Multiple sequence alignment - TraesCS1D01G017700

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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 TraesCS1D01G017700 chr1D 100.000 4586 0 0 1 4586 7877992 7873407 0.000000e+00 8469.0
1 TraesCS1D01G017700 chr1D 90.009 2172 149 38 1 2131 7900302 7898158 0.000000e+00 2747.0
2 TraesCS1D01G017700 chr1D 91.249 1657 120 16 2199 3852 7898130 7896496 0.000000e+00 2233.0
3 TraesCS1D01G017700 chr1D 90.931 1235 100 8 2337 3560 7210747 7211980 0.000000e+00 1650.0
4 TraesCS1D01G017700 chr1D 89.533 1242 114 8 2308 3543 7352986 7354217 0.000000e+00 1559.0
5 TraesCS1D01G017700 chr1D 85.355 915 102 21 1076 1985 7209248 7210135 0.000000e+00 918.0
6 TraesCS1D01G017700 chr1D 80.355 901 135 24 1078 1976 7351453 7352313 0.000000e+00 645.0
7 TraesCS1D01G017700 chr1D 84.874 595 69 4 1 583 7207057 7207642 8.550000e-162 580.0
8 TraesCS1D01G017700 chr1D 81.176 595 78 10 1 578 7350285 7350862 9.050000e-122 448.0
9 TraesCS1D01G017700 chr1D 86.967 399 40 5 997 1389 7208066 7208458 5.450000e-119 438.0
10 TraesCS1D01G017700 chr1D 79.100 622 78 31 3957 4570 7896344 7895767 9.310000e-102 381.0
11 TraesCS1D01G017700 chr1D 84.973 366 40 7 3486 3843 7378588 7378946 1.570000e-94 357.0
12 TraesCS1D01G017700 chr1D 86.186 333 36 7 3516 3843 7216779 7217106 7.300000e-93 351.0
13 TraesCS1D01G017700 chr1D 92.593 108 7 1 2018 2124 7352684 7352791 2.210000e-33 154.0
14 TraesCS1D01G017700 chr1D 86.047 86 5 1 3852 3937 7217208 7217286 8.170000e-13 86.1
15 TraesCS1D01G017700 chr1B 93.542 2168 105 17 1524 3671 10069732 10067580 0.000000e+00 3195.0
16 TraesCS1D01G017700 chr1B 87.494 2199 186 50 1 2164 9596116 9598260 0.000000e+00 2455.0
17 TraesCS1D01G017700 chr1B 92.071 1690 96 10 2164 3835 10081078 10079409 0.000000e+00 2344.0
18 TraesCS1D01G017700 chr1B 88.909 1659 131 24 2164 3792 9598227 9599862 0.000000e+00 1995.0
19 TraesCS1D01G017700 chr1B 89.681 1192 90 17 997 2165 10082225 10081044 0.000000e+00 1489.0
20 TraesCS1D01G017700 chr1B 89.855 621 33 10 3957 4570 10067167 10066570 0.000000e+00 771.0
21 TraesCS1D01G017700 chr1B 88.648 599 59 4 1 590 10073467 10072869 0.000000e+00 721.0
22 TraesCS1D01G017700 chr1B 82.538 859 101 26 1 823 10083714 10082869 0.000000e+00 710.0
23 TraesCS1D01G017700 chr1B 89.286 476 47 2 997 1471 10070290 10069818 1.100000e-165 593.0
24 TraesCS1D01G017700 chr1B 90.106 283 26 1 3657 3937 10067433 10067151 2.610000e-97 366.0
25 TraesCS1D01G017700 chr1B 88.704 301 31 2 3545 3843 10065348 10065049 9.380000e-97 364.0
26 TraesCS1D01G017700 chr1B 82.796 186 25 5 4233 4415 9600304 9600485 4.750000e-35 159.0
27 TraesCS1D01G017700 chr1B 87.407 135 15 2 3553 3686 10066531 10066398 2.210000e-33 154.0
28 TraesCS1D01G017700 chr1B 82.353 187 22 8 4232 4413 10066316 10066136 7.950000e-33 152.0
29 TraesCS1D01G017700 chr1B 91.589 107 6 2 901 1004 10070913 10070807 1.330000e-30 145.0
30 TraesCS1D01G017700 chr1B 97.333 75 1 1 821 895 10070424 10070351 4.820000e-25 126.0
31 TraesCS1D01G017700 chr1B 97.222 72 1 1 824 895 10082356 10082286 2.240000e-23 121.0
32 TraesCS1D01G017700 chr1B 83.212 137 14 4 4169 4305 9701269 9701396 2.900000e-22 117.0
33 TraesCS1D01G017700 chr1B 85.321 109 7 6 901 1004 10082664 10082560 2.260000e-18 104.0
34 TraesCS1D01G017700 chr1A 90.687 1514 115 7 2327 3836 9550379 9548888 0.000000e+00 1991.0
35 TraesCS1D01G017700 chr1A 90.757 1255 105 8 2314 3560 9356531 9355280 0.000000e+00 1664.0
36 TraesCS1D01G017700 chr1A 87.487 983 85 26 997 1972 9551863 9550912 0.000000e+00 1099.0
37 TraesCS1D01G017700 chr1A 87.594 927 88 14 1003 1923 9358077 9357172 0.000000e+00 1050.0
38 TraesCS1D01G017700 chr1A 88.538 602 48 4 1 590 9359808 9359216 0.000000e+00 710.0
39 TraesCS1D01G017700 chr1A 87.914 604 43 15 1 583 9554586 9553992 0.000000e+00 684.0
40 TraesCS1D01G017700 chr1A 85.577 104 15 0 2013 2116 9550693 9550590 4.850000e-20 110.0
41 TraesCS1D01G017700 chr1A 88.158 76 5 3 824 899 9358210 9358139 2.270000e-13 87.9
42 TraesCS1D01G017700 chr3D 81.227 1108 191 15 2341 3441 4967403 4966306 0.000000e+00 878.0
43 TraesCS1D01G017700 chr3A 96.875 32 1 0 55 86 10955142 10955111 2.000000e-03 54.7


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 TraesCS1D01G017700 chr1D 7873407 7877992 4585 True 8469.000000 8469 100.000000 1 4586 1 chr1D.!!$R1 4585
1 TraesCS1D01G017700 chr1D 7895767 7900302 4535 True 1787.000000 2747 86.786000 1 4570 3 chr1D.!!$R2 4569
2 TraesCS1D01G017700 chr1D 7207057 7211980 4923 False 896.500000 1650 87.031750 1 3560 4 chr1D.!!$F2 3559
3 TraesCS1D01G017700 chr1D 7350285 7354217 3932 False 701.500000 1559 85.914250 1 3543 4 chr1D.!!$F4 3542
4 TraesCS1D01G017700 chr1D 7216779 7217286 507 False 218.550000 351 86.116500 3516 3937 2 chr1D.!!$F3 421
5 TraesCS1D01G017700 chr1B 9596116 9600485 4369 False 1536.333333 2455 86.399667 1 4415 3 chr1B.!!$F2 4414
6 TraesCS1D01G017700 chr1B 10079409 10083714 4305 True 953.600000 2344 89.366600 1 3835 5 chr1B.!!$R2 3834
7 TraesCS1D01G017700 chr1B 10065049 10073467 8418 True 658.700000 3195 89.882300 1 4570 10 chr1B.!!$R1 4569
8 TraesCS1D01G017700 chr1A 9548888 9554586 5698 True 971.000000 1991 87.916250 1 3836 4 chr1A.!!$R2 3835
9 TraesCS1D01G017700 chr1A 9355280 9359808 4528 True 877.975000 1664 88.761750 1 3560 4 chr1A.!!$R1 3559
10 TraesCS1D01G017700 chr3D 4966306 4967403 1097 True 878.000000 878 81.227000 2341 3441 1 chr3D.!!$R1 1100

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
451 506 1.566298 AACCTGACCTCTGGGCCATC 61.566 60.0 6.72 1.40 39.04 3.51 F
1490 6013 1.059098 AGTGGATCTGGCACAACTGA 58.941 50.0 3.83 0.00 38.70 3.41 F
1520 6043 0.110056 CACGGCACAACTGATTCAGC 60.110 55.0 13.64 0.00 34.37 4.26 F
3297 8284 0.321653 GGTCTCGTGATTGGCCAACT 60.322 55.0 23.27 10.38 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 6023 0.110056 CTGAATCAGTTGTGCCGTGC 60.110 55.000 1.31 0.0 0.0 5.34 R
3444 8431 0.888619 CTTCCTCTGACACCGCACTA 59.111 55.000 0.00 0.0 0.0 2.74 R
3465 8452 7.710475 CACATTGTATGTATACCTCACACATCA 59.290 37.037 0.00 0.0 42.7 3.07 R
4364 11994 0.034186 GCCCACACATTCCATCTCCA 60.034 55.000 0.00 0.0 0.0 3.86 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
135 142 3.682696 TCTCTTGAACAGCGTACTAGGA 58.317 45.455 0.00 0.00 0.00 2.94
169 200 3.069586 CGGTAAAGACCTGGCATCTCATA 59.930 47.826 0.00 0.00 44.46 2.15
173 204 5.957771 AAAGACCTGGCATCTCATAGTTA 57.042 39.130 0.00 0.00 0.00 2.24
183 214 8.837788 TGGCATCTCATAGTTAATAACATCAG 57.162 34.615 5.89 0.00 0.00 2.90
215 246 3.102204 TGATGAGCTTCTGGAGATGACA 58.898 45.455 0.00 0.00 0.00 3.58
216 247 3.132467 TGATGAGCTTCTGGAGATGACAG 59.868 47.826 0.00 0.00 37.30 3.51
277 308 2.003301 GAGCTTCATGGAAGAACGTCC 58.997 52.381 10.01 0.11 41.71 4.79
302 333 2.821546 TCTATGGCGCTGACATTGTAC 58.178 47.619 7.64 0.00 31.56 2.90
336 367 2.820197 GGGTGAAAAAGGATGGTGTCTC 59.180 50.000 0.00 0.00 0.00 3.36
368 405 5.674525 CATGCTAACTTCCTGGTTGATCTA 58.325 41.667 0.00 0.00 0.00 1.98
451 506 1.566298 AACCTGACCTCTGGGCCATC 61.566 60.000 6.72 1.40 39.04 3.51
695 825 7.769044 GGAGTAGATTTCAAATGCTAACACCTA 59.231 37.037 0.00 0.00 0.00 3.08
767 3247 4.383335 CCCTTGTGGCATGAGCAATAAATT 60.383 41.667 0.00 0.00 44.61 1.82
910 4248 8.658840 ATCTTCCTCTACTTAACAGAAGACTT 57.341 34.615 2.63 0.00 41.63 3.01
970 4308 8.316497 TGAGAGAATATCTTCCTCTTTCACAT 57.684 34.615 0.00 0.00 38.84 3.21
1061 4433 3.568443 CCTTCCCCTCCTTAGTACTCTC 58.432 54.545 0.00 0.00 0.00 3.20
1083 5558 6.013379 TCTCAACAGAACAAACCAGGATATCT 60.013 38.462 2.05 0.00 0.00 1.98
1243 5718 1.277557 GCTCACTGTTCTCCTGTGGAT 59.722 52.381 0.00 0.00 41.79 3.41
1437 5912 4.041691 ACCAACTTCAATACCAGTAGCAGT 59.958 41.667 0.00 0.00 0.00 4.40
1488 6011 3.639099 CAGTGGATCTGGCACAACT 57.361 52.632 3.83 0.00 38.70 3.16
1489 6012 1.162698 CAGTGGATCTGGCACAACTG 58.837 55.000 3.83 0.00 38.70 3.16
1490 6013 1.059098 AGTGGATCTGGCACAACTGA 58.941 50.000 3.83 0.00 38.70 3.41
1491 6014 1.632409 AGTGGATCTGGCACAACTGAT 59.368 47.619 3.83 0.00 38.70 2.90
1492 6015 2.040813 AGTGGATCTGGCACAACTGATT 59.959 45.455 3.83 0.00 38.70 2.57
1493 6016 2.421424 GTGGATCTGGCACAACTGATTC 59.579 50.000 0.00 0.00 38.70 2.52
1494 6017 2.040145 TGGATCTGGCACAACTGATTCA 59.960 45.455 0.00 0.00 38.70 2.57
1495 6018 2.681848 GGATCTGGCACAACTGATTCAG 59.318 50.000 12.17 12.17 38.70 3.02
1496 6019 2.189594 TCTGGCACAACTGATTCAGG 57.810 50.000 17.66 3.74 38.70 3.86
1497 6020 1.699083 TCTGGCACAACTGATTCAGGA 59.301 47.619 17.66 0.33 38.70 3.86
1498 6021 2.082231 CTGGCACAACTGATTCAGGAG 58.918 52.381 17.66 11.45 38.70 3.69
1499 6022 1.699083 TGGCACAACTGATTCAGGAGA 59.301 47.619 17.66 0.00 35.51 3.71
1500 6023 2.289882 TGGCACAACTGATTCAGGAGAG 60.290 50.000 17.66 9.08 35.51 3.20
1501 6024 1.736681 GCACAACTGATTCAGGAGAGC 59.263 52.381 17.66 14.29 35.51 4.09
1508 6031 1.078848 ATTCAGGAGAGCACGGCAC 60.079 57.895 0.00 0.00 0.00 5.01
1520 6043 0.110056 CACGGCACAACTGATTCAGC 60.110 55.000 13.64 0.00 34.37 4.26
1521 6044 1.237285 ACGGCACAACTGATTCAGCC 61.237 55.000 13.64 8.52 38.73 4.85
1529 6055 1.356124 ACTGATTCAGCCTCACCTGT 58.644 50.000 13.64 0.00 34.37 4.00
1555 6081 1.812571 AGTATTTGGCCACTCAAAGCG 59.187 47.619 3.88 0.00 39.59 4.68
1562 6088 1.676014 GGCCACTCAAAGCGACTACAT 60.676 52.381 0.00 0.00 0.00 2.29
1601 6127 5.839262 TGTTCACGAGCAGTAACAAATAG 57.161 39.130 0.00 0.00 0.00 1.73
1666 6192 4.393062 CACATGTTTATGTCTGGGTGTCTC 59.607 45.833 0.00 0.00 45.53 3.36
1673 6199 2.248248 TGTCTGGGTGTCTCCTTACAG 58.752 52.381 0.00 0.00 36.25 2.74
1694 6223 1.522668 TGTGCGGTTGAAGATCTTGG 58.477 50.000 14.00 0.00 0.00 3.61
1713 6242 3.371965 TGGACCTTACTGTGGATACCTC 58.628 50.000 0.00 0.00 0.00 3.85
1764 6302 1.482182 TCTGATTGGCGACAGCTACAT 59.518 47.619 0.00 0.00 44.54 2.29
2129 7028 5.746307 TGCACTTCTTAGAATGCATGATC 57.254 39.130 19.95 0.00 42.92 2.92
2130 7029 5.187687 TGCACTTCTTAGAATGCATGATCA 58.812 37.500 19.95 0.00 42.92 2.92
2158 7057 5.335819 GGAGCTCTAACGATGATTACTACCC 60.336 48.000 14.64 0.00 0.00 3.69
2165 7064 3.773119 ACGATGATTACTACCCCACAACT 59.227 43.478 0.00 0.00 0.00 3.16
2166 7065 4.142004 ACGATGATTACTACCCCACAACTC 60.142 45.833 0.00 0.00 0.00 3.01
2167 7066 3.880047 TGATTACTACCCCACAACTCG 57.120 47.619 0.00 0.00 0.00 4.18
2168 7067 2.498481 TGATTACTACCCCACAACTCGG 59.502 50.000 0.00 0.00 0.00 4.63
2169 7068 2.307496 TTACTACCCCACAACTCGGA 57.693 50.000 0.00 0.00 0.00 4.55
2170 7069 1.843368 TACTACCCCACAACTCGGAG 58.157 55.000 2.83 2.83 0.00 4.63
2171 7070 1.218316 CTACCCCACAACTCGGAGC 59.782 63.158 4.58 0.00 0.00 4.70
2172 7071 1.229082 TACCCCACAACTCGGAGCT 60.229 57.895 4.58 0.00 0.00 4.09
2173 7072 1.255667 TACCCCACAACTCGGAGCTC 61.256 60.000 4.71 4.71 0.00 4.09
2174 7073 2.286523 CCCCACAACTCGGAGCTCT 61.287 63.158 14.64 0.00 0.00 4.09
2175 7074 0.970937 CCCCACAACTCGGAGCTCTA 60.971 60.000 14.64 1.15 0.00 2.43
2176 7075 0.895530 CCCACAACTCGGAGCTCTAA 59.104 55.000 14.64 0.80 0.00 2.10
2177 7076 1.404315 CCCACAACTCGGAGCTCTAAC 60.404 57.143 14.64 0.00 0.00 2.34
2178 7077 1.546476 CCACAACTCGGAGCTCTAACT 59.454 52.381 14.64 0.00 0.00 2.24
2179 7078 2.753452 CCACAACTCGGAGCTCTAACTA 59.247 50.000 14.64 0.00 0.00 2.24
2180 7079 3.381908 CCACAACTCGGAGCTCTAACTAT 59.618 47.826 14.64 0.00 0.00 2.12
2181 7080 4.355437 CACAACTCGGAGCTCTAACTATG 58.645 47.826 14.64 8.76 0.00 2.23
2182 7081 4.096532 CACAACTCGGAGCTCTAACTATGA 59.903 45.833 14.64 0.18 0.00 2.15
2183 7082 4.890581 ACAACTCGGAGCTCTAACTATGAT 59.109 41.667 14.64 0.00 0.00 2.45
2184 7083 5.361285 ACAACTCGGAGCTCTAACTATGATT 59.639 40.000 14.64 0.00 0.00 2.57
2185 7084 6.546403 ACAACTCGGAGCTCTAACTATGATTA 59.454 38.462 14.64 0.00 0.00 1.75
2186 7085 6.563222 ACTCGGAGCTCTAACTATGATTAC 57.437 41.667 14.64 0.00 0.00 1.89
2187 7086 6.300703 ACTCGGAGCTCTAACTATGATTACT 58.699 40.000 14.64 0.00 0.00 2.24
2188 7087 7.451732 ACTCGGAGCTCTAACTATGATTACTA 58.548 38.462 14.64 0.00 0.00 1.82
2189 7088 7.388500 ACTCGGAGCTCTAACTATGATTACTAC 59.612 40.741 14.64 0.00 0.00 2.73
2190 7089 6.368243 TCGGAGCTCTAACTATGATTACTACG 59.632 42.308 14.64 2.22 0.00 3.51
2191 7090 6.316319 GGAGCTCTAACTATGATTACTACGC 58.684 44.000 14.64 0.00 0.00 4.42
2192 7091 6.256912 AGCTCTAACTATGATTACTACGCC 57.743 41.667 0.00 0.00 0.00 5.68
2193 7092 5.768662 AGCTCTAACTATGATTACTACGCCA 59.231 40.000 0.00 0.00 0.00 5.69
2194 7093 5.857517 GCTCTAACTATGATTACTACGCCAC 59.142 44.000 0.00 0.00 0.00 5.01
2195 7094 6.514541 GCTCTAACTATGATTACTACGCCACA 60.515 42.308 0.00 0.00 0.00 4.17
2196 7095 7.337480 TCTAACTATGATTACTACGCCACAA 57.663 36.000 0.00 0.00 0.00 3.33
2197 7096 7.948357 TCTAACTATGATTACTACGCCACAAT 58.052 34.615 0.00 0.00 0.00 2.71
2206 7138 4.742438 ACTACGCCACAATAAAGTTGTG 57.258 40.909 12.62 12.62 46.79 3.33
2214 7146 6.638873 CGCCACAATAAAGTTGTGTTTGATTA 59.361 34.615 16.80 0.00 46.05 1.75
3064 8048 1.473257 GCGTCATATCCAGCAAGTCCA 60.473 52.381 0.00 0.00 0.00 4.02
3244 8231 2.163509 TGCACGAGCTAGAGAAGAAGT 58.836 47.619 6.36 0.00 42.74 3.01
3259 8246 2.277084 AGAAGTTGTGTGTTGTCGGAC 58.723 47.619 0.00 0.00 0.00 4.79
3289 8276 5.360999 TGTATTCAGATGAGGTCTCGTGATT 59.639 40.000 0.00 0.00 34.00 2.57
3297 8284 0.321653 GGTCTCGTGATTGGCCAACT 60.322 55.000 23.27 10.38 0.00 3.16
3444 8431 1.208293 GCAGTCTCGGAGGAGGAATTT 59.792 52.381 4.96 0.00 40.85 1.82
3465 8452 0.247736 GTGCGGTGTCAGAGGAAGAT 59.752 55.000 0.00 0.00 0.00 2.40
3481 8468 6.266558 AGAGGAAGATGATGTGTGAGGTATAC 59.733 42.308 0.00 0.00 0.00 1.47
3497 8500 8.148351 GTGAGGTATACATACAATGTGTGGTAT 58.852 37.037 14.40 11.78 44.60 2.73
3622 10992 3.891586 CTGCCTTGCTTGCTGTGCG 62.892 63.158 0.00 0.00 0.00 5.34
3676 11050 8.633075 ACATCAGTTTATTTGTTTGTTCACTG 57.367 30.769 0.00 0.00 33.19 3.66
3691 11067 6.500684 TGTTCACTGCTCTTGATAAATTCC 57.499 37.500 0.00 0.00 0.00 3.01
3708 11084 9.346725 GATAAATTCCGATGGAAAATATTGCTC 57.653 33.333 1.86 0.00 45.41 4.26
3709 11085 5.712152 ATTCCGATGGAAAATATTGCTCC 57.288 39.130 1.86 9.11 45.41 4.70
3716 11093 6.610075 ATGGAAAATATTGCTCCAACAGTT 57.390 33.333 18.69 4.58 42.41 3.16
3730 11121 7.119699 TGCTCCAACAGTTAATTCTTGATACAG 59.880 37.037 0.00 0.00 0.00 2.74
3759 11150 0.110486 TGAGAGGTGACAAAAGGCCC 59.890 55.000 0.00 0.00 0.00 5.80
3813 11209 6.708949 AGAAAAATTGCATTTCATTCTGCTGT 59.291 30.769 12.50 0.00 38.86 4.40
3843 11241 5.801531 ATGCATTATGGATGAGCATTGTT 57.198 34.783 0.00 0.00 42.76 2.83
3844 11242 4.939271 TGCATTATGGATGAGCATTGTTG 58.061 39.130 0.00 0.00 38.03 3.33
3880 11372 0.174845 TTCCGGTGCGACAGATAAGG 59.825 55.000 0.00 0.00 0.00 2.69
3890 11384 3.914364 GCGACAGATAAGGCAAGTTTTTG 59.086 43.478 0.00 0.00 37.36 2.44
3891 11385 4.556699 GCGACAGATAAGGCAAGTTTTTGT 60.557 41.667 0.00 0.00 36.65 2.83
3892 11386 5.519722 CGACAGATAAGGCAAGTTTTTGTT 58.480 37.500 0.00 0.00 36.65 2.83
3893 11387 5.977129 CGACAGATAAGGCAAGTTTTTGTTT 59.023 36.000 0.00 0.00 36.65 2.83
3894 11388 6.475402 CGACAGATAAGGCAAGTTTTTGTTTT 59.525 34.615 0.00 0.00 36.65 2.43
3895 11389 7.010091 CGACAGATAAGGCAAGTTTTTGTTTTT 59.990 33.333 0.00 0.00 36.65 1.94
3896 11390 7.973601 ACAGATAAGGCAAGTTTTTGTTTTTG 58.026 30.769 0.00 0.00 36.65 2.44
3937 11431 2.629617 CACAACTCAGCTCCCCAATTTT 59.370 45.455 0.00 0.00 0.00 1.82
3938 11432 3.070015 CACAACTCAGCTCCCCAATTTTT 59.930 43.478 0.00 0.00 0.00 1.94
3939 11433 4.280677 CACAACTCAGCTCCCCAATTTTTA 59.719 41.667 0.00 0.00 0.00 1.52
3940 11434 5.047092 CACAACTCAGCTCCCCAATTTTTAT 60.047 40.000 0.00 0.00 0.00 1.40
3941 11435 5.543790 ACAACTCAGCTCCCCAATTTTTATT 59.456 36.000 0.00 0.00 0.00 1.40
3942 11436 6.043127 ACAACTCAGCTCCCCAATTTTTATTT 59.957 34.615 0.00 0.00 0.00 1.40
3943 11437 6.686484 ACTCAGCTCCCCAATTTTTATTTT 57.314 33.333 0.00 0.00 0.00 1.82
3944 11438 7.078249 ACTCAGCTCCCCAATTTTTATTTTT 57.922 32.000 0.00 0.00 0.00 1.94
3962 11456 3.963383 TTTTCTTGAAACGGACTCAGC 57.037 42.857 0.00 0.00 0.00 4.26
3963 11457 2.910688 TTCTTGAAACGGACTCAGCT 57.089 45.000 0.00 0.00 0.00 4.24
3964 11458 2.440539 TCTTGAAACGGACTCAGCTC 57.559 50.000 0.00 0.00 0.00 4.09
3965 11459 1.000955 TCTTGAAACGGACTCAGCTCC 59.999 52.381 0.00 0.00 0.00 4.70
3966 11460 0.034896 TTGAAACGGACTCAGCTCCC 59.965 55.000 0.00 0.00 0.00 4.30
3967 11461 1.079057 GAAACGGACTCAGCTCCCC 60.079 63.158 0.00 0.00 0.00 4.81
3968 11462 1.827399 GAAACGGACTCAGCTCCCCA 61.827 60.000 0.00 0.00 0.00 4.96
3969 11463 1.415672 AAACGGACTCAGCTCCCCAA 61.416 55.000 0.00 0.00 0.00 4.12
3970 11464 1.201429 AACGGACTCAGCTCCCCAAT 61.201 55.000 0.00 0.00 0.00 3.16
3971 11465 1.201429 ACGGACTCAGCTCCCCAATT 61.201 55.000 0.00 0.00 0.00 2.32
3972 11466 0.035056 CGGACTCAGCTCCCCAATTT 60.035 55.000 0.00 0.00 0.00 1.82
4022 11516 7.173390 AGTTTTAGTTTACAGCAACATCTCTCC 59.827 37.037 0.00 0.00 0.00 3.71
4023 11517 4.899352 AGTTTACAGCAACATCTCTCCT 57.101 40.909 0.00 0.00 0.00 3.69
4025 11519 2.680312 TACAGCAACATCTCTCCTGC 57.320 50.000 0.00 0.00 34.96 4.85
4026 11520 0.689055 ACAGCAACATCTCTCCTGCA 59.311 50.000 0.00 0.00 37.26 4.41
4034 11528 1.554160 CATCTCTCCTGCAGGTTGACT 59.446 52.381 31.58 15.24 36.34 3.41
4040 11534 3.449018 TCTCCTGCAGGTTGACTAATCTC 59.551 47.826 31.58 0.00 36.34 2.75
4055 11549 9.996554 TTGACTAATCTCTCATGAACAAAGTTA 57.003 29.630 0.00 0.00 0.00 2.24
4056 11550 9.996554 TGACTAATCTCTCATGAACAAAGTTAA 57.003 29.630 0.00 0.00 0.00 2.01
4090 11585 6.993786 AAACTAGCTAGGCAAGAGAAATTC 57.006 37.500 24.35 0.00 0.00 2.17
4102 11598 7.177216 AGGCAAGAGAAATTCACACATATTTGA 59.823 33.333 0.00 0.00 0.00 2.69
4135 11632 2.439507 GCCTGTCATATTCCCTCCTTCA 59.560 50.000 0.00 0.00 0.00 3.02
4142 11639 0.915364 ATTCCCTCCTTCAGGTCTGC 59.085 55.000 0.00 0.00 41.51 4.26
4147 11644 2.164865 CTCCTTCAGGTCTGCGCACT 62.165 60.000 5.66 0.00 36.34 4.40
4163 11660 0.866906 CACTGCCAAGCACACAAACG 60.867 55.000 0.00 0.00 33.79 3.60
4172 11669 2.294074 AGCACACAAACGTATGGTTGT 58.706 42.857 12.71 12.71 39.30 3.32
4192 11689 6.312672 GGTTGTTTTTCTTCTTTGCAGCTAAA 59.687 34.615 0.00 0.00 0.00 1.85
4213 11710 4.582701 AAAATTGTCGCAGTCATGGAAA 57.417 36.364 0.00 0.00 0.00 3.13
4216 11713 4.882671 ATTGTCGCAGTCATGGAAATAC 57.117 40.909 0.00 0.00 0.00 1.89
4225 11722 5.366460 CAGTCATGGAAATACTGCTGATCT 58.634 41.667 0.00 0.00 34.73 2.75
4227 11724 6.423302 CAGTCATGGAAATACTGCTGATCTAC 59.577 42.308 0.00 0.00 34.73 2.59
4261 11890 1.379309 AACCCTGTGCCGTGTTGTT 60.379 52.632 0.00 0.00 0.00 2.83
4266 11895 1.653094 CTGTGCCGTGTTGTTGTGGT 61.653 55.000 0.00 0.00 0.00 4.16
4273 11902 2.030363 CCGTGTTGTTGTGGTTGCATAT 60.030 45.455 0.00 0.00 0.00 1.78
4279 11908 4.433186 TGTTGTGGTTGCATATACTTGC 57.567 40.909 0.00 0.00 43.07 4.01
4281 11910 4.082841 TGTTGTGGTTGCATATACTTGCTG 60.083 41.667 0.00 0.00 43.18 4.41
4324 11953 3.423162 TTGTGCGTGCAACAAGGGC 62.423 57.895 0.00 0.00 35.74 5.19
4340 11969 2.178273 GCCGCCGTGTGGAAATTC 59.822 61.111 7.56 0.00 37.49 2.17
4341 11970 2.622011 GCCGCCGTGTGGAAATTCA 61.622 57.895 7.56 0.00 37.49 2.57
4349 11978 3.443037 CGTGTGGAAATTCAAGCAACAA 58.557 40.909 0.00 0.00 0.00 2.83
4356 11986 6.203338 GTGGAAATTCAAGCAACAATGACATT 59.797 34.615 0.00 0.00 0.00 2.71
4362 11992 1.073177 GCAACAATGACATTGCCTGC 58.927 50.000 27.06 27.06 44.42 4.85
4364 11994 1.274167 CAACAATGACATTGCCTGCCT 59.726 47.619 24.85 4.67 43.98 4.75
4365 11995 0.892755 ACAATGACATTGCCTGCCTG 59.107 50.000 24.85 3.27 43.98 4.85
4368 11998 0.395311 ATGACATTGCCTGCCTGGAG 60.395 55.000 0.00 0.00 38.35 3.86
4369 11999 1.300963 GACATTGCCTGCCTGGAGA 59.699 57.895 0.00 0.00 38.35 3.71
4370 12000 0.106819 GACATTGCCTGCCTGGAGAT 60.107 55.000 0.00 0.00 38.35 2.75
4371 12001 0.395311 ACATTGCCTGCCTGGAGATG 60.395 55.000 0.00 0.00 38.35 2.90
4382 12012 1.409241 CCTGGAGATGGAATGTGTGGG 60.409 57.143 0.00 0.00 0.00 4.61
4419 12050 2.356125 GCAGATGGGGCAGAAGAGTAAA 60.356 50.000 0.00 0.00 0.00 2.01
4442 12074 5.323371 CAAAGTCTTTTGTTCCAACTCCA 57.677 39.130 0.00 0.00 39.05 3.86
4444 12076 2.952310 AGTCTTTTGTTCCAACTCCAGC 59.048 45.455 0.00 0.00 0.00 4.85
4445 12077 1.946768 TCTTTTGTTCCAACTCCAGCG 59.053 47.619 0.00 0.00 0.00 5.18
4446 12078 1.946768 CTTTTGTTCCAACTCCAGCGA 59.053 47.619 0.00 0.00 0.00 4.93
4447 12079 2.270352 TTTGTTCCAACTCCAGCGAT 57.730 45.000 0.00 0.00 0.00 4.58
4448 12080 2.270352 TTGTTCCAACTCCAGCGATT 57.730 45.000 0.00 0.00 0.00 3.34
4449 12081 1.808411 TGTTCCAACTCCAGCGATTC 58.192 50.000 0.00 0.00 0.00 2.52
4450 12082 1.347707 TGTTCCAACTCCAGCGATTCT 59.652 47.619 0.00 0.00 0.00 2.40
4451 12083 1.734465 GTTCCAACTCCAGCGATTCTG 59.266 52.381 0.00 0.00 42.49 3.02
4452 12084 1.266178 TCCAACTCCAGCGATTCTGA 58.734 50.000 0.00 0.00 45.72 3.27
4453 12085 1.833630 TCCAACTCCAGCGATTCTGAT 59.166 47.619 0.00 0.00 45.72 2.90
4454 12086 1.938577 CCAACTCCAGCGATTCTGATG 59.061 52.381 0.00 0.00 45.72 3.07
4455 12087 2.625737 CAACTCCAGCGATTCTGATGT 58.374 47.619 0.00 0.00 45.72 3.06
4456 12088 3.430790 CCAACTCCAGCGATTCTGATGTA 60.431 47.826 0.00 0.00 45.72 2.29
4457 12089 4.375272 CAACTCCAGCGATTCTGATGTAT 58.625 43.478 0.00 0.00 45.72 2.29
4458 12090 3.987547 ACTCCAGCGATTCTGATGTATG 58.012 45.455 0.00 0.00 45.72 2.39
4459 12091 3.244009 ACTCCAGCGATTCTGATGTATGG 60.244 47.826 0.00 0.00 45.72 2.74
4460 12092 2.700371 TCCAGCGATTCTGATGTATGGT 59.300 45.455 0.00 0.00 45.72 3.55
4461 12093 3.062763 CCAGCGATTCTGATGTATGGTC 58.937 50.000 0.00 0.00 45.72 4.02
4462 12094 3.062763 CAGCGATTCTGATGTATGGTCC 58.937 50.000 0.00 0.00 45.72 4.46
4463 12095 2.700371 AGCGATTCTGATGTATGGTCCA 59.300 45.455 0.00 0.00 0.00 4.02
4464 12096 3.062763 GCGATTCTGATGTATGGTCCAG 58.937 50.000 0.00 0.00 0.00 3.86
4465 12097 3.062763 CGATTCTGATGTATGGTCCAGC 58.937 50.000 0.00 0.00 0.00 4.85
4466 12098 2.602257 TTCTGATGTATGGTCCAGCG 57.398 50.000 0.00 0.00 0.00 5.18
4467 12099 1.775385 TCTGATGTATGGTCCAGCGA 58.225 50.000 0.00 0.00 0.00 4.93
4468 12100 2.319844 TCTGATGTATGGTCCAGCGAT 58.680 47.619 0.00 0.00 0.00 4.58
4474 12106 2.700371 TGTATGGTCCAGCGATTCTGAT 59.300 45.455 0.00 0.00 45.72 2.90
4475 12107 2.251409 ATGGTCCAGCGATTCTGATG 57.749 50.000 0.00 0.00 45.72 3.07
4479 12111 3.062763 GGTCCAGCGATTCTGATGTATG 58.937 50.000 0.00 0.00 45.72 2.39
4494 12126 8.844865 TCTGATGTATGGTCCTATAATATGCT 57.155 34.615 0.00 0.00 0.00 3.79
4506 12138 6.558775 TCCTATAATATGCTGGGACTGAAACT 59.441 38.462 0.00 0.00 0.00 2.66
4526 12158 7.173218 TGAAACTGACTCTGTTCCAACATATTC 59.827 37.037 2.11 0.00 38.41 1.75
4531 12163 5.794894 ACTCTGTTCCAACATATTCGAAGT 58.205 37.500 3.35 0.00 38.41 3.01
4542 12174 6.663944 ACATATTCGAAGTTCTAGGTTTGC 57.336 37.500 3.35 0.00 0.00 3.68
4543 12175 5.585047 ACATATTCGAAGTTCTAGGTTTGCC 59.415 40.000 3.35 0.00 0.00 4.52
4546 12178 4.877378 TCGAAGTTCTAGGTTTGCCTTA 57.123 40.909 0.56 0.00 44.18 2.69
4550 12182 5.469084 CGAAGTTCTAGGTTTGCCTTAAGTT 59.531 40.000 0.97 0.00 44.18 2.66
4563 12195 9.806203 GTTTGCCTTAAGTTAAACCTCTTTAAA 57.194 29.630 15.59 0.00 34.33 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 200 5.189736 TCTCCACAGGCTGATGTTATTAACT 59.810 40.000 23.66 0.00 0.00 2.24
173 204 4.164796 TCATCTCCACAGGCTGATGTTATT 59.835 41.667 23.66 0.00 36.04 1.40
183 214 0.469070 AGCTCATCATCTCCACAGGC 59.531 55.000 0.00 0.00 0.00 4.85
233 264 1.804748 CCGCTTGTAGACCCTTGTTTC 59.195 52.381 0.00 0.00 0.00 2.78
239 270 0.325296 TCATCCCGCTTGTAGACCCT 60.325 55.000 0.00 0.00 0.00 4.34
277 308 2.134201 TGTCAGCGCCATAGATTACG 57.866 50.000 2.29 0.00 0.00 3.18
302 333 2.672996 CACCCAGTTCTTGGCCCG 60.673 66.667 0.00 0.00 46.32 6.13
336 367 0.745845 AAGTTAGCATGCTCTGGGCG 60.746 55.000 26.57 0.00 45.43 6.13
368 405 0.749091 CATCATGTGGATGTGCCGGT 60.749 55.000 1.90 0.00 46.81 5.28
391 437 1.133598 GCAATACATCAGCAGCAGCAA 59.866 47.619 3.17 0.00 45.49 3.91
451 506 3.052082 CGTCCCAGTGCAGCCAAG 61.052 66.667 0.00 0.00 0.00 3.61
628 708 1.569479 GCACAACTCCGACTGCCTTC 61.569 60.000 0.00 0.00 0.00 3.46
695 825 5.702670 CACACTCAAACCACTAGAACATGAT 59.297 40.000 0.00 0.00 0.00 2.45
767 3247 5.769484 ATGCAAAATGCCAATCAAAACAA 57.231 30.435 0.00 0.00 44.23 2.83
970 4308 7.102847 TGACTTCATTGGTATATACACGACA 57.897 36.000 14.70 0.70 0.00 4.35
1061 4433 7.106239 ACTAGATATCCTGGTTTGTTCTGTTG 58.894 38.462 0.00 0.00 32.13 3.33
1083 5558 4.442052 GCTTCACAGATGCACTATGGACTA 60.442 45.833 0.00 0.00 33.71 2.59
1243 5718 9.126151 GAAAGGATATGATATGTCTCGGAGATA 57.874 37.037 11.46 9.10 33.89 1.98
1437 5912 1.059584 TCCACAGTGGAAGAGGGCAA 61.060 55.000 20.84 0.00 45.00 4.52
1472 5947 2.119801 ATCAGTTGTGCCAGATCCAC 57.880 50.000 0.00 0.00 0.00 4.02
1480 6003 2.354259 CTCTCCTGAATCAGTTGTGCC 58.646 52.381 9.63 0.00 0.00 5.01
1481 6004 1.736681 GCTCTCCTGAATCAGTTGTGC 59.263 52.381 9.63 9.61 0.00 4.57
1483 6006 2.611473 CGTGCTCTCCTGAATCAGTTGT 60.611 50.000 9.63 0.00 0.00 3.32
1484 6007 1.998315 CGTGCTCTCCTGAATCAGTTG 59.002 52.381 9.63 1.71 0.00 3.16
1485 6008 1.066573 CCGTGCTCTCCTGAATCAGTT 60.067 52.381 9.63 0.00 0.00 3.16
1486 6009 0.534412 CCGTGCTCTCCTGAATCAGT 59.466 55.000 9.63 0.00 0.00 3.41
1487 6010 0.809241 GCCGTGCTCTCCTGAATCAG 60.809 60.000 2.68 2.68 0.00 2.90
1488 6011 1.219124 GCCGTGCTCTCCTGAATCA 59.781 57.895 0.00 0.00 0.00 2.57
1489 6012 1.086634 GTGCCGTGCTCTCCTGAATC 61.087 60.000 0.00 0.00 0.00 2.52
1490 6013 1.078848 GTGCCGTGCTCTCCTGAAT 60.079 57.895 0.00 0.00 0.00 2.57
1491 6014 2.038814 TTGTGCCGTGCTCTCCTGAA 62.039 55.000 0.00 0.00 0.00 3.02
1492 6015 2.506957 TTGTGCCGTGCTCTCCTGA 61.507 57.895 0.00 0.00 0.00 3.86
1493 6016 2.031012 TTGTGCCGTGCTCTCCTG 59.969 61.111 0.00 0.00 0.00 3.86
1494 6017 2.031163 GTTGTGCCGTGCTCTCCT 59.969 61.111 0.00 0.00 0.00 3.69
1495 6018 2.031163 AGTTGTGCCGTGCTCTCC 59.969 61.111 0.00 0.00 0.00 3.71
1496 6019 0.671781 ATCAGTTGTGCCGTGCTCTC 60.672 55.000 0.00 0.00 0.00 3.20
1497 6020 0.250467 AATCAGTTGTGCCGTGCTCT 60.250 50.000 0.00 0.00 0.00 4.09
1498 6021 0.166814 GAATCAGTTGTGCCGTGCTC 59.833 55.000 0.00 0.00 0.00 4.26
1499 6022 0.534877 TGAATCAGTTGTGCCGTGCT 60.535 50.000 0.00 0.00 0.00 4.40
1500 6023 0.110056 CTGAATCAGTTGTGCCGTGC 60.110 55.000 1.31 0.00 0.00 5.34
1501 6024 0.110056 GCTGAATCAGTTGTGCCGTG 60.110 55.000 12.29 0.00 33.43 4.94
1508 6031 2.082231 CAGGTGAGGCTGAATCAGTTG 58.918 52.381 12.29 0.00 33.43 3.16
1529 6055 4.365514 TGAGTGGCCAAATACTGAAAGA 57.634 40.909 7.24 0.00 37.43 2.52
1601 6127 1.396996 CAACGGGCTTGTATGCACTAC 59.603 52.381 0.00 0.00 33.50 2.73
1666 6192 1.588674 TCAACCGCACAACTGTAAGG 58.411 50.000 2.34 2.34 39.30 2.69
1673 6199 2.350772 CCAAGATCTTCAACCGCACAAC 60.351 50.000 4.57 0.00 0.00 3.32
1694 6223 2.361438 CCGAGGTATCCACAGTAAGGTC 59.639 54.545 0.00 0.00 0.00 3.85
1741 6279 0.392193 AGCTGTCGCCAATCAGAAGG 60.392 55.000 0.00 0.00 36.60 3.46
2128 7027 1.751351 CATCGTTAGAGCTCCCAGTGA 59.249 52.381 10.93 2.81 0.00 3.41
2129 7028 1.751351 TCATCGTTAGAGCTCCCAGTG 59.249 52.381 10.93 2.69 0.00 3.66
2130 7029 2.145397 TCATCGTTAGAGCTCCCAGT 57.855 50.000 10.93 0.00 0.00 4.00
2158 7057 1.546476 AGTTAGAGCTCCGAGTTGTGG 59.454 52.381 10.93 0.00 0.00 4.17
2165 7064 6.368243 CGTAGTAATCATAGTTAGAGCTCCGA 59.632 42.308 10.93 0.00 0.00 4.55
2166 7065 6.535811 CGTAGTAATCATAGTTAGAGCTCCG 58.464 44.000 10.93 0.00 0.00 4.63
2167 7066 6.316319 GCGTAGTAATCATAGTTAGAGCTCC 58.684 44.000 10.93 0.00 0.00 4.70
2168 7067 6.072618 TGGCGTAGTAATCATAGTTAGAGCTC 60.073 42.308 5.27 5.27 0.00 4.09
2169 7068 5.768662 TGGCGTAGTAATCATAGTTAGAGCT 59.231 40.000 0.00 0.00 0.00 4.09
2170 7069 5.857517 GTGGCGTAGTAATCATAGTTAGAGC 59.142 44.000 0.00 0.00 0.00 4.09
2171 7070 6.967135 TGTGGCGTAGTAATCATAGTTAGAG 58.033 40.000 0.00 0.00 0.00 2.43
2172 7071 6.947644 TGTGGCGTAGTAATCATAGTTAGA 57.052 37.500 0.00 0.00 0.00 2.10
2173 7072 9.687210 TTATTGTGGCGTAGTAATCATAGTTAG 57.313 33.333 0.00 0.00 0.00 2.34
2175 7074 8.951787 TTTATTGTGGCGTAGTAATCATAGTT 57.048 30.769 0.00 0.00 0.00 2.24
2176 7075 8.202137 ACTTTATTGTGGCGTAGTAATCATAGT 58.798 33.333 0.00 0.00 0.00 2.12
2177 7076 8.589335 ACTTTATTGTGGCGTAGTAATCATAG 57.411 34.615 0.00 0.00 0.00 2.23
2178 7077 8.822855 CAACTTTATTGTGGCGTAGTAATCATA 58.177 33.333 0.00 0.00 0.00 2.15
2179 7078 7.335924 ACAACTTTATTGTGGCGTAGTAATCAT 59.664 33.333 0.00 0.00 0.00 2.45
2180 7079 6.651643 ACAACTTTATTGTGGCGTAGTAATCA 59.348 34.615 0.00 0.00 0.00 2.57
2181 7080 6.959311 CACAACTTTATTGTGGCGTAGTAATC 59.041 38.462 11.16 0.00 44.33 1.75
2182 7081 6.837992 CACAACTTTATTGTGGCGTAGTAAT 58.162 36.000 11.16 0.00 44.33 1.89
2183 7082 6.230849 CACAACTTTATTGTGGCGTAGTAA 57.769 37.500 11.16 0.00 44.33 2.24
2184 7083 5.849357 CACAACTTTATTGTGGCGTAGTA 57.151 39.130 11.16 0.00 44.33 1.82
2185 7084 4.742438 CACAACTTTATTGTGGCGTAGT 57.258 40.909 11.16 0.00 44.33 2.73
2193 7092 8.194104 TGCAGTAATCAAACACAACTTTATTGT 58.806 29.630 0.00 0.00 0.00 2.71
2194 7093 8.572828 TGCAGTAATCAAACACAACTTTATTG 57.427 30.769 0.00 0.00 0.00 1.90
2195 7094 9.030301 GTTGCAGTAATCAAACACAACTTTATT 57.970 29.630 0.00 0.00 36.52 1.40
2196 7095 7.651704 GGTTGCAGTAATCAAACACAACTTTAT 59.348 33.333 0.00 0.00 38.11 1.40
2197 7096 6.975772 GGTTGCAGTAATCAAACACAACTTTA 59.024 34.615 0.00 0.00 38.11 1.85
2206 7138 8.391106 CAGATACTAAGGTTGCAGTAATCAAAC 58.609 37.037 0.00 0.00 31.35 2.93
2214 7146 5.878406 ATAGCAGATACTAAGGTTGCAGT 57.122 39.130 0.00 0.00 37.24 4.40
3013 7997 3.380004 CGGGATATCATCTCAGGAGCTAC 59.620 52.174 4.83 0.00 0.00 3.58
3064 8048 2.027192 ACATCCCGAAGCTGTACACATT 60.027 45.455 0.00 0.00 0.00 2.71
3244 8231 2.103432 ACCATAGTCCGACAACACACAA 59.897 45.455 0.40 0.00 0.00 3.33
3259 8246 6.569418 CGAGACCTCATCTGAATACACCATAG 60.569 46.154 0.00 0.00 38.00 2.23
3289 8276 2.589540 CTCGCCCATAGTTGGCCA 59.410 61.111 0.00 0.00 46.48 5.36
3297 8284 2.971901 TCTCTATGACCTCGCCCATA 57.028 50.000 0.00 0.00 0.00 2.74
3426 8413 3.702045 CACTAAATTCCTCCTCCGAGACT 59.298 47.826 0.00 0.00 38.52 3.24
3444 8431 0.888619 CTTCCTCTGACACCGCACTA 59.111 55.000 0.00 0.00 0.00 2.74
3465 8452 7.710475 CACATTGTATGTATACCTCACACATCA 59.290 37.037 0.00 0.00 42.70 3.07
3572 10927 5.444744 AGCATTTATACAGGGTTGGTACA 57.555 39.130 0.00 0.00 0.00 2.90
3674 11048 5.059161 TCCATCGGAATTTATCAAGAGCAG 58.941 41.667 0.00 0.00 0.00 4.24
3676 11050 6.377327 TTTCCATCGGAATTTATCAAGAGC 57.623 37.500 0.00 0.00 41.71 4.09
3691 11067 5.163622 ACTGTTGGAGCAATATTTTCCATCG 60.164 40.000 15.72 13.34 40.48 3.84
3730 11121 7.809806 CCTTTTGTCACCTCTCACAAATTTATC 59.190 37.037 0.00 0.00 41.10 1.75
3735 11126 3.319122 GCCTTTTGTCACCTCTCACAAAT 59.681 43.478 0.00 0.00 41.10 2.32
3794 11187 4.219944 ACTGACAGCAGAATGAAATGCAAT 59.780 37.500 1.25 0.00 45.17 3.56
3813 11209 5.471116 GCTCATCCATAATGCATGTTACTGA 59.529 40.000 0.00 0.00 35.17 3.41
3843 11241 3.559655 CGGAATCAGAATGTTTATCGGCA 59.440 43.478 0.00 0.00 37.40 5.69
3844 11242 3.058914 CCGGAATCAGAATGTTTATCGGC 60.059 47.826 0.00 0.00 37.64 5.54
3849 11247 2.675844 CGCACCGGAATCAGAATGTTTA 59.324 45.455 9.46 0.00 37.40 2.01
3880 11372 6.345644 CCAGCAAAACAAAAACAAAAACTTGC 60.346 34.615 0.00 0.00 37.50 4.01
3890 11384 7.532682 TTCTGTTATCCAGCAAAACAAAAAC 57.467 32.000 0.00 0.00 41.25 2.43
3891 11385 6.257630 GCTTCTGTTATCCAGCAAAACAAAAA 59.742 34.615 0.00 0.00 41.25 1.94
3892 11386 5.752955 GCTTCTGTTATCCAGCAAAACAAAA 59.247 36.000 0.00 0.00 41.25 2.44
3893 11387 5.163468 TGCTTCTGTTATCCAGCAAAACAAA 60.163 36.000 0.00 0.00 39.32 2.83
3894 11388 4.340666 TGCTTCTGTTATCCAGCAAAACAA 59.659 37.500 0.00 0.00 39.32 2.83
3895 11389 3.888323 TGCTTCTGTTATCCAGCAAAACA 59.112 39.130 0.00 0.00 39.32 2.83
3896 11390 4.229876 GTGCTTCTGTTATCCAGCAAAAC 58.770 43.478 0.00 0.00 43.73 2.43
3941 11435 3.945285 AGCTGAGTCCGTTTCAAGAAAAA 59.055 39.130 0.00 0.00 31.33 1.94
3942 11436 3.541632 AGCTGAGTCCGTTTCAAGAAAA 58.458 40.909 0.00 0.00 31.33 2.29
3943 11437 3.131396 GAGCTGAGTCCGTTTCAAGAAA 58.869 45.455 0.00 0.00 0.00 2.52
3944 11438 2.548067 GGAGCTGAGTCCGTTTCAAGAA 60.548 50.000 0.00 0.00 0.00 2.52
3945 11439 1.000955 GGAGCTGAGTCCGTTTCAAGA 59.999 52.381 0.00 0.00 0.00 3.02
3946 11440 1.433534 GGAGCTGAGTCCGTTTCAAG 58.566 55.000 0.00 0.00 0.00 3.02
3947 11441 0.034896 GGGAGCTGAGTCCGTTTCAA 59.965 55.000 0.00 0.00 37.50 2.69
3948 11442 1.671742 GGGAGCTGAGTCCGTTTCA 59.328 57.895 0.00 0.00 37.50 2.69
3949 11443 1.079057 GGGGAGCTGAGTCCGTTTC 60.079 63.158 0.00 0.00 37.50 2.78
3950 11444 1.415672 TTGGGGAGCTGAGTCCGTTT 61.416 55.000 0.00 0.00 37.50 3.60
3951 11445 1.201429 ATTGGGGAGCTGAGTCCGTT 61.201 55.000 0.00 0.00 37.50 4.44
3952 11446 1.201429 AATTGGGGAGCTGAGTCCGT 61.201 55.000 0.00 0.00 37.50 4.69
3953 11447 0.035056 AAATTGGGGAGCTGAGTCCG 60.035 55.000 0.00 0.00 37.50 4.79
3954 11448 1.004745 TGAAATTGGGGAGCTGAGTCC 59.995 52.381 0.00 0.00 35.64 3.85
3955 11449 2.496899 TGAAATTGGGGAGCTGAGTC 57.503 50.000 0.00 0.00 0.00 3.36
3956 11450 2.309755 TGATGAAATTGGGGAGCTGAGT 59.690 45.455 0.00 0.00 0.00 3.41
3957 11451 2.686915 GTGATGAAATTGGGGAGCTGAG 59.313 50.000 0.00 0.00 0.00 3.35
3958 11452 2.621407 GGTGATGAAATTGGGGAGCTGA 60.621 50.000 0.00 0.00 0.00 4.26
3959 11453 1.753073 GGTGATGAAATTGGGGAGCTG 59.247 52.381 0.00 0.00 0.00 4.24
3960 11454 1.642762 AGGTGATGAAATTGGGGAGCT 59.357 47.619 0.00 0.00 0.00 4.09
3961 11455 2.149973 AGGTGATGAAATTGGGGAGC 57.850 50.000 0.00 0.00 0.00 4.70
3962 11456 3.434309 ACAAGGTGATGAAATTGGGGAG 58.566 45.455 0.00 0.00 0.00 4.30
3963 11457 3.541242 ACAAGGTGATGAAATTGGGGA 57.459 42.857 0.00 0.00 0.00 4.81
3964 11458 3.577848 TGAACAAGGTGATGAAATTGGGG 59.422 43.478 0.00 0.00 0.00 4.96
3965 11459 4.870123 TGAACAAGGTGATGAAATTGGG 57.130 40.909 0.00 0.00 0.00 4.12
3966 11460 6.457355 TCAATGAACAAGGTGATGAAATTGG 58.543 36.000 0.00 0.00 0.00 3.16
3967 11461 7.949903 TTCAATGAACAAGGTGATGAAATTG 57.050 32.000 0.00 0.00 0.00 2.32
3969 11463 9.643693 GTATTTCAATGAACAAGGTGATGAAAT 57.356 29.630 13.35 13.35 44.02 2.17
3970 11464 8.637099 TGTATTTCAATGAACAAGGTGATGAAA 58.363 29.630 0.00 0.00 38.98 2.69
3971 11465 8.175925 TGTATTTCAATGAACAAGGTGATGAA 57.824 30.769 0.00 0.00 0.00 2.57
3972 11466 7.448161 ACTGTATTTCAATGAACAAGGTGATGA 59.552 33.333 0.00 0.00 0.00 2.92
4022 11516 4.462508 TGAGAGATTAGTCAACCTGCAG 57.537 45.455 6.78 6.78 0.00 4.41
4023 11517 4.467438 TCATGAGAGATTAGTCAACCTGCA 59.533 41.667 0.00 0.00 0.00 4.41
4025 11519 6.401394 TGTTCATGAGAGATTAGTCAACCTG 58.599 40.000 0.00 0.00 0.00 4.00
4026 11520 6.611613 TGTTCATGAGAGATTAGTCAACCT 57.388 37.500 0.00 0.00 0.00 3.50
4034 11528 8.846943 TGCTTAACTTTGTTCATGAGAGATTA 57.153 30.769 0.00 0.00 0.00 1.75
4040 11534 4.860907 GGCATGCTTAACTTTGTTCATGAG 59.139 41.667 18.92 0.00 34.79 2.90
4072 11567 4.006319 GTGTGAATTTCTCTTGCCTAGCT 58.994 43.478 0.00 0.00 0.00 3.32
4088 11583 9.356433 CTATGCAACAATTCAAATATGTGTGAA 57.644 29.630 0.00 0.00 38.09 3.18
4090 11585 7.254185 GGCTATGCAACAATTCAAATATGTGTG 60.254 37.037 0.00 0.00 0.00 3.82
4102 11598 6.239120 GGAATATGACAGGCTATGCAACAATT 60.239 38.462 0.00 0.00 0.00 2.32
4135 11632 4.254709 TTGGCAGTGCGCAGACCT 62.255 61.111 12.22 0.27 45.17 3.85
4142 11639 2.610700 TTTGTGTGCTTGGCAGTGCG 62.611 55.000 9.45 0.00 40.08 5.34
4147 11644 1.001924 CATACGTTTGTGTGCTTGGCA 60.002 47.619 0.00 0.00 35.60 4.92
4157 11654 6.859017 AGAAGAAAAACAACCATACGTTTGT 58.141 32.000 5.27 1.42 35.57 2.83
4163 11660 6.292328 GCTGCAAAGAAGAAAAACAACCATAC 60.292 38.462 0.00 0.00 0.00 2.39
4192 11689 4.582701 TTTCCATGACTGCGACAATTTT 57.417 36.364 0.00 0.00 0.00 1.82
4197 11694 3.261580 CAGTATTTCCATGACTGCGACA 58.738 45.455 0.00 0.00 34.64 4.35
4209 11706 5.283457 ACCAGTAGATCAGCAGTATTTCC 57.717 43.478 0.00 0.00 0.00 3.13
4213 11710 6.491714 AATCAACCAGTAGATCAGCAGTAT 57.508 37.500 0.00 0.00 0.00 2.12
4216 11713 7.255035 CCATTAAATCAACCAGTAGATCAGCAG 60.255 40.741 0.00 0.00 0.00 4.24
4219 11716 8.616076 GTTCCATTAAATCAACCAGTAGATCAG 58.384 37.037 0.00 0.00 0.00 2.90
4220 11717 7.556275 GGTTCCATTAAATCAACCAGTAGATCA 59.444 37.037 0.00 0.00 38.57 2.92
4221 11718 7.013369 GGGTTCCATTAAATCAACCAGTAGATC 59.987 40.741 12.44 0.00 40.21 2.75
4222 11719 6.833933 GGGTTCCATTAAATCAACCAGTAGAT 59.166 38.462 12.44 0.00 40.21 1.98
4225 11722 5.949354 CAGGGTTCCATTAAATCAACCAGTA 59.051 40.000 12.44 0.00 40.21 2.74
4227 11724 4.772100 ACAGGGTTCCATTAAATCAACCAG 59.228 41.667 12.44 8.18 40.21 4.00
4273 11902 0.250727 GGACTGGGTTGCAGCAAGTA 60.251 55.000 8.49 0.00 0.00 2.24
4279 11908 0.179020 TTGACAGGACTGGGTTGCAG 60.179 55.000 4.14 0.00 34.19 4.41
4281 11910 1.270550 CATTTGACAGGACTGGGTTGC 59.729 52.381 4.14 0.00 34.19 4.17
4285 11914 0.251297 TGGCATTTGACAGGACTGGG 60.251 55.000 4.14 0.00 34.19 4.45
4324 11953 0.109781 CTTGAATTTCCACACGGCGG 60.110 55.000 13.24 2.35 0.00 6.13
4340 11969 2.734606 CAGGCAATGTCATTGTTGCTTG 59.265 45.455 23.27 15.10 46.79 4.01
4349 11978 0.395311 CTCCAGGCAGGCAATGTCAT 60.395 55.000 0.00 0.00 35.29 3.06
4356 11986 1.284111 ATTCCATCTCCAGGCAGGCA 61.284 55.000 0.00 0.00 37.29 4.75
4360 11990 0.994247 ACACATTCCATCTCCAGGCA 59.006 50.000 0.00 0.00 0.00 4.75
4361 11991 1.386533 CACACATTCCATCTCCAGGC 58.613 55.000 0.00 0.00 0.00 4.85
4362 11992 1.409241 CCCACACATTCCATCTCCAGG 60.409 57.143 0.00 0.00 0.00 4.45
4364 11994 0.034186 GCCCACACATTCCATCTCCA 60.034 55.000 0.00 0.00 0.00 3.86
4365 11995 0.034186 TGCCCACACATTCCATCTCC 60.034 55.000 0.00 0.00 0.00 3.71
4382 12012 0.593128 CTGCTGGGTAACAACAGTGC 59.407 55.000 0.00 0.00 38.25 4.40
4434 12066 1.938577 CATCAGAATCGCTGGAGTTGG 59.061 52.381 0.00 0.00 44.98 3.77
4435 12067 2.625737 ACATCAGAATCGCTGGAGTTG 58.374 47.619 0.00 0.00 44.98 3.16
4438 12070 3.244009 ACCATACATCAGAATCGCTGGAG 60.244 47.826 0.00 0.00 44.98 3.86
4440 12072 3.062763 GACCATACATCAGAATCGCTGG 58.937 50.000 0.00 0.00 44.98 4.85
4442 12074 2.700371 TGGACCATACATCAGAATCGCT 59.300 45.455 0.00 0.00 0.00 4.93
4444 12076 3.062763 GCTGGACCATACATCAGAATCG 58.937 50.000 0.00 0.00 0.00 3.34
4445 12077 3.062763 CGCTGGACCATACATCAGAATC 58.937 50.000 0.00 0.00 0.00 2.52
4446 12078 2.700371 TCGCTGGACCATACATCAGAAT 59.300 45.455 0.00 0.00 0.00 2.40
4447 12079 2.107366 TCGCTGGACCATACATCAGAA 58.893 47.619 0.00 0.00 0.00 3.02
4448 12080 1.775385 TCGCTGGACCATACATCAGA 58.225 50.000 0.00 0.00 0.00 3.27
4449 12081 2.827800 ATCGCTGGACCATACATCAG 57.172 50.000 0.00 0.00 0.00 2.90
4450 12082 2.700371 AGAATCGCTGGACCATACATCA 59.300 45.455 0.00 0.00 0.00 3.07
4451 12083 3.062763 CAGAATCGCTGGACCATACATC 58.937 50.000 0.00 0.00 41.07 3.06
4452 12084 2.700371 TCAGAATCGCTGGACCATACAT 59.300 45.455 0.00 0.00 44.98 2.29
4453 12085 2.107366 TCAGAATCGCTGGACCATACA 58.893 47.619 0.00 0.00 44.98 2.29
4454 12086 2.890808 TCAGAATCGCTGGACCATAC 57.109 50.000 0.00 0.00 44.98 2.39
4455 12087 2.700371 ACATCAGAATCGCTGGACCATA 59.300 45.455 0.00 0.00 44.98 2.74
4456 12088 1.487976 ACATCAGAATCGCTGGACCAT 59.512 47.619 0.00 0.00 44.98 3.55
4457 12089 0.904649 ACATCAGAATCGCTGGACCA 59.095 50.000 0.00 0.00 44.98 4.02
4458 12090 2.890808 TACATCAGAATCGCTGGACC 57.109 50.000 0.00 0.00 44.98 4.46
4459 12091 3.062763 CCATACATCAGAATCGCTGGAC 58.937 50.000 0.00 0.00 44.98 4.02
4460 12092 2.700371 ACCATACATCAGAATCGCTGGA 59.300 45.455 0.00 0.00 44.98 3.86
4461 12093 3.062763 GACCATACATCAGAATCGCTGG 58.937 50.000 0.00 0.00 44.98 4.85
4462 12094 3.062763 GGACCATACATCAGAATCGCTG 58.937 50.000 0.00 0.00 46.31 5.18
4463 12095 2.968574 AGGACCATACATCAGAATCGCT 59.031 45.455 0.00 0.00 0.00 4.93
4464 12096 3.393089 AGGACCATACATCAGAATCGC 57.607 47.619 0.00 0.00 0.00 4.58
4468 12100 9.271921 AGCATATTATAGGACCATACATCAGAA 57.728 33.333 0.00 0.00 0.00 3.02
4474 12106 6.156256 GTCCCAGCATATTATAGGACCATACA 59.844 42.308 0.00 0.00 38.25 2.29
4475 12107 6.384305 AGTCCCAGCATATTATAGGACCATAC 59.616 42.308 3.46 0.00 43.92 2.39
4479 12111 4.777896 TCAGTCCCAGCATATTATAGGACC 59.222 45.833 3.46 0.00 43.92 4.46
4494 12126 2.398588 ACAGAGTCAGTTTCAGTCCCA 58.601 47.619 0.00 0.00 0.00 4.37
4506 12138 5.400066 TCGAATATGTTGGAACAGAGTCA 57.600 39.130 13.18 0.95 43.10 3.41


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

AutoCloner maintained by Alex Coulton.