Multiple sequence alignment - TraesCS2B01G383700

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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 TraesCS2B01G383700 chr2B 100.000 3101 0 0 1 3101 547098122 547095022 0.000000e+00 5727.0
1 TraesCS2B01G383700 chr2B 87.842 1464 138 19 820 2249 547441440 547439983 0.000000e+00 1681.0
2 TraesCS2B01G383700 chr2B 86.496 1481 136 34 820 2254 547430455 547428993 0.000000e+00 1568.0
3 TraesCS2B01G383700 chr2B 90.244 410 29 5 2427 2831 547428999 547428596 2.740000e-145 525.0
4 TraesCS2B01G383700 chr2B 88.443 424 48 1 1366 1789 547436078 547435656 7.670000e-141 510.0
5 TraesCS2B01G383700 chr2B 78.395 486 101 4 1551 2034 731711120 731711603 2.320000e-81 313.0
6 TraesCS2B01G383700 chr2B 85.921 277 32 4 1976 2249 547433003 547432731 3.910000e-74 289.0
7 TraesCS2B01G383700 chr2B 92.784 194 14 0 2908 3101 547428579 547428386 6.550000e-72 281.0
8 TraesCS2B01G383700 chr2B 79.545 440 49 12 1830 2253 655299706 655299292 3.050000e-70 276.0
9 TraesCS2B01G383700 chr2D 93.394 1105 64 4 1732 2831 468945476 468944376 0.000000e+00 1628.0
10 TraesCS2B01G383700 chr2D 92.191 922 55 12 820 1736 468950630 468949721 0.000000e+00 1288.0
11 TraesCS2B01G383700 chr2D 89.786 793 71 6 1305 2090 468984575 468983786 0.000000e+00 1007.0
12 TraesCS2B01G383700 chr2D 76.590 1179 234 26 993 2154 469227144 469225991 7.350000e-171 610.0
13 TraesCS2B01G383700 chr2D 88.060 469 44 6 1775 2235 468958023 468957559 2.100000e-151 545.0
14 TraesCS2B01G383700 chr2D 89.858 424 43 0 1366 1789 468977502 468977079 2.100000e-151 545.0
15 TraesCS2B01G383700 chr2D 91.386 267 22 1 2836 3101 468944397 468944131 6.320000e-97 364.0
16 TraesCS2B01G383700 chr2D 89.286 56 6 0 2367 2422 621316896 621316841 1.540000e-08 71.3
17 TraesCS2B01G383700 chr2A 91.707 832 69 0 1366 2197 608898484 608897653 0.000000e+00 1155.0
18 TraesCS2B01G383700 chr2A 90.352 881 53 5 2177 3057 608896556 608895708 0.000000e+00 1127.0
19 TraesCS2B01G383700 chr2A 88.626 888 93 4 1366 2249 608921122 608920239 0.000000e+00 1074.0
20 TraesCS2B01G383700 chr2A 92.125 546 43 0 1465 2010 608917977 608917432 0.000000e+00 771.0
21 TraesCS2B01G383700 chrUn 96.904 646 14 5 1 644 91454298 91454939 0.000000e+00 1077.0
22 TraesCS2B01G383700 chr7A 96.749 646 15 5 1 644 720450544 720449903 0.000000e+00 1072.0
23 TraesCS2B01G383700 chr7A 78.308 1111 197 27 984 2077 10380412 10381495 0.000000e+00 676.0
24 TraesCS2B01G383700 chr7A 78.165 1090 187 23 999 2076 10830814 10831864 0.000000e+00 647.0
25 TraesCS2B01G383700 chr3B 96.325 653 18 5 1 651 114599508 114600156 0.000000e+00 1068.0
26 TraesCS2B01G383700 chr3B 96.296 648 17 6 1 645 519418054 519417411 0.000000e+00 1057.0
27 TraesCS2B01G383700 chr5A 96.313 651 18 5 1 649 226950902 226951548 0.000000e+00 1064.0
28 TraesCS2B01G383700 chr5A 90.909 55 2 3 2370 2423 702491934 702491882 1.540000e-08 71.3
29 TraesCS2B01G383700 chr3A 96.440 646 15 5 1 644 621591259 621590620 0.000000e+00 1059.0
30 TraesCS2B01G383700 chr7D 96.302 649 15 7 1 644 376952739 376952095 0.000000e+00 1057.0
31 TraesCS2B01G383700 chr7D 77.787 1148 205 31 984 2117 11260972 11262083 0.000000e+00 662.0
32 TraesCS2B01G383700 chr6A 96.296 648 17 6 1 645 171847739 171847096 0.000000e+00 1057.0
33 TraesCS2B01G383700 chr4D 96.024 654 18 6 1 650 455617343 455616694 0.000000e+00 1057.0
34 TraesCS2B01G383700 chr4A 77.993 1086 193 24 999 2076 726577161 726576114 9.380000e-180 640.0
35 TraesCS2B01G383700 chr4B 94.340 53 3 0 2371 2423 400385010 400384958 7.130000e-12 82.4
36 TraesCS2B01G383700 chr5D 90.566 53 5 0 2370 2422 54693730 54693678 1.540000e-08 71.3
37 TraesCS2B01G383700 chr5D 89.286 56 6 0 2370 2425 233060009 233059954 1.540000e-08 71.3
38 TraesCS2B01G383700 chr3D 89.474 57 5 1 2367 2423 10835214 10835159 1.540000e-08 71.3
39 TraesCS2B01G383700 chr3D 90.741 54 4 1 2371 2423 49783568 49783515 1.540000e-08 71.3


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 TraesCS2B01G383700 chr2B 547095022 547098122 3100 True 5727.0 5727 100.000000 1 3101 1 chr2B.!!$R1 3100
1 TraesCS2B01G383700 chr2B 547428386 547441440 13054 True 809.0 1681 88.621667 820 3101 6 chr2B.!!$R3 2281
2 TraesCS2B01G383700 chr2D 468949721 468950630 909 True 1288.0 1288 92.191000 820 1736 1 chr2D.!!$R1 916
3 TraesCS2B01G383700 chr2D 468983786 468984575 789 True 1007.0 1007 89.786000 1305 2090 1 chr2D.!!$R4 785
4 TraesCS2B01G383700 chr2D 468944131 468945476 1345 True 996.0 1628 92.390000 1732 3101 2 chr2D.!!$R7 1369
5 TraesCS2B01G383700 chr2D 469225991 469227144 1153 True 610.0 610 76.590000 993 2154 1 chr2D.!!$R5 1161
6 TraesCS2B01G383700 chr2A 608895708 608898484 2776 True 1141.0 1155 91.029500 1366 3057 2 chr2A.!!$R1 1691
7 TraesCS2B01G383700 chr2A 608917432 608921122 3690 True 922.5 1074 90.375500 1366 2249 2 chr2A.!!$R2 883
8 TraesCS2B01G383700 chrUn 91454298 91454939 641 False 1077.0 1077 96.904000 1 644 1 chrUn.!!$F1 643
9 TraesCS2B01G383700 chr7A 720449903 720450544 641 True 1072.0 1072 96.749000 1 644 1 chr7A.!!$R1 643
10 TraesCS2B01G383700 chr7A 10380412 10381495 1083 False 676.0 676 78.308000 984 2077 1 chr7A.!!$F1 1093
11 TraesCS2B01G383700 chr7A 10830814 10831864 1050 False 647.0 647 78.165000 999 2076 1 chr7A.!!$F2 1077
12 TraesCS2B01G383700 chr3B 114599508 114600156 648 False 1068.0 1068 96.325000 1 651 1 chr3B.!!$F1 650
13 TraesCS2B01G383700 chr3B 519417411 519418054 643 True 1057.0 1057 96.296000 1 645 1 chr3B.!!$R1 644
14 TraesCS2B01G383700 chr5A 226950902 226951548 646 False 1064.0 1064 96.313000 1 649 1 chr5A.!!$F1 648
15 TraesCS2B01G383700 chr3A 621590620 621591259 639 True 1059.0 1059 96.440000 1 644 1 chr3A.!!$R1 643
16 TraesCS2B01G383700 chr7D 376952095 376952739 644 True 1057.0 1057 96.302000 1 644 1 chr7D.!!$R1 643
17 TraesCS2B01G383700 chr7D 11260972 11262083 1111 False 662.0 662 77.787000 984 2117 1 chr7D.!!$F1 1133
18 TraesCS2B01G383700 chr6A 171847096 171847739 643 True 1057.0 1057 96.296000 1 645 1 chr6A.!!$R1 644
19 TraesCS2B01G383700 chr4D 455616694 455617343 649 True 1057.0 1057 96.024000 1 650 1 chr4D.!!$R1 649
20 TraesCS2B01G383700 chr4A 726576114 726577161 1047 True 640.0 640 77.993000 999 2076 1 chr4A.!!$R1 1077

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
706 712 0.107361 CGTGGGGTTATCCAAGGACC 60.107 60.0 0.00 0.0 38.72 4.46 F
1095 1121 0.107993 TCGAGATCGACGGGTACAGT 60.108 55.0 13.42 0.0 44.22 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 4801 0.179215 GCTGCATTTCTTCGACGGTG 60.179 55.0 0.0 0.00 0.00 4.94 R
2785 18007 0.036765 TCAATACGGTGACCTGGCAC 60.037 55.0 0.0 11.32 38.05 5.01 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
198 199 4.394729 TCTACATCCGGTTGAAGCTTTTT 58.605 39.130 19.34 0.00 0.00 1.94
199 200 3.643159 ACATCCGGTTGAAGCTTTTTC 57.357 42.857 19.34 0.00 0.00 2.29
200 201 2.955660 ACATCCGGTTGAAGCTTTTTCA 59.044 40.909 19.34 0.00 0.00 2.69
202 203 3.915437 TCCGGTTGAAGCTTTTTCATC 57.085 42.857 0.00 0.00 0.00 2.92
203 204 3.486383 TCCGGTTGAAGCTTTTTCATCT 58.514 40.909 0.00 0.00 0.00 2.90
204 205 4.647611 TCCGGTTGAAGCTTTTTCATCTA 58.352 39.130 0.00 0.00 0.00 1.98
205 206 5.253330 TCCGGTTGAAGCTTTTTCATCTAT 58.747 37.500 0.00 0.00 0.00 1.98
249 252 3.443045 CAACATGAGGGGGTGCGC 61.443 66.667 0.00 0.00 0.00 6.09
393 398 0.818445 TGGCGAAACGGGCTGTAAAA 60.818 50.000 0.00 0.00 0.00 1.52
394 399 0.311477 GGCGAAACGGGCTGTAAAAA 59.689 50.000 0.00 0.00 0.00 1.94
417 422 0.616395 TGGCGGGGTGAGATCTACAA 60.616 55.000 0.00 0.00 0.00 2.41
419 424 0.824759 GCGGGGTGAGATCTACAACT 59.175 55.000 0.00 0.00 0.00 3.16
502 508 3.543536 GATGAGGATGGGGGCGAGC 62.544 68.421 0.00 0.00 0.00 5.03
674 680 8.570068 AAAAACTTATATACGAAAAGGAGGCA 57.430 30.769 0.00 0.00 0.00 4.75
675 681 7.787725 AAACTTATATACGAAAAGGAGGCAG 57.212 36.000 0.00 0.00 0.00 4.85
676 682 5.298347 ACTTATATACGAAAAGGAGGCAGC 58.702 41.667 0.00 0.00 0.00 5.25
677 683 2.218953 TATACGAAAAGGAGGCAGCG 57.781 50.000 0.00 0.00 0.00 5.18
678 684 0.535335 ATACGAAAAGGAGGCAGCGA 59.465 50.000 0.00 0.00 0.00 4.93
679 685 0.108804 TACGAAAAGGAGGCAGCGAG 60.109 55.000 0.00 0.00 0.00 5.03
680 686 1.374758 CGAAAAGGAGGCAGCGAGT 60.375 57.895 0.00 0.00 0.00 4.18
681 687 1.630244 CGAAAAGGAGGCAGCGAGTG 61.630 60.000 0.00 0.00 0.00 3.51
682 688 0.320771 GAAAAGGAGGCAGCGAGTGA 60.321 55.000 0.00 0.00 0.00 3.41
683 689 0.108585 AAAAGGAGGCAGCGAGTGAA 59.891 50.000 0.00 0.00 0.00 3.18
684 690 0.321122 AAAGGAGGCAGCGAGTGAAG 60.321 55.000 0.00 0.00 0.00 3.02
685 691 2.794820 AAGGAGGCAGCGAGTGAAGC 62.795 60.000 0.00 0.00 0.00 3.86
686 692 3.184683 GAGGCAGCGAGTGAAGCG 61.185 66.667 0.00 0.00 40.04 4.68
694 700 4.681978 GAGTGAAGCGCGTGGGGT 62.682 66.667 8.43 0.00 0.00 4.95
695 701 4.250305 AGTGAAGCGCGTGGGGTT 62.250 61.111 8.43 0.73 0.00 4.11
696 702 2.357760 GTGAAGCGCGTGGGGTTA 60.358 61.111 8.43 0.00 0.00 2.85
697 703 1.743995 GTGAAGCGCGTGGGGTTAT 60.744 57.895 8.43 0.00 0.00 1.89
698 704 1.448893 TGAAGCGCGTGGGGTTATC 60.449 57.895 8.43 0.00 0.00 1.75
699 705 2.124860 AAGCGCGTGGGGTTATCC 60.125 61.111 8.43 0.00 0.00 2.59
700 706 2.862674 GAAGCGCGTGGGGTTATCCA 62.863 60.000 8.43 0.00 37.22 3.41
701 707 2.437002 GCGCGTGGGGTTATCCAA 60.437 61.111 8.43 0.00 38.72 3.53
702 708 2.469516 GCGCGTGGGGTTATCCAAG 61.470 63.158 8.43 0.00 38.72 3.61
703 709 1.817941 CGCGTGGGGTTATCCAAGG 60.818 63.158 0.00 0.00 38.72 3.61
704 710 1.605453 GCGTGGGGTTATCCAAGGA 59.395 57.895 0.00 0.00 38.72 3.36
705 711 0.746923 GCGTGGGGTTATCCAAGGAC 60.747 60.000 0.00 0.00 38.72 3.85
706 712 0.107361 CGTGGGGTTATCCAAGGACC 60.107 60.000 0.00 0.00 38.72 4.46
707 713 0.996583 GTGGGGTTATCCAAGGACCA 59.003 55.000 0.00 0.00 38.72 4.02
708 714 1.064685 GTGGGGTTATCCAAGGACCAG 60.065 57.143 0.00 0.00 38.72 4.00
709 715 0.551396 GGGGTTATCCAAGGACCAGG 59.449 60.000 0.00 0.00 37.22 4.45
710 716 1.591768 GGGTTATCCAAGGACCAGGA 58.408 55.000 8.02 8.02 38.50 3.86
711 717 1.920351 GGGTTATCCAAGGACCAGGAA 59.080 52.381 9.48 0.00 37.48 3.36
712 718 2.356844 GGGTTATCCAAGGACCAGGAAC 60.357 54.545 9.48 4.91 37.48 3.62
713 719 2.356844 GGTTATCCAAGGACCAGGAACC 60.357 54.545 9.48 9.64 37.48 3.62
714 720 2.576648 GTTATCCAAGGACCAGGAACCT 59.423 50.000 9.48 0.00 37.48 3.50
715 721 1.760405 ATCCAAGGACCAGGAACCTT 58.240 50.000 14.13 14.13 45.87 3.50
719 725 1.821088 AAGGACCAGGAACCTTGTCT 58.179 50.000 19.55 7.67 43.69 3.41
720 726 1.821088 AGGACCAGGAACCTTGTCTT 58.179 50.000 19.55 12.56 38.36 3.01
721 727 1.421646 AGGACCAGGAACCTTGTCTTG 59.578 52.381 19.55 0.00 38.36 3.02
722 728 1.239347 GACCAGGAACCTTGTCTTGC 58.761 55.000 15.03 0.00 36.26 4.01
723 729 0.535102 ACCAGGAACCTTGTCTTGCG 60.535 55.000 0.00 0.00 0.00 4.85
724 730 1.237285 CCAGGAACCTTGTCTTGCGG 61.237 60.000 0.00 0.00 0.00 5.69
725 731 1.600916 AGGAACCTTGTCTTGCGGC 60.601 57.895 0.00 0.00 0.00 6.53
726 732 1.600916 GGAACCTTGTCTTGCGGCT 60.601 57.895 0.00 0.00 0.00 5.52
727 733 1.172812 GGAACCTTGTCTTGCGGCTT 61.173 55.000 0.00 0.00 0.00 4.35
728 734 0.238553 GAACCTTGTCTTGCGGCTTC 59.761 55.000 0.00 0.00 0.00 3.86
729 735 1.172812 AACCTTGTCTTGCGGCTTCC 61.173 55.000 0.00 0.00 0.00 3.46
730 736 1.600636 CCTTGTCTTGCGGCTTCCA 60.601 57.895 0.00 0.00 0.00 3.53
731 737 1.576421 CTTGTCTTGCGGCTTCCAC 59.424 57.895 0.00 0.00 0.00 4.02
732 738 1.856265 CTTGTCTTGCGGCTTCCACC 61.856 60.000 0.00 0.00 0.00 4.61
733 739 3.056328 GTCTTGCGGCTTCCACCC 61.056 66.667 0.00 0.00 0.00 4.61
734 740 3.249189 TCTTGCGGCTTCCACCCT 61.249 61.111 0.00 0.00 0.00 4.34
735 741 2.282462 CTTGCGGCTTCCACCCTT 60.282 61.111 0.00 0.00 0.00 3.95
736 742 1.903404 CTTGCGGCTTCCACCCTTT 60.903 57.895 0.00 0.00 0.00 3.11
737 743 1.866853 CTTGCGGCTTCCACCCTTTC 61.867 60.000 0.00 0.00 0.00 2.62
738 744 3.062466 GCGGCTTCCACCCTTTCC 61.062 66.667 0.00 0.00 0.00 3.13
739 745 2.361230 CGGCTTCCACCCTTTCCC 60.361 66.667 0.00 0.00 0.00 3.97
740 746 2.037367 GGCTTCCACCCTTTCCCC 59.963 66.667 0.00 0.00 0.00 4.81
741 747 2.548547 GGCTTCCACCCTTTCCCCT 61.549 63.158 0.00 0.00 0.00 4.79
742 748 1.465172 GCTTCCACCCTTTCCCCTT 59.535 57.895 0.00 0.00 0.00 3.95
743 749 0.178932 GCTTCCACCCTTTCCCCTTT 60.179 55.000 0.00 0.00 0.00 3.11
744 750 1.924731 CTTCCACCCTTTCCCCTTTC 58.075 55.000 0.00 0.00 0.00 2.62
745 751 1.429299 CTTCCACCCTTTCCCCTTTCT 59.571 52.381 0.00 0.00 0.00 2.52
746 752 0.777446 TCCACCCTTTCCCCTTTCTG 59.223 55.000 0.00 0.00 0.00 3.02
747 753 0.482887 CCACCCTTTCCCCTTTCTGT 59.517 55.000 0.00 0.00 0.00 3.41
748 754 1.133167 CCACCCTTTCCCCTTTCTGTT 60.133 52.381 0.00 0.00 0.00 3.16
749 755 2.239400 CACCCTTTCCCCTTTCTGTTC 58.761 52.381 0.00 0.00 0.00 3.18
750 756 2.144450 ACCCTTTCCCCTTTCTGTTCT 58.856 47.619 0.00 0.00 0.00 3.01
751 757 2.518407 ACCCTTTCCCCTTTCTGTTCTT 59.482 45.455 0.00 0.00 0.00 2.52
752 758 2.893489 CCCTTTCCCCTTTCTGTTCTTG 59.107 50.000 0.00 0.00 0.00 3.02
753 759 2.297315 CCTTTCCCCTTTCTGTTCTTGC 59.703 50.000 0.00 0.00 0.00 4.01
754 760 3.225940 CTTTCCCCTTTCTGTTCTTGCT 58.774 45.455 0.00 0.00 0.00 3.91
755 761 2.568623 TCCCCTTTCTGTTCTTGCTC 57.431 50.000 0.00 0.00 0.00 4.26
756 762 1.073923 TCCCCTTTCTGTTCTTGCTCC 59.926 52.381 0.00 0.00 0.00 4.70
757 763 1.074566 CCCCTTTCTGTTCTTGCTCCT 59.925 52.381 0.00 0.00 0.00 3.69
758 764 2.431454 CCCTTTCTGTTCTTGCTCCTC 58.569 52.381 0.00 0.00 0.00 3.71
759 765 2.431454 CCTTTCTGTTCTTGCTCCTCC 58.569 52.381 0.00 0.00 0.00 4.30
760 766 2.431454 CTTTCTGTTCTTGCTCCTCCC 58.569 52.381 0.00 0.00 0.00 4.30
761 767 0.693049 TTCTGTTCTTGCTCCTCCCC 59.307 55.000 0.00 0.00 0.00 4.81
762 768 1.078848 CTGTTCTTGCTCCTCCCCG 60.079 63.158 0.00 0.00 0.00 5.73
763 769 2.269241 GTTCTTGCTCCTCCCCGG 59.731 66.667 0.00 0.00 0.00 5.73
764 770 3.717294 TTCTTGCTCCTCCCCGGC 61.717 66.667 0.00 0.00 0.00 6.13
765 771 4.722535 TCTTGCTCCTCCCCGGCT 62.723 66.667 0.00 0.00 0.00 5.52
766 772 4.168291 CTTGCTCCTCCCCGGCTC 62.168 72.222 0.00 0.00 0.00 4.70
770 776 3.151022 CTCCTCCCCGGCTCAGAC 61.151 72.222 0.00 0.00 0.00 3.51
771 777 3.965026 CTCCTCCCCGGCTCAGACA 62.965 68.421 0.00 0.00 0.00 3.41
772 778 2.765807 CCTCCCCGGCTCAGACAT 60.766 66.667 0.00 0.00 0.00 3.06
773 779 2.370445 CCTCCCCGGCTCAGACATT 61.370 63.158 0.00 0.00 0.00 2.71
774 780 1.144936 CTCCCCGGCTCAGACATTC 59.855 63.158 0.00 0.00 0.00 2.67
775 781 2.202932 CCCCGGCTCAGACATTCG 60.203 66.667 0.00 0.00 0.00 3.34
776 782 2.579201 CCCGGCTCAGACATTCGT 59.421 61.111 0.00 0.00 0.00 3.85
777 783 1.811266 CCCGGCTCAGACATTCGTG 60.811 63.158 0.00 0.00 0.00 4.35
778 784 1.079819 CCGGCTCAGACATTCGTGT 60.080 57.895 0.00 0.00 0.00 4.49
779 785 1.354337 CCGGCTCAGACATTCGTGTG 61.354 60.000 0.00 0.00 37.75 3.82
780 786 1.354337 CGGCTCAGACATTCGTGTGG 61.354 60.000 0.00 0.00 37.04 4.17
781 787 1.639298 GGCTCAGACATTCGTGTGGC 61.639 60.000 0.00 0.00 37.04 5.01
782 788 0.671781 GCTCAGACATTCGTGTGGCT 60.672 55.000 0.00 0.00 38.20 4.75
783 789 1.800805 CTCAGACATTCGTGTGGCTT 58.199 50.000 0.00 0.00 34.48 4.35
784 790 1.462283 CTCAGACATTCGTGTGGCTTG 59.538 52.381 0.00 0.00 34.48 4.01
785 791 0.110056 CAGACATTCGTGTGGCTTGC 60.110 55.000 0.00 0.00 34.48 4.01
786 792 0.534877 AGACATTCGTGTGGCTTGCA 60.535 50.000 0.00 0.00 32.09 4.08
787 793 0.523072 GACATTCGTGTGGCTTGCAT 59.477 50.000 0.00 0.00 0.00 3.96
788 794 0.523072 ACATTCGTGTGGCTTGCATC 59.477 50.000 0.00 0.00 0.00 3.91
789 795 0.521867 CATTCGTGTGGCTTGCATCG 60.522 55.000 0.00 0.00 0.00 3.84
790 796 0.673333 ATTCGTGTGGCTTGCATCGA 60.673 50.000 0.00 0.00 0.00 3.59
791 797 1.291184 TTCGTGTGGCTTGCATCGAG 61.291 55.000 0.00 0.00 0.00 4.04
792 798 2.482374 GTGTGGCTTGCATCGAGC 59.518 61.111 0.00 0.00 45.96 5.03
801 807 2.812499 GCATCGAGCGGAACCCTA 59.188 61.111 0.00 0.00 0.00 3.53
802 808 1.300233 GCATCGAGCGGAACCCTAG 60.300 63.158 0.00 0.00 0.00 3.02
803 809 1.735376 GCATCGAGCGGAACCCTAGA 61.735 60.000 0.00 0.00 0.00 2.43
804 810 0.962489 CATCGAGCGGAACCCTAGAT 59.038 55.000 0.00 0.00 0.00 1.98
805 811 1.068194 CATCGAGCGGAACCCTAGATC 60.068 57.143 0.00 0.00 0.00 2.75
806 812 1.164662 TCGAGCGGAACCCTAGATCG 61.165 60.000 0.00 0.00 0.00 3.69
807 813 1.164662 CGAGCGGAACCCTAGATCGA 61.165 60.000 0.00 0.00 0.00 3.59
808 814 0.594110 GAGCGGAACCCTAGATCGAG 59.406 60.000 0.00 0.00 0.00 4.04
809 815 0.824182 AGCGGAACCCTAGATCGAGG 60.824 60.000 14.60 14.60 36.23 4.63
810 816 0.822532 GCGGAACCCTAGATCGAGGA 60.823 60.000 22.35 0.00 39.15 3.71
811 817 1.240256 CGGAACCCTAGATCGAGGAG 58.760 60.000 22.35 14.45 39.15 3.69
812 818 0.963225 GGAACCCTAGATCGAGGAGC 59.037 60.000 22.35 10.84 39.15 4.70
813 819 1.479757 GGAACCCTAGATCGAGGAGCT 60.480 57.143 22.35 6.72 39.15 4.09
814 820 2.312390 GAACCCTAGATCGAGGAGCTT 58.688 52.381 22.35 10.52 39.15 3.74
815 821 3.488363 GAACCCTAGATCGAGGAGCTTA 58.512 50.000 22.35 0.00 39.15 3.09
816 822 3.596940 ACCCTAGATCGAGGAGCTTAA 57.403 47.619 22.35 0.00 39.15 1.85
817 823 3.224269 ACCCTAGATCGAGGAGCTTAAC 58.776 50.000 22.35 0.00 39.15 2.01
818 824 3.223435 CCCTAGATCGAGGAGCTTAACA 58.777 50.000 22.35 0.00 39.15 2.41
853 860 4.367023 CGCCCAAACCCTCGTCGA 62.367 66.667 0.00 0.00 0.00 4.20
894 901 4.767892 CCCCTGCCTTCCCCCTCT 62.768 72.222 0.00 0.00 0.00 3.69
898 905 3.003173 TGCCTTCCCCCTCTGTCG 61.003 66.667 0.00 0.00 0.00 4.35
900 907 3.787001 CCTTCCCCCTCTGTCGCC 61.787 72.222 0.00 0.00 0.00 5.54
919 933 2.725312 GCTCTCCACGCCCAGATCA 61.725 63.158 0.00 0.00 0.00 2.92
922 936 1.448540 CTCCACGCCCAGATCACAC 60.449 63.158 0.00 0.00 0.00 3.82
941 955 4.091939 GACGTTTCCCCCTCCCCG 62.092 72.222 0.00 0.00 0.00 5.73
967 989 4.776322 CATCGCCACCGCCCTTGA 62.776 66.667 0.00 0.00 0.00 3.02
968 990 3.797353 ATCGCCACCGCCCTTGAT 61.797 61.111 0.00 0.00 0.00 2.57
971 993 4.424711 GCCACCGCCCTTGATCCA 62.425 66.667 0.00 0.00 0.00 3.41
974 996 1.103398 CCACCGCCCTTGATCCATTC 61.103 60.000 0.00 0.00 0.00 2.67
978 1000 1.529244 GCCCTTGATCCATTCCCCG 60.529 63.158 0.00 0.00 0.00 5.73
979 1001 1.922821 CCCTTGATCCATTCCCCGT 59.077 57.895 0.00 0.00 0.00 5.28
1009 1035 2.821366 CTCCCACGATGGCAGCAC 60.821 66.667 2.73 0.00 35.79 4.40
1010 1036 3.320879 CTCCCACGATGGCAGCACT 62.321 63.158 2.73 0.00 35.79 4.40
1095 1121 0.107993 TCGAGATCGACGGGTACAGT 60.108 55.000 13.42 0.00 44.22 3.55
1211 1247 0.673644 GATACACACGCCAACAGCCT 60.674 55.000 0.00 0.00 38.78 4.58
1476 1524 4.456280 TGAGTGCGATCTAACTGTCATT 57.544 40.909 2.19 0.00 0.00 2.57
1547 4644 1.707427 ACCCTCAGACTTGGCAGAAAT 59.293 47.619 0.00 0.00 0.00 2.17
1649 4746 4.427661 GCTCGCAGCACGGTCTCT 62.428 66.667 0.00 0.00 41.89 3.10
1662 4759 1.202200 CGGTCTCTAGTCTTCAAGGCG 60.202 57.143 0.00 0.00 0.00 5.52
1704 4801 1.537202 GGCAAGTGTGGACAGAACATC 59.463 52.381 0.00 0.00 0.00 3.06
1828 4925 4.833390 AGAAATGGTCAGGCACTTACTAC 58.167 43.478 0.00 0.00 34.60 2.73
1887 4984 6.713903 AGATGATGTGTGAAGACATTCTTTGT 59.286 34.615 0.00 0.00 42.79 2.83
1888 4985 6.063640 TGATGTGTGAAGACATTCTTTGTG 57.936 37.500 0.00 0.00 39.18 3.33
1917 5014 0.392706 ATGTTGAGACTGTGGCGACA 59.607 50.000 0.33 0.33 38.70 4.35
1919 5016 1.202639 TGTTGAGACTGTGGCGACAAT 60.203 47.619 2.34 0.00 46.06 2.71
1923 5020 1.195448 GAGACTGTGGCGACAATGTTG 59.805 52.381 2.34 0.00 46.06 3.33
2054 5151 0.822164 AAGAAATCATGCCCTGCTGC 59.178 50.000 0.00 0.00 0.00 5.25
2077 16164 6.183360 TGCCTCAGTAAATATCTTGGAGAGAC 60.183 42.308 0.00 0.00 37.17 3.36
2158 16253 1.107114 ATGTAGCCACCTGAGACGAG 58.893 55.000 0.00 0.00 0.00 4.18
2178 16273 4.929808 CGAGGTAGTGTATGCTTCACTTTT 59.070 41.667 12.41 2.38 42.50 2.27
2264 17476 4.957684 AGTCTTAGTAACCTGTGTGCTT 57.042 40.909 0.00 0.00 0.00 3.91
2315 17527 0.179012 TGGAACCCCCTGTTTTCGTC 60.179 55.000 0.00 0.00 37.29 4.20
2494 17711 5.661312 ACTCAATACATAGCCACCTGAACTA 59.339 40.000 0.00 0.00 0.00 2.24
2526 17743 5.649395 CCTTAGTTTGCAGAGATCATTGGAA 59.351 40.000 0.00 0.00 0.00 3.53
2532 17749 6.446781 TTGCAGAGATCATTGGAATCTTTC 57.553 37.500 0.00 0.00 0.00 2.62
2685 17906 6.798315 AGTTCTTCTGAATGTTCTGTGATG 57.202 37.500 0.00 0.00 34.40 3.07
2690 17911 7.392418 TCTTCTGAATGTTCTGTGATGATCTT 58.608 34.615 0.00 0.00 0.00 2.40
2699 17921 6.367149 TGTTCTGTGATGATCTTCTTTTCTCG 59.633 38.462 9.75 0.00 0.00 4.04
2753 17975 4.072131 TCTAAGGTGCCAAGCTGTTTAAG 58.928 43.478 0.00 0.00 33.40 1.85
2781 18003 9.197694 CCGATCAATTAGTACCTTTGAGAATAG 57.802 37.037 8.23 0.00 33.26 1.73
2782 18004 9.751542 CGATCAATTAGTACCTTTGAGAATAGT 57.248 33.333 8.23 0.00 33.26 2.12
2788 18010 9.765795 ATTAGTACCTTTGAGAATAGTATGTGC 57.234 33.333 0.00 0.00 0.00 4.57
2793 18015 5.431765 CTTTGAGAATAGTATGTGCCAGGT 58.568 41.667 0.00 0.00 0.00 4.00
2831 18053 5.606348 TTTGCAGGTGAAGGTTATGTTTT 57.394 34.783 0.00 0.00 0.00 2.43
2832 18054 5.606348 TTGCAGGTGAAGGTTATGTTTTT 57.394 34.783 0.00 0.00 0.00 1.94
2853 18075 2.990740 TTTTGCAGGGGAGGTTATGT 57.009 45.000 0.00 0.00 0.00 2.29
2854 18076 2.990740 TTTGCAGGGGAGGTTATGTT 57.009 45.000 0.00 0.00 0.00 2.71
2855 18077 2.990740 TTGCAGGGGAGGTTATGTTT 57.009 45.000 0.00 0.00 0.00 2.83
2856 18078 2.214376 TGCAGGGGAGGTTATGTTTG 57.786 50.000 0.00 0.00 0.00 2.93
2910 18132 9.413048 TCCAACAAAAATGGAATTCGTTAATAC 57.587 29.630 0.00 0.00 43.84 1.89
2927 18149 8.984764 TCGTTAATACCATAGTTATGTGCAATC 58.015 33.333 0.00 0.00 31.82 2.67
2999 18221 3.529085 GTTTCTGTTCACGTTTCGTAGC 58.471 45.455 0.00 0.00 38.32 3.58
3001 18223 1.002576 TCTGTTCACGTTTCGTAGCGA 60.003 47.619 5.15 0.00 38.32 4.93
3042 18264 5.090757 GCGTAATGGTAAACTTAAACCTGC 58.909 41.667 0.00 0.00 36.67 4.85
3066 18288 8.026026 TGCTCGTTCAATTTGCTAAATCAAATA 58.974 29.630 2.65 0.00 43.56 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 252 0.813210 GGAGGCTTCTGCAGAATCGG 60.813 60.000 28.57 18.26 41.91 4.18
393 398 2.615227 GATCTCACCCCGCCATGCTT 62.615 60.000 0.00 0.00 0.00 3.91
394 399 3.092511 ATCTCACCCCGCCATGCT 61.093 61.111 0.00 0.00 0.00 3.79
596 602 1.369839 GAAGCTTTGGCCGGTCTAGC 61.370 60.000 21.34 21.34 39.73 3.42
599 605 2.358737 CGAAGCTTTGGCCGGTCT 60.359 61.111 7.97 0.00 39.73 3.85
651 657 6.260271 GCTGCCTCCTTTTCGTATATAAGTTT 59.740 38.462 0.00 0.00 0.00 2.66
652 658 5.758784 GCTGCCTCCTTTTCGTATATAAGTT 59.241 40.000 0.00 0.00 0.00 2.66
653 659 5.298347 GCTGCCTCCTTTTCGTATATAAGT 58.702 41.667 0.00 0.00 0.00 2.24
654 660 4.386049 CGCTGCCTCCTTTTCGTATATAAG 59.614 45.833 0.00 0.00 0.00 1.73
655 661 4.038282 TCGCTGCCTCCTTTTCGTATATAA 59.962 41.667 0.00 0.00 0.00 0.98
656 662 3.570975 TCGCTGCCTCCTTTTCGTATATA 59.429 43.478 0.00 0.00 0.00 0.86
657 663 2.364324 TCGCTGCCTCCTTTTCGTATAT 59.636 45.455 0.00 0.00 0.00 0.86
658 664 1.752498 TCGCTGCCTCCTTTTCGTATA 59.248 47.619 0.00 0.00 0.00 1.47
659 665 0.535335 TCGCTGCCTCCTTTTCGTAT 59.465 50.000 0.00 0.00 0.00 3.06
660 666 0.108804 CTCGCTGCCTCCTTTTCGTA 60.109 55.000 0.00 0.00 0.00 3.43
661 667 1.374758 CTCGCTGCCTCCTTTTCGT 60.375 57.895 0.00 0.00 0.00 3.85
662 668 1.374758 ACTCGCTGCCTCCTTTTCG 60.375 57.895 0.00 0.00 0.00 3.46
663 669 0.320771 TCACTCGCTGCCTCCTTTTC 60.321 55.000 0.00 0.00 0.00 2.29
664 670 0.108585 TTCACTCGCTGCCTCCTTTT 59.891 50.000 0.00 0.00 0.00 2.27
665 671 0.321122 CTTCACTCGCTGCCTCCTTT 60.321 55.000 0.00 0.00 0.00 3.11
666 672 1.294780 CTTCACTCGCTGCCTCCTT 59.705 57.895 0.00 0.00 0.00 3.36
667 673 2.977178 CTTCACTCGCTGCCTCCT 59.023 61.111 0.00 0.00 0.00 3.69
668 674 2.817396 GCTTCACTCGCTGCCTCC 60.817 66.667 0.00 0.00 0.00 4.30
669 675 3.184683 CGCTTCACTCGCTGCCTC 61.185 66.667 0.00 0.00 0.00 4.70
677 683 2.775032 TAACCCCACGCGCTTCACTC 62.775 60.000 5.73 0.00 0.00 3.51
678 684 2.180159 ATAACCCCACGCGCTTCACT 62.180 55.000 5.73 0.00 0.00 3.41
679 685 1.702491 GATAACCCCACGCGCTTCAC 61.702 60.000 5.73 0.00 0.00 3.18
680 686 1.448893 GATAACCCCACGCGCTTCA 60.449 57.895 5.73 0.00 0.00 3.02
681 687 2.178235 GGATAACCCCACGCGCTTC 61.178 63.158 5.73 0.00 0.00 3.86
682 688 2.124860 GGATAACCCCACGCGCTT 60.125 61.111 5.73 0.00 0.00 4.68
683 689 2.869503 CTTGGATAACCCCACGCGCT 62.870 60.000 5.73 0.00 35.62 5.92
684 690 2.437002 TTGGATAACCCCACGCGC 60.437 61.111 5.73 0.00 35.62 6.86
685 691 1.817941 CCTTGGATAACCCCACGCG 60.818 63.158 3.53 3.53 35.62 6.01
686 692 0.746923 GTCCTTGGATAACCCCACGC 60.747 60.000 0.00 0.00 35.62 5.34
687 693 0.107361 GGTCCTTGGATAACCCCACG 60.107 60.000 0.00 0.00 35.62 4.94
688 694 0.996583 TGGTCCTTGGATAACCCCAC 59.003 55.000 0.00 0.00 35.62 4.61
689 695 1.295020 CTGGTCCTTGGATAACCCCA 58.705 55.000 0.00 0.00 34.81 4.96
690 696 0.551396 CCTGGTCCTTGGATAACCCC 59.449 60.000 0.00 0.00 34.81 4.95
691 697 1.591768 TCCTGGTCCTTGGATAACCC 58.408 55.000 0.00 0.00 34.81 4.11
692 698 2.356844 GGTTCCTGGTCCTTGGATAACC 60.357 54.545 5.26 7.13 31.76 2.85
693 699 2.576648 AGGTTCCTGGTCCTTGGATAAC 59.423 50.000 7.22 2.62 31.76 1.89
694 700 2.929301 AGGTTCCTGGTCCTTGGATAA 58.071 47.619 7.22 0.00 31.76 1.75
695 701 2.661176 AGGTTCCTGGTCCTTGGATA 57.339 50.000 7.22 0.00 31.76 2.59
696 702 1.760405 AAGGTTCCTGGTCCTTGGAT 58.240 50.000 19.19 2.42 41.75 3.41
697 703 3.274823 AAGGTTCCTGGTCCTTGGA 57.725 52.632 19.19 0.80 41.75 3.53
700 706 1.821088 AGACAAGGTTCCTGGTCCTT 58.179 50.000 19.37 15.97 43.79 3.36
701 707 1.421646 CAAGACAAGGTTCCTGGTCCT 59.578 52.381 19.37 7.14 37.65 3.85
702 708 1.897560 CAAGACAAGGTTCCTGGTCC 58.102 55.000 19.37 5.55 37.65 4.46
703 709 1.239347 GCAAGACAAGGTTCCTGGTC 58.761 55.000 16.30 16.30 37.30 4.02
704 710 0.535102 CGCAAGACAAGGTTCCTGGT 60.535 55.000 0.00 0.00 43.02 4.00
705 711 1.237285 CCGCAAGACAAGGTTCCTGG 61.237 60.000 0.00 0.00 43.02 4.45
706 712 1.856265 GCCGCAAGACAAGGTTCCTG 61.856 60.000 0.00 0.00 43.02 3.86
707 713 1.600916 GCCGCAAGACAAGGTTCCT 60.601 57.895 0.00 0.00 43.02 3.36
708 714 1.172812 AAGCCGCAAGACAAGGTTCC 61.173 55.000 0.00 0.00 43.02 3.62
709 715 0.238553 GAAGCCGCAAGACAAGGTTC 59.761 55.000 0.00 0.00 43.02 3.62
710 716 1.172812 GGAAGCCGCAAGACAAGGTT 61.173 55.000 0.00 0.00 43.02 3.50
711 717 1.600916 GGAAGCCGCAAGACAAGGT 60.601 57.895 0.00 0.00 43.02 3.50
712 718 1.600636 TGGAAGCCGCAAGACAAGG 60.601 57.895 0.00 0.00 43.02 3.61
713 719 1.576421 GTGGAAGCCGCAAGACAAG 59.424 57.895 0.00 0.00 43.02 3.16
714 720 1.896660 GGTGGAAGCCGCAAGACAA 60.897 57.895 0.00 0.00 43.02 3.18
715 721 2.281484 GGTGGAAGCCGCAAGACA 60.281 61.111 0.00 0.00 43.02 3.41
724 730 0.178932 AAAGGGGAAAGGGTGGAAGC 60.179 55.000 0.00 0.00 0.00 3.86
725 731 1.429299 AGAAAGGGGAAAGGGTGGAAG 59.571 52.381 0.00 0.00 0.00 3.46
726 732 1.146982 CAGAAAGGGGAAAGGGTGGAA 59.853 52.381 0.00 0.00 0.00 3.53
727 733 0.777446 CAGAAAGGGGAAAGGGTGGA 59.223 55.000 0.00 0.00 0.00 4.02
728 734 0.482887 ACAGAAAGGGGAAAGGGTGG 59.517 55.000 0.00 0.00 0.00 4.61
729 735 2.158460 AGAACAGAAAGGGGAAAGGGTG 60.158 50.000 0.00 0.00 0.00 4.61
730 736 2.144450 AGAACAGAAAGGGGAAAGGGT 58.856 47.619 0.00 0.00 0.00 4.34
731 737 2.893489 CAAGAACAGAAAGGGGAAAGGG 59.107 50.000 0.00 0.00 0.00 3.95
732 738 2.297315 GCAAGAACAGAAAGGGGAAAGG 59.703 50.000 0.00 0.00 0.00 3.11
733 739 3.225940 AGCAAGAACAGAAAGGGGAAAG 58.774 45.455 0.00 0.00 0.00 2.62
734 740 3.222603 GAGCAAGAACAGAAAGGGGAAA 58.777 45.455 0.00 0.00 0.00 3.13
735 741 2.489073 GGAGCAAGAACAGAAAGGGGAA 60.489 50.000 0.00 0.00 0.00 3.97
736 742 1.073923 GGAGCAAGAACAGAAAGGGGA 59.926 52.381 0.00 0.00 0.00 4.81
737 743 1.074566 AGGAGCAAGAACAGAAAGGGG 59.925 52.381 0.00 0.00 0.00 4.79
738 744 2.431454 GAGGAGCAAGAACAGAAAGGG 58.569 52.381 0.00 0.00 0.00 3.95
739 745 2.431454 GGAGGAGCAAGAACAGAAAGG 58.569 52.381 0.00 0.00 0.00 3.11
740 746 2.431454 GGGAGGAGCAAGAACAGAAAG 58.569 52.381 0.00 0.00 0.00 2.62
741 747 1.073923 GGGGAGGAGCAAGAACAGAAA 59.926 52.381 0.00 0.00 0.00 2.52
742 748 0.693049 GGGGAGGAGCAAGAACAGAA 59.307 55.000 0.00 0.00 0.00 3.02
743 749 1.544825 CGGGGAGGAGCAAGAACAGA 61.545 60.000 0.00 0.00 0.00 3.41
744 750 1.078848 CGGGGAGGAGCAAGAACAG 60.079 63.158 0.00 0.00 0.00 3.16
745 751 2.592993 CCGGGGAGGAGCAAGAACA 61.593 63.158 0.00 0.00 45.00 3.18
746 752 2.269241 CCGGGGAGGAGCAAGAAC 59.731 66.667 0.00 0.00 45.00 3.01
747 753 3.717294 GCCGGGGAGGAGCAAGAA 61.717 66.667 2.18 0.00 45.00 2.52
748 754 4.722535 AGCCGGGGAGGAGCAAGA 62.723 66.667 2.18 0.00 45.00 3.02
749 755 4.168291 GAGCCGGGGAGGAGCAAG 62.168 72.222 2.18 0.00 45.00 4.01
753 759 3.151022 GTCTGAGCCGGGGAGGAG 61.151 72.222 2.18 0.00 45.00 3.69
754 760 2.822643 AATGTCTGAGCCGGGGAGGA 62.823 60.000 2.18 0.00 45.00 3.71
755 761 2.317149 GAATGTCTGAGCCGGGGAGG 62.317 65.000 2.18 0.00 44.97 4.30
756 762 1.144936 GAATGTCTGAGCCGGGGAG 59.855 63.158 2.18 0.00 0.00 4.30
757 763 2.721167 CGAATGTCTGAGCCGGGGA 61.721 63.158 2.18 0.00 0.00 4.81
758 764 2.202932 CGAATGTCTGAGCCGGGG 60.203 66.667 2.18 0.00 0.00 5.73
759 765 1.811266 CACGAATGTCTGAGCCGGG 60.811 63.158 2.18 0.00 0.00 5.73
760 766 1.079819 ACACGAATGTCTGAGCCGG 60.080 57.895 0.00 0.00 31.55 6.13
761 767 1.354337 CCACACGAATGTCTGAGCCG 61.354 60.000 0.00 0.00 36.72 5.52
762 768 1.639298 GCCACACGAATGTCTGAGCC 61.639 60.000 0.00 0.00 36.72 4.70
763 769 0.671781 AGCCACACGAATGTCTGAGC 60.672 55.000 0.00 0.00 36.72 4.26
764 770 1.462283 CAAGCCACACGAATGTCTGAG 59.538 52.381 0.00 0.00 36.72 3.35
765 771 1.511850 CAAGCCACACGAATGTCTGA 58.488 50.000 0.00 0.00 36.72 3.27
766 772 0.110056 GCAAGCCACACGAATGTCTG 60.110 55.000 0.00 0.00 36.72 3.51
767 773 0.534877 TGCAAGCCACACGAATGTCT 60.535 50.000 0.00 0.00 36.72 3.41
768 774 0.523072 ATGCAAGCCACACGAATGTC 59.477 50.000 0.00 0.00 36.72 3.06
769 775 0.523072 GATGCAAGCCACACGAATGT 59.477 50.000 0.00 0.00 40.80 2.71
770 776 0.521867 CGATGCAAGCCACACGAATG 60.522 55.000 0.00 0.00 0.00 2.67
771 777 0.673333 TCGATGCAAGCCACACGAAT 60.673 50.000 0.00 0.00 34.41 3.34
772 778 1.291184 CTCGATGCAAGCCACACGAA 61.291 55.000 0.00 0.00 36.00 3.85
773 779 1.737735 CTCGATGCAAGCCACACGA 60.738 57.895 0.00 0.00 35.45 4.35
774 780 2.780643 CTCGATGCAAGCCACACG 59.219 61.111 0.00 0.00 0.00 4.49
775 781 2.482374 GCTCGATGCAAGCCACAC 59.518 61.111 0.00 0.00 42.31 3.82
776 782 3.120385 CGCTCGATGCAAGCCACA 61.120 61.111 3.34 0.00 43.06 4.17
777 783 3.869272 CCGCTCGATGCAAGCCAC 61.869 66.667 3.34 0.00 43.06 5.01
778 784 3.604129 TTCCGCTCGATGCAAGCCA 62.604 57.895 3.34 0.00 43.06 4.75
779 785 2.819595 TTCCGCTCGATGCAAGCC 60.820 61.111 3.34 0.00 43.06 4.35
780 786 2.401195 GTTCCGCTCGATGCAAGC 59.599 61.111 0.00 0.00 43.06 4.01
781 787 2.464459 GGGTTCCGCTCGATGCAAG 61.464 63.158 0.00 0.00 43.06 4.01
782 788 1.609635 TAGGGTTCCGCTCGATGCAA 61.610 55.000 0.00 0.00 43.06 4.08
783 789 2.016393 CTAGGGTTCCGCTCGATGCA 62.016 60.000 0.00 0.00 43.06 3.96
784 790 1.300233 CTAGGGTTCCGCTCGATGC 60.300 63.158 0.00 0.00 38.57 3.91
785 791 0.962489 ATCTAGGGTTCCGCTCGATG 59.038 55.000 0.00 0.00 30.24 3.84
786 792 1.249407 GATCTAGGGTTCCGCTCGAT 58.751 55.000 0.00 0.00 33.08 3.59
787 793 1.164662 CGATCTAGGGTTCCGCTCGA 61.165 60.000 0.00 0.00 0.00 4.04
788 794 1.164662 TCGATCTAGGGTTCCGCTCG 61.165 60.000 0.00 0.00 0.00 5.03
789 795 0.594110 CTCGATCTAGGGTTCCGCTC 59.406 60.000 0.00 0.00 0.00 5.03
790 796 0.824182 CCTCGATCTAGGGTTCCGCT 60.824 60.000 5.34 0.00 32.55 5.52
791 797 0.822532 TCCTCGATCTAGGGTTCCGC 60.823 60.000 13.08 0.00 37.24 5.54
792 798 1.240256 CTCCTCGATCTAGGGTTCCG 58.760 60.000 13.08 0.00 37.24 4.30
793 799 0.963225 GCTCCTCGATCTAGGGTTCC 59.037 60.000 13.08 0.00 37.24 3.62
794 800 1.989706 AGCTCCTCGATCTAGGGTTC 58.010 55.000 13.08 3.45 37.24 3.62
795 801 2.463047 AAGCTCCTCGATCTAGGGTT 57.537 50.000 13.08 2.69 37.24 4.11
796 802 3.224269 GTTAAGCTCCTCGATCTAGGGT 58.776 50.000 13.08 0.29 37.24 4.34
797 803 3.004944 GTGTTAAGCTCCTCGATCTAGGG 59.995 52.174 13.08 5.59 37.24 3.53
798 804 3.004944 GGTGTTAAGCTCCTCGATCTAGG 59.995 52.174 6.96 6.96 38.06 3.02
799 805 3.004944 GGGTGTTAAGCTCCTCGATCTAG 59.995 52.174 0.00 0.00 0.00 2.43
800 806 2.957006 GGGTGTTAAGCTCCTCGATCTA 59.043 50.000 0.00 0.00 0.00 1.98
801 807 1.757699 GGGTGTTAAGCTCCTCGATCT 59.242 52.381 0.00 0.00 0.00 2.75
802 808 1.757699 AGGGTGTTAAGCTCCTCGATC 59.242 52.381 0.00 0.00 0.00 3.69
803 809 1.757699 GAGGGTGTTAAGCTCCTCGAT 59.242 52.381 1.45 0.00 36.78 3.59
804 810 1.183549 GAGGGTGTTAAGCTCCTCGA 58.816 55.000 1.45 0.00 36.78 4.04
805 811 3.742983 GAGGGTGTTAAGCTCCTCG 57.257 57.895 1.45 0.00 36.78 4.63
806 812 0.896226 ACGAGGGTGTTAAGCTCCTC 59.104 55.000 6.79 6.79 41.62 3.71
807 813 0.896226 GACGAGGGTGTTAAGCTCCT 59.104 55.000 0.00 0.00 0.00 3.69
808 814 0.896226 AGACGAGGGTGTTAAGCTCC 59.104 55.000 0.00 0.00 0.00 4.70
809 815 1.135053 GGAGACGAGGGTGTTAAGCTC 60.135 57.143 0.00 0.00 0.00 4.09
810 816 0.896226 GGAGACGAGGGTGTTAAGCT 59.104 55.000 0.00 0.00 0.00 3.74
811 817 3.437746 GGAGACGAGGGTGTTAAGC 57.562 57.895 0.00 0.00 0.00 3.09
882 889 4.475135 GCGACAGAGGGGGAAGGC 62.475 72.222 0.00 0.00 0.00 4.35
889 896 4.200283 GAGAGCGGCGACAGAGGG 62.200 72.222 12.98 0.00 0.00 4.30
900 907 3.781770 GATCTGGGCGTGGAGAGCG 62.782 68.421 0.00 0.00 35.00 5.03
903 917 1.609210 TGTGATCTGGGCGTGGAGA 60.609 57.895 0.00 0.00 0.00 3.71
919 933 2.845795 AGGGGGAAACGTCGGTGT 60.846 61.111 0.00 0.00 0.00 4.16
922 936 4.091939 GGGAGGGGGAAACGTCGG 62.092 72.222 0.00 0.00 0.00 4.79
966 988 2.830514 GGGGGACGGGGAATGGATC 61.831 68.421 0.00 0.00 0.00 3.36
967 989 2.776963 GGGGGACGGGGAATGGAT 60.777 66.667 0.00 0.00 0.00 3.41
968 990 4.356561 TGGGGGACGGGGAATGGA 62.357 66.667 0.00 0.00 0.00 3.41
970 992 4.123545 GGTGGGGGACGGGGAATG 62.124 72.222 0.00 0.00 0.00 2.67
978 1000 4.097361 GGAGCTTCGGTGGGGGAC 62.097 72.222 0.00 0.00 0.00 4.46
1009 1035 0.879765 CTTTCTGTTGGCCTCTGCAG 59.120 55.000 7.63 7.63 40.13 4.41
1010 1036 0.538057 CCTTTCTGTTGGCCTCTGCA 60.538 55.000 3.32 0.00 40.13 4.41
1085 1111 1.480954 CCTTATGCAGACTGTACCCGT 59.519 52.381 3.99 0.00 0.00 5.28
1095 1121 1.152694 GCCCATGCCCTTATGCAGA 60.153 57.895 0.00 0.00 45.93 4.26
1118 1144 0.036306 GGTGGACCGGATGAACTTGT 59.964 55.000 9.46 0.00 0.00 3.16
1194 1230 2.825982 AGGCTGTTGGCGTGTGTA 59.174 55.556 0.00 0.00 44.18 2.90
1211 1247 1.076014 TAGACTGAGACGTGGCCCA 59.924 57.895 0.00 0.00 0.00 5.36
1303 1339 3.057019 CTGAGAAAACCGATGACGACAA 58.943 45.455 0.00 0.00 42.66 3.18
1476 1524 1.600023 CCGCAACAAGTGGTTCCTTA 58.400 50.000 0.00 0.00 43.15 2.69
1547 4644 3.004315 CGCCTCTAGCAGTTTTCCAAAAA 59.996 43.478 0.00 0.00 44.04 1.94
1649 4746 0.532573 CAGCTCCGCCTTGAAGACTA 59.467 55.000 0.00 0.00 0.00 2.59
1662 4759 1.000283 CTCATCGGTCCATACAGCTCC 60.000 57.143 0.00 0.00 0.00 4.70
1704 4801 0.179215 GCTGCATTTCTTCGACGGTG 60.179 55.000 0.00 0.00 0.00 4.94
1806 4903 4.532521 AGTAGTAAGTGCCTGACCATTTCT 59.467 41.667 0.00 0.00 0.00 2.52
1828 4925 1.226686 GCATACCGATCTGCAGCCAG 61.227 60.000 9.47 1.82 40.54 4.85
1887 4984 5.525012 CACAGTCTCAACATCAAGAGTTTCA 59.475 40.000 0.00 0.00 33.63 2.69
1888 4985 5.049818 CCACAGTCTCAACATCAAGAGTTTC 60.050 44.000 0.00 0.00 33.63 2.78
1917 5014 3.806380 CTGATCAGCTAGAGCCAACATT 58.194 45.455 10.38 0.00 43.38 2.71
1919 5016 2.975732 CTGATCAGCTAGAGCCAACA 57.024 50.000 10.38 0.00 43.38 3.33
1942 5039 2.276732 TCTTTTAGCCTGCTGCAGTT 57.723 45.000 26.41 17.01 44.83 3.16
2054 5151 7.595819 AGTCTCTCCAAGATATTTACTGAGG 57.404 40.000 0.00 0.00 36.11 3.86
2158 16253 5.701290 AGTGAAAAGTGAAGCATACACTACC 59.299 40.000 10.00 4.86 46.01 3.18
2315 17527 0.877649 AGACGCACACAGCAACAGAG 60.878 55.000 0.00 0.00 46.13 3.35
2434 17651 5.006552 GCTGACACAAGAATCTAAGATGAGC 59.993 44.000 0.00 0.00 0.00 4.26
2443 17660 2.693069 CGGAAGCTGACACAAGAATCT 58.307 47.619 0.00 0.00 0.00 2.40
2576 17793 3.611025 TTCTTCCCCAAAAGACACCAT 57.389 42.857 0.00 0.00 35.06 3.55
2590 17807 5.802465 TGCAGGAGATATGATCATTCTTCC 58.198 41.667 14.65 16.61 0.00 3.46
2666 17887 7.549842 AGAAGATCATCACAGAACATTCAGAAG 59.450 37.037 0.10 0.00 0.00 2.85
2753 17975 4.448210 TCAAAGGTACTAATTGATCGGGC 58.552 43.478 0.00 0.00 38.49 6.13
2781 18003 0.533491 TACGGTGACCTGGCACATAC 59.467 55.000 18.44 6.41 40.52 2.39
2782 18004 1.491668 ATACGGTGACCTGGCACATA 58.508 50.000 18.44 12.29 40.52 2.29
2783 18005 0.618458 AATACGGTGACCTGGCACAT 59.382 50.000 18.44 10.95 40.52 3.21
2784 18006 0.321210 CAATACGGTGACCTGGCACA 60.321 55.000 18.44 6.80 40.52 4.57
2785 18007 0.036765 TCAATACGGTGACCTGGCAC 60.037 55.000 0.00 11.32 38.05 5.01
2786 18008 0.908910 ATCAATACGGTGACCTGGCA 59.091 50.000 0.00 0.00 0.00 4.92
2788 18010 3.812156 TGTATCAATACGGTGACCTGG 57.188 47.619 0.00 0.00 36.06 4.45
2793 18015 4.574421 CCTGCAAATGTATCAATACGGTGA 59.426 41.667 0.00 0.00 36.06 4.02
2833 18055 3.252554 ACATAACCTCCCCTGCAAAAA 57.747 42.857 0.00 0.00 0.00 1.94
2834 18056 2.990740 ACATAACCTCCCCTGCAAAA 57.009 45.000 0.00 0.00 0.00 2.44
2835 18057 2.896685 CAAACATAACCTCCCCTGCAAA 59.103 45.455 0.00 0.00 0.00 3.68
2836 18058 2.524306 CAAACATAACCTCCCCTGCAA 58.476 47.619 0.00 0.00 0.00 4.08
2837 18059 1.272425 CCAAACATAACCTCCCCTGCA 60.272 52.381 0.00 0.00 0.00 4.41
2838 18060 1.005450 TCCAAACATAACCTCCCCTGC 59.995 52.381 0.00 0.00 0.00 4.85
2839 18061 3.449746 TTCCAAACATAACCTCCCCTG 57.550 47.619 0.00 0.00 0.00 4.45
2840 18062 3.309848 CCATTCCAAACATAACCTCCCCT 60.310 47.826 0.00 0.00 0.00 4.79
2841 18063 3.031013 CCATTCCAAACATAACCTCCCC 58.969 50.000 0.00 0.00 0.00 4.81
2842 18064 3.699538 GACCATTCCAAACATAACCTCCC 59.300 47.826 0.00 0.00 0.00 4.30
2843 18065 4.600062 AGACCATTCCAAACATAACCTCC 58.400 43.478 0.00 0.00 0.00 4.30
2844 18066 4.640647 GGAGACCATTCCAAACATAACCTC 59.359 45.833 0.00 0.00 37.20 3.85
2845 18067 4.044065 TGGAGACCATTCCAAACATAACCT 59.956 41.667 0.00 0.00 44.09 3.50
2846 18068 4.340617 TGGAGACCATTCCAAACATAACC 58.659 43.478 0.00 0.00 44.09 2.85
2856 18078 8.517878 CAATCAATTATGTATGGAGACCATTCC 58.482 37.037 8.59 1.73 42.23 3.01
2910 18132 6.293626 GCCTGTAAGATTGCACATAACTATGG 60.294 42.308 1.98 0.00 35.10 2.74
2927 18149 1.929836 GATCTCGCAAGTGCCTGTAAG 59.070 52.381 0.00 0.00 37.91 2.34
2999 18221 2.494059 CCATAAGGCCCATTACACTCG 58.506 52.381 0.00 0.00 0.00 4.18
3021 18243 6.148315 ACGAGCAGGTTTAAGTTTACCATTAC 59.852 38.462 8.93 0.00 36.87 1.89
3042 18264 8.526681 GCTATTTGATTTAGCAAATTGAACGAG 58.473 33.333 15.48 6.66 43.83 4.18
3066 18288 5.474876 CCCTGAAATAACTTTGAGACAAGCT 59.525 40.000 0.00 0.00 28.03 3.74


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

AutoCloner maintained by Alex Coulton.