Multiple sequence alignment - TraesCS4B01G013200

Loading Multiple Alignment...

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 TraesCS4B01G013200 chr4B 100.000 4021 0 0 1 4021 9384797 9388817 0.000000e+00 7426.0
1 TraesCS4B01G013200 chr4B 88.439 173 12 4 3406 3572 9357531 9357361 6.810000e-48 202.0
2 TraesCS4B01G013200 chr4B 85.455 110 16 0 1681 1790 624862334 624862225 9.130000e-22 115.0
3 TraesCS4B01G013200 chr4B 100.000 37 0 0 3858 3894 9357285 9357249 7.210000e-08 69.4
4 TraesCS4B01G013200 chr4A 93.581 2913 136 24 146 3037 598438070 598435188 0.000000e+00 4296.0
5 TraesCS4B01G013200 chr4A 80.839 548 97 7 1048 1594 632989712 632990252 1.340000e-114 424.0
6 TraesCS4B01G013200 chr4A 80.762 551 98 7 1048 1597 632999846 632999303 1.340000e-114 424.0
7 TraesCS4B01G013200 chr4A 79.926 538 88 15 1048 1578 685834820 685835344 1.050000e-100 377.0
8 TraesCS4B01G013200 chr4A 92.720 261 11 1 3761 4021 598434389 598434137 1.770000e-98 370.0
9 TraesCS4B01G013200 chr4A 90.000 170 14 2 3419 3588 598434798 598434632 2.430000e-52 217.0
10 TraesCS4B01G013200 chr4A 88.889 180 4 6 3077 3242 598435057 598434880 1.460000e-49 207.0
11 TraesCS4B01G013200 chr4A 90.850 153 13 1 3611 3763 11275900 11276051 1.890000e-48 204.0
12 TraesCS4B01G013200 chr4A 90.196 153 15 0 3610 3762 736341850 736341698 2.450000e-47 200.0
13 TraesCS4B01G013200 chr4A 86.792 106 11 2 2163 2268 123275896 123275998 9.130000e-22 115.0
14 TraesCS4B01G013200 chr4A 82.258 124 15 6 2166 2287 246807129 246807247 2.560000e-17 100.0
15 TraesCS4B01G013200 chr4A 89.706 68 7 0 82 149 701348198 701348131 1.990000e-13 87.9
16 TraesCS4B01G013200 chr4D 94.956 2042 68 11 146 2168 5291253 5289228 0.000000e+00 3168.0
17 TraesCS4B01G013200 chr4D 96.265 589 12 5 2448 3030 5288750 5288166 0.000000e+00 957.0
18 TraesCS4B01G013200 chr4D 89.400 500 21 13 3057 3533 5288094 5287604 5.750000e-168 601.0
19 TraesCS4B01G013200 chr4D 94.505 182 10 0 3761 3942 5287230 5287049 8.510000e-72 281.0
20 TraesCS4B01G013200 chr4D 84.255 235 31 4 3372 3604 5236366 5236136 1.450000e-54 224.0
21 TraesCS4B01G013200 chr4D 87.273 110 11 2 3799 3905 5236117 5236008 5.460000e-24 122.0
22 TraesCS4B01G013200 chr4D 93.827 81 5 0 3940 4020 5286599 5286519 5.460000e-24 122.0
23 TraesCS4B01G013200 chr5B 81.569 548 93 7 1048 1594 677537460 677538000 2.850000e-121 446.0
24 TraesCS4B01G013200 chr5B 81.307 551 95 7 1048 1597 677545037 677544494 1.330000e-119 440.0
25 TraesCS4B01G013200 chr5B 80.360 555 93 12 1048 1597 643460763 643461306 1.350000e-109 407.0
26 TraesCS4B01G013200 chr5B 80.275 218 33 9 2162 2377 606923502 606923711 5.380000e-34 156.0
27 TraesCS4B01G013200 chr5D 81.939 526 84 9 1048 1572 537088083 537088598 6.170000e-118 435.0
28 TraesCS4B01G013200 chr5D 80.987 547 95 8 1048 1593 537162868 537162330 3.710000e-115 425.0
29 TraesCS4B01G013200 chr5D 80.360 555 93 12 1048 1597 512534366 512534909 1.350000e-109 407.0
30 TraesCS4B01G013200 chr5D 80.657 274 39 8 2160 2425 473469713 473469980 2.450000e-47 200.0
31 TraesCS4B01G013200 chr5D 87.248 149 15 4 4 149 543118920 543118773 2.490000e-37 167.0
32 TraesCS4B01G013200 chr5D 87.850 107 10 2 2162 2268 348955335 348955232 5.460000e-24 122.0
33 TraesCS4B01G013200 chr5D 87.805 82 7 2 69 149 42799930 42799851 4.280000e-15 93.5
34 TraesCS4B01G013200 chr5A 79.099 555 100 12 1048 1597 640724667 640725210 6.350000e-98 368.0
35 TraesCS4B01G013200 chr1B 94.156 154 9 0 3610 3763 623824570 623824417 6.720000e-58 235.0
36 TraesCS4B01G013200 chr1B 89.262 149 13 3 1 149 29972255 29972110 2.470000e-42 183.0
37 TraesCS4B01G013200 chr1B 85.047 107 13 2 2162 2268 336122854 336122957 5.500000e-19 106.0
38 TraesCS4B01G013200 chr3D 91.558 154 13 0 3610 3763 611903940 611903787 3.150000e-51 213.0
39 TraesCS4B01G013200 chr3D 90.728 151 10 1 3613 3763 347272783 347272929 8.810000e-47 198.0
40 TraesCS4B01G013200 chr3D 85.981 107 11 2 2162 2268 448339970 448340072 1.180000e-20 111.0
41 TraesCS4B01G013200 chr3D 100.000 28 0 0 964 991 410998977 410999004 7.000000e-03 52.8
42 TraesCS4B01G013200 chr3A 90.789 152 14 0 3612 3763 745728436 745728587 1.890000e-48 204.0
43 TraesCS4B01G013200 chr2A 90.196 153 15 0 3611 3763 550682130 550681978 2.450000e-47 200.0
44 TraesCS4B01G013200 chr1D 90.385 156 9 5 3612 3763 74389351 74389198 2.450000e-47 200.0
45 TraesCS4B01G013200 chr7D 89.103 156 15 2 3609 3764 52522939 52522786 4.100000e-45 193.0
46 TraesCS4B01G013200 chr7D 87.586 145 18 0 5 149 107820087 107819943 6.910000e-38 169.0
47 TraesCS4B01G013200 chr7D 81.890 127 15 6 5 125 136390551 136390675 2.560000e-17 100.0
48 TraesCS4B01G013200 chr7D 97.778 45 1 0 81 125 151525857 151525901 1.200000e-10 78.7
49 TraesCS4B01G013200 chr1A 88.764 89 8 2 72 160 564317457 564317543 1.530000e-19 108.0
50 TraesCS4B01G013200 chr7A 74.194 279 52 13 2158 2425 578444486 578444755 9.200000e-17 99.0
51 TraesCS4B01G013200 chr2D 86.747 83 9 2 79 160 622477110 622477191 1.540000e-14 91.6
52 TraesCS4B01G013200 chr7B 100.000 32 0 0 3874 3905 552706214 552706245 4.340000e-05 60.2
53 TraesCS4B01G013200 chr7B 100.000 32 0 0 3874 3905 552753202 552753233 4.340000e-05 60.2
54 TraesCS4B01G013200 chr7B 100.000 28 0 0 964 991 13817407 13817434 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 TraesCS4B01G013200 chr4B 9384797 9388817 4020 False 7426.0 7426 100.0000 1 4021 1 chr4B.!!$F1 4020
1 TraesCS4B01G013200 chr4A 598434137 598438070 3933 True 1272.5 4296 91.2975 146 4021 4 chr4A.!!$R4 3875
2 TraesCS4B01G013200 chr4A 632989712 632990252 540 False 424.0 424 80.8390 1048 1594 1 chr4A.!!$F4 546
3 TraesCS4B01G013200 chr4A 632999303 632999846 543 True 424.0 424 80.7620 1048 1597 1 chr4A.!!$R1 549
4 TraesCS4B01G013200 chr4A 685834820 685835344 524 False 377.0 377 79.9260 1048 1578 1 chr4A.!!$F5 530
5 TraesCS4B01G013200 chr4D 5286519 5291253 4734 True 1025.8 3168 93.7906 146 4020 5 chr4D.!!$R2 3874
6 TraesCS4B01G013200 chr5B 677537460 677538000 540 False 446.0 446 81.5690 1048 1594 1 chr5B.!!$F3 546
7 TraesCS4B01G013200 chr5B 677544494 677545037 543 True 440.0 440 81.3070 1048 1597 1 chr5B.!!$R1 549
8 TraesCS4B01G013200 chr5B 643460763 643461306 543 False 407.0 407 80.3600 1048 1597 1 chr5B.!!$F2 549
9 TraesCS4B01G013200 chr5D 537088083 537088598 515 False 435.0 435 81.9390 1048 1572 1 chr5D.!!$F3 524
10 TraesCS4B01G013200 chr5D 537162330 537162868 538 True 425.0 425 80.9870 1048 1593 1 chr5D.!!$R3 545
11 TraesCS4B01G013200 chr5D 512534366 512534909 543 False 407.0 407 80.3600 1048 1597 1 chr5D.!!$F2 549
12 TraesCS4B01G013200 chr5A 640724667 640725210 543 False 368.0 368 79.0990 1048 1597 1 chr5A.!!$F1 549

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
119 120 0.032130 AATCCCACGGATCGATGACG 59.968 55.000 0.54 10.24 42.27 4.35 F
737 746 0.516877 CAAGTATGCCCGTGTGTGTG 59.483 55.000 0.00 0.00 0.00 3.82 F
1645 1670 1.077086 TGGAATGTGCACCATGGCT 59.923 52.632 15.69 0.00 32.82 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1658 1683 0.106819 GGGCCACTGCTCAATCTGAT 60.107 55.0 4.39 0.00 38.13 2.90 R
1875 1900 0.392998 AGTATTCGTTGGCTGCCCTG 60.393 55.0 17.53 5.87 0.00 4.45 R
3071 3660 0.373716 CTGGTCGCCGTTATTCTTGC 59.626 55.0 0.00 0.00 0.00 4.01 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
64 65 9.921637 ATAATAAAATAAAATGTATGCCCACGG 57.078 29.630 0.00 0.00 0.00 4.94
100 101 4.267503 TGCGCACACGGACGTACA 62.268 61.111 5.66 0.00 40.57 2.90
101 102 3.031457 GCGCACACGGACGTACAA 61.031 61.111 0.30 0.00 40.57 2.41
102 103 2.377310 GCGCACACGGACGTACAAT 61.377 57.895 0.30 0.00 40.57 2.71
103 104 1.700029 CGCACACGGACGTACAATC 59.300 57.895 0.00 0.00 34.97 2.67
104 105 1.680105 CGCACACGGACGTACAATCC 61.680 60.000 0.00 3.46 34.97 3.01
105 106 1.356527 GCACACGGACGTACAATCCC 61.357 60.000 0.00 0.00 31.99 3.85
106 107 0.038067 CACACGGACGTACAATCCCA 60.038 55.000 0.00 0.00 31.99 4.37
107 108 0.037975 ACACGGACGTACAATCCCAC 60.038 55.000 0.00 0.00 31.99 4.61
108 109 1.074319 CACGGACGTACAATCCCACG 61.074 60.000 0.00 0.00 43.63 4.94
109 110 1.517694 CGGACGTACAATCCCACGG 60.518 63.158 0.00 0.00 42.35 4.94
110 111 1.892338 GGACGTACAATCCCACGGA 59.108 57.895 0.00 0.00 42.35 4.69
111 112 0.462789 GGACGTACAATCCCACGGAT 59.537 55.000 0.00 0.00 45.46 4.18
112 113 1.537562 GGACGTACAATCCCACGGATC 60.538 57.143 0.00 0.00 42.27 3.36
113 114 0.101759 ACGTACAATCCCACGGATCG 59.898 55.000 0.00 0.00 42.27 3.69
114 115 0.382873 CGTACAATCCCACGGATCGA 59.617 55.000 0.00 0.00 42.27 3.59
115 116 1.000607 CGTACAATCCCACGGATCGAT 60.001 52.381 0.00 0.00 42.27 3.59
116 117 2.404215 GTACAATCCCACGGATCGATG 58.596 52.381 0.54 0.00 42.27 3.84
117 118 1.119684 ACAATCCCACGGATCGATGA 58.880 50.000 0.54 0.00 42.27 2.92
118 119 1.202533 ACAATCCCACGGATCGATGAC 60.203 52.381 0.54 0.00 42.27 3.06
119 120 0.032130 AATCCCACGGATCGATGACG 59.968 55.000 0.54 10.24 42.27 4.35
120 121 1.107538 ATCCCACGGATCGATGACGT 61.108 55.000 16.37 16.37 38.09 4.34
123 124 2.104331 ACGGATCGATGACGTGGC 59.896 61.111 20.02 0.00 39.64 5.01
124 125 2.104132 CGGATCGATGACGTGGCA 59.896 61.111 0.54 0.00 40.69 4.92
125 126 2.230940 CGGATCGATGACGTGGCAC 61.231 63.158 7.79 7.79 40.69 5.01
126 127 1.883084 GGATCGATGACGTGGCACC 60.883 63.158 12.86 0.00 40.69 5.01
127 128 2.202743 ATCGATGACGTGGCACCG 60.203 61.111 12.86 9.47 40.69 4.94
130 131 3.788766 GATGACGTGGCACCGCAC 61.789 66.667 12.86 6.25 0.00 5.34
143 144 2.954868 CGCACGCGGGTAGATGAC 60.955 66.667 11.45 0.00 35.56 3.06
144 145 2.183300 GCACGCGGGTAGATGACA 59.817 61.111 11.45 0.00 0.00 3.58
149 150 1.956170 GCGGGTAGATGACATGGCG 60.956 63.158 0.00 0.00 0.00 5.69
214 216 1.099689 TGACGATGGACAGCGATACA 58.900 50.000 17.27 10.31 43.75 2.29
231 233 5.163913 GCGATACAGAAATACATCAGCCATC 60.164 44.000 0.00 0.00 0.00 3.51
259 261 3.141398 TCAAGCCTCACACAATCTCAAC 58.859 45.455 0.00 0.00 0.00 3.18
262 264 1.511850 CCTCACACAATCTCAACGCA 58.488 50.000 0.00 0.00 0.00 5.24
263 265 2.079158 CCTCACACAATCTCAACGCAT 58.921 47.619 0.00 0.00 0.00 4.73
264 266 2.485426 CCTCACACAATCTCAACGCATT 59.515 45.455 0.00 0.00 0.00 3.56
315 321 3.118811 ACTCTGCTAAATCTCAGCTGACC 60.119 47.826 13.74 0.00 40.65 4.02
318 324 2.197577 GCTAAATCTCAGCTGACCGAC 58.802 52.381 13.74 0.00 36.07 4.79
320 326 3.066900 GCTAAATCTCAGCTGACCGACTA 59.933 47.826 13.74 4.66 36.07 2.59
322 328 3.512033 AATCTCAGCTGACCGACTAAC 57.488 47.619 13.74 0.00 0.00 2.34
325 331 0.956633 TCAGCTGACCGACTAACGTT 59.043 50.000 13.74 5.88 40.78 3.99
326 332 2.153645 TCAGCTGACCGACTAACGTTA 58.846 47.619 13.74 7.94 40.78 3.18
434 440 1.350019 ACCTCCCTTTGTTCTTACGGG 59.650 52.381 0.00 0.00 36.21 5.28
435 441 1.626825 CCTCCCTTTGTTCTTACGGGA 59.373 52.381 0.00 0.00 41.47 5.14
436 442 2.614734 CCTCCCTTTGTTCTTACGGGAC 60.615 54.545 0.00 0.00 38.95 4.46
437 443 2.302157 CTCCCTTTGTTCTTACGGGACT 59.698 50.000 0.00 0.00 38.95 3.85
438 444 2.301009 TCCCTTTGTTCTTACGGGACTC 59.699 50.000 0.00 0.00 38.95 3.36
439 445 2.614734 CCCTTTGTTCTTACGGGACTCC 60.615 54.545 0.00 0.00 37.05 3.85
440 446 2.302157 CCTTTGTTCTTACGGGACTCCT 59.698 50.000 0.00 0.00 0.00 3.69
441 447 3.512724 CCTTTGTTCTTACGGGACTCCTA 59.487 47.826 0.00 0.00 0.00 2.94
447 453 4.096190 TCTTACGGGACTCCTATACCTG 57.904 50.000 0.00 0.00 36.28 4.00
460 466 1.863662 ATACCTGCCTATCGCCGACG 61.864 60.000 0.00 0.00 42.01 5.12
584 591 5.613358 AGCTTCCAAGTAAATTTCACGAG 57.387 39.130 0.00 0.00 0.00 4.18
585 592 4.083271 AGCTTCCAAGTAAATTTCACGAGC 60.083 41.667 0.00 0.00 0.00 5.03
711 720 5.642919 TGTATGTTTGTCCCGGTGTATTAAC 59.357 40.000 0.00 0.00 0.00 2.01
718 727 4.183865 GTCCCGGTGTATTAACCTTGTAC 58.816 47.826 0.00 0.00 38.14 2.90
737 746 0.516877 CAAGTATGCCCGTGTGTGTG 59.483 55.000 0.00 0.00 0.00 3.82
742 751 2.050168 GCCCGTGTGTGTGCAATG 60.050 61.111 0.00 0.00 0.00 2.82
766 775 4.985409 GGTGAGAAATGTATGATCCGAGTC 59.015 45.833 0.00 0.00 0.00 3.36
823 832 3.452024 GACGGAGGCTACGAGCGAC 62.452 68.421 28.69 7.64 43.62 5.19
826 835 2.023041 GAGGCTACGAGCGACGAC 59.977 66.667 12.62 0.00 43.62 4.34
840 849 1.416373 GACGACGACAGTTTTCCCTC 58.584 55.000 0.00 0.00 0.00 4.30
844 853 2.605338 CGACGACAGTTTTCCCTCGTTA 60.605 50.000 0.00 0.00 39.40 3.18
1634 1659 4.634703 TGCACCGGCGTGGAATGT 62.635 61.111 6.01 0.00 45.35 2.71
1645 1670 1.077086 TGGAATGTGCACCATGGCT 59.923 52.632 15.69 0.00 32.82 4.75
1650 1675 2.282391 GTGCACCATGGCTGGACA 60.282 61.111 23.94 10.22 46.37 4.02
1657 1682 1.340405 ACCATGGCTGGACAGTTGATC 60.340 52.381 13.04 0.00 46.37 2.92
1658 1683 1.340308 CCATGGCTGGACAGTTGATCA 60.340 52.381 0.00 0.00 46.37 2.92
1662 1687 2.286872 GGCTGGACAGTTGATCATCAG 58.713 52.381 6.55 0.88 0.00 2.90
1665 1690 4.197750 GCTGGACAGTTGATCATCAGATT 58.802 43.478 6.55 0.00 33.72 2.40
1668 1693 5.425630 TGGACAGTTGATCATCAGATTGAG 58.574 41.667 6.55 0.00 33.72 3.02
1875 1900 2.741517 GCAGGAGAAGCTCTCAAAGTTC 59.258 50.000 13.06 0.00 45.12 3.01
1881 1906 0.767375 AGCTCTCAAAGTTCAGGGCA 59.233 50.000 8.89 0.00 38.75 5.36
1914 1939 1.552337 TCTCTGCTGTCCATGGAGTTC 59.448 52.381 16.81 3.99 0.00 3.01
1995 2020 1.406205 GCCTTCTACAGCCAGAACCTC 60.406 57.143 0.00 0.00 31.34 3.85
2139 2164 3.310860 CTACTGGGTCACCGTGGCC 62.311 68.421 14.20 14.20 42.67 5.36
2184 2209 1.627329 GTACTCCCTCCGGTCCTTTTT 59.373 52.381 0.00 0.00 0.00 1.94
2210 2235 8.798859 AGTCAGCATATAAGTTTTTGTCTGAT 57.201 30.769 0.00 0.00 31.82 2.90
2211 2236 9.890629 AGTCAGCATATAAGTTTTTGTCTGATA 57.109 29.630 0.00 0.00 31.82 2.15
2276 2301 9.941325 AATTATCAACATTCACAAAGCCAAATA 57.059 25.926 0.00 0.00 0.00 1.40
2388 2420 5.163733 GGTACGAAGTTTGACTGGACAAAAA 60.164 40.000 0.00 0.00 37.78 1.94
2389 2421 5.576447 ACGAAGTTTGACTGGACAAAAAT 57.424 34.783 0.00 0.00 37.78 1.82
2393 2425 7.072030 CGAAGTTTGACTGGACAAAAATCTAG 58.928 38.462 0.00 0.00 40.62 2.43
2401 2433 4.196193 TGGACAAAAATCTAGTATGCGGG 58.804 43.478 0.00 0.00 0.00 6.13
2409 2441 6.937436 AAATCTAGTATGCGGGGTAAAAAG 57.063 37.500 0.00 0.00 0.00 2.27
2413 2445 0.331954 TATGCGGGGTAAAAAGGGCA 59.668 50.000 0.00 0.00 34.60 5.36
2460 2951 2.184322 GGCTCATGCGAGACCGAA 59.816 61.111 0.00 0.00 42.05 4.30
2509 3000 9.752961 CACATTAATTTGAGCATCCATGAATTA 57.247 29.630 0.00 0.00 0.00 1.40
2510 3001 9.754382 ACATTAATTTGAGCATCCATGAATTAC 57.246 29.630 0.00 0.00 0.00 1.89
2553 3049 4.043310 TCCTTGGTTTCTTCATGATGTCCT 59.957 41.667 8.33 0.00 0.00 3.85
2657 3153 1.508632 TCTTCTTCGCAAACTTCGGG 58.491 50.000 0.00 0.00 0.00 5.14
3030 3526 4.971830 CGTCCATGAATTAATGCATGACAC 59.028 41.667 30.59 24.32 43.43 3.67
3031 3527 5.284079 GTCCATGAATTAATGCATGACACC 58.716 41.667 30.59 15.03 43.43 4.16
3032 3528 4.954826 TCCATGAATTAATGCATGACACCA 59.045 37.500 30.59 11.28 43.43 4.17
3033 3529 5.045215 CCATGAATTAATGCATGACACCAC 58.955 41.667 30.59 0.00 43.43 4.16
3048 3583 4.401202 TGACACCACGCATCTTATCTTCTA 59.599 41.667 0.00 0.00 0.00 2.10
3049 3584 5.069119 TGACACCACGCATCTTATCTTCTAT 59.931 40.000 0.00 0.00 0.00 1.98
3050 3585 6.264518 TGACACCACGCATCTTATCTTCTATA 59.735 38.462 0.00 0.00 0.00 1.31
3051 3586 7.039714 TGACACCACGCATCTTATCTTCTATAT 60.040 37.037 0.00 0.00 0.00 0.86
3052 3587 7.316640 ACACCACGCATCTTATCTTCTATATC 58.683 38.462 0.00 0.00 0.00 1.63
3054 3589 7.487509 CACCACGCATCTTATCTTCTATATCAG 59.512 40.741 0.00 0.00 0.00 2.90
3055 3590 6.977502 CCACGCATCTTATCTTCTATATCAGG 59.022 42.308 0.00 0.00 0.00 3.86
3056 3591 6.977502 CACGCATCTTATCTTCTATATCAGGG 59.022 42.308 0.00 0.00 0.00 4.45
3058 3593 7.397476 ACGCATCTTATCTTCTATATCAGGGAA 59.603 37.037 0.00 0.00 0.00 3.97
3059 3594 8.420222 CGCATCTTATCTTCTATATCAGGGAAT 58.580 37.037 0.00 0.00 0.00 3.01
3071 3660 4.542906 ATCAGGGAATTTAGAAAGGGGG 57.457 45.455 0.00 0.00 0.00 5.40
3085 3680 2.478033 GGGGGCAAGAATAACGGCG 61.478 63.158 4.80 4.80 0.00 6.46
3211 3824 9.787532 CCATTGTGTTGTTAAGGTTATATTGAG 57.212 33.333 0.00 0.00 0.00 3.02
3242 3856 5.464722 GTGTGGATGTATGAGCATTGACTAG 59.535 44.000 0.00 0.00 0.00 2.57
3357 3976 9.855021 AAGTTTACAGAATTAAATACCATGCAC 57.145 29.630 0.00 0.00 0.00 4.57
3371 3990 0.528466 ATGCACGTCGAGTAGGCATG 60.528 55.000 11.55 0.00 39.88 4.06
3372 3991 2.517450 GCACGTCGAGTAGGCATGC 61.517 63.158 9.90 9.90 0.00 4.06
3373 3992 1.153842 CACGTCGAGTAGGCATGCA 60.154 57.895 21.36 0.00 0.00 3.96
3374 3993 0.528466 CACGTCGAGTAGGCATGCAT 60.528 55.000 21.36 16.31 0.00 3.96
3379 3998 3.793492 CGTCGAGTAGGCATGCATATATG 59.207 47.826 21.36 8.45 0.00 1.78
3445 4064 8.268850 ATTGCATCTCAATAAGTTAACGAACT 57.731 30.769 0.00 0.00 43.24 3.01
3452 4071 9.362539 TCTCAATAAGTTAACGAACTGGTATTC 57.637 33.333 0.00 0.00 45.50 1.75
3453 4072 9.367444 CTCAATAAGTTAACGAACTGGTATTCT 57.633 33.333 0.00 0.00 45.50 2.40
3502 4123 6.346678 CGAACAGCTAGAAAGAACAAACTACC 60.347 42.308 0.00 0.00 0.00 3.18
3534 4155 4.039124 ACAATCCTGCTTTTTGGAACGAAT 59.961 37.500 0.00 0.00 35.81 3.34
3535 4156 4.871933 ATCCTGCTTTTTGGAACGAATT 57.128 36.364 0.00 0.00 35.81 2.17
3536 4157 3.976169 TCCTGCTTTTTGGAACGAATTG 58.024 40.909 0.00 0.00 0.00 2.32
3556 4177 6.811253 ATTGTTAAGCTGGTAAACATTCGA 57.189 33.333 0.00 0.00 33.44 3.71
3581 4202 4.922471 AAATCGAGTAGGCTTAGACTCC 57.078 45.455 9.69 0.00 39.15 3.85
3593 4214 2.151502 TAGACTCCCTCTGAAGGCTG 57.848 55.000 0.00 0.00 41.85 4.85
3596 4217 1.221293 CTCCCTCTGAAGGCTGCTG 59.779 63.158 0.00 0.00 41.85 4.41
3597 4218 2.254737 CTCCCTCTGAAGGCTGCTGG 62.255 65.000 0.00 0.00 41.85 4.85
3599 4220 1.078567 CCTCTGAAGGCTGCTGGTC 60.079 63.158 0.00 0.00 35.37 4.02
3600 4221 1.447489 CTCTGAAGGCTGCTGGTCG 60.447 63.158 0.00 0.00 0.00 4.79
3601 4222 1.881903 CTCTGAAGGCTGCTGGTCGA 61.882 60.000 0.00 0.00 0.00 4.20
3602 4223 1.004560 CTGAAGGCTGCTGGTCGAA 60.005 57.895 0.00 0.00 0.00 3.71
3604 4225 2.032681 AAGGCTGCTGGTCGAACC 59.967 61.111 0.00 0.00 39.22 3.62
3632 4253 3.569250 TTTTTAGAAATGGAGGCGTGC 57.431 42.857 0.00 0.00 0.00 5.34
3633 4254 1.459450 TTTAGAAATGGAGGCGTGCC 58.541 50.000 1.67 1.67 0.00 5.01
3650 4300 3.882326 CCCCGGCCTCTGCATCAT 61.882 66.667 0.00 0.00 40.13 2.45
3651 4301 2.593725 CCCGGCCTCTGCATCATG 60.594 66.667 0.00 0.00 40.13 3.07
3653 4303 1.072678 CCGGCCTCTGCATCATGAT 59.927 57.895 1.18 1.18 40.13 2.45
3654 4304 1.235281 CCGGCCTCTGCATCATGATG 61.235 60.000 28.04 28.04 41.60 3.07
3666 4316 0.958822 TCATGATGATGCATGCAGCC 59.041 50.000 31.30 22.02 44.08 4.85
3668 4318 1.273327 CATGATGATGCATGCAGCCAT 59.727 47.619 31.30 29.37 44.83 4.40
3669 4319 0.958822 TGATGATGCATGCAGCCATC 59.041 50.000 35.18 35.18 44.83 3.51
3670 4320 1.248486 GATGATGCATGCAGCCATCT 58.752 50.000 34.86 20.95 44.83 2.90
3671 4321 1.613925 GATGATGCATGCAGCCATCTT 59.386 47.619 34.86 23.70 44.83 2.40
3672 4322 2.351706 TGATGCATGCAGCCATCTTA 57.648 45.000 31.30 10.43 44.83 2.10
3673 4323 2.871453 TGATGCATGCAGCCATCTTAT 58.129 42.857 31.30 9.02 44.83 1.73
3674 4324 3.227614 TGATGCATGCAGCCATCTTATT 58.772 40.909 31.30 8.21 44.83 1.40
3676 4326 4.828387 TGATGCATGCAGCCATCTTATTAA 59.172 37.500 31.30 7.33 44.83 1.40
3678 4328 4.935702 TGCATGCAGCCATCTTATTAAAC 58.064 39.130 18.46 0.00 44.83 2.01
3679 4329 4.401837 TGCATGCAGCCATCTTATTAAACA 59.598 37.500 18.46 0.00 44.83 2.83
3685 4335 5.979517 GCAGCCATCTTATTAAACAATCCAC 59.020 40.000 0.00 0.00 0.00 4.02
3686 4336 6.201517 CAGCCATCTTATTAAACAATCCACG 58.798 40.000 0.00 0.00 0.00 4.94
3695 4345 9.498307 CTTATTAAACAATCCACGAAATACCAC 57.502 33.333 0.00 0.00 0.00 4.16
3698 4348 5.776173 AACAATCCACGAAATACCACAAA 57.224 34.783 0.00 0.00 0.00 2.83
3699 4349 5.371115 ACAATCCACGAAATACCACAAAG 57.629 39.130 0.00 0.00 0.00 2.77
3701 4351 5.300792 ACAATCCACGAAATACCACAAAGTT 59.699 36.000 0.00 0.00 0.00 2.66
3705 4355 7.330900 TCCACGAAATACCACAAAGTTTTAA 57.669 32.000 0.00 0.00 0.00 1.52
3708 4358 8.536407 CCACGAAATACCACAAAGTTTTAAAAG 58.464 33.333 0.00 0.00 0.00 2.27
3709 4359 9.078753 CACGAAATACCACAAAGTTTTAAAAGT 57.921 29.630 0.00 1.03 0.00 2.66
3711 4361 9.078753 CGAAATACCACAAAGTTTTAAAAGTGT 57.921 29.630 9.02 7.39 0.00 3.55
3719 4369 8.583765 CACAAAGTTTTAAAAGTGTTACAGCTC 58.416 33.333 9.02 0.00 0.00 4.09
3721 4371 5.507974 AGTTTTAAAAGTGTTACAGCTCGC 58.492 37.500 7.49 0.00 0.00 5.03
3749 4399 6.542852 CGGAGCGAATCAAGAAAATAAAAGA 58.457 36.000 0.00 0.00 0.00 2.52
3750 4400 6.684555 CGGAGCGAATCAAGAAAATAAAAGAG 59.315 38.462 0.00 0.00 0.00 2.85
3753 4403 8.956617 AGCGAATCAAGAAAATAAAAGAGAAC 57.043 30.769 0.00 0.00 0.00 3.01
3754 4404 8.787852 AGCGAATCAAGAAAATAAAAGAGAACT 58.212 29.630 0.00 0.00 0.00 3.01
3819 4620 3.177920 GAGCACGACAGAGCAGCG 61.178 66.667 0.00 0.00 36.39 5.18
3924 4725 1.532090 CGTGAGTGAGCGACTATGACC 60.532 57.143 0.00 0.00 33.83 4.02
3998 5251 2.856760 TCTTGGTAGGCTGATCTCCT 57.143 50.000 11.05 11.05 37.72 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.921637 CCGTGGGCATACATTTTATTTTATTAT 57.078 29.630 0.00 0.00 0.00 1.28
77 78 2.125713 TCCGTGTGCGCACCTATG 60.126 61.111 35.72 23.18 42.39 2.23
78 79 2.125673 GTCCGTGTGCGCACCTAT 60.126 61.111 35.72 0.00 42.39 2.57
79 80 4.710695 CGTCCGTGTGCGCACCTA 62.711 66.667 35.72 17.55 42.39 3.08
82 83 3.759828 GTACGTCCGTGTGCGCAC 61.760 66.667 33.11 33.11 41.97 5.34
83 84 3.769875 TTGTACGTCCGTGTGCGCA 62.770 57.895 5.66 5.66 36.67 6.09
84 85 2.274834 GATTGTACGTCCGTGTGCGC 62.275 60.000 0.00 0.00 36.67 6.09
85 86 1.680105 GGATTGTACGTCCGTGTGCG 61.680 60.000 1.98 0.00 37.95 5.34
86 87 1.356527 GGGATTGTACGTCCGTGTGC 61.357 60.000 1.98 0.00 36.58 4.57
87 88 0.038067 TGGGATTGTACGTCCGTGTG 60.038 55.000 1.98 0.00 36.58 3.82
88 89 0.037975 GTGGGATTGTACGTCCGTGT 60.038 55.000 1.98 0.00 36.58 4.49
89 90 1.074319 CGTGGGATTGTACGTCCGTG 61.074 60.000 1.98 1.04 36.58 4.94
90 91 1.213537 CGTGGGATTGTACGTCCGT 59.786 57.895 10.08 0.00 36.58 4.69
91 92 1.517694 CCGTGGGATTGTACGTCCG 60.518 63.158 10.08 1.28 38.56 4.79
92 93 0.462789 ATCCGTGGGATTGTACGTCC 59.537 55.000 8.26 8.26 39.79 4.79
93 94 1.849097 GATCCGTGGGATTGTACGTC 58.151 55.000 0.00 0.00 43.27 4.34
94 95 0.101759 CGATCCGTGGGATTGTACGT 59.898 55.000 0.00 0.00 43.27 3.57
95 96 0.382873 TCGATCCGTGGGATTGTACG 59.617 55.000 10.85 4.85 43.27 3.67
96 97 2.035449 TCATCGATCCGTGGGATTGTAC 59.965 50.000 10.85 0.00 43.27 2.90
97 98 2.035449 GTCATCGATCCGTGGGATTGTA 59.965 50.000 10.85 0.74 43.27 2.41
98 99 1.119684 TCATCGATCCGTGGGATTGT 58.880 50.000 10.85 0.00 43.27 2.71
99 100 1.502231 GTCATCGATCCGTGGGATTG 58.498 55.000 0.00 5.65 43.27 2.67
100 101 0.032130 CGTCATCGATCCGTGGGATT 59.968 55.000 0.00 0.00 43.27 3.01
101 102 1.107538 ACGTCATCGATCCGTGGGAT 61.108 55.000 16.40 0.00 46.28 3.85
102 103 1.751544 ACGTCATCGATCCGTGGGA 60.752 57.895 16.40 0.00 40.62 4.37
103 104 1.588932 CACGTCATCGATCCGTGGG 60.589 63.158 27.39 12.21 45.97 4.61
104 105 3.997561 CACGTCATCGATCCGTGG 58.002 61.111 27.39 15.55 45.97 4.94
106 107 2.104331 GCCACGTCATCGATCCGT 59.896 61.111 12.53 12.53 40.62 4.69
107 108 2.104132 TGCCACGTCATCGATCCG 59.896 61.111 11.37 11.37 40.62 4.18
108 109 1.883084 GGTGCCACGTCATCGATCC 60.883 63.158 0.00 0.00 40.62 3.36
109 110 2.230940 CGGTGCCACGTCATCGATC 61.231 63.158 3.99 0.00 42.76 3.69
110 111 2.202743 CGGTGCCACGTCATCGAT 60.203 61.111 3.99 0.00 42.76 3.59
113 114 3.788766 GTGCGGTGCCACGTCATC 61.789 66.667 0.00 0.00 35.98 2.92
126 127 2.954020 ATGTCATCTACCCGCGTGCG 62.954 60.000 4.92 7.38 39.44 5.34
127 128 1.227263 ATGTCATCTACCCGCGTGC 60.227 57.895 4.92 0.00 0.00 5.34
128 129 0.875908 CCATGTCATCTACCCGCGTG 60.876 60.000 4.92 0.00 0.00 5.34
129 130 1.441729 CCATGTCATCTACCCGCGT 59.558 57.895 4.92 0.00 0.00 6.01
130 131 1.956170 GCCATGTCATCTACCCGCG 60.956 63.158 0.00 0.00 0.00 6.46
131 132 1.956170 CGCCATGTCATCTACCCGC 60.956 63.158 0.00 0.00 0.00 6.13
132 133 1.956170 GCGCCATGTCATCTACCCG 60.956 63.158 0.00 0.00 0.00 5.28
133 134 1.956170 CGCGCCATGTCATCTACCC 60.956 63.158 0.00 0.00 0.00 3.69
134 135 2.598632 GCGCGCCATGTCATCTACC 61.599 63.158 23.24 0.00 0.00 3.18
135 136 2.598632 GGCGCGCCATGTCATCTAC 61.599 63.158 43.55 12.83 35.81 2.59
136 137 2.280119 GGCGCGCCATGTCATCTA 60.280 61.111 43.55 0.00 35.81 1.98
214 216 3.470709 CCGTGATGGCTGATGTATTTCT 58.529 45.455 0.00 0.00 0.00 2.52
259 261 0.381445 TGGCCATTCGATCAAATGCG 59.619 50.000 0.00 0.00 35.68 4.73
262 264 3.956199 AGTTCATGGCCATTCGATCAAAT 59.044 39.130 17.92 0.00 0.00 2.32
263 265 3.355378 AGTTCATGGCCATTCGATCAAA 58.645 40.909 17.92 0.00 0.00 2.69
264 266 3.003394 AGTTCATGGCCATTCGATCAA 57.997 42.857 17.92 0.00 0.00 2.57
315 321 5.051240 AGACTGTTTTGCTTAACGTTAGTCG 60.051 40.000 8.23 2.91 46.00 4.18
318 324 7.964545 AAAAGACTGTTTTGCTTAACGTTAG 57.035 32.000 8.23 4.48 0.00 2.34
434 440 2.424246 GCGATAGGCAGGTATAGGAGTC 59.576 54.545 0.00 0.00 42.87 3.36
435 441 2.448453 GCGATAGGCAGGTATAGGAGT 58.552 52.381 0.00 0.00 42.87 3.85
565 572 4.059511 TCGCTCGTGAAATTTACTTGGAA 58.940 39.130 0.00 0.00 0.00 3.53
584 591 2.495939 CGTGTGCTTATTTTGTCTCGC 58.504 47.619 0.00 0.00 0.00 5.03
585 592 2.495939 GCGTGTGCTTATTTTGTCTCG 58.504 47.619 0.00 0.00 38.39 4.04
711 720 2.006888 CACGGGCATACTTGTACAAGG 58.993 52.381 33.11 19.78 42.53 3.61
718 727 0.516877 CACACACACGGGCATACTTG 59.483 55.000 0.00 0.00 0.00 3.16
737 746 5.278660 GGATCATACATTTCTCACCCATTGC 60.279 44.000 0.00 0.00 0.00 3.56
742 751 4.202264 ACTCGGATCATACATTTCTCACCC 60.202 45.833 0.00 0.00 0.00 4.61
766 775 0.443869 GGCAGCATATTCCGCATACG 59.556 55.000 0.00 0.00 39.67 3.06
823 832 0.318445 ACGAGGGAAAACTGTCGTCG 60.318 55.000 7.48 7.48 41.68 5.12
826 835 2.064014 GGTAACGAGGGAAAACTGTCG 58.936 52.381 0.00 0.00 38.40 4.35
844 853 4.070552 GAAGCAGAGGACGGCGGT 62.071 66.667 13.24 0.00 41.73 5.68
998 1023 3.125376 GCCCCATTCTCCGCCATCT 62.125 63.158 0.00 0.00 0.00 2.90
1551 1576 1.215655 CGGCGAAGATGATTCCGACC 61.216 60.000 0.00 0.00 42.43 4.79
1557 1582 1.227674 GAGGCCGGCGAAGATGATT 60.228 57.895 22.54 0.00 0.00 2.57
1630 1655 3.702802 CCAGCCATGGTGCACATT 58.297 55.556 20.43 1.46 42.17 2.71
1645 1670 5.425196 TCAATCTGATGATCAACTGTCCA 57.575 39.130 0.00 0.00 31.51 4.02
1650 1675 4.876679 CACTGCTCAATCTGATGATCAACT 59.123 41.667 0.00 0.00 31.51 3.16
1657 1682 1.022735 GGCCACTGCTCAATCTGATG 58.977 55.000 0.00 0.00 37.74 3.07
1658 1683 0.106819 GGGCCACTGCTCAATCTGAT 60.107 55.000 4.39 0.00 38.13 2.90
1662 1687 2.825836 CCGGGCCACTGCTCAATC 60.826 66.667 4.39 0.00 38.12 2.67
1869 1894 1.455383 CGTTGGCTGCCCTGAACTTT 61.455 55.000 17.53 0.00 0.00 2.66
1875 1900 0.392998 AGTATTCGTTGGCTGCCCTG 60.393 55.000 17.53 5.87 0.00 4.45
1881 1906 1.827969 AGCAGAGAGTATTCGTTGGCT 59.172 47.619 0.00 0.00 0.00 4.75
1929 1954 1.971167 GGTGCCGATGAGGTGCAAA 60.971 57.895 0.00 0.00 43.70 3.68
1995 2020 3.221771 TGGGAAGATGTCCTTTTGTGTG 58.778 45.455 0.00 0.00 46.92 3.82
2184 2209 9.890629 ATCAGACAAAAACTTATATGCTGACTA 57.109 29.630 0.00 0.00 32.74 2.59
2211 2236 9.522804 GTTCGATGAAAGTAGAGATACTTTGAT 57.477 33.333 15.94 13.43 46.66 2.57
2216 2241 9.175312 TGTAAGTTCGATGAAAGTAGAGATACT 57.825 33.333 0.00 0.00 0.00 2.12
2250 2275 8.851541 ATTTGGCTTTGTGAATGTTGATAATT 57.148 26.923 0.00 0.00 0.00 1.40
2251 2276 9.941325 TTATTTGGCTTTGTGAATGTTGATAAT 57.059 25.926 0.00 0.00 0.00 1.28
2252 2277 9.770097 TTTATTTGGCTTTGTGAATGTTGATAA 57.230 25.926 0.00 0.00 0.00 1.75
2352 2377 9.881529 GTCAAACTTCGTACCAAATTTATGTTA 57.118 29.630 0.00 0.00 0.00 2.41
2354 2379 8.073768 CAGTCAAACTTCGTACCAAATTTATGT 58.926 33.333 0.00 0.00 0.00 2.29
2355 2380 7.537306 CCAGTCAAACTTCGTACCAAATTTATG 59.463 37.037 0.00 0.00 0.00 1.90
2356 2381 7.446013 TCCAGTCAAACTTCGTACCAAATTTAT 59.554 33.333 0.00 0.00 0.00 1.40
2357 2382 6.766944 TCCAGTCAAACTTCGTACCAAATTTA 59.233 34.615 0.00 0.00 0.00 1.40
2360 2385 4.514066 GTCCAGTCAAACTTCGTACCAAAT 59.486 41.667 0.00 0.00 0.00 2.32
2363 2388 2.431419 TGTCCAGTCAAACTTCGTACCA 59.569 45.455 0.00 0.00 0.00 3.25
2364 2389 3.102052 TGTCCAGTCAAACTTCGTACC 57.898 47.619 0.00 0.00 0.00 3.34
2365 2390 5.473796 TTTTGTCCAGTCAAACTTCGTAC 57.526 39.130 0.00 0.00 37.10 3.67
2366 2391 6.540914 AGATTTTTGTCCAGTCAAACTTCGTA 59.459 34.615 0.00 0.00 37.10 3.43
2368 2393 5.821204 AGATTTTTGTCCAGTCAAACTTCG 58.179 37.500 0.00 0.00 37.10 3.79
2369 2394 7.931275 ACTAGATTTTTGTCCAGTCAAACTTC 58.069 34.615 0.00 0.00 37.10 3.01
2388 2420 4.202430 CCCTTTTTACCCCGCATACTAGAT 60.202 45.833 0.00 0.00 0.00 1.98
2389 2421 3.135167 CCCTTTTTACCCCGCATACTAGA 59.865 47.826 0.00 0.00 0.00 2.43
2393 2425 0.742505 GCCCTTTTTACCCCGCATAC 59.257 55.000 0.00 0.00 0.00 2.39
2401 2433 0.702316 TCCCTCCTGCCCTTTTTACC 59.298 55.000 0.00 0.00 0.00 2.85
2409 2441 1.076485 TACGTACTCCCTCCTGCCC 60.076 63.158 0.00 0.00 0.00 5.36
2413 2445 4.567327 GCATATAGGTACGTACTCCCTCCT 60.567 50.000 24.07 14.44 0.00 3.69
2453 2944 7.467675 GTGTAACAAAACTAACCAATTCGGTCT 60.468 37.037 0.83 0.00 42.81 3.85
2460 2951 7.556996 TGTGTAGGTGTAACAAAACTAACCAAT 59.443 33.333 0.00 0.00 39.98 3.16
2509 3000 1.065854 GCTGGATCAAGTACCTGCAGT 60.066 52.381 13.81 3.45 45.76 4.40
2510 3001 1.661341 GCTGGATCAAGTACCTGCAG 58.339 55.000 6.78 6.78 45.76 4.41
2553 3049 2.290832 TGCCCATCACTAGCATGAACAA 60.291 45.455 0.00 0.00 30.82 2.83
2612 3108 1.591594 CGCGTACAGGATGGCGAAT 60.592 57.895 0.00 0.00 45.02 3.34
2657 3153 2.521708 AAGGTGGTGCTGTTGGGC 60.522 61.111 0.00 0.00 0.00 5.36
3030 3526 6.977502 CCTGATATAGAAGATAAGATGCGTGG 59.022 42.308 0.00 0.00 0.00 4.94
3031 3527 6.977502 CCCTGATATAGAAGATAAGATGCGTG 59.022 42.308 0.00 0.00 0.00 5.34
3032 3528 6.892456 TCCCTGATATAGAAGATAAGATGCGT 59.108 38.462 0.00 0.00 0.00 5.24
3033 3529 7.340122 TCCCTGATATAGAAGATAAGATGCG 57.660 40.000 0.00 0.00 0.00 4.73
3048 3583 5.459683 GCCCCCTTTCTAAATTCCCTGATAT 60.460 44.000 0.00 0.00 0.00 1.63
3049 3584 4.141018 GCCCCCTTTCTAAATTCCCTGATA 60.141 45.833 0.00 0.00 0.00 2.15
3050 3585 3.374208 GCCCCCTTTCTAAATTCCCTGAT 60.374 47.826 0.00 0.00 0.00 2.90
3051 3586 2.024369 GCCCCCTTTCTAAATTCCCTGA 60.024 50.000 0.00 0.00 0.00 3.86
3052 3587 2.292192 TGCCCCCTTTCTAAATTCCCTG 60.292 50.000 0.00 0.00 0.00 4.45
3054 3589 2.543037 TGCCCCCTTTCTAAATTCCC 57.457 50.000 0.00 0.00 0.00 3.97
3055 3590 3.708451 TCTTGCCCCCTTTCTAAATTCC 58.292 45.455 0.00 0.00 0.00 3.01
3056 3591 5.939764 ATTCTTGCCCCCTTTCTAAATTC 57.060 39.130 0.00 0.00 0.00 2.17
3058 3593 5.359860 CGTTATTCTTGCCCCCTTTCTAAAT 59.640 40.000 0.00 0.00 0.00 1.40
3059 3594 4.703093 CGTTATTCTTGCCCCCTTTCTAAA 59.297 41.667 0.00 0.00 0.00 1.85
3062 3651 2.620627 CCGTTATTCTTGCCCCCTTTCT 60.621 50.000 0.00 0.00 0.00 2.52
3071 3660 0.373716 CTGGTCGCCGTTATTCTTGC 59.626 55.000 0.00 0.00 0.00 4.01
3159 3767 5.126067 GGTATCACACACAAGCAATCCTAT 58.874 41.667 0.00 0.00 0.00 2.57
3211 3824 4.455533 TGCTCATACATCCACACTGAAAAC 59.544 41.667 0.00 0.00 0.00 2.43
3212 3825 4.650734 TGCTCATACATCCACACTGAAAA 58.349 39.130 0.00 0.00 0.00 2.29
3321 3939 5.594199 ATTCTGTAAACTTGGTTACCCCT 57.406 39.130 0.00 0.00 33.76 4.79
3357 3976 2.354109 ATATGCATGCCTACTCGACG 57.646 50.000 16.68 0.00 0.00 5.12
3371 3990 3.338818 AAACGCAGTGCACATATATGC 57.661 42.857 21.04 18.05 45.00 3.14
3402 4021 8.604035 AGATGCAATACAAATTAACTCTGTACG 58.396 33.333 0.00 0.00 0.00 3.67
3415 4034 9.767684 CGTTAACTTATTGAGATGCAATACAAA 57.232 29.630 3.71 0.00 46.31 2.83
3445 4064 9.753674 AGATTTGGTAATGAGAAAAGAATACCA 57.246 29.630 0.00 0.00 40.60 3.25
3452 4071 7.315890 GGTTGGAGATTTGGTAATGAGAAAAG 58.684 38.462 0.00 0.00 0.00 2.27
3453 4072 6.072175 CGGTTGGAGATTTGGTAATGAGAAAA 60.072 38.462 0.00 0.00 0.00 2.29
3502 4123 6.183360 CCAAAAAGCAGGATTGTATGGTCTAG 60.183 42.308 0.00 0.00 0.00 2.43
3534 4155 6.811253 ATCGAATGTTTACCAGCTTAACAA 57.189 33.333 0.00 0.00 35.62 2.83
3535 4156 6.811253 AATCGAATGTTTACCAGCTTAACA 57.189 33.333 0.00 0.00 36.35 2.41
3536 4157 9.615295 TTTAAATCGAATGTTTACCAGCTTAAC 57.385 29.630 0.00 0.00 0.00 2.01
3556 4177 7.435305 GGAGTCTAAGCCTACTCGATTTAAAT 58.565 38.462 0.00 0.00 42.51 1.40
3569 4190 2.625617 CCTTCAGAGGGAGTCTAAGCCT 60.626 54.545 0.00 0.00 39.55 4.58
3572 4193 2.430332 CAGCCTTCAGAGGGAGTCTAAG 59.570 54.545 1.81 0.00 43.75 2.18
3581 4202 1.078567 GACCAGCAGCCTTCAGAGG 60.079 63.158 0.00 0.00 46.50 3.69
3612 4233 2.230266 GGCACGCCTCCATTTCTAAAAA 59.770 45.455 0.00 0.00 0.00 1.94
3613 4234 1.816224 GGCACGCCTCCATTTCTAAAA 59.184 47.619 0.00 0.00 0.00 1.52
3614 4235 1.459450 GGCACGCCTCCATTTCTAAA 58.541 50.000 0.00 0.00 0.00 1.85
3617 4238 2.044946 GGGCACGCCTCCATTTCT 60.045 61.111 8.20 0.00 36.10 2.52
3618 4239 3.140814 GGGGCACGCCTCCATTTC 61.141 66.667 8.20 0.00 36.10 2.17
3633 4254 3.882326 ATGATGCAGAGGCCGGGG 61.882 66.667 2.18 0.00 40.13 5.73
3648 4298 0.673437 TGGCTGCATGCATCATCATG 59.327 50.000 22.97 8.76 44.93 3.07
3650 4300 0.958822 GATGGCTGCATGCATCATCA 59.041 50.000 34.72 25.17 45.15 3.07
3651 4301 1.248486 AGATGGCTGCATGCATCATC 58.752 50.000 33.79 33.79 45.15 2.92
3653 4303 2.351706 TAAGATGGCTGCATGCATCA 57.648 45.000 22.97 21.78 45.15 3.07
3654 4304 3.936372 AATAAGATGGCTGCATGCATC 57.064 42.857 22.97 17.75 45.15 3.91
3657 4307 4.935702 TGTTTAATAAGATGGCTGCATGC 58.064 39.130 11.82 11.82 41.94 4.06
3658 4308 6.643770 GGATTGTTTAATAAGATGGCTGCATG 59.356 38.462 0.50 0.00 0.00 4.06
3659 4309 6.324512 TGGATTGTTTAATAAGATGGCTGCAT 59.675 34.615 0.50 0.00 0.00 3.96
3660 4310 5.655974 TGGATTGTTTAATAAGATGGCTGCA 59.344 36.000 0.50 0.00 0.00 4.41
3661 4311 5.979517 GTGGATTGTTTAATAAGATGGCTGC 59.020 40.000 0.00 0.00 0.00 5.25
3662 4312 6.038161 TCGTGGATTGTTTAATAAGATGGCTG 59.962 38.462 0.00 0.00 0.00 4.85
3664 4314 6.371809 TCGTGGATTGTTTAATAAGATGGC 57.628 37.500 0.00 0.00 0.00 4.40
3668 4318 9.451002 TGGTATTTCGTGGATTGTTTAATAAGA 57.549 29.630 0.00 0.00 0.00 2.10
3669 4319 9.498307 GTGGTATTTCGTGGATTGTTTAATAAG 57.502 33.333 0.00 0.00 0.00 1.73
3670 4320 9.011095 TGTGGTATTTCGTGGATTGTTTAATAA 57.989 29.630 0.00 0.00 0.00 1.40
3671 4321 8.563123 TGTGGTATTTCGTGGATTGTTTAATA 57.437 30.769 0.00 0.00 0.00 0.98
3672 4322 7.455641 TGTGGTATTTCGTGGATTGTTTAAT 57.544 32.000 0.00 0.00 0.00 1.40
3673 4323 6.879276 TGTGGTATTTCGTGGATTGTTTAA 57.121 33.333 0.00 0.00 0.00 1.52
3674 4324 6.879276 TTGTGGTATTTCGTGGATTGTTTA 57.121 33.333 0.00 0.00 0.00 2.01
3676 4326 5.300792 ACTTTGTGGTATTTCGTGGATTGTT 59.699 36.000 0.00 0.00 0.00 2.83
3678 4328 5.371115 ACTTTGTGGTATTTCGTGGATTG 57.629 39.130 0.00 0.00 0.00 2.67
3679 4329 6.399639 AAACTTTGTGGTATTTCGTGGATT 57.600 33.333 0.00 0.00 0.00 3.01
3685 4335 9.078753 ACACTTTTAAAACTTTGTGGTATTTCG 57.921 29.630 17.40 0.00 0.00 3.46
3693 4343 8.460831 AGCTGTAACACTTTTAAAACTTTGTG 57.539 30.769 13.55 13.55 0.00 3.33
3695 4345 7.513041 GCGAGCTGTAACACTTTTAAAACTTTG 60.513 37.037 0.00 0.00 0.00 2.77
3698 4348 5.065474 TGCGAGCTGTAACACTTTTAAAACT 59.935 36.000 0.00 0.00 0.00 2.66
3699 4349 5.267776 TGCGAGCTGTAACACTTTTAAAAC 58.732 37.500 0.00 0.00 0.00 2.43
3701 4351 5.487153 TTGCGAGCTGTAACACTTTTAAA 57.513 34.783 0.00 0.00 0.00 1.52
3705 4355 1.264288 GCTTGCGAGCTGTAACACTTT 59.736 47.619 19.25 0.00 45.65 2.66
3708 4358 1.130613 CGCTTGCGAGCTGTAACAC 59.869 57.895 23.42 0.00 46.96 3.32
3709 4359 2.027073 CCGCTTGCGAGCTGTAACA 61.027 57.895 23.42 0.00 46.96 2.41
3711 4361 1.446099 CTCCGCTTGCGAGCTGTAA 60.446 57.895 23.42 5.45 46.96 2.41
3712 4362 2.181777 CTCCGCTTGCGAGCTGTA 59.818 61.111 23.42 7.85 46.96 2.74
3721 4371 1.078709 TTCTTGATTCGCTCCGCTTG 58.921 50.000 0.00 0.00 0.00 4.01
3725 4375 6.542852 TCTTTTATTTTCTTGATTCGCTCCG 58.457 36.000 0.00 0.00 0.00 4.63
3727 4377 9.056306 GTTCTCTTTTATTTTCTTGATTCGCTC 57.944 33.333 0.00 0.00 0.00 5.03
3728 4378 8.787852 AGTTCTCTTTTATTTTCTTGATTCGCT 58.212 29.630 0.00 0.00 0.00 4.93
3729 4379 8.956617 AGTTCTCTTTTATTTTCTTGATTCGC 57.043 30.769 0.00 0.00 0.00 4.70
3740 4390 7.148407 CGACCAGCATGTAGTTCTCTTTTATTT 60.148 37.037 0.00 0.00 0.00 1.40
3744 4394 3.997021 CGACCAGCATGTAGTTCTCTTTT 59.003 43.478 0.00 0.00 0.00 2.27
3746 4396 2.826128 TCGACCAGCATGTAGTTCTCTT 59.174 45.455 0.00 0.00 0.00 2.85
3749 4399 2.563179 AGTTCGACCAGCATGTAGTTCT 59.437 45.455 0.00 0.00 0.00 3.01
3750 4400 2.960819 AGTTCGACCAGCATGTAGTTC 58.039 47.619 0.00 0.00 0.00 3.01
3753 4403 5.183014 TGTATAGTTCGACCAGCATGTAG 57.817 43.478 0.00 0.00 0.00 2.74
3754 4404 5.585820 TTGTATAGTTCGACCAGCATGTA 57.414 39.130 0.00 0.00 0.00 2.29
3755 4405 4.465632 TTGTATAGTTCGACCAGCATGT 57.534 40.909 0.00 0.00 0.00 3.21
3757 4407 4.189231 GGTTTGTATAGTTCGACCAGCAT 58.811 43.478 0.00 0.00 0.00 3.79
3758 4408 3.007074 TGGTTTGTATAGTTCGACCAGCA 59.993 43.478 0.00 0.00 32.60 4.41
3759 4409 3.592059 TGGTTTGTATAGTTCGACCAGC 58.408 45.455 0.00 0.00 32.60 4.85
3819 4620 1.377202 TTGCCACCTCGATGCTTCC 60.377 57.895 0.00 0.00 0.00 3.46
3998 5251 3.191669 CGTTATAGGCGTTCATGTTCCA 58.808 45.455 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.