Multiple sequence alignment - TraesCS3A01G443800

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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 TraesCS3A01G443800 chr3A 100.000 5132 0 0 1 5132 685125530 685120399 0.000000e+00 9478
1 TraesCS3A01G443800 chr3D 93.818 3219 119 36 1961 5132 548250943 548247758 0.000000e+00 4769
2 TraesCS3A01G443800 chr3D 89.129 1205 94 16 789 1970 548252154 548250964 0.000000e+00 1465
3 TraesCS3A01G443800 chr3D 84.810 790 56 34 59 808 548252944 548252179 0.000000e+00 736
4 TraesCS3A01G443800 chr3D 93.431 137 6 3 2763 2897 54716801 54716936 3.130000e-47 200
5 TraesCS3A01G443800 chr3D 93.431 137 6 3 2763 2897 520650514 520650379 3.130000e-47 200
6 TraesCS3A01G443800 chr3B 91.058 2080 122 28 1445 3500 725711513 725709474 0.000000e+00 2752
7 TraesCS3A01G443800 chr3B 94.174 1562 62 5 3597 5132 725709474 725707916 0.000000e+00 2353
8 TraesCS3A01G443800 chr3B 85.380 513 55 13 789 1294 725712039 725711540 9.850000e-142 514
9 TraesCS3A01G443800 chr3B 83.946 517 28 24 270 771 725712580 725712104 1.310000e-120 444
10 TraesCS3A01G443800 chr2D 95.181 415 18 2 2262 2674 352630726 352631140 0.000000e+00 654
11 TraesCS3A01G443800 chr2D 86.667 240 14 9 2659 2897 352631371 352631593 3.070000e-62 250
12 TraesCS3A01G443800 chr2D 93.431 137 6 3 2763 2897 577120792 577120657 3.130000e-47 200
13 TraesCS3A01G443800 chr6D 93.431 137 6 3 2763 2897 469922851 469922716 3.130000e-47 200
14 TraesCS3A01G443800 chr6D 93.431 137 6 3 2763 2897 469924281 469924146 3.130000e-47 200
15 TraesCS3A01G443800 chr2B 93.431 137 6 3 2763 2897 766560127 766559992 3.130000e-47 200


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 TraesCS3A01G443800 chr3A 685120399 685125530 5131 True 9478.000000 9478 100.000000 1 5132 1 chr3A.!!$R1 5131
1 TraesCS3A01G443800 chr3D 548247758 548252944 5186 True 2323.333333 4769 89.252333 59 5132 3 chr3D.!!$R2 5073
2 TraesCS3A01G443800 chr3B 725707916 725712580 4664 True 1515.750000 2752 88.639500 270 5132 4 chr3B.!!$R1 4862
3 TraesCS3A01G443800 chr2D 352630726 352631593 867 False 452.000000 654 90.924000 2262 2897 2 chr2D.!!$F1 635

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
717 777 0.251341 TTCTTGCCTCCCCTGCTTTC 60.251 55.0 0.00 0.0 0.00 2.62 F
1279 1405 0.110056 GATGGAGCAACAGTTGTGCG 60.110 55.0 14.88 0.0 0.00 5.34 F
1741 1883 0.308376 AACGCAACGCCACGTAATTT 59.692 45.0 0.00 0.0 42.68 1.82 F
2764 3191 0.313043 TTCTCCGTATCCGCCGATTC 59.687 55.0 0.00 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 1864 0.308376 AAATTACGTGGCGTTGCGTT 59.692 45.0 0.00 0.00 41.54 4.84 R
3093 3521 0.178967 TTGCAGTTGGAGAATGGCCA 60.179 50.0 8.56 8.56 0.00 5.36 R
3097 3525 1.542492 AGCCTTGCAGTTGGAGAATG 58.458 50.0 6.65 0.00 0.00 2.67 R
4683 5148 1.882989 GCGAGCTCTGGGACTTCACT 61.883 60.0 12.85 0.00 0.00 3.41 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
25 26 4.496336 GGCCGCTTCCTCCATGCT 62.496 66.667 0.00 0.00 0.00 3.79
26 27 2.899339 GCCGCTTCCTCCATGCTC 60.899 66.667 0.00 0.00 0.00 4.26
27 28 2.587194 CCGCTTCCTCCATGCTCG 60.587 66.667 0.00 0.00 0.00 5.03
28 29 2.587194 CGCTTCCTCCATGCTCGG 60.587 66.667 0.00 0.00 0.00 4.63
29 30 2.899339 GCTTCCTCCATGCTCGGC 60.899 66.667 0.00 0.00 0.00 5.54
30 31 2.586245 CTTCCTCCATGCTCGGCA 59.414 61.111 1.01 1.01 44.86 5.69
31 32 1.078214 CTTCCTCCATGCTCGGCAA 60.078 57.895 2.68 0.00 43.62 4.52
32 33 0.465097 CTTCCTCCATGCTCGGCAAT 60.465 55.000 2.68 0.00 43.62 3.56
33 34 0.464373 TTCCTCCATGCTCGGCAATC 60.464 55.000 2.68 0.00 43.62 2.67
34 35 1.153107 CCTCCATGCTCGGCAATCA 60.153 57.895 2.68 0.00 43.62 2.57
35 36 0.536687 CCTCCATGCTCGGCAATCAT 60.537 55.000 2.68 0.00 43.62 2.45
36 37 1.315690 CTCCATGCTCGGCAATCATT 58.684 50.000 2.68 0.00 43.62 2.57
37 38 1.001706 CTCCATGCTCGGCAATCATTG 60.002 52.381 2.68 0.00 43.62 2.82
38 39 1.026584 CCATGCTCGGCAATCATTGA 58.973 50.000 0.00 0.00 43.62 2.57
39 40 1.268896 CCATGCTCGGCAATCATTGAC 60.269 52.381 0.00 0.00 43.62 3.18
45 46 3.629858 GGCAATCATTGACGCCTTC 57.370 52.632 17.69 0.00 41.50 3.46
46 47 1.098050 GGCAATCATTGACGCCTTCT 58.902 50.000 17.69 0.00 41.50 2.85
47 48 2.288666 GGCAATCATTGACGCCTTCTA 58.711 47.619 17.69 0.00 41.50 2.10
48 49 2.880890 GGCAATCATTGACGCCTTCTAT 59.119 45.455 17.69 0.00 41.50 1.98
49 50 3.316308 GGCAATCATTGACGCCTTCTATT 59.684 43.478 17.69 0.00 41.50 1.73
50 51 4.531332 GCAATCATTGACGCCTTCTATTC 58.469 43.478 0.00 0.00 0.00 1.75
51 52 4.274459 GCAATCATTGACGCCTTCTATTCT 59.726 41.667 0.00 0.00 0.00 2.40
52 53 5.466728 GCAATCATTGACGCCTTCTATTCTA 59.533 40.000 0.00 0.00 0.00 2.10
53 54 6.564873 GCAATCATTGACGCCTTCTATTCTAC 60.565 42.308 0.00 0.00 0.00 2.59
54 55 5.854010 TCATTGACGCCTTCTATTCTACT 57.146 39.130 0.00 0.00 0.00 2.57
55 56 6.954487 TCATTGACGCCTTCTATTCTACTA 57.046 37.500 0.00 0.00 0.00 1.82
56 57 6.736123 TCATTGACGCCTTCTATTCTACTAC 58.264 40.000 0.00 0.00 0.00 2.73
57 58 5.511234 TTGACGCCTTCTATTCTACTACC 57.489 43.478 0.00 0.00 0.00 3.18
73 74 2.552315 ACTACCACGCCATTTCTTGTTG 59.448 45.455 0.00 0.00 0.00 3.33
80 81 1.730446 GCCATTTCTTGTTGAGCTCGC 60.730 52.381 9.64 5.16 0.00 5.03
81 82 1.464687 CCATTTCTTGTTGAGCTCGCG 60.465 52.381 9.64 0.00 0.00 5.87
107 113 6.018425 CGATCGACAGAAAGATTCATCCATTT 60.018 38.462 10.26 0.00 0.00 2.32
109 115 7.539712 TCGACAGAAAGATTCATCCATTTAC 57.460 36.000 0.00 0.00 0.00 2.01
111 117 6.238484 CGACAGAAAGATTCATCCATTTACCC 60.238 42.308 0.00 0.00 0.00 3.69
114 120 6.017605 CAGAAAGATTCATCCATTTACCCGAG 60.018 42.308 0.00 0.00 0.00 4.63
115 121 3.744660 AGATTCATCCATTTACCCGAGC 58.255 45.455 0.00 0.00 0.00 5.03
119 125 4.908601 TCATCCATTTACCCGAGCATAT 57.091 40.909 0.00 0.00 0.00 1.78
120 126 4.578871 TCATCCATTTACCCGAGCATATG 58.421 43.478 0.00 0.00 0.00 1.78
126 132 7.047891 TCCATTTACCCGAGCATATGATAATC 58.952 38.462 6.97 0.00 0.00 1.75
127 133 6.260936 CCATTTACCCGAGCATATGATAATCC 59.739 42.308 6.97 0.00 0.00 3.01
128 134 3.526931 ACCCGAGCATATGATAATCCG 57.473 47.619 6.97 0.00 0.00 4.18
168 179 6.523201 CGAATTGCCGAATAGTAAAATATGCC 59.477 38.462 0.00 0.00 0.00 4.40
170 181 3.187637 TGCCGAATAGTAAAATATGCCGC 59.812 43.478 0.00 0.00 0.00 6.53
171 182 3.723835 GCCGAATAGTAAAATATGCCGCG 60.724 47.826 0.00 0.00 0.00 6.46
176 187 6.629649 CGAATAGTAAAATATGCCGCGAAAAA 59.370 34.615 8.23 0.00 0.00 1.94
180 191 6.027749 AGTAAAATATGCCGCGAAAAAGAAG 58.972 36.000 8.23 0.00 0.00 2.85
181 192 4.434713 AAATATGCCGCGAAAAAGAAGT 57.565 36.364 8.23 0.00 0.00 3.01
183 194 4.795970 ATATGCCGCGAAAAAGAAGTAG 57.204 40.909 8.23 0.00 0.00 2.57
330 347 4.400884 TCCCTCTCATTCTTTTCTCTCTCG 59.599 45.833 0.00 0.00 0.00 4.04
371 388 4.423625 TTAAGGAGGGATTAAGAGCAGC 57.576 45.455 0.00 0.00 0.00 5.25
512 550 1.216178 GGCACATTTTGATGCGGCT 59.784 52.632 0.00 0.00 43.02 5.52
607 653 2.641746 CCTGTCCCCTCTCCCCTCT 61.642 68.421 0.00 0.00 0.00 3.69
610 656 2.133201 TCCCCTCTCCCCTCTCCT 59.867 66.667 0.00 0.00 0.00 3.69
636 692 2.487968 CCCAAACCCCTCCCCCTTT 61.488 63.158 0.00 0.00 0.00 3.11
669 725 1.309347 CTGAGCAGGAGGAGGAGGA 59.691 63.158 0.00 0.00 0.00 3.71
670 726 0.756442 CTGAGCAGGAGGAGGAGGAG 60.756 65.000 0.00 0.00 0.00 3.69
671 727 1.457455 GAGCAGGAGGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
672 728 1.938596 AGCAGGAGGAGGAGGAGGA 60.939 63.158 0.00 0.00 0.00 3.71
673 729 1.457455 GCAGGAGGAGGAGGAGGAG 60.457 68.421 0.00 0.00 0.00 3.69
674 730 1.232792 CAGGAGGAGGAGGAGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
675 731 1.087725 AGGAGGAGGAGGAGGAGGA 59.912 63.158 0.00 0.00 0.00 3.71
676 732 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
677 733 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
678 734 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
679 735 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
680 736 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
690 746 2.115427 GGAGGAGGAGGAAGAAGAAGG 58.885 57.143 0.00 0.00 0.00 3.46
717 777 0.251341 TTCTTGCCTCCCCTGCTTTC 60.251 55.000 0.00 0.00 0.00 2.62
718 778 1.136329 TCTTGCCTCCCCTGCTTTCT 61.136 55.000 0.00 0.00 0.00 2.52
719 779 0.251519 CTTGCCTCCCCTGCTTTCTT 60.252 55.000 0.00 0.00 0.00 2.52
725 785 2.643232 CCCCTGCTTTCTTGCTGCC 61.643 63.158 0.00 0.00 0.00 4.85
732 792 1.954258 GCTTTCTTGCTGCCTCTCCAT 60.954 52.381 0.00 0.00 0.00 3.41
733 793 1.743958 CTTTCTTGCTGCCTCTCCATG 59.256 52.381 0.00 0.00 0.00 3.66
750 810 2.558359 CCATGTCCCCTGTTTTTCTCAC 59.442 50.000 0.00 0.00 0.00 3.51
751 811 3.490348 CATGTCCCCTGTTTTTCTCACT 58.510 45.455 0.00 0.00 0.00 3.41
752 812 3.662759 TGTCCCCTGTTTTTCTCACTT 57.337 42.857 0.00 0.00 0.00 3.16
753 813 3.551846 TGTCCCCTGTTTTTCTCACTTC 58.448 45.455 0.00 0.00 0.00 3.01
754 814 3.202151 TGTCCCCTGTTTTTCTCACTTCT 59.798 43.478 0.00 0.00 0.00 2.85
768 828 4.224594 TCTCACTTCTCATGGATTCTTGCT 59.775 41.667 0.00 0.00 0.00 3.91
771 831 3.280295 CTTCTCATGGATTCTTGCTGCT 58.720 45.455 0.00 0.00 0.00 4.24
772 832 3.361281 TCTCATGGATTCTTGCTGCTT 57.639 42.857 0.00 0.00 0.00 3.91
773 833 3.276857 TCTCATGGATTCTTGCTGCTTC 58.723 45.455 0.00 0.00 0.00 3.86
774 834 3.054582 TCTCATGGATTCTTGCTGCTTCT 60.055 43.478 0.00 0.00 0.00 2.85
776 836 2.119801 TGGATTCTTGCTGCTTCTCC 57.880 50.000 0.00 1.14 0.00 3.71
777 837 1.352017 TGGATTCTTGCTGCTTCTCCA 59.648 47.619 0.00 3.77 0.00 3.86
779 839 2.358267 GGATTCTTGCTGCTTCTCCATG 59.642 50.000 0.00 0.00 0.00 3.66
780 840 2.574006 TTCTTGCTGCTTCTCCATGT 57.426 45.000 0.00 0.00 0.00 3.21
782 842 1.093159 CTTGCTGCTTCTCCATGTCC 58.907 55.000 0.00 0.00 0.00 4.02
783 843 0.322816 TTGCTGCTTCTCCATGTCCC 60.323 55.000 0.00 0.00 0.00 4.46
804 867 4.324874 CCCCTGTTTCTTCTCATCTTCCAT 60.325 45.833 0.00 0.00 0.00 3.41
808 871 6.260493 CCTGTTTCTTCTCATCTTCCATGATC 59.740 42.308 0.00 0.00 0.00 2.92
855 962 8.130469 ACATTTTTCATGCTTGATTTTGGTTTC 58.870 29.630 2.75 0.00 0.00 2.78
884 998 2.893489 GTTGATTTCTTGCCCTGAACCT 59.107 45.455 0.00 0.00 0.00 3.50
886 1000 4.380843 TGATTTCTTGCCCTGAACCTAA 57.619 40.909 0.00 0.00 0.00 2.69
887 1001 4.934356 TGATTTCTTGCCCTGAACCTAAT 58.066 39.130 0.00 0.00 0.00 1.73
893 1007 3.926058 TGCCCTGAACCTAATAGGAAC 57.074 47.619 14.17 6.91 37.67 3.62
912 1029 6.331369 GGAACTTTTCCTTGTTGATGATGA 57.669 37.500 0.00 0.00 46.57 2.92
913 1030 6.152379 GGAACTTTTCCTTGTTGATGATGAC 58.848 40.000 0.00 0.00 46.57 3.06
914 1031 6.239008 GGAACTTTTCCTTGTTGATGATGACA 60.239 38.462 0.00 0.00 46.57 3.58
917 1034 5.947228 TTTCCTTGTTGATGATGACAGAC 57.053 39.130 0.00 0.00 0.00 3.51
922 1039 2.026915 TGTTGATGATGACAGACAGGGG 60.027 50.000 0.00 0.00 0.00 4.79
925 1042 0.545171 ATGATGACAGACAGGGGCAG 59.455 55.000 0.00 0.00 0.00 4.85
951 1068 5.610791 AGGGAGAAGAAGGGGATAAAAGTA 58.389 41.667 0.00 0.00 0.00 2.24
953 1070 6.330514 AGGGAGAAGAAGGGGATAAAAGTATC 59.669 42.308 0.00 0.00 36.18 2.24
954 1071 6.101296 GGGAGAAGAAGGGGATAAAAGTATCA 59.899 42.308 0.00 0.00 38.33 2.15
957 1074 5.291905 AGAAGGGGATAAAAGTATCACGG 57.708 43.478 0.00 0.00 40.58 4.94
993 1110 1.375098 GATCCTGCTCTTGTGCCTGC 61.375 60.000 0.00 0.00 0.00 4.85
1026 1143 1.135915 CCAGGAGACCTCGTCAATCTG 59.864 57.143 0.00 0.00 34.60 2.90
1054 1171 2.963432 GCATGTTTGCTATTGGTTGCT 58.037 42.857 0.00 0.00 45.77 3.91
1055 1172 3.328505 GCATGTTTGCTATTGGTTGCTT 58.671 40.909 0.00 0.00 45.77 3.91
1069 1186 2.746362 GGTTGCTTGGACATTCTCTCTG 59.254 50.000 0.00 0.00 0.00 3.35
1076 1193 1.473080 GGACATTCTCTCTGCTCTGGC 60.473 57.143 0.00 0.00 39.26 4.85
1086 1203 3.902467 TCTCTGCTCTGGCTGATTGATAT 59.098 43.478 0.00 0.00 43.52 1.63
1087 1204 3.997681 CTCTGCTCTGGCTGATTGATATG 59.002 47.826 0.00 0.00 43.52 1.78
1088 1205 3.644738 TCTGCTCTGGCTGATTGATATGA 59.355 43.478 0.00 0.00 40.57 2.15
1089 1206 4.286291 TCTGCTCTGGCTGATTGATATGAT 59.714 41.667 0.00 0.00 40.57 2.45
1090 1207 4.324267 TGCTCTGGCTGATTGATATGATG 58.676 43.478 0.00 0.00 39.59 3.07
1165 1290 4.999950 GTGTGCTCTGGGGATAAGATATTG 59.000 45.833 0.00 0.00 0.00 1.90
1199 1324 6.698008 TGCTGTGGAATTTGTTGATATAGG 57.302 37.500 0.00 0.00 0.00 2.57
1227 1352 3.608506 CGTTATAGATCATACTGCGTGCC 59.391 47.826 0.00 0.00 0.00 5.01
1238 1363 1.806542 ACTGCGTGCCTGTTATTCTTG 59.193 47.619 0.00 0.00 0.00 3.02
1239 1364 0.521291 TGCGTGCCTGTTATTCTTGC 59.479 50.000 0.00 0.00 0.00 4.01
1240 1365 0.179163 GCGTGCCTGTTATTCTTGCC 60.179 55.000 0.00 0.00 0.00 4.52
1260 1386 4.227538 GCCATGTACTGTAGCACGTATAG 58.772 47.826 0.00 0.00 0.00 1.31
1279 1405 0.110056 GATGGAGCAACAGTTGTGCG 60.110 55.000 14.88 0.00 0.00 5.34
1288 1414 2.825086 ACAGTTGTGCGTCTGTTTTC 57.175 45.000 0.00 0.00 41.33 2.29
1293 1419 4.621034 CAGTTGTGCGTCTGTTTTCTTTTT 59.379 37.500 0.00 0.00 0.00 1.94
1294 1420 4.857037 AGTTGTGCGTCTGTTTTCTTTTTC 59.143 37.500 0.00 0.00 0.00 2.29
1295 1421 4.427096 TGTGCGTCTGTTTTCTTTTTCA 57.573 36.364 0.00 0.00 0.00 2.69
1296 1422 4.992688 TGTGCGTCTGTTTTCTTTTTCAT 58.007 34.783 0.00 0.00 0.00 2.57
1297 1423 6.125327 TGTGCGTCTGTTTTCTTTTTCATA 57.875 33.333 0.00 0.00 0.00 2.15
1298 1424 5.968848 TGTGCGTCTGTTTTCTTTTTCATAC 59.031 36.000 0.00 0.00 0.00 2.39
1319 1445 7.561722 TCATACTACTAGGAGCAATTCTTGTCT 59.438 37.037 0.36 0.00 0.00 3.41
1375 1501 6.441274 CCAATGCCATATTGTTAGATCACAC 58.559 40.000 0.00 0.00 0.00 3.82
1463 1596 3.181461 TGTTAAAGGCATTGGTGGTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
1501 1634 3.275999 GAAGCTTTCGCATACCCCTTTA 58.724 45.455 0.00 0.00 39.10 1.85
1609 1751 2.322355 AGAAGAATATGCAGCGCAGT 57.678 45.000 11.47 0.00 43.65 4.40
1692 1834 6.074888 GCGCGAAATATTTGAATATTGCAACT 60.075 34.615 12.10 0.00 39.89 3.16
1722 1864 2.604046 TAAAAGGCAAAAGGCGCAAA 57.396 40.000 10.83 0.00 46.16 3.68
1741 1883 0.308376 AACGCAACGCCACGTAATTT 59.692 45.000 0.00 0.00 42.68 1.82
1773 1915 6.476243 TTCACGAGGCTCTTTAAATTACAC 57.524 37.500 13.50 0.00 0.00 2.90
1798 1940 5.464168 AGAATTTAGTACGTGTTACAGCGT 58.536 37.500 14.71 14.71 44.02 5.07
1815 1957 3.438087 CAGCGTGAAATTTCTCTGATGGT 59.562 43.478 18.64 6.98 0.00 3.55
1819 1961 3.436704 GTGAAATTTCTCTGATGGTGCGA 59.563 43.478 18.64 0.00 0.00 5.10
1827 1969 3.686241 TCTCTGATGGTGCGAAATTTCTG 59.314 43.478 15.92 10.41 0.00 3.02
1841 1983 5.275881 CGAAATTTCTGAATATTGCAACGGC 60.276 40.000 15.92 0.00 41.68 5.68
1880 2023 9.665264 CTAGGAAATAAAAGGAATGCGATAAAC 57.335 33.333 0.00 0.00 0.00 2.01
1892 2035 1.667467 GCGATAAACGGCAAAAAGGCA 60.667 47.619 0.00 0.00 44.47 4.75
1914 2057 1.474077 GAACTGCCAGGCCACTTAATG 59.526 52.381 9.64 0.00 0.00 1.90
1937 2080 5.821995 TGTTCAGTTCTGAATGTCAACATGA 59.178 36.000 16.55 0.00 36.56 3.07
2036 2209 1.663643 GTCATTGTCGGAATGCGCTTA 59.336 47.619 9.73 0.00 0.00 3.09
2046 2219 5.178809 GTCGGAATGCGCTTACCTATTTTAT 59.821 40.000 9.73 0.00 0.00 1.40
2113 2286 5.960113 TGGCACATATGTTCCATTTTGTAC 58.040 37.500 21.49 0.71 36.45 2.90
2123 2296 7.517614 TGTTCCATTTTGTACTCTGCAATTA 57.482 32.000 0.00 0.00 0.00 1.40
2170 2343 3.325870 TGTCGATTCAGCAATCTTTCGT 58.674 40.909 0.00 0.00 36.93 3.85
2176 2349 7.162708 GTCGATTCAGCAATCTTTCGTTTATTC 59.837 37.037 0.00 0.00 36.93 1.75
2246 2425 0.541392 AGGTTACATCTGCATCGCCA 59.459 50.000 0.00 0.00 0.00 5.69
2255 2434 1.426816 CTGCATCGCCACTGCTACAG 61.427 60.000 0.00 0.00 40.34 2.74
2258 2437 1.725641 CATCGCCACTGCTACAGAAA 58.274 50.000 0.78 0.00 35.18 2.52
2259 2438 2.283298 CATCGCCACTGCTACAGAAAT 58.717 47.619 0.78 0.00 35.18 2.17
2285 2464 1.734655 AGCCTGTTCTGAAGGAGGAA 58.265 50.000 16.20 0.00 36.91 3.36
2330 2509 1.686052 CTTGCAGTAGCTCTAGGAGGG 59.314 57.143 0.00 0.00 42.74 4.30
2488 2667 6.765989 AGTTTTTGAGGGGCTTTTAATTTCAC 59.234 34.615 0.00 0.00 0.00 3.18
2712 3139 2.876368 AAAGGCGGCATTCTCCTCCG 62.876 60.000 13.08 0.00 45.46 4.63
2741 3168 4.161001 GGAATTTCTTCATGAGGTGCCAAT 59.839 41.667 4.57 0.00 32.70 3.16
2742 3169 5.337813 GGAATTTCTTCATGAGGTGCCAATT 60.338 40.000 4.57 5.91 32.70 2.32
2760 3187 3.053662 TTTTTCTCCGTATCCGCCG 57.946 52.632 0.00 0.00 0.00 6.46
2761 3188 0.531657 TTTTTCTCCGTATCCGCCGA 59.468 50.000 0.00 0.00 0.00 5.54
2762 3189 0.748450 TTTTCTCCGTATCCGCCGAT 59.252 50.000 0.00 0.00 0.00 4.18
2763 3190 0.748450 TTTCTCCGTATCCGCCGATT 59.252 50.000 0.00 0.00 0.00 3.34
2764 3191 0.313043 TTCTCCGTATCCGCCGATTC 59.687 55.000 0.00 0.00 0.00 2.52
2765 3192 0.536687 TCTCCGTATCCGCCGATTCT 60.537 55.000 0.00 0.00 0.00 2.40
2784 3211 6.552445 ATTCTCTAGAGTAGTGGCATGTTT 57.448 37.500 19.21 0.00 0.00 2.83
2847 3274 3.921119 TGAACTCATGATTGTTGGTGC 57.079 42.857 5.16 0.00 0.00 5.01
2849 3276 2.592102 ACTCATGATTGTTGGTGCCT 57.408 45.000 0.00 0.00 0.00 4.75
2853 3280 3.991773 CTCATGATTGTTGGTGCCTTTTG 59.008 43.478 0.00 0.00 0.00 2.44
2871 3298 4.668138 TTTGCTCCCCAGGTTAATTACT 57.332 40.909 0.00 0.00 0.00 2.24
2873 3300 5.782677 TTGCTCCCCAGGTTAATTACTTA 57.217 39.130 0.00 0.00 0.00 2.24
2900 3327 1.153628 CCGTCGTCATCCCAACCTC 60.154 63.158 0.00 0.00 0.00 3.85
2916 3343 1.209747 ACCTCGTAAATCTCTTGGGGC 59.790 52.381 0.00 0.00 0.00 5.80
3033 3461 8.729756 TGTGTTTCCTATTATTGTTCTGATGTG 58.270 33.333 0.00 0.00 0.00 3.21
3048 3476 2.745821 TGATGTGCAAGAAGAGCATCAC 59.254 45.455 9.19 0.00 44.79 3.06
3054 3482 2.810274 GCAAGAAGAGCATCACAAGTGA 59.190 45.455 5.24 5.24 44.59 3.41
3071 3499 8.345565 TCACAAGTGATAGCTTTTCTTTCTTTC 58.654 33.333 0.00 0.00 34.14 2.62
3072 3500 8.348507 CACAAGTGATAGCTTTTCTTTCTTTCT 58.651 33.333 0.00 0.00 0.00 2.52
3081 3509 5.510349 GCTTTTCTTTCTTTCTTGCCATCCT 60.510 40.000 0.00 0.00 0.00 3.24
3110 3538 1.188863 AATGGCCATTCTCCAACTGC 58.811 50.000 25.73 0.00 37.13 4.40
3111 3539 0.040058 ATGGCCATTCTCCAACTGCA 59.960 50.000 14.09 0.00 37.13 4.41
3186 3614 0.179084 ATACATCGGCACCAACTCCG 60.179 55.000 0.00 0.00 46.52 4.63
3286 3722 7.833682 TGCAATGAATCTTATTGACCTTTCCTA 59.166 33.333 0.00 0.00 37.65 2.94
3338 3774 1.222936 CATGACCCCTCCTGCTGTC 59.777 63.158 0.00 0.00 0.00 3.51
3470 3906 5.220548 GCCTTCGATGATATTCAATGATCCG 60.221 44.000 0.00 0.00 0.00 4.18
3511 3947 1.777272 ACTGAGCTTCTTCTTTGGGGT 59.223 47.619 0.00 0.00 0.00 4.95
3573 4009 9.436957 ACTTCCATTAGTGAATAGTACAAACTG 57.563 33.333 0.00 0.00 36.36 3.16
3815 4251 7.033791 CCTGATGATTGTTCAATTCCTCTTTG 58.966 38.462 0.00 0.00 34.96 2.77
3927 4389 2.368221 AGCAGATAGGAGAATGACCAGC 59.632 50.000 0.00 0.00 0.00 4.85
3941 4403 3.124921 CAGCGGCTTTACCCCACG 61.125 66.667 0.00 0.00 33.26 4.94
4172 4634 4.593956 AGCATTTCAAAGGCTAAGCTAGT 58.406 39.130 7.70 0.00 35.82 2.57
4333 4795 3.181437 ACCCCTGGTGTATTTTCTTCGTT 60.181 43.478 0.00 0.00 32.98 3.85
4334 4796 3.190535 CCCCTGGTGTATTTTCTTCGTTG 59.809 47.826 0.00 0.00 0.00 4.10
4359 4821 3.071479 TCGACATAGGGTTTCAACTTGC 58.929 45.455 0.00 0.00 0.00 4.01
4443 4905 9.125026 CCAAACTGGCAACTTTATATATCTCTT 57.875 33.333 0.00 0.00 37.61 2.85
4465 4930 9.211485 CTCTTCAATTTTAGACATTTGCCATTT 57.789 29.630 0.00 0.00 0.00 2.32
4470 4935 9.206870 CAATTTTAGACATTTGCCATTTGTAGT 57.793 29.630 0.00 0.00 0.00 2.73
4473 4938 9.853555 TTTTAGACATTTGCCATTTGTAGTATG 57.146 29.630 0.00 0.00 0.00 2.39
4476 4941 6.095440 AGACATTTGCCATTTGTAGTATGGTC 59.905 38.462 0.00 0.00 43.65 4.02
4665 5130 3.461458 TGAATGGCACCTATGGTTGGATA 59.539 43.478 0.00 0.00 31.02 2.59
4683 5148 4.777366 TGGATAAGGTCATCTCTGTTGACA 59.223 41.667 6.20 0.00 44.22 3.58
4881 5346 2.916934 TGCCCCAATGTAAAGGTACTCT 59.083 45.455 0.00 0.00 38.49 3.24
4986 5455 6.443849 AGAGGTTAATGGAACTACTCAATCCA 59.556 38.462 0.00 0.00 46.60 3.41
5023 5492 0.178767 CCATTCCGAGGATGACTGCA 59.821 55.000 0.00 0.00 0.00 4.41
5064 5533 1.136147 GTGCTGCAAGAGATTGCCG 59.864 57.895 2.77 5.38 46.82 5.69
5097 5566 9.605275 CTAATGAGAAAGATTCAAGGACATGTA 57.395 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.496336 AGCATGGAGGAAGCGGCC 62.496 66.667 0.00 0.00 0.00 6.13
9 10 2.899339 GAGCATGGAGGAAGCGGC 60.899 66.667 0.00 0.00 0.00 6.53
10 11 2.587194 CGAGCATGGAGGAAGCGG 60.587 66.667 0.00 0.00 0.00 5.52
11 12 2.587194 CCGAGCATGGAGGAAGCG 60.587 66.667 0.00 0.00 0.00 4.68
12 13 2.899339 GCCGAGCATGGAGGAAGC 60.899 66.667 0.00 0.00 0.00 3.86
13 14 0.465097 ATTGCCGAGCATGGAGGAAG 60.465 55.000 0.00 0.00 38.76 3.46
14 15 0.464373 GATTGCCGAGCATGGAGGAA 60.464 55.000 0.00 0.00 38.76 3.36
15 16 1.146930 GATTGCCGAGCATGGAGGA 59.853 57.895 0.00 0.00 38.76 3.71
16 17 0.536687 ATGATTGCCGAGCATGGAGG 60.537 55.000 0.00 0.00 38.76 4.30
17 18 1.001706 CAATGATTGCCGAGCATGGAG 60.002 52.381 0.00 0.00 38.76 3.86
18 19 1.026584 CAATGATTGCCGAGCATGGA 58.973 50.000 0.00 0.00 38.76 3.41
19 20 1.026584 TCAATGATTGCCGAGCATGG 58.973 50.000 0.00 0.00 38.76 3.66
20 21 1.596220 CGTCAATGATTGCCGAGCATG 60.596 52.381 2.00 0.00 38.76 4.06
21 22 0.659427 CGTCAATGATTGCCGAGCAT 59.341 50.000 2.00 0.00 38.76 3.79
22 23 1.980951 GCGTCAATGATTGCCGAGCA 61.981 55.000 13.09 0.00 33.22 4.26
23 24 1.297893 GCGTCAATGATTGCCGAGC 60.298 57.895 13.09 5.64 33.22 5.03
24 25 1.353103 GGCGTCAATGATTGCCGAG 59.647 57.895 13.09 0.00 37.81 4.63
25 26 3.496711 GGCGTCAATGATTGCCGA 58.503 55.556 13.09 0.00 37.81 5.54
28 29 4.274459 AGAATAGAAGGCGTCAATGATTGC 59.726 41.667 2.69 2.39 0.00 3.56
29 30 5.998454 AGAATAGAAGGCGTCAATGATTG 57.002 39.130 2.69 0.00 0.00 2.67
30 31 6.821388 AGTAGAATAGAAGGCGTCAATGATT 58.179 36.000 2.69 0.00 0.00 2.57
31 32 6.412362 AGTAGAATAGAAGGCGTCAATGAT 57.588 37.500 2.69 0.00 0.00 2.45
32 33 5.854010 AGTAGAATAGAAGGCGTCAATGA 57.146 39.130 2.69 0.00 0.00 2.57
33 34 5.921408 GGTAGTAGAATAGAAGGCGTCAATG 59.079 44.000 2.69 0.00 0.00 2.82
34 35 5.597182 TGGTAGTAGAATAGAAGGCGTCAAT 59.403 40.000 2.69 0.00 0.00 2.57
35 36 4.951715 TGGTAGTAGAATAGAAGGCGTCAA 59.048 41.667 2.69 0.00 0.00 3.18
36 37 4.337555 GTGGTAGTAGAATAGAAGGCGTCA 59.662 45.833 2.69 0.00 0.00 4.35
37 38 4.554330 CGTGGTAGTAGAATAGAAGGCGTC 60.554 50.000 0.00 0.00 0.00 5.19
38 39 3.314635 CGTGGTAGTAGAATAGAAGGCGT 59.685 47.826 0.00 0.00 0.00 5.68
39 40 3.852572 GCGTGGTAGTAGAATAGAAGGCG 60.853 52.174 0.00 0.00 0.00 5.52
40 41 3.552478 GGCGTGGTAGTAGAATAGAAGGC 60.552 52.174 0.00 0.00 0.00 4.35
41 42 3.635373 TGGCGTGGTAGTAGAATAGAAGG 59.365 47.826 0.00 0.00 0.00 3.46
42 43 4.913335 TGGCGTGGTAGTAGAATAGAAG 57.087 45.455 0.00 0.00 0.00 2.85
43 44 5.864418 AATGGCGTGGTAGTAGAATAGAA 57.136 39.130 0.00 0.00 0.00 2.10
44 45 5.597182 AGAAATGGCGTGGTAGTAGAATAGA 59.403 40.000 0.00 0.00 0.00 1.98
45 46 5.844004 AGAAATGGCGTGGTAGTAGAATAG 58.156 41.667 0.00 0.00 0.00 1.73
46 47 5.864418 AGAAATGGCGTGGTAGTAGAATA 57.136 39.130 0.00 0.00 0.00 1.75
47 48 4.755266 AGAAATGGCGTGGTAGTAGAAT 57.245 40.909 0.00 0.00 0.00 2.40
48 49 4.250464 CAAGAAATGGCGTGGTAGTAGAA 58.750 43.478 0.00 0.00 0.00 2.10
49 50 3.259876 ACAAGAAATGGCGTGGTAGTAGA 59.740 43.478 0.00 0.00 0.00 2.59
50 51 3.596214 ACAAGAAATGGCGTGGTAGTAG 58.404 45.455 0.00 0.00 0.00 2.57
51 52 3.688694 ACAAGAAATGGCGTGGTAGTA 57.311 42.857 0.00 0.00 0.00 1.82
52 53 2.552315 CAACAAGAAATGGCGTGGTAGT 59.448 45.455 0.00 0.00 0.00 2.73
53 54 2.811431 TCAACAAGAAATGGCGTGGTAG 59.189 45.455 0.00 0.00 0.00 3.18
54 55 2.811431 CTCAACAAGAAATGGCGTGGTA 59.189 45.455 0.00 0.00 0.00 3.25
55 56 1.608590 CTCAACAAGAAATGGCGTGGT 59.391 47.619 0.00 0.00 0.00 4.16
56 57 1.666888 GCTCAACAAGAAATGGCGTGG 60.667 52.381 0.00 0.00 0.00 4.94
57 58 1.267806 AGCTCAACAAGAAATGGCGTG 59.732 47.619 0.00 0.00 0.00 5.34
80 81 2.185262 TGAATCTTTCTGTCGATCGCG 58.815 47.619 11.09 0.00 39.35 5.87
81 82 3.183373 GGATGAATCTTTCTGTCGATCGC 59.817 47.826 11.09 6.41 0.00 4.58
107 113 4.097437 GTCGGATTATCATATGCTCGGGTA 59.903 45.833 0.00 0.00 0.00 3.69
109 115 3.448686 GTCGGATTATCATATGCTCGGG 58.551 50.000 0.00 0.00 0.00 5.14
111 117 4.016113 TCGTCGGATTATCATATGCTCG 57.984 45.455 0.00 0.00 0.00 5.03
114 120 5.507974 TCGTATCGTCGGATTATCATATGC 58.492 41.667 0.00 0.00 34.00 3.14
115 121 6.086896 GCATCGTATCGTCGGATTATCATATG 59.913 42.308 0.00 0.00 34.00 1.78
119 125 3.189702 TGCATCGTATCGTCGGATTATCA 59.810 43.478 0.00 0.00 34.00 2.15
120 126 3.754955 TGCATCGTATCGTCGGATTATC 58.245 45.455 0.00 0.00 34.00 1.75
126 132 0.590481 TCGTTGCATCGTATCGTCGG 60.590 55.000 16.21 0.00 0.00 4.79
127 133 1.185189 TTCGTTGCATCGTATCGTCG 58.815 50.000 16.21 0.00 0.00 5.12
128 134 3.522362 CAATTCGTTGCATCGTATCGTC 58.478 45.455 16.21 0.00 0.00 4.20
152 163 7.853929 TCTTTTTCGCGGCATATTTTACTATTC 59.146 33.333 6.13 0.00 0.00 1.75
168 179 3.180980 TCGTTGTCTACTTCTTTTTCGCG 59.819 43.478 0.00 0.00 0.00 5.87
170 181 6.001725 CGATTCGTTGTCTACTTCTTTTTCG 58.998 40.000 0.00 0.00 0.00 3.46
171 182 6.297353 CCGATTCGTTGTCTACTTCTTTTTC 58.703 40.000 5.20 0.00 0.00 2.29
176 187 3.087031 TCCCGATTCGTTGTCTACTTCT 58.913 45.455 5.20 0.00 0.00 2.85
180 191 3.498927 TTCTCCCGATTCGTTGTCTAC 57.501 47.619 5.20 0.00 0.00 2.59
181 192 3.181479 CCATTCTCCCGATTCGTTGTCTA 60.181 47.826 5.20 0.00 0.00 2.59
183 194 1.933853 CCATTCTCCCGATTCGTTGTC 59.066 52.381 5.20 0.00 0.00 3.18
330 347 0.179073 TTAGCAAGATCGCCTCTGCC 60.179 55.000 0.00 0.00 33.29 4.85
417 444 6.980051 AATTACTTACTGCCTAAAACGGAG 57.020 37.500 0.00 0.00 0.00 4.63
421 455 9.608617 GTGAGAAAATTACTTACTGCCTAAAAC 57.391 33.333 0.00 0.00 0.00 2.43
478 516 1.804748 GTGCCTAGGAAAAACGTGAGG 59.195 52.381 14.75 0.00 0.00 3.86
512 550 2.270434 AATGGTGGAGCTTAGGAGGA 57.730 50.000 0.00 0.00 0.00 3.71
607 653 1.850755 GGTTTGGGGGAGGACAGGA 60.851 63.158 0.00 0.00 0.00 3.86
610 656 2.861974 GGGGTTTGGGGGAGGACA 60.862 66.667 0.00 0.00 0.00 4.02
636 692 0.178767 CTCAGGTGCCGATGATTGGA 59.821 55.000 1.99 0.00 0.00 3.53
669 725 2.292851 CCTTCTTCTTCCTCCTCCTCCT 60.293 54.545 0.00 0.00 0.00 3.69
670 726 2.115427 CCTTCTTCTTCCTCCTCCTCC 58.885 57.143 0.00 0.00 0.00 4.30
671 727 1.484653 GCCTTCTTCTTCCTCCTCCTC 59.515 57.143 0.00 0.00 0.00 3.71
672 728 1.203364 TGCCTTCTTCTTCCTCCTCCT 60.203 52.381 0.00 0.00 0.00 3.69
673 729 1.065782 GTGCCTTCTTCTTCCTCCTCC 60.066 57.143 0.00 0.00 0.00 4.30
674 730 1.625818 TGTGCCTTCTTCTTCCTCCTC 59.374 52.381 0.00 0.00 0.00 3.71
675 731 1.627834 CTGTGCCTTCTTCTTCCTCCT 59.372 52.381 0.00 0.00 0.00 3.69
676 732 1.339535 CCTGTGCCTTCTTCTTCCTCC 60.340 57.143 0.00 0.00 0.00 4.30
677 733 1.349357 ACCTGTGCCTTCTTCTTCCTC 59.651 52.381 0.00 0.00 0.00 3.71
678 734 1.439543 ACCTGTGCCTTCTTCTTCCT 58.560 50.000 0.00 0.00 0.00 3.36
679 735 2.278332 AACCTGTGCCTTCTTCTTCC 57.722 50.000 0.00 0.00 0.00 3.46
680 736 3.481453 AGAAACCTGTGCCTTCTTCTTC 58.519 45.455 0.00 0.00 0.00 2.87
690 746 1.527433 GGGAGGCAAGAAACCTGTGC 61.527 60.000 0.00 0.00 37.77 4.57
717 777 0.747283 GGACATGGAGAGGCAGCAAG 60.747 60.000 0.00 0.00 0.00 4.01
718 778 1.300963 GGACATGGAGAGGCAGCAA 59.699 57.895 0.00 0.00 0.00 3.91
719 779 2.673200 GGGACATGGAGAGGCAGCA 61.673 63.158 0.00 0.00 0.00 4.41
725 785 2.887151 AAAACAGGGGACATGGAGAG 57.113 50.000 0.00 0.00 0.00 3.20
732 792 3.202151 AGAAGTGAGAAAAACAGGGGACA 59.798 43.478 0.00 0.00 0.00 4.02
733 793 3.815962 GAGAAGTGAGAAAAACAGGGGAC 59.184 47.826 0.00 0.00 0.00 4.46
750 810 3.280295 AGCAGCAAGAATCCATGAGAAG 58.720 45.455 0.00 0.00 0.00 2.85
751 811 3.361281 AGCAGCAAGAATCCATGAGAA 57.639 42.857 0.00 0.00 0.00 2.87
752 812 3.054582 AGAAGCAGCAAGAATCCATGAGA 60.055 43.478 0.00 0.00 0.00 3.27
753 813 3.280295 AGAAGCAGCAAGAATCCATGAG 58.720 45.455 0.00 0.00 0.00 2.90
754 814 3.276857 GAGAAGCAGCAAGAATCCATGA 58.723 45.455 0.00 0.00 0.00 3.07
768 828 0.842030 ACAGGGGACATGGAGAAGCA 60.842 55.000 0.00 0.00 0.00 3.91
771 831 2.348472 AGAAACAGGGGACATGGAGAA 58.652 47.619 0.00 0.00 0.00 2.87
772 832 2.044793 AGAAACAGGGGACATGGAGA 57.955 50.000 0.00 0.00 0.00 3.71
773 833 2.307098 AGAAGAAACAGGGGACATGGAG 59.693 50.000 0.00 0.00 0.00 3.86
774 834 2.305927 GAGAAGAAACAGGGGACATGGA 59.694 50.000 0.00 0.00 0.00 3.41
776 836 3.423539 TGAGAAGAAACAGGGGACATG 57.576 47.619 0.00 0.00 0.00 3.21
777 837 3.848975 AGATGAGAAGAAACAGGGGACAT 59.151 43.478 0.00 0.00 0.00 3.06
779 839 3.990959 AGATGAGAAGAAACAGGGGAC 57.009 47.619 0.00 0.00 0.00 4.46
780 840 3.264450 GGAAGATGAGAAGAAACAGGGGA 59.736 47.826 0.00 0.00 0.00 4.81
782 842 4.292186 TGGAAGATGAGAAGAAACAGGG 57.708 45.455 0.00 0.00 0.00 4.45
783 843 5.494724 TCATGGAAGATGAGAAGAAACAGG 58.505 41.667 0.00 0.00 0.00 4.00
804 867 5.359756 CAAGGAACATCCAGATTACGATCA 58.640 41.667 0.00 0.00 39.61 2.92
808 871 3.063997 GTGCAAGGAACATCCAGATTACG 59.936 47.826 0.00 0.00 39.61 3.18
855 962 2.751806 GGCAAGAAATCAACAGAGGAGG 59.248 50.000 0.00 0.00 0.00 4.30
893 1007 6.016860 TGTCTGTCATCATCAACAAGGAAAAG 60.017 38.462 0.00 0.00 0.00 2.27
906 1021 0.545171 CTGCCCCTGTCTGTCATCAT 59.455 55.000 0.00 0.00 0.00 2.45
909 1026 2.304056 CCCTGCCCCTGTCTGTCAT 61.304 63.158 0.00 0.00 0.00 3.06
910 1027 2.930019 CCCTGCCCCTGTCTGTCA 60.930 66.667 0.00 0.00 0.00 3.58
912 1029 2.608988 CTCCCTGCCCCTGTCTGT 60.609 66.667 0.00 0.00 0.00 3.41
913 1030 3.406200 CCTCCCTGCCCCTGTCTG 61.406 72.222 0.00 0.00 0.00 3.51
914 1031 4.748798 CCCTCCCTGCCCCTGTCT 62.749 72.222 0.00 0.00 0.00 3.41
917 1034 3.950861 TTCTCCCTCCCTGCCCCTG 62.951 68.421 0.00 0.00 0.00 4.45
922 1039 1.631071 CCCTTCTTCTCCCTCCCTGC 61.631 65.000 0.00 0.00 0.00 4.85
925 1042 0.029577 ATCCCCTTCTTCTCCCTCCC 60.030 60.000 0.00 0.00 0.00 4.30
951 1068 2.117156 GCTGAAGCCATGCCGTGAT 61.117 57.895 0.00 0.00 34.31 3.06
953 1070 4.170062 CGCTGAAGCCATGCCGTG 62.170 66.667 0.00 0.00 37.91 4.94
954 1071 4.704833 ACGCTGAAGCCATGCCGT 62.705 61.111 0.00 0.00 37.91 5.68
957 1074 0.171903 ATCAAACGCTGAAGCCATGC 59.828 50.000 0.00 0.00 37.67 4.06
993 1110 2.025767 CTCCTGGCGTCATCTCCCTG 62.026 65.000 0.00 0.00 0.00 4.45
1035 1152 3.680937 CCAAGCAACCAATAGCAAACATG 59.319 43.478 0.00 0.00 0.00 3.21
1039 1156 2.961741 TGTCCAAGCAACCAATAGCAAA 59.038 40.909 0.00 0.00 0.00 3.68
1040 1157 2.591923 TGTCCAAGCAACCAATAGCAA 58.408 42.857 0.00 0.00 0.00 3.91
1041 1158 2.284754 TGTCCAAGCAACCAATAGCA 57.715 45.000 0.00 0.00 0.00 3.49
1042 1159 3.445096 AGAATGTCCAAGCAACCAATAGC 59.555 43.478 0.00 0.00 0.00 2.97
1043 1160 4.946157 AGAGAATGTCCAAGCAACCAATAG 59.054 41.667 0.00 0.00 0.00 1.73
1044 1161 4.922206 AGAGAATGTCCAAGCAACCAATA 58.078 39.130 0.00 0.00 0.00 1.90
1048 1165 2.746362 CAGAGAGAATGTCCAAGCAACC 59.254 50.000 0.00 0.00 0.00 3.77
1049 1166 2.161211 GCAGAGAGAATGTCCAAGCAAC 59.839 50.000 0.00 0.00 0.00 4.17
1051 1168 1.627329 AGCAGAGAGAATGTCCAAGCA 59.373 47.619 0.00 0.00 0.00 3.91
1052 1169 2.093553 AGAGCAGAGAGAATGTCCAAGC 60.094 50.000 0.00 0.00 0.00 4.01
1053 1170 3.523547 CAGAGCAGAGAGAATGTCCAAG 58.476 50.000 0.00 0.00 0.00 3.61
1054 1171 2.235650 CCAGAGCAGAGAGAATGTCCAA 59.764 50.000 0.00 0.00 0.00 3.53
1055 1172 1.829849 CCAGAGCAGAGAGAATGTCCA 59.170 52.381 0.00 0.00 0.00 4.02
1069 1186 3.690139 CCATCATATCAATCAGCCAGAGC 59.310 47.826 0.00 0.00 40.32 4.09
1076 1193 6.628919 TGCAAAGACCATCATATCAATCAG 57.371 37.500 0.00 0.00 0.00 2.90
1086 1203 1.005097 AGGAGCATGCAAAGACCATCA 59.995 47.619 21.98 0.00 0.00 3.07
1087 1204 1.404391 CAGGAGCATGCAAAGACCATC 59.596 52.381 21.98 5.57 0.00 3.51
1088 1205 1.471119 CAGGAGCATGCAAAGACCAT 58.529 50.000 21.98 0.00 0.00 3.55
1089 1206 0.609957 CCAGGAGCATGCAAAGACCA 60.610 55.000 21.98 0.00 0.00 4.02
1090 1207 0.610232 ACCAGGAGCATGCAAAGACC 60.610 55.000 21.98 14.08 0.00 3.85
1199 1324 8.576281 CACGCAGTATGATCTATAACGAATAAC 58.424 37.037 0.00 0.00 41.61 1.89
1205 1330 3.608506 GGCACGCAGTATGATCTATAACG 59.391 47.826 0.00 0.00 41.61 3.18
1227 1352 6.238211 GCTACAGTACATGGCAAGAATAACAG 60.238 42.308 0.00 0.00 0.00 3.16
1238 1363 2.572191 TACGTGCTACAGTACATGGC 57.428 50.000 0.00 0.00 0.00 4.40
1239 1364 5.684550 TCTATACGTGCTACAGTACATGG 57.315 43.478 0.00 0.00 0.00 3.66
1240 1365 6.072673 TCCATCTATACGTGCTACAGTACATG 60.073 42.308 0.00 0.00 0.00 3.21
1260 1386 0.110056 CGCACAACTGTTGCTCCATC 60.110 55.000 19.82 3.03 0.00 3.51
1288 1414 9.606631 AGAATTGCTCCTAGTAGTATGAAAAAG 57.393 33.333 0.00 0.00 0.00 2.27
1319 1445 3.374988 CGCTGAAGGAAATCATGCAGTAA 59.625 43.478 5.07 0.00 0.00 2.24
1362 1488 7.857734 TTCTTCAACTTGTGTGATCTAACAA 57.142 32.000 11.62 11.62 35.14 2.83
1371 1497 4.923893 TGCAGAATTCTTCAACTTGTGTG 58.076 39.130 4.86 0.00 0.00 3.82
1463 1596 3.445805 AGCTTCCTCTGTAGTAGTGCTTC 59.554 47.826 0.00 0.00 0.00 3.86
1501 1634 0.874607 GAACGCTTCGTCGCCCATAT 60.875 55.000 0.00 0.00 39.99 1.78
1609 1751 6.350949 GCAAAGAGCCTCCCAAATACAATAAA 60.351 38.462 0.00 0.00 37.23 1.40
1692 1834 5.221621 CCTTTTGCCTTTTATTTCCCAGACA 60.222 40.000 0.00 0.00 0.00 3.41
1722 1864 0.308376 AAATTACGTGGCGTTGCGTT 59.692 45.000 0.00 0.00 41.54 4.84
1741 1883 5.344743 AAGAGCCTCGTGAATTCTCATAA 57.655 39.130 7.05 0.00 33.05 1.90
1773 1915 5.275142 CGCTGTAACACGTACTAAATTCTCG 60.275 44.000 0.00 0.00 33.46 4.04
1793 1935 3.438087 ACCATCAGAGAAATTTCACGCTG 59.562 43.478 19.99 20.36 0.00 5.18
1798 1940 3.673902 TCGCACCATCAGAGAAATTTCA 58.326 40.909 19.99 0.00 0.00 2.69
1815 1957 5.285845 CGTTGCAATATTCAGAAATTTCGCA 59.714 36.000 12.42 10.19 0.00 5.10
1819 1961 4.869861 GGCCGTTGCAATATTCAGAAATTT 59.130 37.500 0.59 0.00 40.13 1.82
1827 1969 0.865639 GCACGGCCGTTGCAATATTC 60.866 55.000 33.23 12.96 40.13 1.75
1841 1983 2.572191 TTCCTAGATAACGTGCACGG 57.428 50.000 39.21 23.04 44.95 4.94
1880 2023 0.934436 CAGTTCGTGCCTTTTTGCCG 60.934 55.000 0.00 0.00 0.00 5.69
1892 2035 1.764571 TAAGTGGCCTGGCAGTTCGT 61.765 55.000 22.05 7.97 0.00 3.85
2067 2240 4.781775 ATATGGATGGACCGGTTAAACA 57.218 40.909 9.42 6.62 42.61 2.83
2068 2241 6.737254 CATATATGGATGGACCGGTTAAAC 57.263 41.667 9.42 0.00 42.61 2.01
2123 2296 6.362283 GCGCAACAATACAAAGTGAACTAAAT 59.638 34.615 0.30 0.00 0.00 1.40
2166 2339 9.737427 TTTGAACAAGCAATAAGAATAAACGAA 57.263 25.926 0.00 0.00 0.00 3.85
2176 2349 9.515020 TGAACTTAACTTTGAACAAGCAATAAG 57.485 29.630 0.00 0.00 30.17 1.73
2246 2425 7.070074 ACAGGCTAGTAATATTTCTGTAGCAGT 59.930 37.037 14.93 11.09 35.60 4.40
2255 2434 8.204836 TCCTTCAGAACAGGCTAGTAATATTTC 58.795 37.037 0.00 0.00 0.00 2.17
2258 2437 6.268847 CCTCCTTCAGAACAGGCTAGTAATAT 59.731 42.308 0.00 0.00 0.00 1.28
2259 2438 5.598830 CCTCCTTCAGAACAGGCTAGTAATA 59.401 44.000 0.00 0.00 0.00 0.98
2330 2509 3.376918 GCCAAACCTCCTGCAGCC 61.377 66.667 8.66 0.00 0.00 4.85
2712 3139 3.631227 CCTCATGAAGAAATTCCTGGCTC 59.369 47.826 0.00 0.00 0.00 4.70
2751 3178 3.075884 ACTCTAGAGAATCGGCGGATAC 58.924 50.000 26.57 3.06 42.67 2.24
2752 3179 3.420300 ACTCTAGAGAATCGGCGGATA 57.580 47.619 26.57 0.00 42.67 2.59
2753 3180 2.279935 ACTCTAGAGAATCGGCGGAT 57.720 50.000 26.57 0.04 42.67 4.18
2754 3181 2.104451 ACTACTCTAGAGAATCGGCGGA 59.896 50.000 26.57 0.00 42.67 5.54
2755 3182 2.224549 CACTACTCTAGAGAATCGGCGG 59.775 54.545 26.57 8.60 42.67 6.13
2756 3183 2.224549 CCACTACTCTAGAGAATCGGCG 59.775 54.545 26.57 0.00 42.67 6.46
2757 3184 2.030628 GCCACTACTCTAGAGAATCGGC 60.031 54.545 26.57 24.19 42.67 5.54
2758 3185 3.215151 TGCCACTACTCTAGAGAATCGG 58.785 50.000 26.57 19.44 42.67 4.18
2759 3186 4.277174 ACATGCCACTACTCTAGAGAATCG 59.723 45.833 26.57 12.56 42.67 3.34
2760 3187 5.782893 ACATGCCACTACTCTAGAGAATC 57.217 43.478 26.57 8.99 0.00 2.52
2761 3188 6.552445 AAACATGCCACTACTCTAGAGAAT 57.448 37.500 26.57 7.44 0.00 2.40
2762 3189 6.360370 AAAACATGCCACTACTCTAGAGAA 57.640 37.500 26.57 3.18 0.00 2.87
2763 3190 7.396339 TCTTAAAACATGCCACTACTCTAGAGA 59.604 37.037 26.57 9.01 0.00 3.10
2764 3191 7.548097 TCTTAAAACATGCCACTACTCTAGAG 58.452 38.462 18.49 18.49 0.00 2.43
2765 3192 7.476540 TCTTAAAACATGCCACTACTCTAGA 57.523 36.000 0.00 0.00 0.00 2.43
2784 3211 7.069331 TCAGGAAGCAAGGTTTTGATTTCTTAA 59.931 33.333 0.00 0.00 44.14 1.85
2847 3274 2.302587 TTAACCTGGGGAGCAAAAGG 57.697 50.000 0.00 0.00 35.82 3.11
2849 3276 5.005628 AGTAATTAACCTGGGGAGCAAAA 57.994 39.130 0.00 0.00 0.00 2.44
2853 3280 4.995487 CGATAAGTAATTAACCTGGGGAGC 59.005 45.833 0.00 0.00 0.00 4.70
2871 3298 3.434641 GGATGACGACGGATAGACGATAA 59.565 47.826 0.00 0.00 40.26 1.75
2873 3300 1.805345 GGATGACGACGGATAGACGAT 59.195 52.381 0.00 0.00 40.26 3.73
2900 3327 2.223572 GCAATGCCCCAAGAGATTTACG 60.224 50.000 0.00 0.00 0.00 3.18
3022 3450 2.810274 GCTCTTCTTGCACATCAGAACA 59.190 45.455 0.00 0.00 0.00 3.18
3033 3461 2.810274 TCACTTGTGATGCTCTTCTTGC 59.190 45.455 0.00 0.00 0.00 4.01
3048 3476 9.178427 CAAGAAAGAAAGAAAAGCTATCACTTG 57.822 33.333 0.00 0.00 0.00 3.16
3054 3482 6.655078 TGGCAAGAAAGAAAGAAAAGCTAT 57.345 33.333 0.00 0.00 0.00 2.97
3057 3485 4.687948 GGATGGCAAGAAAGAAAGAAAAGC 59.312 41.667 0.00 0.00 0.00 3.51
3058 3486 6.094193 AGGATGGCAAGAAAGAAAGAAAAG 57.906 37.500 0.00 0.00 0.00 2.27
3064 3492 5.630121 TGTAGAAGGATGGCAAGAAAGAAA 58.370 37.500 0.00 0.00 0.00 2.52
3081 3509 4.526970 GAGAATGGCCATTTCCTGTAGAA 58.473 43.478 31.13 0.00 0.00 2.10
3090 3518 1.551883 GCAGTTGGAGAATGGCCATTT 59.448 47.619 31.13 20.32 34.90 2.32
3093 3521 0.178967 TTGCAGTTGGAGAATGGCCA 60.179 50.000 8.56 8.56 0.00 5.36
3097 3525 1.542492 AGCCTTGCAGTTGGAGAATG 58.458 50.000 6.65 0.00 0.00 2.67
3110 3538 4.332268 GTCTCTGCTTGAATTCTAGCCTTG 59.668 45.833 30.36 22.07 42.61 3.61
3111 3539 4.224818 AGTCTCTGCTTGAATTCTAGCCTT 59.775 41.667 30.36 12.70 42.61 4.35
3219 3647 9.455847 GAAAATGAGGCAATTCATAATGTAGTC 57.544 33.333 0.00 0.00 36.81 2.59
3274 3710 8.197592 TGAGTAACAGTAATAGGAAAGGTCAA 57.802 34.615 0.00 0.00 0.00 3.18
3338 3774 4.311816 AGCAGTTTTGAAGTTCATGTGG 57.688 40.909 6.36 0.00 0.00 4.17
3470 3906 3.550678 GTCATTACCGAGGATCAACGAAC 59.449 47.826 11.34 0.00 33.17 3.95
3530 3966 8.469309 AATGGAAGTCAAGGGATGTAATTATG 57.531 34.615 0.00 0.00 0.00 1.90
3531 3967 9.799106 CTAATGGAAGTCAAGGGATGTAATTAT 57.201 33.333 0.00 0.00 0.00 1.28
3842 4278 7.357429 TGCATATCAGAGATGGATAGTATGG 57.643 40.000 7.15 0.00 31.27 2.74
3927 4389 2.125269 CCTCGTGGGGTAAAGCCG 60.125 66.667 0.00 0.00 38.44 5.52
3941 4403 2.733227 CGCAACAATTCCTTCATGCCTC 60.733 50.000 0.00 0.00 0.00 4.70
3988 4450 2.956964 CGGACGATCCTCGCTTGC 60.957 66.667 0.00 0.00 45.12 4.01
4320 4782 9.831054 CTATGTCGAATACAACGAAGAAAATAC 57.169 33.333 0.00 0.00 42.70 1.89
4333 4795 6.045072 AGTTGAAACCCTATGTCGAATACA 57.955 37.500 0.00 0.00 43.86 2.29
4334 4796 6.674760 GCAAGTTGAAACCCTATGTCGAATAC 60.675 42.308 7.16 0.00 0.00 1.89
4443 4905 9.421806 CTACAAATGGCAAATGTCTAAAATTGA 57.578 29.630 11.22 0.00 0.00 2.57
4465 4930 8.783093 CAAATTGTCAGAAAAGACCATACTACA 58.217 33.333 0.00 0.00 37.73 2.74
4470 4935 6.716628 AGAGCAAATTGTCAGAAAAGACCATA 59.283 34.615 0.00 0.00 37.73 2.74
4473 4938 5.218139 CAGAGCAAATTGTCAGAAAAGACC 58.782 41.667 0.00 0.00 37.73 3.85
4476 4941 4.613944 TGCAGAGCAAATTGTCAGAAAAG 58.386 39.130 0.00 0.00 34.76 2.27
4665 5130 3.643320 TCACTGTCAACAGAGATGACCTT 59.357 43.478 16.71 0.00 46.59 3.50
4683 5148 1.882989 GCGAGCTCTGGGACTTCACT 61.883 60.000 12.85 0.00 0.00 3.41
4881 5346 1.004277 GTCTATTTGTGCCACCAGGGA 59.996 52.381 0.00 0.00 40.01 4.20
4904 5369 2.031069 TCACTGAACGAAGGAAGACTCG 60.031 50.000 0.00 0.00 0.00 4.18
4915 5380 0.033504 GTCTTGGGCTCACTGAACGA 59.966 55.000 0.00 0.00 0.00 3.85
4986 5455 0.814010 GGCTTTCGATGTGCCGGTAT 60.814 55.000 1.90 0.00 37.11 2.73
5064 5533 7.914346 CCTTGAATCTTTCTCATTAGCATCAAC 59.086 37.037 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.