Multiple sequence alignment - TraesCS6A01G401500

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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 TraesCS6A01G401500 chr6A 100.000 3609 0 0 1 3609 609974926 609971318 0.000000e+00 6665.0
1 TraesCS6A01G401500 chr6D 92.505 2028 132 11 864 2882 463447875 463445859 0.000000e+00 2885.0
2 TraesCS6A01G401500 chr6D 94.213 553 32 0 3057 3609 370701323 370701875 0.000000e+00 845.0
3 TraesCS6A01G401500 chr6D 78.571 252 22 21 1 238 463448587 463448354 1.750000e-28 137.0
4 TraesCS6A01G401500 chr6D 87.059 85 11 0 864 948 463448081 463447997 2.970000e-16 97.1
5 TraesCS6A01G401500 chr6B 90.549 2169 167 14 864 2999 706627786 706625623 0.000000e+00 2835.0
6 TraesCS6A01G401500 chr6B 77.907 430 44 35 310 726 706628279 706627888 1.690000e-53 220.0
7 TraesCS6A01G401500 chr6B 78.431 306 28 28 1 288 706628667 706628382 8.020000e-37 165.0
8 TraesCS6A01G401500 chr3D 95.298 553 24 2 3057 3609 352854385 352854935 0.000000e+00 876.0
9 TraesCS6A01G401500 chr3D 94.756 553 27 2 3057 3609 358537725 358537175 0.000000e+00 859.0
10 TraesCS6A01G401500 chr1D 94.604 556 29 1 3054 3609 88931611 88932165 0.000000e+00 859.0
11 TraesCS6A01G401500 chr1D 94.575 553 30 0 3057 3609 320014507 320015059 0.000000e+00 856.0
12 TraesCS6A01G401500 chr1D 94.394 553 31 0 3057 3609 313282485 313283037 0.000000e+00 850.0
13 TraesCS6A01G401500 chr1D 90.244 41 3 1 594 634 474052463 474052424 7.000000e-03 52.8
14 TraesCS6A01G401500 chr7D 94.575 553 26 4 3058 3609 170006421 170006970 0.000000e+00 852.0
15 TraesCS6A01G401500 chr2D 94.245 556 27 5 3056 3609 101338668 101339220 0.000000e+00 845.0
16 TraesCS6A01G401500 chr4D 94.065 556 24 8 3057 3609 495029779 495029230 0.000000e+00 835.0
17 TraesCS6A01G401500 chr4D 100.000 40 0 0 593 632 507685731 507685770 1.390000e-09 75.0
18 TraesCS6A01G401500 chr4B 89.212 241 22 1 873 1113 402794602 402794366 7.580000e-77 298.0
19 TraesCS6A01G401500 chr4B 88.655 238 23 1 873 1110 138680234 138680467 1.640000e-73 287.0
20 TraesCS6A01G401500 chr4B 97.500 40 1 0 593 632 656266132 656266093 6.470000e-08 69.4
21 TraesCS6A01G401500 chr1B 85.000 260 33 3 854 1113 123078862 123079115 3.570000e-65 259.0
22 TraesCS6A01G401500 chr1B 87.444 223 28 0 891 1113 123149772 123149994 1.290000e-64 257.0
23 TraesCS6A01G401500 chr5A 97.500 40 1 0 593 632 692844262 692844301 6.470000e-08 69.4
24 TraesCS6A01G401500 chr5A 94.872 39 0 2 311 348 121944160 121944123 3.890000e-05 60.2
25 TraesCS6A01G401500 chr5A 100.000 31 0 0 308 338 123292920 123292890 1.400000e-04 58.4
26 TraesCS6A01G401500 chr3A 92.683 41 3 0 308 348 184258682 184258642 3.890000e-05 60.2


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 TraesCS6A01G401500 chr6A 609971318 609974926 3608 True 6665.000000 6665 100.000000 1 3609 1 chr6A.!!$R1 3608
1 TraesCS6A01G401500 chr6D 463445859 463448587 2728 True 1039.700000 2885 86.045000 1 2882 3 chr6D.!!$R1 2881
2 TraesCS6A01G401500 chr6D 370701323 370701875 552 False 845.000000 845 94.213000 3057 3609 1 chr6D.!!$F1 552
3 TraesCS6A01G401500 chr6B 706625623 706628667 3044 True 1073.333333 2835 82.295667 1 2999 3 chr6B.!!$R1 2998
4 TraesCS6A01G401500 chr3D 352854385 352854935 550 False 876.000000 876 95.298000 3057 3609 1 chr3D.!!$F1 552
5 TraesCS6A01G401500 chr3D 358537175 358537725 550 True 859.000000 859 94.756000 3057 3609 1 chr3D.!!$R1 552
6 TraesCS6A01G401500 chr1D 88931611 88932165 554 False 859.000000 859 94.604000 3054 3609 1 chr1D.!!$F1 555
7 TraesCS6A01G401500 chr1D 320014507 320015059 552 False 856.000000 856 94.575000 3057 3609 1 chr1D.!!$F3 552
8 TraesCS6A01G401500 chr1D 313282485 313283037 552 False 850.000000 850 94.394000 3057 3609 1 chr1D.!!$F2 552
9 TraesCS6A01G401500 chr7D 170006421 170006970 549 False 852.000000 852 94.575000 3058 3609 1 chr7D.!!$F1 551
10 TraesCS6A01G401500 chr2D 101338668 101339220 552 False 845.000000 845 94.245000 3056 3609 1 chr2D.!!$F1 553
11 TraesCS6A01G401500 chr4D 495029230 495029779 549 True 835.000000 835 94.065000 3057 3609 1 chr4D.!!$R1 552

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
762 895 0.037326 CTGAAACCTGCACGCCTCTA 60.037 55.0 0.0 0.0 0.00 2.43 F
774 907 0.038709 CGCCTCTAGCTACCTGATGC 60.039 60.0 0.0 0.0 40.39 3.91 F
1641 1852 0.036765 ATGTAGTTGCTTCCGGCGAA 60.037 50.0 9.3 0.0 45.43 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1572 1783 0.237498 GGAGCGGTGGTTTTTCTTCG 59.763 55.0 0.0 0.0 0.0 3.79 R
2274 2494 0.602905 ACGTAACAGGCACAGCTTCC 60.603 55.0 0.0 0.0 0.0 3.46 R
3110 3352 0.325933 CTTCACAGCCCATCAGTCCA 59.674 55.0 0.0 0.0 0.0 4.02 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
45 46 3.374402 CCACGCCTCACTCCGACT 61.374 66.667 0.00 0.00 0.00 4.18
50 51 2.795297 CCTCACTCCGACTCTCGC 59.205 66.667 0.00 0.00 38.82 5.03
55 56 3.213402 CTCCGACTCTCGCCCTCC 61.213 72.222 0.00 0.00 38.82 4.30
169 190 3.254617 GGACACCCCGAACCCCTT 61.255 66.667 0.00 0.00 0.00 3.95
174 195 2.609610 CCCCGAACCCCTTCCTCA 60.610 66.667 0.00 0.00 0.00 3.86
175 196 2.001269 CCCCGAACCCCTTCCTCAT 61.001 63.158 0.00 0.00 0.00 2.90
176 197 1.527370 CCCGAACCCCTTCCTCATC 59.473 63.158 0.00 0.00 0.00 2.92
178 199 1.144057 CGAACCCCTTCCTCATCCG 59.856 63.158 0.00 0.00 0.00 4.18
179 200 1.327690 CGAACCCCTTCCTCATCCGA 61.328 60.000 0.00 0.00 0.00 4.55
180 201 1.132500 GAACCCCTTCCTCATCCGAT 58.868 55.000 0.00 0.00 0.00 4.18
181 202 1.070914 GAACCCCTTCCTCATCCGATC 59.929 57.143 0.00 0.00 0.00 3.69
182 203 0.764752 ACCCCTTCCTCATCCGATCC 60.765 60.000 0.00 0.00 0.00 3.36
183 204 1.484444 CCCCTTCCTCATCCGATCCC 61.484 65.000 0.00 0.00 0.00 3.85
184 205 1.484444 CCCTTCCTCATCCGATCCCC 61.484 65.000 0.00 0.00 0.00 4.81
185 206 1.668294 CTTCCTCATCCGATCCCCG 59.332 63.158 0.00 0.00 38.18 5.73
186 207 2.441822 CTTCCTCATCCGATCCCCGC 62.442 65.000 0.00 0.00 36.84 6.13
187 208 2.919856 CCTCATCCGATCCCCGCT 60.920 66.667 0.00 0.00 36.84 5.52
188 209 2.653702 CTCATCCGATCCCCGCTC 59.346 66.667 0.00 0.00 36.84 5.03
189 210 2.917751 TCATCCGATCCCCGCTCC 60.918 66.667 0.00 0.00 36.84 4.70
190 211 4.008933 CATCCGATCCCCGCTCCC 62.009 72.222 0.00 0.00 36.84 4.30
191 212 4.241076 ATCCGATCCCCGCTCCCT 62.241 66.667 0.00 0.00 36.84 4.20
192 213 4.916314 TCCGATCCCCGCTCCCTC 62.916 72.222 0.00 0.00 36.84 4.30
238 259 2.601966 ATCGGATCCCCTCTCGCC 60.602 66.667 6.06 0.00 0.00 5.54
251 292 4.316823 TCGCCCACCCTCCTCTGT 62.317 66.667 0.00 0.00 0.00 3.41
253 294 2.284995 GCCCACCCTCCTCTGTCT 60.285 66.667 0.00 0.00 0.00 3.41
256 297 1.611851 CCACCCTCCTCTGTCTGCT 60.612 63.158 0.00 0.00 0.00 4.24
288 329 2.522638 GCCGATTAACCGCTCGTGG 61.523 63.158 0.00 0.00 33.11 4.94
289 330 1.153706 CCGATTAACCGCTCGTGGT 60.154 57.895 0.00 0.00 46.67 4.16
340 466 1.202256 GGGCGTATTAGTTTTGGCTGC 60.202 52.381 0.00 0.00 0.00 5.25
366 492 2.882927 TGCGCTCTTACGGTTATGAT 57.117 45.000 9.73 0.00 0.00 2.45
370 496 2.726760 CGCTCTTACGGTTATGATGCTC 59.273 50.000 0.00 0.00 0.00 4.26
371 497 3.717707 GCTCTTACGGTTATGATGCTCA 58.282 45.455 0.00 0.00 0.00 4.26
387 513 2.424601 TGCTCATCTGTAAATTGCTGCC 59.575 45.455 0.00 0.00 0.00 4.85
400 526 2.796651 CTGCCGCCTGAAATCAGC 59.203 61.111 4.87 0.65 42.47 4.26
410 536 2.211806 CTGAAATCAGCAGAGCTAGGC 58.788 52.381 0.00 0.91 36.40 3.93
412 538 2.211806 GAAATCAGCAGAGCTAGGCAG 58.788 52.381 11.25 3.79 36.40 4.85
438 564 3.112205 ATGCTGATCCTGCCCGGAC 62.112 63.158 0.73 0.00 46.80 4.79
448 574 0.172803 CTGCCCGGACTGTGTAGTAC 59.827 60.000 0.73 0.00 37.25 2.73
464 590 5.844914 GTGTAGTACGCAGTAATAGACGATG 59.155 44.000 9.00 0.00 44.94 3.84
474 600 3.503827 AATAGACGATGCGTTCACTGA 57.496 42.857 0.00 0.00 41.37 3.41
518 645 5.962433 TGTTACTCCTGCATAGTCTTGTAC 58.038 41.667 5.20 0.00 0.00 2.90
519 646 5.715279 TGTTACTCCTGCATAGTCTTGTACT 59.285 40.000 5.20 0.00 42.62 2.73
522 649 5.511363 ACTCCTGCATAGTCTTGTACTACT 58.489 41.667 0.00 0.00 43.47 2.57
526 653 5.299531 CCTGCATAGTCTTGTACTACTAGCA 59.700 44.000 16.58 16.58 43.47 3.49
539 666 5.024785 ACTACTAGCATAAAACAGCTCCC 57.975 43.478 0.00 0.00 42.05 4.30
540 667 3.283259 ACTAGCATAAAACAGCTCCCC 57.717 47.619 0.00 0.00 42.05 4.81
541 668 2.846827 ACTAGCATAAAACAGCTCCCCT 59.153 45.455 0.00 0.00 42.05 4.79
544 671 4.316025 AGCATAAAACAGCTCCCCTAAA 57.684 40.909 0.00 0.00 36.00 1.85
568 695 6.239217 TCTAATATTGCATCTGGACAGTGT 57.761 37.500 0.00 0.00 0.00 3.55
571 698 1.229975 TTGCATCTGGACAGTGTGCG 61.230 55.000 10.41 5.39 40.90 5.34
574 701 3.939837 ATCTGGACAGTGTGCGGCG 62.940 63.158 18.15 0.51 30.27 6.46
578 705 3.649986 GACAGTGTGCGGCGCTTT 61.650 61.111 33.26 12.60 35.42 3.51
589 716 1.822581 CGGCGCTTTTTATTACAGCC 58.177 50.000 7.64 0.00 39.68 4.85
609 738 8.732746 ACAGCCATCTAAAACGTCTTATATTT 57.267 30.769 0.00 0.00 0.00 1.40
611 740 7.587757 CAGCCATCTAAAACGTCTTATATTTGC 59.412 37.037 0.00 0.00 0.00 3.68
613 742 8.129211 GCCATCTAAAACGTCTTATATTTGCTT 58.871 33.333 0.00 0.00 0.00 3.91
621 750 7.108841 ACGTCTTATATTTGCTTACAGAGGA 57.891 36.000 0.00 0.00 0.00 3.71
623 752 7.707035 ACGTCTTATATTTGCTTACAGAGGAAG 59.293 37.037 0.00 0.00 37.01 3.46
654 785 7.701809 TTTGGTTTTTACGGATCAATTGTTC 57.298 32.000 5.13 6.65 0.00 3.18
669 800 8.599624 ATCAATTGTTCTAAATTCCCAGTCAT 57.400 30.769 5.13 0.00 0.00 3.06
676 807 7.942341 TGTTCTAAATTCCCAGTCATTTACAGT 59.058 33.333 0.00 0.00 0.00 3.55
710 843 5.195001 ACCACACACATCAATTTTACACC 57.805 39.130 0.00 0.00 0.00 4.16
715 848 5.221224 ACACACATCAATTTTACACCACTGG 60.221 40.000 0.00 0.00 0.00 4.00
730 863 4.984194 TGGACAAGTGTGCAGCTT 57.016 50.000 1.04 0.00 41.48 3.74
732 865 2.566833 TGGACAAGTGTGCAGCTTAT 57.433 45.000 1.04 0.00 41.48 1.73
733 866 2.153645 TGGACAAGTGTGCAGCTTATG 58.846 47.619 1.04 0.00 41.48 1.90
750 883 5.641709 GCTTATGCTTCCTTTACTGAAACC 58.358 41.667 0.00 0.00 36.03 3.27
751 884 5.416013 GCTTATGCTTCCTTTACTGAAACCT 59.584 40.000 0.00 0.00 36.03 3.50
752 885 6.623767 GCTTATGCTTCCTTTACTGAAACCTG 60.624 42.308 0.00 0.00 36.03 4.00
753 886 2.884639 TGCTTCCTTTACTGAAACCTGC 59.115 45.455 0.00 0.00 0.00 4.85
754 887 2.884639 GCTTCCTTTACTGAAACCTGCA 59.115 45.455 0.00 0.00 0.00 4.41
755 888 3.304726 GCTTCCTTTACTGAAACCTGCAC 60.305 47.826 0.00 0.00 0.00 4.57
756 889 2.489971 TCCTTTACTGAAACCTGCACG 58.510 47.619 0.00 0.00 0.00 5.34
757 890 1.069227 CCTTTACTGAAACCTGCACGC 60.069 52.381 0.00 0.00 0.00 5.34
758 891 0.948678 TTTACTGAAACCTGCACGCC 59.051 50.000 0.00 0.00 0.00 5.68
759 892 0.107831 TTACTGAAACCTGCACGCCT 59.892 50.000 0.00 0.00 0.00 5.52
760 893 0.320421 TACTGAAACCTGCACGCCTC 60.320 55.000 0.00 0.00 0.00 4.70
761 894 1.302033 CTGAAACCTGCACGCCTCT 60.302 57.895 0.00 0.00 0.00 3.69
762 895 0.037326 CTGAAACCTGCACGCCTCTA 60.037 55.000 0.00 0.00 0.00 2.43
763 896 0.037326 TGAAACCTGCACGCCTCTAG 60.037 55.000 0.00 0.00 0.00 2.43
764 897 1.362406 GAAACCTGCACGCCTCTAGC 61.362 60.000 0.00 0.00 38.52 3.42
765 898 1.831652 AAACCTGCACGCCTCTAGCT 61.832 55.000 0.00 0.00 40.39 3.32
766 899 0.970937 AACCTGCACGCCTCTAGCTA 60.971 55.000 0.00 0.00 40.39 3.32
767 900 1.066587 CCTGCACGCCTCTAGCTAC 59.933 63.158 0.00 0.00 40.39 3.58
768 901 1.066587 CTGCACGCCTCTAGCTACC 59.933 63.158 0.00 0.00 40.39 3.18
769 902 1.379977 TGCACGCCTCTAGCTACCT 60.380 57.895 0.00 0.00 40.39 3.08
770 903 1.066587 GCACGCCTCTAGCTACCTG 59.933 63.158 0.00 0.00 40.39 4.00
771 904 1.384989 GCACGCCTCTAGCTACCTGA 61.385 60.000 0.00 0.00 40.39 3.86
772 905 1.323412 CACGCCTCTAGCTACCTGAT 58.677 55.000 0.00 0.00 40.39 2.90
773 906 1.000827 CACGCCTCTAGCTACCTGATG 60.001 57.143 0.00 0.00 40.39 3.07
774 907 0.038709 CGCCTCTAGCTACCTGATGC 60.039 60.000 0.00 0.00 40.39 3.91
775 908 0.320050 GCCTCTAGCTACCTGATGCC 59.680 60.000 0.00 0.00 38.99 4.40
776 909 2.008242 CCTCTAGCTACCTGATGCCT 57.992 55.000 0.00 0.00 0.00 4.75
777 910 1.617850 CCTCTAGCTACCTGATGCCTG 59.382 57.143 0.00 0.00 0.00 4.85
778 911 2.315176 CTCTAGCTACCTGATGCCTGT 58.685 52.381 0.00 0.00 0.00 4.00
779 912 2.295909 CTCTAGCTACCTGATGCCTGTC 59.704 54.545 0.00 0.00 0.00 3.51
780 913 1.342819 CTAGCTACCTGATGCCTGTCC 59.657 57.143 0.00 0.00 0.00 4.02
781 914 1.227380 GCTACCTGATGCCTGTCCG 60.227 63.158 0.00 0.00 0.00 4.79
782 915 1.443407 CTACCTGATGCCTGTCCGG 59.557 63.158 0.00 0.00 0.00 5.14
783 916 2.032860 CTACCTGATGCCTGTCCGGG 62.033 65.000 0.00 0.00 0.00 5.73
784 917 4.181010 CCTGATGCCTGTCCGGGG 62.181 72.222 0.00 0.00 0.00 5.73
791 924 4.659172 CCTGTCCGGGGCTTGCAA 62.659 66.667 0.00 0.00 0.00 4.08
792 925 2.361610 CTGTCCGGGGCTTGCAAT 60.362 61.111 0.00 0.00 0.00 3.56
793 926 1.978617 CTGTCCGGGGCTTGCAATT 60.979 57.895 0.00 0.00 0.00 2.32
794 927 0.679640 CTGTCCGGGGCTTGCAATTA 60.680 55.000 0.00 0.00 0.00 1.40
795 928 0.251386 TGTCCGGGGCTTGCAATTAA 60.251 50.000 0.00 0.00 0.00 1.40
796 929 0.172578 GTCCGGGGCTTGCAATTAAC 59.827 55.000 0.00 0.00 0.00 2.01
797 930 0.251386 TCCGGGGCTTGCAATTAACA 60.251 50.000 0.00 0.00 0.00 2.41
798 931 0.823460 CCGGGGCTTGCAATTAACAT 59.177 50.000 0.00 0.00 0.00 2.71
799 932 1.206849 CCGGGGCTTGCAATTAACATT 59.793 47.619 0.00 0.00 0.00 2.71
800 933 2.428890 CCGGGGCTTGCAATTAACATTA 59.571 45.455 0.00 0.00 0.00 1.90
801 934 3.118956 CCGGGGCTTGCAATTAACATTAA 60.119 43.478 0.00 0.00 0.00 1.40
802 935 4.111916 CGGGGCTTGCAATTAACATTAAG 58.888 43.478 0.00 0.00 0.00 1.85
803 936 4.381505 CGGGGCTTGCAATTAACATTAAGT 60.382 41.667 0.00 0.00 0.00 2.24
804 937 5.487433 GGGGCTTGCAATTAACATTAAGTT 58.513 37.500 0.00 0.00 44.27 2.66
805 938 5.580691 GGGGCTTGCAATTAACATTAAGTTC 59.419 40.000 0.00 0.00 41.64 3.01
806 939 6.162777 GGGCTTGCAATTAACATTAAGTTCA 58.837 36.000 0.00 0.00 41.64 3.18
807 940 6.090763 GGGCTTGCAATTAACATTAAGTTCAC 59.909 38.462 0.00 0.00 41.64 3.18
808 941 6.868339 GGCTTGCAATTAACATTAAGTTCACT 59.132 34.615 0.00 0.00 41.64 3.41
809 942 7.148755 GGCTTGCAATTAACATTAAGTTCACTG 60.149 37.037 0.00 0.00 41.64 3.66
810 943 7.619982 GCTTGCAATTAACATTAAGTTCACTGC 60.620 37.037 0.00 0.00 41.64 4.40
817 950 1.234615 TTAAGTTCACTGCGCCTGCC 61.235 55.000 4.18 0.00 41.78 4.85
839 972 3.865745 CCTGTTTCTGAGCTATGTTACGG 59.134 47.826 0.00 0.00 0.00 4.02
850 983 3.997021 GCTATGTTACGGCTGCATATTCT 59.003 43.478 0.50 0.00 0.00 2.40
851 984 5.047306 AGCTATGTTACGGCTGCATATTCTA 60.047 40.000 0.50 0.00 34.82 2.10
852 985 5.289675 GCTATGTTACGGCTGCATATTCTAG 59.710 44.000 0.50 0.00 0.00 2.43
853 986 4.665833 TGTTACGGCTGCATATTCTAGT 57.334 40.909 0.50 0.00 0.00 2.57
855 988 5.769367 TGTTACGGCTGCATATTCTAGTAG 58.231 41.667 0.50 0.00 0.00 2.57
858 991 3.322254 ACGGCTGCATATTCTAGTAGCTT 59.678 43.478 0.50 0.00 42.17 3.74
859 992 4.523173 ACGGCTGCATATTCTAGTAGCTTA 59.477 41.667 0.50 0.00 42.17 3.09
862 1066 6.254589 CGGCTGCATATTCTAGTAGCTTATTC 59.745 42.308 0.50 0.00 42.17 1.75
871 1075 6.315091 TCTAGTAGCTTATTCACGGATCAC 57.685 41.667 0.00 0.00 0.00 3.06
892 1096 8.970859 ATCACTTATTCTAAATTCCCAGTCAG 57.029 34.615 0.00 0.00 0.00 3.51
895 1099 7.824289 CACTTATTCTAAATTCCCAGTCAGTCA 59.176 37.037 0.00 0.00 0.00 3.41
923 1129 1.225855 TGTGAAACCGCACAGCTTAG 58.774 50.000 0.00 0.00 43.35 2.18
936 1142 5.388475 CGCACAGCTTAGTTTTACACTACTG 60.388 44.000 0.00 0.00 37.74 2.74
962 1169 5.450818 AAGGGTGCAAGTTATGATTCCTA 57.549 39.130 0.00 0.00 0.00 2.94
967 1174 5.049129 GGTGCAAGTTATGATTCCTATGCTC 60.049 44.000 0.00 0.00 33.87 4.26
977 1184 2.113860 TCCTATGCTCAAACCTGCAC 57.886 50.000 0.00 0.00 42.26 4.57
978 1185 1.350684 TCCTATGCTCAAACCTGCACA 59.649 47.619 0.00 0.00 42.26 4.57
981 1188 1.180029 ATGCTCAAACCTGCACATCC 58.820 50.000 0.00 0.00 42.26 3.51
982 1189 1.236616 TGCTCAAACCTGCACATCCG 61.237 55.000 0.00 0.00 33.94 4.18
1008 1216 4.860907 GCTAAATTGCCTGTCATGAGTTTG 59.139 41.667 0.00 0.00 0.00 2.93
1017 1225 4.756642 CCTGTCATGAGTTTGCTGACTTTA 59.243 41.667 0.00 0.00 39.94 1.85
1021 1229 6.486320 TGTCATGAGTTTGCTGACTTTAATCA 59.514 34.615 0.00 0.00 39.94 2.57
1122 1330 3.347411 GCTCACCGCTTCGAACTAT 57.653 52.632 0.00 0.00 35.14 2.12
1125 1333 0.245266 TCACCGCTTCGAACTATGCA 59.755 50.000 7.73 0.00 0.00 3.96
1141 1349 2.821366 CATCTGCACCTGGTCCGC 60.821 66.667 0.00 0.00 0.00 5.54
1152 1360 2.182030 GGTCCGCCGAGAACTGAG 59.818 66.667 0.00 0.00 0.00 3.35
1158 1366 1.807573 GCCGAGAACTGAGCCTTCG 60.808 63.158 0.00 0.00 0.00 3.79
1233 1441 1.002868 GGCACTGCTGATGTCTGGT 60.003 57.895 0.00 0.00 0.00 4.00
1248 1456 0.321564 CTGGTCATTTCTCGGTGCCA 60.322 55.000 0.00 0.00 0.00 4.92
1258 1466 1.364626 CTCGGTGCCACAGAATGAGC 61.365 60.000 0.00 0.00 39.69 4.26
1265 1473 1.743091 GCCACAGAATGAGCCTGAGAG 60.743 57.143 0.00 0.00 39.69 3.20
1272 1480 2.548464 ATGAGCCTGAGAGTCTCCTT 57.452 50.000 17.57 0.35 0.00 3.36
1273 1481 1.554836 TGAGCCTGAGAGTCTCCTTG 58.445 55.000 17.57 6.95 0.00 3.61
1279 1487 2.634940 CCTGAGAGTCTCCTTGTGGAAA 59.365 50.000 17.57 0.00 42.66 3.13
1396 1607 1.275291 TGAAGGACGATGGTCTTGACC 59.725 52.381 12.54 12.54 42.97 4.02
1453 1664 3.106827 TCTGTTGATATGGAGCCTGACA 58.893 45.455 0.00 0.00 0.00 3.58
1471 1682 3.248630 AATGGGAACGCGTTGCACG 62.249 57.895 37.98 0.00 45.88 5.34
1494 1705 1.628846 GTTAGTCAGGCTGGGGAAGAA 59.371 52.381 15.73 0.00 0.00 2.52
1536 1747 1.957186 TTACAGTGCAACGGACGCC 60.957 57.895 0.00 0.00 45.86 5.68
1562 1773 0.461961 GAAGCTACCGAGAGTGCCAT 59.538 55.000 0.00 0.00 0.00 4.40
1563 1774 0.905357 AAGCTACCGAGAGTGCCATT 59.095 50.000 0.00 0.00 0.00 3.16
1572 1783 2.626840 GAGAGTGCCATTGAGAAGACC 58.373 52.381 0.00 0.00 0.00 3.85
1581 1792 4.023193 GCCATTGAGAAGACCGAAGAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
1585 1796 3.875134 TGAGAAGACCGAAGAAAAACCAC 59.125 43.478 0.00 0.00 0.00 4.16
1626 1837 4.494484 CTGTCACTGATTCGTCCAATGTA 58.506 43.478 0.00 0.00 0.00 2.29
1638 1849 0.451783 CCAATGTAGTTGCTTCCGGC 59.548 55.000 0.00 0.00 42.22 6.13
1641 1852 0.036765 ATGTAGTTGCTTCCGGCGAA 60.037 50.000 9.30 0.00 45.43 4.70
1677 1888 3.842925 TTCTGGAGCCCCACGCAAC 62.843 63.158 0.00 0.00 41.38 4.17
1707 1918 3.059325 GGCAGAAGCAACTTATATCGCTG 60.059 47.826 0.00 0.00 44.61 5.18
1722 1933 2.964911 GCTGTACAGGAGCGCTAAG 58.035 57.895 23.95 5.68 0.00 2.18
1761 1972 1.003959 TATCGTTGTGGCTGCTGCA 60.004 52.632 17.89 0.88 41.91 4.41
1962 2173 9.046296 GGTAGGTGATAGCATACATATATTTGC 57.954 37.037 4.58 4.58 35.34 3.68
1997 2208 3.921119 TTCGTGCTGCTTTCATCAAAT 57.079 38.095 0.00 0.00 0.00 2.32
2144 2358 7.150783 CTTAAAAGCTCTGCCTGTTATCTTT 57.849 36.000 0.00 0.00 0.00 2.52
2149 2363 5.320277 AGCTCTGCCTGTTATCTTTTCTTT 58.680 37.500 0.00 0.00 0.00 2.52
2163 2377 1.028905 TTCTTTTGTTGGCCGTCCAG 58.971 50.000 0.00 0.00 44.53 3.86
2217 2432 6.484288 TCAGATTCTTGCCTTTCTAATTCCA 58.516 36.000 0.00 0.00 0.00 3.53
2271 2491 6.633500 ATCATATGTTCATTTTACCCGTGG 57.367 37.500 1.90 0.00 0.00 4.94
2274 2494 3.992260 TGTTCATTTTACCCGTGGTTG 57.008 42.857 0.72 0.00 37.09 3.77
2275 2497 2.623889 TGTTCATTTTACCCGTGGTTGG 59.376 45.455 0.72 0.00 37.09 3.77
2307 2529 5.605327 CCTGTTACGTTTTGTTGTCTATCG 58.395 41.667 0.00 0.00 0.00 2.92
2355 2577 4.281182 TCTTGACTTCTGTAACTCCTGTCC 59.719 45.833 0.00 0.00 0.00 4.02
2377 2599 3.130516 CGAGTTGGTCTGTAGCCTATCAA 59.869 47.826 0.00 0.00 0.00 2.57
2403 2625 7.615582 ATTTCGCAGACATTTCTATTTCAGA 57.384 32.000 0.00 0.00 34.32 3.27
2441 2663 3.674753 GTGTCAATTTTGCACTACCATGC 59.325 43.478 0.00 0.00 46.32 4.06
2455 2677 2.632377 ACCATGCTCGGATTTACTGTG 58.368 47.619 0.00 0.00 0.00 3.66
2492 2714 8.289618 GCAGAGTTCTAATAAACATCAAACACA 58.710 33.333 0.00 0.00 0.00 3.72
2661 2884 7.124573 TGTATCCTGAAACTAGTGTATGCAT 57.875 36.000 3.79 3.79 0.00 3.96
2753 2976 3.136626 ACTCCTCCTGGGCATGTAAATAC 59.863 47.826 0.00 0.00 34.39 1.89
2791 3014 2.698274 GTTGCTTTCCCTCCTTTGGAAA 59.302 45.455 4.56 4.56 46.81 3.13
2837 3060 1.105457 TGCTGCTGCTTCAGTTTGTT 58.895 45.000 17.00 0.00 40.48 2.83
2890 3114 8.122952 CCGTGGATATTTTTATCTGTCTTGTTC 58.877 37.037 0.00 0.00 0.00 3.18
2957 3199 3.372206 TGCCGAATTTTTGGTTTGTGTTG 59.628 39.130 0.00 0.00 34.01 3.33
2964 3206 7.201600 CGAATTTTTGGTTTGTGTTGAAGGAAT 60.202 33.333 0.00 0.00 0.00 3.01
2969 3211 6.734104 TGGTTTGTGTTGAAGGAATTTTTG 57.266 33.333 0.00 0.00 0.00 2.44
2978 3220 8.040727 GTGTTGAAGGAATTTTTGGCCTATATT 58.959 33.333 3.32 0.00 0.00 1.28
2982 3224 8.421002 TGAAGGAATTTTTGGCCTATATTTAGC 58.579 33.333 3.32 0.00 0.00 3.09
2985 3227 7.015584 AGGAATTTTTGGCCTATATTTAGCTGG 59.984 37.037 3.32 0.00 0.00 4.85
2999 3241 4.871871 TTAGCTGGGATTACATTTGGGA 57.128 40.909 0.00 0.00 0.00 4.37
3000 3242 3.979501 AGCTGGGATTACATTTGGGAT 57.020 42.857 0.00 0.00 0.00 3.85
3001 3243 3.569491 AGCTGGGATTACATTTGGGATG 58.431 45.455 0.00 0.00 0.00 3.51
3002 3244 2.629617 GCTGGGATTACATTTGGGATGG 59.370 50.000 0.00 0.00 0.00 3.51
3003 3245 2.629617 CTGGGATTACATTTGGGATGGC 59.370 50.000 0.00 0.00 0.00 4.40
3004 3246 2.247111 TGGGATTACATTTGGGATGGCT 59.753 45.455 0.00 0.00 0.00 4.75
3005 3247 2.893489 GGGATTACATTTGGGATGGCTC 59.107 50.000 0.00 0.00 0.00 4.70
3006 3248 2.893489 GGATTACATTTGGGATGGCTCC 59.107 50.000 0.00 0.00 41.26 4.70
3007 3249 2.051334 TTACATTTGGGATGGCTCCG 57.949 50.000 0.00 0.00 43.11 4.63
3008 3250 0.182537 TACATTTGGGATGGCTCCGG 59.817 55.000 0.00 0.00 43.11 5.14
3009 3251 1.227102 CATTTGGGATGGCTCCGGA 59.773 57.895 2.93 2.93 43.11 5.14
3010 3252 0.178981 CATTTGGGATGGCTCCGGAT 60.179 55.000 3.57 0.00 43.11 4.18
3011 3253 0.111253 ATTTGGGATGGCTCCGGATC 59.889 55.000 3.57 0.00 43.11 3.36
3012 3254 0.988145 TTTGGGATGGCTCCGGATCT 60.988 55.000 3.57 0.00 43.11 2.75
3013 3255 1.699054 TTGGGATGGCTCCGGATCTG 61.699 60.000 3.57 0.00 43.11 2.90
3014 3256 2.746359 GGATGGCTCCGGATCTGG 59.254 66.667 15.09 15.09 0.00 3.86
3015 3257 2.143419 GGATGGCTCCGGATCTGGT 61.143 63.158 20.32 0.00 0.00 4.00
3016 3258 1.700042 GGATGGCTCCGGATCTGGTT 61.700 60.000 20.32 1.85 0.00 3.67
3017 3259 0.250081 GATGGCTCCGGATCTGGTTC 60.250 60.000 20.32 12.47 0.00 3.62
3018 3260 1.700042 ATGGCTCCGGATCTGGTTCC 61.700 60.000 20.32 20.24 0.00 3.62
3024 3266 4.986467 GGATCTGGTTCCGGCAAT 57.014 55.556 0.00 0.00 0.00 3.56
3025 3267 3.191182 GGATCTGGTTCCGGCAATT 57.809 52.632 0.00 0.00 0.00 2.32
3026 3268 2.341846 GGATCTGGTTCCGGCAATTA 57.658 50.000 0.00 0.00 0.00 1.40
3027 3269 2.650322 GGATCTGGTTCCGGCAATTAA 58.350 47.619 0.00 0.00 0.00 1.40
3028 3270 2.618709 GGATCTGGTTCCGGCAATTAAG 59.381 50.000 0.00 0.00 0.00 1.85
3029 3271 2.871096 TCTGGTTCCGGCAATTAAGT 57.129 45.000 0.00 0.00 0.00 2.24
3030 3272 3.149005 TCTGGTTCCGGCAATTAAGTT 57.851 42.857 0.00 0.00 0.00 2.66
3031 3273 3.078837 TCTGGTTCCGGCAATTAAGTTC 58.921 45.455 0.00 0.00 0.00 3.01
3032 3274 2.163613 CTGGTTCCGGCAATTAAGTTCC 59.836 50.000 0.00 0.00 0.00 3.62
3033 3275 1.131693 GGTTCCGGCAATTAAGTTCCG 59.868 52.381 7.02 7.02 41.41 4.30
3034 3276 1.808343 GTTCCGGCAATTAAGTTCCGT 59.192 47.619 12.69 0.00 40.23 4.69
3035 3277 2.188062 TCCGGCAATTAAGTTCCGTT 57.812 45.000 12.69 0.00 40.23 4.44
3036 3278 3.331478 TCCGGCAATTAAGTTCCGTTA 57.669 42.857 12.69 0.00 40.23 3.18
3037 3279 3.002102 TCCGGCAATTAAGTTCCGTTAC 58.998 45.455 12.69 0.00 40.23 2.50
3038 3280 2.743126 CCGGCAATTAAGTTCCGTTACA 59.257 45.455 12.69 0.00 40.23 2.41
3039 3281 3.425227 CCGGCAATTAAGTTCCGTTACAC 60.425 47.826 12.69 0.00 40.23 2.90
3040 3282 3.425227 CGGCAATTAAGTTCCGTTACACC 60.425 47.826 5.82 0.00 37.33 4.16
3041 3283 3.754850 GGCAATTAAGTTCCGTTACACCT 59.245 43.478 0.00 0.00 0.00 4.00
3042 3284 4.379082 GGCAATTAAGTTCCGTTACACCTG 60.379 45.833 0.00 0.00 0.00 4.00
3043 3285 4.379082 GCAATTAAGTTCCGTTACACCTGG 60.379 45.833 0.00 0.00 0.00 4.45
3044 3286 3.405823 TTAAGTTCCGTTACACCTGGG 57.594 47.619 0.00 0.00 0.00 4.45
3045 3287 1.134228 AAGTTCCGTTACACCTGGGT 58.866 50.000 0.00 0.00 0.00 4.51
3110 3352 1.538666 GGCCTGTTATCCATGGGCT 59.461 57.895 13.02 2.14 42.14 5.19
3141 3383 2.550855 GGCTGTGAAGACATGAAGACCA 60.551 50.000 0.00 0.00 0.00 4.02
3216 3458 4.507756 TGGCGATCAACTATGAAGATTTCG 59.492 41.667 0.00 0.00 39.49 3.46
3466 3709 1.477685 AACATCGTGTCCCCCGTCTT 61.478 55.000 0.00 0.00 0.00 3.01
3531 3775 0.035439 AGATCCGCCGGTTTTGACAT 60.035 50.000 1.63 0.00 0.00 3.06
3543 3787 3.004315 GGTTTTGACATCGACATTGGTGT 59.996 43.478 0.00 0.00 42.49 4.16
3603 3847 2.513897 GGCCCCTTCAATCGTCGG 60.514 66.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.277404 GAGGAGGAGGGCGAGAGT 59.723 66.667 0.00 0.00 0.00 3.24
45 46 2.598467 GAGAGGAGGAGGGCGAGA 59.402 66.667 0.00 0.00 0.00 4.04
50 51 3.368501 TGGGGGAGAGGAGGAGGG 61.369 72.222 0.00 0.00 0.00 4.30
55 56 1.275421 GGGAAAGTGGGGGAGAGGAG 61.275 65.000 0.00 0.00 0.00 3.69
155 175 2.933834 AGGAAGGGGTTCGGGGTG 60.934 66.667 0.00 0.00 0.00 4.61
156 176 2.609921 GAGGAAGGGGTTCGGGGT 60.610 66.667 0.00 0.00 0.00 4.95
161 181 1.070914 GATCGGATGAGGAAGGGGTTC 59.929 57.143 0.00 0.00 0.00 3.62
169 190 2.917751 GCGGGGATCGGATGAGGA 60.918 66.667 0.00 0.00 39.69 3.71
174 195 4.241076 AGGGAGCGGGGATCGGAT 62.241 66.667 0.00 0.00 39.69 4.18
175 196 4.916314 GAGGGAGCGGGGATCGGA 62.916 72.222 0.00 0.00 39.69 4.55
186 207 4.787280 AGAGTGGGCGGGAGGGAG 62.787 72.222 0.00 0.00 0.00 4.30
207 228 4.460683 CGATCGAAACCCCGGCCA 62.461 66.667 10.26 0.00 0.00 5.36
238 259 1.197430 AAGCAGACAGAGGAGGGTGG 61.197 60.000 0.00 0.00 0.00 4.61
240 261 0.907230 GGAAGCAGACAGAGGAGGGT 60.907 60.000 0.00 0.00 0.00 4.34
251 292 1.304962 TAGCTGGACGGGAAGCAGA 60.305 57.895 0.00 0.00 42.06 4.26
253 294 3.019003 GCTAGCTGGACGGGAAGCA 62.019 63.158 7.70 0.00 42.06 3.91
256 297 3.458163 CGGCTAGCTGGACGGGAA 61.458 66.667 19.01 0.00 33.56 3.97
299 340 2.131294 CTAGAATCCCGACCTCCGCG 62.131 65.000 0.00 0.00 36.84 6.46
300 341 1.660917 CTAGAATCCCGACCTCCGC 59.339 63.158 0.00 0.00 36.84 5.54
301 342 1.660917 GCTAGAATCCCGACCTCCG 59.339 63.158 0.00 0.00 38.18 4.63
304 345 1.833049 CCCGCTAGAATCCCGACCT 60.833 63.158 0.00 0.00 0.00 3.85
305 346 2.735237 CCCGCTAGAATCCCGACC 59.265 66.667 0.00 0.00 0.00 4.79
306 347 2.029221 GCCCGCTAGAATCCCGAC 59.971 66.667 0.00 0.00 0.00 4.79
307 348 2.963928 TACGCCCGCTAGAATCCCGA 62.964 60.000 0.00 0.00 0.00 5.14
340 466 1.154205 CCGTAAGAGCGCAATCCCAG 61.154 60.000 11.47 0.00 43.02 4.45
366 492 2.424601 GGCAGCAATTTACAGATGAGCA 59.575 45.455 0.00 0.00 0.00 4.26
370 496 1.831343 GCGGCAGCAATTTACAGATG 58.169 50.000 3.18 0.00 44.35 2.90
387 513 0.743701 AGCTCTGCTGATTTCAGGCG 60.744 55.000 9.49 0.00 43.94 5.52
400 526 2.733669 AGCTGGCTGCCTAGCTCTG 61.734 63.158 28.32 10.43 46.76 3.35
416 542 1.897615 GGGCAGGATCAGCATCAGC 60.898 63.158 10.94 0.00 42.56 4.26
417 543 1.597302 CGGGCAGGATCAGCATCAG 60.597 63.158 10.94 0.00 0.00 2.90
418 544 2.507452 CGGGCAGGATCAGCATCA 59.493 61.111 10.94 0.00 0.00 3.07
419 545 2.281345 CCGGGCAGGATCAGCATC 60.281 66.667 0.00 2.83 45.00 3.91
420 546 2.769621 TCCGGGCAGGATCAGCAT 60.770 61.111 0.91 0.00 45.98 3.79
438 564 5.006068 TCGTCTATTACTGCGTACTACACAG 59.994 44.000 3.14 3.14 34.62 3.66
449 575 3.061139 GTGAACGCATCGTCTATTACTGC 60.061 47.826 0.00 0.00 39.99 4.40
450 576 4.205181 CAGTGAACGCATCGTCTATTACTG 59.795 45.833 0.00 0.00 39.99 2.74
451 577 4.095932 TCAGTGAACGCATCGTCTATTACT 59.904 41.667 0.00 0.00 39.99 2.24
464 590 1.070309 CAGAGCAAGTTCAGTGAACGC 60.070 52.381 26.17 23.64 45.96 4.84
474 600 4.125703 CAGAGTTGAGAACAGAGCAAGTT 58.874 43.478 0.00 0.00 0.00 2.66
518 645 4.101741 AGGGGAGCTGTTTTATGCTAGTAG 59.898 45.833 0.00 0.00 39.91 2.57
519 646 4.037927 AGGGGAGCTGTTTTATGCTAGTA 58.962 43.478 0.00 0.00 39.91 1.82
522 649 5.444744 TTTAGGGGAGCTGTTTTATGCTA 57.555 39.130 0.00 0.00 39.91 3.49
539 666 8.853077 TGTCCAGATGCAATATTAGATTTAGG 57.147 34.615 0.00 0.00 0.00 2.69
540 667 9.499479 ACTGTCCAGATGCAATATTAGATTTAG 57.501 33.333 0.40 0.00 0.00 1.85
541 668 9.276590 CACTGTCCAGATGCAATATTAGATTTA 57.723 33.333 0.40 0.00 0.00 1.40
544 671 6.709397 CACACTGTCCAGATGCAATATTAGAT 59.291 38.462 0.40 0.00 0.00 1.98
553 680 1.668793 CGCACACTGTCCAGATGCA 60.669 57.895 20.23 0.00 41.07 3.96
568 695 1.466697 GCTGTAATAAAAAGCGCCGCA 60.467 47.619 13.36 0.00 0.00 5.69
571 698 2.931512 TGGCTGTAATAAAAAGCGCC 57.068 45.000 2.29 0.00 37.83 6.53
574 701 7.753580 ACGTTTTAGATGGCTGTAATAAAAAGC 59.246 33.333 0.00 0.00 31.99 3.51
575 702 9.274065 GACGTTTTAGATGGCTGTAATAAAAAG 57.726 33.333 0.00 0.00 33.74 2.27
576 703 9.005777 AGACGTTTTAGATGGCTGTAATAAAAA 57.994 29.630 0.00 0.00 28.90 1.94
577 704 8.556213 AGACGTTTTAGATGGCTGTAATAAAA 57.444 30.769 0.00 0.00 28.90 1.52
578 705 8.556213 AAGACGTTTTAGATGGCTGTAATAAA 57.444 30.769 0.00 0.00 31.16 1.40
633 764 9.634163 ATTTAGAACAATTGATCCGTAAAAACC 57.366 29.630 13.59 0.00 0.00 3.27
648 779 9.308000 TGTAAATGACTGGGAATTTAGAACAAT 57.692 29.630 0.00 0.00 30.84 2.71
669 800 5.123502 TGTGGTTTTCGCAGTTAACTGTAAA 59.876 36.000 30.90 26.54 45.45 2.01
676 807 2.747989 TGTGTGTGGTTTTCGCAGTTAA 59.252 40.909 0.00 0.00 36.43 2.01
685 816 6.536941 GGTGTAAAATTGATGTGTGTGGTTTT 59.463 34.615 0.00 0.00 0.00 2.43
691 822 5.221224 CCAGTGGTGTAAAATTGATGTGTGT 60.221 40.000 0.00 0.00 0.00 3.72
727 860 5.416013 AGGTTTCAGTAAAGGAAGCATAAGC 59.584 40.000 0.00 0.00 42.56 3.09
728 861 6.623767 GCAGGTTTCAGTAAAGGAAGCATAAG 60.624 42.308 0.00 0.00 0.00 1.73
729 862 5.183140 GCAGGTTTCAGTAAAGGAAGCATAA 59.817 40.000 0.00 0.00 0.00 1.90
730 863 4.700213 GCAGGTTTCAGTAAAGGAAGCATA 59.300 41.667 0.00 0.00 0.00 3.14
731 864 3.507622 GCAGGTTTCAGTAAAGGAAGCAT 59.492 43.478 0.00 0.00 0.00 3.79
732 865 2.884639 GCAGGTTTCAGTAAAGGAAGCA 59.115 45.455 0.00 0.00 0.00 3.91
733 866 2.884639 TGCAGGTTTCAGTAAAGGAAGC 59.115 45.455 0.00 0.00 0.00 3.86
734 867 3.058914 CGTGCAGGTTTCAGTAAAGGAAG 60.059 47.826 0.00 0.00 0.00 3.46
735 868 2.875933 CGTGCAGGTTTCAGTAAAGGAA 59.124 45.455 0.00 0.00 0.00 3.36
736 869 2.489971 CGTGCAGGTTTCAGTAAAGGA 58.510 47.619 0.00 0.00 0.00 3.36
737 870 1.069227 GCGTGCAGGTTTCAGTAAAGG 60.069 52.381 8.40 0.00 0.00 3.11
738 871 1.069227 GGCGTGCAGGTTTCAGTAAAG 60.069 52.381 8.40 0.00 0.00 1.85
739 872 0.948678 GGCGTGCAGGTTTCAGTAAA 59.051 50.000 8.40 0.00 0.00 2.01
740 873 0.107831 AGGCGTGCAGGTTTCAGTAA 59.892 50.000 8.40 0.00 0.00 2.24
741 874 0.320421 GAGGCGTGCAGGTTTCAGTA 60.320 55.000 8.40 0.00 0.00 2.74
742 875 1.598130 GAGGCGTGCAGGTTTCAGT 60.598 57.895 8.40 0.00 0.00 3.41
743 876 0.037326 TAGAGGCGTGCAGGTTTCAG 60.037 55.000 8.40 0.00 0.00 3.02
744 877 0.037326 CTAGAGGCGTGCAGGTTTCA 60.037 55.000 8.40 0.00 0.00 2.69
745 878 1.362406 GCTAGAGGCGTGCAGGTTTC 61.362 60.000 8.40 6.26 0.00 2.78
746 879 1.376037 GCTAGAGGCGTGCAGGTTT 60.376 57.895 8.40 0.00 0.00 3.27
747 880 2.266055 GCTAGAGGCGTGCAGGTT 59.734 61.111 8.40 0.00 0.00 3.50
756 889 0.320050 GGCATCAGGTAGCTAGAGGC 59.680 60.000 17.01 17.01 38.25 4.70
757 890 1.617850 CAGGCATCAGGTAGCTAGAGG 59.382 57.143 0.00 0.00 0.00 3.69
758 891 2.295909 GACAGGCATCAGGTAGCTAGAG 59.704 54.545 0.00 0.00 0.00 2.43
759 892 2.311463 GACAGGCATCAGGTAGCTAGA 58.689 52.381 0.00 0.00 0.00 2.43
760 893 1.342819 GGACAGGCATCAGGTAGCTAG 59.657 57.143 0.00 0.00 0.00 3.42
761 894 1.414158 GGACAGGCATCAGGTAGCTA 58.586 55.000 0.00 0.00 0.00 3.32
762 895 1.680522 CGGACAGGCATCAGGTAGCT 61.681 60.000 0.00 0.00 0.00 3.32
763 896 1.227380 CGGACAGGCATCAGGTAGC 60.227 63.158 0.00 0.00 0.00 3.58
764 897 1.443407 CCGGACAGGCATCAGGTAG 59.557 63.158 0.00 0.00 0.00 3.18
765 898 2.063979 CCCGGACAGGCATCAGGTA 61.064 63.158 0.73 0.00 39.21 3.08
766 899 3.402681 CCCGGACAGGCATCAGGT 61.403 66.667 0.73 0.00 39.21 4.00
767 900 4.181010 CCCCGGACAGGCATCAGG 62.181 72.222 0.73 1.71 39.21 3.86
774 907 3.944250 ATTGCAAGCCCCGGACAGG 62.944 63.158 0.73 0.00 40.63 4.00
775 908 0.679640 TAATTGCAAGCCCCGGACAG 60.680 55.000 0.73 0.00 0.00 3.51
776 909 0.251386 TTAATTGCAAGCCCCGGACA 60.251 50.000 0.73 0.00 0.00 4.02
777 910 0.172578 GTTAATTGCAAGCCCCGGAC 59.827 55.000 0.73 0.00 0.00 4.79
778 911 0.251386 TGTTAATTGCAAGCCCCGGA 60.251 50.000 0.73 0.00 0.00 5.14
779 912 0.823460 ATGTTAATTGCAAGCCCCGG 59.177 50.000 4.94 0.00 0.00 5.73
780 913 2.671130 AATGTTAATTGCAAGCCCCG 57.329 45.000 4.94 0.00 0.00 5.73
781 914 5.084818 ACTTAATGTTAATTGCAAGCCCC 57.915 39.130 4.94 0.00 0.00 5.80
782 915 6.090763 GTGAACTTAATGTTAATTGCAAGCCC 59.909 38.462 4.94 0.00 39.30 5.19
783 916 6.868339 AGTGAACTTAATGTTAATTGCAAGCC 59.132 34.615 4.94 0.00 39.30 4.35
784 917 7.619982 GCAGTGAACTTAATGTTAATTGCAAGC 60.620 37.037 4.94 0.00 46.20 4.01
785 918 7.409661 CGCAGTGAACTTAATGTTAATTGCAAG 60.410 37.037 4.94 0.00 46.86 4.01
786 919 6.362016 CGCAGTGAACTTAATGTTAATTGCAA 59.638 34.615 0.00 0.00 46.86 4.08
787 920 5.855925 CGCAGTGAACTTAATGTTAATTGCA 59.144 36.000 15.95 0.00 46.86 4.08
788 921 5.220024 GCGCAGTGAACTTAATGTTAATTGC 60.220 40.000 0.30 10.19 44.56 3.56
789 922 5.286082 GGCGCAGTGAACTTAATGTTAATTG 59.714 40.000 10.83 0.00 39.30 2.32
790 923 5.183140 AGGCGCAGTGAACTTAATGTTAATT 59.817 36.000 10.83 0.00 39.30 1.40
791 924 4.700213 AGGCGCAGTGAACTTAATGTTAAT 59.300 37.500 10.83 0.00 39.30 1.40
792 925 4.069304 AGGCGCAGTGAACTTAATGTTAA 58.931 39.130 10.83 0.00 39.30 2.01
793 926 3.435327 CAGGCGCAGTGAACTTAATGTTA 59.565 43.478 10.83 0.00 39.30 2.41
794 927 2.226437 CAGGCGCAGTGAACTTAATGTT 59.774 45.455 10.83 0.00 42.38 2.71
795 928 1.806542 CAGGCGCAGTGAACTTAATGT 59.193 47.619 10.83 0.00 0.00 2.71
796 929 1.466360 GCAGGCGCAGTGAACTTAATG 60.466 52.381 10.83 0.00 38.36 1.90
797 930 0.804989 GCAGGCGCAGTGAACTTAAT 59.195 50.000 10.83 0.00 38.36 1.40
798 931 1.234615 GGCAGGCGCAGTGAACTTAA 61.235 55.000 10.83 0.00 41.24 1.85
799 932 1.671054 GGCAGGCGCAGTGAACTTA 60.671 57.895 10.83 0.00 41.24 2.24
800 933 2.980233 GGCAGGCGCAGTGAACTT 60.980 61.111 10.83 0.00 41.24 2.66
806 939 4.586235 AAACAGGGCAGGCGCAGT 62.586 61.111 10.83 5.84 41.24 4.40
807 940 3.741476 GAAACAGGGCAGGCGCAG 61.741 66.667 10.83 1.27 41.24 5.18
808 941 4.269523 AGAAACAGGGCAGGCGCA 62.270 61.111 10.83 0.00 41.24 6.09
809 942 3.741476 CAGAAACAGGGCAGGCGC 61.741 66.667 0.00 0.00 37.44 6.53
810 943 2.032528 TCAGAAACAGGGCAGGCG 59.967 61.111 0.00 0.00 0.00 5.52
817 950 3.865745 CCGTAACATAGCTCAGAAACAGG 59.134 47.826 0.00 0.00 0.00 4.00
839 972 7.201393 CGTGAATAAGCTACTAGAATATGCAGC 60.201 40.741 0.00 0.00 0.00 5.25
850 983 6.710597 AAGTGATCCGTGAATAAGCTACTA 57.289 37.500 0.00 0.00 0.00 1.82
851 984 5.599999 AAGTGATCCGTGAATAAGCTACT 57.400 39.130 0.00 0.00 0.00 2.57
852 985 7.868415 AGAATAAGTGATCCGTGAATAAGCTAC 59.132 37.037 0.00 0.00 0.00 3.58
853 986 7.952671 AGAATAAGTGATCCGTGAATAAGCTA 58.047 34.615 0.00 0.00 0.00 3.32
855 988 8.589335 TTAGAATAAGTGATCCGTGAATAAGC 57.411 34.615 0.00 0.00 0.00 3.09
859 992 9.057089 GGAATTTAGAATAAGTGATCCGTGAAT 57.943 33.333 0.00 0.00 0.00 2.57
862 1066 6.765989 TGGGAATTTAGAATAAGTGATCCGTG 59.234 38.462 0.00 0.00 0.00 4.94
871 1075 7.824289 TGTGACTGACTGGGAATTTAGAATAAG 59.176 37.037 0.00 0.00 0.00 1.73
884 1088 1.971357 AGTTACCTGTGACTGACTGGG 59.029 52.381 0.00 0.00 45.82 4.45
906 1112 1.961793 AACTAAGCTGTGCGGTTTCA 58.038 45.000 0.00 0.00 34.65 2.69
923 1129 5.506815 GCACCCTTTTCCAGTAGTGTAAAAC 60.507 44.000 0.00 0.00 30.68 2.43
936 1142 5.405935 AATCATAACTTGCACCCTTTTCC 57.594 39.130 0.00 0.00 0.00 3.13
962 1169 1.180029 GGATGTGCAGGTTTGAGCAT 58.820 50.000 0.00 0.00 43.44 3.79
967 1174 0.447801 GCTACGGATGTGCAGGTTTG 59.552 55.000 0.00 0.00 0.00 2.93
977 1184 3.206150 ACAGGCAATTTAGCTACGGATG 58.794 45.455 0.00 0.00 34.17 3.51
978 1185 3.118408 TGACAGGCAATTTAGCTACGGAT 60.118 43.478 0.00 0.00 34.17 4.18
981 1188 3.871006 TCATGACAGGCAATTTAGCTACG 59.129 43.478 0.00 0.00 34.17 3.51
982 1189 4.878397 ACTCATGACAGGCAATTTAGCTAC 59.122 41.667 0.00 0.00 34.17 3.58
1008 1216 5.730010 GCTGCAGAGATTGATTAAAGTCAGC 60.730 44.000 20.43 0.00 35.89 4.26
1017 1225 3.054582 TCTTCCAGCTGCAGAGATTGATT 60.055 43.478 20.43 0.00 0.00 2.57
1021 1229 2.421670 CCATCTTCCAGCTGCAGAGATT 60.422 50.000 20.43 0.00 0.00 2.40
1125 1333 4.101448 GGCGGACCAGGTGCAGAT 62.101 66.667 12.28 0.00 35.26 2.90
1141 1349 1.153745 CCGAAGGCTCAGTTCTCGG 60.154 63.158 8.50 8.50 46.14 4.63
1158 1366 2.896443 CCTTCAGCCTCCTCGTCC 59.104 66.667 0.00 0.00 0.00 4.79
1233 1441 0.684535 TCTGTGGCACCGAGAAATGA 59.315 50.000 16.26 0.00 0.00 2.57
1248 1456 2.818921 AGACTCTCAGGCTCATTCTGT 58.181 47.619 0.00 0.00 34.15 3.41
1258 1466 1.930251 TCCACAAGGAGACTCTCAGG 58.070 55.000 8.35 2.27 42.68 3.86
1265 1473 5.153950 AGTATCAGTTTCCACAAGGAGAC 57.846 43.478 0.00 0.00 46.74 3.36
1272 1480 6.461648 GCTCTATGCTAGTATCAGTTTCCACA 60.462 42.308 0.00 0.00 38.95 4.17
1273 1481 5.923684 GCTCTATGCTAGTATCAGTTTCCAC 59.076 44.000 0.00 0.00 38.95 4.02
1279 1487 2.490115 GCCGCTCTATGCTAGTATCAGT 59.510 50.000 0.00 0.00 40.11 3.41
1419 1630 6.071165 CCATATCAACAGAGGAAAGGCTTTTT 60.071 38.462 14.66 5.79 0.00 1.94
1453 1664 2.642700 GTGCAACGCGTTCCCATT 59.357 55.556 23.92 0.00 0.00 3.16
1471 1682 1.198759 TCCCCAGCCTGACTAACACC 61.199 60.000 0.00 0.00 0.00 4.16
1473 1684 0.984230 CTTCCCCAGCCTGACTAACA 59.016 55.000 0.00 0.00 0.00 2.41
1494 1705 4.383880 CCAGATGATGAGAATGTGACTGGT 60.384 45.833 0.00 0.00 37.95 4.00
1500 1711 6.036844 CACTGTAACCAGATGATGAGAATGTG 59.963 42.308 0.00 0.00 41.50 3.21
1536 1747 2.420722 ACTCTCGGTAGCTTCTTTCTCG 59.579 50.000 0.00 0.00 0.00 4.04
1562 1773 4.334481 GTGGTTTTTCTTCGGTCTTCTCAA 59.666 41.667 0.00 0.00 0.00 3.02
1563 1774 3.875134 GTGGTTTTTCTTCGGTCTTCTCA 59.125 43.478 0.00 0.00 0.00 3.27
1572 1783 0.237498 GGAGCGGTGGTTTTTCTTCG 59.763 55.000 0.00 0.00 0.00 3.79
1581 1792 1.208535 TCGATATTTTGGAGCGGTGGT 59.791 47.619 0.00 0.00 0.00 4.16
1585 1796 1.202651 AGGGTCGATATTTTGGAGCGG 60.203 52.381 0.00 0.00 0.00 5.52
1638 1849 1.075425 CGTCAGGCTTGCTCTCTTCG 61.075 60.000 0.00 0.00 0.00 3.79
1641 1852 1.476007 AACCGTCAGGCTTGCTCTCT 61.476 55.000 0.00 0.00 42.76 3.10
1677 1888 2.186160 TTGCTTCTGCCACCACACG 61.186 57.895 0.00 0.00 38.71 4.49
1707 1918 1.335496 CTCTCCTTAGCGCTCCTGTAC 59.665 57.143 16.34 0.00 0.00 2.90
1761 1972 2.815945 CGCCATCCCCATCAGAGCT 61.816 63.158 0.00 0.00 0.00 4.09
1962 2173 7.855545 AGCAGCACGAATAATAGTTTAAGATG 58.144 34.615 0.00 0.00 0.00 2.90
1967 2178 7.603963 TGAAAGCAGCACGAATAATAGTTTA 57.396 32.000 0.00 0.00 0.00 2.01
1979 2190 4.232221 AGAAATTTGATGAAAGCAGCACG 58.768 39.130 0.00 0.00 40.65 5.34
1997 2208 9.658799 CTATGATCTACCTGAACAAAAGAGAAA 57.341 33.333 0.00 0.00 31.27 2.52
2085 2299 4.380841 ACATGCATGGTTCATCAATCAC 57.619 40.909 29.41 0.00 0.00 3.06
2144 2358 1.028905 CTGGACGGCCAACAAAAGAA 58.971 50.000 13.37 0.00 45.41 2.52
2149 2363 3.637911 ATAATACTGGACGGCCAACAA 57.362 42.857 13.37 0.00 45.41 2.83
2163 2377 9.856488 TTCCTCGCAATACTATCAGAATAATAC 57.144 33.333 0.00 0.00 0.00 1.89
2217 2432 6.891388 TGATCCAACAACCCGTAATACTATT 58.109 36.000 0.00 0.00 0.00 1.73
2248 2466 6.126409 ACCACGGGTAAAATGAACATATGAT 58.874 36.000 10.38 0.00 32.11 2.45
2267 2485 2.639286 GCACAGCTTCCAACCACG 59.361 61.111 0.00 0.00 0.00 4.94
2271 2491 1.266989 GTAACAGGCACAGCTTCCAAC 59.733 52.381 0.00 0.00 0.00 3.77
2274 2494 0.602905 ACGTAACAGGCACAGCTTCC 60.603 55.000 0.00 0.00 0.00 3.46
2275 2497 1.226746 AACGTAACAGGCACAGCTTC 58.773 50.000 0.00 0.00 0.00 3.86
2307 2529 9.852091 GATATCTTGGAAATTCTGGCAATATTC 57.148 33.333 0.00 0.00 0.00 1.75
2355 2577 2.688446 TGATAGGCTACAGACCAACTCG 59.312 50.000 0.00 0.00 0.00 4.18
2361 2583 5.504173 GCGAAATTTTGATAGGCTACAGACC 60.504 44.000 9.75 0.00 0.00 3.85
2377 2599 8.514594 TCTGAAATAGAAATGTCTGCGAAATTT 58.485 29.630 0.00 6.45 32.78 1.82
2416 2638 6.676950 CATGGTAGTGCAAAATTGACACTAA 58.323 36.000 21.12 13.30 42.98 2.24
2417 2639 5.335583 GCATGGTAGTGCAAAATTGACACTA 60.336 40.000 18.13 18.13 44.43 2.74
2418 2640 4.559300 GCATGGTAGTGCAAAATTGACACT 60.559 41.667 19.49 19.49 44.43 3.55
2441 2663 2.416547 CAGTTGGCACAGTAAATCCGAG 59.583 50.000 0.00 0.00 42.39 4.63
2455 2677 1.002544 AGAACTCTGCTACCAGTTGGC 59.997 52.381 0.00 0.00 40.09 4.52
2492 2714 8.463930 TGGTTGATTCTCTGAAAAGTAAACAT 57.536 30.769 0.00 0.00 0.00 2.71
2575 2797 3.976701 ATTTCCGTGAGCAGCCGGG 62.977 63.158 2.18 0.00 44.32 5.73
2582 2804 1.009829 AATCGAGCATTTCCGTGAGC 58.990 50.000 0.00 0.00 0.00 4.26
2661 2884 1.474320 CGGCATCGGGTATTTCTCCAA 60.474 52.381 0.00 0.00 0.00 3.53
2791 3014 1.770324 CTGGCCAAGGAGGGACTTT 59.230 57.895 7.01 0.00 41.55 2.66
2837 3060 2.895404 ACGGAAGAAGTTACAGTGGCTA 59.105 45.455 0.00 0.00 0.00 3.93
2890 3114 2.160813 GTGTATACAAACTGCAACCCGG 59.839 50.000 7.25 0.00 0.00 5.73
2930 3172 2.524569 ACCAAAAATTCGGCACCAAG 57.475 45.000 0.00 0.00 0.00 3.61
2932 3174 2.093447 ACAAACCAAAAATTCGGCACCA 60.093 40.909 0.00 0.00 0.00 4.17
2957 3199 8.642432 AGCTAAATATAGGCCAAAAATTCCTTC 58.358 33.333 5.01 0.00 0.00 3.46
2964 3206 5.772004 TCCCAGCTAAATATAGGCCAAAAA 58.228 37.500 5.01 0.00 0.00 1.94
2969 3211 6.062258 TGTAATCCCAGCTAAATATAGGCC 57.938 41.667 0.00 0.00 0.00 5.19
2978 3220 4.871871 TCCCAAATGTAATCCCAGCTAA 57.128 40.909 0.00 0.00 0.00 3.09
2982 3224 2.629617 GCCATCCCAAATGTAATCCCAG 59.370 50.000 0.00 0.00 0.00 4.45
2985 3227 2.893489 GGAGCCATCCCAAATGTAATCC 59.107 50.000 0.00 0.00 40.03 3.01
2999 3241 1.700042 GGAACCAGATCCGGAGCCAT 61.700 60.000 17.84 0.00 0.00 4.40
3000 3242 2.367202 GGAACCAGATCCGGAGCCA 61.367 63.158 17.84 0.00 0.00 4.75
3001 3243 2.506472 GGAACCAGATCCGGAGCC 59.494 66.667 17.84 7.36 0.00 4.70
3007 3249 2.341846 TAATTGCCGGAACCAGATCC 57.658 50.000 5.05 0.00 36.05 3.36
3008 3250 3.279434 ACTTAATTGCCGGAACCAGATC 58.721 45.455 5.05 0.00 0.00 2.75
3009 3251 3.366052 ACTTAATTGCCGGAACCAGAT 57.634 42.857 5.05 0.00 0.00 2.90
3010 3252 2.871096 ACTTAATTGCCGGAACCAGA 57.129 45.000 5.05 0.00 0.00 3.86
3011 3253 2.163613 GGAACTTAATTGCCGGAACCAG 59.836 50.000 5.05 0.00 0.00 4.00
3012 3254 2.164338 GGAACTTAATTGCCGGAACCA 58.836 47.619 5.05 0.00 0.00 3.67
3013 3255 1.131693 CGGAACTTAATTGCCGGAACC 59.868 52.381 5.05 0.00 40.08 3.62
3014 3256 2.537639 CGGAACTTAATTGCCGGAAC 57.462 50.000 5.05 0.00 40.08 3.62
3019 3261 3.754850 AGGTGTAACGGAACTTAATTGCC 59.245 43.478 0.00 0.00 38.12 4.52
3020 3262 4.379082 CCAGGTGTAACGGAACTTAATTGC 60.379 45.833 0.00 0.00 38.12 3.56
3021 3263 4.155280 CCCAGGTGTAACGGAACTTAATTG 59.845 45.833 0.00 0.00 38.12 2.32
3022 3264 4.202493 ACCCAGGTGTAACGGAACTTAATT 60.202 41.667 0.00 0.00 38.12 1.40
3023 3265 3.328637 ACCCAGGTGTAACGGAACTTAAT 59.671 43.478 0.00 0.00 38.12 1.40
3024 3266 2.705127 ACCCAGGTGTAACGGAACTTAA 59.295 45.455 0.00 0.00 38.12 1.85
3025 3267 2.037511 CACCCAGGTGTAACGGAACTTA 59.962 50.000 8.75 0.00 40.91 2.24
3026 3268 1.134228 ACCCAGGTGTAACGGAACTT 58.866 50.000 0.00 0.00 38.12 2.66
3027 3269 0.395312 CACCCAGGTGTAACGGAACT 59.605 55.000 8.75 0.00 40.91 3.01
3028 3270 1.232621 GCACCCAGGTGTAACGGAAC 61.233 60.000 17.82 0.00 46.90 3.62
3029 3271 1.071814 GCACCCAGGTGTAACGGAA 59.928 57.895 17.82 0.00 46.90 4.30
3030 3272 1.823169 GAGCACCCAGGTGTAACGGA 61.823 60.000 17.82 0.00 46.90 4.69
3031 3273 1.375523 GAGCACCCAGGTGTAACGG 60.376 63.158 17.82 0.00 46.90 4.44
3032 3274 1.375523 GGAGCACCCAGGTGTAACG 60.376 63.158 17.82 0.00 46.90 3.18
3033 3275 4.716003 GGAGCACCCAGGTGTAAC 57.284 61.111 17.82 9.43 46.90 2.50
3043 3285 2.266055 CCTCAACGAGGGAGCACC 59.734 66.667 1.84 0.00 45.43 5.01
3051 3293 0.612174 TCCAGGACTCCCTCAACGAG 60.612 60.000 0.00 0.00 42.02 4.18
3052 3294 0.898789 GTCCAGGACTCCCTCAACGA 60.899 60.000 12.94 0.00 42.02 3.85
3110 3352 0.325933 CTTCACAGCCCATCAGTCCA 59.674 55.000 0.00 0.00 0.00 4.02
3141 3383 3.705051 TCCGGACACAGGTATAGTCTTT 58.295 45.455 0.00 0.00 32.98 2.52
3216 3458 7.859875 GGTTACATAGAGTCGGTTACATAGAAC 59.140 40.741 4.88 0.00 0.00 3.01
3531 3775 4.819088 TCTCAATGAAAACACCAATGTCGA 59.181 37.500 0.00 0.00 38.45 4.20


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

AutoCloner maintained by Alex Coulton.