Multiple sequence alignment - TraesCS1B01G314200

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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 TraesCS1B01G314200 chr1B 100.000 3643 0 0 1 3643 539125828 539129470 0.000000e+00 6728.0
1 TraesCS1B01G314200 chr1B 93.617 47 2 1 3205 3251 498685740 498685785 6.530000e-08 69.4
2 TraesCS1B01G314200 chr1B 95.122 41 2 0 3205 3245 118515930 118515890 8.440000e-07 65.8
3 TraesCS1B01G314200 chr1B 97.222 36 1 0 3170 3205 325262215 325262180 1.090000e-05 62.1
4 TraesCS1B01G314200 chr1D 93.702 1842 96 8 1186 3011 401160073 401161910 0.000000e+00 2741.0
5 TraesCS1B01G314200 chr1D 88.097 1067 67 30 127 1187 401158967 401159979 0.000000e+00 1212.0
6 TraesCS1B01G314200 chr1D 92.019 639 45 6 3009 3643 401168969 401169605 0.000000e+00 893.0
7 TraesCS1B01G314200 chr1D 96.739 92 2 1 2999 3089 401168886 401168977 6.300000e-33 152.0
8 TraesCS1B01G314200 chr1D 95.122 41 2 0 3205 3245 75109280 75109240 8.440000e-07 65.8
9 TraesCS1B01G314200 chr1D 100.000 31 0 0 52 82 328437563 328437533 1.410000e-04 58.4
10 TraesCS1B01G314200 chr1A 95.303 958 31 5 1030 1977 497274436 497275389 0.000000e+00 1507.0
11 TraesCS1B01G314200 chr1A 91.875 800 40 7 2710 3505 497275388 497276166 0.000000e+00 1094.0
12 TraesCS1B01G314200 chr1A 88.288 666 60 9 344 999 497272814 497273471 0.000000e+00 782.0
13 TraesCS1B01G314200 chr1A 90.769 130 10 2 192 319 497268264 497268135 4.840000e-39 172.0
14 TraesCS1B01G314200 chr1A 100.000 35 0 0 1 35 497267593 497267627 8.440000e-07 65.8
15 TraesCS1B01G314200 chr1A 94.595 37 0 2 310 345 497272797 497272832 5.080000e-04 56.5
16 TraesCS1B01G314200 chr4B 88.889 81 9 0 490 570 180696380 180696300 2.310000e-17 100.0
17 TraesCS1B01G314200 chr4B 87.719 57 6 1 3205 3260 482662710 482662654 8.440000e-07 65.8
18 TraesCS1B01G314200 chr2A 89.024 82 6 2 3169 3250 567376859 567376937 8.330000e-17 99.0
19 TraesCS1B01G314200 chr5D 87.952 83 6 3 490 570 31264058 31263978 1.080000e-15 95.3
20 TraesCS1B01G314200 chrUn 93.478 46 3 0 3205 3250 79505425 79505470 6.530000e-08 69.4
21 TraesCS1B01G314200 chrUn 100.000 31 0 0 3175 3205 32240944 32240974 1.410000e-04 58.4
22 TraesCS1B01G314200 chr2B 97.436 39 1 0 52 90 448777229 448777191 2.350000e-07 67.6
23 TraesCS1B01G314200 chr2B 96.774 31 1 0 3172 3202 30131367 30131397 7.000000e-03 52.8
24 TraesCS1B01G314200 chr7D 95.122 41 2 0 3205 3245 561921877 561921837 8.440000e-07 65.8
25 TraesCS1B01G314200 chr6B 100.000 31 0 0 3175 3205 415885016 415884986 1.410000e-04 58.4
26 TraesCS1B01G314200 chr7A 81.944 72 4 7 317 388 16105125 16105187 7.000000e-03 52.8
27 TraesCS1B01G314200 chr3D 100.000 28 0 0 3175 3202 107672219 107672246 7.000000e-03 52.8
28 TraesCS1B01G314200 chr3B 100.000 28 0 0 3175 3202 127932735 127932708 7.000000e-03 52.8
29 TraesCS1B01G314200 chr3A 81.944 72 4 7 317 388 745088948 745089010 7.000000e-03 52.8


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 TraesCS1B01G314200 chr1B 539125828 539129470 3642 False 6728.000 6728 100.00000 1 3643 1 chr1B.!!$F2 3642
1 TraesCS1B01G314200 chr1D 401158967 401161910 2943 False 1976.500 2741 90.89950 127 3011 2 chr1D.!!$F1 2884
2 TraesCS1B01G314200 chr1D 401168886 401169605 719 False 522.500 893 94.37900 2999 3643 2 chr1D.!!$F2 644
3 TraesCS1B01G314200 chr1A 497272797 497276166 3369 False 859.875 1507 92.51525 310 3505 4 chr1A.!!$F2 3195

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
603 613 0.034670 GCTTCCCTGACAATCCAGCT 60.035 55.0 0.00 0.0 32.97 4.24 F
1124 2081 0.465287 TTGACAGTCTGTGAGCTGCA 59.535 50.0 11.04 0.0 36.26 4.41 F
2242 3311 0.037046 GAGCCCAATTTTGTGCCCTG 60.037 55.0 0.00 0.0 31.60 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1901 2970 0.253327 CCTTGTACAGGGGAGCCTTC 59.747 60.0 16.14 0.0 39.39 3.46 R
2487 3556 0.323816 TCGACCTCATGCCACTCTCT 60.324 55.0 0.00 0.0 0.00 3.10 R
3183 4328 1.006832 CTGCGACAAGTAATTCCGGG 58.993 55.0 0.00 0.0 0.00 5.73 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
28 29 9.802039 TGGTATTATTTCATAATTGGTACTCCC 57.198 33.333 0.00 0.00 36.82 4.30
32 33 4.682778 TTCATAATTGGTACTCCCTCCG 57.317 45.455 0.00 0.00 0.00 4.63
33 34 3.649843 TCATAATTGGTACTCCCTCCGT 58.350 45.455 0.00 0.00 0.00 4.69
34 35 4.035112 TCATAATTGGTACTCCCTCCGTT 58.965 43.478 0.00 0.00 0.00 4.44
35 36 4.100498 TCATAATTGGTACTCCCTCCGTTC 59.900 45.833 0.00 0.00 0.00 3.95
36 37 1.946984 ATTGGTACTCCCTCCGTTCA 58.053 50.000 0.00 0.00 0.00 3.18
37 38 0.971386 TTGGTACTCCCTCCGTTCAC 59.029 55.000 0.00 0.00 0.00 3.18
38 39 1.246056 TGGTACTCCCTCCGTTCACG 61.246 60.000 0.00 0.00 39.44 4.35
39 40 1.153881 GTACTCCCTCCGTTCACGC 60.154 63.158 0.00 0.00 38.18 5.34
40 41 1.604308 TACTCCCTCCGTTCACGCA 60.604 57.895 0.00 0.00 38.18 5.24
41 42 1.870055 TACTCCCTCCGTTCACGCAC 61.870 60.000 0.00 0.00 38.18 5.34
42 43 3.220999 CTCCCTCCGTTCACGCACA 62.221 63.158 0.00 0.00 38.18 4.57
43 44 3.041940 CCCTCCGTTCACGCACAC 61.042 66.667 0.00 0.00 38.18 3.82
44 45 2.029073 CCTCCGTTCACGCACACT 59.971 61.111 0.00 0.00 38.18 3.55
45 46 2.310233 CCTCCGTTCACGCACACTG 61.310 63.158 0.00 0.00 38.18 3.66
46 47 2.943345 CTCCGTTCACGCACACTGC 61.943 63.158 0.00 0.00 40.69 4.40
47 48 2.967076 CCGTTCACGCACACTGCT 60.967 61.111 0.00 0.00 42.25 4.24
48 49 2.246397 CGTTCACGCACACTGCTG 59.754 61.111 0.00 0.00 42.25 4.41
49 50 2.237066 CGTTCACGCACACTGCTGA 61.237 57.895 0.00 0.00 42.25 4.26
50 51 1.560004 CGTTCACGCACACTGCTGAT 61.560 55.000 0.00 0.00 42.25 2.90
51 52 0.110509 GTTCACGCACACTGCTGATG 60.111 55.000 0.00 0.00 42.25 3.07
52 53 0.249826 TTCACGCACACTGCTGATGA 60.250 50.000 0.00 0.00 42.25 2.92
53 54 0.668401 TCACGCACACTGCTGATGAG 60.668 55.000 0.00 0.00 42.25 2.90
54 55 0.947660 CACGCACACTGCTGATGAGT 60.948 55.000 0.00 0.62 42.25 3.41
55 56 0.603065 ACGCACACTGCTGATGAGTA 59.397 50.000 0.00 0.00 42.25 2.59
56 57 1.205655 ACGCACACTGCTGATGAGTAT 59.794 47.619 0.00 0.00 42.25 2.12
57 58 1.857217 CGCACACTGCTGATGAGTATC 59.143 52.381 0.00 0.00 42.25 2.24
58 59 2.736400 CGCACACTGCTGATGAGTATCA 60.736 50.000 0.00 0.00 46.75 2.15
59 60 3.264947 GCACACTGCTGATGAGTATCAA 58.735 45.455 0.00 0.00 45.21 2.57
60 61 3.063180 GCACACTGCTGATGAGTATCAAC 59.937 47.826 0.00 0.00 45.21 3.18
61 62 5.389531 GCACACTGCTGATGAGTATCAACA 61.390 45.833 0.00 0.00 45.21 3.33
74 75 6.867550 TGAGTATCAACAATCTCTACAGGTG 58.132 40.000 0.00 0.00 45.97 4.00
75 76 6.127338 TGAGTATCAACAATCTCTACAGGTGG 60.127 42.308 0.00 0.00 45.97 4.61
76 77 5.958380 AGTATCAACAATCTCTACAGGTGGA 59.042 40.000 0.00 0.00 0.00 4.02
77 78 5.965033 ATCAACAATCTCTACAGGTGGAT 57.035 39.130 0.00 0.00 0.00 3.41
78 79 5.344743 TCAACAATCTCTACAGGTGGATC 57.655 43.478 0.00 0.00 0.00 3.36
79 80 5.026121 TCAACAATCTCTACAGGTGGATCT 58.974 41.667 0.00 0.00 0.00 2.75
80 81 5.485353 TCAACAATCTCTACAGGTGGATCTT 59.515 40.000 0.00 0.00 0.00 2.40
81 82 5.606348 ACAATCTCTACAGGTGGATCTTC 57.394 43.478 0.00 0.00 0.00 2.87
82 83 4.407296 ACAATCTCTACAGGTGGATCTTCC 59.593 45.833 0.00 0.00 36.96 3.46
83 84 3.757947 TCTCTACAGGTGGATCTTCCA 57.242 47.619 8.82 0.00 45.98 3.53
91 92 3.006061 TGGATCTTCCATCCACCGT 57.994 52.632 0.00 0.00 42.67 4.83
92 93 0.541392 TGGATCTTCCATCCACCGTG 59.459 55.000 0.00 0.00 42.67 4.94
93 94 0.815615 GGATCTTCCATCCACCGTGC 60.816 60.000 0.00 0.00 38.09 5.34
94 95 0.107703 GATCTTCCATCCACCGTGCA 60.108 55.000 0.00 0.00 0.00 4.57
95 96 0.392998 ATCTTCCATCCACCGTGCAC 60.393 55.000 6.82 6.82 0.00 4.57
96 97 1.302431 CTTCCATCCACCGTGCACA 60.302 57.895 18.64 0.00 0.00 4.57
97 98 1.577328 CTTCCATCCACCGTGCACAC 61.577 60.000 18.64 0.00 0.00 3.82
98 99 2.032528 CCATCCACCGTGCACACT 59.967 61.111 18.64 0.00 0.00 3.55
99 100 2.327343 CCATCCACCGTGCACACTG 61.327 63.158 18.64 10.60 0.00 3.66
100 101 2.669569 ATCCACCGTGCACACTGC 60.670 61.111 18.64 0.00 45.29 4.40
101 102 3.182590 ATCCACCGTGCACACTGCT 62.183 57.895 18.64 0.00 45.31 4.24
102 103 1.826340 ATCCACCGTGCACACTGCTA 61.826 55.000 18.64 2.48 45.31 3.49
103 104 1.375908 CCACCGTGCACACTGCTAT 60.376 57.895 18.64 0.00 45.31 2.97
104 105 0.955428 CCACCGTGCACACTGCTATT 60.955 55.000 18.64 0.00 45.31 1.73
105 106 1.674519 CCACCGTGCACACTGCTATTA 60.675 52.381 18.64 0.00 45.31 0.98
106 107 2.073056 CACCGTGCACACTGCTATTAA 58.927 47.619 18.64 0.00 45.31 1.40
107 108 2.073816 ACCGTGCACACTGCTATTAAC 58.926 47.619 18.64 0.00 45.31 2.01
108 109 1.396996 CCGTGCACACTGCTATTAACC 59.603 52.381 18.64 0.00 45.31 2.85
109 110 1.396996 CGTGCACACTGCTATTAACCC 59.603 52.381 18.64 0.00 45.31 4.11
110 111 1.743394 GTGCACACTGCTATTAACCCC 59.257 52.381 13.17 0.00 45.31 4.95
111 112 1.340600 TGCACACTGCTATTAACCCCC 60.341 52.381 0.00 0.00 45.31 5.40
112 113 1.663695 CACACTGCTATTAACCCCCG 58.336 55.000 0.00 0.00 0.00 5.73
113 114 0.107361 ACACTGCTATTAACCCCCGC 60.107 55.000 0.00 0.00 0.00 6.13
114 115 0.107410 CACTGCTATTAACCCCCGCA 60.107 55.000 0.00 0.00 0.00 5.69
115 116 0.843984 ACTGCTATTAACCCCCGCAT 59.156 50.000 0.00 0.00 0.00 4.73
116 117 1.238439 CTGCTATTAACCCCCGCATG 58.762 55.000 0.00 0.00 0.00 4.06
117 118 0.179004 TGCTATTAACCCCCGCATGG 60.179 55.000 0.00 0.00 0.00 3.66
118 119 0.109723 GCTATTAACCCCCGCATGGA 59.890 55.000 0.00 0.00 37.49 3.41
119 120 1.882352 GCTATTAACCCCCGCATGGAG 60.882 57.143 0.00 0.00 37.49 3.86
120 121 1.697432 CTATTAACCCCCGCATGGAGA 59.303 52.381 0.00 0.00 37.49 3.71
121 122 0.474184 ATTAACCCCCGCATGGAGAG 59.526 55.000 0.00 0.00 37.49 3.20
122 123 0.619255 TTAACCCCCGCATGGAGAGA 60.619 55.000 0.00 0.00 37.49 3.10
123 124 1.048724 TAACCCCCGCATGGAGAGAG 61.049 60.000 0.00 0.00 37.49 3.20
124 125 2.765807 CCCCCGCATGGAGAGAGT 60.766 66.667 0.00 0.00 37.49 3.24
125 126 1.457643 CCCCCGCATGGAGAGAGTA 60.458 63.158 0.00 0.00 37.49 2.59
152 153 8.988934 TCTTGTAAAAGATATTATGGCGATCAC 58.011 33.333 0.00 0.00 0.00 3.06
166 167 3.859386 GGCGATCACCTTGCAATAAAAAG 59.141 43.478 0.00 0.00 35.78 2.27
167 168 3.304293 GCGATCACCTTGCAATAAAAAGC 59.696 43.478 0.00 0.00 34.05 3.51
172 173 5.288804 TCACCTTGCAATAAAAAGCACTTC 58.711 37.500 0.00 0.00 41.05 3.01
178 179 5.153513 TGCAATAAAAAGCACTTCGATGTC 58.846 37.500 0.13 0.00 35.51 3.06
179 180 5.153513 GCAATAAAAAGCACTTCGATGTCA 58.846 37.500 0.13 0.00 0.00 3.58
180 181 5.629020 GCAATAAAAAGCACTTCGATGTCAA 59.371 36.000 0.13 0.00 0.00 3.18
181 182 6.143758 GCAATAAAAAGCACTTCGATGTCAAA 59.856 34.615 0.13 0.00 0.00 2.69
182 183 7.306515 GCAATAAAAAGCACTTCGATGTCAAAA 60.307 33.333 0.13 0.00 0.00 2.44
183 184 8.538856 CAATAAAAAGCACTTCGATGTCAAAAA 58.461 29.630 0.13 0.00 0.00 1.94
229 231 2.359107 GGTTCGTCGGGGGTTTCC 60.359 66.667 0.00 0.00 0.00 3.13
253 255 1.907255 AGGGAGTTTTTCTACGAGGGG 59.093 52.381 0.00 0.00 0.00 4.79
397 407 4.408821 GCTGCCCGTGTCCATCCA 62.409 66.667 0.00 0.00 0.00 3.41
410 420 4.673298 ATCCACCGCGCACGTTCA 62.673 61.111 8.75 0.00 37.70 3.18
490 500 3.471620 TCCAGCTGGGACTGTCAC 58.528 61.111 32.23 6.62 42.15 3.67
491 501 1.152247 TCCAGCTGGGACTGTCACT 60.152 57.895 32.23 0.00 42.15 3.41
492 502 1.004080 CCAGCTGGGACTGTCACTG 60.004 63.158 26.14 11.99 40.01 3.66
541 551 2.196925 CGACCAGGCCGAGAGCTAT 61.197 63.158 0.00 0.00 43.05 2.97
547 557 0.758685 AGGCCGAGAGCTATGCTTCT 60.759 55.000 0.00 0.00 39.88 2.85
549 559 0.387202 GCCGAGAGCTATGCTTCTGA 59.613 55.000 0.00 0.00 39.88 3.27
583 593 0.041238 TCGAGGGGTTCATGGAGAGT 59.959 55.000 0.00 0.00 0.00 3.24
589 599 1.680249 GGGTTCATGGAGAGTGCTTCC 60.680 57.143 0.00 0.00 0.00 3.46
595 605 0.471780 TGGAGAGTGCTTCCCTGACA 60.472 55.000 0.00 0.00 0.00 3.58
598 608 2.626840 GAGAGTGCTTCCCTGACAATC 58.373 52.381 0.00 0.00 0.00 2.67
599 609 1.280421 AGAGTGCTTCCCTGACAATCC 59.720 52.381 0.00 0.00 0.00 3.01
603 613 0.034670 GCTTCCCTGACAATCCAGCT 60.035 55.000 0.00 0.00 32.97 4.24
612 622 2.106338 TGACAATCCAGCTCAGTTTCCA 59.894 45.455 0.00 0.00 0.00 3.53
622 632 3.834813 AGCTCAGTTTCCATCAGACAGTA 59.165 43.478 0.00 0.00 0.00 2.74
626 636 3.921021 CAGTTTCCATCAGACAGTACGTC 59.079 47.826 0.00 9.05 45.77 4.34
694 704 1.892862 CCAGAGGCATAGCAGCAGC 60.893 63.158 0.00 0.00 42.56 5.25
834 851 2.294078 GGCTAGGTGGAGCAGGTGT 61.294 63.158 0.00 0.00 44.76 4.16
843 860 1.148273 GAGCAGGTGTGGTGGTTCA 59.852 57.895 0.00 0.00 33.41 3.18
853 870 2.203153 GTGGTTCAGGCACACCGT 60.203 61.111 0.00 0.00 42.76 4.83
854 871 2.203139 TGGTTCAGGCACACCGTG 60.203 61.111 0.00 0.00 42.76 4.94
855 872 2.978010 GGTTCAGGCACACCGTGG 60.978 66.667 3.03 0.00 42.76 4.94
904 924 3.376935 CTGCTCGGCCCTGATTCGT 62.377 63.158 0.00 0.00 0.00 3.85
913 933 0.749649 CCCTGATTCGTCTCTCCCTG 59.250 60.000 0.00 0.00 0.00 4.45
944 966 4.906792 CGCTGCCTCCTAGCCTGC 62.907 72.222 0.00 0.00 37.90 4.85
1000 1022 3.042682 TGGTTGGTTCTAGTCCTGTCAA 58.957 45.455 7.86 0.00 0.00 3.18
1003 1025 3.981071 TGGTTCTAGTCCTGTCAATGG 57.019 47.619 7.86 0.00 0.00 3.16
1124 2081 0.465287 TTGACAGTCTGTGAGCTGCA 59.535 50.000 11.04 0.00 36.26 4.41
1348 2407 4.022849 GCACTGGGATGGCATATTTCTAAC 60.023 45.833 0.00 0.00 0.00 2.34
1355 2414 7.284489 TGGGATGGCATATTTCTAACTTAACAC 59.716 37.037 0.00 0.00 0.00 3.32
1447 2506 1.814586 GTGCCTAGCAGCTGCAGAG 60.815 63.158 38.24 31.36 45.16 3.35
1484 2543 4.382754 GCGATGATTTTCTGAAACACCAAC 59.617 41.667 1.58 0.25 0.00 3.77
1494 2553 2.174639 TGAAACACCAACTGGATGACCT 59.825 45.455 1.86 0.00 38.94 3.85
1513 2572 9.220767 GATGACCTTTGTTTACTAGTCAAGAAT 57.779 33.333 0.00 0.00 37.74 2.40
1590 2649 6.426328 TGAGCTCTGTTCTCTTCAATCTTTTC 59.574 38.462 16.19 0.00 0.00 2.29
1642 2701 7.287466 ACAGAGCCATTGCCATTGTTATAATAA 59.713 33.333 0.00 0.00 38.69 1.40
1711 2779 1.686110 AAGCTCCTCTGTACGGGGG 60.686 63.158 15.21 15.21 0.00 5.40
1867 2936 2.028385 GGAATCTGTCCGTGTACCTTGT 60.028 50.000 0.00 0.00 36.40 3.16
1901 2970 2.544267 GGACTGGTCTGTTTCTCAAACG 59.456 50.000 0.67 0.00 44.28 3.60
1940 3009 0.110486 TGGAAGTTGCCCTCTCCAAC 59.890 55.000 0.00 0.00 42.11 3.77
1963 3032 2.358737 CGACCCTTCTTTGCCGCT 60.359 61.111 0.00 0.00 0.00 5.52
2019 3088 2.280628 GAGCCCGTAATCTGGAAACTG 58.719 52.381 0.00 0.00 0.00 3.16
2025 3094 3.623060 CCGTAATCTGGAAACTGACATGG 59.377 47.826 0.00 0.00 41.39 3.66
2026 3095 3.623060 CGTAATCTGGAAACTGACATGGG 59.377 47.826 0.00 0.00 41.39 4.00
2031 3100 1.971167 GAAACTGACATGGGCGGCA 60.971 57.895 12.47 0.00 0.00 5.69
2177 3246 2.111043 CCTGTGGTGGCTGTCGTT 59.889 61.111 0.00 0.00 0.00 3.85
2214 3283 0.987294 CCTCACATCAACCCCTGACT 59.013 55.000 0.00 0.00 36.69 3.41
2217 3286 2.567169 CTCACATCAACCCCTGACTACA 59.433 50.000 0.00 0.00 36.69 2.74
2231 3300 4.521146 CTGACTACATTCAAGAGCCCAAT 58.479 43.478 0.00 0.00 0.00 3.16
2234 3303 5.774690 TGACTACATTCAAGAGCCCAATTTT 59.225 36.000 0.00 0.00 0.00 1.82
2240 3309 0.686789 AAGAGCCCAATTTTGTGCCC 59.313 50.000 0.00 0.00 31.60 5.36
2242 3311 0.037046 GAGCCCAATTTTGTGCCCTG 60.037 55.000 0.00 0.00 31.60 4.45
2246 3315 1.270785 CCCAATTTTGTGCCCTGGTTC 60.271 52.381 0.00 0.00 0.00 3.62
2279 3348 4.351938 TCCAAGCCGGACGTCACG 62.352 66.667 18.91 17.44 39.64 4.35
2326 3395 1.956170 CAGACACGTGCACCTGGAC 60.956 63.158 17.22 12.13 0.00 4.02
2327 3396 2.108157 GACACGTGCACCTGGACA 59.892 61.111 17.22 0.00 36.05 4.02
2331 3400 2.972505 CGTGCACCTGGACACCAC 60.973 66.667 12.15 8.94 36.05 4.16
2355 3424 2.058595 TACCCGCTCTGCTTCCCTC 61.059 63.158 0.00 0.00 0.00 4.30
2392 3461 0.462047 GACTTCCGTATGCCACCCAG 60.462 60.000 0.00 0.00 0.00 4.45
2398 3467 1.542547 CCGTATGCCACCCAGGATAAC 60.543 57.143 0.00 0.00 41.22 1.89
2399 3468 1.140052 CGTATGCCACCCAGGATAACA 59.860 52.381 0.00 0.00 41.22 2.41
2403 3472 0.618458 GCCACCCAGGATAACAGTCA 59.382 55.000 0.00 0.00 41.22 3.41
2411 3480 1.743958 AGGATAACAGTCACGTCCTCG 59.256 52.381 0.00 0.00 34.26 4.63
2444 3513 5.179368 CGAGCCATACATTTTGATATCGGTT 59.821 40.000 0.00 0.00 0.00 4.44
2461 3530 1.622232 GTTAGTCGCCCGTACAACTC 58.378 55.000 0.00 0.00 0.00 3.01
2462 3531 0.527565 TTAGTCGCCCGTACAACTCC 59.472 55.000 0.00 0.00 0.00 3.85
2465 3534 2.433664 CGCCCGTACAACTCCACC 60.434 66.667 0.00 0.00 0.00 4.61
2468 3537 0.108472 GCCCGTACAACTCCACCTAC 60.108 60.000 0.00 0.00 0.00 3.18
2477 3546 3.009723 CAACTCCACCTACGCATTTGAT 58.990 45.455 0.00 0.00 0.00 2.57
2487 3556 2.710377 ACGCATTTGATACCAGCTCAA 58.290 42.857 0.00 0.00 0.00 3.02
2499 3568 1.370609 CAGCTCAAGAGAGTGGCATG 58.629 55.000 0.32 0.00 44.00 4.06
2525 3594 4.090057 GGCGAGCAACTGCCGTTC 62.090 66.667 12.11 0.00 42.22 3.95
2526 3595 3.345808 GCGAGCAACTGCCGTTCA 61.346 61.111 12.11 0.00 43.38 3.18
2528 3597 1.421485 CGAGCAACTGCCGTTCATC 59.579 57.895 0.00 0.00 43.38 2.92
2590 3659 1.122632 TCTCACAAGTACGGCCCCAA 61.123 55.000 0.00 0.00 0.00 4.12
2602 3671 0.824109 GGCCCCAATCAAAGCTTACC 59.176 55.000 0.00 0.00 0.00 2.85
2619 3688 1.874019 CCGCATCCGAGTCTCAACG 60.874 63.158 0.00 0.00 36.29 4.10
2625 3694 0.250597 TCCGAGTCTCAACGTCTGGA 60.251 55.000 0.00 0.00 0.00 3.86
2698 3767 4.095483 AGGAGCATGAAGAAATTAACGCAG 59.905 41.667 0.00 0.00 0.00 5.18
2703 3772 2.224917 TGAAGAAATTAACGCAGGGGGT 60.225 45.455 0.00 0.00 0.00 4.95
2757 3826 1.265365 GCTCTGTTGTCTTGGCAGAAC 59.735 52.381 0.00 0.00 38.58 3.01
2767 3836 2.125512 GGCAGAACGACAGCGGAT 60.126 61.111 0.00 0.00 43.17 4.18
2896 3965 2.485814 GAGATTGTTGTCTCCTGCCAAC 59.514 50.000 0.00 0.00 38.94 3.77
2930 3999 0.548682 AGGATCTGCAGTTCCCCTGT 60.549 55.000 31.51 16.29 43.55 4.00
2931 4000 0.107459 GGATCTGCAGTTCCCCTGTC 60.107 60.000 27.13 6.63 43.55 3.51
2956 4025 2.514592 ATGCACCCATCGCCTTCG 60.515 61.111 0.00 0.00 0.00 3.79
2965 4034 0.508641 CATCGCCTTCGCTTTATCCG 59.491 55.000 0.00 0.00 35.26 4.18
2976 4047 9.090692 GCCTTCGCTTTATCCGTATAAATAATA 57.909 33.333 0.00 0.00 37.04 0.98
3036 4110 5.521372 AGAAGCTTGCTTTTTAACTGCAAAG 59.479 36.000 2.10 2.75 44.49 2.77
3083 4228 7.601073 TCATTGCTCATAGTTTCTACACTTG 57.399 36.000 0.00 0.00 0.00 3.16
3173 4318 0.179009 CCCCACTGGCCAGTCATATG 60.179 60.000 35.79 22.99 40.20 1.78
3183 4328 0.320247 CAGTCATATGCTCCCTCCGC 60.320 60.000 0.00 0.00 0.00 5.54
3284 4429 0.820891 AACTGCACTGTTCTGCCCTG 60.821 55.000 0.00 0.00 36.21 4.45
3301 4446 3.099141 CCCTGTGGCCTTTTTACATCAT 58.901 45.455 3.32 0.00 0.00 2.45
3302 4447 3.515104 CCCTGTGGCCTTTTTACATCATT 59.485 43.478 3.32 0.00 0.00 2.57
3303 4448 4.381932 CCCTGTGGCCTTTTTACATCATTC 60.382 45.833 3.32 0.00 0.00 2.67
3304 4449 4.463891 CCTGTGGCCTTTTTACATCATTCT 59.536 41.667 3.32 0.00 0.00 2.40
3305 4450 5.389859 TGTGGCCTTTTTACATCATTCTG 57.610 39.130 3.32 0.00 0.00 3.02
3306 4451 4.176271 GTGGCCTTTTTACATCATTCTGC 58.824 43.478 3.32 0.00 0.00 4.26
3307 4452 4.082026 GTGGCCTTTTTACATCATTCTGCT 60.082 41.667 3.32 0.00 0.00 4.24
3308 4453 4.527816 TGGCCTTTTTACATCATTCTGCTT 59.472 37.500 3.32 0.00 0.00 3.91
3309 4454 5.011943 TGGCCTTTTTACATCATTCTGCTTT 59.988 36.000 3.32 0.00 0.00 3.51
3310 4455 5.934043 GGCCTTTTTACATCATTCTGCTTTT 59.066 36.000 0.00 0.00 0.00 2.27
3311 4456 6.128472 GGCCTTTTTACATCATTCTGCTTTTG 60.128 38.462 0.00 0.00 0.00 2.44
3312 4457 6.646240 GCCTTTTTACATCATTCTGCTTTTGA 59.354 34.615 0.00 0.00 0.00 2.69
3313 4458 7.171337 GCCTTTTTACATCATTCTGCTTTTGAA 59.829 33.333 0.00 0.00 0.00 2.69
3314 4459 8.706035 CCTTTTTACATCATTCTGCTTTTGAAG 58.294 33.333 0.00 0.00 0.00 3.02
3315 4460 9.467258 CTTTTTACATCATTCTGCTTTTGAAGA 57.533 29.630 0.00 0.00 30.63 2.87
3316 4461 8.801715 TTTTACATCATTCTGCTTTTGAAGAC 57.198 30.769 0.00 0.00 32.79 3.01
3317 4462 7.509141 TTACATCATTCTGCTTTTGAAGACA 57.491 32.000 0.00 0.00 32.79 3.41
3318 4463 5.766222 ACATCATTCTGCTTTTGAAGACAC 58.234 37.500 0.00 0.00 32.79 3.67
3319 4464 5.300034 ACATCATTCTGCTTTTGAAGACACA 59.700 36.000 0.00 0.00 32.79 3.72
3320 4465 6.015688 ACATCATTCTGCTTTTGAAGACACAT 60.016 34.615 0.00 0.00 32.79 3.21
3376 4541 2.411748 TCGATGTTCGACATGCTGAAAC 59.588 45.455 5.41 0.00 44.82 2.78
3415 4580 1.741770 GGTTGTGCCGCTACCTCTG 60.742 63.158 1.43 0.00 39.42 3.35
3427 4592 5.360591 CCGCTACCTCTGATCAGTATTTTT 58.639 41.667 21.92 5.19 0.00 1.94
3479 4644 9.950496 AACATCTTGTCTCACTGATAAATAGTT 57.050 29.630 0.00 0.00 0.00 2.24
3486 4651 9.151471 TGTCTCACTGATAAATAGTTTTGTAGC 57.849 33.333 0.00 0.00 0.00 3.58
3498 4663 8.480643 AATAGTTTTGTAGCAGTACTAGCTTG 57.519 34.615 20.08 0.00 43.25 4.01
3525 4690 1.613061 CCCCTCCCCGTGCTTAAAT 59.387 57.895 0.00 0.00 0.00 1.40
3526 4691 0.841289 CCCCTCCCCGTGCTTAAATA 59.159 55.000 0.00 0.00 0.00 1.40
3527 4692 1.476291 CCCCTCCCCGTGCTTAAATAC 60.476 57.143 0.00 0.00 0.00 1.89
3538 4712 8.768019 CCCCGTGCTTAAATACTAGTAAATAAC 58.232 37.037 6.70 5.57 0.00 1.89
3590 4764 4.836125 TCAGTTTCAAAGGTTCTGATGC 57.164 40.909 0.00 0.00 31.51 3.91
3608 4782 0.179056 GCGCTATTTGGTAGGCCTGA 60.179 55.000 17.99 0.00 35.27 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.883311 CGGAGGGAGTACCAATTATGAAATAAT 59.117 37.037 0.00 0.00 43.74 1.28
7 8 7.147444 ACGGAGGGAGTACCAATTATGAAATAA 60.147 37.037 0.00 0.00 42.26 1.40
8 9 6.328148 ACGGAGGGAGTACCAATTATGAAATA 59.672 38.462 0.00 0.00 43.89 1.40
9 10 5.132144 ACGGAGGGAGTACCAATTATGAAAT 59.868 40.000 0.00 0.00 43.89 2.17
10 11 4.472108 ACGGAGGGAGTACCAATTATGAAA 59.528 41.667 0.00 0.00 43.89 2.69
11 12 4.035112 ACGGAGGGAGTACCAATTATGAA 58.965 43.478 0.00 0.00 43.89 2.57
12 13 3.649843 ACGGAGGGAGTACCAATTATGA 58.350 45.455 0.00 0.00 43.89 2.15
13 14 4.141801 TGAACGGAGGGAGTACCAATTATG 60.142 45.833 0.00 0.00 43.89 1.90
14 15 4.035112 TGAACGGAGGGAGTACCAATTAT 58.965 43.478 0.00 0.00 43.89 1.28
15 16 3.196254 GTGAACGGAGGGAGTACCAATTA 59.804 47.826 0.00 0.00 43.89 1.40
16 17 2.027469 GTGAACGGAGGGAGTACCAATT 60.027 50.000 0.00 0.00 43.89 2.32
17 18 1.553704 GTGAACGGAGGGAGTACCAAT 59.446 52.381 0.00 0.00 43.89 3.16
18 19 0.971386 GTGAACGGAGGGAGTACCAA 59.029 55.000 0.00 0.00 43.89 3.67
19 20 1.246056 CGTGAACGGAGGGAGTACCA 61.246 60.000 0.00 0.00 37.44 3.25
20 21 1.509923 CGTGAACGGAGGGAGTACC 59.490 63.158 0.00 0.00 35.96 3.34
21 22 1.153881 GCGTGAACGGAGGGAGTAC 60.154 63.158 4.84 0.00 40.23 2.73
22 23 1.604308 TGCGTGAACGGAGGGAGTA 60.604 57.895 4.84 0.00 40.23 2.59
23 24 2.915659 TGCGTGAACGGAGGGAGT 60.916 61.111 4.84 0.00 40.23 3.85
24 25 2.432628 GTGCGTGAACGGAGGGAG 60.433 66.667 4.84 0.00 41.17 4.30
25 26 3.228017 TGTGCGTGAACGGAGGGA 61.228 61.111 4.84 0.00 41.17 4.20
26 27 3.041940 GTGTGCGTGAACGGAGGG 61.042 66.667 4.84 0.00 41.17 4.30
27 28 2.029073 AGTGTGCGTGAACGGAGG 59.971 61.111 4.84 0.00 41.17 4.30
28 29 2.943345 GCAGTGTGCGTGAACGGAG 61.943 63.158 4.84 0.00 41.17 4.63
29 30 2.964925 GCAGTGTGCGTGAACGGA 60.965 61.111 4.84 0.00 40.23 4.69
38 39 2.897436 TGATACTCATCAGCAGTGTGC 58.103 47.619 0.00 0.00 45.46 4.57
39 40 4.248058 TGTTGATACTCATCAGCAGTGTG 58.752 43.478 0.70 0.00 44.53 3.82
40 41 4.541973 TGTTGATACTCATCAGCAGTGT 57.458 40.909 0.70 0.00 44.53 3.55
44 45 6.231258 AGAGATTGTTGATACTCATCAGCA 57.769 37.500 0.70 0.70 46.76 4.41
45 46 7.205992 TGTAGAGATTGTTGATACTCATCAGC 58.794 38.462 0.00 0.00 42.11 4.26
46 47 7.866898 CCTGTAGAGATTGTTGATACTCATCAG 59.133 40.741 0.00 0.00 42.11 2.90
47 48 7.343057 ACCTGTAGAGATTGTTGATACTCATCA 59.657 37.037 0.00 0.00 39.47 3.07
48 49 7.651304 CACCTGTAGAGATTGTTGATACTCATC 59.349 40.741 0.00 0.00 32.59 2.92
49 50 7.418368 CCACCTGTAGAGATTGTTGATACTCAT 60.418 40.741 0.00 0.00 32.59 2.90
50 51 6.127338 CCACCTGTAGAGATTGTTGATACTCA 60.127 42.308 0.00 0.00 32.59 3.41
51 52 6.096987 TCCACCTGTAGAGATTGTTGATACTC 59.903 42.308 0.00 0.00 0.00 2.59
52 53 5.958380 TCCACCTGTAGAGATTGTTGATACT 59.042 40.000 0.00 0.00 0.00 2.12
53 54 6.222038 TCCACCTGTAGAGATTGTTGATAC 57.778 41.667 0.00 0.00 0.00 2.24
54 55 6.841229 AGATCCACCTGTAGAGATTGTTGATA 59.159 38.462 0.00 0.00 0.00 2.15
55 56 5.664908 AGATCCACCTGTAGAGATTGTTGAT 59.335 40.000 0.00 0.00 0.00 2.57
56 57 5.026121 AGATCCACCTGTAGAGATTGTTGA 58.974 41.667 0.00 0.00 0.00 3.18
57 58 5.350504 AGATCCACCTGTAGAGATTGTTG 57.649 43.478 0.00 0.00 0.00 3.33
58 59 5.104735 GGAAGATCCACCTGTAGAGATTGTT 60.105 44.000 0.00 0.00 36.28 2.83
59 60 4.407296 GGAAGATCCACCTGTAGAGATTGT 59.593 45.833 0.00 0.00 36.28 2.71
60 61 4.406972 TGGAAGATCCACCTGTAGAGATTG 59.593 45.833 0.00 0.00 42.67 2.67
61 62 4.624913 TGGAAGATCCACCTGTAGAGATT 58.375 43.478 0.00 0.00 42.67 2.40
62 63 4.271807 TGGAAGATCCACCTGTAGAGAT 57.728 45.455 0.00 0.00 42.67 2.75
63 64 3.757947 TGGAAGATCCACCTGTAGAGA 57.242 47.619 0.00 0.00 42.67 3.10
74 75 0.815615 GCACGGTGGATGGAAGATCC 60.816 60.000 10.60 0.00 38.66 3.36
75 76 0.107703 TGCACGGTGGATGGAAGATC 60.108 55.000 10.60 0.00 0.00 2.75
76 77 0.392998 GTGCACGGTGGATGGAAGAT 60.393 55.000 10.60 0.00 0.00 2.40
77 78 1.003839 GTGCACGGTGGATGGAAGA 60.004 57.895 10.60 0.00 0.00 2.87
78 79 1.302431 TGTGCACGGTGGATGGAAG 60.302 57.895 13.13 0.00 0.00 3.46
79 80 1.599518 GTGTGCACGGTGGATGGAA 60.600 57.895 13.13 0.00 0.00 3.53
80 81 2.031919 GTGTGCACGGTGGATGGA 59.968 61.111 13.13 0.00 0.00 3.41
81 82 2.032528 AGTGTGCACGGTGGATGG 59.967 61.111 13.13 0.00 36.20 3.51
82 83 2.969806 GCAGTGTGCACGGTGGATG 61.970 63.158 13.13 3.84 44.26 3.51
83 84 2.669569 GCAGTGTGCACGGTGGAT 60.670 61.111 13.13 0.00 44.26 3.41
92 93 1.389555 GGGGGTTAATAGCAGTGTGC 58.610 55.000 0.00 0.00 45.46 4.57
93 94 1.663695 CGGGGGTTAATAGCAGTGTG 58.336 55.000 0.00 0.00 0.00 3.82
94 95 0.107361 GCGGGGGTTAATAGCAGTGT 60.107 55.000 0.00 0.00 0.00 3.55
95 96 0.107410 TGCGGGGGTTAATAGCAGTG 60.107 55.000 0.00 0.00 33.57 3.66
96 97 0.843984 ATGCGGGGGTTAATAGCAGT 59.156 50.000 0.00 0.00 41.34 4.40
97 98 1.238439 CATGCGGGGGTTAATAGCAG 58.762 55.000 0.00 0.00 41.34 4.24
98 99 0.179004 CCATGCGGGGGTTAATAGCA 60.179 55.000 0.00 0.00 42.28 3.49
99 100 0.109723 TCCATGCGGGGGTTAATAGC 59.890 55.000 0.00 0.00 37.22 2.97
100 101 1.697432 TCTCCATGCGGGGGTTAATAG 59.303 52.381 0.00 0.00 38.77 1.73
101 102 1.697432 CTCTCCATGCGGGGGTTAATA 59.303 52.381 0.00 0.00 38.77 0.98
102 103 0.474184 CTCTCCATGCGGGGGTTAAT 59.526 55.000 0.00 0.00 38.77 1.40
103 104 0.619255 TCTCTCCATGCGGGGGTTAA 60.619 55.000 0.00 0.00 38.77 2.01
104 105 1.002403 TCTCTCCATGCGGGGGTTA 59.998 57.895 0.00 0.00 38.77 2.85
105 106 2.285368 TCTCTCCATGCGGGGGTT 60.285 61.111 0.00 0.00 38.77 4.11
106 107 2.238319 TACTCTCTCCATGCGGGGGT 62.238 60.000 0.00 0.00 38.77 4.95
107 108 0.833834 ATACTCTCTCCATGCGGGGG 60.834 60.000 0.00 0.00 39.19 5.40
108 109 0.605589 GATACTCTCTCCATGCGGGG 59.394 60.000 0.00 0.00 37.22 5.73
109 110 1.626686 AGATACTCTCTCCATGCGGG 58.373 55.000 0.00 0.00 38.37 6.13
110 111 2.363680 ACAAGATACTCTCTCCATGCGG 59.636 50.000 0.00 0.00 31.03 5.69
111 112 3.724508 ACAAGATACTCTCTCCATGCG 57.275 47.619 0.00 0.00 31.03 4.73
112 113 7.268586 TCTTTTACAAGATACTCTCTCCATGC 58.731 38.462 0.00 0.00 33.80 4.06
143 144 2.121291 TTATTGCAAGGTGATCGCCA 57.879 45.000 26.71 6.40 0.00 5.69
152 153 4.545610 TCGAAGTGCTTTTTATTGCAAGG 58.454 39.130 4.94 0.00 41.10 3.61
192 193 7.705325 ACGAACCAAAGTGTATACTGCTAATAG 59.295 37.037 4.17 0.00 37.19 1.73
229 231 0.989890 CGTAGAAAAACTCCCTCGCG 59.010 55.000 0.00 0.00 0.00 5.87
356 366 1.587613 GAGATCGTGAGCGTGAGGC 60.588 63.158 0.00 0.00 44.05 4.70
357 367 1.064946 GGAGATCGTGAGCGTGAGG 59.935 63.158 0.00 0.00 39.49 3.86
358 368 1.064946 GGGAGATCGTGAGCGTGAG 59.935 63.158 0.00 0.00 39.49 3.51
359 369 2.761195 CGGGAGATCGTGAGCGTGA 61.761 63.158 0.00 0.00 39.49 4.35
360 370 2.278206 CGGGAGATCGTGAGCGTG 60.278 66.667 0.00 0.00 39.49 5.34
361 371 4.194720 GCGGGAGATCGTGAGCGT 62.195 66.667 0.00 0.00 39.49 5.07
362 372 4.933064 GGCGGGAGATCGTGAGCG 62.933 72.222 0.00 0.00 39.92 5.03
363 373 4.933064 CGGCGGGAGATCGTGAGC 62.933 72.222 0.00 0.00 0.00 4.26
415 425 2.734673 GCAGCAGAAGACCGCGAAG 61.735 63.158 8.23 0.00 0.00 3.79
417 427 3.989787 TGCAGCAGAAGACCGCGA 61.990 61.111 8.23 0.00 0.00 5.87
487 497 2.997315 CTCCAGCGGGTCCAGTGA 60.997 66.667 1.81 0.00 34.93 3.41
488 498 4.767255 GCTCCAGCGGGTCCAGTG 62.767 72.222 1.81 0.00 34.93 3.66
541 551 1.293498 GAAGCGGAGGTCAGAAGCA 59.707 57.895 0.00 0.00 37.06 3.91
583 593 0.322816 GCTGGATTGTCAGGGAAGCA 60.323 55.000 0.00 0.00 35.43 3.91
589 599 2.486472 AACTGAGCTGGATTGTCAGG 57.514 50.000 0.00 0.00 41.77 3.86
595 605 3.265221 TCTGATGGAAACTGAGCTGGATT 59.735 43.478 0.00 0.00 0.00 3.01
598 608 2.289882 TGTCTGATGGAAACTGAGCTGG 60.290 50.000 0.00 0.00 0.00 4.85
599 609 3.001414 CTGTCTGATGGAAACTGAGCTG 58.999 50.000 0.00 0.00 0.00 4.24
603 613 3.572682 ACGTACTGTCTGATGGAAACTGA 59.427 43.478 0.00 0.00 0.00 3.41
622 632 0.669077 GACCTCGCCTATGATGACGT 59.331 55.000 0.00 0.00 0.00 4.34
626 636 1.290324 CCGGACCTCGCCTATGATG 59.710 63.158 0.00 0.00 37.59 3.07
627 637 2.574955 GCCGGACCTCGCCTATGAT 61.575 63.158 5.05 0.00 37.59 2.45
748 765 0.747644 CTTGCCGTGCCATGGTATGA 60.748 55.000 22.39 1.44 0.00 2.15
751 768 2.045438 CCTTGCCGTGCCATGGTA 60.045 61.111 14.67 5.86 0.00 3.25
795 812 1.613630 AGCTGTTCCATCCGGTCCT 60.614 57.895 0.00 0.00 0.00 3.85
823 840 2.337879 GAACCACCACACCTGCTCCA 62.338 60.000 0.00 0.00 0.00 3.86
834 851 2.194597 GGTGTGCCTGAACCACCA 59.805 61.111 3.28 0.00 46.33 4.17
843 860 0.109723 ACAATAACCACGGTGTGCCT 59.890 50.000 7.45 0.00 31.34 4.75
853 870 1.743623 CTGCCGCCGACAATAACCA 60.744 57.895 0.00 0.00 0.00 3.67
854 871 3.098555 CTGCCGCCGACAATAACC 58.901 61.111 0.00 0.00 0.00 2.85
855 872 2.403586 GCTGCCGCCGACAATAAC 59.596 61.111 0.00 0.00 0.00 1.89
904 924 1.670949 GATGCTGCGTCAGGGAGAGA 61.671 60.000 16.63 0.00 35.87 3.10
962 984 2.048127 AAGTCGCTTCTCCGTGCC 60.048 61.111 0.00 0.00 0.00 5.01
1000 1022 1.760086 CCCTCCTCGAGCTCACCAT 60.760 63.158 15.40 0.00 0.00 3.55
1003 1025 3.071206 TGCCCTCCTCGAGCTCAC 61.071 66.667 15.40 0.00 0.00 3.51
1484 2543 6.464222 TGACTAGTAAACAAAGGTCATCCAG 58.536 40.000 0.00 0.00 35.89 3.86
1494 2553 6.770785 ACAGCCATTCTTGACTAGTAAACAAA 59.229 34.615 0.00 0.00 0.00 2.83
1513 2572 3.306641 GGCAACCAAATTTATCACAGCCA 60.307 43.478 11.39 0.00 38.27 4.75
1590 2649 8.996271 TGCTTCTTCAGTATCATAATAAGCATG 58.004 33.333 0.00 0.00 37.39 4.06
1642 2701 5.934625 ACTGCTGATGAGTTCTAAAATTCGT 59.065 36.000 0.00 0.00 0.00 3.85
1660 2728 2.420642 AGTAGTTCATGCACACTGCTG 58.579 47.619 11.00 0.00 45.31 4.41
1867 2936 1.613317 CCAGTCCCGACAGCATACCA 61.613 60.000 0.00 0.00 0.00 3.25
1901 2970 0.253327 CCTTGTACAGGGGAGCCTTC 59.747 60.000 16.14 0.00 39.39 3.46
1940 3009 1.014564 GCAAAGAAGGGTCGTCGGAG 61.015 60.000 0.00 0.00 0.00 4.63
2019 3088 3.134127 GGTCTTGCCGCCCATGTC 61.134 66.667 0.00 0.00 0.00 3.06
2025 3094 2.954611 GACAAAGGTCTTGCCGCC 59.045 61.111 0.00 0.00 43.70 6.13
2031 3100 2.173569 ACTGCAAGGAGACAAAGGTCTT 59.826 45.455 0.00 0.00 46.19 3.01
2039 3108 0.764369 ACCCTGACTGCAAGGAGACA 60.764 55.000 4.39 0.00 39.30 3.41
2049 3118 0.747255 CCGACTATCCACCCTGACTG 59.253 60.000 0.00 0.00 0.00 3.51
2171 3240 2.446994 ACCCTGTCCCCAACGACA 60.447 61.111 0.00 0.00 40.44 4.35
2177 3246 1.692749 GGCATAGACCCTGTCCCCA 60.693 63.158 0.00 0.00 32.18 4.96
2187 3256 2.565841 GGTTGATGTGAGGGCATAGAC 58.434 52.381 0.00 0.00 0.00 2.59
2214 3283 5.782047 CACAAAATTGGGCTCTTGAATGTA 58.218 37.500 0.00 0.00 0.00 2.29
2231 3300 0.821711 CCTCGAACCAGGGCACAAAA 60.822 55.000 0.00 0.00 0.00 2.44
2234 3303 2.847234 ACCTCGAACCAGGGCACA 60.847 61.111 0.00 0.00 37.96 4.57
2309 3378 2.421739 GTCCAGGTGCACGTGTCT 59.578 61.111 31.20 12.55 0.00 3.41
2381 3450 2.438021 GACTGTTATCCTGGGTGGCATA 59.562 50.000 0.00 0.00 35.26 3.14
2383 3452 0.618458 GACTGTTATCCTGGGTGGCA 59.382 55.000 0.00 0.00 35.26 4.92
2387 3456 1.549170 GACGTGACTGTTATCCTGGGT 59.451 52.381 0.00 0.00 0.00 4.51
2392 3461 1.202268 CCGAGGACGTGACTGTTATCC 60.202 57.143 0.00 0.00 37.88 2.59
2398 3467 2.258591 CCACCGAGGACGTGACTG 59.741 66.667 0.00 0.00 41.22 3.51
2399 3468 2.203451 ACCACCGAGGACGTGACT 60.203 61.111 0.00 0.00 41.22 3.41
2403 3472 3.300765 GACCACCACCGAGGACGT 61.301 66.667 0.00 0.00 41.22 4.34
2426 3495 6.367969 GGCGACTAACCGATATCAAAATGTAT 59.632 38.462 3.12 0.00 0.00 2.29
2444 3513 0.608856 TGGAGTTGTACGGGCGACTA 60.609 55.000 0.00 0.00 33.52 2.59
2461 3530 2.872245 CTGGTATCAAATGCGTAGGTGG 59.128 50.000 0.00 0.00 0.00 4.61
2462 3531 2.287915 GCTGGTATCAAATGCGTAGGTG 59.712 50.000 0.00 0.00 0.00 4.00
2465 3534 3.457234 TGAGCTGGTATCAAATGCGTAG 58.543 45.455 0.00 0.00 0.00 3.51
2468 3537 2.938451 TCTTGAGCTGGTATCAAATGCG 59.062 45.455 0.00 0.00 36.30 4.73
2477 3546 0.898320 GCCACTCTCTTGAGCTGGTA 59.102 55.000 0.00 0.00 43.85 3.25
2487 3556 0.323816 TCGACCTCATGCCACTCTCT 60.324 55.000 0.00 0.00 0.00 3.10
2499 3568 3.760035 TTGCTCGCCCTCGACCTC 61.760 66.667 0.00 0.00 40.21 3.85
2602 3671 1.134530 GACGTTGAGACTCGGATGCG 61.135 60.000 0.00 0.00 0.00 4.73
2619 3688 0.690762 TAGCACCACCCTTTCCAGAC 59.309 55.000 0.00 0.00 0.00 3.51
2625 3694 3.157087 CAACTCAATAGCACCACCCTTT 58.843 45.455 0.00 0.00 0.00 3.11
2703 3772 2.089936 CAGGTAAACGTAGCGCGCA 61.090 57.895 35.10 16.82 46.11 6.09
2757 3826 1.588404 GACATGTAACATCCGCTGTCG 59.412 52.381 0.00 0.00 36.98 4.35
2840 3909 1.343465 CGAGTACACACCTCCCAGTTT 59.657 52.381 0.00 0.00 0.00 2.66
2896 3965 4.479993 CCTGAAGGCCTGCTCCGG 62.480 72.222 13.40 6.39 0.00 5.14
2930 3999 1.137675 CGATGGGTGCATCAGAGAAGA 59.862 52.381 0.00 0.00 0.00 2.87
2931 4000 1.579698 CGATGGGTGCATCAGAGAAG 58.420 55.000 0.00 0.00 0.00 2.85
2976 4047 6.323739 ACTGTGAAATAAAAGTGTCCAATGGT 59.676 34.615 0.00 0.00 0.00 3.55
3036 4110 2.816087 CAGAGGTGCATGGCATTATACC 59.184 50.000 13.80 13.80 41.91 2.73
3083 4228 4.755266 TCCACAAGGTAAGCTTCCTATC 57.245 45.455 15.17 0.00 34.56 2.08
3149 4294 1.152546 ACTGGCCAGTGGGGAAAAC 60.153 57.895 37.39 0.00 40.75 2.43
3183 4328 1.006832 CTGCGACAAGTAATTCCGGG 58.993 55.000 0.00 0.00 0.00 5.73
3215 4360 4.096382 CCTTCCATCCCAAATTACTTGTCG 59.904 45.833 0.00 0.00 32.65 4.35
3284 4429 4.082026 AGCAGAATGATGTAAAAAGGCCAC 60.082 41.667 5.01 0.00 39.69 5.01
3301 4446 7.771183 AGTTTAATGTGTCTTCAAAAGCAGAA 58.229 30.769 0.00 0.00 0.00 3.02
3302 4447 7.333528 AGTTTAATGTGTCTTCAAAAGCAGA 57.666 32.000 0.00 0.00 0.00 4.26
3303 4448 7.992180 AAGTTTAATGTGTCTTCAAAAGCAG 57.008 32.000 0.00 0.00 0.00 4.24
3304 4449 8.031864 TCAAAGTTTAATGTGTCTTCAAAAGCA 58.968 29.630 0.00 0.00 0.00 3.91
3305 4450 8.406172 TCAAAGTTTAATGTGTCTTCAAAAGC 57.594 30.769 0.00 0.00 0.00 3.51
3312 4457 9.758651 GGGTAAAATCAAAGTTTAATGTGTCTT 57.241 29.630 0.00 0.00 0.00 3.01
3313 4458 9.143155 AGGGTAAAATCAAAGTTTAATGTGTCT 57.857 29.630 0.00 0.00 0.00 3.41
3314 4459 9.758651 AAGGGTAAAATCAAAGTTTAATGTGTC 57.241 29.630 0.00 0.00 0.00 3.67
3356 4521 2.474526 GGTTTCAGCATGTCGAACATCG 60.475 50.000 0.00 0.00 36.53 3.84
3376 4541 9.300681 ACAACCATCATCCATATTGTAATAAGG 57.699 33.333 0.58 0.58 32.42 2.69
3427 4592 4.701651 CCATCCTCTTAACATGCTCAACAA 59.298 41.667 0.00 0.00 0.00 2.83
3430 4595 4.842531 TCCATCCTCTTAACATGCTCAA 57.157 40.909 0.00 0.00 0.00 3.02
3479 4644 3.596214 GGCAAGCTAGTACTGCTACAAA 58.404 45.455 16.73 0.00 40.22 2.83
3572 4746 2.030805 AGCGCATCAGAACCTTTGAAAC 60.031 45.455 11.47 0.00 0.00 2.78
3590 4764 2.325583 TTCAGGCCTACCAAATAGCG 57.674 50.000 3.98 0.00 39.06 4.26
3608 4782 2.556782 GGTAGCCCTAAAGCCCAAGTTT 60.557 50.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.