Multiple sequence alignment - TraesCS4B01G029300

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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 TraesCS4B01G029300 chr4B 100.000 4656 0 0 1 4656 21550279 21554934 0.000000e+00 8599.0
1 TraesCS4B01G029300 chr4D 90.423 4563 233 92 210 4656 11920578 11916104 0.000000e+00 5818.0
2 TraesCS4B01G029300 chr4A 89.399 1698 122 28 2422 4082 590587562 590589238 0.000000e+00 2085.0
3 TraesCS4B01G029300 chr4A 83.654 1456 80 65 210 1588 590585702 590587076 0.000000e+00 1225.0
4 TraesCS4B01G029300 chr4A 85.863 481 46 9 1797 2256 590587073 590587552 4.190000e-135 492.0
5 TraesCS4B01G029300 chr4A 90.559 286 18 6 4372 4656 590590059 590590336 2.050000e-98 370.0
6 TraesCS4B01G029300 chr4A 82.653 196 20 10 524 717 490605687 490605870 1.340000e-35 161.0
7 TraesCS4B01G029300 chr4A 100.000 41 0 0 1 41 733551959 733551919 5.000000e-10 76.8
8 TraesCS4B01G029300 chr2D 87.500 232 20 7 701 932 379717890 379717668 4.620000e-65 259.0
9 TraesCS4B01G029300 chr7B 94.118 51 2 1 1 51 684806870 684806821 5.000000e-10 76.8
10 TraesCS4B01G029300 chr3B 100.000 41 0 0 1 41 478014962 478014922 5.000000e-10 76.8
11 TraesCS4B01G029300 chr3B 91.667 48 3 1 4 51 825753499 825753453 1.080000e-06 65.8
12 TraesCS4B01G029300 chr2A 97.778 45 0 1 1 44 31673037 31672993 5.000000e-10 76.8
13 TraesCS4B01G029300 chr1B 97.619 42 1 0 1 42 121793465 121793506 6.460000e-09 73.1
14 TraesCS4B01G029300 chr6A 97.561 41 1 0 4 44 567117 567077 2.320000e-08 71.3
15 TraesCS4B01G029300 chr2B 93.478 46 3 0 1 46 774084524 774084479 8.360000e-08 69.4
16 TraesCS4B01G029300 chr5B 89.091 55 4 2 1 54 483052254 483052307 3.010000e-07 67.6


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 TraesCS4B01G029300 chr4B 21550279 21554934 4655 False 8599 8599 100.00000 1 4656 1 chr4B.!!$F1 4655
1 TraesCS4B01G029300 chr4D 11916104 11920578 4474 True 5818 5818 90.42300 210 4656 1 chr4D.!!$R1 4446
2 TraesCS4B01G029300 chr4A 590585702 590590336 4634 False 1043 2085 87.36875 210 4656 4 chr4A.!!$F2 4446

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
64 65 0.031721 GCTAGCGCCTAACCGTGTAT 59.968 55.0 2.29 0.0 0.00 2.29 F
84 85 0.040246 GCTACGCGAGGATCACTACC 60.040 60.0 15.93 0.0 33.17 3.18 F
498 520 0.040514 CGCTCTCGCTATCACCTCTG 60.041 60.0 0.00 0.0 0.00 3.35 F
1394 1493 0.253630 TCCCAACTGCCTTATCCCCT 60.254 55.0 0.00 0.0 0.00 4.79 F
1592 1691 0.406361 AATAGTTCCACGGGGGCAAA 59.594 50.0 2.42 0.0 36.21 3.68 F
1909 2008 0.466007 TGATGTGGGCATGATTCCCG 60.466 55.0 0.00 0.0 46.92 5.14 F
3488 3670 0.036388 CCCTAGTTCCAGCAGCGAAA 60.036 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 1912 0.105913 GACCCAGGGGAAAACCAACA 60.106 55.0 11.37 0.0 42.91 3.33 R
1980 2081 0.890996 CAGAGCAACCAACCCCTGTC 60.891 60.0 0.00 0.0 0.00 3.51 R
2410 2558 0.251916 CACCGCCCCAATCAGAGTTA 59.748 55.0 0.00 0.0 0.00 2.24 R
2577 2731 1.165270 AAACGCATAAGTGTGGCCTC 58.835 50.0 3.32 0.0 40.16 4.70 R
3488 3670 1.542492 TAGGAGAAAGGCTCGTCGTT 58.458 50.0 0.00 0.0 44.91 3.85 R
3607 3789 0.035881 TGAGAGGGAGCAAGCTGTTG 59.964 55.0 0.00 0.0 36.67 3.33 R
4455 5202 0.597898 GTAGCTTCCTCGCCCGATTC 60.598 60.0 0.00 0.0 0.00 2.52 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
38 39 1.228094 GGCTGGAGATGCCCTAAGC 60.228 63.158 0.00 0.00 44.32 3.09
47 48 2.825264 GCCCTAAGCATCCTCGCT 59.175 61.111 0.00 0.00 46.67 4.93
48 49 2.050269 GCCCTAAGCATCCTCGCTA 58.950 57.895 0.00 0.00 42.89 4.26
49 50 0.037790 GCCCTAAGCATCCTCGCTAG 60.038 60.000 0.00 0.00 42.89 3.42
50 51 0.037790 CCCTAAGCATCCTCGCTAGC 60.038 60.000 4.06 4.06 42.89 3.42
51 52 0.387878 CCTAAGCATCCTCGCTAGCG 60.388 60.000 30.91 30.91 42.89 4.26
52 53 1.006314 CTAAGCATCCTCGCTAGCGC 61.006 60.000 31.82 16.67 42.89 5.92
53 54 2.421877 TAAGCATCCTCGCTAGCGCC 62.422 60.000 31.82 14.44 42.89 6.53
54 55 4.292178 GCATCCTCGCTAGCGCCT 62.292 66.667 31.82 12.95 39.59 5.52
55 56 2.920645 GCATCCTCGCTAGCGCCTA 61.921 63.158 31.82 18.60 39.59 3.93
56 57 1.660355 CATCCTCGCTAGCGCCTAA 59.340 57.895 31.82 16.80 39.59 2.69
57 58 0.664767 CATCCTCGCTAGCGCCTAAC 60.665 60.000 31.82 0.00 39.59 2.34
58 59 1.807495 ATCCTCGCTAGCGCCTAACC 61.807 60.000 31.82 0.00 39.59 2.85
59 60 2.353607 CTCGCTAGCGCCTAACCG 60.354 66.667 31.82 9.72 39.59 4.44
60 61 3.122250 CTCGCTAGCGCCTAACCGT 62.122 63.158 31.82 0.00 39.59 4.83
61 62 2.954868 CGCTAGCGCCTAACCGTG 60.955 66.667 26.07 0.00 0.00 4.94
62 63 2.183555 GCTAGCGCCTAACCGTGT 59.816 61.111 2.29 0.00 0.00 4.49
63 64 1.434696 GCTAGCGCCTAACCGTGTA 59.565 57.895 2.29 0.00 0.00 2.90
64 65 0.031721 GCTAGCGCCTAACCGTGTAT 59.968 55.000 2.29 0.00 0.00 2.29
65 66 1.767289 CTAGCGCCTAACCGTGTATG 58.233 55.000 2.29 0.00 0.00 2.39
66 67 0.249155 TAGCGCCTAACCGTGTATGC 60.249 55.000 2.29 0.00 0.00 3.14
67 68 1.520787 GCGCCTAACCGTGTATGCT 60.521 57.895 0.00 0.00 0.00 3.79
68 69 0.249155 GCGCCTAACCGTGTATGCTA 60.249 55.000 0.00 0.00 0.00 3.49
69 70 1.484356 CGCCTAACCGTGTATGCTAC 58.516 55.000 0.00 0.00 0.00 3.58
70 71 1.484356 GCCTAACCGTGTATGCTACG 58.516 55.000 0.00 0.00 40.98 3.51
71 72 1.484356 CCTAACCGTGTATGCTACGC 58.516 55.000 0.00 0.00 40.04 4.42
77 78 3.867723 GTGTATGCTACGCGAGGAT 57.132 52.632 15.93 15.03 39.91 3.24
78 79 1.687628 GTGTATGCTACGCGAGGATC 58.312 55.000 15.93 7.63 37.43 3.36
79 80 1.001706 GTGTATGCTACGCGAGGATCA 60.002 52.381 15.93 9.90 37.43 2.92
80 81 1.001706 TGTATGCTACGCGAGGATCAC 60.002 52.381 15.93 11.46 37.43 3.06
81 82 1.267261 GTATGCTACGCGAGGATCACT 59.733 52.381 15.93 0.00 37.43 3.41
82 83 1.605753 ATGCTACGCGAGGATCACTA 58.394 50.000 15.93 0.00 28.05 2.74
83 84 0.661552 TGCTACGCGAGGATCACTAC 59.338 55.000 15.93 0.00 33.17 2.73
84 85 0.040246 GCTACGCGAGGATCACTACC 60.040 60.000 15.93 0.00 33.17 3.18
85 86 0.235144 CTACGCGAGGATCACTACCG 59.765 60.000 15.93 0.00 33.17 4.02
86 87 0.462581 TACGCGAGGATCACTACCGT 60.463 55.000 15.93 4.81 38.80 4.83
87 88 1.298413 CGCGAGGATCACTACCGTG 60.298 63.158 0.00 0.00 42.59 4.94
88 89 1.807886 GCGAGGATCACTACCGTGT 59.192 57.895 0.00 0.00 41.89 4.49
89 90 1.019673 GCGAGGATCACTACCGTGTA 58.980 55.000 0.00 0.00 41.89 2.90
90 91 1.268437 GCGAGGATCACTACCGTGTAC 60.268 57.143 0.00 0.00 41.89 2.90
91 92 1.332997 CGAGGATCACTACCGTGTACC 59.667 57.143 0.00 0.00 41.89 3.34
92 93 1.332997 GAGGATCACTACCGTGTACCG 59.667 57.143 0.00 0.00 41.89 4.02
93 94 1.098050 GGATCACTACCGTGTACCGT 58.902 55.000 0.00 0.00 41.89 4.83
94 95 1.064654 GGATCACTACCGTGTACCGTC 59.935 57.143 0.00 0.00 41.89 4.79
95 96 2.012673 GATCACTACCGTGTACCGTCT 58.987 52.381 0.00 0.00 41.89 4.18
96 97 1.442769 TCACTACCGTGTACCGTCTC 58.557 55.000 0.00 0.00 41.89 3.36
97 98 1.002430 TCACTACCGTGTACCGTCTCT 59.998 52.381 0.00 0.00 41.89 3.10
98 99 1.808945 CACTACCGTGTACCGTCTCTT 59.191 52.381 0.00 0.00 36.39 2.85
99 100 2.079925 ACTACCGTGTACCGTCTCTTC 58.920 52.381 0.00 0.00 33.66 2.87
100 101 1.399791 CTACCGTGTACCGTCTCTTCC 59.600 57.143 0.00 0.00 33.66 3.46
101 102 0.251077 ACCGTGTACCGTCTCTTCCT 60.251 55.000 0.00 0.00 33.66 3.36
102 103 0.450983 CCGTGTACCGTCTCTTCCTC 59.549 60.000 0.00 0.00 33.66 3.71
103 104 1.451067 CGTGTACCGTCTCTTCCTCT 58.549 55.000 0.00 0.00 0.00 3.69
104 105 2.625737 CGTGTACCGTCTCTTCCTCTA 58.374 52.381 0.00 0.00 0.00 2.43
105 106 2.351111 CGTGTACCGTCTCTTCCTCTAC 59.649 54.545 0.00 0.00 0.00 2.59
106 107 2.682352 GTGTACCGTCTCTTCCTCTACC 59.318 54.545 0.00 0.00 0.00 3.18
107 108 2.306805 TGTACCGTCTCTTCCTCTACCA 59.693 50.000 0.00 0.00 0.00 3.25
108 109 2.599408 ACCGTCTCTTCCTCTACCAA 57.401 50.000 0.00 0.00 0.00 3.67
109 110 3.103080 ACCGTCTCTTCCTCTACCAAT 57.897 47.619 0.00 0.00 0.00 3.16
110 111 2.761208 ACCGTCTCTTCCTCTACCAATG 59.239 50.000 0.00 0.00 0.00 2.82
111 112 3.024547 CCGTCTCTTCCTCTACCAATGA 58.975 50.000 0.00 0.00 0.00 2.57
112 113 3.447586 CCGTCTCTTCCTCTACCAATGAA 59.552 47.826 0.00 0.00 0.00 2.57
113 114 4.081642 CCGTCTCTTCCTCTACCAATGAAA 60.082 45.833 0.00 0.00 0.00 2.69
114 115 5.395768 CCGTCTCTTCCTCTACCAATGAAAT 60.396 44.000 0.00 0.00 0.00 2.17
115 116 5.521735 CGTCTCTTCCTCTACCAATGAAATG 59.478 44.000 0.00 0.00 0.00 2.32
116 117 6.628175 CGTCTCTTCCTCTACCAATGAAATGA 60.628 42.308 0.00 0.00 0.00 2.57
117 118 7.278875 GTCTCTTCCTCTACCAATGAAATGAT 58.721 38.462 0.00 0.00 0.00 2.45
118 119 8.424918 GTCTCTTCCTCTACCAATGAAATGATA 58.575 37.037 0.00 0.00 0.00 2.15
119 120 8.424918 TCTCTTCCTCTACCAATGAAATGATAC 58.575 37.037 0.00 0.00 0.00 2.24
120 121 7.210174 TCTTCCTCTACCAATGAAATGATACG 58.790 38.462 0.00 0.00 0.00 3.06
121 122 5.297547 TCCTCTACCAATGAAATGATACGC 58.702 41.667 0.00 0.00 0.00 4.42
122 123 5.056480 CCTCTACCAATGAAATGATACGCA 58.944 41.667 0.00 0.00 0.00 5.24
123 124 5.702670 CCTCTACCAATGAAATGATACGCAT 59.297 40.000 0.00 0.00 39.43 4.73
124 125 6.873605 CCTCTACCAATGAAATGATACGCATA 59.126 38.462 0.00 0.00 35.78 3.14
125 126 7.387673 CCTCTACCAATGAAATGATACGCATAA 59.612 37.037 0.00 0.00 35.78 1.90
126 127 8.083462 TCTACCAATGAAATGATACGCATAAC 57.917 34.615 0.00 0.00 35.78 1.89
172 173 8.674263 AAATCATACTGAGAATCCTAAAGCAG 57.326 34.615 0.00 0.00 0.00 4.24
173 174 5.605534 TCATACTGAGAATCCTAAAGCAGC 58.394 41.667 0.00 0.00 0.00 5.25
174 175 3.988976 ACTGAGAATCCTAAAGCAGCA 57.011 42.857 0.00 0.00 0.00 4.41
175 176 4.500499 ACTGAGAATCCTAAAGCAGCAT 57.500 40.909 0.00 0.00 0.00 3.79
176 177 5.620738 ACTGAGAATCCTAAAGCAGCATA 57.379 39.130 0.00 0.00 0.00 3.14
177 178 5.609423 ACTGAGAATCCTAAAGCAGCATAG 58.391 41.667 0.00 0.00 0.00 2.23
178 179 4.965814 TGAGAATCCTAAAGCAGCATAGG 58.034 43.478 15.18 15.18 40.09 2.57
179 180 4.202398 TGAGAATCCTAAAGCAGCATAGGG 60.202 45.833 19.19 6.36 39.36 3.53
180 181 3.976654 AGAATCCTAAAGCAGCATAGGGA 59.023 43.478 19.19 10.78 39.36 4.20
181 182 4.600983 AGAATCCTAAAGCAGCATAGGGAT 59.399 41.667 19.19 12.27 39.36 3.85
182 183 3.777106 TCCTAAAGCAGCATAGGGATG 57.223 47.619 19.19 0.64 39.36 3.51
183 184 3.317406 TCCTAAAGCAGCATAGGGATGA 58.683 45.455 19.19 3.00 39.36 2.92
184 185 3.716353 TCCTAAAGCAGCATAGGGATGAA 59.284 43.478 19.19 2.71 39.36 2.57
185 186 4.352001 TCCTAAAGCAGCATAGGGATGAAT 59.648 41.667 19.19 0.00 39.36 2.57
186 187 5.075493 CCTAAAGCAGCATAGGGATGAATT 58.925 41.667 13.99 0.00 35.95 2.17
187 188 5.182760 CCTAAAGCAGCATAGGGATGAATTC 59.817 44.000 13.99 0.00 35.95 2.17
188 189 3.151912 AGCAGCATAGGGATGAATTCC 57.848 47.619 2.27 0.00 44.62 3.01
222 223 4.020662 TGTGACCATAAAAATTTCCCCAGC 60.021 41.667 0.00 0.00 0.00 4.85
249 250 7.233348 GCTCTAAAATCCATATGAAATGGGGAA 59.767 37.037 3.65 0.00 39.60 3.97
334 355 2.435059 GCTCTGGCCGTTCTCACC 60.435 66.667 0.00 0.00 0.00 4.02
496 518 4.933483 CGCTCTCGCTATCACCTC 57.067 61.111 0.00 0.00 0.00 3.85
497 519 2.326222 CGCTCTCGCTATCACCTCT 58.674 57.895 0.00 0.00 0.00 3.69
498 520 0.040514 CGCTCTCGCTATCACCTCTG 60.041 60.000 0.00 0.00 0.00 3.35
1063 1119 4.760047 CGGGTGCTGGGGAGTTCG 62.760 72.222 0.00 0.00 0.00 3.95
1240 1317 4.037446 TGCTTTTAACCGTTTCAGCTCAAT 59.963 37.500 9.29 0.00 0.00 2.57
1280 1373 2.226315 AGAGTGGTGCCATGAGCCA 61.226 57.895 0.00 0.00 42.71 4.75
1283 1376 0.625316 AGTGGTGCCATGAGCCATTA 59.375 50.000 0.00 0.00 42.71 1.90
1305 1398 3.094572 GCTACCTCTACCTGTACACCAA 58.905 50.000 0.00 0.00 0.00 3.67
1306 1399 3.705072 GCTACCTCTACCTGTACACCAAT 59.295 47.826 0.00 0.00 0.00 3.16
1373 1466 3.056821 GCCATTTTCCCTTCACAACCTAC 60.057 47.826 0.00 0.00 0.00 3.18
1383 1482 1.697432 TCACAACCTACCTCCCAACTG 59.303 52.381 0.00 0.00 0.00 3.16
1394 1493 0.253630 TCCCAACTGCCTTATCCCCT 60.254 55.000 0.00 0.00 0.00 4.79
1403 1502 1.051812 CCTTATCCCCTCATGACGCT 58.948 55.000 0.00 0.00 0.00 5.07
1411 1510 2.544685 CCCTCATGACGCTAGAACTTG 58.455 52.381 0.00 0.00 0.00 3.16
1425 1524 7.148407 ACGCTAGAACTTGGAAAATGTATGAAG 60.148 37.037 0.00 0.00 0.00 3.02
1436 1535 8.906867 TGGAAAATGTATGAAGAATCTGGATTC 58.093 33.333 13.59 13.59 45.66 2.52
1499 1598 8.682710 GTGTTCTTACATTAGAATGGCCATTTA 58.317 33.333 31.13 20.74 40.70 1.40
1589 1688 0.835276 AGTAATAGTTCCACGGGGGC 59.165 55.000 2.42 0.00 36.21 5.80
1592 1691 0.406361 AATAGTTCCACGGGGGCAAA 59.594 50.000 2.42 0.00 36.21 3.68
1604 1703 4.717629 GGCAAAGAAACCCCGCGC 62.718 66.667 0.00 0.00 0.00 6.86
1711 1810 6.424032 AGACATAGACAGTAGACACCATGTA 58.576 40.000 0.00 0.00 0.00 2.29
1712 1811 6.319152 AGACATAGACAGTAGACACCATGTAC 59.681 42.308 0.00 0.00 0.00 2.90
1809 1908 3.605749 ATTCTGGGGTCGCCACACG 62.606 63.158 4.12 0.00 45.62 4.49
1813 1912 3.688159 GGGGTCGCCACACGTACT 61.688 66.667 0.00 0.00 44.19 2.73
1845 1944 2.755103 CCCTGGGTCTTAATTGAACTGC 59.245 50.000 3.97 0.00 0.00 4.40
1873 1972 8.099364 TGATGAAATTTCTCTTTGTGTAGGTC 57.901 34.615 18.64 0.93 0.00 3.85
1878 1977 1.623811 TCTCTTTGTGTAGGTCCAGCC 59.376 52.381 0.00 0.00 37.58 4.85
1909 2008 0.466007 TGATGTGGGCATGATTCCCG 60.466 55.000 0.00 0.00 46.92 5.14
1980 2081 4.588106 TGGGAACATGCATATTTATGGGTG 59.412 41.667 0.00 0.00 32.37 4.61
2038 2166 8.984891 CAGTCTTGCAACAATATATTTTTGGA 57.015 30.769 20.52 16.90 30.35 3.53
2116 2246 2.088104 TGGGCAATGTGGTTTGGTTA 57.912 45.000 0.00 0.00 0.00 2.85
2120 2250 3.007398 GGGCAATGTGGTTTGGTTATTCA 59.993 43.478 0.00 0.00 0.00 2.57
2144 2274 6.258287 CAGCTGGTTTTAGAGAGATTCTCATG 59.742 42.308 15.83 0.00 45.73 3.07
2162 2292 7.063934 TCTCATGACAGCAGATAATGATTCT 57.936 36.000 0.00 0.00 0.00 2.40
2206 2341 7.120923 TGTTAACTTCTACTGGTTTGAGAGT 57.879 36.000 7.22 0.00 0.00 3.24
2208 2343 7.494625 TGTTAACTTCTACTGGTTTGAGAGTTG 59.505 37.037 7.22 0.00 0.00 3.16
2236 2371 4.478203 TCAAATGATTCCACAGTTTGGGA 58.522 39.130 0.00 0.00 46.92 4.37
2256 2391 4.820173 GGGAGGTTAAAATCATACTTCGGG 59.180 45.833 0.00 0.00 0.00 5.14
2257 2392 4.820173 GGAGGTTAAAATCATACTTCGGGG 59.180 45.833 0.00 0.00 0.00 5.73
2258 2393 5.434408 GAGGTTAAAATCATACTTCGGGGT 58.566 41.667 0.00 0.00 0.00 4.95
2259 2394 5.823312 AGGTTAAAATCATACTTCGGGGTT 58.177 37.500 0.00 0.00 0.00 4.11
2260 2395 5.650703 AGGTTAAAATCATACTTCGGGGTTG 59.349 40.000 0.00 0.00 0.00 3.77
2261 2396 5.648960 GGTTAAAATCATACTTCGGGGTTGA 59.351 40.000 0.00 0.00 0.00 3.18
2262 2397 6.151480 GGTTAAAATCATACTTCGGGGTTGAA 59.849 38.462 0.00 0.00 0.00 2.69
2263 2398 7.309316 GGTTAAAATCATACTTCGGGGTTGAAA 60.309 37.037 0.00 0.00 0.00 2.69
2264 2399 6.658188 AAAATCATACTTCGGGGTTGAAAA 57.342 33.333 0.00 0.00 0.00 2.29
2265 2400 6.850752 AAATCATACTTCGGGGTTGAAAAT 57.149 33.333 0.00 0.00 0.00 1.82
2266 2401 6.850752 AATCATACTTCGGGGTTGAAAATT 57.149 33.333 0.00 0.00 0.00 1.82
2267 2402 6.850752 ATCATACTTCGGGGTTGAAAATTT 57.149 33.333 0.00 0.00 0.00 1.82
2269 2404 5.770663 TCATACTTCGGGGTTGAAAATTTGA 59.229 36.000 0.00 0.00 0.00 2.69
2270 2405 4.316205 ACTTCGGGGTTGAAAATTTGAC 57.684 40.909 0.00 0.00 0.00 3.18
2271 2406 3.069016 ACTTCGGGGTTGAAAATTTGACC 59.931 43.478 9.16 9.16 0.00 4.02
2274 2422 3.707102 TCGGGGTTGAAAATTTGACCTTT 59.293 39.130 14.63 0.00 32.73 3.11
2278 2426 6.461788 CGGGGTTGAAAATTTGACCTTTCTAA 60.462 38.462 14.63 0.00 33.55 2.10
2279 2427 7.450074 GGGGTTGAAAATTTGACCTTTCTAAT 58.550 34.615 14.63 0.00 33.55 1.73
2292 2440 9.581289 TTGACCTTTCTAATTTGGAACTGAATA 57.419 29.630 0.00 0.00 0.00 1.75
2293 2441 9.581289 TGACCTTTCTAATTTGGAACTGAATAA 57.419 29.630 0.00 0.00 0.00 1.40
2326 2474 7.712264 TGAGTTTGAAAAACTGCATAAATGG 57.288 32.000 9.97 0.00 0.00 3.16
2332 2480 2.678471 AACTGCATAAATGGCCTTGC 57.322 45.000 3.32 6.28 35.67 4.01
2365 2513 8.306038 CCATTTAAGTCAATGTCCTGAAATTCA 58.694 33.333 0.00 0.00 32.95 2.57
2369 2517 6.906157 AGTCAATGTCCTGAAATTCATTGT 57.094 33.333 12.42 0.00 43.97 2.71
2385 2533 4.382291 TCATTGTTGTACCAGTACCACAC 58.618 43.478 12.84 5.16 40.12 3.82
2394 2542 2.884639 ACCAGTACCACACAATGAAAGC 59.115 45.455 0.00 0.00 0.00 3.51
2400 2548 3.221771 ACCACACAATGAAAGCAAGCTA 58.778 40.909 0.00 0.00 0.00 3.32
2410 2558 7.067859 ACAATGAAAGCAAGCTATGTGTATGAT 59.932 33.333 0.00 0.00 0.00 2.45
2416 2568 7.060383 AGCAAGCTATGTGTATGATAACTCT 57.940 36.000 0.00 0.00 0.00 3.24
2417 2569 6.927936 AGCAAGCTATGTGTATGATAACTCTG 59.072 38.462 0.00 0.00 0.00 3.35
2425 2577 4.757149 GTGTATGATAACTCTGATTGGGGC 59.243 45.833 0.00 0.00 0.00 5.80
2444 2597 1.905512 GGTGGAGTTGCGGGTAGAT 59.094 57.895 0.00 0.00 0.00 1.98
2500 2654 1.691434 TGGTGCTCACATGTACACAGA 59.309 47.619 20.83 5.63 34.69 3.41
2501 2655 2.069273 GGTGCTCACATGTACACAGAC 58.931 52.381 20.83 5.98 34.69 3.51
2619 2783 3.997021 AGAAATCGTGAGCTGTTTGTAGG 59.003 43.478 0.00 0.00 0.00 3.18
2626 2790 4.377897 GTGAGCTGTTTGTAGGTAAGTGT 58.622 43.478 0.00 0.00 0.00 3.55
2758 2930 3.026630 TCTTGGATGAGTGACGTCAAC 57.973 47.619 21.95 17.41 36.34 3.18
2771 2943 3.916172 TGACGTCAACGAATAACTAGTGC 59.084 43.478 17.62 0.00 43.02 4.40
2793 2965 4.496341 GCGATTATGTTGAGTGGTTCATGG 60.496 45.833 0.00 0.00 35.27 3.66
2974 3146 4.641989 CCCTCCCAATTCTTAGTCACAATG 59.358 45.833 0.00 0.00 0.00 2.82
3018 3190 4.931601 CACAACTGCTAAGCTGTATCTTCA 59.068 41.667 0.00 0.00 39.66 3.02
3071 3243 7.801716 ACTTCACTAGCAACAATACAGAAAA 57.198 32.000 0.00 0.00 0.00 2.29
3154 3331 5.070981 TCATTATTGTTCCTAGCTGGAGGAG 59.929 44.000 5.39 0.00 46.43 3.69
3195 3372 6.635030 TGCTGATGATCGTATAGTAGTTGT 57.365 37.500 0.00 0.00 0.00 3.32
3196 3373 6.438763 TGCTGATGATCGTATAGTAGTTGTG 58.561 40.000 0.00 0.00 0.00 3.33
3244 3421 4.159135 GCTCCTGGATCACATTGTTTCATT 59.841 41.667 0.00 0.00 0.00 2.57
3246 3423 4.082081 TCCTGGATCACATTGTTTCATTGC 60.082 41.667 0.00 0.00 0.00 3.56
3249 3426 6.198650 TGGATCACATTGTTTCATTGCTAG 57.801 37.500 0.00 0.00 0.00 3.42
3303 3483 1.466167 CAAGAACTGTGGATTCCAGCG 59.534 52.381 5.39 2.61 32.34 5.18
3368 3550 6.401394 CAGGACTGAATTCACTGTCTTGATA 58.599 40.000 24.19 0.00 43.10 2.15
3375 3557 8.667076 TGAATTCACTGTCTTGATATGGTATG 57.333 34.615 3.38 0.00 0.00 2.39
3457 3639 4.628333 CACAGCATGATCCCACAAAATTTC 59.372 41.667 0.00 0.00 39.69 2.17
3488 3670 0.036388 CCCTAGTTCCAGCAGCGAAA 60.036 55.000 0.00 0.00 0.00 3.46
3595 3777 4.279169 CCTGGCAATTTTGTGAAGAAGAGA 59.721 41.667 0.00 0.00 0.00 3.10
3601 3783 6.201425 GCAATTTTGTGAAGAAGAGAAATGCA 59.799 34.615 0.00 0.00 0.00 3.96
3607 3789 4.391523 GTGAAGAAGAGAAATGCAGACTCC 59.608 45.833 11.97 1.71 0.00 3.85
3613 3795 2.157738 AGAAATGCAGACTCCAACAGC 58.842 47.619 0.00 0.00 0.00 4.40
3662 3844 2.478033 GGGGCTGGATAAAACCGCG 61.478 63.158 0.00 0.00 33.07 6.46
3817 4008 1.801771 CTCCAAAAACGTCGCATGGTA 59.198 47.619 8.79 0.00 32.90 3.25
3830 4021 3.134623 TCGCATGGTATCCTTTGAGACAT 59.865 43.478 0.00 0.00 34.33 3.06
3839 4030 4.288670 TCCTTTGAGACATCGATACGTC 57.711 45.455 0.00 2.31 0.00 4.34
3847 4038 2.089201 ACATCGATACGTCTGGTGTCA 58.911 47.619 0.00 0.00 36.64 3.58
3881 4072 1.704387 TTACCGCTGACATGCATGCG 61.704 55.000 26.53 22.38 40.98 4.73
3948 4140 0.248907 GCGCTGCTCGTATACCTCAA 60.249 55.000 0.00 0.00 41.07 3.02
3962 4154 5.907197 ATACCTCAAAATAATGTCTCGCG 57.093 39.130 0.00 0.00 0.00 5.87
3972 4164 2.765108 ATGTCTCGCGTACTGATGAG 57.235 50.000 5.77 0.00 0.00 2.90
4048 4240 6.348540 CCTTCACTGTATTTTACTGTTGAGCC 60.349 42.308 0.00 0.00 38.55 4.70
4074 4266 5.174943 GTGTGCTTGCAATTGTTTACCTAAC 59.825 40.000 7.40 0.00 37.26 2.34
4126 4413 6.154021 AGCAAGATTTTGTGGCTAAATCTCAT 59.846 34.615 17.05 6.21 46.35 2.90
4153 4455 8.934697 AGTACATACTCCCAATCTTAATAAGCA 58.065 33.333 0.00 0.00 0.00 3.91
4198 4501 1.430707 GCGGGCGGCGTTCTAAATTA 61.431 55.000 9.37 0.00 0.00 1.40
4416 5162 9.350357 CACCATTCTTTTCAAGAGAATAACATG 57.650 33.333 2.92 0.00 40.82 3.21
4455 5202 1.073216 CTAGTCGAGGCAGCACAACG 61.073 60.000 0.00 0.00 0.00 4.10
4542 5293 3.602491 CGAAGAACATGCGCTATAACTGC 60.602 47.826 9.73 0.58 0.00 4.40
4547 5298 3.123804 ACATGCGCTATAACTGCACTAC 58.876 45.455 9.73 0.00 42.11 2.73
4564 5315 3.951680 CACTACCAACAGGGAAACACTTT 59.048 43.478 0.00 0.00 41.15 2.66
4572 5323 6.398095 CAACAGGGAAACACTTTCTTTCTTT 58.602 36.000 0.00 0.00 39.59 2.52
4647 5398 3.142393 CAGCCCCGGACATAGGAG 58.858 66.667 0.73 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 4.471761 GCTTAGGGCATCTCCAGC 57.528 61.111 0.00 0.00 41.35 4.85
30 31 0.037790 CTAGCGAGGATGCTTAGGGC 60.038 60.000 0.00 0.00 44.46 5.19
31 32 0.037790 GCTAGCGAGGATGCTTAGGG 60.038 60.000 0.00 0.00 44.46 3.53
32 33 0.387878 CGCTAGCGAGGATGCTTAGG 60.388 60.000 32.98 0.00 44.46 2.69
33 34 1.006314 GCGCTAGCGAGGATGCTTAG 61.006 60.000 39.52 7.40 44.46 2.18
34 35 1.007271 GCGCTAGCGAGGATGCTTA 60.007 57.895 39.52 0.00 44.46 3.09
35 36 2.279784 GCGCTAGCGAGGATGCTT 60.280 61.111 39.52 0.00 44.46 3.91
37 38 2.421877 TTAGGCGCTAGCGAGGATGC 62.422 60.000 39.52 20.51 46.35 3.91
38 39 0.664767 GTTAGGCGCTAGCGAGGATG 60.665 60.000 39.52 11.13 46.35 3.51
39 40 1.660917 GTTAGGCGCTAGCGAGGAT 59.339 57.895 39.52 22.38 46.35 3.24
40 41 2.487532 GGTTAGGCGCTAGCGAGGA 61.488 63.158 39.52 20.17 46.35 3.71
41 42 2.027751 GGTTAGGCGCTAGCGAGG 59.972 66.667 39.52 12.74 46.35 4.63
42 43 2.353607 CGGTTAGGCGCTAGCGAG 60.354 66.667 39.52 13.54 46.35 5.03
43 44 3.136123 ACGGTTAGGCGCTAGCGA 61.136 61.111 39.52 17.48 46.35 4.93
44 45 2.327002 TACACGGTTAGGCGCTAGCG 62.327 60.000 32.22 32.22 46.35 4.26
45 46 0.031721 ATACACGGTTAGGCGCTAGC 59.968 55.000 7.64 4.06 44.18 3.42
46 47 1.767289 CATACACGGTTAGGCGCTAG 58.233 55.000 7.64 0.00 0.00 3.42
47 48 0.249155 GCATACACGGTTAGGCGCTA 60.249 55.000 7.64 0.00 0.00 4.26
48 49 1.520787 GCATACACGGTTAGGCGCT 60.521 57.895 7.64 0.00 0.00 5.92
49 50 0.249155 TAGCATACACGGTTAGGCGC 60.249 55.000 0.00 0.00 0.00 6.53
50 51 1.484356 GTAGCATACACGGTTAGGCG 58.516 55.000 0.00 0.00 42.43 5.52
51 52 1.484356 CGTAGCATACACGGTTAGGC 58.516 55.000 0.00 0.00 43.24 3.93
66 67 0.235144 CGGTAGTGATCCTCGCGTAG 59.765 60.000 5.77 1.91 30.95 3.51
67 68 0.462581 ACGGTAGTGATCCTCGCGTA 60.463 55.000 5.77 0.00 30.95 4.42
68 69 1.748122 ACGGTAGTGATCCTCGCGT 60.748 57.895 5.77 0.00 30.95 6.01
69 70 3.108343 ACGGTAGTGATCCTCGCG 58.892 61.111 0.00 0.00 30.95 5.87
85 86 2.682352 GGTAGAGGAAGAGACGGTACAC 59.318 54.545 0.00 0.00 0.00 2.90
86 87 2.306805 TGGTAGAGGAAGAGACGGTACA 59.693 50.000 0.00 0.00 0.00 2.90
87 88 2.996631 TGGTAGAGGAAGAGACGGTAC 58.003 52.381 0.00 0.00 0.00 3.34
88 89 3.726557 TTGGTAGAGGAAGAGACGGTA 57.273 47.619 0.00 0.00 0.00 4.02
89 90 2.599408 TTGGTAGAGGAAGAGACGGT 57.401 50.000 0.00 0.00 0.00 4.83
90 91 3.024547 TCATTGGTAGAGGAAGAGACGG 58.975 50.000 0.00 0.00 0.00 4.79
91 92 4.720649 TTCATTGGTAGAGGAAGAGACG 57.279 45.455 0.00 0.00 0.00 4.18
92 93 6.644347 TCATTTCATTGGTAGAGGAAGAGAC 58.356 40.000 0.00 0.00 0.00 3.36
93 94 6.874278 TCATTTCATTGGTAGAGGAAGAGA 57.126 37.500 0.00 0.00 0.00 3.10
94 95 7.383572 CGTATCATTTCATTGGTAGAGGAAGAG 59.616 40.741 0.00 0.00 0.00 2.85
95 96 7.210174 CGTATCATTTCATTGGTAGAGGAAGA 58.790 38.462 0.00 0.00 0.00 2.87
96 97 6.073548 GCGTATCATTTCATTGGTAGAGGAAG 60.074 42.308 0.00 0.00 0.00 3.46
97 98 5.758296 GCGTATCATTTCATTGGTAGAGGAA 59.242 40.000 0.00 0.00 0.00 3.36
98 99 5.163353 TGCGTATCATTTCATTGGTAGAGGA 60.163 40.000 0.00 0.00 0.00 3.71
99 100 5.056480 TGCGTATCATTTCATTGGTAGAGG 58.944 41.667 0.00 0.00 0.00 3.69
100 101 6.791887 ATGCGTATCATTTCATTGGTAGAG 57.208 37.500 0.00 0.00 29.16 2.43
101 102 7.095816 CGTTATGCGTATCATTTCATTGGTAGA 60.096 37.037 0.00 0.00 36.63 2.59
102 103 7.009440 CGTTATGCGTATCATTTCATTGGTAG 58.991 38.462 0.00 0.00 36.63 3.18
103 104 6.565060 GCGTTATGCGTATCATTTCATTGGTA 60.565 38.462 0.00 0.00 43.66 3.25
104 105 5.747565 CGTTATGCGTATCATTTCATTGGT 58.252 37.500 0.00 0.00 36.63 3.67
105 106 4.612614 GCGTTATGCGTATCATTTCATTGG 59.387 41.667 0.00 0.00 43.66 3.16
106 107 5.713851 GCGTTATGCGTATCATTTCATTG 57.286 39.130 0.00 0.00 43.66 2.82
149 150 7.474507 ATGCTGCTTTAGGATTCTCAGTATGAT 60.475 37.037 0.00 0.00 38.35 2.45
150 151 6.183361 ATGCTGCTTTAGGATTCTCAGTATGA 60.183 38.462 0.00 0.00 37.08 2.15
151 152 5.363101 TGCTGCTTTAGGATTCTCAGTATG 58.637 41.667 0.00 0.00 37.54 2.39
152 153 5.620738 TGCTGCTTTAGGATTCTCAGTAT 57.379 39.130 0.00 0.00 0.00 2.12
153 154 5.620738 ATGCTGCTTTAGGATTCTCAGTA 57.379 39.130 0.00 0.00 33.06 2.74
154 155 3.988976 TGCTGCTTTAGGATTCTCAGT 57.011 42.857 0.00 0.00 0.00 3.41
155 156 4.996122 CCTATGCTGCTTTAGGATTCTCAG 59.004 45.833 18.57 0.00 38.53 3.35
156 157 4.202398 CCCTATGCTGCTTTAGGATTCTCA 60.202 45.833 22.64 0.00 38.53 3.27
157 158 4.040952 TCCCTATGCTGCTTTAGGATTCTC 59.959 45.833 22.64 0.00 38.53 2.87
158 159 3.976654 TCCCTATGCTGCTTTAGGATTCT 59.023 43.478 22.64 0.00 38.53 2.40
159 160 4.357918 TCCCTATGCTGCTTTAGGATTC 57.642 45.455 22.64 0.00 38.53 2.52
160 161 4.352001 TCATCCCTATGCTGCTTTAGGATT 59.648 41.667 22.64 11.66 38.53 3.01
161 162 3.912528 TCATCCCTATGCTGCTTTAGGAT 59.087 43.478 22.64 16.92 40.85 3.24
162 163 3.317406 TCATCCCTATGCTGCTTTAGGA 58.683 45.455 22.64 15.76 37.74 2.94
163 164 3.777106 TCATCCCTATGCTGCTTTAGG 57.223 47.619 17.20 17.20 35.69 2.69
164 165 5.182760 GGAATTCATCCCTATGCTGCTTTAG 59.817 44.000 7.93 2.36 43.00 1.85
165 166 5.072741 GGAATTCATCCCTATGCTGCTTTA 58.927 41.667 7.93 0.00 43.00 1.85
166 167 3.893813 GGAATTCATCCCTATGCTGCTTT 59.106 43.478 7.93 0.00 43.00 3.51
167 168 3.494332 GGAATTCATCCCTATGCTGCTT 58.506 45.455 7.93 0.00 43.00 3.91
168 169 3.151912 GGAATTCATCCCTATGCTGCT 57.848 47.619 7.93 0.00 43.00 4.24
192 193 9.061435 GGGAAATTTTTATGGTCACAAAATTCA 57.939 29.630 12.20 0.00 38.54 2.57
193 194 8.511321 GGGGAAATTTTTATGGTCACAAAATTC 58.489 33.333 12.20 4.95 38.54 2.17
194 195 8.001292 TGGGGAAATTTTTATGGTCACAAAATT 58.999 29.630 0.00 8.48 40.29 1.82
195 196 7.521669 TGGGGAAATTTTTATGGTCACAAAAT 58.478 30.769 0.00 0.00 32.62 1.82
196 197 6.900194 TGGGGAAATTTTTATGGTCACAAAA 58.100 32.000 0.00 0.00 0.00 2.44
197 198 6.500589 TGGGGAAATTTTTATGGTCACAAA 57.499 33.333 0.00 0.00 0.00 2.83
198 199 5.512232 GCTGGGGAAATTTTTATGGTCACAA 60.512 40.000 0.00 0.00 0.00 3.33
199 200 4.020662 GCTGGGGAAATTTTTATGGTCACA 60.021 41.667 0.00 0.00 0.00 3.58
200 201 4.503910 GCTGGGGAAATTTTTATGGTCAC 58.496 43.478 0.00 0.00 0.00 3.67
201 202 3.194542 CGCTGGGGAAATTTTTATGGTCA 59.805 43.478 0.00 0.00 0.00 4.02
202 203 3.780902 CGCTGGGGAAATTTTTATGGTC 58.219 45.455 0.00 0.00 0.00 4.02
203 204 2.093711 GCGCTGGGGAAATTTTTATGGT 60.094 45.455 0.00 0.00 0.00 3.55
204 205 2.168313 AGCGCTGGGGAAATTTTTATGG 59.832 45.455 10.39 0.00 0.00 2.74
205 206 3.131046 AGAGCGCTGGGGAAATTTTTATG 59.869 43.478 18.48 0.00 0.00 1.90
206 207 3.365472 AGAGCGCTGGGGAAATTTTTAT 58.635 40.909 18.48 0.00 0.00 1.40
207 208 2.802719 AGAGCGCTGGGGAAATTTTTA 58.197 42.857 18.48 0.00 0.00 1.52
208 209 1.632589 AGAGCGCTGGGGAAATTTTT 58.367 45.000 18.48 0.00 0.00 1.94
209 210 2.507407 TAGAGCGCTGGGGAAATTTT 57.493 45.000 18.48 0.00 0.00 1.82
210 211 2.507407 TTAGAGCGCTGGGGAAATTT 57.493 45.000 18.48 0.00 0.00 1.82
211 212 2.507407 TTTAGAGCGCTGGGGAAATT 57.493 45.000 18.48 0.00 0.00 1.82
212 213 2.507407 TTTTAGAGCGCTGGGGAAAT 57.493 45.000 18.48 0.00 0.00 2.17
213 214 2.365582 GATTTTAGAGCGCTGGGGAAA 58.634 47.619 18.48 10.95 0.00 3.13
214 215 1.408266 GGATTTTAGAGCGCTGGGGAA 60.408 52.381 18.48 4.82 0.00 3.97
222 223 6.349611 CCCCATTTCATATGGATTTTAGAGCG 60.350 42.308 2.13 0.00 41.64 5.03
254 255 2.631062 TGGTGTCTTGTCACGGTTCTAT 59.369 45.455 0.00 0.00 39.00 1.98
483 505 1.268999 GCAGACAGAGGTGATAGCGAG 60.269 57.143 0.00 0.00 0.00 5.03
489 511 0.814457 GAGACGCAGACAGAGGTGAT 59.186 55.000 0.00 0.00 0.00 3.06
495 517 0.602905 TGAGACGAGACGCAGACAGA 60.603 55.000 0.00 0.00 0.00 3.41
496 518 0.449786 ATGAGACGAGACGCAGACAG 59.550 55.000 0.00 0.00 0.00 3.51
497 519 0.881796 AATGAGACGAGACGCAGACA 59.118 50.000 0.00 0.00 0.00 3.41
498 520 1.131504 AGAATGAGACGAGACGCAGAC 59.868 52.381 0.00 0.00 0.00 3.51
701 724 3.807538 CATGCTGCTGGTCGTGGC 61.808 66.667 0.00 0.00 0.00 5.01
706 732 3.857854 CGCGACATGCTGCTGGTC 61.858 66.667 0.00 12.25 43.27 4.02
734 760 4.498520 CATGCTGCTGCTGCTGGC 62.499 66.667 27.67 20.58 40.48 4.85
996 1052 0.652592 GGAAGAACGGCGACATCATG 59.347 55.000 16.62 0.00 0.00 3.07
1113 1190 0.179056 CGTGAGGGTTGACACCAAGT 60.179 55.000 0.00 0.00 46.43 3.16
1280 1373 5.139001 GGTGTACAGGTAGAGGTAGCTAAT 58.861 45.833 0.00 0.00 35.13 1.73
1283 1376 2.310945 TGGTGTACAGGTAGAGGTAGCT 59.689 50.000 0.00 0.00 37.48 3.32
1345 1438 3.161866 GTGAAGGGAAAATGGCAAGGTA 58.838 45.455 0.00 0.00 0.00 3.08
1360 1453 1.358152 TGGGAGGTAGGTTGTGAAGG 58.642 55.000 0.00 0.00 0.00 3.46
1373 1466 0.183731 GGGATAAGGCAGTTGGGAGG 59.816 60.000 0.00 0.00 0.00 4.30
1383 1482 0.603975 GCGTCATGAGGGGATAAGGC 60.604 60.000 16.66 0.00 0.00 4.35
1394 1493 3.953712 TTCCAAGTTCTAGCGTCATGA 57.046 42.857 0.00 0.00 0.00 3.07
1411 1510 8.906867 TGAATCCAGATTCTTCATACATTTTCC 58.093 33.333 18.55 0.00 45.55 3.13
1455 1554 7.308782 AGAACACTCACTTGTTAGAACTTTG 57.691 36.000 0.00 0.00 39.88 2.77
1499 1598 2.092429 AGTCACACCATATTGCCGGAAT 60.092 45.455 5.05 4.90 0.00 3.01
1566 1665 4.284234 GCCCCCGTGGAACTATTACTTATA 59.716 45.833 0.00 0.00 35.39 0.98
1567 1666 3.072038 GCCCCCGTGGAACTATTACTTAT 59.928 47.826 0.00 0.00 35.39 1.73
1568 1667 2.435437 GCCCCCGTGGAACTATTACTTA 59.565 50.000 0.00 0.00 35.39 2.24
1582 1681 2.203582 GGGTTTCTTTGCCCCCGT 60.204 61.111 0.00 0.00 38.99 5.28
1589 1688 1.154035 GATGCGCGGGGTTTCTTTG 60.154 57.895 8.83 0.00 0.00 2.77
1592 1691 4.796495 GGGATGCGCGGGGTTTCT 62.796 66.667 8.83 0.00 0.00 2.52
1602 1701 8.536172 AAACAATAGTTTCATCACGGGATGCG 62.536 42.308 23.14 0.00 44.35 4.73
1604 1703 6.194796 AAACAATAGTTTCATCACGGGATG 57.805 37.500 21.99 21.99 44.35 3.51
1617 1716 5.763876 AGAGCTACCCAGAAACAATAGTT 57.236 39.130 0.00 0.00 40.40 2.24
1624 1723 2.745515 ACGAAGAGCTACCCAGAAAC 57.254 50.000 0.00 0.00 0.00 2.78
1690 1789 6.451064 TGTACATGGTGTCTACTGTCTATG 57.549 41.667 0.00 0.00 0.00 2.23
1700 1799 9.905713 ACATAAAATATCTTGTACATGGTGTCT 57.094 29.630 8.74 0.00 0.00 3.41
1809 1908 2.235891 CCAGGGGAAAACCAACAGTAC 58.764 52.381 0.00 0.00 42.91 2.73
1813 1912 0.105913 GACCCAGGGGAAAACCAACA 60.106 55.000 11.37 0.00 42.91 3.33
1845 1944 7.907045 CCTACACAAAGAGAAATTTCATCATCG 59.093 37.037 19.99 6.49 0.00 3.84
1873 1972 3.328931 ACATCATGGTTAGGATAGGCTGG 59.671 47.826 0.00 0.00 0.00 4.85
1898 1997 4.192317 AGAAGTTCTTACGGGAATCATGC 58.808 43.478 0.00 0.00 0.00 4.06
1980 2081 0.890996 CAGAGCAACCAACCCCTGTC 60.891 60.000 0.00 0.00 0.00 3.51
2038 2166 7.856894 GCAATCATTATTTGTTGTTGCAACTTT 59.143 29.630 28.61 10.52 38.23 2.66
2101 2229 4.925054 CAGCTGAATAACCAAACCACATTG 59.075 41.667 8.42 0.00 0.00 2.82
2106 2236 3.237268 ACCAGCTGAATAACCAAACCA 57.763 42.857 17.39 0.00 0.00 3.67
2116 2246 6.956497 AGAATCTCTCTAAAACCAGCTGAAT 58.044 36.000 17.39 0.00 30.22 2.57
2120 2250 6.155910 TCATGAGAATCTCTCTAAAACCAGCT 59.844 38.462 11.92 0.00 43.73 4.24
2144 2274 9.160496 CCCTATTAAGAATCATTATCTGCTGTC 57.840 37.037 0.00 0.00 0.00 3.51
2236 2371 5.446260 ACCCCGAAGTATGATTTTAACCT 57.554 39.130 0.00 0.00 0.00 3.50
2262 2397 9.546428 CAGTTCCAAATTAGAAAGGTCAAATTT 57.454 29.630 0.00 0.00 33.07 1.82
2263 2398 8.923270 TCAGTTCCAAATTAGAAAGGTCAAATT 58.077 29.630 0.00 0.00 0.00 1.82
2264 2399 8.477419 TCAGTTCCAAATTAGAAAGGTCAAAT 57.523 30.769 0.00 0.00 0.00 2.32
2265 2400 7.889873 TCAGTTCCAAATTAGAAAGGTCAAA 57.110 32.000 0.00 0.00 0.00 2.69
2266 2401 7.889873 TTCAGTTCCAAATTAGAAAGGTCAA 57.110 32.000 0.00 0.00 0.00 3.18
2267 2402 9.581289 TTATTCAGTTCCAAATTAGAAAGGTCA 57.419 29.630 0.00 0.00 0.00 4.02
2269 2404 9.588096 AGTTATTCAGTTCCAAATTAGAAAGGT 57.412 29.630 0.00 0.00 0.00 3.50
2278 2426 9.739276 TCATCTTGTAGTTATTCAGTTCCAAAT 57.261 29.630 0.00 0.00 0.00 2.32
2279 2427 9.219603 CTCATCTTGTAGTTATTCAGTTCCAAA 57.780 33.333 0.00 0.00 0.00 3.28
2292 2440 7.702348 GCAGTTTTTCAAACTCATCTTGTAGTT 59.298 33.333 0.00 0.00 37.54 2.24
2293 2441 7.148086 TGCAGTTTTTCAAACTCATCTTGTAGT 60.148 33.333 0.00 0.00 0.00 2.73
2300 2448 8.437742 CCATTTATGCAGTTTTTCAAACTCATC 58.562 33.333 13.14 3.41 0.00 2.92
2301 2449 7.095102 GCCATTTATGCAGTTTTTCAAACTCAT 60.095 33.333 13.77 13.77 0.00 2.90
2303 2451 6.347644 GGCCATTTATGCAGTTTTTCAAACTC 60.348 38.462 0.00 0.00 0.00 3.01
2332 2480 5.238650 GGACATTGACTTAAATGGTATCCCG 59.761 44.000 2.34 0.00 41.06 5.14
2340 2488 9.865321 ATGAATTTCAGGACATTGACTTAAATG 57.135 29.630 5.21 0.00 42.21 2.32
2347 2495 6.925165 ACAACAATGAATTTCAGGACATTGAC 59.075 34.615 20.30 0.00 46.81 3.18
2369 2517 4.691326 TCATTGTGTGGTACTGGTACAA 57.309 40.909 12.14 0.00 38.70 2.41
2385 2533 6.788243 TCATACACATAGCTTGCTTTCATTG 58.212 36.000 0.00 0.00 0.00 2.82
2394 2542 9.486497 AATCAGAGTTATCATACACATAGCTTG 57.514 33.333 0.00 0.00 0.00 4.01
2400 2548 6.537355 CCCCAATCAGAGTTATCATACACAT 58.463 40.000 0.00 0.00 0.00 3.21
2410 2558 0.251916 CACCGCCCCAATCAGAGTTA 59.748 55.000 0.00 0.00 0.00 2.24
2416 2568 2.534396 AACTCCACCGCCCCAATCA 61.534 57.895 0.00 0.00 0.00 2.57
2417 2569 2.046285 CAACTCCACCGCCCCAATC 61.046 63.158 0.00 0.00 0.00 2.67
2425 2577 1.956629 ATCTACCCGCAACTCCACCG 61.957 60.000 0.00 0.00 0.00 4.94
2463 2617 5.299949 AGCACCAGGATTTTTGAACATTTC 58.700 37.500 0.00 0.00 0.00 2.17
2500 2654 2.034879 CATTCTGAAGCGCACCCGT 61.035 57.895 11.47 0.00 36.67 5.28
2501 2655 1.298157 TTCATTCTGAAGCGCACCCG 61.298 55.000 11.47 0.00 31.83 5.28
2534 2688 5.773176 TGGCGTAGACTATAGATGAATCCAA 59.227 40.000 6.78 0.00 34.59 3.53
2577 2731 1.165270 AAACGCATAAGTGTGGCCTC 58.835 50.000 3.32 0.00 40.16 4.70
2758 2930 7.167635 ACTCAACATAATCGCACTAGTTATTCG 59.832 37.037 0.00 0.00 0.00 3.34
2771 2943 4.035558 CCCATGAACCACTCAACATAATCG 59.964 45.833 0.00 0.00 37.67 3.34
2793 2965 7.885922 TCTGTATACTGAGATTCTCATCTACCC 59.114 40.741 16.48 5.00 40.14 3.69
2974 3146 5.584649 TGTGCACTAGTTAGGAATATGCAAC 59.415 40.000 19.41 0.00 42.71 4.17
3018 3190 2.154462 CCATCACACGAAAAGCCTCTT 58.846 47.619 0.00 0.00 0.00 2.85
3071 3243 9.790344 TTTATGAACCATCAACAAAATGGAAAT 57.210 25.926 9.04 2.75 45.51 2.17
3154 3331 6.025789 ATCAGCAGCTAGCAGATATTGTCAC 61.026 44.000 18.83 0.00 46.24 3.67
3177 3354 8.726068 CAGATCTCACAACTACTATACGATCAT 58.274 37.037 0.00 0.00 0.00 2.45
3180 3357 6.999272 ACCAGATCTCACAACTACTATACGAT 59.001 38.462 0.00 0.00 0.00 3.73
3195 3372 3.055819 GCAGAGTTGGTAACCAGATCTCA 60.056 47.826 0.00 0.00 33.81 3.27
3196 3373 3.196685 AGCAGAGTTGGTAACCAGATCTC 59.803 47.826 0.00 0.00 33.81 2.75
3244 3421 6.550108 CCCTCCTACTCTTTATGTAACTAGCA 59.450 42.308 0.00 0.00 0.00 3.49
3246 3423 7.296098 TCCCCTCCTACTCTTTATGTAACTAG 58.704 42.308 0.00 0.00 0.00 2.57
3249 3426 6.997942 ATCCCCTCCTACTCTTTATGTAAC 57.002 41.667 0.00 0.00 0.00 2.50
3303 3483 5.331876 ACTCATTCCTTAGCAGTACAGTC 57.668 43.478 0.00 0.00 0.00 3.51
3375 3557 7.927092 GGGTCAGTTTCTTAGTAACAGATATCC 59.073 40.741 4.66 0.62 0.00 2.59
3386 3568 6.842676 AGAAATGAAGGGTCAGTTTCTTAGT 58.157 36.000 0.00 0.00 41.92 2.24
3467 3649 2.124529 GCTGCTGGAACTAGGGGC 60.125 66.667 0.00 0.00 0.00 5.80
3488 3670 1.542492 TAGGAGAAAGGCTCGTCGTT 58.458 50.000 0.00 0.00 44.91 3.85
3595 3777 2.283145 AGCTGTTGGAGTCTGCATTT 57.717 45.000 0.00 0.00 33.36 2.32
3601 3783 0.036022 GGAGCAAGCTGTTGGAGTCT 59.964 55.000 0.00 0.00 33.87 3.24
3607 3789 0.035881 TGAGAGGGAGCAAGCTGTTG 59.964 55.000 0.00 0.00 36.67 3.33
3613 3795 2.301296 TCTGAACTTGAGAGGGAGCAAG 59.699 50.000 0.00 0.00 45.27 4.01
3817 4008 4.861210 GACGTATCGATGTCTCAAAGGAT 58.139 43.478 8.54 0.00 38.40 3.24
3830 4021 2.103537 TCTGACACCAGACGTATCGA 57.896 50.000 0.00 0.00 44.01 3.59
3839 4030 0.179116 CCGCTGAGATCTGACACCAG 60.179 60.000 0.00 1.50 41.74 4.00
3847 4038 0.461961 GGTAAGCACCGCTGAGATCT 59.538 55.000 0.00 0.00 39.62 2.75
3896 4087 1.628846 CACCACCCTGTATATAGCCCC 59.371 57.143 0.00 0.00 0.00 5.80
3948 4140 5.588240 TCATCAGTACGCGAGACATTATTT 58.412 37.500 15.93 0.00 0.00 1.40
3972 4164 9.590451 TCTCATGGCAAATTTATTCATTTCTTC 57.410 29.630 0.00 0.00 0.00 2.87
4048 4240 1.569708 AAACAATTGCAAGCACACCG 58.430 45.000 4.94 0.00 0.00 4.94
4074 4266 4.836125 AGTACACATTCCACAGCAAAAG 57.164 40.909 0.00 0.00 0.00 2.27
4153 4455 4.082463 CCAATAATACACAAAACACCGCCT 60.082 41.667 0.00 0.00 0.00 5.52
4221 4529 7.786030 TGGATGTCCAAAAGTTCAAAATGTTA 58.214 30.769 0.00 0.00 44.35 2.41
4276 4586 6.572167 TGTGTCATTATTTCTTCATGCACA 57.428 33.333 0.00 0.00 34.99 4.57
4336 4661 4.989279 ATGTTTCTGAATATGTGGTGGC 57.011 40.909 0.00 0.00 0.00 5.01
4433 5180 0.609406 TGTGCTGCCTCGACTAGTCT 60.609 55.000 20.34 0.00 0.00 3.24
4455 5202 0.597898 GTAGCTTCCTCGCCCGATTC 60.598 60.000 0.00 0.00 0.00 2.52
4542 5293 3.208747 AGTGTTTCCCTGTTGGTAGTG 57.791 47.619 0.00 0.00 34.77 2.74
4547 5298 4.402474 AGAAAGAAAGTGTTTCCCTGTTGG 59.598 41.667 0.00 0.00 40.54 3.77
4564 5315 6.569994 GCTTCGACAGGACTACTAAAGAAAGA 60.570 42.308 0.00 0.00 0.00 2.52
4572 5323 2.391616 TCGCTTCGACAGGACTACTA 57.608 50.000 0.00 0.00 0.00 1.82
4597 5348 4.830046 TCAATAGGCAGTAGCTAGAAGAGG 59.170 45.833 0.00 0.00 41.70 3.69
4602 5353 4.793201 TCAGTCAATAGGCAGTAGCTAGA 58.207 43.478 0.00 0.00 41.70 2.43
4603 5354 5.476599 AGATCAGTCAATAGGCAGTAGCTAG 59.523 44.000 0.00 0.00 41.70 3.42
4604 5355 5.389520 AGATCAGTCAATAGGCAGTAGCTA 58.610 41.667 0.00 0.00 41.70 3.32


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

AutoCloner maintained by Alex Coulton.