Multiple sequence alignment - TraesCS7A01G050900

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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 TraesCS7A01G050900 chr7A 100.000 3544 0 0 1 3544 24541044 24537501 0.000000e+00 6545.0
1 TraesCS7A01G050900 chr7A 92.794 2248 123 20 1318 3544 24627138 24629367 0.000000e+00 3217.0
2 TraesCS7A01G050900 chr7A 95.380 909 35 4 412 1318 538762275 538763178 0.000000e+00 1439.0
3 TraesCS7A01G050900 chr7A 95.270 909 38 3 412 1318 183473372 183472467 0.000000e+00 1435.0
4 TraesCS7A01G050900 chr7A 94.609 909 37 4 412 1318 183467756 183466858 0.000000e+00 1397.0
5 TraesCS7A01G050900 chr7A 94.279 909 43 5 412 1318 672286457 672285556 0.000000e+00 1382.0
6 TraesCS7A01G050900 chr7A 93.729 909 45 3 412 1318 579317524 579316626 0.000000e+00 1352.0
7 TraesCS7A01G050900 chr7A 82.159 880 127 24 1989 2862 24624504 24625359 0.000000e+00 728.0
8 TraesCS7A01G050900 chr7A 98.305 413 7 0 1 413 7037789 7037377 0.000000e+00 725.0
9 TraesCS7A01G050900 chr7A 98.297 411 7 0 1 411 634857044 634857454 0.000000e+00 721.0
10 TraesCS7A01G050900 chr7A 98.063 413 8 0 1 413 1650308 1650720 0.000000e+00 719.0
11 TraesCS7A01G050900 chr7A 97.831 415 9 0 1 415 7031238 7030824 0.000000e+00 717.0
12 TraesCS7A01G050900 chr7A 79.528 762 126 23 1323 2061 25006675 25007429 1.890000e-142 516.0
13 TraesCS7A01G050900 chr7A 77.074 458 80 16 2246 2691 25007717 25008161 1.270000e-59 241.0
14 TraesCS7A01G050900 chr7D 96.661 2246 52 12 1318 3544 23510011 23512252 0.000000e+00 3711.0
15 TraesCS7A01G050900 chr7D 84.034 1428 179 30 1324 2725 23999893 24001297 0.000000e+00 1328.0
16 TraesCS7A01G050900 chr7D 83.936 1438 180 32 1324 2725 24114361 24115783 0.000000e+00 1328.0
17 TraesCS7A01G050900 chr7D 82.960 1338 187 23 1324 2643 23541341 23540027 0.000000e+00 1170.0
18 TraesCS7A01G050900 chr7D 79.870 616 91 23 1995 2600 23507191 23507783 1.520000e-113 420.0
19 TraesCS7A01G050900 chr4A 93.413 1594 86 14 1318 2903 708300199 708298617 0.000000e+00 2344.0
20 TraesCS7A01G050900 chr4A 84.928 1035 98 34 2522 3544 708259411 708258423 0.000000e+00 994.0
21 TraesCS7A01G050900 chr4A 91.200 625 46 6 2924 3544 708298506 708297887 0.000000e+00 841.0
22 TraesCS7A01G050900 chr4A 78.994 795 132 26 1307 2076 708916541 708915757 8.780000e-141 510.0
23 TraesCS7A01G050900 chr4A 79.541 567 97 14 1526 2073 710413460 710412894 1.540000e-103 387.0
24 TraesCS7A01G050900 chr4A 76.201 458 83 17 2246 2691 708914058 708913615 5.960000e-53 219.0
25 TraesCS7A01G050900 chr4A 76.201 458 83 17 2246 2691 708915481 708915038 5.960000e-53 219.0
26 TraesCS7A01G050900 chr2A 93.399 909 53 6 412 1318 669120186 669121089 0.000000e+00 1339.0
27 TraesCS7A01G050900 chr2A 93.399 909 47 8 413 1318 705845904 705845006 0.000000e+00 1334.0
28 TraesCS7A01G050900 chr2A 98.063 413 8 0 1 413 2426485 2426897 0.000000e+00 719.0
29 TraesCS7A01G050900 chr1A 93.092 912 55 3 412 1321 193336807 193335902 0.000000e+00 1328.0
30 TraesCS7A01G050900 chr5A 92.755 911 49 9 412 1318 524931194 524932091 0.000000e+00 1301.0
31 TraesCS7A01G050900 chr6A 98.540 411 6 0 1 411 47094958 47095368 0.000000e+00 726.0
32 TraesCS7A01G050900 chr6A 98.063 413 8 0 1 413 47087995 47088407 0.000000e+00 719.0
33 TraesCS7A01G050900 chr6A 84.314 255 39 1 2303 2556 310681614 310681868 7.600000e-62 248.0
34 TraesCS7A01G050900 chr3A 98.063 413 8 0 1 413 51730151 51730563 0.000000e+00 719.0
35 TraesCS7A01G050900 chr3A 97.156 422 12 0 1 422 735536818 735537239 0.000000e+00 713.0
36 TraesCS7A01G050900 chr1D 77.647 510 94 15 1580 2070 413778604 413779112 3.460000e-75 292.0
37 TraesCS7A01G050900 chrUn 77.899 457 78 12 2246 2691 90117275 90116831 2.710000e-66 263.0
38 TraesCS7A01G050900 chr7B 87.671 73 8 1 2301 2372 41522242 41522170 2.270000e-12 84.2


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 TraesCS7A01G050900 chr7A 24537501 24541044 3543 True 6545.0 6545 100.0000 1 3544 1 chr7A.!!$R3 3543
1 TraesCS7A01G050900 chr7A 24624504 24629367 4863 False 1972.5 3217 87.4765 1318 3544 2 chr7A.!!$F4 2226
2 TraesCS7A01G050900 chr7A 538762275 538763178 903 False 1439.0 1439 95.3800 412 1318 1 chr7A.!!$F2 906
3 TraesCS7A01G050900 chr7A 183472467 183473372 905 True 1435.0 1435 95.2700 412 1318 1 chr7A.!!$R5 906
4 TraesCS7A01G050900 chr7A 183466858 183467756 898 True 1397.0 1397 94.6090 412 1318 1 chr7A.!!$R4 906
5 TraesCS7A01G050900 chr7A 672285556 672286457 901 True 1382.0 1382 94.2790 412 1318 1 chr7A.!!$R7 906
6 TraesCS7A01G050900 chr7A 579316626 579317524 898 True 1352.0 1352 93.7290 412 1318 1 chr7A.!!$R6 906
7 TraesCS7A01G050900 chr7A 25006675 25008161 1486 False 378.5 516 78.3010 1323 2691 2 chr7A.!!$F5 1368
8 TraesCS7A01G050900 chr7D 23507191 23512252 5061 False 2065.5 3711 88.2655 1318 3544 2 chr7D.!!$F3 2226
9 TraesCS7A01G050900 chr7D 23999893 24001297 1404 False 1328.0 1328 84.0340 1324 2725 1 chr7D.!!$F1 1401
10 TraesCS7A01G050900 chr7D 24114361 24115783 1422 False 1328.0 1328 83.9360 1324 2725 1 chr7D.!!$F2 1401
11 TraesCS7A01G050900 chr7D 23540027 23541341 1314 True 1170.0 1170 82.9600 1324 2643 1 chr7D.!!$R1 1319
12 TraesCS7A01G050900 chr4A 708297887 708300199 2312 True 1592.5 2344 92.3065 1318 3544 2 chr4A.!!$R3 2226
13 TraesCS7A01G050900 chr4A 708258423 708259411 988 True 994.0 994 84.9280 2522 3544 1 chr4A.!!$R1 1022
14 TraesCS7A01G050900 chr4A 710412894 710413460 566 True 387.0 387 79.5410 1526 2073 1 chr4A.!!$R2 547
15 TraesCS7A01G050900 chr4A 708913615 708916541 2926 True 316.0 510 77.1320 1307 2691 3 chr4A.!!$R4 1384
16 TraesCS7A01G050900 chr2A 669120186 669121089 903 False 1339.0 1339 93.3990 412 1318 1 chr2A.!!$F2 906
17 TraesCS7A01G050900 chr2A 705845006 705845904 898 True 1334.0 1334 93.3990 413 1318 1 chr2A.!!$R1 905
18 TraesCS7A01G050900 chr1A 193335902 193336807 905 True 1328.0 1328 93.0920 412 1321 1 chr1A.!!$R1 909
19 TraesCS7A01G050900 chr5A 524931194 524932091 897 False 1301.0 1301 92.7550 412 1318 1 chr5A.!!$F1 906
20 TraesCS7A01G050900 chr1D 413778604 413779112 508 False 292.0 292 77.6470 1580 2070 1 chr1D.!!$F1 490

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
45 46 0.307760 GCACACAAAGTGTTCCTCCG 59.692 55.0 0.00 0.00 45.08 4.63 F
53 54 0.609131 AGTGTTCCTCCGGCAAATGG 60.609 55.0 0.00 0.00 0.00 3.16 F
584 605 0.748450 ACGAAAGGTCACACGGAAGA 59.252 50.0 0.00 0.00 0.00 2.87 F
1954 3580 0.389948 ACTGCGATGGAACCGTTCTC 60.390 55.0 11.03 1.33 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 3037 1.202463 ACTCCCTCGAAGCAATCATCG 60.202 52.381 0.00 0.00 40.31 3.84 R
1687 3295 1.351076 AAACCCCAAGCCTGGAAATG 58.649 50.000 1.80 0.00 46.92 2.32 R
2419 4173 1.615883 TCTTATCGATCAGCTGAGCCC 59.384 52.381 25.34 13.84 0.00 5.19 R
2804 4585 1.260538 TGCAGGGGTCAGTCAGCTAG 61.261 60.000 0.00 0.00 0.00 3.42 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
19 20 2.922740 ACCCAGTTACATTGTGACGT 57.077 45.000 6.11 0.00 0.00 4.34
21 22 3.547746 ACCCAGTTACATTGTGACGTTT 58.452 40.909 6.11 0.00 0.00 3.60
23 24 3.304391 CCCAGTTACATTGTGACGTTTGG 60.304 47.826 10.01 10.01 0.00 3.28
24 25 3.314080 CCAGTTACATTGTGACGTTTGGT 59.686 43.478 6.11 0.00 0.00 3.67
25 26 4.512198 CCAGTTACATTGTGACGTTTGGTA 59.488 41.667 6.11 0.00 0.00 3.25
26 27 5.333798 CCAGTTACATTGTGACGTTTGGTAG 60.334 44.000 6.11 0.00 0.00 3.18
27 28 4.212636 AGTTACATTGTGACGTTTGGTAGC 59.787 41.667 6.11 0.00 0.00 3.58
28 29 2.566913 ACATTGTGACGTTTGGTAGCA 58.433 42.857 0.00 0.00 0.00 3.49
29 30 2.289547 ACATTGTGACGTTTGGTAGCAC 59.710 45.455 0.00 0.00 0.00 4.40
30 31 2.025589 TTGTGACGTTTGGTAGCACA 57.974 45.000 0.00 0.34 37.66 4.57
31 32 1.292061 TGTGACGTTTGGTAGCACAC 58.708 50.000 1.04 1.04 34.85 3.82
32 33 1.292061 GTGACGTTTGGTAGCACACA 58.708 50.000 11.43 0.00 0.00 3.72
33 34 1.666700 GTGACGTTTGGTAGCACACAA 59.333 47.619 11.43 0.00 0.00 3.33
34 35 2.096174 GTGACGTTTGGTAGCACACAAA 59.904 45.455 11.43 0.00 34.48 2.83
35 36 2.353269 TGACGTTTGGTAGCACACAAAG 59.647 45.455 11.43 1.31 37.27 2.77
40 41 4.102649 GTTTGGTAGCACACAAAGTGTTC 58.897 43.478 6.34 0.00 45.08 3.18
42 43 2.092646 TGGTAGCACACAAAGTGTTCCT 60.093 45.455 0.00 3.24 45.08 3.36
43 44 2.548480 GGTAGCACACAAAGTGTTCCTC 59.452 50.000 0.00 0.00 45.08 3.71
45 46 0.307760 GCACACAAAGTGTTCCTCCG 59.692 55.000 0.00 0.00 45.08 4.63
46 47 0.944386 CACACAAAGTGTTCCTCCGG 59.056 55.000 0.00 0.00 45.08 5.14
47 48 0.818040 ACACAAAGTGTTCCTCCGGC 60.818 55.000 0.00 0.00 45.08 6.13
48 49 0.817634 CACAAAGTGTTCCTCCGGCA 60.818 55.000 0.00 0.00 0.00 5.69
50 51 1.028905 CAAAGTGTTCCTCCGGCAAA 58.971 50.000 0.00 0.00 0.00 3.68
53 54 0.609131 AGTGTTCCTCCGGCAAATGG 60.609 55.000 0.00 0.00 0.00 3.16
54 55 1.304052 TGTTCCTCCGGCAAATGGG 60.304 57.895 0.00 0.00 0.00 4.00
55 56 1.001393 GTTCCTCCGGCAAATGGGA 60.001 57.895 0.00 0.00 0.00 4.37
58 59 1.000896 CCTCCGGCAAATGGGAGTT 60.001 57.895 0.00 0.00 46.83 3.01
59 60 1.315257 CCTCCGGCAAATGGGAGTTG 61.315 60.000 0.00 0.00 46.83 3.16
71 72 7.514784 CAAATGGGAGTTGCATAATCTCATA 57.485 36.000 10.61 1.60 32.99 2.15
72 73 7.591165 CAAATGGGAGTTGCATAATCTCATAG 58.409 38.462 10.61 5.31 32.99 2.23
73 74 5.894298 TGGGAGTTGCATAATCTCATAGT 57.106 39.130 0.00 0.00 0.00 2.12
74 75 5.858381 TGGGAGTTGCATAATCTCATAGTC 58.142 41.667 0.00 0.00 0.00 2.59
75 76 5.366477 TGGGAGTTGCATAATCTCATAGTCA 59.634 40.000 0.00 0.00 0.00 3.41
78 79 7.763528 GGGAGTTGCATAATCTCATAGTCATAG 59.236 40.741 0.00 0.00 0.00 2.23
79 80 8.526978 GGAGTTGCATAATCTCATAGTCATAGA 58.473 37.037 0.00 0.00 0.00 1.98
80 81 9.920133 GAGTTGCATAATCTCATAGTCATAGAA 57.080 33.333 0.00 0.00 0.00 2.10
104 105 9.495754 GAAACATGTATAAGTCATGAAGAAAGC 57.504 33.333 0.00 0.00 43.47 3.51
105 106 8.565896 AACATGTATAAGTCATGAAGAAAGCA 57.434 30.769 0.00 0.00 43.47 3.91
106 107 8.565896 ACATGTATAAGTCATGAAGAAAGCAA 57.434 30.769 11.92 0.00 43.47 3.91
107 108 9.182214 ACATGTATAAGTCATGAAGAAAGCAAT 57.818 29.630 11.92 0.00 43.47 3.56
110 111 8.830580 TGTATAAGTCATGAAGAAAGCAATAGC 58.169 33.333 0.00 0.00 42.56 2.97
111 112 7.870509 ATAAGTCATGAAGAAAGCAATAGCA 57.129 32.000 0.00 0.00 45.49 3.49
112 113 6.579666 AAGTCATGAAGAAAGCAATAGCAA 57.420 33.333 0.00 0.00 45.49 3.91
113 114 5.947443 AGTCATGAAGAAAGCAATAGCAAC 58.053 37.500 0.00 0.00 45.49 4.17
114 115 5.474532 AGTCATGAAGAAAGCAATAGCAACA 59.525 36.000 0.00 0.00 45.49 3.33
115 116 6.152323 AGTCATGAAGAAAGCAATAGCAACAT 59.848 34.615 0.00 0.00 45.49 2.71
116 117 7.337689 AGTCATGAAGAAAGCAATAGCAACATA 59.662 33.333 0.00 0.00 45.49 2.29
117 118 7.430502 GTCATGAAGAAAGCAATAGCAACATAC 59.569 37.037 0.00 0.00 45.49 2.39
119 120 8.615211 CATGAAGAAAGCAATAGCAACATACTA 58.385 33.333 0.00 0.00 45.49 1.82
121 122 9.008965 TGAAGAAAGCAATAGCAACATACTAAA 57.991 29.630 0.00 0.00 45.49 1.85
122 123 9.278734 GAAGAAAGCAATAGCAACATACTAAAC 57.721 33.333 0.00 0.00 45.49 2.01
123 124 7.464358 AGAAAGCAATAGCAACATACTAAACG 58.536 34.615 0.00 0.00 45.49 3.60
125 126 7.553881 AAGCAATAGCAACATACTAAACGAT 57.446 32.000 0.00 0.00 45.49 3.73
126 127 7.178712 AGCAATAGCAACATACTAAACGATC 57.821 36.000 0.00 0.00 45.49 3.69
127 128 6.065153 GCAATAGCAACATACTAAACGATCG 58.935 40.000 14.88 14.88 41.58 3.69
128 129 6.581370 CAATAGCAACATACTAAACGATCGG 58.419 40.000 20.98 3.61 0.00 4.18
129 130 3.454375 AGCAACATACTAAACGATCGGG 58.546 45.455 20.98 8.89 0.00 5.14
134 135 3.633525 ACATACTAAACGATCGGGTGCTA 59.366 43.478 20.98 3.41 0.00 3.49
135 136 4.098349 ACATACTAAACGATCGGGTGCTAA 59.902 41.667 20.98 0.00 0.00 3.09
136 137 3.160777 ACTAAACGATCGGGTGCTAAG 57.839 47.619 20.98 8.87 0.00 2.18
137 138 1.859080 CTAAACGATCGGGTGCTAAGC 59.141 52.381 20.98 0.00 0.00 3.09
139 140 1.108776 AACGATCGGGTGCTAAGCTA 58.891 50.000 20.98 0.00 0.00 3.32
140 141 1.108776 ACGATCGGGTGCTAAGCTAA 58.891 50.000 20.98 0.00 0.00 3.09
142 143 2.061773 CGATCGGGTGCTAAGCTAATG 58.938 52.381 7.38 0.00 0.00 1.90
143 144 2.417719 GATCGGGTGCTAAGCTAATGG 58.582 52.381 0.00 0.00 0.00 3.16
145 146 1.834896 TCGGGTGCTAAGCTAATGGAA 59.165 47.619 0.00 0.00 0.00 3.53
146 147 2.438021 TCGGGTGCTAAGCTAATGGAAT 59.562 45.455 0.00 0.00 0.00 3.01
147 148 2.549754 CGGGTGCTAAGCTAATGGAATG 59.450 50.000 0.00 0.00 0.00 2.67
148 149 2.887152 GGGTGCTAAGCTAATGGAATGG 59.113 50.000 0.00 0.00 0.00 3.16
149 150 2.887152 GGTGCTAAGCTAATGGAATGGG 59.113 50.000 0.00 0.00 0.00 4.00
150 151 3.555966 GTGCTAAGCTAATGGAATGGGT 58.444 45.455 0.00 0.00 0.00 4.51
151 152 3.565902 GTGCTAAGCTAATGGAATGGGTC 59.434 47.826 0.00 0.00 0.00 4.46
152 153 3.201930 TGCTAAGCTAATGGAATGGGTCA 59.798 43.478 0.00 0.00 0.00 4.02
153 154 4.141181 TGCTAAGCTAATGGAATGGGTCAT 60.141 41.667 0.00 0.00 0.00 3.06
154 155 4.217118 GCTAAGCTAATGGAATGGGTCATG 59.783 45.833 0.00 0.00 0.00 3.07
155 156 3.959495 AGCTAATGGAATGGGTCATGT 57.041 42.857 0.00 0.00 0.00 3.21
156 157 3.825328 AGCTAATGGAATGGGTCATGTC 58.175 45.455 0.00 0.00 0.00 3.06
157 158 3.202818 AGCTAATGGAATGGGTCATGTCA 59.797 43.478 0.00 0.00 0.00 3.58
158 159 3.953612 GCTAATGGAATGGGTCATGTCAA 59.046 43.478 0.00 0.00 0.00 3.18
159 160 4.586001 GCTAATGGAATGGGTCATGTCAAT 59.414 41.667 0.00 0.00 0.00 2.57
160 161 5.278660 GCTAATGGAATGGGTCATGTCAATC 60.279 44.000 0.00 0.00 0.00 2.67
162 163 3.623703 TGGAATGGGTCATGTCAATCAG 58.376 45.455 0.00 0.00 0.00 2.90
163 164 3.266513 TGGAATGGGTCATGTCAATCAGA 59.733 43.478 0.00 0.00 0.00 3.27
164 165 4.079615 TGGAATGGGTCATGTCAATCAGAT 60.080 41.667 0.00 0.00 0.00 2.90
165 166 4.518211 GGAATGGGTCATGTCAATCAGATC 59.482 45.833 0.00 0.00 0.00 2.75
167 168 4.783560 TGGGTCATGTCAATCAGATCAT 57.216 40.909 0.00 0.00 0.00 2.45
168 169 5.120054 TGGGTCATGTCAATCAGATCATT 57.880 39.130 0.00 0.00 0.00 2.57
172 173 6.459298 GGGTCATGTCAATCAGATCATTCAAC 60.459 42.308 0.00 0.00 0.00 3.18
174 175 7.496920 GGTCATGTCAATCAGATCATTCAACTA 59.503 37.037 0.00 0.00 0.00 2.24
177 178 9.665264 CATGTCAATCAGATCATTCAACTAATG 57.335 33.333 0.00 0.00 45.47 1.90
189 190 4.801330 TCAACTAATGATGTGACCTCGT 57.199 40.909 0.00 0.00 31.50 4.18
190 191 5.147330 TCAACTAATGATGTGACCTCGTT 57.853 39.130 1.18 1.18 31.50 3.85
191 192 6.275494 TCAACTAATGATGTGACCTCGTTA 57.725 37.500 3.19 3.19 31.50 3.18
195 196 6.873997 ACTAATGATGTGACCTCGTTAATCA 58.126 36.000 4.52 0.00 0.00 2.57
197 198 7.822334 ACTAATGATGTGACCTCGTTAATCAAA 59.178 33.333 4.52 0.00 0.00 2.69
198 199 7.630242 AATGATGTGACCTCGTTAATCAAAT 57.370 32.000 0.00 0.00 0.00 2.32
199 200 8.731275 AATGATGTGACCTCGTTAATCAAATA 57.269 30.769 0.00 0.00 0.00 1.40
201 202 7.970384 TGATGTGACCTCGTTAATCAAATAAC 58.030 34.615 0.00 0.00 33.40 1.89
205 206 7.442969 TGTGACCTCGTTAATCAAATAACAACT 59.557 33.333 0.00 0.00 35.89 3.16
207 208 7.876068 TGACCTCGTTAATCAAATAACAACTCT 59.124 33.333 0.00 0.00 35.89 3.24
208 209 8.617290 ACCTCGTTAATCAAATAACAACTCTT 57.383 30.769 0.00 0.00 35.89 2.85
209 210 9.063615 ACCTCGTTAATCAAATAACAACTCTTT 57.936 29.630 0.00 0.00 35.89 2.52
224 225 8.934023 AACAACTCTTTATTCATGGTTAGGAA 57.066 30.769 0.00 0.00 0.00 3.36
225 226 8.934023 ACAACTCTTTATTCATGGTTAGGAAA 57.066 30.769 0.00 0.00 29.52 3.13
227 228 7.611213 ACTCTTTATTCATGGTTAGGAAACG 57.389 36.000 0.00 0.00 36.39 3.60
228 229 7.166167 ACTCTTTATTCATGGTTAGGAAACGT 58.834 34.615 0.00 0.00 36.39 3.99
229 230 8.316214 ACTCTTTATTCATGGTTAGGAAACGTA 58.684 33.333 0.00 0.00 36.39 3.57
230 231 9.158233 CTCTTTATTCATGGTTAGGAAACGTAA 57.842 33.333 0.00 0.00 36.39 3.18
231 232 8.938906 TCTTTATTCATGGTTAGGAAACGTAAC 58.061 33.333 0.00 0.00 36.39 2.50
232 233 7.614124 TTATTCATGGTTAGGAAACGTAACC 57.386 36.000 19.71 19.71 46.71 2.85
239 240 5.934921 GGTTAGGAAACGTAACCATCTTTG 58.065 41.667 20.87 0.00 46.08 2.77
241 242 6.373495 GGTTAGGAAACGTAACCATCTTTGAT 59.627 38.462 20.87 0.00 46.08 2.57
245 246 7.813645 AGGAAACGTAACCATCTTTGATTAAC 58.186 34.615 12.35 0.00 0.00 2.01
246 247 6.739550 GGAAACGTAACCATCTTTGATTAACG 59.260 38.462 6.14 0.00 0.00 3.18
247 248 7.360269 GGAAACGTAACCATCTTTGATTAACGA 60.360 37.037 6.14 0.00 0.00 3.85
248 249 6.642683 ACGTAACCATCTTTGATTAACGAG 57.357 37.500 0.00 0.00 0.00 4.18
249 250 5.063060 ACGTAACCATCTTTGATTAACGAGC 59.937 40.000 0.00 0.00 0.00 5.03
251 252 6.474427 CGTAACCATCTTTGATTAACGAGCTA 59.526 38.462 0.00 0.00 0.00 3.32
252 253 6.910536 AACCATCTTTGATTAACGAGCTAG 57.089 37.500 0.00 0.00 0.00 3.42
254 255 6.043411 ACCATCTTTGATTAACGAGCTAGTC 58.957 40.000 0.00 0.00 0.00 2.59
255 256 6.042777 CCATCTTTGATTAACGAGCTAGTCA 58.957 40.000 0.00 0.00 0.00 3.41
256 257 6.535150 CCATCTTTGATTAACGAGCTAGTCAA 59.465 38.462 0.00 0.00 0.00 3.18
257 258 7.254252 CCATCTTTGATTAACGAGCTAGTCAAG 60.254 40.741 0.00 0.00 31.56 3.02
258 259 6.688578 TCTTTGATTAACGAGCTAGTCAAGT 58.311 36.000 0.00 0.00 31.56 3.16
260 261 7.968956 TCTTTGATTAACGAGCTAGTCAAGTAG 59.031 37.037 0.00 0.00 31.56 2.57
261 262 6.997239 TGATTAACGAGCTAGTCAAGTAGA 57.003 37.500 0.00 0.00 0.00 2.59
262 263 7.017498 TGATTAACGAGCTAGTCAAGTAGAG 57.983 40.000 0.00 0.00 0.00 2.43
263 264 5.814764 TTAACGAGCTAGTCAAGTAGAGG 57.185 43.478 0.00 0.00 0.00 3.69
264 265 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
265 266 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
268 269 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
269 270 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
270 271 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
271 272 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
273 274 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
275 276 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
276 277 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
277 278 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
278 279 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
279 280 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
280 281 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
281 282 3.951037 AGAGGCATACTAGTGACACTCTG 59.049 47.826 12.39 9.04 33.23 3.35
283 284 4.090090 AGGCATACTAGTGACACTCTGTT 58.910 43.478 12.39 0.00 0.00 3.16
284 285 4.528596 AGGCATACTAGTGACACTCTGTTT 59.471 41.667 12.39 5.23 0.00 2.83
285 286 4.627467 GGCATACTAGTGACACTCTGTTTG 59.373 45.833 12.39 16.63 0.00 2.93
286 287 5.230942 GCATACTAGTGACACTCTGTTTGT 58.769 41.667 12.39 5.61 0.00 2.83
290 291 9.424319 CATACTAGTGACACTCTGTTTGTTTAT 57.576 33.333 12.39 0.00 0.00 1.40
291 292 7.715265 ACTAGTGACACTCTGTTTGTTTATG 57.285 36.000 12.39 0.00 0.00 1.90
293 294 8.418662 ACTAGTGACACTCTGTTTGTTTATGTA 58.581 33.333 12.39 0.00 0.00 2.29
296 297 8.774586 AGTGACACTCTGTTTGTTTATGTATTC 58.225 33.333 1.07 0.00 0.00 1.75
297 298 8.556194 GTGACACTCTGTTTGTTTATGTATTCA 58.444 33.333 0.00 0.00 0.00 2.57
298 299 8.556194 TGACACTCTGTTTGTTTATGTATTCAC 58.444 33.333 0.00 0.00 0.00 3.18
299 300 8.445275 ACACTCTGTTTGTTTATGTATTCACA 57.555 30.769 0.00 0.00 39.52 3.58
300 301 8.342634 ACACTCTGTTTGTTTATGTATTCACAC 58.657 33.333 0.00 0.00 37.54 3.82
301 302 7.803189 CACTCTGTTTGTTTATGTATTCACACC 59.197 37.037 0.00 0.00 37.54 4.16
302 303 7.719633 ACTCTGTTTGTTTATGTATTCACACCT 59.280 33.333 0.00 0.00 37.54 4.00
303 304 7.870826 TCTGTTTGTTTATGTATTCACACCTG 58.129 34.615 0.00 0.00 37.54 4.00
304 305 7.500892 TCTGTTTGTTTATGTATTCACACCTGT 59.499 33.333 0.00 0.00 37.54 4.00
306 307 9.290988 TGTTTGTTTATGTATTCACACCTGTAT 57.709 29.630 0.00 0.00 37.54 2.29
316 317 6.677781 ATTCACACCTGTATTATGTTTCCG 57.322 37.500 0.00 0.00 0.00 4.30
317 318 4.509616 TCACACCTGTATTATGTTTCCGG 58.490 43.478 0.00 0.00 0.00 5.14
319 320 4.698304 CACACCTGTATTATGTTTCCGGTT 59.302 41.667 0.00 0.00 0.00 4.44
320 321 5.875910 CACACCTGTATTATGTTTCCGGTTA 59.124 40.000 0.00 0.00 0.00 2.85
321 322 6.372103 CACACCTGTATTATGTTTCCGGTTAA 59.628 38.462 0.00 0.00 0.00 2.01
323 324 8.266473 ACACCTGTATTATGTTTCCGGTTAATA 58.734 33.333 0.00 0.00 0.00 0.98
325 326 8.266473 ACCTGTATTATGTTTCCGGTTAATACA 58.734 33.333 21.19 21.19 41.59 2.29
326 327 9.111613 CCTGTATTATGTTTCCGGTTAATACAA 57.888 33.333 21.91 8.78 42.45 2.41
334 335 6.879993 TGTTTCCGGTTAATACAATTCTAGCA 59.120 34.615 0.00 0.00 0.00 3.49
335 336 7.554835 TGTTTCCGGTTAATACAATTCTAGCAT 59.445 33.333 0.00 0.00 0.00 3.79
336 337 7.490962 TTCCGGTTAATACAATTCTAGCATG 57.509 36.000 0.00 0.00 0.00 4.06
337 338 6.822442 TCCGGTTAATACAATTCTAGCATGA 58.178 36.000 0.00 0.00 0.00 3.07
338 339 7.276658 TCCGGTTAATACAATTCTAGCATGAA 58.723 34.615 0.00 0.00 0.00 2.57
339 340 7.936847 TCCGGTTAATACAATTCTAGCATGAAT 59.063 33.333 0.00 0.00 38.19 2.57
340 341 9.214957 CCGGTTAATACAATTCTAGCATGAATA 57.785 33.333 0.00 0.00 35.82 1.75
398 399 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
410 411 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
584 605 0.748450 ACGAAAGGTCACACGGAAGA 59.252 50.000 0.00 0.00 0.00 2.87
589 612 4.630069 CGAAAGGTCACACGGAAGATAAAT 59.370 41.667 0.00 0.00 0.00 1.40
877 902 2.805657 GCACCTTTTGAGTCCTGTACGT 60.806 50.000 0.00 0.00 0.00 3.57
978 1004 0.964358 ACGACGACTTCTTCCCCGAT 60.964 55.000 0.00 0.00 0.00 4.18
1042 1068 1.602311 CAAGTCCAGTGCTTCTGCTT 58.398 50.000 4.40 1.88 42.38 3.91
1416 3017 3.449018 AGCTCAGTAACCATGGTGTAGAG 59.551 47.826 20.60 22.00 0.00 2.43
1582 3186 1.573376 AGATCCTAGACTGGCCTGACT 59.427 52.381 17.64 17.65 0.00 3.41
1655 3259 4.441356 GCCAACACATCCTGAAAACTTCAA 60.441 41.667 0.00 0.00 39.58 2.69
1667 3271 6.294176 CCTGAAAACTTCAAGTCACCTATTGG 60.294 42.308 0.00 0.00 39.58 3.16
1687 3295 5.344743 TGGTCAGAGATATCACTTTCCAC 57.655 43.478 14.55 5.09 0.00 4.02
1708 3329 3.106827 CATTTCCAGGCTTGGGGTTTAT 58.893 45.455 15.86 0.00 45.10 1.40
1954 3580 0.389948 ACTGCGATGGAACCGTTCTC 60.390 55.000 11.03 1.33 0.00 2.87
1955 3581 1.079405 TGCGATGGAACCGTTCTCC 60.079 57.895 11.03 0.00 0.00 3.71
1991 3621 3.726517 CGTCGGTGGCTTGCAAGG 61.727 66.667 27.10 10.71 0.00 3.61
2236 3973 1.762708 ATGCCAGGGTTTACGGATTG 58.237 50.000 0.00 0.00 0.00 2.67
2254 4005 6.257630 ACGGATTGAAAAACCATTTTGTCAAG 59.742 34.615 8.33 0.00 38.96 3.02
2375 4129 5.187772 TGCAAAGAAAGAGAGGCTATCAGTA 59.812 40.000 12.28 0.00 0.00 2.74
2419 4173 3.449528 TGAGAGAGAAATCGAGCCATG 57.550 47.619 0.00 0.00 0.00 3.66
2436 4190 1.274447 CATGGGCTCAGCTGATCGATA 59.726 52.381 18.63 3.22 0.00 2.92
2446 4200 5.129634 TCAGCTGATCGATAAGAAGAGACT 58.870 41.667 13.74 0.00 0.00 3.24
2667 4446 6.751425 TCAACAACACATGTCATTTCAAGTTC 59.249 34.615 0.00 0.00 42.99 3.01
2804 4585 3.319122 AGTTGAAACAGATCCAAGCCAAC 59.681 43.478 0.00 0.00 34.55 3.77
2832 4613 0.105760 TGACCCCTGCAACAACCAAT 60.106 50.000 0.00 0.00 0.00 3.16
3102 5627 0.315568 GATTGGCGGCTATCGAGTCT 59.684 55.000 16.71 0.00 42.43 3.24
3146 5671 2.819608 GGACCTTGCAAATGCTTACTCA 59.180 45.455 0.00 0.00 42.66 3.41
3173 5698 6.893958 ATGCTTTTCTCATAGTCAAGTACG 57.106 37.500 0.00 0.00 0.00 3.67
3214 5743 9.770097 TTGATCTCTACTTTAGCCATGAAATAG 57.230 33.333 0.00 0.00 0.00 1.73
3507 6555 7.350467 CAATTGATCTGAATATGTCAACTCCG 58.650 38.462 0.00 0.00 35.22 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.304391 CCAAACGTCACAATGTAACTGGG 60.304 47.826 0.00 0.00 0.00 4.45
2 3 3.314080 ACCAAACGTCACAATGTAACTGG 59.686 43.478 0.00 0.00 0.00 4.00
3 4 4.545823 ACCAAACGTCACAATGTAACTG 57.454 40.909 0.00 0.00 0.00 3.16
5 6 4.024725 TGCTACCAAACGTCACAATGTAAC 60.025 41.667 0.00 0.00 0.00 2.50
7 8 3.495377 GTGCTACCAAACGTCACAATGTA 59.505 43.478 0.00 0.00 0.00 2.29
9 10 2.289274 TGTGCTACCAAACGTCACAATG 59.711 45.455 1.90 0.00 35.08 2.82
12 13 1.292061 GTGTGCTACCAAACGTCACA 58.708 50.000 0.34 0.34 35.57 3.58
13 14 1.292061 TGTGTGCTACCAAACGTCAC 58.708 50.000 0.00 0.00 31.47 3.67
14 15 2.025589 TTGTGTGCTACCAAACGTCA 57.974 45.000 0.00 0.00 31.47 4.35
16 17 2.096819 CACTTTGTGTGCTACCAAACGT 59.903 45.455 0.00 0.00 40.06 3.99
17 18 2.715268 CACTTTGTGTGCTACCAAACG 58.285 47.619 0.00 0.00 40.06 3.60
18 19 4.102649 GAACACTTTGTGTGCTACCAAAC 58.897 43.478 4.01 0.00 46.79 2.93
19 20 3.129638 GGAACACTTTGTGTGCTACCAAA 59.870 43.478 8.51 0.00 46.79 3.28
21 22 2.092646 AGGAACACTTTGTGTGCTACCA 60.093 45.455 8.51 0.00 46.79 3.25
23 24 2.548480 GGAGGAACACTTTGTGTGCTAC 59.452 50.000 8.51 3.85 46.79 3.58
24 25 2.805295 CGGAGGAACACTTTGTGTGCTA 60.805 50.000 8.51 0.00 46.79 3.49
25 26 1.680338 GGAGGAACACTTTGTGTGCT 58.320 50.000 8.51 2.39 46.79 4.40
26 27 0.307760 CGGAGGAACACTTTGTGTGC 59.692 55.000 4.01 2.15 46.79 4.57
42 43 1.976474 GCAACTCCCATTTGCCGGA 60.976 57.895 5.05 0.00 43.02 5.14
43 44 2.573340 GCAACTCCCATTTGCCGG 59.427 61.111 0.00 0.00 43.02 6.13
47 48 5.840243 TGAGATTATGCAACTCCCATTTG 57.160 39.130 0.00 0.00 0.00 2.32
48 49 7.293073 ACTATGAGATTATGCAACTCCCATTT 58.707 34.615 0.00 0.00 0.00 2.32
50 51 6.043590 TGACTATGAGATTATGCAACTCCCAT 59.956 38.462 0.00 0.00 0.00 4.00
53 54 8.526978 TCTATGACTATGAGATTATGCAACTCC 58.473 37.037 0.00 0.00 0.00 3.85
54 55 9.920133 TTCTATGACTATGAGATTATGCAACTC 57.080 33.333 0.00 0.00 0.00 3.01
78 79 9.495754 GCTTTCTTCATGACTTATACATGTTTC 57.504 33.333 2.30 0.00 43.56 2.78
79 80 9.013229 TGCTTTCTTCATGACTTATACATGTTT 57.987 29.630 2.30 0.00 43.56 2.83
80 81 8.565896 TGCTTTCTTCATGACTTATACATGTT 57.434 30.769 2.30 0.00 43.56 2.71
84 85 8.830580 GCTATTGCTTTCTTCATGACTTATACA 58.169 33.333 0.00 0.00 36.03 2.29
85 86 8.830580 TGCTATTGCTTTCTTCATGACTTATAC 58.169 33.333 0.00 0.00 40.48 1.47
87 88 7.870509 TGCTATTGCTTTCTTCATGACTTAT 57.129 32.000 0.00 0.00 40.48 1.73
89 90 6.016024 TGTTGCTATTGCTTTCTTCATGACTT 60.016 34.615 0.00 0.00 40.48 3.01
90 91 5.474532 TGTTGCTATTGCTTTCTTCATGACT 59.525 36.000 0.00 0.00 40.48 3.41
91 92 5.702865 TGTTGCTATTGCTTTCTTCATGAC 58.297 37.500 0.00 0.00 40.48 3.06
92 93 5.963176 TGTTGCTATTGCTTTCTTCATGA 57.037 34.783 0.00 0.00 40.48 3.07
93 94 7.478322 AGTATGTTGCTATTGCTTTCTTCATG 58.522 34.615 0.00 0.00 40.48 3.07
94 95 7.636150 AGTATGTTGCTATTGCTTTCTTCAT 57.364 32.000 0.00 0.17 40.48 2.57
95 96 8.560355 TTAGTATGTTGCTATTGCTTTCTTCA 57.440 30.769 0.00 0.00 40.48 3.02
96 97 9.278734 GTTTAGTATGTTGCTATTGCTTTCTTC 57.721 33.333 0.00 0.00 40.48 2.87
97 98 7.962918 CGTTTAGTATGTTGCTATTGCTTTCTT 59.037 33.333 0.00 0.00 40.48 2.52
98 99 7.333423 TCGTTTAGTATGTTGCTATTGCTTTCT 59.667 33.333 0.00 0.00 40.48 2.52
99 100 7.461107 TCGTTTAGTATGTTGCTATTGCTTTC 58.539 34.615 0.00 0.00 40.48 2.62
100 101 7.372451 TCGTTTAGTATGTTGCTATTGCTTT 57.628 32.000 0.00 0.00 40.48 3.51
101 102 6.978343 TCGTTTAGTATGTTGCTATTGCTT 57.022 33.333 0.00 0.00 40.48 3.91
103 104 6.065153 CGATCGTTTAGTATGTTGCTATTGC 58.935 40.000 7.03 0.00 40.20 3.56
104 105 6.346598 CCCGATCGTTTAGTATGTTGCTATTG 60.347 42.308 15.09 0.00 0.00 1.90
105 106 5.694910 CCCGATCGTTTAGTATGTTGCTATT 59.305 40.000 15.09 0.00 0.00 1.73
106 107 5.221382 ACCCGATCGTTTAGTATGTTGCTAT 60.221 40.000 15.09 0.00 0.00 2.97
107 108 4.098349 ACCCGATCGTTTAGTATGTTGCTA 59.902 41.667 15.09 0.00 0.00 3.49
108 109 3.118884 ACCCGATCGTTTAGTATGTTGCT 60.119 43.478 15.09 0.00 0.00 3.91
109 110 3.000925 CACCCGATCGTTTAGTATGTTGC 59.999 47.826 15.09 0.00 0.00 4.17
110 111 3.000925 GCACCCGATCGTTTAGTATGTTG 59.999 47.826 15.09 0.00 0.00 3.33
111 112 3.118884 AGCACCCGATCGTTTAGTATGTT 60.119 43.478 15.09 0.00 0.00 2.71
112 113 2.429610 AGCACCCGATCGTTTAGTATGT 59.570 45.455 15.09 0.00 0.00 2.29
113 114 3.093717 AGCACCCGATCGTTTAGTATG 57.906 47.619 15.09 2.63 0.00 2.39
114 115 4.795308 GCTTAGCACCCGATCGTTTAGTAT 60.795 45.833 15.09 1.60 0.00 2.12
115 116 3.489738 GCTTAGCACCCGATCGTTTAGTA 60.490 47.826 15.09 0.00 0.00 1.82
116 117 2.737679 GCTTAGCACCCGATCGTTTAGT 60.738 50.000 15.09 2.94 0.00 2.24
117 118 1.859080 GCTTAGCACCCGATCGTTTAG 59.141 52.381 15.09 2.28 0.00 1.85
119 120 0.249398 AGCTTAGCACCCGATCGTTT 59.751 50.000 15.09 0.00 0.00 3.60
121 122 1.108776 TTAGCTTAGCACCCGATCGT 58.891 50.000 15.09 0.00 0.00 3.73
122 123 2.061773 CATTAGCTTAGCACCCGATCG 58.938 52.381 8.51 8.51 0.00 3.69
123 124 2.037251 TCCATTAGCTTAGCACCCGATC 59.963 50.000 7.07 0.00 0.00 3.69
125 126 1.491668 TCCATTAGCTTAGCACCCGA 58.508 50.000 7.07 0.00 0.00 5.14
126 127 2.325583 TTCCATTAGCTTAGCACCCG 57.674 50.000 7.07 0.00 0.00 5.28
127 128 2.887152 CCATTCCATTAGCTTAGCACCC 59.113 50.000 7.07 0.00 0.00 4.61
128 129 2.887152 CCCATTCCATTAGCTTAGCACC 59.113 50.000 7.07 0.00 0.00 5.01
129 130 3.555966 ACCCATTCCATTAGCTTAGCAC 58.444 45.455 7.07 0.00 0.00 4.40
134 135 4.210331 GACATGACCCATTCCATTAGCTT 58.790 43.478 0.00 0.00 0.00 3.74
135 136 3.202818 TGACATGACCCATTCCATTAGCT 59.797 43.478 0.00 0.00 0.00 3.32
136 137 3.554934 TGACATGACCCATTCCATTAGC 58.445 45.455 0.00 0.00 0.00 3.09
137 138 5.829391 TGATTGACATGACCCATTCCATTAG 59.171 40.000 0.00 0.00 0.00 1.73
139 140 4.612401 TGATTGACATGACCCATTCCATT 58.388 39.130 0.00 0.00 0.00 3.16
140 141 4.079615 TCTGATTGACATGACCCATTCCAT 60.080 41.667 0.00 0.00 0.00 3.41
142 143 3.889815 TCTGATTGACATGACCCATTCC 58.110 45.455 0.00 0.00 0.00 3.01
143 144 5.128205 TGATCTGATTGACATGACCCATTC 58.872 41.667 0.00 1.66 0.00 2.67
145 146 4.783560 TGATCTGATTGACATGACCCAT 57.216 40.909 0.00 0.00 0.00 4.00
146 147 4.783560 ATGATCTGATTGACATGACCCA 57.216 40.909 0.00 0.00 0.00 4.51
147 148 5.128205 TGAATGATCTGATTGACATGACCC 58.872 41.667 0.00 0.00 0.00 4.46
148 149 6.318144 AGTTGAATGATCTGATTGACATGACC 59.682 38.462 0.00 0.00 0.00 4.02
149 150 7.317842 AGTTGAATGATCTGATTGACATGAC 57.682 36.000 0.00 0.00 0.00 3.06
150 151 9.623000 ATTAGTTGAATGATCTGATTGACATGA 57.377 29.630 0.00 0.00 0.00 3.07
151 152 9.665264 CATTAGTTGAATGATCTGATTGACATG 57.335 33.333 0.00 0.00 46.94 3.21
165 166 5.582269 ACGAGGTCACATCATTAGTTGAATG 59.418 40.000 0.00 0.00 45.57 2.67
167 168 5.147330 ACGAGGTCACATCATTAGTTGAA 57.853 39.130 0.00 0.00 38.03 2.69
168 169 4.801330 ACGAGGTCACATCATTAGTTGA 57.199 40.909 0.00 0.00 39.12 3.18
172 173 7.770801 TTGATTAACGAGGTCACATCATTAG 57.229 36.000 0.00 0.00 0.00 1.73
174 175 7.630242 ATTTGATTAACGAGGTCACATCATT 57.370 32.000 0.00 0.00 0.00 2.57
177 178 7.970384 TGTTATTTGATTAACGAGGTCACATC 58.030 34.615 0.00 0.00 35.30 3.06
178 179 7.915293 TGTTATTTGATTAACGAGGTCACAT 57.085 32.000 0.00 0.00 35.30 3.21
180 181 7.803724 AGTTGTTATTTGATTAACGAGGTCAC 58.196 34.615 0.00 0.00 35.30 3.67
182 183 8.252964 AGAGTTGTTATTTGATTAACGAGGTC 57.747 34.615 0.00 0.00 35.30 3.85
183 184 8.617290 AAGAGTTGTTATTTGATTAACGAGGT 57.383 30.769 0.00 0.00 35.30 3.85
199 200 8.934023 TTCCTAACCATGAATAAAGAGTTGTT 57.066 30.769 0.00 0.00 0.00 2.83
201 202 7.962918 CGTTTCCTAACCATGAATAAAGAGTTG 59.037 37.037 0.00 0.00 0.00 3.16
205 206 8.938906 GTTACGTTTCCTAACCATGAATAAAGA 58.061 33.333 0.00 0.00 0.00 2.52
207 208 7.664731 TGGTTACGTTTCCTAACCATGAATAAA 59.335 33.333 14.43 0.00 45.42 1.40
208 209 7.166851 TGGTTACGTTTCCTAACCATGAATAA 58.833 34.615 14.43 0.00 45.42 1.40
209 210 6.709281 TGGTTACGTTTCCTAACCATGAATA 58.291 36.000 14.43 0.00 45.42 1.75
211 212 4.970711 TGGTTACGTTTCCTAACCATGAA 58.029 39.130 14.43 0.00 45.42 2.57
216 217 5.702209 TCAAAGATGGTTACGTTTCCTAACC 59.298 40.000 9.76 9.76 42.49 2.85
221 222 6.739550 CGTTAATCAAAGATGGTTACGTTTCC 59.260 38.462 0.00 0.00 31.90 3.13
222 223 7.512297 TCGTTAATCAAAGATGGTTACGTTTC 58.488 34.615 0.00 0.00 31.90 2.78
223 224 7.424227 TCGTTAATCAAAGATGGTTACGTTT 57.576 32.000 0.00 0.00 31.90 3.60
224 225 6.401796 GCTCGTTAATCAAAGATGGTTACGTT 60.402 38.462 0.00 0.00 31.90 3.99
225 226 5.063060 GCTCGTTAATCAAAGATGGTTACGT 59.937 40.000 0.00 0.00 31.90 3.57
227 228 6.663944 AGCTCGTTAATCAAAGATGGTTAC 57.336 37.500 0.00 0.00 31.90 2.50
228 229 7.553334 ACTAGCTCGTTAATCAAAGATGGTTA 58.447 34.615 0.00 0.00 30.84 2.85
229 230 6.407202 ACTAGCTCGTTAATCAAAGATGGTT 58.593 36.000 0.00 0.00 33.49 3.67
230 231 5.978814 ACTAGCTCGTTAATCAAAGATGGT 58.021 37.500 0.00 0.00 0.00 3.55
231 232 6.042777 TGACTAGCTCGTTAATCAAAGATGG 58.957 40.000 0.00 0.00 0.00 3.51
232 233 7.276658 ACTTGACTAGCTCGTTAATCAAAGATG 59.723 37.037 0.00 0.00 0.00 2.90
233 234 7.324178 ACTTGACTAGCTCGTTAATCAAAGAT 58.676 34.615 0.00 0.00 0.00 2.40
235 236 6.952935 ACTTGACTAGCTCGTTAATCAAAG 57.047 37.500 0.00 0.00 0.00 2.77
236 237 7.823665 TCTACTTGACTAGCTCGTTAATCAAA 58.176 34.615 0.00 0.00 0.00 2.69
237 238 7.387119 TCTACTTGACTAGCTCGTTAATCAA 57.613 36.000 0.00 0.00 0.00 2.57
238 239 6.038382 CCTCTACTTGACTAGCTCGTTAATCA 59.962 42.308 0.00 0.00 0.00 2.57
239 240 6.432107 CCTCTACTTGACTAGCTCGTTAATC 58.568 44.000 0.00 0.00 0.00 1.75
241 242 4.096081 GCCTCTACTTGACTAGCTCGTTAA 59.904 45.833 0.00 0.00 0.00 2.01
245 246 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
246 247 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
247 248 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
248 249 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
249 250 6.993308 TCACTAGTATGCCTCTACTTGACTAG 59.007 42.308 0.00 0.00 40.35 2.57
251 252 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
252 253 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
254 255 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
255 256 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
256 257 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
257 258 5.008217 CAGAGTGTCACTAGTATGCCTCTAC 59.992 48.000 5.21 0.00 0.00 2.59
258 259 5.126779 CAGAGTGTCACTAGTATGCCTCTA 58.873 45.833 5.21 0.00 0.00 2.43
260 261 3.697045 ACAGAGTGTCACTAGTATGCCTC 59.303 47.826 5.21 0.00 0.00 4.70
261 262 3.702792 ACAGAGTGTCACTAGTATGCCT 58.297 45.455 5.21 0.00 0.00 4.75
262 263 4.457834 AACAGAGTGTCACTAGTATGCC 57.542 45.455 5.21 0.00 0.00 4.40
263 264 5.230942 ACAAACAGAGTGTCACTAGTATGC 58.769 41.667 5.21 0.00 0.00 3.14
264 265 7.715265 AAACAAACAGAGTGTCACTAGTATG 57.285 36.000 5.21 5.56 0.00 2.39
265 266 9.424319 CATAAACAAACAGAGTGTCACTAGTAT 57.576 33.333 5.21 0.00 0.00 2.12
268 269 7.715265 ACATAAACAAACAGAGTGTCACTAG 57.285 36.000 5.21 4.44 0.00 2.57
269 270 9.772973 AATACATAAACAAACAGAGTGTCACTA 57.227 29.630 5.21 0.00 0.00 2.74
270 271 8.677148 AATACATAAACAAACAGAGTGTCACT 57.323 30.769 4.81 4.81 0.00 3.41
271 272 8.556194 TGAATACATAAACAAACAGAGTGTCAC 58.444 33.333 0.00 0.00 0.00 3.67
273 274 8.556194 TGTGAATACATAAACAAACAGAGTGTC 58.444 33.333 0.00 0.00 0.00 3.67
275 276 7.803189 GGTGTGAATACATAAACAAACAGAGTG 59.197 37.037 0.00 0.00 39.39 3.51
276 277 7.719633 AGGTGTGAATACATAAACAAACAGAGT 59.280 33.333 0.00 0.00 39.39 3.24
277 278 8.017373 CAGGTGTGAATACATAAACAAACAGAG 58.983 37.037 0.00 0.00 39.39 3.35
278 279 7.500892 ACAGGTGTGAATACATAAACAAACAGA 59.499 33.333 0.00 0.00 39.39 3.41
279 280 7.648142 ACAGGTGTGAATACATAAACAAACAG 58.352 34.615 0.00 0.00 39.39 3.16
280 281 7.575414 ACAGGTGTGAATACATAAACAAACA 57.425 32.000 0.00 0.00 39.39 2.83
290 291 7.279090 CGGAAACATAATACAGGTGTGAATACA 59.721 37.037 0.00 0.00 0.00 2.29
291 292 7.254658 CCGGAAACATAATACAGGTGTGAATAC 60.255 40.741 0.00 0.00 0.00 1.89
293 294 5.588648 CCGGAAACATAATACAGGTGTGAAT 59.411 40.000 0.00 0.00 0.00 2.57
296 297 4.258543 ACCGGAAACATAATACAGGTGTG 58.741 43.478 9.46 0.00 30.60 3.82
297 298 4.563140 ACCGGAAACATAATACAGGTGT 57.437 40.909 9.46 0.00 30.60 4.16
298 299 6.988622 TTAACCGGAAACATAATACAGGTG 57.011 37.500 9.46 0.00 31.97 4.00
299 300 8.266473 TGTATTAACCGGAAACATAATACAGGT 58.734 33.333 22.31 0.00 42.13 4.00
300 301 8.665643 TGTATTAACCGGAAACATAATACAGG 57.334 34.615 22.31 0.00 42.13 4.00
307 308 9.048446 GCTAGAATTGTATTAACCGGAAACATA 57.952 33.333 9.46 0.00 0.00 2.29
308 309 7.554835 TGCTAGAATTGTATTAACCGGAAACAT 59.445 33.333 9.46 0.00 0.00 2.71
309 310 6.879993 TGCTAGAATTGTATTAACCGGAAACA 59.120 34.615 9.46 1.34 0.00 2.83
310 311 7.311364 TGCTAGAATTGTATTAACCGGAAAC 57.689 36.000 9.46 0.00 0.00 2.78
312 313 7.276658 TCATGCTAGAATTGTATTAACCGGAA 58.723 34.615 9.46 0.00 0.00 4.30
313 314 6.822442 TCATGCTAGAATTGTATTAACCGGA 58.178 36.000 9.46 0.00 0.00 5.14
314 315 7.490962 TTCATGCTAGAATTGTATTAACCGG 57.509 36.000 0.00 0.00 0.00 5.28
389 390 4.349342 ACTGAAGGAAATATGCCCTAGAGG 59.651 45.833 0.00 0.00 39.47 3.69
392 393 5.010719 TCGTACTGAAGGAAATATGCCCTAG 59.989 44.000 0.00 0.00 31.36 3.02
394 395 3.709653 TCGTACTGAAGGAAATATGCCCT 59.290 43.478 0.00 0.00 0.00 5.19
395 396 4.058817 CTCGTACTGAAGGAAATATGCCC 58.941 47.826 0.00 0.00 0.00 5.36
396 397 3.495001 GCTCGTACTGAAGGAAATATGCC 59.505 47.826 0.00 0.00 0.00 4.40
398 399 5.985530 TCATGCTCGTACTGAAGGAAATATG 59.014 40.000 0.00 0.00 0.00 1.78
399 400 6.040955 TCTCATGCTCGTACTGAAGGAAATAT 59.959 38.462 0.00 0.00 0.00 1.28
400 401 5.359860 TCTCATGCTCGTACTGAAGGAAATA 59.640 40.000 0.00 0.00 0.00 1.40
402 403 3.509967 TCTCATGCTCGTACTGAAGGAAA 59.490 43.478 0.00 0.00 0.00 3.13
403 404 3.089284 TCTCATGCTCGTACTGAAGGAA 58.911 45.455 0.00 0.00 0.00 3.36
404 405 2.723273 TCTCATGCTCGTACTGAAGGA 58.277 47.619 0.00 0.00 0.00 3.36
406 407 3.838120 TGTTCTCATGCTCGTACTGAAG 58.162 45.455 0.00 0.00 0.00 3.02
408 409 3.506067 TCTTGTTCTCATGCTCGTACTGA 59.494 43.478 0.00 0.00 0.00 3.41
409 410 3.838120 TCTTGTTCTCATGCTCGTACTG 58.162 45.455 0.00 0.00 0.00 2.74
410 411 3.119316 CCTCTTGTTCTCATGCTCGTACT 60.119 47.826 0.00 0.00 0.00 2.73
877 902 5.076873 CCAAAAACCTTATCACCCTTCTCA 58.923 41.667 0.00 0.00 0.00 3.27
978 1004 0.240145 CGTTGCTGAGGTAGTCGACA 59.760 55.000 19.50 0.48 0.00 4.35
1042 1068 2.631062 AGAACACATACGGGACAACAGA 59.369 45.455 0.00 0.00 0.00 3.41
1345 2944 7.585573 GCAAGATGAATATGAACGTTTGATCTC 59.414 37.037 0.46 0.00 0.00 2.75
1436 3037 1.202463 ACTCCCTCGAAGCAATCATCG 60.202 52.381 0.00 0.00 40.31 3.84
1576 3180 1.480137 CTTGAGGTAGAGGCAGTCAGG 59.520 57.143 0.00 0.00 0.00 3.86
1667 3271 7.011857 GGAAATGTGGAAAGTGATATCTCTGAC 59.988 40.741 8.03 5.72 0.00 3.51
1687 3295 1.351076 AAACCCCAAGCCTGGAAATG 58.649 50.000 1.80 0.00 46.92 2.32
1820 3446 4.443063 CACAAAGTAGTCGTCATCGTCAAA 59.557 41.667 0.00 0.00 38.33 2.69
1954 3580 2.505628 CTGTCATCGACCATGAGAGG 57.494 55.000 4.22 0.00 45.38 3.69
1991 3621 2.093447 CACCACACCCCATCTCTTAGAC 60.093 54.545 0.00 0.00 0.00 2.59
2203 3939 4.943093 ACCCTGGCATTTAATTTTGATTGC 59.057 37.500 0.00 0.00 0.00 3.56
2236 3973 8.479313 AGAAACTCTTGACAAAATGGTTTTTC 57.521 30.769 0.00 0.00 32.72 2.29
2254 4005 8.041323 TCAATTAGTCCATGACCTTAGAAACTC 58.959 37.037 0.00 0.00 32.18 3.01
2375 4129 4.772624 TGGTCAACAGAATAGTCTACAGCT 59.227 41.667 0.00 0.00 30.85 4.24
2419 4173 1.615883 TCTTATCGATCAGCTGAGCCC 59.384 52.381 25.34 13.84 0.00 5.19
2436 4190 5.712446 TCATGTACAGTGCTAGTCTCTTCTT 59.288 40.000 0.33 0.00 0.00 2.52
2446 4200 5.221641 ACCTTCACTTTCATGTACAGTGCTA 60.222 40.000 0.33 6.53 38.27 3.49
2569 4343 9.947433 AAACATTGGTCATAATTTGATCACATT 57.053 25.926 11.62 11.62 45.19 2.71
2745 4526 0.038599 AGCACATGACCAGCAATCCA 59.961 50.000 0.00 0.00 0.00 3.41
2804 4585 1.260538 TGCAGGGGTCAGTCAGCTAG 61.261 60.000 0.00 0.00 0.00 3.42
3146 5671 6.648192 ACTTGACTATGAGAAAAGCATAGCT 58.352 36.000 9.77 0.00 45.71 3.32
3149 5674 7.544622 ACGTACTTGACTATGAGAAAAGCATA 58.455 34.615 0.00 0.00 0.00 3.14
3214 5743 3.989167 TGCATGCTGCTTAATTTGTTCAC 59.011 39.130 20.33 0.00 45.31 3.18
3252 5789 2.813754 GTTCAACTGAACCTGCATGCTA 59.186 45.455 20.33 4.40 46.42 3.49
3253 5790 1.610522 GTTCAACTGAACCTGCATGCT 59.389 47.619 20.33 0.00 46.42 3.79


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

AutoCloner maintained by Alex Coulton.