Multiple sequence alignment - TraesCS1B01G211200

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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 TraesCS1B01G211200 chr1B 100.000 4128 0 0 1 4128 384302003 384297876 0.000000e+00 7624.0
1 TraesCS1B01G211200 chr1B 85.853 721 70 15 2432 3142 34777018 34777716 0.000000e+00 737.0
2 TraesCS1B01G211200 chr1B 85.853 721 70 15 2432 3142 34794346 34795044 0.000000e+00 737.0
3 TraesCS1B01G211200 chr1D 90.486 2775 179 37 1402 4128 282950808 282948071 0.000000e+00 3583.0
4 TraesCS1B01G211200 chr1D 88.984 1398 76 39 1 1362 282952161 282950806 0.000000e+00 1657.0
5 TraesCS1B01G211200 chr1D 100.000 29 0 0 464 492 360473047 360473075 2.000000e-03 54.7
6 TraesCS1B01G211200 chr1A 88.340 2187 153 43 1402 3556 354939919 354937803 0.000000e+00 2532.0
7 TraesCS1B01G211200 chr1A 96.422 531 16 1 3599 4126 354937719 354937189 0.000000e+00 872.0
8 TraesCS1B01G211200 chr1A 84.531 821 38 36 573 1362 354940679 354939917 0.000000e+00 730.0
9 TraesCS1B01G211200 chr1A 88.017 242 28 1 2 242 354941509 354941268 6.750000e-73 285.0
10 TraesCS1B01G211200 chr1A 86.842 76 10 0 494 569 354940838 354940763 7.350000e-13 86.1
11 TraesCS1B01G211200 chr2B 86.159 867 98 15 2243 3099 65472562 65473416 0.000000e+00 917.0
12 TraesCS1B01G211200 chr4A 82.550 298 32 10 2766 3061 196609536 196609257 1.150000e-60 244.0
13 TraesCS1B01G211200 chr4A 90.000 120 11 1 3146 3264 196609226 196609107 1.990000e-33 154.0
14 TraesCS1B01G211200 chr4A 100.000 30 0 0 464 493 165711874 165711903 5.760000e-04 56.5
15 TraesCS1B01G211200 chr5B 88.618 123 13 1 3145 3266 397964580 397964702 9.250000e-32 148.0
16 TraesCS1B01G211200 chr5B 96.875 32 1 0 464 495 10464494 10464463 2.000000e-03 54.7
17 TraesCS1B01G211200 chr3D 94.444 36 2 0 457 492 143246471 143246506 5.760000e-04 56.5
18 TraesCS1B01G211200 chr7D 100.000 29 0 0 464 492 613714563 613714535 2.000000e-03 54.7
19 TraesCS1B01G211200 chr5A 94.286 35 2 0 457 491 43255425 43255391 2.000000e-03 54.7
20 TraesCS1B01G211200 chr2A 96.875 32 1 0 464 495 727188141 727188110 2.000000e-03 54.7
21 TraesCS1B01G211200 chr2D 100.000 28 0 0 464 491 562180438 562180411 7.000000e-03 52.8


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 TraesCS1B01G211200 chr1B 384297876 384302003 4127 True 7624.00 7624 100.0000 1 4128 1 chr1B.!!$R1 4127
1 TraesCS1B01G211200 chr1B 34777018 34777716 698 False 737.00 737 85.8530 2432 3142 1 chr1B.!!$F1 710
2 TraesCS1B01G211200 chr1B 34794346 34795044 698 False 737.00 737 85.8530 2432 3142 1 chr1B.!!$F2 710
3 TraesCS1B01G211200 chr1D 282948071 282952161 4090 True 2620.00 3583 89.7350 1 4128 2 chr1D.!!$R1 4127
4 TraesCS1B01G211200 chr1A 354937189 354941509 4320 True 901.02 2532 88.8304 2 4126 5 chr1A.!!$R1 4124
5 TraesCS1B01G211200 chr2B 65472562 65473416 854 False 917.00 917 86.1590 2243 3099 1 chr2B.!!$F1 856


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
963 1331 0.398381 CTTCCTCCTCTCCTCCCCAG 60.398 65.0 0.00 0.0 0.00 4.45 F
1229 1615 0.036765 ATCCTGTTCTTGGCGCGTTA 60.037 50.0 8.43 0.0 0.00 3.18 F
1237 1623 0.247537 CTTGGCGCGTTACGGAAATC 60.248 55.0 8.43 0.0 43.93 2.17 F
1395 1782 0.319728 TTCTGTCTCCAGTCTGCTGC 59.680 55.0 0.00 0.0 41.26 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2274 1.066430 TCGGCATGGGTGTTCTACTTC 60.066 52.381 0.00 0.0 0.00 3.01 R
2787 3207 1.593469 CAGCACATCAGAAGATCAGCG 59.407 52.381 0.00 0.0 36.62 5.18 R
2999 3419 2.414994 ATTACAGCAGCAGCATCAGT 57.585 45.000 3.17 0.0 45.49 3.41 R
3290 3716 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.0 0.00 3.72 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 2.031682 GTGATGGTGTTGCTCAGTTGAC 60.032 50.000 0.00 0.00 0.00 3.18
68 69 4.142249 CGTAGTATCCACATGGTGAGAACA 60.142 45.833 0.00 0.00 35.23 3.18
78 79 3.744238 TGGTGAGAACAAGAATCACGA 57.256 42.857 0.00 0.00 43.39 4.35
82 83 4.150804 GGTGAGAACAAGAATCACGAGAAC 59.849 45.833 0.00 0.00 43.39 3.01
210 212 3.068307 GCCTAGACCTCTCTCGCAAATAA 59.932 47.826 0.00 0.00 0.00 1.40
226 228 8.740123 TCGCAAATAAGTAATCCAAAAGGATA 57.260 30.769 0.00 0.00 0.00 2.59
288 531 3.982316 CTTGATGCGGCAGCCCTCA 62.982 63.158 16.43 7.86 44.33 3.86
317 560 1.292223 CGGTCGGATGTCCAACACT 59.708 57.895 0.00 0.00 35.14 3.55
335 578 6.016276 CCAACACTTATTTCTTAGTGCCAGTT 60.016 38.462 0.00 0.00 44.34 3.16
393 636 5.010314 ACTTCCACGTAAAGTCACACATAGA 59.990 40.000 9.14 0.00 31.36 1.98
454 697 8.101419 ACTCCTTCCGTAAAGAAATGTAAGATT 58.899 33.333 0.00 0.00 37.12 2.40
504 768 3.408634 AGGGAGTACAAAAACATCCACG 58.591 45.455 0.00 0.00 0.00 4.94
542 806 4.020218 TGTCTTCATCGACAATCTCCCTTT 60.020 41.667 0.00 0.00 40.69 3.11
636 988 3.566523 GACCGTCATCGTTAGGATCATC 58.433 50.000 0.00 0.00 31.28 2.92
655 1007 5.221880 TCATCTTTTACATGTGCAAAGTGC 58.778 37.500 22.29 0.00 45.29 4.40
721 1078 2.298411 GCGATGAAAAACATGGGCAT 57.702 45.000 0.00 0.00 39.56 4.40
737 1099 2.886859 CATCCGCGTGATGGTACTC 58.113 57.895 22.32 0.00 45.99 2.59
757 1119 1.278238 CGCGTCCACAGAATTAGGTC 58.722 55.000 0.00 0.00 0.00 3.85
763 1125 3.773119 GTCCACAGAATTAGGTCTGGGTA 59.227 47.826 7.10 0.00 45.98 3.69
764 1126 4.409247 GTCCACAGAATTAGGTCTGGGTAT 59.591 45.833 7.10 0.00 45.98 2.73
765 1127 5.601313 GTCCACAGAATTAGGTCTGGGTATA 59.399 44.000 7.10 0.00 45.98 1.47
800 1167 1.823610 AGGACGGGTCTGCTTAACTAC 59.176 52.381 0.00 0.00 0.00 2.73
801 1168 1.823610 GGACGGGTCTGCTTAACTACT 59.176 52.381 0.00 0.00 0.00 2.57
802 1169 2.233186 GGACGGGTCTGCTTAACTACTT 59.767 50.000 0.00 0.00 0.00 2.24
879 1246 1.833630 AGTCTGATCATCAAGGCGGAA 59.166 47.619 0.00 0.00 0.00 4.30
956 1324 4.214327 CGCCGCTTCCTCCTCTCC 62.214 72.222 0.00 0.00 0.00 3.71
960 1328 2.131067 CGCTTCCTCCTCTCCTCCC 61.131 68.421 0.00 0.00 0.00 4.30
963 1331 0.398381 CTTCCTCCTCTCCTCCCCAG 60.398 65.000 0.00 0.00 0.00 4.45
969 1337 1.074623 CTCTCCTCCCCAGCCTCAT 60.075 63.158 0.00 0.00 0.00 2.90
970 1338 1.074926 TCTCCTCCCCAGCCTCATC 60.075 63.158 0.00 0.00 0.00 2.92
971 1339 1.383664 CTCCTCCCCAGCCTCATCA 60.384 63.158 0.00 0.00 0.00 3.07
1207 1593 2.683968 CCAAGCTGCTGTACGTTCTTA 58.316 47.619 1.35 0.00 0.00 2.10
1209 1595 3.684788 CCAAGCTGCTGTACGTTCTTATT 59.315 43.478 1.35 0.00 0.00 1.40
1210 1596 4.868171 CCAAGCTGCTGTACGTTCTTATTA 59.132 41.667 1.35 0.00 0.00 0.98
1211 1597 5.523916 CCAAGCTGCTGTACGTTCTTATTAT 59.476 40.000 1.35 0.00 0.00 1.28
1212 1598 6.292381 CCAAGCTGCTGTACGTTCTTATTATC 60.292 42.308 1.35 0.00 0.00 1.75
1213 1599 5.290386 AGCTGCTGTACGTTCTTATTATCC 58.710 41.667 0.00 0.00 0.00 2.59
1214 1600 5.069251 AGCTGCTGTACGTTCTTATTATCCT 59.931 40.000 0.00 0.00 0.00 3.24
1215 1601 5.175856 GCTGCTGTACGTTCTTATTATCCTG 59.824 44.000 0.00 0.00 0.00 3.86
1221 1607 8.697846 TGTACGTTCTTATTATCCTGTTCTTG 57.302 34.615 0.00 0.00 0.00 3.02
1224 1610 5.276868 CGTTCTTATTATCCTGTTCTTGGCG 60.277 44.000 0.00 0.00 0.00 5.69
1229 1615 0.036765 ATCCTGTTCTTGGCGCGTTA 60.037 50.000 8.43 0.00 0.00 3.18
1230 1616 0.947180 TCCTGTTCTTGGCGCGTTAC 60.947 55.000 8.43 0.00 0.00 2.50
1232 1618 2.222953 CTGTTCTTGGCGCGTTACGG 62.223 60.000 8.43 0.00 43.93 4.02
1234 1620 1.300775 TTCTTGGCGCGTTACGGAA 60.301 52.632 8.43 3.83 43.93 4.30
1237 1623 0.247537 CTTGGCGCGTTACGGAAATC 60.248 55.000 8.43 0.00 43.93 2.17
1238 1624 1.957711 TTGGCGCGTTACGGAAATCG 61.958 55.000 8.43 1.92 43.93 3.34
1251 1637 4.608818 CGGAAATCGTCATACGTACATG 57.391 45.455 0.00 0.00 43.14 3.21
1252 1638 3.121463 CGGAAATCGTCATACGTACATGC 60.121 47.826 0.00 0.00 43.14 4.06
1267 1653 4.218635 CGTACATGCCATGTAGATCTAGGT 59.781 45.833 17.57 0.00 45.62 3.08
1362 1749 1.483004 TCCAACCGCCTCAAATCGATA 59.517 47.619 0.00 0.00 0.00 2.92
1363 1750 1.597663 CCAACCGCCTCAAATCGATAC 59.402 52.381 0.00 0.00 0.00 2.24
1364 1751 1.597663 CAACCGCCTCAAATCGATACC 59.402 52.381 0.00 0.00 0.00 2.73
1365 1752 1.120530 ACCGCCTCAAATCGATACCT 58.879 50.000 0.00 0.00 0.00 3.08
1366 1753 1.068741 ACCGCCTCAAATCGATACCTC 59.931 52.381 0.00 0.00 0.00 3.85
1367 1754 1.605712 CCGCCTCAAATCGATACCTCC 60.606 57.143 0.00 0.00 0.00 4.30
1368 1755 1.784525 GCCTCAAATCGATACCTCCG 58.215 55.000 0.00 0.00 0.00 4.63
1369 1756 1.605712 GCCTCAAATCGATACCTCCGG 60.606 57.143 0.00 0.00 0.00 5.14
1370 1757 1.687123 CCTCAAATCGATACCTCCGGT 59.313 52.381 0.00 0.00 40.16 5.28
1371 1758 2.102588 CCTCAAATCGATACCTCCGGTT 59.897 50.000 0.00 0.00 37.09 4.44
1372 1759 3.431766 CCTCAAATCGATACCTCCGGTTT 60.432 47.826 0.00 0.00 40.49 3.27
1373 1760 4.189231 CTCAAATCGATACCTCCGGTTTT 58.811 43.478 0.00 0.00 38.15 2.43
1374 1761 4.581868 TCAAATCGATACCTCCGGTTTTT 58.418 39.130 0.00 0.00 38.15 1.94
1375 1762 4.632688 TCAAATCGATACCTCCGGTTTTTC 59.367 41.667 0.00 0.00 38.15 2.29
1376 1763 4.482952 AATCGATACCTCCGGTTTTTCT 57.517 40.909 0.00 0.00 37.09 2.52
1377 1764 3.967332 TCGATACCTCCGGTTTTTCTT 57.033 42.857 0.00 0.00 37.09 2.52
1378 1765 3.853475 TCGATACCTCCGGTTTTTCTTC 58.147 45.455 0.00 0.00 37.09 2.87
1379 1766 3.512724 TCGATACCTCCGGTTTTTCTTCT 59.487 43.478 0.00 0.00 37.09 2.85
1380 1767 3.617263 CGATACCTCCGGTTTTTCTTCTG 59.383 47.826 0.00 0.00 37.09 3.02
1381 1768 4.576879 GATACCTCCGGTTTTTCTTCTGT 58.423 43.478 0.00 0.00 37.09 3.41
1382 1769 2.847441 ACCTCCGGTTTTTCTTCTGTC 58.153 47.619 0.00 0.00 27.29 3.51
1383 1770 2.438392 ACCTCCGGTTTTTCTTCTGTCT 59.562 45.455 0.00 0.00 27.29 3.41
1384 1771 3.067833 CCTCCGGTTTTTCTTCTGTCTC 58.932 50.000 0.00 0.00 0.00 3.36
1385 1772 3.067833 CTCCGGTTTTTCTTCTGTCTCC 58.932 50.000 0.00 0.00 0.00 3.71
1386 1773 2.436542 TCCGGTTTTTCTTCTGTCTCCA 59.563 45.455 0.00 0.00 0.00 3.86
1387 1774 2.808543 CCGGTTTTTCTTCTGTCTCCAG 59.191 50.000 0.00 0.00 40.25 3.86
1388 1775 3.467803 CGGTTTTTCTTCTGTCTCCAGT 58.532 45.455 0.00 0.00 39.82 4.00
1389 1776 3.495001 CGGTTTTTCTTCTGTCTCCAGTC 59.505 47.826 0.00 0.00 39.82 3.51
1390 1777 4.709250 GGTTTTTCTTCTGTCTCCAGTCT 58.291 43.478 0.00 0.00 39.82 3.24
1391 1778 4.513318 GGTTTTTCTTCTGTCTCCAGTCTG 59.487 45.833 0.00 0.00 39.82 3.51
1392 1779 3.393089 TTTCTTCTGTCTCCAGTCTGC 57.607 47.619 0.00 0.00 39.82 4.26
1393 1780 2.300956 TCTTCTGTCTCCAGTCTGCT 57.699 50.000 0.00 0.00 39.82 4.24
1394 1781 1.891811 TCTTCTGTCTCCAGTCTGCTG 59.108 52.381 0.00 0.00 39.82 4.41
1395 1782 0.319728 TTCTGTCTCCAGTCTGCTGC 59.680 55.000 0.00 0.00 41.26 5.25
1396 1783 0.829182 TCTGTCTCCAGTCTGCTGCA 60.829 55.000 0.88 0.88 41.26 4.41
1397 1784 0.390078 CTGTCTCCAGTCTGCTGCAG 60.390 60.000 23.31 23.31 41.26 4.41
1398 1785 1.117749 TGTCTCCAGTCTGCTGCAGT 61.118 55.000 27.24 8.26 41.26 4.40
1399 1786 0.891373 GTCTCCAGTCTGCTGCAGTA 59.109 55.000 27.24 10.46 41.26 2.74
1400 1787 1.480137 GTCTCCAGTCTGCTGCAGTAT 59.520 52.381 27.24 15.27 41.26 2.12
1421 1808 4.127566 TGATGCTCATTTCGATCTGTGA 57.872 40.909 0.00 0.00 0.00 3.58
1425 1812 2.030213 GCTCATTTCGATCTGTGACTGC 59.970 50.000 0.00 0.00 0.00 4.40
1526 1913 1.817099 CATGAACCAGGAGGAGCGC 60.817 63.158 0.00 0.00 38.69 5.92
1564 1951 0.536233 TGCAAGTGCGTAACCACCAT 60.536 50.000 0.00 0.00 45.83 3.55
1570 1957 0.951525 TGCGTAACCACCATCAACCG 60.952 55.000 0.00 0.00 0.00 4.44
1571 1958 1.791662 CGTAACCACCATCAACCGC 59.208 57.895 0.00 0.00 0.00 5.68
1609 1997 8.982723 ACCTCTTCAATTAGTATACATCACACT 58.017 33.333 5.50 0.00 0.00 3.55
1659 2055 3.630312 TGCAGACACGCATCACTAGTATA 59.370 43.478 0.00 0.00 36.86 1.47
1660 2056 4.222886 GCAGACACGCATCACTAGTATAG 58.777 47.826 0.00 0.00 46.50 1.31
1661 2057 6.661613 TGCAGACACGCATCACTAGTATAGT 61.662 44.000 0.00 0.00 45.34 2.12
1662 2058 7.404565 TGCAGACACGCATCACTAGTATAGTA 61.405 42.308 0.00 0.00 43.60 1.82
1663 2059 8.649733 TGCAGACACGCATCACTAGTATAGTAT 61.650 40.741 0.00 0.00 43.60 2.12
1678 2074 7.597288 AGTATAGTATGCCAGTTACACATCA 57.403 36.000 0.00 0.00 0.00 3.07
1688 2084 5.350365 GCCAGTTACACATCACTTTCGATTA 59.650 40.000 0.00 0.00 0.00 1.75
1708 2107 1.373246 CAAATGCCACCAGTTGCCG 60.373 57.895 0.00 0.00 39.73 5.69
1749 2148 6.153510 AGCCATCCTTTCCTGTTATTCTTTTC 59.846 38.462 0.00 0.00 0.00 2.29
1785 2186 6.862711 ACTAGATGATGTGATTCATTGCAG 57.137 37.500 0.00 0.00 36.48 4.41
1791 2192 5.195185 TGATGTGATTCATTGCAGTACCAT 58.805 37.500 0.00 0.00 36.83 3.55
1798 2199 5.756195 TTCATTGCAGTACCATGCTTATC 57.244 39.130 8.39 0.00 46.63 1.75
1887 2292 7.921786 TTAAGAATGAAGTAGAACACCCATG 57.078 36.000 0.00 0.00 0.00 3.66
1888 2293 4.265073 AGAATGAAGTAGAACACCCATGC 58.735 43.478 0.00 0.00 0.00 4.06
1904 2309 2.559668 CCATGCCGATGATTTTATGCCT 59.440 45.455 0.00 0.00 0.00 4.75
1905 2310 3.571571 CATGCCGATGATTTTATGCCTG 58.428 45.455 0.00 0.00 0.00 4.85
1906 2311 2.653726 TGCCGATGATTTTATGCCTGT 58.346 42.857 0.00 0.00 0.00 4.00
1909 2314 4.081752 TGCCGATGATTTTATGCCTGTTTT 60.082 37.500 0.00 0.00 0.00 2.43
1951 2357 9.466497 TCAGAAAATGGTATTTTCTAATCTGCT 57.534 29.630 22.12 3.44 44.30 4.24
2113 2519 4.023193 CGCACAAGGGTTATATCAAATCCC 60.023 45.833 0.00 0.00 38.50 3.85
2123 2530 6.787458 GGTTATATCAAATCCCCATTTTCCCT 59.213 38.462 0.00 0.00 28.97 4.20
2146 2553 6.016610 CCTCTCTAATCAGCTCCACTAACTAC 60.017 46.154 0.00 0.00 0.00 2.73
2147 2554 5.527951 TCTCTAATCAGCTCCACTAACTACG 59.472 44.000 0.00 0.00 0.00 3.51
2148 2555 2.873133 ATCAGCTCCACTAACTACGC 57.127 50.000 0.00 0.00 0.00 4.42
2150 2557 2.100197 TCAGCTCCACTAACTACGCAT 58.900 47.619 0.00 0.00 0.00 4.73
2151 2558 2.496070 TCAGCTCCACTAACTACGCATT 59.504 45.455 0.00 0.00 0.00 3.56
2152 2559 3.056107 TCAGCTCCACTAACTACGCATTT 60.056 43.478 0.00 0.00 0.00 2.32
2153 2560 3.684788 CAGCTCCACTAACTACGCATTTT 59.315 43.478 0.00 0.00 0.00 1.82
2154 2561 3.933332 AGCTCCACTAACTACGCATTTTC 59.067 43.478 0.00 0.00 0.00 2.29
2155 2562 3.063588 GCTCCACTAACTACGCATTTTCC 59.936 47.826 0.00 0.00 0.00 3.13
2156 2563 4.504858 CTCCACTAACTACGCATTTTCCT 58.495 43.478 0.00 0.00 0.00 3.36
2157 2564 4.901868 TCCACTAACTACGCATTTTCCTT 58.098 39.130 0.00 0.00 0.00 3.36
2158 2565 5.310451 TCCACTAACTACGCATTTTCCTTT 58.690 37.500 0.00 0.00 0.00 3.11
2159 2566 5.766174 TCCACTAACTACGCATTTTCCTTTT 59.234 36.000 0.00 0.00 0.00 2.27
2160 2567 5.856455 CCACTAACTACGCATTTTCCTTTTG 59.144 40.000 0.00 0.00 0.00 2.44
2166 2573 4.141855 ACGCATTTTCCTTTTGTACTCG 57.858 40.909 0.00 0.00 0.00 4.18
2281 2688 7.255139 GGCGATATCTTTACCATTGCTTACTTT 60.255 37.037 0.34 0.00 31.04 2.66
2282 2689 8.770828 GCGATATCTTTACCATTGCTTACTTTA 58.229 33.333 0.34 0.00 0.00 1.85
2291 2698 5.770162 ACCATTGCTTACTTTATCCTATGGC 59.230 40.000 0.00 0.00 33.87 4.40
2292 2699 5.769662 CCATTGCTTACTTTATCCTATGGCA 59.230 40.000 0.00 0.00 0.00 4.92
2293 2700 6.265196 CCATTGCTTACTTTATCCTATGGCAA 59.735 38.462 0.00 0.00 40.52 4.52
2338 2745 7.201696 GGAAAATTCAAGGAAACAAAAAGGACC 60.202 37.037 0.00 0.00 0.00 4.46
2398 2805 4.929808 GTGAAGGACTACAACCAGTATGTG 59.070 45.833 0.00 0.00 32.27 3.21
2504 2916 3.320826 ACCAACCCTTTTATGTGACAAGC 59.679 43.478 0.00 0.00 0.00 4.01
2574 2992 0.909610 TTGGTCTCCCAGCCTAGGTG 60.910 60.000 11.31 7.47 43.15 4.00
2680 3098 3.181480 GCACAGCAAGAAAAGGTAACCAA 60.181 43.478 0.00 0.00 37.17 3.67
2696 3114 0.950836 CCAACCATGCGTGTTCTCAA 59.049 50.000 4.96 0.00 0.00 3.02
2697 3115 1.541147 CCAACCATGCGTGTTCTCAAT 59.459 47.619 4.96 0.00 0.00 2.57
2703 3121 3.670055 CCATGCGTGTTCTCAATTCAAAC 59.330 43.478 4.96 0.00 0.00 2.93
2715 3133 4.075682 TCAATTCAAACCATACTTGCCGA 58.924 39.130 0.00 0.00 0.00 5.54
2721 3139 2.038387 ACCATACTTGCCGACAATCC 57.962 50.000 0.00 0.00 34.61 3.01
2722 3140 1.559682 ACCATACTTGCCGACAATCCT 59.440 47.619 0.00 0.00 34.61 3.24
2723 3141 2.769663 ACCATACTTGCCGACAATCCTA 59.230 45.455 0.00 0.00 34.61 2.94
2725 3143 4.196193 CCATACTTGCCGACAATCCTAAA 58.804 43.478 0.00 0.00 34.61 1.85
2741 3159 5.270893 TCCTAAAATCGATCGTTCCATCA 57.729 39.130 15.94 0.00 0.00 3.07
2787 3207 7.510549 TTTAGGCCTGATGATTATTAGTTGC 57.489 36.000 17.99 0.00 0.00 4.17
2887 3307 4.101448 GATCGCTGGGTGGCAGGT 62.101 66.667 0.00 0.00 0.00 4.00
2968 3388 7.823310 AGAATCTACAAACAGAGTAGTCGAGTA 59.177 37.037 0.00 0.00 39.86 2.59
2975 3395 7.389884 ACAAACAGAGTAGTCGAGTAGAACATA 59.610 37.037 0.00 0.00 0.00 2.29
2995 3415 9.535270 GAACATAAAATTCTTGAGAAAGAGACG 57.465 33.333 0.00 0.00 37.61 4.18
3001 3421 9.930693 AAAATTCTTGAGAAAGAGACGTATACT 57.069 29.630 0.56 0.00 37.61 2.12
3002 3422 8.918961 AATTCTTGAGAAAGAGACGTATACTG 57.081 34.615 0.56 0.00 37.61 2.74
3003 3423 7.683437 TTCTTGAGAAAGAGACGTATACTGA 57.317 36.000 0.56 0.00 0.00 3.41
3195 3617 4.439057 AGCGAGAAGTTGTTTAGTTGTGA 58.561 39.130 0.00 0.00 0.00 3.58
3301 3727 0.392327 TGGTGGAGTGTGTGTGTGTG 60.392 55.000 0.00 0.00 0.00 3.82
3302 3728 0.392461 GGTGGAGTGTGTGTGTGTGT 60.392 55.000 0.00 0.00 0.00 3.72
3303 3729 0.726827 GTGGAGTGTGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
3304 3730 0.323302 TGGAGTGTGTGTGTGTGTGT 59.677 50.000 0.00 0.00 0.00 3.72
3305 3731 0.726827 GGAGTGTGTGTGTGTGTGTG 59.273 55.000 0.00 0.00 0.00 3.82
3345 3771 4.466567 TTCACAGTTTTGTACGCAGATG 57.533 40.909 0.00 0.00 35.25 2.90
3347 3773 3.493129 TCACAGTTTTGTACGCAGATGTC 59.507 43.478 0.00 0.00 35.25 3.06
3348 3774 3.494626 CACAGTTTTGTACGCAGATGTCT 59.505 43.478 0.00 0.00 35.25 3.41
3349 3775 4.684242 CACAGTTTTGTACGCAGATGTCTA 59.316 41.667 0.00 0.00 35.25 2.59
3395 3828 2.547211 TCGAGCGTCTTACCTACTATGC 59.453 50.000 0.00 0.00 0.00 3.14
3412 3845 5.790593 ACTATGCGGAGAGAGTTTTGTTAA 58.209 37.500 5.28 0.00 0.00 2.01
3415 3848 2.157085 GCGGAGAGAGTTTTGTTAACCG 59.843 50.000 2.48 0.00 40.60 4.44
3420 3853 5.277202 GGAGAGAGTTTTGTTAACCGTGTTC 60.277 44.000 2.48 0.00 0.00 3.18
3422 3855 5.522824 AGAGAGTTTTGTTAACCGTGTTCTC 59.477 40.000 2.48 10.04 0.00 2.87
3462 3895 6.146184 TCTGTAATGAGAGAAAAGAAGTTGCG 59.854 38.462 0.00 0.00 0.00 4.85
3465 3898 0.868406 AGAGAAAAGAAGTTGCGCCG 59.132 50.000 4.18 0.00 0.00 6.46
3492 3925 5.715434 TTGTGCTTACCCCATAAGAAAAC 57.285 39.130 0.00 0.00 42.75 2.43
3495 3928 3.009253 TGCTTACCCCATAAGAAAACGGA 59.991 43.478 0.00 0.00 42.75 4.69
3496 3929 3.626217 GCTTACCCCATAAGAAAACGGAG 59.374 47.826 0.00 0.00 42.75 4.63
3497 3930 2.124277 ACCCCATAAGAAAACGGAGC 57.876 50.000 0.00 0.00 0.00 4.70
3498 3931 1.353022 ACCCCATAAGAAAACGGAGCA 59.647 47.619 0.00 0.00 0.00 4.26
3499 3932 1.743394 CCCCATAAGAAAACGGAGCAC 59.257 52.381 0.00 0.00 0.00 4.40
3511 3944 2.004583 CGGAGCACGGATTAAGTTGA 57.995 50.000 0.00 0.00 39.42 3.18
3512 3945 2.343101 CGGAGCACGGATTAAGTTGAA 58.657 47.619 0.00 0.00 39.42 2.69
3513 3946 2.093783 CGGAGCACGGATTAAGTTGAAC 59.906 50.000 0.00 0.00 39.42 3.18
3516 3949 5.116882 GGAGCACGGATTAAGTTGAACTAT 58.883 41.667 0.00 0.00 0.00 2.12
3517 3950 5.006746 GGAGCACGGATTAAGTTGAACTATG 59.993 44.000 0.00 0.00 0.00 2.23
3520 3955 6.823689 AGCACGGATTAAGTTGAACTATGAAT 59.176 34.615 0.00 0.00 0.00 2.57
3522 3957 7.429340 GCACGGATTAAGTTGAACTATGAATTG 59.571 37.037 0.00 0.12 0.00 2.32
3539 3974 6.968263 TGAATTGTTTGTAACCCATCAAGA 57.032 33.333 0.00 0.00 0.00 3.02
3543 3978 6.723298 TTGTTTGTAACCCATCAAGAATGT 57.277 33.333 0.00 0.00 33.13 2.71
3546 3981 5.720371 TTGTAACCCATCAAGAATGTTGG 57.280 39.130 0.00 0.00 43.32 3.77
3556 3991 6.421801 CCATCAAGAATGTTGGTGTTTTTCTC 59.578 38.462 2.70 0.00 40.23 2.87
3557 3992 6.522625 TCAAGAATGTTGGTGTTTTTCTCA 57.477 33.333 0.00 0.00 0.00 3.27
3558 3993 6.329496 TCAAGAATGTTGGTGTTTTTCTCAC 58.671 36.000 0.00 0.00 35.36 3.51
3559 3994 5.913137 AGAATGTTGGTGTTTTTCTCACA 57.087 34.783 0.00 0.00 37.52 3.58
3560 3995 6.279513 AGAATGTTGGTGTTTTTCTCACAA 57.720 33.333 0.00 0.00 37.52 3.33
3561 3996 6.696411 AGAATGTTGGTGTTTTTCTCACAAA 58.304 32.000 0.00 0.00 37.52 2.83
3562 3997 7.158021 AGAATGTTGGTGTTTTTCTCACAAAA 58.842 30.769 0.00 0.00 37.52 2.44
3563 3998 7.659390 AGAATGTTGGTGTTTTTCTCACAAAAA 59.341 29.630 0.00 0.00 37.52 1.94
3595 4063 2.699954 ACGTTTCATGGAGTGGTGATC 58.300 47.619 0.00 0.00 0.00 2.92
3755 4238 0.319555 CTGCTTCCGTCTCCGTTTCA 60.320 55.000 0.00 0.00 0.00 2.69
3907 4390 4.619227 ACGTCGCACCAACCCAGG 62.619 66.667 0.00 0.00 0.00 4.45
3982 4465 2.036414 TGCAGCTCCTCTCCTCGT 59.964 61.111 0.00 0.00 0.00 4.18
3994 4477 3.443925 CCTCGTGCCTCGCTCTCA 61.444 66.667 0.00 0.00 39.67 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 5.339008 TGTTCTCACCATGTGGATACTAC 57.661 43.478 5.96 0.00 38.94 2.73
49 50 4.832248 TCTTGTTCTCACCATGTGGATAC 58.168 43.478 5.96 0.00 38.94 2.24
51 52 4.371624 TTCTTGTTCTCACCATGTGGAT 57.628 40.909 5.96 0.00 38.94 3.41
78 79 2.027745 AGCATCACATCAAGGACGTTCT 60.028 45.455 0.00 0.00 0.00 3.01
82 83 2.014335 TGAGCATCACATCAAGGACG 57.986 50.000 0.00 0.00 42.56 4.79
133 134 2.029623 GCACCAGGAGCAATGATCATT 58.970 47.619 15.36 15.36 0.00 2.57
134 135 1.688772 GCACCAGGAGCAATGATCAT 58.311 50.000 1.18 1.18 0.00 2.45
226 228 5.719085 TCAACATGGCCAAACTATAAACCAT 59.281 36.000 10.96 0.00 38.42 3.55
317 560 7.011499 TCACCTAACTGGCACTAAGAAATAA 57.989 36.000 0.00 0.00 40.22 1.40
335 578 2.302733 TGCAGTGCAGATTCTTCACCTA 59.697 45.455 15.37 0.00 33.32 3.08
393 636 3.618507 GCACATAAGCAGAGAGGTTGTCT 60.619 47.826 0.00 0.00 38.62 3.41
478 742 6.263617 GTGGATGTTTTTGTACTCCCTTTGTA 59.736 38.462 0.00 0.00 0.00 2.41
481 745 4.277423 CGTGGATGTTTTTGTACTCCCTTT 59.723 41.667 0.00 0.00 0.00 3.11
482 746 3.818773 CGTGGATGTTTTTGTACTCCCTT 59.181 43.478 0.00 0.00 0.00 3.95
483 747 3.408634 CGTGGATGTTTTTGTACTCCCT 58.591 45.455 0.00 0.00 0.00 4.20
486 750 3.002862 TGTGCGTGGATGTTTTTGTACTC 59.997 43.478 0.00 0.00 0.00 2.59
487 751 2.946329 TGTGCGTGGATGTTTTTGTACT 59.054 40.909 0.00 0.00 0.00 2.73
488 752 3.341857 TGTGCGTGGATGTTTTTGTAC 57.658 42.857 0.00 0.00 0.00 2.90
489 753 4.106197 GTTTGTGCGTGGATGTTTTTGTA 58.894 39.130 0.00 0.00 0.00 2.41
490 754 2.926838 GTTTGTGCGTGGATGTTTTTGT 59.073 40.909 0.00 0.00 0.00 2.83
491 755 2.283884 GGTTTGTGCGTGGATGTTTTTG 59.716 45.455 0.00 0.00 0.00 2.44
492 756 2.167487 AGGTTTGTGCGTGGATGTTTTT 59.833 40.909 0.00 0.00 0.00 1.94
504 768 0.874607 AGACACGTCGAGGTTTGTGC 60.875 55.000 8.27 0.27 35.79 4.57
721 1078 2.767445 CGGAGTACCATCACGCGGA 61.767 63.158 12.47 5.24 35.59 5.54
737 1099 0.108329 ACCTAATTCTGTGGACGCGG 60.108 55.000 12.47 0.00 0.00 6.46
800 1167 1.436983 GCCCGCCAAATCCGTCTAAG 61.437 60.000 0.00 0.00 0.00 2.18
801 1168 1.450669 GCCCGCCAAATCCGTCTAA 60.451 57.895 0.00 0.00 0.00 2.10
802 1169 2.188469 GCCCGCCAAATCCGTCTA 59.812 61.111 0.00 0.00 0.00 2.59
850 1217 2.493278 TGATGATCAGACTCGTGAGCAA 59.507 45.455 0.09 0.00 45.45 3.91
851 1218 2.094675 TGATGATCAGACTCGTGAGCA 58.905 47.619 0.09 0.00 46.31 4.26
854 1221 2.159184 GCCTTGATGATCAGACTCGTGA 60.159 50.000 0.09 0.00 0.00 4.35
879 1246 2.550180 GCTCGGCTTTTCTGACTTTCTT 59.450 45.455 0.00 0.00 0.00 2.52
956 1324 0.841961 TGATTGATGAGGCTGGGGAG 59.158 55.000 0.00 0.00 0.00 4.30
960 1328 1.386533 GTGGTGATTGATGAGGCTGG 58.613 55.000 0.00 0.00 0.00 4.85
963 1331 0.753111 GGGGTGGTGATTGATGAGGC 60.753 60.000 0.00 0.00 0.00 4.70
969 1337 2.966732 GCTCCGGGGTGGTGATTGA 61.967 63.158 1.62 0.00 39.52 2.57
970 1338 2.438434 GCTCCGGGGTGGTGATTG 60.438 66.667 1.62 0.00 39.52 2.67
971 1339 4.096003 CGCTCCGGGGTGGTGATT 62.096 66.667 7.11 0.00 39.52 2.57
1207 1593 1.299541 CGCGCCAAGAACAGGATAAT 58.700 50.000 0.00 0.00 0.00 1.28
1209 1595 0.036765 AACGCGCCAAGAACAGGATA 60.037 50.000 5.73 0.00 0.00 2.59
1210 1596 0.036765 TAACGCGCCAAGAACAGGAT 60.037 50.000 5.73 0.00 0.00 3.24
1211 1597 0.947180 GTAACGCGCCAAGAACAGGA 60.947 55.000 5.73 0.00 0.00 3.86
1212 1598 1.495951 GTAACGCGCCAAGAACAGG 59.504 57.895 5.73 0.00 0.00 4.00
1213 1599 1.129809 CGTAACGCGCCAAGAACAG 59.870 57.895 5.73 0.00 0.00 3.16
1214 1600 2.311701 CCGTAACGCGCCAAGAACA 61.312 57.895 5.73 0.00 39.71 3.18
1215 1601 1.559149 TTCCGTAACGCGCCAAGAAC 61.559 55.000 5.73 0.00 39.71 3.01
1221 1607 2.318696 CGATTTCCGTAACGCGCC 59.681 61.111 5.73 0.00 39.71 6.53
1230 1616 3.121463 GCATGTACGTATGACGATTTCCG 60.121 47.826 5.94 0.00 46.05 4.30
1231 1617 3.183775 GGCATGTACGTATGACGATTTCC 59.816 47.826 5.94 0.00 46.05 3.13
1232 1618 3.799963 TGGCATGTACGTATGACGATTTC 59.200 43.478 5.94 0.00 46.05 2.17
1234 1620 3.446310 TGGCATGTACGTATGACGATT 57.554 42.857 5.94 0.00 46.05 3.34
1237 1623 2.469826 ACATGGCATGTACGTATGACG 58.530 47.619 30.56 1.24 42.78 4.35
1238 1624 4.866921 TCTACATGGCATGTACGTATGAC 58.133 43.478 31.06 0.00 44.38 3.06
1239 1625 5.476945 AGATCTACATGGCATGTACGTATGA 59.523 40.000 31.06 25.74 44.38 2.15
1240 1626 5.714047 AGATCTACATGGCATGTACGTATG 58.286 41.667 31.06 22.12 44.38 2.39
1241 1627 5.984695 AGATCTACATGGCATGTACGTAT 57.015 39.130 31.06 23.83 44.38 3.06
1242 1628 5.414765 CCTAGATCTACATGGCATGTACGTA 59.585 44.000 31.06 20.89 44.38 3.57
1243 1629 4.218635 CCTAGATCTACATGGCATGTACGT 59.781 45.833 31.06 22.90 44.38 3.57
1244 1630 4.218635 ACCTAGATCTACATGGCATGTACG 59.781 45.833 31.06 25.37 44.38 3.67
1245 1631 5.336849 GGACCTAGATCTACATGGCATGTAC 60.337 48.000 31.06 22.64 44.38 2.90
1246 1632 4.772624 GGACCTAGATCTACATGGCATGTA 59.227 45.833 31.99 31.99 44.38 2.29
1247 1633 3.580458 GGACCTAGATCTACATGGCATGT 59.420 47.826 33.18 33.18 46.92 3.21
1248 1634 3.367806 CGGACCTAGATCTACATGGCATG 60.368 52.174 25.31 25.31 0.00 4.06
1249 1635 2.828520 CGGACCTAGATCTACATGGCAT 59.171 50.000 0.00 0.00 0.00 4.40
1250 1636 2.239400 CGGACCTAGATCTACATGGCA 58.761 52.381 0.00 0.00 0.00 4.92
1251 1637 1.067495 GCGGACCTAGATCTACATGGC 60.067 57.143 0.00 0.00 0.00 4.40
1252 1638 1.546476 GGCGGACCTAGATCTACATGG 59.454 57.143 0.00 1.54 0.00 3.66
1306 1693 1.079127 CCTTGGAACGAGGCGACAT 60.079 57.895 0.00 0.00 0.00 3.06
1364 1751 3.067833 GGAGACAGAAGAAAAACCGGAG 58.932 50.000 9.46 0.00 0.00 4.63
1365 1752 2.436542 TGGAGACAGAAGAAAAACCGGA 59.563 45.455 9.46 0.00 35.01 5.14
1366 1753 2.846193 TGGAGACAGAAGAAAAACCGG 58.154 47.619 0.00 0.00 35.01 5.28
1379 1766 3.875390 TGCAGCAGACTGGAGACA 58.125 55.556 4.26 0.00 44.63 3.41
1383 1770 1.560505 TCATACTGCAGCAGACTGGA 58.439 50.000 29.70 16.39 44.63 3.86
1384 1771 2.210961 CATCATACTGCAGCAGACTGG 58.789 52.381 29.70 14.42 44.63 4.00
1385 1772 2.742204 AGCATCATACTGCAGCAGACTG 60.742 50.000 29.70 22.55 44.77 3.51
1386 1773 1.485480 AGCATCATACTGCAGCAGACT 59.515 47.619 29.70 12.29 44.77 3.24
1387 1774 1.865970 GAGCATCATACTGCAGCAGAC 59.134 52.381 29.70 8.59 44.77 3.51
1388 1775 1.483415 TGAGCATCATACTGCAGCAGA 59.517 47.619 29.70 12.88 42.56 4.26
1389 1776 1.949465 TGAGCATCATACTGCAGCAG 58.051 50.000 21.54 21.54 42.56 4.24
1526 1913 3.449227 TGGCGCAGGGACTCGTAG 61.449 66.667 10.83 0.00 34.60 3.51
1559 1946 0.107508 ATGAGGAGCGGTTGATGGTG 60.108 55.000 0.00 0.00 0.00 4.17
1564 1951 0.690192 TGGAAATGAGGAGCGGTTGA 59.310 50.000 0.00 0.00 0.00 3.18
1570 1957 2.026822 TGAAGAGGTGGAAATGAGGAGC 60.027 50.000 0.00 0.00 0.00 4.70
1571 1958 3.988976 TGAAGAGGTGGAAATGAGGAG 57.011 47.619 0.00 0.00 0.00 3.69
1609 1997 8.262715 TCGTAATAACTGAATGAAGAAATGCA 57.737 30.769 0.00 0.00 0.00 3.96
1653 2044 8.573885 GTGATGTGTAACTGGCATACTATACTA 58.426 37.037 0.00 0.00 38.04 1.82
1659 2055 4.826274 AGTGATGTGTAACTGGCATACT 57.174 40.909 0.00 0.00 38.04 2.12
1660 2056 5.445939 CGAAAGTGATGTGTAACTGGCATAC 60.446 44.000 0.00 0.00 38.04 2.39
1661 2057 4.629634 CGAAAGTGATGTGTAACTGGCATA 59.370 41.667 0.00 0.00 38.04 3.14
1662 2058 3.436704 CGAAAGTGATGTGTAACTGGCAT 59.563 43.478 0.00 0.00 38.04 4.40
1663 2059 2.805671 CGAAAGTGATGTGTAACTGGCA 59.194 45.455 0.00 0.00 38.04 4.92
1678 2074 4.704540 TGGTGGCATTTGATAATCGAAAGT 59.295 37.500 0.00 0.00 0.00 2.66
1712 2111 1.117150 GGATGGCTCCAATGCACAAT 58.883 50.000 0.00 0.00 41.64 2.71
1749 2148 5.070180 ACATCATCTAGTTCTCCTGGTGATG 59.930 44.000 13.45 13.45 41.02 3.07
1785 2186 8.298140 ACTCGAGTATTTAGATAAGCATGGTAC 58.702 37.037 18.46 0.00 0.00 3.34
1791 2192 7.201145 GGTCAACTCGAGTATTTAGATAAGCA 58.799 38.462 20.39 0.00 0.00 3.91
1798 2199 6.816640 TCAAATGGGTCAACTCGAGTATTTAG 59.183 38.462 20.39 13.18 0.00 1.85
1871 2274 1.066430 TCGGCATGGGTGTTCTACTTC 60.066 52.381 0.00 0.00 0.00 3.01
1883 2288 2.559668 AGGCATAAAATCATCGGCATGG 59.440 45.455 0.00 0.00 0.00 3.66
1887 2292 3.715628 AACAGGCATAAAATCATCGGC 57.284 42.857 0.00 0.00 0.00 5.54
1944 2350 9.632807 GATAAATAGTTAGACGATCAGCAGATT 57.367 33.333 0.00 0.00 33.72 2.40
1945 2351 9.019656 AGATAAATAGTTAGACGATCAGCAGAT 57.980 33.333 0.00 0.00 37.13 2.90
1951 2357 6.863645 GCAGCAGATAAATAGTTAGACGATCA 59.136 38.462 0.00 0.00 0.00 2.92
2100 2506 7.836142 AGAGGGAAAATGGGGATTTGATATAA 58.164 34.615 0.00 0.00 0.00 0.98
2113 2519 5.046288 AGCTGATTAGAGAGGGAAAATGG 57.954 43.478 0.00 0.00 0.00 3.16
2123 2530 5.527951 CGTAGTTAGTGGAGCTGATTAGAGA 59.472 44.000 0.00 0.00 0.00 3.10
2146 2553 4.141855 ACGAGTACAAAAGGAAAATGCG 57.858 40.909 0.00 0.00 0.00 4.73
2147 2554 4.148174 GCAACGAGTACAAAAGGAAAATGC 59.852 41.667 0.00 0.00 0.00 3.56
2148 2555 5.277825 TGCAACGAGTACAAAAGGAAAATG 58.722 37.500 0.00 0.00 0.00 2.32
2150 2557 4.396790 ACTGCAACGAGTACAAAAGGAAAA 59.603 37.500 0.00 0.00 0.00 2.29
2151 2558 3.942748 ACTGCAACGAGTACAAAAGGAAA 59.057 39.130 0.00 0.00 0.00 3.13
2152 2559 3.537580 ACTGCAACGAGTACAAAAGGAA 58.462 40.909 0.00 0.00 0.00 3.36
2153 2560 3.188159 ACTGCAACGAGTACAAAAGGA 57.812 42.857 0.00 0.00 0.00 3.36
2154 2561 3.963383 AACTGCAACGAGTACAAAAGG 57.037 42.857 0.00 0.00 0.00 3.11
2281 2688 6.730507 TCTTGACCTGATATTGCCATAGGATA 59.269 38.462 0.00 0.00 32.86 2.59
2282 2689 5.549228 TCTTGACCTGATATTGCCATAGGAT 59.451 40.000 0.00 0.00 32.86 3.24
2289 2696 5.009410 CCAATCTTCTTGACCTGATATTGCC 59.991 44.000 0.00 0.00 0.00 4.52
2291 2698 7.870509 TTCCAATCTTCTTGACCTGATATTG 57.129 36.000 0.00 0.00 0.00 1.90
2292 2699 8.884124 TTTTCCAATCTTCTTGACCTGATATT 57.116 30.769 0.00 0.00 0.00 1.28
2293 2700 9.484806 AATTTTCCAATCTTCTTGACCTGATAT 57.515 29.630 0.00 0.00 0.00 1.63
2398 2805 2.625790 ACCTCGTGCTAGATTCCTCATC 59.374 50.000 0.00 0.00 0.00 2.92
2504 2916 2.806608 AAGCCATGTGTCAAGCTTTG 57.193 45.000 0.00 0.00 42.74 2.77
2574 2992 4.510340 ACAAGACGACCAACACAAGTTATC 59.490 41.667 0.00 0.00 35.85 1.75
2680 3098 2.503331 TGAATTGAGAACACGCATGGT 58.497 42.857 0.00 0.00 0.00 3.55
2688 3106 6.446318 GCAAGTATGGTTTGAATTGAGAACA 58.554 36.000 0.00 0.00 0.00 3.18
2696 3114 3.417101 TGTCGGCAAGTATGGTTTGAAT 58.583 40.909 0.00 0.00 0.00 2.57
2697 3115 2.852449 TGTCGGCAAGTATGGTTTGAA 58.148 42.857 0.00 0.00 0.00 2.69
2703 3121 2.332063 AGGATTGTCGGCAAGTATGG 57.668 50.000 9.01 0.00 38.10 2.74
2715 3133 5.424757 TGGAACGATCGATTTTAGGATTGT 58.575 37.500 24.34 0.00 38.60 2.71
2721 3139 6.344572 TGTTGATGGAACGATCGATTTTAG 57.655 37.500 24.34 0.00 37.38 1.85
2722 3140 6.714492 CATGTTGATGGAACGATCGATTTTA 58.286 36.000 24.34 4.21 37.38 1.52
2723 3141 5.572211 CATGTTGATGGAACGATCGATTTT 58.428 37.500 24.34 5.50 37.38 1.82
2725 3143 4.801147 CATGTTGATGGAACGATCGATT 57.199 40.909 24.34 12.31 37.38 3.34
2741 3159 6.887626 AAAAACCGTCTATTGTACCATGTT 57.112 33.333 0.00 0.00 0.00 2.71
2787 3207 1.593469 CAGCACATCAGAAGATCAGCG 59.407 52.381 0.00 0.00 36.62 5.18
2884 3304 3.181439 CCTCAAACTTCTCCAGGAAACCT 60.181 47.826 0.00 0.00 33.07 3.50
2887 3307 3.496870 GCTCCTCAAACTTCTCCAGGAAA 60.497 47.826 0.00 0.00 32.74 3.13
2902 3322 3.226429 GACGTGGCAGTGCTCCTCA 62.226 63.158 16.11 0.78 0.00 3.86
2975 3395 9.930693 AGTATACGTCTCTTTCTCAAGAATTTT 57.069 29.630 0.00 0.00 38.63 1.82
2982 3402 6.095580 AGCATCAGTATACGTCTCTTTCTCAA 59.904 38.462 0.00 0.00 0.00 3.02
2983 3403 5.590663 AGCATCAGTATACGTCTCTTTCTCA 59.409 40.000 0.00 0.00 0.00 3.27
2995 3415 2.831333 ACAGCAGCAGCATCAGTATAC 58.169 47.619 3.17 0.00 45.49 1.47
2998 3418 3.548745 ATTACAGCAGCAGCATCAGTA 57.451 42.857 3.17 0.00 45.49 2.74
2999 3419 2.414994 ATTACAGCAGCAGCATCAGT 57.585 45.000 3.17 0.00 45.49 3.41
3000 3420 5.212934 CAATTATTACAGCAGCAGCATCAG 58.787 41.667 3.17 0.00 45.49 2.90
3001 3421 4.498513 GCAATTATTACAGCAGCAGCATCA 60.499 41.667 3.17 0.00 45.49 3.07
3002 3422 3.979495 GCAATTATTACAGCAGCAGCATC 59.021 43.478 3.17 0.00 45.49 3.91
3003 3423 3.549423 CGCAATTATTACAGCAGCAGCAT 60.549 43.478 3.17 0.00 45.49 3.79
3195 3617 4.021229 AGCATCACATTCCATGACACAAT 58.979 39.130 0.00 0.00 0.00 2.71
3290 3716 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3291 3717 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3292 3718 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
3301 3727 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
3302 3728 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
3303 3729 1.265635 ACAACACACACACACACACAC 59.734 47.619 0.00 0.00 0.00 3.82
3304 3730 1.598882 ACAACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
3305 3731 2.697431 AACAACACACACACACACAC 57.303 45.000 0.00 0.00 0.00 3.82
3345 3771 4.238514 CCAAACGCCTCTGCTATATAGAC 58.761 47.826 14.16 5.69 34.43 2.59
3347 3773 3.990469 CACCAAACGCCTCTGCTATATAG 59.010 47.826 5.30 5.30 34.43 1.31
3348 3774 3.386726 ACACCAAACGCCTCTGCTATATA 59.613 43.478 0.00 0.00 34.43 0.86
3349 3775 2.170607 ACACCAAACGCCTCTGCTATAT 59.829 45.455 0.00 0.00 34.43 0.86
3395 3828 3.183775 CACGGTTAACAAAACTCTCTCCG 59.816 47.826 8.10 0.00 40.94 4.63
3412 3845 0.603569 CAGCCTACAGAGAACACGGT 59.396 55.000 0.00 0.00 0.00 4.83
3415 3848 4.993029 AGATACAGCCTACAGAGAACAC 57.007 45.455 0.00 0.00 0.00 3.32
3420 3853 6.701145 TTACAGAAGATACAGCCTACAGAG 57.299 41.667 0.00 0.00 0.00 3.35
3422 3855 7.013750 TCTCATTACAGAAGATACAGCCTACAG 59.986 40.741 0.00 0.00 0.00 2.74
3471 3904 3.754323 CGTTTTCTTATGGGGTAAGCACA 59.246 43.478 0.00 0.00 39.73 4.57
3480 3913 1.396996 CGTGCTCCGTTTTCTTATGGG 59.603 52.381 0.00 0.00 0.00 4.00
3492 3925 2.004583 TCAACTTAATCCGTGCTCCG 57.995 50.000 0.00 0.00 0.00 4.63
3495 3928 5.730550 TCATAGTTCAACTTAATCCGTGCT 58.269 37.500 0.00 0.00 0.00 4.40
3496 3929 6.417191 TTCATAGTTCAACTTAATCCGTGC 57.583 37.500 0.00 0.00 0.00 5.34
3497 3930 8.450964 ACAATTCATAGTTCAACTTAATCCGTG 58.549 33.333 0.00 0.00 0.00 4.94
3498 3931 8.561738 ACAATTCATAGTTCAACTTAATCCGT 57.438 30.769 0.00 0.00 0.00 4.69
3499 3932 9.840427 AAACAATTCATAGTTCAACTTAATCCG 57.160 29.630 0.00 0.00 0.00 4.18
3505 3938 9.744468 GGTTACAAACAATTCATAGTTCAACTT 57.256 29.630 0.00 0.00 0.00 2.66
3506 3939 8.357402 GGGTTACAAACAATTCATAGTTCAACT 58.643 33.333 0.00 0.00 0.00 3.16
3507 3940 8.138712 TGGGTTACAAACAATTCATAGTTCAAC 58.861 33.333 0.00 0.00 0.00 3.18
3508 3941 8.239038 TGGGTTACAAACAATTCATAGTTCAA 57.761 30.769 0.00 0.00 0.00 2.69
3509 3942 7.825331 TGGGTTACAAACAATTCATAGTTCA 57.175 32.000 0.00 0.00 0.00 3.18
3510 3943 8.519526 TGATGGGTTACAAACAATTCATAGTTC 58.480 33.333 0.00 0.00 0.00 3.01
3511 3944 8.415950 TGATGGGTTACAAACAATTCATAGTT 57.584 30.769 0.00 0.00 0.00 2.24
3512 3945 8.415950 TTGATGGGTTACAAACAATTCATAGT 57.584 30.769 0.00 0.00 0.00 2.12
3513 3946 8.739039 TCTTGATGGGTTACAAACAATTCATAG 58.261 33.333 0.00 0.00 32.22 2.23
3516 3949 6.968263 TCTTGATGGGTTACAAACAATTCA 57.032 33.333 0.00 0.00 32.22 2.57
3517 3950 7.872483 ACATTCTTGATGGGTTACAAACAATTC 59.128 33.333 0.00 0.00 40.21 2.17
3520 3955 6.723298 ACATTCTTGATGGGTTACAAACAA 57.277 33.333 0.00 0.00 40.21 2.83
3522 3957 5.925969 CCAACATTCTTGATGGGTTACAAAC 59.074 40.000 0.00 0.00 41.01 2.93
3539 3974 7.736447 TTTTTGTGAGAAAAACACCAACATT 57.264 28.000 0.00 0.00 37.45 2.71
3568 4003 4.401202 ACCACTCCATGAAACGTTCTTTTT 59.599 37.500 0.00 0.00 0.00 1.94
3580 4029 1.065926 GCACAGATCACCACTCCATGA 60.066 52.381 0.00 0.00 0.00 3.07



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

AutoCloner maintained by Alex Coulton.