Multiple sequence alignment - TraesCS2D01G063000

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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 TraesCS2D01G063000 chr2D 100.000 3114 0 0 1 3114 27061401 27064514 0.000000e+00 5751.0
1 TraesCS2D01G063000 chr2A 85.926 1755 166 49 1335 3050 29262114 29263826 0.000000e+00 1797.0
2 TraesCS2D01G063000 chr2A 89.826 747 40 12 562 1278 29261357 29262097 0.000000e+00 926.0
3 TraesCS2D01G063000 chr2A 84.024 507 39 16 24 506 29257172 29257660 1.700000e-122 449.0
4 TraesCS2D01G063000 chr2B 89.938 805 33 14 1359 2123 42264388 42265184 0.000000e+00 994.0
5 TraesCS2D01G063000 chr2B 89.985 659 35 8 365 1021 42263159 42263788 0.000000e+00 822.0
6 TraesCS2D01G063000 chr2B 84.228 596 41 15 144 713 42238662 42239230 5.910000e-147 531.0
7 TraesCS2D01G063000 chr2B 85.907 518 45 18 2160 2673 42265193 42265686 7.650000e-146 527.0
8 TraesCS2D01G063000 chr2B 86.181 398 30 13 2660 3052 42265704 42266081 1.040000e-109 407.0
9 TraesCS2D01G063000 chr2B 98.810 168 2 0 1102 1269 42264173 42264340 1.820000e-77 300.0
10 TraesCS2D01G063000 chr2B 77.577 388 52 9 1 369 42261966 42262337 5.270000e-48 202.0
11 TraesCS2D01G063000 chr6B 82.222 135 18 3 1106 1234 38971328 38971462 9.130000e-21 111.0
12 TraesCS2D01G063000 chr6D 81.618 136 19 3 1105 1234 24029265 24029400 1.180000e-19 108.0
13 TraesCS2D01G063000 chr7D 94.340 53 3 0 1188 1240 490881599 490881547 7.160000e-12 82.4
14 TraesCS2D01G063000 chr7B 94.340 53 3 0 1188 1240 519524386 519524334 7.160000e-12 82.4
15 TraesCS2D01G063000 chr7A 92.453 53 4 0 1188 1240 556921225 556921173 3.330000e-10 76.8


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 TraesCS2D01G063000 chr2D 27061401 27064514 3113 False 5751.000000 5751 100.000000 1 3114 1 chr2D.!!$F1 3113
1 TraesCS2D01G063000 chr2A 29257172 29263826 6654 False 1057.333333 1797 86.592000 24 3050 3 chr2A.!!$F1 3026
2 TraesCS2D01G063000 chr2B 42261966 42266081 4115 False 542.000000 994 88.066333 1 3052 6 chr2B.!!$F2 3051
3 TraesCS2D01G063000 chr2B 42238662 42239230 568 False 531.000000 531 84.228000 144 713 1 chr2B.!!$F1 569

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
324 355 0.388520 GAATCCACAACGCCAAAGCC 60.389 55.0 0.00 0.00 34.57 4.35 F
1281 6146 0.039911 AAGGTACCCTCGAGCTCTGT 59.960 55.0 12.85 6.25 30.89 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 6332 0.102120 CTCACGCCTGCAAAACCAAA 59.898 50.0 0.0 0.0 0.0 3.28 R
3077 8045 0.032267 TGTTGTGTGCGTATCGTCCA 59.968 50.0 0.0 0.0 0.0 4.02 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
20 21 2.695314 GCGTTGGAGATGCCCTTAG 58.305 57.895 0.00 0.00 34.03 2.18
22 23 1.138266 GCGTTGGAGATGCCCTTAGTA 59.862 52.381 0.00 0.00 34.03 1.82
26 27 4.202264 CGTTGGAGATGCCCTTAGTAAGAT 60.202 45.833 11.66 0.00 34.97 2.40
31 32 5.163195 GGAGATGCCCTTAGTAAGATTGGAA 60.163 44.000 11.66 0.00 0.00 3.53
43 44 6.183347 AGTAAGATTGGAAGACCCTGATTTG 58.817 40.000 0.00 0.00 35.38 2.32
47 48 4.935352 TTGGAAGACCCTGATTTGTTTG 57.065 40.909 0.00 0.00 35.38 2.93
54 56 5.660460 AGACCCTGATTTGTTTGTTTCAAC 58.340 37.500 0.00 0.00 0.00 3.18
69 71 6.175712 TGTTTCAACATTTCAGCCAAAAAC 57.824 33.333 0.00 0.00 33.17 2.43
73 75 5.240891 TCAACATTTCAGCCAAAAACAACA 58.759 33.333 0.00 0.00 0.00 3.33
80 82 5.843673 TCAGCCAAAAACAACAATAGACA 57.156 34.783 0.00 0.00 0.00 3.41
103 107 9.123709 GACAGAAATTTAACAAAATCGCATACA 57.876 29.630 0.00 0.00 0.00 2.29
123 127 7.642669 CATACATTTCTCGGTGCTATCATTTT 58.357 34.615 0.00 0.00 0.00 1.82
154 158 5.455056 ACTCGGTTATATCAGGATCACAC 57.545 43.478 0.00 0.00 0.00 3.82
156 160 4.219919 TCGGTTATATCAGGATCACACCA 58.780 43.478 0.00 0.00 0.00 4.17
164 168 3.096852 TCAGGATCACACCAATAGTCGT 58.903 45.455 0.00 0.00 0.00 4.34
169 173 2.937591 TCACACCAATAGTCGTCGAAC 58.062 47.619 0.00 0.00 0.00 3.95
251 272 1.603455 CAAACCCACACGAGCCCAT 60.603 57.895 0.00 0.00 0.00 4.00
252 273 1.303317 AAACCCACACGAGCCCATC 60.303 57.895 0.00 0.00 0.00 3.51
324 355 0.388520 GAATCCACAACGCCAAAGCC 60.389 55.000 0.00 0.00 34.57 4.35
335 366 2.332654 CCAAAGCCGTGCCACCTAC 61.333 63.158 0.00 0.00 0.00 3.18
357 388 3.403057 CGACACGTCGCCACCAAG 61.403 66.667 6.65 0.00 46.50 3.61
358 389 3.041940 GACACGTCGCCACCAAGG 61.042 66.667 0.00 0.00 41.84 3.61
360 391 3.041940 CACGTCGCCACCAAGGAC 61.042 66.667 0.00 0.00 41.22 3.85
363 394 3.998672 GTCGCCACCAAGGACGGA 61.999 66.667 0.00 0.00 41.22 4.69
375 1241 0.687757 AGGACGGATAAGGAGCAGCA 60.688 55.000 0.00 0.00 0.00 4.41
394 1260 1.040339 AGCGGTGAGGAGAGACATCC 61.040 60.000 0.00 0.00 39.89 3.51
509 1380 1.918293 ATGAACAGTCCGAGCCCCA 60.918 57.895 0.00 0.00 0.00 4.96
544 5075 0.731514 CGGAGTTTCTGCGCGACTTA 60.732 55.000 12.10 0.00 38.60 2.24
545 5076 1.425412 GGAGTTTCTGCGCGACTTAA 58.575 50.000 12.10 0.00 0.00 1.85
546 5077 1.390463 GGAGTTTCTGCGCGACTTAAG 59.610 52.381 12.10 0.00 0.00 1.85
547 5078 2.059541 GAGTTTCTGCGCGACTTAAGT 58.940 47.619 12.10 8.13 0.00 2.24
548 5079 2.475487 GAGTTTCTGCGCGACTTAAGTT 59.525 45.455 12.10 0.00 0.00 2.66
549 5080 2.221055 AGTTTCTGCGCGACTTAAGTTG 59.779 45.455 17.30 17.30 0.00 3.16
556 5087 2.159181 CGACTTAAGTTGCCGGTGG 58.841 57.895 10.02 0.00 0.00 4.61
557 5088 0.601841 CGACTTAAGTTGCCGGTGGT 60.602 55.000 10.02 0.00 0.00 4.16
687 5219 1.082756 GCGCACGAAAAGTCAGTGG 60.083 57.895 0.30 0.00 36.48 4.00
761 5293 1.079543 GTCACCATCGCTGCTCAGT 60.080 57.895 0.00 0.00 0.00 3.41
970 5502 2.506962 CCCGGGCGCCTATAAACA 59.493 61.111 28.56 0.00 0.00 2.83
972 5504 2.241880 CCGGGCGCCTATAAACACG 61.242 63.158 28.56 18.21 0.00 4.49
1041 5574 3.755434 GCAACCAGCAGTGCTTCT 58.245 55.556 16.89 0.00 44.79 2.85
1042 5575 1.578423 GCAACCAGCAGTGCTTCTC 59.422 57.895 16.89 0.00 44.79 2.87
1043 5576 0.888285 GCAACCAGCAGTGCTTCTCT 60.888 55.000 16.89 0.00 44.79 3.10
1047 5580 1.694150 ACCAGCAGTGCTTCTCTACAA 59.306 47.619 16.89 0.00 36.40 2.41
1084 5617 2.028748 CCAGCTGAACAATTTCTTGGGG 60.029 50.000 17.39 0.00 36.64 4.96
1088 5621 3.862264 GCTGAACAATTTCTTGGGGCTTC 60.862 47.826 0.00 0.00 36.64 3.86
1099 5939 0.260230 TGGGGCTTCGAGAGAGAGAT 59.740 55.000 0.00 0.00 43.69 2.75
1100 5940 0.958822 GGGGCTTCGAGAGAGAGATC 59.041 60.000 0.00 0.00 43.69 2.75
1270 6135 1.203052 TCGACGACATGAAAGGTACCC 59.797 52.381 8.74 0.00 0.00 3.69
1273 6138 1.203994 ACGACATGAAAGGTACCCTCG 59.796 52.381 8.74 6.35 30.89 4.63
1275 6140 2.479730 CGACATGAAAGGTACCCTCGAG 60.480 54.545 8.74 5.13 30.89 4.04
1276 6141 1.207329 ACATGAAAGGTACCCTCGAGC 59.793 52.381 8.74 0.00 30.89 5.03
1277 6142 1.482593 CATGAAAGGTACCCTCGAGCT 59.517 52.381 8.74 0.00 30.89 4.09
1278 6143 1.183549 TGAAAGGTACCCTCGAGCTC 58.816 55.000 8.74 2.73 30.89 4.09
1280 6145 1.135333 GAAAGGTACCCTCGAGCTCTG 59.865 57.143 12.85 5.69 30.89 3.35
1281 6146 0.039911 AAGGTACCCTCGAGCTCTGT 59.960 55.000 12.85 6.25 30.89 3.41
1287 6152 0.610687 CCCTCGAGCTCTGTTCCTTT 59.389 55.000 12.85 0.00 0.00 3.11
1289 6154 1.404851 CCTCGAGCTCTGTTCCTTTCC 60.405 57.143 12.85 0.00 0.00 3.13
1290 6155 1.548269 CTCGAGCTCTGTTCCTTTCCT 59.452 52.381 12.85 0.00 0.00 3.36
1292 6157 1.548269 CGAGCTCTGTTCCTTTCCTCT 59.452 52.381 12.85 0.00 0.00 3.69
1293 6158 2.755655 CGAGCTCTGTTCCTTTCCTCTA 59.244 50.000 12.85 0.00 0.00 2.43
1294 6159 3.181491 CGAGCTCTGTTCCTTTCCTCTAG 60.181 52.174 12.85 0.00 0.00 2.43
1296 6161 4.421131 AGCTCTGTTCCTTTCCTCTAGAA 58.579 43.478 0.00 0.00 0.00 2.10
1297 6162 4.841246 AGCTCTGTTCCTTTCCTCTAGAAA 59.159 41.667 0.00 0.00 42.28 2.52
1314 6179 9.927668 CCTCTAGAAAGATTAGATTGATTCTCC 57.072 37.037 0.00 0.00 35.79 3.71
1317 6182 9.487790 CTAGAAAGATTAGATTGATTCTCCACC 57.512 37.037 0.00 0.00 35.79 4.61
1318 6183 7.865820 AGAAAGATTAGATTGATTCTCCACCA 58.134 34.615 0.00 0.00 35.79 4.17
1319 6184 7.772757 AGAAAGATTAGATTGATTCTCCACCAC 59.227 37.037 0.00 0.00 35.79 4.16
1320 6185 5.934781 AGATTAGATTGATTCTCCACCACC 58.065 41.667 0.00 0.00 35.79 4.61
1321 6186 2.698855 AGATTGATTCTCCACCACCG 57.301 50.000 0.00 0.00 0.00 4.94
1322 6187 2.187958 AGATTGATTCTCCACCACCGA 58.812 47.619 0.00 0.00 0.00 4.69
1323 6188 2.093447 AGATTGATTCTCCACCACCGAC 60.093 50.000 0.00 0.00 0.00 4.79
1324 6189 0.323629 TTGATTCTCCACCACCGACC 59.676 55.000 0.00 0.00 0.00 4.79
1325 6190 0.834261 TGATTCTCCACCACCGACCA 60.834 55.000 0.00 0.00 0.00 4.02
1326 6191 0.391263 GATTCTCCACCACCGACCAC 60.391 60.000 0.00 0.00 0.00 4.16
1327 6192 1.838073 ATTCTCCACCACCGACCACC 61.838 60.000 0.00 0.00 0.00 4.61
1328 6193 3.238497 CTCCACCACCGACCACCA 61.238 66.667 0.00 0.00 0.00 4.17
1329 6194 3.238497 TCCACCACCGACCACCAG 61.238 66.667 0.00 0.00 0.00 4.00
1330 6195 3.238497 CCACCACCGACCACCAGA 61.238 66.667 0.00 0.00 0.00 3.86
1331 6196 2.343758 CACCACCGACCACCAGAG 59.656 66.667 0.00 0.00 0.00 3.35
1332 6197 2.923035 ACCACCGACCACCAGAGG 60.923 66.667 0.00 0.00 0.00 3.69
1333 6198 3.706373 CCACCGACCACCAGAGGG 61.706 72.222 0.00 0.00 41.29 4.30
1334 6199 2.603473 CACCGACCACCAGAGGGA 60.603 66.667 0.00 0.00 38.05 4.20
1335 6200 1.990060 CACCGACCACCAGAGGGAT 60.990 63.158 0.00 0.00 38.05 3.85
1336 6201 1.686110 ACCGACCACCAGAGGGATC 60.686 63.158 0.00 0.00 38.05 3.36
1337 6202 2.786495 CCGACCACCAGAGGGATCG 61.786 68.421 0.00 0.00 38.05 3.69
1338 6203 2.786495 CGACCACCAGAGGGATCGG 61.786 68.421 0.00 0.00 38.05 4.18
1339 6204 1.381327 GACCACCAGAGGGATCGGA 60.381 63.158 0.00 0.00 38.05 4.55
1340 6205 0.760945 GACCACCAGAGGGATCGGAT 60.761 60.000 0.00 0.00 38.05 4.18
1341 6206 0.326618 ACCACCAGAGGGATCGGATT 60.327 55.000 0.00 0.00 38.05 3.01
1342 6207 0.394565 CCACCAGAGGGATCGGATTC 59.605 60.000 0.00 0.00 38.05 2.52
1343 6208 0.394565 CACCAGAGGGATCGGATTCC 59.605 60.000 7.27 7.27 38.05 3.01
1351 6216 0.178918 GGATCGGATTCCTCCTCCCT 60.179 60.000 0.30 0.00 39.65 4.20
1352 6217 0.972883 GATCGGATTCCTCCTCCCTG 59.027 60.000 0.30 0.00 39.65 4.45
1354 6219 0.397254 TCGGATTCCTCCTCCCTGAC 60.397 60.000 0.30 0.00 39.65 3.51
1356 6221 1.057275 GGATTCCTCCTCCCTGACCC 61.057 65.000 0.00 0.00 38.65 4.46
1357 6222 0.326618 GATTCCTCCTCCCTGACCCA 60.327 60.000 0.00 0.00 0.00 4.51
1374 6239 1.747355 CCCAGCACATGTTTCTCCATC 59.253 52.381 0.00 0.00 0.00 3.51
1377 6242 0.734889 GCACATGTTTCTCCATCGGG 59.265 55.000 0.00 0.00 0.00 5.14
1401 6271 2.121538 GGAAATCTTGCCCCGGCTC 61.122 63.158 7.35 0.00 42.51 4.70
1458 6329 3.429085 CTTTGCTCAAAGTGTGTGTGTC 58.571 45.455 12.81 0.00 42.02 3.67
1459 6330 1.378531 TGCTCAAAGTGTGTGTGTCC 58.621 50.000 0.00 0.00 0.00 4.02
1460 6331 1.339535 TGCTCAAAGTGTGTGTGTCCA 60.340 47.619 0.00 0.00 0.00 4.02
1461 6332 1.949525 GCTCAAAGTGTGTGTGTCCAT 59.050 47.619 0.00 0.00 0.00 3.41
1468 6341 3.096092 AGTGTGTGTGTCCATTTGGTTT 58.904 40.909 0.00 0.00 36.34 3.27
1793 6666 5.430886 TGCTCCGTCATGTAGTAGTAGTAA 58.569 41.667 0.00 0.00 0.00 2.24
1795 6668 6.017357 TGCTCCGTCATGTAGTAGTAGTAATG 60.017 42.308 0.00 0.00 0.00 1.90
1796 6669 6.017275 GCTCCGTCATGTAGTAGTAGTAATGT 60.017 42.308 0.00 0.00 0.00 2.71
1798 6671 8.284945 TCCGTCATGTAGTAGTAGTAATGTTT 57.715 34.615 0.00 0.00 0.00 2.83
1799 6672 8.186163 TCCGTCATGTAGTAGTAGTAATGTTTG 58.814 37.037 0.00 0.00 0.00 2.93
1829 6731 2.036387 GAGACCTTCTCTAGCTTCCCC 58.964 57.143 0.00 0.00 40.30 4.81
1838 6740 2.362329 CTAGCTTCCCCGCTCTGCTC 62.362 65.000 0.00 0.00 41.30 4.26
1844 6746 3.767806 CCCGCTCTGCTCTGCTCA 61.768 66.667 0.00 0.00 0.00 4.26
1848 6750 1.521141 GCTCTGCTCTGCTCATCCA 59.479 57.895 0.00 0.00 0.00 3.41
1849 6751 0.107081 GCTCTGCTCTGCTCATCCAT 59.893 55.000 0.00 0.00 0.00 3.41
1852 6754 1.153025 TGCTCTGCTCATCCATGGC 60.153 57.895 6.96 0.00 0.00 4.40
1858 6760 2.514592 CTCATCCATGGCGGCGTT 60.515 61.111 6.96 0.00 33.14 4.84
1859 6761 2.823593 TCATCCATGGCGGCGTTG 60.824 61.111 6.96 2.44 33.14 4.10
1860 6762 3.133464 CATCCATGGCGGCGTTGT 61.133 61.111 6.96 0.00 33.14 3.32
1881 6783 2.959030 TGTTGGGATCTCTAGATGGTCG 59.041 50.000 0.00 0.00 34.37 4.79
1893 6795 0.517316 GATGGTCGCTGTTGGTGTTC 59.483 55.000 0.00 0.00 0.00 3.18
1914 6819 8.336080 GTGTTCTCTTGTACTTTTGAAACTAGG 58.664 37.037 0.00 0.00 0.00 3.02
1956 6861 3.482436 TGTATTCTTGCTTCGGTTTGGT 58.518 40.909 0.00 0.00 0.00 3.67
1957 6862 3.886505 TGTATTCTTGCTTCGGTTTGGTT 59.113 39.130 0.00 0.00 0.00 3.67
1958 6863 4.339814 TGTATTCTTGCTTCGGTTTGGTTT 59.660 37.500 0.00 0.00 0.00 3.27
1959 6864 5.531659 TGTATTCTTGCTTCGGTTTGGTTTA 59.468 36.000 0.00 0.00 0.00 2.01
2036 6941 3.244976 CGCAAAATGTTCCCAATCAGAC 58.755 45.455 0.00 0.00 0.00 3.51
2111 7020 2.670414 GGTGAATGAAAGAGACTCTGCG 59.330 50.000 5.55 0.00 0.00 5.18
2117 7026 2.558795 TGAAAGAGACTCTGCGCTAGTT 59.441 45.455 9.73 3.70 0.00 2.24
2146 7059 1.569479 GGAGCGTGCTGTTCCTGTTC 61.569 60.000 0.00 0.00 44.14 3.18
2147 7060 1.569479 GAGCGTGCTGTTCCTGTTCC 61.569 60.000 0.00 0.00 0.00 3.62
2148 7061 1.598130 GCGTGCTGTTCCTGTTCCT 60.598 57.895 0.00 0.00 0.00 3.36
2149 7062 1.845809 GCGTGCTGTTCCTGTTCCTG 61.846 60.000 0.00 0.00 0.00 3.86
2150 7063 0.532862 CGTGCTGTTCCTGTTCCTGT 60.533 55.000 0.00 0.00 0.00 4.00
2151 7064 1.680338 GTGCTGTTCCTGTTCCTGTT 58.320 50.000 0.00 0.00 0.00 3.16
2152 7065 1.334869 GTGCTGTTCCTGTTCCTGTTG 59.665 52.381 0.00 0.00 0.00 3.33
2153 7066 0.954452 GCTGTTCCTGTTCCTGTTGG 59.046 55.000 0.00 0.00 0.00 3.77
2154 7067 1.609208 CTGTTCCTGTTCCTGTTGGG 58.391 55.000 0.00 0.00 0.00 4.12
2155 7068 0.467290 TGTTCCTGTTCCTGTTGGGC 60.467 55.000 0.00 0.00 34.39 5.36
2224 7137 7.872113 AAGTCCCAAAGATAATCACAATCTC 57.128 36.000 0.00 0.00 32.48 2.75
2232 7145 7.856145 AAGATAATCACAATCTCACTGTTCC 57.144 36.000 0.00 0.00 32.48 3.62
2234 7147 2.455674 TCACAATCTCACTGTTCCGG 57.544 50.000 0.00 0.00 0.00 5.14
2285 7199 0.904649 ACATCAGGCCAGATCGACAA 59.095 50.000 7.84 0.00 0.00 3.18
2304 7218 3.044986 CAACAAACTGAGATTGGCAACG 58.955 45.455 0.00 0.00 42.51 4.10
2333 7249 1.051812 ATGATGACCCCACTCGATCC 58.948 55.000 0.00 0.00 0.00 3.36
2335 7251 2.088674 GATGACCCCACTCGATCCGG 62.089 65.000 0.00 0.00 0.00 5.14
2369 7285 1.153061 ACTCTGTCTCCGTCCCACA 59.847 57.895 0.00 0.00 0.00 4.17
2381 7299 2.151202 CGTCCCACAATACAACAAGCT 58.849 47.619 0.00 0.00 0.00 3.74
2384 7302 1.612950 CCCACAATACAACAAGCTGCA 59.387 47.619 1.02 0.00 0.00 4.41
2388 7306 2.294233 ACAATACAACAAGCTGCAGTGG 59.706 45.455 16.64 7.70 0.00 4.00
2489 7412 9.204570 GCTAGACAAGTGTCAAACTTCTAAATA 57.795 33.333 13.66 0.00 46.60 1.40
2570 7493 2.569853 TCAGATAAAAAGGGGCTCGTCA 59.430 45.455 0.00 0.00 0.00 4.35
2572 7495 3.313526 CAGATAAAAAGGGGCTCGTCATG 59.686 47.826 0.00 0.00 0.00 3.07
2573 7496 1.459450 TAAAAAGGGGCTCGTCATGC 58.541 50.000 0.00 0.00 0.00 4.06
2628 7556 2.051879 TTTCTGTTGCTCTCGTCTCG 57.948 50.000 0.00 0.00 0.00 4.04
2631 7559 1.867919 CTGTTGCTCTCGTCTCGGGT 61.868 60.000 0.00 0.00 0.00 5.28
2707 7666 6.708676 CAATTGAGTTGCCAGAAAGAAAAAC 58.291 36.000 0.00 0.00 0.00 2.43
2757 7716 4.933330 TGATGAGTCGGTGTTATCTTAGC 58.067 43.478 0.00 0.00 0.00 3.09
2781 7740 4.461081 CCAAAAGTTAATTCCGGGACATCA 59.539 41.667 0.00 0.00 0.00 3.07
2791 7750 4.577988 TCCGGGACATCAGGAAATTTAA 57.422 40.909 0.00 0.00 0.00 1.52
2816 7775 9.830975 AATTTAACTAGTCAAAATGCCAAACTT 57.169 25.926 13.87 0.00 0.00 2.66
2875 7834 0.976641 AGATGGACGGCAAACTGAGA 59.023 50.000 0.00 0.00 0.00 3.27
2880 7839 1.610624 GGACGGCAAACTGAGATTGGA 60.611 52.381 4.61 0.00 0.00 3.53
2888 7847 4.618489 GCAAACTGAGATTGGACAAAATCG 59.382 41.667 4.61 0.00 40.75 3.34
2894 7853 7.923888 ACTGAGATTGGACAAAATCGATATTG 58.076 34.615 0.00 0.00 40.75 1.90
2904 7872 5.163632 ACAAAATCGATATTGTCATGCTGCA 60.164 36.000 4.13 4.13 34.84 4.41
2930 7898 3.852286 ACTCGTGTGCATTATTTCGGTA 58.148 40.909 0.00 0.00 0.00 4.02
2935 7903 5.868258 TCGTGTGCATTATTTCGGTAGTTAA 59.132 36.000 0.00 0.00 0.00 2.01
2950 7918 4.201920 GGTAGTTAATTTGCTGCAGCCTAC 60.202 45.833 34.64 30.14 41.18 3.18
2958 7926 2.603473 TGCAGCCTACCCGTCAGT 60.603 61.111 0.00 0.00 0.00 3.41
3003 7971 5.939764 TGTCTCATGTCAGCTTTAGGTAT 57.060 39.130 0.00 0.00 0.00 2.73
3030 7998 0.251916 CCAAACTACATCTGGCCGGA 59.748 55.000 18.80 18.80 0.00 5.14
3052 8020 1.269517 GCCAACTCGCAATCAAAACCA 60.270 47.619 0.00 0.00 0.00 3.67
3053 8021 2.801342 GCCAACTCGCAATCAAAACCAA 60.801 45.455 0.00 0.00 0.00 3.67
3054 8022 3.452474 CCAACTCGCAATCAAAACCAAA 58.548 40.909 0.00 0.00 0.00 3.28
3055 8023 3.245048 CCAACTCGCAATCAAAACCAAAC 59.755 43.478 0.00 0.00 0.00 2.93
3056 8024 4.111916 CAACTCGCAATCAAAACCAAACT 58.888 39.130 0.00 0.00 0.00 2.66
3057 8025 3.705604 ACTCGCAATCAAAACCAAACTG 58.294 40.909 0.00 0.00 0.00 3.16
3058 8026 2.468831 TCGCAATCAAAACCAAACTGC 58.531 42.857 0.00 0.00 0.00 4.40
3059 8027 1.526464 CGCAATCAAAACCAAACTGCC 59.474 47.619 0.00 0.00 0.00 4.85
3060 8028 2.559440 GCAATCAAAACCAAACTGCCA 58.441 42.857 0.00 0.00 0.00 4.92
3061 8029 3.140623 GCAATCAAAACCAAACTGCCAT 58.859 40.909 0.00 0.00 0.00 4.40
3062 8030 4.314121 GCAATCAAAACCAAACTGCCATA 58.686 39.130 0.00 0.00 0.00 2.74
3063 8031 4.152223 GCAATCAAAACCAAACTGCCATAC 59.848 41.667 0.00 0.00 0.00 2.39
3064 8032 5.295950 CAATCAAAACCAAACTGCCATACA 58.704 37.500 0.00 0.00 0.00 2.29
3065 8033 4.314740 TCAAAACCAAACTGCCATACAC 57.685 40.909 0.00 0.00 0.00 2.90
3066 8034 3.701542 TCAAAACCAAACTGCCATACACA 59.298 39.130 0.00 0.00 0.00 3.72
3067 8035 3.726291 AAACCAAACTGCCATACACAC 57.274 42.857 0.00 0.00 0.00 3.82
3068 8036 1.234821 ACCAAACTGCCATACACACG 58.765 50.000 0.00 0.00 0.00 4.49
3069 8037 1.202710 ACCAAACTGCCATACACACGA 60.203 47.619 0.00 0.00 0.00 4.35
3070 8038 2.083774 CCAAACTGCCATACACACGAT 58.916 47.619 0.00 0.00 0.00 3.73
3071 8039 2.159531 CCAAACTGCCATACACACGATG 60.160 50.000 0.00 0.00 0.00 3.84
3072 8040 2.472695 AACTGCCATACACACGATGT 57.527 45.000 0.00 0.00 46.06 3.06
3081 8049 2.827604 CACACGATGTGTCCTGGAC 58.172 57.895 19.96 19.96 43.92 4.02
3082 8050 1.008875 CACACGATGTGTCCTGGACG 61.009 60.000 21.15 11.76 43.92 4.79
3083 8051 1.176619 ACACGATGTGTCCTGGACGA 61.177 55.000 21.15 11.21 43.92 4.20
3084 8052 0.173481 CACGATGTGTCCTGGACGAT 59.827 55.000 21.15 15.33 34.95 3.73
3085 8053 1.404035 CACGATGTGTCCTGGACGATA 59.596 52.381 21.15 10.64 34.95 2.92
3086 8054 1.404391 ACGATGTGTCCTGGACGATAC 59.596 52.381 21.15 14.41 34.95 2.24
3087 8055 1.597199 CGATGTGTCCTGGACGATACG 60.597 57.143 21.15 18.55 34.95 3.06
3088 8056 0.102481 ATGTGTCCTGGACGATACGC 59.898 55.000 21.15 5.77 34.95 4.42
3089 8057 1.245376 TGTGTCCTGGACGATACGCA 61.245 55.000 21.15 8.35 34.95 5.24
3090 8058 0.801067 GTGTCCTGGACGATACGCAC 60.801 60.000 21.15 8.75 34.95 5.34
3091 8059 1.245376 TGTCCTGGACGATACGCACA 61.245 55.000 21.15 0.00 34.95 4.57
3092 8060 0.801067 GTCCTGGACGATACGCACAC 60.801 60.000 11.71 0.00 0.00 3.82
3093 8061 1.214325 CCTGGACGATACGCACACA 59.786 57.895 0.00 0.00 0.00 3.72
3094 8062 0.389296 CCTGGACGATACGCACACAA 60.389 55.000 0.00 0.00 0.00 3.33
3095 8063 0.713883 CTGGACGATACGCACACAAC 59.286 55.000 0.00 0.00 0.00 3.32
3096 8064 0.032267 TGGACGATACGCACACAACA 59.968 50.000 0.00 0.00 0.00 3.33
3097 8065 0.437295 GGACGATACGCACACAACAC 59.563 55.000 0.00 0.00 0.00 3.32
3098 8066 1.415374 GACGATACGCACACAACACT 58.585 50.000 0.00 0.00 0.00 3.55
3099 8067 1.385743 GACGATACGCACACAACACTC 59.614 52.381 0.00 0.00 0.00 3.51
3100 8068 1.269361 ACGATACGCACACAACACTCA 60.269 47.619 0.00 0.00 0.00 3.41
3101 8069 1.790043 CGATACGCACACAACACTCAA 59.210 47.619 0.00 0.00 0.00 3.02
3102 8070 2.219903 CGATACGCACACAACACTCAAA 59.780 45.455 0.00 0.00 0.00 2.69
3103 8071 3.120683 CGATACGCACACAACACTCAAAT 60.121 43.478 0.00 0.00 0.00 2.32
3104 8072 2.755836 ACGCACACAACACTCAAATC 57.244 45.000 0.00 0.00 0.00 2.17
3105 8073 1.003972 ACGCACACAACACTCAAATCG 60.004 47.619 0.00 0.00 0.00 3.34
3106 8074 1.260297 CGCACACAACACTCAAATCGA 59.740 47.619 0.00 0.00 0.00 3.59
3107 8075 2.286125 CGCACACAACACTCAAATCGAA 60.286 45.455 0.00 0.00 0.00 3.71
3108 8076 3.035942 GCACACAACACTCAAATCGAAC 58.964 45.455 0.00 0.00 0.00 3.95
3109 8077 3.279950 CACACAACACTCAAATCGAACG 58.720 45.455 0.00 0.00 0.00 3.95
3110 8078 2.286833 ACACAACACTCAAATCGAACGG 59.713 45.455 0.00 0.00 0.00 4.44
3111 8079 1.871039 ACAACACTCAAATCGAACGGG 59.129 47.619 0.00 0.00 0.00 5.28
3112 8080 1.196808 CAACACTCAAATCGAACGGGG 59.803 52.381 0.00 0.00 0.00 5.73
3113 8081 0.682852 ACACTCAAATCGAACGGGGA 59.317 50.000 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.103153 CCAATCTTACTAAGGGCATCTCCA 59.897 45.833 0.00 0.00 36.21 3.86
9 10 5.667626 TCTTCCAATCTTACTAAGGGCATCT 59.332 40.000 0.00 0.00 0.00 2.90
10 11 5.760743 GTCTTCCAATCTTACTAAGGGCATC 59.239 44.000 0.00 0.00 0.00 3.91
11 12 5.398012 GGTCTTCCAATCTTACTAAGGGCAT 60.398 44.000 0.00 0.00 0.00 4.40
12 13 4.080526 GGTCTTCCAATCTTACTAAGGGCA 60.081 45.833 0.00 0.00 0.00 5.36
13 14 4.452825 GGTCTTCCAATCTTACTAAGGGC 58.547 47.826 0.00 0.00 0.00 5.19
20 21 5.946377 ACAAATCAGGGTCTTCCAATCTTAC 59.054 40.000 0.00 0.00 38.24 2.34
22 23 5.003096 ACAAATCAGGGTCTTCCAATCTT 57.997 39.130 0.00 0.00 38.24 2.40
26 27 4.285863 ACAAACAAATCAGGGTCTTCCAA 58.714 39.130 0.00 0.00 38.24 3.53
31 32 5.186797 TGTTGAAACAAACAAATCAGGGTCT 59.813 36.000 0.00 0.00 37.12 3.85
43 44 5.793026 TTGGCTGAAATGTTGAAACAAAC 57.207 34.783 0.00 0.00 43.03 2.93
47 48 6.175712 TGTTTTTGGCTGAAATGTTGAAAC 57.824 33.333 0.00 0.00 0.00 2.78
54 56 7.224362 TGTCTATTGTTGTTTTTGGCTGAAATG 59.776 33.333 0.00 0.00 0.00 2.32
73 75 9.906660 TGCGATTTTGTTAAATTTCTGTCTATT 57.093 25.926 0.00 0.00 34.16 1.73
103 107 6.732154 CATCAAAATGATAGCACCGAGAAAT 58.268 36.000 0.00 0.00 34.28 2.17
123 127 5.509670 CCTGATATAACCGAGTTCAGCATCA 60.510 44.000 0.00 0.00 33.97 3.07
154 158 2.267188 TTCCGTTCGACGACTATTGG 57.733 50.000 0.00 0.00 46.05 3.16
156 160 4.367386 AGATTTCCGTTCGACGACTATT 57.633 40.909 0.00 0.00 46.05 1.73
164 168 3.837213 AAGTCGTAGATTTCCGTTCGA 57.163 42.857 0.00 0.00 40.67 3.71
169 173 2.664568 TCGCAAAAGTCGTAGATTTCCG 59.335 45.455 0.00 0.00 40.67 4.30
251 272 2.990514 TGAATTTTCATCGTTCGAGCGA 59.009 40.909 26.29 26.29 45.32 4.93
252 273 3.084278 GTGAATTTTCATCGTTCGAGCG 58.916 45.455 16.09 16.09 39.73 5.03
253 274 3.120338 TGGTGAATTTTCATCGTTCGAGC 60.120 43.478 0.80 0.00 41.19 5.03
254 275 4.394795 GTGGTGAATTTTCATCGTTCGAG 58.605 43.478 0.80 0.00 41.19 4.04
305 335 0.388520 GGCTTTGGCGTTGTGGATTC 60.389 55.000 0.00 0.00 39.81 2.52
324 355 3.179265 CGCTTCGTAGGTGGCACG 61.179 66.667 12.17 0.00 40.72 5.34
352 383 0.831307 GCTCCTTATCCGTCCTTGGT 59.169 55.000 0.00 0.00 0.00 3.67
356 387 0.687757 TGCTGCTCCTTATCCGTCCT 60.688 55.000 0.00 0.00 0.00 3.85
357 388 0.249657 CTGCTGCTCCTTATCCGTCC 60.250 60.000 0.00 0.00 0.00 4.79
358 389 0.878086 GCTGCTGCTCCTTATCCGTC 60.878 60.000 8.53 0.00 36.03 4.79
360 391 1.953138 CGCTGCTGCTCCTTATCCG 60.953 63.158 14.03 0.00 36.97 4.18
362 393 1.144936 ACCGCTGCTGCTCCTTATC 59.855 57.895 14.03 0.00 36.97 1.75
363 394 1.153289 CACCGCTGCTGCTCCTTAT 60.153 57.895 14.03 0.00 36.97 1.73
375 1241 1.040339 GGATGTCTCTCCTCACCGCT 61.040 60.000 0.00 0.00 32.18 5.52
378 1244 0.741915 GACGGATGTCTCTCCTCACC 59.258 60.000 0.00 0.00 42.08 4.02
414 1280 4.373116 GTCACCGGAGCGCCAAGA 62.373 66.667 9.46 0.00 0.00 3.02
484 1355 2.158957 GCTCGGACTGTTCATGGGATTA 60.159 50.000 0.00 0.00 0.00 1.75
509 1380 3.138798 CGGGAGTGATCGGTCCGT 61.139 66.667 11.88 0.00 36.38 4.69
552 5083 4.675029 CACCGACCACCGACCACC 62.675 72.222 0.00 0.00 41.76 4.61
553 5084 4.675029 CCACCGACCACCGACCAC 62.675 72.222 0.00 0.00 41.76 4.16
578 5109 2.119801 ATGTACTGGTCGTACTCCGT 57.880 50.000 0.00 0.14 46.89 4.69
595 5126 3.126831 GCTTTGGATCCGTCTGTCTATG 58.873 50.000 7.39 0.00 0.00 2.23
669 5200 1.082756 CCACTGACTTTTCGTGCGC 60.083 57.895 0.00 0.00 0.00 6.09
755 5287 1.673337 TGCCATGTGAGCACTGAGC 60.673 57.895 1.99 2.89 46.19 4.26
756 5288 4.707791 TGCCATGTGAGCACTGAG 57.292 55.556 1.99 0.00 34.69 3.35
761 5293 0.394216 GGTATGGTGCCATGTGAGCA 60.394 55.000 13.57 0.00 37.82 4.26
1036 5569 5.462398 TCGAGTTCAAGTTTTGTAGAGAAGC 59.538 40.000 0.00 0.00 0.00 3.86
1039 5572 6.645415 GGATTCGAGTTCAAGTTTTGTAGAGA 59.355 38.462 0.00 0.00 0.00 3.10
1041 5574 6.285224 TGGATTCGAGTTCAAGTTTTGTAGA 58.715 36.000 0.00 0.00 0.00 2.59
1042 5575 6.539649 TGGATTCGAGTTCAAGTTTTGTAG 57.460 37.500 0.00 0.00 0.00 2.74
1043 5576 5.049680 GCTGGATTCGAGTTCAAGTTTTGTA 60.050 40.000 0.00 0.00 0.00 2.41
1047 5580 3.499918 CAGCTGGATTCGAGTTCAAGTTT 59.500 43.478 5.57 0.00 0.00 2.66
1084 5617 1.069906 GCTCGATCTCTCTCTCGAAGC 60.070 57.143 0.00 0.00 42.73 3.86
1088 5621 0.867746 CCTGCTCGATCTCTCTCTCG 59.132 60.000 0.00 0.00 36.25 4.04
1099 5939 2.824546 GATGCCCATCCTGCTCGA 59.175 61.111 0.00 0.00 31.76 4.04
1100 5940 2.664185 CGATGCCCATCCTGCTCG 60.664 66.667 2.88 0.00 34.40 5.03
1105 5970 2.911143 GTCCACGATGCCCATCCT 59.089 61.111 2.88 0.00 34.40 3.24
1270 6135 1.548269 AGGAAAGGAACAGAGCTCGAG 59.452 52.381 8.45 8.45 0.00 4.04
1273 6138 4.020543 TCTAGAGGAAAGGAACAGAGCTC 58.979 47.826 5.27 5.27 0.00 4.09
1275 6140 4.810191 TTCTAGAGGAAAGGAACAGAGC 57.190 45.455 0.00 0.00 0.00 4.09
1292 6157 8.992349 TGGTGGAGAATCAATCTAATCTTTCTA 58.008 33.333 0.00 0.00 38.96 2.10
1293 6158 7.772757 GTGGTGGAGAATCAATCTAATCTTTCT 59.227 37.037 0.00 0.00 38.96 2.52
1294 6159 7.012799 GGTGGTGGAGAATCAATCTAATCTTTC 59.987 40.741 0.00 0.00 38.96 2.62
1296 6161 6.360618 GGTGGTGGAGAATCAATCTAATCTT 58.639 40.000 0.00 0.00 38.96 2.40
1297 6162 5.453903 CGGTGGTGGAGAATCAATCTAATCT 60.454 44.000 0.00 0.00 38.96 2.40
1298 6163 4.752101 CGGTGGTGGAGAATCAATCTAATC 59.248 45.833 0.00 0.00 38.96 1.75
1299 6164 4.408921 TCGGTGGTGGAGAATCAATCTAAT 59.591 41.667 0.00 0.00 38.96 1.73
1300 6165 3.772572 TCGGTGGTGGAGAATCAATCTAA 59.227 43.478 0.00 0.00 38.96 2.10
1302 6167 2.093447 GTCGGTGGTGGAGAATCAATCT 60.093 50.000 0.00 0.00 42.61 2.40
1303 6168 2.280628 GTCGGTGGTGGAGAATCAATC 58.719 52.381 0.00 0.00 36.25 2.67
1304 6169 1.065418 GGTCGGTGGTGGAGAATCAAT 60.065 52.381 0.00 0.00 36.25 2.57
1305 6170 0.323629 GGTCGGTGGTGGAGAATCAA 59.676 55.000 0.00 0.00 36.25 2.57
1306 6171 0.834261 TGGTCGGTGGTGGAGAATCA 60.834 55.000 0.00 0.00 36.25 2.57
1307 6172 0.391263 GTGGTCGGTGGTGGAGAATC 60.391 60.000 0.00 0.00 0.00 2.52
1308 6173 1.677552 GTGGTCGGTGGTGGAGAAT 59.322 57.895 0.00 0.00 0.00 2.40
1309 6174 2.513259 GGTGGTCGGTGGTGGAGAA 61.513 63.158 0.00 0.00 0.00 2.87
1310 6175 2.920912 GGTGGTCGGTGGTGGAGA 60.921 66.667 0.00 0.00 0.00 3.71
1311 6176 3.238497 TGGTGGTCGGTGGTGGAG 61.238 66.667 0.00 0.00 0.00 3.86
1312 6177 3.238497 CTGGTGGTCGGTGGTGGA 61.238 66.667 0.00 0.00 0.00 4.02
1313 6178 3.238497 TCTGGTGGTCGGTGGTGG 61.238 66.667 0.00 0.00 0.00 4.61
1314 6179 2.343758 CTCTGGTGGTCGGTGGTG 59.656 66.667 0.00 0.00 0.00 4.17
1315 6180 2.923035 CCTCTGGTGGTCGGTGGT 60.923 66.667 0.00 0.00 32.25 4.16
1316 6181 3.706373 CCCTCTGGTGGTCGGTGG 61.706 72.222 0.00 0.00 35.66 4.61
1317 6182 1.961180 GATCCCTCTGGTGGTCGGTG 61.961 65.000 0.00 0.00 0.00 4.94
1318 6183 1.686110 GATCCCTCTGGTGGTCGGT 60.686 63.158 0.00 0.00 0.00 4.69
1319 6184 2.786495 CGATCCCTCTGGTGGTCGG 61.786 68.421 0.00 0.00 32.49 4.79
1320 6185 2.786495 CCGATCCCTCTGGTGGTCG 61.786 68.421 0.00 0.00 34.36 4.79
1321 6186 0.760945 ATCCGATCCCTCTGGTGGTC 60.761 60.000 0.00 0.00 0.00 4.02
1322 6187 0.326618 AATCCGATCCCTCTGGTGGT 60.327 55.000 0.00 0.00 0.00 4.16
1323 6188 0.394565 GAATCCGATCCCTCTGGTGG 59.605 60.000 0.00 0.00 0.00 4.61
1324 6189 0.394565 GGAATCCGATCCCTCTGGTG 59.605 60.000 0.00 0.00 33.05 4.17
1325 6190 0.266152 AGGAATCCGATCCCTCTGGT 59.734 55.000 0.00 0.00 40.59 4.00
1326 6191 0.972883 GAGGAATCCGATCCCTCTGG 59.027 60.000 6.41 0.00 42.36 3.86
1327 6192 0.972883 GGAGGAATCCGATCCCTCTG 59.027 60.000 12.99 0.00 44.43 3.35
1328 6193 0.863956 AGGAGGAATCCGATCCCTCT 59.136 55.000 12.99 0.00 44.43 3.69
1329 6194 1.262417 GAGGAGGAATCCGATCCCTC 58.738 60.000 5.07 5.07 44.32 4.30
1330 6195 0.178918 GGAGGAGGAATCCGATCCCT 60.179 60.000 4.14 4.89 40.59 4.20
1331 6196 1.195442 GGGAGGAGGAATCCGATCCC 61.195 65.000 19.03 19.03 40.59 3.85
1332 6197 0.178918 AGGGAGGAGGAATCCGATCC 60.179 60.000 10.70 10.70 37.75 3.36
1333 6198 0.972883 CAGGGAGGAGGAATCCGATC 59.027 60.000 0.00 0.00 37.75 3.69
1334 6199 0.563173 TCAGGGAGGAGGAATCCGAT 59.437 55.000 0.00 0.00 37.75 4.18
1335 6200 0.397254 GTCAGGGAGGAGGAATCCGA 60.397 60.000 0.00 0.00 37.75 4.55
1336 6201 1.403687 GGTCAGGGAGGAGGAATCCG 61.404 65.000 0.00 0.00 37.75 4.18
1337 6202 1.057275 GGGTCAGGGAGGAGGAATCC 61.057 65.000 0.00 0.00 35.99 3.01
1338 6203 0.326618 TGGGTCAGGGAGGAGGAATC 60.327 60.000 0.00 0.00 0.00 2.52
1339 6204 0.327000 CTGGGTCAGGGAGGAGGAAT 60.327 60.000 0.00 0.00 0.00 3.01
1340 6205 1.081092 CTGGGTCAGGGAGGAGGAA 59.919 63.158 0.00 0.00 0.00 3.36
1341 6206 2.780693 CTGGGTCAGGGAGGAGGA 59.219 66.667 0.00 0.00 0.00 3.71
1342 6207 3.086600 GCTGGGTCAGGGAGGAGG 61.087 72.222 0.00 0.00 31.21 4.30
1343 6208 2.284921 TGCTGGGTCAGGGAGGAG 60.285 66.667 0.00 0.00 31.21 3.69
1351 6216 1.545428 GGAGAAACATGTGCTGGGTCA 60.545 52.381 0.00 0.00 0.00 4.02
1352 6217 1.168714 GGAGAAACATGTGCTGGGTC 58.831 55.000 0.00 0.00 0.00 4.46
1354 6219 1.747355 GATGGAGAAACATGTGCTGGG 59.253 52.381 0.00 0.00 0.00 4.45
1356 6221 1.399440 CCGATGGAGAAACATGTGCTG 59.601 52.381 0.00 0.00 0.00 4.41
1357 6222 1.679944 CCCGATGGAGAAACATGTGCT 60.680 52.381 0.00 0.00 0.00 4.40
1374 6239 0.817654 GCAAGATTTCCTTTCCCCCG 59.182 55.000 0.00 0.00 31.42 5.73
1401 6271 7.230027 AGATATAGATCTGGCCAAAGAAAAGG 58.770 38.462 7.01 0.00 41.12 3.11
1452 6323 2.865551 CTGCAAAACCAAATGGACACAC 59.134 45.455 6.42 0.00 38.94 3.82
1458 6329 0.249826 ACGCCTGCAAAACCAAATGG 60.250 50.000 0.00 0.00 42.17 3.16
1459 6330 0.860533 CACGCCTGCAAAACCAAATG 59.139 50.000 0.00 0.00 0.00 2.32
1460 6331 0.749649 TCACGCCTGCAAAACCAAAT 59.250 45.000 0.00 0.00 0.00 2.32
1461 6332 0.102120 CTCACGCCTGCAAAACCAAA 59.898 50.000 0.00 0.00 0.00 3.28
1793 6666 7.283329 AGAAGGTCTCTCTTACAAACAAACAT 58.717 34.615 0.00 0.00 0.00 2.71
1795 6668 7.179927 GAGAAGGTCTCTCTTACAAACAAAC 57.820 40.000 0.00 0.00 46.32 2.93
1810 6712 1.686741 CGGGGAAGCTAGAGAAGGTCT 60.687 57.143 0.00 0.00 39.59 3.85
1829 6731 1.592131 GGATGAGCAGAGCAGAGCG 60.592 63.158 0.00 0.00 35.48 5.03
1838 6740 3.285215 GCCGCCATGGATGAGCAG 61.285 66.667 18.40 0.00 42.00 4.24
1844 6746 3.133464 CACAACGCCGCCATGGAT 61.133 61.111 18.40 0.00 42.00 3.41
1848 6750 3.669344 CCAACACAACGCCGCCAT 61.669 61.111 0.00 0.00 0.00 4.40
1852 6754 1.635663 GAGATCCCAACACAACGCCG 61.636 60.000 0.00 0.00 0.00 6.46
1857 6759 4.104086 ACCATCTAGAGATCCCAACACAA 58.896 43.478 0.00 0.00 31.21 3.33
1858 6760 3.706594 GACCATCTAGAGATCCCAACACA 59.293 47.826 0.00 0.00 31.21 3.72
1859 6761 3.243569 CGACCATCTAGAGATCCCAACAC 60.244 52.174 0.00 0.00 31.21 3.32
1860 6762 2.959030 CGACCATCTAGAGATCCCAACA 59.041 50.000 0.00 0.00 31.21 3.33
1881 6783 3.467803 AGTACAAGAGAACACCAACAGC 58.532 45.455 0.00 0.00 0.00 4.40
1893 6795 8.088981 TCTAGCCTAGTTTCAAAAGTACAAGAG 58.911 37.037 0.00 0.00 0.00 2.85
1914 6819 4.100808 ACAGACCCATCTTCATCTTCTAGC 59.899 45.833 0.00 0.00 30.42 3.42
1957 6862 9.913310 TCACCAAATCCAACATATCTTACATAA 57.087 29.630 0.00 0.00 0.00 1.90
1958 6863 9.559732 CTCACCAAATCCAACATATCTTACATA 57.440 33.333 0.00 0.00 0.00 2.29
1959 6864 7.503566 CCTCACCAAATCCAACATATCTTACAT 59.496 37.037 0.00 0.00 0.00 2.29
2036 6941 2.463553 AATCAATCATGCAACGCTCG 57.536 45.000 0.00 0.00 0.00 5.03
2111 7020 1.874320 GCTCCCGCCTGATTAACTAGC 60.874 57.143 0.00 0.00 0.00 3.42
2117 7026 2.499205 CACGCTCCCGCCTGATTA 59.501 61.111 0.00 0.00 38.22 1.75
2150 7063 3.613877 TATCAGCGCCGTTGCCCAA 62.614 57.895 2.29 0.00 34.65 4.12
2151 7064 3.613877 TTATCAGCGCCGTTGCCCA 62.614 57.895 2.29 0.00 34.65 5.36
2152 7065 2.822255 TTATCAGCGCCGTTGCCC 60.822 61.111 2.29 0.00 34.65 5.36
2153 7066 2.036764 GACTTATCAGCGCCGTTGCC 62.037 60.000 2.29 0.00 34.65 4.52
2154 7067 1.348594 GACTTATCAGCGCCGTTGC 59.651 57.895 2.29 0.00 0.00 4.17
2155 7068 1.429148 GGGACTTATCAGCGCCGTTG 61.429 60.000 2.29 0.00 0.00 4.10
2224 7137 1.961793 TTCCAAGTTCCGGAACAGTG 58.038 50.000 40.66 34.87 43.47 3.66
2232 7145 7.145932 ACTTCAGATATTTTTCCAAGTTCCG 57.854 36.000 0.00 0.00 0.00 4.30
2234 7147 7.329471 GGCAACTTCAGATATTTTTCCAAGTTC 59.671 37.037 0.00 0.00 31.59 3.01
2285 7199 2.033299 CACGTTGCCAATCTCAGTTTGT 59.967 45.455 0.00 0.00 0.00 2.83
2304 7218 2.092968 TGGGGTCATCATAGAGCAACAC 60.093 50.000 0.00 0.00 37.74 3.32
2310 7224 2.587522 TCGAGTGGGGTCATCATAGAG 58.412 52.381 0.00 0.00 0.00 2.43
2314 7228 1.051812 GGATCGAGTGGGGTCATCAT 58.948 55.000 0.00 0.00 0.00 2.45
2315 7229 1.391933 CGGATCGAGTGGGGTCATCA 61.392 60.000 0.00 0.00 0.00 3.07
2318 7232 2.758327 CCGGATCGAGTGGGGTCA 60.758 66.667 0.00 0.00 0.00 4.02
2319 7233 2.441532 TCCGGATCGAGTGGGGTC 60.442 66.667 0.00 0.00 0.00 4.46
2333 7249 2.146342 AGTGATGCACAAGAAACTCCG 58.854 47.619 0.00 0.00 36.74 4.63
2335 7251 3.812053 ACAGAGTGATGCACAAGAAACTC 59.188 43.478 0.00 0.00 36.74 3.01
2369 7285 1.270550 GCCACTGCAGCTTGTTGTATT 59.729 47.619 15.27 0.00 37.47 1.89
2452 7375 1.555075 CTTGTCTAGCCCAGCCAAGTA 59.445 52.381 0.00 0.00 0.00 2.24
2582 7505 9.983024 TCAGTCCATAAACCCTTTGAATAATAA 57.017 29.630 0.00 0.00 0.00 1.40
2602 7530 2.670414 CGAGAGCAACAGAAATCAGTCC 59.330 50.000 0.00 0.00 0.00 3.85
2603 7531 3.321497 ACGAGAGCAACAGAAATCAGTC 58.679 45.455 0.00 0.00 0.00 3.51
2628 7556 3.196685 AGCTGAGTCTTAATCAGTGACCC 59.803 47.826 0.00 0.00 44.92 4.46
2631 7559 3.129462 CCGAGCTGAGTCTTAATCAGTGA 59.871 47.826 0.00 0.00 44.92 3.41
2694 7653 7.269477 ACATCTTCTCTGTTTTTCTTTCTGG 57.731 36.000 0.00 0.00 0.00 3.86
2697 7656 8.621286 TGGTAACATCTTCTCTGTTTTTCTTTC 58.379 33.333 0.00 0.00 46.17 2.62
2757 7716 3.158676 TGTCCCGGAATTAACTTTTGGG 58.841 45.455 0.73 0.00 34.45 4.12
2806 7765 7.148069 GGTTTAAGATACTGCTAAGTTTGGCAT 60.148 37.037 3.33 0.00 43.81 4.40
2807 7766 6.150474 GGTTTAAGATACTGCTAAGTTTGGCA 59.850 38.462 2.90 2.90 42.59 4.92
2816 7775 4.463539 TGTGTCCGGTTTAAGATACTGCTA 59.536 41.667 0.00 0.00 0.00 3.49
2880 7839 5.163632 TGCAGCATGACAATATCGATTTTGT 60.164 36.000 27.32 27.32 39.69 2.83
2888 7847 6.034363 CGAGTACTATGCAGCATGACAATATC 59.966 42.308 18.81 6.48 39.69 1.63
2894 7853 2.791560 CACGAGTACTATGCAGCATGAC 59.208 50.000 18.81 12.63 39.69 3.06
2896 7855 2.537214 CACACGAGTACTATGCAGCATG 59.463 50.000 18.81 10.34 40.87 4.06
2897 7856 2.814269 CACACGAGTACTATGCAGCAT 58.186 47.619 13.73 13.73 0.00 3.79
2904 7872 5.690409 CCGAAATAATGCACACGAGTACTAT 59.310 40.000 0.00 0.00 0.00 2.12
2930 7898 2.755103 GGTAGGCTGCAGCAAATTAACT 59.245 45.455 37.63 25.21 44.36 2.24
2935 7903 1.750399 CGGGTAGGCTGCAGCAAAT 60.750 57.895 37.63 25.06 44.36 2.32
2971 7939 3.598299 TGACATGAGACATCATCGCAAA 58.402 40.909 0.00 0.00 44.58 3.68
2972 7940 3.192466 CTGACATGAGACATCATCGCAA 58.808 45.455 0.00 0.00 44.58 4.85
2973 7941 2.817901 CTGACATGAGACATCATCGCA 58.182 47.619 0.00 0.00 44.58 5.10
3003 7971 3.370846 CCAGATGTAGTTTGGCATCTCCA 60.371 47.826 4.30 0.00 46.03 3.86
3028 7996 0.960364 TTGATTGCGAGTTGGCCTCC 60.960 55.000 3.32 0.00 36.82 4.30
3030 7998 1.000274 GTTTTGATTGCGAGTTGGCCT 60.000 47.619 3.32 0.00 0.00 5.19
3040 8008 2.559440 TGGCAGTTTGGTTTTGATTGC 58.441 42.857 0.00 0.00 0.00 3.56
3052 8020 2.483877 CACATCGTGTGTATGGCAGTTT 59.516 45.455 9.19 0.00 43.08 2.66
3053 8021 2.076100 CACATCGTGTGTATGGCAGTT 58.924 47.619 9.19 0.00 43.08 3.16
3054 8022 1.725641 CACATCGTGTGTATGGCAGT 58.274 50.000 9.19 0.00 43.08 4.40
3065 8033 0.173481 ATCGTCCAGGACACATCGTG 59.827 55.000 20.13 1.23 39.88 4.35
3066 8034 1.404391 GTATCGTCCAGGACACATCGT 59.596 52.381 20.13 1.08 32.09 3.73
3067 8035 1.597199 CGTATCGTCCAGGACACATCG 60.597 57.143 20.13 13.70 32.09 3.84
3068 8036 1.864435 GCGTATCGTCCAGGACACATC 60.864 57.143 20.13 6.15 32.09 3.06
3069 8037 0.102481 GCGTATCGTCCAGGACACAT 59.898 55.000 20.13 12.59 32.09 3.21
3070 8038 1.245376 TGCGTATCGTCCAGGACACA 61.245 55.000 20.13 5.53 32.09 3.72
3071 8039 0.801067 GTGCGTATCGTCCAGGACAC 60.801 60.000 20.13 9.27 32.09 3.67
3072 8040 1.245376 TGTGCGTATCGTCCAGGACA 61.245 55.000 20.13 7.26 32.72 4.02
3073 8041 0.801067 GTGTGCGTATCGTCCAGGAC 60.801 60.000 9.92 9.92 0.00 3.85
3074 8042 1.245376 TGTGTGCGTATCGTCCAGGA 61.245 55.000 0.00 0.00 0.00 3.86
3075 8043 0.389296 TTGTGTGCGTATCGTCCAGG 60.389 55.000 0.00 0.00 0.00 4.45
3076 8044 0.713883 GTTGTGTGCGTATCGTCCAG 59.286 55.000 0.00 0.00 0.00 3.86
3077 8045 0.032267 TGTTGTGTGCGTATCGTCCA 59.968 50.000 0.00 0.00 0.00 4.02
3078 8046 0.437295 GTGTTGTGTGCGTATCGTCC 59.563 55.000 0.00 0.00 0.00 4.79
3079 8047 1.385743 GAGTGTTGTGTGCGTATCGTC 59.614 52.381 0.00 0.00 0.00 4.20
3080 8048 1.269361 TGAGTGTTGTGTGCGTATCGT 60.269 47.619 0.00 0.00 0.00 3.73
3081 8049 1.414378 TGAGTGTTGTGTGCGTATCG 58.586 50.000 0.00 0.00 0.00 2.92
3082 8050 3.870723 TTTGAGTGTTGTGTGCGTATC 57.129 42.857 0.00 0.00 0.00 2.24
3083 8051 3.120683 CGATTTGAGTGTTGTGTGCGTAT 60.121 43.478 0.00 0.00 0.00 3.06
3084 8052 2.219903 CGATTTGAGTGTTGTGTGCGTA 59.780 45.455 0.00 0.00 0.00 4.42
3085 8053 1.003972 CGATTTGAGTGTTGTGTGCGT 60.004 47.619 0.00 0.00 0.00 5.24
3086 8054 1.260297 TCGATTTGAGTGTTGTGTGCG 59.740 47.619 0.00 0.00 0.00 5.34
3087 8055 3.035942 GTTCGATTTGAGTGTTGTGTGC 58.964 45.455 0.00 0.00 0.00 4.57
3088 8056 3.279950 CGTTCGATTTGAGTGTTGTGTG 58.720 45.455 0.00 0.00 0.00 3.82
3089 8057 2.286833 CCGTTCGATTTGAGTGTTGTGT 59.713 45.455 0.00 0.00 0.00 3.72
3090 8058 2.349438 CCCGTTCGATTTGAGTGTTGTG 60.349 50.000 0.00 0.00 0.00 3.33
3091 8059 1.871039 CCCGTTCGATTTGAGTGTTGT 59.129 47.619 0.00 0.00 0.00 3.32
3092 8060 1.196808 CCCCGTTCGATTTGAGTGTTG 59.803 52.381 0.00 0.00 0.00 3.33
3093 8061 1.071071 TCCCCGTTCGATTTGAGTGTT 59.929 47.619 0.00 0.00 0.00 3.32
3094 8062 0.682852 TCCCCGTTCGATTTGAGTGT 59.317 50.000 0.00 0.00 0.00 3.55
3095 8063 3.525619 TCCCCGTTCGATTTGAGTG 57.474 52.632 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.