Multiple sequence alignment - TraesCS3B01G591300

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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 TraesCS3B01G591300 chr3B 100.000 5381 0 0 1 5381 816004415 816009795 0.000000e+00 9937.0
1 TraesCS3B01G591300 chr3B 77.528 534 109 8 1 524 815974907 815975439 1.460000e-80 311.0
2 TraesCS3B01G591300 chr3B 80.449 445 43 22 1336 1770 406133569 406133159 3.150000e-77 300.0
3 TraesCS3B01G591300 chr3B 72.646 446 84 21 144 588 815869606 815869198 4.400000e-21 113.0
4 TraesCS3B01G591300 chr3B 91.071 56 5 0 144 199 813805395 813805450 5.780000e-10 76.8
5 TraesCS3B01G591300 chr3B 93.182 44 2 1 4770 4812 692011129 692011086 4.500000e-06 63.9
6 TraesCS3B01G591300 chr3D 93.805 1259 59 11 3513 4756 606082906 606081652 0.000000e+00 1875.0
7 TraesCS3B01G591300 chr3D 93.107 1030 40 16 2520 3522 606084180 606083155 0.000000e+00 1480.0
8 TraesCS3B01G591300 chr3D 87.257 1028 57 27 752 1770 606085968 606085006 0.000000e+00 1105.0
9 TraesCS3B01G591300 chr3D 87.240 768 56 22 1765 2521 606084958 606084222 0.000000e+00 837.0
10 TraesCS3B01G591300 chr3D 89.105 514 37 8 4874 5381 606081418 606080918 5.920000e-174 621.0
11 TraesCS3B01G591300 chr3D 85.957 470 39 15 302 756 606086460 606086003 1.360000e-130 477.0
12 TraesCS3B01G591300 chr3D 92.578 256 19 0 1 256 606086719 606086464 8.510000e-98 368.0
13 TraesCS3B01G591300 chr3D 71.649 582 130 24 20 588 606305140 606305699 1.570000e-25 128.0
14 TraesCS3B01G591300 chr3A 87.988 1282 77 43 513 1770 738129083 738130311 0.000000e+00 1443.0
15 TraesCS3B01G591300 chr3A 92.992 899 47 9 3848 4743 738132109 738132994 0.000000e+00 1297.0
16 TraesCS3B01G591300 chr3A 96.898 548 15 1 2520 3065 738130943 738131490 0.000000e+00 917.0
17 TraesCS3B01G591300 chr3A 93.359 527 24 7 3067 3585 738131575 738132098 0.000000e+00 769.0
18 TraesCS3B01G591300 chr3A 91.158 475 25 5 1 471 738128626 738129087 3.540000e-176 628.0
19 TraesCS3B01G591300 chr3A 89.201 463 22 11 4919 5381 738133720 738134154 2.190000e-153 553.0
20 TraesCS3B01G591300 chr3A 80.816 735 109 16 1 709 738109637 738110365 1.020000e-151 547.0
21 TraesCS3B01G591300 chr3A 92.953 298 18 3 2078 2373 738130369 738130665 1.070000e-116 431.0
22 TraesCS3B01G591300 chr3A 93.333 150 6 1 2376 2521 738130752 738130901 9.070000e-53 219.0
23 TraesCS3B01G591300 chr3A 75.455 220 34 12 141 356 737945006 737944803 7.420000e-14 89.8
24 TraesCS3B01G591300 chr3A 71.848 341 81 12 26 357 737823654 737823988 3.450000e-12 84.2
25 TraesCS3B01G591300 chr2B 82.329 249 36 5 5133 5373 726705022 726704774 5.460000e-50 209.0
26 TraesCS3B01G591300 chr2B 82.329 249 36 5 5133 5373 726745911 726745663 5.460000e-50 209.0
27 TraesCS3B01G591300 chr2B 86.131 137 18 1 4866 5002 225571504 225571639 4.340000e-31 147.0
28 TraesCS3B01G591300 chr5D 88.983 118 11 2 4866 4982 517846820 517846936 1.560000e-30 145.0
29 TraesCS3B01G591300 chr5D 83.740 123 17 3 4866 4987 242356140 242356020 4.400000e-21 113.0
30 TraesCS3B01G591300 chr5D 95.556 45 2 0 4770 4814 552795171 552795127 7.480000e-09 73.1
31 TraesCS3B01G591300 chr5B 87.500 120 11 4 4866 4982 650551903 650552021 9.400000e-28 135.0
32 TraesCS3B01G591300 chr5B 86.066 122 17 0 4866 4987 259537605 259537484 1.220000e-26 132.0
33 TraesCS3B01G591300 chr5A 85.606 132 13 3 4866 4997 369631589 369631714 3.380000e-27 134.0
34 TraesCS3B01G591300 chr5A 85.593 118 15 2 4866 4982 645267293 645267409 7.320000e-24 122.0
35 TraesCS3B01G591300 chr7A 91.139 79 6 1 4876 4954 105627946 105628023 7.370000e-19 106.0
36 TraesCS3B01G591300 chr4B 93.103 58 3 1 4758 4814 552766705 552766648 3.450000e-12 84.2
37 TraesCS3B01G591300 chr1B 88.710 62 5 2 4758 4817 566846831 566846770 2.080000e-09 75.0
38 TraesCS3B01G591300 chr1B 97.222 36 1 0 493 528 26091091 26091126 1.620000e-05 62.1
39 TraesCS3B01G591300 chr2A 87.931 58 6 1 4758 4814 766966398 766966455 3.480000e-07 67.6
40 TraesCS3B01G591300 chr1D 90.000 50 3 2 4770 4817 419743059 419743010 4.500000e-06 63.9
41 TraesCS3B01G591300 chr1D 86.207 58 7 1 4758 4814 472542586 472542529 1.620000e-05 62.1


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 TraesCS3B01G591300 chr3B 816004415 816009795 5380 False 9937.000000 9937 100.000000 1 5381 1 chr3B.!!$F3 5380
1 TraesCS3B01G591300 chr3B 815974907 815975439 532 False 311.000000 311 77.528000 1 524 1 chr3B.!!$F2 523
2 TraesCS3B01G591300 chr3D 606080918 606086719 5801 True 966.142857 1875 89.864143 1 5381 7 chr3D.!!$R1 5380
3 TraesCS3B01G591300 chr3A 738128626 738134154 5528 False 782.125000 1443 92.235250 1 5381 8 chr3A.!!$F3 5380
4 TraesCS3B01G591300 chr3A 738109637 738110365 728 False 547.000000 547 80.816000 1 709 1 chr3A.!!$F2 708

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
970 1055 0.250338 AGAAAAGCCCGCGACTTTCT 60.250 50.000 21.90 18.10 36.35 2.52 F
1242 1340 0.033405 TCGAGGACTTCTGGGGGTAG 60.033 60.000 0.00 0.00 0.00 3.18 F
1295 1393 0.180406 CCCCCTCTCGTTTATGTGGG 59.820 60.000 0.00 0.00 36.90 4.61 F
1535 1634 0.234625 TGCAAGTGAAATCGTCGTGC 59.765 50.000 0.00 8.45 33.76 5.34 F
1536 1635 0.234625 GCAAGTGAAATCGTCGTGCA 59.765 50.000 9.77 0.00 33.51 4.57 F
1643 1745 0.245539 TAGGCAGTAAGTGGACACGC 59.754 55.000 0.00 0.00 36.20 5.34 F
2501 2760 1.130938 TGCTGAATAGTGTGCATTGCG 59.869 47.619 3.84 0.00 0.00 4.85 F
3658 4335 0.828022 TGTATCTTACCGGCCACCAG 59.172 55.000 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2236 1.388547 AAACCGAAGCTTGCTGTTGA 58.611 45.000 2.10 0.0 0.00 3.18 R
3023 3328 1.922570 CAGCTTCATTGGCAGCATTC 58.077 50.000 10.29 0.0 38.61 2.67 R
3287 3692 2.032550 CAGTGTTCTGCTGTTCAAGGTG 59.967 50.000 0.00 0.0 34.79 4.00 R
3306 3711 5.505173 AACAGGTCAAGTTTCATCAACAG 57.495 39.130 0.00 0.0 37.93 3.16 R
3335 3740 7.506114 AGAAGACATAGAAACACAGTAAACCA 58.494 34.615 0.00 0.0 0.00 3.67 R
3608 4283 2.645730 ACACGCAGAAAGCAAAAACA 57.354 40.000 0.00 0.0 46.13 2.83 R
4074 4756 0.105593 CTCATGTATCCACGGCAGCT 59.894 55.000 0.00 0.0 0.00 4.24 R
5059 6303 0.673644 ACGGCAATCCCAGAGTTTCG 60.674 55.000 0.00 0.0 0.00 3.46 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
67 68 1.141053 AGGCAATATCCAAGACCGTCC 59.859 52.381 0.00 0.00 0.00 4.79
105 109 2.456119 CGTCCATGCAGACTTCGGC 61.456 63.158 4.76 0.00 37.57 5.54
132 136 1.620819 AGTCCACAGATTGCGACTTCT 59.379 47.619 0.00 0.00 34.07 2.85
138 142 2.826128 ACAGATTGCGACTTCTGACCTA 59.174 45.455 10.90 0.00 41.53 3.08
141 145 1.334160 TTGCGACTTCTGACCTACCA 58.666 50.000 0.00 0.00 0.00 3.25
201 205 4.039366 GGCTCGGAGAATATTACCTTCAGT 59.961 45.833 9.69 0.00 34.09 3.41
216 220 1.967319 TCAGTGGAACAAACAGGCTC 58.033 50.000 0.00 0.00 44.16 4.70
241 248 1.938016 GCGGGCGTAAACGGATGATAT 60.938 52.381 4.49 0.00 40.23 1.63
297 304 5.310857 ACCAGAGAAAAGGTTCACTATCCTT 59.689 40.000 0.00 0.00 44.71 3.36
561 583 1.279527 CGTTCGTGAGCTTGGCGTAA 61.280 55.000 0.00 0.00 0.00 3.18
582 604 1.338337 ACCAGGCTGAGAATATCGTCG 59.662 52.381 17.94 0.00 0.00 5.12
605 627 0.905357 AGAATTGACCACCTCTCCGG 59.095 55.000 0.00 0.00 39.35 5.14
691 731 1.001974 CCTCCATCTTTGTGTCCGTGA 59.998 52.381 0.00 0.00 0.00 4.35
738 781 3.000376 GTCGATCGTTTATTGTTCGGTCC 60.000 47.826 15.94 0.00 32.08 4.46
758 840 4.270325 GTCCACGAGACAAACCATATAAGC 59.730 45.833 5.64 0.00 45.55 3.09
787 869 1.269936 ACAAACCTAACCGGACACGAG 60.270 52.381 9.46 0.00 44.60 4.18
798 880 0.322546 GGACACGAGGATTGGGCTTT 60.323 55.000 0.00 0.00 0.00 3.51
802 884 1.402968 CACGAGGATTGGGCTTTGATG 59.597 52.381 0.00 0.00 0.00 3.07
811 893 2.182537 GCTTTGATGGGCCTTGCG 59.817 61.111 4.53 0.00 0.00 4.85
878 963 7.911205 CGTTTTTCTACTACTAGTCTCCATCTG 59.089 40.741 0.00 0.00 0.00 2.90
970 1055 0.250338 AGAAAAGCCCGCGACTTTCT 60.250 50.000 21.90 18.10 36.35 2.52
1242 1340 0.033405 TCGAGGACTTCTGGGGGTAG 60.033 60.000 0.00 0.00 0.00 3.18
1295 1393 0.180406 CCCCCTCTCGTTTATGTGGG 59.820 60.000 0.00 0.00 36.90 4.61
1320 1418 4.434195 GATTGGATCCTCTCCCCTAAGAT 58.566 47.826 14.23 0.00 44.23 2.40
1321 1419 4.302004 TTGGATCCTCTCCCCTAAGATT 57.698 45.455 14.23 0.00 44.23 2.40
1322 1420 3.591789 TGGATCCTCTCCCCTAAGATTG 58.408 50.000 14.23 0.00 44.23 2.67
1323 1421 3.209843 TGGATCCTCTCCCCTAAGATTGA 59.790 47.826 14.23 0.00 44.23 2.57
1333 1431 2.550978 CCTAAGATTGATTGGCGTCGT 58.449 47.619 0.00 0.00 0.00 4.34
1334 1432 2.540101 CCTAAGATTGATTGGCGTCGTC 59.460 50.000 0.00 0.00 0.00 4.20
1402 1501 1.837439 AGTTAGTGGATGCGATTGGGA 59.163 47.619 0.00 0.00 0.00 4.37
1431 1530 3.119495 AGGTAGCCATTGATTTTGCGTTC 60.119 43.478 0.00 0.00 0.00 3.95
1432 1531 2.368655 AGCCATTGATTTTGCGTTCC 57.631 45.000 0.00 0.00 0.00 3.62
1487 1586 3.194116 CGCCGTGGGTATATACTGGTTAT 59.806 47.826 12.54 0.00 0.00 1.89
1489 1588 5.068198 CGCCGTGGGTATATACTGGTTATAT 59.932 44.000 12.54 0.00 37.22 0.86
1496 1595 6.042897 GGGTATATACTGGTTATATGAGGCCC 59.957 46.154 12.54 0.00 34.69 5.80
1514 1613 1.208776 CCCGGGTTTCCTTGTAGTAGG 59.791 57.143 14.18 0.00 36.59 3.18
1527 1626 5.473504 CCTTGTAGTAGGTTGCAAGTGAAAT 59.526 40.000 0.00 0.00 38.59 2.17
1531 1630 3.746492 AGTAGGTTGCAAGTGAAATCGTC 59.254 43.478 0.00 0.00 0.00 4.20
1534 1633 2.298300 GTTGCAAGTGAAATCGTCGTG 58.702 47.619 0.00 0.00 0.00 4.35
1535 1634 0.234625 TGCAAGTGAAATCGTCGTGC 59.765 50.000 0.00 8.45 33.76 5.34
1536 1635 0.234625 GCAAGTGAAATCGTCGTGCA 59.765 50.000 9.77 0.00 33.51 4.57
1553 1652 3.645975 AGTTTTGTCCGGTGCGCG 61.646 61.111 0.00 0.00 0.00 6.86
1590 1692 7.676043 TGAGATTAGGAGGCTTATATAACAGCT 59.324 37.037 6.42 0.00 36.20 4.24
1591 1693 8.442660 AGATTAGGAGGCTTATATAACAGCTT 57.557 34.615 6.42 0.00 36.20 3.74
1592 1694 9.548631 AGATTAGGAGGCTTATATAACAGCTTA 57.451 33.333 6.42 0.00 36.20 3.09
1595 1697 7.560796 AGGAGGCTTATATAACAGCTTATGT 57.439 36.000 6.42 0.00 46.97 2.29
1596 1698 7.616313 AGGAGGCTTATATAACAGCTTATGTC 58.384 38.462 6.42 0.00 43.00 3.06
1597 1699 7.235606 AGGAGGCTTATATAACAGCTTATGTCA 59.764 37.037 6.42 0.00 43.00 3.58
1598 1700 7.332182 GGAGGCTTATATAACAGCTTATGTCAC 59.668 40.741 6.42 0.00 43.00 3.67
1599 1701 6.868864 AGGCTTATATAACAGCTTATGTCACG 59.131 38.462 6.42 0.00 43.00 4.35
1600 1702 6.645415 GGCTTATATAACAGCTTATGTCACGT 59.355 38.462 6.42 0.00 43.00 4.49
1601 1703 7.359264 GGCTTATATAACAGCTTATGTCACGTG 60.359 40.741 9.94 9.94 43.00 4.49
1602 1704 7.381408 GCTTATATAACAGCTTATGTCACGTGA 59.619 37.037 15.76 15.76 43.00 4.35
1603 1705 9.411801 CTTATATAACAGCTTATGTCACGTGAT 57.588 33.333 23.12 9.40 43.00 3.06
1605 1707 8.972262 ATATAACAGCTTATGTCACGTGATAG 57.028 34.615 23.12 16.63 43.00 2.08
1606 1708 3.448686 ACAGCTTATGTCACGTGATAGC 58.551 45.455 23.12 24.23 37.75 2.97
1607 1709 3.119137 ACAGCTTATGTCACGTGATAGCA 60.119 43.478 29.47 21.80 37.75 3.49
1608 1710 3.865164 CAGCTTATGTCACGTGATAGCAA 59.135 43.478 29.47 21.04 0.00 3.91
1609 1711 4.026228 CAGCTTATGTCACGTGATAGCAAG 60.026 45.833 29.47 26.67 0.00 4.01
1610 1712 3.865745 GCTTATGTCACGTGATAGCAAGT 59.134 43.478 26.09 13.17 37.19 3.16
1611 1713 5.041287 GCTTATGTCACGTGATAGCAAGTA 58.959 41.667 26.09 12.40 34.92 2.24
1612 1714 5.051641 GCTTATGTCACGTGATAGCAAGTAC 60.052 44.000 26.09 13.43 34.92 2.73
1613 1715 3.226346 TGTCACGTGATAGCAAGTACC 57.774 47.619 23.12 5.00 34.92 3.34
1614 1716 2.182825 GTCACGTGATAGCAAGTACCG 58.817 52.381 23.12 0.00 34.92 4.02
1615 1717 0.921347 CACGTGATAGCAAGTACCGC 59.079 55.000 10.90 0.00 34.92 5.68
1616 1718 0.524816 ACGTGATAGCAAGTACCGCG 60.525 55.000 0.00 0.00 34.92 6.46
1631 1733 1.019278 CCGCGTGTTTCATAGGCAGT 61.019 55.000 4.92 0.00 0.00 4.40
1642 1744 2.165641 TCATAGGCAGTAAGTGGACACG 59.834 50.000 0.00 0.00 36.20 4.49
1643 1745 0.245539 TAGGCAGTAAGTGGACACGC 59.754 55.000 0.00 0.00 36.20 5.34
1667 1769 5.333875 CCGTGTTCTGATTGATGCATATCTG 60.334 44.000 0.00 4.60 34.31 2.90
1750 1858 5.652014 ACCATGATTATTTGATGGACACGTT 59.348 36.000 0.00 0.00 39.29 3.99
1759 1867 3.799366 TGATGGACACGTTGTTGTAGTT 58.201 40.909 0.00 0.00 0.00 2.24
1761 1869 2.195096 TGGACACGTTGTTGTAGTTCG 58.805 47.619 0.00 0.00 0.00 3.95
1762 1870 2.195922 GGACACGTTGTTGTAGTTCGT 58.804 47.619 0.00 0.00 35.12 3.85
1763 1871 2.217167 GGACACGTTGTTGTAGTTCGTC 59.783 50.000 0.00 0.00 32.47 4.20
1764 1872 3.111098 GACACGTTGTTGTAGTTCGTCT 58.889 45.455 0.00 0.00 32.47 4.18
1765 1873 4.282068 GACACGTTGTTGTAGTTCGTCTA 58.718 43.478 0.00 0.00 32.47 2.59
1766 1874 4.863491 ACACGTTGTTGTAGTTCGTCTAT 58.137 39.130 0.00 0.00 32.47 1.98
1768 1876 6.437928 ACACGTTGTTGTAGTTCGTCTATTA 58.562 36.000 0.00 0.00 32.47 0.98
1788 1951 5.765576 TTATTAGGCTTTGGTAGGTGACA 57.234 39.130 0.00 0.00 0.00 3.58
1842 2005 6.626623 GCATCCAAATGTATCTCTTTGTGCTT 60.627 38.462 0.00 0.00 34.29 3.91
1858 2021 8.081633 TCTTTGTGCTTCTGTTAACCAATAATG 58.918 33.333 2.48 0.00 0.00 1.90
1861 2024 4.142491 TGCTTCTGTTAACCAATAATGCCG 60.142 41.667 2.48 0.00 0.00 5.69
1862 2025 4.351192 CTTCTGTTAACCAATAATGCCGC 58.649 43.478 2.48 0.00 0.00 6.53
1872 2035 9.685828 TTAACCAATAATGCCGCTATTAATTTC 57.314 29.630 0.00 0.00 0.00 2.17
1878 2041 6.699575 AATGCCGCTATTAATTTCTTGACT 57.300 33.333 0.00 0.00 0.00 3.41
1901 2064 5.993055 TGATCACTCAATCACACATATGGT 58.007 37.500 7.80 0.00 30.76 3.55
1941 2106 7.298122 TCGTCATTTTCTTATTTCTCTTGTGC 58.702 34.615 0.00 0.00 0.00 4.57
1982 2150 9.247861 ACTTTTCTAGCATCTATGGAAATGTTT 57.752 29.630 0.00 0.00 33.59 2.83
1990 2158 9.412460 AGCATCTATGGAAATGTTTTATCTTGA 57.588 29.630 0.00 0.00 0.00 3.02
1994 2162 9.919416 TCTATGGAAATGTTTTATCTTGATGGA 57.081 29.630 0.00 0.00 0.00 3.41
1998 2166 9.656040 TGGAAATGTTTTATCTTGATGGAAATG 57.344 29.630 0.00 0.00 0.00 2.32
1999 2167 9.657419 GGAAATGTTTTATCTTGATGGAAATGT 57.343 29.630 0.00 0.00 0.00 2.71
2006 2174 8.648698 TTTATCTTGATGGAAATGTTGGAAGA 57.351 30.769 0.00 0.00 0.00 2.87
2018 2186 9.276590 GGAAATGTTGGAAGATTTTTCTGAAAT 57.723 29.630 3.31 0.00 32.74 2.17
2023 2191 9.748708 TGTTGGAAGATTTTTCTGAAATACTTG 57.251 29.630 15.89 0.00 0.00 3.16
2024 2192 9.965824 GTTGGAAGATTTTTCTGAAATACTTGA 57.034 29.630 15.89 5.77 0.00 3.02
2063 2232 4.961435 ACGTTTCTTTTCCGGTTGTTTA 57.039 36.364 0.00 0.00 0.00 2.01
2067 2236 6.183360 ACGTTTCTTTTCCGGTTGTTTAGATT 60.183 34.615 0.00 0.00 0.00 2.40
2068 2237 6.358822 CGTTTCTTTTCCGGTTGTTTAGATTC 59.641 38.462 0.00 0.00 0.00 2.52
2069 2238 6.945938 TTCTTTTCCGGTTGTTTAGATTCA 57.054 33.333 0.00 0.00 0.00 2.57
2070 2239 6.945938 TCTTTTCCGGTTGTTTAGATTCAA 57.054 33.333 0.00 0.00 0.00 2.69
2071 2240 6.731164 TCTTTTCCGGTTGTTTAGATTCAAC 58.269 36.000 0.00 0.00 41.88 3.18
2072 2241 6.319152 TCTTTTCCGGTTGTTTAGATTCAACA 59.681 34.615 0.00 0.00 43.64 3.33
2073 2242 5.682943 TTCCGGTTGTTTAGATTCAACAG 57.317 39.130 0.00 5.96 43.64 3.16
2074 2243 3.500680 TCCGGTTGTTTAGATTCAACAGC 59.499 43.478 0.00 0.00 43.64 4.40
2075 2244 3.252215 CCGGTTGTTTAGATTCAACAGCA 59.748 43.478 9.60 0.00 43.64 4.41
2076 2245 4.261405 CCGGTTGTTTAGATTCAACAGCAA 60.261 41.667 9.60 0.00 43.64 3.91
2097 2266 5.513141 GCAAGCTTCGGTTTTAAGAATGATC 59.487 40.000 0.00 0.00 0.00 2.92
2158 2328 9.512588 CCTATTGCTTCTAACAATGAAGGATAT 57.487 33.333 0.00 0.00 40.53 1.63
2228 2398 3.093574 CGCAAGACGCACTCATAAATTG 58.906 45.455 0.00 0.00 42.60 2.32
2356 2527 8.598075 GGTTAAGTTTGTGTAATATGGTACTCG 58.402 37.037 0.00 0.00 0.00 4.18
2369 2540 4.019792 TGGTACTCGTACTTGACACCTA 57.980 45.455 7.12 0.00 36.36 3.08
2495 2754 4.497006 CCATTAAGCTGCTGAATAGTGTGC 60.497 45.833 11.86 0.00 0.00 4.57
2501 2760 1.130938 TGCTGAATAGTGTGCATTGCG 59.869 47.619 3.84 0.00 0.00 4.85
2541 2843 3.673902 TCAGGATGATTTCTTTCGTGCA 58.326 40.909 0.00 0.00 42.56 4.57
2571 2873 7.758528 AGCTTGCTTCAGAAATTTGATTATGTC 59.241 33.333 0.00 0.00 0.00 3.06
3023 3328 6.775629 AGGAAAGAGTAGCTATCTGGACTAAG 59.224 42.308 0.00 0.00 0.00 2.18
3067 3372 9.519191 TGCTCAGGTATGTATTATAAAATGCAT 57.481 29.630 0.00 0.00 46.30 3.96
3200 3605 4.760204 GTGTAGCCCTTTACAGTGTGATTT 59.240 41.667 5.88 0.00 34.41 2.17
3287 3692 5.725110 CTGAAAGGATGTATGCAGTACAC 57.275 43.478 10.03 6.04 45.59 2.90
3306 3711 2.017049 ACACCTTGAACAGCAGAACAC 58.983 47.619 0.00 0.00 0.00 3.32
3335 3740 7.453393 TGATGAAACTTGACCTGTTATCTTCT 58.547 34.615 0.00 0.00 0.00 2.85
3426 3832 4.796606 ACCAAATATTCCAGCTGTGCTAT 58.203 39.130 13.81 3.32 36.40 2.97
3439 3845 4.712337 AGCTGTGCTATGTAACTCCTAAGT 59.288 41.667 0.00 0.00 36.99 2.24
3499 3907 8.283291 GTCTGTTATTCTCCGGCTATATTTTTG 58.717 37.037 0.00 0.00 0.00 2.44
3654 4331 1.903860 ACAGTTGTATCTTACCGGCCA 59.096 47.619 0.00 0.00 0.00 5.36
3655 4332 2.277084 CAGTTGTATCTTACCGGCCAC 58.723 52.381 0.00 0.00 0.00 5.01
3658 4335 0.828022 TGTATCTTACCGGCCACCAG 59.172 55.000 0.00 0.00 0.00 4.00
3659 4336 0.828677 GTATCTTACCGGCCACCAGT 59.171 55.000 0.00 0.00 0.00 4.00
3758 4435 1.534729 CTGCACCTAAAGGACCAACC 58.465 55.000 2.23 0.00 38.94 3.77
3780 4457 2.301346 AGTGTGTTTTTCCAGCTGGAG 58.699 47.619 33.16 9.70 46.36 3.86
3796 4473 2.890945 CTGGAGGGGAAAAACAATTCGT 59.109 45.455 0.00 0.00 0.00 3.85
3809 4486 9.281075 GAAAAACAATTCGTAGCCGTATTTTAT 57.719 29.630 0.00 0.00 32.63 1.40
3820 4497 3.305897 GCCGTATTTTATGCTGGTTTTGC 59.694 43.478 0.00 0.00 0.00 3.68
3823 4500 4.381505 CGTATTTTATGCTGGTTTTGCCCT 60.382 41.667 0.00 0.00 36.04 5.19
3900 4579 9.508567 GAAGCTCCATTGATAAATGTTCTTAAC 57.491 33.333 2.00 0.00 0.00 2.01
3949 4628 6.986250 TCTCTGATATGCACTCGTTCATTAT 58.014 36.000 0.00 0.00 0.00 1.28
3958 4637 5.049474 TGCACTCGTTCATTATCATTATGCC 60.049 40.000 0.00 0.00 0.00 4.40
4025 4704 9.308000 CCTGAGTAAATTCTATCACCTATCTCT 57.692 37.037 0.00 0.00 0.00 3.10
4027 4706 8.580720 TGAGTAAATTCTATCACCTATCTCTGC 58.419 37.037 0.00 0.00 0.00 4.26
4074 4756 9.328845 AGTACTATTAACGGTTTTGTTTTCTGA 57.671 29.630 0.00 0.00 33.32 3.27
4077 4759 5.570234 TTAACGGTTTTGTTTTCTGAGCT 57.430 34.783 0.00 0.00 33.32 4.09
4166 4848 7.148407 CGTTTATTAGTTTCTGAGCACATTCCT 60.148 37.037 0.00 0.00 0.00 3.36
4263 4945 0.950555 TCATGTGAGTCGCTTGCACC 60.951 55.000 13.31 0.00 0.00 5.01
4323 5005 0.098376 CATCGCCTCTTTCTGCTTGC 59.902 55.000 0.00 0.00 0.00 4.01
4386 5068 1.702491 GCTACACCGTTTGATCCCGC 61.702 60.000 0.00 0.00 0.00 6.13
4498 5180 3.441572 CGGATGCTGTTTTCTGAAGGATT 59.558 43.478 0.00 0.00 0.00 3.01
4521 5203 7.922505 TTTATTATGTGTGTTTGCTGTGAAC 57.077 32.000 0.00 0.00 0.00 3.18
4557 5239 2.587612 TCTAACATCGTTGCGTTTGC 57.412 45.000 0.00 0.00 43.20 3.68
4564 5246 2.424640 GTTGCGTTTGCCGTCGTC 60.425 61.111 0.00 0.00 41.78 4.20
4583 5265 4.034858 TCGTCGTACTCCATAAGTCACATC 59.965 45.833 0.00 0.00 39.55 3.06
4618 5301 7.817478 TGAAGAGTTATATTTTGTGAGAAGCGA 59.183 33.333 0.00 0.00 0.00 4.93
4687 5373 1.070758 ACGTGAGATGGTTTCAGTGCT 59.929 47.619 0.00 0.00 0.00 4.40
4705 5391 6.376299 TCAGTGCTGAAGATTGCTCAATTATT 59.624 34.615 0.00 0.00 36.53 1.40
4714 5400 9.798994 GAAGATTGCTCAATTATTTGTCATTCT 57.201 29.630 0.00 5.94 33.73 2.40
4735 5421 5.935945 TCTAAACTTGGAAGTCATGGTTGA 58.064 37.500 0.00 0.00 38.57 3.18
4743 5429 6.968263 TGGAAGTCATGGTTGAAATTACAA 57.032 33.333 0.00 0.00 32.48 2.41
4747 5433 7.255801 GGAAGTCATGGTTGAAATTACAAAGGA 60.256 37.037 0.00 0.00 32.48 3.36
4756 5442 7.595130 GGTTGAAATTACAAAGGATCAGTTCAC 59.405 37.037 0.00 0.00 0.00 3.18
4760 5446 7.823745 AATTACAAAGGATCAGTTCACACTT 57.176 32.000 0.00 0.00 0.00 3.16
4765 5451 3.515562 AGGATCAGTTCACACTTCCTCT 58.484 45.455 0.00 0.00 35.98 3.69
4779 5516 5.221661 ACACTTCCTCTGTTCGGAATTACTT 60.222 40.000 0.00 0.00 39.64 2.24
4799 5536 8.786826 TTACTTGTCGGAGAAATGAATGTATT 57.213 30.769 0.00 0.00 39.69 1.89
4800 5537 9.878667 TTACTTGTCGGAGAAATGAATGTATTA 57.121 29.630 0.00 0.00 39.69 0.98
4801 5538 8.425577 ACTTGTCGGAGAAATGAATGTATTAG 57.574 34.615 0.00 0.00 39.69 1.73
4802 5539 8.258007 ACTTGTCGGAGAAATGAATGTATTAGA 58.742 33.333 0.00 0.00 39.69 2.10
4805 5586 8.204160 TGTCGGAGAAATGAATGTATTAGACAT 58.796 33.333 0.00 0.00 45.99 3.06
5009 6253 8.253810 TGGAGAGAGTATGTCACAAGAAATTAG 58.746 37.037 0.00 0.00 0.00 1.73
5013 6257 9.862371 GAGAGTATGTCACAAGAAATTAGAGAA 57.138 33.333 0.00 0.00 0.00 2.87
5037 6281 2.928801 TACTGCTTCTGTGGCAAGAA 57.071 45.000 10.32 10.32 39.30 2.52
5038 6282 2.057137 ACTGCTTCTGTGGCAAGAAA 57.943 45.000 11.42 0.00 39.30 2.52
5044 6288 1.761449 TCTGTGGCAAGAAAACAGCA 58.239 45.000 0.00 0.00 40.89 4.41
5055 6299 3.374745 AGAAAACAGCACAAATGAAGCG 58.625 40.909 0.00 0.00 0.00 4.68
5059 6303 1.002468 ACAGCACAAATGAAGCGTCAC 60.002 47.619 3.91 0.00 36.31 3.67
5071 6315 1.006571 GCGTCACGAAACTCTGGGA 60.007 57.895 0.00 0.00 0.00 4.37
5076 6320 0.804989 CACGAAACTCTGGGATTGCC 59.195 55.000 0.00 0.00 0.00 4.52
5086 6330 1.223487 GGGATTGCCGTGCCTTAGA 59.777 57.895 0.00 0.00 33.83 2.10
5100 6344 5.593010 GTGCCTTAGATAGAACCACAGTAG 58.407 45.833 0.00 0.00 0.00 2.57
5130 6374 7.633193 ACACCAAATACAGTAAAGTTCACAA 57.367 32.000 0.00 0.00 0.00 3.33
5131 6375 7.477494 ACACCAAATACAGTAAAGTTCACAAC 58.523 34.615 0.00 0.00 0.00 3.32
5153 6399 5.854157 ACAGTGTATATTTCTGTTTTCGCG 58.146 37.500 0.00 0.00 39.00 5.87
5178 6424 4.022416 GCATCATAAACAACAGGGTGTTCA 60.022 41.667 2.77 0.00 40.86 3.18
5275 6521 8.355169 CGGCATAGTACCAAACTAAGATAACTA 58.645 37.037 0.00 0.00 43.87 2.24
5355 6605 2.125147 CGCGGATTCTGCTTCCCA 60.125 61.111 15.23 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.273327 GCCACAAGGATTTGTTGGGAG 59.727 52.381 2.13 0.00 45.01 4.30
105 109 1.002134 AATCTGTGGACTTGGCCGG 60.002 57.895 0.00 0.00 0.00 6.13
138 142 0.040058 TCCTTGCTGCCATCATTGGT 59.960 50.000 0.00 0.00 45.57 3.67
141 145 3.301794 TGTATCCTTGCTGCCATCATT 57.698 42.857 0.00 0.00 0.00 2.57
201 205 2.250939 CGCGAGCCTGTTTGTTCCA 61.251 57.895 0.00 0.00 0.00 3.53
367 382 2.680913 CGCGCTTCTGGTTTCTGGG 61.681 63.158 5.56 0.00 0.00 4.45
414 436 1.144057 CGATAAGGGGAAGCACGCT 59.856 57.895 0.00 0.00 34.86 5.07
475 497 2.796483 ATTAAGCTGACGCACCCGCA 62.796 55.000 0.00 0.00 38.40 5.69
536 558 3.493830 AAGCTCACGAACGTCGGCA 62.494 57.895 17.64 0.00 45.59 5.69
538 560 2.372690 CCAAGCTCACGAACGTCGG 61.373 63.158 11.13 0.00 45.59 4.79
541 563 2.410638 TACGCCAAGCTCACGAACGT 62.411 55.000 9.62 6.27 36.17 3.99
548 570 0.605319 CCTGGTTTACGCCAAGCTCA 60.605 55.000 0.00 0.00 38.18 4.26
561 583 2.223829 CGACGATATTCTCAGCCTGGTT 60.224 50.000 0.00 0.00 0.00 3.67
582 604 1.210722 GAGAGGTGGTCAATTCTCCCC 59.789 57.143 0.00 0.00 31.95 4.81
716 759 3.000376 GGACCGAACAATAAACGATCGAC 60.000 47.826 24.34 0.79 35.65 4.20
738 781 3.245284 CCGCTTATATGGTTTGTCTCGTG 59.755 47.826 0.00 0.00 0.00 4.35
750 793 2.502213 TGTCACCGACCGCTTATATG 57.498 50.000 0.00 0.00 0.00 1.78
755 837 1.890510 GGTTTGTCACCGACCGCTT 60.891 57.895 0.00 0.00 35.12 4.68
777 859 2.186903 CCCAATCCTCGTGTCCGG 59.813 66.667 0.00 0.00 33.95 5.14
787 869 1.689243 GGCCCATCAAAGCCCAATCC 61.689 60.000 0.00 0.00 43.76 3.01
1125 1223 1.079057 GAAGGTCCAGGCGTTCTCC 60.079 63.158 8.31 0.00 32.44 3.71
1188 1286 1.454479 GATGGGGTGGATGGTGCTG 60.454 63.158 0.00 0.00 0.00 4.41
1431 1530 0.817634 TGGACCGCAACAAACTGAGG 60.818 55.000 0.00 0.00 41.65 3.86
1432 1531 1.069022 CATGGACCGCAACAAACTGAG 60.069 52.381 0.00 0.00 0.00 3.35
1487 1586 0.917333 AAGGAAACCCGGGCCTCATA 60.917 55.000 24.08 0.00 0.00 2.15
1489 1588 2.856988 AAGGAAACCCGGGCCTCA 60.857 61.111 24.08 0.00 0.00 3.86
1496 1595 3.332034 CAACCTACTACAAGGAAACCCG 58.668 50.000 0.00 0.00 39.15 5.28
1514 1613 2.298300 CACGACGATTTCACTTGCAAC 58.702 47.619 0.00 0.00 0.00 4.17
1527 1626 1.484227 CGGACAAAACTGCACGACGA 61.484 55.000 0.00 0.00 0.00 4.20
1531 1630 1.010125 CACCGGACAAAACTGCACG 60.010 57.895 9.46 0.00 0.00 5.34
1534 1633 2.051345 CGCACCGGACAAAACTGC 60.051 61.111 9.46 4.30 0.00 4.40
1535 1634 2.051345 GCGCACCGGACAAAACTG 60.051 61.111 9.46 0.00 0.00 3.16
1536 1635 3.645975 CGCGCACCGGACAAAACT 61.646 61.111 9.46 0.00 0.00 2.66
1553 1652 0.249657 CTAATCTCAGACCCAGGCGC 60.250 60.000 0.00 0.00 0.00 6.53
1556 1655 2.324541 CCTCCTAATCTCAGACCCAGG 58.675 57.143 0.00 0.00 0.00 4.45
1563 1662 7.978975 GCTGTTATATAAGCCTCCTAATCTCAG 59.021 40.741 0.00 0.00 33.12 3.35
1590 1692 5.345702 GGTACTTGCTATCACGTGACATAA 58.654 41.667 22.71 12.56 0.00 1.90
1591 1693 4.496840 CGGTACTTGCTATCACGTGACATA 60.497 45.833 22.71 9.63 0.00 2.29
1592 1694 3.733988 CGGTACTTGCTATCACGTGACAT 60.734 47.826 22.71 8.85 0.00 3.06
1593 1695 2.414957 CGGTACTTGCTATCACGTGACA 60.415 50.000 22.71 8.81 0.00 3.58
1594 1696 2.182825 CGGTACTTGCTATCACGTGAC 58.817 52.381 22.71 9.19 0.00 3.67
1595 1697 1.468565 GCGGTACTTGCTATCACGTGA 60.469 52.381 22.48 22.48 0.00 4.35
1596 1698 0.921347 GCGGTACTTGCTATCACGTG 59.079 55.000 9.94 9.94 0.00 4.49
1597 1699 0.524816 CGCGGTACTTGCTATCACGT 60.525 55.000 0.00 0.00 0.00 4.49
1598 1700 0.524816 ACGCGGTACTTGCTATCACG 60.525 55.000 12.47 0.00 0.00 4.35
1599 1701 0.921347 CACGCGGTACTTGCTATCAC 59.079 55.000 12.47 0.00 0.00 3.06
1600 1702 0.528924 ACACGCGGTACTTGCTATCA 59.471 50.000 12.47 0.00 0.00 2.15
1601 1703 1.636988 AACACGCGGTACTTGCTATC 58.363 50.000 12.47 0.00 0.00 2.08
1602 1704 1.997606 GAAACACGCGGTACTTGCTAT 59.002 47.619 12.47 0.00 0.00 2.97
1603 1705 1.269673 TGAAACACGCGGTACTTGCTA 60.270 47.619 12.47 0.00 0.00 3.49
1604 1706 0.531090 TGAAACACGCGGTACTTGCT 60.531 50.000 12.47 0.00 0.00 3.91
1605 1707 0.515564 ATGAAACACGCGGTACTTGC 59.484 50.000 12.47 0.00 0.00 4.01
1606 1708 2.347452 CCTATGAAACACGCGGTACTTG 59.653 50.000 12.47 0.56 0.00 3.16
1607 1709 2.613691 CCTATGAAACACGCGGTACTT 58.386 47.619 12.47 0.00 0.00 2.24
1608 1710 1.738030 GCCTATGAAACACGCGGTACT 60.738 52.381 12.47 0.00 0.00 2.73
1609 1711 0.648958 GCCTATGAAACACGCGGTAC 59.351 55.000 12.47 4.69 0.00 3.34
1610 1712 0.246910 TGCCTATGAAACACGCGGTA 59.753 50.000 12.47 0.00 0.00 4.02
1611 1713 1.004320 TGCCTATGAAACACGCGGT 60.004 52.632 12.47 2.05 0.00 5.68
1612 1714 1.019278 ACTGCCTATGAAACACGCGG 61.019 55.000 12.47 1.27 0.00 6.46
1613 1715 1.635844 TACTGCCTATGAAACACGCG 58.364 50.000 3.53 3.53 0.00 6.01
1614 1716 3.000727 ACTTACTGCCTATGAAACACGC 58.999 45.455 0.00 0.00 0.00 5.34
1615 1717 3.370978 CCACTTACTGCCTATGAAACACG 59.629 47.826 0.00 0.00 0.00 4.49
1616 1718 4.392138 GTCCACTTACTGCCTATGAAACAC 59.608 45.833 0.00 0.00 0.00 3.32
1631 1733 0.598158 GAACACGGCGTGTCCACTTA 60.598 55.000 41.29 0.00 46.79 2.24
1642 1744 0.804364 TGCATCAATCAGAACACGGC 59.196 50.000 0.00 0.00 0.00 5.68
1643 1745 4.753610 AGATATGCATCAATCAGAACACGG 59.246 41.667 0.19 0.00 33.21 4.94
1654 1756 4.301637 CAAGCTTGCAGATATGCATCAA 57.698 40.909 16.98 0.00 44.94 2.57
1750 1858 8.004087 AGCCTAATAATAGACGAACTACAACA 57.996 34.615 0.00 0.00 33.62 3.33
1759 1867 6.552350 ACCTACCAAAGCCTAATAATAGACGA 59.448 38.462 0.00 0.00 0.00 4.20
1761 1869 7.656542 GTCACCTACCAAAGCCTAATAATAGAC 59.343 40.741 0.00 0.00 0.00 2.59
1762 1870 7.346175 TGTCACCTACCAAAGCCTAATAATAGA 59.654 37.037 0.00 0.00 0.00 1.98
1763 1871 7.506114 TGTCACCTACCAAAGCCTAATAATAG 58.494 38.462 0.00 0.00 0.00 1.73
1764 1872 7.440505 TGTCACCTACCAAAGCCTAATAATA 57.559 36.000 0.00 0.00 0.00 0.98
1765 1873 6.321821 TGTCACCTACCAAAGCCTAATAAT 57.678 37.500 0.00 0.00 0.00 1.28
1766 1874 5.765576 TGTCACCTACCAAAGCCTAATAA 57.234 39.130 0.00 0.00 0.00 1.40
1768 1876 4.288626 TCTTGTCACCTACCAAAGCCTAAT 59.711 41.667 0.00 0.00 0.00 1.73
1806 1969 7.924412 AGATACATTTGGATGCATCACAAATTC 59.076 33.333 31.86 28.05 41.41 2.17
1812 1975 6.630444 AAGAGATACATTTGGATGCATCAC 57.370 37.500 27.25 16.88 38.15 3.06
1814 1977 6.916387 CACAAAGAGATACATTTGGATGCATC 59.084 38.462 18.81 18.81 40.05 3.91
1842 2005 3.616219 AGCGGCATTATTGGTTAACAGA 58.384 40.909 8.10 0.00 0.00 3.41
1858 2021 5.734855 TCAGTCAAGAAATTAATAGCGGC 57.265 39.130 0.00 0.00 0.00 6.53
1861 2024 9.102757 TGAGTGATCAGTCAAGAAATTAATAGC 57.897 33.333 27.30 0.00 37.79 2.97
1878 2041 5.993055 ACCATATGTGTGATTGAGTGATCA 58.007 37.500 1.24 0.00 33.81 2.92
1953 2121 8.896744 CATTTCCATAGATGCTAGAAAAGTTCA 58.103 33.333 0.00 0.00 30.86 3.18
1982 2150 8.827832 ATCTTCCAACATTTCCATCAAGATAA 57.172 30.769 0.00 0.00 29.54 1.75
1983 2151 8.827832 AATCTTCCAACATTTCCATCAAGATA 57.172 30.769 0.00 0.00 30.82 1.98
1984 2152 7.729124 AATCTTCCAACATTTCCATCAAGAT 57.271 32.000 0.00 0.00 32.03 2.40
1985 2153 7.543359 AAATCTTCCAACATTTCCATCAAGA 57.457 32.000 0.00 0.00 0.00 3.02
1986 2154 8.611654 AAAAATCTTCCAACATTTCCATCAAG 57.388 30.769 0.00 0.00 0.00 3.02
1987 2155 8.431222 AGAAAAATCTTCCAACATTTCCATCAA 58.569 29.630 0.00 0.00 0.00 2.57
1988 2156 7.874016 CAGAAAAATCTTCCAACATTTCCATCA 59.126 33.333 0.00 0.00 0.00 3.07
1989 2157 8.090214 TCAGAAAAATCTTCCAACATTTCCATC 58.910 33.333 0.00 0.00 0.00 3.51
1990 2158 7.965718 TCAGAAAAATCTTCCAACATTTCCAT 58.034 30.769 0.00 0.00 0.00 3.41
1991 2159 7.358770 TCAGAAAAATCTTCCAACATTTCCA 57.641 32.000 0.00 0.00 0.00 3.53
1992 2160 8.661352 TTTCAGAAAAATCTTCCAACATTTCC 57.339 30.769 0.00 0.00 0.00 3.13
1997 2165 9.748708 CAAGTATTTCAGAAAAATCTTCCAACA 57.251 29.630 0.00 0.00 0.00 3.33
1998 2166 9.965824 TCAAGTATTTCAGAAAAATCTTCCAAC 57.034 29.630 0.00 0.00 0.00 3.77
2028 2196 7.213891 GGAAAAGAAACGTAATCTCGAATTTCG 59.786 37.037 12.54 12.54 42.10 3.46
2063 2232 1.808945 CCGAAGCTTGCTGTTGAATCT 59.191 47.619 2.10 0.00 0.00 2.40
2067 2236 1.388547 AAACCGAAGCTTGCTGTTGA 58.611 45.000 2.10 0.00 0.00 3.18
2068 2237 2.208326 AAAACCGAAGCTTGCTGTTG 57.792 45.000 2.10 0.00 0.00 3.33
2069 2238 3.630312 TCTTAAAACCGAAGCTTGCTGTT 59.370 39.130 2.10 0.94 0.00 3.16
2070 2239 3.211045 TCTTAAAACCGAAGCTTGCTGT 58.789 40.909 2.10 0.00 0.00 4.40
2071 2240 3.896648 TCTTAAAACCGAAGCTTGCTG 57.103 42.857 2.10 0.00 0.00 4.41
2072 2241 4.518970 TCATTCTTAAAACCGAAGCTTGCT 59.481 37.500 2.10 0.00 0.00 3.91
2073 2242 4.794169 TCATTCTTAAAACCGAAGCTTGC 58.206 39.130 2.10 0.00 0.00 4.01
2074 2243 6.611381 TGATCATTCTTAAAACCGAAGCTTG 58.389 36.000 2.10 0.00 0.00 4.01
2075 2244 6.817765 TGATCATTCTTAAAACCGAAGCTT 57.182 33.333 0.00 0.00 0.00 3.74
2076 2245 7.396540 AATGATCATTCTTAAAACCGAAGCT 57.603 32.000 15.36 0.00 0.00 3.74
2158 2328 5.126707 GGGAATCTAACTTACAGTCTTCGGA 59.873 44.000 0.00 0.00 0.00 4.55
2317 2488 8.406297 ACACAAACTTAACCTTCAGAAATTCTC 58.594 33.333 0.00 0.00 0.00 2.87
2501 2760 3.717707 TGAAGACAAGCTACAGTGTCAC 58.282 45.455 16.51 11.05 45.40 3.67
2541 2843 6.639632 TCAAATTTCTGAAGCAAGCTAGTT 57.360 33.333 0.00 0.00 0.00 2.24
2660 2965 9.249053 TGGATATTGTTGTAAAGGCTGAAATAA 57.751 29.630 0.00 0.00 0.00 1.40
3023 3328 1.922570 CAGCTTCATTGGCAGCATTC 58.077 50.000 10.29 0.00 38.61 2.67
3162 3566 2.159170 GCTACACAGTCAGGTCATCCTC 60.159 54.545 0.00 0.00 43.07 3.71
3222 3627 7.594351 TTATGCACATAAAATGGGAGCATTA 57.406 32.000 16.32 9.06 42.76 1.90
3287 3692 2.032550 CAGTGTTCTGCTGTTCAAGGTG 59.967 50.000 0.00 0.00 34.79 4.00
3306 3711 5.505173 AACAGGTCAAGTTTCATCAACAG 57.495 39.130 0.00 0.00 37.93 3.16
3335 3740 7.506114 AGAAGACATAGAAACACAGTAAACCA 58.494 34.615 0.00 0.00 0.00 3.67
3439 3845 9.820229 CGTATGTTGCAAGAAGAGTTAAAATAA 57.180 29.630 0.00 0.00 0.00 1.40
3499 3907 8.479280 CAATTAAATGCTTACACAAGTTGACAC 58.521 33.333 10.54 0.00 34.00 3.67
3537 4205 2.899900 TGCTACAGAGGACACTGTCAAT 59.100 45.455 11.34 0.00 46.36 2.57
3608 4283 2.645730 ACACGCAGAAAGCAAAAACA 57.354 40.000 0.00 0.00 46.13 2.83
3750 4427 3.517602 GAAAAACACACTTGGTTGGTCC 58.482 45.455 0.00 0.00 30.94 4.46
3758 4435 2.426738 TCCAGCTGGAAAAACACACTTG 59.573 45.455 33.41 1.41 42.18 3.16
3780 4457 2.414957 CGGCTACGAATTGTTTTTCCCC 60.415 50.000 0.00 0.00 44.60 4.81
3796 4473 5.677598 GCAAAACCAGCATAAAATACGGCTA 60.678 40.000 0.00 0.00 34.25 3.93
3809 4486 2.364002 GTTTTCTAGGGCAAAACCAGCA 59.636 45.455 6.91 0.00 42.05 4.41
3820 4497 0.254747 TGGATGGCCGTTTTCTAGGG 59.745 55.000 0.00 0.00 36.79 3.53
3823 4500 1.459450 GCTTGGATGGCCGTTTTCTA 58.541 50.000 0.00 0.00 36.79 2.10
3941 4620 9.846248 GGAGTATTTGGCATAATGATAATGAAC 57.154 33.333 0.00 0.00 0.00 3.18
3949 4628 4.133820 CGTGGGAGTATTTGGCATAATGA 58.866 43.478 0.00 0.00 0.00 2.57
3958 4637 6.978343 TTTAGAATGACGTGGGAGTATTTG 57.022 37.500 0.00 0.00 0.00 2.32
4003 4682 7.448777 TCGCAGAGATAGGTGATAGAATTTACT 59.551 37.037 0.00 0.00 0.00 2.24
4025 4704 3.369052 CCCTCACCTATTTGTACTTCGCA 60.369 47.826 0.00 0.00 0.00 5.10
4027 4706 4.159879 ACTCCCTCACCTATTTGTACTTCG 59.840 45.833 0.00 0.00 0.00 3.79
4074 4756 0.105593 CTCATGTATCCACGGCAGCT 59.894 55.000 0.00 0.00 0.00 4.24
4077 4759 0.469494 ATGCTCATGTATCCACGGCA 59.531 50.000 0.00 0.00 0.00 5.69
4222 4904 2.102578 CAATGAACCCAATGGAGTCCC 58.897 52.381 6.74 0.00 34.81 4.46
4263 4945 2.756760 ACACAATGCAATCCAGGCTTAG 59.243 45.455 0.00 0.00 0.00 2.18
4306 4988 0.250467 AAGCAAGCAGAAAGAGGCGA 60.250 50.000 0.00 0.00 34.54 5.54
4309 4991 0.956633 TGCAAGCAAGCAGAAAGAGG 59.043 50.000 0.00 0.00 40.11 3.69
4498 5180 7.138081 CAGTTCACAGCAAACACACATAATAA 58.862 34.615 0.00 0.00 0.00 1.40
4521 5203 7.307042 CGATGTTAGATTATGTCTTCCAAGCAG 60.307 40.741 0.00 0.00 38.42 4.24
4557 5239 1.667724 ACTTATGGAGTACGACGACGG 59.332 52.381 12.58 0.00 44.46 4.79
4564 5246 8.873215 AATTAAGATGTGACTTATGGAGTACG 57.127 34.615 0.00 0.00 39.19 3.67
4618 5301 2.738846 CACTGCAGCTCAAACGAGTTAT 59.261 45.455 15.27 0.00 32.72 1.89
4687 5373 9.577110 GAATGACAAATAATTGAGCAATCTTCA 57.423 29.630 0.00 0.00 38.94 3.02
4705 5391 7.040478 CCATGACTTCCAAGTTTAGAATGACAA 60.040 37.037 0.00 0.00 39.88 3.18
4714 5400 7.595819 ATTTCAACCATGACTTCCAAGTTTA 57.404 32.000 0.00 0.00 39.88 2.01
4724 5410 7.451255 TGATCCTTTGTAATTTCAACCATGACT 59.549 33.333 0.00 0.00 34.61 3.41
4727 5413 7.605449 ACTGATCCTTTGTAATTTCAACCATG 58.395 34.615 0.00 0.00 0.00 3.66
4735 5421 7.823745 AGTGTGAACTGATCCTTTGTAATTT 57.176 32.000 0.00 0.00 0.00 1.82
4743 5429 3.906846 AGAGGAAGTGTGAACTGATCCTT 59.093 43.478 1.65 0.00 37.42 3.36
4747 5433 4.636249 GAACAGAGGAAGTGTGAACTGAT 58.364 43.478 0.00 0.00 0.00 2.90
4760 5446 4.617530 CGACAAGTAATTCCGAACAGAGGA 60.618 45.833 0.00 0.00 35.69 3.71
4765 5451 3.256383 TCTCCGACAAGTAATTCCGAACA 59.744 43.478 0.00 0.00 0.00 3.18
4779 5516 7.552459 TGTCTAATACATTCATTTCTCCGACA 58.448 34.615 0.00 0.00 31.43 4.35
4810 5602 9.492973 GGTGAAAAACTGTTACACCTTATACTA 57.507 33.333 23.98 0.00 44.91 1.82
4811 5603 8.387190 GGTGAAAAACTGTTACACCTTATACT 57.613 34.615 23.98 0.00 44.91 2.12
4983 6227 6.611613 ATTTCTTGTGACATACTCTCTCCA 57.388 37.500 0.00 0.00 0.00 3.86
5009 6253 5.157067 GCCACAGAAGCAGTAAATTTTCTC 58.843 41.667 0.00 0.00 0.00 2.87
5013 6257 4.584325 TCTTGCCACAGAAGCAGTAAATTT 59.416 37.500 0.00 0.00 42.17 1.82
5037 6281 2.098934 TGACGCTTCATTTGTGCTGTTT 59.901 40.909 0.00 0.00 0.00 2.83
5038 6282 1.675483 TGACGCTTCATTTGTGCTGTT 59.325 42.857 0.00 0.00 0.00 3.16
5044 6288 2.612212 AGTTTCGTGACGCTTCATTTGT 59.388 40.909 0.00 0.00 33.11 2.83
5055 6299 1.464997 GCAATCCCAGAGTTTCGTGAC 59.535 52.381 0.00 0.00 0.00 3.67
5059 6303 0.673644 ACGGCAATCCCAGAGTTTCG 60.674 55.000 0.00 0.00 0.00 3.46
5071 6315 3.467803 GTTCTATCTAAGGCACGGCAAT 58.532 45.455 0.00 0.00 0.00 3.56
5076 6320 3.119101 ACTGTGGTTCTATCTAAGGCACG 60.119 47.826 0.00 0.00 0.00 5.34
5086 6330 7.913789 TGGTGTTTTATCTACTGTGGTTCTAT 58.086 34.615 0.00 0.00 0.00 1.98
5130 6374 5.163893 CCGCGAAAACAGAAATATACACTGT 60.164 40.000 8.23 0.00 45.02 3.55
5131 6375 5.255596 CCGCGAAAACAGAAATATACACTG 58.744 41.667 8.23 0.00 37.62 3.66
5153 6399 2.166254 CACCCTGTTGTTTATGATGCCC 59.834 50.000 0.00 0.00 0.00 5.36
5178 6424 8.691661 ACACTTTTACCAATAACAGTTCAGAT 57.308 30.769 0.00 0.00 30.43 2.90
5275 6521 4.615912 CGTTTTCGCATGGGAGAAATCTTT 60.616 41.667 15.97 0.00 41.45 2.52
5355 6605 1.948145 CTTGAGTAGTAGGATCGCCGT 59.052 52.381 0.00 0.00 39.96 5.68


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

AutoCloner maintained by Alex Coulton.