Multiple sequence alignment - TraesCS7D01G080700

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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 TraesCS7D01G080700 chr7D 100.000 3826 0 0 1 3826 47480734 47484559 0.000000e+00 7066.0
1 TraesCS7D01G080700 chr7D 83.016 1207 180 17 1641 2825 47449520 47448317 0.000000e+00 1070.0
2 TraesCS7D01G080700 chr7D 87.435 573 60 7 924 1489 47450274 47449707 0.000000e+00 649.0
3 TraesCS7D01G080700 chr7D 96.471 170 6 0 253 422 576195326 576195157 8.090000e-72 281.0
4 TraesCS7D01G080700 chr7D 95.455 176 7 1 252 426 604569204 604569379 2.910000e-71 279.0
5 TraesCS7D01G080700 chr7D 95.930 172 6 1 249 420 102575937 102576107 1.050000e-70 278.0
6 TraesCS7D01G080700 chr4A 91.932 2516 149 16 415 2894 662565807 662568304 0.000000e+00 3472.0
7 TraesCS7D01G080700 chr4A 82.890 1204 184 17 1641 2825 662232465 662233665 0.000000e+00 1062.0
8 TraesCS7D01G080700 chr4A 86.713 572 46 13 2889 3455 662568342 662568888 3.270000e-170 608.0
9 TraesCS7D01G080700 chr4A 85.839 572 65 6 924 1489 662231719 662232280 9.150000e-166 593.0
10 TraesCS7D01G080700 chr4A 92.328 378 23 3 3450 3824 662589213 662589587 2.020000e-147 532.0
11 TraesCS7D01G080700 chr4A 83.700 454 65 6 1041 1488 621806463 621806013 1.640000e-113 420.0
12 TraesCS7D01G080700 chr7A 94.977 1951 88 3 946 2894 50136019 50137961 0.000000e+00 3051.0
13 TraesCS7D01G080700 chr7A 95.962 941 32 6 2889 3826 50137999 50138936 0.000000e+00 1522.0
14 TraesCS7D01G080700 chr7A 82.285 1208 187 18 1641 2825 49994048 49995251 0.000000e+00 1020.0
15 TraesCS7D01G080700 chr7A 87.215 571 61 7 926 1489 49993289 49993854 1.160000e-179 640.0
16 TraesCS7D01G080700 chr7A 87.129 303 11 6 660 945 50135622 50135913 6.170000e-83 318.0
17 TraesCS7D01G080700 chr7A 92.760 221 10 3 415 629 50135408 50135628 7.980000e-82 315.0
18 TraesCS7D01G080700 chr7A 90.196 153 15 0 104 256 50135259 50135411 2.330000e-47 200.0
19 TraesCS7D01G080700 chrUn 92.941 1360 81 5 1548 2894 264862735 264861378 0.000000e+00 1965.0
20 TraesCS7D01G080700 chrUn 92.941 1360 81 5 1548 2894 299069070 299070427 0.000000e+00 1965.0
21 TraesCS7D01G080700 chrUn 89.490 942 73 13 2889 3824 264861340 264860419 0.000000e+00 1168.0
22 TraesCS7D01G080700 chrUn 89.490 942 73 13 2889 3824 299070465 299071386 0.000000e+00 1168.0
23 TraesCS7D01G080700 chrUn 91.626 824 40 6 684 1490 264863545 264862734 0.000000e+00 1112.0
24 TraesCS7D01G080700 chrUn 91.626 824 40 6 684 1490 299068260 299069071 0.000000e+00 1112.0
25 TraesCS7D01G080700 chrUn 92.164 268 17 1 420 687 264866145 264865882 3.610000e-100 375.0
26 TraesCS7D01G080700 chrUn 92.164 268 17 1 420 687 280426777 280427040 3.610000e-100 375.0
27 TraesCS7D01G080700 chrUn 92.164 268 17 1 420 687 280433790 280434053 3.610000e-100 375.0
28 TraesCS7D01G080700 chrUn 92.164 268 17 1 420 687 305064565 305064302 3.610000e-100 375.0
29 TraesCS7D01G080700 chrUn 88.372 129 15 0 104 232 264866274 264866146 5.120000e-34 156.0
30 TraesCS7D01G080700 chrUn 88.372 129 15 0 104 232 280426648 280426776 5.120000e-34 156.0
31 TraesCS7D01G080700 chrUn 88.372 129 15 0 104 232 280433661 280433789 5.120000e-34 156.0
32 TraesCS7D01G080700 chrUn 88.372 129 15 0 104 232 305064694 305064566 5.120000e-34 156.0
33 TraesCS7D01G080700 chr5B 83.040 454 68 6 1041 1488 690102711 690103161 1.660000e-108 403.0
34 TraesCS7D01G080700 chr5B 77.664 488 99 5 1641 2126 712009094 712008615 4.840000e-74 289.0
35 TraesCS7D01G080700 chr5B 77.664 488 99 5 1641 2126 712026546 712026067 4.840000e-74 289.0
36 TraesCS7D01G080700 chr2D 97.605 167 4 0 252 418 451960657 451960823 1.740000e-73 287.0
37 TraesCS7D01G080700 chr6D 97.024 168 5 0 252 419 286634345 286634178 2.250000e-72 283.0
38 TraesCS7D01G080700 chr6D 96.450 169 6 0 252 420 45503516 45503348 2.910000e-71 279.0
39 TraesCS7D01G080700 chr5D 97.024 168 5 0 253 420 486175298 486175131 2.250000e-72 283.0
40 TraesCS7D01G080700 chr5D 95.402 174 8 0 250 423 382430436 382430609 1.050000e-70 278.0
41 TraesCS7D01G080700 chr3D 96.364 165 6 0 252 416 402850632 402850796 4.870000e-69 272.0
42 TraesCS7D01G080700 chr3D 94.595 37 2 0 212 248 445619914 445619878 1.480000e-04 58.4
43 TraesCS7D01G080700 chr6B 91.870 123 6 2 3704 3826 230607096 230606978 6.570000e-38 169.0
44 TraesCS7D01G080700 chr3B 89.362 47 5 0 202 248 584531247 584531201 4.130000e-05 60.2
45 TraesCS7D01G080700 chr3A 94.595 37 2 0 212 248 587391240 587391204 1.480000e-04 58.4


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 TraesCS7D01G080700 chr7D 47480734 47484559 3825 False 7066.0 7066 100.000000 1 3826 1 chr7D.!!$F1 3825
1 TraesCS7D01G080700 chr7D 47448317 47450274 1957 True 859.5 1070 85.225500 924 2825 2 chr7D.!!$R2 1901
2 TraesCS7D01G080700 chr4A 662565807 662568888 3081 False 2040.0 3472 89.322500 415 3455 2 chr4A.!!$F3 3040
3 TraesCS7D01G080700 chr4A 662231719 662233665 1946 False 827.5 1062 84.364500 924 2825 2 chr4A.!!$F2 1901
4 TraesCS7D01G080700 chr7A 50135259 50138936 3677 False 1081.2 3051 92.204800 104 3826 5 chr7A.!!$F2 3722
5 TraesCS7D01G080700 chr7A 49993289 49995251 1962 False 830.0 1020 84.750000 926 2825 2 chr7A.!!$F1 1899
6 TraesCS7D01G080700 chrUn 299068260 299071386 3126 False 1415.0 1965 91.352333 684 3824 3 chrUn.!!$F3 3140
7 TraesCS7D01G080700 chrUn 264860419 264866274 5855 True 955.2 1965 90.918600 104 3824 5 chrUn.!!$R1 3720

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
252 253 0.100682 CGGTCGAGTCGATCCAACAT 59.899 55.0 19.75 0.00 38.42 2.71 F
2066 4700 0.179004 TGGAAGAAACCACGTGGCAT 60.179 50.0 34.26 22.99 39.32 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 4707 0.179067 TGACGTGGTCCTTGGTGAAC 60.179 55.0 0.0 0.0 0.0 3.18 R
3330 6040 0.617820 GTCCTTCTCCCTAGTGCCCA 60.618 60.0 0.0 0.0 0.0 5.36 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
21 22 3.963428 AGGATCTACAACACCTGACAC 57.037 47.619 0.00 0.00 0.00 3.67
22 23 2.567615 AGGATCTACAACACCTGACACC 59.432 50.000 0.00 0.00 0.00 4.16
23 24 2.301870 GGATCTACAACACCTGACACCA 59.698 50.000 0.00 0.00 0.00 4.17
24 25 3.055094 GGATCTACAACACCTGACACCAT 60.055 47.826 0.00 0.00 0.00 3.55
25 26 4.161565 GGATCTACAACACCTGACACCATA 59.838 45.833 0.00 0.00 0.00 2.74
26 27 5.163301 GGATCTACAACACCTGACACCATAT 60.163 44.000 0.00 0.00 0.00 1.78
27 28 5.339008 TCTACAACACCTGACACCATATC 57.661 43.478 0.00 0.00 0.00 1.63
28 29 5.023452 TCTACAACACCTGACACCATATCT 58.977 41.667 0.00 0.00 0.00 1.98
29 30 4.207891 ACAACACCTGACACCATATCTC 57.792 45.455 0.00 0.00 0.00 2.75
30 31 3.190079 CAACACCTGACACCATATCTCG 58.810 50.000 0.00 0.00 0.00 4.04
31 32 2.457598 ACACCTGACACCATATCTCGT 58.542 47.619 0.00 0.00 0.00 4.18
32 33 2.832129 ACACCTGACACCATATCTCGTT 59.168 45.455 0.00 0.00 0.00 3.85
33 34 4.021229 ACACCTGACACCATATCTCGTTA 58.979 43.478 0.00 0.00 0.00 3.18
34 35 4.649674 ACACCTGACACCATATCTCGTTAT 59.350 41.667 0.00 0.00 0.00 1.89
35 36 5.128827 ACACCTGACACCATATCTCGTTATT 59.871 40.000 0.00 0.00 0.00 1.40
36 37 5.463392 CACCTGACACCATATCTCGTTATTG 59.537 44.000 0.00 0.00 0.00 1.90
37 38 4.449068 CCTGACACCATATCTCGTTATTGC 59.551 45.833 0.00 0.00 0.00 3.56
38 39 4.048504 TGACACCATATCTCGTTATTGCG 58.951 43.478 0.00 0.00 0.00 4.85
39 40 2.800544 ACACCATATCTCGTTATTGCGC 59.199 45.455 0.00 0.00 0.00 6.09
40 41 2.799978 CACCATATCTCGTTATTGCGCA 59.200 45.455 5.66 5.66 0.00 6.09
41 42 2.800544 ACCATATCTCGTTATTGCGCAC 59.199 45.455 11.12 0.00 0.00 5.34
42 43 2.159973 CCATATCTCGTTATTGCGCACG 60.160 50.000 11.12 11.33 37.77 5.34
43 44 0.850217 TATCTCGTTATTGCGCACGC 59.150 50.000 11.12 8.33 42.35 5.34
53 54 4.794241 GCGCACGCACGATGAACC 62.794 66.667 10.65 0.00 41.49 3.62
54 55 3.112075 CGCACGCACGATGAACCT 61.112 61.111 0.00 0.00 34.06 3.50
55 56 2.778679 GCACGCACGATGAACCTC 59.221 61.111 0.00 0.00 0.00 3.85
56 57 3.071459 GCACGCACGATGAACCTCG 62.071 63.158 0.00 0.00 44.14 4.63
57 58 2.809601 ACGCACGATGAACCTCGC 60.810 61.111 0.00 0.00 42.35 5.03
58 59 3.554692 CGCACGATGAACCTCGCC 61.555 66.667 0.00 0.00 42.35 5.54
59 60 2.434185 GCACGATGAACCTCGCCA 60.434 61.111 0.00 0.00 42.35 5.69
60 61 2.456119 GCACGATGAACCTCGCCAG 61.456 63.158 0.00 0.00 42.35 4.85
61 62 2.125512 ACGATGAACCTCGCCAGC 60.126 61.111 0.00 0.00 42.35 4.85
62 63 2.185350 CGATGAACCTCGCCAGCT 59.815 61.111 0.00 0.00 0.00 4.24
63 64 1.448540 CGATGAACCTCGCCAGCTT 60.449 57.895 0.00 0.00 0.00 3.74
64 65 1.021390 CGATGAACCTCGCCAGCTTT 61.021 55.000 0.00 0.00 0.00 3.51
65 66 0.449388 GATGAACCTCGCCAGCTTTG 59.551 55.000 0.00 0.00 0.00 2.77
66 67 1.589716 ATGAACCTCGCCAGCTTTGC 61.590 55.000 0.00 0.00 0.00 3.68
67 68 1.968540 GAACCTCGCCAGCTTTGCT 60.969 57.895 3.68 0.00 40.77 3.91
79 80 2.983229 AGCTTTGCTGACTACATCCAG 58.017 47.619 0.00 0.00 37.57 3.86
80 81 2.568956 AGCTTTGCTGACTACATCCAGA 59.431 45.455 0.00 0.00 37.57 3.86
81 82 2.675348 GCTTTGCTGACTACATCCAGAC 59.325 50.000 0.00 0.00 32.37 3.51
82 83 2.654749 TTGCTGACTACATCCAGACG 57.345 50.000 0.00 0.00 32.37 4.18
83 84 0.817654 TGCTGACTACATCCAGACGG 59.182 55.000 0.00 0.00 32.37 4.79
85 86 1.202313 GCTGACTACATCCAGACGGAC 60.202 57.143 0.00 0.00 46.79 4.79
86 87 2.092323 CTGACTACATCCAGACGGACA 58.908 52.381 0.00 0.00 46.79 4.02
87 88 2.492088 CTGACTACATCCAGACGGACAA 59.508 50.000 0.00 0.00 46.79 3.18
88 89 3.096852 TGACTACATCCAGACGGACAAT 58.903 45.455 0.00 0.00 46.79 2.71
89 90 3.130516 TGACTACATCCAGACGGACAATC 59.869 47.826 0.00 0.00 46.79 2.67
90 91 3.366396 ACTACATCCAGACGGACAATCT 58.634 45.455 0.00 0.00 46.79 2.40
91 92 2.969628 ACATCCAGACGGACAATCTC 57.030 50.000 0.00 0.00 46.79 2.75
92 93 2.461695 ACATCCAGACGGACAATCTCT 58.538 47.619 0.00 0.00 46.79 3.10
93 94 2.428890 ACATCCAGACGGACAATCTCTC 59.571 50.000 0.00 0.00 46.79 3.20
94 95 1.095600 TCCAGACGGACAATCTCTCG 58.904 55.000 0.00 0.00 35.91 4.04
95 96 1.095600 CCAGACGGACAATCTCTCGA 58.904 55.000 0.00 0.00 0.00 4.04
96 97 1.064803 CCAGACGGACAATCTCTCGAG 59.935 57.143 5.93 5.93 0.00 4.04
97 98 1.064803 CAGACGGACAATCTCTCGAGG 59.935 57.143 13.56 3.44 0.00 4.63
98 99 1.065345 AGACGGACAATCTCTCGAGGA 60.065 52.381 13.56 9.31 0.00 3.71
99 100 1.332375 GACGGACAATCTCTCGAGGAG 59.668 57.143 13.56 8.94 43.12 3.69
100 101 0.665835 CGGACAATCTCTCGAGGAGG 59.334 60.000 13.56 7.95 42.10 4.30
101 102 1.747552 CGGACAATCTCTCGAGGAGGA 60.748 57.143 13.56 9.17 42.10 3.71
102 103 2.593026 GGACAATCTCTCGAGGAGGAT 58.407 52.381 13.56 11.04 42.10 3.24
143 144 1.089112 TGCGAATTCACAGGCTCATG 58.911 50.000 6.22 0.00 0.00 3.07
176 177 2.246091 AGAGAGAGTTTGCCCTAGCT 57.754 50.000 0.00 0.00 40.80 3.32
177 178 1.830477 AGAGAGAGTTTGCCCTAGCTG 59.170 52.381 0.00 0.00 40.80 4.24
183 184 1.377725 TTTGCCCTAGCTGCTGAGC 60.378 57.895 13.43 12.48 46.64 4.26
193 194 3.672295 CTGCTGAGCGGAAGGGGAC 62.672 68.421 7.70 0.00 37.02 4.46
204 205 1.271707 GGAAGGGGACGAAATGTTGGA 60.272 52.381 0.00 0.00 0.00 3.53
208 209 2.890945 AGGGGACGAAATGTTGGAAAAG 59.109 45.455 0.00 0.00 0.00 2.27
210 211 2.029380 GGGACGAAATGTTGGAAAAGGG 60.029 50.000 0.00 0.00 0.00 3.95
212 213 1.343142 ACGAAATGTTGGAAAAGGGGC 59.657 47.619 0.00 0.00 0.00 5.80
240 241 0.107848 AATAAAGGTGGCCGGTCGAG 60.108 55.000 0.00 0.00 0.00 4.04
252 253 0.100682 CGGTCGAGTCGATCCAACAT 59.899 55.000 19.75 0.00 38.42 2.71
253 254 1.332686 CGGTCGAGTCGATCCAACATA 59.667 52.381 19.75 0.00 38.42 2.29
254 255 2.728922 GGTCGAGTCGATCCAACATAC 58.271 52.381 19.75 2.47 38.42 2.39
255 256 2.358267 GGTCGAGTCGATCCAACATACT 59.642 50.000 19.75 0.00 38.42 2.12
256 257 3.548415 GGTCGAGTCGATCCAACATACTC 60.548 52.174 19.75 0.52 38.42 2.59
257 258 2.617308 TCGAGTCGATCCAACATACTCC 59.383 50.000 12.09 0.00 34.42 3.85
258 259 2.287668 CGAGTCGATCCAACATACTCCC 60.288 54.545 6.73 0.00 34.42 4.30
259 260 2.959707 GAGTCGATCCAACATACTCCCT 59.040 50.000 0.00 0.00 32.27 4.20
260 261 3.375699 AGTCGATCCAACATACTCCCTT 58.624 45.455 0.00 0.00 0.00 3.95
261 262 3.385111 AGTCGATCCAACATACTCCCTTC 59.615 47.826 0.00 0.00 0.00 3.46
262 263 2.361119 TCGATCCAACATACTCCCTTCG 59.639 50.000 0.00 0.00 0.00 3.79
263 264 2.100916 CGATCCAACATACTCCCTTCGT 59.899 50.000 0.00 0.00 0.00 3.85
264 265 3.430374 CGATCCAACATACTCCCTTCGTT 60.430 47.826 0.00 0.00 0.00 3.85
265 266 3.604875 TCCAACATACTCCCTTCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
266 267 2.235402 TCCAACATACTCCCTTCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
267 268 2.236395 CCAACATACTCCCTTCGTTCCT 59.764 50.000 0.00 0.00 0.00 3.36
268 269 3.449737 CCAACATACTCCCTTCGTTCCTA 59.550 47.826 0.00 0.00 0.00 2.94
269 270 4.081309 CCAACATACTCCCTTCGTTCCTAA 60.081 45.833 0.00 0.00 0.00 2.69
270 271 5.484715 CAACATACTCCCTTCGTTCCTAAA 58.515 41.667 0.00 0.00 0.00 1.85
271 272 5.952347 ACATACTCCCTTCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
272 273 7.270047 CAACATACTCCCTTCGTTCCTAAATA 58.730 38.462 0.00 0.00 0.00 1.40
273 274 6.814043 ACATACTCCCTTCGTTCCTAAATAC 58.186 40.000 0.00 0.00 0.00 1.89
274 275 6.610425 ACATACTCCCTTCGTTCCTAAATACT 59.390 38.462 0.00 0.00 0.00 2.12
275 276 7.125356 ACATACTCCCTTCGTTCCTAAATACTT 59.875 37.037 0.00 0.00 0.00 2.24
276 277 5.731591 ACTCCCTTCGTTCCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
277 278 5.247792 ACTCCCTTCGTTCCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
278 279 5.727434 TCCCTTCGTTCCTAAATACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
279 280 5.482878 TCCCTTCGTTCCTAAATACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
280 281 5.581085 CCCTTCGTTCCTAAATACTTGTCTG 59.419 44.000 0.00 0.00 0.00 3.51
281 282 6.164176 CCTTCGTTCCTAAATACTTGTCTGT 58.836 40.000 0.00 0.00 0.00 3.41
282 283 6.310711 CCTTCGTTCCTAAATACTTGTCTGTC 59.689 42.308 0.00 0.00 0.00 3.51
283 284 6.585695 TCGTTCCTAAATACTTGTCTGTCT 57.414 37.500 0.00 0.00 0.00 3.41
284 285 7.692460 TCGTTCCTAAATACTTGTCTGTCTA 57.308 36.000 0.00 0.00 0.00 2.59
285 286 7.759465 TCGTTCCTAAATACTTGTCTGTCTAG 58.241 38.462 0.00 0.00 0.00 2.43
286 287 7.609146 TCGTTCCTAAATACTTGTCTGTCTAGA 59.391 37.037 0.00 0.00 0.00 2.43
311 312 9.385902 GACATTTCAAATGAATATCACATACGG 57.614 33.333 17.30 0.00 33.54 4.02
312 313 9.119418 ACATTTCAAATGAATATCACATACGGA 57.881 29.630 17.30 0.00 33.54 4.69
315 316 9.119418 TTTCAAATGAATATCACATACGGATGT 57.881 29.630 7.68 7.68 39.20 3.06
327 328 6.650427 ACATACGGATGTGTGTAGACATAT 57.350 37.500 13.83 1.68 46.96 1.78
328 329 7.050970 ACATACGGATGTGTGTAGACATATT 57.949 36.000 13.83 0.00 46.96 1.28
329 330 7.497595 ACATACGGATGTGTGTAGACATATTT 58.502 34.615 13.83 0.00 46.96 1.40
330 331 7.985184 ACATACGGATGTGTGTAGACATATTTT 59.015 33.333 13.83 0.00 46.96 1.82
331 332 9.471084 CATACGGATGTGTGTAGACATATTTTA 57.529 33.333 0.00 0.00 36.67 1.52
332 333 9.692749 ATACGGATGTGTGTAGACATATTTTAG 57.307 33.333 3.74 0.07 36.67 1.85
333 334 7.778083 ACGGATGTGTGTAGACATATTTTAGA 58.222 34.615 3.74 0.00 36.67 2.10
334 335 7.921214 ACGGATGTGTGTAGACATATTTTAGAG 59.079 37.037 3.74 0.00 36.67 2.43
335 336 7.921214 CGGATGTGTGTAGACATATTTTAGAGT 59.079 37.037 3.74 0.00 36.67 3.24
358 359 9.400638 GAGTATAGATTCACTCATTTTACTCCG 57.599 37.037 0.00 0.00 40.74 4.63
359 360 8.915036 AGTATAGATTCACTCATTTTACTCCGT 58.085 33.333 0.00 0.00 0.00 4.69
362 363 9.698309 ATAGATTCACTCATTTTACTCCGTATG 57.302 33.333 0.00 0.00 0.00 2.39
363 364 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
364 365 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
365 366 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
366 367 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
367 368 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
368 369 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
369 370 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
370 371 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
371 372 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
372 373 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
373 374 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
374 375 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
375 376 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
376 377 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
377 378 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
378 379 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
379 380 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
380 381 6.367695 TCCGTATGTAGTCACTTGTTGAAATG 59.632 38.462 0.00 0.00 35.39 2.32
381 382 6.015504 CGTATGTAGTCACTTGTTGAAATGC 58.984 40.000 0.00 0.00 35.39 3.56
382 383 4.829064 TGTAGTCACTTGTTGAAATGCC 57.171 40.909 0.00 0.00 35.39 4.40
383 384 4.460263 TGTAGTCACTTGTTGAAATGCCT 58.540 39.130 0.00 0.00 35.39 4.75
384 385 5.616270 TGTAGTCACTTGTTGAAATGCCTA 58.384 37.500 0.00 0.00 35.39 3.93
385 386 5.700832 TGTAGTCACTTGTTGAAATGCCTAG 59.299 40.000 0.00 0.00 35.39 3.02
386 387 4.973168 AGTCACTTGTTGAAATGCCTAGA 58.027 39.130 0.00 0.00 35.39 2.43
387 388 5.376625 AGTCACTTGTTGAAATGCCTAGAA 58.623 37.500 0.00 0.00 35.39 2.10
388 389 5.827797 AGTCACTTGTTGAAATGCCTAGAAA 59.172 36.000 0.00 0.00 35.39 2.52
389 390 6.016777 AGTCACTTGTTGAAATGCCTAGAAAG 60.017 38.462 0.00 0.00 35.39 2.62
390 391 6.017109 GTCACTTGTTGAAATGCCTAGAAAGA 60.017 38.462 0.00 0.00 35.39 2.52
391 392 6.017109 TCACTTGTTGAAATGCCTAGAAAGAC 60.017 38.462 0.00 0.00 0.00 3.01
392 393 5.827797 ACTTGTTGAAATGCCTAGAAAGACA 59.172 36.000 0.00 0.00 0.00 3.41
393 394 6.321181 ACTTGTTGAAATGCCTAGAAAGACAA 59.679 34.615 0.00 0.00 0.00 3.18
394 395 6.317789 TGTTGAAATGCCTAGAAAGACAAG 57.682 37.500 0.00 0.00 0.00 3.16
395 396 5.827797 TGTTGAAATGCCTAGAAAGACAAGT 59.172 36.000 0.00 0.00 0.00 3.16
396 397 6.995686 TGTTGAAATGCCTAGAAAGACAAGTA 59.004 34.615 0.00 0.00 0.00 2.24
397 398 7.665559 TGTTGAAATGCCTAGAAAGACAAGTAT 59.334 33.333 0.00 0.00 0.00 2.12
398 399 8.515414 GTTGAAATGCCTAGAAAGACAAGTATT 58.485 33.333 0.00 0.00 0.00 1.89
399 400 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
400 401 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
402 403 8.738645 AATGCCTAGAAAGACAAGTATTTAGG 57.261 34.615 5.26 5.26 0.00 2.69
403 404 7.490657 TGCCTAGAAAGACAAGTATTTAGGA 57.509 36.000 11.40 0.00 26.70 2.94
404 405 7.913789 TGCCTAGAAAGACAAGTATTTAGGAA 58.086 34.615 11.40 1.02 26.70 3.36
405 406 7.822822 TGCCTAGAAAGACAAGTATTTAGGAAC 59.177 37.037 11.40 0.00 26.70 3.62
406 407 7.010275 GCCTAGAAAGACAAGTATTTAGGAACG 59.990 40.741 11.40 0.00 26.70 3.95
407 408 7.491696 CCTAGAAAGACAAGTATTTAGGAACGG 59.508 40.741 4.01 0.00 26.70 4.44
408 409 7.001099 AGAAAGACAAGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
409 410 7.097834 AGAAAGACAAGTATTTAGGAACGGAG 58.902 38.462 0.00 0.00 0.00 4.63
410 411 5.340439 AGACAAGTATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
411 412 4.161754 AGACAAGTATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
412 413 4.098894 ACAAGTATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
413 414 4.161754 ACAAGTATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
434 435 9.719433 AGGGAGTACTTGGTATATAACTTACAA 57.281 33.333 0.00 0.00 0.00 2.41
460 466 6.531503 ACATGAGCTAGCTGAAGTAGTTAA 57.468 37.500 24.99 0.00 0.00 2.01
478 484 9.988350 AGTAGTTAATTCATTTGCTAATTCACG 57.012 29.630 0.00 0.00 28.96 4.35
499 505 2.352960 GCCAGTTATGTTGAGCTAGTGC 59.647 50.000 0.00 0.00 40.05 4.40
707 3056 3.990318 ACTTTTCTTTCCAAAGGAGCG 57.010 42.857 0.00 0.00 35.82 5.03
753 3102 0.832135 TCAGGAAGGGCTGACTTCGT 60.832 55.000 9.20 7.60 46.06 3.85
829 3195 2.032894 CGTTGTGATGCAAAGTCGTCTT 60.033 45.455 0.00 0.00 39.03 3.01
846 3212 7.616313 AGTCGTCTTATCTTCTCCTTCAAATT 58.384 34.615 0.00 0.00 0.00 1.82
847 3213 8.750298 AGTCGTCTTATCTTCTCCTTCAAATTA 58.250 33.333 0.00 0.00 0.00 1.40
848 3214 9.367444 GTCGTCTTATCTTCTCCTTCAAATTAA 57.633 33.333 0.00 0.00 0.00 1.40
919 3285 4.795970 TGCAAAGTCTCTTCTTCGTTTC 57.204 40.909 0.00 0.00 0.00 2.78
941 3307 3.731867 CGTCCCTTTGCACAGCATATTTC 60.732 47.826 0.00 0.00 38.76 2.17
1034 3511 2.757508 CTCGCTGCTCCTCTCCCA 60.758 66.667 0.00 0.00 0.00 4.37
1039 3516 3.003173 TGCTCCTCTCCCAACCCG 61.003 66.667 0.00 0.00 0.00 5.28
1050 3527 1.257055 CCCAACCCGAACAATGGCAT 61.257 55.000 0.00 0.00 0.00 4.40
1052 3529 0.887247 CAACCCGAACAATGGCATCA 59.113 50.000 0.00 0.00 0.00 3.07
1069 3546 3.589988 CATCACGTCCTCTTAGCACTTT 58.410 45.455 0.00 0.00 0.00 2.66
1080 3557 5.129485 CCTCTTAGCACTTTTCTCCATCCTA 59.871 44.000 0.00 0.00 0.00 2.94
1522 4046 2.264794 CCTAGTCACGGTGCACCC 59.735 66.667 29.95 15.82 0.00 4.61
1531 4055 1.543802 CACGGTGCACCCAAAATGTAT 59.456 47.619 29.95 1.59 0.00 2.29
1553 4078 7.726291 TGTATTACCTTTTTCCCTTCATTGACA 59.274 33.333 0.00 0.00 0.00 3.58
1596 4125 6.293790 CCACGTAGAGTTTACATCCGATATCA 60.294 42.308 3.12 0.00 0.00 2.15
1633 4255 8.042944 AGCAGTCTGTCTAGTTAGTTACTTAC 57.957 38.462 0.93 0.00 38.33 2.34
1698 4332 3.099438 CTGAGCCATGCAGAAGCG 58.901 61.111 0.00 0.00 46.23 4.68
1878 4512 3.394836 GCCGAGGACTTGCTCCCT 61.395 66.667 0.00 0.00 40.53 4.20
1885 4519 1.194781 GGACTTGCTCCCTGGAGTCA 61.195 60.000 14.45 9.99 43.70 3.41
1943 4577 1.931551 GCCGCGAGCGAATATTCAA 59.068 52.632 19.72 0.00 42.83 2.69
1947 4581 2.222931 CCGCGAGCGAATATTCAAACAA 60.223 45.455 19.72 0.00 42.83 2.83
1954 4588 7.621991 CGAGCGAATATTCAAACAATTAGACT 58.378 34.615 15.57 0.00 0.00 3.24
1967 4601 7.971183 AACAATTAGACTCCTTCTTTGAGAC 57.029 36.000 0.00 0.00 35.55 3.36
1974 4608 3.325135 ACTCCTTCTTTGAGACGGTCATT 59.675 43.478 11.27 0.00 35.36 2.57
2004 4638 1.340088 TGGACCCTAAGCGTGTGTTA 58.660 50.000 0.00 0.00 0.00 2.41
2066 4700 0.179004 TGGAAGAAACCACGTGGCAT 60.179 50.000 34.26 22.99 39.32 4.40
2073 4707 3.945285 AGAAACCACGTGGCATATTTAGG 59.055 43.478 34.26 7.12 39.32 2.69
2608 5270 0.878086 GGCGAGCATCCAGAGCTAAC 60.878 60.000 0.00 0.00 43.58 2.34
2707 5369 2.092429 TGCTCTTCAGTTTTGAGTGGGT 60.092 45.455 0.00 0.00 34.15 4.51
2745 5407 3.673902 ACAACGGATGATGTGAACATGA 58.326 40.909 0.00 0.00 36.57 3.07
2762 5424 3.075134 ACATGAAGGAAGAAGGAAGGCTT 59.925 43.478 0.00 0.00 0.00 4.35
2843 5505 3.574074 GAGTGCCACCACCATGCCT 62.574 63.158 0.00 0.00 43.09 4.75
3185 5893 5.222254 ACCTAATAAAGAAAACCCAGAGCCA 60.222 40.000 0.00 0.00 0.00 4.75
3322 6032 1.811860 GCACAGCCAGCATTTAGGG 59.188 57.895 0.00 0.00 0.00 3.53
3355 6065 3.436243 CACTAGGGAGAAGGACTGTCTT 58.564 50.000 7.85 0.00 0.00 3.01
3357 6067 4.642885 CACTAGGGAGAAGGACTGTCTTAG 59.357 50.000 7.85 0.00 0.00 2.18
3413 6124 6.931281 CACAAATATGGAACGGATAGAGTGAT 59.069 38.462 0.00 0.00 0.00 3.06
3473 6184 4.256920 CTCCAACTGAATCAACTAGTGGG 58.743 47.826 0.00 0.00 36.95 4.61
3655 6370 2.099062 CTCGAAGCACGGCAATGC 59.901 61.111 0.00 0.00 46.50 3.56
3676 6391 3.184986 GCCAATTCTGTGTGCAATTTGTC 59.815 43.478 0.00 0.00 0.00 3.18
3748 6463 8.528044 TGGATGTTTAAGTTAGGTTTCAAGTT 57.472 30.769 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.008049 GGTGTCAGGTGTTGTAGATCCTT 59.992 47.826 0.00 0.00 0.00 3.36
1 2 2.567615 GGTGTCAGGTGTTGTAGATCCT 59.432 50.000 0.00 0.00 0.00 3.24
2 3 2.301870 TGGTGTCAGGTGTTGTAGATCC 59.698 50.000 0.00 0.00 0.00 3.36
3 4 3.678056 TGGTGTCAGGTGTTGTAGATC 57.322 47.619 0.00 0.00 0.00 2.75
4 5 5.663106 AGATATGGTGTCAGGTGTTGTAGAT 59.337 40.000 0.00 0.00 0.00 1.98
5 6 5.023452 AGATATGGTGTCAGGTGTTGTAGA 58.977 41.667 0.00 0.00 0.00 2.59
6 7 5.344743 AGATATGGTGTCAGGTGTTGTAG 57.655 43.478 0.00 0.00 0.00 2.74
7 8 4.142249 CGAGATATGGTGTCAGGTGTTGTA 60.142 45.833 0.00 0.00 0.00 2.41
8 9 3.368427 CGAGATATGGTGTCAGGTGTTGT 60.368 47.826 0.00 0.00 0.00 3.32
9 10 3.190079 CGAGATATGGTGTCAGGTGTTG 58.810 50.000 0.00 0.00 0.00 3.33
10 11 2.832129 ACGAGATATGGTGTCAGGTGTT 59.168 45.455 0.00 0.00 0.00 3.32
11 12 2.457598 ACGAGATATGGTGTCAGGTGT 58.542 47.619 0.00 0.00 0.00 4.16
12 13 3.526931 AACGAGATATGGTGTCAGGTG 57.473 47.619 0.00 0.00 0.00 4.00
13 14 5.601662 CAATAACGAGATATGGTGTCAGGT 58.398 41.667 0.00 0.00 0.00 4.00
14 15 4.449068 GCAATAACGAGATATGGTGTCAGG 59.551 45.833 0.00 0.00 0.00 3.86
15 16 4.148871 CGCAATAACGAGATATGGTGTCAG 59.851 45.833 0.00 0.00 34.06 3.51
16 17 4.048504 CGCAATAACGAGATATGGTGTCA 58.951 43.478 0.00 0.00 34.06 3.58
17 18 3.120991 GCGCAATAACGAGATATGGTGTC 60.121 47.826 0.30 0.00 34.06 3.67
18 19 2.800544 GCGCAATAACGAGATATGGTGT 59.199 45.455 0.30 0.00 34.06 4.16
19 20 2.799978 TGCGCAATAACGAGATATGGTG 59.200 45.455 8.16 0.00 34.06 4.17
20 21 2.800544 GTGCGCAATAACGAGATATGGT 59.199 45.455 14.00 0.00 34.06 3.55
21 22 2.159973 CGTGCGCAATAACGAGATATGG 60.160 50.000 14.00 0.00 42.32 2.74
22 23 2.718789 GCGTGCGCAATAACGAGATATG 60.719 50.000 20.53 0.00 42.32 1.78
23 24 1.455786 GCGTGCGCAATAACGAGATAT 59.544 47.619 20.53 0.00 42.32 1.63
24 25 0.850217 GCGTGCGCAATAACGAGATA 59.150 50.000 20.53 0.00 42.32 1.98
25 26 1.636340 GCGTGCGCAATAACGAGAT 59.364 52.632 20.53 0.00 42.32 2.75
26 27 3.077705 GCGTGCGCAATAACGAGA 58.922 55.556 20.53 0.00 42.32 4.04
36 37 4.794241 GGTTCATCGTGCGTGCGC 62.794 66.667 9.85 9.85 42.35 6.09
37 38 3.071459 GAGGTTCATCGTGCGTGCG 62.071 63.158 0.00 0.00 0.00 5.34
38 39 2.778679 GAGGTTCATCGTGCGTGC 59.221 61.111 0.00 0.00 0.00 5.34
39 40 3.071459 GCGAGGTTCATCGTGCGTG 62.071 63.158 8.52 0.00 44.53 5.34
40 41 2.809601 GCGAGGTTCATCGTGCGT 60.810 61.111 8.52 0.00 44.53 5.24
41 42 3.554692 GGCGAGGTTCATCGTGCG 61.555 66.667 8.52 0.00 44.53 5.34
42 43 2.434185 TGGCGAGGTTCATCGTGC 60.434 61.111 8.52 0.00 44.53 5.34
43 44 2.456119 GCTGGCGAGGTTCATCGTG 61.456 63.158 8.52 1.76 44.53 4.35
44 45 2.125512 GCTGGCGAGGTTCATCGT 60.126 61.111 8.52 0.00 44.53 3.73
45 46 1.021390 AAAGCTGGCGAGGTTCATCG 61.021 55.000 13.73 2.51 45.48 3.84
46 47 0.449388 CAAAGCTGGCGAGGTTCATC 59.551 55.000 13.73 0.00 39.03 2.92
47 48 1.589716 GCAAAGCTGGCGAGGTTCAT 61.590 55.000 13.73 0.00 39.03 2.57
48 49 2.260869 GCAAAGCTGGCGAGGTTCA 61.261 57.895 13.73 0.00 39.03 3.18
49 50 1.968540 AGCAAAGCTGGCGAGGTTC 60.969 57.895 13.73 2.61 39.03 3.62
50 51 2.113986 AGCAAAGCTGGCGAGGTT 59.886 55.556 7.40 7.40 41.82 3.50
59 60 2.568956 TCTGGATGTAGTCAGCAAAGCT 59.431 45.455 0.00 0.00 40.77 3.74
60 61 2.675348 GTCTGGATGTAGTCAGCAAAGC 59.325 50.000 0.00 0.00 0.00 3.51
61 62 2.926200 CGTCTGGATGTAGTCAGCAAAG 59.074 50.000 0.00 0.00 0.00 2.77
62 63 2.353704 CCGTCTGGATGTAGTCAGCAAA 60.354 50.000 0.00 0.00 37.49 3.68
63 64 1.204704 CCGTCTGGATGTAGTCAGCAA 59.795 52.381 0.00 0.00 37.49 3.91
64 65 0.817654 CCGTCTGGATGTAGTCAGCA 59.182 55.000 0.00 0.00 37.49 4.41
65 66 1.103803 TCCGTCTGGATGTAGTCAGC 58.896 55.000 0.00 0.00 40.17 4.26
71 72 7.882765 TCGAGAGATTGTCCGTCTGGATGTA 62.883 48.000 0.00 0.00 40.65 2.29
73 74 4.792384 TCGAGAGATTGTCCGTCTGGATG 61.792 52.174 0.00 0.00 40.65 3.51
74 75 2.684038 TCGAGAGATTGTCCGTCTGGAT 60.684 50.000 0.00 0.00 40.65 3.41
75 76 1.095600 CGAGAGATTGTCCGTCTGGA 58.904 55.000 0.00 0.00 43.88 3.86
76 77 1.064803 CTCGAGAGATTGTCCGTCTGG 59.935 57.143 6.58 0.00 40.84 3.86
77 78 1.064803 CCTCGAGAGATTGTCCGTCTG 59.935 57.143 15.71 0.00 40.84 3.51
78 79 1.065345 TCCTCGAGAGATTGTCCGTCT 60.065 52.381 15.71 0.00 40.84 4.18
79 80 1.332375 CTCCTCGAGAGATTGTCCGTC 59.668 57.143 15.71 0.00 46.50 4.79
80 81 1.384525 CTCCTCGAGAGATTGTCCGT 58.615 55.000 15.71 0.00 46.50 4.69
81 82 0.665835 CCTCCTCGAGAGATTGTCCG 59.334 60.000 15.71 0.00 46.50 4.79
82 83 2.060050 TCCTCCTCGAGAGATTGTCC 57.940 55.000 15.71 0.00 46.50 4.02
83 84 2.225491 CGATCCTCCTCGAGAGATTGTC 59.775 54.545 15.71 3.98 46.50 3.18
84 85 2.226330 CGATCCTCCTCGAGAGATTGT 58.774 52.381 15.71 0.00 46.50 2.71
85 86 1.539388 CCGATCCTCCTCGAGAGATTG 59.461 57.143 15.71 15.40 46.50 2.67
86 87 1.422024 TCCGATCCTCCTCGAGAGATT 59.578 52.381 15.71 0.72 46.50 2.40
87 88 1.003118 CTCCGATCCTCCTCGAGAGAT 59.997 57.143 15.71 12.83 46.50 2.75
88 89 0.394938 CTCCGATCCTCCTCGAGAGA 59.605 60.000 15.71 8.14 46.50 3.10
89 90 1.234615 GCTCCGATCCTCCTCGAGAG 61.235 65.000 15.71 9.35 41.12 3.20
90 91 1.228003 GCTCCGATCCTCCTCGAGA 60.228 63.158 15.71 0.00 41.12 4.04
91 92 2.612567 CGCTCCGATCCTCCTCGAG 61.613 68.421 5.13 5.13 41.12 4.04
92 93 2.592001 CGCTCCGATCCTCCTCGA 60.592 66.667 0.00 0.00 41.12 4.04
93 94 3.665226 CCGCTCCGATCCTCCTCG 61.665 72.222 0.00 0.00 38.37 4.63
94 95 3.984749 GCCGCTCCGATCCTCCTC 61.985 72.222 0.00 0.00 0.00 3.71
95 96 4.841617 TGCCGCTCCGATCCTCCT 62.842 66.667 0.00 0.00 0.00 3.69
96 97 3.620785 ATGCCGCTCCGATCCTCC 61.621 66.667 0.00 0.00 0.00 4.30
97 98 2.356793 CATGCCGCTCCGATCCTC 60.357 66.667 0.00 0.00 0.00 3.71
98 99 4.615815 GCATGCCGCTCCGATCCT 62.616 66.667 6.36 0.00 37.77 3.24
99 100 2.786539 TATGCATGCCGCTCCGATCC 62.787 60.000 16.68 0.00 43.06 3.36
100 101 1.357258 CTATGCATGCCGCTCCGATC 61.357 60.000 16.68 0.00 43.06 3.69
101 102 1.375140 CTATGCATGCCGCTCCGAT 60.375 57.895 16.68 2.16 43.06 4.18
102 103 2.029518 CTATGCATGCCGCTCCGA 59.970 61.111 16.68 0.00 43.06 4.55
120 121 1.064654 GAGCCTGTGAATTCGCATTCC 59.935 52.381 21.33 12.49 38.50 3.01
122 123 1.825090 TGAGCCTGTGAATTCGCATT 58.175 45.000 21.33 10.68 35.63 3.56
143 144 2.102925 CTCTCTCTTCCAGGCTTCATCC 59.897 54.545 0.00 0.00 0.00 3.51
176 177 3.706373 GTCCCCTTCCGCTCAGCA 61.706 66.667 0.00 0.00 0.00 4.41
177 178 4.821589 CGTCCCCTTCCGCTCAGC 62.822 72.222 0.00 0.00 0.00 4.26
183 184 0.802494 CAACATTTCGTCCCCTTCCG 59.198 55.000 0.00 0.00 0.00 4.30
193 194 1.668628 CGCCCCTTTTCCAACATTTCG 60.669 52.381 0.00 0.00 0.00 3.46
204 205 2.764637 ATTCGTGCCTCGCCCCTTTT 62.765 55.000 0.00 0.00 39.67 2.27
208 209 1.436983 CTTTATTCGTGCCTCGCCCC 61.437 60.000 0.00 0.00 39.67 5.80
210 211 0.743345 ACCTTTATTCGTGCCTCGCC 60.743 55.000 0.00 0.00 39.67 5.54
212 213 1.006832 CCACCTTTATTCGTGCCTCG 58.993 55.000 0.00 0.00 41.41 4.63
240 241 3.718815 GAAGGGAGTATGTTGGATCGAC 58.281 50.000 0.00 0.00 0.00 4.20
243 244 3.821421 ACGAAGGGAGTATGTTGGATC 57.179 47.619 0.00 0.00 0.00 3.36
252 253 6.438425 ACAAGTATTTAGGAACGAAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
253 254 5.247792 ACAAGTATTTAGGAACGAAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
254 255 5.731591 ACAAGTATTTAGGAACGAAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
255 256 5.482878 AGACAAGTATTTAGGAACGAAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
256 257 5.581085 CAGACAAGTATTTAGGAACGAAGGG 59.419 44.000 0.00 0.00 0.00 3.95
257 258 6.164176 ACAGACAAGTATTTAGGAACGAAGG 58.836 40.000 0.00 0.00 0.00 3.46
258 259 7.091443 AGACAGACAAGTATTTAGGAACGAAG 58.909 38.462 0.00 0.00 0.00 3.79
259 260 6.989659 AGACAGACAAGTATTTAGGAACGAA 58.010 36.000 0.00 0.00 0.00 3.85
260 261 6.585695 AGACAGACAAGTATTTAGGAACGA 57.414 37.500 0.00 0.00 0.00 3.85
261 262 7.759465 TCTAGACAGACAAGTATTTAGGAACG 58.241 38.462 0.00 0.00 0.00 3.95
285 286 9.385902 CCGTATGTGATATTCATTTGAAATGTC 57.614 33.333 16.62 8.24 37.61 3.06
286 287 9.119418 TCCGTATGTGATATTCATTTGAAATGT 57.881 29.630 16.62 2.38 37.61 2.71
289 290 9.119418 ACATCCGTATGTGATATTCATTTGAAA 57.881 29.630 0.00 0.00 44.79 2.69
290 291 8.675705 ACATCCGTATGTGATATTCATTTGAA 57.324 30.769 0.00 0.00 44.79 2.69
305 306 7.946655 AAATATGTCTACACACATCCGTATG 57.053 36.000 0.00 0.00 38.07 2.39
306 307 9.692749 CTAAAATATGTCTACACACATCCGTAT 57.307 33.333 0.00 0.00 38.07 3.06
307 308 8.905850 TCTAAAATATGTCTACACACATCCGTA 58.094 33.333 0.00 0.00 38.07 4.02
308 309 7.778083 TCTAAAATATGTCTACACACATCCGT 58.222 34.615 0.00 0.00 38.07 4.69
309 310 7.921214 ACTCTAAAATATGTCTACACACATCCG 59.079 37.037 0.00 0.00 38.07 4.18
332 333 9.400638 CGGAGTAAAATGAGTGAATCTATACTC 57.599 37.037 0.00 0.00 42.77 2.59
333 334 8.915036 ACGGAGTAAAATGAGTGAATCTATACT 58.085 33.333 0.00 0.00 41.94 2.12
351 352 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
352 353 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
353 354 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
354 355 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
355 356 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
356 357 6.534059 CATTTCAACAAGTGACTACATACGG 58.466 40.000 0.00 0.00 35.39 4.02
357 358 6.015504 GCATTTCAACAAGTGACTACATACG 58.984 40.000 0.00 0.00 35.39 3.06
358 359 6.149474 AGGCATTTCAACAAGTGACTACATAC 59.851 38.462 0.00 0.00 35.84 2.39
359 360 6.237901 AGGCATTTCAACAAGTGACTACATA 58.762 36.000 0.00 0.00 35.84 2.29
360 361 5.072741 AGGCATTTCAACAAGTGACTACAT 58.927 37.500 0.00 0.00 35.84 2.29
361 362 4.460263 AGGCATTTCAACAAGTGACTACA 58.540 39.130 0.00 0.00 35.84 2.74
362 363 5.932303 TCTAGGCATTTCAACAAGTGACTAC 59.068 40.000 0.00 0.00 38.51 2.73
363 364 6.109156 TCTAGGCATTTCAACAAGTGACTA 57.891 37.500 0.00 0.00 38.51 2.59
364 365 4.973168 TCTAGGCATTTCAACAAGTGACT 58.027 39.130 0.00 0.00 40.60 3.41
365 366 5.689383 TTCTAGGCATTTCAACAAGTGAC 57.311 39.130 0.00 0.00 35.39 3.67
366 367 6.017109 GTCTTTCTAGGCATTTCAACAAGTGA 60.017 38.462 0.00 0.00 0.00 3.41
367 368 6.145535 GTCTTTCTAGGCATTTCAACAAGTG 58.854 40.000 0.00 0.00 0.00 3.16
368 369 5.827797 TGTCTTTCTAGGCATTTCAACAAGT 59.172 36.000 0.00 0.00 29.10 3.16
369 370 6.317789 TGTCTTTCTAGGCATTTCAACAAG 57.682 37.500 0.00 0.00 29.10 3.16
370 371 6.321181 ACTTGTCTTTCTAGGCATTTCAACAA 59.679 34.615 0.00 0.00 35.56 2.83
371 372 5.827797 ACTTGTCTTTCTAGGCATTTCAACA 59.172 36.000 0.00 0.00 35.56 3.33
372 373 6.319141 ACTTGTCTTTCTAGGCATTTCAAC 57.681 37.500 0.00 0.00 35.56 3.18
373 374 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
374 375 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
376 377 9.178758 CCTAAATACTTGTCTTTCTAGGCATTT 57.821 33.333 0.00 0.00 35.56 2.32
377 378 8.548877 TCCTAAATACTTGTCTTTCTAGGCATT 58.451 33.333 0.00 0.00 35.56 3.56
378 379 8.090788 TCCTAAATACTTGTCTTTCTAGGCAT 57.909 34.615 0.00 0.00 35.56 4.40
379 380 7.490657 TCCTAAATACTTGTCTTTCTAGGCA 57.509 36.000 0.00 0.00 33.22 4.75
380 381 7.010275 CGTTCCTAAATACTTGTCTTTCTAGGC 59.990 40.741 0.00 0.00 0.00 3.93
381 382 7.491696 CCGTTCCTAAATACTTGTCTTTCTAGG 59.508 40.741 0.00 0.00 0.00 3.02
382 383 8.248945 TCCGTTCCTAAATACTTGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
383 384 8.125978 TCCGTTCCTAAATACTTGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
384 385 7.001099 TCCGTTCCTAAATACTTGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
385 386 6.313164 CCTCCGTTCCTAAATACTTGTCTTTC 59.687 42.308 0.00 0.00 0.00 2.62
386 387 6.171213 CCTCCGTTCCTAAATACTTGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
387 388 5.338137 CCCTCCGTTCCTAAATACTTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
388 389 4.161754 CCCTCCGTTCCTAAATACTTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
389 390 4.161001 TCCCTCCGTTCCTAAATACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
390 391 4.098894 TCCCTCCGTTCCTAAATACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
391 392 4.161754 ACTCCCTCCGTTCCTAAATACTTG 59.838 45.833 0.00 0.00 0.00 3.16
392 393 4.359996 ACTCCCTCCGTTCCTAAATACTT 58.640 43.478 0.00 0.00 0.00 2.24
393 394 3.991683 ACTCCCTCCGTTCCTAAATACT 58.008 45.455 0.00 0.00 0.00 2.12
394 395 4.892345 AGTACTCCCTCCGTTCCTAAATAC 59.108 45.833 0.00 0.00 0.00 1.89
395 396 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
396 397 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
397 398 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
398 399 3.094572 CAAGTACTCCCTCCGTTCCTAA 58.905 50.000 0.00 0.00 0.00 2.69
399 400 2.622452 CCAAGTACTCCCTCCGTTCCTA 60.622 54.545 0.00 0.00 0.00 2.94
400 401 1.558233 CAAGTACTCCCTCCGTTCCT 58.442 55.000 0.00 0.00 0.00 3.36
401 402 0.535797 CCAAGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
402 403 1.264295 ACCAAGTACTCCCTCCGTTC 58.736 55.000 0.00 0.00 0.00 3.95
403 404 2.610438 TACCAAGTACTCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
404 405 2.842645 ATACCAAGTACTCCCTCCGT 57.157 50.000 0.00 0.00 0.00 4.69
405 406 6.008960 AGTTATATACCAAGTACTCCCTCCG 58.991 44.000 0.00 0.00 0.00 4.63
406 407 7.852550 AAGTTATATACCAAGTACTCCCTCC 57.147 40.000 0.00 0.00 0.00 4.30
407 408 9.359653 TGTAAGTTATATACCAAGTACTCCCTC 57.640 37.037 0.00 0.00 0.00 4.30
408 409 9.719433 TTGTAAGTTATATACCAAGTACTCCCT 57.281 33.333 0.00 0.00 0.00 4.20
434 435 6.723298 ACTACTTCAGCTAGCTCATGTATT 57.277 37.500 16.15 6.48 0.00 1.89
460 466 4.158394 ACTGGCGTGAATTAGCAAATGAAT 59.842 37.500 3.06 0.00 34.54 2.57
478 484 2.352960 GCACTAGCTCAACATAACTGGC 59.647 50.000 0.00 0.00 37.91 4.85
499 505 3.423154 GAGCGCCCCTCACAAACG 61.423 66.667 2.29 0.00 40.45 3.60
541 547 6.490566 ACACTTTGTAGAAACGAACTTTGT 57.509 33.333 0.00 0.00 0.00 2.83
707 3056 1.407258 TGGTTGTTACAACTGCTTGGC 59.593 47.619 24.67 9.29 0.00 4.52
753 3102 7.607223 GCTAAGCTAAGTACTACTCTATGGCTA 59.393 40.741 0.00 0.00 0.00 3.93
784 3150 6.201806 CGACTTGAAACAGTCAATTCTTCTCT 59.798 38.462 2.00 0.00 45.27 3.10
869 3235 6.017605 CCACATGTGGTCAGCTATCTTAATTC 60.018 42.308 32.94 0.00 45.53 2.17
870 3236 5.824624 CCACATGTGGTCAGCTATCTTAATT 59.175 40.000 32.94 0.00 45.53 1.40
871 3237 5.371526 CCACATGTGGTCAGCTATCTTAAT 58.628 41.667 32.94 0.00 45.53 1.40
872 3238 4.769688 CCACATGTGGTCAGCTATCTTAA 58.230 43.478 32.94 0.00 45.53 1.85
873 3239 4.406648 CCACATGTGGTCAGCTATCTTA 57.593 45.455 32.94 0.00 45.53 2.10
874 3240 3.272574 CCACATGTGGTCAGCTATCTT 57.727 47.619 32.94 0.00 45.53 2.40
875 3241 2.996249 CCACATGTGGTCAGCTATCT 57.004 50.000 32.94 0.00 45.53 1.98
919 3285 1.382522 ATATGCTGTGCAAAGGGACG 58.617 50.000 5.91 0.00 43.62 4.79
941 3307 2.531508 GGGTACGTGCGAACTTTATACG 59.468 50.000 0.00 0.00 40.30 3.06
1034 3511 0.887933 GTGATGCCATTGTTCGGGTT 59.112 50.000 0.00 0.00 0.00 4.11
1039 3516 1.398390 GAGGACGTGATGCCATTGTTC 59.602 52.381 0.00 0.00 0.00 3.18
1050 3527 3.321111 AGAAAAGTGCTAAGAGGACGTGA 59.679 43.478 0.00 0.00 41.78 4.35
1052 3529 3.306156 GGAGAAAAGTGCTAAGAGGACGT 60.306 47.826 0.00 0.00 41.78 4.34
1069 3546 2.761416 GCAGGAGGGATAGGATGGAGAA 60.761 54.545 0.00 0.00 0.00 2.87
1158 3647 4.208403 AGCTGGTGCAGGTTGCCA 62.208 61.111 0.00 0.00 44.23 4.92
1248 3737 3.307906 ACCACTGTCGGCGCCTTA 61.308 61.111 26.68 9.93 0.00 2.69
1260 3749 4.664677 GCGGACGACAGCACCACT 62.665 66.667 5.07 0.00 37.19 4.00
1500 4024 0.899019 TGCACCGTGACTAGGCAATA 59.101 50.000 0.00 0.00 0.00 1.90
1501 4025 0.673644 GTGCACCGTGACTAGGCAAT 60.674 55.000 5.22 0.00 36.08 3.56
1502 4026 1.301401 GTGCACCGTGACTAGGCAA 60.301 57.895 5.22 0.00 36.08 4.52
1522 4046 9.942850 ATGAAGGGAAAAAGGTAATACATTTTG 57.057 29.630 15.15 0.00 40.61 2.44
1531 4055 5.009210 CGTGTCAATGAAGGGAAAAAGGTAA 59.991 40.000 0.00 0.00 0.00 2.85
1553 4078 4.112634 CGTGGTTGTATCATCTTGATCGT 58.887 43.478 0.00 0.00 38.26 3.73
1596 4125 0.390860 AGACTGCTCGTTTGACTGCT 59.609 50.000 0.00 0.00 0.00 4.24
1809 4443 3.490793 ATCGTCGAGCGCATCCTGG 62.491 63.158 11.47 0.00 41.07 4.45
1885 4519 2.746277 GTCAACAAGGCGGCCGAT 60.746 61.111 33.48 14.48 0.00 4.18
1943 4577 6.647067 CGTCTCAAAGAAGGAGTCTAATTGTT 59.353 38.462 0.00 0.00 34.56 2.83
1947 4581 4.773149 ACCGTCTCAAAGAAGGAGTCTAAT 59.227 41.667 14.61 0.00 45.13 1.73
1954 4588 3.323691 TCAATGACCGTCTCAAAGAAGGA 59.676 43.478 14.61 0.00 45.13 3.36
1967 4601 1.399440 CCAAGTGATGCTCAATGACCG 59.601 52.381 0.00 0.00 0.00 4.79
1974 4608 1.951209 TAGGGTCCAAGTGATGCTCA 58.049 50.000 0.00 0.00 0.00 4.26
1984 4618 0.470766 AACACACGCTTAGGGTCCAA 59.529 50.000 0.00 0.00 31.20 3.53
2004 4638 3.390521 TCGCCGCCATTCTCAGGT 61.391 61.111 0.00 0.00 0.00 4.00
2066 4700 4.563993 CGTGGTCCTTGGTGAACCTAAATA 60.564 45.833 0.37 0.00 36.82 1.40
2073 4707 0.179067 TGACGTGGTCCTTGGTGAAC 60.179 55.000 0.00 0.00 0.00 3.18
2745 5407 5.504853 CAAGATAAGCCTTCCTTCTTCCTT 58.495 41.667 0.00 0.00 34.95 3.36
2762 5424 2.024176 GCTCCTTTCGGTGCAAGATA 57.976 50.000 0.00 0.00 46.48 1.98
2843 5505 7.771361 TGTTTCCATCTTTATTAGGTCGCATAA 59.229 33.333 0.00 0.00 0.00 1.90
2880 5542 6.488769 TTACTCCCACTTTTACTGAGACAA 57.511 37.500 0.00 0.00 0.00 3.18
3330 6040 0.617820 GTCCTTCTCCCTAGTGCCCA 60.618 60.000 0.00 0.00 0.00 5.36
3355 6065 7.500892 ACAGAACAATATGTGTGGTTTTGTCTA 59.499 33.333 0.00 0.00 40.60 2.59
3357 6067 6.417635 CACAGAACAATATGTGTGGTTTTGTC 59.582 38.462 0.00 0.00 42.46 3.18
3413 6124 2.479837 CAACGGCTCTGTTGTACTCAA 58.520 47.619 12.21 0.00 43.28 3.02
3655 6370 3.426191 CGACAAATTGCACACAGAATTGG 59.574 43.478 0.00 0.00 0.00 3.16
3676 6391 6.584942 GGGTCTAATTTTCTTTTACCAAAGCG 59.415 38.462 0.00 0.00 39.56 4.68
3748 6463 6.260050 GTGCCATATTTAATTCCAGTTCGAGA 59.740 38.462 0.00 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.