Multiple sequence alignment - TraesCS6B01G307600

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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 TraesCS6B01G307600 chr6B 100.000 4567 0 0 1 4567 551788469 551793035 0.000000e+00 8434
1 TraesCS6B01G307600 chr6B 90.909 176 16 0 3966 4141 233030266 233030091 2.120000e-58 237
2 TraesCS6B01G307600 chr4D 90.837 2412 111 39 1600 3980 57472709 57475041 0.000000e+00 3129
3 TraesCS6B01G307600 chr4D 89.515 639 32 16 957 1576 57471968 57472590 0.000000e+00 776
4 TraesCS6B01G307600 chr4D 94.366 213 8 2 4358 4567 57475346 57475557 1.580000e-84 324
5 TraesCS6B01G307600 chr4D 89.407 236 11 6 4138 4361 57475038 57475271 7.480000e-73 285
6 TraesCS6B01G307600 chr4B 91.309 1795 84 37 830 2593 86058548 86060301 0.000000e+00 2385
7 TraesCS6B01G307600 chr4B 91.603 1048 53 17 2932 3969 86060579 86061601 0.000000e+00 1415
8 TraesCS6B01G307600 chr4B 92.674 778 54 2 1 778 575816440 575817214 0.000000e+00 1118
9 TraesCS6B01G307600 chr4B 92.545 778 55 2 1 778 575841731 575842505 0.000000e+00 1112
10 TraesCS6B01G307600 chr4B 90.769 780 69 2 1 780 376414917 376415693 0.000000e+00 1038
11 TraesCS6B01G307600 chr4B 96.190 210 7 1 4358 4567 86061905 86062113 4.380000e-90 342
12 TraesCS6B01G307600 chr4B 88.789 223 11 3 4144 4361 86061617 86061830 1.260000e-65 261
13 TraesCS6B01G307600 chr4B 93.913 115 3 2 2590 2701 86060463 86060576 2.180000e-38 171
14 TraesCS6B01G307600 chrUn 97.311 781 20 1 1 781 2322966 2323745 0.000000e+00 1325
15 TraesCS6B01G307600 chr2B 92.702 781 53 3 1 781 282965132 282965908 0.000000e+00 1123
16 TraesCS6B01G307600 chr2B 92.784 776 53 2 1 776 453066886 453066114 0.000000e+00 1120
17 TraesCS6B01G307600 chr2B 91.282 780 67 1 1 779 254335521 254336300 0.000000e+00 1062
18 TraesCS6B01G307600 chr2B 93.902 164 10 0 3977 4140 214378248 214378085 9.810000e-62 248
19 TraesCS6B01G307600 chr2A 92.526 776 55 2 1 776 715896684 715895912 0.000000e+00 1109
20 TraesCS6B01G307600 chr2A 90.805 783 67 5 1 782 159635642 159636420 0.000000e+00 1042
21 TraesCS6B01G307600 chr4A 87.171 912 73 20 3081 3980 539300501 539299622 0.000000e+00 996
22 TraesCS6B01G307600 chr4A 85.177 904 72 28 830 1698 539302377 539301501 0.000000e+00 870
23 TraesCS6B01G307600 chr4A 89.677 620 37 17 1776 2377 539301504 539300894 0.000000e+00 765
24 TraesCS6B01G307600 chr4A 95.238 210 6 2 4361 4567 539299332 539299124 3.410000e-86 329
25 TraesCS6B01G307600 chr4A 91.284 218 13 1 4144 4361 539299621 539299410 4.470000e-75 292
26 TraesCS6B01G307600 chr4A 91.813 171 14 0 3970 4140 87406082 87406252 5.910000e-59 239
27 TraesCS6B01G307600 chr5A 95.152 165 8 0 3976 4140 82305599 82305763 1.260000e-65 261
28 TraesCS6B01G307600 chr5A 92.771 166 12 0 3975 4140 269823460 269823295 1.640000e-59 241
29 TraesCS6B01G307600 chr5B 93.373 166 11 0 3978 4143 145828344 145828179 3.530000e-61 246
30 TraesCS6B01G307600 chr1D 91.908 173 13 1 3977 4149 175953969 175954140 1.640000e-59 241
31 TraesCS6B01G307600 chr1D 97.015 134 4 0 2939 3072 68403174 68403307 4.600000e-55 226
32 TraesCS6B01G307600 chr1D 97.015 134 4 0 2939 3072 254527062 254527195 4.600000e-55 226
33 TraesCS6B01G307600 chr1D 97.015 134 4 0 2939 3072 298349174 298349041 4.600000e-55 226
34 TraesCS6B01G307600 chr1D 97.015 134 4 0 2939 3072 459903261 459903128 4.600000e-55 226
35 TraesCS6B01G307600 chr6D 92.073 164 13 0 3978 4141 90890444 90890281 9.880000e-57 231
36 TraesCS6B01G307600 chr3D 88.889 189 17 4 3954 4140 547631262 547631448 3.550000e-56 230
37 TraesCS6B01G307600 chr3D 97.015 134 4 0 2939 3072 589262070 589261937 4.600000e-55 226
38 TraesCS6B01G307600 chr5D 97.015 134 4 0 2939 3072 432436707 432436840 4.600000e-55 226
39 TraesCS6B01G307600 chr1A 97.015 134 4 0 2939 3072 532075147 532075280 4.600000e-55 226


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 TraesCS6B01G307600 chr6B 551788469 551793035 4566 False 8434.0 8434 100.00000 1 4567 1 chr6B.!!$F1 4566
1 TraesCS6B01G307600 chr4D 57471968 57475557 3589 False 1128.5 3129 91.03125 957 4567 4 chr4D.!!$F1 3610
2 TraesCS6B01G307600 chr4B 575816440 575817214 774 False 1118.0 1118 92.67400 1 778 1 chr4B.!!$F2 777
3 TraesCS6B01G307600 chr4B 575841731 575842505 774 False 1112.0 1112 92.54500 1 778 1 chr4B.!!$F3 777
4 TraesCS6B01G307600 chr4B 376414917 376415693 776 False 1038.0 1038 90.76900 1 780 1 chr4B.!!$F1 779
5 TraesCS6B01G307600 chr4B 86058548 86062113 3565 False 914.8 2385 92.36080 830 4567 5 chr4B.!!$F4 3737
6 TraesCS6B01G307600 chrUn 2322966 2323745 779 False 1325.0 1325 97.31100 1 781 1 chrUn.!!$F1 780
7 TraesCS6B01G307600 chr2B 282965132 282965908 776 False 1123.0 1123 92.70200 1 781 1 chr2B.!!$F2 780
8 TraesCS6B01G307600 chr2B 453066114 453066886 772 True 1120.0 1120 92.78400 1 776 1 chr2B.!!$R2 775
9 TraesCS6B01G307600 chr2B 254335521 254336300 779 False 1062.0 1062 91.28200 1 779 1 chr2B.!!$F1 778
10 TraesCS6B01G307600 chr2A 715895912 715896684 772 True 1109.0 1109 92.52600 1 776 1 chr2A.!!$R1 775
11 TraesCS6B01G307600 chr2A 159635642 159636420 778 False 1042.0 1042 90.80500 1 782 1 chr2A.!!$F1 781
12 TraesCS6B01G307600 chr4A 539299124 539302377 3253 True 650.4 996 89.70940 830 4567 5 chr4A.!!$R1 3737

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
874 878 0.403750 TAAACCCTCAACCCCCACCT 60.404 55.0 0.00 0.0 0.00 4.00 F
1514 1595 0.034186 TTGGGGGATTGTAGCTGCTG 60.034 55.0 13.43 0.0 0.00 4.41 F
1737 1922 0.036010 AAGGTGACCGCCATTCTCTG 60.036 55.0 0.00 0.0 0.00 3.35 F
2797 3223 0.540365 CTGCCCCCAGTTCAACATGT 60.540 55.0 0.00 0.0 34.31 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 3160 1.743252 GGCCACTGTAGCTGCTCAC 60.743 63.158 4.91 3.89 0.00 3.51 R
2894 3320 0.179000 AATCTCACAGGGACATCGCC 59.821 55.000 0.00 0.00 0.00 5.54 R
2999 3426 0.465824 GCCTGCTCATGGATTCAGCT 60.466 55.000 5.11 0.00 34.03 4.24 R
4355 4831 1.213013 CGTCGAACACCCTGAGGAG 59.787 63.158 0.00 0.00 36.73 3.69 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
145 146 3.243501 ACTTCGGACAACGTAGCTAAACA 60.244 43.478 0.00 0.00 42.86 2.83
398 399 3.483901 GGACGACGCGCAATAAAATTACA 60.484 43.478 5.73 0.00 0.00 2.41
489 490 4.697756 CGTTGGGGAAGGAGCGCA 62.698 66.667 11.47 0.00 0.00 6.09
533 534 3.552068 CCATGGTGCGTATCAAGACGATA 60.552 47.826 2.57 0.00 45.82 2.92
591 594 1.880646 GCTTTTGTAGCCTTCCGTGGA 60.881 52.381 0.00 0.00 44.48 4.02
592 595 2.076863 CTTTTGTAGCCTTCCGTGGAG 58.923 52.381 0.00 0.00 0.00 3.86
658 661 4.789012 ATTTTGATGCGATGAACCTTGT 57.211 36.364 0.00 0.00 0.00 3.16
727 731 1.408702 GTTGAACCTTGCTGCCTTTCA 59.591 47.619 0.00 0.00 0.00 2.69
803 807 4.036567 CAGTATGTCGTGGTATTTCCGA 57.963 45.455 0.00 0.00 39.52 4.55
804 808 4.426416 CAGTATGTCGTGGTATTTCCGAA 58.574 43.478 0.00 0.00 39.52 4.30
805 809 4.266976 CAGTATGTCGTGGTATTTCCGAAC 59.733 45.833 0.00 0.00 39.52 3.95
806 810 3.604875 ATGTCGTGGTATTTCCGAACT 57.395 42.857 0.00 0.00 39.52 3.01
807 811 2.679450 TGTCGTGGTATTTCCGAACTG 58.321 47.619 0.00 0.00 39.52 3.16
808 812 2.036217 TGTCGTGGTATTTCCGAACTGT 59.964 45.455 0.00 0.00 39.52 3.55
809 813 3.062042 GTCGTGGTATTTCCGAACTGTT 58.938 45.455 0.00 0.00 39.52 3.16
810 814 3.061322 TCGTGGTATTTCCGAACTGTTG 58.939 45.455 0.00 0.00 39.52 3.33
811 815 3.061322 CGTGGTATTTCCGAACTGTTGA 58.939 45.455 0.00 0.00 39.52 3.18
812 816 3.120786 CGTGGTATTTCCGAACTGTTGAC 60.121 47.826 0.00 0.00 39.52 3.18
813 817 4.062991 GTGGTATTTCCGAACTGTTGACT 58.937 43.478 0.00 0.00 39.52 3.41
814 818 5.232463 GTGGTATTTCCGAACTGTTGACTA 58.768 41.667 0.00 0.00 39.52 2.59
815 819 5.873164 GTGGTATTTCCGAACTGTTGACTAT 59.127 40.000 0.00 0.00 39.52 2.12
816 820 6.035758 GTGGTATTTCCGAACTGTTGACTATC 59.964 42.308 0.00 0.00 39.52 2.08
817 821 6.103997 GGTATTTCCGAACTGTTGACTATCA 58.896 40.000 0.00 0.00 0.00 2.15
818 822 6.761714 GGTATTTCCGAACTGTTGACTATCAT 59.238 38.462 0.00 0.00 0.00 2.45
819 823 7.924412 GGTATTTCCGAACTGTTGACTATCATA 59.076 37.037 0.00 0.00 0.00 2.15
820 824 9.309516 GTATTTCCGAACTGTTGACTATCATAA 57.690 33.333 0.00 0.00 0.00 1.90
821 825 8.964476 ATTTCCGAACTGTTGACTATCATAAT 57.036 30.769 0.00 0.00 0.00 1.28
822 826 8.420374 TTTCCGAACTGTTGACTATCATAATC 57.580 34.615 0.00 0.00 0.00 1.75
823 827 6.513180 TCCGAACTGTTGACTATCATAATCC 58.487 40.000 0.00 0.00 0.00 3.01
824 828 5.402568 CCGAACTGTTGACTATCATAATCCG 59.597 44.000 0.00 0.00 0.00 4.18
825 829 5.107837 CGAACTGTTGACTATCATAATCCGC 60.108 44.000 0.00 0.00 0.00 5.54
826 830 4.299155 ACTGTTGACTATCATAATCCGCG 58.701 43.478 0.00 0.00 0.00 6.46
827 831 3.649073 TGTTGACTATCATAATCCGCGG 58.351 45.455 22.12 22.12 0.00 6.46
828 832 2.993899 GTTGACTATCATAATCCGCGGG 59.006 50.000 27.83 8.93 0.00 6.13
868 872 3.007635 CGTCTCATTAAACCCTCAACCC 58.992 50.000 0.00 0.00 0.00 4.11
874 878 0.403750 TAAACCCTCAACCCCCACCT 60.404 55.000 0.00 0.00 0.00 4.00
875 879 1.301160 AAACCCTCAACCCCCACCTT 61.301 55.000 0.00 0.00 0.00 3.50
912 923 1.078848 CTTCCAGTTCTGCCCTCCG 60.079 63.158 0.00 0.00 0.00 4.63
979 1002 1.075482 CCTTCCTCAAGCCAAGCCA 59.925 57.895 0.00 0.00 0.00 4.75
980 1003 1.246737 CCTTCCTCAAGCCAAGCCAC 61.247 60.000 0.00 0.00 0.00 5.01
1012 1035 1.532604 AAGCTCGATGGACCACGTGA 61.533 55.000 19.30 0.00 0.00 4.35
1172 1201 1.295101 CCCAAATTCGGGGTTTGCC 59.705 57.895 0.00 0.00 43.21 4.52
1232 1262 1.087501 GCCTTGTTCACGGAATCTCC 58.912 55.000 0.00 0.00 0.00 3.71
1280 1334 4.442706 TGTTCTGCGAGATTTTAGGGATC 58.557 43.478 0.00 0.00 0.00 3.36
1281 1335 4.162320 TGTTCTGCGAGATTTTAGGGATCT 59.838 41.667 0.00 0.00 36.60 2.75
1282 1336 5.119694 GTTCTGCGAGATTTTAGGGATCTT 58.880 41.667 0.00 0.00 34.13 2.40
1283 1337 4.950050 TCTGCGAGATTTTAGGGATCTTC 58.050 43.478 0.00 0.00 34.13 2.87
1284 1338 4.651503 TCTGCGAGATTTTAGGGATCTTCT 59.348 41.667 0.00 0.00 34.13 2.85
1285 1339 5.129485 TCTGCGAGATTTTAGGGATCTTCTT 59.871 40.000 0.00 0.00 34.13 2.52
1286 1340 5.360591 TGCGAGATTTTAGGGATCTTCTTC 58.639 41.667 0.00 0.00 34.13 2.87
1287 1341 5.129485 TGCGAGATTTTAGGGATCTTCTTCT 59.871 40.000 0.00 0.00 34.13 2.85
1288 1342 5.694458 GCGAGATTTTAGGGATCTTCTTCTC 59.306 44.000 0.00 0.45 34.13 2.87
1289 1343 6.684111 GCGAGATTTTAGGGATCTTCTTCTCA 60.684 42.308 0.00 0.00 34.13 3.27
1290 1344 7.441017 CGAGATTTTAGGGATCTTCTTCTCAT 58.559 38.462 0.00 0.00 34.13 2.90
1291 1345 7.384660 CGAGATTTTAGGGATCTTCTTCTCATG 59.615 40.741 0.00 0.00 34.13 3.07
1292 1346 7.516452 AGATTTTAGGGATCTTCTTCTCATGG 58.484 38.462 0.00 0.00 29.77 3.66
1293 1347 5.636903 TTTAGGGATCTTCTTCTCATGGG 57.363 43.478 0.00 0.00 0.00 4.00
1294 1348 3.428063 AGGGATCTTCTTCTCATGGGA 57.572 47.619 0.00 0.00 0.00 4.37
1295 1349 3.952043 AGGGATCTTCTTCTCATGGGAT 58.048 45.455 0.00 0.00 0.00 3.85
1393 1468 5.334879 CCGATGCTAGTTGTTTTAGCTGTTT 60.335 40.000 0.00 0.00 43.07 2.83
1399 1474 3.636764 AGTTGTTTTAGCTGTTTCAGGGG 59.363 43.478 0.00 0.00 31.21 4.79
1468 1549 5.008331 GGGGTTCTTTTTAACTCAGGGTAG 58.992 45.833 0.00 0.00 31.01 3.18
1514 1595 0.034186 TTGGGGGATTGTAGCTGCTG 60.034 55.000 13.43 0.00 0.00 4.41
1515 1596 1.825622 GGGGGATTGTAGCTGCTGC 60.826 63.158 13.43 12.15 40.05 5.25
1612 1797 8.568794 TCGGTGATAATTTTGTAATGTTTGTCA 58.431 29.630 0.00 0.00 0.00 3.58
1648 1833 5.862924 TTCTTAGCATTGCTCTGTTGTAC 57.137 39.130 15.81 0.00 40.44 2.90
1667 1852 3.120321 ACGGTGTGAGCACTTGAAATA 57.880 42.857 1.99 0.00 44.65 1.40
1668 1853 3.674997 ACGGTGTGAGCACTTGAAATAT 58.325 40.909 1.99 0.00 44.65 1.28
1692 1877 3.296854 GGACATTATTGGGAAGGGGAAC 58.703 50.000 0.00 0.00 0.00 3.62
1728 1913 1.659098 CTAATCGTTGAAGGTGACCGC 59.341 52.381 0.00 0.00 0.00 5.68
1730 1915 2.107041 ATCGTTGAAGGTGACCGCCA 62.107 55.000 0.00 0.00 0.00 5.69
1731 1916 1.671054 CGTTGAAGGTGACCGCCAT 60.671 57.895 0.00 0.00 0.00 4.40
1733 1918 0.521735 GTTGAAGGTGACCGCCATTC 59.478 55.000 0.00 0.00 0.00 2.67
1734 1919 0.400213 TTGAAGGTGACCGCCATTCT 59.600 50.000 0.00 0.00 0.00 2.40
1735 1920 0.036388 TGAAGGTGACCGCCATTCTC 60.036 55.000 0.00 0.00 0.00 2.87
1736 1921 0.250513 GAAGGTGACCGCCATTCTCT 59.749 55.000 0.00 0.00 0.00 3.10
1737 1922 0.036010 AAGGTGACCGCCATTCTCTG 60.036 55.000 0.00 0.00 0.00 3.35
1752 1937 5.163163 CCATTCTCTGTCATATTGGGAAGGA 60.163 44.000 0.00 0.00 0.00 3.36
1939 2124 1.134670 GGGATCACCAGCTGTGTAGAC 60.135 57.143 13.81 0.00 45.61 2.59
2009 2194 1.497286 TGGCCAAGTTCCAGGTACTTT 59.503 47.619 0.61 0.00 34.60 2.66
2379 2586 4.177165 TCGTACCGTGTTTGTGTATGAT 57.823 40.909 0.00 0.00 0.00 2.45
2389 2596 8.661257 CCGTGTTTGTGTATGATTTATCTGTTA 58.339 33.333 0.00 0.00 0.00 2.41
2407 2614 7.843490 TCTGTTAATGGTGTATTTAGTCAGC 57.157 36.000 0.00 0.00 0.00 4.26
2439 2647 8.743085 ATAGCATACATATGTTCCATCATTCC 57.257 34.615 14.77 0.00 36.11 3.01
2440 2648 6.545567 AGCATACATATGTTCCATCATTCCA 58.454 36.000 14.77 0.00 36.11 3.53
2441 2649 7.179966 AGCATACATATGTTCCATCATTCCAT 58.820 34.615 14.77 0.00 36.11 3.41
2442 2650 7.122204 AGCATACATATGTTCCATCATTCCATG 59.878 37.037 14.77 7.93 36.11 3.66
2443 2651 5.717078 ACATATGTTCCATCATTCCATGC 57.283 39.130 1.41 0.00 0.00 4.06
2480 2690 7.255208 CGTGATATGTTCCATCCATGATTTGAA 60.255 37.037 0.00 0.00 0.00 2.69
2481 2691 8.582437 GTGATATGTTCCATCCATGATTTGAAT 58.418 33.333 0.00 0.00 0.00 2.57
2494 2704 9.358406 TCCATGATTTGAATATAAGCAATGAGT 57.642 29.630 0.00 0.00 0.00 3.41
2518 2728 6.867816 GTCAGTGATTTGGATAATTGTTTGCA 59.132 34.615 0.00 0.00 0.00 4.08
2530 2740 7.009815 GGATAATTGTTTGCATGACATGTCAAG 59.990 37.037 31.00 26.98 43.58 3.02
2582 2793 5.240623 CAGATAGGTAGGTCAGATGACAGAC 59.759 48.000 14.52 10.66 46.47 3.51
2612 3007 0.662619 TTTCTTCGTGCAGTTGGCTG 59.337 50.000 0.00 0.00 45.15 4.85
2623 3018 2.031157 GCAGTTGGCTGTGTCGTTAAAT 60.031 45.455 0.00 0.00 44.32 1.40
2689 3087 7.027874 ACTCTAATAATGTTTGTCCCTCCAA 57.972 36.000 0.00 0.00 0.00 3.53
2792 3218 2.166907 TTTTTCTGCCCCCAGTTCAA 57.833 45.000 0.00 0.00 40.09 2.69
2797 3223 0.540365 CTGCCCCCAGTTCAACATGT 60.540 55.000 0.00 0.00 34.31 3.21
2833 3259 1.019278 ACGGCTGCCTATTTGTCACG 61.019 55.000 17.92 1.48 0.00 4.35
2858 3284 7.190335 AGACATCTAGTAGTGTAGTCAGTCT 57.810 40.000 12.77 0.00 0.00 3.24
2863 3289 9.347934 CATCTAGTAGTGTAGTCAGTCTTTTTG 57.652 37.037 0.00 0.00 0.00 2.44
2894 3320 1.948145 GCCTCAAGCATCTGGATCAAG 59.052 52.381 0.00 0.00 42.97 3.02
2895 3321 2.573369 CCTCAAGCATCTGGATCAAGG 58.427 52.381 0.00 0.00 0.00 3.61
2966 3393 6.357367 AGTTGAAAATAAGCATAGATCCGGT 58.643 36.000 0.00 0.00 0.00 5.28
2999 3426 3.637769 AGGTCAACCTTTTAAACTGCCA 58.362 40.909 0.00 0.00 46.09 4.92
3238 3666 6.099701 TGCAGGGTTACATACACTTCATCTAT 59.900 38.462 0.00 0.00 37.10 1.98
3239 3667 7.289084 TGCAGGGTTACATACACTTCATCTATA 59.711 37.037 0.00 0.00 37.10 1.31
3240 3668 7.599245 GCAGGGTTACATACACTTCATCTATAC 59.401 40.741 0.00 0.00 37.10 1.47
3289 3717 9.914834 TTTATACCTGAATAAACCAGCAGTTAT 57.085 29.630 0.00 0.00 37.88 1.89
3404 3837 0.250234 CCAGGAGGTTGAATCGCTCA 59.750 55.000 0.00 0.00 0.00 4.26
3461 3894 2.102252 GCTCCAGAAGATGAAGACGGAT 59.898 50.000 0.00 0.00 0.00 4.18
3474 3907 1.003580 AGACGGATGCAACCAATGAGT 59.996 47.619 14.03 1.88 0.00 3.41
3649 4082 4.663334 TCCAGAGTCTCTAGCAACACTAA 58.337 43.478 0.94 0.00 0.00 2.24
3696 4134 6.051717 TGAGAAGTCCAGAGAAGAGTTTTTG 58.948 40.000 0.00 0.00 0.00 2.44
3712 4150 6.944862 AGAGTTTTTGGCTGAGAGATTAATGT 59.055 34.615 0.00 0.00 0.00 2.71
3724 4162 7.568349 TGAGAGATTAATGTGTCTAAATGGCT 58.432 34.615 10.55 0.00 0.00 4.75
3735 4173 2.364324 TCTAAATGGCTCCGCGATACTT 59.636 45.455 8.23 0.00 0.00 2.24
3783 4221 6.381481 TTGCATAGCACATCCTTTATCTTG 57.619 37.500 0.00 0.00 38.71 3.02
3884 4326 5.608676 TGGCACAAATTTGCATACAATTG 57.391 34.783 18.12 3.24 44.94 2.32
3885 4327 5.061853 TGGCACAAATTTGCATACAATTGT 58.938 33.333 18.12 16.68 44.94 2.71
3886 4328 5.530171 TGGCACAAATTTGCATACAATTGTT 59.470 32.000 17.78 1.87 44.94 2.83
3887 4329 6.707608 TGGCACAAATTTGCATACAATTGTTA 59.292 30.769 17.78 3.36 44.94 2.41
3953 4404 5.916318 TCAAATGTCTCAAGCAAACCAAAT 58.084 33.333 0.00 0.00 0.00 2.32
3991 4442 2.845363 TTTTGTACTCCCTCCGTTCC 57.155 50.000 0.00 0.00 0.00 3.62
3992 4443 2.019807 TTTGTACTCCCTCCGTTCCT 57.980 50.000 0.00 0.00 0.00 3.36
3993 4444 2.905415 TTGTACTCCCTCCGTTCCTA 57.095 50.000 0.00 0.00 0.00 2.94
3994 4445 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3995 4446 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3996 4447 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3997 4448 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3998 4449 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3999 4450 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
4000 4451 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
4001 4452 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4002 4453 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4003 4454 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4004 4455 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4005 4456 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4006 4457 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4007 4458 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
4008 4459 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
4070 4521 9.798994 AGATGCATTTCAAGTTTAGATTCATTC 57.201 29.630 0.00 0.00 0.00 2.67
4071 4522 9.577110 GATGCATTTCAAGTTTAGATTCATTCA 57.423 29.630 0.00 0.00 0.00 2.57
4073 4524 9.932207 TGCATTTCAAGTTTAGATTCATTCATT 57.068 25.926 0.00 0.00 0.00 2.57
4078 4529 9.985730 TTCAAGTTTAGATTCATTCATTTTGCT 57.014 25.926 0.00 0.00 0.00 3.91
4079 4530 9.630098 TCAAGTTTAGATTCATTCATTTTGCTC 57.370 29.630 0.00 0.00 0.00 4.26
4080 4531 8.866956 CAAGTTTAGATTCATTCATTTTGCTCC 58.133 33.333 0.00 0.00 0.00 4.70
4081 4532 7.253422 AGTTTAGATTCATTCATTTTGCTCCG 58.747 34.615 0.00 0.00 0.00 4.63
4082 4533 6.757897 TTAGATTCATTCATTTTGCTCCGT 57.242 33.333 0.00 0.00 0.00 4.69
4083 4534 7.857734 TTAGATTCATTCATTTTGCTCCGTA 57.142 32.000 0.00 0.00 0.00 4.02
4084 4535 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
4085 4536 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
4086 4537 4.291540 TCATTCATTTTGCTCCGTATGC 57.708 40.909 0.00 0.00 0.00 3.14
4087 4538 3.693578 TCATTCATTTTGCTCCGTATGCA 59.306 39.130 0.00 0.00 38.80 3.96
4088 4539 4.338964 TCATTCATTTTGCTCCGTATGCAT 59.661 37.500 3.79 3.79 40.34 3.96
4089 4540 4.717233 TTCATTTTGCTCCGTATGCATT 57.283 36.364 3.54 0.00 40.34 3.56
4090 4541 4.291540 TCATTTTGCTCCGTATGCATTC 57.708 40.909 3.54 0.00 40.34 2.67
4091 4542 3.066621 TCATTTTGCTCCGTATGCATTCC 59.933 43.478 3.54 0.00 40.34 3.01
4092 4543 2.121291 TTTGCTCCGTATGCATTCCA 57.879 45.000 3.54 0.00 40.34 3.53
4093 4544 2.346766 TTGCTCCGTATGCATTCCAT 57.653 45.000 3.54 0.00 40.34 3.41
4094 4545 1.882912 TGCTCCGTATGCATTCCATC 58.117 50.000 3.54 0.00 35.31 3.51
4095 4546 1.417517 TGCTCCGTATGCATTCCATCT 59.582 47.619 3.54 0.00 35.31 2.90
4096 4547 2.632512 TGCTCCGTATGCATTCCATCTA 59.367 45.455 3.54 0.00 35.31 1.98
4097 4548 3.070878 TGCTCCGTATGCATTCCATCTAA 59.929 43.478 3.54 0.00 35.31 2.10
4098 4549 4.256920 GCTCCGTATGCATTCCATCTAAT 58.743 43.478 3.54 0.00 35.34 1.73
4099 4550 4.093998 GCTCCGTATGCATTCCATCTAATG 59.906 45.833 3.54 0.00 39.41 1.90
4117 4568 9.829507 CATCTAATGGAATCTCTACAAAGACTT 57.170 33.333 0.00 0.00 0.00 3.01
4122 4573 9.965902 AATGGAATCTCTACAAAGACTTACATT 57.034 29.630 0.00 0.00 30.67 2.71
4123 4574 9.965902 ATGGAATCTCTACAAAGACTTACATTT 57.034 29.630 0.00 0.00 0.00 2.32
4129 4580 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
4130 4581 9.152595 CTCTACAAAGACTTACATTTAGGAACC 57.847 37.037 0.00 0.00 0.00 3.62
4131 4582 8.098912 TCTACAAAGACTTACATTTAGGAACCC 58.901 37.037 0.00 0.00 0.00 4.11
4132 4583 6.607019 ACAAAGACTTACATTTAGGAACCCA 58.393 36.000 0.00 0.00 0.00 4.51
4133 4584 6.715264 ACAAAGACTTACATTTAGGAACCCAG 59.285 38.462 0.00 0.00 0.00 4.45
4134 4585 5.437191 AGACTTACATTTAGGAACCCAGG 57.563 43.478 0.00 0.00 0.00 4.45
4135 4586 4.227527 AGACTTACATTTAGGAACCCAGGG 59.772 45.833 2.85 2.85 0.00 4.45
4136 4587 4.180723 ACTTACATTTAGGAACCCAGGGA 58.819 43.478 14.54 0.00 0.00 4.20
4137 4588 4.227527 ACTTACATTTAGGAACCCAGGGAG 59.772 45.833 14.54 0.00 0.00 4.30
4138 4589 2.644151 ACATTTAGGAACCCAGGGAGT 58.356 47.619 14.54 0.00 0.00 3.85
4139 4590 3.810623 ACATTTAGGAACCCAGGGAGTA 58.189 45.455 14.54 0.00 0.00 2.59
4140 4591 3.522343 ACATTTAGGAACCCAGGGAGTAC 59.478 47.826 14.54 0.00 0.00 2.73
4149 4600 3.323775 ACCCAGGGAGTACAAAAGAAGA 58.676 45.455 14.54 0.00 0.00 2.87
4231 4698 0.548926 TCCAACAGATGCCCCCTACA 60.549 55.000 0.00 0.00 0.00 2.74
4234 4701 1.004745 CAACAGATGCCCCCTACAACT 59.995 52.381 0.00 0.00 0.00 3.16
4316 4783 4.824515 CCGGCGTCTCCTCCTCCT 62.825 72.222 6.01 0.00 0.00 3.69
4317 4784 3.213402 CGGCGTCTCCTCCTCCTC 61.213 72.222 0.00 0.00 0.00 3.71
4318 4785 3.213402 GGCGTCTCCTCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
4319 4786 3.894947 GCGTCTCCTCCTCCTCGC 61.895 72.222 0.00 0.00 37.17 5.03
4320 4787 3.213402 CGTCTCCTCCTCCTCGCC 61.213 72.222 0.00 0.00 0.00 5.54
4483 5040 2.725008 GACGCGCTCCAGCTCTAT 59.275 61.111 5.73 0.00 39.32 1.98
4484 5041 1.516365 GGACGCGCTCCAGCTCTATA 61.516 60.000 18.80 0.00 39.21 1.31
4532 5089 1.673808 CGGACTGCTACACCTACCCC 61.674 65.000 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
398 399 7.375834 GGTGGTTAGGAAATTTCTTTTCGATT 58.624 34.615 17.42 0.00 43.95 3.34
489 490 2.967599 TCTGTCATACGCTCAGCATT 57.032 45.000 0.00 0.00 0.00 3.56
533 534 1.649321 TCTGTCTTGCCCTCATCTGT 58.351 50.000 0.00 0.00 0.00 3.41
591 594 5.048713 GCAATGACCTAAGCAACTAAACACT 60.049 40.000 0.00 0.00 0.00 3.55
592 595 5.154222 GCAATGACCTAAGCAACTAAACAC 58.846 41.667 0.00 0.00 0.00 3.32
658 661 1.047002 CCCAACAGGGCATCAAACAA 58.953 50.000 0.00 0.00 35.34 2.83
683 687 4.324267 GTTACACCATAACAGGTTCAGCT 58.676 43.478 0.00 0.00 40.77 4.24
782 786 4.036567 TCGGAAATACCACGACATACTG 57.963 45.455 0.00 0.00 38.90 2.74
783 787 4.159135 AGTTCGGAAATACCACGACATACT 59.841 41.667 0.00 0.00 38.90 2.12
784 788 4.266976 CAGTTCGGAAATACCACGACATAC 59.733 45.833 0.00 0.00 38.90 2.39
785 789 4.082081 ACAGTTCGGAAATACCACGACATA 60.082 41.667 0.00 0.00 38.90 2.29
786 790 3.259064 CAGTTCGGAAATACCACGACAT 58.741 45.455 0.00 0.00 38.90 3.06
787 791 2.036217 ACAGTTCGGAAATACCACGACA 59.964 45.455 0.00 0.00 38.90 4.35
788 792 2.680577 ACAGTTCGGAAATACCACGAC 58.319 47.619 0.00 0.00 38.90 4.34
789 793 3.061322 CAACAGTTCGGAAATACCACGA 58.939 45.455 0.00 0.00 38.90 4.35
790 794 3.061322 TCAACAGTTCGGAAATACCACG 58.939 45.455 0.00 0.00 38.90 4.94
791 795 4.062991 AGTCAACAGTTCGGAAATACCAC 58.937 43.478 0.00 0.00 38.90 4.16
792 796 4.345859 AGTCAACAGTTCGGAAATACCA 57.654 40.909 0.00 0.00 38.90 3.25
793 797 6.103997 TGATAGTCAACAGTTCGGAAATACC 58.896 40.000 0.00 0.00 0.00 2.73
794 798 7.772332 ATGATAGTCAACAGTTCGGAAATAC 57.228 36.000 0.00 0.00 0.00 1.89
796 800 8.964476 ATTATGATAGTCAACAGTTCGGAAAT 57.036 30.769 0.00 0.00 0.00 2.17
797 801 7.494625 GGATTATGATAGTCAACAGTTCGGAAA 59.505 37.037 0.00 0.00 0.00 3.13
798 802 6.984474 GGATTATGATAGTCAACAGTTCGGAA 59.016 38.462 0.00 0.00 0.00 4.30
799 803 6.513180 GGATTATGATAGTCAACAGTTCGGA 58.487 40.000 0.00 0.00 0.00 4.55
800 804 5.402568 CGGATTATGATAGTCAACAGTTCGG 59.597 44.000 0.00 0.00 0.00 4.30
801 805 5.107837 GCGGATTATGATAGTCAACAGTTCG 60.108 44.000 0.00 0.00 0.00 3.95
802 806 5.107837 CGCGGATTATGATAGTCAACAGTTC 60.108 44.000 0.00 0.00 0.00 3.01
803 807 4.745125 CGCGGATTATGATAGTCAACAGTT 59.255 41.667 0.00 0.00 0.00 3.16
804 808 4.299155 CGCGGATTATGATAGTCAACAGT 58.701 43.478 0.00 0.00 0.00 3.55
805 809 3.675225 CCGCGGATTATGATAGTCAACAG 59.325 47.826 24.07 0.00 0.00 3.16
806 810 3.554129 CCCGCGGATTATGATAGTCAACA 60.554 47.826 30.73 0.00 0.00 3.33
807 811 2.993899 CCCGCGGATTATGATAGTCAAC 59.006 50.000 30.73 0.00 0.00 3.18
808 812 2.611971 GCCCGCGGATTATGATAGTCAA 60.612 50.000 30.73 0.00 0.00 3.18
809 813 1.067142 GCCCGCGGATTATGATAGTCA 60.067 52.381 30.73 0.00 0.00 3.41
810 814 1.641577 GCCCGCGGATTATGATAGTC 58.358 55.000 30.73 0.00 0.00 2.59
811 815 0.108804 CGCCCGCGGATTATGATAGT 60.109 55.000 30.73 0.00 35.56 2.12
812 816 1.421410 GCGCCCGCGGATTATGATAG 61.421 60.000 30.73 7.40 40.19 2.08
813 817 1.447140 GCGCCCGCGGATTATGATA 60.447 57.895 30.73 0.00 40.19 2.15
814 818 2.742372 GCGCCCGCGGATTATGAT 60.742 61.111 30.73 0.00 40.19 2.45
815 819 4.980805 GGCGCCCGCGGATTATGA 62.981 66.667 30.73 0.00 43.06 2.15
826 830 3.148031 CTAGGGTTCTACGGCGCCC 62.148 68.421 23.46 9.43 41.36 6.13
827 831 2.416260 CTAGGGTTCTACGGCGCC 59.584 66.667 19.07 19.07 0.00 6.53
828 832 2.279318 GCTAGGGTTCTACGGCGC 60.279 66.667 6.90 0.00 0.00 6.53
868 872 2.933834 AAGGGGACGGAAGGTGGG 60.934 66.667 0.00 0.00 0.00 4.61
874 878 1.980772 GAGTCGGAAGGGGACGGAA 60.981 63.158 0.00 0.00 39.38 4.30
875 879 2.362120 GAGTCGGAAGGGGACGGA 60.362 66.667 0.00 0.00 39.38 4.69
912 923 0.598419 GGCTGTGCTTTTCTTGGTGC 60.598 55.000 0.00 0.00 0.00 5.01
979 1002 1.531149 CGAGCTTCACGATTTGGTTGT 59.469 47.619 0.00 0.00 0.00 3.32
980 1003 1.798223 TCGAGCTTCACGATTTGGTTG 59.202 47.619 0.00 0.00 34.85 3.77
1172 1201 1.523758 GCCCTAAACCGCATCATAGG 58.476 55.000 0.00 0.00 35.68 2.57
1176 1205 2.124901 CGGCCCTAAACCGCATCA 60.125 61.111 0.00 0.00 44.90 3.07
1206 1236 2.398554 CGTGAACAAGGCATCGGGG 61.399 63.158 0.00 0.00 0.00 5.73
1232 1262 1.747745 GAATCCCCCGAACCAACCG 60.748 63.158 0.00 0.00 0.00 4.44
1241 1271 0.461339 ACAAATCGACGAATCCCCCG 60.461 55.000 0.00 0.00 0.00 5.73
1280 1334 4.778213 TTACCCATCCCATGAGAAGAAG 57.222 45.455 0.00 0.00 0.00 2.85
1281 1335 4.977739 AGATTACCCATCCCATGAGAAGAA 59.022 41.667 0.00 0.00 31.20 2.52
1282 1336 4.570926 AGATTACCCATCCCATGAGAAGA 58.429 43.478 0.00 0.00 31.20 2.87
1283 1337 4.349048 TGAGATTACCCATCCCATGAGAAG 59.651 45.833 0.00 0.00 31.20 2.85
1284 1338 4.306391 TGAGATTACCCATCCCATGAGAA 58.694 43.478 0.00 0.00 31.20 2.87
1285 1339 3.906218 CTGAGATTACCCATCCCATGAGA 59.094 47.826 0.00 0.00 31.20 3.27
1286 1340 3.008813 CCTGAGATTACCCATCCCATGAG 59.991 52.174 0.00 0.00 31.20 2.90
1287 1341 2.981784 CCTGAGATTACCCATCCCATGA 59.018 50.000 0.00 0.00 31.20 3.07
1288 1342 2.981784 TCCTGAGATTACCCATCCCATG 59.018 50.000 0.00 0.00 31.20 3.66
1289 1343 2.982488 GTCCTGAGATTACCCATCCCAT 59.018 50.000 0.00 0.00 31.20 4.00
1290 1344 2.408565 GTCCTGAGATTACCCATCCCA 58.591 52.381 0.00 0.00 31.20 4.37
1291 1345 1.344763 CGTCCTGAGATTACCCATCCC 59.655 57.143 0.00 0.00 31.20 3.85
1292 1346 1.344763 CCGTCCTGAGATTACCCATCC 59.655 57.143 0.00 0.00 31.20 3.51
1293 1347 2.297597 CTCCGTCCTGAGATTACCCATC 59.702 54.545 0.00 0.00 34.11 3.51
1294 1348 2.320781 CTCCGTCCTGAGATTACCCAT 58.679 52.381 0.00 0.00 34.11 4.00
1295 1349 1.688311 CCTCCGTCCTGAGATTACCCA 60.688 57.143 0.00 0.00 34.11 4.51
1393 1468 1.770658 CCAAGTATCTCATGCCCCTGA 59.229 52.381 0.00 0.00 0.00 3.86
1399 1474 4.265073 AGAACAACCCAAGTATCTCATGC 58.735 43.478 0.00 0.00 0.00 4.06
1468 1549 5.738909 TCAGGTCTTTCCATCTCAAATCTC 58.261 41.667 0.00 0.00 39.02 2.75
1514 1595 9.145865 GCTTACTGAAATTCCTACATATCTAGC 57.854 37.037 0.00 0.00 0.00 3.42
1515 1596 9.646427 GGCTTACTGAAATTCCTACATATCTAG 57.354 37.037 0.00 0.00 0.00 2.43
1516 1597 8.594550 GGGCTTACTGAAATTCCTACATATCTA 58.405 37.037 0.00 0.00 0.00 1.98
1615 1800 8.239998 AGAGCAATGCTAAGAAAATTACAGAAC 58.760 33.333 8.12 0.00 39.88 3.01
1667 1852 3.375207 CCCCTTCCCAATAATGTCCCAAT 60.375 47.826 0.00 0.00 0.00 3.16
1668 1853 2.023501 CCCCTTCCCAATAATGTCCCAA 60.024 50.000 0.00 0.00 0.00 4.12
1692 1877 4.270084 ACGATTAGTGTAAACCATGCATCG 59.730 41.667 0.00 0.00 35.57 3.84
1728 1913 5.068636 CCTTCCCAATATGACAGAGAATGG 58.931 45.833 0.00 0.00 0.00 3.16
1730 1915 5.907662 TCTCCTTCCCAATATGACAGAGAAT 59.092 40.000 0.00 0.00 0.00 2.40
1731 1916 5.280499 TCTCCTTCCCAATATGACAGAGAA 58.720 41.667 0.00 0.00 0.00 2.87
1733 1918 5.620738 TTCTCCTTCCCAATATGACAGAG 57.379 43.478 0.00 0.00 0.00 3.35
1734 1919 5.726308 TCTTTCTCCTTCCCAATATGACAGA 59.274 40.000 0.00 0.00 0.00 3.41
1735 1920 5.994250 TCTTTCTCCTTCCCAATATGACAG 58.006 41.667 0.00 0.00 0.00 3.51
1736 1921 6.581388 ATCTTTCTCCTTCCCAATATGACA 57.419 37.500 0.00 0.00 0.00 3.58
1737 1922 7.740805 ACTATCTTTCTCCTTCCCAATATGAC 58.259 38.462 0.00 0.00 0.00 3.06
1752 1937 8.887717 GCATGTTTCATGTAGAACTATCTTTCT 58.112 33.333 10.68 0.00 39.28 2.52
1939 2124 3.964875 GCGGGCACACCACAGTTG 61.965 66.667 0.00 0.00 40.22 3.16
2083 2273 6.040391 TGGCTAAACTCAATACAAACAAAGCT 59.960 34.615 0.00 0.00 0.00 3.74
2361 2568 7.820386 ACAGATAAATCATACACAAACACGGTA 59.180 33.333 0.00 0.00 0.00 4.02
2389 2596 5.086104 ACTCGCTGACTAAATACACCATT 57.914 39.130 0.00 0.00 0.00 3.16
2393 2600 7.434307 TGCTATTTACTCGCTGACTAAATACAC 59.566 37.037 0.00 0.00 0.00 2.90
2407 2614 8.757164 TGGAACATATGTATGCTATTTACTCG 57.243 34.615 9.21 0.00 37.19 4.18
2480 2690 7.994911 TCCAAATCACTGACTCATTGCTTATAT 59.005 33.333 0.00 0.00 0.00 0.86
2481 2691 7.337938 TCCAAATCACTGACTCATTGCTTATA 58.662 34.615 0.00 0.00 0.00 0.98
2494 2704 6.990798 TGCAAACAATTATCCAAATCACTGA 58.009 32.000 0.00 0.00 0.00 3.41
2530 2740 7.872483 TGCAAAGAGATTTTTCCCAAGTATTTC 59.128 33.333 0.00 0.00 0.00 2.17
2582 2793 8.873830 CAACTGCACGAAGAAATATATATAGGG 58.126 37.037 0.00 0.00 0.00 3.53
2587 2798 6.202762 CAGCCAACTGCACGAAGAAATATATA 59.797 38.462 0.00 0.00 44.83 0.86
2612 3007 7.965045 AGCTCTTGATTCTAATTTAACGACAC 58.035 34.615 0.00 0.00 0.00 3.67
2689 3087 4.968080 GGGAGGAAGCCAGATGATAGATAT 59.032 45.833 0.00 0.00 0.00 1.63
2747 3160 1.743252 GGCCACTGTAGCTGCTCAC 60.743 63.158 4.91 3.89 0.00 3.51
2792 3218 5.562696 CGTGCAAAGTTTAGGAATGACATGT 60.563 40.000 0.00 0.00 0.00 3.21
2797 3223 2.227865 GCCGTGCAAAGTTTAGGAATGA 59.772 45.455 0.00 0.00 0.00 2.57
2833 3259 7.270047 AGACTGACTACACTACTAGATGTCTC 58.730 42.308 0.00 0.00 0.00 3.36
2839 3265 8.687292 TCAAAAAGACTGACTACACTACTAGA 57.313 34.615 0.00 0.00 0.00 2.43
2841 3267 7.813148 GCATCAAAAAGACTGACTACACTACTA 59.187 37.037 0.00 0.00 0.00 1.82
2843 3269 6.423905 TGCATCAAAAAGACTGACTACACTAC 59.576 38.462 0.00 0.00 0.00 2.73
2845 3271 5.368145 TGCATCAAAAAGACTGACTACACT 58.632 37.500 0.00 0.00 0.00 3.55
2894 3320 0.179000 AATCTCACAGGGACATCGCC 59.821 55.000 0.00 0.00 0.00 5.54
2895 3321 1.137872 AGAATCTCACAGGGACATCGC 59.862 52.381 0.00 0.00 0.00 4.58
2999 3426 0.465824 GCCTGCTCATGGATTCAGCT 60.466 55.000 5.11 0.00 34.03 4.24
3268 3696 9.338622 GTTATATAACTGCTGGTTTATTCAGGT 57.661 33.333 16.82 0.00 39.17 4.00
3289 3717 4.442893 GGCCGATATATGCTGCCTGTTATA 60.443 45.833 0.00 0.00 39.05 0.98
3474 3907 0.874175 CTGTTCACGCACGACTCCAA 60.874 55.000 0.00 0.00 0.00 3.53
3577 4010 2.030274 GTCGGGGGACAATTTGAAAGTG 60.030 50.000 3.59 3.59 0.00 3.16
3649 4082 9.281371 CTCATGGAAGTAATGATCATGTTACAT 57.719 33.333 17.39 15.59 37.20 2.29
3696 4134 7.041508 CCATTTAGACACATTAATCTCTCAGCC 60.042 40.741 0.00 0.00 0.00 4.85
3724 4162 4.380841 ACATTTAGTCAAGTATCGCGGA 57.619 40.909 6.13 0.00 0.00 5.54
3767 4205 6.485984 ACATGAGATCAAGATAAAGGATGTGC 59.514 38.462 0.00 0.00 0.00 4.57
3799 4238 6.109359 ACTGGCAAGTTACAGAGATTATGAC 58.891 40.000 12.27 0.00 38.09 3.06
3871 4313 9.330063 TCCAAATTTGTAACAATTGTATGCAAA 57.670 25.926 24.16 24.16 38.21 3.68
3872 4314 8.893219 TCCAAATTTGTAACAATTGTATGCAA 57.107 26.923 12.39 14.11 39.16 4.08
3980 4431 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3981 4432 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3982 4433 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
4044 4495 9.798994 GAATGAATCTAAACTTGAAATGCATCT 57.201 29.630 0.00 0.00 0.00 2.90
4045 4496 9.577110 TGAATGAATCTAAACTTGAAATGCATC 57.423 29.630 0.00 0.00 0.00 3.91
4047 4498 9.932207 AATGAATGAATCTAAACTTGAAATGCA 57.068 25.926 0.00 0.00 0.00 3.96
4052 4503 9.985730 AGCAAAATGAATGAATCTAAACTTGAA 57.014 25.926 0.00 0.00 0.00 2.69
4053 4504 9.630098 GAGCAAAATGAATGAATCTAAACTTGA 57.370 29.630 0.00 0.00 0.00 3.02
4054 4505 8.866956 GGAGCAAAATGAATGAATCTAAACTTG 58.133 33.333 0.00 0.00 0.00 3.16
4055 4506 7.756722 CGGAGCAAAATGAATGAATCTAAACTT 59.243 33.333 0.00 0.00 0.00 2.66
4056 4507 7.094205 ACGGAGCAAAATGAATGAATCTAAACT 60.094 33.333 0.00 0.00 0.00 2.66
4057 4508 7.029563 ACGGAGCAAAATGAATGAATCTAAAC 58.970 34.615 0.00 0.00 0.00 2.01
4058 4509 7.156876 ACGGAGCAAAATGAATGAATCTAAA 57.843 32.000 0.00 0.00 0.00 1.85
4059 4510 6.757897 ACGGAGCAAAATGAATGAATCTAA 57.242 33.333 0.00 0.00 0.00 2.10
4060 4511 7.520453 GCATACGGAGCAAAATGAATGAATCTA 60.520 37.037 0.00 0.00 0.00 1.98
4061 4512 6.732154 CATACGGAGCAAAATGAATGAATCT 58.268 36.000 0.00 0.00 0.00 2.40
4062 4513 5.400485 GCATACGGAGCAAAATGAATGAATC 59.600 40.000 0.00 0.00 0.00 2.52
4063 4514 5.163530 TGCATACGGAGCAAAATGAATGAAT 60.164 36.000 0.00 0.00 39.39 2.57
4064 4515 4.157472 TGCATACGGAGCAAAATGAATGAA 59.843 37.500 0.00 0.00 39.39 2.57
4065 4516 3.693578 TGCATACGGAGCAAAATGAATGA 59.306 39.130 0.00 0.00 39.39 2.57
4066 4517 4.031418 TGCATACGGAGCAAAATGAATG 57.969 40.909 0.00 0.00 39.39 2.67
4067 4518 4.924305 ATGCATACGGAGCAAAATGAAT 57.076 36.364 0.00 0.00 46.27 2.57
4068 4519 4.439974 GGAATGCATACGGAGCAAAATGAA 60.440 41.667 0.00 0.00 46.27 2.57
4069 4520 3.066621 GGAATGCATACGGAGCAAAATGA 59.933 43.478 0.00 0.00 46.27 2.57
4070 4521 3.181488 TGGAATGCATACGGAGCAAAATG 60.181 43.478 0.00 0.00 46.27 2.32
4071 4522 3.023119 TGGAATGCATACGGAGCAAAAT 58.977 40.909 0.00 0.00 46.27 1.82
4072 4523 2.441410 TGGAATGCATACGGAGCAAAA 58.559 42.857 0.00 0.00 46.27 2.44
4073 4524 2.121291 TGGAATGCATACGGAGCAAA 57.879 45.000 0.00 0.00 46.27 3.68
4074 4525 2.158769 AGATGGAATGCATACGGAGCAA 60.159 45.455 0.00 0.00 46.27 3.91
4076 4527 2.175878 AGATGGAATGCATACGGAGC 57.824 50.000 0.00 0.00 0.00 4.70
4077 4528 5.791367 CATTAGATGGAATGCATACGGAG 57.209 43.478 0.00 0.00 30.43 4.63
4091 4542 9.829507 AAGTCTTTGTAGAGATTCCATTAGATG 57.170 33.333 0.00 0.00 0.00 2.90
4096 4547 9.965902 AATGTAAGTCTTTGTAGAGATTCCATT 57.034 29.630 0.00 0.00 0.00 3.16
4097 4548 9.965902 AAATGTAAGTCTTTGTAGAGATTCCAT 57.034 29.630 0.00 0.00 0.00 3.41
4103 4554 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
4104 4555 9.152595 GGTTCCTAAATGTAAGTCTTTGTAGAG 57.847 37.037 0.00 0.00 0.00 2.43
4105 4556 8.098912 GGGTTCCTAAATGTAAGTCTTTGTAGA 58.901 37.037 0.00 0.00 0.00 2.59
4106 4557 7.881232 TGGGTTCCTAAATGTAAGTCTTTGTAG 59.119 37.037 0.00 0.00 0.00 2.74
4107 4558 7.747690 TGGGTTCCTAAATGTAAGTCTTTGTA 58.252 34.615 0.00 0.00 0.00 2.41
4108 4559 6.607019 TGGGTTCCTAAATGTAAGTCTTTGT 58.393 36.000 0.00 0.00 0.00 2.83
4109 4560 6.151144 CCTGGGTTCCTAAATGTAAGTCTTTG 59.849 42.308 0.00 0.00 0.00 2.77
4110 4561 6.246163 CCTGGGTTCCTAAATGTAAGTCTTT 58.754 40.000 0.00 0.00 0.00 2.52
4111 4562 5.281037 CCCTGGGTTCCTAAATGTAAGTCTT 60.281 44.000 3.97 0.00 0.00 3.01
4112 4563 4.227527 CCCTGGGTTCCTAAATGTAAGTCT 59.772 45.833 3.97 0.00 0.00 3.24
4113 4564 4.226620 TCCCTGGGTTCCTAAATGTAAGTC 59.773 45.833 13.56 0.00 0.00 3.01
4114 4565 4.180723 TCCCTGGGTTCCTAAATGTAAGT 58.819 43.478 13.56 0.00 0.00 2.24
4115 4566 4.227527 ACTCCCTGGGTTCCTAAATGTAAG 59.772 45.833 13.56 0.00 0.00 2.34
4116 4567 4.180723 ACTCCCTGGGTTCCTAAATGTAA 58.819 43.478 13.56 0.00 0.00 2.41
4117 4568 3.810623 ACTCCCTGGGTTCCTAAATGTA 58.189 45.455 13.56 0.00 0.00 2.29
4118 4569 2.644151 ACTCCCTGGGTTCCTAAATGT 58.356 47.619 13.56 0.00 0.00 2.71
4119 4570 3.521937 TGTACTCCCTGGGTTCCTAAATG 59.478 47.826 13.56 0.00 0.00 2.32
4120 4571 3.810623 TGTACTCCCTGGGTTCCTAAAT 58.189 45.455 13.56 0.00 0.00 1.40
4121 4572 3.278987 TGTACTCCCTGGGTTCCTAAA 57.721 47.619 13.56 0.00 0.00 1.85
4122 4573 3.278987 TTGTACTCCCTGGGTTCCTAA 57.721 47.619 13.56 1.68 0.00 2.69
4123 4574 3.278987 TTTGTACTCCCTGGGTTCCTA 57.721 47.619 13.56 0.00 0.00 2.94
4124 4575 2.127651 TTTGTACTCCCTGGGTTCCT 57.872 50.000 13.56 0.00 0.00 3.36
4125 4576 2.374170 TCTTTTGTACTCCCTGGGTTCC 59.626 50.000 13.56 0.16 0.00 3.62
4126 4577 3.782656 TCTTTTGTACTCCCTGGGTTC 57.217 47.619 13.56 2.73 0.00 3.62
4127 4578 3.720002 TCTTCTTTTGTACTCCCTGGGTT 59.280 43.478 13.56 3.64 0.00 4.11
4128 4579 3.072622 GTCTTCTTTTGTACTCCCTGGGT 59.927 47.826 13.56 0.00 0.00 4.51
4129 4580 3.676093 GTCTTCTTTTGTACTCCCTGGG 58.324 50.000 6.33 6.33 0.00 4.45
4130 4581 3.244112 ACGTCTTCTTTTGTACTCCCTGG 60.244 47.826 0.00 0.00 0.00 4.45
4131 4582 3.991367 ACGTCTTCTTTTGTACTCCCTG 58.009 45.455 0.00 0.00 0.00 4.45
4132 4583 4.321824 GCTACGTCTTCTTTTGTACTCCCT 60.322 45.833 0.00 0.00 0.00 4.20
4133 4584 3.925299 GCTACGTCTTCTTTTGTACTCCC 59.075 47.826 0.00 0.00 0.00 4.30
4134 4585 4.807443 AGCTACGTCTTCTTTTGTACTCC 58.193 43.478 0.00 0.00 0.00 3.85
4135 4586 7.462988 GCATAAGCTACGTCTTCTTTTGTACTC 60.463 40.741 0.00 0.00 37.91 2.59
4136 4587 6.310711 GCATAAGCTACGTCTTCTTTTGTACT 59.689 38.462 0.00 0.00 37.91 2.73
4137 4588 6.467648 GCATAAGCTACGTCTTCTTTTGTAC 58.532 40.000 0.00 0.00 37.91 2.90
4138 4589 6.642683 GCATAAGCTACGTCTTCTTTTGTA 57.357 37.500 0.00 0.00 37.91 2.41
4139 4590 5.532025 GCATAAGCTACGTCTTCTTTTGT 57.468 39.130 0.00 0.00 37.91 2.83
4231 4698 4.699522 GGCGGTTGCGGGAGAGTT 62.700 66.667 0.00 0.00 44.10 3.01
4355 4831 1.213013 CGTCGAACACCCTGAGGAG 59.787 63.158 0.00 0.00 36.73 3.69


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

AutoCloner maintained by Alex Coulton.