Multiple sequence alignment - TraesCS4D01G135100

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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 TraesCS4D01G135100 chr4D 100.000 3729 0 0 1 3729 121966633 121970361 0.000000e+00 6887
1 TraesCS4D01G135100 chr4A 93.989 1830 71 19 1924 3726 449119991 449118174 0.000000e+00 2734
2 TraesCS4D01G135100 chr4A 90.798 1315 68 15 25 1322 449121860 449120582 0.000000e+00 1709
3 TraesCS4D01G135100 chr4A 84.651 430 29 19 1499 1908 449120452 449120040 9.710000e-106 394
4 TraesCS4D01G135100 chr4B 93.587 1840 63 20 1924 3726 184862642 184864463 0.000000e+00 2693
5 TraesCS4D01G135100 chr4B 92.062 1096 33 14 257 1322 184860970 184862041 0.000000e+00 1493
6 TraesCS4D01G135100 chr4B 83.982 437 38 16 1495 1908 184862162 184862589 1.260000e-104 390


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 TraesCS4D01G135100 chr4D 121966633 121970361 3728 False 6887.000000 6887 100.000000 1 3729 1 chr4D.!!$F1 3728
1 TraesCS4D01G135100 chr4A 449118174 449121860 3686 True 1612.333333 2734 89.812667 25 3726 3 chr4A.!!$R1 3701
2 TraesCS4D01G135100 chr4B 184860970 184864463 3493 False 1525.333333 2693 89.877000 257 3726 3 chr4B.!!$F1 3469

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
44 45 0.264359 AGAGGGACAGGGATCTCTGG 59.736 60.0 26.23 8.85 38.98 3.86 F
1299 1346 0.108329 GCGCTAGGACCAAAGCAGTA 60.108 55.0 16.50 0.00 38.70 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1408 0.038892 AACCGCATAGTTGACGACGT 60.039 50.0 0.0 0.0 0.00 4.34 R
3158 3325 0.730265 ACTCGATCTCACTGTCGCTC 59.270 55.0 0.0 0.0 37.74 5.03 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
22 23 4.723248 GAATTTGATGAAGACCGGACAAC 58.277 43.478 9.46 0.28 0.00 3.32
23 24 2.178912 TTGATGAAGACCGGACAACC 57.821 50.000 9.46 0.00 0.00 3.77
41 42 2.727103 CGAGAGGGACAGGGATCTC 58.273 63.158 0.00 0.00 35.82 2.75
44 45 0.264359 AGAGGGACAGGGATCTCTGG 59.736 60.000 26.23 8.85 38.98 3.86
49 50 0.671251 GACAGGGATCTCTGGCGTAG 59.329 60.000 26.23 0.31 38.98 3.51
90 91 4.298332 CACTGACATGTGGGTTTAAAAGC 58.702 43.478 1.15 0.00 34.56 3.51
113 114 2.032681 GGTCCACCTGCCAGTGAC 59.967 66.667 4.85 0.00 40.34 3.67
115 116 3.625897 TCCACCTGCCAGTGACCG 61.626 66.667 4.85 0.00 40.34 4.79
120 121 0.981183 ACCTGCCAGTGACCGAATTA 59.019 50.000 0.00 0.00 0.00 1.40
125 126 2.236146 TGCCAGTGACCGAATTACATCT 59.764 45.455 0.00 0.00 0.00 2.90
132 133 4.868171 GTGACCGAATTACATCTTGCAGTA 59.132 41.667 0.00 0.00 0.00 2.74
133 134 5.523916 GTGACCGAATTACATCTTGCAGTAT 59.476 40.000 0.00 0.00 0.00 2.12
138 139 6.203530 CCGAATTACATCTTGCAGTATGTCAT 59.796 38.462 16.58 10.51 39.31 3.06
168 169 3.993736 GAGTCCTTTGAAAGAGAGTGCTC 59.006 47.826 6.49 2.58 41.62 4.26
170 171 2.039084 TCCTTTGAAAGAGAGTGCTCCC 59.961 50.000 6.49 0.00 42.30 4.30
183 184 2.746277 CTCCCGCCGGTTTCTTGG 60.746 66.667 1.90 0.00 0.00 3.61
221 222 7.245604 TGACGGAAGAAAAACAAAAACTCTAC 58.754 34.615 0.00 0.00 0.00 2.59
224 225 8.248253 ACGGAAGAAAAACAAAAACTCTACAAT 58.752 29.630 0.00 0.00 0.00 2.71
276 277 2.411904 GAAGACCTGATCGATCATGGC 58.588 52.381 27.43 25.79 36.02 4.40
293 294 3.007473 TGGCTCAATCATGATTCAGCA 57.993 42.857 35.49 23.02 45.15 4.41
314 315 4.377635 GCAGTACCTACTCGATCGATCTTC 60.378 50.000 19.78 6.03 33.46 2.87
316 317 2.144730 ACCTACTCGATCGATCTTCCG 58.855 52.381 19.78 10.63 0.00 4.30
410 419 1.590665 TGCACCGCATTGAAATGGG 59.409 52.632 11.92 11.92 45.68 4.00
456 474 2.717044 TACATCCAGGTGCGGTCGG 61.717 63.158 0.00 0.00 0.00 4.79
494 513 9.539139 GTATAGCTGTACGTACATTACAGTATG 57.461 37.037 27.50 14.00 45.62 2.39
495 514 6.688637 AGCTGTACGTACATTACAGTATGA 57.311 37.500 27.50 1.48 45.62 2.15
505 524 4.240888 CATTACAGTATGAGATGCTCCCG 58.759 47.826 0.00 0.00 39.69 5.14
658 678 2.758979 ACCTGCTGTATGCTAAGTACGT 59.241 45.455 0.00 0.00 43.37 3.57
659 679 3.949754 ACCTGCTGTATGCTAAGTACGTA 59.050 43.478 0.00 0.00 43.37 3.57
660 680 4.400251 ACCTGCTGTATGCTAAGTACGTAA 59.600 41.667 0.00 0.00 43.37 3.18
1048 1092 2.573341 GATGGAAGACGACGACGCGA 62.573 60.000 15.93 0.00 43.96 5.87
1049 1093 2.573689 GGAAGACGACGACGCGAG 60.574 66.667 15.93 9.24 43.96 5.03
1050 1094 3.231954 GAAGACGACGACGCGAGC 61.232 66.667 15.93 2.83 43.96 5.03
1059 1103 4.702081 GACGCGAGCGGTGTGAGT 62.702 66.667 21.69 0.00 44.69 3.41
1212 1259 1.070275 CAGGGAGCGATGCTATGCA 59.930 57.895 0.00 0.00 44.86 3.96
1248 1295 1.033574 CCTACATCCACCGTCTCCTC 58.966 60.000 0.00 0.00 0.00 3.71
1296 1343 0.955428 CAAGCGCTAGGACCAAAGCA 60.955 55.000 12.05 0.00 38.70 3.91
1299 1346 0.108329 GCGCTAGGACCAAAGCAGTA 60.108 55.000 16.50 0.00 38.70 2.74
1309 1356 3.585862 ACCAAAGCAGTACACTACATCG 58.414 45.455 0.00 0.00 0.00 3.84
1314 1361 6.266323 CAAAGCAGTACACTACATCGTCTAT 58.734 40.000 0.00 0.00 0.00 1.98
1328 1375 6.257169 CATCGTCTATGTACGTCCTTTTTC 57.743 41.667 0.00 0.00 43.31 2.29
1329 1376 5.633830 TCGTCTATGTACGTCCTTTTTCT 57.366 39.130 0.00 0.00 43.31 2.52
1330 1377 6.017400 TCGTCTATGTACGTCCTTTTTCTT 57.983 37.500 0.00 0.00 43.31 2.52
1331 1378 6.449698 TCGTCTATGTACGTCCTTTTTCTTT 58.550 36.000 0.00 0.00 43.31 2.52
1332 1379 6.925165 TCGTCTATGTACGTCCTTTTTCTTTT 59.075 34.615 0.00 0.00 43.31 2.27
1333 1380 8.081633 TCGTCTATGTACGTCCTTTTTCTTTTA 58.918 33.333 0.00 0.00 43.31 1.52
1334 1381 8.866956 CGTCTATGTACGTCCTTTTTCTTTTAT 58.133 33.333 0.00 0.00 38.07 1.40
1343 1390 9.981114 ACGTCCTTTTTCTTTTATTTGATTGAT 57.019 25.926 0.00 0.00 0.00 2.57
1367 1414 7.260558 TGAGAAAATCATCTATCTACGTCGT 57.739 36.000 2.21 2.21 31.12 4.34
1368 1415 7.353497 TGAGAAAATCATCTATCTACGTCGTC 58.647 38.462 0.00 0.00 31.12 4.20
1369 1416 7.012044 TGAGAAAATCATCTATCTACGTCGTCA 59.988 37.037 0.00 0.00 31.12 4.35
1370 1417 7.704271 AGAAAATCATCTATCTACGTCGTCAA 58.296 34.615 0.00 0.00 0.00 3.18
1371 1418 7.644551 AGAAAATCATCTATCTACGTCGTCAAC 59.355 37.037 0.00 0.00 0.00 3.18
1372 1419 6.621316 AATCATCTATCTACGTCGTCAACT 57.379 37.500 0.00 0.00 0.00 3.16
1373 1420 7.725818 AATCATCTATCTACGTCGTCAACTA 57.274 36.000 0.00 0.00 0.00 2.24
1374 1421 7.908827 ATCATCTATCTACGTCGTCAACTAT 57.091 36.000 0.00 0.00 0.00 2.12
1375 1422 7.118422 TCATCTATCTACGTCGTCAACTATG 57.882 40.000 0.00 0.90 0.00 2.23
1376 1423 5.340010 TCTATCTACGTCGTCAACTATGC 57.660 43.478 0.00 0.00 0.00 3.14
1377 1424 2.447089 TCTACGTCGTCAACTATGCG 57.553 50.000 0.00 0.00 0.00 4.73
1378 1425 1.063027 TCTACGTCGTCAACTATGCGG 59.937 52.381 0.00 0.00 0.00 5.69
1379 1426 0.804364 TACGTCGTCAACTATGCGGT 59.196 50.000 0.00 0.00 0.00 5.68
1380 1427 0.038892 ACGTCGTCAACTATGCGGTT 60.039 50.000 0.00 0.00 0.00 4.44
1381 1428 1.065358 CGTCGTCAACTATGCGGTTT 58.935 50.000 0.00 0.00 0.00 3.27
1382 1429 1.058695 CGTCGTCAACTATGCGGTTTC 59.941 52.381 0.00 0.00 0.00 2.78
1383 1430 2.334838 GTCGTCAACTATGCGGTTTCT 58.665 47.619 0.00 0.00 0.00 2.52
1387 1434 2.092211 GTCAACTATGCGGTTTCTGTCG 59.908 50.000 0.00 0.00 0.00 4.35
1388 1435 1.393539 CAACTATGCGGTTTCTGTCGG 59.606 52.381 0.00 0.00 0.00 4.79
1393 1440 2.654912 GCGGTTTCTGTCGGTGTCG 61.655 63.158 0.00 0.00 37.82 4.35
1400 1447 4.094887 GGTTTCTGTCGGTGTCGTAGTATA 59.905 45.833 0.00 0.00 37.69 1.47
1401 1448 5.220931 GGTTTCTGTCGGTGTCGTAGTATAT 60.221 44.000 0.00 0.00 37.69 0.86
1402 1449 5.413969 TTCTGTCGGTGTCGTAGTATATG 57.586 43.478 0.00 0.00 37.69 1.78
1403 1450 3.249320 TCTGTCGGTGTCGTAGTATATGC 59.751 47.826 0.00 0.00 37.69 3.14
1404 1451 2.944349 TGTCGGTGTCGTAGTATATGCA 59.056 45.455 0.00 0.00 37.69 3.96
1407 1454 4.381863 GTCGGTGTCGTAGTATATGCATTG 59.618 45.833 3.54 0.00 37.69 2.82
1415 1463 7.055598 GTCGTAGTATATGCATTGTTCGTTTC 58.944 38.462 3.54 0.00 0.00 2.78
1423 1471 3.243367 TGCATTGTTCGTTTCCCTTTGAG 60.243 43.478 0.00 0.00 0.00 3.02
1425 1473 2.721425 TGTTCGTTTCCCTTTGAGGT 57.279 45.000 0.00 0.00 31.93 3.85
1426 1474 3.007473 TGTTCGTTTCCCTTTGAGGTT 57.993 42.857 0.00 0.00 31.93 3.50
1427 1475 4.153673 TGTTCGTTTCCCTTTGAGGTTA 57.846 40.909 0.00 0.00 31.93 2.85
1428 1476 4.525024 TGTTCGTTTCCCTTTGAGGTTAA 58.475 39.130 0.00 0.00 31.93 2.01
1429 1477 4.577283 TGTTCGTTTCCCTTTGAGGTTAAG 59.423 41.667 0.00 0.00 31.93 1.85
1430 1478 3.746940 TCGTTTCCCTTTGAGGTTAAGG 58.253 45.455 0.00 0.00 41.51 2.69
1431 1479 3.136992 TCGTTTCCCTTTGAGGTTAAGGT 59.863 43.478 0.00 0.00 40.47 3.50
1432 1480 3.887110 CGTTTCCCTTTGAGGTTAAGGTT 59.113 43.478 0.00 0.00 40.47 3.50
1433 1481 4.340097 CGTTTCCCTTTGAGGTTAAGGTTT 59.660 41.667 0.00 0.00 40.47 3.27
1434 1482 5.532032 CGTTTCCCTTTGAGGTTAAGGTTTA 59.468 40.000 0.00 0.00 40.47 2.01
1435 1483 6.513884 CGTTTCCCTTTGAGGTTAAGGTTTAC 60.514 42.308 0.00 0.00 40.47 2.01
1436 1484 4.989277 TCCCTTTGAGGTTAAGGTTTACC 58.011 43.478 0.00 0.00 40.47 2.85
1453 1501 5.465935 GTTTACCTGCATTTCCAATTTCGA 58.534 37.500 0.00 0.00 0.00 3.71
1456 1504 4.019174 ACCTGCATTTCCAATTTCGATCT 58.981 39.130 0.00 0.00 0.00 2.75
1459 1507 5.528690 CCTGCATTTCCAATTTCGATCTCTA 59.471 40.000 0.00 0.00 0.00 2.43
1460 1508 6.293298 CCTGCATTTCCAATTTCGATCTCTAG 60.293 42.308 0.00 0.00 0.00 2.43
1461 1509 5.008019 TGCATTTCCAATTTCGATCTCTAGC 59.992 40.000 0.00 0.00 0.00 3.42
1462 1510 5.238214 GCATTTCCAATTTCGATCTCTAGCT 59.762 40.000 0.00 0.00 0.00 3.32
1463 1511 6.238593 GCATTTCCAATTTCGATCTCTAGCTT 60.239 38.462 0.00 0.00 0.00 3.74
1474 1523 8.771920 TTCGATCTCTAGCTTTGTTGAATTTA 57.228 30.769 0.00 0.00 0.00 1.40
1475 1524 8.771920 TCGATCTCTAGCTTTGTTGAATTTAA 57.228 30.769 0.00 0.00 0.00 1.52
1477 1526 9.994432 CGATCTCTAGCTTTGTTGAATTTAATT 57.006 29.630 0.00 0.00 0.00 1.40
1484 1533 8.986477 AGCTTTGTTGAATTTAATTATTCGCT 57.014 26.923 0.00 0.00 37.34 4.93
1486 1535 9.675553 GCTTTGTTGAATTTAATTATTCGCTTC 57.324 29.630 0.00 0.00 37.34 3.86
1562 1635 1.201769 CGTTCAACGCGGTCAACTATG 60.202 52.381 9.78 0.00 33.65 2.23
1564 1637 1.705256 TCAACGCGGTCAACTATGTC 58.295 50.000 12.47 0.00 0.00 3.06
1611 1684 3.334583 TCTGGTCAGTCCTGCAATTAC 57.665 47.619 0.00 0.00 37.07 1.89
1614 1687 2.308570 TGGTCAGTCCTGCAATTACCAT 59.691 45.455 1.78 0.00 37.07 3.55
1615 1688 2.684881 GGTCAGTCCTGCAATTACCATG 59.315 50.000 0.00 0.00 0.00 3.66
1616 1689 3.347216 GTCAGTCCTGCAATTACCATGT 58.653 45.455 0.00 0.00 0.00 3.21
1623 1708 5.861787 GTCCTGCAATTACCATGTTGTTAAC 59.138 40.000 0.00 0.00 0.00 2.01
1625 1710 5.863397 CCTGCAATTACCATGTTGTTAACTG 59.137 40.000 7.22 0.00 0.00 3.16
1635 1720 6.372659 ACCATGTTGTTAACTGATCTCATGTC 59.627 38.462 7.22 0.00 32.40 3.06
1639 1724 5.151297 TGTTAACTGATCTCATGTCTGCA 57.849 39.130 7.22 0.00 0.00 4.41
1640 1725 5.737860 TGTTAACTGATCTCATGTCTGCAT 58.262 37.500 7.22 0.00 35.32 3.96
1675 1760 6.089249 GGGGGTTATTTTTGCTGATAGATG 57.911 41.667 0.00 0.00 0.00 2.90
1678 1763 6.323739 GGGGTTATTTTTGCTGATAGATGGAA 59.676 38.462 0.00 0.00 0.00 3.53
1679 1764 7.147742 GGGGTTATTTTTGCTGATAGATGGAAA 60.148 37.037 0.00 0.00 0.00 3.13
1680 1765 8.257306 GGGTTATTTTTGCTGATAGATGGAAAA 58.743 33.333 0.00 0.00 33.06 2.29
1712 1812 4.482386 CATGCATATGTAAATGGCAGAGC 58.518 43.478 0.00 0.00 0.00 4.09
1733 1833 1.059913 GGGAGGTATGGATGGTGGAG 58.940 60.000 0.00 0.00 0.00 3.86
1805 1905 1.704641 TACCATCCCTCCACGATCTG 58.295 55.000 0.00 0.00 0.00 2.90
1839 1939 0.856641 CACCCGTGTCGTTGTTACTG 59.143 55.000 0.00 0.00 0.00 2.74
1840 1940 0.746063 ACCCGTGTCGTTGTTACTGA 59.254 50.000 0.00 0.00 0.00 3.41
1849 1949 3.550678 GTCGTTGTTACTGAATCCGATCC 59.449 47.826 0.00 0.00 0.00 3.36
1852 1952 4.025730 CGTTGTTACTGAATCCGATCCATG 60.026 45.833 0.00 0.00 0.00 3.66
1854 1954 3.454447 TGTTACTGAATCCGATCCATGGT 59.546 43.478 12.58 0.00 0.00 3.55
1874 1974 6.043327 TGGTTTTATATTCGATCACAAGCG 57.957 37.500 0.00 0.00 35.07 4.68
1877 1977 1.139989 ATATTCGATCACAAGCGCCG 58.860 50.000 2.29 0.00 33.40 6.46
1886 1986 2.317609 ACAAGCGCCGTGTGATCAC 61.318 57.895 19.27 19.27 40.79 3.06
1889 1989 0.458543 AAGCGCCGTGTGATCACTAG 60.459 55.000 25.55 18.24 41.89 2.57
1890 1990 1.153823 GCGCCGTGTGATCACTAGT 60.154 57.895 25.55 0.00 41.89 2.57
1891 1991 0.099968 GCGCCGTGTGATCACTAGTA 59.900 55.000 25.55 3.34 41.89 1.82
1892 1992 1.823828 CGCCGTGTGATCACTAGTAC 58.176 55.000 25.55 14.57 41.89 2.73
1893 1993 1.400846 CGCCGTGTGATCACTAGTACT 59.599 52.381 25.55 0.00 41.89 2.73
1897 1997 4.730035 GCCGTGTGATCACTAGTACTGTAC 60.730 50.000 25.55 9.93 41.89 2.90
1908 2008 7.704271 TCACTAGTACTGTACAAGATATGCAC 58.296 38.462 19.27 0.00 0.00 4.57
1909 2009 6.633234 CACTAGTACTGTACAAGATATGCACG 59.367 42.308 19.27 0.00 0.00 5.34
1913 2013 3.804325 ACTGTACAAGATATGCACGCATC 59.196 43.478 7.99 0.00 37.82 3.91
1914 2014 3.791245 TGTACAAGATATGCACGCATCA 58.209 40.909 7.99 0.00 37.82 3.07
1916 2016 3.680642 ACAAGATATGCACGCATCAAC 57.319 42.857 7.99 1.76 37.82 3.18
1917 2017 2.355756 ACAAGATATGCACGCATCAACC 59.644 45.455 7.99 0.00 37.82 3.77
1921 2058 0.251634 TATGCACGCATCAACCTGGA 59.748 50.000 7.99 0.00 37.82 3.86
1922 2059 0.394762 ATGCACGCATCAACCTGGAT 60.395 50.000 0.00 0.00 29.42 3.41
1927 2064 1.451927 GCATCAACCTGGATCGGCA 60.452 57.895 0.00 0.00 0.00 5.69
1939 2076 5.473504 ACCTGGATCGGCATGATAAATTAAC 59.526 40.000 0.00 0.00 37.47 2.01
1944 2081 7.882791 TGGATCGGCATGATAAATTAACTATGT 59.117 33.333 0.00 0.00 37.47 2.29
1945 2082 8.391106 GGATCGGCATGATAAATTAACTATGTC 58.609 37.037 0.00 0.00 37.47 3.06
1951 2088 7.693951 GCATGATAAATTAACTATGTCGGATGC 59.306 37.037 0.00 0.00 0.00 3.91
1952 2089 7.346208 TGATAAATTAACTATGTCGGATGCG 57.654 36.000 0.00 0.00 0.00 4.73
1953 2090 4.468095 AAATTAACTATGTCGGATGCGC 57.532 40.909 0.00 0.00 0.00 6.09
1954 2091 1.483316 TTAACTATGTCGGATGCGCG 58.517 50.000 0.00 0.00 0.00 6.86
1955 2092 0.664224 TAACTATGTCGGATGCGCGA 59.336 50.000 12.10 0.00 0.00 5.87
1958 2095 3.817274 TATGTCGGATGCGCGACGG 62.817 63.158 12.10 10.67 37.89 4.79
1974 2116 1.153107 CGGCATGCAGATGGAGGAA 60.153 57.895 21.36 0.00 0.00 3.36
2020 2162 1.306997 ACCATCCGGGACATGGAGT 60.307 57.895 23.72 3.23 43.32 3.85
2091 2233 1.152715 CTACCTCGACCTCCTCCCC 60.153 68.421 0.00 0.00 0.00 4.81
2161 2306 0.890090 CCGATCCCTCTCCGGTACTC 60.890 65.000 0.00 0.00 38.55 2.59
2173 2318 2.025981 TCCGGTACTCTACTACCTGCAA 60.026 50.000 0.00 0.00 34.93 4.08
2188 2333 7.865707 ACTACCTGCAAATCGATTAATCAATC 58.134 34.615 11.83 0.00 37.74 2.67
2506 2670 2.898729 TTGACCCCGTACGTGTTAAA 57.101 45.000 15.21 7.21 0.00 1.52
2572 2736 2.099756 AGCACTTGAAACAAGCTTGGAC 59.900 45.455 29.18 19.10 29.98 4.02
2655 2819 0.390340 GCATTCGAGAGCACTGACCA 60.390 55.000 6.32 0.00 0.00 4.02
2683 2847 1.160137 CAGTTAACAGCAGGTCAGCC 58.840 55.000 8.61 0.00 34.23 4.85
2704 2868 1.153449 CAGTCGGCGCCTATTTGGA 60.153 57.895 26.68 10.44 38.35 3.53
2714 2878 2.095263 CGCCTATTTGGAACACCAACAG 60.095 50.000 0.00 0.00 42.44 3.16
2862 3028 4.436050 CGTACCATTTCTCAACTGTGATGC 60.436 45.833 0.00 0.00 31.85 3.91
2991 3157 7.618502 TTGTTGTTGTTCAGTGTTACTATGT 57.381 32.000 0.00 0.00 0.00 2.29
2992 3158 7.618502 TGTTGTTGTTCAGTGTTACTATGTT 57.381 32.000 0.00 0.00 0.00 2.71
3052 3219 8.837788 TGTGCATCTATCATTATAAACCAGAG 57.162 34.615 0.00 0.00 0.00 3.35
3060 3227 6.147864 TCATTATAAACCAGAGCAATTGGC 57.852 37.500 7.72 0.00 45.30 4.52
3104 3271 5.351465 TCTTCAGAGTTCAGTTGTTGTGTTC 59.649 40.000 0.00 0.00 0.00 3.18
3158 3325 5.105997 GGAAAGACAAAAGGGACTCATCATG 60.106 44.000 0.00 0.00 38.49 3.07
3176 3343 0.729690 TGAGCGACAGTGAGATCGAG 59.270 55.000 5.86 0.00 40.86 4.04
3178 3345 1.131504 GAGCGACAGTGAGATCGAGTT 59.868 52.381 5.86 0.00 40.86 3.01
3351 3518 2.928396 AACTGGGGCTACCGCTGT 60.928 61.111 7.29 7.29 46.81 4.40
3503 3676 8.903820 CAAAGGAGAAGGAGAAAAGAAAAGTTA 58.096 33.333 0.00 0.00 0.00 2.24
3525 3698 2.507407 ATTTGCAGGGGAACGTACAT 57.493 45.000 0.00 0.00 0.00 2.29
3608 3781 1.137872 CAGGTAGCCCACTCACTGATC 59.862 57.143 0.00 0.00 33.72 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.379499 GGTTGTCCGGTCTTCATCAAATTC 60.379 45.833 0.00 0.00 0.00 2.17
1 2 3.506067 GGTTGTCCGGTCTTCATCAAATT 59.494 43.478 0.00 0.00 0.00 1.82
2 3 3.081804 GGTTGTCCGGTCTTCATCAAAT 58.918 45.455 0.00 0.00 0.00 2.32
3 4 2.500229 GGTTGTCCGGTCTTCATCAAA 58.500 47.619 0.00 0.00 0.00 2.69
4 5 2.178912 GGTTGTCCGGTCTTCATCAA 57.821 50.000 0.00 0.00 0.00 2.57
5 6 3.927555 GGTTGTCCGGTCTTCATCA 57.072 52.632 0.00 0.00 0.00 3.07
16 17 1.592223 CTGTCCCTCTCGGTTGTCC 59.408 63.158 0.00 0.00 0.00 4.02
17 18 1.592223 CCTGTCCCTCTCGGTTGTC 59.408 63.158 0.00 0.00 0.00 3.18
18 19 1.913762 CCCTGTCCCTCTCGGTTGT 60.914 63.158 0.00 0.00 0.00 3.32
19 20 0.978146 ATCCCTGTCCCTCTCGGTTG 60.978 60.000 0.00 0.00 0.00 3.77
20 21 0.688087 GATCCCTGTCCCTCTCGGTT 60.688 60.000 0.00 0.00 0.00 4.44
21 22 1.075896 GATCCCTGTCCCTCTCGGT 60.076 63.158 0.00 0.00 0.00 4.69
22 23 0.825840 GAGATCCCTGTCCCTCTCGG 60.826 65.000 0.00 0.00 0.00 4.63
23 24 0.184933 AGAGATCCCTGTCCCTCTCG 59.815 60.000 0.00 0.00 39.27 4.04
35 36 0.249238 CTGCACTACGCCAGAGATCC 60.249 60.000 0.00 0.00 41.33 3.36
41 42 2.099263 ACTGTATACTGCACTACGCCAG 59.901 50.000 9.48 0.00 41.33 4.85
44 45 3.766151 TCAACTGTATACTGCACTACGC 58.234 45.455 9.48 0.00 42.89 4.42
49 50 2.673368 GTGGCTCAACTGTATACTGCAC 59.327 50.000 9.48 5.25 0.00 4.57
54 55 4.188247 TGTCAGTGGCTCAACTGTATAC 57.812 45.455 12.37 0.00 46.33 1.47
55 56 4.222810 ACATGTCAGTGGCTCAACTGTATA 59.777 41.667 12.37 3.99 46.33 1.47
58 59 1.141657 ACATGTCAGTGGCTCAACTGT 59.858 47.619 12.37 0.00 46.33 3.55
80 81 2.696187 TGGACCAACCTGCTTTTAAACC 59.304 45.455 0.00 0.00 39.86 3.27
81 82 3.491964 GGTGGACCAACCTGCTTTTAAAC 60.492 47.826 0.00 0.00 39.86 2.01
84 85 1.989706 GGTGGACCAACCTGCTTTTA 58.010 50.000 0.00 0.00 39.86 1.52
106 107 3.063997 GCAAGATGTAATTCGGTCACTGG 59.936 47.826 0.00 0.00 0.00 4.00
113 114 5.523552 TGACATACTGCAAGATGTAATTCGG 59.476 40.000 11.98 0.00 35.73 4.30
115 116 7.859377 CCAATGACATACTGCAAGATGTAATTC 59.141 37.037 15.74 5.61 35.34 2.17
120 121 4.847198 TCCAATGACATACTGCAAGATGT 58.153 39.130 11.87 11.87 37.39 3.06
125 126 4.650734 TCAACTCCAATGACATACTGCAA 58.349 39.130 0.00 0.00 0.00 4.08
132 133 4.647564 AAGGACTCAACTCCAATGACAT 57.352 40.909 0.00 0.00 31.94 3.06
133 134 4.136796 CAAAGGACTCAACTCCAATGACA 58.863 43.478 0.00 0.00 31.94 3.58
138 139 5.104527 TCTCTTTCAAAGGACTCAACTCCAA 60.105 40.000 0.00 0.00 31.94 3.53
168 169 1.457009 TTTTCCAAGAAACCGGCGGG 61.457 55.000 31.78 12.53 40.11 6.13
170 171 3.949031 TTTTTCCAAGAAACCGGCG 57.051 47.368 0.00 0.00 0.00 6.46
190 191 6.937886 TTTGTTTTTCTTCCGTCAAGTTTC 57.062 33.333 0.00 0.00 33.27 2.78
191 192 7.439955 AGTTTTTGTTTTTCTTCCGTCAAGTTT 59.560 29.630 0.00 0.00 33.27 2.66
192 193 6.926826 AGTTTTTGTTTTTCTTCCGTCAAGTT 59.073 30.769 0.00 0.00 33.27 2.66
193 194 6.452242 AGTTTTTGTTTTTCTTCCGTCAAGT 58.548 32.000 0.00 0.00 33.27 3.16
200 201 8.743099 CGATTGTAGAGTTTTTGTTTTTCTTCC 58.257 33.333 0.00 0.00 0.00 3.46
237 238 6.708502 GGTCTTCCTGGCTAGATTTAGATTTC 59.291 42.308 0.00 0.00 0.00 2.17
276 277 5.366460 AGGTACTGCTGAATCATGATTGAG 58.634 41.667 25.34 25.34 37.18 3.02
293 294 4.317488 GGAAGATCGATCGAGTAGGTACT 58.683 47.826 23.84 3.38 46.37 2.73
410 419 2.137177 TAAGTGCACCCCAAGCCCTC 62.137 60.000 14.63 0.00 0.00 4.30
426 439 2.872245 CCTGGATGTACGCACCAATAAG 59.128 50.000 6.87 0.00 33.14 1.73
456 474 1.662629 CAGCTATACGCATGCATAGGC 59.337 52.381 19.57 14.97 42.61 3.93
458 476 3.543889 CGTACAGCTATACGCATGCATAG 59.456 47.826 19.57 17.96 41.28 2.23
494 513 3.917760 CCGGGTCGGGAGCATCTC 61.918 72.222 0.00 0.00 44.15 2.75
505 524 0.106149 CCATACTAAGTGGCCGGGTC 59.894 60.000 2.18 0.00 0.00 4.46
658 678 7.514721 ACAGGAGACAAATGGAAACTACTTTA 58.485 34.615 0.00 0.00 0.00 1.85
659 679 6.365520 ACAGGAGACAAATGGAAACTACTTT 58.634 36.000 0.00 0.00 0.00 2.66
660 680 5.941788 ACAGGAGACAAATGGAAACTACTT 58.058 37.500 0.00 0.00 0.00 2.24
716 750 0.806868 CTTGCATGCCTGTGAATCGT 59.193 50.000 16.68 0.00 0.00 3.73
1048 1092 2.262915 GCTAGCACTCACACCGCT 59.737 61.111 10.63 0.00 39.80 5.52
1049 1093 3.181967 CGCTAGCACTCACACCGC 61.182 66.667 16.45 0.00 0.00 5.68
1050 1094 2.507102 CCGCTAGCACTCACACCG 60.507 66.667 16.45 0.00 0.00 4.94
1051 1095 1.961180 ATCCCGCTAGCACTCACACC 61.961 60.000 16.45 0.00 0.00 4.16
1052 1096 0.528684 GATCCCGCTAGCACTCACAC 60.529 60.000 16.45 0.00 0.00 3.82
1053 1097 0.970427 TGATCCCGCTAGCACTCACA 60.970 55.000 16.45 6.19 0.00 3.58
1054 1098 0.390860 ATGATCCCGCTAGCACTCAC 59.609 55.000 16.45 3.51 0.00 3.51
1055 1099 1.069204 GAATGATCCCGCTAGCACTCA 59.931 52.381 16.45 11.25 0.00 3.41
1056 1100 1.342819 AGAATGATCCCGCTAGCACTC 59.657 52.381 16.45 5.76 0.00 3.51
1057 1101 1.342819 GAGAATGATCCCGCTAGCACT 59.657 52.381 16.45 0.00 0.00 4.40
1058 1102 1.342819 AGAGAATGATCCCGCTAGCAC 59.657 52.381 16.45 0.97 0.00 4.40
1059 1103 1.709578 AGAGAATGATCCCGCTAGCA 58.290 50.000 16.45 0.00 0.00 3.49
1060 1104 2.823154 AGTAGAGAATGATCCCGCTAGC 59.177 50.000 4.06 4.06 0.00 3.42
1061 1105 3.366883 GCAGTAGAGAATGATCCCGCTAG 60.367 52.174 0.00 0.00 0.00 3.42
1062 1106 2.558795 GCAGTAGAGAATGATCCCGCTA 59.441 50.000 0.00 0.00 0.00 4.26
1113 1157 2.034999 GCCGGTGGTGGAATTGGA 59.965 61.111 1.90 0.00 0.00 3.53
1212 1259 3.771160 GCAGACGATCCCACGGGT 61.771 66.667 1.07 0.00 37.61 5.28
1248 1295 1.423721 CGTGCTGATGATGGTCGTGG 61.424 60.000 0.00 0.00 0.00 4.94
1343 1390 7.012044 TGACGACGTAGATAGATGATTTTCTCA 59.988 37.037 0.00 0.00 38.53 3.27
1344 1391 7.353497 TGACGACGTAGATAGATGATTTTCTC 58.647 38.462 0.00 0.00 0.00 2.87
1345 1392 7.260558 TGACGACGTAGATAGATGATTTTCT 57.739 36.000 0.00 0.00 0.00 2.52
1346 1393 7.644551 AGTTGACGACGTAGATAGATGATTTTC 59.355 37.037 0.00 0.00 0.00 2.29
1347 1394 7.481642 AGTTGACGACGTAGATAGATGATTTT 58.518 34.615 0.00 0.00 0.00 1.82
1348 1395 7.028926 AGTTGACGACGTAGATAGATGATTT 57.971 36.000 0.00 0.00 0.00 2.17
1349 1396 6.621316 AGTTGACGACGTAGATAGATGATT 57.379 37.500 0.00 0.00 0.00 2.57
1350 1397 7.624554 GCATAGTTGACGACGTAGATAGATGAT 60.625 40.741 0.00 0.00 0.00 2.45
1351 1398 6.347483 GCATAGTTGACGACGTAGATAGATGA 60.347 42.308 0.00 0.00 0.00 2.92
1352 1399 5.790988 GCATAGTTGACGACGTAGATAGATG 59.209 44.000 0.00 2.39 0.00 2.90
1353 1400 5.389620 CGCATAGTTGACGACGTAGATAGAT 60.390 44.000 0.00 0.00 0.00 1.98
1354 1401 4.084693 CGCATAGTTGACGACGTAGATAGA 60.085 45.833 0.00 0.00 0.00 1.98
1355 1402 4.142397 CGCATAGTTGACGACGTAGATAG 58.858 47.826 0.00 0.00 0.00 2.08
1356 1403 3.059393 CCGCATAGTTGACGACGTAGATA 60.059 47.826 0.00 0.00 0.00 1.98
1357 1404 2.286831 CCGCATAGTTGACGACGTAGAT 60.287 50.000 0.00 0.00 0.00 1.98
1358 1405 1.063027 CCGCATAGTTGACGACGTAGA 59.937 52.381 0.00 0.00 0.00 2.59
1359 1406 1.202110 ACCGCATAGTTGACGACGTAG 60.202 52.381 0.00 0.00 0.00 3.51
1360 1407 0.804364 ACCGCATAGTTGACGACGTA 59.196 50.000 0.00 0.00 0.00 3.57
1361 1408 0.038892 AACCGCATAGTTGACGACGT 60.039 50.000 0.00 0.00 0.00 4.34
1362 1409 1.058695 GAAACCGCATAGTTGACGACG 59.941 52.381 0.00 0.00 0.00 5.12
1363 1410 2.092211 CAGAAACCGCATAGTTGACGAC 59.908 50.000 0.00 0.00 0.00 4.34
1364 1411 2.288579 ACAGAAACCGCATAGTTGACGA 60.289 45.455 0.00 0.00 0.00 4.20
1365 1412 2.066262 ACAGAAACCGCATAGTTGACG 58.934 47.619 0.00 0.00 0.00 4.35
1366 1413 2.092211 CGACAGAAACCGCATAGTTGAC 59.908 50.000 0.00 0.00 0.00 3.18
1367 1414 2.333926 CGACAGAAACCGCATAGTTGA 58.666 47.619 0.00 0.00 0.00 3.18
1368 1415 1.393539 CCGACAGAAACCGCATAGTTG 59.606 52.381 0.00 0.00 0.00 3.16
1369 1416 1.001633 ACCGACAGAAACCGCATAGTT 59.998 47.619 0.00 0.00 0.00 2.24
1370 1417 0.606604 ACCGACAGAAACCGCATAGT 59.393 50.000 0.00 0.00 0.00 2.12
1371 1418 0.999406 CACCGACAGAAACCGCATAG 59.001 55.000 0.00 0.00 0.00 2.23
1372 1419 0.319083 ACACCGACAGAAACCGCATA 59.681 50.000 0.00 0.00 0.00 3.14
1373 1420 0.949105 GACACCGACAGAAACCGCAT 60.949 55.000 0.00 0.00 0.00 4.73
1374 1421 1.593209 GACACCGACAGAAACCGCA 60.593 57.895 0.00 0.00 0.00 5.69
1375 1422 2.654912 CGACACCGACAGAAACCGC 61.655 63.158 0.00 0.00 38.22 5.68
1376 1423 0.040157 TACGACACCGACAGAAACCG 60.040 55.000 0.00 0.00 39.50 4.44
1377 1424 1.000938 ACTACGACACCGACAGAAACC 60.001 52.381 0.00 0.00 39.50 3.27
1378 1425 2.412421 ACTACGACACCGACAGAAAC 57.588 50.000 0.00 0.00 39.50 2.78
1379 1426 5.731406 GCATATACTACGACACCGACAGAAA 60.731 44.000 0.00 0.00 39.50 2.52
1380 1427 4.260907 GCATATACTACGACACCGACAGAA 60.261 45.833 0.00 0.00 39.50 3.02
1381 1428 3.249320 GCATATACTACGACACCGACAGA 59.751 47.826 0.00 0.00 39.50 3.41
1382 1429 3.002965 TGCATATACTACGACACCGACAG 59.997 47.826 0.00 0.00 39.50 3.51
1383 1430 2.944349 TGCATATACTACGACACCGACA 59.056 45.455 0.00 0.00 39.50 4.35
1387 1434 5.107989 CGAACAATGCATATACTACGACACC 60.108 44.000 0.00 0.00 0.00 4.16
1388 1435 5.457799 ACGAACAATGCATATACTACGACAC 59.542 40.000 0.00 0.00 0.00 3.67
1393 1440 6.482308 AGGGAAACGAACAATGCATATACTAC 59.518 38.462 0.00 0.00 0.00 2.73
1400 1447 3.320541 TCAAAGGGAAACGAACAATGCAT 59.679 39.130 0.00 0.00 0.00 3.96
1401 1448 2.690497 TCAAAGGGAAACGAACAATGCA 59.310 40.909 0.00 0.00 0.00 3.96
1402 1449 3.308530 CTCAAAGGGAAACGAACAATGC 58.691 45.455 0.00 0.00 0.00 3.56
1403 1450 3.317993 ACCTCAAAGGGAAACGAACAATG 59.682 43.478 0.00 0.00 40.58 2.82
1404 1451 3.562182 ACCTCAAAGGGAAACGAACAAT 58.438 40.909 0.00 0.00 40.58 2.71
1407 1454 4.023450 CCTTAACCTCAAAGGGAAACGAAC 60.023 45.833 0.00 0.00 40.58 3.95
1415 1463 4.765339 CAGGTAAACCTTAACCTCAAAGGG 59.235 45.833 0.00 0.00 46.09 3.95
1423 1471 4.525100 TGGAAATGCAGGTAAACCTTAACC 59.475 41.667 0.00 0.00 46.09 2.85
1425 1473 6.926630 ATTGGAAATGCAGGTAAACCTTAA 57.073 33.333 0.00 0.00 46.09 1.85
1426 1474 6.926630 AATTGGAAATGCAGGTAAACCTTA 57.073 33.333 0.00 0.00 46.09 2.69
1427 1475 5.823861 AATTGGAAATGCAGGTAAACCTT 57.176 34.783 0.00 0.00 46.09 3.50
1429 1477 4.625311 CGAAATTGGAAATGCAGGTAAACC 59.375 41.667 0.00 0.00 0.00 3.27
1430 1478 5.465935 TCGAAATTGGAAATGCAGGTAAAC 58.534 37.500 0.00 0.00 0.00 2.01
1431 1479 5.713792 TCGAAATTGGAAATGCAGGTAAA 57.286 34.783 0.00 0.00 0.00 2.01
1432 1480 5.652014 AGATCGAAATTGGAAATGCAGGTAA 59.348 36.000 0.00 0.00 0.00 2.85
1433 1481 5.192927 AGATCGAAATTGGAAATGCAGGTA 58.807 37.500 0.00 0.00 0.00 3.08
1434 1482 4.019174 AGATCGAAATTGGAAATGCAGGT 58.981 39.130 0.00 0.00 0.00 4.00
1435 1483 4.337555 AGAGATCGAAATTGGAAATGCAGG 59.662 41.667 0.00 0.00 0.00 4.85
1436 1484 5.496133 AGAGATCGAAATTGGAAATGCAG 57.504 39.130 0.00 0.00 0.00 4.41
1445 1493 7.065216 TCAACAAAGCTAGAGATCGAAATTG 57.935 36.000 0.00 0.00 0.00 2.32
1459 1507 8.986477 AGCGAATAATTAAATTCAACAAAGCT 57.014 26.923 0.00 0.00 35.93 3.74
1460 1508 9.675553 GAAGCGAATAATTAAATTCAACAAAGC 57.324 29.630 0.00 0.00 35.93 3.51
1562 1635 0.389948 ATGGACAAGAAGCGGTCGAC 60.390 55.000 7.13 7.13 34.87 4.20
1564 1637 0.389817 TGATGGACAAGAAGCGGTCG 60.390 55.000 0.00 0.00 34.87 4.79
1611 1684 6.596888 AGACATGAGATCAGTTAACAACATGG 59.403 38.462 8.61 2.98 38.35 3.66
1614 1687 5.409520 GCAGACATGAGATCAGTTAACAACA 59.590 40.000 8.61 0.00 0.00 3.33
1615 1688 5.409520 TGCAGACATGAGATCAGTTAACAAC 59.590 40.000 8.61 0.00 0.00 3.32
1616 1689 5.550290 TGCAGACATGAGATCAGTTAACAA 58.450 37.500 8.61 0.00 0.00 2.83
1623 1708 5.562506 ACAAAATGCAGACATGAGATCAG 57.437 39.130 0.00 0.00 36.36 2.90
1625 1710 7.061905 CAGAAAACAAAATGCAGACATGAGATC 59.938 37.037 0.00 0.00 36.36 2.75
1635 1720 2.769893 CCCCCAGAAAACAAAATGCAG 58.230 47.619 0.00 0.00 0.00 4.41
1680 1765 8.399425 CCATTTACATATGCATGCAACATTTTT 58.601 29.630 26.68 8.86 35.39 1.94
1699 1792 1.673168 CTCCCAGCTCTGCCATTTAC 58.327 55.000 0.00 0.00 0.00 2.01
1701 1794 1.305623 CCTCCCAGCTCTGCCATTT 59.694 57.895 0.00 0.00 0.00 2.32
1712 1812 0.767375 CCACCATCCATACCTCCCAG 59.233 60.000 0.00 0.00 0.00 4.45
1818 1918 1.950130 TAACAACGACACGGGTGCG 60.950 57.895 0.00 0.50 36.62 5.34
1823 1923 2.410730 GGATTCAGTAACAACGACACGG 59.589 50.000 0.00 0.00 0.00 4.94
1827 1927 3.550678 GGATCGGATTCAGTAACAACGAC 59.449 47.826 0.00 0.00 0.00 4.34
1828 1928 3.193903 TGGATCGGATTCAGTAACAACGA 59.806 43.478 0.00 0.00 0.00 3.85
1829 1929 3.517602 TGGATCGGATTCAGTAACAACG 58.482 45.455 0.00 0.00 0.00 4.10
1830 1930 4.273480 CCATGGATCGGATTCAGTAACAAC 59.727 45.833 5.56 0.00 0.00 3.32
1831 1931 4.080582 ACCATGGATCGGATTCAGTAACAA 60.081 41.667 21.47 0.00 0.00 2.83
1832 1932 3.454447 ACCATGGATCGGATTCAGTAACA 59.546 43.478 21.47 0.00 0.00 2.41
1833 1933 4.073293 ACCATGGATCGGATTCAGTAAC 57.927 45.455 21.47 0.00 0.00 2.50
1834 1934 4.771114 AACCATGGATCGGATTCAGTAA 57.229 40.909 21.47 0.00 0.00 2.24
1839 1939 7.333423 TCGAATATAAAACCATGGATCGGATTC 59.667 37.037 21.47 16.79 0.00 2.52
1840 1940 7.165485 TCGAATATAAAACCATGGATCGGATT 58.835 34.615 21.47 10.20 0.00 3.01
1849 1949 6.574832 CGCTTGTGATCGAATATAAAACCATG 59.425 38.462 0.00 0.00 0.00 3.66
1852 1952 4.904154 GCGCTTGTGATCGAATATAAAACC 59.096 41.667 0.00 0.00 0.00 3.27
1854 1954 4.318475 CGGCGCTTGTGATCGAATATAAAA 60.318 41.667 7.64 0.00 0.00 1.52
1877 1977 7.142306 TCTTGTACAGTACTAGTGATCACAC 57.858 40.000 27.02 16.11 46.24 3.82
1884 1984 6.633234 CGTGCATATCTTGTACAGTACTAGTG 59.367 42.308 18.21 12.21 40.62 2.74
1886 1986 5.625721 GCGTGCATATCTTGTACAGTACTAG 59.374 44.000 14.17 14.17 40.62 2.57
1889 1989 4.109766 TGCGTGCATATCTTGTACAGTAC 58.890 43.478 3.49 3.49 40.62 2.73
1890 1990 4.379339 TGCGTGCATATCTTGTACAGTA 57.621 40.909 0.00 0.00 40.62 2.74
1891 1991 3.245518 TGCGTGCATATCTTGTACAGT 57.754 42.857 0.00 0.00 40.62 3.55
1892 1992 3.803778 TGATGCGTGCATATCTTGTACAG 59.196 43.478 7.42 0.00 40.62 2.74
1893 1993 3.791245 TGATGCGTGCATATCTTGTACA 58.209 40.909 7.42 0.00 40.62 2.90
1897 1997 2.615447 AGGTTGATGCGTGCATATCTTG 59.385 45.455 7.42 0.00 36.70 3.02
1908 2008 2.537560 GCCGATCCAGGTTGATGCG 61.538 63.158 0.00 0.00 0.00 4.73
1909 2009 0.820891 ATGCCGATCCAGGTTGATGC 60.821 55.000 0.00 0.00 0.00 3.91
1913 2013 2.549064 TATCATGCCGATCCAGGTTG 57.451 50.000 0.00 0.00 35.39 3.77
1914 2014 3.576078 TTTATCATGCCGATCCAGGTT 57.424 42.857 0.00 0.00 35.39 3.50
1916 2016 5.707298 AGTTAATTTATCATGCCGATCCAGG 59.293 40.000 0.00 0.00 35.39 4.45
1917 2017 6.808008 AGTTAATTTATCATGCCGATCCAG 57.192 37.500 0.00 0.00 35.39 3.86
1921 2058 7.064609 CCGACATAGTTAATTTATCATGCCGAT 59.935 37.037 0.00 0.00 38.21 4.18
1922 2059 6.367695 CCGACATAGTTAATTTATCATGCCGA 59.632 38.462 0.00 0.00 0.00 5.54
1927 2064 7.413000 GCGCATCCGACATAGTTAATTTATCAT 60.413 37.037 0.30 0.00 36.29 2.45
1951 2088 4.289379 CATCTGCATGCCGTCGCG 62.289 66.667 16.68 0.00 38.08 5.87
1952 2089 3.945434 CCATCTGCATGCCGTCGC 61.945 66.667 16.68 0.00 0.00 5.19
1953 2090 2.202919 TCCATCTGCATGCCGTCG 60.203 61.111 16.68 4.47 0.00 5.12
1954 2091 1.890979 CCTCCATCTGCATGCCGTC 60.891 63.158 16.68 0.00 0.00 4.79
1955 2092 1.913951 TTCCTCCATCTGCATGCCGT 61.914 55.000 16.68 0.00 0.00 5.68
1958 2095 1.022735 CACTTCCTCCATCTGCATGC 58.977 55.000 11.82 11.82 0.00 4.06
1959 2096 2.286872 GTCACTTCCTCCATCTGCATG 58.713 52.381 0.00 0.00 0.00 4.06
2161 2306 7.946655 TGATTAATCGATTTGCAGGTAGTAG 57.053 36.000 17.19 0.00 0.00 2.57
2173 2318 9.277783 CTTAAGGGAGTGATTGATTAATCGATT 57.722 33.333 17.57 16.15 44.55 3.34
2506 2670 3.034635 AGACTCATCGCCCTGTAGAATT 58.965 45.455 0.00 0.00 0.00 2.17
2572 2736 8.982685 GTACTGTACTTGTGATATTGATGATGG 58.017 37.037 10.64 0.00 0.00 3.51
2655 2819 4.040461 ACCTGCTGTTAACTGTACTGTCAT 59.960 41.667 13.27 0.00 0.00 3.06
2683 2847 1.144057 AAATAGGCGCCGACTGAGG 59.856 57.895 23.20 0.00 0.00 3.86
2704 2868 0.751643 GGTCCAGTGCTGTTGGTGTT 60.752 55.000 0.00 0.00 37.02 3.32
2714 2878 2.435805 TCTATCTTCATGGGTCCAGTGC 59.564 50.000 0.00 0.00 0.00 4.40
2862 3028 5.886960 AAGTAACTTTGCAGGATTAGCTG 57.113 39.130 0.00 0.00 0.00 4.24
2880 3046 6.330004 TGAAGAACATGTACACGGTAAGTA 57.670 37.500 0.00 0.00 0.00 2.24
3030 3197 7.912056 TGCTCTGGTTTATAATGATAGATGC 57.088 36.000 0.00 0.00 0.00 3.91
3052 3219 1.474077 CAGTTCTACCAGGCCAATTGC 59.526 52.381 5.01 0.00 40.16 3.56
3060 3227 3.264450 AGACCCAATTCAGTTCTACCAGG 59.736 47.826 0.00 0.00 0.00 4.45
3104 3271 4.191544 TGAAGAAGCGAGGATTATGGTTG 58.808 43.478 0.00 0.00 0.00 3.77
3158 3325 0.730265 ACTCGATCTCACTGTCGCTC 59.270 55.000 0.00 0.00 37.74 5.03
3176 3343 3.733337 TCAGAAAGGCAGACTCTTCAAC 58.267 45.455 0.00 0.00 0.00 3.18
3178 3345 4.630644 AATCAGAAAGGCAGACTCTTCA 57.369 40.909 0.00 0.00 0.00 3.02
3351 3518 9.496873 TTTGGATAACTAACGAAAAGAATGAGA 57.503 29.630 0.00 0.00 0.00 3.27
3381 3548 0.036388 TTGGCTACCTACTGTGCTGC 60.036 55.000 0.00 0.00 0.00 5.25
3503 3676 2.303600 TGTACGTTCCCCTGCAAATACT 59.696 45.455 0.00 0.00 0.00 2.12
3608 3781 5.053145 CAGGCTAGCTGGTAGATTAACTTG 58.947 45.833 15.72 2.74 0.00 3.16
3684 3863 7.556635 TCTGAACTGAAACTATGCTAGCTACTA 59.443 37.037 17.23 4.32 0.00 1.82


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

AutoCloner maintained by Alex Coulton.