Multiple sequence alignment - TraesCS7D01G243300

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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 TraesCS7D01G243300 chr7D 100.000 3547 0 0 1 3547 209519795 209523341 0.000000e+00 6551
1 TraesCS7D01G243300 chr7D 90.179 224 14 3 1 216 213885295 213885518 5.800000e-73 285
2 TraesCS7D01G243300 chr7D 87.054 224 14 7 2768 2979 393624863 393625083 4.580000e-59 239
3 TraesCS7D01G243300 chr7B 94.135 1995 83 12 792 2755 192041657 192039666 0.000000e+00 3005
4 TraesCS7D01G243300 chr7B 89.573 585 25 20 2982 3547 192039654 192039087 0.000000e+00 710
5 TraesCS7D01G243300 chr7B 88.506 435 32 8 216 644 192086209 192085787 8.780000e-141 510
6 TraesCS7D01G243300 chr7B 93.506 154 10 0 216 369 192087333 192087180 2.750000e-56 230
7 TraesCS7D01G243300 chr7B 92.208 154 12 0 216 369 192086771 192086618 5.960000e-53 219
8 TraesCS7D01G243300 chr7B 87.565 193 17 3 459 651 192043822 192043637 2.140000e-52 217
9 TraesCS7D01G243300 chr7A 94.302 1720 46 18 1064 2759 222290593 222292284 0.000000e+00 2586
10 TraesCS7D01G243300 chr7A 91.372 452 24 9 2978 3422 222292352 222292795 3.920000e-169 604
11 TraesCS7D01G243300 chr7A 85.579 527 58 9 216 735 222286780 222287295 1.450000e-148 536
12 TraesCS7D01G243300 chr7A 91.071 224 12 2 1 217 661856830 661857052 2.680000e-76 296
13 TraesCS7D01G243300 chr7A 90.135 223 14 5 1 216 313743834 313744055 2.080000e-72 283
14 TraesCS7D01G243300 chr7A 85.153 229 19 9 2765 2980 218936411 218936185 1.660000e-53 220
15 TraesCS7D01G243300 chr7A 86.893 206 12 8 2768 2962 446368799 446369000 2.140000e-52 217
16 TraesCS7D01G243300 chr7A 96.183 131 3 2 3419 3547 222294272 222294402 2.770000e-51 213
17 TraesCS7D01G243300 chr5D 91.964 224 11 2 1 217 143170425 143170648 1.240000e-79 307
18 TraesCS7D01G243300 chr5D 84.649 228 20 9 2765 2979 546697750 546697975 2.770000e-51 213
19 TraesCS7D01G243300 chr4D 90.708 226 11 5 1 216 118136381 118136606 3.460000e-75 292
20 TraesCS7D01G243300 chr4D 90.308 227 13 3 1 218 404772742 404772516 4.480000e-74 289
21 TraesCS7D01G243300 chr3D 90.583 223 14 2 3 218 71244944 71244722 4.480000e-74 289
22 TraesCS7D01G243300 chr4A 90.222 225 15 1 1 218 89955888 89955664 1.610000e-73 287
23 TraesCS7D01G243300 chr3A 89.778 225 16 1 1 218 190856220 190856444 7.500000e-72 281
24 TraesCS7D01G243300 chr6D 86.842 228 14 10 2765 2979 472139091 472139315 1.270000e-59 241
25 TraesCS7D01G243300 chr4B 87.678 211 14 6 2765 2963 121191779 121191569 5.920000e-58 235
26 TraesCS7D01G243300 chr2A 85.463 227 18 9 2765 2979 529559369 529559146 4.610000e-54 222
27 TraesCS7D01G243300 chr2A 85.520 221 18 11 2772 2980 487745927 487746145 5.960000e-53 219
28 TraesCS7D01G243300 chr2B 89.697 165 10 4 2772 2930 636489391 636489554 1.670000e-48 204


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 TraesCS7D01G243300 chr7D 209519795 209523341 3546 False 6551.000000 6551 100.000000 1 3547 1 chr7D.!!$F1 3546
1 TraesCS7D01G243300 chr7B 192039087 192043822 4735 True 1310.666667 3005 90.424333 459 3547 3 chr7B.!!$R1 3088
2 TraesCS7D01G243300 chr7B 192085787 192087333 1546 True 319.666667 510 91.406667 216 644 3 chr7B.!!$R2 428
3 TraesCS7D01G243300 chr7A 222286780 222294402 7622 False 984.750000 2586 91.859000 216 3547 4 chr7A.!!$F4 3331

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
103 104 0.036010 AAATGTGGAGAGAGGTGCGG 60.036 55.0 0.00 0.0 0.00 5.69 F
398 1516 0.175760 GCTTGATGTCTAGCCGTGGA 59.824 55.0 5.33 0.0 38.48 4.02 F
694 3603 0.182061 AGCATGAATGTGGATCGGCT 59.818 50.0 0.00 0.0 0.00 5.52 F
1631 7574 0.106619 ACCTCCGTATCCTCGAGCTT 60.107 55.0 6.99 0.0 0.00 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1038 6953 2.415893 GCATTCACCCATCTTTCGGTTG 60.416 50.000 0.00 0.0 0.00 3.77 R
1535 7478 2.566913 GCGAGTATGAGAGAGGACAGA 58.433 52.381 0.00 0.0 0.00 3.41 R
2433 8376 1.605738 CGGCTACCGGGCTAGGTAT 60.606 63.158 6.32 0.0 44.88 2.73 R
3248 9223 0.247460 TGCCGTCTGACCATCTCTTG 59.753 55.000 1.55 0.0 0.00 3.02 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
47 48 1.985473 TTGCTCAGCAATGAGGTTGT 58.015 45.000 8.40 0.00 43.99 3.32
48 49 1.241165 TGCTCAGCAATGAGGTTGTG 58.759 50.000 0.00 0.00 40.07 3.33
49 50 0.524862 GCTCAGCAATGAGGTTGTGG 59.475 55.000 7.33 0.00 40.07 4.17
50 51 1.171308 CTCAGCAATGAGGTTGTGGG 58.829 55.000 0.00 0.00 40.07 4.61
51 52 0.770499 TCAGCAATGAGGTTGTGGGA 59.230 50.000 0.00 0.00 40.07 4.37
52 53 1.171308 CAGCAATGAGGTTGTGGGAG 58.829 55.000 0.00 0.00 40.07 4.30
53 54 1.067295 AGCAATGAGGTTGTGGGAGA 58.933 50.000 0.00 0.00 40.07 3.71
54 55 1.637553 AGCAATGAGGTTGTGGGAGAT 59.362 47.619 0.00 0.00 40.07 2.75
55 56 2.846206 AGCAATGAGGTTGTGGGAGATA 59.154 45.455 0.00 0.00 40.07 1.98
56 57 3.266772 AGCAATGAGGTTGTGGGAGATAA 59.733 43.478 0.00 0.00 40.07 1.75
57 58 3.629398 GCAATGAGGTTGTGGGAGATAAG 59.371 47.826 0.00 0.00 40.07 1.73
58 59 4.202441 CAATGAGGTTGTGGGAGATAAGG 58.798 47.826 0.00 0.00 33.01 2.69
59 60 3.199442 TGAGGTTGTGGGAGATAAGGA 57.801 47.619 0.00 0.00 0.00 3.36
60 61 3.736094 TGAGGTTGTGGGAGATAAGGAT 58.264 45.455 0.00 0.00 0.00 3.24
61 62 3.455910 TGAGGTTGTGGGAGATAAGGATG 59.544 47.826 0.00 0.00 0.00 3.51
62 63 3.711704 GAGGTTGTGGGAGATAAGGATGA 59.288 47.826 0.00 0.00 0.00 2.92
63 64 4.111577 AGGTTGTGGGAGATAAGGATGAA 58.888 43.478 0.00 0.00 0.00 2.57
64 65 4.080299 AGGTTGTGGGAGATAAGGATGAAC 60.080 45.833 0.00 0.00 0.00 3.18
65 66 3.819564 TGTGGGAGATAAGGATGAACG 57.180 47.619 0.00 0.00 0.00 3.95
66 67 3.371034 TGTGGGAGATAAGGATGAACGA 58.629 45.455 0.00 0.00 0.00 3.85
67 68 3.384789 TGTGGGAGATAAGGATGAACGAG 59.615 47.826 0.00 0.00 0.00 4.18
68 69 2.965831 TGGGAGATAAGGATGAACGAGG 59.034 50.000 0.00 0.00 0.00 4.63
69 70 2.289133 GGGAGATAAGGATGAACGAGGC 60.289 54.545 0.00 0.00 0.00 4.70
70 71 2.365617 GGAGATAAGGATGAACGAGGCA 59.634 50.000 0.00 0.00 0.00 4.75
71 72 3.181465 GGAGATAAGGATGAACGAGGCAA 60.181 47.826 0.00 0.00 0.00 4.52
72 73 4.054671 GAGATAAGGATGAACGAGGCAAG 58.945 47.826 0.00 0.00 0.00 4.01
73 74 2.691409 TAAGGATGAACGAGGCAAGG 57.309 50.000 0.00 0.00 0.00 3.61
74 75 0.678048 AAGGATGAACGAGGCAAGGC 60.678 55.000 0.00 0.00 0.00 4.35
88 89 4.574599 GGCAAGGCCTTATCTGTAAATG 57.425 45.455 20.00 3.17 46.69 2.32
89 90 3.954258 GGCAAGGCCTTATCTGTAAATGT 59.046 43.478 20.00 0.00 46.69 2.71
90 91 4.202050 GGCAAGGCCTTATCTGTAAATGTG 60.202 45.833 20.00 2.34 46.69 3.21
91 92 4.202050 GCAAGGCCTTATCTGTAAATGTGG 60.202 45.833 20.00 1.10 0.00 4.17
92 93 5.192927 CAAGGCCTTATCTGTAAATGTGGA 58.807 41.667 20.00 0.00 0.00 4.02
93 94 5.041191 AGGCCTTATCTGTAAATGTGGAG 57.959 43.478 0.00 0.00 0.00 3.86
94 95 4.721776 AGGCCTTATCTGTAAATGTGGAGA 59.278 41.667 0.00 0.00 0.00 3.71
95 96 5.059833 GGCCTTATCTGTAAATGTGGAGAG 58.940 45.833 0.00 0.00 0.00 3.20
96 97 5.163301 GGCCTTATCTGTAAATGTGGAGAGA 60.163 44.000 0.00 0.00 0.00 3.10
97 98 5.988561 GCCTTATCTGTAAATGTGGAGAGAG 59.011 44.000 0.00 0.00 0.00 3.20
98 99 6.520272 CCTTATCTGTAAATGTGGAGAGAGG 58.480 44.000 0.00 0.00 0.00 3.69
99 100 6.098982 CCTTATCTGTAAATGTGGAGAGAGGT 59.901 42.308 0.00 0.00 0.00 3.85
100 101 4.808414 TCTGTAAATGTGGAGAGAGGTG 57.192 45.455 0.00 0.00 0.00 4.00
101 102 3.055819 TCTGTAAATGTGGAGAGAGGTGC 60.056 47.826 0.00 0.00 0.00 5.01
102 103 2.271800 GTAAATGTGGAGAGAGGTGCG 58.728 52.381 0.00 0.00 0.00 5.34
103 104 0.036010 AAATGTGGAGAGAGGTGCGG 60.036 55.000 0.00 0.00 0.00 5.69
104 105 1.194781 AATGTGGAGAGAGGTGCGGT 61.195 55.000 0.00 0.00 0.00 5.68
105 106 1.194781 ATGTGGAGAGAGGTGCGGTT 61.195 55.000 0.00 0.00 0.00 4.44
106 107 1.371558 GTGGAGAGAGGTGCGGTTT 59.628 57.895 0.00 0.00 0.00 3.27
107 108 0.250338 GTGGAGAGAGGTGCGGTTTT 60.250 55.000 0.00 0.00 0.00 2.43
108 109 0.472471 TGGAGAGAGGTGCGGTTTTT 59.528 50.000 0.00 0.00 0.00 1.94
142 143 9.886132 AATTGTCATAGTTTACTTTCTATCCGT 57.114 29.630 0.00 0.00 0.00 4.69
143 144 8.922058 TTGTCATAGTTTACTTTCTATCCGTC 57.078 34.615 0.00 0.00 0.00 4.79
144 145 8.058667 TGTCATAGTTTACTTTCTATCCGTCA 57.941 34.615 0.00 0.00 0.00 4.35
145 146 8.188799 TGTCATAGTTTACTTTCTATCCGTCAG 58.811 37.037 0.00 0.00 0.00 3.51
146 147 8.404000 GTCATAGTTTACTTTCTATCCGTCAGA 58.596 37.037 0.00 0.00 0.00 3.27
147 148 9.132923 TCATAGTTTACTTTCTATCCGTCAGAT 57.867 33.333 0.00 0.00 39.15 2.90
155 156 8.514330 ACTTTCTATCCGTCAGATATAGATCC 57.486 38.462 0.00 0.00 36.84 3.36
156 157 8.333235 ACTTTCTATCCGTCAGATATAGATCCT 58.667 37.037 0.00 0.00 36.84 3.24
157 158 9.839817 CTTTCTATCCGTCAGATATAGATCCTA 57.160 37.037 0.00 0.00 36.84 2.94
175 176 7.972301 AGATCCTATATTATAAGATGGCAGGC 58.028 38.462 2.80 0.00 0.00 4.85
176 177 7.570232 AGATCCTATATTATAAGATGGCAGGCA 59.430 37.037 0.00 0.00 0.00 4.75
177 178 6.889198 TCCTATATTATAAGATGGCAGGCAC 58.111 40.000 0.00 0.00 0.00 5.01
178 179 6.443527 TCCTATATTATAAGATGGCAGGCACA 59.556 38.462 0.00 0.00 0.00 4.57
179 180 6.540189 CCTATATTATAAGATGGCAGGCACAC 59.460 42.308 0.00 0.00 0.00 3.82
180 181 2.638480 TATAAGATGGCAGGCACACC 57.362 50.000 0.00 0.00 0.00 4.16
181 182 0.625316 ATAAGATGGCAGGCACACCA 59.375 50.000 0.00 0.00 41.01 4.17
183 184 0.251922 AAGATGGCAGGCACACCATT 60.252 50.000 0.00 0.00 45.56 3.16
184 185 0.625316 AGATGGCAGGCACACCATTA 59.375 50.000 0.00 0.00 45.56 1.90
185 186 1.216175 AGATGGCAGGCACACCATTAT 59.784 47.619 0.00 0.00 45.56 1.28
186 187 1.610522 GATGGCAGGCACACCATTATC 59.389 52.381 0.00 0.00 45.56 1.75
187 188 0.330941 TGGCAGGCACACCATTATCA 59.669 50.000 0.00 0.00 39.06 2.15
188 189 0.740737 GGCAGGCACACCATTATCAC 59.259 55.000 0.00 0.00 39.06 3.06
189 190 0.740737 GCAGGCACACCATTATCACC 59.259 55.000 0.00 0.00 39.06 4.02
190 191 1.954733 GCAGGCACACCATTATCACCA 60.955 52.381 0.00 0.00 39.06 4.17
191 192 2.445427 CAGGCACACCATTATCACCAA 58.555 47.619 0.00 0.00 39.06 3.67
192 193 3.025978 CAGGCACACCATTATCACCAAT 58.974 45.455 0.00 0.00 39.06 3.16
193 194 3.448301 CAGGCACACCATTATCACCAATT 59.552 43.478 0.00 0.00 39.06 2.32
194 195 3.701040 AGGCACACCATTATCACCAATTC 59.299 43.478 0.00 0.00 39.06 2.17
195 196 3.489059 GGCACACCATTATCACCAATTCG 60.489 47.826 0.00 0.00 35.26 3.34
196 197 3.489059 GCACACCATTATCACCAATTCGG 60.489 47.826 0.00 0.00 42.50 4.30
197 198 3.944650 CACACCATTATCACCAATTCGGA 59.055 43.478 1.54 0.00 38.63 4.55
198 199 4.580167 CACACCATTATCACCAATTCGGAT 59.420 41.667 1.54 0.00 38.63 4.18
199 200 5.067674 CACACCATTATCACCAATTCGGATT 59.932 40.000 1.54 0.00 38.63 3.01
200 201 5.656416 ACACCATTATCACCAATTCGGATTT 59.344 36.000 0.00 0.00 38.63 2.17
201 202 6.154363 ACACCATTATCACCAATTCGGATTTT 59.846 34.615 0.00 0.00 38.63 1.82
202 203 7.041107 CACCATTATCACCAATTCGGATTTTT 58.959 34.615 0.00 0.00 38.63 1.94
203 204 8.194104 CACCATTATCACCAATTCGGATTTTTA 58.806 33.333 0.00 0.00 38.63 1.52
204 205 8.923270 ACCATTATCACCAATTCGGATTTTTAT 58.077 29.630 0.00 0.00 38.63 1.40
210 211 8.801882 TCACCAATTCGGATTTTTATAAGAGT 57.198 30.769 0.00 0.00 38.63 3.24
211 212 9.893634 TCACCAATTCGGATTTTTATAAGAGTA 57.106 29.630 0.00 0.00 38.63 2.59
325 888 0.813821 CTCCTCATCTGTCGCAGTCA 59.186 55.000 6.72 0.00 32.61 3.41
328 891 1.408340 CCTCATCTGTCGCAGTCATCT 59.592 52.381 6.72 0.00 32.61 2.90
331 894 2.232208 TCATCTGTCGCAGTCATCTTGT 59.768 45.455 6.72 0.00 32.61 3.16
391 1509 1.268794 CGACTCCGGCTTGATGTCTAG 60.269 57.143 0.00 0.00 0.00 2.43
397 1515 2.682893 GCTTGATGTCTAGCCGTGG 58.317 57.895 5.33 0.00 38.48 4.94
398 1516 0.175760 GCTTGATGTCTAGCCGTGGA 59.824 55.000 5.33 0.00 38.48 4.02
420 1544 1.304962 GAGGGGCCCGAAAACCATT 60.305 57.895 18.95 0.00 0.00 3.16
466 1590 4.664677 ACGCGTCAGCCACCACTC 62.665 66.667 5.58 0.00 41.18 3.51
495 1619 1.706287 GGACTTCTTTCCCATCGCGC 61.706 60.000 0.00 0.00 0.00 6.86
537 1661 2.767505 GCGACTTTGAAAGAGGGAAGA 58.232 47.619 12.53 0.00 0.00 2.87
540 1664 3.078097 GACTTTGAAAGAGGGAAGAGGC 58.922 50.000 12.53 0.00 0.00 4.70
545 1669 2.100989 GAAAGAGGGAAGAGGCGTAGA 58.899 52.381 0.00 0.00 0.00 2.59
563 1687 1.069204 AGAGTTTGCGTCTTGAGCTCA 59.931 47.619 13.74 13.74 35.28 4.26
572 1696 3.497118 CGTCTTGAGCTCAGTAGACTTG 58.503 50.000 31.42 20.37 33.66 3.16
573 1697 3.189495 CGTCTTGAGCTCAGTAGACTTGA 59.811 47.826 31.42 11.55 33.66 3.02
574 1698 4.481463 GTCTTGAGCTCAGTAGACTTGAC 58.519 47.826 29.34 18.38 33.28 3.18
575 1699 4.217550 GTCTTGAGCTCAGTAGACTTGACT 59.782 45.833 29.34 0.00 33.28 3.41
576 1700 4.830046 TCTTGAGCTCAGTAGACTTGACTT 59.170 41.667 17.43 0.00 0.00 3.01
577 1701 4.775058 TGAGCTCAGTAGACTTGACTTC 57.225 45.455 13.74 0.00 0.00 3.01
585 1709 5.480422 TCAGTAGACTTGACTTCAATAGCCA 59.520 40.000 0.00 0.00 35.02 4.75
596 1720 0.394762 CAATAGCCAGAGCAAGCCCA 60.395 55.000 0.00 0.00 43.56 5.36
613 1737 2.224018 GCCCAACAAAGCTTCAATGTGA 60.224 45.455 0.00 0.00 0.00 3.58
688 3597 2.038820 TGTCAGACAGCATGAATGTGGA 59.961 45.455 8.55 4.19 39.69 4.02
690 3599 3.311871 GTCAGACAGCATGAATGTGGATC 59.688 47.826 8.55 0.00 39.69 3.36
691 3600 2.287103 CAGACAGCATGAATGTGGATCG 59.713 50.000 8.55 0.00 39.69 3.69
692 3601 1.600957 GACAGCATGAATGTGGATCGG 59.399 52.381 8.55 0.00 39.69 4.18
693 3602 0.309922 CAGCATGAATGTGGATCGGC 59.690 55.000 0.00 0.00 39.69 5.54
694 3603 0.182061 AGCATGAATGTGGATCGGCT 59.818 50.000 0.00 0.00 0.00 5.52
695 3604 0.590195 GCATGAATGTGGATCGGCTC 59.410 55.000 0.00 0.00 0.00 4.70
698 3607 2.203070 AATGTGGATCGGCTCGGC 60.203 61.111 0.00 0.00 0.00 5.54
705 3614 3.701604 GATCGGCTCGGCTGTCGTT 62.702 63.158 0.09 0.00 40.32 3.85
726 3635 1.367840 GACACGTTCACTCTGGCCT 59.632 57.895 3.32 0.00 0.00 5.19
735 3644 4.441495 CGTTCACTCTGGCCTACATGAATA 60.441 45.833 3.32 0.00 30.74 1.75
740 3649 2.981784 TCTGGCCTACATGAATATGGCT 59.018 45.455 3.32 0.00 42.84 4.75
743 3652 3.138098 TGGCCTACATGAATATGGCTTGA 59.862 43.478 3.32 0.00 42.84 3.02
749 3658 6.649973 CCTACATGAATATGGCTTGAAGAGAG 59.350 42.308 0.00 0.00 38.66 3.20
752 3661 6.099413 ACATGAATATGGCTTGAAGAGAGAGA 59.901 38.462 0.00 0.00 38.66 3.10
753 3662 6.159299 TGAATATGGCTTGAAGAGAGAGAG 57.841 41.667 0.00 0.00 0.00 3.20
768 6013 9.581099 GAAGAGAGAGAGTTTTAGAATAACAGG 57.419 37.037 0.00 0.00 0.00 4.00
802 6110 1.202915 GGGTTTTAGGTTGGTTCGGGA 60.203 52.381 0.00 0.00 0.00 5.14
806 6114 4.325972 GTTTTAGGTTGGTTCGGGATGTA 58.674 43.478 0.00 0.00 0.00 2.29
824 6132 1.269998 GTAAGAGTCTGACGTGGCAGT 59.730 52.381 2.05 0.00 37.20 4.40
856 6164 4.108287 ACCATCCAAACCCCCTTTAGTTTA 59.892 41.667 0.00 0.00 34.52 2.01
868 6177 6.319399 CCCCTTTAGTTTAGTGTAAATTGCG 58.681 40.000 0.00 0.00 0.00 4.85
937 6246 6.599638 AGACTAAAAGTATCTGGTCCAAATGC 59.400 38.462 0.00 0.00 0.00 3.56
981 6290 5.332205 GCGCGATATATAGACGGTACTACTC 60.332 48.000 12.10 0.00 0.00 2.59
988 6297 3.289407 AGACGGTACTACTCCCCTAAC 57.711 52.381 0.00 0.00 0.00 2.34
1038 6953 6.583050 CGTAGTATTAAGCTGGAGTATCTTGC 59.417 42.308 0.00 0.00 34.58 4.01
1111 7054 0.887933 CCATTTTGAACACTCCCCCG 59.112 55.000 0.00 0.00 0.00 5.73
1535 7478 4.057428 GTCTGCCACCTCGACGCT 62.057 66.667 0.00 0.00 0.00 5.07
1550 7493 2.566913 GACGCTCTGTCCTCTCTCATA 58.433 52.381 0.00 0.00 42.04 2.15
1631 7574 0.106619 ACCTCCGTATCCTCGAGCTT 60.107 55.000 6.99 0.00 0.00 3.74
2424 8367 3.487879 CCGTGCGTGTGTGATATACTGTA 60.488 47.826 0.00 0.00 0.00 2.74
2433 8376 8.504005 CGTGTGTGATATACTGTACTGATGATA 58.496 37.037 6.77 2.31 0.00 2.15
2585 8532 1.153667 GTGAGCGAGGAAGAGGCAG 60.154 63.158 0.00 0.00 0.00 4.85
2623 8570 4.164988 TCCTCCTCCATTCCTCTTCATTTC 59.835 45.833 0.00 0.00 0.00 2.17
2636 8585 7.670364 TCCTCTTCATTTCCCTTTTTCATTTC 58.330 34.615 0.00 0.00 0.00 2.17
2665 8614 5.422012 TGATTTCCATGAGAGTGTGCTACTA 59.578 40.000 0.00 0.00 40.53 1.82
2666 8615 4.991153 TTCCATGAGAGTGTGCTACTAG 57.009 45.455 0.00 0.00 40.53 2.57
2667 8616 2.690497 TCCATGAGAGTGTGCTACTAGC 59.310 50.000 0.61 0.61 40.53 3.42
2700 8669 4.286297 TGGACTGTTAAGCTACAAGCAT 57.714 40.909 1.22 0.00 45.56 3.79
2755 8724 4.067896 AGCCTGTGAGAAGTGTGTATTTG 58.932 43.478 0.00 0.00 0.00 2.32
2759 8728 6.017440 GCCTGTGAGAAGTGTGTATTTGTTTA 60.017 38.462 0.00 0.00 0.00 2.01
2760 8729 7.352739 CCTGTGAGAAGTGTGTATTTGTTTAC 58.647 38.462 0.00 0.00 0.00 2.01
2763 8732 7.225931 TGTGAGAAGTGTGTATTTGTTTACTCC 59.774 37.037 0.00 0.00 0.00 3.85
2765 8734 7.990886 TGAGAAGTGTGTATTTGTTTACTCCTT 59.009 33.333 0.00 0.00 0.00 3.36
2767 8736 9.185680 AGAAGTGTGTATTTGTTTACTCCTTTT 57.814 29.630 0.00 0.00 0.00 2.27
2768 8737 9.447040 GAAGTGTGTATTTGTTTACTCCTTTTC 57.553 33.333 0.00 0.00 0.00 2.29
2770 8739 9.841295 AGTGTGTATTTGTTTACTCCTTTTCTA 57.159 29.630 0.00 0.00 0.00 2.10
2780 8749 8.680001 TGTTTACTCCTTTTCTAAAGTCAAACC 58.320 33.333 0.00 0.00 0.00 3.27
2781 8750 8.900781 GTTTACTCCTTTTCTAAAGTCAAACCT 58.099 33.333 0.00 0.00 0.00 3.50
2783 8752 6.659824 ACTCCTTTTCTAAAGTCAAACCTCA 58.340 36.000 0.00 0.00 0.00 3.86
2784 8753 7.290813 ACTCCTTTTCTAAAGTCAAACCTCAT 58.709 34.615 0.00 0.00 0.00 2.90
2785 8754 8.437575 ACTCCTTTTCTAAAGTCAAACCTCATA 58.562 33.333 0.00 0.00 0.00 2.15
2786 8755 9.284968 CTCCTTTTCTAAAGTCAAACCTCATAA 57.715 33.333 0.00 0.00 0.00 1.90
2787 8756 9.635404 TCCTTTTCTAAAGTCAAACCTCATAAA 57.365 29.630 0.00 0.00 0.00 1.40
2788 8757 9.899226 CCTTTTCTAAAGTCAAACCTCATAAAG 57.101 33.333 0.00 0.00 0.00 1.85
2852 8821 9.836076 AATGTGAAATCATTATCATTAGATGCG 57.164 29.630 0.00 0.00 36.44 4.73
2853 8822 8.382030 TGTGAAATCATTATCATTAGATGCGT 57.618 30.769 0.00 0.00 35.67 5.24
2854 8823 8.498358 TGTGAAATCATTATCATTAGATGCGTC 58.502 33.333 0.00 0.00 35.67 5.19
2855 8824 7.685712 GTGAAATCATTATCATTAGATGCGTCG 59.314 37.037 0.00 0.00 35.67 5.12
2856 8825 7.384932 TGAAATCATTATCATTAGATGCGTCGT 59.615 33.333 0.00 0.00 35.67 4.34
2857 8826 6.638168 ATCATTATCATTAGATGCGTCGTG 57.362 37.500 0.00 1.72 35.67 4.35
2858 8827 5.768317 TCATTATCATTAGATGCGTCGTGA 58.232 37.500 12.08 12.08 35.67 4.35
2859 8828 5.629435 TCATTATCATTAGATGCGTCGTGAC 59.371 40.000 11.98 0.00 35.67 3.67
2860 8829 3.717400 ATCATTAGATGCGTCGTGACT 57.283 42.857 11.98 0.00 31.91 3.41
2861 8830 3.503827 TCATTAGATGCGTCGTGACTT 57.496 42.857 0.00 0.00 0.00 3.01
2862 8831 4.625972 TCATTAGATGCGTCGTGACTTA 57.374 40.909 0.00 0.00 0.00 2.24
2863 8832 4.989044 TCATTAGATGCGTCGTGACTTAA 58.011 39.130 0.00 0.00 0.00 1.85
2864 8833 5.404096 TCATTAGATGCGTCGTGACTTAAA 58.596 37.500 0.00 0.00 0.00 1.52
2865 8834 6.040247 TCATTAGATGCGTCGTGACTTAAAT 58.960 36.000 0.00 0.00 0.00 1.40
2866 8835 6.533723 TCATTAGATGCGTCGTGACTTAAATT 59.466 34.615 0.00 0.00 0.00 1.82
2867 8836 6.715344 TTAGATGCGTCGTGACTTAAATTT 57.285 33.333 0.00 0.00 0.00 1.82
2868 8837 5.204673 AGATGCGTCGTGACTTAAATTTC 57.795 39.130 0.00 0.00 0.00 2.17
2869 8838 3.799137 TGCGTCGTGACTTAAATTTCC 57.201 42.857 0.00 0.00 0.00 3.13
2870 8839 3.132160 TGCGTCGTGACTTAAATTTCCA 58.868 40.909 0.00 0.00 0.00 3.53
2871 8840 3.749088 TGCGTCGTGACTTAAATTTCCAT 59.251 39.130 0.00 0.00 0.00 3.41
2872 8841 4.930405 TGCGTCGTGACTTAAATTTCCATA 59.070 37.500 0.00 0.00 0.00 2.74
2873 8842 5.583061 TGCGTCGTGACTTAAATTTCCATAT 59.417 36.000 0.00 0.00 0.00 1.78
2874 8843 6.092944 TGCGTCGTGACTTAAATTTCCATATT 59.907 34.615 0.00 0.00 0.00 1.28
2875 8844 6.410914 GCGTCGTGACTTAAATTTCCATATTG 59.589 38.462 0.00 0.00 0.00 1.90
2876 8845 7.461107 CGTCGTGACTTAAATTTCCATATTGT 58.539 34.615 0.00 0.00 0.00 2.71
2877 8846 8.597227 CGTCGTGACTTAAATTTCCATATTGTA 58.403 33.333 0.00 0.00 0.00 2.41
2944 8913 9.773328 TGATCGAAGTTTGATTTCATACAATTC 57.227 29.630 7.06 0.60 31.54 2.17
2945 8914 9.994432 GATCGAAGTTTGATTTCATACAATTCT 57.006 29.630 7.06 0.00 31.54 2.40
3028 9000 4.226803 GCACATGCGGACAACAAC 57.773 55.556 0.00 0.00 0.00 3.32
3033 9005 2.095768 CACATGCGGACAACAACCTTAG 60.096 50.000 0.00 0.00 0.00 2.18
3039 9011 2.416547 CGGACAACAACCTTAGCATGAG 59.583 50.000 0.00 0.00 0.00 2.90
3051 9023 7.681259 ACCTTAGCATGAGCATATGGATATA 57.319 36.000 4.56 0.00 45.49 0.86
3148 9123 1.959282 CAGTTTTCAGCCTTGCTTCCT 59.041 47.619 0.00 0.00 36.40 3.36
3164 9139 0.252103 TCCTGGTACCCTGTCCTGTC 60.252 60.000 10.07 0.00 0.00 3.51
3165 9140 0.544357 CCTGGTACCCTGTCCTGTCA 60.544 60.000 10.07 0.00 0.00 3.58
3166 9141 1.573108 CTGGTACCCTGTCCTGTCAT 58.427 55.000 10.07 0.00 0.00 3.06
3167 9142 1.208052 CTGGTACCCTGTCCTGTCATG 59.792 57.143 10.07 0.00 0.00 3.07
3169 9144 1.628846 GGTACCCTGTCCTGTCATGTT 59.371 52.381 0.00 0.00 0.00 2.71
3170 9145 2.354805 GGTACCCTGTCCTGTCATGTTC 60.355 54.545 0.00 0.00 0.00 3.18
3171 9146 0.693049 ACCCTGTCCTGTCATGTTCC 59.307 55.000 0.00 0.00 0.00 3.62
3172 9147 0.987294 CCCTGTCCTGTCATGTTCCT 59.013 55.000 0.00 0.00 0.00 3.36
3173 9148 1.352352 CCCTGTCCTGTCATGTTCCTT 59.648 52.381 0.00 0.00 0.00 3.36
3174 9149 2.571653 CCCTGTCCTGTCATGTTCCTTA 59.428 50.000 0.00 0.00 0.00 2.69
3175 9150 3.009033 CCCTGTCCTGTCATGTTCCTTAA 59.991 47.826 0.00 0.00 0.00 1.85
3248 9223 5.278604 ACACACGAAAAACTATTTGAAGCC 58.721 37.500 0.00 0.00 0.00 4.35
3249 9224 5.163602 ACACACGAAAAACTATTTGAAGCCA 60.164 36.000 0.00 0.00 0.00 4.75
3335 9313 4.163458 TGACAGCTTATCGTTTCGTACA 57.837 40.909 0.00 0.00 0.00 2.90
3413 9391 1.077169 GAATTTTGGACCACTCCCCCT 59.923 52.381 0.00 0.00 35.34 4.79
3438 10896 7.687941 TTCAATTTCTTTAGATCGGAAAGCT 57.312 32.000 14.84 0.00 34.51 3.74
3534 11000 0.110419 TTGCAATTTCCGAGCGAACG 60.110 50.000 0.00 0.00 0.00 3.95
3540 11006 1.798234 TTTCCGAGCGAACGACCTGA 61.798 55.000 0.00 0.00 35.09 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.241165 CACAACCTCATTGCTGAGCA 58.759 50.000 1.40 1.40 46.39 4.26
30 31 0.524862 CCACAACCTCATTGCTGAGC 59.475 55.000 0.00 0.00 46.39 4.26
32 33 0.770499 TCCCACAACCTCATTGCTGA 59.230 50.000 0.00 0.00 42.62 4.26
33 34 1.171308 CTCCCACAACCTCATTGCTG 58.829 55.000 0.00 0.00 42.62 4.41
34 35 1.067295 TCTCCCACAACCTCATTGCT 58.933 50.000 0.00 0.00 42.62 3.91
35 36 2.134789 ATCTCCCACAACCTCATTGC 57.865 50.000 0.00 0.00 42.62 3.56
36 37 4.080356 TCCTTATCTCCCACAACCTCATTG 60.080 45.833 0.00 0.00 44.60 2.82
37 38 4.111577 TCCTTATCTCCCACAACCTCATT 58.888 43.478 0.00 0.00 0.00 2.57
38 39 3.736094 TCCTTATCTCCCACAACCTCAT 58.264 45.455 0.00 0.00 0.00 2.90
39 40 3.199442 TCCTTATCTCCCACAACCTCA 57.801 47.619 0.00 0.00 0.00 3.86
40 41 3.711704 TCATCCTTATCTCCCACAACCTC 59.288 47.826 0.00 0.00 0.00 3.85
41 42 3.736094 TCATCCTTATCTCCCACAACCT 58.264 45.455 0.00 0.00 0.00 3.50
42 43 4.200092 GTTCATCCTTATCTCCCACAACC 58.800 47.826 0.00 0.00 0.00 3.77
43 44 3.871594 CGTTCATCCTTATCTCCCACAAC 59.128 47.826 0.00 0.00 0.00 3.32
44 45 3.772572 TCGTTCATCCTTATCTCCCACAA 59.227 43.478 0.00 0.00 0.00 3.33
45 46 3.371034 TCGTTCATCCTTATCTCCCACA 58.629 45.455 0.00 0.00 0.00 4.17
46 47 3.243907 CCTCGTTCATCCTTATCTCCCAC 60.244 52.174 0.00 0.00 0.00 4.61
47 48 2.965831 CCTCGTTCATCCTTATCTCCCA 59.034 50.000 0.00 0.00 0.00 4.37
48 49 2.289133 GCCTCGTTCATCCTTATCTCCC 60.289 54.545 0.00 0.00 0.00 4.30
49 50 2.365617 TGCCTCGTTCATCCTTATCTCC 59.634 50.000 0.00 0.00 0.00 3.71
50 51 3.735237 TGCCTCGTTCATCCTTATCTC 57.265 47.619 0.00 0.00 0.00 2.75
51 52 3.181461 CCTTGCCTCGTTCATCCTTATCT 60.181 47.826 0.00 0.00 0.00 1.98
52 53 3.134458 CCTTGCCTCGTTCATCCTTATC 58.866 50.000 0.00 0.00 0.00 1.75
53 54 2.746472 GCCTTGCCTCGTTCATCCTTAT 60.746 50.000 0.00 0.00 0.00 1.73
54 55 1.406887 GCCTTGCCTCGTTCATCCTTA 60.407 52.381 0.00 0.00 0.00 2.69
55 56 0.678048 GCCTTGCCTCGTTCATCCTT 60.678 55.000 0.00 0.00 0.00 3.36
56 57 1.078143 GCCTTGCCTCGTTCATCCT 60.078 57.895 0.00 0.00 0.00 3.24
57 58 2.115291 GGCCTTGCCTCGTTCATCC 61.115 63.158 0.00 0.00 46.69 3.51
58 59 3.502572 GGCCTTGCCTCGTTCATC 58.497 61.111 0.00 0.00 46.69 2.92
68 69 4.202050 CCACATTTACAGATAAGGCCTTGC 60.202 45.833 28.77 19.04 0.00 4.01
69 70 5.192927 TCCACATTTACAGATAAGGCCTTG 58.807 41.667 28.77 14.69 0.00 3.61
70 71 5.191722 TCTCCACATTTACAGATAAGGCCTT 59.808 40.000 24.18 24.18 0.00 4.35
71 72 4.721776 TCTCCACATTTACAGATAAGGCCT 59.278 41.667 0.00 0.00 0.00 5.19
72 73 5.036117 TCTCCACATTTACAGATAAGGCC 57.964 43.478 0.00 0.00 0.00 5.19
73 74 5.918608 TCTCTCCACATTTACAGATAAGGC 58.081 41.667 0.00 0.00 0.00 4.35
74 75 6.098982 ACCTCTCTCCACATTTACAGATAAGG 59.901 42.308 0.00 0.00 0.00 2.69
75 76 6.983307 CACCTCTCTCCACATTTACAGATAAG 59.017 42.308 0.00 0.00 0.00 1.73
76 77 6.630413 GCACCTCTCTCCACATTTACAGATAA 60.630 42.308 0.00 0.00 0.00 1.75
77 78 5.163405 GCACCTCTCTCCACATTTACAGATA 60.163 44.000 0.00 0.00 0.00 1.98
78 79 4.383552 GCACCTCTCTCCACATTTACAGAT 60.384 45.833 0.00 0.00 0.00 2.90
79 80 3.055819 GCACCTCTCTCCACATTTACAGA 60.056 47.826 0.00 0.00 0.00 3.41
80 81 3.265791 GCACCTCTCTCCACATTTACAG 58.734 50.000 0.00 0.00 0.00 2.74
81 82 2.353704 CGCACCTCTCTCCACATTTACA 60.354 50.000 0.00 0.00 0.00 2.41
82 83 2.271800 CGCACCTCTCTCCACATTTAC 58.728 52.381 0.00 0.00 0.00 2.01
83 84 1.207089 CCGCACCTCTCTCCACATTTA 59.793 52.381 0.00 0.00 0.00 1.40
84 85 0.036010 CCGCACCTCTCTCCACATTT 60.036 55.000 0.00 0.00 0.00 2.32
85 86 1.194781 ACCGCACCTCTCTCCACATT 61.195 55.000 0.00 0.00 0.00 2.71
86 87 1.194781 AACCGCACCTCTCTCCACAT 61.195 55.000 0.00 0.00 0.00 3.21
87 88 1.407656 AAACCGCACCTCTCTCCACA 61.408 55.000 0.00 0.00 0.00 4.17
88 89 0.250338 AAAACCGCACCTCTCTCCAC 60.250 55.000 0.00 0.00 0.00 4.02
89 90 0.472471 AAAAACCGCACCTCTCTCCA 59.528 50.000 0.00 0.00 0.00 3.86
90 91 3.324207 AAAAACCGCACCTCTCTCC 57.676 52.632 0.00 0.00 0.00 3.71
116 117 9.886132 ACGGATAGAAAGTAAACTATGACAATT 57.114 29.630 0.00 0.00 30.74 2.32
117 118 9.530633 GACGGATAGAAAGTAAACTATGACAAT 57.469 33.333 0.00 0.00 30.74 2.71
118 119 8.525316 TGACGGATAGAAAGTAAACTATGACAA 58.475 33.333 0.00 0.00 30.74 3.18
119 120 8.058667 TGACGGATAGAAAGTAAACTATGACA 57.941 34.615 0.00 0.00 30.74 3.58
120 121 8.404000 TCTGACGGATAGAAAGTAAACTATGAC 58.596 37.037 0.00 0.00 30.74 3.06
121 122 8.515695 TCTGACGGATAGAAAGTAAACTATGA 57.484 34.615 0.00 0.00 30.74 2.15
129 130 9.616156 GGATCTATATCTGACGGATAGAAAGTA 57.384 37.037 9.78 0.00 39.89 2.24
130 131 8.333235 AGGATCTATATCTGACGGATAGAAAGT 58.667 37.037 9.78 0.00 39.89 2.66
131 132 8.746052 AGGATCTATATCTGACGGATAGAAAG 57.254 38.462 9.78 7.25 39.89 2.62
149 150 9.094578 GCCTGCCATCTTATAATATAGGATCTA 57.905 37.037 2.38 0.00 0.00 1.98
150 151 7.570232 TGCCTGCCATCTTATAATATAGGATCT 59.430 37.037 2.38 0.00 0.00 2.75
151 152 7.659390 GTGCCTGCCATCTTATAATATAGGATC 59.341 40.741 2.38 0.00 0.00 3.36
152 153 7.127801 TGTGCCTGCCATCTTATAATATAGGAT 59.872 37.037 0.00 0.00 0.00 3.24
153 154 6.443527 TGTGCCTGCCATCTTATAATATAGGA 59.556 38.462 0.00 0.00 0.00 2.94
154 155 6.540189 GTGTGCCTGCCATCTTATAATATAGG 59.460 42.308 0.00 0.00 0.00 2.57
155 156 6.540189 GGTGTGCCTGCCATCTTATAATATAG 59.460 42.308 0.00 0.00 0.00 1.31
156 157 6.012945 TGGTGTGCCTGCCATCTTATAATATA 60.013 38.462 0.00 0.00 35.27 0.86
157 158 5.222109 TGGTGTGCCTGCCATCTTATAATAT 60.222 40.000 0.00 0.00 35.27 1.28
158 159 4.103943 TGGTGTGCCTGCCATCTTATAATA 59.896 41.667 0.00 0.00 35.27 0.98
159 160 3.117550 TGGTGTGCCTGCCATCTTATAAT 60.118 43.478 0.00 0.00 35.27 1.28
160 161 2.240921 TGGTGTGCCTGCCATCTTATAA 59.759 45.455 0.00 0.00 35.27 0.98
161 162 1.843206 TGGTGTGCCTGCCATCTTATA 59.157 47.619 0.00 0.00 35.27 0.98
162 163 0.625316 TGGTGTGCCTGCCATCTTAT 59.375 50.000 0.00 0.00 35.27 1.73
163 164 0.625316 ATGGTGTGCCTGCCATCTTA 59.375 50.000 0.00 0.00 41.24 2.10
164 165 0.251922 AATGGTGTGCCTGCCATCTT 60.252 50.000 3.93 0.00 44.03 2.40
165 166 0.625316 TAATGGTGTGCCTGCCATCT 59.375 50.000 3.93 0.00 44.03 2.90
166 167 1.610522 GATAATGGTGTGCCTGCCATC 59.389 52.381 3.93 0.00 44.03 3.51
167 168 1.063792 TGATAATGGTGTGCCTGCCAT 60.064 47.619 0.00 0.00 46.51 4.40
168 169 0.330941 TGATAATGGTGTGCCTGCCA 59.669 50.000 0.00 0.00 39.33 4.92
169 170 0.740737 GTGATAATGGTGTGCCTGCC 59.259 55.000 0.00 0.00 35.27 4.85
170 171 0.740737 GGTGATAATGGTGTGCCTGC 59.259 55.000 0.00 0.00 35.27 4.85
171 172 2.127271 TGGTGATAATGGTGTGCCTG 57.873 50.000 0.00 0.00 35.27 4.85
172 173 2.897271 TTGGTGATAATGGTGTGCCT 57.103 45.000 0.00 0.00 35.27 4.75
173 174 3.489059 CGAATTGGTGATAATGGTGTGCC 60.489 47.826 0.00 0.00 0.00 5.01
174 175 3.489059 CCGAATTGGTGATAATGGTGTGC 60.489 47.826 0.00 0.00 0.00 4.57
175 176 3.944650 TCCGAATTGGTGATAATGGTGTG 59.055 43.478 0.00 0.00 39.52 3.82
176 177 4.229304 TCCGAATTGGTGATAATGGTGT 57.771 40.909 0.00 0.00 39.52 4.16
177 178 5.772825 AATCCGAATTGGTGATAATGGTG 57.227 39.130 0.00 0.00 39.52 4.17
178 179 6.790232 AAAATCCGAATTGGTGATAATGGT 57.210 33.333 0.00 0.00 39.52 3.55
184 185 9.408648 ACTCTTATAAAAATCCGAATTGGTGAT 57.591 29.630 0.00 0.00 39.52 3.06
185 186 8.801882 ACTCTTATAAAAATCCGAATTGGTGA 57.198 30.769 0.00 0.00 39.52 4.02
199 200 9.982651 GTGGCATGTATCTCTACTCTTATAAAA 57.017 33.333 0.00 0.00 0.00 1.52
200 201 9.368416 AGTGGCATGTATCTCTACTCTTATAAA 57.632 33.333 0.00 0.00 0.00 1.40
201 202 8.797438 CAGTGGCATGTATCTCTACTCTTATAA 58.203 37.037 0.00 0.00 0.00 0.98
202 203 7.394641 CCAGTGGCATGTATCTCTACTCTTATA 59.605 40.741 0.00 0.00 0.00 0.98
203 204 6.210385 CCAGTGGCATGTATCTCTACTCTTAT 59.790 42.308 0.00 0.00 0.00 1.73
204 205 5.536538 CCAGTGGCATGTATCTCTACTCTTA 59.463 44.000 0.00 0.00 0.00 2.10
205 206 4.343526 CCAGTGGCATGTATCTCTACTCTT 59.656 45.833 0.00 0.00 0.00 2.85
206 207 3.894427 CCAGTGGCATGTATCTCTACTCT 59.106 47.826 0.00 0.00 0.00 3.24
207 208 3.639094 ACCAGTGGCATGTATCTCTACTC 59.361 47.826 9.78 0.00 0.00 2.59
208 209 3.386078 CACCAGTGGCATGTATCTCTACT 59.614 47.826 9.78 0.00 0.00 2.57
209 210 3.133003 ACACCAGTGGCATGTATCTCTAC 59.867 47.826 9.78 0.00 34.19 2.59
210 211 3.374764 ACACCAGTGGCATGTATCTCTA 58.625 45.455 9.78 0.00 34.19 2.43
211 212 2.191400 ACACCAGTGGCATGTATCTCT 58.809 47.619 9.78 0.00 34.19 3.10
212 213 2.698855 ACACCAGTGGCATGTATCTC 57.301 50.000 9.78 0.00 34.19 2.75
213 214 3.107601 ACTACACCAGTGGCATGTATCT 58.892 45.455 9.78 0.00 35.62 1.98
214 215 3.543680 ACTACACCAGTGGCATGTATC 57.456 47.619 9.78 0.00 35.62 2.24
325 888 1.513158 CGCACCTCCTCGACAAGAT 59.487 57.895 0.00 0.00 0.00 2.40
328 891 2.430382 GAACCGCACCTCCTCGACAA 62.430 60.000 0.00 0.00 0.00 3.18
331 894 2.282958 AGAACCGCACCTCCTCGA 60.283 61.111 0.00 0.00 0.00 4.04
391 1509 4.554036 GCCCCTCATCTCCACGGC 62.554 72.222 0.00 0.00 0.00 5.68
393 1511 3.866582 GGGCCCCTCATCTCCACG 61.867 72.222 12.23 0.00 0.00 4.94
395 1513 3.634157 TTCGGGCCCCTCATCTCCA 62.634 63.158 18.66 0.00 0.00 3.86
396 1514 1.921869 TTTTCGGGCCCCTCATCTCC 61.922 60.000 18.66 0.00 0.00 3.71
397 1515 0.748367 GTTTTCGGGCCCCTCATCTC 60.748 60.000 18.66 0.00 0.00 2.75
398 1516 1.303282 GTTTTCGGGCCCCTCATCT 59.697 57.895 18.66 0.00 0.00 2.90
454 1578 2.997315 CCGAGGAGTGGTGGCTGA 60.997 66.667 0.00 0.00 0.00 4.26
466 1590 0.108138 AAAGAAGTCCGATGCCGAGG 60.108 55.000 0.00 0.00 38.22 4.63
495 1619 1.152839 ACACCCAAAACACCTCCGG 60.153 57.895 0.00 0.00 0.00 5.14
537 1661 0.317479 AAGACGCAAACTCTACGCCT 59.683 50.000 0.00 0.00 0.00 5.52
540 1664 1.387084 GCTCAAGACGCAAACTCTACG 59.613 52.381 0.00 0.00 0.00 3.51
545 1669 1.202580 ACTGAGCTCAAGACGCAAACT 60.203 47.619 18.85 0.00 0.00 2.66
563 1687 5.717178 TCTGGCTATTGAAGTCAAGTCTACT 59.283 40.000 0.00 0.00 39.97 2.57
572 1696 2.354199 GCTTGCTCTGGCTATTGAAGTC 59.646 50.000 0.00 0.00 39.59 3.01
573 1697 2.363683 GCTTGCTCTGGCTATTGAAGT 58.636 47.619 0.00 0.00 39.59 3.01
574 1698 1.674962 GGCTTGCTCTGGCTATTGAAG 59.325 52.381 0.00 0.00 39.59 3.02
575 1699 1.683011 GGGCTTGCTCTGGCTATTGAA 60.683 52.381 0.00 0.00 39.59 2.69
576 1700 0.107017 GGGCTTGCTCTGGCTATTGA 60.107 55.000 0.00 0.00 39.59 2.57
577 1701 0.394762 TGGGCTTGCTCTGGCTATTG 60.395 55.000 0.00 0.00 39.59 1.90
585 1709 0.468771 AGCTTTGTTGGGCTTGCTCT 60.469 50.000 0.00 0.00 34.96 4.09
596 1720 2.948979 TCCGTCACATTGAAGCTTTGTT 59.051 40.909 0.00 0.00 0.00 2.83
613 1737 3.432326 GGAGACCAAGAAGCATATTCCGT 60.432 47.826 0.00 0.00 0.00 4.69
673 3582 1.671979 CCGATCCACATTCATGCTGT 58.328 50.000 0.00 0.00 0.00 4.40
676 3585 0.590195 GAGCCGATCCACATTCATGC 59.410 55.000 0.00 0.00 0.00 4.06
685 3594 3.838271 GACAGCCGAGCCGATCCA 61.838 66.667 0.00 0.00 0.00 3.41
688 3597 3.701604 GAACGACAGCCGAGCCGAT 62.702 63.158 0.00 0.00 41.76 4.18
692 3601 4.415332 TCCGAACGACAGCCGAGC 62.415 66.667 0.00 0.00 41.76 5.03
693 3602 2.504244 GTCCGAACGACAGCCGAG 60.504 66.667 0.00 0.00 41.54 4.63
694 3603 3.289062 TGTCCGAACGACAGCCGA 61.289 61.111 0.00 0.00 46.80 5.54
705 3614 1.658114 CCAGAGTGAACGTGTCCGA 59.342 57.895 0.00 0.00 37.88 4.55
708 3617 0.601558 TAGGCCAGAGTGAACGTGTC 59.398 55.000 5.01 0.00 0.00 3.67
726 3635 7.288621 TCTCTCTCTTCAAGCCATATTCATGTA 59.711 37.037 0.00 0.00 0.00 2.29
735 3644 4.906747 AAACTCTCTCTCTTCAAGCCAT 57.093 40.909 0.00 0.00 0.00 4.40
743 3652 8.038351 GCCTGTTATTCTAAAACTCTCTCTCTT 58.962 37.037 0.00 0.00 0.00 2.85
749 3658 4.259850 CGCGCCTGTTATTCTAAAACTCTC 60.260 45.833 0.00 0.00 0.00 3.20
752 3661 3.370061 GTCGCGCCTGTTATTCTAAAACT 59.630 43.478 0.00 0.00 0.00 2.66
753 3662 3.667050 GTCGCGCCTGTTATTCTAAAAC 58.333 45.455 0.00 0.00 0.00 2.43
766 6011 4.436998 CCTTCTTCCGTCGCGCCT 62.437 66.667 0.00 0.00 0.00 5.52
768 6013 4.736896 ACCCTTCTTCCGTCGCGC 62.737 66.667 0.00 0.00 0.00 6.86
802 6110 1.893137 TGCCACGTCAGACTCTTACAT 59.107 47.619 0.00 0.00 0.00 2.29
806 6114 0.315568 GACTGCCACGTCAGACTCTT 59.684 55.000 10.93 0.00 37.51 2.85
824 6132 3.430453 GGGTTTGGATGGTTTCAGATGA 58.570 45.455 0.00 0.00 0.00 2.92
826 6134 2.559705 GGGGGTTTGGATGGTTTCAGAT 60.560 50.000 0.00 0.00 0.00 2.90
856 6164 2.422127 CCGAAATCCCGCAATTTACACT 59.578 45.455 0.00 0.00 0.00 3.55
868 6177 0.880718 GATCCAGCGTCCGAAATCCC 60.881 60.000 0.00 0.00 0.00 3.85
882 6191 0.616371 AAATTGTCCGGACCGATCCA 59.384 50.000 31.19 9.27 46.67 3.41
909 6218 7.786046 TTGGACCAGATACTTTTAGTCTACA 57.214 36.000 0.00 0.00 0.00 2.74
921 6230 2.223340 CGCAAGCATTTGGACCAGATAC 60.223 50.000 0.00 0.00 34.79 2.24
937 6246 1.328680 CCTCACCAAATCGATCGCAAG 59.671 52.381 11.09 0.00 0.00 4.01
981 6290 3.054361 ACCAGTAGCATTTCTGTTAGGGG 60.054 47.826 0.00 0.00 0.00 4.79
988 6297 2.430465 ACTGCACCAGTAGCATTTCTG 58.570 47.619 0.00 0.00 43.46 3.02
1038 6953 2.415893 GCATTCACCCATCTTTCGGTTG 60.416 50.000 0.00 0.00 0.00 3.77
1111 7054 3.348119 AGCAAAGCTTTTAGTAGAGGCC 58.652 45.455 9.53 0.00 33.89 5.19
1535 7478 2.566913 GCGAGTATGAGAGAGGACAGA 58.433 52.381 0.00 0.00 0.00 3.41
1550 7493 3.288308 CTGCTTCCAGTCGGCGAGT 62.288 63.158 11.20 11.78 34.31 4.18
2424 8367 3.245658 ACCGGGCTAGGTATATCATCAGT 60.246 47.826 6.32 0.00 43.89 3.41
2433 8376 1.605738 CGGCTACCGGGCTAGGTAT 60.606 63.158 6.32 0.00 44.88 2.73
2510 8454 9.925545 TCCATGACTAACCTATAGTAGTACAAA 57.074 33.333 2.52 0.00 0.00 2.83
2511 8455 9.925545 TTCCATGACTAACCTATAGTAGTACAA 57.074 33.333 2.52 0.00 0.00 2.41
2512 8456 9.570468 CTTCCATGACTAACCTATAGTAGTACA 57.430 37.037 2.52 4.89 0.00 2.90
2513 8457 9.790344 TCTTCCATGACTAACCTATAGTAGTAC 57.210 37.037 0.00 0.00 0.00 2.73
2531 8478 8.768955 GCAGTACACTATTTATCTTCTTCCATG 58.231 37.037 0.00 0.00 0.00 3.66
2623 8570 5.488262 AATCACTGGGAAATGAAAAAGGG 57.512 39.130 0.00 0.00 0.00 3.95
2636 8585 3.276857 CACTCTCATGGAAATCACTGGG 58.723 50.000 0.00 0.00 0.00 4.45
2665 8614 4.357918 ACAGTCCAAAGTTCATAGTGCT 57.642 40.909 0.00 0.00 0.00 4.40
2666 8615 6.554334 TTAACAGTCCAAAGTTCATAGTGC 57.446 37.500 0.00 0.00 0.00 4.40
2667 8616 6.428159 AGCTTAACAGTCCAAAGTTCATAGTG 59.572 38.462 0.00 0.00 0.00 2.74
2676 8625 4.515191 TGCTTGTAGCTTAACAGTCCAAAG 59.485 41.667 0.00 0.00 42.97 2.77
2755 8724 8.900781 AGGTTTGACTTTAGAAAAGGAGTAAAC 58.099 33.333 4.56 8.51 0.00 2.01
2759 8728 6.659824 TGAGGTTTGACTTTAGAAAAGGAGT 58.340 36.000 4.56 0.00 0.00 3.85
2760 8729 7.751768 ATGAGGTTTGACTTTAGAAAAGGAG 57.248 36.000 4.56 0.00 0.00 3.69
2826 8795 9.836076 CGCATCTAATGATAATGATTTCACATT 57.164 29.630 0.00 0.00 42.17 2.71
2829 8798 7.685712 CGACGCATCTAATGATAATGATTTCAC 59.314 37.037 0.00 0.00 0.00 3.18
2830 8799 7.384932 ACGACGCATCTAATGATAATGATTTCA 59.615 33.333 0.00 0.00 0.00 2.69
2831 8800 7.685712 CACGACGCATCTAATGATAATGATTTC 59.314 37.037 0.00 0.00 0.00 2.17
2832 8801 7.384932 TCACGACGCATCTAATGATAATGATTT 59.615 33.333 0.00 0.00 0.00 2.17
2833 8802 6.868339 TCACGACGCATCTAATGATAATGATT 59.132 34.615 0.00 0.00 0.00 2.57
2834 8803 6.309009 GTCACGACGCATCTAATGATAATGAT 59.691 38.462 0.00 0.00 0.00 2.45
2835 8804 5.629435 GTCACGACGCATCTAATGATAATGA 59.371 40.000 0.00 0.00 0.00 2.57
2836 8805 5.631096 AGTCACGACGCATCTAATGATAATG 59.369 40.000 0.00 0.00 36.20 1.90
2837 8806 5.773575 AGTCACGACGCATCTAATGATAAT 58.226 37.500 0.00 0.00 36.20 1.28
2838 8807 5.183014 AGTCACGACGCATCTAATGATAA 57.817 39.130 0.00 0.00 36.20 1.75
2839 8808 4.830826 AGTCACGACGCATCTAATGATA 57.169 40.909 0.00 0.00 36.20 2.15
2840 8809 3.717400 AGTCACGACGCATCTAATGAT 57.283 42.857 0.00 0.00 36.20 2.45
2841 8810 3.503827 AAGTCACGACGCATCTAATGA 57.496 42.857 0.00 0.00 36.20 2.57
2842 8811 5.696260 TTTAAGTCACGACGCATCTAATG 57.304 39.130 0.00 0.00 36.20 1.90
2843 8812 6.903883 AATTTAAGTCACGACGCATCTAAT 57.096 33.333 0.00 0.00 36.20 1.73
2844 8813 6.183360 GGAAATTTAAGTCACGACGCATCTAA 60.183 38.462 0.00 0.00 36.20 2.10
2845 8814 5.290158 GGAAATTTAAGTCACGACGCATCTA 59.710 40.000 0.00 0.00 36.20 1.98
2846 8815 4.092968 GGAAATTTAAGTCACGACGCATCT 59.907 41.667 0.00 0.00 36.20 2.90
2847 8816 4.142988 TGGAAATTTAAGTCACGACGCATC 60.143 41.667 0.00 0.00 36.20 3.91
2848 8817 3.749088 TGGAAATTTAAGTCACGACGCAT 59.251 39.130 0.00 0.00 36.20 4.73
2849 8818 3.132160 TGGAAATTTAAGTCACGACGCA 58.868 40.909 0.00 0.00 36.20 5.24
2850 8819 3.799137 TGGAAATTTAAGTCACGACGC 57.201 42.857 0.00 0.00 36.20 5.19
2851 8820 7.461107 ACAATATGGAAATTTAAGTCACGACG 58.539 34.615 0.00 0.00 36.20 5.12
2918 8887 9.773328 GAATTGTATGAAATCAAACTTCGATCA 57.227 29.630 0.00 0.00 0.00 2.92
2919 8888 9.994432 AGAATTGTATGAAATCAAACTTCGATC 57.006 29.630 0.00 0.00 0.00 3.69
2960 8929 2.200373 ATACTCCTGCGGTGCTTTTT 57.800 45.000 0.00 0.00 0.00 1.94
2961 8930 2.200373 AATACTCCTGCGGTGCTTTT 57.800 45.000 0.00 0.00 0.00 2.27
2962 8931 2.200373 AAATACTCCTGCGGTGCTTT 57.800 45.000 0.00 0.00 0.00 3.51
2963 8932 2.200373 AAAATACTCCTGCGGTGCTT 57.800 45.000 0.00 0.00 0.00 3.91
2964 8933 3.007635 GTTAAAATACTCCTGCGGTGCT 58.992 45.455 0.00 0.00 0.00 4.40
2965 8934 3.007635 AGTTAAAATACTCCTGCGGTGC 58.992 45.455 0.00 0.00 0.00 5.01
2966 8935 3.306166 CGAGTTAAAATACTCCTGCGGTG 59.694 47.826 0.00 0.00 41.18 4.94
2967 8936 3.056322 ACGAGTTAAAATACTCCTGCGGT 60.056 43.478 0.00 0.00 41.18 5.68
2968 8937 3.306166 CACGAGTTAAAATACTCCTGCGG 59.694 47.826 0.00 0.00 41.18 5.69
2969 8938 4.171005 TCACGAGTTAAAATACTCCTGCG 58.829 43.478 0.00 0.00 41.18 5.18
2970 8939 6.663944 AATCACGAGTTAAAATACTCCTGC 57.336 37.500 0.00 0.00 41.18 4.85
2971 8940 6.961554 GCAAATCACGAGTTAAAATACTCCTG 59.038 38.462 0.00 0.00 41.18 3.86
2972 8941 6.879458 AGCAAATCACGAGTTAAAATACTCCT 59.121 34.615 0.00 0.00 41.18 3.69
2973 8942 7.073342 AGCAAATCACGAGTTAAAATACTCC 57.927 36.000 0.00 0.00 41.18 3.85
2974 8943 7.180748 GGAGCAAATCACGAGTTAAAATACTC 58.819 38.462 0.00 0.00 40.90 2.59
2975 8944 6.093633 GGGAGCAAATCACGAGTTAAAATACT 59.906 38.462 0.00 0.00 0.00 2.12
2976 8945 6.255950 GGGAGCAAATCACGAGTTAAAATAC 58.744 40.000 0.00 0.00 0.00 1.89
2977 8946 6.431198 GGGAGCAAATCACGAGTTAAAATA 57.569 37.500 0.00 0.00 0.00 1.40
2978 8947 5.310720 GGGAGCAAATCACGAGTTAAAAT 57.689 39.130 0.00 0.00 0.00 1.82
3007 8976 2.027073 GTTGTCCGCATGTGCTCGA 61.027 57.895 0.00 0.00 39.32 4.04
3019 8991 2.162408 GCTCATGCTAAGGTTGTTGTCC 59.838 50.000 0.00 0.00 36.03 4.02
3033 9005 9.293404 ACCATTATTATATCCATATGCTCATGC 57.707 33.333 0.00 0.00 40.20 4.06
3051 9023 9.391006 ACGAGTTTACATGTTCATACCATTATT 57.609 29.630 2.30 0.00 0.00 1.40
3066 9040 4.875536 TGATTATGCAGCACGAGTTTACAT 59.124 37.500 0.00 0.00 0.00 2.29
3164 9139 4.202101 TGCTGTGTTGGTTTAAGGAACATG 60.202 41.667 0.00 0.00 40.13 3.21
3165 9140 3.957497 TGCTGTGTTGGTTTAAGGAACAT 59.043 39.130 0.00 0.00 40.13 2.71
3166 9141 3.129638 GTGCTGTGTTGGTTTAAGGAACA 59.870 43.478 0.00 0.00 40.13 3.18
3167 9142 3.129638 TGTGCTGTGTTGGTTTAAGGAAC 59.870 43.478 0.00 0.00 37.53 3.62
3169 9144 2.948979 CTGTGCTGTGTTGGTTTAAGGA 59.051 45.455 0.00 0.00 0.00 3.36
3170 9145 2.687935 ACTGTGCTGTGTTGGTTTAAGG 59.312 45.455 0.00 0.00 0.00 2.69
3171 9146 5.270853 GTTACTGTGCTGTGTTGGTTTAAG 58.729 41.667 0.00 0.00 0.00 1.85
3172 9147 4.096682 GGTTACTGTGCTGTGTTGGTTTAA 59.903 41.667 0.00 0.00 0.00 1.52
3173 9148 3.628487 GGTTACTGTGCTGTGTTGGTTTA 59.372 43.478 0.00 0.00 0.00 2.01
3174 9149 2.425668 GGTTACTGTGCTGTGTTGGTTT 59.574 45.455 0.00 0.00 0.00 3.27
3175 9150 2.021457 GGTTACTGTGCTGTGTTGGTT 58.979 47.619 0.00 0.00 0.00 3.67
3248 9223 0.247460 TGCCGTCTGACCATCTCTTG 59.753 55.000 1.55 0.00 0.00 3.02
3249 9224 0.247736 GTGCCGTCTGACCATCTCTT 59.752 55.000 1.55 0.00 0.00 2.85
3264 9239 3.982241 GGGCTGTGCACTTGTGCC 61.982 66.667 24.68 24.68 42.56 5.01
3294 9269 5.245075 TGTCAAAGTTCACCAAAGGAAAAGT 59.755 36.000 0.00 0.00 0.00 2.66
3295 9270 5.719173 TGTCAAAGTTCACCAAAGGAAAAG 58.281 37.500 0.00 0.00 0.00 2.27
3335 9313 3.578716 TGAGCTGGTAGTAAAGAGCAGTT 59.421 43.478 0.00 0.00 42.98 3.16
3413 9391 8.110860 AGCTTTCCGATCTAAAGAAATTGAAA 57.889 30.769 17.11 0.00 36.27 2.69
3438 10896 2.829720 ACGGTACTGTTCAAGATGCCTA 59.170 45.455 0.04 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.