Multiple sequence alignment - TraesCS3D01G326800

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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 TraesCS3D01G326800 chr3D 100.000 3880 0 0 1 3880 438644467 438640588 0.000000e+00 7166
1 TraesCS3D01G326800 chr3D 82.522 452 55 17 1 441 43036084 43036522 3.660000e-100 375
2 TraesCS3D01G326800 chr3D 81.778 450 50 23 1 441 553166638 553167064 7.980000e-92 348
3 TraesCS3D01G326800 chr3B 88.354 3469 217 89 1 3413 574830938 574827601 0.000000e+00 3995
4 TraesCS3D01G326800 chr3B 88.260 2334 164 49 1562 3880 574829401 574827163 0.000000e+00 2691
5 TraesCS3D01G326800 chr3A 88.898 1279 78 28 2534 3799 577634924 577633697 0.000000e+00 1517
6 TraesCS3D01G326800 chr3A 92.533 991 36 12 547 1535 577636662 577635708 0.000000e+00 1386
7 TraesCS3D01G326800 chr3A 90.067 745 55 6 1562 2305 577635647 577634921 0.000000e+00 948
8 TraesCS3D01G326800 chr6D 83.111 450 44 18 1 441 36059205 36059631 7.870000e-102 381
9 TraesCS3D01G326800 chr7D 82.628 449 54 17 1 441 617269656 617270088 3.660000e-100 375
10 TraesCS3D01G326800 chr5B 82.444 450 55 18 1 442 358002415 358001982 4.730000e-99 372
11 TraesCS3D01G326800 chr2D 82.340 453 55 20 1 442 247368816 247369254 1.700000e-98 370
12 TraesCS3D01G326800 chr5D 82.405 449 51 21 1 441 403943642 403943214 2.200000e-97 366
13 TraesCS3D01G326800 chr5D 85.650 223 24 8 229 446 404033230 404033449 1.080000e-55 228
14 TraesCS3D01G326800 chr1D 82.040 451 55 19 3 441 411056732 411057168 1.020000e-95 361
15 TraesCS3D01G326800 chr1D 92.547 161 9 1 1 161 352375931 352375774 1.080000e-55 228
16 TraesCS3D01G326800 chr1B 81.978 455 55 21 1 444 24693980 24693542 1.020000e-95 361
17 TraesCS3D01G326800 chr2B 81.739 460 55 18 1 441 692621954 692622403 1.330000e-94 357
18 TraesCS3D01G326800 chr6A 80.942 446 61 20 1 441 34212852 34212426 8.040000e-87 331
19 TraesCS3D01G326800 chr6A 85.124 242 27 7 208 441 715424 715664 5.010000e-59 239
20 TraesCS3D01G326800 chr2A 87.963 216 22 4 229 441 58405123 58404909 6.440000e-63 252


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 TraesCS3D01G326800 chr3D 438640588 438644467 3879 True 7166.000000 7166 100.000000 1 3880 1 chr3D.!!$R1 3879
1 TraesCS3D01G326800 chr3B 574827163 574830938 3775 True 3343.000000 3995 88.307000 1 3880 2 chr3B.!!$R1 3879
2 TraesCS3D01G326800 chr3A 577633697 577636662 2965 True 1283.666667 1517 90.499333 547 3799 3 chr3A.!!$R1 3252

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
129 130 0.104144 TTCCAGGGAAGGGGAGAACA 60.104 55.0 0.00 0.00 34.02 3.18 F
607 609 0.107214 TGGGTGGTATTGCAGCTAGC 60.107 55.0 6.62 6.62 45.96 3.42 F
1267 1279 0.110486 TTTGCTTTCCTCTTCCCGCT 59.890 50.0 0.00 0.00 0.00 5.52 F
1989 2038 0.036294 GGTACAGCAGAACCTCACCC 60.036 60.0 0.00 0.00 32.72 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1346 0.032678 GATCGCGGATGACCATCACT 59.967 55.0 6.13 0.0 39.54 3.41 R
1974 2023 0.038744 AATGGGGTGAGGTTCTGCTG 59.961 55.0 0.00 0.0 0.00 4.41 R
2707 2769 0.623723 AGATGGGTTACATGCCGGTT 59.376 50.0 1.90 0.0 40.72 4.44 R
3620 3706 0.602106 CATCTCCGGTGCTATGCCTG 60.602 60.0 0.00 0.0 0.00 4.85 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
66 67 3.293337 CCATCATTCCAAGAAGGCATCA 58.707 45.455 0.00 0.00 37.29 3.07
102 103 3.771160 GGAGGTGGTCGGCGACAT 61.771 66.667 37.13 21.65 33.68 3.06
114 115 2.032634 GCGACATTGGCGAGTTCCA 61.033 57.895 17.84 0.00 0.00 3.53
129 130 0.104144 TTCCAGGGAAGGGGAGAACA 60.104 55.000 0.00 0.00 34.02 3.18
155 156 1.687493 GGGGGAGAGAGTGGGAGTG 60.687 68.421 0.00 0.00 0.00 3.51
156 157 1.687493 GGGGAGAGAGTGGGAGTGG 60.687 68.421 0.00 0.00 0.00 4.00
157 158 1.687493 GGGAGAGAGTGGGAGTGGG 60.687 68.421 0.00 0.00 0.00 4.61
158 159 1.079438 GGAGAGAGTGGGAGTGGGT 59.921 63.158 0.00 0.00 0.00 4.51
159 160 1.261238 GGAGAGAGTGGGAGTGGGTG 61.261 65.000 0.00 0.00 0.00 4.61
160 161 0.251832 GAGAGAGTGGGAGTGGGTGA 60.252 60.000 0.00 0.00 0.00 4.02
161 162 0.252012 AGAGAGTGGGAGTGGGTGAG 60.252 60.000 0.00 0.00 0.00 3.51
162 163 1.893919 GAGAGTGGGAGTGGGTGAGC 61.894 65.000 0.00 0.00 0.00 4.26
163 164 3.302347 GAGTGGGAGTGGGTGAGCG 62.302 68.421 0.00 0.00 0.00 5.03
164 165 3.311110 GTGGGAGTGGGTGAGCGA 61.311 66.667 0.00 0.00 0.00 4.93
165 166 2.997315 TGGGAGTGGGTGAGCGAG 60.997 66.667 0.00 0.00 0.00 5.03
166 167 2.680352 GGGAGTGGGTGAGCGAGA 60.680 66.667 0.00 0.00 0.00 4.04
167 168 2.716017 GGGAGTGGGTGAGCGAGAG 61.716 68.421 0.00 0.00 0.00 3.20
168 169 1.979693 GGAGTGGGTGAGCGAGAGT 60.980 63.158 0.00 0.00 0.00 3.24
169 170 1.214062 GAGTGGGTGAGCGAGAGTG 59.786 63.158 0.00 0.00 0.00 3.51
170 171 2.219325 GAGTGGGTGAGCGAGAGTGG 62.219 65.000 0.00 0.00 0.00 4.00
171 172 2.997315 TGGGTGAGCGAGAGTGGG 60.997 66.667 0.00 0.00 0.00 4.61
172 173 2.680352 GGGTGAGCGAGAGTGGGA 60.680 66.667 0.00 0.00 0.00 4.37
173 174 2.716017 GGGTGAGCGAGAGTGGGAG 61.716 68.421 0.00 0.00 0.00 4.30
174 175 1.979693 GGTGAGCGAGAGTGGGAGT 60.980 63.158 0.00 0.00 0.00 3.85
193 194 2.716017 GGGTGAGCGAGAGTGGGAG 61.716 68.421 0.00 0.00 0.00 4.30
209 210 0.977395 GGAGTGGGTGACTAAGCACT 59.023 55.000 0.00 0.00 38.78 4.40
244 245 1.935933 GTTCTAACGGCCGTCATCAT 58.064 50.000 34.29 18.74 0.00 2.45
273 274 2.954611 GCCTCTGGCCGACAAAAC 59.045 61.111 0.00 0.00 44.06 2.43
302 303 1.101049 CGGGCCCCACATGTCATAAC 61.101 60.000 18.66 0.00 0.00 1.89
330 331 5.003121 GCTTAAAATGTAACGATTCGGCAAC 59.997 40.000 11.29 5.96 0.00 4.17
336 337 0.611714 AACGATTCGGCAACTAGGGT 59.388 50.000 11.29 0.00 0.00 4.34
337 338 0.611714 ACGATTCGGCAACTAGGGTT 59.388 50.000 11.29 0.00 35.86 4.11
349 350 2.594131 ACTAGGGTTTTTGGAACAGCC 58.406 47.619 0.00 0.00 42.39 4.85
457 459 6.417191 TTTACTCTTCATTACGAACATGCC 57.583 37.500 0.00 0.00 0.00 4.40
471 473 1.233019 CATGCCGGCTCCTTCATAAG 58.767 55.000 29.70 0.00 0.00 1.73
497 499 3.020102 GCAACAAGCCACGCTAATG 57.980 52.632 0.00 0.00 38.25 1.90
498 500 1.072666 GCAACAAGCCACGCTAATGC 61.073 55.000 3.50 3.50 38.25 3.56
499 501 0.523072 CAACAAGCCACGCTAATGCT 59.477 50.000 0.00 0.00 38.25 3.79
500 502 1.737236 CAACAAGCCACGCTAATGCTA 59.263 47.619 0.00 0.00 38.25 3.49
501 503 2.107950 ACAAGCCACGCTAATGCTAA 57.892 45.000 0.00 0.00 38.25 3.09
502 504 2.643551 ACAAGCCACGCTAATGCTAAT 58.356 42.857 0.00 0.00 38.25 1.73
607 609 0.107214 TGGGTGGTATTGCAGCTAGC 60.107 55.000 6.62 6.62 45.96 3.42
658 660 1.065928 GTAGACGCAGACGATGGGG 59.934 63.158 12.41 1.98 45.85 4.96
875 878 1.153289 CCCACTCGCAGGATTGGAG 60.153 63.158 2.42 0.00 43.74 3.86
1260 1272 2.573915 CTCCCCTACTTTGCTTTCCTCT 59.426 50.000 0.00 0.00 0.00 3.69
1261 1273 2.986728 TCCCCTACTTTGCTTTCCTCTT 59.013 45.455 0.00 0.00 0.00 2.85
1262 1274 3.009143 TCCCCTACTTTGCTTTCCTCTTC 59.991 47.826 0.00 0.00 0.00 2.87
1264 1276 3.348119 CCTACTTTGCTTTCCTCTTCCC 58.652 50.000 0.00 0.00 0.00 3.97
1265 1277 1.897560 ACTTTGCTTTCCTCTTCCCG 58.102 50.000 0.00 0.00 0.00 5.14
1267 1279 0.110486 TTTGCTTTCCTCTTCCCGCT 59.890 50.000 0.00 0.00 0.00 5.52
1268 1280 0.321653 TTGCTTTCCTCTTCCCGCTC 60.322 55.000 0.00 0.00 0.00 5.03
1269 1281 1.296715 GCTTTCCTCTTCCCGCTCA 59.703 57.895 0.00 0.00 0.00 4.26
1271 1283 0.742635 CTTTCCTCTTCCCGCTCAGC 60.743 60.000 0.00 0.00 0.00 4.26
1272 1284 1.194781 TTTCCTCTTCCCGCTCAGCT 61.195 55.000 0.00 0.00 0.00 4.24
1273 1285 1.194781 TTCCTCTTCCCGCTCAGCTT 61.195 55.000 0.00 0.00 0.00 3.74
1274 1286 1.449246 CCTCTTCCCGCTCAGCTTG 60.449 63.158 0.00 0.00 0.00 4.01
1333 1346 3.634448 TGTTTTTCCTTTTCGCTGATGGA 59.366 39.130 0.00 0.00 0.00 3.41
1334 1347 4.229876 GTTTTTCCTTTTCGCTGATGGAG 58.770 43.478 0.00 0.00 0.00 3.86
1335 1348 2.859165 TTCCTTTTCGCTGATGGAGT 57.141 45.000 0.00 0.00 0.00 3.85
1336 1349 2.099141 TCCTTTTCGCTGATGGAGTG 57.901 50.000 0.00 0.00 0.00 3.51
1337 1350 1.623311 TCCTTTTCGCTGATGGAGTGA 59.377 47.619 0.00 0.00 39.55 3.41
1338 1351 2.237143 TCCTTTTCGCTGATGGAGTGAT 59.763 45.455 0.00 0.00 40.96 3.06
1339 1352 2.353889 CCTTTTCGCTGATGGAGTGATG 59.646 50.000 0.00 0.00 40.96 3.07
1340 1353 2.028420 TTTCGCTGATGGAGTGATGG 57.972 50.000 0.00 0.00 40.96 3.51
1386 1399 5.456192 CGACAACTTCGCTAGATTTGAAT 57.544 39.130 0.00 0.00 41.87 2.57
1404 1417 1.917872 ATCCCTAGCTCCATCGTCTC 58.082 55.000 0.00 0.00 0.00 3.36
1452 1465 0.868177 GACCGGTGTTTGTTTTGCCG 60.868 55.000 14.63 0.00 41.82 5.69
1535 1549 2.356673 CTGCTCTGCTGTGCACGA 60.357 61.111 15.21 1.93 37.71 4.35
1536 1550 2.662857 TGCTCTGCTGTGCACGAC 60.663 61.111 15.21 7.19 37.71 4.34
1537 1551 2.356793 GCTCTGCTGTGCACGACT 60.357 61.111 13.13 0.00 33.79 4.18
1538 1552 2.665395 GCTCTGCTGTGCACGACTG 61.665 63.158 13.13 10.58 33.79 3.51
1539 1553 2.662857 TCTGCTGTGCACGACTGC 60.663 61.111 13.13 13.79 46.86 4.40
1554 1568 4.292208 TGCGCGTTGTGCAAGTCG 62.292 61.111 8.43 0.00 46.28 4.18
1556 1570 4.000557 CGCGTTGTGCAAGTCGCT 62.001 61.111 21.59 0.00 46.97 4.93
1559 1573 1.369209 CGTTGTGCAAGTCGCTTGG 60.369 57.895 17.36 4.19 41.31 3.61
1560 1574 1.727467 GTTGTGCAAGTCGCTTGGT 59.273 52.632 17.36 0.00 41.31 3.67
1578 1626 4.202245 TGGTGCCTCTACAATTCTACAC 57.798 45.455 0.00 0.00 0.00 2.90
1652 1700 2.701951 TGCTGCCTGATGATGAGTGATA 59.298 45.455 0.00 0.00 0.00 2.15
1657 1706 3.244146 GCCTGATGATGAGTGATACTGCT 60.244 47.826 0.00 0.00 0.00 4.24
1663 1712 4.745351 TGATGAGTGATACTGCTAGGGAT 58.255 43.478 0.00 0.00 0.00 3.85
1684 1733 3.034635 TCTCTAGGGACAATTCAGAGCC 58.965 50.000 0.00 0.00 34.12 4.70
1686 1735 2.768527 TCTAGGGACAATTCAGAGCCAG 59.231 50.000 0.00 0.00 0.00 4.85
1691 1740 2.746362 GGACAATTCAGAGCCAGTCAAG 59.254 50.000 0.00 0.00 0.00 3.02
1692 1741 3.557898 GGACAATTCAGAGCCAGTCAAGA 60.558 47.826 0.00 0.00 0.00 3.02
1695 1744 4.284490 ACAATTCAGAGCCAGTCAAGACTA 59.716 41.667 1.86 0.00 40.20 2.59
1702 1751 5.121454 CAGAGCCAGTCAAGACTACATTTTC 59.879 44.000 1.86 0.00 40.20 2.29
1707 1756 4.999950 CAGTCAAGACTACATTTTCTGCCT 59.000 41.667 1.86 0.00 40.20 4.75
1709 1758 6.312426 CAGTCAAGACTACATTTTCTGCCTAG 59.688 42.308 1.86 0.00 40.20 3.02
1739 1788 2.363306 ATGTTGGTGAAGTTCTGCCA 57.637 45.000 13.34 13.34 0.00 4.92
1763 1812 3.340814 AATGGCAGTCTCCTAACACTG 57.659 47.619 0.00 0.00 42.61 3.66
1767 1816 3.327757 TGGCAGTCTCCTAACACTGATTT 59.672 43.478 3.24 0.00 42.37 2.17
1770 1819 4.390297 GCAGTCTCCTAACACTGATTTGTC 59.610 45.833 3.24 0.00 42.37 3.18
1771 1820 5.541845 CAGTCTCCTAACACTGATTTGTCA 58.458 41.667 0.00 0.00 42.37 3.58
1775 1824 7.721399 AGTCTCCTAACACTGATTTGTCATTTT 59.279 33.333 0.00 0.00 0.00 1.82
1783 1832 8.638685 ACACTGATTTGTCATTTTTCTCTTTG 57.361 30.769 0.00 0.00 0.00 2.77
1808 1857 4.563337 TCAGATATACGTGTTCTTCCCG 57.437 45.455 0.00 0.00 0.00 5.14
1850 1899 3.987868 TGAAGCACATCAAGAAGTACGTC 59.012 43.478 0.00 0.00 0.00 4.34
1892 1941 3.243724 AGTCTCCAGGGCTATATTGGTC 58.756 50.000 0.00 0.00 33.65 4.02
1898 1947 1.070758 AGGGCTATATTGGTCGTGCAG 59.929 52.381 0.00 0.00 0.00 4.41
1977 2026 1.822506 GGAGGTTTTCCAGGTACAGC 58.177 55.000 0.00 0.00 46.01 4.40
1978 2027 1.073284 GGAGGTTTTCCAGGTACAGCA 59.927 52.381 0.00 0.00 46.01 4.41
1979 2028 2.427506 GAGGTTTTCCAGGTACAGCAG 58.572 52.381 0.00 0.00 43.73 4.24
1980 2029 2.038557 GAGGTTTTCCAGGTACAGCAGA 59.961 50.000 0.00 0.00 43.73 4.26
1981 2030 2.441750 AGGTTTTCCAGGTACAGCAGAA 59.558 45.455 0.00 0.00 43.73 3.02
1982 2031 2.552743 GGTTTTCCAGGTACAGCAGAAC 59.447 50.000 0.00 0.00 40.31 3.01
1983 2032 2.552743 GTTTTCCAGGTACAGCAGAACC 59.447 50.000 0.00 0.00 35.91 3.62
1985 2034 1.267121 TCCAGGTACAGCAGAACCTC 58.733 55.000 0.00 0.00 44.43 3.85
1986 2035 0.976641 CCAGGTACAGCAGAACCTCA 59.023 55.000 0.00 0.00 44.43 3.86
1987 2036 1.338200 CCAGGTACAGCAGAACCTCAC 60.338 57.143 0.00 0.00 44.43 3.51
1988 2037 0.977395 AGGTACAGCAGAACCTCACC 59.023 55.000 0.00 0.00 42.60 4.02
1989 2038 0.036294 GGTACAGCAGAACCTCACCC 60.036 60.000 0.00 0.00 32.72 4.61
1990 2039 0.036294 GTACAGCAGAACCTCACCCC 60.036 60.000 0.00 0.00 0.00 4.95
1991 2040 0.472925 TACAGCAGAACCTCACCCCA 60.473 55.000 0.00 0.00 0.00 4.96
2077 2133 0.586802 GAAGCAACGAACCACAGGAC 59.413 55.000 0.00 0.00 0.00 3.85
2080 2136 2.660552 AACGAACCACAGGACGCG 60.661 61.111 3.53 3.53 32.29 6.01
2239 2295 4.622260 AGTTGCACTAATTTTGGGCATT 57.378 36.364 8.56 0.00 34.03 3.56
2257 2313 3.745480 GCATTAGTAGAGCCAGCCAATCA 60.745 47.826 0.00 0.00 0.00 2.57
2258 2314 4.454678 CATTAGTAGAGCCAGCCAATCAA 58.545 43.478 0.00 0.00 0.00 2.57
2261 2317 2.012673 GTAGAGCCAGCCAATCAAGTG 58.987 52.381 0.00 0.00 0.00 3.16
2271 2327 3.584848 AGCCAATCAAGTGTCTAGTTCCT 59.415 43.478 0.00 0.00 0.00 3.36
2301 2357 4.164796 AGCAATATGGTGAACATCAGAGGA 59.835 41.667 0.00 0.00 41.03 3.71
2302 2358 4.883585 GCAATATGGTGAACATCAGAGGAA 59.116 41.667 0.00 0.00 41.03 3.36
2303 2359 5.220931 GCAATATGGTGAACATCAGAGGAAC 60.221 44.000 0.00 0.00 41.03 3.62
2304 2360 5.698741 ATATGGTGAACATCAGAGGAACA 57.301 39.130 0.00 0.00 41.03 3.18
2308 2364 4.042062 TGGTGAACATCAGAGGAACAAGAT 59.958 41.667 0.00 0.00 0.00 2.40
2309 2365 4.394300 GGTGAACATCAGAGGAACAAGATG 59.606 45.833 0.00 0.00 42.61 2.90
2341 2397 9.817809 CCTTGATAGTTATAGTAAAAGCTGTCA 57.182 33.333 0.00 0.00 0.00 3.58
2431 2493 5.945144 AGTTCCATTAACTACGGGTATGT 57.055 39.130 0.00 0.00 46.85 2.29
2433 2495 7.047460 AGTTCCATTAACTACGGGTATGTAG 57.953 40.000 0.00 0.00 46.85 2.74
2464 2526 3.573967 CAGACCCATTTTAGGCACAAACT 59.426 43.478 0.00 0.00 0.00 2.66
2473 2535 9.131791 CCATTTTAGGCACAAACTAATATAGGT 57.868 33.333 0.00 0.00 31.12 3.08
2477 2539 6.808321 AGGCACAAACTAATATAGGTCAGA 57.192 37.500 0.00 0.00 0.00 3.27
2482 2544 9.331282 GCACAAACTAATATAGGTCAGAGAAAT 57.669 33.333 0.00 0.00 0.00 2.17
2511 2573 8.514594 TGACAATCTTTTAAATGCCTGTTCTAG 58.485 33.333 8.36 0.00 0.00 2.43
2589 2651 9.842775 TTGATGATATTTATCTATGGGAGATGC 57.157 33.333 0.00 0.00 45.05 3.91
2605 2667 5.477291 GGGAGATGCACTACAATAGCTACTA 59.523 44.000 0.00 0.00 0.00 1.82
2622 2684 5.474876 AGCTACTAAATCTTGCTTGTTTGCT 59.525 36.000 0.00 0.00 0.00 3.91
2630 2692 5.261209 TCTTGCTTGTTTGCTAACACATT 57.739 34.783 13.36 0.00 43.66 2.71
2651 2713 4.952262 TCATGCTTCTATCACTTGTTGC 57.048 40.909 0.00 0.00 0.00 4.17
2667 2729 0.111061 TTGCTGCATGACACCCTCTT 59.889 50.000 1.84 0.00 0.00 2.85
2683 2745 7.514721 ACACCCTCTTCATTTTTCAGTACTTA 58.485 34.615 0.00 0.00 0.00 2.24
2688 2750 9.092876 CCTCTTCATTTTTCAGTACTTAGCTAG 57.907 37.037 0.00 0.00 0.00 3.42
2689 2751 9.862371 CTCTTCATTTTTCAGTACTTAGCTAGA 57.138 33.333 0.00 0.00 0.00 2.43
2725 2787 2.218603 CTAACCGGCATGTAACCCATC 58.781 52.381 0.00 0.00 0.00 3.51
2768 2830 6.560253 ACAAAACAGCTACCAAGAATACAG 57.440 37.500 0.00 0.00 0.00 2.74
2774 2836 7.182817 ACAGCTACCAAGAATACAGATTACA 57.817 36.000 0.00 0.00 0.00 2.41
2890 2952 6.237569 CGCTATGTTGTATGACAGTACACAAG 60.238 42.308 0.00 0.00 34.50 3.16
2891 2953 6.590292 GCTATGTTGTATGACAGTACACAAGT 59.410 38.462 0.00 0.00 34.50 3.16
2892 2954 6.785488 ATGTTGTATGACAGTACACAAGTG 57.215 37.500 0.00 0.00 34.50 3.16
2893 2955 5.908341 TGTTGTATGACAGTACACAAGTGA 58.092 37.500 7.28 0.00 34.50 3.41
2894 2956 5.983118 TGTTGTATGACAGTACACAAGTGAG 59.017 40.000 7.28 0.00 34.50 3.51
2895 2957 5.134202 TGTATGACAGTACACAAGTGAGG 57.866 43.478 7.28 0.00 32.41 3.86
2896 2958 4.587262 TGTATGACAGTACACAAGTGAGGT 59.413 41.667 7.28 0.00 32.41 3.85
2897 2959 3.452755 TGACAGTACACAAGTGAGGTG 57.547 47.619 7.28 3.49 41.95 4.00
2898 2960 3.028130 TGACAGTACACAAGTGAGGTGA 58.972 45.455 7.28 0.00 39.53 4.02
2899 2961 3.449377 TGACAGTACACAAGTGAGGTGAA 59.551 43.478 7.28 0.00 39.53 3.18
2900 2962 4.051922 GACAGTACACAAGTGAGGTGAAG 58.948 47.826 7.28 0.00 39.53 3.02
2901 2963 3.181465 ACAGTACACAAGTGAGGTGAAGG 60.181 47.826 7.28 0.00 39.53 3.46
2902 2964 3.039011 AGTACACAAGTGAGGTGAAGGT 58.961 45.455 7.28 0.00 39.53 3.50
2903 2965 2.622064 ACACAAGTGAGGTGAAGGTC 57.378 50.000 7.28 0.00 39.53 3.85
2971 3039 2.593026 ACCCATTCGCTTGGAGAAAAA 58.407 42.857 5.15 0.00 39.25 1.94
2972 3040 2.296190 ACCCATTCGCTTGGAGAAAAAC 59.704 45.455 5.15 0.00 39.25 2.43
2975 3043 0.309612 TTCGCTTGGAGAAAAACGGC 59.690 50.000 0.00 0.00 0.00 5.68
2978 3046 1.729149 CGCTTGGAGAAAAACGGCATC 60.729 52.381 0.00 0.00 0.00 3.91
2989 3057 1.514678 AACGGCATCGCTTCAAGCAA 61.515 50.000 10.73 0.00 42.58 3.91
3086 3154 4.454161 TCCTCATGTTGTACCATTGTTTCG 59.546 41.667 0.00 0.00 0.00 3.46
3087 3155 4.215399 CCTCATGTTGTACCATTGTTTCGT 59.785 41.667 0.00 0.00 0.00 3.85
3111 3179 8.592998 CGTGAACTTTATAGAACATACAGAACC 58.407 37.037 0.00 0.00 0.00 3.62
3237 3314 0.675208 GTGTGTGTGTGTGGTGGTGA 60.675 55.000 0.00 0.00 0.00 4.02
3254 3331 3.622612 TGGTGATATGCGTGATGAACTTG 59.377 43.478 0.00 0.00 0.00 3.16
3258 3338 5.509272 GTGATATGCGTGATGAACTTGTTTG 59.491 40.000 0.00 0.00 0.00 2.93
3259 3339 2.118228 TGCGTGATGAACTTGTTTGC 57.882 45.000 0.00 0.00 0.00 3.68
3260 3340 1.403323 TGCGTGATGAACTTGTTTGCA 59.597 42.857 0.00 0.00 0.00 4.08
3261 3341 2.159324 TGCGTGATGAACTTGTTTGCAA 60.159 40.909 0.00 0.00 0.00 4.08
3262 3342 3.052036 GCGTGATGAACTTGTTTGCAAT 58.948 40.909 0.00 0.00 33.65 3.56
3263 3343 4.225984 GCGTGATGAACTTGTTTGCAATA 58.774 39.130 0.00 0.00 33.65 1.90
3264 3344 4.858692 GCGTGATGAACTTGTTTGCAATAT 59.141 37.500 0.00 0.00 33.65 1.28
3265 3345 6.027131 GCGTGATGAACTTGTTTGCAATATA 58.973 36.000 0.00 0.00 33.65 0.86
3266 3346 6.021468 GCGTGATGAACTTGTTTGCAATATAC 60.021 38.462 0.00 0.00 33.65 1.47
3267 3347 6.468956 CGTGATGAACTTGTTTGCAATATACC 59.531 38.462 0.00 0.00 33.65 2.73
3268 3348 6.751888 GTGATGAACTTGTTTGCAATATACCC 59.248 38.462 0.00 0.00 33.65 3.69
3269 3349 5.652994 TGAACTTGTTTGCAATATACCCC 57.347 39.130 0.00 0.00 33.65 4.95
3270 3350 5.080337 TGAACTTGTTTGCAATATACCCCA 58.920 37.500 0.00 0.00 33.65 4.96
3271 3351 5.047660 TGAACTTGTTTGCAATATACCCCAC 60.048 40.000 0.00 0.00 33.65 4.61
3272 3352 4.411927 ACTTGTTTGCAATATACCCCACA 58.588 39.130 0.00 0.00 33.65 4.17
3273 3353 4.835615 ACTTGTTTGCAATATACCCCACAA 59.164 37.500 0.00 4.41 33.65 3.33
3274 3354 5.305644 ACTTGTTTGCAATATACCCCACAAA 59.694 36.000 0.00 0.00 33.65 2.83
3275 3355 5.808366 TGTTTGCAATATACCCCACAAAA 57.192 34.783 0.00 0.00 0.00 2.44
3276 3356 6.174720 TGTTTGCAATATACCCCACAAAAA 57.825 33.333 0.00 0.00 0.00 1.94
3336 3416 4.800471 GCATTGTAAGCATTTACTCAAGGC 59.200 41.667 0.00 0.00 42.83 4.35
3359 3439 5.177511 GCAAAGGGAAAATTGCTCTGTTTAC 59.822 40.000 3.41 0.00 46.42 2.01
3388 3468 4.435651 CCTTCGTTTGGAATTAACTCTCGC 60.436 45.833 0.00 0.00 33.26 5.03
3417 3497 5.773239 TTTCATCGACAGTTAATTCCGAC 57.227 39.130 0.00 0.00 31.85 4.79
3438 3524 2.819726 CGGAGGGAGTAGGATGTAGCAT 60.820 54.545 0.00 0.00 0.00 3.79
3458 3544 4.201851 GCATCTAGCAACATACCACAGTTG 60.202 45.833 0.00 0.00 45.91 3.16
3522 3608 0.253327 CTGGGCTGGGGTTTACTCTC 59.747 60.000 0.00 0.00 0.00 3.20
3545 3631 4.365514 TCATGAAAGAAAGGGTAGTGCA 57.634 40.909 0.00 0.00 0.00 4.57
3569 3655 1.165270 ATCTTGCCGGTACTGTTTGC 58.835 50.000 1.90 0.00 0.00 3.68
3593 3679 2.211353 GGAACGCTACTCTGATCACC 57.789 55.000 0.00 0.00 0.00 4.02
3669 3755 5.726980 ATGACAGGAATTGCAAAGCTAAA 57.273 34.783 1.71 0.00 0.00 1.85
3671 3757 4.340666 TGACAGGAATTGCAAAGCTAAACA 59.659 37.500 1.71 0.00 0.00 2.83
3756 3842 2.223782 GCTGGACAAACAAGTGAATGCA 60.224 45.455 0.00 0.00 0.00 3.96
3776 3862 0.179105 AAACAGCGACCACACGTACA 60.179 50.000 0.00 0.00 35.59 2.90
3808 3894 4.043037 GACCAGGTCGTCCTAACAATAG 57.957 50.000 3.05 0.00 43.07 1.73
3859 3946 2.467566 ACACTAAAGCCTGTAACCGG 57.532 50.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.485582 CTCCGACGACGACAGCAT 59.514 61.111 9.28 0.00 42.66 3.79
21 22 2.098680 GAGCTCCGACGACGACAG 59.901 66.667 9.28 5.40 42.66 3.51
72 73 3.839432 CCTCCCTTCCTCGTCGCC 61.839 72.222 0.00 0.00 0.00 5.54
101 102 0.035056 CTTCCCTGGAACTCGCCAAT 60.035 55.000 0.00 0.00 37.52 3.16
102 103 1.374947 CTTCCCTGGAACTCGCCAA 59.625 57.895 0.00 0.00 37.52 4.52
110 111 0.104144 TGTTCTCCCCTTCCCTGGAA 60.104 55.000 0.00 0.00 0.00 3.53
114 115 0.912006 GCTCTGTTCTCCCCTTCCCT 60.912 60.000 0.00 0.00 0.00 4.20
155 156 2.680352 TCCCACTCTCGCTCACCC 60.680 66.667 0.00 0.00 0.00 4.61
156 157 1.979693 ACTCCCACTCTCGCTCACC 60.980 63.158 0.00 0.00 0.00 4.02
157 158 1.214062 CACTCCCACTCTCGCTCAC 59.786 63.158 0.00 0.00 0.00 3.51
158 159 1.979155 CCACTCCCACTCTCGCTCA 60.979 63.158 0.00 0.00 0.00 4.26
159 160 2.716017 CCCACTCCCACTCTCGCTC 61.716 68.421 0.00 0.00 0.00 5.03
160 161 2.681778 CCCACTCCCACTCTCGCT 60.682 66.667 0.00 0.00 0.00 4.93
161 162 2.997897 ACCCACTCCCACTCTCGC 60.998 66.667 0.00 0.00 0.00 5.03
162 163 1.599606 CTCACCCACTCCCACTCTCG 61.600 65.000 0.00 0.00 0.00 4.04
163 164 1.893919 GCTCACCCACTCCCACTCTC 61.894 65.000 0.00 0.00 0.00 3.20
164 165 1.915769 GCTCACCCACTCCCACTCT 60.916 63.158 0.00 0.00 0.00 3.24
165 166 2.665603 GCTCACCCACTCCCACTC 59.334 66.667 0.00 0.00 0.00 3.51
166 167 3.314331 CGCTCACCCACTCCCACT 61.314 66.667 0.00 0.00 0.00 4.00
167 168 3.302347 CTCGCTCACCCACTCCCAC 62.302 68.421 0.00 0.00 0.00 4.61
168 169 2.997315 CTCGCTCACCCACTCCCA 60.997 66.667 0.00 0.00 0.00 4.37
169 170 2.680352 TCTCGCTCACCCACTCCC 60.680 66.667 0.00 0.00 0.00 4.30
170 171 1.979693 ACTCTCGCTCACCCACTCC 60.980 63.158 0.00 0.00 0.00 3.85
171 172 1.214062 CACTCTCGCTCACCCACTC 59.786 63.158 0.00 0.00 0.00 3.51
172 173 2.279069 CCACTCTCGCTCACCCACT 61.279 63.158 0.00 0.00 0.00 4.00
173 174 2.262915 CCACTCTCGCTCACCCAC 59.737 66.667 0.00 0.00 0.00 4.61
174 175 2.997315 CCCACTCTCGCTCACCCA 60.997 66.667 0.00 0.00 0.00 4.51
193 194 1.202770 ACCAAGTGCTTAGTCACCCAC 60.203 52.381 3.84 0.00 37.68 4.61
260 261 0.310854 GTCAAGGTTTTGTCGGCCAG 59.689 55.000 2.24 0.00 35.73 4.85
266 267 1.281656 CGCCCGTCAAGGTTTTGTC 59.718 57.895 0.00 0.00 38.74 3.18
302 303 2.791417 TCGTTACATTTTAAGCGCGG 57.209 45.000 8.83 0.00 0.00 6.46
330 331 1.893137 GGGCTGTTCCAAAAACCCTAG 59.107 52.381 0.00 0.00 36.21 3.02
336 337 0.827368 GTGGTGGGCTGTTCCAAAAA 59.173 50.000 0.00 0.00 38.72 1.94
337 338 0.032615 AGTGGTGGGCTGTTCCAAAA 60.033 50.000 0.00 0.00 38.72 2.44
386 388 7.296628 TGCTATTGTTCCAAAAACTACCATT 57.703 32.000 0.00 0.00 0.00 3.16
387 389 6.909550 TGCTATTGTTCCAAAAACTACCAT 57.090 33.333 0.00 0.00 0.00 3.55
388 390 6.266558 ACATGCTATTGTTCCAAAAACTACCA 59.733 34.615 0.00 0.00 0.00 3.25
389 391 6.687604 ACATGCTATTGTTCCAAAAACTACC 58.312 36.000 0.00 0.00 0.00 3.18
390 392 9.855021 ATTACATGCTATTGTTCCAAAAACTAC 57.145 29.630 0.00 0.00 0.00 2.73
391 393 9.853555 CATTACATGCTATTGTTCCAAAAACTA 57.146 29.630 0.00 0.00 0.00 2.24
392 394 8.367156 ACATTACATGCTATTGTTCCAAAAACT 58.633 29.630 0.00 0.00 0.00 2.66
393 395 8.434661 CACATTACATGCTATTGTTCCAAAAAC 58.565 33.333 0.00 0.00 0.00 2.43
396 398 6.210385 ACCACATTACATGCTATTGTTCCAAA 59.790 34.615 0.00 0.00 0.00 3.28
430 432 7.044706 GCATGTTCGTAATGAAGAGTAAATTGC 60.045 37.037 0.00 0.00 37.23 3.56
431 433 7.429340 GGCATGTTCGTAATGAAGAGTAAATTG 59.571 37.037 0.00 0.00 37.23 2.32
432 434 7.472543 GGCATGTTCGTAATGAAGAGTAAATT 58.527 34.615 0.00 0.00 37.23 1.82
440 442 1.268032 GCCGGCATGTTCGTAATGAAG 60.268 52.381 24.80 0.00 37.23 3.02
471 473 0.242017 GTGGCTTGTTGCTCATGACC 59.758 55.000 0.00 0.00 42.39 4.02
492 494 7.013083 GCTCCCATGGATGATAATTAGCATTAG 59.987 40.741 16.84 7.82 31.62 1.73
496 498 4.043184 TGCTCCCATGGATGATAATTAGCA 59.957 41.667 15.22 5.78 0.00 3.49
497 499 4.592942 TGCTCCCATGGATGATAATTAGC 58.407 43.478 15.22 7.98 0.00 3.09
498 500 6.479006 TCTTGCTCCCATGGATGATAATTAG 58.521 40.000 15.22 0.00 0.00 1.73
499 501 6.452757 TCTTGCTCCCATGGATGATAATTA 57.547 37.500 15.22 0.00 0.00 1.40
500 502 5.322754 CTCTTGCTCCCATGGATGATAATT 58.677 41.667 15.22 0.00 0.00 1.40
501 503 4.810033 GCTCTTGCTCCCATGGATGATAAT 60.810 45.833 15.22 0.00 36.03 1.28
502 504 3.497405 GCTCTTGCTCCCATGGATGATAA 60.497 47.826 15.22 0.82 36.03 1.75
533 535 3.181423 TGCCCAAAGTAGGAAAGAATGGT 60.181 43.478 0.00 0.00 0.00 3.55
607 609 2.847901 CTCGCAAGCAAGAATGTTCTG 58.152 47.619 0.00 0.00 35.58 3.02
658 660 1.717194 TTTTCTACCGCGATGTCACC 58.283 50.000 8.23 0.00 0.00 4.02
875 878 1.302511 TCGGCCCACTCTGCTTTTC 60.303 57.895 0.00 0.00 0.00 2.29
936 939 2.048503 CGGCTTCGGTTTCGAGGT 60.049 61.111 0.00 0.00 46.75 3.85
1260 1272 1.071699 ACTTTACAAGCTGAGCGGGAA 59.928 47.619 0.00 0.00 0.00 3.97
1261 1273 0.685097 ACTTTACAAGCTGAGCGGGA 59.315 50.000 0.00 0.00 0.00 5.14
1262 1274 2.271800 CTACTTTACAAGCTGAGCGGG 58.728 52.381 0.00 0.00 0.00 6.13
1271 1283 4.967437 ACGACGACTAGCTACTTTACAAG 58.033 43.478 0.00 0.00 0.00 3.16
1272 1284 4.142816 GGACGACGACTAGCTACTTTACAA 60.143 45.833 0.00 0.00 0.00 2.41
1273 1285 3.372206 GGACGACGACTAGCTACTTTACA 59.628 47.826 0.00 0.00 0.00 2.41
1274 1286 3.372206 TGGACGACGACTAGCTACTTTAC 59.628 47.826 0.00 0.00 0.00 2.01
1333 1346 0.032678 GATCGCGGATGACCATCACT 59.967 55.000 6.13 0.00 39.54 3.41
1334 1347 0.946221 GGATCGCGGATGACCATCAC 60.946 60.000 6.13 3.00 39.54 3.06
1335 1348 1.367471 GGATCGCGGATGACCATCA 59.633 57.895 6.13 0.00 39.54 3.07
1336 1349 1.734477 CGGATCGCGGATGACCATC 60.734 63.158 6.13 0.00 37.11 3.51
1337 1350 2.340078 CGGATCGCGGATGACCAT 59.660 61.111 6.13 0.00 35.59 3.55
1338 1351 3.133767 GACGGATCGCGGATGACCA 62.134 63.158 6.13 0.00 35.59 4.02
1339 1352 2.354773 GACGGATCGCGGATGACC 60.355 66.667 6.13 2.04 0.00 4.02
1340 1353 1.370657 GAGACGGATCGCGGATGAC 60.371 63.158 6.13 0.00 0.00 3.06
1386 1399 0.535328 CGAGACGATGGAGCTAGGGA 60.535 60.000 0.00 0.00 0.00 4.20
1535 1549 3.168237 GACTTGCACAACGCGCAGT 62.168 57.895 5.73 0.91 46.97 4.40
1536 1550 2.425773 GACTTGCACAACGCGCAG 60.426 61.111 5.73 0.08 46.97 5.18
1537 1551 4.292208 CGACTTGCACAACGCGCA 62.292 61.111 5.73 0.00 46.97 6.09
1554 1568 2.716217 AGAATTGTAGAGGCACCAAGC 58.284 47.619 0.00 0.00 44.65 4.01
1556 1570 4.041075 TGTGTAGAATTGTAGAGGCACCAA 59.959 41.667 0.00 0.00 0.00 3.67
1559 1573 4.566004 TGTGTGTAGAATTGTAGAGGCAC 58.434 43.478 0.00 0.00 0.00 5.01
1560 1574 4.882842 TGTGTGTAGAATTGTAGAGGCA 57.117 40.909 0.00 0.00 0.00 4.75
1578 1626 5.838529 TCCAATAGTACGTGGTCATATGTG 58.161 41.667 0.00 0.00 36.23 3.21
1652 1700 2.109304 GTCCCTAGAGATCCCTAGCAGT 59.891 54.545 5.76 0.00 35.86 4.40
1657 1706 5.136220 TCTGAATTGTCCCTAGAGATCCCTA 59.864 44.000 0.00 0.00 0.00 3.53
1663 1712 3.034635 GGCTCTGAATTGTCCCTAGAGA 58.965 50.000 0.00 0.00 37.63 3.10
1684 1733 4.999950 AGGCAGAAAATGTAGTCTTGACTG 59.000 41.667 12.99 0.00 0.00 3.51
1686 1735 6.166982 ACTAGGCAGAAAATGTAGTCTTGAC 58.833 40.000 0.00 0.00 0.00 3.18
1691 1740 5.064071 GCTGAACTAGGCAGAAAATGTAGTC 59.936 44.000 16.34 0.00 35.39 2.59
1692 1741 4.938226 GCTGAACTAGGCAGAAAATGTAGT 59.062 41.667 16.34 0.00 35.39 2.73
1695 1744 4.026356 AGCTGAACTAGGCAGAAAATGT 57.974 40.909 16.34 0.00 35.39 2.71
1702 1751 5.468072 CCAACATAATAGCTGAACTAGGCAG 59.532 44.000 0.00 9.74 33.29 4.85
1707 1756 7.620880 ACTTCACCAACATAATAGCTGAACTA 58.379 34.615 0.00 0.00 34.64 2.24
1709 1758 6.743575 ACTTCACCAACATAATAGCTGAAC 57.256 37.500 0.00 0.00 0.00 3.18
1739 1788 4.018960 AGTGTTAGGAGACTGCCATTTCAT 60.019 41.667 0.00 0.00 43.88 2.57
1763 1812 9.480053 TGATTCCAAAGAGAAAAATGACAAATC 57.520 29.630 0.00 0.00 0.00 2.17
1767 1816 7.822161 TCTGATTCCAAAGAGAAAAATGACA 57.178 32.000 0.00 0.00 0.00 3.58
1775 1824 7.782049 ACACGTATATCTGATTCCAAAGAGAA 58.218 34.615 0.00 0.00 0.00 2.87
1783 1832 5.927115 GGGAAGAACACGTATATCTGATTCC 59.073 44.000 0.00 0.00 0.00 3.01
1808 1857 1.080025 CCCCACCTTCTCGTCGTTC 60.080 63.158 0.00 0.00 0.00 3.95
1850 1899 1.277326 TCTCGGCGTTCATCATTTCG 58.723 50.000 6.85 0.00 0.00 3.46
1892 1941 2.320587 GGTGAGGTTCTGCTGCACG 61.321 63.158 0.00 0.00 0.00 5.34
1898 1947 0.890683 CAAATGGGGTGAGGTTCTGC 59.109 55.000 0.00 0.00 0.00 4.26
1973 2022 1.136329 ATGGGGTGAGGTTCTGCTGT 61.136 55.000 0.00 0.00 0.00 4.40
1974 2023 0.038744 AATGGGGTGAGGTTCTGCTG 59.961 55.000 0.00 0.00 0.00 4.41
1975 2024 1.668826 TAATGGGGTGAGGTTCTGCT 58.331 50.000 0.00 0.00 0.00 4.24
1976 2025 2.301346 CATAATGGGGTGAGGTTCTGC 58.699 52.381 0.00 0.00 0.00 4.26
1977 2026 2.301346 GCATAATGGGGTGAGGTTCTG 58.699 52.381 0.00 0.00 0.00 3.02
1978 2027 1.922447 TGCATAATGGGGTGAGGTTCT 59.078 47.619 0.00 0.00 0.00 3.01
1979 2028 2.024414 GTGCATAATGGGGTGAGGTTC 58.976 52.381 0.00 0.00 0.00 3.62
1980 2029 1.640670 AGTGCATAATGGGGTGAGGTT 59.359 47.619 0.00 0.00 0.00 3.50
1981 2030 1.212935 GAGTGCATAATGGGGTGAGGT 59.787 52.381 0.00 0.00 0.00 3.85
1982 2031 1.492176 AGAGTGCATAATGGGGTGAGG 59.508 52.381 0.00 0.00 0.00 3.86
1983 2032 2.171237 TCAGAGTGCATAATGGGGTGAG 59.829 50.000 0.00 0.00 0.00 3.51
1984 2033 2.195727 TCAGAGTGCATAATGGGGTGA 58.804 47.619 0.00 0.00 0.00 4.02
1985 2034 2.715749 TCAGAGTGCATAATGGGGTG 57.284 50.000 0.00 0.00 0.00 4.61
1986 2035 3.202818 TGAATCAGAGTGCATAATGGGGT 59.797 43.478 0.00 0.00 0.00 4.95
1987 2036 3.824133 TGAATCAGAGTGCATAATGGGG 58.176 45.455 0.00 0.00 0.00 4.96
1988 2037 4.037208 GGTTGAATCAGAGTGCATAATGGG 59.963 45.833 0.00 0.00 0.00 4.00
1989 2038 4.260907 CGGTTGAATCAGAGTGCATAATGG 60.261 45.833 0.00 0.00 0.00 3.16
1990 2039 4.260907 CCGGTTGAATCAGAGTGCATAATG 60.261 45.833 0.00 0.00 0.00 1.90
1991 2040 3.879295 CCGGTTGAATCAGAGTGCATAAT 59.121 43.478 0.00 0.00 0.00 1.28
2077 2133 6.742718 CCTTGATATTTATAAGCATTTCCGCG 59.257 38.462 0.00 0.00 36.85 6.46
2239 2295 3.107601 ACTTGATTGGCTGGCTCTACTA 58.892 45.455 2.00 0.00 0.00 1.82
2257 2313 7.661536 TGCTATATCAAGGAACTAGACACTT 57.338 36.000 0.00 0.00 38.49 3.16
2258 2314 7.661536 TTGCTATATCAAGGAACTAGACACT 57.338 36.000 0.00 0.00 38.49 3.55
2261 2317 9.593134 CCATATTGCTATATCAAGGAACTAGAC 57.407 37.037 0.00 0.00 38.49 2.59
2271 2327 9.223099 CTGATGTTCACCATATTGCTATATCAA 57.777 33.333 0.00 0.00 32.56 2.57
2328 2384 9.209175 CTATAGAAAGTTGTGACAGCTTTTACT 57.791 33.333 24.55 19.93 43.00 2.24
2329 2385 7.958025 GCTATAGAAAGTTGTGACAGCTTTTAC 59.042 37.037 24.55 14.84 43.00 2.01
2332 2388 5.997746 TGCTATAGAAAGTTGTGACAGCTTT 59.002 36.000 24.12 24.12 44.95 3.51
2334 2390 5.152623 TGCTATAGAAAGTTGTGACAGCT 57.847 39.130 3.21 0.00 0.00 4.24
2335 2391 5.582269 TGATGCTATAGAAAGTTGTGACAGC 59.418 40.000 3.21 0.00 0.00 4.40
2336 2392 7.413438 GGTTGATGCTATAGAAAGTTGTGACAG 60.413 40.741 3.21 0.00 0.00 3.51
2337 2393 6.371548 GGTTGATGCTATAGAAAGTTGTGACA 59.628 38.462 3.21 0.00 0.00 3.58
2338 2394 6.371548 TGGTTGATGCTATAGAAAGTTGTGAC 59.628 38.462 3.21 0.00 0.00 3.67
2339 2395 6.472016 TGGTTGATGCTATAGAAAGTTGTGA 58.528 36.000 3.21 0.00 0.00 3.58
2340 2396 6.741992 TGGTTGATGCTATAGAAAGTTGTG 57.258 37.500 3.21 0.00 0.00 3.33
2341 2397 7.629222 GCAATGGTTGATGCTATAGAAAGTTGT 60.629 37.037 3.21 0.00 39.46 3.32
2342 2398 6.694411 GCAATGGTTGATGCTATAGAAAGTTG 59.306 38.462 3.21 0.00 39.46 3.16
2426 2488 9.998106 AAATGGGTCTGATACATAACTACATAC 57.002 33.333 0.00 0.00 0.00 2.39
2430 2492 9.490379 CCTAAAATGGGTCTGATACATAACTAC 57.510 37.037 0.00 0.00 0.00 2.73
2431 2493 8.154856 GCCTAAAATGGGTCTGATACATAACTA 58.845 37.037 0.00 0.00 0.00 2.24
2432 2494 6.998673 GCCTAAAATGGGTCTGATACATAACT 59.001 38.462 0.00 0.00 0.00 2.24
2433 2495 6.770785 TGCCTAAAATGGGTCTGATACATAAC 59.229 38.462 0.00 0.00 0.00 1.89
2434 2496 6.770785 GTGCCTAAAATGGGTCTGATACATAA 59.229 38.462 0.00 0.00 0.00 1.90
2435 2497 6.126623 TGTGCCTAAAATGGGTCTGATACATA 60.127 38.462 0.00 0.00 0.00 2.29
2436 2498 5.133221 GTGCCTAAAATGGGTCTGATACAT 58.867 41.667 0.00 0.00 0.00 2.29
2437 2499 4.018870 TGTGCCTAAAATGGGTCTGATACA 60.019 41.667 0.00 0.00 0.00 2.29
2438 2500 4.523083 TGTGCCTAAAATGGGTCTGATAC 58.477 43.478 0.00 0.00 0.00 2.24
2482 2544 9.638239 GAACAGGCATTTAAAAGATTGTCATTA 57.362 29.630 0.00 0.00 0.00 1.90
2564 2626 8.995577 TGCATCTCCCATAGATAAATATCATCA 58.004 33.333 3.45 0.00 43.42 3.07
2569 2631 9.271921 TGTAGTGCATCTCCCATAGATAAATAT 57.728 33.333 0.00 0.00 43.42 1.28
2571 2633 7.559335 TGTAGTGCATCTCCCATAGATAAAT 57.441 36.000 0.00 0.00 43.42 1.40
2575 2637 6.351711 GCTATTGTAGTGCATCTCCCATAGAT 60.352 42.308 0.00 0.00 46.36 1.98
2589 2651 8.879342 AGCAAGATTTAGTAGCTATTGTAGTG 57.121 34.615 0.00 0.00 33.06 2.74
2605 2667 5.659463 TGTGTTAGCAAACAAGCAAGATTT 58.341 33.333 0.00 0.00 46.84 2.17
2622 2684 7.607607 ACAAGTGATAGAAGCATGAATGTGTTA 59.392 33.333 0.00 0.00 0.00 2.41
2630 2692 4.393990 CAGCAACAAGTGATAGAAGCATGA 59.606 41.667 0.00 0.00 0.00 3.07
2651 2713 2.414994 ATGAAGAGGGTGTCATGCAG 57.585 50.000 0.00 0.00 33.21 4.41
2690 2752 4.743493 CCGGTTAGCAAGTGCATATTTTT 58.257 39.130 6.00 0.00 45.16 1.94
2691 2753 3.428862 GCCGGTTAGCAAGTGCATATTTT 60.429 43.478 1.90 0.00 45.16 1.82
2707 2769 0.623723 AGATGGGTTACATGCCGGTT 59.376 50.000 1.90 0.00 40.72 4.44
2710 2772 1.414181 AGAGAGATGGGTTACATGCCG 59.586 52.381 0.00 0.00 40.72 5.69
2725 2787 5.874895 TGTTCATTGCATTCAGAAGAGAG 57.125 39.130 0.00 0.00 0.00 3.20
2768 2830 3.070018 CCTCGCAATGGGATCTGTAATC 58.930 50.000 0.00 0.00 0.00 1.75
2774 2836 1.794714 AGTACCTCGCAATGGGATCT 58.205 50.000 0.00 0.00 0.00 2.75
2890 2952 2.495084 GTTCCTTGACCTTCACCTCAC 58.505 52.381 0.00 0.00 0.00 3.51
2891 2953 1.420138 GGTTCCTTGACCTTCACCTCA 59.580 52.381 0.00 0.00 36.73 3.86
2892 2954 2.186532 GGTTCCTTGACCTTCACCTC 57.813 55.000 0.00 0.00 36.73 3.85
2900 2962 4.022329 CACCATGTTTTAGGTTCCTTGACC 60.022 45.833 0.00 0.00 40.11 4.02
2901 2963 4.825085 TCACCATGTTTTAGGTTCCTTGAC 59.175 41.667 0.00 0.00 35.52 3.18
2902 2964 5.055265 TCACCATGTTTTAGGTTCCTTGA 57.945 39.130 0.00 0.00 35.52 3.02
2903 2965 5.982890 ATCACCATGTTTTAGGTTCCTTG 57.017 39.130 0.00 0.00 35.52 3.61
2912 2974 7.981789 TGTAACTGCAAAAATCACCATGTTTTA 59.018 29.630 0.00 0.00 0.00 1.52
2914 2976 6.257630 GTGTAACTGCAAAAATCACCATGTTT 59.742 34.615 0.00 0.00 0.00 2.83
2971 3039 1.965930 TTGCTTGAAGCGATGCCGT 60.966 52.632 13.05 0.00 46.26 5.68
2972 3040 1.512734 GTTGCTTGAAGCGATGCCG 60.513 57.895 10.76 0.00 46.26 5.69
2975 3043 2.163010 AGAATGGTTGCTTGAAGCGATG 59.837 45.455 10.76 0.00 46.26 3.84
2978 3046 2.712057 AAGAATGGTTGCTTGAAGCG 57.288 45.000 13.05 0.00 46.26 4.68
2989 3057 2.880890 GCATGCGATCCTTAAGAATGGT 59.119 45.455 0.00 0.00 0.00 3.55
3086 3154 8.592998 CGGTTCTGTATGTTCTATAAAGTTCAC 58.407 37.037 0.00 0.00 0.00 3.18
3087 3155 8.525316 TCGGTTCTGTATGTTCTATAAAGTTCA 58.475 33.333 0.00 0.00 0.00 3.18
3111 3179 1.989165 GCTCTCAGCACACTAGTTTCG 59.011 52.381 0.00 0.00 41.89 3.46
3237 3314 4.082841 TGCAAACAAGTTCATCACGCATAT 60.083 37.500 0.00 0.00 0.00 1.78
3276 3356 6.038050 CCACCATGTATTGCAAACAAGTTTTT 59.962 34.615 1.71 0.00 39.69 1.94
3277 3357 5.526846 CCACCATGTATTGCAAACAAGTTTT 59.473 36.000 1.71 0.00 39.69 2.43
3278 3358 5.055812 CCACCATGTATTGCAAACAAGTTT 58.944 37.500 1.71 0.00 39.69 2.66
3279 3359 4.343526 TCCACCATGTATTGCAAACAAGTT 59.656 37.500 1.71 0.00 39.69 2.66
3280 3360 3.894427 TCCACCATGTATTGCAAACAAGT 59.106 39.130 1.71 8.67 39.69 3.16
3281 3361 4.517952 TCCACCATGTATTGCAAACAAG 57.482 40.909 1.71 6.62 39.69 3.16
3282 3362 4.081752 GGATCCACCATGTATTGCAAACAA 60.082 41.667 6.95 0.00 38.25 2.83
3283 3363 3.446873 GGATCCACCATGTATTGCAAACA 59.553 43.478 6.95 9.96 38.79 2.83
3284 3364 3.701040 AGGATCCACCATGTATTGCAAAC 59.299 43.478 15.82 4.00 42.04 2.93
3285 3365 3.700539 CAGGATCCACCATGTATTGCAAA 59.299 43.478 15.82 0.00 42.04 3.68
3286 3366 3.289836 CAGGATCCACCATGTATTGCAA 58.710 45.455 15.82 0.00 42.04 4.08
3287 3367 2.423231 CCAGGATCCACCATGTATTGCA 60.423 50.000 15.82 0.00 42.04 4.08
3288 3368 2.158623 TCCAGGATCCACCATGTATTGC 60.159 50.000 15.82 0.00 42.04 3.56
3336 3416 6.515832 AGTAAACAGAGCAATTTTCCCTTTG 58.484 36.000 0.00 0.00 0.00 2.77
3359 3439 9.379791 AGAGTTAATTCCAAACGAAGGTAATAG 57.620 33.333 0.00 0.00 32.78 1.73
3368 3448 2.664568 CGCGAGAGTTAATTCCAAACGA 59.335 45.455 0.00 0.00 32.00 3.85
3388 3468 1.645034 ACTGTCGATGAAATGAGCCG 58.355 50.000 0.00 0.00 0.00 5.52
3417 3497 1.249407 GCTACATCCTACTCCCTCCG 58.751 60.000 0.00 0.00 0.00 4.63
3438 3524 4.617253 ACAACTGTGGTATGTTGCTAGA 57.383 40.909 0.00 0.00 45.07 2.43
3522 3608 4.761739 TGCACTACCCTTTCTTTCATGAAG 59.238 41.667 8.41 3.62 36.67 3.02
3545 3631 2.679082 ACAGTACCGGCAAGATATCCT 58.321 47.619 0.00 0.00 0.00 3.24
3569 3655 0.809385 TCAGAGTAGCGTTCCGGAAG 59.191 55.000 19.50 12.94 0.00 3.46
3593 3679 2.421424 GCCTACACAAAGATGGAAGCTG 59.579 50.000 0.00 0.00 24.31 4.24
3620 3706 0.602106 CATCTCCGGTGCTATGCCTG 60.602 60.000 0.00 0.00 0.00 4.85
3669 3755 0.884704 GCCGGCCGATCATGTTATGT 60.885 55.000 30.73 0.00 0.00 2.29
3671 3757 1.302511 GGCCGGCCGATCATGTTAT 60.303 57.895 33.60 0.00 0.00 1.89
3756 3842 0.932399 GTACGTGTGGTCGCTGTTTT 59.068 50.000 0.00 0.00 0.00 2.43
3776 3862 3.314331 CCTGGTCCCTGTGCGAGT 61.314 66.667 0.00 0.00 0.00 4.18
3808 3894 3.879295 TGGATGCTGTTAGCTTAATCTGC 59.121 43.478 0.00 0.00 42.97 4.26


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

AutoCloner maintained by Alex Coulton.