Multiple sequence alignment - TraesCS1B01G310100

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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 TraesCS1B01G310100 chr1B 100.000 4025 0 0 1 4025 532692297 532696321 0.000000e+00 7433.0
1 TraesCS1B01G310100 chr1B 79.742 1397 235 31 1234 2611 353273942 353272575 0.000000e+00 968.0
2 TraesCS1B01G310100 chr1B 88.211 246 16 4 438 670 532663397 532663642 8.520000e-72 281.0
3 TraesCS1B01G310100 chr1B 93.750 176 8 2 304 479 532662444 532662616 1.110000e-65 261.0
4 TraesCS1B01G310100 chr1D 92.128 3633 186 45 431 4011 397284496 397288080 0.000000e+00 5033.0
5 TraesCS1B01G310100 chr1D 78.322 143 25 5 164 302 122900578 122900438 1.990000e-13 87.9
6 TraesCS1B01G310100 chr1D 86.538 52 5 2 216 265 130615104 130615053 5.620000e-04 56.5
7 TraesCS1B01G310100 chr1A 89.822 3262 177 62 838 4021 494799386 494802570 0.000000e+00 4041.0
8 TraesCS1B01G310100 chr1A 90.541 148 14 0 304 451 494798959 494799106 3.170000e-46 196.0
9 TraesCS1B01G310100 chr2D 95.278 1207 56 1 1096 2302 432871710 432870505 0.000000e+00 1912.0
10 TraesCS1B01G310100 chr2D 95.122 82 2 1 2365 2444 432870494 432870413 1.170000e-25 128.0
11 TraesCS1B01G310100 chr3D 82.374 1912 312 19 1062 2959 452619466 452617566 0.000000e+00 1640.0
12 TraesCS1B01G310100 chr3D 93.750 48 3 0 1101 1148 558745258 558745211 5.580000e-09 73.1
13 TraesCS1B01G310100 chr3A 82.402 1915 304 24 1062 2958 595061499 595059600 0.000000e+00 1639.0
14 TraesCS1B01G310100 chr3B 81.462 1915 324 25 1062 2959 594745328 594743428 0.000000e+00 1541.0
15 TraesCS1B01G310100 chr5B 79.885 1397 233 31 1234 2611 411026771 411025404 0.000000e+00 979.0
16 TraesCS1B01G310100 chr7A 79.786 1400 235 32 1231 2611 608482232 608483602 0.000000e+00 974.0
17 TraesCS1B01G310100 chr7A 100.000 30 0 0 218 247 255583576 255583547 5.620000e-04 56.5
18 TraesCS1B01G310100 chr7D 83.710 442 68 4 2298 2737 236582801 236582362 8.050000e-112 414.0
19 TraesCS1B01G310100 chr6B 79.394 330 30 12 3 301 504566007 504566329 8.820000e-47 198.0
20 TraesCS1B01G310100 chr5A 80.347 173 23 8 136 302 638760331 638760498 1.960000e-23 121.0
21 TraesCS1B01G310100 chr6D 79.747 158 22 9 153 301 357774824 357774980 5.500000e-19 106.0
22 TraesCS1B01G310100 chr5D 86.813 91 11 1 174 264 424134147 424134058 2.560000e-17 100.0
23 TraesCS1B01G310100 chr4A 78.912 147 23 7 120 264 546552216 546552356 4.280000e-15 93.5
24 TraesCS1B01G310100 chr2B 93.750 48 3 0 1101 1148 68608918 68608871 5.580000e-09 73.1
25 TraesCS1B01G310100 chr2A 93.750 48 3 0 1101 1148 683562725 683562678 5.580000e-09 73.1


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 TraesCS1B01G310100 chr1B 532692297 532696321 4024 False 7433.0 7433 100.0000 1 4025 1 chr1B.!!$F1 4024
1 TraesCS1B01G310100 chr1B 353272575 353273942 1367 True 968.0 968 79.7420 1234 2611 1 chr1B.!!$R1 1377
2 TraesCS1B01G310100 chr1B 532662444 532663642 1198 False 271.0 281 90.9805 304 670 2 chr1B.!!$F2 366
3 TraesCS1B01G310100 chr1D 397284496 397288080 3584 False 5033.0 5033 92.1280 431 4011 1 chr1D.!!$F1 3580
4 TraesCS1B01G310100 chr1A 494798959 494802570 3611 False 2118.5 4041 90.1815 304 4021 2 chr1A.!!$F1 3717
5 TraesCS1B01G310100 chr2D 432870413 432871710 1297 True 1020.0 1912 95.2000 1096 2444 2 chr2D.!!$R1 1348
6 TraesCS1B01G310100 chr3D 452617566 452619466 1900 True 1640.0 1640 82.3740 1062 2959 1 chr3D.!!$R1 1897
7 TraesCS1B01G310100 chr3A 595059600 595061499 1899 True 1639.0 1639 82.4020 1062 2958 1 chr3A.!!$R1 1896
8 TraesCS1B01G310100 chr3B 594743428 594745328 1900 True 1541.0 1541 81.4620 1062 2959 1 chr3B.!!$R1 1897
9 TraesCS1B01G310100 chr5B 411025404 411026771 1367 True 979.0 979 79.8850 1234 2611 1 chr5B.!!$R1 1377
10 TraesCS1B01G310100 chr7A 608482232 608483602 1370 False 974.0 974 79.7860 1231 2611 1 chr7A.!!$F1 1380

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
958 1825 0.108804 TTCAACTCGACTCCATCCGC 60.109 55.000 0.0 0.0 0.00 5.54 F
979 1848 0.250684 TCCAAAGCCTTCACGCATCA 60.251 50.000 0.0 0.0 0.00 3.07 F
982 1854 0.607489 AAAGCCTTCACGCATCAGCT 60.607 50.000 0.0 0.0 39.10 4.24 F
1044 1922 1.226435 CGAGCCGTCCTCTTCTTCG 60.226 63.158 0.0 0.0 38.49 3.79 F
2274 3171 1.301244 CGTGCCACTGCTCAACTCT 60.301 57.895 0.0 0.0 38.71 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3393 0.171455 GCACGACCTTCTCGATCACT 59.829 55.000 0.00 0.00 46.14 3.41 R
2640 3537 2.364186 TCCTCCTCGCTGATGGCA 60.364 61.111 0.00 0.00 41.91 4.92 R
2979 3876 2.204090 ACGGTGGAGGTGGGGAAT 60.204 61.111 0.00 0.00 0.00 3.01 R
3015 3912 2.535574 TCGAAGAATGATTCACGATGCG 59.464 45.455 18.03 5.15 36.45 4.73 R
3770 4735 0.173708 CTCGACCAGGAGTACTTGGC 59.826 60.000 12.69 5.92 45.50 4.52 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
17 18 4.796231 GAAGGCGCGCGAGGAAGA 62.796 66.667 37.18 0.00 0.00 2.87
18 19 4.803426 AAGGCGCGCGAGGAAGAG 62.803 66.667 37.18 1.14 0.00 2.85
22 23 4.421479 CGCGCGAGGAAGAGTGGT 62.421 66.667 28.94 0.00 0.00 4.16
23 24 2.811317 GCGCGAGGAAGAGTGGTG 60.811 66.667 12.10 0.00 0.00 4.17
24 25 2.125912 CGCGAGGAAGAGTGGTGG 60.126 66.667 0.00 0.00 0.00 4.61
25 26 2.435059 GCGAGGAAGAGTGGTGGC 60.435 66.667 0.00 0.00 0.00 5.01
26 27 2.125912 CGAGGAAGAGTGGTGGCG 60.126 66.667 0.00 0.00 0.00 5.69
27 28 2.435059 GAGGAAGAGTGGTGGCGC 60.435 66.667 0.00 0.00 0.00 6.53
28 29 2.925170 AGGAAGAGTGGTGGCGCT 60.925 61.111 7.64 0.00 0.00 5.92
29 30 2.435059 GGAAGAGTGGTGGCGCTC 60.435 66.667 7.64 0.23 0.00 5.03
30 31 2.811317 GAAGAGTGGTGGCGCTCG 60.811 66.667 7.64 0.00 36.88 5.03
31 32 3.575351 GAAGAGTGGTGGCGCTCGT 62.575 63.158 7.64 0.00 36.88 4.18
32 33 3.865929 AAGAGTGGTGGCGCTCGTG 62.866 63.158 7.64 0.00 36.88 4.35
33 34 4.357947 GAGTGGTGGCGCTCGTGA 62.358 66.667 7.64 0.00 0.00 4.35
34 35 4.664677 AGTGGTGGCGCTCGTGAC 62.665 66.667 7.64 0.00 0.00 3.67
43 44 3.749064 GCTCGTGACGGCTGAGGA 61.749 66.667 4.70 0.00 0.00 3.71
44 45 3.069980 GCTCGTGACGGCTGAGGAT 62.070 63.158 4.70 0.00 0.00 3.24
45 46 1.226802 CTCGTGACGGCTGAGGATG 60.227 63.158 4.70 0.00 0.00 3.51
46 47 2.202797 CGTGACGGCTGAGGATGG 60.203 66.667 0.00 0.00 0.00 3.51
47 48 2.982130 GTGACGGCTGAGGATGGT 59.018 61.111 0.00 0.00 0.00 3.55
48 49 1.153549 GTGACGGCTGAGGATGGTC 60.154 63.158 0.00 0.00 0.00 4.02
49 50 2.105128 GACGGCTGAGGATGGTCG 59.895 66.667 0.00 0.00 36.57 4.79
50 51 3.432051 GACGGCTGAGGATGGTCGG 62.432 68.421 0.00 0.00 34.68 4.79
51 52 4.227134 CGGCTGAGGATGGTCGGG 62.227 72.222 0.00 0.00 0.00 5.14
52 53 3.866582 GGCTGAGGATGGTCGGGG 61.867 72.222 0.00 0.00 0.00 5.73
53 54 3.866582 GCTGAGGATGGTCGGGGG 61.867 72.222 0.00 0.00 0.00 5.40
54 55 2.041922 CTGAGGATGGTCGGGGGA 60.042 66.667 0.00 0.00 0.00 4.81
55 56 2.041922 TGAGGATGGTCGGGGGAG 60.042 66.667 0.00 0.00 0.00 4.30
56 57 2.844839 GAGGATGGTCGGGGGAGG 60.845 72.222 0.00 0.00 0.00 4.30
57 58 4.499116 AGGATGGTCGGGGGAGGG 62.499 72.222 0.00 0.00 0.00 4.30
77 78 4.778143 GTTGCTGGCCGGATCCGT 62.778 66.667 31.22 0.00 37.81 4.69
78 79 4.776322 TTGCTGGCCGGATCCGTG 62.776 66.667 31.22 22.89 37.81 4.94
83 84 4.467084 GGCCGGATCCGTGCAGAA 62.467 66.667 33.72 0.00 37.36 3.02
84 85 2.892425 GCCGGATCCGTGCAGAAG 60.892 66.667 30.59 17.93 36.29 2.85
85 86 2.202932 CCGGATCCGTGCAGAAGG 60.203 66.667 31.22 10.74 37.81 3.46
86 87 2.892425 CGGATCCGTGCAGAAGGC 60.892 66.667 26.35 0.00 45.13 4.35
87 88 2.514824 GGATCCGTGCAGAAGGCC 60.515 66.667 0.00 0.00 43.89 5.19
88 89 2.892425 GATCCGTGCAGAAGGCCG 60.892 66.667 0.00 0.00 43.89 6.13
108 109 3.551407 GGGAGGACCGGATCTGGC 61.551 72.222 21.17 12.92 36.97 4.85
109 110 3.917760 GGAGGACCGGATCTGGCG 61.918 72.222 21.17 1.27 0.00 5.69
110 111 4.593864 GAGGACCGGATCTGGCGC 62.594 72.222 21.17 12.66 0.00 6.53
112 113 4.899239 GGACCGGATCTGGCGCTG 62.899 72.222 21.17 0.11 0.00 5.18
113 114 4.148825 GACCGGATCTGGCGCTGT 62.149 66.667 21.17 0.00 0.00 4.40
114 115 4.148825 ACCGGATCTGGCGCTGTC 62.149 66.667 21.17 0.02 0.00 3.51
117 118 3.838271 GGATCTGGCGCTGTCGGA 61.838 66.667 7.64 0.88 35.95 4.55
118 119 2.583593 GATCTGGCGCTGTCGGAC 60.584 66.667 7.64 0.00 35.95 4.79
119 120 4.148825 ATCTGGCGCTGTCGGACC 62.149 66.667 7.64 0.00 35.95 4.46
127 128 4.087892 CTGTCGGACCAGCAGGGG 62.088 72.222 5.55 0.00 42.91 4.79
128 129 4.954118 TGTCGGACCAGCAGGGGT 62.954 66.667 5.55 0.00 46.02 4.95
129 130 2.682494 GTCGGACCAGCAGGGGTA 60.682 66.667 0.00 0.00 42.53 3.69
130 131 2.363795 TCGGACCAGCAGGGGTAG 60.364 66.667 0.00 0.00 42.53 3.18
131 132 4.162690 CGGACCAGCAGGGGTAGC 62.163 72.222 0.00 0.00 42.53 3.58
132 133 3.798511 GGACCAGCAGGGGTAGCC 61.799 72.222 1.07 1.07 42.53 3.93
133 134 3.009115 GACCAGCAGGGGTAGCCA 61.009 66.667 14.06 0.00 42.53 4.75
134 135 2.286425 ACCAGCAGGGGTAGCCAT 60.286 61.111 14.06 1.68 40.07 4.40
135 136 2.194056 CCAGCAGGGGTAGCCATG 59.806 66.667 20.88 20.88 0.00 3.66
136 137 2.194056 CAGCAGGGGTAGCCATGG 59.806 66.667 25.47 7.63 0.00 3.66
137 138 2.286425 AGCAGGGGTAGCCATGGT 60.286 61.111 23.34 23.34 0.00 3.55
138 139 2.124151 GCAGGGGTAGCCATGGTG 60.124 66.667 25.47 11.74 0.00 4.17
139 140 2.597340 CAGGGGTAGCCATGGTGG 59.403 66.667 17.69 0.00 41.55 4.61
140 141 2.696125 AGGGGTAGCCATGGTGGG 60.696 66.667 14.67 0.00 38.19 4.61
141 142 3.820843 GGGGTAGCCATGGTGGGG 61.821 72.222 14.67 0.00 38.19 4.96
142 143 3.820843 GGGTAGCCATGGTGGGGG 61.821 72.222 14.67 0.00 38.19 5.40
143 144 3.021263 GGTAGCCATGGTGGGGGT 61.021 66.667 14.67 0.00 38.19 4.95
144 145 2.275418 GTAGCCATGGTGGGGGTG 59.725 66.667 14.67 0.00 38.19 4.61
145 146 3.020647 TAGCCATGGTGGGGGTGG 61.021 66.667 14.67 0.00 38.19 4.61
169 170 4.120755 GCTGGGGGCTTGAGGAGG 62.121 72.222 0.00 0.00 38.06 4.30
176 177 4.874528 GCTTGAGGAGGCAGATCC 57.125 61.111 0.00 0.00 39.89 3.36
177 178 1.227497 GCTTGAGGAGGCAGATCCG 60.227 63.158 0.00 0.00 44.65 4.18
178 179 1.227497 CTTGAGGAGGCAGATCCGC 60.227 63.158 0.00 0.00 44.65 5.54
195 196 4.047125 CCCCGCCACCACCTTCAT 62.047 66.667 0.00 0.00 0.00 2.57
196 197 2.751436 CCCGCCACCACCTTCATG 60.751 66.667 0.00 0.00 0.00 3.07
197 198 2.751436 CCGCCACCACCTTCATGG 60.751 66.667 0.00 0.00 46.10 3.66
198 199 2.751436 CGCCACCACCTTCATGGG 60.751 66.667 0.00 0.00 44.81 4.00
199 200 2.362889 GCCACCACCTTCATGGGG 60.363 66.667 0.00 0.00 44.81 4.96
200 201 2.362889 CCACCACCTTCATGGGGC 60.363 66.667 5.71 0.00 42.40 5.80
201 202 2.362889 CACCACCTTCATGGGGCC 60.363 66.667 0.00 0.00 44.81 5.80
202 203 3.672503 ACCACCTTCATGGGGCCC 61.673 66.667 18.17 18.17 44.81 5.80
203 204 4.820744 CCACCTTCATGGGGCCCG 62.821 72.222 19.83 4.26 38.11 6.13
271 272 3.483869 GGTGGAGGGGCCTGCTAG 61.484 72.222 0.84 0.00 37.63 3.42
272 273 2.689034 GTGGAGGGGCCTGCTAGT 60.689 66.667 0.84 0.00 37.63 2.57
273 274 2.688666 TGGAGGGGCCTGCTAGTG 60.689 66.667 0.84 0.00 37.63 2.74
274 275 3.483869 GGAGGGGCCTGCTAGTGG 61.484 72.222 0.84 0.00 0.00 4.00
275 276 2.689034 GAGGGGCCTGCTAGTGGT 60.689 66.667 0.84 0.00 0.00 4.16
276 277 3.011517 AGGGGCCTGCTAGTGGTG 61.012 66.667 0.84 0.00 0.00 4.17
277 278 4.115199 GGGGCCTGCTAGTGGTGG 62.115 72.222 0.84 0.00 0.00 4.61
278 279 4.803908 GGGCCTGCTAGTGGTGGC 62.804 72.222 0.84 8.29 44.22 5.01
349 350 3.256631 TCTCTGCTTCCAAAATCCAAAGC 59.743 43.478 0.00 0.00 43.41 3.51
359 360 5.721000 TCCAAAATCCAAAGCTGATATGGTT 59.279 36.000 12.94 3.06 33.91 3.67
408 409 4.213482 TGATATAGTCGTGACACCGATGAG 59.787 45.833 0.00 0.00 39.34 2.90
414 415 2.427095 TCGTGACACCGATGAGATGAAT 59.573 45.455 0.00 0.00 30.63 2.57
415 416 2.537214 CGTGACACCGATGAGATGAATG 59.463 50.000 0.00 0.00 0.00 2.67
416 417 3.734902 CGTGACACCGATGAGATGAATGA 60.735 47.826 0.00 0.00 0.00 2.57
417 418 3.801050 GTGACACCGATGAGATGAATGAG 59.199 47.826 0.00 0.00 0.00 2.90
536 1362 1.065273 CGCATTGATCAGGCAAGCC 59.935 57.895 18.05 2.02 0.00 4.35
643 1490 2.441532 ATCCCGACCGTCCATCGT 60.442 61.111 0.00 0.00 37.90 3.73
660 1507 1.689582 GTCCCCGATCCAACCCTCT 60.690 63.158 0.00 0.00 0.00 3.69
671 1518 3.104512 TCCAACCCTCTACATACCACTG 58.895 50.000 0.00 0.00 0.00 3.66
674 1521 3.468071 ACCCTCTACATACCACTGACA 57.532 47.619 0.00 0.00 0.00 3.58
675 1522 3.995636 ACCCTCTACATACCACTGACAT 58.004 45.455 0.00 0.00 0.00 3.06
676 1523 3.961408 ACCCTCTACATACCACTGACATC 59.039 47.826 0.00 0.00 0.00 3.06
697 1552 1.154035 CCTTCAAACAATCGCGCCC 60.154 57.895 0.00 0.00 0.00 6.13
717 1572 7.381139 CGCGCCCATAAAATAAGTGAAAATAAT 59.619 33.333 0.00 0.00 0.00 1.28
732 1587 9.490379 AGTGAAAATAATACCGCTAAGATAAGG 57.510 33.333 0.00 0.00 0.00 2.69
742 1597 6.852664 ACCGCTAAGATAAGGAAAAACAATG 58.147 36.000 0.00 0.00 0.00 2.82
773 1628 1.751351 CTGAGATGAGACGGGCAGTAA 59.249 52.381 0.00 0.00 0.00 2.24
880 1737 3.879295 GCTCGTATATATACCTACGCCCA 59.121 47.826 15.70 0.00 40.30 5.36
943 1810 3.068448 CCATCGGCATCCAATTCATTCAA 59.932 43.478 0.00 0.00 0.00 2.69
944 1811 3.781079 TCGGCATCCAATTCATTCAAC 57.219 42.857 0.00 0.00 0.00 3.18
945 1812 3.355378 TCGGCATCCAATTCATTCAACT 58.645 40.909 0.00 0.00 0.00 3.16
946 1813 3.378112 TCGGCATCCAATTCATTCAACTC 59.622 43.478 0.00 0.00 0.00 3.01
947 1814 3.699067 GGCATCCAATTCATTCAACTCG 58.301 45.455 0.00 0.00 0.00 4.18
948 1815 3.378112 GGCATCCAATTCATTCAACTCGA 59.622 43.478 0.00 0.00 0.00 4.04
950 1817 4.095483 GCATCCAATTCATTCAACTCGACT 59.905 41.667 0.00 0.00 0.00 4.18
951 1818 5.728898 GCATCCAATTCATTCAACTCGACTC 60.729 44.000 0.00 0.00 0.00 3.36
953 1820 4.002982 CCAATTCATTCAACTCGACTCCA 58.997 43.478 0.00 0.00 0.00 3.86
954 1821 4.637534 CCAATTCATTCAACTCGACTCCAT 59.362 41.667 0.00 0.00 0.00 3.41
955 1822 5.220739 CCAATTCATTCAACTCGACTCCATC 60.221 44.000 0.00 0.00 0.00 3.51
956 1823 3.526931 TCATTCAACTCGACTCCATCC 57.473 47.619 0.00 0.00 0.00 3.51
957 1824 2.159240 TCATTCAACTCGACTCCATCCG 60.159 50.000 0.00 0.00 0.00 4.18
958 1825 0.108804 TTCAACTCGACTCCATCCGC 60.109 55.000 0.00 0.00 0.00 5.54
959 1826 1.874019 CAACTCGACTCCATCCGCG 60.874 63.158 0.00 0.00 0.00 6.46
979 1848 0.250684 TCCAAAGCCTTCACGCATCA 60.251 50.000 0.00 0.00 0.00 3.07
982 1854 0.607489 AAAGCCTTCACGCATCAGCT 60.607 50.000 0.00 0.00 39.10 4.24
1040 1918 4.516195 GCCCGAGCCGTCCTCTTC 62.516 72.222 0.00 0.00 38.49 2.87
1041 1919 2.756283 CCCGAGCCGTCCTCTTCT 60.756 66.667 0.00 0.00 38.49 2.85
1044 1922 1.226435 CGAGCCGTCCTCTTCTTCG 60.226 63.158 0.00 0.00 38.49 3.79
1053 1931 1.595993 CCTCTTCTTCGTCCTCGCCA 61.596 60.000 0.00 0.00 36.96 5.69
1425 2309 1.415672 TTCTCCCGGTTGGTGAGCTT 61.416 55.000 0.00 0.00 37.88 3.74
1467 2351 4.200283 CTCCTCACGCTCGCCTCC 62.200 72.222 0.00 0.00 0.00 4.30
1692 2576 2.182030 GAGAGGTGGACTTCGGCG 59.818 66.667 0.00 0.00 0.00 6.46
1806 2695 2.543802 CGATGACGCCGAGCCTCTA 61.544 63.158 0.00 0.00 0.00 2.43
1896 2785 2.174107 CAGACGTACGACCGCGAA 59.826 61.111 24.41 0.00 41.64 4.70
1917 2806 1.738830 CATTACGCGGTGGTTCGGT 60.739 57.895 12.47 0.00 0.00 4.69
1944 2841 3.228017 TCGACGTGCCCCAAGACA 61.228 61.111 0.00 0.00 0.00 3.41
1956 2853 1.673665 CAAGACAGGCCAGGTGCTC 60.674 63.158 5.01 0.00 40.92 4.26
2127 3024 1.897398 GCATGACCGCGTCGTTTCTT 61.897 55.000 4.92 0.00 34.95 2.52
2158 3055 2.441532 CGGCCTCGTTCTCCCCTA 60.442 66.667 0.00 0.00 0.00 3.53
2274 3171 1.301244 CGTGCCACTGCTCAACTCT 60.301 57.895 0.00 0.00 38.71 3.24
2475 3372 2.800736 GTCCATACGTACCGCCGT 59.199 61.111 0.00 0.00 44.50 5.68
2478 3375 2.404789 CATACGTACCGCCGTCGT 59.595 61.111 0.00 4.89 42.00 4.34
2496 3393 3.072468 CTCGGCCGGAACCCACTA 61.072 66.667 27.83 0.26 0.00 2.74
2562 3459 4.008933 AAGAAGGACGCGCTGGCT 62.009 61.111 5.73 0.00 36.88 4.75
2611 3508 3.414136 AACGTGGGCAAGCTGGTGA 62.414 57.895 0.00 0.00 0.00 4.02
3026 3923 3.195002 CGTGGCCGCATCGTGAAT 61.195 61.111 18.18 0.00 0.00 2.57
3027 3924 2.709475 GTGGCCGCATCGTGAATC 59.291 61.111 12.58 0.00 0.00 2.52
3028 3925 2.106074 GTGGCCGCATCGTGAATCA 61.106 57.895 12.58 0.00 0.00 2.57
3035 3936 2.347939 CCGCATCGTGAATCATTCTTCG 60.348 50.000 0.00 4.32 0.00 3.79
3036 3937 2.535574 CGCATCGTGAATCATTCTTCGA 59.464 45.455 16.22 16.22 39.40 3.71
3042 3943 5.351458 TCGTGAATCATTCTTCGATGACAT 58.649 37.500 11.99 0.00 38.75 3.06
3043 3944 5.812127 TCGTGAATCATTCTTCGATGACATT 59.188 36.000 11.99 0.55 38.75 2.71
3161 4064 7.052873 TCTAGGCTGTAGTACGATTCTTTAGT 58.947 38.462 0.00 0.00 0.00 2.24
3165 4068 5.735638 GCTGTAGTACGATTCTTTAGTCCCC 60.736 48.000 0.00 0.00 0.00 4.81
3251 4161 3.432592 TCGTTCTTCGTTGTTGTTGTGAA 59.567 39.130 0.00 0.00 40.80 3.18
3260 4170 6.252281 TCGTTGTTGTTGTGAAATCTTGTAC 58.748 36.000 0.00 0.00 0.00 2.90
3261 4171 5.168856 CGTTGTTGTTGTGAAATCTTGTACG 59.831 40.000 0.00 0.00 0.00 3.67
3262 4172 5.804692 TGTTGTTGTGAAATCTTGTACGT 57.195 34.783 0.00 0.00 0.00 3.57
3263 4173 6.905544 TGTTGTTGTGAAATCTTGTACGTA 57.094 33.333 0.00 0.00 0.00 3.57
3264 4174 7.304919 TGTTGTTGTGAAATCTTGTACGTAA 57.695 32.000 0.00 0.00 0.00 3.18
3265 4175 7.921787 TGTTGTTGTGAAATCTTGTACGTAAT 58.078 30.769 0.00 0.00 0.00 1.89
3311 4224 7.141363 AGTTGTACAAATTGTGCTCATTCTTC 58.859 34.615 10.51 0.00 33.97 2.87
3312 4225 6.882610 TGTACAAATTGTGCTCATTCTTCT 57.117 33.333 14.77 0.00 33.97 2.85
3313 4226 7.977789 TGTACAAATTGTGCTCATTCTTCTA 57.022 32.000 14.77 0.00 33.97 2.10
3314 4227 8.032952 TGTACAAATTGTGCTCATTCTTCTAG 57.967 34.615 14.77 0.00 33.97 2.43
3315 4228 7.661437 TGTACAAATTGTGCTCATTCTTCTAGT 59.339 33.333 14.77 0.00 33.97 2.57
3318 4231 8.416329 ACAAATTGTGCTCATTCTTCTAGTTTT 58.584 29.630 0.00 0.00 0.00 2.43
3323 4236 6.425114 TGTGCTCATTCTTCTAGTTTTCTCAC 59.575 38.462 0.00 0.00 0.00 3.51
3649 4606 7.728532 TCCACTGCTAATCTAACCTACATGATA 59.271 37.037 0.00 0.00 0.00 2.15
3651 4608 7.815068 CACTGCTAATCTAACCTACATGATACC 59.185 40.741 0.00 0.00 0.00 2.73
3652 4609 7.038941 ACTGCTAATCTAACCTACATGATACCC 60.039 40.741 0.00 0.00 0.00 3.69
3663 4620 6.070656 CCTACATGATACCCCATTGACAATT 58.929 40.000 0.00 0.00 0.00 2.32
3664 4621 6.550854 CCTACATGATACCCCATTGACAATTT 59.449 38.462 0.00 0.00 0.00 1.82
3668 4625 4.402155 TGATACCCCATTGACAATTTGCTC 59.598 41.667 0.00 0.00 0.00 4.26
3684 4641 1.416401 TGCTCGGTTCCTTTCTTGTCT 59.584 47.619 0.00 0.00 0.00 3.41
3714 4671 2.172483 GATGCACTCCAGGGTGTCGT 62.172 60.000 0.00 0.00 39.21 4.34
3715 4672 2.048127 GCACTCCAGGGTGTCGTC 60.048 66.667 0.00 0.00 39.21 4.20
3765 4730 0.620556 ACCATTGATCTGCCGTTCCT 59.379 50.000 0.00 0.00 0.00 3.36
3766 4731 1.004745 ACCATTGATCTGCCGTTCCTT 59.995 47.619 0.00 0.00 0.00 3.36
3767 4732 2.094675 CCATTGATCTGCCGTTCCTTT 58.905 47.619 0.00 0.00 0.00 3.11
3768 4733 3.278574 CCATTGATCTGCCGTTCCTTTA 58.721 45.455 0.00 0.00 0.00 1.85
3769 4734 3.694072 CCATTGATCTGCCGTTCCTTTAA 59.306 43.478 0.00 0.00 0.00 1.52
3770 4735 4.201950 CCATTGATCTGCCGTTCCTTTAAG 60.202 45.833 0.00 0.00 0.00 1.85
3771 4736 2.356135 TGATCTGCCGTTCCTTTAAGC 58.644 47.619 0.00 0.00 0.00 3.09
3772 4737 1.671328 GATCTGCCGTTCCTTTAAGCC 59.329 52.381 0.00 0.00 0.00 4.35
3847 4812 2.811873 GCGGTGCCTATCATCTTTCCAT 60.812 50.000 0.00 0.00 0.00 3.41
3848 4813 3.070018 CGGTGCCTATCATCTTTCCATC 58.930 50.000 0.00 0.00 0.00 3.51
3849 4814 3.416156 GGTGCCTATCATCTTTCCATCC 58.584 50.000 0.00 0.00 0.00 3.51
3850 4815 3.416156 GTGCCTATCATCTTTCCATCCC 58.584 50.000 0.00 0.00 0.00 3.85
3851 4816 3.055328 TGCCTATCATCTTTCCATCCCA 58.945 45.455 0.00 0.00 0.00 4.37
3852 4817 3.462954 TGCCTATCATCTTTCCATCCCAA 59.537 43.478 0.00 0.00 0.00 4.12
3853 4818 3.823304 GCCTATCATCTTTCCATCCCAAC 59.177 47.826 0.00 0.00 0.00 3.77
3854 4819 4.401925 CCTATCATCTTTCCATCCCAACC 58.598 47.826 0.00 0.00 0.00 3.77
3855 4820 2.826674 TCATCTTTCCATCCCAACCC 57.173 50.000 0.00 0.00 0.00 4.11
3856 4821 1.064758 TCATCTTTCCATCCCAACCCG 60.065 52.381 0.00 0.00 0.00 5.28
3857 4822 0.999712 ATCTTTCCATCCCAACCCGT 59.000 50.000 0.00 0.00 0.00 5.28
3858 4823 0.037590 TCTTTCCATCCCAACCCGTG 59.962 55.000 0.00 0.00 0.00 4.94
3859 4824 1.595093 CTTTCCATCCCAACCCGTGC 61.595 60.000 0.00 0.00 0.00 5.34
3860 4825 3.910914 TTCCATCCCAACCCGTGCG 62.911 63.158 0.00 0.00 0.00 5.34
3899 4882 4.254709 AGCCTCACGTTGCTGCCA 62.255 61.111 3.38 0.00 36.23 4.92
3902 4885 2.610694 CCTCACGTTGCTGCCACTG 61.611 63.158 2.24 0.63 0.00 3.66
4011 5001 4.864247 GCGTGAAATTAAAATGTGCCTGAT 59.136 37.500 0.00 0.00 0.00 2.90
4014 5004 6.197096 CGTGAAATTAAAATGTGCCTGATAGC 59.803 38.462 0.00 0.00 0.00 2.97
4023 5013 8.696043 AAAATGTGCCTGATAGCATTATAAGA 57.304 30.769 0.00 0.00 46.24 2.10
4024 5014 8.874744 AAATGTGCCTGATAGCATTATAAGAT 57.125 30.769 0.00 0.00 46.24 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.803426 CTCTTCCTCGCGCGCCTT 62.803 66.667 27.95 0.00 0.00 4.35
5 6 4.421479 ACCACTCTTCCTCGCGCG 62.421 66.667 26.76 26.76 0.00 6.86
6 7 2.811317 CACCACTCTTCCTCGCGC 60.811 66.667 0.00 0.00 0.00 6.86
7 8 2.125912 CCACCACTCTTCCTCGCG 60.126 66.667 0.00 0.00 0.00 5.87
8 9 2.435059 GCCACCACTCTTCCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
9 10 2.125912 CGCCACCACTCTTCCTCG 60.126 66.667 0.00 0.00 0.00 4.63
10 11 2.435059 GCGCCACCACTCTTCCTC 60.435 66.667 0.00 0.00 0.00 3.71
11 12 2.925170 AGCGCCACCACTCTTCCT 60.925 61.111 2.29 0.00 0.00 3.36
12 13 2.435059 GAGCGCCACCACTCTTCC 60.435 66.667 2.29 0.00 0.00 3.46
13 14 2.811317 CGAGCGCCACCACTCTTC 60.811 66.667 2.29 0.00 0.00 2.87
14 15 3.616721 ACGAGCGCCACCACTCTT 61.617 61.111 2.29 0.00 0.00 2.85
15 16 4.363990 CACGAGCGCCACCACTCT 62.364 66.667 2.29 0.00 0.00 3.24
16 17 4.357947 TCACGAGCGCCACCACTC 62.358 66.667 2.29 0.00 0.00 3.51
17 18 4.664677 GTCACGAGCGCCACCACT 62.665 66.667 2.29 0.00 0.00 4.00
26 27 3.069980 ATCCTCAGCCGTCACGAGC 62.070 63.158 0.00 0.00 0.00 5.03
27 28 1.226802 CATCCTCAGCCGTCACGAG 60.227 63.158 0.00 0.00 0.00 4.18
28 29 2.710902 CCATCCTCAGCCGTCACGA 61.711 63.158 0.00 0.00 0.00 4.35
29 30 2.202797 CCATCCTCAGCCGTCACG 60.203 66.667 0.00 0.00 0.00 4.35
30 31 1.153549 GACCATCCTCAGCCGTCAC 60.154 63.158 0.00 0.00 0.00 3.67
31 32 2.710902 CGACCATCCTCAGCCGTCA 61.711 63.158 0.00 0.00 0.00 4.35
32 33 2.105128 CGACCATCCTCAGCCGTC 59.895 66.667 0.00 0.00 0.00 4.79
33 34 3.461773 CCGACCATCCTCAGCCGT 61.462 66.667 0.00 0.00 0.00 5.68
34 35 4.227134 CCCGACCATCCTCAGCCG 62.227 72.222 0.00 0.00 0.00 5.52
35 36 3.866582 CCCCGACCATCCTCAGCC 61.867 72.222 0.00 0.00 0.00 4.85
36 37 3.866582 CCCCCGACCATCCTCAGC 61.867 72.222 0.00 0.00 0.00 4.26
37 38 2.041922 TCCCCCGACCATCCTCAG 60.042 66.667 0.00 0.00 0.00 3.35
38 39 2.041922 CTCCCCCGACCATCCTCA 60.042 66.667 0.00 0.00 0.00 3.86
39 40 2.844839 CCTCCCCCGACCATCCTC 60.845 72.222 0.00 0.00 0.00 3.71
40 41 4.499116 CCCTCCCCCGACCATCCT 62.499 72.222 0.00 0.00 0.00 3.24
60 61 4.778143 ACGGATCCGGCCAGCAAC 62.778 66.667 35.87 0.00 44.69 4.17
61 62 4.776322 CACGGATCCGGCCAGCAA 62.776 66.667 35.87 0.00 44.69 3.91
66 67 4.467084 TTCTGCACGGATCCGGCC 62.467 66.667 35.87 25.55 44.69 6.13
67 68 2.892425 CTTCTGCACGGATCCGGC 60.892 66.667 35.87 32.26 44.69 6.13
68 69 2.202932 CCTTCTGCACGGATCCGG 60.203 66.667 35.87 25.13 44.69 5.14
69 70 2.892425 GCCTTCTGCACGGATCCG 60.892 66.667 32.20 32.20 46.03 4.18
70 71 2.514824 GGCCTTCTGCACGGATCC 60.515 66.667 0.00 0.00 43.89 3.36
71 72 2.892425 CGGCCTTCTGCACGGATC 60.892 66.667 0.00 0.00 43.89 3.36
91 92 3.551407 GCCAGATCCGGTCCTCCC 61.551 72.222 0.00 0.00 0.00 4.30
92 93 3.917760 CGCCAGATCCGGTCCTCC 61.918 72.222 0.00 0.00 0.00 4.30
93 94 4.593864 GCGCCAGATCCGGTCCTC 62.594 72.222 0.00 0.00 0.00 3.71
95 96 4.899239 CAGCGCCAGATCCGGTCC 62.899 72.222 2.29 0.00 33.76 4.46
96 97 4.148825 ACAGCGCCAGATCCGGTC 62.149 66.667 2.29 0.00 33.76 4.79
97 98 4.148825 GACAGCGCCAGATCCGGT 62.149 66.667 2.29 0.00 36.81 5.28
100 101 3.838271 TCCGACAGCGCCAGATCC 61.838 66.667 2.29 0.00 35.83 3.36
101 102 2.583593 GTCCGACAGCGCCAGATC 60.584 66.667 2.29 0.00 35.83 2.75
102 103 4.148825 GGTCCGACAGCGCCAGAT 62.149 66.667 2.29 0.00 35.83 2.90
110 111 4.087892 CCCCTGCTGGTCCGACAG 62.088 72.222 9.00 4.33 41.41 3.51
111 112 3.533079 TACCCCTGCTGGTCCGACA 62.533 63.158 9.00 0.00 39.91 4.35
112 113 2.682494 TACCCCTGCTGGTCCGAC 60.682 66.667 9.00 0.00 39.91 4.79
113 114 2.363795 CTACCCCTGCTGGTCCGA 60.364 66.667 9.00 0.00 39.91 4.55
114 115 4.162690 GCTACCCCTGCTGGTCCG 62.163 72.222 9.00 0.00 39.91 4.79
115 116 3.798511 GGCTACCCCTGCTGGTCC 61.799 72.222 9.00 0.00 39.91 4.46
116 117 2.378634 ATGGCTACCCCTGCTGGTC 61.379 63.158 9.00 0.00 39.91 4.02
117 118 2.286425 ATGGCTACCCCTGCTGGT 60.286 61.111 9.00 3.69 42.62 4.00
118 119 2.194056 CATGGCTACCCCTGCTGG 59.806 66.667 1.89 1.89 0.00 4.85
119 120 2.194056 CCATGGCTACCCCTGCTG 59.806 66.667 0.00 0.00 0.00 4.41
120 121 2.286425 ACCATGGCTACCCCTGCT 60.286 61.111 13.04 0.00 0.00 4.24
121 122 2.124151 CACCATGGCTACCCCTGC 60.124 66.667 13.04 0.00 0.00 4.85
122 123 2.597340 CCACCATGGCTACCCCTG 59.403 66.667 13.04 0.00 0.00 4.45
123 124 2.696125 CCCACCATGGCTACCCCT 60.696 66.667 13.04 0.00 35.79 4.79
124 125 3.820843 CCCCACCATGGCTACCCC 61.821 72.222 13.04 0.00 35.79 4.95
125 126 3.820843 CCCCCACCATGGCTACCC 61.821 72.222 13.04 0.00 35.79 3.69
126 127 3.021263 ACCCCCACCATGGCTACC 61.021 66.667 13.04 0.00 35.79 3.18
127 128 2.275418 CACCCCCACCATGGCTAC 59.725 66.667 13.04 0.00 35.79 3.58
128 129 3.020647 CCACCCCCACCATGGCTA 61.021 66.667 13.04 0.00 35.79 3.93
152 153 4.120755 CCTCCTCAAGCCCCCAGC 62.121 72.222 0.00 0.00 44.25 4.85
153 154 4.120755 GCCTCCTCAAGCCCCCAG 62.121 72.222 0.00 0.00 0.00 4.45
155 156 4.120755 CTGCCTCCTCAAGCCCCC 62.121 72.222 0.00 0.00 0.00 5.40
156 157 2.336484 GATCTGCCTCCTCAAGCCCC 62.336 65.000 0.00 0.00 0.00 5.80
157 158 1.148048 GATCTGCCTCCTCAAGCCC 59.852 63.158 0.00 0.00 0.00 5.19
158 159 1.148048 GGATCTGCCTCCTCAAGCC 59.852 63.158 0.00 0.00 32.18 4.35
159 160 1.227497 CGGATCTGCCTCCTCAAGC 60.227 63.158 0.00 0.00 32.77 4.01
160 161 1.227497 GCGGATCTGCCTCCTCAAG 60.227 63.158 16.13 0.00 32.77 3.02
161 162 2.903357 GCGGATCTGCCTCCTCAA 59.097 61.111 16.13 0.00 32.77 3.02
178 179 4.047125 ATGAAGGTGGTGGCGGGG 62.047 66.667 0.00 0.00 0.00 5.73
179 180 2.751436 CATGAAGGTGGTGGCGGG 60.751 66.667 0.00 0.00 0.00 6.13
180 181 2.751436 CCATGAAGGTGGTGGCGG 60.751 66.667 0.00 0.00 34.46 6.13
181 182 2.751436 CCCATGAAGGTGGTGGCG 60.751 66.667 0.00 0.00 37.57 5.69
182 183 2.362889 CCCCATGAAGGTGGTGGC 60.363 66.667 0.00 0.00 37.57 5.01
183 184 2.362889 GCCCCATGAAGGTGGTGG 60.363 66.667 0.00 0.00 37.57 4.61
184 185 2.362889 GGCCCCATGAAGGTGGTG 60.363 66.667 0.00 0.00 37.57 4.17
185 186 3.672503 GGGCCCCATGAAGGTGGT 61.673 66.667 12.23 0.00 37.57 4.16
186 187 4.820744 CGGGCCCCATGAAGGTGG 62.821 72.222 18.66 0.00 39.05 4.61
254 255 3.483869 CTAGCAGGCCCCTCCACC 61.484 72.222 0.00 0.00 37.29 4.61
255 256 2.689034 ACTAGCAGGCCCCTCCAC 60.689 66.667 0.00 0.00 37.29 4.02
256 257 2.688666 CACTAGCAGGCCCCTCCA 60.689 66.667 0.00 0.00 37.29 3.86
257 258 3.483869 CCACTAGCAGGCCCCTCC 61.484 72.222 0.00 0.00 0.00 4.30
258 259 2.689034 ACCACTAGCAGGCCCCTC 60.689 66.667 0.00 0.00 0.00 4.30
259 260 3.011517 CACCACTAGCAGGCCCCT 61.012 66.667 0.00 0.00 0.00 4.79
260 261 4.115199 CCACCACTAGCAGGCCCC 62.115 72.222 0.00 0.00 0.00 5.80
261 262 4.803908 GCCACCACTAGCAGGCCC 62.804 72.222 0.00 0.00 41.25 5.80
296 297 1.647346 TTACTACCAAATCGCTGGCG 58.353 50.000 8.80 8.80 40.45 5.69
297 298 5.689819 CATTATTACTACCAAATCGCTGGC 58.310 41.667 0.00 0.00 40.45 4.85
298 299 5.238432 TGCATTATTACTACCAAATCGCTGG 59.762 40.000 0.00 0.00 42.68 4.85
299 300 6.299023 TGCATTATTACTACCAAATCGCTG 57.701 37.500 0.00 0.00 0.00 5.18
300 301 6.935741 TTGCATTATTACTACCAAATCGCT 57.064 33.333 0.00 0.00 0.00 4.93
301 302 7.359595 TGATTGCATTATTACTACCAAATCGC 58.640 34.615 0.00 0.00 0.00 4.58
302 303 9.546909 GATGATTGCATTATTACTACCAAATCG 57.453 33.333 0.00 0.00 34.11 3.34
408 409 1.936547 GTGCGGTTCTCCTCATTCATC 59.063 52.381 0.00 0.00 30.80 2.92
414 415 2.599281 TCCGTGCGGTTCTCCTCA 60.599 61.111 10.60 0.00 36.47 3.86
415 416 2.126031 GTCCGTGCGGTTCTCCTC 60.126 66.667 10.60 0.00 36.47 3.71
416 417 3.692406 GGTCCGTGCGGTTCTCCT 61.692 66.667 10.60 0.00 36.47 3.69
643 1490 0.398098 GTAGAGGGTTGGATCGGGGA 60.398 60.000 0.00 0.00 0.00 4.81
654 1501 3.468071 TGTCAGTGGTATGTAGAGGGT 57.532 47.619 0.00 0.00 0.00 4.34
656 1503 4.219115 AGGATGTCAGTGGTATGTAGAGG 58.781 47.826 0.00 0.00 0.00 3.69
660 1507 4.265856 AGGAGGATGTCAGTGGTATGTA 57.734 45.455 0.00 0.00 0.00 2.29
671 1518 3.181506 GCGATTGTTTGAAGGAGGATGTC 60.182 47.826 0.00 0.00 0.00 3.06
674 1521 2.009774 CGCGATTGTTTGAAGGAGGAT 58.990 47.619 0.00 0.00 0.00 3.24
675 1522 1.438651 CGCGATTGTTTGAAGGAGGA 58.561 50.000 0.00 0.00 0.00 3.71
676 1523 0.179189 GCGCGATTGTTTGAAGGAGG 60.179 55.000 12.10 0.00 0.00 4.30
717 1572 7.825270 TCATTGTTTTTCCTTATCTTAGCGGTA 59.175 33.333 0.00 0.00 0.00 4.02
728 1583 5.751028 CCGCTTTGTTCATTGTTTTTCCTTA 59.249 36.000 0.00 0.00 0.00 2.69
730 1585 4.119136 CCGCTTTGTTCATTGTTTTTCCT 58.881 39.130 0.00 0.00 0.00 3.36
732 1587 3.555547 AGCCGCTTTGTTCATTGTTTTTC 59.444 39.130 0.00 0.00 0.00 2.29
742 1597 1.396301 CTCATCTCAGCCGCTTTGTTC 59.604 52.381 0.00 0.00 0.00 3.18
773 1628 4.719369 GACCGTGACGCGAGGCTT 62.719 66.667 15.93 0.00 44.77 4.35
818 1673 1.622811 AGCTGTGGAGAACTGGAGAAG 59.377 52.381 0.00 0.00 0.00 2.85
943 1810 2.750637 ACGCGGATGGAGTCGAGT 60.751 61.111 12.47 0.00 34.83 4.18
944 1811 2.024871 GACGCGGATGGAGTCGAG 59.975 66.667 12.47 0.00 35.73 4.04
945 1812 3.515286 GGACGCGGATGGAGTCGA 61.515 66.667 12.47 0.00 45.30 4.20
946 1813 2.829043 TTTGGACGCGGATGGAGTCG 62.829 60.000 12.47 0.00 45.30 4.18
947 1814 1.079405 TTTGGACGCGGATGGAGTC 60.079 57.895 12.47 0.00 43.84 3.36
948 1815 1.079127 CTTTGGACGCGGATGGAGT 60.079 57.895 12.47 0.00 0.00 3.85
950 1817 2.435938 GCTTTGGACGCGGATGGA 60.436 61.111 12.47 0.00 0.00 3.41
951 1818 3.508840 GGCTTTGGACGCGGATGG 61.509 66.667 12.47 0.00 0.00 3.51
953 1820 1.745489 GAAGGCTTTGGACGCGGAT 60.745 57.895 12.47 0.00 0.00 4.18
954 1821 2.358247 GAAGGCTTTGGACGCGGA 60.358 61.111 12.47 0.00 0.00 5.54
955 1822 2.668212 TGAAGGCTTTGGACGCGG 60.668 61.111 12.47 0.00 0.00 6.46
956 1823 2.556287 GTGAAGGCTTTGGACGCG 59.444 61.111 3.53 3.53 0.00 6.01
957 1824 2.556287 CGTGAAGGCTTTGGACGC 59.444 61.111 0.00 0.00 0.00 5.19
958 1825 1.577328 ATGCGTGAAGGCTTTGGACG 61.577 55.000 17.80 17.80 0.00 4.79
959 1826 0.169009 GATGCGTGAAGGCTTTGGAC 59.831 55.000 0.00 0.00 0.00 4.02
979 1848 2.282745 GGCAACCAGAAGGCAGCT 60.283 61.111 0.00 0.00 37.91 4.24
982 1854 4.577677 TGCGGCAACCAGAAGGCA 62.578 61.111 0.00 0.00 39.06 4.75
986 1858 3.364442 CCATTGCGGCAACCAGAA 58.636 55.556 18.94 0.00 0.00 3.02
1023 1901 4.516195 GAAGAGGACGGCTCGGGC 62.516 72.222 0.00 0.00 37.82 6.13
1024 1902 2.286127 GAAGAAGAGGACGGCTCGGG 62.286 65.000 0.00 0.00 0.00 5.14
1025 1903 1.139947 GAAGAAGAGGACGGCTCGG 59.860 63.158 0.00 0.00 0.00 4.63
1026 1904 1.226435 CGAAGAAGAGGACGGCTCG 60.226 63.158 0.00 0.00 0.00 5.03
1027 1905 0.179158 GACGAAGAAGAGGACGGCTC 60.179 60.000 0.00 0.00 0.00 4.70
1028 1906 1.596895 GGACGAAGAAGAGGACGGCT 61.597 60.000 0.00 0.00 34.03 5.52
1029 1907 1.153804 GGACGAAGAAGAGGACGGC 60.154 63.158 0.00 0.00 0.00 5.68
1030 1908 0.452585 GAGGACGAAGAAGAGGACGG 59.547 60.000 0.00 0.00 0.00 4.79
1031 1909 0.097325 CGAGGACGAAGAAGAGGACG 59.903 60.000 0.00 0.00 42.66 4.79
1032 1910 0.179158 GCGAGGACGAAGAAGAGGAC 60.179 60.000 0.00 0.00 42.66 3.85
1033 1911 1.313812 GGCGAGGACGAAGAAGAGGA 61.314 60.000 0.00 0.00 42.66 3.71
1034 1912 1.139947 GGCGAGGACGAAGAAGAGG 59.860 63.158 0.00 0.00 42.66 3.69
1035 1913 0.457851 ATGGCGAGGACGAAGAAGAG 59.542 55.000 0.00 0.00 42.66 2.85
1036 1914 1.404391 GTATGGCGAGGACGAAGAAGA 59.596 52.381 0.00 0.00 42.66 2.87
1037 1915 1.405821 AGTATGGCGAGGACGAAGAAG 59.594 52.381 0.00 0.00 42.66 2.85
1038 1916 1.404391 GAGTATGGCGAGGACGAAGAA 59.596 52.381 0.00 0.00 42.66 2.52
1039 1917 1.022735 GAGTATGGCGAGGACGAAGA 58.977 55.000 0.00 0.00 42.66 2.87
1040 1918 0.030908 GGAGTATGGCGAGGACGAAG 59.969 60.000 0.00 0.00 42.66 3.79
1041 1919 0.395311 AGGAGTATGGCGAGGACGAA 60.395 55.000 0.00 0.00 42.66 3.85
1044 1922 1.102222 ACGAGGAGTATGGCGAGGAC 61.102 60.000 0.00 0.00 0.00 3.85
1152 2030 2.804090 GACACGGACGCGAAGACC 60.804 66.667 15.93 9.70 0.00 3.85
1275 2159 2.515757 TTGAACCGCTGCAGCACA 60.516 55.556 36.03 25.32 42.21 4.57
1668 2552 3.775654 GTCCACCTCTCCGCCAGG 61.776 72.222 0.00 0.00 37.03 4.45
1692 2576 4.033894 CCGACGAGGGCAATCATC 57.966 61.111 0.00 0.00 35.97 2.92
1896 2785 0.808453 CGAACCACCGCGTAATGGAT 60.808 55.000 23.44 14.37 39.46 3.41
1944 2841 0.543749 GATTAGTGAGCACCTGGCCT 59.456 55.000 3.32 0.00 46.50 5.19
1956 2853 1.565305 GCACGAGCTCCAGATTAGTG 58.435 55.000 8.47 9.56 37.91 2.74
2127 3024 1.188219 AGGCCGAGAGCTTCTTCACA 61.188 55.000 0.00 0.00 43.05 3.58
2430 3327 4.694233 CTGAGCACGGTGGCAGCT 62.694 66.667 15.48 6.92 42.17 4.24
2478 3375 3.588817 TAGTGGGTTCCGGCCGAGA 62.589 63.158 30.73 19.83 0.00 4.04
2496 3393 0.171455 GCACGACCTTCTCGATCACT 59.829 55.000 0.00 0.00 46.14 3.41
2640 3537 2.364186 TCCTCCTCGCTGATGGCA 60.364 61.111 0.00 0.00 41.91 4.92
2700 3597 3.449227 TTCACGATCGCCTCCGCT 61.449 61.111 16.60 0.00 0.00 5.52
2979 3876 2.204090 ACGGTGGAGGTGGGGAAT 60.204 61.111 0.00 0.00 0.00 3.01
2981 3878 3.899545 GAGACGGTGGAGGTGGGGA 62.900 68.421 0.00 0.00 0.00 4.81
3015 3912 2.535574 TCGAAGAATGATTCACGATGCG 59.464 45.455 18.03 5.15 36.45 4.73
3018 3915 5.351458 TGTCATCGAAGAATGATTCACGAT 58.649 37.500 23.51 23.51 44.98 3.73
3026 3923 7.614124 TCAATTCAATGTCATCGAAGAATGA 57.386 32.000 0.00 0.00 43.58 2.57
3027 3924 7.590322 GGATCAATTCAATGTCATCGAAGAATG 59.410 37.037 0.00 0.00 43.58 2.67
3028 3925 7.519488 CGGATCAATTCAATGTCATCGAAGAAT 60.519 37.037 0.00 0.00 43.58 2.40
3035 3936 5.991606 TCCTACGGATCAATTCAATGTCATC 59.008 40.000 0.00 0.00 0.00 2.92
3036 3937 5.928976 TCCTACGGATCAATTCAATGTCAT 58.071 37.500 0.00 0.00 0.00 3.06
3042 3943 3.938963 GCTGTTCCTACGGATCAATTCAA 59.061 43.478 0.00 0.00 31.98 2.69
3043 3944 3.197766 AGCTGTTCCTACGGATCAATTCA 59.802 43.478 0.00 0.00 31.98 2.57
3089 3991 9.398170 CCAATTTTGTACAACAATTCTCTACAG 57.602 33.333 8.07 4.78 38.00 2.74
3090 3992 8.908903 ACCAATTTTGTACAACAATTCTCTACA 58.091 29.630 8.07 0.00 38.00 2.74
3091 3993 9.744468 AACCAATTTTGTACAACAATTCTCTAC 57.256 29.630 8.07 0.00 38.00 2.59
3146 4049 3.129988 CACGGGGACTAAAGAATCGTACT 59.870 47.826 0.00 0.00 0.00 2.73
3149 4052 1.206371 CCACGGGGACTAAAGAATCGT 59.794 52.381 0.00 0.00 35.59 3.73
3165 4068 2.678836 TCTGTGTTTGTGTTTACCCACG 59.321 45.455 0.00 0.00 38.20 4.94
3311 4224 4.008074 TCTGCCAAGGTGAGAAAACTAG 57.992 45.455 0.00 0.00 0.00 2.57
3312 4225 4.640771 ATCTGCCAAGGTGAGAAAACTA 57.359 40.909 0.00 0.00 0.00 2.24
3313 4226 3.515602 ATCTGCCAAGGTGAGAAAACT 57.484 42.857 0.00 0.00 0.00 2.66
3314 4227 3.858503 GCAATCTGCCAAGGTGAGAAAAC 60.859 47.826 0.00 0.00 37.42 2.43
3315 4228 2.297033 GCAATCTGCCAAGGTGAGAAAA 59.703 45.455 0.00 0.00 37.42 2.29
3318 4231 0.401356 TGCAATCTGCCAAGGTGAGA 59.599 50.000 0.00 0.00 44.23 3.27
3323 4236 5.644636 ACAAAATTATTGCAATCTGCCAAGG 59.355 36.000 16.86 3.03 44.23 3.61
3366 4282 1.065701 CATCCGCGACAACTAGCTAGT 59.934 52.381 20.95 20.95 38.39 2.57
3371 4287 1.999051 GTGCATCCGCGACAACTAG 59.001 57.895 8.23 0.00 42.97 2.57
3649 4606 1.545582 CGAGCAAATTGTCAATGGGGT 59.454 47.619 0.00 0.12 0.00 4.95
3651 4608 1.545582 ACCGAGCAAATTGTCAATGGG 59.454 47.619 0.00 0.00 0.00 4.00
3652 4609 3.244976 GAACCGAGCAAATTGTCAATGG 58.755 45.455 0.00 0.00 0.00 3.16
3663 4620 2.158813 AGACAAGAAAGGAACCGAGCAA 60.159 45.455 0.00 0.00 0.00 3.91
3664 4621 1.416401 AGACAAGAAAGGAACCGAGCA 59.584 47.619 0.00 0.00 0.00 4.26
3668 4625 3.386768 TGAGAGACAAGAAAGGAACCG 57.613 47.619 0.00 0.00 0.00 4.44
3714 4671 4.393155 AGCCCATGTGAAGCGCGA 62.393 61.111 12.10 0.00 0.00 5.87
3715 4672 3.869272 GAGCCCATGTGAAGCGCG 61.869 66.667 0.00 0.00 0.00 6.86
3765 4730 3.306502 CGACCAGGAGTACTTGGCTTAAA 60.307 47.826 12.69 0.00 45.50 1.52
3766 4731 2.232941 CGACCAGGAGTACTTGGCTTAA 59.767 50.000 12.69 0.00 45.50 1.85
3767 4732 1.822990 CGACCAGGAGTACTTGGCTTA 59.177 52.381 12.69 0.00 45.50 3.09
3768 4733 0.608640 CGACCAGGAGTACTTGGCTT 59.391 55.000 12.69 0.00 45.50 4.35
3769 4734 0.251653 TCGACCAGGAGTACTTGGCT 60.252 55.000 12.69 1.86 45.50 4.75
3770 4735 0.173708 CTCGACCAGGAGTACTTGGC 59.826 60.000 12.69 5.92 45.50 4.52
3771 4736 1.835494 TCTCGACCAGGAGTACTTGG 58.165 55.000 11.41 11.41 46.74 3.61
3772 4737 2.557056 TGTTCTCGACCAGGAGTACTTG 59.443 50.000 0.00 0.00 35.91 3.16
3860 4825 2.547123 TTAGGACAGGGGAGAGGGCC 62.547 65.000 0.00 0.00 0.00 5.80
3861 4826 0.400670 ATTAGGACAGGGGAGAGGGC 60.401 60.000 0.00 0.00 0.00 5.19
3862 4827 1.062121 TGATTAGGACAGGGGAGAGGG 60.062 57.143 0.00 0.00 0.00 4.30
3863 4828 2.324541 CTGATTAGGACAGGGGAGAGG 58.675 57.143 0.00 0.00 0.00 3.69
3864 4829 1.691434 GCTGATTAGGACAGGGGAGAG 59.309 57.143 0.00 0.00 36.09 3.20
3898 4881 2.754946 ATGCCTTTGCCATTTCAGTG 57.245 45.000 0.00 0.00 36.33 3.66
3899 4882 2.164219 CGTATGCCTTTGCCATTTCAGT 59.836 45.455 0.00 0.00 36.33 3.41
3902 4885 1.135141 TGCGTATGCCTTTGCCATTTC 60.135 47.619 4.05 0.00 41.78 2.17
3935 4919 1.576421 CAGCAGAAAGACAACGCCC 59.424 57.895 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.