428 3077 1 chr7A.!!$F10 649
19 TraesCS2A01G224400 chr7A 658495298 658495947 649 True 1013 1013 94.7690 2428 3077 1 chr7A.!!$R3 649
20 TraesCS2A01G224400 chr3A 136875599 136876592 993 False 1404 1404 92.1530 1 994 1 chr3A.!!$F1 993

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
203 204 0.179108 CGGTTTCTCCCTGATCGGTC 60.179 60.000 0.0 0.0 0.00 4.79 F
882 883 1.071699 TGCCTTCCACACCAAGTAGAC 59.928 52.381 0.0 0.0 0.00 2.59 F
1024 1025 0.034863 GGAACGAAAGGGGTGCCATA 60.035 55.000 0.0 0.0 32.91 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1006 0.034863 TATGGCACCCCTTTCGTTCC 60.035 55.0 0.0 0.0 0.00 3.62 R
2081 2084 0.110147 CGTCTCACAGGTCTGTCGTC 60.110 60.0 0.0 0.0 42.83 4.20 R
2256 2259 0.248054 CTCGCTCAGCTTCTCTCGAC 60.248 60.0 0.0 0.0 0.00 4.20 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
30 31 2.592287 GTTTGGAACCGCCGTCCA 60.592 61.111 0.00 0.00 40.66 4.02
64 65 1.896660 GGCTGGTTGCGTCCTTTCA 60.897 57.895 0.00 0.00 44.05 2.69
83 84 0.398522 ATGGGTGAGTATCCGGCTCA 60.399 55.000 6.20 6.20 40.28 4.26
91 92 3.580022 TGAGTATCCGGCTCATCATGAAT 59.420 43.478 0.00 0.00 37.98 2.57
118 119 2.479730 CCCGAACATAGTCCGTCTTCAG 60.480 54.545 0.00 0.00 0.00 3.02
203 204 0.179108 CGGTTTCTCCCTGATCGGTC 60.179 60.000 0.00 0.00 0.00 4.79
335 336 2.491693 GTTGATGCGAAGGGGATTTTCA 59.508 45.455 0.00 0.00 0.00 2.69
450 451 7.622502 ACCCCTACGGTAATATTGTCTTTAT 57.377 36.000 0.00 0.00 45.97 1.40
541 542 3.515286 GACACCGGCGGATCTCGA 61.515 66.667 35.78 0.00 42.43 4.04
563 564 2.156920 GGGGGTCCCAAACTGTGTA 58.843 57.895 10.98 0.00 44.65 2.90
579 580 4.202161 ACTGTGTATCTTGGATCGATGGTC 60.202 45.833 0.54 0.00 0.00 4.02
583 584 4.344968 TGTATCTTGGATCGATGGTCACAT 59.655 41.667 0.54 0.00 40.85 3.21
641 642 3.391626 CCTCTCTATGGAGGTAAAACCCC 59.608 52.174 6.21 0.00 45.65 4.95
649 650 1.072806 GAGGTAAAACCCCACGTCCTT 59.927 52.381 0.00 0.00 39.75 3.36
836 837 5.163794 GGTTTTACATGGAGTCGGTTACATG 60.164 44.000 9.78 9.78 44.61 3.21
844 845 1.831736 AGTCGGTTACATGAGAAGGGG 59.168 52.381 0.00 0.00 0.00 4.79
859 860 2.267961 GGGTCTTCGGTCGCCAAT 59.732 61.111 0.00 0.00 0.00 3.16
882 883 1.071699 TGCCTTCCACACCAAGTAGAC 59.928 52.381 0.00 0.00 0.00 2.59
957 958 2.637919 AGCCCATGGATAACAGGCT 58.362 52.632 15.22 8.59 43.70 4.58
1003 1004 2.689073 ACTCCCTCAGTCACCATGG 58.311 57.895 11.19 11.19 0.00 3.66
1004 1005 1.222936 CTCCCTCAGTCACCATGGC 59.777 63.158 13.04 0.00 0.00 4.40
1005 1006 2.124983 CCCTCAGTCACCATGGCG 60.125 66.667 13.04 1.26 0.00 5.69
1006 1007 2.124983 CCTCAGTCACCATGGCGG 60.125 66.667 13.04 4.40 42.50 6.13
1007 1008 2.659063 CCTCAGTCACCATGGCGGA 61.659 63.158 13.04 7.19 38.63 5.54
1008 1009 1.296392 CTCAGTCACCATGGCGGAA 59.704 57.895 13.04 0.00 38.63 4.30
1009 1010 1.003839 TCAGTCACCATGGCGGAAC 60.004 57.895 13.04 4.94 38.63 3.62
1022 1023 2.114411 GGAACGAAAGGGGTGCCA 59.886 61.111 0.00 0.00 32.91 4.92
1023 1024 1.304134 GGAACGAAAGGGGTGCCAT 60.304 57.895 0.00 0.00 32.91 4.40
1024 1025 0.034863 GGAACGAAAGGGGTGCCATA 60.035 55.000 0.00 0.00 32.91 2.74
1025 1026 1.379527 GAACGAAAGGGGTGCCATAG 58.620 55.000 0.00 0.00 0.00 2.23
1026 1027 0.679960 AACGAAAGGGGTGCCATAGC 60.680 55.000 0.00 0.00 40.48 2.97
1027 1028 2.180204 CGAAAGGGGTGCCATAGCG 61.180 63.158 0.00 0.00 44.31 4.26
1028 1029 1.223487 GAAAGGGGTGCCATAGCGA 59.777 57.895 0.00 0.00 44.31 4.93
1029 1030 1.077716 AAAGGGGTGCCATAGCGAC 60.078 57.895 0.00 0.00 44.31 5.19
1030 1031 2.869503 AAAGGGGTGCCATAGCGACG 62.870 60.000 0.00 0.00 44.31 5.12
1031 1032 3.845259 GGGGTGCCATAGCGACGA 61.845 66.667 0.00 0.00 44.31 4.20
1032 1033 2.185867 GGGTGCCATAGCGACGAA 59.814 61.111 0.00 0.00 44.31 3.85
1033 1034 1.227556 GGGTGCCATAGCGACGAAT 60.228 57.895 0.00 0.00 44.31 3.34
1034 1035 1.222115 GGGTGCCATAGCGACGAATC 61.222 60.000 0.00 0.00 44.31 2.52
1035 1036 1.222115 GGTGCCATAGCGACGAATCC 61.222 60.000 0.00 0.00 44.31 3.01
1036 1037 0.529773 GTGCCATAGCGACGAATCCA 60.530 55.000 0.00 0.00 44.31 3.41
1037 1038 0.529773 TGCCATAGCGACGAATCCAC 60.530 55.000 0.00 0.00 44.31 4.02
1038 1039 0.529773 GCCATAGCGACGAATCCACA 60.530 55.000 0.00 0.00 0.00 4.17
1039 1040 1.934589 CCATAGCGACGAATCCACAA 58.065 50.000 0.00 0.00 0.00 3.33
1040 1041 2.276201 CCATAGCGACGAATCCACAAA 58.724 47.619 0.00 0.00 0.00 2.83
1041 1042 2.872245 CCATAGCGACGAATCCACAAAT 59.128 45.455 0.00 0.00 0.00 2.32
1042 1043 3.303329 CCATAGCGACGAATCCACAAATG 60.303 47.826 0.00 0.00 0.00 2.32
1043 1044 2.093306 AGCGACGAATCCACAAATGA 57.907 45.000 0.00 0.00 0.00 2.57
1044 1045 2.422597 AGCGACGAATCCACAAATGAA 58.577 42.857 0.00 0.00 0.00 2.57
1045 1046 2.416547 AGCGACGAATCCACAAATGAAG 59.583 45.455 0.00 0.00 0.00 3.02
1046 1047 2.774007 CGACGAATCCACAAATGAAGC 58.226 47.619 0.00 0.00 0.00 3.86
1047 1048 2.476185 CGACGAATCCACAAATGAAGCC 60.476 50.000 0.00 0.00 0.00 4.35
1048 1049 2.487762 GACGAATCCACAAATGAAGCCA 59.512 45.455 0.00 0.00 0.00 4.75
1049 1050 2.228822 ACGAATCCACAAATGAAGCCAC 59.771 45.455 0.00 0.00 0.00 5.01
1050 1051 2.728846 CGAATCCACAAATGAAGCCACG 60.729 50.000 0.00 0.00 0.00 4.94
1051 1052 2.198827 ATCCACAAATGAAGCCACGA 57.801 45.000 0.00 0.00 0.00 4.35
1052 1053 1.234821 TCCACAAATGAAGCCACGAC 58.765 50.000 0.00 0.00 0.00 4.34
1053 1054 0.950836 CCACAAATGAAGCCACGACA 59.049 50.000 0.00 0.00 0.00 4.35
1054 1055 1.336440 CCACAAATGAAGCCACGACAA 59.664 47.619 0.00 0.00 0.00 3.18
1055 1056 2.384382 CACAAATGAAGCCACGACAAC 58.616 47.619 0.00 0.00 0.00 3.32
1056 1057 2.020720 ACAAATGAAGCCACGACAACA 58.979 42.857 0.00 0.00 0.00 3.33
1057 1058 2.622942 ACAAATGAAGCCACGACAACAT 59.377 40.909 0.00 0.00 0.00 2.71
1058 1059 3.818210 ACAAATGAAGCCACGACAACATA 59.182 39.130 0.00 0.00 0.00 2.29
1059 1060 4.458989 ACAAATGAAGCCACGACAACATAT 59.541 37.500 0.00 0.00 0.00 1.78
1060 1061 4.882671 AATGAAGCCACGACAACATATC 57.117 40.909 0.00 0.00 0.00 1.63
1061 1062 3.326836 TGAAGCCACGACAACATATCA 57.673 42.857 0.00 0.00 0.00 2.15
1062 1063 3.261580 TGAAGCCACGACAACATATCAG 58.738 45.455 0.00 0.00 0.00 2.90
1063 1064 3.262420 GAAGCCACGACAACATATCAGT 58.738 45.455 0.00 0.00 0.00 3.41
1064 1065 3.334583 AGCCACGACAACATATCAGTT 57.665 42.857 0.00 0.00 0.00 3.16
1065 1066 3.262420 AGCCACGACAACATATCAGTTC 58.738 45.455 0.00 0.00 0.00 3.01
1066 1067 2.351726 GCCACGACAACATATCAGTTCC 59.648 50.000 0.00 0.00 0.00 3.62
1067 1068 2.603110 CCACGACAACATATCAGTTCCG 59.397 50.000 0.00 0.00 33.53 4.30
1068 1069 2.603110 CACGACAACATATCAGTTCCGG 59.397 50.000 0.00 0.00 32.38 5.14
1069 1070 2.232941 ACGACAACATATCAGTTCCGGT 59.767 45.455 0.00 0.00 32.38 5.28
1070 1071 3.444742 ACGACAACATATCAGTTCCGGTA 59.555 43.478 0.00 0.00 32.38 4.02
1071 1072 4.082081 ACGACAACATATCAGTTCCGGTAA 60.082 41.667 0.00 0.00 32.38 2.85
1072 1073 4.266976 CGACAACATATCAGTTCCGGTAAC 59.733 45.833 0.00 4.94 38.46 2.50
1074 1075 5.416947 ACAACATATCAGTTCCGGTAACTC 58.583 41.667 14.09 0.00 45.64 3.01
1075 1076 5.046878 ACAACATATCAGTTCCGGTAACTCA 60.047 40.000 14.09 4.90 45.64 3.41
1076 1077 5.670792 ACATATCAGTTCCGGTAACTCAA 57.329 39.130 14.09 8.01 45.64 3.02
1077 1078 6.235231 ACATATCAGTTCCGGTAACTCAAT 57.765 37.500 14.09 12.90 45.64 2.57
1078 1079 6.650120 ACATATCAGTTCCGGTAACTCAATT 58.350 36.000 14.09 5.13 45.64 2.32
1079 1080 6.538742 ACATATCAGTTCCGGTAACTCAATTG 59.461 38.462 14.09 0.00 45.64 2.32
1080 1081 4.610605 TCAGTTCCGGTAACTCAATTGA 57.389 40.909 8.12 8.12 45.64 2.57
1081 1082 4.566004 TCAGTTCCGGTAACTCAATTGAG 58.434 43.478 29.74 29.74 45.64 3.02
1082 1083 4.282449 TCAGTTCCGGTAACTCAATTGAGA 59.718 41.667 36.15 16.53 45.64 3.27
1083 1084 5.046591 TCAGTTCCGGTAACTCAATTGAGAT 60.047 40.000 36.15 28.26 45.64 2.75
1084 1085 5.063944 CAGTTCCGGTAACTCAATTGAGATG 59.936 44.000 36.15 20.80 45.64 2.90
1085 1086 3.531538 TCCGGTAACTCAATTGAGATGC 58.468 45.455 36.15 28.07 44.74 3.91
1086 1087 2.614057 CCGGTAACTCAATTGAGATGCC 59.386 50.000 36.15 33.06 44.74 4.40
1087 1088 3.951979 GGTAACTCAATTGAGATGCCG 57.048 47.619 36.15 14.52 44.74 5.69
1088 1089 2.614057 GGTAACTCAATTGAGATGCCGG 59.386 50.000 36.15 13.83 44.74 6.13
1089 1090 2.496899 AACTCAATTGAGATGCCGGT 57.503 45.000 36.15 14.46 44.74 5.28
1090 1091 1.742761 ACTCAATTGAGATGCCGGTG 58.257 50.000 36.15 12.44 44.74 4.94
1091 1092 0.379669 CTCAATTGAGATGCCGGTGC 59.620 55.000 28.13 0.00 44.74 5.01
1092 1093 2.282807 CTCAATTGAGATGCCGGTGCA 61.283 52.381 28.13 0.00 44.51 4.57
1093 1094 3.772557 CTCAATTGAGATGCCGGTGCAA 61.773 50.000 28.13 1.05 44.07 4.08
1094 1095 5.220785 CTCAATTGAGATGCCGGTGCAAA 62.221 47.826 28.13 0.00 44.07 3.68
1095 1096 6.632556 CTCAATTGAGATGCCGGTGCAAAA 62.633 45.833 28.13 0.00 44.07 2.44
1100 1101 4.889807 TGCCGGTGCAAAAGTAGT 57.110 50.000 1.90 0.00 46.66 2.73
1101 1102 2.326222 TGCCGGTGCAAAAGTAGTG 58.674 52.632 1.90 0.00 46.66 2.74
1102 1103 1.169661 TGCCGGTGCAAAAGTAGTGG 61.170 55.000 1.90 0.00 46.66 4.00
1103 1104 1.862602 GCCGGTGCAAAAGTAGTGGG 61.863 60.000 1.90 0.00 37.47 4.61
1104 1105 0.250553 CCGGTGCAAAAGTAGTGGGA 60.251 55.000 0.00 0.00 0.00 4.37
1105 1106 1.613255 CCGGTGCAAAAGTAGTGGGAT 60.613 52.381 0.00 0.00 0.00 3.85
1114 1115 6.212791 TGCAAAAGTAGTGGGATAAGTAGTCT 59.787 38.462 0.00 0.00 0.00 3.24
1120 1121 5.326200 AGTGGGATAAGTAGTCTTTCACG 57.674 43.478 0.00 0.00 35.36 4.35
1125 1126 2.719426 AAGTAGTCTTTCACGGGTCG 57.281 50.000 0.00 0.00 0.00 4.79
1128 1129 3.149196 AGTAGTCTTTCACGGGTCGTAA 58.851 45.455 0.00 0.00 38.32 3.18
1148 1151 3.637998 AGAAGTAGTCGTTCTCGCAAA 57.362 42.857 0.00 0.00 36.96 3.68
1149 1152 3.973657 AGAAGTAGTCGTTCTCGCAAAA 58.026 40.909 0.00 0.00 36.96 2.44
1153 1156 4.225208 AGTAGTCGTTCTCGCAAAAGTAC 58.775 43.478 0.00 0.00 36.96 2.73
1159 1162 3.432252 CGTTCTCGCAAAAGTACTGGAAT 59.568 43.478 0.00 0.00 0.00 3.01
1190 1193 0.311477 GCGGATCGAAGAGGGAGTAC 59.689 60.000 0.00 0.00 43.63 2.73
1233 1236 0.314935 GGGTCACGACACGGAACTTA 59.685 55.000 0.00 0.00 0.00 2.24
1268 1271 0.821517 TCGCGGGTCAATGATAGTGT 59.178 50.000 6.13 0.00 0.00 3.55
1273 1276 4.127171 GCGGGTCAATGATAGTGTTACAT 58.873 43.478 0.00 0.00 0.00 2.29
1439 1442 2.038269 GGCGTTCTTGGCGATTCCA 61.038 57.895 0.00 0.00 44.85 3.53
1447 1450 1.674637 TGGCGATTCCAAAGACGGA 59.325 52.632 0.00 0.00 43.21 4.69
1458 1461 4.543689 TCCAAAGACGGAGGTAGATGTAT 58.456 43.478 0.00 0.00 0.00 2.29
1480 1483 0.517316 GGTGTCAATGTGGTCTTCGC 59.483 55.000 0.00 0.00 0.00 4.70
1484 1487 2.268298 GTCAATGTGGTCTTCGCGTAT 58.732 47.619 5.77 0.00 0.00 3.06
1639 1642 4.379243 CGGGTCTTGGCAGCGACT 62.379 66.667 15.53 0.00 0.00 4.18
1649 1652 2.278466 CAGCGACTAGAGCGGCAG 60.278 66.667 1.45 0.00 40.04 4.85
1669 1672 3.883744 AAGGCCGACGGTTCAGCAG 62.884 63.158 16.73 0.00 0.00 4.24
1796 1799 2.125350 GAACGAGGGCAGAGGCAG 60.125 66.667 0.00 0.00 43.71 4.85
1808 1811 3.240134 GAGGCAGGAGGTCAACGCA 62.240 63.158 0.00 0.00 0.00 5.24
1836 1839 2.974148 CGCTGTGAAGCAGGTGCA 60.974 61.111 4.48 0.00 45.14 4.57
1842 1845 0.665369 GTGAAGCAGGTGCAATGTGC 60.665 55.000 4.48 7.88 45.16 4.57
1871 1874 4.832608 ACGAATTCCGGCGAGGCC 62.833 66.667 9.30 0.00 46.75 5.19
1904 1907 2.758327 TCGGTCGGGTCTGGATGG 60.758 66.667 0.00 0.00 0.00 3.51
1929 1932 4.521062 GCGGACATGCTCGAGGCT 62.521 66.667 15.58 0.00 42.39 4.58
1960 1963 0.322277 AGATGGTGAAGGTGCTGCAG 60.322 55.000 10.11 10.11 0.00 4.41
1975 1978 2.496817 CAGCAGCGGAGGACCTAC 59.503 66.667 0.00 0.00 0.00 3.18
1983 1986 1.921294 GGAGGACCTACGAGGAGGA 59.079 63.158 8.63 0.00 37.67 3.71
1994 1997 1.819905 GAGGAGGAAGAAGGCGGAG 59.180 63.158 0.00 0.00 0.00 4.63
1997 2000 1.518302 GAGGAAGAAGGCGGAGGAC 59.482 63.158 0.00 0.00 0.00 3.85
1998 2001 1.229209 AGGAAGAAGGCGGAGGACA 60.229 57.895 0.00 0.00 0.00 4.02
2048 2051 4.016706 GTACTGCGGGGCTGGTGT 62.017 66.667 0.00 0.00 0.00 4.16
2081 2084 2.202492 CTCCTGCCGAAGACGACG 60.202 66.667 0.00 0.00 42.66 5.12
2085 2088 3.304764 CTGCCGAAGACGACGACGA 62.305 63.158 15.32 0.00 42.66 4.20
2121 2124 0.442699 GGCGGCAGTAAGAGAAAACG 59.557 55.000 3.07 0.00 0.00 3.60
2125 2128 1.126296 GGCAGTAAGAGAAAACGCGAC 59.874 52.381 15.93 0.00 0.00 5.19
2130 2133 1.687628 AAGAGAAAACGCGACGAGAG 58.312 50.000 15.93 0.00 0.00 3.20
2135 2138 0.313043 AAAACGCGACGAGAGGAAGA 59.687 50.000 15.93 0.00 0.00 2.87
2162 2165 0.327259 CATGGATCGGGCATGAGGAT 59.673 55.000 0.00 0.00 0.00 3.24
2185 2188 3.531207 CTCCCTCGGCTCGATGCA 61.531 66.667 8.71 0.00 45.15 3.96
2279 2282 2.284258 AGAAGCTGAGCGAGGGGT 60.284 61.111 0.00 0.00 0.00 4.95
2280 2283 2.185608 GAAGCTGAGCGAGGGGTC 59.814 66.667 0.00 0.00 41.07 4.46
2281 2284 3.708220 GAAGCTGAGCGAGGGGTCG 62.708 68.421 0.00 0.00 43.60 4.79
2310 2314 2.183811 CTGCCCTCTCTCTGCGTG 59.816 66.667 0.00 0.00 0.00 5.34
2338 2342 3.038280 CGCAGGAGGGAGAGATCG 58.962 66.667 0.00 0.00 0.00 3.69
2344 2348 0.113385 GGAGGGAGAGATCGATGGGA 59.887 60.000 0.54 0.00 0.00 4.37
2360 2364 1.755008 GGAGAGAGGGTGGAGACCG 60.755 68.421 0.00 0.00 44.23 4.79
2370 2374 0.454196 GTGGAGACCGAGAGAAGAGC 59.546 60.000 0.00 0.00 0.00 4.09
2390 2394 1.074167 AGAGATGGGGATCGGGCTT 60.074 57.895 0.00 0.00 0.00 4.35
2420 2424 0.695803 AGGTTGGATGGCCTCTAGGG 60.696 60.000 3.32 0.00 35.18 3.53
2897 2923 9.490379 GGGTTGATATAAACGACAAGAATAGAT 57.510 33.333 0.00 0.00 0.00 1.98
2931 2957 4.158764 TCATGAAGAATGCAATGCACATGA 59.841 37.500 24.85 24.85 43.04 3.07
2992 3019 4.390603 GCAATGCAAACAATGATGACATGT 59.609 37.500 0.00 0.00 36.79 3.21
3052 3079 4.618920 ACGAATAACTGGAAGACACCTT 57.381 40.909 0.00 0.00 37.43 3.50
3078 3105 1.002624 GGACTCGGGGCATCACAAA 60.003 57.895 0.00 0.00 0.00 2.83
3138 3166 0.482446 ATGGCACCAGAGGGAAACAA 59.518 50.000 0.00 0.00 38.05 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.839946 AGCCCTCCGAACATAGCATT 59.160 50.000 0.00 0.00 0.00 3.56
64 65 0.398522 TGAGCCGGATACTCACCCAT 60.399 55.000 5.05 0.00 39.21 4.00
83 84 4.229304 TGTTCGGGTTACCATTCATGAT 57.771 40.909 2.98 0.00 36.13 2.45
91 92 1.477700 CGGACTATGTTCGGGTTACCA 59.522 52.381 2.98 0.00 36.13 3.25
118 119 4.521256 AGGATGGCGAGTCTTCTTCTATAC 59.479 45.833 0.00 0.00 0.00 1.47
335 336 1.832912 GATGACCTCTCGGGCCATT 59.167 57.895 4.39 0.00 37.62 3.16
366 367 1.362717 CTATGATCGCCCGTTCGGT 59.637 57.895 10.36 0.00 0.00 4.69
450 451 0.250684 TTGATGGCTCGCCTTGTCAA 60.251 50.000 9.65 13.01 36.94 3.18
524 525 3.471244 CTCGAGATCCGCCGGTGTC 62.471 68.421 15.14 5.84 38.37 3.67
526 527 2.119147 CTACTCGAGATCCGCCGGTG 62.119 65.000 21.68 8.42 38.37 4.94
541 542 0.104090 ACAGTTTGGGACCCCCTACT 60.104 55.000 8.45 5.76 45.70 2.57
554 555 5.118990 CCATCGATCCAAGATACACAGTTT 58.881 41.667 0.00 0.00 0.00 2.66
563 564 3.389002 TCATGTGACCATCGATCCAAGAT 59.611 43.478 0.00 0.00 0.00 2.40
579 580 1.079127 GTGTCCCCCGTCTCATGTG 60.079 63.158 0.00 0.00 0.00 3.21
583 584 1.125093 ACATTGTGTCCCCCGTCTCA 61.125 55.000 0.00 0.00 0.00 3.27
641 642 6.908870 TCAATATCAATCAAGAAGGACGTG 57.091 37.500 0.00 0.00 0.00 4.49
814 815 5.795972 TCATGTAACCGACTCCATGTAAAA 58.204 37.500 0.00 0.00 36.81 1.52
836 837 1.511768 CGACCGAAGACCCCTTCTC 59.488 63.158 0.00 0.00 45.06 2.87
844 845 0.721718 CAAGATTGGCGACCGAAGAC 59.278 55.000 0.00 0.00 0.00 3.01
859 860 0.550914 ACTTGGTGTGGAAGGCAAGA 59.449 50.000 0.00 0.00 0.00 3.02
997 998 1.674322 CCTTTCGTTCCGCCATGGT 60.674 57.895 14.67 0.00 39.52 3.55
998 999 2.406616 CCCTTTCGTTCCGCCATGG 61.407 63.158 7.63 7.63 40.09 3.66
999 1000 2.406616 CCCCTTTCGTTCCGCCATG 61.407 63.158 0.00 0.00 0.00 3.66
1000 1001 2.045340 CCCCTTTCGTTCCGCCAT 60.045 61.111 0.00 0.00 0.00 4.40
1001 1002 3.562232 ACCCCTTTCGTTCCGCCA 61.562 61.111 0.00 0.00 0.00 5.69
1002 1003 3.053896 CACCCCTTTCGTTCCGCC 61.054 66.667 0.00 0.00 0.00 6.13
1003 1004 3.733960 GCACCCCTTTCGTTCCGC 61.734 66.667 0.00 0.00 0.00 5.54
1004 1005 3.053896 GGCACCCCTTTCGTTCCG 61.054 66.667 0.00 0.00 0.00 4.30
1005 1006 0.034863 TATGGCACCCCTTTCGTTCC 60.035 55.000 0.00 0.00 0.00 3.62
1006 1007 1.379527 CTATGGCACCCCTTTCGTTC 58.620 55.000 0.00 0.00 0.00 3.95
1007 1008 0.679960 GCTATGGCACCCCTTTCGTT 60.680 55.000 0.00 0.00 38.54 3.85
1008 1009 1.077716 GCTATGGCACCCCTTTCGT 60.078 57.895 0.00 0.00 38.54 3.85
1009 1010 2.180204 CGCTATGGCACCCCTTTCG 61.180 63.158 0.74 0.00 38.60 3.46
1010 1011 1.095807 GTCGCTATGGCACCCCTTTC 61.096 60.000 0.74 0.00 38.60 2.62
1011 1012 1.077716 GTCGCTATGGCACCCCTTT 60.078 57.895 0.74 0.00 38.60 3.11
1012 1013 2.590092 GTCGCTATGGCACCCCTT 59.410 61.111 0.74 0.00 38.60 3.95
1013 1014 3.849951 CGTCGCTATGGCACCCCT 61.850 66.667 0.74 0.00 38.60 4.79
1014 1015 2.660258 ATTCGTCGCTATGGCACCCC 62.660 60.000 0.74 0.00 38.60 4.95
1015 1016 1.222115 GATTCGTCGCTATGGCACCC 61.222 60.000 0.74 0.00 38.60 4.61
1016 1017 1.222115 GGATTCGTCGCTATGGCACC 61.222 60.000 0.74 0.00 38.60 5.01
1017 1018 0.529773 TGGATTCGTCGCTATGGCAC 60.530 55.000 0.74 0.00 38.60 5.01
1018 1019 0.529773 GTGGATTCGTCGCTATGGCA 60.530 55.000 0.74 0.00 38.60 4.92
1019 1020 0.529773 TGTGGATTCGTCGCTATGGC 60.530 55.000 0.00 0.00 0.00 4.40
1020 1021 1.934589 TTGTGGATTCGTCGCTATGG 58.065 50.000 0.00 0.00 0.00 2.74
1021 1022 3.555547 TCATTTGTGGATTCGTCGCTATG 59.444 43.478 0.00 0.00 0.00 2.23
1022 1023 3.792401 TCATTTGTGGATTCGTCGCTAT 58.208 40.909 0.00 0.00 0.00 2.97
1023 1024 3.239587 TCATTTGTGGATTCGTCGCTA 57.760 42.857 0.00 0.00 0.00 4.26
1024 1025 2.093306 TCATTTGTGGATTCGTCGCT 57.907 45.000 0.00 0.00 0.00 4.93
1025 1026 2.774007 CTTCATTTGTGGATTCGTCGC 58.226 47.619 0.00 0.00 0.00 5.19
1026 1027 2.476185 GGCTTCATTTGTGGATTCGTCG 60.476 50.000 0.00 0.00 0.00 5.12
1027 1028 2.487762 TGGCTTCATTTGTGGATTCGTC 59.512 45.455 0.00 0.00 0.00 4.20
1028 1029 2.228822 GTGGCTTCATTTGTGGATTCGT 59.771 45.455 0.00 0.00 0.00 3.85
1029 1030 2.728846 CGTGGCTTCATTTGTGGATTCG 60.729 50.000 0.00 0.00 0.00 3.34
1030 1031 2.487762 TCGTGGCTTCATTTGTGGATTC 59.512 45.455 0.00 0.00 0.00 2.52
1031 1032 2.228822 GTCGTGGCTTCATTTGTGGATT 59.771 45.455 0.00 0.00 0.00 3.01
1032 1033 1.812571 GTCGTGGCTTCATTTGTGGAT 59.187 47.619 0.00 0.00 0.00 3.41
1033 1034 1.234821 GTCGTGGCTTCATTTGTGGA 58.765 50.000 0.00 0.00 0.00 4.02
1034 1035 0.950836 TGTCGTGGCTTCATTTGTGG 59.049 50.000 0.00 0.00 0.00 4.17
1035 1036 2.223456 TGTTGTCGTGGCTTCATTTGTG 60.223 45.455 0.00 0.00 0.00 3.33
1036 1037 2.020720 TGTTGTCGTGGCTTCATTTGT 58.979 42.857 0.00 0.00 0.00 2.83
1037 1038 2.772568 TGTTGTCGTGGCTTCATTTG 57.227 45.000 0.00 0.00 0.00 2.32
1038 1039 4.699735 TGATATGTTGTCGTGGCTTCATTT 59.300 37.500 0.00 0.00 0.00 2.32
1039 1040 4.260985 TGATATGTTGTCGTGGCTTCATT 58.739 39.130 0.00 0.00 0.00 2.57
1040 1041 3.872696 TGATATGTTGTCGTGGCTTCAT 58.127 40.909 0.00 0.00 0.00 2.57
1041 1042 3.261580 CTGATATGTTGTCGTGGCTTCA 58.738 45.455 0.00 0.00 0.00 3.02
1042 1043 3.262420 ACTGATATGTTGTCGTGGCTTC 58.738 45.455 0.00 0.00 0.00 3.86
1043 1044 3.334583 ACTGATATGTTGTCGTGGCTT 57.665 42.857 0.00 0.00 0.00 4.35
1044 1045 3.262420 GAACTGATATGTTGTCGTGGCT 58.738 45.455 0.00 0.00 0.00 4.75
1045 1046 2.351726 GGAACTGATATGTTGTCGTGGC 59.648 50.000 0.00 0.00 0.00 5.01
1046 1047 2.603110 CGGAACTGATATGTTGTCGTGG 59.397 50.000 0.00 0.00 0.00 4.94
1047 1048 2.603110 CCGGAACTGATATGTTGTCGTG 59.397 50.000 0.00 0.00 0.00 4.35
1048 1049 2.232941 ACCGGAACTGATATGTTGTCGT 59.767 45.455 9.46 0.00 0.00 4.34
1049 1050 2.888594 ACCGGAACTGATATGTTGTCG 58.111 47.619 9.46 0.00 0.00 4.35
1050 1051 5.713822 GTTACCGGAACTGATATGTTGTC 57.286 43.478 9.46 0.00 34.96 3.18
1062 1063 4.201822 GCATCTCAATTGAGTTACCGGAAC 60.202 45.833 29.80 8.67 42.60 3.62
1063 1064 3.938963 GCATCTCAATTGAGTTACCGGAA 59.061 43.478 29.80 12.52 42.60 4.30
1064 1065 3.531538 GCATCTCAATTGAGTTACCGGA 58.468 45.455 29.80 13.40 42.60 5.14
1065 1066 2.614057 GGCATCTCAATTGAGTTACCGG 59.386 50.000 29.80 16.72 42.60 5.28
1066 1067 2.285220 CGGCATCTCAATTGAGTTACCG 59.715 50.000 30.08 30.08 42.60 4.02
1067 1068 2.614057 CCGGCATCTCAATTGAGTTACC 59.386 50.000 29.80 24.41 42.60 2.85
1068 1069 3.063997 CACCGGCATCTCAATTGAGTTAC 59.936 47.826 29.80 18.72 42.60 2.50
1069 1070 3.270027 CACCGGCATCTCAATTGAGTTA 58.730 45.455 29.80 15.90 42.60 2.24
1070 1071 2.086869 CACCGGCATCTCAATTGAGTT 58.913 47.619 29.80 21.43 42.60 3.01
1071 1072 1.742761 CACCGGCATCTCAATTGAGT 58.257 50.000 29.80 17.26 42.60 3.41
1072 1073 0.379669 GCACCGGCATCTCAATTGAG 59.620 55.000 26.56 26.56 40.78 3.02
1073 1074 2.481212 GCACCGGCATCTCAATTGA 58.519 52.632 8.12 8.12 40.72 2.57
1084 1085 1.579429 CCACTACTTTTGCACCGGC 59.421 57.895 0.00 0.00 41.68 6.13
1085 1086 0.250553 TCCCACTACTTTTGCACCGG 60.251 55.000 0.00 0.00 0.00 5.28
1086 1087 1.821216 ATCCCACTACTTTTGCACCG 58.179 50.000 0.00 0.00 0.00 4.94
1087 1088 4.332828 ACTTATCCCACTACTTTTGCACC 58.667 43.478 0.00 0.00 0.00 5.01
1088 1089 6.171213 ACTACTTATCCCACTACTTTTGCAC 58.829 40.000 0.00 0.00 0.00 4.57
1089 1090 6.212791 AGACTACTTATCCCACTACTTTTGCA 59.787 38.462 0.00 0.00 0.00 4.08
1090 1091 6.641474 AGACTACTTATCCCACTACTTTTGC 58.359 40.000 0.00 0.00 0.00 3.68
1091 1092 9.152595 GAAAGACTACTTATCCCACTACTTTTG 57.847 37.037 0.00 0.00 35.05 2.44
1092 1093 8.877195 TGAAAGACTACTTATCCCACTACTTTT 58.123 33.333 0.00 0.00 35.05 2.27
1093 1094 8.312564 GTGAAAGACTACTTATCCCACTACTTT 58.687 37.037 0.00 0.00 35.05 2.66
1094 1095 7.362747 CGTGAAAGACTACTTATCCCACTACTT 60.363 40.741 0.00 0.00 35.05 2.24
1095 1096 6.095160 CGTGAAAGACTACTTATCCCACTACT 59.905 42.308 0.00 0.00 35.05 2.57
1096 1097 6.264088 CGTGAAAGACTACTTATCCCACTAC 58.736 44.000 0.00 0.00 35.05 2.73
1097 1098 5.359009 CCGTGAAAGACTACTTATCCCACTA 59.641 44.000 0.00 0.00 35.05 2.74
1098 1099 4.159879 CCGTGAAAGACTACTTATCCCACT 59.840 45.833 0.00 0.00 35.05 4.00
1099 1100 4.430908 CCGTGAAAGACTACTTATCCCAC 58.569 47.826 0.00 0.00 35.05 4.61
1100 1101 3.449737 CCCGTGAAAGACTACTTATCCCA 59.550 47.826 0.00 0.00 35.05 4.37
1101 1102 3.450096 ACCCGTGAAAGACTACTTATCCC 59.550 47.826 0.00 0.00 35.05 3.85
1102 1103 4.680702 GACCCGTGAAAGACTACTTATCC 58.319 47.826 0.00 0.00 35.05 2.59
1103 1104 4.142513 ACGACCCGTGAAAGACTACTTATC 60.143 45.833 0.00 0.00 39.18 1.75
1104 1105 3.760684 ACGACCCGTGAAAGACTACTTAT 59.239 43.478 0.00 0.00 39.18 1.73
1105 1106 3.149196 ACGACCCGTGAAAGACTACTTA 58.851 45.455 0.00 0.00 39.18 2.24
1114 1115 3.569701 ACTACTTCTTACGACCCGTGAAA 59.430 43.478 1.93 0.00 41.39 2.69
1120 1121 3.438434 AGAACGACTACTTCTTACGACCC 59.562 47.826 0.00 0.00 0.00 4.46
1125 1126 4.075763 TGCGAGAACGACTACTTCTTAC 57.924 45.455 0.00 0.00 42.66 2.34
1128 1129 3.637998 TTTGCGAGAACGACTACTTCT 57.362 42.857 0.00 0.00 42.66 2.85
1137 1140 2.400399 TCCAGTACTTTTGCGAGAACG 58.600 47.619 0.00 0.00 42.93 3.95
1148 1151 5.717119 CGTGTACCACTTATTCCAGTACTT 58.283 41.667 0.00 0.00 35.45 2.24
1149 1152 4.381292 GCGTGTACCACTTATTCCAGTACT 60.381 45.833 0.00 0.00 35.45 2.73
1153 1156 1.924524 CGCGTGTACCACTTATTCCAG 59.075 52.381 0.00 0.00 31.34 3.86
1159 1162 0.099259 CGATCCGCGTGTACCACTTA 59.901 55.000 4.92 0.00 34.64 2.24
1175 1178 4.537751 TGAATGAGTACTCCCTCTTCGAT 58.462 43.478 20.11 1.44 32.50 3.59
1178 1181 5.452636 GGACATGAATGAGTACTCCCTCTTC 60.453 48.000 20.11 16.05 32.50 2.87
1190 1193 4.442403 CGAACATCTACGGACATGAATGAG 59.558 45.833 0.00 0.00 0.00 2.90
1233 1236 2.739132 GAAGACCCCGTGGACGTT 59.261 61.111 0.00 0.00 37.74 3.99
1268 1271 2.662637 CGAACGGCTACGAAACATGTAA 59.337 45.455 0.00 0.00 44.60 2.41
1273 1276 0.311790 ACTCGAACGGCTACGAAACA 59.688 50.000 0.00 0.00 44.60 2.83
1397 1400 2.884894 ACCTTTTCGAGTTGACGAGT 57.115 45.000 0.00 0.00 43.04 4.18
1439 1442 5.189145 ACCAAATACATCTACCTCCGTCTTT 59.811 40.000 0.00 0.00 0.00 2.52
1447 1450 6.599244 CACATTGACACCAAATACATCTACCT 59.401 38.462 0.00 0.00 35.67 3.08
1458 1461 2.616376 CGAAGACCACATTGACACCAAA 59.384 45.455 0.00 0.00 35.67 3.28
1484 1487 2.435234 CCGCCCGGAATCGTCAAA 60.435 61.111 0.73 0.00 37.50 2.69
1498 1501 0.601057 ACTATGTTTTGTTGCCCCGC 59.399 50.000 0.00 0.00 0.00 6.13
1607 1610 2.671070 CCGACAACCAGGGATGCT 59.329 61.111 0.00 0.00 0.00 3.79
1639 1642 4.473520 GGCCTTGCTGCCGCTCTA 62.474 66.667 0.70 0.00 42.54 2.43
1649 1652 3.423154 CTGAACCGTCGGCCTTGC 61.423 66.667 12.28 0.00 0.00 4.01
1709 1712 0.250381 CTCCCTCCATGCTGCTGATC 60.250 60.000 0.00 0.00 0.00 2.92
1711 1714 3.040206 GCTCCCTCCATGCTGCTGA 62.040 63.158 0.00 0.00 0.00 4.26
1765 1768 0.725686 TCGTTCGAGGAGATGACGAC 59.274 55.000 2.35 0.00 37.24 4.34
1787 1790 1.376553 GTTGACCTCCTGCCTCTGC 60.377 63.158 0.00 0.00 38.26 4.26
1796 1799 3.423154 CCGCTTGCGTTGACCTCC 61.423 66.667 13.97 0.00 0.00 4.30
1824 1827 1.661480 GCACATTGCACCTGCTTCA 59.339 52.632 0.00 0.00 44.26 3.02
1836 1839 0.593128 GTCAAGTTCAGCGGCACATT 59.407 50.000 1.45 0.00 0.00 2.71
1842 1845 1.128692 GGAATTCGTCAAGTTCAGCGG 59.871 52.381 0.00 0.00 0.00 5.52
1845 1848 1.128692 GCCGGAATTCGTCAAGTTCAG 59.871 52.381 5.05 0.00 37.11 3.02
1871 1874 4.394712 GACCCTGCACCCCTGTCG 62.395 72.222 0.00 0.00 0.00 4.35
1929 1932 4.147449 CCATCTCGCCAGCCGTCA 62.147 66.667 0.00 0.00 38.35 4.35
1960 1963 3.127352 CTCGTAGGTCCTCCGCTGC 62.127 68.421 0.00 0.00 39.05 5.25
1975 1978 2.010582 CTCCGCCTTCTTCCTCCTCG 62.011 65.000 0.00 0.00 0.00 4.63
1983 1986 1.604378 CCATGTCCTCCGCCTTCTT 59.396 57.895 0.00 0.00 0.00 2.52
1994 1997 2.511600 CTTCGCGACCCCATGTCC 60.512 66.667 9.15 0.00 41.18 4.02
2081 2084 0.110147 CGTCTCACAGGTCTGTCGTC 60.110 60.000 0.00 0.00 42.83 4.20
2085 2088 1.908793 CCCCGTCTCACAGGTCTGT 60.909 63.158 0.00 0.00 46.17 3.41
2110 2113 2.413765 CCTCTCGTCGCGTTTTCTCTTA 60.414 50.000 5.77 0.00 0.00 2.10
2121 2124 1.720694 CTCCCTCTTCCTCTCGTCGC 61.721 65.000 0.00 0.00 0.00 5.19
2125 2128 2.131067 GGCCTCCCTCTTCCTCTCG 61.131 68.421 0.00 0.00 0.00 4.04
2130 2133 1.064824 ATCCATGGCCTCCCTCTTCC 61.065 60.000 6.96 0.00 0.00 3.46
2135 2138 2.851102 CCGATCCATGGCCTCCCT 60.851 66.667 6.96 0.00 0.00 4.20
2162 2165 2.598467 GAGCCGAGGGAGAGGAGA 59.402 66.667 0.00 0.00 0.00 3.71
2168 2171 3.531207 TGCATCGAGCCGAGGGAG 61.531 66.667 10.41 0.17 44.83 4.30
2185 2188 4.640855 CCACTCGGTCACACGCGT 62.641 66.667 5.58 5.58 31.17 6.01
2232 2235 4.821589 CGTCCTTCCTCCAGCGCC 62.822 72.222 2.29 0.00 0.00 6.53
2256 2259 0.248054 CTCGCTCAGCTTCTCTCGAC 60.248 60.000 0.00 0.00 0.00 4.20
2338 2342 0.263172 TCTCCACCCTCTCTCCCATC 59.737 60.000 0.00 0.00 0.00 3.51
2344 2348 1.208844 TCTCGGTCTCCACCCTCTCT 61.209 60.000 0.00 0.00 40.01 3.10
2360 2364 1.608590 CCCATCTCTCGCTCTTCTCTC 59.391 57.143 0.00 0.00 0.00 3.20
2370 2374 2.936912 GCCCGATCCCCATCTCTCG 61.937 68.421 0.00 0.00 0.00 4.04
2390 2394 2.196595 CATCCAACCTCCTCTAACCCA 58.803 52.381 0.00 0.00 0.00 4.51
2416 2420 3.093835 CGGCCCAACCATCCCCTA 61.094 66.667 0.00 0.00 39.03 3.53
2529 2552 5.239525 CCAAACCCTCTGTACTTTCTTTCTG 59.760 44.000 0.00 0.00 0.00 3.02
2673 2696 3.802866 TGGGTTCAAAAATGGTTCAAGC 58.197 40.909 0.00 0.00 0.00 4.01
2897 2923 5.474189 TGCATTCTTCATGATGTTGTCTTGA 59.526 36.000 8.33 0.00 38.73 3.02
2931 2957 7.717436 TGCCATTTTGCATTTCATCATAATCAT 59.283 29.630 0.00 0.00 36.04 2.45
3071 3098 4.431416 TGTAGTGGTGGAGTTTTGTGAT 57.569 40.909 0.00 0.00 0.00 3.06
3078 3105 2.972348 TCCTCTTGTAGTGGTGGAGTT 58.028 47.619 0.00 0.00 31.13 3.01
3116 3143 2.196997 TTTCCCTCTGGTGCCATCCG 62.197 60.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.