Multiple sequence alignment - TraesCS4B01G008200

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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 TraesCS4B01G008200 chr4B 100.000 3329 0 0 1 3329 5454819 5458147 0.000000e+00 6148.0
1 TraesCS4B01G008200 chr4B 91.726 701 56 2 1 701 146681732 146682430 0.000000e+00 972.0
2 TraesCS4B01G008200 chr4B 87.705 122 15 0 700 821 300265363 300265484 3.460000e-30 143.0
3 TraesCS4B01G008200 chr4B 100.000 42 0 0 2989 3030 5457765 5457806 9.900000e-11 78.7
4 TraesCS4B01G008200 chr4B 100.000 42 0 0 2947 2988 5457807 5457848 9.900000e-11 78.7
5 TraesCS4B01G008200 chr4D 87.436 2149 173 46 891 2991 3601026 3598927 0.000000e+00 2383.0
6 TraesCS4B01G008200 chr4D 91.298 701 57 4 1 701 351701889 351701193 0.000000e+00 953.0
7 TraesCS4B01G008200 chr4D 96.746 338 11 0 2991 3328 3598969 3598632 6.230000e-157 564.0
8 TraesCS4B01G008200 chr4D 92.135 89 5 2 741 829 291527369 291527283 1.250000e-24 124.0
9 TraesCS4B01G008200 chr4D 88.889 90 9 1 730 819 235713110 235713022 3.510000e-20 110.0
10 TraesCS4B01G008200 chr4A 83.843 1962 159 73 840 2747 601039787 601041644 0.000000e+00 1722.0
11 TraesCS4B01G008200 chr4A 94.375 320 14 2 3009 3328 601041755 601042070 3.860000e-134 488.0
12 TraesCS4B01G008200 chr6D 92.275 699 50 4 3 701 9476549 9475855 0.000000e+00 989.0
13 TraesCS4B01G008200 chr6D 86.777 121 13 3 709 828 124743381 124743263 7.490000e-27 132.0
14 TraesCS4B01G008200 chr3D 91.785 706 45 6 4 701 407214573 407213873 0.000000e+00 970.0
15 TraesCS4B01G008200 chr2D 91.465 703 56 3 1 701 89921426 89920726 0.000000e+00 963.0
16 TraesCS4B01G008200 chr2D 88.372 129 14 1 700 828 348420 348293 1.600000e-33 154.0
17 TraesCS4B01G008200 chr2D 100.000 29 0 0 2897 2925 617975719 617975691 2.000000e-03 54.7
18 TraesCS4B01G008200 chr7B 91.298 701 58 3 1 701 72517636 72518333 0.000000e+00 953.0
19 TraesCS4B01G008200 chr2A 90.728 701 63 2 1 701 592369024 592369722 0.000000e+00 933.0
20 TraesCS4B01G008200 chr7D 90.442 701 64 3 1 701 182494937 182494240 0.000000e+00 920.0
21 TraesCS4B01G008200 chr3B 90.442 701 63 4 1 701 385394290 385393594 0.000000e+00 920.0
22 TraesCS4B01G008200 chr3B 81.857 700 117 10 3 698 819844898 819845591 6.190000e-162 580.0
23 TraesCS4B01G008200 chr3B 85.057 87 11 2 3148 3233 42917250 42917335 1.650000e-13 87.9
24 TraesCS4B01G008200 chr3B 82.796 93 16 0 700 792 345431573 345431665 2.130000e-12 84.2
25 TraesCS4B01G008200 chr2B 87.597 129 15 1 700 828 797083461 797083334 7.440000e-32 148.0
26 TraesCS4B01G008200 chr2B 83.186 113 19 0 700 812 168062602 168062714 1.630000e-18 104.0
27 TraesCS4B01G008200 chr3A 87.302 126 15 1 700 825 561758799 561758923 3.460000e-30 143.0
28 TraesCS4B01G008200 chr5D 87.500 72 6 2 705 774 164590860 164590930 2.750000e-11 80.5


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 TraesCS4B01G008200 chr4B 5454819 5458147 3328 False 2101.8 6148 100.000 1 3329 3 chr4B.!!$F3 3328
1 TraesCS4B01G008200 chr4B 146681732 146682430 698 False 972.0 972 91.726 1 701 1 chr4B.!!$F1 700
2 TraesCS4B01G008200 chr4D 3598632 3601026 2394 True 1473.5 2383 92.091 891 3328 2 chr4D.!!$R4 2437
3 TraesCS4B01G008200 chr4D 351701193 351701889 696 True 953.0 953 91.298 1 701 1 chr4D.!!$R3 700
4 TraesCS4B01G008200 chr4A 601039787 601042070 2283 False 1105.0 1722 89.109 840 3328 2 chr4A.!!$F1 2488
5 TraesCS4B01G008200 chr6D 9475855 9476549 694 True 989.0 989 92.275 3 701 1 chr6D.!!$R1 698
6 TraesCS4B01G008200 chr3D 407213873 407214573 700 True 970.0 970 91.785 4 701 1 chr3D.!!$R1 697
7 TraesCS4B01G008200 chr2D 89920726 89921426 700 True 963.0 963 91.465 1 701 1 chr2D.!!$R2 700
8 TraesCS4B01G008200 chr7B 72517636 72518333 697 False 953.0 953 91.298 1 701 1 chr7B.!!$F1 700
9 TraesCS4B01G008200 chr2A 592369024 592369722 698 False 933.0 933 90.728 1 701 1 chr2A.!!$F1 700
10 TraesCS4B01G008200 chr7D 182494240 182494937 697 True 920.0 920 90.442 1 701 1 chr7D.!!$R1 700
11 TraesCS4B01G008200 chr3B 385393594 385394290 696 True 920.0 920 90.442 1 701 1 chr3B.!!$R1 700
12 TraesCS4B01G008200 chr3B 819844898 819845591 693 False 580.0 580 81.857 3 698 1 chr3B.!!$F3 695

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
706 721 0.031721 AGTCCAAGTCGGTTGTCGTC 59.968 55.0 0.00 0.00 40.32 4.20 F
959 974 0.040351 ACTGGAGAGCAGGCTCAGTA 59.960 55.0 22.12 7.47 44.99 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1768 1838 0.250166 CCCCGTCTTTTTCTGGTCGT 60.250 55.0 0.0 0.0 0.00 4.34 R
2775 2921 0.177141 TGAAACTCGGCCCGAATAGG 59.823 55.0 7.5 0.0 34.74 2.57 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
87 88 3.469008 TCCACGGCTTCCACATTATAG 57.531 47.619 0.00 0.00 0.00 1.31
98 99 7.013655 GGCTTCCACATTATAGTCATGTCAAAT 59.986 37.037 0.00 0.00 32.25 2.32
151 152 7.496920 TCTTGATCATGGTCTTCACATCAATAC 59.503 37.037 7.64 0.00 37.37 1.89
157 158 4.081142 TGGTCTTCACATCAATACGTCCAT 60.081 41.667 0.00 0.00 0.00 3.41
160 161 5.812642 GTCTTCACATCAATACGTCCATTCT 59.187 40.000 0.00 0.00 0.00 2.40
195 196 3.131755 CACATACTCTGATGCAGACTGGA 59.868 47.826 4.26 0.73 35.39 3.86
196 197 3.966006 ACATACTCTGATGCAGACTGGAT 59.034 43.478 9.49 9.49 35.39 3.41
230 231 2.104132 CGACGATGCACATCCGGA 59.896 61.111 6.61 6.61 34.40 5.14
293 298 4.946157 TCGAAAAGATAGGTTACGGTCTCT 59.054 41.667 0.00 0.00 0.00 3.10
387 392 2.738521 CAGAACTGCACCGACCGG 60.739 66.667 6.94 6.94 42.03 5.28
405 410 2.364324 CCGGTTGAGCAGGCTACTATTA 59.636 50.000 0.00 0.00 0.00 0.98
507 512 9.506018 TTGATATTCACTTTGTTCATGAGAAGA 57.494 29.630 17.31 5.74 33.63 2.87
540 545 0.606401 AGTTCGGGTGCTCCATGTTG 60.606 55.000 7.20 0.00 34.36 3.33
552 557 3.397482 CTCCATGTTGCTACTATGGCTC 58.603 50.000 18.00 0.00 40.87 4.70
611 617 8.353423 ACTAAGCCATTTCAAGACATACATTT 57.647 30.769 0.00 0.00 0.00 2.32
614 620 7.230849 AGCCATTTCAAGACATACATTTCAA 57.769 32.000 0.00 0.00 0.00 2.69
616 622 7.762615 AGCCATTTCAAGACATACATTTCAATG 59.237 33.333 0.00 0.00 42.10 2.82
617 623 7.010738 GCCATTTCAAGACATACATTTCAATGG 59.989 37.037 4.58 0.00 40.70 3.16
701 716 3.064931 GTTTCCTAGTCCAAGTCGGTTG 58.935 50.000 0.00 0.00 35.57 3.77
702 717 2.005370 TCCTAGTCCAAGTCGGTTGT 57.995 50.000 0.00 0.00 33.87 3.32
703 718 1.891150 TCCTAGTCCAAGTCGGTTGTC 59.109 52.381 0.00 0.00 33.87 3.18
704 719 1.402456 CCTAGTCCAAGTCGGTTGTCG 60.402 57.143 0.00 0.00 40.90 4.35
705 720 1.268899 CTAGTCCAAGTCGGTTGTCGT 59.731 52.381 0.00 0.00 40.32 4.34
706 721 0.031721 AGTCCAAGTCGGTTGTCGTC 59.968 55.000 0.00 0.00 40.32 4.20
707 722 0.942884 GTCCAAGTCGGTTGTCGTCC 60.943 60.000 0.00 0.00 40.32 4.79
709 724 2.355481 AAGTCGGTTGTCGTCCGC 60.355 61.111 0.00 0.00 46.49 5.54
710 725 2.853290 AAGTCGGTTGTCGTCCGCT 61.853 57.895 0.00 0.00 46.49 5.52
711 726 1.518056 AAGTCGGTTGTCGTCCGCTA 61.518 55.000 0.00 0.00 46.49 4.26
712 727 1.138247 GTCGGTTGTCGTCCGCTAT 59.862 57.895 0.00 0.00 46.49 2.97
713 728 0.864797 GTCGGTTGTCGTCCGCTATC 60.865 60.000 0.00 0.00 46.49 2.08
714 729 1.028330 TCGGTTGTCGTCCGCTATCT 61.028 55.000 0.00 0.00 46.49 1.98
715 730 0.866061 CGGTTGTCGTCCGCTATCTG 60.866 60.000 0.00 0.00 41.48 2.90
716 731 0.454600 GGTTGTCGTCCGCTATCTGA 59.545 55.000 0.00 0.00 0.00 3.27
717 732 1.546834 GTTGTCGTCCGCTATCTGAC 58.453 55.000 0.00 0.00 0.00 3.51
723 738 4.513519 CCGCTATCTGACGGCAAA 57.486 55.556 0.00 0.00 43.44 3.68
724 739 2.301505 CCGCTATCTGACGGCAAAG 58.698 57.895 0.00 0.00 43.44 2.77
725 740 1.638467 CGCTATCTGACGGCAAAGC 59.362 57.895 9.34 9.34 0.00 3.51
726 741 0.807667 CGCTATCTGACGGCAAAGCT 60.808 55.000 15.56 0.00 0.00 3.74
727 742 1.373570 GCTATCTGACGGCAAAGCTT 58.626 50.000 11.61 0.00 0.00 3.74
728 743 1.740025 GCTATCTGACGGCAAAGCTTT 59.260 47.619 5.69 5.69 0.00 3.51
729 744 2.162408 GCTATCTGACGGCAAAGCTTTT 59.838 45.455 9.53 0.00 0.00 2.27
730 745 3.366374 GCTATCTGACGGCAAAGCTTTTT 60.366 43.478 9.53 0.00 0.00 1.94
753 768 3.376546 TCTGCTAGCAGACGGCAA 58.623 55.556 37.64 19.05 46.80 4.52
754 769 1.671166 TCTGCTAGCAGACGGCAAA 59.329 52.632 37.64 18.34 46.80 3.68
755 770 0.390340 TCTGCTAGCAGACGGCAAAG 60.390 55.000 37.64 15.06 46.80 2.77
756 771 2.769270 TCTGCTAGCAGACGGCAAAGA 61.769 52.381 37.64 17.11 46.80 2.52
757 772 4.241416 TCTGCTAGCAGACGGCAAAGAA 62.241 50.000 37.64 16.20 46.80 2.52
761 776 1.576421 GCAGACGGCAAAGAAGTGG 59.424 57.895 0.00 0.00 43.97 4.00
762 777 1.576421 CAGACGGCAAAGAAGTGGC 59.424 57.895 0.00 0.00 40.55 5.01
763 778 0.886490 CAGACGGCAAAGAAGTGGCT 60.886 55.000 0.00 0.00 41.74 4.75
764 779 0.886490 AGACGGCAAAGAAGTGGCTG 60.886 55.000 0.00 0.00 41.74 4.85
765 780 0.884704 GACGGCAAAGAAGTGGCTGA 60.885 55.000 0.00 0.00 41.74 4.26
766 781 0.250901 ACGGCAAAGAAGTGGCTGAT 60.251 50.000 0.00 0.00 41.74 2.90
767 782 0.169672 CGGCAAAGAAGTGGCTGATG 59.830 55.000 0.00 0.00 41.74 3.07
768 783 0.529378 GGCAAAGAAGTGGCTGATGG 59.471 55.000 0.00 0.00 40.77 3.51
769 784 1.251251 GCAAAGAAGTGGCTGATGGT 58.749 50.000 0.00 0.00 0.00 3.55
770 785 2.436417 GCAAAGAAGTGGCTGATGGTA 58.564 47.619 0.00 0.00 0.00 3.25
771 786 2.819608 GCAAAGAAGTGGCTGATGGTAA 59.180 45.455 0.00 0.00 0.00 2.85
772 787 3.255642 GCAAAGAAGTGGCTGATGGTAAA 59.744 43.478 0.00 0.00 0.00 2.01
773 788 4.082026 GCAAAGAAGTGGCTGATGGTAAAT 60.082 41.667 0.00 0.00 0.00 1.40
774 789 5.404946 CAAAGAAGTGGCTGATGGTAAATG 58.595 41.667 0.00 0.00 0.00 2.32
775 790 4.307032 AGAAGTGGCTGATGGTAAATGT 57.693 40.909 0.00 0.00 0.00 2.71
776 791 4.012374 AGAAGTGGCTGATGGTAAATGTG 58.988 43.478 0.00 0.00 0.00 3.21
777 792 3.719268 AGTGGCTGATGGTAAATGTGA 57.281 42.857 0.00 0.00 0.00 3.58
778 793 4.240881 AGTGGCTGATGGTAAATGTGAT 57.759 40.909 0.00 0.00 0.00 3.06
779 794 4.202441 AGTGGCTGATGGTAAATGTGATC 58.798 43.478 0.00 0.00 0.00 2.92
780 795 4.080129 AGTGGCTGATGGTAAATGTGATCT 60.080 41.667 0.00 0.00 0.00 2.75
781 796 4.641989 GTGGCTGATGGTAAATGTGATCTT 59.358 41.667 0.00 0.00 0.00 2.40
782 797 5.126061 GTGGCTGATGGTAAATGTGATCTTT 59.874 40.000 0.00 0.00 0.00 2.52
783 798 5.125900 TGGCTGATGGTAAATGTGATCTTTG 59.874 40.000 0.00 0.00 0.00 2.77
784 799 5.039333 GCTGATGGTAAATGTGATCTTTGC 58.961 41.667 0.00 0.00 0.00 3.68
785 800 5.581126 TGATGGTAAATGTGATCTTTGCC 57.419 39.130 6.21 6.21 38.43 4.52
788 803 5.581126 TGGTAAATGTGATCTTTGCCATC 57.419 39.130 10.43 0.00 41.51 3.51
789 804 5.015515 TGGTAAATGTGATCTTTGCCATCA 58.984 37.500 10.43 0.00 41.51 3.07
790 805 5.125900 TGGTAAATGTGATCTTTGCCATCAG 59.874 40.000 10.43 0.00 41.51 2.90
791 806 3.795623 AATGTGATCTTTGCCATCAGC 57.204 42.857 0.00 0.00 44.14 4.26
792 807 1.466856 TGTGATCTTTGCCATCAGCC 58.533 50.000 0.00 0.00 42.71 4.85
793 808 1.272037 TGTGATCTTTGCCATCAGCCA 60.272 47.619 0.00 0.00 42.71 4.75
794 809 1.404391 GTGATCTTTGCCATCAGCCAG 59.596 52.381 0.00 0.00 42.71 4.85
795 810 1.005097 TGATCTTTGCCATCAGCCAGT 59.995 47.619 0.00 0.00 42.71 4.00
796 811 2.097825 GATCTTTGCCATCAGCCAGTT 58.902 47.619 0.00 0.00 42.71 3.16
797 812 1.999648 TCTTTGCCATCAGCCAGTTT 58.000 45.000 0.00 0.00 42.71 2.66
798 813 2.318908 TCTTTGCCATCAGCCAGTTTT 58.681 42.857 0.00 0.00 42.71 2.43
799 814 2.699846 TCTTTGCCATCAGCCAGTTTTT 59.300 40.909 0.00 0.00 42.71 1.94
830 845 2.861462 TTTTTGGAAGCTGACGGTTG 57.139 45.000 0.00 0.00 0.00 3.77
831 846 1.757682 TTTTGGAAGCTGACGGTTGT 58.242 45.000 0.00 0.00 0.00 3.32
832 847 2.623878 TTTGGAAGCTGACGGTTGTA 57.376 45.000 0.00 0.00 0.00 2.41
833 848 1.873698 TTGGAAGCTGACGGTTGTAC 58.126 50.000 0.00 0.00 0.00 2.90
834 849 0.753867 TGGAAGCTGACGGTTGTACA 59.246 50.000 0.00 0.00 0.00 2.90
835 850 1.346395 TGGAAGCTGACGGTTGTACAT 59.654 47.619 0.00 0.00 0.00 2.29
836 851 1.732259 GGAAGCTGACGGTTGTACATG 59.268 52.381 0.00 0.00 0.00 3.21
837 852 2.413837 GAAGCTGACGGTTGTACATGT 58.586 47.619 2.69 2.69 0.00 3.21
838 853 2.080286 AGCTGACGGTTGTACATGTC 57.920 50.000 0.00 13.54 0.00 3.06
849 864 5.548406 GGTTGTACATGTCCTAACAGAGTT 58.452 41.667 0.00 0.00 39.20 3.01
959 974 0.040351 ACTGGAGAGCAGGCTCAGTA 59.960 55.000 22.12 7.47 44.99 2.74
1110 1134 1.398958 GCTCTCTCTCCGGATGCCTT 61.399 60.000 3.57 0.00 0.00 4.35
1161 1185 0.684805 CCTACTGCCTCTTCTCCGGT 60.685 60.000 0.00 0.00 0.00 5.28
1162 1186 1.409802 CCTACTGCCTCTTCTCCGGTA 60.410 57.143 0.00 0.00 0.00 4.02
1190 1214 3.771160 CCGCCGGAAGCAGGTACT 61.771 66.667 5.05 0.00 44.04 2.73
1193 1217 3.003113 GCCGGAAGCAGGTACTCGT 62.003 63.158 5.05 0.00 42.97 4.18
1194 1218 1.153823 CCGGAAGCAGGTACTCGTG 60.154 63.158 0.00 0.00 34.60 4.35
1242 1266 0.459237 CTTCCGCGAGCAAGATCTGT 60.459 55.000 8.23 0.00 0.00 3.41
1258 1286 5.186198 AGATCTGTCCGGGTTTTAGATTTG 58.814 41.667 0.00 0.00 0.00 2.32
1285 1313 2.417787 GGTTCAGATTTTGGGCTGATGC 60.418 50.000 0.00 0.00 40.51 3.91
1327 1361 3.501950 GTGTTAACCTGCTAAATGCTGC 58.498 45.455 2.48 0.00 43.37 5.25
1341 1375 3.616956 ATGCTGCTGAAACTGTAGCTA 57.383 42.857 15.92 0.00 40.37 3.32
1363 1407 6.292596 GCTAGAATTCAGTTCTTAATCCTGCG 60.293 42.308 8.44 0.00 44.80 5.18
1371 1415 4.452455 AGTTCTTAATCCTGCGTTGAGTTG 59.548 41.667 0.00 0.00 0.00 3.16
1372 1416 4.002906 TCTTAATCCTGCGTTGAGTTGT 57.997 40.909 0.00 0.00 0.00 3.32
1386 1430 3.728845 TGAGTTGTCAGTTGAGGCTAAC 58.271 45.455 0.00 0.00 0.00 2.34
1392 1436 1.156736 CAGTTGAGGCTAACGTTGGG 58.843 55.000 11.99 4.87 35.73 4.12
1413 1466 3.698040 GGACACATTCAGATGCTGGATTT 59.302 43.478 0.00 0.00 36.72 2.17
1417 1470 4.398358 CACATTCAGATGCTGGATTTCTGT 59.602 41.667 0.00 0.00 38.39 3.41
1430 1483 6.219417 TGGATTTCTGTGTGATGTTTTGTT 57.781 33.333 0.00 0.00 0.00 2.83
1438 1491 9.868277 TTCTGTGTGATGTTTTGTTTTTAATCT 57.132 25.926 0.00 0.00 0.00 2.40
1439 1492 9.868277 TCTGTGTGATGTTTTGTTTTTAATCTT 57.132 25.926 0.00 0.00 0.00 2.40
1440 1493 9.904647 CTGTGTGATGTTTTGTTTTTAATCTTG 57.095 29.630 0.00 0.00 0.00 3.02
1466 1519 9.478019 GTGTAAGAACATAGACAAATCGAATTG 57.522 33.333 11.66 11.66 38.08 2.32
1477 1530 6.484643 AGACAAATCGAATTGGGATGATACTG 59.515 38.462 17.14 0.00 34.56 2.74
1490 1543 4.811557 GGATGATACTGTTCCTGCAAGTAC 59.188 45.833 0.00 0.00 0.00 2.73
1492 1545 3.580895 TGATACTGTTCCTGCAAGTACCA 59.419 43.478 0.00 0.00 0.00 3.25
1533 1586 4.143543 TGAGATTTGATGGTTGCAGACAA 58.856 39.130 0.00 0.00 0.00 3.18
1554 1607 4.866508 ACCGAGATTGTTCTGAACTGTA 57.133 40.909 20.18 7.41 30.30 2.74
1567 1620 7.703621 TGTTCTGAACTGTACACTGTTAAGTAC 59.296 37.037 20.18 14.26 37.47 2.73
1571 1630 9.557338 CTGAACTGTACACTGTTAAGTACTATC 57.443 37.037 0.00 0.00 40.84 2.08
1581 1640 6.116711 TGTTAAGTACTATCAAACTGCCCA 57.883 37.500 0.00 0.00 0.00 5.36
1591 1650 4.365514 TCAAACTGCCCACTTTGATCTA 57.634 40.909 0.00 0.00 32.62 1.98
1604 1663 6.713903 CCACTTTGATCTATGATAGGCATTGT 59.286 38.462 0.00 0.00 38.44 2.71
1608 1667 5.563592 TGATCTATGATAGGCATTGTTGGG 58.436 41.667 0.00 0.00 38.44 4.12
1613 1672 2.240921 TGATAGGCATTGTTGGGCTACA 59.759 45.455 0.00 0.00 44.77 2.74
1614 1673 2.889170 TAGGCATTGTTGGGCTACAA 57.111 45.000 7.88 7.88 41.81 2.41
1632 1693 9.654663 GGGCTACAATCTCGATAAGTATAAAAT 57.345 33.333 0.00 0.00 0.00 1.82
1656 1717 5.674525 TGACATTTATTCCTGCGAGAATCT 58.325 37.500 4.44 0.00 37.62 2.40
1666 1727 4.705507 TCCTGCGAGAATCTAGTGTTACTT 59.294 41.667 0.00 0.00 0.00 2.24
1683 1752 8.041323 AGTGTTACTTGTATCTTCCATGGTTAG 58.959 37.037 12.58 10.73 0.00 2.34
1687 1756 7.016153 ACTTGTATCTTCCATGGTTAGACAA 57.984 36.000 12.58 15.50 0.00 3.18
1688 1757 7.633789 ACTTGTATCTTCCATGGTTAGACAAT 58.366 34.615 12.58 4.38 0.00 2.71
1690 1759 7.194112 TGTATCTTCCATGGTTAGACAATCA 57.806 36.000 12.58 10.01 0.00 2.57
1695 1764 5.102953 TCCATGGTTAGACAATCAAGAGG 57.897 43.478 12.58 0.00 0.00 3.69
1739 1809 3.073062 AGTTGTGTACTTTCCTGCAGGAT 59.927 43.478 35.42 23.21 44.98 3.24
1750 1820 1.698532 CCTGCAGGATGAAGCTAGGAT 59.301 52.381 29.88 0.00 41.90 3.24
1766 1836 1.050988 GGATAGGGCTGGAGAGTGCA 61.051 60.000 0.00 0.00 0.00 4.57
1767 1837 1.055040 GATAGGGCTGGAGAGTGCAT 58.945 55.000 0.00 0.00 0.00 3.96
1768 1838 2.251818 GATAGGGCTGGAGAGTGCATA 58.748 52.381 0.00 0.00 0.00 3.14
1769 1839 1.414158 TAGGGCTGGAGAGTGCATAC 58.586 55.000 0.00 0.00 0.00 2.39
1778 1848 2.094182 GGAGAGTGCATACGACCAGAAA 60.094 50.000 0.00 0.00 0.00 2.52
1824 1903 0.685097 TACAAGGCGGCAAAGAGACT 59.315 50.000 13.08 0.00 0.00 3.24
1847 1926 3.325753 GGTGGTCCTGCTCCTGCT 61.326 66.667 0.00 0.00 40.48 4.24
1848 1927 2.046507 GTGGTCCTGCTCCTGCTG 60.047 66.667 0.00 0.00 40.48 4.41
1849 1928 4.025858 TGGTCCTGCTCCTGCTGC 62.026 66.667 0.00 0.00 40.48 5.25
1850 1929 4.792804 GGTCCTGCTCCTGCTGCC 62.793 72.222 0.00 0.00 40.48 4.85
1895 1989 1.585651 GGTCTGGAGGAGGAGGAGGA 61.586 65.000 0.00 0.00 0.00 3.71
1898 1992 1.547755 TGGAGGAGGAGGAGGAGGT 60.548 63.158 0.00 0.00 0.00 3.85
2014 2108 4.342951 CGGGGAATGTCCTGTGTTACTATA 59.657 45.833 0.00 0.00 36.57 1.31
2115 2209 2.270352 ATTTCAACGTGCTTCTGGGA 57.730 45.000 0.00 0.00 0.00 4.37
2127 2221 0.687757 TTCTGGGAGCTGCCGTCTAT 60.688 55.000 20.39 0.00 37.63 1.98
2223 2317 4.715523 CCCGCTTCCAGGCCGAAA 62.716 66.667 0.00 0.00 0.00 3.46
2239 2333 2.325761 CGAAACCAACTCCTGTAGACG 58.674 52.381 0.00 0.00 0.00 4.18
2240 2334 2.030540 CGAAACCAACTCCTGTAGACGA 60.031 50.000 0.00 0.00 0.00 4.20
2244 2338 0.456312 CAACTCCTGTAGACGACGCC 60.456 60.000 0.00 0.00 0.00 5.68
2338 2432 3.491104 GCGTTCGGACTGAATTAGAGGAT 60.491 47.826 0.00 0.00 39.21 3.24
2360 2454 4.989279 ATTTCAATGCCTTGCGAGTTAT 57.011 36.364 0.00 0.00 32.11 1.89
2361 2455 7.094805 GGATATTTCAATGCCTTGCGAGTTATA 60.095 37.037 0.00 0.00 32.11 0.98
2369 2463 4.517453 TGCCTTGCGAGTTATACTGTTTTT 59.483 37.500 0.00 0.00 0.00 1.94
2370 2464 5.086727 GCCTTGCGAGTTATACTGTTTTTC 58.913 41.667 0.00 0.00 0.00 2.29
2371 2465 5.628134 CCTTGCGAGTTATACTGTTTTTCC 58.372 41.667 0.00 0.00 0.00 3.13
2432 2526 9.543783 AGTTCTATTTCTTGTTTTCGAGTAAGT 57.456 29.630 0.00 0.00 33.26 2.24
2442 2536 1.517257 CGAGTAAGTGGCAGGAGCG 60.517 63.158 0.00 0.00 43.41 5.03
2443 2537 1.890894 GAGTAAGTGGCAGGAGCGA 59.109 57.895 0.00 0.00 43.41 4.93
2474 2570 8.713708 ATATTAGAAGTAGATGGTGCTACAGT 57.286 34.615 0.00 0.00 42.47 3.55
2485 2581 5.873179 TGGTGCTACAGTTATTTACAAGC 57.127 39.130 0.00 0.00 32.82 4.01
2486 2582 5.309638 TGGTGCTACAGTTATTTACAAGCA 58.690 37.500 0.00 0.00 37.11 3.91
2488 2584 5.642063 GGTGCTACAGTTATTTACAAGCAGA 59.358 40.000 0.00 0.00 38.85 4.26
2499 2595 9.624697 GTTATTTACAAGCAGACATTTGAATGA 57.375 29.630 10.48 0.00 39.67 2.57
2535 2632 6.595772 CACTATTTCTGTGCAAGATACCTC 57.404 41.667 0.00 0.00 33.93 3.85
2541 2638 2.932614 CTGTGCAAGATACCTCGGAAAG 59.067 50.000 0.00 0.00 0.00 2.62
2556 2653 4.710324 TCGGAAAGTCCACATTTACTTGT 58.290 39.130 0.00 0.00 35.91 3.16
2559 2656 5.390567 CGGAAAGTCCACATTTACTTGTAGC 60.391 44.000 0.00 0.00 35.91 3.58
2562 2659 4.579869 AGTCCACATTTACTTGTAGCTGG 58.420 43.478 0.00 0.00 0.00 4.85
2575 2672 2.107378 TGTAGCTGGTGGTTGGATTTGA 59.893 45.455 0.00 0.00 0.00 2.69
2637 2734 2.159234 GCTTTCAACAGCAGCAGACTAG 59.841 50.000 0.00 0.00 39.83 2.57
2639 2736 0.036952 TCAACAGCAGCAGACTAGGC 60.037 55.000 0.00 0.00 0.00 3.93
2714 2811 5.220854 CCTGTTTTCAGTTCATGTTCGAAGT 60.221 40.000 0.00 0.00 45.68 3.01
2724 2821 6.202954 AGTTCATGTTCGAAGTAACTTTCCTG 59.797 38.462 0.00 0.00 0.00 3.86
2735 2832 5.308825 AGTAACTTTCCTGTGTGAATCTGG 58.691 41.667 0.00 0.00 0.00 3.86
2747 2893 2.027745 GTGAATCTGGGAAGCTCACTGA 60.028 50.000 0.00 0.00 34.80 3.41
2750 2896 2.550830 TCTGGGAAGCTCACTGAAAC 57.449 50.000 0.00 0.00 0.00 2.78
2751 2897 1.072331 TCTGGGAAGCTCACTGAAACC 59.928 52.381 0.00 0.00 0.00 3.27
2752 2898 1.072965 CTGGGAAGCTCACTGAAACCT 59.927 52.381 0.00 0.00 0.00 3.50
2753 2899 2.303022 CTGGGAAGCTCACTGAAACCTA 59.697 50.000 0.00 0.00 0.00 3.08
2754 2900 2.912956 TGGGAAGCTCACTGAAACCTAT 59.087 45.455 0.00 0.00 0.00 2.57
2755 2901 3.274288 GGGAAGCTCACTGAAACCTATG 58.726 50.000 0.00 0.00 0.00 2.23
2756 2902 3.307762 GGGAAGCTCACTGAAACCTATGT 60.308 47.826 0.00 0.00 0.00 2.29
2757 2903 4.327680 GGAAGCTCACTGAAACCTATGTT 58.672 43.478 0.00 0.00 35.82 2.71
2768 2914 4.846779 AAACCTATGTTTCGTTGTGCAT 57.153 36.364 0.00 0.00 40.68 3.96
2769 2915 5.950758 AAACCTATGTTTCGTTGTGCATA 57.049 34.783 0.00 0.00 40.68 3.14
2770 2916 6.509418 AAACCTATGTTTCGTTGTGCATAT 57.491 33.333 0.00 0.00 40.68 1.78
2771 2917 6.509418 AACCTATGTTTCGTTGTGCATATT 57.491 33.333 0.00 0.00 0.00 1.28
2772 2918 6.119144 ACCTATGTTTCGTTGTGCATATTC 57.881 37.500 0.00 0.00 0.00 1.75
2773 2919 5.645929 ACCTATGTTTCGTTGTGCATATTCA 59.354 36.000 0.00 0.00 0.00 2.57
2774 2920 6.183360 ACCTATGTTTCGTTGTGCATATTCAG 60.183 38.462 0.00 0.00 0.00 3.02
2775 2921 3.820689 TGTTTCGTTGTGCATATTCAGC 58.179 40.909 0.00 0.00 0.00 4.26
2776 2922 3.171277 GTTTCGTTGTGCATATTCAGCC 58.829 45.455 0.00 0.00 0.00 4.85
2777 2923 2.401583 TCGTTGTGCATATTCAGCCT 57.598 45.000 0.00 0.00 0.00 4.58
2778 2924 3.535280 TCGTTGTGCATATTCAGCCTA 57.465 42.857 0.00 0.00 0.00 3.93
2779 2925 4.071961 TCGTTGTGCATATTCAGCCTAT 57.928 40.909 0.00 0.00 0.00 2.57
2780 2926 4.450976 TCGTTGTGCATATTCAGCCTATT 58.549 39.130 0.00 0.00 0.00 1.73
2781 2927 4.511454 TCGTTGTGCATATTCAGCCTATTC 59.489 41.667 0.00 0.00 0.00 1.75
2782 2928 4.609113 CGTTGTGCATATTCAGCCTATTCG 60.609 45.833 0.00 0.00 0.00 3.34
2783 2929 3.402110 TGTGCATATTCAGCCTATTCGG 58.598 45.455 0.00 0.00 0.00 4.30
2784 2930 2.744202 GTGCATATTCAGCCTATTCGGG 59.256 50.000 0.00 0.00 0.00 5.14
2791 2937 2.504519 GCCTATTCGGGCCGAGTT 59.495 61.111 29.05 21.92 45.92 3.01
2792 2938 1.153229 GCCTATTCGGGCCGAGTTT 60.153 57.895 29.05 19.46 45.92 2.66
2793 2939 1.158484 GCCTATTCGGGCCGAGTTTC 61.158 60.000 29.05 14.21 45.92 2.78
2794 2940 0.177141 CCTATTCGGGCCGAGTTTCA 59.823 55.000 29.05 14.85 37.14 2.69
2795 2941 1.571919 CTATTCGGGCCGAGTTTCAG 58.428 55.000 29.05 16.53 37.14 3.02
2796 2942 0.177141 TATTCGGGCCGAGTTTCAGG 59.823 55.000 29.05 0.00 37.14 3.86
2797 2943 1.550130 ATTCGGGCCGAGTTTCAGGA 61.550 55.000 29.30 12.24 37.14 3.86
2798 2944 1.550130 TTCGGGCCGAGTTTCAGGAT 61.550 55.000 29.30 0.00 37.14 3.24
2837 2983 8.486210 ACCTCACTTTAAGTTATGATGCTGATA 58.514 33.333 0.00 0.00 0.00 2.15
2903 3050 6.438425 AGTTTCATGGCAAATCAAATACTCCT 59.562 34.615 0.00 0.00 0.00 3.69
2924 3071 4.941263 CCTTCCGATCCAAAATAAGTGTCA 59.059 41.667 0.00 0.00 0.00 3.58
2925 3072 5.065218 CCTTCCGATCCAAAATAAGTGTCAG 59.935 44.000 0.00 0.00 0.00 3.51
2978 3125 8.071967 AGTAGTATGTTTTTCTTTGTTTACGGC 58.928 33.333 0.00 0.00 0.00 5.68
2979 3126 6.797454 AGTATGTTTTTCTTTGTTTACGGCA 58.203 32.000 0.00 0.00 0.00 5.69
2980 3127 6.915843 AGTATGTTTTTCTTTGTTTACGGCAG 59.084 34.615 0.00 0.00 0.00 4.85
2981 3128 5.061920 TGTTTTTCTTTGTTTACGGCAGT 57.938 34.783 0.00 0.00 0.00 4.40
2982 3129 6.192234 TGTTTTTCTTTGTTTACGGCAGTA 57.808 33.333 0.00 0.00 0.00 2.74
2983 3130 6.028987 TGTTTTTCTTTGTTTACGGCAGTAC 58.971 36.000 0.00 0.00 31.60 2.73
2984 3131 5.814764 TTTTCTTTGTTTACGGCAGTACA 57.185 34.783 0.00 0.00 31.60 2.90
2985 3132 4.799419 TTCTTTGTTTACGGCAGTACAC 57.201 40.909 6.38 6.38 34.89 2.90
2986 3133 3.794717 TCTTTGTTTACGGCAGTACACA 58.205 40.909 11.27 11.27 40.53 3.72
2987 3134 4.382291 TCTTTGTTTACGGCAGTACACAT 58.618 39.130 15.19 0.00 41.45 3.21
2988 3135 4.212425 TCTTTGTTTACGGCAGTACACATG 59.788 41.667 15.19 11.68 41.45 3.21
2989 3136 2.418692 TGTTTACGGCAGTACACATGG 58.581 47.619 11.27 0.00 38.26 3.66
2990 3137 2.037381 TGTTTACGGCAGTACACATGGA 59.963 45.455 11.27 0.00 38.26 3.41
2991 3138 2.665649 TTACGGCAGTACACATGGAG 57.334 50.000 0.00 0.00 31.60 3.86
2992 3139 0.821517 TACGGCAGTACACATGGAGG 59.178 55.000 0.00 0.00 0.00 4.30
2993 3140 1.192146 ACGGCAGTACACATGGAGGT 61.192 55.000 0.00 0.00 0.00 3.85
2994 3141 0.821517 CGGCAGTACACATGGAGGTA 59.178 55.000 0.00 0.00 0.00 3.08
2995 3142 1.202417 CGGCAGTACACATGGAGGTAG 60.202 57.143 0.00 0.00 0.00 3.18
2996 3143 1.831736 GGCAGTACACATGGAGGTAGT 59.168 52.381 0.00 0.00 0.00 2.73
2997 3144 3.028850 GGCAGTACACATGGAGGTAGTA 58.971 50.000 0.00 0.00 0.00 1.82
2998 3145 3.068307 GGCAGTACACATGGAGGTAGTAG 59.932 52.174 0.00 0.00 0.00 2.57
2999 3146 3.700038 GCAGTACACATGGAGGTAGTAGT 59.300 47.826 0.00 0.00 0.00 2.73
3000 3147 4.885907 GCAGTACACATGGAGGTAGTAGTA 59.114 45.833 0.00 0.00 0.00 1.82
3001 3148 5.535406 GCAGTACACATGGAGGTAGTAGTAT 59.465 44.000 0.00 0.00 0.00 2.12
3002 3149 6.515200 GCAGTACACATGGAGGTAGTAGTATG 60.515 46.154 0.00 0.00 0.00 2.39
3006 3153 7.253905 ACACATGGAGGTAGTAGTATGTTTT 57.746 36.000 0.00 0.00 0.00 2.43
3007 3154 7.686434 ACACATGGAGGTAGTAGTATGTTTTT 58.314 34.615 0.00 0.00 0.00 1.94
3057 3204 9.556030 GACAGGTTAAGCATGTACTTAATTTTC 57.444 33.333 7.52 2.16 42.70 2.29
3058 3205 9.073475 ACAGGTTAAGCATGTACTTAATTTTCA 57.927 29.630 7.52 0.00 42.44 2.69
3105 3252 3.954904 GAGCAGGTCCACTAGAGATTGTA 59.045 47.826 0.00 0.00 0.00 2.41
3136 3283 9.604626 GAGAAACAACAGCTTATATTGCATATC 57.395 33.333 0.00 0.00 0.00 1.63
3328 3475 9.757227 GCATTTACAGGGCAAATTATAAACATA 57.243 29.630 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 9.710900 GTTGAACATCAAAGGAAATTTTAGGAT 57.289 29.630 0.00 0.00 38.22 3.24
87 88 5.107607 ACGTAAGAACACGATTTGACATGAC 60.108 40.000 0.00 0.00 44.69 3.06
98 99 5.984926 ACCTTTCAAATACGTAAGAACACGA 59.015 36.000 0.00 0.00 44.69 4.35
151 152 3.868077 GGTGAGAGAATGAAGAATGGACG 59.132 47.826 0.00 0.00 0.00 4.79
157 158 6.438741 AGAGTATGTGGTGAGAGAATGAAGAA 59.561 38.462 0.00 0.00 0.00 2.52
160 161 5.716703 TCAGAGTATGTGGTGAGAGAATGAA 59.283 40.000 0.00 0.00 0.00 2.57
195 196 1.691976 TCGAGTGTCTGGACAACCAAT 59.308 47.619 4.92 0.00 46.32 3.16
196 197 1.116308 TCGAGTGTCTGGACAACCAA 58.884 50.000 4.92 0.00 46.32 3.67
243 244 7.045126 ACCAAGAAATCAAATTGTTACCGAA 57.955 32.000 0.00 0.00 0.00 4.30
293 298 2.202797 GCTTCAGCGGATGAGCGA 60.203 61.111 3.92 0.00 39.68 4.93
387 392 9.877178 ACAATATATAATAGTAGCCTGCTCAAC 57.123 33.333 0.00 0.00 0.00 3.18
426 431 4.289672 AGGATTCCCAGACATGTAAACAGT 59.710 41.667 0.00 0.00 33.88 3.55
500 505 2.259917 TGTCCAAGAGCCATCTTCTCA 58.740 47.619 0.00 0.00 44.15 3.27
507 512 1.611673 CCGAACTTGTCCAAGAGCCAT 60.612 52.381 13.69 0.00 40.79 4.40
540 545 3.004106 CAGCAAATTGGAGCCATAGTAGC 59.996 47.826 0.00 0.00 0.00 3.58
611 617 1.358877 CTCGATGACGTTGCCATTGA 58.641 50.000 5.74 5.74 40.69 2.57
614 620 3.799753 GCTCGATGACGTTGCCAT 58.200 55.556 0.00 0.00 40.69 4.40
617 623 2.167861 GGAGGCTCGATGACGTTGC 61.168 63.158 8.69 0.00 40.69 4.17
662 677 6.601332 AGGAAACTTGTGATCTAAGGAACAA 58.399 36.000 12.73 5.00 37.44 2.83
707 722 0.807667 AGCTTTGCCGTCAGATAGCG 60.808 55.000 0.00 0.00 34.01 4.26
708 723 1.373570 AAGCTTTGCCGTCAGATAGC 58.626 50.000 0.00 0.00 0.00 2.97
709 724 4.425577 AAAAAGCTTTGCCGTCAGATAG 57.574 40.909 13.54 0.00 0.00 2.08
727 742 3.106242 TCTGCTAGCAGACGTCAAAAA 57.894 42.857 37.64 16.91 46.80 1.94
728 743 2.812358 TCTGCTAGCAGACGTCAAAA 57.188 45.000 37.64 17.62 46.80 2.44
737 752 0.390340 TCTTTGCCGTCTGCTAGCAG 60.390 55.000 34.48 34.48 44.86 4.24
738 753 0.034756 TTCTTTGCCGTCTGCTAGCA 59.965 50.000 18.22 18.22 42.00 3.49
739 754 0.723981 CTTCTTTGCCGTCTGCTAGC 59.276 55.000 8.10 8.10 42.00 3.42
740 755 1.728971 CACTTCTTTGCCGTCTGCTAG 59.271 52.381 0.00 0.00 42.00 3.42
741 756 1.608025 CCACTTCTTTGCCGTCTGCTA 60.608 52.381 0.00 0.00 42.00 3.49
742 757 0.886490 CCACTTCTTTGCCGTCTGCT 60.886 55.000 0.00 0.00 42.00 4.24
743 758 1.576421 CCACTTCTTTGCCGTCTGC 59.424 57.895 0.00 0.00 41.77 4.26
744 759 0.886490 AGCCACTTCTTTGCCGTCTG 60.886 55.000 0.00 0.00 0.00 3.51
745 760 0.886490 CAGCCACTTCTTTGCCGTCT 60.886 55.000 0.00 0.00 0.00 4.18
746 761 0.884704 TCAGCCACTTCTTTGCCGTC 60.885 55.000 0.00 0.00 0.00 4.79
747 762 0.250901 ATCAGCCACTTCTTTGCCGT 60.251 50.000 0.00 0.00 0.00 5.68
748 763 0.169672 CATCAGCCACTTCTTTGCCG 59.830 55.000 0.00 0.00 0.00 5.69
749 764 0.529378 CCATCAGCCACTTCTTTGCC 59.471 55.000 0.00 0.00 0.00 4.52
750 765 1.251251 ACCATCAGCCACTTCTTTGC 58.749 50.000 0.00 0.00 0.00 3.68
751 766 5.047802 ACATTTACCATCAGCCACTTCTTTG 60.048 40.000 0.00 0.00 0.00 2.77
752 767 5.047802 CACATTTACCATCAGCCACTTCTTT 60.048 40.000 0.00 0.00 0.00 2.52
753 768 4.460382 CACATTTACCATCAGCCACTTCTT 59.540 41.667 0.00 0.00 0.00 2.52
754 769 4.012374 CACATTTACCATCAGCCACTTCT 58.988 43.478 0.00 0.00 0.00 2.85
755 770 4.009675 TCACATTTACCATCAGCCACTTC 58.990 43.478 0.00 0.00 0.00 3.01
756 771 4.032960 TCACATTTACCATCAGCCACTT 57.967 40.909 0.00 0.00 0.00 3.16
757 772 3.719268 TCACATTTACCATCAGCCACT 57.281 42.857 0.00 0.00 0.00 4.00
758 773 4.202441 AGATCACATTTACCATCAGCCAC 58.798 43.478 0.00 0.00 0.00 5.01
759 774 4.508551 AGATCACATTTACCATCAGCCA 57.491 40.909 0.00 0.00 0.00 4.75
760 775 5.585390 CAAAGATCACATTTACCATCAGCC 58.415 41.667 0.00 0.00 0.00 4.85
761 776 5.039333 GCAAAGATCACATTTACCATCAGC 58.961 41.667 0.00 0.00 0.00 4.26
762 777 5.125900 TGGCAAAGATCACATTTACCATCAG 59.874 40.000 0.00 0.00 29.89 2.90
763 778 5.015515 TGGCAAAGATCACATTTACCATCA 58.984 37.500 0.00 0.00 29.89 3.07
764 779 5.581126 TGGCAAAGATCACATTTACCATC 57.419 39.130 0.00 0.00 29.89 3.51
765 780 5.657745 TGATGGCAAAGATCACATTTACCAT 59.342 36.000 9.39 9.39 43.42 3.55
766 781 5.015515 TGATGGCAAAGATCACATTTACCA 58.984 37.500 0.00 0.00 37.45 3.25
767 782 5.581126 TGATGGCAAAGATCACATTTACC 57.419 39.130 0.00 0.00 0.00 2.85
768 783 5.039333 GCTGATGGCAAAGATCACATTTAC 58.961 41.667 4.85 0.00 41.35 2.01
769 784 4.098349 GGCTGATGGCAAAGATCACATTTA 59.902 41.667 4.85 0.00 44.01 1.40
770 785 3.118884 GGCTGATGGCAAAGATCACATTT 60.119 43.478 4.85 0.00 44.01 2.32
771 786 2.429610 GGCTGATGGCAAAGATCACATT 59.570 45.455 4.85 0.00 44.01 2.71
772 787 2.029623 GGCTGATGGCAAAGATCACAT 58.970 47.619 4.85 0.00 44.01 3.21
773 788 1.272037 TGGCTGATGGCAAAGATCACA 60.272 47.619 4.85 0.00 46.03 3.58
774 789 1.466856 TGGCTGATGGCAAAGATCAC 58.533 50.000 4.85 0.00 46.03 3.06
775 790 3.983229 TGGCTGATGGCAAAGATCA 57.017 47.368 4.85 0.00 46.03 2.92
811 826 2.096248 ACAACCGTCAGCTTCCAAAAA 58.904 42.857 0.00 0.00 0.00 1.94
812 827 1.757682 ACAACCGTCAGCTTCCAAAA 58.242 45.000 0.00 0.00 0.00 2.44
813 828 2.215196 GTACAACCGTCAGCTTCCAAA 58.785 47.619 0.00 0.00 0.00 3.28
814 829 1.139256 TGTACAACCGTCAGCTTCCAA 59.861 47.619 0.00 0.00 0.00 3.53
815 830 0.753867 TGTACAACCGTCAGCTTCCA 59.246 50.000 0.00 0.00 0.00 3.53
816 831 1.732259 CATGTACAACCGTCAGCTTCC 59.268 52.381 0.00 0.00 0.00 3.46
817 832 2.412089 GACATGTACAACCGTCAGCTTC 59.588 50.000 14.98 0.00 0.00 3.86
818 833 2.413837 GACATGTACAACCGTCAGCTT 58.586 47.619 14.98 0.00 0.00 3.74
819 834 1.337823 GGACATGTACAACCGTCAGCT 60.338 52.381 19.20 0.00 0.00 4.24
820 835 1.076332 GGACATGTACAACCGTCAGC 58.924 55.000 19.20 5.40 0.00 4.26
821 836 2.743636 AGGACATGTACAACCGTCAG 57.256 50.000 11.55 1.37 0.00 3.51
822 837 3.321396 TGTTAGGACATGTACAACCGTCA 59.679 43.478 11.55 12.76 0.00 4.35
823 838 3.916761 TGTTAGGACATGTACAACCGTC 58.083 45.455 11.55 7.25 0.00 4.79
824 839 3.575256 TCTGTTAGGACATGTACAACCGT 59.425 43.478 11.55 0.00 34.72 4.83
825 840 4.174009 CTCTGTTAGGACATGTACAACCG 58.826 47.826 11.55 9.17 34.72 4.44
826 841 5.148651 ACTCTGTTAGGACATGTACAACC 57.851 43.478 11.55 1.54 34.72 3.77
827 842 6.929606 AGAAACTCTGTTAGGACATGTACAAC 59.070 38.462 11.55 12.71 34.72 3.32
828 843 7.062749 AGAAACTCTGTTAGGACATGTACAA 57.937 36.000 11.55 0.00 34.72 2.41
829 844 6.665992 AGAAACTCTGTTAGGACATGTACA 57.334 37.500 11.55 4.87 34.72 2.90
830 845 7.964604 AAAGAAACTCTGTTAGGACATGTAC 57.035 36.000 0.00 0.00 34.72 2.90
831 846 8.974060 AAAAAGAAACTCTGTTAGGACATGTA 57.026 30.769 0.00 0.00 34.72 2.29
832 847 7.881775 AAAAAGAAACTCTGTTAGGACATGT 57.118 32.000 0.00 0.00 34.72 3.21
890 905 6.777213 TTAGGGCTTGTTGTTTTTCACTAA 57.223 33.333 0.00 0.00 0.00 2.24
959 974 0.332632 TATGGCTTTCTTGGCTGGCT 59.667 50.000 2.00 0.00 0.00 4.75
1093 1117 1.680522 GCAAGGCATCCGGAGAGAGA 61.681 60.000 11.34 0.00 0.00 3.10
1193 1217 0.966875 TAGTAAAGAGACGGGCGCCA 60.967 55.000 30.85 0.00 0.00 5.69
1194 1218 0.248949 CTAGTAAAGAGACGGGCGCC 60.249 60.000 21.18 21.18 0.00 6.53
1242 1266 3.343617 CAGAGCAAATCTAAAACCCGGA 58.656 45.455 0.73 0.00 36.10 5.14
1285 1313 3.741476 GCACTCGCCAGCCAAAGG 61.741 66.667 0.00 0.00 0.00 3.11
1288 1316 2.979676 CTTGCACTCGCCAGCCAA 60.980 61.111 0.00 0.00 37.32 4.52
1291 1319 3.730761 CACCTTGCACTCGCCAGC 61.731 66.667 0.00 0.00 37.32 4.85
1292 1320 0.602638 TAACACCTTGCACTCGCCAG 60.603 55.000 0.00 0.00 37.32 4.85
1327 1361 7.816995 AGAACTGAATTCTAGCTACAGTTTCAG 59.183 37.037 21.10 20.24 46.38 3.02
1363 1407 2.565841 AGCCTCAACTGACAACTCAAC 58.434 47.619 0.00 0.00 0.00 3.18
1371 1415 1.798813 CCAACGTTAGCCTCAACTGAC 59.201 52.381 0.00 0.00 0.00 3.51
1372 1416 1.270625 CCCAACGTTAGCCTCAACTGA 60.271 52.381 0.00 0.00 0.00 3.41
1386 1430 1.131126 GCATCTGAATGTGTCCCAACG 59.869 52.381 0.00 0.00 35.18 4.10
1392 1436 4.639310 AGAAATCCAGCATCTGAATGTGTC 59.361 41.667 0.00 0.00 35.18 3.67
1413 1466 9.868277 AAGATTAAAAACAAAACATCACACAGA 57.132 25.926 0.00 0.00 0.00 3.41
1417 1470 9.429359 ACACAAGATTAAAAACAAAACATCACA 57.571 25.926 0.00 0.00 0.00 3.58
1435 1488 8.873830 CGATTTGTCTATGTTCTTACACAAGAT 58.126 33.333 0.00 0.00 40.47 2.40
1436 1489 8.085909 TCGATTTGTCTATGTTCTTACACAAGA 58.914 33.333 0.00 0.00 39.06 3.02
1437 1490 8.239681 TCGATTTGTCTATGTTCTTACACAAG 57.760 34.615 0.00 0.00 37.03 3.16
1438 1491 8.596271 TTCGATTTGTCTATGTTCTTACACAA 57.404 30.769 0.00 0.00 37.03 3.33
1439 1492 8.771920 ATTCGATTTGTCTATGTTCTTACACA 57.228 30.769 0.00 0.00 37.03 3.72
1440 1493 9.478019 CAATTCGATTTGTCTATGTTCTTACAC 57.522 33.333 11.07 0.00 37.03 2.90
1452 1505 6.484643 CAGTATCATCCCAATTCGATTTGTCT 59.515 38.462 16.46 1.30 0.00 3.41
1454 1507 6.122277 ACAGTATCATCCCAATTCGATTTGT 58.878 36.000 16.46 2.59 0.00 2.83
1466 1519 3.209410 CTTGCAGGAACAGTATCATCCC 58.791 50.000 0.00 0.00 33.55 3.85
1477 1530 4.037446 TCAAAACATGGTACTTGCAGGAAC 59.963 41.667 1.40 0.00 0.00 3.62
1533 1586 3.753294 ACAGTTCAGAACAATCTCGGT 57.247 42.857 15.85 0.00 32.03 4.69
1536 1589 5.986135 ACAGTGTACAGTTCAGAACAATCTC 59.014 40.000 15.85 2.97 32.03 2.75
1537 1590 5.918608 ACAGTGTACAGTTCAGAACAATCT 58.081 37.500 15.85 2.61 35.88 2.40
1540 1593 7.101054 ACTTAACAGTGTACAGTTCAGAACAA 58.899 34.615 15.85 0.00 0.00 2.83
1542 1595 7.919621 AGTACTTAACAGTGTACAGTTCAGAAC 59.080 37.037 13.28 5.00 40.84 3.01
1554 1607 6.649557 GGCAGTTTGATAGTACTTAACAGTGT 59.350 38.462 0.00 0.00 34.06 3.55
1581 1640 7.230108 CCAACAATGCCTATCATAGATCAAAGT 59.770 37.037 0.00 0.00 34.33 2.66
1591 1650 2.761786 AGCCCAACAATGCCTATCAT 57.238 45.000 0.00 0.00 36.87 2.45
1604 1663 6.665992 ATACTTATCGAGATTGTAGCCCAA 57.334 37.500 0.00 0.00 37.49 4.12
1632 1693 6.115446 AGATTCTCGCAGGAATAAATGTCAA 58.885 36.000 1.81 0.00 36.24 3.18
1637 1698 6.821388 ACACTAGATTCTCGCAGGAATAAAT 58.179 36.000 0.00 0.00 36.24 1.40
1656 1717 7.490657 ACCATGGAAGATACAAGTAACACTA 57.509 36.000 21.47 0.00 0.00 2.74
1666 1727 7.194112 TGATTGTCTAACCATGGAAGATACA 57.806 36.000 21.47 12.93 0.00 2.29
1707 1776 7.442969 CAGGAAAGTACACAACTGGTTATGTTA 59.557 37.037 2.73 0.00 38.88 2.41
1713 1782 2.949644 GCAGGAAAGTACACAACTGGTT 59.050 45.455 0.00 0.00 38.88 3.67
1739 1809 1.220493 TCCAGCCCTATCCTAGCTTCA 59.780 52.381 0.00 0.00 33.70 3.02
1750 1820 1.414158 GTATGCACTCTCCAGCCCTA 58.586 55.000 0.00 0.00 0.00 3.53
1766 1836 2.354403 CCCCGTCTTTTTCTGGTCGTAT 60.354 50.000 0.00 0.00 0.00 3.06
1767 1837 1.001181 CCCCGTCTTTTTCTGGTCGTA 59.999 52.381 0.00 0.00 0.00 3.43
1768 1838 0.250166 CCCCGTCTTTTTCTGGTCGT 60.250 55.000 0.00 0.00 0.00 4.34
1769 1839 0.250166 ACCCCGTCTTTTTCTGGTCG 60.250 55.000 0.00 0.00 0.00 4.79
1778 1848 1.486145 ATGTCCCGAACCCCGTCTTT 61.486 55.000 0.00 0.00 36.31 2.52
1816 1895 1.071471 CCACCACGCCAGTCTCTTT 59.929 57.895 0.00 0.00 0.00 2.52
1862 1941 3.256960 GACCTTCCCCTGCCACCA 61.257 66.667 0.00 0.00 0.00 4.17
1895 1989 1.286305 ACCTGAACCAACCACCACCT 61.286 55.000 0.00 0.00 0.00 4.00
1898 1992 1.228793 CCACCTGAACCAACCACCA 59.771 57.895 0.00 0.00 0.00 4.17
2115 2209 1.141881 CAACGGATAGACGGCAGCT 59.858 57.895 0.00 0.00 38.39 4.24
2127 2221 3.923864 AGCACGACCAGCAACGGA 61.924 61.111 0.00 0.00 0.00 4.69
2151 2245 2.245532 GTGATTGCGCGCCGTATC 59.754 61.111 30.77 25.98 0.00 2.24
2164 2258 2.164219 CACAATAAGCCGCAAAGGTGAT 59.836 45.455 0.00 0.00 43.70 3.06
2223 2317 0.879765 CGTCGTCTACAGGAGTTGGT 59.120 55.000 0.00 0.00 0.00 3.67
2244 2338 3.730761 GCTGCAGCCACCACTTCG 61.731 66.667 28.76 0.00 34.31 3.79
2338 2432 6.765989 AGTATAACTCGCAAGGCATTGAAATA 59.234 34.615 16.56 0.43 38.83 1.40
2360 2454 2.103432 TCTGACCAGCGGAAAAACAGTA 59.897 45.455 1.50 0.00 0.00 2.74
2361 2455 1.134220 TCTGACCAGCGGAAAAACAGT 60.134 47.619 1.50 0.00 0.00 3.55
2369 2463 2.565391 TGAAAACTATCTGACCAGCGGA 59.435 45.455 1.50 0.00 36.05 5.54
2370 2464 2.972625 TGAAAACTATCTGACCAGCGG 58.027 47.619 0.00 0.00 0.00 5.52
2371 2465 4.508124 GGTATGAAAACTATCTGACCAGCG 59.492 45.833 0.00 0.00 0.00 5.18
2432 2526 3.838244 ATATAAAGTTCGCTCCTGCCA 57.162 42.857 0.00 0.00 35.36 4.92
2468 2564 9.546909 CAAATGTCTGCTTGTAAATAACTGTAG 57.453 33.333 0.00 0.00 0.00 2.74
2474 2570 9.844790 CTCATTCAAATGTCTGCTTGTAAATAA 57.155 29.630 2.85 0.00 37.65 1.40
2525 2622 3.056107 TGTGGACTTTCCGAGGTATCTTG 60.056 47.826 0.00 0.00 40.17 3.02
2535 2632 5.390567 GCTACAAGTAAATGTGGACTTTCCG 60.391 44.000 0.00 0.00 40.17 4.30
2541 2638 4.154195 CACCAGCTACAAGTAAATGTGGAC 59.846 45.833 0.00 0.00 34.02 4.02
2556 2653 2.879756 GCTCAAATCCAACCACCAGCTA 60.880 50.000 0.00 0.00 0.00 3.32
2559 2656 1.815003 GAGCTCAAATCCAACCACCAG 59.185 52.381 9.40 0.00 0.00 4.00
2562 2659 1.815003 CCAGAGCTCAAATCCAACCAC 59.185 52.381 17.77 0.00 0.00 4.16
2575 2672 1.519719 GCCGATCAAGTCCAGAGCT 59.480 57.895 0.00 0.00 0.00 4.09
2637 2734 0.957888 GAGTTCAGACTTGGCAGGCC 60.958 60.000 2.62 2.62 35.88 5.19
2639 2736 1.345741 TCAGAGTTCAGACTTGGCAGG 59.654 52.381 0.00 0.00 35.88 4.85
2714 2811 4.349636 TCCCAGATTCACACAGGAAAGTTA 59.650 41.667 0.00 0.00 0.00 2.24
2724 2821 2.079925 GTGAGCTTCCCAGATTCACAC 58.920 52.381 0.00 0.00 36.70 3.82
2735 2832 3.944087 ACATAGGTTTCAGTGAGCTTCC 58.056 45.455 0.00 0.00 0.00 3.46
2750 2896 6.117911 TGAATATGCACAACGAAACATAGG 57.882 37.500 0.00 0.00 0.00 2.57
2751 2897 5.678483 GCTGAATATGCACAACGAAACATAG 59.322 40.000 0.00 0.00 0.00 2.23
2752 2898 5.448496 GGCTGAATATGCACAACGAAACATA 60.448 40.000 0.00 0.00 0.00 2.29
2753 2899 4.414852 GCTGAATATGCACAACGAAACAT 58.585 39.130 0.00 0.00 0.00 2.71
2754 2900 3.365868 GGCTGAATATGCACAACGAAACA 60.366 43.478 0.00 0.00 0.00 2.83
2755 2901 3.119849 AGGCTGAATATGCACAACGAAAC 60.120 43.478 0.00 0.00 0.00 2.78
2756 2902 3.081061 AGGCTGAATATGCACAACGAAA 58.919 40.909 0.00 0.00 0.00 3.46
2757 2903 2.710377 AGGCTGAATATGCACAACGAA 58.290 42.857 0.00 0.00 0.00 3.85
2758 2904 2.401583 AGGCTGAATATGCACAACGA 57.598 45.000 0.00 0.00 0.00 3.85
2759 2905 4.609113 CGAATAGGCTGAATATGCACAACG 60.609 45.833 0.00 0.00 0.00 4.10
2760 2906 4.319766 CCGAATAGGCTGAATATGCACAAC 60.320 45.833 0.00 0.00 0.00 3.32
2761 2907 3.814842 CCGAATAGGCTGAATATGCACAA 59.185 43.478 0.00 0.00 0.00 3.33
2762 2908 3.402110 CCGAATAGGCTGAATATGCACA 58.598 45.455 0.00 0.00 0.00 4.57
2763 2909 2.744202 CCCGAATAGGCTGAATATGCAC 59.256 50.000 0.00 0.00 39.21 4.57
2764 2910 3.057969 CCCGAATAGGCTGAATATGCA 57.942 47.619 0.00 0.00 39.21 3.96
2775 2921 0.177141 TGAAACTCGGCCCGAATAGG 59.823 55.000 7.50 0.00 34.74 2.57
2776 2922 1.571919 CTGAAACTCGGCCCGAATAG 58.428 55.000 7.50 0.00 34.74 1.73
2777 2923 0.177141 CCTGAAACTCGGCCCGAATA 59.823 55.000 7.50 0.00 34.74 1.75
2778 2924 1.078426 CCTGAAACTCGGCCCGAAT 60.078 57.895 7.50 0.00 34.74 3.34
2779 2925 1.550130 ATCCTGAAACTCGGCCCGAA 61.550 55.000 7.50 0.00 34.74 4.30
2780 2926 1.987855 ATCCTGAAACTCGGCCCGA 60.988 57.895 5.37 5.37 0.00 5.14
2781 2927 1.815421 CATCCTGAAACTCGGCCCG 60.815 63.158 0.00 0.00 0.00 6.13
2782 2928 0.181350 ATCATCCTGAAACTCGGCCC 59.819 55.000 0.00 0.00 0.00 5.80
2783 2929 1.134401 TGATCATCCTGAAACTCGGCC 60.134 52.381 0.00 0.00 0.00 6.13
2784 2930 2.315925 TGATCATCCTGAAACTCGGC 57.684 50.000 0.00 0.00 0.00 5.54
2785 2931 8.090831 TCTATTTATGATCATCCTGAAACTCGG 58.909 37.037 12.53 0.04 0.00 4.63
2786 2932 8.920665 GTCTATTTATGATCATCCTGAAACTCG 58.079 37.037 12.53 0.51 0.00 4.18
2787 2933 9.213799 GGTCTATTTATGATCATCCTGAAACTC 57.786 37.037 12.53 0.00 0.00 3.01
2788 2934 8.943085 AGGTCTATTTATGATCATCCTGAAACT 58.057 33.333 12.53 0.20 0.00 2.66
2789 2935 9.213799 GAGGTCTATTTATGATCATCCTGAAAC 57.786 37.037 12.53 5.64 0.00 2.78
2790 2936 8.937835 TGAGGTCTATTTATGATCATCCTGAAA 58.062 33.333 12.53 7.64 0.00 2.69
2791 2937 8.370940 GTGAGGTCTATTTATGATCATCCTGAA 58.629 37.037 12.53 4.00 0.00 3.02
2792 2938 7.732140 AGTGAGGTCTATTTATGATCATCCTGA 59.268 37.037 12.53 1.82 0.00 3.86
2793 2939 7.905265 AGTGAGGTCTATTTATGATCATCCTG 58.095 38.462 12.53 0.00 0.00 3.86
2794 2940 8.503428 AAGTGAGGTCTATTTATGATCATCCT 57.497 34.615 12.53 10.48 0.00 3.24
2903 3050 4.394920 GCTGACACTTATTTTGGATCGGAA 59.605 41.667 0.00 0.00 0.00 4.30
2946 3093 8.843885 ACAAAGAAAAACATACTACTACCTCC 57.156 34.615 0.00 0.00 0.00 4.30
2960 3107 6.021232 GTGTACTGCCGTAAACAAAGAAAAAC 60.021 38.462 3.89 0.00 34.56 2.43
2977 3124 3.700038 ACTACTACCTCCATGTGTACTGC 59.300 47.826 0.00 0.00 0.00 4.40
2978 3125 6.546403 ACATACTACTACCTCCATGTGTACTG 59.454 42.308 0.00 0.00 0.00 2.74
2979 3126 6.670617 ACATACTACTACCTCCATGTGTACT 58.329 40.000 0.00 0.00 0.00 2.73
2980 3127 6.956202 ACATACTACTACCTCCATGTGTAC 57.044 41.667 0.00 0.00 0.00 2.90
2981 3128 7.966339 AAACATACTACTACCTCCATGTGTA 57.034 36.000 0.00 0.00 0.00 2.90
2982 3129 6.869206 AAACATACTACTACCTCCATGTGT 57.131 37.500 0.00 0.00 0.00 3.72
2983 3130 8.041323 AGAAAAACATACTACTACCTCCATGTG 58.959 37.037 0.00 0.00 0.00 3.21
2984 3131 8.147244 AGAAAAACATACTACTACCTCCATGT 57.853 34.615 0.00 0.00 0.00 3.21
2985 3132 9.449719 AAAGAAAAACATACTACTACCTCCATG 57.550 33.333 0.00 0.00 0.00 3.66
2986 3133 9.449719 CAAAGAAAAACATACTACTACCTCCAT 57.550 33.333 0.00 0.00 0.00 3.41
2987 3134 8.434392 ACAAAGAAAAACATACTACTACCTCCA 58.566 33.333 0.00 0.00 0.00 3.86
2988 3135 8.843885 ACAAAGAAAAACATACTACTACCTCC 57.156 34.615 0.00 0.00 0.00 4.30
2994 3141 8.071967 GCCGTAAACAAAGAAAAACATACTACT 58.928 33.333 0.00 0.00 0.00 2.57
2995 3142 7.856894 TGCCGTAAACAAAGAAAAACATACTAC 59.143 33.333 0.00 0.00 0.00 2.73
2996 3143 7.928103 TGCCGTAAACAAAGAAAAACATACTA 58.072 30.769 0.00 0.00 0.00 1.82
2997 3144 6.797454 TGCCGTAAACAAAGAAAAACATACT 58.203 32.000 0.00 0.00 0.00 2.12
2998 3145 6.693978 ACTGCCGTAAACAAAGAAAAACATAC 59.306 34.615 0.00 0.00 0.00 2.39
2999 3146 6.797454 ACTGCCGTAAACAAAGAAAAACATA 58.203 32.000 0.00 0.00 0.00 2.29
3000 3147 5.656480 ACTGCCGTAAACAAAGAAAAACAT 58.344 33.333 0.00 0.00 0.00 2.71
3001 3148 5.061920 ACTGCCGTAAACAAAGAAAAACA 57.938 34.783 0.00 0.00 0.00 2.83
3002 3149 6.021232 GTGTACTGCCGTAAACAAAGAAAAAC 60.021 38.462 3.89 0.00 34.56 2.43
3006 3153 4.190001 TGTGTACTGCCGTAAACAAAGAA 58.810 39.130 8.69 0.00 40.11 2.52
3007 3154 3.794717 TGTGTACTGCCGTAAACAAAGA 58.205 40.909 8.69 0.00 40.11 2.52
3019 3166 4.378459 GCTTAACCTGTCAATGTGTACTGC 60.378 45.833 0.00 0.00 0.00 4.40
3057 3204 6.673154 TGCACATCTTGTTCTTCTGATATG 57.327 37.500 0.00 0.00 0.00 1.78
3058 3205 7.555195 TCATTGCACATCTTGTTCTTCTGATAT 59.445 33.333 0.00 0.00 0.00 1.63
3089 3236 8.453238 TTCTCTATGTACAATCTCTAGTGGAC 57.547 38.462 0.00 0.00 35.02 4.02
3091 3238 8.687242 TGTTTCTCTATGTACAATCTCTAGTGG 58.313 37.037 0.00 0.00 0.00 4.00
3105 3252 8.616076 GCAATATAAGCTGTTGTTTCTCTATGT 58.384 33.333 0.00 0.00 0.00 2.29
3136 3283 7.438757 CAGATTGACACAGGAATCTCTCTAATG 59.561 40.741 0.00 0.00 36.90 1.90


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

AutoCloner maintained by Alex Coulton.